Citrus Sinensis ID: 023816

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270------
Protein Sequence
MTTTNGVASLRLISDEIDGFDLSPSDTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSDVKRIKDYLTRDVNLGNEGRGINKRKARESCDLSSSPPSVITSSSSPSSPSSPFRSPSILSSSAPCSPPSTLDSPTSRLKMTISD
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccEEEEEcccHHHHHHHHHHHHHcccEEEEEccHHHHHHHHcccHHHHccccccccccEEEEEcccccccHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccEEEEEccccHHHHHHHHHccccccccccccHHHHHHHHHHHHHcccccccccccHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccHHHHHccccc
Secondary Structure Prediction (SSPRO)
ccccccEEEEEcccccccccccccccccccEEEEEcccHHHHHHHHHHHHHcccEEEEEccHHHHHHHHccccccccccccccEEEEEEEEcccccccHHHHHHHHHHccccccccEEEEEccccHHHHHHHHHccccHHcccccccHHccccccccccEEEEEccccHHHHHHHHHccHHHHccccccHHHHHHHHHHHHHccccccccccccHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mtttngvaSLRLIsdeidgfdlspsdteeVHVLavddsfvdRKVIERLLTISSCKVTAVDSGRRALqflgldeeqsingfdglkVDLIITdycmpgmtgYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSIcfcfpfffpsnnleqdssalreipvviMSSENILARIDRCLEdgaedfivkpvklsdvkRIKDYLTrdvnlgnegrginkrkarescdlsssppsvitsssspsspsspfrspsilsssapcsppstldsptsrlkmtisd
Flexible Loop (DISEMBL)
mtttngvaslrlisdeidgfdlspsDTEEVHVlavddsfvdrKVIERLLtissckvtavdSGRRALQFlgldeeqsingfdgLKVDLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGaedfivkpvklsdvkrikdyltrdvnlgnegrginkrkarescdlsssppsvitsssspsspsSPFRSPSILsssapcsppstldsptsrlkmtisd
Low Complexity Region (SEG)
MTTTNGVASLRLISDEIDGFDLSPSDTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTiivflnlqnlflfilsicfcfpfffpsnnlEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSDVKRIKDYLTRDVNLGNEGRGINKRKARESCDLsssppsvitsssspsspsspfrspsilsssapcsppsTLDSPTSRLKMTISD
Disordered region (IsUnstruct)
***********LISDEIDGFD*****TEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSDVKRIKDYLTRDVNL**********************************************************************
Disordered Region (DISOPRED)
******************************HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKV*************FLNLQNLFLFILSIC****************SALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSDVKRIKDYL****************************************************************************
Disordered Region (DISEMBL)
MTTTNGVASLRLISDEIDGFDLSPSDTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSDVKRIKDYLTRDVNLGNEGRGINKR************************************************************
Disordered Region (DISPRO)
***********L*********L*****EEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSDVKRIKDYLTRDV************************************************************************
Transmembrane Helix (TMHMM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MTTTNGVASLRLISDEIDGFDLSPSDTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSDVKRIKDYLTRDVNLGNEGRGINKRKARESCDLSSSPPSVITSSSSPSSPSSPFRSPSILSSSAPCSPPSTLDSPTSRLKMTISD
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	276	2.2.26 [Sep-21-2011]
Q9ZWS9	231	Two-component response re	yes	no	0.793	0.948	0.490	2e-55
O82798	259	Two-component response re	no	no	0.615	0.656	0.538	2e-53
Q9ZWS6	186	Two-component response re	no	no	0.521	0.774	0.547	7e-46
Q9SB04	184	Two-component response re	no	no	0.471	0.706	0.568	9e-45
Q7G8V2	206	Two-component response re	no	no	0.474	0.635	0.540	1e-43
Q9ZWS7	206	Two-component response re	no	no	0.565	0.757	0.502	6e-43
Q9SHC2	164	Two-component response re	no	no	0.5	0.841	0.451	4e-36
O80366	234	Two-component response re	no	no	0.474	0.559	0.451	6e-36
Q9FPR6	153	Two-component response re	no	no	0.471	0.849	0.459	8e-36
O80365	225	Two-component response re	no	no	0.467	0.573	0.455	5e-35

>sp|Q9ZWS9|ARR3_ARATH Two-component response regulator ARR3 OS=Arabidopsis thaliana GN=ARR3 PE=2 SV=1

 Score =  216 bits (549), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 133/271 (49%), Positives = 163/271 (60%), Gaps = 52/271 (19%)

Query: 1   MTTTNGVASLR---LISDEIDGFDLSPSDTEEVHVLAVDDSFVDRKVIERLLTISSCKVT 57
           M    GV+ LR   +I   I   +  P D+++VHVLAVDDS VDR VIERLL I+SCKVT
Sbjct: 1   MAKDGGVSCLRRSEMIGIGIGELESPPLDSDQVHVLAVDDSLVDRIVIERLLRITSCKVT 60

Query: 58  AVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVTTPFNFLYS 117
           AVDSG RAL+FLGLD++++   FD LKVDLIITDYCMPGMTGYELLKKIK +T F     
Sbjct: 61  AVDSGWRALEFLGLDDDKAAVEFDRLKVDLIITDYCMPGMTGYELLKKIKESTSF----- 115

Query: 118 TIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLE 177
                                                 +E+PVVIMSSEN++ RIDRCLE
Sbjct: 116 --------------------------------------KEVPVVIMSSENVMTRIDRCLE 137

Query: 178 DGAEDFIVKPVKLSDVKRIKDYLTRDVNLGNEGRGINKRKARESCDLS--SSPPSVITSS 235
           +GAEDF++KPVKL+DVKR++ YLTRDV +  EG   NKRK          S+  S+ +S 
Sbjct: 138 EGAEDFLLKPVKLADVKRLRSYLTRDVKVAAEG---NKRKLTTPPPPPPLSATSSMESSD 194

Query: 236 SSPSSPSSPFRSPSILSSSAPCSPPSTLDSP 266
           S+  SP S       L+ S P S  S +DSP
Sbjct: 195 STVESPLSMVDDEDSLTMS-PESATSLVDSP 224

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. Type-A response regulators seem to act as negative regulators of the cytokinin signaling.
Arabidopsis thaliana (taxid: 3702)

>sp|O82798|ARR4_ARATH Two-component response regulator ARR4 OS=Arabidopsis thaliana GN=ARR4 PE=1 SV=1

 Score =  209 bits (531), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 119/221 (53%), Positives = 140/221 (63%), Gaps = 51/221 (23%)

Query: 1   MTTTNGVASLR----LISDEIDGFDLSPSDTEEVHVLAVDDSFVDRKVIERLLTISSCKV 56
           M    GV+ LR    +    I G + +P D +EVHVLAVDDS VDR VIERLL I+SCKV
Sbjct: 1   MARDGGVSCLRRSEMMSVGGIGGIESAPLDLDEVHVLAVDDSLVDRIVIERLLRITSCKV 60

Query: 57  TAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVTTPFNFLY 116
           TAVDSG RAL+FLGLD E++   FD LKVDLIITDYCMPGMTGYELLKKIK         
Sbjct: 61  TAVDSGWRALEFLGLDNEKASAEFDRLKVDLIITDYCMPGMTGYELLKKIK--------- 111

Query: 117 STIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCL 176
                                             +SS  RE+PVVIMSSEN+L RIDRCL
Sbjct: 112 ----------------------------------ESSNFREVPVVIMSSENVLTRIDRCL 137

Query: 177 EDGAEDFIVKPVKLSDVKRIKDYLTRDVNLGNEGRGINKRK 217
           E+GA+DF++KPVKL+DVKR++ +LT+DV L N     NKRK
Sbjct: 138 EEGAQDFLLKPVKLADVKRLRSHLTKDVKLSNG----NKRK 174

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. Type-A response regulators seem to act as negative regulators of the cytokinin signaling. Modulates red light signaling through its interaction with the phytochrome B photoreceptor.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9ZWS6|ARR6_ARATH Two-component response regulator ARR6 OS=Arabidopsis thaliana GN=ARR6 PE=1 SV=2

 Score =  184 bits (467), Expect = 7e-46,   Method: Compositional matrix adjust.
 Identities = 103/188 (54%), Positives = 121/188 (64%), Gaps = 44/188 (23%)

Query: 30  VHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLII 89
           +HVLAVDDS VDRK IERLL +SSCKVT VDS  RALQ+LGLD E+   GF+ LKV+LI+
Sbjct: 25  LHVLAVDDSHVDRKFIERLLRVSSCKVTVVDSATRALQYLGLDVEEKSVGFEDLKVNLIM 84

Query: 90  TDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLE 149
           TDY MPGMTGYELLKKIK                                          
Sbjct: 85  TDYSMPGMTGYELLKKIK------------------------------------------ 102

Query: 150 QDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSDVKRIKDYLTRDVNLGNE 209
            +SSA RE+PVVIMSSENIL RIDRCLE+GAEDF++KPVKLSDVKR++D L +  +L   
Sbjct: 103 -ESSAFREVPVVIMSSENILPRIDRCLEEGAEDFLLKPVKLSDVKRLRDSLMKVEDLSF- 160

Query: 210 GRGINKRK 217
            + I KR+
Sbjct: 161 TKSIQKRE 168

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. Type-A response regulators seem to act as negative regulators of the cytokinin signaling.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SB04|ARR5_ARATH Two-component response regulator ARR5 OS=Arabidopsis thaliana GN=ARR5 PE=1 SV=2

 Score =  180 bits (457), Expect = 9e-45,   Method: Compositional matrix adjust.
 Identities = 99/174 (56%), Positives = 114/174 (65%), Gaps = 44/174 (25%)

Query: 30  VHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLD-EEQSINGFDGLKVDLI 88
           +HVLAVDDS VDRK IERLL +SSCKVT VDS  RALQ+LGLD E  S  GF+ LK++LI
Sbjct: 25  LHVLAVDDSMVDRKFIERLLRVSSCKVTVVDSATRALQYLGLDGENNSSVGFEDLKINLI 84

Query: 89  ITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNL 148
           +TDY MPGMTGYELLKKIK                                         
Sbjct: 85  MTDYSMPGMTGYELLKKIK----------------------------------------- 103

Query: 149 EQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSDVKRIKDYLTR 202
             +SSA REIPVVIMSSENIL RIDRCLE+GAEDF++KPVKL+DVKR++D L +
Sbjct: 104 --ESSAFREIPVVIMSSENILPRIDRCLEEGAEDFLLKPVKLADVKRLRDSLMK 155

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. Type-A response regulators seem to act as negative regulators of the cytokinin signaling.

Arabidopsis thaliana (taxid: 3702)

>sp|Q7G8V2|ARR15_ARATH Two-component response regulator ARR15 OS=Arabidopsis thaliana GN=ARR15 PE=1 SV=1

 Score =  176 bits (447), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 94/174 (54%), Positives = 115/174 (66%), Gaps = 43/174 (24%)

Query: 29  EVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLI 88
           E+HVLAVDDSFVDRKVIERLL IS+CKVT V+SG RALQ+LGLD +   +G   LKV+LI
Sbjct: 17  ELHVLAVDDSFVDRKVIERLLKISACKVTTVESGTRALQYLGLDGDNGSSGLKDLKVNLI 76

Query: 89  ITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNL 148
           +TDY MPG+TGYELLKKIK                                         
Sbjct: 77  VTDYSMPGLTGYELLKKIK----------------------------------------- 95

Query: 149 EQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSDVKRIKDYLTR 202
             +SSALREIPVVIMSSENI  RI++C+ +GAE+F++KPVKL+DVKR+K+ + R
Sbjct: 96  --ESSALREIPVVIMSSENIQPRIEQCMIEGAEEFLLKPVKLADVKRLKELIMR 147

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. Type-A response regulators seem to act as negative regulators of the cytokinin signaling.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9ZWS7|ARR7_ARATH Two-component response regulator ARR7 OS=Arabidopsis thaliana GN=ARR7 PE=1 SV=1

 Score =  174 bits (441), Expect = 6e-43,   Method: Compositional matrix adjust.
 Identities = 103/205 (50%), Positives = 127/205 (61%), Gaps = 49/205 (23%)

Query: 19  GFDLSPSDTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSIN 78
           G DL+ + T E+HVLAVDDS VDRKVIERLL ISSCKVT V+SG RALQ+LGLD  +  +
Sbjct: 14  GGDLTVT-TPELHVLAVDDSIVDRKVIERLLRISSCKVTTVESGTRALQYLGLDGGKGAS 72

Query: 79  GFDGLKVDLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFC 138
               LKV+LI+TDY MPG++GY+LLKKIK                               
Sbjct: 73  NLKDLKVNLIVTDYSMPGLSGYDLLKKIK------------------------------- 101

Query: 139 FPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSDVKRIKD 198
                       +SSA RE+PVVIMSSENIL RI  CL++GAE+F++KPVKL+DVKRIK 
Sbjct: 102 ------------ESSAFREVPVVIMSSENILPRIQECLKEGAEEFLLKPVKLADVKRIKQ 149

Query: 199 YLTRDVNLGNEGRGI---NKRKARE 220
            + R  N   E + +   NKRK +E
Sbjct: 150 LIMR--NEAEECKILSHSNKRKLQE 172

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. Type-A response regulators seem to act as negative regulators of the cytokinin signaling.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SHC2|ARR16_ARATH Two-component response regulator ARR16 OS=Arabidopsis thaliana GN=ARR16 PE=1 SV=1

 Score =  151 bits (382), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 83/184 (45%), Positives = 110/184 (59%), Gaps = 46/184 (25%)

Query: 20  FDLSPSDTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGL-DEEQSIN 78
             L     EE+HVLAVDD+ +DRK++ERLL IS CKVT  ++  RAL++LGL D+ Q I+
Sbjct: 19  HHLHHGHDEELHVLAVDDNLIDRKLVERLLKISCCKVTTAENALRALEYLGLGDQNQHID 78

Query: 79  GF--DGLKVDLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSIC 136
               + +KV LIITDYCMPGMTG+ELLKK+K                             
Sbjct: 79  ALTCNVMKVSLIITDYCMPGMTGFELLKKVK----------------------------- 109

Query: 137 FCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSDVKRI 196
                         +SS LRE+PVVIMSSENI  RI++CL  GA+ F+ KP+KL+DV+++
Sbjct: 110 --------------ESSNLREVPVVIMSSENIPTRINKCLASGAQMFMQKPLKLADVEKL 155

Query: 197 KDYL 200
           K +L
Sbjct: 156 KCHL 159

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. Type-A response regulators seem to act as negative regulators of the cytokinin signaling.

Arabidopsis thaliana (taxid: 3702)

>sp|O80366|ARR9_ARATH Two-component response regulator ARR9 OS=Arabidopsis thaliana GN=ARR9 PE=1 SV=1

 Score =  151 bits (381), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 83/184 (45%), Positives = 108/184 (58%), Gaps = 53/184 (28%)

Query: 29  EVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSIN---------- 78
           + HVLAVDDS  DRK+IERLL  SSC+VT VDSG +AL+FLGL +    N          
Sbjct: 8   QFHVLAVDDSLFDRKLIERLLQKSSCQVTTVDSGSKALEFLGLRQSTDSNDPNAFSKAPV 67

Query: 79  GFDGLKVDLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFC 138
               ++V+LIITDYCMPGMTGY+LLKK+K                               
Sbjct: 68  NHQVVEVNLIITDYCMPGMTGYDLLKKVK------------------------------- 96

Query: 139 FPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSDVKRIKD 198
                       +SSA R+IPVVIMSSEN+ ARI RCLE+GAE+F +KPV+L+D+ ++K 
Sbjct: 97  ------------ESSAFRDIPVVIMSSENVPARISRCLEEGAEEFFLKPVRLADLNKLKP 144

Query: 199 YLTR 202
           ++ +
Sbjct: 145 HMMK 148

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. Type-A response regulators seem to act as negative regulators of the cytokinin signaling.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FPR6|ARR17_ARATH Two-component response regulator ARR17 OS=Arabidopsis thaliana GN=ARR17 PE=2 SV=1

 Score =  150 bits (380), Expect = 8e-36,   Method: Compositional matrix adjust.
 Identities = 80/174 (45%), Positives = 109/174 (62%), Gaps = 44/174 (25%)

Query: 28  EEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDG-LKVD 86
           EE+HVLAVDD+ +DRK++ER+L ISSCKVT  ++G RAL++LGL + Q  +     +KV+
Sbjct: 18  EELHVLAVDDNLIDRKLVERILKISSCKVTTAENGLRALEYLGLGDPQQTDSLTNVMKVN 77

Query: 87  LIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSN 146
           LIITDYCMPGMTG+ELLKK+K                                       
Sbjct: 78  LIITDYCMPGMTGFELLKKVK--------------------------------------- 98

Query: 147 NLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSDVKRIKDYL 200
               +SS L+E+PVVI+SSENI  RI++CL  GA+ F+ KP+KLSDV+++K +L
Sbjct: 99  ----ESSNLKEVPVVILSSENIPTRINKCLASGAQMFMQKPLKLSDVEKLKCHL 148

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. Type-A response regulators seem to act as negative regulators of the cytokinin signaling.

Arabidopsis thaliana (taxid: 3702)

>sp|O80365|ARR8_ARATH Two-component response regulator ARR8 OS=Arabidopsis thaliana GN=ARR8 PE=1 SV=1

 Score =  148 bits (373), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 82/180 (45%), Positives = 107/180 (59%), Gaps = 51/180 (28%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLD-EEQSINGF-------DG 82
           HVLAVDDS  DRK+IERLL  SSC+VT VDSG +AL+FLGL  ++   N           
Sbjct: 10  HVLAVDDSLFDRKMIERLLQKSSCQVTTVDSGSKALEFLGLRVDDNDPNALSTSPQIHQE 69

Query: 83  LKVDLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFF 142
           ++++LIITDYCMPGMTGY+LLKK+K                                   
Sbjct: 70  VEINLIITDYCMPGMTGYDLLKKVK----------------------------------- 94

Query: 143 FPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSDVKRIKDYLTR 202
                   +S+A R IPVVIMSSEN+ ARI RCLE+GAE+F +KPVKL+D+ ++K ++ +
Sbjct: 95  --------ESAAFRSIPVVIMSSENVPARISRCLEEGAEEFFLKPVKLADLTKLKPHMMK 146

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. Type-A response regulators seem to act as negative regulators of the cytokinin signaling.

Arabidopsis thaliana (taxid: 3702)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	276
296086487	221	unnamed protein product [Vitis vinifera]	0.786	0.981	0.593	1e-67
147768948	210	hypothetical protein VITISV_026384 [Viti	0.605	0.795	0.658	3e-66
255558348	258	two-component sensor protein histidine p	0.811	0.868	0.564	2e-64
449434875	233	PREDICTED: two-component response regula	0.637	0.755	0.586	2e-60
148608690	209	response regulator, partial [Malus x dom	0.735	0.971	0.583	1e-56
148608687	212	response regulator, partial [Malus x dom	0.543	0.707	0.627	1e-56
309951224	255	putative A-type response regulator 1a [P	0.826	0.894	0.551	3e-56
309951226	257	putative A-type response regulator 1b [P	0.644	0.692	0.573	5e-56
297849384	258	hypothetical protein ARALYDRAFT_888316 [	0.804	0.860	0.470	7e-56
224135721	223	type-a response regulator [Populus trich	0.782	0.968	0.511	9e-55

>gi|296086487|emb|CBI32076.3| unnamed protein product [Vitis vinifera]

 Score =  262 bits (670), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 162/273 (59%), Positives = 178/273 (65%), Gaps = 56/273 (20%)

Query: 5   NGVASLRLISDEIDGFDLSPSDTEE-VHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGR 63
           +GV S R + DEI GFDLSP  +EE  HVLAVDDS VDRKVIERLL ISSCKVTAVDSGR
Sbjct: 4   SGVLSRRNMPDEIGGFDLSPGHSEEEAHVLAVDDSLVDRKVIERLLKISSCKVTAVDSGR 63

Query: 64  RALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFL 123
           RALQFLGLDEE++  G DGLKVDLIITDYCMPGMTGYELLKKIK ++ F           
Sbjct: 64  RALQFLGLDEEKNSAGLDGLKVDLIITDYCMPGMTGYELLKKIKESSTF----------- 112

Query: 124 NLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDF 183
                                           RE PVVIMSSENIL RIDRCLE+GAEDF
Sbjct: 113 --------------------------------RETPVVIMSSENILTRIDRCLEEGAEDF 140

Query: 184 IVKPVKLSDVKRIKDYLTRDVNLGNEGRGINKRKARESCDLSSSPPSVITSSSSPSSPSS 243
           IVKPVKLSDVKR+KDY+TR+   GNEGRGINKRK  E+CD+S S  S   S SS SS  S
Sbjct: 141 IVKPVKLSDVKRLKDYMTREDRDGNEGRGINKRKLGEACDVSPSLSSSPPSISSSSSSWS 200

Query: 244 PFRSPSILSSSAPCSPPSTLDSPTSRLKMTISD 276
                         S P++LDSPT RLK +  D
Sbjct: 201 AP------------SSPTSLDSPTRRLKTSTCD 221

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147768948|emb|CAN69259.1| hypothetical protein VITISV_026384 [Vitis vinifera]

 Score =  258 bits (658), Expect = 3e-66,   Method: Compositional matrix adjust.
 Identities = 139/211 (65%), Positives = 149/211 (70%), Gaps = 44/211 (20%)

Query: 15  DEIDGFDLSPSDTEE-VHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDE 73
           DEI GFDLSP  +EE  HVLAVDDS VDRKVIERLL ISSCKVTAVDSGRRALQFLGLDE
Sbjct: 3   DEIGGFDLSPGHSEEEAHVLAVDDSLVDRKVIERLLKISSCKVTAVDSGRRALQFLGLDE 62

Query: 74  EQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFIL 133
           E++  G DGLKVDLIITDYCMPGMTGYELLKKIK                          
Sbjct: 63  EKNSAGLDGLKVDLIITDYCMPGMTGYELLKKIK-------------------------- 96

Query: 134 SICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSDV 193
                            +SS  RE PVVIMSSENIL RIDRCLE+GAEDFIVKPVKLSDV
Sbjct: 97  -----------------ESSTFRETPVVIMSSENILTRIDRCLEEGAEDFIVKPVKLSDV 139

Query: 194 KRIKDYLTRDVNLGNEGRGINKRKARESCDL 224
           KR+KDY+TR+   GNEGRGINKRK  E+CD+
Sbjct: 140 KRLKDYMTREDRDGNEGRGINKRKLGEACDV 170

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255558348|ref|XP_002520201.1| two-component sensor protein histidine protein kinase, putative [Ricinus communis] gi|223540693|gb|EEF42256.1| two-component sensor protein histidine protein kinase, putative [Ricinus communis]

 Score =  251 bits (641), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 166/294 (56%), Positives = 191/294 (64%), Gaps = 70/294 (23%)

Query: 5   NGVASLRLISDEIDGFDLSPSDTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRR 64
           NG+AS R  S++I+GF+ S  D +EVHVLAVDDS VDRKVIERLL I+SCKVTAVDSGRR
Sbjct: 4   NGIASRRWRSEKIEGFEFSSCDNDEVHVLAVDDSLVDRKVIERLLKITSCKVTAVDSGRR 63

Query: 65  ALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLN 124
           ALQFLGLDEE+S +   GLKVDLIITDYCMPGMTGYELLKKIK                 
Sbjct: 64  ALQFLGLDEEKSTS-IQGLKVDLIITDYCMPGMTGYELLKKIK----------------- 105

Query: 125 LQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFI 184
                                     +SS  REIPVVIMSSEN++ARIDRCLE+GAEDF+
Sbjct: 106 --------------------------ESSTFREIPVVIMSSENVMARIDRCLEEGAEDFL 139

Query: 185 VKPVKLSDVKRIKDYLT-RDVNLGNE----------GRGINKRKARESCDLSSSPPSVIT 233
           VKPVKLSDVKRI+DY+T R++ L ++          G  +NKRK+R+S DLSSSPPS+  
Sbjct: 140 VKPVKLSDVKRIRDYMTARELKLKSQQTSHNFNNSTGNNVNKRKSRDSFDLSSSPPSISF 199

Query: 234 SSSSPSSPSSPFRSPSILSS--------------SAPCSPPSTLDSPTSRLKMT 273
           SSSS S   S   SPS  S               SAPCSP S LDSPT RLKM+
Sbjct: 200 SSSSLSPSPSSLSSPSSPSPCGSPSWSPSPMLSFSAPCSPTS-LDSPTRRLKMS 252

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449434875|ref|XP_004135221.1| PREDICTED: two-component response regulator ARR3-like [Cucumis sativus] gi|449478516|ref|XP_004155339.1| PREDICTED: two-component response regulator ARR3-like [Cucumis sativus]

 Score =  238 bits (607), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 129/220 (58%), Positives = 147/220 (66%), Gaps = 44/220 (20%)

Query: 5   NGVASLRLISDEIDGFDLSPSDTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRR 64
           N + S R  SD++DG D  P+   EVHVLAVDDS VDR VIERLL +++C+VTAVDSG R
Sbjct: 4   NHIFSRRRRSDQLDGLDRFPTSDSEVHVLAVDDSLVDRTVIERLLRLTACRVTAVDSGIR 63

Query: 65  ALQFLGL-DEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFL 123
           ALQ+LGL DE  S  GFDGLKVD+IITDYCMPGMTGYELLKKIK                
Sbjct: 64  ALQYLGLQDETNSQVGFDGLKVDMIITDYCMPGMTGYELLKKIK---------------- 107

Query: 124 NLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDF 183
                                      +SS LREIPVVIMSSEN++ARIDRCLE+GAEDF
Sbjct: 108 ---------------------------ESSTLREIPVVIMSSENVVARIDRCLEEGAEDF 140

Query: 184 IVKPVKLSDVKRIKDYLTRDVNLGNEGRGINKRKARESCD 223
           IVKPVKLSDVKR+++Y+  D   GNE  GINKRK RE CD
Sbjct: 141 IVKPVKLSDVKRLREYMVGDEKTGNERSGINKRKLREPCD 180

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|148608690|gb|ABQ95669.1| response regulator, partial [Malus x domestica]

 Score =  226 bits (575), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 147/252 (58%), Positives = 163/252 (64%), Gaps = 49/252 (19%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQS-INGFDGLKVDLII 89
           HVLAVDDS VDRKVIERLL ISSC+VT VDSGRRALQFLGLDEE+S   GFDGLKVDLII
Sbjct: 1   HVLAVDDSLVDRKVIERLLKISSCRVTTVDSGRRALQFLGLDEEKSSTAGFDGLKVDLII 60

Query: 90  TDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLE 149
           TDYCMPGMTGYELLKKIK                                          
Sbjct: 61  TDYCMPGMTGYELLKKIK------------------------------------------ 78

Query: 150 QDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSDVKRIKDYLT--RDVNLG 207
            +SS  +  PVVIMSSEN+LARIDRCLE+GAEDFIVKPVKL+DVKR+KDY+T  RDV + 
Sbjct: 79  -ESSTFKATPVVIMSSENVLARIDRCLEEGAEDFIVKPVKLADVKRLKDYMTTARDVGVE 137

Query: 208 NEGRGINKRKARESCD---LSSSPPSVITSSSSPSSPSSPFRSPSILSSSAPCSPPSTLD 264
             G G+NKRK RE CD     S P    +S SS SS  S   SP + SS +  S P+ LD
Sbjct: 138 ESGGGMNKRKLREPCDPTIAPSPPSIFPSSPSSSSSSPSKSPSPPLSSSFSAPSSPTPLD 197

Query: 265 SPTSRLKMTISD 276
           SP  RLKMT +D
Sbjct: 198 SPIRRLKMTNAD 209

Source: Malus x domestica

Species: Malus x domestica

Genus: Malus

Family: Rosaceae

Order: Rosales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|148608687|gb|ABQ95668.1| response regulator, partial [Malus x domestica]

 Score =  226 bits (575), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 123/196 (62%), Positives = 134/196 (68%), Gaps = 46/196 (23%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQS-INGFDGLKVDLII 89
           HVLAVDDS VDRKVIERLL ISSC+VT VDSGRRALQFLGLDEE+S   GFDGLKVDLII
Sbjct: 1   HVLAVDDSLVDRKVIERLLKISSCRVTTVDSGRRALQFLGLDEEKSSTAGFDGLKVDLII 60

Query: 90  TDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLE 149
           TDYCMPGMTGYELLKKIK                                          
Sbjct: 61  TDYCMPGMTGYELLKKIK------------------------------------------ 78

Query: 150 QDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSDVKRIKDYLT--RDVNLG 207
            +SS  +  PVVIMSSEN+LARIDRCLE+GAEDFIVKPVKL+DVKR+KDY+T  RDV + 
Sbjct: 79  -ESSTFKATPVVIMSSENVLARIDRCLEEGAEDFIVKPVKLADVKRLKDYMTTARDVGVE 137

Query: 208 NEGRGINKRKARESCD 223
             G G+NKRK RE CD
Sbjct: 138 ESGGGMNKRKLREPCD 153

Source: Malus x domestica

Species: Malus x domestica

Genus: Malus

Family: Rosaceae

Order: Rosales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|309951224|emb|CBX43982.1| putative A-type response regulator 1a [Populus x canadensis]

 Score =  224 bits (571), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 162/294 (55%), Positives = 183/294 (62%), Gaps = 66/294 (22%)

Query: 3   TTNGVASLRLISDEIDGFDLSP---SDTEE--VHVLAVDDSFVDRKVIERLLTISSCKVT 57
           ++N +AS R +S+++DGFDLSP   SD EE  VHVLAVDDS VDRKVIERLL ISSCKVT
Sbjct: 2   SSNSIASNRWMSEKMDGFDLSPNSNSDNEEEGVHVLAVDDSLVDRKVIERLLKISSCKVT 61

Query: 58  AVDSGRRALQFLG-LDEEQSIN--------GFDGLKVDLIITDYCMPGMTGYELLKKIKV 108
           AVDSG RAL+ LG LDEE   +        GFD LKVDLIITDYCMPGMTGYELLKKIK 
Sbjct: 62  AVDSGWRALKLLGLLDEEDKSSSSSSSSSAGFDVLKVDLIITDYCMPGMTGYELLKKIKE 121

Query: 109 TTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENI 168
           +T F                                           REIPVVIMSSEN+
Sbjct: 122 STTF-------------------------------------------REIPVVIMSSENV 138

Query: 169 LARIDRCLEDGAEDFIVKPVKLSDVKRIKDYL-TRDVN--LGNEGR---GINKRKARESC 222
           +ARIDRCLE+GAEDFIVKPVKLSDVKRI+DY+ +R+V      E R    INKRK +E  
Sbjct: 139 VARIDRCLEEGAEDFIVKPVKLSDVKRIRDYMASREVRSVQNQEERSSSNINKRKLQECF 198

Query: 223 D---LSSSPPSVITSSSSPSSPSSPFRSPSILSSSAPCSPPSTLDSPTSRLKMT 273
           D    SS P    +S S PS   S   SP  L SS+    PS+LDSPT RLKMT
Sbjct: 199 DLSLSSSPPSISSSSLSYPSRSPSLTPSPPSLFSSSAPCSPSSLDSPTRRLKMT 252

Source: Populus x canadensis

Species: Populus x canadensis

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|309951226|emb|CBX43983.1| putative A-type response regulator 1b [Populus x canadensis]

 Score =  223 bits (569), Expect = 5e-56,   Method: Compositional matrix adjust.
 Identities = 137/239 (57%), Positives = 155/239 (64%), Gaps = 61/239 (25%)

Query: 3   TTNGVASLRLISDEIDGFDLSP---SDTEE--VHVLAVDDSFVDRKVIERLLTISSCKVT 57
           ++N +AS R +S+++DGFDLSP   SD EE  VHVLAVDDS VDRKVIERLL ISSCKVT
Sbjct: 2   SSNSIASNRWMSEKMDGFDLSPNSNSDNEEEGVHVLAVDDSLVDRKVIERLLKISSCKVT 61

Query: 58  AVDSGRRALQFLG-LDEEQSIN------GFDGLKVDLIITDYCMPGMTGYELLKKIKVTT 110
           AVDSG RAL+ LG LDEE   +      GFD LKVDLIITDYCMPGMTGYELLKKIK +T
Sbjct: 62  AVDSGWRALKLLGLLDEEDKSSSSSSSAGFDVLKVDLIITDYCMPGMTGYELLKKIKEST 121

Query: 111 PFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILA 170
            F                                           REIPVVIMSSEN++A
Sbjct: 122 TF-------------------------------------------REIPVVIMSSENVVA 138

Query: 171 RIDRCLEDGAEDFIVKPVKLSDVKRIKDYL-TRDVN--LGNEGR---GINKRKARESCD 223
           RIDRCLE+GAEDFIVKPVKLSDVKRI+DY+ +R+V      E R    INKRK +E  D
Sbjct: 139 RIDRCLEEGAEDFIVKPVKLSDVKRIRDYMASREVRSVQNQEERSSSNINKRKLQECFD 197

Source: Populus x canadensis

Species: Populus x canadensis

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297849384|ref|XP_002892573.1| hypothetical protein ARALYDRAFT_888316 [Arabidopsis lyrata subsp. lyrata] gi|297338415|gb|EFH68832.1| hypothetical protein ARALYDRAFT_888316 [Arabidopsis lyrata subsp. lyrata]

 Score =  223 bits (568), Expect = 7e-56,   Method: Compositional matrix adjust.
 Identities = 142/302 (47%), Positives = 173/302 (57%), Gaps = 80/302 (26%)

Query: 1   MTTTNGVASLRLISD-EIDGFDLSPSDTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAV 59
           M    GV+ LR+     + G + +P D +EVHVLAVDDS VDR VIERLL I+SCKVTAV
Sbjct: 1   MARDGGVSCLRMSEMMNVGGIESAPLDLDEVHVLAVDDSLVDRIVIERLLRITSCKVTAV 60

Query: 60  DSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTI 119
           DSG RAL+FLGLD E++   FD LKVDLIITDYCMPGMTGYELLKKIK            
Sbjct: 61  DSGWRALEFLGLDNEKASAEFDRLKVDLIITDYCMPGMTGYELLKKIK------------ 108

Query: 120 IVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDG 179
                                          +SS  RE+PVVIMSSEN+L RIDRCLE+G
Sbjct: 109 -------------------------------ESSNFREVPVVIMSSENVLTRIDRCLEEG 137

Query: 180 AEDFIVKPVKLSDVKRIKDYLTRDVNLGNEGRGINKRKARESCD---------------- 223
           A+DF++KPVKL+DVKR++++LT+DV L N     NKRK  +  D                
Sbjct: 138 AQDFLLKPVKLADVKRLRNHLTKDVKLSNG----NKRKLPDDSDSVNSSLPPPSPPLTIS 193

Query: 224 LSSSPPSVITSSSSPSSP---------SSPFRSP----SILSSSAPCSPPSTLDSPTSRL 270
             SSPP  I++ SS SSP         +SP  +P     +L++S   SP    DSP  R 
Sbjct: 194 PESSPPLTISTESSDSSPQLSPVEMFSTSPLSTPIDDDDVLTTSPESSPE---DSPIRRQ 250

Query: 271 KM 272
           KM
Sbjct: 251 KM 252

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224135721|ref|XP_002322144.1| type-a response regulator [Populus trichocarpa] gi|222869140|gb|EEF06271.1| type-a response regulator [Populus trichocarpa] gi|309951242|emb|CBX43991.1| putative A-type response regulator 10 [Populus x canadensis]

 Score =  219 bits (558), Expect = 9e-55,   Method: Compositional matrix adjust.
 Identities = 135/264 (51%), Positives = 160/264 (60%), Gaps = 48/264 (18%)

Query: 3   TTNGVASLRLISDEIDGFDLSPSDTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSG 62
            T G    R +++E+     S S +EE+HVLAVDDSFVDRKVIERLL ISSCKVT V+SG
Sbjct: 2   ATAGEILRRSLTEEVGFSKGSVSGSEELHVLAVDDSFVDRKVIERLLKISSCKVTVVESG 61

Query: 63  RRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVF 122
            RALQ+LGLD E+S  GF+ LK++LI+TDY MPGMTGYELLKKIK               
Sbjct: 62  SRALQYLGLDGEKSSVGFNDLKINLIMTDYSMPGMTGYELLKKIK--------------- 106

Query: 123 LNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAED 182
                                       +SSA REIPVVIMSSENILARIDRCLE+GAE+
Sbjct: 107 ----------------------------ESSAFREIPVVIMSSENILARIDRCLEEGAEE 138

Query: 183 FIVKPVKLSDVKRIKDYLTRDVNLGNEGRGINKRKARESCDLSSSPPSVITSSSSPSSPS 242
           +I+KPVKLSDVKRIKD +        + R + KR  RE C  S S P ++ SSSSP+   
Sbjct: 139 YILKPVKLSDVKRIKDVIMGGDGEQKKRRSVRKR-GREDCFYSLSQPQLVQSSSSPAFDF 197

Query: 243 SPFRSPSILSSSAPCSPPSTLDSP 266
                PS L SS+P S  S    P
Sbjct: 198 ----LPSELQSSSPFSTLSLSKRP 217

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

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	276
TAIR|locus:2025911	231	ARR3 "response regulator 3" [A	0.405	0.484	0.652	3.3e-55
TAIR|locus:2194584	259	ARR4 "response regulator 4" [A	0.405	0.432	0.663	1.4e-54
TAIR|locus:2170723	186	ARR6 "response regulator 6" [A	0.307	0.456	0.705	1.6e-47
TAIR|locus:2097870	184	RR5 "response regulator 5" [Ar	0.300	0.451	0.714	2.9e-46
TAIR|locus:2027237	206	ARR15 "response regulator 15"	0.311	0.417	0.720	1.2e-45
TAIR|locus:2011286	206	ARR7 "response regulator 7" [A	0.336	0.451	0.648	1.2e-45
TAIR|locus:2102509	153	RR17 "response regulator 17" [	0.289	0.522	0.629	3.5e-38
TAIR|locus:2080590	234	ARR9 "response regulator 9" [A	0.304	0.358	0.574	7.3e-38
TAIR|locus:2040282	225	RR3 "response regulator 3" [Ar	0.315	0.386	0.562	2.4e-37
UNIPROTKB|Q4GZK2	201	rr9 "Type A response regulator	0.278	0.383	0.658	2.7e-36

TAIR|locus:2025911 ARR3 "response regulator 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 351 (128.6 bits), Expect = 3.3e-55, Sum P(2) = 3.3e-55
 Identities = 75/115 (65%), Positives = 88/115 (76%)

Query:     1 MTTTNGVASLR---LISDEIDGFDLSPSDTEEVHVLAVDDSFVDRKVIERLLTISSCKVT 57
             M    GV+ LR   +I   I   +  P D+++VHVLAVDDS VDR VIERLL I+SCKVT
Sbjct:     1 MAKDGGVSCLRRSEMIGIGIGELESPPLDSDQVHVLAVDDSLVDRIVIERLLRITSCKVT 60

Query:    58 AVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVTTPF 112
             AVDSG RAL+FLGLD++++   FD LKVDLIITDYCMPGMTGYELLKKIK +T F
Sbjct:    61 AVDSGWRALEFLGLDDDKAAVEFDRLKVDLIITDYCMPGMTGYELLKKIKESTSF 115

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

GO:0000160 "phosphorelay signal transduction system" evidence=IEA;IDA;TAS

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

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

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

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

GO:0007623 "circadian rhythm" evidence=IMP

GO:0042752 "regulation of circadian rhythm" evidence=IGI

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

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

TAIR|locus:2194584 ARR4 "response regulator 4" [Arabidopsis thaliana (taxid:3702)]

 Score = 352 (129.0 bits), Expect = 1.4e-54, Sum P(2) = 1.4e-54
 Identities = 77/116 (66%), Positives = 89/116 (76%)

Query:     1 MTTTNGVASLR---LIS-DEIDGFDLSPSDTEEVHVLAVDDSFVDRKVIERLLTISSCKV 56
             M    GV+ LR   ++S   I G + +P D +EVHVLAVDDS VDR VIERLL I+SCKV
Sbjct:     1 MARDGGVSCLRRSEMMSVGGIGGIESAPLDLDEVHVLAVDDSLVDRIVIERLLRITSCKV 60

Query:    57 TAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVTTPF 112
             TAVDSG RAL+FLGLD E++   FD LKVDLIITDYCMPGMTGYELLKKIK ++ F
Sbjct:    61 TAVDSGWRALEFLGLDNEKASAEFDRLKVDLIITDYCMPGMTGYELLKKIKESSNF 116

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

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

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0005515 "protein binding" evidence=IPI

GO:0005737 "cytoplasm" evidence=IDA

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

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

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

GO:0009793 "embryo development ending in seed dormancy" evidence=IMP

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

GO:0042752 "regulation of circadian rhythm" evidence=IGI

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

GO:0004674 "protein serine/threonine kinase activity" evidence=IDA

GO:0046777 "protein autophosphorylation" evidence=IDA

GO:0006612 "protein targeting to membrane" evidence=RCA

GO:0009963 "positive regulation of flavonoid biosynthetic process" evidence=RCA

GO:0010363 "regulation of plant-type hypersensitive response" evidence=RCA

TAIR|locus:2170723 ARR6 "response regulator 6" [Arabidopsis thaliana (taxid:3702)]

 Score = 300 (110.7 bits), Expect = 1.6e-47, Sum P(2) = 1.6e-47
 Identities = 60/85 (70%), Positives = 70/85 (82%)

Query:    28 EEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDL 87
             + +HVLAVDDS VDRK IERLL +SSCKVT VDS  RALQ+LGLD E+   GF+ LKV+L
Sbjct:    23 DPLHVLAVDDSHVDRKFIERLLRVSSCKVTVVDSATRALQYLGLDVEEKSVGFEDLKVNL 82

Query:    88 IITDYCMPGMTGYELLKKIKVTTPF 112
             I+TDY MPGMTGYELLKKIK ++ F
Sbjct:    83 IMTDYSMPGMTGYELLKKIKESSAF 107

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

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

GO:0005634 "nucleus" evidence=ISM;IDA

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

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

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

GO:0005515 "protein binding" evidence=IPI

GO:0007623 "circadian rhythm" evidence=RCA

TAIR|locus:2097870 RR5 "response regulator 5" [Arabidopsis thaliana (taxid:3702)]

 Score = 294 (108.6 bits), Expect = 2.9e-46, Sum P(2) = 2.9e-46
 Identities = 60/84 (71%), Positives = 69/84 (82%)

Query:    30 VHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLD-EEQSINGFDGLKVDLI 88
             +HVLAVDDS VDRK IERLL +SSCKVT VDS  RALQ+LGLD E  S  GF+ LK++LI
Sbjct:    25 LHVLAVDDSMVDRKFIERLLRVSSCKVTVVDSATRALQYLGLDGENNSSVGFEDLKINLI 84

Query:    89 ITDYCMPGMTGYELLKKIKVTTPF 112
             +TDY MPGMTGYELLKKIK ++ F
Sbjct:    85 MTDYSMPGMTGYELLKKIKESSAF 108

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

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

GO:0005634 "nucleus" evidence=ISM;IDA

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

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

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

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

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

GO:0005515 "protein binding" evidence=IPI

GO:0005737 "cytoplasm" evidence=IDA

GO:0006612 "protein targeting to membrane" evidence=RCA

GO:0009963 "positive regulation of flavonoid biosynthetic process" evidence=RCA

GO:0010363 "regulation of plant-type hypersensitive response" evidence=RCA

TAIR|locus:2027237 ARR15 "response regulator 15" [Arabidopsis thaliana (taxid:3702)]

 Score = 311 (114.5 bits), Expect = 1.2e-45, Sum P(2) = 1.2e-45
 Identities = 62/86 (72%), Positives = 72/86 (83%)

Query:    22 LSPSDTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFD 81
             LS S + E+HVLAVDDSFVDRKVIERLL IS+CKVT V+SG RALQ+LGLD +   +G  
Sbjct:    10 LSSSSSPELHVLAVDDSFVDRKVIERLLKISACKVTTVESGTRALQYLGLDGDNGSSGLK 69

Query:    82 GLKVDLIITDYCMPGMTGYELLKKIK 107
              LKV+LI+TDY MPG+TGYELLKKIK
Sbjct:    70 DLKVNLIVTDYSMPGLTGYELLKKIK 95

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

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

GO:0005634 "nucleus" evidence=ISM;IDA

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

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

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

GO:0005515 "protein binding" evidence=IPI

GO:0005737 "cytoplasm" evidence=IDA

GO:0007623 "circadian rhythm" evidence=RCA

TAIR|locus:2011286 ARR7 "response regulator 7" [Arabidopsis thaliana (taxid:3702)]

 Score = 295 (108.9 bits), Expect = 1.2e-45, Sum P(2) = 1.2e-45
 Identities = 61/94 (64%), Positives = 75/94 (79%)

Query:    19 GFDLSPSDTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSIN 78
             G DL+ + T E+HVLAVDDS VDRKVIERLL ISSCKVT V+SG RALQ+LGLD  +  +
Sbjct:    14 GGDLTVT-TPELHVLAVDDSIVDRKVIERLLRISSCKVTTVESGTRALQYLGLDGGKGAS 72

Query:    79 GFDGLKVDLIITDYCMPGMTGYELLKKIKVTTPF 112
                 LKV+LI+TDY MPG++GY+LLKKIK ++ F
Sbjct:    73 NLKDLKVNLIVTDYSMPGLSGYDLLKKIKESSAF 106

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

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

GO:0005634 "nucleus" evidence=ISM;IDA

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

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

GO:0019827 "stem cell maintenance" evidence=IMP

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

GO:0005515 "protein binding" evidence=IPI

GO:0010200 "response to chitin" evidence=IEP

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:2102509 RR17 "response regulator 17" [Arabidopsis thaliana (taxid:3702)]

 Score = 274 (101.5 bits), Expect = 3.5e-38, Sum P(2) = 3.5e-38
 Identities = 51/81 (62%), Positives = 67/81 (82%)

Query:    28 EEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDG-LKVD 86
             EE+HVLAVDD+ +DRK++ER+L ISSCKVT  ++G RAL++LGL + Q  +     +KV+
Sbjct:    18 EELHVLAVDDNLIDRKLVERILKISSCKVTTAENGLRALEYLGLGDPQQTDSLTNVMKVN 77

Query:    87 LIITDYCMPGMTGYELLKKIK 107
             LIITDYCMPGMTG+ELLKK+K
Sbjct:    78 LIITDYCMPGMTGFELLKKVK 98

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

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

GO:0005634 "nucleus" evidence=ISM

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

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

TAIR|locus:2080590 ARR9 "response regulator 9" [Arabidopsis thaliana (taxid:3702)]

 Score = 247 (92.0 bits), Expect = 7.3e-38, Sum P(2) = 7.3e-38
 Identities = 54/94 (57%), Positives = 67/94 (71%)

Query:    29 EVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGL---DEEQSINGFDG--- 82
             + HVLAVDDS  DRK+IERLL  SSC+VT VDSG +AL+FLGL    +    N F     
Sbjct:     8 QFHVLAVDDSLFDRKLIERLLQKSSCQVTTVDSGSKALEFLGLRQSTDSNDPNAFSKAPV 67

Query:    83 ----LKVDLIITDYCMPGMTGYELLKKIKVTTPF 112
                 ++V+LIITDYCMPGMTGY+LLKK+K ++ F
Sbjct:    68 NHQVVEVNLIITDYCMPGMTGYDLLKKVKESSAF 101

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

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

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0005515 "protein binding" evidence=IPI

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

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

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

GO:0009740 "gibberellic acid mediated signaling pathway" evidence=RCA

GO:0010162 "seed dormancy process" evidence=RCA

TAIR|locus:2040282 RR3 "response regulator 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 246 (91.7 bits), Expect = 2.4e-37, Sum P(2) = 2.4e-37
 Identities = 54/96 (56%), Positives = 69/96 (71%)

Query:    26 DTE-EVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLD-EEQSINGFDG- 82
             +TE + HVLAVDDS  DRK+IERLL  SSC+VT VDSG +AL+FLGL  ++   N     
Sbjct:     4 ETESKFHVLAVDDSLFDRKMIERLLQKSSCQVTTVDSGSKALEFLGLRVDDNDPNALSTS 63

Query:    83 ------LKVDLIITDYCMPGMTGYELLKKIKVTTPF 112
                   ++++LIITDYCMPGMTGY+LLKK+K +  F
Sbjct:    64 PQIHQEVEINLIITDYCMPGMTGYDLLKKVKESAAF 99

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

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

GO:0005634 "nucleus" evidence=ISM;IDA

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

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

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

GO:0005515 "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

UNIPROTKB|Q4GZK2 rr9 "Type A response regulator 9" [Oryza sativa Indica Group (taxid:39946)]

 Score = 239 (89.2 bits), Expect = 2.7e-36, Sum P(2) = 2.7e-36
 Identities = 54/82 (65%), Positives = 61/82 (74%)

Query:    31 HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGL-DEEQSINGFDG----LKV 85
             HVLAVDDS  DRK+IERLL  SS +VT VDSG +AL+FLGL D E S          + V
Sbjct:    10 HVLAVDDSLPDRKLIERLLKTSSFQVTTVDSGSKALEFLGLHDHEDSPISTQSDQQEVAV 69

Query:    86 DLIITDYCMPGMTGYELLKKIK 107
             +LIITDYCMPGMTGY+LLKKIK
Sbjct:    70 NLIITDYCMPGMTGYDLLKKIK 91

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

---

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

Fail to connect to STRING server

---

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	276
PLN03029	222	PLN03029, PLN03029, type-a response regulator prot	1e-50
cd00156	113	cd00156, REC, Signal receiver domain; originally t	2e-19
COG0784	130	COG0784, CheY, FOG: CheY-like receiver [Signal tra	8e-17
pfam00072	111	pfam00072, Response_reg, Response regulator receiv	1e-15
COG3706	435	COG3706, PleD, Response regulator containing a Che	1e-11
COG2204	464	COG2204, AtoC, Response regulator containing CheY-	8e-10
COG3437	360	COG3437, COG3437, Response regulator containing a	1e-09
PRK15347	921	PRK15347, PRK15347, two component system sensor ki	1e-07
TIGR01818	463	TIGR01818, ntrC, nitrogen regulation protein NR(I)	2e-07
COG2197	211	COG2197, CitB, Response regulator containing a Che	1e-06
COG4753	475	COG4753, COG4753, Response regulator containing Ch	2e-06
smart00448	55	smart00448, REC, cheY-homologous receiver domain	3e-06
COG2201	350	COG2201, CheB, Chemotaxis response regulator conta	2e-05
COG0745	229	COG0745, OmpR, Response regulators consisting of a	2e-05
PRK09581	457	PRK09581, pleD, response regulator PleD; Reviewed	3e-05
PRK00742	354	PRK00742, PRK00742, chemotaxis-specific methyleste	3e-05
PRK09390	202	PRK09390, fixJ, response regulator FixJ; Provision	2e-04
PRK10693	303	PRK10693, PRK10693, response regulator of RpoS; Pr	3e-04
PRK10923	469	PRK10923, glnG, nitrogen regulation protein NR(I);	0.002
COG3947	361	COG3947, COG3947, Response regulator containing Ch	0.003
PRK11107	919	PRK11107, PRK11107, hybrid sensory histidine kinas	0.004
CHL00148	240	CHL00148, orf27, Ycf27; Reviewed	0.004
PRK10651	216	PRK10651, PRK10651, transcriptional regulator NarL	0.004

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

 Score =  165 bits (420), Expect = 1e-50
 Identities = 91/234 (38%), Positives = 121/234 (51%), Gaps = 54/234 (23%)

Query: 22  LSPSDTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQ------ 75
           +  +   + HVLAVDDS +DRK+IE+LL  SS +VT VDSG +AL+FLGL E+       
Sbjct: 1   MGITTESQFHVLAVDDSLIDRKLIEKLLKTSSYQVTTVDSGSKALKFLGLHEDDRSNPDT 60

Query: 76  ---SINGFDGLKVDLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFI 132
              S N    ++V+LIITDYCMPGMTGY+LLKKIK                         
Sbjct: 61  PSVSPNSHQEVEVNLIITDYCMPGMTGYDLLKKIK------------------------- 95

Query: 133 LSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSD 192
                             +SS+LR IPVVIMSSEN+ +RI RCLE+GAE+F +KPV+LSD
Sbjct: 96  ------------------ESSSLRNIPVVIMSSENVPSRITRCLEEGAEEFFLKPVQLSD 137

Query: 193 VKRIKDYL--TRDVNLGNEGRGINKRKARESCDLSSSPPSVITSSSSPSSPSSP 244
           + R+K ++  T+  N   E +   ++                   S P     P
Sbjct: 138 LNRLKPHMMKTKSKNQKQENQEKQEKLEESEIQSEKQEQPSQQPQSQPQPQQQP 191

Length = 222

>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 = 80.7 bits (200), Expect = 2e-19
 Identities = 38/169 (22%), Positives = 61/169 (36%), Gaps = 57/169 (33%)

Query: 33  LAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDY 92
           L VDD  + R+++ RLL     +V   + G  AL  L              K DLI+ D 
Sbjct: 1   LIVDDDPLIRELLRRLLEKEGYEVVEAEDGEEALALL-----------AEEKPDLILLDI 49

Query: 93  CMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDS 152
            MPGM G ELL++I+                                             
Sbjct: 50  MMPGMDGLELLRRIR--------------------------------------------- 64

Query: 153 SALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSD-VKRIKDYL 200
               +IP++ +++          L+ GA+D++ KP    + + RI+  L
Sbjct: 65  KRGPDIPIIFLTAHGDDEDAVEALKAGADDYLTKPFSPEELLARIRALL 113

Length = 113

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

 Score = 74.5 bits (183), Expect = 8e-17
 Identities = 41/180 (22%), Positives = 71/180 (39%), Gaps = 58/180 (32%)

Query: 26  DTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRR-ALQFLGLDEEQSINGFDGLK 84
               + VL VDD  V+R++++RLL     +V     G   AL+ L           +  +
Sbjct: 2   LLSGLRVLVVDDEPVNRRLLKRLLEDLGYEVVEAADGEEEALELLR----------ELPQ 51

Query: 85  VDLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFP 144
            DLI+ D  MPGM G ELL++++                                     
Sbjct: 52  PDLILLDINMPGMDGIELLRRLR------------------------------------- 74

Query: 145 SNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSD--VKRIKDYLTR 202
                   +    IPV+++++    A  +R L  GA+D++ KP+ L +  +  ++  L R
Sbjct: 75  --------ARGPNIPVILLTAYADEADRERALAAGADDYLTKPIFLEEELLAALRRLLAR 126

Length = 130

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

 Score = 70.7 bits (174), Expect = 1e-15
 Identities = 38/167 (22%), Positives = 59/167 (35%), Gaps = 57/167 (34%)

Query: 32  VLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITD 91
           VL VDD  + R+++ +LL      V   D G  AL+ L              + DLI+ D
Sbjct: 1   VLIVDDDPLIRELLRQLLEKEGYVVAEADDGEEALELL-----------KEKRPDLILLD 49

Query: 92  YCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQD 151
             MPGM G ELL++I+   P                                        
Sbjct: 50  IRMPGMDGLELLRRIRRRPP---------------------------------------- 69

Query: 152 SSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSD-VKRIK 197
                  PV+++++          L+ GA DF+ KP    + V  ++
Sbjct: 70  -----TTPVIVLTAHGDEEDAVEALKAGANDFLSKPFDPEELVAALR 111

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

 Score = 63.9 bits (156), Expect = 1e-11
 Identities = 34/157 (21%), Positives = 55/157 (35%), Gaps = 54/157 (34%)

Query: 32  VLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITD 91
           +L VDD    R+ + R+L +   +V     G  AL  L             L  DL++ D
Sbjct: 135 ILVVDDDATQRERLRRILQVEGFRVVEATDGEEALLQL-----------AELPPDLVLLD 183

Query: 92  YCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQD 151
             MP M G EL  +++                                            
Sbjct: 184 ANMPDMDGLELCTRLR-------------------------------------------Q 200

Query: 152 SSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPV 188
               R+IP++++SS++    + R  E G  D+I KP+
Sbjct: 201 LERTRDIPIILLSSKDDDELVVRAFELGVNDYITKPI 237

Length = 435

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

 Score = 58.5 bits (142), Expect = 8e-10
 Identities = 38/160 (23%), Positives = 58/160 (36%), Gaps = 56/160 (35%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
            +L VDD    R+++E+ L ++  +V   +S   AL+ L                DL++ 
Sbjct: 6   RILVVDDDPDIRELLEQALELAGYEVVTAESAEEALEALSESP-----------FDLVLL 54

Query: 91  DYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQ 150
           D  MPGM G ELLK+IK                                           
Sbjct: 55  DIRMPGMDGLELLKEIK------------------------------------------- 71

Query: 151 DSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKL 190
             S   ++PV++M+    +      L  GA DF+ KP  L
Sbjct: 72  --SRDPDLPVIVMTGHGDIDTAVEALRLGAFDFLEKPFDL 109

Length = 464

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

 Score = 57.8 bits (140), Expect = 1e-09
 Identities = 39/186 (20%), Positives = 71/186 (38%), Gaps = 54/186 (29%)

Query: 18  DGFDLSPSDTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSI 77
                     E++ VL VDD   + + + +LL +   +V   ++G  AL+   L +E+  
Sbjct: 3   QSMQGKNEPDEKLTVLLVDDEPDNLEALRQLLRMIGYRVIEAENGEEALK---LLQEE-- 57

Query: 78  NGFDGLKVDLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICF 137
                   DL++ D  MP M G E+L K+K  +P            + + + + +L+   
Sbjct: 58  ------PPDLVLLDVRMPEMDGAEVLNKLKAMSP------------STRRIPVILLTAY- 98

Query: 138 CFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSDVK-RI 196
                           A  E                R LE GA+D++ KP+   ++  R+
Sbjct: 99  ----------------ADSED-------------RQRALEAGADDYLSKPISPKELVARV 129

Query: 197 KDYLTR 202
             +L  
Sbjct: 130 SSHLQL 135

Length = 360

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

 Score = 52.3 bits (126), Expect = 1e-07
 Identities = 40/181 (22%), Positives = 64/181 (35%), Gaps = 57/181 (31%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
            +L VDD   +R +I  +L     +VT   SG  AL+ LG    Q          DL++ 
Sbjct: 692 QILLVDDVETNRDIIGMMLVELGQQVTTAASGTEALE-LG---RQHR-------FDLVLM 740

