Citrus Sinensis ID: 027234

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220------
Protein Sequence
MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQSGSVEGGAQQPKPFEESDDSYSVNEGTSNSRKDEEEEAEKRLKKPRLVWSVELHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGVSPQQGNSFVSSNIG
Secondary Structure (PSIPRED)
cccEEEEEccHHHHHHHHHHccccccEEEEEcccccccHHHHHHHHHccccccEEEEEccccHHHHHHHHHHcccccccccccHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccHHHHHHHHHccccccccHHHHHHHHHHHHHHccccccccccEEEcccccccHHHHHHHHHHHHHHHHccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccEEEEEccHHHHHHHHHHHccccccEEEEEcccccccHHHHHHHHHHHccccEEEEEcccccHHHHHHHHccHHHHEEccccHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEcHHHHHHHHHHHHHHcccccccHHHHHHHccccccHHHHHHHHHHHHHHHHHHccccccccccccccccc
Coil and Loop (DISEMBL)
mgfsvtkcNRAEIALDMLRtnkngydivisdvhmpdmdgFKLLELVglemdlpvIMMCAHGskevvmkgvthdacdyltkpvrIEELKNIWQHVVRKRKNErkdleqsgsveggaqqpkpfeesddsysvnegtsnsrkDEEEEAEKRLKKPRLVWSVELHQQFVSAVKElgfdkagpkKILElmnipgltreNVASHLQKHRLYLSrlsgvspqqgnsfvssnig
Flexible Loop (DISEMBL)
mgfsvtkcNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKnerkdleqsgsveggaqqpkpfeesddsysvnegtsnsrkdeeEEAEKrlkkprlvwsVELHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSrlsgvspqqgnsfvssnig
Low Complexity Region (SEG)
MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQSGSVEGGAQQPKPFEESDDSYSVNEGTSNSRKDEEEEAEKRLKKPRLVWSVELHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGVSPQQGNSFVSSNIG
Disordered region (IsUnstruct)
*****TKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVR********************************************************RLVWSVELHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYL********************
Disordered Region (DISOPRED)
MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQSGSVEGGAQQPKPFEESDDSYSVNEGTSNSRKDEEEEAEKRLKKPRLVWSVELHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRL**********************
Disordered Region (DISEMBL)
MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVR*****************************************************KKPRLVWSVELHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGVSPQQGNSFVSSNIG
Disordered Region (DISPRO)
MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKN**************************************************KPRLVWSVELHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLS****************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQSGSVEGGAQQPKPFEESDDSYSVNEGTSNSRKDEEEEAEKRLKKPRLVWSVELHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGVSPQQGNSFVSSNIG
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	226	2.2.26 [Sep-21-2011]
Q9ZWJ9	664	Two-component response re	yes	no	0.955	0.325	0.676	5e-79
Q940D0	690	Two-component response re	no	no	0.955	0.313	0.643	2e-78
P62598	596	Two-component response re	no	no	0.889	0.337	0.548	6e-64
Q9FXD6	521	Two-component response re	no	no	0.907	0.393	0.572	2e-59
O49397	552	Two-component response re	no	no	0.929	0.380	0.546	3e-57
Q8L9Y3	382	Two-component response re	no	no	0.960	0.568	0.512	4e-57
Q9FGT7	635	Two-component response re	no	no	0.902	0.321	0.537	5e-54
Q9LZJ8	426	Putative two-component re	no	no	0.969	0.514	0.417	5e-38
Q9M9B9	407	Putative two-component re	no	no	0.973	0.540	0.367	1e-35
Q7Y0W3	341	Two-component response re	N/A	no	0.991	0.656	0.351	5e-35

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

 Score =  293 bits (751), Expect = 5e-79,   Method: Compositional matrix adjust.
 Identities = 157/232 (67%), Positives = 178/232 (76%), Gaps = 16/232 (6%)

Query: 3   FSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGS 62
           + VTKCNRAE AL +LR NKNG+DIVISDVHMPDMDGFKLLE VGLEMDLPVIMM A  S
Sbjct: 52  YRVTKCNRAESALSLLRKNKNGFDIVISDVHMPDMDGFKLLEHVGLEMDLPVIMMSADDS 111

Query: 63  KEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQS-GSVE--GG---AQ 116
           K VV+KGVTH A DYL KPVRIE LKNIWQHVVRK++NE    E S GS+E  GG    Q
Sbjct: 112 KSVVLKGVTHGAVDYLIKPVRIEALKNIWQHVVRKKRNEWNVSEHSGGSIEDTGGDRDRQ 171

Query: 117 QPKPFEESDDSYSVNEGTS-NSRKDEEEEAEKR---------LKKPRLVWSVELHQQFVS 166
           Q    +  ++S SVNEG   +SRK +EEE + +         LKKPR+VWSVELHQQFV+
Sbjct: 172 QQHREDADNNSSSVNEGNGRSSRKRKEEEVDDQGDDKEDSSSLKKPRVVWSVELHQQFVA 231

Query: 167 AVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGVSPQQGN 218
           AV +LG DKA PKKILE+MN+PGLTRENVASHLQK+R+YL RL GVS  QGN
Sbjct: 232 AVNQLGVDKAVPKKILEMMNVPGLTRENVASHLQKYRIYLRRLGGVSQHQGN 283

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 =  291 bits (746), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 157/244 (64%), Positives = 183/244 (75%), Gaps = 28/244 (11%)

Query: 3   FSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGS 62
           + VTKCNRAE+AL +LR NK+G+DIVISDVHMPDMDGFKLLE VGLEMDLPVIMM A  S
Sbjct: 61  YEVTKCNRAEMALSLLRKNKHGFDIVISDVHMPDMDGFKLLEHVGLEMDLPVIMMSADDS 120

Query: 63  KEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQSGSVE--GGAQQPK- 119
           K VV+KGVTH A DYL KPVR+E LKNIWQHVVRKR++E    E SGS+E  G  QQ + 
Sbjct: 121 KSVVLKGVTHGAVDYLIKPVRMEALKNIWQHVVRKRRSEWSVPEHSGSIEETGERQQQQH 180

Query: 120 ----------PFEES--DDSYSVNEGT---SNSRKDEEEEAEKR----------LKKPRL 154
                       E++  D+S SVNEG    S+SRK ++EE E++          LKKPR+
Sbjct: 181 RGGGGGAAVSGGEDAVDDNSSSVNEGNNWRSSSRKRKDEEGEEQGDDKDEDASNLKKPRV 240

Query: 155 VWSVELHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGVSP 214
           VWSVELHQQFV+AV +LG +KA PKKILELMN+PGLTRENVASHLQK+R+YL RL GVS 
Sbjct: 241 VWSVELHQQFVAAVNQLGVEKAVPKKILELMNVPGLTRENVASHLQKYRIYLRRLGGVSQ 300

Query: 215 QQGN 218
            QGN
Sbjct: 301 HQGN 304

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 =  243 bits (621), Expect = 6e-64,   Method: Compositional matrix adjust.
 Identities = 129/235 (54%), Positives = 157/235 (66%), Gaps = 34/235 (14%)

Query: 3   FSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGS 62
           + VT  N+A+ AL++LR NKN +D+VISDV MPDMDGFKLLELVGLEMDLPVIM+ AH  
Sbjct: 41  YHVTTTNQAQKALELLRENKNKFDLVISDVDMPDMDGFKLLELVGLEMDLPVIMLSAHSD 100

Query: 63  KEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQSGSVEGGAQQPKPFE 122
            + VMKGVTH ACDYL KPVRIEELKNIWQHVVR R ++ +    +G    G        
Sbjct: 101 PKYVMKGVTHGACDYLLKPVRIEELKNIWQHVVRSRFDKNRGSNNNGDKRDG-------- 152

Query: 123 ESDDSYSVNEGTSNSRKDEEEEAEKR--------------------LKKPRLVWSVELHQ 162
                 S NEG  NS ++  +   KR                     KK R+VW+VELH+
Sbjct: 153 ------SGNEGVGNSDQNNGKGNRKRKDQYNEDEDEDRDDNDDSCAQKKQRVVWTVELHK 206

Query: 163 QFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGVSPQQG 217
           +FV+AV +LG++KA PKKIL+LMN+  LTRENVASHLQK RLYL R+SGV+ QQ 
Sbjct: 207 KFVAAVNQLGYEKAMPKKILDLMNVEKLTRENVASHLQKFRLYLKRISGVANQQA 261

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 =  228 bits (582), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 126/220 (57%), Positives = 154/220 (70%), Gaps = 15/220 (6%)

Query: 3   FSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGS 62
           + VT C  A  AL +LR  K+GYDIVISDV+MPDMDGFKLLE VGLE+DLPVIMM   G 
Sbjct: 35  YEVTTCGLAREALRLLRERKDGYDIVISDVNMPDMDGFKLLEHVGLELDLPVIMMSVDGE 94

Query: 63  KEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQSGSVEGGAQQPKPFE 122
              VMKGV H ACDYL KP+R++ELK IWQHV+RK+  E +D+E  G  EGGA     ++
Sbjct: 95  TSRVMKGVQHGACDYLLKPIRMKELKIIWQHVLRKKLQEVRDIEGCG-YEGGADWITRYD 153

Query: 123 ESDDSYSVNEGTSNSRKDEEEEAEKRL------------KKPRLVWSVELHQQFVSAVKE 170
           E+       E  S  +K ++ + EK+L            KK R+VWS ELH +FV+AV +
Sbjct: 154 EA-HFLGGGEDVSFGKKRKDFDFEKKLLQDESDPSSSSSKKARVVWSFELHHKFVNAVNQ 212

Query: 171 LGFD-KAGPKKILELMNIPGLTRENVASHLQKHRLYLSRL 209
           +G D KAGPKKIL+LMN+P LTRENVASHLQK+RLYLSRL
Sbjct: 213 IGCDHKAGPKKILDLMNVPWLTRENVASHLQKYRLYLSRL 252

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 =  221 bits (563), Expect = 3e-57,   Method: Compositional matrix adjust.
 Identities = 118/216 (54%), Positives = 149/216 (68%), Gaps = 6/216 (2%)

Query: 3   FSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGS 62
           + VT  N+A+ AL++LR NKN +D+VISDV MPDMDGFKLLELVGLEMDLPVIM+ AH  
Sbjct: 41  YHVTTTNQAQTALELLRENKNKFDLVISDVDMPDMDGFKLLELVGLEMDLPVIMLSAHSD 100

Query: 63  KEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQSGSVEGGAQQPKPFE 122
            + VMKGV H ACDYL KPVRIEELKNIWQHVVRK K ++     S    G     K   
Sbjct: 101 PKYVMKGVKHGACDYLLKPVRIEELKNIWQHVVRKSKLKKNKSNVS---NGSGNCDKANR 157

Query: 123 ESDDSYSVNEGTSNSRKDEEEEAEKRLKKPRLVWSVELHQQFVSAVKELGFDKAGPKKIL 182
           +  + Y   E       +++  A+   KKPR++W+ ELH +F++AV  LG ++A PKKIL
Sbjct: 158 KRKEQYEEEEEEERGNDNDDPTAQ---KKPRVLWTHELHNKFLAAVDHLGVERAVPKKIL 214

Query: 183 ELMNIPGLTRENVASHLQKHRLYLSRLSGVSPQQGN 218
           +LMN+  LTRENVASHLQK R+ L ++S  + QQ N
Sbjct: 215 DLMNVDKLTRENVASHLQKFRVALKKVSDDAIQQAN 250

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 =  221 bits (562), Expect = 4e-57,   Method: Compositional matrix adjust.
 Identities = 120/234 (51%), Positives = 154/234 (65%), Gaps = 17/234 (7%)

Query: 3   FSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGL-EMDLPVIMMCAHG 61
           + VT C++A++AL +LR  K+ +D+V+SDVHMP M+G+ LL+ VGL EMDLPVIMM   G
Sbjct: 35  YQVTICSQADVALTILRERKDSFDLVLSDVHMPGMNGYNLLQQVGLLEMDLPVIMMSVDG 94

Query: 62  SKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDL---------EQSGSVE 112
               VM G+ H ACDYL KP+R EELKNIWQHVVR++   +K+L         + SGS+E
Sbjct: 95  RTTTVMTGINHGACDYLIKPIRPEELKNIWQHVVRRKCVMKKELRSSQALEDNKNSGSLE 154

Query: 113 GGAQQPKPFEESDDSYSVNEGTSNSRKDEEEEAEKRL-------KKPRLVWSVELHQQFV 165
                     E       N+     R  + ++ E  L       KK R+VWS+ELHQQFV
Sbjct: 155 TVVVSVSECSEESLMKCRNKKKKKKRSVDRDDNEDDLLLDPGNSKKSRVVWSIELHQQFV 214

Query: 166 SAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGVSPQQGNS 219
           +AV +LG DKA PK+ILELMN+PGL+RENVASHLQK RLYL RLSG + Q  +S
Sbjct: 215 NAVNKLGIDKAVPKRILELMNVPGLSRENVASHLQKFRLYLKRLSGEASQSNDS 268

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 =  211 bits (536), Expect = 5e-54,   Method: Compositional matrix adjust.
 Identities = 115/214 (53%), Positives = 148/214 (69%), Gaps = 10/214 (4%)

Query: 3   FSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGS 62
           + VTK   +  AL+MLR N N +D+VISDV MPD DGFKLLE +GLEMDLPVIM+ AH  
Sbjct: 42  YHVTKTMESRKALEMLRENSNMFDLVISDVEMPDTDGFKLLE-IGLEMDLPVIMLSAHSD 100

Query: 63  KEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDL---EQSGSVEGGAQQPK 119
            + VMKG+ H ACDYL KPV ++EL+NIW HVV+K       L    +S SV   +++ K
Sbjct: 101 YDSVMKGIIHGACDYLVKPVGLKELQNIWHHVVKKNIKSYAKLLPPSESDSVPSASRKRK 160

Query: 120 PFEESDDS----YSVNEGTSNSRKDEEEEAEKRLKKPRLVWSVELHQQFVSAVKELGFDK 175
             ++ +DS     S  E       +++ +     KKPR+VWS ELHQ+FVSAV++LG DK
Sbjct: 161 --DKVNDSGDEDDSDREEDDGEGSEQDGDGSGTRKKPRVVWSQELHQKFVSAVQQLGLDK 218

Query: 176 AGPKKILELMNIPGLTRENVASHLQKHRLYLSRL 209
           A PKKIL+LM+I GLTRENVASHLQK+RLYL ++
Sbjct: 219 AVPKKILDLMSIEGLTRENVASHLQKYRLYLKKI 252

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  157 bits (397), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 98/235 (41%), Positives = 137/235 (58%), Gaps = 16/235 (6%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHG 61
            + VTK    E A+  L  NK+  D+VI D HMPD++G   L ++G +MDLPV++M    
Sbjct: 62  SYQVTKYESGEEAMAFLMKNKHEIDLVIWDFHMPDINGLDALNIIGKQMDLPVVIMSHEY 121

Query: 62  SKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQSGSVEGGAQQPKPF 121
            KE VM+ + + ACD+L KPV  E +  +W+HV RKR + +  L++ G  E G  +  P 
Sbjct: 122 KKETVMESIKYGACDFLVKPVSKEVIAVLWRHVYRKRMS-KSGLDKPG--ESGTVESDPD 178

Query: 122 E----ESDDSYSVNEGTSNSRKDEEEEAEKRLKKPRLVWSVELHQQFVSAVKELG-FDKA 176
           E    E D+ Y  NE  S +  D +EE +   KKPR+ W+ ELH +F  AV+++G  +KA
Sbjct: 179 EYDDLEQDNLYESNEEGSKNTCDHKEE-KSPTKKPRMQWTPELHHKFEVAVEKMGSLEKA 237

Query: 177 GPKKILELM----NIPGLTRENVASHLQKHRLYLSRLSGVSPQQGN-SFVSSNIG 226
            PK IL+ M    N+ GLTR NVASHLQK+R   S     +PQ+    FV  N G
Sbjct: 238 FPKTILKYMQEELNVQGLTRNNVASHLQKYR--QSSKKTCTPQEPQEDFVWGNAG 290

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

Arabidopsis thaliana (taxid: 3702)

>sp|Q9M9B9|ARR19_ARATH Putative two-component response regulator ARR19 OS=Arabidopsis thaliana GN=ARR19 PE=2 SV=2

 Score =  149 bits (377), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 87/237 (36%), Positives = 135/237 (56%), Gaps = 17/237 (7%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHG 61
            + V+    AE AL  L + K+  +IVI D HMP +DG + L+ +  ++DLPV++M    
Sbjct: 57  AYQVSIETDAEKALAFLTSCKHEINIVIWDFHMPGIDGLQALKSITSKLDLPVVIMSDDN 116

Query: 62  SKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQSGSVEGGAQQPKPF 121
             E VMK   + ACDY+ KPV+ E + NIWQH+VRKR   + D+         ++  +P 
Sbjct: 117 QTESVMKATFYGACDYVVKPVKEEVMANIWQHIVRKRLIFKPDVAPPKPRMTWSEVFQPV 176

Query: 122 E-----------ESDDSYSVNEGTSNSRKDEEEEAEKRLKKPRLVWSVELHQQFVSAVKE 170
           +           +  DS ++N G  N  ++ E++  K+ +KPR+ W+ ELHQ+F+ A++ 
Sbjct: 177 QSHLVPTDGLDRDHFDSITINGG--NGIQNMEKKQGKKPRKPRMTWTEELHQKFLEAIEI 234

Query: 171 L-GFDKAGPKKILEL---MNIPGLTRENVASHLQKHRLYLSRLSGVSPQQGNSFVSS 223
           + G +KA PK ++E    M I G+TR NVASHLQKHR+ L         QGN + ++
Sbjct: 235 IGGIEKANPKVLVECLQEMRIEGITRSNVASHLQKHRINLEENQIPQQTQGNGWATA 291

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

Arabidopsis thaliana (taxid: 3702)

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

 Score =  147 bits (371), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 84/239 (35%), Positives = 122/239 (51%), Gaps = 15/239 (6%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHG 61
            + VT       A+  +  N    D+VISD   P  DG  +L+ V  +  +P ++M + G
Sbjct: 34  SYKVTTYKNVREAVPFILDNPQIVDLVISDAFFPTEDGLLILQEVTSKFGIPTVIMASSG 93

Query: 62  SKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQSGSVEGGAQQPKPF 121
               VMK V + A D+L KPVRIEEL NIWQH+ RK+  + K+    G++E     P   
Sbjct: 94  DTNTVMKYVANGAFDFLLKPVRIEELSNIWQHIFRKQMQDHKNNNMVGNLEKPGHPPSIL 153

Query: 122 EESDDSYSVNEGTSNSRKDEEEEAEKR---------------LKKPRLVWSVELHQQFVS 166
             +  + +    T+        E E R               L K RL W+ +LH+QF++
Sbjct: 154 AMARATPATTRSTATEASLAPLENEVRDDMVNYNGEITDIRDLGKSRLTWTTQLHRQFIA 213

Query: 167 AVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGVSPQQGNSFVSSNI 225
           AV  LG DKA PKKIL +M +  LTRE VASHLQK+R+ L +    + + G +  S+ +
Sbjct: 214 AVNHLGEDKAVPKKILGIMKVKHLTREQVASHLQKYRMQLKKSIPTTSKHGATLSSTAL 272

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	226
298103716	670	putative B-type response regulator 13 [P	0.973	0.328	0.724	1e-87
313184318	674	putative type-b response regulator (sens	0.973	0.326	0.727	2e-87
255556280	682	sensor histidine kinase, putative [Ricin	0.973	0.322	0.722	2e-87
224106962	634	type-b response regulator [Populus trich	0.973	0.347	0.724	4e-87
449464732	673	PREDICTED: two-component response regula	0.973	0.326	0.714	1e-86
224130444	671	type-b response regulator [Populus trich	0.973	0.327	0.724	2e-86
356521815	679	PREDICTED: two-component response regula	0.973	0.324	0.718	6e-86
298103714	690	putative B-type response regulator 12 [P	0.973	0.318	0.711	2e-85
356556050	672	PREDICTED: two-component response regula	0.977	0.328	0.7	3e-85
356564542	677	PREDICTED: two-component response regula	0.955	0.319	0.723	6e-85

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

 Score =  328 bits (840), Expect = 1e-87,   Method: Compositional matrix adjust.
 Identities = 168/232 (72%), Positives = 187/232 (80%), Gaps = 12/232 (5%)

Query: 3   FSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGS 62
           + VTKCNRAEIAL +LR N+NGYDIVISDVHMPDMDGFKLLEL+GLEMDLPVIMM A   
Sbjct: 41  YEVTKCNRAEIALSLLRENRNGYDIVISDVHMPDMDGFKLLELIGLEMDLPVIMMSADDG 100

Query: 63  KEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQSGSVEGGAQQP-KPF 121
           K VVMKGVTH ACDYL KP+RIE LKNIWQHVVRKRKNE KDLEQSGSVE G  +P K  
Sbjct: 101 KNVVMKGVTHGACDYLIKPIRIEALKNIWQHVVRKRKNEWKDLEQSGSVEEGGDRPQKQS 160

Query: 122 EESDDSYSVNEGT-SNSRKDE-------EEEAEKRLKKPRLVWSVELHQQFVSAVKELGF 173
           E++D S S NEG+  NS++ +       E +    LKKPR+VWSVELHQQFV+AV +LG 
Sbjct: 161 EDADYSSSANEGSWKNSKRRKDEEEEADERDDTSTLKKPRVVWSVELHQQFVAAVNQLGI 220

Query: 174 DKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGVSPQQ---GNSFVS 222
           DKA PKKILELMN+PGLTRENVASHLQK+RLYL RLSGVS  Q   GNSF+S
Sbjct: 221 DKAVPKKILELMNVPGLTRENVASHLQKYRLYLRRLSGVSQHQSGMGNSFIS 272

Source: Populus x canadensis

Species: Populus x canadensis

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  327 bits (839), Expect = 2e-87,   Method: Compositional matrix adjust.
 Identities = 168/231 (72%), Positives = 186/231 (80%), Gaps = 11/231 (4%)

Query: 3   FSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGS 62
           + VTKCNRAEIAL +LR NKNG+DIVISDVHMPDMDGFKLLE VGLEMDLPVIMM A   
Sbjct: 57  YEVTKCNRAEIALSLLRENKNGFDIVISDVHMPDMDGFKLLEQVGLEMDLPVIMMSADDG 116

Query: 63  KEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQSGSVEGGAQQPKPFE 122
           + VVMKGVTH ACDYL KPVRIE LKNIWQHVVRK+KNE KD+EQSGSVE G +Q KP E
Sbjct: 117 QSVVMKGVTHGACDYLIKPVRIEALKNIWQHVVRKKKNEWKDVEQSGSVEEGDRQQKPSE 176

Query: 123 ESDDSYSVNEGT-SNSRKDE-------EEEAEKRLKKPRLVWSVELHQQFVSAVKELGFD 174
           ++D S S NEGT  NS++ +       E +    LKKPR+VWSVELHQQFV AV +LG D
Sbjct: 177 DADYSSSANEGTWKNSKRRKDEEEETDERDDSSTLKKPRVVWSVELHQQFVGAVNQLGID 236

Query: 175 KAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGVSPQQ---GNSFVS 222
           KA PKKILELMN+PGLTRENVASHLQK+RLYL RLSGVS  Q   GNSF+S
Sbjct: 237 KAVPKKILELMNVPGLTRENVASHLQKYRLYLRRLSGVSQHQNNLGNSFMS 287

Source: Malus x domestica

Species: Malus x domestica

Genus: Malus

Family: Rosaceae

Order: Rosales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  327 bits (838), Expect = 2e-87,   Method: Compositional matrix adjust.
 Identities = 167/231 (72%), Positives = 186/231 (80%), Gaps = 11/231 (4%)

Query: 3   FSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGS 62
           + VTKCNRAE AL +LR NKNGYDIVISDVHMPDMDGFKLLE +GLEMDLPVIMM A  +
Sbjct: 57  YEVTKCNRAETALSLLRENKNGYDIVISDVHMPDMDGFKLLEHIGLEMDLPVIMMSADEA 116

Query: 63  KEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQSGSVEGGAQQPKPFE 122
           K VVMKGVTH ACDYL KPVRIE LKNIWQHVVRK++NE KDLEQSGSVE G +QPK  E
Sbjct: 117 KSVVMKGVTHGACDYLIKPVRIEALKNIWQHVVRKKRNEWKDLEQSGSVEEGDRQPKQSE 176

Query: 123 ESDDSYSVNEGT-SNSRKDE-------EEEAEKRLKKPRLVWSVELHQQFVSAVKELGFD 174
           ++D S S NEG   NS+K +       E +    LKKPR+VWSVELHQQFV+AV +LG D
Sbjct: 177 DADYSSSANEGNWRNSKKRKDEEEEGDERDDTSTLKKPRVVWSVELHQQFVAAVNQLGID 236

Query: 175 KAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGVSPQQ---GNSFVS 222
           KA PKKILELMN+PGLTRENVASHLQK+RLYL RLSGVS  Q   GN+F+S
Sbjct: 237 KAVPKKILELMNVPGLTRENVASHLQKYRLYLRRLSGVSQHQNNLGNAFIS 287

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

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 =  326 bits (836), Expect = 4e-87,   Method: Compositional matrix adjust.
 Identities = 168/232 (72%), Positives = 188/232 (81%), Gaps = 12/232 (5%)

Query: 3   FSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGS 62
           + VTKCNRAEIAL +LR N+NGYDIVISDVHMPDMDGFKLLEL+GLEMDLPVIMM A   
Sbjct: 51  YEVTKCNRAEIALSLLRENRNGYDIVISDVHMPDMDGFKLLELIGLEMDLPVIMMSADDG 110

Query: 63  KEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQSGSV-EGGAQQPKPF 121
           K VVMKGVTH ACDYL KP+RIE LKNIWQHVVRKRKNE KDLEQSGSV EGG +Q K  
Sbjct: 111 KNVVMKGVTHGACDYLIKPIRIEALKNIWQHVVRKRKNEWKDLEQSGSVEEGGDRQQKQS 170

Query: 122 EESDDSYSVNEGT-SNSRKDE-------EEEAEKRLKKPRLVWSVELHQQFVSAVKELGF 173
           E++D S S NEG+  NS++ +       E +    LKKPR+VWSVELHQQFV+AV +LG 
Sbjct: 171 EDADYSSSANEGSWKNSKRRKDEEEEADERDDTSTLKKPRVVWSVELHQQFVAAVHQLGI 230

Query: 174 DKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGVSPQQ---GNSFVS 222
           DKA PKKILELMN+PGLTRENVASHLQK+RLYL RLSGVS  Q   GNSF++
Sbjct: 231 DKAVPKKILELMNVPGLTRENVASHLQKYRLYLRRLSGVSQHQSGMGNSFIN 282

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

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 =  324 bits (831), Expect = 1e-86,   Method: Compositional matrix adjust.
 Identities = 165/231 (71%), Positives = 186/231 (80%), Gaps = 11/231 (4%)

Query: 3   FSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGS 62
           ++VTKCNRAEIAL MLR NKNG+DIV+SDVHMPDMDGFKLLE VGLEMDLPVIMM A   
Sbjct: 61  YAVTKCNRAEIALSMLRENKNGFDIVLSDVHMPDMDGFKLLEQVGLEMDLPVIMMSADDG 120

Query: 63  KEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQSGSVEGGAQQPKPFE 122
           K VVMKGV H ACDYL KPVRIE L+N+WQHVVRKRK E KDLEQSGSV+ G ++    E
Sbjct: 121 KNVVMKGVIHGACDYLIKPVRIEALRNLWQHVVRKRKTEWKDLEQSGSVDEGDREQNLSE 180

Query: 123 ESDDSYSVNEGTSNS---RKDEEEEAEKR-----LKKPRLVWSVELHQQFVSAVKELGFD 174
            ++ S S  EG+ NS   R+D EEE E+R     LKKPR+VWSVELHQQFV+AV +LG D
Sbjct: 181 GANYSSSAYEGSWNSSKRRRDAEEEPEERDDTSTLKKPRVVWSVELHQQFVAAVNQLGID 240

Query: 175 KAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGVSPQQG---NSFVS 222
           KA PKKILELMN+PGLTRENVASHLQK+RLYL RLSGVSP Q    NSF++
Sbjct: 241 KAVPKKILELMNVPGLTRENVASHLQKYRLYLRRLSGVSPHQSNLNNSFIN 291

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224130444|ref|XP_002328610.1| type-b response regulator [Populus trichocarpa] gi|222838592|gb|EEE76957.1| type-b response regulator [Populus trichocarpa]

 Score =  323 bits (829), Expect = 2e-86,   Method: Compositional matrix adjust.
 Identities = 168/232 (72%), Positives = 185/232 (79%), Gaps = 12/232 (5%)

Query: 3   FSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGS 62
           + VTKCNRAEIAL +LR NKNGYDIVISDVHMPDMDGFKLLE +GLEMDLPVIMM A   
Sbjct: 58  YEVTKCNRAEIALSLLRENKNGYDIVISDVHMPDMDGFKLLEQIGLEMDLPVIMMSADDG 117

Query: 63  KEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQSGSV-EGGAQQPKPF 121
           K VVMKGVTH ACDYL KP+RIE LKNIWQHVVRKRKNE KDLEQSGSV EGG +Q K  
Sbjct: 118 KNVVMKGVTHGACDYLIKPIRIEALKNIWQHVVRKRKNEWKDLEQSGSVEEGGDRQQKQP 177

Query: 122 EESDDSYSVNEGTSNSRK--------DEEEEAEKRLKKPRLVWSVELHQQFVSAVKELGF 173
           E++D S S NEG+  + K         EE +    LKKPR+VWSVELHQQFV+AV +LG 
Sbjct: 178 EDADYSSSANEGSWKNSKRRKDEEEEAEERDDTSALKKPRVVWSVELHQQFVAAVNQLGI 237

Query: 174 DKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGVSPQQ---GNSFVS 222
           DKA PKKILELMN+PGLTRENVASHLQK+RLYL RLSGVS  Q   G+SF+S
Sbjct: 238 DKAVPKKILELMNVPGLTRENVASHLQKYRLYLRRLSGVSQHQNGMGSSFIS 289

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  322 bits (826), Expect = 6e-86,   Method: Compositional matrix adjust.
 Identities = 166/231 (71%), Positives = 183/231 (79%), Gaps = 11/231 (4%)

Query: 3   FSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGS 62
           + VTKCNRAE AL +LR NKNG+DIVISDVHMPDMDGFKLLE +GLEMDLPVIMM A   
Sbjct: 57  YEVTKCNRAETALSLLRENKNGFDIVISDVHMPDMDGFKLLEHIGLEMDLPVIMMSADDG 116

Query: 63  KEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQSGSVEGGAQQPKPFE 122
           K VVMKGVTH ACDYL KPVRIE LKNIWQHVVRKRKNE KD EQSGS E G +QPK  +
Sbjct: 117 KSVVMKGVTHGACDYLIKPVRIEALKNIWQHVVRKRKNEWKDAEQSGSAEEGDRQPKASD 176

Query: 123 ESDDSYSVNEGT-SNSRK-------DEEEEAEKRLKKPRLVWSVELHQQFVSAVKELGFD 174
           E+D S S NEG+  NS+K        E+ +    LKKPR+VWSVELHQQFV+AV +LG D
Sbjct: 177 EADYSSSANEGSWRNSKKRRDEEEEAEDRDDTSTLKKPRVVWSVELHQQFVAAVDQLGID 236

Query: 175 KAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGVSPQQ---GNSFVS 222
           KA PKKILELMN+PGLTRENVASHLQK+RLYL RLSGVS  Q    NSF+S
Sbjct: 237 KAVPKKILELMNVPGLTRENVASHLQKYRLYLRRLSGVSQHQNNMNNSFLS 287

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|298103714|emb|CBM42558.1| putative B-type response regulator 12 [Populus x canadensis]

 Score =  321 bits (822), Expect = 2e-85,   Method: Compositional matrix adjust.
 Identities = 165/232 (71%), Positives = 185/232 (79%), Gaps = 12/232 (5%)

Query: 3   FSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGS 62
           + VTKCNRAEIAL +LR NKNGYDIVISDVHMPDMDGFKLLE +GLEMDLPVIMM A   
Sbjct: 58  YEVTKCNRAEIALSLLRENKNGYDIVISDVHMPDMDGFKLLEQIGLEMDLPVIMMSADDG 117

Query: 63  KEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQSGSV-EGGAQQPKPF 121
           K VVMKGVTH ACDYL KP+RIE LKNIWQHVVRKRKNE +DLEQSGSV EGG +Q K  
Sbjct: 118 KNVVMKGVTHGACDYLIKPIRIEALKNIWQHVVRKRKNEWRDLEQSGSVEEGGDRQQKQP 177

Query: 122 EESDDSYSVNEGTSNSRK--------DEEEEAEKRLKKPRLVWSVELHQQFVSAVKELGF 173
           E++D S S NEG+  + K         EE +    LKKPR+VWSVELHQQFV+AV +LG 
Sbjct: 178 EDADYSSSANEGSWKNSKRRKDEEEETEERDDTSALKKPRVVWSVELHQQFVAAVNQLGI 237

Query: 174 DKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGVSPQQ---GNSFVS 222
           DKA PKKILELMN+PGLTRENVASHLQK+RLYL R+SGVS  Q   G++F+S
Sbjct: 238 DKAVPKKILELMNVPGLTRENVASHLQKYRLYLRRVSGVSQHQNGMGSTFIS 289

Source: Populus x canadensis

Species: Populus x canadensis

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356556050|ref|XP_003546340.1| PREDICTED: two-component response regulator ARR2-like [Glycine max]

 Score =  320 bits (820), Expect = 3e-85,   Method: Compositional matrix adjust.
 Identities = 161/230 (70%), Positives = 185/230 (80%), Gaps = 9/230 (3%)

Query: 3   FSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGS 62
           + VTKC RAE+AL +LR NKNG+DIV+SDVHMPDMDGFKLLE +GLEMDLPVIMM A   
Sbjct: 53  YEVTKCQRAEVALSLLRENKNGFDIVLSDVHMPDMDGFKLLEHIGLEMDLPVIMMSADDG 112

Query: 63  KEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQSGSVEGGAQQPKPFE 122
           K VVMKGVTH ACDYL KPVRIE LKNIWQHV+RKRKN  +D+EQSGSVE G Q PK  +
Sbjct: 113 KHVVMKGVTHGACDYLIKPVRIEALKNIWQHVIRKRKNGLRDVEQSGSVEEGDQPPKVSD 172

Query: 123 ESDDSYSVNEGTSNSRK------DEEEEAEKRLKKPRLVWSVELHQQFVSAVKELGFDKA 176
           + D S SVNE  S+ ++       +E++    LKKPR+VWSVELHQQF++AV +LG DKA
Sbjct: 173 DGDYSSSVNEARSSKKRRDEDEEGDEKDDSSTLKKPRVVWSVELHQQFMAAVNQLGIDKA 232

Query: 177 GPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGVSPQQG---NSFVSS 223
            PKKILELMN+PGLTRENVASHLQK+RLYL RLSGVS QQG   NSF+SS
Sbjct: 233 VPKKILELMNVPGLTRENVASHLQKYRLYLRRLSGVSQQQGNLNNSFMSS 282

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356564542|ref|XP_003550512.1| PREDICTED: two-component response regulator ARR2-like [Glycine max]

 Score =  319 bits (817), Expect = 6e-85,   Method: Compositional matrix adjust.
 Identities = 162/224 (72%), Positives = 178/224 (79%), Gaps = 8/224 (3%)

Query: 3   FSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGS 62
           + VTKCNRAE AL +LR NKNG+DIVISDVHMPDMDGFKLLE +GLEMDLPVIMM A   
Sbjct: 57  YEVTKCNRAETALSLLRENKNGFDIVISDVHMPDMDGFKLLEHIGLEMDLPVIMMSADDG 116

Query: 63  KEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQSGSVEGGAQQPKPFE 122
           K VVMKGVTH ACDYL KPVRIE LKNIWQHVVRKRKNE KD EQSGS E G + PK  +
Sbjct: 117 KSVVMKGVTHGACDYLIKPVRIEALKNIWQHVVRKRKNEWKDAEQSGSAEEGDRHPKASD 176

Query: 123 ESDDSYSVNEGT-SNSRK-------DEEEEAEKRLKKPRLVWSVELHQQFVSAVKELGFD 174
           E+D S S NEG+  NS+K        E+ +    LKKPR+VWSVELHQQFV+AV +LG D
Sbjct: 177 EADYSSSANEGSWRNSKKRRDEEEEAEDRDDTSTLKKPRVVWSVELHQQFVAAVDQLGID 236

Query: 175 KAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGVSPQQGN 218
           KA PKKILELMN+PGLTRENVASHLQK+RLYL RLSGVS  Q N
Sbjct: 237 KAVPKKILELMNVPGLTRENVASHLQKYRLYLRRLSGVSQHQNN 280

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	226
TAIR|locus:2130095	664	RR2 "response regulator 2" [Ar	0.955	0.325	0.681	5.9e-73
TAIR|locus:2040194	596	RR12 "response regulator 12" [	0.924	0.350	0.591	1.5e-60
TAIR|locus:2008585	521	ARR11 "response regulator 11"	0.911	0.395	0.570	1.2e-56
TAIR|locus:2116587	552	RR10 "response regulator 10" [	0.929	0.380	0.546	8.6e-56
TAIR|locus:2065398	382	RR14 "response regulator 14" [	0.761	0.450	0.521	4.6e-41
TAIR|locus:2093668	690	RR1 "response regulator 1" [Ar	0.637	0.208	0.593	8.3e-40
UNIPROTKB|Q7Y0W3	341	Q7Y0W3 "Two-component response	0.977	0.648	0.360	2.3e-32
UNIPROTKB|Q7Y0W5	341	EHD1 "Two-component response r	0.977	0.648	0.360	2.3e-32
TAIR|locus:2155954	292	APRR4 "pseudo-response regulat	0.871	0.674	0.370	7.9e-30
TAIR|locus:2141020	535	APRR2 [Arabidopsis thaliana (t	0.460	0.194	0.383	2.3e-22

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

 Score = 737 (264.5 bits), Expect = 5.9e-73, P = 5.9e-73
 Identities = 158/232 (68%), Positives = 181/232 (78%)

Query:     3 FSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGS 62
             + VTKCNRAE AL +LR NKNG+DIVISDVHMPDMDGFKLLE VGLEMDLPVIMM A  S
Sbjct:    52 YRVTKCNRAESALSLLRKNKNGFDIVISDVHMPDMDGFKLLEHVGLEMDLPVIMMSADDS 111

Query:    63 KEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQSG-SVE--GGAQ--Q 117
             K VV+KGVTH A DYL KPVRIE LKNIWQHVVRK++NE    E SG S+E  GG +  Q
Sbjct:   112 KSVVLKGVTHGAVDYLIKPVRIEALKNIWQHVVRKKRNEWNVSEHSGGSIEDTGGDRDRQ 171

Query:   118 PKPFEESDD-SYSVNEGTS-NSRKDEEEEAEKR---------LKKPRLVWSVELHQQFVS 166
              +  E++D+ S SVNEG   +SRK +EEE + +         LKKPR+VWSVELHQQFV+
Sbjct:   172 QQHREDADNNSSSVNEGNGRSSRKRKEEEVDDQGDDKEDSSSLKKPRVVWSVELHQQFVA 231

Query:   167 AVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGVSPQQGN 218
             AV +LG DKA PKKILE+MN+PGLTRENVASHLQK+R+YL RL GVS  QGN
Sbjct:   232 AVNQLGVDKAVPKKILEMMNVPGLTRENVASHLQKYRIYLRRLGGVSQHQGN 283

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

 Score = 620 (223.3 bits), Expect = 1.5e-60, P = 1.5e-60
 Identities = 133/225 (59%), Positives = 162/225 (72%)

Query:     3 FSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGS 62
             + VT  N+A+ AL++LR NKN +D+VISDV MPDMDGFKLLELVGLEMDLPVIM+ AH  
Sbjct:    41 YHVTTTNQAQKALELLRENKNKFDLVISDVDMPDMDGFKLLELVGLEMDLPVIMLSAHSD 100

Query:    63 KEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQSGSVEGGAQQPKPFE 122
              + VMKGVTH ACDYL KPVRIEELKNIWQHVVR R ++ +    +G    G+   +   
Sbjct:   101 PKYVMKGVTHGACDYLLKPVRIEELKNIWQHVVRSRFDKNRGSNNNGDKRDGSGN-EGVG 159

Query:   123 ESDDSYSVNEGTSN-SRKDE--EEEAEKR--------LKKPRLVWSVELHQQFVSAVKEL 171
              SD     N G  N  RKD+  E+E E R         KK R+VW+VELH++FV+AV +L
Sbjct:   160 NSDQ----NNGKGNRKRKDQYNEDEDEDRDDNDDSCAQKKQRVVWTVELHKKFVAAVNQL 215

Query:   172 GFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGVSPQQ 216
             G++KA PKKIL+LMN+  LTRENVASHLQK RLYL R+SGV+ QQ
Sbjct:   216 GYEKAMPKKILDLMNVEKLTRENVASHLQKFRLYLKRISGVANQQ 260

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

 Score = 583 (210.3 bits), Expect = 1.2e-56, P = 1.2e-56
 Identities = 125/219 (57%), Positives = 152/219 (69%)

Query:     3 FSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGS 62
             + VT C  A  AL +LR  K+GYDIVISDV+MPDMDGFKLLE VGLE+DLPVIMM   G 
Sbjct:    35 YEVTTCGLAREALRLLRERKDGYDIVISDVNMPDMDGFKLLEHVGLELDLPVIMMSVDGE 94

Query:    63 KEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQSGSVEGGAQQPKPFE 122
                VMKGV H ACDYL KP+R++ELK IWQHV+RK+  E +D+E  G  EGGA     ++
Sbjct:    95 TSRVMKGVQHGACDYLLKPIRMKELKIIWQHVLRKKLQEVRDIEGCG-YEGGADWITRYD 153

Query:   123 ES-------DDSYSVNEGTSNSRK----DEEEEAEKRLKKPRLVWSVELHQQFVSAVKEL 171
             E+       D S+       +  K    DE + +    KK R+VWS ELH +FV+AV ++
Sbjct:   154 EAHFLGGGEDVSFGKKRKDFDFEKKLLQDESDPSSSSSKKARVVWSFELHHKFVNAVNQI 213

Query:   172 GFD-KAGPKKILELMNIPGLTRENVASHLQKHRLYLSRL 209
             G D KAGPKKIL+LMN+P LTRENVASHLQK+RLYLSRL
Sbjct:   214 GCDHKAGPKKILDLMNVPWLTRENVASHLQKYRLYLSRL 252

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 = 575 (207.5 bits), Expect = 8.6e-56, P = 8.6e-56
 Identities = 118/216 (54%), Positives = 150/216 (69%)

Query:     3 FSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGS 62
             + VT  N+A+ AL++LR NKN +D+VISDV MPDMDGFKLLELVGLEMDLPVIM+ AH  
Sbjct:    41 YHVTTTNQAQTALELLRENKNKFDLVISDVDMPDMDGFKLLELVGLEMDLPVIMLSAHSD 100

Query:    63 KEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQSGSVEGGAQQPKPFE 122
              + VMKGV H ACDYL KPVRIEELKNIWQHVVRK K ++    +S    G     K   
Sbjct:   101 PKYVMKGVKHGACDYLLKPVRIEELKNIWQHVVRKSKLKKN---KSNVSNGSGNCDKANR 157

Query:   123 ESDDSYSVNEGTSNSRKDEEEEAEKRLKKPRLVWSVELHQQFVSAVKELGFDKAGPKKIL 182
             +  + Y   E       +++  A+K   KPR++W+ ELH +F++AV  LG ++A PKKIL
Sbjct:   158 KRKEQYEEEEEEERGNDNDDPTAQK---KPRVLWTHELHNKFLAAVDHLGVERAVPKKIL 214

Query:   183 ELMNIPGLTRENVASHLQKHRLYLSRLSGVSPQQGN 218
             +LMN+  LTRENVASHLQK R+ L ++S  + QQ N
Sbjct:   215 DLMNVDKLTRENVASHLQKFRVALKKVSDDAIQQAN 250

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

 Score = 436 (158.5 bits), Expect = 4.6e-41, P = 4.6e-41
 Identities = 98/188 (52%), Positives = 123/188 (65%)

Query:    48 LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQ 107
             LEMDLPVIMM   G    VM G+ H ACDYL KP+R EELKNIWQHVVR++   +K+L  
Sbjct:    81 LEMDLPVIMMSVDGRTTTVMTGINHGACDYLIKPIRPEELKNIWQHVVRRKCVMKKELRS 140

Query:   108 SGSVE----GGAQQP---KPFEESDDSYSV--NEGTSNSRKDEEEEAEKRL-------KK 151
             S ++E     G+ +       E S++S     N+     R  + ++ E  L       KK
Sbjct:   141 SQALEDNKNSGSLETVVVSVSECSEESLMKCRNKKKKKKRSVDRDDNEDDLLLDPGNSKK 200

Query:   152 PRLVWSVELHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSG 211
              R+VWS+ELHQQFV+AV +LG DKA PK+ILELMN+PGL+RENVASHLQK RLYL RLSG
Sbjct:   201 SRVVWSIELHQQFVNAVNKLGIDKAVPKRILELMNVPGLSRENVASHLQKFRLYLKRLSG 260

Query:   212 VSPQQGNS 219
              + Q  +S
Sbjct:   261 EASQSNDS 268

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

 Score = 429 (156.1 bits), Expect = 8.3e-40, P = 8.3e-40
 Identities = 95/160 (59%), Positives = 112/160 (70%)

Query:     3 FSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGS 62
             + VTKCNRAE+AL +LR NK+G+DIVISDVHMPDMDGFKLLE VGLEMDLPVIMM A  S
Sbjct:    61 YEVTKCNRAEMALSLLRKNKHGFDIVISDVHMPDMDGFKLLEHVGLEMDLPVIMMSADDS 120

Query:    63 KEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQSGSVE---------- 112
             K VV+KGVTH A DYL KPVR+E LKNIWQHVVRKR++E    E SGS+E          
Sbjct:   121 KSVVLKGVTHGAVDYLIKPVRMEALKNIWQHVVRKRRSEWSVPEHSGSIEETGERQQQQH 180

Query:   113 ---GGAQQPKPFEES--DDSYSVNEGTSNSRKDEEEEAEK 147
                GG       E++  D+S SVNEG +N R    +  ++
Sbjct:   181 RGGGGGAAVSGGEDAVDDNSSSVNEG-NNWRSSSRKRKDE 219

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

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

 Score = 354 (129.7 bits), Expect = 2.3e-32, P = 2.3e-32
 Identities = 85/236 (36%), Positives = 125/236 (52%)

Query:     3 FSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGS 62
             + VT       A+  +  N    D+VISD   P  DG  +L+ V  +  +P ++M + G 
Sbjct:    35 YKVTTYKNVREAVPFILDNPQIVDLVISDAFFPTEDGLLILQEVTSKFGIPTVIMASSGD 94

Query:    63 KEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQSGSVEGGAQQPKPFE 122
                VMK V + A D+L KPVRIEEL NIWQH+ RK+  + K+    G++E     P    
Sbjct:    95 TNTVMKYVANGAFDFLLKPVRIEELSNIWQHIFRKQMQDHKNNNMVGNLEKPGHPPSILA 154

Query:   123 ESDDSYSVNEGTS---------NSRKDEE-----EEAEKR-LKKPRLVWSVELHQQFVSA 167
              +  + +    T+         N  +D+      E  + R L K RL W+ +LH+QF++A
Sbjct:   155 MARATPATTRSTATEASLAPLENEVRDDMVNYNGEITDIRDLGKSRLTWTTQLHRQFIAA 214

Query:   168 VKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGVSPQQGNSFVSS 223
             V  LG DKA PKKIL +M +  LTRE VASHLQK+R+ L +    + + G +  S+
Sbjct:   215 VNHLGEDKAVPKKILGIMKVKHLTREQVASHLQKYRMQLKKSIPTTSKHGATLSST 270

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 = 354 (129.7 bits), Expect = 2.3e-32, P = 2.3e-32
 Identities = 85/236 (36%), Positives = 125/236 (52%)

Query:     3 FSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGS 62
             + VT       A+  +  N    D+VISD   P  DG  +L+ V  +  +P ++M + G 
Sbjct:    35 YKVTTYKNVREAVPFILDNPQIVDLVISDAFFPTEDGLLILQEVTSKFGIPTVIMASSGD 94

Query:    63 KEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQSGSVEGGAQQPKPFE 122
                VMK V + A D+L KPVRIEEL NIWQH+ RK+  + K+    G++E     P    
Sbjct:    95 TNTVMKYVANGAFDFLLKPVRIEELSNIWQHIFRKQMQDHKNNNMVGNLEKPGHPPSILA 154

Query:   123 ESDDSYSVNEGTS---------NSRKDEE-----EEAEKR-LKKPRLVWSVELHQQFVSA 167
              +  + +    T+         N  +D+      E  + R L K RL W+ +LH+QF++A
Sbjct:   155 MARATPATTRSTATEASLAPLENEVRDDMVNYNGEITDIRDLGKSRLTWTTQLHRQFIAA 214

Query:   168 VKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGVSPQQGNSFVSS 223
             V  LG DKA PKKIL +M +  LTRE VASHLQK+R+ L +    + + G +  S+
Sbjct:   215 VNHLGEDKAVPKKILGIMKVKHLTREQVASHLQKYRMQLKKSIPTTSKHGATLSST 270

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

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

 Score = 330 (121.2 bits), Expect = 7.9e-30, P = 7.9e-30
 Identities = 77/208 (37%), Positives = 118/208 (56%)

Query:     3 FSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGS 62
             + VT CN    A+  LR ++N +D+ +  V+  + D F+ L  +G EMDLP+I++    S
Sbjct:    66 YQVTICNEVNKAMHTLRNHRNRFDLAMIQVNNAEGDIFRFLSEIGSEMDLPIIIISEDDS 125

Query:    63 KEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDL---------EQSGSVEG 113
              + V K + + A DYL KP+R E+L+ +++H+V+K +  R  +         E+S SV G
Sbjct:   126 VKSVKKWMINGAADYLIKPIRPEDLRIVFKHLVKKMRERRSVVTGEAEKAAGEKSSSV-G 184

Query:   114 GAQQPKPFEESDDSYSVNEGTSNSRKDEEEEA-EKRLKKPRLVWSVELHQQFVSAVKELG 172
              +    P +    S    E     R D  + A     KK R+VW  ELHQ F++AV  LG
Sbjct:   185 DSTIRNPNKSKRSSCLEAEVNEEDRHDHNDRACASSAKKRRVVWDEELHQNFLNAVDFLG 244

Query:   173 FDKAGPKKILELMNIPGLTRENVASHLQ 200
              ++A PKKIL++M +  ++RENVASHLQ
Sbjct:   245 LERAVPKKILDVMKVDYISRENVASHLQ 272

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

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

GO:0005634 "nucleus" evidence=ISM

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

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

TAIR|locus:2141020 APRR2 [Arabidopsis thaliana (taxid:3702)]

 Score = 165 (63.1 bits), Expect = 2.3e-22, Sum P(2) = 2.3e-22
 Identities = 41/107 (38%), Positives = 60/107 (56%)

Query:    99 KNERKDLEQSGSVEGGAQQPKPFEESDDSYSVNEGTSNSRKDE--EEEAEKRLKKPRLVW 156
             K ER D E+    E G    +   +S D +   + T    K    +  +  +  + ++ W
Sbjct:   243 KEERGDSEKEEEGETGDLISEK-TDSVDIHKKEDETKPINKSSGIKNVSGNKTSRKKVDW 301

Query:   157 SVELHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHR 203
             + ELH++FV AV++LG D+A P +ILELM +  LTR NVASHLQK R
Sbjct:   302 TPELHKKFVQAVEQLGVDQAIPSRILELMKVGTLTRHNVASHLQKFR 348

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:0007623 "circadian rhythm" evidence=RCA;TAS

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

GO:0005515 "protein binding" evidence=IPI

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	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	226
cd00156	113	cd00156, REC, Signal receiver domain; originally t	4e-20
TIGR01557	57	TIGR01557, myb_SHAQKYF, myb-like DNA-binding domai	3e-19
pfam00072	111	pfam00072, Response_reg, Response regulator receiv	8e-19
COG2204	464	COG2204, AtoC, Response regulator containing CheY-	1e-16
COG0745	229	COG0745, OmpR, Response regulators consisting of a	2e-15
COG0784	130	COG0784, CheY, FOG: CheY-like receiver [Signal tra	8e-15
PLN03162	526	PLN03162, PLN03162, golden-2 like transcription fa	1e-14
COG3437	360	COG3437, COG3437, Response regulator containing a	1e-10
COG3706	435	COG3706, PleD, Response regulator containing a Che	2e-10
COG4753	475	COG4753, COG4753, Response regulator containing Ch	1e-09
PRK15479	221	PRK15479, PRK15479, transcriptional regulatory pro	3e-09
PRK15115	444	PRK15115, PRK15115, response regulator GlrR; Provi	6e-09
TIGR01818	463	TIGR01818, ntrC, nitrogen regulation protein NR(I)	8e-09
PRK10923	469	PRK10923, glnG, nitrogen regulation protein NR(I);	1e-08
PRK10841	924	PRK10841, PRK10841, hybrid sensory kinase in two-c	2e-08
PRK10610	129	PRK10610, PRK10610, chemotaxis regulatory protein	2e-08
COG4566	202	COG4566, TtrR, Response regulator [Signal transduc	4e-08
COG4565	224	COG4565, CitB, Response regulator of citrate/malat	6e-08
COG2197	211	COG2197, CitB, Response regulator containing a Che	1e-07
PRK11361	457	PRK11361, PRK11361, acetoacetate metabolism regula	3e-07
PRK09390	202	PRK09390, fixJ, response regulator FixJ; Provision	3e-07
PRK11083	228	PRK11083, PRK11083, DNA-binding response regulator	3e-07
PRK09581	457	PRK09581, pleD, response regulator PleD; Reviewed	4e-07
COG3947	361	COG3947, COG3947, Response regulator containing Ch	4e-07
PRK10365	441	PRK10365, PRK10365, transcriptional regulatory pro	4e-07
pfam00249	47	pfam00249, Myb_DNA-binding, Myb-like DNA-binding d	2e-06
TIGR01387	218	TIGR01387, cztR_silR_copR, heavy metal response re	2e-06
CHL00148	240	CHL00148, orf27, Ycf27; Reviewed	3e-06
PRK10643	222	PRK10643, PRK10643, DNA-binding transcriptional re	4e-06
PRK11517	223	PRK11517, PRK11517, transcriptional regulatory pro	4e-06
PRK09836	227	PRK09836, PRK09836, DNA-binding transcriptional ac	6e-06
PRK11107	919	PRK11107, PRK11107, hybrid sensory histidine kinas	1e-05
PRK10955	232	PRK10955, PRK10955, DNA-binding transcriptional re	1e-05
COG2201	350	COG2201, CheB, Chemotaxis response regulator conta	1e-04
PLN03029	222	PLN03029, PLN03029, type-a response regulator prot	2e-04
COG4567	182	COG4567, COG4567, Response regulator consisting of	2e-04
PRK10161	229	PRK10161, PRK10161, transcriptional regulator PhoB	3e-04
PRK09468	239	PRK09468, ompR, osmolarity response regulator; Pro	3e-04
TIGR02956	968	TIGR02956, TMAO_torS, TMAO reductase sytem sensor	3e-04
TIGR02154	226	TIGR02154, PhoB, phosphate regulon transcriptional	4e-04
PRK15347	921	PRK15347, PRK15347, two component system sensor ki	5e-04
smart00448	55	smart00448, REC, cheY-homologous receiver domain	8e-04
PRK10529	225	PRK10529, PRK10529, DNA-binding transcriptional ac	0.001
PRK09581	457	PRK09581, pleD, response regulator PleD; Reviewed	0.002
TIGR02875	262	TIGR02875, spore_0_A, sporulation transcription fa	0.002
PRK10816	223	PRK10816, PRK10816, DNA-binding transcriptional re	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 = 81.9 bits (203), Expect = 4e-20
 Identities = 33/95 (34%), Positives = 50/95 (52%), Gaps = 3/95 (3%)

Query: 1   MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLL-ELVGLEMDLPVIMMCA 59
            G+ V +    E AL +L   K   D+++ D+ MP MDG +LL  +     D+P+I + A
Sbjct: 20  EGYEVVEAEDGEEALALLAEEK--PDLILLDIMMPGMDGLELLRRIRKRGPDIPIIFLTA 77

Query: 60  HGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHV 94
           HG  E  ++ +   A DYLTKP   EEL    + +
Sbjct: 78  HGDDEDAVEALKAGADDYLTKPFSPEELLARIRAL 112

Length = 113

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

 Score = 77.8 bits (192), Expect = 3e-19
 Identities = 34/55 (61%), Positives = 45/55 (81%), Gaps = 1/55 (1%)

Query: 151 KPRLVWSVELHQQFVSAVKELG-FDKAGPKKILELMNIPGLTRENVASHLQKHRL 204
           KPR+VW+ +LH +F+ AV++LG  D A PK+ILELM + GLTR+ VASHLQK+RL
Sbjct: 1   KPRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYRL 55

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

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

 Score = 78.0 bits (193), Expect = 8e-19
 Identities = 30/91 (32%), Positives = 51/91 (56%), Gaps = 3/91 (3%)

Query: 1   MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLL-ELVGLEMDLPVIMMCA 59
            G+ V + +  E AL++L+  +   D+++ D+ MP MDG +LL  +       PVI++ A
Sbjct: 21  EGYVVAEADDGEEALELLKEKR--PDLILLDIRMPGMDGLELLRRIRRRPPTTPVIVLTA 78

Query: 60  HGSKEVVMKGVTHDACDYLTKPVRIEELKNI 90
           HG +E  ++ +   A D+L+KP   EEL   
Sbjct: 79  HGDEEDAVEALKAGANDFLSKPFDPEELVAA 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 = 77.7 bits (192), Expect = 1e-16
 Identities = 35/104 (33%), Positives = 59/104 (56%), Gaps = 3/104 (2%)

Query: 1   MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLL-ELVGLEMDLPVIMMCA 59
            G+ V     AE AL+ L   ++ +D+V+ D+ MP MDG +LL E+   + DLPVI+M  
Sbjct: 27  AGYEVVTAESAEEALEALS--ESPFDLVLLDIRMPGMDGLELLKEIKSRDPDLPVIVMTG 84

Query: 60  HGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERK 103
           HG  +  ++ +   A D+L KP  ++ L  I +  +  R+ +R+
Sbjct: 85  HGDIDTAVEALRLGAFDFLEKPFDLDRLLAIVERALELRELQRE 128

Length = 464

>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 = 71.9 bits (177), Expect = 2e-15
 Identities = 28/88 (31%), Positives = 43/88 (48%), Gaps = 5/88 (5%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV--GLEMDLPVIMMCA 59
           G+ V      E AL+  R      D+V+ D+ +PD+DG +L   +        P+I++ A
Sbjct: 24  GYEVDVAADGEEALEAAREQ---PDLVLLDLMLPDLDGLELCRRLRAKKGSGPPIIVLTA 80

Query: 60  HGSKEVVMKGVTHDACDYLTKPVRIEEL 87
              +E  + G+   A DYLTKP    EL
Sbjct: 81  RDDEEDRVLGLEAGADDYLTKPFSPREL 108

Length = 229

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

 Score = 68.3 bits (167), Expect = 8e-15
 Identities = 31/104 (29%), Positives = 58/104 (55%), Gaps = 4/104 (3%)

Query: 1   MGFSVTKC-NRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV-GLEMDLPVIMMC 58
           +G+ V +  +  E AL++LR      D+++ D++MP MDG +LL  +     ++PVI++ 
Sbjct: 28  LGYEVVEAADGEEEALELLRELPQ-PDLILLDINMPGMDGIELLRRLRARGPNIPVILLT 86

Query: 59  AHGSKEVVMKGVTHDACDYLTKPVRIEE-LKNIWQHVVRKRKNE 101
           A+  +    + +   A DYLTKP+ +EE L    + ++ +   E
Sbjct: 87  AYADEADRERALAAGADDYLTKPIFLEEELLAALRRLLARAAAE 130

Length = 130

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

 Score = 71.7 bits (175), Expect = 1e-14
 Identities = 36/89 (40%), Positives = 56/89 (62%)

Query: 123 ESDDSYSVNEGTSNSRKDEEEEAEKRLKKPRLVWSVELHQQFVSAVKELGFDKAGPKKIL 182
           +S +  SV+   + +     + A    KK ++ W+ ELH++FV AV++LG +KA P +IL
Sbjct: 207 DSGECSSVDRKDNQASPKSCKNAAPGKKKAKVDWTPELHRRFVHAVEQLGVEKAFPSRIL 266

Query: 183 ELMNIPGLTRENVASHLQKHRLYLSRLSG 211
           ELM +  LTR N+ASHLQK+R +   L+ 
Sbjct: 267 ELMGVQCLTRHNIASHLQKYRSHRRHLAA 295

Length = 526

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

 Score = 59.7 bits (145), Expect = 1e-10
 Identities = 34/115 (29%), Positives = 60/115 (52%), Gaps = 6/115 (5%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEM----DLPVIMM 57
           G+ V +    E AL +L+      D+V+ DV MP+MDG ++L  +         +PVI++
Sbjct: 38  GYRVIEAENGEEALKLLQEEP--PDLVLLDVRMPEMDGAEVLNKLKAMSPSTRRIPVILL 95

Query: 58  CAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQSGSVE 112
            A+   E   + +   A DYL+KP+  +EL       ++ ++NE   L+Q+  +E
Sbjct: 96  TAYADSEDRQRALEAGADDYLSKPISPKELVARVSSHLQLKRNEDFLLDQNLYLE 150

Length = 360

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

 Score = 59.6 bits (145), Expect = 2e-10
 Identities = 35/113 (30%), Positives = 57/113 (50%), Gaps = 8/113 (7%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLE---MDLPVIMMC 58
           GF V +    E AL  L       D+V+ D +MPDMDG +L   +       D+P+I++ 
Sbjct: 156 GFRVVEATDGEEALLQLAELP--PDLVLLDANMPDMDGLELCTRLRQLERTRDIPIILLS 213

Query: 59  AHGSKEVVMKGVTHDACDYLTKPVRIEELK-NIWQHVVRKRKNE--RKDLEQS 108
           +    E+V++       DY+TKP+   EL+  + + + RKR     R+ LE+ 
Sbjct: 214 SKDDDELVVRAFELGVNDYITKPIEEGELRARLRRQLRRKRYERQLRESLERL 266

Length = 435

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

 Score = 57.0 bits (138), Expect = 1e-09
 Identities = 27/92 (29%), Positives = 50/92 (54%), Gaps = 3/92 (3%)

Query: 14  ALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEM-DLPVIMMCAHGSKEVVMKGVTH 72
           AL++++  +   DIVI+D++MP MDG  L++ +  +  D   I++  +   E   K +  
Sbjct: 40  ALELIQ--ETQPDIVITDINMPGMDGLDLIKAIKEQSPDTEFIILSGYDEFEYAKKAMKL 97

Query: 73  DACDYLTKPVRIEELKNIWQHVVRKRKNERKD 104
              DYL KPV   EL+   + ++ K + ++K 
Sbjct: 98  GVKDYLLKPVDKAELEEALKKIIGKLEEQQKV 129

Length = 475

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

 Score = 54.7 bits (132), Expect = 3e-09
 Identities = 34/112 (30%), Positives = 61/112 (54%), Gaps = 3/112 (2%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLL-ELVGLEMDLPVIMMCAH 60
           GF+V  C    +A D L  ++  Y + + D++MP MDG ++L  L      LPV+++ A 
Sbjct: 24  GFAV-DCVFDGLAADHLLQSEM-YALAVLDINMPGMDGLEVLQRLRKRGQTLPVLLLTAR 81

Query: 61  GSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQSGSVE 112
            +    +KG+   A DYL KP  +EEL    + ++R+   + ++++Q G + 
Sbjct: 82  SAVADRVKGLNVGADDYLPKPFELEELDARLRALLRRSAGQVQEVQQLGELI 133

Length = 221

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

 Score = 54.8 bits (132), Expect = 6e-09
 Identities = 31/87 (35%), Positives = 48/87 (55%), Gaps = 3/87 (3%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLL-ELVGLEMDLPVIMMCAH 60
           G+SV      + AL +L  N+   D+VISD+ M +MDG +L  E+  ++  +PVI++ AH
Sbjct: 29  GYSVVTAESGQEALRVL--NREKVDLVISDLRMDEMDGMQLFAEIQKVQPGMPVIILTAH 86

Query: 61  GSKEVVMKGVTHDACDYLTKPVRIEEL 87
           GS    +         +LTKPV  + L
Sbjct: 87  GSIPDAVAATQQGVFSFLTKPVDRDAL 113

Length = 444

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

 Score = 54.7 bits (132), Expect = 8e-09
 Identities = 26/96 (27%), Positives = 43/96 (44%), Gaps = 5/96 (5%)

Query: 26  DIVISDVHMPDMDGFKLL-ELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTKPVRI 84
           D++I+DV MP  DG  LL ++      LPVI+M AH   +  +      A +YL KP  +
Sbjct: 44  DLLITDVRMPGEDGLDLLPQIKKRHPQLPVIVMTAHSDLDTAVAAYQRGAFEYLPKPFDL 103

Query: 85  EELKNIWQHVVRKRKNERKDLEQSGSVEGGAQQPKP 120
           +E   +    V +     ++     +  G A+    
Sbjct: 104 DEAVTL----VERALAHAQEQVALPADAGEAEDSAE 135

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

 Score = 54.1 bits (130), Expect = 1e-08
 Identities = 29/86 (33%), Positives = 42/86 (48%), Gaps = 3/86 (3%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMD-LPVIMMCAH 60
           G + T        L+ L +     D+++SD+ MP MDG  LL+ +      LPVI+M AH
Sbjct: 27  GLTCTTFENGNEVLEALASKTP--DVLLSDIRMPGMDGLALLKQIKQRHPMLPVIIMTAH 84

Query: 61  GSKEVVMKGVTHDACDYLTKPVRIEE 86
              +  +      A DYL KP  I+E
Sbjct: 85  SDLDAAVSAYQQGAFDYLPKPFDIDE 110

Length = 469

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

 Score = 53.8 bits (130), Expect = 2e-08
 Identities = 38/116 (32%), Positives = 58/116 (50%), Gaps = 32/116 (27%)

Query: 1   MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLE-LVGLEMDLPVIMMCA 59
           +G+     N    AL++L  +KN  DIV++DV+MP+MDG++L + L  L + LPVI    
Sbjct: 824 LGYQCKTANDGVDALNVL--SKNHIDIVLTDVNMPNMDGYRLTQRLRQLGLTLPVI---- 877

Query: 60  HGSKEVVMKGVTHDA-------C------DYLTKPVRIEELKN---IWQHVVRKRK 99
                    GVT +A       C        L+KPV ++ LK    ++   VRK +
Sbjct: 878 ---------GVTANALAEEKQRCLEAGMDSCLSKPVTLDVLKQTLTVYAERVRKSR 924

Length = 924

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

 Score = 51.1 bits (122), Expect = 2e-08
 Identities = 27/71 (38%), Positives = 40/71 (56%), Gaps = 5/71 (7%)

Query: 14  ALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIMMCAHGSKEVVMKGV 70
           AL+ L+    G+  VISD +MP+MDG +LL+ +   G    LPV+M+ A   KE ++   
Sbjct: 42  ALNKLQAG--GFGFVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAA 99

Query: 71  THDACDYLTKP 81
              A  Y+ KP
Sbjct: 100 QAGASGYVVKP 110

Length = 129

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

 Score = 51.5 bits (124), Expect = 4e-08
 Identities = 27/88 (30%), Positives = 42/88 (47%), Gaps = 3/88 (3%)

Query: 1   MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLE-LVGLEMDLPVIMMCA 59
            GF V     AE  L     ++ G   ++ DV MP M G +L + L    + LPVI +  
Sbjct: 27  AGFQVKCFASAEEFLAAAPLDRPG--CLLLDVRMPGMSGLELQDRLAERGIRLPVIFLTG 84

Query: 60  HGSKEVVMKGVTHDACDYLTKPVRIEEL 87
           HG   + ++ +   A D+L KP   ++L
Sbjct: 85  HGDIPMAVQAMKAGAVDFLEKPFSEQDL 112

Length = 202

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

 Score = 51.1 bits (123), Expect = 6e-08
 Identities = 32/111 (28%), Positives = 51/111 (45%), Gaps = 6/111 (5%)

Query: 2   GFS-VTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLL-ELVGLEMDLPVIMMCA 59
           GFS V      E A  ++   K   D+++ D++MPD +G +LL EL      + VI++ A
Sbjct: 25  GFSVVGTAGTLEEAKMIIEEFKP--DLILLDIYMPDGNGIELLPELRSQHYPVDVIVITA 82

Query: 60  HGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRK--NERKDLEQS 108
               E + + + +   DYL KP   E L+       +KR      + L Q 
Sbjct: 83  ASDMETIKEALRYGVVDYLIKPFTFERLQQALTRYRQKRHALESHQQLSQK 133

Length = 224

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

 Score = 50.0 bits (120), Expect = 1e-07
 Identities = 28/84 (33%), Positives = 44/84 (52%), Gaps = 3/84 (3%)

Query: 5   VTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEM-DLPVIMMCAHGSK 63
           V + +  E ALD+ R  K   D+V+ D+ MP MDG + L+ +     D+ V+++ AH   
Sbjct: 29  VGEASNGEEALDLARELK--PDVVLLDLSMPGMDGLEALKQLRARGPDIKVVVLTAHDDP 86

Query: 64  EVVMKGVTHDACDYLTKPVRIEEL 87
             V++ +   A  YL K    EEL
Sbjct: 87  AYVIRALRAGADGYLLKDASPEEL 110

Length = 211

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

 Score = 50.2 bits (120), Expect = 3e-07
 Identities = 32/88 (36%), Positives = 50/88 (56%), Gaps = 3/88 (3%)

Query: 26  DIVISDVHMPDMDGFKLL-ELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTKPVRI 84
           D+V+ D+ MP+MDG K L E+   E   PVI+M A+   E  ++ +   A DY+ KP  +
Sbjct: 50  DVVLMDIRMPEMDGIKALKEMRSHETRTPVILMTAYAEVETAVEALRCGAFDYVIKPFDL 109

Query: 85  EELKNIWQHVVRKR--KNERKDLEQSGS 110
           +EL  I Q  ++ +  K E + L Q+ S
Sbjct: 110 DELNLIVQRALQLQSMKKEIRHLHQALS 137

Length = 457

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

 Score = 48.8 bits (117), Expect = 3e-07
 Identities = 29/81 (35%), Positives = 42/81 (51%), Gaps = 3/81 (3%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLL-ELVGLEMDLPVIMMCAH 60
           GF V     A+  LD L   + G   V++DV MP +DG +LL  L      LPVI+M  H
Sbjct: 27  GFEVRLFESAQAFLDALPGLRFG--CVVTDVRMPGIDGIELLRRLKARGSPLPVIVMTGH 84

Query: 61  GSKEVVMKGVTHDACDYLTKP 81
           G   + ++ +   A D++ KP
Sbjct: 85  GDVPLAVEAMKLGAVDFIEKP 105

Length = 202

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

 Score = 49.2 bits (118), Expect = 3e-07
 Identities = 34/83 (40%), Positives = 46/83 (55%), Gaps = 7/83 (8%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLL-ELVGLEMDLPVIMMCAH 60
           GF+V    R   ALD LR      D+VI DV +PD+ GF+L  +L+     LPVI + A 
Sbjct: 27  GFTVEWFERGLPALDKLRQQ--PPDLVILDVGLPDISGFELCRQLLAFHPALPVIFLTAR 84

Query: 61  GSKEV--VMKGVTHDACDYLTKP 81
            S EV  ++ G+   A DY+ KP
Sbjct: 85  -SDEVDRLV-GLEIGADDYVAKP 105

Length = 228

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

 Score = 49.5 bits (119), Expect = 4e-07
 Identities = 25/83 (30%), Positives = 43/83 (51%), Gaps = 5/83 (6%)

Query: 3   FSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGF---KLLELVGLEMDLPVIMMCA 59
           ++V   +    A+ +    +   DI++ DV MP MDGF   + L+       +PV+M+ A
Sbjct: 27  YTVLTASSGAEAIAICEREQ--PDIILLDVMMPGMDGFEVCRRLKSDPATTHIPVVMVTA 84

Query: 60  HGSKEVVMKGVTHDACDYLTKPV 82
               E  ++G+   A D+LTKP+
Sbjct: 85  LDDPEDRVRGLEAGADDFLTKPI 107

Length = 457

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

 Score = 49.5 bits (118), Expect = 4e-07
 Identities = 34/113 (30%), Positives = 53/113 (46%), Gaps = 12/113 (10%)

Query: 5   VTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLE-LVGLEMDLPVIMMCAHGSK 63
           V  C+    ALD+L   K   D++  D+ MP M+G +  E +  +E  +P+I + +H   
Sbjct: 27  VRSCSHPVEALDLLEVFK--PDLIFLDIVMPYMNGIEFAEQVRDIESAVPIIFISSHAEY 84

Query: 64  EVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQSGSVEGGAQ 116
                G+  D  DYL KPV  E+L       + +R    K +E +   E G Q
Sbjct: 85  ADDSFGMNLD--DYLPKPVTPEKL----NRAIDRRL---KRVELTAEEESGTQ 128

Length = 361

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

 Score = 49.6 bits (118), Expect = 4e-07
 Identities = 30/88 (34%), Positives = 50/88 (56%), Gaps = 3/88 (3%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLL-ELVGLEMDLPVIMMCAH 60
           G++V   N    AL+ +R  +  +D+V+ DV M +MDG   L E+  L   +PV++M A+
Sbjct: 29  GYNVALANSGRQALEQVR--EQVFDLVLCDVRMAEMDGIATLKEIKALNPAIPVLIMTAY 86

Query: 61  GSKEVVMKGVTHDACDYLTKPVRIEELK 88
            S E  ++ +   A DYL KP+  + L+
Sbjct: 87  SSVETAVEALKTGALDYLIKPLDFDNLQ 114

Length = 441

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

 Score = 43.3 bits (103), Expect = 2e-06
 Identities = 12/51 (23%), Positives = 20/51 (39%), Gaps = 4/51 (7%)

Query: 153 RLVWSVELHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHR 203
           R  W+ E  +  + AVK+ G       KI + +  PG T     +    + 
Sbjct: 1   RGPWTPEEDELLIEAVKKHGNGN--WSKIAKHL--PGRTDNQCKNRWNNYL 47

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

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

 Score = 46.7 bits (111), Expect = 2e-06
 Identities = 26/67 (38%), Positives = 38/67 (56%), Gaps = 1/67 (1%)

Query: 22  KNGYDIVISDVHMPDMDGFKLLE-LVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTK 80
           K+ YD++I DV +P MDG+++L+ L       PV+ + A  S    +KG+   A DYL K
Sbjct: 40  KDDYDLIILDVMLPGMDGWQILQTLRRSGKQTPVLFLTARDSVADKVKGLDLGADDYLVK 99

Query: 81  PVRIEEL 87
           P    EL
Sbjct: 100 PFSFSEL 106

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|214376 CHL00148, orf27, Ycf27; Reviewed

 Score = 46.2 bits (110), Expect = 3e-06
 Identities = 35/117 (29%), Positives = 61/117 (52%), Gaps = 4/117 (3%)

Query: 1   MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAH 60
           +G+ V   +  E AL + R  +   D+VI DV MP +DG+ + + +  E D+P+IM+ A 
Sbjct: 29  IGYEVITASDGEEALKLFRKEQP--DLVILDVMMPKLDGYGVCQEIRKESDVPIIMLTAL 86

Query: 61  GSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK--RKNERKDLEQSGSVEGGA 115
           G     + G+   A DY+ KP   +EL+   + V+R+  +K+    +  S  +  G 
Sbjct: 87  GDVSDRITGLELGADDYVVKPFSPKELEARIRSVLRRTNKKSFSSKIPNSSIIRIGF 143

Length = 240

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

 Score = 45.8 bits (109), Expect = 4e-06
 Identities = 27/86 (31%), Positives = 47/86 (54%), Gaps = 1/86 (1%)

Query: 25  YDIVISDVHMPDMDGFKLLELVGLE-MDLPVIMMCAHGSKEVVMKGVTHDACDYLTKPVR 83
           Y +V+ D+ +PD DG  LL     +   LPV+++ A  + E  + G+   A DYL KP  
Sbjct: 45  YSLVVLDLGLPDEDGLHLLRRWRQKKYTLPVLILTARDTLEDRVAGLDVGADDYLVKPFA 104

Query: 84  IEELKNIWQHVVRKRKNERKDLEQSG 109
           +EEL    + ++R+ + + ++  Q G
Sbjct: 105 LEELHARIRALIRRHQGQGENELQVG 130

Length = 222

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

 Score = 45.7 bits (108), Expect = 4e-06
 Identities = 23/66 (34%), Positives = 38/66 (57%)

Query: 22  KNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTKP 81
           K+ Y ++I D+ +P MDG+++L+ +      PVI + A  S +  ++G+   A DYL KP
Sbjct: 42  KDDYALIILDIMLPGMDGWQILQTLRTAKQTPVICLTARDSVDDRVRGLDSGANDYLVKP 101

Query: 82  VRIEEL 87
               EL
Sbjct: 102 FSFSEL 107

Length = 223

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

 Score = 45.3 bits (107), Expect = 6e-06
 Identities = 21/65 (32%), Positives = 40/65 (61%), Gaps = 1/65 (1%)

Query: 24  GYDIVISDVHMPDMDGFKLLELV-GLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTKPV 82
            YD++I D+ +PD++G+ ++ ++      +P++++ A G+ E  +KG+   A DYL KP 
Sbjct: 44  DYDLIILDIMLPDVNGWDIVRMLRSANKGMPILLLTALGTIEHRVKGLELGADDYLVKPF 103

Query: 83  RIEEL 87
              EL
Sbjct: 104 AFAEL 108

Length = 227

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

 Score = 45.6 bits (109), Expect = 1e-05
 Identities = 28/95 (29%), Positives = 48/95 (50%), Gaps = 17/95 (17%)

Query: 5   VTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIMMCAH- 60
           V  C+    A++  +     +D+++ D+ MP MDG +  EL+       + P+I + AH 
Sbjct: 694 VVLCDSGHQAVEQAKQRP--FDLILMDIQMPGMDGIRACELIRQLPHNQNTPIIAVTAHA 751

Query: 61  --GSKEVVMK-GVTHDACDYLTKPVRIEE--LKNI 90
             G +E ++  G+     DYL KP  I+E  LK +
Sbjct: 752 MAGERERLLSAGMD----DYLAKP--IDEAMLKQV 780

Length = 919

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

 Score = 44.4 bits (105), Expect = 1e-05
 Identities = 31/86 (36%), Positives = 45/86 (52%), Gaps = 3/86 (3%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHG 61
           GF+V   +  E ALD+L    +  D+++ DV MP  +G   L+ +      PVIM+ A G
Sbjct: 25  GFNVIVAHDGEQALDLL---DDSIDLLLLDVMMPKKNGIDTLKELRQTHQTPVIMLTARG 81

Query: 62  SKEVVMKGVTHDACDYLTKPVRIEEL 87
           S+   + G+   A DYL KP    EL
Sbjct: 82  SELDRVLGLELGADDYLPKPFNDREL 107

Length = 232

>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 = 1e-04
 Identities = 32/128 (25%), Positives = 52/128 (40%), Gaps = 11/128 (8%)

Query: 6   TKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCA--HGSK 63
           T  N  E A+D ++  K   D++  DV MP MDG + L  +     LPVIM+ +      
Sbjct: 32  TARNGRE-AIDKVKKLKP--DVITLDVEMPVMDGLEALRKIMRLRPLPVIMVSSLTEEGA 88

Query: 64  EVVMKGVTHDACDYLTKPVRI------EELKNIWQHVVRKRKNERKDLEQSGSVEGGAQQ 117
           E  ++ +   A D++ KP         E  + + + V    +  RK L         A +
Sbjct: 89  EATLEALELGAVDFIAKPSGGISLGLDEVAELLIEKVRAAARQNRKSLRTPEPPRAPAFR 148

Query: 118 PKPFEESD 125
           P     + 
Sbjct: 149 PVKPGPAA 156

Length = 350

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

 Score = 40.8 bits (95), Expect = 2e-04
 Identities = 33/143 (23%), Positives = 67/143 (46%), Gaps = 17/143 (11%)

Query: 26  DIVISDVHMPDMDGFKLLELVGLE---MDLPVIMMCAHGSKEVVMKGVTHDACDYLTKPV 82
           +++I+D  MP M G+ LL+ +       ++PV++M +      + + +   A ++  KPV
Sbjct: 74  NLIITDYCMPGMTGYDLLKKIKESSSLRNIPVVIMSSENVPSRITRCLEEGAEEFFLKPV 133

Query: 83  RIEELKNIWQHVVR-KRKNERKDLE-----------QSGSVEGGAQQPKPFEESDDSYSV 130
           ++ +L  +  H+++ K KN++++ +           QS   E  +QQP+   +       
Sbjct: 134 QLSDLNRLKPHMMKTKSKNQKQENQEKQEKLEESEIQSEKQEQPSQQPQSQPQPQQQPQQ 193

Query: 131 NEGTSNSRKDEEEEAEKRLKKPR 153
               +N RK  EE       +PR
Sbjct: 194 P--NNNKRKAMEEGLSPDRTRPR 214

Length = 222

>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 = 40.1 bits (94), Expect = 2e-04
 Identities = 24/87 (27%), Positives = 42/87 (48%), Gaps = 3/87 (3%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV-GLEMDLPVIMMCAH 60
           GF+V      E AL   RT    Y +V  D+ + D  G  ++E +     D+ ++++  +
Sbjct: 33  GFAVVTAESVEEALAAARTAPPAYAVV--DLKLGDGSGLAVIEALRERRADMRIVVLTGY 90

Query: 61  GSKEVVMKGVTHDACDYLTKPVRIEEL 87
            S    ++ V   ACDYL KP   +++
Sbjct: 91  ASIATAVEAVKLGACDYLAKPADADDI 117

Length = 182

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

 Score = 40.5 bits (94), Expect = 3e-04
 Identities = 28/99 (28%), Positives = 53/99 (53%), Gaps = 5/99 (5%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEM---DLPVIMMC 58
           GF   +    + A++ L  N+   D+++ D  +P   G + ++ +  E    D+PV+M+ 
Sbjct: 26  GFQPVEAEDYDSAVNQL--NEPWPDLILLDWMLPGGSGIQFIKHLKRESMTRDIPVVMLT 83

Query: 59  AHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
           A G +E  ++G+   A DY+TKP   +EL    + V+R+
Sbjct: 84  ARGEEEDRVRGLETGADDYITKPFSPKELVARIKAVMRR 122

Length = 229

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

 Score = 40.3 bits (95), Expect = 3e-04
 Identities = 36/144 (25%), Positives = 63/144 (43%), Gaps = 15/144 (10%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLE-LVGLEMDLPVIMMCAH 60
           GF V     AE  +D L T ++ + +++ D+ +P  DG  +   L       P+IM+ A 
Sbjct: 29  GFQVRSAANAE-QMDRLLTRES-FHLMVLDLMLPGEDGLSICRRLRSQNNPTPIIMLTAK 86

Query: 61  GSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQSGSVEGG-AQQPK 119
           G +   + G+   A DYL KP    EL    + V+R++  E         + G  +Q+ +
Sbjct: 87  GEEVDRIVGLEIGADDYLPKPFNPRELLARIRAVLRRQAPE---------LPGAPSQEEE 137

Query: 120 PFEESDDSYSVNEGTSNSRKDEEE 143
                   + +N GT    + +E 
Sbjct: 138 VIAFGK--FKLNLGTRELFRGDEP 159

Length = 239

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

 Score = 40.9 bits (96), Expect = 3e-04
 Identities = 31/138 (22%), Positives = 61/138 (44%), Gaps = 6/138 (4%)

Query: 1   MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLL----ELVGLEMDLPVIM 56
           +G  VT     + AL+    +++ +D+ + D+++PD DG  LL     + G + ++  I 
Sbjct: 725 LGHKVTLAESGQSALECF--HQHAFDLALLDINLPDGDGVTLLQQLRAIYGAKNEVKFIA 782

Query: 57  MCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQSGSVEGGAQ 116
             AH   E V + +      +L KPV  E+L  +   ++   K+  +    S S    + 
Sbjct: 783 FSAHVFNEDVAQYLAAGFDGFLAKPVVEEQLTAMIAVILAGGKSNTEAPVLSASPSFDSA 842

Query: 117 QPKPFEESDDSYSVNEGT 134
                 ++DD    N+ +
Sbjct: 843 SVIENAQADDIPESNQAS 860

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|131209 TIGR02154, PhoB, phosphate regulon transcriptional regulatory protein PhoB

 Score = 40.0 bits (94), Expect = 4e-04
 Identities = 27/89 (30%), Positives = 46/89 (51%), Gaps = 5/89 (5%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLL-ELVGLEM--DLPVIMMC 58
           G+ V +    + AL ++  N+ G D+++ D  +P   G +L   L        +P+IM+ 
Sbjct: 26  GYDVVEAGDGDEALTLI--NERGPDLILLDWMLPGTSGIELCRRLRRRPETRAIPIIMLT 83

Query: 59  AHGSKEVVMKGVTHDACDYLTKPVRIEEL 87
           A G +E  ++G+   A DY+TKP    EL
Sbjct: 84  ARGEEEDRVRGLETGADDYITKPFSPREL 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|237951 PRK15347, PRK15347, two component system sensor kinase SsrA; Provisional

 Score = 40.4 bits (95), Expect = 5e-04
 Identities = 19/68 (27%), Positives = 36/68 (52%), Gaps = 5/68 (7%)

Query: 25  YDIVISDVHMPDMDGFKLLEL-----VGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT 79
           +D+V+ D+ MP +DG +  +L       L+ D  ++ + A+ + E + +        YLT
Sbjct: 735 FDLVLMDIRMPGLDGLETTQLWRDDPNNLDPDCMIVALTANAAPEEIHRCKKAGMNHYLT 794

Query: 80  KPVRIEEL 87
           KPV + +L
Sbjct: 795 KPVTLAQL 802

Length = 921

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

 Score = 36.0 bits (84), Expect = 8e-04
 Identities = 11/35 (31%), Positives = 20/35 (57%), Gaps = 2/35 (5%)

Query: 1  MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMP 35
           G+ V +    E AL++L+  K   D+++ D+ MP
Sbjct: 23 EGYEVDEATDGEEALELLKEEK--PDLILLDIMMP 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|182522 PRK10529, PRK10529, DNA-binding transcriptional activator KdpE; Provisional

 Score = 38.6 bits (90), Expect = 0.001
 Identities = 20/62 (32%), Positives = 34/62 (54%)

Query: 26  DIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTKPVRIE 85
           D++I D+ +PD DG + +  +     +PVI++ A   +   +  +   A DYL+KP  I 
Sbjct: 47  DLIILDLGLPDGDGIEFIRDLRQWSAIPVIVLSARSEESDKIAALDAGADDYLSKPFGIG 106

Query: 86  EL 87
           EL
Sbjct: 107 EL 108

Length = 225

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

 Score = 38.3 bits (90), Expect = 0.002
 Identities = 28/112 (25%), Positives = 50/112 (44%), Gaps = 8/112 (7%)

Query: 3   FSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLL-ELVGLEMD--LPVIMMCA 59
           F V   +    AL      +  YD+VI   +  + D  +L  +L   E    +P++++  
Sbjct: 179 FRVVVVSDPSEALF--NAAETNYDLVIVSANFENYDPLRLCSQLRSKERTRYVPILLLVD 236

Query: 60  HGSKEVVMKGVTHDACDYLTKPV-RIEELKNIWQHVVRKRKNE--RKDLEQS 108
                 ++K +     DYL +P+ + E L  +   + RKR  +  R +LEQS
Sbjct: 237 EDDDPRLVKALELGVNDYLMRPIDKNELLARVRTQIRRKRYQDALRNNLEQS 288

Length = 457

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

 Score = 38.2 bits (89), Expect = 0.002
 Identities = 21/65 (32%), Positives = 34/65 (52%), Gaps = 3/65 (4%)

Query: 26  DIVISDVHMPDMDGFKLLELVGLEMDLP---VIMMCAHGSKEVVMKGVTHDACDYLTKPV 82
           D+V+ D+ MP +DG  +LE +          VIM+ A G +++  + V   A  Y+ KP 
Sbjct: 50  DVVVLDIIMPHLDGIGVLEKLNEIELSARPRVIMLSAFGQEKITQRAVALGADYYVLKPF 109

Query: 83  RIEEL 87
            +E L
Sbjct: 110 DLEIL 114

Spo0A, the stage 0 sporulation protein A, is a transcription factor critical for the initiation of sporulation. It contains a response regulator receiver domain (pfam00072). In Bacillus subtilis, it works together with response regulator Spo0F and the phosphotransferase Spo0B, both of which are missing from at least some sporulating species and thus not part of the endospore forming bacteria minimal gene set. Spo0A, however, is universal among endospore-forming species [Cellular processes, Sporulation and germination]. Length = 262

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

 Score = 37.8 bits (88), Expect = 0.002
 Identities = 25/78 (32%), Positives = 46/78 (58%), Gaps = 1/78 (1%)

Query: 21  NKNGYDIVISDVHMPDMDGFKLLE-LVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT 79
           N++  DI I D+ +PD DG  L+      ++ LP++++ A  S +  ++ ++  A DY+T
Sbjct: 41  NEHLPDIAIVDLGLPDEDGLSLIRRWRSNDVSLPILVLTARESWQDKVEVLSAGADDYVT 100

Query: 80  KPVRIEELKNIWQHVVRK 97
           KP  IEE+    Q ++R+
Sbjct: 101 KPFHIEEVMARMQALMRR 118

Length = 223

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	226
COG4565	224	CitB Response regulator of citrate/malate metaboli	99.86
COG4753	475	Response regulator containing CheY-like receiver d	99.85
COG0745	229	OmpR Response regulators consisting of a CheY-like	99.83
COG2204	464	AtoC Response regulator containing CheY-like recei	99.78
COG4566	202	TtrR Response regulator [Signal transduction mecha	99.77
COG2197	211	CitB Response regulator containing a CheY-like rec	99.75
PRK10046	225	dpiA two-component response regulator DpiA; Provis	99.74
PF00072	112	Response_reg: Response regulator receiver domain;	99.73
PRK11475	207	DNA-binding transcriptional activator BglJ; Provis	99.72
COG4567	182	Response regulator consisting of a CheY-like recei	99.71
COG3437	360	Response regulator containing a CheY-like receiver	99.7
PLN03162	526	golden-2 like transcription factor; Provisional	99.67
PRK10430	239	DNA-binding transcriptional activator DcuR; Provis	99.65
COG3706	435	PleD Response regulator containing a CheY-like rec	99.61
PRK10840	216	transcriptional regulator RcsB; Provisional	99.6
PLN03029	222	type-a response regulator protein; Provisional	99.58
COG3947	361	Response regulator containing CheY-like receiver a	99.58
PRK09958	204	DNA-binding transcriptional activator EvgA; Provis	99.58
PRK11173	237	two-component response regulator; Provisional	99.58
COG0784	130	CheY FOG: CheY-like receiver [Signal transduction	99.57
KOG0519	786	consensus Sensory transduction histidine kinase [S	99.57
PRK10529	225	DNA-binding transcriptional activator KdpE; Provis	99.56
PRK10766	221	DNA-binding transcriptional regulator TorR; Provis	99.56
PRK09483	217	response regulator; Provisional	99.55
PRK10816	223	DNA-binding transcriptional regulator PhoP; Provis	99.55
PRK09836	227	DNA-binding transcriptional activator CusR; Provis	99.53
PRK10841	924	hybrid sensory kinase in two-component regulatory	99.53
PRK10643	222	DNA-binding transcriptional regulator BasR; Provis	99.52
PRK10360	196	DNA-binding transcriptional activator UhpA; Provis	99.52
PRK10701	240	DNA-binding transcriptional regulator RstA; Provis	99.52
PRK13856	241	two-component response regulator VirG; Provisional	99.51
PRK10161	229	transcriptional regulator PhoB; Provisional	99.5
PRK09468	239	ompR osmolarity response regulator; Provisional	99.5
PRK11517	223	transcriptional regulatory protein YedW; Provision	99.5
PRK10336	219	DNA-binding transcriptional regulator QseB; Provis	99.49
PRK10955	232	DNA-binding transcriptional regulator CpxR; Provis	99.49
TIGR03787	227	marine_sort_RR proteobacterial dedicated sortase s	99.48
TIGR02154	226	PhoB phosphate regulon transcriptional regulatory	99.48
CHL00148	240	orf27 Ycf27; Reviewed	99.48
TIGR01387	218	cztR_silR_copR heavy metal response regulator. Mem	99.48
TIGR02915	445	PEP_resp_reg putative PEP-CTERM system response re	99.48
PRK10693	303	response regulator of RpoS; Provisional	99.47
PRK09935	210	transcriptional regulator FimZ; Provisional	99.47
PRK09581	457	pleD response regulator PleD; Reviewed	99.46
PRK11083	228	DNA-binding response regulator CreB; Provisional	99.46
PRK11107	919	hybrid sensory histidine kinase BarA; Provisional	99.46
PRK15347	921	two component system sensor kinase SsrA; Provision	99.46
PRK10100	216	DNA-binding transcriptional regulator CsgD; Provis	99.46
PRK11466	914	hybrid sensory histidine kinase TorS; Provisional	99.45
TIGR01557	57	myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF c	99.45
TIGR02875	262	spore_0_A sporulation transcription factor Spo0A.	99.45
TIGR02956	968	TMAO_torS TMAO reductase sytem sensor TorS. This p	99.43
PRK15115	444	response regulator GlrR; Provisional	99.43
PRK10923	469	glnG nitrogen regulation protein NR(I); Provisiona	99.42
TIGR01818	463	ntrC nitrogen regulation protein NR(I). This model	99.41
PRK14084	246	two-component response regulator; Provisional	99.41
PRK10403	215	transcriptional regulator NarP; Provisional	99.41
PRK11361	457	acetoacetate metabolism regulatory protein AtoC; P	99.4
PRK10365	441	transcriptional regulatory protein ZraR; Provision	99.4
PRK09959	1197	hybrid sensory histidine kinase in two-component r	99.38
PRK10710	240	DNA-binding transcriptional regulator BaeR; Provis	99.38
PRK11697	238	putative two-component response-regulatory protein	99.38
PRK11091	779	aerobic respiration control sensor protein ArcB; P	99.36
PRK15411	207	rcsA colanic acid capsular biosynthesis activation	99.36
PRK15369	211	two component system sensor kinase SsrB; Provision	99.34
PRK15479	221	transcriptional regulatory protein TctD; Provision	99.34
COG3707	194	AmiR Response regulator with putative antiterminat	99.34
PRK12555	337	chemotaxis-specific methylesterase; Provisional	99.32
PRK10651	216	transcriptional regulator NarL; Provisional	99.32
PRK09581	457	pleD response regulator PleD; Reviewed	99.31
PRK13435	145	response regulator; Provisional	99.28
PRK09390	202	fixJ response regulator FixJ; Provisional	99.27
PRK13558	665	bacterio-opsin activator; Provisional	99.22
PRK10610	129	chemotaxis regulatory protein CheY; Provisional	99.2
COG2201	350	CheB Chemotaxis response regulator containing a Ch	99.2
PRK00742	354	chemotaxis-specific methylesterase; Provisional	99.19
PRK09191	261	two-component response regulator; Provisional	99.13
cd00156	113	REC Signal receiver domain; originally thought to	99.11
PRK13837	828	two-component VirA-like sensor kinase; Provisional	99.09
PRK13557	540	histidine kinase; Provisional	98.94
COG3279	244	LytT Response regulator of the LytR/AlgR family [T	98.85
COG3706	435	PleD Response regulator containing a CheY-like rec	98.75
PRK15029	755	arginine decarboxylase; Provisional	98.57
PRK11107	919	hybrid sensory histidine kinase BarA; Provisional	97.58
PF00165	42	HTH_AraC: Bacterial regulatory helix-turn-helix pr	96.93
PF03709	115	OKR_DC_1_N: Orn/Lys/Arg decarboxylase, N-terminal	96.67
PRK09685	302	DNA-binding transcriptional activator FeaR; Provis	96.37
cd02071	122	MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 bin	96.02
TIGR03815	322	CpaE_hom_Actino helicase/secretion neighborhood Cp	96.0
PF02796	45	HTH_7: Helix-turn-helix domain of resolvase; Inter	95.95
TIGR00640	132	acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal	95.5
cd04728	248	ThiG Thiazole synthase (ThiG) is the tetrameric en	95.49
PRK02261	137	methylaspartate mutase subunit S; Provisional	95.33
PRK00208	250	thiG thiazole synthase; Reviewed	95.33
PRK10219	107	DNA-binding transcriptional regulator SoxS; Provis	95.2
PRK11511	127	DNA-binding transcriptional activator MarA; Provis	94.71
PRK09978	274	DNA-binding transcriptional regulator GadX; Provis	94.7
cd02067	119	B12-binding B12 binding domain (B12-BD). This doma	94.45
PRK10130	350	transcriptional regulator EutR; Provisional	94.34
TIGR01501	134	MthylAspMutase methylaspartate mutase, S subunit.	93.95
smart00448	55	REC cheY-homologous receiver domain. CheY regulate	93.49
TIGR02297	287	HpaA 4-hydroxyphenylacetate catabolism regulatory	93.26
PRK10371	302	DNA-binding transcriptional regulator MelR; Provis	92.99
PRK00043	212	thiE thiamine-phosphate pyrophosphorylase; Reviewe	92.64
PF00440	47	TetR_N: Bacterial regulatory proteins, tetR family	92.52
PF06490	109	FleQ: Flagellar regulatory protein FleQ; InterPro:	92.38
PF02954	42	HTH_8: Bacterial regulatory protein, Fis family; I	92.37
TIGR02311	249	HpaI 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldola	92.33
TIGR00343	287	pyridoxal 5'-phosphate synthase, synthase subunit	91.57
cd04727	283	pdxS PdxS is a subunit of the pyridoxal 5'-phospha	91.29
PRK13503	278	transcriptional activator RhaS; Provisional	90.88
PRK15044	295	transcriptional regulator SirC; Provisional	90.87
PRK09940	253	transcriptional regulator YdeO; Provisional	90.7
smart00342	84	HTH_ARAC helix_turn_helix, arabinose operon contro	90.65
PRK15320	251	transcriptional activator SprB; Provisional	90.62
PRK10558	256	alpha-dehydro-beta-deoxy-D-glucarate aldolase; Pro	90.57
PF00249	48	Myb_DNA-binding: Myb-like DNA-binding domain; Inte	90.56
COG4943	524	Predicted signal transduction protein containing s	90.45
PRK01130	221	N-acetylmannosamine-6-phosphate 2-epimerase; Provi	90.31
PRK15186	291	AraC family transcriptional regulator; Provisional	90.05
CHL00162	267	thiG thiamin biosynthesis protein G; Validated	90.0
cd02072	128	Glm_B12_BD B12 binding domain of glutamate mutase	89.92
PRK13502	282	transcriptional activator RhaR; Provisional	89.87
PRK15185	309	transcriptional regulator HilD; Provisional	89.76
COG2207	127	AraC AraC-type DNA-binding domain-containing prote	89.71
PF13384	50	HTH_23: Homeodomain-like domain; PDB: 2X48_C.	89.69
TIGR03239	249	GarL 2-dehydro-3-deoxyglucarate aldolase. In E. co	89.3
COG4977	328	Transcriptional regulator containing an amidase do	89.28
PRK07896	289	nicotinate-nucleotide pyrophosphorylase; Provision	88.94
TIGR01334	277	modD putative molybdenum utilization protein ModD.	88.92
PF13936	44	HTH_38: Helix-turn-helix domain; PDB: 2W48_A.	88.78
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	88.57
PRK12704	520	phosphodiesterase; Provisional	88.48
PLN02591	250	tryptophan synthase	88.43
PF02310	121	B12-binding: B12 binding domain; InterPro: IPR0061	88.35
cd04729	219	NanE N-acetylmannosamine-6-phosphate epimerase (Na	88.33
cd04724	242	Tryptophan_synthase_alpha Ttryptophan synthase (TR	88.29
PRK10572	290	DNA-binding transcriptional regulator AraC; Provis	88.27
PRK10128	267	2-keto-3-deoxy-L-rhamnonate aldolase; Provisional	88.11
TIGR00007	230	phosphoribosylformimino-5-aminoimidazole carboxami	87.87
PF13443	63	HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3	87.8
TIGR02531	88	yecD_yerC TrpR-related protein YerC/YecD. This mod	87.8
COG3355	126	Predicted transcriptional regulator [Transcription	87.29
PRK09393	322	ftrA transcriptional activator FtrA; Provisional	87.2
PRK09426	714	methylmalonyl-CoA mutase; Reviewed	87.13
PRK13111	258	trpA tryptophan synthase subunit alpha; Provisiona	86.77
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	86.42
TIGR00262	256	trpA tryptophan synthase, alpha subunit. Tryptopha	86.12
PRK06096	284	molybdenum transport protein ModD; Provisional	86.11
PRK15340	216	transcriptional regulator InvF; Provisional	86.09
PRK00748	233	1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)met	86.02
PF02001	106	DUF134: Protein of unknown function DUF134; InterP	85.93
TIGR02366	176	DHAK_reg probable dihydroxyacetone kinase regulato	85.91
cd04723	233	HisA_HisF Phosphoribosylformimino-5-aminoimidazole	85.8
cd00564	196	TMP_TenI Thiamine monophosphate synthase (TMP synt	85.6
TIGR01321	94	TrpR trp operon repressor, proteobacterial. This m	84.98
PRK13587	234	1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)met	84.93
TIGR03151	307	enACPred_II putative enoyl-(acyl-carrier-protein)	84.78
PRK05848	273	nicotinate-nucleotide pyrophosphorylase; Provision	84.42
PRK15399	713	lysine decarboxylase LdcC; Provisional	84.37
PRK13501	290	transcriptional activator RhaR; Provisional	84.35
COG5001	663	Predicted signal transduction protein containing a	84.3
cd02069	213	methionine_synthase_B12_BD B12 binding domain of m	84.22
PRK11840	326	bifunctional sulfur carrier protein/thiazole synth	84.19
CHL00200	263	trpA tryptophan synthase alpha subunit; Provisiona	84.07
PRK09975	213	DNA-binding transcriptional regulator EnvR; Provis	84.07
PRK15400	714	lysine decarboxylase CadA; Provisional	83.94
PRK13500	312	transcriptional activator RhaR; Provisional	83.54
TIGR01764	49	excise DNA binding domain, excisionase family. An	83.52
PF01381	55	HTH_3: Helix-turn-helix; InterPro: IPR001387 This	83.51
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	83.36
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	83.17
TIGR00735	254	hisF imidazoleglycerol phosphate synthase, cyclase	83.09
PRK07428	288	nicotinate-nucleotide pyrophosphorylase; Provision	82.97
PF04131	192	NanE: Putative N-acetylmannosamine-6-phosphate epi	82.79
PF12728	51	HTH_17: Helix-turn-helix domain	82.7
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	82.61
PHA01976	67	helix-turn-helix protein	82.53
COG2185	143	Sbm Methylmalonyl-CoA mutase, C-terminal domain/su	82.3
cd02070	201	corrinoid_protein_B12-BD B12 binding domain of cor	82.16
PF03328	221	HpcH_HpaI: HpcH/HpaI aldolase/citrate lyase family	82.06
TIGR01361	260	DAHP_synth_Bsub phospho-2-dehydro-3-deoxyheptonate	81.89
TIGR01305	343	GMP_reduct_1 guanosine monophosphate reductase, eu	81.78
PF04297	101	UPF0122: Putative helix-turn-helix protein, YlxM /	81.42
PRK14996	192	TetR family transcriptional regulator; Provisional	81.2
PRK08385	278	nicotinate-nucleotide pyrophosphorylase; Provision	81.05
TIGR00122	69	birA_repr_reg BirA biotin operon repressor domain.	81.04
PF01729	169	QRPTase_C: Quinolinate phosphoribosyl transferase,	80.7
TIGR00693	196	thiE thiamine-phosphate pyrophosphorylase. This mo	80.67
smart00342	84	HTH_ARAC helix_turn_helix, arabinose operon contro	80.5
cd00452	190	KDPG_aldolase KDPG and KHG aldolase. This family b	80.49
PRK09480	194	slmA division inhibitor protein; Provisional	80.35
TIGR01610	95	phage_O_Nterm phage replication protein O, N-termi	80.34
PRK00767	197	transcriptional regulator BetI; Validated	80.29
PRK13756	205	tetracycline repressor protein TetR; Provisional	80.24
PRK02083	253	imidazole glycerol phosphate synthase subunit HisF	80.12
PF10078	89	DUF2316: Uncharacterized protein conserved in bact	80.06
PF12844	64	HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_	80.02
PRK04180	293	pyridoxal biosynthesis lyase PdxS; Provisional	80.01

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

Probab=99.86  E-value=5.8e-21  Score=147.03  Aligned_cols=100  Identities=28%  Similarity=0.414  Sum_probs=91.1

Q ss_pred             CcE-EEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            2 GFS-VTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         2 g~~-V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      ||. |.+|.+.++|..+++...  |||||+|+-||+.+|++|+..++ ++..+-||++|+-.+.+.+.+|+++||.|||.
T Consensus        25 gF~~vg~A~~~~ea~~~i~~~~--pDLILLDiYmPd~~Gi~lL~~ir~~~~~~DVI~iTAA~d~~tI~~alr~Gv~DYLi  102 (224)
T COG4565          25 GFSVVGTAGTLEEAKMIIEEFK--PDLILLDIYMPDGNGIELLPELRSQHYPVDVIVITAASDMETIKEALRYGVVDYLI  102 (224)
T ss_pred             CceEEEeeccHHHHHHHHHhhC--CCEEEEeeccCCCccHHHHHHHHhcCCCCCEEEEeccchHHHHHHHHhcCchhhee
Confidence            566 568999999999999977  99999999999999999999998 56788999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHhhhhh
Q 027234           80 KPVRIEELKNIWQHVVRKRKNERK  103 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~~~~~~~  103 (226)
                      |||..+.|..++.+..+.+.....
T Consensus       103 KPf~~eRl~~aL~~y~~~r~~l~~  126 (224)
T COG4565         103 KPFTFERLQQALTRYRQKRHALES  126 (224)
T ss_pred             cceeHHHHHHHHHHHHHHHHHHhh
Confidence            999999999999998877665443

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

Probab=99.85  E-value=1.1e-20  Score=162.84  Aligned_cols=101  Identities=29%  Similarity=0.499  Sum_probs=92.3

Q ss_pred             CCcE-EEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEE
Q 027234            1 MGFS-VTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYL   78 (226)
Q Consensus         1 lg~~-V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl   78 (226)
                      +||+ |.+|.||.+|++.+.+..  |||||+|++||+|||+++++.++ ..|++.+|++|++++++++.+|+++|+.|||
T Consensus        26 ~g~eiVgtA~NG~eAleli~e~~--pDiviTDI~MP~mdGLdLI~~ike~~p~~~~IILSGy~eFeYak~Am~lGV~dYL  103 (475)
T COG4753          26 LGIEVVGTAANGKEALELIQETQ--PDIVITDINMPGMDGLDLIKAIKEQSPDTEFIILSGYDEFEYAKKAMKLGVKDYL  103 (475)
T ss_pred             cCCeEEEecccHHHHHHHHHhcC--CCEEEEecCCCCCcHHHHHHHHHHhCCCceEEEEeccchhHHHHHHHhcCchhhe
Confidence            4777 559999999999999977  99999999999999999999998 6789999999999999999999999999999


Q ss_pred             eCCCCHHHHHHHHHHHHHHHhhhhh
Q 027234           79 TKPVRIEELKNIWQHVVRKRKNERK  103 (226)
Q Consensus        79 ~KP~~~~~L~~~l~~~~~~~~~~~~  103 (226)
                      +||++.++|..++.++.........
T Consensus       104 LKP~~k~eL~~~L~ki~~kl~~~~~  128 (475)
T COG4753         104 LKPVDKAELEEALKKIIGKLEEQQK  128 (475)
T ss_pred             eCcCCHHHHHHHHHHHHHHHHHHHh
Confidence            9999999999999998876554433

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

Probab=99.83  E-value=8.3e-20  Score=146.59  Aligned_cols=96  Identities=30%  Similarity=0.485  Sum_probs=89.5

Q ss_pred             CcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhc--CCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            2 GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGL--EMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         2 g~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~--~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      ||+|..+.++.+|++.+..  . ||+||+|++||++||+++|++++.  ...+|||++|+.++.+....+++.|||||+.
T Consensus        24 g~~v~~~~~~~~a~~~~~~--~-~dlviLD~~lP~~dG~~~~~~iR~~~~~~~PIi~Lta~~~~~d~v~gl~~GADDYl~  100 (229)
T COG0745          24 GYEVDVAADGEEALEAARE--Q-PDLVLLDLMLPDLDGLELCRRLRAKKGSGPPIIVLTARDDEEDRVLGLEAGADDYLT  100 (229)
T ss_pred             CCEEEEECCHHHHHHHHhc--C-CCEEEEECCCCCCCHHHHHHHHHhhcCCCCcEEEEECCCcHHHHHHHHhCcCCeeee
Confidence            8999999999999999986  4 999999999999999999999983  4678999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHhh
Q 027234           80 KPVRIEELKNIWQHVVRKRKN  100 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~~~~  100 (226)
                      |||++.+|...++.++++...
T Consensus       101 KPf~~~EL~ARi~a~lRR~~~  121 (229)
T COG0745         101 KPFSPRELLARLRALLRRNAG  121 (229)
T ss_pred             CCCCHHHHHHHHHHHHCcCcC
Confidence            999999999999999976543

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

Probab=99.78  E-value=3.3e-18  Score=147.89  Aligned_cols=98  Identities=34%  Similarity=0.615  Sum_probs=92.0

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||.|.++.++.+|++.+....  ||+||+|+.||++||+++++.++ ..+.+|||++|++.+.+.+..|++.||.|||.
T Consensus        27 ~G~~v~~a~~~~~al~~i~~~~--~~lvl~Di~mp~~~Gl~ll~~i~~~~~~~pVI~~Tg~g~i~~AV~A~k~GA~Dfl~  104 (464)
T COG2204          27 AGYEVVTAESAEEALEALSESP--FDLVLLDIRMPGMDGLELLKEIKSRDPDLPVIVMTGHGDIDTAVEALRLGAFDFLE  104 (464)
T ss_pred             cCCeEEEeCCHHHHHHHHhcCC--CCEEEEecCCCCCchHHHHHHHHhhCCCCCEEEEeCCCCHHHHHHHHhcCcceeee
Confidence            3899999999999999999865  99999999999999999999997 56899999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHhh
Q 027234           80 KPVRIEELKNIWQHVVRKRKN  100 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~~~~  100 (226)
                      |||+++.|...+++++..++.
T Consensus       105 KP~~~~~L~~~v~ral~~~~~  125 (464)
T COG2204         105 KPFDLDRLLAIVERALELREL  125 (464)
T ss_pred             CCCCHHHHHHHHHHHHHHhhh
Confidence            999999999999999886544

>COG4566 TtrR Response regulator [Signal transduction mechanisms]

Probab=99.77  E-value=3.7e-18  Score=129.18  Aligned_cols=99  Identities=25%  Similarity=0.447  Sum_probs=89.8

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||+|.++.++++.|.......  |-++|+|+.||+|+|+++.+++. .....|||++|++.+..-..++++.||.|||.
T Consensus        27 ~G~~v~~~~s~~~fL~~~~~~~--pGclllDvrMPg~sGlelq~~L~~~~~~~PVIfiTGhgDIpmaV~AmK~GAvDFLe  104 (202)
T COG4566          27 AGFQVKCFASAEEFLAAAPLDR--PGCLLLDVRMPGMSGLELQDRLAERGIRLPVIFLTGHGDIPMAVQAMKAGAVDFLE  104 (202)
T ss_pred             CCceeeeecCHHHHHhhccCCC--CCeEEEecCCCCCchHHHHHHHHhcCCCCCEEEEeCCCChHHHHHHHHcchhhHHh
Confidence            3899999999999998865544  89999999999999999999997 56789999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHhhh
Q 027234           80 KPVRIEELKNIWQHVVRKRKNE  101 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~~~~~  101 (226)
                      |||+...|..++++.+......
T Consensus       105 KP~~~q~Lldav~~Al~~~~~~  126 (202)
T COG4566         105 KPFSEQDLLDAVERALARDASR  126 (202)
T ss_pred             CCCchHHHHHHHHHHHHHHHHH
Confidence            9999999999999998765443

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

Probab=99.75  E-value=2.9e-17  Score=130.57  Aligned_cols=99  Identities=29%  Similarity=0.398  Sum_probs=90.1

Q ss_pred             cE-EEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEeC
Q 027234            3 FS-VTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTK   80 (226)
Q Consensus         3 ~~-V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~K   80 (226)
                      ++ |.++.++.++++.+....  ||+||+|+.||+++|+++++.|+ ..++++|+++|.+.+.....++++.||+||+.|
T Consensus        26 ~~vv~~a~~~~~~l~~~~~~~--pdvvl~Dl~mP~~~G~e~~~~l~~~~p~~~vvvlt~~~~~~~v~~al~~Ga~Gyl~K  103 (211)
T COG2197          26 LEVVGEASNGEEALDLARELK--PDVVLLDLSMPGMDGLEALKQLRARGPDIKVVVLTAHDDPAYVIRALRAGADGYLLK  103 (211)
T ss_pred             CEEEEEeCCHHHHHHHhhhcC--CCEEEEcCCCCCCChHHHHHHHHHHCCCCcEEEEeccCCHHHHHHHHHcCCCEEEeC
Confidence            55 557888999999988866  99999999999999999999998 678899999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHhhhhh
Q 027234           81 PVRIEELKNIWQHVVRKRKNERK  103 (226)
Q Consensus        81 P~~~~~L~~~l~~~~~~~~~~~~  103 (226)
                      ..++++|..+++.+..+.....+
T Consensus       104 ~~~~~~l~~ai~~v~~G~~~~~~  126 (211)
T COG2197         104 DASPEELVEAIRAVAAGGTYLPP  126 (211)
T ss_pred             CCCHHHHHHHHHHHHCCCeEeCH
Confidence            99999999999999877655444

>PRK10046 dpiA two-component response regulator DpiA; Provisional

Probab=99.74  E-value=1.1e-16  Score=128.46  Aligned_cols=97  Identities=25%  Similarity=0.325  Sum_probs=87.6

Q ss_pred             CcE-EEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhc-CCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            2 GFS-VTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGL-EMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         2 g~~-V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~-~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      |+. |..+.++.+|++.+....  ||+||+|+.||+++|+++++.++. .+..|||++|+..+.+...+++..||++|+.
T Consensus        29 ~~~~v~~a~~~~~al~~~~~~~--pdlvllD~~mp~~~gle~~~~l~~~~~~~~iivls~~~~~~~~~~al~~Ga~~yl~  106 (225)
T PRK10046         29 GFSQILLAGNLAQARMMIERFK--PGLILLDNYLPDGRGINLLHELVQAHYPGDVVFTTAASDMETVSEAVRCGVFDYLI  106 (225)
T ss_pred             CcEEEEEECCHHHHHHHHHhcC--CCEEEEeCCCCCCcHHHHHHHHHhcCCCCCEEEEEcCCCHHHHHHHHHcCccEEEE
Confidence            464 678999999999998866  999999999999999999999974 5678999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHhh
Q 027234           80 KPVRIEELKNIWQHVVRKRKN  100 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~~~~  100 (226)
                      ||++.++|...++++..+...
T Consensus       107 Kp~~~~~L~~~i~~~~~~~~~  127 (225)
T PRK10046        107 KPIAYERLGQTLTRFRQRKHM  127 (225)
T ss_pred             CCcCHHHHHHHHHHHHHHHHH
Confidence            999999999999988766543

>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=99.73  E-value=1e-16  Score=114.19  Aligned_cols=90  Identities=32%  Similarity=0.591  Sum_probs=84.2

Q ss_pred             CCc-EEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEE
Q 027234            1 MGF-SVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYL   78 (226)
Q Consensus         1 lg~-~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl   78 (226)
                      .|| .|..+.++.+|++.+....  ||+||+|+.||+++|+++++.|+ ..+.+|+|++|...+.....++++.|+++||
T Consensus        21 ~~~~~v~~~~~~~~~~~~~~~~~--~d~iiid~~~~~~~~~~~~~~i~~~~~~~~ii~~t~~~~~~~~~~~~~~g~~~~l   98 (112)
T PF00072_consen   21 AGYEEVTTASSGEEALELLKKHP--PDLIIIDLELPDGDGLELLEQIRQINPSIPIIVVTDEDDSDEVQEALRAGADDYL   98 (112)
T ss_dssp             TTEEEEEEESSHHHHHHHHHHST--ESEEEEESSSSSSBHHHHHHHHHHHTTTSEEEEEESSTSHHHHHHHHHTTESEEE
T ss_pred             CCCCEEEEECCHHHHHHHhcccC--ceEEEEEeeeccccccccccccccccccccEEEecCCCCHHHHHHHHHCCCCEEE
Confidence            378 8999999999999999977  99999999999999999999997 4568999999999999999999999999999


Q ss_pred             eCCCCHHHHHHHHH
Q 027234           79 TKPVRIEELKNIWQ   92 (226)
Q Consensus        79 ~KP~~~~~L~~~l~   92 (226)
                      .||++.++|..+++
T Consensus        99 ~kp~~~~~l~~~i~  112 (112)
T PF00072_consen   99 SKPFSPEELRAAIN  112 (112)
T ss_dssp             ESSSSHHHHHHHHH
T ss_pred             ECCCCHHHHHHhhC
Confidence            99999999998874

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 ....

>PRK11475 DNA-binding transcriptional activator BglJ; Provisional

Probab=99.72  E-value=8.5e-17  Score=127.37  Aligned_cols=96  Identities=10%  Similarity=0.123  Sum_probs=84.2

Q ss_pred             CcEEEEECCHHHHHHHHHhCCCCceEEE---EccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHH-hCCcce
Q 027234            2 GFSVTKCNRAEIALDMLRTNKNGYDIVI---SDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGV-THDACD   76 (226)
Q Consensus         2 g~~V~~~~~~~eal~~l~~~~~~~DlVl---~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~-~~ga~~   76 (226)
                      ||.|..+.+++++++.+....  ||+||   +|+.||+++|+++++.++ ..+.+|||++|+.++......++ +.||.|
T Consensus        17 ~~~v~~~~~~~~~l~~~~~~~--pd~vl~dl~d~~mp~~~Gl~~~~~l~~~~p~~~iIvlt~~~~~~~~~~~~~~~Ga~g   94 (207)
T PRK11475         17 PYKLHTFSSQSSFQDAMSRIS--FSAVIFSLSAMRSERREGLSCLTELAIKFPRMRRLVIADDDIEARLIGSLSPSPLDG   94 (207)
T ss_pred             eeEEEEeCCHHHHHHHhccCC--CCEEEeeccccCCCCCCHHHHHHHHHHHCCCCCEEEEeCCCCHHHHHHHHHHcCCeE
Confidence            567789999999999988755  99998   788999999999999997 56889999999988777666665 799999


Q ss_pred             EEeCCCCHHHHHHHHHHHHHHHh
Q 027234           77 YLTKPVRIEELKNIWQHVVRKRK   99 (226)
Q Consensus        77 yl~KP~~~~~L~~~l~~~~~~~~   99 (226)
                      ||.||.+.++|..+++.++.+..
T Consensus        95 yl~K~~~~~eL~~aI~~v~~G~~  117 (207)
T PRK11475         95 VLSKASTLEILQQELFLSLNGVR  117 (207)
T ss_pred             EEecCCCHHHHHHHHHHHHCCCc
Confidence            99999999999999999987654

>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=3.1e-17  Score=119.61  Aligned_cols=90  Identities=24%  Similarity=0.436  Sum_probs=84.7

Q ss_pred             CcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEeC
Q 027234            2 GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTK   80 (226)
Q Consensus         2 g~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~K   80 (226)
                      ||.|.+|.+.+||+..+++..  |.-.++|+.|.+.+|+.+++.|+ ...+..+|++|++.+...+..|++.||++||.|
T Consensus        33 Gf~v~~a~~~~eal~~art~~--PayAvvDlkL~~gsGL~~i~~lr~~~~d~rivvLTGy~sIATAV~AvKlGA~~YLaK  110 (182)
T COG4567          33 GFAVVTAESVEEALAAARTAP--PAYAVVDLKLGDGSGLAVIEALRERRADMRIVVLTGYASIATAVEAVKLGACDYLAK  110 (182)
T ss_pred             CceeEeeccHHHHHHHHhcCC--CceEEEEeeecCCCchHHHHHHHhcCCcceEEEEecchHHHHHHHHHHhhhhhhcCC
Confidence            899999999999999999976  99999999999999999999998 567899999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHH
Q 027234           81 PVRIEELKNIWQH   93 (226)
Q Consensus        81 P~~~~~L~~~l~~   93 (226)
                      |-+.+++..++.+
T Consensus       111 PAdaDdi~aAl~~  123 (182)
T COG4567         111 PADADDILAALLR  123 (182)
T ss_pred             CCChHHHHHHHhh
Confidence            9999999877654

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

Probab=99.70  E-value=1e-16  Score=132.53  Aligned_cols=95  Identities=31%  Similarity=0.492  Sum_probs=87.6

Q ss_pred             CcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhc-CC---CCcEEEEeccCCHHHHHHHHhCCcceE
Q 027234            2 GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGL-EM---DLPVIMMCAHGSKEVVMKGVTHDACDY   77 (226)
Q Consensus         2 g~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~-~~---~~pvI~ls~~~~~~~~~~a~~~ga~~y   77 (226)
                      ||.|..|.+|++|+++..++.  ||+||+|++||+|||+++|++|+. .+   .+|++++|++.+.+...+++..||++|
T Consensus        38 ~y~v~~ae~g~~a~kl~~~~~--~dlvllD~~mp~mdg~ev~~~lk~~~p~t~~ip~i~lT~~~d~~~~~~~~~~g~~dy  115 (360)
T COG3437          38 GYRVIEAENGEEALKLLQEEP--PDLVLLDVRMPEMDGAEVLNKLKAMSPSTRRIPVILLTAYADSEDRQRALEAGADDY  115 (360)
T ss_pred             ccceeeecCchHHHHHhcccC--CceEEeeccCCCccHHHHHHHHHhcCCcccccceEEEeecCChHHHHHHHHhhHHHH
Confidence            799999999999999998876  999999999999999999999985 55   589999999999999999999999999


Q ss_pred             EeCCCCHHHHHHHHHHHHHHH
Q 027234           78 LTKPVRIEELKNIWQHVVRKR   98 (226)
Q Consensus        78 l~KP~~~~~L~~~l~~~~~~~   98 (226)
                      |.||+++.+|...+...+..+
T Consensus       116 l~KP~~~~~l~~rv~~~~q~k  136 (360)
T COG3437         116 LSKPISPKELVARVSSHLQLK  136 (360)
T ss_pred             hcCCCCHHHHHHHHHHHHHHH
Confidence            999999999999997666544

>PLN03162 golden-2 like transcription factor; Provisional

Probab=99.67  E-value=6.9e-17  Score=132.44  Aligned_cols=62  Identities=52%  Similarity=0.761  Sum_probs=59.3

Q ss_pred             ccCCceeeeHhhHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhccc
Q 027234          149 LKKPRLVWSVELHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLS  210 (226)
Q Consensus       149 ~~~~~~~~~~~l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~  210 (226)
                      .+|+++.||.+||++|+.+++++|.++++||.|+++|++++||+++|+|||||||.+++|+-
T Consensus       233 ~KKpRLrWTpELH~rFVeAV~qLG~dKATPK~ILelMnV~GLTRenVKSHLQKYRl~rk~l~  294 (526)
T PLN03162        233 KKKAKVDWTPELHRRFVHAVEQLGVEKAFPSRILELMGVQCLTRHNIASHLQKYRSHRRHLA  294 (526)
T ss_pred             CCCCcccCCHHHHHHHHHHHHHhCcCccchHHHHHHcCCCCcCHHHHHHHHHHHHHhccccc
Confidence            57899999999999999999999999999999999999999999999999999999998653

>PRK10430 DNA-binding transcriptional activator DcuR; Provisional

Probab=99.65  E-value=1.1e-14  Score=117.82  Aligned_cols=96  Identities=19%  Similarity=0.346  Sum_probs=83.1

Q ss_pred             CcE-EEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            2 GFS-VTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         2 g~~-V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      |+. +..+.++.++++.+......||+||+|+.||+++|+++++.++ ..+.+|+|++|+..+......++..|+++|+.
T Consensus        26 ~~~~~~~~~~~~~a~~~~~~~~~~~DlvilD~~~p~~~G~eli~~l~~~~~~~~vI~ls~~~~~~~~~~al~~Ga~~yl~  105 (239)
T PRK10430         26 GFQCCGTASTLEQAKEIIFNSDTPIDLILLDIYMQQENGLDLLPVLHEAGCKSDVIVISSAADAATIKDSLHYGVVDYLI  105 (239)
T ss_pred             CceEEEEeCCHHHHHHHHHhcCCCCCEEEEecCCCCCCcHHHHHHHHhhCCCCCEEEEECCCcHHHHHHHHHcCCCEEEe
Confidence            455 4478899999998863223399999999999999999999997 45789999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHH
Q 027234           80 KPVRIEELKNIWQHVVRK   97 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~   97 (226)
                      ||++.++|..++.++...
T Consensus       106 Kp~~~~~l~~~i~~~~~~  123 (239)
T PRK10430        106 KPFQASRFEEALTGWRQK  123 (239)
T ss_pred             CCCCHHHHHHHHHHHHHH
Confidence            999999999999876543

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

Probab=99.61  E-value=1.1e-14  Score=125.36  Aligned_cols=97  Identities=31%  Similarity=0.537  Sum_probs=90.0

Q ss_pred             CcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcC---CCCcEEEEeccCCHHHHHHHHhCCcceEE
Q 027234            2 GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLE---MDLPVIMMCAHGSKEVVMKGVTHDACDYL   78 (226)
Q Consensus         2 g~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~---~~~pvI~ls~~~~~~~~~~a~~~ga~~yl   78 (226)
                      ||.|..+.++.+|+..+.+..  ||+||+|+.||++||+++|+.++..   ..+|||++++.++.....+|++.|+.||+
T Consensus       156 g~~v~~a~~~~~Al~~~~e~~--~dlil~d~~mp~~dg~el~~~lr~~~~t~~ipii~~~~~~d~~~~~~Af~~G~~Dyi  233 (435)
T COG3706         156 GFRVVEATDGEEALLQLAELP--PDLVLLDANMPDMDGLELCTRLRQLERTRDIPIILLSSKDDDELVVRAFELGVNDYI  233 (435)
T ss_pred             cceeeeecCHHHHHHHHhcCC--CcEEEEecCCCccCHHHHHHHHhcccccccccEEEEecccchHHHHHHHHcCCcceE
Confidence            799999999999999999876  9999999999999999999999743   46899999999999999999999999999


Q ss_pred             eCCCCHHHHHHHHHHHHHHHhh
Q 027234           79 TKPVRIEELKNIWQHVVRKRKN  100 (226)
Q Consensus        79 ~KP~~~~~L~~~l~~~~~~~~~  100 (226)
                      .||+...+|...+.+.++..+.
T Consensus       234 ~kPi~~~~l~~Rl~~~l~~~~~  255 (435)
T COG3706         234 TKPIEEGELRARLRRQLRRKRY  255 (435)
T ss_pred             ecCCCHHHHHHHHHHHHHhhhH
Confidence            9999999999999988877664

>PRK10840 transcriptional regulator RcsB; Provisional

Probab=99.60  E-value=1.4e-14  Score=115.34  Aligned_cols=93  Identities=16%  Similarity=0.251  Sum_probs=84.0

Q ss_pred             EEEECCHHHHHHHHHhCCCCceEEEEccCCCC---CCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEeC
Q 027234            5 VTKCNRAEIALDMLRTNKNGYDIVISDVHMPD---MDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTK   80 (226)
Q Consensus         5 V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~---~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~K   80 (226)
                      |..+.++.++++.+....  ||+||+|+.||+   ++|+++++.++ ..+.+|||++|...+......+++.||++|+.|
T Consensus        32 v~~~~~~~~~~~~~~~~~--~DlvllD~~l~~~~~~~g~~~~~~l~~~~~~~~iIvls~~~~~~~~~~a~~~Ga~~yl~K  109 (216)
T PRK10840         32 VGEFEDSTALINNLPKLD--AHVLITDLSMPGDKYGDGITLIKYIKRHFPSLSIIVLTMNNNPAILSAVLDLDIEGIVLK  109 (216)
T ss_pred             EEEECCHHHHHHHHHhCC--CCEEEEeCcCCCCCCCCHHHHHHHHHHHCCCCcEEEEEecCCHHHHHHHHHCCCeEEEEC
Confidence            667899999999998766  999999999999   59999999997 457899999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHh
Q 027234           81 PVRIEELKNIWQHVVRKRK   99 (226)
Q Consensus        81 P~~~~~L~~~l~~~~~~~~   99 (226)
                      |.+.++|..+++.+..+..
T Consensus       110 ~~~~~~l~~ai~~v~~g~~  128 (216)
T PRK10840        110 QGAPTDLPKALAALQKGKK  128 (216)
T ss_pred             CCCHHHHHHHHHHHHCCCe
Confidence            9999999999998876543

>PLN03029 type-a response regulator protein; Provisional

Probab=99.58  E-value=6.6e-14  Score=112.24  Aligned_cols=98  Identities=22%  Similarity=0.500  Sum_probs=85.1

Q ss_pred             CCcEEEEECCHHHHHHHHHhCC------------------CCceEEEEccCCCCCCHHHHHHHHhcC---CCCcEEEEec
Q 027234            1 MGFSVTKCNRAEIALDMLRTNK------------------NGYDIVISDVHMPDMDGFKLLELVGLE---MDLPVIMMCA   59 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~------------------~~~DlVl~D~~mp~~dG~~l~~~l~~~---~~~pvI~ls~   59 (226)
                      .||+|.++.++.+|++.+....                  ..+|+||+|+.||+++|+++++.++..   ..+|+|++|+
T Consensus        31 ~g~~v~~a~sg~~al~~l~~~~~d~~~p~~~~~~~~~~~~~~~dlVllD~~mp~~~G~e~l~~ir~~~~~~~ipvIils~  110 (222)
T PLN03029         31 SSYQVTTVDSGSKALKFLGLHEDDRSNPDTPSVSPNSHQEVEVNLIITDYCMPGMTGYDLLKKIKESSSLRNIPVVIMSS  110 (222)
T ss_pred             cCceEEEECCHHHHHHHHHhccccccccccccccccccccccCCEEEEcCCCCCCCHHHHHHHHHhccccCCCcEEEEeC
Confidence            4899999999999999986532                  126799999999999999999999743   4789999999


Q ss_pred             cCCHHHHHHHHhCCcceEEeCCCCHHHHHHHHHHHHHHH
Q 027234           60 HGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKR   98 (226)
Q Consensus        60 ~~~~~~~~~a~~~ga~~yl~KP~~~~~L~~~l~~~~~~~   98 (226)
                      ........+++..|+++||.||++..+|...+.+++..+
T Consensus       111 ~~~~~~~~~al~~Ga~dyl~KP~~~~~L~~l~~~~~~~~  149 (222)
T PLN03029        111 ENVPSRITRCLEEGAEEFFLKPVQLSDLNRLKPHMMKTK  149 (222)
T ss_pred             CCCHHHHHHHHHhCchheEECCCCHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999988877765543

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

Probab=99.58  E-value=3.8e-15  Score=119.81  Aligned_cols=91  Identities=32%  Similarity=0.540  Sum_probs=81.8

Q ss_pred             CcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEeC
Q 027234            2 GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTK   80 (226)
Q Consensus         2 g~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~K   80 (226)
                      |..+..|+...+|++.+....  ||||++|+.||+|+|++|+++++ ..+.+|||++|++.  ++...++.+.++|||+|
T Consensus        24 ~~~~~~~~~~~eal~~Le~~k--pDLifldI~mp~~ngiefaeQvr~i~~~v~iifIssh~--eya~dsf~~n~~dYl~K   99 (361)
T COG3947          24 GHEVRSCSHPVEALDLLEVFK--PDLIFLDIVMPYMNGIEFAEQVRDIESAVPIIFISSHA--EYADDSFGMNLDDYLPK   99 (361)
T ss_pred             cchhhccCCHHHHHHHHHhcC--CCEEEEEeecCCccHHHHHHHHHHhhccCcEEEEecch--hhhhhhcccchHhhccC
Confidence            456788999999999999987  99999999999999999999997 45789999999975  56777888899999999


Q ss_pred             CCCHHHHHHHHHHHHH
Q 027234           81 PVRIEELKNIWQHVVR   96 (226)
Q Consensus        81 P~~~~~L~~~l~~~~~   96 (226)
                      |++++.|..++.++.+
T Consensus       100 Pvt~ekLnraIdr~~k  115 (361)
T COG3947         100 PVTPEKLNRAIDRRLK  115 (361)
T ss_pred             CCCHHHHHHHHHHHhc
Confidence            9999999999988763

>PRK09958 DNA-binding transcriptional activator EvgA; Provisional

Probab=99.58  E-value=1e-13  Score=108.76  Aligned_cols=94  Identities=18%  Similarity=0.243  Sum_probs=85.2

Q ss_pred             CcEEE-EECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhc-CCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            2 GFSVT-KCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGL-EMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         2 g~~V~-~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~-~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      ||.+. .+.++.++++.+....  ||+|++|+.||+++|+++++.++. .+..|+|++++..+......++..|+++|+.
T Consensus        24 ~~~v~~~~~~~~~~~~~~~~~~--~dlvi~d~~~~~~~g~~~~~~l~~~~~~~~ii~ls~~~~~~~~~~~~~~ga~~~i~  101 (204)
T PRK09958         24 DIEILAELTEGGSAVQRVETLK--PDIVIIDVDIPGVNGIQVLETLRKRQYSGIIIIVSAKNDHFYGKHCADAGANGFVS  101 (204)
T ss_pred             CCEEEEEeCCHHHHHHHHHccC--CCEEEEeCCCCCCCHHHHHHHHHhhCCCCeEEEEeCCCCHHHHHHHHHCCCCEEEe
Confidence            67776 6899999999998765  999999999999999999999974 5678999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHH
Q 027234           80 KPVRIEELKNIWQHVVRK   97 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~   97 (226)
                      ||++.++|...++.+.++
T Consensus       102 kp~~~~~l~~~i~~~~~~  119 (204)
T PRK09958        102 KKEGMNNIIAAIEAAKNG  119 (204)
T ss_pred             cCCCHHHHHHHHHHHHcC
Confidence            999999999999988754

>PRK11173 two-component response regulator; Provisional

Probab=99.58  E-value=4.4e-14  Score=113.74  Aligned_cols=96  Identities=20%  Similarity=0.369  Sum_probs=88.3

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEeC
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTK   80 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~K   80 (226)
                      .||.|..+.++.++++.+....  ||+||+|+.||+++|+++++.++..+.+|+|++|+..+......++..||++|+.|
T Consensus        26 ~g~~v~~~~~~~~~~~~~~~~~--~dlvild~~l~~~~g~~~~~~lr~~~~~pii~lt~~~~~~~~~~~~~~ga~d~l~k  103 (237)
T PRK11173         26 EGYDVFEATDGAEMHQILSEND--INLVIMDINLPGKNGLLLARELREQANVALMFLTGRDNEVDKILGLEIGADDYITK  103 (237)
T ss_pred             cCCEEEEECCHHHHHHHHhhCC--CCEEEEcCCCCCCCHHHHHHHHhcCCCCCEEEEECCCCHHHHHHHHHCCCCEEEEC
Confidence            3789999999999999998765  99999999999999999999998667899999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHH
Q 027234           81 PVRIEELKNIWQHVVRKR   98 (226)
Q Consensus        81 P~~~~~L~~~l~~~~~~~   98 (226)
                      |++..+|...++.+++..
T Consensus       104 P~~~~eL~~~i~~~l~r~  121 (237)
T PRK11173        104 PFNPRELTIRARNLLSRT  121 (237)
T ss_pred             CCCHHHHHHHHHHHHhcc
Confidence            999999999999887653

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

Probab=99.57  E-value=6.2e-14  Score=102.27  Aligned_cols=93  Identities=32%  Similarity=0.576  Sum_probs=80.0

Q ss_pred             CCcEEEEECCHH-HHHHHHHhC-CCCceEEEEccCCCCCCHHHHHHHHhcC-CCCcEEEEeccCCHHHHHHHHhCCcceE
Q 027234            1 MGFSVTKCNRAE-IALDMLRTN-KNGYDIVISDVHMPDMDGFKLLELVGLE-MDLPVIMMCAHGSKEVVMKGVTHDACDY   77 (226)
Q Consensus         1 lg~~V~~~~~~~-eal~~l~~~-~~~~DlVl~D~~mp~~dG~~l~~~l~~~-~~~pvI~ls~~~~~~~~~~a~~~ga~~y   77 (226)
                      +||.|..+.++. +|++.++.. .  ||+|++|+.||++||+++++.++.. ..+|+|++|+.........++..|+++|
T Consensus        28 ~g~~v~~a~~g~~~al~~~~~~~~--~dlii~D~~mp~~~G~~~~~~l~~~~~~~pvv~~t~~~~~~~~~~~~~~g~~~~  105 (130)
T COG0784          28 LGYEVVEAADGEEEALELLRELPQ--PDLILLDINMPGMDGIELLRRLRARGPNIPVILLTAYADEADRERALAAGADDY  105 (130)
T ss_pred             cCCeEEEeCChHHHHHHHHHhCCC--CCEEEEeCCCCCCCHHHHHHHHHhCCCCCCEEEEEcCcCHHHHHHHHHcCCCeE
Confidence            368899999995 999999975 4  9999999999999999999999855 6788888999988887777899999999


Q ss_pred             EeCCCCHHH-HHHHHHHHH
Q 027234           78 LTKPVRIEE-LKNIWQHVV   95 (226)
Q Consensus        78 l~KP~~~~~-L~~~l~~~~   95 (226)
                      +.||+...+ |...+.+.+
T Consensus       106 l~kP~~~~~~l~~~i~~~~  124 (130)
T COG0784         106 LTKPIFLEEELLAALRRLL  124 (130)
T ss_pred             EcCCCCcHHHHHHHHHHHH
Confidence            999977766 677776544

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

Probab=99.57  E-value=8.9e-15  Score=136.00  Aligned_cols=94  Identities=28%  Similarity=0.528  Sum_probs=85.9

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcC--CCCcEEEEeccCCHHHHHHHHhCCcceEE
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLE--MDLPVIMMCAHGSKEVVMKGVTHDACDYL   78 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~--~~~pvI~ls~~~~~~~~~~a~~~ga~~yl   78 (226)
                      +|.+|+++.+|.||++.+... +.||+||+|++||.|||++..++|+..  ..+|||.+|+....+...+|++.|.++||
T Consensus       689 ~g~~~~~~~sg~e~l~~~~~~-~~y~~ifmD~qMP~mDG~e~~~~irk~~~~~~pIvAlTa~~~~~~~~~c~~~Gmd~yl  767 (786)
T KOG0519|consen  689 LGAEVTEVNSGQEALDKLKPP-HSYDVIFMDLQMPEMDGYEATREIRKKERWHLPIVALTADADPSTEEECLEVGMDGYL  767 (786)
T ss_pred             hCCeeEeecCcHHHHHhcCCC-CcccEEEEEcCCcccchHHHHHHHHHhhcCCCCEEEEecCCcHHHHHHHHHhCCceEE
Confidence            588999999999999999822 459999999999999999999999743  58999999999999999999999999999


Q ss_pred             eCCCCHHHHHHHHHHHH
Q 027234           79 TKPVRIEELKNIWQHVV   95 (226)
Q Consensus        79 ~KP~~~~~L~~~l~~~~   95 (226)
                      .|||+.+.|...+.+++
T Consensus       768 ~KP~~~~~l~~~l~~~~  784 (786)
T KOG0519|consen  768 SKPFTLEKLVKILREFL  784 (786)
T ss_pred             cccccHHHHHHHHHHHh
Confidence            99999999999988775

>PRK10529 DNA-binding transcriptional activator KdpE; Provisional

Probab=99.56  E-value=7.1e-14  Score=111.35  Aligned_cols=95  Identities=27%  Similarity=0.403  Sum_probs=87.3

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEeC
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTK   80 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~K   80 (226)
                      .||.+..+.++.+++..+....  ||+||+|+.||+++|+++++.++..+.+|+|++|+..+.+....++..|+++|+.|
T Consensus        24 ~g~~v~~~~~~~~~~~~~~~~~--~dlvild~~l~~~~g~~~~~~lr~~~~~pvi~lt~~~~~~~~~~~~~~ga~~~l~k  101 (225)
T PRK10529         24 DGMRVFEAETLQRGLLEAATRK--PDLIILDLGLPDGDGIEFIRDLRQWSAIPVIVLSARSEESDKIAALDAGADDYLSK  101 (225)
T ss_pred             CCCEEEEeCCHHHHHHHHhcCC--CCEEEEeCCCCCCCHHHHHHHHHcCCCCCEEEEECCCCHHHHHHHHHcCCCEEEeC
Confidence            3788999999999999887755  99999999999999999999998777899999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHH
Q 027234           81 PVRIEELKNIWQHVVRK   97 (226)
Q Consensus        81 P~~~~~L~~~l~~~~~~   97 (226)
                      |++.++|...++.+++.
T Consensus       102 P~~~~~l~~~i~~~~~~  118 (225)
T PRK10529        102 PFGIGELQARLRVALRR  118 (225)
T ss_pred             CCCHHHHHHHHHHHHhh
Confidence            99999999999887764

>PRK10766 DNA-binding transcriptional regulator TorR; Provisional

Probab=99.56  E-value=9.1e-14  Score=110.41  Aligned_cols=95  Identities=19%  Similarity=0.385  Sum_probs=87.9

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEeC
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTK   80 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~K   80 (226)
                      .||.|..+.++.++++.+....  ||+|++|..||+++|+++++.++..+.+|+|++++..+......++..||++|+.|
T Consensus        25 ~~~~v~~~~~~~~~~~~~~~~~--~dlvild~~l~~~~g~~~~~~lr~~~~~~ii~l~~~~~~~~~~~~l~~Ga~d~l~k  102 (221)
T PRK10766         25 EGYTVSEAASGAGMREIMQNQH--VDLILLDINLPGEDGLMLTRELRSRSTVGIILVTGRTDSIDRIVGLEMGADDYVTK  102 (221)
T ss_pred             cCCEEEEECCHHHHHHHHhcCC--CCEEEEeCCCCCCCHHHHHHHHHhCCCCCEEEEECCCcHHHHHHHHHcCCCcEEeC
Confidence            3789999999999999988765  99999999999999999999998667899999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHH
Q 027234           81 PVRIEELKNIWQHVVRK   97 (226)
Q Consensus        81 P~~~~~L~~~l~~~~~~   97 (226)
                      |++..+|...+..+++.
T Consensus       103 P~~~~~L~~~i~~~~~r  119 (221)
T PRK10766        103 PLELRELLVRVKNLLWR  119 (221)
T ss_pred             CCCHHHHHHHHHHHHhh
Confidence            99999999999988765

>PRK09483 response regulator; Provisional

Probab=99.55  E-value=1.3e-13  Score=109.16  Aligned_cols=96  Identities=25%  Similarity=0.371  Sum_probs=86.3

Q ss_pred             CcEEE-EECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            2 GFSVT-KCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         2 g~~V~-~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      |+.+. .+.++.+++..+....  ||+||+|+.+|+++|+++++.++ ..+.+|+|++|...+......++..|+++|+.
T Consensus        26 ~~~~v~~~~~~~~~~~~~~~~~--~dlvi~d~~~~~~~g~~~~~~l~~~~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~  103 (217)
T PRK09483         26 GIKVVGEACCGEDAVKWCRTNA--VDVVLMDMNMPGIGGLEATRKILRYTPDVKIIMLTVHTENPLPAKVMQAGAAGYLS  103 (217)
T ss_pred             CCEEEEEeCCHHHHHHHHHhcC--CCEEEEeCCCCCCCHHHHHHHHHHHCCCCeEEEEeCCCCHHHHHHHHHcCCCEEEe
Confidence            56665 7899999999998866  99999999999999999999986 46789999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHh
Q 027234           80 KPVRIEELKNIWQHVVRKRK   99 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~~~   99 (226)
                      ||++.++|...++.+..+..
T Consensus       104 k~~~~~~l~~~i~~~~~g~~  123 (217)
T PRK09483        104 KGAAPQEVVSAIRSVHSGQR  123 (217)
T ss_pred             CCCCHHHHHHHHHHHHCCCc
Confidence            99999999999999876543

>PRK10816 DNA-binding transcriptional regulator PhoP; Provisional

Probab=99.55  E-value=1.1e-13  Score=110.26  Aligned_cols=95  Identities=31%  Similarity=0.435  Sum_probs=87.4

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhc-CCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGL-EMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~-~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||.|..+.++.+|+..+....  ||+|++|+.||+++|+++++.++. .+.+|+|++|+..+.+....++..||++|+.
T Consensus        23 ~g~~v~~~~~~~~~l~~~~~~~--~dlvild~~l~~~~g~~l~~~lr~~~~~~pii~ls~~~~~~~~~~~l~~Ga~d~l~  100 (223)
T PRK10816         23 AGHQVDAAEDAKEADYYLNEHL--PDIAIVDLGLPDEDGLSLIRRWRSNDVSLPILVLTARESWQDKVEVLSAGADDYVT  100 (223)
T ss_pred             CCCEEEEECCHHHHHHHHhhCC--CCEEEEECCCCCCCHHHHHHHHHhcCCCCCEEEEEcCCCHHHHHHHHHcCCCeeEe
Confidence            3789999999999999998766  999999999999999999999974 5789999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHH
Q 027234           80 KPVRIEELKNIWQHVVRK   97 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~   97 (226)
                      ||++..+|...+..++++
T Consensus       101 kp~~~~eL~~~i~~~~~~  118 (223)
T PRK10816        101 KPFHIEEVMARMQALMRR  118 (223)
T ss_pred             CCCCHHHHHHHHHHHHhc
Confidence            999999999999988764

>PRK09836 DNA-binding transcriptional activator CusR; Provisional

Probab=99.53  E-value=2e-13  Score=109.04  Aligned_cols=95  Identities=27%  Similarity=0.548  Sum_probs=86.7

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhc-CCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGL-EMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~-~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||.|..+.++.++++.+....  ||+||+|+.||+++|+++++.++. .+.+|+|++|+..+.+....++..||++|+.
T Consensus        23 ~g~~v~~~~~~~~~~~~~~~~~--~dlvild~~~~~~~g~~~~~~lr~~~~~~pii~ls~~~~~~~~~~~~~~Ga~~~l~  100 (227)
T PRK09836         23 AGFVVDLADNGLNGYHLAMTGD--YDLIILDIMLPDVNGWDIVRMLRSANKGMPILLLTALGTIEHRVKGLELGADDYLV  100 (227)
T ss_pred             CCCEEEEECCHHHHHHHHhhCC--CCEEEEECCCCCCCHHHHHHHHHhcCCCCCEEEEEcCCCHHHHHHHHhCCCCEEEe
Confidence            3788999999999999887765  999999999999999999999974 4789999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHH
Q 027234           80 KPVRIEELKNIWQHVVRK   97 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~   97 (226)
                      ||++.++|...++.+++.
T Consensus       101 kp~~~~~l~~~i~~~~~~  118 (227)
T PRK09836        101 KPFAFAELLARVRTLLRR  118 (227)
T ss_pred             CCCCHHHHHHHHHHHHhc
Confidence            999999999999887653

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

Probab=99.53  E-value=1.3e-13  Score=130.93  Aligned_cols=96  Identities=30%  Similarity=0.490  Sum_probs=88.6

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhc-CCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGL-EMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~-~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      +||.|..+.++.+|++.+....  ||+||+|+.||+|+|+++++.+++ .+.+|||++|+....+...++++.|+++||.
T Consensus       824 ~G~~v~~a~~g~eal~~l~~~~--~DlVl~D~~mP~mdG~el~~~ir~~~~~~pII~lTa~~~~~~~~~~~~aG~d~~L~  901 (924)
T PRK10841        824 LGYQCKTANDGVDALNVLSKNH--IDIVLTDVNMPNMDGYRLTQRLRQLGLTLPVIGVTANALAEEKQRCLEAGMDSCLS  901 (924)
T ss_pred             cCCEEEEECCHHHHHHHHHhCC--CCEEEEcCCCCCCCHHHHHHHHHhcCCCCCEEEEECCCCHHHHHHHHHCCCCEEEe
Confidence            5899999999999999998866  999999999999999999999984 5679999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHH
Q 027234           80 KPVRIEELKNIWQHVVRKR   98 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~~   98 (226)
                      ||++.++|...+.++....
T Consensus       902 KPv~~~~L~~~L~~~~~~~  920 (924)
T PRK10841        902 KPVTLDVLKQTLTVYAERV  920 (924)
T ss_pred             CCCCHHHHHHHHHHHHHHh
Confidence            9999999999999876543

>PRK10643 DNA-binding transcriptional regulator BasR; Provisional

Probab=99.52  E-value=3.1e-13  Score=107.02  Aligned_cols=96  Identities=30%  Similarity=0.517  Sum_probs=87.1

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||.|..+.++.++++.+....  ||+|++|+.||+++|+++++.++ ..+.+|+|++|+..+......++..|+++|+.
T Consensus        23 ~~~~v~~~~~~~~~~~~~~~~~--~d~illd~~~~~~~g~~~~~~l~~~~~~~pii~ls~~~~~~~~~~~~~~ga~~~l~  100 (222)
T PRK10643         23 EGYACDCASTAREAEALLESGH--YSLVVLDLGLPDEDGLHLLRRWRQKKYTLPVLILTARDTLEDRVAGLDVGADDYLV  100 (222)
T ss_pred             CCCEEEEeCCHHHHHHHHHhCC--CCEEEEECCCCCCCHHHHHHHHHhcCCCCcEEEEECCCCHHHHHHHHhcCCCeEEe
Confidence            3788889999999999988765  99999999999999999999997 44779999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHH
Q 027234           80 KPVRIEELKNIWQHVVRKR   98 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~~   98 (226)
                      ||++.++|...++.+++..
T Consensus       101 kp~~~~~l~~~i~~~~~~~  119 (222)
T PRK10643        101 KPFALEELHARIRALIRRH  119 (222)
T ss_pred             CCCCHHHHHHHHHHHHhhh
Confidence            9999999999998877643

>PRK10360 DNA-binding transcriptional activator UhpA; Provisional

Probab=99.52  E-value=8.1e-13  Score=102.93  Aligned_cols=92  Identities=25%  Similarity=0.383  Sum_probs=82.7

Q ss_pred             CcE-EEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEeC
Q 027234            2 GFS-VTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTK   80 (226)
Q Consensus         2 g~~-V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~K   80 (226)
                      |+. +..+.++.+++..+....  ||+||+|+.||+++|+++++.++  +.+|+|++|...+.+....++..|+++|+.|
T Consensus        26 ~~~~~~~~~~~~~~l~~~~~~~--~dlvi~d~~~~~~~g~~~~~~l~--~~~~vi~~s~~~~~~~~~~~~~~ga~~~i~k  101 (196)
T PRK10360         26 DLQVVAEFGSGREALAGLPGRG--VQVCICDISMPDISGLELLSQLP--KGMATIMLSVHDSPALVEQALNAGARGFLSK  101 (196)
T ss_pred             CcEEEEEECCHHHHHHHHhcCC--CCEEEEeCCCCCCCHHHHHHHHc--cCCCEEEEECCCCHHHHHHHHHcCCcEEEEC
Confidence            344 568899999999998765  99999999999999999999886  3689999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHH
Q 027234           81 PVRIEELKNIWQHVVRK   97 (226)
Q Consensus        81 P~~~~~L~~~l~~~~~~   97 (226)
                      |++.++|..+++.+.++
T Consensus       102 p~~~~~l~~~i~~~~~~  118 (196)
T PRK10360        102 RCSPDELIAAVHTVATG  118 (196)
T ss_pred             CCCHHHHHHHHHHHHcC
Confidence            99999999999988764

>PRK10701 DNA-binding transcriptional regulator RstA; Provisional

Probab=99.52  E-value=2.9e-13  Score=109.07  Aligned_cols=95  Identities=20%  Similarity=0.295  Sum_probs=86.8

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEeC
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTK   80 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~K   80 (226)
                      .||.|..+.++.++++.+....  ||+||+|+.||+++|+++++.++.....|+|++++..+......++..|+++|+.|
T Consensus        24 ~g~~v~~~~~~~~~l~~~~~~~--~dlvild~~l~~~~g~~~~~~ir~~~~~pii~l~~~~~~~~~~~~~~~Ga~d~l~k  101 (240)
T PRK10701         24 HDIDVTVEPRGDRAEATILREQ--PDLVLLDIMLPGKDGMTICRDLRPKWQGPIVLLTSLDSDMNHILALEMGACDYILK  101 (240)
T ss_pred             cCCEEEEeCCHHHHHHHHhhCC--CCEEEEeCCCCCCCHHHHHHHHHhcCCCCEEEEECCCCHHHHHHHHHcCCCEEEEC
Confidence            3788999999999999998766  99999999999999999999998666789999999888888889999999999999


Q ss_pred             CCCHHHHHHHHHHHHHH
Q 027234           81 PVRIEELKNIWQHVVRK   97 (226)
Q Consensus        81 P~~~~~L~~~l~~~~~~   97 (226)
                      |++..+|...+..+++.
T Consensus       102 P~~~~~l~~~i~~~l~~  118 (240)
T PRK10701        102 TTPPAVLLARLRLHLRQ  118 (240)
T ss_pred             CCCHHHHHHHHHHHHhc
Confidence            99999999999887765

>PRK13856 two-component response regulator VirG; Provisional

Probab=99.51  E-value=3.1e-13  Score=109.22  Aligned_cols=95  Identities=19%  Similarity=0.349  Sum_probs=85.0

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcCCCCcEEEEecc-CCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAH-GSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~~~~pvI~ls~~-~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||.|..+.++.++++.+....  ||+||+|+.||+++|+++++.++....+|+|++|+. .+......++..||++|+.
T Consensus        24 ~~~~v~~~~~~~~~~~~~~~~~--~dlvi~d~~l~~~~g~~l~~~i~~~~~~pii~lt~~~~~~~~~~~~l~~Ga~~yl~  101 (241)
T PRK13856         24 HAFKVTAVADSQQFNRVLASET--VDVVVVDLNLGREDGLEIVRSLATKSDVPIIIISGDRLEEADKVVALELGATDFIA  101 (241)
T ss_pred             cCCEEEEECCHHHHHHHHhhCC--CCEEEEeCCCCCCCHHHHHHHHHhcCCCcEEEEECCCCcHHHHHHHHhcCcCeEEe
Confidence            3788999999999999988766  999999999999999999999986678999999985 4667778999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHH
Q 027234           80 KPVRIEELKNIWQHVVRK   97 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~   97 (226)
                      ||++.++|...++.+++.
T Consensus       102 kP~~~~eL~~~i~~~l~~  119 (241)
T PRK13856        102 KPFGTREFLARIRVALRV  119 (241)
T ss_pred             CCCCHHHHHHHHHHHHhh
Confidence            999999999999887764

>PRK10161 transcriptional regulator PhoB; Provisional

Probab=99.50  E-value=4.8e-13  Score=106.91  Aligned_cols=94  Identities=29%  Similarity=0.495  Sum_probs=86.1

Q ss_pred             CcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcC---CCCcEEEEeccCCHHHHHHHHhCCcceEE
Q 027234            2 GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLE---MDLPVIMMCAHGSKEVVMKGVTHDACDYL   78 (226)
Q Consensus         2 g~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~---~~~pvI~ls~~~~~~~~~~a~~~ga~~yl   78 (226)
                      ||++..+.++.++++.+....  ||+||+|+.||+++|+++++.++..   +.+|+|++|+..+......++..||++|+
T Consensus        26 g~~v~~~~~~~~~~~~~~~~~--~dlvild~~l~~~~g~~~~~~l~~~~~~~~~pvi~ls~~~~~~~~~~~~~~Ga~~~l  103 (229)
T PRK10161         26 GFQPVEAEDYDSAVNQLNEPW--PDLILLDWMLPGGSGIQFIKHLKRESMTRDIPVVMLTARGEEEDRVRGLETGADDYI  103 (229)
T ss_pred             CCEEEEECCHHHHHHHHhccC--CCEEEEeCCCCCCCHHHHHHHHHhccccCCCCEEEEECCCCHHHHHHHHHcCCCEEE
Confidence            788999999999999988765  9999999999999999999999743   57899999999999999999999999999


Q ss_pred             eCCCCHHHHHHHHHHHHHH
Q 027234           79 TKPVRIEELKNIWQHVVRK   97 (226)
Q Consensus        79 ~KP~~~~~L~~~l~~~~~~   97 (226)
                      .||++.++|...++.++++
T Consensus       104 ~kp~~~~~L~~~i~~~~~~  122 (229)
T PRK10161        104 TKPFSPKELVARIKAVMRR  122 (229)
T ss_pred             ECCCCHHHHHHHHHHHHhc
Confidence            9999999999999988764

>PRK09468 ompR osmolarity response regulator; Provisional

Probab=99.50  E-value=4.6e-13  Score=107.77  Aligned_cols=95  Identities=27%  Similarity=0.449  Sum_probs=87.1

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhc-CCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGL-EMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~-~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||.|..+.++.++++.+....  ||+||+|+.||+++|+++++.++. .+.+|+|++++..+......++..|+++|+.
T Consensus        28 ~g~~v~~~~~~~~~~~~~~~~~--~dlvild~~l~~~~g~~~~~~lr~~~~~~pii~ls~~~~~~~~~~~l~~Ga~~~l~  105 (239)
T PRK09468         28 QGFQVRSAANAEQMDRLLTRES--FHLMVLDLMLPGEDGLSICRRLRSQNNPTPIIMLTAKGEEVDRIVGLEIGADDYLP  105 (239)
T ss_pred             CCCEEEEECCHHHHHHHHhcCC--CCEEEEeCCCCCCCHHHHHHHHHhcCCCCCEEEEECCCcHHHHHHHHhcCCCeEEE
Confidence            3789999999999999988765  999999999999999999999974 4689999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHH
Q 027234           80 KPVRIEELKNIWQHVVRK   97 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~   97 (226)
                      ||++.++|...+..++++
T Consensus       106 kP~~~~~L~~~i~~~~~r  123 (239)
T PRK09468        106 KPFNPRELLARIRAVLRR  123 (239)
T ss_pred             CCCCHHHHHHHHHHHhcc
Confidence            999999999999988754

>PRK11517 transcriptional regulatory protein YedW; Provisional

Probab=99.50  E-value=5.4e-13  Score=105.91  Aligned_cols=95  Identities=26%  Similarity=0.489  Sum_probs=86.9

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEeC
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTK   80 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~K   80 (226)
                      .||.|..+.++.+++..+....  ||+|++|+.||+++|+++++.++....+|+|++++..+.+....++..||++|+.|
T Consensus        23 ~~~~v~~~~~~~~~l~~~~~~~--~dlvi~d~~~~~~~g~~~~~~l~~~~~~~ii~ls~~~~~~~~~~a~~~Ga~~~l~k  100 (223)
T PRK11517         23 AGYVIDAVSDGRDGLYLALKDD--YALIILDIMLPGMDGWQILQTLRTAKQTPVICLTARDSVDDRVRGLDSGANDYLVK  100 (223)
T ss_pred             CCCEEEEECCHHHHHHHHhcCC--CCEEEEECCCCCCCHHHHHHHHHcCCCCCEEEEECCCCHHHHHHHHhcCCCEEEEC
Confidence            3788889999999999988765  99999999999999999999998667899999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHH
Q 027234           81 PVRIEELKNIWQHVVRK   97 (226)
Q Consensus        81 P~~~~~L~~~l~~~~~~   97 (226)
                      |++.++|...++.++++
T Consensus       101 p~~~~~l~~~i~~~~~~  117 (223)
T PRK11517        101 PFSFSELLARVRAQLRQ  117 (223)
T ss_pred             CCCHHHHHHHHHHHHcc
Confidence            99999999999887653

>PRK10336 DNA-binding transcriptional regulator QseB; Provisional

Probab=99.49  E-value=5.6e-13  Score=105.42  Aligned_cols=94  Identities=29%  Similarity=0.440  Sum_probs=85.9

Q ss_pred             CcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhc-CCCCcEEEEeccCCHHHHHHHHhCCcceEEeC
Q 027234            2 GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGL-EMDLPVIMMCAHGSKEVVMKGVTHDACDYLTK   80 (226)
Q Consensus         2 g~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~-~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~K   80 (226)
                      ||.+..+.++.+++..+....  ||+||+|+.||+++|+++++.++. .+.+|+|++|...+.+....++..||++|+.|
T Consensus        24 ~~~v~~~~~~~~~~~~~~~~~--~dlvild~~l~~~~g~~~~~~i~~~~~~~~ii~lt~~~~~~~~~~~~~~ga~~~i~k  101 (219)
T PRK10336         24 GFSVDWFTQGRQGKEALYSAP--YDAVILDLTLPGMDGRDILREWREKGQREPVLILTARDALAERVEGLRLGADDYLCK  101 (219)
T ss_pred             CCEEEEeCCHHHHHHHHhhCC--CCEEEEECCCCCCCHHHHHHHHHhcCCCCcEEEEECCCCHHHHHHHHhCCCCeEEEC
Confidence            788889999999999888755  999999999999999999999974 57899999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHH
Q 027234           81 PVRIEELKNIWQHVVRK   97 (226)
Q Consensus        81 P~~~~~L~~~l~~~~~~   97 (226)
                      |++.++|...++.+++.
T Consensus       102 p~~~~~l~~~i~~~~~~  118 (219)
T PRK10336        102 PFALIEVAARLEALMRR  118 (219)
T ss_pred             CCCHHHHHHHHHHHHhc
Confidence            99999999999887654

>PRK10955 DNA-binding transcriptional regulator CpxR; Provisional

Probab=99.49  E-value=6.2e-13  Score=106.19  Aligned_cols=95  Identities=34%  Similarity=0.505  Sum_probs=85.1

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEeC
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTK   80 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~K   80 (226)
                      .||.|..+.++.++++.+. ..  ||+||+|+.||+++|+++++.++....+|+|++|+..+......+++.|+++|+.|
T Consensus        24 ~~~~v~~~~~~~~~~~~~~-~~--~d~vl~d~~~~~~~g~~~~~~l~~~~~~~ii~lt~~~~~~~~~~~~~~ga~~~l~k  100 (232)
T PRK10955         24 EGFNVIVAHDGEQALDLLD-DS--IDLLLLDVMMPKKNGIDTLKELRQTHQTPVIMLTARGSELDRVLGLELGADDYLPK  100 (232)
T ss_pred             CCCEEEEeCCHHHHHHHhh-cC--CCEEEEeCCCCCCcHHHHHHHHHhcCCCcEEEEECCCCHHHHHHHHHcCCCEEEcC
Confidence            3788889999999999886 34  99999999999999999999998554599999999999989999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHH
Q 027234           81 PVRIEELKNIWQHVVRKR   98 (226)
Q Consensus        81 P~~~~~L~~~l~~~~~~~   98 (226)
                      |++.++|...++.++++.
T Consensus       101 p~~~~~l~~~i~~~~~~~  118 (232)
T PRK10955        101 PFNDRELVARIRAILRRS  118 (232)
T ss_pred             CCCHHHHHHHHHHHHhcc
Confidence            999999999998887653

>TIGR03787 marine_sort_RR proteobacterial dedicated sortase system response regulator

Probab=99.48  E-value=9.1e-13  Score=105.08  Aligned_cols=95  Identities=26%  Similarity=0.388  Sum_probs=86.3

Q ss_pred             CcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCC--CCHHHHHHHHhc-CCCCcEEEEeccCCHHHHHHHHhCCcceEE
Q 027234            2 GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPD--MDGFKLLELVGL-EMDLPVIMMCAHGSKEVVMKGVTHDACDYL   78 (226)
Q Consensus         2 g~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~--~dG~~l~~~l~~-~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl   78 (226)
                      ||.|..+.++.+++..+....  ||+|++|+.||+  .+|+++++.++. .+.+|+|++|+..+......++..||++|+
T Consensus        24 ~~~v~~~~~~~~~~~~~~~~~--~dlvild~~l~~~~~~g~~~~~~i~~~~~~~pii~ls~~~~~~~~~~~~~~Ga~~~l  101 (227)
T TIGR03787        24 GYQVTTYADRPSAMQAFRQRL--PDLAIIDIGLGEEIDGGFMLCQDLRSLSATLPIIFLTARDSDFDTVSGLRLGADDYL  101 (227)
T ss_pred             CcEEEEecCHHHHHHHHHhCC--CCEEEEECCCCCCCCCHHHHHHHHHhcCCCCCEEEEECCCCHHHHHHHHhcCCCEEE
Confidence            788888999999999998766  999999999998  589999999974 467999999999999999999999999999


Q ss_pred             eCCCCHHHHHHHHHHHHHHH
Q 027234           79 TKPVRIEELKNIWQHVVRKR   98 (226)
Q Consensus        79 ~KP~~~~~L~~~l~~~~~~~   98 (226)
                      .||++.++|...++.++++.
T Consensus       102 ~kp~~~~~l~~~i~~~~~~~  121 (227)
T TIGR03787       102 TKDISLPHLLARITALFRRA  121 (227)
T ss_pred             ECCCCHHHHHHHHHHHHHhh
Confidence            99999999999999887654

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.

>TIGR02154 PhoB phosphate regulon transcriptional regulatory protein PhoB

Probab=99.48  E-value=7.1e-13  Score=105.15  Aligned_cols=94  Identities=28%  Similarity=0.502  Sum_probs=85.8

Q ss_pred             CcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcC---CCCcEEEEeccCCHHHHHHHHhCCcceEE
Q 027234            2 GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLE---MDLPVIMMCAHGSKEVVMKGVTHDACDYL   78 (226)
Q Consensus         2 g~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~---~~~pvI~ls~~~~~~~~~~a~~~ga~~yl   78 (226)
                      |+.|..+.++.+++..+....  ||+|++|+.||+++|+++++.++..   +.+|+|++|+..+......++..|+++|+
T Consensus        26 ~~~v~~~~~~~~~~~~~~~~~--~d~vi~d~~~~~~~g~~~~~~l~~~~~~~~~~ii~ls~~~~~~~~~~~~~~Ga~~~l  103 (226)
T TIGR02154        26 GYDVVEAGDGDEALTLINERG--PDLILLDWMLPGTSGIELCRRLRRRPETRAIPIIMLTARGEEEDRVRGLETGADDYI  103 (226)
T ss_pred             CCEEEEEcCHHHHHHHHHhcC--CCEEEEECCCCCCcHHHHHHHHHccccCCCCCEEEEecCCCHHHHHHHHhcCcceEE
Confidence            688888999999999998765  9999999999999999999999743   57899999999999999999999999999


Q ss_pred             eCCCCHHHHHHHHHHHHHH
Q 027234           79 TKPVRIEELKNIWQHVVRK   97 (226)
Q Consensus        79 ~KP~~~~~L~~~l~~~~~~   97 (226)
                      .||++.++|...+..++++
T Consensus       104 ~kp~~~~~l~~~i~~~~~~  122 (226)
T TIGR02154       104 TKPFSPRELLARIKAVLRR  122 (226)
T ss_pred             eCCCCHHHHHHHHHHHhcc
Confidence            9999999999999888754

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.

>CHL00148 orf27 Ycf27; Reviewed

Probab=99.48  E-value=8.3e-13  Score=106.01  Aligned_cols=95  Identities=34%  Similarity=0.574  Sum_probs=86.8

Q ss_pred             CcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEeCC
Q 027234            2 GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTKP   81 (226)
Q Consensus         2 g~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~KP   81 (226)
                      ||.|..+.++.+++..+....  ||+|++|+.||+++|+++++.++..+.+|+|++|+..+......++..||++|+.||
T Consensus        30 ~~~v~~~~~~~~~l~~~~~~~--~d~illd~~~~~~~g~~~~~~l~~~~~~~ii~ls~~~~~~~~~~~~~~Ga~~~l~kp  107 (240)
T CHL00148         30 GYEVITASDGEEALKLFRKEQ--PDLVILDVMMPKLDGYGVCQEIRKESDVPIIMLTALGDVSDRITGLELGADDYVVKP  107 (240)
T ss_pred             CCEEEEeCCHHHHHHHHHhcC--CCEEEEeCCCCCCCHHHHHHHHHhcCCCcEEEEECCCCHHhHHHHHHCCCCEEEeCC
Confidence            688888999999999888765  999999999999999999999986678999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHH
Q 027234           82 VRIEELKNIWQHVVRKR   98 (226)
Q Consensus        82 ~~~~~L~~~l~~~~~~~   98 (226)
                      ++.++|...+..+++..
T Consensus       108 ~~~~~L~~~i~~~~~~~  124 (240)
T CHL00148        108 FSPKELEARIRSVLRRT  124 (240)
T ss_pred             CCHHHHHHHHHHHHhhc
Confidence            99999999998887543

>TIGR01387 cztR_silR_copR heavy metal response regulator

Probab=99.48  E-value=7.8e-13  Score=104.44  Aligned_cols=94  Identities=30%  Similarity=0.530  Sum_probs=86.5

Q ss_pred             CcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEeC
Q 027234            2 GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTK   80 (226)
Q Consensus         2 g~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~K   80 (226)
                      ||.+..+.++.++++.+....  ||+|++|+.||+++|+++++.++ ..+.+|+|++|+..+......++..|+++|+.|
T Consensus        22 ~~~v~~~~~~~~~~~~~~~~~--~dlvl~d~~~~~~~g~~~~~~l~~~~~~~~iivls~~~~~~~~~~~~~~Ga~~~l~k   99 (218)
T TIGR01387        22 GYVVDAASNGRDGLHLALKDD--YDLIILDVMLPGMDGWQILQTLRRSGKQTPVLFLTARDSVADKVKGLDLGADDYLVK   99 (218)
T ss_pred             CCEEEEECCHHHHHHHHhcCC--CCEEEEeCCCCCCCHHHHHHHHHccCCCCcEEEEEcCCCHHHHHHHHHcCCCeEEEC
Confidence            688889999999999998766  99999999999999999999997 457899999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHH
Q 027234           81 PVRIEELKNIWQHVVRK   97 (226)
Q Consensus        81 P~~~~~L~~~l~~~~~~   97 (226)
                      |++.++|...++.++++
T Consensus       100 p~~~~~l~~~i~~~~~~  116 (218)
T TIGR01387       100 PFSFSELLARVRTLLRR  116 (218)
T ss_pred             CCCHHHHHHHHHHHhcc
Confidence            99999999999887754

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.

>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator

Probab=99.48  E-value=6.1e-13  Score=117.09  Aligned_cols=94  Identities=21%  Similarity=0.380  Sum_probs=86.4

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCC-----CCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCc
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPD-----MDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDA   74 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~-----~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga   74 (226)
                      .||.|..+.++.+|++.+....  ||+||+|+.||+     ++|+++++.++ ..+.+|||++|+..+.+...++++.||
T Consensus        19 ~~~~v~~a~~~~~al~~l~~~~--~dlvllD~~mp~~~~~~~~g~~~l~~i~~~~~~~piI~lt~~~~~~~~~~a~~~Ga   96 (445)
T TIGR02915        19 ADYELAVAADRESAIALVRRHE--PAVVTLDLGLPPDADGASEGLAALQQILAIAPDTKVIVITGNDDRENAVKAIGLGA   96 (445)
T ss_pred             CCCeEEEeCCHHHHHHHHhhCC--CCEEEEeCCCCCCcCCCCCHHHHHHHHHhhCCCCCEEEEecCCCHHHHHHHHHCCc
Confidence            3789999999999999998866  999999999996     89999999987 567899999999999999999999999


Q ss_pred             ceEEeCCCCHHHHHHHHHHHHH
Q 027234           75 CDYLTKPVRIEELKNIWQHVVR   96 (226)
Q Consensus        75 ~~yl~KP~~~~~L~~~l~~~~~   96 (226)
                      ++||.||++.++|..++++++.
T Consensus        97 ~dyl~KP~~~~~L~~~i~~~~~  118 (445)
T TIGR02915        97 YDFYQKPIDPDVLKLIVDRAFH  118 (445)
T ss_pred             cEEEeCCCCHHHHHHHHhhhhh
Confidence            9999999999999999887765

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).

>PRK10693 response regulator of RpoS; Provisional

Probab=99.47  E-value=6.8e-13  Score=111.21  Aligned_cols=88  Identities=24%  Similarity=0.365  Sum_probs=79.4

Q ss_pred             EECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEeCCC-CH
Q 027234            7 KCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTKPV-RI   84 (226)
Q Consensus         7 ~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~KP~-~~   84 (226)
                      .+.++.+|++.+....  ||+||+|+.||+++|+++++.++ ..+.+|+|++|+..+.+...++++.|+++|+.||+ +.
T Consensus         2 ~a~~g~~al~~l~~~~--pDlVL~D~~mp~~~Gle~~~~ir~~~~~ipiI~lt~~~~~~~~~~al~~Ga~dyl~KP~~~~   79 (303)
T PRK10693          2 LAANGVDALELLGGFT--PDLIICDLAMPRMNGIEFVEHLRNRGDQTPVLVISATENMADIAKALRLGVQDVLLKPVKDL   79 (303)
T ss_pred             EeCCHHHHHHHHhcCC--CCEEEEeCCCCCCCHHHHHHHHHhcCCCCcEEEEECCCCHHHHHHHHHCCCcEEEECCCCcH
Confidence            4789999999998865  99999999999999999999997 44679999999999999999999999999999999 58


Q ss_pred             HHHHHHHHHHHH
Q 027234           85 EELKNIWQHVVR   96 (226)
Q Consensus        85 ~~L~~~l~~~~~   96 (226)
                      ++|...+.+.++
T Consensus        80 ~~L~~~i~~~l~   91 (303)
T PRK10693         80 NRLREMVFACLY   91 (303)
T ss_pred             HHHHHHHHHHhh
Confidence            999888877654

>PRK09935 transcriptional regulator FimZ; Provisional

Probab=99.47  E-value=2.9e-12  Score=100.58  Aligned_cols=94  Identities=19%  Similarity=0.369  Sum_probs=83.9

Q ss_pred             CcEEE-EECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhc-CCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            2 GFSVT-KCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGL-EMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         2 g~~V~-~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~-~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      ++.+. .+.++.++++.+....  ||+|++|+.||+++|+++++.++. .+.+|+|++|+..+......++..|+++|+.
T Consensus        28 ~~~~~~~~~~~~~~~~~~~~~~--~dlvild~~l~~~~g~~~~~~l~~~~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~  105 (210)
T PRK09935         28 ELQIVLKTDDYRITIDYLRTRP--VDLIIMDIDLPGTDGFTFLKRIKQIQSTVKVLFLSSKSECFYAGRAIQAGANGFVS  105 (210)
T ss_pred             CceEEEEeCCHHHHHHHHHhcC--CCEEEEeCCCCCCCHHHHHHHHHHhCCCCcEEEEECCCcHHHHHHHHHcCCCEEEe
Confidence            46664 6889999999988755  999999999999999999999974 5679999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHH
Q 027234           80 KPVRIEELKNIWQHVVRK   97 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~   97 (226)
                      ||++.++|...++.++.+
T Consensus       106 kp~~~~~l~~~i~~~l~~  123 (210)
T PRK09935        106 KCNDQNDIFHAVQMILSG  123 (210)
T ss_pred             CCCCHHHHHHHHHHHHcC
Confidence            999999999999887764

>PRK09581 pleD response regulator PleD; Reviewed

Probab=99.46  E-value=3.7e-13  Score=117.92  Aligned_cols=93  Identities=20%  Similarity=0.355  Sum_probs=84.1

Q ss_pred             cEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhc---CCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            3 FSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGL---EMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         3 ~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~---~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      +.+..+.++.+|+..+....  ||+||+|+.||+++|+++++.+++   .+.+|+|++|+..+.+...+++..||++||.
T Consensus       179 ~~~~~~~~~~~a~~~~~~~~--~d~vi~d~~~p~~~g~~l~~~i~~~~~~~~~~ii~ls~~~~~~~~~~a~~~Ga~d~l~  256 (457)
T PRK09581        179 FRVVVVSDPSEALFNAAETN--YDLVIVSANFENYDPLRLCSQLRSKERTRYVPILLLVDEDDDPRLVKALELGVNDYLM  256 (457)
T ss_pred             ceeeeecChHHHHHhcccCC--CCEEEecCCCCCchHhHHHHHHHhccccCCCcEEEEeCCCChHHHHHHHHccchhhhh
Confidence            45667899999999988766  999999999999999999999974   2689999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHH
Q 027234           80 KPVRIEELKNIWQHVVRK   97 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~   97 (226)
                      ||+++++|...+......
T Consensus       257 kp~~~~~l~~~i~~~~~~  274 (457)
T PRK09581        257 RPIDKNELLARVRTQIRR  274 (457)
T ss_pred             CCCcHHHHHHHHHHHHHH
Confidence            999999999988876654

>PRK11083 DNA-binding response regulator CreB; Provisional

Probab=99.46  E-value=1.1e-12  Score=104.35  Aligned_cols=95  Identities=34%  Similarity=0.492  Sum_probs=86.0

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhc-CCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGL-EMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~-~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||.|..+.++.+++..+....  ||+|++|+.||+.+|+++++.++. .+.+|+|++|+..+......++..|+++|+.
T Consensus        26 ~~~~v~~~~~~~~~~~~~~~~~--~dlvl~d~~~~~~~g~~~~~~l~~~~~~~~ii~ls~~~~~~~~~~a~~~Ga~~~l~  103 (228)
T PRK11083         26 EGFTVEWFERGLPALDKLRQQP--PDLVILDVGLPDISGFELCRQLLAFHPALPVIFLTARSDEVDRLVGLEIGADDYVA  103 (228)
T ss_pred             CCCEEEEEcCHHHHHHHHhcCC--CCEEEEeCCCCCCCHHHHHHHHHhhCCCCCEEEEEcCCcHHHHHHHhhcCCCeEEE
Confidence            3788888999999999988765  999999999999999999999974 4789999999999998899999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHH
Q 027234           80 KPVRIEELKNIWQHVVRK   97 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~   97 (226)
                      ||++.++|...++.++++
T Consensus       104 kp~~~~~l~~~i~~~~~~  121 (228)
T PRK11083        104 KPFSPREVAARVRTILRR  121 (228)
T ss_pred             CCCCHHHHHHHHHHHHCc
Confidence            999999999999887654

>PRK11107 hybrid sensory histidine kinase BarA; Provisional

Probab=99.46  E-value=5.6e-13  Score=126.70  Aligned_cols=95  Identities=24%  Similarity=0.419  Sum_probs=87.3

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhc---CCCCcEEEEeccCCHHHHHHHHhCCcceE
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGL---EMDLPVIMMCAHGSKEVVMKGVTHDACDY   77 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~---~~~~pvI~ls~~~~~~~~~~a~~~ga~~y   77 (226)
                      +||.|..+.++.+|++.+....  ||+||+|+.||+|||+++++.++.   .+.+|||++|+....+...+++..|+++|
T Consensus       690 ~~~~v~~~~~~~~al~~~~~~~--~dlil~D~~mp~~~g~~~~~~lr~~~~~~~~pii~lt~~~~~~~~~~~~~~G~~~~  767 (919)
T PRK11107        690 QVEHVVLCDSGHQAVEQAKQRP--FDLILMDIQMPGMDGIRACELIRQLPHNQNTPIIAVTAHAMAGERERLLSAGMDDY  767 (919)
T ss_pred             cCCEEEEECCHHHHHHHHHhCC--CCEEEEeCCCCCCcHHHHHHHHHhcccCCCCCEEEEeCCCCHHHHHHHHHcCCCeE
Confidence            4789999999999999998866  999999999999999999999974   35799999999999999999999999999


Q ss_pred             EeCCCCHHHHHHHHHHHHHH
Q 027234           78 LTKPVRIEELKNIWQHVVRK   97 (226)
Q Consensus        78 l~KP~~~~~L~~~l~~~~~~   97 (226)
                      |.||++..+|...+.++...
T Consensus       768 l~KP~~~~~L~~~l~~~~~~  787 (919)
T PRK11107        768 LAKPIDEAMLKQVLLRYKPG  787 (919)
T ss_pred             eeCCCCHHHHHHHHHHHccc
Confidence            99999999999999887643

>PRK15347 two component system sensor kinase SsrA; Provisional

Probab=99.46  E-value=6.9e-13  Score=126.17  Aligned_cols=94  Identities=26%  Similarity=0.449  Sum_probs=86.6

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcC-----CCCcEEEEeccCCHHHHHHHHhCCcc
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLE-----MDLPVIMMCAHGSKEVVMKGVTHDAC   75 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~-----~~~pvI~ls~~~~~~~~~~a~~~ga~   75 (226)
                      +||+|..+.++.+|++.+....  ||+||+|+.||++||+++++.++..     +.+|||++|+..+.....+++..|++
T Consensus       713 ~g~~v~~a~~~~~al~~~~~~~--~dlil~D~~mp~~~G~~~~~~ir~~~~~~~~~~pii~lt~~~~~~~~~~~~~~G~~  790 (921)
T PRK15347        713 LGQQVTTAASGTEALELGRQHR--FDLVLMDIRMPGLDGLETTQLWRDDPNNLDPDCMIVALTANAAPEEIHRCKKAGMN  790 (921)
T ss_pred             cCCEEEEECCHHHHHHHHhcCC--CCEEEEeCCCCCCCHHHHHHHHHhchhhcCCCCcEEEEeCCCCHHHHHHHHHCCCC
Confidence            4899999999999999998866  9999999999999999999999742     56899999999999999999999999


Q ss_pred             eEEeCCCCHHHHHHHHHHHHH
Q 027234           76 DYLTKPVRIEELKNIWQHVVR   96 (226)
Q Consensus        76 ~yl~KP~~~~~L~~~l~~~~~   96 (226)
                      +||.||++.++|...+.++..
T Consensus       791 ~~l~KP~~~~~L~~~l~~~~~  811 (921)
T PRK15347        791 HYLTKPVTLAQLARALELAAE  811 (921)
T ss_pred             EEEECCCCHHHHHHHHHHHHh
Confidence            999999999999999987754

>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional

Probab=99.46  E-value=8.8e-13  Score=105.16  Aligned_cols=91  Identities=12%  Similarity=0.099  Sum_probs=74.6

Q ss_pred             EEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHH-HHHh-cCCCCcEEEEeccCCHHHHHHHHh--CCcceEEeC
Q 027234            5 VTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLL-ELVG-LEMDLPVIMMCAHGSKEVVMKGVT--HDACDYLTK   80 (226)
Q Consensus         5 V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~-~~l~-~~~~~pvI~ls~~~~~~~~~~a~~--~ga~~yl~K   80 (226)
                      +..+.++.++++.+.  .  ||+||+|+.||+++|++++ +.++ ..+.++||++|+..+.  ...++.  .||.||+.|
T Consensus        37 ~~~~~~~~~~~~~~~--~--~DvvllDi~~p~~~G~~~~~~~i~~~~p~~~vvvlt~~~~~--~~~~~~~~~Ga~G~l~K  110 (216)
T PRK10100         37 TGKLHNIQRSLDDIS--S--GSIILLDMMEADKKLIHYWQDTLSRKNNNIKILLLNTPEDY--PYREIENWPHINGVFYA  110 (216)
T ss_pred             eEEEcCHHHhhccCC--C--CCEEEEECCCCCccHHHHHHHHHHHhCCCCcEEEEECCchh--HHHHHHHhcCCeEEEEC
Confidence            446789999988743  2  8999999999999999997 5566 5678999999998763  344455  599999999


Q ss_pred             CCCHHHHHHHHHHHHHHHhhh
Q 027234           81 PVRIEELKNIWQHVVRKRKNE  101 (226)
Q Consensus        81 P~~~~~L~~~l~~~~~~~~~~  101 (226)
                      +.+.++|..+++.+..+....
T Consensus       111 ~~~~~~L~~aI~~v~~G~~~~  131 (216)
T PRK10100        111 MEDQERVVNGLQGVLRGECYF  131 (216)
T ss_pred             CCCHHHHHHHHHHHHcCCccc
Confidence            999999999999998765543

>PRK11466 hybrid sensory histidine kinase TorS; Provisional

Probab=99.45  E-value=7e-13  Score=126.13  Aligned_cols=96  Identities=24%  Similarity=0.319  Sum_probs=87.2

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      +||.|..+.++.+|++.+... .+||+||+|+.||++||+++++.++ ..+.+|+|++|+.........++..|+++||.
T Consensus       704 ~g~~v~~a~~~~~al~~~~~~-~~~Dlvl~D~~mp~~~G~~~~~~lr~~~~~~~ii~~t~~~~~~~~~~~~~~g~~~~l~  782 (914)
T PRK11466        704 SGAQVVAVGNAAQALETLQNS-EPFAAALVDFDLPDYDGITLARQLAQQYPSLVLIGFSAHVIDETLRQRTSSLFRGIIP  782 (914)
T ss_pred             cCCceEEeCCHHHHHHHHHcC-CCCCEEEEeCCCCCCCHHHHHHHHHhhCCCCCEEEEeCCCchhhHHHHHhcCcCCEEe
Confidence            489999999999999988643 2489999999999999999999997 45789999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHH
Q 027234           80 KPVRIEELKNIWQHVVRK   97 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~   97 (226)
                      ||++.++|...+.+++..
T Consensus       783 KP~~~~~L~~~i~~~~~~  800 (914)
T PRK11466        783 KPVPREVLGQLLAHYLQL  800 (914)
T ss_pred             CCCCHHHHHHHHHHHhhh
Confidence            999999999999998754

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

Probab=99.45  E-value=1.6e-13  Score=85.23  Aligned_cols=55  Identities=62%  Similarity=0.957  Sum_probs=51.8

Q ss_pred             CCceeeeHhhHHHHHHHHHHhCC-CCCCchHHHHhhCCCCCCHHHHHHHhhhhhhh
Q 027234          151 KPRLVWSVELHQQFVSAVKELGF-DKAGPKKILELMNIPGLTRENVASHLQKHRLY  205 (226)
Q Consensus       151 ~~~~~~~~~l~~~Fi~~~~~~g~-~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~  205 (226)
                      ++++.||.++|..|+.+++.+|. +.+.|+.|.++|..+++|.++|+||+||||..
T Consensus         1 k~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~~k   56 (57)
T TIGR01557         1 KPRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYRLK   56 (57)
T ss_pred             CCCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHHcc
Confidence            47789999999999999999998 88999999999999999999999999999864

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

>TIGR02875 spore_0_A sporulation transcription factor Spo0A

Probab=99.45  E-value=1.4e-12  Score=106.79  Aligned_cols=93  Identities=26%  Similarity=0.422  Sum_probs=82.3

Q ss_pred             cEE-EEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcC-CC--CcEEEEeccCCHHHHHHHHhCCcceEE
Q 027234            3 FSV-TKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLE-MD--LPVIMMCAHGSKEVVMKGVTHDACDYL   78 (226)
Q Consensus         3 ~~V-~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~-~~--~pvI~ls~~~~~~~~~~a~~~ga~~yl   78 (226)
                      +.+ ..+.++.++++.+....  ||+||+|+.||++||+++++.++.. ..  +|+|++|+.........++..|+++|+
T Consensus        28 ~~~~~~a~~~~eal~~l~~~~--~DlvllD~~mp~~dG~~~l~~i~~~~~~~~~~iI~lt~~~~~~~~~~~~~~G~~~~l  105 (262)
T TIGR02875        28 MEVVGVAHNGVDALELIKEQQ--PDVVVLDIIMPHLDGIGVLEKLNEIELSARPRVIMLSAFGQEKITQRAVALGADYYV  105 (262)
T ss_pred             eEEEEEeCCHHHHHHHHHhcC--CCEEEEeCCCCCCCHHHHHHHHHhhccccCCeEEEEeCCCCHHHHHHHHHCCCCEEE
Confidence            444 47899999999998866  9999999999999999999999743 33  789999999999999999999999999


Q ss_pred             eCCCCHHHHHHHHHHHHHH
Q 027234           79 TKPVRIEELKNIWQHVVRK   97 (226)
Q Consensus        79 ~KP~~~~~L~~~l~~~~~~   97 (226)
                      .||++.++|...+.++...
T Consensus       106 ~KP~~~~~L~~~i~~~~~~  124 (262)
T TIGR02875       106 LKPFDLEILAARIRQLAWG  124 (262)
T ss_pred             ECCCCHHHHHHHHHHHHcc
Confidence            9999999999999887643

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.

>TIGR02956 TMAO_torS TMAO reductase sytem sensor TorS

Probab=99.43  E-value=1.4e-12  Score=124.68  Aligned_cols=95  Identities=25%  Similarity=0.386  Sum_probs=87.2

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcC-CC---CcEEEEeccCCHHHHHHHHhCCcce
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLE-MD---LPVIMMCAHGSKEVVMKGVTHDACD   76 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~-~~---~pvI~ls~~~~~~~~~~a~~~ga~~   76 (226)
                      +||+|..+.++.+|++.+....  ||+||+|+.||+++|+++++.++.. +.   +|||++|+....+...+++..|+++
T Consensus       725 ~g~~v~~~~~~~~a~~~l~~~~--~dlvl~D~~mp~~~g~~~~~~ir~~~~~~~~~pii~lta~~~~~~~~~~~~~G~~~  802 (968)
T TIGR02956       725 LGHKVTLAESGQSALECFHQHA--FDLALLDINLPDGDGVTLLQQLRAIYGAKNEVKFIAFSAHVFNEDVAQYLAAGFDG  802 (968)
T ss_pred             cCCEEEEECCHHHHHHHHHCCC--CCEEEECCCCCCCCHHHHHHHHHhCccccCCCeEEEEECCCCHHHHHHHHHCCCCE
Confidence            5899999999999999998865  9999999999999999999999743 33   8999999999999999999999999


Q ss_pred             EEeCCCCHHHHHHHHHHHHHH
Q 027234           77 YLTKPVRIEELKNIWQHVVRK   97 (226)
Q Consensus        77 yl~KP~~~~~L~~~l~~~~~~   97 (226)
                      ||.||++.++|...+.+++..
T Consensus       803 ~l~KP~~~~~L~~~l~~~~~~  823 (968)
T TIGR02956       803 FLAKPVVEEQLTAMIAVILAG  823 (968)
T ss_pred             EEeCCCCHHHHHHHHHHHhcc
Confidence            999999999999999988753

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).

>PRK15115 response regulator GlrR; Provisional

Probab=99.43  E-value=1.7e-12  Score=114.23  Aligned_cols=95  Identities=32%  Similarity=0.544  Sum_probs=87.2

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||.|..+.++.+|++.+....  ||+||+|+.||+++|+++++.++ ..+.+|||++|+..+.....+++..|+.+|+.
T Consensus        28 ~g~~v~~~~~~~eal~~l~~~~--~dlvilD~~lp~~~g~~ll~~l~~~~~~~pvIvlt~~~~~~~~~~a~~~Ga~~~l~  105 (444)
T PRK15115         28 EGYSVVTAESGQEALRVLNREK--VDLVISDLRMDEMDGMQLFAEIQKVQPGMPVIILTAHGSIPDAVAATQQGVFSFLT  105 (444)
T ss_pred             CCCEEEEeCCHHHHHHHHhcCC--CCEEEEcCCCCCCCHHHHHHHHHhcCCCCcEEEEECCCCHHHHHHHHhcChhhhcc
Confidence            4789999999999999998766  99999999999999999999987 45779999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHH
Q 027234           80 KPVRIEELKNIWQHVVRK   97 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~   97 (226)
                      ||++.++|...+..++..
T Consensus       106 KP~~~~~L~~~l~~~~~~  123 (444)
T PRK15115        106 KPVDRDALYKAIDDALEQ  123 (444)
T ss_pred             CCCCHHHHHHHHHHHHHh
Confidence            999999999999887754

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

Probab=99.42  E-value=3.3e-12  Score=113.18  Aligned_cols=95  Identities=31%  Similarity=0.542  Sum_probs=87.4

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||.|..+.++.+|+..+....  ||+||+|+.||+++|+++++.++ ..+.+|+|++|+..+.+....+++.|+.+|+.
T Consensus        26 ~g~~v~~~~s~~~al~~l~~~~--~DlvllD~~lp~~dgl~~l~~ir~~~~~~pvIvlt~~~~~~~~~~a~~~Ga~~~l~  103 (469)
T PRK10923         26 AGLTCTTFENGNEVLEALASKT--PDVLLSDIRMPGMDGLALLKQIKQRHPMLPVIIMTAHSDLDAAVSAYQQGAFDYLP  103 (469)
T ss_pred             cCCEEEEECCHHHHHHHHhcCC--CCEEEECCCCCCCCHHHHHHHHHhhCCCCeEEEEECCCCHHHHHHHHhcCcceEEe
Confidence            4789999999999999998866  99999999999999999999997 45779999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHH
Q 027234           80 KPVRIEELKNIWQHVVRK   97 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~   97 (226)
                      ||++.++|...+.+++..
T Consensus       104 KP~~~~~L~~~i~~~l~~  121 (469)
T PRK10923        104 KPFDIDEAVALVERAISH  121 (469)
T ss_pred             cCCcHHHHHHHHHHHHHH
Confidence            999999999999887654

>TIGR01818 ntrC nitrogen regulation protein NR(I)

Probab=99.41  E-value=3.9e-12  Score=112.53  Aligned_cols=95  Identities=29%  Similarity=0.512  Sum_probs=86.9

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||.|..+.++.+|+..+....  ||+||+|+.||+++|+++++.++ ..+.+|+|++|+..+.....+++..|+++|+.
T Consensus        21 ~g~~v~~~~~~~~al~~~~~~~--~DlVllD~~~p~~~g~~ll~~l~~~~~~~~vIvlt~~~~~~~~~~a~~~Ga~~~l~   98 (463)
T TIGR01818        21 AGYEVRTFGNAASVLRALARGQ--PDLLITDVRMPGEDGLDLLPQIKKRHPQLPVIVMTAHSDLDTAVAAYQRGAFEYLP   98 (463)
T ss_pred             cCCEEEEECCHHHHHHHHhcCC--CCEEEEcCCCCCCCHHHHHHHHHHhCCCCeEEEEeCCCCHHHHHHHHHcCcceeec
Confidence            4789999999999999998765  99999999999999999999997 45779999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHH
Q 027234           80 KPVRIEELKNIWQHVVRK   97 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~   97 (226)
                      ||++.++|...+.+++..
T Consensus        99 KP~~~~~L~~~i~~~l~~  116 (463)
T TIGR01818        99 KPFDLDEAVTLVERALAH  116 (463)
T ss_pred             CCCCHHHHHHHHHHHHHH
Confidence            999999999999887653

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.

>PRK14084 two-component response regulator; Provisional

Probab=99.41  E-value=4.1e-12  Score=103.02  Aligned_cols=90  Identities=22%  Similarity=0.406  Sum_probs=78.0

Q ss_pred             EEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhc-CCCCcEEEEeccCCHHHHHHHHhCCcceEEeCCC
Q 027234            4 SVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGL-EMDLPVIMMCAHGSKEVVMKGVTHDACDYLTKPV   82 (226)
Q Consensus         4 ~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~-~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~KP~   82 (226)
                      .|..+.++.+++..+....  ||+|++|+.||+++|+++++.++. .+..++|++|+..  +...++++.|+.+||.||+
T Consensus        28 ~v~~~~~~~~~l~~~~~~~--~dlv~lDi~m~~~~G~~~~~~i~~~~~~~~iI~~t~~~--~~~~~~~~~~~~~yl~KP~  103 (246)
T PRK14084         28 EINEAENVKETLEALLINQ--YDIIFLDINLMDESGIELAAKIQKMKEPPAIIFATAHD--QFAVKAFELNATDYILKPF  103 (246)
T ss_pred             EEEEECCHHHHHHHHHhcC--CCEEEEeCCCCCCCHHHHHHHHHhcCCCCEEEEEecCh--HHHHHHHhcCCcEEEECCC
Confidence            4678999999999998765  999999999999999999999974 4556788888765  4567899999999999999


Q ss_pred             CHHHHHHHHHHHHHH
Q 027234           83 RIEELKNIWQHVVRK   97 (226)
Q Consensus        83 ~~~~L~~~l~~~~~~   97 (226)
                      +.++|..+++++...
T Consensus       104 ~~~~l~~~l~~~~~~  118 (246)
T PRK14084        104 EQKRIEQAVNKVRAT  118 (246)
T ss_pred             CHHHHHHHHHHHHHh
Confidence            999999999988654

>PRK10403 transcriptional regulator NarP; Provisional

Probab=99.41  E-value=1.4e-11  Score=96.76  Aligned_cols=94  Identities=20%  Similarity=0.298  Sum_probs=82.7

Q ss_pred             CcEEE-EECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhc-CCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            2 GFSVT-KCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGL-EMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         2 g~~V~-~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~-~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      ++.+. .+.++.+++..+....  ||+|++|..||+++|+++++.++. .+..|+++++...+......++..|+++|+.
T Consensus        31 ~~~~~~~~~~~~~~~~~~~~~~--~dlvi~d~~~~~~~~~~~~~~l~~~~~~~~ii~l~~~~~~~~~~~~~~~g~~~~i~  108 (215)
T PRK10403         31 GFEVVAEAGDGASAIDLANRLD--PDVILLDLNMKGMSGLDTLNALRRDGVTAQIIILTVSDASSDVFALIDAGADGYLL  108 (215)
T ss_pred             CCEEEEEeCCHHHHHHHHHhcC--CCEEEEecCCCCCcHHHHHHHHHHhCCCCeEEEEeCCCChHHHHHHHHcCCCeEEe
Confidence            45654 6889999999887765  999999999999999999999974 4678999999988888899999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHH
Q 027234           80 KPVRIEELKNIWQHVVRK   97 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~   97 (226)
                      ||++.++|...++.+..+
T Consensus       109 kp~~~~~l~~~i~~~~~~  126 (215)
T PRK10403        109 KDSDPEVLLEAIRAGAKG  126 (215)
T ss_pred             cCCCHHHHHHHHHHHhCC
Confidence            999999999999887653

>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional

Probab=99.40  E-value=2.7e-12  Score=113.39  Aligned_cols=94  Identities=33%  Similarity=0.533  Sum_probs=86.2

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||.|..+.++.+|+..+....  ||+|++|+.||+++|+++++.++ ..+.+|+|++|+..+.+....++..|+.+|+.
T Consensus        27 ~g~~v~~~~~~~~al~~l~~~~--~dlillD~~~p~~~g~~ll~~i~~~~~~~pvI~lt~~~~~~~~~~a~~~Ga~d~l~  104 (457)
T PRK11361         27 QGFETHCANNGRTALHLFADIH--PDVVLMDIRMPEMDGIKALKEMRSHETRTPVILMTAYAEVETAVEALRCGAFDYVI  104 (457)
T ss_pred             CCCEEEEECCHHHHHHHHhcCC--CCEEEEeCCCCCCCHHHHHHHHHhcCCCCCEEEEeCCCCHHHHHHHHHCCccEEEe
Confidence            4789999999999999998766  99999999999999999999987 45789999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHH
Q 027234           80 KPVRIEELKNIWQHVVR   96 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~   96 (226)
                      ||++.++|...+.+++.
T Consensus       105 KP~~~~~L~~~i~~~l~  121 (457)
T PRK11361        105 KPFDLDELNLIVQRALQ  121 (457)
T ss_pred             cccCHHHHHHHHhhhcc
Confidence            99999999998887654

>PRK10365 transcriptional regulatory protein ZraR; Provisional

Probab=99.40  E-value=2.4e-12  Score=113.14  Aligned_cols=95  Identities=31%  Similarity=0.566  Sum_probs=86.9

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      +||.|..+.++.+++..+....  ||+||+|+.||+++|+++++.++ ..+.+|+|++|++.+.+....++..|+.+|+.
T Consensus        28 ~g~~v~~~~~~~~al~~l~~~~--~DlvilD~~m~~~~G~~~~~~ir~~~~~~~vi~lt~~~~~~~~~~a~~~ga~~~l~  105 (441)
T PRK10365         28 WGYNVALANSGRQALEQVREQV--FDLVLCDVRMAEMDGIATLKEIKALNPAIPVLIMTAYSSVETAVEALKTGALDYLI  105 (441)
T ss_pred             CCCeEEEeCCHHHHHHHHhcCC--CCEEEEeCCCCCCCHHHHHHHHHhhCCCCeEEEEECCCCHHHHHHHHHhhhHHHhc
Confidence            4789999999999999998765  99999999999999999999997 45789999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHH
Q 027234           80 KPVRIEELKNIWQHVVRK   97 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~   97 (226)
                      ||++.+.|...+.+++..
T Consensus       106 Kp~~~~~L~~~l~~~l~~  123 (441)
T PRK10365        106 KPLDFDNLQATLEKALAH  123 (441)
T ss_pred             CCCCHHHHHHHHHHHHHH
Confidence            999999999999887654

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

Probab=99.38  E-value=4.7e-12  Score=123.70  Aligned_cols=94  Identities=28%  Similarity=0.481  Sum_probs=86.8

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      +||+|..+.++.+|++.+....  ||+||+|+.||+++|+++++.++ ..+.+|+|++|+..+.....+++..|+++||.
T Consensus       981 ~g~~v~~~~~~~~al~~~~~~~--~dlil~D~~mp~~~g~~~~~~i~~~~~~~pii~lt~~~~~~~~~~~~~~G~~~~l~ 1058 (1197)
T PRK09959        981 LGYDVDEATDGVQALHKVSMQH--YDLLITDVNMPNMDGFELTRKLREQNSSLPIWGLTANAQANEREKGLSCGMNLCLF 1058 (1197)
T ss_pred             cCCEEEEECCHHHHHHHhhcCC--CCEEEEeCCCCCCCHHHHHHHHHhcCCCCCEEEEECCCCHHHHHHHHHCCCCEEEe
Confidence            4899999999999999998766  99999999999999999999997 45779999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHH
Q 027234           80 KPVRIEELKNIWQHVVR   96 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~   96 (226)
                      ||++.++|...++++..
T Consensus      1059 KP~~~~~L~~~l~~~~~ 1075 (1197)
T PRK09959       1059 KPLTLDVLKTHLSQLHQ 1075 (1197)
T ss_pred             CCCCHHHHHHHHHHHhh
Confidence            99999999999987653

>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional

Probab=99.38  E-value=1.1e-11  Score=99.46  Aligned_cols=94  Identities=22%  Similarity=0.383  Sum_probs=86.0

Q ss_pred             CcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEeCC
Q 027234            2 GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTKP   81 (226)
Q Consensus         2 g~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~KP   81 (226)
                      ||.|..+.++.+++..+....  ||+|++|..||+++|+++++.++..+.+|+|+++...+......++..|+++|+.||
T Consensus        34 ~~~v~~~~~~~~~~~~~~~~~--~dlvl~d~~~~~~~g~~~~~~l~~~~~~pii~l~~~~~~~~~~~~~~~ga~~~l~kp  111 (240)
T PRK10710         34 SYATTLLSHGDEVLPYVRQTP--PDLILLDLMLPGTDGLTLCREIRRFSDIPIVMVTAKIEEIDRLLGLEIGADDYICKP  111 (240)
T ss_pred             CCEEEEeCCHHHHHHHHhhCC--CCEEEEeCCCCCCCHHHHHHHHHhcCCCCEEEEEcCCCHHHHHHHHhcCCCeEEECC
Confidence            688889999999999998765  999999999999999999999986678999999999988888999999999999999


Q ss_pred             CCHHHHHHHHHHHHHH
Q 027234           82 VRIEELKNIWQHVVRK   97 (226)
Q Consensus        82 ~~~~~L~~~l~~~~~~   97 (226)
                      ++.++|...+..++..
T Consensus       112 ~~~~~L~~~i~~~~~~  127 (240)
T PRK10710        112 YSPREVVARVKTILRR  127 (240)
T ss_pred             CCHHHHHHHHHHHHhh
Confidence            9999999998887654

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

Probab=99.38  E-value=7.3e-12  Score=100.92  Aligned_cols=89  Identities=26%  Similarity=0.443  Sum_probs=76.1

Q ss_pred             EEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEeCCCCH
Q 027234            5 VTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTKPVRI   84 (226)
Q Consensus         5 V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~KP~~~   84 (226)
                      +..+.++.++++.+....  ||+||+|+.||+++|+++++.++.....++|++|++.  +...+++..|+.+||.||++.
T Consensus        30 ~~~~~~~~~~l~~~~~~~--~dlv~lDi~~~~~~G~~~~~~l~~~~~~~ii~vt~~~--~~~~~a~~~~~~~yl~KP~~~  105 (238)
T PRK11697         30 VGECSNAIEAIGAIHRLK--PDVVFLDIQMPRISGLELVGMLDPEHMPYIVFVTAFD--EYAIKAFEEHAFDYLLKPIDP  105 (238)
T ss_pred             EEEeCCHHHHHHHHHhcC--CCEEEEeCCCCCCCHHHHHHHhcccCCCEEEEEeccH--HHHHHHHhcCCcEEEECCCCH
Confidence            457889999999988765  9999999999999999999988643445688888765  567889999999999999999


Q ss_pred             HHHHHHHHHHHHH
Q 027234           85 EELKNIWQHVVRK   97 (226)
Q Consensus        85 ~~L~~~l~~~~~~   97 (226)
                      ++|...+.++...
T Consensus       106 ~~l~~~l~~~~~~  118 (238)
T PRK11697        106 ARLAKTLARLRQE  118 (238)
T ss_pred             HHHHHHHHHHHHh
Confidence            9999999988653

>PRK11091 aerobic respiration control sensor protein ArcB; Provisional

Probab=99.36  E-value=6.7e-12  Score=117.69  Aligned_cols=94  Identities=24%  Similarity=0.401  Sum_probs=81.8

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcC---CC-CcEEEEeccCCHHHHHHHHhCCcce
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLE---MD-LPVIMMCAHGSKEVVMKGVTHDACD   76 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~---~~-~pvI~ls~~~~~~~~~~a~~~ga~~   76 (226)
                      +||.|..+.++.+|++.+....  ||+||+|+.||++||+++++.|+..   +. +|+|++|+.... ....++..|+++
T Consensus       548 ~g~~v~~a~~~~eal~~~~~~~--~Dlvl~D~~mp~~~G~e~~~~ir~~~~~~~~~~ii~~ta~~~~-~~~~~~~~G~~~  624 (779)
T PRK11091        548 LGNSVDVAMTGKEALEMFDPDE--YDLVLLDIQLPDMTGLDIARELRERYPREDLPPLVALTANVLK-DKKEYLDAGMDD  624 (779)
T ss_pred             cCCEEEEECCHHHHHHHhhcCC--CCEEEEcCCCCCCCHHHHHHHHHhccccCCCCcEEEEECCchH-hHHHHHHCCCCE
Confidence            4899999999999999998765  9999999999999999999999743   34 488888886654 467899999999


Q ss_pred             EEeCCCCHHHHHHHHHHHHHH
Q 027234           77 YLTKPVRIEELKNIWQHVVRK   97 (226)
Q Consensus        77 yl~KP~~~~~L~~~l~~~~~~   97 (226)
                      ||.||++.++|...+++++..
T Consensus       625 ~l~KP~~~~~L~~~l~~~~~~  645 (779)
T PRK11091        625 VLSKPLSVPALTAMIKKFWDT  645 (779)
T ss_pred             EEECCCCHHHHHHHHHHHhcc
Confidence            999999999999999988643

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

Probab=99.36  E-value=6.4e-12  Score=99.70  Aligned_cols=91  Identities=9%  Similarity=0.061  Sum_probs=75.7

Q ss_pred             EEEECCHHHHHHHHHhCCCCceEEEEccC--CCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcce-EEeC
Q 027234            5 VTKCNRAEIALDMLRTNKNGYDIVISDVH--MPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACD-YLTK   80 (226)
Q Consensus         5 V~~~~~~~eal~~l~~~~~~~DlVl~D~~--mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~-yl~K   80 (226)
                      |..++++.++++.+....  ||+||+|+.  ||.++|.++++.++ ..+.+++|++|+..+..... ++..|+.+ |+.|
T Consensus        30 v~~~~~~~~~~~~~~~~~--pDlvLlDl~~~l~~~~g~~~i~~i~~~~p~~~iivlt~~~~~~~~~-~~~~~~~~~~~~K  106 (207)
T PRK15411         30 INDIETVDDLAIACDSLR--PSVVFINEDCFIHDASNSQRIKQIINQHPNTLFIVFMAIANIHFDE-YLLVRKNLLISSK  106 (207)
T ss_pred             EEecCCHHHHHHHHhccC--CCEEEEeCcccCCCCChHHHHHHHHHHCCCCeEEEEECCCchhHHH-HHHHHhhceeeec
Confidence            568899999999988765  999999966  88889999999997 56889999999988776543 55555554 8899


Q ss_pred             CCCHHHHHHHHHHHHHHH
Q 027234           81 PVRIEELKNIWQHVVRKR   98 (226)
Q Consensus        81 P~~~~~L~~~l~~~~~~~   98 (226)
                      +.++++|..+++.+..+.
T Consensus       107 ~~~~~~L~~aI~~v~~g~  124 (207)
T PRK15411        107 SIKPESLDDLLGDILKKE  124 (207)
T ss_pred             cCCHHHHHHHHHHHHcCC
Confidence            999999999999987654

>PRK15369 two component system sensor kinase SsrB; Provisional

Probab=99.34  E-value=1.8e-11  Score=95.49  Aligned_cols=93  Identities=17%  Similarity=0.265  Sum_probs=82.4

Q ss_pred             cEE-EEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhc-CCCCcEEEEeccCCHHHHHHHHhCCcceEEeC
Q 027234            3 FSV-TKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGL-EMDLPVIMMCAHGSKEVVMKGVTHDACDYLTK   80 (226)
Q Consensus         3 ~~V-~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~-~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~K   80 (226)
                      +.+ ..+.++.++++.+....  ||+|++|..||+++|+++++.++. .+..|+|++|...+......++..|+.+|+.|
T Consensus        29 ~~~~~~~~~~~~~~~~~~~~~--~dlvl~d~~~~~~~~~~~~~~l~~~~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~k  106 (211)
T PRK15369         29 YKIVGQVDNGLEVYNACRQLE--PDIVILDLGLPGMNGLDVIPQLHQRWPAMNILVLTARQEEHMASRTLAAGALGYVLK  106 (211)
T ss_pred             cEEEEEECCHHHHHHHHHhcC--CCEEEEeCCCCCCCHHHHHHHHHHHCCCCcEEEEeCCCCHHHHHHHHHhCCCEEEeC
Confidence            454 47889999998887765  999999999999999999999874 57789999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHH
Q 027234           81 PVRIEELKNIWQHVVRK   97 (226)
Q Consensus        81 P~~~~~L~~~l~~~~~~   97 (226)
                      |++..+|...+..+..+
T Consensus       107 p~~~~~l~~~i~~~~~~  123 (211)
T PRK15369        107 KSPQQILLAAIQTVAVG  123 (211)
T ss_pred             CCCHHHHHHHHHHHHCC
Confidence            99999999999887654

>PRK15479 transcriptional regulatory protein TctD; Provisional

Probab=99.34  E-value=3.1e-11  Score=95.46  Aligned_cols=95  Identities=31%  Similarity=0.536  Sum_probs=85.4

Q ss_pred             CcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEeC
Q 027234            2 GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTK   80 (226)
Q Consensus         2 g~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~K   80 (226)
                      |+.+..+.++.++++.+....  ||+|++|+.+|+++|+++++.++ ..+.+|+|+++...+.....+++..|+++|+.|
T Consensus        24 ~~~v~~~~~~~~~~~~~~~~~--~d~vild~~~~~~~~~~~~~~i~~~~~~~~ii~lt~~~~~~~~~~~~~~g~~~~i~k  101 (221)
T PRK15479         24 GFAVDCVFDGLAADHLLQSEM--YALAVLDINMPGMDGLEVLQRLRKRGQTLPVLLLTARSAVADRVKGLNVGADDYLPK  101 (221)
T ss_pred             CCEEEEeCCHHHHHHHHhhCC--CCEEEEeCCCCCCcHHHHHHHHHhcCCCCCEEEEECCCCHHHHHHHHHcCCCeeEeC
Confidence            677888999999998887755  99999999999999999999997 456799999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHH
Q 027234           81 PVRIEELKNIWQHVVRKR   98 (226)
Q Consensus        81 P~~~~~L~~~l~~~~~~~   98 (226)
                      |++..+|...++.++++.
T Consensus       102 p~~~~~l~~~i~~~~~~~  119 (221)
T PRK15479        102 PFELEELDARLRALLRRS  119 (221)
T ss_pred             CCCHHHHHHHHHHHHhhh
Confidence            999999999998877643

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

Probab=99.34  E-value=1.7e-11  Score=93.69  Aligned_cols=100  Identities=21%  Similarity=0.341  Sum_probs=84.6

Q ss_pred             CcE-EEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEeC
Q 027234            2 GFS-VTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTK   80 (226)
Q Consensus         2 g~~-V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~K   80 (226)
                      ||+ |.++.++.++.+.+....  ||+||+|+.||..|-.+-+.....+...|+|++++++++.....++..||.+|+.|
T Consensus        29 g~~~Vg~~~~~~~~~~~~~~~~--pDvVildie~p~rd~~e~~~~~~~~~~~piv~lt~~s~p~~i~~a~~~Gv~ayivk  106 (194)
T COG3707          29 GYQRVGEAADGLEAVEVCERLQ--PDVVILDIEMPRRDIIEALLLASENVARPIVALTAYSDPALIEAAIEAGVMAYIVK  106 (194)
T ss_pred             CCeEeeeecccccchhHHHhcC--CCEEEEecCCCCccHHHHHHHhhcCCCCCEEEEEccCChHHHHHHHHcCCeEEEec
Confidence            677 457778889999998877  99999999999999544444445667889999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHhhhhh
Q 027234           81 PVRIEELKNIWQHVVRKRKNERK  103 (226)
Q Consensus        81 P~~~~~L~~~l~~~~~~~~~~~~  103 (226)
                      |+++..|...+.-+.......++
T Consensus       107 pi~~~rl~p~L~vA~srf~~~~~  129 (194)
T COG3707         107 PLDESRLLPILDVAVSRFEERRA  129 (194)
T ss_pred             CcchhhhhHHHHHHHHHHHHHHH
Confidence            99999999998887766555443

>PRK12555 chemotaxis-specific methylesterase; Provisional

Probab=99.32  E-value=1.9e-11  Score=104.02  Aligned_cols=92  Identities=18%  Similarity=0.279  Sum_probs=75.8

Q ss_pred             CcEEE-EECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcCCCCcEEEEeccCC--HHHHHHHHhCCcceEE
Q 027234            2 GFSVT-KCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGS--KEVVMKGVTHDACDYL   78 (226)
Q Consensus         2 g~~V~-~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~~~~pvI~ls~~~~--~~~~~~a~~~ga~~yl   78 (226)
                      ||+|. .+.++.+|++.+....  ||+|++|+.||+|+|+++++.++....+|+|++++...  .....++++.|+++|+
T Consensus        25 ~~~vv~~a~~~~eal~~l~~~~--pDlVllD~~mp~~~G~e~l~~l~~~~~~pvivvs~~~~~~~~~~~~al~~Ga~d~l  102 (337)
T PRK12555         25 DHEVVWVATDGAQAVERCAAQP--PDVILMDLEMPRMDGVEATRRIMAERPCPILIVTSLTERNASRVFEAMGAGALDAV  102 (337)
T ss_pred             CCEEEEEECCHHHHHHHHhccC--CCEEEEcCCCCCCCHHHHHHHHHHHCCCcEEEEeCCCCcCHHHHHHHHhcCceEEE
Confidence            56765 7899999999998866  99999999999999999999997656689999998754  5667789999999999


Q ss_pred             eCCC---------CHHHHHHHHHHHH
Q 027234           79 TKPV---------RIEELKNIWQHVV   95 (226)
Q Consensus        79 ~KP~---------~~~~L~~~l~~~~   95 (226)
                      .||+         ..++|...++.+.
T Consensus       103 ~KP~~~~~~~~~~~~~~l~~~i~~~~  128 (337)
T PRK12555        103 DTPTLGIGAGLEEYAAELLAKIDQIG  128 (337)
T ss_pred             ECCCCCcchhHHHHHHHHHHHHHHHh
Confidence            9999         4445555555443

>PRK10651 transcriptional regulator NarL; Provisional

Probab=99.32  E-value=6.8e-11  Score=92.97  Aligned_cols=93  Identities=19%  Similarity=0.369  Sum_probs=83.1

Q ss_pred             cEE-EEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEeC
Q 027234            3 FSV-TKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTK   80 (226)
Q Consensus         3 ~~V-~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~K   80 (226)
                      +.+ ..+.++.+++..+....  ||+|++|+.+|+++|+++++.++ ..+..|+|+++...+......++..|+++|+.|
T Consensus        32 ~~~~~~~~~~~~~~~~~~~~~--~dlvl~d~~l~~~~~~~~~~~l~~~~~~~~vi~l~~~~~~~~~~~~~~~g~~~~i~k  109 (216)
T PRK10651         32 ITVVGEASNGEQGIELAESLD--PDLILLDLNMPGMNGLETLDKLREKSLSGRIVVFSVSNHEEDVVTALKRGADGYLLK  109 (216)
T ss_pred             cEEEEEeCCHHHHHHHHHhCC--CCEEEEeCCCCCCcHHHHHHHHHHhCCCCcEEEEeCCCCHHHHHHHHHcCCCEEEeC
Confidence            443 46889999999998765  99999999999999999999987 456789999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHH
Q 027234           81 PVRIEELKNIWQHVVRK   97 (226)
Q Consensus        81 P~~~~~L~~~l~~~~~~   97 (226)
                      |++.++|...+..++.+
T Consensus       110 ~~~~~~l~~~i~~~~~~  126 (216)
T PRK10651        110 DMEPEDLLKALQQAAAG  126 (216)
T ss_pred             CCCHHHHHHHHHHHHCC
Confidence            99999999999998764

>PRK09581 pleD response regulator PleD; Reviewed

Probab=99.31  E-value=4.1e-11  Score=104.99  Aligned_cols=96  Identities=27%  Similarity=0.431  Sum_probs=87.1

Q ss_pred             CcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcC---CCCcEEEEeccCCHHHHHHHHhCCcceEE
Q 027234            2 GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLE---MDLPVIMMCAHGSKEVVMKGVTHDACDYL   78 (226)
Q Consensus         2 g~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~---~~~pvI~ls~~~~~~~~~~a~~~ga~~yl   78 (226)
                      ||.|..+.++.+++..+....  ||+|++|+.||+.+|+++++.++..   +.+|+|++|+..+.....+++..|+++|+
T Consensus        26 ~~~v~~~~~~~~~~~~~~~~~--~dlvi~d~~~~~~~g~~l~~~i~~~~~~~~~~ii~~s~~~~~~~~~~~~~~ga~~~l  103 (457)
T PRK09581         26 YYTVLTASSGAEAIAICEREQ--PDIILLDVMMPGMDGFEVCRRLKSDPATTHIPVVMVTALDDPEDRVRGLEAGADDFL  103 (457)
T ss_pred             CCEEEEeCCHHHHHHHHhhcC--CCEEEEeCCCCCCCHHHHHHHHHcCcccCCCCEEEEECCCCHHHHHHHHHCCCCEEE
Confidence            688999999999999998765  9999999999999999999999753   36899999999999999999999999999


Q ss_pred             eCCCCHHHHHHHHHHHHHHHh
Q 027234           79 TKPVRIEELKNIWQHVVRKRK   99 (226)
Q Consensus        79 ~KP~~~~~L~~~l~~~~~~~~   99 (226)
                      .||++.++|..++..+.+...
T Consensus       104 ~kp~~~~~l~~~i~~~~~~~~  124 (457)
T PRK09581        104 TKPINDVALFARVKSLTRLKM  124 (457)
T ss_pred             ECCCCHHHHHHHHHHHHHHHH
Confidence            999999999999988776543

>PRK13435 response regulator; Provisional

Probab=99.28  E-value=4.8e-11  Score=88.87  Aligned_cols=94  Identities=17%  Similarity=0.238  Sum_probs=78.8

Q ss_pred             CcEEE-EECCHHHHHHHHHhCCCCceEEEEccCCC-CCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            2 GFSVT-KCNRAEIALDMLRTNKNGYDIVISDVHMP-DMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         2 g~~V~-~~~~~~eal~~l~~~~~~~DlVl~D~~mp-~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      ||.+. .++++.++++.+....  ||+|++|..++ +.+|+++++.++..+.+|+|+++...+   ...++..|+++|+.
T Consensus        29 ~~~~~~~~~~~~~~~~~~~~~~--~dliivd~~~~~~~~~~~~~~~l~~~~~~pii~ls~~~~---~~~~~~~ga~~~l~  103 (145)
T PRK13435         29 GHEVVGIAMSSEQAIALGRRRQ--PDVALVDVHLADGPTGVEVARRLSADGGVEVVFMTGNPE---RVPHDFAGALGVIA  103 (145)
T ss_pred             CCeEEEeeCCHHHHHHHhhhcC--CCEEEEeeecCCCCcHHHHHHHHHhCCCCCEEEEeCCHH---HHHHHhcCcceeEe
Confidence            67766 7899999999887655  99999999998 589999999987667899999987543   24677899999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHhh
Q 027234           80 KPVRIEELKNIWQHVVRKRKN  100 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~~~~  100 (226)
                      ||++.++|...++++..+...
T Consensus       104 kp~~~~~l~~~i~~~~~~~~~  124 (145)
T PRK13435        104 KPYSPRGVARALSYLSARRVG  124 (145)
T ss_pred             CCCCHHHHHHHHHHHHhcCcc
Confidence            999999999999988754443

>PRK09390 fixJ response regulator FixJ; Provisional

Probab=99.27  E-value=5.6e-11  Score=92.16  Aligned_cols=95  Identities=31%  Similarity=0.518  Sum_probs=85.2

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||.+..+.++.++++.+....  ||+|++|..||+++|+++++.++ ..+.+|+|+++...+......++..|+.+|+.
T Consensus        26 ~~~~v~~~~~~~~~~~~~~~~~--~d~ii~d~~~~~~~~~~~~~~l~~~~~~~~ii~l~~~~~~~~~~~~~~~g~~~~l~  103 (202)
T PRK09390         26 AGFEVRLFESAQAFLDALPGLR--FGCVVTDVRMPGIDGIELLRRLKARGSPLPVIVMTGHGDVPLAVEAMKLGAVDFIE  103 (202)
T ss_pred             CCCeEEEeCCHHHHHHHhccCC--CCEEEEeCCCCCCcHHHHHHHHHhcCCCCCEEEEECCCCHHHHHHHHHcChHHHhh
Confidence            3688889999999999988765  99999999999999999999997 45678999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHH
Q 027234           80 KPVRIEELKNIWQHVVRK   97 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~   97 (226)
                      ||++...+...+..++..
T Consensus       104 ~p~~~~~l~~~l~~~~~~  121 (202)
T PRK09390        104 KPFEDERLIGAIERALAQ  121 (202)
T ss_pred             CCCCHHHHHHHHHHHHHh
Confidence            999999999888877654

>PRK13558 bacterio-opsin activator; Provisional

Probab=99.22  E-value=8e-11  Score=108.60  Aligned_cols=94  Identities=23%  Similarity=0.303  Sum_probs=81.6

Q ss_pred             CcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEeC
Q 027234            2 GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTK   80 (226)
Q Consensus         2 g~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~K   80 (226)
                      ||.|..+.++.+++..+....  ||+||+|+.||+++|+++++.++ ..+.+|+|++|+..+.+...+++..|+.+|+.|
T Consensus        31 ~~~v~~~~~~~~al~~~~~~~--~Dlvl~d~~lp~~~g~~~l~~l~~~~~~~piI~lt~~~~~~~~~~al~~Ga~dyl~k  108 (665)
T PRK13558         31 RLDVTQIRDFVAARDRVEAGE--IDCVVADHEPDGFDGLALLEAVRQTTAVPPVVVVPTAGDEAVARRAVDADAAAYVPA  108 (665)
T ss_pred             CcceEeeCCHHHHHHHhhccC--CCEEEEeccCCCCcHHHHHHHHHhcCCCCCEEEEECCCCHHHHHHHHhcCcceEEec
Confidence            688999999999999998765  99999999999999999999997 457899999999999999999999999999999


Q ss_pred             CCCHH--HHHHHHHHHHHH
Q 027234           81 PVRIE--ELKNIWQHVVRK   97 (226)
Q Consensus        81 P~~~~--~L~~~l~~~~~~   97 (226)
                      |....  .+...+...+..
T Consensus       109 ~~~~~~~~l~~~i~~~~~~  127 (665)
T PRK13558        109 VSDDATAAIAERIESAVPE  127 (665)
T ss_pred             cchhHHHHHHHHHHHhhhc
Confidence            97643  555566555543

>PRK10610 chemotaxis regulatory protein CheY; Provisional

Probab=99.20  E-value=7.4e-10  Score=78.78  Aligned_cols=93  Identities=31%  Similarity=0.559  Sum_probs=81.4

Q ss_pred             Cc-EEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcC---CCCcEEEEeccCCHHHHHHHHhCCcceE
Q 027234            2 GF-SVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLE---MDLPVIMMCAHGSKEVVMKGVTHDACDY   77 (226)
Q Consensus         2 g~-~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~---~~~pvI~ls~~~~~~~~~~a~~~ga~~y   77 (226)
                      |+ .+..+.++.+++..+....  +|++++|..+++++|+++++.++..   +.+|+++++...+......++..|+.+|
T Consensus        29 ~~~~~~~~~~~~~~~~~~~~~~--~di~l~d~~~~~~~~~~~~~~l~~~~~~~~~~~i~~~~~~~~~~~~~~~~~g~~~~  106 (129)
T PRK10610         29 GFNNVEEAEDGVDALNKLQAGG--FGFVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGY  106 (129)
T ss_pred             CCCeEEEeCCHHHHHHHhhccC--CCEEEEcCCCCCCCHHHHHHHHHhCCCcCCCcEEEEECCCCHHHHHHHHHhCCCeE
Confidence            55 3667889999999887755  9999999999999999999999743   4689999998888888899999999999


Q ss_pred             EeCCCCHHHHHHHHHHHHH
Q 027234           78 LTKPVRIEELKNIWQHVVR   96 (226)
Q Consensus        78 l~KP~~~~~L~~~l~~~~~   96 (226)
                      +.||++.+++...++++++
T Consensus       107 i~~p~~~~~l~~~l~~~~~  125 (129)
T PRK10610        107 VVKPFTAATLEEKLNKIFE  125 (129)
T ss_pred             EECCCCHHHHHHHHHHHHH
Confidence            9999999999999988764

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

Probab=99.20  E-value=8.2e-11  Score=98.63  Aligned_cols=78  Identities=29%  Similarity=0.453  Sum_probs=70.5

Q ss_pred             EEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcCCCCcEEEEeccCCH--HHHHHHHhCCcceEEeCC
Q 027234            4 SVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSK--EVVMKGVTHDACDYLTKP   81 (226)
Q Consensus         4 ~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~~~~pvI~ls~~~~~--~~~~~a~~~ga~~yl~KP   81 (226)
                      .|.++.|+.+|++.+....  ||+|.+|+.||.|||+++++.+-+...+|||++|+....  +...+++++||.||+.||
T Consensus        29 vv~~a~ng~~a~~~~~~~~--PDVi~ld~emp~mdgl~~l~~im~~~p~pVimvsslt~~g~~~t~~al~~gAvD~i~kp  106 (350)
T COG2201          29 VVGTARNGREAIDKVKKLK--PDVITLDVEMPVMDGLEALRKIMRLRPLPVIMVSSLTEEGAEATLEALELGAVDFIAKP  106 (350)
T ss_pred             EEEecCCHHHHHHHHHhcC--CCEEEEecccccccHHHHHHHHhcCCCCcEEEEeccccccHHHHHHHHhcCcceeecCC
Confidence            4678999999999999987  999999999999999999999977788999999976654  677899999999999999


Q ss_pred             CC
Q 027234           82 VR   83 (226)
Q Consensus        82 ~~   83 (226)
                      ..
T Consensus       107 ~~  108 (350)
T COG2201         107 SG  108 (350)
T ss_pred             Cc
Confidence            74

>PRK00742 chemotaxis-specific methylesterase; Provisional

Probab=99.19  E-value=2.6e-10  Score=97.66  Aligned_cols=80  Identities=26%  Similarity=0.401  Sum_probs=68.9

Q ss_pred             CcEEE-EECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcCCCCcEEEEeccC--CHHHHHHHHhCCcceEE
Q 027234            2 GFSVT-KCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHG--SKEVVMKGVTHDACDYL   78 (226)
Q Consensus         2 g~~V~-~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~~~~pvI~ls~~~--~~~~~~~a~~~ga~~yl   78 (226)
                      |+.+. .+.++.++++.+....  ||+|++|+.||+++|+++++.++....+|+|++|+..  ......+++..|+++|+
T Consensus        28 ~~~vv~~a~~~~~al~~~~~~~--~DlVllD~~mp~~dgle~l~~i~~~~~~piIvls~~~~~~~~~~~~al~~Ga~d~l  105 (354)
T PRK00742         28 DIEVVGTAPDGLEAREKIKKLN--PDVITLDVEMPVMDGLDALEKIMRLRPTPVVMVSSLTERGAEITLRALELGAVDFV  105 (354)
T ss_pred             CCEEEEEECCHHHHHHHHhhhC--CCEEEEeCCCCCCChHHHHHHHHHhCCCCEEEEecCCCCCHHHHHHHHhCCCcEEE
Confidence            56766 8899999999998766  9999999999999999999999754449999999753  34667789999999999


Q ss_pred             eCCCC
Q 027234           79 TKPVR   83 (226)
Q Consensus        79 ~KP~~   83 (226)
                      .||+.
T Consensus       106 ~kP~~  110 (354)
T PRK00742        106 TKPFL  110 (354)
T ss_pred             eCCcc
Confidence            99994

>PRK09191 two-component response regulator; Provisional

Probab=99.13  E-value=9e-10  Score=89.93  Aligned_cols=92  Identities=18%  Similarity=0.335  Sum_probs=76.3

Q ss_pred             CcEEE-EECCHHHHHHHHHhCCCCceEEEEccCCCC-CCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            2 GFSVT-KCNRAEIALDMLRTNKNGYDIVISDVHMPD-MDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         2 g~~V~-~~~~~~eal~~l~~~~~~~DlVl~D~~mp~-~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      |+.+. .+.++.++++.+....  ||+||+|+.||+ ++|+++++.++....+|+|++|+..+....  +...|+.+|+.
T Consensus       161 ~~~~~~~~~~~~~~l~~l~~~~--~dlvi~d~~~~~~~~g~e~l~~l~~~~~~pii~ls~~~~~~~~--~~~~~~~~~l~  236 (261)
T PRK09191        161 GHRVTGIARTRAEAVALAKKTR--PGLILADIQLADGSSGIDAVNDILKTFDVPVIFITAFPERLLT--GERPEPAFLIT  236 (261)
T ss_pred             CCEEEEEECCHHHHHHHHhccC--CCEEEEecCCCCCCCHHHHHHHHHHhCCCCEEEEeCCCcHHHH--HHhcccCceEE
Confidence            67776 6889999999998765  999999999995 899999999874348999999997765443  34467889999


Q ss_pred             CCCCHHHHHHHHHHHHHH
Q 027234           80 KPVRIEELKNIWQHVVRK   97 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~   97 (226)
                      ||++.++|...++++...
T Consensus       237 kP~~~~~l~~~i~~~~~~  254 (261)
T PRK09191        237 KPFQPDTVKAAISQALFF  254 (261)
T ss_pred             CCCCHHHHHHHHHHHHhc
Confidence            999999999999887643

>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=99.11  E-value=1.5e-09  Score=74.13  Aligned_cols=91  Identities=36%  Similarity=0.603  Sum_probs=80.0

Q ss_pred             CcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhc-CCCCcEEEEeccCCHHHHHHHHhCCcceEEeC
Q 027234            2 GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGL-EMDLPVIMMCAHGSKEVVMKGVTHDACDYLTK   80 (226)
Q Consensus         2 g~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~-~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~K   80 (226)
                      |+.+..+.+..+++..+....  +|++++|..+++.+|+++++.++. .+.+|+++++..........++..|+.+|+.|
T Consensus        21 ~~~~~~~~~~~~~~~~~~~~~--~~~ii~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~i~~   98 (113)
T cd00156          21 GYEVVEAEDGEEALALLAEEK--PDLILLDIMMPGMDGLELLRRIRKRGPDIPIIFLTAHGDDEDAVEALKAGADDYLTK   98 (113)
T ss_pred             CceEEEecCHHHHHHHHHhCC--CCEEEEecCCCCCchHHHHHHHHHhCCCCCEEEEEecccHHHHHHHHHcChhhHccC
Confidence            678888889999999888765  999999999999999999998874 46789999998877888889999999999999


Q ss_pred             CCCHHHHHHHHHHH
Q 027234           81 PVRIEELKNIWQHV   94 (226)
Q Consensus        81 P~~~~~L~~~l~~~   94 (226)
                      |++...|...+..+
T Consensus        99 p~~~~~l~~~l~~~  112 (113)
T cd00156          99 PFSPEELLARIRAL  112 (113)
T ss_pred             CCCHHHHHHHHHhh
Confidence            99999998887653

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

Probab=99.09  E-value=9.8e-10  Score=103.84  Aligned_cols=93  Identities=13%  Similarity=0.198  Sum_probs=83.7

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      +||+|..+.++.++++.+......||+||+  .||+++|+++++.++ ..+.+|||++|+........+++..| ++||.
T Consensus       720 ~G~~v~~~~s~~~al~~l~~~~~~~DlVll--~~~~~~g~~l~~~l~~~~~~ipIIvls~~~~~~~~~~~~~~G-~d~L~  796 (828)
T PRK13837        720 LGYEPVGFSTLAAAIAWISKGPERFDLVLV--DDRLLDEEQAAAALHAAAPTLPIILGGNSKTMALSPDLLASV-AEILA  796 (828)
T ss_pred             CCCEEEEeCCHHHHHHHHHhCCCCceEEEE--CCCCCCHHHHHHHHHhhCCCCCEEEEeCCCchhhhhhHhhcc-CcEEe
Confidence            489999999999999999764334799999  799999999999997 55789999999999999999999999 99999


Q ss_pred             CCCCHHHHHHHHHHHHH
Q 027234           80 KPVRIEELKNIWQHVVR   96 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~   96 (226)
                      ||++..+|..++.++++
T Consensus       797 KP~~~~~L~~~l~~~l~  813 (828)
T PRK13837        797 KPISSRTLAYALRTALA  813 (828)
T ss_pred             CCCCHHHHHHHHHHHHc
Confidence            99999999999998875

>PRK13557 histidine kinase; Provisional

Probab=98.94  E-value=9.6e-09  Score=91.91  Aligned_cols=95  Identities=21%  Similarity=0.339  Sum_probs=83.9

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCC-CCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEE
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPD-MDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYL   78 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~-~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl   78 (226)
                      .||.+..+.++.++++.+... ..||+|++|..||+ ++|+++++.++ ..+.+|+|+++...+......++..|+.+|+
T Consensus       438 ~~~~v~~~~~~~~~~~~~~~~-~~~d~vi~d~~~~~~~~~~~~~~~l~~~~~~~~ii~~~~~~~~~~~~~~~~~g~~~~l  516 (540)
T PRK13557        438 FGYRTLVASNGREALEILDSH-PEVDLLFTDLIMPGGMNGVMLAREARRRQPKIKVLLTTGYAEASIERTDAGGSEFDIL  516 (540)
T ss_pred             cCCeEEEeCCHHHHHHHHhcC-CCceEEEEeccCCCCCCHHHHHHHHHHhCCCCcEEEEcCCCchhhhhhhccccCCcee
Confidence            378899999999999998653 23999999999997 99999999997 4577999999999888888889999999999


Q ss_pred             eCCCCHHHHHHHHHHHHH
Q 027234           79 TKPVRIEELKNIWQHVVR   96 (226)
Q Consensus        79 ~KP~~~~~L~~~l~~~~~   96 (226)
                      .||++.++|...++.++.
T Consensus       517 ~kp~~~~~l~~~l~~~~~  534 (540)
T PRK13557        517 NKPYRRAELARRVRMVLD  534 (540)
T ss_pred             eCCCCHHHHHHHHHHHhc
Confidence            999999999999887664

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

Probab=98.85  E-value=1e-08  Score=83.29  Aligned_cols=87  Identities=28%  Similarity=0.469  Sum_probs=76.3

Q ss_pred             EECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhc-CCCCcEEEEeccCCHHHHHHHHhCCcceEEeCCCCHH
Q 027234            7 KCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGL-EMDLPVIMMCAHGSKEVVMKGVTHDACDYLTKPVRIE   85 (226)
Q Consensus         7 ~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~-~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~KP~~~~   85 (226)
                      .+.++.++++.+....  ||++++|+.||+++|+++...++. .+..+|+++|++.  +++..+++..|.+|+.||++.+
T Consensus        32 ~~~~~~~~~~~~~~~~--~~~~fldI~~~~~~G~ela~~i~~~~~~~~Ivfvt~~~--~~a~~afev~a~d~i~kp~~~~  107 (244)
T COG3279          32 EAENGEEALQLLQGLR--PDLVFLDIAMPDINGIELAARIRKGDPRPAIVFVTAHD--EYAVAAFEVEALDYLLKPISEE  107 (244)
T ss_pred             eeccchhhHHHHhccC--CCeEEEeeccCccchHHHHHHhcccCCCCeEEEEEehH--HHHHHHHhHHHHhhhcCcchHH
Confidence            6889999999999876  999999999999999999999985 4567788899865  5677788999999999999999


Q ss_pred             HHHHHHHHHHHH
Q 027234           86 ELKNIWQHVVRK   97 (226)
Q Consensus        86 ~L~~~l~~~~~~   97 (226)
                      .|...+.+..+.
T Consensus       108 ~l~~~l~~~~~~  119 (244)
T COG3279         108 RLAKTLERLRRY  119 (244)
T ss_pred             HHHHHHHHHHHH
Confidence            999999876554

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

Probab=98.75  E-value=1.7e-08  Score=87.29  Aligned_cols=95  Identities=33%  Similarity=0.404  Sum_probs=84.4

Q ss_pred             cEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEeCCC
Q 027234            3 FSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTKPV   82 (226)
Q Consensus         3 ~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~KP~   82 (226)
                      |+|.++..+..++..+..+.  ||.+++|+.||+|+|+++++.++..+.. ++++|...+.....+++++|++++|+||.
T Consensus        13 ~~v~~a~~g~~~l~~~~~~~--~~~~lld~~m~~~~~~~~~~~lk~~~~~-~v~~t~~~~~~~~~~~~~~~~~~~l~~~~   89 (435)
T COG3706          13 KEVATAKKGLIALAILLDHK--PDYKLLDVMMPGMDGFELCRRLKAEPAT-VVMVTALDDSAPRVRGLKAGADDFLTKPV   89 (435)
T ss_pred             hhhhhccchHHHHHHHhcCC--CCeEEeecccCCcCchhHHHHHhcCCcc-eEEEEecCCCCcchhHHhhhhhhhccCCC
Confidence            45777899999999999876  9999999999999999999999876655 88899999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHHhh
Q 027234           83 RIEELKNIWQHVVRKRKN  100 (226)
Q Consensus        83 ~~~~L~~~l~~~~~~~~~  100 (226)
                      +...+......+.+....
T Consensus        90 ~~~~~~~r~~~l~~~k~~  107 (435)
T COG3706          90 NDSQLFLRAKSLVRLKCS  107 (435)
T ss_pred             ChHHHHHhhhhhccchhh
Confidence            999999888887655443

>PRK15029 arginine decarboxylase; Provisional

Probab=98.57  E-value=5.2e-07  Score=83.55  Aligned_cols=91  Identities=10%  Similarity=0.105  Sum_probs=68.1

Q ss_pred             CCcEEEEECCHHHHHHHHHh-CCCCceEEEEccCCCCCCHH----HHHHHHhc-CCCCcEEEEeccCC--HHHHHHHHhC
Q 027234            1 MGFSVTKCNRAEIALDMLRT-NKNGYDIVISDVHMPDMDGF----KLLELVGL-EMDLPVIMMCAHGS--KEVVMKGVTH   72 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~-~~~~~DlVl~D~~mp~~dG~----~l~~~l~~-~~~~pvI~ls~~~~--~~~~~~a~~~   72 (226)
                      .||+|..+.++.+|++.+.. ..  ||+||+|++||+++|+    ++++.|+. .+++|||++|+..+  .......+ -
T Consensus        31 ~G~eV~~a~s~~dAl~~l~~~~~--~DlVLLD~~LPd~dG~~~~~ell~~IR~~~~~iPIIlLTar~~~~~~~~~~~~-~  107 (755)
T PRK15029         31 QNVTVIKSTSFDDGFAILSSNEA--IDCLMFSYQMEHPDEHQNVRQLIGKLHERQQNVPVFLLGDREKALAAMDRDLL-E  107 (755)
T ss_pred             CCCEEEEECCHHHHHHHHHhcCC--CcEEEEECCCCCCccchhHHHHHHHHHhhCCCCCEEEEEcCCcccccCCHHHH-H
Confidence            38999999999999999976 35  9999999999999997    89999984 56899999999886  22222222 2


Q ss_pred             CcceEEeCCCCHHHH-HHHHHHH
Q 027234           73 DACDYLTKPVRIEEL-KNIWQHV   94 (226)
Q Consensus        73 ga~~yl~KP~~~~~L-~~~l~~~   94 (226)
                      -+.+|+.+--+..++ ...+...
T Consensus       108 ~~~~~~~~~~~~~~~~~~~~~~~  130 (755)
T PRK15029        108 LVDEFAWILEDTADFIAGRAVAA  130 (755)
T ss_pred             hhheEEEecCCCHHHHHHHHHHH
Confidence            367888776554443 3334444

>PRK11107 hybrid sensory histidine kinase BarA; Provisional

Probab=97.58  E-value=0.00052  Score=65.72  Aligned_cols=89  Identities=16%  Similarity=0.130  Sum_probs=70.0

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHH-HHhc--CCCCcEEEEeccCCHHHHHHHHhCCcceE
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLE-LVGL--EMDLPVIMMCAHGSKEVVMKGVTHDACDY   77 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~-~l~~--~~~~pvI~ls~~~~~~~~~~a~~~ga~~y   77 (226)
                      +||.|..+.+..+    +....  ||++++|..||++++...+. .++.  ....++|+++..........+...|+++|
T Consensus       559 ~g~~v~~~~~~~~----l~~~~--~d~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~g~~~~  632 (919)
T PRK11107        559 TPLEVTYSPTLSQ----LPEAH--YDILLLGLPVTFREPLTMLHERLAKAKSMTDFLILALPCHEQVLAEQLKQDGADAC  632 (919)
T ss_pred             CCCEEEEcCCHHH----hccCC--CCEEEecccCCCCCCHHHHHHHHHhhhhcCCcEEEEeCCcchhhHHHHhhCCCceE
Confidence            4788888888777    34434  99999999999988776654 3332  23456788888888888899999999999


Q ss_pred             EeCCCCHHHHHHHHHHHH
Q 027234           78 LTKPVRIEELKNIWQHVV   95 (226)
Q Consensus        78 l~KP~~~~~L~~~l~~~~   95 (226)
                      +.||++..++...+....
T Consensus       633 l~kp~~~~~l~~~l~~~~  650 (919)
T PRK11107        633 LSKPLSHTRLLPALLEPC  650 (919)
T ss_pred             ECCCCCHHHHHHHHHHhh
Confidence            999999999988887643

>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A

Probab=96.93  E-value=0.00029  Score=40.86  Aligned_cols=31  Identities=32%  Similarity=0.278  Sum_probs=22.9

Q ss_pred             HHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          181 ILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       181 I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      |.+++.. ++++++||+++++|++||+|+|+.
T Consensus         1 I~~~~~~-~~~l~~iA~~~g~S~~~f~r~Fk~   31 (42)
T PF00165_consen    1 IEENLQQ-KLTLEDIAEQAGFSPSYFSRLFKK   31 (42)
T ss_dssp             HHTTT-S-S--HHHHHHHHTS-HHHHHHHHHH
T ss_pred             CCccccC-CCCHHHHHHHHCCCHHHHHHHHHH
Confidence            4566677 699999999999999999998864

>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=96.67  E-value=0.018  Score=41.18  Aligned_cols=92  Identities=13%  Similarity=0.183  Sum_probs=66.2

Q ss_pred             CcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCC--CCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEE
Q 027234            2 GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPD--MDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYL   78 (226)
Q Consensus         2 g~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~--~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl   78 (226)
                      ||+|+.+.+.++++..+++. ..+..|++|+. ++  ....++++.++ .+..+||.+++.....+.+-...-..+++|+
T Consensus        17 ~~~vv~~~~~dd~~~~i~~~-~~i~avvi~~d-~~~~~~~~~ll~~i~~~~~~iPVFl~~~~~~~~~l~~~~l~~v~~~i   94 (115)
T PF03709_consen   17 GREVVDADSTDDALAIIESF-TDIAAVVISWD-GEEEDEAQELLDKIRERNFGIPVFLLAERDTTEDLPAEVLGEVDGFI   94 (115)
T ss_dssp             TTEEEEESSHHHHHHHHHCT-TTEEEEEEECH-HHHHHHHHHHHHHHHHHSTT-EEEEEESCCHHHCCCHHHHCCESEEE
T ss_pred             CCEEEEeCChHHHHHHHHhC-CCeeEEEEEcc-cccchhHHHHHHHHHHhCCCCCEEEEecCCCcccCCHHHHhhccEEE
Confidence            79999999999999999986 45899999986 22  23566788887 6789999999986644444444555688898


Q ss_pred             eCCC-CHHHHHHHHHHHH
Q 027234           79 TKPV-RIEELKNIWQHVV   95 (226)
Q Consensus        79 ~KP~-~~~~L~~~l~~~~   95 (226)
                      ...- +++.+...+..+.
T Consensus        95 ~l~~~t~~fia~rI~~Aa  112 (115)
T PF03709_consen   95 WLFEDTAEFIARRIEAAA  112 (115)
T ss_dssp             ETTTTTHHHHHHHHHHHH
T ss_pred             EecCCCHHHHHHHHHHHH
Confidence            7754 4455555555544

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.

>PRK09685 DNA-binding transcriptional activator FeaR; Provisional

Probab=96.37  E-value=0.0014  Score=54.75  Aligned_cols=42  Identities=19%  Similarity=0.032  Sum_probs=37.2

Q ss_pred             HHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCCCCCCCCCCC
Q 027234          180 KILELMNIPGLTRENVASHLQKHRLYLSRLSGVSPQQGNSFV  221 (226)
Q Consensus       180 ~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~~~~~~~~~~  221 (226)
                      .|.+++.+|+||.+.||.++++|++||+|+|+-.++.+..|+
T Consensus       205 ~I~~~l~~~~ls~~~lA~~~giS~r~L~r~Fk~~G~T~~~yi  246 (302)
T PRK09685        205 LIDQSIQEEILRPEWIAGELGISVRSLYRLFAEQGLVVAQYI  246 (302)
T ss_pred             HHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHHcCCCHHHHH
Confidence            699999999999999999999999999999997766665554

>cd02071 MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 binding domain

Probab=96.02  E-value=0.17  Score=36.48  Aligned_cols=89  Identities=12%  Similarity=-0.005  Sum_probs=63.7

Q ss_pred             CcEEEEE---CCHHHHHHHHHhCCCCceEEEEccCCCCCC--HHHHHHHHhcC-CCCcEEEEeccCCHHHHHHHHhCCcc
Q 027234            2 GFSVTKC---NRAEIALDMLRTNKNGYDIVISDVHMPDMD--GFKLLELVGLE-MDLPVIMMCAHGSKEVVMKGVTHDAC   75 (226)
Q Consensus         2 g~~V~~~---~~~~eal~~l~~~~~~~DlVl~D~~mp~~d--G~~l~~~l~~~-~~~pvI~ls~~~~~~~~~~a~~~ga~   75 (226)
                      ||+|...   ...++..+.+.+..  ||+|.+...++..-  --++++.+++. +....+++.+....+...+..++|++
T Consensus        27 G~~vi~lG~~vp~e~~~~~a~~~~--~d~V~iS~~~~~~~~~~~~~~~~L~~~~~~~i~i~~GG~~~~~~~~~~~~~G~d  104 (122)
T cd02071          27 GFEVIYTGLRQTPEEIVEAAIQED--VDVIGLSSLSGGHMTLFPEVIELLRELGAGDILVVGGGIIPPEDYELLKEMGVA  104 (122)
T ss_pred             CCEEEECCCCCCHHHHHHHHHHcC--CCEEEEcccchhhHHHHHHHHHHHHhcCCCCCEEEEECCCCHHHHHHHHHCCCC
Confidence            7887643   35778888888876  99999998876432  24456666643 43445566665666777888899999


Q ss_pred             eEEeCCCCHHHHHHHHH
Q 027234           76 DYLTKPVRIEELKNIWQ   92 (226)
Q Consensus        76 ~yl~KP~~~~~L~~~l~   92 (226)
                      +|+..--+.++....++
T Consensus       105 ~~~~~~~~~~~~~~~~~  121 (122)
T cd02071         105 EIFGPGTSIEEIIDKIR  121 (122)
T ss_pred             EEECCCCCHHHHHHHHh
Confidence            99999888888766543

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.

>TIGR03815 CpaE_hom_Actino helicase/secretion neighborhood CpaE-like protein

Probab=96.00  E-value=0.032  Score=47.15  Aligned_cols=84  Identities=12%  Similarity=0.020  Sum_probs=56.9

Q ss_pred             CcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHH-HHHhcCCCCcEEEE-eccCCHHHHHHHHhCCcceEEe
Q 027234            2 GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLL-ELVGLEMDLPVIMM-CAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         2 g~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~-~~l~~~~~~pvI~l-s~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      |.++..+.+..++-.....    -.+|++|..+     ...+ ...- -....++++ +...+.+....++..|+.+||.
T Consensus         1 ~~~~~~~~~~~~~~~~~~~----~~~v~~~~~~-----~~~~~~~~~-p~~~~vv~v~~~~~~~~~~~~a~~~Ga~~~l~   70 (322)
T TIGR03815         1 GVELDVAPDPEAARRAWAR----APLVLVDADM-----AEACAAAGL-PRRRRVVLVGGGEPGGALWRAAAAVGAEHVAV   70 (322)
T ss_pred             CCceEEccCchhhhhcccc----CCeEEECchh-----hhHHHhccC-CCCCCEEEEeCCCCCHHHHHHHHHhChhheee
Confidence            5677788877766444332    5788998543     1111 1111 122335544 4455788999999999999999


Q ss_pred             CCCCHHHHHHHHHHHH
Q 027234           80 KPVRIEELKNIWQHVV   95 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~   95 (226)
                      +|++..+|...+.++.
T Consensus        71 ~P~~~~~l~~~l~~~~   86 (322)
T TIGR03815        71 LPEAEGWLVELLADLD   86 (322)
T ss_pred             CCCCHHHHHHHHHhhc
Confidence            9999999999988763

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.

>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms

Probab=95.95  E-value=0.0037  Score=36.80  Aligned_cols=31  Identities=23%  Similarity=0.285  Sum_probs=24.0

Q ss_pred             HHHHhhCCCCCCHHHHHHHhhhhhhhhhcccC
Q 027234          180 KILELMNIPGLTRENVASHLQKHRLYLSRLSG  211 (226)
Q Consensus       180 ~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~  211 (226)
                      .|.+++.. |.++.+||..+++||+.+||+..
T Consensus        13 ~i~~l~~~-G~si~~IA~~~gvsr~TvyR~l~   43 (45)
T PF02796_consen   13 EIKELYAE-GMSIAEIAKQFGVSRSTVYRYLN   43 (45)
T ss_dssp             HHHHHHHT-T--HHHHHHHTTS-HHHHHHHHC
T ss_pred             HHHHHHHC-CCCHHHHHHHHCcCHHHHHHHHh
Confidence            47777777 79999999999999999999754

Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....

>TIGR00640 acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal domain

Probab=95.50  E-value=0.44  Score=34.89  Aligned_cols=92  Identities=9%  Similarity=-0.057  Sum_probs=63.3

Q ss_pred             CcEEEE---ECCHHHHHHHHHhCCCCceEEEEccCCCC-CCHH-HHHHHHhcC-CCCcEEEEeccCCHHHHHHHHhCCcc
Q 027234            2 GFSVTK---CNRAEIALDMLRTNKNGYDIVISDVHMPD-MDGF-KLLELVGLE-MDLPVIMMCAHGSKEVVMKGVTHDAC   75 (226)
Q Consensus         2 g~~V~~---~~~~~eal~~l~~~~~~~DlVl~D~~mp~-~dG~-~l~~~l~~~-~~~pvI~ls~~~~~~~~~~a~~~ga~   75 (226)
                      ||+|..   ..+.+++.+...+..  +|+|.+.-.+.. +..+ ++++.|++. .....|++-+....+......++|++
T Consensus        30 GfeVi~lg~~~s~e~~v~aa~e~~--adii~iSsl~~~~~~~~~~~~~~L~~~g~~~i~vivGG~~~~~~~~~l~~~Gvd  107 (132)
T TIGR00640        30 GFDVDVGPLFQTPEEIARQAVEAD--VHVVGVSSLAGGHLTLVPALRKELDKLGRPDILVVVGGVIPPQDFDELKEMGVA  107 (132)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHcC--CCEEEEcCchhhhHHHHHHHHHHHHhcCCCCCEEEEeCCCChHhHHHHHHCCCC
Confidence            788774   446888888888866  999988776643 3332 344566543 32233445544455667778999999


Q ss_pred             eEEeCCCCHHHHHHHHHHHH
Q 027234           76 DYLTKPVRIEELKNIWQHVV   95 (226)
Q Consensus        76 ~yl~KP~~~~~L~~~l~~~~   95 (226)
                      +|+..--+..++...+.+.+
T Consensus       108 ~~~~~gt~~~~i~~~l~~~~  127 (132)
T TIGR00640       108 EIFGPGTPIPESAIFLLKKL  127 (132)
T ss_pred             EEECCCCCHHHHHHHHHHHH
Confidence            99999888888888777644

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.

>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=95.49  E-value=0.39  Score=38.84  Aligned_cols=89  Identities=20%  Similarity=0.251  Sum_probs=64.2

Q ss_pred             CcEEE-EE-CCHHHHHHHHHhCCCCceEEEEccCCC---------CCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHH
Q 027234            2 GFSVT-KC-NRAEIALDMLRTNKNGYDIVISDVHMP---------DMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGV   70 (226)
Q Consensus         2 g~~V~-~~-~~~~eal~~l~~~~~~~DlVl~D~~mp---------~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~   70 (226)
                      ||.|. .| +|...|-.+.. ..  +++|     ||         +..-.++++.+++..++|||+=.+-...+.+.+++
T Consensus       123 Gf~vlpyc~dd~~~ar~l~~-~G--~~~v-----mPlg~pIGsg~Gi~~~~~I~~I~e~~~vpVI~egGI~tpeda~~Am  194 (248)
T cd04728         123 GFTVLPYCTDDPVLAKRLED-AG--CAAV-----MPLGSPIGSGQGLLNPYNLRIIIERADVPVIVDAGIGTPSDAAQAM  194 (248)
T ss_pred             CCEEEEEeCCCHHHHHHHHH-cC--CCEe-----CCCCcCCCCCCCCCCHHHHHHHHHhCCCcEEEeCCCCCHHHHHHHH
Confidence            78877 44 45666655544 33  8887     66         22126778888766789999888888999999999


Q ss_pred             hCCcceEE-----eCCCCHHHHHHHHHHHHHHH
Q 027234           71 THDACDYL-----TKPVRIEELKNIWQHVVRKR   98 (226)
Q Consensus        71 ~~ga~~yl-----~KP~~~~~L~~~l~~~~~~~   98 (226)
                      ++|+++.+     .|.-++..+.......+..-
T Consensus       195 elGAdgVlV~SAIt~a~dP~~ma~af~~Av~aG  227 (248)
T cd04728         195 ELGADAVLLNTAIAKAKDPVAMARAFKLAVEAG  227 (248)
T ss_pred             HcCCCEEEEChHhcCCCCHHHHHHHHHHHHHHH
Confidence            99999988     46566777777776665443

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).

>PRK02261 methylaspartate mutase subunit S; Provisional

Probab=95.33  E-value=0.4  Score=35.36  Aligned_cols=92  Identities=16%  Similarity=0.037  Sum_probs=65.9

Q ss_pred             CcEEEE---ECCHHHHHHHHHhCCCCceEEEEccCCCCC--CHHHHHHHHhcC-C-CCcEEEEeccC------CHHHHHH
Q 027234            2 GFSVTK---CNRAEIALDMLRTNKNGYDIVISDVHMPDM--DGFKLLELVGLE-M-DLPVIMMCAHG------SKEVVMK   68 (226)
Q Consensus         2 g~~V~~---~~~~~eal~~l~~~~~~~DlVl~D~~mp~~--dG~~l~~~l~~~-~-~~pvI~ls~~~------~~~~~~~   68 (226)
                      ||+|+.   .-..++..+.+.+..  ||+|.+...|+..  .--++++.++.. + ++++ ++.+..      ..+...+
T Consensus        31 G~eVi~LG~~vp~e~i~~~a~~~~--~d~V~lS~~~~~~~~~~~~~~~~L~~~~~~~~~i-~vGG~~~~~~~~~~~~~~~  107 (137)
T PRK02261         31 GFEVINLGVMTSQEEFIDAAIETD--ADAILVSSLYGHGEIDCRGLREKCIEAGLGDILL-YVGGNLVVGKHDFEEVEKK  107 (137)
T ss_pred             CCEEEECCCCCCHHHHHHHHHHcC--CCEEEEcCccccCHHHHHHHHHHHHhcCCCCCeE-EEECCCCCCccChHHHHHH
Confidence            788774   346788888888876  9999999988753  234556677633 3 4444 444432      3455677


Q ss_pred             HHhCCcceEEeCCCCHHHHHHHHHHHHH
Q 027234           69 GVTHDACDYLTKPVRIEELKNIWQHVVR   96 (226)
Q Consensus        69 a~~~ga~~yl~KP~~~~~L~~~l~~~~~   96 (226)
                      +.++|++..+...-+.+++...+++.+.
T Consensus       108 l~~~G~~~vf~~~~~~~~i~~~l~~~~~  135 (137)
T PRK02261        108 FKEMGFDRVFPPGTDPEEAIDDLKKDLN  135 (137)
T ss_pred             HHHcCCCEEECcCCCHHHHHHHHHHHhc
Confidence            8899999999999999999888877653

>PRK00208 thiG thiazole synthase; Reviewed

Probab=95.33  E-value=0.46  Score=38.49  Aligned_cols=88  Identities=19%  Similarity=0.231  Sum_probs=63.8

Q ss_pred             CcEEE-EE-CCHHHHHHHHHhCCCCceEEEEccCCC---------CCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHH
Q 027234            2 GFSVT-KC-NRAEIALDMLRTNKNGYDIVISDVHMP---------DMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGV   70 (226)
Q Consensus         2 g~~V~-~~-~~~~eal~~l~~~~~~~DlVl~D~~mp---------~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~   70 (226)
                      ||.|. .| +|...|-.+.. ..  +|+|     ||         +..-.++++.+++..++|||+=.+-...+.+.+++
T Consensus       123 Gf~vlpyc~~d~~~ak~l~~-~G--~~~v-----mPlg~pIGsg~gi~~~~~i~~i~e~~~vpVIveaGI~tpeda~~Am  194 (250)
T PRK00208        123 GFVVLPYCTDDPVLAKRLEE-AG--CAAV-----MPLGAPIGSGLGLLNPYNLRIIIEQADVPVIVDAGIGTPSDAAQAM  194 (250)
T ss_pred             CCEEEEEeCCCHHHHHHHHH-cC--CCEe-----CCCCcCCCCCCCCCCHHHHHHHHHhcCCeEEEeCCCCCHHHHHHHH
Confidence            78877 44 45666655544 33  8887     76         12125677888765789999988889999999999


Q ss_pred             hCCcceEE-----eCCCCHHHHHHHHHHHHHH
Q 027234           71 THDACDYL-----TKPVRIEELKNIWQHVVRK   97 (226)
Q Consensus        71 ~~ga~~yl-----~KP~~~~~L~~~l~~~~~~   97 (226)
                      ++|+++.+     .|.-++..+.......+..
T Consensus       195 elGAdgVlV~SAItka~dP~~ma~af~~Av~a  226 (250)
T PRK00208        195 ELGADAVLLNTAIAVAGDPVAMARAFKLAVEA  226 (250)
T ss_pred             HcCCCEEEEChHhhCCCCHHHHHHHHHHHHHH
Confidence            99999988     4656677777777666543

>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional

Probab=95.20  E-value=0.02  Score=40.14  Aligned_cols=50  Identities=22%  Similarity=0.270  Sum_probs=37.8

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC-CCCCCCCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV-SPQQGNSF  220 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~-~~~~~~~~  220 (226)
                      +...+..+..         .|.+++.. .++++++|.++++|+++|.|+|+- .++.+..|
T Consensus         3 ~~~~~~~~~~---------~i~~~~~~-~~~~~~lA~~~~~S~~~l~r~f~~~~g~s~~~~   53 (107)
T PRK10219          3 HQKIIQTLIA---------WIDEHIDQ-PLNIDVVAKKSGYSKWYLQRMFRTVTHQTLGDY   53 (107)
T ss_pred             hHHHHHHHHH---------HHHHhcCC-CCCHHHHHHHHCCCHHHHHHHHHHHHCcCHHHH
Confidence            4455666666         58888877 699999999999999999997765 35554443

>PRK11511 DNA-binding transcriptional activator MarA; Provisional

Probab=94.71  E-value=0.012  Score=42.80  Aligned_cols=41  Identities=15%  Similarity=0.129  Sum_probs=33.9

Q ss_pred             HHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCCC-CCCCCCCC
Q 027234          180 KILELMNIPGLTRENVASHLQKHRLYLSRLSGVS-PQQGNSFV  221 (226)
Q Consensus       180 ~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~~-~~~~~~~~  221 (226)
                      .|.+++.. .++++++|+++++|+.+|.|+|+-. ++++..|+
T Consensus        17 ~I~~~~~~-~~sl~~lA~~~g~S~~~l~r~Fk~~~G~s~~~~l   58 (127)
T PRK11511         17 WIEDNLES-PLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYI   58 (127)
T ss_pred             HHHHhcCC-CCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHHHH
Confidence            58888887 6999999999999999999988754 66665553

>PRK09978 DNA-binding transcriptional regulator GadX; Provisional

Probab=94.70  E-value=0.015  Score=48.02  Aligned_cols=41  Identities=15%  Similarity=0.024  Sum_probs=34.6

Q ss_pred             HHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCCCCCCCCCCC
Q 027234          180 KILELMNIPGLTRENVASHLQKHRLYLSRLSGVSPQQGNSFV  221 (226)
Q Consensus       180 ~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~~~~~~~~~~  221 (226)
                      .|.+++.. .++++++|+++++|+++|+|+|+..++++..|+
T Consensus       150 yI~~~~~~-~lsl~~lA~~~g~S~~~L~R~Fk~~G~S~~~yl  190 (274)
T PRK09978        150 VINNNIAH-EWTLARIASELLMSPSLLKKKLREEETSYSQLL  190 (274)
T ss_pred             HHHhcccC-CCCHHHHHHHHCcCHHHHHHHHHhcCCCHHHHH
Confidence            58888887 799999999999999999999987666555543

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

Probab=94.45  E-value=0.28  Score=34.91  Aligned_cols=78  Identities=9%  Similarity=-0.079  Sum_probs=52.4

Q ss_pred             CcEEEE---ECCHHHHHHHHHhCCCCceEEEEccCCCC--CCHHHHHHHHhcCCC-CcEEEEeccCCHHHHHHHHhCCcc
Q 027234            2 GFSVTK---CNRAEIALDMLRTNKNGYDIVISDVHMPD--MDGFKLLELVGLEMD-LPVIMMCAHGSKEVVMKGVTHDAC   75 (226)
Q Consensus         2 g~~V~~---~~~~~eal~~l~~~~~~~DlVl~D~~mp~--~dG~~l~~~l~~~~~-~pvI~ls~~~~~~~~~~a~~~ga~   75 (226)
                      ||+|..   ..+.++..+.+.+..  ||+|.+...+..  .+..++++.+++... -+.|++.+.........+...|++
T Consensus        27 G~~V~~lg~~~~~~~l~~~~~~~~--pdvV~iS~~~~~~~~~~~~~i~~l~~~~~~~~~i~vGG~~~~~~~~~~~~~G~D  104 (119)
T cd02067          27 GFEVIDLGVDVPPEEIVEAAKEED--ADAIGLSGLLTTHMTLMKEVIEELKEAGLDDIPVLVGGAIVTRDFKFLKEIGVD  104 (119)
T ss_pred             CCEEEECCCCCCHHHHHHHHHHcC--CCEEEEeccccccHHHHHHHHHHHHHcCCCCCeEEEECCCCChhHHHHHHcCCe
Confidence            778754   335678888888876  999999887654  244666777774432 334556655554444578889998


Q ss_pred             eEEeCC
Q 027234           76 DYLTKP   81 (226)
Q Consensus        76 ~yl~KP   81 (226)
                      +|+...
T Consensus       105 ~~~~~~  110 (119)
T cd02067         105 AYFGPA  110 (119)
T ss_pred             EEECCH
Confidence            887643

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.

>PRK10130 transcriptional regulator EutR; Provisional

Probab=94.34  E-value=0.018  Score=49.36  Aligned_cols=50  Identities=22%  Similarity=0.280  Sum_probs=40.8

Q ss_pred             HHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC-CCCCCCCCC
Q 027234          162 QQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV-SPQQGNSFV  221 (226)
Q Consensus       162 ~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~-~~~~~~~~~  221 (226)
                      ..++..+..         .|.+++..+ +|+++||.++++|+++|.|.|+- .++.+..|+
T Consensus       239 ~~~v~~~~~---------~i~~~~~~~-ltv~~lA~~~gvS~r~L~r~Fk~~~G~sp~~yl  289 (350)
T PRK10130        239 RRLLSRARE---------YVLENMSEP-VTVLDLCNQLHVSRRTLQNAFHAILGIGPNAWL  289 (350)
T ss_pred             HHHHHHHHH---------HHHhhhcCC-CCHHHHHHHHCCCHHHHHHHHHHHHCcCHHHHH
Confidence            566777777         688999884 99999999999999999998854 677666553

>TIGR01501 MthylAspMutase methylaspartate mutase, S subunit

Probab=93.95  E-value=1.6  Score=32.03  Aligned_cols=92  Identities=10%  Similarity=-0.049  Sum_probs=62.8

Q ss_pred             CcEEE---EECCHHHHHHHHHhCCCCceEEEEccCCCC-CCH-HHHHHHHhcC-CCCcEEEEeccC-----CHH-HHHHH
Q 027234            2 GFSVT---KCNRAEIALDMLRTNKNGYDIVISDVHMPD-MDG-FKLLELVGLE-MDLPVIMMCAHG-----SKE-VVMKG   69 (226)
Q Consensus         2 g~~V~---~~~~~~eal~~l~~~~~~~DlVl~D~~mp~-~dG-~~l~~~l~~~-~~~pvI~ls~~~-----~~~-~~~~a   69 (226)
                      ||+|.   ..-+.++.++.+.+..  +|+|-+...|.. +.. -++.+.+++. ..-+++++-+..     +.. ...++
T Consensus        29 GfeVi~LG~~v~~e~~v~aa~~~~--adiVglS~l~~~~~~~~~~~~~~l~~~gl~~~~vivGG~~vi~~~d~~~~~~~l  106 (134)
T TIGR01501        29 GFNVVNLGVLSPQEEFIKAAIETK--ADAILVSSLYGHGEIDCKGLRQKCDEAGLEGILLYVGGNLVVGKQDFPDVEKRF  106 (134)
T ss_pred             CCEEEECCCCCCHHHHHHHHHHcC--CCEEEEecccccCHHHHHHHHHHHHHCCCCCCEEEecCCcCcChhhhHHHHHHH
Confidence            78876   3557889999988866  999999888754 222 3344566532 323445555531     111 24467


Q ss_pred             HhCCcceEEeCCCCHHHHHHHHHHHH
Q 027234           70 VTHDACDYLTKPVRIEELKNIWQHVV   95 (226)
Q Consensus        70 ~~~ga~~yl~KP~~~~~L~~~l~~~~   95 (226)
                      .++|++..+...-.++++...+++.+
T Consensus       107 ~~~Gv~~vF~pgt~~~~iv~~l~~~~  132 (134)
T TIGR01501       107 KEMGFDRVFAPGTPPEVVIADLKKDL  132 (134)
T ss_pred             HHcCCCEEECcCCCHHHHHHHHHHHh
Confidence            88999999998889999988887765

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.

>smart00448 REC cheY-homologous receiver domain

Probab=93.49  E-value=0.22  Score=27.76  Aligned_cols=32  Identities=34%  Similarity=0.706  Sum_probs=25.4

Q ss_pred             CcEEEEECCHHHHHHHHHhCCCCceEEEEccCCC
Q 027234            2 GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMP   35 (226)
Q Consensus         2 g~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp   35 (226)
                      |+.+..+.+..+++..+....  +|++++|..++
T Consensus        24 ~~~~~~~~~~~~~~~~~~~~~--~~~vi~~~~~~   55 (55)
T smart00448       24 GYEVDEATDGEEALELLKEEK--PDLILLDIMMP   55 (55)
T ss_pred             CcEEEEeCCHHHHHHHHHhcC--CCEEEEeccCC
Confidence            677788888888888887655  89999987654

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

>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA

Probab=93.26  E-value=0.033  Score=46.04  Aligned_cols=40  Identities=18%  Similarity=0.046  Sum_probs=34.3

Q ss_pred             HHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC-CCCCCCCC
Q 027234          180 KILELMNIPGLTRENVASHLQKHRLYLSRLSGV-SPQQGNSF  220 (226)
Q Consensus       180 ~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~-~~~~~~~~  220 (226)
                      .|.+++.. .+|++++|+++++|++||.|+|+. +++.+..|
T Consensus       194 ~I~~~~~~-~~sl~~lA~~~~~S~~~l~r~Fk~~~G~t~~~y  234 (287)
T TIGR02297       194 LIEENYKQ-HLRLPEYADRLGISESRLNDICRRFSALSPKRL  234 (287)
T ss_pred             HHHHhhcc-CCCHHHHHHHHCCCHHHHHHHHHHHhCCCHHHH
Confidence            47788887 799999999999999999998887 77666555

This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway.

>PRK10371 DNA-binding transcriptional regulator MelR; Provisional

Probab=92.99  E-value=0.044  Score=45.96  Aligned_cols=41  Identities=20%  Similarity=0.184  Sum_probs=34.2

Q ss_pred             HHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC-CCCCCCCCC
Q 027234          180 KILELMNIPGLTRENVASHLQKHRLYLSRLSGV-SPQQGNSFV  221 (226)
Q Consensus       180 ~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~-~~~~~~~~~  221 (226)
                      .|.+++.. .+|++++|+++++|+++|+|+|+- .++.+..|+
T Consensus       199 ~i~~~~~~-~~tl~~lA~~~~~S~~~l~r~Fk~~~G~t~~~~l  240 (302)
T PRK10371        199 FIAENYDQ-ALTINDVAEHVKLNANYAMGIFQRVMQLTMKQYI  240 (302)
T ss_pred             HHHHhhcC-CCCHHHHHHHHCcCHHHHHHHHHHHhCCCHHHHH
Confidence            58888874 899999999999999999999987 466655543

>PRK00043 thiE thiamine-phosphate pyrophosphorylase; Reviewed

Probab=92.64  E-value=2.4  Score=33.16  Aligned_cols=69  Identities=19%  Similarity=0.188  Sum_probs=49.7

Q ss_pred             EECCHHHHHHHHHhCCCCceEEEEccCCCCC--------CHHHHHHHHhcCC-CCcEEEEeccCCHHHHHHHHhCCcceE
Q 027234            7 KCNRAEIALDMLRTNKNGYDIVISDVHMPDM--------DGFKLLELVGLEM-DLPVIMMCAHGSKEVVMKGVTHDACDY   77 (226)
Q Consensus         7 ~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~--------dG~~l~~~l~~~~-~~pvI~ls~~~~~~~~~~a~~~ga~~y   77 (226)
                      .+.+..++.+...   .++|.|.+.-..|..        .|++.++.++... ++||++..+- +.+.+..++..|++++
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            3456677766654   338999887555543        3588888886444 4898877665 6788889999999998


Q ss_pred             Ee
Q 027234           78 LT   79 (226)
Q Consensus        78 l~   79 (226)
                      ..
T Consensus       186 ~~  187 (212)
T PRK00043        186 AV  187 (212)
T ss_pred             EE
Confidence            84

>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor

Probab=92.52  E-value=0.17  Score=29.78  Aligned_cols=32  Identities=6%  Similarity=0.017  Sum_probs=26.8

Q ss_pred             HHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          181 ILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       181 I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      ++....-.++|++.||+.+++++..+|+-|..
T Consensus         8 l~~~~G~~~~s~~~Ia~~~gvs~~~~y~~f~~   39 (47)
T PF00440_consen    8 LFAEKGYEAVSIRDIARRAGVSKGSFYRYFPS   39 (47)
T ss_dssp             HHHHHHTTTSSHHHHHHHHTSCHHHHHHHCSS
T ss_pred             HHHHhCHHhCCHHHHHHHHccchhhHHHHcCC
Confidence            44455567899999999999999999998864

Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....

>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=92.38  E-value=1.2  Score=31.34  Aligned_cols=85  Identities=13%  Similarity=0.199  Sum_probs=54.2

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHH-hcCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV-GLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l-~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      +|+++..+++.+- ........  .+.+++-..-.. ...++++.+ +..+.+|++++.........     ..+.+-|.
T Consensus        22 lGe~~~~~~~~~~-~~~~~~~~--~~~~~v~~g~~~-~~~~~l~~l~~~~~~~Pvlllg~~~~~~~~-----~nvvg~Le   92 (109)
T PF06490_consen   22 LGEQCEAVSSSDW-SQADWSSP--WEACAVILGSCS-KLAELLKELLKWAPHIPVLLLGEHDSPEEL-----PNVVGELE   92 (109)
T ss_pred             cCCCeEEecHHHH-HHhhhhcC--CcEEEEEecCch-hHHHHHHHHHhhCCCCCEEEECCCCccccc-----cCeeEecC
Confidence            5777777765433 23333332  444444332222 445666666 47789999999887766111     12778899


Q ss_pred             CCCCHHHHHHHHHHH
Q 027234           80 KPVRIEELKNIWQHV   94 (226)
Q Consensus        80 KP~~~~~L~~~l~~~   94 (226)
                      -|++..+|...+++.
T Consensus        93 ~Pl~Y~qLt~~L~~c  107 (109)
T PF06490_consen   93 EPLNYPQLTDALHRC  107 (109)
T ss_pred             CCCCHHHHHHHHHHh
Confidence            999999999998874

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).

>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]

Probab=92.37  E-value=0.11  Score=29.90  Aligned_cols=30  Identities=23%  Similarity=0.074  Sum_probs=23.4

Q ss_pred             HHHHhhCCCCCCHHHHHHHhhhhhhhhhcc
Q 027234          180 KILELMNIPGLTRENVASHLQKHRLYLSRL  209 (226)
Q Consensus       180 ~I~~~~~~~~lt~~~va~~l~~~r~~l~r~  209 (226)
                      .|.+.+...+-++...|..||++|+.|||.
T Consensus         9 ~i~~aL~~~~gn~~~aA~~Lgisr~tL~~k   38 (42)
T PF02954_consen    9 LIRQALERCGGNVSKAARLLGISRRTLYRK   38 (42)
T ss_dssp             HHHHHHHHTTT-HHHHHHHHTS-HHHHHHH
T ss_pred             HHHHHHHHhCCCHHHHHHHHCCCHHHHHHH
Confidence            466666677889999999999999999974

It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....

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

Probab=92.33  E-value=2.6  Score=34.37  Aligned_cols=83  Identities=12%  Similarity=0.041  Sum_probs=60.7

Q ss_pred             CHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhc--CCCCcEEEEeccCCHHHHHHHHhCCcceEE-eCCCCHHH
Q 027234           10 RAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGL--EMDLPVIMMCAHGSKEVVMKGVTHDACDYL-TKPVRIEE   86 (226)
Q Consensus        10 ~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~--~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl-~KP~~~~~   86 (226)
                      ......+.+....  +|.|++|++-...|--++...++.  .....+++=....+...+.+++..|+++.+ +|--+.++
T Consensus        21 ~~p~~~e~~~~~g--~D~v~iDlEH~~~~~~~~~~~~~a~~~~g~~~~VRv~~~~~~~i~~~Ld~Ga~gIivP~v~s~e~   98 (249)
T TIGR02311        21 ADPYAAEICAGAG--FDWLLIDGEHAPNDVRTILSQLQALAPYPSSPVVRPAIGDPVLIKQLLDIGAQTLLVPMIETAEQ   98 (249)
T ss_pred             CCcHHHHHHHhcC--CCEEEEeccCCCCCHHHHHHHHHHHHhcCCCcEEECCCCCHHHHHHHhCCCCCEEEecCcCCHHH
Confidence            3345667777654  999999999888887777776652  334455555555667789999999999987 66778888


Q ss_pred             HHHHHHHH
Q 027234           87 LKNIWQHV   94 (226)
Q Consensus        87 L~~~l~~~   94 (226)
                      ++.+++..
T Consensus        99 a~~~v~~~  106 (249)
T TIGR02311        99 AEAAVAAT  106 (249)
T ss_pred             HHHHHHHc
Confidence            77777664

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.

>TIGR00343 pyridoxal 5'-phosphate synthase, synthase subunit Pdx1

Probab=91.57  E-value=3.5  Score=34.20  Aligned_cols=89  Identities=15%  Similarity=-0.010  Sum_probs=63.5

Q ss_pred             EECCHHHHHHHHHhCCCCceEEEEccC-------------------------CC-----------CCCHHHHHHHHhcCC
Q 027234            7 KCNRAEIALDMLRTNKNGYDIVISDVH-------------------------MP-----------DMDGFKLLELVGLEM   50 (226)
Q Consensus         7 ~~~~~~eal~~l~~~~~~~DlVl~D~~-------------------------mp-----------~~dG~~l~~~l~~~~   50 (226)
                      -|++..||+..+...   +|+|=+-..                         |.           ...|+++++.+++..
T Consensus       120 d~~~l~EAlrai~~G---admI~Tt~e~gTg~v~~av~hlr~~~~~~~~~~~~~~~~~~~~~a~~~~~~~elLkei~~~~  196 (287)
T TIGR00343       120 GARDLGEALRRINEG---AAMIRTKGEAGTGNIVEAVRHMRKINEEIRQIQNMLEEEDLAAVAKELRVPVELLLEVLKLG  196 (287)
T ss_pred             cCCCHHHHHHHHHCC---CCEEeccccCCCccHHHHHHHHHHHHHHHHHHhcccchhHHhhhhcccCCCHHHHHHHHHhC
Confidence            467888888887743   677765521                         10           125888998887666


Q ss_pred             CCcEE--EEeccCCHHHHHHHHhCCcceEE-----eCCCCHHHHHHHHHHHHHHH
Q 027234           51 DLPVI--MMCAHGSKEVVMKGVTHDACDYL-----TKPVRIEELKNIWQHVVRKR   98 (226)
Q Consensus        51 ~~pvI--~ls~~~~~~~~~~a~~~ga~~yl-----~KP~~~~~L~~~l~~~~~~~   98 (226)
                      .+|||  ...+-..++.+..++++||++++     .|.-++......+...+...
T Consensus       197 ~iPVV~fAiGGI~TPedAa~~melGAdGVaVGSaI~ks~dP~~~akafv~ai~~~  251 (287)
T TIGR00343       197 KLPVVNFAAGGVATPADAALMMQLGADGVFVGSGIFKSSNPEKLAKAIVEATTHY  251 (287)
T ss_pred             CCCEEEeccCCCCCHHHHHHHHHcCCCEEEEhHHhhcCCCHHHHHHHHHHHHHHc
Confidence            79998  56666689999999999999987     44556777766666665543

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.

>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=91.29  E-value=4.1  Score=33.71  Aligned_cols=88  Identities=13%  Similarity=0.051  Sum_probs=63.3

Q ss_pred             EECCHHHHHHHHHhCCCCceEEEEccC---------------------------------C--CCCCHHHHHHHHhcCCC
Q 027234            7 KCNRAEIALDMLRTNKNGYDIVISDVH---------------------------------M--PDMDGFKLLELVGLEMD   51 (226)
Q Consensus         7 ~~~~~~eal~~l~~~~~~~DlVl~D~~---------------------------------m--p~~dG~~l~~~l~~~~~   51 (226)
                      -|++.+||+...+.   ++|+|=+-+.                                 .  ....|+++++.+.+...
T Consensus       118 D~stleEal~a~~~---Gad~I~TTl~gyT~~~~~~~~~~~~i~~~i~~~~gyt~~t~~~~~~~~~~d~elLk~l~~~~~  194 (283)
T cd04727         118 GARNLGEALRRISE---GAAMIRTKGEAGTGNVVEAVRHMRAVNGEIRKLQSMSEEELYAVAKEIQAPYELVKETAKLGR  194 (283)
T ss_pred             cCCCHHHHHHHHHC---CCCEEEecCCCCCCcHHHHHHHHHHHHHHHHHHhCCCHHHHHhhhcccCCCHHHHHHHHHhcC
Confidence            47788999988874   3788877651                                 1  12347888988876667


Q ss_pred             CcEE--EEeccCCHHHHHHHHhCCcceEEe-----CCCCHHHHHHHHHHHHHH
Q 027234           52 LPVI--MMCAHGSKEVVMKGVTHDACDYLT-----KPVRIEELKNIWQHVVRK   97 (226)
Q Consensus        52 ~pvI--~ls~~~~~~~~~~a~~~ga~~yl~-----KP~~~~~L~~~l~~~~~~   97 (226)
                      +|||  ...+-..++.+..+++.||++++.     +.-++......+...+..
T Consensus       195 iPVV~iAeGGI~Tpena~~v~e~GAdgVaVGSAI~~a~dP~~~tk~f~~ai~~  247 (283)
T cd04727         195 LPVVNFAAGGVATPADAALMMQLGADGVFVGSGIFKSENPEKRARAIVEAVTH  247 (283)
T ss_pred             CCeEEEEeCCCCCHHHHHHHHHcCCCEEEEcHHhhcCCCHHHHHHHHHHHHHh
Confidence            9997  566666899999999999999874     334566666666555544

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.