Query: 91  DYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQ 150
           D  MPG+ G E  +  +                                      NNL+ 
Sbjct: 741 DIRMPGLDGLETTQLWRDD-----------------------------------PNNLD- 764

Query: 151 DSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSDVKRIKDY-----LTRDVN 205
                 +  +V +++      I RC + G   ++ KPV L+ + R  +      L R + 
Sbjct: 765 -----PDCMIVALTANAAPEEIHRCKKAGMNHYLTKPVTLAQLARALELAAEYQLLRGIE 819

Query: 206 L 206
           L
Sbjct: 820 L 820

Length = 921

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

 Score = 51.7 bits (124), Expect = 2e-07
 Identities = 34/161 (21%), Positives = 57/161 (35%), Gaps = 56/161 (34%)

Query: 32  VLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITD 91
           V  VDD    R V+E+ L+ +  +V    +    L+ L   +            DL+ITD
Sbjct: 1   VWVVDDDRSIRWVLEKALSRAGYEVRTFGNAASVLRALARGQP-----------DLLITD 49

Query: 92  YCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQD 151
             MPG  G +LL +IK   P                                        
Sbjct: 50  VRMPGEDGLDLLPQIKKRHP---------------------------------------- 69

Query: 152 SSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSD 192
                ++PV++M++ + L       + GA +++ KP  L +
Sbjct: 70  -----QLPVIVMTAHSDLDTAVAAYQRGAFEYLPKPFDLDE 105

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

 Score = 47.7 bits (114), Expect = 1e-06
 Identities = 34/160 (21%), Positives = 57/160 (35%), Gaps = 58/160 (36%)

Query: 31  HVLAVDDSFVDRKVIERLL-TISSCKVTAV-DSGRRALQFLGLDEEQSINGFDGLKVDLI 88
            VL VDD  + R+ + +LL      +V     +G  AL                LK D++
Sbjct: 2   KVLIVDDHPLVREGLRQLLELEPDLEVVGEASNGEEALDLA-----------RELKPDVV 50

Query: 89  ITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNL 148
           + D  MPGM G E LK+++   P                                     
Sbjct: 51  LLDLSMPGMDGLEALKQLRARGP------------------------------------- 73

Query: 149 EQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPV 188
                   +I VV++++ +  A + R L  GA+ +++K  
Sbjct: 74  --------DIKVVVLTAHDDPAYVIRALRAGADGYLLKDA 105

Length = 211

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

 Score = 48.1 bits (115), Expect = 2e-06
 Identities = 26/83 (31%), Positives = 43/83 (51%), Gaps = 14/83 (16%)

Query: 32  VLAVDDSFVDRKVIERLLTISSCKVTAV---DSGRRALQFLGLDEEQSINGFDGLKVDLI 88
           VL VDD  + R+ ++ L+   +  +  V    +G+ AL+ +   +E           D++
Sbjct: 4   VLIVDDEPLIREGLKSLIDWEALGIEVVGTAANGKEALELI---QETQ--------PDIV 52

Query: 89  ITDYCMPGMTGYELLKKIKVTTP 111
           ITD  MPGM G +L+K IK  +P
Sbjct: 53  ITDINMPGMDGLDLIKAIKEQSP 75

Length = 475

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

 Score = 43.3 bits (103), Expect = 3e-06
 Identities = 19/65 (29%), Positives = 28/65 (43%), Gaps = 11/65 (16%)

Query: 31 HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
           +L VDD  + R++++ LL     +V     G  AL+ L              K DLI+ 
Sbjct: 2  RILVVDDDPLLRELLKALLEKEGYEVDEATDGEEALELL-----------KEEKPDLILL 50

Query: 91 DYCMP 95
          D  MP
Sbjct: 51 DIMMP 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|225111 COG2201, CheB, Chemotaxis response regulator containing a CheY-like receiver domain and a methylesterase domain [Cell motility and secretion / Signal transduction mechanisms]

 Score = 45.0 bits (107), Expect = 2e-05
 Identities = 44/161 (27%), Positives = 56/161 (34%), Gaps = 63/161 (39%)

Query: 32  VLAVDDSFVDRKVIERLLTISSCKVTAV---DSGRRALQFLGLDEEQSINGFDGLKVDLI 88
           VL VDDS + RKVI  +L  S   +  V    +GR A+  +             LK D+I
Sbjct: 4   VLVVDDSALMRKVISDIL-NSDPDIEVVGTARNGREAIDKVK-----------KLKPDVI 51

Query: 89  ITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNL 148
             D  MP M G E L+KI    P                                     
Sbjct: 52  TLDVEMPVMDGLEALRKIMRLRP------------------------------------- 74

Query: 149 EQDSSALREIPVVIMSS--ENILARIDRCLEDGAEDFIVKP 187
                    +PV+++SS  E         LE GA DFI KP
Sbjct: 75  ---------LPVIMVSSLTEEGAEATLEALELGAVDFIAKP 106

Length = 350

>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 = 44.2 bits (105), Expect = 2e-05
 Identities = 26/173 (15%), Positives = 57/173 (32%), Gaps = 57/173 (32%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
            +L V+D     ++++  L     +V     G  AL+                  DL++ 
Sbjct: 2   RILLVEDDPELAELLKEYLEEEGYEVDVAADGEEALEAAREQ------------PDLVLL 49

Query: 91  DYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQ 150
           D  +P + G EL ++++                                           
Sbjct: 50  DLMLPDLDGLELCRRLR------------------------------------------- 66

Query: 151 DSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSD-VKRIKDYLTR 202
            +      P++++++ +        LE GA+D++ KP    + + R++  L R
Sbjct: 67  -AKKGSGPPIIVLTARDDEEDRVLGLEAGADDYLTKPFSPRELLARLRALLRR 118

Length = 229

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

 Score = 44.9 bits (107), Expect = 3e-05
 Identities = 45/175 (25%), Positives = 70/175 (40%), Gaps = 62/175 (35%)

Query: 32  VLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITD 91
           +L VDD   + K++E  L      V    SG  A+     + EQ          D+I+ D
Sbjct: 5   ILVVDDIPANVKLLEAKLLAEYYTVLTASSGAEAIAIC--EREQ---------PDIILLD 53

Query: 92  YCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQD 151
             MPGM G+E+ +++K                                            
Sbjct: 54  VMMPGMDGFEVCRRLK-------------------------------------------S 70

Query: 152 SSALREIPVVIMSS-ENILARIDRCLEDGAEDFIVKPVKLSDVK---RIKDYLTR 202
             A   IPVV++++ ++   R+ R LE GA+DF+ KP+  +DV    R+K  LTR
Sbjct: 71  DPATTHIPVVMVTALDDPEDRV-RGLEAGADDFLTKPI--NDVALFARVKS-LTR 121

Length = 457

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

 Score = 44.4 bits (106), Expect = 3e-05
 Identities = 51/231 (22%), Positives = 79/231 (34%), Gaps = 80/231 (34%)

Query: 32  VLAVDDSFVDRKVIERLLT-ISSCKV--TAVDSGRRALQFLGLDEEQSINGFDGLKVDLI 88
           VL VDDS   R++I  +L      +V  TA D G  A + +    ++       L  D+I
Sbjct: 6   VLVVDDSAFMRRLISEILNSDPDIEVVGTAPD-GLEAREKI----KK-------LNPDVI 53

Query: 89  ITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNL 148
             D  MP M G + L+KI                                          
Sbjct: 54  TLDVEMPVMDGLDALEKIM----------------------------------------- 72

Query: 149 EQDSSALREIPVVIMSS------ENILARIDRCLEDGAEDFIVKPV--KLSDVKRIKDYL 200
                 LR  PVV++SS      E  L    R LE GA DF+ KP       +   K+ L
Sbjct: 73  -----RLRPTPVVMVSSLTERGAEITL----RALELGAVDFVTKPFLGISLGMDEYKEEL 123

Query: 201 TRDVNLGNEGRGINKRKARESCDLSSSPPSVITSSSSPSSPSSPFRSPSIL 251
              V      R    R    +    ++  +   +++  +  ++P  S  ++
Sbjct: 124 AEKV------RAA-ARARVRALPPRAAAAARAAAAAPAALAAAPLLSSKLV 167

Length = 354

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

 Score = 40.8 bits (96), Expect = 2e-04
 Identities = 24/81 (29%), Positives = 39/81 (48%), Gaps = 11/81 (13%)

Query: 27  TEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVD 86
           +++  V  VDD    R  +  LL  +  +V   +S   A  FL        +   GL+  
Sbjct: 1   SDKGVVHVVDDDEAMRDSLAFLLDSAGFEVRLFES---AQAFL--------DALPGLRFG 49

Query: 87  LIITDYCMPGMTGYELLKKIK 107
            ++TD  MPG+ G ELL+++K
Sbjct: 50  CVVTDVRMPGIDGIELLRRLK 70

Length = 202

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

 Score = 41.1 bits (97), Expect = 3e-04
 Identities = 29/142 (20%), Positives = 48/142 (33%), Gaps = 58/142 (40%)

Query: 57  TAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVTTPFNFLY 116
               +G  AL+ L            G   DLII D  MP M G E ++ +          
Sbjct: 1   VLAANGVDALELL-----------GGFTPDLIICDLAMPRMNGIEFVEHL---------- 39

Query: 117 STIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCL 176
                                            +        PV+++S+   +A I + L
Sbjct: 40  -------------------------------RNRGDQ----TPVLVISATENMADIAKAL 64

Query: 177 EDGAEDFIVKPVKLSDVKRIKD 198
             G +D ++KPVK  D+ R+++
Sbjct: 65  RLGVQDVLLKPVK--DLNRLRE 84

Length = 303

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

 Score = 39.5 bits (92), Expect = 0.002
 Identities = 26/80 (32%), Positives = 36/80 (45%), Gaps = 11/80 (13%)

Query: 32  VLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITD 91
           V  VDD    R V+ER L  +    T  ++G   L+ L                D++++D
Sbjct: 6   VWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLEALASKTP-----------DVLLSD 54

Query: 92  YCMPGMTGYELLKKIKVTTP 111
             MPGM G  LLK+IK   P
Sbjct: 55  IRMPGMDGLALLKQIKQRHP 74

Length = 469

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

 Score = 37.9 bits (88), Expect = 0.003
 Identities = 19/76 (25%), Positives = 33/76 (43%), Gaps = 11/76 (14%)

Query: 32  VLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITD 91
           ++ VDD     K++  +L+ +  +V +      AL  L           +  K DLI  D
Sbjct: 3   IIIVDDDAAIVKLLSVILSRAGHEVRSCSHPVEALDLL-----------EVFKPDLIFLD 51

Query: 92  YCMPGMTGYELLKKIK 107
             MP M G E  ++++
Sbjct: 52  IVMPYMNGIEFAEQVR 67

Length = 361

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

 Score = 38.3 bits (90), Expect = 0.004
 Identities = 24/76 (31%), Positives = 37/76 (48%), Gaps = 11/76 (14%)

Query: 32  VLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITD 91
           V+AVDD+  + K+I  LL      V   DSG +A++     +++          DLI+ D
Sbjct: 670 VMAVDDNPANLKLIGALLEEQVEHVVLCDSGHQAVE---QAKQRPF--------DLILMD 718

Query: 92  YCMPGMTGYELLKKIK 107
             MPGM G    + I+
Sbjct: 719 IQMPGMDGIRACELIR 734

Length = 919

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

 Score = 37.8 bits (88), Expect = 0.004
 Identities = 22/77 (28%), Positives = 37/77 (48%), Gaps = 11/77 (14%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
            +L VDD    RK++E  L+I   +V     G           E+++  F   + DL+I 
Sbjct: 8   KILVVDDEAYIRKILETRLSIIGYEVITASDG-----------EEALKLFRKEQPDLVIL 56

Query: 91  DYCMPGMTGYELLKKIK 107
           D  MP + GY + ++I+
Sbjct: 57  DVMMPKLDGYGVCQEIR 73

Length = 240

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

 Score = 37.3 bits (87), Expect = 0.004
 Identities = 20/67 (29%), Positives = 33/67 (49%), Gaps = 15/67 (22%)

Query: 67  QFLGLDEEQSI-----NGFDGLKV------DLIITDYCMPGMTGYELLKKIKVTTPFNFL 115
           Q + +  + ++     NG  G+++      DLI+ D  MPGM G E L K++  +    L
Sbjct: 24  QLISMAPDITVVGEASNGEQGIELAESLDPDLILLDLNMPGMNGLETLDKLREKS----L 79

Query: 116 YSTIIVF 122
              I+VF
Sbjct: 80  SGRIVVF 86

Length = 216

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	276
COG0745	229	OmpR Response regulators consisting of a CheY-like	99.87
COG2204	464	AtoC Response regulator containing CheY-like recei	99.85
COG4753	475	Response regulator containing CheY-like receiver d	99.84
PF00072	112	Response_reg: Response regulator receiver domain;	99.84
PLN03029	222	type-a response regulator protein; Provisional	99.84
COG4565	224	CitB Response regulator of citrate/malate metaboli	99.81
COG0784	130	CheY FOG: CheY-like receiver [Signal transduction	99.8
KOG0519	786	consensus Sensory transduction histidine kinase [S	99.8
COG3437	360	Response regulator containing a CheY-like receiver	99.79
COG2197	211	CitB Response regulator containing a CheY-like rec	99.77
COG4566	202	TtrR Response regulator [Signal transduction mecha	99.76
PRK10046	225	dpiA two-component response regulator DpiA; Provis	99.75
PRK10816	223	DNA-binding transcriptional regulator PhoP; Provis	99.72
PRK10529	225	DNA-binding transcriptional activator KdpE; Provis	99.72
PRK10643	222	DNA-binding transcriptional regulator BasR; Provis	99.72
PRK09836	227	DNA-binding transcriptional activator CusR; Provis	99.72
PRK10841	924	hybrid sensory kinase in two-component regulatory	99.72
PRK10336	219	DNA-binding transcriptional regulator QseB; Provis	99.71
PRK11173	237	two-component response regulator; Provisional	99.71
PRK11083	228	DNA-binding response regulator CreB; Provisional	99.71
PRK11107	919	hybrid sensory histidine kinase BarA; Provisional	99.7
PRK15347	921	two component system sensor kinase SsrA; Provision	99.7
PRK10430	239	DNA-binding transcriptional activator DcuR; Provis	99.69
PRK09468	239	ompR osmolarity response regulator; Provisional	99.69
COG3706	435	PleD Response regulator containing a CheY-like rec	99.69
PRK10766	221	DNA-binding transcriptional regulator TorR; Provis	99.69
PRK10701	240	DNA-binding transcriptional regulator RstA; Provis	99.69
TIGR03787	227	marine_sort_RR proteobacterial dedicated sortase s	99.69
PRK11466	914	hybrid sensory histidine kinase TorS; Provisional	99.69
PRK10161	229	transcriptional regulator PhoB; Provisional	99.68
PRK10955	232	DNA-binding transcriptional regulator CpxR; Provis	99.68
TIGR02154	226	PhoB phosphate regulon transcriptional regulatory	99.68
TIGR02956	968	TMAO_torS TMAO reductase sytem sensor TorS. This p	99.68
CHL00148	240	orf27 Ycf27; Reviewed	99.67
PRK10840	216	transcriptional regulator RcsB; Provisional	99.67
PRK09958	204	DNA-binding transcriptional activator EvgA; Provis	99.66
PRK09483	217	response regulator; Provisional	99.66
PRK11517	223	transcriptional regulatory protein YedW; Provision	99.66
PRK13856	241	two-component response regulator VirG; Provisional	99.66
TIGR01387	218	cztR_silR_copR heavy metal response regulator. Mem	99.65
PRK11091	779	aerobic respiration control sensor protein ArcB; P	99.65
TIGR02875	262	spore_0_A sporulation transcription factor Spo0A.	99.65
PRK09935	210	transcriptional regulator FimZ; Provisional	99.65
PRK10923	469	glnG nitrogen regulation protein NR(I); Provisiona	99.65
COG3947	361	Response regulator containing CheY-like receiver a	99.64
PRK09581	457	pleD response regulator PleD; Reviewed	99.64
PRK14084	246	two-component response regulator; Provisional	99.63
PRK15115	444	response regulator GlrR; Provisional	99.63
PRK11361	457	acetoacetate metabolism regulatory protein AtoC; P	99.63
PRK10365	441	transcriptional regulatory protein ZraR; Provision	99.63
PRK09959	1197	hybrid sensory histidine kinase in two-component r	99.63
PRK10360	196	DNA-binding transcriptional activator UhpA; Provis	99.61
TIGR02915	445	PEP_resp_reg putative PEP-CTERM system response re	99.61
PRK15479	221	transcriptional regulatory protein TctD; Provision	99.61
PRK09390	202	fixJ response regulator FixJ; Provisional	99.6
PRK11697	238	putative two-component response-regulatory protein	99.6
PRK10710	240	DNA-binding transcriptional regulator BaeR; Provis	99.6
COG4567	182	Response regulator consisting of a CheY-like recei	99.6
TIGR01818	463	ntrC nitrogen regulation protein NR(I). This model	99.59
PRK12555	337	chemotaxis-specific methylesterase; Provisional	99.59
PRK15369	211	two component system sensor kinase SsrB; Provision	99.55
PRK10403	215	transcriptional regulator NarP; Provisional	99.54
PRK10651	216	transcriptional regulator NarL; Provisional	99.54
PRK09581	457	pleD response regulator PleD; Reviewed	99.54
PRK13558	665	bacterio-opsin activator; Provisional	99.54
PRK00742	354	chemotaxis-specific methylesterase; Provisional	99.54
PRK10610	129	chemotaxis regulatory protein CheY; Provisional	99.52
PRK13435	145	response regulator; Provisional	99.5
COG2201	350	CheB Chemotaxis response regulator containing a Ch	99.5
PRK10100	216	DNA-binding transcriptional regulator CsgD; Provis	99.47
PRK11475	207	DNA-binding transcriptional activator BglJ; Provis	99.43
cd00156	113	REC Signal receiver domain; originally thought to	99.41
PRK13837	828	two-component VirA-like sensor kinase; Provisional	99.39
PRK15411	207	rcsA colanic acid capsular biosynthesis activation	99.38
PRK09191	261	two-component response regulator; Provisional	99.35
COG3707	194	AmiR Response regulator with putative antiterminat	99.35
PRK13557	540	histidine kinase; Provisional	99.34
PRK10693	303	response regulator of RpoS; Provisional	99.28
PRK15029	755	arginine decarboxylase; Provisional	99.15
COG3279	244	LytT Response regulator of the LytR/AlgR family [T	99.14
PRK11107	919	hybrid sensory histidine kinase BarA; Provisional	98.52
COG3706	435	PleD Response regulator containing a CheY-like rec	98.06
smart00448	55	REC cheY-homologous receiver domain. CheY regulate	97.98
PF06490	109	FleQ: Flagellar regulatory protein FleQ; InterPro:	97.39
PRK10618	894	phosphotransfer intermediate protein in two-compon	97.16
cd02071	122	MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 bin	96.81
PF03709	115	OKR_DC_1_N: Orn/Lys/Arg decarboxylase, N-terminal	96.64
PRK02261	137	methylaspartate mutase subunit S; Provisional	96.47
cd02067	119	B12-binding B12 binding domain (B12-BD). This doma	96.27
TIGR00640	132	acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal	96.19
PRK15399	713	lysine decarboxylase LdcC; Provisional	94.55
PF02310	121	B12-binding: B12 binding domain; InterPro: IPR0061	94.44
PRK15400	714	lysine decarboxylase CadA; Provisional	94.09
TIGR03815	322	CpaE_hom_Actino helicase/secretion neighborhood Cp	93.52
COG2185	143	Sbm Methylmalonyl-CoA mutase, C-terminal domain/su	93.05
TIGR01501	134	MthylAspMutase methylaspartate mutase, S subunit.	92.22
PRK00208	250	thiG thiazole synthase; Reviewed	91.06
cd04728	248	ThiG Thiazole synthase (ThiG) is the tetrameric en	90.05
cd02069	213	methionine_synthase_B12_BD B12 binding domain of m	89.75
PF01408	120	GFO_IDH_MocA: Oxidoreductase family, NAD-binding R	89.29
cd02068	127	radical_SAM_B12_BD B12 binding domain_like associa	88.02
cd02072	128	Glm_B12_BD B12 binding domain of glutamate mutase	87.83
cd02070	201	corrinoid_protein_B12-BD B12 binding domain of cor	87.8
PRK09426	714	methylmalonyl-CoA mutase; Reviewed	86.41
PRK01130	221	N-acetylmannosamine-6-phosphate 2-epimerase; Provi	85.3
PRK13111	258	trpA tryptophan synthase subunit alpha; Provisiona	83.98
PF02254	116	TrkA_N: TrkA-N domain; InterPro: IPR003148 The reg	83.05
TIGR00262	256	trpA tryptophan synthase, alpha subunit. Tryptopha	82.83
PRK12704	520	phosphodiesterase; Provisional	81.44
TIGR02370	197	pyl_corrinoid methyltransferase cognate corrinoid	81.28
COG4999	140	Uncharacterized domain of BarA-like signal transdu	81.08
COG0512	191	PabA Anthranilate/para-aminobenzoate synthases com	80.98
PRK00278	260	trpC indole-3-glycerol-phosphate synthase; Reviewe	80.6
PRK10558	256	alpha-dehydro-beta-deoxy-D-glucarate aldolase; Pro	80.06

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

Probab=99.87  E-value=2.2e-21  Score=175.03  Aligned_cols=118  Identities=21%  Similarity=0.360  Sum_probs=106.2

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhh
Q 023816           30 VHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVT  109 (276)
Q Consensus        30 ~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~  109 (276)
                      ++||||||++..++.|..+|+..||+|..+.+|++|++.+           ... ||+||+|++||++||++++++||+.
T Consensus         1 ~~ILiveDd~~i~~~l~~~L~~~g~~v~~~~~~~~a~~~~-----------~~~-~dlviLD~~lP~~dG~~~~~~iR~~   68 (229)
T COG0745           1 MRILLVEDDPELAELLKEYLEEEGYEVDVAADGEEALEAA-----------REQ-PDLVLLDLMLPDLDGLELCRRLRAK   68 (229)
T ss_pred             CeEEEEcCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHH-----------hcC-CCEEEEECCCCCCCHHHHHHHHHhh
Confidence            4899999999999999999999999999999999999998           566 9999999999999999999999953


Q ss_pred             CCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCC
Q 023816          110 TPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVK  189 (276)
Q Consensus       110 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~  189 (276)
                      .                                            ...+|||++|+..+..+...++++|||||++||++
T Consensus        69 ~--------------------------------------------~~~~PIi~Lta~~~~~d~v~gl~~GADDYl~KPf~  104 (229)
T COG0745          69 K--------------------------------------------GSGPPIIVLTARDDEEDRVLGLEAGADDYLTKPFS  104 (229)
T ss_pred             c--------------------------------------------CCCCcEEEEECCCcHHHHHHHHhCcCCeeeeCCCC
Confidence            1                                            22689999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHh
Q 023816          190 LSDVKRIKDYLTRD  203 (276)
Q Consensus       190 ~~~L~~~~~~l~~~  203 (276)
                      +.+|..-++.+.|.
T Consensus       105 ~~EL~ARi~a~lRR  118 (229)
T COG0745         105 PRELLARLRALLRR  118 (229)
T ss_pred             HHHHHHHHHHHHCc
Confidence            99995555554443

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

Probab=99.85  E-value=1.3e-20  Score=185.79  Aligned_cols=125  Identities=33%  Similarity=0.493  Sum_probs=114.5

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHh
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKV  108 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~  108 (276)
                      ..+||||||+...|+.++..|+..||.|..+.|+++|++.+           ....||+||+|+.||++||++++++|++
T Consensus         4 ~~~iLvVDDd~~ir~~l~~~L~~~G~~v~~a~~~~~al~~i-----------~~~~~~lvl~Di~mp~~~Gl~ll~~i~~   72 (464)
T COG2204           4 MARILVVDDDPDIRELLEQALELAGYEVVTAESAEEALEAL-----------SESPFDLVLLDIRMPGMDGLELLKEIKS   72 (464)
T ss_pred             cCCEEEEeCCHHHHHHHHHHHHHcCCeEEEeCCHHHHHHHH-----------hcCCCCEEEEecCCCCCchHHHHHHHHh
Confidence            45799999999999999999999999999999999999999           4447999999999999999999999999


Q ss_pred             hCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCC
Q 023816          109 TTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPV  188 (276)
Q Consensus       109 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv  188 (276)
                      ..|                                             .+|||++|++.+.+.+.+|++.||.|||.||+
T Consensus        73 ~~~---------------------------------------------~~pVI~~Tg~g~i~~AV~A~k~GA~Dfl~KP~  107 (464)
T COG2204          73 RDP---------------------------------------------DLPVIVMTGHGDIDTAVEALRLGAFDFLEKPF  107 (464)
T ss_pred             hCC---------------------------------------------CCCEEEEeCCCCHHHHHHHHhcCcceeeeCCC
Confidence            888                                             89999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHhhhcccc
Q 023816          189 KLSDVKRIKDYLTRDVNLGNE  209 (276)
Q Consensus       189 ~~~~L~~~~~~l~~~~~~~~~  209 (276)
                      +.++|..++........+..+
T Consensus       108 ~~~~L~~~v~ral~~~~~~~e  128 (464)
T COG2204         108 DLDRLLAIVERALELRELQRE  128 (464)
T ss_pred             CHHHHHHHHHHHHHHhhhhhh
Confidence            999997777776665555443

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

Probab=99.84  E-value=1.7e-20  Score=185.16  Aligned_cols=121  Identities=26%  Similarity=0.495  Sum_probs=110.8

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHh--hCCCEEEE-ECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHH
Q 023816           29 EVHVLAVDDSFVDRKVIERLLT--ISSCKVTA-VDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKK  105 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~--~~g~~v~~-a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~  105 (276)
                      +.+||||||++..|+.|+.++.  ..|++++. |.||+||++.+           ++..|||||+|+.||+|||+++++.
T Consensus         1 MykVlIVDDE~lIr~GLk~lI~w~~~g~eiVgtA~NG~eAleli-----------~e~~pDiviTDI~MP~mdGLdLI~~   69 (475)
T COG4753           1 MYKVLIVDDEPLIREGLKSLIDWEALGIEVVGTAANGKEALELI-----------QETQPDIVITDINMPGMDGLDLIKA   69 (475)
T ss_pred             CeeEEEecChHHHHHHHHHhCChhhcCCeEEEecccHHHHHHHH-----------HhcCCCEEEEecCCCCCcHHHHHHH
Confidence            4689999999999999999995  66898775 99999999999           8889999999999999999999999


Q ss_pred             HHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEe
Q 023816          106 IKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIV  185 (276)
Q Consensus       106 Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~  185 (276)
                      +++..|                                             .+-+|++|++++-+.+.+|++.|+.|||.
T Consensus        70 ike~~p---------------------------------------------~~~~IILSGy~eFeYak~Am~lGV~dYLL  104 (475)
T COG4753          70 IKEQSP---------------------------------------------DTEFIILSGYDEFEYAKKAMKLGVKDYLL  104 (475)
T ss_pred             HHHhCC---------------------------------------------CceEEEEeccchhHHHHHHHhcCchhhee
Confidence            999888                                             89999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHhhh
Q 023816          186 KPVKLSDVKRIKDYLTRDVN  205 (276)
Q Consensus       186 KPv~~~~L~~~~~~l~~~~~  205 (276)
                      ||++.++|..++..+.....
T Consensus       105 KP~~k~eL~~~L~ki~~kl~  124 (475)
T COG4753         105 KPVDKAELEEALKKIIGKLE  124 (475)
T ss_pred             CcCCHHHHHHHHHHHHHHHH
Confidence            99999999777666655443

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

Probab=99.84  E-value=8e-20  Score=140.51  Aligned_cols=110  Identities=33%  Similarity=0.572  Sum_probs=104.0

Q ss_pred             EEEEeCCHHHHHHHHHHHhhCCC-EEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhhC
Q 023816           32 VLAVDDSFVDRKVIERLLTISSC-KVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVTT  110 (276)
Q Consensus        32 VLIVdD~~~~~~~L~~~L~~~g~-~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~~  110 (276)
                      ||||||++..++.++++|+..|+ ++..+.++.+|++.+           +...||+||+|+.||+++|.++++.||...
T Consensus         1 Ilivd~~~~~~~~l~~~l~~~~~~~v~~~~~~~~~~~~~-----------~~~~~d~iiid~~~~~~~~~~~~~~i~~~~   69 (112)
T PF00072_consen    1 ILIVDDDPEIRELLEKLLERAGYEEVTTASSGEEALELL-----------KKHPPDLIIIDLELPDGDGLELLEQIRQIN   69 (112)
T ss_dssp             EEEEESSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHH-----------HHSTESEEEEESSSSSSBHHHHHHHHHHHT
T ss_pred             cEEEECCHHHHHHHHHHHHhCCCCEEEEECCHHHHHHHh-----------cccCceEEEEEeeecccccccccccccccc
Confidence            79999999999999999999999 999999999999999           567799999999999999999999999877


Q ss_pred             CCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCCH
Q 023816          111 PFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKL  190 (276)
Q Consensus       111 p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~~  190 (276)
                      +                                             .+|+|++|...+.....+++++|+++||.||++.
T Consensus        70 ~---------------------------------------------~~~ii~~t~~~~~~~~~~~~~~g~~~~l~kp~~~  104 (112)
T PF00072_consen   70 P---------------------------------------------SIPIIVVTDEDDSDEVQEALRAGADDYLSKPFSP  104 (112)
T ss_dssp             T---------------------------------------------TSEEEEEESSTSHHHHHHHHHTTESEEEESSSSH
T ss_pred             c---------------------------------------------cccEEEecCCCCHHHHHHHHHCCCCEEEECCCCH
Confidence            6                                             8999999999999999999999999999999999


Q ss_pred             HHHHHHH
Q 023816          191 SDVKRIK  197 (276)
Q Consensus       191 ~~L~~~~  197 (276)
                      ++|.+.+
T Consensus       105 ~~l~~~i  111 (112)
T PF00072_consen  105 EELRAAI  111 (112)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHhh
Confidence            9996654

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 ....

>PLN03029 type-a response regulator protein; Provisional

Probab=99.84  E-value=2.5e-19  Score=159.26  Aligned_cols=136  Identities=61%  Similarity=1.000  Sum_probs=111.3

Q ss_pred             CCCCccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccc---------cccCCCCCceeEEEEecCCC
Q 023816           25 SDTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQ---------SINGFDGLKVDLIITDYCMP   95 (276)
Q Consensus        25 ~~~~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~---------~~~~~~~~~~DlIL~D~~mp   95 (276)
                      .....++||||||+...+..++++|+..||++..+.++.+|+..+......         .-+.-....+|+||+|++||
T Consensus         4 ~~~~~~~VLiVdd~~~~~~~l~~~L~~~g~~v~~a~sg~~al~~l~~~~~d~~~p~~~~~~~~~~~~~~~dlVllD~~mp   83 (222)
T PLN03029          4 TTESQFHVLAVDDSLIDRKLIEKLLKTSSYQVTTVDSGSKALKFLGLHEDDRSNPDTPSVSPNSHQEVEVNLIITDYCMP   83 (222)
T ss_pred             CCCCCccEEEEeCCHHHHHHHHHHHHHcCceEEEECCHHHHHHHHHhccccccccccccccccccccccCCEEEEcCCCC
Confidence            345689999999999999999999999999999999999999988432100         00000233578999999999


Q ss_pred             CCCHHHHHHHHHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHH
Q 023816           96 GMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRC  175 (276)
Q Consensus        96 ~~~G~ell~~Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~a  175 (276)
                      +++|++++++|++...                                           ...+|||++|+........++
T Consensus        84 ~~~G~e~l~~ir~~~~-------------------------------------------~~~ipvIils~~~~~~~~~~a  120 (222)
T PLN03029         84 GMTGYDLLKKIKESSS-------------------------------------------LRNIPVVIMSSENVPSRITRC  120 (222)
T ss_pred             CCCHHHHHHHHHhccc-------------------------------------------cCCCcEEEEeCCCCHHHHHHH
Confidence            9999999999996321                                           236899999999999999999


Q ss_pred             HhcCCCeEEeCCCCHHHHHHHHHHHHHh
Q 023816          176 LEDGAEDFIVKPVKLSDVKRIKDYLTRD  203 (276)
Q Consensus       176 l~~Ga~d~l~KPv~~~~L~~~~~~l~~~  203 (276)
                      ++.|+++||.||+...+|.+++..+.+.
T Consensus       121 l~~Ga~dyl~KP~~~~~L~~l~~~~~~~  148 (222)
T PLN03029        121 LEEGAEEFFLKPVQLSDLNRLKPHMMKT  148 (222)
T ss_pred             HHhCchheEECCCCHHHHHHHHHHHHHH
Confidence            9999999999999999997777665544

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

Probab=99.81  E-value=5.3e-19  Score=159.28  Aligned_cols=131  Identities=18%  Similarity=0.358  Sum_probs=116.0

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhh-CCCEEE-EECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHH
Q 023816           30 VHVLAVDDSFVDRKVIERLLTI-SSCKVT-AVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIK  107 (276)
Q Consensus        30 ~~VLIVdD~~~~~~~L~~~L~~-~g~~v~-~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir  107 (276)
                      ++||||||++.+.++-+++++. .||.+. .+.++++|...+           ...+|||||+|+.||+.+|++++.+||
T Consensus         1 i~VLIiEDD~mVaeih~~yv~~~~gF~~vg~A~~~~ea~~~i-----------~~~~pDLILLDiYmPd~~Gi~lL~~ir   69 (224)
T COG4565           1 INVLIIEDDPMVAEIHRRYVKQIPGFSVVGTAGTLEEAKMII-----------EEFKPDLILLDIYMPDGNGIELLPELR   69 (224)
T ss_pred             CcEEEEcCchHHHHHHHHHHHhCCCceEEEeeccHHHHHHHH-----------HhhCCCEEEEeeccCCCccHHHHHHHH
Confidence            5899999999999999999985 588766 599999999999           677899999999999999999999999


Q ss_pred             hhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCC
Q 023816          108 VTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKP  187 (276)
Q Consensus       108 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KP  187 (276)
                      ..+.                                             ++-||++|+-++.+.+.+|+..|+.|||.||
T Consensus        70 ~~~~---------------------------------------------~~DVI~iTAA~d~~tI~~alr~Gv~DYLiKP  104 (224)
T COG4565          70 SQHY---------------------------------------------PVDVIVITAASDMETIKEALRYGVVDYLIKP  104 (224)
T ss_pred             hcCC---------------------------------------------CCCEEEEeccchHHHHHHHHhcCchhheecc
Confidence            8776                                             8999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHhhhccccccccchh
Q 023816          188 VKLSDVKRIKDYLTRDVNLGNEGRGINKR  216 (276)
Q Consensus       188 v~~~~L~~~~~~l~~~~~~~~~~~~~~~~  216 (276)
                      |..+.+.+.++.+.+.+..-...+..+..
T Consensus       105 f~~eRl~~aL~~y~~~r~~l~~~~~~sQ~  133 (224)
T COG4565         105 FTFERLQQALTRYRQKRHALESHQQLSQK  133 (224)
T ss_pred             eeHHHHHHHHHHHHHHHHHHhhhcccCHH
Confidence            99999988888887776665554444443

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

Probab=99.80  E-value=2.8e-18  Score=134.81  Aligned_cols=116  Identities=35%  Similarity=0.610  Sum_probs=101.8

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHH-HHHHHhcccccccccCCCCC-ceeEEEEecCCCCCCHHHHHH
Q 023816           27 TEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGR-RALQFLGLDEEQSINGFDGL-KVDLIITDYCMPGMTGYELLK  104 (276)
Q Consensus        27 ~~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~-~al~~l~~~~~~~~~~~~~~-~~DlIL~D~~mp~~~G~ell~  104 (276)
                      +...+||+|||++..++.++..|...|+.+..+.+|. +|+..+           +.. .||+|++|+.||++||+++++
T Consensus         3 ~~~~~vLivdD~~~~~~~~~~~l~~~g~~v~~a~~g~~~al~~~-----------~~~~~~dlii~D~~mp~~~G~~~~~   71 (130)
T COG0784           3 LSGLRVLVVDDEPVNRRLLKRLLEDLGYEVVEAADGEEEALELL-----------RELPQPDLILLDINMPGMDGIELLR   71 (130)
T ss_pred             CCCcEEEEEcCCHHHHHHHHHHHHHcCCeEEEeCChHHHHHHHH-----------HhCCCCCEEEEeCCCCCCCHHHHHH
Confidence            4578999999999999999999999999999999995 999999           566 599999999999999999999


Q ss_pred             HHHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEE
Q 023816          105 KIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFI  184 (276)
Q Consensus       105 ~Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l  184 (276)
                      ++|...+                                             .+|+|++|++........+++.|+++|+
T Consensus        72 ~l~~~~~---------------------------------------------~~pvv~~t~~~~~~~~~~~~~~g~~~~l  106 (130)
T COG0784          72 RLRARGP---------------------------------------------NIPVILLTAYADEADRERALAAGADDYL  106 (130)
T ss_pred             HHHhCCC---------------------------------------------CCCEEEEEcCcCHHHHHHHHHcCCCeEE
Confidence            9997422                                             6788999999988877788999999999


Q ss_pred             eCCCCHHH-HHHHHH
Q 023816          185 VKPVKLSD-VKRIKD  198 (276)
Q Consensus       185 ~KPv~~~~-L~~~~~  198 (276)
                      .||+...+ +...+.
T Consensus       107 ~kP~~~~~~l~~~i~  121 (130)
T COG0784         107 TKPIFLEEELLAALR  121 (130)
T ss_pred             cCCCCcHHHHHHHHH
Confidence            99977666 544444

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

Probab=99.80  E-value=3.1e-19  Score=185.43  Aligned_cols=120  Identities=31%  Similarity=0.493  Sum_probs=109.1

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHH
Q 023816           27 TEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKI  106 (276)
Q Consensus        27 ~~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~I  106 (276)
                      ..+.+||+||||++++++...+|+..|++++.+.+|.||++.+.          ..+.||+|+||+|||.|||+|+.++|
T Consensus       664 l~g~~iLlvddn~vn~~Va~~~l~~~g~~~~~~~sg~e~l~~~~----------~~~~y~~ifmD~qMP~mDG~e~~~~i  733 (786)
T KOG0519|consen  664 LTGPKILLVDDNPVNRKVATGMLKKLGAEVTEVNSGQEALDKLK----------PPHSYDVIFMDLQMPEMDGYEATREI  733 (786)
T ss_pred             ccCCceEEEecccchHHHHHHHHHHhCCeeEeecCcHHHHHhcC----------CCCcccEEEEEcCCcccchHHHHHHH
Confidence            44789999999999999999999999999999999999999993          25789999999999999999999999


Q ss_pred             HhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeC
Q 023816          107 KVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVK  186 (276)
Q Consensus       107 r~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~K  186 (276)
                      |++..                                            -++|||+||+..+.+...+|++.|+|.||.|
T Consensus       734 rk~~~--------------------------------------------~~~pIvAlTa~~~~~~~~~c~~~Gmd~yl~K  769 (786)
T KOG0519|consen  734 RKKER--------------------------------------------WHLPIVALTADADPSTEEECLEVGMDGYLSK  769 (786)
T ss_pred             HHhhc--------------------------------------------CCCCEEEEecCCcHHHHHHHHHhCCceEEcc
Confidence            98653                                            2799999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHH
Q 023816          187 PVKLSDVKRIKDYL  200 (276)
Q Consensus       187 Pv~~~~L~~~~~~l  200 (276)
                      |++.+.+..++.++
T Consensus       770 P~~~~~l~~~l~~~  783 (786)
T KOG0519|consen  770 PFTLEKLVKILREF  783 (786)
T ss_pred             cccHHHHHHHHHHH
Confidence            99988886665544

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

Probab=99.79  E-value=1.3e-18  Score=166.21  Aligned_cols=126  Identities=29%  Similarity=0.489  Sum_probs=115.3

Q ss_pred             CCCCCCCCCCccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCC
Q 023816           19 GFDLSPSDTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMT   98 (276)
Q Consensus        19 ~~~~~~~~~~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~   98 (276)
                      ++.+...+...++||+|||.+.++..+..+|+..||.+..++||++|++..           .+..+|+||+|++||+|+
T Consensus         4 ~~~~~~~~~~~~~vl~vDD~~~~~~~~~~lL~~~~y~v~~ae~g~~a~kl~-----------~~~~~dlvllD~~mp~md   72 (360)
T COG3437           4 SMQGKNEPDEKLTVLLVDDEPDNLEALRQLLRMIGYRVIEAENGEEALKLL-----------QEEPPDLVLLDVRMPEMD   72 (360)
T ss_pred             ccCCCCCCcccceEEEecCchhHHHHHHHHHHhcccceeeecCchHHHHHh-----------cccCCceEEeeccCCCcc
Confidence            466777788899999999999999999999999999999999999999998           566799999999999999


Q ss_pred             HHHHHHHHHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhc
Q 023816           99 GYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLED  178 (276)
Q Consensus        99 G~ell~~Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~  178 (276)
                      |+|++.+|++..|                                          ..+.+||+++|+..+.....+|+++
T Consensus        73 g~ev~~~lk~~~p------------------------------------------~t~~ip~i~lT~~~d~~~~~~~~~~  110 (360)
T COG3437          73 GAEVLNKLKAMSP------------------------------------------STRRIPVILLTAYADSEDRQRALEA  110 (360)
T ss_pred             HHHHHHHHHhcCC------------------------------------------cccccceEEEeecCChHHHHHHHHh
Confidence            9999999998666                                          3458999999999999999999999


Q ss_pred             CCCeEEeCCCCHHHHHHHH
Q 023816          179 GAEDFIVKPVKLSDVKRIK  197 (276)
Q Consensus       179 Ga~d~l~KPv~~~~L~~~~  197 (276)
                      |++|||.||+++.+|...+
T Consensus       111 g~~dyl~KP~~~~~l~~rv  129 (360)
T COG3437         111 GADDYLSKPISPKELVARV  129 (360)
T ss_pred             hHHHHhcCCCCHHHHHHHH
Confidence            9999999999999985444

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

Probab=99.77  E-value=1.2e-17  Score=148.51  Aligned_cols=118  Identities=29%  Similarity=0.506  Sum_probs=108.0

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhCC-CEEEE-ECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHH
Q 023816           30 VHVLAVDDSFVDRKVIERLLTISS-CKVTA-VDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIK  107 (276)
Q Consensus        30 ~~VLIVdD~~~~~~~L~~~L~~~g-~~v~~-a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir  107 (276)
                      ++||||||++..|..++.+|...+ ++|+. +.||.++++.+           +...||+||+|+.||+++|++++++|+
T Consensus         1 ~~vlivDDh~l~r~gl~~~L~~~~~~~vv~~a~~~~~~l~~~-----------~~~~pdvvl~Dl~mP~~~G~e~~~~l~   69 (211)
T COG2197           1 IKVLIVDDHPLVREGLRQLLELEPDLEVVGEASNGEEALDLA-----------RELKPDVVLLDLSMPGMDGLEALKQLR   69 (211)
T ss_pred             CeEEEECCcHHHHHHHHHHHhhCCCCEEEEEeCCHHHHHHHh-----------hhcCCCEEEEcCCCCCCChHHHHHHHH
Confidence            479999999999999999998766 88665 88899999997           788999999999999999999999999


Q ss_pred             hhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCC
Q 023816          108 VTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKP  187 (276)
Q Consensus       108 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KP  187 (276)
                      +..|                                             +++||++|.+.+...+.+++++||++|+.|.
T Consensus        70 ~~~p---------------------------------------------~~~vvvlt~~~~~~~v~~al~~Ga~Gyl~K~  104 (211)
T COG2197          70 ARGP---------------------------------------------DIKVVVLTAHDDPAYVIRALRAGADGYLLKD  104 (211)
T ss_pred             HHCC---------------------------------------------CCcEEEEeccCCHHHHHHHHHcCCCEEEeCC
Confidence            9888                                             8899999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHh
Q 023816          188 VKLSDVKRIKDYLTRD  203 (276)
Q Consensus       188 v~~~~L~~~~~~l~~~  203 (276)
                      .+.+++.+.++.+...
T Consensus       105 ~~~~~l~~ai~~v~~G  120 (211)
T COG2197         105 ASPEELVEAIRAVAAG  120 (211)
T ss_pred             CCHHHHHHHHHHHHCC
Confidence            9999997777766544

>COG4566 TtrR Response regulator [Signal transduction mechanisms]

Probab=99.76  E-value=1e-17  Score=148.82  Aligned_cols=115  Identities=24%  Similarity=0.327  Sum_probs=105.6

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHh
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKV  108 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~  108 (276)
                      ..-|.||||+...|+.+..+|...||++..+.++++.|+..           ....+-++|+|+.||+++|.|+..++++
T Consensus         4 ~~~V~vVDDD~~vr~al~~Ll~s~G~~v~~~~s~~~fL~~~-----------~~~~pGclllDvrMPg~sGlelq~~L~~   72 (202)
T COG4566           4 EPLVHVVDDDESVRDALAFLLESAGFQVKCFASAEEFLAAA-----------PLDRPGCLLLDVRMPGMSGLELQDRLAE   72 (202)
T ss_pred             CCeEEEEcCcHHHHHHHHHHHHhCCceeeeecCHHHHHhhc-----------cCCCCCeEEEecCCCCCchHHHHHHHHh
Confidence            45688999999999999999999999999999999999886           5667999999999999999999999998


Q ss_pred             hCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCC
Q 023816          109 TTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPV  188 (276)
Q Consensus       109 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv  188 (276)
                      ...                                             ..|||++|++.+.....+|+++||.|||.||+
T Consensus        73 ~~~---------------------------------------------~~PVIfiTGhgDIpmaV~AmK~GAvDFLeKP~  107 (202)
T COG4566          73 RGI---------------------------------------------RLPVIFLTGHGDIPMAVQAMKAGAVDFLEKPF  107 (202)
T ss_pred             cCC---------------------------------------------CCCEEEEeCCCChHHHHHHHHcchhhHHhCCC
Confidence            766                                             89999999999999999999999999999999


Q ss_pred             CHHHHHHHHHH
Q 023816          189 KLSDVKRIKDY  199 (276)
Q Consensus       189 ~~~~L~~~~~~  199 (276)
                      +.+.|...+..
T Consensus       108 ~~q~Lldav~~  118 (202)
T COG4566         108 SEQDLLDAVER  118 (202)
T ss_pred             chHHHHHHHHH
Confidence            99998555444

>PRK10046 dpiA two-component response regulator DpiA; Provisional

Probab=99.75  E-value=6.1e-17  Score=142.05  Aligned_cols=120  Identities=15%  Similarity=0.245  Sum_probs=107.2

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhh-CCCE-EEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHH
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTI-SSCK-VTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKI  106 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~-~g~~-v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~I  106 (276)
                      +++||||||++..+..++.+|.. .++. +..+.++.+|++.+           ....||+||+|+.||+++|+++++.|
T Consensus         4 ~~~ilivdd~~~~~~~l~~~L~~~~~~~~v~~a~~~~~al~~~-----------~~~~pdlvllD~~mp~~~gle~~~~l   72 (225)
T PRK10046          4 PLTLLIVEDETPLAEMHAEYIRHIPGFSQILLAGNLAQARMMI-----------ERFKPGLILLDNYLPDGRGINLLHEL   72 (225)
T ss_pred             cceEEEECCCHHHHHHHHHHHHhCCCcEEEEEECCHHHHHHHH-----------HhcCCCEEEEeCCCCCCcHHHHHHHH
Confidence            68999999999999999999986 4785 56799999999998           66789999999999999999999999


Q ss_pred             HhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeC
Q 023816          107 KVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVK  186 (276)
Q Consensus       107 r~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~K  186 (276)
                      +...+                                             +++||++|+..+.....++++.||++|+.|
T Consensus        73 ~~~~~---------------------------------------------~~~iivls~~~~~~~~~~al~~Ga~~yl~K  107 (225)
T PRK10046         73 VQAHY---------------------------------------------PGDVVFTTAASDMETVSEAVRCGVFDYLIK  107 (225)
T ss_pred             HhcCC---------------------------------------------CCCEEEEEcCCCHHHHHHHHHcCccEEEEC
Confidence            97655                                             679999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHhh
Q 023816          187 PVKLSDVKRIKDYLTRDV  204 (276)
Q Consensus       187 Pv~~~~L~~~~~~l~~~~  204 (276)
                      |++.++|...+..+....
T Consensus       108 p~~~~~L~~~i~~~~~~~  125 (225)
T PRK10046        108 PIAYERLGQTLTRFRQRK  125 (225)
T ss_pred             CcCHHHHHHHHHHHHHHH
Confidence            999999977776655443

>PRK10816 DNA-binding transcriptional regulator PhoP; Provisional

Probab=99.72  E-value=2.3e-16  Score=134.49  Aligned_cols=117  Identities=22%  Similarity=0.411  Sum_probs=106.4

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhh
Q 023816           30 VHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVT  109 (276)
Q Consensus        30 ~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~  109 (276)
                      ++||+|||+...+..+...|+..|+.+..+.++.+|+..+           ....||+|++|+.||+++|+++++.++..
T Consensus         1 m~iLlv~d~~~~~~~l~~~L~~~g~~v~~~~~~~~~l~~~-----------~~~~~dlvild~~l~~~~g~~l~~~lr~~   69 (223)
T PRK10816          1 MRVLVVEDNALLRHHLKVQLQDAGHQVDAAEDAKEADYYL-----------NEHLPDIAIVDLGLPDEDGLSLIRRWRSN   69 (223)
T ss_pred             CeEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHH-----------hhCCCCEEEEECCCCCCCHHHHHHHHHhc
Confidence            4799999999999999999999999999999999999988           56689999999999999999999999975


Q ss_pred             CCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCC
Q 023816          110 TPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVK  189 (276)
Q Consensus       110 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~  189 (276)
                      .+                                             .+|+|++++..+.....++++.|++||+.||++
T Consensus        70 ~~---------------------------------------------~~pii~ls~~~~~~~~~~~l~~Ga~d~l~kp~~  104 (223)
T PRK10816         70 DV---------------------------------------------SLPILVLTARESWQDKVEVLSAGADDYVTKPFH  104 (223)
T ss_pred             CC---------------------------------------------CCCEEEEEcCCCHHHHHHHHHcCCCeeEeCCCC
Confidence            55                                             789999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHH
Q 023816          190 LSDVKRIKDYLTR  202 (276)
Q Consensus       190 ~~~L~~~~~~l~~  202 (276)
                      ..++...+..+.+
T Consensus       105 ~~eL~~~i~~~~~  117 (223)
T PRK10816        105 IEEVMARMQALMR  117 (223)
T ss_pred             HHHHHHHHHHHHh
Confidence            9999665555544

>PRK10529 DNA-binding transcriptional activator KdpE; Provisional

Probab=99.72  E-value=2.9e-16  Score=133.73  Aligned_cols=116  Identities=25%  Similarity=0.382  Sum_probs=104.6

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhh
Q 023816           30 VHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVT  109 (276)
Q Consensus        30 ~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~  109 (276)
                      .+||+|||++..+..+...|+..|+.+..+.++.+++..+           ....||+||+|+.||+++|++++++|++.
T Consensus         2 ~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~~~~~~-----------~~~~~dlvild~~l~~~~g~~~~~~lr~~   70 (225)
T PRK10529          2 TNVLIVEDEQAIRRFLRTALEGDGMRVFEAETLQRGLLEA-----------ATRKPDLIILDLGLPDGDGIEFIRDLRQW   70 (225)
T ss_pred             CEEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHH-----------hcCCCCEEEEeCCCCCCCHHHHHHHHHcC
Confidence            5899999999999999999999999999999999999887           56679999999999999999999999952


Q ss_pred             CCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCC
Q 023816          110 TPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVK  189 (276)
Q Consensus       110 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~  189 (276)
                       +                                             .+|+|++|+........++++.|++||+.||++
T Consensus        71 -~---------------------------------------------~~pvi~lt~~~~~~~~~~~~~~ga~~~l~kP~~  104 (225)
T PRK10529         71 -S---------------------------------------------AIPVIVLSARSEESDKIAALDAGADDYLSKPFG  104 (225)
T ss_pred             -C---------------------------------------------CCCEEEEECCCCHHHHHHHHHcCCCEEEeCCCC
Confidence             2                                             589999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHH
Q 023816          190 LSDVKRIKDYLTR  202 (276)
Q Consensus       190 ~~~L~~~~~~l~~  202 (276)
                      .+++...+..+.+
T Consensus       105 ~~~l~~~i~~~~~  117 (225)
T PRK10529        105 IGELQARLRVALR  117 (225)
T ss_pred             HHHHHHHHHHHHh
Confidence            9999666655544

>PRK10643 DNA-binding transcriptional regulator BasR; Provisional

Probab=99.72  E-value=3.3e-16  Score=131.84  Aligned_cols=117  Identities=23%  Similarity=0.386  Sum_probs=105.8

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhh
Q 023816           30 VHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVT  109 (276)
Q Consensus        30 ~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~  109 (276)
                      ++||+|||+...+..+...|...|+.+..+.++.+++..+           ....||+|++|+.||+++|+++++.++..
T Consensus         1 ~~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~-----------~~~~~d~illd~~~~~~~g~~~~~~l~~~   69 (222)
T PRK10643          1 MKILIVEDDTLLLQGLILALQTEGYACDCASTAREAEALL-----------ESGHYSLVVLDLGLPDEDGLHLLRRWRQK   69 (222)
T ss_pred             CEEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHH-----------HhCCCCEEEEECCCCCCCHHHHHHHHHhc
Confidence            4799999999999999999999999999999999999988           56679999999999999999999999975


Q ss_pred             CCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCC
Q 023816          110 TPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVK  189 (276)
Q Consensus       110 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~  189 (276)
                      .+                                             .+|+|++|+........++++.|++||+.||++
T Consensus        70 ~~---------------------------------------------~~pii~ls~~~~~~~~~~~~~~ga~~~l~kp~~  104 (222)
T PRK10643         70 KY---------------------------------------------TLPVLILTARDTLEDRVAGLDVGADDYLVKPFA  104 (222)
T ss_pred             CC---------------------------------------------CCcEEEEECCCCHHHHHHHHhcCCCeEEeCCCC
Confidence            55                                             689999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHH
Q 023816          190 LSDVKRIKDYLTR  202 (276)
Q Consensus       190 ~~~L~~~~~~l~~  202 (276)
                      .+++...+..+.+
T Consensus       105 ~~~l~~~i~~~~~  117 (222)
T PRK10643        105 LEELHARIRALIR  117 (222)
T ss_pred             HHHHHHHHHHHHh
Confidence            9999666655443

>PRK09836 DNA-binding transcriptional activator CusR; Provisional

Probab=99.72  E-value=3.2e-16  Score=134.01  Aligned_cols=117  Identities=22%  Similarity=0.410  Sum_probs=105.9

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhh
Q 023816           30 VHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVT  109 (276)
Q Consensus        30 ~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~  109 (276)
                      ++||+|||++..+..+...|+..|+.+..+.++.++++.+           ....||+||+|+.||+++|+++++.+++.
T Consensus         1 m~iliv~d~~~~~~~l~~~L~~~g~~v~~~~~~~~~~~~~-----------~~~~~dlvild~~~~~~~g~~~~~~lr~~   69 (227)
T PRK09836          1 MKLLIVEDEKKTGEYLTKGLTEAGFVVDLADNGLNGYHLA-----------MTGDYDLIILDIMLPDVNGWDIVRMLRSA   69 (227)
T ss_pred             CeEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHH-----------hhCCCCEEEEECCCCCCCHHHHHHHHHhc
Confidence            4799999999999999999999999999999999999987           56679999999999999999999999975


Q ss_pred             CCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCC
Q 023816          110 TPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVK  189 (276)
Q Consensus       110 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~  189 (276)
                      .+                                             .+|+|++|+........++++.|++||+.||++
T Consensus        70 ~~---------------------------------------------~~pii~ls~~~~~~~~~~~~~~Ga~~~l~kp~~  104 (227)
T PRK09836         70 NK---------------------------------------------GMPILLLTALGTIEHRVKGLELGADDYLVKPFA  104 (227)
T ss_pred             CC---------------------------------------------CCCEEEEEcCCCHHHHHHHHhCCCCEEEeCCCC
Confidence            55                                             789999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHH
Q 023816          190 LSDVKRIKDYLTR  202 (276)
Q Consensus       190 ~~~L~~~~~~l~~  202 (276)
                      .+++...+..+.+
T Consensus       105 ~~~l~~~i~~~~~  117 (227)
T PRK09836        105 FAELLARVRTLLR  117 (227)
T ss_pred             HHHHHHHHHHHHh
Confidence            9999665555443

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

Probab=99.72  E-value=1.7e-16  Score=167.14  Aligned_cols=120  Identities=26%  Similarity=0.511  Sum_probs=110.7

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHH
Q 023816           27 TEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKI  106 (276)
Q Consensus        27 ~~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~I  106 (276)
                      ...++||||||++.+++.+.++|+..||++..+.+|.+|++.+           ....||+||+|+.||+|+|+++++.|
T Consensus       799 ~~~~~ILvVdD~~~~~~~l~~~L~~~G~~v~~a~~g~eal~~l-----------~~~~~DlVl~D~~mP~mdG~el~~~i  867 (924)
T PRK10841        799 NDDMMILVVDDHPINRRLLADQLGSLGYQCKTANDGVDALNVL-----------SKNHIDIVLTDVNMPNMDGYRLTQRL  867 (924)
T ss_pred             CCCCEEEEECCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHH-----------HhCCCCEEEEcCCCCCCCHHHHHHHH
Confidence            3567999999999999999999999999999999999999999           56789999999999999999999999


Q ss_pred             HhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeC
Q 023816          107 KVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVK  186 (276)
Q Consensus       107 r~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~K  186 (276)
                      |+..+                                             .+|||++|+....+...+|++.|+++||.|
T Consensus       868 r~~~~---------------------------------------------~~pII~lTa~~~~~~~~~~~~aG~d~~L~K  902 (924)
T PRK10841        868 RQLGL---------------------------------------------TLPVIGVTANALAEEKQRCLEAGMDSCLSK  902 (924)
T ss_pred             HhcCC---------------------------------------------CCCEEEEECCCCHHHHHHHHHCCCCEEEeC
Confidence            97555                                             689999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHH
Q 023816          187 PVKLSDVKRIKDYLTR  202 (276)
Q Consensus       187 Pv~~~~L~~~~~~l~~  202 (276)
                      |++..+|.+.+..+.+
T Consensus       903 Pv~~~~L~~~L~~~~~  918 (924)
T PRK10841        903 PVTLDVLKQTLTVYAE  918 (924)
T ss_pred             CCCHHHHHHHHHHHHH
Confidence            9999999887776554