>PRK13503 transcriptional activator RhaS; Provisional

Probab=90.88  E-value=0.18  Score=41.42  Aligned_cols=40  Identities=10%  Similarity=0.028  Sum_probs=32.0

Q ss_pred             HHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC-CCCCCCCC
Q 027234          180 KILELMNIPGLTRENVASHLQKHRLYLSRLSGV-SPQQGNSF  220 (226)
Q Consensus       180 ~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~-~~~~~~~~  220 (226)
                      .|.+++.. .+|++++|+++++|++||.|+||. +++++..|
T Consensus       179 ~I~~~~~~-~~tl~~lA~~~~lS~~~l~r~Fk~~~G~S~~~y  219 (278)
T PRK13503        179 WLEDHFAE-EVNWEALADQFSLSLRTLHRQLKQQTGLTPQRY  219 (278)
T ss_pred             HHHHhhcC-CCCHHHHHHHHCCCHHHHHHHHHHHhCcCHHHH
Confidence            57788877 899999999999999999998853 35554443

>PRK15044 transcriptional regulator SirC; Provisional

Probab=90.87  E-value=0.1  Score=43.33  Aligned_cols=36  Identities=17%  Similarity=0.077  Sum_probs=31.0

Q ss_pred             HHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCCCCCC
Q 027234          180 KILELMNIPGLTRENVASHLQKHRLYLSRLSGVSPQQ  216 (226)
Q Consensus       180 ~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~~~~~  216 (226)
                      .|.+++.. .++++++|+++++|+++|+|.|+..++.
T Consensus       200 ~I~~nl~~-~~SLeeLA~~lgmS~~tL~R~Fk~eg~T  235 (295)
T PRK15044        200 IIISDLTR-KWSQAEVAGKLFMSVSSLKRKLAAEEVS  235 (295)
T ss_pred             HHHhCccc-CCCHHHHHHHhCCCHHHHHHHHHHcCCC
Confidence            67788877 6999999999999999999999865443

>PRK09940 transcriptional regulator YdeO; Provisional

Probab=90.70  E-value=0.076  Score=43.37  Aligned_cols=40  Identities=5%  Similarity=-0.071  Sum_probs=32.1

Q ss_pred             HHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCCCCCCCCCC
Q 027234          180 KILELMNIPGLTRENVASHLQKHRLYLSRLSGVSPQQGNSF  220 (226)
Q Consensus       180 ~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~~~~~~~~~  220 (226)
                      .|.+++.. .+|++++|+++++|+++|.|+|+..++.+..|
T Consensus       142 ~I~~~~~~-~~tl~~LA~~~gmS~s~l~R~FK~~G~T~~ey  181 (253)
T PRK09940        142 IVNMKLAH-PWKLKDICDCLYISESLLKKKLKQEQTTFSQI  181 (253)
T ss_pred             HHHHhhcC-CCCHHHHHHHHCcCHHHHHHHHHHcCCCHHHH
Confidence            46666766 69999999999999999999998765554444

>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein

Probab=90.65  E-value=0.11  Score=33.97  Aligned_cols=40  Identities=15%  Similarity=0.152  Sum_probs=29.3

Q ss_pred             HHHhhCCCCCCHHHHHHHhhh-hhhhhhccc-CCCCCCCCCC
Q 027234          181 ILELMNIPGLTRENVASHLQK-HRLYLSRLS-GVSPQQGNSF  220 (226)
Q Consensus       181 I~~~~~~~~lt~~~va~~l~~-~r~~l~r~~-~~~~~~~~~~  220 (226)
                      +.+.+...++++++||..+|. +.++|+|.| +..++.|..|
T Consensus        42 a~~~l~~~~~~~~~ia~~~g~~s~~~f~r~Fk~~~g~sp~~~   83 (84)
T smart00342       42 ARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGVTPSEY   83 (84)
T ss_pred             HHHHHHcCCCCHHHHHHHhCCCChHHHHHHHHHHHCcChhhc
Confidence            344444448999999999999 999999977 4455555443

>PRK15320 transcriptional activator SprB; Provisional

Probab=90.62  E-value=0.77  Score=35.95  Aligned_cols=76  Identities=16%  Similarity=0.046  Sum_probs=48.3

Q ss_pred             CcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEeC
Q 027234            2 GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTK   80 (226)
Q Consensus         2 g~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~K   80 (226)
                      |..|.+|.+....+..++..   ||.+++=.--|..--+-+-.....-++-||++++..--.....-..-.|+.+|+.|
T Consensus        27 ~~~~~t~~~l~~ll~~l~~~---p~a~lil~l~p~eh~~lf~~l~~~l~~~~v~vv~d~l~~~dr~vl~~~g~~~~~l~  102 (251)
T PRK15320         27 EKCVKTCNSLTALLHSLSDM---PDAGLILALNPHEHVYLFHALLTRLQNRKVLVVADRLYYIDRCVLQYFGVMDYVLK  102 (251)
T ss_pred             ccchhhhhhHHHHHHHHhhC---CCceEEEeeCchhHHHHHHHHHHHcCCCceEEEecceeehhhhhhhhhcchhHHHH
Confidence            34567777777777777753   77766644445544333322223456789999998766655555555788888766

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

Probab=90.57  E-value=5.2  Score=32.76  Aligned_cols=80  Identities=11%  Similarity=0.096  Sum_probs=58.7

Q ss_pred             HHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh--cCCCCcEEEEeccCCHHHHHHHHhCCcceEEeCCC-CHHHHH
Q 027234           12 EIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG--LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTKPV-RIEELK   88 (226)
Q Consensus        12 ~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~--~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~KP~-~~~~L~   88 (226)
                      ..+.+.+....  +|.|++|++-..+|--++...++  +...++.++=....+...+.++++.|+.+.+..=+ +.++.+
T Consensus        30 p~~~e~~a~~G--~D~v~iD~EHg~~~~~~~~~~i~a~~~~g~~~lVRvp~~~~~~i~r~LD~Ga~giivP~v~tae~a~  107 (256)
T PRK10558         30 PITTEVLGLAG--FDWLVLDGEHAPNDVSTFIPQLMALKGSASAPVVRVPTNEPVIIKRLLDIGFYNFLIPFVETAEEAR  107 (256)
T ss_pred             cHHHHHHHhcC--CCEEEEccccCCCCHHHHHHHHHHHhhcCCCcEEECCCCCHHHHHHHhCCCCCeeeecCcCCHHHHH
Confidence            45667777654  99999999998888877777665  33455666666667889999999999999986544 456665


Q ss_pred             HHHHH
Q 027234           89 NIWQH   93 (226)
Q Consensus        89 ~~l~~   93 (226)
                      .+++.
T Consensus       108 ~~v~a  112 (256)
T PRK10558        108 RAVAS  112 (256)
T ss_pred             HHHHH
Confidence            55544

>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins

Probab=90.56  E-value=0.83  Score=26.87  Aligned_cols=47  Identities=32%  Similarity=0.352  Sum_probs=34.4

Q ss_pred             eeeeHhhHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhh
Q 027234          154 LVWSVELHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHR  203 (226)
Q Consensus       154 ~~~~~~l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r  203 (226)
                      ..||.+.+..|+.++.++|..  .-+.|-+.|. .+-|..++-+|.++++
T Consensus         2 ~~Wt~eE~~~l~~~v~~~g~~--~W~~Ia~~~~-~~Rt~~qc~~~~~~~~   48 (48)
T PF00249_consen    2 GPWTEEEDEKLLEAVKKYGKD--NWKKIAKRMP-GGRTAKQCRSRYQNLL   48 (48)
T ss_dssp             -SS-HHHHHHHHHHHHHSTTT--HHHHHHHHHS-SSSTHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHHHhCCc--HHHHHHHHcC-CCCCHHHHHHHHHhhC
Confidence            459999999999999998854  3556777766 3777788877776653

These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....

>COG4943 Predicted signal transduction protein containing sensor and EAL domains [Signal transduction mechanisms]

Probab=90.45  E-value=0.16  Score=44.77  Aligned_cols=56  Identities=13%  Similarity=-0.051  Sum_probs=47.3

Q ss_pred             cccccCCCCCCccchHHHHHHhccCCceeeeHhhHHHHHHHHHHhCCCCCCchHHHHh
Q 027234          127 SYSVNEGTSNSRKDEEEEAEKRLKKPRLVWSVELHQQFVSAVKELGFDKAGPKKILEL  184 (226)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~Fi~~~~~~g~~~~~p~~I~~~  184 (226)
                      ...++.....+++-.+.|++.||..+...|  ..|+.||+++|+.|+....+..++++
T Consensus       284 v~YQPIV~la~GkcvGaEAL~RW~~~dG~~--vsPd~FIplAE~sG~ie~iT~~Vi~~  339 (524)
T COG4943         284 VHYQPIVDLATGKCVGAEALARWPQEDGTV--VSPDVFIPLAEESGMIEQITDYVIRN  339 (524)
T ss_pred             EEecceeEccCCcEecHHHHhcCcccCCCc--cChHHhhhHHhhcCchHHHHHHHHHH
Confidence            345666778889999999999999998886  78999999999999988777777653

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

Probab=90.31  E-value=2.5  Score=33.59  Aligned_cols=72  Identities=21%  Similarity=0.289  Sum_probs=51.2

Q ss_pred             EEECCHHHHHHHHHhCCCCceEEEEccC-------CCCCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEE
Q 027234            6 TKCNRAEIALDMLRTNKNGYDIVISDVH-------MPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYL   78 (226)
Q Consensus         6 ~~~~~~~eal~~l~~~~~~~DlVl~D~~-------mp~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl   78 (226)
                      ..+.+.+++.....   .++|+|.+...       .+...++++++.++...++|++...+-.+.+.+.+++..||++.+
T Consensus       124 ~~v~t~ee~~~a~~---~G~d~i~~~~~g~t~~~~~~~~~~~~~i~~i~~~~~iPvia~GGI~t~~~~~~~l~~GadgV~  200 (221)
T PRK01130        124 ADCSTLEEGLAAQK---LGFDFIGTTLSGYTEETKKPEEPDFALLKELLKAVGCPVIAEGRINTPEQAKKALELGAHAVV  200 (221)
T ss_pred             EeCCCHHHHHHHHH---cCCCEEEcCCceeecCCCCCCCcCHHHHHHHHHhCCCCEEEECCCCCHHHHHHHHHCCCCEEE
Confidence            34567777765444   23888865321       122335788888876667999998888889999999999999987


Q ss_pred             eC
Q 027234           79 TK   80 (226)
Q Consensus        79 ~K   80 (226)
                      .=
T Consensus       201 iG  202 (221)
T PRK01130        201 VG  202 (221)
T ss_pred             Ec
Confidence            53

>PRK15186 AraC family transcriptional regulator; Provisional

Probab=90.05  E-value=0.12  Score=43.19  Aligned_cols=37  Identities=11%  Similarity=-0.023  Sum_probs=30.3

Q ss_pred             HHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCCCCCCC
Q 027234          180 KILELMNIPGLTRENVASHLQKHRLYLSRLSGVSPQQG  217 (226)
Q Consensus       180 ~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~~~~~~  217 (226)
                      .|..++.. .+|++++|++++||+++|+|.|+..++..
T Consensus       189 ~I~~~~~~-~~sl~~lA~~~gmS~stl~R~Fk~~g~s~  225 (291)
T PRK15186        189 IIISDISR-KWALKDISDSLYMSCSTLKRKLKQENTSF  225 (291)
T ss_pred             HHHhCccC-CCCHHHHHHHHCcCHHHHHHHHHHcCCCH
Confidence            46666665 89999999999999999999998754443

>CHL00162 thiG thiamin biosynthesis protein G; Validated

Probab=90.00  E-value=8.7  Score=31.40  Aligned_cols=94  Identities=16%  Similarity=0.225  Sum_probs=64.0

Q ss_pred             CcEEEE--ECCHHHHHHHHHhCCCCceEEEEccCCCCCCH-----HHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCc
Q 027234            2 GFSVTK--CNRAEIALDMLRTNKNGYDIVISDVHMPDMDG-----FKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDA   74 (226)
Q Consensus         2 g~~V~~--~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG-----~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga   74 (226)
                      ||.|..  ..|..-|-++.+..   +. +++=+.-|-..|     -..++.|.+++++|||+=.+-...+.+..++++|+
T Consensus       137 GF~VlPY~~~D~v~a~rLed~G---c~-aVMPlgsPIGSg~Gl~n~~~l~~i~e~~~vpVivdAGIgt~sDa~~AmElGa  212 (267)
T CHL00162        137 GFTVLPYINADPMLAKHLEDIG---CA-TVMPLGSPIGSGQGLQNLLNLQIIIENAKIPVIIDAGIGTPSEASQAMELGA  212 (267)
T ss_pred             CCEEeecCCCCHHHHHHHHHcC---Ce-EEeeccCcccCCCCCCCHHHHHHHHHcCCCcEEEeCCcCCHHHHHHHHHcCC
Confidence            566652  33455555444332   32 233344443333     34567777778899999999999999999999999


Q ss_pred             ceEE-----eCCCCHHHHHHHHHHHHHHHh
Q 027234           75 CDYL-----TKPVRIEELKNIWQHVVRKRK   99 (226)
Q Consensus        75 ~~yl-----~KP~~~~~L~~~l~~~~~~~~   99 (226)
                      ++.+     .|.-++.++...++.....-+
T Consensus       213 DgVL~nSaIakA~dP~~mA~a~~~AV~AGR  242 (267)
T CHL00162        213 SGVLLNTAVAQAKNPEQMAKAMKLAVQAGR  242 (267)
T ss_pred             CEEeecceeecCCCHHHHHHHHHHHHHHHH
Confidence            9987     567888888888888765433

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

Probab=89.92  E-value=6  Score=28.81  Aligned_cols=88  Identities=14%  Similarity=0.026  Sum_probs=59.8

Q ss_pred             CcEEE---EECCHHHHHHHHHhCCCCceEEEEccCCCC-CCH-HHHHHHHhcC-C-CCcEEEEeccC-----C-HHHHHH
Q 027234            2 GFSVT---KCNRAEIALDMLRTNKNGYDIVISDVHMPD-MDG-FKLLELVGLE-M-DLPVIMMCAHG-----S-KEVVMK   68 (226)
Q Consensus         2 g~~V~---~~~~~~eal~~l~~~~~~~DlVl~D~~mp~-~dG-~~l~~~l~~~-~-~~pvI~ls~~~-----~-~~~~~~   68 (226)
                      ||+|.   ..-+.++.++.+.+..  +|+|.+...|.. +.. -++.+.+++. . +++|+ +.+..     + .+...+
T Consensus        27 GfeVidLG~~v~~e~~v~aa~~~~--adiVglS~L~t~~~~~~~~~~~~l~~~gl~~v~vi-vGG~~~i~~~d~~~~~~~  103 (128)
T cd02072          27 GFNVVNLGVLSPQEEFIDAAIETD--ADAILVSSLYGHGEIDCKGLREKCDEAGLKDILLY-VGGNLVVGKQDFEDVEKR  103 (128)
T ss_pred             CCEEEECCCCCCHHHHHHHHHHcC--CCEEEEeccccCCHHHHHHHHHHHHHCCCCCCeEE-EECCCCCChhhhHHHHHH
Confidence            78876   3457888888888866  999999888865 333 3445566533 2 44443 44431     1 234566


Q ss_pred             HHhCCcceEEeCCCCHHHHHHHHH
Q 027234           69 GVTHDACDYLTKPVRIEELKNIWQ   92 (226)
Q Consensus        69 a~~~ga~~yl~KP~~~~~L~~~l~   92 (226)
                      ..++|++..+...-+++++...|+
T Consensus       104 L~~~Gv~~vf~pgt~~~~i~~~l~  127 (128)
T cd02072         104 FKEMGFDRVFAPGTPPEEAIADLK  127 (128)
T ss_pred             HHHcCCCEEECcCCCHHHHHHHHh
Confidence            888999999998888888876654

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.

>PRK13502 transcriptional activator RhaR; Provisional

Probab=89.87  E-value=0.12  Score=42.55  Aligned_cols=40  Identities=8%  Similarity=0.030  Sum_probs=33.5

Q ss_pred             HHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC-CCCCCCCC
Q 027234          180 KILELMNIPGLTRENVASHLQKHRLYLSRLSGV-SPQQGNSF  220 (226)
Q Consensus       180 ~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~-~~~~~~~~  220 (226)
                      .|.+++.. .++.+++|..+++|++||+|+|+. +++.+..|
T Consensus       184 ~I~~~~~~-~~~~~~lA~~~~iS~~~L~r~fk~~~G~t~~~y  224 (282)
T PRK13502        184 ALANSLEC-PFALDAFCQQEQCSERVLRQQFRAQTGMTINQY  224 (282)
T ss_pred             HHHhcccC-CCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHHH
Confidence            47778877 599999999999999999999985 67765544

>PRK15185 transcriptional regulator HilD; Provisional

Probab=89.76  E-value=0.14  Score=42.90  Aligned_cols=39  Identities=15%  Similarity=-0.021  Sum_probs=31.1

Q ss_pred             HHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCCCCCCCCC
Q 027234          180 KILELMNIPGLTRENVASHLQKHRLYLSRLSGVSPQQGNS  219 (226)
Q Consensus       180 ~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~~~~~~~~  219 (226)
                      .|.+++.. .++++++|+++++|+++|+|.|+..++++..
T Consensus       214 ~I~~n~~~-~~SledLA~~lgmS~~tL~R~FK~~G~S~~~  252 (309)
T PRK15185        214 IISSSPSR-QWKLTDVADHIFMSTSTLKRKLAEEGTSFSD  252 (309)
T ss_pred             HHHhCccC-CCCHHHHHHHHCcCHHHHHHHHHHcCCCHHH
Confidence            46666665 7899999999999999999999865555443

>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]

Probab=89.71  E-value=0.085  Score=37.43  Aligned_cols=37  Identities=32%  Similarity=0.229  Sum_probs=29.4

Q ss_pred             HHHhhCCCCCCHHHHHHHhhhhhhhhhcccC-CCCCCCC
Q 027234          181 ILELMNIPGLTRENVASHLQKHRLYLSRLSG-VSPQQGN  218 (226)
Q Consensus       181 I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~-~~~~~~~  218 (226)
                      |.+++.. +++++.||.++++|+.+|.|.|+ ..+..+.
T Consensus        29 i~~~~~~-~~~l~~la~~~g~S~~~l~r~f~~~~g~s~~   66 (127)
T COG2207          29 IEENLAE-PLTLEDLARRLGMSRRTLSRLFKKETGTSPS   66 (127)
T ss_pred             HHHHhcC-CCCHHHHHHHHCCCHHHHHHHHHHHHCCCHH
Confidence            5565555 69999999999999999999887 5555443

>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C

Probab=89.69  E-value=0.12  Score=30.67  Aligned_cols=34  Identities=21%  Similarity=0.235  Sum_probs=21.4

Q ss_pred             HHHhhCCCCCCHHHHHHHhhhhhhhhhcccCCCCC
Q 027234          181 ILELMNIPGLTRENVASHLQKHRLYLSRLSGVSPQ  215 (226)
Q Consensus       181 I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~~~~  215 (226)
                      |+..... +.|..+||.+|++|++.+||..+--.+
T Consensus        10 ii~l~~~-G~s~~~ia~~lgvs~~Tv~~w~kr~~~   43 (50)
T PF13384_consen   10 IIRLLRE-GWSIREIAKRLGVSRSTVYRWIKRYRE   43 (50)
T ss_dssp             HHHHHHH-T--HHHHHHHHTS-HHHHHHHHT----
T ss_pred             HHHHHHC-CCCHHHHHHHHCcCHHHHHHHHHHccc
Confidence            4444444 999999999999999999986554333

>TIGR03239 GarL 2-dehydro-3-deoxyglucarate aldolase

Probab=89.30  E-value=5.4  Score=32.55  Aligned_cols=81  Identities=11%  Similarity=0.089  Sum_probs=59.1

Q ss_pred             HHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh--cCCCCcEEEEeccCCHHHHHHHHhCCcceEEeCCC-CHHHH
Q 027234           11 AEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG--LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTKPV-RIEEL   87 (226)
Q Consensus        11 ~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~--~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~KP~-~~~~L   87 (226)
                      ...+.+.+....  +|.|++|++-..+|--++...++  +...++.++=....+...+.++++.|+.+.+..=+ +.++.
T Consensus        22 sp~~~e~~a~~G--~D~v~iD~EHg~~~~~~~~~~~~a~~~~g~~~~VRvp~~~~~~i~r~LD~Ga~gIivP~v~taeea   99 (249)
T TIGR03239        22 NPITTEVLGLAG--FDWLLLDGEHAPNDVLTFIPQLMALKGSASAPVVRPPWNEPVIIKRLLDIGFYNFLIPFVESAEEA   99 (249)
T ss_pred             CcHHHHHHHhcC--CCEEEEecccCCCCHHHHHHHHHHHhhcCCCcEEECCCCCHHHHHHHhcCCCCEEEecCcCCHHHH
Confidence            345667777644  99999999998888777777665  33455556656667889999999999999986544 45666


Q ss_pred             HHHHHH
Q 027234           88 KNIWQH   93 (226)
Q Consensus        88 ~~~l~~   93 (226)
                      +.+++.
T Consensus       100 ~~~v~a  105 (249)
T TIGR03239       100 ERAVAA  105 (249)
T ss_pred             HHHHHH
Confidence            555543

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

>COG4977 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]

Probab=89.28  E-value=0.3  Score=41.39  Aligned_cols=41  Identities=20%  Similarity=0.196  Sum_probs=32.9

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      +.++..+++.          +..++.. .++++++|.++++|+++|-|+|+.
T Consensus       219 ~~~l~~~i~~----------me~nle~-plsl~~LA~~~~~S~R~leRlF~~  259 (328)
T COG4977         219 DPRLLRAIEL----------MEANLEE-PLSLEELADRAGLSRRQLERLFRA  259 (328)
T ss_pred             CHHHHHHHHH----------HHHhhcC-CcCHHHHHHHhCCCHHHHHHHHHH
Confidence            4556555555          6677777 899999999999999999998764

>PRK07896 nicotinate-nucleotide pyrophosphorylase; Provisional

Probab=88.94  E-value=3  Score=34.81  Aligned_cols=67  Identities=9%  Similarity=0.027  Sum_probs=46.6

Q ss_pred             EEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHH---HHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEE
Q 027234            5 VTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLE---LVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYL   78 (226)
Q Consensus         5 V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~---~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl   78 (226)
                      .+.+.+.++|.+.+..   ++|+|++|    +|+--++-+   .++....-..+..|+.-+.+.+......|+|.+-
T Consensus       203 eVEv~tl~ea~eal~~---gaDiI~LD----nm~~e~vk~av~~~~~~~~~v~ieaSGGI~~~ni~~yA~tGvD~Is  272 (289)
T PRK07896        203 EVEVDSLEQLDEVLAE---GAELVLLD----NFPVWQTQEAVQRRDARAPTVLLESSGGLTLDTAAAYAETGVDYLA  272 (289)
T ss_pred             EEEcCCHHHHHHHHHc---CCCEEEeC----CCCHHHHHHHHHHHhccCCCEEEEEECCCCHHHHHHHHhcCCCEEE
Confidence            4578899999999874   38999999    344333322   3332333335678888999999999999988654

>TIGR01334 modD putative molybdenum utilization protein ModD

Probab=88.92  E-value=3.1  Score=34.55  Aligned_cols=69  Identities=16%  Similarity=0.167  Sum_probs=47.7

Q ss_pred             EEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEE
Q 027234            6 TKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYL   78 (226)
Q Consensus         6 ~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl   78 (226)
                      +.+.+.++|.+.+..   ++|+|++| +|+..+=.+..+.++....-..+-.|+.-+.+.+......|++-+.
T Consensus       193 VEv~tleea~ea~~~---GaDiI~lD-n~~~e~l~~~v~~l~~~~~~~~leasGGI~~~ni~~ya~~GvD~is  261 (277)
T TIGR01334       193 VEADTIEQALTVLQA---SPDILQLD-KFTPQQLHHLHERLKFFDHIPTLAAAGGINPENIADYIEAGIDLFI  261 (277)
T ss_pred             EECCCHHHHHHHHHc---CcCEEEEC-CCCHHHHHHHHHHHhccCCCEEEEEECCCCHHHHHHHHhcCCCEEE
Confidence            467899999999874   38999999 3433333333444442222335678888999999888888988654

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.

>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A

Probab=88.78  E-value=0.39  Score=27.88  Aligned_cols=29  Identities=28%  Similarity=0.441  Sum_probs=18.6

Q ss_pred             HHHHhhCCCCCCHHHHHHHhhhhhhhhhcc
Q 027234          180 KILELMNIPGLTRENVASHLQKHRLYLSRL  209 (226)
Q Consensus       180 ~I~~~~~~~~lt~~~va~~l~~~r~~l~r~  209 (226)
                      .|..... .|.+..+||..|++|++.++|.
T Consensus        12 ~I~~l~~-~G~s~~~IA~~lg~s~sTV~re   40 (44)
T PF13936_consen   12 QIEALLE-QGMSIREIAKRLGRSRSTVSRE   40 (44)
T ss_dssp             HHHHHHC-S---HHHHHHHTT--HHHHHHH
T ss_pred             HHHHHHH-cCCCHHHHHHHHCcCcHHHHHH
Confidence            3555554 5999999999999999998873

>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=88.57  E-value=0.15  Score=27.62  Aligned_cols=23  Identities=30%  Similarity=0.364  Sum_probs=16.9

Q ss_pred             CCCHHHHHHHhhhhhhhhhcccC
Q 027234          189 GLTRENVASHLQKHRLYLSRLSG  211 (226)
Q Consensus       189 ~lt~~~va~~l~~~r~~l~r~~~  211 (226)
                      .+|+++||+.++.+|..+.|+++
T Consensus         2 ~mtr~diA~~lG~t~ETVSR~l~   24 (32)
T PF00325_consen    2 PMTRQDIADYLGLTRETVSRILK   24 (32)
T ss_dssp             E--HHHHHHHHTS-HHHHHHHHH
T ss_pred             CcCHHHHHHHhCCcHHHHHHHHH
Confidence            36899999999999999888643

These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....

>PRK12704 phosphodiesterase; Provisional

Probab=88.48  E-value=1.3  Score=40.13  Aligned_cols=45  Identities=16%  Similarity=0.169  Sum_probs=39.2

Q ss_pred             CcEEEEeccCCHH--HHHHHHhCCcceEEeCCCCHHHHHHHHHHHHH
Q 027234           52 LPVIMMCAHGSKE--VVMKGVTHDACDYLTKPVRIEELKNIWQHVVR   96 (226)
Q Consensus        52 ~pvI~ls~~~~~~--~~~~a~~~ga~~yl~KP~~~~~L~~~l~~~~~   96 (226)
                      ..+|++|+++...  .+..++..++.|+..||+..+++...++.-+.
T Consensus       250 p~~v~ls~~~~~rre~a~~~l~~l~~dg~i~P~~iee~~~~~~~~~~  296 (520)
T PRK12704        250 PEAVILSGFDPIRREIARLALEKLVQDGRIHPARIEEMVEKARKEVD  296 (520)
T ss_pred             CCeEEEecCChhhHHHHHHHHHHHHhcCCcCCCCHHHHHHHHHHHHH
Confidence            3588899988775  88999999999999999999999988887665

>PLN02591 tryptophan synthase

Probab=88.43  E-value=2.6  Score=34.38  Aligned_cols=56  Identities=9%  Similarity=0.177  Sum_probs=42.7

Q ss_pred             HHHHHHHHhcCCCCcEEEEeccCC------HHHHHHHHhCCcceEEeCCCCHHHHHHHHHHH
Q 027234           39 GFKLLELVGLEMDLPVIMMCAHGS------KEVVMKGVTHDACDYLTKPVRIEELKNIWQHV   94 (226)
Q Consensus        39 G~~l~~~l~~~~~~pvI~ls~~~~------~~~~~~a~~~ga~~yl~KP~~~~~L~~~l~~~   94 (226)
                      .+++++.++...++|+|+|+-.+.      .....++.++|+++.|.-.+..++........
T Consensus        66 ~~~~~~~~r~~~~~p~ilm~Y~N~i~~~G~~~F~~~~~~aGv~GviipDLP~ee~~~~~~~~  127 (250)
T PLN02591         66 VISMLKEVAPQLSCPIVLFTYYNPILKRGIDKFMATIKEAGVHGLVVPDLPLEETEALRAEA  127 (250)
T ss_pred             HHHHHHHHhcCCCCCEEEEecccHHHHhHHHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHH
Confidence            366667776557789988876553      24578899999999999999988887766655

>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=88.35  E-value=5.7  Score=27.93  Aligned_cols=75  Identities=15%  Similarity=0.188  Sum_probs=44.4

Q ss_pred             CcEEEEE---CCHHHHHHHHHhCCCCceEEEEccC-CCCC-CHHHHHHHHhc-CCCCcEEEEeccCCHHHHHHHHh--CC
Q 027234            2 GFSVTKC---NRAEIALDMLRTNKNGYDIVISDVH-MPDM-DGFKLLELVGL-EMDLPVIMMCAHGSKEVVMKGVT--HD   73 (226)
Q Consensus         2 g~~V~~~---~~~~eal~~l~~~~~~~DlVl~D~~-mp~~-dG~~l~~~l~~-~~~~pvI~ls~~~~~~~~~~a~~--~g   73 (226)
                      ||+|...   .+.++..+.+....  ||+|.+... .+.. ...++++.++. .++++++ +-+..-.......++  .|
T Consensus        28 G~~v~~~d~~~~~~~l~~~~~~~~--pd~V~iS~~~~~~~~~~~~l~~~~k~~~p~~~iv-~GG~~~t~~~~~~l~~~~~  104 (121)
T PF02310_consen   28 GHEVDILDANVPPEELVEALRAER--PDVVGISVSMTPNLPEAKRLARAIKERNPNIPIV-VGGPHATADPEEILREYPG  104 (121)
T ss_dssp             TBEEEEEESSB-HHHHHHHHHHTT--CSEEEEEESSSTHHHHHHHHHHHHHTTCTTSEEE-EEESSSGHHHHHHHHHHHT
T ss_pred             CCeEEEECCCCCHHHHHHHHhcCC--CcEEEEEccCcCcHHHHHHHHHHHHhcCCCCEEE-EECCchhcChHHHhccCcC
Confidence            7887755   24577778888866  999999984 4443 34566677764 4555555 444333333333343  56


Q ss_pred             cceEEe
Q 027234           74 ACDYLT   79 (226)
Q Consensus        74 a~~yl~   79 (226)
                      +|..+.
T Consensus       105 ~D~vv~  110 (121)
T PF02310_consen  105 IDYVVR  110 (121)
T ss_dssp             SEEEEE
T ss_pred             cceecC
Confidence            665443

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 ....

>cd04729 NanE N-acetylmannosamine-6-phosphate epimerase (NanE) converts N-acetylmannosamine-6-phosphate to N-acetylglucosamine-6-phosphate

Probab=88.33  E-value=4.4  Score=32.14  Aligned_cols=71  Identities=23%  Similarity=0.283  Sum_probs=50.7

Q ss_pred             EECCHHHHHHHHHhCCCCceEEEEccC-------CCCCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            7 KCNRAEIALDMLRTNKNGYDIVISDVH-------MPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         7 ~~~~~~eal~~l~~~~~~~DlVl~D~~-------mp~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .+.+.+++......   ++|.+.+...       .....++++++.++...++|++...+-.+.+.+.+++..||++.+.
T Consensus       129 ~v~t~~ea~~a~~~---G~d~i~~~~~g~t~~~~~~~~~~~~~l~~i~~~~~ipvia~GGI~~~~~~~~~l~~GadgV~v  205 (219)
T cd04729         129 DISTLEEALNAAKL---GFDIIGTTLSGYTEETAKTEDPDFELLKELRKALGIPVIAEGRINSPEQAAKALELGADAVVV  205 (219)
T ss_pred             ECCCHHHHHHHHHc---CCCEEEccCccccccccCCCCCCHHHHHHHHHhcCCCEEEeCCCCCHHHHHHHHHCCCCEEEE
Confidence            45677777655542   3888755321       1123457888888765689999988888899999999999999875


Q ss_pred             C
Q 027234           80 K   80 (226)
Q Consensus        80 K   80 (226)
                      -
T Consensus       206 G  206 (219)
T cd04729         206 G  206 (219)
T ss_pred             c
Confidence            3

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.

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

Probab=88.29  E-value=2.8  Score=33.96  Aligned_cols=56  Identities=9%  Similarity=0.158  Sum_probs=39.8

Q ss_pred             HHHHHHHHhcCCCCcEEEEeccCC------HHHHHHHHhCCcceEEeCCCCHHHHHHHHHHH
Q 027234           39 GFKLLELVGLEMDLPVIMMCAHGS------KEVVMKGVTHDACDYLTKPVRIEELKNIWQHV   94 (226)
Q Consensus        39 G~~l~~~l~~~~~~pvI~ls~~~~------~~~~~~a~~~ga~~yl~KP~~~~~L~~~l~~~   94 (226)
                      ++++++.++...++|+++|+-.+.      ......+.++|+++.+.-....+++...++.+
T Consensus        64 ~~~~~~~vr~~~~~pv~lm~y~n~~~~~G~~~fi~~~~~aG~~giiipDl~~ee~~~~~~~~  125 (242)
T cd04724          64 VLELVKEIRKKNTIPIVLMGYYNPILQYGLERFLRDAKEAGVDGLIIPDLPPEEAEEFREAA  125 (242)
T ss_pred             HHHHHHHHhhcCCCCEEEEEecCHHHHhCHHHHHHHHHHCCCcEEEECCCCHHHHHHHHHHH
Confidence            455666666555789888776553      55677889999999999777777665555544

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.

>PRK10572 DNA-binding transcriptional regulator AraC; Provisional

Probab=88.27  E-value=0.34  Score=40.10  Aligned_cols=40  Identities=18%  Similarity=0.063  Sum_probs=31.9

Q ss_pred             HHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCCC-CCCCCCC
Q 027234          180 KILELMNIPGLTRENVASHLQKHRLYLSRLSGVS-PQQGNSF  220 (226)
Q Consensus       180 ~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~~-~~~~~~~  220 (226)
                      .|..++.. .++++++|+++++|++||.|+||-. ++.+..|
T Consensus       191 ~i~~~~~~-~isl~~lA~~~~lS~~~l~r~Fk~~~G~tp~~~  231 (290)
T PRK10572        191 YISDHLAS-EFDIESVAQHVCLSPSRLAHLFRQQLGISVLRW  231 (290)
T ss_pred             HHHhcccC-CCCHHHHHHHHCCCHHHHHHHHHHHHCcCHHHH
Confidence            46677774 9999999999999999999988764 5555444

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

Probab=88.11  E-value=7.7  Score=32.03  Aligned_cols=80  Identities=15%  Similarity=0.127  Sum_probs=57.1

Q ss_pred             HHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh--cCCCCcEEEEeccCCHHHHHHHHhCCcceEEeCCCCH-HHHH
Q 027234           12 EIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG--LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTKPVRI-EELK   88 (226)
Q Consensus        12 ~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~--~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~KP~~~-~~L~   88 (226)
                      -.+.+.+....  +|.|++|++-...|--++...++  ....++.++-....+...+.++++.||.+.+..=++. ++.+
T Consensus        29 p~~~E~~a~~G--fD~v~iD~EHg~~~~~~l~~~i~a~~~~g~~~lVRvp~~~~~~i~r~LD~GA~GIivP~V~saeeA~  106 (267)
T PRK10128         29 SYMAEIAATSG--YDWLLIDGEHAPNTIQDLYHQLQAIAPYASQPVIRPVEGSKPLIKQVLDIGAQTLLIPMVDTAEQAR  106 (267)
T ss_pred             cHHHHHHHHcC--CCEEEEccccCCCCHHHHHHHHHHHHhcCCCeEEECCCCCHHHHHHHhCCCCCeeEecCcCCHHHHH
Confidence            45566676644  99999999998887777766664  3344555555566778889999999999999776544 5555


Q ss_pred             HHHHH
Q 027234           89 NIWQH   93 (226)
Q Consensus        89 ~~l~~   93 (226)
                      .+++.
T Consensus       107 ~~V~a  111 (267)
T PRK10128        107 QVVSA  111 (267)
T ss_pred             HHHHh
Confidence            44443

>TIGR00007 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase

Probab=87.87  E-value=4  Score=32.56  Aligned_cols=68  Identities=16%  Similarity=0.183  Sum_probs=49.9

Q ss_pred             CHHHHHHHHHhCCCCce-EEEEccCCCCC-CH--HHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234           10 RAEIALDMLRTNKNGYD-IVISDVHMPDM-DG--FKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus        10 ~~~eal~~l~~~~~~~D-lVl~D~~mp~~-dG--~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      +..+..+.+.+..  ++ ++++|+.--++ .|  +++++.+++...+|+++-.+-.+.+.+.+++..||++.+.
T Consensus       146 ~~~~~~~~~~~~g--~~~ii~~~~~~~g~~~g~~~~~i~~i~~~~~ipvia~GGi~~~~di~~~~~~Gadgv~i  217 (230)
T TIGR00007       146 SLEELAKRLEELG--LEGIIYTDISRDGTLSGPNFELTKELVKAVNVPVIASGGVSSIDDLIALKKLGVYGVIV  217 (230)
T ss_pred             CHHHHHHHHHhCC--CCEEEEEeecCCCCcCCCCHHHHHHHHHhCCCCEEEeCCCCCHHHHHHHHHCCCCEEEE
Confidence            4455556565543  67 77788854332 22  6778888766789999888888999999999999999875

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).

>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A

Probab=87.80  E-value=0.24  Score=30.88  Aligned_cols=33  Identities=30%  Similarity=0.355  Sum_probs=24.0

Q ss_pred             HHHhhCCCCCCHHHHHHHhhhhhhhhhcccCCC
Q 027234          181 ILELMNIPGLTRENVASHLQKHRLYLSRLSGVS  213 (226)
Q Consensus       181 I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~~  213 (226)
                      |.+.|...++|...+|...+++++.++++++-.
T Consensus         2 L~~~m~~~~it~~~La~~~gis~~tl~~~~~~~   34 (63)
T PF13443_consen    2 LKELMAERGITQKDLARKTGISRSTLSRILNGK   34 (63)
T ss_dssp             HHHHHHHTT--HHHHHHHHT--HHHHHHHHTTT
T ss_pred             HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcc
Confidence            455677779999999999999999999987744

>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD

Probab=87.80  E-value=0.3  Score=33.13  Aligned_cols=32  Identities=13%  Similarity=0.269  Sum_probs=26.8

Q ss_pred             HHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          180 KILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       180 ~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .|...+.. +.|..+||..+++||+.+||+.+.
T Consensus        42 ~I~~ll~~-G~S~~eIA~~LgISrsTIyRi~R~   73 (88)
T TIGR02531        42 QVAKMLKQ-GKTYSDIEAETGASTATISRVKRC   73 (88)
T ss_pred             HHHHHHHC-CCCHHHHHHHHCcCHHHHHHHHHh
Confidence            36566666 899999999999999999997763

This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=87.29  E-value=0.41  Score=34.63  Aligned_cols=38  Identities=21%  Similarity=0.253  Sum_probs=30.3

Q ss_pred             hCCCCCCchHHHHhh-CCCCCCHHHHHHHhhhhhhhhhc
Q 027234          171 LGFDKAGPKKILELM-NIPGLTRENVASHLQKHRLYLSR  208 (226)
Q Consensus       171 ~g~~~~~p~~I~~~~-~~~~lt~~~va~~l~~~r~~l~r  208 (226)
                      +|+....-.....++ .+..+|++.||+.|+.+|+..||
T Consensus        23 ~GLs~~Dv~v~~~LL~~~~~~tvdelae~lnr~rStv~r   61 (126)
T COG3355          23 YGLSELDVEVYKALLEENGPLTVDELAEILNRSRSTVYR   61 (126)
T ss_pred             hCCcHHHHHHHHHHHhhcCCcCHHHHHHHHCccHHHHHH
Confidence            466665555666666 57799999999999999998776

>PRK09393 ftrA transcriptional activator FtrA; Provisional

Probab=87.20  E-value=0.47  Score=40.03  Aligned_cols=41  Identities=7%  Similarity=-0.065  Sum_probs=32.6

Q ss_pred             HHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCCC-CCCCCCCC
Q 027234          180 KILELMNIPGLTRENVASHLQKHRLYLSRLSGVS-PQQGNSFV  221 (226)
Q Consensus       180 ~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~~-~~~~~~~~  221 (226)
                      .|.+++.. .++++++|+++++|+++|+|+|+-. ++.+..|+
T Consensus       226 ~i~~~~~~-~~sl~~lA~~~~~S~~~l~r~fk~~~g~s~~~~~  267 (322)
T PRK09393        226 WMRAHLAE-PHTVASLAARAAMSPRTFLRRFEAATGMTPAEWL  267 (322)
T ss_pred             HHHhccCC-CCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHHHH
Confidence            46677666 6999999999999999999988753 66655543

>PRK09426 methylmalonyl-CoA mutase; Reviewed

Probab=87.13  E-value=7.6  Score=36.72  Aligned_cols=93  Identities=11%  Similarity=-0.061  Sum_probs=62.3

Q ss_pred             CcEEEE---ECCHHHHHHHHHhCCCCceEEEEccCCCCC--CHHHHHHHHhcCCCCcE-EEEeccCCHHHHHHHHhCCcc
Q 027234            2 GFSVTK---CNRAEIALDMLRTNKNGYDIVISDVHMPDM--DGFKLLELVGLEMDLPV-IMMCAHGSKEVVMKGVTHDAC   75 (226)
Q Consensus         2 g~~V~~---~~~~~eal~~l~~~~~~~DlVl~D~~mp~~--dG~~l~~~l~~~~~~pv-I~ls~~~~~~~~~~a~~~ga~   75 (226)
                      ||+|..   ..+.+++.+...+..  +|+|.+...+...  ..-.+++.|+....-.+ |++.+....+........|++
T Consensus       610 GfeV~~~~~~~s~e~~v~aa~~~~--a~ivvlcs~d~~~~e~~~~l~~~Lk~~G~~~v~vl~GG~~~~~~~~~l~~aGvD  687 (714)
T PRK09426        610 GFDVDIGPLFQTPEEAARQAVEND--VHVVGVSSLAAGHKTLVPALIEALKKLGREDIMVVVGGVIPPQDYDFLYEAGVA  687 (714)
T ss_pred             CeeEecCCCCCCHHHHHHHHHHcC--CCEEEEeccchhhHHHHHHHHHHHHhcCCCCcEEEEeCCCChhhHHHHHhCCCC
Confidence            788753   246788888887765  8988877665442  34456677775432123 345544234444567889999


Q ss_pred             eEEeCCCCHHHHHHHHHHHHH
Q 027234           76 DYLTKPVRIEELKNIWQHVVR   96 (226)
Q Consensus        76 ~yl~KP~~~~~L~~~l~~~~~   96 (226)
                      +|+..-.+..++...+.+.+.
T Consensus       688 ~~i~~g~d~~~~L~~l~~~l~  708 (714)
T PRK09426        688 AIFGPGTVIADAAIDLLELLS  708 (714)
T ss_pred             EEECCCCCHHHHHHHHHHHHH
Confidence            999999998888877777664

>PRK13111 trpA tryptophan synthase subunit alpha; Provisional

Probab=86.77  E-value=3.6  Score=33.74  Aligned_cols=56  Identities=11%  Similarity=0.205  Sum_probs=42.1

Q ss_pred             HHHHHHHHh-cCCCCcEEEEeccCC------HHHHHHHHhCCcceEEeCCCCHHHHHHHHHHH
Q 027234           39 GFKLLELVG-LEMDLPVIMMCAHGS------KEVVMKGVTHDACDYLTKPVRIEELKNIWQHV   94 (226)
Q Consensus        39 G~~l~~~l~-~~~~~pvI~ls~~~~------~~~~~~a~~~ga~~yl~KP~~~~~L~~~l~~~   94 (226)
                      .+++++.++ ..+++|+++|+-...      .....++.++|+++.|.-.+..++....+...
T Consensus        76 ~~~~~~~~r~~~~~~p~vlm~Y~N~i~~~G~e~f~~~~~~aGvdGviipDLp~ee~~~~~~~~  138 (258)
T PRK13111         76 VFELVREIREKDPTIPIVLMTYYNPIFQYGVERFAADAAEAGVDGLIIPDLPPEEAEELRAAA  138 (258)
T ss_pred             HHHHHHHHHhcCCCCCEEEEecccHHhhcCHHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHH
Confidence            366667776 557899998885442      35678899999999999888888777666554

>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis

Probab=86.42  E-value=0.075  Score=33.97  Aligned_cols=39  Identities=28%  Similarity=0.309  Sum_probs=29.5

Q ss_pred             hCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcc
Q 027234          171 LGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRL  209 (226)
Q Consensus       171 ~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~  209 (226)
                      +|+....-+....++.....|..+||..++++|+..|+.
T Consensus         4 ~gLs~~E~~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~   42 (68)
T PF01978_consen    4 LGLSENEAKVYLALLKNGPATAEEIAEELGISRSTVYRA   42 (68)
T ss_dssp             HCHHHHHHHHHHHHHHHCHEEHHHHHHHHTSSHHHHHHH
T ss_pred             CCcCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHH
Confidence            444444444556666777999999999999999988874

TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.

>TIGR00262 trpA tryptophan synthase, alpha subunit

Probab=86.12  E-value=4.4  Score=33.17  Aligned_cols=56  Identities=18%  Similarity=0.202  Sum_probs=42.0

Q ss_pred             HHHHHHHHhcC-CCCcEEEEeccCC------HHHHHHHHhCCcceEEeCCCCHHHHHHHHHHH
Q 027234           39 GFKLLELVGLE-MDLPVIMMCAHGS------KEVVMKGVTHDACDYLTKPVRIEELKNIWQHV   94 (226)
Q Consensus        39 G~~l~~~l~~~-~~~pvI~ls~~~~------~~~~~~a~~~ga~~yl~KP~~~~~L~~~l~~~   94 (226)
                      .+++++.++.. .++|+++|+-...      .....++.++|+++.+.-....++....++.+
T Consensus        74 ~~~~v~~ir~~~~~~plv~m~Y~Npi~~~G~e~f~~~~~~aGvdgviipDlp~ee~~~~~~~~  136 (256)
T TIGR00262        74 CFELLKKVRQKHPNIPIGLLTYYNLIFRKGVEEFYAKCKEVGVDGVLVADLPLEESGDLVEAA  136 (256)
T ss_pred             HHHHHHHHHhcCCCCCEEEEEeccHHhhhhHHHHHHHHHHcCCCEEEECCCChHHHHHHHHHH
Confidence            45556777644 6889887776654      46788899999999999988888776655554

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.

>PRK06096 molybdenum transport protein ModD; Provisional

Probab=86.11  E-value=5.6  Score=33.13  Aligned_cols=70  Identities=9%  Similarity=0.087  Sum_probs=47.3

Q ss_pred             EEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEE
Q 027234            5 VTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYL   78 (226)
Q Consensus         5 V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl   78 (226)
                      .+.+.+.++|.+.++..   +|+|++| +|+..+=-+..+.++....-..+-.|+.-+.+.+......|+|-..
T Consensus       193 eVEv~tleqa~ea~~ag---aDiI~LD-n~~~e~l~~av~~~~~~~~~~~leaSGGI~~~ni~~yA~tGvD~Is  262 (284)
T PRK06096        193 VVEADTPKEAIAALRAQ---PDVLQLD-KFSPQQATEIAQIAPSLAPHCTLSLAGGINLNTLKNYADCGIRLFI  262 (284)
T ss_pred             EEECCCHHHHHHHHHcC---CCEEEEC-CCCHHHHHHHHHHhhccCCCeEEEEECCCCHHHHHHHHhcCCCEEE
Confidence            35678999999998743   8999999 3332222233333332122345678888999999998899988654

>PRK15340 transcriptional regulator InvF; Provisional

Probab=86.09  E-value=0.4  Score=38.22  Aligned_cols=47  Identities=11%  Similarity=0.014  Sum_probs=32.3

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      -..|++..|.-|+    ...|++.... ..+++++|+++++|++||+|+|+-
T Consensus       102 ~~~~~r~~e~y~l----~~~Ll~~~~~-~~sleeLA~~~gvS~r~f~RlFk~  148 (216)
T PRK15340        102 VLALLRKSESYWL----VGYLLAQSTS-GNTMRMLGEDYGVSYTHFRRLCSR  148 (216)
T ss_pred             HHHHHHHHHHHHH----HHHHHhCccC-CCCHHHHHHHHCcCHHHHHHHHHH
Confidence            3455555554432    1134444443 689999999999999999998875

>PRK00748 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase; Validated

Probab=86.02  E-value=5.4  Score=31.81  Aligned_cols=68  Identities=13%  Similarity=0.120  Sum_probs=50.5

Q ss_pred             CHHHHHHHHHhCCCCce-EEEEccCCCC-CCH--HHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCC-cceEEe
Q 027234           10 RAEIALDMLRTNKNGYD-IVISDVHMPD-MDG--FKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHD-ACDYLT   79 (226)
Q Consensus        10 ~~~eal~~l~~~~~~~D-lVl~D~~mp~-~dG--~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~g-a~~yl~   79 (226)
                      +..+..+.+....  ++ ++++|...-+ ..|  +++++.+++...+|+|.-.+-.+.+.+.++++.| +++.+.
T Consensus       147 ~~~e~~~~~~~~g--~~~ii~~~~~~~g~~~G~d~~~i~~l~~~~~ipvia~GGi~~~~di~~~~~~g~~~gv~v  219 (233)
T PRK00748        147 TAEDLAKRFEDAG--VKAIIYTDISRDGTLSGPNVEATRELAAAVPIPVIASGGVSSLDDIKALKGLGAVEGVIV  219 (233)
T ss_pred             CHHHHHHHHHhcC--CCEEEEeeecCcCCcCCCCHHHHHHHHHhCCCCEEEeCCCCCHHHHHHHHHcCCccEEEE
Confidence            3456666666543  66 7888876433 244  6788888766679999888888999999999988 998875

>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function

Probab=85.93  E-value=0.34  Score=33.98  Aligned_cols=30  Identities=23%  Similarity=0.428  Sum_probs=25.4

Q ss_pred             HHhhCCCCCCHHHHHHHhhhhhhhhhcccC
Q 027234          182 LELMNIPGLTRENVASHLQKHRLYLSRLSG  211 (226)
Q Consensus       182 ~~~~~~~~lt~~~va~~l~~~r~~l~r~~~  211 (226)
                      +.+++-.++++++-|..||+||..|.|+..
T Consensus        50 iRL~D~egl~QeeaA~~MgVSR~T~~ril~   79 (106)
T PF02001_consen   50 IRLVDYEGLSQEEAAERMGVSRPTFQRILE   79 (106)
T ss_pred             HHHHHHcCCCHHHHHHHcCCcHHHHHHHHH
Confidence            345667799999999999999999998754

>TIGR02366 DHAK_reg probable dihydroxyacetone kinase regulator

Probab=85.91  E-value=1.1  Score=33.96  Aligned_cols=32  Identities=13%  Similarity=0.127  Sum_probs=26.9

Q ss_pred             HHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          181 ILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       181 I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      +++...-+.+|+++||.+-+++|+.||+=|+.
T Consensus        15 Ll~~k~~~~ITV~~I~~~AgvsR~TFY~hF~d   46 (176)
T TIGR02366        15 LMEVQAFSKISVSDIMSTAQIRRQTFYNHFQD   46 (176)
T ss_pred             HHHHCCCccCCHHHHHHHhCCCHHHHHHHCCC
Confidence            45556677899999999999999999987763

The seed alignment for this family was built from a set of closely related uncharacterized proteins associated with operons for the type of bacterial dihydroxyacetone kinase that transfers PEP-derived phosphate from a phosphoprotein, as in phosphotransferase system transport, rather than from ATP. Members have a TetR transcriptional regulator domain (pfam00440) at the N-terminus and sequence homology throughout.

>cd04723 HisA_HisF Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase (HisA) and the cyclase subunit of imidazoleglycerol phosphate synthase (HisF)

Probab=85.80  E-value=6  Score=31.85  Aligned_cols=69  Identities=23%  Similarity=0.199  Sum_probs=53.2

Q ss_pred             CCHHHHHHHHHhCCCCceEEEEccCCCCC-CH--HHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            9 NRAEIALDMLRTNKNGYDIVISDVHMPDM-DG--FKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         9 ~~~~eal~~l~~~~~~~DlVl~D~~mp~~-dG--~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .+..+.++.+....  -.++++|+..-++ .|  +++++.+.+...+|+++-.+-.+.+.+.+++..|+++.+.
T Consensus       146 ~~~~~~~~~~~~~~--~~li~~di~~~G~~~g~~~~~~~~i~~~~~ipvi~~GGi~s~edi~~l~~~G~~~viv  217 (233)
T cd04723         146 IGPEELLRRLAKWP--EELIVLDIDRVGSGQGPDLELLERLAARADIPVIAAGGVRSVEDLELLKKLGASGALV  217 (233)
T ss_pred             CCHHHHHHHHHHhC--CeEEEEEcCccccCCCcCHHHHHHHHHhcCCCEEEeCCCCCHHHHHHHHHcCCCEEEE
Confidence            35677777776542  4699999976542 33  6677888766789999888889999999999999998874

The ProFAR isomerase catalyzes the fourth step in histidine biosynthesis, an isomerisation of the aminoaldose moiety of ProFAR to the aminoketose of PRFAR (N-(5'-phospho-D-1'-ribulosylformimino)-5-amino-1-(5''-phospho-ribosyl)-4-imidazolecarboxamide). In bacteria and archaea, ProFAR isomerase is encoded by the HisA gene. The Imidazole glycerol phosphate synthase (IGPS) catalyzes the fifth step of histidine biosynthesis, the formation of the imidazole ring. IGPS converts N1-(5'-phosphoribulosyl)-formimino-5-aminoimidazole-4-carboxamide ribonucleotide (PRFAR) to imidazole glycerol phosphate (ImGP) and 5'-(5-aminoimidazole-4-carboxamide) ribonucleotide (AICAR). This conversion involves two tightly coupled reactions in distinct active sites of IGPS. The two catalytic domains can be fused, like in fungi and pl

>cd00564 TMP_TenI Thiamine monophosphate synthase (TMP synthase)/TenI

Probab=85.60  E-value=7  Score=29.83  Aligned_cols=68  Identities=21%  Similarity=0.181  Sum_probs=48.5

Q ss_pred             ECCHHHHHHHHHhCCCCceEEEEccCCCC--------CCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            8 CNRAEIALDMLRTNKNGYDIVISDVHMPD--------MDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         8 ~~~~~eal~~l~~~~~~~DlVl~D~~mp~--------~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      +.+..++.+....   ++|.|+++-..|.        ..|++.++.++...++||++..+- +.+.+..+...|++++..
T Consensus       102 ~~t~~~~~~~~~~---g~d~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pv~a~GGi-~~~~i~~~~~~Ga~~i~~  177 (196)
T cd00564         102 THSLEEALRAEEL---GADYVGFGPVFPTPTKPGAGPPLGLELLREIAELVEIPVVAIGGI-TPENAAEVLAAGADGVAV  177 (196)
T ss_pred             CCCHHHHHHHhhc---CCCEEEECCccCCCCCCCCCCCCCHHHHHHHHHhCCCCEEEECCC-CHHHHHHHHHcCCCEEEE
Confidence            3456676665542   3899988755442        356788888876577898877765 567888899999998764

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.

>TIGR01321 TrpR trp operon repressor, proteobacterial

Probab=84.98  E-value=0.43  Score=32.70  Aligned_cols=33  Identities=15%  Similarity=0.087  Sum_probs=27.1

Q ss_pred             CCCCCHHHHHHHhhhhhhhhhcccCCCCCCCCC
Q 027234          187 IPGLTRENVASHLQKHRLYLSRLSGVSPQQGNS  219 (226)
Q Consensus       187 ~~~lt~~~va~~l~~~r~~l~r~~~~~~~~~~~  219 (226)
                      ..++|..+||.++|+|+++..|..+.-...+++
T Consensus        53 ~~~~tQrEIa~~lGiS~atIsR~sn~lk~~~~~   85 (94)
T TIGR01321        53 NGNMSQREIASKLGVSIATITRGSNNLKTMDPN   85 (94)
T ss_pred             hCCCCHHHHHHHhCCChhhhhHHHhhcccCCHH
Confidence            358999999999999999999987766654443

This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.

>PRK13587 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase; Provisional

Probab=84.93  E-value=8.4  Score=31.08  Aligned_cols=68  Identities=13%  Similarity=0.091  Sum_probs=51.1

Q ss_pred             HHHHHHHHHhCCCCceEEEEccCCCCC-CH--HHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234           11 AEIALDMLRTNKNGYDIVISDVHMPDM-DG--FKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus        11 ~~eal~~l~~~~~~~DlVl~D~~mp~~-dG--~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      ..+.++.+.... .-.++++|+..-++ .|  +++++.+.+..++|+++-.+-.+.+.+.++++.|+++.+.
T Consensus       150 ~~~~~~~~~~~g-~~~ii~tdi~~dGt~~G~~~~li~~l~~~~~ipvi~~GGi~s~edi~~l~~~G~~~viv  220 (234)
T PRK13587        150 LFSFVRQLSDIP-LGGIIYTDIAKDGKMSGPNFELTGQLVKATTIPVIASGGIRHQQDIQRLASLNVHAAII  220 (234)
T ss_pred             HHHHHHHHHHcC-CCEEEEecccCcCCCCccCHHHHHHHHHhCCCCEEEeCCCCCHHHHHHHHHcCCCEEEE
Confidence            355555555432 13799999987553 44  6677888766789999888888999999999999999885

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

Probab=84.78  E-value=9.1  Score=32.24  Aligned_cols=72  Identities=17%  Similarity=0.144  Sum_probs=53.3

Q ss_pred             EEECCHHHHHHHHHhCCCCceEEEEccCCC-----CCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEeC
Q 027234            6 TKCNRAEIALDMLRTNKNGYDIVISDVHMP-----DMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTK   80 (226)
Q Consensus         6 ~~~~~~~eal~~l~~~~~~~DlVl~D~~mp-----~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~K   80 (226)
                      ..+.+.++|....+.   ++|.|++.-.-.     ...-+.++..++...++|||.--+-.+.+.+..++..||++...=
T Consensus       114 ~~v~s~~~a~~a~~~---GaD~Ivv~g~eagGh~g~~~~~~ll~~v~~~~~iPviaaGGI~~~~~~~~al~~GA~gV~iG  190 (307)
T TIGR03151       114 PVVASVALAKRMEKA---GADAVIAEGMESGGHIGELTTMALVPQVVDAVSIPVIAAGGIADGRGMAAAFALGAEAVQMG  190 (307)
T ss_pred             EEcCCHHHHHHHHHc---CCCEEEEECcccCCCCCCCcHHHHHHHHHHHhCCCEEEECCCCCHHHHHHHHHcCCCEeecc
Confidence            356788888766553   389988744311     223588888887666799998888888999999999999997743

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.

>PRK05848 nicotinate-nucleotide pyrophosphorylase; Provisional

Probab=84.42  E-value=8.7  Score=31.83  Aligned_cols=67  Identities=18%  Similarity=0.178  Sum_probs=46.6

Q ss_pred             EEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh---cCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            6 TKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG---LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         6 ~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~---~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      +.+++.+||.+.++.   ++|+|.+|-    |+--++-+.++   ....-..|..|+.-+.+.+.+....|+|.+-.
T Consensus       187 VEv~tleea~~A~~~---GaDiI~LDn----~~~e~l~~~v~~~~~~~~~~~ieAsGgIt~~ni~~ya~~GvD~Isv  256 (273)
T PRK05848        187 IECESLEEAKNAMNA---GADIVMCDN----MSVEEIKEVVAYRNANYPHVLLEASGNITLENINAYAKSGVDAISS  256 (273)
T ss_pred             EEeCCHHHHHHHHHc---CCCEEEECC----CCHHHHHHHHHHhhccCCCeEEEEECCCCHHHHHHHHHcCCCEEEe
Confidence            478899999999874   389999883    33333333333   11122356688888999999999999987653

>PRK15399 lysine decarboxylase LdcC; Provisional

Probab=84.37  E-value=11  Score=35.68  Aligned_cols=91  Identities=16%  Similarity=0.067  Sum_probs=58.1

Q ss_pred             CcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEeC
Q 027234            2 GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTK   80 (226)
Q Consensus         2 g~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~K   80 (226)
                      ||+|..+.+..++...+++. ...+.|++|..-.   ...+++.++ .+..+||++++.......+-...-.-+++|+..
T Consensus        30 ~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~---~~~~~~~~~~~~~~~Pv~~~~~~~~~~~~~~~~~~~~~~~~~~  105 (713)
T PRK15399         30 GFQTIWPQNSVDLLKFIEHN-PRICGVIFDWDEY---SLDLCSDINQLNEYLPLYAFINTHSTMDVSVQDMRMALWFFEY  105 (713)
T ss_pred             CcEEEEecCHHHHHHHHhcc-cceeEEEEecccc---hHHHHHHHHHhCCCCCEEEEcCccccccCChhHhhhcceeeee
Confidence            89999999999999998854 5688999995332   355788776 668999999876543332222222235566654


Q ss_pred             CC-CHHHHHHHHHHHHH
Q 027234           81 PV-RIEELKNIWQHVVR   96 (226)
Q Consensus        81 P~-~~~~L~~~l~~~~~   96 (226)
                      -- +.+.+...+....+
T Consensus       106 ~~~~~~~~a~~i~~~~~  122 (713)
T PRK15399        106 ALGAAEDIAIRIRQYTN  122 (713)
T ss_pred             ccCCHHHHHHHHHHHHH
Confidence            32 34444444444433

>PRK13501 transcriptional activator RhaR; Provisional

Probab=84.35  E-value=0.55  Score=38.91  Aligned_cols=31  Identities=10%  Similarity=0.003  Sum_probs=27.1

Q ss_pred             HHHHhhCCCCCCHHHHHHHhhhhhhhhhcccC
Q 027234          180 KILELMNIPGLTRENVASHLQKHRLYLSRLSG  211 (226)
Q Consensus       180 ~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~  211 (226)
                      .|.+++.. .++++++|+++++|++||+|+|+
T Consensus       184 ~I~~~~~e-~~sl~~lA~~~~lS~~~l~r~Fk  214 (290)
T PRK13501        184 ALQQSLGA-YFDMADFCHKNQLVERSLKQLFR  214 (290)
T ss_pred             HHHHhhcc-CCCHHHHHHHHCcCHHHHHHHHH
Confidence            46677766 79999999999999999999876

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

Probab=84.30  E-value=1.8  Score=37.89  Aligned_cols=74  Identities=19%  Similarity=0.054  Sum_probs=53.9

Q ss_pred             cccccCCCCCCccchHHHHHHhccCCceeeeHhhHHHHHHHHHHhCCCCCCchHHHH----hh---------CCCCCCHH
Q 027234          127 SYSVNEGTSNSRKDEEEEAEKRLKKPRLVWSVELHQQFVSAVKELGFDKAGPKKILE----LM---------NIPGLTRE  193 (226)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~Fi~~~~~~g~~~~~p~~I~~----~~---------~~~~lt~~  193 (226)
                      ...++.....+++....|++.||.+|..+|  ..|+.|+..+|+.|.....+..++.    .+         +. +++-.
T Consensus       418 V~fQPiVDi~~gkt~a~EALaRWhspe~G~--vpPd~F~~iAErsG~i~~ltR~ll~~Alrea~~W~~~~Rvs~-NlSa~  494 (663)
T COG5001         418 VHFQPIVDIVSGKTIALEALARWHSPEIGP--VPPDVFIGIAERSGQIVELTRLLLAKALREARAWPMDVRVSI-NLSAR  494 (663)
T ss_pred             eeceeeeeecccchHHHHHHHhhcCCccCC--CChHHhhhhHhhcCchHHHHHHHHHHHHHHhccCCCCceEEE-ecCHH
Confidence            345566677888899999999999999998  6789999999999987666554442    11         22 45666


Q ss_pred             HHHHHhhhhh
Q 027234          194 NVASHLQKHR  203 (226)
Q Consensus       194 ~va~~l~~~r  203 (226)
                      +++++=+.-|
T Consensus       495 dl~~~e~v~~  504 (663)
T COG5001         495 DLASMENVRR  504 (663)
T ss_pred             HHhhHHhHHH
Confidence            7776655433

>cd02069 methionine_synthase_B12_BD B12 binding domain of methionine synthase

Probab=84.22  E-value=6.6  Score=31.22  Aligned_cols=78  Identities=17%  Similarity=0.218  Sum_probs=49.2

Q ss_pred             CcEEEEEC---CHHHHHHHHHhCCCCceEEEEccCCCC-CC-HHHHHHHHhcC-CCCcEEEEeccCCHHHHHH---HHhC
Q 027234            2 GFSVTKCN---RAEIALDMLRTNKNGYDIVISDVHMPD-MD-GFKLLELVGLE-MDLPVIMMCAHGSKEVVMK---GVTH   72 (226)
Q Consensus         2 g~~V~~~~---~~~eal~~l~~~~~~~DlVl~D~~mp~-~d-G~~l~~~l~~~-~~~pvI~ls~~~~~~~~~~---a~~~   72 (226)
                      ||+|....   ..++.++.+.+..  ||+|.+...|+. +. --++++.++.. .+++|++=...-+.+....   +-..
T Consensus       116 G~~Vi~LG~~vp~e~~v~~~~~~~--~~~V~lS~~~~~~~~~~~~~i~~L~~~~~~~~i~vGG~~~~~~~~~~~~~~~~~  193 (213)
T cd02069         116 GYEVIDLGVMVPIEKILEAAKEHK--ADIIGLSGLLVPSLDEMVEVAEEMNRRGIKIPLLIGGAATSRKHTAVKIAPEYD  193 (213)
T ss_pred             CCEEEECCCCCCHHHHHHHHHHcC--CCEEEEccchhccHHHHHHHHHHHHhcCCCCeEEEEChhcCHHHHhhhhccccC
Confidence            77876433   5788888888877  999999998875 33 24456677643 4555554333333333322   2457


Q ss_pred             CcceEEeCC
Q 027234           73 DACDYLTKP   81 (226)
Q Consensus        73 ga~~yl~KP   81 (226)
                      |||+|-.-.
T Consensus       194 gad~y~~da  202 (213)
T cd02069         194 GPVVYVKDA  202 (213)
T ss_pred             CCceEecCH
Confidence            999887543

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

>PRK11840 bifunctional sulfur carrier protein/thiazole synthase protein; Provisional

Probab=84.19  E-value=20  Score=30.48  Aligned_cols=93  Identities=12%  Similarity=0.124  Sum_probs=62.4

Q ss_pred             CcEE-E-EECCHHHHHHHHHhCCCCceEEEEccCCC-----CCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCc
Q 027234            2 GFSV-T-KCNRAEIALDMLRTNKNGYDIVISDVHMP-----DMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDA   74 (226)
Q Consensus         2 g~~V-~-~~~~~~eal~~l~~~~~~~DlVl~D~~mp-----~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga   74 (226)
                      ||.| . +++|...|-.+..- .  | +.++=+--|     +..--+.++.+...+.+|||+=.+-...+.+..|+++|+
T Consensus       197 Gf~v~~yc~~d~~~a~~l~~~-g--~-~avmPl~~pIGsg~gv~~p~~i~~~~e~~~vpVivdAGIg~~sda~~AmelGa  272 (326)
T PRK11840        197 GFQVMVYCSDDPIAAKRLEDA-G--A-VAVMPLGAPIGSGLGIQNPYTIRLIVEGATVPVLVDAGVGTASDAAVAMELGC  272 (326)
T ss_pred             CCEEEEEeCCCHHHHHHHHhc-C--C-EEEeeccccccCCCCCCCHHHHHHHHHcCCCcEEEeCCCCCHHHHHHHHHcCC
Confidence            7777 3 44566666655543 2  5 222221111     122344556665567899999999999999999999999


Q ss_pred             ceEE-----eCCCCHHHHHHHHHHHHHHH
Q 027234           75 CDYL-----TKPVRIEELKNIWQHVVRKR   98 (226)
Q Consensus        75 ~~yl-----~KP~~~~~L~~~l~~~~~~~   98 (226)
                      ++.|     .|--++-.+..+.+.....-
T Consensus       273 dgVL~nSaIa~a~dPv~Ma~A~~~av~aG  301 (326)
T PRK11840        273 DGVLMNTAIAEAKNPVLMARAMKLAVEAG  301 (326)
T ss_pred             CEEEEcceeccCCCHHHHHHHHHHHHHHH
Confidence            9987     46778888888887776543

>CHL00200 trpA tryptophan synthase alpha subunit; Provisional

Probab=84.07  E-value=5.4  Score=32.82  Aligned_cols=56  Identities=13%  Similarity=0.140  Sum_probs=42.0

Q ss_pred             HHHHHHHHhcCCCCcEEEEeccCC------HHHHHHHHhCCcceEEeCCCCHHHHHHHHHHH
Q 027234           39 GFKLLELVGLEMDLPVIMMCAHGS------KEVVMKGVTHDACDYLTKPVRIEELKNIWQHV   94 (226)
Q Consensus        39 G~~l~~~l~~~~~~pvI~ls~~~~------~~~~~~a~~~ga~~yl~KP~~~~~L~~~l~~~   94 (226)
                      .+++++.++...++|+++|+-...      .....++.++|+++.+.-.+..++....++.+
T Consensus        79 ~~~~~~~~r~~~~~p~vlm~Y~N~i~~~G~e~F~~~~~~aGvdgviipDLP~ee~~~~~~~~  140 (263)
T CHL00200         79 ILSILSEVNGEIKAPIVIFTYYNPVLHYGINKFIKKISQAGVKGLIIPDLPYEESDYLISVC  140 (263)
T ss_pred             HHHHHHHHhcCCCCCEEEEecccHHHHhCHHHHHHHHHHcCCeEEEecCCCHHHHHHHHHHH
Confidence            466667777557899888876543      35688899999999999988888866555544

>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional

Probab=84.07  E-value=1.4  Score=34.56  Aligned_cols=42  Identities=12%  Similarity=0.082  Sum_probs=33.5

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .++.++++.+          +......++.|+++||...|+||..+|+-|+.
T Consensus        13 r~~Il~aa~~----------lf~~~G~~~~ti~~Ia~~agvsk~t~Y~~F~s   54 (213)
T PRK09975         13 RQELIETAIA----------QFALRGVSNTTLNDIADAANVTRGAIYWHFEN   54 (213)
T ss_pred             HHHHHHHHHH----------HHHHcCcccCCHHHHHHHcCCCHHHHHHHcCC
Confidence            4567777776          44455667899999999999999999998864

>PRK15400 lysine decarboxylase CadA; Provisional

Probab=83.94  E-value=10  Score=35.79  Aligned_cols=91  Identities=15%  Similarity=0.155  Sum_probs=57.0

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||+|..+.+..+++..+++. .....|++|..-   ....+++.++ .+..+||+++........+-...-.-+++|+.
T Consensus        29 ~~~~v~~~~~~~~~~~~~~~~-~~~~~~~~~~~~---~~~~~~~~~~~~~~~~Pv~~~~~~~~~~~~~~~~l~~~~~~~~  104 (714)
T PRK15400         29 LNFQIVYPNDRDDLLKLIENN-ARLCGVIFDWDK---YNLELCEEISKMNENLPLYAFANTYSTLDVSLNDLRLQVSFFE  104 (714)
T ss_pred             CCcEEEEeCCHHHHHHHHhcc-cceeEEEEecch---hhHHHHHHHHHhCCCCCEEEEccccccccCChHHhhhccceee
Confidence            389999999999999998854 458899999532   2245778776 66899999987654332221112223455555


Q ss_pred             CC-CCHHHHHHHHHHHH
Q 027234           80 KP-VRIEELKNIWQHVV   95 (226)
Q Consensus        80 KP-~~~~~L~~~l~~~~   95 (226)
                      .- -+++.+...+.+..
T Consensus       105 ~~~~~~~~~a~~i~~~~  121 (714)
T PRK15400        105 YALGAADDIANKIKQTT  121 (714)
T ss_pred             eccCCHHHHHHHHHHHH
Confidence            32 23444444444443

>PRK13500 transcriptional activator RhaR; Provisional

Probab=83.54  E-value=0.61  Score=39.25  Aligned_cols=40  Identities=5%  Similarity=0.026  Sum_probs=33.1

Q ss_pred             HHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC-CCCCCCCC
Q 027234          180 KILELMNIPGLTRENVASHLQKHRLYLSRLSGV-SPQQGNSF  220 (226)
Q Consensus       180 ~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~-~~~~~~~~  220 (226)
                      .|.+++.. .++++++|+.+++|++||.|+||. +++.+..|
T Consensus       214 yI~~~~~e-~isl~~lA~~~~iS~~~L~r~FK~~tG~T~~~y  254 (312)
T PRK13500        214 RLAASLKS-PFALDKFCDEASCSERVLRQQFRQQTGMTINQY  254 (312)
T ss_pred             HHHHcccC-CCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHHH
Confidence            57778877 599999999999999999998885 46665544

>TIGR01764 excise DNA binding domain, excisionase family

Probab=83.52  E-value=0.6  Score=27.07  Aligned_cols=23  Identities=30%  Similarity=0.160  Sum_probs=20.0

Q ss_pred             CCHHHHHHHhhhhhhhhhcccCC
Q 027234          190 LTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       190 lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      +|..++|.+|+++++.+|+.-+.
T Consensus         2 lt~~e~a~~lgis~~ti~~~~~~   24 (49)
T TIGR01764         2 LTVEEAAEYLGVSKDTVYRLIHE   24 (49)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHc
Confidence            68999999999999999986544

An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).

>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould)

Probab=83.51  E-value=0.61  Score=28.07  Aligned_cols=28  Identities=25%  Similarity=0.331  Sum_probs=21.6

Q ss_pred             hCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          185 MNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       185 ~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      +..-++|..++|..+++++++++++..-
T Consensus         5 r~~~gls~~~la~~~gis~~~i~~~~~g   32 (55)
T PF01381_consen    5 RKEKGLSQKELAEKLGISRSTISRIENG   32 (55)
T ss_dssp             HHHTTS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred             HHHcCCCHHHHHHHhCCCcchhHHHhcC
Confidence            3345899999999999999999987554

; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....

>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets

Probab=83.36  E-value=0.93  Score=27.36  Aligned_cols=23  Identities=22%  Similarity=0.252  Sum_probs=18.6

Q ss_pred             CCCCCCHHHHHHHhhhhhhhhhc
Q 027234          186 NIPGLTRENVASHLQKHRLYLSR  208 (226)
Q Consensus       186 ~~~~lt~~~va~~l~~~r~~l~r  208 (226)
                      +.+.+|.+++|..|++|++.++|
T Consensus        12 ~~~~it~~eLa~~l~vS~rTi~~   34 (55)
T PF08279_consen   12 SKEPITAKELAEELGVSRRTIRR   34 (55)
T ss_dssp             TTTSBEHHHHHHHCTS-HHHHHH
T ss_pred             cCCCcCHHHHHHHhCCCHHHHHH
Confidence            34459999999999999998776

The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....

>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=83.17  E-value=0.83  Score=27.06  Aligned_cols=29  Identities=31%  Similarity=0.460  Sum_probs=22.0

Q ss_pred             HHHhhCCCCCCHHHHHHHhhhhhhhhhcc
Q 027234          181 ILELMNIPGLTRENVASHLQKHRLYLSRL  209 (226)
Q Consensus       181 I~~~~~~~~lt~~~va~~l~~~r~~l~r~  209 (226)
                      |+...-..++|..+||..||+|+...+++
T Consensus        12 vi~~~y~~~~t~~eIa~~lg~s~~~V~~~   40 (50)
T PF04545_consen   12 VIRLRYFEGLTLEEIAERLGISRSTVRRI   40 (50)
T ss_dssp             HHHHHHTST-SHHHHHHHHTSCHHHHHHH
T ss_pred             HHHHHhcCCCCHHHHHHHHCCcHHHHHHH
Confidence            33333366999999999999999988764

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....

>TIGR00735 hisF imidazoleglycerol phosphate synthase, cyclase subunit

Probab=83.09  E-value=23  Score=28.75  Aligned_cols=80  Identities=19%  Similarity=0.209  Sum_probs=51.7

Q ss_pred             HHHHHHHHHhCCCCceE-EEEccCCCC-CCH--HHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCC-cceEEe------
Q 027234           11 AEIALDMLRTNKNGYDI-VISDVHMPD-MDG--FKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHD-ACDYLT------   79 (226)
Q Consensus        11 ~~eal~~l~~~~~~~Dl-Vl~D~~mp~-~dG--~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~g-a~~yl~------   79 (226)
                      ..+..+.+.+..  +|. +++|+.--+ +.|  +++++.++...++|||...+-.+.+.+.+++..| +++.+.      
T Consensus       157 ~~~~~~~l~~~G--~~~iivt~i~~~g~~~g~~~~~~~~i~~~~~ipvia~GGi~s~~di~~~~~~g~~dgv~~g~a~~~  234 (254)
T TIGR00735       157 AVEWAKEVEKLG--AGEILLTSMDKDGTKSGYDLELTKAVSEAVKIPVIASGGAGKPEHFYEAFTKGKADAALAASVFHY  234 (254)
T ss_pred             HHHHHHHHHHcC--CCEEEEeCcCcccCCCCCCHHHHHHHHHhCCCCEEEeCCCCCHHHHHHHHHcCCcceeeEhHHHhC
Confidence            344555555533  674 444542211 122  5778888766789999988899999999999988 888543      


Q ss_pred             CCCCHHHHHHHHH
Q 027234           80 KPVRIEELKNIWQ   92 (226)
Q Consensus        80 KP~~~~~L~~~l~   92 (226)
                      .-++..+++..++
T Consensus       235 ~~~~~~~~~~~~~  247 (254)
T TIGR00735       235 REITIGEVKEYLA  247 (254)
T ss_pred             CCCCHHHHHHHHH
Confidence            3455565554443

>PRK07428 nicotinate-nucleotide pyrophosphorylase; Provisional

Probab=82.97  E-value=9.5  Score=31.87  Aligned_cols=68  Identities=13%  Similarity=0.020  Sum_probs=45.0

Q ss_pred             EEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhc-CCCCcEEEEeccCCHHHHHHHHhCCcceEE
Q 027234            6 TKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGL-EMDLPVIMMCAHGSKEVVMKGVTHDACDYL   78 (226)
Q Consensus         6 ~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~-~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl   78 (226)
                      .++.+.+||.+.+..   ++|+|.+|-.-| .+=-+..+.++. .+.+| +..++.-+.+.+.+....|++..-
T Consensus       201 VEv~tleea~eA~~~---GaD~I~LDn~~~-e~l~~av~~~~~~~~~i~-leAsGGIt~~ni~~ya~tGvD~Is  269 (288)
T PRK07428        201 VETETLEQVQEALEY---GADIIMLDNMPV-DLMQQAVQLIRQQNPRVK-IEASGNITLETIRAVAETGVDYIS  269 (288)
T ss_pred             EECCCHHHHHHHHHc---CCCEEEECCCCH-HHHHHHHHHHHhcCCCeE-EEEECCCCHHHHHHHHHcCCCEEE
Confidence            467899999999863   389999992222 111112233332 34454 557777888888888999998755

>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=82.79  E-value=5.6  Score=31.00  Aligned_cols=69  Identities=12%  Similarity=0.043  Sum_probs=49.1

Q ss_pred             CcEEEEECCHHHHHHHHHhCCCCceEEEEccCC---CCCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEE
Q 027234            2 GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHM---PDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYL   78 (226)
Q Consensus         2 g~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~m---p~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl   78 (226)
                      ++.|......+++-+++...   .|+|=+|...   | ..--++++.++...   .++|...+..+....|.++|+| ++
T Consensus        45 ~~~V~ITPT~~ev~~l~~aG---adIIAlDaT~R~Rp-~~l~~li~~i~~~~---~l~MADist~ee~~~A~~~G~D-~I  116 (192)
T PF04131_consen   45 DSDVYITPTLKEVDALAEAG---ADIIALDATDRPRP-ETLEELIREIKEKY---QLVMADISTLEEAINAAELGFD-II  116 (192)
T ss_dssp             TSS--BS-SHHHHHHHHHCT----SEEEEE-SSSS-S-S-HHHHHHHHHHCT---SEEEEE-SSHHHHHHHHHTT-S-EE
T ss_pred             CCCeEECCCHHHHHHHHHcC---CCEEEEecCCCCCC-cCHHHHHHHHHHhC---cEEeeecCCHHHHHHHHHcCCC-EE
Confidence            35677777889998888853   7999999865   5 66777888888655   6778888999999999999976 44

; GO: 0047465 N-acylglucosamine-6-phosphate 2-epimerase activity, 0006051 N-acetylmannosamine metabolic process; PDB: 1Y0E_B 3IGS_A 1YXY_A 3Q58_B.

>PF12728 HTH_17: Helix-turn-helix domain

Probab=82.70  E-value=0.69  Score=27.51  Aligned_cols=23  Identities=26%  Similarity=0.124  Sum_probs=20.1

Q ss_pred             CCHHHHHHHhhhhhhhhhcccCC
Q 027234          190 LTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       190 lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      +|.+++|..|++|++.+|+..+.
T Consensus         2 lt~~e~a~~l~is~~tv~~~~~~   24 (51)
T PF12728_consen    2 LTVKEAAELLGISRSTVYRWIRQ   24 (51)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHc
Confidence            78999999999999999986543

>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A

Probab=82.61  E-value=1.1  Score=26.26  Aligned_cols=26  Identities=27%  Similarity=0.382  Sum_probs=20.1

Q ss_pred             hhCCCCCCHHHHHHHhhhhhhhhhcc
Q 027234          184 LMNIPGLTRENVASHLQKHRLYLSRL  209 (226)
Q Consensus       184 ~~~~~~lt~~~va~~l~~~r~~l~r~  209 (226)
                      +..++++|+.++|..+++|+...++.
T Consensus        12 l~~~~~~t~~ela~~~~is~~tv~~~   37 (48)
T PF13412_consen   12 LRENPRITQKELAEKLGISRSTVNRY   37 (48)
T ss_dssp             HHHCTTS-HHHHHHHHTS-HHHHHHH
T ss_pred             HHHcCCCCHHHHHHHhCCCHHHHHHH
Confidence            44578899999999999999987763

...

>PHA01976 helix-turn-helix protein

Probab=82.53  E-value=0.57  Score=29.53  Aligned_cols=31  Identities=3%  Similarity=0.109  Sum_probs=25.8

Q ss_pred             HHHHhhCCCCCCHHHHHHHhhhhhhhhhccc
Q 027234          180 KILELMNIPGLTRENVASHLQKHRLYLSRLS  210 (226)
Q Consensus       180 ~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~  210 (226)
                      .|.......++|..++|..+++++++++++-
T Consensus         6 rl~~~R~~~glt~~~lA~~~gvs~~~v~~~e   36 (67)
T PHA01976          6 QLIKARNARAWSAPELSRRAGVRHSLIYDFE   36 (67)
T ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Confidence            4566666779999999999999999999853

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

Probab=82.30  E-value=18  Score=26.85  Aligned_cols=92  Identities=12%  Similarity=-0.018  Sum_probs=59.9

Q ss_pred             CCcEEE---EECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHH----HHHhcCCCCcEE-EEeccCCHHHHHHHHhC
Q 027234            1 MGFSVT---KCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLL----ELVGLEMDLPVI-MMCAHGSKEVVMKGVTH   72 (226)
Q Consensus         1 lg~~V~---~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~----~~l~~~~~~pvI-~ls~~~~~~~~~~a~~~   72 (226)
                      .||+|.   ...+++|+.+..-+..  .|+|.+...-.+  ..+++    +.++...--.|+ +.-+.-..+......++
T Consensus        39 ~GfeVi~~g~~~tp~e~v~aA~~~d--v~vIgvSsl~g~--h~~l~~~lve~lre~G~~~i~v~~GGvip~~d~~~l~~~  114 (143)
T COG2185          39 AGFEVINLGLFQTPEEAVRAAVEED--VDVIGVSSLDGG--HLTLVPGLVEALREAGVEDILVVVGGVIPPGDYQELKEM  114 (143)
T ss_pred             CCceEEecCCcCCHHHHHHHHHhcC--CCEEEEEeccch--HHHHHHHHHHHHHHhCCcceEEeecCccCchhHHHHHHh
Confidence            478876   4678899998886655  888877643322  23333    444433322333 45555566677777889


Q ss_pred             CcceEEeCCCCHHHHHHHHHHHHH
Q 027234           73 DACDYLTKPVRIEELKNIWQHVVR   96 (226)
Q Consensus        73 ga~~yl~KP~~~~~L~~~l~~~~~   96 (226)
                      |++.++..-....+...-+...+.
T Consensus       115 G~~~if~pgt~~~~~~~~v~~~l~  138 (143)
T COG2185         115 GVDRIFGPGTPIEEALSDLLTRLG  138 (143)
T ss_pred             CcceeeCCCCCHHHHHHHHHHHHH
Confidence            999999988888777666555443

>cd02070 corrinoid_protein_B12-BD B12 binding domain of corrinoid proteins

Probab=82.16  E-value=11  Score=29.60  Aligned_cols=74  Identities=19%  Similarity=0.162  Sum_probs=48.0

Q ss_pred             CcEEEEE---CCHHHHHHHHHhCCCCceEEEEccCCCCC--CHHHHHHHHhcC-C--CCcEEEEeccCCHHHHHHHHhCC
Q 027234            2 GFSVTKC---NRAEIALDMLRTNKNGYDIVISDVHMPDM--DGFKLLELVGLE-M--DLPVIMMCAHGSKEVVMKGVTHD   73 (226)
Q Consensus         2 g~~V~~~---~~~~eal~~l~~~~~~~DlVl~D~~mp~~--dG~~l~~~l~~~-~--~~pvI~ls~~~~~~~~~~a~~~g   73 (226)
                      ||+|...   -..++..+.+.+..  ||+|-+...|+..  ...++++.++.. +  +++|++=-..-..+   -+-..|
T Consensus       110 G~~vi~lG~~~p~~~l~~~~~~~~--~d~v~lS~~~~~~~~~~~~~i~~lr~~~~~~~~~i~vGG~~~~~~---~~~~~G  184 (201)
T cd02070         110 GFEVIDLGRDVPPEEFVEAVKEHK--PDILGLSALMTTTMGGMKEVIEALKEAGLRDKVKVMVGGAPVNQE---FADEIG  184 (201)
T ss_pred             CCEEEECCCCCCHHHHHHHHHHcC--CCEEEEeccccccHHHHHHHHHHHHHCCCCcCCeEEEECCcCCHH---HHHHcC
Confidence            7887743   35678888888876  9999999988663  334556677643 3  45555433333322   456679


Q ss_pred             cceEEeC
Q 027234           74 ACDYLTK   80 (226)
Q Consensus        74 a~~yl~K   80 (226)
                      ||.|-.-
T Consensus       185 aD~~~~d  191 (201)
T cd02070         185 ADGYAED  191 (201)
T ss_pred             CcEEECC
Confidence            9988753

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.

>PF03328 HpcH_HpaI: HpcH/HpaI aldolase/citrate lyase family; InterPro: IPR005000 This family includes 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase (4

Probab=82.06  E-value=22  Score=28.13  Aligned_cols=85  Identities=12%  Similarity=0.039  Sum_probs=52.3

Q ss_pred             ECCHHHHHHHHHhCCCCceEEEEccCCCC---------CCHHHHHHHHhc--CCCCcEEEEeccCCHHHHHH---HHhCC
Q 027234            8 CNRAEIALDMLRTNKNGYDIVISDVHMPD---------MDGFKLLELVGL--EMDLPVIMMCAHGSKEVVMK---GVTHD   73 (226)
Q Consensus         8 ~~~~~eal~~l~~~~~~~DlVl~D~~mp~---------~dG~~l~~~l~~--~~~~pvI~ls~~~~~~~~~~---a~~~g   73 (226)
                      -.+..+.++.+....  +|.|++|+.-..         .+-.+++..+..  .....+++=....+.....+   ++..|
T Consensus         7 p~~~~~~~~~a~~~g--~D~vilDlEd~~~~~~K~~ar~~~~~~~~~~~~~~~~~~~~~VRvn~~~~~~~~~Dl~~l~~g   84 (221)
T PF03328_consen    7 PANSPKMLEKAAASG--ADFVILDLEDGVPPDEKDEAREDLAEALRSIRAARAAGSEIIVRVNSLDSPHIERDLEALDAG   84 (221)
T ss_dssp             ESTSHHHHHHHHTTC--SSEEEEESSTTSSGGGHHHHHHHHHHHHHHHHHHTTSSSEEEEE-SSTTCHHHHHHHHHHHTT
T ss_pred             eCCCHHHHHHHHhcC--CCEEEEeCcccCCcccchhhHHHHHHHHHhhcccccccccceecCCCCCcchhhhhhhhcccC
Confidence            345556677776655  999999998755         344445555542  22345555444444444555   99999


Q ss_pred             cceEEeCC-CCHHHHHHHHHHH
Q 027234           74 ACDYLTKP-VRIEELKNIWQHV   94 (226)
Q Consensus        74 a~~yl~KP-~~~~~L~~~l~~~   94 (226)
                      +++.+..= -+.+++...++.+
T Consensus        85 ~~gI~lP~ves~~~~~~~~~~~  106 (221)
T PF03328_consen   85 ADGIVLPKVESAEDARQAVAAL  106 (221)
T ss_dssp             SSEEEETT--SHHHHHHHHHHH
T ss_pred             CCeeeccccCcHHHHHHHHHHH
Confidence            99987544 4677777766654

1.2 from EC) and 4-hydroxy-2-oxovalerate aldolase (4.1.2 from EC). ; GO: 0016830 carbon-carbon lyase activity, 0006725 cellular aromatic compound metabolic process; PDB: 1DXF_B 1DXE_A 3QZ6_A 3QLL_C 3QQW_F 3OYZ_A 3PUG_A 3OYX_A 1IZC_A 2V5K_B ....

>TIGR01361 DAHP_synth_Bsub phospho-2-dehydro-3-deoxyheptonate aldolase

Probab=81.89  E-value=18  Score=29.73  Aligned_cols=84  Identities=12%  Similarity=0.193  Sum_probs=51.6

Q ss_pred             CHHHHHHHHHhCCCCceEEEEccCC----CC---CCHHHHHHHHhcCCCCcEEEEeccC-C-----HHHHHHHHhCCcce
Q 027234           10 RAEIALDMLRTNKNGYDIVISDVHM----PD---MDGFKLLELVGLEMDLPVIMMCAHG-S-----KEVVMKGVTHDACD   76 (226)
Q Consensus        10 ~~~eal~~l~~~~~~~DlVl~D~~m----p~---~dG~~l~~~l~~~~~~pvI~ls~~~-~-----~~~~~~a~~~ga~~   76 (226)
                      +...|++.+.+. +..+++||.-..    |.   .--+..+..+++.++.||++=+.+. .     ......|..+||++
T Consensus       147 e~~~Ave~i~~~-Gn~~i~l~~rG~s~y~~~~~~~~dl~~i~~lk~~~~~pV~~ds~Hs~G~r~~~~~~~~aAva~Ga~g  225 (260)
T TIGR01361       147 EWLYAAEYILSS-GNGNVILCERGIRTFEKATRNTLDLSAVPVLKKETHLPIIVDPSHAAGRRDLVIPLAKAAIAAGADG  225 (260)
T ss_pred             HHHHHHHHHHHc-CCCcEEEEECCCCCCCCCCcCCcCHHHHHHHHHhhCCCEEEcCCCCCCccchHHHHHHHHHHcCCCE
Confidence            355677888754 346899988522    21   1223444566655678988745543 2     35566799999998


Q ss_pred             -EEeCC-------------CCHHHHHHHHHHH
Q 027234           77 -YLTKP-------------VRIEELKNIWQHV   94 (226)
Q Consensus        77 -yl~KP-------------~~~~~L~~~l~~~   94 (226)
                       +|.|=             +++++|...++.+
T Consensus       226 l~iE~H~t~d~a~~D~~~sl~p~~l~~lv~~i  257 (260)
T TIGR01361       226 LMIEVHPDPEKALSDSKQQLTPEEFKRLVKEL  257 (260)
T ss_pred             EEEEeCCCccccCCcchhcCCHHHHHHHHHHH
Confidence             66662             5556666555543

The member of this family from Synechocystis PCC 6803, CcmA, was shown to be essential for carboxysome formation. However, no other candidate for this enzyme is present in that species, chorismate biosynthesis does occur, other species having this protein lack carboxysomes but appear to make chorismate, and a requirement of CcmA for carboxysome formation does not prohibit a role in chorismate biosynthesis.

>TIGR01305 GMP_reduct_1 guanosine monophosphate reductase, eukaryotic

Probab=81.78  E-value=9.8  Score=32.45  Aligned_cols=57  Identities=16%  Similarity=0.029  Sum_probs=41.9

Q ss_pred             CceEEEEccCCCCCCH-HHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEeC
Q 027234           24 GYDIVISDVHMPDMDG-FKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTK   80 (226)
Q Consensus        24 ~~DlVl~D~~mp~~dG-~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~K   80 (226)
                      .+|+|++|.--..... ++.+++|+....-+.|+--.-...+.+..++.+|||+...-
T Consensus       121 ~~d~iviD~AhGhs~~~i~~ik~ir~~~p~~~viaGNV~T~e~a~~Li~aGAD~ikVg  178 (343)
T TIGR01305       121 QLKFICLDVANGYSEHFVEFVKLVREAFPEHTIMAGNVVTGEMVEELILSGADIVKVG  178 (343)
T ss_pred             CCCEEEEECCCCcHHHHHHHHHHHHhhCCCCeEEEecccCHHHHHHHHHcCCCEEEEc
Confidence            4899999997765443 67788888554334444444677889999999999998644

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.

>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT)

Probab=81.42  E-value=1.3  Score=30.88  Aligned_cols=28  Identities=29%  Similarity=0.288  Sum_probs=20.8

Q ss_pred             HHHHhhCCCCCCHHHHHHHhhhhhhhhh
Q 027234          180 KILELMNIPGLTRENVASHLQKHRLYLS  207 (226)
Q Consensus       180 ~I~~~~~~~~lt~~~va~~l~~~r~~l~  207 (226)
                      .+++.+-.++++..+||..+++||...|
T Consensus        24 ~~l~lyy~eDlSlsEIAe~~~iSRqaV~   51 (101)
T PF04297_consen   24 EILELYYEEDLSLSEIAEELGISRQAVY   51 (101)
T ss_dssp             HHHHHHCTS---HHHHHHHCTS-HHHHH
T ss_pred             HHHHHHHccCCCHHHHHHHHCCCHHHHH
Confidence            5778888889999999999999999765

Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.

>PRK14996 TetR family transcriptional regulator; Provisional

Probab=81.20  E-value=1.7  Score=33.49  Aligned_cols=42  Identities=12%  Similarity=0.040  Sum_probs=32.5

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .++.+.++.+          +...-.-.+.|+++||.+.|+||..+|+-|+.
T Consensus        10 R~~Il~aA~~----------lf~e~G~~~tSi~~Ia~~aGvsk~~lY~~F~s   51 (192)
T PRK14996         10 REVILQAAMR----------VALAEGFAAMTVRRIASEAQVAAGQVHHHFSS   51 (192)
T ss_pred             HHHHHHHHHH----------HHHhcChhhccHHHHHHHhCCCcHHHHHHcCC
Confidence            4566677666          33444566889999999999999999998874

>PRK08385 nicotinate-nucleotide pyrophosphorylase; Provisional

Probab=81.05  E-value=14  Score=30.75  Aligned_cols=69  Identities=16%  Similarity=0.096  Sum_probs=46.8

Q ss_pred             EEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhc-C-CCCcEEEEeccCCHHHHHHHHhCCcceEE
Q 027234            6 TKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGL-E-MDLPVIMMCAHGSKEVVMKGVTHDACDYL   78 (226)
Q Consensus         6 ~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~-~-~~~pvI~ls~~~~~~~~~~a~~~ga~~yl   78 (226)
                      +.+.+.+++.+.+...   +|+|++|-..|. +=-+..+.++. . ..-..+..|+.-+.+.+....+.|+|.+-
T Consensus       187 VEv~~leea~~a~~ag---aDiI~LDn~~~e-~l~~~v~~l~~~~~~~~~~leaSGGI~~~ni~~yA~tGvD~Is  257 (278)
T PRK08385        187 VEVESLEDALKAAKAG---ADIIMLDNMTPE-EIREVIEALKREGLRERVKIEVSGGITPENIEEYAKLDVDVIS  257 (278)
T ss_pred             EEeCCHHHHHHHHHcC---cCEEEECCCCHH-HHHHHHHHHHhcCcCCCEEEEEECCCCHHHHHHHHHcCCCEEE
Confidence            4788999999998743   799999955433 11122233332 1 12345678888899999999999988654

>TIGR00122 birA_repr_reg BirA biotin operon repressor domain

Probab=81.04  E-value=0.54  Score=30.03  Aligned_cols=29  Identities=17%  Similarity=0.304  Sum_probs=24.4

Q ss_pred             HHHHhhCCCCCCHHHHHHHhhhhhhhhhc
Q 027234          180 KILELMNIPGLTRENVASHLQKHRLYLSR  208 (226)
Q Consensus       180 ~I~~~~~~~~lt~~~va~~l~~~r~~l~r  208 (226)
                      .|++.+.+...+..++|.++++||+..++
T Consensus         4 ~il~~L~~~~~~~~eLa~~l~vS~~tv~~   32 (69)
T TIGR00122         4 RLLALLADNPFSGEKLGEALGMSRTAVNK   32 (69)
T ss_pred             HHHHHHHcCCcCHHHHHHHHCCCHHHHHH
Confidence            46667777788999999999999998776

This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.

>PF01729 QRPTase_C: Quinolinate phosphoribosyl transferase, C-terminal domain; InterPro: IPR002638 Quinolinate phosphoribosyl transferase (QPRTase) or nicotinate-nucleotide pyrophosphorylase 2

Probab=80.70  E-value=5.8  Score=30.35  Aligned_cols=69  Identities=16%  Similarity=-0.006  Sum_probs=45.8

Q ss_pred             EEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEE
Q 027234            6 TKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYL   78 (226)
Q Consensus         6 ~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl   78 (226)
                      ..+.+.+++.+.++..   +|+|.+|-.-| .+=-++.+.++....-..|..|+.-+.+.+.+..+.|+|.+-
T Consensus        85 VEv~~~ee~~ea~~~g---~d~I~lD~~~~-~~~~~~v~~l~~~~~~v~ie~SGGI~~~ni~~ya~~gvD~is  153 (169)
T PF01729_consen   85 VEVENLEEAEEALEAG---ADIIMLDNMSP-EDLKEAVEELRELNPRVKIEASGGITLENIAEYAKTGVDVIS  153 (169)
T ss_dssp             EEESSHHHHHHHHHTT----SEEEEES-CH-HHHHHHHHHHHHHTTTSEEEEESSSSTTTHHHHHHTT-SEEE
T ss_pred             EEcCCHHHHHHHHHhC---CCEEEecCcCH-HHHHHHHHHHhhcCCcEEEEEECCCCHHHHHHHHhcCCCEEE
Confidence            4688899999998853   89999996544 112223334443333367778888888888888899987654

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 ....

>TIGR00693 thiE thiamine-phosphate pyrophosphorylase

Probab=80.67  E-value=16  Score=28.24  Aligned_cols=69  Identities=16%  Similarity=0.193  Sum_probs=47.9

Q ss_pred             EECCHHHHHHHHHhCCCCceEEEEccCCCC--------CCHHHHHHHHhc-CCCCcEEEEeccCCHHHHHHHHhCCcceE
Q 027234            7 KCNRAEIALDMLRTNKNGYDIVISDVHMPD--------MDGFKLLELVGL-EMDLPVIMMCAHGSKEVVMKGVTHDACDY   77 (226)
Q Consensus         7 ~~~~~~eal~~l~~~~~~~DlVl~D~~mp~--------~dG~~l~~~l~~-~~~~pvI~ls~~~~~~~~~~a~~~ga~~y   77 (226)
                      .|.+..++.+..+   .++|.|.++-..|.        ..|++.++.+.. .+.+||+++.+- +.+.+.+++..|++++
T Consensus       102 s~h~~~e~~~a~~---~g~dyi~~~~v~~t~~k~~~~~~~g~~~l~~~~~~~~~~pv~a~GGI-~~~~~~~~~~~G~~gv  177 (196)
T TIGR00693       102 STHNLEELAEAEA---EGADYIGFGPIFPTPTKKDPAPPAGVELLREIAATSIDIPIVAIGGI-TLENAAEVLAAGADGV  177 (196)
T ss_pred             eCCCHHHHHHHhH---cCCCEEEECCccCCCCCCCCCCCCCHHHHHHHHHhcCCCCEEEECCc-CHHHHHHHHHcCCCEE
Confidence            4556677665443   23899988765542        247888888763 356898777654 5788888889999887


Q ss_pred             Ee
Q 027234           78 LT   79 (226)
Q Consensus        78 l~   79 (226)
                      ..
T Consensus       178 a~  179 (196)
T TIGR00693       178 AV  179 (196)
T ss_pred             EE
Confidence            63

This model includes ThiE from Bacillus subtilis but excludes its paralog, the regulatory protein TenI, and neighbors of TenI.

>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein

Probab=80.50  E-value=0.68  Score=29.98  Aligned_cols=24  Identities=33%  Similarity=0.217  Sum_probs=21.2

Q ss_pred             CCCHHHHHHHhhhhhhhhhcccCC
Q 027234          189 GLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       189 ~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      ++++++||.++++++.+|+|+|+.
T Consensus         1 ~~~~~~la~~~~~s~~~l~~~f~~   24 (84)
T smart00342        1 PLTLEDLAEALGMSPRHLQRLFKK   24 (84)
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHHH
Confidence            478999999999999999997764

>cd00452 KDPG_aldolase KDPG and KHG aldolase

Probab=80.49  E-value=12  Score=29.07  Aligned_cols=68  Identities=10%  Similarity=-0.046  Sum_probs=50.0

Q ss_pred             EECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhc-CCCCcEEEEeccCCHHHHHHHHhCCcceEEeC
Q 027234            7 KCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGL-EMDLPVIMMCAHGSKEVVMKGVTHDACDYLTK   80 (226)
Q Consensus         7 ~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~-~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~K   80 (226)
                      -+.+.+|+.+.++.   ++|.|-++- .+.. |.++++.++. .+.+|++.+.+ -+.+.....++.|+++.-.-
T Consensus       103 gv~t~~e~~~A~~~---Gad~i~~~p-~~~~-g~~~~~~l~~~~~~~p~~a~GG-I~~~n~~~~~~~G~~~v~v~  171 (190)
T cd00452         103 GVATPTEIMQALEL---GADIVKLFP-AEAV-GPAYIKALKGPFPQVRFMPTGG-VSLDNAAEWLAAGVVAVGGG  171 (190)
T ss_pred             CcCCHHHHHHHHHC---CCCEEEEcC-Cccc-CHHHHHHHHhhCCCCeEEEeCC-CCHHHHHHHHHCCCEEEEEc
Confidence            45688898888763   389998853 3333 9999999874 34688776655 48889999999998876643

This family belongs to the class I adolases whose reaction mechanism involves Schiff base formation between a substrate carbonyl and lysine residue in the active site. 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase, is best known for its role in the Entner-Doudoroff pathway of bacteria, where it catalyzes the reversible cleavage of KDPG to pyruvate and glyceraldehyde-3-phosphate. 2-keto-4-hydroxyglutarate (KHG) aldolase, which has enzymatic specificity toward glyoxylate, forming KHG in the presence of pyruvate, and is capable of regulating glyoxylate levels in the glyoxylate bypass, an alternate pathway when bacteria are grown on acetate carbon sources.

>PRK09480 slmA division inhibitor protein; Provisional

Probab=80.35  E-value=2.7  Score=32.14  Aligned_cols=44  Identities=16%  Similarity=0.117  Sum_probs=34.0

Q ss_pred             hhHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          159 ELHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       159 ~l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .-.++.+.++..         .+.+.-. .+.|+++||.+.|+||..+|+-|+.
T Consensus        10 ~~r~~Il~aa~~---------l~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~   53 (194)
T PRK09480         10 ERREQILQALAQ---------MLESPPG-ERITTAKLAARVGVSEAALYRHFPS   53 (194)
T ss_pred             hHHHHHHHHHHH---------HHHhcCC-CccCHHHHHHHhCCCHhHHHHHCCC
Confidence            345677777777         2445423 5999999999999999999998875

>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain

Probab=80.34  E-value=2.5  Score=28.92  Aligned_cols=46  Identities=13%  Similarity=0.119  Sum_probs=31.8

Q ss_pred             HHHHHHHHhCCCCCCchHHHHhh--------CCCCCCHHHHHHHhhhhhhhhhc
Q 027234          163 QFVSAVKELGFDKAGPKKILELM--------NIPGLTRENVASHLQKHRLYLSR  208 (226)
Q Consensus       163 ~Fi~~~~~~g~~~~~p~~I~~~~--------~~~~lt~~~va~~l~~~r~~l~r  208 (226)
                      .+++.+..+++....-+.++.+.        ..+.+|..++|+.++++|..+.|
T Consensus        13 ~~~e~l~~~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr   66 (95)
T TIGR01610        13 ELQEALPGADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSD   66 (95)
T ss_pred             HHHHHHHhCCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHH
Confidence            44444445555544444444443        46689999999999999998887

This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.

>PRK00767 transcriptional regulator BetI; Validated

Probab=80.29  E-value=2.7  Score=32.22  Aligned_cols=43  Identities=16%  Similarity=0.105  Sum_probs=33.6

Q ss_pred             hHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          160 LHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       160 l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      -.++.+.++.+          +...-...+.|.+.||++.|+++..+|+-|+.
T Consensus        10 ~r~~Il~aA~~----------lf~~~G~~~~s~~~Ia~~aGvs~gslY~~F~~   52 (197)
T PRK00767         10 RRQQLIDATLR----------AIGEVGLLDATIAQIARRAGVSTGIISHYFGG   52 (197)
T ss_pred             HHHHHHHHHHH----------HHHHcCcccCCHHHHHHHhCCCHHHHHHHhCC
Confidence            34567777776          44444566889999999999999999998864

>PRK13756 tetracycline repressor protein TetR; Provisional

Probab=80.24  E-value=2.4  Score=33.50  Aligned_cols=42  Identities=21%  Similarity=0.264  Sum_probs=33.6

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .++++.++.+          +++.-..+++|+..||.++++++..+|+-|+.
T Consensus         6 re~Il~aA~~----------l~~e~G~~~lsmr~lA~~lgv~~~slY~hf~~   47 (205)
T PRK13756          6 KEKVIDSALE----------LLNEVGIEGLTTRKLAQKLGVEQPTLYWHVKN   47 (205)
T ss_pred             HHHHHHHHHH----------HHHHcCcccCCHHHHHHHhCCCchHHHHHcCC
Confidence            3566677666          55555677899999999999999999998764

>PRK02083 imidazole glycerol phosphate synthase subunit HisF; Provisional

Probab=80.12  E-value=30  Score=28.03  Aligned_cols=80  Identities=21%  Similarity=0.224  Sum_probs=52.8

Q ss_pred             HHHHHHHHHhCCCCce-EEEEccCC-CCCCH--HHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhC-CcceEEe------
Q 027234           11 AEIALDMLRTNKNGYD-IVISDVHM-PDMDG--FKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTH-DACDYLT------   79 (226)
Q Consensus        11 ~~eal~~l~~~~~~~D-lVl~D~~m-p~~dG--~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~-ga~~yl~------   79 (226)
                      ..+..+.+....  ++ ++++|+.- ..+.|  +++++.+.+...+|+|.-.+-.+.+...++++. |+++.+.      
T Consensus       155 ~~~~~~~~~~~g--~~~ii~~~i~~~g~~~g~d~~~i~~~~~~~~ipvia~GGv~s~~d~~~~~~~~G~~gvivg~al~~  232 (253)
T PRK02083        155 AVEWAKEVEELG--AGEILLTSMDRDGTKNGYDLELTRAVSDAVNVPVIASGGAGNLEHFVEAFTEGGADAALAASIFHF  232 (253)
T ss_pred             HHHHHHHHHHcC--CCEEEEcCCcCCCCCCCcCHHHHHHHHhhCCCCEEEECCCCCHHHHHHHHHhCCccEEeEhHHHHc
Confidence            344555555433  65 66766542 11222  667788876668999988888889999999975 9988775      


Q ss_pred             CCCCHHHHHHHHH
Q 027234           80 KPVRIEELKNIWQ   92 (226)
Q Consensus        80 KP~~~~~L~~~l~   92 (226)
                      .-++..+++..++
T Consensus       233 ~~~~~~~~~~~~~  245 (253)
T PRK02083        233 GEITIGELKAYLA  245 (253)
T ss_pred             CCCCHHHHHHHHH
Confidence            3466666655443

>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function

Probab=80.06  E-value=1.4  Score=29.80  Aligned_cols=42  Identities=17%  Similarity=0.184  Sum_probs=35.0

Q ss_pred             HHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCCCCCCCCCCCC
Q 027234          180 KILELMNIPGLTRENVASHLQKHRLYLSRLSGVSPQQGNSFVS  222 (226)
Q Consensus       180 ~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~~~~~~~~~~~  222 (226)
                      .+.+|+...++|.++||..|+.|-.++.++....+.. +..||
T Consensus        14 ELq~nf~~~~ls~~~ia~dL~~s~~~le~vL~l~~~~-~~~vW   55 (89)
T PF10078_consen   14 ELQANFELSGLSLEQIAADLGTSPEHLEQVLNLKQPF-PEDVW   55 (89)
T ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCC-cccch
Confidence            4677888889999999999999999999998888554 44455

>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B

Probab=80.02  E-value=0.87  Score=28.37  Aligned_cols=30  Identities=30%  Similarity=0.438  Sum_probs=21.5

Q ss_pred             HHHhhCCCCCCHHHHHHHhhhhhhhhhccc
Q 027234          181 ILELMNIPGLTRENVASHLQKHRLYLSRLS  210 (226)
Q Consensus       181 I~~~~~~~~lt~~~va~~l~~~r~~l~r~~  210 (226)
                      |.+.+..-++|+.++|..+++++++++++-
T Consensus         4 lk~~r~~~~lt~~~~a~~~~i~~~~i~~~e   33 (64)
T PF12844_consen    4 LKELREEKGLTQKDLAEKLGISRSTISKIE   33 (64)
T ss_dssp             HHHHHHHCT--HHHHHHHHTS-HHHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHCcCHHHHHHHH
Confidence            444555669999999999999999999863

>PRK04180 pyridoxal biosynthesis lyase PdxS; Provisional

Probab=80.01  E-value=11  Score=31.36  Aligned_cols=94  Identities=12%  Similarity=0.031  Sum_probs=65.9

Q ss_pred             EECCHHHHHHHHHhCCCCceEEEEc------------------------cC-CC----------CCCHHHHHHHHhcCCC
Q 027234            7 KCNRAEIALDMLRTNKNGYDIVISD------------------------VH-MP----------DMDGFKLLELVGLEMD   51 (226)
Q Consensus         7 ~~~~~~eal~~l~~~~~~~DlVl~D------------------------~~-mp----------~~dG~~l~~~l~~~~~   51 (226)
                      -|++..||+..+...   +|+|=+-                        +. +.          ...++++++.+++...
T Consensus       127 d~~~l~EAlrai~~G---admI~Ttge~gtg~v~~av~h~r~~~~~i~~L~gyt~~~~~~~a~~~~~~~elL~ei~~~~~  203 (293)
T PRK04180        127 GARNLGEALRRIAEG---AAMIRTKGEAGTGNVVEAVRHMRQINGEIRRLTSMSEDELYTAAKELQAPYELVKEVAELGR  203 (293)
T ss_pred             cCCCHHHHHHHHHCC---CCeeeccCCCCCccHHHHHHHHHHHHHHHHHHhCCCHHHHHhhccccCCCHHHHHHHHHhCC
Confidence            467888888887753   6877665                        11 11          1247888888876667


Q ss_pred             CcEE--EEeccCCHHHHHHHHhCCcceEE-----eCCCCHHHHHHHHHHHHHHHhhhhh
Q 027234           52 LPVI--MMCAHGSKEVVMKGVTHDACDYL-----TKPVRIEELKNIWQHVVRKRKNERK  103 (226)
Q Consensus        52 ~pvI--~ls~~~~~~~~~~a~~~ga~~yl-----~KP~~~~~L~~~l~~~~~~~~~~~~  103 (226)
                      +|||  ...+-..++.+..++++||++++     .|.-++......+...+........
T Consensus       204 iPVV~~AeGGI~TPedaa~vme~GAdgVaVGSaI~ks~dP~~~akafv~ai~~~~~~~~  262 (293)
T PRK04180        204 LPVVNFAAGGIATPADAALMMQLGADGVFVGSGIFKSGDPEKRARAIVEATTHYDDPEV  262 (293)
T ss_pred             CCEEEEEeCCCCCHHHHHHHHHhCCCEEEEcHHhhcCCCHHHHHHHHHHHHHHcCCHHH
Confidence            9998  56666689999999999999987     3455777777777776655444333

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	226
1irz_A	64	Solution Structure Of Arr10-B Belonging To The Garp		4e-16
1l5y_A	155	Crystal Structure Of Mg2+ / Bef3-bound Receiver Dom		4e-10
1qkk_A	155	Crystal Structure Of The Receiver Domain And Linker		8e-10
3ffx_A	128	Crystal Structure Of Chey Triple Mutant F14e, N59r,		4e-08
1ymv_A	129	Signal Transduction Protein Chey Mutant With Phe 14		2e-07
3ffw_A	128	Crystal Structure Of Chey Triple Mutant F14q, N59k,		2e-07
1hey_A	128	Investigating The Structural Determinants Of The P2		2e-07
1d4z_A	128	Crystal Structure Of Chey-95iv, A Hyperactive Chey		2e-07
1ymu_A	130	Signal Transduction Protein Chey Mutant With Met 17		2e-07
1cye_A	129	Three Dimensional Structure Of Chemotactic Che Y Pr		2e-07
1ab5_A	125	Structure Of Chey Mutant F14n, V21t Length = 125		2e-07
1ehc_A	128	Structure Of Signal Transduction Protein Chey Lengt		2e-07
3fft_A	128	Crystal Structure Of Chey Double Mutant F14e, E89r		2e-07
1e6l_A	127	Two-Component Signal Transduction System D13a Mutan		2e-07
1eay_A	128	Chey-Binding (P2) Domain Of Chea In Complex With Ch		2e-07
3rvn_A	132	Structure Of The Chey-Bef3 Complex With Substitutio		2e-07
1e6k_A	130	Two-Component Signal Transduction System D12a Mutan		3e-07
1cey_A	128	Assignments, Secondary Structure, Global Fold, And		3e-07
1djm_A	129	Solution Structure Of Bef3-Activated Chey From Esch		3e-07
1vlz_A	128	Uncoupled Phosphorylation And Activation In Bacteri		3e-07
1ab6_A	125	Structure Of Chey Mutant F14n, V86t Length = 125		3e-07
3myy_A	128	Structure Of E. Coli Chey Mutant A113p Bound To Ber		3e-07
1mih_A	129	A Role For Chey Glu 89 In Chez-Mediated Dephosphory		4e-07
3oo0_A	129	Structure Of Apo Chey A113p Length = 129		4e-07
3rvj_A	132	Structure Of The Chey-Bef3 Complex With Substitutio		4e-07
3fgz_A	128	Crystal Structure Of Chey Triple Mutant F14e, N59m,		5e-07
3rvl_A	132	Structure Of The Chey-Bef3 Complex With Substitutio		5e-07
3rvp_A	132	Structure Of The Chey-Bef3 Complex With Substitutio		6e-07
2ayx_A	254	Solution Structure Of The E.Coli Rcsc C-Terminus (R		6e-07
1dbw_A	126	Crystal Structure Of Fixj-N Length = 126		7e-07
3olx_A	129	Structural And Functional Effects Of Substitution A		8e-07
5chy_A	128	Structure Of Chemotaxis Protein Chey Length = 128		8e-07
6chy_A	128	Structure Of Chemotaxis Protein Chey Length = 128		9e-07
2ayz_A	133	Solution Structure Of The E.Coli Rcsc C-Terminus (R		9e-07
3f7n_A	128	Crystal Structure Of Chey Triple Mutant F14e, N59m,		9e-07
3olw_A	129	Structural And Functional Effects Of Substitution A		1e-06
3olv_A	129	Structural And Functional Effects Of Substitution A		1e-06
1jbe_A	128	1.08 A Structure Of Apo-Chey Reveals Meta-Active Co		2e-06
1e6m_A	128	Two-Component Signal Transduction System D57a Mutan		2e-06
3oly_A	129	Structural And Functional Effects Of Substitution A		2e-06
1c4w_A	128	1.9 A Structure Of A-Thiophosphonate Modified Chey		2e-06
1dc7_A	124	Structure Of A Transiently Phosphorylated "switch"		2e-06
1zdm_A	129	Crystal Structure Of Activated Chey Bound To Xe Len		2e-06
1j56_A	124	Minimized Average Structure Of Beryllofluoride-Acti		2e-06
3r0j_A	250	Structure Of Phop From Mycobacterium Tuberculosis L		2e-06
1krw_A	124	Solution Structure And Backbone Dynamics Of Beryllo		2e-06
2id7_A	128	1.75 A Structure Of T87i Phosphono-Chey Length = 12		2e-06
2che_A	128	Structure Of The Mg2+-Bound Form Of Chey And Mechan		4e-06
1d5w_A	126	Phosphorylated Fixj Receiver Domain Length = 126		5e-06
2fka_A	129	Crystal Structure Of Mg(2+) And Bef(3)(-)-Bound Che		5e-06
2id9_A	128	1.85 A Structure Of T87iY106W PHOSPHONO-Chey Length		6e-06
1udr_A	129	Chey Mutant With Lys 91 Replaced By Asp, Lys 92 Rep		1e-05
1dc8_A	124	Structure Of A Transiently Phosphorylated "switch"		1e-05
3t6k_A	136	Crystal Structure Of A Hypothetical Response Regula		2e-05
2chy_A	128	Three-Dimensional Structure Of Chey, The Response R		2e-05
1u8t_A	128	Crystal Structure Of Chey D13k Y106w Alone And In C		3e-05
3jte_A	143	Crystal Structure Of Response Regulator Receiver Do		4e-05
1p6u_A	129	Nmr Structure Of The Bef3-Activated Structure Of Th		4e-05
1ys6_A	233	Crystal Structure Of The Response Regulatory Protei		5e-05
2oqr_A	230	The Structure Of The Response Regulator Regx3 From		7e-05
3nnn_A	122	Bef3 Activated Drrd Receiver Domain Length = 122		2e-04
3to5_A	134	High Resolution Structure Of Chey3 From Vibrio Chol		2e-04
1yio_A	208	Crystallographic Structure Of Response Regulator St		2e-04
1zes_A	125	Bef3- Activated Phob Receiver Domain Length = 125		2e-04
1b00_A	127	Phob Receiver Domain From Escherichia Coli Length =		2e-04
1dz3_A	130	Domain-Swapping In The Sporulation Response Regulat		2e-04
3gt7_A	154	Crystal Structure Of Signal Receiver Domain Of Sign		3e-04
1nxo_A	120	Micarec Ph7.0 Length = 120		3e-04
2pkx_A	121	E.Coli Response Regulator Phop Receiver Domain Leng		4e-04
3cfy_A	137	Crystal Structure Of Signal Receiver Domain Of Puta		4e-04
3q9s_A	249	Crystal Structure Of Rra(1-215) From Deinococcus Ra		5e-04
1zit_A	121	Structure Of The Receiver Domain Of Ntrc4 From Aqui		5e-04
1kgs_A	225	Crystal Structure At 1.50 A Of An OmprPHOB HOMOLOG		6e-04
3cu5_A	141	Crystal Structure Of A Two Component Transcriptiona		7e-04
2jb9_A	127	Phob Response Regulator Receiver Domain Constitutiv		8e-04
2zwm_A	130	Crystal Structure Of Yycf Receiver Domain From Baci		9e-04

>pdb|1IRZ|A Chain A, Solution Structure Of Arr10-B Belonging To The Garp Family Of Plant Myb-Related Dna Binding Motifs Of The Arabidopsis Response Regulators Length = 64

Iteration: 1
 Score = 81.3 bits (199), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 37/61 (60%), Positives = 50/61 (81%)
Query: 150 KKPRLVWSVELHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRL 209
           KKPR++W+ ELH +F++AV  LG ++A PKKIL+LMN+  LTRENVASHLQK R+ L ++
Sbjct: 4   KKPRVLWTHELHNKFLAAVDHLGVERAVPKKILDLMNVDKLTRENVASHLQKFRVALKKV 63
Query: 210 S 210
           S
Sbjct: 64  S 64

>pdb|1L5Y|A Chain A, Crystal Structure Of Mg2+ / Bef3-bound Receiver Domain Of Sinorhizobium Meliloti Dctd Length = 155

Iteration: 1
 Score = 61.2 bits (147), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 33/99 (33%), Positives = 54/99 (54%), Gaps = 3/99 (3%)
Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLL-ELVGLEMDLPVIMMCAH 60
           GF+V+    A  AL  L  +  G  IVISD+ MP MDG  L  +++ L+ DLP+I++  H
Sbjct: 27  GFTVSSFASATEALAGLSADFAG--IVISDIRMPGMDGLALFRKILALDPDLPMILVTGH 84
Query: 61  GSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRK 99
           G   + ++ +   A D++ KP   + L    +   +KR+
Sbjct: 85  GDIPMAVQAIQDGAYDFIAKPFAADRLVQSARRAEKKRR 123

>pdb|1QKK|A Chain A, Crystal Structure Of The Receiver Domain And Linker Region Of Dctd From Sinorhizobium Meliloti Length = 155

Iteration: 1
 Score = 60.5 bits (145), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 33/99 (33%), Positives = 53/99 (53%), Gaps = 3/99 (3%)
Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLL-ELVGLEMDLPVIMMCAH 60
           GF+V+    A  AL  L  +  G  IVISD+ MP MDG  L  +++ L+ DLP+I++  H
Sbjct: 27  GFTVSSFASATEALAGLSADFAG--IVISDIRMPGMDGLALFRKILALDPDLPMILVTGH 84
Query: 61  GSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRK 99
           G   + ++ +   A D++ KP   + L    +    KR+
Sbjct: 85  GDIPMAVQAIQDGAYDFIAKPFAADRLVQSARRAEEKRR 123

>pdb|3FFX|A Chain A, Crystal Structure Of Chey Triple Mutant F14e, N59r, E89h Complexed With Bef3- And Mn2+ Length = 128

Iteration: 1
 Score = 54.7 bits (130), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 34/101 (33%), Positives = 49/101 (48%), Gaps = 6/101 (5%)
Query: 1   MGFSVTKCNRAEIALDML-RTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIM 56
           +GF+      AE  +D L +    GY  VISD  MP+MDG +LL+ +   G    LPV+M
Sbjct: 27  LGFN--NVEEAEDGVDALNKLQAGGYGFVISDWRMPNMDGLELLKTIRADGAMSALPVLM 84
Query: 57  MCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
           + AH  KE ++      A  Y+ KP     L+     +  K
Sbjct: 85  VTAHAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEK 125

>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 = 52.8 bits (125), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 33/101 (32%), Positives = 49/101 (48%), Gaps = 6/101 (5%)
Query: 1   MGFSVTKCNRAEIALDML-RTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIM 56
           +GF+      AE  +D L +    GY  VISD +MP+MDG +LL+ +   G    LPV+M
Sbjct: 28  LGFN--NVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGAMSALPVLM 85
Query: 57  MCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
           + A   KE ++      A  Y+ KP     L+     +  K
Sbjct: 86  VTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEK 126

>pdb|3FFW|A Chain A, Crystal Structure Of Chey Triple Mutant F14q, N59k, E89y Complexed With Bef3- And Mn2+ Length = 128

Iteration: 1
 Score = 52.8 bits (125), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 33/101 (32%), Positives = 49/101 (48%), Gaps = 6/101 (5%)
Query: 1   MGFSVTKCNRAEIALDML-RTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIM 56
           +GF+      AE  +D L +    GY  VISD  MP+MDG +LL+ +   G    LPV+M
Sbjct: 27  LGFN--NVEEAEDGVDALNKLQAGGYGFVISDWKMPNMDGLELLKTIRADGAMSALPVLM 84
Query: 57  MCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
           + A+  KE ++      A  Y+ KP     L+     +  K
Sbjct: 85  VTAYAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEK 125

>pdb|1HEY|A Chain A, Investigating The Structural Determinants Of The P21-Like Triphosphate And Mg2+ Binding Site Length = 128

Iteration: 1
 Score = 52.8 bits (125), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 33/101 (32%), Positives = 49/101 (48%), Gaps = 6/101 (5%)
Query: 1   MGFSVTKCNRAEIALDML-RTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIM 56
           +GF+      AE  +D L +    GY  VISD +MP+MDG +LL+ +   G    LPV+M
Sbjct: 27  LGFN--NVEDAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGAMSALPVLM 84
Query: 57  MCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
           + A   KE ++      A  Y+ KP     L+     +  K
Sbjct: 85  VTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEK 125

>pdb|1D4Z|A Chain A, Crystal Structure Of Chey-95iv, A Hyperactive Chey Mutant Length = 128

Iteration: 1
 Score = 52.8 bits (125), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 34/101 (33%), Positives = 49/101 (48%), Gaps = 6/101 (5%)
Query: 1   MGFSVTKCNRAEIALDML-RTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIM 56
           +GF+      AE  +D L +    GY  VISD +MP+MDG +LL+ +   G    LPV+M
Sbjct: 27  LGFN--NVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGAMSALPVLM 84
Query: 57  MCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
           + A   KE V+      A  Y+ KP     L+     +  K
Sbjct: 85  VTAEAKKENVIAAAQAGASGYVVKPFTAATLEEKLNKIFEK 125

>pdb|1YMU|A Chain A, Signal Transduction Protein Chey Mutant With Met 17 Replaced By Gly (M17g) Length = 130

Iteration: 1
 Score = 52.4 bits (124), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 33/101 (32%), Positives = 49/101 (48%), Gaps = 6/101 (5%)
Query: 1   MGFSVTKCNRAEIALDML-RTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIM 56
           +GF+      AE  +D L +    GY  VISD +MP+MDG +LL+ +   G    LPV+M
Sbjct: 29  LGFN--NVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGAMSALPVLM 86
Query: 57  MCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
           + A   KE ++      A  Y+ KP     L+     +  K
Sbjct: 87  VTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEK 127

>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 = 52.4 bits (124), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 33/101 (32%), Positives = 49/101 (48%), Gaps = 6/101 (5%)
Query: 1   MGFSVTKCNRAEIALDML-RTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIM 56
           +GF+      AE  +D L +    GY  VISD +MP+MDG +LL+ +   G    LPV+M
Sbjct: 28  LGFN--NVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGAMSALPVLM 85
Query: 57  MCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
           + A   KE ++      A  Y+ KP     L+     +  K
Sbjct: 86  VTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEK 126

>pdb|1AB5|A Chain A, Structure Of Chey Mutant F14n, V21t Length = 125

Iteration: 1
 Score = 52.4 bits (124), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 33/101 (32%), Positives = 49/101 (48%), Gaps = 6/101 (5%)
Query: 1   MGFSVTKCNRAEIALDML-RTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIM 56
           +GF+      AE  +D L +    GY  VISD +MP+MDG +LL+ +   G    LPV+M
Sbjct: 24  LGFN--NVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGAMSALPVLM 81
Query: 57  MCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
           + A   KE ++      A  Y+ KP     L+     +  K
Sbjct: 82  VTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEK 122

>pdb|1EHC|A Chain A, Structure Of Signal Transduction Protein Chey Length = 128

Iteration: 1
 Score = 52.4 bits (124), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 33/101 (32%), Positives = 49/101 (48%), Gaps = 6/101 (5%)
Query: 1   MGFSVTKCNRAEIALDML-RTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIM 56
           +GF+      AE  +D L +    GY  VISD +MP+MDG +LL+ +   G    LPV+M
Sbjct: 27  LGFN--NVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGAMSALPVLM 84
Query: 57  MCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
           + A   KE ++      A  Y+ KP     L+     +  K
Sbjct: 85  VTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEK 125

>pdb|3FFT|A Chain A, Crystal Structure Of Chey Double Mutant F14e, E89r Complexed With Bef3- And Mn2+ Length = 128

Iteration: 1
 Score = 52.0 bits (123), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 33/101 (32%), Positives = 49/101 (48%), Gaps = 6/101 (5%)
Query: 1   MGFSVTKCNRAEIALDML-RTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIM 56
           +GF+      AE  +D L +    GY  VISD +MP+MDG +LL+ +   G    LPV+M
Sbjct: 27  LGFN--NVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGAMSALPVLM 84
Query: 57  MCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
           + A   KE ++      A  Y+ KP     L+     +  K
Sbjct: 85  VTARAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEK 125

>pdb|1E6L|A Chain A, Two-Component Signal Transduction System D13a Mutant Of Chey Length = 127

Iteration: 1
 Score = 52.0 bits (123), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 33/101 (32%), Positives = 49/101 (48%), Gaps = 6/101 (5%)
Query: 1   MGFSVTKCNRAEIALDML-RTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIM 56
           +GF+      AE  +D L +    GY  VISD +MP+MDG +LL+ +   G    LPV+M
Sbjct: 26  LGFN--NVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGAMSALPVLM 83
Query: 57  MCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
           + A   KE ++      A  Y+ KP     L+     +  K
Sbjct: 84  VTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEK 124

>pdb|1EAY|A Chain A, Chey-Binding (P2) Domain Of Chea In Complex With Chey From Escherichia Coli Length = 128

Iteration: 1
 Score = 52.0 bits (123), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 33/101 (32%), Positives = 49/101 (48%), Gaps = 6/101 (5%)
Query: 1   MGFSVTKCNRAEIALDML-RTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIM 56
           +GF+      AE  +D L +    GY  VISD +MP+MDG +LL+ +   G    LPV+M
Sbjct: 27  LGFN--NVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGAMSALPVLM 84
Query: 57  MCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
           + A   KE ++      A  Y+ KP     L+     +  K
Sbjct: 85  VTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEK 125

>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 = 52.0 bits (123), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 33/101 (32%), Positives = 49/101 (48%), Gaps = 6/101 (5%)
Query: 1   MGFSVTKCNRAEIALDML-RTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIM 56
           +GF+      AE  +D L +    GY  VISD  MP+MDG +LL+ +   G    LPV+M
Sbjct: 31  LGFN--NVEEAEDGVDALNKLQAGGYGFVISDWDMPNMDGLELLKTIRADGAMSALPVLM 88
Query: 57  MCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
           + A+  KE ++      A  Y+ KP     L+     +  K
Sbjct: 89  VTAYAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEK 129

>pdb|1E6K|A Chain A, Two-Component Signal Transduction System D12a Mutant Of Chey Length = 130

Iteration: 1
 Score = 52.0 bits (123), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 33/101 (32%), Positives = 49/101 (48%), Gaps = 6/101 (5%)
Query: 1   MGFSVTKCNRAEIALDML-RTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIM 56
           +GF+      AE  +D L +    GY  VISD +MP+MDG +LL+ +   G    LPV+M
Sbjct: 29  LGFN--NVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGAMSALPVLM 86
Query: 57  MCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
           + A   KE ++      A  Y+ KP     L+     +  K
Sbjct: 87  VTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEK 127

>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 = 52.0 bits (123), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 33/101 (32%), Positives = 49/101 (48%), Gaps = 6/101 (5%)
Query: 1   MGFSVTKCNRAEIALDML-RTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIM 56
           +GF+      AE  +D L +    GY  VISD +MP+MDG +LL+ +   G    LPV+M
Sbjct: 27  LGFN--NVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGAMSALPVLM 84
Query: 57  MCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
           + A   KE ++      A  Y+ KP     L+     +  K
Sbjct: 85  VTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEK 125

>pdb|1DJM|A Chain A, Solution Structure Of Bef3-Activated Chey From Escherichia Coli Length = 129

Iteration: 1
 Score = 52.0 bits (123), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 33/101 (32%), Positives = 49/101 (48%), Gaps = 6/101 (5%)
Query: 1   MGFSVTKCNRAEIALDML-RTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIM 56
           +GF+      AE  +D L +    GY  VISD +MP+MDG +LL+ +   G    LPV+M
Sbjct: 28  LGFN--NVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGAMSALPVLM 85
Query: 57  MCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
           + A   KE ++      A  Y+ KP     L+     +  K
Sbjct: 86  VTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEK 126

>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 = 52.0 bits (123), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 33/101 (32%), Positives = 49/101 (48%), Gaps = 6/101 (5%)
Query: 1   MGFSVTKCNRAEIALDML-RTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIM 56
           +GF+      AE  +D L +    GY  VISD +MP+MDG +LL+ +   G    LPV+M
Sbjct: 27  LGFN--NVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGAMSALPVLM 84
Query: 57  MCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
           + A   KE ++      A  Y+ KP     L+     +  K
Sbjct: 85  VIAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEK 125

>pdb|1AB6|A Chain A, Structure Of Chey Mutant F14n, V86t Length = 125

Iteration: 1
 Score = 51.6 bits (122), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 33/101 (32%), Positives = 48/101 (47%), Gaps = 6/101 (5%)
Query: 1   MGFSVTKCNRAEIALDML-RTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIM 56
           +GF+      AE  +D L +    GY  VISD +MP+MDG +LL+ +   G    LPV+M
Sbjct: 24  LGFN--NVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGAMSALPVLM 81
Query: 57  MCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
             A   KE ++      A  Y+ KP     L+     +  K
Sbjct: 82  TTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEK 122

>pdb|3MYY|A Chain A, Structure Of E. Coli Chey Mutant A113p Bound To Beryllium Fluoride Length = 128

Iteration: 1
 Score = 51.6 bits (122), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 31/85 (36%), Positives = 45/85 (52%), Gaps = 6/85 (7%)
Query: 1   MGFSVTKCNRAEIALDML-RTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIM 56
           +GF+      AE  +D L +    GY  VISD +MP+MDG +LL+ +   G    LPV+M
Sbjct: 27  LGFN--NVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGAMSALPVLM 84
Query: 57  MCAHGSKEVVMKGVTHDACDYLTKP 81
           + A   KE ++      A  Y+ KP
Sbjct: 85  VTAEAKKENIIAAAQAGASGYVVKP 109

>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 = 51.2 bits (121), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 33/101 (32%), Positives = 48/101 (47%), Gaps = 6/101 (5%)
Query: 1   MGFSVTKCNRAEIALDML-RTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIM 56
           +GF+      AE  +D L +    GY  VISD  MP+MDG +LL+ +   G    LPV+M
Sbjct: 28  LGFN--NVEEAEDGVDALNKLQAGGYGFVISDWRMPNMDGLELLKTIRADGAMSALPVLM 85
Query: 57  MCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
           + A   KE ++      A  Y+ KP     L+     +  K
Sbjct: 86  VTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEK 126

>pdb|3OO0|A Chain A, Structure Of Apo Chey A113p Length = 129

Iteration: 1
 Score = 51.2 bits (121), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 31/85 (36%), Positives = 45/85 (52%), Gaps = 6/85 (7%)
Query: 1   MGFSVTKCNRAEIALDML-RTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIM 56
           +GF+      AE  +D L +    GY  VISD +MP+MDG +LL+ +   G    LPV+M
Sbjct: 28  LGFN--NVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGAMSALPVLM 85
Query: 57  MCAHGSKEVVMKGVTHDACDYLTKP 81
           + A   KE ++      A  Y+ KP
Sbjct: 86  VTAEAKKENIIAAAQAGASGYVVKP 110

>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 = 51.2 bits (121), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 33/101 (32%), Positives = 48/101 (47%), Gaps = 6/101 (5%)
Query: 1   MGFSVTKCNRAEIALDML-RTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIM 56
           +GF+      AE  +D L +    GY  VISD  MP+MDG +LL+ +   G    LPV+M
Sbjct: 31  LGFN--NVEEAEDGVDALNKLQAGGYGFVISDWDMPNMDGLELLKTIRADGAMSALPVLM 88
Query: 57  MCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
           + A   KE ++      A  Y+ KP     L+     +  K
Sbjct: 89  VTAQAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEK 129

>pdb|3FGZ|A Chain A, Crystal Structure Of Chey Triple Mutant F14e, N59m, E89r Complexed With Bef3- And Mn2+ Length = 128

Iteration: 1
 Score = 50.8 bits (120), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 33/101 (32%), Positives = 48/101 (47%), Gaps = 6/101 (5%)
Query: 1   MGFSVTKCNRAEIALDML-RTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIM 56
           +GF+      AE  +D L +    GY  VISD  MP+MDG +LL+ +   G    LPV+M
Sbjct: 27  LGFN--NVEEAEDGVDALNKLQAGGYGFVISDWMMPNMDGLELLKTIRADGAMSALPVLM 84
Query: 57  MCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
           + A   KE ++      A  Y+ KP     L+     +  K
Sbjct: 85  VTARAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEK 125

>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 = 50.8 bits (120), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 33/101 (32%), Positives = 48/101 (47%), Gaps = 6/101 (5%)
Query: 1   MGFSVTKCNRAEIALDML-RTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIM 56
           +GF+      AE  +D L +    GY  VISD  MP+MDG +LL+ +   G    LPV+M
Sbjct: 31  LGFN--NVEEAEDGVDALNKLQAGGYGFVISDWDMPNMDGLELLKTIRADGAMSALPVLM 88
Query: 57  MCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
           + A   KE ++      A  Y+ KP     L+     +  K
Sbjct: 89  VTARAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEK 129

>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 = 50.8 bits (120), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 33/101 (32%), Positives = 48/101 (47%), Gaps = 6/101 (5%)
Query: 1   MGFSVTKCNRAEIALDML-RTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIM 56
           +GF+      AE  +D L +    GY  VISD  MP+MDG +LL+ +   G    LPV+M
Sbjct: 31  LGFN--NVEEAEDGVDALNKLQAGGYGFVISDWDMPNMDGLELLKTIRADGAMSALPVLM 88
Query: 57  MCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
           + A   KE ++      A  Y+ KP     L+     +  K
Sbjct: 89  VTAKAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEK 129

>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 = 50.8 bits (120), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 34/104 (32%), Positives = 59/104 (56%), Gaps = 6/104 (5%)
Query: 1   MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV-GLEMDLPVIMMCA 59
           +G+     N    AL++L  +KN  DIV+SDV+MP+MDG++L + +  L + LPVI + A
Sbjct: 152 LGYQCKTANDGVDALNVL--SKNHIDIVLSDVNMPNMDGYRLTQRIRQLGLTLPVIGVTA 209
Query: 60  HGSKEVVMKGVTHDACDYLTKPVRIEELK---NIWQHVVRKRKN 100
           +   E   + +       L+KPV ++ +K    ++   VRK ++
Sbjct: 210 NALAEEKQRCLESGMDSCLSKPVTLDVIKQTLTLYAERVRKSRD 253

>pdb|1DBW|A Chain A, Crystal Structure Of Fixj-N Length = 126

Iteration: 1
 Score = 50.4 bits (119), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 31/99 (31%), Positives = 56/99 (56%), Gaps = 7/99 (7%)
Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAH 60
           GF+V     AE  L      +NG  ++++D+ MPDM G +LL  +G L++++P I++  H
Sbjct: 27  GFAVKMHQSAEAFLAFAPDVRNG--VLVTDLRMPDMSGVELLRNLGDLKINIPSIVITGH 84
Query: 61  GSKEVVMKGVTHDACDYLTKP----VRIEELKNIWQHVV 95
           G   + ++ +   A D++ KP    V IE ++   +H+V
Sbjct: 85  GDVPMAVEAMKAGAVDFIEKPFEDTVIIEAIERASEHLV 123

>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 = 50.4 bits (119), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 32/101 (31%), Positives = 49/101 (48%), Gaps = 6/101 (5%)
Query: 1   MGFSVTKCNRAEIALDML-RTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIM 56
           +GF+      AE  +D L +    GY  VISD +MP+MDG +LL+ +   G    LPV+M
Sbjct: 28  LGFN--NVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGAMSALPVLM 85
Query: 57  MCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
           + +   KE ++      A  Y+ KP     L+     +  K
Sbjct: 86  VTSEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEK 126

>pdb|5CHY|A Chain A, Structure Of Chemotaxis Protein Chey Length = 128

Iteration: 1
 Score = 50.4 bits (119), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 31/92 (33%), Positives = 47/92 (51%), Gaps = 6/92 (6%)
Query: 1   MGFSVTKCNRAEIALDML-RTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIM 56
           +GF+      AE  +D L +    GY  VISD +MP+MDG +LL+ +   G    LPV+M
Sbjct: 27  LGFN--NVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGAMSALPVLM 84
Query: 57  MCAHGSKEVVMKGVTHDACDYLTKPVRIEELK 88
           + A   KE ++      A  ++ KP     L+
Sbjct: 85  VTAEAKKENIIAAAQAGASGWVVKPFTAATLE 116

>pdb|6CHY|A Chain A, Structure Of Chemotaxis Protein Chey Length = 128

Iteration: 1
 Score = 50.4 bits (119), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 31/92 (33%), Positives = 47/92 (51%), Gaps = 6/92 (6%)
Query: 1   MGFSVTKCNRAEIALDML-RTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIM 56
           +GF+      AE  +D L +    GY  VISD +MP+MDG +LL+ +   G    LPV+M
Sbjct: 27  LGFN--NVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGAMSALPVLM 84
Query: 57  MCAHGSKEVVMKGVTHDACDYLTKPVRIEELK 88
           + A   KE ++      A  ++ KP     L+
Sbjct: 85  VIAEAKKENIIAAAQAGASGWVVKPFTAATLE 116

>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 = 50.1 bits (118), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 36/106 (33%), Positives = 62/106 (58%), Gaps = 10/106 (9%)
Query: 1   MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV-GLEMDLPVIMMCA 59
           +G+     N    AL++L  +KN  DIV+SDV+MP+MDG++L + +  L + LPVI + A
Sbjct: 31  LGYQCKTANDGVDALNVL--SKNHIDIVLSDVNMPNMDGYRLTQRIRQLGLTLPVIGVTA 88
Query: 60  HGSKEVVMKGVTH--DACDYLTKPVRIEELK---NIWQHVVRKRKN 100
           +   E   + +    D+C  L+KPV ++ +K    ++   VRK ++
Sbjct: 89  NALAEEKQRCLESGMDSC--LSKPVTLDVIKQTLTLYAERVRKSRD 132

>pdb|3F7N|A Chain A, Crystal Structure Of Chey Triple Mutant F14e, N59m, E89l Complexed With Bef3- And Mn2+ Length = 128

Iteration: 1
 Score = 50.1 bits (118), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 33/101 (32%), Positives = 48/101 (47%), Gaps = 6/101 (5%)
Query: 1   MGFSVTKCNRAEIALDML-RTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIM 56
           +GF+      AE  +D L +    GY  VISD  MP+MDG +LL+ +   G    LPV+M
Sbjct: 27  LGFN--NVEEAEDGVDALNKLQAGGYGFVISDWMMPNMDGLELLKTIRADGAMSALPVLM 84
Query: 57  MCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
           + A   KE ++      A  Y+ KP     L+     +  K
Sbjct: 85  VTALAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEK 125

>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 = 50.1 bits (118), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 32/101 (31%), Positives = 48/101 (47%), Gaps = 6/101 (5%)
Query: 1   MGFSVTKCNRAEIALDML-RTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIM 56
           +GF+      AE  +D L +    GY  VISD +MP+MDG +LL+ +   G    LPV+M
Sbjct: 28  LGFN--NVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGAMSALPVLM 85
Query: 57  MCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
           +     KE ++      A  Y+ KP     L+     +  K
Sbjct: 86  VTTEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEK 126

>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 = 49.7 bits (117), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 32/101 (31%), Positives = 48/101 (47%), Gaps = 6/101 (5%)
Query: 1   MGFSVTKCNRAEIALDML-RTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIM 56
           +GF+      AE  +D L +    GY  VISD +MP+MDG +LL+ +   G    LPV+M
Sbjct: 28  LGFN--NVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGAMSALPVLM 85
Query: 57  MCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
           +     KE ++      A  Y+ KP     L+     +  K
Sbjct: 86  VTVEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEK 126

>pdb|1JBE|A Chain A, 1.08 A Structure Of Apo-Chey Reveals Meta-Active Conformation Length = 128

Iteration: 1
 Score = 49.3 bits (116), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 32/101 (31%), Positives = 48/101 (47%), Gaps = 6/101 (5%)
Query: 1   MGFSVTKCNRAEIALDML-RTNKNGYDIVISDVHMPDMDGFKLLELVGLEM---DLPVIM 56
           +GF+      AE  +D L +    GY  VISD +MP+MDG +LL+ +        LPV+M
Sbjct: 27  LGFN--NVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRAXXAMSALPVLM 84
Query: 57  MCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
           + A   KE ++      A  Y+ KP     L+     +  K
Sbjct: 85  VTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEK 125