>PRK10336 DNA-binding transcriptional regulator QseB; Provisional

Probab=99.71  E-value=4.9e-16  Score=130.88  Aligned_cols=117  Identities=26%  Similarity=0.416  Sum_probs=106.2

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhh
Q 023816           30 VHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVT  109 (276)
Q Consensus        30 ~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~  109 (276)
                      ++||+|||++..+..+...|+..|+++..+.++.+++..+           ....||+||+|+.||+++|+++++.|+..
T Consensus         1 ~~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~-----------~~~~~dlvild~~l~~~~g~~~~~~i~~~   69 (219)
T PRK10336          1 MRILLIEDDMLIGDGIKTGLSKMGFSVDWFTQGRQGKEAL-----------YSAPYDAVILDLTLPGMDGRDILREWREK   69 (219)
T ss_pred             CeEEEEcCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHH-----------hhCCCCEEEEECCCCCCCHHHHHHHHHhc
Confidence            4799999999999999999999999999999999999988           55679999999999999999999999976


Q ss_pred             CCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCC
Q 023816          110 TPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVK  189 (276)
Q Consensus       110 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~  189 (276)
                      .+                                             .+|+|++|+........++++.|+++|+.||++
T Consensus        70 ~~---------------------------------------------~~~ii~lt~~~~~~~~~~~~~~ga~~~i~kp~~  104 (219)
T PRK10336         70 GQ---------------------------------------------REPVLILTARDALAERVEGLRLGADDYLCKPFA  104 (219)
T ss_pred             CC---------------------------------------------CCcEEEEECCCCHHHHHHHHhCCCCeEEECCCC
Confidence            55                                             789999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHH
Q 023816          190 LSDVKRIKDYLTR  202 (276)
Q Consensus       190 ~~~L~~~~~~l~~  202 (276)
                      .+++...+..+.+
T Consensus       105 ~~~l~~~i~~~~~  117 (219)
T PRK10336        105 LIEVAARLEALMR  117 (219)
T ss_pred             HHHHHHHHHHHHh
Confidence            9999766665544

>PRK11173 two-component response regulator; Provisional

Probab=99.71  E-value=4.4e-16  Score=134.93  Aligned_cols=118  Identities=22%  Similarity=0.397  Sum_probs=105.3

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHH
Q 023816           28 EEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIK  107 (276)
Q Consensus        28 ~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir  107 (276)
                      ...+||+|||++..+..+...|+..|+.+..+.++.++++.+           ....||+||+|+.||+++|+++++.|+
T Consensus         2 ~~~~iLiv~dd~~~~~~l~~~L~~~g~~v~~~~~~~~~~~~~-----------~~~~~dlvild~~l~~~~g~~~~~~lr   70 (237)
T PRK11173          2 QTPHILIVEDELVTRNTLKSIFEAEGYDVFEATDGAEMHQIL-----------SENDINLVIMDINLPGKNGLLLARELR   70 (237)
T ss_pred             CCCeEEEEeCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHH-----------hhCCCCEEEEcCCCCCCCHHHHHHHHh
Confidence            346899999999999999999999999999999999999988           566899999999999999999999999


Q ss_pred             hhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCC
Q 023816          108 VTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKP  187 (276)
Q Consensus       108 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KP  187 (276)
                      +. +                                             .+|+|++++.........+++.|++||+.||
T Consensus        71 ~~-~---------------------------------------------~~pii~lt~~~~~~~~~~~~~~ga~d~l~kP  104 (237)
T PRK11173         71 EQ-A---------------------------------------------NVALMFLTGRDNEVDKILGLEIGADDYITKP  104 (237)
T ss_pred             cC-C---------------------------------------------CCCEEEEECCCCHHHHHHHHHCCCCEEEECC
Confidence            52 3                                             5899999999998889999999999999999


Q ss_pred             CCHHHHHHHHHHHHH
Q 023816          188 VKLSDVKRIKDYLTR  202 (276)
Q Consensus       188 v~~~~L~~~~~~l~~  202 (276)
                      ++..+|...+..+.+
T Consensus       105 ~~~~eL~~~i~~~l~  119 (237)
T PRK11173        105 FNPRELTIRARNLLS  119 (237)
T ss_pred             CCHHHHHHHHHHHHh
Confidence            999999655544443

>PRK11083 DNA-binding response regulator CreB; Provisional

Probab=99.71  E-value=6.3e-16  Score=130.62  Aligned_cols=118  Identities=24%  Similarity=0.350  Sum_probs=106.2

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHH
Q 023816           28 EEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIK  107 (276)
Q Consensus        28 ~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir  107 (276)
                      .+++||+|||++..+..+...|...|+.+..+.++.+++..+           ....||+||+|+.||+++|+++++.|+
T Consensus         2 ~~~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~-----------~~~~~dlvl~d~~~~~~~g~~~~~~l~   70 (228)
T PRK11083          2 QQPTILLVEDEQAIADTLVYALQSEGFTVEWFERGLPALDKL-----------RQQPPDLVILDVGLPDISGFELCRQLL   70 (228)
T ss_pred             CCCEEEEEeCCHHHHHHHHHHHHHCCCEEEEEcCHHHHHHHH-----------hcCCCCEEEEeCCCCCCCHHHHHHHHH
Confidence            357899999999999999999999999999999999999988           566799999999999999999999999


Q ss_pred             hhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCC
Q 023816          108 VTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKP  187 (276)
Q Consensus       108 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KP  187 (276)
                      ...+                                             .+|+|++|+.........+++.|+++|+.||
T Consensus        71 ~~~~---------------------------------------------~~~ii~ls~~~~~~~~~~a~~~Ga~~~l~kp  105 (228)
T PRK11083         71 AFHP---------------------------------------------ALPVIFLTARSDEVDRLVGLEIGADDYVAKP  105 (228)
T ss_pred             hhCC---------------------------------------------CCCEEEEEcCCcHHHHHHHhhcCCCeEEECC
Confidence            7655                                             7899999999988888999999999999999


Q ss_pred             CCHHHHHHHHHHHH
Q 023816          188 VKLSDVKRIKDYLT  201 (276)
Q Consensus       188 v~~~~L~~~~~~l~  201 (276)
                      ++.++|...+..+.
T Consensus       106 ~~~~~l~~~i~~~~  119 (228)
T PRK11083        106 FSPREVAARVRTIL  119 (228)
T ss_pred             CCHHHHHHHHHHHH
Confidence            99999866555544

>PRK11107 hybrid sensory histidine kinase BarA; Provisional

Probab=99.70  E-value=2.8e-16  Score=160.71  Aligned_cols=121  Identities=26%  Similarity=0.404  Sum_probs=109.6

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHH
Q 023816           27 TEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKI  106 (276)
Q Consensus        27 ~~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~I  106 (276)
                      ..+++||||||++.++..++.+|+..|+.+..+.+|++|++.+           ....||+||+|+.||++||+++++.|
T Consensus       665 ~~~~~vLivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~al~~~-----------~~~~~dlil~D~~mp~~~g~~~~~~l  733 (919)
T PRK11107        665 RLPLTVMAVDDNPANLKLIGALLEEQVEHVVLCDSGHQAVEQA-----------KQRPFDLILMDIQMPGMDGIRACELI  733 (919)
T ss_pred             cCCCeEEEEeCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHH-----------HhCCCCEEEEeCCCCCCcHHHHHHHH
Confidence            3468999999999999999999999999999999999999998           66789999999999999999999999


Q ss_pred             HhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeC
Q 023816          107 KVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVK  186 (276)
Q Consensus       107 r~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~K  186 (276)
                      |+...                                           ...+|||++|+........+|++.|+++|+.|
T Consensus       734 r~~~~-------------------------------------------~~~~pii~lt~~~~~~~~~~~~~~G~~~~l~K  770 (919)
T PRK11107        734 RQLPH-------------------------------------------NQNTPIIAVTAHAMAGERERLLSAGMDDYLAK  770 (919)
T ss_pred             Hhccc-------------------------------------------CCCCCEEEEeCCCCHHHHHHHHHcCCCeEeeC
Confidence            96321                                           23689999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHH
Q 023816          187 PVKLSDVKRIKDYLT  201 (276)
Q Consensus       187 Pv~~~~L~~~~~~l~  201 (276)
                      |++..+|.+.+..+.
T Consensus       771 P~~~~~L~~~l~~~~  785 (919)
T PRK11107        771 PIDEAMLKQVLLRYK  785 (919)
T ss_pred             CCCHHHHHHHHHHHc
Confidence            999999977776654

>PRK15347 two component system sensor kinase SsrA; Provisional

Probab=99.70  E-value=3.6e-16  Score=160.25  Aligned_cols=122  Identities=25%  Similarity=0.418  Sum_probs=108.8

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHH
Q 023816           28 EEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIK  107 (276)
Q Consensus        28 ~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir  107 (276)
                      ..++||||||++.+++.+.++|+..|+++..+.+|++|++.+           ....||+||+|++||+++|++++++||
T Consensus       689 ~~~~iLivdd~~~~~~~l~~~L~~~g~~v~~a~~~~~al~~~-----------~~~~~dlil~D~~mp~~~G~~~~~~ir  757 (921)
T PRK15347        689 WQLQILLVDDVETNRDIIGMMLVELGQQVTTAASGTEALELG-----------RQHRFDLVLMDIRMPGLDGLETTQLWR  757 (921)
T ss_pred             ccCCEEEEeCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHH-----------hcCCCCEEEEeCCCCCCCHHHHHHHHH
Confidence            357999999999999999999999999999999999999998           667899999999999999999999999


Q ss_pred             hhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCC
Q 023816          108 VTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKP  187 (276)
Q Consensus       108 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KP  187 (276)
                      +...                                         .....+|||++|+........++++.|+++||.||
T Consensus       758 ~~~~-----------------------------------------~~~~~~pii~lt~~~~~~~~~~~~~~G~~~~l~KP  796 (921)
T PRK15347        758 DDPN-----------------------------------------NLDPDCMIVALTANAAPEEIHRCKKAGMNHYLTKP  796 (921)
T ss_pred             hchh-----------------------------------------hcCCCCcEEEEeCCCCHHHHHHHHHCCCCEEEECC
Confidence            6321                                         01237899999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHH
Q 023816          188 VKLSDVKRIKDYLT  201 (276)
Q Consensus       188 v~~~~L~~~~~~l~  201 (276)
                      ++..+|...+..+.
T Consensus       797 ~~~~~L~~~l~~~~  810 (921)
T PRK15347        797 VTLAQLARALELAA  810 (921)
T ss_pred             CCHHHHHHHHHHHH
Confidence            99999977776554

>PRK10430 DNA-binding transcriptional activator DcuR; Provisional

Probab=99.69  E-value=9.1e-16  Score=135.53  Aligned_cols=119  Identities=22%  Similarity=0.297  Sum_probs=103.9

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhh-CCCEEE-EECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHH
Q 023816           30 VHVLAVDDSFVDRKVIERLLTI-SSCKVT-AVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIK  107 (276)
Q Consensus        30 ~~VLIVdD~~~~~~~L~~~L~~-~g~~v~-~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir  107 (276)
                      ++||||||++..+..+..+|.. .++.+. .+.++.++++.+..         ....||+||+|+.||+++|+++++.|+
T Consensus         2 ~~VLivdd~~~~~~~l~~~L~~~~~~~~~~~~~~~~~a~~~~~~---------~~~~~DlvilD~~~p~~~G~eli~~l~   72 (239)
T PRK10430          2 INVLIVDDDAMVAELNRRYVAQIPGFQCCGTASTLEQAKEIIFN---------SDTPIDLILLDIYMQQENGLDLLPVLH   72 (239)
T ss_pred             eeEEEEcCCHHHHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHh---------cCCCCCEEEEecCCCCCCcHHHHHHHH
Confidence            6899999999999999999986 477655 68999999988721         135699999999999999999999999


Q ss_pred             hhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCC
Q 023816          108 VTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKP  187 (276)
Q Consensus       108 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KP  187 (276)
                      +..|                                             .+|||++|+..+.....++++.|+++|+.||
T Consensus        73 ~~~~---------------------------------------------~~~vI~ls~~~~~~~~~~al~~Ga~~yl~Kp  107 (239)
T PRK10430         73 EAGC---------------------------------------------KSDVIVISSAADAATIKDSLHYGVVDYLIKP  107 (239)
T ss_pred             hhCC---------------------------------------------CCCEEEEECCCcHHHHHHHHHcCCCEEEeCC
Confidence            8666                                             7899999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHH
Q 023816          188 VKLSDVKRIKDYLTR  202 (276)
Q Consensus       188 v~~~~L~~~~~~l~~  202 (276)
                      ++.++|...+..+..
T Consensus       108 ~~~~~l~~~i~~~~~  122 (239)
T PRK10430        108 FQASRFEEALTGWRQ  122 (239)
T ss_pred             CCHHHHHHHHHHHHH
Confidence            999999777766543

>PRK09468 ompR osmolarity response regulator; Provisional

Probab=99.69  E-value=1.3e-15  Score=131.50  Aligned_cols=118  Identities=21%  Similarity=0.375  Sum_probs=107.1

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHh
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKV  108 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~  108 (276)
                      ..+||||||++..+..+...|...|+.+..+.+++++++.+           ....||+||+|+.||+++|+++++.|+.
T Consensus         5 ~~~iLiv~d~~~~~~~l~~~L~~~g~~v~~~~~~~~~~~~~-----------~~~~~dlvild~~l~~~~g~~~~~~lr~   73 (239)
T PRK09468          5 NYKILVVDDDMRLRALLERYLTEQGFQVRSAANAEQMDRLL-----------TRESFHLMVLDLMLPGEDGLSICRRLRS   73 (239)
T ss_pred             CCeEEEEcCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHH-----------hcCCCCEEEEeCCCCCCCHHHHHHHHHh
Confidence            56899999999999999999999999999999999999988           5678999999999999999999999997


Q ss_pred             hCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCC
Q 023816          109 TTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPV  188 (276)
Q Consensus       109 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv  188 (276)
                      ..+                                             .+|||++++.........+++.|++||+.||+
T Consensus        74 ~~~---------------------------------------------~~pii~ls~~~~~~~~~~~l~~Ga~~~l~kP~  108 (239)
T PRK09468         74 QNN---------------------------------------------PTPIIMLTAKGEEVDRIVGLEIGADDYLPKPF  108 (239)
T ss_pred             cCC---------------------------------------------CCCEEEEECCCcHHHHHHHHhcCCCeEEECCC
Confidence            554                                             78999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHH
Q 023816          189 KLSDVKRIKDYLTR  202 (276)
Q Consensus       189 ~~~~L~~~~~~l~~  202 (276)
                      +.++|...+..+.+
T Consensus       109 ~~~~L~~~i~~~~~  122 (239)
T PRK09468        109 NPRELLARIRAVLR  122 (239)
T ss_pred             CHHHHHHHHHHHhc
Confidence            99999666655443

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

Probab=99.69  E-value=5.6e-16  Score=152.05  Aligned_cols=123  Identities=30%  Similarity=0.529  Sum_probs=110.2

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHH
Q 023816           28 EEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIK  107 (276)
Q Consensus        28 ~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir  107 (276)
                      .+.+||+|||+...++.++++|...|+++..+.++.+|+..+           .+..||+||+|+.||++||+++++++|
T Consensus       131 ~~~kILvvdD~~~~~~~l~~~L~~~g~~v~~a~~~~~Al~~~-----------~e~~~dlil~d~~mp~~dg~el~~~lr  199 (435)
T COG3706         131 APKKILVVDDDATQRERLRRILQVEGFRVVEATDGEEALLQL-----------AELPPDLVLLDANMPDMDGLELCTRLR  199 (435)
T ss_pred             cCceEEEEcCcHHHHHHHHHHHHhccceeeeecCHHHHHHHH-----------hcCCCcEEEEecCCCccCHHHHHHHHh
Confidence            578999999999999999999999999999999999999999           667999999999999999999999999


Q ss_pred             hhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCC
Q 023816          108 VTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKP  187 (276)
Q Consensus       108 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KP  187 (276)
                      ....                                           .+.+|||++++.++.....+|++.|++|||.||
T Consensus       200 ~~~~-------------------------------------------t~~ipii~~~~~~d~~~~~~Af~~G~~Dyi~kP  236 (435)
T COG3706         200 QLER-------------------------------------------TRDIPIILLSSKDDDELVVRAFELGVNDYITKP  236 (435)
T ss_pred             cccc-------------------------------------------cccccEEEEecccchHHHHHHHHcCCcceEecC
Confidence            7443                                           368999999999999999999999999999999


Q ss_pred             CCHHHH-HHHHHHHHHhh
Q 023816          188 VKLSDV-KRIKDYLTRDV  204 (276)
Q Consensus       188 v~~~~L-~~~~~~l~~~~  204 (276)
                      +...++ .++.+.+.+..
T Consensus       237 i~~~~l~~Rl~~~l~~~~  254 (435)
T COG3706         237 IEEGELRARLRRQLRRKR  254 (435)
T ss_pred             CCHHHHHHHHHHHHHhhh
Confidence            997777 45444444443

>PRK10766 DNA-binding transcriptional regulator TorR; Provisional

Probab=99.69  E-value=1.4e-15  Score=129.32  Aligned_cols=117  Identities=23%  Similarity=0.387  Sum_probs=104.8

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHh
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKV  108 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~  108 (276)
                      ..+||+|||+...+..+...|...|+.+..+.++.++++.+           ....||+|++|+.||+++|+++++.++.
T Consensus         2 ~~~iLlv~d~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~-----------~~~~~dlvild~~l~~~~g~~~~~~lr~   70 (221)
T PRK10766          2 SYHILVVEDEPVTRARLQGYFEQEGYTVSEAASGAGMREIM-----------QNQHVDLILLDINLPGEDGLMLTRELRS   70 (221)
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHH-----------hcCCCCEEEEeCCCCCCCHHHHHHHHHh
Confidence            35899999999999999999999999999999999999988           5667999999999999999999999996


Q ss_pred             hCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCC
Q 023816          109 TTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPV  188 (276)
Q Consensus       109 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv  188 (276)
                      . +                                             .+|+|++++........++++.||+||+.||+
T Consensus        71 ~-~---------------------------------------------~~~ii~l~~~~~~~~~~~~l~~Ga~d~l~kP~  104 (221)
T PRK10766         71 R-S---------------------------------------------TVGIILVTGRTDSIDRIVGLEMGADDYVTKPL  104 (221)
T ss_pred             C-C---------------------------------------------CCCEEEEECCCcHHHHHHHHHcCCCcEEeCCC
Confidence            2 2                                             68999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHH
Q 023816          189 KLSDVKRIKDYLTR  202 (276)
Q Consensus       189 ~~~~L~~~~~~l~~  202 (276)
                      +..+|...+..+.+
T Consensus       105 ~~~~L~~~i~~~~~  118 (221)
T PRK10766        105 ELRELLVRVKNLLW  118 (221)
T ss_pred             CHHHHHHHHHHHHh
Confidence            99998655554443

>PRK10701 DNA-binding transcriptional regulator RstA; Provisional

Probab=99.69  E-value=1.3e-15  Score=131.83  Aligned_cols=116  Identities=22%  Similarity=0.253  Sum_probs=103.6

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhh
Q 023816           30 VHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVT  109 (276)
Q Consensus        30 ~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~  109 (276)
                      .+||+|||++..+..+...|+..|+.+..+.++.++++.+           ....||+||+|+.||+++|+++++.|+..
T Consensus         2 ~~iLivedd~~~~~~l~~~L~~~g~~v~~~~~~~~~l~~~-----------~~~~~dlvild~~l~~~~g~~~~~~ir~~   70 (240)
T PRK10701          2 NKIVFVEDDAEVGSLIAAYLAKHDIDVTVEPRGDRAEATI-----------LREQPDLVLLDIMLPGKDGMTICRDLRPK   70 (240)
T ss_pred             ceEEEEeCCHHHHHHHHHHHHHcCCEEEEeCCHHHHHHHH-----------hhCCCCEEEEeCCCCCCCHHHHHHHHHhc
Confidence            4899999999999999999999999999999999999988           66789999999999999999999999962


Q ss_pred             CCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCC
Q 023816          110 TPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVK  189 (276)
Q Consensus       110 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~  189 (276)
                      .                                              +.|+|++++........++++.|++||+.||++
T Consensus        71 ~----------------------------------------------~~pii~l~~~~~~~~~~~~~~~Ga~d~l~kP~~  104 (240)
T PRK10701         71 W----------------------------------------------QGPIVLLTSLDSDMNHILALEMGACDYILKTTP  104 (240)
T ss_pred             C----------------------------------------------CCCEEEEECCCCHHHHHHHHHcCCCEEEECCCC
Confidence            2                                              579999999888888889999999999999999


Q ss_pred             HHHHHHHHHHHHH
Q 023816          190 LSDVKRIKDYLTR  202 (276)
Q Consensus       190 ~~~L~~~~~~l~~  202 (276)
                      ..++...+..+.+
T Consensus       105 ~~~l~~~i~~~l~  117 (240)
T PRK10701        105 PAVLLARLRLHLR  117 (240)
T ss_pred             HHHHHHHHHHHHh
Confidence            9998655554443

>TIGR03787 marine_sort_RR proteobacterial dedicated sortase system response regulator

Probab=99.69  E-value=1.5e-15  Score=129.46  Aligned_cols=116  Identities=20%  Similarity=0.259  Sum_probs=104.4

Q ss_pred             EEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCC--CCHHHHHHHHHh
Q 023816           31 HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPG--MTGYELLKKIKV  108 (276)
Q Consensus        31 ~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~--~~G~ell~~Ir~  108 (276)
                      +||+|||+...+..+...|+..|+.+..+.++++++..+           ....||+|++|+.||+  .+|+++++.++.
T Consensus         2 ~iLivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~-----------~~~~~dlvild~~l~~~~~~g~~~~~~i~~   70 (227)
T TIGR03787         2 RIAIVEDEAAIRENYADALKRQGYQVTTYADRPSAMQAF-----------RQRLPDLAIIDIGLGEEIDGGFMLCQDLRS   70 (227)
T ss_pred             eEEEEeCCHHHHHHHHHHHHHCCcEEEEecCHHHHHHHH-----------HhCCCCEEEEECCCCCCCCCHHHHHHHHHh
Confidence            699999999999999999999999999999999999988           5678999999999998  589999999997


Q ss_pred             hCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCC
Q 023816          109 TTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPV  188 (276)
Q Consensus       109 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv  188 (276)
                      ..+                                             .+|+|++|+.........++++||++|+.||+
T Consensus        71 ~~~---------------------------------------------~~pii~ls~~~~~~~~~~~~~~Ga~~~l~kp~  105 (227)
T TIGR03787        71 LSA---------------------------------------------TLPIIFLTARDSDFDTVSGLRLGADDYLTKDI  105 (227)
T ss_pred             cCC---------------------------------------------CCCEEEEECCCCHHHHHHHHhcCCCEEEECCC
Confidence            555                                             68999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHH
Q 023816          189 KLSDVKRIKDYLTR  202 (276)
Q Consensus       189 ~~~~L~~~~~~l~~  202 (276)
                      +..++...+..+.+
T Consensus       106 ~~~~l~~~i~~~~~  119 (227)
T TIGR03787       106 SLPHLLARITALFR  119 (227)
T ss_pred             CHHHHHHHHHHHHH
Confidence            99998665555444

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.

>PRK11466 hybrid sensory histidine kinase TorS; Provisional

Probab=99.69  E-value=5.6e-16  Score=159.47  Aligned_cols=121  Identities=17%  Similarity=0.288  Sum_probs=109.6

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHH
Q 023816           27 TEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKI  106 (276)
Q Consensus        27 ~~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~I  106 (276)
                      ..+.+||||||++.++..+..+|+..||+|..+.++.+|++.+.          ....||+||+|++||+++|+++++.|
T Consensus       679 ~~~~~vLivdD~~~~~~~l~~~L~~~g~~v~~a~~~~~al~~~~----------~~~~~Dlvl~D~~mp~~~G~~~~~~l  748 (914)
T PRK11466        679 LDGLRLLLIEDNPLTQRITAEMLNTSGAQVVAVGNAAQALETLQ----------NSEPFAAALVDFDLPDYDGITLARQL  748 (914)
T ss_pred             cCCcceEEEeCCHHHHHHHHHHHHhcCCceEEeCCHHHHHHHHH----------cCCCCCEEEEeCCCCCCCHHHHHHHH
Confidence            34679999999999999999999999999999999999999872          23468999999999999999999999


Q ss_pred             HhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeC
Q 023816          107 KVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVK  186 (276)
Q Consensus       107 r~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~K  186 (276)
                      |+..|                                             .+|||++|+........++++.|+++||.|
T Consensus       749 r~~~~---------------------------------------------~~~ii~~t~~~~~~~~~~~~~~g~~~~l~K  783 (914)
T PRK11466        749 AQQYP---------------------------------------------SLVLIGFSAHVIDETLRQRTSSLFRGIIPK  783 (914)
T ss_pred             HhhCC---------------------------------------------CCCEEEEeCCCchhhHHHHHhcCcCCEEeC
Confidence            98666                                             799999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHH
Q 023816          187 PVKLSDVKRIKDYLTR  202 (276)
Q Consensus       187 Pv~~~~L~~~~~~l~~  202 (276)
                      |++.++|...+..+.+
T Consensus       784 P~~~~~L~~~i~~~~~  799 (914)
T PRK11466        784 PVPREVLGQLLAHYLQ  799 (914)
T ss_pred             CCCHHHHHHHHHHHhh
Confidence            9999999877776654

>PRK10161 transcriptional regulator PhoB; Provisional

Probab=99.68  E-value=1.8e-15  Score=129.60  Aligned_cols=119  Identities=26%  Similarity=0.396  Sum_probs=105.8

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhh
Q 023816           30 VHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVT  109 (276)
Q Consensus        30 ~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~  109 (276)
                      .+||+|||++..+..+...|+..|+++..+.++.++++.+           ....||+||+|+.||+++|+++++.|++.
T Consensus         3 ~~Ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~~~~~~-----------~~~~~dlvild~~l~~~~g~~~~~~l~~~   71 (229)
T PRK10161          3 RRILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQL-----------NEPWPDLILLDWMLPGGSGIQFIKHLKRE   71 (229)
T ss_pred             CeEEEEcCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHH-----------hccCCCEEEEeCCCCCCCHHHHHHHHHhc
Confidence            6799999999999999999999999999999999999988           56679999999999999999999999963


Q ss_pred             CCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCC
Q 023816          110 TPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVK  189 (276)
Q Consensus       110 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~  189 (276)
                      ..                                           ...+|+|++|+..+.....+++++|+++|+.||++
T Consensus        72 ~~-------------------------------------------~~~~pvi~ls~~~~~~~~~~~~~~Ga~~~l~kp~~  108 (229)
T PRK10161         72 SM-------------------------------------------TRDIPVVMLTARGEEEDRVRGLETGADDYITKPFS  108 (229)
T ss_pred             cc-------------------------------------------cCCCCEEEEECCCCHHHHHHHHHcCCCEEEECCCC
Confidence            21                                           12689999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHH
Q 023816          190 LSDVKRIKDYLTR  202 (276)
Q Consensus       190 ~~~L~~~~~~l~~  202 (276)
                      ..+|...+..+.+
T Consensus       109 ~~~L~~~i~~~~~  121 (229)
T PRK10161        109 PKELVARIKAVMR  121 (229)
T ss_pred             HHHHHHHHHHHHh
Confidence            9999666665544

>PRK10955 DNA-binding transcriptional regulator CpxR; Provisional

Probab=99.68  E-value=1.8e-15  Score=128.79  Aligned_cols=115  Identities=27%  Similarity=0.424  Sum_probs=102.6

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhh
Q 023816           30 VHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVT  109 (276)
Q Consensus        30 ~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~  109 (276)
                      .+||+|||++..+..+...|+..|+.+..+.++.++++.+           . ..||+||+|+.||+++|+++++.|++.
T Consensus         2 ~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~-----------~-~~~d~vl~d~~~~~~~g~~~~~~l~~~   69 (232)
T PRK10955          2 NKILLVDDDRELTSLLKELLEMEGFNVIVAHDGEQALDLL-----------D-DSIDLLLLDVMMPKKNGIDTLKELRQT   69 (232)
T ss_pred             ceEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHh-----------h-cCCCEEEEeCCCCCCcHHHHHHHHHhc
Confidence            4899999999999999999999999999999999999977           4 369999999999999999999999963


Q ss_pred             CCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCC
Q 023816          110 TPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVK  189 (276)
Q Consensus       110 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~  189 (276)
                      .                                              ++|+|++|+........++++.|+++|+.||++
T Consensus        70 ~----------------------------------------------~~~ii~lt~~~~~~~~~~~~~~ga~~~l~kp~~  103 (232)
T PRK10955         70 H----------------------------------------------QTPVIMLTARGSELDRVLGLELGADDYLPKPFN  103 (232)
T ss_pred             C----------------------------------------------CCcEEEEECCCCHHHHHHHHHcCCCEEEcCCCC
Confidence            2                                              379999999999888899999999999999999


Q ss_pred             HHHHHHHHHHHHH
Q 023816          190 LSDVKRIKDYLTR  202 (276)
Q Consensus       190 ~~~L~~~~~~l~~  202 (276)
                      .+++...+..+.+
T Consensus       104 ~~~l~~~i~~~~~  116 (232)
T PRK10955        104 DRELVARIRAILR  116 (232)
T ss_pred             HHHHHHHHHHHHh
Confidence            9999666655544

>TIGR02154 PhoB phosphate regulon transcriptional regulatory protein PhoB

Probab=99.68  E-value=1.8e-15  Score=127.36  Aligned_cols=120  Identities=27%  Similarity=0.451  Sum_probs=105.7

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHh
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKV  108 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~  108 (276)
                      ..+||+|||++..+..+...|+..|+++..+.++++++..+           ....||+||+|+.||+++|+++++.|+.
T Consensus         2 ~~~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~-----------~~~~~d~vi~d~~~~~~~g~~~~~~l~~   70 (226)
T TIGR02154         2 TRRILVVEDEPAIRELIAYNLEKAGYDVVEAGDGDEALTLI-----------NERGPDLILLDWMLPGTSGIELCRRLRR   70 (226)
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHHCCCEEEEEcCHHHHHHHH-----------HhcCCCEEEEECCCCCCcHHHHHHHHHc
Confidence            36899999999999999999999999999999999999988           5667999999999999999999999986


Q ss_pred             hCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCC
Q 023816          109 TTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPV  188 (276)
Q Consensus       109 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv  188 (276)
                      ..+                                           ...+|||++|+..+.....++++.|+++|+.||+
T Consensus        71 ~~~-------------------------------------------~~~~~ii~ls~~~~~~~~~~~~~~Ga~~~l~kp~  107 (226)
T TIGR02154        71 RPE-------------------------------------------TRAIPIIMLTARGEEEDRVRGLETGADDYITKPF  107 (226)
T ss_pred             ccc-------------------------------------------CCCCCEEEEecCCCHHHHHHHHhcCcceEEeCCC
Confidence            421                                           1268999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHH
Q 023816          189 KLSDVKRIKDYLTR  202 (276)
Q Consensus       189 ~~~~L~~~~~~l~~  202 (276)
                      +.+++...+..+.+
T Consensus       108 ~~~~l~~~i~~~~~  121 (226)
T TIGR02154       108 SPRELLARIKAVLR  121 (226)
T ss_pred             CHHHHHHHHHHHhc
Confidence            99998666655543

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.

>TIGR02956 TMAO_torS TMAO reductase sytem sensor TorS

Probab=99.68  E-value=7.5e-16  Score=158.94  Aligned_cols=124  Identities=25%  Similarity=0.359  Sum_probs=110.3

Q ss_pred             CCCccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHH
Q 023816           26 DTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKK  105 (276)
Q Consensus        26 ~~~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~  105 (276)
                      ..+..+||||||++.++..+.++|+..||+|..+.+|.+|++.+           ....||+||+|++||+++|+++++.
T Consensus       699 ~~~~~~iLvvdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l-----------~~~~~dlvl~D~~mp~~~g~~~~~~  767 (968)
T TIGR02956       699 DLPPQRVLLVEDNEVNQMVAQGFLTRLGHKVTLAESGQSALECF-----------HQHAFDLALLDINLPDGDGVTLLQQ  767 (968)
T ss_pred             cccccceEEEcCcHHHHHHHHHHHHHcCCEEEEECCHHHHHHHH-----------HCCCCCEEEECCCCCCCCHHHHHHH
Confidence            44566899999999999999999999999999999999999999           5678999999999999999999999


Q ss_pred             HHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEe
Q 023816          106 IKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIV  185 (276)
Q Consensus       106 Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~  185 (276)
                      ||...+.                                          ...+|||++|+........++++.|+++|+.
T Consensus       768 ir~~~~~------------------------------------------~~~~pii~lta~~~~~~~~~~~~~G~~~~l~  805 (968)
T TIGR02956       768 LRAIYGA------------------------------------------KNEVKFIAFSAHVFNEDVAQYLAAGFDGFLA  805 (968)
T ss_pred             HHhCccc------------------------------------------cCCCeEEEEECCCCHHHHHHHHHCCCCEEEe
Confidence            9975440                                          0028999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHH
Q 023816          186 KPVKLSDVKRIKDYLTR  202 (276)
Q Consensus       186 KPv~~~~L~~~~~~l~~  202 (276)
                      ||++..+|...+..+..
T Consensus       806 KP~~~~~L~~~l~~~~~  822 (968)
T TIGR02956       806 KPVVEEQLTAMIAVILA  822 (968)
T ss_pred             CCCCHHHHHHHHHHHhc
Confidence            99999999877766543

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).

>CHL00148 orf27 Ycf27; Reviewed

Probab=99.67  E-value=3.3e-15  Score=127.80  Aligned_cols=118  Identities=27%  Similarity=0.477  Sum_probs=106.0

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHH
Q 023816           28 EEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIK  107 (276)
Q Consensus        28 ~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir  107 (276)
                      +.++||+|||++..+..+...|...|+.+..+.++.+++..+           ....||+||+|+.||+++|+++++.++
T Consensus         5 ~~~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~~l~~~-----------~~~~~d~illd~~~~~~~g~~~~~~l~   73 (240)
T CHL00148          5 SKEKILVVDDEAYIRKILETRLSIIGYEVITASDGEEALKLF-----------RKEQPDLVILDVMMPKLDGYGVCQEIR   73 (240)
T ss_pred             CCceEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHH-----------HhcCCCEEEEeCCCCCCCHHHHHHHHH
Confidence            467999999999999999999999999999999999999988           566799999999999999999999999


Q ss_pred             hhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCC
Q 023816          108 VTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKP  187 (276)
Q Consensus       108 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KP  187 (276)
                      +. +                                             .+|+|++|+........++++.|+++|+.||
T Consensus        74 ~~-~---------------------------------------------~~~ii~ls~~~~~~~~~~~~~~Ga~~~l~kp  107 (240)
T CHL00148         74 KE-S---------------------------------------------DVPIIMLTALGDVSDRITGLELGADDYVVKP  107 (240)
T ss_pred             hc-C---------------------------------------------CCcEEEEECCCCHHhHHHHHHCCCCEEEeCC
Confidence            63 3                                             6899999999999888999999999999999


Q ss_pred             CCHHHHHHHHHHHHH
Q 023816          188 VKLSDVKRIKDYLTR  202 (276)
Q Consensus       188 v~~~~L~~~~~~l~~  202 (276)
                      ++.++|...+..+.+
T Consensus       108 ~~~~~L~~~i~~~~~  122 (240)
T CHL00148        108 FSPKELEARIRSVLR  122 (240)
T ss_pred             CCHHHHHHHHHHHHh
Confidence            999999666655543

>PRK10840 transcriptional regulator RcsB; Provisional

Probab=99.67  E-value=2.1e-15  Score=130.56  Aligned_cols=119  Identities=23%  Similarity=0.328  Sum_probs=105.4

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhCCC-E-EEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCC---CCHHHH
Q 023816           28 EEVHVLAVDDSFVDRKVIERLLTISSC-K-VTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPG---MTGYEL  102 (276)
Q Consensus        28 ~~~~VLIVdD~~~~~~~L~~~L~~~g~-~-v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~---~~G~el  102 (276)
                      +.++||||||++..+..++..|+..++ . +..+.++.++++.+           ....||+||+|+.||+   .+|.++
T Consensus         2 ~~~~Ilivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~~~~~~-----------~~~~~DlvllD~~l~~~~~~~g~~~   70 (216)
T PRK10840          2 NNMNVIIADDHPIVLFGIRKSLEQIEWVNVVGEFEDSTALINNL-----------PKLDAHVLITDLSMPGDKYGDGITL   70 (216)
T ss_pred             CceEEEEECCcHHHHHHHHHHHhcCCCCEEEEEECCHHHHHHHH-----------HhCCCCEEEEeCcCCCCCCCCHHHH
Confidence            458999999999999999999987664 4 55689999999988           5667999999999999   599999


Q ss_pred             HHHHHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCe
Q 023816          103 LKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAED  182 (276)
Q Consensus       103 l~~Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d  182 (276)
                      +++|++..|                                             .+|||++|+..+.....++++.|+++
T Consensus        71 ~~~l~~~~~---------------------------------------------~~~iIvls~~~~~~~~~~a~~~Ga~~  105 (216)
T PRK10840         71 IKYIKRHFP---------------------------------------------SLSIIVLTMNNNPAILSAVLDLDIEG  105 (216)
T ss_pred             HHHHHHHCC---------------------------------------------CCcEEEEEecCCHHHHHHHHHCCCeE
Confidence            999998776                                             78999999999999999999999999


Q ss_pred             EEeCCCCHHHHHHHHHHHHH
Q 023816          183 FIVKPVKLSDVKRIKDYLTR  202 (276)
Q Consensus       183 ~l~KPv~~~~L~~~~~~l~~  202 (276)
                      |+.||.+.++|...+..+..
T Consensus       106 yl~K~~~~~~l~~ai~~v~~  125 (216)
T PRK10840        106 IVLKQGAPTDLPKALAALQK  125 (216)
T ss_pred             EEECCCCHHHHHHHHHHHHC
Confidence            99999999999777766554

>PRK09958 DNA-binding transcriptional activator EvgA; Provisional

Probab=99.66  E-value=3.8e-15  Score=124.77  Aligned_cols=117  Identities=21%  Similarity=0.367  Sum_probs=105.9

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhCCCEEE-EECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHh
Q 023816           30 VHVLAVDDSFVDRKVIERLLTISSCKVT-AVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKV  108 (276)
Q Consensus        30 ~~VLIVdD~~~~~~~L~~~L~~~g~~v~-~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~  108 (276)
                      ++||+|||++..+..+...|+..|+++. .+.++.++++.+           ....||+|++|+.||+++|+++++.++.
T Consensus         1 m~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~~-----------~~~~~dlvi~d~~~~~~~g~~~~~~l~~   69 (204)
T PRK09958          1 MNAIIIDDHPLAIAAIRNLLIKNDIEILAELTEGGSAVQRV-----------ETLKPDIVIIDVDIPGVNGIQVLETLRK   69 (204)
T ss_pred             CcEEEECCcHHHHHHHHHHHhcCCCEEEEEeCCHHHHHHHH-----------HccCCCEEEEeCCCCCCCHHHHHHHHHh
Confidence            4799999999999999999999999987 699999999988           5667999999999999999999999997


Q ss_pred             hCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCC
Q 023816          109 TTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPV  188 (276)
Q Consensus       109 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv  188 (276)
                      ..+                                             ..|+|++++........++++.|+++|+.||+
T Consensus        70 ~~~---------------------------------------------~~~ii~ls~~~~~~~~~~~~~~ga~~~i~kp~  104 (204)
T PRK09958         70 RQY---------------------------------------------SGIIIIVSAKNDHFYGKHCADAGANGFVSKKE  104 (204)
T ss_pred             hCC---------------------------------------------CCeEEEEeCCCCHHHHHHHHHCCCCEEEecCC
Confidence            655                                             67899999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHH
Q 023816          189 KLSDVKRIKDYLTR  202 (276)
Q Consensus       189 ~~~~L~~~~~~l~~  202 (276)
                      +.+++...+..+.+
T Consensus       105 ~~~~l~~~i~~~~~  118 (204)
T PRK09958        105 GMNNIIAAIEAAKN  118 (204)
T ss_pred             CHHHHHHHHHHHHc
Confidence            99999777766654

>PRK09483 response regulator; Provisional

Probab=99.66  E-value=3.7e-15  Score=125.95  Aligned_cols=118  Identities=25%  Similarity=0.367  Sum_probs=106.3

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhC-CCEEE-EECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHH
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTIS-SCKVT-AVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKI  106 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~-g~~v~-~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~I  106 (276)
                      +++||||||++..+..++.+|+.. |+++. .+.+++++++.+           ....||+||+|+.+|+++|+++++.|
T Consensus         1 m~~ilivd~~~~~~~~l~~~L~~~~~~~~v~~~~~~~~~~~~~-----------~~~~~dlvi~d~~~~~~~g~~~~~~l   69 (217)
T PRK09483          1 MINVLLVDDHELVRAGIRRILEDIKGIKVVGEACCGEDAVKWC-----------RTNAVDVVLMDMNMPGIGGLEATRKI   69 (217)
T ss_pred             CeEEEEECCcHHHHHHHHHHHccCCCCEEEEEeCCHHHHHHHH-----------HhcCCCEEEEeCCCCCCCHHHHHHHH
Confidence            368999999999999999999874 88876 689999999988           56689999999999999999999999


Q ss_pred             HhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeC
Q 023816          107 KVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVK  186 (276)
Q Consensus       107 r~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~K  186 (276)
                      ++..|                                             .+|+|++|.........+++..|+++|+.|
T Consensus        70 ~~~~~---------------------------------------------~~~ii~ls~~~~~~~~~~~~~~g~~~~l~k  104 (217)
T PRK09483         70 LRYTP---------------------------------------------DVKIIMLTVHTENPLPAKVMQAGAAGYLSK  104 (217)
T ss_pred             HHHCC---------------------------------------------CCeEEEEeCCCCHHHHHHHHHcCCCEEEeC
Confidence            98766                                             789999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHH
Q 023816          187 PVKLSDVKRIKDYLTR  202 (276)
Q Consensus       187 Pv~~~~L~~~~~~l~~  202 (276)
                      |++.+++...+..+.+
T Consensus       105 ~~~~~~l~~~i~~~~~  120 (217)
T PRK09483        105 GAAPQEVVSAIRSVHS  120 (217)
T ss_pred             CCCHHHHHHHHHHHHC
Confidence            9999999777766654

>PRK11517 transcriptional regulatory protein YedW; Provisional

Probab=99.66  E-value=4.5e-15  Score=125.66  Aligned_cols=115  Identities=24%  Similarity=0.443  Sum_probs=103.5

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhh
Q 023816           30 VHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVT  109 (276)
Q Consensus        30 ~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~  109 (276)
                      ++||+|||++..+..+...|+..|+.+..+.++.+++..+           ....||+|++|+.||+++|+++++.+++.
T Consensus         1 m~iliv~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~l~~~-----------~~~~~dlvi~d~~~~~~~g~~~~~~l~~~   69 (223)
T PRK11517          1 MKILLIEDNQRTQEWVTQGLSEAGYVIDAVSDGRDGLYLA-----------LKDDYALIILDIMLPGMDGWQILQTLRTA   69 (223)
T ss_pred             CEEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHH-----------hcCCCCEEEEECCCCCCCHHHHHHHHHcC
Confidence            4799999999999999999999999999999999999988           56679999999999999999999999852


Q ss_pred             CCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCC
Q 023816          110 TPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVK  189 (276)
Q Consensus       110 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~  189 (276)
                       +                                             .+|+|++++........++++.||++|+.||++
T Consensus        70 -~---------------------------------------------~~~ii~ls~~~~~~~~~~a~~~Ga~~~l~kp~~  103 (223)
T PRK11517         70 -K---------------------------------------------QTPVICLTARDSVDDRVRGLDSGANDYLVKPFS  103 (223)
T ss_pred             -C---------------------------------------------CCCEEEEECCCCHHHHHHHHhcCCCEEEECCCC
Confidence             2                                             589999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHH
Q 023816          190 LSDVKRIKDYLT  201 (276)
Q Consensus       190 ~~~L~~~~~~l~  201 (276)
                      .+++...+..+.
T Consensus       104 ~~~l~~~i~~~~  115 (223)
T PRK11517        104 FSELLARVRAQL  115 (223)
T ss_pred             HHHHHHHHHHHH
Confidence            999866555444

>PRK13856 two-component response regulator VirG; Provisional

Probab=99.66  E-value=4.3e-15  Score=129.60  Aligned_cols=115  Identities=30%  Similarity=0.443  Sum_probs=101.2

Q ss_pred             EEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhhC
Q 023816           31 HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVTT  110 (276)
Q Consensus        31 ~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~~  110 (276)
                      +||+|||++..+..+...|+..|+.+..+.++.++++.+           ....||+||+|+.||+++|+++++.|+.. 
T Consensus         3 ~ILived~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~-----------~~~~~dlvi~d~~l~~~~g~~l~~~i~~~-   70 (241)
T PRK13856          3 HVLVIDDDVAMRHLIVEYLTIHAFKVTAVADSQQFNRVL-----------ASETVDVVVVDLNLGREDGLEIVRSLATK-   70 (241)
T ss_pred             eEEEEeCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHH-----------hhCCCCEEEEeCCCCCCCHHHHHHHHHhc-
Confidence            799999999999999999999999999999999999988           66789999999999999999999999852 


Q ss_pred             CCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCC-CHHHHHHHHhcCCCeEEeCCCC
Q 023816          111 PFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSEN-ILARIDRCLEDGAEDFIVKPVK  189 (276)
Q Consensus       111 p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~-~~~~~~~al~~Ga~d~l~KPv~  189 (276)
                      +                                             .+|+|++|+.. ......++++.||++|+.||++
T Consensus        71 ~---------------------------------------------~~pii~lt~~~~~~~~~~~~l~~Ga~~yl~kP~~  105 (241)
T PRK13856         71 S---------------------------------------------DVPIIIISGDRLEEADKVVALELGATDFIAKPFG  105 (241)
T ss_pred             C---------------------------------------------CCcEEEEECCCCcHHHHHHHHhcCcCeEEeCCCC
Confidence            2                                             58999999854 5667789999999999999999


Q ss_pred             HHHHHHHHHHHHH
Q 023816          190 LSDVKRIKDYLTR  202 (276)
Q Consensus       190 ~~~L~~~~~~l~~  202 (276)
                      ..+|...+..+.+
T Consensus       106 ~~eL~~~i~~~l~  118 (241)
T PRK13856        106 TREFLARIRVALR  118 (241)
T ss_pred             HHHHHHHHHHHHh
Confidence            9998655554443

>TIGR01387 cztR_silR_copR heavy metal response regulator

Probab=99.65  E-value=5.3e-15  Score=124.17  Aligned_cols=114  Identities=28%  Similarity=0.473  Sum_probs=103.6

Q ss_pred             EEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhhCC
Q 023816           32 VLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVTTP  111 (276)
Q Consensus        32 VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~~p  111 (276)
                      ||+|||++..+..+...|...|+.+..+.++.+++..+           ....||+|++|+.||+++|+++++.++...+
T Consensus         1 iliidd~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~-----------~~~~~dlvl~d~~~~~~~g~~~~~~l~~~~~   69 (218)
T TIGR01387         1 ILVVEDEQKTAEYLQQGLSESGYVVDAASNGRDGLHLA-----------LKDDYDLIILDVMLPGMDGWQILQTLRRSGK   69 (218)
T ss_pred             CEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHH-----------hcCCCCEEEEeCCCCCCCHHHHHHHHHccCC
Confidence            58999999999999999999999999999999999988           5667999999999999999999999997555


Q ss_pred             CCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCCHH
Q 023816          112 FNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLS  191 (276)
Q Consensus       112 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~~~  191 (276)
                                                                   .+|||++++........+++++|+++|+.||++.+
T Consensus        70 ---------------------------------------------~~~iivls~~~~~~~~~~~~~~Ga~~~l~kp~~~~  104 (218)
T TIGR01387        70 ---------------------------------------------QTPVLFLTARDSVADKVKGLDLGADDYLVKPFSFS  104 (218)
T ss_pred             ---------------------------------------------CCcEEEEEcCCCHHHHHHHHHcCCCeEEECCCCHH
Confidence                                                         78999999999999999999999999999999999


Q ss_pred             HHHHHHHHHH
Q 023816          192 DVKRIKDYLT  201 (276)
Q Consensus       192 ~L~~~~~~l~  201 (276)
                      ++...+..+.
T Consensus       105 ~l~~~i~~~~  114 (218)
T TIGR01387       105 ELLARVRTLL  114 (218)
T ss_pred             HHHHHHHHHh
Confidence            9866555544

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.

>PRK11091 aerobic respiration control sensor protein ArcB; Provisional

Probab=99.65  E-value=2.4e-15  Score=153.13  Aligned_cols=120  Identities=21%  Similarity=0.395  Sum_probs=104.9

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHH
Q 023816           27 TEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKI  106 (276)
Q Consensus        27 ~~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~I  106 (276)
                      ...++||||||++.++..+..+|+..||.+..+.+|++|++.+           ....||+||+|+.||+++|++++++|
T Consensus       523 ~~~~~ILivdD~~~~~~~l~~~L~~~g~~v~~a~~~~eal~~~-----------~~~~~Dlvl~D~~mp~~~G~e~~~~i  591 (779)
T PRK11091        523 LPALNILLVEDIELNVIVARSVLEKLGNSVDVAMTGKEALEMF-----------DPDEYDLVLLDIQLPDMTGLDIAREL  591 (779)
T ss_pred             ccccceEEEcCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHh-----------hcCCCCEEEEcCCCCCCCHHHHHHHH
Confidence            4468999999999999999999999999999999999999998           66789999999999999999999999


Q ss_pred             HhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCC-CeEEEEecCCCHHHHHHHHhcCCCeEEe
Q 023816          107 KVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALRE-IPVVIMSSENILARIDRCLEDGAEDFIV  185 (276)
Q Consensus       107 r~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-ipiV~ls~~~~~~~~~~al~~Ga~d~l~  185 (276)
                      |+..+                                           ... +|||++|++... ...++++.|+++||.
T Consensus       592 r~~~~-------------------------------------------~~~~~~ii~~ta~~~~-~~~~~~~~G~~~~l~  627 (779)
T PRK11091        592 RERYP-------------------------------------------REDLPPLVALTANVLK-DKKEYLDAGMDDVLS  627 (779)
T ss_pred             Hhccc-------------------------------------------cCCCCcEEEEECCchH-hHHHHHHCCCCEEEE
Confidence            97442                                           013 488999987654 467899999999999


Q ss_pred             CCCCHHHHHHHHHHHH
Q 023816          186 KPVKLSDVKRIKDYLT  201 (276)
Q Consensus       186 KPv~~~~L~~~~~~l~  201 (276)
                      ||++..+|...+..+.
T Consensus       628 KP~~~~~L~~~l~~~~  643 (779)
T PRK11091        628 KPLSVPALTAMIKKFW  643 (779)
T ss_pred             CCCCHHHHHHHHHHHh
Confidence            9999999977776654

>TIGR02875 spore_0_A sporulation transcription factor Spo0A

Probab=99.65  E-value=5.1e-15  Score=131.70  Aligned_cols=119  Identities=19%  Similarity=0.315  Sum_probs=103.0

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhC-CCEEE-EECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHH
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTIS-SCKVT-AVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKI  106 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~-g~~v~-~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~I  106 (276)
                      +++||+|||++..+..+...|... ++.+. .+.++.++++.+           ....||+||+|+.||+++|+++++.|
T Consensus         2 ~~~vLivdd~~~~~~~l~~~L~~~~~~~~~~~a~~~~eal~~l-----------~~~~~DlvllD~~mp~~dG~~~l~~i   70 (262)
T TIGR02875         2 KIRIVIADDNKEFCNLLKEYLAAQPDMEVVGVAHNGVDALELI-----------KEQQPDVVVLDIIMPHLDGIGVLEKL   70 (262)
T ss_pred             CcEEEEEcCCHHHHHHHHHHHhcCCCeEEEEEeCCHHHHHHHH-----------HhcCCCEEEEeCCCCCCCHHHHHHHH
Confidence            579999999999999999999854 56655 699999999998           56789999999999999999999999


Q ss_pred             HhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeC
Q 023816          107 KVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVK  186 (276)
Q Consensus       107 r~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~K  186 (276)
                      ++..+                                           ...+|+|++|+........++++.|+++|+.|
T Consensus        71 ~~~~~-------------------------------------------~~~~~iI~lt~~~~~~~~~~~~~~G~~~~l~K  107 (262)
T TIGR02875        71 NEIEL-------------------------------------------SARPRVIMLSAFGQEKITQRAVALGADYYVLK  107 (262)
T ss_pred             Hhhcc-------------------------------------------ccCCeEEEEeCCCCHHHHHHHHHCCCCEEEEC
Confidence            97543                                           11379999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHH
Q 023816          187 PVKLSDVKRIKDYLT  201 (276)
Q Consensus       187 Pv~~~~L~~~~~~l~  201 (276)
                      |++.++|...+..+.
T Consensus       108 P~~~~~L~~~i~~~~  122 (262)
T TIGR02875       108 PFDLEILAARIRQLA  122 (262)
T ss_pred             CCCHHHHHHHHHHHH
Confidence            999999966665543

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.