>pdb|1E6M|A Chain A, Two-Component Signal Transduction System D57a Mutant Of Chey Length = 128

Iteration: 1
 Score = 49.3 bits (116), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 32/101 (31%), Positives = 48/101 (47%), Gaps = 6/101 (5%)
Query: 1   MGFSVTKCNRAEIALDML-RTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIM 56
           +GF+      AE  +D L +    GY  VIS  +MP+MDG +LL+ +   G    LPV+M
Sbjct: 27  LGFN--NVEEAEDGVDALNKLQAGGYGFVISAWNMPNMDGLELLKTIRADGAMSALPVLM 84
Query: 57  MCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
           + A   KE ++      A  Y+ KP     L+     +  K
Sbjct: 85  VTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEK 125

>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 = 49.3 bits (116), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 32/101 (31%), Positives = 48/101 (47%), Gaps = 6/101 (5%)
Query: 1   MGFSVTKCNRAEIALDML-RTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIM 56
           +GF+      AE  +D L +    GY  VISD +MP+MDG +LL+ +   G    LPV+M
Sbjct: 28  LGFN--NVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGAMSALPVLM 85
Query: 57  MCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
           +     KE ++      A  Y+ KP     L+     +  K
Sbjct: 86  VTMEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEK 126

>pdb|1C4W|A Chain A, 1.9 A Structure Of A-Thiophosphonate Modified Chey D57c Length = 128

Iteration: 1
 Score = 49.3 bits (116), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 32/101 (31%), Positives = 48/101 (47%), Gaps = 6/101 (5%)
Query: 1   MGFSVTKCNRAEIALDML-RTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIM 56
           +GF+      AE  +D L +    GY  VIS  +MP+MDG +LL+ +   G    LPV+M
Sbjct: 27  LGFN--NVEEAEDGVDALNKLQAGGYGFVISXWNMPNMDGLELLKTIRADGAMSALPVLM 84
Query: 57  MCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
           + A   KE ++      A  Y+ KP     L+     +  K
Sbjct: 85  VTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEK 125

>pdb|1DC7|A Chain A, Structure Of A Transiently Phosphorylated "switch" In Bacterial Signal Transduction Length = 124

Iteration: 1
 Score = 49.3 bits (116), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 25/62 (40%), Positives = 35/62 (56%), Gaps = 1/62 (1%)
Query: 26  DIVISDVHMPDMDGFKLLELVGLEMD-LPVIMMCAHGSKEVVMKGVTHDACDYLTKPVRI 84
           D+++SD+ MP MDG  LL+ +      LPVI+M AH   +  +      A DYL KP  I
Sbjct: 49  DVLLSDIRMPGMDGLALLKQIKQRHPMLPVIIMTAHSDLDAAVSAYQQGAFDYLPKPFDI 108
Query: 85  EE 86
           +E
Sbjct: 109 DE 110

>pdb|1ZDM|A Chain A, Crystal Structure Of Activated Chey Bound To Xe Length = 129

Iteration: 1
 Score = 48.9 bits (115), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 32/101 (31%), Positives = 48/101 (47%), Gaps = 6/101 (5%)
Query: 1   MGFSVTKCNRAEIALDML-RTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIM 56
           +GF+      AE  +D L +    GY  VIS  +MP+MDG +LL+ +   G    LPV+M
Sbjct: 28  LGFN--NVEEAEDGVDALNKLQAGGYGFVISXWNMPNMDGLELLKTIRADGAMSALPVLM 85
Query: 57  MCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
           + A   KE ++      A  Y+ KP     L+     +  K
Sbjct: 86  VTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEK 126

>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 = 48.9 bits (115), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 25/62 (40%), Positives = 35/62 (56%), Gaps = 1/62 (1%)
Query: 26  DIVISDVHMPDMDGFKLLELVGLEMD-LPVIMMCAHGSKEVVMKGVTHDACDYLTKPVRI 84
           D+++SD+ MP MDG  LL+ +      LPVI+M AH   +  +      A DYL KP  I
Sbjct: 49  DVLLSDIRMPGMDGLALLKQIKQRHPMLPVIIMTAHSDLDAAVSAYQQGAFDYLPKPFDI 108
Query: 85  EE 86
           +E
Sbjct: 109 DE 110

>pdb|3R0J|A Chain A, Structure Of Phop From Mycobacterium Tuberculosis Length = 250

Iteration: 1
 Score = 48.9 bits (115), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 31/97 (31%), Positives = 48/97 (49%), Gaps = 3/97 (3%)
Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLE-MDLPVIMMCAH 60
           GF V        ALD  R  +   D VI DV  P  DGF +L  +  + +D P + + A 
Sbjct: 47  GFEVYTATNGAQALDRARETRP--DAVILDVXXPGXDGFGVLRRLRADGIDAPALFLTAR 104
Query: 61  GSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
            S +  + G+T    DY+TKP  +EE+    + ++R+
Sbjct: 105 DSLQDKIAGLTLGGDDYVTKPFSLEEVVARLRVILRR 141

>pdb|1KRW|A Chain A, Solution Structure And Backbone Dynamics Of Beryllofluoride- Activated Ntrc Receiver Domain Length = 124

Iteration: 1
 Score = 48.9 bits (115), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 25/62 (40%), Positives = 35/62 (56%), Gaps = 1/62 (1%)
Query: 26  DIVISDVHMPDMDGFKLLELVGLEMD-LPVIMMCAHGSKEVVMKGVTHDACDYLTKPVRI 84
           D+++SD+ MP MDG  LL+ +      LPVI+M AH   +  +      A DYL KP  I
Sbjct: 49  DVLLSDIRMPGMDGLALLKQIKQRHPMLPVIIMTAHSDLDAAVSAYQQGAFDYLPKPFDI 108
Query: 85  EE 86
           +E
Sbjct: 109 DE 110

>pdb|2ID7|A Chain A, 1.75 A Structure Of T87i Phosphono-Chey Length = 128

Iteration: 1
 Score = 48.9 bits (115), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 32/101 (31%), Positives = 48/101 (47%), Gaps = 6/101 (5%)
Query: 1   MGFSVTKCNRAEIALDML-RTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIM 56
           +GF+      AE  +D L +    GY  VIS  +MP+MDG +LL+ +   G    LPV+M
Sbjct: 27  LGFN--NVEEAEDGVDALNKLQAGGYGFVISXWNMPNMDGLELLKTIRADGAMSALPVLM 84
Query: 57  MCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
           + A   KE ++      A  Y+ KP     L+     +  K
Sbjct: 85  VIAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEK 125

>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 = 48.1 bits (113), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 30/101 (29%), Positives = 49/101 (48%), Gaps = 6/101 (5%)
Query: 1   MGFSVTKCNRAEIALDML-RTNKNGYDIVISDVHMPDMDGFKLLELVGLE---MDLPVIM 56
           +GF+      AE  +D L +    G+  +ISD +MP+MDG +LL+ +  +     LPV+M
Sbjct: 27  LGFN--NVEEAEDGVDALNKLQAGGFGFIISDWNMPNMDGLELLKTIRADSAMSALPVLM 84
Query: 57  MCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
           + A   KE ++      A  Y+ KP     L+     +  K
Sbjct: 85  VTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEK 125

>pdb|1D5W|A Chain A, Phosphorylated Fixj Receiver Domain Length = 126

Iteration: 1
 Score = 47.8 bits (112), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 30/99 (30%), Positives = 55/99 (55%), Gaps = 7/99 (7%)
Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAH 60
           GF+V     AE  L      +NG  ++++ + MPDM G +LL  +G L++++P I++  H
Sbjct: 27  GFAVKMHQSAEAFLAFAPDVRNG--VLVTXLRMPDMSGVELLRNLGDLKINIPSIVITGH 84
Query: 61  GSKEVVMKGVTHDACDYLTKP----VRIEELKNIWQHVV 95
           G   + ++ +   A D++ KP    V IE ++   +H+V
Sbjct: 85  GDVPMAVEAMKAGAVDFIEKPFEDTVIIEAIERASEHLV 123

>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 = 47.8 bits (112), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 30/101 (29%), Positives = 49/101 (48%), Gaps = 6/101 (5%)
Query: 1   MGFSVTKCNRAEIALDML-RTNKNGYDIVISDVHMPDMDGFKLLELVGLE---MDLPVIM 56
           +GF+      AE  +D L +    G+  +ISD +MP+MDG +LL+ +  +     LPV+M
Sbjct: 28  LGFN--NVEEAEDGVDALNKLQAGGFGFIISDWNMPNMDGLELLKTIRADSAMSALPVLM 85
Query: 57  MCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
           + A   KE ++      A  Y+ KP     L+     +  K
Sbjct: 86  VTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEK 126

>pdb|2ID9|A Chain A, 1.85 A Structure Of T87iY106W PHOSPHONO-Chey Length = 128

Iteration: 1
 Score = 47.4 bits (111), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 30/92 (32%), Positives = 46/92 (50%), Gaps = 6/92 (6%)
Query: 1   MGFSVTKCNRAEIALDML-RTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIM 56
           +GF+      AE  +D L +    GY  VIS  +MP+MDG +LL+ +   G    LPV+M
Sbjct: 27  LGFN--NVEEAEDGVDALNKLQAGGYGFVISXWNMPNMDGLELLKTIRADGAMSALPVLM 84
Query: 57  MCAHGSKEVVMKGVTHDACDYLTKPVRIEELK 88
           + A   KE ++      A  ++ KP     L+
Sbjct: 85  VIAEAKKENIIAAAQAGASGWVVKPFTAATLE 116

>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 = 47.0 bits (110), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 32/101 (31%), Positives = 47/101 (46%), Gaps = 6/101 (5%)
Query: 1   MGFSVTKCNRAEIALDML-RTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIM 56
           +GF+      AE  +D L +    GY  VISD +MP+MDG +LL+ +   G    LPV+M
Sbjct: 28  LGFN--NVEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRADGAMSALPVLM 85
Query: 57  MCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
           + A    E +       A  Y+ KP     L+     +  K
Sbjct: 86  VTAEADAENIKALAQAGASGYVVKPFTAATLEEKLNKIFEK 126

>pdb|1DC8|A Chain A, Structure Of A Transiently Phosphorylated "switch" In Bacterial Signal Transduction Length = 124

Iteration: 1
 Score = 46.6 bits (109), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/62 (38%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 26  DIVISDVHMPDMDGFKLLELVGLEMD-LPVIMMCAHGSKEVVMKGVTHDACDYLTKPVRI 84
           D+++S + MP MDG  LL+ +      LPVI+M AH   +  +      A DYL KP  I
Sbjct: 49  DVLLSXIRMPGMDGLALLKQIKQRHPMLPVIIMTAHSDLDAAVSAYQQGAFDYLPKPFDI 108
Query: 85  EE 86
           +E
Sbjct: 109 DE 110

>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 = 45.4 bits (106), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 33/97 (34%), Positives = 46/97 (47%), Gaps = 9/97 (9%)
Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIMMC 58
           G+ V +    E AL  +   KN  D +I DV +P +DG+ L + V    L   LP++ + 
Sbjct: 28  GYEVRRAASGEEALQQI--YKNLPDALICDVLLPGIDGYTLCKRVRQHPLTKTLPILXLT 85
Query: 59  AHGSKEVVMKGVTHDACDYLTKPVRIEEL----KNIW 91
           A G     + G    A DYL KP   +EL    KNI 
Sbjct: 86  AQGDISAKIAGFEAGANDYLAKPFEPQELVYRVKNIL 122

>pdb|2CHY|A Chain A, Three-Dimensional Structure Of Chey, The Response Regulator Of Bacterial Chemotaxis Length = 128

Iteration: 1
 Score = 45.4 bits (106), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 29/101 (28%), Positives = 48/101 (47%), Gaps = 6/101 (5%)
Query: 1   MGFSVTKCNRAEIALDML-RTNKNGYDIVISDVHMPDMDGFKLLELVGLE---MDLPVIM 56
           +GF+      AE  +D L +    G+  +I D +MP+MDG +LL+ +  +     LPV+M
Sbjct: 27  LGFN--NVEEAEDGVDALNKLQAGGFGFIICDWNMPNMDGLELLKTIRADSAMSALPVLM 84
Query: 57  MCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
           + A   KE ++      A  Y+ KP     L+     +  K
Sbjct: 85  VTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEK 125

>pdb|1U8T|A Chain A, Crystal Structure Of Chey D13k Y106w Alone And In Complex With A Flim Peptide Length = 128

Iteration: 1
 Score = 45.1 bits (105), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 28/92 (30%), Positives = 44/92 (47%), Gaps = 6/92 (6%)
Query: 1   MGFSVTKCNRAEIALDML-RTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIM 56
           +GF+      AE  +D L +    GY  VISD + P+ DG +LL+ +   G    LPV+ 
Sbjct: 27  LGFN--NVEEAEDGVDALNKLQAGGYGFVISDWNXPNXDGLELLKTIRADGAXSALPVLX 84
Query: 57  MCAHGSKEVVMKGVTHDACDYLTKPVRIEELK 88
           + A   KE ++      A  ++ KP     L+
Sbjct: 85  VTAEAKKENIIAAAQAGASGWVVKPFTAATLE 116

>pdb|3JTE|A Chain A, Crystal Structure Of Response Regulator Receiver Domain Protein From Clostridium Thermocellum Length = 143

Iteration: 1
 Score = 44.7 bits (104), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 27/93 (29%), Positives = 48/93 (51%), Gaps = 5/93 (5%)
Query: 15  LDMLRTNKNGYDIVISDVHMPDMDGFKLL-ELVGLEMDLPVIMMCAHGSKEVVMKGVTHD 73
           L +   N N  D+VI+D+ MP + G  +L E+  +   + VI++  HG  +  +  +   
Sbjct: 40  LRIFTENCNSIDVVITDMKMPKLSGMDILREIKKITPHMAVIILTGHGDLDNAILAMKEG 99
Query: 74  ACDYLTKPVRIEELKNIWQHVVRKRK----NER 102
           A +YL KPV  ++L     + + ++K    NER
Sbjct: 100 AFEYLRKPVTAQDLSIAINNAINRKKLLMENER 132

>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 = 44.7 bits (104), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 26/76 (34%), Positives = 39/76 (51%), Gaps = 3/76 (3%)
Query: 22  KNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIMMCAHGSKEVVMKGVTHDACDYL 78
           +N + +VISD +MP MDG  LL+ V           I++ A G + +V K     A + L
Sbjct: 49  QNPHHLVISDFNMPKMDGLGLLQAVRANPATKKAAFIILTAQGDRALVQKAAALGANNVL 108
Query: 79  TKPVRIEELKNIWQHV 94
            KP  IE++K   + V
Sbjct: 109 AKPFTIEKMKAAIEAV 124

>pdb|1YS6|A Chain A, Crystal Structure Of The Response Regulatory Protein Prra From Mycobacterium Tuberculosis Length = 233

Iteration: 1
 Score = 44.7 bits (104), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 32/100 (32%), Positives = 55/100 (55%), Gaps = 7/100 (7%)
Query: 2   GFSV-TKCNRAEIALDMLRT-NKNGYDIVISDVHMPDMDGFKLL-ELVGLEMDLPVIMMC 58
           GF V T  + AE     LR+  +N  D ++ D++MP +DG  ++  L  ++ D+PV ++ 
Sbjct: 31  GFEVATAVDGAE----ALRSATENRPDAIVLDINMPVLDGVSVVTALRAMDNDVPVCVLS 86
Query: 59  AHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKR 98
           A  S +  + G+   A DYL KP  + EL    + ++R+R
Sbjct: 87  ARSSVDDRVAGLEAGADDYLVKPFVLAELVARVKALLRRR 126

>pdb|2OQR|A Chain A, The Structure Of The Response Regulator Regx3 From Mycobacterium Tuberculosis Length = 230

Iteration: 1
 Score = 43.9 bits (102), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 33/113 (29%), Positives = 55/113 (48%), Gaps = 3/113 (2%)
Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHG 61
           GF  T       AL     ++ G DIV+ D+ +P M G  + + +     +PVIM+ A  
Sbjct: 28  GFEATVVTDGPAAL--AEFDRAGADIVLLDLMLPGMSGTDVCKQLRARSSVPVIMVTARD 85
Query: 62  SKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQSGSVEGG 114
           S+   + G+   A DY+TKP    EL    + V+R+  ++  ++   G +E G
Sbjct: 86  SEIDKVVGLELGADDYVTKPYSARELIARIRAVLRRGGDDDSEM-SDGVLESG 137

>pdb|3NNN|A Chain A, Bef3 Activated Drrd Receiver Domain Length = 122

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 29/97 (29%), Positives = 52/97 (53%), Gaps = 3/97 (3%)
Query: 3   FSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLE-MDLPVIMMCAHG 61
           F+V  C   E  + M       +D+VI D+ +P  DG+++L+ +    ++ PV+M+ A  
Sbjct: 27  FTVDVCYDGEEGMYM--ALNEPFDVVILDIMLPVHDGWEILKSMRESGVNTPVLMLTALS 84
Query: 62  SKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKR 98
             E  +KG+   A DYL KP  + EL    + ++R++
Sbjct: 85  DVEYRVKGLNMGADDYLPKPFDLRELIARVRALIRRK 121

>pdb|3TO5|A Chain A, High Resolution Structure Of Chey3 From Vibrio Cholerae Length = 134

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 28/92 (30%), Positives = 48/92 (52%), Gaps = 6/92 (6%)
Query: 1   MGFSVTK-CNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMD---LPVIM 56
           +GF+ T+  +    AL ML+  K  +D V++D +MP M G  LL+ +  + +   LPV+M
Sbjct: 35  LGFNNTQEADDGLTALPMLK--KGDFDFVVTDWNMPGMQGIDLLKNIRADEELKHLPVLM 92
Query: 57  MCAHGSKEVVMKGVTHDACDYLTKPVRIEELK 88
           + A   +E +++        Y+ KP     LK
Sbjct: 93  ITAEAKREQIIEAAQAGVNGYIVKPFTAATLK 124

>pdb|1YIO|A Chain A, Crystallographic Structure Of Response Regulator Styr From Pseudomonas Fluorescens Length = 208

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 33/123 (26%), Positives = 60/123 (48%), Gaps = 9/123 (7%)
Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLE-LVGLEMDLPVIMMCAH 60
           GF V   + A   L+  R  ++G   ++ D+ MP M G +L E L  +   +P++ + AH
Sbjct: 28  GFEVETFDCASTFLEHRRPEQHG--CLVLDMRMPGMSGIELQEQLTAISDGIPIVFITAH 85
Query: 61  GSKEVVMKGVTHDACDYLTKPVRIEEL-----KNIWQHVVRKRKNERKD-LEQSGSVEGG 114
           G   + ++ +   A ++L KP   + L     + +  +  R++  E +D LEQ  S   G
Sbjct: 86  GDIPMTVRAMKAGAIEFLPKPFEEQALLDAIEQGLQLNAERRQARETQDQLEQLFSSLTG 145
Query: 115 AQQ 117
            +Q
Sbjct: 146 REQ 148

>pdb|1ZES|A Chain A, Bef3- Activated Phob Receiver Domain Length = 125

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 27/99 (27%), Positives = 53/99 (53%), Gaps = 5/99 (5%)
Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIMMC 58
           GF   +    + A++ L  N+   D+++ D  +P   G + ++ +    +  D+PV+M+ 
Sbjct: 26  GFQPVEAEDYDSAVNQL--NEPWPDLILLDWMLPGGSGIQFIKHLKRESMTRDIPVVMLT 83
Query: 59  AHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
           A G +E  ++G+   A DY+TKP   +EL    + V+R+
Sbjct: 84  ARGEEEDRVRGLETGADDYITKPFSPKELVARIKAVMRR 122

>pdb|1B00|A Chain A, Phob Receiver Domain From Escherichia Coli Length = 127

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 27/99 (27%), Positives = 53/99 (53%), Gaps = 5/99 (5%)
Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIMMC 58
           GF   +    + A++ L  N+   D+++ D  +P   G + ++ +    +  D+PV+M+ 
Sbjct: 26  GFQPVEAEDYDSAVNQL--NEPWPDLILLDWMLPGGSGIQFIKHLKRESMTRDIPVVMLT 83
Query: 59  AHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
           A G +E  ++G+   A DY+TKP   +EL    + V+R+
Sbjct: 84  ARGEEEDRVRGLETGADDYITKPFSPKELVARIKAVMRR 122

>pdb|1DZ3|A Chain A, Domain-Swapping In The Sporulation Response Regulator Spo0a Length = 130

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/74 (35%), Positives = 40/74 (54%), Gaps = 2/74 (2%)
Query: 26  DIVISDVHMPDMDGFKLLELV--GLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTKPVR 83
           DI++ D+ MP +DG  +LE +  G E    VIM+ A G ++V  K V   A  ++ KP  
Sbjct: 50  DILLLDIIMPHLDGLAVLERIRAGFEHQPNVIMLTAFGQEDVTKKAVELGASYFILKPFD 109
Query: 84  IEELKNIWQHVVRK 97
           +E L +  + V  K
Sbjct: 110 MENLAHHIRQVYGK 123

>pdb|3GT7|A Chain A, Crystal Structure Of Signal Receiver Domain Of Signal Transduction Histidine Kinase From Syntrophus Aciditrophicus Length = 154

Iteration: 1
 Score = 42.0 bits (97), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 22/61 (36%), Positives = 36/61 (59%), Gaps = 3/61 (4%)
Query: 26  DIVISDVHMPDMDGFKLLELVGLEMDL---PVIMMCAHGSKEVVMKGVTHDACDYLTKPV 82
           D++ISDV MP+MDG+ L   +  + DL   PVI++        V++ +   A D++TKP 
Sbjct: 53  DLIISDVLMPEMDGYALCRWLKGQPDLRTIPVILLTILSDPRDVVRSLECGADDFITKPC 112
Query: 83  R 83
           +
Sbjct: 113 K 113

>pdb|1NXO|A Chain A, Micarec Ph7.0 Length = 120

Iteration: 1
 Score = 42.0 bits (97), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 21/72 (29%), Positives = 43/72 (59%)
Query: 26  DIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTKPVRIE 85
           DI+I D+ +P++DG ++ + +     +P++M+ A  S+   + G+   A DY+TKP    
Sbjct: 47  DIIILDLMLPEIDGLEVAKTIRKTSSVPILMLSAKDSEFDKVIGLELGADDYVTKPFSNR 106
Query: 86  ELKNIWQHVVRK 97
           EL+   + ++R+
Sbjct: 107 ELQARVKALLRR 118

>pdb|2PKX|A Chain A, E.Coli Response Regulator Phop Receiver Domain Length = 121

Iteration: 1
 Score = 41.6 bits (96), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 25/78 (32%), Positives = 45/78 (57%), Gaps = 1/78 (1%)
Query: 21  NKNGYDIVISDVHMPDMDGFKLLE-LVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT 79
           N++  DI I D+ +PD DG  L+      ++ LP++++ A  S +  ++ ++  A DY+T
Sbjct: 41  NEHIPDIAIVDLGLPDEDGLSLIRRWRSNDVSLPILVLTARESWQDKVEVLSAGADDYVT 100
Query: 80  KPVRIEELKNIWQHVVRK 97
           KP  IEE+    Q + R+
Sbjct: 101 KPFHIEEVXARXQALXRR 118

>pdb|3CFY|A Chain A, Crystal Structure Of Signal Receiver Domain Of Putative Luxo Repressor Protein From Vibrio Parahaemolyticus Length = 137

Iteration: 1
 Score = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 22/65 (33%), Positives = 39/65 (60%), Gaps = 3/65 (4%)
Query: 27  IVISDVHMPDMDGFKLLELVGLEMDLP--VIMMCAHGSKEVVMKGVTHDACDYLTKPVRI 84
           ++I D+ +PDM G  +L+ +  + D+P  VI+  AHGS ++ +  +   A D+L KP+  
Sbjct: 51  LIILDLKLPDMSGEDVLDWIN-QNDIPTSVIIATAHGSVDLAVNLIQKGAEDFLEKPINA 109
Query: 85  EELKN 89
           + LK 
Sbjct: 110 DRLKT 114

>pdb|3Q9S|A Chain A, Crystal Structure Of Rra(1-215) From Deinococcus Radiodurans Length = 249

Iteration: 1
 Score = 41.2 bits (95), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 26/100 (26%), Positives = 53/100 (53%), Gaps = 2/100 (2%)
Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHG 61
           G+ V   + A   L  ++  ++  D+++ D+ +PD DG  +++ +     LP+I++ A  
Sbjct: 61  GYVVDHADSAXNGL--IKAREDHPDLILLDLGLPDFDGGDVVQRLRKNSALPIIVLTARD 118
Query: 62  SKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNE 101
           + E  ++ +   A DYL KP   +EL    +  +R+R +E
Sbjct: 119 TVEEKVRLLGLGADDYLIKPFHPDELLARVKVQLRQRTSE 158

>pdb|1ZIT|A Chain A, Structure Of The Receiver Domain Of Ntrc4 From Aquifex Aeolicus Length = 121

Iteration: 1
 Score = 40.8 bits (94), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 1/70 (1%)
Query: 25  YDIVISDVHMPDMDGFKLLELVGLEM-DLPVIMMCAHGSKEVVMKGVTHDACDYLTKPVR 83
           + +++ DV MPD DG   ++ +     D  VI++  HGS +  +K +   A ++L KP  
Sbjct: 46  FPVIVLDVWMPDGDGVNFIDFIKENSPDSVVIVITGHGSVDTAVKAIKKGAYEFLEKPFS 105
Query: 84  IEELKNIWQH 93
           +E      +H
Sbjct: 106 VERFLLTIKH 115

>pdb|1KGS|A Chain A, Crystal Structure At 1.50 A Of An OmprPHOB HOMOLOG FROM THERMOTOGA Maritima Length = 225

Iteration: 1
 Score = 40.8 bits (94), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 27/80 (33%), Positives = 46/80 (57%), Gaps = 2/80 (2%)
Query: 25  YDIVISDVHMPDMDGFKLLELVGLE-MDLPVIMMCAHGSKEVVMKGVTHDACDYLTKPVR 83
           +D+VI D+ +P  DG+++L+      ++ PV+ + A    E  +KG+   A DYL KP  
Sbjct: 47  FDVVILDIXLPVHDGWEILKSXRESGVNTPVLXLTALSDVEYRVKGLNXGADDYLPKPFD 106
Query: 84  IEELKNIWQHVVRKRKNERK 103
           + EL    + ++R RK+E K
Sbjct: 107 LRELIARVRALIR-RKSESK 125

>pdb|3CU5|A Chain A, Crystal Structure Of A Two Component Transcriptional Regulator Arac From Clostridium Phytofermentans Isdg Length = 141

Iteration: 1
 Score = 40.4 bits (93), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 25/90 (27%), Positives = 47/90 (52%), Gaps = 7/90 (7%)
Query: 8   CNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLE-LVGLEMDLPVIMMCAHGSKEVV 66
            N  +IAL      K+  +++++DV MP MDG +L++ ++ L  D  VI M  +  KE +
Sbjct: 39  INAIQIAL------KHPPNVLLTDVRMPRMDGIELVDNILKLYPDCSVIFMSGYSDKEYL 92
Query: 67  MKGVTHDACDYLTKPVRIEELKNIWQHVVR 96
              +   A  Y+ KP+   E+ +  +  ++
Sbjct: 93  KAAIKFRAIRYVEKPIDPSEIMDALKQSIQ 122

>pdb|2JB9|A Chain A, Phob Response Regulator Receiver Domain Constitutively- Active Double Mutant D10a And D53e. Length = 127

Iteration: 1
 Score = 40.4 bits (93), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 26/99 (26%), Positives = 53/99 (53%), Gaps = 5/99 (5%)
Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIMMC 58
           GF   +    + A++ L  N+   D+++ +  +P   G + ++ +    +  D+PV+M+ 
Sbjct: 26  GFQPVEAEDYDSAVNQL--NEPWPDLILLEWMLPGGSGIQFIKHLKRESMTRDIPVVMLT 83
Query: 59  AHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
           A G +E  ++G+   A DY+TKP   +EL    + V+R+
Sbjct: 84  ARGEEEDRVRGLETGADDYITKPFSPKELVARIKAVMRR 122

>pdb|2ZWM|A Chain A, Crystal Structure Of Yycf Receiver Domain From Bacillus Subtilis Length = 130

Iteration: 1
 Score = 40.4 bits (93), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 25/80 (31%), Positives = 44/80 (55%), Gaps = 6/80 (7%)
Query: 26  DIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTKPVRIE 85
           D+++ D+ +P+ DG ++   V  + D+P+IM+ A  S+   + G+   A DY+TKP    
Sbjct: 48  DLILLDIMLPNKDGVEVCREVRKKYDMPIIMLTAKDSEIDKVIGLEIGADDYVTKPFSTR 107
Query: 86  ELKNIWQHVVRKRKNERKDL 105
           EL      + R + N R+ L
Sbjct: 108 EL------LARVKANLRRQL 121

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	226
1irz_A	64	ARR10-B; helix-turn-helix, DNA binding protein; NM	8e-29
1srr_A	124	SPO0F, sporulation response regulatory protein; as	6e-23
3jte_A	143	Response regulator receiver protein; structural ge	8e-23
3cfy_A	137	Putative LUXO repressor protein; structural genomi	2e-22
3hdv_A	136	Response regulator; PSI-II, structural genomics, P	2e-22
2qxy_A	142	Response regulator; regulation of transcription, N	3e-21
1dc7_A	124	NTRC, nitrogen regulation protein; receiver domain	5e-21
3hdg_A	137	Uncharacterized protein; two-component sensor acti	1e-20
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	1e-20
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	2e-20
4dad_A	146	Putative pilus assembly-related protein; response	2e-20
3hv2_A	153	Response regulator/HD domain protein; PSI-2, NYSGX	6e-20
1qkk_A	155	DCTD, C4-dicarboxylate transport transcriptional r	1e-19
3kcn_A	151	Adenylate cyclase homolog; SGX, PSI 2, structural	1e-19
2jk1_A	139	HUPR, hydrogenase transcriptional regulatory prote	1e-19
2rjn_A	154	Response regulator receiver:metal-dependent phosph	2e-19
1dbw_A	126	Transcriptional regulatory protein FIXJ; doubly wo	4e-19
3luf_A	259	Two-component system response regulator/ggdef doma	1e-18
3luf_A	259	Two-component system response regulator/ggdef doma	5e-14
2qr3_A	140	Two-component system response regulator; structura	2e-18
1w25_A	459	Stalked-cell differentiation controlling protein;	3e-17
1w25_A	459	Stalked-cell differentiation controlling protein;	2e-12
3rqi_A	184	Response regulator protein; structural genomics, s	3e-17
3cg0_A	140	Response regulator receiver modulated diguanylate	3e-17
3eq2_A	394	Probable two-component response regulator; adaptor	5e-17
1yio_A	208	Response regulatory protein; transcription regulat	9e-17
3bre_A	358	Probable two-component response regulator; protein	1e-16
3i42_A	127	Response regulator receiver domain protein (CHEY-	2e-16
2ayx_A	254	Sensor kinase protein RCSC; two independent struct	3e-16
3kto_A	136	Response regulator receiver protein; PSI-II,struct	1e-15
1p6q_A	129	CHEY2; chemotaxis, signal transduction, response r	2e-15
3eqz_A	135	Response regulator; structural genomics, unknown f	2e-15
3h5i_A	140	Response regulator/sensory box protein/ggdef domai	2e-15
3cnb_A	143	DNA-binding response regulator, MERR family; signa	2e-15
3crn_A	132	Response regulator receiver domain protein, CHEY-;	3e-15
3snk_A	135	Response regulator CHEY-like protein; P-loop conta	3e-15
3m6m_D	143	Sensory/regulatory protein RPFC; RPFF, REC, enoyl-	1e-14
3grc_A	140	Sensor protein, kinase; protein structure initiati	2e-14
1jbe_A	128	Chemotaxis protein CHEY; signaling protein; 1.08A	2e-14
1mb3_A	124	Cell division response regulator DIVK; signal tran	2e-14
3cu5_A	141	Two component transcriptional regulator, ARAC FAM;	3e-14
3hzh_A	157	Chemotaxis response regulator (CHEY-3); phosphatas	3e-14
2rdm_A	132	Response regulator receiver protein; structural ge	3e-14
3ilh_A	146	Two component response regulator; NYSGXRC, PSI-II,	4e-14
3c97_A	140	Signal transduction histidine kinase; structural g	7e-14
1dcf_A	136	ETR1 protein; beta-alpha five sandwich, transferas	8e-14
3eod_A	130	Protein HNR; response regulator, phosphoprotein, t	1e-13
2b4a_A	138	BH3024; flavodoxin-like fold, structural genomics,	1e-13
3n0r_A	286	Response regulator; sigma factor, receiver, two-co	2e-13
1ys7_A	233	Transcriptional regulatory protein PRRA; response	2e-13
3h1g_A	129	Chemotaxis protein CHEY homolog; sulfate-bound CHE	2e-13
3r0j_A	250	Possible two component system response transcript	3e-13
3q9s_A	249	DNA-binding response regulator; DNA binding protei	4e-13
3a10_A	116	Response regulator; phosphoacceptor, signaling pro	6e-13
2qvg_A	143	Two component response regulator; NYSGXRC, PSI-2,	6e-13
3lua_A	140	Response regulator receiver protein; two-component	7e-13
2qzj_A	136	Two-component response regulator; 11017X, PSI-II,	7e-13
3nhm_A	133	Response regulator; protein structure initiative I	1e-12
3n53_A	140	Response regulator receiver modulated diguanylate;	2e-12
1kgs_A	225	DRRD, DNA binding response regulator D; DNA-bindin	2e-12
1s8n_A	205	Putative antiterminator; RV1626, structural genomi	2e-12
3lte_A	132	Response regulator; structural genomics, PSI, prot	2e-12
3gt7_A	154	Sensor protein; structural genomics, signal receiv	4e-12
1zh2_A	121	KDP operon transcriptional regulatory protein KDPE	5e-12
2pl1_A	121	Transcriptional regulatory protein PHOP; CHEY-like	6e-12
3f6p_A	120	Transcriptional regulatory protein YYCF; unphospho	1e-11
2gwr_A	238	DNA-binding response regulator MTRA; two-component	2e-11
2a9o_A	120	Response regulator; essential protein, YYCF/YYCG h	2e-11
1k66_A	149	Phytochrome response regulator RCPB; CHEY homologu	2e-11
2qv0_A	143	Protein MRKE; structural genomics, transcription,	2e-11
1i3c_A	149	Response regulator RCP1; phytochrome, signaling pr	2e-11
3cg4_A	142	Response regulator receiver domain protein (CHEY-;	3e-11
3kht_A	144	Response regulator; PSI-II, 11023K, structural gen	4e-11
2oqr_A	230	Sensory transduction protein REGX3; response regul	5e-11
2zay_A	147	Response regulator receiver protein; structural ge	5e-11
2j48_A	119	Two-component sensor kinase; pseudo-receiver, circ	6e-11
1tmy_A	120	CHEY protein, TMY; chemotaxis, phosphoryl transfer	7e-11
3c3m_A	138	Response regulator receiver protein; structural ge	7e-11
2r25_B	133	Osmosensing histidine protein kinase SLN1; alpha5-	1e-10
1qo0_D	196	AMIR; binding protein, gene regulator, receptor; 2	1e-10
3heb_A	152	Response regulator receiver domain protein (CHEY);	3e-10
3t6k_A	136	Response regulator receiver; flavodoxin-like, stru	7e-10
3gl9_A	122	Response regulator; beta-sheet, surrounded by alph	7e-10
1mvo_A	136	PHOP response regulator; phosphate regulon, transc	3e-09
1xhf_A	123	DYE resistance, aerobic respiration control protei	3e-09
1zgz_A	122	Torcad operon transcriptional regulatory protein;	5e-09
2jba_A	127	Phosphate regulon transcriptional regulatory PROT;	6e-09
3mm4_A	206	Histidine kinase homolog; receiver domain, CKI1, c	7e-09
2gkg_A	127	Response regulator homolog; social motility, recei	8e-09
3kyj_B	145	CHEY6 protein, putative histidine protein kinase;	2e-08
2hqr_A	223	Putative transcriptional regulator; phosporylation	4e-08
3t8y_A	164	CHEB, chemotaxis response regulator protein-glutam	4e-08
2qsj_A	154	DNA-binding response regulator, LUXR family; struc	4e-08
1dz3_A	130	Stage 0 sporulation protein A; response regulator,	5e-08
2pln_A	137	HP1043, response regulator; signaling protein; 1.8	7e-08
1p2f_A	220	Response regulator; DRRB, OMPR/PHOB, transcription	8e-08
1a2o_A	349	CHEB methylesterase; bacterial chemotaxis, adaptat	1e-07
1k68_A	140	Phytochrome response regulator RCPA; phosphorylate	2e-07
3f6c_A	134	Positive transcription regulator EVGA; structural	3e-06
3b2n_A	133	Uncharacterized protein Q99UF4; structural genomic	1e-05
4e7p_A	150	Response regulator; DNA binding, cytosol, transcri	1e-04
3cz5_A	153	Two-component response regulator, LUXR family; str	4e-04

>1irz_A ARR10-B; helix-turn-helix, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: a.4.1.11 Length = 64

 Score =  102 bits (255), Expect = 8e-29
 Identities = 37/61 (60%), Positives = 50/61 (81%)

Query: 150 KKPRLVWSVELHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRL 209
           KKPR++W+ ELH +F++AV  LG ++A PKKIL+LMN+  LTRENVASHLQK R+ L ++
Sbjct: 4   KKPRVLWTHELHNKFLAAVDHLGVERAVPKKILDLMNVDKLTRENVASHLQKFRVALKKV 63

Query: 210 S 210
           S
Sbjct: 64  S 64

>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 = 88.7 bits (221), Expect = 6e-23
 Identities = 23/100 (23%), Positives = 54/100 (54%), Gaps = 3/100 (3%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV-GLEMDLPVIMMCAH 60
           G+   +      ALD++   +   D+V+ D+ +P MDG ++L+ +  ++ ++ VI+M A+
Sbjct: 27  GYQTFQAANGLQALDIVTKER--PDLVLLDMKIPGMDGIEILKRMKVIDENIRVIIMTAY 84

Query: 61  GSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKN 100
           G  +++ +     A  +  KP  I+E+++  +  +  + N
Sbjct: 85  GELDMIQESKELGALTHFAKPFDIDEIRDAVKKYLPLKSN 124

>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 = 89.1 bits (222), Expect = 8e-23
 Identities = 27/102 (26%), Positives = 48/102 (47%), Gaps = 7/102 (6%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV-GLEMDLPVIMMCAH 60
           G  V   + +   L +   N N  D+VI+D+ MP + G  +L  +  +   + VI++  H
Sbjct: 27  GNEVLTASSSTEGLRIFTENCNSIDVVITDMKMPKLSGMDILREIKKITPHMAVIILTGH 86

Query: 61  GSKEV---VMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRK 99
           G  +     MK     A +YL KPV  ++L     + + ++K
Sbjct: 87  GDLDNAILAMK---EGAFEYLRKPVTAQDLSIAINNAINRKK 125

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

 Score = 88.0 bits (219), Expect = 2e-22
 Identities = 22/109 (20%), Positives = 50/109 (45%), Gaps = 5/109 (4%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV-GLEMDLPVIMMCAH 60
            + +        A+  +  +K    ++I D+ +PDM G  +L+ +   ++   VI+  AH
Sbjct: 28  PYDIFHVETGRDAIQFIERSK--PQLIILDLKLPDMSGEDVLDWINQNDIPTSVIIATAH 85

Query: 61  GSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKR--KNERKDLEQ 107
           GS ++ +  +   A D+L KP+  + LK      +++   ++  +    
Sbjct: 86  GSVDLAVNLIQKGAEDFLEKPINADRLKTSVALHLKRAKLEDLVEGHHH 134

>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 = 87.7 bits (218), Expect = 2e-22
 Identities = 20/104 (19%), Positives = 39/104 (37%), Gaps = 3/104 (2%)

Query: 1   MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLE--MDLPVIMMC 58
            G      + AE A   L   K    ++I+D+ M    G  L+  +       L +I++ 
Sbjct: 30  RGIDAVGADGAEEARLYLHYQKR-IGLMITDLRMQPESGLDLIRTIRASERAALSIIVVS 88

Query: 59  AHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNER 102
                E  +  +     D+L KPV + +L  +    ++  +   
Sbjct: 89  GDTDVEEAVDVMHLGVVDFLLKPVDLGKLLELVNKELKIGEGHH 132

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

 Score = 84.9 bits (211), Expect = 3e-21
 Identities = 25/107 (23%), Positives = 45/107 (42%), Gaps = 4/107 (3%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV-GLEMDLPVIMMCAH 60
           GF+V      + A   LR  K   D+V  DV     +   L+  +     D  V ++ A+
Sbjct: 28  GFNVIWAKNEQEAFTFLRREK--IDLVFVDV-FEGEESLNLIRRIREEFPDTKVAVLSAY 84

Query: 61  GSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQ 107
             K++++  V   A DY+ KP R++ L    + ++         L +
Sbjct: 85  VDKDLIINSVKAGAVDYILKPFRLDYLLERVKKIISSTPRVTVSLRK 131

>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 = 83.7 bits (208), Expect = 5e-21
 Identities = 29/99 (29%), Positives = 45/99 (45%), Gaps = 3/99 (3%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV-GLEMDLPVIMMCAH 60
           G + T        L  L +     D+++SD+ MP MDG  LL+ +      LPVI+M AH
Sbjct: 27  GLTCTTFENGNEVLAALASKT--PDVLLSDIRMPGMDGLALLKQIKQRHPMLPVIIMTAH 84

Query: 61  GSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRK 99
              +  +      A DYL KP  I+E   + +  +   +
Sbjct: 85  SDLDAAVSAYQQGAFDYLPKPFDIDEAVALVERAISHYQ 123

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

 Score = 83.4 bits (207), Expect = 1e-20
 Identities = 17/103 (16%), Positives = 38/103 (36%), Gaps = 3/103 (2%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV-GLEMDLPVIMMCAH 60
              V      E    +   +    D++I+D+ MP + G ++L+ +        VI++ A 
Sbjct: 31  FPEVWSAGDGEEGERLFGLHA--PDVIITDIRMPKLGGLEMLDRIKAGGAKPYVIVISAF 88

Query: 61  GSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERK 103
              +  +K +      +L KP+    L    +     +  +  
Sbjct: 89  SEMKYFIKAIELGVHLFLPKPIEPGRLMETLEDFRHIKLAKEG 131

>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 = 87.9 bits (219), Expect = 1e-20
 Identities = 25/102 (24%), Positives = 54/102 (52%), Gaps = 3/102 (2%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV-GLEMDLPVIMMCAH 60
           G  V    R + A  +L   +  +++V+ D+ +PD++G ++L+ +     +  VI++  H
Sbjct: 24  GIKVESAERGKEAYKLLS--EKHFNVVLLDLLLPDVNGLEILKWIKERSPETEVIVITGH 81

Query: 61  GSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNER 102
           G+ +  ++ +   A D+LTKP  +EE++      +  RK  +
Sbjct: 82  GTIKTAVEAMKMGAYDFLTKPCMLEEIELTINKAIEHRKLRK 123

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

 Score = 87.5 bits (218), Expect = 2e-20
 Identities = 23/110 (20%), Positives = 46/110 (41%), Gaps = 3/110 (2%)

Query: 1   MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV-GLEMDLPVIMMCA 59
            G+          A   ++  +  + +++ DV MPD DG   ++ +     D  VI++  
Sbjct: 23  EGYHPDTAKTLREAEKKIK--ELFFPVIVLDVWMPDGDGVNFIDFIKENSPDSVVIVITG 80

Query: 60  HGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQSG 109
           HGS +  +K +   A ++L KP  +E      +H   +   +    E+  
Sbjct: 81  HGSVDTAVKAIKKGAYEFLEKPFSVERFLLTIKHAFEEYSKKAPPQEEIE 130

>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 = 82.8 bits (205), Expect = 2e-20
 Identities = 17/99 (17%), Positives = 34/99 (34%), Gaps = 2/99 (2%)

Query: 2   GFSVTKCNRAEIALDMLRT-NKNGYDIVISDVHMPDMDGFKLLE-LVGLEMDLPVIMMCA 59
           G           A  + RT   + +DI++ D    D      +E L  L   L  +++  
Sbjct: 44  GRYRVTRTVGRAAQIVQRTDGLDAFDILMIDGAALDTAELAAIEKLSRLHPGLTCLLVTT 103

Query: 60  HGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKR 98
             S + ++  +     D L  P+    L +  +    + 
Sbjct: 104 DASSQTLLDAMRAGVRDVLRWPLEPRALDDALKRAAAQC 142

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

 Score = 81.9 bits (203), Expect = 6e-20
 Identities = 26/110 (23%), Positives = 48/110 (43%), Gaps = 6/110 (5%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV-GLEMDLPVIMMCAH 60
            +++     A  AL +L + +   D+VIS  H+P MDG  LL  +         I++   
Sbjct: 38  PYTLHFARDATQALQLLASRE--VDLVISAAHLPQMDGPTLLARIHQQYPSTTRILLTGD 95

Query: 61  GSKEVVMKGVTHDAC-DYLTKPVRIEELKNIWQHVVRKR--KNERKDLEQ 107
              +++ K +       YL+KP   +EL    +  +  +  + ER  L+ 
Sbjct: 96  PDLKLIAKAINEGEIYRYLSKPWDDQELLLALRQALEHQHSERERLRLQD 145

>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 = 81.4 bits (202), Expect = 1e-19
 Identities = 32/99 (32%), Positives = 51/99 (51%), Gaps = 3/99 (3%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLE-LVGLEMDLPVIMMCAH 60
           GF+V+    A  AL  L  +     IVISD+ MP MDG  L   ++ L+ DLP+I++  H
Sbjct: 27  GFTVSSFASATEALAGLSADF--AGIVISDIRMPGMDGLALFRKILALDPDLPMILVTGH 84

Query: 61  GSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRK 99
           G   + ++ +   A D++ KP   + L    +    KR+
Sbjct: 85  GDIPMAVQAIQDGAYDFIAKPFAADRLVQSARRAEEKRR 123

>3kcn_A Adenylate cyclase homolog; SGX, PSI 2, structural genomics, protein structure initiative; 2.45A {Rhodopirellula baltica} Length = 151

 Score = 81.1 bits (201), Expect = 1e-19
 Identities = 19/111 (17%), Positives = 51/111 (45%), Gaps = 5/111 (4%)

Query: 1   MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV-GLEMDLPVIMMCA 59
             F VT C     AL  ++ + + + +++ D+ MP M+G ++++    +  +   +M+  
Sbjct: 26  FDFEVTTCESGPEALACIKKS-DPFSVIMVDMRMPGMEGTEVIQKARLISPNSVYLMLTG 84

Query: 60  HGSKEVVMKGVTH-DACDYLTKPVRIEELKNIWQHVVRKR--KNERKDLEQ 107
           +      M+ V       +L KP ++ ++K      +++      +++L +
Sbjct: 85  NQDLTTAMEAVNEGQVFRFLNKPCQMSDIKAAINAGIKQYDLVTSKEELLK 135

>2jk1_A HUPR, hydrogenase transcriptional regulatory protein HU; nucleotide-binding, transcription regulation; 2.10A {Rhodobacter capsulatus} PDB: 2vui_B 2vuh_B Length = 139

 Score = 80.6 bits (200), Expect = 1e-19
 Identities = 24/110 (21%), Positives = 41/110 (37%), Gaps = 6/110 (5%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV-GLEMDLPVIMMCAH 60
            F V     AE A+ +L   +    ++I D  MP   G   L  V     +   I++  +
Sbjct: 24  DFDVLTAQGAEAAIAILE--EEWVQVIICDQRMPGRTGVDFLTEVRERWPETVRIIITGY 81

Query: 61  GSKEVVMKGVTH-DACDYLTKPVRIEELKNIWQHVVRKR--KNERKDLEQ 107
                +M  +       +LTKP   E+L +  ++  R      E + L  
Sbjct: 82  TDSASMMAAINDAGIHQFLTKPWHPEQLLSSARNAARMFTLARENERLSL 131

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

 Score = 80.7 bits (200), Expect = 2e-19
 Identities = 23/110 (20%), Positives = 47/110 (42%), Gaps = 6/110 (5%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV-GLEMDLPVIMMCAH 60
           G ++        AL+ L+       +VISD+ MP+M G   LE V     D+  +++  +
Sbjct: 31  GCNIITFTSPLDALEALKGTS--VQLVISDMRMPEMGGEVFLEQVAKSYPDIERVVISGY 88

Query: 61  GSKEVVMKGVTHDACD-YLTKPVRIEELKNIWQHVVRKR--KNERKDLEQ 107
              +  +  V       +L KP   E++  + +  ++    + E   L++
Sbjct: 89  ADAQATIDAVNRGKISRFLLKPWEDEDVFKVVEKGLQLAFLREENLRLQE 138

>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 = 78.7 bits (195), Expect = 4e-19
 Identities = 26/99 (26%), Positives = 48/99 (48%), Gaps = 3/99 (3%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLE-LVGLEMDLPVIMMCAH 60
           GF+V     AE  L      +NG  ++++D+ MPDM G +LL  L  L++++P I++  H
Sbjct: 27  GFAVKMHQSAEAFLAFAPDVRNG--VLVTDLRMPDMSGVELLRNLGDLKINIPSIVITGH 84

Query: 61  GSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRK 99
           G   + ++ +   A D++ KP     +    +       
Sbjct: 85  GDVPMAVEAMKAGAVDFIEKPFEDTVIIEAIERASEHLV 123

>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 = 80.4 bits (199), Expect = 1e-18
 Identities = 22/111 (19%), Positives = 46/111 (41%), Gaps = 6/111 (5%)

Query: 1   MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV----GLEMDLPVIM 56
               V + + A  AL  L  +     +V+ D +MP++DG  L+ ++      +  L +I 
Sbjct: 147 QLLQVHEASHAREALATLEQHPA-IRLVLVDYYMPEIDGISLVRMLRERYSKQ-QLAIIG 204

Query: 57  MCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQ 107
           +     + +  + +   A D+L +P   EEL+    H +   +    +   
Sbjct: 205 ISVSDKRGLSARYLKQGANDFLNQPFEPEELQCRVSHNLEALEQFNSEGHH 255

>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 = 68.1 bits (167), Expect = 5e-14
 Identities = 17/102 (16%), Positives = 41/102 (40%), Gaps = 4/102 (3%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHG 61
           G  +   +  E      + ++  Y + + D+ +PD    + ++++ LE  LPV+++ A  
Sbjct: 29  GLEIDAFDTLE-GARHCQGDE--YVVALVDLTLPDAPSGEAVKVL-LERGLPVVILTADI 84

Query: 62  SKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERK 103
           S++     +     DY+ K  R      +          + +
Sbjct: 85  SEDKREAWLEAGVLDYVMKDSRHSLQYAVGLVHRLYLNQQIE 126

>2qr3_A Two-component system response regulator; structural genomics, signal receiver, PSI-2, protein structu initiative; 1.80A {Bacteroides fragilis} Length = 140

 Score = 77.6 bits (192), Expect = 2e-18
 Identities = 20/112 (17%), Positives = 46/112 (41%), Gaps = 8/112 (7%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPD-----MDGFKLLELV-GLEMDLPVI 55
              V   +       +LR      ++V+ D++         +G   L  +     DLPV+
Sbjct: 27  FSKVITLSSPVSLSTVLREEN--PEVVLLDMNFTSGINNGNEGLFWLHEIKRQYRDLPVV 84

Query: 56  MMCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQ 107
           +  A+   ++ ++G+   A D++ KP   ++L     +   + K+ +K+   
Sbjct: 85  LFTAYADIDLAVRGIKEGASDFVVKPWDNQKLLETLLNAASQAKDGKKEGHH 136

>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 = 78.7 bits (194), Expect = 3e-17
 Identities = 26/105 (24%), Positives = 45/105 (42%), Gaps = 6/105 (5%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIMMC 58
            + V+       AL M   +    DI++ DV MP MDGF +   +        +PV+++ 
Sbjct: 25  YYEVSTAMDGPTALAMAARDL--PDIILLDVMMPGMDGFTVCRKLKDDPTTRHIPVVLIT 82

Query: 59  AHGSKEVVMKGVTHDACDYLTKPVRIEELK-NIWQHVVRKRKNER 102
           A   +   ++G+   A D+LTKP+    L   +      K   + 
Sbjct: 83  ALDGRGDRIQGLESGASDFLTKPIDDVMLFARVRSLTRFKLVIDE 127

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

 Score = 64.8 bits (158), Expect = 2e-12
 Identities = 20/105 (19%), Positives = 42/105 (40%), Gaps = 8/105 (7%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLE---MDLPVIMMC 58
              V + +  +  +    +     D+VI +    + DG +    +  E     LPV+ M 
Sbjct: 176 HRPVIESDPEKAKI----SAGGPVDLVIVNAAAKNFDGLRFTAALRSEERTRQLPVLAMV 231

Query: 59  AHGSKEVVMKGVTHDACDYLTKPVRIEELK-NIWQHVVRKRKNER 102
               +  ++K +     D L++P+  +EL   +   + RKR  + 
Sbjct: 232 DPDDRGRMVKALEIGVNDILSRPIDPQELSARVKTQIQRKRYTDY 276

>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 = 75.4 bits (186), Expect = 3e-17
 Identities = 21/102 (20%), Positives = 47/102 (46%), Gaps = 3/102 (2%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLL-ELVGLEMDLPVIMMCAH 60
           G++V + +  + AL +    K  ++ +   +H+ +  G  L+  L  L+ D  ++++  +
Sbjct: 31  GYAVRQAHNKDEALKLAGAEK--FEFITVXLHLGNDSGLSLIAPLCDLQPDARILVLTGY 88

Query: 61  GSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNER 102
            S    ++ V   A +YL KP  +E +    Q    + + E 
Sbjct: 89  ASIATAVQAVKDGADNYLAKPANVESILAALQTNASEVQAEE 130

>3cg0_A Response regulator receiver modulated diguanylate with PAS/PAC sensor; signal receiver domain, diguanylate cyclase; 2.15A {Desulfovibrio desulfuricans subsp} Length = 140

 Score = 74.1 bits (183), Expect = 3e-17
 Identities = 22/109 (20%), Positives = 43/109 (39%), Gaps = 4/109 (3%)

Query: 1   MGFSVTK-CNRAEIALDMLRTNKNGYDIVISDVHM-PDMDGFKLLELVGLEMDLPVIMMC 58
           +G+ V    +  E A+      +   DI + D+ +   +DG +    +    +LP+I + 
Sbjct: 32  LGYDVLGVFDNGEEAVRCAPDLR--PDIALVDIMLCGALDGVETAARLAAGCNLPIIFIT 89

Query: 59  AHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQ 107
           +    E   +    +   YL KPV  + L    +  + K+K E      
Sbjct: 90  SSQDVETFQRAKRVNPFGYLAKPVAADTLHRSIEMAIHKKKLEEGHHHH 138

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

 Score = 78.0 bits (192), Expect = 5e-17
 Identities = 21/88 (23%), Positives = 40/88 (45%), Gaps = 3/88 (3%)

Query: 1   MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLE-LVGLEMDLPVIMMCA 59
             F V +       L +  + +   D+VI D+ MP +DG +L+  +     + P+I++  
Sbjct: 28  SNFKVLQALNGLQGLQIFESEQ--PDLVICDLRMPQIDGLELIRRIRQTASETPIIVLSG 85

Query: 60  HGSKEVVMKGVTHDACDYLTKPVRIEEL 87
            G     ++ +   A DYL KP+    +
Sbjct: 86  AGVMSDAVEALRLGAADYLIKPLEDLAV 113

>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 = 74.6 bits (184), Expect = 9e-17
 Identities = 25/113 (22%), Positives = 52/113 (46%), Gaps = 3/113 (2%)

Query: 1   MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLL-ELVGLEMDLPVIMMCA 59
            GF V   + A   L+  R  +  +  ++ D+ MP M G +L  +L  +   +P++ + A
Sbjct: 27  AGFEVETFDCASTFLEHRRPEQ--HGCLVLDMRMPGMSGIELQEQLTAISDGIPIVFITA 84

Query: 60  HGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQSGSVE 112
           HG   + ++ +   A ++L KP   + L +  +  ++     R+  E    +E
Sbjct: 85  HGDIPMTVRAMKAGAIEFLPKPFEEQALLDAIEQGLQLNAERRQARETQDQLE 137

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

 Score = 76.3 bits (188), Expect = 1e-16
 Identities = 22/90 (24%), Positives = 35/90 (38%), Gaps = 5/90 (5%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIMMC 58
           G     C+  + A+ +    K    +++ D+ MP +DG  LL          D+P+I++ 
Sbjct: 43  GIDFHFCSDPQQAVAVANQIK--PTVILQDLVMPGVDGLTLLAAYRGNPATRDIPIIVLS 100

Query: 59  AHGSKEVVMKGVTHDACDYLTKPVRIEELK 88
                 V        A DYL K     EL 
Sbjct: 101 TKEEPTVKSAAFAAGANDYLVKLPDAIELV 130

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

 Score = 72.2 bits (178), Expect = 2e-16
 Identities = 23/103 (22%), Positives = 40/103 (38%), Gaps = 6/103 (5%)

Query: 1   MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIMM 57
           +GF          AL  + T    YD V  D+++PD  G  L++ +    +E     + +
Sbjct: 26  LGFQADYVMSGTDALHAMSTRG--YDAVFIDLNLPDTSGLALVKQLRALPMEKTSKFVAV 83

Query: 58  CAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKN 100
                 ++  K        YL KP+ I  L+ I Q +     +
Sbjct: 84  SGFAKNDLG-KEACELFDFYLEKPIDIASLEPILQSIEGHHHH 125

>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 = 74.4 bits (183), Expect = 3e-16
 Identities = 32/109 (29%), Positives = 53/109 (48%), Gaps = 15/109 (13%)

Query: 1   MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV-GLEMDLPVIMMCA 59
           +G+     N    AL++L   KN  DIV+SDV+MP+MDG++L + +  L + LPVI + A
Sbjct: 152 LGYQCKTANDGVDALNVLS--KNHIDIVLSDVNMPNMDGYRLTQRIRQLGLTLPVIGVTA 209

Query: 60  HGSKEVVMKGVTHDAC------DYLTKPVRIEELKNIWQHVVRKRKNER 102
           +      +       C        L+KPV ++ +K        + +  R
Sbjct: 210 N-----ALAE-EKQRCLESGMDSCLSKPVTLDVIKQTLTLYAERVRKSR 252

>3kto_A Response regulator receiver protein; PSI-II,structural genomics, protein structure initiative; 1.98A {Pseudoalteromonas atlantica T6C} Length = 136

 Score = 70.3 bits (173), Expect = 1e-15
 Identities = 22/109 (20%), Positives = 41/109 (37%), Gaps = 5/109 (4%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDM--DGFKLLE-LVGLEMDLPVIMMC 58
             ++     AE  +    ++      +I + H+ D    G +LLE LV     LP I+M 
Sbjct: 30  DVTIQCFASAESFMRQQISDDAI--GMIIEAHLEDKKDSGIELLETLVKRGFHLPTIVMA 87

Query: 59  AHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQ 107
           +       ++ +   A D++ KP     L +  Q ++   K        
Sbjct: 88  SSSDIPTAVRAMRASAADFIEKPFIEHVLVHDVQQIINGAKEGHHHHHH 136

>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 = 69.5 bits (171), Expect = 2e-15
 Identities = 28/91 (30%), Positives = 43/91 (47%), Gaps = 5/91 (5%)

Query: 12  EIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIMMCAHGSKEVVMK 68
           E  + ++  N   + +VISD +MP MDG  LL+ V           I++ A G + +V K
Sbjct: 41  EQGMKIMAQNP--HHLVISDFNMPKMDGLGLLQAVRANPATKKAAFIILTAQGDRALVQK 98

Query: 69  GVTHDACDYLTKPVRIEELKNIWQHVVRKRK 99
                A + L KP  IE++K   + V    K
Sbjct: 99  AAALGANNVLAKPFTIEKMKAAIEAVFGALK 129

>3eqz_A Response regulator; structural genomics, unknown function, PSI-2, protein struct initiative; 2.15A {Colwellia psychrerythraea} Length = 135

 Score = 69.6 bits (171), Expect = 2e-15
 Identities = 24/92 (26%), Positives = 39/92 (42%), Gaps = 9/92 (9%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLL-ELVGLEMDLPVIMMCAH 60
             +V        A   L  NK   DI+I D+ MPDMDG +++  L   +    +I++  +
Sbjct: 27  FGNVEAFQHPR-AFLTLSLNK--QDIIILDLMMPDMDGIEVIRHLAEHKSPASLILISGY 83

Query: 61  G-----SKEVVMKGVTHDACDYLTKPVRIEEL 87
                 S E +      +  +  TKP+  E L
Sbjct: 84  DSGVLHSAETLALSCGLNVINTFTKPINTEVL 115

>3h5i_A Response regulator/sensory box protein/ggdef domain protein; structural genomics, transcription, PSI-2; 1.90A {Carboxydothermus hydrogenoformans z-2901} Length = 140

 Score = 69.5 bits (171), Expect = 2e-15
 Identities = 24/108 (22%), Positives = 45/108 (41%), Gaps = 2/108 (1%)

Query: 1   MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMP-DMDGFKLLELVGLEMDLPVIMMCA 59
            G++V      E A++ +       D+++ D+ +   MDG +    +    +LPV+ + A
Sbjct: 28  YGYTVEIALTGEAAVEKVSGGWY-PDLILMDIELGEGMDGVQTALAIQQISELPVVFLTA 86

Query: 60  HGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQ 107
           H    VV K  +  A  Y+ K    + L  I +  +R  +      E 
Sbjct: 87  HTEPAVVEKIRSVTAYGYVMKSATEQVLITIVEMALRLYEANVHANEG 134

>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 = 69.1 bits (170), Expect = 2e-15
 Identities = 26/106 (24%), Positives = 42/106 (39%), Gaps = 6/106 (5%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEM---DLPVIMMC 58
              +        A D+L T K   D+V+ D+ M  MDGF +   +       ++ VI M 
Sbjct: 34  YAKIKIAYNPFDAGDLLHTVK--PDVVMLDLMMVGMDGFSICHRIKSTPATANIIVIAMT 91

Query: 59  AHGSKEVVMKGVTHDACDYLTKPVRIEELK-NIWQHVVRKRKNERK 103
              + + V + V   A     KP+    L+  I Q V +K+     
Sbjct: 92  GALTDDNVSRIVALGAETCFGKPLNFTLLEKTIKQLVEQKKATSEG 137

>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 = 69.0 bits (169), Expect = 3e-15
 Identities = 22/102 (21%), Positives = 45/102 (44%), Gaps = 3/102 (2%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLL-ELVGLEMDLPVIMMCAH 60
           G+ V     A   L  +      +++ +  + +PDM+G +LL +   L   +  IM+  +
Sbjct: 27  GYEVEIAATAGEGLAKIENEF--FNLALFXIKLPDMEGTELLEKAHKLRPGMKKIMVTGY 84

Query: 61  GSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNER 102
            S E  +  +   A  Y+ KPV   +L    +  + +++ E 
Sbjct: 85  ASLENSVFSLNAGADAYIMKPVNPRDLLEKIKEKLDEQEKEG 126

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

 Score = 68.9 bits (169), Expect = 3e-15
 Identities = 19/87 (21%), Positives = 33/87 (37%), Gaps = 3/87 (3%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV-GLEMDLPVIMMCAH 60
            + V      +         +    IVI D+   D+ G   +     L   +P+I +   
Sbjct: 39  IYDVRVSETDDFLKGPPADTR--PGIVILDLGGGDLLGKPGIVEARALWATVPLIAVSDE 96

Query: 61  GSKEVVMKGVTHDACDYLTKPVRIEEL 87
            + E     V  +A D+L KP+  +EL
Sbjct: 97  LTSEQTRVLVRMNASDWLHKPLDGKEL 123

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

 Score = 67.2 bits (165), Expect = 1e-14
 Identities = 29/111 (26%), Positives = 46/111 (41%), Gaps = 21/111 (18%)

Query: 1   MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGF------KLLELVGLEMDLPV 54
            G  V   N AE  LD +   +  YD VI D+HMP M+G       ++++  G+    PV
Sbjct: 37  AGHKVLCVNGAEQVLDAMA--EEDYDAVIVDLHMPGMNGLDMLKQLRVMQASGMR-YTPV 93

Query: 55  IMMCAHGSKEVVMKGVTHDAC------DYLTKPVRIEELKNIWQHVVRKRK 99
           +++ A      V       AC       +L KPV   +L +    +    +
Sbjct: 94  VVLSAD-----VTPE-AIRACEQAGARAFLAKPVVAAKLLDTLADLAVSTR 138

>3grc_A Sensor protein, kinase; protein structure initiative II(PSI II), NYSGXRC, 11025B, structural genomics; 2.21A {Polaromonas SP} Length = 140

 Score = 67.2 bits (165), Expect = 2e-14
 Identities = 20/90 (22%), Positives = 37/90 (41%), Gaps = 6/90 (6%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIMMC 58
           GF     + A  AL+ +      Y  +  D+++PD DG  L+  +       DL ++++ 
Sbjct: 30  GFDSDMVHSAAQALEQVARRP--YAAMTVDLNLPDQDGVSLIRALRRDSRTRDLAIVVVS 87

Query: 59  AHGS-KEVVMKGVTHDACDYLTKPVRIEEL 87
           A+    E+           +L KP+    L
Sbjct: 88  ANAREGELEFNSQPLAVSTWLEKPIDENLL 117

>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 = 66.9 bits (164), Expect = 2e-14
 Identities = 27/78 (34%), Positives = 40/78 (51%), Gaps = 5/78 (6%)

Query: 14  ALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIMMCAHGSKEVVMKGV 70
           AL+ L+     Y  VISD +MP+MDG +LL+ +        LPV+M+ A   KE ++   
Sbjct: 41  ALNKLQAGG--YGFVISDWNMPNMDGLELLKTIRAXXAMSALPVLMVTAEAKKENIIAAA 98

Query: 71  THDACDYLTKPVRIEELK 88
              A  Y+ KP     L+
Sbjct: 99  QAGASGYVVKPFTAATLE 116

>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 = 66.4 bits (163), Expect = 2e-14
 Identities = 22/109 (20%), Positives = 45/109 (41%), Gaps = 21/109 (19%)

Query: 1   MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGF---KLLELVGLEMDLPVIMM 57
            G+   +      AL + R NK   D+++ D+ +P++ G    K L+       +PV+ +
Sbjct: 24  QGYETLQTREGLSALSIARENK--PDLILMDIQLPEISGLEVTKWLKEDDDLAHIPVVAV 81

Query: 58  CAHGSKEVVMKGVTHD--AC------DYLTKPVRIEELKNIWQHVVRKR 98
            A       MKG   D           Y++KP+ +       + ++ ++
Sbjct: 82  TAF-----AMKG---DEERIREGGCEAYISKPISVVHFLETIKRLLERQ 122

>3cu5_A Two component transcriptional regulator, ARAC FAM; structural genomics, protein structure initiative; 2.60A {Clostridium phytofermentans isdg} Length = 141

 Score = 66.4 bits (163), Expect = 3e-14
 Identities = 22/109 (20%), Positives = 49/109 (44%), Gaps = 4/109 (3%)

Query: 1   MGFSVT-KCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV-GLEMDLPVIMMC 58
           + F    + +    A+ +   +    +++++DV MP MDG +L++ +  L  D  VI M 
Sbjct: 27  LSFDQIDQADDGINAIQIALKHP--PNVLLTDVRMPRMDGIELVDNILKLYPDCSVIFMS 84

Query: 59  AHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQ 107
            +  KE +   +   A  Y+ KP+   E+ +  +  ++     +   + 
Sbjct: 85  GYSDKEYLKAAIKFRAIRYVEKPIDPSEIMDALKQSIQTVLQHQAQQDS 133

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

 Score = 66.8 bits (163), Expect = 3e-14
 Identities = 22/87 (25%), Positives = 40/87 (45%), Gaps = 1/87 (1%)

Query: 12  EIALDMLRTNKNGYDIVISDVHMPDMDGFKLL-ELVGLEMDLPVIMMCAHGSKEVVMKGV 70
           E A+   + +    DIV   + MP MDG   L  ++  + +  VIM+ A G +++V   +
Sbjct: 71  EEAVIKYKNHYPNIDIVTLXITMPKMDGITCLSNIMEFDKNARVIMISALGKEQLVKDCL 130

Query: 71  THDACDYLTKPVRIEELKNIWQHVVRK 97
              A  ++ KP+   ++      V  K
Sbjct: 131 IKGAKTFIVKPLDRAKVLQRVMSVFVK 157

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

 Score = 66.1 bits (162), Expect = 3e-14
 Identities = 23/104 (22%), Positives = 46/104 (44%), Gaps = 7/104 (6%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPD-MDGFKLLELVGLEM--DLPVIMMC 58
           GF VT  +    A++ML++     D V++D+      DG+++  +   E+  ++P++ + 
Sbjct: 29  GFLVTAVSSGAKAIEMLKSGA-AIDGVVTDIRFCQPPDGWQVARVA-REIDPNMPIVYIS 86

Query: 59  AHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNER 102
            H + E    GV       L KP    +L      ++  R+   
Sbjct: 87  GHAALEWASNGVPDSI--ILEKPFTSAQLITAVSQLLNAREGHH 128

>3ilh_A Two component response regulator; NYSGXRC, PSI-II, protein S initiative, structural genomics; 2.59A {Cytophaga hutchinsonii} Length = 146

 Score = 66.2 bits (162), Expect = 4e-14
 Identities = 19/96 (19%), Positives = 43/96 (44%), Gaps = 9/96 (9%)

Query: 14  ALDMLRTNKNG---YDIVISDVHMPDMDGFKLLELV-----GLEMDLPVIMMCAHGSKEV 65
           A++ L           I+  D++MP ++G++L++L       ++    V ++ +      
Sbjct: 47  AINKLNELYAAGRWPSIICIDINMPGINGWELIDLFKQHFQPMKNKSIVCLLSSSLDPRD 106

Query: 66  VMKGVTHDACD-YLTKPVRIEELKNIWQHVVRKRKN 100
             K    D  D Y++KP+    L N++  V+ +  +
Sbjct: 107 QAKAEASDWVDYYVSKPLTANALNNLYNKVLNEGHH 142

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

 Score = 65.3 bits (160), Expect = 7e-14
 Identities = 18/112 (16%), Positives = 38/112 (33%), Gaps = 17/112 (15%)

Query: 1   MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGF------KLLELVGLEMDLPV 54
               +T       AL   +  +  +D++I D+ MP MDG       +  E         +
Sbjct: 33  CTNDITVVTNGLQALQAYQNRQ--FDVIIMDIQMPVMDGLEAVSEIRNYERTHNTKRASI 90

Query: 55  IMMCAHGSKEVVMKGVTHDAC---DYLTKPVRIEELKNIWQHVVRKRKNERK 103
           I + A       +           +Y++KP+   +L+++      +      
Sbjct: 91  IAITAD-----TIDD-DRPGAELDEYVSKPLNPNQLRDVVLTCHSEGAEGHH 136

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

 Score = 65.2 bits (160), Expect = 8e-14
 Identities = 18/110 (16%), Positives = 43/110 (39%), Gaps = 21/110 (19%)

Query: 1   MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKL------LELVGLEMDLPV 54
           +G  VT  +  E  L ++    + + +V  DV MP ++ +++                 +
Sbjct: 30  LGCEVTTVSSNEECLRVVS---HEHKVVFMDVCMPGVENYQIALRIHEKFTKQRHQRPLL 86

Query: 55  IMMCAHGSKEVVMKGVTHDAC------DYLTKPVRIEELKNIWQHVVRKR 98
           + +  +       K  T + C        L KPV ++ ++++   ++  R
Sbjct: 87  VALSGN-----TDKS-TKEKCMSFGLDGVLLKPVSLDNIRDVLSDLLEPR 130

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

 Score = 64.5 bits (158), Expect = 1e-13
 Identities = 24/88 (27%), Positives = 40/88 (45%), Gaps = 4/88 (4%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLL-ELVGLEMDLPVIMMCAH 60
           G +         AL++L       D++I D+ MP M+G KLL  +       PV+++ A 
Sbjct: 31  GATTVLAADGVDALELLGGFT--PDLMICDIAMPRMNGLKLLEHIRNRGDQTPVLVISAT 88

Query: 61  GSKEVVMKGVTHDACDYLTKPVR-IEEL 87
            +   + K +     D L KPV+ +  L
Sbjct: 89  ENMADIAKALRLGVEDVLLKPVKDLNRL 116

>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 = 64.9 bits (159), Expect = 1e-13
 Identities = 18/87 (20%), Positives = 30/87 (34%), Gaps = 5/87 (5%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLL-ELVGLEMDLPVIMMCAH 60
           G  VT                +  D++I    + D+  F LL  +        V+++   
Sbjct: 39  GAEVTVHPSGSAFFQHRS-QLSTCDLLIVSDQLVDLSIFSLLDIVKEQTKQPSVLILTTG 97

Query: 61  GSKEVVMKGVTHDACDYLTKPVRIEEL 87
                +++   H    YL KP  I EL
Sbjct: 98  R--HELIESSEH-NLSYLQKPFAISEL 121

>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 = 67.1 bits (164), Expect = 2e-13
 Identities = 22/104 (21%), Positives = 42/104 (40%), Gaps = 6/104 (5%)

Query: 1   MGFSVT-KCNRAEIALDMLRTNKNGYDIVISDVHMPD-MDGFKLLELVGLEMDLPVIMMC 58
           +G  VT        AL+ +        +V++D+ + D   G   ++ +   MD+PVI + 
Sbjct: 183 LGHDVTDIAATRGEALEAVTRRT--PGLVLADIQLADGSSGIDAVKDILGRMDVPVIFIT 240

Query: 59  AHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNER 102
           A    E ++ G   +    +TKP + E +K      +       
Sbjct: 241 AFP--ERLLTGERPEPTFLITKPFQPETVKAAIGQALFFHPRRT 282

>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 = 66.0 bits (162), Expect = 2e-13
 Identities = 27/87 (31%), Positives = 44/87 (50%), Gaps = 3/87 (3%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLL-ELVGLEMDLPVIMMCAH 60
           GF V        AL     N+   D ++ D++MP +DG  ++  L  ++ D+PV ++ A 
Sbjct: 31  GFEVATAVDGAEALRSATENR--PDAIVLDINMPVLDGVSVVTALRAMDNDVPVCVLSAR 88

Query: 61  GSKEVVMKGVTHDACDYLTKPVRIEEL 87
            S +  + G+   A DYL KP  + EL
Sbjct: 89  SSVDDRVAGLEAGADDYLVKPFVLAEL 115

>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 = 64.1 bits (157), Expect = 2e-13
 Identities = 25/91 (27%), Positives = 46/91 (50%), Gaps = 5/91 (5%)

Query: 2   GF-SVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIMM 57
           G+  V +      A + L  N +   ++I+D +MP+M+G  L++ V       ++P+IM+
Sbjct: 29  GYEDVLEAEHGVEAWEKLDANAD-TKVLITDWNMPEMNGLDLVKKVRSDSRFKEIPIIMI 87

Query: 58  CAHGSKEVVMKGVTHDACDYLTKPVRIEELK 88
            A G K  V+  +     +Y+ KP   + LK
Sbjct: 88  TAEGGKAEVITALKAGVNNYIVKPFTPQVLK 118

>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 = 65.9 bits (160), Expect = 3e-13
 Identities = 35/108 (32%), Positives = 51/108 (47%), Gaps = 3/108 (2%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLL-ELVGLEMDLPVIMMCAH 60
           GF V        ALD  R  +   D VI DV MP MDGF +L  L    +D P + + A 
Sbjct: 47  GFEVYTATNGAQALDRARETR--PDAVILDVXMPGMDGFGVLRRLRADGIDAPALFLTAR 104

Query: 61  GSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQS 108
            S +  + G+T    DY+TKP  +EE+    + ++R+     K+    
Sbjct: 105 DSLQDKIAGLTLGGDDYVTKPFSLEEVVARLRVILRRAGKGNKEPRNV 152

>3q9s_A DNA-binding response regulator; DNA binding protein; 2.40A {Deinococcus radiodurans} Length = 249

 Score = 65.3 bits (160), Expect = 4e-13
 Identities = 24/86 (27%), Positives = 44/86 (51%), Gaps = 2/86 (2%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHG 61
           G+ V   + A   L   R +    D+++ D+ +PD DG  +++ +     LP+I++ A  
Sbjct: 61  GYVVDHADSAMNGLIKAREDH--PDLILLDLGLPDFDGGDVVQRLRKNSALPIIVLTARD 118

Query: 62  SKEVVMKGVTHDACDYLTKPVRIEEL 87
           + E  ++ +   A DYL KP   +EL
Sbjct: 119 TVEEKVRLLGLGADDYLIKPFHPDEL 144

>3a10_A Response regulator; phosphoacceptor, signaling protein; HET: MSE PG4; 1.63A {Thermotoga maritima} PDB: 3a0r_B* 3a0u_A* Length = 116

 Score = 62.5 bits (153), Expect = 6e-13
 Identities = 22/87 (25%), Positives = 39/87 (44%), Gaps = 5/87 (5%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLL-ELVGLEMDLPVIMMCAH 60
           G+ +      E AL    +    YD+VI D+ MP + G ++  E+   + D  +I++ A+
Sbjct: 25  GYEIDTAENGEEALKKFFSGN--YDLVILDIEMPGISGLEVAGEIRKKKKDAKIILLTAY 82

Query: 61  GSKEVVMKGVTHDACDYLTKPVRIEEL 87
                 M     D  +Y+ K    +EL
Sbjct: 83  SHYRSDMSSWAAD--EYVVKSFNFDEL 107

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

 Score = 63.0 bits (154), Expect = 6e-13
 Identities = 21/98 (21%), Positives = 43/98 (43%), Gaps = 10/98 (10%)

Query: 14  ALDMLR----TNKNGYDIVISDVHMPDMDGFKLLELV----GLEMDLPVIMMCAHGSKEV 65
           ALDML      NK    +++ D+++P M+G + L+ +        D+ V ++ A  + + 
Sbjct: 45  ALDMLYGRNKENKIHPKLILLDINIPKMNGIEFLKELRDDSSFT-DIEVFVLTAAYTSKD 103

Query: 66  VMKGVTHDACDYLTKPVRIEEL-KNIWQHVVRKRKNER 102
            +   + +   +L KP+   E  K  W     +  +  
Sbjct: 104 KLAFESLNIRGHLIKPLDYGEAIKLFWILQSMEGHHHH 141

>3lua_A Response regulator receiver protein; two-component signal transduction system, histidine kinase, phosphorelay, receiver domain, nysgxrc; 2.40A {Clostridium thermocellum} Length = 140

 Score = 62.7 bits (153), Expect = 7e-13
 Identities = 16/109 (14%), Positives = 43/109 (39%), Gaps = 5/109 (4%)

Query: 3   FSVTKCNRAEIALDMLRTNKNGYDIVISDVHMP-DMDGFKLLELVGLEM---DLPVIMMC 58
           +   +    +    + + + +   ++I D+  P + +G ++L  +       + PVI+  
Sbjct: 30  YDFIEVENLKKFYSIFK-DLDSITLIIMDIAFPVEKEGLEVLSAIRNNSRTANTPVIIAT 88

Query: 59  AHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQ 107
              +       +     DY+ KP   + L+N  + V++  +  R+    
Sbjct: 89  KSDNPGYRHAALKFKVSDYILKPYPTKRLENSVRSVLKICQRFREGHHH 137

>2qzj_A Two-component response regulator; 11017X, PSI-II, structural genomics; 2.89A {Clostridium difficile} Length = 136

 Score = 62.5 bits (153), Expect = 7e-13
 Identities = 21/86 (24%), Positives = 41/86 (47%), Gaps = 2/86 (2%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHG 61
           G S+      E A+  + +NK  YD++  ++ + D DG+ L + +      P++ M    
Sbjct: 28  GISIDLAYNCEEAIGKIFSNK--YDLIFLEIILSDGDGWTLCKKIRNVTTCPIVYMTYIN 85

Query: 62  SKEVVMKGVTHDACDYLTKPVRIEEL 87
             + ++  +     DYL KP+ +E L
Sbjct: 86  EDQSILNALNSGGDDYLIKPLNLEIL 111

>3nhm_A Response regulator; protein structure initiative II(PSI II), NYSGXRC, structural genomics; 2.19A {Myxococcus xanthus} Length = 133

 Score = 61.8 bits (151), Expect = 1e-12
 Identities = 24/109 (22%), Positives = 37/109 (33%), Gaps = 6/109 (5%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEM---DLPVIMMC 58
            F  T        L     +    D++ISDV+M  MDG+ L      E     +PVI + 
Sbjct: 27  EFDCTTAADGASGLQQALAHP--PDVLISDVNMDGMDGYALCGHFRSEPTLKHIPVIFVS 84

Query: 59  AHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQ 107
            +                YL KPV+   L      ++ + + E      
Sbjct: 85  GYAP-RTEGPADQPVPDAYLVKPVKPPVLIAQLHALLARAEAEGHHHHH 132

>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 = 61.4 bits (150), Expect = 2e-12
 Identities = 24/114 (21%), Positives = 50/114 (43%), Gaps = 14/114 (12%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIMMC 58
            + V +    + AL+ +  +    D+VI D+ +   +   L   +       ++P+I++ 
Sbjct: 26  EYLVIESKNEKEALEQIDHHH--PDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILLF 83

Query: 59  AHGSKEVVMKGVTHDACDYLTKPVRIEEL----KNIWQHVVRKRKNERKDLEQS 108
           +   KE ++ G+   A DYLTKP    +L    +        + +N   DL ++
Sbjct: 84  SSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHL-----RTQNYYSDLRKN 132

>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 = 62.8 bits (154), Expect = 2e-12
 Identities = 28/87 (32%), Positives = 46/87 (52%), Gaps = 3/87 (3%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLE-LVGLEMDLPVIMMCAH 60
            F+V  C   E  + M       +D+VI D+ +P  DG+++L+ +    ++ PV+M+ A 
Sbjct: 26  MFTVDVCYDGEEGMYMALNEP--FDVVILDIMLPVHDGWEILKSMRESGVNTPVLMLTAL 83

Query: 61  GSKEVVMKGVTHDACDYLTKPVRIEEL 87
              E  +KG+   A DYL KP  + EL
Sbjct: 84  SDVEYRVKGLNMGADDYLPKPFDLREL 110

>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 = 62.8 bits (153), Expect = 2e-12
 Identities = 20/78 (25%), Positives = 35/78 (44%)

Query: 26  DIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTKPVRIE 85
           D+VI DV MP  DG      +  +   P++++ A   +++V +     A  YL KP  I 
Sbjct: 60  DLVIMDVKMPRRDGIDAASEIASKRIAPIVVLTAFSQRDLVERARDAGAMAYLVKPFSIS 119

Query: 86  ELKNIWQHVVRKRKNERK 103
           +L    +  V + +    
Sbjct: 120 DLIPAIELAVSRFREITA 137

>3lte_A Response regulator; structural genomics, PSI, protein structure initiative, NYSG YORK structural genomix research consortium, nysgxrc; 2.00A {Bermanella marisrubri} Length = 132

 Score = 61.0 bits (149), Expect = 2e-12
 Identities = 22/88 (25%), Positives = 38/88 (43%), Gaps = 4/88 (4%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV--GLEMDLPVIMMCA 59
            + V   +    A   L T +    I+  D+ MP +DG  ++  +      + P I++ +
Sbjct: 30  HWQVEIAHNGFDAGIKLSTFE--PAIMTLDLSMPKLDGLDVIRSLRQNKVANQPKILVVS 87

Query: 60  HGSKEVVMKGVTHDACDYLTKPVRIEEL 87
              K  + + VT  A DYL KP   + L
Sbjct: 88  GLDKAKLQQAVTEGADDYLEKPFDNDAL 115

>3gt7_A Sensor protein; structural genomics, signal receiver domain, kinase, PSI-2, protein structure initiative; 2.30A {Syntrophus aciditrophicus SB} Length = 154

 Score = 61.1 bits (149), Expect = 4e-12
 Identities = 27/119 (22%), Positives = 56/119 (47%), Gaps = 6/119 (5%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGF---KLLELVGLEMDLPVIMMC 58
           G+          A+  L   +   D++ISDV MP+MDG+   + L+       +PVI++ 
Sbjct: 31  GYQTEHVRNGREAVRFLSLTR--PDLIISDVLMPEMDGYALCRWLKGQPDLRTIPVILLT 88

Query: 59  AHGSKEVVMKGVTHDACDYLTKPVRIEELKN-IWQHVVRKRKNERKDLEQSGSVEGGAQ 116
                  V++ +   A D++TKP +   L + + + +   ++ E +   +S ++  G +
Sbjct: 89  ILSDPRDVVRSLECGADDFITKPCKDVVLASHVKRLLSGVKRTEERYSRESITLAFGNE 147

>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 = 59.8 bits (146), Expect = 5e-12
 Identities = 25/86 (29%), Positives = 41/86 (47%), Gaps = 2/86 (2%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHG 61
           G  V +    +  L    T K   D++I D+ +PD DG + +  +     +PVI++ A  
Sbjct: 25  GMRVFEAETLQRGLLEAATRK--PDLIILDLGLPDGDGIEFIRDLRQWSAVPVIVLSARS 82

Query: 62  SKEVVMKGVTHDACDYLTKPVRIEEL 87
            +   +  +   A DYL+KP  I EL
Sbjct: 83  EESDKIAALDAGADDYLSKPFGIGEL 108

>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 = 59.8 bits (146), Expect = 6e-12
 Identities = 27/87 (31%), Positives = 45/87 (51%), Gaps = 3/87 (3%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLL-ELVGLEMDLPVIMMCAH 60
           G  V     A+ A   L  +    DI I D+ +PD DG  L+      ++ LP++++ A 
Sbjct: 24  GHQVDDAEDAKEADYYLNEH--IPDIAIVDLGLPDEDGLSLIRRWRSNDVSLPILVLTAR 81

Query: 61  GSKEVVMKGVTHDACDYLTKPVRIEEL 87
            S +  ++ ++  A DY+TKP  IEE+
Sbjct: 82  ESWQDKVEVLSAGADDYVTKPFHIEEV 108

>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 = 58.6 bits (143), Expect = 1e-11
 Identities = 25/86 (29%), Positives = 47/86 (54%), Gaps = 2/86 (2%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHG 61
           G+ V   +    A++M+   +   D+++ D+ +P+ DG ++   V  + D+P+IM+ A  
Sbjct: 26  GYEVHCAHDGNEAVEMVEELQ--PDLILLDIMLPNKDGVEVCREVRKKYDMPIIMLTAKD 83

Query: 62  SKEVVMKGVTHDACDYLTKPVRIEEL 87
           S+   + G+   A DY+TKP    EL
Sbjct: 84  SEIDKVIGLEIGADDYVTKPFSTREL 109

>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 = 60.6 bits (148), Expect = 2e-11
 Identities = 23/86 (26%), Positives = 43/86 (50%), Gaps = 2/86 (2%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHG 61
           GF          AL  +R  +   D+V+ D+ +P M+G  +  ++  +  +P++M+ A  
Sbjct: 29  GFDTAVIGDGTQALTAVRELR--PDLVLLDLMLPGMNGIDVCRVLRADSGVPIVMLTAKT 86

Query: 62  SKEVVMKGVTHDACDYLTKPVRIEEL 87
               V+ G+   A DY+ KP + +EL
Sbjct: 87  DTVDVVLGLESGADDYIMKPFKPKEL 112

>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 = 58.2 bits (142), Expect = 2e-11
 Identities = 24/86 (27%), Positives = 44/86 (51%), Gaps = 2/86 (2%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHG 61
           G+ V        AL+     +   DI+I D+ +P++DG ++ + +     +P++M+ A  
Sbjct: 25  GYEVVTAFNGREALEQFEAEQ--PDIIILDLMLPEIDGLEVAKTIRKTSSVPILMLSAKD 82

Query: 62  SKEVVMKGVTHDACDYLTKPVRIEEL 87
           S+   + G+   A DY+TKP    EL
Sbjct: 83  SEFDKVIGLELGADDYVTKPFSNREL 108

>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 = 58.8 bits (143), Expect = 2e-11
 Identities = 19/101 (18%), Positives = 43/101 (42%), Gaps = 18/101 (17%)

Query: 14  ALDMLRTNKNGY--------DIVISDVHMPDMDGFKLLELVGLE---MDLPVIMMCAHGS 62
           ALD L    +           +++ D+++P  DG ++L+ +  +     +PV++M    +
Sbjct: 44  ALDFLYQTGSYCNPDIAPRPAVILLDLNLPGTDGREVLQEIKQDEVLKKIPVVIMTTSSN 103

Query: 63  KEVVMKGVTHDACDYLTKPVRIEELKNI-------WQHVVR 96
            + +    ++    Y+ KP+ I+ L          W  +V 
Sbjct: 104 PKDIEICYSYSISSYIVKPLEIDRLTETVQTFIKYWLDIVV 144

>2qv0_A Protein MRKE; structural genomics, transcription, PSI-2, protein structure initiative; 2.40A {Klebsiella pneumoniae} Length = 143

 Score = 58.8 bits (143), Expect = 2e-11
 Identities = 24/105 (22%), Positives = 44/105 (41%), Gaps = 5/105 (4%)

Query: 5   VTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMC-AHGSK 63
           V   +     L  L+ NK   D +  D+++P +DG  L + +      P I+   A   K
Sbjct: 38  VGSFDDGLDVLKFLQHNK--VDAIFLDINIPSLDGVLLAQNISQFAHKPFIVFITAW--K 93

Query: 64  EVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQS 108
           E  ++    +A DY+ KP +   + N+ Q +    + +    E  
Sbjct: 94  EHAVEAFELEAFDYILKPYQESRIINMLQKLTTAWEQQNNAAEGH 138

>1i3c_A Response regulator RCP1; phytochrome, signaling protein; 1.90A {Synechocystis SP} SCOP: c.23.1.1 PDB: 1jlk_A Length = 149

 Score = 58.8 bits (143), Expect = 2e-11
 Identities = 16/100 (16%), Positives = 41/100 (41%), Gaps = 15/100 (15%)

Query: 12  EIALDMLRTNKNGY-----DIVISDVHMPDMDGFKLLELVGLE---MDLPVIMMCAHGSK 63
             A+  L+           ++++ D+++P  DG ++L  +        +PV+++    ++
Sbjct: 44  LAAMAFLQQQGEYENSPRPNLILLDLNLPKKDGREVLAEIKQNPDLKRIPVVVLTTSHNE 103

Query: 64  EVVMKGVTHDACDYLTKPV-------RIEELKNIWQHVVR 96
           + V+         YLTK          ++ +++ W   V 
Sbjct: 104 DDVIASYELHVNCYLTKSRNLKDLFKMVQGIESFWLETVT 143

>3cg4_A Response regulator receiver domain protein (CHEY-; structural genomics, unknown function; HET: MSE; 1.61A {Methanospirillum hungatei jf-1} Length = 142

 Score = 58.3 bits (142), Expect = 3e-11
 Identities = 24/89 (26%), Positives = 44/89 (49%), Gaps = 5/89 (5%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIMMC 58
           GF +   +     +D+L+       +V+ D+ MP MDG+  +  +    LE  + ++M+ 
Sbjct: 31  GFHIISADSGGQCIDLLKKGF--SGVVLLDIMMPGMDGWDTIRAILDNSLEQGIAIVMLT 88

Query: 59  AHGSKEVVMKGVTHDACDYLTKPVRIEEL 87
           A  + +  M G+     DY+TKP   E+L
Sbjct: 89  AKNAPDAKMIGLQEYVVDYITKPFDNEDL 117

>3kht_A Response regulator; PSI-II, 11023K, structural genomics, Pro structure initiative, NEW YORK SGX research center for STRU genomics, nysgxrc; 2.10A {Hahella chejuensis} Length = 144

 Score = 58.0 bits (141), Expect = 4e-11
 Identities = 15/92 (16%), Positives = 32/92 (34%), Gaps = 17/92 (18%)

Query: 1   MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGF---KLLELVGLEMDLPVIMM 57
           +   +   +    AL  ++  K  YD++I D+ +P  +GF     +   G     P++++
Sbjct: 30  IHCQLEFVDNGAKALYQVQQAK--YDLIILDIGLPIANGFEVMSAVRKPGANQHTPIVIL 87

Query: 58  CAHGSKEVVMKGVTHDAC------DYLTKPVR 83
             +     V        C        + K   
Sbjct: 88  TDN-----VSDD-RAKQCMAAGASSVVDKSSN 113

>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 = 59.4 bits (145), Expect = 5e-11
 Identities = 27/86 (31%), Positives = 39/86 (45%), Gaps = 2/86 (2%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHG 61
           GF  T       AL          DIV+ D+ +P M G  + + +     +PVIM+ A  
Sbjct: 28  GFEATVVTDGPAALAEFDRAG--ADIVLLDLMLPGMSGTDVCKQLRARSSVPVIMVTARD 85

Query: 62  SKEVVMKGVTHDACDYLTKPVRIEEL 87
           S+   + G+   A DY+TKP    EL
Sbjct: 86  SEIDKVVGLELGADDYVTKPYSAREL 111

>2zay_A Response regulator receiver protein; structural genomics, NYSGXRC, target 11006U, protein structure initiative; 2.00A {Desulfuromonas acetoxidans} Length = 147

 Score = 57.6 bits (140), Expect = 5e-11
 Identities = 18/89 (20%), Positives = 37/89 (41%), Gaps = 5/89 (5%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIMMC 58
           GF + +C  A  A+ +         ++I++ +MP + G  L   +        +PVI + 
Sbjct: 32  GFDIIQCGNAIEAVPVAVKTH--PHLIITEANMPKISGMDLFNSLKKNPQTASIPVIALS 89

Query: 59  AHGSKEVVMKGVTHDACDYLTKPVRIEEL 87
              + +   + +     D++ KPV    L
Sbjct: 90  GRATAKEEAQLLDMGFIDFIAKPVNAIRL 118

>2j48_A Two-component sensor kinase; pseudo-receiver, circadian clock, transferase, response regulator, histidine protein kinase; NMR {Synechococcus elongatus} Length = 119

 Score = 56.7 bits (138), Expect = 6e-11
 Identities = 18/89 (20%), Positives = 33/89 (37%), Gaps = 8/89 (8%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIMMC 58
           GF V        ALD L   +    +++     PD     LL+ +     +   P+++  
Sbjct: 25  GFKVIWLVDGSTALDQLDLLQ--PIVILMAWPPPDQSCLLLLQHLREHQADPHPPLVLFL 82

Query: 59  AHGSKEVVMKGVTHDACDYLTKPVRIEEL 87
                +     +T  A   L+KP+  + L
Sbjct: 83  GEPPVD---PLLTAQASAILSKPLDPQLL 108

>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 = 56.7 bits (138), Expect = 7e-11
 Identities = 17/63 (26%), Positives = 37/63 (58%), Gaps = 1/63 (1%)

Query: 26  DIVISDVHMPDMDGFKLL-ELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTKPVRI 84
           DIV  D+ MP+M+G   + E++ ++ +  +I+  A G + +V++ +   A D++ KP + 
Sbjct: 49  DIVTMDITMPEMNGIDAIKEIMKIDPNAKIIVCSAMGQQAMVIEAIKAGAKDFIVKPFQP 108

Query: 85  EEL 87
             +
Sbjct: 109 SRV 111

>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 = 57.2 bits (139), Expect = 7e-11
 Identities = 21/89 (23%), Positives = 35/89 (39%), Gaps = 5/89 (5%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGF---KLLELVGLEMDLPVIMMC 58
           G+        E  L+ L       D+V+ D+ M  MDG+   + ++      D+PV+M+ 
Sbjct: 27  GYRPITAFSGEECLEALNATP--PDLVLLDIMMEPMDGWETLERIKTDPATRDIPVLMLT 84

Query: 59  AHGSKEVVMKGVTHDACDYLTKPVRIEEL 87
           A                DY+ KP    +L
Sbjct: 85  AKPLTPEEANEYGSYIEDYILKPTTHHQL 113

>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 = 56.4 bits (137), Expect = 1e-10
 Identities = 19/104 (18%), Positives = 40/104 (38%), Gaps = 21/104 (20%)

Query: 12  EIALDMLR---TNKNGYDIVISDVHMPDMDGF----KLLELVGLEMDLPVIMMCAHGSKE 64
           + A D ++   +    Y+++  DV MP +DG      +   +G     P++ + A     
Sbjct: 37  QEAFDKVKELTSKGENYNMIFMDVQMPKVDGLLSTKMIRRDLGY--TSPIVALTAF---- 90

Query: 65  VVMKGVTHDAC------DYLTKPVRIEELKNIWQHVVRKRKNER 102
                     C       +L+KP++  +LK I        + ++
Sbjct: 91  -ADDS-NIKECLESGMNGFLSKPIKRPKLKTILTEFCAAYQGKK 132

>1qo0_D AMIR; binding protein, gene regulator, receptor; 2.25A {Pseudomonas aeruginosa} SCOP: c.23.1.3 Length = 196

 Score = 57.8 bits (139), Expect = 1e-10
 Identities = 21/151 (13%), Positives = 45/151 (29%), Gaps = 12/151 (7%)

Query: 1   MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAH 60
           +G SV +C     A D+        D+V + +            L        ++ +  +
Sbjct: 35  IGCSVRQCWPPPEAFDV------PVDVVFTSIFQNRHHDEIAALLAAGTPRTTLVALVEY 88

Query: 61  GSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQSGSVEGGAQQPKP 120
            S  V+ + +  +    +T+P+    +        R+   E   L+Q           + 
Sbjct: 89  ESPAVLSQIIELECHGVITQPLDAHRVLP-VLVSARRISEEMAKLKQKTEQLQDRIAGQA 147

Query: 121 FEESDDSYSVNEGTSNSRKDEEEEAEKRLKK 151
                               +E EA + L +
Sbjct: 148 R-----INQAKVLLMQRHGWDEREAHQHLSR 173

>3heb_A Response regulator receiver domain protein (CHEY); NYSGXRC, PSI-II, respose regulator, structure initiative, structural genomics; 2.40A {Rhodospirillum rubrum} Length = 152

 Score = 55.8 bits (135), Expect = 3e-10
 Identities = 21/93 (22%), Positives = 38/93 (40%), Gaps = 10/93 (10%)

Query: 5   VTKCNRAEIALDMLRTNKNGY-------DIVISDVHMPDMDGFKLLELVGLE---MDLPV 54
           +        AL+ L  +            +V+ D+++PDM G  +L+LV         PV
Sbjct: 33  IIAFTDGTSALNYLFGDDKSGRVSAGRAQLVLLDLNLPDMTGIDILKLVKENPHTRRSPV 92

Query: 55  IMMCAHGSKEVVMKGVTHDACDYLTKPVRIEEL 87
           +++     +  + +     A  Y+TKPV  E  
Sbjct: 93  VILTTTDDQREIQRCYDLGANVYITKPVNYENF 125

>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 = 54.5 bits (132), Expect = 7e-10
 Identities = 29/89 (32%), Positives = 42/89 (47%), Gaps = 5/89 (5%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGF---KLLELVGLEMDLPVIMMC 58
           G+ V +    E AL  +  N    D +I DV +P +DG+   K +    L   LP++M+ 
Sbjct: 28  GYEVRRAASGEEALQQIYKNL--PDALICDVLLPGIDGYTLCKRVRQHPLTKTLPILMLT 85

Query: 59  AHGSKEVVMKGVTHDACDYLTKPVRIEEL 87
           A G     + G    A DYL KP   +EL
Sbjct: 86  AQGDISAKIAGFEAGANDYLAKPFEPQEL 114

>3gl9_A Response regulator; beta-sheet, surrounded by alpha helices, BOTH sides, signaling protein; HET: BFD; 1.80A {Thermotoga maritima} PDB: 3dgf_C 3dge_C Length = 122

 Score = 54.0 bits (130), Expect = 7e-10
 Identities = 23/89 (25%), Positives = 43/89 (48%), Gaps = 5/89 (5%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLE---MDLPVIMMC 58
           G+ V +    +IAL+ L       D+++  + MP MDGF +L+ +  +     +PVI++ 
Sbjct: 26  GYEVIEAENGQIALEKLSEFT--PDLIVLXIMMPVMDGFTVLKKLQEKEEWKRIPVIVLT 83

Query: 59  AHGSKEVVMKGVTHDACDYLTKPVRIEEL 87
           A G +E     ++  A   + KP    + 
Sbjct: 84  AKGGEEDESLALSLGARKVMRKPFSPSQF 112

>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 = 52.9 bits (128), Expect = 3e-09
 Identities = 25/87 (28%), Positives = 45/87 (51%), Gaps = 3/87 (3%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLL-ELVGLEMDLPVIMMCAH 60
           G+ V   +  E AL    T K   D+++ DV +P +DG ++  +L   ++  P++M+ A 
Sbjct: 27  GYDVITASDGEEALKKAETEK--PDLIVLDVMLPKLDGIEVCKQLRQQKLMFPILMLTAK 84

Query: 61  GSKEVVMKGVTHDACDYLTKPVRIEEL 87
             +   + G+   A DY+TKP    E+
Sbjct: 85  DEEFDKVLGLELGADDYMTKPFSPREV 111

>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 = 52.1 bits (126), Expect = 3e-09
 Identities = 18/86 (20%), Positives = 39/86 (45%), Gaps = 2/86 (2%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHG 61
           G+ V +         +L       ++VI D+++P  +G  L   +  + ++ ++ +    
Sbjct: 27  GYDVFEATDGAEMHQILSEYD--INLVIMDINLPGKNGLLLARELREQANVALMFLTGRD 84

Query: 62  SKEVVMKGVTHDACDYLTKPVRIEEL 87
           ++   + G+   A DY+TKP    EL
Sbjct: 85  NEVDKILGLEIGADDYITKPFNPREL 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 = 51.7 bits (125), Expect = 5e-09
 Identities = 18/86 (20%), Positives = 43/86 (50%), Gaps = 2/86 (2%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHG 61
           G++V+         ++++      D+++ D+++PD +G  L   +     + +I++    
Sbjct: 26  GYTVSVTASGAGLREIMQ--NQSVDLILLDINLPDENGLMLTRALRERSTVGIILVTGRS 83

Query: 62  SKEVVMKGVTHDACDYLTKPVRIEEL 87
            +   + G+   A DY+TKP+ + EL
Sbjct: 84  DRIDRIVGLEMGADDYVTKPLELREL 109

>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 = 51.7 bits (125), Expect = 6e-09
 Identities = 24/89 (26%), Positives = 42/89 (47%), Gaps = 5/89 (5%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGF---KLLELVGLEMDLPVIMMC 58
           GF   +    + A++ L       D+++    +P   G    K L    +  D+PV+M+ 
Sbjct: 26  GFQPVEAEDYDSAVNQLNEPW--PDLILLAWMLPGGSGIQFIKHLRRESMTRDIPVVMLT 83

Query: 59  AHGSKEVVMKGVTHDACDYLTKPVRIEEL 87
           A G +E  ++G+   A D +TKP   +EL
Sbjct: 84  ARGEEEDRVRGLETGADDCITKPFSPKEL 112

>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 = 52.8 bits (127), Expect = 7e-09
 Identities = 26/132 (19%), Positives = 46/132 (34%), Gaps = 34/132 (25%)

Query: 1   MGFS-VTKCNRAEIALDMLRTNKNG-----------YDIVISDVHMPDMDGF-------K 41
           MG S V +C+  + AL ++                 +D +  D  MP+MDG+       K
Sbjct: 84  MGVSEVEQCDSGKEALRLVTEGLTQREEQGSVDKLPFDYIFMDCQMPEMDGYEATREIRK 143

Query: 42  LLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDAC------DYLTKPVRIEELKNIWQHVV 95
           + +  G+    P+I +  H                      +L K   + +L N+ + + 
Sbjct: 144 VEKSYGVR--TPIIAVSGH-----DPGSEEARETIQAGMDAFLDKS--LNQLANVIREIE 194

Query: 96  RKRKNERKDLEQ 107
            KR  E      
Sbjct: 195 SKRHLEHHHHHH 206

>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 = 51.4 bits (124), Expect = 8e-09
 Identities = 16/90 (17%), Positives = 43/90 (47%), Gaps = 7/90 (7%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHM-PDMDGF---KLLELVGLEMDLPVIMM 57
           GF+V +    + +++ +R ++   D+V+  V +    +G+     L+      ++P++++
Sbjct: 29  GFTVDETTDGKGSVEQIRRDR--PDLVVLAVDLSAGQNGYLICGKLKKDDDLKNVPIVII 86

Query: 58  CAHGSKEVVMKGVTHDACDYLTKPVRIEEL 87
                     + +   A +Y+ KPV  ++L
Sbjct: 87  GNPDGFAQH-RKLKAHADEYVAKPVDADQL 115

>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 = 50.7 bits (122), Expect = 2e-08
 Identities = 18/72 (25%), Positives = 30/72 (41%), Gaps = 3/72 (4%)

Query: 12  EIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSK--EVVMKG 69
           + ALD L    N  D+++ D+ MP MDG + L    L+    + M+ +          + 
Sbjct: 49  QEALDKLAAQPN-VDLILLDIEMPVMDGMEFLRHAKLKTRAKICMLSSVAVSGSPHAARA 107

Query: 70  VTHDACDYLTKP 81
               A   + KP
Sbjct: 108 RELGADGVVAKP 119

>2hqr_A Putative transcriptional regulator; phosporylation-independent response regulator, H. pylori, SY dimer, signaling protein; NMR {Helicobacter pylori} Length = 223

 Score = 50.9 bits (123), Expect = 4e-08
 Identities = 16/88 (18%), Positives = 32/88 (36%), Gaps = 8/88 (9%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLE-LVGLEMDLPVIMMCAH 60
           GF        E    ++      YD+V+    + D +    +  +      + V++   +
Sbjct: 24  GFMADVTESLEDGEYLMDIR--NYDLVM----VSDKNALSFVSRIKEKHSSIVVLVSSDN 77

Query: 61  GSKEVVMKGVTHDACDYLTKP-VRIEEL 87
            + E  +      A DY+ KP   I+ L
Sbjct: 78  PTSEEEVHAFEQGADDYIAKPYRSIKAL 105

>3t8y_A CHEB, chemotaxis response regulator protein-glutamate methylesterase; CHEA, hydrolase; 1.90A {Thermotoga maritima} Length = 164

 Score = 50.0 bits (120), Expect = 4e-08
 Identities = 17/73 (23%), Positives = 39/73 (53%), Gaps = 4/73 (5%)

Query: 11  AEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSK--EVVMK 68
              A++     K   D++  D+ MP+++G + L+L+  +    VIM+ +   +   + ++
Sbjct: 60  GLEAVEKAIELK--PDVITMDIEMPNLNGIEALKLIMKKAPTRVIMVSSLTEEGAAITIE 117

Query: 69  GVTHDACDYLTKP 81
            + + A D++TKP
Sbjct: 118 ALRNGAVDFITKP 130

>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 = 4e-08
 Identities = 12/63 (19%), Positives = 27/63 (42%), Gaps = 1/63 (1%)

Query: 26  DIVISDVHMPDMDGFKLL-ELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTKPVRI 84
           D+++ DV++PD +    L  L   +    V ++      E++   +   A  ++ K    
Sbjct: 52  DLILLDVNLPDAEAIDGLVRLKRFDPSNAVALISGETDHELIRAALEAGADGFIPKSADP 111

Query: 85  EEL 87
           + L
Sbjct: 112 QVL 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 = 49.1 bits (118), Expect = 5e-08
 Identities = 22/64 (34%), Positives = 35/64 (54%), Gaps = 2/64 (3%)

Query: 26  DIVISDVHMPDMDGFKLLELVGLEMDLP--VIMMCAHGSKEVVMKGVTHDACDYLTKPVR 83
           DI++ D+ MP +DG  +LE +    +    VIM+ A G ++V  K V   A  ++ KP  
Sbjct: 50  DILLLDIIMPHLDGLAVLERIRAGFEHQPNVIMLTAFGQEDVTKKAVELGASYFILKPFD 109

Query: 84  IEEL 87
           +E L
Sbjct: 110 MENL 113

>2pln_A HP1043, response regulator; signaling protein; 1.80A {Helicobacter pylori} PDB: 2hqo_A Length = 137

 Score = 48.7 bits (117), Expect = 7e-08
 Identities = 16/88 (18%), Positives = 32/88 (36%), Gaps = 8/88 (9%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLE-LVGLEMDLPVIMMCAH 60
           GF        E    ++      YD+V+    + D +    +  +      + V++   +
Sbjct: 42  GFMADVTESLEDGEYLMDIRN--YDLVM----VSDKNALSFVSRIKEKHSSIVVLVSSDN 95

Query: 61  GSKEVVMKGVTHDACDYLTKP-VRIEEL 87
            + E  +      A DY+ KP   I+ L
Sbjct: 96  PTSEEEVHAFEQGADDYIAKPYRSIKAL 123

>1p2f_A Response regulator; DRRB, OMPR/PHOB, transcription; HET: MSE; 1.80A {Thermotoga maritima} SCOP: a.4.6.1 c.23.1.1 PDB: 3nns_A* Length = 220

 Score = 50.2 bits (121), Expect = 8e-08
 Identities = 23/84 (27%), Positives = 38/84 (45%), Gaps = 5/84 (5%)

Query: 5   VTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLL-ELVGLEMDLPVIMMCAHGSK 63
           V      E  L+     +  + +V+ DV +PD  G+++   +     +  VI++      
Sbjct: 28  VKTFLTGEDFLND----EEAFHVVVLDVMLPDYSGYEICRMIKETRPETWVILLTLLSDD 83

Query: 64  EVVMKGVTHDACDYLTKPVRIEEL 87
           E V+KG    A DY+TKP   E L
Sbjct: 84  ESVLKGFEAGADDYVTKPFNPEIL 107

>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 = 50.2 bits (121), Expect = 1e-07
 Identities = 23/73 (31%), Positives = 39/73 (53%), Gaps = 4/73 (5%)

Query: 11  AEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSK--EVVMK 68
             +A D+++      D++  DV MP MDG   LE +     +PV+M+ +   K  EV ++
Sbjct: 38  PLVARDLIKKFN--PDVLTLDVEMPRMDGLDFLEKLMRLRPMPVVMVSSLTGKGSEVTLR 95

Query: 69  GVTHDACDYLTKP 81
            +   A D++TKP
Sbjct: 96  ALELGAIDFVTKP 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 = 48.0 bits (114), Expect = 2e-07
 Identities = 15/98 (15%), Positives = 40/98 (40%), Gaps = 15/98 (15%)

Query: 14  ALDMLR-----TNKNGYDIVISDVHMPDMDGFKLLELVGLE---MDLPVIMMCAHGSKEV 65
           A+  LR      N +  D+++  +++P  DG ++L  +  +     +PV+++    +++ 
Sbjct: 40  AMAYLRQEGEYANASRPDLILLXLNLPKKDGREVLAEIKSDPTLKRIPVVVLSTSINEDD 99

Query: 66  VMKGVTHDACDYLTKPV-------RIEELKNIWQHVVR 96
           +          Y+TK          ++ ++  W     
Sbjct: 100 IFHSYDLHVNCYITKSANLSQLFQIVKGIEEFWLSTAT 137

>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 = 3e-06
 Identities = 14/63 (22%), Positives = 28/63 (44%), Gaps = 1/63 (1%)

Query: 26  DIVISDVHMPDMDGFKLL-ELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTKPVRI 84
           DIVI DV +P ++G ++L  L   +    +I++ A              A  +++K   +
Sbjct: 48  DIVIIDVDIPGVNGIQVLETLRKRQYSGIIIIVSAKNDHFYGKHCADAGANGFVSKKEGM 107

Query: 85  EEL 87
             +
Sbjct: 108 NNI 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 = 42.5 bits (101), Expect = 1e-05
 Identities = 20/63 (31%), Positives = 33/63 (52%), Gaps = 1/63 (1%)

Query: 26  DIVISDVHMPDMDGFKLL-ELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTKPVRI 84
           ++VI D+ MP M G ++L E+    +++ VI++          K V +D   Y+ K   I
Sbjct: 51  NVVILDIEMPGMTGLEVLAEIRKKHLNIKVIIVTTFKRPGYFEKAVVNDVDAYVLKERSI 110

Query: 85  EEL 87
           EEL
Sbjct: 111 EEL 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 = 1e-04
 Identities = 16/63 (25%), Positives = 28/63 (44%), Gaps = 1/63 (1%)

Query: 26  DIVISDVHMPDMDGFKLLE-LVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTKPVRI 84
           DI I DV MP   G ++LE +   +++  V+++          + V      Y+ K   I
Sbjct: 68  DIAILDVEMPVKTGLEVLEWIRSEKLETKVVVVTTFKRAGYFERAVKAGVDAYVLKERSI 127

Query: 85  EEL 87
            +L
Sbjct: 128 ADL 130

>3cz5_A Two-component response regulator, LUXR family; structural genomics, protein structure initiative; 2.70A {Aurantimonas SP} Length = 153

 Score = 38.7 bits (91), Expect = 4e-04
 Identities = 14/63 (22%), Positives = 25/63 (39%), Gaps = 1/63 (1%)

Query: 26  DIVISDVHMPDMDGFKLL-ELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTKPVRI 84
           DIV+ D+ +P   G +    +   +    +++   H      +K     A  Y+TK    
Sbjct: 53  DIVVMDLTLPGPGGIEATRHIRQWDGAARILIFTMHQGSAFALKAFEAGASGYVTKSSDP 112

Query: 85  EEL 87
            EL
Sbjct: 113 AEL 115

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	226
3to5_A	134	CHEY homolog; alpha(5)beta(5), chemotaxis, FLIM, p	99.9
3rqi_A	184	Response regulator protein; structural genomics, s	99.87
3gl9_A	122	Response regulator; beta-sheet, surrounded by alph	99.83
1irz_A	64	ARR10-B; helix-turn-helix, DNA binding protein; NM	99.83
3f6p_A	120	Transcriptional regulatory protein YYCF; unphospho	99.83
3t6k_A	136	Response regulator receiver; flavodoxin-like, stru	99.82
2lpm_A	123	Two-component response regulator; transcription re	99.81
1s8n_A	205	Putative antiterminator; RV1626, structural genomi	99.8
3crn_A	132	Response regulator receiver domain protein, CHEY-;	99.79
2r25_B	133	Osmosensing histidine protein kinase SLN1; alpha5-	99.79
2pl1_A	121	Transcriptional regulatory protein PHOP; CHEY-like	99.78
1yio_A	208	Response regulatory protein; transcription regulat	99.78
1a04_A	215	Nitrate/nitrite response regulator protein NARL; s	99.78
3sy8_A	400	ROCR; TIM barrel phosphodiesterase-A, transcriptio	99.78
1dbw_A	126	Transcriptional regulatory protein FIXJ; doubly wo	99.78
1zgz_A	122	Torcad operon transcriptional regulatory protein;	99.78
3cfy_A	137	Putative LUXO repressor protein; structural genomi	99.78
3n0r_A	286	Response regulator; sigma factor, receiver, two-co	99.78
1xhf_A	123	DYE resistance, aerobic respiration control protei	99.78
2a9o_A	120	Response regulator; essential protein, YYCF/YYCG h	99.77
3hv2_A	153	Response regulator/HD domain protein; PSI-2, NYSGX	99.77
3gt7_A	154	Sensor protein; structural genomics, signal receiv	99.77
2qzj_A	136	Two-component response regulator; 11017X, PSI-II,	99.77
3m6m_D	143	Sensory/regulatory protein RPFC; RPFF, REC, enoyl-	99.77
1srr_A	124	SPO0F, sporulation response regulatory protein; as	99.77
3h1g_A	129	Chemotaxis protein CHEY homolog; sulfate-bound CHE	99.77
3jte_A	143	Response regulator receiver protein; structural ge	99.76
3r0j_A	250	Possible two component system response transcript	99.76
3b2n_A	133	Uncharacterized protein Q99UF4; structural genomic	99.76
1tmy_A	120	CHEY protein, TMY; chemotaxis, phosphoryl transfer	99.76
3kto_A	136	Response regulator receiver protein; PSI-II,struct	99.76
1zh2_A	121	KDP operon transcriptional regulatory protein KDPE	99.75
3hdg_A	137	Uncharacterized protein; two-component sensor acti	99.75
3h5i_A	140	Response regulator/sensory box protein/ggdef domai	99.75
1jbe_A	128	Chemotaxis protein CHEY; signaling protein; 1.08A	99.75
3luf_A	259	Two-component system response regulator/ggdef doma	99.75
3grc_A	140	Sensor protein, kinase; protein structure initiati	99.75
3lua_A	140	Response regulator receiver protein; two-component	99.75
3eod_A	130	Protein HNR; response regulator, phosphoprotein, t	99.75
3nhm_A	133	Response regulator; protein structure initiative I	99.74
3c3w_A	225	Two component transcriptional regulatory protein;	99.74
3klo_A	225	Transcriptional regulator VPST; REC domain, HTH do	99.74
1p6q_A	129	CHEY2; chemotaxis, signal transduction, response r	99.74
1i3c_A	149	Response regulator RCP1; phytochrome, signaling pr	99.74
2zay_A	147	Response regulator receiver protein; structural ge	99.74
4e7p_A	150	Response regulator; DNA binding, cytosol, transcri	99.74
1mb3_A	124	Cell division response regulator DIVK; signal tran	99.74
3cu5_A	141	Two component transcriptional regulator, ARAC FAM;	99.74
1dz3_A	130	Stage 0 sporulation protein A; response regulator,	99.74
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	99.73
1mvo_A	136	PHOP response regulator; phosphate regulon, transc	99.73
2ayx_A	254	Sensor kinase protein RCSC; two independent struct	99.73
3kht_A	144	Response regulator; PSI-II, 11023K, structural gen	99.73
3kcn_A	151	Adenylate cyclase homolog; SGX, PSI 2, structural	99.73
3hdv_A	136	Response regulator; PSI-II, structural genomics, P	99.73
3mm4_A	206	Histidine kinase homolog; receiver domain, CKI1, c	99.73
3q9s_A	249	DNA-binding response regulator; DNA binding protei	99.73
2rjn_A	154	Response regulator receiver:metal-dependent phosph	99.73
3snk_A	135	Response regulator CHEY-like protein; P-loop conta	99.73
3ilh_A	146	Two component response regulator; NYSGXRC, PSI-II,	99.73
3i42_A	127	Response regulator receiver domain protein (CHEY-	99.73
3cnb_A	143	DNA-binding response regulator, MERR family; signa	99.73
3f6c_A	134	Positive transcription regulator EVGA; structural	99.73
1k68_A	140	Phytochrome response regulator RCPA; phosphorylate	99.73
3heb_A	152	Response regulator receiver domain protein (CHEY);	99.72
2jba_A	127	Phosphate regulon transcriptional regulatory PROT;	99.72
3n53_A	140	Response regulator receiver modulated diguanylate;	99.72
3hzh_A	157	Chemotaxis response regulator (CHEY-3); phosphatas	99.72
1k66_A	149	Phytochrome response regulator RCPB; CHEY homologu	99.72
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	99.72
3cg0_A	140	Response regulator receiver modulated diguanylate	99.72
4dad_A	146	Putative pilus assembly-related protein; response	99.72
1kgs_A	225	DRRD, DNA binding response regulator D; DNA-bindin	99.71
3c3m_A	138	Response regulator receiver protein; structural ge	99.71
2jk1_A	139	HUPR, hydrogenase transcriptional regulatory prote	99.71
2qxy_A	142	Response regulator; regulation of transcription, N	99.71
1qkk_A	155	DCTD, C4-dicarboxylate transport transcriptional r	99.71
3eul_A	152	Possible nitrate/nitrite response transcriptional	99.71
3eq2_A	394	Probable two-component response regulator; adaptor	99.7
3bre_A	358	Probable two-component response regulator; protein	99.7
3a10_A	116	Response regulator; phosphoacceptor, signaling pro	99.7
1w25_A	459	Stalked-cell differentiation controlling protein;	99.7
2qr3_A	140	Two-component system response regulator; structura	99.7
3cg4_A	142	Response regulator receiver domain protein (CHEY-;	99.7
3lte_A	132	Response regulator; structural genomics, PSI, prot	99.7
3cz5_A	153	Two-component response regulator, LUXR family; str	99.69
1ys7_A	233	Transcriptional regulatory protein PRRA; response	99.69
2oqr_A	230	Sensory transduction protein REGX3; response regul	99.68
2qvg_A	143	Two component response regulator; NYSGXRC, PSI-2,	99.67
2gkg_A	127	Response regulator homolog; social motility, recei	99.66
2gwr_A	238	DNA-binding response regulator MTRA; two-component	99.66
1dcf_A	136	ETR1 protein; beta-alpha five sandwich, transferas	99.66
2qv0_A	143	Protein MRKE; structural genomics, transcription,	99.66
2qsj_A	154	DNA-binding response regulator, LUXR family; struc	99.65
3kyj_B	145	CHEY6 protein, putative histidine protein kinase;	99.64
2rdm_A	132	Response regulator receiver protein; structural ge	99.64
3c97_A	140	Signal transduction histidine kinase; structural g	99.64
1p2f_A	220	Response regulator; DRRB, OMPR/PHOB, transcription	99.63
1dc7_A	124	NTRC, nitrogen regulation protein; receiver domain	99.62
3eqz_A	135	Response regulator; structural genomics, unknown f	99.62
2pln_A	137	HP1043, response regulator; signaling protein; 1.8	99.61
3t8y_A	164	CHEB, chemotaxis response regulator protein-glutam	99.61
1qo0_D	196	AMIR; binding protein, gene regulator, receptor; 2	99.61
2j48_A	119	Two-component sensor kinase; pseudo-receiver, circ	99.59
2hqr_A	223	Putative transcriptional regulator; phosporylation	99.56
2b4a_A	138	BH3024; flavodoxin-like fold, structural genomics,	99.55
1a2o_A	349	CHEB methylesterase; bacterial chemotaxis, adaptat	99.52
3luf_A	259	Two-component system response regulator/ggdef doma	99.46
2vyc_A	755	Biodegradative arginine decarboxylase; pyridoxal p	99.44
3cwo_X	237	Beta/alpha-barrel protein based on 1THF and 1TMY;	99.36
1w25_A	459	Stalked-cell differentiation controlling protein;	98.96
3n75_A	715	LDC, lysine decarboxylase, inducible; pyridoxal-5'	97.48
3cwo_X	237	Beta/alpha-barrel protein based on 1THF and 1TMY;	97.21
3lsg_A	103	Two-component response regulator YESN; structural	96.15
2k9s_A	107	Arabinose operon regulatory protein; activator, ar	95.48
3mkl_A	120	HTH-type transcriptional regulator GADX; PSI2, MCS	95.37
3oou_A	108	LIN2118 protein; protein structure initiative, PSI	95.22
3mn2_A	108	Probable ARAC family transcriptional regulator; st	95.19
3oio_A	113	Transcriptional regulator (ARAC-type DNA-binding c	95.01
1wv2_A	265	Thiazole moeity, thiazole biosynthesis protein THI	94.83
1bl0_A	129	Protein (multiple antibiotic resistance protein),	94.78
2yxb_A	161	Coenzyme B12-dependent mutase; alpha/beta, structu	94.37
3q7r_A	121	Transcriptional regulatory protein; CHXR, receiver	93.67
3q58_A	229	N-acetylmannosamine-6-phosphate 2-epimerase; TIM b	93.49
3gbg_A	276	TCP pilus virulence regulatory protein; cupin, hel	93.39
2htm_A	268	Thiazole biosynthesis protein THIG; thiamin biosyn	92.65
1u8b_A	133	ADA polyprotein; protein-DNA complex, methylation,	92.5
3igs_A	232	N-acetylmannosamine-6-phosphate 2-epimerase 2; ene	92.09
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	92.05
2w7n_A	101	TRFB transcriptional repressor protein; INCP, plas	90.23
2zcm_A	192	Biofilm operon icaabcd HTH-type negative transcri	89.83
1jko_C	52	HIN recombinase, DNA-invertase HIN; water-mediated	89.55
3knw_A	212	Putative transcriptional regulator (TETR/ACRR FAM;	88.05
3qkx_A	188	Uncharacterized HTH-type transcriptional regulato;	87.96
3ppb_A	195	Putative TETR family transcription regulator; DNA-	87.9
3rd3_A	197	Probable transcriptional regulator; 2.40A {Pseudom	87.81
3kkc_A	177	TETR family transcriptional regulator; APC20805, s	87.8
3o63_A	243	Probable thiamine-phosphate pyrophosphorylase; thi	87.5
1geq_A	248	Tryptophan synthase alpha-subunit; hyperthermophIl	87.47
1xi3_A	215	Thiamine phosphate pyrophosphorylase; structural g	87.3
3qbm_A	199	TETR transcriptional regulator; DNA/RNA-binding th	87.18
2iu5_A	195	DHAS, YCEG, HTH-type dhaklm operon transcriptional	87.12
3b81_A	203	Transcriptional regulator, ACRR family; NP_350189.	86.81
2ekc_A	262	AQ_1548, tryptophan synthase alpha chain; structur	86.74
3vp5_A	189	Transcriptional regulator; heme, sensor protein, T	86.7
3lwj_A	202	Putative TETR-family transcriptional regulator; st	86.61
1yad_A	221	Regulatory protein TENI; TIM barrel, transcription	86.59
3him_A	211	Probable transcriptional regulator; TETR, bacteria	86.53
3e7l_A	63	Transcriptional regulator (NTRC family); sigma43 a	86.52
3he0_A	196	Transcriptional regulator, TETR family; ACRR, vibr	86.45
3dcf_A	218	Transcriptional regulator of the TETR/ACRR family;	86.4
3kz9_A	206	SMCR; transcriptional regulator, quorum S DNA-bind	86.2
3col_A	196	Putative transcription regulator; structural genom	85.81
2fq4_A	192	Transcriptional regulator, TETR family; DNA-bindin	85.78
3lhq_A	220	Acrab operon repressor (TETR/ACRR family); structu	85.77
3on4_A	191	Transcriptional regulator, TETR family; structural	85.74
3vnd_A	267	TSA, tryptophan synthase alpha chain; psychrophili	85.66
1sgm_A	191	Putative HTH-type transcriptional regulator YXAF;	85.63
3f1b_A	203	TETR-like transcriptional regulator; APC5888, rhod	85.62
2fd5_A	180	Transcriptional regulator; DNA-binding protein, st	85.38
1neq_A	74	DNA-binding protein NER; NMR {Enterobacteria phage	85.32
1ka9_F	252	Imidazole glycerol phosphtate synthase; riken stru	85.29
2x48_A	55	CAG38821; archeal virus, viral protein; 2.60A {Sul	85.23
3qqa_A	216	CMER; alpha-helical, helix-turn-helix, DNA-binding	85.19
1pb6_A	212	Hypothetical transcriptional regulator YCDC; helix	85.12
2w6r_A	266	Imidazole glycerol phosphate synthase subunit HISF	85.11
3nrg_A	217	TETR family transcriptional regulator; structural	85.08
3o07_A	291	Pyridoxine biosynthesis protein SNZ1; (beta/alpha)	85.05
2g7s_A	194	Transcriptional regulator, TETR family; APC5906, P	84.91
2v57_A	190	TETR family transcriptional repressor LFRR; DNA-bi	84.91
4fe7_A	412	Xylose operon regulatory protein; HTH_ARAC, helix-	84.84
1zk8_A	183	Transcriptional regulator, TETR family; TETR membe	84.74
2qko_A	215	Possible transcriptional regulator, TETR family P;	84.63
3dew_A	206	Transcriptional regulator, TETR family; S genomics	84.59
3vpr_A	190	Transcriptional regulator, TETR family; all alpha,	84.56
2ras_A	212	Transcriptional regulator, TETR family; bacterial	84.52
2rae_A	207	Transcriptional regulator, ACRR family protein; TE	84.48
3cwr_A	208	Transcriptional regulator, TETR family; YP_425770.	84.34
3bru_A	222	Regulatory protein, TETR family; structural genomi	84.33
2hxo_A	237	Putative TETR-family transcriptional regulator; TE	84.25
3egq_A	170	TETR family transcriptional regulator; DNA-binding	84.24
4hku_A	178	LMO2814 protein, TETR transcriptional regulator; s	84.23
2qtq_A	213	Transcriptional regulator, TETR family; transcript	84.2
3ccy_A	203	Putative TETR-family transcriptional regulator; AP	84.07
2dg7_A	195	Putative transcriptional regulator; helix-turn-hel	84.02
1qop_A	268	Tryptophan synthase alpha chain; lyase, carbon-oxy	83.82
3on2_A	199	Probable transcriptional regulator; protein struct	83.82
3aqt_A	245	Bacterial regulatory proteins, TETR family; helix-	83.73
4adt_A	297	Pyridoxine biosynthetic enzyme PDX1 homologue, PU;	83.68
3t76_A	88	VANU, transcriptional regulator vanug; structural	83.64
3bni_A	229	Putative TETR-family transcriptional regulator; st	83.64
3gzi_A	218	Transcriptional regulator, TETR family; TETR famil	83.52
2yve_A	185	Transcriptional regulator; helix-turn-helix, TETR-	83.39
1ccw_A	137	Protein (glutamate mutase); coenzyme B12, radical	83.3
2oi8_A	216	Putative regulatory protein SCO4313; TETR, structu	83.21
3anp_C	204	Transcriptional repressor, TETR family; all alpha	83.17
3dpj_A	194	Transcription regulator, TETR family; APC88616, si	83.15
3s5r_A	216	Transcriptional regulator TETR family; DNA/RNA-bin	82.99
3fiw_A	211	Putative TETR-family transcriptional regulator; TE	82.99
3g7r_A	221	Putative transcriptional regulator; TETR, all-heli	82.95
3f0c_A	216	TETR-molecule A, transcriptional regulator; MCSG,P	82.8
1umq_A	81	Photosynthetic apparatus regulatory protein; DNA-b	82.7
3rh2_A	212	Hypothetical TETR-like transcriptional regulator;	82.68
1thf_D	253	HISF protein; thermophIle, TIM-barrel, histidine b	82.68
1rkt_A	205	Protein YFIR; transcription regulator, structural	82.61
2d6y_A	202	Putative TETR family regulatory protein; helix-tur	82.47
2a6c_A	83	Helix-turn-helix motif; putative transcriptional r	82.4
2dg8_A	193	Putative TETR-family transcriptional regulatory P;	82.38
1r69_A	69	Repressor protein CI; gene regulating protein; 2.0	82.2
2xdn_A	210	HTH-type transcriptional regulator TTGR; transcrip	82.15
2w53_A	219	Repressor, SMet; antibiotic resistance, multi-drug	82.12
2qwt_A	196	Transcriptional regulator, TETR family; structural	82.09
3qq6_A	78	HTH-type transcriptional regulator SINR; helix-tur	82.07
3geu_A	189	Intercellular adhesion protein R; TETR family, int	82.01
2zb9_A	214	Putative transcriptional regulator; transcription	81.88
2hku_A	215	A putative transcriptional regulator; structural g	81.84
2g7l_A	243	TETR-family transcriptional regulator; APC6062, pr	81.67
3kts_A	192	Glycerol uptake operon antiterminator regulatory;	81.66
2kpj_A	94	SOS-response transcriptional repressor, LEXA; NESG	81.61
3kp1_A	763	D-ornithine aminomutase E component; 5 aminomutase	81.59
2f07_A	197	YVDT; helix-turn-helix, transcription; HET: BTB; 2	81.57
2of7_A	260	Putative TETR-family transcriptional regulator; AP	81.56
1zug_A	71	Phage 434 CRO protein; gene regulating protein, tr	81.53
1ntc_A	91	Protein (nitrogen regulation protein (NTRC)); heli	81.5
2gjl_A	328	Hypothetical protein PA1024; 2-nitropropane dioxyg	81.49
3lsj_A	220	DEST; transcriptional repressor, TETR family, DNA-	81.49
3nnr_A	228	Transcriptional regulator, TETR family; TETR-famil	81.45
2ibd_A	204	Possible transcriptional regulator; probable trans	81.44
1z0x_A	220	Transcriptional regulator, TETR family; structural	81.39
2qib_A	231	TETR-family transcriptional regulator; HTH DNA bin	81.35
2o7t_A	199	Transcriptional regulator; transcription regulator	81.32
3nxc_A	212	HTH-type protein SLMA; nucleoid occlusion, cell di	81.2
3crj_A	199	Transcription regulator; APC88200, TETR, structura	81.1
3mvp_A	217	TETR/ACRR transcriptional regulator; PSI, MCSG, st	81.05
3b7h_A	78	Prophage LP1 protein 11; structural genomics, PSI2	80.8
1qo2_A	241	Molecule: N-((5-phosphoribosyl)-formimino)-5-amino	80.79
2y2z_A	267	SIM16, SIMR, putative repressor simreg2; transcrip	80.75
2ao9_A	155	Phage protein; structural genomics, nine-fold NCS.	80.74
1ui5_A	215	A-factor receptor homolog; helix-turn-helix, alpha	80.54
3hta_A	217	EBRA repressor; TETR family, DNA binding protein,	80.45
2xij_A	762	Methylmalonyl-COA mutase, mitochondrial; isomerase	80.43
3trb_A	104	Virulence-associated protein I; mobIle and extrach	80.29
2xi8_A	66	Putative transcription regulator; HTH DNA-binding	80.29
3s8q_A	82	R-M controller protein; protein-DNA complex, helix	80.26
1xm3_A	264	Thiazole biosynthesis protein THIG; structural gen	80.22
3cdl_A	203	Transcriptional regulator AEFR; APC88582, TETR, ps	80.18
2iai_A	230	Putative transcriptional regulator SCO3833; struct	80.16
3pas_A	195	TETR family transcription regulator; structural ge	80.07
1y0e_A	223	Putative N-acetylmannosamine-6-phosphate 2-epimer;	80.01

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

Probab=99.90  E-value=1.6e-23  Score=153.97  Aligned_cols=94  Identities=28%  Similarity=0.568  Sum_probs=86.9

Q ss_pred             CCcE-EEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcC---CCCcEEEEeccCCHHHHHHHHhCCcce
Q 027234            1 MGFS-VTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLE---MDLPVIMMCAHGSKEVVMKGVTHDACD   76 (226)
Q Consensus         1 lg~~-V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~---~~~pvI~ls~~~~~~~~~~a~~~ga~~   76 (226)
                      +||. |.+|.||.+|++.+++..  ||+||+|++||+|||+++++.|+..   +++|||++|+..+.+...++++.||++
T Consensus        35 ~G~~~v~~a~~g~~al~~~~~~~--~DlillD~~MP~mdG~el~~~ir~~~~~~~ipvI~lTa~~~~~~~~~~~~~Ga~~  112 (134)
T 3to5_A           35 LGFNNTQEADDGLTALPMLKKGD--FDFVVTDWNMPGMQGIDLLKNIRADEELKHLPVLMITAEAKREQIIEAAQAGVNG  112 (134)
T ss_dssp             TTCCCEEEESSHHHHHHHHHHHC--CSEEEEESCCSSSCHHHHHHHHHHSTTTTTCCEEEEESSCCHHHHHHHHHTTCCE
T ss_pred             cCCcEEEEECCHHHHHHHHHhCC--CCEEEEcCCCCCCCHHHHHHHHHhCCCCCCCeEEEEECCCCHHHHHHHHHCCCCE
Confidence            5886 678999999999999877  9999999999999999999999843   579999999999999999999999999


Q ss_pred             EEeCCCCHHHHHHHHHHHHH
Q 027234           77 YLTKPVRIEELKNIWQHVVR   96 (226)
Q Consensus        77 yl~KP~~~~~L~~~l~~~~~   96 (226)
                      ||.|||++++|...++++++
T Consensus       113 yl~KP~~~~~L~~~i~~~l~  132 (134)
T 3to5_A          113 YIVKPFTAATLKEKLDKIFE  132 (134)
T ss_dssp             EEESSCCHHHHHHHHHHHCC
T ss_pred             EEECCCCHHHHHHHHHHHHh
Confidence            99999999999999998764

>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=4.6e-22  Score=153.45  Aligned_cols=98  Identities=19%  Similarity=0.395  Sum_probs=90.7

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||.|..|.++.+|++.+....  ||+||+|+.||+++|+++++.++ ..+.+|||++|+..+.+...+++..||++||.
T Consensus        30 ~g~~v~~~~~~~~al~~~~~~~--~dlvl~D~~lp~~~g~~~~~~l~~~~~~~~ii~lt~~~~~~~~~~a~~~Ga~~~l~  107 (184)
T 3rqi_A           30 RGYAVRQAHNKDEALKLAGAEK--FEFITVXLHLGNDSGLSLIAPLCDLQPDARILVLTGYASIATAVQAVKDGADNYLA  107 (184)
T ss_dssp             TTCEEEEECSHHHHHHHHTTSC--CSEEEECSEETTEESHHHHHHHHHHCTTCEEEEEESSCCHHHHHHHHHHTCSEEEE
T ss_pred             CCCEEEEeCCHHHHHHHHhhCC--CCEEEEeccCCCccHHHHHHHHHhcCCCCCEEEEeCCCCHHHHHHHHHhCHHHhee
Confidence            4899999999999999998866  99999999999999999999997 46789999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHhh
Q 027234           80 KPVRIEELKNIWQHVVRKRKN  100 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~~~~  100 (226)
                      ||++.++|...+++++.....
T Consensus       108 KP~~~~~L~~~i~~~~~~~~~  128 (184)
T 3rqi_A          108 KPANVESILAALQTNASEVQA  128 (184)
T ss_dssp             SSCCHHHHHHHTSTTHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHhhh
Confidence            999999999999988766543

>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=99.83  E-value=8.9e-20  Score=131.12  Aligned_cols=93  Identities=26%  Similarity=0.446  Sum_probs=86.8

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcC---CCCcEEEEeccCCHHHHHHHHhCCcceE
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLE---MDLPVIMMCAHGSKEVVMKGVTHDACDY   77 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~---~~~pvI~ls~~~~~~~~~~a~~~ga~~y   77 (226)
                      .||+|..+.++.+|++.+....  ||+||+|+.||+++|+++++.++..   +.+|||++|+..+.+...++++.||++|
T Consensus        25 ~g~~v~~~~~~~~al~~l~~~~--~dlvllD~~~p~~~g~~~~~~l~~~~~~~~~pii~~s~~~~~~~~~~~~~~Ga~~~  102 (122)
T 3gl9_A           25 EGYEVIEAENGQIALEKLSEFT--PDLIVLXIMMPVMDGFTVLKKLQEKEEWKRIPVIVLTAKGGEEDESLALSLGARKV  102 (122)
T ss_dssp             TTCEEEEESSHHHHHHHHTTBC--CSEEEECSCCSSSCHHHHHHHHHTSTTTTTSCEEEEESCCSHHHHHHHHHTTCSEE
T ss_pred             CCcEEEEeCCHHHHHHHHHhcC--CCEEEEeccCCCCcHHHHHHHHHhcccccCCCEEEEecCCchHHHHHHHhcChhhh
Confidence            4899999999999999998866  9999999999999999999999743   5799999999999999999999999999


Q ss_pred             EeCCCCHHHHHHHHHHHH
Q 027234           78 LTKPVRIEELKNIWQHVV   95 (226)
Q Consensus        78 l~KP~~~~~L~~~l~~~~   95 (226)
                      |.||++.++|...+++++
T Consensus       103 l~KP~~~~~L~~~i~~~l  120 (122)
T 3gl9_A          103 MRKPFSPSQFIEEVKHLL  120 (122)
T ss_dssp             EESSCCHHHHHHHHHHHH
T ss_pred             ccCCCCHHHHHHHHHHHh
Confidence            999999999999998876

>1irz_A ARR10-B; helix-turn-helix, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: a.4.1.11

Probab=99.83  E-value=7.4e-21  Score=118.84  Aligned_cols=61  Identities=59%  Similarity=0.958  Sum_probs=58.8

Q ss_pred             ccCCceeeeHhhHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcc
Q 027234          149 LKKPRLVWSVELHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRL  209 (226)
Q Consensus       149 ~~~~~~~~~~~l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~  209 (226)
                      .+++++.||.++|.+|+.+++++|.+++.|+.|+++|++++||+++|+|||||||.+++|+
T Consensus         3 ~~k~r~~WT~elH~~Fv~Av~~LG~~~AtPk~Il~~M~v~gLT~~~VkSHLQKYR~~l~r~   63 (64)
T 1irz_A            3 QKKPRVLWTHELHNKFLAAVDHLGVERAVPKKILDLMNVDKLTRENVASHLQKFRVALKKV   63 (64)
T ss_dssp             CCCSSCSSCHHHHHHHHHHHHHHCTTTCCHHHHHHHHCCTTCCHHHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHhCCCCCCcHHHHHHcCCCCCCHHHHHHHHHHHHHHHHcc
Confidence            3679999999999999999999999999999999999999999999999999999999986

>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=99.83  E-value=6.3e-20  Score=131.46  Aligned_cols=94  Identities=28%  Similarity=0.445  Sum_probs=88.1

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEeC
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTK   80 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~K   80 (226)
                      .||+|..+.++.+|++.+....  ||+||+|+.||+++|+++++.++....+|+|++|+..+......+++.||++||.|
T Consensus        25 ~g~~v~~~~~~~~al~~~~~~~--~dlii~D~~~p~~~g~~~~~~lr~~~~~~ii~~t~~~~~~~~~~~~~~ga~~~l~K  102 (120)
T 3f6p_A           25 EGYEVHCAHDGNEAVEMVEELQ--PDLILLDIMLPNKDGVEVCREVRKKYDMPIIMLTAKDSEIDKVIGLEIGADDYVTK  102 (120)
T ss_dssp             TTCEEEEESSHHHHHHHHHTTC--CSEEEEETTSTTTHHHHHHHHHHTTCCSCEEEEEESSCHHHHHHHHHTTCCEEEEE
T ss_pred             CCEEEEEeCCHHHHHHHHhhCC--CCEEEEeCCCCCCCHHHHHHHHHhcCCCCEEEEECCCChHHHHHHHhCCcceeEcC
Confidence            4899999999999999999876  99999999999999999999998777899999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHH
Q 027234           81 PVRIEELKNIWQHVVR   96 (226)
Q Consensus        81 P~~~~~L~~~l~~~~~   96 (226)
                      |++.++|...++++++
T Consensus       103 P~~~~~l~~~i~~~l~  118 (120)
T 3f6p_A          103 PFSTRELLARVKANLR  118 (120)
T ss_dssp             SCCHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHHHh
Confidence            9999999999988764

>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=99.82  E-value=2.1e-19  Score=131.56  Aligned_cols=97  Identities=30%  Similarity=0.507  Sum_probs=88.7