>PRK09935 transcriptional regulator FimZ; Provisional

Probab=99.65  E-value=9.1e-15  Score=122.07  Aligned_cols=120  Identities=27%  Similarity=0.398  Sum_probs=105.9

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhC-CCEEE-EECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHH
Q 023816           27 TEEVHVLAVDDSFVDRKVIERLLTIS-SCKVT-AVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLK  104 (276)
Q Consensus        27 ~~~~~VLIVdD~~~~~~~L~~~L~~~-g~~v~-~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~  104 (276)
                      |++.+||+|||++..+..++..|... ++.+. .+.++.+++..+           ....||+|++|+.||+++|.++++
T Consensus         1 ~~~~~iliv~d~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~dlvild~~l~~~~g~~~~~   69 (210)
T PRK09935          1 MKPASVIIMDTHPIIRMSIEVLLQKNSELQIVLKTDDYRITIDYL-----------RTRPVDLIIMDIDLPGTDGFTFLK   69 (210)
T ss_pred             CCcceEEEECCcHHHHHHHHHHHhhCCCceEEEEeCCHHHHHHHH-----------HhcCCCEEEEeCCCCCCCHHHHHH
Confidence            35789999999999999999999876 57876 588999999887           566899999999999999999999


Q ss_pred             HHHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEE
Q 023816          105 KIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFI  184 (276)
Q Consensus       105 ~Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l  184 (276)
                      .++...|                                             .+|||++|+........++++.|+++|+
T Consensus        70 ~l~~~~~---------------------------------------------~~~ii~ls~~~~~~~~~~~~~~g~~~~l  104 (210)
T PRK09935         70 RIKQIQS---------------------------------------------TVKVLFLSSKSECFYAGRAIQAGANGFV  104 (210)
T ss_pred             HHHHhCC---------------------------------------------CCcEEEEECCCcHHHHHHHHHcCCCEEE
Confidence            9997666                                             6899999999998899999999999999


Q ss_pred             eCCCCHHHHHHHHHHHHH
Q 023816          185 VKPVKLSDVKRIKDYLTR  202 (276)
Q Consensus       185 ~KPv~~~~L~~~~~~l~~  202 (276)
                      .||++..+|...+..+..
T Consensus       105 ~kp~~~~~l~~~i~~~l~  122 (210)
T PRK09935        105 SKCNDQNDIFHAVQMILS  122 (210)
T ss_pred             eCCCCHHHHHHHHHHHHc
Confidence            999999999776665543

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

Probab=99.65  E-value=5.7e-15  Score=142.78  Aligned_cols=118  Identities=31%  Similarity=0.467  Sum_probs=107.9

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHH
Q 023816           28 EEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIK  107 (276)
Q Consensus        28 ~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir  107 (276)
                      .+.+||||||++..+..+++.|+..|+.+..+.++.+|+..+           ....||+||+|+.||+++|+++++.|+
T Consensus         2 ~~~~ILiVdd~~~~~~~L~~~L~~~g~~v~~~~s~~~al~~l-----------~~~~~DlvllD~~lp~~dgl~~l~~ir   70 (469)
T PRK10923          2 QRGIVWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLEAL-----------ASKTPDVLLSDIRMPGMDGLALLKQIK   70 (469)
T ss_pred             CCCeEEEEECCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHH-----------hcCCCCEEEECCCCCCCCHHHHHHHHH
Confidence            346899999999999999999999999999999999999998           667899999999999999999999999


Q ss_pred             hhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCC
Q 023816          108 VTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKP  187 (276)
Q Consensus       108 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KP  187 (276)
                      +..+                                             .+|+|++|++.......++++.|+.+|+.||
T Consensus        71 ~~~~---------------------------------------------~~pvIvlt~~~~~~~~~~a~~~Ga~~~l~KP  105 (469)
T PRK10923         71 QRHP---------------------------------------------MLPVIIMTAHSDLDAAVSAYQQGAFDYLPKP  105 (469)
T ss_pred             hhCC---------------------------------------------CCeEEEEECCCCHHHHHHHHhcCcceEEecC
Confidence            7666                                             7899999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHH
Q 023816          188 VKLSDVKRIKDYLT  201 (276)
Q Consensus       188 v~~~~L~~~~~~l~  201 (276)
                      ++.+++...+..+.
T Consensus       106 ~~~~~L~~~i~~~l  119 (469)
T PRK10923        106 FDIDEAVALVERAI  119 (469)
T ss_pred             CcHHHHHHHHHHHH
Confidence            99999876665544

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

Probab=99.64  E-value=8.2e-16  Score=144.63  Aligned_cols=120  Identities=26%  Similarity=0.406  Sum_probs=108.3

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhh
Q 023816           30 VHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVT  109 (276)
Q Consensus        30 ~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~  109 (276)
                      ++|+||||+....+.|..+|++.|+.+..++...+|+..+           ...+||||++|+.||+|||+|+++++|..
T Consensus         1 ~~~iiVDdd~a~~~~l~~iLs~~~~~~~~~~~~~eal~~L-----------e~~kpDLifldI~mp~~ngiefaeQvr~i   69 (361)
T COG3947           1 PRIIIVDDDAAIVKLLSVILSRAGHEVRSCSHPVEALDLL-----------EVFKPDLIFLDIVMPYMNGIEFAEQVRDI   69 (361)
T ss_pred             CcEEEEcchHHHHHHHHHHHHhccchhhccCCHHHHHHHH-----------HhcCCCEEEEEeecCCccHHHHHHHHHHh
Confidence            4799999999999999999999998899999999999999           78899999999999999999999999987


Q ss_pred             CCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCC
Q 023816          110 TPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVK  189 (276)
Q Consensus       110 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~  189 (276)
                      .+                                             .+|||++|++..  ....+...-+.|||.|||+
T Consensus        70 ~~---------------------------------------------~v~iifIssh~e--ya~dsf~~n~~dYl~KPvt  102 (361)
T COG3947          70 ES---------------------------------------------AVPIIFISSHAE--YADDSFGMNLDDYLPKPVT  102 (361)
T ss_pred             hc---------------------------------------------cCcEEEEecchh--hhhhhcccchHhhccCCCC
Confidence            77                                             899999999875  4556667778999999999


Q ss_pred             HHHHHHHHHHHHHhhhcc
Q 023816          190 LSDVKRIKDYLTRDVNLG  207 (276)
Q Consensus       190 ~~~L~~~~~~l~~~~~~~  207 (276)
                      .+.|.+.+++..+.....
T Consensus       103 ~ekLnraIdr~~k~ve~~  120 (361)
T COG3947         103 PEKLNRAIDRRLKRVELT  120 (361)
T ss_pred             HHHHHHHHHHHhcccccc
Confidence            999999998887665543

>PRK09581 pleD response regulator PleD; Reviewed

Probab=99.64  E-value=2.4e-15  Score=140.31  Aligned_cols=118  Identities=20%  Similarity=0.331  Sum_probs=103.6

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHH
Q 023816           27 TEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKI  106 (276)
Q Consensus        27 ~~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~I  106 (276)
                      ....+||+|||++..++.+.++|.. .+.+..+.++++|+..+           ...+||+||+|+.||+++|++++++|
T Consensus       153 ~~~~~vlivdd~~~~~~~l~~~l~~-~~~~~~~~~~~~a~~~~-----------~~~~~d~vi~d~~~p~~~g~~l~~~i  220 (457)
T PRK09581        153 DEDGRILLVDDDVSQAERIANILKE-EFRVVVVSDPSEALFNA-----------AETNYDLVIVSANFENYDPLRLCSQL  220 (457)
T ss_pred             ccCceEEEEecccchHHHHHHHHhh-cceeeeecChHHHHHhc-----------ccCCCCEEEecCCCCCchHhHHHHHH
Confidence            3467899999999999999999964 57777899999999987           67889999999999999999999999


Q ss_pred             HhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeC
Q 023816          107 KVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVK  186 (276)
Q Consensus       107 r~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~K  186 (276)
                      ++...                                           ...+|||++|++.+.....+|++.|+.||+.|
T Consensus       221 ~~~~~-------------------------------------------~~~~~ii~ls~~~~~~~~~~a~~~Ga~d~l~k  257 (457)
T PRK09581        221 RSKER-------------------------------------------TRYVPILLLVDEDDDPRLVKALELGVNDYLMR  257 (457)
T ss_pred             Hhccc-------------------------------------------cCCCcEEEEeCCCChHHHHHHHHccchhhhhC
Confidence            96331                                           12799999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHH
Q 023816          187 PVKLSDVKRIKDY  199 (276)
Q Consensus       187 Pv~~~~L~~~~~~  199 (276)
                      |++.++|...+..
T Consensus       258 p~~~~~l~~~i~~  270 (457)
T PRK09581        258 PIDKNELLARVRT  270 (457)
T ss_pred             CCcHHHHHHHHHH
Confidence            9999998554443

>PRK14084 two-component response regulator; Provisional

Probab=99.63  E-value=8.8e-15  Score=128.27  Aligned_cols=115  Identities=20%  Similarity=0.288  Sum_probs=98.9

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhCC-C-EEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHH
Q 023816           30 VHVLAVDDSFVDRKVIERLLTISS-C-KVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIK  107 (276)
Q Consensus        30 ~~VLIVdD~~~~~~~L~~~L~~~g-~-~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir  107 (276)
                      ++||||||++..+..++.+|+..+ + .+..+.++++++..+           .+..||+|++|+.||+++|+++++.|+
T Consensus         1 ~~ilivdd~~~~~~~l~~~l~~~~~~~~v~~~~~~~~~l~~~-----------~~~~~dlv~lDi~m~~~~G~~~~~~i~   69 (246)
T PRK14084          1 MKALIVDDEPLARNELTYLLNEIGGFEEINEAENVKETLEAL-----------LINQYDIIFLDINLMDESGIELAAKIQ   69 (246)
T ss_pred             CEEEEECCCHHHHHHHHHHHHhCCCceEEEEECCHHHHHHHH-----------HhcCCCEEEEeCCCCCCCHHHHHHHHH
Confidence            589999999999999999998765 4 466799999999988           556799999999999999999999999


Q ss_pred             hhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCC
Q 023816          108 VTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKP  187 (276)
Q Consensus       108 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KP  187 (276)
                      ...+                                             ..+||++|++..  ...++++.|+.+|+.||
T Consensus        70 ~~~~---------------------------------------------~~~iI~~t~~~~--~~~~~~~~~~~~yl~KP  102 (246)
T PRK14084         70 KMKE---------------------------------------------PPAIIFATAHDQ--FAVKAFELNATDYILKP  102 (246)
T ss_pred             hcCC---------------------------------------------CCEEEEEecChH--HHHHHHhcCCcEEEECC
Confidence            7554                                             578888887654  56689999999999999


Q ss_pred             CCHHHHHHHHHHHHH
Q 023816          188 VKLSDVKRIKDYLTR  202 (276)
Q Consensus       188 v~~~~L~~~~~~l~~  202 (276)
                      ++.++|.+.+..+.+
T Consensus       103 ~~~~~l~~~l~~~~~  117 (246)
T PRK14084        103 FEQKRIEQAVNKVRA  117 (246)
T ss_pred             CCHHHHHHHHHHHHH
Confidence            999999777766643

>PRK15115 response regulator GlrR; Provisional

Probab=99.63  E-value=6e-15  Score=141.48  Aligned_cols=120  Identities=29%  Similarity=0.436  Sum_probs=109.1

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHH
Q 023816           27 TEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKI  106 (276)
Q Consensus        27 ~~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~I  106 (276)
                      ....+||||||++..+..+...|+..||.+..+.++.+|+..+           ....||+||+|+.||+++|+++++.+
T Consensus         3 ~~~~~vLiVdd~~~~~~~l~~~L~~~g~~v~~~~~~~eal~~l-----------~~~~~dlvilD~~lp~~~g~~ll~~l   71 (444)
T PRK15115          3 RKPAHLLLVDDDPGLLKLLGMRLTSEGYSVVTAESGQEALRVL-----------NREKVDLVISDLRMDEMDGMQLFAEI   71 (444)
T ss_pred             CCCCeEEEEECCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHH-----------hcCCCCEEEEcCCCCCCCHHHHHHHH
Confidence            3468999999999999999999999999999999999999988           56789999999999999999999999


Q ss_pred             HhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeC
Q 023816          107 KVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVK  186 (276)
Q Consensus       107 r~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~K  186 (276)
                      ++..+                                             .+|||++|+........++++.|+.||+.|
T Consensus        72 ~~~~~---------------------------------------------~~pvIvlt~~~~~~~~~~a~~~Ga~~~l~K  106 (444)
T PRK15115         72 QKVQP---------------------------------------------GMPVIILTAHGSIPDAVAATQQGVFSFLTK  106 (444)
T ss_pred             HhcCC---------------------------------------------CCcEEEEECCCCHHHHHHHHhcChhhhccC
Confidence            97665                                             789999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHH
Q 023816          187 PVKLSDVKRIKDYLTR  202 (276)
Q Consensus       187 Pv~~~~L~~~~~~l~~  202 (276)
                      |++.++|...+..+.+
T Consensus       107 P~~~~~L~~~l~~~~~  122 (444)
T PRK15115        107 PVDRDALYKAIDDALE  122 (444)
T ss_pred             CCCHHHHHHHHHHHHH
Confidence            9999999766665544

>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional

Probab=99.63  E-value=7.5e-15  Score=140.84  Aligned_cols=117  Identities=24%  Similarity=0.440  Sum_probs=107.0

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHh
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKV  108 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~  108 (276)
                      ..+||||||++..+..+...|+..|+++..+.++.+|+..+           ....||+||+|+.||+++|+++++.++.
T Consensus         4 ~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l-----------~~~~~dlillD~~~p~~~g~~ll~~i~~   72 (457)
T PRK11361          4 INRILIVDDEDNVRRMLSTAFALQGFETHCANNGRTALHLF-----------ADIHPDVVLMDIRMPEMDGIKALKEMRS   72 (457)
T ss_pred             CCeEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHH-----------hcCCCCEEEEeCCCCCCCHHHHHHHHHh
Confidence            55899999999999999999999999999999999999998           5667999999999999999999999997


Q ss_pred             hCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCC
Q 023816          109 TTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPV  188 (276)
Q Consensus       109 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv  188 (276)
                      ..+                                             .+|||++|+..+.....++++.|++||+.||+
T Consensus        73 ~~~---------------------------------------------~~pvI~lt~~~~~~~~~~a~~~Ga~d~l~KP~  107 (457)
T PRK11361         73 HET---------------------------------------------RTPVILMTAYAEVETAVEALRCGAFDYVIKPF  107 (457)
T ss_pred             cCC---------------------------------------------CCCEEEEeCCCCHHHHHHHHHCCccEEEeccc
Confidence            655                                             78999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHH
Q 023816          189 KLSDVKRIKDYLT  201 (276)
Q Consensus       189 ~~~~L~~~~~~l~  201 (276)
                      +.+++...+..+.
T Consensus       108 ~~~~L~~~i~~~l  120 (457)
T PRK11361        108 DLDELNLIVQRAL  120 (457)
T ss_pred             CHHHHHHHHhhhc
Confidence            9999876665543

>PRK10365 transcriptional regulatory protein ZraR; Provisional

Probab=99.63  E-value=5.7e-15  Score=140.79  Aligned_cols=117  Identities=29%  Similarity=0.498  Sum_probs=107.3

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHH
Q 023816           28 EEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIK  107 (276)
Q Consensus        28 ~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir  107 (276)
                      ..++||||||+...+..++..|+..|+++..+.++.+++..+           ....||+||+|+.||+++|+++++.|+
T Consensus         4 ~~~~Ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l-----------~~~~~DlvilD~~m~~~~G~~~~~~ir   72 (441)
T PRK10365          4 DNIDILVVDDDISHCTILQALLRGWGYNVALANSGRQALEQV-----------REQVFDLVLCDVRMAEMDGIATLKEIK   72 (441)
T ss_pred             CcceEEEEECCHHHHHHHHHHHHHCCCeEEEeCCHHHHHHHH-----------hcCCCCEEEEeCCCCCCCHHHHHHHHH
Confidence            368999999999999999999999999999999999999988           566799999999999999999999999


Q ss_pred             hhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCC
Q 023816          108 VTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKP  187 (276)
Q Consensus       108 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KP  187 (276)
                      +..+                                             .+|||++|++.......++++.|+.+|+.||
T Consensus        73 ~~~~---------------------------------------------~~~vi~lt~~~~~~~~~~a~~~ga~~~l~Kp  107 (441)
T PRK10365         73 ALNP---------------------------------------------AIPVLIMTAYSSVETAVEALKTGALDYLIKP  107 (441)
T ss_pred             hhCC---------------------------------------------CCeEEEEECCCCHHHHHHHHHhhhHHHhcCC
Confidence            8666                                             7899999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHH
Q 023816          188 VKLSDVKRIKDYL  200 (276)
Q Consensus       188 v~~~~L~~~~~~l  200 (276)
                      ++.++|...+...
T Consensus       108 ~~~~~L~~~l~~~  120 (441)
T PRK10365        108 LDFDNLQATLEKA  120 (441)
T ss_pred             CCHHHHHHHHHHH
Confidence            9999986665544

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

Probab=99.63  E-value=8.2e-15  Score=155.45  Aligned_cols=117  Identities=26%  Similarity=0.410  Sum_probs=108.5

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHh
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKV  108 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~  108 (276)
                      ..+||||||++.++..+..+|+..|+++..+.++.+|++.+           ....||+||+|++||+++|+++++.|+.
T Consensus       958 ~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~-----------~~~~~dlil~D~~mp~~~g~~~~~~i~~ 1026 (1197)
T PRK09959        958 KLSILIADDHPTNRLLLKRQLNLLGYDVDEATDGVQALHKV-----------SMQHYDLLITDVNMPNMDGFELTRKLRE 1026 (1197)
T ss_pred             CceEEEcCCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHh-----------hcCCCCEEEEeCCCCCCCHHHHHHHHHh
Confidence            57899999999999999999999999999999999999998           6778999999999999999999999997


Q ss_pred             hCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCC
Q 023816          109 TTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPV  188 (276)
Q Consensus       109 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv  188 (276)
                      ..+                                             .+|||++|+........++++.|+++||.||+
T Consensus      1027 ~~~---------------------------------------------~~pii~lt~~~~~~~~~~~~~~G~~~~l~KP~ 1061 (1197)
T PRK09959       1027 QNS---------------------------------------------SLPIWGLTANAQANEREKGLSCGMNLCLFKPL 1061 (1197)
T ss_pred             cCC---------------------------------------------CCCEEEEECCCCHHHHHHHHHCCCCEEEeCCC
Confidence            555                                             68999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHH
Q 023816          189 KLSDVKRIKDYLT  201 (276)
Q Consensus       189 ~~~~L~~~~~~l~  201 (276)
                      +.++|.+.+..+.
T Consensus      1062 ~~~~L~~~l~~~~ 1074 (1197)
T PRK09959       1062 TLDVLKTHLSQLH 1074 (1197)
T ss_pred             CHHHHHHHHHHHh
Confidence            9999977776554

>PRK10360 DNA-binding transcriptional activator UhpA; Provisional

Probab=99.61  E-value=2.3e-14  Score=119.39  Aligned_cols=114  Identities=26%  Similarity=0.436  Sum_probs=100.6

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhC-CCE-EEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHH
Q 023816           30 VHVLAVDDSFVDRKVIERLLTIS-SCK-VTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIK  107 (276)
Q Consensus        30 ~~VLIVdD~~~~~~~L~~~L~~~-g~~-v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir  107 (276)
                      ++||||||++..+..++..|... ++. +..+.++.++++.+           .+..||+||+|+.||+++|+++++.++
T Consensus         2 ~~ilivd~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~l~~~-----------~~~~~dlvi~d~~~~~~~g~~~~~~l~   70 (196)
T PRK10360          2 ITVALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALAGL-----------PGRGVQVCICDISMPDISGLELLSQLP   70 (196)
T ss_pred             eEEEEECCcHHHHHHHHHHHccCCCcEEEEEECCHHHHHHHH-----------hcCCCCEEEEeCCCCCCCHHHHHHHHc
Confidence            68999999999999999999754 665 45789999999998           667899999999999999999999886


Q ss_pred             hhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCC
Q 023816          108 VTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKP  187 (276)
Q Consensus       108 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KP  187 (276)
                      .                                                .+|||++++........++++.|+++|+.||
T Consensus        71 ~------------------------------------------------~~~vi~~s~~~~~~~~~~~~~~ga~~~i~kp  102 (196)
T PRK10360         71 K------------------------------------------------GMATIMLSVHDSPALVEQALNAGARGFLSKR  102 (196)
T ss_pred             c------------------------------------------------CCCEEEEECCCCHHHHHHHHHcCCcEEEECC
Confidence            2                                                5789999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHH
Q 023816          188 VKLSDVKRIKDYLTR  202 (276)
Q Consensus       188 v~~~~L~~~~~~l~~  202 (276)
                      ++.+++...+..+.+
T Consensus       103 ~~~~~l~~~i~~~~~  117 (196)
T PRK10360        103 CSPDELIAAVHTVAT  117 (196)
T ss_pred             CCHHHHHHHHHHHHc
Confidence            999999777666554

>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator

Probab=99.61  E-value=1.1e-14  Score=139.79  Aligned_cols=112  Identities=19%  Similarity=0.302  Sum_probs=101.9

Q ss_pred             EEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCC-----CCHHHHHHHH
Q 023816           32 VLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPG-----MTGYELLKKI  106 (276)
Q Consensus        32 VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~-----~~G~ell~~I  106 (276)
                      ||||||++..+..+...|  .||++..+.++.+|++.+           ....||+||+|+.||+     ++|+++++++
T Consensus         1 ILivddd~~~~~~l~~~l--~~~~v~~a~~~~~al~~l-----------~~~~~dlvllD~~mp~~~~~~~~g~~~l~~i   67 (445)
T TIGR02915         1 LLIVEDDLGLQKQLKWSF--ADYELAVAADRESAIALV-----------RRHEPAVVTLDLGLPPDADGASEGLAALQQI   67 (445)
T ss_pred             CEEEECCHHHHHHHHHHh--CCCeEEEeCCHHHHHHHH-----------hhCCCCEEEEeCCCCCCcCCCCCHHHHHHHH
Confidence            689999999999999888  799999999999999999           5668999999999996     8999999999


Q ss_pred             HhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeC
Q 023816          107 KVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVK  186 (276)
Q Consensus       107 r~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~K  186 (276)
                      +...|                                             .+|||++|+..+.+...++++.||+|||.|
T Consensus        68 ~~~~~---------------------------------------------~~piI~lt~~~~~~~~~~a~~~Ga~dyl~K  102 (445)
T TIGR02915        68 LAIAP---------------------------------------------DTKVIVITGNDDRENAVKAIGLGAYDFYQK  102 (445)
T ss_pred             HhhCC---------------------------------------------CCCEEEEecCCCHHHHHHHHHCCccEEEeC
Confidence            98776                                             799999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHH
Q 023816          187 PVKLSDVKRIKDYLT  201 (276)
Q Consensus       187 Pv~~~~L~~~~~~l~  201 (276)
                      |++.++|...+..+.
T Consensus       103 P~~~~~L~~~i~~~~  117 (445)
T TIGR02915       103 PIDPDVLKLIVDRAF  117 (445)
T ss_pred             CCCHHHHHHHHhhhh
Confidence            999999866665443

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).

>PRK15479 transcriptional regulatory protein TctD; Provisional

Probab=99.61  E-value=4.6e-14  Score=118.71  Aligned_cols=117  Identities=26%  Similarity=0.410  Sum_probs=105.0

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhh
Q 023816           30 VHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVT  109 (276)
Q Consensus        30 ~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~  109 (276)
                      ++||++||++..+..++..|...|+.+..+.++.++++.+           ....||+|++|+.+|+++|+++++.++..
T Consensus         1 ~~ilivd~~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~-----------~~~~~d~vild~~~~~~~~~~~~~~i~~~   69 (221)
T PRK15479          1 MRLLLAEDNRELAHWLEKALVQNGFAVDCVFDGLAADHLL-----------QSEMYALAVLDINMPGMDGLEVLQRLRKR   69 (221)
T ss_pred             CeEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHH-----------hhCCCCEEEEeCCCCCCcHHHHHHHHHhc
Confidence            4799999999999999999999999999999999999887           55679999999999999999999999976


Q ss_pred             CCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCC
Q 023816          110 TPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVK  189 (276)
Q Consensus       110 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~  189 (276)
                      .+                                             .+|+|++++........++++.|+++|+.||++
T Consensus        70 ~~---------------------------------------------~~~ii~lt~~~~~~~~~~~~~~g~~~~i~kp~~  104 (221)
T PRK15479         70 GQ---------------------------------------------TLPVLLLTARSAVADRVKGLNVGADDYLPKPFE  104 (221)
T ss_pred             CC---------------------------------------------CCCEEEEECCCCHHHHHHHHHcCCCeeEeCCCC
Confidence            55                                             689999999999888899999999999999999


Q ss_pred             HHHHHHHHHHHHH
Q 023816          190 LSDVKRIKDYLTR  202 (276)
Q Consensus       190 ~~~L~~~~~~l~~  202 (276)
                      ..++...+..+.+
T Consensus       105 ~~~l~~~i~~~~~  117 (221)
T PRK15479        105 LEELDARLRALLR  117 (221)
T ss_pred             HHHHHHHHHHHHh
Confidence            9998666655443

>PRK09390 fixJ response regulator FixJ; Provisional

Probab=99.60  E-value=3.9e-14  Score=115.94  Aligned_cols=118  Identities=28%  Similarity=0.410  Sum_probs=105.6

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHH
Q 023816           28 EEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIK  107 (276)
Q Consensus        28 ~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir  107 (276)
                      +..+||+|||++..+..+...|...|+.+..+.++.+++..+           ....||+||+|+.||+++|+++++.|+
T Consensus         2 ~~~~iliv~~~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~-----------~~~~~d~ii~d~~~~~~~~~~~~~~l~   70 (202)
T PRK09390          2 DKGVVHVVDDDEAMRDSLAFLLDSAGFEVRLFESAQAFLDAL-----------PGLRFGCVVTDVRMPGIDGIELLRRLK   70 (202)
T ss_pred             CCCEEEEEeCCHHHHHHHHHHHHHCCCeEEEeCCHHHHHHHh-----------ccCCCCEEEEeCCCCCCcHHHHHHHHH
Confidence            457899999999999999999999999999999999999888           567799999999999999999999999


Q ss_pred             hhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCC
Q 023816          108 VTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKP  187 (276)
Q Consensus       108 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KP  187 (276)
                      ...+                                             .+|+|++++.........+++.|+.+|+.||
T Consensus        71 ~~~~---------------------------------------------~~~ii~l~~~~~~~~~~~~~~~g~~~~l~~p  105 (202)
T PRK09390         71 ARGS---------------------------------------------PLPVIVMTGHGDVPLAVEAMKLGAVDFIEKP  105 (202)
T ss_pred             hcCC---------------------------------------------CCCEEEEECCCCHHHHHHHHHcChHHHhhCC
Confidence            7555                                             7899999999998899999999999999999


Q ss_pred             CCHHHHHHHHHHHH
Q 023816          188 VKLSDVKRIKDYLT  201 (276)
Q Consensus       188 v~~~~L~~~~~~l~  201 (276)
                      +...++...+....
T Consensus       106 ~~~~~l~~~l~~~~  119 (202)
T PRK09390        106 FEDERLIGAIERAL  119 (202)
T ss_pred             CCHHHHHHHHHHHH
Confidence            99988865555433

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

Probab=99.60  E-value=3e-14  Score=123.77  Aligned_cols=115  Identities=23%  Similarity=0.350  Sum_probs=96.3

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhCC-CE-EEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHH
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTISS-CK-VTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKI  106 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~g-~~-v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~I  106 (276)
                      +++||||||++..+..++..|+..| +. +..+.++.+++..+           ....||+|++|+.||+++|+++++.+
T Consensus         1 m~~IlIvdd~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~l~~~-----------~~~~~dlv~lDi~~~~~~G~~~~~~l   69 (238)
T PRK11697          1 MIKVLIVDDEPLAREELRELLQEEGDIEIVGECSNAIEAIGAI-----------HRLKPDVVFLDIQMPRISGLELVGML   69 (238)
T ss_pred             CcEEEEECCCHHHHHHHHHHHhhCCCcEEEEEeCCHHHHHHHH-----------HhcCCCEEEEeCCCCCCCHHHHHHHh
Confidence            3799999999999999999999887 34 34689999999988           55679999999999999999999988


Q ss_pred             HhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeC
Q 023816          107 KVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVK  186 (276)
Q Consensus       107 r~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~K  186 (276)
                      +.. +                                             ..+||++|++.  +...++++.|+.+||.|
T Consensus        70 ~~~-~---------------------------------------------~~~ii~vt~~~--~~~~~a~~~~~~~yl~K  101 (238)
T PRK11697         70 DPE-H---------------------------------------------MPYIVFVTAFD--EYAIKAFEEHAFDYLLK  101 (238)
T ss_pred             ccc-C---------------------------------------------CCEEEEEeccH--HHHHHHHhcCCcEEEEC
Confidence            631 1                                             34688888765  46678999999999999


Q ss_pred             CCCHHHHHHHHHHHHH
Q 023816          187 PVKLSDVKRIKDYLTR  202 (276)
Q Consensus       187 Pv~~~~L~~~~~~l~~  202 (276)
                      |++.+++...+..+.+
T Consensus       102 P~~~~~l~~~l~~~~~  117 (238)
T PRK11697        102 PIDPARLAKTLARLRQ  117 (238)
T ss_pred             CCCHHHHHHHHHHHHH
Confidence            9999999777776654

>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional

Probab=99.60  E-value=7.5e-14  Score=119.45  Aligned_cols=116  Identities=25%  Similarity=0.362  Sum_probs=103.5

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHh
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKV  108 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~  108 (276)
                      ..+||+|||+...+..+...|...|+.+..+.++.+++..+           ....||+||+|+.||+++|+++++.|+.
T Consensus        10 ~~~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~-----------~~~~~dlvl~d~~~~~~~g~~~~~~l~~   78 (240)
T PRK10710         10 TPRILIVEDEPKLGQLLIDYLQAASYATTLLSHGDEVLPYV-----------RQTPPDLILLDLMLPGTDGLTLCREIRR   78 (240)
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHH-----------hhCCCCEEEEeCCCCCCCHHHHHHHHHh
Confidence            34899999999999999999999999999999999999988           5667999999999999999999999985


Q ss_pred             hCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCC
Q 023816          109 TTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPV  188 (276)
Q Consensus       109 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv  188 (276)
                       .+                                             .+|+|++++.........+++.|+++|+.||+
T Consensus        79 -~~---------------------------------------------~~pii~l~~~~~~~~~~~~~~~ga~~~l~kp~  112 (240)
T PRK10710         79 -FS---------------------------------------------DIPIVMVTAKIEEIDRLLGLEIGADDYICKPY  112 (240)
T ss_pred             -cC---------------------------------------------CCCEEEEEcCCCHHHHHHHHhcCCCeEEECCC
Confidence             22                                             58999999998888888999999999999999


Q ss_pred             CHHHHHHHHHHHH
Q 023816          189 KLSDVKRIKDYLT  201 (276)
Q Consensus       189 ~~~~L~~~~~~l~  201 (276)
                      +.++|...+..+.
T Consensus       113 ~~~~L~~~i~~~~  125 (240)
T PRK10710        113 SPREVVARVKTIL  125 (240)
T ss_pred             CHHHHHHHHHHHH
Confidence            9999866555443

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

Probab=99.60  E-value=1.5e-14  Score=125.34  Aligned_cols=111  Identities=17%  Similarity=0.256  Sum_probs=105.4

Q ss_pred             EEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhhC
Q 023816           31 HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVTT  110 (276)
Q Consensus        31 ~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~~  110 (276)
                      +.|||||+..+.+.|.+.|++.||.|.++.+.+||+..+           +...|.-.++|+.|.+.+|+++++.|++..
T Consensus        11 ~lllvdDD~~f~~~LaRa~e~RGf~v~~a~~~~eal~~a-----------rt~~PayAvvDlkL~~gsGL~~i~~lr~~~   79 (182)
T COG4567          11 SLLLVDDDTPFLRTLARAMERRGFAVVTAESVEEALAAA-----------RTAPPAYAVVDLKLGDGSGLAVIEALRERR   79 (182)
T ss_pred             eeEEecCChHHHHHHHHHHhccCceeEeeccHHHHHHHH-----------hcCCCceEEEEeeecCCCchHHHHHHHhcC
Confidence            789999999999999999999999999999999999999           778899999999999999999999999988


Q ss_pred             CCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCCH
Q 023816          111 PFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKL  190 (276)
Q Consensus       111 p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~~  190 (276)
                      +                                             +..||++|++.+.....+|++.||.+||.||.+.
T Consensus        80 ~---------------------------------------------d~rivvLTGy~sIATAV~AvKlGA~~YLaKPAda  114 (182)
T COG4567          80 A---------------------------------------------DMRIVVLTGYASIATAVEAVKLGACDYLAKPADA  114 (182)
T ss_pred             C---------------------------------------------cceEEEEecchHHHHHHHHHHhhhhhhcCCCCCh
Confidence            7                                             8999999999999999999999999999999999


Q ss_pred             HHHHHHH
Q 023816          191 SDVKRIK  197 (276)
Q Consensus       191 ~~L~~~~  197 (276)
                      +++.+.+
T Consensus       115 Ddi~aAl  121 (182)
T COG4567         115 DDILAAL  121 (182)
T ss_pred             HHHHHHH
Confidence            9985543

>TIGR01818 ntrC nitrogen regulation protein NR(I)

Probab=99.59  E-value=2.8e-14  Score=137.33  Aligned_cols=113  Identities=30%  Similarity=0.465  Sum_probs=104.1

Q ss_pred             EEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhhCC
Q 023816           32 VLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVTTP  111 (276)
Q Consensus        32 VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~~p  111 (276)
                      ||||||++..+..+...|+..|+.+..+.++.+|+..+           ....||+||+|+.||+++|+++++.|++..+
T Consensus         1 ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~-----------~~~~~DlVllD~~~p~~~g~~ll~~l~~~~~   69 (463)
T TIGR01818         1 VWVVDDDRSIRWVLEKALSRAGYEVRTFGNAASVLRAL-----------ARGQPDLLITDVRMPGEDGLDLLPQIKKRHP   69 (463)
T ss_pred             CEEEECCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHH-----------hcCCCCEEEEcCCCCCCCHHHHHHHHHHhCC
Confidence            68999999999999999999999999999999999988           5667999999999999999999999998666


Q ss_pred             CCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCCHH
Q 023816          112 FNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLS  191 (276)
Q Consensus       112 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~~~  191 (276)
                                                                   .+|||++|++.......++++.|+.||+.||++.+
T Consensus        70 ---------------------------------------------~~~vIvlt~~~~~~~~~~a~~~Ga~~~l~KP~~~~  104 (463)
T TIGR01818        70 ---------------------------------------------QLPVIVMTAHSDLDTAVAAYQRGAFEYLPKPFDLD  104 (463)
T ss_pred             ---------------------------------------------CCeEEEEeCCCCHHHHHHHHHcCcceeecCCCCHH
Confidence                                                         78999999999999999999999999999999999


Q ss_pred             HHHHHHHHH
Q 023816          192 DVKRIKDYL  200 (276)
Q Consensus       192 ~L~~~~~~l  200 (276)
                      +|...+..+
T Consensus       105 ~L~~~i~~~  113 (463)
T TIGR01818       105 EAVTLVERA  113 (463)
T ss_pred             HHHHHHHHH
Confidence            987666554

This model represents NtrC, a DNA-binding response regulator that is phosphorylated by NtrB and interacts with sigma-54. NtrC usually controls the expression of glutamine synthase, GlnA, and may be called GlnL, GlnG, etc.

>PRK12555 chemotaxis-specific methylesterase; Provisional

Probab=99.59  E-value=3e-14  Score=133.06  Aligned_cols=102  Identities=25%  Similarity=0.353  Sum_probs=90.3

Q ss_pred             cEEEEEeCCHHHHHHHHHHH-hhCCCEEE-EECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHH
Q 023816           30 VHVLAVDDSFVDRKVIERLL-TISSCKVT-AVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIK  107 (276)
Q Consensus        30 ~~VLIVdD~~~~~~~L~~~L-~~~g~~v~-~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir  107 (276)
                      ++||+|||++..++.++++| +..++++. .+.++++|++.+           .+..||+|++|+.||+|+|++++++|+
T Consensus         1 ~~VLvVdd~~~~~~~l~~~L~~~~~~~vv~~a~~~~eal~~l-----------~~~~pDlVllD~~mp~~~G~e~l~~l~   69 (337)
T PRK12555          1 MRIGIVNDSPLAVEALRRALARDPDHEVVWVATDGAQAVERC-----------AAQPPDVILMDLEMPRMDGVEATRRIM   69 (337)
T ss_pred             CEEEEEeCCHHHHHHHHHHHhhCCCCEEEEEECCHHHHHHHH-----------hccCCCEEEEcCCCCCCCHHHHHHHHH
Confidence            48999999999999999999 56788887 689999999998           667899999999999999999999998


Q ss_pred             hhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCC--HHHHHHHHhcCCCeEEe
Q 023816          108 VTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENI--LARIDRCLEDGAEDFIV  185 (276)
Q Consensus       108 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~--~~~~~~al~~Ga~d~l~  185 (276)
                      +..                                              ++|+|++++...  .....++++.|+.+|+.
T Consensus        70 ~~~----------------------------------------------~~pvivvs~~~~~~~~~~~~al~~Ga~d~l~  103 (337)
T PRK12555         70 AER----------------------------------------------PCPILIVTSLTERNASRVFEAMGAGALDAVD  103 (337)
T ss_pred             HHC----------------------------------------------CCcEEEEeCCCCcCHHHHHHHHhcCceEEEE
Confidence            643                                              479999998754  45677899999999999


Q ss_pred             CCC
Q 023816          186 KPV  188 (276)
Q Consensus       186 KPv  188 (276)
                      ||+
T Consensus       104 KP~  106 (337)
T PRK12555        104 TPT  106 (337)
T ss_pred             CCC
Confidence            999

>PRK15369 two component system sensor kinase SsrB; Provisional

Probab=99.55  E-value=2.9e-13  Score=111.19  Aligned_cols=118  Identities=20%  Similarity=0.340  Sum_probs=103.3

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhC-CCEEE-EECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHH
Q 023816           28 EEVHVLAVDDSFVDRKVIERLLTIS-SCKVT-AVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKK  105 (276)
Q Consensus        28 ~~~~VLIVdD~~~~~~~L~~~L~~~-g~~v~-~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~  105 (276)
                      ..++||+|||++..+..+...|... ++.+. .+.++.++++.+           ....||+|++|+.|++++|+++++.
T Consensus         2 ~~~~iliv~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~dlvl~d~~~~~~~~~~~~~~   70 (211)
T PRK15369          2 KNYKILLVDDHELIINGIKNMLAPYPRYKIVGQVDNGLEVYNAC-----------RQLEPDIVILDLGLPGMNGLDVIPQ   70 (211)
T ss_pred             CccEEEEECCcHHHHHHHHHHHccCCCcEEEEEECCHHHHHHHH-----------HhcCCCEEEEeCCCCCCCHHHHHHH
Confidence            4689999999999999999999865 46654 689999999887           5678999999999999999999999


Q ss_pred             HHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEe
Q 023816          106 IKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIV  185 (276)
Q Consensus       106 Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~  185 (276)
                      +++..+                                             .+|+|++++.........+++.|+.+|+.
T Consensus        71 l~~~~~---------------------------------------------~~~ii~ls~~~~~~~~~~~~~~g~~~~l~  105 (211)
T PRK15369         71 LHQRWP---------------------------------------------AMNILVLTARQEEHMASRTLAAGALGYVL  105 (211)
T ss_pred             HHHHCC---------------------------------------------CCcEEEEeCCCCHHHHHHHHHhCCCEEEe
Confidence            997655                                             68999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHH
Q 023816          186 KPVKLSDVKRIKDYLT  201 (276)
Q Consensus       186 KPv~~~~L~~~~~~l~  201 (276)
                      ||++..+|...+....
T Consensus       106 kp~~~~~l~~~i~~~~  121 (211)
T PRK15369        106 KKSPQQILLAAIQTVA  121 (211)
T ss_pred             CCCCHHHHHHHHHHHH
Confidence            9999999866665544

>PRK10403 transcriptional regulator NarP; Provisional

Probab=99.54  E-value=3.5e-13  Score=112.02  Aligned_cols=118  Identities=20%  Similarity=0.353  Sum_probs=103.5

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhh-CCCEEE-EECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHH
Q 023816           28 EEVHVLAVDDSFVDRKVIERLLTI-SSCKVT-AVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKK  105 (276)
Q Consensus        28 ~~~~VLIVdD~~~~~~~L~~~L~~-~g~~v~-~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~  105 (276)
                      .+++||+|||++..+..+...|+. .++.+. .+.++.++++.+           ....||+||+|+.||+++|+++++.
T Consensus         5 ~~~~ilii~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~dlvi~d~~~~~~~~~~~~~~   73 (215)
T PRK10403          5 TPFQVLIVDDHPLMRRGVRQLLELDPGFEVVAEAGDGASAIDLA-----------NRLDPDVILLDLNMKGMSGLDTLNA   73 (215)
T ss_pred             eeEEEEEEcCCHHHHHHHHHHHhcCCCCEEEEEeCCHHHHHHHH-----------HhcCCCEEEEecCCCCCcHHHHHHH
Confidence            458999999999999999999975 577775 589999999987           5667999999999999999999999


Q ss_pred             HHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEe
Q 023816          106 IKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIV  185 (276)
Q Consensus       106 Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~  185 (276)
                      ++...+                                             ..|+++++..........+++.|+++|+.
T Consensus        74 l~~~~~---------------------------------------------~~~ii~l~~~~~~~~~~~~~~~g~~~~i~  108 (215)
T PRK10403         74 LRRDGV---------------------------------------------TAQIIILTVSDASSDVFALIDAGADGYLL  108 (215)
T ss_pred             HHHhCC---------------------------------------------CCeEEEEeCCCChHHHHHHHHcCCCeEEe
Confidence            998665                                             67899999988888888999999999999


Q ss_pred             CCCCHHHHHHHHHHHH
Q 023816          186 KPVKLSDVKRIKDYLT  201 (276)
Q Consensus       186 KPv~~~~L~~~~~~l~  201 (276)
                      ||++..++...++.+.
T Consensus       109 kp~~~~~l~~~i~~~~  124 (215)
T PRK10403        109 KDSDPEVLLEAIRAGA  124 (215)
T ss_pred             cCCCHHHHHHHHHHHh
Confidence            9999999876666543

>PRK10651 transcriptional regulator NarL; Provisional

Probab=99.54  E-value=3.7e-13  Score=112.25  Aligned_cols=120  Identities=24%  Similarity=0.436  Sum_probs=104.9

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhC-CCEEE-EECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHH
Q 023816           27 TEEVHVLAVDDSFVDRKVIERLLTIS-SCKVT-AVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLK  104 (276)
Q Consensus        27 ~~~~~VLIVdD~~~~~~~L~~~L~~~-g~~v~-~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~  104 (276)
                      ....+||+|||++..+..++.+|... ++.+. .+.++++++..+           ....||+||+|+.+|+++|+++++
T Consensus         4 ~~~~~iliv~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~dlvl~d~~l~~~~~~~~~~   72 (216)
T PRK10651          4 QEPATILLIDDHPMLRTGVKQLISMAPDITVVGEASNGEQGIELA-----------ESLDPDLILLDLNMPGMNGLETLD   72 (216)
T ss_pred             CcceEEEEECCCHHHHHHHHHHHccCCCcEEEEEeCCHHHHHHHH-----------HhCCCCEEEEeCCCCCCcHHHHHH
Confidence            45689999999999999999999764 56654 589999999988           566799999999999999999999


Q ss_pred             HHHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEE
Q 023816          105 KIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFI  184 (276)
Q Consensus       105 ~Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l  184 (276)
                      .++...+                                             ..|+++++..........+++.|+++|+
T Consensus        73 ~l~~~~~---------------------------------------------~~~vi~l~~~~~~~~~~~~~~~g~~~~i  107 (216)
T PRK10651         73 KLREKSL---------------------------------------------SGRIVVFSVSNHEEDVVTALKRGADGYL  107 (216)
T ss_pred             HHHHhCC---------------------------------------------CCcEEEEeCCCCHHHHHHHHHcCCCEEE
Confidence            9998666                                             6799999999998999999999999999


Q ss_pred             eCCCCHHHHHHHHHHHHH
Q 023816          185 VKPVKLSDVKRIKDYLTR  202 (276)
Q Consensus       185 ~KPv~~~~L~~~~~~l~~  202 (276)
                      .||++..+|...+..+.+
T Consensus       108 ~k~~~~~~l~~~i~~~~~  125 (216)
T PRK10651        108 LKDMEPEDLLKALQQAAA  125 (216)
T ss_pred             eCCCCHHHHHHHHHHHHC
Confidence            999999998766665543

>PRK09581 pleD response regulator PleD; Reviewed

Probab=99.54  E-value=2.8e-13  Score=126.42  Aligned_cols=120  Identities=31%  Similarity=0.447  Sum_probs=106.6

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhh
Q 023816           30 VHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVT  109 (276)
Q Consensus        30 ~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~  109 (276)
                      .+||+|||++..+..+.+.|...|+++..+.++.++++.+           .+..||+|++|+.||+.+|+++++.|+..
T Consensus         3 ~~ilii~~~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~-----------~~~~~dlvi~d~~~~~~~g~~l~~~i~~~   71 (457)
T PRK09581          3 ARILVVDDIPANVKLLEAKLLAEYYTVLTASSGAEAIAIC-----------EREQPDIILLDVMMPGMDGFEVCRRLKSD   71 (457)
T ss_pred             CeEEEEeCCHHHHHHHHHHHHhCCCEEEEeCCHHHHHHHH-----------hhcCCCEEEEeCCCCCCCHHHHHHHHHcC
Confidence            4899999999999999999998999999999999999998           66789999999999999999999999863


Q ss_pred             CCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCC
Q 023816          110 TPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVK  189 (276)
Q Consensus       110 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~  189 (276)
                      .+                                           ...+|||++++........++++.|+++|+.||++
T Consensus        72 ~~-------------------------------------------~~~~~ii~~s~~~~~~~~~~~~~~ga~~~l~kp~~  108 (457)
T PRK09581         72 PA-------------------------------------------TTHIPVVMVTALDDPEDRVRGLEAGADDFLTKPIN  108 (457)
T ss_pred             cc-------------------------------------------cCCCCEEEEECCCCHHHHHHHHHCCCCEEEECCCC
Confidence            21                                           12689999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHh
Q 023816          190 LSDVKRIKDYLTRD  203 (276)
Q Consensus       190 ~~~L~~~~~~l~~~  203 (276)
                      .++|...+..+.+.
T Consensus       109 ~~~l~~~i~~~~~~  122 (457)
T PRK09581        109 DVALFARVKSLTRL  122 (457)
T ss_pred             HHHHHHHHHHHHHH
Confidence            99997666665543

>PRK13558 bacterio-opsin activator; Provisional

Probab=99.54  E-value=9.2e-14  Score=139.23  Aligned_cols=107  Identities=21%  Similarity=0.184  Sum_probs=99.1

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHH
Q 023816           28 EEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIK  107 (276)
Q Consensus        28 ~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir  107 (276)
                      +.++||||||++.++..+.++|...||.+..+.++.+++..+           ....||+||+|+.||+++|++++++|+
T Consensus         6 ~~~~ILivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~al~~~-----------~~~~~Dlvl~d~~lp~~~g~~~l~~l~   74 (665)
T PRK13558          6 PTRGVLFVGDDPEAGPVDCDLDEDGRLDVTQIRDFVAARDRV-----------EAGEIDCVVADHEPDGFDGLALLEAVR   74 (665)
T ss_pred             cceeEEEEccCcchHHHHHHHhhccCcceEeeCCHHHHHHHh-----------hccCCCEEEEeccCCCCcHHHHHHHHH
Confidence            468999999999999999999999999999999999999988           566799999999999999999999999


Q ss_pred             hhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCC
Q 023816          108 VTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKP  187 (276)
Q Consensus       108 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KP  187 (276)
                      ...+                                             .+|||++|+..+.....++++.|+.||+.||
T Consensus        75 ~~~~---------------------------------------------~~piI~lt~~~~~~~~~~al~~Ga~dyl~k~  109 (665)
T PRK13558         75 QTTA---------------------------------------------VPPVVVVPTAGDEAVARRAVDADAAAYVPAV  109 (665)
T ss_pred             hcCC---------------------------------------------CCCEEEEECCCCHHHHHHHHhcCcceEEecc
Confidence            7666                                             7899999999999999999999999999999


Q ss_pred             CCH
Q 023816          188 VKL  190 (276)
Q Consensus       188 v~~  190 (276)
                      ...
T Consensus       110 ~~~  112 (665)
T PRK13558        110 SDD  112 (665)
T ss_pred             chh
Confidence            753

>PRK00742 chemotaxis-specific methylesterase; Provisional

Probab=99.54  E-value=2e-13  Score=128.17  Aligned_cols=106  Identities=35%  Similarity=0.430  Sum_probs=92.4

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhC-CCEEE-EECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHH
Q 023816           27 TEEVHVLAVDDSFVDRKVIERLLTIS-SCKVT-AVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLK  104 (276)
Q Consensus        27 ~~~~~VLIVdD~~~~~~~L~~~L~~~-g~~v~-~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~  104 (276)
                      |.+++||||||+...+..+++.|+.. ++.+. .+.+++++++.+           ....||+|++|+.||+++|+++++
T Consensus         1 m~~~~ILiVdd~~~~~~~L~~~L~~~~~~~vv~~a~~~~~al~~~-----------~~~~~DlVllD~~mp~~dgle~l~   69 (354)
T PRK00742          1 MMKIRVLVVDDSAFMRRLISEILNSDPDIEVVGTAPDGLEAREKI-----------KKLNPDVITLDVEMPVMDGLDALE   69 (354)
T ss_pred             CCccEEEEECCCHHHHHHHHHHHhhCCCCEEEEEECCHHHHHHHH-----------hhhCCCEEEEeCCCCCCChHHHHH
Confidence            35689999999999999999999876 88887 799999999988           667899999999999999999999


Q ss_pred             HHHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCC--CHHHHHHHHhcCCCe
Q 023816          105 KIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSEN--ILARIDRCLEDGAED  182 (276)
Q Consensus       105 ~Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~--~~~~~~~al~~Ga~d  182 (276)
                      +|++..                                              ++|+|++|+..  ......++++.|++|
T Consensus        70 ~i~~~~----------------------------------------------~~piIvls~~~~~~~~~~~~al~~Ga~d  103 (354)
T PRK00742         70 KIMRLR----------------------------------------------PTPVVMVSSLTERGAEITLRALELGAVD  103 (354)
T ss_pred             HHHHhC----------------------------------------------CCCEEEEecCCCCCHHHHHHHHhCCCcE
Confidence            999633                                              27999999753  345677899999999


Q ss_pred             EEeCCCC
Q 023816          183 FIVKPVK  189 (276)
Q Consensus       183 ~l~KPv~  189 (276)
                      |+.||+.
T Consensus       104 ~l~kP~~  110 (354)
T PRK00742        104 FVTKPFL  110 (354)
T ss_pred             EEeCCcc
Confidence            9999994

>PRK10610 chemotaxis regulatory protein CheY; Provisional

Probab=99.52  E-value=1.7e-12  Score=96.90  Aligned_cols=120  Identities=28%  Similarity=0.463  Sum_probs=102.7

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhCCCE-EEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHH
Q 023816           28 EEVHVLAVDDSFVDRKVIERLLTISSCK-VTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKI  106 (276)
Q Consensus        28 ~~~~VLIVdD~~~~~~~L~~~L~~~g~~-v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~I  106 (276)
                      +.++|+++|++......+...|...|+. +..+.++.+++..+           ....+|++++|..+++++|+++++.+
T Consensus         4 ~~~~il~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~-----------~~~~~di~l~d~~~~~~~~~~~~~~l   72 (129)
T PRK10610          4 KELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKL-----------QAGGFGFVISDWNMPNMDGLELLKTI   72 (129)
T ss_pred             ccceEEEEcCCHHHHHHHHHHHHHcCCCeEEEeCCHHHHHHHh-----------hccCCCEEEEcCCCCCCCHHHHHHHH
Confidence            4579999999999999999999988984 77789999999887           55679999999999999999999999


Q ss_pred             HhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeC
Q 023816          107 KVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVK  186 (276)
Q Consensus       107 r~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~K  186 (276)
                      ++...                                           ...+|+++++..........+++.|+.+|+.|
T Consensus        73 ~~~~~-------------------------------------------~~~~~~i~~~~~~~~~~~~~~~~~g~~~~i~~  109 (129)
T PRK10610         73 RADGA-------------------------------------------MSALPVLMVTAEAKKENIIAAAQAGASGYVVK  109 (129)
T ss_pred             HhCCC-------------------------------------------cCCCcEEEEECCCCHHHHHHHHHhCCCeEEEC
Confidence            96432                                           12578999998888888889999999999999


Q ss_pred             CCCHHHHHHHHHHHH
Q 023816          187 PVKLSDVKRIKDYLT  201 (276)
Q Consensus       187 Pv~~~~L~~~~~~l~  201 (276)
                      |++..++...+..+.
T Consensus       110 p~~~~~l~~~l~~~~  124 (129)
T PRK10610        110 PFTAATLEEKLNKIF  124 (129)
T ss_pred             CCCHHHHHHHHHHHH
Confidence            999999866655543

>PRK13435 response regulator; Provisional

Probab=99.50  E-value=1.1e-12  Score=106.09  Aligned_cols=115  Identities=23%  Similarity=0.290  Sum_probs=97.3

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhCCCEEE-EECCHHHHHHHhcccccccccCCCCCceeEEEEecCCC-CCCHHHHHH
Q 023816           27 TEEVHVLAVDDSFVDRKVIERLLTISSCKVT-AVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMP-GMTGYELLK  104 (276)
Q Consensus        27 ~~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~-~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp-~~~G~ell~  104 (276)
                      +.+++||++||+...+..+...|+..|+++. .+.+++++++.+           ....||+|++|+.++ +.+|+++++
T Consensus         3 ~~~~~iliid~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~-----------~~~~~dliivd~~~~~~~~~~~~~~   71 (145)
T PRK13435          3 LRQLKVLIVEDEALIALELEKLVEEAGHEVVGIAMSSEQAIALG-----------RRRQPDVALVDVHLADGPTGVEVAR   71 (145)
T ss_pred             cccceEEEEcCcHHHHHHHHHHHHhcCCeEEEeeCCHHHHHHHh-----------hhcCCCEEEEeeecCCCCcHHHHHH
Confidence            4578999999999999999999999999987 689999999987           456799999999998 589999999


Q ss_pred             HHHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEE
Q 023816          105 KIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFI  184 (276)
Q Consensus       105 ~Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l  184 (276)
                      .+++. +                                             .+|+|++++...   ...++..|+++|+
T Consensus        72 ~l~~~-~---------------------------------------------~~pii~ls~~~~---~~~~~~~ga~~~l  102 (145)
T PRK13435         72 RLSAD-G---------------------------------------------GVEVVFMTGNPE---RVPHDFAGALGVI  102 (145)
T ss_pred             HHHhC-C---------------------------------------------CCCEEEEeCCHH---HHHHHhcCcceeE
Confidence            99752 2                                             589999987643   3467889999999


Q ss_pred             eCCCCHHHHHHHHHHHH
Q 023816          185 VKPVKLSDVKRIKDYLT  201 (276)
Q Consensus       185 ~KPv~~~~L~~~~~~l~  201 (276)
                      .||++.+++.+.+..+.
T Consensus       103 ~kp~~~~~l~~~i~~~~  119 (145)
T PRK13435        103 AKPYSPRGVARALSYLS  119 (145)
T ss_pred             eCCCCHHHHHHHHHHHH
Confidence            99999999977665553

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

Probab=99.50  E-value=1.5e-13  Score=131.74  Aligned_cols=104  Identities=39%  Similarity=0.512  Sum_probs=92.3

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhCC-CEEE-EECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHH
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTISS-CKVT-AVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKI  106 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~g-~~v~-~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~I  106 (276)
                      .++||+|||+...|+.|.++|...+ ++++ .+.||.+|++++           .+..||+|.+|+.||.|||++++++|
T Consensus         1 ~irVlvVddsal~R~~i~~~l~~~~~i~vv~~a~ng~~a~~~~-----------~~~~PDVi~ld~emp~mdgl~~l~~i   69 (350)
T COG2201           1 KIRVLVVDDSALMRKVISDILNSDPDIEVVGTARNGREAIDKV-----------KKLKPDVITLDVEMPVMDGLEALRKI   69 (350)
T ss_pred             CcEEEEEcCcHHHHHHHHHHHhcCCCeEEEEecCCHHHHHHHH-----------HhcCCCEEEEecccccccHHHHHHHH
Confidence            4799999999999999999999888 5554 699999999999           78899999999999999999999999


Q ss_pred             HhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCH--HHHHHHHhcCCCeEE
Q 023816          107 KVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENIL--ARIDRCLEDGAEDFI  184 (276)
Q Consensus       107 r~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~--~~~~~al~~Ga~d~l  184 (276)
                      .+..                                              ++|||++++-...  +...+|++.||.||+
T Consensus        70 m~~~----------------------------------------------p~pVimvsslt~~g~~~t~~al~~gAvD~i  103 (350)
T COG2201          70 MRLR----------------------------------------------PLPVIMVSSLTEEGAEATLEALELGAVDFI  103 (350)
T ss_pred             hcCC----------------------------------------------CCcEEEEeccccccHHHHHHHHhcCcceee
Confidence            9753                                              6999999886554  456689999999999


Q ss_pred             eCCCC
Q 023816          185 VKPVK  189 (276)
Q Consensus       185 ~KPv~  189 (276)
                      .||..
T Consensus       104 ~kp~~  108 (350)
T COG2201         104 AKPSG  108 (350)
T ss_pred             cCCCc
Confidence            99974

>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional

Probab=99.47  E-value=1.3e-12  Score=116.95  Aligned_cols=117  Identities=10%  Similarity=0.086  Sum_probs=96.7

Q ss_pred             CCCccEEEEEeCCHHHHHHHHHHHhhCCCEE-EEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHH-
Q 023816           26 DTEEVHVLAVDDSFVDRKVIERLLTISSCKV-TAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELL-  103 (276)
Q Consensus        26 ~~~~~~VLIVdD~~~~~~~L~~~L~~~g~~v-~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell-  103 (276)
                      .+...+|++|||++..+..|..+|. .++.+ ..+.++.++++.+           .  .|||||+|+.||+++|++++ 
T Consensus         7 ~~~~~~~~~v~~~~l~~~~l~~~L~-~~~~v~~~~~~~~~~~~~~-----------~--~~DvvllDi~~p~~~G~~~~~   72 (216)
T PRK10100          7 SSHGHTLLLITKPSLQATALLQHLK-QSLAITGKLHNIQRSLDDI-----------S--SGSIILLDMMEADKKLIHYWQ   72 (216)
T ss_pred             cccCceEEEEeChHhhhHHHHHHHH-HhCCCeEEEcCHHHhhccC-----------C--CCCEEEEECCCCCccHHHHHH
Confidence            4557789999999999999999998 55554 4578999998865           3  39999999999999999997 


Q ss_pred             HHHHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHh--cCCC
Q 023816          104 KKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLE--DGAE  181 (276)
Q Consensus       104 ~~Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~--~Ga~  181 (276)
                      +.|++..|                                             .++||++|+..+  ....++.  .||.
T Consensus        73 ~~i~~~~p---------------------------------------------~~~vvvlt~~~~--~~~~~~~~~~Ga~  105 (216)
T PRK10100         73 DTLSRKNN---------------------------------------------NIKILLLNTPED--YPYREIENWPHIN  105 (216)
T ss_pred             HHHHHhCC---------------------------------------------CCcEEEEECCch--hHHHHHHHhcCCe
Confidence            56888777                                             799999999876  3445555  5999


Q ss_pred             eEEeCCCCHHHHHHHHHHHHHh
Q 023816          182 DFIVKPVKLSDVKRIKDYLTRD  203 (276)
Q Consensus       182 d~l~KPv~~~~L~~~~~~l~~~  203 (276)
                      +|+.|+.+.++|.+.++.+...
T Consensus       106 G~l~K~~~~~~L~~aI~~v~~G  127 (216)
T PRK10100        106 GVFYAMEDQERVVNGLQGVLRG  127 (216)
T ss_pred             EEEECCCCHHHHHHHHHHHHcC
Confidence            9999999999998777766543

>PRK11475 DNA-binding transcriptional activator BglJ; Provisional

Probab=99.43  E-value=2.6e-12  Score=114.35  Aligned_cols=105  Identities=14%  Similarity=0.182  Sum_probs=88.4

Q ss_pred             HHHHHHHHhh---CCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEE---EecCCCCCCHHHHHHHHHhhCCCCcc
Q 023816           42 RKVIERLLTI---SSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLII---TDYCMPGMTGYELLKKIKVTTPFNFL  115 (276)
Q Consensus        42 ~~~L~~~L~~---~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL---~D~~mp~~~G~ell~~Ir~~~p~~~~  115 (276)
                      |..+..+|+.   .|+.+..+.+++++++.+           ....||++|   +|+.||+++|++++++|++..|    
T Consensus         3 r~gi~~lL~~~~~~~~~v~~~~~~~~~l~~~-----------~~~~pd~vl~dl~d~~mp~~~Gl~~~~~l~~~~p----   67 (207)
T PRK11475          3 SIGIESLFRKFPGNPYKLHTFSSQSSFQDAM-----------SRISFSAVIFSLSAMRSERREGLSCLTELAIKFP----   67 (207)
T ss_pred             hHHHHHHHhcCCCCeeEEEEeCCHHHHHHHh-----------ccCCCCEEEeeccccCCCCCCHHHHHHHHHHHCC----
Confidence            6778888864   356667899999999988           666799998   6888999999999999999888    


Q ss_pred             cchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHH-hcCCCeEEeCCCCHHHHH
Q 023816          116 YSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCL-EDGAEDFIVKPVKLSDVK  194 (276)
Q Consensus       116 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al-~~Ga~d~l~KPv~~~~L~  194 (276)
                                                               +++||++|+..+.....+++ ++||.+|+.||.+.++|.
T Consensus        68 -----------------------------------------~~~iIvlt~~~~~~~~~~~~~~~Ga~gyl~K~~~~~eL~  106 (207)
T PRK11475         68 -----------------------------------------RMRRLVIADDDIEARLIGSLSPSPLDGVLSKASTLEILQ  106 (207)
T ss_pred             -----------------------------------------CCCEEEEeCCCCHHHHHHHHHHcCCeEEEecCCCHHHHH
Confidence                                                     89999999988776666655 799999999999999997


Q ss_pred             HHHHHHHH
Q 023816          195 RIKDYLTR  202 (276)
Q Consensus       195 ~~~~~l~~  202 (276)
                      +.++.+.+
T Consensus       107 ~aI~~v~~  114 (207)
T PRK11475        107 QELFLSLN  114 (207)
T ss_pred             HHHHHHHC
Confidence            77766554