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhc---CCCCcEEEEeccCCHHHHHHHHhCCcceE
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGL---EMDLPVIMMCAHGSKEVVMKGVTHDACDY   77 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~---~~~~pvI~ls~~~~~~~~~~a~~~ga~~y   77 (226)
                      .||.|..+.++.+|++.+....  ||+||+|+.||+++|+++++.++.   .+.+|||++|+..+.+...+++..||++|
T Consensus        27 ~g~~v~~~~~~~~al~~~~~~~--~dlvl~D~~lp~~~g~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~~~~~ga~~~  104 (136)
T 3t6k_A           27 AGYEVRRAASGEEALQQIYKNL--PDALICDVLLPGIDGYTLCKRVRQHPLTKTLPILMLTAQGDISAKIAGFEAGANDY  104 (136)
T ss_dssp             TTCEEEEESSHHHHHHHHHHSC--CSEEEEESCCSSSCHHHHHHHHHHSGGGTTCCEEEEECTTCHHHHHHHHHHTCSEE
T ss_pred             CCCEEEEeCCHHHHHHHHHhCC--CCEEEEeCCCCCCCHHHHHHHHHcCCCcCCccEEEEecCCCHHHHHHHHhcCcceE
Confidence            4899999999999999999876  999999999999999999999974   35799999999999999999999999999


Q ss_pred             EeCCCCHHHHHHHHHHHHHHHh
Q 027234           78 LTKPVRIEELKNIWQHVVRKRK   99 (226)
Q Consensus        78 l~KP~~~~~L~~~l~~~~~~~~   99 (226)
                      |.||++.++|...+++++.+..
T Consensus       105 l~KP~~~~~L~~~i~~~l~~~~  126 (136)
T 3t6k_A          105 LAKPFEPQELVYRVKNILARTT  126 (136)
T ss_dssp             EETTCCHHHHHHHHHHHHHC--
T ss_pred             EeCCCCHHHHHHHHHHHHhccC
Confidence            9999999999999999886543

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

Probab=99.81  E-value=1.9e-21  Score=140.60  Aligned_cols=89  Identities=26%  Similarity=0.445  Sum_probs=78.2

Q ss_pred             CCcEEE-EECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVT-KCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~-~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      +||+|. +|.|+.+|++.+++..  ||+||+|++||+|||+++++.+++ .++|||++|++.+...   +.++|+++||.
T Consensus        31 ~G~~v~~~a~~g~eAl~~~~~~~--~DlvllDi~mP~~~G~el~~~lr~-~~ipvI~lTa~~~~~~---~~~~g~~~yl~  104 (123)
T 2lpm_A           31 LGHEVAATASRMQEALDIARKGQ--FDIAIIDVNLDGEPSYPVADILAE-RNVPFIFATGYGSKGL---DTRYSNIPLLT  104 (123)
T ss_dssp             HCCCCCBCSCCHHHHHHHHHHCC--SSEEEECSSSSSCCSHHHHHHHHH-TCCSSCCBCTTCTTSC---CSSSCSCSCBC
T ss_pred             CCCEEEEEECCHHHHHHHHHhCC--CCEEEEecCCCCCCHHHHHHHHHc-CCCCEEEEecCccHHH---HHhCCCCcEEE
Confidence            489875 7899999999999876  999999999999999999999985 4799999999876543   45679999999


Q ss_pred             CCCCHHHHHHHHHHHH
Q 027234           80 KPVRIEELKNIWQHVV   95 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~   95 (226)
                      |||+.++|..+++++.
T Consensus       105 KP~~~~~L~~~l~~~~  120 (123)
T 2lpm_A          105 KPFLDSELEAVLVQIS  120 (123)
T ss_dssp             SSSSHHHHHHHHSTTC
T ss_pred             CCCCHHHHHHHHHHHH
Confidence            9999999999887653

>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=99.80  E-value=5.9e-19  Score=137.97  Aligned_cols=99  Identities=23%  Similarity=0.410  Sum_probs=90.3

Q ss_pred             CCcEEE-EECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVT-KCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~-~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||.|. .+.++.+|++.+....  ||+||+|+.||+++|+++++.++.....|||++|+..+.+....++..||++||.
T Consensus        36 ~g~~v~~~~~~~~~al~~~~~~~--~dlvi~D~~~p~~~g~~~~~~l~~~~~~pii~lt~~~~~~~~~~~~~~ga~~~l~  113 (205)
T 1s8n_A           36 EGYEIVGEAGDGQEAVELAELHK--PDLVIMDVKMPRRDGIDAASEIASKRIAPIVVLTAFSQRDLVERARDAGAMAYLV  113 (205)
T ss_dssp             TTCEEEEEESSHHHHHHHHHHHC--CSEEEEESSCSSSCHHHHHHHHHHTTCSCEEEEEEGGGHHHHHTTGGGSCEEEEE
T ss_pred             CCCEEEEEeCCHHHHHHHHhhcC--CCEEEEeCCCCCCChHHHHHHHHhcCCCCEEEEecCCCHHHHHHHHhcCCcEEEe
Confidence            489988 8999999999998876  9999999999999999999999865556999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHhhh
Q 027234           80 KPVRIEELKNIWQHVVRKRKNE  101 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~~~~~  101 (226)
                      ||++.++|...++.++......
T Consensus       114 KP~~~~~L~~~i~~~~~~~~~~  135 (205)
T 1s8n_A          114 KPFSISDLIPAIELAVSRFREI  135 (205)
T ss_dssp             ESCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHHH
Confidence            9999999999999998765443

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

Probab=99.79  E-value=2.5e-18  Score=124.94  Aligned_cols=100  Identities=23%  Similarity=0.361  Sum_probs=91.2

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||.|..+.++.+|++.+....  ||+||+|+.||+++|+++++.++ ..+.+|+|++|+..+.+....+++.||++||.
T Consensus        26 ~g~~v~~~~~~~~al~~~~~~~--~dlvl~D~~l~~~~g~~~~~~l~~~~~~~~ii~~s~~~~~~~~~~~~~~ga~~~l~  103 (132)
T 3crn_A           26 EGYEVEIAATAGEGLAKIENEF--FNLALFXIKLPDMEGTELLEKAHKLRPGMKKIMVTGYASLENSVFSLNAGADAYIM  103 (132)
T ss_dssp             TTCEEEEESSHHHHHHHHHHSC--CSEEEECSBCSSSBHHHHHHHHHHHCTTSEEEEEESCCCHHHHHHHHHTTCSEEEE
T ss_pred             CCceEEEeCCHHHHHHHHhcCC--CCEEEEecCCCCCchHHHHHHHHhhCCCCcEEEEeccccHHHHHHHHhccchhhcc
Confidence            4799999999999999998866  99999999999999999999997 45789999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHhhhh
Q 027234           80 KPVRIEELKNIWQHVVRKRKNER  102 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~~~~~~  102 (226)
                      ||++.++|...+++++++.....
T Consensus       104 KP~~~~~L~~~i~~~~~~~~~~~  126 (132)
T 3crn_A          104 KPVNPRDLLEKIKEKLDEQEKEG  126 (132)
T ss_dssp             SSCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHhcccCCC
Confidence            99999999999999887655433

>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=99.79  E-value=6.7e-19  Score=128.38  Aligned_cols=93  Identities=19%  Similarity=0.438  Sum_probs=84.4

Q ss_pred             Cc-EEEEECCHHHHHHHHHh-----CCCCceEEEEccCCCCCCHHHHHHHHhc--CCCCcEEEEeccCCHHHHHHHHhCC
Q 027234            2 GF-SVTKCNRAEIALDMLRT-----NKNGYDIVISDVHMPDMDGFKLLELVGL--EMDLPVIMMCAHGSKEVVMKGVTHD   73 (226)
Q Consensus         2 g~-~V~~~~~~~eal~~l~~-----~~~~~DlVl~D~~mp~~dG~~l~~~l~~--~~~~pvI~ls~~~~~~~~~~a~~~g   73 (226)
                      || .|..+.++.+|++.+..     ..  ||+||+|+.||+++|+++++.++.  .+.+|||++|+..+.+...++++.|
T Consensus        26 g~~~v~~~~~~~~al~~~~~~~~~~~~--~dlvllD~~mp~~~G~~~~~~lr~~~~~~~~ii~lt~~~~~~~~~~~~~~g  103 (133)
T 2r25_B           26 GIENIELACDGQEAFDKVKELTSKGEN--YNMIFMDVQMPKVDGLLSTKMIRRDLGYTSPIVALTAFADDSNIKECLESG  103 (133)
T ss_dssp             TCCCEEEESSHHHHHHHHHHHHHHTCC--CSEEEECSCCSSSCHHHHHHHHHHHSCCCSCEEEEESCCSHHHHHHHHHTT
T ss_pred             CCceEEEECCHHHHHHHHHHHHhcCCC--CCEEEEeCCCCCCChHHHHHHHHhhcCCCCCEEEEECCCCHHHHHHHHHcC
Confidence            66 48889999999999986     55  999999999999999999999974  3578999999999999999999999


Q ss_pred             cceEEeCCCCHHHHHHHHHHHHH
Q 027234           74 ACDYLTKPVRIEELKNIWQHVVR   96 (226)
Q Consensus        74 a~~yl~KP~~~~~L~~~l~~~~~   96 (226)
                      |++||.||++.++|...+++++.
T Consensus       104 a~~~l~KP~~~~~L~~~l~~~~~  126 (133)
T 2r25_B          104 MNGFLSKPIKRPKLKTILTEFCA  126 (133)
T ss_dssp             CSEEEESSCCHHHHHHHHHHHCT
T ss_pred             CCEEEeCCCCHHHHHHHHHHHHH
Confidence            99999999999999999988754

>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=99.78  E-value=4.7e-18  Score=121.14  Aligned_cols=95  Identities=31%  Similarity=0.435  Sum_probs=88.2

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||.|..+.++.+|++.+....  ||+||+|+.||+++|+++++.++ ..+.+|+|++|+..+.....++++.|+++|+.
T Consensus        23 ~g~~v~~~~~~~~a~~~~~~~~--~dlil~D~~l~~~~g~~~~~~l~~~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~  100 (121)
T 2pl1_A           23 AGHQVDDAEDAKEADYYLNEHI--PDIAIVDLGLPDEDGLSLIRRWRSNDVSLPILVLTARESWQDKVEVLSAGADDYVT  100 (121)
T ss_dssp             TTCEEEEESSHHHHHHHHHHSC--CSEEEECSCCSSSCHHHHHHHHHHTTCCSCEEEEESCCCHHHHHHHHHTTCSEEEE
T ss_pred             cCCEEEEeCCHHHHHHHHhccC--CCEEEEecCCCCCCHHHHHHHHHhcCCCCCEEEEecCCCHHHHHHHHHcCccceEE
Confidence            4799999999999999999876  99999999999999999999997 45689999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHH
Q 027234           80 KPVRIEELKNIWQHVVRK   97 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~   97 (226)
                      ||++.++|...++++++.
T Consensus       101 kp~~~~~l~~~i~~~~~~  118 (121)
T 2pl1_A          101 KPFHIEEVMARMQALMRR  118 (121)
T ss_dssp             SSCCHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHh
Confidence            999999999999988754

>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=99.78  E-value=2.1e-18  Score=134.93  Aligned_cols=97  Identities=23%  Similarity=0.445  Sum_probs=89.1

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||.|..+.++.+|++.+....  ||+||+|+.||+++|+++++.++ ..+.+|||++|+..+.+....+++.||++||.
T Consensus        27 ~g~~v~~~~~~~~al~~~~~~~--~dlvl~D~~lp~~~g~~~~~~l~~~~~~~~ii~ls~~~~~~~~~~a~~~Ga~~~l~  104 (208)
T 1yio_A           27 AGFEVETFDCASTFLEHRRPEQ--HGCLVLDMRMPGMSGIELQEQLTAISDGIPIVFITAHGDIPMTVRAMKAGAIEFLP  104 (208)
T ss_dssp             TTCEEEEESSHHHHHHHCCTTS--CEEEEEESCCSSSCHHHHHHHHHHTTCCCCEEEEESCTTSCCCHHHHHTTEEEEEE
T ss_pred             CCceEEEcCCHHHHHHhhhccC--CCEEEEeCCCCCCCHHHHHHHHHhcCCCCCEEEEeCCCCHHHHHHHHHCCCcEEEe
Confidence            4799999999999999988765  99999999999999999999998 45789999999999988899999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHh
Q 027234           80 KPVRIEELKNIWQHVVRKRK   99 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~~~   99 (226)
                      ||++.++|...+++++++..
T Consensus       105 Kp~~~~~L~~~i~~~~~~~~  124 (208)
T 1yio_A          105 KPFEEQALLDAIEQGLQLNA  124 (208)
T ss_dssp             SSCCHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHhhhh
Confidence            99999999999999887654

>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=99.78  E-value=2.8e-18  Score=134.99  Aligned_cols=94  Identities=18%  Similarity=0.360  Sum_probs=87.2

Q ss_pred             CcEE-EEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            2 GFSV-TKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         2 g~~V-~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      ||.| ..+.++.+|++.+....  ||+||+|+.||+++|+++++.++ ..+.+|||++|+..+.+....++..||++||.
T Consensus        30 ~~~vv~~~~~~~~al~~~~~~~--~dlvllD~~lp~~~g~~~~~~lr~~~~~~~ii~ls~~~~~~~~~~~~~~Ga~~~l~  107 (215)
T 1a04_A           30 DITVVGEASNGEQGIELAESLD--PDLILLDLNMPGMNGLETLDKLREKSLSGRIVVFSVSNHEEDVVTALKRGADGYLL  107 (215)
T ss_dssp             TEEEEEEESSHHHHHHHHHHHC--CSEEEEETTSTTSCHHHHHHHHHHSCCCSEEEEEECCCCHHHHHHHHHTTCSEEEE
T ss_pred             CcEEEEEeCCHHHHHHHHHhcC--CCEEEEeCCCCCCcHHHHHHHHHHhCCCCcEEEEECCCCHHHHHHHHHcCCcEEEe
Confidence            4777 68999999999998876  99999999999999999999998 45689999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHH
Q 027234           80 KPVRIEELKNIWQHVVRK   97 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~   97 (226)
                      ||++.++|..+++.++++
T Consensus       108 Kp~~~~~L~~~i~~~~~~  125 (215)
T 1a04_A          108 KDMEPEDLLKALHQAAAG  125 (215)
T ss_dssp             TTCCHHHHHHHHHHHHHS
T ss_pred             CCCCHHHHHHHHHHHHcC
Confidence            999999999999998865

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

Probab=99.78  E-value=9e-21  Score=163.33  Aligned_cols=166  Identities=17%  Similarity=0.231  Sum_probs=119.3

Q ss_pred             CcEEEEECCHHHHHHHHHh-CCCCceEEEEccCCCCCCHHHHHHHHhc-CCCCcEEEEeccCCH-----HHHHHHHhCCc
Q 027234            2 GFSVTKCNRAEIALDMLRT-NKNGYDIVISDVHMPDMDGFKLLELVGL-EMDLPVIMMCAHGSK-----EVVMKGVTHDA   74 (226)
Q Consensus         2 g~~V~~~~~~~eal~~l~~-~~~~~DlVl~D~~mp~~dG~~l~~~l~~-~~~~pvI~ls~~~~~-----~~~~~a~~~ga   74 (226)
                      ||.|.++.++.+|++.+.. ..  ||+||+|+.||+|||+++++.++. .+.+|||++|+..+.     ....+++..||
T Consensus        28 ~~~v~~a~~g~eal~~l~~~~~--~DlvllDi~mP~~dG~ell~~l~~~~~~~~ii~~s~~~~~~~~~~~~~~~a~~~ga  105 (400)
T 3sy8_A           28 PGSILEAADGKEAVAILESCGH--VDIAICDLQMSGMDGLAFLRHASLSGKVHSVILSSEVDPILRQATISMIECLGLNF  105 (400)
T ss_dssp             SEEEEEESSHHHHHHHHHHHSC--EEEEEECSSCSSSCHHHHHHHHHHHTCEEEEEESCCCCGGGHHHHHHHHHTTTCEE
T ss_pred             CcEEEEecCHHHHHHHHhhCCC--CCEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEcCchHHHHHHHHHHHHHcCCee
Confidence            6889999999999999987 46  999999999999999999999984 455667777776665     66788999999


Q ss_pred             ceEEeCCCCHHHHHHHHHHHHHHHhhhhhhhhhccCccCCCCCC---CCcccCC-CcccccCCCCCCccchHHHHHHhcc
Q 027234           75 CDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQSGSVEGGAQQP---KPFEESD-DSYSVNEGTSNSRKDEEEEAEKRLK  150 (226)
Q Consensus        75 ~~yl~KP~~~~~L~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~  150 (226)
                      ++||.||++.++|...+++++...........    ........   ......+ ....++......+...+.|++.||.
T Consensus       106 ~~yl~KP~~~~~L~~~i~~~~~~~~~~~~~~~----~~~~~~~~~l~~al~~~~~~~~~QPiv~~~~~~~~g~EaL~R~~  181 (400)
T 3sy8_A          106 LGDLGKPFSLERITALLTRYNARRQDLPRQIE----VAELPSVADVVRGLDNGEFEAYYQPKVALDGGGLIGAEVLARWN  181 (400)
T ss_dssp             EEECCSSCCHHHHHHHHHHHHHHTTSCCCC-------CCCCCHHHHHHHHHTTCEEEEEEEEEESSSCCEEEEEEEEEEE
T ss_pred             ccCcCCCcCHHHHHHHHHHHHHhhhhhhhhhh----hhcccHHHHHHHHHHCCcEEEEEeCeEEcCCCCEEEEEEEEEEe
Confidence            99999999999999999998765432111000    00000000   0000000 1223344455566677888899999


Q ss_pred             CCceeeeHhhHHHHHHHHHHhCCCC
Q 027234          151 KPRLVWSVELHQQFVSAVKELGFDK  175 (226)
Q Consensus       151 ~~~~~~~~~l~~~Fi~~~~~~g~~~  175 (226)
                      ++..++  ..|..|++.+++.|+..
T Consensus       182 ~~~~~~--i~p~~fi~~ae~~~l~~  204 (400)
T 3sy8_A          182 HPHLGV--LPPSHFLYVMETYNLVD  204 (400)
T ss_dssp             ETTTEE--ECGGGTHHHHHHTTCHH
T ss_pred             cCCCCE--ECHHHHHHHHHHCCCHH
Confidence            988775  56889999999998743

>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=99.78  E-value=3.5e-18  Score=123.00  Aligned_cols=94  Identities=24%  Similarity=0.484  Sum_probs=87.1

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhc-CCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGL-EMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~-~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||.|..+.++.++++.+....  ||+||+|+.||+++|+++++.++. .+.+|+|++|+..+.+...++++.|+++||.
T Consensus        26 ~~~~v~~~~~~~~~~~~~~~~~--~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~ii~~s~~~~~~~~~~~~~~ga~~~l~  103 (126)
T 1dbw_A           26 NGFAVKMHQSAEAFLAFAPDVR--NGVLVTDLRMPDMSGVELLRNLGDLKINIPSIVITGHGDVPMAVEAMKAGAVDFIE  103 (126)
T ss_dssp             TTCEEEEESCHHHHHHHGGGCC--SEEEEEECCSTTSCHHHHHHHHHHTTCCCCEEEEECTTCHHHHHHHHHTTCSEEEE
T ss_pred             CCcEEEEeCCHHHHHHHHhcCC--CCEEEEECCCCCCCHHHHHHHHHhcCCCCCEEEEECCCCHHHHHHHHHhCHHHhee
Confidence            3789999999999999998766  999999999999999999999974 5789999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHH
Q 027234           80 KPVRIEELKNIWQHVVR   96 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~   96 (226)
                      ||++.++|...++++++
T Consensus       104 Kp~~~~~l~~~i~~~~~  120 (126)
T 1dbw_A          104 KPFEDTVIIEAIERASE  120 (126)
T ss_dssp             SSCCHHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHHH
Confidence            99999999999998764

>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=99.78  E-value=5.8e-18  Score=120.97  Aligned_cols=95  Identities=19%  Similarity=0.394  Sum_probs=88.5

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEeC
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTK   80 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~K   80 (226)
                      .||.|..+.++.++++.+....  ||+||+|+.||+++|+++++.++..+.+|+|++|+..+......+++.|+++|+.|
T Consensus        25 ~~~~v~~~~~~~~~~~~~~~~~--~dlvi~d~~l~~~~g~~~~~~l~~~~~~~ii~~s~~~~~~~~~~~~~~ga~~~l~K  102 (122)
T 1zgz_A           25 EGYTVSVTASGAGLREIMQNQS--VDLILLDINLPDENGLMLTRALRERSTVGIILVTGRSDRIDRIVGLEMGADDYVTK  102 (122)
T ss_dssp             TTCEEEEESSHHHHHHHHHHSC--CSEEEEESCCSSSCHHHHHHHHHTTCCCEEEEEESSCCHHHHHHHHHHTCSEEEES
T ss_pred             CCCeEEEecCHHHHHHHHhcCC--CCEEEEeCCCCCCChHHHHHHHHhcCCCCEEEEECCCChhhHHHHHHhCHHHHccC
Confidence            3789999999999999998866  99999999999999999999998777899999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHH
Q 027234           81 PVRIEELKNIWQHVVRK   97 (226)
Q Consensus        81 P~~~~~L~~~l~~~~~~   97 (226)
                      |++.++|...++++++.
T Consensus       103 p~~~~~l~~~i~~~~~~  119 (122)
T 1zgz_A          103 PLELRELVVRVKNLLWR  119 (122)
T ss_dssp             SCCHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHH
Confidence            99999999999988754

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

Probab=99.78  E-value=6.3e-18  Score=123.78  Aligned_cols=98  Identities=23%  Similarity=0.448  Sum_probs=89.9

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhc-CCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGL-EMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~-~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||.|..+.++.+|++.+....  ||+||+|+.||+++|+++++.++. .+.+|+|++|+..+.+....+++.|+++||.
T Consensus        27 ~g~~v~~~~~~~~a~~~l~~~~--~dlvllD~~l~~~~g~~l~~~l~~~~~~~~ii~ls~~~~~~~~~~~~~~ga~~~l~  104 (137)
T 3cfy_A           27 EPYDIFHVETGRDAIQFIERSK--PQLIILDLKLPDMSGEDVLDWINQNDIPTSVIIATAHGSVDLAVNLIQKGAEDFLE  104 (137)
T ss_dssp             SSSEEEEESSHHHHHHHHHHHC--CSEEEECSBCSSSBHHHHHHHHHHTTCCCEEEEEESSCCHHHHHHHHHTTCSEEEE
T ss_pred             cCceEEEeCCHHHHHHHHHhcC--CCEEEEecCCCCCCHHHHHHHHHhcCCCCCEEEEEecCcHHHHHHHHHCCccEEEe
Confidence            3799999999999999998876  999999999999999999999984 5789999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHhh
Q 027234           80 KPVRIEELKNIWQHVVRKRKN  100 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~~~~  100 (226)
                      ||++.++|...++++++....
T Consensus       105 KP~~~~~L~~~i~~~~~~~~~  125 (137)
T 3cfy_A          105 KPINADRLKTSVALHLKRAKL  125 (137)
T ss_dssp             SSCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHH
Confidence            999999999999998875443

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

Probab=99.78  E-value=1.6e-19  Score=148.91  Aligned_cols=95  Identities=22%  Similarity=0.327  Sum_probs=86.2

Q ss_pred             CCcEEE-EECCHHHHHHHHHhCCCCceEEEEccCCC-CCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEE
Q 027234            1 MGFSVT-KCNRAEIALDMLRTNKNGYDIVISDVHMP-DMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYL   78 (226)
Q Consensus         1 lg~~V~-~~~~~~eal~~l~~~~~~~DlVl~D~~mp-~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl   78 (226)
                      +||.|. +|.||.+|++.+....  ||+||+|+.|| +|||+++++.|+..+++|||++|+..  +...+++..|+++||
T Consensus       183 ~g~~v~~~a~~g~eAl~~~~~~~--~dlvl~D~~MPd~mdG~e~~~~ir~~~~~piI~lT~~~--~~~~~~~~~G~~~~l  258 (286)
T 3n0r_A          183 LGHDVTDIAATRGEALEAVTRRT--PGLVLADIQLADGSSGIDAVKDILGRMDVPVIFITAFP--ERLLTGERPEPTFLI  258 (286)
T ss_dssp             TTCEEEEEESSHHHHHHHHHHCC--CSEEEEESCCTTSCCTTTTTHHHHHHTTCCEEEEESCG--GGGCCSSSCCCSSEE
T ss_pred             cCceEEEEeCCHHHHHHHHHhCC--CCEEEEcCCCCCCCCHHHHHHHHHhcCCCCEEEEeCCH--HHHHHHHhCCCcEEE
Confidence            489999 9999999999999876  99999999999 89999999999855599999999985  356779999999999


Q ss_pred             eCCCCHHHHHHHHHHHHHHHh
Q 027234           79 TKPVRIEELKNIWQHVVRKRK   99 (226)
Q Consensus        79 ~KP~~~~~L~~~l~~~~~~~~   99 (226)
                      .||++.++|...+.+++....
T Consensus       259 ~KP~~~~~L~~~i~~~l~~~~  279 (286)
T 3n0r_A          259 TKPFQPETVKAAIGQALFFHP  279 (286)
T ss_dssp             ESSCCHHHHHHHHHHHHHHSC
T ss_pred             eCCCCHHHHHHHHHHHHHhCC
Confidence            999999999999999987543

>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=99.78  E-value=4.7e-18  Score=121.63  Aligned_cols=95  Identities=19%  Similarity=0.355  Sum_probs=88.2

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEeC
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTK   80 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~K   80 (226)
                      .||.|..+.++.+|++.+....  ||+||+|+.||+++|+++++.++..+.+|+|++|+..+......+++.|+++||.|
T Consensus        26 ~~~~v~~~~~~~~a~~~~~~~~--~dlvi~D~~l~~~~g~~~~~~l~~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~K  103 (123)
T 1xhf_A           26 EGYDVFEATDGAEMHQILSEYD--INLVIMDINLPGKNGLLLARELREQANVALMFLTGRDNEVDKILGLEIGADDYITK  103 (123)
T ss_dssp             TTCEEEEESSHHHHHHHHHHSC--CSEEEECSSCSSSCHHHHHHHHHHHCCCEEEEEESCCSHHHHHHHHHHTCSEEEES
T ss_pred             CCcEEEEeCCHHHHHHHHhcCC--CCEEEEcCCCCCCCHHHHHHHHHhCCCCcEEEEECCCChHHHHHHHhcCcceEEeC
Confidence            3799999999999999998866  99999999999999999999998557899999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHH
Q 027234           81 PVRIEELKNIWQHVVRK   97 (226)
Q Consensus        81 P~~~~~L~~~l~~~~~~   97 (226)
                      |++.++|...++++++.
T Consensus       104 P~~~~~l~~~i~~~~~~  120 (123)
T 1xhf_A          104 PFNPRELTIRARNLLSR  120 (123)
T ss_dssp             SCCHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHH
Confidence            99999999999988754

>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=99.77  E-value=3.9e-18  Score=121.26  Aligned_cols=94  Identities=27%  Similarity=0.468  Sum_probs=87.6

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEeC
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTK   80 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~K   80 (226)
                      .||.|..+.++.+|++.+....  ||+||+|+.||+++|+++++.++..+.+|+|++|+..+......+++.|+++||.|
T Consensus        24 ~~~~v~~~~~~~~a~~~~~~~~--~dlvl~D~~l~~~~g~~~~~~l~~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~K  101 (120)
T 2a9o_A           24 EGYEVVTAFNGREALEQFEAEQ--PDIIILDLMLPEIDGLEVAKTIRKTSSVPILMLSAKDSEFDKVIGLELGADDYVTK  101 (120)
T ss_dssp             TTCEEEEESSHHHHHHHHHHHC--CSEEEECSSCSSSCHHHHHHHHHHHCCCCEEEEESCCSHHHHHHHHHHTCSEEEES
T ss_pred             cCcEEEEecCHHHHHHHHHhCC--CCEEEEeccCCCCCHHHHHHHHHhCCCCCEEEEecCCchHHHHHHHhCCHhheEeC
Confidence            3799999999999999998866  99999999999999999999998667899999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHH
Q 027234           81 PVRIEELKNIWQHVVR   96 (226)
Q Consensus        81 P~~~~~L~~~l~~~~~   96 (226)
                      |++.++|...++++++
T Consensus       102 p~~~~~l~~~i~~~~~  117 (120)
T 2a9o_A          102 PFSNRELQARVKALLR  117 (120)
T ss_dssp             SCCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHc
Confidence            9999999999988765

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

Probab=99.77  E-value=7.2e-18  Score=125.61  Aligned_cols=101  Identities=25%  Similarity=0.407  Sum_probs=92.9

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCC-cceEE
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHD-ACDYL   78 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~g-a~~yl   78 (226)
                      .||.|..+.++.+|++.+....  ||+||+|+.||+++|+++++.++ ..+.+|||++|+..+.+...+++..| +++||
T Consensus        37 ~g~~v~~~~~~~~a~~~l~~~~--~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~~l  114 (153)
T 3hv2_A           37 LPYTLHFARDATQALQLLASRE--VDLVISAAHLPQMDGPTLLARIHQQYPSTTRILLTGDPDLKLIAKAINEGEIYRYL  114 (153)
T ss_dssp             SSCEEEEESSHHHHHHHHHHSC--CSEEEEESCCSSSCHHHHHHHHHHHCTTSEEEEECCCCCHHHHHHHHHTTCCSEEE
T ss_pred             cCcEEEEECCHHHHHHHHHcCC--CCEEEEeCCCCcCcHHHHHHHHHhHCCCCeEEEEECCCCHHHHHHHHhCCCcceEE
Confidence            3799999999999999999876  99999999999999999999997 45789999999999999999999999 99999


Q ss_pred             eCCCCHHHHHHHHHHHHHHHhhhhh
Q 027234           79 TKPVRIEELKNIWQHVVRKRKNERK  103 (226)
Q Consensus        79 ~KP~~~~~L~~~l~~~~~~~~~~~~  103 (226)
                      .||++.++|..+++++++.....+.
T Consensus       115 ~KP~~~~~l~~~i~~~l~~~~~~~~  139 (153)
T 3hv2_A          115 SKPWDDQELLLALRQALEHQHSERE  139 (153)
T ss_dssp             CSSCCHHHHHHHHHHHHHHHHHHHT
T ss_pred             eCCCCHHHHHHHHHHHHHHhHHHhh
Confidence            9999999999999999887665443

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

Probab=99.77  E-value=3.9e-18  Score=127.39  Aligned_cols=98  Identities=26%  Similarity=0.435  Sum_probs=90.7

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcC---CCCcEEEEeccCCHHHHHHHHhCCcceE
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLE---MDLPVIMMCAHGSKEVVMKGVTHDACDY   77 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~---~~~pvI~ls~~~~~~~~~~a~~~ga~~y   77 (226)
                      .||.|..+.++.+|++.+....  ||+||+|+.||+++|+++++.++..   +.+|||++|+..+.+...+++..|+++|
T Consensus        30 ~g~~v~~~~~~~~al~~l~~~~--~dlii~D~~l~~~~g~~~~~~lr~~~~~~~~pii~~s~~~~~~~~~~~~~~g~~~~  107 (154)
T 3gt7_A           30 TGYQTEHVRNGREAVRFLSLTR--PDLIISDVLMPEMDGYALCRWLKGQPDLRTIPVILLTILSDPRDVVRSLECGADDF  107 (154)
T ss_dssp             TTCEEEEESSHHHHHHHHTTCC--CSEEEEESCCSSSCHHHHHHHHHHSTTTTTSCEEEEECCCSHHHHHHHHHHCCSEE
T ss_pred             CCCEEEEeCCHHHHHHHHHhCC--CCEEEEeCCCCCCCHHHHHHHHHhCCCcCCCCEEEEECCCChHHHHHHHHCCCCEE
Confidence            4899999999999999998866  9999999999999999999999854   6799999999999999999999999999


Q ss_pred             EeCCCCHHHHHHHHHHHHHHHhh
Q 027234           78 LTKPVRIEELKNIWQHVVRKRKN  100 (226)
Q Consensus        78 l~KP~~~~~L~~~l~~~~~~~~~  100 (226)
                      |.||++.++|...+++++.+...
T Consensus       108 l~KP~~~~~l~~~i~~~l~~~~~  130 (154)
T 3gt7_A          108 ITKPCKDVVLASHVKRLLSGVKR  130 (154)
T ss_dssp             EESSCCHHHHHHHHHHHHHHTCC
T ss_pred             EeCCCCHHHHHHHHHHHHHHHHh
Confidence            99999999999999999876544

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

Probab=99.77  E-value=4.7e-18  Score=124.30  Aligned_cols=97  Identities=23%  Similarity=0.421  Sum_probs=89.3

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEeC
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTK   80 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~K   80 (226)
                      .||.|..+.++.+|++.+....  ||+||+|+.||+++|+++++.++....+|+|++|+..+.+....+++.|+++||.|
T Consensus        27 ~g~~v~~~~~~~~al~~~~~~~--~dlvllD~~l~~~~g~~l~~~l~~~~~~~ii~ls~~~~~~~~~~~~~~ga~~~l~K  104 (136)
T 2qzj_A           27 KGISIDLAYNCEEAIGKIFSNK--YDLIFLEIILSDGDGWTLCKKIRNVTTCPIVYMTYINEDQSILNALNSGGDDYLIK  104 (136)
T ss_dssp             TTCEEEEESSHHHHHHHHHHCC--CSEEEEESEETTEEHHHHHHHHHTTCCCCEEEEESCCCHHHHHHHHHTTCCEEEES
T ss_pred             CCCEEEEECCHHHHHHHHHhcC--CCEEEEeCCCCCCCHHHHHHHHccCCCCCEEEEEcCCCHHHHHHHHHcCCcEEEEC
Confidence            3789999999999999998866  99999999999999999999998655899999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHh
Q 027234           81 PVRIEELKNIWQHVVRKRK   99 (226)
Q Consensus        81 P~~~~~L~~~l~~~~~~~~   99 (226)
                      |++.++|...+++++++..
T Consensus       105 P~~~~~L~~~l~~~~~~~~  123 (136)
T 2qzj_A          105 PLNLEILYAKVKAILRRMN  123 (136)
T ss_dssp             SCCHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHhh
Confidence            9999999999999876543

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

Probab=99.77  E-value=4.4e-18  Score=125.62  Aligned_cols=95  Identities=29%  Similarity=0.448  Sum_probs=84.5

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhc-----CCCCcEEEEeccCCHHHHHHHHhCCcc
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGL-----EMDLPVIMMCAHGSKEVVMKGVTHDAC   75 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~-----~~~~pvI~ls~~~~~~~~~~a~~~ga~   75 (226)
                      .||.|..+.++.+|++.+....  ||+||+|+.||+++|+++++.++.     .+.+|+|++|+..+.+....+++.||+
T Consensus        37 ~g~~v~~~~~~~~al~~~~~~~--~dlvl~D~~mp~~~g~~~~~~lr~~~~~~~~~~pii~~s~~~~~~~~~~~~~~Ga~  114 (143)
T 3m6m_D           37 AGHKVLCVNGAEQVLDAMAEED--YDAVIVDLHMPGMNGLDMLKQLRVMQASGMRYTPVVVLSADVTPEAIRACEQAGAR  114 (143)
T ss_dssp             --CEEEEESSHHHHHHHHHHSC--CSEEEEESCCSSSCHHHHHHHHHHHHHTTCCCCCEEEEESCCCHHHHHHHHHTTCS
T ss_pred             cCCeEEEeCCHHHHHHHHhcCC--CCEEEEeCCCCCCCHHHHHHHHHhchhccCCCCeEEEEeCCCCHHHHHHHHHcChh
Confidence            3789999999999999998866  999999999999999999999862     246899999999999999999999999


Q ss_pred             eEEeCCCCHHHHHHHHHHHHHH
Q 027234           76 DYLTKPVRIEELKNIWQHVVRK   97 (226)
Q Consensus        76 ~yl~KP~~~~~L~~~l~~~~~~   97 (226)
                      +||.||++.++|...+.++...
T Consensus       115 ~~l~KP~~~~~L~~~l~~~~~~  136 (143)
T 3m6m_D          115 AFLAKPVVAAKLLDTLADLAVS  136 (143)
T ss_dssp             EEEESSCCHHHHHHHHHHHC--
T ss_pred             heeeCCCCHHHHHHHHHHHHHh
Confidence            9999999999999999887644

>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=99.77  E-value=3.3e-18  Score=122.73  Aligned_cols=94  Identities=23%  Similarity=0.469  Sum_probs=86.9

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhc-CCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGL-EMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~-~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||.|..+.++.+|++.+....  ||+||+|+.||+++|+++++.++. .+.+|+|++|+..+.+...++++.|+++||.
T Consensus        26 ~~~~v~~~~~~~~a~~~~~~~~--~dlvl~D~~l~~~~g~~~~~~l~~~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~  103 (124)
T 1srr_A           26 EGYQTFQAANGLQALDIVTKER--PDLVLLDMKIPGMDGIEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHFA  103 (124)
T ss_dssp             TTCEEEEESSHHHHHHHHHHHC--CSEEEEESCCTTCCHHHHHHHHHHHCTTCEEEEEESSCCHHHHHHHHHHTCCCEEE
T ss_pred             CCcEEEEeCCHHHHHHHHhccC--CCEEEEecCCCCCCHHHHHHHHHHhCCCCCEEEEEccCchHHHHHHHhcChHhhcc
Confidence            3799999999999999998866  999999999999999999999974 5789999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHH
Q 027234           80 KPVRIEELKNIWQHVVR   96 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~   96 (226)
                      ||++.++|...++++++
T Consensus       104 KP~~~~~l~~~i~~~~~  120 (124)
T 1srr_A          104 KPFDIDEIRDAVKKYLP  120 (124)
T ss_dssp             SSCCHHHHHHHHHHHSC
T ss_pred             CCCCHHHHHHHHHHHhc
Confidence            99999999999988753

>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=99.77  E-value=7.6e-18  Score=121.92  Aligned_cols=95  Identities=27%  Similarity=0.525  Sum_probs=85.4

Q ss_pred             CCcE-EEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcC---CCCcEEEEeccCCHHHHHHHHhCCcce
Q 027234            1 MGFS-VTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLE---MDLPVIMMCAHGSKEVVMKGVTHDACD   76 (226)
Q Consensus         1 lg~~-V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~---~~~pvI~ls~~~~~~~~~~a~~~ga~~   76 (226)
                      .||. |..+.++.+|++.+... ..||+||+|+.||+++|+++++.++..   +.+|||++|+..+.....++++.||++
T Consensus        28 ~g~~~v~~~~~~~~a~~~~~~~-~~~dlvi~D~~~p~~~g~~~~~~lr~~~~~~~~pii~~s~~~~~~~~~~~~~~g~~~  106 (129)
T 3h1g_A           28 LGYEDVLEAEHGVEAWEKLDAN-ADTKVLITDWNMPEMNGLDLVKKVRSDSRFKEIPIIMITAEGGKAEVITALKAGVNN  106 (129)
T ss_dssp             TTCCCEEEESSHHHHHHHHHHC-TTCCEEEECSCCSSSCHHHHHHHHHTSTTCTTCCEEEEESCCSHHHHHHHHHHTCCE
T ss_pred             cCCcEEEEeCCHHHHHHHHHhC-CCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCCCeEEEEeCCCChHHHHHHHHcCccE
Confidence            3775 88999999999988764 239999999999999999999999743   578999999999999999999999999


Q ss_pred             EEeCCCCHHHHHHHHHHHHH
Q 027234           77 YLTKPVRIEELKNIWQHVVR   96 (226)
Q Consensus        77 yl~KP~~~~~L~~~l~~~~~   96 (226)
                      ||.||++.++|...++.++.
T Consensus       107 ~l~KP~~~~~L~~~l~~~l~  126 (129)
T 3h1g_A          107 YIVKPFTPQVLKEKLEVVLG  126 (129)
T ss_dssp             EEESCCCHHHHHHHHHHHHC
T ss_pred             EEeCCCCHHHHHHHHHHHhc
Confidence            99999999999999998864

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

Probab=99.76  E-value=1.8e-17  Score=121.71  Aligned_cols=102  Identities=25%  Similarity=0.457  Sum_probs=91.8

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||.|..+.++.+|++.+......||+||+|+.||+++|+++++.++ ..+.+|||++|+..+.+...+++..|+++||.
T Consensus        26 ~g~~v~~~~~~~~a~~~~~~~~~~~dlvi~d~~l~~~~g~~~~~~l~~~~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~  105 (143)
T 3jte_A           26 DGNEVLTASSSTEGLRIFTENCNSIDVVITDMKMPKLSGMDILREIKKITPHMAVIILTGHGDLDNAILAMKEGAFEYLR  105 (143)
T ss_dssp             TTCEEEEESSHHHHHHHHHHTTTTCCEEEEESCCSSSCHHHHHHHHHHHCTTCEEEEEECTTCHHHHHHHHHTTCSEEEE
T ss_pred             CCceEEEeCCHHHHHHHHHhCCCCCCEEEEeCCCCCCcHHHHHHHHHHhCCCCeEEEEECCCCHHHHHHHHHhCcceeEe
Confidence            47999999999999999984223499999999999999999999997 55789999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHhhhh
Q 027234           80 KPVRIEELKNIWQHVVRKRKNER  102 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~~~~~~  102 (226)
                      ||++.++|..++++++++....+
T Consensus       106 kp~~~~~l~~~l~~~~~~~~~~~  128 (143)
T 3jte_A          106 KPVTAQDLSIAINNAINRKKLLM  128 (143)
T ss_dssp             SSCCHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999998766544

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

Probab=99.76  E-value=1e-17  Score=135.03  Aligned_cols=97  Identities=34%  Similarity=0.528  Sum_probs=90.3

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhc-CCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGL-EMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~-~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||+|..+.++.+|++.+....  ||+||+|+.||++||+++++.++. .+.+|||++|+..+.+....+++.||++||.
T Consensus        46 ~g~~v~~~~~~~~al~~~~~~~--~dlvllD~~lp~~~g~~~~~~lr~~~~~~~ii~lt~~~~~~~~~~~~~~Ga~~yl~  123 (250)
T 3r0j_A           46 QGFEVYTATNGAQALDRARETR--PDAVILDVXMPGMDGFGVLRRLRADGIDAPALFLTARDSLQDKIAGLTLGGDDYVT  123 (250)
T ss_dssp             TTCEEEEESSHHHHHHHHHHHC--CSEEEEESCCSSSCHHHHHHHHHHTTCCCCEEEEECSTTHHHHHHHHTSTTCEEEE
T ss_pred             CCCEEEEECCHHHHHHHHHhCC--CCEEEEeCCCCCCCHHHHHHHHHhcCCCCCEEEEECCCCHHHHHHHHHcCCcEEEe
Confidence            4799999999999999999876  999999999999999999999984 5789999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHh
Q 027234           80 KPVRIEELKNIWQHVVRKRK   99 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~~~   99 (226)
                      ||++.++|..+++.++++..
T Consensus       124 Kp~~~~~L~~~i~~~~~~~~  143 (250)
T 3r0j_A          124 KPFSLEEVVARLRVILRRAG  143 (250)
T ss_dssp             SSCCHHHHHHHHHHHHHHHC
T ss_pred             CCCCHHHHHHHHHHHHHhhc
Confidence            99999999999999987643

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

Probab=99.76  E-value=1e-17  Score=121.80  Aligned_cols=94  Identities=22%  Similarity=0.338  Sum_probs=85.2

Q ss_pred             cEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEeCC
Q 027234            3 FSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTKP   81 (226)
Q Consensus         3 ~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~KP   81 (226)
                      +.|..+.++.+|++.+....  ||+||+|+.||+++|+++++.++ ..+.+|||++|+..+.+...++++.|+++||.||
T Consensus        30 ~~v~~~~~~~~al~~~~~~~--~dlvilD~~lp~~~g~~~~~~l~~~~~~~~ii~ls~~~~~~~~~~~~~~ga~~~l~Kp  107 (133)
T 3b2n_A           30 EILADTDNGLDAMKLIEEYN--PNVVILDIEMPGMTGLEVLAEIRKKHLNIKVIIVTTFKRPGYFEKAVVNDVDAYVLKE  107 (133)
T ss_dssp             EEEEEESCHHHHHHHHHHHC--CSEEEECSSCSSSCHHHHHHHHHHTTCSCEEEEEESCCCHHHHHHHHHTTCSEEEETT
T ss_pred             EEEEEcCCHHHHHHHHhhcC--CCEEEEecCCCCCCHHHHHHHHHHHCCCCcEEEEecCCCHHHHHHHHHcCCcEEEECC
Confidence            45678999999999998866  99999999999999999999997 4578999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHH
Q 027234           82 VRIEELKNIWQHVVRKR   98 (226)
Q Consensus        82 ~~~~~L~~~l~~~~~~~   98 (226)
                      ++.++|...+++++++.
T Consensus       108 ~~~~~L~~~i~~~~~~~  124 (133)
T 3b2n_A          108 RSIEELVETINKVNNGE  124 (133)
T ss_dssp             SCHHHHHHHHHHHHC--
T ss_pred             CCHHHHHHHHHHHHcCC
Confidence            99999999999887543

>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=99.76  E-value=8e-18  Score=119.86  Aligned_cols=93  Identities=22%  Similarity=0.434  Sum_probs=85.1

Q ss_pred             CCcE-EEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEE
Q 027234            1 MGFS-VTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYL   78 (226)
Q Consensus         1 lg~~-V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl   78 (226)
                      .||+ +..+.++.+|++.+....  ||+||+|+.||+++|+++++.++ ..+.+|+|++|+..+.+...++++.|+++|+
T Consensus        25 ~g~~vv~~~~~~~~a~~~~~~~~--~dlil~D~~l~~~~g~~~~~~l~~~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l  102 (120)
T 1tmy_A           25 AGYEVAGEATNGREAVEKYKELK--PDIVTMDITMPEMNGIDAIKEIMKIDPNAKIIVCSAMGQQAMVIEAIKAGAKDFI  102 (120)
T ss_dssp             TTCEEEEEESSHHHHHHHHHHHC--CSEEEEECSCGGGCHHHHHHHHHHHCTTCCEEEEECTTCHHHHHHHHHTTCCEEE
T ss_pred             cCcEEEEEECCHHHHHHHHHhcC--CCEEEEeCCCCCCcHHHHHHHHHhhCCCCeEEEEeCCCCHHHHHHHHHhCcceeE
Confidence            3788 568999999999998876  99999999999999999999997 4578999999999999999999999999999


Q ss_pred             eCCCCHHHHHHHHHHHH
Q 027234           79 TKPVRIEELKNIWQHVV   95 (226)
Q Consensus        79 ~KP~~~~~L~~~l~~~~   95 (226)
                      .||++.++|...+++++
T Consensus       103 ~KP~~~~~l~~~i~~~~  119 (120)
T 1tmy_A          103 VKPFQPSRVVEALNKVS  119 (120)
T ss_dssp             ESSCCHHHHHHHHHHHC
T ss_pred             eCCCCHHHHHHHHHHHh
Confidence            99999999999988753

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

Probab=99.76  E-value=3.2e-18  Score=125.06  Aligned_cols=98  Identities=20%  Similarity=0.298  Sum_probs=90.4

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCC--CCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceE
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPD--MDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDY   77 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~--~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~y   77 (226)
                      .||+|..+.++.+|++.+.+..  ||+||+|+.||+  ++|+++++.++ ..+.+|||++|+..+.+...+++..|+++|
T Consensus        29 ~g~~v~~~~~~~~a~~~l~~~~--~dlvi~D~~l~~~~~~g~~~~~~l~~~~~~~~ii~~s~~~~~~~~~~~~~~ga~~~  106 (136)
T 3kto_A           29 LDVTIQCFASAESFMRQQISDD--AIGMIIEAHLEDKKDSGIELLETLVKRGFHLPTIVMASSSDIPTAVRAMRASAADF  106 (136)
T ss_dssp             SSSEEEEESSHHHHTTSCCCTT--EEEEEEETTGGGBTTHHHHHHHHHHHTTCCCCEEEEESSCCHHHHHHHHHTTCSEE
T ss_pred             CCcEEEEeCCHHHHHHHHhccC--CCEEEEeCcCCCCCccHHHHHHHHHhCCCCCCEEEEEcCCCHHHHHHHHHcChHHh
Confidence            3899999999999999998766  999999999999  99999999998 457899999999999999999999999999


Q ss_pred             EeCCCCHHHHHHHHHHHHHHHhh
Q 027234           78 LTKPVRIEELKNIWQHVVRKRKN  100 (226)
Q Consensus        78 l~KP~~~~~L~~~l~~~~~~~~~  100 (226)
                      |.||++.++|..+++++..+...
T Consensus       107 l~KP~~~~~l~~~i~~~~~~~~~  129 (136)
T 3kto_A          107 IEKPFIEHVLVHDVQQIINGAKE  129 (136)
T ss_dssp             EESSBCHHHHHHHHHHHHHHHC-
T ss_pred             eeCCCCHHHHHHHHHHHHhccCC
Confidence            99999999999999999877654

>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=99.75  E-value=9.7e-18  Score=119.39  Aligned_cols=95  Identities=27%  Similarity=0.400  Sum_probs=88.2

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEeC
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTK   80 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~K   80 (226)
                      .||.|..+.++.+++..+....  ||+||+|+.||+++|+++++.++..+.+|+|++|+..+......+++.|+++|+.|
T Consensus        24 ~~~~v~~~~~~~~~~~~~~~~~--~dlvi~D~~l~~~~g~~~~~~l~~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~K  101 (121)
T 1zh2_A           24 DGMRVFEAETLQRGLLEAATRK--PDLIILDLGLPDGDGIEFIRDLRQWSAVPVIVLSARSEESDKIAALDAGADDYLSK  101 (121)
T ss_dssp             TTCEEEEESSHHHHHHHHHHHC--CSEEEEESEETTEEHHHHHHHHHTTCCCCEEEEESCCSHHHHHHHHHHTCSEEEES
T ss_pred             CCCEEEEeCCHHHHHHHHhcCC--CCEEEEeCCCCCCcHHHHHHHHHhCCCCcEEEEECCCCHHHHHHHHhcCCCeEEeC
Confidence            3789999999999999988766  99999999999999999999998667899999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHH
Q 027234           81 PVRIEELKNIWQHVVRK   97 (226)
Q Consensus        81 P~~~~~L~~~l~~~~~~   97 (226)
                      |++.++|...+++++++
T Consensus       102 p~~~~~l~~~i~~~~~~  118 (121)
T 1zh2_A          102 PFGIGELQARLRVALRR  118 (121)
T ss_dssp             SCCHHHHHHHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHHHh
Confidence            99999999999988764

>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=99.75  E-value=1.1e-17  Score=121.98  Aligned_cols=100  Identities=17%  Similarity=0.257  Sum_probs=91.9

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||.|..+.++.+|++.+....  ||+||+|+.||+++|+++++.++ ..+.+|||++|+..+.+...+++..|+++||.
T Consensus        30 ~~~~v~~~~~~~~a~~~l~~~~--~dlvi~d~~l~~~~g~~~~~~l~~~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~  107 (137)
T 3hdg_A           30 HFPEVWSAGDGEEGERLFGLHA--PDVIITDIRMPKLGGLEMLDRIKAGGAKPYVIVISAFSEMKYFIKAIELGVHLFLP  107 (137)
T ss_dssp             TCSCEEEESSHHHHHHHHHHHC--CSEEEECSSCSSSCHHHHHHHHHHTTCCCEEEECCCCCCHHHHHHHHHHCCSEECC
T ss_pred             cCcEEEEECCHHHHHHHHhccC--CCEEEEeCCCCCCCHHHHHHHHHhcCCCCcEEEEecCcChHHHHHHHhCCcceeEc
Confidence            3688999999999999999876  99999999999999999999997 45789999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHhhhh
Q 027234           80 KPVRIEELKNIWQHVVRKRKNER  102 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~~~~~~  102 (226)
                      ||++.++|...+++++++.....
T Consensus       108 kP~~~~~l~~~i~~~~~~~~~~~  130 (137)
T 3hdg_A          108 KPIEPGRLMETLEDFRHIKLAKE  130 (137)
T ss_dssp             SSCCHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCHHHHHHHHHHHHHHHhcCC
Confidence            99999999999999988766543

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

Probab=99.75  E-value=5.1e-18  Score=124.58  Aligned_cols=100  Identities=23%  Similarity=0.315  Sum_probs=91.2

Q ss_pred             CCcEEEEECCHHHHHHHHHh-CCCCceEEEEccCCCC-CCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEE
Q 027234            1 MGFSVTKCNRAEIALDMLRT-NKNGYDIVISDVHMPD-MDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYL   78 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~-~~~~~DlVl~D~~mp~-~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl   78 (226)
                      .||.|..+.++.+|++.+.. ..  ||+||+|+.||+ ++|+++++.++..+.+|||++|+..+.+...+++..|+++||
T Consensus        28 ~g~~v~~~~~~~~a~~~l~~~~~--~dlvi~D~~l~~~~~g~~~~~~l~~~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l  105 (140)
T 3h5i_A           28 YGYTVEIALTGEAAVEKVSGGWY--PDLILMDIELGEGMDGVQTALAIQQISELPVVFLTAHTEPAVVEKIRSVTAYGYV  105 (140)
T ss_dssp             TTCEEEEESSHHHHHHHHHTTCC--CSEEEEESSCSSSCCHHHHHHHHHHHCCCCEEEEESSSSCCCCGGGGGSCEEEEE
T ss_pred             cCCEEEEecChHHHHHHHhcCCC--CCEEEEeccCCCCCCHHHHHHHHHhCCCCCEEEEECCCCHHHHHHHHhCCCcEEE
Confidence            48999999999999999987 45  999999999995 999999999987789999999999988888899999999999


Q ss_pred             eCCCCHHHHHHHHHHHHHHHhhhh
Q 027234           79 TKPVRIEELKNIWQHVVRKRKNER  102 (226)
Q Consensus        79 ~KP~~~~~L~~~l~~~~~~~~~~~  102 (226)
                      .||++.++|...++++++..+...
T Consensus       106 ~KP~~~~~l~~~i~~~l~~~~~~~  129 (140)
T 3h5i_A          106 MKSATEQVLITIVEMALRLYEANV  129 (140)
T ss_dssp             ETTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             eCCCCHHHHHHHHHHHHHHHHhhc
Confidence            999999999999999988766544

>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=99.75  E-value=3.1e-17  Score=118.11  Aligned_cols=95  Identities=33%  Similarity=0.561  Sum_probs=86.7

Q ss_pred             CCc-EEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhc---CCCCcEEEEeccCCHHHHHHHHhCCcce
Q 027234            1 MGF-SVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGL---EMDLPVIMMCAHGSKEVVMKGVTHDACD   76 (226)
Q Consensus         1 lg~-~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~---~~~~pvI~ls~~~~~~~~~~a~~~ga~~   76 (226)
                      .|| .|..+.++.+|++.+....  ||+||+|+.||+++|+++++.++.   .+.+|+|++|+..+.+....+++.|+++
T Consensus        27 ~~~~~v~~~~~~~~a~~~~~~~~--~dlvi~D~~l~~~~g~~l~~~l~~~~~~~~~~ii~~s~~~~~~~~~~~~~~ga~~  104 (128)
T 1jbe_A           27 LGFNNVEEAEDGVDALNKLQAGG--YGFVISDWNMPNMDGLELLKTIRAXXAMSALPVLMVTAEAKKENIIAAAQAGASG  104 (128)
T ss_dssp             TTCCCEEEESSHHHHHHHHTTCC--CCEEEEESCCSSSCHHHHHHHHHC--CCTTCCEEEEESSCCHHHHHHHHHTTCSE
T ss_pred             cCCcEEEeeCCHHHHHHHHHhcC--CCEEEEeCCCCCCCHHHHHHHHHhhcccCCCcEEEEecCccHHHHHHHHHhCcCc
Confidence            367 6889999999999998765  999999999999999999999975   3578999999999999999999999999


Q ss_pred             EEeCCCCHHHHHHHHHHHHHH
Q 027234           77 YLTKPVRIEELKNIWQHVVRK   97 (226)
Q Consensus        77 yl~KP~~~~~L~~~l~~~~~~   97 (226)
                      |+.||++.++|...++++++.
T Consensus       105 ~l~KP~~~~~l~~~i~~~~~~  125 (128)
T 1jbe_A          105 YVVKPFTAATLEEKLNKIFEK  125 (128)
T ss_dssp             EEESSCCHHHHHHHHHHHHHH
T ss_pred             eeecCCCHHHHHHHHHHHHHH
Confidence            999999999999999988754

>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=99.75  E-value=9.1e-18  Score=136.41  Aligned_cols=99  Identities=22%  Similarity=0.361  Sum_probs=88.5

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcC---CCCcEEEEeccCCHHHHHHHHhCCcceE
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLE---MDLPVIMMCAHGSKEVVMKGVTHDACDY   77 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~---~~~pvI~ls~~~~~~~~~~a~~~ga~~y   77 (226)
                      .||.|..+.++.+|++.+... ..||+||+|+.||++||+++++.++..   ..+|||++|+..+.....++++.||++|
T Consensus       147 ~~~~v~~a~~~~eal~~l~~~-~~~dlvllD~~mP~~dG~~l~~~lr~~~~~~~~~ii~~s~~~~~~~~~~a~~~Ga~~y  225 (259)
T 3luf_A          147 QLLQVHEASHAREALATLEQH-PAIRLVLVDYYMPEIDGISLVRMLRERYSKQQLAIIGISVSDKRGLSARYLKQGANDF  225 (259)
T ss_dssp             TTCEEEEESSHHHHHHHHHHC-TTEEEEEECSCCSSSCHHHHHHHHHHHCCTTTSEEEEEECSSSSSHHHHHHHTTCSEE
T ss_pred             cCcEEEEeCCHHHHHHHHhcC-CCCCEEEEcCCCCCCCHHHHHHHHHhccCCCCCeEEEEEccCCHHHHHHHHhcChhhe
Confidence            378999999999999999874 238999999999999999999999743   3589999999999999999999999999


Q ss_pred             EeCCCCHHHHHHHHHHHHHHHhh
Q 027234           78 LTKPVRIEELKNIWQHVVRKRKN  100 (226)
Q Consensus        78 l~KP~~~~~L~~~l~~~~~~~~~  100 (226)
                      |.||++.++|...++++++....
T Consensus       226 l~KP~~~~~L~~~i~~~l~~~~~  248 (259)
T 3luf_A          226 LNQPFEPEELQCRVSHNLEALEQ  248 (259)
T ss_dssp             EESSCCHHHHHHHHHHHHHHHHC
T ss_pred             EcCCCCHHHHHHHHHHHHHhHhh
Confidence            99999999999999999876543

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

Probab=99.75  E-value=9.5e-18  Score=122.80  Aligned_cols=100  Identities=19%  Similarity=0.333  Sum_probs=89.1

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhc---CCCCcEEEEeccCCHHHHH-HHHhCCcce
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGL---EMDLPVIMMCAHGSKEVVM-KGVTHDACD   76 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~---~~~~pvI~ls~~~~~~~~~-~a~~~ga~~   76 (226)
                      .||.|..+.++.+|++.+....  ||+||+|+.||+++|+++++.++.   .+.+|||++|+..+..... .++..|+++
T Consensus        29 ~g~~v~~~~~~~~a~~~l~~~~--~dlvi~d~~l~~~~g~~~~~~l~~~~~~~~~~ii~~s~~~~~~~~~~~~~~~g~~~  106 (140)
T 3grc_A           29 GGFDSDMVHSAAQALEQVARRP--YAAMTVDLNLPDQDGVSLIRALRRDSRTRDLAIVVVSANAREGELEFNSQPLAVST  106 (140)
T ss_dssp             TTCEEEEECSHHHHHHHHHHSC--CSEEEECSCCSSSCHHHHHHHHHTSGGGTTCEEEEECTTHHHHHHHHCCTTTCCCE
T ss_pred             CCCeEEEECCHHHHHHHHHhCC--CCEEEEeCCCCCCCHHHHHHHHHhCcccCCCCEEEEecCCChHHHHHHhhhcCCCE
Confidence            4899999999999999999876  999999999999999999999974   4689999999988877777 899999999


Q ss_pred             EEeCCCCHHHHHHHHHHHHHHHhhhh
Q 027234           77 YLTKPVRIEELKNIWQHVVRKRKNER  102 (226)
Q Consensus        77 yl~KP~~~~~L~~~l~~~~~~~~~~~  102 (226)
                      ||.||++.++|...+++++++.....
T Consensus       107 ~l~kP~~~~~l~~~i~~~l~~~~~~~  132 (140)
T 3grc_A          107 WLEKPIDENLLILSLHRAIDNMAEGK  132 (140)
T ss_dssp             EECSSCCHHHHHHHHHHHHHHHC---
T ss_pred             EEeCCCCHHHHHHHHHHHHHhcCCCC
Confidence            99999999999999999988765433

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

Probab=99.75  E-value=2.7e-18  Score=125.85  Aligned_cols=98  Identities=15%  Similarity=0.339  Sum_probs=89.2

Q ss_pred             CCcEEEEECCHHHHHHHHHh-CCCCceEEEEccCCC-CCCHHHHHHHHhc---CCCCcEEEEeccCCHHHHHHHHhCCcc
Q 027234            1 MGFSVTKCNRAEIALDMLRT-NKNGYDIVISDVHMP-DMDGFKLLELVGL---EMDLPVIMMCAHGSKEVVMKGVTHDAC   75 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~-~~~~~DlVl~D~~mp-~~dG~~l~~~l~~---~~~~pvI~ls~~~~~~~~~~a~~~ga~   75 (226)
                      .||+|..+.++.+|++.+.. ..  ||+||+|+.|| +++|+++++.++.   .+.+|||++|+..+.+...+++..|++
T Consensus        28 ~~~~v~~~~~~~~a~~~l~~~~~--~dlvi~D~~l~~~~~g~~~~~~l~~~~~~~~~~ii~ls~~~~~~~~~~~~~~g~~  105 (140)
T 3lua_A           28 GEYDFIEVENLKKFYSIFKDLDS--ITLIIMDIAFPVEKEGLEVLSAIRNNSRTANTPVIIATKSDNPGYRHAALKFKVS  105 (140)
T ss_dssp             CCCEEEEECSHHHHHTTTTTCCC--CSEEEECSCSSSHHHHHHHHHHHHHSGGGTTCCEEEEESCCCHHHHHHHHHSCCS
T ss_pred             cCccEEEECCHHHHHHHHhcCCC--CcEEEEeCCCCCCCcHHHHHHHHHhCcccCCCCEEEEeCCCCHHHHHHHHHcCCC
Confidence            48999999999999999988 76  99999999999 9999999999975   578999999999999999999999999


Q ss_pred             eEEeCCCCHHHHHHHHHHHHHHHhh
Q 027234           76 DYLTKPVRIEELKNIWQHVVRKRKN  100 (226)
Q Consensus        76 ~yl~KP~~~~~L~~~l~~~~~~~~~  100 (226)
                      +||.||++.++|..++++++++...
T Consensus       106 ~~l~KP~~~~~l~~~i~~~~~~~~~  130 (140)
T 3lua_A          106 DYILKPYPTKRLENSVRSVLKICQR  130 (140)
T ss_dssp             EEEESSCCTTHHHHHHHHHHCC---
T ss_pred             EEEECCCCHHHHHHHHHHHHHhccc
Confidence            9999999999999999999876544

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

Probab=99.75  E-value=8.8e-18  Score=121.45  Aligned_cols=96  Identities=26%  Similarity=0.386  Sum_probs=81.2

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||.|..+.++.+|++.+....  ||+||+|+.||+++|+++++.++ ..+.+|+|++|+..+.+...++++.|+++||.
T Consensus        30 ~g~~v~~~~~~~~a~~~l~~~~--~dlvi~d~~l~~~~g~~~~~~l~~~~~~~~ii~~t~~~~~~~~~~~~~~g~~~~l~  107 (130)
T 3eod_A           30 LGATTVLAADGVDALELLGGFT--PDLMICDIAMPRMNGLKLLEHIRNRGDQTPVLVISATENMADIAKALRLGVEDVLL  107 (130)
T ss_dssp             TTCEEEEESCHHHHHHHHTTCC--CSEEEECCC-----CHHHHHHHHHTTCCCCEEEEECCCCHHHHHHHHHHCCSEEEE
T ss_pred             CCceEEEeCCHHHHHHHHhcCC--CCEEEEecCCCCCCHHHHHHHHHhcCCCCCEEEEEcCCCHHHHHHHHHcCCCEEEe
Confidence            4899999999999999998866  99999999999999999999997 55789999999999999999999999999999


Q ss_pred             CCC-CHHHHHHHHHHHHHHH
Q 027234           80 KPV-RIEELKNIWQHVVRKR   98 (226)
Q Consensus        80 KP~-~~~~L~~~l~~~~~~~   98 (226)
                      ||+ +.++|...+++++.++
T Consensus       108 KP~~~~~~l~~~i~~~l~~~  127 (130)
T 3eod_A          108 KPVKDLNRLREMVFACLYPS  127 (130)
T ss_dssp             SCC---CHHHHHHHHHHC--
T ss_pred             CCCCcHHHHHHHHHHHhchh
Confidence            999 9999999999987654

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

Probab=99.74  E-value=2.1e-17  Score=119.76  Aligned_cols=97  Identities=23%  Similarity=0.283  Sum_probs=84.2

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhc---CCCCcEEEEeccCCHHHHHHHHhCCcceE
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGL---EMDLPVIMMCAHGSKEVVMKGVTHDACDY   77 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~---~~~~pvI~ls~~~~~~~~~~a~~~ga~~y   77 (226)
                      .||.|..+.++.+|++.+....  ||+||+|+.||+++|+++++.++.   .+.+|||++|+..+... ..++..|+++|
T Consensus        26 ~~~~v~~~~~~~~a~~~l~~~~--~dlvi~d~~l~~~~g~~~~~~l~~~~~~~~~pii~~s~~~~~~~-~~~~~~g~~~~  102 (133)
T 3nhm_A           26 GEFDCTTAADGASGLQQALAHP--PDVLISDVNMDGMDGYALCGHFRSEPTLKHIPVIFVSGYAPRTE-GPADQPVPDAY  102 (133)
T ss_dssp             TTSEEEEESSHHHHHHHHHHSC--CSEEEECSSCSSSCHHHHHHHHHHSTTTTTCCEEEEESCCC------TTSCCCSEE
T ss_pred             CCcEEEEECCHHHHHHHHhcCC--CCEEEEeCCCCCCCHHHHHHHHHhCCccCCCCEEEEeCCCcHhH-HHHhhcCCceE
Confidence            3789999999999999999876  999999999999999999999985   35799999999888877 89999999999


Q ss_pred             EeCCCCHHHHHHHHHHHHHHHhh
Q 027234           78 LTKPVRIEELKNIWQHVVRKRKN  100 (226)
Q Consensus        78 l~KP~~~~~L~~~l~~~~~~~~~  100 (226)
                      |.||++.++|...+++++++...
T Consensus       103 l~KP~~~~~l~~~i~~~l~~~~~  125 (133)
T 3nhm_A          103 LVKPVKPPVLIAQLHALLARAEA  125 (133)
T ss_dssp             EESSCCHHHHHHHHHHHHHHHC-
T ss_pred             EeccCCHHHHHHHHHHHHhhhcc
Confidence            99999999999999999987654

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

Probab=99.74  E-value=3.7e-18  Score=135.60  Aligned_cols=95  Identities=21%  Similarity=0.308  Sum_probs=87.7

Q ss_pred             cEE-EEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEeC
Q 027234            3 FSV-TKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTK   80 (226)
Q Consensus         3 ~~V-~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~K   80 (226)
                      |.+ ..+.++.+|++.+....  ||+||+|+.||+++|+++++.++ ..+.+|||++|+..+.+....+++.||++||.|
T Consensus        27 ~~vv~~~~~~~~al~~l~~~~--~dlvllD~~lp~~~g~~~~~~lr~~~~~~~ii~lt~~~~~~~~~~~~~~Ga~~~l~K  104 (225)
T 3c3w_A           27 LDVVGEAGSVAEAMARVPAAR--PDVAVLDVRLPDGNGIELCRDLLSRMPDLRCLILTSYTSDEAMLDAILAGASGYVVK  104 (225)
T ss_dssp             EEEEEEESSHHHHHHHHHHHC--CSEEEECSEETTEEHHHHHHHHHHHCTTCEEEEGGGSSSHHHHHHHHHHTCCCHHHH
T ss_pred             cEEEEEECCHHHHHHHHhhcC--CCEEEEeCCCCCCCHHHHHHHHHHhCCCCcEEEEECCCCHHHHHHHHHCCCCEEEEC
Confidence            774 57999999999998876  99999999999999999999997 467899999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHh
Q 027234           81 PVRIEELKNIWQHVVRKRK   99 (226)
Q Consensus        81 P~~~~~L~~~l~~~~~~~~   99 (226)
                      |++.++|...++.++++..
T Consensus       105 p~~~~~L~~~i~~~~~~~~  123 (225)
T 3c3w_A          105 DIKGMELARAVKDVGAGRS  123 (225)
T ss_dssp             HHHHHHHHHHHHHHHHHGG
T ss_pred             CCCHHHHHHHHHHHHcCCe
Confidence            9999999999999987654

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

Probab=99.74  E-value=2.1e-18  Score=136.83  Aligned_cols=95  Identities=5%  Similarity=-0.069  Sum_probs=82.4

Q ss_pred             CcEEEE-ECCHHHHHH-HHHhCCCCceEEEEccCCCCCCHHHHHHHHhc--CCCCcEEEEeccCCHHHHHHHHhCCcceE
Q 027234            2 GFSVTK-CNRAEIALD-MLRTNKNGYDIVISDVHMPDMDGFKLLELVGL--EMDLPVIMMCAHGSKEVVMKGVTHDACDY   77 (226)
Q Consensus         2 g~~V~~-~~~~~eal~-~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~--~~~~pvI~ls~~~~~~~~~~a~~~ga~~y   77 (226)
                      ||.|.. +.++.+++. .+....  ||+||+|+.||++||+++++.++.  .+++|||++|+..+......++..||++|
T Consensus        32 ~~~v~~~~~~~~~~~~~~~~~~~--~dlvllD~~mp~~~G~~~~~~lr~~~~~~~~ii~lt~~~~~~~~~~~~~~Ga~~~  109 (225)
T 3klo_A           32 PLALEITPFSELWLEENKPESRS--IQMLVIDYSRISDDVLTDYSSFKHISCPDAKEVIINCPQDIEHKLLFKWNNLAGV  109 (225)
T ss_dssp             SEEEEEECGGGHHHHTTCSGGGG--CCEEEEEGGGCCHHHHHHHHHHHHHHCTTCEEEEEEECTTCCHHHHTTSTTEEEE
T ss_pred             CceEEEEeCCcHHHHHHHhhccC--CCEEEEeCCCCCCCHHHHHHHHHHhhCCCCcEEEEECCcchhHHHHHHHhCCCEE
Confidence            677754 456666665 466655  999999999999999999999975  68899999999999888999999999999


Q ss_pred             EeCCCCHHHHHHHHHHHHHHH
Q 027234           78 LTKPVRIEELKNIWQHVVRKR   98 (226)
Q Consensus        78 l~KP~~~~~L~~~l~~~~~~~   98 (226)
                      |.||++.++|..+++.++++.
T Consensus       110 l~Kp~~~~~L~~~i~~~~~~~  130 (225)
T 3klo_A          110 FYIDDDMDTLIKGMSKILQDE  130 (225)
T ss_dssp             EETTCCHHHHHHHHHHHHTTC
T ss_pred             EecCCCHHHHHHHHHHHHCCC
Confidence            999999999999999988654

>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=99.74  E-value=1.7e-17  Score=119.67  Aligned_cols=94  Identities=32%  Similarity=0.540  Sum_probs=86.1

Q ss_pred             CCc-EEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcC---CCCcEEEEeccCCHHHHHHHHhCCcce
Q 027234            1 MGF-SVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLE---MDLPVIMMCAHGSKEVVMKGVTHDACD   76 (226)
Q Consensus         1 lg~-~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~---~~~pvI~ls~~~~~~~~~~a~~~ga~~   76 (226)
                      .|| .|..+.++.+|++.+....  ||+||+|+.||+++|+++++.++..   +.+|+|++|+..+.+....+++.|+++
T Consensus        29 ~g~~~v~~~~~~~~a~~~~~~~~--~dlvl~D~~l~~~~g~~~~~~l~~~~~~~~~~ii~~s~~~~~~~~~~~~~~g~~~  106 (129)
T 1p6q_A           29 LGFKQITAAGDGEQGMKIMAQNP--HHLVISDFNMPKMDGLGLLQAVRANPATKKAAFIILTAQGDRALVQKAAALGANN  106 (129)
T ss_dssp             TTCSCEECCSSHHHHHHHHHTSC--CSEEEECSSSCSSCHHHHHHHHTTCTTSTTCEEEECCSCCCHHHHHHHHHHTCSC
T ss_pred             CCCcEEEecCCHHHHHHHHHcCC--CCEEEEeCCCCCCCHHHHHHHHhcCccccCCCEEEEeCCCCHHHHHHHHHcCCCE
Confidence            377 7889999999999998866  9999999999999999999999853   578999999999999999999999999


Q ss_pred             EEeCCCCHHHHHHHHHHHHH
Q 027234           77 YLTKPVRIEELKNIWQHVVR   96 (226)
Q Consensus        77 yl~KP~~~~~L~~~l~~~~~   96 (226)
                      |+.||++.++|...++++++
T Consensus       107 ~l~KP~~~~~l~~~i~~~~~  126 (129)
T 1p6q_A          107 VLAKPFTIEKMKAAIEAVFG  126 (129)
T ss_dssp             EECCCSSHHHHHHHHHHHHH
T ss_pred             EEECCCCHHHHHHHHHHHHH
Confidence            99999999999999988764

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

Probab=99.74  E-value=4.4e-17  Score=120.83  Aligned_cols=94  Identities=17%  Similarity=0.298  Sum_probs=84.3

Q ss_pred             EEEEECCHHHHHHHHHhC-----CCCceEEEEccCCCCCCHHHHHHHHhcC---CCCcEEEEeccCCHHHHHHHHhCCcc
Q 027234            4 SVTKCNRAEIALDMLRTN-----KNGYDIVISDVHMPDMDGFKLLELVGLE---MDLPVIMMCAHGSKEVVMKGVTHDAC   75 (226)
Q Consensus         4 ~V~~~~~~~eal~~l~~~-----~~~~DlVl~D~~mp~~dG~~l~~~l~~~---~~~pvI~ls~~~~~~~~~~a~~~ga~   75 (226)
                      .|..+.++.+|++.+...     ...||+||+|+.||+++|+++++.++..   +.+|||++|+..+.+...++++.||+
T Consensus        36 ~v~~~~~~~~al~~l~~~~~~~~~~~~dlillD~~lp~~~g~~l~~~l~~~~~~~~~piiils~~~~~~~~~~~~~~ga~  115 (149)
T 1i3c_A           36 ELIILRDGLAAMAFLQQQGEYENSPRPNLILLDLNLPKKDGREVLAEIKQNPDLKRIPVVVLTTSHNEDDVIASYELHVN  115 (149)
T ss_dssp             EEEEECSHHHHHHHHTTCGGGTTCCCCSEEEECSCCSSSCHHHHHHHHHHCTTTTTSCEEEEESCCCHHHHHHHHHTTCS
T ss_pred             cEEEeCCHHHHHHHHHhccccccCCCCCEEEEeCCCCCCcHHHHHHHHHhCcCcCCCeEEEEECCCChHHHHHHHHcCCc
Confidence            789999999999999752     0239999999999999999999999754   57899999999999999999999999


Q ss_pred             eEEeCCCCHHHHHHHHHHHHHH
Q 027234           76 DYLTKPVRIEELKNIWQHVVRK   97 (226)
Q Consensus        76 ~yl~KP~~~~~L~~~l~~~~~~   97 (226)
                      +||.||++.++|..+++++.+.
T Consensus       116 ~~l~KP~~~~~L~~~i~~~~~~  137 (149)
T 1i3c_A          116 CYLTKSRNLKDLFKMVQGIESF  137 (149)
T ss_dssp             EEEECCSSHHHHHHHHHHHHHH
T ss_pred             EEEECCCCHHHHHHHHHHHHHH
Confidence            9999999999999999988653

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

Probab=99.74  E-value=3.4e-17  Score=120.80  Aligned_cols=97  Identities=20%  Similarity=0.388  Sum_probs=89.7

Q ss_pred             CcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhc---CCCCcEEEEeccCCHHHHHHHHhCCcceEE
Q 027234            2 GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGL---EMDLPVIMMCAHGSKEVVMKGVTHDACDYL   78 (226)
Q Consensus         2 g~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~---~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl   78 (226)
                      ||+|..+.++.+|++.+....  ||+||+|+.||+++|+++++.++.   .+.+|||++|+..+.+....++..|+++||
T Consensus        32 g~~v~~~~~~~~a~~~l~~~~--~dlii~d~~l~~~~g~~~~~~l~~~~~~~~~pii~ls~~~~~~~~~~~~~~g~~~~l  109 (147)
T 2zay_A           32 GFDIIQCGNAIEAVPVAVKTH--PHLIITEANMPKISGMDLFNSLKKNPQTASIPVIALSGRATAKEEAQLLDMGFIDFI  109 (147)
T ss_dssp             TEEEEEESSHHHHHHHHHHHC--CSEEEEESCCSSSCHHHHHHHHHTSTTTTTSCEEEEESSCCHHHHHHHHHHTCSEEE
T ss_pred             CCeEEEeCCHHHHHHHHHcCC--CCEEEEcCCCCCCCHHHHHHHHHcCcccCCCCEEEEeCCCCHHHHHHHHhCCCCEEE
Confidence            789999999999999999876  999999999999999999999985   467999999999999999999999999999


Q ss_pred             eCCCCHHHHHHHHHHHHHHHhh
Q 027234           79 TKPVRIEELKNIWQHVVRKRKN  100 (226)
Q Consensus        79 ~KP~~~~~L~~~l~~~~~~~~~  100 (226)
                      .||++.++|...++++++....
T Consensus       110 ~kp~~~~~L~~~i~~~~~~~~~  131 (147)
T 2zay_A          110 AKPVNAIRLSARIKRVLKLLYE  131 (147)
T ss_dssp             ESSCCHHHHHHHHHHHHHHHC-
T ss_pred             eCCCCHHHHHHHHHHHHHHHHh
Confidence            9999999999999999876544

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

Probab=99.74  E-value=2.7e-17  Score=122.05  Aligned_cols=96  Identities=24%  Similarity=0.363  Sum_probs=89.0

Q ss_pred             cEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEeCC
Q 027234            3 FSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTKP   81 (226)
Q Consensus         3 ~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~KP   81 (226)
                      |.|..+.++.+|++.+....  ||+||+|+.||+++|+++++.++ ..+.+|||++|+..+.+...++++.|+++||.||
T Consensus        47 ~~v~~~~~~~~al~~l~~~~--~dlii~D~~l~~~~g~~~~~~l~~~~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~Kp  124 (150)
T 4e7p_A           47 ESVLQAKNGQEAIQLLEKES--VDIAILDVEMPVKTGLEVLEWIRSEKLETKVVVVTTFKRAGYFERAVKAGVDAYVLKE  124 (150)
T ss_dssp             EEEEEESSHHHHHHHHTTSC--CSEEEECSSCSSSCHHHHHHHHHHTTCSCEEEEEESCCCHHHHHHHHHTTCSEEEETT
T ss_pred             EEEEEECCHHHHHHHhhccC--CCEEEEeCCCCCCcHHHHHHHHHHhCCCCeEEEEeCCCCHHHHHHHHHCCCcEEEecC
Confidence            77899999999999998876  99999999999999999999997 4578999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHhh
Q 027234           82 VRIEELKNIWQHVVRKRKN  100 (226)
Q Consensus        82 ~~~~~L~~~l~~~~~~~~~  100 (226)
                      ++.++|..++++++++...
T Consensus       125 ~~~~~l~~~i~~~~~~~~~  143 (150)
T 4e7p_A          125 RSIADLMQTLHTVLEGRKE  143 (150)
T ss_dssp             SCHHHHHHHHHHHHTTCCE
T ss_pred             CCHHHHHHHHHHHHcCCEE
Confidence            9999999999999876543

>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=99.74  E-value=1.7e-17  Score=118.67  Aligned_cols=94  Identities=18%  Similarity=0.392  Sum_probs=80.5

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcC---CCCcEEEEeccCCHHHHHHHHhCCcceE
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLE---MDLPVIMMCAHGSKEVVMKGVTHDACDY   77 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~---~~~pvI~ls~~~~~~~~~~a~~~ga~~y   77 (226)
                      .||.|..+.++.+|++.+....  ||+||+|+.||+++|+++++.++..   +.+|+|++|+..+.+....+++.|+++|
T Consensus        24 ~~~~v~~~~~~~~a~~~~~~~~--~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~  101 (124)
T 1mb3_A           24 QGYETLQTREGLSALSIARENK--PDLILMDIQLPEISGLEVTKWLKEDDDLAHIPVVAVTAFAMKGDEERIREGGCEAY  101 (124)
T ss_dssp             TTCEEEEESCHHHHHHHHHHHC--CSEEEEESBCSSSBHHHHHHHHHHSTTTTTSCEEEEC------CHHHHHHHTCSEE
T ss_pred             cCcEEEEeCCHHHHHHHHhcCC--CCEEEEeCCCCCCCHHHHHHHHHcCccccCCcEEEEECCCCHHHHHHHHhCCCCEE
Confidence            3789999999999999998866  9999999999999999999999753   5789999999988888899999999999


Q ss_pred             EeCCCCHHHHHHHHHHHHH
Q 027234           78 LTKPVRIEELKNIWQHVVR   96 (226)
Q Consensus        78 l~KP~~~~~L~~~l~~~~~   96 (226)
                      |.||++.++|...+++++.
T Consensus       102 l~KP~~~~~l~~~i~~~~~  120 (124)
T 1mb3_A          102 ISKPISVVHFLETIKRLLE  120 (124)
T ss_dssp             ECSSCCHHHHHHHHHHHHS
T ss_pred             EeCCCCHHHHHHHHHHHHh
Confidence            9999999999999988764

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

Probab=99.74  E-value=8.7e-18  Score=123.64  Aligned_cols=96  Identities=23%  Similarity=0.400  Sum_probs=81.2

Q ss_pred             CcEEE-EECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            2 GFSVT-KCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         2 g~~V~-~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      ||.+. .+.++.+|++.+....  ||+||+|+.||+++|+++++.++ ..+.+|+|++|+..+.+....+++.|+++||.
T Consensus        28 ~~~~~~~~~~~~~al~~~~~~~--~dlvllD~~lp~~~g~~l~~~l~~~~~~~~ii~ls~~~~~~~~~~~~~~ga~~~l~  105 (141)
T 3cu5_A           28 SFDQIDQADDGINAIQIALKHP--PNVLLTDVRMPRMDGIELVDNILKLYPDCSVIFMSGYSDKEYLKAAIKFRAIRYVE  105 (141)
T ss_dssp             CCSEEEEESSHHHHHHHHTTSC--CSEEEEESCCSSSCHHHHHHHHHHHCTTCEEEEECCSTTTCCC------CCCEEEC
T ss_pred             CcEEeeecccHHHHHHHHhcCC--CCEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEeCCCcHHHHHHHHhCCccEEEe
Confidence            67766 8999999999998765  99999999999999999999997 45789999999998888888999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHh
Q 027234           80 KPVRIEELKNIWQHVVRKRK   99 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~~~   99 (226)
                      ||++.++|...++++++...
T Consensus       106 KP~~~~~L~~~i~~~~~~~~  125 (141)
T 3cu5_A          106 KPIDPSEIMDALKQSIQTVL  125 (141)
T ss_dssp             SSCCHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHH
Confidence            99999999999999886554

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

Probab=99.74  E-value=1.5e-17  Score=120.38  Aligned_cols=94  Identities=31%  Similarity=0.483  Sum_probs=85.8

Q ss_pred             CcEEE-EECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhc--CCCCcEEEEeccCCHHHHHHHHhCCcceEE
Q 027234            2 GFSVT-KCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGL--EMDLPVIMMCAHGSKEVVMKGVTHDACDYL   78 (226)
Q Consensus         2 g~~V~-~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~--~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl   78 (226)
                      ||.+. .+.++.+|++.+....  ||+||+|+.||+++|+++++.++.  .+.+|+|++|+..+.+...++++.|+++||
T Consensus        27 ~~~~~~~~~~~~~a~~~~~~~~--~dlvllD~~l~~~~g~~~~~~l~~~~~~~~~ii~ls~~~~~~~~~~~~~~ga~~~l  104 (130)
T 1dz3_A           27 DMEVIGTAYNGQDCLQMLEEKR--PDILLLDIIMPHLDGLAVLERIRAGFEHQPNVIMLTAFGQEDVTKKAVELGASYFI  104 (130)
T ss_dssp             TEEEEEEESSHHHHHHHHHHHC--CSEEEEESCCSSSCHHHHHHHHHHHCSSCCEEEEEEETTCHHHHHHHHHTTCEEEE
T ss_pred             CceEEEEeCCHHHHHHHHhcCC--CCEEEEecCCCCCCHHHHHHHHHhcCCCCCcEEEEecCCCHHHHHHHHHcCCCEEE
Confidence            67765 8999999999998866  999999999999999999999974  467899999999999999999999999999


Q ss_pred             eCCCCHHHHHHHHHHHHHH
Q 027234           79 TKPVRIEELKNIWQHVVRK   97 (226)
Q Consensus        79 ~KP~~~~~L~~~l~~~~~~   97 (226)
                      .||++.++|...++++++.
T Consensus       105 ~KP~~~~~l~~~i~~~~~~  123 (130)
T 1dz3_A          105 LKPFDMENLAHHIRQVYGK  123 (130)
T ss_dssp             ECSSCCTTHHHHHHHHHHC
T ss_pred             eCCCCHHHHHHHHHHHhcC
Confidence            9999999999999988754

>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=99.73  E-value=6e-18  Score=144.15  Aligned_cols=97  Identities=23%  Similarity=0.429  Sum_probs=90.5

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||.|..+.++.+|++.+....  ||+||+|+.||+|||+++++.++ ..+.+|||++|++.+.+...++++.||++||.
T Consensus        23 ~g~~v~~a~~~~eal~~l~~~~--~DlvllDi~mP~~dG~ell~~lr~~~~~~pvI~lT~~~~~~~~~~a~~~Ga~~yl~  100 (368)
T 3dzd_A           23 EGYHPDTAKTLREAEKKIKELF--FPVIVLDVWMPDGDGVNFIDFIKENSPDSVVIVITGHGSVDTAVKAIKKGAYEFLE  100 (368)
T ss_dssp             TTCEEEEESSHHHHHHHHHHBC--CSEEEEESEETTEETTTHHHHHHHHCTTCEEEEEECSSCCHHHHHHHHHTCCEEEE
T ss_pred             cCCEEEEECCHHHHHHHHHhCC--CCEEEEeCCCCCCCHHHHHHHHHhhCCCCeEEEEeCCCCHHHHHHHHhcCcceEEe
Confidence            4899999999999999999877  99999999999999999999997 56789999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHh
Q 027234           80 KPVRIEELKNIWQHVVRKRK   99 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~~~   99 (226)
                      ||++.++|...+++++....
T Consensus       101 KP~~~~~L~~~i~~~l~~~~  120 (368)
T 3dzd_A          101 KPFSVERFLLTIKHAFEEYS  120 (368)
T ss_dssp             SSCCHHHHHHHHHHHHHHHS
T ss_pred             CCCCHHHHHHHHHHHHHHhh
Confidence            99999999999999887543

>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=99.73  E-value=2.1e-17  Score=120.30  Aligned_cols=96  Identities=26%  Similarity=0.464  Sum_probs=87.7

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhc-CCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGL-EMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~-~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||.|..+.++.+|++.+....  ||+||+|+.||+++|+++++.++. .+.+|+|++|+..+......+++.|+++||.
T Consensus        26 ~g~~v~~~~~~~~a~~~~~~~~--~dlvl~D~~l~~~~g~~~~~~l~~~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~  103 (136)
T 1mvo_A           26 SGYDVITASDGEEALKKAETEK--PDLIVLDVMLPKLDGIEVCKQLRQQKLMFPILMLTAKDEEFDKVLGLELGADDYMT  103 (136)
T ss_dssp             TTCEEEEESSHHHHHHHHHHHC--CSEEEEESSCSSSCHHHHHHHHHHTTCCCCEEEEECTTCCCCHHHHHHTTCCEEEE
T ss_pred             CCcEEEEecCHHHHHHHHhhcC--CCEEEEecCCCCCCHHHHHHHHHcCCCCCCEEEEECCCCHHHHHHHHhCCCCEEEE
Confidence            3799999999999999998866  999999999999999999999984 4789999999998888888999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHH
Q 027234           80 KPVRIEELKNIWQHVVRKR   98 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~~   98 (226)
                      ||++.++|...++++++..
T Consensus       104 KP~~~~~l~~~i~~~~~~~  122 (136)
T 1mvo_A          104 KPFSPREVNARVKAILRRS  122 (136)
T ss_dssp             SSCCHHHHHHHHHHHHHTC
T ss_pred             CCCCHHHHHHHHHHHHHhh
Confidence            9999999999999887653

>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=99.73  E-value=1.7e-17  Score=134.41  Aligned_cols=98  Identities=30%  Similarity=0.497  Sum_probs=90.3

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhc-CCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGL-EMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~-~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      +||+|..+.++.+|++.+....  ||+||+|+.||+|||+++++.|+. .+.+|||++|+..+.+...++++.|+++||.
T Consensus       152 ~g~~v~~a~~~~eal~~l~~~~--~dlvl~D~~mp~~~G~~l~~~ir~~~~~~piI~lt~~~~~~~~~~~~~~G~~~~l~  229 (254)
T 2ayx_A          152 LGYQCKTANDGVDALNVLSKNH--IDIVLSDVNMPNMDGYRLTQRIRQLGLTLPVIGVTANALAEEKQRCLESGMDSCLS  229 (254)
T ss_dssp             HTSEEEEECCSHHHHHHHHHSC--CSEEEEEESSCSSCCHHHHHHHHHHHCCSCEEEEESSTTSHHHHHHHHCCCEEEEE
T ss_pred             cCCEEEEECCHHHHHHHHHhCC--CCEEEEcCCCCCCCHHHHHHHHHhcCCCCcEEEEECCCCHHHHHHHHHcCCceEEE
Confidence            3899999999999999999876  999999999999999999999974 4689999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHhh
Q 027234           80 KPVRIEELKNIWQHVVRKRKN  100 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~~~~  100 (226)
                      ||++.++|...+++++...+.
T Consensus       230 KP~~~~~L~~~l~~~~~~~~~  250 (254)
T 2ayx_A          230 KPVTLDVIKQTLTLYAERVRK  250 (254)
T ss_dssp             SSCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHhhh
Confidence            999999999999998866543

>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=99.73  E-value=4.7e-17  Score=119.73  Aligned_cols=97  Identities=15%  Similarity=0.292  Sum_probs=89.0

Q ss_pred             CcE--EEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhc---CCCCcEEEEeccCCHHHHHHHHhCCcce
Q 027234            2 GFS--VTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGL---EMDLPVIMMCAHGSKEVVMKGVTHDACD   76 (226)
Q Consensus         2 g~~--V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~---~~~~pvI~ls~~~~~~~~~~a~~~ga~~   76 (226)
                      ||.  |..+.++.+|++.+....  ||+||+|+.||+++|+++++.++.   .+.+|||++|+..+.+...+++..|+++
T Consensus        29 ~~~~~v~~~~~~~~a~~~l~~~~--~dlii~D~~l~~~~g~~~~~~lr~~~~~~~~pii~~s~~~~~~~~~~~~~~ga~~  106 (144)
T 3kht_A           29 DIHCQLEFVDNGAKALYQVQQAK--YDLIILDIGLPIANGFEVMSAVRKPGANQHTPIVILTDNVSDDRAKQCMAAGASS  106 (144)
T ss_dssp             TCCEEEEEESSHHHHHHHHTTCC--CSEEEECTTCGGGCHHHHHHHHHSSSTTTTCCEEEEETTCCHHHHHHHHHTTCSE
T ss_pred             CCCeeEEEECCHHHHHHHhhcCC--CCEEEEeCCCCCCCHHHHHHHHHhcccccCCCEEEEeCCCCHHHHHHHHHcCCCE
Confidence            555  889999999999998866  999999999999999999999985   4679999999999999999999999999


Q ss_pred             EEeCCC-CHHHHHHHHHHHHHHHhh
Q 027234           77 YLTKPV-RIEELKNIWQHVVRKRKN  100 (226)
Q Consensus        77 yl~KP~-~~~~L~~~l~~~~~~~~~  100 (226)
                      ||.||+ +.++|..+++++++....
T Consensus       107 ~l~Kp~~~~~~l~~~i~~~l~~~~~  131 (144)
T 3kht_A          107 VVDKSSNNVTDFYGRIYAIFSYWLT  131 (144)
T ss_dssp             EEECCTTSHHHHHHHHHHHHHHHHH
T ss_pred             EEECCCCcHHHHHHHHHHHHHHHHh
Confidence            999999 999999999999876543

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

Probab=99.73  E-value=6.1e-17  Score=120.24  Aligned_cols=101  Identities=18%  Similarity=0.414  Sum_probs=91.3

Q ss_pred             CcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCC-cceEEe
Q 027234            2 GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHD-ACDYLT   79 (226)
Q Consensus         2 g~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~g-a~~yl~   79 (226)
                      ||.|..+.++.+|++.+.+.. +||+||+|+.||+++|+++++.++ ..+.+|||++|+..+.+...+++..| +++||.
T Consensus        27 ~~~v~~~~~~~~a~~~l~~~~-~~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~~l~  105 (151)
T 3kcn_A           27 DFEVTTCESGPEALACIKKSD-PFSVIMVDMRMPGMEGTEVIQKARLISPNSVYLMLTGNQDLTTAMEAVNEGQVFRFLN  105 (151)
T ss_dssp             TSEEEEESSHHHHHHHHHHSC-CCSEEEEESCCSSSCHHHHHHHHHHHCSSCEEEEEECGGGHHHHHHHHHHTCCSEEEE
T ss_pred             CceEEEeCCHHHHHHHHHcCC-CCCEEEEeCCCCCCcHHHHHHHHHhcCCCcEEEEEECCCCHHHHHHHHHcCCeeEEEc
Confidence            789999999999999998763 259999999999999999999997 46789999999999999999999999 999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHhhhhh
Q 027234           80 KPVRIEELKNIWQHVVRKRKNERK  103 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~~~~~~~  103 (226)
                      ||++.++|..+++.+++.......
T Consensus       106 KP~~~~~L~~~i~~~l~~~~~~~~  129 (151)
T 3kcn_A          106 KPCQMSDIKAAINAGIKQYDLVTS  129 (151)
T ss_dssp             SSCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999887665443

>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=99.73  E-value=5.6e-17  Score=118.06  Aligned_cols=98  Identities=19%  Similarity=0.312  Sum_probs=87.6

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcC--CCCcEEEEeccCCHHHHHHHHhCCcceEE
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLE--MDLPVIMMCAHGSKEVVMKGVTHDACDYL   78 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~--~~~pvI~ls~~~~~~~~~~a~~~ga~~yl   78 (226)
                      .||+|..+.++.+|+..+... ..||+||+|+.||+++|+++++.++..  +.+|+|++|+..+.+...++++.|+++||
T Consensus        30 ~g~~v~~~~~~~~a~~~~~~~-~~~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l  108 (136)
T 3hdv_A           30 RGIDAVGADGAEEARLYLHYQ-KRIGLMITDLRMQPESGLDLIRTIRASERAALSIIVVSGDTDVEEAVDVMHLGVVDFL  108 (136)
T ss_dssp             TTCCEEEESSHHHHHHHHHHC-TTEEEEEECSCCSSSCHHHHHHHHHTSTTTTCEEEEEESSCCHHHHHHHHHTTCSEEE
T ss_pred             cCceEEEeCCHHHHHHHHHhC-CCCcEEEEeccCCCCCHHHHHHHHHhcCCCCCCEEEEeCCCChHHHHHHHhCCcceEE
Confidence            489999999999999998764 349999999999999999999999853  78999999999999999999999999999


Q ss_pred             eCCCCHHHHHHHHHHHHHHHh
Q 027234           79 TKPVRIEELKNIWQHVVRKRK   99 (226)
Q Consensus        79 ~KP~~~~~L~~~l~~~~~~~~   99 (226)
                      .||++.++|..+++++..+..
T Consensus       109 ~KP~~~~~l~~~i~~~~~~~~  129 (136)
T 3hdv_A          109 LKPVDLGKLLELVNKELKIGE  129 (136)
T ss_dssp             ESSCCHHHHHHHHHHHHC---
T ss_pred             eCCCCHHHHHHHHHHHhcCch
Confidence            999999999999999876554

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

Probab=99.73  E-value=1.7e-17  Score=130.19  Aligned_cols=98  Identities=24%  Similarity=0.481  Sum_probs=83.5

Q ss_pred             CCc-EEEEECCHHHHHHHHHhC-----------CCCceEEEEccCCCCCCHHHHHHHHhc-----CCCCcEEEEeccC-C
Q 027234            1 MGF-SVTKCNRAEIALDMLRTN-----------KNGYDIVISDVHMPDMDGFKLLELVGL-----EMDLPVIMMCAHG-S   62 (226)
Q Consensus         1 lg~-~V~~~~~~~eal~~l~~~-----------~~~~DlVl~D~~mp~~dG~~l~~~l~~-----~~~~pvI~ls~~~-~   62 (226)
                      +|| .|..+.++.+|++.+...           ...||+||+|+.||+++|+++++.|+.     .+.+|||++|+.. +
T Consensus        84 ~g~~~v~~a~~~~eal~~l~~~~~~~~~~~~~~~~~~dlillD~~lp~~~G~el~~~lr~~~~~~~~~~piI~ls~~~~~  163 (206)
T 3mm4_A           84 MGVSEVEQCDSGKEALRLVTEGLTQREEQGSVDKLPFDYIFMDCQMPEMDGYEATREIRKVEKSYGVRTPIIAVSGHDPG  163 (206)
T ss_dssp             TTCSEEEEESSHHHHHHHHHHHHHHHHHHTCSSCCSCSEEEEESCCSSSCHHHHHHHHHHHHHTTTCCCCEEEEESSCCC
T ss_pred             cCCCeeeeeCCHHHHHHHHHhhcccccccccccCCCCCEEEEcCCCCCCCHHHHHHHHHhhhhhcCCCCcEEEEECCCCc
Confidence            477 899999999999999874           113999999999999999999999975     3789999999998 7


Q ss_pred             HHHHHHHHhCCcceEEeCCCCHHHHHHHHHHHHHHHhh
Q 027234           63 KEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKN  100 (226)
Q Consensus        63 ~~~~~~a~~~ga~~yl~KP~~~~~L~~~l~~~~~~~~~  100 (226)
                      .+...+++..|+++||.||++  +|..++++++..+..
T Consensus       164 ~~~~~~~~~~Ga~~~l~KP~~--~L~~~i~~~l~~~~~  199 (206)
T 3mm4_A          164 SEEARETIQAGMDAFLDKSLN--QLANVIREIESKRHL  199 (206)
T ss_dssp             HHHHHHHHHHTCSEEEETTCT--THHHHHHHHC-----
T ss_pred             HHHHHHHHhCCCCEEEcCcHH--HHHHHHHHHHhhhHH
Confidence            888999999999999999999  899999988765543

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

Probab=99.73  E-value=1.7e-17  Score=133.96  Aligned_cols=96  Identities=27%  Similarity=0.415  Sum_probs=90.0

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEeC
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTK   80 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~K   80 (226)
                      .||.|..+.++.+|++.+....  ||+||+|+.||+++|+++++.++..+.+|||++|+..+.+...+++..||++||.|
T Consensus        60 ~g~~v~~~~~~~~al~~~~~~~--~DlvllD~~lp~~~G~~l~~~lr~~~~~~iI~lt~~~~~~~~~~a~~~Ga~~yl~K  137 (249)
T 3q9s_A           60 AGYVVDHADSAMNGLIKAREDH--PDLILLDLGLPDFDGGDVVQRLRKNSALPIIVLTARDTVEEKVRLLGLGADDYLIK  137 (249)
T ss_dssp             TTCEEEEESSHHHHHHHHHHSC--CSEEEEECCSCHHHHHHHHHHHHTTCCCCEEEEESCCSHHHHHHHHHHTCSEEEES
T ss_pred             CCCEEEEeCCHHHHHHHHhcCC--CCEEEEcCCCCCCCHHHHHHHHHcCCCCCEEEEECCCCHHHHHHHHHCCCcEEEEC
Confidence            3789999999999999999876  99999999999999999999998878899999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHH
Q 027234           81 PVRIEELKNIWQHVVRKR   98 (226)
Q Consensus        81 P~~~~~L~~~l~~~~~~~   98 (226)
                      |++.++|..+++.++++.
T Consensus       138 p~~~~~L~~~i~~~l~~~  155 (249)
T 3q9s_A          138 PFHPDELLARVKVQLRQR  155 (249)
T ss_dssp             SCCHHHHHHHHHHHHCCC
T ss_pred             CCCHHHHHHHHHHHHhhc
Confidence            999999999999987643

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

Probab=99.73  E-value=8.2e-17  Score=119.85  Aligned_cols=100  Identities=21%  Similarity=0.323  Sum_probs=91.2

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCC-cceEE
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHD-ACDYL   78 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~g-a~~yl   78 (226)
                      .||.|..+.++.+|++.+....  ||+||+|+.||+++|+++++.++ ..+.+|||++|+..+......++..| +++||
T Consensus        30 ~g~~v~~~~~~~~a~~~l~~~~--~dlvi~d~~l~~~~g~~~~~~l~~~~~~~~ii~ls~~~~~~~~~~~~~~g~~~~~l  107 (154)
T 2rjn_A           30 LGCNIITFTSPLDALEALKGTS--VQLVISDMRMPEMGGEVFLEQVAKSYPDIERVVISGYADAQATIDAVNRGKISRFL  107 (154)
T ss_dssp             TTCEEEEESCHHHHHHHHTTSC--CSEEEEESSCSSSCHHHHHHHHHHHCTTSEEEEEECGGGHHHHHHHHHTTCCSEEE
T ss_pred             cCCeEEEeCCHHHHHHHHhcCC--CCEEEEecCCCCCCHHHHHHHHHHhCCCCcEEEEecCCCHHHHHHHHhccchheee
Confidence            4799999999999999999866  99999999999999999999997 45789999999999999999999998 99999


Q ss_pred             eCCCCHHHHHHHHHHHHHHHhhhh
Q 027234           79 TKPVRIEELKNIWQHVVRKRKNER  102 (226)
Q Consensus        79 ~KP~~~~~L~~~l~~~~~~~~~~~  102 (226)
                      .||++.++|...+++++......+
T Consensus       108 ~kP~~~~~L~~~i~~~~~~~~~~~  131 (154)
T 2rjn_A          108 LKPWEDEDVFKVVEKGLQLAFLRE  131 (154)
T ss_dssp             ESSCCHHHHHHHHHHHHHHHHHHH
T ss_pred             eCCCCHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999987665433

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

Probab=99.73  E-value=1.7e-18  Score=126.25  Aligned_cols=95  Identities=21%  Similarity=0.174  Sum_probs=86.6

Q ss_pred             CC-cEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEE
Q 027234            1 MG-FSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYL   78 (226)
Q Consensus         1 lg-~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl   78 (226)
                      .| |.|..+.++.+|++.+....  ||+||+|+.||+++|+++++.++ ..+.+|+|++|+..+.+...++++.|+++||
T Consensus        37 ~g~~~v~~~~~~~~a~~~l~~~~--~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l  114 (135)
T 3snk_A           37 LAIYDVRVSETDDFLKGPPADTR--PGIVILDLGGGDLLGKPGIVEARALWATVPLIAVSDELTSEQTRVLVRMNASDWL  114 (135)
T ss_dssp             TSSEEEEEECGGGGGGCCCTTCC--CSEEEEEEETTGGGGSTTHHHHHGGGTTCCEEEEESCCCHHHHHHHHHTTCSEEE
T ss_pred             cCCeEEEEeccHHHHHHHHhccC--CCEEEEeCCCCCchHHHHHHHHHhhCCCCcEEEEeCCCCHHHHHHHHHcCcHhhc
Confidence            37 99999999999999998766  99999999999999999999998 4468999999999999999999999999999


Q ss_pred             eCCCCHHHHHHHHHHHHHH
Q 027234           79 TKPVRIEELKNIWQHVVRK   97 (226)
Q Consensus        79 ~KP~~~~~L~~~l~~~~~~   97 (226)
                      .||++.++|...+++++++
T Consensus       115 ~KP~~~~~L~~~i~~~~~~  133 (135)
T 3snk_A          115 HKPLDGKELLNAVTFHDTG  133 (135)
T ss_dssp             ESSCCHHHHHHHHHHTC--
T ss_pred             cCCCCHHHHHHHHHHHhcc
Confidence            9999999999999887653

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

Probab=99.73  E-value=5.1e-17  Score=119.38  Aligned_cols=95  Identities=19%  Similarity=0.345  Sum_probs=87.0

Q ss_pred             Cc--EEEEECCHHHHHHHHHh-----CCCCceEEEEccCCCCCCHHHHHHHHhc-----CCCCcEEEEeccCCHHHHHHH
Q 027234            2 GF--SVTKCNRAEIALDMLRT-----NKNGYDIVISDVHMPDMDGFKLLELVGL-----EMDLPVIMMCAHGSKEVVMKG   69 (226)
Q Consensus         2 g~--~V~~~~~~~eal~~l~~-----~~~~~DlVl~D~~mp~~dG~~l~~~l~~-----~~~~pvI~ls~~~~~~~~~~a   69 (226)
                      ||  .|..+.++.+|++.+..     ..  ||+||+|+.||+++|+++++.++.     .+.+|+|++|+..+.+....+
T Consensus        33 ~~~~~v~~~~~~~~a~~~l~~~~~~~~~--~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~~~~~ii~~t~~~~~~~~~~~  110 (146)
T 3ilh_A           33 HRVEEIQSVTSGNAAINKLNELYAAGRW--PSIICIDINMPGINGWELIDLFKQHFQPMKNKSIVCLLSSSLDPRDQAKA  110 (146)
T ss_dssp             CCEEEEEEESSHHHHHHHHHHHHTSSCC--CSEEEEESSCSSSCHHHHHHHHHHHCGGGTTTCEEEEECSSCCHHHHHHH
T ss_pred             CCCeeeeecCCHHHHHHHHHHhhccCCC--CCEEEEcCCCCCCCHHHHHHHHHHhhhhccCCCeEEEEeCCCChHHHHHH
Confidence            56  88999999999999987     66  999999999999999999999975     468999999999999999999


Q ss_pred             HhCC-cceEEeCCCCHHHHHHHHHHHHHHH
Q 027234           70 VTHD-ACDYLTKPVRIEELKNIWQHVVRKR   98 (226)
Q Consensus        70 ~~~g-a~~yl~KP~~~~~L~~~l~~~~~~~   98 (226)
                      +..| +++||.||++.++|..++++...+.
T Consensus       111 ~~~g~~~~~l~KP~~~~~L~~~i~~~~~~~  140 (146)
T 3ilh_A          111 EASDWVDYYVSKPLTANALNNLYNKVLNEG  140 (146)
T ss_dssp             HHCSSCCEEECSSCCHHHHHHHHHHHHCC-
T ss_pred             HhcCCcceeeeCCCCHHHHHHHHHHHHHhc
Confidence            9999 9999999999999999999987543

>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=99.73  E-value=1.3e-17  Score=120.05  Aligned_cols=94  Identities=24%  Similarity=0.373  Sum_probs=84.3

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhc---CCCCcEEEEeccCCHHHHHHHHhCCcceE
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGL---EMDLPVIMMCAHGSKEVVMKGVTHDACDY   77 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~---~~~~pvI~ls~~~~~~~~~~a~~~ga~~y   77 (226)
                      .||.|..+.++.+|++.+....  ||+||+|+.||+++|+++++.++.   .+.+|+|++|+..+... ..++..|+++|
T Consensus        26 ~g~~v~~~~~~~~a~~~l~~~~--~dlii~D~~l~~~~g~~~~~~l~~~~~~~~~~ii~~s~~~~~~~-~~~~~~g~~~~  102 (127)
T 3i42_A           26 LGFQADYVMSGTDALHAMSTRG--YDAVFIDLNLPDTSGLALVKQLRALPMEKTSKFVAVSGFAKNDL-GKEACELFDFY  102 (127)
T ss_dssp             TTEEEEEESSHHHHHHHHHHSC--CSEEEEESBCSSSBHHHHHHHHHHSCCSSCCEEEEEECC-CTTC-CHHHHHHCSEE
T ss_pred             cCCCEEEECCHHHHHHHHHhcC--CCEEEEeCCCCCCCHHHHHHHHHhhhccCCCCEEEEECCcchhH-HHHHHHhhHHh
Confidence            4899999999999999999876  999999999999999999999984   57899999999988877 88999999999


Q ss_pred             EeCCCCHHHHHHHHHHHHHH
Q 027234           78 LTKPVRIEELKNIWQHVVRK   97 (226)
Q Consensus        78 l~KP~~~~~L~~~l~~~~~~   97 (226)
                      |.||++.++|...+++..+.
T Consensus       103 l~KP~~~~~L~~~i~~~~~~  122 (127)
T 3i42_A          103 LEKPIDIASLEPILQSIEGH  122 (127)
T ss_dssp             EESSCCHHHHHHHHHHHC--
T ss_pred             eeCCCCHHHHHHHHHHhhcc
Confidence            99999999999999987654

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

Probab=99.73  E-value=7.4e-17  Score=118.08  Aligned_cols=97  Identities=25%  Similarity=0.323  Sum_probs=89.4

Q ss_pred             CCcE-EEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhc---CCCCcEEEEeccCCHHHHHHHHhCCcce
Q 027234            1 MGFS-VTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGL---EMDLPVIMMCAHGSKEVVMKGVTHDACD   76 (226)
Q Consensus         1 lg~~-V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~---~~~~pvI~ls~~~~~~~~~~a~~~ga~~   76 (226)
                      .||. |..+.++.+|++.+....  ||+||+|+.||+++|+++++.++.   .+.+|||++|+..+......++..|+++
T Consensus        32 ~~~~~v~~~~~~~~a~~~l~~~~--~dlii~d~~l~~~~g~~~~~~l~~~~~~~~~~ii~~s~~~~~~~~~~~~~~g~~~  109 (143)
T 3cnb_A           32 FPYAKIKIAYNPFDAGDLLHTVK--PDVVMLDLMMVGMDGFSICHRIKSTPATANIIVIAMTGALTDDNVSRIVALGAET  109 (143)
T ss_dssp             CTTCEEEEECSHHHHHHHHHHTC--CSEEEEETTCTTSCHHHHHHHHHTSTTTTTSEEEEEESSCCHHHHHHHHHTTCSE
T ss_pred             cCccEEEEECCHHHHHHHHHhcC--CCEEEEecccCCCcHHHHHHHHHhCccccCCcEEEEeCCCCHHHHHHHHhcCCcE
Confidence            4788 899999999999999876  999999999999999999999975   4679999999999999999999999999


Q ss_pred             EEeCCCCHHHHHHHHHHHHHHHh
Q 027234           77 YLTKPVRIEELKNIWQHVVRKRK   99 (226)
Q Consensus        77 yl~KP~~~~~L~~~l~~~~~~~~   99 (226)
                      ||.||++.++|...+++++++..
T Consensus       110 ~l~kP~~~~~l~~~i~~~~~~~~  132 (143)
T 3cnb_A          110 CFGKPLNFTLLEKTIKQLVEQKK  132 (143)
T ss_dssp             EEESSCCHHHHHHHHHHHHHTTC
T ss_pred             EEeCCCCHHHHHHHHHHHHHhhc
Confidence            99999999999999999987544

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

Probab=99.73  E-value=7.1e-18  Score=122.45  Aligned_cols=97  Identities=18%  Similarity=0.212  Sum_probs=86.2

Q ss_pred             CCcEEE-EECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEE
Q 027234            1 MGFSVT-KCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYL   78 (226)
Q Consensus         1 lg~~V~-~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl   78 (226)
                      .||.+. .+.++.+|++.+....  ||+||+|+.||+++|+++++.++ ..+.+|+|++|+..+.+...++++.|+++||
T Consensus        24 ~g~~v~~~~~~~~~a~~~~~~~~--~dlii~d~~l~~~~g~~~~~~l~~~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l  101 (134)
T 3f6c_A           24 NDIEILAELTEGGSAVQRVETLK--PDIVIIDVDIPGVNGIQVLETLRKRQYSGIIIIVSAKNDHFYGKHCADAGANGFV  101 (134)
T ss_dssp             TTEEEEEEESSSTTHHHHHHHHC--CSEEEEETTCSSSCHHHHHHHHHHTTCCSEEEEEECC---CTHHHHHHTTCSEEE
T ss_pred             CCcEEEEEcCCHHHHHHHHHhcC--CCEEEEecCCCCCChHHHHHHHHhcCCCCeEEEEeCCCChHHHHHHHHhCCCEEE
Confidence            378887 8999999999999876  99999999999999999999998 5578999999999998899999999999999


Q ss_pred             eCCCCHHHHHHHHHHHHHHHh
Q 027234           79 TKPVRIEELKNIWQHVVRKRK   99 (226)
Q Consensus        79 ~KP~~~~~L~~~l~~~~~~~~   99 (226)
                      .||++.++|..++++++++..
T Consensus       102 ~kp~~~~~l~~~i~~~~~~~~  122 (134)
T 3f6c_A          102 SKKEGMNNIIAAIEAAKNGYC  122 (134)
T ss_dssp             EGGGCTHHHHHHHHHHHTTCC
T ss_pred             eCCCCHHHHHHHHHHHHCCCE
Confidence            999999999999999886543

>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=99.73  E-value=8.3e-17  Score=117.15  Aligned_cols=96  Identities=17%  Similarity=0.302  Sum_probs=87.9

Q ss_pred             Cc--EEEEECCHHHHHHHHHh-------CCCCceEEEEccCCCCCCHHHHHHHHhcC---CCCcEEEEeccCCHHHHHHH
Q 027234            2 GF--SVTKCNRAEIALDMLRT-------NKNGYDIVISDVHMPDMDGFKLLELVGLE---MDLPVIMMCAHGSKEVVMKG   69 (226)
Q Consensus         2 g~--~V~~~~~~~eal~~l~~-------~~~~~DlVl~D~~mp~~dG~~l~~~l~~~---~~~pvI~ls~~~~~~~~~~a   69 (226)
                      ||  .|..+.++.+|++.+..       ..  ||+||+|+.||+++|+++++.++..   +.+|+|++|+..+.+...++
T Consensus        26 ~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~--~dlvi~d~~~~~~~g~~~~~~l~~~~~~~~~pii~ls~~~~~~~~~~~  103 (140)
T 1k68_A           26 TVPHEVVTVRDGMEAMAYLRQEGEYANASR--PDLILLXLNLPKKDGREVLAEIKSDPTLKRIPVVVLSTSINEDDIFHS  103 (140)
T ss_dssp             SSCCEEEEECSHHHHHHHHTTCGGGGSCCC--CSEEEECSSCSSSCHHHHHHHHHHSTTGGGSCEEEEESCCCHHHHHHH
T ss_pred             CCCceEEEECCHHHHHHHHHcccccccCCC--CcEEEEecCCCcccHHHHHHHHHcCcccccccEEEEecCCcHHHHHHH
Confidence            56  89999999999999987       45  9999999999999999999999854   57999999999999999999


Q ss_pred             HhCCcceEEeCCCCHHHHHHHHHHHHHHHh
Q 027234           70 VTHDACDYLTKPVRIEELKNIWQHVVRKRK   99 (226)
Q Consensus        70 ~~~ga~~yl~KP~~~~~L~~~l~~~~~~~~   99 (226)
                      ++.|+++||.||++.++|...++++++...
T Consensus       104 ~~~g~~~~l~kP~~~~~l~~~i~~~~~~~~  133 (140)
T 1k68_A          104 YDLHVNCYITKSANLSQLFQIVKGIEEFWL  133 (140)
T ss_dssp             HHTTCSEEEECCSSHHHHHHHHHHHHHHHH
T ss_pred             HHhchhheecCCCCHHHHHHHHHHHHHHHc
Confidence            999999999999999999999999986543

>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=99.72  E-value=9.5e-17  Score=119.23  Aligned_cols=97  Identities=24%  Similarity=0.370  Sum_probs=86.0

Q ss_pred             Cc--EEEEECCHHHHHHHHHh-------CCCCceEEEEccCCCCCCHHHHHHHHhc---CCCCcEEEEeccCCHHHHHHH
Q 027234            2 GF--SVTKCNRAEIALDMLRT-------NKNGYDIVISDVHMPDMDGFKLLELVGL---EMDLPVIMMCAHGSKEVVMKG   69 (226)
Q Consensus         2 g~--~V~~~~~~~eal~~l~~-------~~~~~DlVl~D~~mp~~dG~~l~~~l~~---~~~~pvI~ls~~~~~~~~~~a   69 (226)
                      ||  .|..+.++.+|++.+..       ....||+||+|+.||+++|+++++.++.   .+.+|||++|+..+.+...++
T Consensus        28 g~~~~v~~~~~~~~al~~l~~~~~~~~~~~~~~dliilD~~l~~~~g~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~~  107 (152)
T 3heb_A           28 GVNNEIIAFTDGTSALNYLFGDDKSGRVSAGRAQLVLLDLNLPDMTGIDILKLVKENPHTRRSPVVILTTTDDQREIQRC  107 (152)
T ss_dssp             TCCCCEEEESSHHHHHHHHHCTTSSSGGGTTCBEEEEECSBCSSSBHHHHHHHHHHSTTTTTSCEEEEESCCCHHHHHHH
T ss_pred             CCcceEEEeCCHHHHHHHHhccccccccccCCCCEEEEeCCCCCCcHHHHHHHHHhcccccCCCEEEEecCCCHHHHHHH
Confidence            56  79999999999999961       1134999999999999999999999975   367899999999999999999


Q ss_pred             HhCCcceEEeCCCCHHHHHHHHHHHHHHH
Q 027234           70 VTHDACDYLTKPVRIEELKNIWQHVVRKR   98 (226)
Q Consensus        70 ~~~ga~~yl~KP~~~~~L~~~l~~~~~~~   98 (226)
                      ++.|+++||.||++.++|..+++++.+..
T Consensus       108 ~~~g~~~~l~KP~~~~~l~~~i~~~~~~~  136 (152)
T 3heb_A          108 YDLGANVYITKPVNYENFANAIRQLGLFF  136 (152)
T ss_dssp             HHTTCSEEEECCSSHHHHHHHHHHHHHHH
T ss_pred             HHCCCcEEEeCCCCHHHHHHHHHHHHHHH
Confidence            99999999999999999999999986543

>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=99.72  E-value=1.2e-17  Score=120.06  Aligned_cols=95  Identities=26%  Similarity=0.436  Sum_probs=86.9

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcC---CCCcEEEEeccCCHHHHHHHHhCCcceE
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLE---MDLPVIMMCAHGSKEVVMKGVTHDACDY   77 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~---~~~pvI~ls~~~~~~~~~~a~~~ga~~y   77 (226)
                      .||.|..+.++.+|++.+....  ||+||+|+.||+++|+++++.++..   +.+|+|++|+..+.+...++++.|+++|
T Consensus        25 ~g~~v~~~~~~~~a~~~~~~~~--~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~~~ii~~s~~~~~~~~~~~~~~ga~~~  102 (127)
T 2jba_A           25 NGFQPVEAEDYDSAVNQLNEPW--PDLILLAWMLPGGSGIQFIKHLRRESMTRDIPVVMLTARGEEEDRVRGLETGADDC  102 (127)
T ss_dssp             TTCEEEEECSHHHHHTTCSSSC--CSEEEEESEETTEEHHHHHHHHHTSTTTTTSCEEEEEETTHHHHHHTTCCCSCSEE
T ss_pred             CCceEEEeCCHHHHHHHHhccC--CCEEEEecCCCCCCHHHHHHHHHhCcccCCCCEEEEeCCCCHHHHHHHHhcCCCeE
Confidence            3789999999999999988765  9999999999999999999999854   6799999999999999999999999999


Q ss_pred             EeCCCCHHHHHHHHHHHHHH
Q 027234           78 LTKPVRIEELKNIWQHVVRK   97 (226)
Q Consensus        78 l~KP~~~~~L~~~l~~~~~~   97 (226)
                      |.||++.++|...++++++.
T Consensus       103 l~Kp~~~~~l~~~i~~~~~~  122 (127)
T 2jba_A          103 ITKPFSPKELVARIKAVMRR  122 (127)
T ss_dssp             EEESCCHHHHHHHHHHHHHC
T ss_pred             EeCCCCHHHHHHHHHHHHhc
Confidence            99999999999999988753

>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=99.72  E-value=2.1e-17  Score=121.02  Aligned_cols=99  Identities=22%  Similarity=0.345  Sum_probs=81.3

Q ss_pred             cEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcC---CCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            3 FSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLE---MDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         3 ~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~---~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      |.|..+.++.+|++.+.+..  ||+||+|+.||+++|+++++.++..   +.+|+|++|+..+.+...++++.|+++||.
T Consensus        27 ~~v~~~~~~~~a~~~~~~~~--~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~  104 (140)
T 3n53_A           27 YLVIESKNEKEALEQIDHHH--PDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILLFSSEHKEAIVNGLHSGADDYLT  104 (140)
T ss_dssp             SEEEEESSHHHHHHHHHHHC--CSEEEEETTC------CHHHHHHTSTTCTTCCEEEEECC----CTTTTTTCCCSEEEE
T ss_pred             ceEEEeCCHHHHHHHHhcCC--CCEEEEeCCCCCCcHHHHHHHHHcCcccCCCCEEEEecCCCHHHHHHHHhcCCCeeee
Confidence            78899999999999999876  9999999999999999999999854   689999999999888899999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHhhhhh
Q 027234           80 KPVRIEELKNIWQHVVRKRKNERK  103 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~~~~~~~  103 (226)
                      ||++.++|..++++++++......
T Consensus       105 KP~~~~~l~~~i~~~~~~~~~~~~  128 (140)
T 3n53_A          105 KPFNRNDLLSRIEIHLRTQNYYSD  128 (140)
T ss_dssp             SSCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHhhHHHHHH
Confidence            999999999999999987766544

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

Probab=99.72  E-value=6.5e-17  Score=121.04  Aligned_cols=95  Identities=24%  Similarity=0.373  Sum_probs=86.5

Q ss_pred             CCcEEE-EECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEE
Q 027234            1 MGFSVT-KCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYL   78 (226)
Q Consensus         1 lg~~V~-~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl   78 (226)
                      .||.|. .+.++.+|++.+......||+||+|+.||+++|+++++.|+ ..+.+|||++|+..+.+...++++.|+++||
T Consensus        59 ~g~~v~~~~~~~~~al~~l~~~~~~~dliilD~~l~~~~g~~~~~~lr~~~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l  138 (157)
T 3hzh_A           59 EGFNIIDTAADGEEAVIKYKNHYPNIDIVTLXITMPKMDGITCLSNIMEFDKNARVIMISALGKEQLVKDCLIKGAKTFI  138 (157)
T ss_dssp             TTCEEEEEESSHHHHHHHHHHHGGGCCEEEECSSCSSSCHHHHHHHHHHHCTTCCEEEEESCCCHHHHHHHHHTTCSEEE
T ss_pred             CCCeEEEEECCHHHHHHHHHhcCCCCCEEEEeccCCCccHHHHHHHHHhhCCCCcEEEEeccCcHHHHHHHHHcCCCEEE
Confidence            378988 99999999999988611289999999999999999999997 4678999999999999999999999999999


Q ss_pred             eCCCCHHHHHHHHHHHH
Q 027234           79 TKPVRIEELKNIWQHVV   95 (226)
Q Consensus        79 ~KP~~~~~L~~~l~~~~   95 (226)
                      .||++.++|...+++++
T Consensus       139 ~KP~~~~~l~~~i~~~l  155 (157)
T 3hzh_A          139 VKPLDRAKVLQRVMSVF  155 (157)
T ss_dssp             ESSCCHHHHHHHHHHTT
T ss_pred             eCCCCHHHHHHHHHHHh
Confidence            99999999999998765

>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=99.72  E-value=1.3e-16  Score=117.53  Aligned_cols=95  Identities=21%  Similarity=0.457  Sum_probs=87.6

Q ss_pred             Cc--EEEEECCHHHHHHHHHh----------CCCCceEEEEccCCCCCCHHHHHHHHhcC---CCCcEEEEeccCCHHHH
Q 027234            2 GF--SVTKCNRAEIALDMLRT----------NKNGYDIVISDVHMPDMDGFKLLELVGLE---MDLPVIMMCAHGSKEVV   66 (226)
Q Consensus         2 g~--~V~~~~~~~eal~~l~~----------~~~~~DlVl~D~~mp~~dG~~l~~~l~~~---~~~pvI~ls~~~~~~~~   66 (226)
                      ||  .|..+.++.+|++.+..          ..  ||+||+|+.||+++|+++++.++..   +.+|+|++|+..+.+..
T Consensus        30 g~~~~v~~~~~~~~al~~l~~~~~~~~~~~~~~--~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~~~ii~~t~~~~~~~~  107 (149)
T 1k66_A           30 GVVNPIYRCITGDQALDFLYQTGSYCNPDIAPR--PAVILLDLNLPGTDGREVLQEIKQDEVLKKIPVVIMTTSSNPKDI  107 (149)
T ss_dssp             TBCSCEEEECSHHHHHHHHHTCCSSSCGGGCCC--CSEEEECSCCSSSCHHHHHHHHTTSTTGGGSCEEEEESCCCHHHH
T ss_pred             CCCceEEEECCHHHHHHHHHhcccccCcccCCC--CcEEEEECCCCCCCHHHHHHHHHhCcccCCCeEEEEeCCCCHHHH
Confidence            66  89999999999999986          45  9999999999999999999999854   57999999999999999


Q ss_pred             HHHHhCCcceEEeCCCCHHHHHHHHHHHHHHH
Q 027234           67 MKGVTHDACDYLTKPVRIEELKNIWQHVVRKR   98 (226)
Q Consensus        67 ~~a~~~ga~~yl~KP~~~~~L~~~l~~~~~~~   98 (226)
                      ..+++.|+++||.||++.++|...++++++..
T Consensus       108 ~~~~~~g~~~~l~kP~~~~~l~~~i~~~~~~~  139 (149)
T 1k66_A          108 EICYSYSISSYIVKPLEIDRLTETVQTFIKYW  139 (149)
T ss_dssp             HHHHHTTCSEEEECCSSHHHHHHHHHHHHHHH
T ss_pred             HHHHHCCCCEEEeCCCCHHHHHHHHHHHHHHh
Confidence            99999999999999999999999999998654

>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=99.72  E-value=7.8e-17  Score=138.17  Aligned_cols=96  Identities=26%  Similarity=0.551  Sum_probs=89.8

Q ss_pred             CcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEeC
Q 027234            2 GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTK   80 (226)
Q Consensus         2 g~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~K   80 (226)
                      ||.|..+.++.+|++.+....  ||+||+|+.||++||+++++.++ ..+.+|||++|++.+.+...++++.||++||.|
T Consensus        24 g~~v~~a~~~~eal~~l~~~~--~DlvllD~~mp~~dG~ell~~lr~~~~~~pvIvlT~~~~~~~~~~a~~~Ga~dyl~K  101 (387)
T 1ny5_A           24 GIKVESAERGKEAYKLLSEKH--FNVVLLDLLLPDVNGLEILKWIKERSPETEVIVITGHGTIKTAVEAMKMGAYDFLTK  101 (387)
T ss_dssp             TCEEEEESSHHHHHHHHHHSC--CSEEEEESBCSSSBHHHHHHHHHHHCTTSEEEEEEETTCHHHHHHHHTTTCCEEEEE
T ss_pred             CCEEEEECCHHHHHHHHHhCC--CCEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEeCCCCHHHHHHHHhcCceEEecC
Confidence            799999999999999999876  99999999999999999999997 467899999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHh
Q 027234           81 PVRIEELKNIWQHVVRKRK   99 (226)
Q Consensus        81 P~~~~~L~~~l~~~~~~~~   99 (226)
                      |++.++|...+++++..+.
T Consensus       102 P~~~~~L~~~i~~~l~~~~  120 (387)
T 1ny5_A          102 PCMLEEIELTINKAIEHRK  120 (387)
T ss_dssp             SCCHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHH
Confidence            9999999999999886544

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

Probab=99.72  E-value=1.1e-16  Score=116.81  Aligned_cols=98  Identities=22%  Similarity=0.375  Sum_probs=90.0

Q ss_pred             CcEEE-EECCHHHHHHHHHhCCCCceEEEEccCCC-CCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            2 GFSVT-KCNRAEIALDMLRTNKNGYDIVISDVHMP-DMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         2 g~~V~-~~~~~~eal~~l~~~~~~~DlVl~D~~mp-~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      ||+|. .+.++.+|++.+....  ||+||+|+.|| +++|+++++.++..+.+|||++|+..+......++..|+++||.
T Consensus        33 g~~v~~~~~~~~~a~~~~~~~~--~dlii~d~~~~~~~~g~~~~~~l~~~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~  110 (140)
T 3cg0_A           33 GYDVLGVFDNGEEAVRCAPDLR--PDIALVDIMLCGALDGVETAARLAAGCNLPIIFITSSQDVETFQRAKRVNPFGYLA  110 (140)
T ss_dssp             TCEEEEEESSHHHHHHHHHHHC--CSEEEEESSCCSSSCHHHHHHHHHHHSCCCEEEEECCCCHHHHHHHHTTCCSEEEE
T ss_pred             CCeeEEEECCHHHHHHHHHhCC--CCEEEEecCCCCCCCHHHHHHHHHhCCCCCEEEEecCCCHHHHHHHHhcCCCEEEe
Confidence            78998 5999999999999876  99999999998 79999999999854889999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHhhh
Q 027234           80 KPVRIEELKNIWQHVVRKRKNE  101 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~~~~~  101 (226)
                      ||++.++|...+++++++....
T Consensus       111 kp~~~~~l~~~i~~~~~~~~~~  132 (140)
T 3cg0_A          111 KPVAADTLHRSIEMAIHKKKLE  132 (140)
T ss_dssp             ESCCHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCHHHHHHHHHHHHhccccC
Confidence            9999999999999998765543

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

Probab=99.72  E-value=2.4e-17  Score=121.61  Aligned_cols=95  Identities=16%  Similarity=0.273  Sum_probs=86.8

Q ss_pred             C-cEEEEECCHHHHHHHHHh--CCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceE
Q 027234            2 G-FSVTKCNRAEIALDMLRT--NKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDY   77 (226)
Q Consensus         2 g-~~V~~~~~~~eal~~l~~--~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~y   77 (226)
                      | |.|..+.++.+++..+..  ..  ||+||+|+.||+++|+++++.++ ..+.+|||++|+..+.+...++++.||++|
T Consensus        44 g~~~v~~~~~~~~~~~~~~~~~~~--~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~ii~lt~~~~~~~~~~~~~~ga~~~  121 (146)
T 4dad_A           44 GRYRVTRTVGRAAQIVQRTDGLDA--FDILMIDGAALDTAELAAIEKLSRLHPGLTCLLVTTDASSQTLLDAMRAGVRDV  121 (146)
T ss_dssp             CSCEEEEECCCHHHHTTCHHHHTT--CSEEEEECTTCCHHHHHHHHHHHHHCTTCEEEEEESCCCHHHHHHHHTTTEEEE
T ss_pred             CCeEEEEeCCHHHHHHHHHhcCCC--CCEEEEeCCCCCccHHHHHHHHHHhCCCCcEEEEeCCCCHHHHHHHHHhCCcee
Confidence            5 999999999998877654  66  99999999999999999999997 557899999999999999999999999999


Q ss_pred             EeCCCCHHHHHHHHHHHHHHH
Q 027234           78 LTKPVRIEELKNIWQHVVRKR   98 (226)
Q Consensus        78 l~KP~~~~~L~~~l~~~~~~~   98 (226)
                      |.||++.++|..++++++++.
T Consensus       122 l~Kp~~~~~L~~~i~~~~~~~  142 (146)
T 4dad_A          122 LRWPLEPRALDDALKRAAAQC  142 (146)
T ss_dssp             EESSCCHHHHHHHHHHHHHTC
T ss_pred             EcCCCCHHHHHHHHHHHHhhh
Confidence            999999999999999988653

>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=99.71  E-value=8.9e-17  Score=127.01  Aligned_cols=96  Identities=30%  Similarity=0.518  Sum_probs=89.4

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhc-CCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGL-EMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~-~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||.|..+.++.+|++.+....  ||+||+|+.||+++|+++++.++. .+.+|||++|+..+.+....++..||++||.
T Consensus        25 ~g~~v~~~~~~~~a~~~~~~~~--~dlvllD~~l~~~~g~~~~~~lr~~~~~~~ii~ls~~~~~~~~~~~~~~ga~~~l~  102 (225)
T 1kgs_A           25 EMFTVDVCYDGEEGMYMALNEP--FDVVILDIMLPVHDGWEILKSMRESGVNTPVLMLTALSDVEYRVKGLNMGADDYLP  102 (225)
T ss_dssp             TTCEEEEESSHHHHHHHHHHSC--CSEEEEESCCSSSCHHHHHHHHHHTTCCCCEEEEESSCHHHHHHHTCCCCCSEEEE
T ss_pred             CCCEEEEECCHHHHHHHHhcCC--CCEEEEeCCCCCCCHHHHHHHHHhcCCCCCEEEEeCCCCHHHHHHHHhCCccEEEe
Confidence            3799999999999999999876  999999999999999999999984 5789999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHH
Q 027234           80 KPVRIEELKNIWQHVVRKR   98 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~~   98 (226)
                      ||++.++|...++.++++.
T Consensus       103 Kp~~~~~l~~~i~~~~~~~  121 (225)
T 1kgs_A          103 KPFDLRELIARVRALIRRK  121 (225)
T ss_dssp             SSCCHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHhhc
Confidence            9999999999999998764

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

Probab=99.71  E-value=5.3e-17  Score=118.76  Aligned_cols=95  Identities=26%  Similarity=0.397  Sum_probs=84.3

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcC---CCCcEEEEeccCCHHHHHHHHhCCcceE
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLE---MDLPVIMMCAHGSKEVVMKGVTHDACDY   77 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~---~~~pvI~ls~~~~~~~~~~a~~~ga~~y   77 (226)
                      .||.|..+.++.+|++.+....  ||+||+|+.||+++|+++++.++..   +.+|||++|+..+......++..|+++|
T Consensus        26 ~g~~v~~~~~~~~al~~l~~~~--~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~~~ii~ls~~~~~~~~~~~~~~~~~~~  103 (138)
T 3c3m_A           26 GGYRPITAFSGEECLEALNATP--PDLVLLDIMMEPMDGWETLERIKTDPATRDIPVLMLTAKPLTPEEANEYGSYIEDY  103 (138)
T ss_dssp             TTCEEEEESSHHHHHHHHHHSC--CSEEEEESCCSSSCHHHHHHHHHHSTTTTTSCEEEEESSCCCHHHHHHTTTTCSEE
T ss_pred             cCceEEEeCCHHHHHHHHhccC--CCEEEEeCCCCCCCHHHHHHHHHcCcccCCCCEEEEECCCChHHHHHHhhcCHhhe
Confidence            4799999999999999999876  9999999999999999999999743   4789999999877666667778889999


Q ss_pred             EeCCCCHHHHHHHHHHHHHH
Q 027234           78 LTKPVRIEELKNIWQHVVRK   97 (226)
Q Consensus        78 l~KP~~~~~L~~~l~~~~~~   97 (226)
                      |.||++.++|...+++++..
T Consensus       104 l~KP~~~~~L~~~i~~~~~~  123 (138)
T 3c3m_A          104 ILKPTTHHQLYEAIEHVLAR  123 (138)
T ss_dssp             EECCCHHHHHHHHHHHHHSC
T ss_pred             EeCCCCHHHHHHHHHHHHHH
Confidence            99999999999999988754

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

Probab=99.71  E-value=1.4e-16  Score=116.56  Aligned_cols=95  Identities=23%  Similarity=0.309  Sum_probs=85.3

Q ss_pred             cEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhC-CcceEEeC
Q 027234            3 FSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTH-DACDYLTK   80 (226)
Q Consensus         3 ~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~-ga~~yl~K   80 (226)
                      |.|..+.++.+|++.+....  ||+||+|+.||+++|+++++.++ ..+.+|+|++|+..+......++.. |+++||.|
T Consensus        25 ~~v~~~~~~~~a~~~~~~~~--~dlvl~D~~lp~~~g~~~~~~l~~~~~~~~ii~~s~~~~~~~~~~~~~~~ga~~~l~K  102 (139)
T 2jk1_A           25 FDVLTAQGAEAAIAILEEEW--VQVIICDQRMPGRTGVDFLTEVRERWPETVRIIITGYTDSASMMAAINDAGIHQFLTK  102 (139)
T ss_dssp             SCEEEESSHHHHHHHHHHSC--EEEEEEESCCSSSCHHHHHHHHHHHCTTSEEEEEESCTTCHHHHHHHHHTTCCEEEES
T ss_pred             ceEEEcCCHHHHHHHHhcCC--CCEEEEeCCCCCCcHHHHHHHHHHhCCCCcEEEEeCCCChHHHHHHHHhhchhhhccC
Confidence            77889999999999998866  99999999999999999999997 4578999999999888888888875 59999999


Q ss_pred             CCCHHHHHHHHHHHHHHHh
Q 027234           81 PVRIEELKNIWQHVVRKRK   99 (226)
Q Consensus        81 P~~~~~L~~~l~~~~~~~~   99 (226)
                      |++.++|...++++++...
T Consensus       103 P~~~~~L~~~i~~~~~~~~  121 (139)
T 2jk1_A          103 PWHPEQLLSSARNAARMFT  121 (139)
T ss_dssp             SCCHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHH
Confidence            9999999999999886544

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

Probab=99.71  E-value=7.4e-17  Score=118.27  Aligned_cols=99  Identities=24%  Similarity=0.386  Sum_probs=87.9

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||+|..+.++.+|++.+....  ||+||+|+ ||+++|+++++.++ ..+.+|+|++|+..+.+....++..|+++||.
T Consensus        27 ~g~~v~~~~~~~~a~~~l~~~~--~dlvi~d~-~~~~~g~~~~~~l~~~~~~~pii~ls~~~~~~~~~~~~~~g~~~~l~  103 (142)
T 2qxy_A           27 DGFNVIWAKNEQEAFTFLRREK--IDLVFVDV-FEGEESLNLIRRIREEFPDTKVAVLSAYVDKDLIINSVKAGAVDYIL  103 (142)
T ss_dssp             GTCEEEEESSHHHHHHHHTTSC--CSEEEEEC-TTTHHHHHHHHHHHHHCTTCEEEEEESCCCHHHHHHHHHHTCSCEEE
T ss_pred             CCCEEEEECCHHHHHHHHhccC--CCEEEEeC-CCCCcHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHCCcceeEe
Confidence            3799999999999999999866  99999999 99999999999997 45689999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHhhhh
Q 027234           80 KPVRIEELKNIWQHVVRKRKNER  102 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~~~~~~  102 (226)
                      ||++.++|...+++++++.....
T Consensus       104 kP~~~~~l~~~i~~~~~~~~~~~  126 (142)
T 2qxy_A          104 KPFRLDYLLERVKKIISSTPRVT  126 (142)
T ss_dssp             SSCCHHHHHHHHHHHHHC-----
T ss_pred             CCCCHHHHHHHHHHHHhhccccc
Confidence            99999999999999987654433

>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=99.71  E-value=1.2e-16  Score=119.12  Aligned_cols=98  Identities=33%  Similarity=0.542  Sum_probs=90.4

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||+|..+.++.+|++.+....  ||+||+|+.||+++|+++++.++ ..+.+|||++|+..+.+....++..|+++||.
T Consensus        26 ~g~~v~~~~~~~~a~~~l~~~~--~dliild~~l~~~~g~~~~~~l~~~~~~~pii~ls~~~~~~~~~~~~~~g~~~~l~  103 (155)
T 1qkk_A           26 AGFTVSSFASATEALAGLSADF--AGIVISDIRMPGMDGLALFRKILALDPDLPMILVTGHGDIPMAVQAIQDGAYDFIA  103 (155)
T ss_dssp             TTCEEEEESCHHHHHHTCCTTC--CSEEEEESCCSSSCHHHHHHHHHHHCTTSCEEEEECGGGHHHHHHHHHTTCCEEEE
T ss_pred             cCcEEEEECCHHHHHHHHHhCC--CCEEEEeCCCCCCCHHHHHHHHHhhCCCCCEEEEECCCChHHHHHHHhcCCCeEEe
Confidence            4899999999999999998766  99999999999999999999997 45789999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHhh
Q 027234           80 KPVRIEELKNIWQHVVRKRKN  100 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~~~~  100 (226)
                      ||++.++|...+++++.....
T Consensus       104 kP~~~~~L~~~i~~~~~~~~~  124 (155)
T 1qkk_A          104 KPFAADRLVQSARRAEEKRRL  124 (155)
T ss_dssp             SSCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHH
Confidence            999999999999999876554

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

Probab=99.71  E-value=1.6e-16  Score=118.01  Aligned_cols=95  Identities=22%  Similarity=0.383  Sum_probs=86.1

Q ss_pred             EEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEeCCCC
Q 027234            5 VTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTKPVR   83 (226)
Q Consensus         5 V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~KP~~   83 (226)
                      |..+.++.+|++.+....  ||+||+|+.||+++|+++++.++ ..+.+|||++|+..+.....++++.||++||.||++
T Consensus        44 v~~~~~~~~a~~~l~~~~--~dlii~d~~l~~~~g~~~~~~l~~~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~Kp~~  121 (152)
T 3eul_A           44 VGEADDGAAALELIKAHL--PDVALLDYRMPGMDGAQVAAAVRSYELPTRVLLISAHDEPAIVYQALQQGAAGFLLKDST  121 (152)
T ss_dssp             EEEESSHHHHHHHHHHHC--CSEEEEETTCSSSCHHHHHHHHHHTTCSCEEEEEESCCCHHHHHHHHHTTCSEEEETTCC
T ss_pred             EEEeCCHHHHHHHHHhcC--CCEEEEeCCCCCCCHHHHHHHHHhcCCCCeEEEEEccCCHHHHHHHHHcCCCEEEecCCC
Confidence            558999999999999876  99999999999999999999997 557899999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHhhh
Q 027234           84 IEELKNIWQHVVRKRKNE  101 (226)
Q Consensus        84 ~~~L~~~l~~~~~~~~~~  101 (226)
                      .++|..++++++.+....
T Consensus       122 ~~~l~~~i~~~~~~~~~~  139 (152)
T 3eul_A          122 RTEIVKAVLDCAKGRDVV  139 (152)
T ss_dssp             HHHHHHHHHHHHHCC---
T ss_pred             HHHHHHHHHHHHcCCeee
Confidence            999999999998765543