>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=99.41  E-value=8.7e-12  Score=88.14  Aligned_cols=110  Identities=33%  Similarity=0.559  Sum_probs=97.3

Q ss_pred             EEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhhCCC
Q 023816           33 LAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVTTPF  112 (276)
Q Consensus        33 LIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~~p~  112 (276)
                      |++|+++..+..+...++..|+.+..+.+..+++..+           ....+|++++|..+++.+|+++++.++...+ 
T Consensus         1 l~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~-----------~~~~~~~ii~~~~~~~~~~~~~~~~l~~~~~-   68 (113)
T cd00156           1 LIVDDDPLIRELLRRLLEKEGYEVVEAEDGEEALALL-----------AEEKPDLILLDIMMPGMDGLELLRRIRKRGP-   68 (113)
T ss_pred             CeecCcHHHHHHHHHHHhhcCceEEEecCHHHHHHHH-----------HhCCCCEEEEecCCCCCchHHHHHHHHHhCC-
Confidence            4789999999999999998899999999999999888           5567999999999999999999999997544 


Q ss_pred             CcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCCHHH
Q 023816          113 NFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSD  192 (276)
Q Consensus       113 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~~~~  192 (276)
                                                                  .+|+++++..........+++.|+.+|+.||++..+
T Consensus        69 --------------------------------------------~~~~i~~~~~~~~~~~~~~~~~~~~~~i~~p~~~~~  104 (113)
T cd00156          69 --------------------------------------------DIPIIFLTAHGDDEDAVEALKAGADDYLTKPFSPEE  104 (113)
T ss_pred             --------------------------------------------CCCEEEEEecccHHHHHHHHHcChhhHccCCCCHHH
Confidence                                                        689999988877778888999999999999999988


Q ss_pred             HHHHHH
Q 023816          193 VKRIKD  198 (276)
Q Consensus       193 L~~~~~  198 (276)
                      +.+.+.
T Consensus       105 l~~~l~  110 (113)
T cd00156         105 LLARIR  110 (113)
T ss_pred             HHHHHH
Confidence            866554

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

Probab=99.39  E-value=8.7e-12  Score=129.38  Aligned_cols=117  Identities=12%  Similarity=0.143  Sum_probs=103.6

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHh
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKV  108 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~  108 (276)
                      +.+||||||++..+..+++.|+..||++..+.+++++++.+..         ....||+||+  .||+++|.++++.|+.
T Consensus       697 ~~~ILvVddd~~~~~~l~~~L~~~G~~v~~~~s~~~al~~l~~---------~~~~~DlVll--~~~~~~g~~l~~~l~~  765 (828)
T PRK13837        697 GETVLLVEPDDATLERYEEKLAALGYEPVGFSTLAAAIAWISK---------GPERFDLVLV--DDRLLDEEQAAAALHA  765 (828)
T ss_pred             CCEEEEEcCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHHh---------CCCCceEEEE--CCCCCCHHHHHHHHHh
Confidence            4589999999999999999999999999999999999998821         1234899999  7999999999999998


Q ss_pred             hCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCC
Q 023816          109 TTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPV  188 (276)
Q Consensus       109 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv  188 (276)
                      ..+                                             .+|||++++........++++.| +|||.||+
T Consensus       766 ~~~---------------------------------------------~ipIIvls~~~~~~~~~~~~~~G-~d~L~KP~  799 (828)
T PRK13837        766 AAP---------------------------------------------TLPIILGGNSKTMALSPDLLASV-AEILAKPI  799 (828)
T ss_pred             hCC---------------------------------------------CCCEEEEeCCCchhhhhhHhhcc-CcEEeCCC
Confidence            666                                             79999999999988999999999 99999999


Q ss_pred             CHHHHHHHHHHHHH
Q 023816          189 KLSDVKRIKDYLTR  202 (276)
Q Consensus       189 ~~~~L~~~~~~l~~  202 (276)
                      +..+|...+..+.+
T Consensus       800 ~~~~L~~~l~~~l~  813 (828)
T PRK13837        800 SSRTLAYALRTALA  813 (828)
T ss_pred             CHHHHHHHHHHHHc
Confidence            99999777766553

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

Probab=99.38  E-value=9.3e-12  Score=110.04  Aligned_cols=115  Identities=10%  Similarity=0.073  Sum_probs=95.0

Q ss_pred             EEEEEeCCHHHHHHHHHHHhhCC--CEE-EEECCHHHHHHHhcccccccccCCCCCceeEEEEecC--CCCCCHHHHHHH
Q 023816           31 HVLAVDDSFVDRKVIERLLTISS--CKV-TAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYC--MPGMTGYELLKK  105 (276)
Q Consensus        31 ~VLIVdD~~~~~~~L~~~L~~~g--~~v-~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~--mp~~~G~ell~~  105 (276)
                      .||||||++..+..++.+|...+  +++ ..+.++.++++.+           +..+|||||+|+.  |++.+|.+++++
T Consensus         2 ~~lIvDD~~~~~~gl~~~L~~~~~~~~vv~~~~~~~~~~~~~-----------~~~~pDlvLlDl~~~l~~~~g~~~i~~   70 (207)
T PRK15411          2 STIIMDLCSYTRLGLTGYLLSRGVKKREINDIETVDDLAIAC-----------DSLRPSVVFINEDCFIHDASNSQRIKQ   70 (207)
T ss_pred             CEEEEcCCHHHHHHHHHHHHhCCCcceEEEecCCHHHHHHHH-----------hccCCCEEEEeCcccCCCCChHHHHHH
Confidence            58999999999999999998655  344 4689999999988           5668999999976  888899999999


Q ss_pred             HHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCe-EE
Q 023816          106 IKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAED-FI  184 (276)
Q Consensus       106 Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d-~l  184 (276)
                      |++..|                                             .++||++|+..+..... ++..|+.. |+
T Consensus        71 i~~~~p---------------------------------------------~~~iivlt~~~~~~~~~-~~~~~~~~~~~  104 (207)
T PRK15411         71 IINQHP---------------------------------------------NTLFIVFMAIANIHFDE-YLLVRKNLLIS  104 (207)
T ss_pred             HHHHCC---------------------------------------------CCeEEEEECCCchhHHH-HHHHHhhceee
Confidence            999888                                             79999999987766543 55555544 88


Q ss_pred             eCCCCHHHHHHHHHHHHH
Q 023816          185 VKPVKLSDVKRIKDYLTR  202 (276)
Q Consensus       185 ~KPv~~~~L~~~~~~l~~  202 (276)
                      .|+.+.++|.+.++.+..
T Consensus       105 ~K~~~~~~L~~aI~~v~~  122 (207)
T PRK15411        105 SKSIKPESLDDLLGDILK  122 (207)
T ss_pred             eccCCHHHHHHHHHHHHc
Confidence            999999999777766543

>PRK09191 two-component response regulator; Provisional

Probab=99.35  E-value=3.3e-11  Score=106.14  Aligned_cols=114  Identities=18%  Similarity=0.221  Sum_probs=96.0

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhCCCEEE-EECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCC-CCHHHHHHHH
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTISSCKVT-AVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPG-MTGYELLKKI  106 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~g~~v~-~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~-~~G~ell~~I  106 (276)
                      ..+|||+||++..+..++..|+..|+.+. .+.++.+++..+           .+..||+||+|+.||+ ++|+++++.+
T Consensus       137 ~~~~liidd~~~~~~~l~~~L~~~~~~~~~~~~~~~~~l~~l-----------~~~~~dlvi~d~~~~~~~~g~e~l~~l  205 (261)
T PRK09191        137 ATRVLIIEDEPIIAMDLEQLVESLGHRVTGIARTRAEAVALA-----------KKTRPGLILADIQLADGSSGIDAVNDI  205 (261)
T ss_pred             CCeEEEEcCcHHHHHHHHHHHhcCCCEEEEEECCHHHHHHHH-----------hccCCCEEEEecCCCCCCCHHHHHHHH
Confidence            46899999999999999999999999988 689999999988           5668999999999995 8999999999


Q ss_pred             HhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeC
Q 023816          107 KVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVK  186 (276)
Q Consensus       107 r~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~K  186 (276)
                      +...                                              .+|+|++|+......  .+...|+.+|+.|
T Consensus       206 ~~~~----------------------------------------------~~pii~ls~~~~~~~--~~~~~~~~~~l~k  237 (261)
T PRK09191        206 LKTF----------------------------------------------DVPVIFITAFPERLL--TGERPEPAFLITK  237 (261)
T ss_pred             HHhC----------------------------------------------CCCEEEEeCCCcHHH--HHHhcccCceEEC
Confidence            8521                                              489999998766443  3445678899999


Q ss_pred             CCCHHHHHHHHHHHH
Q 023816          187 PVKLSDVKRIKDYLT  201 (276)
Q Consensus       187 Pv~~~~L~~~~~~l~  201 (276)
                      |++.+++...+..+.
T Consensus       238 P~~~~~l~~~i~~~~  252 (261)
T PRK09191        238 PFQPDTVKAAISQAL  252 (261)
T ss_pred             CCCHHHHHHHHHHHH
Confidence            999999977666544

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

Probab=99.35  E-value=6.8e-12  Score=111.73  Aligned_cols=114  Identities=26%  Similarity=0.309  Sum_probs=95.7

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhCCCEEEE-ECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHH
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTISSCKVTA-VDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIK  107 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~-a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir  107 (276)
                      ..+||++||++..+..+...|...||.++. +.++-++....           ..+.||+||+|+.||..|-.+.+-...
T Consensus         5 ~lrvlv~~d~~i~~~~i~~~l~eag~~~Vg~~~~~~~~~~~~-----------~~~~pDvVildie~p~rd~~e~~~~~~   73 (194)
T COG3707           5 LLRVLVADDEALTRMDIREGLLEAGYQRVGEAADGLEAVEVC-----------ERLQPDVVILDIEMPRRDIIEALLLAS   73 (194)
T ss_pred             ccceeeccccccchhhHHHHHHHcCCeEeeeecccccchhHH-----------HhcCCCEEEEecCCCCccHHHHHHHhh
Confidence            578999999999999999999999997665 77777777776           678999999999999999444333333


Q ss_pred             hhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCC
Q 023816          108 VTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKP  187 (276)
Q Consensus       108 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KP  187 (276)
                       .++                                             .-|||++|++++++.+..++++|+..||+||
T Consensus        74 -~~~---------------------------------------------~~piv~lt~~s~p~~i~~a~~~Gv~ayivkp  107 (194)
T COG3707          74 -ENV---------------------------------------------ARPIVALTAYSDPALIEAAIEAGVMAYIVKP  107 (194)
T ss_pred             -cCC---------------------------------------------CCCEEEEEccCChHHHHHHHHcCCeEEEecC
Confidence             223                                             6799999999999999999999999999999


Q ss_pred             CCHHHHHHHHHH
Q 023816          188 VKLSDVKRIKDY  199 (276)
Q Consensus       188 v~~~~L~~~~~~  199 (276)
                      ++...|.-+++-
T Consensus       108 i~~~rl~p~L~v  119 (194)
T COG3707         108 LDESRLLPILDV  119 (194)
T ss_pred             cchhhhhHHHHH
Confidence            999888665543

>PRK13557 histidine kinase; Provisional

Probab=99.34  E-value=3.2e-11  Score=115.02  Aligned_cols=118  Identities=24%  Similarity=0.318  Sum_probs=104.4

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCC-CCHHHHHHHHH
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPG-MTGYELLKKIK  107 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~-~~G~ell~~Ir  107 (276)
                      ..+||+|||+...+..+.+.|+..|+++..+.++.++++.+.          ....||+|++|..||+ ++|+++++.|+
T Consensus       415 ~~~iliv~~~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~----------~~~~~d~vi~d~~~~~~~~~~~~~~~l~  484 (540)
T PRK13557        415 TETILIVDDRPDVAELARMILEDFGYRTLVASNGREALEILD----------SHPEVDLLFTDLIMPGGMNGVMLAREAR  484 (540)
T ss_pred             CceEEEEcCcHHHHHHHHHHHHhcCCeEEEeCCHHHHHHHHh----------cCCCceEEEEeccCCCCCCHHHHHHHHH
Confidence            458999999999999999999999999999999999999882          2336999999999997 99999999999


Q ss_pred             hhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCC
Q 023816          108 VTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKP  187 (276)
Q Consensus       108 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KP  187 (276)
                      ...+                                             .+|+|++++.........++..|+.+|+.||
T Consensus       485 ~~~~---------------------------------------------~~~ii~~~~~~~~~~~~~~~~~g~~~~l~kp  519 (540)
T PRK13557        485 RRQP---------------------------------------------KIKVLLTTGYAEASIERTDAGGSEFDILNKP  519 (540)
T ss_pred             HhCC---------------------------------------------CCcEEEEcCCCchhhhhhhccccCCceeeCC
Confidence            8666                                             6899999999888888889999999999999


Q ss_pred             CCHHHHHHHHHHHH
Q 023816          188 VKLSDVKRIKDYLT  201 (276)
Q Consensus       188 v~~~~L~~~~~~l~  201 (276)
                      ++.++|...+..+.
T Consensus       520 ~~~~~l~~~l~~~~  533 (540)
T PRK13557        520 YRRAELARRVRMVL  533 (540)
T ss_pred             CCHHHHHHHHHHHh
Confidence            99999866665543

>PRK10693 response regulator of RpoS; Provisional

Probab=99.28  E-value=3.8e-11  Score=111.48  Aligned_cols=87  Identities=31%  Similarity=0.560  Sum_probs=76.1

Q ss_pred             EECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhhCCCCcccchheehhhhhhhhhhhhhccc
Q 023816           58 AVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICF  137 (276)
Q Consensus        58 ~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~  137 (276)
                      .+.++++|++.+           +...||+||+|+.||+++|++++++|++..+                          
T Consensus         2 ~a~~g~~al~~l-----------~~~~pDlVL~D~~mp~~~Gle~~~~ir~~~~--------------------------   44 (303)
T PRK10693          2 LAANGVDALELL-----------GGFTPDLIICDLAMPRMNGIEFVEHLRNRGD--------------------------   44 (303)
T ss_pred             EeCCHHHHHHHH-----------hcCCCCEEEEeCCCCCCCHHHHHHHHHhcCC--------------------------
Confidence            467899999988           5678999999999999999999999997555                          


Q ss_pred             cCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCC-CHHHHHHHHHHH
Q 023816          138 CFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPV-KLSDVKRIKDYL  200 (276)
Q Consensus       138 ~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv-~~~~L~~~~~~l  200 (276)
                                         .+|||++|+....+...++++.|++||+.||+ +.+++.+.+...
T Consensus        45 -------------------~ipiI~lt~~~~~~~~~~al~~Ga~dyl~KP~~~~~~L~~~i~~~   89 (303)
T PRK10693         45 -------------------QTPVLVISATENMADIAKALRLGVQDVLLKPVKDLNRLREMVFAC   89 (303)
T ss_pred             -------------------CCcEEEEECCCCHHHHHHHHHCCCcEEEECCCCcHHHHHHHHHHH
Confidence                               68999999999999999999999999999999 478886555443

>PRK15029 arginine decarboxylase; Provisional

Probab=99.15  E-value=3.4e-10  Score=118.03  Aligned_cols=107  Identities=19%  Similarity=0.250  Sum_probs=88.8

Q ss_pred             cEEEEEeCCHH--------HHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCC-CceeEEEEecCCCCCCHH
Q 023816           30 VHVLAVDDSFV--------DRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDG-LKVDLIITDYCMPGMTGY  100 (276)
Q Consensus        30 ~~VLIVdD~~~--------~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~-~~~DlIL~D~~mp~~~G~  100 (276)
                      ++||||||+..        .++.|+..|+..||+|..+.++++|++.+           +. ..||+||+|+.||+++|+
T Consensus         1 MkILIVDDD~~~~~~~~~~i~~~L~~~Le~~G~eV~~a~s~~dAl~~l-----------~~~~~~DlVLLD~~LPd~dG~   69 (755)
T PRK15029          1 MKVLIVESEFLHQDTWVGNAVERLADALSQQNVTVIKSTSFDDGFAIL-----------SSNEAIDCLMFSYQMEHPDEH   69 (755)
T ss_pred             CeEEEEeCCcccccchhHHHHHHHHHHHHHCCCEEEEECCHHHHHHHH-----------HhcCCCcEEEEECCCCCCccc
Confidence            37999999995        69999999999999999999999999998           44 589999999999999997


Q ss_pred             ----HHHHHHHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCC--HHHHHH
Q 023816          101 ----ELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENI--LARIDR  174 (276)
Q Consensus       101 ----ell~~Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~--~~~~~~  174 (276)
                          +++++||+..+                                             .+|||++|+...  ......
T Consensus        70 ~~~~ell~~IR~~~~---------------------------------------------~iPIIlLTar~~~~~~~~~~  104 (755)
T PRK15029         70 QNVRQLIGKLHERQQ---------------------------------------------NVPVFLLGDREKALAAMDRD  104 (755)
T ss_pred             hhHHHHHHHHHhhCC---------------------------------------------CCCEEEEEcCCcccccCCHH
Confidence                89999997555                                             799999999886  333334


Q ss_pred             HHhcCCCeEEeCCCCHHHH
Q 023816          175 CLEDGAEDFIVKPVKLSDV  193 (276)
Q Consensus       175 al~~Ga~d~l~KPv~~~~L  193 (276)
                      .++ -++.|+-+-....+.
T Consensus       105 ~~~-~~~~~~~~~~~~~~~  122 (755)
T PRK15029        105 LLE-LVDEFAWILEDTADF  122 (755)
T ss_pred             HHH-hhheEEEecCCCHHH
Confidence            333 377888886655553

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

Probab=99.14  E-value=2.3e-10  Score=104.28  Aligned_cols=117  Identities=28%  Similarity=0.488  Sum_probs=98.9

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhC-CCEEE-EECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHH
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTIS-SCKVT-AVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKI  106 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~-g~~v~-~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~I  106 (276)
                      +++|+++||++..++.+..++... .+++. .+.++.++++.+           +...+|++++|+.||+++|+++.+.|
T Consensus         1 m~~i~i~dd~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~~~~fldI~~~~~~G~ela~~i   69 (244)
T COG3279           1 MLKVLIVDDEPLAREELRRILNEIPDIEIVGEAENGEEALQLL-----------QGLRPDLVFLDIAMPDINGIELAARI   69 (244)
T ss_pred             CCcEEEecCCHHHHHHHHHHHHhhhhcCeeeeeccchhhHHHH-----------hccCCCeEEEeeccCccchHHHHHHh
Confidence            368999999999999999999832 23333 588999999998           66699999999999999999999999


Q ss_pred             HhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeC
Q 023816          107 KVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVK  186 (276)
Q Consensus       107 r~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~K  186 (276)
                      +...+                                             ..+||++|++..  ....+.+..|.|||.|
T Consensus        70 ~~~~~---------------------------------------------~~~Ivfvt~~~~--~a~~afev~a~d~i~k  102 (244)
T COG3279          70 RKGDP---------------------------------------------RPAIVFVTAHDE--YAVAAFEVEALDYLLK  102 (244)
T ss_pred             cccCC---------------------------------------------CCeEEEEEehHH--HHHHHHhHHHHhhhcC
Confidence            97655                                             789999998865  5556778899999999


Q ss_pred             CCCHHHHHHHHHHHHHh
Q 023816          187 PVKLSDVKRIKDYLTRD  203 (276)
Q Consensus       187 Pv~~~~L~~~~~~l~~~  203 (276)
                      |+..+++...+.++.+.
T Consensus       103 p~~~~~l~~~l~~~~~~  119 (244)
T COG3279         103 PISEERLAKTLERLRRY  119 (244)
T ss_pred             cchHHHHHHHHHHHHHH
Confidence            99999998887765554

>PRK11107 hybrid sensory histidine kinase BarA; Provisional

Probab=98.52  E-value=2e-06  Score=88.67  Aligned_cols=115  Identities=11%  Similarity=0.061  Sum_probs=93.1

Q ss_pred             CCCccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHH
Q 023816           26 DTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKK  105 (276)
Q Consensus        26 ~~~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~  105 (276)
                      ...+.+|+++||++..++.+.++|...|+.+..+.++.+    +           ....||++++|+.||+.++.+.+..
T Consensus       533 ~~~g~~ili~d~~~~~~~~l~~~L~~~g~~v~~~~~~~~----l-----------~~~~~d~il~~~~~~~~~~~~~~~~  597 (919)
T PRK11107        533 CLAGKRLLYVEPNSAAAQATLDILSETPLEVTYSPTLSQ----L-----------PEAHYDILLLGLPVTFREPLTMLHE  597 (919)
T ss_pred             ccCCCeEEEEeCCHHHHHHHHHHHHHCCCEEEEcCCHHH----h-----------ccCCCCEEEecccCCCCCCHHHHHH
Confidence            345679999999999999999999999999999999877    3           3457999999999999887765555


Q ss_pred             HHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEe
Q 023816          106 IKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIV  185 (276)
Q Consensus       106 Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~  185 (276)
                      .....+                                           ....++++++..........+.+.|+++|+.
T Consensus       598 ~~~~~~-------------------------------------------~~~~~~i~~~~~~~~~~~~~~~~~g~~~~l~  634 (919)
T PRK11107        598 RLAKAK-------------------------------------------SMTDFLILALPCHEQVLAEQLKQDGADACLS  634 (919)
T ss_pred             HHHhhh-------------------------------------------hcCCcEEEEeCCcchhhHHHHhhCCCceEEC
Confidence            543221                                           1134677788888888889999999999999


Q ss_pred             CCCCHHHHHHHHH
Q 023816          186 KPVKLSDVKRIKD  198 (276)
Q Consensus       186 KPv~~~~L~~~~~  198 (276)
                      ||+...++...+.
T Consensus       635 kp~~~~~l~~~l~  647 (919)
T PRK11107        635 KPLSHTRLLPALL  647 (919)
T ss_pred             CCCCHHHHHHHHH
Confidence            9999998855554

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

Probab=98.06  E-value=3.7e-06  Score=83.33  Aligned_cols=91  Identities=34%  Similarity=0.450  Sum_probs=77.0

Q ss_pred             CEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhhCCCCcccchheehhhhhhhhhhhh
Q 023816           54 CKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFIL  133 (276)
Q Consensus        54 ~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~~p~~~~~~~~~~~~~~~~~~~~~~  133 (276)
                      ++|..+..|.+|+..+           ..+++|.+|+|+.||+++|+++++.++...                       
T Consensus        13 ~~v~~a~~g~~~l~~~-----------~~~~~~~~lld~~m~~~~~~~~~~~lk~~~-----------------------   58 (435)
T COG3706          13 KEVATAKKGLIALAIL-----------LDHKPDYKLLDVMMPGMDGFELCRRLKAEP-----------------------   58 (435)
T ss_pred             hhhhhccchHHHHHHH-----------hcCCCCeEEeecccCCcCchhHHHHHhcCC-----------------------
Confidence            5677799999999999           778999999999999999999999999621                       


Q ss_pred             hccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCCHHHHHHHHHHHHH
Q 023816          134 SICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSDVKRIKDYLTR  202 (276)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~~~~L~~~~~~l~~  202 (276)
                                              ..++++|.....+...+.+++|+++|++||++-..+..-...+.+
T Consensus        59 ------------------------~~~v~~t~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~r~~~l~~  103 (435)
T COG3706          59 ------------------------ATVVMVTALDDSAPRVRGLKAGADDFLTKPVNDSQLFLRAKSLVR  103 (435)
T ss_pred             ------------------------cceEEEEecCCCCcchhHHhhhhhhhccCCCChHHHHHhhhhhcc
Confidence                                    228889999999999999999999999999998887444444433

>smart00448 REC cheY-homologous receiver domain

Probab=97.98  E-value=5.9e-05  Score=46.46  Aligned_cols=55  Identities=35%  Similarity=0.532  Sum_probs=48.5

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCC
Q 023816           30 VHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMP   95 (276)
Q Consensus        30 ~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp   95 (276)
                      ++|++++|+...+..+.+.+...|+++..+.++.++++.+           ....+|++++|+.++
T Consensus         1 ~~i~i~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~-----------~~~~~~~vi~~~~~~   55 (55)
T smart00448        1 MRILVVDDDPLLRELLKALLEREGYEVDEATDGEEALELL-----------KEEKPDLILLDIMMP   55 (55)
T ss_pred             CeEEEEcCCHHHHHHHHHHHhhcCcEEEEeCCHHHHHHHH-----------HhcCCCEEEEeccCC
Confidence            3789999999999999999999999999999999999887           455799999998654

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

>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=97.39  E-value=0.002  Score=52.17  Aligned_cols=105  Identities=17%  Similarity=0.182  Sum_probs=73.8

Q ss_pred             EEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEE-EEecCCCCCCHHHHHHHHHhh
Q 023816           31 HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLI-ITDYCMPGMTGYELLKKIKVT  109 (276)
Q Consensus        31 ~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlI-L~D~~mp~~~G~ell~~Ir~~  109 (276)
                      ||||||||..-+..|+.+|+-.|+.+..+....- ....           .....+.+ +..-..+  ...+.++.+.+.
T Consensus         1 kILvIddd~~R~~~L~~ILeFlGe~~~~~~~~~~-~~~~-----------~~~~~~~~~v~~g~~~--~~~~~l~~l~~~   66 (109)
T PF06490_consen    1 KILVIDDDAERRQRLSTILEFLGEQCEAVSSSDW-SQAD-----------WSSPWEACAVILGSCS--KLAELLKELLKW   66 (109)
T ss_pred             CEEEECCcHHHHHhhhhhhhhcCCCeEEecHHHH-HHhh-----------hhcCCcEEEEEecCch--hHHHHHHHHHhh
Confidence            6999999999999999999999999998886543 1111           12233333 3333333  566788899888


Q ss_pred             CCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCC
Q 023816          110 TPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVK  189 (276)
Q Consensus       110 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~  189 (276)
                      .|                                             .+||+++.........     ..+-+-|..|++
T Consensus        67 ~~---------------------------------------------~~Pvlllg~~~~~~~~-----~nvvg~Le~Pl~   96 (109)
T PF06490_consen   67 AP---------------------------------------------HIPVLLLGEHDSPEEL-----PNVVGELEEPLN   96 (109)
T ss_pred             CC---------------------------------------------CCCEEEECCCCccccc-----cCeeEecCCCCC
Confidence            87                                             8999999877665111     115666889999


Q ss_pred             HHHHHHHHHH
Q 023816          190 LSDVKRIKDY  199 (276)
Q Consensus       190 ~~~L~~~~~~  199 (276)
                      ..+|...+.+
T Consensus        97 Y~qLt~~L~~  106 (109)
T PF06490_consen   97 YPQLTDALHR  106 (109)
T ss_pred             HHHHHHHHHH
Confidence            9998655443

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).

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

Probab=97.16  E-value=0.00072  Score=72.38  Aligned_cols=52  Identities=25%  Similarity=0.146  Sum_probs=44.7

Q ss_pred             CCCccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCC
Q 023816           26 DTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCM   94 (276)
Q Consensus        26 ~~~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~m   94 (276)
                      ..++.+||+|||++.+++.+.++|+..||+|..++++      .           .+..||+||+|+++
T Consensus       686 ~l~g~~vLlvdD~~~~r~~l~~~L~~~G~~v~~a~~~------~-----------~~~~~Dlvl~D~~~  737 (894)
T PRK10618        686 LLDGVTVLLDITSEEVRKIVTRQLENWGATCITPDER------L-----------ISQEYDIFLTDNPS  737 (894)
T ss_pred             cCCCCEEEEEeCCHHHHHHHHHHHHHCCCEEEEcCcc------c-----------cCCCCCEEEECCCC
Confidence            3456899999999999999999999999999998763      1           45579999999984

>cd02071 MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 binding domain

Probab=96.81  E-value=0.036  Score=45.25  Aligned_cols=103  Identities=15%  Similarity=0.043  Sum_probs=73.5

Q ss_pred             eCCHHHHHHHHHHHhhCCCEEEEE---CCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCC--HHHHHHHHHhhC
Q 023816           36 DDSFVDRKVIERLLTISSCKVTAV---DSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMT--GYELLKKIKVTT  110 (276)
Q Consensus        36 dD~~~~~~~L~~~L~~~g~~v~~a---~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~--G~ell~~Ir~~~  110 (276)
                      |.+..=...+..+|+..||+|...   ...++.++.+           .+.++|+|.+...+...-  --++++.+++..
T Consensus        10 d~H~lG~~~~~~~l~~~G~~vi~lG~~vp~e~~~~~a-----------~~~~~d~V~iS~~~~~~~~~~~~~~~~L~~~~   78 (122)
T cd02071          10 DGHDRGAKVIARALRDAGFEVIYTGLRQTPEEIVEAA-----------IQEDVDVIGLSSLSGGHMTLFPEVIELLRELG   78 (122)
T ss_pred             ChhHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHH-----------HHcCCCEEEEcccchhhHHHHHHHHHHHHhcC
Confidence            556666677888899999999983   3467777777           677899999988765322  235566666543


Q ss_pred             CCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCCH
Q 023816          111 PFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKL  190 (276)
Q Consensus       111 p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~~  190 (276)
                      +                                             +-+.+++-+....+...+..++|.+.|+-.-.+.
T Consensus        79 ~---------------------------------------------~~i~i~~GG~~~~~~~~~~~~~G~d~~~~~~~~~  113 (122)
T cd02071          79 A---------------------------------------------GDILVVGGGIIPPEDYELLKEMGVAEIFGPGTSI  113 (122)
T ss_pred             C---------------------------------------------CCCEEEEECCCCHHHHHHHHHCCCCEEECCCCCH
Confidence            3                                             3344556655556677888899999999998777


Q ss_pred             HHHH
Q 023816          191 SDVK  194 (276)
Q Consensus       191 ~~L~  194 (276)
                      +++.
T Consensus       114 ~~~~  117 (122)
T cd02071         114 EEII  117 (122)
T ss_pred             HHHH
Confidence            7763

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.

>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=96.64  E-value=0.027  Score=45.88  Aligned_cols=96  Identities=17%  Similarity=0.208  Sum_probs=74.3

Q ss_pred             HHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCC--CCHHHHHHHHHhhCCCCcccchh
Q 023816           42 RKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPG--MTGYELLKKIKVTTPFNFLYSTI  119 (276)
Q Consensus        42 ~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~--~~G~ell~~Ir~~~p~~~~~~~~  119 (276)
                      .+.|...|+..|++|+.+.+.++++..+.          ....++.|++||. ++  ....+++++|++...        
T Consensus         6 ~~~l~~~L~~~~~~vv~~~~~dd~~~~i~----------~~~~i~avvi~~d-~~~~~~~~~ll~~i~~~~~--------   66 (115)
T PF03709_consen    6 SRELAEALEQRGREVVDADSTDDALAIIE----------SFTDIAAVVISWD-GEEEDEAQELLDKIRERNF--------   66 (115)
T ss_dssp             HHHHHHHHHHTTTEEEEESSHHHHHHHHH----------CTTTEEEEEEECH-HHHHHHHHHHHHHHHHHST--------
T ss_pred             HHHHHHHHHHCCCEEEEeCChHHHHHHHH----------hCCCeeEEEEEcc-cccchhHHHHHHHHHHhCC--------
Confidence            35677788889999999999999999994          3457999999997 22  235678999998776        


Q ss_pred             eehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCCHHHH
Q 023816          120 IVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSDV  193 (276)
Q Consensus       120 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~~~~L  193 (276)
                                                           .+||.+++.....+.+....-..+++|+-..-+-.+.
T Consensus        67 -------------------------------------~iPVFl~~~~~~~~~l~~~~l~~v~~~i~l~~~t~~f  103 (115)
T PF03709_consen   67 -------------------------------------GIPVFLLAERDTTEDLPAEVLGEVDGFIWLFEDTAEF  103 (115)
T ss_dssp             -------------------------------------T-EEEEEESCCHHHCCCHHHHCCESEEEETTTTTHHH
T ss_pred             -------------------------------------CCCEEEEecCCCcccCCHHHHhhccEEEEecCCCHHH
Confidence                                                 8999999987765555556666788999987766665

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.

>PRK02261 methylaspartate mutase subunit S; Provisional

Probab=96.47  E-value=0.13  Score=43.41  Aligned_cols=110  Identities=15%  Similarity=0.070  Sum_probs=78.3

Q ss_pred             CccEEEEE----eCCHHHHHHHHHHHhhCCCEEEEEC---CHHHHHHHhcccccccccCCCCCceeEEEEecCCCCC--C
Q 023816           28 EEVHVLAV----DDSFVDRKVIERLLTISSCKVTAVD---SGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGM--T   98 (276)
Q Consensus        28 ~~~~VLIV----dD~~~~~~~L~~~L~~~g~~v~~a~---~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~--~   98 (276)
                      .+.+||+.    |.+..-...+..+|+..||+|+...   ..++.++.+           .+..+|+|.+...+...  .
T Consensus         2 ~~~~vl~~~~~gD~H~lG~~iv~~~lr~~G~eVi~LG~~vp~e~i~~~a-----------~~~~~d~V~lS~~~~~~~~~   70 (137)
T PRK02261          2 KKKTVVLGVIGADCHAVGNKILDRALTEAGFEVINLGVMTSQEEFIDAA-----------IETDADAILVSSLYGHGEID   70 (137)
T ss_pred             CCCEEEEEeCCCChhHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHH-----------HHcCCCEEEEcCccccCHHH
Confidence            45677777    7778888889999999999999843   467777777           67789999999887743  2


Q ss_pred             HHHHHHHHHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCC------CHHHH
Q 023816           99 GYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSEN------ILARI  172 (276)
Q Consensus        99 G~ell~~Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~------~~~~~  172 (276)
                      ..++++++++..+                                            +.++| ++-+.-      ..+..
T Consensus        71 ~~~~~~~L~~~~~--------------------------------------------~~~~i-~vGG~~~~~~~~~~~~~  105 (137)
T PRK02261         71 CRGLREKCIEAGL--------------------------------------------GDILL-YVGGNLVVGKHDFEEVE  105 (137)
T ss_pred             HHHHHHHHHhcCC--------------------------------------------CCCeE-EEECCCCCCccChHHHH
Confidence            3467777775422                                            13443 333322      34466


Q ss_pred             HHHHhcCCCeEEeCCCCHHHH
Q 023816          173 DRCLEDGAEDFIVKPVKLSDV  193 (276)
Q Consensus       173 ~~al~~Ga~d~l~KPv~~~~L  193 (276)
                      .++.+.|++.+.....+.+++
T Consensus       106 ~~l~~~G~~~vf~~~~~~~~i  126 (137)
T PRK02261        106 KKFKEMGFDRVFPPGTDPEEA  126 (137)
T ss_pred             HHHHHcCCCEEECcCCCHHHH
Confidence            788999998888888776666

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

Probab=96.27  E-value=0.06  Score=43.14  Aligned_cols=96  Identities=11%  Similarity=0.094  Sum_probs=66.6

Q ss_pred             eCCHHHHHHHHHHHhhCCCEEEEE---CCHHHHHHHhcccccccccCCCCCceeEEEEecCCCC--CCHHHHHHHHHhhC
Q 023816           36 DDSFVDRKVIERLLTISSCKVTAV---DSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPG--MTGYELLKKIKVTT  110 (276)
Q Consensus        36 dD~~~~~~~L~~~L~~~g~~v~~a---~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~--~~G~ell~~Ir~~~  110 (276)
                      |....-...+..+|+..||+|...   .+.++.++.+           .+.+||+|.+...+..  .+..++++.+|+..
T Consensus        10 e~H~lG~~~~~~~l~~~G~~V~~lg~~~~~~~l~~~~-----------~~~~pdvV~iS~~~~~~~~~~~~~i~~l~~~~   78 (119)
T cd02067          10 DGHDIGKNIVARALRDAGFEVIDLGVDVPPEEIVEAA-----------KEEDADAIGLSGLLTTHMTLMKEVIEELKEAG   78 (119)
T ss_pred             chhhHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHH-----------HHcCCCEEEEeccccccHHHHHHHHHHHHHcC
Confidence            556667788999999999999763   3456777777           6778999999886544  23456777777642


Q ss_pred             CCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCC
Q 023816          111 PFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKP  187 (276)
Q Consensus       111 p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KP  187 (276)
                      +                                             +-+.|++.+.........+.+.|++.|+...
T Consensus        79 ~---------------------------------------------~~~~i~vGG~~~~~~~~~~~~~G~D~~~~~~  110 (119)
T cd02067          79 L---------------------------------------------DDIPVLVGGAIVTRDFKFLKEIGVDAYFGPA  110 (119)
T ss_pred             C---------------------------------------------CCCeEEEECCCCChhHHHHHHcCCeEEECCH
Confidence            2                                             2344556665555555678899997776643

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.

>TIGR00640 acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal domain

Probab=96.19  E-value=0.28  Score=41.26  Aligned_cols=105  Identities=14%  Similarity=0.069  Sum_probs=69.6

Q ss_pred             eCCHHHHHHHHHHHhhCCCEEEE---ECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCC-CC-HHHHHHHHHhhC
Q 023816           36 DDSFVDRKVIERLLTISSCKVTA---VDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPG-MT-GYELLKKIKVTT  110 (276)
Q Consensus        36 dD~~~~~~~L~~~L~~~g~~v~~---a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~-~~-G~ell~~Ir~~~  110 (276)
                      |-+..-.+.+..+|+..||+|..   ..+.++.++.+           .+.++|+|.+.-.+.. +. --++++.|++..
T Consensus        13 D~Hd~g~~iv~~~l~~~GfeVi~lg~~~s~e~~v~aa-----------~e~~adii~iSsl~~~~~~~~~~~~~~L~~~g   81 (132)
T TIGR00640        13 DGHDRGAKVIATAYADLGFDVDVGPLFQTPEEIARQA-----------VEADVHVVGVSSLAGGHLTLVPALRKELDKLG   81 (132)
T ss_pred             CccHHHHHHHHHHHHhCCcEEEECCCCCCHHHHHHHH-----------HHcCCCEEEEcCchhhhHHHHHHHHHHHHhcC
Confidence            34445556788899999999987   44678888887           5678999887755432 11 224555565422


Q ss_pred             CCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCCH
Q 023816          111 PFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKL  190 (276)
Q Consensus       111 p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~~  190 (276)
                      +                                            ..++ |++-+....++..+..++|+++|+..--+.
T Consensus        82 ~--------------------------------------------~~i~-vivGG~~~~~~~~~l~~~Gvd~~~~~gt~~  116 (132)
T TIGR00640        82 R--------------------------------------------PDIL-VVVGGVIPPQDFDELKEMGVAEIFGPGTPI  116 (132)
T ss_pred             C--------------------------------------------CCCE-EEEeCCCChHhHHHHHHCCCCEEECCCCCH
Confidence            2                                            1333 444433445567788899999999998887


Q ss_pred             HHHHHH
Q 023816          191 SDVKRI  196 (276)
Q Consensus       191 ~~L~~~  196 (276)
                      .++...
T Consensus       117 ~~i~~~  122 (132)
T TIGR00640       117 PESAIF  122 (132)
T ss_pred             HHHHHH
Confidence            776443

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.

>PRK15399 lysine decarboxylase LdcC; Provisional

Probab=94.55  E-value=0.47  Score=50.35  Aligned_cols=69  Identities=16%  Similarity=0.178  Sum_probs=51.9

Q ss_pred             cEEEEEeCCH-HH-----HHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHH
Q 023816           30 VHVLAVDDSF-VD-----RKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELL  103 (276)
Q Consensus        30 ~~VLIVdD~~-~~-----~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell  103 (276)
                      ++|+||+++. .+     .+.|.+.|+..||+|..+.+.++++..+.          .....+.|++|+.-.   ..+++
T Consensus         1 ~~~~~i~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~----------~~~~~~~~~~~~~~~---~~~~~   67 (713)
T PRK15399          1 MNIIAIMGPHGVFYKDEPIKELESALQAQGFQTIWPQNSVDLLKFIE----------HNPRICGVIFDWDEY---SLDLC   67 (713)
T ss_pred             CcEEEEecccccccccHHHHHHHHHHHHCCcEEEEecCHHHHHHHHh----------cccceeEEEEecccc---hHHHH
Confidence            4688887764 11     45567778889999999999999999883          345688999996432   35588


Q ss_pred             HHHHhhCC
Q 023816          104 KKIKVTTP  111 (276)
Q Consensus       104 ~~Ir~~~p  111 (276)
                      +++|+...
T Consensus        68 ~~~~~~~~   75 (713)
T PRK15399         68 SDINQLNE   75 (713)
T ss_pred             HHHHHhCC
Confidence            99987665

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

Probab=94.44  E-value=0.51  Score=37.24  Aligned_cols=64  Identities=14%  Similarity=0.150  Sum_probs=46.7

Q ss_pred             CCHHHHHHHHHHHhhCCCEEEEE---CCHHHHHHHhcccccccccCCCCCceeEEEEec-CCCCC-CHHHHHHHHHhhCC
Q 023816           37 DSFVDRKVIERLLTISSCKVTAV---DSGRRALQFLGLDEEQSINGFDGLKVDLIITDY-CMPGM-TGYELLKKIKVTTP  111 (276)
Q Consensus        37 D~~~~~~~L~~~L~~~g~~v~~a---~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~-~mp~~-~G~ell~~Ir~~~p  111 (276)
                      -.+.-...+..+|++.||+|...   .+.++..+.+           ...+||+|.+.. ..+.. ...++++.+|+..|
T Consensus        12 ~~~lGl~~la~~l~~~G~~v~~~d~~~~~~~l~~~~-----------~~~~pd~V~iS~~~~~~~~~~~~l~~~~k~~~p   80 (121)
T PF02310_consen   12 VHPLGLLYLAAYLRKAGHEVDILDANVPPEELVEAL-----------RAERPDVVGISVSMTPNLPEAKRLARAIKERNP   80 (121)
T ss_dssp             STSHHHHHHHHHHHHTTBEEEEEESSB-HHHHHHHH-----------HHTTCSEEEEEESSSTHHHHHHHHHHHHHTTCT
T ss_pred             chhHHHHHHHHHHHHCCCeEEEECCCCCHHHHHHHH-----------hcCCCcEEEEEccCcCcHHHHHHHHHHHHhcCC
Confidence            34667888999999999999875   2346666666           556899999998 44443 35678888887666

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

>PRK15400 lysine decarboxylase CadA; Provisional

Probab=94.09  E-value=0.55  Score=49.83  Aligned_cols=69  Identities=16%  Similarity=0.232  Sum_probs=51.2

Q ss_pred             cEEEEEeCCH-H-----HHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHH
Q 023816           30 VHVLAVDDSF-V-----DRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELL  103 (276)
Q Consensus        30 ~~VLIVdD~~-~-----~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell  103 (276)
                      ++||+|+++. .     -.+.|.+.|+..||+|..+.+.++++..+.          .....+.|++|+.-   ...+++
T Consensus         1 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~----------~~~~~~~~~~~~~~---~~~~~~   67 (714)
T PRK15400          1 MNVIAILNHMGVYFKEEPIRELHRALERLNFQIVYPNDRDDLLKLIE----------NNARLCGVIFDWDK---YNLELC   67 (714)
T ss_pred             CcEEEEccccccccccHHHHHHHHHHHHCCcEEEEeCCHHHHHHHHh----------cccceeEEEEecch---hhHHHH
Confidence            4678887662 1     145677788899999999999999999883          34568899999643   225588


Q ss_pred             HHHHhhCC
Q 023816          104 KKIKVTTP  111 (276)
Q Consensus       104 ~~Ir~~~p  111 (276)
                      +.+|+...
T Consensus        68 ~~~~~~~~   75 (714)
T PRK15400         68 EEISKMNE   75 (714)
T ss_pred             HHHHHhCC
Confidence            88987655

>TIGR03815 CpaE_hom_Actino helicase/secretion neighborhood CpaE-like protein

Probab=93.52  E-value=0.25  Score=46.25  Aligned_cols=41  Identities=24%  Similarity=0.070  Sum_probs=33.8

Q ss_pred             EE-EEecCCCHHHHHHHHhcCCCeEEeCCCCHHHHHHHHHHH
Q 023816          160 VV-IMSSENILARIDRCLEDGAEDFIVKPVKLSDVKRIKDYL  200 (276)
Q Consensus       160 iV-~ls~~~~~~~~~~al~~Ga~d~l~KPv~~~~L~~~~~~l  200 (276)
                      +| +.....+.+....|++.|+.||+.+|+...+|.+.+..+
T Consensus        44 vv~v~~~~~~~~~~~~a~~~Ga~~~l~~P~~~~~l~~~l~~~   85 (322)
T TIGR03815        44 VVLVGGGEPGGALWRAAAAVGAEHVAVLPEAEGWLVELLADL   85 (322)
T ss_pred             EEEEeCCCCCHHHHHHHHHhChhheeeCCCCHHHHHHHHHhh
Confidence            55 444466788999999999999999999999997777665

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.

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

Probab=93.05  E-value=3.6  Score=35.61  Aligned_cols=118  Identities=17%  Similarity=0.134  Sum_probs=78.2

Q ss_pred             CccEEEEE----eCCHHHHHHHHHHHhhCCCEEEE---ECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCC-C-C
Q 023816           28 EEVHVLAV----DDSFVDRKVIERLLTISSCKVTA---VDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPG-M-T   98 (276)
Q Consensus        28 ~~~~VLIV----dD~~~~~~~L~~~L~~~g~~v~~---a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~-~-~   98 (276)
                      ...+||+.    |-...-.+++.+.|...||+|..   ..+.+|+++.+           .+...|+|.+...-.+ + .
T Consensus        11 ~rprvlvak~GlDgHd~gakvia~~l~d~GfeVi~~g~~~tp~e~v~aA-----------~~~dv~vIgvSsl~g~h~~l   79 (143)
T COG2185          11 ARPRVLVAKLGLDGHDRGAKVIARALADAGFEVINLGLFQTPEEAVRAA-----------VEEDVDVIGVSSLDGGHLTL   79 (143)
T ss_pred             CCceEEEeccCccccccchHHHHHHHHhCCceEEecCCcCCHHHHHHHH-----------HhcCCCEEEEEeccchHHHH
Confidence            46677765    66667789999999999999987   77899999887           5567888776542111 1 1


Q ss_pred             HHHHHHHHHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhc
Q 023816           99 GYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLED  178 (276)
Q Consensus        99 G~ell~~Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~  178 (276)
                      .-++.+.+|+...                                            .++. |+.-+.-..++..+..+.
T Consensus        80 ~~~lve~lre~G~--------------------------------------------~~i~-v~~GGvip~~d~~~l~~~  114 (143)
T COG2185          80 VPGLVEALREAGV--------------------------------------------EDIL-VVVGGVIPPGDYQELKEM  114 (143)
T ss_pred             HHHHHHHHHHhCC--------------------------------------------cceE-EeecCccCchhHHHHHHh
Confidence            2345555555433                                            2333 344444445666777789


Q ss_pred             CCCeEEeCCCCHHHH-HHHHHHHH
Q 023816          179 GAEDFIVKPVKLSDV-KRIKDYLT  201 (276)
Q Consensus       179 Ga~d~l~KPv~~~~L-~~~~~~l~  201 (276)
                      |++.++..-.+..+. ..+++.+.
T Consensus       115 G~~~if~pgt~~~~~~~~v~~~l~  138 (143)
T COG2185         115 GVDRIFGPGTPIEEALSDLLTRLG  138 (143)
T ss_pred             CcceeeCCCCCHHHHHHHHHHHHH
Confidence            999999987777775 34444443

>TIGR01501 MthylAspMutase methylaspartate mutase, S subunit

Probab=92.22  E-value=3.6  Score=35.02  Aligned_cols=59  Identities=15%  Similarity=0.099  Sum_probs=42.7

Q ss_pred             HHHHHHHHHHHhhCCCEEEE---ECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCC--HHHHHHHHHh
Q 023816           39 FVDRKVIERLLTISSCKVTA---VDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMT--GYELLKKIKV  108 (276)
Q Consensus        39 ~~~~~~L~~~L~~~g~~v~~---a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~--G~ell~~Ir~  108 (276)
                      ..-.+.+..+|+..||+|..   .-+.++.++.+           .+..+|+|.+...|...-  --++.+++++
T Consensus        15 diGk~iv~~~l~~~GfeVi~LG~~v~~e~~v~aa-----------~~~~adiVglS~l~~~~~~~~~~~~~~l~~   78 (134)
T TIGR01501        15 AVGNKILDHAFTNAGFNVVNLGVLSPQEEFIKAA-----------IETKADAILVSSLYGHGEIDCKGLRQKCDE   78 (134)
T ss_pred             hHhHHHHHHHHHHCCCEEEECCCCCCHHHHHHHH-----------HHcCCCEEEEecccccCHHHHHHHHHHHHH
Confidence            34456788899999999997   44677788777           567899999998775322  3345666664

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.

>PRK00208 thiG thiazole synthase; Reviewed

Probab=91.06  E-value=3.3  Score=38.96  Aligned_cols=29  Identities=17%  Similarity=0.421  Sum_probs=26.3

Q ss_pred             CCeEEEEecCCCHHHHHHHHhcCCCeEEe
Q 023816          157 EIPVVIMSSENILARIDRCLEDGAEDFIV  185 (276)
Q Consensus       157 ~ipiV~ls~~~~~~~~~~al~~Ga~d~l~  185 (276)
                      .+|||+=.+-..++++.+|++.|++..+.
T Consensus       175 ~vpVIveaGI~tpeda~~AmelGAdgVlV  203 (250)
T PRK00208        175 DVPVIVDAGIGTPSDAAQAMELGADAVLL  203 (250)
T ss_pred             CCeEEEeCCCCCHHHHHHHHHcCCCEEEE
Confidence            68999888888999999999999999865

>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=90.05  E-value=2.2  Score=39.98  Aligned_cols=29  Identities=17%  Similarity=0.421  Sum_probs=26.1

Q ss_pred             CCeEEEEecCCCHHHHHHHHhcCCCeEEe
Q 023816          157 EIPVVIMSSENILARIDRCLEDGAEDFIV  185 (276)
Q Consensus       157 ~ipiV~ls~~~~~~~~~~al~~Ga~d~l~  185 (276)
                      ++|||+=.+-...++..+|++.||+..+.
T Consensus       175 ~vpVI~egGI~tpeda~~AmelGAdgVlV  203 (248)
T cd04728         175 DVPVIVDAGIGTPSDAAQAMELGADAVLL  203 (248)
T ss_pred             CCcEEEeCCCCCHHHHHHHHHcCCCEEEE
Confidence            68998888888999999999999999865

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).

>cd02069 methionine_synthase_B12_BD B12 binding domain of methionine synthase

Probab=89.75  E-value=3.1  Score=37.55  Aligned_cols=70  Identities=11%  Similarity=0.134  Sum_probs=51.7

Q ss_pred             ccEEEEE----eCCHHHHHHHHHHHhhCCCEEEEEC---CHHHHHHHhcccccccccCCCCCceeEEEEecCCCC-CC-H
Q 023816           29 EVHVLAV----DDSFVDRKVIERLLTISSCKVTAVD---SGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPG-MT-G   99 (276)
Q Consensus        29 ~~~VLIV----dD~~~~~~~L~~~L~~~g~~v~~a~---~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~-~~-G   99 (276)
                      .-+|++.    |.+.+=...+..+|+..||+|+...   ..++.++.+           .+.++|+|.+...|+. +. -
T Consensus        88 ~~~vvl~t~~gd~HdiG~~iv~~~l~~~G~~Vi~LG~~vp~e~~v~~~-----------~~~~~~~V~lS~~~~~~~~~~  156 (213)
T cd02069          88 KGKIVLATVKGDVHDIGKNLVGVILSNNGYEVIDLGVMVPIEKILEAA-----------KEHKADIIGLSGLLVPSLDEM  156 (213)
T ss_pred             CCeEEEEeCCCchhHHHHHHHHHHHHhCCCEEEECCCCCCHHHHHHHH-----------HHcCCCEEEEccchhccHHHH
Confidence            4567766    6677777888889999999999843   466777777           6789999999988764 22 3


Q ss_pred             HHHHHHHHhh
Q 023816          100 YELLKKIKVT  109 (276)
Q Consensus       100 ~ell~~Ir~~  109 (276)
                      .++++.|++.
T Consensus       157 ~~~i~~L~~~  166 (213)
T cd02069         157 VEVAEEMNRR  166 (213)
T ss_pred             HHHHHHHHhc
Confidence            4567777754

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

>PF01408 GFO_IDH_MocA: Oxidoreductase family, NAD-binding Rossmann fold; InterPro: IPR000683 This group of enzymes utilise NADP or NAD, and is known as the GFO/IDH/MOCA family in UniProtKB/Swiss-Prot

Probab=89.29  E-value=5  Score=31.31  Aligned_cols=47  Identities=13%  Similarity=0.291  Sum_probs=34.4

Q ss_pred             CCeEEEEecCCCHHHHHHHHhcCCCeEEeCCC--CHHHHHHHHHHHHHh
Q 023816          157 EIPVVIMSSENILARIDRCLEDGAEDFIVKPV--KLSDVKRIKDYLTRD  203 (276)
Q Consensus       157 ~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv--~~~~L~~~~~~l~~~  203 (276)
                      ++-+|........+....+++.|..=|+.||+  +.+++.++++...+.
T Consensus        64 D~V~I~tp~~~h~~~~~~~l~~g~~v~~EKP~~~~~~~~~~l~~~a~~~  112 (120)
T PF01408_consen   64 DAVIIATPPSSHAEIAKKALEAGKHVLVEKPLALTLEEAEELVEAAKEK  112 (120)
T ss_dssp             SEEEEESSGGGHHHHHHHHHHTTSEEEEESSSSSSHHHHHHHHHHHHHH
T ss_pred             CEEEEecCCcchHHHHHHHHHcCCEEEEEcCCcCCHHHHHHHHHHHHHh
Confidence            33444444444567788999999999999999  788888877766654

GFO is a glucose--fructose oxidoreductase, which converts D-glucose and D-fructose into D-gluconolactone and D-glucitol in the sorbitol-gluconate pathway. MOCA is a rhizopine catabolism protein which may catalyse the NADH-dependent dehydrogenase reaction involved in rhizopine catabolism. Other proteins belonging to this family include Gal80, a negative regulator for the expression of lactose and galactose metabolic genes; and several hypothetical proteins from yeast, Escherichia coli and Bacillus subtilis. The oxidoreductase, N-terminal domain is almost always associated with the oxidoreductase, C-terminal domain (see IPR004104 from INTERPRO).; GO: 0016491 oxidoreductase activity; PDB: 1LC0_A 1LC3_A 1GCU_A 3IP3_E 3CEA_C 3EVN_A 3NTQ_A 3NTR_B 3NT5_A 3MZ0_A ....

>cd02068 radical_SAM_B12_BD B12 binding domain_like associated with radical SAM domain

Probab=88.02  E-value=8.2  Score=31.12  Aligned_cols=61  Identities=18%  Similarity=0.159  Sum_probs=43.5

Q ss_pred             HHHHHHHHHHhhCCCEEEEE--CCHHHHHHHhcccccccccCCCC-CceeEEEEecCCCCC-CHHHHHHHHHhhCC
Q 023816           40 VDRKVIERLLTISSCKVTAV--DSGRRALQFLGLDEEQSINGFDG-LKVDLIITDYCMPGM-TGYELLKKIKVTTP  111 (276)
Q Consensus        40 ~~~~~L~~~L~~~g~~v~~a--~~g~~al~~l~~~~~~~~~~~~~-~~~DlIL~D~~mp~~-~G~ell~~Ir~~~p  111 (276)
                      .-...+..+|...|+.+...  ...++.++.+           .. .+||+|.+...-... ...++++.||+..|
T Consensus         3 lgl~~~aa~l~~~g~~v~~~~~~~~~~~~~~~-----------~~~~~pdiv~~S~~~~~~~~~~~~~~~ik~~~p   67 (127)
T cd02068           3 LGLAYLAAVLEDAGFIVAEHDVLSADDIVEDI-----------KELLKPDVVGISLMTSAIYEALELAKIAKEVLP   67 (127)
T ss_pred             chHHHHHHHHHHCCCeeeecCCCCHHHHHHHH-----------HHhcCCCEEEEeeccccHHHHHHHHHHHHHHCC
Confidence            34567888899899887663  3455566665           33 689999998744443 46679999998777

This domain shows similarity with B12 (adenosylcobamide) binding domains found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase, but it lacks the signature motif Asp-X-His-X-X-Gly, which contains the histidine that acts as a cobalt ligand. The function of this domain remains unclear.

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

Probab=87.83  E-value=15  Score=31.11  Aligned_cols=100  Identities=13%  Similarity=0.078  Sum_probs=67.2

Q ss_pred             HHHHHHHHHHHhhCCCEEEE---ECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCC-CC-HHHHHHHHHhhCCCC
Q 023816           39 FVDRKVIERLLTISSCKVTA---VDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPG-MT-GYELLKKIKVTTPFN  113 (276)
Q Consensus        39 ~~~~~~L~~~L~~~g~~v~~---a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~-~~-G~ell~~Ir~~~p~~  113 (276)
                      ..-.+.+..+|+..||+|.-   ..+.++.++.+           .+.++|+|.+..-|.. +. .-++.+.+++.    
T Consensus        13 diGkniv~~~L~~~GfeVidLG~~v~~e~~v~aa-----------~~~~adiVglS~L~t~~~~~~~~~~~~l~~~----   77 (128)
T cd02072          13 AVGNKILDHAFTEAGFNVVNLGVLSPQEEFIDAA-----------IETDADAILVSSLYGHGEIDCKGLREKCDEA----   77 (128)
T ss_pred             HHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHH-----------HHcCCCEEEEeccccCCHHHHHHHHHHHHHC----
Confidence            34557788899999999987   34667777777           5678999999887754 22 33566666652    


Q ss_pred             cccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCC-----C-HHHHHHHHhcCCCeEEeCC
Q 023816          114 FLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSEN-----I-LARIDRCLEDGAEDFIVKP  187 (276)
Q Consensus       114 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~-----~-~~~~~~al~~Ga~d~l~KP  187 (276)
                                                              ..++++|+ +-+.-     + .++..+..+.|++..+...
T Consensus        78 ----------------------------------------gl~~v~vi-vGG~~~i~~~d~~~~~~~L~~~Gv~~vf~pg  116 (128)
T cd02072          78 ----------------------------------------GLKDILLY-VGGNLVVGKQDFEDVEKRFKEMGFDRVFAPG  116 (128)
T ss_pred             ----------------------------------------CCCCCeEE-EECCCCCChhhhHHHHHHHHHcCCCEEECcC
Confidence                                                    22344443 33321     1 3345678899999999887


Q ss_pred             CCHHHHH
Q 023816          188 VKLSDVK  194 (276)
Q Consensus       188 v~~~~L~  194 (276)
                      -+++++.
T Consensus       117 t~~~~i~  123 (128)
T cd02072         117 TPPEEAI  123 (128)
T ss_pred             CCHHHHH
Confidence            7777763

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.