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

Probab=99.70  E-value=4.9e-17  Score=139.49  Aligned_cols=95  Identities=23%  Similarity=0.478  Sum_probs=84.3

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||+|..+.++.+|++.+....  ||+||+|+.||+|||+++++.++ ..+++|||++|+..+.+...++++.||++||.
T Consensus        28 ~g~~v~~a~~~~~al~~~~~~~--~dlvllD~~mp~~~G~~~~~~lr~~~~~~pii~lt~~~~~~~~~~a~~~ga~~yl~  105 (394)
T 3eq2_A           28 SNFKVLQALNGLQGLQIFESEQ--PDLVICDLRMPQIDGLELIRRIRQTASETPIIVLSGAGVMSDAVEALRLGAADYLI  105 (394)
T ss_dssp             TTEEEEECSSHHHHHHHHHHSC--CSEEEECCCSSSSCTHHHHHHHHHTTCCCCEEEC---CHHHHHHHHHHHTCSEECC
T ss_pred             CCCEEEEECCHHHHHHHHhhCC--CCEEEEcCCCCCCCHHHHHHHHHhhCCCCcEEEEEcCCCHHHHHHHHhcChhhEEE
Confidence            4899999999999999999876  99999999999999999999998 45789999999999999999999999999999


Q ss_pred             CCC-CHHHHHHHHHHHHHH
Q 027234           80 KPV-RIEELKNIWQHVVRK   97 (226)
Q Consensus        80 KP~-~~~~L~~~l~~~~~~   97 (226)
                      ||+ ..+.|...+++++..
T Consensus       106 KP~~~~~~l~~~i~~~~~~  124 (394)
T 3eq2_A          106 KPLEDLAVLEHSVRRALDR  124 (394)
T ss_dssp             SSCSCTHHHHHHHHHHHHH
T ss_pred             CCCChHHHHHHHHHHHHhh
Confidence            999 688888888877654

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

Probab=99.70  E-value=2e-16  Score=133.62  Aligned_cols=92  Identities=24%  Similarity=0.349  Sum_probs=85.7

Q ss_pred             CcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcC---CCCcEEEEeccCCHHHHHHHHhCCcceEE
Q 027234            2 GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLE---MDLPVIMMCAHGSKEVVMKGVTHDACDYL   78 (226)
Q Consensus         2 g~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~---~~~pvI~ls~~~~~~~~~~a~~~ga~~yl   78 (226)
                      ||.|..+.++.+|++.+....  ||+||+|+.||+|||+++++.++..   +.+|||++|+..+.+....+++.||++||
T Consensus        43 ~~~v~~~~~~~~al~~~~~~~--~dlvl~D~~mp~~~G~~~~~~l~~~~~~~~~~ii~~s~~~~~~~~~~a~~~Ga~~~l  120 (358)
T 3bre_A           43 GIDFHFCSDPQQAVAVANQIK--PTVILQDLVMPGVDGLTLLAAYRGNPATRDIPIIVLSTKEEPTVKSAAFAAGANDYL  120 (358)
T ss_dssp             TEEEEEECCHHHHHHHHHHHC--CSEEEEESBCSSSBHHHHHHHHTTSTTTTTSCEEEEESSCCHHHHHHHHHTTCSEEE
T ss_pred             CcEEEEeCCHHHHHHHHHhCC--CCEEEEeCCCCCCCHHHHHHHHhcCcccCCCcEEEEeCCCCHHHHHHHHhcChheEe
Confidence            789999999999999998876  9999999999999999999999853   57999999999999999999999999999


Q ss_pred             eCCCCHHHHHHHHHHHH
Q 027234           79 TKPVRIEELKNIWQHVV   95 (226)
Q Consensus        79 ~KP~~~~~L~~~l~~~~   95 (226)
                      .||++.++|...+..+.
T Consensus       121 ~Kp~~~~~l~~~v~~~~  137 (358)
T 3bre_A          121 VKLPDAIELVARIRYHS  137 (358)
T ss_dssp             ESCCCHHHHHHHHHHHH
T ss_pred             eccCCHHHHHHHHHHHH
Confidence            99999999999988764

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

Probab=99.70  E-value=6.5e-17  Score=114.42  Aligned_cols=91  Identities=23%  Similarity=0.420  Sum_probs=81.4

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||.|..+.++.+|++.+....  ||+||+|+.||+++|+++++.++ ..+.+|+|++|+..+..  ..++..|+++|+.
T Consensus        24 ~~~~v~~~~~~~~a~~~~~~~~--~dlvl~D~~l~~~~g~~~~~~l~~~~~~~~ii~~s~~~~~~--~~~~~~g~~~~l~   99 (116)
T 3a10_A           24 EGYEIDTAENGEEALKKFFSGN--YDLVILDIEMPGISGLEVAGEIRKKKKDAKIILLTAYSHYR--SDMSSWAADEYVV   99 (116)
T ss_dssp             TTCEEEEESSHHHHHHHHHHSC--CSEEEECSCCSSSCHHHHHHHHHHHCTTCCEEEEESCGGGG--GCGGGGGSSEEEE
T ss_pred             CCCEEEEeCCHHHHHHHHhcCC--CCEEEEECCCCCCCHHHHHHHHHccCCCCeEEEEECCcchH--HHHHhccccceEE
Confidence            3799999999999999998866  99999999999999999999997 45789999999876655  7788999999999


Q ss_pred             CCCCHHHHHHHHHHHH
Q 027234           80 KPVRIEELKNIWQHVV   95 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~   95 (226)
                      ||++.++|...+++++
T Consensus       100 Kp~~~~~l~~~i~~~~  115 (116)
T 3a10_A          100 KSFNFDELKEKVKKLL  115 (116)
T ss_dssp             CCSSTHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHh
Confidence            9999999999888753

>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=99.70  E-value=1.7e-16  Score=138.47  Aligned_cols=98  Identities=27%  Similarity=0.385  Sum_probs=90.0

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcC---CCCcEEEEeccCCHHHHHHHHhCCcceE
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLE---MDLPVIMMCAHGSKEVVMKGVTHDACDY   77 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~---~~~pvI~ls~~~~~~~~~~a~~~ga~~y   77 (226)
                      .||.|..+.++.+|++.+....  ||+||+|+.||+|||+++++.++..   +.+|||++|+..+.+...++++.||++|
T Consensus        24 ~~~~v~~a~~~~~al~~~~~~~--~dlvllD~~mp~~~G~~~~~~l~~~~~~~~~pii~lt~~~~~~~~~~a~~~Ga~~~  101 (459)
T 1w25_A           24 EYYEVSTAMDGPTALAMAARDL--PDIILLDVMMPGMDGFTVCRKLKDDPTTRHIPVVLITALDGRGDRIQGLESGASDF  101 (459)
T ss_dssp             TTCEEEEESSHHHHHHHHHHHC--CSEEEEESCCSSSCHHHHHHHHHHSTTTTTSCEEEEECSSCHHHHHHHHHHTCCEE
T ss_pred             cCCEEEEECCHHHHHHHHhcCC--CCEEEEcCCCCCCCHHHHHHHHhcCcccCCCCEEEEECCCCHHHHHHHHHcCCCEE
Confidence            3799999999999999998876  9999999999999999999999853   5789999999999999999999999999


Q ss_pred             EeCCCCHHHHHHHHHHHHHHHhh
Q 027234           78 LTKPVRIEELKNIWQHVVRKRKN  100 (226)
Q Consensus        78 l~KP~~~~~L~~~l~~~~~~~~~  100 (226)
                      |.||++.++|...++.+++....
T Consensus       102 l~KP~~~~~l~~~i~~~~~~~~~  124 (459)
T 1w25_A          102 LTKPIDDVMLFARVRSLTRFKLV  124 (459)
T ss_dssp             EESSCCHHHHHHHHHHHHHHHHH
T ss_pred             EeCCCCHHHHHHHHHHHHHHHhh
Confidence            99999999999999998876543

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

Probab=99.70  E-value=1.7e-16  Score=115.89  Aligned_cols=97  Identities=20%  Similarity=0.308  Sum_probs=88.0

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCC-----CCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCc
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMP-----DMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDA   74 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp-----~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga   74 (226)
                      .||.|..+.++.+|++.+....  ||+||+|+.||     +++|+++++.++ ..+.+|+|++|+..+.+....+++.|+
T Consensus        26 ~g~~v~~~~~~~~a~~~l~~~~--~dlvi~d~~~~~~~~~~~~g~~~~~~l~~~~~~~~ii~ls~~~~~~~~~~~~~~g~  103 (140)
T 2qr3_A           26 HFSKVITLSSPVSLSTVLREEN--PEVVLLDMNFTSGINNGNEGLFWLHEIKRQYRDLPVVLFTAYADIDLAVRGIKEGA  103 (140)
T ss_dssp             TSSEEEEECCHHHHHHHHHHSC--EEEEEEETTTTC-----CCHHHHHHHHHHHCTTCCEEEEEEGGGHHHHHHHHHTTC
T ss_pred             CCcEEEEeCCHHHHHHHHHcCC--CCEEEEeCCcCCCCCCCccHHHHHHHHHhhCcCCCEEEEECCCCHHHHHHHHHcCc
Confidence            3799999999999999999876  99999999999     999999999997 457899999999999999999999999


Q ss_pred             ceEEeCCCCHHHHHHHHHHHHHHHh
Q 027234           75 CDYLTKPVRIEELKNIWQHVVRKRK   99 (226)
Q Consensus        75 ~~yl~KP~~~~~L~~~l~~~~~~~~   99 (226)
                      ++||.||++.++|...+++++++..
T Consensus       104 ~~~l~kp~~~~~l~~~l~~~~~~~~  128 (140)
T 2qr3_A          104 SDFVVKPWDNQKLLETLLNAASQAK  128 (140)
T ss_dssp             CEEEEESCCHHHHHHHHHHHHTCC-
T ss_pred             hheeeCCCCHHHHHHHHHHHHHhcc
Confidence            9999999999999999999876543

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

Probab=99.70  E-value=5.4e-17  Score=118.92  Aligned_cols=98  Identities=24%  Similarity=0.450  Sum_probs=89.4

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhc---CCCCcEEEEeccCCHHHHHHHHhCCcceE
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGL---EMDLPVIMMCAHGSKEVVMKGVTHDACDY   77 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~---~~~~pvI~ls~~~~~~~~~~a~~~ga~~y   77 (226)
                      .||+|..+.++.+|++.+....  ||+||+|+.||+++|+++++.++.   .+.+|||++|+..+.+....+++.|+++|
T Consensus        30 ~g~~v~~~~~~~~a~~~l~~~~--~dlii~d~~l~~~~g~~~~~~l~~~~~~~~~pii~~s~~~~~~~~~~~~~~g~~~~  107 (142)
T 3cg4_A           30 AGFHIISADSGGQCIDLLKKGF--SGVVLLDIMMPGMDGWDTIRAILDNSLEQGIAIVMLTAKNAPDAKMIGLQEYVVDY  107 (142)
T ss_dssp             TTCEEEEESSHHHHHHHHHTCC--CEEEEEESCCSSSCHHHHHHHHHHTTCCTTEEEEEEECTTCCCCSSTTGGGGEEEE
T ss_pred             CCeEEEEeCCHHHHHHHHHhcC--CCEEEEeCCCCCCCHHHHHHHHHhhcccCCCCEEEEECCCCHHHHHHHHhcCccEE
Confidence            3799999999999999999876  999999999999999999999975   46789999999988888889999999999


Q ss_pred             EeCCCCHHHHHHHHHHHHHHHhh
Q 027234           78 LTKPVRIEELKNIWQHVVRKRKN  100 (226)
Q Consensus        78 l~KP~~~~~L~~~l~~~~~~~~~  100 (226)
                      |.||++.++|...++++++..+.
T Consensus       108 l~kp~~~~~l~~~i~~~~~~~~~  130 (142)
T 3cg4_A          108 ITKPFDNEDLIEKTTFFMGFVRN  130 (142)
T ss_dssp             EESSCCHHHHHHHHHHHHHHHHH
T ss_pred             EeCCCCHHHHHHHHHHHHHHHhh
Confidence            99999999999999999876554

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

Probab=99.70  E-value=1.9e-16  Score=114.51  Aligned_cols=96  Identities=21%  Similarity=0.266  Sum_probs=81.0

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcCC---CCcEEEEeccCCHHHHHHHHhCCcceE
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEM---DLPVIMMCAHGSKEVVMKGVTHDACDY   77 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~~---~~pvI~ls~~~~~~~~~~a~~~ga~~y   77 (226)
                      .||.|..+.++.+|++.+....  ||+||+|+.||+++|+++++.++...   .++||+++..... ...++++.|+++|
T Consensus        29 ~g~~v~~~~~~~~a~~~l~~~~--~dlii~d~~l~~~~g~~~~~~l~~~~~~~~~~ii~~~~~~~~-~~~~~~~~g~~~~  105 (132)
T 3lte_A           29 DHWQVEIAHNGFDAGIKLSTFE--PAIMTLDLSMPKLDGLDVIRSLRQNKVANQPKILVVSGLDKA-KLQQAVTEGADDY  105 (132)
T ss_dssp             TTCEEEEESSHHHHHHHHHHTC--CSEEEEESCBTTBCHHHHHHHHHTTTCSSCCEEEEECCSCSH-HHHHHHHHTCCEE
T ss_pred             CCcEEEEeCCHHHHHHHHHhcC--CCEEEEecCCCCCCHHHHHHHHHhcCccCCCeEEEEeCCChH-HHHHHHHhChHHH
Confidence            4799999999999999999876  99999999999999999999998543   3555656655554 7889999999999


Q ss_pred             EeCCCCHHHHHHHHHHHHHHHh
Q 027234           78 LTKPVRIEELKNIWQHVVRKRK   99 (226)
Q Consensus        78 l~KP~~~~~L~~~l~~~~~~~~   99 (226)
                      |.||++.++|...+++...+..
T Consensus       106 l~kP~~~~~l~~~i~~~~~~~~  127 (132)
T 3lte_A          106 LEKPFDNDALLDRIHDLVNEGH  127 (132)
T ss_dssp             ECSSCCHHHHHHHHHHHHC---
T ss_pred             hhCCCCHHHHHHHHHHHcCCCC
Confidence            9999999999999998876543

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

Probab=99.69  E-value=1.4e-16  Score=118.41  Aligned_cols=97  Identities=21%  Similarity=0.360  Sum_probs=89.1

Q ss_pred             CcEEE-EECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            2 GFSVT-KCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         2 g~~V~-~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      ||.|. .+.++.+|++.+....  ||+||+|+.||+++|+++++.++ ..+.+|||++|+..+.+....++..|+++||.
T Consensus        30 ~~~v~~~~~~~~~a~~~l~~~~--~dlii~D~~l~~~~g~~~~~~l~~~~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~  107 (153)
T 3cz5_A           30 GYAVVAEAADAGEAYRLYRETT--PDIVVMDLTLPGPGGIEATRHIRQWDGAARILIFTMHQGSAFALKAFEAGASGYVT  107 (153)
T ss_dssp             TEEEEEEESSHHHHHHHHHTTC--CSEEEECSCCSSSCHHHHHHHHHHHCTTCCEEEEESCCSHHHHHHHHHTTCSEEEE
T ss_pred             CcEEEEEeCCHHHHHHHHhcCC--CCEEEEecCCCCCCHHHHHHHHHHhCCCCeEEEEECCCCHHHHHHHHHCCCcEEEe
Confidence            78887 8999999999999876  99999999999999999999997 45789999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHhh
Q 027234           80 KPVRIEELKNIWQHVVRKRKN  100 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~~~~  100 (226)
                      ||++.++|...+++++++...
T Consensus       108 kp~~~~~L~~~i~~~~~~~~~  128 (153)
T 3cz5_A          108 KSSDPAELVQAIEAILAGRRA  128 (153)
T ss_dssp             TTSCTTHHHHHHHHHTTTCCE
T ss_pred             cCCCHHHHHHHHHHHHhCCcc
Confidence            999999999999998765543

>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=99.69  E-value=1.2e-16  Score=127.00  Aligned_cols=97  Identities=29%  Similarity=0.469  Sum_probs=89.5

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhc-CCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGL-EMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~-~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||.|..+.++.+|++.+....  ||+||+|+.||+++|+++++.++. .+.+|||++|+..+.+....++..||++||.
T Consensus        30 ~g~~v~~~~~~~~a~~~~~~~~--~dlvllD~~l~~~~g~~~~~~l~~~~~~~~ii~lt~~~~~~~~~~~~~~ga~~~l~  107 (233)
T 1ys7_A           30 SGFEVATAVDGAEALRSATENR--PDAIVLDINMPVLDGVSVVTALRAMDNDVPVCVLSARSSVDDRVAGLEAGADDYLV  107 (233)
T ss_dssp             TTCEEEEESSHHHHHHHHHHSC--CSEEEEESSCSSSCHHHHHHHHHHTTCCCCEEEEECCCTTTCCCTTTTTTCSEEEE
T ss_pred             CCCEEEEECCHHHHHHHHHhCC--CCEEEEeCCCCCCCHHHHHHHHHhcCCCCCEEEEEcCCCHHHHHHHHHcCCCEEEe
Confidence            3799999999999999999876  999999999999999999999984 5789999999999988889999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHh
Q 027234           80 KPVRIEELKNIWQHVVRKRK   99 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~~~   99 (226)
                      ||++.++|...++.++++..
T Consensus       108 Kp~~~~~L~~~i~~~~~~~~  127 (233)
T 1ys7_A          108 KPFVLAELVARVKALLRRRG  127 (233)
T ss_dssp             SSCCHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHhhcc
Confidence            99999999999999987643

>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=99.68  E-value=1.2e-16  Score=126.77  Aligned_cols=96  Identities=30%  Similarity=0.409  Sum_probs=89.0

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEeC
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTK   80 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~K   80 (226)
                      .||.|..+.++.+|++.+....  ||+||+|+.||+++|+++++.++..+.+|||++|+..+......+++.||++||.|
T Consensus        27 ~g~~v~~~~~~~~al~~~~~~~--~dlvllD~~l~~~~g~~~~~~l~~~~~~~ii~lt~~~~~~~~~~~~~~ga~~~l~K  104 (230)
T 2oqr_A           27 EGFEATVVTDGPAALAEFDRAG--ADIVLLDLMLPGMSGTDVCKQLRARSSVPVIMVTARDSEIDKVVGLELGADDYVTK  104 (230)
T ss_dssp             TTCEEEEECSHHHHHHHHHHHC--CSEEEEESSCSSSCHHHHHHHHHHHCSCSEEEEECCHHHHHHHHHHHHCCSCCCCS
T ss_pred             CCCEEEEECCHHHHHHHHhccC--CCEEEEECCCCCCCHHHHHHHHHcCCCCCEEEEeCCCcHHHHHHHHHcCCCEEEeC
Confidence            3789999999999999998866  99999999999999999999998668899999999988888999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHH
Q 027234           81 PVRIEELKNIWQHVVRKR   98 (226)
Q Consensus        81 P~~~~~L~~~l~~~~~~~   98 (226)
                      |++.++|...++.++++.
T Consensus       105 p~~~~~l~~~i~~~~~~~  122 (230)
T 2oqr_A          105 PYSARELIARIRAVLRRG  122 (230)
T ss_dssp             SCCHHHHHHHHHHHHTTT
T ss_pred             CCCHHHHHHHHHHHHhhc
Confidence            999999999999987653

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

Probab=99.67  E-value=1.1e-15  Score=112.08  Aligned_cols=92  Identities=18%  Similarity=0.277  Sum_probs=83.8

Q ss_pred             Cc--EEEEECCHHHHHHHHHh------CCCCceEEEEccCCCCCCHHHHHHHHhcC---CCCcEEEEeccCCHHHHHHHH
Q 027234            2 GF--SVTKCNRAEIALDMLRT------NKNGYDIVISDVHMPDMDGFKLLELVGLE---MDLPVIMMCAHGSKEVVMKGV   70 (226)
Q Consensus         2 g~--~V~~~~~~~eal~~l~~------~~~~~DlVl~D~~mp~~dG~~l~~~l~~~---~~~pvI~ls~~~~~~~~~~a~   70 (226)
                      ||  .|..+.++.+|++.+..      ..  ||+||+|+.||+++|+++++.++..   +.+|+|++|+..+.+....++
T Consensus        31 g~~~~v~~~~~~~~a~~~l~~~~~~~~~~--~dlii~D~~l~~~~g~~~~~~l~~~~~~~~~~ii~ls~~~~~~~~~~~~  108 (143)
T 2qvg_A           31 SSLIKIEIAKSGNQALDMLYGRNKENKIH--PKLILLDINIPKMNGIEFLKELRDDSSFTDIEVFVLTAAYTSKDKLAFE  108 (143)
T ss_dssp             CTTCCEEEESSHHHHHHHHHTCTTCCCCC--CSEEEEETTCTTSCHHHHHHHHTTSGGGTTCEEEEEESCCCHHHHHHHT
T ss_pred             CCCceEEEECCHHHHHHHHHhcccccCCC--CCEEEEecCCCCCCHHHHHHHHHcCccccCCcEEEEeCCCCHHHHHHHH
Confidence            55  89999999999999986      44  9999999999999999999999854   689999999999999999999


Q ss_pred             hCCcceEEeCCCCHHHHHHHHHHHH
Q 027234           71 THDACDYLTKPVRIEELKNIWQHVV   95 (226)
Q Consensus        71 ~~ga~~yl~KP~~~~~L~~~l~~~~   95 (226)
                      +.|+++||.||++.++|..++....
T Consensus       109 ~~g~~~~l~kP~~~~~L~~~~~~~~  133 (143)
T 2qvg_A          109 SLNIRGHLIKPLDYGEAIKLFWILQ  133 (143)
T ss_dssp             TTTCCEEEESSCCHHHHHHHHHHHH
T ss_pred             hcCCCeEEECCCCHHHHHHHHHHHH
Confidence            9999999999999999999876643

>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=99.66  E-value=6.9e-16  Score=110.35  Aligned_cols=92  Identities=16%  Similarity=0.385  Sum_probs=84.7

Q ss_pred             CcEEEEECCHHHHHHHHHhCCCCceEEEEccCCC-CCCHHHHHHHHhcC---CCCcEEEEeccCCHHHHHHHHhCCcceE
Q 027234            2 GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMP-DMDGFKLLELVGLE---MDLPVIMMCAHGSKEVVMKGVTHDACDY   77 (226)
Q Consensus         2 g~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp-~~dG~~l~~~l~~~---~~~pvI~ls~~~~~~~~~~a~~~ga~~y   77 (226)
                      ||+|..+.++.+|++.+....  ||+||+|+.|| +++|+++++.++..   +.+|+|++ +..+.+....++..|+++|
T Consensus        29 g~~v~~~~~~~~a~~~~~~~~--~dlvi~d~~~~~~~~g~~~~~~l~~~~~~~~~~ii~~-~~~~~~~~~~~~~~g~~~~  105 (127)
T 2gkg_A           29 GFTVDETTDGKGSVEQIRRDR--PDLVVLAVDLSAGQNGYLICGKLKKDDDLKNVPIVII-GNPDGFAQHRKLKAHADEY  105 (127)
T ss_dssp             TCEEEEECCHHHHHHHHHHHC--CSEEEEESBCGGGCBHHHHHHHHHHSTTTTTSCEEEE-ECGGGHHHHHHSTTCCSEE
T ss_pred             CceEEEecCHHHHHHHHHhcC--CCEEEEeCCCCCCCCHHHHHHHHhcCccccCCCEEEE-ecCCchhHHHHHHhCcchh
Confidence            799999999999999999876  99999999999 99999999999853   68999999 8888888899999999999


Q ss_pred             EeCCCCHHHHHHHHHHHHH
Q 027234           78 LTKPVRIEELKNIWQHVVR   96 (226)
Q Consensus        78 l~KP~~~~~L~~~l~~~~~   96 (226)
                      +.||++.++|...++++++
T Consensus       106 l~kp~~~~~l~~~i~~~~~  124 (127)
T 2gkg_A          106 VAKPVDADQLVERAGALIG  124 (127)
T ss_dssp             EESSCCHHHHHHHHHHHHC
T ss_pred             eeCCCCHHHHHHHHHHHHc
Confidence            9999999999999988763

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

Probab=99.66  E-value=2.8e-16  Score=125.53  Aligned_cols=95  Identities=25%  Similarity=0.451  Sum_probs=88.1

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEeC
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTK   80 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~K   80 (226)
                      .||+|..+.++.+|++.+....  ||+||+|+.||+++|+++++.++..+.+|||++|+..+......++..||++||.|
T Consensus        28 ~g~~v~~~~~~~~al~~l~~~~--~dlvilD~~l~~~~g~~~~~~lr~~~~~~ii~lt~~~~~~~~~~~~~~Ga~~~l~K  105 (238)
T 2gwr_A           28 EGFDTAVIGDGTQALTAVRELR--PDLVLLDLMLPGMNGIDVCRVLRADSGVPIVMLTAKTDTVDVVLGLESGADDYIMK  105 (238)
T ss_dssp             TTCEEEEECCGGGHHHHHHHHC--CSEEEEESSCSSSCHHHHHHHHHTTCCCCEEEEEETTCCSCHHHHHHTTCCEEEEE
T ss_pred             CCCEEEEECCHHHHHHHHHhCC--CCEEEEeCCCCCCCHHHHHHHHHhCCCCcEEEEeCCCCHHHHHHHHHCCCCEEEeC
Confidence            3799999999999999998876  99999999999999999999998667899999999999888999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHH
Q 027234           81 PVRIEELKNIWQHVVRK   97 (226)
Q Consensus        81 P~~~~~L~~~l~~~~~~   97 (226)
                      |++.++|...++.++++
T Consensus       106 p~~~~~L~~~i~~~~~~  122 (238)
T 2gwr_A          106 PFKPKELVARVRARLRR  122 (238)
T ss_dssp             SCCHHHHHHHHHHHCCC
T ss_pred             CCCHHHHHHHHHHHHhh
Confidence            99999999999988654

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

Probab=99.66  E-value=7.5e-16  Score=112.12  Aligned_cols=93  Identities=17%  Similarity=0.329  Sum_probs=81.3

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCC----CC-cEEEEeccCCHHHHHHHHhCCc
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEM----DL-PVIMMCAHGSKEVVMKGVTHDA   74 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~----~~-pvI~ls~~~~~~~~~~a~~~ga   74 (226)
                      .||.|..+.++.+|++.+...   +|+||+|+.||+++|+++++.++ ..+    .. ++|++|+..+.....++++.|+
T Consensus        30 ~g~~v~~~~~~~~a~~~~~~~---~dlvllD~~lp~~~g~~~~~~l~~~~~~~~~~~~~ii~~s~~~~~~~~~~~~~~ga  106 (136)
T 1dcf_A           30 LGCEVTTVSSNEECLRVVSHE---HKVVFMDVCMPGVENYQIALRIHEKFTKQRHQRPLLVALSGNTDKSTKEKCMSFGL  106 (136)
T ss_dssp             TTCEEEEESSHHHHHHHCCTT---CSEEEEECCSSTTTTTHHHHHHHHHHC-CCSCCCEEEEEESCCSHHHHHHHHHTTC
T ss_pred             cCCeEEEeCCHHHHHHHHhcc---CCEEEEeCCCCCCcHHHHHHHHHHhhhhccCCCceEEEEeCCCCHHHHHHHHHcCC
Confidence            479999999999999988642   49999999999999999999986 222    23 5788999999999999999999


Q ss_pred             ceEEeCCCCHHHHHHHHHHHHH
Q 027234           75 CDYLTKPVRIEELKNIWQHVVR   96 (226)
Q Consensus        75 ~~yl~KP~~~~~L~~~l~~~~~   96 (226)
                      ++||.||++.++|...+++++.
T Consensus       107 ~~~l~KP~~~~~L~~~l~~~~~  128 (136)
T 1dcf_A          107 DGVLLKPVSLDNIRDVLSDLLE  128 (136)
T ss_dssp             CEEEESSCCHHHHHHHHHHHHS
T ss_pred             CeEEECCCCHHHHHHHHHHHhc
Confidence            9999999999999999988764

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

Probab=99.66  E-value=2.5e-15  Score=110.20  Aligned_cols=95  Identities=20%  Similarity=0.332  Sum_probs=82.6

Q ss_pred             CcE-EEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcC-CCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            2 GFS-VTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLE-MDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         2 g~~-V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~-~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      ||. |..+.++.+|++.+....  ||+||+|+.||+++|+++++.++.. +.+|||++|+..+  ...+++..|+++||.
T Consensus        34 ~~~~v~~~~~~~~al~~l~~~~--~dlvi~d~~l~~~~g~~~~~~l~~~~~~~~ii~~s~~~~--~~~~~~~~g~~~~l~  109 (143)
T 2qv0_A           34 QMEIVGSFDDGLDVLKFLQHNK--VDAIFLDINIPSLDGVLLAQNISQFAHKPFIVFITAWKE--HAVEAFELEAFDYIL  109 (143)
T ss_dssp             CCEEEEEESCHHHHHHHHHHCC--CSEEEECSSCSSSCHHHHHHHHTTSTTCCEEEEEESCCT--THHHHHHTTCSEEEE
T ss_pred             CceEEEEeCCHHHHHHHHHhCC--CCEEEEecCCCCCCHHHHHHHHHccCCCceEEEEeCCHH--HHHHHHhCCcceEEe
Confidence            677 458999999999999876  9999999999999999999999854 4567888888743  567889999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHhh
Q 027234           80 KPVRIEELKNIWQHVVRKRKN  100 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~~~~  100 (226)
                      ||++.++|...++++++..+.
T Consensus       110 KP~~~~~l~~~i~~~~~~~~~  130 (143)
T 2qv0_A          110 KPYQESRIINMLQKLTTAWEQ  130 (143)
T ss_dssp             SSCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHh
Confidence            999999999999998876554

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

Probab=99.65  E-value=2.5e-16  Score=117.13  Aligned_cols=97  Identities=16%  Similarity=0.237  Sum_probs=77.7

Q ss_pred             Cc-EEEEECCHHHHHHHHHh-CCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEE
Q 027234            2 GF-SVTKCNRAEIALDMLRT-NKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYL   78 (226)
Q Consensus         2 g~-~V~~~~~~~eal~~l~~-~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl   78 (226)
                      || .|..+.++.+|++.+.. ..  ||+||+|+.||+++|+++++.++ ..+.+|||++|+..+.+....++..|+++||
T Consensus        28 g~~~v~~~~~~~~a~~~l~~~~~--~dlvi~d~~l~~~~g~~~~~~l~~~~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l  105 (154)
T 2qsj_A           28 SGMRVEGAETVSDALAFLEADNT--VDLILLDVNLPDAEAIDGLVRLKRFDPSNAVALISGETDHELIRAALEAGADGFI  105 (154)
T ss_dssp             TTEEEEEESSHHHHHHHHHTTCC--CSEEEECC------CHHHHHHHHHHCTTSEEEEC-----CHHHHHHHHTTCCBBC
T ss_pred             CceEEEEecCHHHHHHHHhccCC--CCEEEEeCCCCCCchHHHHHHHHHhCCCCeEEEEeCCCCHHHHHHHHHccCCEEE
Confidence            67 68899999999999988 66  99999999999999999999997 4578999999999888899999999999999


Q ss_pred             eCCCCHHHHHHHHHHHHHHHhh
Q 027234           79 TKPVRIEELKNIWQHVVRKRKN  100 (226)
Q Consensus        79 ~KP~~~~~L~~~l~~~~~~~~~  100 (226)
                      .||++.++|...+++++++...
T Consensus       106 ~kp~~~~~L~~~l~~~~~~~~~  127 (154)
T 2qsj_A          106 PKSADPQVLIHAVSLILEGEIF  127 (154)
T ss_dssp             CTTSCHHHHHHHHHHHHTTCCB
T ss_pred             eCCCCHHHHHHHHHHHHcCCEE
Confidence            9999999999999998865543

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

Probab=99.64  E-value=3.7e-16  Score=115.11  Aligned_cols=90  Identities=21%  Similarity=0.303  Sum_probs=72.5

Q ss_pred             CcEEE-EECCHHHHHHHHHhC-CCCceEEEEccCCCCCCHHHHHHHHhcCCCCcEEEEec--cCCHHHHHHHHhCCcceE
Q 027234            2 GFSVT-KCNRAEIALDMLRTN-KNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCA--HGSKEVVMKGVTHDACDY   77 (226)
Q Consensus         2 g~~V~-~~~~~~eal~~l~~~-~~~~DlVl~D~~mp~~dG~~l~~~l~~~~~~pvI~ls~--~~~~~~~~~a~~~ga~~y   77 (226)
                      ||.+. .+.++.+|++.+... .  ||+||+|+.||+++|+++++.++.....|+|++++  ..+.+...++++.|+++|
T Consensus        38 ~~~~v~~~~~~~~al~~l~~~~~--~dlvilD~~l~~~~g~~~~~~lr~~~~~~iiil~~~~~~~~~~~~~~~~~ga~~~  115 (145)
T 3kyj_B           38 DFKVVAQAANGQEALDKLAAQPN--VDLILLDIEMPVMDGMEFLRHAKLKTRAKICMLSSVAVSGSPHAARARELGADGV  115 (145)
T ss_dssp             TEEEEEEESSHHHHHHHHHHCTT--CCEEEECTTSCCCTTCHHHHHHHHHCCCEEC-CBSSCSTTSSHHHHHHHTTCSCC
T ss_pred             CceEEEEECCHHHHHHHHhcCCC--CCEEEEeCCCCCCCHHHHHHHHHhcCCCCeEEEEEeccCChHHHHHHHhCCCCEE
Confidence            67754 899999999999886 5  99999999999999999999998655689999987  556677889999999999


Q ss_pred             EeCCCCHHHHHHHHHH
Q 027234           78 LTKPVRIEELKNIWQH   93 (226)
Q Consensus        78 l~KP~~~~~L~~~l~~   93 (226)
                      |.||++.++|...++.
T Consensus       116 l~KP~~~~~l~~~i~~  131 (145)
T 3kyj_B          116 VAKPSGTVSHDLEEKT  131 (145)
T ss_dssp             CBCCCSCC------CT
T ss_pred             EeCCCCHHHHHHHHHH
Confidence            9999997666555443

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

Probab=99.64  E-value=2.2e-15  Score=108.77  Aligned_cols=95  Identities=23%  Similarity=0.452  Sum_probs=84.7

Q ss_pred             CCcEEEEECCHHHHHHHHHhC-CCCceEEEEccCCCC-CCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceE
Q 027234            1 MGFSVTKCNRAEIALDMLRTN-KNGYDIVISDVHMPD-MDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDY   77 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~-~~~~DlVl~D~~mp~-~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~y   77 (226)
                      .||.|..+.++.+|++.+... .  ||+||+|+.||+ ++|+++++.++ ..+.+|+|++|+..+.+....++..|  +|
T Consensus        28 ~g~~v~~~~~~~~a~~~l~~~~~--~dlvi~d~~l~~~~~g~~~~~~l~~~~~~~~ii~~s~~~~~~~~~~~~~~~--~~  103 (132)
T 2rdm_A           28 AGFLVTAVSSGAKAIEMLKSGAA--IDGVVTDIRFCQPPDGWQVARVAREIDPNMPIVYISGHAALEWASNGVPDS--II  103 (132)
T ss_dssp             TTCEEEEESSHHHHHHHHHTTCC--CCEEEEESCCSSSSCHHHHHHHHHHHCTTCCEEEEESSCCTTHHHHSCTTC--EE
T ss_pred             cCCEEEEECCHHHHHHHHHcCCC--CCEEEEeeeCCCCCCHHHHHHHHHhcCCCCCEEEEeCCccHHHHHhhcCCc--ce
Confidence            479999999999999999885 5  999999999997 99999999997 45689999999999888888887776  79


Q ss_pred             EeCCCCHHHHHHHHHHHHHHHh
Q 027234           78 LTKPVRIEELKNIWQHVVRKRK   99 (226)
Q Consensus        78 l~KP~~~~~L~~~l~~~~~~~~   99 (226)
                      |.||++.++|...++++..+..
T Consensus       104 l~kP~~~~~l~~~i~~~~~~~~  125 (132)
T 2rdm_A          104 LEKPFTSAQLITAVSQLLNARE  125 (132)
T ss_dssp             EESSCCHHHHHHHHHHHHHTTC
T ss_pred             EeCCCCHHHHHHHHHHHHhcCC
Confidence            9999999999999999886544

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

Probab=99.64  E-value=5.7e-16  Score=113.41  Aligned_cols=94  Identities=18%  Similarity=0.318  Sum_probs=79.1

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhc------CCCCcEEEEeccCCHHHHHHHHhCCc
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGL------EMDLPVIMMCAHGSKEVVMKGVTHDA   74 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~------~~~~pvI~ls~~~~~~~~~~a~~~ga   74 (226)
                      .||.|..+.++.+|++.+....  ||+||+|+.||+++|+++++.++.      .+.+|+|++|+.......   ...|+
T Consensus        33 ~~~~v~~~~~~~~al~~l~~~~--~dlvllD~~lp~~~g~~~~~~l~~~~~~~~~~~~~ii~~s~~~~~~~~---~~~g~  107 (140)
T 3c97_A           33 CTNDITVVTNGLQALQAYQNRQ--FDVIIMDIQMPVMDGLEAVSEIRNYERTHNTKRASIIAITADTIDDDR---PGAEL  107 (140)
T ss_dssp             TCSEEEEESSHHHHHHHHHHSC--CSEEEECTTCCSSCHHHHHHHHHHHHHHHTCCCCCCEEEESSCCSCCC---CCSSC
T ss_pred             cCCceEEECCHHHHHHHHhcCC--CCEEEEeCCCCCCcHHHHHHHHHhhhhhcCCCceEEEEEeCccchhHH---HhCCh
Confidence            3788999999999999998866  999999999999999999999974      367899999986654332   27899


Q ss_pred             ceEEeCCCCHHHHHHHHHHHHHHHh
Q 027234           75 CDYLTKPVRIEELKNIWQHVVRKRK   99 (226)
Q Consensus        75 ~~yl~KP~~~~~L~~~l~~~~~~~~   99 (226)
                      ++||.||++.++|..++++++.+..
T Consensus       108 ~~~l~KP~~~~~L~~~i~~~~~~~~  132 (140)
T 3c97_A          108 DEYVSKPLNPNQLRDVVLTCHSEGA  132 (140)
T ss_dssp             SEEEESSCCHHHHHHHHHHHHC---
T ss_pred             hheEeCCCCHHHHHHHHHHHhCCCC
Confidence            9999999999999999999876543

>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=99.63  E-value=2.2e-15  Score=118.75  Aligned_cols=91  Identities=25%  Similarity=0.378  Sum_probs=83.9

Q ss_pred             EEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhc-CCCCcEEEEeccCCHHHHHHHHhCCcceEEeCCC
Q 027234            4 SVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGL-EMDLPVIMMCAHGSKEVVMKGVTHDACDYLTKPV   82 (226)
Q Consensus         4 ~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~-~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~KP~   82 (226)
                      .|..+.++.+|++.+  ..  ||+||+|+.||+++|+++++.++. .+.+|||++|+..+.+....++..||++||.||+
T Consensus        27 ~v~~~~~~~~al~~~--~~--~dlvllD~~lp~~~g~~~~~~lr~~~~~~~ii~lt~~~~~~~~~~~~~~ga~~~l~Kp~  102 (220)
T 1p2f_A           27 RVKTFLTGEDFLNDE--EA--FHVVVLDVMLPDYSGYEICRMIKETRPETWVILLTLLSDDESVLKGFEAGADDYVTKPF  102 (220)
T ss_dssp             EEEEESSHHHHHHCC--SC--CSEEEEESBCSSSBHHHHHHHHHHHCTTSEEEEEESCCSHHHHHHHHHHTCSEEEESSC
T ss_pred             CEEEECCHHHHHHhc--CC--CCEEEEeCCCCCCCHHHHHHHHHhcCCCCcEEEEEcCCCHHHHHHHHHcCCCEEEECCC
Confidence            688999999999877  44  999999999999999999999984 4789999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHHH
Q 027234           83 RIEELKNIWQHVVRKR   98 (226)
Q Consensus        83 ~~~~L~~~l~~~~~~~   98 (226)
                      +.++|...++.++++.
T Consensus       103 ~~~~L~~~i~~~~~~~  118 (220)
T 1p2f_A          103 NPEILLARVKRFLERE  118 (220)
T ss_dssp             CHHHHHHHHHHHHHHC
T ss_pred             CHHHHHHHHHHHHccc
Confidence            9999999999988753

>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=99.62  E-value=1.7e-17  Score=118.50  Aligned_cols=95  Identities=31%  Similarity=0.532  Sum_probs=86.3

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||.|..+.++.++++.+....  ||+||+|+.||+++|+++++.++ ..+.+|+|++|+..+.+....++..|+++|+.
T Consensus        26 ~~~~v~~~~~~~~~~~~~~~~~--~dlvi~d~~~~~~~g~~~~~~l~~~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~  103 (124)
T 1dc7_A           26 AGLTCTTFENGNEVLAALASKT--PDVLLSDIRMPGMDGLALLKQIKQRHPMLPVIIMTAHSDLDAAVSAYQQGAFDYLP  103 (124)
T ss_dssp             TTCCCEECCCTTHHHHHSSSCC--CSCEEECSCSSHHHHCSTHHHHHHHCTTSCCCCBCCSTTSTTTTSSCTTCCCCCBC
T ss_pred             CCcEEEEeCCHHHHHHHHhcCC--CCEEEEeeecCCCCHHHHHHHHHhhCCCCCEEEEecCCCHHHHHHHHhcCcceEee
Confidence            3788899999999999998765  99999999999999999999997 45789999999998888888999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHH
Q 027234           80 KPVRIEELKNIWQHVVRK   97 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~   97 (226)
                      ||++.++|...++++++.
T Consensus       104 kp~~~~~l~~~i~~~~~~  121 (124)
T 1dc7_A          104 KPFDIDEAVALVERAISH  121 (124)
T ss_dssp             SSCCHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHh
Confidence            999999999999988754

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

Probab=99.62  E-value=4.4e-16  Score=112.79  Aligned_cols=94  Identities=21%  Similarity=0.315  Sum_probs=83.2

Q ss_pred             CcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCH-----HHHHHHHhCCcc
Q 027234            2 GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSK-----EVVMKGVTHDAC   75 (226)
Q Consensus         2 g~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~-----~~~~~a~~~ga~   75 (226)
                      |+.|..++++.++++.+..  . ||+||+|+.||+++|+++++.++ ..+.+|+|++|+..+.     +....+++.|++
T Consensus        27 ~~~v~~~~~~~~~~~~~~~--~-~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~ii~~s~~~~~~~~~~~~~~~~~~~g~~  103 (135)
T 3eqz_A           27 FGNVEAFQHPRAFLTLSLN--K-QDIIILDLMMPDMDGIEVIRHLAEHKSPASLILISGYDSGVLHSAETLALSCGLNVI  103 (135)
T ss_dssp             CSCEEEESCHHHHTTSCCC--T-TEEEEEECCTTTTHHHHHHHHHHHTTCCCEEEEEESSCHHHHHHHHHHHHHTTCEEE
T ss_pred             cceeeeecCHHHHHHhhcc--C-CCEEEEeCCCCCCCHHHHHHHHHhCCCCCCEEEEEeccchhHHHHHHHHHHcCCCcc
Confidence            5678999999999988764  3 99999999999999999999997 5578999999998875     677789999999


Q ss_pred             eEEeCCCCHHHHHHHHHHHHHHH
Q 027234           76 DYLTKPVRIEELKNIWQHVVRKR   98 (226)
Q Consensus        76 ~yl~KP~~~~~L~~~l~~~~~~~   98 (226)
                      +||.||++.++|...++++..+.
T Consensus       104 ~~l~KP~~~~~l~~~l~~~~~~~  126 (135)
T 3eqz_A          104 NTFTKPINTEVLTCFLTSLSNRQ  126 (135)
T ss_dssp             EEEESSCCHHHHHHHHHHHSCCC
T ss_pred             eeeCCCCCHHHHHHHHHHHHhhc
Confidence            99999999999999999987544

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

Probab=99.61  E-value=5e-15  Score=107.82  Aligned_cols=91  Identities=19%  Similarity=0.307  Sum_probs=83.4

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcCC-CCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEM-DLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~~-~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||.|..+.++.+|++.+....  ||+||    ||+++|+++++.++..+ .+|||++|+..+.+....++..|+++||.
T Consensus        41 ~g~~v~~~~~~~~al~~l~~~~--~dlvi----~~~~~g~~~~~~l~~~~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~  114 (137)
T 2pln_A           41 KGFMADVTESLEDGEYLMDIRN--YDLVM----VSDKNALSFVSRIKEKHSSIVVLVSSDNPTSEEEVHAFEQGADDYIA  114 (137)
T ss_dssp             TTCEEEEESCHHHHHHHHHHSC--CSEEE----ECSTTHHHHHHHHHHHSTTSEEEEEESSCCHHHHHHHHHTTCSEEEE
T ss_pred             cCcEEEEeCCHHHHHHHHHcCC--CCEEE----EcCccHHHHHHHHHhcCCCccEEEEeCCCCHHHHHHHHHcCCceeee
Confidence            4899999999999999999876  99999    99999999999997447 89999999999999999999999999999


Q ss_pred             CCC-CHHHHHHHHHHHHHH
Q 027234           80 KPV-RIEELKNIWQHVVRK   97 (226)
Q Consensus        80 KP~-~~~~L~~~l~~~~~~   97 (226)
                      ||+ +.++|...+++++.+
T Consensus       115 kP~~~~~~l~~~i~~~~~~  133 (137)
T 2pln_A          115 KPYRSIKALVARIEARLRF  133 (137)
T ss_dssp             SSCSCHHHHHHHHHHHTC-
T ss_pred             CCCCCHHHHHHHHHHHHhh
Confidence            999 999999999988654

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

Probab=99.61  E-value=3e-15  Score=112.88  Aligned_cols=90  Identities=22%  Similarity=0.355  Sum_probs=76.9

Q ss_pred             EEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcCCCCcEEEEeccCCHH--HHHHHHhCCcceEEeCCC
Q 027234            5 VTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKE--VVMKGVTHDACDYLTKPV   82 (226)
Q Consensus         5 V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~~~~pvI~ls~~~~~~--~~~~a~~~ga~~yl~KP~   82 (226)
                      |..+.++.+|++.+....  ||+||+|+.||+++|+++++.++....+|+|++|+..+..  ...+++..||++||.||+
T Consensus        54 v~~~~~~~~al~~l~~~~--~dlvilD~~l~~~~g~~l~~~lr~~~~~~ii~~s~~~~~~~~~~~~~~~~ga~~~l~KP~  131 (164)
T 3t8y_A           54 VGFAKDGLEAVEKAIELK--PDVITMDIEMPNLNGIEALKLIMKKAPTRVIMVSSLTEEGAAITIEALRNGAVDFITKPH  131 (164)
T ss_dssp             EEEESSHHHHHHHHHHHC--CSEEEECSSCSSSCHHHHHHHHHHHSCCEEEEEESSCCTTCHHHHHHHHTTCCEEEECSS
T ss_pred             EEecCCHHHHHHHhccCC--CCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEecCCccchHHHHHHHHcCcCEEEeCCC
Confidence            458999999999999876  9999999999999999999999854449999999877653  677899999999999999


Q ss_pred             C---------HHHHHHHHHHHHH
Q 027234           83 R---------IEELKNIWQHVVR   96 (226)
Q Consensus        83 ~---------~~~L~~~l~~~~~   96 (226)
                      +         .++|...+++++.
T Consensus       132 ~~~~l~~r~~~~~l~~~i~~~~~  154 (164)
T 3t8y_A          132 GSISLTFRQVAPELLEKIRQAMN  154 (164)
T ss_dssp             SSSCGGGGGGHHHHHHHHHHHTT
T ss_pred             CHHHHHHHhhhHHHHHHHHHHhC
Confidence            9         5666666666553

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

Probab=99.61  E-value=1.1e-15  Score=118.44  Aligned_cols=92  Identities=14%  Similarity=0.205  Sum_probs=81.6

Q ss_pred             CcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcC-CCCcEEEEeccCCHHHHHHHHhCCcceEEeC
Q 027234            2 GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLE-MDLPVIMMCAHGSKEVVMKGVTHDACDYLTK   80 (226)
Q Consensus         2 g~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~-~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~K   80 (226)
                      ||.|..+.++.+|+    ...  ||+||+|+.||+++|+ +++.++.. +.+|||++|+..+.+....+++.|+++||.|
T Consensus        36 g~~v~~~~~~~~al----~~~--~dlvl~D~~mp~~~g~-l~~~~~~~~~~~~ii~lt~~~~~~~~~~a~~~ga~~~l~K  108 (196)
T 1qo0_D           36 GCSVRQCWPPPEAF----DVP--VDVVFTSIFQNRHHDE-IAALLAAGTPRTTLVALVEYESPAVLSQIIELECHGVITQ  108 (196)
T ss_dssp             TCEEEEECSCCSSC----SSC--CSEEEEECCSSTHHHH-HHHHHHHSCTTCEEEEEECCCSHHHHHHHHHHTCSEEEES
T ss_pred             CCeEEEecCchhhC----CCC--CCEEEEeCCCCccchH-HHHHHhccCCCCCEEEEEcCCChHHHHHHHHcCCCeeEec
Confidence            78888888887766    334  9999999999999999 88888765 8899999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHhh
Q 027234           81 PVRIEELKNIWQHVVRKRKN  100 (226)
Q Consensus        81 P~~~~~L~~~l~~~~~~~~~  100 (226)
                      |++.++|...++.++.....
T Consensus       109 P~~~~~L~~~l~~~~~~~~~  128 (196)
T 1qo0_D          109 PLDAHRVLPVLVSARRISEE  128 (196)
T ss_dssp             SCCGGGHHHHHHHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHHHHHHH
Confidence            99999999999988765543

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

Probab=99.59  E-value=2.7e-15  Score=105.65  Aligned_cols=90  Identities=21%  Similarity=0.226  Sum_probs=81.1

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcC---CCCcEEEEeccCCHHHHHHHHhCCcceE
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLE---MDLPVIMMCAHGSKEVVMKGVTHDACDY   77 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~---~~~pvI~ls~~~~~~~~~~a~~~ga~~y   77 (226)
                      .||+|..+.++.++++.+....  ||+||+|+.||+++|+++++.++..   +.+|+|++|+..+..   .++..|+++|
T Consensus        24 ~g~~v~~~~~~~~~~~~l~~~~--~dlii~d~~~~~~~~~~~~~~l~~~~~~~~~~ii~~~~~~~~~---~~~~~g~~~~   98 (119)
T 2j48_A           24 AGFKVIWLVDGSTALDQLDLLQ--PIVILMAWPPPDQSCLLLLQHLREHQADPHPPLVLFLGEPPVD---PLLTAQASAI   98 (119)
T ss_dssp             TTCEEEEESCHHHHHHHHHHHC--CSEEEEECSTTCCTHHHHHHHHHHTCCCSSCCCEEEESSCCSS---HHHHHHCSEE
T ss_pred             CCcEEEEecCHHHHHHHHHhcC--CCEEEEecCCCCCCHHHHHHHHHhccccCCCCEEEEeCCCCch---hhhhcCHHHh
Confidence            4899999999999999999876  9999999999999999999999744   679999999887766   8899999999


Q ss_pred             EeCCCCHHHHHHHHHHHH
Q 027234           78 LTKPVRIEELKNIWQHVV   95 (226)
Q Consensus        78 l~KP~~~~~L~~~l~~~~   95 (226)
                      +.||++.++|...+++++
T Consensus        99 l~kp~~~~~l~~~l~~~~  116 (119)
T 2j48_A           99 LSKPLDPQLLLTTLQGLC  116 (119)
T ss_dssp             CSSCSTTHHHHHHHHTTC
T ss_pred             ccCCCCHHHHHHHHHHHh
Confidence            999999999998887654

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

Probab=99.56  E-value=9.4e-15  Score=115.29  Aligned_cols=90  Identities=19%  Similarity=0.315  Sum_probs=83.7

Q ss_pred             CcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcCC-CCcEEEEeccCCHHHHHHHHhCCcceEEeC
Q 027234            2 GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEM-DLPVIMMCAHGSKEVVMKGVTHDACDYLTK   80 (226)
Q Consensus         2 g~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~~-~~pvI~ls~~~~~~~~~~a~~~ga~~yl~K   80 (226)
                      ||.|..+.++.+|++.+....  ||+||    ||+++|+++++.++..+ .+|||++|+..+.+....++..||++||.|
T Consensus        24 g~~v~~~~~~~~al~~l~~~~--~dlvi----lp~~~g~~~~~~lr~~~~~~~ii~lt~~~~~~~~~~~~~~Ga~~~l~K   97 (223)
T 2hqr_A           24 GFMADVTESLEDGEYLMDIRN--YDLVM----VSDKNALSFVSRIKEKHSSIVVLVSSDNPTSEEEVHAFEQGADDYIAK   97 (223)
T ss_dssp             TCCEEEESSHHHHHHHHTTSC--CSEEE----ECCTTHHHHHHHHHHHCTTSEEEEEESSCCHHHHHHHHHHTCSEEEET
T ss_pred             CcEEEEECCHHHHHHHHhcCC--CCEEE----eCCCCHHHHHHHHHhCCCCCcEEEEECCCCHHHHHHHHHcCCCEEEEC
Confidence            789999999999999998866  99999    99999999999997446 899999999999999999999999999999


Q ss_pred             CC-CHHHHHHHHHHHHHH
Q 027234           81 PV-RIEELKNIWQHVVRK   97 (226)
Q Consensus        81 P~-~~~~L~~~l~~~~~~   97 (226)
                      |+ +.++|...++.++++
T Consensus        98 p~~~~~~L~~~i~~~~~~  115 (223)
T 2hqr_A           98 PYRSIKALVARIEARLRF  115 (223)
T ss_dssp             TCSCTHHHHHHHHHHTSS
T ss_pred             CCCCHHHHHHHHHHHhcc
Confidence            99 999999999998754

>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=99.55  E-value=3.2e-15  Score=109.02  Aligned_cols=90  Identities=20%  Similarity=0.247  Sum_probs=78.1

Q ss_pred             CCcEEEEECCHHHHHHHHHh-CCCCceEEEEccCCCCCCHHHHHHHHhc-CCCCcEEEEe-ccCCHHHHHHHHhCCcceE
Q 027234            1 MGFSVTKCNRAEIALDMLRT-NKNGYDIVISDVHMPDMDGFKLLELVGL-EMDLPVIMMC-AHGSKEVVMKGVTHDACDY   77 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~-~~~~~DlVl~D~~mp~~dG~~l~~~l~~-~~~~pvI~ls-~~~~~~~~~~a~~~ga~~y   77 (226)
                      .||.|..+.++.+|++.+.. ..  ||+||+|+.||+++|+++++.++. .+.+|+|++| +..+... .+++   +++|
T Consensus        38 ~g~~v~~~~~~~~al~~l~~~~~--~dlvilD~~l~~~~g~~~~~~l~~~~~~~~ii~ls~~~~~~~~-~~~~---~~~~  111 (138)
T 2b4a_A           38 LGAEVTVHPSGSAFFQHRSQLST--CDLLIVSDQLVDLSIFSLLDIVKEQTKQPSVLILTTGRHELIE-SSEH---NLSY  111 (138)
T ss_dssp             TTCEEEEESSHHHHHHTGGGGGS--CSEEEEETTCTTSCHHHHHHHHTTSSSCCEEEEEESCC--CCC-CSSS---CEEE
T ss_pred             cCCEEEEeCCHHHHHHHHHhCCC--CCEEEEeCCCCCCCHHHHHHHHHhhCCCCCEEEEECCCCCHHH-HHHH---HHhe
Confidence            47999999999999999988 76  999999999999999999999984 5689999999 8776665 5665   9999


Q ss_pred             EeCCCCHHHHHHHHHHHHH
Q 027234           78 LTKPVRIEELKNIWQHVVR   96 (226)
Q Consensus        78 l~KP~~~~~L~~~l~~~~~   96 (226)
                      |.||++.++|...+++++.
T Consensus       112 l~KP~~~~~L~~~i~~~~~  130 (138)
T 2b4a_A          112 LQKPFAISELRAAIDYHKP  130 (138)
T ss_dssp             EESSCCHHHHHHHHHHTCC
T ss_pred             eeCCCCHHHHHHHHHHHHH
Confidence            9999999999999987654

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

Probab=99.52  E-value=5.5e-14  Score=118.79  Aligned_cols=94  Identities=28%  Similarity=0.422  Sum_probs=81.3

Q ss_pred             CcE-EEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcCCCCcEEEEeccCCH--HHHHHHHhCCcceEE
Q 027234            2 GFS-VTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSK--EVVMKGVTHDACDYL   78 (226)
Q Consensus         2 g~~-V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~~~~pvI~ls~~~~~--~~~~~a~~~ga~~yl   78 (226)
                      ||+ |..+.++.+|++.+....  ||+|++|+.||++||+++++.|+....+|||++|+..+.  +...++++.|+++||
T Consensus        28 g~~vv~~a~~~~eAl~~l~~~~--pDlVllDi~mp~~dGlell~~l~~~~p~pVIvlS~~~~~~~~~~~~al~~Ga~d~l  105 (349)
T 1a2o_A           28 DMEMVATAPDPLVARDLIKKFN--PDVLTLDVEMPRMDGLDFLEKLMRLRPMPVVMVSSLTGKGSEVTLRALELGAIDFV  105 (349)
T ss_dssp             TEEEEEEESSHHHHHHHHHHHC--CSEEEEECCCSSSCHHHHHHHHHHSSCCCEEEEECCTHHHHHHHHHHHHHTCCEEE
T ss_pred             CcEEEEEeCCHHHHHHHHhccC--CCEEEEECCCCCCCHHHHHHHHHhcCCCcEEEEECCCcccHHHHHHHHhCCceEEE
Confidence            678 569999999999999876  999999999999999999999985444999999998775  458899999999999


Q ss_pred             eCCCCH---------HHHHHHHHHHHHH
Q 027234           79 TKPVRI---------EELKNIWQHVVRK   97 (226)
Q Consensus        79 ~KP~~~---------~~L~~~l~~~~~~   97 (226)
                      .||++.         ++|...++.+.+.
T Consensus       106 ~KP~~~~~~~l~~~~~~L~~~I~~~~~~  133 (349)
T 1a2o_A          106 TKPQLGIREGMLAYSEMIAEKVRTAARA  133 (349)
T ss_dssp             ECSSSSCSSCHHHHHHHHHHHHHHHHHC
T ss_pred             ECCCCccchhHHHHHHHHHHHHHHHHhh
Confidence            999983         7777777776553

>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=99.46  E-value=5.7e-14  Score=113.90  Aligned_cols=80  Identities=18%  Similarity=0.273  Sum_probs=66.1

Q ss_pred             CcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEeCC
Q 027234            2 GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTKP   81 (226)
Q Consensus         2 g~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~KP   81 (226)
                      ||.|..+ ++.+++..+....  ||+||+|++||++||+++++.++.. .+|||++|+..+.+...++++.||++||.||
T Consensus        29 ~~~v~~~-~~~~~~~~~~~~~--~dlvllD~~mP~~~G~~~~~~lr~~-~~pvi~lt~~~~~~~~~~a~~~Ga~dyl~Kp  104 (259)
T 3luf_A           29 GLEIDAF-DTLEGARHCQGDE--YVVALVDLTLPDAPSGEAVKVLLER-GLPVVILTADISEDKREAWLEAGVLDYVMKD  104 (259)
T ss_dssp             CCEEEEE-SSTGGGTTCCTTT--EEEEEEESCBTTBTTSHHHHHHHHT-TCCEEEEECC-CHHHHHHHHHTTCCEEEECS
T ss_pred             CeEEEEe-ChHHHHHHhhcCC--CcEEEEeCCCCCCCHHHHHHHHHhC-CCCEEEEEccCCHHHHHHHHHCCCcEEEeCC
Confidence            5666544 5556665555544  9999999999999999999999753 6899999999999999999999999999999


Q ss_pred             CCHH
Q 027234           82 VRIE   85 (226)
Q Consensus        82 ~~~~   85 (226)
                      +...
T Consensus       105 ~~~~  108 (259)
T 3luf_A          105 SRHS  108 (259)
T ss_dssp             SHHH
T ss_pred             chhH
Confidence            6543

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

Probab=99.44  E-value=8.8e-14  Score=128.38  Aligned_cols=97  Identities=9%  Similarity=0.123  Sum_probs=86.6

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCC----CCHHHHHHHHh-cCCCCcEEEEeccCC-HHHHHHHHhCCc
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPD----MDGFKLLELVG-LEMDLPVIMMCAHGS-KEVVMKGVTHDA   74 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~----~dG~~l~~~l~-~~~~~pvI~ls~~~~-~~~~~~a~~~ga   74 (226)
                      .||+|..+.++++|+..+.+. ..||+||+|++||+    +||+++++.|+ ..+.+|||++|+..+ .+....++..||
T Consensus        31 ~g~~v~~a~~g~~al~~~~~~-~~~d~vilDi~lp~~~~~~~G~~ll~~iR~~~~~iPIi~lTa~~~~~~d~~~~l~~ga  109 (755)
T 2vyc_A           31 QNVTVIKSTSFDDGFAILSSN-EAIDCLMFSYQMEHPDEHQNVRQLIGKLHERQQNVPVFLLGDREKALAAMDRDLLELV  109 (755)
T ss_dssp             TTCEEEEESSHHHHHHHHTTT-CCCSEEEEECCCCSHHHHHHHHHHHHHHHHHSTTCCEEEEECHHHHHHTCSHHHHHHC
T ss_pred             CCCEEEEECCHHHHHHHHhcC-CCCcEEEEeCCCCcccccccHHHHHHHHHHhCCCCCEEEEecCCcchhhccHhHhhcC
Confidence            389999999999999999874 23999999999999    99999999998 456899999999877 677888899999


Q ss_pred             ceEEeCCCCHHH-HHHHHHHHHHHH
Q 027234           75 CDYLTKPVRIEE-LKNIWQHVVRKR   98 (226)
Q Consensus        75 ~~yl~KP~~~~~-L~~~l~~~~~~~   98 (226)
                      +||+.||++..+ |...|+.++++.
T Consensus       110 ddyi~kpf~~~efl~~ri~a~~rr~  134 (755)
T 2vyc_A          110 DEFAWILEDTADFIAGRAVAAMTRY  134 (755)
T ss_dssp             SEEEETTTSCHHHHHHHHHHHHHHH
T ss_pred             CceEeCCCCCHHHHHHHHHHHHHHh
Confidence            999999999999 888898888664

>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=99.36  E-value=5.5e-13  Score=105.69  Aligned_cols=92  Identities=21%  Similarity=0.347  Sum_probs=78.8

Q ss_pred             cEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhc-CCCCcEEEEeccCCHHHHHHHHhCCcceEEeCC
Q 027234            3 FSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGL-EMDLPVIMMCAHGSKEVVMKGVTHDACDYLTKP   81 (226)
Q Consensus         3 ~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~-~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~KP   81 (226)
                      +.|..+.++.+|++.+....  ||+||+|+.||+++|+++++.++. .+..++++++.....+...++++.|+++|+.||
T Consensus         6 ~~v~~~~~~~~a~~~~~~~~--~dlvl~D~~~p~~~g~~~~~~l~~~~~~~~i~vi~~~~~~~~~~~~~~~Ga~~~l~kp   83 (237)
T 3cwo_X            6 LIVDDATNGREAVEKYKELK--PDIVTMDITMPEMNGIDAIKEIMKIDPNAKIIVCSAMGQQAMVIEAIKAGAKDFIVNT   83 (237)
T ss_dssp             EEEECCCSSSTTHHHHHHHC--CSCEEEECCSTTSSHHHHHHHHHHHSSSCCEEEECCSSTHHHHHHHHHTTCCEEEESH
T ss_pred             EEEEECCCHHHHHHHHHhcC--CCEEEEeCCCCCCCHHHHHHHHHHhCCCCCEEEEECCCCHHHHHHHHHCCHHheEeCC
Confidence            56778899999999999876  999999999999999999999873 456677777777778889999999999999999


Q ss_pred             --CCHHHHHHHHHHHHH
Q 027234           82 --VRIEELKNIWQHVVR   96 (226)
Q Consensus        82 --~~~~~L~~~l~~~~~   96 (226)
                        ++..++...+.+.+.
T Consensus        84 ~~~~~~~l~~~i~~~~~  100 (237)
T 3cwo_X           84 AAVENPSLITQIAQTFG  100 (237)
T ss_dssp             HHHHCTHHHHHHHHHHT
T ss_pred             cccChHHHHHHHHHHhC
Confidence              777788777776654

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

Probab=98.96  E-value=1.3e-08  Score=88.49  Aligned_cols=96  Identities=19%  Similarity=0.307  Sum_probs=79.8

Q ss_pred             cEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcC---CCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            3 FSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLE---MDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         3 ~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~---~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      +.+....++.+++ ......  ||++++|..||+|+|+++++.++..   ..+|++++|+.........++..|+++|+.
T Consensus       176 ~~~~~~~~~~~~~-~~~~~~--~dlil~D~~mp~~dG~~~~~~ir~~~~~~~~pii~lt~~~~~~~~~~~l~~Ga~d~~~  252 (459)
T 1w25_A          176 HRPVIESDPEKAK-ISAGGP--VDLVIVNAAAKNFDGLRFTAALRSEERTRQLPVLAMVDPDDRGRMVKALEIGVNDILS  252 (459)
T ss_dssp             SEEEEECCHHHHH-HHHHSS--CSEEEEETTCSSSCHHHHHHHHHTSGGGTTCCEEEEECTTCHHHHHHHHHTTCCEEEE
T ss_pred             cceeeccCHHHHh-hhccCC--CCEEEEecCCCCCcHHHHHHHHHhCccccCCcEEEEcCCCchHHHHHHHhcccccccc
Confidence            4456677777776 334444  9999999999999999999999743   468999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHhhh
Q 027234           80 KPVRIEELKNIWQHVVRKRKNE  101 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~~~~~  101 (226)
                      ||++.+++...+..+.......
T Consensus       253 kp~~~~~l~~~v~~~~~~~~~~  274 (459)
T 1w25_A          253 RPIDPQELSARVKTQIQRKRYT  274 (459)
T ss_dssp             SSCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHHH
Confidence            9999999998888877655443

>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=97.48  E-value=0.00015  Score=66.44  Aligned_cols=93  Identities=16%  Similarity=0.172  Sum_probs=70.3

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||+|..+.++++|+..++++ ..+++||+|+.|+   +.++++.|+ .++++||++++............-.++++|+.
T Consensus        29 ~g~~V~~a~s~~Da~~~i~~~-~~i~avIld~d~~---~~~ll~~Ir~~~~~iPVFl~~~~~~~~~~~~~~~~~~~~~~~  104 (715)
T 3n75_A           29 LNFQIVYPNDRDDLLKLIENN-ARLCGVIFDWDKY---NLELCEEISKMNENLPLYAFANTYSTLDVSLNDLRLQISFFE  104 (715)
T ss_dssp             TTCEEECCSSHHHHHHHHHHC-TTEEEEEEEHHHH---HHHHHHHHHHHCTTCEEEEECCTTCCCCGGGTTSCCEEEEEC
T ss_pred             CCcEEEEeCCHHHHHHHHHhC-CCceEEEEecccc---HHHHHHHHHHhCCCCCEEEEecCCcccccchhhhhccCeEEE
Confidence            389999999999999999876 4589999999886   788999997 67899999998875433222112357899998


Q ss_pred             CCC-CHHHHHHHHHHHHHH
Q 027234           80 KPV-RIEELKNIWQHVVRK   97 (226)
Q Consensus        80 KP~-~~~~L~~~l~~~~~~   97 (226)
                      +.. +++.+...+.+..+.
T Consensus       105 ~~~~~~~~~~~~~~~~~~~  123 (715)
T 3n75_A          105 YALGAAEDIANKIKQTTDE  123 (715)
T ss_dssp             CCTTCHHHHHHHHHHHHHH
T ss_pred             eCCCCHHHHHHHHHHHHHH
Confidence            875 556655556555443

>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=97.21  E-value=0.0022  Score=49.76  Aligned_cols=82  Identities=16%  Similarity=0.201  Sum_probs=63.3

Q ss_pred             CHHHHHHHHHhCCCCceEEEEcc-CCCCCCH--HHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEE------eC
Q 027234           10 RAEIALDMLRTNKNGYDIVISDV-HMPDMDG--FKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYL------TK   80 (226)
Q Consensus        10 ~~~eal~~l~~~~~~~DlVl~D~-~mp~~dG--~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl------~K   80 (226)
                      +..+.+..+.... ..+++++++ .++.++|  .++++.++...++|+|.+++....+...++++.|+++++      .+
T Consensus       131 ~~~~~i~~~~~~~-~~~vli~~~~~~g~~~g~~~~~i~~~~~~~~~Pvia~~g~~~~~~~~~~~~~G~~~~~vg~a~~~~  209 (237)
T 3cwo_X          131 LLRDWVVEVEKRG-AGEILLTSIDRDGTKSGYDTEMIRFVRPLTTLPIIASGGAGKMEHFLEAFLAGADAALAASVFHFR  209 (237)
T ss_dssp             EHHHHHHHHHHHT-CSEEEEEETTTTTCCSCCCHHHHHHHGGGCCSCEEEESCCCSHHHHHHHHHHTCSEEEESHHHHTT
T ss_pred             CHHHHHHHHhhcC-CCeEEEEecCCCCccccccHHHHHHHHHhcCCCEEecCCCCCHHHHHHHHHcCcHHHhhhHHHHcC
Confidence            4556655555432 257899987 6677777  456777776678999999999999999999999999985      78


Q ss_pred             CCCHHHHHHHHH
Q 027234           81 PVRIEELKNIWQ   92 (226)
Q Consensus        81 P~~~~~L~~~l~   92 (226)
                      |++..++...++
T Consensus       210 ~~~~~~~~~~l~  221 (237)
T 3cwo_X          210 EIDVRELKEYLK  221 (237)
T ss_dssp             SSCHHHHHHHHH
T ss_pred             CCCHHHHHHHHH
Confidence            999998877543

>3lsg_A Two-component response regulator YESN; structural genomics, PSI-2, protein structure initiative, MCSG; 2.05A {Fusobacterium nucleatum}

Probab=96.15  E-value=0.0029  Score=43.04  Aligned_cols=40  Identities=18%  Similarity=0.007  Sum_probs=33.6

Q ss_pred             HHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCCC-CCCCCC
Q 027234          180 KILELMNIPGLTRENVASHLQKHRLYLSRLSGVS-PQQGNS  219 (226)
Q Consensus       180 ~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~~-~~~~~~  219 (226)
                      .|.+++..+.++++++|+++++|+++|+|+|+.. ++.+..
T Consensus        10 ~i~~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~~~g~s~~~   50 (103)
T 3lsg_A           10 IIEESYTDSQFTLSVLSEKLDLSSGYLSIMFKKNFGIPFQD   50 (103)
T ss_dssp             HHHHHTTCTTCCHHHHHHHTTCCHHHHHHHHHHHHSSCHHH
T ss_pred             HHHHHccCCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHH
Confidence            6888998889999999999999999999988754 554433

>2k9s_A Arabinose operon regulatory protein; activator, arabinose catabolism, carbohydrate metabolism, cytoplasm, DNA-binding, repressor, transcription; NMR {Escherichia coli}

Probab=95.48  E-value=0.0063  Score=41.62  Aligned_cols=41  Identities=20%  Similarity=0.058  Sum_probs=33.3

Q ss_pred             HHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCCC-CCCCCCC
Q 027234          180 KILELMNIPGLTRENVASHLQKHRLYLSRLSGVS-PQQGNSF  220 (226)
Q Consensus       180 ~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~~-~~~~~~~  220 (226)
                      .|.+++.++.++++++|+++++|+++|+|+|+.. ++.+..|
T Consensus        11 ~i~~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~~~G~s~~~~   52 (107)
T 2k9s_A           11 YISDHLADSNFDIASVAQHVCLSPSRLSHLFRQQLGISVLSW   52 (107)
T ss_dssp             HHHHTSSCSSCCHHHHHHHTTSCHHHHHHHHHHHHSSCHHHH
T ss_pred             HHHHHhccCCCCHHHHHHHHCCCHHHHHHHHHHHHCcCHHHH
Confidence            5888888679999999999999999999988753 5554433

>3mkl_A HTH-type transcriptional regulator GADX; PSI2, MCSG, structural genomics, protein structure initiativ midwest center for structural genomics; 2.15A {Escherichia coli}

Probab=95.37  E-value=0.0012  Score=46.35  Aligned_cols=40  Identities=15%  Similarity=0.010  Sum_probs=32.7

Q ss_pred             HHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCCCCCCCCCC
Q 027234          180 KILELMNIPGLTRENVASHLQKHRLYLSRLSGVSPQQGNSF  220 (226)
Q Consensus       180 ~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~~~~~~~~~  220 (226)
                      .|.+++.. .++++++|.++++|+++|+|+|+..++.+..|
T Consensus        15 ~i~~~~~~-~~~~~~lA~~~~~S~~~l~r~fk~~G~s~~~~   54 (120)
T 3mkl_A           15 VINNNIAH-EWTLARIASELLMSPSLLKKKLREEETSYSQL   54 (120)
T ss_dssp             HHHTSTTS-CCCHHHHHHHTTCCHHHHHHHHHHTTCCHHHH
T ss_pred             HHHHhccC-CCCHHHHHHHHCcCHHHHHHHHHHcCCCHHHH
Confidence            57777776 89999999999999999999988765554443

>3oou_A LIN2118 protein; protein structure initiative, PSI-2, structural genomics, MI center for structural genomics, MCSG, unknown function; HET: BTB; 1.57A {Listeria innocua}

Probab=95.22  E-value=0.006  Score=41.80  Aligned_cols=39  Identities=15%  Similarity=0.250  Sum_probs=32.0

Q ss_pred             HHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCCC-CCCCCC
Q 027234          180 KILELMNIPGLTRENVASHLQKHRLYLSRLSGVS-PQQGNS  219 (226)
Q Consensus       180 ~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~~-~~~~~~  219 (226)
                      .|.+++.. .++++++|+++++|+++|+|+|+.. ++.+..
T Consensus        13 ~i~~~~~~-~~~~~~lA~~~~~S~~~l~r~fk~~~G~s~~~   52 (108)
T 3oou_A           13 YITEHFSE-GMSLKTLGNDFHINAVYLGQLFQKEMGEHFTD   52 (108)
T ss_dssp             HHHHHTTS-CCCHHHHHHHHTSCHHHHHHHHHHHHSSCHHH
T ss_pred             HHHHHhcC-CCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHH
Confidence            58888877 8999999999999999999988654 554433

>3mn2_A Probable ARAC family transcriptional regulator; structural genomics, PSI-2, protein structure initiative; 1.80A {Rhodopseudomonas palustris}

Probab=95.19  E-value=0.011  Score=40.35  Aligned_cols=40  Identities=13%  Similarity=-0.115  Sum_probs=32.1

Q ss_pred             HHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCCC-CCCCCCC
Q 027234          180 KILELMNIPGLTRENVASHLQKHRLYLSRLSGVS-PQQGNSF  220 (226)
Q Consensus       180 ~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~~-~~~~~~~  220 (226)
                      .|.+++.. .++++++|+++++|+++|+|+|+.. ++.+..|
T Consensus        10 ~i~~~~~~-~~~~~~lA~~~~~s~~~l~r~fk~~~G~s~~~~   50 (108)
T 3mn2_A           10 YIEANWMR-PITIEKLTALTGISSRGIFKAFQRSRGYSPMAF   50 (108)
T ss_dssp             HHHHHTTS-CCCHHHHHHHHTCCHHHHHHHHHHHTSSCHHHH
T ss_pred             HHHHcccC-CCCHHHHHHHHCCCHHHHHHHHHHHhCcCHHHH
Confidence            58888877 5999999999999999999988753 5554433

>3oio_A Transcriptional regulator (ARAC-type DNA-binding containing proteins); PSI-2, midwest center for structural genomics; 1.65A {Chromobacterium violaceum}

Probab=95.01  E-value=0.0081  Score=41.50  Aligned_cols=40  Identities=15%  Similarity=0.102  Sum_probs=31.8

Q ss_pred             HHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCCC-CCCCCCC
Q 027234          180 KILELMNIPGLTRENVASHLQKHRLYLSRLSGVS-PQQGNSF  220 (226)
Q Consensus       180 ~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~~-~~~~~~~  220 (226)
                      .|.+++.. .++++++|.++++|+++|+|+|+.. ++.+..|
T Consensus        15 ~i~~~~~~-~~~~~~lA~~~~~S~~~l~r~fk~~~G~s~~~~   55 (113)
T 3oio_A           15 LMEANIEE-PLSTDDIAYYVGVSRRQLERLFKQYLGTVPSKY   55 (113)
T ss_dssp             HHHTCSSS-CCCHHHHHHHHTSCHHHHHHHHHHHTSSCHHHH
T ss_pred             HHHhhhcC-CCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHHH
Confidence            48788877 4999999999999999999987654 5554433

>1wv2_A Thiazole moeity, thiazole biosynthesis protein THIG; structural genomics, protein structure initiative, PSI; 2.90A {Pseudomonas aeruginosa} SCOP: c.1.31.1

Probab=94.83  E-value=0.37  Score=38.30  Aligned_cols=91  Identities=14%  Similarity=0.085  Sum_probs=64.9

Q ss_pred             CcEEE--EECCHHHHHHHHHhCCCCceEEEEccCCCC-----CCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCc
Q 027234            2 GFSVT--KCNRAEIALDMLRTNKNGYDIVISDVHMPD-----MDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDA   74 (226)
Q Consensus         2 g~~V~--~~~~~~eal~~l~~~~~~~DlVl~D~~mp~-----~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga   74 (226)
                      ||.|.  +.+|...|-.+.. ..  +++| +.+..|-     ...+++++.+++..++|||+=.+-...+.+..++++|+
T Consensus       135 Gf~Vlpy~~dd~~~akrl~~-~G--~~aV-mPlg~pIGsG~Gi~~~~lI~~I~e~~~vPVI~eGGI~TPsDAa~AmeLGA  210 (265)
T 1wv2_A          135 GFDVMVYTSDDPIIARQLAE-IG--CIAV-MPLAGLIGSGLGICNPYNLRIILEEAKVPVLVDAGVGTASDAAIAMELGC  210 (265)
T ss_dssp             TCEEEEEECSCHHHHHHHHH-SC--CSEE-EECSSSTTCCCCCSCHHHHHHHHHHCSSCBEEESCCCSHHHHHHHHHHTC
T ss_pred             CCEEEEEeCCCHHHHHHHHH-hC--CCEE-EeCCccCCCCCCcCCHHHHHHHHhcCCCCEEEeCCCCCHHHHHHHHHcCC
Confidence            78877  4556666665544 33  7887 5544432     22378889888778899999888889999999999999


Q ss_pred             ceEEe-----CCCCHHHHHHHHHHHHH
Q 027234           75 CDYLT-----KPVRIEELKNIWQHVVR   96 (226)
Q Consensus        75 ~~yl~-----KP~~~~~L~~~l~~~~~   96 (226)
                      ++.+.     |.-++..+...+...+.
T Consensus       211 dgVlVgSAI~~a~dP~~ma~af~~Av~  237 (265)
T 1wv2_A          211 EAVLMNTAIAHAKDPVMMAEAMKHAIV  237 (265)
T ss_dssp             SEEEESHHHHTSSSHHHHHHHHHHHHH
T ss_pred             CEEEEChHHhCCCCHHHHHHHHHHHHH
Confidence            99884     44556666666655543

>1bl0_A Protein (multiple antibiotic resistance protein), DNA (5'- D(*CP*CP*GP*AP*TP*GP*CP*CP*AP*CP*GP*TP*TP*TP*TP*GP*CP*TP*AP *AP*AP*TP* CP*C)-3')...; transcriptional activator; HET: DNA; 2.30A {Escherichia coli} SCOP: a.4.1.8 a.4.1.8 PDB: 1xs9_A

Probab=94.78  E-value=0.0094  Score=42.26  Aligned_cols=49  Identities=12%  Similarity=0.079  Sum_probs=37.0

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCCC-CCCCCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGVS-PQQGNS  219 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~~-~~~~~~  219 (226)
                      +..++..+..         .|.+++.. .++++++|+++++|+++|+|+|+-. ++.+..
T Consensus         9 ~~~~i~~~~~---------~i~~~~~~-~~sl~~lA~~~~~S~~~l~r~fk~~~G~s~~~   58 (129)
T 1bl0_A            9 DAITIHSILD---------WIEDNLES-PLSLEKVSERSGYSKWHLQRMFKKETGHSLGQ   58 (129)
T ss_dssp             CHHHHHHHHH---------HHHTTTTS-CCCCHHHHHHSSSCHHHHHHHHHHHHSSCHHH
T ss_pred             hHHHHHHHHH---------HHHHccCC-CCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHH
Confidence            3455555555         58888887 4999999999999999999988753 554433

>2yxb_A Coenzyme B12-dependent mutase; alpha/beta, structural genomics, NPPSFA, national project on structural and functional analyses; 1.80A {Aeropyrum pernix}

Probab=94.37  E-value=0.98  Score=33.08  Aligned_cols=95  Identities=11%  Similarity=0.083  Sum_probs=63.7

Q ss_pred             CcEEEE---ECCHHHHHHHHHhCCCCceEEEEccCCCC-CC-HHHHHHHHhcC--CCCcEEEEeccCCHHHHHHHHhCCc
Q 027234            2 GFSVTK---CNRAEIALDMLRTNKNGYDIVISDVHMPD-MD-GFKLLELVGLE--MDLPVIMMCAHGSKEVVMKGVTHDA   74 (226)
Q Consensus         2 g~~V~~---~~~~~eal~~l~~~~~~~DlVl~D~~mp~-~d-G~~l~~~l~~~--~~~pvI~ls~~~~~~~~~~a~~~ga   74 (226)
                      ||+|..   ..+.++..+.+.+..  ||+|.+...+.. +. --++++.++..  .+++|+ +.+.........+...|+
T Consensus        46 G~eVi~lG~~~p~e~lv~aa~~~~--~diV~lS~~~~~~~~~~~~~i~~L~~~g~~~i~v~-vGG~~~~~~~~~l~~~G~  122 (161)
T 2yxb_A           46 GFEVVYTGLRQTPEQVAMAAVQED--VDVIGVSILNGAHLHLMKRLMAKLRELGADDIPVV-LGGTIPIPDLEPLRSLGI  122 (161)
T ss_dssp             TCEEECCCSBCCHHHHHHHHHHTT--CSEEEEEESSSCHHHHHHHHHHHHHHTTCTTSCEE-EEECCCHHHHHHHHHTTC
T ss_pred             CCEEEECCCCCCHHHHHHHHHhcC--CCEEEEEeechhhHHHHHHHHHHHHhcCCCCCEEE-EeCCCchhcHHHHHHCCC
Confidence            788873   346788889988876  999999888764 22 23345566533  256654 555555555555678999


Q ss_pred             ceEEeCCCCHHHHHHHHHHHHHHHh
Q 027234           75 CDYLTKPVRIEELKNIWQHVVRKRK   99 (226)
Q Consensus        75 ~~yl~KP~~~~~L~~~l~~~~~~~~   99 (226)
                      ++++..--+..+....+..++..+.
T Consensus       123 d~v~~~~~~~~~~~~~~~~~~~~~~  147 (161)
T 2yxb_A          123 REIFLPGTSLGEIIEKVRKLAEEKR  147 (161)
T ss_dssp             CEEECTTCCHHHHHHHHHHHHHHHH
T ss_pred             cEEECCCCCHHHHHHHHHHHHHHhh
Confidence            9877665666777777777776543

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

Probab=93.67  E-value=0.29  Score=32.92  Aligned_cols=64  Identities=16%  Similarity=0.216  Sum_probs=50.0

Q ss_pred             ceEEEEccCC-CCCCHHHHHHHHh---cCCCCcEEEEeccCCHHHHHHHHhCCcceEEeCCCCHHHHHHHHHHHHHH
Q 027234           25 YDIVISDVHM-PDMDGFKLLELVG---LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK   97 (226)
Q Consensus        25 ~DlVl~D~~m-p~~dG~~l~~~l~---~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~KP~~~~~L~~~l~~~~~~   97 (226)
                      .|+|+|...+ |.        .+.   .....-+|++-..-+.+...+.+..||. ||..|+++..|..+|+..++.
T Consensus        51 AdlIfCEYlLLPe--------~ifS~k~~~~~dliVLfD~F~EEa~v~vLd~Ga~-yLlrPIT~kvldAvIraFLrq  118 (121)
T 3q7r_A           51 ADLVVCEYSLLPR--------EIRSPKSLEGSFVLVLLDFFDEETSVDLLDRGFW-YLIRPITPRILKSAISLFLSQ  118 (121)
T ss_dssp             EEEEEEEGGGSCT--------TCCCCTTCCSCEEEEEESSCCHHHHHHHHHTTCE-EEESCCCHHHHHHHHHHHHHH
T ss_pred             ceeEEEeeecChH--------HhcCCCCCCcccEEEEehhhchHHHHHHHhCCce-eEeccCcHHHHHHHHHHHHhc
Confidence            5888888754 32        121   1234557888888888999999999999 999999999999999988764

>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=93.49  E-value=0.46  Score=37.08  Aligned_cols=71  Identities=10%  Similarity=0.189  Sum_probs=54.5

Q ss_pred             EEECCHHHHHHHHHhCCCCceEEEEccC------CCCCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            6 TKCNRAEIALDMLRTNKNGYDIVISDVH------MPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         6 ~~~~~~~eal~~l~~~~~~~DlVl~D~~------mp~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      ..+.+.+++....+.   ++|.|.+...      .+...++++++.++.. ++|+|.-++-.+.+.+.+++..||++.+.
T Consensus       134 ~~v~t~eea~~a~~~---Gad~Ig~~~~g~t~~~~~~~~~~~li~~l~~~-~ipvIA~GGI~t~~d~~~~~~~GadgV~V  209 (229)
T 3q58_A          134 ADCSTVNEGISCHQK---GIEFIGTTLSGYTGPITPVEPDLAMVTQLSHA-GCRVIAEGRYNTPALAANAIEHGAWAVTV  209 (229)
T ss_dssp             EECSSHHHHHHHHHT---TCSEEECTTTTSSSSCCCSSCCHHHHHHHHTT-TCCEEEESSCCSHHHHHHHHHTTCSEEEE
T ss_pred             EecCCHHHHHHHHhC---CCCEEEecCccCCCCCcCCCCCHHHHHHHHHc-CCCEEEECCCCCHHHHHHHHHcCCCEEEE
Confidence            356788888777653   3899865332      2334568889988765 89999998888999999999999999985


Q ss_pred             C
Q 027234           80 K   80 (226)
Q Consensus        80 K   80 (226)
                      =
T Consensus       210 G  210 (229)
T 3q58_A          210 G  210 (229)
T ss_dssp             C
T ss_pred             c
Confidence            3

>3gbg_A TCP pilus virulence regulatory protein; cupin, helix-turn-helix, ARAC family, activator, DNA-binding transcription, transcription regulation; HET: PAM; 1.90A {Vibrio cholerae}

Probab=93.39  E-value=0.02  Score=45.80  Aligned_cols=40  Identities=8%  Similarity=0.081  Sum_probs=34.3

Q ss_pred             HHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCCCCCCCCCC
Q 027234          180 KILELMNIPGLTRENVASHLQKHRLYLSRLSGVSPQQGNSF  220 (226)
Q Consensus       180 ~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~~~~~~~~~  220 (226)
                      .|.+++.. .+|++++|+++++|+++|.|+||..++.+..|
T Consensus       177 ~i~~~~~~-~~sl~~lA~~~~~S~~~l~r~fk~~G~t~~~~  216 (276)
T 3gbg_A          177 LVKSDITR-NWRWADICGELRTNRMILKKELESRGVKFREL  216 (276)
T ss_dssp             HHHHTTTS-CCCHHHHHHHHTCCHHHHHHHHHTTTCCHHHH
T ss_pred             HHHHhhcC-CCCHHHHHHHHCcCHHHHHHHHHHcCCCHHHH
Confidence            47778877 89999999999999999999998777666544

>2htm_A Thiazole biosynthesis protein THIG; thiamin biosynthesis, THIG, thermus thermophilus HB8, structural genomics, NPPSFA; 2.30A {Thermus thermophilus}

Probab=92.65  E-value=0.41  Score=38.14  Aligned_cols=91  Identities=16%  Similarity=0.115  Sum_probs=62.3

Q ss_pred             CcEEE-EE-CCHHHHHHHHHhCCCCceEEEEccCCCCCCH-----HHHHHHHhc-CCC-CcEEEEeccCCHHHHHHHHhC
Q 027234            2 GFSVT-KC-NRAEIALDMLRTNKNGYDIVISDVHMPDMDG-----FKLLELVGL-EMD-LPVIMMCAHGSKEVVMKGVTH   72 (226)
Q Consensus         2 g~~V~-~~-~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG-----~~l~~~l~~-~~~-~pvI~ls~~~~~~~~~~a~~~   72 (226)
                      ||.|. .| .|...|-.+.. ..  +++| +.+..|-..|     .++++.++. ..+ +|||+=.+-...+.+..++++
T Consensus       124 Gf~Vlpy~~~D~~~ak~l~~-~G--~~aV-mPlg~pIGsG~Gi~~~~~L~~i~~~~~~~vPVI~~GGI~tpsDAa~AmeL  199 (268)
T 2htm_A          124 DFLVLPYMGPDLVLAKRLAA-LG--TATV-MPLAAPIGSGWGVRTRALLELFAREKASLPPVVVDAGLGLPSHAAEVMEL  199 (268)
T ss_dssp             TCEECCEECSCHHHHHHHHH-HT--CSCB-EEBSSSTTTCCCSTTHHHHHHHHHTTTTSSCBEEESCCCSHHHHHHHHHT
T ss_pred             CCEEeeccCCCHHHHHHHHh-cC--CCEE-EecCccCcCCcccCCHHHHHHHHHhcCCCCeEEEeCCCCCHHHHHHHHHc
Confidence            78876 34 56655554444 33  7776 5555443222     556787775 677 999998888899999999999


Q ss_pred             CcceEE-----eCCCCHHHHHHHHHHHHH
Q 027234           73 DACDYL-----TKPVRIEELKNIWQHVVR   96 (226)
Q Consensus        73 ga~~yl-----~KP~~~~~L~~~l~~~~~   96 (226)
                      |+++.+     .|.-++..+...+...+.
T Consensus       200 GAdgVlVgSAI~~a~dP~~ma~af~~Av~  228 (268)
T 2htm_A          200 GLDAVLVNTAIAEAQDPPAMAEAFRLAVE  228 (268)
T ss_dssp             TCCEEEESHHHHTSSSHHHHHHHHHHHHH
T ss_pred             CCCEEEEChHHhCCCCHHHHHHHHHHHHH
Confidence            999988     455556666666665543

>1u8b_A ADA polyprotein; protein-DNA complex, methylation, zinc, helix-turn-helix, metal binding protein/DNA complex; 2.10A {Escherichia coli} PDB: 1zgw_A* 1wpk_A* 1adn_A 1eyf_A

Probab=92.50  E-value=0.046  Score=38.78  Aligned_cols=34  Identities=18%  Similarity=0.172  Sum_probs=27.1

Q ss_pred             CCCCCHHHHHHHhhhhhhhhhcccC-CCCCCCCCC
Q 027234          187 IPGLTRENVASHLQKHRLYLSRLSG-VSPQQGNSF  220 (226)
Q Consensus       187 ~~~lt~~~va~~l~~~r~~l~r~~~-~~~~~~~~~  220 (226)
                      .+++++++||.++|+|.+||+|+|+ ..++.+..|
T Consensus        91 ~~~~sl~~lA~~~g~S~~~f~r~Fk~~~G~tp~~y  125 (133)
T 1u8b_A           91 ETPVTLEALADQVAMSPFHLHRLFKATTGMTPKAW  125 (133)
T ss_dssp             SSCCCHHHHHHHHTSCHHHHHHHHHHHTSSCHHHH
T ss_pred             cCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHHH
Confidence            6789999999999999999999874 344444433

>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=92.09  E-value=0.85  Score=35.61  Aligned_cols=70  Identities=17%  Similarity=0.215  Sum_probs=53.2

Q ss_pred             EEECCHHHHHHHHHhCCCCceEEEEccC------CCCCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            6 TKCNRAEIALDMLRTNKNGYDIVISDVH------MPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         6 ~~~~~~~eal~~l~~~~~~~DlVl~D~~------mp~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      ..+.+.+++....+.   ++|.|.+...      .+...++++++.++.. ++|+|.-++-.+.+.+.+++..||++.+.
T Consensus       134 ~~v~t~eea~~a~~~---Gad~Ig~~~~g~t~~~~~~~~~~~~i~~l~~~-~ipvIA~GGI~t~~d~~~~~~~GadgV~V  209 (232)
T 3igs_A          134 ADCSSVDDGLACQRL---GADIIGTTMSGYTTPDTPEEPDLPLVKALHDA-GCRVIAEGRYNSPALAAEAIRYGAWAVTV  209 (232)
T ss_dssp             EECCSHHHHHHHHHT---TCSEEECTTTTSSSSSCCSSCCHHHHHHHHHT-TCCEEEESCCCSHHHHHHHHHTTCSEEEE
T ss_pred             EeCCCHHHHHHHHhC---CCCEEEEcCccCCCCCCCCCCCHHHHHHHHhc-CCcEEEECCCCCHHHHHHHHHcCCCEEEE
Confidence            356788888776653   3899864322      1234468889888765 89999888888899999999999999985

>1tc3_C Protein (TC3 transposase); DNA binding, helix-turn-helix, TC1/mariner family, complex (transposase/DNA), DNA binding protein/DNA complex; HET: DNA; 2.45A {Caenorhabditis elegans} SCOP: a.4.1.2

Probab=92.05  E-value=0.068  Score=30.25  Aligned_cols=34  Identities=3%  Similarity=0.002  Sum_probs=25.1

Q ss_pred             HHHhhCCCCCCHHHHHHHhhhhhhhhhcccCCCCC
Q 027234          181 ILELMNIPGLTRENVASHLQKHRLYLSRLSGVSPQ  215 (226)
Q Consensus       181 I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~~~~  215 (226)
                      |+..+. .+++..+||..|++|+..+++..+....
T Consensus        14 i~~~~~-~g~s~~~IA~~lgis~~Tv~~~~~~~~~   47 (51)
T 1tc3_C           14 LDVMKL-LNVSLHEMSRKISRSRHCIRVYLKDPVS   47 (51)
T ss_dssp             HHHHHH-TTCCHHHHHHHHTCCHHHHHHHHHCSTT
T ss_pred             HHHHHH-cCCCHHHHHHHHCcCHHHHHHHHhhHHh
Confidence            444443 4899999999999999999885444333

>2w7n_A TRFB transcriptional repressor protein; INCP, plasmid, repressor, DNA-binding, transcription/DNA; HET: BRU; 1.85A {Escherichia coli}

Probab=90.23  E-value=0.13  Score=34.88  Aligned_cols=46  Identities=22%  Similarity=0.233  Sum_probs=30.0

Q ss_pred             HHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhc
Q 027234          162 QQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSR  208 (226)
Q Consensus       162 ~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r  208 (226)
                      .+|-.++..+.++... -.|-..+=++|+|..+||..||+||....|
T Consensus         8 ~eFe~~~~~l~~~~~~-~~~A~lyYv~g~tQ~eIA~~lGiSR~~Vsr   53 (101)
T 2w7n_A            8 SQFQEAIQGLEVGQQT-IEIARGVLVDGKPQATFATSLGLTRGAVSQ   53 (101)
T ss_dssp             HHHHHHHTTCCCCHHH-HHHHHHHHTTCCCHHHHHHHHTCCHHHHHH
T ss_pred             HHHHHHHccCChHHHH-HHHHHHHHHcCCCHHHHHHHHCCCHHHHHH
Confidence            4555555444332222 234445556799999999999999997655

>2zcm_A Biofilm operon icaabcd HTH-type negative transcri regulator ICAR; helix-turn-helix, TETR family, repressor; 1.33A {Staphylococcus epidermidis} PDB: 2zcn_A

Probab=89.83  E-value=0.3  Score=36.00  Aligned_cols=44  Identities=7%  Similarity=0.137  Sum_probs=35.7

Q ss_pred             hhHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          159 ELHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       159 ~l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      ..+.+++.++.+          +...-.-.+.|+++||.+.|+||..+|+-|+.
T Consensus         7 ~~~~~Il~aA~~----------lf~~~G~~~~t~~~IA~~agvs~~tlY~~F~s   50 (192)
T 2zcm_A            7 HMKDKIIDNAIT----------LFSEKGYDGTTLDDISKSVNIKKASLYYHYDN   50 (192)
T ss_dssp             -CHHHHHHHHHH----------HHHHHCTTTCCHHHHHHHTTCCHHHHHHHTCC
T ss_pred             hhHHHHHHHHHH----------HHHHcCcccCCHHHHHHHhCCChHHHHHHCCC
Confidence            456788888888          44445667899999999999999999998874

>1jko_C HIN recombinase, DNA-invertase HIN; water-mediated recognition, protein-DNA complex, A10G mutant, DNA binding protein/DNA complex; 2.24A {Synthetic} SCOP: a.4.1.2 PDB: 1ijw_C* 1jj6_C* 1jj8_C* 1hcr_A 1jkp_C 1jkq_C 1jkr_C

Probab=89.55  E-value=0.16  Score=28.93  Aligned_cols=32  Identities=25%  Similarity=0.171  Sum_probs=24.8

Q ss_pred             HHHhhCCCCCCHHHHHHHhhhhhhhhhcccCCC
Q 027234          181 ILELMNIPGLTRENVASHLQKHRLYLSRLSGVS  213 (226)
Q Consensus       181 I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~~  213 (226)
                      |++.+.. +.+..+||..+++|++.+||..+..
T Consensus        14 i~~l~~~-g~s~~~ia~~lgvs~~Tv~r~l~~~   45 (52)
T 1jko_C           14 ISRLLEK-GHPRQQLAIIFGIGVSTLYRYFPAS   45 (52)
T ss_dssp             HHHHHHT-TCCHHHHHHTTSCCHHHHHHHSCTT
T ss_pred             HHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHc
Confidence            4444433 7999999999999999999865543

>3knw_A Putative transcriptional regulator (TETR/ACRR FAM; TETR-like protein, MCSG, PSI, structural genomics, protein S initiative; 2.45A {Acinetobacter SP}

Probab=88.05  E-value=0.47  Score=35.30  Aligned_cols=44  Identities=5%  Similarity=-0.040  Sum_probs=35.8

Q ss_pred             hhHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          159 ELHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       159 ~l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .-.++++.++.+          ++......++|+++||.+.|+||..+|+-|+.
T Consensus        14 ~~r~~Il~aa~~----------l~~~~G~~~~ti~~IA~~agvs~~t~Y~~F~s   57 (212)
T 3knw_A           14 AKRQHILDSGFH----------LVLRKGFVGVGLQEILKTSGVPKGSFYHYFES   57 (212)
T ss_dssp             HHHHHHHHHHHH----------HHHHHCSTTCCHHHHHHHHTCCHHHHHHHCSS
T ss_pred             hhHHHHHHHHHH----------HHHHcCCccCCHHHHHHHhCCChHHHHHHCCC
Confidence            345678888888          44445677999999999999999999998874

>3qkx_A Uncharacterized HTH-type transcriptional regulato; structural genomics, joint center for structural genomics; HET: MSE; 2.35A {Haemophilus influenzae}

Probab=87.96  E-value=0.49  Score=34.38  Aligned_cols=43  Identities=14%  Similarity=0.050  Sum_probs=34.3

Q ss_pred             hHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          160 LHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       160 l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      ..++++.++.+          +...-...++|+++||.+.|+||..+|+-|+.
T Consensus         9 ~r~~Il~aa~~----------l~~~~G~~~~ti~~Ia~~agvs~~t~Y~~F~s   51 (188)
T 3qkx_A            9 LAEQIFSATDR----------LMAREGLNQLSMLKLAKEANVAAGTIYLYFKN   51 (188)
T ss_dssp             HHHHHHHHHHH----------HHHHSCSTTCCHHHHHHHHTCCHHHHHHHSSS
T ss_pred             HHHHHHHHHHH----------HHHhcCcccCCHHHHHHHhCCCcchHHHHcCC
Confidence            34677777777          44445666899999999999999999998864

>3ppb_A Putative TETR family transcription regulator; DNA-binding, helix-turn-helix motif, HTH motif, DNA/RNA-BIND helical bundle fold; HET: MSE PG4; 2.10A {Shewanella loihica}

Probab=87.90  E-value=0.51  Score=34.45  Aligned_cols=42  Identities=10%  Similarity=0.023  Sum_probs=34.0

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .++++.++..          ++..-...++|+++||.+.++||..+|+-|+.
T Consensus        11 r~~Il~aa~~----------l~~~~G~~~~tv~~Ia~~agvs~~t~Y~~F~s   52 (195)
T 3ppb_A           11 KQAILETALQ----------LFVSQGFHGTSTATIAREAGVATGTLFHHFPS   52 (195)
T ss_dssp             HHHHHHHHHH----------HHHHTCSTTSCHHHHHHHHTCCHHHHHHHCSS
T ss_pred             HHHHHHHHHH----------HHHhcCcccCCHHHHHHHhCCChhHHHHHcCC
Confidence            4577777777          44445667899999999999999999998874

>3rd3_A Probable transcriptional regulator; 2.40A {Pseudomonas aeruginosa}

Probab=87.81  E-value=0.61  Score=34.13  Aligned_cols=44  Identities=7%  Similarity=0.084  Sum_probs=35.5

Q ss_pred             hhHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          159 ELHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       159 ~l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      ...++++.++.+          +...-.-.+.|+++||.+.++||..+|+-|+.
T Consensus        10 ~~r~~Il~aa~~----------lf~~~G~~~~t~~~IA~~agvs~~tlY~~F~s   53 (197)
T 3rd3_A           10 DTRQHLLDTGYR----------IMAVKGFSGVGLNEILQSAGVPKGSFYHYFKS   53 (197)
T ss_dssp             CHHHHHHHHHHH----------HHHHHCSTTCCHHHHHHHHTCCHHHHTTTCSC
T ss_pred             hHHHHHHHHHHH----------HHHHCCcccCCHHHHHHHhCCChhhHHHHcCC
Confidence            345678888888          33444667899999999999999999998874

>3kkc_A TETR family transcriptional regulator; APC20805, structural genomics, PSI-2, protein structure initiative; 2.50A {Streptococcus agalactiae 2603V}

Probab=87.80  E-value=0.43  Score=34.49  Aligned_cols=43  Identities=12%  Similarity=0.026  Sum_probs=33.3

Q ss_pred             hHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          160 LHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       160 l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      -.++++.++.+          ++..-.-.+.|+++||.+.|+||..+|+-|+.
T Consensus        13 tr~~Il~aa~~----------l~~~~G~~~~tv~~Ia~~agvs~~t~Y~~F~s   55 (177)
T 3kkc_A           13 TKVAIYNAFIS----------LLQENDYSKITVQDVIGLANVGRSTFYSHYES   55 (177)
T ss_dssp             HHHHHHHHHHH----------HTTTSCTTTCCHHHHHHHHCCCHHHHTTTCSS
T ss_pred             HHHHHHHHHHH----------HHHhCChhHhhHHHHHHHhCCcHhhHHHHcCC
Confidence            34577777777          33334556789999999999999999998875

>3o63_A Probable thiamine-phosphate pyrophosphorylase; thiamin biosynthesis, TIM barrel, transferase; 2.35A {Mycobacterium tuberculosis}

Probab=87.50  E-value=6.7  Score=30.71  Aligned_cols=83  Identities=8%  Similarity=0.018  Sum_probs=57.3

Q ss_pred             EECCHHHHHHHHHhCCCCceEEEEccCCCC-------CCHHHHHHHHhcC--CCCcEEEEeccCCHHHHHHHHhCCcceE
Q 027234            7 KCNRAEIALDMLRTNKNGYDIVISDVHMPD-------MDGFKLLELVGLE--MDLPVIMMCAHGSKEVVMKGVTHDACDY   77 (226)
Q Consensus         7 ~~~~~~eal~~l~~~~~~~DlVl~D~~mp~-------~dG~~l~~~l~~~--~~~pvI~ls~~~~~~~~~~a~~~ga~~y   77 (226)
                      .|.+.+|+......   ++|.|.+.-..|.       .-|++.++.+...  .++|++.+.+- +.+.+...+..||+++
T Consensus       141 S~ht~~Ea~~A~~~---GaDyI~vgpvf~T~tK~~~~~~gl~~l~~~~~~~~~~iPvvAiGGI-~~~ni~~~~~aGa~gv  216 (243)
T 3o63_A          141 STHDPDQVAAAAAG---DADYFCVGPCWPTPTKPGRAAPGLGLVRVAAELGGDDKPWFAIGGI-NAQRLPAVLDAGARRI  216 (243)
T ss_dssp             EECSHHHHHHHHHS---SCSEEEECCSSCCCC-----CCCHHHHHHHHTC---CCCEEEESSC-CTTTHHHHHHTTCCCE
T ss_pred             eCCCHHHHHHHhhC---CCCEEEEcCccCCCCCCCcchhhHHHHHHHHHhccCCCCEEEecCC-CHHHHHHHHHcCCCEE
Confidence            57888888776653   3899998654433       2378888888754  48999998876 6677888899999998


Q ss_pred             Ee-----CCCCHHHHHHHHHH
Q 027234           78 LT-----KPVRIEELKNIWQH   93 (226)
Q Consensus        78 l~-----KP~~~~~L~~~l~~   93 (226)
                      ..     +.-++......+..
T Consensus       217 av~sai~~a~dp~~a~~~l~~  237 (243)
T 3o63_A          217 VVVRAITSADDPRAAAEQLRS  237 (243)
T ss_dssp             EESHHHHTCSSHHHHHHHHHH
T ss_pred             EEeHHHhCCCCHHHHHHHHHH
Confidence            74     44455444444333

>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=87.47  E-value=1.9  Score=33.61  Aligned_cols=50  Identities=10%  Similarity=0.169  Sum_probs=36.6

Q ss_pred             HHHHHHHhcCCCCcEEEEeccCC------HHHHHHHHhCCcceEEeCCCCHHHHHH
Q 027234           40 FKLLELVGLEMDLPVIMMCAHGS------KEVVMKGVTHDACDYLTKPVRIEELKN   89 (226)
Q Consensus        40 ~~l~~~l~~~~~~pvI~ls~~~~------~~~~~~a~~~ga~~yl~KP~~~~~L~~   89 (226)
                      +++++.+++..++||++++....      .+....++..||++.+.-....++...
T Consensus        69 ~~~i~~i~~~~~~pv~~~~~~~~~~~~~~~~~~~~~~~~Gad~v~~~~~~~~~~~~  124 (248)
T 1geq_A           69 FWIVKEFRRHSSTPIVLMTYYNPIYRAGVRNFLAEAKASGVDGILVVDLPVFHAKE  124 (248)
T ss_dssp             HHHHHHHHTTCCCCEEEEECHHHHHHHCHHHHHHHHHHHTCCEEEETTCCGGGHHH
T ss_pred             HHHHHHHHhhCCCCEEEEeccchhhhcCHHHHHHHHHHCCCCEEEECCCChhhHHH
Confidence            67778887666789988874333      467788999999999987666555443

>1xi3_A Thiamine phosphate pyrophosphorylase; structural genomics, southeast collaboratory for structural genomics, hyperthermophIle; 1.70A {Pyrococcus furiosus} SCOP: c.1.3.1

Probab=87.30  E-value=5.7  Score=29.84  Aligned_cols=68  Identities=15%  Similarity=0.144  Sum_probs=48.3

Q ss_pred             EECCHHHHHHHHHhCCCCceEEEEccCCCC-------CCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEE
Q 027234            7 KCNRAEIALDMLRTNKNGYDIVISDVHMPD-------MDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYL   78 (226)
Q Consensus         7 ~~~~~~eal~~l~~~~~~~DlVl~D~~mp~-------~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl   78 (226)
                      .+.+..++...... .  +|.|+++-..|.       ..+++.++.++...++|+++..+-. .+.+.+++..|++++.
T Consensus       114 ~~~t~~e~~~~~~~-g--~d~i~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~pvia~GGI~-~~nv~~~~~~Ga~gv~  188 (215)
T 1xi3_A          114 SVYSLEEALEAEKK-G--ADYLGAGSVFPTKTKEDARVIGLEGLRKIVESVKIPVVAIGGIN-KDNAREVLKTGVDGIA  188 (215)
T ss_dssp             EESSHHHHHHHHHH-T--CSEEEEECSSCC----CCCCCHHHHHHHHHHHCSSCEEEESSCC-TTTHHHHHTTTCSEEE
T ss_pred             ecCCHHHHHHHHhc-C--CCEEEEcCCccCCCCCCCCCcCHHHHHHHHHhCCCCEEEECCcC-HHHHHHHHHcCCCEEE
Confidence            35677777655432 3  899998754443       3578888888655578988766655 7777778889999885

>3qbm_A TETR transcriptional regulator; DNA/RNA-binding three-helical bundle, structural genomics, J center for structural genomics, JCSG; HET: MSE PGE; 1.80A {Chloroflexus aurantiacus}

Probab=87.18  E-value=0.67  Score=33.96  Aligned_cols=43  Identities=7%  Similarity=0.085  Sum_probs=34.5

Q ss_pred             hHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          160 LHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       160 l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      -.++++.++.+          ++..-.-.++|+++||.+.|+|+..+|+-|+.
T Consensus         8 ~r~~Il~aa~~----------l~~~~G~~~~t~~~IA~~agvs~~t~Y~~F~s   50 (199)
T 3qbm_A            8 TRERVVAQAAA----------LFNVSGYAGTAISDIMAATGLEKGGIYRHFES   50 (199)
T ss_dssp             HHHHHHHHHHH----------HHHHHCSTTCCHHHHHHHHTCCHHHHHTTCSS
T ss_pred             HHHHHHHHHHH----------HHHHhCcCcCCHHHHHHHhCCCccHHHHhCCC
Confidence            34677778777          44445667899999999999999999998874

>2iu5_A DHAS, YCEG, HTH-type dhaklm operon transcriptional activator; synthase, TETR family; 1.6A {Lactococcus lactis subsp} SCOP: a.4.1.9 a.121.1.1

Probab=87.12  E-value=0.56  Score=34.63  Aligned_cols=43  Identities=7%  Similarity=0.083  Sum_probs=33.5

Q ss_pred             hHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          160 LHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       160 l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      -.++++.++.+          +...-.-.+.|+++||.+.|+||..||+-|+.
T Consensus        14 ~r~~Il~aa~~----------lf~~~G~~~~tv~~Ia~~agvs~~t~Y~~F~s   56 (195)
T 2iu5_A           14 TQKIIAKAFKD----------LMQSNAYHQISVSDIMQTAKIRRQTFYNYFQN   56 (195)
T ss_dssp             HHHHHHHHHHH----------HHHHSCGGGCCHHHHHHHHTSCGGGGGGTCSS
T ss_pred             HHHHHHHHHHH----------HHHhCCCCeeCHHHHHHHhCCCHHHHHHHcCC
Confidence            35677777777          33334556799999999999999999998864

>3b81_A Transcriptional regulator, ACRR family; NP_350189.1, predicted DNA-binding transcriptional regulator TETR/ACRR family; 2.10A {Clostridium acetobutylicum atcc 824}

Probab=86.81  E-value=0.72  Score=33.97  Aligned_cols=44  Identities=9%  Similarity=0.012  Sum_probs=35.2

Q ss_pred             hhHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          159 ELHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       159 ~l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .-.++++.++.+          ++..-.-.+.|+++||.+.|+|+..+|+-|+.
T Consensus        11 ~~r~~Il~aA~~----------lf~~~G~~~~s~~~Ia~~agvs~~t~Y~~F~s   54 (203)
T 3b81_A           11 NKRTELANKIWD----------IFIANGYENTTLAFIINKLGISKGALYHYFSS   54 (203)
T ss_dssp             HHHHHHHHHHHH----------HHHHHCSTTCCHHHHHHHHTCCHHHHHTTCSS
T ss_pred             HHHHHHHHHHHH----------HHHHcCcccCcHHHHHHHhCCCchhHHHHcCC
Confidence            345678888887          34445666899999999999999999998874

>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=86.74  E-value=3  Score=33.02  Aligned_cols=56  Identities=14%  Similarity=0.207  Sum_probs=39.1

Q ss_pred             HHHHHHHHhcCC-CCcEEEEeccCC------HHHHHHHHhCCcceEEeCCCCHHHHHHHHHHH
Q 027234           39 GFKLLELVGLEM-DLPVIMMCAHGS------KEVVMKGVTHDACDYLTKPVRIEELKNIWQHV   94 (226)
Q Consensus        39 G~~l~~~l~~~~-~~pvI~ls~~~~------~~~~~~a~~~ga~~yl~KP~~~~~L~~~l~~~   94 (226)
                      .+++++.++... ++|+++++-...      ......+...|+++++.-.+..+++...+..+
T Consensus        81 ~~~~v~~ir~~~~~~Pi~~m~y~n~v~~~g~~~f~~~~~~aG~dgvii~dl~~ee~~~~~~~~  143 (262)
T 2ekc_A           81 VLELSETLRKEFPDIPFLLMTYYNPIFRIGLEKFCRLSREKGIDGFIVPDLPPEEAEELKAVM  143 (262)
T ss_dssp             HHHHHHHHHHHCTTSCEEEECCHHHHHHHCHHHHHHHHHHTTCCEEECTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhcCCCCEEEEecCcHHHHhhHHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHH
Confidence            345677777554 899999753321      34567788999999999888887765555443

>3vp5_A Transcriptional regulator; heme, sensor protein, TETR superf transcription; HET: HEM; 1.90A {Lactococcus lactis} PDB: 3vox_A 3vok_A*

Probab=86.70  E-value=0.64  Score=34.33  Aligned_cols=43  Identities=7%  Similarity=-0.050  Sum_probs=34.4

Q ss_pred             hHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          160 LHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       160 l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      -.++++.++.+          ++..-.-.++|+++||.+.|+||..+|+-|+.
T Consensus        13 tr~~Il~aa~~----------l~~~~G~~~~ti~~Ia~~agvs~~t~Y~~F~~   55 (189)
T 3vp5_A           13 KRNRVYDACLN----------EFQTHSFHEAKIMHIVKALDIPRGSFYQYFED   55 (189)
T ss_dssp             HHHHHHHHHHH----------HHHHSCTTTCCHHHHHHHHTCCHHHHHHHCSS
T ss_pred             HHHHHHHHHHH----------HHHHCCcccccHHHHHHHhCCChHHHHHHCCC
Confidence            34677777777          44455667899999999999999999998864

>3lwj_A Putative TETR-family transcriptional regulator; structural G joint center for structural genomics, JCSG, protein structu initiative; 2.07A {Syntrophomonas wolfei subsp}

Probab=86.61  E-value=0.61  Score=34.39  Aligned_cols=44  Identities=5%  Similarity=-0.082  Sum_probs=35.0

Q ss_pred             hhHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          159 ELHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       159 ~l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .-.++++.++.+          ++..-.-.++|+++||.+.|+||..+|+-|+.
T Consensus        12 ~~r~~Il~aa~~----------l~~~~G~~~~t~~~Ia~~agvs~~t~Y~~F~s   55 (202)
T 3lwj_A           12 ERRQKILTCSLD----------LFIEKGYYNTSIRDIIALSEVGTGTFYNYFVD   55 (202)
T ss_dssp             HHHHHHHHHHHH----------HHHHHCTTTCCHHHHHHHHCSCHHHHHHHCSS
T ss_pred             HHHHHHHHHHHH----------HHHHcCcccCCHHHHHHHhCCCchhHHHHcCC
Confidence            345677778777          44445667899999999999999999998874

>1yad_A Regulatory protein TENI; TIM barrel, transcription; 2.10A {Bacillus subtilis} PDB: 3qh2_A*

Probab=86.59  E-value=2.9  Score=31.94  Aligned_cols=69  Identities=16%  Similarity=0.143  Sum_probs=49.1

Q ss_pred             EECCHHHHHHHHHhCCCCceEEEEccCCCC-------CCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            7 KCNRAEIALDMLRTNKNGYDIVISDVHMPD-------MDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         7 ~~~~~~eal~~l~~~~~~~DlVl~D~~mp~-------~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .+.+.+++......   +.|.|+++-..+.       ..|++.++.++...++|+++..+- +.+.+.+++..|++++..
T Consensus       116 sv~t~~~~~~a~~~---gaD~i~~~~~f~~~~~~g~~~~~~~~l~~~~~~~~~pvia~GGI-~~~nv~~~~~~Ga~gv~v  191 (221)
T 1yad_A          116 SVHSLEEAVQAEKE---DADYVLFGHVFETDCKKGLEGRGVSLLSDIKQRISIPVIAIGGM-TPDRLRDVKQAGADGIAV  191 (221)
T ss_dssp             EECSHHHHHHHHHT---TCSEEEEECCC----------CHHHHHHHHHHHCCSCEEEESSC-CGGGHHHHHHTTCSEEEE
T ss_pred             EcCCHHHHHHHHhC---CCCEEEECCccccCCCCCCCCCCHHHHHHHHHhCCCCEEEECCC-CHHHHHHHHHcCCCEEEE
Confidence            46678887766553   3899998764332       236778888765457898877766 788888999999998764

>3him_A Probable transcriptional regulator; TETR, bacterial, RHA1, PSI-2, MCSG, structural midwest center for structural genomics; 2.20A {Rhodococcus jostii}

Probab=86.53  E-value=0.64  Score=34.37  Aligned_cols=43  Identities=12%  Similarity=0.026  Sum_probs=35.0

Q ss_pred             hHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          160 LHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       160 l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      -.++++.++.+          ++..-.-.++|+++||.+.|+||..||+-|+.
T Consensus        17 ~r~~Il~aa~~----------l~~~~G~~~~t~~~Ia~~agvs~~t~Y~~F~s   59 (211)
T 3him_A           17 AAARIRAAAIE----------VFAAKGYGATTTREIAASLDMSPGAVYPHYKT   59 (211)
T ss_dssp             HHHHHHHHHHH----------HHHHHCSTTCCHHHHHHHTTCCTTSSTTTCSS
T ss_pred             HHHHHHHHHHH----------HHHHcCCCcCCHHHHHHHhCCCcChhhhcCCC
Confidence            35677888887          44445667899999999999999999998874

>3e7l_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+ ATPase, response regulator, transcriptional activator, ATP-binding; 2.25A {Aquifex aeolicus} PDB: 4fth_A

Probab=86.52  E-value=0.44  Score=28.97  Aligned_cols=30  Identities=17%  Similarity=-0.017  Sum_probs=24.5

Q ss_pred             HHHHhhCCCCCCHHHHHHHhhhhhhhhhcc
Q 027234          180 KILELMNIPGLTRENVASHLQKHRLYLSRL  209 (226)
Q Consensus       180 ~I~~~~~~~~lt~~~va~~l~~~r~~l~r~  209 (226)
                      .|.+.+...+-++...|..||++|+.|||.
T Consensus        23 ~i~~aL~~~~gn~~~aA~~LGisr~tL~rk   52 (63)
T 3e7l_A           23 FIEEKLREYDYDLKRTAEEIGIDLSNLYRK   52 (63)
T ss_dssp             HHHHHHHHTTTCHHHHHHHHTCCHHHHHHH
T ss_pred             HHHHHHHHhCCCHHHHHHHHCcCHHHHHHH
Confidence            455666566778999999999999999974

>3he0_A Transcriptional regulator, TETR family; ACRR, vibrio parahaemolytic structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.20A {Vibrio parahaemolyticus}

Probab=86.45  E-value=0.8  Score=33.50  Aligned_cols=42  Identities=14%  Similarity=0.186  Sum_probs=34.0

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .++++.++..          ++..-...+.|+++||.+.|+||..||+-|+.
T Consensus        13 r~~il~aa~~----------lf~~~G~~~~tv~~Ia~~agvs~~t~Y~~F~s   54 (196)
T 3he0_A           13 RDQILAAAEQ----------LIAESGFQGLSMQKLANEAGVAAGTIYRYFSD   54 (196)
T ss_dssp             HHHHHHHHHH----------HHHHHCTTTCCHHHHHHHHTSCHHHHHTTCSS
T ss_pred             HHHHHHHHHH----------HHHHhCcccCCHHHHHHHhCCCcchHHHhcCC
Confidence            4677777777          34444667899999999999999999998874

>3dcf_A Transcriptional regulator of the TETR/ACRR family; YP_290855.1, structural genomics, joint center for structural genomics, JCSG; 2.50A {Thermobifida fusca YX}

Probab=86.40  E-value=0.68  Score=34.49  Aligned_cols=44  Identities=7%  Similarity=0.079  Sum_probs=35.6

Q ss_pred             hhHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          159 ELHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       159 ~l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      ...++++.++.+          ++......++|+++||.+.++||..||+-|+.
T Consensus        31 ~~r~~Il~aa~~----------l~~~~G~~~~tv~~Ia~~agvs~~t~Y~~F~s   74 (218)
T 3dcf_A           31 DRRTQIIKVATE----------LFREKGYYATSLDDIADRIGFTKPAIYYYFKS   74 (218)
T ss_dssp             HHHHHHHHHHHH----------HHHHTCTTTCCHHHHHHHHTCCHHHHHHHCSS
T ss_pred             chHHHHHHHHHH----------HHHHcCcccCcHHHHHHHhCCCHHHHHHHcCC
Confidence            345778888887          44555667899999999999999999998864

>3kz9_A SMCR; transcriptional regulator, quorum S DNA-binding, transcription regulation, transcription regula; HET: MSE; 2.10A {Vibrio vulnificus} PDB: 2pbx_A

Probab=86.20  E-value=0.71  Score=33.98  Aligned_cols=43  Identities=14%  Similarity=0.015  Sum_probs=35.0

Q ss_pred             hHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          160 LHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       160 l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      -.++++.++..          ++..-...++|+++||.+.|+||..+|+-|+.
T Consensus        18 ~r~~Il~aa~~----------l~~~~G~~~~s~~~Ia~~agvs~~t~Y~~F~s   60 (206)
T 3kz9_A           18 RKQQLMEIALE----------VFARRGIGRGGHADIAEIAQVSVATVFNYFPT   60 (206)
T ss_dssp             HHHHHHHHHHH----------HHHHSCCSSCCHHHHHHHHTSCHHHHHHHCCS
T ss_pred             HHHHHHHHHHH----------HHHhcCcccccHHHHHHHhCCCHHHHHHHcCC
Confidence            35678888887          44455677899999999999999999998874

>3col_A Putative transcription regulator; structural genomics, PSI-2, protein structure initiative, midwest CENT structural genomics, MCSG; HET: MSE; 2.10A {Lactobacillus plantarum WCFS1}

Probab=85.81  E-value=0.61  Score=34.02  Aligned_cols=43  Identities=14%  Similarity=0.063  Sum_probs=34.3

Q ss_pred             hHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          160 LHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       160 l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      -.++++.++.+          ++..-...++|+++||...|+||..+|+-|+.
T Consensus        11 ~r~~Il~aa~~----------l~~~~G~~~~ti~~Ia~~agvs~~t~Y~~F~s   53 (196)
T 3col_A           11 KQVKIQDAVAA----------IILAEGPAGVSTTKVAKRVGIAQSNVYLYFKN   53 (196)
T ss_dssp             HHHHHHHHHHH----------HHHHHCGGGCCHHHHHHHHTSCHHHHHTTCSS
T ss_pred             HHHHHHHHHHH----------HHHhcCcccCCHHHHHHHhCCcHHHHHHHhCC
Confidence            35677788777          33334666899999999999999999998874

>2fq4_A Transcriptional regulator, TETR family; DNA-binding protein, bacillu structural genomics, PSI, protein structure initiative; 1.79A {Bacillus cereus} SCOP: a.4.1.9 a.121.1.1

Probab=85.78  E-value=0.76  Score=33.84  Aligned_cols=44  Identities=16%  Similarity=0.151  Sum_probs=35.4

Q ss_pred             hhHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          159 ELHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       159 ~l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      ...++++.++.+          +...-.-.+.|+++||.+.|+||..+|+-|+.
T Consensus        12 ~~r~~Il~aA~~----------lf~e~G~~~~t~~~IA~~agvsk~tlY~~F~s   55 (192)
T 2fq4_A           12 ETQKAILSASYE----------LLLESGFKAVTVDKIAERAKVSKATIYKWWPN   55 (192)
T ss_dssp             HHHHHHHHHHHH----------HHHHHCTTTCCHHHHHHHHTCCHHHHHHHCSS
T ss_pred             HHHHHHHHHHHH----------HHHHcCcccccHHHHHHHcCCCHHHHHHHCCC
Confidence            345678888888          44445667899999999999999999998764

>3lhq_A Acrab operon repressor (TETR/ACRR family); structural genomics, IDP02616, csgid, DNA-binding, transcription, transcription regulation; 1.56A {Salmonella enterica subsp} PDB: 3bcg_A 2qop_A

Probab=85.77  E-value=0.74  Score=34.21  Aligned_cols=43  Identities=7%  Similarity=0.014  Sum_probs=34.4

Q ss_pred             hHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          160 LHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       160 l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      ..++++.++.+          ++..-.-.++|+++||.+.|+|+..||+-|+.
T Consensus        15 ~r~~Il~aa~~----------l~~~~G~~~~ti~~Ia~~agvs~~t~Y~~F~s   57 (220)
T 3lhq_A           15 TRQHILDVALR----------LFSQQGVSATSLAEIANAAGVTRGAIYWHFKN   57 (220)
T ss_dssp             HHHHHHHHHHH----------HHHHHCSTTCCHHHHHHHHTCCHHHHHHHCSS
T ss_pred             HHHHHHHHHHH----------HHHHcCcccCCHHHHHHHhCCCceeehhhcCC
Confidence            35677888877          33444666899999999999999999998874

>3on4_A Transcriptional regulator, TETR family; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics; HET: MSE; 1.85A {Legionella pneumophila subsp}

Probab=85.74  E-value=0.53  Score=34.28  Aligned_cols=43  Identities=2%  Similarity=0.091  Sum_probs=34.5

Q ss_pred             hHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          160 LHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       160 l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      -.++++.++.+          ++..-.-.+.|+++||.+.|+|+..+|+-|+.
T Consensus        11 ~r~~Il~aa~~----------l~~~~G~~~~t~~~IA~~agvs~~t~Y~~F~s   53 (191)
T 3on4_A           11 TKERILAVAEA----------LIQKDGYNAFSFKDIATAINIKTASIHYHFPS   53 (191)
T ss_dssp             HHHHHHHHHHH----------HHHHHCGGGCCHHHHHHHHTCCHHHHHHHCSS
T ss_pred             HHHHHHHHHHH----------HHHHhCcccCCHHHHHHHhCCCcchhhhcCCC
Confidence            35677778777          44445666899999999999999999998874

>3vnd_A TSA, tryptophan synthase alpha chain; psychrophilic enzyme, cold adaptation; HET: PE8; 2.60A {Shewanella frigidimarina}

Probab=85.66  E-value=1.6  Score=34.80  Aligned_cols=78  Identities=22%  Similarity=0.255  Sum_probs=51.4

Q ss_pred             HHHHHHhCCCCceEEEEccC--CCCCCH--------------------HHHHHHHhcC-CCCcEEEEeccCC------HH
Q 027234           14 ALDMLRTNKNGYDIVISDVH--MPDMDG--------------------FKLLELVGLE-MDLPVIMMCAHGS------KE   64 (226)
Q Consensus        14 al~~l~~~~~~~DlVl~D~~--mp~~dG--------------------~~l~~~l~~~-~~~pvI~ls~~~~------~~   64 (226)
                      .+..+.+  .+.|+|=+++=  -|-+||                    +++++.++.. .++|+++++-.+.      ..
T Consensus        37 ~~~~l~~--~GaD~iElgiPfSDP~aDGp~Iq~a~~~AL~~G~~~~~~~~~v~~ir~~~~~~Pivlm~Y~npv~~~g~e~  114 (267)
T 3vnd_A           37 IIQTLVD--NGADALELGFPFSDPLADGPVIQGANLRSLAAGTTSSDCFDIITKVRAQHPDMPIGLLLYANLVFANGIDE  114 (267)
T ss_dssp             HHHHHHH--TTCSSEEEECCCSCCTTCCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCTTCCEEEEECHHHHHHHCHHH
T ss_pred             HHHHHHH--cCCCEEEECCCCCCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCEEEEecCcHHHHhhHHH
Confidence            3444444  34899888842  244443                    5666677654 7899998865332      45


Q ss_pred             HHHHHHhCCcceEEeCCCCHHHHHHHHHH
Q 027234           65 VVMKGVTHDACDYLTKPVRIEELKNIWQH   93 (226)
Q Consensus        65 ~~~~a~~~ga~~yl~KP~~~~~L~~~l~~   93 (226)
                      ...++.+.|+++.+.-....++....++.
T Consensus       115 f~~~~~~aGvdgvii~Dlp~ee~~~~~~~  143 (267)
T 3vnd_A          115 FYTKAQAAGVDSVLIADVPVEESAPFSKA  143 (267)
T ss_dssp             HHHHHHHHTCCEEEETTSCGGGCHHHHHH
T ss_pred             HHHHHHHcCCCEEEeCCCCHhhHHHHHHH
Confidence            67889999999999987777765444433

>1sgm_A Putative HTH-type transcriptional regulator YXAF; structural genomics, PSI, protein structure initiative; 2.00A {Bacillus subtilis} SCOP: a.4.1.9 a.121.1.1

Probab=85.63  E-value=0.72  Score=33.54  Aligned_cols=42  Identities=5%  Similarity=0.024  Sum_probs=33.8

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .++++.++.+          ++..-.-.++|+++||.+.|+||..+|+-|+.
T Consensus         8 r~~Il~aa~~----------l~~~~G~~~~t~~~Ia~~agvs~~t~Y~~F~~   49 (191)
T 1sgm_A            8 REKILHTASR----------LSQLQGYHATGLNQIVKESGAPKGSLYHFFPN   49 (191)
T ss_dssp             HHHHHHHHHH----------HHHHHCTTTCCHHHHHHHHCCCSCHHHHSTTT
T ss_pred             HHHHHHHHHH----------HHHHcCccccCHHHHHHHHCCCchhHHHHccc
Confidence            4567777777          44445666899999999999999999998874

>3f1b_A TETR-like transcriptional regulator; APC5888, rhodococcus SP. RHA1, structural genomics, PS protein structure initiative; 2.40A {Rhodococcus}

Probab=85.62  E-value=0.76  Score=33.78  Aligned_cols=42  Identities=14%  Similarity=0.180  Sum_probs=33.8

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .++++.++.+          ++..-...++|+++||.+.++||..||+-|+.
T Consensus        16 r~~Il~aa~~----------l~~~~G~~~~ti~~Ia~~agvs~~t~Y~~F~s   57 (203)
T 3f1b_A           16 EQQMLDAAVD----------VFSDRGFHETSMDAIAAKAEISKPMLYLYYGS   57 (203)
T ss_dssp             HHHHHHHHHH----------HHHHHCTTTCCHHHHHHHTTSCHHHHHHHCCS
T ss_pred             HHHHHHHHHH----------HHHHcCcccccHHHHHHHhCCchHHHHHHhCC
Confidence            4567777777          44444667899999999999999999998864

>2fd5_A Transcriptional regulator; DNA-binding protein, structural G PSI, protein structure initiative, midwest center for struc genomics, MCSG; 1.70A {Pseudomonas aeruginosa} SCOP: a.4.1.9 a.121.1.1

Probab=85.38  E-value=1.1  Score=32.40  Aligned_cols=42  Identities=7%  Similarity=-0.158  Sum_probs=33.9

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .++++.++.+          ++..-.-.+.|+++||.+.|+|+..+|+-|+.
T Consensus         9 r~~Il~aA~~----------l~~~~G~~~~s~~~IA~~agvs~~tly~~F~s   50 (180)
T 2fd5_A            9 RARILGAATQ----------ALLERGAVEPSVGEVMGAAGLTVGGFYAHFQS   50 (180)
T ss_dssp             HHHHHHHHHH----------HHHHHTTTSCCHHHHHHHTTCCGGGGGGTCSC
T ss_pred             HHHHHHHHHH----------HHHHhCcccCCHHHHHHHhCCCccHHHHHCCC
Confidence            4677777777          34445566899999999999999999998874

>1neq_A DNA-binding protein NER; NMR {Enterobacteria phage MU} SCOP: a.35.1.2 PDB: 1ner_A

Probab=85.32  E-value=0.51  Score=29.80  Aligned_cols=32  Identities=6%  Similarity=0.043  Sum_probs=26.9

Q ss_pred             HHHHhhCCCCCCHHHHHHHhhhhhhhhhcccC
Q 027234          180 KILELMNIPGLTRENVASHLQKHRLYLSRLSG  211 (226)
Q Consensus       180 ~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~  211 (226)
                      .|...+...++|..++|..+|++++++++...
T Consensus        13 ri~~~l~~~glT~~~LA~~~Gvs~stls~~~~   44 (74)
T 1neq_A           13 DVIAGLKKRKLSLSALSRQFGYAPTTLANALE   44 (74)
T ss_dssp             HHHHHHHTTSCCHHHHHHHHSSCHHHHHHTTT
T ss_pred             HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            56666667799999999999999999998744

>1ka9_F Imidazole glycerol phosphtate synthase; riken structural genomics/proteomics initiative, RSGI, structural genomics, transferase; 2.30A {Thermus thermophilus} SCOP: c.1.2.1

Probab=85.29  E-value=7.6  Score=30.04  Aligned_cols=78  Identities=17%  Similarity=0.150  Sum_probs=53.4

Q ss_pred             HHHHHHHHhCCCCce-EEEEccCCCC-CC--HHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEe------CC
Q 027234           12 EIALDMLRTNKNGYD-IVISDVHMPD-MD--GFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT------KP   81 (226)
Q Consensus        12 ~eal~~l~~~~~~~D-lVl~D~~mp~-~d--G~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~------KP   81 (226)
                      .+..+.+.+..  ++ +++++..-.+ ..  .+++++.++...++|+|...+-.+.+.+.++++.|+++.+.      .|
T Consensus       155 ~e~~~~~~~~G--~~~i~~~~~~~~g~~~g~~~~~i~~l~~~~~ipvia~GGI~~~~d~~~~~~~Gadgv~vgsal~~~~  232 (252)
T 1ka9_F          155 VEWAVKGVELG--AGEILLTSMDRDGTKEGYDLRLTRMVAEAVGVPVIASGGAGRMEHFLEAFQAGAEAALAASVFHFGE  232 (252)
T ss_dssp             HHHHHHHHHHT--CCEEEEEETTTTTTCSCCCHHHHHHHHHHCSSCEEEESCCCSHHHHHHHHHTTCSEEEESHHHHTTS
T ss_pred             HHHHHHHHHcC--CCEEEEecccCCCCcCCCCHHHHHHHHHHcCCCEEEeCCCCCHHHHHHHHHCCCHHHHHHHHHHcCC
Confidence            44444444432  56 5556554222 12  38889988866789999988888889999999999999874      36


Q ss_pred             CCHHHHHHHH
Q 027234           82 VRIEELKNIW   91 (226)
Q Consensus        82 ~~~~~L~~~l   91 (226)
                      +++.++...+
T Consensus       233 ~~~~~~~~~l  242 (252)
T 1ka9_F          233 IPIPKLKRYL  242 (252)
T ss_dssp             SCHHHHHHHH
T ss_pred             CCHHHHHHHH
Confidence            6777765543

>2x48_A CAG38821; archeal virus, viral protein; 2.60A {Sulfolobus islandicus rod-shaped virusorganism_taxid}

Probab=85.23  E-value=0.38  Score=28.06  Aligned_cols=23  Identities=22%  Similarity=0.206  Sum_probs=20.6

Q ss_pred             CCCCHHHHHHHhhhhhhhhhccc
Q 027234          188 PGLTRENVASHLQKHRLYLSRLS  210 (226)
Q Consensus       188 ~~lt~~~va~~l~~~r~~l~r~~  210 (226)
                      .++|..+||..|++|++.+++..
T Consensus        30 ~g~s~~eIA~~lgis~~TV~~~l   52 (55)
T 2x48_A           30 MGYTVQQIANALGVSERKVRRYL   52 (55)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHH
Confidence            48999999999999999998754

>3qqa_A CMER; alpha-helical, helix-turn-helix, DNA-binding, transcription regulation, transcription repressor, drug binding, transcri; HET: TCH; 2.20A {Campylobacter jejuni} PDB: 3hgy_A* 3qps_A* 2qco_A 3hgg_A*

Probab=85.19  E-value=0.87  Score=33.88  Aligned_cols=44  Identities=2%  Similarity=-0.112  Sum_probs=35.7

Q ss_pred             hhHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          159 ELHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       159 ~l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .-.++++.++.+          ++..-...++|+++||.+.|+|+..+|+-|+.
T Consensus        19 ~~r~~Il~aA~~----------lf~~~G~~~~t~~~IA~~agvs~~tlY~~F~s   62 (216)
T 3qqa_A           19 ARQEKIKAVALE----------LFLTKGYQETSLSDIIKLSGGSYSNIYDGFKS   62 (216)
T ss_dssp             HHHHHHHHHHHH----------HHHHTCTTTCCHHHHHHHHTTSCCSSSCSCCS
T ss_pred             HHHHHHHHHHHH----------HHHHcChhhCCHHHHHHHhCCCHHHHHHhcCC
Confidence            345678888888          44555677899999999999999999998864

>1pb6_A Hypothetical transcriptional regulator YCDC; helix-loop-helix, dimer, structural genomics, PSI, protein structure initiative; 2.50A {Escherichia coli} PDB: 3loc_A*

Probab=85.12  E-value=0.8  Score=33.96  Aligned_cols=44  Identities=14%  Similarity=0.089  Sum_probs=35.3

Q ss_pred             hhHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          159 ELHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       159 ~l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .-.++++.++.+          ++..-.-.++|+++||.+.|+|+..+|+-|+.
T Consensus        18 ~~r~~Il~aa~~----------l~~~~G~~~~s~~~Ia~~agvs~~t~Y~~F~s   61 (212)
T 1pb6_A           18 AKKKAILSAALD----------TFSQFGFHGTRLEQIAELAGVSKTNLLYYFPS   61 (212)
T ss_dssp             HHHHHHHHHHHH----------HHHHHCTTTCCHHHHHHHTTSCHHHHHHHSSS
T ss_pred             HHHHHHHHHHHH----------HHHHcCcchhhHHHHHHHHCCChhHHHHhCCC
Confidence            345678888888          34444667899999999999999999998864

>2w6r_A Imidazole glycerol phosphate synthase subunit HISF; lyase, fusion protein, cobalamin, precorrin, novel fold, VIT; 2.10A {Thermotoga maritima}

Probab=85.11  E-value=5.4  Score=31.23  Aligned_cols=68  Identities=12%  Similarity=0.093  Sum_probs=47.3

Q ss_pred             HHHHHHHHHhCCCCceEEEE-ccCCCC-CC--HHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEeC
Q 027234           11 AEIALDMLRTNKNGYDIVIS-DVHMPD-MD--GFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTK   80 (226)
Q Consensus        11 ~~eal~~l~~~~~~~DlVl~-D~~mp~-~d--G~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~K   80 (226)
                      ..+..+.+....  ++.|++ ++.-.+ ..  .+++++.++...++|+|...+-.+.+.+.+++..||++.+.=
T Consensus       158 ~~e~~~~~~~~G--~~~i~~t~~~~~g~~~g~~~~~i~~l~~~~~ipvia~GGI~~~ed~~~~~~~Gadgv~vg  229 (266)
T 2w6r_A          158 LRDWVVEVEKRG--AGEILLTSIDRDGTKSGYDTEMIRFVRPLTTLPIIASGGAGKMEHFLEAFLAGADAALAA  229 (266)
T ss_dssp             HHHHHHHHHHTT--CSEEEEEETTTTTTCSCCCHHHHHHHGGGCCSCEEEESCCCSHHHHHHHHHHTCSEEEES
T ss_pred             HHHHHHHHHHcC--CCEEEEEeecCCCCcCCCCHHHHHHHHHHcCCCEEEeCCCCCHHHHHHHHHcCCHHHHcc
Confidence            445545555533  666554 433111 12  378889998777899999999888899999999999998743

>3nrg_A TETR family transcriptional regulator; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; 2.56A {Chloroflexus aurantiacus}

Probab=85.08  E-value=0.74  Score=34.31  Aligned_cols=44  Identities=2%  Similarity=0.024  Sum_probs=35.3

Q ss_pred             hhHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          159 ELHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       159 ~l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .-.++++.++.+          +...-...+.|+++||.+.++|+..+|+-|+.
T Consensus        13 ~~r~~Il~aA~~----------lf~~~G~~~~t~~~IA~~agvs~~tlY~~F~s   56 (217)
T 3nrg_A           13 EKRSRLIDVLLD----------EFAQNDYDSVSINRITERAGIAKGSFYQYFAD   56 (217)
T ss_dssp             HHHHHHHHHHHH----------HHHHSCGGGCCHHHHHHHHTCCTTGGGGTCSS
T ss_pred             HHHHHHHHHHHH----------HHHhcCcccCCHHHHHHHhCCcHHHHHHHcCC
Confidence            345678888887          44445666899999999999999999998875

>3o07_A Pyridoxine biosynthesis protein SNZ1; (beta/alpha)8-barrel, pyridoxal 5-phosphate synthase, PLP G3 SNO1, biosynthetic protein; HET: 1GP; 1.80A {Saccharomyces cerevisiae} PDB: 3o06_A 3o05_A* 3fem_A

Probab=85.05  E-value=7.7  Score=31.11  Aligned_cols=96  Identities=14%  Similarity=0.034  Sum_probs=68.3

Q ss_pred             EEEECCHHHHHHHHHhCCCCceEEEEccC-------------------------C-CC----------CCHHHHHHHHhc
Q 027234            5 VTKCNRAEIALDMLRTNKNGYDIVISDVH-------------------------M-PD----------MDGFKLLELVGL   48 (226)
Q Consensus         5 V~~~~~~~eal~~l~~~~~~~DlVl~D~~-------------------------m-p~----------~dG~~l~~~l~~   48 (226)
                      |.-|.|..||+..+...   .|+|=+-..                         | ..          ...+++++.+++
T Consensus       119 v~~~~~l~EAlrri~eG---A~mIrTtge~gtg~v~~av~h~r~~~~~i~~l~g~~t~~el~~~a~~~~ad~elI~~Ike  195 (291)
T 3o07_A          119 VCGAKDLGEALRRINEG---AAMIRTKGEAGTGDVSEAVKHIRRITEEIKACQQLKSEDDIAKVAEEMRVPVSLLKDVLE  195 (291)
T ss_dssp             EEEESSHHHHHHHHHHT---CSEEEECCCTTSCCTHHHHHHHHHHHHHHHHHHTCCCHHHHHHHHHHHTSCHHHHHHHHH
T ss_pred             EeeCCCHHHHHHHHHCC---CCEEEecCcCCCccHHHHHHHHHHHHHHHHHHHcCCCHHHhhhcccccCCCHHHHHHHHH
Confidence            34688999999999865   688876411                         2 11          234677888876


Q ss_pred             CCCCcEEEE--eccCCHHHHHHHHhCCcceEE-----eCCCCHHHHHHHHHHHHHHHhhhhh
Q 027234           49 EMDLPVIMM--CAHGSKEVVMKGVTHDACDYL-----TKPVRIEELKNIWQHVVRKRKNERK  103 (226)
Q Consensus        49 ~~~~pvI~l--s~~~~~~~~~~a~~~ga~~yl-----~KP~~~~~L~~~l~~~~~~~~~~~~  103 (226)
                      ...+|||++  .+-...+.+..+++.|+++.+     .+.-++......+...+........
T Consensus       196 ~~~IPVV~IAnGGI~TpedA~~~le~GaDGVmVGrAI~~s~DP~~~Akafv~Av~~~~~~~~  257 (291)
T 3o07_A          196 KGKLPVVNFAAGGVATPADAALLMQLGCDGVFVGSGIFKSSNPVRLATAVVEATTHFDNPSK  257 (291)
T ss_dssp             HTSCSSCEEBCSSCCSHHHHHHHHHTTCSCEEECGGGGGSSCHHHHHHHHHHHHHTTTCHHH
T ss_pred             ccCCCEEEecCCCCCCHHHHHHHHHhCCCEEEEchHHhCCCCHHHHHHHHHHHHHhccCHHH
Confidence            688999887  333468999999999999987     4456678887777777765443333

>2g7s_A Transcriptional regulator, TETR family; APC5906, PSI, protein structure initiat midwest center for structural genomics, MCSG; HET: MSE; 1.40A {Agrobacterium tumefaciens str} SCOP: a.4.1.9 a.121.1.1

Probab=84.91  E-value=0.57  Score=34.15  Aligned_cols=43  Identities=0%  Similarity=0.004  Sum_probs=33.9

Q ss_pred             hHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          160 LHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       160 l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      -.++++.++.+          ++..-.-.++|+++||.+.|+||..+|+-|+.
T Consensus         9 ~r~~Il~aa~~----------l~~~~G~~~~ti~~Ia~~agvs~~t~Y~~F~s   51 (194)
T 2g7s_A            9 KADDILQCART----------LIIRGGYNSFSYADISQVVGIRNASIHHHFPS   51 (194)
T ss_dssp             HHHHHHHHHHH----------HHHHHCGGGCCHHHHHHHHCCCHHHHHHHCSS
T ss_pred             hHHHHHHHHHH----------HHHHcCcccCCHHHHHHHhCCCchHHHHHcCC
Confidence            35677777777          33344566899999999999999999998874

>2v57_A TETR family transcriptional repressor LFRR; DNA-binding, transcription regulation; HET: PRL; 1.90A {Mycobacterium smegmatis} PDB: 2wgb_A

Probab=84.91  E-value=0.59  Score=34.16  Aligned_cols=42  Identities=12%  Similarity=0.086  Sum_probs=34.7

Q ss_pred             hhHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          159 ELHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       159 ~l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      ...++++.++.+         .+.+.   .+.|+++||.+.|+|+..||+-|+.
T Consensus        14 ~~r~~Il~aA~~---------lf~~~---~~~t~~~Ia~~agvs~~t~Y~~F~s   55 (190)
T 2v57_A           14 RTRRAILDAAML---------VLADH---PTAALGDIAAAAGVGRSTVHRYYPE   55 (190)
T ss_dssp             HHHHHHHHHHHH---------HHTTC---TTCCHHHHHHHHTCCHHHHHHHCSS
T ss_pred             HHHHHHHHHHHH---------HHHHc---CCCCHHHHHHHhCCCHHHHHHHcCC
Confidence            345678888888         35555   6999999999999999999998864

>4fe7_A Xylose operon regulatory protein; HTH_ARAC, helix-turn-helix, PBP, periplasmic binding protein binding transcription regulator, DNA xylose; HET: XYS; 2.90A {Escherichia coli} PDB: 4fe4_A

Probab=84.84  E-value=0.37  Score=40.63  Aligned_cols=37  Identities=14%  Similarity=0.014  Sum_probs=30.5

Q ss_pred             HHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCCC-CCCC
Q 027234          180 KILELMNIPGLTRENVASHLQKHRLYLSRLSGVS-PQQG  217 (226)
Q Consensus       180 ~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~~-~~~~  217 (226)
                      .|.+++.. .++++++|+++++|+++|+|+|+.. ++.+
T Consensus       313 ~i~~~~~~-~~~~~~~a~~~~~s~~~l~r~f~~~~g~s~  350 (412)
T 4fe7_A          313 YIRNHACK-GIKVDQVLDAVGISRSNLEKRFKEEVGETI  350 (412)
T ss_dssp             HHHHHGGG-TCCHHHHHHHTTCCHHHHHHHHHHHHSSCH
T ss_pred             HHHhhccC-CCCHHHHHHHHCcCHHHHHHHHHHHHCcCH
Confidence            57788765 9999999999999999999988654 4443

>1zk8_A Transcriptional regulator, TETR family; TETR member,transcriptional regulator, STRU genomics, PSI, protein structure initiative; 2.15A {Bacillus cereus atcc 14579} SCOP: a.4.1.9 a.121.1.1

Probab=84.74  E-value=0.76  Score=33.36  Aligned_cols=42  Identities=19%  Similarity=0.122  Sum_probs=33.0

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .++++.++.+          ++..-.-.+.|+++||.+.|+||..+|+-|+.
T Consensus        10 r~~Il~aa~~----------l~~~~G~~~~t~~~Ia~~agvs~~t~Y~~F~s   51 (183)
T 1zk8_A           10 LQKIVETAAE----------IADANGVQEVTLASLAQTLGVRSPSLYNHVKG   51 (183)
T ss_dssp             HHHHHHHHHH----------HHHHHCGGGCCHHHHHHHHTSCHHHHTTTCSS
T ss_pred             HHHHHHHHHH----------HHHhcCccccCHHHHHHHcCCCchHHHHHcCC
Confidence            4567777777          33334556899999999999999999998864

>2qko_A Possible transcriptional regulator, TETR family P; TETR family protein, structural genomics, P protein structure initiative; 2.35A {Rhodococcus SP}

Probab=84.63  E-value=0.78  Score=34.40  Aligned_cols=44  Identities=23%  Similarity=0.116  Sum_probs=35.5

Q ss_pred             hhHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          159 ELHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       159 ~l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .-.++++.++.+          ++..-.-.++|+++||.+.++||..||+-|+.
T Consensus        28 ~~r~~Il~aa~~----------lf~~~G~~~~tv~~IA~~agvs~~t~Y~~F~s   71 (215)
T 2qko_A           28 ERRAALVNAAIE----------VLAREGARGLTFRAVDVEANVPKGTASNYFPS   71 (215)
T ss_dssp             HHHHHHHHHHHH----------HHHHTCTTTCCHHHHHHHSSSTTTCHHHHCSC
T ss_pred             HHHHHHHHHHHH----------HHHHhChhhccHHHHHHHcCCCcchHHHhCCC
Confidence            345678888887          44445666899999999999999999998864

>3dew_A Transcriptional regulator, TETR family; S genomics, PSI-2, protein structure initiative, midwest CENT structural genomics, MCSG; HET: MSE; 1.75A {Geobacter sulfurreducens}

Probab=84.59  E-value=0.63  Score=34.22  Aligned_cols=43  Identities=12%  Similarity=0.121  Sum_probs=34.1

Q ss_pred             hHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          160 LHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       160 l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      ..++++.++.+          ++..-...++|+++||.+.|+||..||+-|+.
T Consensus         9 ~r~~Il~aa~~----------l~~~~G~~~~t~~~Ia~~agvs~~t~Y~~F~s   51 (206)
T 3dew_A            9 CRSRLMEVATE----------LFAQKGFYGVSIRELAQAAGASISMISYHFGG   51 (206)
T ss_dssp             HHHHHHHHHHH----------HHHHHCGGGCCHHHHHHHHTCCHHHHHHHSCH
T ss_pred             HHHHHHHHHHH----------HHhcCCcccCcHHHHHHHhCCCHHHHHHHcCC
Confidence            34677778777          44445666899999999999999999998863

>3vpr_A Transcriptional regulator, TETR family; all alpha, helix-turn-helix, transcriptional repressor, DNA protein; 2.27A {Thermus thermophilus}

Probab=84.56  E-value=0.82  Score=33.51  Aligned_cols=42  Identities=10%  Similarity=0.132  Sum_probs=32.9

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .++++.++.+          +...-.-.+.|+++||.+.|+||..+|+-|+.
T Consensus         5 r~~Il~aA~~----------lf~~~G~~~~s~~~IA~~agvsk~t~Y~~F~s   46 (190)
T 3vpr_A            5 RDRILEEAAK----------LFTEKGYEATSVQDLAQALGLSKAALYHHFGS   46 (190)
T ss_dssp             HHHHHHHHHH----------HHHHHCSTTCCHHHHHHHHTCCHHHHHHHHSS
T ss_pred             HHHHHHHHHH----------HHHHhCcccCCHHHHHHHhCCCHHHHHHHcCC
Confidence            3566677776          44445667899999999999999999997764

>2ras_A Transcriptional regulator, TETR family; bacterial regulatory proteins, DNA-binding, DNA binding 3-helical bundle fold; 1.80A {Novosphingobium aromaticivorans}

Probab=84.52  E-value=1.1  Score=33.36  Aligned_cols=43  Identities=23%  Similarity=0.257  Sum_probs=34.6

Q ss_pred             hHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          160 LHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       160 l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      ..++++.++.+          ++..-.-.+.|+++||.+.|+|+..+|+-|+.
T Consensus        12 ~r~~Il~aA~~----------lf~~~G~~~~s~~~IA~~agvs~~t~Y~~F~s   54 (212)
T 2ras_A           12 MRARLVDVAQA----------IVEERGGAGLTLSELAARAGISQANLSRYFET   54 (212)
T ss_dssp             HHHHHHHHHHH----------HHHHHTSSCCCHHHHHHHHTSCHHHHTTTCSS
T ss_pred             HHHHHHHHHHH----------HHHHhCcccCcHHHHHHHhCCCHHHHHHHcCC
Confidence            35678888887          33444566899999999999999999998874

>2rae_A Transcriptional regulator, ACRR family protein; TETR/ACRR family transcriptional regulator, structural genom 2, RHA08332, MCSG; 2.20A {Rhodococcus SP}

Probab=84.48  E-value=0.9  Score=33.64  Aligned_cols=44  Identities=14%  Similarity=0.051  Sum_probs=35.1

Q ss_pred             hHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCCC
Q 027234          160 LHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGVS  213 (226)
Q Consensus       160 l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~~  213 (226)
                      ..++++.++.+          ++..-...++|+++||.+.|+||..||+-|+.-
T Consensus        18 ~r~~Il~aa~~----------l~~~~G~~~~ti~~Ia~~agvs~~t~Y~~F~sK   61 (207)
T 2rae_A           18 TQDRISTVGIE----------LFTEQGFDATSVDEVAEASGIARRTLFRYFPSK   61 (207)
T ss_dssp             HHHHHHHHHHH----------HHHHHCTTTSCHHHHHHHTTSCHHHHHHHCSST
T ss_pred             HHHHHHHHHHH----------HHHHcCcccCCHHHHHHHhCCCcchHhhhCCCH
Confidence            45677778777          444455668999999999999999999988754

>3cwr_A Transcriptional regulator, TETR family; YP_425770.1, transcriptional regulator of TETR family, bacterial regulatory proteins; 1.50A {Rhodospirillum rubrum atcc 11170}

Probab=84.34  E-value=0.66  Score=34.21  Aligned_cols=44  Identities=23%  Similarity=0.229  Sum_probs=35.4

Q ss_pred             hhHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          159 ELHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       159 ~l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .-.++++.++.+          ++..-...++|+++||.+.|+|+..+|+-|+.
T Consensus        17 ~~r~~Il~aa~~----------lf~~~G~~~~ti~~Ia~~agvs~~t~Y~~F~s   60 (208)
T 3cwr_A           17 VVRESIVGAAQR----------LLSSGGAAAMTMEGVASEAGIAKKTLYRFASG   60 (208)
T ss_dssp             HHHHHHHHHHHH----------HHHHHCGGGCCHHHHHHHHTCCHHHHHHHCSS
T ss_pred             HHHHHHHHHHHH----------HHHHcCHHhccHHHHHHHhCCCHHHHHHHcCC
Confidence            345788888888          44444666899999999999999999998864

>3bru_A Regulatory protein, TETR family; structural genomics, APC88928, PSI-2, protein structur initiative; 2.30A {Rhodobacter sphaeroides 2}

Probab=84.33  E-value=0.94  Score=33.90  Aligned_cols=44  Identities=11%  Similarity=0.006  Sum_probs=35.3

Q ss_pred             hhHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          159 ELHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       159 ~l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .-.++++.++.+          ++..-.-.++|+++||.+.|+||..||+-|+.
T Consensus        30 ~~r~~Il~aA~~----------l~~~~G~~~~t~~~IA~~aGvs~~t~Y~~F~s   73 (222)
T 3bru_A           30 LAHQSLIRAGLE----------HLTEKGYSSVGVDEILKAARVPKGSFYHYFRN   73 (222)
T ss_dssp             GHHHHHHHHHHH----------HHHHSCTTTCCHHHHHHHHTCCHHHHHHHCSS
T ss_pred             hHHHHHHHHHHH----------HHHHcCCCcCcHHHHHHHhCCCcchhhhhCCC
Confidence            345678888888          44445666899999999999999999998864

>2hxo_A Putative TETR-family transcriptional regulator; TETR transcriptional regulator, structural genomics, PSI-2, structure initiative; 2.40A {Streptomyces coelicolor}

Probab=84.25  E-value=1.4  Score=34.11  Aligned_cols=42  Identities=21%  Similarity=0.167  Sum_probs=34.4

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .++++.++..          ++..-...++|+..||.++++++..||+-|+.
T Consensus        18 r~~Il~aA~~----------l~~~~G~~~~s~~~IA~~aGvs~~tlY~hF~~   59 (237)
T 2hxo_A           18 RERIVGAAVE----------LLDTVGERGLTFRALAERLATGPGAIYWHITG   59 (237)
T ss_dssp             HHHHHHHHHH----------HHHHTTTTTCCHHHHHHHHTSCGGGGGGTCCC
T ss_pred             HHHHHHHHHH----------HHHhcCcccCCHHHHHHHHCCChHHHHHhcCC
Confidence            5677777777          44555667899999999999999999998874

>3egq_A TETR family transcriptional regulator; DNA-binding, transcription regulation, bacterial regulatory DNA/RNA-binding 3-helical bundle fold; HET: MSE PE8; 2.55A {Archaeoglobus fulgidus}

Probab=84.24  E-value=0.59  Score=33.55  Aligned_cols=42  Identities=7%  Similarity=-0.009  Sum_probs=31.7

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .++++.++.+          ++..-.-.++|+++||.+.|+||..+|+-|+.
T Consensus         6 r~~Il~aa~~----------l~~~~G~~~~t~~~Ia~~agvs~~t~Y~~F~s   47 (170)
T 3egq_A            6 SVRIIEAALR----------LYMKKPPHEVSIEEIAREAKVSKSLIFYHFES   47 (170)
T ss_dssp             HHHHHHHHHH----------HHTTSCGGGCCHHHHHHHHTSCHHHHHHHCSS
T ss_pred             HHHHHHHHHH----------HHHhcCCccCcHHHHHHHhCCCchhHHHHcCC
Confidence            4566666666          33333445789999999999999999998864

>4hku_A LMO2814 protein, TETR transcriptional regulator; structural genomics, PSI-biology; 2.30A {Listeria monocytogenes}

Probab=84.23  E-value=0.92  Score=33.07  Aligned_cols=42  Identities=14%  Similarity=0.104  Sum_probs=32.8

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .++++.++.+          +...-.-.+.|+++||.+.|+|+..+|+-|+.
T Consensus         9 Re~Il~aA~~----------lf~~~G~~~~s~~~IA~~aGvs~~tlY~~F~s   50 (178)
T 4hku_A            9 QEIILNMAEK----------IIYEKGMEKTTLYDIASNLNVTHAALYKHYRN   50 (178)
T ss_dssp             HHHHHHHHHH----------HHHHHCGGGCCHHHHHHHTTSCGGGGGGTCSS
T ss_pred             HHHHHHHHHH----------HHHHhCcccccHHHHHHHhCcCHhHHHHHCCC
Confidence            3567777777          33334556889999999999999999998874

>2qtq_A Transcriptional regulator, TETR family; transcription regulator, DNA/RNA-binding 3-helical bundle FO turn helix motif, HTH motif; HET: MSE; 1.85A {Novosphingobium aromaticivorans} PDB: 2rha_A*

Probab=84.20  E-value=0.79  Score=33.99  Aligned_cols=44  Identities=5%  Similarity=0.070  Sum_probs=34.8

Q ss_pred             hhHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          159 ELHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       159 ~l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      ...++++.++.+          ++..-.-.++|+++||.+.++||..+|+-|+.
T Consensus        16 ~~r~~Il~aa~~----------lf~~~G~~~~t~~~Ia~~agvs~~t~Y~~F~s   59 (213)
T 2qtq_A           16 GARDLLLQTASN----------IMREGDVVDISLSELSLRSGLNSALVKYYFGN   59 (213)
T ss_dssp             THHHHHHHHHHH----------HHHHHTSSCCCHHHHHHHHCCCHHHHHHHHSS
T ss_pred             hHHHHHHHHHHH----------HHHHcCcccccHHHHHHHhCCChhhHhHhcCC
Confidence            345677888877          34445566899999999999999999998864

>3ccy_A Putative TETR-family transcriptional regulator; APC88698, structural G PSI-2, protein structure initiative; HET: MSE; 2.01A {Bordetella parapertussis 12822}

Probab=84.07  E-value=1.3  Score=32.73  Aligned_cols=43  Identities=5%  Similarity=0.057  Sum_probs=34.5

Q ss_pred             hHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          160 LHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       160 l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      -.++++.++.+          +...-.-.+.|+++||...|+||..||+-|+.
T Consensus        15 ~r~~Il~aA~~----------lf~~~G~~~~s~~~Ia~~agvs~~t~Y~yF~s   57 (203)
T 3ccy_A           15 IRDTIIERAAA----------MFARQGYSETSIGDIARACECSKSRLYHYFDS   57 (203)
T ss_dssp             HHHHHHHHHHH----------HHHHTCTTTSCHHHHHHHTTCCGGGGTTTCSC
T ss_pred             HHHHHHHHHHH----------HHHHcCcccCCHHHHHHHhCCCcCeeeeeeCC
Confidence            35677888877          44444666899999999999999999998864

>2dg7_A Putative transcriptional regulator; helix-turn-helix motif, TETR family, gene regulation; 2.30A {Streptomyces coelicolor}

Probab=84.02  E-value=0.65  Score=34.19  Aligned_cols=45  Identities=16%  Similarity=0.049  Sum_probs=34.8

Q ss_pred             hHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCCCC
Q 027234          160 LHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGVSP  214 (226)
Q Consensus       160 l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~~~  214 (226)
                      -.++++.++.+          ++..-...++|+++||.+.|+||..||+-|+.-.
T Consensus         8 ~r~~Il~aA~~----------l~~~~G~~~~t~~~Ia~~agvs~~t~Y~~F~sK~   52 (195)
T 2dg7_A            8 AEQRLKRAALE----------LYSEHGYDNVTVTDIAERAGLTRRSYFRYFPDKR   52 (195)
T ss_dssp             HHHHHHHHHHH----------HHHHSCGGGCCHHHHHHHTTCCHHHHHHHCSSTT
T ss_pred             HHHHHHHHHHH----------HHHhcCccccCHHHHHHHhCCCHHHHHHHcCCHH
Confidence            34677777777          3444456689999999999999999999887643

>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=83.82  E-value=2.8  Score=33.26  Aligned_cols=72  Identities=18%  Similarity=0.212  Sum_probs=49.3

Q ss_pred             CCceEEEEccCC--CCCC--------------------HHHHHHHHhcC-CCCcEEEEeccC------CHHHHHHHHhCC
Q 027234           23 NGYDIVISDVHM--PDMD--------------------GFKLLELVGLE-MDLPVIMMCAHG------SKEVVMKGVTHD   73 (226)
Q Consensus        23 ~~~DlVl~D~~m--p~~d--------------------G~~l~~~l~~~-~~~pvI~ls~~~------~~~~~~~a~~~g   73 (226)
                      .+.|+|-+|+-.  |-+|                    ++++++.++.. .++|+++++-..      .......+...|
T Consensus        43 ~GaD~ieig~P~sdp~~DG~~i~~a~~~al~~G~~~~~~~~~v~~ir~~~~~~Pv~lm~y~n~v~~~g~~~~~~~~~~aG  122 (268)
T 1qop_A           43 AGADALELGVPFSDPLADGPTIQNANLRAFAAGVTPAQCFEMLAIIREKHPTIPIGLLMYANLVFNNGIDAFYARCEQVG  122 (268)
T ss_dssp             TTCSSEEEECCCSCCTTCCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCSSSCEEEEECHHHHHTTCHHHHHHHHHHHT
T ss_pred             CCCCEEEECCCCCCccCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCEEEEEcccHHHHhhHHHHHHHHHHcC
Confidence            348999998733  3333                    34667777765 689998875222      146677889999


Q ss_pred             cceEEeCCCCHHHHHHHHHHH
Q 027234           74 ACDYLTKPVRIEELKNIWQHV   94 (226)
Q Consensus        74 a~~yl~KP~~~~~L~~~l~~~   94 (226)
                      +++++.-....+++...++.+
T Consensus       123 adgii~~d~~~e~~~~~~~~~  143 (268)
T 1qop_A          123 VDSVLVADVPVEESAPFRQAA  143 (268)
T ss_dssp             CCEEEETTCCGGGCHHHHHHH
T ss_pred             CCEEEEcCCCHHHHHHHHHHH
Confidence            999999888776655554443

>3on2_A Probable transcriptional regulator; protein structure initiative, PSI-2, structural genomics, MI center for structural genomics, MCSG; HET: MSE PG6; 1.96A {Rhodococcus jostii}

Probab=83.82  E-value=0.73  Score=33.69  Aligned_cols=43  Identities=16%  Similarity=0.139  Sum_probs=29.2

Q ss_pred             hHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          160 LHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       160 l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      ..++++.++.+          ++..-...++|+++||.+.|+|+..+|+-|+.
T Consensus        13 ~r~~Il~aA~~----------lf~~~G~~~~t~~~IA~~agvs~~t~Y~~F~s   55 (199)
T 3on2_A           13 LRRVLLARAES----------TLEKDGVDGLSLRQLAREAGVSHAAPSKHFRD   55 (199)
T ss_dssp             HHHHHHHHHHH----------HHHHHCGGGCCHHHHHHHTC-----CCCSSSS
T ss_pred             HHHHHHHHHHH----------HHHhcChhhhhHHHHHHHhCCChHHHHHHhCC
Confidence            34677777777          34444566899999999999999999998874

>3aqt_A Bacterial regulatory proteins, TETR family; helix-turn-helix, all alpha, transcription, transcription RE transcription regulator; 2.50A {Corynebacterium glutamicum} PDB: 3aqs_A

Probab=83.73  E-value=0.93  Score=34.96  Aligned_cols=44  Identities=0%  Similarity=0.012  Sum_probs=34.6

Q ss_pred             hhHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          159 ELHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       159 ~l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      ...++++.++.+          ++..-...++|+++||.+.++||..||+-|+.
T Consensus        46 ~~r~~Il~aA~~----------lf~~~G~~~~t~~~IA~~aGvs~~t~Y~~F~s   89 (245)
T 3aqt_A           46 QTRARLITSART----------LMAERGVDNVGIAEITEGANIGTGTFYNYFPD   89 (245)
T ss_dssp             HHHHHHHHHHHH----------HHHHHCGGGCCHHHHHHHTTSCGGGGGGTCSS
T ss_pred             HHHHHHHHHHHH----------HHHhcCcccCcHHHHHHHhCCChHHHHHHcCC
Confidence            345677778777          33444566899999999999999999998874

>4adt_A Pyridoxine biosynthetic enzyme PDX1 homologue, PU; transferase, pyridoxal 5-phosphate biosynthesis; 2.42A {Plasmodium berghei} PDB: 4adu_A* 4ads_A

Probab=83.68  E-value=16  Score=29.51  Aligned_cols=89  Identities=11%  Similarity=0.091  Sum_probs=59.6

Q ss_pred             EEEECCHHHHHHHHHhCCCCceEEEEccC-------------------------CCC----------CCHHHHHHHHhcC
Q 027234            5 VTKCNRAEIALDMLRTNKNGYDIVISDVH-------------------------MPD----------MDGFKLLELVGLE   49 (226)
Q Consensus         5 V~~~~~~~eal~~l~~~~~~~DlVl~D~~-------------------------mp~----------~dG~~l~~~l~~~   49 (226)
                      |..+.+..||...+...   +|+|.+...                         |+.          ...+++++.++..
T Consensus       129 vv~v~~~~Ea~~a~~~G---ad~I~v~g~~gTG~~~~~v~h~~~~~~eir~l~~~~~d~L~t~~~~~~~~~~ll~~i~~~  205 (297)
T 4adt_A          129 VCGCTNLGEALRRISEG---ASMIRTKGEAGTGNIIEAIKHIRTVNNEIKYLCSLDESEVYNFAKKLRAPIDLILLTRKL  205 (297)
T ss_dssp             EEEESSHHHHHHHHHHT---CSEEEECCCTTSCCCHHHHHHHHHHHHHHHHHHHSCTTTHHHHHHHHTCCHHHHHHHHHH
T ss_pred             EEEeCCHHHHHHHHhCC---CCEEEECCCcCCCchHHHHHHHHHhhhhhhhhccccccccccccccCCCCHHHHHHHHHh
Confidence            44688999999888753   788888743                         111          1125667777655


Q ss_pred             CCCcEEE--EeccCCHHHHHHHHhCCcceEEe-----CCCCHHHHHHHHHHHHH
Q 027234           50 MDLPVIM--MCAHGSKEVVMKGVTHDACDYLT-----KPVRIEELKNIWQHVVR   96 (226)
Q Consensus        50 ~~~pvI~--ls~~~~~~~~~~a~~~ga~~yl~-----KP~~~~~L~~~l~~~~~   96 (226)
                      ..+|+|+  .++-.+.+.+..++..||++++.     |.-++......+...+.
T Consensus       206 ~~iPVivvA~GGI~t~~dv~~~~~~GAdgVlVGsai~~a~dp~~~~~~l~~ai~  259 (297)
T 4adt_A          206 KRLPVVNFAAGGIATPADAAMCMQLGMDGVFVGSGIFESENPQKMASSIVMAVS  259 (297)
T ss_dssp             TSCSSEEEEESCCCSHHHHHHHHHTTCSCEEESHHHHTSSCHHHHHHHHHHHHH
T ss_pred             cCCCeEEEecCCCCCHHHHHHHHHcCCCEEEEhHHHHcCCCHHHHHHHHHHHHH
Confidence            5678874  44555889999999999999884     45566555555554444

>3bni_A Putative TETR-family transcriptional regulator; structural genomics, APC7281; HET: PG4; 2.30A {Streptomyces coelicolor A3}

Probab=83.64  E-value=1  Score=34.21  Aligned_cols=44  Identities=18%  Similarity=0.175  Sum_probs=35.3

Q ss_pred             hhHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          159 ELHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       159 ~l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .-.++++.++.+          ++..-.-.++|+++||...++||..||+-|+.
T Consensus        43 ~~r~~Il~aA~~----------l~~~~G~~~~tv~~IA~~AGvs~~t~Y~~F~s   86 (229)
T 3bni_A           43 ERLTRILDACAD----------LLDEVGYDALSTRAVALRADVPIGSVYRFFGN   86 (229)
T ss_dssp             HHHHHHHHHHHH----------HHHHHCTTTCCHHHHHHHHTCCHHHHHHHCSS
T ss_pred             HHHHHHHHHHHH----------HHHhcChhhccHHHHHHHHCCCchhHHHHcCC
Confidence            345678888888          34445667899999999999999999998874

>3gzi_A Transcriptional regulator, TETR family; TETR family transcriptional regulator, structural genomics, center for structural genomics, JCSG; 2.05A {Shewanella loihica pv-4}

Probab=83.52  E-value=0.87  Score=33.97  Aligned_cols=43  Identities=9%  Similarity=0.072  Sum_probs=35.0

Q ss_pred             hHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          160 LHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       160 l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      ..++++.++.+          ++..-...++|+++||.+.|+|+..+|+-|+.
T Consensus        18 ~r~~Il~aA~~----------l~~~~G~~~~t~~~IA~~agvs~~t~Y~~F~s   60 (218)
T 3gzi_A           18 NRDKLILAARN----------LFIERPYAQVSIREIASLAGTDPGLIRYYFGS   60 (218)
T ss_dssp             HHHHHHHHHHH----------HHHTSCCSCCCHHHHHHHHTSCTHHHHHHHSS
T ss_pred             HHHHHHHHHHH----------HHHHCCCCcCCHHHHHHHhCCCHHHHHHHcCC
Confidence            45678888888          44445666899999999999999999998864

>2yve_A Transcriptional regulator; helix-turn-helix, TETR-family; HET: MBT; 1.40A {Corynebacterium glutamicum} PDB: 1v7b_A 2zoy_A 2yvh_A 2dh0_A* 2zoz_A*

Probab=83.39  E-value=1  Score=32.96  Aligned_cols=42  Identities=7%  Similarity=0.015  Sum_probs=32.5

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .++++.++..          ++..-...++|+++||.+.|+||..+|+-|+.
T Consensus         6 r~~Il~aa~~----------l~~~~G~~~~t~~~Ia~~agvs~~t~Y~~F~s   47 (185)
T 2yve_A            6 KEMILRTAID----------YIGEYSLETLSYDSLAEATGLSKSGLIYHFPS   47 (185)
T ss_dssp             HHHHHHHHHH----------HHHHSCSTTCCHHHHHHHHCCCHHHHHHHCSS
T ss_pred             HHHHHHHHHH----------HHHHcChhhccHHHHHHHhCCChHHHHHhCcC
Confidence            3456666666          34444566899999999999999999998864

>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=83.30  E-value=9.7  Score=26.75  Aligned_cols=90  Identities=10%  Similarity=-0.062  Sum_probs=59.4

Q ss_pred             CcEEE---EECCHHHHHHHHHhCCCCceEEEEccCCCCC-C-HHHHHHHHhcC-C-CCcEEEEecc-----CCHH-HHHH
Q 027234            2 GFSVT---KCNRAEIALDMLRTNKNGYDIVISDVHMPDM-D-GFKLLELVGLE-M-DLPVIMMCAH-----GSKE-VVMK   68 (226)
Q Consensus         2 g~~V~---~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~-d-G~~l~~~l~~~-~-~~pvI~ls~~-----~~~~-~~~~   68 (226)
                      ||+|.   ...+.++..+.+.+..  +|+|.+...+... . --++++.+++. . +++|+ +.+.     .+.. ....
T Consensus        31 G~~Vi~lG~~~p~e~~v~~a~~~~--~d~v~lS~~~~~~~~~~~~~i~~l~~~g~~~i~v~-vGG~~~~~~~~~~~~~~~  107 (137)
T 1ccw_A           31 GFNVVNIGVLSPQELFIKAAIETK--ADAILVSSLYGQGEIDCKGLRQKCDEAGLEGILLY-VGGNIVVGKQHWPDVEKR  107 (137)
T ss_dssp             TCEEEEEEEEECHHHHHHHHHHHT--CSEEEEEECSSTHHHHHTTHHHHHHHTTCTTCEEE-EEESCSSSSCCHHHHHHH
T ss_pred             CCEEEECCCCCCHHHHHHHHHhcC--CCEEEEEecCcCcHHHHHHHHHHHHhcCCCCCEEE-EECCCcCchHhhhhhHHH
Confidence            78876   4567899999998876  9999999888542 1 12345556532 2 46654 4443     2222 2455


Q ss_pred             HHhCCcceEEeCCCCHHHHHHHHHHH
Q 027234           69 GVTHDACDYLTKPVRIEELKNIWQHV   94 (226)
Q Consensus        69 a~~~ga~~yl~KP~~~~~L~~~l~~~   94 (226)
                      +.+.|++.|+.---+..++...+...
T Consensus       108 ~~~~G~d~~~~~g~~~~~~~~~l~~~  133 (137)
T 1ccw_A          108 FKDMGYDRVYAPGTPPEVGIADLKKD  133 (137)
T ss_dssp             HHHTTCSEECCTTCCHHHHHHHHHHH
T ss_pred             HHHCCCCEEECCCCCHHHHHHHHHHH
Confidence            78899999998777777776665543

>2oi8_A Putative regulatory protein SCO4313; TETR, structural genomics, PSI-2, P structure initiative; 2.50A {Streptomyces coelicolor} SCOP: a.4.1.9 a.121.1.1

Probab=83.21  E-value=1.4  Score=33.37  Aligned_cols=44  Identities=11%  Similarity=0.077  Sum_probs=35.8

Q ss_pred             hhHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          159 ELHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       159 ~l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      ...++++.++.+          ++..-...++|+++||.+.++|+..+|+-|+.
T Consensus        16 ~~r~~il~aA~~----------l~~~~G~~~~s~~~IA~~agvs~~t~Y~~F~~   59 (216)
T 2oi8_A           16 QVRAEIKDHAWE----------QIATAGASALSLNAIAKRMGMSGPALYRYFDG   59 (216)
T ss_dssp             HHHHHHHHHHHH----------HHHHHCTTSCCHHHHHHHTTCCHHHHHTTCSS
T ss_pred             HHHHHHHHHHHH----------HHHhcCcccCCHHHHHHHhCCCHHHHHHHcCC
Confidence            445678888887          44455667899999999999999999998874

>3anp_C Transcriptional repressor, TETR family; all alpha protein, DNA, acyl-COA; HET: DCC DAO; 1.95A {Thermus thermophilus} PDB: 3ang_C*

Probab=83.17  E-value=1.2  Score=33.06  Aligned_cols=43  Identities=12%  Similarity=0.047  Sum_probs=34.0

Q ss_pred             hHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          160 LHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       160 l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      -.++++.++.+          +...-.-.+.|+++||...|+||..||+-|+.
T Consensus        10 ~r~~Il~aA~~----------lf~~~G~~~~t~~~Ia~~Agvs~gt~Y~yF~s   52 (204)
T 3anp_C           10 RRERIFRAAME----------LFRNRGFQETTATEIAKAAHVSRGTFFNYYPY   52 (204)
T ss_dssp             HHHHHHHHHHH----------HHHHHCTTTCCHHHHHHHHTSCHHHHHHHCSS
T ss_pred             HHHHHHHHHHH----------HHHHcCcccccHHHHHHHcCCchHHHHHHcCC
Confidence            34677888877          33344566899999999999999999998865

>3dpj_A Transcription regulator, TETR family; APC88616, silicibacter pomeroyi DSS, structural genomics, PSI-2, protein structure initiative; HET: MES; 1.90A {Silicibacter pomeroyi}

Probab=83.15  E-value=1.2  Score=32.60  Aligned_cols=43  Identities=12%  Similarity=0.051  Sum_probs=34.5

Q ss_pred             hHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          160 LHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       160 l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      -.++++.++..          ++..-.-.++|+++||.+.|+|+..+|+-|+.
T Consensus         9 ~r~~Il~aA~~----------l~~~~G~~~~t~~~IA~~Agvs~~tly~~F~s   51 (194)
T 3dpj_A            9 TRDQIVAAADE----------LFYRQGFAQTSFVDISAAVGISRGNFYYHFKT   51 (194)
T ss_dssp             HHHHHHHHHHH----------HHHHHCTTTCCHHHHHHHHTCCHHHHHHHCSS
T ss_pred             HHHHHHHHHHH----------HHHHcCcccCCHHHHHHHHCCChHHHHHHcCC
Confidence            35677778777          44445667999999999999999999998864

>3s5r_A Transcriptional regulator TETR family; DNA/RNA-binding 3-helical bundle, tetracyclin repressor-like structural genomics; 2.60A {Syntrophus aciditrophicus}

Probab=82.99  E-value=1  Score=33.51  Aligned_cols=43  Identities=9%  Similarity=0.111  Sum_probs=34.6

Q ss_pred             hHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          160 LHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       160 l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      ..++++.++.+          ++..-.-.++|+++||.+.++||..+|+-|+.
T Consensus        11 ~r~~Il~aa~~----------l~~~~G~~~~ti~~Ia~~agvs~~t~Y~~F~s   53 (216)
T 3s5r_A           11 TRELLLDAATT----------LFAEQGIAATTMAEIAASVGVNPAMIHYYFKT   53 (216)
T ss_dssp             HHHHHHHHHHH----------HHHHHCTTTCCHHHHHHTTTCCHHHHHHHCSS
T ss_pred             HHHHHHHHHHH----------HHHHcCcccCCHHHHHHHHCCCHHHHHHHcCC
Confidence            35677788777          44445667899999999999999999998864

>3fiw_A Putative TETR-family transcriptional regulator; TETR-family transcriptional regulator streptomyces, structur genomics, PSI-2; 2.20A {Streptomyces coelicolor}

Probab=82.99  E-value=0.92  Score=34.44  Aligned_cols=42  Identities=12%  Similarity=0.236  Sum_probs=34.1

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .++++.++.+          ++..-...++|++.||.++++++..+|+-|+.
T Consensus        27 r~~Il~aA~~----------l~~~~G~~~~s~~~IA~~aGvs~~tlY~~F~~   68 (211)
T 3fiw_A           27 RETVITEALD----------LLDEVGLDGVSTRRLAKRLGVEQPSLYWYFRT   68 (211)
T ss_dssp             HHHHHHHHHH----------HHHHHCGGGCCHHHHHHHHTSCTHHHHTTCSS
T ss_pred             HHHHHHHHHH----------HHHhcCcccCCHHHHHHHhCCChhHHHHHcCC
Confidence            5677888877          44444566899999999999999999998864

>3g7r_A Putative transcriptional regulator; TETR, all-helical, structural genomics, PSI-2, protein structure initiative; 1.38A {Streptomyces coelicolor A3}

Probab=82.95  E-value=1.2  Score=33.68  Aligned_cols=44  Identities=16%  Similarity=0.156  Sum_probs=35.8

Q ss_pred             hhHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          159 ELHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       159 ~l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .-.++++.++.+          ++..-.-.+.|+++||.+.|+|+..+|+-|+.
T Consensus        35 ~~r~~Il~aA~~----------lf~~~G~~~~t~~~IA~~AGvs~~tlY~~F~s   78 (221)
T 3g7r_A           35 EARARLLGTATR----------IFYAEGIHSVGIDRITAEAQVTRATLYRHFSG   78 (221)
T ss_dssp             HHHHHHHHHHHH----------HHHHHCSTTSCHHHHHHHHTCCHHHHHHHCSS
T ss_pred             hHHHHHHHHHHH----------HHHHhCcccCCHHHHHHHhCCCHHHHHHHCCC
Confidence            446788888888          44445667899999999999999999998874

>3f0c_A TETR-molecule A, transcriptional regulator; MCSG,PSI, SAD, structural genomics, protein structure initiative; 2.96A {Cytophaga hutchinsonii}

Probab=82.80  E-value=1.2  Score=33.20  Aligned_cols=43  Identities=12%  Similarity=0.024  Sum_probs=34.2

Q ss_pred             hHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          160 LHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       160 l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      ..++++.++.+          ++..-.-.+.|+++||.+.|+|+..+|+-|+.
T Consensus        12 ~r~~Il~aA~~----------lf~~~G~~~~ti~~Ia~~agvs~~t~Y~~F~s   54 (216)
T 3f0c_A           12 KLELIINAAQK----------RFAHYGLCKTTMNEIASDVGMGKASLYYYFPD   54 (216)
T ss_dssp             HHHHHHHHHHH----------HHHHHCSSSCCHHHHHHHHTCCHHHHHHHCSS
T ss_pred             HHHHHHHHHHH----------HHHHcCCCcCCHHHHHHHhCCCHHHHHHHcCC
Confidence            35677778777          33444566899999999999999999998864

>3rh2_A Hypothetical TETR-like transcriptional regulator; DNA/RNA-binding 3-helical bundle, structural genomics, joint for structural genomics; 2.42A {Shewanella amazonensis}

Probab=82.68  E-value=0.84  Score=34.05  Aligned_cols=42  Identities=17%  Similarity=0.126  Sum_probs=32.8

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .++++.++.+          +...-.-.++|+++||.+.|+||..+|+-|+.
T Consensus         5 r~~Il~aA~~----------lf~~~G~~~~s~~~IA~~Agvs~~t~Y~~F~s   46 (212)
T 3rh2_A            5 RDKIIQASLE----------LFNEHGERTITTNHIAAHLDISPGNLYYHFRN   46 (212)
T ss_dssp             HHHHHHHHHH----------HHHHHCGGGCCHHHHHHHHTCCHHHHHHHCSS
T ss_pred             HHHHHHHHHH----------HHHHcCcccCCHHHHHHHhCCCHHHHHHHCCC
Confidence            3466677776          33444566899999999999999999998864

>1thf_D HISF protein; thermophIle, TIM-barrel, histidine biosynthesis, lyase, phosphate-binding sites; 1.45A {Thermotoga maritima} SCOP: c.1.2.1 PDB: 2wjz_A 2a0n_A* 1gpw_A 1vh7_A 2rkx_A 3iio_A 3iip_A* 3iiv_A

Probab=82.68  E-value=15  Score=28.38  Aligned_cols=78  Identities=14%  Similarity=0.176  Sum_probs=52.4

Q ss_pred             HHHHHHHHHhCCCCceE-EEEccCCCC-CC--HHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEe------C
Q 027234           11 AEIALDMLRTNKNGYDI-VISDVHMPD-MD--GFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT------K   80 (226)
Q Consensus        11 ~~eal~~l~~~~~~~Dl-Vl~D~~mp~-~d--G~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~------K   80 (226)
                      ..+..+.+....  ++. ++++..-.+ ..  .+++++.++...++|||.-.+-.+.+.+.++++.|+++.+.      .
T Consensus       153 ~~e~~~~~~~~G--~~~i~~~~~~~~g~~~g~~~~~~~~l~~~~~ipvia~GGI~~~~d~~~~~~~Gadgv~vGsal~~~  230 (253)
T 1thf_D          153 LRDWVVEVEKRG--AGEILLTSIDRDGTKSGYDTEMIRFVRPLTTLPIIASGGAGKMEHFLEAFLAGADAALAASVFHFR  230 (253)
T ss_dssp             HHHHHHHHHHTT--CSEEEEEETTTTTSCSCCCHHHHHHHGGGCCSCEEEESCCCSHHHHHHHHHTTCSEEEESHHHHTT
T ss_pred             HHHHHHHHHHCC--CCEEEEEeccCCCCCCCCCHHHHHHHHHhcCCCEEEECCCCCHHHHHHHHHcCChHHHHHHHHHcC
Confidence            445555555533  674 445554222 12  37888888866789999888888889999999999999874      3


Q ss_pred             CCCHHHHHHH
Q 027234           81 PVRIEELKNI   90 (226)
Q Consensus        81 P~~~~~L~~~   90 (226)
                      |+++.++...
T Consensus       231 ~~~~~~~~~~  240 (253)
T 1thf_D          231 EIDVRELKEY  240 (253)
T ss_dssp             CSCHHHHHHH
T ss_pred             CCCHHHHHHH
Confidence            5565555444

>1rkt_A Protein YFIR; transcription regulator, structural genomics, PSI, protein S initiative, midwest center for structural genomics, MCSG; 1.95A {Bacillus subtilis} SCOP: a.4.1.9 a.121.1.1

Probab=82.61  E-value=1.5  Score=32.55  Aligned_cols=42  Identities=12%  Similarity=0.014  Sum_probs=34.0

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .++++.++.+          +...-.-.+.|+++||.+.|+|+..+|+-|+.
T Consensus        14 r~~Il~aA~~----------lf~~~Gy~~ts~~~IA~~agvs~gtlY~yF~s   55 (205)
T 1rkt_A           14 QAEILEAAKT----------VFKRKGFELTTMKDVVEESGFSRGGVYLYFSS   55 (205)
T ss_dssp             HHHHHHHHHH----------HHHHHCSTTCCHHHHHHHHTSCHHHHHTTCSC
T ss_pred             HHHHHHHHHH----------HHHHcCcccCCHHHHHHHHCCCcchhhhhCCC
Confidence            4577888887          33444667899999999999999999998874

>2d6y_A Putative TETR family regulatory protein; helix-turn-helix, gene regulation; HET: TLA; 2.30A {Streptomyces coelicolor} SCOP: a.4.1.9 a.121.1.1

Probab=82.47  E-value=1.1  Score=33.36  Aligned_cols=42  Identities=12%  Similarity=0.179  Sum_probs=33.6

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .++++.++.+          +...-.-.+.|+++||.+.|+|+..+|+-|+.
T Consensus        10 r~~Il~aA~~----------lf~~~G~~~~s~~~IA~~aGvs~~tiY~~F~s   51 (202)
T 2d6y_A           10 KARIFEAAVA----------EFARHGIAGARIDRIAAEARANKQLIYAYYGN   51 (202)
T ss_dssp             HHHHHHHHHH----------HHHHHTTTSCCHHHHHHHHTCCHHHHHHHHSS
T ss_pred             HHHHHHHHHH----------HHHHcCcccCCHHHHHHHhCCCHHHHHHHcCC
Confidence            4677788877          33444566899999999999999999998764

>2a6c_A Helix-turn-helix motif; putative transcriptional regulator, structural genomics, JOI for structural genomics, JCSG; HET: CIT; 1.90A {Nitrosomonas europaea} SCOP: a.35.1.13

Probab=82.40  E-value=0.57  Score=29.92  Aligned_cols=32  Identities=25%  Similarity=0.188  Sum_probs=26.6

Q ss_pred             HHHHhhCCCCCCHHHHHHHhhhhhhhhhcccC
Q 027234          180 KILELMNIPGLTRENVASHLQKHRLYLSRLSG  211 (226)
Q Consensus       180 ~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~  211 (226)
                      .|.+.+..-++|..++|..+++++++++++.+
T Consensus        22 ~l~~~r~~~glsq~elA~~~gis~~~is~~e~   53 (83)
T 2a6c_A           22 VLQEHLRNSGLTQFKAAELLGVTQPRVSDLMR   53 (83)
T ss_dssp             HHHHHHHTTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            35666667799999999999999999998643

>2dg8_A Putative TETR-family transcriptional regulatory P; helix-turn-helix motif, gene regulation; 2.21A {Streptomyces coelicolor}

Probab=82.38  E-value=0.88  Score=33.48  Aligned_cols=43  Identities=7%  Similarity=0.032  Sum_probs=33.5

Q ss_pred             hHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          160 LHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       160 l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      ..++++.++.+          ++..-...++|+++||.+.|+||..||+-|+.
T Consensus        10 ~r~~Il~aa~~----------l~~~~G~~~~ti~~IA~~agvs~~t~Y~~F~s   52 (193)
T 2dg8_A           10 RRERILAATLD----------LIAEEGIARVSHRRIAQRAGVPLGSMTYHFTG   52 (193)
T ss_dssp             HHHHHHHHHHH----------HHHHHCGGGCCHHHHHHHHTSCTHHHHHHCSS
T ss_pred             HHHHHHHHHHH----------HHHHhChhhccHHHHHHHhCCCchhhheeCCC
Confidence            34567777777          33444566899999999999999999998864

>1r69_A Repressor protein CI; gene regulating protein; 2.00A {Phage 434} SCOP: a.35.1.2 PDB: 1pra_A 1per_L 1rpe_L* 2or1_L* 1r63_A 2r63_A 1sq8_A

Probab=82.20  E-value=0.43  Score=28.89  Aligned_cols=31  Identities=13%  Similarity=0.180  Sum_probs=24.6

Q ss_pred             HHHhhCCCCCCHHHHHHHhhhhhhhhhcccC
Q 027234          181 ILELMNIPGLTRENVASHLQKHRLYLSRLSG  211 (226)
Q Consensus       181 I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~  211 (226)
                      |.+.+..-++|..++|..+++++++++++-.
T Consensus         6 l~~~r~~~glsq~~lA~~~gis~~~i~~~e~   36 (69)
T 1r69_A            6 VKSKRIQLGLNQAELAQKVGTTQQSIEQLEN   36 (69)
T ss_dssp             HHHHHHHTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            4445555689999999999999999988643

>2xdn_A HTH-type transcriptional regulator TTGR; transcription regulation, TETR family; 2.20A {Pseudomonas putida} PDB: 2uxu_A* 2uxi_A* 2uxo_A* 2uxp_A* 2uxh_A*

Probab=82.15  E-value=1.3  Score=33.05  Aligned_cols=43  Identities=12%  Similarity=-0.002  Sum_probs=34.4

Q ss_pred             hHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          160 LHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       160 l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      -.++++.++.+          +...-.-.+.|+++||.+.|+|+..+|+-|+.
T Consensus        12 ~r~~Il~aA~~----------lf~~~G~~~~s~~~IA~~aGvskgtlY~~F~s   54 (210)
T 2xdn_A           12 TRAQIIEAAER----------AFYKRGVARTTLADIAELAGVTRGAIYWHFNN   54 (210)
T ss_dssp             HHHHHHHHHHH----------HHHHHCSTTCCHHHHHHHHTCCTTHHHHHCSS
T ss_pred             HHHHHHHHHHH----------HHHHcCcccCcHHHHHHHHCCChHHHHHHhCC
Confidence            34678888888          33444666899999999999999999998864

>2w53_A Repressor, SMet; antibiotic resistance, multi-drug efflux pump, transcription regulation, transcriptional repressor, DNA binding; 2.00A {Stenotrophomonas maltophilia} PDB: 3p9t_A*

Probab=82.12  E-value=1.5  Score=32.78  Aligned_cols=42  Identities=10%  Similarity=-0.015  Sum_probs=33.9

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .++++.++.+          +...-.-.+.|+++||...|+||..+|+-|+.
T Consensus        13 r~~Il~aA~~----------lf~~~G~~~~s~~~IA~~aGvskgtlY~~F~s   54 (219)
T 2w53_A           13 REGILDAAEA----------CFHEHGVARTTLEMIGARAGYTRGAVYWHFKN   54 (219)
T ss_dssp             HHHHHHHHHH----------HHHHHCTTTCCHHHHHHHHTSCHHHHHTTCSS
T ss_pred             HHHHHHHHHH----------HHHHhCcccCCHHHHHHHhCCCchHHhhcCCC
Confidence            4677888887          33444566899999999999999999998864

>2qwt_A Transcriptional regulator, TETR family; structural genomics, PSI-2, protein structure initiative; 2.30A {Mycobacterium vanbaalenii pyr-1}

Probab=82.09  E-value=1.3  Score=32.79  Aligned_cols=41  Identities=7%  Similarity=0.070  Sum_probs=33.0

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .++++.++.+         .+.+ -.. +.|+++||.+.|+|+..+|+-|+.
T Consensus        15 r~~Il~aA~~---------lf~~-~G~-~~t~~~IA~~agvs~~tlY~~F~s   55 (196)
T 2qwt_A           15 RARVLEVAYD---------TFAA-EGL-GVPMDEIARRAGVGAGTVYRHFPT   55 (196)
T ss_dssp             HHHHHHHHHH---------HHHH-TCT-TSCHHHHHHHTTSCHHHHHHHCSS
T ss_pred             HHHHHHHHHH---------HHHh-cCC-CCCHHHHHHHhCCCHHHHHHHCCC
Confidence            4678888888         2444 345 799999999999999999998864

>3qq6_A HTH-type transcriptional regulator SINR; helix-turn-helix motif, biofilm, repressor, SINI; 1.90A {Bacillus subtilis}

Probab=82.07  E-value=0.42  Score=30.27  Aligned_cols=32  Identities=19%  Similarity=0.270  Sum_probs=25.5

Q ss_pred             HHHHhhCCCCCCHHHHHHHhhhhhhhhhcccC
Q 027234          180 KILELMNIPGLTRENVASHLQKHRLYLSRLSG  211 (226)
Q Consensus       180 ~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~  211 (226)
                      .|.+....-++|+.++|..+++++++++++-.
T Consensus        14 ~ik~~R~~~gltq~elA~~~gis~~~is~~E~   45 (78)
T 3qq6_A           14 RIKQYRKEKGYSLSELAEKAGVAKSYLSSIER   45 (78)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            34444555699999999999999999998743

>3geu_A Intercellular adhesion protein R; TETR family, intercellular adhesion regulator, IDP00851, DNA repressor, transcription; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=82.01  E-value=0.58  Score=34.20  Aligned_cols=42  Identities=10%  Similarity=0.131  Sum_probs=32.7

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .++++.++.+          ++..-.-.++|+++||.+.|+||..+|+-|+.
T Consensus         5 r~~Il~aa~~----------l~~~~G~~~~ti~~IA~~agvs~~t~Y~~F~s   46 (189)
T 3geu_A            5 KDKIIDNAIT----------LFSEKGYDGTTLDDIAKSVNIKKASLYYHFDS   46 (189)
T ss_dssp             HHHHHHHHHH----------HHHHHHHHHCCHHHHHHHTTCCHHHHTTTCSS
T ss_pred             HHHHHHHHHH----------HHHHcCcccCCHHHHHHHhCCCHHHHHHHhCC
Confidence            4567777777          33333455799999999999999999998874

>2zb9_A Putative transcriptional regulator; transcription regulator, TETR family, helix-turn-helix, DNA- binding, transcription regulation; 2.25A {Streptomyces coelicolor}

Probab=81.88  E-value=0.87  Score=34.02  Aligned_cols=44  Identities=25%  Similarity=0.160  Sum_probs=34.8

Q ss_pred             hhHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          159 ELHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       159 ~l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      ...++++.++.+          ++..-.-.++|+++||.+.|+|+..||+-|+.
T Consensus        23 ~~r~~Il~aA~~----------lf~~~G~~~~t~~~IA~~agvs~~t~Y~~F~s   66 (214)
T 2zb9_A           23 EVRAEVLHAVGE----------LLLTEGTAQLTFERVARVSGVSKTTLYKWWPS   66 (214)
T ss_dssp             HHHHHHHHHHHH----------HHHHHCGGGCCHHHHHHHHCCCHHHHHHHCSS
T ss_pred             HHHHHHHHHHHH----------HHHHhCcccCCHHHHHHHHCCCHHHHHHHCCC
Confidence            345678888877          44445556899999999999999999998864

>2hku_A A putative transcriptional regulator; structural genomics, APC6040, TET rhodococcus SP. RHA1, PSI-2, protein structure initiative; HET: PG4; 2.00A {Rhodococcus SP} SCOP: a.4.1.9 a.121.1.1

Probab=81.84  E-value=1.2  Score=33.40  Aligned_cols=43  Identities=16%  Similarity=0.236  Sum_probs=35.0

Q ss_pred             hhHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          159 ELHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       159 ~l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      ...++++.++.+         .+.+ -. .+.|+++||.+.++|+..+|+-|+.
T Consensus        20 ~~r~~Il~aA~~---------lf~~-~G-~~~s~~~IA~~aGvs~~tlY~~F~s   62 (215)
T 2hku_A           20 QTRDALFTAATE---------LFLE-HG-EGVPITQICAAAGAHPNQVTYYYGS   62 (215)
T ss_dssp             CHHHHHHHHHHH---------HHHH-HC-TTSCHHHHHHHHTCCHHHHHHHHSS
T ss_pred             HHHHHHHHHHHH---------HHHH-hC-CCcCHHHHHHHhCCCHHHHHHHcCC
Confidence            346788888888         2444 45 7999999999999999999998764

>2g7l_A TETR-family transcriptional regulator; APC6062, protein structure initiativ midwest center for structural genomics, MCSG; 2.10A {Streptomyces coelicolor} SCOP: a.4.1.9 a.121.1.1

Probab=81.67  E-value=1.5  Score=34.11  Aligned_cols=42  Identities=12%  Similarity=0.104  Sum_probs=34.5

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .++++.++..          ++..-...++|+..||.++++++..||+-|+.
T Consensus        21 r~~Il~AA~~----------l~~e~G~~~~S~~~IA~~aGvs~~tlY~hF~s   62 (243)
T 2g7l_A           21 RRWIVDTAVA----------LMRAEGLEKVTMRRLAQELDTGPASLYVYVAN   62 (243)
T ss_dssp             HHHHHHHHHH----------HHHHHCSSSCCHHHHHHHTTSCHHHHTTTCCS
T ss_pred             HHHHHHHHHH----------HHHhcCchhcCHHHHHHHHCCChhHHHHHcCC
Confidence            5677777777          44555667899999999999999999998874

>3kts_A Glycerol uptake operon antiterminator regulatory; structural genomics, PSI-2, protein structur initiative; HET: UNL; 2.75A {Listeria monocytogenes str}

Probab=81.66  E-value=2.7  Score=31.80  Aligned_cols=62  Identities=15%  Similarity=0.186  Sum_probs=48.5

Q ss_pred             HHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234           12 EIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus        12 ~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      +.+++.+.+..  ||+|   -.||+.-- ++++.+++..++|+|.=-.-.+.+.+..|+++||+..-+
T Consensus       117 ~~~~~~i~~~~--PD~i---EiLPGi~p-~iI~~i~~~~~~PiIaGGlI~~~edv~~al~aGA~aVsT  178 (192)
T 3kts_A          117 NKGVALIQKVQ--PDCI---ELLPGIIP-EQVQKMTQKLHIPVIAGGLIETSEQVNQVIASGAIAVTT  178 (192)
T ss_dssp             HHHHHHHHHHC--CSEE---EEECTTCH-HHHHHHHHHHCCCEEEESSCCSHHHHHHHHTTTEEEEEE
T ss_pred             HHHHHHHhhcC--CCEE---EECCchhH-HHHHHHHHhcCCCEEEECCcCCHHHHHHHHHcCCeEEEe
Confidence            45778888876  9987   34587543 688888877789998766677889999999999997654

>2kpj_A SOS-response transcriptional repressor, LEXA; NESG, GFT, structural genomics, PSI-2, protein structure initiative; NMR {Eubacterium rectale atcc 33656}

Probab=81.61  E-value=0.84  Score=29.82  Aligned_cols=32  Identities=6%  Similarity=0.027  Sum_probs=25.4

Q ss_pred             HHHHhhCCCCCCHHHHHHHhhhhhhhhhcccC
Q 027234          180 KILELMNIPGLTRENVASHLQKHRLYLSRLSG  211 (226)
Q Consensus       180 ~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~  211 (226)
                      .|.+.+..-++|..++|..+++++++++++..
T Consensus        13 ~lk~~r~~~glsq~~lA~~~gis~~~is~~e~   44 (94)
T 2kpj_A           13 NLNSYIAKSEKTQLEIAKSIGVSPQTFNTWCK   44 (94)
T ss_dssp             HHHHHHTTSSSCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHh
Confidence            35666677789999999999999998887643

>3kp1_A D-ornithine aminomutase E component; 5 aminomutase (OAM), metal binding protein; HET: PLP B12 5AD; 2.01A {Clostridium sticklandii} PDB: 3kow_A* 3koy_A* 3koz_A* 3kp0_A* 3kox_A*

Probab=81.59  E-value=13  Score=33.55  Aligned_cols=91  Identities=14%  Similarity=0.103  Sum_probs=60.8

Q ss_pred             CcEEEE---ECCHHHHHHHHHhCCCCceEEEEccCCCC----CCHHH-HHHHHhcC-C--CCcEEEEeccCCHHHHHHHH
Q 027234            2 GFSVTK---CNRAEIALDMLRTNKNGYDIVISDVHMPD----MDGFK-LLELVGLE-M--DLPVIMMCAHGSKEVVMKGV   70 (226)
Q Consensus         2 g~~V~~---~~~~~eal~~l~~~~~~~DlVl~D~~mp~----~dG~~-l~~~l~~~-~--~~pvI~ls~~~~~~~~~~a~   70 (226)
                      ||+|..   .-..++.++.+.+..  +|+|.+...|..    +..+. +++.+++. .  .++|++=-.....+.   +.
T Consensus       634 GFEVIDLGvdVPpEeIVeAA~Eed--ADVVGLSsLLTt~dihL~~MkevIelLrE~GlrDkIkVIVGGa~~tqd~---Ak  708 (763)
T 3kp1_A          634 GVEVHYLGTSVPVEKLVDAAIELK--ADAILASTIISHDDIHYKNMKRIHELAVEKGIRDKIMIGCGGTQVTPEV---AV  708 (763)
T ss_dssp             TCEEEECCSSBCHHHHHHHHHHTT--CSEEEEECCCCGGGHHHHHHHHHHHHHHHTTCTTTSEEEEECTTCCHHH---HH
T ss_pred             CCEEEECCCCCCHHHHHHHHHHcC--CCEEEEeccccCchhhHHHHHHHHHHHHhcCCCCCCEEEEECCCCCHHH---HH
Confidence            788863   347889999999877  999999988876    34433 44555532 2  245544222333333   35


Q ss_pred             hCCcceEEeCCCCHHHHHHHHHHHHHH
Q 027234           71 THDACDYLTKPVRIEELKNIWQHVVRK   97 (226)
Q Consensus        71 ~~ga~~yl~KP~~~~~L~~~l~~~~~~   97 (226)
                      ..||+.|..-.....++...|...+..
T Consensus       709 eIGADa~f~DATeAVeVA~~Ll~~l~e  735 (763)
T 3kp1_A          709 KQGVDAGFGRGSKGIHVATFLVKKRRE  735 (763)
T ss_dssp             TTTCSEEECTTCCHHHHHHHHHHHHHH
T ss_pred             HcCCcEEECCcchHHHHHHHHHHHHHH
Confidence            899999999888888777776665544

>2f07_A YVDT; helix-turn-helix, transcription; HET: BTB; 2.30A {Bacillus subtilis subsp}

Probab=81.57  E-value=1.5  Score=32.44  Aligned_cols=43  Identities=5%  Similarity=0.021  Sum_probs=34.1

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGVS  213 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~~  213 (226)
                      .++++.++.+          +...-.-.+.|+++||.+.|+||..+|+-|+.-
T Consensus        12 r~~Il~aA~~----------lf~~~G~~~~s~~~Ia~~Agvskgt~Y~yF~sK   54 (197)
T 2f07_A           12 YEKILQAAIE----------VISEKGLDKASISDIVKKAGTAQGTFYLYFSSK   54 (197)
T ss_dssp             HHHHHHHHHH----------HHHHHCTTTCCHHHHHHHHTSCHHHHHHHCSSS
T ss_pred             HHHHHHHHHH----------HHHHhCcccCCHHHHHHHhCCCchHHHHhCCCH
Confidence            4567777777          444455668999999999999999999988753

>2of7_A Putative TETR-family transcriptional regulator; APC7240, streptomyces coelicolor A3, structural genomics, PSI-2; 2.30A {Streptomyces coelicolor}

Probab=81.56  E-value=1.4  Score=34.37  Aligned_cols=44  Identities=11%  Similarity=0.058  Sum_probs=35.2

Q ss_pred             hhHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          159 ELHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       159 ~l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      ...++++.++.+          ++..-...++|+++||...++|+..||+-|+.
T Consensus        48 ~tr~~Il~AA~~----------lf~e~G~~~~Ti~~IA~~AGvs~~t~Y~yF~s   91 (260)
T 2of7_A           48 RTREAIRAATYG----------LIRQQGYEATTVEQIAERAEVSPSTVLRYFPT   91 (260)
T ss_dssp             HHHHHHHHHHHH----------HHHHHCSTTCCHHHHHHHHTSCHHHHHHHCSS
T ss_pred             HHHHHHHHHHHH----------HHHHhCcccccHHHHHHHhCCChHHHHHHcCC
Confidence            345678888887          44445677899999999999999999998864

>1zug_A Phage 434 CRO protein; gene regulating protein, transcription regulation; NMR {Phage 434} SCOP: a.35.1.2 PDB: 2cro_A 3cro_L*

Probab=81.53  E-value=0.47  Score=28.90  Aligned_cols=32  Identities=6%  Similarity=0.071  Sum_probs=25.3

Q ss_pred             HHHHhhCCCCCCHHHHHHHhhhhhhhhhcccC
Q 027234          180 KILELMNIPGLTRENVASHLQKHRLYLSRLSG  211 (226)
Q Consensus       180 ~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~  211 (226)
                      .|.+.+..-++|..++|..+++++++++++..
T Consensus         7 ~l~~~r~~~glsq~~lA~~~gis~~~i~~~e~   38 (71)
T 1zug_A            7 RLKKRRIALKMTQTELATKAGVKQQSIQLIEA   38 (71)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence            34455555689999999999999999998644

>1ntc_A Protein (nitrogen regulation protein (NTRC)); helix-turn-helix, FIS, four-helix bundle, transcription regulation; NMR {Salmonella typhimurium} SCOP: a.4.1.12

Probab=81.50  E-value=0.33  Score=31.98  Aligned_cols=30  Identities=10%  Similarity=-0.038  Sum_probs=24.9

Q ss_pred             HHHHhhCCCCCCHHHHHHHhhhhhhhhhcc
Q 027234          180 KILELMNIPGLTRENVASHLQKHRLYLSRL  209 (226)
Q Consensus       180 ~I~~~~~~~~lt~~~va~~l~~~r~~l~r~  209 (226)
                      .|.+.+...+-++...|..||+||..|||.
T Consensus        55 ~i~~aL~~~~gn~~~aA~~LGIsr~tL~rk   84 (91)
T 1ntc_A           55 LLTTALRHTQGHKQEAARLLGWGAATLTAK   84 (91)
T ss_dssp             HHHHHHHHTTTCTTHHHHHTTCCHHHHHHH
T ss_pred             HHHHHHHHhCCCHHHHHHHHCcCHHHHHHH
Confidence            566666666778899999999999999974

>2gjl_A Hypothetical protein PA1024; 2-nitropropane dioxygenase, 2-nitropropane, FMN, oxidoreduct; HET: FMN; 2.00A {Pseudomonas aeruginosa PAO1} PDB: 2gjn_A*

Probab=81.49  E-value=12  Score=30.32  Aligned_cols=70  Identities=21%  Similarity=0.236  Sum_probs=51.8

Q ss_pred             EECCHHHHHHHHHhCCCCceEEEEccCCC----C---CCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            7 KCNRAEIALDMLRTNKNGYDIVISDVHMP----D---MDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         7 ~~~~~~eal~~l~~~~~~~DlVl~D~~mp----~---~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .+.+.+++......   ++|.|+++-.-+    +   ...+++++.++...++|||+-.+-.+.+.+.+++..||++...
T Consensus       124 ~v~t~~~a~~~~~~---GaD~i~v~g~~~GG~~G~~~~~~~~~l~~v~~~~~iPviaaGGI~~~~~v~~al~~GAdgV~v  200 (328)
T 2gjl_A          124 KCTAVRHALKAERL---GVDAVSIDGFECAGHPGEDDIPGLVLLPAAANRLRVPIIASGGFADGRGLVAALALGADAINM  200 (328)
T ss_dssp             EESSHHHHHHHHHT---TCSEEEEECTTCSBCCCSSCCCHHHHHHHHHTTCCSCEEEESSCCSHHHHHHHHHHTCSEEEE
T ss_pred             eCCCHHHHHHHHHc---CCCEEEEECCCCCcCCCCccccHHHHHHHHHHhcCCCEEEECCCCCHHHHHHHHHcCCCEEEE
Confidence            46777887766553   379888853222    1   2567888888766789999888877888999999999998774

>3lsj_A DEST; transcriptional repressor, TETR family, DNA-binding, transcription, transcription regulation; HET: PLM COA; 2.30A {Pseudomonas aeruginosa} PDB: 3lsp_A* 3lsr_A*

Probab=81.49  E-value=0.93  Score=33.98  Aligned_cols=43  Identities=14%  Similarity=0.063  Sum_probs=33.2

Q ss_pred             hHHHHHHHHHHhCCCCCCchHHHH-hhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          160 LHQQFVSAVKELGFDKAGPKKILE-LMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       160 l~~~Fi~~~~~~g~~~~~p~~I~~-~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      ..++++.++.+          ++. .-.-.++|+++||.+.|+||..||+-|+.
T Consensus        12 ~r~~Il~aa~~----------l~~~~~G~~~~ti~~Ia~~Agvs~~t~Y~~F~s   55 (220)
T 3lsj_A           12 TRHALMSAARH----------LMESGRGFGSLSLREVTRAAGIVPAGFYRHFSD   55 (220)
T ss_dssp             HHHHHHHHHHH----------HTTTSCCGGGCCHHHHHHHHTSCGGGGTTTCSS
T ss_pred             HHHHHHHHHHH----------HHHhCCCcccCCHHHHHHHhCCChhHHHHHcCC
Confidence            34677777777          333 44455789999999999999999998874

>3nnr_A Transcriptional regulator, TETR family; TETR-family transcriptional regulator, structural genomics, center for structural genomics, JCSG; HET: MSE; 2.49A {Marinobacter aquaeolei}

Probab=81.45  E-value=0.98  Score=34.16  Aligned_cols=42  Identities=14%  Similarity=0.080  Sum_probs=33.3

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .++++.++.+          ++..-.-.++|+++||.+.|+||..||+-|+.
T Consensus         7 r~~Il~aA~~----------lf~~~G~~~~t~~~IA~~Agvs~~t~Y~~F~s   48 (228)
T 3nnr_A            7 RDKILLSSLE----------LFNDKGERNITTNHIAAHLAISPGNLYYHFRN   48 (228)
T ss_dssp             HHHHHHHHHH----------HHHHHCGGGCCHHHHHHHHTCCHHHHHHHCSS
T ss_pred             HHHHHHHHHH----------HHHHhChhhcCHHHHHHHhCCCCccchhcCCC
Confidence            4567777777          44444666899999999999999999998864

>2ibd_A Possible transcriptional regulator; probable transcriptional regulatory protein, rhodococcus SP. structural genomics, PSI-2; 1.50A {Rhodococcus SP}

Probab=81.44  E-value=1.4  Score=32.66  Aligned_cols=44  Identities=7%  Similarity=-0.021  Sum_probs=35.0

Q ss_pred             hhHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          159 ELHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       159 ~l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      ...++++.++.+          +.....-.+.|+++||.+.|+||..+|+-|+.
T Consensus        14 ~~r~~Il~aA~~----------lf~~~G~~~~s~~~IA~~agvs~~tlY~~F~s   57 (204)
T 2ibd_A           14 GRRTELLDIAAT----------LFAERGLRATTVRDIADAAGILSGSLYHHFDS   57 (204)
T ss_dssp             HHHHHHHHHHHH----------HHHHHCSTTCCHHHHHHHTTSCHHHHHHHCSC
T ss_pred             hhHHHHHHHHHH----------HHHHcCchhcCHHHHHHHhCCCchhHHHhcCC
Confidence            345678888888          44445667899999999999999999998764

>1z0x_A Transcriptional regulator, TETR family; structural genomics, PSI, P structure initiative; 2.40A {Enterococcus faecalis} SCOP: a.4.1.9 a.121.1.1

Probab=81.39  E-value=1.2  Score=34.01  Aligned_cols=42  Identities=17%  Similarity=0.141  Sum_probs=32.9

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhh-CCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELM-NIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~-~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .++++.++..          ++..- ...++|+..||.++++++..+|+-|+.
T Consensus         7 r~~Il~aA~~----------l~~~~~G~~~~s~~~IA~~aGvs~~tlY~~F~s   49 (220)
T 1z0x_A            7 KDTIIAAAFS----------LLEKSPTLEQLSMRKVAKQLGVQAPAIYWYFKN   49 (220)
T ss_dssp             HHHHHHHHHH----------HHHHSCCGGGCCHHHHHHHHTSCHHHHHTTCSS
T ss_pred             HHHHHHHHHH----------HHHhcCCcccCCHHHHHHHcCCCHHHHHHhcCC
Confidence            4566667666          44444 556899999999999999999998874

>2qib_A TETR-family transcriptional regulator; HTH DNA binding, STRU genomics, MCSG, PSI-2, protein structure initiative; HET: P6G; 1.70A {Streptomyces coelicolor A3}

Probab=81.35  E-value=0.99  Score=34.39  Aligned_cols=43  Identities=12%  Similarity=0.081  Sum_probs=33.9

Q ss_pred             hHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          160 LHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       160 l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      -.++++.++.+          ++..-.-.++|+++||.+.++||..||+-|+.
T Consensus        14 ~r~~Il~AA~~----------l~~~~G~~~~tv~~IA~~agvs~~t~Y~~F~s   56 (231)
T 2qib_A           14 RRQQLIGVALD----------LFSRRSPDEVSIDEIASAAGISRPLVYHYFPG   56 (231)
T ss_dssp             HHHHHHHHHHH----------HHHHSCGGGCCHHHHHHHHTSCHHHHHHHCSS
T ss_pred             HHHHHHHHHHH----------HHHHcCchhcCHHHHHHHhCCCHHHHHHHCCC
Confidence            35677777777          34444556899999999999999999998864

>2o7t_A Transcriptional regulator; transcription regulator, DNA/RNA-binding 3-helical bundle FO turn helix motif, HTH motif; HET: UNL; 2.10A {Corynebacterium glutamicum} SCOP: a.4.1.9 a.121.1.1

Probab=81.32  E-value=1  Score=33.27  Aligned_cols=42  Identities=17%  Similarity=0.100  Sum_probs=33.2

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .++++.++.+          ++..-.-.+.|+++||.+.|+||..+|+-|+.
T Consensus        10 r~~Il~aA~~----------lf~~~G~~~~t~~~IA~~agvs~~tlY~~F~s   51 (199)
T 2o7t_A           10 REHIITTTCN----------LYRTHHHDSLTMENIAEQAGVGVATLYRNFPD   51 (199)
T ss_dssp             HHHHHHHHHH----------HHHHSCGGGCCHHHHHHHHTCCHHHHHHHCSS
T ss_pred             HHHHHHHHHH----------HHHHCCCccCCHHHHHHHhCCCHHHHHHHcCC
Confidence            4567777777          33444556889999999999999999998864

>3nxc_A HTH-type protein SLMA; nucleoid occlusion, cell division, TETR family member, DNA B protein; 2.50A {Escherichia coli}

Probab=81.20  E-value=1.1  Score=33.09  Aligned_cols=43  Identities=9%  Similarity=0.035  Sum_probs=29.8

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .++++.++.+         .+.......++|+++||.+.|+||..+|+-|+.
T Consensus        26 r~~Il~aA~~---------~lf~~~G~~~~t~~~Ia~~agvs~~t~Y~~F~s   68 (212)
T 3nxc_A           26 REEILQSLAL---------MLESSDGSQRITTAKLAASVGVSEAALYRHFPS   68 (212)
T ss_dssp             HHHHHHHHHH---------HHHC------CCHHHHHHHTTSCHHHHHTTCSS
T ss_pred             HHHHHHHHHH---------HHHhcCChhhcCHHHHHHHhCCChhHHHHHCCC
Confidence            4677777666         233444556899999999999999999998874

>3crj_A Transcription regulator; APC88200, TETR, structura genomics, PSI-2, protein structure initiative; HET: MSE; 2.60A {Haloarcula marismortui atcc 43049}

Probab=81.10  E-value=1.8  Score=32.05  Aligned_cols=43  Identities=14%  Similarity=0.107  Sum_probs=34.3

Q ss_pred             hHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          160 LHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       160 l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      ..++++.++.+          +...-.-.+.|+++||...|+|+..+|+-|+.
T Consensus        15 ~r~~Il~aA~~----------lf~~~G~~~~s~~~IA~~agvsk~tlY~yF~s   57 (199)
T 3crj_A           15 QTEEIMQATYR----------ALREHGYADLTIQRIADEYGKSTAAVHYYYDT   57 (199)
T ss_dssp             HHHHHHHHHHH----------HHHHHTTTTCCHHHHHHHHTSCHHHHHTTCSS
T ss_pred             HHHHHHHHHHH----------HHHHcCcccCCHHHHHHHhCCChhHHhhhcCC
Confidence            35677888887          34444566899999999999999999998864

>3mvp_A TETR/ACRR transcriptional regulator; PSI, MCSG, structural genomics, midwest center for structura genomics, protein structure initiative; 1.85A {Streptococcus mutans}

Probab=81.05  E-value=1.1  Score=33.35  Aligned_cols=44  Identities=11%  Similarity=0.072  Sum_probs=34.7

Q ss_pred             hhHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          159 ELHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       159 ~l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .-.++++.++.+          ++..-.-.++|+++||.+.|+|+..+|+-|+.
T Consensus        26 ~~r~~Il~aA~~----------l~~~~G~~~~t~~~Ia~~agvs~~t~Y~~F~s   69 (217)
T 3mvp_A           26 EKRNKILQVAKD----------LFSDKTYFNVTTNEIAKKADVSVGTLYAYFAS   69 (217)
T ss_dssp             HHHHHHHHHHHH----------HHHHHCGGGCCHHHHHHHHTSCHHHHHHHCSS
T ss_pred             hHHHHHHHHHHH----------HHHHcCccccCHHHHHHHhCCChhHHHHHcCC
Confidence            345678888877          33444566899999999999999999998864

>3b7h_A Prophage LP1 protein 11; structural genomics, PSI2, MCSG, protein structure initiative, midwest center for structural genomics; 2.00A {Lactobacillus plantarum WCFS1}

Probab=80.80  E-value=0.51  Score=29.41  Aligned_cols=31  Identities=19%  Similarity=0.226  Sum_probs=24.8

Q ss_pred             HHHhhCCCCCCHHHHHHHhhhhhhhhhcccC
Q 027234          181 ILELMNIPGLTRENVASHLQKHRLYLSRLSG  211 (226)
Q Consensus       181 I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~  211 (226)
                      |.+.+...++|..++|..+++++++++++..
T Consensus        12 l~~~r~~~g~sq~~lA~~~gis~~~i~~~e~   42 (78)
T 3b7h_A           12 LMELITQQNLTINRVATLAGLNQSTVNAMFE   42 (78)
T ss_dssp             HHHHHHHTTCCHHHHHHHHTCCHHHHHHHHC
T ss_pred             HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            4444555689999999999999999998644

>1qo2_A Molecule: N-((5-phosphoribosyl)-formimino)-5-aminoimidazol- 4-carboxamid ribonucleotid...; isomerase, histidine biosynthesis; 1.85A {Thermotoga maritima} SCOP: c.1.2.1 PDB: 2cff_A 2w79_A

Probab=80.79  E-value=9.9  Score=29.27  Aligned_cols=78  Identities=14%  Similarity=0.226  Sum_probs=54.4

Q ss_pred             CHHHHHHHHHhCCCCce-EEEEccC----CCCCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhC-----C-cceEE
Q 027234           10 RAEIALDMLRTNKNGYD-IVISDVH----MPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTH-----D-ACDYL   78 (226)
Q Consensus        10 ~~~eal~~l~~~~~~~D-lVl~D~~----mp~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~-----g-a~~yl   78 (226)
                      +..+....+.+..  ++ ++++++.    +.+. .+++++.++...++|||...+-.+.+.+.++++.     | +++.+
T Consensus       145 ~~~e~~~~~~~~G--~~~i~~t~~~~~g~~~g~-~~~~i~~l~~~~~iPvia~GGI~~~~d~~~~~~~~~~~~G~adgv~  221 (241)
T 1qo2_A          145 DPVSLLKRLKEYG--LEEIVHTEIEKDGTLQEH-DFSLTKKIAIEAEVKVLAAGGISSENSLKTAQKVHTETNGLLKGVI  221 (241)
T ss_dssp             CHHHHHHHHHTTT--CCEEEEEETTHHHHTCCC-CHHHHHHHHHHHTCEEEEESSCCSHHHHHHHHHHHHHTTTSEEEEE
T ss_pred             CHHHHHHHHHhCC--CCEEEEEeecccccCCcC-CHHHHHHHHHhcCCcEEEECCCCCHHHHHHHHhcccccCCeEeEEE
Confidence            4556555555533  67 5555543    2233 3888888876668999998888888999999988     9 99877


Q ss_pred             e------CCCCHHHHHHH
Q 027234           79 T------KPVRIEELKNI   90 (226)
Q Consensus        79 ~------KP~~~~~L~~~   90 (226)
                      .      .+++..++...
T Consensus       222 vgsal~~~~~~~~~~~~~  239 (241)
T 1qo2_A          222 VGRAFLEGILTVEVMKRY  239 (241)
T ss_dssp             ECHHHHTTSSCHHHHHHH
T ss_pred             eeHHHHcCCCCHHHHHHH
Confidence            4      47777776543

>2y2z_A SIM16, SIMR, putative repressor simreg2; transcription, simocyclinone regulator, TETR-family; 1.95A {Streptomyces antibioticus} PDB: 2y30_A* 2y31_A* 3zql_A

Probab=80.75  E-value=1.8  Score=34.31  Aligned_cols=42  Identities=17%  Similarity=0.172  Sum_probs=34.6

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .++++.++..          ++..-...++|+..||.++++++..||+-|+.
T Consensus        29 r~~Il~AA~~----------L~~e~G~~~~Smr~IA~~aGVs~~tlY~hF~~   70 (267)
T 2y2z_A           29 RDQIVRAAVK----------VADTEGVEAASMRRVAAELGAGTMSLYYYVPT   70 (267)
T ss_dssp             HHHHHHHHHH----------HHHHHCTTTCCHHHHHHHHTCCHHHHHTTCCS
T ss_pred             HHHHHHHHHH----------HHHhcCcccCCHHHHHHHhCCCHHHHHHHcCC
Confidence            5677778777          44555677999999999999999999998864

>2ao9_A Phage protein; structural genomics, nine-fold NCS., PSI, protein structure initiative, midwest center for structural genomics, MCSG, U function; 1.90A {Bacillus cereus} SCOP: a.4.1.17

Probab=80.74  E-value=1.5  Score=32.01  Aligned_cols=21  Identities=24%  Similarity=0.221  Sum_probs=19.7

Q ss_pred             CCCCHHHHHHHhhhhhhhhhc
Q 027234          188 PGLTRENVASHLQKHRLYLSR  208 (226)
Q Consensus       188 ~~lt~~~va~~l~~~r~~l~r  208 (226)
                      .++|+.+||..||+||..|||
T Consensus        47 ~~lTv~eIA~~LGIS~~TLyr   67 (155)
T 2ao9_A           47 EKRTQDEMANELGINRTTLWE   67 (155)
T ss_dssp             CCCCHHHHHHHHTCCHHHHHH
T ss_pred             cCCCHHHHHHHhCCCHHHHHH
Confidence            379999999999999999997

>1ui5_A A-factor receptor homolog; helix-turn-helix, alpha-helix-bundle, antibiotic; 2.40A {Streptomyces coelicolor} SCOP: a.4.1.9 a.121.1.1 PDB: 1ui6_A

Probab=80.54  E-value=1.6  Score=32.79  Aligned_cols=43  Identities=9%  Similarity=0.070  Sum_probs=34.0

Q ss_pred             hHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          160 LHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       160 l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      -.++++.++.+          +...-.-.+.|+++||.+.|+||..||+-|+.
T Consensus        10 ~r~~Il~aA~~----------lf~~~Gy~~ts~~~IA~~AGvskgtlY~~F~s   52 (215)
T 1ui5_A           10 TRATIIGAAAD----------LFDRRGYESTTLSEIVAHAGVTKGALYFHFAA   52 (215)
T ss_dssp             HHHHHHHHHHH----------HHHHHCTTTCCHHHHHHHHTCCHHHHHHHCSS
T ss_pred             HHHHHHHHHHH----------HHHHhCcccCCHHHHHHHhCCCchhhHhhCCC
Confidence            34677778777          33444566899999999999999999998864

>3hta_A EBRA repressor; TETR family, DNA binding protein, multidrug resistance, MULT binding protein, DNA-binding, transcription; 2.30A {Streptomyces lividans} PDB: 3hth_A* 3hti_A* 3htj_A* 3iuv_A

Probab=80.45  E-value=1.1  Score=33.79  Aligned_cols=43  Identities=16%  Similarity=0.136  Sum_probs=34.1

Q ss_pred             hHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          160 LHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       160 l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      ..++++.++.+          ++..-.-.++|+++||.+.|+||..||+-|+.
T Consensus        29 ~r~~Il~AA~~----------lf~~~G~~~~t~~~IA~~aGvs~~tlY~~F~s   71 (217)
T 3hta_A           29 RRQRIIDAAIR----------VVGQKGIAGLSHRTVAAEADVPLGSTTYHFAT   71 (217)
T ss_dssp             HHHHHHHHHHH----------HHHHHTGGGCCHHHHHHHHTCCHHHHHHHCSS
T ss_pred             HHHHHHHHHHH----------HHHHcCcccCCHHHHHHHcCCCcchhhhcCCC
Confidence            35678888887          33334556899999999999999999998864

>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=80.43  E-value=10  Score=34.82  Aligned_cols=96  Identities=10%  Similarity=-0.040  Sum_probs=63.3

Q ss_pred             CCcEEEEE---CCHHHHHHHHHhCCCCceEEEEccCCCC-CC-HHHHHHHHhcC-C-CCcEEEEeccCCHHHHHHHHhCC
Q 027234            1 MGFSVTKC---NRAEIALDMLRTNKNGYDIVISDVHMPD-MD-GFKLLELVGLE-M-DLPVIMMCAHGSKEVVMKGVTHD   73 (226)
Q Consensus         1 lg~~V~~~---~~~~eal~~l~~~~~~~DlVl~D~~mp~-~d-G~~l~~~l~~~-~-~~pvI~ls~~~~~~~~~~a~~~g   73 (226)
                      .||+|..-   .+.++.++.+.+..  +|+|.+...|.. +. .-++++.|+.. . +++ |++-+.........+.+.|
T Consensus       631 ~GfeVi~lG~~v~~eeiv~aA~e~~--adiVglSsl~~~~~~~~~~vi~~Lr~~G~~dv~-VivGG~~P~~d~~~l~~~G  707 (762)
T 2xij_A          631 LGFDVDIGPLFQTPREVAQQAVDAD--VHAVGVSTLAAGHKTLVPELIKELNSLGRPDIL-VMCGGVIPPQDYEFLFEVG  707 (762)
T ss_dssp             TTCEEEECCTTCCHHHHHHHHHHTT--CSEEEEEECSSCHHHHHHHHHHHHHHTTCTTSE-EEEEESCCGGGHHHHHHHT
T ss_pred             CCeEEeeCCCCCCHHHHHHHHHHcC--CCEEEEeeecHHHHHHHHHHHHHHHhcCCCCCE-EEEeCCCCcccHHHHHhCC
Confidence            37888743   36788888888866  999998887754 22 34455666633 2 333 3344322222344467899


Q ss_pred             cceEEeCCCCHHHHHHHHHHHHHHHh
Q 027234           74 ACDYLTKPVRIEELKNIWQHVVRKRK   99 (226)
Q Consensus        74 a~~yl~KP~~~~~L~~~l~~~~~~~~   99 (226)
                      +++|+..--+..+....+...+..+.
T Consensus       708 aD~~f~pgtd~~e~~~~i~~~l~~~~  733 (762)
T 2xij_A          708 VSNVFGPGTRIPKAAVQVLDDIEKCL  733 (762)
T ss_dssp             CCEEECTTCCHHHHHHHHHHHHHHHH
T ss_pred             CCEEeCCCCCHHHHHHHHHHHHHHHh
Confidence            99999877788888888877775544

>3trb_A Virulence-associated protein I; mobIle and extrachromosomal element functions, DNA binding P; 2.00A {Coxiella burnetii}

Probab=80.29  E-value=0.94  Score=30.55  Aligned_cols=27  Identities=15%  Similarity=0.162  Sum_probs=24.2

Q ss_pred             hhCCCCCCHHHHHHHhhhhhhhhhccc
Q 027234          184 LMNIPGLTRENVASHLQKHRLYLSRLS  210 (226)
Q Consensus       184 ~~~~~~lt~~~va~~l~~~r~~l~r~~  210 (226)
                      .+..-++|..++|..+++|+++++++-
T Consensus        22 lr~~~gltq~eLA~~lGis~~~is~ie   48 (104)
T 3trb_A           22 LGFLDKMSANQLAKHLAIPTNRVTAIL   48 (104)
T ss_dssp             HHHTTSCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHcCCCHHHHHHHHCcCHHHHHHHH
Confidence            577889999999999999999999863

>2xi8_A Putative transcription regulator; HTH DNA-binding motif; HET: GOL; 1.21A {Enterococcus faecalis} PDB: 2gzu_A 1utx_A* 2xj3_A 2xiu_A

Probab=80.29  E-value=0.38  Score=28.84  Aligned_cols=31  Identities=10%  Similarity=0.174  Sum_probs=24.8

Q ss_pred             HHHhhCCCCCCHHHHHHHhhhhhhhhhcccC
Q 027234          181 ILELMNIPGLTRENVASHLQKHRLYLSRLSG  211 (226)
Q Consensus       181 I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~  211 (226)
                      |.+.+...++|..++|..+++++++++++..
T Consensus         6 l~~~r~~~g~s~~~lA~~~gis~~~i~~~e~   36 (66)
T 2xi8_A            6 LKLIREKKKISQSELAALLEVSRQTINGIEK   36 (66)
T ss_dssp             HHHHHHHTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            4444555689999999999999999998644

>3s8q_A R-M controller protein; protein-DNA complex, helix-turn-helix; HET: DNA; 2.10A {Enterobacter SP} SCOP: a.35.1.0 PDB: 3clc_A* 3ufd_A*

Probab=80.26  E-value=0.54  Score=29.77  Aligned_cols=30  Identities=27%  Similarity=0.391  Sum_probs=24.9

Q ss_pred             HHHhhCCCCCCHHHHHHHhhhhhhhhhccc
Q 027234          181 ILELMNIPGLTRENVASHLQKHRLYLSRLS  210 (226)
Q Consensus       181 I~~~~~~~~lt~~~va~~l~~~r~~l~r~~  210 (226)
                      |.+.+...++|..++|..+++++++++++-
T Consensus        16 lk~~R~~~glsq~~lA~~~gis~~~i~~~e   45 (82)
T 3s8q_A           16 IKKIRLEKGMTQEDLAYKSNLDRTYISGIE   45 (82)
T ss_dssp             HHHHHHHTTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHhCcCHHHHHHHH
Confidence            444555669999999999999999999864

>1xm3_A Thiazole biosynthesis protein THIG; structural genomics, protein structure initiative, PSI, NESG, northeast structural genomics consortium; 1.80A {Bacillus subtilis} SCOP: c.1.31.1 PDB: 1tyg_A

Probab=80.22  E-value=3.5  Score=32.68  Aligned_cols=76  Identities=16%  Similarity=0.132  Sum_probs=50.5

Q ss_pred             CcEEE--EECCHHHHHHHHHhCCCCceEEEEccCC-C---CCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcc
Q 027234            2 GFSVT--KCNRAEIALDMLRTNKNGYDIVISDVHM-P---DMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDAC   75 (226)
Q Consensus         2 g~~V~--~~~~~~eal~~l~~~~~~~DlVl~D~~m-p---~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~   75 (226)
                      |+.+.  ++.+.+++....+. .  .|.|+.=-.. +   +..+.++++.+++..++|||+..+-.+.+.+.+++..||+
T Consensus       126 g~~vi~~~~~~~~~a~~~~~~-g--ad~v~~~~~~~Gt~~~~~~~~~l~~i~~~~~iPviv~gGI~t~eda~~~~~~GAd  202 (264)
T 1xm3_A          126 GFIVLPYTSDDVVLARKLEEL-G--VHAIMPGASPIGSGQGILNPLNLSFIIEQAKVPVIVDAGIGSPKDAAYAMELGAD  202 (264)
T ss_dssp             TCCEEEEECSCHHHHHHHHHH-T--CSCBEECSSSTTCCCCCSCHHHHHHHHHHCSSCBEEESCCCSHHHHHHHHHTTCS
T ss_pred             CeEEEEEcCCCHHHHHHHHHh-C--CCEEEECCcccCCCCCCCCHHHHHHHHhcCCCCEEEEeCCCCHHHHHHHHHcCCC
Confidence            44444  44566666555443 2  5766330000 1   1234778888876678999999998889999999999999


Q ss_pred             eEEeC
Q 027234           76 DYLTK   80 (226)
Q Consensus        76 ~yl~K   80 (226)
                      +.+.=
T Consensus       203 gViVG  207 (264)
T 1xm3_A          203 GVLLN  207 (264)
T ss_dssp             EEEES
T ss_pred             EEEEc
Confidence            98843

>3cdl_A Transcriptional regulator AEFR; APC88582, TETR, pseudomonas syringae PV. tomato STR. DC3000, structural genomics, PSI-2; HET: MSE; 2.36A {Pseudomonas syringae PV}

Probab=80.18  E-value=1.9  Score=31.93  Aligned_cols=43  Identities=7%  Similarity=-0.048  Sum_probs=34.0

Q ss_pred             hHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          160 LHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       160 l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      ..++++.++.+          +...-.-.+.|+++||++.|+|+..+|+-|+.
T Consensus        10 ~r~~Il~aA~~----------lf~~~G~~~~s~~~IA~~aGvsk~tlY~~F~s   52 (203)
T 3cdl_A           10 KRESIVQAAIA----------EFGDRGFEITSMDRIAARAEVSKRTVYNHFPS   52 (203)
T ss_dssp             HHHHHHHHHHH----------HHHHHCTTTCCHHHHHHHTTSCHHHHHTTSSS
T ss_pred             HHHHHHHHHHH----------HHHHcCchhcCHHHHHHHhCCCHHHHHHHCCC
Confidence            35677888887          33344566899999999999999999998874

>2iai_A Putative transcriptional regulator SCO3833; structural genomics, TETR, unknow function, PSI-2, protein structure initiative; 1.65A {Streptomyces coelicolor}

Probab=80.16  E-value=1.7  Score=32.91  Aligned_cols=41  Identities=7%  Similarity=0.045  Sum_probs=32.0

Q ss_pred             HHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          162 QQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       162 ~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      ++++.++.+          ++..-.-.++|+++||.+.++||..||+-|+.
T Consensus        33 ~~Il~aA~~----------lf~~~G~~~~t~~~IA~~Agvs~~t~Y~~F~s   73 (230)
T 2iai_A           33 ETLLSVAVQ----------VFIERGYDGTSMEHLSKAAGISKSSIYHHVTG   73 (230)
T ss_dssp             SCHHHHHHH----------HHHHHCTTTCCHHHHHHHHTSCHHHHTTTCSS
T ss_pred             HHHHHHHHH----------HHHHcCccccCHHHHHHHHCCChhHHHHhCCC
Confidence            355666666          33444566899999999999999999998864

>3pas_A TETR family transcription regulator; structural genomics, joint center for structural genomics, J protein structure initiative; HET: MSE; 1.90A {Marinobacter aquaeolei}

Probab=80.07  E-value=0.56  Score=34.22  Aligned_cols=43  Identities=9%  Similarity=-0.065  Sum_probs=33.0

Q ss_pred             hHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          160 LHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       160 l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      -.++++.++.+          ++..-.-.++|+++||.+.|+||..+|+-|+.
T Consensus         9 ~r~~Il~aa~~----------l~~~~G~~~~t~~~Ia~~agvs~~t~Y~~F~s   51 (195)
T 3pas_A            9 KRIAFLEATVR----------EVADHGFSATSVGKIAKAAGLSPATLYIYYED   51 (195)
T ss_dssp             HHHHHHHHHHH----------HHHHHHHHHCCHHHHHHHHTSCHHHHHHHCSS
T ss_pred             HHHHHHHHHHH----------HHHHcChHhcCHHHHHHHhCCCchHHHHHcCC
Confidence            34677777777          33333445799999999999999999998874

>1y0e_A Putative N-acetylmannosamine-6-phosphate 2-epimer; mannac-6-P epimerase, NANE, structural genomics, protein STR initiative, PSI; 1.95A {Staphylococcus aureus subsp} SCOP: c.1.2.5

Probab=80.01  E-value=8  Score=29.31  Aligned_cols=71  Identities=17%  Similarity=0.149  Sum_probs=49.0

Q ss_pred             EECCHHHHHHHHHhCCCCceEEEEccC-----CC----CCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceE
Q 027234            7 KCNRAEIALDMLRTNKNGYDIVISDVH-----MP----DMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDY   77 (226)
Q Consensus         7 ~~~~~~eal~~l~~~~~~~DlVl~D~~-----mp----~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~y   77 (226)
                      .+.+.+++......   +.|+|.+...     .+    ...++++++.++...++|||...+-.+.+.+.+++..||+++
T Consensus       125 ~~~t~~e~~~~~~~---G~d~i~~~~~g~t~~~~~~~~~~~~~~~~~~~~~~~~ipvia~GGI~~~~~~~~~~~~Gad~v  201 (223)
T 1y0e_A          125 DIATVEEAKNAARL---GFDYIGTTLHGYTSYTQGQLLYQNDFQFLKDVLQSVDAKVIAEGNVITPDMYKRVMDLGVHCS  201 (223)
T ss_dssp             ECSSHHHHHHHHHT---TCSEEECTTTTSSTTSTTCCTTHHHHHHHHHHHHHCCSEEEEESSCCSHHHHHHHHHTTCSEE
T ss_pred             cCCCHHHHHHHHHc---CCCEEEeCCCcCcCCCCCCCCCcccHHHHHHHHhhCCCCEEEecCCCCHHHHHHHHHcCCCEE
Confidence            45567777765442   3788765321     01    123456778887556799998888779999999999999998


Q ss_pred             EeC
Q 027234           78 LTK   80 (226)
Q Consensus        78 l~K   80 (226)
                      +.=
T Consensus       202 ~vG  204 (223)
T 1y0e_A          202 VVG  204 (223)
T ss_dssp             EEC
T ss_pred             EEC
Confidence            853

---

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	226
d1irza_	64	a.4.1.11 (A:) Arr10-B {Thale cress (Arabidopsis th	5e-27
d1dz3a_	123	c.23.1.1 (A:) Sporulation response regulator Spo0A	3e-19
d1zesa1	121	c.23.1.1 (A:3-123) PhoB receiver domain {Escherich	3e-16
d1a04a2	138	c.23.1.1 (A:5-142) Nitrate/nitrite response regula	6e-16
d2a9pa1	117	c.23.1.1 (A:2-118) DNA-binding response regulator	9e-16
d1peya_	119	c.23.1.1 (A:) Sporulation response regulator Spo0F	1e-15
d1dcfa_	134	c.23.1.2 (A:) Receiver domain of the ethylene rece	4e-15
d1u0sy_	118	c.23.1.1 (Y:) CheY protein {Thermotoga maritima [T	4e-15
d1jbea_	128	c.23.1.1 (A:) CheY protein {Escherichia coli [TaxI	8e-15
d1qkka_	140	c.23.1.1 (A:) Transcriptional regulatory protein D	4e-14
d1s8na_	190	c.23.1.1 (A:) Probable two-component system transc	4e-14
d1krwa_	123	c.23.1.1 (A:) NTRC receiver domain {Salmonella typ	4e-14
d1zgza1	120	c.23.1.1 (A:2-121) TorCAD operon transcriptional r	1e-13
d1a2oa1	140	c.23.1.1 (A:1-140) Methylesterase CheB, N-terminal	1e-13
d2r25b1	128	c.23.1.1 (B:1087-1214) Response regulator Sin1 {Ba	2e-13
d1xhfa1	121	c.23.1.1 (A:2-122) Aerobic respiration control pro	2e-13
d2b4aa1	118	c.23.1.1 (A:2-119) Hypothetical protein BH3024 {Ba	2e-13
d1i3ca_	144	c.23.1.1 (A:) Response regulator for cyanobacteria	4e-13
d2ayxa1	133	c.23.1.1 (A:817-949) Sensor kinase protein RcsC, C	8e-13
d1k68a_	140	c.23.1.1 (A:) Response regulator for cyanobacteria	9e-13
d1yioa2	128	c.23.1.1 (A:3-130) Response regulatory protein Sty	1e-12
d1ny5a1	137	c.23.1.1 (A:1-137) Transcriptional activator sigm5	1e-12
d1p6qa_	129	c.23.1.1 (A:) CheY protein {Sinorhizobium meliloti	1e-12
d1zh2a1	119	c.23.1.1 (A:2-120) Transcriptional regulatory prot	2e-12
d1mb3a_	123	c.23.1.1 (A:) Cell division response regulator Div	2e-12
d1dbwa_	123	c.23.1.1 (A:) Transcriptional regulatory protein F	5e-12
d1kgsa2	122	c.23.1.1 (A:2-123) PhoB receiver domain {Thermotog	7e-12
d1mvoa_	121	c.23.1.1 (A:) PhoP receiver domain {Bacillus subti	5e-11
d1k66a_	149	c.23.1.1 (A:) Response regulator for cyanobacteria	9e-11
d1ys7a2	121	c.23.1.1 (A:7-127) Transcriptional regulatory prot	1e-10
d1p2fa2	120	c.23.1.1 (A:1-120) Response regulator DrrB {Thermo	7e-10
d2pl1a1	119	c.23.1.1 (A:1-119) PhoP receiver domain {Escherich	9e-10
d1w25a2	153	c.23.1.1 (A:141-293) Response regulator PleD, rece	3e-09
d1w25a1	139	c.23.1.1 (A:2-140) Response regulator PleD, receiv	7e-09
d1qo0d_	189	c.23.1.3 (D:) Positive regulator of the amidase op	6e-08

>d1irza_ a.4.1.11 (A:) Arr10-B {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 64

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: GARP response regulators
domain: Arr10-B
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

 Score = 96.5 bits (240), Expect = 5e-27
 Identities = 37/61 (60%), Positives = 50/61 (81%)

Query: 150 KKPRLVWSVELHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRL 209
           KKPR++W+ ELH +F++AV  LG ++A PKKIL+LMN+  LTRENVASHLQK R+ L ++
Sbjct: 4   KKPRVLWTHELHNKFLAAVDHLGVERAVPKKILDLMNVDKLTRENVASHLQKFRVALKKV 63

Query: 210 S 210
           S
Sbjct: 64  S 64

>d1dz3a_ c.23.1.1 (A:) Sporulation response regulator Spo0A {Bacillus stearothermophilus [TaxId: 1422]} Length = 123

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Sporulation response regulator Spo0A
species: Bacillus stearothermophilus [TaxId: 1422]

 Score = 77.9 bits (192), Expect = 3e-19
 Identities = 29/98 (29%), Positives = 46/98 (46%), Gaps = 4/98 (4%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV--GLEMDLPVIMMCA 59
              +      +  L ML   +   DI++ D+ MP +DG  +LE +  G E    VIM+ A
Sbjct: 27  MEVIGTAYNGQDCLQMLEEKR--PDILLLDIIMPHLDGLAVLERIRAGFEHQPNVIMLTA 84

Query: 60  HGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
            G ++V  K V   A  ++ KP  +E L +  + V  K
Sbjct: 85  FGQEDVTKKAVELGASYFILKPFDMENLAHHIRQVYGK 122

>d1zesa1 c.23.1.1 (A:3-123) PhoB receiver domain {Escherichia coli [TaxId: 562]} Length = 121

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: PhoB receiver domain
species: Escherichia coli [TaxId: 562]

 Score = 69.9 bits (171), Expect = 3e-16
 Identities = 26/99 (26%), Positives = 52/99 (52%), Gaps = 5/99 (5%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIMMC 58
           GF   +    + A++ L   +   D+++ D  +P   G + ++ +    +  D+PV+M+ 
Sbjct: 24  GFQPVEAEDYDSAVNQLN--EPWPDLILLDWMLPGGSGIQFIKHLKRESMTRDIPVVMLT 81

Query: 59  AHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
           A G +E  ++G+   A DY+TKP   +EL    + V+R+
Sbjct: 82  ARGEEEDRVRGLETGADDYITKPFSPKELVARIKAVMRR 120

>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 = 69.5 bits (170), Expect = 6e-16
 Identities = 18/99 (18%), Positives = 41/99 (41%), Gaps = 3/99 (3%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLL-ELVGLEMDLPVIMMCAH 60
              V + +  E  +++  +     D+++ D++MP M+G + L +L    +   +++    
Sbjct: 28  ITVVGEASNGEQGIELAESLD--PDLILLDLNMPGMNGLETLDKLREKSLSGRIVVFSVS 85

Query: 61  GSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRK 99
             +E V+  +   A  YL K +  E+L            
Sbjct: 86  NHEEDVVTALKRGADGYLLKDMEPEDLLKALHQAAAGEM 124

>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 = 68.5 bits (167), Expect = 9e-16
 Identities = 25/96 (26%), Positives = 50/96 (52%), Gaps = 2/96 (2%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHG 61
           G+ V        AL+     +   DI+I D+ +P++DG ++ + +     +P++M+ A  
Sbjct: 24  GYEVVTAFNGREALEQFEAEQ--PDIIILDLMLPEIDGLEVAKTIRKTSSVPILMLSAKD 81

Query: 62  SKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
           S+   + G+   A DY+TKP    EL+   + ++R+
Sbjct: 82  SEFDKVIGLELGADDYVTKPFSNRELQARVKALLRR 117

>d1peya_ c.23.1.1 (A:) Sporulation response regulator Spo0F {Bacillus subtilis [TaxId: 1423]} Length = 119

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Sporulation response regulator Spo0F
species: Bacillus subtilis [TaxId: 1423]

 Score = 68.4 bits (167), Expect = 1e-15
 Identities = 22/90 (24%), Positives = 49/90 (54%), Gaps = 3/90 (3%)

Query: 1   MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLL-ELVGLEMDLPVIMMCA 59
            G+   +      ALD++   +   D+V+ D+ +P MDG ++L  +  ++ ++ VI+M A
Sbjct: 24  EGYQTFQAANGLQALDIVTKER--PDLVLLDMKIPGMDGIEILKRMKVIDENIRVIIMTA 81

Query: 60  HGSKEVVMKGVTHDACDYLTKPVRIEELKN 89
           +G  +++ +     A  +  KP  I+E+++
Sbjct: 82  YGELDMIQESKELGALTHFAKPFDIDEIRD 111

>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 = 67.7 bits (165), Expect = 4e-15
 Identities = 17/104 (16%), Positives = 44/104 (42%), Gaps = 9/104 (8%)

Query: 1   MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEM------DLPV 54
           +G  VT  +  E  L +     + + +V  DV MP ++ +++   +  +          +
Sbjct: 30  LGCEVTTVSSNEECLRV---VSHEHKVVFMDVCMPGVENYQIALRIHEKFTKQRHQRPLL 86

Query: 55  IMMCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKR 98
           + +  +  K    K ++      L KPV ++ ++++   ++  R
Sbjct: 87  VALSGNTDKSTKEKCMSFGLDGVLLKPVSLDNIRDVLSDLLEPR 130

>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 = 66.9 bits (163), Expect = 4e-15
 Identities = 20/91 (21%), Positives = 44/91 (48%), Gaps = 3/91 (3%)

Query: 5   VTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLL-ELVGLEMDLPVIMMCAHGSK 63
             +      A++  +  K   DIV  D+ MP+M+G   + E++ ++ +  +I+  A G +
Sbjct: 29  AGEATNGREAVEKYKELK--PDIVTMDITMPEMNGIDAIKEIMKIDPNAKIIVCSAMGQQ 86

Query: 64  EVVMKGVTHDACDYLTKPVRIEELKNIWQHV 94
            +V++ +   A D++ KP +   +      V
Sbjct: 87  AMVIEAIKAGAKDFIVKPFQPSRVVEALNKV 117

>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 = 65.1 bits (158), Expect = 4e-14
 Identities = 33/118 (27%), Positives = 58/118 (49%), Gaps = 3/118 (2%)

Query: 1   MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLL-ELVGLEMDLPVIMMCA 59
            GF+V+    A  AL  L  +     IVISD+ MP MDG  L  +++ L+ DLP+I++  
Sbjct: 23  AGFTVSSFASATEALAGLSADF--AGIVISDIRMPGMDGLALFRKILALDPDLPMILVTG 80

Query: 60  HGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQSGSVEGGAQQ 117
           HG   + ++ +   A D++ KP   + L    +    KR+   ++     + E  ++ 
Sbjct: 81  HGDIPMAVQAIQDGAYDFIAKPFAADRLVQSARRAEEKRRLVMENRSLRRAAEAASEG 138

>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 = 66.0 bits (160), Expect = 4e-14
 Identities = 32/178 (17%), Positives = 69/178 (38%), Gaps = 14/178 (7%)

Query: 1   MGFSVTK-CNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCA 59
            G+ +       + A+++   +K   D+VI DV MP  DG      +  +   P++++ A
Sbjct: 26  EGYEIVGEAGDGQEAVELAELHK--PDLVIMDVKMPRRDGIDAASEIASKRIAPIVVLTA 83

Query: 60  HGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQSGSVEGGAQQPK 119
              +++V +     A  YL KP  I +L    +  V + +       +  ++    +  K
Sbjct: 84  FSQRDLVERARDAGAMAYLVKPFSISDLIPAIELAVSRFREITALEGEVATLSERLETRK 143

Query: 120 PFEESDDSYSVNEGTSNSRKDEEEEAEKRLKKPRLVWSVELHQQFVSAVKELGFDKAG 177
             E +        G +      E +A K +++     +    +  +  V E+  +  G
Sbjct: 144 LVERAKGLLQTKHGMT------EPDAFKWIQR-----AAMDRRTTMKRVAEVVLETLG 190

>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 = 64.4 bits (156), Expect = 4e-14
 Identities = 29/100 (29%), Positives = 45/100 (45%), Gaps = 3/100 (3%)

Query: 1   MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLL-ELVGLEMDLPVIMMCA 59
            G + T        L  L +     D+++SD+ MP MDG  LL ++      LPVI+M A
Sbjct: 26  AGLTCTTFENGNEVLAALASKT--PDVLLSDIRMPGMDGLALLKQIKQRHPMLPVIIMTA 83

Query: 60  HGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRK 99
           H   +  +      A DYL KP  I+E   + +  +   +
Sbjct: 84  HSDLDAAVSAYQQGAFDYLPKPFDIDEAVALVERAISHYQ 123

>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 = 63.1 bits (153), Expect = 1e-13
 Identities = 18/96 (18%), Positives = 48/96 (50%), Gaps = 2/96 (2%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHG 61
           G++V+         ++++      D+++ D+++PD +G  L   +     + +I++    
Sbjct: 25  GYTVSVTASGAGLREIMQ--NQSVDLILLDINLPDENGLMLTRALRERSTVGIILVTGRS 82

Query: 62  SKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
            +   + G+   A DY+TKP+ + EL    ++++ +
Sbjct: 83  DRIDRIVGLEMGADDYVTKPLELRELVVRVKNLLWR 118

>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 = 63.4 bits (154), Expect = 1e-13
 Identities = 26/102 (25%), Positives = 46/102 (45%), Gaps = 6/102 (5%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHG 61
              V       +A D+++      D++  DV MP MDG   LE +     +PV+M+ +  
Sbjct: 29  MEMVATAPDPLVARDLIKKFN--PDVLTLDVEMPRMDGLDFLEKLMRLRPMPVVMVSSLT 86

Query: 62  SK--EVVMKGVTHDACDYLTKPVRI--EELKNIWQHVVRKRK 99
            K  EV ++ +   A D++TKP     E +    + +  K +
Sbjct: 87  GKGSEVTLRALELGAIDFVTKPQLGIREGMLAYSEMIAEKVR 128

>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 = 63.1 bits (153), Expect = 2e-13
 Identities = 17/88 (19%), Positives = 38/88 (43%), Gaps = 2/88 (2%)

Query: 14  ALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV--GLEMDLPVIMMCAHGSKEVVMKGVT 71
            +  L +    Y+++  DV MP +DG    +++   L    P++ + A      + + + 
Sbjct: 41  KVKELTSKGENYNMIFMDVQMPKVDGLLSTKMIRRDLGYTSPIVALTAFADDSNIKECLE 100

Query: 72  HDACDYLTKPVRIEELKNIWQHVVRKRK 99
                +L+KP++  +LK I        +
Sbjct: 101 SGMNGFLSKPIKRPKLKTILTEFCAAYQ 128

>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 = 62.7 bits (152), Expect = 2e-13
 Identities = 18/96 (18%), Positives = 45/96 (46%), Gaps = 2/96 (2%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHG 61
           G+ V +         +L   +   ++VI D+++P  +G  L   +  + ++ ++ +    
Sbjct: 26  GYDVFEATDGAEMHQILS--EYDINLVIMDINLPGKNGLLLARELREQANVALMFLTGRD 83

Query: 62  SKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
           ++   + G+   A DY+TKP    EL    ++++ +
Sbjct: 84  NEVDKILGLEIGADDYITKPFNPRELTIRARNLLSR 119

>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 = 62.6 bits (152), Expect = 2e-13
 Identities = 18/88 (20%), Positives = 32/88 (36%), Gaps = 5/88 (5%)

Query: 1   MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLL-ELVGLEMDLPVIMMCA 59
           +G  VT                +  D++I    + D+  F LL  +        V+++  
Sbjct: 25  LGAEVTVHPSGSAFFQHRSQL-STCDLLIVSDQLVDLSIFSLLDIVKEQTKQPSVLILTT 83

Query: 60  HGSKEVVMKGVTHDACDYLTKPVRIEEL 87
                 +++   H+   YL KP  I EL
Sbjct: 84  GR--HELIESSEHNL-SYLQKPFAISEL 108

>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 = 62.4 bits (151), Expect = 4e-13
 Identities = 16/106 (15%), Positives = 43/106 (40%), Gaps = 8/106 (7%)

Query: 1   MGFSVTKCNRAEIALDMLRTNKNG-----YDIVISDVHMPDMDGFKLLELV---GLEMDL 52
           +   +        A+  L+           ++++ D+++P  DG ++L  +        +
Sbjct: 28  IDHELIILRDGLAAMAFLQQQGEYENSPRPNLILLDLNLPKKDGREVLAEIKQNPDLKRI 87

Query: 53  PVIMMCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKR 98
           PV+++    +++ V+         YLTK   +++L  + Q +    
Sbjct: 88  PVVVLTTSHNEDDVIASYELHVNCYLTKSRNLKDLFKMVQGIESFW 133

>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 = 61.3 bits (148), Expect = 8e-13
 Identities = 31/103 (30%), Positives = 52/103 (50%), Gaps = 3/103 (2%)

Query: 1   MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLL-ELVGLEMDLPVIMMCA 59
           +G+     N    AL++L  N    DIV+SDV+MP+MDG++L   +  L + LPVI + A
Sbjct: 31  LGYQCKTANDGVDALNVLSKNH--IDIVLSDVNMPNMDGYRLTQRIRQLGLTLPVIGVTA 88

Query: 60  HGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNER 102
           +   E   + +       L+KPV ++ +K        + +  R
Sbjct: 89  NALAEEKQRCLESGMDSCLSKPVTLDVIKQTLTLYAERVRKSR 131

>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 = 61.2 bits (148), Expect = 9e-13
 Identities = 18/104 (17%), Positives = 44/104 (42%), Gaps = 8/104 (7%)

Query: 1   MGFSVTKCNRAEIALDMLRT-----NKNGYDIVISDVHMPDMDGFKLLELVGLEM---DL 52
           +   V        A+  LR      N +  D+++ D+++P  DG ++L  +  +     +
Sbjct: 27  VPHEVVTVRDGMEAMAYLRQEGEYANASRPDLILLDLNLPKKDGREVLAEIKSDPTLKRI 86

Query: 53  PVIMMCAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVR 96
           PV+++    +++ +          Y+TK   + +L  I + +  
Sbjct: 87  PVVVLSTSINEDDIFHSYDLHVNCYITKSANLSQLFQIVKGIEE 130

>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 = 60.5 bits (146), Expect = 1e-12
 Identities = 23/104 (22%), Positives = 49/104 (47%), Gaps = 3/104 (2%)

Query: 1   MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV-GLEMDLPVIMMCA 59
            GF V   + A   L+  R  +  +  ++ D+ MP M G +L E +  +   +P++ + A
Sbjct: 25  AGFEVETFDCASTFLEHRRPEQ--HGCLVLDMRMPGMSGIELQEQLTAISDGIPIVFITA 82

Query: 60  HGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERK 103
           HG   + ++ +   A ++L KP   + L +  +  ++     R+
Sbjct: 83  HGDIPMTVRAMKAGAIEFLPKPFEEQALLDAIEQGLQLNAERRQ 126

>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 = 60.8 bits (147), Expect = 1e-12
 Identities = 20/102 (19%), Positives = 41/102 (40%), Gaps = 1/102 (0%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHG 61
           G  V    R + A  +L        + +  +         L  +     +  VI++  HG
Sbjct: 24  GIKVESAERGKEAYKLLSEKHFNVVL-LDLLLPDVNGLEILKWIKERSPETEVIVITGHG 82

Query: 62  SKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNERK 103
           + +  ++ +   A D+LTKP  +EE++      +  RK  ++
Sbjct: 83  TIKTAVEAMKMGAYDFLTKPCMLEEIELTINKAIEHRKLRKE 124

>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 = 60.4 bits (146), Expect = 1e-12
 Identities = 29/98 (29%), Positives = 46/98 (46%), Gaps = 5/98 (5%)

Query: 5   VTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIMMCAHG 61
           +T     E  + ++   +N + +VISD +MP MDG  LL+ V           I++ A G
Sbjct: 34  ITAAGDGEQGMKIMA--QNPHHLVISDFNMPKMDGLGLLQAVRANPATKKAAFIILTAQG 91

Query: 62  SKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRK 99
            + +V K     A + L KP  IE++K   + V    K
Sbjct: 92  DRALVQKAAALGANNVLAKPFTIEKMKAAIEAVFGALK 129

>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 = 60.1 bits (145), Expect = 2e-12
 Identities = 26/98 (26%), Positives = 46/98 (46%), Gaps = 2/98 (2%)

Query: 1   MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAH 60
            G  V +    +  L    T K   D++I D+ +PD DG + +  +     +PVI++ A 
Sbjct: 23  DGMRVFEAETLQRGLLEAATRK--PDLIILDLGLPDGDGIEFIRDLRQWSAVPVIVLSAR 80

Query: 61  GSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKR 98
             +   +  +   A DYL+KP  I EL+   +  +R+ 
Sbjct: 81  SEESDKIAALDAGADDYLSKPFGIGELQARLRVALRRH 118

>d1mb3a_ c.23.1.1 (A:) Cell division response regulator DivK {Caulobacter crescentus [TaxId: 155892]} Length = 123

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Cell division response regulator DivK
species: Caulobacter crescentus [TaxId: 155892]

 Score = 60.0 bits (145), Expect = 2e-12
 Identities = 17/101 (16%), Positives = 44/101 (43%), Gaps = 5/101 (4%)

Query: 1   MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIMM 57
            G+   +      AL + R NK   D+++ D+ +P++ G ++ + +        +PV+ +
Sbjct: 24  QGYETLQTREGLSALSIARENK--PDLILMDIQLPEISGLEVTKWLKEDDDLAHIPVVAV 81

Query: 58  CAHGSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKR 98
            A   K    +        Y++KP+ +       + ++ ++
Sbjct: 82  TAFAMKGDEERIREGGCEAYISKPISVVHFLETIKRLLERQ 122

>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 = 58.9 bits (142), Expect = 5e-12
 Identities = 25/99 (25%), Positives = 48/99 (48%), Gaps = 7/99 (7%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGF-KLLELVGLEMDLPVIMMCAH 60
           GF+V     AE  L      +    ++++D+ MPDM G   L  L  L++++P I++  H
Sbjct: 27  GFAVKMHQSAEAFLAFAPDVR--NGVLVTDLRMPDMSGVELLRNLGDLKINIPSIVITGH 84

Query: 61  GSKEVVMKGVTHDACDYLTKPVRIEEL----KNIWQHVV 95
           G   + ++ +   A D++ KP     +    +   +H+V
Sbjct: 85  GDVPMAVEAMKAGAVDFIEKPFEDTVIIEAIERASEHLV 123

>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 = 58.2 bits (140), Expect = 7e-12
 Identities = 30/101 (29%), Positives = 48/101 (47%), Gaps = 4/101 (3%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDM-DGFKLLELVGLEMDLPVIMMCAH 60
            F+V  C   E  + M       +D+VI D+ +P       L  +    ++ PV+M+ A 
Sbjct: 25  MFTVDVCYDGEEGMYMAL--NEPFDVVILDIMLPVHDGWEILKSMRESGVNTPVLMLTAL 82

Query: 61  GSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRKNE 101
              E  +KG+   A DYL KP  + EL    + ++R RK+E
Sbjct: 83  SDVEYRVKGLNMGADDYLPKPFDLRELIARVRALIR-RKSE 122

>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 = 55.8 bits (134), Expect = 5e-11
 Identities = 26/97 (26%), Positives = 48/97 (49%), Gaps = 3/97 (3%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDG-FKLLELVGLEMDLPVIMMCAH 60
           G+ V   +  E AL    T K   D+++ DV +P +DG     +L   ++  P++M+ A 
Sbjct: 26  GYDVITASDGEEALKKAETEK--PDLIVLDVMLPKLDGIEVCKQLRQQKLMFPILMLTAK 83

Query: 61  GSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
             +   + G+   A DY+TKP    E+    + ++R+
Sbjct: 84  DEEFDKVLGLELGADDYMTKPFSPREVNARVKAILRR 120

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

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulator for cyanobacterial phytochrome
species: Calothrix sp. pcc 7601, RcpB [TaxId: 1188]

 Score = 56.0 bits (134), Expect = 9e-11
 Identities = 14/90 (15%), Positives = 39/90 (43%), Gaps = 3/90 (3%)

Query: 10  RAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIMMCAHGSKEVV 66
             +              +++ D+++P  DG ++L+ +    +   +PV++M    + + +
Sbjct: 48  LYQTGSYCNPDIAPRPAVILLDLNLPGTDGREVLQEIKQDEVLKKIPVVIMTTSSNPKDI 107

Query: 67  MKGVTHDACDYLTKPVRIEELKNIWQHVVR 96
               ++    Y+ KP+ I+ L    Q  ++
Sbjct: 108 EICYSYSISSYIVKPLEIDRLTETVQTFIK 137

>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 = 55.0 bits (132), Expect = 1e-10
 Identities = 29/98 (29%), Positives = 49/98 (50%), Gaps = 3/98 (3%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGF-KLLELVGLEMDLPVIMMCAH 60
           GF V        AL     N+   D ++ D++MP +DG   +  L  ++ D+PV ++ A 
Sbjct: 25  GFEVATAVDGAEALRSATENR--PDAIVLDINMPVLDGVSVVTALRAMDNDVPVCVLSAR 82

Query: 61  GSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKR 98
            S +  + G+   A DYL KP  + EL    + ++R+R
Sbjct: 83  SSVDDRVAGLEAGADDYLVKPFVLAELVARVKALLRRR 120

>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 = 53.1 bits (127), Expect = 7e-10
 Identities = 24/96 (25%), Positives = 42/96 (43%), Gaps = 5/96 (5%)

Query: 5   VTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV-GLEMDLPVIMMCAHGSK 63
           V      E  L+        + +V+ DV +PD  G+++  ++     +  VI++      
Sbjct: 28  VKTFLTGEDFLNDEEA----FHVVVLDVMLPDYSGYEICRMIKETRPETWVILLTLLSDD 83

Query: 64  EVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRK 99
           E V+KG    A DY+TKP   E L    +  + + K
Sbjct: 84  ESVLKGFEAGADDYVTKPFNPEILLARVKRFLEREK 119

>d2pl1a1 c.23.1.1 (A:1-119) PhoP receiver domain {Escherichia coli [TaxId: 562]} Length = 119

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: PhoP receiver domain
species: Escherichia coli [TaxId: 562]

 Score = 52.4 bits (125), Expect = 9e-10
 Identities = 28/97 (28%), Positives = 50/97 (51%), Gaps = 3/97 (3%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGF-KLLELVGLEMDLPVIMMCAH 60
           G  V     A+ A   L   ++  DI I D+ +PD DG   +      ++ LP++++ A 
Sbjct: 24  GHQVDDAEDAKEADYYLN--EHIPDIAIVDLGLPDEDGLSLIRRWRSNDVSLPILVLTAR 81

Query: 61  GSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRK 97
            S +  ++ ++  A DY+TKP  IEE+    Q ++R+
Sbjct: 82  ESWQDKVEVLSAGADDYVTKPFHIEEVMARMQALMRR 118

>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 = 52.0 bits (124), Expect = 3e-09
 Identities = 22/113 (19%), Positives = 44/113 (38%), Gaps = 10/113 (8%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELV---GLEMDLPVIMMC 58
              V + +       +        D+VI +    + DG +    +        LPV+ M 
Sbjct: 37  HRPVIESDPE--KAKISAGGP--VDLVIVNAAAKNFDGLRFTAALRSEERTRQLPVLAMV 92

Query: 59  AHGSKEVVMKGVTHDACDYLTKPVRIEELKN-IWQHVVRKRKNE--RKDLEQS 108
               +  ++K +     D L++P+  +EL   +   + RKR  +  R +L+ S
Sbjct: 93  DPDDRGRMVKALEIGVNDILSRPIDPQELSARVKTQIQRKRYTDYLRNNLDHS 145

>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 = 50.6 bits (120), Expect = 7e-09
 Identities = 22/111 (19%), Positives = 45/111 (40%), Gaps = 3/111 (2%)

Query: 2   GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPD-MDGFKLLELVGLEMDLPVIMMCAH 60
            + V+       AL M   +     ++   +   D     + L+       +PV+++ A 
Sbjct: 25  YYEVSTAMDGPTALAMAARDLPDIILLDVMMPGMDGFTVCRKLKDDPTTRHIPVVLITAL 84

Query: 61  GSKEVVMKGVTHDACDYLTKPVRIEELKNIWQHVVRKRK--NERKDLEQSG 109
             +   ++G+   A D+LTKP+    L    + + R +   +E +  E SG
Sbjct: 85  DGRGDRIQGLESGASDFLTKPIDDVMLFARVRSLTRFKLVIDELRQREASG 135

>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 = 48.9 bits (115), Expect = 6e-08
 Identities = 14/142 (9%), Positives = 40/142 (28%), Gaps = 6/142 (4%)

Query: 10  RAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKG 69
                           D+V + +            L        ++ +  + S  V+ + 
Sbjct: 37  SVRQCWPPPEAFDVPVDVVFTSIFQNRHHDEIAALLAAGTPRTTLVALVEYESPAVLSQI 96

Query: 70  VTHDACDYLTKPVRIEELKNIWQHVVRKRKNERKDLEQSGSVEGGAQQPKPFEESDDSYS 129
           +  +    +T+P+    +  +     R  +   K  +++  ++          ++     
Sbjct: 97  IELECHGVITQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQDRIAGQARINQAKVLLM 156

Query: 130 VNEGTSNSRKDEEEEAEKRLKK 151
              G        E EA + L +
Sbjct: 157 QRHGWD------EREAHQHLSR 172

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	226
d2pl1a1	119	PhoP receiver domain {Escherichia coli [TaxId: 562	99.91
d1zh2a1	119	Transcriptional regulatory protein KdpE, N-termina	99.91
d2a9pa1	117	DNA-binding response regulator MicA, N-terminal do	99.91
d1peya_	119	Sporulation response regulator Spo0F {Bacillus sub	99.9
d1ys7a2	121	Transcriptional regulatory protein PrrA, N-termina	99.9
d1kgsa2	122	PhoB receiver domain {Thermotoga maritima [TaxId:	99.9
d1qkka_	140	Transcriptional regulatory protein DctD, receiver	99.9
d1xhfa1	121	Aerobic respiration control protein ArcA, N-termin	99.9
d1ny5a1	137	Transcriptional activator sigm54 (NtrC1), N-termin	99.9
d1dbwa_	123	Transcriptional regulatory protein FixJ, receiver	99.9
d1krwa_	123	NTRC receiver domain {Salmonella typhimurium [TaxI	99.9
d1zesa1	121	PhoB receiver domain {Escherichia coli [TaxId: 562	99.89
d1s8na_	190	Probable two-component system transcriptional regu	99.89
d1mvoa_	121	PhoP receiver domain {Bacillus subtilis [TaxId: 14	99.89
d1zgza1	120	TorCAD operon transcriptional regulator TorD, N-te	99.89
d1u0sy_	118	CheY protein {Thermotoga maritima [TaxId: 2336]}	99.89
d2ayxa1	133	Sensor kinase protein RcsC, C-terminal domain {Esc	99.89
d1w25a1	139	Response regulator PleD, receiver domain {Caulobac	99.88
d1mb3a_	123	Cell division response regulator DivK {Caulobacter	99.88
d1yioa2	128	Response regulatory protein StyR, N-terminal domai	99.87
d1p6qa_	129	CheY protein {Sinorhizobium meliloti, CheY2 [TaxId	99.87
d1jbea_	128	CheY protein {Escherichia coli [TaxId: 562]}	99.87
d1p2fa2	120	Response regulator DrrB {Thermotoga maritima [TaxI	99.87
d2r25b1	128	Response regulator Sin1 {Baker's yeast (Saccharomy	99.87
d1k68a_	140	Response regulator for cyanobacterial phytochrome	99.87
d1i3ca_	144	Response regulator for cyanobacterial phytochrome	99.86
d1a04a2	138	Nitrate/nitrite response regulator (NarL), receive	99.86
d1k66a_	149	Response regulator for cyanobacterial phytochrome	99.86
d1dz3a_	123	Sporulation response regulator Spo0A {Bacillus ste	99.85
d1w25a2	153	Response regulator PleD, receiver domain {Caulobac	99.85
d1dcfa_	134	Receiver domain of the ethylene receptor {Thale cr	99.84
d2b4aa1	118	Hypothetical protein BH3024 {Bacillus halodurans [	99.79
d1qo0d_	189	Positive regulator of the amidase operon AmiR {Pse	99.76
d1irza_	64	Arr10-B {Thale cress (Arabidopsis thaliana) [TaxId	99.75
d1a2oa1	140	Methylesterase CheB, N-terminal domain {Salmonella	99.75
d1bl0a1	54	MarA {Escherichia coli [TaxId: 562]}	97.08
d1d5ya1	54	Rob transcription factor, N-terminal domain {Esche	97.03
d1gdta1	43	gamma,delta resolvase (C-terminal domain) {Escheri	95.47
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	95.25
d2fq4a1	69	Transcriptional regulator BC3163 {Bacillus cereus	94.9
d1jt6a1	71	Multidrug binding protein QacR {Staphylococcus aur	94.09
d2g7la1	68	Putative transcriptional regulator SCO7704 {Strept	93.93
d1rkta1	81	Hypothetical transcriptional regulator YfiR {Bacil	93.8
d2gena1	70	Probable transcriptional regulator PA1836 {Pseudom	93.74
d2iu5a1	71	Transcriptional activator DhaS {Lactococcus lactis	93.74
d1t56a1	73	Ethr repressor {Mycobacterium tuberculosis [TaxId:	93.62
d2fd5a1	76	Probable transcriptional regulator PA3133 {Pseudom	93.6
d1zk8a1	72	Transcriptional regulator BC5000 {Bacillus cereus	93.49
d1v7ba1	74	Transcriptional regulator Cgl2612 {Corynebacterium	93.49
d2fx0a1	73	Hemolysin II regulatory protein, HlyIIR {Bacillus	93.42
d2o7ta1	78	Transcriptional regulator Cgl1640/Cg1846 {Coryneba	93.36
d2g7sa1	74	Putative transcriptional regulator Atu0279 {Agroba	93.29
d2hyja1	75	Putative transcriptional regulator SCO4940 {Strept	93.27
d3c07a1	75	Putative transcriptional regulator SCO4850 {Strept	93.17
d2oi8a1	79	Putative regulatory protein Sco4313 {Streptomyces	93.01
d1pb6a1	72	Hypothetical transcriptional regulator YcdC {Esche	93.0
d2fbqa1	79	Transcriptional regulator PsrA {Pseudomonas aerugi	92.95
d1xrsb1	160	D-lysine 5,6-aminomutase beta subunit KamE, C-term	92.77
d1z0xa1	68	Transcriptional regulator EF0787 {Enterococcus fae	92.75
d2gfna1	77	Probable transcriptional regulator RHA1_ro04631 {R	92.68
d1vi0a1	72	Hypothetical transcriptional regulator YsiA {Bacil	92.66
d2d6ya1	68	Putative regulator SCO4008 {Streptomyces coelicolo	92.64
d2np5a1	69	Transcriptional regulator RHA1_ro04179 {Rhodococcu	92.5
d1ui5a1	71	A-factor receptor homolog CprB {Streptomyces coeli	92.41
d2i10a1	69	Putative transcriptional regulator RHA1_ro09068 {R	92.22
d1sgma1	73	Putative transcriptional regulator YxaF {Bacillus	92.07
d1ccwa_	137	Glutamate mutase, small subunit {Clostridium cochl	91.94
d2id3a1	68	Putative transcriptional regulator SCO5951 {Strept	91.48
d1umqa_	60	Photosynthetic apparatus regulatory protein PprA (	91.22
d2vkva1	62	Tetracyclin repressor (Tet-repressor, TetR) {Esche	90.85
d2g3ba1	72	Putative transcriptional regulator {Rhodococcus sp	90.77
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	90.64
d2g7ga1	65	Putative transcriptional regulator Rha04620 {Rhodo	90.42
d1dxea_	253	2-dehydro-3-deoxy-galactarate aldolase {Escherichi	90.27
d2ao9a1	120	Phage protein BC1890 {Bacillus cereus [TaxId: 1396	89.11
d1xi3a_	206	Thiamin phosphate synthase {Archaeon (Pyrococcus f	89.02
d1o4ua1	170	Quinolinic acid phosphoribosyltransferase (Nicotin	88.88
d2hkua1	70	Putative transcriptional regulator RHA1_ro03468 {R	88.86
d2id6a1	75	Transcriptional regulator TM1030 {Thermotoga marit	88.6
d1etxa_	89	FIS protein {Escherichia coli [TaxId: 562]}	88.33
d1thfd_	253	Cyclase subunit (or domain) of imidazoleglycerolph	87.62
d7reqa2	168	Methylmalonyl-CoA mutase alpha subunit, C-terminal	87.49
d1qpoa1	169	Quinolinic acid phosphoribosyltransferase (Nicotin	87.32
d1y7ya1	69	Restriction-modification controller protein C.AhdI	86.77
d1t33a1	88	Putative transcriptional repressor YbiH {Salmonell	85.96
d1b0na2	68	SinR repressor, DNA-binding domain {Bacillus subti	85.47
d1ntca_	91	DNA-binding domain of NTRC {Salmonella typhimurium	84.89
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	84.75
d1y0ea_	222	Putative N-acetylmannosamine-6-phosphate 2-epimera	84.53
d2icta1	87	Antitoxin HigA {Escherichia coli [TaxId: 562]}	84.29
d2a6ca1	69	HTH-motif protein NE1354 {Nitrosomonas europaea [T	83.43
d2o38a1	89	Hypothetical protein RPA3824 {Rhodopseudomonas pal	83.03
d1g2ha_	61	Transcriptional regulator TyrR, C-terminal domain	83.0
d1h5ya_	252	Cyclase subunit (or domain) of imidazoleglycerolph	82.55
d2np3a1	65	Putative transcriptional regulator SCO0857 {Strept	81.96
d2auwa1	67	Hypothetical protein NE0471 C-terminal domain {Nit	81.59
d1ka9f_	251	Cyclase subunit (or domain) of imidazoleglycerolph	81.48
d2r1jl1	66	P22 C2 repressor, DNA-binding domain {Salmonella b	81.22
d1y9qa1	79	Probable transcriptional regulator VC1968, N-termi	81.17
d1wv2a_	243	Thiazole biosynthesis protein ThiG {Pseudomonas ae	80.82
d1utxa_	66	Putative transcription regulator CylR2 {Enterococc	80.33
d1r8ja2	135	N-terminal domain of the circadian clock protein K	80.28
d1qapa1	167	Quinolinic acid phosphoribosyltransferase (Nicotin	80.14
d1vz0a1	93	Putative partitioning protein ParB/Spo0J {Thermus	80.01

>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=99.91  E-value=4e-24  Score=152.42  Aligned_cols=95  Identities=31%  Similarity=0.435  Sum_probs=90.0

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||+|.+|.++.+|++.+.+..  ||+||+|+.||++||+++++.++ ..+.+|+|++|+..+.+...++++.||++||.
T Consensus        23 ~G~~v~~a~~g~eal~~l~~~~--~dliilD~~mP~~~G~e~~~~i~~~~~~~pvi~lt~~~~~~~~~~a~~~Ga~~yl~  100 (119)
T d2pl1a1          23 AGHQVDDAEDAKEADYYLNEHI--PDIAIVDLGLPDEDGLSLIRRWRSNDVSLPILVLTARESWQDKVEVLSAGADDYVT  100 (119)
T ss_dssp             TTCEEEEESSHHHHHHHHHHSC--CSEEEECSCCSSSCHHHHHHHHHHTTCCSCEEEEESCCCHHHHHHHHHTTCSEEEE
T ss_pred             CCCEEEEECCHHHHHHHHHhcc--cceeehhccCCCchhHHHHHHHHhcCcccceEeeeccCCHHHHHHHHHcCCCEEEE
Confidence            5899999999999999999977  99999999999999999999998 45789999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHH
Q 027234           80 KPVRIEELKNIWQHVVRK   97 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~   97 (226)
                      ||++.++|...+++++++
T Consensus       101 KP~~~~~L~~~v~~~lrR  118 (119)
T d2pl1a1         101 KPFHIEEVMARMQALMRR  118 (119)
T ss_dssp             SSCCHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHcc
Confidence            999999999999999864

>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=99.91  E-value=2.5e-24  Score=153.55  Aligned_cols=96  Identities=27%  Similarity=0.398  Sum_probs=91.5

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEeC
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTK   80 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~K   80 (226)
                      .||+|..|.++++|++.+++..  ||+||+|+.||+++|+++++.+++.+.+|+|++|+..+.+...++++.||++||.|
T Consensus        23 ~g~~v~~a~~~~eal~~l~~~~--~dliilD~~mP~~~G~e~~~~ir~~~~~piI~lt~~~~~~~~~~a~~~Ga~dyl~K  100 (119)
T d1zh2a1          23 DGMRVFEAETLQRGLLEAATRK--PDLIILDLGLPDGDGIEFIRDLRQWSAVPVIVLSARSEESDKIAALDAGADDYLSK  100 (119)
T ss_dssp             TTCEEEEESSHHHHHHHHHHHC--CSEEEEESEETTEEHHHHHHHHHTTCCCCEEEEESCCSHHHHHHHHHHTCSEEEES
T ss_pred             CCCEEEEeCCHHHHHHHHHhcC--CCEEEeccccCCCCCchHHHHHHhccCCcEEEEeccCCHHHHHHHHHcCCCEEEEC
Confidence            5899999999999999999977  99999999999999999999999888899999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHH
Q 027234           81 PVRIEELKNIWQHVVRKR   98 (226)
Q Consensus        81 P~~~~~L~~~l~~~~~~~   98 (226)
                      |++.++|...+++++++.
T Consensus       101 P~~~~~L~~~i~~~lrr~  118 (119)
T d1zh2a1         101 PFGIGELQARLRVALRRH  118 (119)
T ss_dssp             SCCHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHhhh
Confidence            999999999999998653

>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=99.91  E-value=4.3e-24  Score=151.82  Aligned_cols=94  Identities=27%  Similarity=0.468  Sum_probs=90.1

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEeC
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTK   80 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~K   80 (226)
                      .||+|..++++++|++.+.+..  ||+||+|+.||+++|+++++.+++.+++|||++|+..+.+...++++.||++||.|
T Consensus        23 ~g~~v~~a~~~~eal~~~~~~~--~dlillD~~mp~~~G~~~~~~i~~~~~~pvI~lt~~~~~~~~~~a~~~Ga~d~l~K  100 (117)
T d2a9pa1          23 EGYEVVTAFNGREALEQFEAEQ--PDIIILDLMLPEIDGLEVAKTIRKTSSVPILMLSAKDSEFDKVIGLELGADDYVTK  100 (117)
T ss_dssp             TTCEEEEESSHHHHHHHHHHHC--CSEEEECSSCSSSCHHHHHHHHHTTCCCCEEEEESCCSHHHHHHHHHHTCSEEEES
T ss_pred             CCCEEEEECCHHHHHHHHHhcC--CCEEEeccccCCCCccHHHHHHHhCCCCCEEEEecCCCHHHHHHHHHcCCCEEEEC
Confidence            4899999999999999999977  99999999999999999999999888999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHH
Q 027234           81 PVRIEELKNIWQHVVR   96 (226)
Q Consensus        81 P~~~~~L~~~l~~~~~   96 (226)
                      ||+.++|...++++++
T Consensus       101 P~~~~~L~~~i~~~lr  116 (117)
T d2a9pa1         101 PFSNRELQARVKALLR  116 (117)
T ss_dssp             SCCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHhC
Confidence            9999999999998875

>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=99.90  E-value=8.6e-24  Score=150.67  Aligned_cols=93  Identities=24%  Similarity=0.481  Sum_probs=88.0

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||+|.++.++.+|++.+++..  ||+||+|+.||++||+++++.++ ..+++|||++|++.+.+...+|++.||++||.
T Consensus        24 ~g~~v~~a~~g~eal~~~~~~~--~dlillD~~mP~~~G~el~~~lr~~~~~~pvi~lt~~~~~~~~~~a~~~Ga~~yl~  101 (119)
T d1peya_          24 EGYQTFQAANGLQALDIVTKER--PDLVLLDMKIPGMDGIEILKRMKVIDENIRVIIMTAYGELDMIQESKELGALTHFA  101 (119)
T ss_dssp             TTCEEEEESSHHHHHHHHHHHC--CSEEEEESCCTTCCHHHHHHHHHHHCTTCEEEEEESSCCHHHHHHHHHTTCCEEEE
T ss_pred             cCCEEEEeCCHHHHHHHHHhCC--CCEEEEeccCCCCCHHHHHHHHHHhCCCCcEEEEecCCCHHHHHHHHHCCCCEEEE
Confidence            4899999999999999999977  99999999999999999999998 56789999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHH
Q 027234           80 KPVRIEELKNIWQHVV   95 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~   95 (226)
                      ||++.++|..++++++
T Consensus       102 KP~~~~~L~~~v~~~L  117 (119)
T d1peya_         102 KPFDIDEIRDAVKKYL  117 (119)
T ss_dssp             SSCCHHHHHHHHHHHS
T ss_pred             CCCCHHHHHHHHHHHC
Confidence            9999999999998864

>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=99.90  E-value=3.4e-24  Score=153.22  Aligned_cols=96  Identities=29%  Similarity=0.492  Sum_probs=90.4