>cd02070 corrinoid_protein_B12-BD B12 binding domain of corrinoid proteins

Probab=87.80  E-value=9.8  Score=33.56  Aligned_cols=70  Identities=13%  Similarity=0.129  Sum_probs=52.3

Q ss_pred             ccEEEEE----eCCHHHHHHHHHHHhhCCCEEEEE---CCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCC--CH
Q 023816           29 EVHVLAV----DDSFVDRKVIERLLTISSCKVTAV---DSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGM--TG   99 (276)
Q Consensus        29 ~~~VLIV----dD~~~~~~~L~~~L~~~g~~v~~a---~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~--~G   99 (276)
                      ..+||+.    |-+..=...+..+|+..||+|+..   ...++.++.+           .+.+||+|-+...|...  ..
T Consensus        82 ~~~vl~~~~~gd~H~lG~~~v~~~l~~~G~~vi~lG~~~p~~~l~~~~-----------~~~~~d~v~lS~~~~~~~~~~  150 (201)
T cd02070          82 KGKVVIGTVEGDIHDIGKNLVATMLEANGFEVIDLGRDVPPEEFVEAV-----------KEHKPDILGLSALMTTTMGGM  150 (201)
T ss_pred             CCeEEEEecCCccchHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHH-----------HHcCCCEEEEeccccccHHHH
Confidence            4577766    666677888999999999999863   2567777777           67799999999877653  34


Q ss_pred             HHHHHHHHhh
Q 023816          100 YELLKKIKVT  109 (276)
Q Consensus       100 ~ell~~Ir~~  109 (276)
                      .++++.+|+.
T Consensus       151 ~~~i~~lr~~  160 (201)
T cd02070         151 KEVIEALKEA  160 (201)
T ss_pred             HHHHHHHHHC
Confidence            5677777764

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.

>PRK09426 methylmalonyl-CoA mutase; Reviewed

Probab=86.41  E-value=15  Score=39.12  Aligned_cols=109  Identities=16%  Similarity=0.095  Sum_probs=69.8

Q ss_pred             ccEEEEE----eCCHHHHHHHHHHHhhCCCEEEE---ECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCC--CH
Q 023816           29 EVHVLAV----DDSFVDRKVIERLLTISSCKVTA---VDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGM--TG   99 (276)
Q Consensus        29 ~~~VLIV----dD~~~~~~~L~~~L~~~g~~v~~---a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~--~G   99 (276)
                      ..+|++.    |.+..-...+..+|+..||+|..   ..+.+++++.+           .+.++|+|.+-.-+...  ..
T Consensus       582 rpkV~LatlG~d~H~~ra~fv~~~l~~~GfeV~~~~~~~s~e~~v~aa-----------~~~~a~ivvlcs~d~~~~e~~  650 (714)
T PRK09426        582 RPRILVAKMGQDGHDRGAKVIATAFADLGFDVDIGPLFQTPEEAARQA-----------VENDVHVVGVSSLAAGHKTLV  650 (714)
T ss_pred             CceEEEEecCCcchhHhHHHHHHHHHhCCeeEecCCCCCCHHHHHHHH-----------HHcCCCEEEEeccchhhHHHH
Confidence            3455544    23344445678889999999965   24567777777           56678888765444332  24


Q ss_pred             HHHHHHHHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcC
Q 023816          100 YELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDG  179 (276)
Q Consensus       100 ~ell~~Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~G  179 (276)
                      -++++.||+...                                            .+++| ++-+.-..+......++|
T Consensus       651 ~~l~~~Lk~~G~--------------------------------------------~~v~v-l~GG~~~~~~~~~l~~aG  685 (714)
T PRK09426        651 PALIEALKKLGR--------------------------------------------EDIMV-VVGGVIPPQDYDFLYEAG  685 (714)
T ss_pred             HHHHHHHHhcCC--------------------------------------------CCcEE-EEeCCCChhhHHHHHhCC
Confidence            567788886432                                            12333 344432444556788999


Q ss_pred             CCeEEeCCCCHHHH
Q 023816          180 AEDFIVKPVKLSDV  193 (276)
Q Consensus       180 a~d~l~KPv~~~~L  193 (276)
                      +++|+..-.+..++
T Consensus       686 vD~~i~~g~d~~~~  699 (714)
T PRK09426        686 VAAIFGPGTVIADA  699 (714)
T ss_pred             CCEEECCCCCHHHH
Confidence            99999998888776

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

Probab=85.30  E-value=15  Score=32.59  Aligned_cols=30  Identities=27%  Similarity=0.339  Sum_probs=25.4

Q ss_pred             CCeEEEEecCCCHHHHHHHHhcCCCeEEeC
Q 023816          157 EIPVVIMSSENILARIDRCLEDGAEDFIVK  186 (276)
Q Consensus       157 ~ipiV~ls~~~~~~~~~~al~~Ga~d~l~K  186 (276)
                      .+||++..+-...+.+.++++.||+.++.=
T Consensus       173 ~iPvia~GGI~t~~~~~~~l~~GadgV~iG  202 (221)
T PRK01130        173 GCPVIAEGRINTPEQAKKALELGAHAVVVG  202 (221)
T ss_pred             CCCEEEECCCCCHHHHHHHHHCCCCEEEEc
Confidence            589888887778999999999999988663

>PRK13111 trpA tryptophan synthase subunit alpha; Provisional

Probab=83.98  E-value=4.1  Score=37.95  Aligned_cols=46  Identities=17%  Similarity=0.356  Sum_probs=36.4

Q ss_pred             CCeEEEEecCC------CHHHHHHHHhcCCCeEEeCCCCHHHHHHHHHHHHH
Q 023816          157 EIPVVIMSSEN------ILARIDRCLEDGAEDFIVKPVKLSDVKRIKDYLTR  202 (276)
Q Consensus       157 ~ipiV~ls~~~------~~~~~~~al~~Ga~d~l~KPv~~~~L~~~~~~l~~  202 (276)
                      ++|+|+|+=.+      ......+|.++|+++.|...+..++....+..+..
T Consensus        89 ~~p~vlm~Y~N~i~~~G~e~f~~~~~~aGvdGviipDLp~ee~~~~~~~~~~  140 (258)
T PRK13111         89 TIPIVLMTYYNPIFQYGVERFAADAAEAGVDGLIIPDLPPEEAEELRAAAKK  140 (258)
T ss_pred             CCCEEEEecccHHhhcCHHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHHH
Confidence            78999998554      44568899999999999998888887766666544

>PF02254 TrkA_N: TrkA-N domain; InterPro: IPR003148 The regulator of K+ conductance (RCK) domain is found in many ligand-gated K+ channels, most often attached to the intracellular carboxy terminus

Probab=83.05  E-value=15  Score=28.56  Aligned_cols=93  Identities=15%  Similarity=0.114  Sum_probs=57.3

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCH-HHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHh
Q 023816           30 VHVLAVDDSFVDRKVIERLLTISSCKVTAVDSG-RRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKV  108 (276)
Q Consensus        30 ~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g-~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~  108 (276)
                      .+|.+||.++...+.+    ...|+.+...+-. .+.++.++           -.+.+.|++...- +.....++..+|+
T Consensus        22 ~~vvvid~d~~~~~~~----~~~~~~~i~gd~~~~~~l~~a~-----------i~~a~~vv~~~~~-d~~n~~~~~~~r~   85 (116)
T PF02254_consen   22 IDVVVIDRDPERVEEL----REEGVEVIYGDATDPEVLERAG-----------IEKADAVVILTDD-DEENLLIALLARE   85 (116)
T ss_dssp             SEEEEEESSHHHHHHH----HHTTSEEEES-TTSHHHHHHTT-----------GGCESEEEEESSS-HHHHHHHHHHHHH
T ss_pred             CEEEEEECCcHHHHHH----HhcccccccccchhhhHHhhcC-----------ccccCEEEEccCC-HHHHHHHHHHHHH
Confidence            5788888887664433    3456776664332 45666662           2357777777642 2345667778887


Q ss_pred             hCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEe
Q 023816          109 TTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIV  185 (276)
Q Consensus       109 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~  185 (276)
                      ..|                                             ..++++..  .+........+.|++..+.
T Consensus        86 ~~~---------------------------------------------~~~ii~~~--~~~~~~~~l~~~g~d~vi~  115 (116)
T PF02254_consen   86 LNP---------------------------------------------DIRIIARV--NDPENAELLRQAGADHVIS  115 (116)
T ss_dssp             HTT---------------------------------------------TSEEEEEE--SSHHHHHHHHHTT-SEEEE
T ss_pred             HCC---------------------------------------------CCeEEEEE--CCHHHHHHHHHCCcCEEEC
Confidence            666                                             57777666  3455666777899987664

The domain is prevalent among prokaryotic K+ channels, and also found in eukaryotic, high-conductance Ca2+-activated K+ channels (BK channels) [, , ]. Largely involved in redox-linked regulation of potassium channels, the N-terminal part of the RCK domain is predicted to be an active dehydrogenase at least in some cases []. Some have a conserved sequence motif (G-x-G-x-x-G-x(n)-[DE]) for NAD+ binding [], but others do not, reflecting the diversity of ligands for RCK domains. The C-terminal part is less conserved, being absent in some channels, such as the kefC antiporter from Escherichia coli. It is predicted to bind unidentified ligands and to regulate sulphate, sodium and other transporters. The X-ray structure of several RCK domains has been solved [, , ]. It reveals an alpha-beta fold similar to dehydrogenase enzymes. The domain forms a homodimer, producing a cleft between two lobes. It has a composite structure, with an N-terminal (RCK-N), and a C-terminal (RCK-C) subdomain. The RCK-N subdomain forms a Rossmann fold with two alpha helices on one side of a six stranded parallel beta sheet and three alpha helices on the other side. The RCK-C subdomain is an all-beta-strand fold. It forms an extention of the dimer interface and further stabilises the RCK homodimer [, , ]. Ca2+ is a ligand that opens the channel in a concentration-dependent manner. Two Ca2+ ions are located at the base of a cleft between two RCK domains, coordinated by the carboxylate groups of two glutamate residues, and by an aspartate residue [, , ]. RCK domains occur in at least five different contexts: As a single domain on the C terminus of some K+ channels (for example, many prokaryotic K+ channels). As two tandem RCK domains on the C terminus of some transporters that form gating rings (for example, eukaryotic BK channels). The gating ring has an arrangement of eight identical RCK domains, one from each of the four pore-forming subunits and four from the intracellular solution. As two domains, one at the N terminus and another at the C terminus of transporter (for example, the prokaryotic trk system potassium uptake protein A). As a soluble protein (not part of a K+ channel) consisting of two tandem RCK domains. As a soluble protein consisting of a single RCK domain. This entry represents the N-terminal subdomain of RCK.; GO: 0006813 potassium ion transport; PDB: 3L4B_E 1LSS_C 3LLV_A 2FY8_D 2AEF_A 1LNQ_E 3RBX_C 3KXD_A 2AEJ_A 3RBZ_A ....

>TIGR00262 trpA tryptophan synthase, alpha subunit

Probab=82.83  E-value=5.5  Score=36.88  Aligned_cols=46  Identities=17%  Similarity=0.369  Sum_probs=37.4

Q ss_pred             CCeEEEEecCCC------HHHHHHHHhcCCCeEEeCCCCHHHHHHHHHHHHH
Q 023816          157 EIPVVIMSSENI------LARIDRCLEDGAEDFIVKPVKLSDVKRIKDYLTR  202 (276)
Q Consensus       157 ~ipiV~ls~~~~------~~~~~~al~~Ga~d~l~KPv~~~~L~~~~~~l~~  202 (276)
                      ++|+++|+-++.      .....++.++|++..+......++....+..+..
T Consensus        87 ~~plv~m~Y~Npi~~~G~e~f~~~~~~aGvdgviipDlp~ee~~~~~~~~~~  138 (256)
T TIGR00262        87 NIPIGLLTYYNLIFRKGVEEFYAKCKEVGVDGVLVADLPLEESGDLVEAAKK  138 (256)
T ss_pred             CCCEEEEEeccHHhhhhHHHHHHHHHHcCCCEEEECCCChHHHHHHHHHHHH
Confidence            689888888775      6778899999999999998888887766666654

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.

>PRK12704 phosphodiesterase; Provisional

Probab=81.44  E-value=3.5  Score=42.19  Aligned_cols=38  Identities=18%  Similarity=0.223  Sum_probs=32.3

Q ss_pred             CeEEEEecCCCHH--HHHHHHhcCCCeEEeCCCCHHHHHH
Q 023816          158 IPVVIMSSENILA--RIDRCLEDGAEDFIVKPVKLSDVKR  195 (276)
Q Consensus       158 ipiV~ls~~~~~~--~~~~al~~Ga~d~l~KPv~~~~L~~  195 (276)
                      .-+|++|+.+...  ....+++.|+.|++.||+..+++..
T Consensus       250 p~~v~ls~~~~~rre~a~~~l~~l~~dg~i~P~~iee~~~  289 (520)
T PRK12704        250 PEAVILSGFDPIRREIARLALEKLVQDGRIHPARIEEMVE  289 (520)
T ss_pred             CCeEEEecCChhhHHHHHHHHHHHHhcCCcCCCCHHHHHH
Confidence            4678899888765  7889999999999999999999843

>TIGR02370 pyl_corrinoid methyltransferase cognate corrinoid proteins, Methanosarcina family

Probab=81.28  E-value=11  Score=33.28  Aligned_cols=63  Identities=11%  Similarity=0.104  Sum_probs=46.0

Q ss_pred             eCCHHHHHHHHHHHhhCCCEEEEEC---CHHHHHHHhcccccccccCCCCCceeEEEEecCCCCC-C-HHHHHHHHHhh
Q 023816           36 DDSFVDRKVIERLLTISSCKVTAVD---SGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGM-T-GYELLKKIKVT  109 (276)
Q Consensus        36 dD~~~~~~~L~~~L~~~g~~v~~a~---~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~-~-G~ell~~Ir~~  109 (276)
                      |.+.+-...+..+|+..||+|+...   ..++.++.+           ++.+||+|.+...|... . -.++++.+|+.
T Consensus        95 d~H~lG~~~v~~~l~~~G~~vi~LG~~vp~e~~v~~~-----------~~~~pd~v~lS~~~~~~~~~~~~~i~~l~~~  162 (197)
T TIGR02370        95 DVHDIGKNIVVTMLRANGFDVIDLGRDVPIDTVVEKV-----------KKEKPLMLTGSALMTTTMYGQKDINDKLKEE  162 (197)
T ss_pred             chhHHHHHHHHHHHHhCCcEEEECCCCCCHHHHHHHH-----------HHcCCCEEEEccccccCHHHHHHHHHHHHHc
Confidence            4556666778889999999999733   456777777           67899999999877643 2 24567777764

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

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

Probab=81.08  E-value=14  Score=31.63  Aligned_cols=105  Identities=12%  Similarity=0.171  Sum_probs=74.5

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHH-----H
Q 023816           28 EEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYE-----L  102 (276)
Q Consensus        28 ~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~e-----l  102 (276)
                      .+-+.+.||.|-........+|...+.+|+.-...    ..+           -...||.+|+.+-.+-.+...     +
T Consensus        10 ~gk~LayiEpNstAA~~t~~iL~~tpleVtyr~t~----~~l-----------p~~hYD~~Ll~vavtfr~n~tm~~~~l   74 (140)
T COG4999          10 AGKRLAYIEPNSTAAQCTLDILSETPLEVTYRPTF----SAL-----------PPAHYDMMLLGVAVTFRENLTMQHERL   74 (140)
T ss_pred             ccceeEEecCccHHHHHHHHHHhcCCceEEecccc----ccc-----------ChhhhceeeecccccccCCchHHHHHH
Confidence            34578999999999999999999999999875442    222           345799999998766544332     3


Q ss_pred             HHHHHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCe
Q 023816          103 LKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAED  182 (276)
Q Consensus       103 l~~Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d  182 (276)
                      .+.+.-                                               .+--|+.+.+. .....++....|+.+
T Consensus        75 ~~Al~m-----------------------------------------------td~vilalPs~-~qv~AeqLkQ~g~~~  106 (140)
T COG4999          75 AKALSM-----------------------------------------------TDFVILALPSH-AQVNAEQLKQDGAGA  106 (140)
T ss_pred             HHHHhh-----------------------------------------------hcceEEecCcH-HHHhHHHHhhcchHh
Confidence            333331                                               13345555543 345677888999999


Q ss_pred             EEeCCCCHHHHHH
Q 023816          183 FIVKPVKLSDVKR  195 (276)
Q Consensus       183 ~l~KPv~~~~L~~  195 (276)
                      +|.||++.-.|..
T Consensus       107 CllKPls~~rLlp  119 (140)
T COG4999         107 CLLKPLSSTRLLP  119 (140)
T ss_pred             HhhCcchhhhhHH
Confidence            9999999888744

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

Probab=80.98  E-value=4.8  Score=36.42  Aligned_cols=54  Identities=20%  Similarity=0.213  Sum_probs=41.7

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecC
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYC   93 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~   93 (276)
                      +++||+||....+---|..+|+..|+++....|..-.+..+           +..+||.|++.--
T Consensus         1 ~~~IL~IDNyDSFtyNLv~yl~~lg~~v~V~rnd~~~~~~~-----------~~~~pd~iviSPG   54 (191)
T COG0512           1 MMMILLIDNYDSFTYNLVQYLRELGAEVTVVRNDDISLELI-----------EALKPDAIVISPG   54 (191)
T ss_pred             CceEEEEECccchHHHHHHHHHHcCCceEEEECCccCHHHH-----------hhcCCCEEEEcCC
Confidence            36899999877777889999999999998877763333333           5668999998853

>PRK00278 trpC indole-3-glycerol-phosphate synthase; Reviewed

Probab=80.60  E-value=46  Score=30.83  Aligned_cols=29  Identities=24%  Similarity=0.215  Sum_probs=25.8

Q ss_pred             CCeEEEEecCCCHHHHHHHHhcCCCeEEe
Q 023816          157 EIPVVIMSSENILARIDRCLEDGAEDFIV  185 (276)
Q Consensus       157 ~ipiV~ls~~~~~~~~~~al~~Ga~d~l~  185 (276)
                      ..++|..++-...+++.++++.|++.++.
T Consensus       211 ~~~vIaegGI~t~ed~~~~~~~Gad~vlV  239 (260)
T PRK00278        211 DRLVVSESGIFTPEDLKRLAKAGADAVLV  239 (260)
T ss_pred             CCEEEEEeCCCCHHHHHHHHHcCCCEEEE
Confidence            35889999999999999999999999865

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

Probab=80.06  E-value=22  Score=33.02  Aligned_cols=73  Identities=15%  Similarity=0.122  Sum_probs=53.5

Q ss_pred             CCCceeEEEEecCCCCCCHHHHHHHHHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeE
Q 023816           81 DGLKVDLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPV  160 (276)
Q Consensus        81 ~~~~~DlIL~D~~mp~~~G~ell~~Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipi  160 (276)
                      ....||.|++|.+=...|--++...|+....                                            ..++.
T Consensus        37 a~~G~D~v~iD~EHg~~~~~~~~~~i~a~~~--------------------------------------------~g~~~   72 (256)
T PRK10558         37 GLAGFDWLVLDGEHAPNDVSTFIPQLMALKG--------------------------------------------SASAP   72 (256)
T ss_pred             HhcCCCEEEEccccCCCCHHHHHHHHHHHhh--------------------------------------------cCCCc
Confidence            3456999999998888887777777775332                                            14555


Q ss_pred             EEEecCCCHHHHHHHHhcCCCeEEeCCCCHHH-HHHHH
Q 023816          161 VIMSSENILARIDRCLEDGAEDFIVKPVKLSD-VKRIK  197 (276)
Q Consensus       161 V~ls~~~~~~~~~~al~~Ga~d~l~KPv~~~~-L~~~~  197 (276)
                      ++=....+...+.++++.|++..+..=++-.+ .++++
T Consensus        73 lVRvp~~~~~~i~r~LD~Ga~giivP~v~tae~a~~~v  110 (256)
T PRK10558         73 VVRVPTNEPVIIKRLLDIGFYNFLIPFVETAEEARRAV  110 (256)
T ss_pred             EEECCCCCHHHHHHHhCCCCCeeeecCcCCHHHHHHHH
Confidence            55566778899999999999999998765444 44443

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	276
3mm4_A	206	Crystal Structure Of The Receiver Domain Of The His		7e-07
3gt7_A	154	Crystal Structure Of Signal Receiver Domain Of Sign		2e-06
3m6m_D	143	Crystal Structure Of Rpff Complexed With Rec Domain		5e-06

>pdb|3MM4|A Chain A, Crystal Structure Of The Receiver Domain Of The Histidine Kinase Cki1 From Arabidopsis Thaliana Length = 206

Iteration: 1
 Score = 50.8 bits (120), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 34/90 (37%), Positives = 48/90 (53%), Gaps = 6/90 (6%)
Query: 24  PSDTEEVH---VLAVDDSFVDRKVIE-RLLTISSCKVTAVDSGRRALQFL--GLDEEQSI 77
           PSD E +    VL VDD+F+ RKV   +L  +   +V   DSG+ AL+ +  GL + +  
Sbjct: 53  PSDDEFLRGKRVLVVDDNFISRKVATGKLKKMGVSEVEQCDSGKEALRLVTEGLTQREEQ 112
Query: 78  NGFDGLKVDLIITDYCMPGMTGYELLKKIK 107
              D L  D I  D  MP M GYE  ++I+
Sbjct: 113 GSVDKLPFDYIFMDCQMPEMDGYEATREIR 142

>pdb|3GT7|A Chain A, Crystal Structure Of Signal Receiver Domain Of Signal Transduction Histidine Kinase From Syntrophus Aciditrophicus Length = 154

Iteration: 1
 Score = 49.7 bits (117), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 50/193 (25%), Positives = 77/193 (39%), Gaps = 68/193 (35%)
Query: 32  VLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITD 91
           +L V+DS    + ++ +L  +  +   V +GR A++FL L            + DLII+D
Sbjct: 10  ILIVEDSPTQAEHLKHILEETGYQTEHVRNGREAVRFLSLT-----------RPDLIISD 58
Query: 92  YCMPGMTGYELLKKIKVTTPFNFLYSTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXEQD 151
             MP M GY L + +K                                            
Sbjct: 59  VLMPEMDGYALCRWLK-------------------------------------------G 75
Query: 152 SSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVK-----------LSDVKRIKDYL 200
              LR IPV++++  +    + R LE GA+DFI KP K           LS VKR ++  
Sbjct: 76  QPDLRTIPVILLTILSDPRDVVRSLECGADDFITKPCKDVVLASHVKRLLSGVKRTEERY 135
Query: 201 TRD---VNLGNEG 210
           +R+   +  GNEG
Sbjct: 136 SRESITLAFGNEG 148

>pdb|3M6M|D Chain D, Crystal Structure Of Rpff Complexed With Rec Domain Of Rpfc Length = 143

Iteration: 1
 Score = 48.1 bits (113), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 38/157 (24%), Positives = 60/157 (38%), Gaps = 52/157 (33%)
Query: 32  VLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITD 91
           +L  DD   +R V++RLL  +  KV  V+             EQ ++       D +I D
Sbjct: 17  MLVADDHEANRMVLQRLLEKAGHKVLCVNGA-----------EQVLDAMAEEDYDAVIVD 65
Query: 92  YCMPGMTGYELLKKIKVTTPFNFLYSTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXEQD 151
             MPGM G ++LK+++V                                           
Sbjct: 66  LHMPGMNGLDMLKQLRVM-----------------------------------------Q 84
Query: 152 SSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPV 188
           +S +R  PVV++S++     I  C + GA  F+ KPV
Sbjct: 85  ASGMRYTPVVVLSADVTPEAIRACEQAGARAFLAKPV 121

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	276
3luf_A	259	Two-component system response regulator/ggdef doma	1e-20
3luf_A	259	Two-component system response regulator/ggdef doma	1e-15
3bre_A	358	Probable two-component response regulator; protein	6e-19
1w25_A	459	Stalked-cell differentiation controlling protein;	5e-18
1w25_A	459	Stalked-cell differentiation controlling protein;	1e-12
2qvg_A	143	Two component response regulator; NYSGXRC, PSI-2,	7e-18
1k66_A	149	Phytochrome response regulator RCPB; CHEY homologu	2e-17
3ilh_A	146	Two component response regulator; NYSGXRC, PSI-II,	2e-17
3heb_A	152	Response regulator receiver domain protein (CHEY);	2e-17
1i3c_A	149	Response regulator RCP1; phytochrome, signaling pr	4e-16
3eq2_A	394	Probable two-component response regulator; adaptor	2e-15
3i42_A	127	Response regulator receiver domain protein (CHEY-	1e-14
2rjn_A	154	Response regulator receiver:metal-dependent phosph	2e-14
1jbe_A	128	Chemotaxis protein CHEY; signaling protein; 1.08A	2e-14
3hv2_A	153	Response regulator/HD domain protein; PSI-2, NYSGX	2e-14
3jte_A	143	Response regulator receiver protein; structural ge	9e-14
1srr_A	124	SPO0F, sporulation response regulatory protein; as	1e-13
2qxy_A	142	Response regulator; regulation of transcription, N	1e-13
3m6m_D	143	Sensory/regulatory protein RPFC; RPFF, REC, enoyl-	2e-13
3hdg_A	137	Uncharacterized protein; two-component sensor acti	2e-13
3hdv_A	136	Response regulator; PSI-II, structural genomics, P	4e-13
1p6q_A	129	CHEY2; chemotaxis, signal transduction, response r	8e-13
3cfy_A	137	Putative LUXO repressor protein; structural genomi	8e-13
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	1e-12
1dc7_A	124	NTRC, nitrogen regulation protein; receiver domain	1e-12
1qkk_A	155	DCTD, C4-dicarboxylate transport transcriptional r	4e-12
1dcf_A	136	ETR1 protein; beta-alpha five sandwich, transferas	6e-12
3cnb_A	143	DNA-binding response regulator, MERR family; signa	7e-12
1mb3_A	124	Cell division response regulator DIVK; signal tran	9e-12
3kcn_A	151	Adenylate cyclase homolog; SGX, PSI 2, structural	9e-12
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	1e-11
2jk1_A	139	HUPR, hydrogenase transcriptional regulatory prote	2e-11
2ayx_A	254	Sensor kinase protein RCSC; two independent struct	2e-11
3grc_A	140	Sensor protein, kinase; protein structure initiati	2e-11
3gt7_A	154	Sensor protein; structural genomics, signal receiv	6e-11
3h1g_A	129	Chemotaxis protein CHEY homolog; sulfate-bound CHE	8e-11
4dad_A	146	Putative pilus assembly-related protein; response	2e-10
3kht_A	144	Response regulator; PSI-II, 11023K, structural gen	3e-10
2rdm_A	132	Response regulator receiver protein; structural ge	4e-10
3nhm_A	133	Response regulator; protein structure initiative I	8e-10
2zay_A	147	Response regulator receiver protein; structural ge	1e-09
3eqz_A	135	Response regulator; structural genomics, unknown f	1e-09
1tmy_A	120	CHEY protein, TMY; chemotaxis, phosphoryl transfer	2e-09
3kyj_B	145	CHEY6 protein, putative histidine protein kinase;	2e-09
3lua_A	140	Response regulator receiver protein; two-component	3e-09
1k68_A	140	Phytochrome response regulator RCPA; phosphorylate	3e-09
1a2o_A	349	CHEB methylesterase; bacterial chemotaxis, adaptat	3e-09
3c97_A	140	Signal transduction histidine kinase; structural g	3e-09
3c3m_A	138	Response regulator receiver protein; structural ge	6e-09
3h5i_A	140	Response regulator/sensory box protein/ggdef domai	6e-09
1dbw_A	126	Transcriptional regulatory protein FIXJ; doubly wo	7e-09
3hzh_A	157	Chemotaxis response regulator (CHEY-3); phosphatas	8e-09
3cu5_A	141	Two component transcriptional regulator, ARAC FAM;	1e-08
1yio_A	208	Response regulatory protein; transcription regulat	1e-08
2qr3_A	140	Two-component system response regulator; structura	1e-08
3mm4_A	206	Histidine kinase homolog; receiver domain, CKI1, c	2e-08
3t8y_A	164	CHEB, chemotaxis response regulator protein-glutam	3e-08
3rqi_A	184	Response regulator protein; structural genomics, s	3e-08
3eod_A	130	Protein HNR; response regulator, phosphoprotein, t	5e-08
3n53_A	140	Response regulator receiver modulated diguanylate;	6e-08
3crn_A	132	Response regulator receiver domain protein, CHEY-;	7e-08
2j48_A	119	Two-component sensor kinase; pseudo-receiver, circ	1e-07
2qv0_A	143	Protein MRKE; structural genomics, transcription,	4e-07
2b4a_A	138	BH3024; flavodoxin-like fold, structural genomics,	9e-07
1xhf_A	123	DYE resistance, aerobic respiration control protei	1e-06
3cg0_A	140	Response regulator receiver modulated diguanylate	1e-06
2r25_B	133	Osmosensing histidine protein kinase SLN1; alpha5-	2e-06
3snk_A	135	Response regulator CHEY-like protein; P-loop conta	2e-06
1zgz_A	122	Torcad operon transcriptional regulatory protein;	2e-06
3cg4_A	142	Response regulator receiver domain protein (CHEY-;	3e-06
1s8n_A	205	Putative antiterminator; RV1626, structural genomi	6e-06
3r0j_A	250	Possible two component system response transcript	9e-06
3sy8_A	400	ROCR; TIM barrel phosphodiesterase-A, transcriptio	1e-05
2gwr_A	238	DNA-binding response regulator MTRA; two-component	2e-05
3lte_A	132	Response regulator; structural genomics, PSI, prot	2e-05
2qzj_A	136	Two-component response regulator; 11017X, PSI-II,	2e-05
3a10_A	116	Response regulator; phosphoacceptor, signaling pro	3e-05
3kto_A	136	Response regulator receiver protein; PSI-II,struct	4e-05
2oqr_A	230	Sensory transduction protein REGX3; response regul	4e-05
2a9o_A	120	Response regulator; essential protein, YYCF/YYCG h	4e-05
3n0r_A	286	Response regulator; sigma factor, receiver, two-co	5e-05
3f6p_A	120	Transcriptional regulatory protein YYCF; unphospho	5e-05
1zh2_A	121	KDP operon transcriptional regulatory protein KDPE	1e-04
1mvo_A	136	PHOP response regulator; phosphate regulon, transc	1e-04
3t6k_A	136	Response regulator receiver; flavodoxin-like, stru	2e-04
2jba_A	127	Phosphate regulon transcriptional regulatory PROT;	2e-04
1ys7_A	233	Transcriptional regulatory protein PRRA; response	2e-04
1kgs_A	225	DRRD, DNA binding response regulator D; DNA-bindin	3e-04
2gkg_A	127	Response regulator homolog; social motility, recei	3e-04
3gl9_A	122	Response regulator; beta-sheet, surrounded by alph	6e-04

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

 Score = 87.7 bits (218), Expect = 1e-20
 Identities = 34/198 (17%), Positives = 65/198 (32%), Gaps = 54/198 (27%)

Query: 15  DEIDGFDLSPSDTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEE 74
               G        +++ VL VDDS   R      L     +V      R AL  L   E+
Sbjct: 110 QYAVGLVHRLYLNQQIEVLVVDDSRTSRHRTMAQLRKQLLQVHEASHAREALATL---EQ 166

Query: 75  QSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILS 134
                     + L++ DY MP + G  L++ ++                           
Sbjct: 167 HP-------AIRLVLVDYYMPEIDGISLVRMLR--------------------------- 192

Query: 135 ICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSDVK 194
                           +  + +++ ++ +S  +      R L+ GA DF+ +P +  +++
Sbjct: 193 ----------------ERYSKQQLAIIGISVSDKRGLSARYLKQGANDFLNQPFEPEELQ 236

Query: 195 -RIKDYLTRDVNLGNEGR 211
            R+   L       +EG 
Sbjct: 237 CRVSHNLEALEQFNSEGH 254

>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 = 73.5 bits (181), Expect = 1e-15
 Identities = 21/161 (13%), Positives = 47/161 (29%), Gaps = 58/161 (36%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
            +L V+DS   R+++ + +   +             +              G +  + + 
Sbjct: 6   KILIVEDSMTIRRMLIQAIAQQTGLEIDAFDTLEGARHC-----------QGDEYVVALV 54

Query: 91  DYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQ 150
           D  +P     E +K +                                            
Sbjct: 55  DLTLPDAPSGEAVKVLL------------------------------------------- 71

Query: 151 DSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLS 191
                R +PVVI++++    + +  LE G  D+++K  + S
Sbjct: 72  ----ERGLPVVILTADISEDKREAWLEAGVLDYVMKDSRHS 108

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

 Score = 84.4 bits (209), Expect = 6e-19
 Identities = 33/188 (17%), Positives = 61/188 (32%), Gaps = 56/188 (29%)

Query: 21  DLSPSDTEEVHVLAVDDSFVDRKVIERLLT-ISSCKVTAVDSGRRALQFLGLDEEQSING 79
           DL       V VL VDD  +  + + R L   +          ++A+             
Sbjct: 10  DLGAPLDGAVMVLLVDDQAMIGEAVRRSLASEAGIDFHFCSDPQQAVAVA---------- 59

Query: 80  FDGLKVDLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCF 139
            + +K  +I+ D  MPG+ G  LL   +                                
Sbjct: 60  -NQIKPTVILQDLVMPGVDGLTLLAAYR-------------------------------- 86

Query: 140 PFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSDVK-RIKD 198
                       + A R+IP++++S++            GA D++VK     ++  RI+ 
Sbjct: 87  -----------GNPATRDIPIIVLSTKEEPTVKSAAFAAGANDYLVKLPDAIELVARIRY 135

Query: 199 YLTRDVNL 206
           +    + L
Sbjct: 136 HSRSYIAL 143

>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 = 82.2 bits (203), Expect = 5e-18
 Identities = 37/170 (21%), Positives = 61/170 (35%), Gaps = 55/170 (32%)

Query: 32  VLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITD 91
           +L VDD   + +++E  LT    +V+    G  AL     D             D+I+ D
Sbjct: 4   ILVVDDIEANVRLLEAKLTAEYYEVSTAMDGPTALAMAARDL-----------PDIILLD 52

Query: 92  YCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQD 151
             MPGM G+ + +K+K                                           D
Sbjct: 53  VMMPGMDGFTVCRKLK-------------------------------------------D 69

Query: 152 SSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSDVK-RIKDYL 200
               R IPVV++++ +      + LE GA DF+ KP+    +  R++   
Sbjct: 70  DPTTRHIPVVLITALDGRGDRIQGLESGASDFLTKPIDDVMLFARVRSLT 119

>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 = 66.0 bits (161), Expect = 1e-12
 Identities = 27/174 (15%), Positives = 50/174 (28%), Gaps = 57/174 (32%)

Query: 30  VHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLII 89
             VL VDD+    + +   L +    V   D  +  +   G              VDL+I
Sbjct: 153 GRVLIVDDNERQAQRVAAELGVEHRPVIESDPEKAKISAGG-------------PVDLVI 199

Query: 90  TDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLE 149
            +       G      ++                                          
Sbjct: 200 VNAAAKNFDGLRFTAALR------------------------------------------ 217

Query: 150 QDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSDVK-RIKDYLTR 202
                 R++PV+ M   +   R+ + LE G  D + +P+   ++  R+K  + R
Sbjct: 218 -SEERTRQLPVLAMVDPDDRGRMVKALEIGVNDILSRPIDPQELSARVKTQIQR 270

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

 Score = 77.3 bits (191), Expect = 7e-18
 Identities = 30/174 (17%), Positives = 58/174 (33%), Gaps = 51/174 (29%)

Query: 27  TEEVHVLAVDDSFVDRKVIERLLTIS--SCKVTAVDSGRRALQFLGLDEEQSINGFDGLK 84
            ++V +L ++D  VD + +ER+        K+    SG +AL  L        N  + + 
Sbjct: 5   ADKVDILYLEDDEVDIQSVERVFHKISSLIKIEIAKSGNQALDML-----YGRNKENKIH 59

Query: 85  VDLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFP 144
             LI+ D  +P M G E LK+++                                     
Sbjct: 60  PKLILLDINIPKMNGIEFLKELR------------------------------------- 82

Query: 145 SNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSD-VKRIK 197
                 D S+  +I V ++++                  ++KP+   + +K   
Sbjct: 83  ------DDSSFTDIEVFVLTAAYTSKDKLAFESLNIRGHLIKPLDYGEAIKLFW 130

>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 = 76.5 bits (189), Expect = 2e-17
 Identities = 40/187 (21%), Positives = 64/187 (34%), Gaps = 50/187 (26%)

Query: 26  DTEEVHVLAVDDSFVDRKVIERLLTIS--SCKVTAVDSGRRALQFLGLDEEQSINGFDGL 83
                 +L V+DS  D    +RLL        +    +G +AL FL        N     
Sbjct: 3   GNATQPLLVVEDSDEDFSTFQRLLQREGVVNPIYRCITGDQALDFL-YQTGSYCNPDIAP 61

Query: 84  KVDLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFF 143
           +  +I+ D  +PG  G E+L++IK                                    
Sbjct: 62  RPAVILLDLNLPGTDGREVLQEIK------------------------------------ 85

Query: 144 PSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSD----VKRIKDY 199
                      L++IPVVIM++ +    I+ C       +IVKP+++      V+    Y
Sbjct: 86  -------QDEVLKKIPVVIMTTSSNPKDIEICYSYSISSYIVKPLEIDRLTETVQTFIKY 138

Query: 200 LTRDVNL 206
               V L
Sbjct: 139 WLDIVVL 145

>3ilh_A Two component response regulator; NYSGXRC, PSI-II, protein S initiative, structural genomics; 2.59A {Cytophaga hutchinsonii} Length = 146

 Score = 76.2 bits (188), Expect = 2e-17
 Identities = 29/186 (15%), Positives = 59/186 (31%), Gaps = 52/186 (27%)

Query: 22  LSPSDTEEV-HVLAVDDSFVDRKVIERLLTISSC--KVTAVDSGRRALQFLGLDEEQSIN 78
           +S +DT ++  VL +DD  +   +   ++ ++    ++ +V SG  A+  L    E    
Sbjct: 1   MSLADTRKIDSVLLIDDDDIVNFLNTTIIRMTHRVEEIQSVTSGNAAINKL---NELYAA 57

Query: 79  GFDGLKVDLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFC 138
           G       +I  D  MPG+ G+EL+   K                               
Sbjct: 58  GR---WPSIICIDINMPGINGWELIDLFK------------------------------- 83

Query: 139 FPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLED-GAEDFIVKPVKLSDVK-RI 196
                     +       +  V ++SS        +       + ++ KP+  + +    
Sbjct: 84  ----------QHFQPMKNKSIVCLLSSSLDPRDQAKAEASDWVDYYVSKPLTANALNNLY 133

Query: 197 KDYLTR 202
              L  
Sbjct: 134 NKVLNE 139

>3heb_A Response regulator receiver domain protein (CHEY); NYSGXRC, PSI-II, respose regulator, structure initiative, structural genomics; 2.40A {Rhodospirillum rubrum} Length = 152

 Score = 76.2 bits (188), Expect = 2e-17
 Identities = 33/181 (18%), Positives = 71/181 (39%), Gaps = 51/181 (28%)

Query: 27  TEEVHVLAVDDSFVDRKVIERLLTIS--SCKVTAVDSGRRALQFLGLDEEQSINGFDGLK 84
           +  V ++ ++D     ++IE+ +  +  + ++ A   G  AL +L  D++         +
Sbjct: 2   SLSVTIVMIEDDLGHARLIEKNIRRAGVNNEIIAFTDGTSALNYLFGDDKSGRV--SAGR 59

Query: 85  VDLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFP 144
             L++ D  +P MTG ++LK +K                                     
Sbjct: 60  AQLVLLDLNLPDMTGIDILKLVK------------------------------------- 82

Query: 145 SNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSD----VKRIKDYL 200
                 ++   R  PVVI+++ +    I RC + GA  +I KPV   +    ++++  + 
Sbjct: 83  ------ENPHTRRSPVVILTTTDDQREIQRCYDLGANVYITKPVNYENFANAIRQLGLFF 136

Query: 201 T 201
           +
Sbjct: 137 S 137

>1i3c_A Response regulator RCP1; phytochrome, signaling protein; 1.90A {Synechocystis SP} SCOP: c.23.1.1 PDB: 1jlk_A Length = 149

 Score = 72.7 bits (179), Expect = 4e-16
 Identities = 35/190 (18%), Positives = 67/190 (35%), Gaps = 53/190 (27%)

Query: 23  SPSDTEEVHVLAVDDSFVDRKVIERLLTIS--SCKVTAVDSGRRALQFLGLDEEQSINGF 80
           S        +L V+DS  D ++++ +L  S    ++  +  G  A+ FL    +Q     
Sbjct: 2   SDESNPPKVILLVEDSKADSRLVQEVLKTSTIDHELIILRDGLAAMAFL----QQQGEYE 57

Query: 81  DGLKVDLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFP 140
           +  + +LI+ D  +P   G E+L +IK                                 
Sbjct: 58  NSPRPNLILLDLNLPKKDGREVLAEIK--------------------------------- 84

Query: 141 FFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSD----VKRI 196
                      +  L+ IPVV++++ +    +    E     ++ K   L D    V+ I
Sbjct: 85  ----------QNPDLKRIPVVVLTTSHNEDDVIASYELHVNCYLTKSRNLKDLFKMVQGI 134

Query: 197 KDYLTRDVNL 206
           + +    V L
Sbjct: 135 ESFWLETVTL 144

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

 Score = 74.5 bits (183), Expect = 2e-15
 Identities = 33/163 (20%), Positives = 60/163 (36%), Gaps = 56/163 (34%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
            +L +DD  V R+ +   L  S+ KV    +G + LQ             +  + DL+I 
Sbjct: 7   TLLIIDDDEVVRESLAAYLEDSNFKVLQALNGLQGLQIF-----------ESEQPDLVIC 55

Query: 91  DYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQ 150
           D  MP + G EL+++I+ T                                         
Sbjct: 56  DLRMPQIDGLELIRRIRQTAS--------------------------------------- 76

Query: 151 DSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSDV 193
                 E P++++S   +++     L  GA D+++KP++   V
Sbjct: 77  ------ETPIIVLSGAGVMSDAVEALRLGAADYLIKPLEDLAV 113

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

 Score = 68.0 bits (167), Expect = 1e-14
 Identities = 22/175 (12%), Positives = 48/175 (27%), Gaps = 60/175 (34%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
             L V+D     +  + LL +   +   V SG  AL  +     +          D +  
Sbjct: 5   QALIVEDYQAAAETFKELLEMLGFQADYVMSGTDALHAM---STR--------GYDAVFI 53

Query: 91  DYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQ 150
           D  +P  +G  L+K+++                                           
Sbjct: 54  DLNLPDTSGLALVKQLR------------------------------------------- 70

Query: 151 DSSALREIPVVIMSSENILARIDR--CLEDGAEDFIVKPVKLSD-VKRIKDYLTR 202
                +    V +S     A+ D      +  + ++ KP+ ++     ++     
Sbjct: 71  ALPMEKTSKFVAVSG---FAKNDLGKEACELFDFYLEKPIDIASLEPILQSIEGH 122

>2rjn_A Response regulator receiver:metal-dependent phosphohydrolase, HD subdomain; structural genomics, oceanospirillum SP. MED92; 2.10A {Neptuniibacter caesariensis} Length = 154

 Score = 68.4 bits (168), Expect = 2e-14
 Identities = 21/86 (24%), Positives = 35/86 (40%), Gaps = 11/86 (12%)

Query: 26  DTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKV 85
           + +   V+ VDD       ++RL+    C +    S   AL+ L               V
Sbjct: 4   NYKNYTVMLVDDEQPILNSLKRLIKRLGCNIITFTSPLDALEALKGTS-----------V 52

Query: 86  DLIITDYCMPGMTGYELLKKIKVTTP 111
            L+I+D  MP M G   L+++  + P
Sbjct: 53  QLVISDMRMPEMGGEVFLEQVAKSYP 78

>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 = 67.6 bits (166), Expect = 2e-14
 Identities = 35/178 (19%), Positives = 60/178 (33%), Gaps = 58/178 (32%)

Query: 28  EEVHVLAVDDSFVDRKVIERLLTISSCK--VTAVDSGRRALQFLGLDEEQSINGFDGLKV 85
           +E+  L VDD    R+++  LL          A D G  AL  L                
Sbjct: 3   KELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAED-GVDALNKL-----------QAGGY 50

Query: 86  DLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPS 145
             +I+D+ MP M G ELLK I+                                      
Sbjct: 51  GFVISDWNMPNMDGLELLKTIR-------------------------------------- 72

Query: 146 NNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSDVK-RIKDYLTR 202
                   A+  +PV+++++E     I    + GA  ++VKP   + ++ ++     +
Sbjct: 73  -----AXXAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKIFEK 125

>3hv2_A Response regulator/HD domain protein; PSI-2, NYSGXRC, structural genomics, protein structure initiative; 1.50A {Pseudomonas fluorescens pf-5} Length = 153

 Score = 67.6 bits (166), Expect = 2e-14
 Identities = 22/88 (25%), Positives = 36/88 (40%), Gaps = 11/88 (12%)

Query: 24  PSDTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGL 83
            + T    +L VD   V  + +++LL+     +       +ALQ L     +        
Sbjct: 9   ATVTRRPEILLVDSQEVILQRLQQLLSPLPYTLHFARDATQALQLL---ASRE------- 58

Query: 84  KVDLIITDYCMPGMTGYELLKKIKVTTP 111
            VDL+I+   +P M G  LL +I    P
Sbjct: 59  -VDLVISAAHLPQMDGPTLLARIHQQYP 85

>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 = 66.0 bits (162), Expect = 9e-14
 Identities = 31/167 (18%), Positives = 59/167 (35%), Gaps = 60/167 (35%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
            +L +DD     + I+ LL I   +V    S    L+    +            +D++IT
Sbjct: 5   KILVIDDESTILQNIKFLLEIDGNEVLTASSSTEGLRIFTENCNS---------IDVVIT 55

Query: 91  DYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQ 150
           D  MP ++G ++L++IK  TP                                       
Sbjct: 56  DMKMPKLSGMDILREIKKITP--------------------------------------- 76

Query: 151 DSSALREIPVVIMSSENILARID---RCLEDGAEDFIVKPVKLSDVK 194
                  + V+I++       +D     +++GA +++ KPV   D+ 
Sbjct: 77  ------HMAVIILTGH---GDLDNAILAMKEGAFEYLRKPVTAQDLS 114

>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 = 65.2 bits (160), Expect = 1e-13
 Identities = 34/173 (19%), Positives = 57/173 (32%), Gaps = 57/173 (32%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
            +L VDD    R ++  +      +     +G +AL  +              + DL++ 
Sbjct: 5   KILIVDDQSGIRILLNEVFNKEGYQTFQAANGLQALDIV-----------TKERPDLVLL 53

Query: 91  DYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQ 150
           D  +PGM G E+LK++KV                                          
Sbjct: 54  DMKIPGMDGIEILKRMKVIDE--------------------------------------- 74

Query: 151 DSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSDVK-RIKDYLTR 202
                  I V+IM++   L  I    E GA     KP  + +++  +K YL  
Sbjct: 75  ------NIRVIIMTAYGELDMIQESKELGALTHFAKPFDIDEIRDAVKKYLPL 121

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

 Score = 65.3 bits (160), Expect = 1e-13
 Identities = 30/178 (16%), Positives = 57/178 (32%), Gaps = 68/178 (38%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
            V+ VD+S +    ++  L      V    + + A  FL     +        K+DL+  
Sbjct: 6   TVMVVDESRITFLAVKNALEKDGFNVIWAKNEQEAFTFL---RRE--------KIDLVFV 54

Query: 91  DYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQ 150
           D    G     L+++I+   P                                       
Sbjct: 55  DV-FEGEESLNLIRRIREEFP--------------------------------------- 74

Query: 151 DSSALREIPVVIMSSENILARID-----RCLEDGAEDFIVKPVKLSDVK-RIKDYLTR 202
                 +  V ++S     A +D       ++ GA D+I+KP +L  +  R+K  ++ 
Sbjct: 75  ------DTKVAVLS-----AYVDKDLIINSVKAGAVDYILKPFRLDYLLERVKKIISS 121

>3m6m_D Sensory/regulatory protein RPFC; RPFF, REC, enoyl-COA hydratase, lyase-transferase COMP; 2.50A {Xanthomonas campestris PV} Length = 143

 Score = 64.9 bits (159), Expect = 2e-13
 Identities = 37/174 (21%), Positives = 64/174 (36%), Gaps = 52/174 (29%)

Query: 23  SPSDTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDG 82
             +    + +L  DD   +R V++RLL  +  KV  V+   + L  +    E+       
Sbjct: 8   HRARVRSMRMLVADDHEANRMVLQRLLEKAGHKVLCVNGAEQVLDAM---AEED------ 58

Query: 83  LKVDLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFF 142
              D +I D  MPGM G ++LK+++                                   
Sbjct: 59  --YDAVIVDLHMPGMNGLDMLKQLR----------------------------------- 81

Query: 143 FPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSDVKRI 196
                    +S +R  PVV++S++     I  C + GA  F+ KPV  + +   
Sbjct: 82  ------VMQASGMRYTPVVVLSADVTPEAIRACEQAGARAFLAKPVVAAKLLDT 129

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

 Score = 64.5 bits (158), Expect = 2e-13
 Identities = 28/167 (16%), Positives = 52/167 (31%), Gaps = 60/167 (35%)

Query: 32  VLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITD 91
           +L V+D    R+ +  +++    +V +   G    +            F     D+IITD
Sbjct: 10  ILIVEDDTDAREWLSTIISNHFPEVWSAGDGEEGERL-----------FGLHAPDVIITD 58

Query: 92  YCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQD 151
             MP + G E+L +IK                                            
Sbjct: 59  IRMPKLGGLEMLDRIKAGGA---------------------------------------- 78

Query: 152 SSALREIPVVIMS--SENILARIDRCLEDGAEDFIVKPVKLSDVKRI 196
                +  V+++S  SE       + +E G   F+ KP++   +   
Sbjct: 79  -----KPYVIVISAFSEMKYFI--KAIELGVHLFLPKPIEPGRLMET 118

>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 = 64.2 bits (157), Expect = 4e-13
 Identities = 29/161 (18%), Positives = 55/161 (34%), Gaps = 56/161 (34%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
            VL VDD+ V+R+ +   L          D    A  +L   +          ++ L+IT
Sbjct: 9   LVLVVDDNAVNREALILYLKSRGIDAVGADGAEEARLYLHYQK----------RIGLMIT 58

Query: 91  DYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQ 150
           D  M   +G +L++ I+                                           
Sbjct: 59  DLRMQPESGLDLIRTIR------------------------------------------- 75

Query: 151 DSSALREIPVVIMSS-ENILARIDRCLEDGAEDFIVKPVKL 190
            +S    + ++++S   ++   +D  +  G  DF++KPV L
Sbjct: 76  -ASERAALSIIVVSGDTDVEEAVD-VMHLGVVDFLLKPVDL 114

>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 = 62.9 bits (154), Expect = 8e-13
 Identities = 30/177 (16%), Positives = 61/177 (34%), Gaps = 56/177 (31%)

Query: 28  EEVHVLAVDDSFVDRKVIERLLTISSCK-VTAVDSGRRALQFLGLDEEQSINGFDGLKVD 86
           E++ VL VDD    R ++   L     K +TA   G + ++ +    +            
Sbjct: 5   EKIKVLIVDDQVTSRLLLGDALQQLGFKQITAAGDGEQGMKIM---AQN--------PHH 53

Query: 87  LIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSN 146
           L+I+D+ MP M G  LL+ ++                                       
Sbjct: 54  LVISDFNMPKMDGLGLLQAVR--------------------------------------- 74

Query: 147 NLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSDVK-RIKDYLTR 202
                + A ++   +I++++   A + +    GA + + KP  +  +K  I+     
Sbjct: 75  ----ANPATKKAAFIILTAQGDRALVQKAAALGANNVLAKPFTIEKMKAAIEAVFGA 127

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

 Score = 63.3 bits (155), Expect = 8e-13
 Identities = 31/165 (18%), Positives = 58/165 (35%), Gaps = 58/165 (35%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
            VL V+DS     + ++ +      +  V++GR A+QF+  +           K  LII 
Sbjct: 6   RVLLVEDSTSLAILYKQYVKDEPYDIFHVETGRDAIQFI--ERS---------KPQLIIL 54

Query: 91  DYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQ 150
           D  +P M+G ++L  I                                            
Sbjct: 55  DLKLPDMSGEDVLDWINQNDI--------------------------------------- 75

Query: 151 DSSALREIPVVIMSSE-NILARIDRCLEDGAEDFIVKPVKLSDVK 194
                    V+I ++  ++   ++  ++ GAEDF+ KP+    +K
Sbjct: 76  ------PTSVIIATAHGSVDLAVN-LIQKGAEDFLEKPINADRLK 113

>1ny5_A Transcriptional regulator (NTRC family); AAA+ ATPase, sigma54 activator, bacterial transcription, DIM transcription; HET: ADP; 2.40A {Aquifex aeolicus} SCOP: c.23.1.1 c.37.1.20 PDB: 1ny6_A* 3m0e_A* 1zy2_A* Length = 387

 Score = 65.9 bits (162), Expect = 1e-12
 Identities = 32/168 (19%), Positives = 63/168 (37%), Gaps = 62/168 (36%)

Query: 30  VHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLII 89
           ++VL ++D  V R ++E  L++   KV + + G+ A + L    E+          ++++
Sbjct: 1   MNVLVIEDDKVFRGLLEEYLSMKGIKVESAERGKEAYKLL---SEKH--------FNVVL 49

Query: 90  TDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLE 149
            D  +P + G E+LK IK  +P                                      
Sbjct: 50  LDLLLPDVNGLEILKWIKERSP-------------------------------------- 71

Query: 150 QDSSALREIPVVIMSSENILARID---RCLEDGAEDFIVKPVKLSDVK 194
                  E  V++++       I      ++ GA DF+ KP  L +++
Sbjct: 72  -------ETEVIVITGH---GTIKTAVEAMKMGAYDFLTKPCMLEEIE 109

>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 = 62.1 bits (152), Expect = 1e-12
 Identities = 36/166 (21%), Positives = 56/166 (33%), Gaps = 56/166 (33%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
            V  VDD    R V+ER L  +    T  ++G   L  L                D++++
Sbjct: 5   IVWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLAALASKT-----------PDVLLS 53

Query: 91  DYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQ 150
           D  MPGM G  LLK+IK   P                                       
Sbjct: 54  DIRMPGMDGLALLKQIKQRHP--------------------------------------- 74

Query: 151 DSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSDVKRI 196
                  +PV+IM++ + L       + GA D++ KP  + +   +
Sbjct: 75  ------MLPVIIMTAHSDLDAAVSAYQQGAFDYLPKPFDIDEAVAL 114

>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 = 61.8 bits (151), Expect = 4e-12
 Identities = 34/176 (19%), Positives = 58/176 (32%), Gaps = 66/176 (37%)

Query: 27  TEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVD 86
           +    V  +DD    RK +++ L ++   V++  S   AL  L  D              
Sbjct: 1   SAAPSVFLIDDDRDLRKAMQQTLELAGFTVSSFASATEALAGLSADF-----------AG 49

Query: 87  LIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSN 146
           ++I+D  MPGM G  L +KI    P                                   
Sbjct: 50  IVISDIRMPGMDGLALFRKILALDP----------------------------------- 74

Query: 147 NLEQDSSALREIPVVIMSSENILARID---RCLEDGAEDFIVKPVKLSD----VKR 195
                     ++P+++++       I    + ++DGA DFI KP          +R
Sbjct: 75  ----------DLPMILVTGH---GDIPMAVQAIQDGAYDFIAKPFAADRLVQSARR 117

>1dcf_A ETR1 protein; beta-alpha five sandwich, transferase; 2.50A {Arabidopsis thaliana} SCOP: c.23.1.2 Length = 136

 Score = 61.0 bits (149), Expect = 6e-12
 Identities = 32/174 (18%), Positives = 61/174 (35%), Gaps = 56/174 (32%)

Query: 25  SDTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLK 84
           S+   + VL +D++ V R V + LL    C+VT V S    L+ +        +      
Sbjct: 3   SNFTGLKVLVMDENGVSRMVTKGLLVHLGCEVTTVSSNEECLRVVS-------HEH---- 51

Query: 85  VDLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFP 144
             ++  D CMPG+  Y++  +I                                      
Sbjct: 52  -KVVFMDVCMPGVENYQIALRIH------------------------------------- 73

Query: 145 SNNLEQDSSALREIPVVIMSSENILA--RIDRCLEDGAEDFIVKPVKLSDVKRI 196
                      R   +V +S  N     + ++C+  G +  ++KPV L +++ +
Sbjct: 74  --EKFTKQRHQR-PLLVALSG-NTDKSTK-EKCMSFGLDGVLLKPVSLDNIRDV 122

>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 = 60.6 bits (148), Expect = 7e-12
 Identities = 27/184 (14%), Positives = 55/184 (29%), Gaps = 57/184 (30%)

Query: 22  LSPSDTEEVHVLAVDDSFVDRKVIERLLT--ISSCKVTAVDSGRRALQFLGLDEEQSING 79
           +S +   +  +L ++D      ++ + L       K+    +   A   L          
Sbjct: 1   MSLNVKNDFSILIIEDDKEFADMLTQFLENLFPYAKIKIAYNPFDAGDLL---HTV---- 53

Query: 80  FDGLKVDLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCF 139
               K D+++ D  M GM G+ +  +IK                                
Sbjct: 54  ----KPDVVMLDLMMVGMDGFSICHRIK-------------------------------- 77

Query: 140 PFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSDVK-RIKD 198
                 +           I V+ M+       + R +  GAE    KP+  + ++  IK 
Sbjct: 78  ------STPA-----TANIIVIAMTGALTDDNVSRIVALGAETCFGKPLNFTLLEKTIKQ 126

Query: 199 YLTR 202
            + +
Sbjct: 127 LVEQ 130

>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 = 60.2 bits (147), Expect = 9e-12
 Identities = 36/172 (20%), Positives = 59/172 (34%), Gaps = 55/172 (31%)

Query: 32  VLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITD 91
           VL V+D+ ++ K+   LL     +      G  AL       E           DLI+ D
Sbjct: 4   VLIVEDNELNMKLFHDLLEAQGYETLQTREGLSALSIA---RENKP--------DLILMD 52

Query: 92  YCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQD 151
             +P ++G E+ K +K                                           +
Sbjct: 53  IQLPEISGLEVTKWLK-------------------------------------------E 69

Query: 152 SSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSD-VKRIKDYLTR 202
              L  IPVV +++  +    +R  E G E +I KP+ +   ++ IK  L R
Sbjct: 70  DDDLAHIPVVAVTAFAMKGDEERIREGGCEAYISKPISVVHFLETIKRLLER 121

>3kcn_A Adenylate cyclase homolog; SGX, PSI 2, structural genomics, protein structure initiative; 2.45A {Rhodopirellula baltica} Length = 151

 Score = 60.7 bits (148), Expect = 9e-12
 Identities = 22/81 (27%), Positives = 39/81 (48%), Gaps = 11/81 (13%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
            +L VDD +     ++R L+    +VT  +SG  AL  +   +             +I+ 
Sbjct: 6   RILLVDDDYSLLNTLKRNLS-FDFEVTTCESGPEALACIKKSDP----------FSVIMV 54

Query: 91  DYCMPGMTGYELLKKIKVTTP 111
           D  MPGM G E+++K ++ +P
Sbjct: 55  DMRMPGMEGTEVIQKARLISP 75

>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 = 63.2 bits (155), Expect = 1e-11
 Identities = 23/168 (13%), Positives = 44/168 (26%), Gaps = 62/168 (36%)

Query: 32  VLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITD 91
           VL VDD       +  +L           + R A + +                 +I+ D
Sbjct: 3   VLVVDDEESITSSLSAILEEEGYHPDTAKTLREAEKKIKELF-----------FPVIVLD 51

Query: 92  YCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQD 151
             MP   G   +  IK  +P                                        
Sbjct: 52  VWMPDGDGVNFIDFIKENSP---------------------------------------- 71

Query: 152 SSALREIPVVIMSSENILARID---RCLEDGAEDFIVKPVKLSDVKRI 196
                +  V++++       +D   + ++ GA +F+ KP  +      
Sbjct: 72  -----DSVVIVITGH---GSVDTAVKAIKKGAYEFLEKPFSVERFLLT 111

>2jk1_A HUPR, hydrogenase transcriptional regulatory protein HU; nucleotide-binding, transcription regulation; 2.10A {Rhodobacter capsulatus} PDB: 2vui_B 2vuh_B Length = 139

 Score = 59.5 bits (145), Expect = 2e-11
 Identities = 19/80 (23%), Positives = 29/80 (36%), Gaps = 12/80 (15%)

Query: 32  VLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITD 91
           +L VDD       ++  L      V        A+  L  +            V +II D
Sbjct: 4   ILLVDDEPHSLAAMKLALE-DDFDVLTAQGAEAAIAILEEEW-----------VQVIICD 51

Query: 92  YCMPGMTGYELLKKIKVTTP 111
             MPG TG + L +++   P
Sbjct: 52  QRMPGRTGVDFLTEVRERWP 71

>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 = 61.7 bits (150), Expect = 2e-11
 Identities = 37/177 (20%), Positives = 68/177 (38%), Gaps = 58/177 (32%)

Query: 21  DLSPSDTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGF 80
           D + SD +++ +L VDD  ++R+++   L     +    + G  AL  L    +      
Sbjct: 121 DKAVSDNDDMMILVVDDHPINRRLLADQLGSLGYQCKTANDGVDALNVL---SKNH---- 173

Query: 81  DGLKVDLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFP 140
               +D++++D  MP M GY L ++I+                                 
Sbjct: 174 ----IDIVLSDVNMPNMDGYRLTQRIR--------------------------------- 196

Query: 141 FFFPSNNLEQDSSALREIPVVIMSSENILAR-IDRCLEDGAEDFIVKPVKLSDVKRI 196
                   +        +PV+ +++ N LA    RCLE G +  + KPV L  +K+ 
Sbjct: 197 --------QLG----LTLPVIGVTA-NALAEEKQRCLESGMDSCLSKPVTLDVIKQT 240

>3grc_A Sensor protein, kinase; protein structure initiative II(PSI II), NYSGXRC, 11025B, structural genomics; 2.21A {Polaromonas SP} Length = 140

 Score = 59.5 bits (145), Expect = 2e-11
 Identities = 18/179 (10%), Positives = 46/179 (25%), Gaps = 66/179 (36%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
            +L  +D     +++  +L         V S  +AL+ +     +            +  
Sbjct: 8   RILICEDDPDIARLLNLMLEKGGFDSDMVHSAAQALEQV---ARR--------PYAAMTV 56

Query: 91  DYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQ 150
           D  +P   G  L++ ++                                           
Sbjct: 57  DLNLPDQDGVSLIRALR------------------------------------------- 73

Query: 151 DSSALREIPVVIMSSENILARID------RCLEDGAEDFIVKPVKLSD-VKRIKDYLTR 202
             S  R++ +V++S     A                  ++ KP+  +  +  +   +  
Sbjct: 74  RDSRTRDLAIVVVS-----ANAREGELEFNSQPLAVSTWLEKPIDENLLILSLHRAIDN 127

>3gt7_A Sensor protein; structural genomics, signal receiver domain, kinase, PSI-2, protein structure initiative; 2.30A {Syntrophus aciditrophicus SB} Length = 154

 Score = 58.4 bits (142), Expect = 6e-11
 Identities = 41/183 (22%), Positives = 64/183 (34%), Gaps = 65/183 (35%)

Query: 26  DTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKV 85
                 +L V+DS    + ++ +L  +  +   V +GR A++F               + 
Sbjct: 4   SNRAGEILIVEDSPTQAEHLKHILEETGYQTEHVRNGREAVRF-----------LSLTRP 52

Query: 86  DLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPS 145
           DLII+D  MP M GY L + +K                                      
Sbjct: 53  DLIISDVLMPEMDGYALCRWLK-------------------------------------- 74

Query: 146 NNLEQDSSALREIPVVIMSSENILARID-----RCLEDGAEDFIVKPVKLSDVK-RIKDY 199
                    LR IPV++++        D     R LE GA+DFI KP K   +   +K  
Sbjct: 75  -----GQPDLRTIPVILLT-----ILSDPRDVVRSLECGADDFITKPCKDVVLASHVKRL 124

Query: 200 LTR 202
           L+ 
Sbjct: 125 LSG 127

>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 = 57.5 bits (140), Expect = 8e-11
 Identities = 34/159 (21%), Positives = 61/159 (38%), Gaps = 56/159 (35%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCK--VTAVDSGRRALQFLGLDEEQSINGFDGLKVDLI 88
            +L VDDS   R++I+  L+    +  + A   G  A + L  +              ++
Sbjct: 7   KLLVVDDSSTMRRIIKNTLSRLGYEDVLEAEH-GVEAWEKLDANA----------DTKVL 55

Query: 89  ITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNL 148
           ITD+ MP M G +L+KK++                                         
Sbjct: 56  ITDWNMPEMNGLDLVKKVR----------------------------------------- 74

Query: 149 EQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKP 187
               S  +EIP++++++E   A +   L+ G  ++IVKP
Sbjct: 75  --SDSRFKEIPIIMITAEGGKAEVITALKAGVNNYIVKP 111

>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 = 56.6 bits (137), Expect = 2e-10
 Identities = 14/163 (8%), Positives = 40/163 (24%), Gaps = 53/163 (32%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
           ++L   +       + RL+  +         GR A      D   +         D+++ 
Sbjct: 22  NILVASEDASRLAHLARLVGDAGRYRVTRTVGRAAQIVQRTDGLDA--------FDILMI 73

Query: 91  DYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQ 150
           D           ++K+    P                                       
Sbjct: 74  DGAALDTAELAAIEKLSRLHP--------------------------------------- 94

Query: 151 DSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSDV 193
                  +  ++++++     +   +  G  D +  P++   +
Sbjct: 95  ------GLTCLLVTTDASSQTLLDAMRAGVRDVLRWPLEPRAL 131

>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 = 56.5 bits (137), Expect = 3e-10
 Identities = 33/176 (18%), Positives = 58/176 (32%), Gaps = 58/176 (32%)

Query: 31  HVLAVDDSFVDRKVIERLLTIS--SCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLI 88
            VL V+D+  D  +I R+L      C++  VD+G +AL  +   ++           DLI
Sbjct: 7   RVLVVEDNPDDIALIRRVLDRKDIHCQLEFVDNGAKALYQV---QQAKY--------DLI 55

Query: 89  ITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNL 148
           I D  +P   G+E++  ++                                         
Sbjct: 56  ILDIGLPIANGFEVMSAVR----------------------------------------- 74

Query: 149 EQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSD--VKRIKDYLTR 202
                A +  P+VI++      R  +C+  GA   + K          RI    + 
Sbjct: 75  --KPGANQHTPIVILTDNVSDDRAKQCMAAGASSVVDKSSNNVTDFYGRIYAIFSY 128

>2rdm_A Response regulator receiver protein; structural genomics, unknown function, PSI-2, protein struct initiative; HET: MSE; 1.76A {Sinorhizobium medicae} Length = 132

 Score = 55.7 bits (135), Expect = 4e-10
 Identities = 22/86 (25%), Positives = 36/86 (41%), Gaps = 11/86 (12%)

Query: 27  TEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVD 86
            E V +L  DD  +     E  LT +   VTAV SG +A++ L            G  +D
Sbjct: 3   LEAVTILLADDEAILLLDFESTLTDAGFLVTAVSSGAKAIEMLK----------SGAAID 52

Query: 87  LIITDYCMP-GMTGYELLKKIKVTTP 111
            ++TD        G+++ +  +   P
Sbjct: 53  GVVTDIRFCQPPDGWQVARVAREIDP 78

>3nhm_A Response regulator; protein structure initiative II(PSI II), NYSGXRC, structural genomics; 2.19A {Myxococcus xanthus} Length = 133

 Score = 54.9 bits (133), Expect = 8e-10
 Identities = 33/176 (18%), Positives = 53/176 (30%), Gaps = 65/176 (36%)

Query: 32  VLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITD 91
           VL V++S+  R+ +  LL+      T    G   LQ                  D++I+D
Sbjct: 7   VLIVENSWTMRETLRLLLS-GEFDCTTAADGASGLQQA---LAH--------PPDVLISD 54

Query: 92  YCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQD 151
             M GM GY L    +                                            
Sbjct: 55  VNMDGMDGYALCGHFR-------------------------------------------S 71

Query: 152 SSALREIPVVIMSSENILARIDRC----LEDGAEDFIVKPVKLSDVK-RIKDYLTR 202
              L+ IPV+ +S         R      +   + ++VKPVK   +  ++   L R
Sbjct: 72  EPTLKHIPVIFVS-----GYAPRTEGPADQPVPDAYLVKPVKPPVLIAQLHALLAR 122

>2zay_A Response regulator receiver protein; structural genomics, NYSGXRC, target 11006U, protein structure initiative; 2.00A {Desulfuromonas acetoxidans} Length = 147

 Score = 54.9 bits (133), Expect = 1e-09
 Identities = 31/187 (16%), Positives = 53/187 (28%), Gaps = 65/187 (34%)

Query: 22  LSPSDTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFD 81
           +S ++ +   ++ VD            L+     +    +   A+       +       
Sbjct: 1   MSLAEGKWWRIMLVDTQLPALAASISALSQEGFDIIQCGNAIEAVPVA---VKT------ 51

Query: 82  GLKVDLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPF 141
                LIIT+  MP ++G +L   +K                                  
Sbjct: 52  --HPHLIITEANMPKISGMDLFNSLK---------------------------------- 75

Query: 142 FFPSNNLEQDSSALREIPVVIMSSENILARID-----RCLEDGAEDFIVKPVKLSDVK-R 195
                     +     IPV+ +S      R       + L+ G  DFI KPV    +  R
Sbjct: 76  ---------KNPQTASIPVIALS-----GRATAKEEAQLLDMGFIDFIAKPVNAIRLSAR 121

Query: 196 IKDYLTR 202
           IK  L  
Sbjct: 122 IKRVLKL 128

>3eqz_A Response regulator; structural genomics, unknown function, PSI-2, protein struct initiative; 2.15A {Colwellia psychrerythraea} Length = 135

 Score = 54.2 bits (131), Expect = 1e-09
 Identities = 25/178 (14%), Positives = 47/178 (26%), Gaps = 63/178 (35%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
            V  VDD  +   +++ ++      V A     RA   L L+           K D+II 
Sbjct: 5   RVFIVDDDTLTCNLLKTIVEPIFGNVEAFQ-HPRAFLTLSLN-----------KQDIIIL 52

Query: 91  DYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQ 150
           D  MP M G E+++ +                                            
Sbjct: 53  DLMMPDMDGIEVIRHLAEHKS--------------------------------------- 73

Query: 151 DSSALREIPVVIMS---SENILARIDR--CLEDGAEDFIVKPVKLSDVK-RIKDYLTR 202
                    ++++S   S  + +             +   KP+    +   +     R
Sbjct: 74  ------PASLILISGYDSGVLHSAETLALSCGLNVINTFTKPINTEVLTCFLTSLSNR 125

>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 = 53.3 bits (129), Expect = 2e-09
 Identities = 36/164 (21%), Positives = 62/164 (37%), Gaps = 59/164 (35%)

Query: 32  VLAVDDSFVDRKVIERLLTISSCKV--TAVDSGRRALQFLGLDEEQSINGFDGLKVDLII 89
           VL VDD+   R +++ ++T +  +V   A + GR A++     +E        LK D++ 
Sbjct: 5   VLIVDDAAFMRMMLKDIITKAGYEVAGEATN-GREAVE---KYKE--------LKPDIVT 52

Query: 90  TDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLE 149
            D  MP M G + +K+I    P                                      
Sbjct: 53  MDITMPEMNGIDAIKEIMKIDP-------------------------------------- 74

Query: 150 QDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSDV 193
                     +++ S+    A +   ++ GA+DFIVKP + S V
Sbjct: 75  -------NAKIIVCSAMGQQAMVIEAIKAGAKDFIVKPFQPSRV 111

>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 = 53.8 bits (130), Expect = 2e-09
 Identities = 38/194 (19%), Positives = 58/194 (29%), Gaps = 73/194 (37%)

Query: 23  SPSDTEEVHVLAVDDSFVDRKVIERLL-TISSCKV--TAVDSGRRALQFLGLDEEQSING 79
                   +V+ VDD+ + R  I   + T+   KV   A + G+ AL  L          
Sbjct: 7   HHHHGSPYNVMIVDDAAMMRLYIASFIKTLPDFKVVAQAAN-GQEALDKLAAQ------- 58

Query: 80  FDGLKVDLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCF 139
                VDLI+ D  MP M G E L+  K+ T                             
Sbjct: 59  ---PNVDLILLDIEMPVMDGMEFLRHAKLKTR---------------------------- 87

Query: 140 PFFFPSNNLEQDSSALREIPVVIMSS------ENILARIDRCLEDGAEDFIVKP---VKL 190
                               + ++SS       +      R  E GA+  + KP   V  
Sbjct: 88  ------------------AKICMLSSVAVSGSPHAA----RARELGADGVVAKPSGTVSH 125

Query: 191 SDVKRIKDYLTRDV 204
              ++    L R +
Sbjct: 126 DLEEKTGGELARTM 139

>3lua_A Response regulator receiver protein; two-component signal transduction system, histidine kinase, phosphorelay, receiver domain, nysgxrc; 2.40A {Clostridium thermocellum} Length = 140

 Score = 53.4 bits (129), Expect = 3e-09
 Identities = 24/174 (13%), Positives = 49/174 (28%), Gaps = 56/174 (32%)

Query: 32  VLAVDDSFVDRKVIERLLTISSC-KVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
           VL +D    +R+  + +           V++ ++        +           + LII 
Sbjct: 7   VLLIDYFEYEREKTKIIFDNIGEYDFIEVENLKKFYSIFKDLD----------SITLIIM 56

Query: 91  DYCMP-GMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLE 149
           D   P    G E+L  I+                                          
Sbjct: 57  DIAFPVEKEGLEVLSAIR------------------------------------------ 74

Query: 150 QDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSDVK-RIKDYLTR 202
            ++S     PV+I +  +        L+    D+I+KP     ++  ++  L  
Sbjct: 75  -NNSRTANTPVIIATKSDNPGYRHAALKFKVSDYILKPYPTKRLENSVRSVLKI 127

>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 = 53.4 bits (128), Expect = 3e-09
 Identities = 35/174 (20%), Positives = 61/174 (35%), Gaps = 53/174 (30%)

Query: 32  VLAVDDSFVDRKVIERLLTIS--SCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLII 89
           +  V+D+  D ++I+  L  S    +V  V  G  A+ +L  + E +    +  + DLI+
Sbjct: 5   IFLVEDNKADIRLIQEALANSTVPHEVVTVRDGMEAMAYLRQEGEYA----NASRPDLIL 60

Query: 90  TDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLE 149
               +P   G E+L +IK                                          
Sbjct: 61  LXLNLPKKDGREVLAEIK------------------------------------------ 78

Query: 150 QDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSD----VKRIKDY 199
                L+ IPVV++S+      I    +     +I K   LS     VK I+++
Sbjct: 79  -SDPTLKRIPVVVLSTSINEDDIFHSYDLHVNCYITKSANLSQLFQIVKGIEEF 131

>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 = 55.6 bits (135), Expect = 3e-09
 Identities = 37/165 (22%), Positives = 56/165 (33%), Gaps = 71/165 (43%)

Query: 32  VLAVDDSFVDRKVIERLLT-ISSCKV--TAVDSGRRALQFLGLDEEQSINGFDGLKVDLI 88
           VL+VDDS + R+++  ++   S  ++  TA D    A   +                D++
Sbjct: 6   VLSVDDSALMRQIMTEIINSHSDMEMVATAPD-PLVARDLIKK-----------FNPDVL 53

Query: 89  ITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNL 148
             D  MP M G + L+K+    P                                     
Sbjct: 54  TLDVEMPRMDGLDFLEKLMRLRP------------------------------------- 76

Query: 149 EQDSSALREIPVVIMSS------ENILARIDRCLEDGAEDFIVKP 187
                    +PVV++SS      E  L    R LE GA DF+ KP
Sbjct: 77  ---------MPVVMVSSLTGKGSEVTL----RALELGAIDFVTKP 108

>3c97_A Signal transduction histidine kinase; structural genomics, signaling, PSI-2, protein structure initiative; 1.70A {Aspergillus oryzae RIB40} Length = 140

 Score = 53.4 bits (129), Expect = 3e-09
 Identities = 25/80 (31%), Positives = 37/80 (46%), Gaps = 11/80 (13%)

Query: 22  LSPSDTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFD 81
           L PS    + VL  +D+ + R V  + L   +  +T V +G +ALQ     + +    F 
Sbjct: 3   LEPSQIMPLSVLIAEDNDICRLVAAKALEKCTNDITVVTNGLQALQAY---QNRQ---F- 55

Query: 82  GLKVDLIITDYCMPGMTGYE 101
               D+II D  MP M G E
Sbjct: 56  ----DVIIMDIQMPVMDGLE 71

>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 = 52.5 bits (127), Expect = 6e-09
 Identities = 35/177 (19%), Positives = 56/177 (31%), Gaps = 65/177 (36%)

Query: 32  VLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITD 91
           +L VDDS +   V   +L     +     SG   L+ L                DL++ D
Sbjct: 6   ILVVDDSPMIVDVFVTMLERGGYRPITAFSGEECLEAL---NAT--------PPDLVLLD 54

Query: 92  YCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQD 151
             M  M G+E L++IK                                            
Sbjct: 55  IMMEPMDGWETLERIK-------------------------------------------T 71

Query: 152 SSALREIPVVIMSSENILAR---IDRC--LEDGAEDFIVKPVKLSDVK-RIKDYLTR 202
             A R+IPV++++     A+    +         ED+I+KP     +   I+  L R
Sbjct: 72  DPATRDIPVLMLT-----AKPLTPEEANEYGSYIEDYILKPTTHHQLYEAIEHVLAR 123

>3h5i_A Response regulator/sensory box protein/ggdef domain protein; structural genomics, transcription, PSI-2; 1.90A {Carboxydothermus hydrogenoformans z-2901} Length = 140

 Score = 52.6 bits (127), Expect = 6e-09
 Identities = 26/177 (14%), Positives = 53/177 (29%), Gaps = 58/177 (32%)

Query: 28  EEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDL 87
           ++  +L V+DS    K I  +L      V    +G  A++ +            G   DL
Sbjct: 4   KDKKILIVEDSKFQAKTIANILNKYGYTVEIALTGEAAVEKV----------SGGWYPDL 53

Query: 88  IITDYCMPG-MTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSN 146
           I+ D  +   M G +    I+                                       
Sbjct: 54  ILMDIELGEGMDGVQTALAIQ--------------------------------------- 74

Query: 147 NLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSDVK-RIKDYLTR 202
                   + E+PVV +++    A +++     A  +++K      +   ++  L  
Sbjct: 75  -------QISELPVVFLTAHTEPAVVEKIRSVTAYGYVMKSATEQVLITIVEMALRL 124

>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 = 52.1 bits (126), Expect = 7e-09
 Identities = 31/164 (18%), Positives = 54/164 (32%), Gaps = 60/164 (36%)

Query: 28  EEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDL 87
           ++  V  VDD    RK +  +LT++   V    S    L F                  +
Sbjct: 2   QDYTVHIVDDEEPVRKSLAFMLTMNGFAVKMHQSAEAFLAFAPDVR-----------NGV 50

Query: 88  IITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNN 147
           ++TD  MP M+G ELL+ +                                         
Sbjct: 51  LVTDLRMPDMSGVELLRNLG---------------------------------------- 70

Query: 148 LEQDSSALREIPVVIMSSE-NI-LARIDRCLEDGAEDFIVKPVK 189
            +        IP ++++   ++ +A     ++ GA DFI KP +
Sbjct: 71  -DLKI----NIPSIVITGHGDVPMAV--EAMKAGAVDFIEKPFE 107

>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 = 52.6 bits (126), Expect = 8e-09
 Identities = 33/185 (17%), Positives = 54/185 (29%), Gaps = 58/185 (31%)

Query: 21  DLSPSDTEEVHVLAVDDSFVDRKVIERLLTISSCKV--TAVDSGRRALQFLGLDEEQSIN 78
            ++       +VL VDDS    K + ++ T     +  TA D G  A+            
Sbjct: 28  GINYDTGIPFNVLIVDDSVFTVKQLTQIFTSEGFNIIDTAAD-GEEAVIKY--KNHYP-- 82

Query: 79  GFDGLKVDLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFC 138
                 +D++     MP M G   L  I                                
Sbjct: 83  -----NIDIVTLXITMPKMDGITCLSNIMEFDK--------------------------- 110

Query: 139 FPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSDVK-RIK 197
                                V+++S+      +  CL  GA+ FIVKP+  + V  R+ 
Sbjct: 111 ------------------NARVIMISALGKEQLVKDCLIKGAKTFIVKPLDRAKVLQRVM 152

Query: 198 DYLTR 202
               +
Sbjct: 153 SVFVK 157

>3cu5_A Two component transcriptional regulator, ARAC FAM; structural genomics, protein structure initiative; 2.60A {Clostridium phytofermentans isdg} Length = 141

 Score = 51.8 bits (125), Expect = 1e-08
 Identities = 20/95 (21%), Positives = 36/95 (37%), Gaps = 19/95 (20%)

Query: 32  VLAVDDSFVDRKVIERLLTISSCKVTAV---DSGRRALQFLGLDEEQSINGFDGLKVDLI 88
           +L VDD  + R  +   +   +     +   D G  A+Q      +           +++
Sbjct: 5   ILIVDDEKLTRDGLIANINWKALSFDQIDQADDGINAIQIA---LK--------HPPNVL 53

Query: 89  ITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFL 123
           +TD  MP M G EL+  I    P        ++F+
Sbjct: 54  LTDVRMPRMDGIELVDNILKLYP-----DCSVIFM 83

>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 = 53.1 bits (128), Expect = 1e-08
 Identities = 30/194 (15%), Positives = 60/194 (30%), Gaps = 57/194 (29%)

Query: 27  TEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVD 86
           T +  V  VDD    R+ +  LL  +  +V   D     L+                +  
Sbjct: 2   TAKPTVFVVDDDMSVREGLRNLLRSAGFEVETFDCASTFLEHR-----------RPEQHG 50

Query: 87  LIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSN 146
            ++ D  MPGM+G EL +++   +                                    
Sbjct: 51  CLVLDMRMPGMSGIELQEQLTAISD----------------------------------- 75

Query: 147 NLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSD-VKRIKDYLTRDVN 205
                      IP+V +++   +    R ++ GA +F+ KP +    +  I+  L  +  
Sbjct: 76  ----------GIPIVFITAHGDIPMTVRAMKAGAIEFLPKPFEEQALLDAIEQGLQLNAE 125

Query: 206 LGNEGRGINKRKAR 219
                   ++ +  
Sbjct: 126 RRQARETQDQLEQL 139

>2qr3_A Two-component system response regulator; structural genomics, signal receiver, PSI-2, protein structu initiative; 1.80A {Bacteroides fragilis} Length = 140

 Score = 51.4 bits (124), Expect = 1e-08
 Identities = 30/177 (16%), Positives = 52/177 (29%), Gaps = 71/177 (40%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
            ++ VDD+      ++ LL     KV  + S       L  +             ++++ 
Sbjct: 5   TIIIVDDNKGVLTAVQLLLKNHFSKVITLSSPVSLSTVLREEN-----------PEVVLL 53

Query: 91  DYCMP-----GMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPS 145
           D         G  G   L +IK                                      
Sbjct: 54  DMNFTSGINNGNEGLFWLHEIKRQYR---------------------------------- 79

Query: 146 NNLEQDSSALREIPVVIMSSENILARID---RCLEDGAEDFIVKPVK----LSDVKR 195
                      ++PVV+ ++    A ID   R +++GA DF+VKP      L  +  
Sbjct: 80  -----------DLPVVLFTAY---ADIDLAVRGIKEGASDFVVKPWDNQKLLETLLN 122

>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 = 52.5 bits (126), Expect = 2e-08
 Identities = 39/185 (21%), Positives = 69/185 (37%), Gaps = 48/185 (25%)

Query: 23  SPSDTEEVHVLAVDDSFVDRKVIERLLTISSC-KVTAVDSGRRALQFL--GLDEEQSING 79
                    VL VDD+F+ RKV    L      +V   DSG+ AL+ +  GL + +    
Sbjct: 55  DDEFLRGKRVLVVDDNFISRKVATGKLKKMGVSEVEQCDSGKEALRLVTEGLTQREEQGS 114

Query: 80  FDGLKVDLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCF 139
            D L  D I  D  MP M GYE  ++I+                                
Sbjct: 115 VDKLPFDYIFMDCQMPEMDGYEATREIR-------------------------------- 142

Query: 140 PFFFPSNNLEQDSSALREIPVVIMSSENILA-RIDRCLEDGAEDFIVKPV-KLSDVKRIK 197
                    + + S     P++ +S  +  +      ++ G + F+ K + +L++V  I+
Sbjct: 143 ---------KVEKSYGVRTPIIAVSGHDPGSEEARETIQAGMDAFLDKSLNQLANV--IR 191

Query: 198 DYLTR 202
           +  ++
Sbjct: 192 EIESK 196

>3t8y_A CHEB, chemotaxis response regulator protein-glutamate methylesterase; CHEA, hydrolase; 1.90A {Thermotoga maritima} Length = 164

 Score = 51.1 bits (123), Expect = 3e-08
 Identities = 39/174 (22%), Positives = 53/174 (30%), Gaps = 71/174 (40%)

Query: 23  SPSDTEEVHVLAVDDSFVDRKVIERLLT-ISSCKV--TAVDSGRRALQFLGLDEEQSING 79
           S      + VL VDDS   R V++ ++      KV   A D G  A++            
Sbjct: 19  SHMTDRVIRVLVVDDSAFMRMVLKDIIDSQPDMKVVGFAKD-GLEAVEKA---------- 67

Query: 80  FDGLKVDLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCF 139
              LK D+I  D  MP + G E LK I    P                            
Sbjct: 68  -IELKPDVITMDIEMPNLNGIEALKLIMKKAP---------------------------- 98

Query: 140 PFFFPSNNLEQDSSALREIPVVIMSS------ENILARIDRCLEDGAEDFIVKP 187
                               V+++SS         +      L +GA DFI KP
Sbjct: 99  ------------------TRVIMVSSLTEEGAAITI----EALRNGAVDFITKP 130

>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 = 51.5 bits (124), Expect = 3e-08
 Identities = 22/181 (12%), Positives = 54/181 (29%), Gaps = 59/181 (32%)

Query: 24  PSDTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGL 83
           P    + + L +DD+ V    + R L      V    +   AL+  G +           
Sbjct: 2   PGSMSDKNFLVIDDNEVFAGTLARGLERRGYAVRQAHNKDEALKLAGAE----------- 50

Query: 84  KVDLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFF 143
           K + I     +   +G  L+  +    P                                
Sbjct: 51  KFEFITVXLHLGNDSGLSLIAPLCDLQP-------------------------------- 78

Query: 144 PSNNLEQDSSALREIPVVIMSSE-NILARIDRCLEDGAEDFIVKPVKLSDV-KRIKDYLT 201
                        +  +++++   +I   +   ++DGA++++ KP  +  +   ++   +
Sbjct: 79  -------------DARILVLTGYASIATAVQ-AVKDGADNYLAKPANVESILAALQTNAS 124

Query: 202 R 202
            
Sbjct: 125 E 125

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

 Score = 49.8 bits (120), Expect = 5e-08
 Identities = 34/179 (18%), Positives = 54/179 (30%), Gaps = 68/179 (37%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
            +L V+D  V R +++   +           G  AL+              G   DL+I 
Sbjct: 9   QILIVEDEQVFRSLLDSWFSSLGATTVLAADGVDALEL-----------LGGFTPDLMIC 57

Query: 91  DYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQ 150
           D  MP M G +LL+ I+                                           
Sbjct: 58  DIAMPRMNGLKLLEHIRNRGD--------------------------------------- 78

Query: 151 DSSALREIPVVIMSSENILAR---IDR--CLEDGAEDFIVKPVKLSD--VKRIKDYLTR 202
                 + PV+++S     A     D    L  G ED ++KPVK  +   + +   L  
Sbjct: 79  ------QTPVLVIS-----ATENMADIAKALRLGVEDVLLKPVKDLNRLREMVFACLYP 126

>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 = 49.9 bits (120), Expect = 6e-08
 Identities = 30/178 (16%), Positives = 55/178 (30%), Gaps = 66/178 (37%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
            +L +D     R  ++  L  S   V    + + AL+ +  D             DL+I 
Sbjct: 5   KILIIDQQDFSRIELKNFLD-SEYLVIESKNEKEALEQI--DHH---------HPDLVIL 52

Query: 91  DYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQ 150
           D  + G     L  K+K                                           
Sbjct: 53  DMDIIGENSPNLCLKLK------------------------------------------- 69

Query: 151 DSSALREIPVVIMSSENILAR---IDRC--LEDGAEDFIVKPVKLSDVK-RIKDYLTR 202
            S  L+ +P++++      +          L  GA+D++ KP   +D+  RI+ +L  
Sbjct: 70  RSKGLKNVPLILLF-----SSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRT 122

>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 = 49.4 bits (118), Expect = 7e-08
 Identities = 29/173 (16%), Positives = 52/173 (30%), Gaps = 57/173 (32%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
            +L VDD        +++L     +V    +    L  +   E +          +L + 
Sbjct: 5   RILIVDDDTAILDSTKQILEFEGYEVEIAATAGEGLAKI---ENEFF--------NLALF 53

Query: 91  DYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQ 150
              +P M G ELL+K     P                                       
Sbjct: 54  XIKLPDMEGTELLEKAHKLRP--------------------------------------- 74

Query: 151 DSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSDVK-RIKDYLTR 202
                  +  ++++    L      L  GA+ +I+KPV   D+  +IK+ L  
Sbjct: 75  ------GMKKIMVTGYASLENSVFSLNAGADAYIMKPVNPRDLLEKIKEKLDE 121

>2j48_A Two-component sensor kinase; pseudo-receiver, circadian clock, transferase, response regulator, histidine protein kinase; NMR {Synechococcus elongatus} Length = 119

 Score = 48.6 bits (117), Expect = 1e-07
 Identities = 23/176 (13%), Positives = 48/176 (27%), Gaps = 62/176 (35%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
           H+L +++      V+  +LT +  KV  +  G  AL              D L+  +I+ 
Sbjct: 3   HILLLEEEDEAATVVCEMLTAAGFKVIWLVDGSTALDQ-----------LDLLQPIVILM 51

Query: 91  DYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQ 150
            +  P  +   LL+ ++                                           
Sbjct: 52  AWPPPDQSCLLLLQHLR------------------------------------------- 68

Query: 151 DSSALREIPVVIMSSENILARID--RCLEDGAEDFIVKPVKLSD-VKRIKDYLTRD 203
           +  A    P+V+               L   A   + KP+     +  ++     +
Sbjct: 69  EHQADPHPPLVLFL-----GEPPVDPLLTAQASAILSKPLDPQLLLTTLQGLCPPN 119

>2qv0_A Protein MRKE; structural genomics, transcription, PSI-2, protein structure initiative; 2.40A {Klebsiella pneumoniae} Length = 143

 Score = 47.6 bits (114), Expect = 4e-07
 Identities = 25/93 (26%), Positives = 39/93 (41%), Gaps = 18/93 (19%)

Query: 32  VLAVDDSFVDRKVIERLL-TISSCKVTA-VDSGRRALQFLGLDEEQSINGFDGLKVDLII 89
           V+ V+D F+ ++ +  L+ T S  ++    D G   L+FL              KVD I 
Sbjct: 12  VIIVEDEFLAQQELSWLINTHSQMEIVGSFDDGLDVLKFL-----------QHNKVDAIF 60

Query: 90  TDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVF 122
            D  +P + G  L + I       F +   IVF
Sbjct: 61  LDINIPSLDGVLLAQNIS-----QFAHKPFIVF 88

>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 = 46.4 bits (111), Expect = 9e-07
 Identities = 18/98 (18%), Positives = 31/98 (31%), Gaps = 15/98 (15%)

Query: 26  DTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKV 85
             +   V  V+D      +I+  L     +VT   SG    Q                  
Sbjct: 12  HMQPFRVTLVEDEPSHATLIQYHLNQLGAEVTVHPSGSAFFQHRSQLS----------TC 61

Query: 86  DLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFL 123
           DL+I    +  ++ + LL  +K  T         ++ L
Sbjct: 62  DLLIVSDQLVDLSIFSLLDIVKEQTK-----QPSVLIL 94

>1xhf_A DYE resistance, aerobic respiration control protein ARCA; two-component system, gene regulation, transcription factor, anoxic redox control; 2.15A {Escherichia coli} SCOP: c.23.1.1 PDB: 1xhe_A Length = 123

 Score = 45.9 bits (110), Expect = 1e-06
 Identities = 16/79 (20%), Positives = 29/79 (36%), Gaps = 11/79 (13%)

Query: 28  EEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDL 87
           +  H+L V+D  V R  ++ +       V     G    Q                 ++L
Sbjct: 2   QTPHILIVEDELVTRNTLKSIFEAEGYDVFEATDGAEMHQI-----------LSEYDINL 50

Query: 88  IITDYCMPGMTGYELLKKI 106
           +I D  +PG  G  L +++
Sbjct: 51  VIMDINLPGKNGLLLAREL 69

>3cg0_A Response regulator receiver modulated diguanylate with PAS/PAC sensor; signal receiver domain, diguanylate cyclase; 2.15A {Desulfovibrio desulfuricans subsp} Length = 140

 Score = 45.6 bits (109), Expect = 1e-06
 Identities = 24/176 (13%), Positives = 49/176 (27%), Gaps = 60/176 (34%)

Query: 25  SDTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAV-DSGRRALQFLGLDEEQSINGFDGL 83
           +  +   VL V+D  +    +   L      V  V D+G  A++               L
Sbjct: 5   ASDDLPGVLIVEDGRLAAATLRIQLESLGYDVLGVFDNGEEAVRC-----------APDL 53

Query: 84  KVDLIITDYCMPG-MTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFF 142
           + D+ + D  + G + G E   ++                                    
Sbjct: 54  RPDIALVDIMLCGALDGVETAARLA----------------------------------- 78

Query: 143 FPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSDVK-RIK 197
                      A   +P++ ++S   +    R        ++ KPV    +   I+
Sbjct: 79  -----------AGCNLPIIFITSSQDVETFQRAKRVNPFGYLAKPVAADTLHRSIE 123

>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 = 45.6 bits (109), Expect = 2e-06
 Identities = 31/179 (17%), Positives = 59/179 (32%), Gaps = 60/179 (33%)

Query: 30  VHVLAVDDSFVDRKVIERLLTISSCK-VTAVDSGRRALQFLGLDEEQSINGFDGLKVDLI 88
           V +L V+D+ V+++VI+R+L +   + +     G+ A   +     +    ++     +I
Sbjct: 3   VKILVVEDNHVNQEVIKRMLNLEGIENIELACDGQEAFDKVKELTSKG-ENYN-----MI 56

Query: 89  ITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNL 148
             D  MP + G    K I+                                         
Sbjct: 57  FMDVQMPKVDGLLSTKMIR----------------------------------------- 75

Query: 149 EQDSSALREIPVVIMS----SENILARIDRCLEDGAEDFIVKPVKLSDVKR-IKDYLTR 202
                     P+V ++      N    I  CLE G   F+ KP+K   +K  + ++   
Sbjct: 76  ---RDLGYTSPIVALTAFADDSN----IKECLESGMNGFLSKPIKRPKLKTILTEFCAA 127

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

 Score = 45.4 bits (108), Expect = 2e-06
 Identities = 18/172 (10%), Positives = 43/172 (25%), Gaps = 57/172 (33%)

Query: 17  IDGFDLSPSDTEEVHVLAV-DDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQ 75
           ++  +   + T+   V     D    R V  RL  ++   V   ++              
Sbjct: 2   MNAINTKVTPTKRKQVALFSSDPNFKRDVATRLDALAIYDVRVSETDDFLKGPPADT--- 58

Query: 76  SINGFDGLKVDLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSI 135
                   +  ++I D     + G   + + +                            
Sbjct: 59  --------RPGIVILDLGGGDLLGKPGIVEAR---------------------------- 82

Query: 136 CFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKP 187
                            +    +P++ +S E    +    +   A D++ KP
Sbjct: 83  -----------------ALWATVPLIAVSDELTSEQTRVLVRMNASDWLHKP 117

>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 = 44.8 bits (107), Expect = 2e-06
 Identities = 16/76 (21%), Positives = 28/76 (36%), Gaps = 11/76 (14%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
           H++ V+D  V +  ++   T     V+   SG    +                 VDLI+ 
Sbjct: 4   HIVIVEDEPVTQARLQSYFTQEGYTVSVTASGAGLREI-----------MQNQSVDLILL 52

Query: 91  DYCMPGMTGYELLKKI 106
           D  +P   G  L + +
Sbjct: 53  DINLPDENGLMLTRAL 68

>3cg4_A Response regulator receiver domain protein (CHEY-; structural genomics, unknown function; HET: MSE; 1.61A {Methanospirillum hungatei jf-1} Length = 142

 Score = 45.2 bits (108), Expect = 3e-06
 Identities = 28/178 (15%), Positives = 63/178 (35%), Gaps = 65/178 (36%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
            V+ VDD    R  ++ +L+ +   + + DSG + +  L   ++            +++ 
Sbjct: 9   DVMIVDDDAHVRIAVKTILSDAGFHIISADSGGQCIDLL---KKG--------FSGVVLL 57

Query: 91  DYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQ 150
           D  MPGM G++ ++ I                                            
Sbjct: 58  DIMMPGMDGWDTIRAIL------------------------------------------- 74

Query: 151 DSSALREIPVVIMSSENILAR---IDRC--LEDGAEDFIVKPVKLSD-VKRIKDYLTR 202
           D+S  + I +V+++     A+     +   L++   D+I KP    D +++   ++  
Sbjct: 75  DNSLEQGIAIVMLT-----AKNAPDAKMIGLQEYVVDYITKPFDNEDLIEKTTFFMGF 127

>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 = 45.1 bits (107), Expect = 6e-06
 Identities = 29/166 (17%), Positives = 56/166 (33%), Gaps = 58/166 (34%)

Query: 32  VLAVDDSFVDRKVIERLLTISSCKVTA-VDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
           VL  +D  + R  +  +L     ++      G+ A++   L E          K DL+I 
Sbjct: 16  VLIAEDEALIRMDLAEMLREEGYEIVGEAGDGQEAVE---LAEL--------HKPDLVIM 64

Query: 91  DYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQ 150
           D  MP   G +   +I                                            
Sbjct: 65  DVKMPRRDGIDAASEI-------------------------------------------- 80

Query: 151 DSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSDVKRI 196
             ++ R  P+V++++ +    ++R  + GA  ++VKP  +SD+   
Sbjct: 81  --ASKRIAPIVVLTAFSQRDLVERARDAGAMAYLVKPFSISDLIPA 124

>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 = 45.1 bits (106), Expect = 9e-06
 Identities = 40/211 (18%), Positives = 69/211 (32%), Gaps = 69/211 (32%)

Query: 23  SPSDTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDG 82
             + T E  VL VDD   +  ++E L                +L+F G +   + NG   
Sbjct: 17  GENTTPEARVLVVDD---EANIVELL--------------SVSLKFQGFEVYTATNGAQA 59

Query: 83  LKV------DLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSIC 136
           L        D +I D  MPGM G+ +L++++                             
Sbjct: 60  LDRARETRPDAVILDVXMPGMDGFGVLRRLRADGI------------------------- 94

Query: 137 FCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSD-VKR 195
                               + P + +++ + L      L  G +D++ KP  L + V R
Sbjct: 95  --------------------DAPALFLTARDSLQDKIAGLTLGGDDYVTKPFSLEEVVAR 134

Query: 196 IKDYLTRDVNLGNEGRGINKRKARESCDLSS 226
           ++  L R      E R +    A    D  +
Sbjct: 135 LRVILRRAGKGNKEPRNVRLTFADIELDEET 165

>3sy8_A ROCR; TIM barrel phosphodiesterase-A, transcription regulator; HET: EPE; 2.50A {Pseudomonas aeruginosa} Length = 400

 Score = 45.0 bits (107), Expect = 1e-05
 Identities = 18/76 (23%), Positives = 28/76 (36%), Gaps = 11/76 (14%)

Query: 29  EVHVLAVDDSFVDRKVIERLL-TISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDL 87
           +++VL ++D    R V    L  +    +     G+ A+  L               VD+
Sbjct: 3   DLNVLVLEDEPFQRLVAVTALKKVVPGSILEAADGKEAVAILESCGH----------VDI 52

Query: 88  IITDYCMPGMTGYELL 103
            I D  M GM G   L
Sbjct: 53  AICDLQMSGMDGLAFL 68

>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 = 44.1 bits (105), Expect = 2e-05
 Identities = 33/178 (18%), Positives = 63/178 (35%), Gaps = 68/178 (38%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
            +L VDD     +++  +L         +  G +AL                L+ DL++ 
Sbjct: 7   RILVVDDDASLAEMLTIVLRGEGFDTAVIGDGTQALTA-----------VRELRPDLVLL 55

Query: 91  DYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQ 150
           D  +PGM G ++ + ++                                           
Sbjct: 56  DLMLPGMNGIDVCRVLR------------------------------------------- 72

Query: 151 DSSALREIPVVIMSSENILAR---IDRC--LEDGAEDFIVKPVKLSDVK-RIKDYLTR 202
              A   +P+V+++     A+   +D    LE GA+D+I+KP K  ++  R++  L R
Sbjct: 73  ---ADSGVPIVMLT-----AKTDTVDVVLGLESGADDYIMKPFKPKELVARVRARLRR 122

>3lte_A Response regulator; structural genomics, PSI, protein structure initiative, NYSG YORK structural genomix research consortium, nysgxrc; 2.00A {Bermanella marisrubri} Length = 132

 Score = 42.2 bits (100), Expect = 2e-05
 Identities = 24/178 (13%), Positives = 51/178 (28%), Gaps = 66/178 (37%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
            +L VDD       IER+L     +V    +G  A                  +  ++  
Sbjct: 8   RILVVDDDQAMAAAIERVLKRDHWQVEIAHNGFDAGIK-----------LSTFEPAIMTL 56

Query: 91  DYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQ 150
           D  MP + G ++++ ++                                           
Sbjct: 57  DLSMPKLDGLDVIRSLR------------------------------------------- 73

Query: 151 DSSALREIPVVIMSSENILAR---IDRC--LEDGAEDFIVKPVKLSDVK-RIKDYLTR 202
             + +   P +++      +          + +GA+D++ KP     +  RI D +  
Sbjct: 74  -QNKVANQPKILVV-----SGLDKAKLQQAVTEGADDYLEKPFDNDALLDRIHDLVNE 125

>2qzj_A Two-component response regulator; 11017X, PSI-II, structural genomics; 2.89A {Clostridium difficile} Length = 136

 Score = 42.5 bits (101), Expect = 2e-05
 Identities = 15/83 (18%), Positives = 27/83 (32%), Gaps = 13/83 (15%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
            +L +D    + + ++  L      +    +   A+                 K DLI  
Sbjct: 6   KILIIDGDKDNCQKLKGFLEEKGISIDLAYNCEEAIGK-----------IFSNKYDLIFL 54

Query: 91  DYCMPGMTGYELLKKI--KVTTP 111
           +  +    G+ L KKI    T P
Sbjct: 55  EIILSDGDGWTLCKKIRNVTTCP 77

>3a10_A Response regulator; phosphoacceptor, signaling protein; HET: MSE PG4; 1.63A {Thermotoga maritima} PDB: 3a0r_B* 3a0u_A* Length = 116

 Score = 41.7 bits (99), Expect = 3e-05
 Identities = 20/77 (25%), Positives = 36/77 (46%), Gaps = 11/77 (14%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
            +L VDD    R++++  L     ++   ++G  AL+            F     DL+I 
Sbjct: 3   RILVVDDEPNIRELLKEELQEEGYEIDTAENGEEALKK-----------FFSGNYDLVIL 51

Query: 91  DYCMPGMTGYELLKKIK 107
           D  MPG++G E+  +I+
Sbjct: 52  DIEMPGISGLEVAGEIR 68

>3kto_A Response regulator receiver protein; PSI-II,structural genomics, protein structure initiative; 1.98A {Pseudoalteromonas atlantica T6C} Length = 136

 Score = 41.4 bits (98), Expect = 4e-05
 Identities = 24/170 (14%), Positives = 46/170 (27%), Gaps = 64/170 (37%)

Query: 25  SDTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLK 84
           S      +  VD     R  + +LL+     +    S    ++    D+           
Sbjct: 2   SLNHHPIIYLVDHQKDARAALSKLLSPLDVTIQCFASAESFMRQQISDDA---------- 51

Query: 85  VDLIITDYCMPGM--TGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFF 142
              +I +  +     +G ELL+ +                                    
Sbjct: 52  -IGMIIEAHLEDKKDSGIELLETLV----------------------------------- 75

Query: 143 FPSNNLEQDSSALREIPVVIMSSENILARID---RCLEDGAEDFIVKPVK 189
                 ++       +P ++M+S    + I    R +   A DFI KP  
Sbjct: 76  ------KRGF----HLPTIVMASS---SDIPTAVRAMRASAADFIEKPFI 112

>2oqr_A Sensory transduction protein REGX3; response regulator, winged-helix-turn-helix, DNA-binding, 3D swapping, two component system; 2.03A {Mycobacterium tuberculosis H37RV} Length = 230

 Score = 42.9 bits (102), Expect = 4e-05
 Identities = 33/162 (20%), Positives = 55/162 (33%), Gaps = 67/162 (41%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
            VL V+D       +  LL     + T V  G  AL             FD    D+++ 
Sbjct: 6   SVLIVEDEESLADPLAFLLRKEGFEATVVTDGPAALAE-----------FDRAGADIVLL 54

Query: 91  DYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQ 150
           D  +PGM+G ++ K+++                                           
Sbjct: 55  DLMLPGMSGTDVCKQLRAR----------------------------------------- 73

Query: 151 DSSALREIPVVIMSSENILAR---IDRC--LEDGAEDFIVKP 187
                  +PV++++     AR   ID+   LE GA+D++ KP
Sbjct: 74  -----SSVPVIMVT-----ARDSEIDKVVGLELGADDYVTKP 105

>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 = 41.3 bits (98), Expect = 4e-05
 Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 11/77 (14%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
            +L VDD      +I+  +T    +V    +GR AL+            F+  + D+II 
Sbjct: 3   KILIVDDEKPISDIIKFNMTKEGYEVVTAFNGREALEQ-----------FEAEQPDIIIL 51

Query: 91  DYCMPGMTGYELLKKIK 107
           D  +P + G E+ K I+
Sbjct: 52  DLMLPEIDGLEVAKTIR 68

>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 = 42.8 bits (101), Expect = 5e-05
 Identities = 27/172 (15%), Positives = 46/172 (26%), Gaps = 66/172 (38%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAV-DSGRRALQFLGLDEEQSINGFDGLKVDLII 89
            VL ++D  V    IE L+      VT +  +   AL+                   L++
Sbjct: 162 EVLIIEDEPVIAADIEALVRELGHDVTDIAATRGEALEA-----------VTRRTPGLVL 210

Query: 90  TDYCMP-GMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNL 148
            D  +  G +G + +K I                                          
Sbjct: 211 ADIQLADGSSGIDAVKDIL----------------------------------------- 229

Query: 149 EQDSSALREIPVVIMS--SENILARIDRCLEDGAEDFIVKPVKLSDVK-RIK 197
                   ++PV+ ++   E    R+           I KP +   VK  I 
Sbjct: 230 -----GRMDVPVIFITAFPE----RLLTGERPEPTFLITKPFQPETVKAAIG 272

>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 = 40.9 bits (97), Expect = 5e-05
 Identities = 17/77 (22%), Positives = 32/77 (41%), Gaps = 11/77 (14%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
            +L VDD      ++E  L     +V     G  A++             + L+ DLI+ 
Sbjct: 4   KILVVDDEKPIADILEFNLRKEGYEVHCAHDGNEAVEM-----------VEELQPDLILL 52

Query: 91  DYCMPGMTGYELLKKIK 107
           D  +P   G E+ ++++
Sbjct: 53  DIMLPNKDGVEVCREVR 69

>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 = 40.1 bits (95), Expect = 1e-04
 Identities = 30/162 (18%), Positives = 53/162 (32%), Gaps = 67/162 (41%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
           +VL V+D    R+ +   L     +V   ++ +R L                 K DLII 
Sbjct: 3   NVLIVEDEQAIRRFLRTALEGDGMRVFEAETLQRGLLE-----------AATRKPDLIIL 51

Query: 91  DYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQ 150
           D  +P   G E ++ ++  +                                        
Sbjct: 52  DLGLPDGDGIEFIRDLRQWS---------------------------------------- 71

Query: 151 DSSALREIPVVIMSSENILAR---IDR--CLEDGAEDFIVKP 187
                  +PV+++S     AR    D+   L+ GA+D++ KP
Sbjct: 72  ------AVPVIVLS-----ARSEESDKIAALDAGADDYLSKP 102

>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 = 40.2 bits (95), Expect = 1e-04
 Identities = 19/77 (24%), Positives = 32/77 (41%), Gaps = 11/77 (14%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
            +L VDD      +++  L  S   V     G  AL+             +  K DLI+ 
Sbjct: 5   KILVVDDEESIVTLLQYNLERSGYDVITASDGEEALKK-----------AETEKPDLIVL 53

Query: 91  DYCMPGMTGYELLKKIK 107
           D  +P + G E+ K+++
Sbjct: 54  DVMLPKLDGIEVCKQLR 70

>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 = 39.8 bits (94), Expect = 2e-04
 Identities = 30/162 (18%), Positives = 52/162 (32%), Gaps = 64/162 (39%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
            +L VDD     +++E +L  +  +V    SG  ALQ                  D +I 
Sbjct: 6   TLLIVDDDDTVAEMLELVLRGAGYEVRRAASGEEALQQ-----------IYKNLPDALIC 54

Query: 91  DYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQ 150
           D  +PG+ GY L K+++                                           
Sbjct: 55  DVLLPGIDGYTLCKRVR------------------------------------------- 71

Query: 151 DSSALREIPVVIMSSENILAR---IDRC--LEDGAEDFIVKP 187
                + +P ++M +    A+     +    E GA D++ KP
Sbjct: 72  QHPLTKTLP-ILMLT----AQGDISAKIAGFEAGANDYLAKP 108

>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 = 39.4 bits (93), Expect = 2e-04
 Identities = 31/162 (19%), Positives = 54/162 (33%), Gaps = 64/162 (39%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
            +L V+D    R+++  +L  +  +    +    A+              +    DLI+ 
Sbjct: 4   RILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQ-----------LNEPWPDLILL 52

Query: 91  DYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQ 150
            + +PG +G + +K ++                                           
Sbjct: 53  AWMLPGGSGIQFIKHLR------------------------------------------- 69

Query: 151 DSSALREIPVVIMSSENILAR---IDRC--LEDGAEDFIVKP 187
             S  R+IP V+M +    AR    DR   LE GA+D I KP
Sbjct: 70  RESMTRDIP-VVMLT----ARGEEEDRVRGLETGADDCITKP 106

>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 = 40.6 bits (96), Expect = 2e-04
 Identities = 21/101 (20%), Positives = 35/101 (34%), Gaps = 26/101 (25%)

Query: 24  PSDTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGL 83
            +      VL VDD   D  V+  L               R L+  G +   +++G + L
Sbjct: 2   DTGVTSPRVLVVDD---DSDVLASL--------------ERGLRLSGFEVATAVDGAEAL 44

Query: 84  KV------DLIITDYCMPGMTGYELLKKI---KVTTPFNFL 115
           +       D I+ D  MP + G  ++  +       P   L
Sbjct: 45  RSATENRPDAIVLDINMPVLDGVSVVTALRAMDNDVPVCVL 85

>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 = 40.1 bits (95), Expect = 3e-04
 Identities = 22/87 (25%), Positives = 35/87 (40%), Gaps = 20/87 (22%)

Query: 31  HVLAVDDSFVDRKV---IERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDL 87
            VL V+D   +R +   I   L      V     G   + ++ L+E            D+
Sbjct: 4   RVLVVED---ERDLADLITEALKKEMFTVDVCYDGEEGM-YMALNEP----------FDV 49

Query: 88  IITDYCMPGMTGYELLKKI---KVTTP 111
           +I D  +P   G+E+LK +    V TP
Sbjct: 50  VILDIMLPVHDGWEILKSMRESGVNTP 76

>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 = 39.0 bits (92), Expect = 3e-04
 Identities = 25/174 (14%), Positives = 52/174 (29%), Gaps = 57/174 (32%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
            +L V+        +   L      V     G+ +++                + DL++ 
Sbjct: 7   KILIVESDTALSATLRSALEGRGFTVDETTDGKGSVEQ-----------IRRDRPDLVVL 55

Query: 91  DYCM-PGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLE 149
              +  G  GY +  K+K                                          
Sbjct: 56  AVDLSAGQNGYLICGKLK------------------------------------------ 73

Query: 150 QDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSD-VKRIKDYLTR 202
                L+ +P+VI+ + +  A+  R L+  A++++ KPV     V+R    +  
Sbjct: 74  -KDDDLKNVPIVIIGNPDGFAQH-RKLKAHADEYVAKPVDADQLVERAGALIGF 125

>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 = 38.2 bits (89), Expect = 6e-04
 Identities = 36/168 (21%), Positives = 60/168 (35%), Gaps = 55/168 (32%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
            VL VDDS V RK++   L     +V   ++G+ AL+ L    E           DLI+ 
Sbjct: 4   KVLLVDDSAVLRKIVSFNLKKEGYEVIEAENGQIALEKL---SEF--------TPDLIVL 52

Query: 91  DYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQ 150
              MP M G+ +LKK++                                           
Sbjct: 53  XIMMPVMDGFTVLKKLQ------------------------------------------- 69

Query: 151 DSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSD-VKRIK 197
           +    + IPV++++++         L  GA   + KP   S  ++ +K
Sbjct: 70  EKEEWKRIPVIVLTAKGGEEDESLALSLGARKVMRKPFSPSQFIEEVK 117