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||+|.+|.++.+|++.+++..  ||+||+|++||++||+++++.++ ..+++|||++|+..+.+...+|++.||++||.
T Consensus        24 ~g~~v~~a~~~~eal~~~~~~~--~dlvl~D~~mP~~~G~el~~~ir~~~~~~piI~lt~~~~~~~~~~a~~~Ga~dyl~  101 (121)
T d1ys7a2          24 SGFEVATAVDGAEALRSATENR--PDAIVLDINMPVLDGVSVVTALRAMDNDVPVCVLSARSSVDDRVAGLEAGADDYLV  101 (121)
T ss_dssp             TTCEEEEESSHHHHHHHHHHSC--CSEEEEESSCSSSCHHHHHHHHHHTTCCCCEEEEECCCTTTCCCTTTTTTCSEEEE
T ss_pred             CCCEEEEECCHHHHHHHHHhCC--CCEEEEEeeccCcccHHHHHHHHhcCCCCEEEEEEeeCCHHHHHHHHHCCCCEEEE
Confidence            4899999999999999999977  99999999999999999999998 45789999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHH
Q 027234           80 KPVRIEELKNIWQHVVRKR   98 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~~   98 (226)
                      ||++.++|...++++++++
T Consensus       102 KP~~~~~L~~~i~~~l~rr  120 (121)
T d1ys7a2         102 KPFVLAELVARVKALLRRR  120 (121)
T ss_dssp             SSCCHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHcC
Confidence            9999999999999998754

>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=99.90  E-value=9.1e-24  Score=151.21  Aligned_cols=96  Identities=30%  Similarity=0.521  Sum_probs=90.5

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||+|.+|.++++|++.+.+..  ||+||+|+.||++||+++++.++ ..+.+|||++|+..+.+...++++.||++||.
T Consensus        24 ~g~~v~~a~~~~~al~~l~~~~--~dlillD~~mp~~~g~~~~~~lr~~~~~~piI~lt~~~~~~~~~~~~~~Ga~~yl~  101 (122)
T d1kgsa2          24 EMFTVDVCYDGEEGMYMALNEP--FDVVILDIMLPVHDGWEILKSMRESGVNTPVLMLTALSDVEYRVKGLNMGADDYLP  101 (122)
T ss_dssp             TTCEEEEESSHHHHHHHHHHSC--CSEEEEESCCSSSCHHHHHHHHHHTTCCCCEEEEESSCHHHHHHHTCCCCCSEEEE
T ss_pred             CCCEEEEEcchHHHHHHHHhhC--ccccccccccccchhHHHHHHHHhcCCCCcEEEEcCCCCHHHHHHHHHcCCceeec
Confidence            4899999999999999999977  99999999999999999999998 45689999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHH
Q 027234           80 KPVRIEELKNIWQHVVRKR   98 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~~   98 (226)
                      ||++.++|...++++++++
T Consensus       102 KP~~~~~L~~~i~~~l~r~  120 (122)
T d1kgsa2         102 KPFDLRELIARVRALIRRK  120 (122)
T ss_dssp             SSCCHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHh
Confidence            9999999999999988754

>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=99.90  E-value=7.9e-24  Score=155.09  Aligned_cols=100  Identities=32%  Similarity=0.520  Sum_probs=92.8

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||.|.++.++.+|++.+.++.  ||+||+|+.||+|||+++++.++ ..+++|||++|++.+.+...+|++.||+|||.
T Consensus        23 ~g~~v~~~~~~~~al~~l~~~~--~dlil~D~~mP~~~G~el~~~lr~~~~~~pvI~lT~~~~~~~~~~a~~~Ga~dyl~  100 (140)
T d1qkka_          23 AGFTVSSFASATEALAGLSADF--AGIVISDIRMPGMDGLALFRKILALDPDLPMILVTGHGDIPMAVQAIQDGAYDFIA  100 (140)
T ss_dssp             TTCEEEEESCHHHHHHTCCTTC--CSEEEEESCCSSSCHHHHHHHHHHHCTTSCEEEEECGGGHHHHHHHHHTTCCEEEE
T ss_pred             CCCEEEEeCChHHHHHHHhccC--cchHHHhhccCCCCHHHHHHHHHHhCCCCcEEEEECCCCHHHHHHHHHcCCCEeec
Confidence            4899999999999999998866  99999999999999999999997 56889999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHhhhh
Q 027234           80 KPVRIEELKNIWQHVVRKRKNER  102 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~~~~~~  102 (226)
                      ||++.++|...+++++..++...
T Consensus       101 KP~~~~~L~~~i~~~~~~~~~~~  123 (140)
T d1qkka_         101 KPFAADRLVQSARRAEEKRRLVM  123 (140)
T ss_dssp             SSCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999887665433

>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=99.90  E-value=1.6e-23  Score=149.63  Aligned_cols=95  Identities=19%  Similarity=0.355  Sum_probs=90.8

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEeC
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTK   80 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~K   80 (226)
                      .||+|..+.++++|++.+.+..  ||+||+|+.||+++|+++++.++..+++|||++|+..+.+...+++++||+|||.|
T Consensus        25 ~g~~v~~a~~~~~al~~l~~~~--~dlii~D~~mp~~~G~~~~~~~r~~~~~pii~lt~~~~~~~~~~a~~~Ga~dyl~K  102 (121)
T d1xhfa1          25 EGYDVFEATDGAEMHQILSEYD--INLVIMDINLPGKNGLLLARELREQANVALMFLTGRDNEVDKILGLEIGADDYITK  102 (121)
T ss_dssp             TTCEEEEESSHHHHHHHHHHSC--CSEEEECSSCSSSCHHHHHHHHHHHCCCEEEEEESCCSHHHHHHHHHHTCSEEEES
T ss_pred             CCCEEEEECChHHHHHHHHhcC--CCEEEeecccCCccCcHHHHHHHhcCCCcEEEEECCCCHHHHHHHHHcCCCEEEeC
Confidence            4899999999999999999976  99999999999999999999998888999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHH
Q 027234           81 PVRIEELKNIWQHVVRK   97 (226)
Q Consensus        81 P~~~~~L~~~l~~~~~~   97 (226)
                      ||++++|..++++++++
T Consensus       103 P~~~~~L~~~v~~~l~R  119 (121)
T d1xhfa1         103 PFNPRELTIRARNLLSR  119 (121)
T ss_dssp             SCCHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHhc
Confidence            99999999999998864

>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=99.90  E-value=2.2e-23  Score=152.18  Aligned_cols=97  Identities=26%  Similarity=0.535  Sum_probs=91.3

Q ss_pred             CcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEeC
Q 027234            2 GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTK   80 (226)
Q Consensus         2 g~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~K   80 (226)
                      ||+|..|.++++|++.+.++.  ||+||+|+.||+++|+++++.++ ..+++|||++|++.+.+...+|++.||+|||.|
T Consensus        24 g~~v~~a~~~~eAl~~l~~~~--~dlvilD~~mp~~~G~e~~~~lr~~~~~~piI~lT~~~~~~~~~~a~~~Ga~dyl~K  101 (137)
T d1ny5a1          24 GIKVESAERGKEAYKLLSEKH--FNVVLLDLLLPDVNGLEILKWIKERSPETEVIVITGHGTIKTAVEAMKMGAYDFLTK  101 (137)
T ss_dssp             TCEEEEESSHHHHHHHHHHSC--CSEEEEESBCSSSBHHHHHHHHHHHCTTSEEEEEEETTCHHHHHHHHTTTCCEEEEE
T ss_pred             CCEEEEECCHHHHHHHhhccc--cccchHHHhhhhhhHHHHHHHHHHhCCCCCEEEEECCCCHHHHHHHHHcCCCEEEeC
Confidence            899999999999999999876  99999999999999999999997 568899999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHhh
Q 027234           81 PVRIEELKNIWQHVVRKRKN  100 (226)
Q Consensus        81 P~~~~~L~~~l~~~~~~~~~  100 (226)
                      |++.++|...++++++.++.
T Consensus       102 P~~~~~L~~~i~~~l~~~~~  121 (137)
T d1ny5a1         102 PCMLEEIELTINKAIEHRKL  121 (137)
T ss_dssp             SCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHHH
Confidence            99999999999998875544

>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=99.90  E-value=2e-23  Score=149.63  Aligned_cols=94  Identities=26%  Similarity=0.513  Sum_probs=88.8

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||+|.+++++++|++.+.+..  ||+||+|++||+|||+++++.++ ..+++|+|++|++.+.+...+|++.||++||.
T Consensus        26 ~g~~v~~a~~~~~al~~~~~~~--~dlvi~D~~mp~~~G~e~~~~lr~~~~~~~iI~lt~~~~~~~~~~a~~~Ga~~yl~  103 (123)
T d1dbwa_          26 NGFAVKMHQSAEAFLAFAPDVR--NGVLVTDLRMPDMSGVELLRNLGDLKINIPSIVITGHGDVPMAVEAMKAGAVDFIE  103 (123)
T ss_dssp             TTCEEEEESCHHHHHHHGGGCC--SEEEEEECCSTTSCHHHHHHHHHHTTCCCCEEEEECTTCHHHHHHHHHTTCSEEEE
T ss_pred             CCCEEEEECCHHHHHHHHhhcC--CcEEEEeccCccccchHHHHHHHhcCCCCeEEEEEeeCCHHHHHHHHHCCCCEEEE
Confidence            4899999999999999999876  99999999999999999999998 56789999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHH
Q 027234           80 KPVRIEELKNIWQHVVR   96 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~   96 (226)
                      ||++.++|..++++++.
T Consensus       104 KP~~~~~L~~~i~~a~e  120 (123)
T d1dbwa_         104 KPFEDTVIIEAIERASE  120 (123)
T ss_dssp             SSCCHHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHHH
Confidence            99999999999998763

>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=99.90  E-value=6.6e-24  Score=152.16  Aligned_cols=96  Identities=30%  Similarity=0.520  Sum_probs=90.6

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||+|.+|.++.+|++.+.+..  ||+||+|++||++||++++++++ ..+.+|||++|+..+.+...+|++.||++||.
T Consensus        26 ~g~~v~~a~~~~~a~~~l~~~~--~dlii~D~~mp~~~G~el~~~l~~~~~~~piI~~t~~~~~~~~~~a~~~Ga~dyl~  103 (123)
T d1krwa_          26 AGLTCTTFENGNEVLAALASKT--PDVLLSDIRMPGMDGLALLKQIKQRHPMLPVIIMTAHSDLDAAVSAYQQGAFDYLP  103 (123)
T ss_dssp             TTCEEEEESSSHHHHHHHTTCC--CSEEEECCSSSSSTTHHHHHHHHHHSSSCCEEESCCCSCHHHHHHHHHHTEEEECS
T ss_pred             CCCEEEEeCCHHHHHHHHHhCC--CCEEEehhhcCCchHHHHHHHHHHhCCCCeEEEEecCCCHHHHHHHHHcCCCeEEe
Confidence            4899999999999999999876  99999999999999999999997 56889999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHH
Q 027234           80 KPVRIEELKNIWQHVVRKR   98 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~~   98 (226)
                      ||++.++|..++++++++.
T Consensus       104 KP~~~~eL~~~i~~~l~~~  122 (123)
T d1krwa_         104 KPFDIDEAVALVERAISHY  122 (123)
T ss_dssp             SCCHHHHHHHHHHHHHHHH
T ss_pred             CcCCHHHHHHHHHHHHHcc
Confidence            9999999999999988653

>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=99.89  E-value=3.3e-23  Score=148.02  Aligned_cols=94  Identities=29%  Similarity=0.478  Sum_probs=88.2

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcC---CCCcEEEEeccCCHHHHHHHHhCCcceE
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLE---MDLPVIMMCAHGSKEVVMKGVTHDACDY   77 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~---~~~pvI~ls~~~~~~~~~~a~~~ga~~y   77 (226)
                      .||+|..|.++.+|++.+.+..  ||+||+|+.||++||+++++.++..   .++|||++|+..+.+...++++.||++|
T Consensus        23 ~g~~v~~a~~~~~al~~l~~~~--~dlil~D~~mp~~~G~~l~~~lr~~~~~~~~pvi~lt~~~~~~~~~~~~~~G~~d~  100 (121)
T d1zesa1          23 NGFQPVEAEDYDSAVNQLNEPW--PDLILLDWMLPGGSGIQFIKHLKRESMTRDIPVVMLTARGEEEDRVRGLETGADDY  100 (121)
T ss_dssp             TTCEEEEECSHHHHHHHSSSSC--CSEEEECSSCTTSCHHHHHHHHHHSTTTTTSCEEEEESCCSHHHHHHHHHHTCSEE
T ss_pred             CCCEEEEECChHHHHHHHHccC--CCEEEeecCCCCCCHHHHHHHHHhCccCCCCeEEEEECCCCHHHHHHHHHCCCCEE
Confidence            4899999999999999999866  9999999999999999999999743   4699999999999999999999999999


Q ss_pred             EeCCCCHHHHHHHHHHHHH
Q 027234           78 LTKPVRIEELKNIWQHVVR   96 (226)
Q Consensus        78 l~KP~~~~~L~~~l~~~~~   96 (226)
                      +.||++.++|...++++++
T Consensus       101 l~KP~~~~~L~~~v~~~lr  119 (121)
T d1zesa1         101 ITKPFSPKELVARIKAVMR  119 (121)
T ss_dssp             EESSCCHHHHHHHHHHHHH
T ss_pred             EECCCCHHHHHHHHHHHHc
Confidence            9999999999999998875

>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=99.89  E-value=3.7e-23  Score=159.07  Aligned_cols=101  Identities=23%  Similarity=0.400  Sum_probs=93.0

Q ss_pred             CCcEEE-EECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVT-KCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~-~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||+|+ +|+|+.+|++.+....  ||+||+|++||+|||+++++.++..+.+|||++|++++.+...+|+++||+|||.
T Consensus        26 ~g~~vv~~a~~g~eal~~~~~~~--pDlvllDi~mP~~dG~e~~~~ir~~~~~pIi~lTa~~~~~~~~~al~~Ga~~yl~  103 (190)
T d1s8na_          26 EGYEIVGEAGDGQEAVELAELHK--PDLVIMDVKMPRRDGIDAASEIASKRIAPIVVLTAFSQRDLVERARDAGAMAYLV  103 (190)
T ss_dssp             TTCEEEEEESSHHHHHHHHHHHC--CSEEEEESSCSSSCHHHHHHHHHHTTCSCEEEEEEGGGHHHHHTTGGGSCEEEEE
T ss_pred             CCCEEEEEECCHHHHHHHHhcCC--CCEEEEeccccCcchHHHHHHHHhcCCCCEEEEeCCCCHHHHHHHHHcCCCEecc
Confidence            489865 8999999999999977  9999999999999999999999977889999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHhhhhh
Q 027234           80 KPVRIEELKNIWQHVVRKRKNERK  103 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~~~~~~~  103 (226)
                      ||+++++|..++..++.+.+....
T Consensus       104 KP~~~~~L~~~i~~~~~~~~~~~~  127 (190)
T d1s8na_         104 KPFSISDLIPAIELAVSRFREITA  127 (190)
T ss_dssp             ESCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHhhHhhhh
Confidence            999999999999998876655443

>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=99.89  E-value=3.3e-23  Score=148.06  Aligned_cols=95  Identities=26%  Similarity=0.470  Sum_probs=89.0

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||+|.+|.++.+|++.+.+..  ||+||+|+.||+++|++++++++ ..+.+|||++|+..+.+...++++.||++||.
T Consensus        25 ~g~~v~~a~~~~~al~~l~~~~--~dlillD~~mp~~~G~~~~~~~r~~~~~~~ii~lt~~~~~~~~~~~~~~Ga~~yl~  102 (121)
T d1mvoa_          25 SGYDVITASDGEEALKKAETEK--PDLIVLDVMLPKLDGIEVCKQLRQQKLMFPILMLTAKDEEFDKVLGLELGADDYMT  102 (121)
T ss_dssp             TTCEEEEESSHHHHHHHHHHHC--CSEEEEESSCSSSCHHHHHHHHHHTTCCCCEEEEECTTCCCCHHHHHHTTCCEEEE
T ss_pred             CCCEEEEECCHHHHHHHHhccc--ccEEEecccccCCCCchhhhhhhccCCCCEEEEEEeeCCHHHHHHHHHCCCCEEEE
Confidence            4899999999999999999877  99999999999999999999998 55678999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHH
Q 027234           80 KPVRIEELKNIWQHVVRK   97 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~   97 (226)
                      |||++++|...+++++++
T Consensus       103 KP~~~~~L~~~i~~~lrR  120 (121)
T d1mvoa_         103 KPFSPREVNARVKAILRR  120 (121)
T ss_dssp             SSCCHHHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHHHcc
Confidence            999999999999998853

>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=99.89  E-value=1.2e-22  Score=144.84  Aligned_cols=95  Identities=19%  Similarity=0.394  Sum_probs=90.7

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEeC
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTK   80 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~K   80 (226)
                      .||+|..|+++++|++.+.+..  ||+||+|+.||++||+++++.++....+|||++|+..+.+...+|+++||++||.|
T Consensus        24 ~g~~v~~a~~~~~a~~~~~~~~--~dliilD~~mp~~~g~~~~~~~~~~~~~piI~lt~~~~~~~~~~a~~~Ga~dyl~K  101 (120)
T d1zgza1          24 EGYTVSVTASGAGLREIMQNQS--VDLILLDINLPDENGLMLTRALRERSTVGIILVTGRSDRIDRIVGLEMGADDYVTK  101 (120)
T ss_dssp             TTCEEEEESSHHHHHHHHHHSC--CSEEEEESCCSSSCHHHHHHHHHTTCCCEEEEEESSCCHHHHHHHHHHTCSEEEES
T ss_pred             CCCEEEEECCHHHHHHHHHhcC--CCEEeeehhhccchhHHHHHHHhccCCCeEEEEEccCCHHHHHHHHHCCCCEEEEC
Confidence            4899999999999999999977  99999999999999999999998888899999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHH
Q 027234           81 PVRIEELKNIWQHVVRK   97 (226)
Q Consensus        81 P~~~~~L~~~l~~~~~~   97 (226)
                      |++.++|..++++++++
T Consensus       102 P~~~~~L~~~i~~~lrR  118 (120)
T d1zgza1         102 PLELRELVVRVKNLLWR  118 (120)
T ss_dssp             SCCHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHcc
Confidence            99999999999998864

>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=99.89  E-value=9.5e-23  Score=144.97  Aligned_cols=92  Identities=23%  Similarity=0.460  Sum_probs=86.2

Q ss_pred             CCcEEE-EECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEE
Q 027234            1 MGFSVT-KCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYL   78 (226)
Q Consensus         1 lg~~V~-~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl   78 (226)
                      .||+|. +|+++.+|++.+++..  ||+||+|++||++||+++++.++ ..+++|||++|++.+.+...++++.||++||
T Consensus        24 ~g~~v~~~a~~~~~al~~~~~~~--~dliilD~~mp~~~G~e~~~~ir~~~~~~pvi~ls~~~~~~~~~~a~~~Ga~~yl  101 (118)
T d1u0sy_          24 AGYEVAGEATNGREAVEKYKELK--PDIVTMDITMPEMNGIDAIKEIMKIDPNAKIIVCSAMGQQAMVIEAIKAGAKDFI  101 (118)
T ss_dssp             TTCEEEEEESSHHHHHHHHHHHC--CSEEEEECSCGGGCHHHHHHHHHHHCTTCCEEEEECTTCHHHHHHHHHTTCCEEE
T ss_pred             cCCceEEEECCHHHHHHHHHhcc--CCEEEEecCCCCCCHHHHHHHHHHhCCCCcEEEEEccCCHHHHHHHHHcCCCEEE
Confidence            489876 7899999999999877  99999999999999999999997 6688999999999999999999999999999


Q ss_pred             eCCCCHHHHHHHHHHH
Q 027234           79 TKPVRIEELKNIWQHV   94 (226)
Q Consensus        79 ~KP~~~~~L~~~l~~~   94 (226)
                      .||+++++|..+++++
T Consensus       102 ~KP~~~~~L~~~l~~v  117 (118)
T d1u0sy_         102 VKPFQPSRVVEALNKV  117 (118)
T ss_dssp             ESSCCHHHHHHHHHHH
T ss_pred             ECCCCHHHHHHHHHHh
Confidence            9999999999998875

>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=99.89  E-value=5.1e-23  Score=149.44  Aligned_cols=98  Identities=31%  Similarity=0.516  Sum_probs=91.0

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      +||+|.+|.++.+|++++....  ||+||+|+.||++||++++++|+ ..+.+|||++|+..+.+...++++.||++||.
T Consensus        31 ~g~~v~~a~~g~ea~~~~~~~~--~dlillD~~mP~~dG~el~~~ir~~~~~~pii~lt~~~~~~~~~~~~~~G~~~~l~  108 (133)
T d2ayxa1          31 LGYQCKTANDGVDALNVLSKNH--IDIVLSDVNMPNMDGYRLTQRIRQLGLTLPVIGVTANALAEEKQRCLESGMDSCLS  108 (133)
T ss_dssp             HTSEEEEECCSHHHHHHHHHSC--CSEEEEEESSCSSCCHHHHHHHHHHHCCSCEEEEESSTTSHHHHHHHHCCCEEEEE
T ss_pred             cCCEEEEECcHHHHHHHHhccC--ceEEEEeccCCCCCHHHHHHHHHHhCCCCCEEEEeccCCHHHHHHHHHcCCCEEEE
Confidence            4899999999999999999876  99999999999999999999998 45689999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHhh
Q 027234           80 KPVRIEELKNIWQHVVRKRKN  100 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~~~~  100 (226)
                      ||++.++|..++++++++.+.
T Consensus       109 KP~~~~~L~~~l~~~~~r~r~  129 (133)
T d2ayxa1         109 KPVTLDVIKQTLTLYAERVRK  129 (133)
T ss_dssp             SSCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHH
Confidence            999999999999998865543

>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=99.88  E-value=3e-22  Score=146.37  Aligned_cols=100  Identities=26%  Similarity=0.367  Sum_probs=91.7

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcC---CCCcEEEEeccCCHHHHHHHHhCCcceE
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLE---MDLPVIMMCAHGSKEVVMKGVTHDACDY   77 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~---~~~pvI~ls~~~~~~~~~~a~~~ga~~y   77 (226)
                      .||+|.+|.|+.+|++.+.+..  ||+||+|+.||+++|+++++.++..   .++|||++|++.+.+...+|++.||+||
T Consensus        24 ~g~~v~~a~~~~eal~~~~~~~--~dlil~D~~~p~~~G~~~~~~ir~~~~~~~~piI~lt~~~~~~~~~~a~~~Ga~dy  101 (139)
T d1w25a1          24 EYYEVSTAMDGPTALAMAARDL--PDIILLDVMMPGMDGFTVCRKLKDDPTTRHIPVVLITALDGRGDRIQGLESGASDF  101 (139)
T ss_dssp             TTCEEEEESSHHHHHHHHHHHC--CSEEEEESCCSSSCHHHHHHHHHHSTTTTTSCEEEEECSSCHHHHHHHHHHTCCEE
T ss_pred             CCCEEEEEccchhhhhhhhccc--ceeeeeeccccCCCchHHHHHhhhcccccCCCEEEEEcCCCHHHHHHHHHcCCCEE
Confidence            4899999999999999999977  9999999999999999999999743   4789999999999999999999999999


Q ss_pred             EeCCCCHHHHHHHHHHHHHHHhhhh
Q 027234           78 LTKPVRIEELKNIWQHVVRKRKNER  102 (226)
Q Consensus        78 l~KP~~~~~L~~~l~~~~~~~~~~~  102 (226)
                      |.||++.++|...++.+++.+....
T Consensus       102 l~KP~~~~~L~~~i~~~lr~~~~~~  126 (139)
T d1w25a1         102 LTKPIDDVMLFARVRSLTRFKLVID  126 (139)
T ss_dssp             EESSCCHHHHHHHHHHHHHHHHHHH
T ss_pred             EECCCCHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999998887655433

>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=99.88  E-value=9.4e-23  Score=146.08  Aligned_cols=94  Identities=18%  Similarity=0.392  Sum_probs=82.3

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcC---CCCcEEEEeccCCHHHHHHHHhCCcceE
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLE---MDLPVIMMCAHGSKEVVMKGVTHDACDY   77 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~---~~~pvI~ls~~~~~~~~~~a~~~ga~~y   77 (226)
                      +||+|.+|.++.+|++.+.+..  ||+||+|++||+|||+++++.|+..   ..+|+|++|+....+...++++.|+++|
T Consensus        24 ~g~~v~~a~~~~~al~~~~~~~--~dlil~D~~mp~~dG~el~~~ir~~~~~~~iPii~lt~~~~~~~~~~~~~~G~~~~  101 (123)
T d1mb3a_          24 QGYETLQTREGLSALSIARENK--PDLILMDIQLPEISGLEVTKWLKEDDDLAHIPVVAVTAFAMKGDEERIREGGCEAY  101 (123)
T ss_dssp             TTCEEEEESCHHHHHHHHHHHC--CSEEEEESBCSSSBHHHHHHHHHHSTTTTTSCEEEEC------CHHHHHHHTCSEE
T ss_pred             CCCEEEEECCHHHHHHHHHhCC--CCEEEEEeccCCCcHHHHHHHHHhCCCcCCCCeEEEEEecCHHHHHHHHHcCCCEE
Confidence            5899999999999999999877  9999999999999999999999844   4689999999999999999999999999


Q ss_pred             EeCCCCHHHHHHHHHHHHH
Q 027234           78 LTKPVRIEELKNIWQHVVR   96 (226)
Q Consensus        78 l~KP~~~~~L~~~l~~~~~   96 (226)
                      |.||++.++|...++++++
T Consensus       102 l~KP~~~~~L~~~i~~~l~  120 (123)
T d1mb3a_         102 ISKPISVVHFLETIKRLLE  120 (123)
T ss_dssp             ECSSCCHHHHHHHHHHHHS
T ss_pred             EECCCCHHHHHHHHHHHHh
Confidence            9999999999999999874

>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=99.87  E-value=1.6e-22  Score=145.90  Aligned_cols=98  Identities=22%  Similarity=0.444  Sum_probs=90.6

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||+|.++.++++|++.+.+..  ||+||+|+.||+++|+++++.++ ..+.+|||++|++.+.+...++++.||++||.
T Consensus        25 ~g~~v~~a~~~~~al~~~~~~~--~dliilD~~mp~~~G~~~~~~i~~~~~~~~ii~lt~~~~~~~~~~a~~~Ga~dyl~  102 (128)
T d1yioa2          25 AGFEVETFDCASTFLEHRRPEQ--HGCLVLDMRMPGMSGIELQEQLTAISDGIPIVFITAHGDIPMTVRAMKAGAIEFLP  102 (128)
T ss_dssp             TTCEEEEESSHHHHHHHCCTTS--CEEEEEESCCSSSCHHHHHHHHHHTTCCCCEEEEESCTTSCCCHHHHHTTEEEEEE
T ss_pred             cCCCccccccHHHHHHHHHhcC--CCEeehhhhcccchhHHHHHHHHhhCCCCeEEEEEEECCHHHHHHHHHCCCCEEEE
Confidence            4899999999999999998866  99999999999999999999998 45779999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHHHhh
Q 027234           80 KPVRIEELKNIWQHVVRKRKN  100 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~~~~  100 (226)
                      ||++.++|...++++++....
T Consensus       103 KP~~~~~L~~~i~~~l~~~~~  123 (128)
T d1yioa2         103 KPFEEQALLDAIEQGLQLNAE  123 (128)
T ss_dssp             SSCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHHHH
Confidence            999999999999999875544

>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=99.87  E-value=4.1e-22  Score=143.86  Aligned_cols=94  Identities=32%  Similarity=0.539  Sum_probs=87.2

Q ss_pred             CCcE-EEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcC---CCCcEEEEeccCCHHHHHHHHhCCcce
Q 027234            1 MGFS-VTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLE---MDLPVIMMCAHGSKEVVMKGVTHDACD   76 (226)
Q Consensus         1 lg~~-V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~---~~~pvI~ls~~~~~~~~~~a~~~ga~~   76 (226)
                      +||. |..++++++|++.+.+..  ||+||+|++||++||+++++.++..   ..+|+|++|+..+.+...++++.|+++
T Consensus        29 ~g~~~v~~a~~~~~al~~l~~~~--~dlii~D~~mP~~~G~el~~~lr~~~~~~~~pii~lt~~~~~~~~~~a~~~G~~~  106 (129)
T d1p6qa_          29 LGFKQITAAGDGEQGMKIMAQNP--HHLVISDFNMPKMDGLGLLQAVRANPATKKAAFIILTAQGDRALVQKAAALGANN  106 (129)
T ss_dssp             TTCSCEECCSSHHHHHHHHHTSC--CSEEEECSSSCSSCHHHHHHHHTTCTTSTTCEEEECCSCCCHHHHHHHHHHTCSC
T ss_pred             CCCeEEEEECCHHHHHHHHHhCC--CCeEEeeeecCCCChHHHHHHHHhCcccCCCeEEEEEecCCHHHHHHHHHCCCCE
Confidence            5884 788999999999999876  9999999999999999999999853   468999999999999999999999999


Q ss_pred             EEeCCCCHHHHHHHHHHHHH
Q 027234           77 YLTKPVRIEELKNIWQHVVR   96 (226)
Q Consensus        77 yl~KP~~~~~L~~~l~~~~~   96 (226)
                      ||.||++.++|..++++++.
T Consensus       107 ~l~KP~~~~~L~~~i~~vl~  126 (129)
T d1p6qa_         107 VLAKPFTIEKMKAAIEAVFG  126 (129)
T ss_dssp             EECCCSSHHHHHHHHHHHHH
T ss_pred             EEECCCCHHHHHHHHHHHHH
Confidence            99999999999999999875

>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=99.87  E-value=4.9e-22  Score=141.66  Aligned_cols=92  Identities=26%  Similarity=0.415  Sum_probs=83.2

Q ss_pred             CcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEeC
Q 027234            2 GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTK   80 (226)
Q Consensus         2 g~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~K   80 (226)
                      || |.++.++.+|++  ...  .||+||+|+.||++||+++++.++ ..+.+|||++|+.++.+...+|++.||+|||.|
T Consensus        26 g~-v~~~~~~~~al~--~~~--~~dlillD~~mP~~~G~~~~~~lr~~~~~~~ii~it~~~~~~~~~~a~~~Ga~dyl~K  100 (120)
T d1p2fa2          26 GR-VKTFLTGEDFLN--DEE--AFHVVVLDVMLPDYSGYEICRMIKETRPETWVILLTLLSDDESVLKGFEAGADDYVTK  100 (120)
T ss_dssp             EE-EEEESSHHHHHH--CCS--CCSEEEEESBCSSSBHHHHHHHHHHHCTTSEEEEEESCCSHHHHHHHHHHTCSEEEES
T ss_pred             CE-EEEECCHHHHHh--cCC--CCCEEEEeCcccccchhHHHHHHhhcCCCCcEEEEecCCCHHHHHHHHHCCCCEEEEC
Confidence            54 888999999986  233  399999999999999999999998 568899999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHH
Q 027234           81 PVRIEELKNIWQHVVRKR   98 (226)
Q Consensus        81 P~~~~~L~~~l~~~~~~~   98 (226)
                      |+++++|...++++++++
T Consensus       101 P~~~~~L~~~i~~~l~r~  118 (120)
T d1p2fa2         101 PFNPEILLARVKRFLERE  118 (120)
T ss_dssp             SCCHHHHHHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHHHHc
Confidence            999999999999998654

>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=99.87  E-value=7.3e-22  Score=142.27  Aligned_cols=96  Identities=19%  Similarity=0.413  Sum_probs=85.3

Q ss_pred             CCcE-EEEECCHHHHHHHHHh---CCCCceEEEEccCCCCCCHHHHHHHHhc--CCCCcEEEEeccCCHHHHHHHHhCCc
Q 027234            1 MGFS-VTKCNRAEIALDMLRT---NKNGYDIVISDVHMPDMDGFKLLELVGL--EMDLPVIMMCAHGSKEVVMKGVTHDA   74 (226)
Q Consensus         1 lg~~-V~~~~~~~eal~~l~~---~~~~~DlVl~D~~mp~~dG~~l~~~l~~--~~~~pvI~ls~~~~~~~~~~a~~~ga   74 (226)
                      +||. |..|.||++|++.+++   ...+||+||+|++||++||+++++.+++  ...+|||++|++.+.+...++++.||
T Consensus        24 ~g~~~v~~a~~g~eAl~~l~~~~~~~~~~dlillD~~mP~~dG~el~~~ir~~~~~~~piI~lT~~~~~~~~~~~~~~G~  103 (128)
T d2r25b1          24 EGIENIELACDGQEAFDKVKELTSKGENYNMIFMDVQMPKVDGLLSTKMIRRDLGYTSPIVALTAFADDSNIKECLESGM  103 (128)
T ss_dssp             TTCCCEEEESSHHHHHHHHHHHHHHTCCCSEEEECSCCSSSCHHHHHHHHHHHSCCCSCEEEEESCCSHHHHHHHHHTTC
T ss_pred             cCCeEEEEEcChHHHHHHHHhhhhccCCCCEEEEEeCCCCCCHHHHHHHHHHccCCCCeEEEEECCCCHHHHHHHHHcCC
Confidence            4785 7889999999999864   1244999999999999999999999973  35689999999999999999999999


Q ss_pred             ceEEeCCCCHHHHHHHHHHHHH
Q 027234           75 CDYLTKPVRIEELKNIWQHVVR   96 (226)
Q Consensus        75 ~~yl~KP~~~~~L~~~l~~~~~   96 (226)
                      ++||.||++.++|..++++++.
T Consensus       104 ~~~l~KP~~~~~L~~~l~~~~~  125 (128)
T d2r25b1         104 NGFLSKPIKRPKLKTILTEFCA  125 (128)
T ss_dssp             SEEEESSCCHHHHHHHHHHHCT
T ss_pred             CEEEECCCCHHHHHHHHHHHHH
Confidence            9999999999999999998754

>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=99.87  E-value=1.3e-21  Score=143.04  Aligned_cols=96  Identities=18%  Similarity=0.313  Sum_probs=86.5

Q ss_pred             CcEEEEECCHHHHHHHHHhC-----CCCceEEEEccCCCCCCHHHHHHHHhcCC---CCcEEEEeccCCHHHHHHHHhCC
Q 027234            2 GFSVTKCNRAEIALDMLRTN-----KNGYDIVISDVHMPDMDGFKLLELVGLEM---DLPVIMMCAHGSKEVVMKGVTHD   73 (226)
Q Consensus         2 g~~V~~~~~~~eal~~l~~~-----~~~~DlVl~D~~mp~~dG~~l~~~l~~~~---~~pvI~ls~~~~~~~~~~a~~~g   73 (226)
                      +|+|..+.||.+|++++.+.     ...||+||+|++||+|||++++++|+..+   ++|||++|+..+.+...+|+++|
T Consensus        28 ~~~v~~a~~g~eAl~~l~~~~~~~~~~~pdlillD~~mP~~dG~el~~~ir~~~~~~~iPvI~ls~~~~~~~~~~a~~~G  107 (140)
T d1k68a_          28 PHEVVTVRDGMEAMAYLRQEGEYANASRPDLILLDLNLPKKDGREVLAEIKSDPTLKRIPVVVLSTSINEDDIFHSYDLH  107 (140)
T ss_dssp             CCEEEEECSHHHHHHHHTTCGGGGSCCCCSEEEECSSCSSSCHHHHHHHHHHSTTGGGSCEEEEESCCCHHHHHHHHHTT
T ss_pred             CeEEEEECCHHHHHHHHHHhHHhhccCCCCEEEEeeccccccChHHHHHHHhCcccCCCcEEEEeCCCCHHHHHHHHHCC
Confidence            57999999999999999652     23489999999999999999999998543   68999999999999999999999


Q ss_pred             cceEEeCCCCHHHHHHHHHHHHHH
Q 027234           74 ACDYLTKPVRIEELKNIWQHVVRK   97 (226)
Q Consensus        74 a~~yl~KP~~~~~L~~~l~~~~~~   97 (226)
                      |++||.||++.++|...++.+.+.
T Consensus       108 a~~yl~KP~~~~~L~~~i~~i~~~  131 (140)
T d1k68a_         108 VNCYITKSANLSQLFQIVKGIEEF  131 (140)
T ss_dssp             CSEEEECCSSHHHHHHHHHHHHHH
T ss_pred             CCEEEECCCCHHHHHHHHHHHHHH
Confidence            999999999999999999987653

>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=99.86  E-value=1.4e-21  Score=143.54  Aligned_cols=96  Identities=17%  Similarity=0.292  Sum_probs=86.5

Q ss_pred             CcEEEEECCHHHHHHHHHhC-----CCCceEEEEccCCCCCCHHHHHHHHhcC---CCCcEEEEeccCCHHHHHHHHhCC
Q 027234            2 GFSVTKCNRAEIALDMLRTN-----KNGYDIVISDVHMPDMDGFKLLELVGLE---MDLPVIMMCAHGSKEVVMKGVTHD   73 (226)
Q Consensus         2 g~~V~~~~~~~eal~~l~~~-----~~~~DlVl~D~~mp~~dG~~l~~~l~~~---~~~pvI~ls~~~~~~~~~~a~~~g   73 (226)
                      +|+|.++.|+.+|++++++.     ...||+||+|++||+|||+++++.|+..   ..+|||++|+..+.+...+|+++|
T Consensus        29 ~~~v~~a~~g~~Al~~l~~~~~~~~~~~pdlIllD~~mP~~~G~el~~~ir~~~~~~~iPvi~lT~~~~~~~~~~a~~~G  108 (144)
T d1i3ca_          29 DHELIILRDGLAAMAFLQQQGEYENSPRPNLILLDLNLPKKDGREVLAEIKQNPDLKRIPVVVLTTSHNEDDVIASYELH  108 (144)
T ss_dssp             CEEEEEECSHHHHHHHHTTCGGGTTCCCCSEEEECSCCSSSCHHHHHHHHHHCTTTTTSCEEEEESCCCHHHHHHHHHTT
T ss_pred             CeEEEEECCHHHHHHHHHhchhhhccCCCCEEEEECccccccchHHHHHHHhCcccCCCeEEEEECCCCHHHHHHHHHCC
Confidence            57899999999999999753     1249999999999999999999999854   468999999999999999999999


Q ss_pred             cceEEeCCCCHHHHHHHHHHHHHH
Q 027234           74 ACDYLTKPVRIEELKNIWQHVVRK   97 (226)
Q Consensus        74 a~~yl~KP~~~~~L~~~l~~~~~~   97 (226)
                      |++||.||++.++|...++++.+.
T Consensus       109 a~~yl~KP~~~~~L~~~i~~l~~~  132 (144)
T d1i3ca_         109 VNCYLTKSRNLKDLFKMVQGIESF  132 (144)
T ss_dssp             CSEEEECCSSHHHHHHHHHHHHHH
T ss_pred             CCEEEECCCCHHHHHHHHHHHHHH
Confidence            999999999999999999887654

>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=99.86  E-value=1.1e-21  Score=143.24  Aligned_cols=95  Identities=18%  Similarity=0.333  Sum_probs=88.5

Q ss_pred             cEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEeCC
Q 027234            3 FSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTKP   81 (226)
Q Consensus         3 ~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~KP   81 (226)
                      +.|.+++++.+|++.+++..  ||+||+|+.||++||+++++.++ ..+.+|+|++|+..+.+...++++.||++||.||
T Consensus        29 ~~v~~a~~~~~al~~~~~~~--~DlvllD~~mP~~~G~el~~~ir~~~~~~~vivlt~~~~~~~~~~a~~~Ga~~yl~Kp  106 (138)
T d1a04a2          29 TVVGEASNGEQGIELAESLD--PDLILLDLNMPGMNGLETLDKLREKSLSGRIVVFSVSNHEEDVVTALKRGADGYLLKD  106 (138)
T ss_dssp             EEEEEESSHHHHHHHHHHHC--CSEEEEETTSTTSCHHHHHHHHHHSCCCSEEEEEECCCCHHHHHHHHHTTCSEEEETT
T ss_pred             EEEEEECCHHHHHHHHHhcC--CCEEEEecCCCCCCHHHHHHHHHhhCCCCCEEEEEEECCHHHHHHHHHcCCCEEEECC
Confidence            45778999999999999877  99999999999999999999998 5678999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHHHh
Q 027234           82 VRIEELKNIWQHVVRKRK   99 (226)
Q Consensus        82 ~~~~~L~~~l~~~~~~~~   99 (226)
                      +++++|..++++++++..
T Consensus       107 ~~~~~L~~~i~~v~~g~~  124 (138)
T d1a04a2         107 MEPEDLLKALHQAAAGEM  124 (138)
T ss_dssp             CCHHHHHHHHHHHHHSCC
T ss_pred             CCHHHHHHHHHHHHCCCC
Confidence            999999999999987544

>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=99.86  E-value=2.7e-21  Score=142.84  Aligned_cols=96  Identities=21%  Similarity=0.441  Sum_probs=87.1

Q ss_pred             Cc--EEEEECCHHHHHHHHHhCC--------CCceEEEEccCCCCCCHHHHHHHHhcCC---CCcEEEEeccCCHHHHHH
Q 027234            2 GF--SVTKCNRAEIALDMLRTNK--------NGYDIVISDVHMPDMDGFKLLELVGLEM---DLPVIMMCAHGSKEVVMK   68 (226)
Q Consensus         2 g~--~V~~~~~~~eal~~l~~~~--------~~~DlVl~D~~mp~~dG~~l~~~l~~~~---~~pvI~ls~~~~~~~~~~   68 (226)
                      ||  +|..|.||.+|++++++..        ..||+||+|++||+|||++++++|++.+   ++|||++|+..+.+...+
T Consensus        30 g~~~~v~~a~~g~eAl~~l~~~~~~~~~~~~~~pdlillD~~mP~~~G~el~~~ir~~~~~~~ipiI~lT~~~~~~~~~~  109 (149)
T d1k66a_          30 GVVNPIYRCITGDQALDFLYQTGSYCNPDIAPRPAVILLDLNLPGTDGREVLQEIKQDEVLKKIPVVIMTTSSNPKDIEI  109 (149)
T ss_dssp             TBCSCEEEECSHHHHHHHHHTCCSSSCGGGCCCCSEEEECSCCSSSCHHHHHHHHTTSTTGGGSCEEEEESCCCHHHHHH
T ss_pred             CCceEEEEECChHHHHHHHHhhccccccccccCCCeEEccccccCCCcHHHHHHHHhccccCCCeEEEEeCCCCHHHHHH
Confidence            55  7899999999999997531        2499999999999999999999998553   689999999999999999


Q ss_pred             HHhCCcceEEeCCCCHHHHHHHHHHHHHH
Q 027234           69 GVTHDACDYLTKPVRIEELKNIWQHVVRK   97 (226)
Q Consensus        69 a~~~ga~~yl~KP~~~~~L~~~l~~~~~~   97 (226)
                      +++.||++||.||++.++|...++++++.
T Consensus       110 ~~~~Ga~~~l~KP~~~~~L~~~i~~~l~~  138 (149)
T d1k66a_         110 CYSYSISSYIVKPLEIDRLTETVQTFIKY  138 (149)
T ss_dssp             HHHTTCSEEEECCSSHHHHHHHHHHHHHH
T ss_pred             HHHCCCCEEEECCCCHHHHHHHHHHHHHH
Confidence            99999999999999999999999999864

>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=99.85  E-value=1.5e-21  Score=139.76  Aligned_cols=91  Identities=29%  Similarity=0.455  Sum_probs=83.0

Q ss_pred             EEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcC-C-CCcEEEEeccCCHHHHHHHHhCCcceEEeCC
Q 027234            4 SVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLE-M-DLPVIMMCAHGSKEVVMKGVTHDACDYLTKP   81 (226)
Q Consensus         4 ~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~-~-~~pvI~ls~~~~~~~~~~a~~~ga~~yl~KP   81 (226)
                      .|.+|.||.+|++.+++..  ||+||+|+.||+|||+++++.+++. + .+|||++|++.+.+...++++.||++||.||
T Consensus        29 ~v~~a~~g~~al~~~~~~~--~dlillD~~mP~~dG~e~~~~ir~~~~~~~~ii~~t~~~~~~~~~~a~~~Ga~~~l~KP  106 (123)
T d1dz3a_          29 VIGTAYNGQDCLQMLEEKR--PDILLLDIIMPHLDGLAVLERIRAGFEHQPNVIMLTAFGQEDVTKKAVELGASYFILKP  106 (123)
T ss_dssp             EEEEESSHHHHHHHHHHHC--CSEEEEESCCSSSCHHHHHHHHHHHCSSCCEEEEEEETTCHHHHHHHHHTTCEEEEECS
T ss_pred             EEEEECCHHHHHHHHHhcC--CCEEEEcCCCCCCCHHHHHHHHHhcCCCCCeEEEEECcCCHHHHHHHHHCCCCEEEECC
Confidence            3568999999999999877  9999999999999999999999843 3 3579999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHH
Q 027234           82 VRIEELKNIWQHVVR   96 (226)
Q Consensus        82 ~~~~~L~~~l~~~~~   96 (226)
                      ++.++|...++++++
T Consensus       107 ~~~~~L~~~i~~v~~  121 (123)
T d1dz3a_         107 FDMENLAHHIRQVYG  121 (123)
T ss_dssp             SCCTTHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHc
Confidence            999999999998875

>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=99.85  E-value=8.7e-21  Score=140.66  Aligned_cols=96  Identities=18%  Similarity=0.305  Sum_probs=84.8

Q ss_pred             CcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcC---CCCcEEEEeccCCHHHHHHHHhCCcceEE
Q 027234            2 GFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLE---MDLPVIMMCAHGSKEVVMKGVTHDACDYL   78 (226)
Q Consensus         2 g~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~---~~~pvI~ls~~~~~~~~~~a~~~ga~~yl   78 (226)
                      ||.|.  .++.+++.++....  ||+||+|++||+|||+++++.||..   +++|||++|+..+.+...+|++.||+|||
T Consensus        37 g~~v~--~~~~~~~~~~~~~~--~DlillD~~mP~~dG~el~~~ir~~~~~~~iPiI~lt~~~~~~~~~~a~~~Ga~d~l  112 (153)
T d1w25a2          37 HRPVI--ESDPEKAKISAGGP--VDLVIVNAAAKNFDGLRFTAALRSEERTRQLPVLAMVDPDDRGRMVKALEIGVNDIL  112 (153)
T ss_dssp             SEEEE--ECCHHHHHHHHHSS--CSEEEEETTCSSSCHHHHHHHHHTSGGGTTCCEEEEECTTCHHHHHHHHHTTCCEEE
T ss_pred             CCEEE--EccHHHHHHHhcCC--CCEEEEECccccccchHHHHHHHhccccccceeEEeecCCCHHHHHHHHhcCcceEE
Confidence            67764  35678888888766  9999999999999999999999743   57999999999999999999999999999


Q ss_pred             eCCCCHHHHHHHHHHHHHHHhhh
Q 027234           79 TKPVRIEELKNIWQHVVRKRKNE  101 (226)
Q Consensus        79 ~KP~~~~~L~~~l~~~~~~~~~~  101 (226)
                      .|||++++|...++.+++.++..
T Consensus       113 ~KP~~~~~L~~~i~~~l~~~~~~  135 (153)
T d1w25a2         113 SRPIDPQELSARVKTQIQRKRYT  135 (153)
T ss_dssp             ESSCCHHHHHHHHHHHHHHHHHH
T ss_pred             ECCCCHHHHHHHHHHHHHHHHHH
Confidence            99999999999999998765543

>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=99.84  E-value=3.8e-21  Score=139.55  Aligned_cols=93  Identities=17%  Similarity=0.337  Sum_probs=84.2

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhc------CCCCcEEEEeccCCHHHHHHHHhCCc
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGL------EMDLPVIMMCAHGSKEVVMKGVTHDA   74 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~------~~~~pvI~ls~~~~~~~~~~a~~~ga   74 (226)
                      +||+|.+|.|+.+|++.+++ .  ||+||+|++||+|||+++++.|++      ...+|||++|++.+.+...++++.|+
T Consensus        30 ~G~~v~~a~~g~eal~~l~~-~--~dlillD~~mP~~dG~el~~~ir~~~~~~~~~~~~ii~lT~~~~~~~~~~~~~~G~  106 (134)
T d1dcfa_          30 LGCEVTTVSSNEECLRVVSH-E--HKVVFMDVCMPGVENYQIALRIHEKFTKQRHQRPLLVALSGNTDKSTKEKCMSFGL  106 (134)
T ss_dssp             TTCEEEEESSHHHHHHHCCT-T--CSEEEEECCSSTTTTTHHHHHHHHHHC-CCSCCCEEEEEESCCSHHHHHHHHHTTC
T ss_pred             CCCEEEEECCHHHHHHHhhc-C--CCeEEEEeccCCCchHHHHHHHHHhcccccCCCCeEEEEeCCCCHHHHHHHHHcCC
Confidence            59999999999999998753 3  999999999999999999999962      13478999999999999999999999


Q ss_pred             ceEEeCCCCHHHHHHHHHHHHH
Q 027234           75 CDYLTKPVRIEELKNIWQHVVR   96 (226)
Q Consensus        75 ~~yl~KP~~~~~L~~~l~~~~~   96 (226)
                      ++||.||++.++|..+++++++
T Consensus       107 ~~~l~KP~~~~~L~~~l~~~l~  128 (134)
T d1dcfa_         107 DGVLLKPVSLDNIRDVLSDLLE  128 (134)
T ss_dssp             CEEEESSCCHHHHHHHHHHHHS
T ss_pred             CEEEECCCCHHHHHHHHHHHhh
Confidence            9999999999999999999874

>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=99.79  E-value=9.6e-20  Score=129.14  Aligned_cols=89  Identities=21%  Similarity=0.344  Sum_probs=75.2

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      .||+|.++.++.+|++.+.+. ..||+||+|+.||+++|+++++.++ ..+.+|||++|+..+.  ..++...|+ |||.
T Consensus        25 ~g~~v~~~~~~~~al~~l~~~-~~~dliilD~~lp~~~G~el~~~ir~~~~~~pii~lt~~~~~--~~~~~~~~~-dyl~  100 (118)
T d2b4aa1          25 LGAEVTVHPSGSAFFQHRSQL-STCDLLIVSDQLVDLSIFSLLDIVKEQTKQPSVLILTTGRHE--LIESSEHNL-SYLQ  100 (118)
T ss_dssp             TTCEEEEESSHHHHHHTGGGG-GSCSEEEEETTCTTSCHHHHHHHHTTSSSCCEEEEEESCC----CCCCSSSCE-EEEE
T ss_pred             cCCCeEEECCHHHHHHHHHhc-CCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCcEEEEECCccH--HHHHhhcCC-CEEE
Confidence            589999999999999877543 2399999999999999999999998 4468999999987653  445677777 8999


Q ss_pred             CCCCHHHHHHHHHH
Q 027234           80 KPVRIEELKNIWQH   93 (226)
Q Consensus        80 KP~~~~~L~~~l~~   93 (226)
                      |||++++|..++++
T Consensus       101 KP~~~~eL~~~i~~  114 (118)
T d2b4aa1         101 KPFAISELRAAIDY  114 (118)
T ss_dssp             SSCCHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHH
Confidence            99999999998875

>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=99.76  E-value=4.9e-19  Score=135.40  Aligned_cols=97  Identities=15%  Similarity=0.176  Sum_probs=86.3

Q ss_pred             CCcEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEeC
Q 027234            1 MGFSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTK   80 (226)
Q Consensus         1 lg~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~K   80 (226)
                      +||+|..|.++.+|++    ..  ||+||+|++||+++|..+.+..+..+.+|||++|++.+.+...+|++.||++||.|
T Consensus        34 ~G~~v~~~~~~~~al~----~~--~Dlvl~D~~mp~~~~~~~~~~~~~~p~~pvI~lta~~~~~~~~~al~~Ga~~yL~K  107 (189)
T d1qo0d_          34 IGCSVRQCWPPPEAFD----VP--VDVVFTSIFQNRHHDEIAALLAAGTPRTTLVALVEYESPAVLSQIIELECHGVITQ  107 (189)
T ss_dssp             HTCEEEEECSCCSSCS----SC--CSEEEEECCSSTHHHHHHHHHHHSCTTCEEEEEECCCSHHHHHHHHHHTCSEEEES
T ss_pred             cCCcceecCCHHHhcc----CC--CCEEEEcCCCCCcHHHHHHHHHHcCCCCCEEEEeccchHHHHHHHHHcCCcEEEEe
Confidence            4899999999999883    34  99999999999999988887777889999999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHHHhhhhh
Q 027234           81 PVRIEELKNIWQHVVRKRKNERK  103 (226)
Q Consensus        81 P~~~~~L~~~l~~~~~~~~~~~~  103 (226)
                      |++.++|...++.+.........
T Consensus       108 P~~~~~L~~~i~~~~~~~~~~~~  130 (189)
T d1qo0d_         108 PLDAHRVLPVLVSARRISEEMAK  130 (189)
T ss_dssp             SCCGGGHHHHHHHHHHHHHHHHH
T ss_pred             cchhhHHHHHHhhcccccccccc
Confidence            99999999999988765554433

>d1irza_ a.4.1.11 (A:) Arr10-B {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: GARP response regulators
domain: Arr10-B
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.75  E-value=9.2e-19  Score=108.25  Aligned_cols=60  Identities=60%  Similarity=0.983  Sum_probs=58.2

Q ss_pred             cCCceeeeHhhHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcc
Q 027234          150 KKPRLVWSVELHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRL  209 (226)
Q Consensus       150 ~~~~~~~~~~l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~  209 (226)
                      +++++.||.++|.+|+.+++++|.+.+.|+.|++.|+++++|+++|+|||||||.++.|+
T Consensus         4 kk~R~~WT~elH~~Fv~Av~~lG~~~atpk~I~~~m~v~~lT~~qV~SHlQKYrl~l~k~   63 (64)
T d1irza_           4 KKPRVLWTHELHNKFLAAVDHLGVERAVPKKILDLMNVDKLTRENVASHLQKFRVALKKV   63 (64)
T ss_dssp             CCSSCSSCHHHHHHHHHHHHHHCTTTCCHHHHHHHHCCTTCCHHHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhCccccchHHHHHHcCCCCCCHHHHHHHHHHHHHHHHhc
Confidence            678999999999999999999999999999999999999999999999999999999886

>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=99.75  E-value=5.6e-18  Score=123.51  Aligned_cols=79  Identities=28%  Similarity=0.384  Sum_probs=66.0

Q ss_pred             cEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcCC-CCcEEEEeccCC-HHHHHHHHhCCcceEEeC
Q 027234            3 FSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEM-DLPVIMMCAHGS-KEVVMKGVTHDACDYLTK   80 (226)
Q Consensus         3 ~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~~-~~pvI~ls~~~~-~~~~~~a~~~ga~~yl~K   80 (226)
                      +.|.+|.||.+|++.+++..  ||+||+|++||+|||+++++.+++.. ..+|++++.... .+...+|++.||++||.|
T Consensus        30 ~~v~~a~~g~~al~~~~~~~--pDlvllDi~MP~~dG~e~~~~ir~~~~~~~i~i~~~~~~~~~~~~~al~~Ga~~yl~K  107 (140)
T d1a2oa1          30 EMVATAPDPLVARDLIKKFN--PDVLTLDVEMPRMDGLDFLEKLMRLRPMPVVMVSSLTGKGSEVTLRALELGAIDFVTK  107 (140)
T ss_dssp             EEEEEESSHHHHHHHHHHHC--CSEEEEECCCSSSCHHHHHHHHHHSSCCCEEEEECCTHHHHHHHHHHHHHTCCEEEEC
T ss_pred             EEEEEECCHHHHHHHHHhcC--CCEEEEcCCCCCCCHHHHHHHHHHhCCCCcEEEEEecCCChHHHHHHHHcCCCEEEEC
Confidence            56788999999999999877  99999999999999999999998544 455555555432 356788999999999999


Q ss_pred             CCC
Q 027234           81 PVR   83 (226)
Q Consensus        81 P~~   83 (226)
                      |+.
T Consensus       108 P~~  110 (140)
T d1a2oa1         108 PQL  110 (140)
T ss_dssp             SSS
T ss_pred             CCC
Confidence            964

>d1bl0a1 a.4.1.8 (A:9-62) MarA {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: AraC type transcriptional activator
domain: MarA
species: Escherichia coli [TaxId: 562]

Probab=97.08  E-value=7.8e-05  Score=43.45  Aligned_cols=40  Identities=15%  Similarity=0.117  Sum_probs=32.2

Q ss_pred             HHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC-CCCCCCCC
Q 027234          180 KILELMNIPGLTRENVASHLQKHRLYLSRLSGV-SPQQGNSF  220 (226)
Q Consensus       180 ~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~-~~~~~~~~  220 (226)
                      .|.+++.. .+|++++|..+++|+++|+|+|+. .++.+..|
T Consensus        11 yI~~~~~~-~~tl~~lA~~~~~s~~~l~r~Fk~~~g~tp~~Y   51 (54)
T d1bl0a1          11 WIEDNLES-PLSLEKVSERSGYSKWHLQRMFKKETGHSLGQY   51 (54)
T ss_dssp             HHHTTTTS-CCCCHHHHHHSSSCHHHHHHHHHHHHSSCHHHH
T ss_pred             HHHhccCC-CCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHHH
Confidence            69999976 899999999999999999997753 34444443

>d1d5ya1 a.4.1.8 (A:3-56) Rob transcription factor, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: AraC type transcriptional activator
domain: Rob transcription factor, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=97.03  E-value=8.5e-05  Score=43.30  Aligned_cols=31  Identities=19%  Similarity=0.171  Sum_probs=28.5

Q ss_pred             HHHHhhCCCCCCHHHHHHHhhhhhhhhhcccC
Q 027234          180 KILELMNIPGLTRENVASHLQKHRLYLSRLSG  211 (226)
Q Consensus       180 ~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~  211 (226)
                      .|.+|+.. .+|++++|+++++|+.+|+|+|+
T Consensus        11 yi~~~~~~-~itl~~lA~~~~~S~~~l~r~Fk   41 (54)
T d1d5ya1          11 WLEGHLDQ-PLSLDNVAAKAGYSKWHLQRMFK   41 (54)
T ss_dssp             HHHTTSSS-SCCCHHHHTTTSSCHHHHHHHHH
T ss_pred             HHHHccCC-CCCHHHHHHHHCcCHHHHHHHHH
Confidence            68899988 59999999999999999999775

>d1gdta1 a.4.1.2 (A:141-183) gamma,delta resolvase (C-terminal domain) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: gamma,delta resolvase (C-terminal domain)
species: Escherichia coli [TaxId: 562]

Probab=95.47  E-value=0.0026  Score=34.45  Aligned_cols=33  Identities=15%  Similarity=0.292  Sum_probs=27.1

Q ss_pred             HHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCCC
Q 027234          180 KILELMNIPGLTRENVASHLQKHRLYLSRLSGVS  213 (226)
Q Consensus       180 ~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~~  213 (226)
                      .|.++.. .++....||.+|+++|...||+.+-+
T Consensus        10 ~V~~L~~-~G~gat~IAk~lgI~R~SVYR~L~~~   42 (43)
T d1gdta1          10 AVLNMWQ-QGLGASHISKTMNIARSTVYKVINES   42 (43)
T ss_dssp             HHHHHHH-TTCCHHHHHHHHTCCHHHHHHHHHSC
T ss_pred             HHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHhhc
Confidence            4666654 59999999999999999999976543

>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: HIN recombinase (DNA-binding domain)
species: Synthetic

Probab=95.25  E-value=0.0047  Score=34.43  Aligned_cols=32  Identities=25%  Similarity=0.171  Sum_probs=25.9

Q ss_pred             HHHhhCCCCCCHHHHHHHhhhhhhhhhcccCCC
Q 027234          181 ILELMNIPGLTRENVASHLQKHRLYLSRLSGVS  213 (226)
Q Consensus       181 I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~~  213 (226)
                      +.+++.. |.++.+||.++++||..+||-|..+
T Consensus        14 a~~l~~~-G~s~~~iA~~~gVSr~TiYry~pa~   45 (47)
T d1ijwc_          14 ISRLLEK-GHPRQQLAIIFGIGVSTLYRYFPAS   45 (47)
T ss_dssp             HHHHHHT-TCCHHHHHHHHTCCHHHHHHHSCST
T ss_pred             HHHHHHC-CCCHHHHHHHHCcCHHHHHhhCCcc
Confidence            4445555 8999999999999999999977543

>d2fq4a1 a.4.1.9 (A:9-77) Transcriptional regulator BC3163 {Bacillus cereus [TaxId: 1396]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator BC3163
species: Bacillus cereus [TaxId: 1396]

Probab=94.90  E-value=0.018  Score=34.57  Aligned_cols=44  Identities=16%  Similarity=0.151  Sum_probs=35.8

Q ss_pred             hhHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          159 ELHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       159 ~l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      +..+.++.++.+          ++..-...++|+.+||.+.|+++..||+-|+.
T Consensus         4 ~~r~~Il~aa~~----------l~~~~G~~~~t~~~Ia~~agvs~~~~y~~F~~   47 (69)
T d2fq4a1           4 ETQKAILSASYE----------LLLESGFKAVTVDKIAERAKVSKATIYKWWPN   47 (69)
T ss_dssp             HHHHHHHHHHHH----------HHHHHCTTTCCHHHHHHHHTCCHHHHHHHCSS
T ss_pred             HHHHHHHHHHHH----------HHHHhCcccCCHHHHHHHHCcCHHHHHHHCCC
Confidence            345677777777          55556677999999999999999999998874

>d1jt6a1 a.4.1.9 (A:2-72) Multidrug binding protein QacR {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Multidrug binding protein QacR
species: Staphylococcus aureus [TaxId: 1280]

Probab=94.09  E-value=0.023  Score=34.28  Aligned_cols=41  Identities=10%  Similarity=0.028  Sum_probs=33.0

Q ss_pred             HHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          162 QQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       162 ~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      ++++.++..          ++......++|+++||.+.++|+..+|+-|+.
T Consensus         4 ~~Il~aa~~----------l~~~~G~~~~s~~~Ia~~agvs~~~~y~~F~~   44 (71)
T d1jt6a1           4 DKILGVAKE----------LFIKNGYNATTTGEIVKLSESSKGNLYYHFKT   44 (71)
T ss_dssp             HHHHHHHHH----------HHHHHCTTTCCHHHHHHHTTCCHHHHHHHHSS
T ss_pred             HHHHHHHHH----------HHHHhCccccCHHHHHHHHCcCHhHHHHHCcC
Confidence            456666666          44555677999999999999999999998874

>d2g7la1 a.4.1.9 (A:16-83) Putative transcriptional regulator SCO7704 {Streptomyces coelicolor [TaxId: 1902]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator SCO7704
species: Streptomyces coelicolor [TaxId: 1902]

Probab=93.93  E-value=0.037  Score=33.02  Aligned_cols=41  Identities=12%  Similarity=0.101  Sum_probs=33.7

Q ss_pred             HHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          162 QQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       162 ~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      ++++.++..          +.....-.++|+..||.+++++|..+|+-|+.
T Consensus         7 ~~Il~aa~~----------l~~~~g~~~~si~~ia~~~gvs~~~~y~hF~~   47 (68)
T d2g7la1           7 RWIVDTAVA----------LMRAEGLEKVTMRRLAQELDTGPASLYVYVAN   47 (68)
T ss_dssp             HHHHHHHHH----------HHHHHCSSSCCHHHHHHHTTSCHHHHTTTCCS
T ss_pred             HHHHHHHHH----------HHHHhCcccCCHHHHHHHHCcCHhHhhHHCcC
Confidence            456677766          55556677999999999999999999998874

>d1rkta1 a.4.1.9 (A:2-82) Hypothetical transcriptional regulator YfiR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Hypothetical transcriptional regulator YfiR
species: Bacillus subtilis [TaxId: 1423]

Probab=93.80  E-value=0.041  Score=33.96  Aligned_cols=42  Identities=12%  Similarity=0.014  Sum_probs=35.2

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      ..+++.++..          ++......++|++.||...|+|+..||+-|+.
T Consensus        13 r~~Il~aa~~----------l~~~~G~~~~ti~~Ia~~agvs~~t~Y~~F~~   54 (81)
T d1rkta1          13 QAEILEAAKT----------VFKRKGFELTTMKDVVEESGFSRGGVYLYFSS   54 (81)
T ss_dssp             HHHHHHHHHH----------HHHHHCSTTCCHHHHHHHHTSCHHHHHTTCSC
T ss_pred             HHHHHHHHHH----------HHHHhCcccCCHHHHHHHhCcCHHHHHHHCcC
Confidence            4567777777          55556788999999999999999999998874

>d2gena1 a.4.1.9 (A:6-75) Probable transcriptional regulator PA1836 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Probable transcriptional regulator PA1836
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=93.74  E-value=0.034  Score=33.26  Aligned_cols=41  Identities=12%  Similarity=0.003  Sum_probs=32.8

Q ss_pred             HHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          162 QQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       162 ~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      ++++.++..          ++......++|+..||.+.++++..+|+-|+.
T Consensus         3 ~~il~aa~~----------l~~~~G~~~~si~~Ia~~agvs~~t~Y~~F~s   43 (70)
T d2gena1           3 DEILQAALA----------CFSEHGVDATTIEMIRDRSGASIGSLYHHFGN   43 (70)
T ss_dssp             HHHHHHHHH----------HHHHHCTTTCCHHHHHHHHCCCHHHHHHHTCS
T ss_pred             HHHHHHHHH----------HHHHhCcccCCHHHHHHHHCcCHHHHHHHCCC
Confidence            356666666          44556677999999999999999999998864

>d2iu5a1 a.4.1.9 (A:1-71) Transcriptional activator DhaS {Lactococcus lactis [TaxId: 1358]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional activator DhaS
species: Lactococcus lactis [TaxId: 1358]

Probab=93.74  E-value=0.035  Score=33.43  Aligned_cols=41  Identities=7%  Similarity=0.088  Sum_probs=32.4

Q ss_pred             HHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          162 QQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       162 ~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      +..+.++.+          ++....-.++|+.+||.+.+++|..+|+-|+.
T Consensus         9 ~~I~~aa~~----------l~~~~G~~~~sv~~Ia~~agvs~~t~Y~~F~~   49 (71)
T d2iu5a1           9 KIIAKAFKD----------LMQSNAYHQISVSDIMQTAKIRRQTFYNYFQN   49 (71)
T ss_dssp             HHHHHHHHH----------HHHHSCGGGCCHHHHHHHHTSCGGGGGGTCSS
T ss_pred             HHHHHHHHH----------HHHHcCcccCCHHHHHHHhCccccHHHHHcCC
Confidence            455566666          44555667899999999999999999998874

>d1t56a1 a.4.1.9 (A:22-94) Ethr repressor {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Ethr repressor
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=93.62  E-value=0.024  Score=34.24  Aligned_cols=42  Identities=10%  Similarity=0.081  Sum_probs=33.9

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .++++.++.+          ++..-...++|+.+||.++++|+..+|+-|+.
T Consensus         5 r~~Il~aa~~----------l~~~~G~~~~t~~~Ia~~agvs~~t~Y~~F~~   46 (73)
T d1t56a1           5 ELAILATAEN----------LLEDRPLADISVDDLAKGAGISRPTFYFYFPS   46 (73)
T ss_dssp             HHHHHHHHHH----------HHHHSCGGGCCHHHHHHHHTCCHHHHHHHCSS
T ss_pred             HHHHHHHHHH----------HHHHhCcccCCHHHHHHHhCCCHHHHHHHCcC
Confidence            3567777777          55555667899999999999999999998864

>d2fd5a1 a.4.1.9 (A:1-76) Probable transcriptional regulator PA3133 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Probable transcriptional regulator PA3133
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=93.60  E-value=0.053  Score=32.92  Aligned_cols=42  Identities=7%  Similarity=-0.158  Sum_probs=33.2

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .++++.++..          ++..-...++|+++||.+.++|+..||+-|+.
T Consensus         9 r~~Il~aa~~----------l~~~~G~~~~si~~Ia~~agvs~~t~Y~~F~~   50 (76)
T d2fd5a1           9 RARILGAATQ----------ALLERGAVEPSVGEVMGAAGLTVGGFYAHFQS   50 (76)
T ss_dssp             HHHHHHHHHH----------HHHHHTTTSCCHHHHHHHTTCCGGGGGGTCSC
T ss_pred             HHHHHHHHHH----------HHHHhCcccccHHHHHHHhCCCccchhhcCCC
Confidence            3567777776          33344677999999999999999999998874

>d1zk8a1 a.4.1.9 (A:6-77) Transcriptional regulator BC5000 {Bacillus cereus [TaxId: 1396]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator BC5000
species: Bacillus cereus [TaxId: 1396]

Probab=93.49  E-value=0.033  Score=33.56  Aligned_cols=42  Identities=19%  Similarity=0.122  Sum_probs=33.2

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .++.+.++.+          ++..-...++|+.+||+++++|+..+|+-|+.
T Consensus         5 ~e~Il~aa~~----------l~~~~G~~~~t~~~Ia~~agvs~~slY~yF~~   46 (72)
T d1zk8a1           5 LQKIVETAAE----------IADANGVQEVTLASLAQTLGVRSPSLYNHVKG   46 (72)
T ss_dssp             HHHHHHHHHH----------HHHHHCGGGCCHHHHHHHHTSCHHHHTTTCSS
T ss_pred             HHHHHHHHHH----------HHHHhCCCcccHHHHHHHhCCCHHHHHHHCcC
Confidence            3456666666          44555667899999999999999999998874

>d1v7ba1 a.4.1.9 (A:1-74) Transcriptional regulator Cgl2612 {Corynebacterium glutamicum [TaxId: 1718]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator Cgl2612
species: Corynebacterium glutamicum [TaxId: 1718]

Probab=93.49  E-value=0.038  Score=33.46  Aligned_cols=42  Identities=7%  Similarity=0.015  Sum_probs=33.7

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .++.+.++.+          ++..-...++|+.+||...++|+..+|+-|+.
T Consensus         6 r~~Il~aa~~----------l~~~~G~~~~s~~~Ia~~agvs~~t~Y~~F~~   47 (74)
T d1v7ba1           6 KEMILRTAID----------YIGEYSLETLSYDSLAEATGLSKSGLIYHFPS   47 (74)
T ss_dssp             HHHHHHHHHH----------HHHHSCSTTCCHHHHHHHHCSCHHHHHHHCSS
T ss_pred             HHHHHHHHHH----------HHHHhCccccCHHHHHHHhCcCcchHhhhCCC
Confidence            3456666666          55555677999999999999999999998874

>d2fx0a1 a.4.1.9 (A:4-76) Hemolysin II regulatory protein, HlyIIR {Bacillus cereus [TaxId: 1396]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Hemolysin II regulatory protein, HlyIIR
species: Bacillus cereus [TaxId: 1396]

Probab=93.42  E-value=0.039  Score=33.45  Aligned_cols=42  Identities=12%  Similarity=0.063  Sum_probs=33.3

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .++++.++.+          +...-...++|+++||++.++|+..+|+-|+.
T Consensus         6 r~~Il~aa~~----------l~~~~G~~~~si~~Ia~~agvs~~~~Y~~F~~   47 (73)
T d2fx0a1           6 MENILKAAKK----------KFGERGYEGTSIQEIAKEAKVNVAMASYYFNG   47 (73)
T ss_dssp             HHHHHHHHHH----------HHHHHCTTTCCHHHHHHHHTSCHHHHHHHHTS
T ss_pred             HHHHHHHHHH----------HHHHhCcccCcHHHHHHHHCcChhHHHHHCcC
Confidence            4567777777          33444566899999999999999999998864

>d2o7ta1 a.4.1.9 (A:1-78) Transcriptional regulator Cgl1640/Cg1846 {Corynebacterium glutamicum [TaxId: 1718]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator Cgl1640/Cg1846
species: Corynebacterium glutamicum [TaxId: 1718]

Probab=93.36  E-value=0.028  Score=34.54  Aligned_cols=42  Identities=17%  Similarity=0.100  Sum_probs=34.0

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .++++.++.+          ++......++|+.+||++.++|+..+|+-|+.
T Consensus         9 r~~Il~aa~~----------l~~~~G~~~~t~~~Ia~~agvs~~t~y~~F~s   50 (78)
T d2o7ta1           9 REHIITTTCN----------LYRTHHHDSLTMENIAEQAGVGVATLYRNFPD   50 (78)
T ss_dssp             HHHHHHHHHH----------HHHHSCGGGCCHHHHHHHHTCCHHHHHHHCSS
T ss_pred             HHHHHHHHHH----------HHHHhCccccCHHHHHHHhCCCHHHHHHHCcC
Confidence            3567777776          55555667899999999999999999998874

>d2g7sa1 a.4.1.9 (A:3-76) Putative transcriptional regulator Atu0279 {Agrobacterium tumefaciens [TaxId: 358]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator Atu0279
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=93.29  E-value=0.028  Score=34.15  Aligned_cols=42  Identities=0%  Similarity=0.021  Sum_probs=33.7

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .+++++++..          ++..-.-.++|+.+||...++++..+|+-|+.
T Consensus         6 r~~Il~aa~~----------l~~~~G~~~~s~~~Ia~~agvs~~~iY~~F~s   47 (74)
T d2g7sa1           6 ADDILQCART----------LIIRGGYNSFSYADISQVVGIRNASIHHHFPS   47 (74)
T ss_dssp             HHHHHHHHHH----------HHHHHCGGGCCHHHHHHHHCCCHHHHHHHCSS
T ss_pred             HHHHHHHHHH----------HHHHhCccccCHHHHHHHHCcCcchHHHHCcC
Confidence            4567777777          34445566899999999999999999998874

>d2hyja1 a.4.1.9 (A:8-82) Putative transcriptional regulator SCO4940 {Streptomyces coelicolor [TaxId: 1902]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator SCO4940
species: Streptomyces coelicolor [TaxId: 1902]

Probab=93.27  E-value=0.036  Score=33.71  Aligned_cols=42  Identities=17%  Similarity=0.227  Sum_probs=33.9

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .++++.++..          ++....-.++|+++||.++++|+..+|+-|+.
T Consensus         7 r~~il~aa~~----------l~~~~G~~~~t~~~Ia~~agvs~~~~Y~~F~~   48 (75)
T d2hyja1           7 RGRILGRAAE----------IASEEGLDGITIGRLAEELEMSKSGVHKHFGT   48 (75)
T ss_dssp             HHHHHHHHHH----------HHHHHCGGGCCHHHHHHHHTCCHHHHHTTCSS
T ss_pred             HHHHHHHHHH----------HHHHhCcccCcHHHHHHHHCcCHHHHHHHCcC
Confidence            4566777776          55555677899999999999999999998864

>d3c07a1 a.4.1.9 (A:15-89) Putative transcriptional regulator SCO4850 {Streptomyces coelicolor [TaxId: 1902]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator SCO4850
species: Streptomyces coelicolor [TaxId: 1902]

Probab=93.17  E-value=0.051  Score=32.86  Aligned_cols=42  Identities=5%  Similarity=-0.118  Sum_probs=34.4

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .++++.++.+          ++......++|+.+||...++|+..+|+-|+.
T Consensus         7 r~~Il~aa~~----------l~~~~G~~~~t~~~Ia~~agvs~~~~y~~F~~   48 (75)
T d3c07a1           7 RALILETAMR----------LFQERGYDRTTMRAIAQEAGVSVGNAYYYFAG   48 (75)
T ss_dssp             HHHHHHHHHH----------HHHHTCSTTCCHHHHHHHHTSCHHHHHHHCSS
T ss_pred             HHHHHHHHHH----------HHHHhCcccCCHHHHHHHHCcCHHHHHHHCcC
Confidence            4677778777          44455677999999999999999999998864

>d2oi8a1 a.4.1.9 (A:8-86) Putative regulatory protein Sco4313 {Streptomyces coelicolor [TaxId: 1902]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative regulatory protein Sco4313
species: Streptomyces coelicolor [TaxId: 1902]

Probab=93.01  E-value=0.066  Score=32.77  Aligned_cols=44  Identities=11%  Similarity=0.077  Sum_probs=35.7

Q ss_pred             hhHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          159 ELHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       159 ~l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      ...++++.++.+          ++..-...++|+++||.+.++|+..||+-|..
T Consensus         9 ~~r~~il~aa~~----------l~~~~G~~~~t~~~Ia~~agvs~~~~Y~~F~~   52 (79)
T d2oi8a1           9 QVRAEIKDHAWE----------QIATAGASALSLNAIAKRMGMSGPALYRYFDG   52 (79)
T ss_dssp             HHHHHHHHHHHH----------HHHHHCTTSCCHHHHHHHTTCCHHHHHTTCSS
T ss_pred             HHHHHHHHHHHH----------HHHHhCccccCHHHHHHHhCCCCCchhhhcCC
Confidence            345677778777          55555677999999999999999999998864

>d1pb6a1 a.4.1.9 (A:14-85) Hypothetical transcriptional regulator YcdC {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Hypothetical transcriptional regulator YcdC
species: Escherichia coli [TaxId: 562]

Probab=93.00  E-value=0.053  Score=32.65  Aligned_cols=42  Identities=14%  Similarity=0.109  Sum_probs=33.6

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .++++.++.+          ++..-...++|+.+||.+.++|+..+|+-|+.
T Consensus         6 r~~Il~aa~~----------l~~~~G~~~~ti~~Ia~~agvs~~t~y~~F~~   47 (72)
T d1pb6a1           6 KKAILSAALD----------TFSQFGFHGTRLEQIAELAGVSKTNLLYYFPS   47 (72)
T ss_dssp             HHHHHHHHHH----------HHHHHCTTTCCHHHHHHHTTSCHHHHHHHSSS
T ss_pred             HHHHHHHHHH----------HHHHhCccccCHHHHHHHhCCChHHHHHHCcC
Confidence            3566666666          45555677999999999999999999998864

>d2fbqa1 a.4.1.9 (A:2-80) Transcriptional regulator PsrA {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator PsrA
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=92.95  E-value=0.057  Score=33.06  Aligned_cols=42  Identities=7%  Similarity=0.056  Sum_probs=33.5

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .++++.++..          ++..-.-.++|+..||...|+|+..+|+-|+.
T Consensus         6 re~Il~aa~~----------~~~~~G~~~~ti~~Ia~~agvs~~s~y~~F~~   47 (79)
T d2fbqa1           6 VERILDAAEQ----------LFAEKGFAETSLRLITSKAGVNLAAVNYHFGS   47 (79)
T ss_dssp             HHHHHHHHHH----------HHHHHCSTTCCHHHHHHHHTSCHHHHHHHTCS
T ss_pred             HHHHHHHHHH----------HHHHhCcccccHHHHHHHHCcChhHHHHHCcC
Confidence            4567777776          44445567999999999999999999998864

>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=92.77  E-value=0.63  Score=32.41  Aligned_cols=92  Identities=9%  Similarity=-0.004  Sum_probs=61.9

Q ss_pred             cEEEE---ECCHHHHHHHHHhCCCCceEEEEccCCCCCCH-H----HHHHHHhcCC-C-CcEEEEeccCCHHHHHHHHhC
Q 027234            3 FSVTK---CNRAEIALDMLRTNKNGYDIVISDVHMPDMDG-F----KLLELVGLEM-D-LPVIMMCAHGSKEVVMKGVTH   72 (226)
Q Consensus         3 ~~V~~---~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG-~----~l~~~l~~~~-~-~pvI~ls~~~~~~~~~~a~~~   72 (226)
                      |+|..   .-+.++.++.+.+..  ||+|-+...|....+ +    ++++.++... . .+.|++-+..-..  ..+.+.
T Consensus        57 ~eVi~LG~~vp~e~~v~~a~e~~--~d~VglS~l~t~~~~h~~~~~~~i~~l~~~g~~d~v~vivGG~~~~~--~~a~~~  132 (160)
T d1xrsb1          57 IDAYNLGSQVANEDFIKKAVELE--ADVLLVSQTVTQKNVHIQNMTHLIELLEAEGLRDRFVLLCGGPRINN--EIAKEL  132 (160)
T ss_dssp             EEEEECCSSBCHHHHHHHHHHTT--CSEEEEECCCCTTSHHHHHHHHHHHHHHHTTCGGGSEEEEECTTCCH--HHHHTT
T ss_pred             eEEEeCCCCCCHHHHHHHHHhcC--CCEEEEeecccccchhHHHHHHHHHHHHHcCCCCceEEEEcCCCCCH--HHHHHc
Confidence            77763   347888999999877  999999999886543 3    3445555332 2 2233344322222  235678


Q ss_pred             CcceEEeCCCCHHHHHHHHHHHHHHH
Q 027234           73 DACDYLTKPVRIEELKNIWQHVVRKR   98 (226)
Q Consensus        73 ga~~yl~KP~~~~~L~~~l~~~~~~~   98 (226)
                      ||+.|...-.+..++...+...++.+
T Consensus       133 GaD~~f~~g~~a~~~a~~l~~~l~~r  158 (160)
T d1xrsb1         133 GYDAGFGPGRFADDVATFAVKTLNDR  158 (160)
T ss_dssp             TCSEEECTTCCHHHHHHHHHHHHHHH
T ss_pred             CCCEEcCCCCCHHHHHHHHHHHHHHh
Confidence            99999999889999888887776544

>d1z0xa1 a.4.1.9 (A:4-71) Transcriptional regulator EF0787 {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator EF0787
species: Enterococcus faecalis [TaxId: 1351]

Probab=92.75  E-value=0.045  Score=32.60  Aligned_cols=42  Identities=12%  Similarity=0.039  Sum_probs=31.8

Q ss_pred             HHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          162 QQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       162 ~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      ++++.++-.         .+.+.-...++|+++||.+.++|+..+|+-|+.
T Consensus         5 ~~Ii~aa~~---------l~~e~~G~~~~t~~~Ia~~agvs~~~iy~hF~~   46 (68)
T d1z0xa1           5 DTIIAAAFS---------LLEKSPTLEQLSMRKVAKQLGVQAPAIYWYFKN   46 (68)
T ss_dssp             HHHHHHHHH---------HHHHSCCGGGCCHHHHHHHHTSCHHHHHTTCSS
T ss_pred             HHHHHHHHH---------HHHHcCCccccCHHHHHHHHCcchhHHHHhcCC
Confidence            456666666         233444566899999999999999999998864

>d2gfna1 a.4.1.9 (A:4-80) Probable transcriptional regulator RHA1_ro04631 {Rhodococcus sp. rha1 [TaxId: 101510]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Probable transcriptional regulator RHA1 ro04631
species: Rhodococcus sp. rha1 [TaxId: 101510]

Probab=92.68  E-value=0.039  Score=33.70  Aligned_cols=42  Identities=19%  Similarity=0.171  Sum_probs=33.3

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .+++++++.+          ++..-.-.++|+.+||+++++|+..||+-|+.
T Consensus         8 r~~Il~aa~~----------l~~~~G~~~~s~~~Ia~~agvs~~~lY~~F~~   49 (77)
T d2gfna1           8 RRALADAVLA----------LIAREGISAVTTRAVAEESGWSTGVLNHYFGS   49 (77)
T ss_dssp             HHHHHHHHHH----------HHHHHCGGGCCHHHHHHHHSSCHHHHHHHTSS
T ss_pred             HHHHHHHHHH----------HHHHhCccccCHHHHHHHHCCCHHHHHHHCcC
Confidence            4567777776          34444566899999999999999999998864

>d1vi0a1 a.4.1.9 (A:6-77) Hypothetical transcriptional regulator YsiA {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Hypothetical transcriptional regulator YsiA
species: Bacillus subtilis [TaxId: 1423]

Probab=92.66  E-value=0.046  Score=32.85  Aligned_cols=41  Identities=10%  Similarity=-0.044  Sum_probs=32.6

Q ss_pred             HHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          162 QQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       162 ~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      ++++.++..          ++..-...++|+.+||...++|+..+|+-|+.
T Consensus         4 ~~Il~aa~~----------l~~~~G~~~~ti~~Ia~~agvs~~~~y~~F~~   44 (72)
T d1vi0a1           4 MQIIDAAVE----------VIAENGYHQSQVSKIAKQAGVADGTIYLYFKN   44 (72)
T ss_dssp             HHHHHHHHH----------HHHHHCGGGCCHHHHHHHHTSCHHHHHHHCSS
T ss_pred             HHHHHHHHH----------HHHHhCcccccHHHHHHHHCcCHHHHHHHCcC
Confidence            456666666          44445666899999999999999999998874

>d2d6ya1 a.4.1.9 (A:7-74) Putative regulator SCO4008 {Streptomyces coelicolor [TaxId: 1902]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative regulator SCO4008
species: Streptomyces coelicolor [TaxId: 1902]

Probab=92.64  E-value=0.057  Score=32.11  Aligned_cols=41  Identities=12%  Similarity=0.178  Sum_probs=32.9

Q ss_pred             HHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          162 QQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       162 ~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      ++++.++.+          ++....-.++|+.+||...++||..+|+-|+.
T Consensus         5 ~~Il~aa~~----------l~~~~G~~~~ti~~Ia~~agvs~~~~Y~~F~~   45 (68)
T d2d6ya1           5 ARIFEAAVA----------EFARHGIAGARIDRIAAEARANKQLIYAYYGN   45 (68)
T ss_dssp             HHHHHHHHH----------HHHHHTTTSCCHHHHHHHHTCCHHHHHHHHSS
T ss_pred             HHHHHHHHH----------HHHHhCccccCHHHHHHHHCcchhHHHHHCcC
Confidence            456666666          55555677999999999999999999998864

>d2np5a1 a.4.1.9 (A:9-77) Transcriptional regulator RHA1_ro04179 {Rhodococcus sp. [TaxId: 1831]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator RHA1 ro04179
species: Rhodococcus sp. [TaxId: 1831]

Probab=92.50  E-value=0.05  Score=32.38  Aligned_cols=42  Identities=10%  Similarity=0.060  Sum_probs=32.9

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .++++.++-.          ++......++|+.+||...++++..+|+-|+.
T Consensus         3 ~e~i~~aa~~----------l~~~~G~~~~ti~~Ia~~agvs~~~iy~~F~s   44 (69)
T d2np5a1           3 PERLAAALFD----------VAAESGLEGASVREVAKRAGVSIGAVQHHFST   44 (69)
T ss_dssp             HHHHHHHHHH----------HHHHHCGGGCCHHHHHHHHTCCHHHHHHHCSS
T ss_pred             HHHHHHHHHH----------HHHHhCccccCHHHHHHHhCCCHHHHHHHCcC
Confidence            3456666666          44555667999999999999999999998864

>d1ui5a1 a.4.1.9 (A:5-75) A-factor receptor homolog CprB {Streptomyces coelicolor [TaxId: 1902]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: A-factor receptor homolog CprB
species: Streptomyces coelicolor [TaxId: 1902]

Probab=92.41  E-value=0.075  Score=31.81  Aligned_cols=42  Identities=10%  Similarity=0.082  Sum_probs=34.8

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .++++.++.+          ++..-...++|++.||...|+|+..+|+-|+.
T Consensus         7 r~~il~aa~~----------l~~~~G~~~~si~~Ia~~agvs~~~~y~~F~s   48 (71)
T d1ui5a1           7 RATIIGAAAD----------LFDRRGYESTTLSEIVAHAGVTKGALYFHFAA   48 (71)
T ss_dssp             HHHHHHHHHH----------HHHHHCTTTCCHHHHHHHHTCCHHHHHHHCSS
T ss_pred             HHHHHHHHHH----------HHHHhCccccCHHHHHHHHCcCHhHHHHHCcC
Confidence            4577777777          45556677999999999999999999998874

>d2i10a1 a.4.1.9 (A:10-78) Putative transcriptional regulator RHA1_ro09068 {Rhodococcus sp. [TaxId: 1831]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator RHA1 ro09068
species: Rhodococcus sp. [TaxId: 1831]

Probab=92.22  E-value=0.072  Score=31.71  Aligned_cols=32  Identities=13%  Similarity=0.052  Sum_probs=26.5

Q ss_pred             HHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          181 ILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       181 I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      +...-.-.++|+.+||.+.++|+..+|+-|+.
T Consensus        12 lf~~~G~~~~ti~~Ia~~agvs~~~~Y~~F~~   43 (69)
T d2i10a1          12 LFWRQGYEGTSITDLTKALGINPPSLYAAFGS   43 (69)
T ss_dssp             HHHHHTTTTCCHHHHHHHHTCCHHHHHHHHCS
T ss_pred             HHHHHCcccCCHHHHHHHhCCChhHHHHHCcC
Confidence            33445667999999999999999999998864

>d1sgma1 a.4.1.9 (A:5-77) Putative transcriptional regulator YxaF {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator YxaF
species: Bacillus subtilis [TaxId: 1423]

Probab=92.07  E-value=0.077  Score=31.88  Aligned_cols=41  Identities=5%  Similarity=0.020  Sum_probs=33.4

Q ss_pred             HHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          162 QQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       162 ~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      ++++.++.+          ++......++|+.+||.+.++|+..+|+-|+.
T Consensus         5 ~~Il~aa~~----------l~~~~G~~~~si~~Ia~~agvs~~~iy~~F~~   45 (73)
T d1sgma1           5 EKILHTASR----------LSQLQGYHATGLNQIVKESGAPKGSLYHFFPN   45 (73)
T ss_dssp             HHHHHHHHH----------HHHHHCTTTCCHHHHHHHHCCCSCHHHHSTTT
T ss_pred             HHHHHHHHH----------HHHHhCcccCCHHHHHHHhCCCHHHHHHHcCC
Confidence            456666666          55566677999999999999999999998865

>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=91.94  E-value=0.49  Score=32.07  Aligned_cols=91  Identities=10%  Similarity=-0.019  Sum_probs=62.7

Q ss_pred             CcEEE---EECCHHHHHHHHHhCCCCceEEEEccCCCCCC-H-HHHHHHHhcC--CCCcEEEEecc-----CC-HHHHHH
Q 027234            2 GFSVT---KCNRAEIALDMLRTNKNGYDIVISDVHMPDMD-G-FKLLELVGLE--MDLPVIMMCAH-----GS-KEVVMK   68 (226)
Q Consensus         2 g~~V~---~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~d-G-~~l~~~l~~~--~~~pvI~ls~~-----~~-~~~~~~   68 (226)
                      ||+|.   .....++.++.+.+..  ||+|.+...|+... . -++++.++..  .++||++ -+.     .. .....+
T Consensus        31 G~~V~~LG~~~p~e~iv~a~~~~~--~d~v~lS~~~~~~~~~~~~~~~~l~~~~~~~i~iiv-GG~~~~~~~~~~~~~~~  107 (137)
T d1ccwa_          31 GFNVVNIGVLSPQELFIKAAIETK--ADAILVSSLYGQGEIDCKGLRQKCDEAGLEGILLYV-GGNIVVGKQHWPDVEKR  107 (137)
T ss_dssp             TCEEEEEEEEECHHHHHHHHHHHT--CSEEEEEECSSTHHHHHTTHHHHHHHTTCTTCEEEE-EESCSSSSCCHHHHHHH
T ss_pred             CCeEEecccccCHHHHHHHHHhcC--CCEEEEeeccccchHHHHHHHHHHHHhccCCCEEEE-eCCcCCCccccHHHHHH
Confidence            78876   4568899999999877  99999999998632 1 1233445432  3566553 332     22 345556


Q ss_pred             HHhCCcceEEeCCCCHHHHHHHHHHHH
Q 027234           69 GVTHDACDYLTKPVRIEELKNIWQHVV   95 (226)
Q Consensus        69 a~~~ga~~yl~KP~~~~~L~~~l~~~~   95 (226)
                      ..++|++..+...-+++++.+.+++-+
T Consensus       108 l~~~Gv~~if~~~t~~~~~~~~l~~~l  134 (137)
T d1ccwa_         108 FKDMGYDRVYAPGTPPEVGIADLKKDL  134 (137)
T ss_dssp             HHHTTCSEECCTTCCHHHHHHHHHHHH
T ss_pred             HHHcCCCEEECCCCCHHHHHHHHHHHh
Confidence            668899999988888999888877654

>d2id3a1 a.4.1.9 (A:13-80) Putative transcriptional regulator SCO5951 {Streptomyces coelicolor [TaxId: 1902]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator SCO5951
species: Streptomyces coelicolor [TaxId: 1902]

Probab=91.48  E-value=0.07  Score=31.66  Aligned_cols=42  Identities=14%  Similarity=0.112  Sum_probs=32.9

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .+.+++++..          ++..-.-.++|+.+||...++|+..+|+-|+.
T Consensus         8 r~~Il~aa~~----------l~~~~G~~~~t~~~Ia~~agvs~~~iY~~F~~   49 (68)
T d2id3a1           8 REAVLLAAGD----------ALAADGFDALDLGEIARRAGVGKTTVYRRWGT   49 (68)
T ss_dssp             HHHHHHHHHH----------HHHHHCGGGCCHHHHHHHHTCCHHHHHHHHCS
T ss_pred             HHHHHHHHHH----------HHHHhCcccCCHHHHHHHHCcCHHHHHHHCcC
Confidence            4566666666          44555667899999999999999999998764

>d1umqa_ a.4.1.12 (A:) Photosynthetic apparatus regulatory protein PprA (RegA), DNA-binding domain {Rhodobacter sphaeroides [TaxId: 1063]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: FIS-like
domain: Photosynthetic apparatus regulatory protein PprA (RegA), DNA-binding domain
species: Rhodobacter sphaeroides [TaxId: 1063]

Probab=91.22  E-value=0.049  Score=31.71  Aligned_cols=30  Identities=23%  Similarity=0.315  Sum_probs=24.9

Q ss_pred             HHHHhhCCCCCCHHHHHHHhhhhhhhhhcc
Q 027234          180 KILELMNIPGLTRENVASHLQKHRLYLSRL  209 (226)
Q Consensus       180 ~I~~~~~~~~lt~~~va~~l~~~r~~l~r~  209 (226)
                      .|.+.+...+-++...|..||+||+.|||.
T Consensus        24 ~I~~aL~~~~gn~~~aA~~LGIsR~TL~rk   53 (60)
T d1umqa_          24 HIQRIYEMCDRNVSETARRLNMHRRTLQRI   53 (60)
T ss_dssp             HHHHHHHHTTSCHHHHHHHHTSCHHHHHHH
T ss_pred             HHHHHHHHhcCcHHHHHHHHCCCHHHHHHH
Confidence            455666666888999999999999999974

>d2vkva1 a.4.1.9 (A:6-67) Tetracyclin repressor (Tet-repressor, TetR) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Tetracyclin repressor (Tet-repressor, TetR)
species: Escherichia coli [TaxId: 562]

Probab=90.85  E-value=0.039  Score=32.26  Aligned_cols=32  Identities=22%  Similarity=0.152  Sum_probs=26.5

Q ss_pred             HHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          181 ILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       181 I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      ++..-...++|+.+||.+.++|+..+|+-|+.
T Consensus        11 l~~~~G~~~~s~~~Ia~~agvs~~tiy~~F~~   42 (62)
T d2vkva1          11 LGNEVGIEGLTTRKLAQKLGVEQPTLYWHVKN   42 (62)
T ss_dssp             HHHHHHHHHCCHHHHHHHHTSCHHHHHHHSCC
T ss_pred             HHHHhCcccCCHHHHHHHhCCCHHHHHHHCCC
Confidence            44444556899999999999999999998875

>d2g3ba1 a.4.1.9 (A:2-73) Putative transcriptional regulator {Rhodococcus sp. rha1 [TaxId: 101510]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator
species: Rhodococcus sp. rha1 [TaxId: 101510]

Probab=90.77  E-value=0.041  Score=33.17  Aligned_cols=42  Identities=17%  Similarity=0.042  Sum_probs=32.5

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .++++.++.+          ++......++|+..||.+.++||..+|+-|+.
T Consensus         4 r~~Il~aa~~----------l~~~~G~~~~ti~~Ia~~agvs~~~ly~~F~~   45 (72)
T d2g3ba1           4 RDAILKASAT----------AIAQRGIRGLRVNDVAEVAGVSPGLLYYHFKD   45 (72)
T ss_dssp             HHHHHHHHHH----------HHHHHHHHHCCHHHHHHHHTSCHHHHHHHHCS
T ss_pred             HHHHHHHHHH----------HHHHhCcccCCHHHHHHHhCcCHHHHHHHCcC
Confidence            3566677766          33444556899999999999999999998864

>d1sfxa_ a.4.5.50 (A:) Hypothetical protein AF2008 {Archaeoglobus fulgidus [TaxId: 2234]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: TrmB-like
domain: Hypothetical protein AF2008
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=90.64  E-value=0.041  Score=36.12  Aligned_cols=48  Identities=17%  Similarity=0.281  Sum_probs=42.2

Q ss_pred             HHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcc
Q 027234          162 QQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRL  209 (226)
Q Consensus       162 ~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~  209 (226)
                      ..++..++.+|+....-+.+.-++..+.+|..+||..++++|+..|+.
T Consensus         7 ~~l~~~L~~lGlt~~e~~v~~~L~~~g~~t~~eia~~~~i~~~~v~~~   54 (109)
T d1sfxa_           7 GELVKALEKLSFKPSDVRIYSLLLERGGMRVSEIARELDLSARFVRDR   54 (109)
T ss_dssp             HHHHHHHHHTCCCHHHHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHHHHhcCCCCHHHHHHHhCCCcchHHHH
Confidence            577888899999988888888888888999999999999999988864

>d2g7ga1 a.4.1.9 (A:9-73) Putative transcriptional regulator Rha04620 {Rhodococcus sp. rha1 [TaxId: 101510]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator Rha04620
species: Rhodococcus sp. rha1 [TaxId: 101510]

Probab=90.42  E-value=0.16  Score=29.81  Aligned_cols=39  Identities=13%  Similarity=0.077  Sum_probs=31.0

Q ss_pred             HHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          162 QQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       162 ~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      ++++.++..         .+.+. .  ++|+.+||.++++++..+|+-|+.
T Consensus         4 ~~Il~aa~~---------l~~~~-G--~~ti~~Ia~~agvs~~~iY~~F~~   42 (65)
T d2g7ga1           4 ERIAEAALE---------LVDRD-G--DFRMPDLARHLNVQVSSIYHHAKG   42 (65)
T ss_dssp             HHHHHHHHH---------HHHHH-S--SCCHHHHHHHTTSCHHHHHTTSCH
T ss_pred             HHHHHHHHH---------HHHHc-C--CCCHHHHHHHhCccccchhhcCCC
Confidence            466777776         35554 3  899999999999999999998763

>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=90.27  E-value=2.1  Score=31.96  Aligned_cols=81  Identities=11%  Similarity=0.075  Sum_probs=59.7

Q ss_pred             CHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh--cCCCCcEEEEeccCCHHHHHHHHhCCcceEEeCCCCH-HH
Q 027234           10 RAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG--LEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTKPVRI-EE   86 (226)
Q Consensus        10 ~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~--~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~KP~~~-~~   86 (226)
                      ......+.+....  +|.|++|+.-...|--++...++  +...++.++=....+...+.+++..||.+.+..-++. ++
T Consensus        25 ~~p~~~ei~a~~G--~Dfv~iD~EHg~~~~~~~~~~i~a~~~~g~~~~VRvp~~~~~~i~~~LD~Ga~GIivP~v~s~ee  102 (253)
T d1dxea_          25 SNPISTEVLGLAG--FDWLVLDGEHAPNDISTFIPQLMALKGSASAPVVRVPTNEPVIIKRLLDIGFYNFLIPFVETKEE  102 (253)
T ss_dssp             CSHHHHHHHTTSC--CSEEEEESSSSSCCHHHHHHHHHHTTTCSSEEEEECSSSCHHHHHHHHHTTCCEEEESCCCSHHH
T ss_pred             CCHHHHHHHHcCC--CCEEEEecccCCCChhHHHHHHHHHhccCCCceecCCCCCHHHHHHHHhcCccEEEecccCCHHH
Confidence            3345566776644  99999999988888777776665  3455666676777899999999999999999876654 55


Q ss_pred             HHHHHH
Q 027234           87 LKNIWQ   92 (226)
Q Consensus        87 L~~~l~   92 (226)
                      .+.+++
T Consensus       103 a~~~v~  108 (253)
T d1dxea_         103 AELAVA  108 (253)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            544444

>d2ao9a1 a.4.1.17 (A:13-132) Phage protein BC1890 {Bacillus cereus [TaxId: 1396]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Nanomeric phage protein-like
domain: Phage protein BC1890
species: Bacillus cereus [TaxId: 1396]

Probab=89.11  E-value=0.058  Score=34.85  Aligned_cols=21  Identities=24%  Similarity=0.221  Sum_probs=18.8

Q ss_pred             CCCCHHHHHHHhhhhhhhhhc
Q 027234          188 PGLTRENVASHLQKHRLYLSR  208 (226)
Q Consensus       188 ~~lt~~~va~~l~~~r~~l~r  208 (226)
                      +.=|.++||.|||+||..|||
T Consensus        35 ekktqeqiAeelGisr~tLyr   55 (120)
T d2ao9a1          35 EKRTQDEMANELGINRTTLWE   55 (120)
T ss_dssp             CCCCHHHHHHHHTCCHHHHHH
T ss_pred             hhhhHHHHHHHhChhHHHHHH
Confidence            345899999999999999997

>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=89.02  E-value=1.7  Score=31.22  Aligned_cols=88  Identities=13%  Similarity=0.140  Sum_probs=62.8

Q ss_pred             EEEECCHHHHHHHHHhCCCCceEEEEccCCCC-------CCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceE
Q 027234            5 VTKCNRAEIALDMLRTNKNGYDIVISDVHMPD-------MDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDY   77 (226)
Q Consensus         5 V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~-------~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~y   77 (226)
                      ...|.+.+++...... .  +|.|.+.-..|.       .-|++.++.+.+...+||+.+-+- +.+....++..|++++
T Consensus       103 g~s~h~~~e~~~a~~~-g--~DYi~~gpvf~T~tk~~~~~~g~~~l~~~~~~~~~Pv~AiGGI-~~~ni~~~~~~Ga~gv  178 (206)
T d1xi3a_         103 GASVYSLEEALEAEKK-G--ADYLGAGSVFPTKTKEDARVIGLEGLRKIVESVKIPVVAIGGI-NKDNAREVLKTGVDGI  178 (206)
T ss_dssp             EEEESSHHHHHHHHHH-T--CSEEEEECSSCC----CCCCCHHHHHHHHHHHCSSCEEEESSC-CTTTHHHHHTTTCSEE
T ss_pred             ccccCCHHHHHHHHhc-C--CCEEEeccccccccccccccccHHHHHHHHHhcCCCEEEECCC-CHHHHHHHHHhCCCEE
Confidence            3467788887766553 3  899998876543       238999998877778999988874 5566788899999998


Q ss_pred             -----EeCCCCHHHHHHHHHHHHH
Q 027234           78 -----LTKPVRIEELKNIWQHVVR   96 (226)
Q Consensus        78 -----l~KP~~~~~L~~~l~~~~~   96 (226)
                           |...-++......+++++.
T Consensus       179 Avis~I~~~~dp~~~~~~l~~~~~  202 (206)
T d1xi3a_         179 AVISAVMGAEDVRKATEELRKIVE  202 (206)
T ss_dssp             EESHHHHTSSSHHHHHHHHHHHHH
T ss_pred             EEhHHHHCCCCHHHHHHHHHHHHH
Confidence                 5555566665555555543

>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=88.88  E-value=0.23  Score=35.20  Aligned_cols=68  Identities=15%  Similarity=0.005  Sum_probs=47.1

Q ss_pred             EEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcce
Q 027234            5 VTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACD   76 (226)
Q Consensus         5 V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~   76 (226)
                      ++.+.+.+++++.+...   +|+|++|=.-|+ +--++.+.++....-..+-.|+.-+.+.+....+.|+|.
T Consensus        82 ~VEv~~~~e~~~a~~~g---~d~i~LDn~~pe-~~k~~~~~lk~~~~~i~lEaSGGI~~~ni~~~a~~GVD~  149 (170)
T d1o4ua1          82 EVEVENLEDALRAVEAG---ADIVMLDNLSPE-EVKDISRRIKDINPNVIVEVSGGITEENVSLYDFETVDV  149 (170)
T ss_dssp             EEEESSHHHHHHHHHTT---CSEEEEESCCHH-HHHHHHHHHHHHCTTSEEEEEECCCTTTGGGGCCTTCCE
T ss_pred             EEEeCcHHHHHHHHhcC---ccEEEEcCcChh-hHhHHHHHHHhhCCcEEEEEECCCCHHHHHHHHHcCCCE
Confidence            45789999999998743   899999933332 222334555533334556688888888888888889883

>d2hkua1 a.4.1.9 (A:18-87) Putative transcriptional regulator RHA1_ro03468 {Rhodococcus sp. RHA1 [TaxId: 101510]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator RHA1 ro03468
species: Rhodococcus sp. RHA1 [TaxId: 101510]

Probab=88.86  E-value=0.21  Score=29.70  Aligned_cols=40  Identities=18%  Similarity=0.222  Sum_probs=31.9

Q ss_pred             HHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          162 QQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       162 ~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      +.++.++.+         .+.+. .. ++|+++||++.|+|+..+|+-|+.
T Consensus         4 ~~Il~aA~~---------l~~~~-G~-~~t~~~Ia~~agvs~~~~Y~~F~~   43 (70)
T d2hkua1           4 DALFTAATE---------LFLEH-GE-GVPITQICAAAGAHPNQVTYYYGS   43 (70)
T ss_dssp             HHHHHHHHH---------HHHHH-CT-TSCHHHHHHHHTCCHHHHHHHHSS
T ss_pred             HHHHHHHHH---------HHHhc-cc-CchHHHHHHHHCCChhhHHhcCCC
Confidence            467777777         35554 44 799999999999999999998764

>d2id6a1 a.4.1.9 (A:1-75) Transcriptional regulator TM1030 {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator TM1030
species: Thermotoga maritima [TaxId: 2336]

Probab=88.60  E-value=0.056  Score=32.77  Aligned_cols=41  Identities=10%  Similarity=0.050  Sum_probs=30.6

Q ss_pred             HHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          162 QQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       162 ~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      +++++++.+          ++..-...++|+.+||.++++|+..+|+-|+.
T Consensus         6 ~~Il~aa~~----------l~~~~G~~~~ti~~Ia~~agvs~~~iY~~F~~   46 (75)
T d2id6a1           6 DAILKAAVE----------VFGKKGYDRATTDEIAEKAGVAKGLIFHYFKN   46 (75)
T ss_dssp             HHHHHHHHH----------HHHHHHHHHCCHHHHHHHHTCCTHHHHHHHSS
T ss_pred             HHHHHHHHH----------HHHHhCccccCHHHHHHHhCCCHHHHHHHCCC
Confidence            455666666          33333455899999999999999999998864

>d1etxa_ a.4.1.12 (A:) FIS protein {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: FIS-like
domain: FIS protein
species: Escherichia coli [TaxId: 562]

Probab=88.33  E-value=0.15  Score=32.09  Aligned_cols=41  Identities=12%  Similarity=0.029  Sum_probs=32.0

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcc
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRL  209 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~  209 (226)
                      .+..+..+|+-        .|.+.+...+-++...|..||++|..|||+
T Consensus        42 ~~~~l~e~E~~--------~i~~aL~~~~gn~~~aA~~LGisR~tL~~k   82 (89)
T d1etxa_          42 YELVLAEVEQP--------LLDMVMQYTRGNATRAALMMGINRGTLRKK   82 (89)
T ss_dssp             HHHHHHHHHHH--------HHHHHHHHTTTCHHHHHHHHTSCHHHHHHH
T ss_pred             HHHHHHHHHHH--------HHHHHHHHcCCcHHHHHHHHCCCHHHHHHH
Confidence            34455555553        577777778899999999999999999974

>d1thfd_ c.1.2.1 (D:) Cyclase subunit (or domain) of imidazoleglycerolphosphate synthase HisF {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: Ribulose-phoshate binding barrel
family: Histidine biosynthesis enzymes
domain: Cyclase subunit (or domain) of imidazoleglycerolphosphate synthase HisF
species: Thermotoga maritima [TaxId: 2336]

Probab=87.62  E-value=3.2  Score=30.68  Aligned_cols=81  Identities=16%  Similarity=0.217  Sum_probs=60.2

Q ss_pred             CHHHHHHHHHhCCCCceEEEEccCCCC-CCH--HHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEe------C
Q 027234           10 RAEIALDMLRTNKNGYDIVISDVHMPD-MDG--FKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT------K   80 (226)
Q Consensus        10 ~~~eal~~l~~~~~~~DlVl~D~~mp~-~dG--~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~------K   80 (226)
                      +..+.+..+.+.. .=.++++|+.--+ +.|  +++++.++.....|+|+-.+-.+.+...+++..|+++.+.      .
T Consensus       152 ~~~~~~~~~~~~g-~~eii~tdI~~dGt~~G~d~~ll~~i~~~~~~pvi~~GGv~s~~di~~l~~~g~~gvivgsal~~~  230 (253)
T d1thfd_         152 LLRDWVVEVEKRG-AGEILLTSIDRDGTKSGYDTEMIRFVRPLTTLPIIASGGAGKMEHFLEAFLAGADAALAASVFHFR  230 (253)
T ss_dssp             EHHHHHHHHHHTT-CSEEEEEETTTTTSCSCCCHHHHHHHGGGCCSCEEEESCCCSHHHHHHHHHTTCSEEEESHHHHTT
T ss_pred             hHHHHHHHHHhcc-CCEEEEEEecccCccCCccccccccccccccceEEEecCCCCHHHHHHHHHCCCCEEEEchHHHcC
Confidence            4567777766643 2359999998755 455  6778888877889999888888899999999999999874      3


Q ss_pred             CCCHHHHHHHH
Q 027234           81 PVRIEELKNIW   91 (226)
Q Consensus        81 P~~~~~L~~~l   91 (226)
                      -++..+++..+
T Consensus       231 ~~~~~~~k~~l  241 (253)
T d1thfd_         231 EIDVRELKEYL  241 (253)
T ss_dssp             CSCHHHHHHHH
T ss_pred             CCCHHHHHHHH
Confidence            45666655443

>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=87.49  E-value=2  Score=29.91  Aligned_cols=83  Identities=13%  Similarity=-0.013  Sum_probs=52.9

Q ss_pred             CCcEEEE---ECCHHHHHHHHHhCCCCceEEEEccCCCCC--CHHHHHHHHhcC--CCCcEEEEeccCCHHHHHHHHhCC
Q 027234            1 MGFSVTK---CNRAEIALDMLRTNKNGYDIVISDVHMPDM--DGFKLLELVGLE--MDLPVIMMCAHGSKEVVMKGVTHD   73 (226)
Q Consensus         1 lg~~V~~---~~~~~eal~~l~~~~~~~DlVl~D~~mp~~--dG~~l~~~l~~~--~~~pvI~ls~~~~~~~~~~a~~~g   73 (226)
                      .||+|..   ..+.++..+.+.+..  +|+|.+...+...  .--++++.|+..  .+++| ++-+....+......+.|
T Consensus        64 ~G~eVi~lg~~~~~e~iv~aa~~~~--advI~iSs~~~~~~~~~~~l~~~L~~~g~~~v~V-ivGG~ip~~d~~~l~~~G  140 (168)
T d7reqa2          64 LGFDVDVGPLFQTPEETARQAVEAD--VHVVGVSSLAGGHLTLVPALRKELDKLGRPDILI-TVGGVIPEQDFDELRKDG  140 (168)
T ss_dssp             TTCEEEECCTTBCHHHHHHHHHHHT--CSEEEEEECSSCHHHHHHHHHHHHHHTTCTTSEE-EEEESCCGGGHHHHHHHT
T ss_pred             CCcceecCCCcCcHHHHHHHHHccC--CCEEEEecCcccchHHHHHHHHHHHhcCCCCeEE-EEeCCCCHHHHHHHHhCC
Confidence            4788875   347889999998876  9999998776552  223344555543  23433 354444455556677899


Q ss_pred             cceEEeCCCCHHH
Q 027234           74 ACDYLTKPVRIEE   86 (226)
Q Consensus        74 a~~yl~KP~~~~~   86 (226)
                      +++.+..--+..+
T Consensus       141 v~~iF~pgt~~~e  153 (168)
T d7reqa2         141 AVEIYTPGTVIPE  153 (168)
T ss_dssp             EEEEECTTCCHHH
T ss_pred             CCEEECcCCCHHH
Confidence            9987765444443

>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=87.32  E-value=0.59  Score=32.90  Aligned_cols=69  Identities=6%  Similarity=-0.099  Sum_probs=47.2

Q ss_pred             EEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceE
Q 027234            5 VTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDY   77 (226)
Q Consensus         5 V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~y   77 (226)
                      .+.+.+.+++.+.+...   +|+|++|=.-|. +=-+.++.++......++-.|+.-+.+.+......|+|..
T Consensus        83 ~VEv~s~~q~~~a~~~~---~diImLDN~sp~-~~k~~v~~~~~~~~~i~lEaSGgI~~~ni~~ya~~GvD~I  151 (169)
T d1qpoa1          83 EVEVDSLEQLDAVLPEK---PELILLDNFAVW-QTQTAVQRRDSRAPTVMLESSGGLSLQTAATYAETGVDYL  151 (169)
T ss_dssp             EEEESSHHHHHHHGGGC---CSEEEEETCCHH-HHHHHHHHHHHHCTTCEEEEESSCCTTTHHHHHHTTCSEE
T ss_pred             EEEeccHHHhhhhhhcC---CcEEEecCcChH-hHHHHHHHhhccCCeeEEEEeCCCCHHHHHHHHHcCCCEE
Confidence            45789999999988753   899999943332 2223334444333345667888888888888888888754

>d1y7ya1 a.35.1.3 (A:5-73) Restriction-modification controller protein C.AhdI {Aeromonas hydrophila [TaxId: 644]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Restriction-modification controller protein C.AhdI
species: Aeromonas hydrophila [TaxId: 644]

Probab=86.77  E-value=0.16  Score=30.06  Aligned_cols=30  Identities=27%  Similarity=0.352  Sum_probs=26.2

Q ss_pred             HHHhhCCCCCCHHHHHHHhhhhhhhhhccc
Q 027234          181 ILELMNIPGLTRENVASHLQKHRLYLSRLS  210 (226)
Q Consensus       181 I~~~~~~~~lt~~~va~~l~~~r~~l~r~~  210 (226)
                      |.+....-++|++++|..+++++++++++-
T Consensus        14 ik~~R~~~gltq~~lA~~~gis~~~i~~~E   43 (69)
T d1y7ya1          14 LRELRTAKGLSQETLAFLSGLDRSYVGGVE   43 (69)
T ss_dssp             HHHHHHHTTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHhHhCCCHHHHHHHH
Confidence            666677779999999999999999999863

>d1t33a1 a.4.1.9 (A:1-88) Putative transcriptional repressor YbiH {Salmonella typhimurium [TaxId: 90371]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional repressor YbiH
species: Salmonella typhimurium [TaxId: 90371]

Probab=85.96  E-value=0.23  Score=30.87  Aligned_cols=41  Identities=12%  Similarity=0.153  Sum_probs=30.8

Q ss_pred             HHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcccCC
Q 027234          161 HQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRLSGV  212 (226)
Q Consensus       161 ~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~  212 (226)
                      .++++.++.+          ++..-.... |..+||++.++|+..+|+-|+.
T Consensus        14 r~~Il~aa~~----------l~~~~G~~~-t~~~Ia~~agvs~~~~Y~~F~s   54 (88)
T d1t33a1          14 KSQLIAAALA----------QFGEYGLHA-TTRDIAALAGQNIAAITYYFGS   54 (88)
T ss_dssp             HHHHHHHHHH----------HHHHHGGGS-CHHHHHHHHTSCHHHHHHHHSS
T ss_pred             HHHHHHHHHH----------HHHHhcccc-CHHHHHHHhCCChhhhhccCCC
Confidence            4677778777          333334445 8899999999999999998864

>d1b0na2 a.35.1.3 (A:1-68) SinR repressor, DNA-binding domain {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: SinR repressor, DNA-binding domain
species: Bacillus subtilis [TaxId: 1423]

Probab=85.47  E-value=0.12  Score=30.51  Aligned_cols=32  Identities=19%  Similarity=0.270  Sum_probs=26.3

Q ss_pred             HHHHhhCCCCCCHHHHHHHhhhhhhhhhcccC
Q 027234          180 KILELMNIPGLTRENVASHLQKHRLYLSRLSG  211 (226)
Q Consensus       180 ~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~  211 (226)
                      .|.+.+..-++|.+++|..+++++++++++-+
T Consensus         5 ~ik~~R~~~gltq~~la~~~gis~~~i~~~E~   36 (68)
T d1b0na2           5 RIKQYRKEKGYSLSELAEKAGVAKSYLSSIER   36 (68)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHc
Confidence            35555666799999999999999999998754

>d1ntca_ a.4.1.12 (A:) DNA-binding domain of NTRC {Salmonella typhimurium [TaxId: 90371]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: FIS-like
domain: DNA-binding domain of NTRC
species: Salmonella typhimurium [TaxId: 90371]

Probab=84.89  E-value=0.21  Score=31.39  Aligned_cols=42  Identities=10%  Similarity=-0.005  Sum_probs=34.4

Q ss_pred             hHHHHHHHHHHhCCCCCCchHHHHhhCCCCCCHHHHHHHhhhhhhhhhcc
Q 027234          160 LHQQFVSAVKELGFDKAGPKKILELMNIPGLTRENVASHLQKHRLYLSRL  209 (226)
Q Consensus       160 l~~~Fi~~~~~~g~~~~~p~~I~~~~~~~~lt~~~va~~l~~~r~~l~r~  209 (226)
                      +...++..+++.        .|...+...+-++...|..||++|..|||.
T Consensus        43 ~l~~~~~~~E~~--------lI~~aL~~~~Gn~~~AA~~LGI~R~TL~~K   84 (91)
T d1ntca_          43 LLSEAQPELERT--------LLTTALRHTQGHKQEAARLLGWGAATLTAK   84 (91)
T ss_dssp             HHHHHHHHHHHH--------HHHHHHHHTTTCTTHHHHHTTCCHHHHHHH
T ss_pred             HHHHHHHHHHHH--------HHHHHHHHhCCcHHHHHHHHCCCHHHHHHH
Confidence            355667777764        677888888999999999999999999974

>d1biaa1 a.4.5.1 (A:1-63) Biotin repressor, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Biotin repressor-like
domain: Biotin repressor, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=84.75  E-value=0.27  Score=28.59  Aligned_cols=29  Identities=17%  Similarity=0.243  Sum_probs=22.7

Q ss_pred             HHHHhhCC-CCCCHHHHHHHhhhhhhhhhc
Q 027234          180 KILELMNI-PGLTRENVASHLQKHRLYLSR  208 (226)
Q Consensus       180 ~I~~~~~~-~~lt~~~va~~l~~~r~~l~r  208 (226)
                      .|++.+.. ..+|.+++|++|++||+..+|
T Consensus         9 ~iL~~L~~~~~~s~~eLa~~l~vS~~ti~r   38 (63)
T d1biaa1           9 KLIALLANGEFHSGEQLGETLGMSRAAINK   38 (63)
T ss_dssp             HHHHHHTTSSCBCHHHHHHHHTSCHHHHHH
T ss_pred             HHHHHHHHCCcCCHHHHHHHHCcCHHHHHH
Confidence            35555544 347999999999999998876

>d1y0ea_ c.1.2.5 (A:) Putative N-acetylmannosamine-6-phosphate 2-epimerase NanE {Staphylococcus aureus [TaxId: 1280]}

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: Ribulose-phoshate binding barrel
family: NanE-like
domain: Putative N-acetylmannosamine-6-phosphate 2-epimerase NanE
species: Staphylococcus aureus [TaxId: 1280]

Probab=84.53  E-value=2  Score=30.64  Aligned_cols=72  Identities=17%  Similarity=0.141  Sum_probs=51.9

Q ss_pred             EEECCHHHHHHHHHhCCCCceEEEEccC-C--------CCCCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcce
Q 027234            6 TKCNRAEIALDMLRTNKNGYDIVISDVH-M--------PDMDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACD   76 (226)
Q Consensus         6 ~~~~~~~eal~~l~~~~~~~DlVl~D~~-m--------p~~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~   76 (226)
                      ....+..+++...+.   +.|.|..-.. .        +....++++.+++...++|||.-.+-.+.+.+.+++++||++
T Consensus       124 ~~~~t~~~a~~~~~~---g~d~i~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~iPVia~GGI~t~~d~~~~~~~GAdg  200 (222)
T d1y0ea_         124 ADIATVEEAKNAARL---GFDYIGTTLHGYTSYTQGQLLYQNDFQFLKDVLQSVDAKVIAEGNVITPDMYKRVMDLGVHC  200 (222)
T ss_dssp             EECSSHHHHHHHHHT---TCSEEECTTTTSSTTSTTCCTTHHHHHHHHHHHHHCCSEEEEESSCCSHHHHHHHHHTTCSE
T ss_pred             ecCCCHHHHHHHHHc---CCCeEEEeccCCcccccCccchhhHHHHHHHHHhcCCCcEEEeCCCCCHHHHHHHHHcCCCE
Confidence            356677888776653   3787764322 1        111236777777777889999888888999999999999999


Q ss_pred             EEeC
Q 027234           77 YLTK   80 (226)
Q Consensus        77 yl~K   80 (226)
                      .+.=
T Consensus       201 V~iG  204 (222)
T d1y0ea_         201 SVVG  204 (222)
T ss_dssp             EEEC
T ss_pred             EEEc
Confidence            9853

>d2icta1 a.35.1.3 (A:8-94) Antitoxin HigA {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Antitoxin HigA
species: Escherichia coli [TaxId: 562]

Probab=84.29  E-value=0.1  Score=32.62  Aligned_cols=29  Identities=21%  Similarity=0.170  Sum_probs=23.9

Q ss_pred             HHHhhCCCCCCHHHHHHHhhhhhhhhhcc
Q 027234          181 ILELMNIPGLTRENVASHLQKHRLYLSRL  209 (226)
Q Consensus       181 I~~~~~~~~lt~~~va~~l~~~r~~l~r~  209 (226)
                      |.+.+..-++|..++|..+|++++++.++
T Consensus         6 lke~r~~~glsq~~LA~~lGvs~~~is~i   34 (87)
T d2icta1           6 IQESLDELNVSLREFARAMEIAPSTASRL   34 (87)
T ss_dssp             HHHHHHHHTCCHHHHHHHHTCCHHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHhhcHHHHHHH
Confidence            44555556999999999999999998875

>d2a6ca1 a.35.1.13 (A:1-69) HTH-motif protein NE1354 {Nitrosomonas europaea [TaxId: 915]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE1354
domain: HTH-motif protein NE1354
species: Nitrosomonas europaea [TaxId: 915]

Probab=83.43  E-value=0.24  Score=29.28  Aligned_cols=32  Identities=25%  Similarity=0.188  Sum_probs=27.3

Q ss_pred             HHHHhhCCCCCCHHHHHHHhhhhhhhhhcccC
Q 027234          180 KILELMNIPGLTRENVASHLQKHRLYLSRLSG  211 (226)
Q Consensus       180 ~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~  211 (226)
                      .|.+.+..-++|..++|..+|+++.+++++..
T Consensus        10 ~i~~~r~~~gltq~elA~~~gv~~~~is~ie~   41 (69)
T d2a6ca1          10 VLQEHLRNSGLTQFKAAELLGVTQPRVSDLMR   41 (69)
T ss_dssp             HHHHHHHTTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHHHcCCCHHHHHHHHHcCHhHHHHHHc
Confidence            46666777899999999999999999998753

>d2o38a1 a.35.1.13 (A:28-116) Hypothetical protein RPA3824 {Rhodopseudomonas palustris [TaxId: 1076]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE1354
domain: Hypothetical protein RPA3824
species: Rhodopseudomonas palustris [TaxId: 1076]

Probab=83.03  E-value=0.17  Score=31.64  Aligned_cols=31  Identities=16%  Similarity=0.218  Sum_probs=26.7

Q ss_pred             HHHHhhCCCCCCHHHHHHHhhhhhhhhhccc
Q 027234          180 KILELMNIPGLTRENVASHLQKHRLYLSRLS  210 (226)
Q Consensus       180 ~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~  210 (226)
                      .|.+.+...|+|..++|.++++++.+++++-
T Consensus        15 ~i~~~r~~~gltq~~lA~~~gis~~~is~ie   45 (89)
T d2o38a1          15 ALNAVIDRARLSQAAAAARLGINQPKVSALR   45 (89)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHHHhhHhHHHHHH
Confidence            3666777789999999999999999999863

>d1g2ha_ a.4.1.12 (A:) Transcriptional regulator TyrR, C-terminal domain {Haemophilus influenzae [TaxId: 727]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: FIS-like
domain: Transcriptional regulator TyrR, C-terminal domain
species: Haemophilus influenzae [TaxId: 727]

Probab=83.00  E-value=0.16  Score=29.52  Aligned_cols=28  Identities=7%  Similarity=0.000  Sum_probs=20.8

Q ss_pred             HHHhhCCCCCCHHHHHHHhhhhhhhhhcc
Q 027234          181 ILELMNIPGLTRENVASHLQKHRLYLSRL  209 (226)
Q Consensus       181 I~~~~~~~~lt~~~va~~l~~~r~~l~r~  209 (226)
                      |.+.+...+ ++...|..||++|+.|||.
T Consensus        26 I~~aL~~~g-n~~~aA~~Lgisr~tL~rK   53 (61)
T d1g2ha_          26 LKLFYAEYP-STRKLAQRLGVSHTAIANK   53 (61)
T ss_dssp             HHHHHHHSC-SHHHHHHHTTSCTHHHHHH
T ss_pred             HHHHHHHCC-CHHHHHHHHCCCHHHHHHH
Confidence            334343434 6789999999999999974

>d1h5ya_ c.1.2.1 (A:) Cyclase subunit (or domain) of imidazoleglycerolphosphate synthase HisF {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: Ribulose-phoshate binding barrel
family: Histidine biosynthesis enzymes
domain: Cyclase subunit (or domain) of imidazoleglycerolphosphate synthase HisF
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=82.55  E-value=5.4  Score=29.41  Aligned_cols=81  Identities=17%  Similarity=0.168  Sum_probs=59.5

Q ss_pred             CHHHHHHHHHhCCCCceEEEEccCCCC-CCH--HHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEeC------
Q 027234           10 RAEIALDMLRTNKNGYDIVISDVHMPD-MDG--FKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLTK------   80 (226)
Q Consensus        10 ~~~eal~~l~~~~~~~DlVl~D~~mp~-~dG--~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~K------   80 (226)
                      +..+.++.+.+.. .=.++++|+.--+ +.|  +++++.++.....|+++--+-.+.+...++...|+++.+.-      
T Consensus       154 ~~~~~~~~~~~~g-~~eii~tdI~~dG~~~G~d~~~~~~i~~~~~~pii~~GGv~~~~di~~l~~~g~~gv~~gs~l~~~  232 (252)
T d1h5ya_         154 DAVKWAKEVEELG-AGEILLTSIDRDGTGLGYDVELIRRVADSVRIPVIASGGAGRVEHFYEAAAAGADAVLAASLFHFR  232 (252)
T ss_dssp             EHHHHHHHHHHHT-CSEEEEEETTTTTTCSCCCHHHHHHHHHHCSSCEEEESCCCSHHHHHHHHHTTCSEEEESHHHHTT
T ss_pred             CHHHHHHHHHhcC-CCEEEEEeecccCccCCcCHHHHHHHHHhcCCCEEEecCCCCHHHHHHHHHCCCCEEEEhhHHHcC
Confidence            4566676666542 2378999997755 455  77888888667899998888888899999999999998753      


Q ss_pred             CCCHHHHHHHH
Q 027234           81 PVRIEELKNIW   91 (226)
Q Consensus        81 P~~~~~L~~~l   91 (226)
                      -++..+++..+
T Consensus       233 ~~~~~~lk~~l  243 (252)
T d1h5ya_         233 VLSIAQVKRYL  243 (252)
T ss_dssp             SSCHHHHHHHH
T ss_pred             CCCHHHHHHHH
Confidence            45566655443

>d2np3a1 a.4.1.9 (A:35-99) Putative transcriptional regulator SCO0857 {Streptomyces coelicolor [TaxId: 1902]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator SCO0857
species: Streptomyces coelicolor [TaxId: 1902]

Probab=81.96  E-value=0.23  Score=28.98  Aligned_cols=28  Identities=7%  Similarity=0.124  Sum_probs=2.1

Q ss_pred             CCCCCCHHHHHHHhhhhhhhhhcccCCC
Q 027234          186 NIPGLTRENVASHLQKHRLYLSRLSGVS  213 (226)
Q Consensus       186 ~~~~lt~~~va~~l~~~r~~l~r~~~~~  213 (226)
                      .-.++|+++||...++|+..+|+-|+.-
T Consensus        13 G~~~~s~~~IA~~agvs~~~ly~~F~sK   40 (65)
T d2np3a1          13 GFDATSLRRIAETAGVDQSLVHHFYGTK   40 (65)
T ss_dssp             ------------------------CCC-
T ss_pred             CcccCCHHHHHHHHCcCHHHHHHHCCCH
Confidence            3457899999999999999999988753

>d2auwa1 a.35.1.10 (A:88-154) Hypothetical protein NE0471 C-terminal domain {Nitrosomonas europaea [TaxId: 915]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE0471 C-terminal domain-like
domain: Hypothetical protein NE0471 C-terminal domain
species: Nitrosomonas europaea [TaxId: 915]

Probab=81.59  E-value=0.25  Score=29.24  Aligned_cols=28  Identities=21%  Similarity=0.145  Sum_probs=22.1

Q ss_pred             HHHhhCCCCCCHHHHHHHhhhhhhhhhc
Q 027234          181 ILELMNIPGLTRENVASHLQKHRLYLSR  208 (226)
Q Consensus       181 I~~~~~~~~lt~~~va~~l~~~r~~l~r  208 (226)
                      +.+....-++|..++|..||+|+..+.+
T Consensus         6 ~k~~R~~~gltQ~elA~~LGvs~~ti~~   33 (67)
T d2auwa1           6 FGDWMHRNNLSLTTAAEALGISRRMVSY   33 (67)
T ss_dssp             HHHHHHHTTCCHHHHHHHHTSCHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHH
Confidence            3444444599999999999999998765

>d1ka9f_ c.1.2.1 (F:) Cyclase subunit (or domain) of imidazoleglycerolphosphate synthase HisF {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: Ribulose-phoshate binding barrel
family: Histidine biosynthesis enzymes
domain: Cyclase subunit (or domain) of imidazoleglycerolphosphate synthase HisF
species: Thermus thermophilus [TaxId: 274]

Probab=81.48  E-value=2.9  Score=30.86  Aligned_cols=69  Identities=17%  Similarity=0.173  Sum_probs=52.8

Q ss_pred             CHHHHHHHHHhCCCCceEEEEccCCCC-CCH--HHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcceEEe
Q 027234           10 RAEIALDMLRTNKNGYDIVISDVHMPD-MDG--FKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDACDYLT   79 (226)
Q Consensus        10 ~~~eal~~l~~~~~~~DlVl~D~~mp~-~dG--~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~~yl~   79 (226)
                      +..+.+..+.+. ..-.++++|+.--+ +.|  +++++.+.....+|+|+-.+..+.+...++++.|+.+.+.
T Consensus       152 ~~~~~~~~~~~~-g~~eii~tdi~~dG~~~G~d~~l~~~i~~~~~~pii~~GGv~~~~dl~~l~~~g~~gvii  223 (251)
T d1ka9f_         152 HAVEWAVKGVEL-GAGEILLTSMDRDGTKEGYDLRLTRMVAEAVGVPVIASGGAGRMEHFLEAFQAGAEAALA  223 (251)
T ss_dssp             EHHHHHHHHHHH-TCCEEEEEETTTTTTCSCCCHHHHHHHHHHCSSCEEEESCCCSHHHHHHHHHTTCSEEEE
T ss_pred             cHHHHHHHHHhc-CCCEEEEEeecccCccCCcchhHHHHHHhhcceeEEEecCCCCHHHHHHHHHCCCCEEEE
Confidence            455666655554 23579999997654 344  7788888777789999888888999999999999999875

>d2r1jl1 a.35.1.2 (L:3-68) P22 C2 repressor, DNA-binding domain {Salmonella bacteriophage P22 [TaxId: 10754]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: P22 C2 repressor, DNA-binding domain
species: Salmonella bacteriophage P22 [TaxId: 10754]

Probab=81.22  E-value=0.14  Score=29.92  Aligned_cols=31  Identities=6%  Similarity=0.063  Sum_probs=25.7

Q ss_pred             HHHHhhCCCCCCHHHHHHHhhhhhhhhhccc
Q 027234          180 KILELMNIPGLTRENVASHLQKHRLYLSRLS  210 (226)
Q Consensus       180 ~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~  210 (226)
                      .|.+.+...++|+.++|..+++++++++++-
T Consensus         7 rik~~R~~~g~tq~~lA~~~gvs~~~i~~~e   37 (66)
T d2r1jl1           7 RIRARRKKLKIRQAALGKMVGVSNVAISQWE   37 (66)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence            4556666679999999999999999998763

>d1y9qa1 a.35.1.8 (A:4-82) Probable transcriptional regulator VC1968, N-terminal domain {Vibrio cholerae [TaxId: 666]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Probable transcriptional regulator VC1968, N-terminal domain
domain: Probable transcriptional regulator VC1968, N-terminal domain
species: Vibrio cholerae [TaxId: 666]

Probab=81.17  E-value=0.3  Score=29.54  Aligned_cols=33  Identities=15%  Similarity=0.173  Sum_probs=26.5

Q ss_pred             HHHhhCCCCCCHHHHHHHhhhhhhhhhcccCCC
Q 027234          181 ILELMNIPGLTRENVASHLQKHRLYLSRLSGVS  213 (226)
Q Consensus       181 I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~~~  213 (226)
                      |.+.+..-++|.+++|..+++++++++++.+-.
T Consensus        13 lr~~R~~~g~sq~~lA~~~gis~~~i~~~E~g~   45 (79)
T d1y9qa1          13 LKNLRKSRGLSLDATAQLTGVSKAMLGQIERGE   45 (79)
T ss_dssp             HHHHHHHTTCCHHHHHHHHSSCHHHHHHHHTTC
T ss_pred             HHHHHHHcCCCHHHHHHHHCcchhHHHHHHcCC
Confidence            455555669999999999999999999875543

>d1wv2a_ c.1.31.1 (A:) Thiazole biosynthesis protein ThiG {Pseudomonas aeruginosa [TaxId: 287]}

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: ThiG-like
family: ThiG-like
domain: Thiazole biosynthesis protein ThiG
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=80.82  E-value=8.6  Score=28.24  Aligned_cols=93  Identities=13%  Similarity=0.062  Sum_probs=62.9

Q ss_pred             CcEEEE-ECCHHHHHHHHHhCCCCceEEEEccCCCC-----CCHHHHHHHHhcCCCCcEEEEeccCCHHHHHHHHhCCcc
Q 027234            2 GFSVTK-CNRAEIALDMLRTNKNGYDIVISDVHMPD-----MDGFKLLELVGLEMDLPVIMMCAHGSKEVVMKGVTHDAC   75 (226)
Q Consensus         2 g~~V~~-~~~~~eal~~l~~~~~~~DlVl~D~~mp~-----~dG~~l~~~l~~~~~~pvI~ls~~~~~~~~~~a~~~ga~   75 (226)
                      ||.|.. +++---+-+.+..-.  ... ++-+.-|-     ..--..++.++.+.++|||+=.+-...+.+..++++|++
T Consensus       127 gF~Vlpy~~~D~v~ak~le~~G--c~~-vMplgsPIGsg~Gi~n~~~l~~i~~~~~vpvivdAGIg~psdaa~AMElG~d  203 (243)
T d1wv2a_         127 GFDVMVYTSDDPIIARQLAEIG--CIA-VMPLAGLIGSGLGICNPYNLRIILEEAKVPVLVDAGVGTASDAAIAMELGCE  203 (243)
T ss_dssp             TCEEEEEECSCHHHHHHHHHSC--CSE-EEECSSSTTCCCCCSCHHHHHHHHHHCSSCBEEESCCCSHHHHHHHHHHTCS
T ss_pred             ceEEEeccCCCHHHHhHHHHcC--cee-eeecccccccccccccHHHHHhccccCCcceEeecccCCHHHHHHHHHccCC
Confidence            566653 332222333444332  444 44555562     333344566666688999999999999999999999999


Q ss_pred             eEEe-----CCCCHHHHHHHHHHHHHH
Q 027234           76 DYLT-----KPVRIEELKNIWQHVVRK   97 (226)
Q Consensus        76 ~yl~-----KP~~~~~L~~~l~~~~~~   97 (226)
                      +.|.     |--++..+...++.....
T Consensus       204 gVLvnsaIa~A~dP~~mA~A~~~Av~a  230 (243)
T d1wv2a_         204 AVLMNTAIAHAKDPVMMAEAMKHAIVA  230 (243)
T ss_dssp             EEEESHHHHTSSSHHHHHHHHHHHHHH
T ss_pred             EEEechHhhcCCCHHHHHHHHHHHHHH
Confidence            9984     678888888888776654

>d1utxa_ a.35.1.3 (A:) Putative transcription regulator CylR2 {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Putative transcription regulator CylR2
species: Enterococcus faecalis [TaxId: 1351]

Probab=80.33  E-value=0.18  Score=29.59  Aligned_cols=32  Identities=9%  Similarity=0.177  Sum_probs=26.2

Q ss_pred             HHHHhhCCCCCCHHHHHHHhhhhhhhhhcccC
Q 027234          180 KILELMNIPGLTRENVASHLQKHRLYLSRLSG  211 (226)
Q Consensus       180 ~I~~~~~~~~lt~~~va~~l~~~r~~l~r~~~  211 (226)
                      .|.+.+...++|..++|..+++++++++++-.
T Consensus         5 ri~~lR~~~g~tq~elA~~~gis~~~is~~e~   36 (66)
T d1utxa_           5 NLKLIREKKKISQSELAALLEVSRQTINGIEK   36 (66)
T ss_dssp             CHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHHHcCCCHHHHHHhcccCHHHHHHHHc
Confidence            45566667799999999999999999988643

>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=80.28  E-value=6.2  Score=26.26  Aligned_cols=94  Identities=13%  Similarity=0.165  Sum_probs=59.0

Q ss_pred             cEEEEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHh-cCCCCcEEEEeccCCHHHH--HHHHhCCcceEEe
Q 027234            3 FSVTKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVG-LEMDLPVIMMCAHGSKEVV--MKGVTHDACDYLT   79 (226)
Q Consensus         3 ~~V~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~-~~~~~pvI~ls~~~~~~~~--~~a~~~ga~~yl~   79 (226)
                      |.+..+.++++.++++++++..+|.+|+--.  +.+-..+...+. +.--.|+|++...+.....  ..-+-+.......
T Consensus        29 Y~l~~~~s~~ef~~~le~~~e~iDcLVl~~~--~~~l~~l~~qL~~~GlLlPaViv~~~~~~~~~~~~~~~~YH~aEv~l  106 (135)
T d1r8ja2          29 YQLQVCESGEMLLEYAQTHRDQIDCLILVAA--NPSFRAVVQQLCFEGVVVPAIVVGDRDSEDPDEPAKEQLYHSAELHL  106 (135)
T ss_dssp             EEEEEECSHHHHHHHHHHSTTSCSEEEEETT--STTHHHHHHHHHHTTCCCCEEEESCCC------CCSSCSSBTTCEEE
T ss_pred             eEEEEcCCHHHHHHHHHhCcccCCEEEEEec--CCccHHHHHHHHhcCccccEEEEecCCCCCCCCCCCceeeeeeeEEc
Confidence            7888999999999999998888999876222  233445556775 4456899888543322111  1111233334455


Q ss_pred             CCCCHHHHHHHHHHHHHHH
Q 027234           80 KPVRIEELKNIWQHVVRKR   98 (226)
Q Consensus        80 KP~~~~~L~~~l~~~~~~~   98 (226)
                      ++-..++|-..|.+++.+-
T Consensus       107 ~~~qL~ql~~~ID~AIsrF  125 (135)
T d1r8ja2         107 GIHQLEQLPYQVDAALAEF  125 (135)
T ss_dssp             CTTCGGGHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHH
Confidence            6666688888888777543

>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=80.14  E-value=7.2  Score=26.93  Aligned_cols=63  Identities=13%  Similarity=0.066  Sum_probs=46.0

Q ss_pred             EEECCHHHHHHHHHhCCCCceEEEEccCCCCCCHHHHHHHHhc-CCCCcEEEEeccCCHHHHHHHHhCCcce
Q 027234            6 TKCNRAEIALDMLRTNKNGYDIVISDVHMPDMDGFKLLELVGL-EMDLPVIMMCAHGSKEVVMKGVTHDACD   76 (226)
Q Consensus         6 ~~~~~~~eal~~l~~~~~~~DlVl~D~~mp~~dG~~l~~~l~~-~~~~pvI~ls~~~~~~~~~~a~~~ga~~   76 (226)
                      +++.+.+++.+.+...   +|+|++|=    |+--++.+.++. .+.+ .+-.|+.-+.+.+......|+|.
T Consensus        84 VEv~~~~~~~~a~~~g---~diImLDN----~~pe~~~~av~~i~~~~-~lEaSGgI~~~ni~~ya~~GVD~  147 (167)
T d1qapa1          84 VEVENLDELDDALKAG---ADIIMLDN----FNTDQMREAVKRVNGQA-RLEVSGNVTAETLREFAETGVDF  147 (167)
T ss_dssp             EEESSHHHHHHHHHTT---CSEEEESS----CCHHHHHHHHHTTCTTC-CEEECCCSCHHHHHHHHHTTCSE
T ss_pred             EecCcHHHHHHHHhcC---CcEEEecC----CCHHHHHHHHHhcCCce-EEEEeCCCCHHHHHHHHHcCCCE
Confidence            5788999999888743   89999994    444455555553 2333 35579989999999999999883

>d1vz0a1 a.4.14.1 (A:116-208) Putative partitioning protein ParB/Spo0J {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: KorB DNA-binding domain-like
family: KorB DNA-binding domain-like
domain: Putative partitioning protein ParB/Spo0J
species: Thermus thermophilus [TaxId: 274]

Probab=80.01  E-value=0.52  Score=29.68  Aligned_cols=21  Identities=38%  Similarity=0.477  Sum_probs=19.1

Q ss_pred             CCCCHHHHHHHhhhhhhhhhc
Q 027234          188 PGLTRENVASHLQKHRLYLSR  208 (226)
Q Consensus       188 ~~lt~~~va~~l~~~r~~l~r  208 (226)
                      -++|.++||..+|+||+|++.
T Consensus        18 ~g~t~~~iA~~~Gks~~~V~~   38 (93)
T d1vz0a1          18 MGLTQEEVARRVGKARSTVAN   38 (93)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHH
T ss_pred             cCCCHHHHHHHHccchHHHHH
Confidence            489999999999999999875