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	276
3to5_A	134	CHEY homolog; alpha(5)beta(5), chemotaxis, FLIM, p	99.95
3gl9_A	122	Response regulator; beta-sheet, surrounded by alph	99.9
3t6k_A	136	Response regulator receiver; flavodoxin-like, stru	99.9
3rqi_A	184	Response regulator protein; structural genomics, s	99.9
2r25_B	133	Osmosensing histidine protein kinase SLN1; alpha5-	99.89
3f6p_A	120	Transcriptional regulatory protein YYCF; unphospho	99.89
1dbw_A	126	Transcriptional regulatory protein FIXJ; doubly wo	99.89
2lpm_A	123	Two-component response regulator; transcription re	99.89
3m6m_D	143	Sensory/regulatory protein RPFC; RPFF, REC, enoyl-	99.88
3crn_A	132	Response regulator receiver domain protein, CHEY-;	99.88
3jte_A	143	Response regulator receiver protein; structural ge	99.88
2pl1_A	121	Transcriptional regulatory protein PHOP; CHEY-like	99.88
1i3c_A	149	Response regulator RCP1; phytochrome, signaling pr	99.88
3h1g_A	129	Chemotaxis protein CHEY homolog; sulfate-bound CHE	99.88
3hv2_A	153	Response regulator/HD domain protein; PSI-2, NYSGX	99.88
3kto_A	136	Response regulator receiver protein; PSI-II,struct	99.88
3eod_A	130	Protein HNR; response regulator, phosphoprotein, t	99.88
1srr_A	124	SPO0F, sporulation response regulatory protein; as	99.88
3gt7_A	154	Sensor protein; structural genomics, signal receiv	99.88
1jbe_A	128	Chemotaxis protein CHEY; signaling protein; 1.08A	99.87
3heb_A	152	Response regulator receiver domain protein (CHEY);	99.87
1xhf_A	123	DYE resistance, aerobic respiration control protei	99.87
3r0j_A	250	Possible two component system response transcript	99.87
1zgz_A	122	Torcad operon transcriptional regulatory protein;	99.87
1tmy_A	120	CHEY protein, TMY; chemotaxis, phosphoryl transfer	99.87
3i42_A	127	Response regulator receiver domain protein (CHEY-	99.87
2zay_A	147	Response regulator receiver protein; structural ge	99.87
3lua_A	140	Response regulator receiver protein; two-component	99.87
4e7p_A	150	Response regulator; DNA binding, cytosol, transcri	99.87
3grc_A	140	Sensor protein, kinase; protein structure initiati	99.87
3b2n_A	133	Uncharacterized protein Q99UF4; structural genomic	99.87
2rjn_A	154	Response regulator receiver:metal-dependent phosph	99.87
3cnb_A	143	DNA-binding response regulator, MERR family; signa	99.87
3kht_A	144	Response regulator; PSI-II, 11023K, structural gen	99.87
3cfy_A	137	Putative LUXO repressor protein; structural genomi	99.87
1p6q_A	129	CHEY2; chemotaxis, signal transduction, response r	99.86
3mm4_A	206	Histidine kinase homolog; receiver domain, CKI1, c	99.86
3hdg_A	137	Uncharacterized protein; two-component sensor acti	99.86
3luf_A	259	Two-component system response regulator/ggdef doma	99.86
2ayx_A	254	Sensor kinase protein RCSC; two independent struct	99.86
3ilh_A	146	Two component response regulator; NYSGXRC, PSI-II,	99.86
1k68_A	140	Phytochrome response regulator RCPA; phosphorylate	99.86
3hdv_A	136	Response regulator; PSI-II, structural genomics, P	99.86
3snk_A	135	Response regulator CHEY-like protein; P-loop conta	99.86
2a9o_A	120	Response regulator; essential protein, YYCF/YYCG h	99.86
4dad_A	146	Putative pilus assembly-related protein; response	99.86
1dcf_A	136	ETR1 protein; beta-alpha five sandwich, transferas	99.86
3f6c_A	134	Positive transcription regulator EVGA; structural	99.86
1qkk_A	155	DCTD, C4-dicarboxylate transport transcriptional r	99.86
3hzh_A	157	Chemotaxis response regulator (CHEY-3); phosphatas	99.86
1k66_A	149	Phytochrome response regulator RCPB; CHEY homologu	99.86
2qzj_A	136	Two-component response regulator; 11017X, PSI-II,	99.85
1mvo_A	136	PHOP response regulator; phosphate regulon, transc	99.85
1yio_A	208	Response regulatory protein; transcription regulat	99.85
2jba_A	127	Phosphate regulon transcriptional regulatory PROT;	99.85
1mb3_A	124	Cell division response regulator DIVK; signal tran	99.85
2qr3_A	140	Two-component system response regulator; structura	99.85
3h5i_A	140	Response regulator/sensory box protein/ggdef domai	99.85
3c3m_A	138	Response regulator receiver protein; structural ge	99.85
3kcn_A	151	Adenylate cyclase homolog; SGX, PSI 2, structural	99.85
3n0r_A	286	Response regulator; sigma factor, receiver, two-co	99.85
1dz3_A	130	Stage 0 sporulation protein A; response regulator,	99.85
2qxy_A	142	Response regulator; regulation of transcription, N	99.85
1zh2_A	121	KDP operon transcriptional regulatory protein KDPE	99.85
3cg0_A	140	Response regulator receiver modulated diguanylate	99.85
3nhm_A	133	Response regulator; protein structure initiative I	99.85
1a04_A	215	Nitrate/nitrite response regulator protein NARL; s	99.85
3cg4_A	142	Response regulator receiver domain protein (CHEY-;	99.84
3eul_A	152	Possible nitrate/nitrite response transcriptional	99.84
3lte_A	132	Response regulator; structural genomics, PSI, prot	99.84
3n53_A	140	Response regulator receiver modulated diguanylate;	99.84
3a10_A	116	Response regulator; phosphoacceptor, signaling pro	99.84
3eq2_A	394	Probable two-component response regulator; adaptor	99.84
3cu5_A	141	Two component transcriptional regulator, ARAC FAM;	99.84
3eqz_A	135	Response regulator; structural genomics, unknown f	99.84
2jk1_A	139	HUPR, hydrogenase transcriptional regulatory prote	99.84
1kgs_A	225	DRRD, DNA binding response regulator D; DNA-bindin	99.84
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	99.84
3q9s_A	249	DNA-binding response regulator; DNA binding protei	99.84
3cz5_A	153	Two-component response regulator, LUXR family; str	99.83
1ys7_A	233	Transcriptional regulatory protein PRRA; response	99.83
2qvg_A	143	Two component response regulator; NYSGXRC, PSI-2,	99.83
2gkg_A	127	Response regulator homolog; social motility, recei	99.83
1s8n_A	205	Putative antiterminator; RV1626, structural genomi	99.83
2qsj_A	154	DNA-binding response regulator, LUXR family; struc	99.82
2rdm_A	132	Response regulator receiver protein; structural ge	99.82
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	99.82
3kyj_B	145	CHEY6 protein, putative histidine protein kinase;	99.81
3klo_A	225	Transcriptional regulator VPST; REC domain, HTH do	99.81
1w25_A	459	Stalked-cell differentiation controlling protein;	99.81
2qv0_A	143	Protein MRKE; structural genomics, transcription,	99.81
3c97_A	140	Signal transduction histidine kinase; structural g	99.81
3bre_A	358	Probable two-component response regulator; protein	99.8
2oqr_A	230	Sensory transduction protein REGX3; response regul	99.8
1dc7_A	124	NTRC, nitrogen regulation protein; receiver domain	99.79
3sy8_A	400	ROCR; TIM barrel phosphodiesterase-A, transcriptio	99.79
1p2f_A	220	Response regulator; DRRB, OMPR/PHOB, transcription	99.79
3c3w_A	225	Two component transcriptional regulatory protein;	99.79
2j48_A	119	Two-component sensor kinase; pseudo-receiver, circ	99.78
2b4a_A	138	BH3024; flavodoxin-like fold, structural genomics,	99.78
2gwr_A	238	DNA-binding response regulator MTRA; two-component	99.78
3t8y_A	164	CHEB, chemotaxis response regulator protein-glutam	99.78
2pln_A	137	HP1043, response regulator; signaling protein; 1.8	99.77
1qo0_D	196	AMIR; binding protein, gene regulator, receptor; 2	99.75
2hqr_A	223	Putative transcriptional regulator; phosporylation	99.75
1a2o_A	349	CHEB methylesterase; bacterial chemotaxis, adaptat	99.72
3luf_A	259	Two-component system response regulator/ggdef doma	99.71
2vyc_A	755	Biodegradative arginine decarboxylase; pyridoxal p	99.65
1w25_A	459	Stalked-cell differentiation controlling protein;	99.22
3cwo_X	237	Beta/alpha-barrel protein based on 1THF and 1TMY;	99.2
2ayx_A	254	Sensor kinase protein RCSC; two independent struct	97.58
3n75_A	715	LDC, lysine decarboxylase, inducible; pyridoxal-5'	97.42
2yxb_A	161	Coenzyme B12-dependent mutase; alpha/beta, structu	96.12
3cwo_X	237	Beta/alpha-barrel protein based on 1THF and 1TMY;	95.78
3q7r_A	121	Transcriptional regulatory protein; CHXR, receiver	94.58
1ccw_A	137	Protein (glutamate mutase); coenzyme B12, radical	93.28
3q58_A	229	N-acetylmannosamine-6-phosphate 2-epimerase; TIM b	91.31
1wv2_A	265	Thiazole moeity, thiazole biosynthesis protein THI	90.93
3igs_A	232	N-acetylmannosamine-6-phosphate 2-epimerase 2; ene	89.53
2ekc_A	262	AQ_1548, tryptophan synthase alpha chain; structur	88.2
2htm_A	268	Thiazole biosynthesis protein THIG; thiamin biosyn	86.66
3vnd_A	267	TSA, tryptophan synthase alpha chain; psychrophili	86.48
1req_A	727	Methylmalonyl-COA mutase; isomerase, intramolecula	85.35
1qop_A	268	Tryptophan synthase alpha chain; lyase, carbon-oxy	84.89
2i2x_B	258	MTAC, methyltransferase 1; TIM barrel and helix bu	84.67
2xij_A	762	Methylmalonyl-COA mutase, mitochondrial; isomerase	84.63
1geq_A	248	Tryptophan synthase alpha-subunit; hyperthermophIl	84.56
3f4w_A	211	Putative hexulose 6 phosphate synthase; humps, mal	82.2
3nav_A	271	Tryptophan synthase alpha chain; alpha subunit, st	81.15
3qja_A	272	IGPS, indole-3-glycerol phosphate synthase; struct	80.88
1y80_A	210	Predicted cobalamin binding protein; corrinoid, fa	80.62

>3to5_A CHEY homolog; alpha(5)beta(5), chemotaxis, FLIM, phosphorylation, motor AC signaling protein; 1.65A {Vibrio cholerae}

Probab=99.95  E-value=3.4e-27  Score=194.64  Aligned_cols=120  Identities=30%  Similarity=0.526  Sum_probs=108.4

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhCCCE-EEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHH
Q 023816           28 EEVHVLAVDDSFVDRKVIERLLTISSCK-VTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKI  106 (276)
Q Consensus        28 ~~~~VLIVdD~~~~~~~L~~~L~~~g~~-v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~I  106 (276)
                      +.+|||||||++.+|+.++.+|+..||+ +..|.||.+|++.+           +...||+||+|++||+|||+|++++|
T Consensus        11 k~~rILiVDD~~~~r~~l~~~L~~~G~~~v~~a~~g~~al~~~-----------~~~~~DlillD~~MP~mdG~el~~~i   79 (134)
T 3to5_A           11 KNMKILIVDDFSTMRRIVKNLLRDLGFNNTQEADDGLTALPML-----------KKGDFDFVVTDWNMPGMQGIDLLKNI   79 (134)
T ss_dssp             TTCCEEEECSCHHHHHHHHHHHHHTTCCCEEEESSHHHHHHHH-----------HHHCCSEEEEESCCSSSCHHHHHHHH
T ss_pred             CCCEEEEEeCCHHHHHHHHHHHHHcCCcEEEEECCHHHHHHHH-----------HhCCCCEEEEcCCCCCCCHHHHHHHH
Confidence            4689999999999999999999999996 66799999999999           56689999999999999999999999


Q ss_pred             HhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeC
Q 023816          107 KVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVK  186 (276)
Q Consensus       107 r~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~K  186 (276)
                      |...                                           ..+++|||++|++...+...+|+++||+|||.|
T Consensus        80 r~~~-------------------------------------------~~~~ipvI~lTa~~~~~~~~~~~~~Ga~~yl~K  116 (134)
T 3to5_A           80 RADE-------------------------------------------ELKHLPVLMITAEAKREQIIEAAQAGVNGYIVK  116 (134)
T ss_dssp             HHST-------------------------------------------TTTTCCEEEEESSCCHHHHHHHHHTTCCEEEES
T ss_pred             HhCC-------------------------------------------CCCCCeEEEEECCCCHHHHHHHHHCCCCEEEEC
Confidence            9632                                           234799999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHH
Q 023816          187 PVKLSDVKRIKDYLT  201 (276)
Q Consensus       187 Pv~~~~L~~~~~~l~  201 (276)
                      |++.++|...+..+.
T Consensus       117 P~~~~~L~~~i~~~l  131 (134)
T 3to5_A          117 PFTAATLKEKLDKIF  131 (134)
T ss_dssp             SCCHHHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHH
Confidence            999999977766554

>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=99.90  E-value=8.4e-23  Score=158.60  Aligned_cols=118  Identities=30%  Similarity=0.392  Sum_probs=107.2

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhh
Q 023816           30 VHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVT  109 (276)
Q Consensus        30 ~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~  109 (276)
                      .+||||||++..++.++.+|+..||++..+.++++|++.+           ....||+||+|+.||+++|++++++||+.
T Consensus         3 ~~ILivdd~~~~~~~l~~~l~~~g~~v~~~~~~~~al~~l-----------~~~~~dlvllD~~~p~~~g~~~~~~l~~~   71 (122)
T 3gl9_A            3 KKVLLVDDSAVLRKIVSFNLKKEGYEVIEAENGQIALEKL-----------SEFTPDLIVLXIMMPVMDGFTVLKKLQEK   71 (122)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHH-----------TTBCCSEEEECSCCSSSCHHHHHHHHHTS
T ss_pred             ceEEEEeCCHHHHHHHHHHHHHCCcEEEEeCCHHHHHHHH-----------HhcCCCEEEEeccCCCCcHHHHHHHHHhc
Confidence            4899999999999999999999999999999999999999           67789999999999999999999999963


Q ss_pred             CCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCC
Q 023816          110 TPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVK  189 (276)
Q Consensus       110 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~  189 (276)
                      ..                                           .+.+|||++|+........++++.|+++|+.||++
T Consensus        72 ~~-------------------------------------------~~~~pii~~s~~~~~~~~~~~~~~Ga~~~l~KP~~  108 (122)
T 3gl9_A           72 EE-------------------------------------------WKRIPVIVLTAKGGEEDESLALSLGARKVMRKPFS  108 (122)
T ss_dssp             TT-------------------------------------------TTTSCEEEEESCCSHHHHHHHHHTTCSEEEESSCC
T ss_pred             cc-------------------------------------------ccCCCEEEEecCCchHHHHHHHhcChhhhccCCCC
Confidence            21                                           23789999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHH
Q 023816          190 LSDVKRIKDYLT  201 (276)
Q Consensus       190 ~~~L~~~~~~l~  201 (276)
                      .++|...+..+.
T Consensus       109 ~~~L~~~i~~~l  120 (122)
T 3gl9_A          109 PSQFIEEVKHLL  120 (122)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHh
Confidence            999976666543

>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=99.90  E-value=5.5e-23  Score=162.40  Aligned_cols=122  Identities=23%  Similarity=0.379  Sum_probs=109.2

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHH
Q 023816           27 TEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKI  106 (276)
Q Consensus        27 ~~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~I  106 (276)
                      |.+.+||||||++..++.++.+|+..||+|..+.++++|++.+           ....||+||+|+.||+++|++++++|
T Consensus         2 m~~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~-----------~~~~~dlvl~D~~lp~~~g~~~~~~l   70 (136)
T 3t6k_A            2 MKPHTLLIVDDDDTVAEMLELVLRGAGYEVRRAASGEEALQQI-----------YKNLPDALICDVLLPGIDGYTLCKRV   70 (136)
T ss_dssp             -CCCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHH-----------HHSCCSEEEEESCCSSSCHHHHHHHH
T ss_pred             CCCCEEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHH-----------HhCCCCEEEEeCCCCCCCHHHHHHHH
Confidence            4568999999999999999999999999999999999999998           56689999999999999999999999


Q ss_pred             HhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeC
Q 023816          107 KVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVK  186 (276)
Q Consensus       107 r~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~K  186 (276)
                      |+..                                           ....+|||++|+..+.....++++.|+++||.|
T Consensus        71 r~~~-------------------------------------------~~~~~pii~~t~~~~~~~~~~~~~~ga~~~l~K  107 (136)
T 3t6k_A           71 RQHP-------------------------------------------LTKTLPILMLTAQGDISAKIAGFEAGANDYLAK  107 (136)
T ss_dssp             HHSG-------------------------------------------GGTTCCEEEEECTTCHHHHHHHHHHTCSEEEET
T ss_pred             HcCC-------------------------------------------CcCCccEEEEecCCCHHHHHHHHhcCcceEEeC
Confidence            9631                                           123789999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHH
Q 023816          187 PVKLSDVKRIKDYLTR  202 (276)
Q Consensus       187 Pv~~~~L~~~~~~l~~  202 (276)
                      |++.++|...+..+.+
T Consensus       108 P~~~~~L~~~i~~~l~  123 (136)
T 3t6k_A          108 PFEPQELVYRVKNILA  123 (136)
T ss_dssp             TCCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHh
Confidence            9999999777766554

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

Probab=99.90  E-value=3.1e-23  Score=172.77  Aligned_cols=122  Identities=17%  Similarity=0.307  Sum_probs=109.4

Q ss_pred             CCCCCccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHH
Q 023816           24 PSDTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELL  103 (276)
Q Consensus        24 ~~~~~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell  103 (276)
                      +..+.+.+||||||++..+..++.+|+..||.|..+.++.+|++.+           ....||+||+|+.||+++|++++
T Consensus         2 ~~~m~~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~-----------~~~~~dlvl~D~~lp~~~g~~~~   70 (184)
T 3rqi_A            2 PGSMSDKNFLVIDDNEVFAGTLARGLERRGYAVRQAHNKDEALKLA-----------GAEKFEFITVXLHLGNDSGLSLI   70 (184)
T ss_dssp             -----CCEEEEECSCHHHHHHHHHHHHHTTCEEEEECSHHHHHHHH-----------TTSCCSEEEECSEETTEESHHHH
T ss_pred             CCCCCCCeEEEEcCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHH-----------hhCCCCEEEEeccCCCccHHHHH
Confidence            3456788999999999999999999999999999999999999999           67789999999999999999999


Q ss_pred             HHHHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeE
Q 023816          104 KKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDF  183 (276)
Q Consensus       104 ~~Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~  183 (276)
                      ++||+..|                                             .+|||++|++.+.+...+|++.||++|
T Consensus        71 ~~l~~~~~---------------------------------------------~~~ii~lt~~~~~~~~~~a~~~Ga~~~  105 (184)
T 3rqi_A           71 APLCDLQP---------------------------------------------DARILVLTGYASIATAVQAVKDGADNY  105 (184)
T ss_dssp             HHHHHHCT---------------------------------------------TCEEEEEESSCCHHHHHHHHHHTCSEE
T ss_pred             HHHHhcCC---------------------------------------------CCCEEEEeCCCCHHHHHHHHHhCHHHh
Confidence            99998776                                             799999999999999999999999999


Q ss_pred             EeCCCCHHHHHHHHHHHH
Q 023816          184 IVKPVKLSDVKRIKDYLT  201 (276)
Q Consensus       184 l~KPv~~~~L~~~~~~l~  201 (276)
                      |.||++.++|...+..+.
T Consensus       106 l~KP~~~~~L~~~i~~~~  123 (184)
T 3rqi_A          106 LAKPANVESILAALQTNA  123 (184)
T ss_dssp             EESSCCHHHHHHHTSTTH
T ss_pred             eeCCCCHHHHHHHHHHHH
Confidence            999999999966655443

>2r25_B Osmosensing histidine protein kinase SLN1; alpha5-BETA5, response regulator, four helix bundle, histidine phosphotransfer (HPT) protein; 1.70A {Saccharomyces cerevisiae} SCOP: c.23.1.1 PDB: 1oxk_B 1oxb_B

Probab=99.89  E-value=1.6e-22  Score=159.26  Aligned_cols=122  Identities=26%  Similarity=0.429  Sum_probs=105.7

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhCCCE-EEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHH
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTISSCK-VTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIK  107 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~g~~-v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir  107 (276)
                      .++||||||++..+..++.+|+..|+. +..+.++.+|++.+.....      ....||+||+|+.||+++|++++++||
T Consensus         2 ~~~ILivdD~~~~~~~l~~~L~~~g~~~v~~~~~~~~al~~~~~~~~------~~~~~dlvllD~~mp~~~G~~~~~~lr   75 (133)
T 2r25_B            2 SVKILVVEDNHVNQEVIKRMLNLEGIENIELACDGQEAFDKVKELTS------KGENYNMIFMDVQMPKVDGLLSTKMIR   75 (133)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHTTCCCEEEESSHHHHHHHHHHHHH------HTCCCSEEEECSCCSSSCHHHHHHHHH
T ss_pred             CceEEEEcCCHHHHHHHHHHHHHcCCceEEEECCHHHHHHHHHHHHh------cCCCCCEEEEeCCCCCCChHHHHHHHH
Confidence            478999999999999999999999974 8889999999998832100      115799999999999999999999999


Q ss_pred             hh-CCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeC
Q 023816          108 VT-TPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVK  186 (276)
Q Consensus       108 ~~-~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~K  186 (276)
                      +. .+                                             .+|||++|++.......++++.|+++||.|
T Consensus        76 ~~~~~---------------------------------------------~~~ii~lt~~~~~~~~~~~~~~ga~~~l~K  110 (133)
T 2r25_B           76 RDLGY---------------------------------------------TSPIVALTAFADDSNIKECLESGMNGFLSK  110 (133)
T ss_dssp             HHSCC---------------------------------------------CSCEEEEESCCSHHHHHHHHHTTCSEEEES
T ss_pred             hhcCC---------------------------------------------CCCEEEEECCCCHHHHHHHHHcCCCEEEeC
Confidence            63 33                                             689999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHH
Q 023816          187 PVKLSDVKRIKDYLT  201 (276)
Q Consensus       187 Pv~~~~L~~~~~~l~  201 (276)
                      |++.++|.+.+..+.
T Consensus       111 P~~~~~L~~~l~~~~  125 (133)
T 2r25_B          111 PIKRPKLKTILTEFC  125 (133)
T ss_dssp             SCCHHHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHH
Confidence            999999987776654

>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=99.89  E-value=3e-22  Score=154.68  Aligned_cols=115  Identities=22%  Similarity=0.375  Sum_probs=105.5

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhh
Q 023816           30 VHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVT  109 (276)
Q Consensus        30 ~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~  109 (276)
                      .+||||||++..++.++..|+..||++..+.++++|++.+           ....||+||+|+.||+++|++++++||+.
T Consensus         3 ~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~-----------~~~~~dlii~D~~~p~~~g~~~~~~lr~~   71 (120)
T 3f6p_A            3 KKILVVDDEKPIADILEFNLRKEGYEVHCAHDGNEAVEMV-----------EELQPDLILLDIMLPNKDGVEVCREVRKK   71 (120)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHH-----------HTTCCSEEEEETTSTTTHHHHHHHHHHTT
T ss_pred             CeEEEEECCHHHHHHHHHHHHhCCEEEEEeCCHHHHHHHH-----------hhCCCCEEEEeCCCCCCCHHHHHHHHHhc
Confidence            5899999999999999999999999999999999999998           56789999999999999999999999952


Q ss_pred             CCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCC
Q 023816          110 TPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVK  189 (276)
Q Consensus       110 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~  189 (276)
                       .                                             ++|||++|+........++++.|+++||.||++
T Consensus        72 -~---------------------------------------------~~~ii~~t~~~~~~~~~~~~~~ga~~~l~KP~~  105 (120)
T 3f6p_A           72 -Y---------------------------------------------DMPIIMLTAKDSEIDKVIGLEIGADDYVTKPFS  105 (120)
T ss_dssp             -C---------------------------------------------CSCEEEEEESSCHHHHHHHHHTTCCEEEEESCC
T ss_pred             -C---------------------------------------------CCCEEEEECCCChHHHHHHHhCCcceeEcCCCC
Confidence             2                                             589999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHH
Q 023816          190 LSDVKRIKDYLT  201 (276)
Q Consensus       190 ~~~L~~~~~~l~  201 (276)
                      .++|...+..+.
T Consensus       106 ~~~l~~~i~~~l  117 (120)
T 3f6p_A          106 TRELLARVKANL  117 (120)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            999976665544

>1dbw_A Transcriptional regulatory protein FIXJ; doubly wound five-stranded beta/alpha fold, nitrogen fixatio regulation; HET: 15P; 1.60A {Sinorhizobium meliloti} SCOP: c.23.1.1 PDB: 1dck_A* 1dcm_A 1d5w_A*

Probab=99.89  E-value=8.4e-22  Score=152.19  Aligned_cols=119  Identities=25%  Similarity=0.377  Sum_probs=109.0

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHH
Q 023816           28 EEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIK  107 (276)
Q Consensus        28 ~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir  107 (276)
                      ...+||||||++..++.++..|+..||.+..+.++.++++.+           ....||+||+|+.||+++|++++++|+
T Consensus         2 ~~~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~-----------~~~~~dlvi~D~~l~~~~g~~~~~~l~   70 (126)
T 1dbw_A            2 QDYTVHIVDDEEPVRKSLAFMLTMNGFAVKMHQSAEAFLAFA-----------PDVRNGVLVTDLRMPDMSGVELLRNLG   70 (126)
T ss_dssp             CCCEEEEEESSHHHHHHHHHHHHHTTCEEEEESCHHHHHHHG-----------GGCCSEEEEEECCSTTSCHHHHHHHHH
T ss_pred             CCCEEEEEcCCHHHHHHHHHHHHhCCcEEEEeCCHHHHHHHH-----------hcCCCCEEEEECCCCCCCHHHHHHHHH
Confidence            357999999999999999999999999999999999999988           556799999999999999999999999


Q ss_pred             hhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCC
Q 023816          108 VTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKP  187 (276)
Q Consensus       108 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KP  187 (276)
                      +..|                                             .+|||++|+........++++.|+++||.||
T Consensus        71 ~~~~---------------------------------------------~~~ii~~s~~~~~~~~~~~~~~ga~~~l~Kp  105 (126)
T 1dbw_A           71 DLKI---------------------------------------------NIPSIVITGHGDVPMAVEAMKAGAVDFIEKP  105 (126)
T ss_dssp             HTTC---------------------------------------------CCCEEEEECTTCHHHHHHHHHTTCSEEEESS
T ss_pred             hcCC---------------------------------------------CCCEEEEECCCCHHHHHHHHHhCHHHheeCC
Confidence            8666                                             7999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHH
Q 023816          188 VKLSDVKRIKDYLTR  202 (276)
Q Consensus       188 v~~~~L~~~~~~l~~  202 (276)
                      ++.++|...+..+.+
T Consensus       106 ~~~~~l~~~i~~~~~  120 (126)
T 1dbw_A          106 FEDTVIIEAIERASE  120 (126)
T ss_dssp             CCHHHHHHHHHHHHT
T ss_pred             CCHHHHHHHHHHHHH
Confidence            999999777766543

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

Probab=99.89  E-value=8.4e-25  Score=178.57  Aligned_cols=112  Identities=17%  Similarity=0.204  Sum_probs=99.3

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhCCCEEE-EECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHH
Q 023816           28 EEVHVLAVDDSFVDRKVIERLLTISSCKVT-AVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKI  106 (276)
Q Consensus        28 ~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~-~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~I  106 (276)
                      .++|||||||++.+++.++.+|+..||+|+ .|.||++|++.+           ++..||+||+|++||+|||++++++|
T Consensus         7 r~~rILiVdD~~~~~~~l~~~L~~~G~~v~~~a~~g~eAl~~~-----------~~~~~DlvllDi~mP~~~G~el~~~l   75 (123)
T 2lpm_A            7 RRLRVLVVEDESMIAMLIEDTLCELGHEVAATASRMQEALDIA-----------RKGQFDIAIIDVNLDGEPSYPVADIL   75 (123)
T ss_dssp             CCCCEEEESSSTTTSHHHHHHHHHHCCCCCBCSCCHHHHHHHH-----------HHCCSSEEEECSSSSSCCSHHHHHHH
T ss_pred             CCCEEEEEeCCHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHH-----------HhCCCCEEEEecCCCCCCHHHHHHHH
Confidence            468999999999999999999999999986 699999999999           56789999999999999999999999


Q ss_pred             HhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeC
Q 023816          107 KVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVK  186 (276)
Q Consensus       107 r~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~K  186 (276)
                      |+  +                                             ++|||++|++.+...   +.++|+.+||.|
T Consensus        76 r~--~---------------------------------------------~ipvI~lTa~~~~~~---~~~~g~~~yl~K  105 (123)
T 2lpm_A           76 AE--R---------------------------------------------NVPFIFATGYGSKGL---DTRYSNIPLLTK  105 (123)
T ss_dssp             HH--T---------------------------------------------CCSSCCBCTTCTTSC---CSSSCSCSCBCS
T ss_pred             Hc--C---------------------------------------------CCCEEEEecCccHHH---HHhCCCCcEEEC
Confidence            96  1                                             589999999876543   457899999999


Q ss_pred             CCCHHHHHHHHHHH
Q 023816          187 PVKLSDVKRIKDYL  200 (276)
Q Consensus       187 Pv~~~~L~~~~~~l  200 (276)
                      |++.++|.+.+.++
T Consensus       106 P~~~~~L~~~l~~~  119 (123)
T 2lpm_A          106 PFLDSELEAVLVQI  119 (123)
T ss_dssp             SSSHHHHHHHHSTT
T ss_pred             CCCHHHHHHHHHHH
Confidence            99999997766544

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

Probab=99.88  E-value=4.1e-22  Score=159.03  Aligned_cols=123  Identities=31%  Similarity=0.518  Sum_probs=105.6

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHH
Q 023816           27 TEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKI  106 (276)
Q Consensus        27 ~~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~I  106 (276)
                      ...++||||||++..+..++.+|+..||.+..+.++++|++.+           ....||+||+|+.||+++|++++++|
T Consensus        12 ~~~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~-----------~~~~~dlvl~D~~mp~~~g~~~~~~l   80 (143)
T 3m6m_D           12 VRSMRMLVADDHEANRMVLQRLLEKAGHKVLCVNGAEQVLDAM-----------AEEDYDAVIVDLHMPGMNGLDMLKQL   80 (143)
T ss_dssp             ---CEEEEECSSHHHHHHHHHHHHC--CEEEEESSHHHHHHHH-----------HHSCCSEEEEESCCSSSCHHHHHHHH
T ss_pred             cccceEEEEeCCHHHHHHHHHHHHHcCCeEEEeCCHHHHHHHH-----------hcCCCCEEEEeCCCCCCCHHHHHHHH
Confidence            4568999999999999999999999999999999999999998           55689999999999999999999999


Q ss_pred             HhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeC
Q 023816          107 KVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVK  186 (276)
Q Consensus       107 r~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~K  186 (276)
                      |+..+                                         ...+.+|||++|+....+...++++.|+++||.|
T Consensus        81 r~~~~-----------------------------------------~~~~~~pii~~s~~~~~~~~~~~~~~Ga~~~l~K  119 (143)
T 3m6m_D           81 RVMQA-----------------------------------------SGMRYTPVVVLSADVTPEAIRACEQAGARAFLAK  119 (143)
T ss_dssp             HHHHH-----------------------------------------TTCCCCCEEEEESCCCHHHHHHHHHTTCSEEEES
T ss_pred             Hhchh-----------------------------------------ccCCCCeEEEEeCCCCHHHHHHHHHcChhheeeC
Confidence            95321                                         1223689999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHH
Q 023816          187 PVKLSDVKRIKDYLT  201 (276)
Q Consensus       187 Pv~~~~L~~~~~~l~  201 (276)
                      |++.++|...+..+.
T Consensus       120 P~~~~~L~~~l~~~~  134 (143)
T 3m6m_D          120 PVVAAKLLDTLADLA  134 (143)
T ss_dssp             SCCHHHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHH
Confidence            999999977776653

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

Probab=99.88  E-value=8.8e-22  Score=153.99  Aligned_cols=118  Identities=21%  Similarity=0.283  Sum_probs=108.6

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHh
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKV  108 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~  108 (276)
                      ..+||||||++..++.++.+|+..||.+..+.++.+|++.+           ....||+||+|+.||+++|++++++|++
T Consensus         3 ~~~Ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~-----------~~~~~dlvl~D~~l~~~~g~~~~~~l~~   71 (132)
T 3crn_A            3 LKRILIVDDDTAILDSTKQILEFEGYEVEIAATAGEGLAKI-----------ENEFFNLALFXIKLPDMEGTELLEKAHK   71 (132)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHH-----------HHSCCSEEEECSBCSSSBHHHHHHHHHH
T ss_pred             ccEEEEEeCCHHHHHHHHHHHHHCCceEEEeCCHHHHHHHH-----------hcCCCCEEEEecCCCCCchHHHHHHHHh
Confidence            57899999999999999999999999999999999999998           4567999999999999999999999998


Q ss_pred             hCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCC
Q 023816          109 TTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPV  188 (276)
Q Consensus       109 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv  188 (276)
                      ..+                                             .+|||++|+........++++.|+++||.||+
T Consensus        72 ~~~---------------------------------------------~~~ii~~s~~~~~~~~~~~~~~ga~~~l~KP~  106 (132)
T 3crn_A           72 LRP---------------------------------------------GMKKIMVTGYASLENSVFSLNAGADAYIMKPV  106 (132)
T ss_dssp             HCT---------------------------------------------TSEEEEEESCCCHHHHHHHHHTTCSEEEESSC
T ss_pred             hCC---------------------------------------------CCcEEEEeccccHHHHHHHHhccchhhccCCC
Confidence            666                                             79999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHH
Q 023816          189 KLSDVKRIKDYLTR  202 (276)
Q Consensus       189 ~~~~L~~~~~~l~~  202 (276)
                      +.++|...++.+.+
T Consensus       107 ~~~~L~~~i~~~~~  120 (132)
T 3crn_A          107 NPRDLLEKIKEKLD  120 (132)
T ss_dssp             CHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHh
Confidence            99999777666543

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

Probab=99.88  E-value=1.6e-21  Score=153.27  Aligned_cols=125  Identities=25%  Similarity=0.395  Sum_probs=112.0

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHH
Q 023816           27 TEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKI  106 (276)
Q Consensus        27 ~~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~I  106 (276)
                      |.+++||||||++..++.++.+|+..|+.+..+.++.+|++.+..         ....||+||+|+.||+++|++++++|
T Consensus         1 M~~~~ilivdd~~~~~~~l~~~l~~~g~~v~~~~~~~~a~~~~~~---------~~~~~dlvi~d~~l~~~~g~~~~~~l   71 (143)
T 3jte_A            1 MSLAKILVIDDESTILQNIKFLLEIDGNEVLTASSSTEGLRIFTE---------NCNSIDVVITDMKMPKLSGMDILREI   71 (143)
T ss_dssp             --CCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHH---------TTTTCCEEEEESCCSSSCHHHHHHHH
T ss_pred             CCCCEEEEEcCCHHHHHHHHHHHHhCCceEEEeCCHHHHHHHHHh---------CCCCCCEEEEeCCCCCCcHHHHHHHH
Confidence            346899999999999999999999999999999999999999821         15689999999999999999999999


Q ss_pred             HhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeC
Q 023816          107 KVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVK  186 (276)
Q Consensus       107 r~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~K  186 (276)
                      |+..|                                             .+|||++|+........++++.|+++||.|
T Consensus        72 ~~~~~---------------------------------------------~~~ii~ls~~~~~~~~~~~~~~g~~~~l~k  106 (143)
T 3jte_A           72 KKITP---------------------------------------------HMAVIILTGHGDLDNAILAMKEGAFEYLRK  106 (143)
T ss_dssp             HHHCT---------------------------------------------TCEEEEEECTTCHHHHHHHHHTTCSEEEES
T ss_pred             HHhCC---------------------------------------------CCeEEEEECCCCHHHHHHHHHhCcceeEeC
Confidence            98776                                             799999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHhhh
Q 023816          187 PVKLSDVKRIKDYLTRDVN  205 (276)
Q Consensus       187 Pv~~~~L~~~~~~l~~~~~  205 (276)
                      |++.++|...+..+.+...
T Consensus       107 p~~~~~l~~~l~~~~~~~~  125 (143)
T 3jte_A          107 PVTAQDLSIAINNAINRKK  125 (143)
T ss_dssp             SCCHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHH
Confidence            9999999877777665443

>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=99.88  E-value=1.7e-21  Score=148.28  Aligned_cols=117  Identities=21%  Similarity=0.400  Sum_probs=107.4

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhh
Q 023816           30 VHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVT  109 (276)
Q Consensus        30 ~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~  109 (276)
                      ++||||||++..+..++..|+..|+.+..+.++.+|++.+           ....||+||+|+.||+++|+++++++++.
T Consensus         1 ~~ilivdd~~~~~~~l~~~l~~~g~~v~~~~~~~~a~~~~-----------~~~~~dlil~D~~l~~~~g~~~~~~l~~~   69 (121)
T 2pl1_A            1 MRVLVVEDNALLRHHLKVQIQDAGHQVDDAEDAKEADYYL-----------NEHIPDIAIVDLGLPDEDGLSLIRRWRSN   69 (121)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHH-----------HHSCCSEEEECSCCSSSCHHHHHHHHHHT
T ss_pred             CeEEEEeCcHHHHHHHHHHHhhcCCEEEEeCCHHHHHHHH-----------hccCCCEEEEecCCCCCCHHHHHHHHHhc
Confidence            4799999999999999999999999999999999999998           45679999999999999999999999976


Q ss_pred             CCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCC
Q 023816          110 TPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVK  189 (276)
Q Consensus       110 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~  189 (276)
                      .+                                             .+|+|++|+........++++.|+++|+.||++
T Consensus        70 ~~---------------------------------------------~~~ii~~s~~~~~~~~~~~~~~g~~~~l~kp~~  104 (121)
T 2pl1_A           70 DV---------------------------------------------SLPILVLTARESWQDKVEVLSAGADDYVTKPFH  104 (121)
T ss_dssp             TC---------------------------------------------CSCEEEEESCCCHHHHHHHHHTTCSEEEESSCC
T ss_pred             CC---------------------------------------------CCCEEEEecCCCHHHHHHHHHcCccceEECCCC
Confidence            55                                             799999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHH
Q 023816          190 LSDVKRIKDYLTR  202 (276)
Q Consensus       190 ~~~L~~~~~~l~~  202 (276)
                      .++|...+..+.+
T Consensus       105 ~~~l~~~i~~~~~  117 (121)
T 2pl1_A          105 IEEVMARMQALMR  117 (121)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            9999777666543

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

Probab=99.88  E-value=2e-21  Score=155.24  Aligned_cols=131  Identities=23%  Similarity=0.375  Sum_probs=108.7

Q ss_pred             CCCCccEEEEEeCCHHHHHHHHHHHhhCCC--EEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHH
Q 023816           25 SDTEEVHVLAVDDSFVDRKVIERLLTISSC--KVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYEL  102 (276)
Q Consensus        25 ~~~~~~~VLIVdD~~~~~~~L~~~L~~~g~--~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~el  102 (276)
                      .....++||||||++..++.++.+|+..|+  .+..+.++.+|++.+....+..    ....||+||+|+.||+++|+++
T Consensus         4 ~~~~~~~ILivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~al~~l~~~~~~~----~~~~~dlillD~~lp~~~g~~l   79 (149)
T 1i3c_A            4 ESNPPKVILLVEDSKADSRLVQEVLKTSTIDHELIILRDGLAAMAFLQQQGEYE----NSPRPNLILLDLNLPKKDGREV   79 (149)
T ss_dssp             --CCCEEEEEECCCHHHHHHHHHHHHSCCSCEEEEEECSHHHHHHHHTTCGGGT----TCCCCSEEEECSCCSSSCHHHH
T ss_pred             ccCCCCeEEEEECCHHHHHHHHHHHHhcCCCccEEEeCCHHHHHHHHHhccccc----cCCCCCEEEEeCCCCCCcHHHH
Confidence            344578999999999999999999998887  8889999999999983210000    0247999999999999999999


Q ss_pred             HHHHHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCe
Q 023816          103 LKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAED  182 (276)
Q Consensus       103 l~~Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d  182 (276)
                      +++||+..                                           ....+|||++|+........++++.||++
T Consensus        80 ~~~l~~~~-------------------------------------------~~~~~piiils~~~~~~~~~~~~~~ga~~  116 (149)
T 1i3c_A           80 LAEIKQNP-------------------------------------------DLKRIPVVVLTTSHNEDDVIASYELHVNC  116 (149)
T ss_dssp             HHHHHHCT-------------------------------------------TTTTSCEEEEESCCCHHHHHHHHHTTCSE
T ss_pred             HHHHHhCc-------------------------------------------CcCCCeEEEEECCCChHHHHHHHHcCCcE
Confidence            99999732                                           12278999999999999999999999999


Q ss_pred             EEeCCCCHHHHHHHHHHHHH
Q 023816          183 FIVKPVKLSDVKRIKDYLTR  202 (276)
Q Consensus       183 ~l~KPv~~~~L~~~~~~l~~  202 (276)
                      ||.||++.++|...++.+.+
T Consensus       117 ~l~KP~~~~~L~~~i~~~~~  136 (149)
T 1i3c_A          117 YLTKSRNLKDLFKMVQGIES  136 (149)
T ss_dssp             EEECCSSHHHHHHHHHHHHH
T ss_pred             EEECCCCHHHHHHHHHHHHH
Confidence            99999999999777776654

>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=99.88  E-value=6.9e-22  Score=154.04  Aligned_cols=122  Identities=28%  Similarity=0.485  Sum_probs=105.8

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhCCCE-EEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHH
Q 023816           27 TEEVHVLAVDDSFVDRKVIERLLTISSCK-VTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKK  105 (276)
Q Consensus        27 ~~~~~VLIVdD~~~~~~~L~~~L~~~g~~-v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~  105 (276)
                      ...++||||||++..++.++.+|+..||. +..+.++.+|++.+.          ....||+||+|+.||+++|++++++
T Consensus         3 ~~~~~iLivdd~~~~~~~l~~~L~~~g~~~v~~~~~~~~a~~~~~----------~~~~~dlvi~D~~~p~~~g~~~~~~   72 (129)
T 3h1g_A            3 LGSMKLLVVDDSSTMRRIIKNTLSRLGYEDVLEAEHGVEAWEKLD----------ANADTKVLITDWNMPEMNGLDLVKK   72 (129)
T ss_dssp             ---CCEEEECSCHHHHHHHHHHHHHTTCCCEEEESSHHHHHHHHH----------HCTTCCEEEECSCCSSSCHHHHHHH
T ss_pred             CCCcEEEEEeCCHHHHHHHHHHHHHcCCcEEEEeCCHHHHHHHHH----------hCCCCCEEEEeCCCCCCCHHHHHHH
Confidence            34679999999999999999999999995 888999999999872          2346999999999999999999999


Q ss_pred             HHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEe
Q 023816          106 IKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIV  185 (276)
Q Consensus       106 Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~  185 (276)
                      ||+..                                           ....+|||++|++.......++++.|+++||.
T Consensus        73 lr~~~-------------------------------------------~~~~~pii~~s~~~~~~~~~~~~~~g~~~~l~  109 (129)
T 3h1g_A           73 VRSDS-------------------------------------------RFKEIPIIMITAEGGKAEVITALKAGVNNYIV  109 (129)
T ss_dssp             HHTST-------------------------------------------TCTTCCEEEEESCCSHHHHHHHHHHTCCEEEE
T ss_pred             HHhcC-------------------------------------------CCCCCeEEEEeCCCChHHHHHHHHcCccEEEe
Confidence            99632                                           12378999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHH
Q 023816          186 KPVKLSDVKRIKDYLT  201 (276)
Q Consensus       186 KPv~~~~L~~~~~~l~  201 (276)
                      ||++.++|.+.++.+.
T Consensus       110 KP~~~~~L~~~l~~~l  125 (129)
T 3h1g_A          110 KPFTPQVLKEKLEVVL  125 (129)
T ss_dssp             SCCCHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHh
Confidence            9999999977776654

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

Probab=99.88  E-value=1.7e-21  Score=155.93  Aligned_cols=122  Identities=22%  Similarity=0.320  Sum_probs=112.4

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHH
Q 023816           27 TEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKI  106 (276)
Q Consensus        27 ~~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~I  106 (276)
                      ..+.+||||||++..+..++.+|+..||.|..+.++.+|++.+           ....||+||+|+.||+++|++++++|
T Consensus        12 ~~~~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l-----------~~~~~dlvi~D~~l~~~~g~~~~~~l   80 (153)
T 3hv2_A           12 TRRPEILLVDSQEVILQRLQQLLSPLPYTLHFARDATQALQLL-----------ASREVDLVISAAHLPQMDGPTLLARI   80 (153)
T ss_dssp             CSCCEEEEECSCHHHHHHHHHHHTTSSCEEEEESSHHHHHHHH-----------HHSCCSEEEEESCCSSSCHHHHHHHH
T ss_pred             cCCceEEEECCCHHHHHHHHHHhcccCcEEEEECCHHHHHHHH-----------HcCCCCEEEEeCCCCcCcHHHHHHHH
Confidence            3468999999999999999999999999999999999999999           55689999999999999999999999


Q ss_pred             HhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcC-CCeEEe
Q 023816          107 KVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDG-AEDFIV  185 (276)
Q Consensus       107 r~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~G-a~d~l~  185 (276)
                      |+..+                                             .+|||++|+........++++.| +++||.
T Consensus        81 ~~~~~---------------------------------------------~~~ii~~s~~~~~~~~~~~~~~g~~~~~l~  115 (153)
T 3hv2_A           81 HQQYP---------------------------------------------STTRILLTGDPDLKLIAKAINEGEIYRYLS  115 (153)
T ss_dssp             HHHCT---------------------------------------------TSEEEEECCCCCHHHHHHHHHTTCCSEEEC
T ss_pred             HhHCC---------------------------------------------CCeEEEEECCCCHHHHHHHHhCCCcceEEe
Confidence            98777                                             79999999999999999999999 999999


Q ss_pred             CCCCHHHHHHHHHHHHHhh
Q 023816          186 KPVKLSDVKRIKDYLTRDV  204 (276)
Q Consensus       186 KPv~~~~L~~~~~~l~~~~  204 (276)
                      ||++.++|...+..+.+..
T Consensus       116 KP~~~~~l~~~i~~~l~~~  134 (153)
T 3hv2_A          116 KPWDDQELLLALRQALEHQ  134 (153)
T ss_dssp             SSCCHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHh
Confidence            9999999987777766543

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

Probab=99.88  E-value=8e-22  Score=154.95  Aligned_cols=121  Identities=17%  Similarity=0.196  Sum_probs=110.9

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCC--CCHHHHHHH
Q 023816           28 EEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPG--MTGYELLKK  105 (276)
Q Consensus        28 ~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~--~~G~ell~~  105 (276)
                      ...+||||||++..++.++.+|+..||++..+.++++|++.+           +...||+||+|+.||+  ++|++++++
T Consensus         5 ~~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l-----------~~~~~dlvi~D~~l~~~~~~g~~~~~~   73 (136)
T 3kto_A            5 HHPIIYLVDHQKDARAALSKLLSPLDVTIQCFASAESFMRQQ-----------ISDDAIGMIIEAHLEDKKDSGIELLET   73 (136)
T ss_dssp             --CEEEEECSCHHHHHHHHHHHTTSSSEEEEESSHHHHTTSC-----------CCTTEEEEEEETTGGGBTTHHHHHHHH
T ss_pred             CCCeEEEEcCCHHHHHHHHHHHHHCCcEEEEeCCHHHHHHHH-----------hccCCCEEEEeCcCCCCCccHHHHHHH
Confidence            467999999999999999999999999999999999999988           6778999999999999  999999999


Q ss_pred             HHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEe
Q 023816          106 IKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIV  185 (276)
Q Consensus       106 Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~  185 (276)
                      ||+..+                                             .+|||++|+........++++.|+++||.
T Consensus        74 l~~~~~---------------------------------------------~~~ii~~s~~~~~~~~~~~~~~ga~~~l~  108 (136)
T 3kto_A           74 LVKRGF---------------------------------------------HLPTIVMASSSDIPTAVRAMRASAADFIE  108 (136)
T ss_dssp             HHHTTC---------------------------------------------CCCEEEEESSCCHHHHHHHHHTTCSEEEE
T ss_pred             HHhCCC---------------------------------------------CCCEEEEEcCCCHHHHHHHHHcChHHhee
Confidence            998666                                             89999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHhh
Q 023816          186 KPVKLSDVKRIKDYLTRDV  204 (276)
Q Consensus       186 KPv~~~~L~~~~~~l~~~~  204 (276)
                      ||++.++|...+..+....
T Consensus       109 KP~~~~~l~~~i~~~~~~~  127 (136)
T 3kto_A          109 KPFIEHVLVHDVQQIINGA  127 (136)
T ss_dssp             SSBCHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHhcc
Confidence            9999999987777766543

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

Probab=99.88  E-value=1.6e-21  Score=150.97  Aligned_cols=121  Identities=28%  Similarity=0.459  Sum_probs=104.9

Q ss_pred             CCCccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHH
Q 023816           26 DTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKK  105 (276)
Q Consensus        26 ~~~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~  105 (276)
                      .+.+.+||||||++..+..++++|+..|+.+..+.++.+|++.+           +...||+||+|+.||+++|++++++
T Consensus         4 ~~~~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l-----------~~~~~dlvi~d~~l~~~~g~~~~~~   72 (130)
T 3eod_A            4 PLVGKQILIVEDEQVFRSLLDSWFSSLGATTVLAADGVDALELL-----------GGFTPDLMICDIAMPRMNGLKLLEH   72 (130)
T ss_dssp             TTTTCEEEEECSCHHHHHHHHHHHHHTTCEEEEESCHHHHHHHH-----------TTCCCSEEEECCC-----CHHHHHH
T ss_pred             CCCCCeEEEEeCCHHHHHHHHHHHHhCCceEEEeCCHHHHHHHH-----------hcCCCCEEEEecCCCCCCHHHHHHH
Confidence            35578999999999999999999999999999999999999999           6778999999999999999999999


Q ss_pred             HHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEe
Q 023816          106 IKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIV  185 (276)
Q Consensus       106 Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~  185 (276)
                      ||+..+                                             .+|||++|+........++++.|+++|+.
T Consensus        73 l~~~~~---------------------------------------------~~~ii~~t~~~~~~~~~~~~~~g~~~~l~  107 (130)
T 3eod_A           73 IRNRGD---------------------------------------------QTPVLVISATENMADIAKALRLGVEDVLL  107 (130)
T ss_dssp             HHHTTC---------------------------------------------CCCEEEEECCCCHHHHHHHHHHCCSEEEE
T ss_pred             HHhcCC---------------------------------------------CCCEEEEEcCCCHHHHHHHHHcCCCEEEe
Confidence            998666                                             79999999999999999999999999999


Q ss_pred             CCC-CHHHHHHHHHHHHH
Q 023816          186 KPV-KLSDVKRIKDYLTR  202 (276)
Q Consensus       186 KPv-~~~~L~~~~~~l~~  202 (276)
                      ||+ +.++|.+.+..+..
T Consensus       108 KP~~~~~~l~~~i~~~l~  125 (130)
T 3eod_A          108 KPVKDLNRLREMVFACLY  125 (130)
T ss_dssp             SCC---CHHHHHHHHHHC
T ss_pred             CCCCcHHHHHHHHHHHhc
Confidence            999 88898777776654

>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=99.88  E-value=1.6e-21  Score=149.83  Aligned_cols=116  Identities=27%  Similarity=0.421  Sum_probs=106.9

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHh
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKV  108 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~  108 (276)
                      ..+||||||++..++.++..|+..||.+..+.++.+|++.+           ....||+||+|+.||+++|++++++|++
T Consensus         3 ~~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~~-----------~~~~~dlvl~D~~l~~~~g~~~~~~l~~   71 (124)
T 1srr_A            3 NEKILIVDDQSGIRILLNEVFNKEGYQTFQAANGLQALDIV-----------TKERPDLVLLDMKIPGMDGIEILKRMKV   71 (124)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHH-----------HHHCCSEEEEESCCTTCCHHHHHHHHHH
T ss_pred             CceEEEEeCCHHHHHHHHHHHHHCCcEEEEeCCHHHHHHHH-----------hccCCCEEEEecCCCCCCHHHHHHHHHH
Confidence            36899999999999999999999999999999999999998           4557999999999999999999999998


Q ss_pred             hCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCC
Q 023816          109 TTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPV  188 (276)
Q Consensus       109 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv  188 (276)
                      ..|                                             .+|||++|+........++++.|+++||.||+
T Consensus        72 ~~~---------------------------------------------~~~ii~~s~~~~~~~~~~~~~~g~~~~l~KP~  106 (124)
T 1srr_A           72 IDE---------------------------------------------NIRVIIMTAYGELDMIQESKELGALTHFAKPF  106 (124)
T ss_dssp             HCT---------------------------------------------TCEEEEEESSCCHHHHHHHHHHTCCCEEESSC
T ss_pred             hCC---------------------------------------------CCCEEEEEccCchHHHHHHHhcChHhhccCCC
Confidence            766                                             79999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHH
Q 023816          189 KLSDVKRIKDYL  200 (276)
Q Consensus       189 ~~~~L~~~~~~l  200 (276)
                      +.++|...+..+
T Consensus       107 ~~~~l~~~i~~~  118 (124)
T 1srr_A          107 DIDEIRDAVKKY  118 (124)
T ss_dssp             CHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHH
Confidence            999997766554

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

Probab=99.88  E-value=3.7e-21  Score=154.86  Aligned_cols=122  Identities=33%  Similarity=0.466  Sum_probs=110.7

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHH
Q 023816           28 EEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIK  107 (276)
Q Consensus        28 ~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir  107 (276)
                      .+.+||||||++..+..++.+|+..||.|..+.++.+|++.+           ....||+||+|+.||+++|+++++.||
T Consensus         6 ~~~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l-----------~~~~~dlii~D~~l~~~~g~~~~~~lr   74 (154)
T 3gt7_A            6 RAGEILIVEDSPTQAEHLKHILEETGYQTEHVRNGREAVRFL-----------SLTRPDLIISDVLMPEMDGYALCRWLK   74 (154)
T ss_dssp             -CCEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHH-----------TTCCCSEEEEESCCSSSCHHHHHHHHH
T ss_pred             CCCcEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHH-----------HhCCCCEEEEeCCCCCCCHHHHHHHHH
Confidence            468999999999999999999999999999999999999999           677899999999999999999999999


Q ss_pred             hhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCC
Q 023816          108 VTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKP  187 (276)
Q Consensus       108 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KP  187 (276)
                      +..                                           ....+|||++|+....+...++++.|+++||.||
T Consensus        75 ~~~-------------------------------------------~~~~~pii~~s~~~~~~~~~~~~~~g~~~~l~KP  111 (154)
T 3gt7_A           75 GQP-------------------------------------------DLRTIPVILLTILSDPRDVVRSLECGADDFITKP  111 (154)
T ss_dssp             HST-------------------------------------------TTTTSCEEEEECCCSHHHHHHHHHHCCSEEEESS
T ss_pred             hCC-------------------------------------------CcCCCCEEEEECCCChHHHHHHHHCCCCEEEeCC
Confidence            742                                           1237999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHh
Q 023816          188 VKLSDVKRIKDYLTRD  203 (276)
Q Consensus       188 v~~~~L~~~~~~l~~~  203 (276)
                      ++.++|...+..+.+.
T Consensus       112 ~~~~~l~~~i~~~l~~  127 (154)
T 3gt7_A          112 CKDVVLASHVKRLLSG  127 (154)
T ss_dssp             CCHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHH
Confidence            9999998777776654

>1jbe_A Chemotaxis protein CHEY; signaling protein; 1.08A {Escherichia coli} SCOP: c.23.1.1 PDB: 3chy_A 1a0o_A 1cey_A 1bdj_A 1eay_A 1f4v_A 1ffg_A 1ffs_A 1ffw_A 1fqw_A 2b1j_A 1chn_A 1djm_A 1kmi_Y* 1d4z_A 3olx_A 3olw_A 1cye_A 2che_A 2chf_A ...

Probab=99.87  E-value=4.9e-21  Score=147.50  Aligned_cols=121  Identities=27%  Similarity=0.440  Sum_probs=107.5

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhCCC-EEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHH
Q 023816           28 EEVHVLAVDDSFVDRKVIERLLTISSC-KVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKI  106 (276)
Q Consensus        28 ~~~~VLIVdD~~~~~~~L~~~L~~~g~-~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~I  106 (276)
                      +.++||||||++..++.++.+|+..|+ .+..+.++.+|++.+           ....||+||+|+.||+++|++++++|
T Consensus         3 ~~~~ilivdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~-----------~~~~~dlvi~D~~l~~~~g~~l~~~l   71 (128)
T 1jbe_A            3 KELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKL-----------QAGGYGFVISDWNMPNMDGLELLKTI   71 (128)
T ss_dssp             TTCCEEEECSCHHHHHHHHHHHHHTTCCCEEEESSHHHHHHHH-----------TTCCCCEEEEESCCSSSCHHHHHHHH
T ss_pred             CccEEEEECCCHHHHHHHHHHHHHcCCcEEEeeCCHHHHHHHH-----------HhcCCCEEEEeCCCCCCCHHHHHHHH
Confidence            467899999999999999999999999 788999999999998           56689999999999999999999999


Q ss_pred             HhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeC
Q 023816          107 KVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVK  186 (276)
Q Consensus       107 r~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~K  186 (276)
                      |+...                                           ...+|||++|+........++++.|+++|+.|
T Consensus        72 ~~~~~-------------------------------------------~~~~~ii~~s~~~~~~~~~~~~~~ga~~~l~K  108 (128)
T 1jbe_A           72 RAXXA-------------------------------------------MSALPVLMVTAEAKKENIIAAAQAGASGYVVK  108 (128)
T ss_dssp             HC--C-------------------------------------------CTTCCEEEEESSCCHHHHHHHHHTTCSEEEES
T ss_pred             Hhhcc-------------------------------------------cCCCcEEEEecCccHHHHHHHHHhCcCceeec
Confidence            96221                                           22689999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHH
Q 023816          187 PVKLSDVKRIKDYLTR  202 (276)
Q Consensus       187 Pv~~~~L~~~~~~l~~  202 (276)
                      |++.++|...++.+.+
T Consensus       109 P~~~~~l~~~i~~~~~  124 (128)
T 1jbe_A          109 PFTAATLEEKLNKIFE  124 (128)
T ss_dssp             SCCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHH
Confidence            9999999777766554

>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=99.87  E-value=3.8e-21  Score=153.33  Aligned_cols=130  Identities=26%  Similarity=0.443  Sum_probs=111.1

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhCCC--EEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHH
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTISSC--KVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKI  106 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~g~--~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~I  106 (276)
                      +++||||||++..++.++++|+..|+  .+..+.++++|++.+.....  .+......||+||+|+.||+++|++++++|
T Consensus         4 ~~~ILivddd~~~~~~l~~~L~~~g~~~~v~~~~~~~~al~~l~~~~~--~~~~~~~~~dliilD~~l~~~~g~~~~~~l   81 (152)
T 3heb_A            4 SVTIVMIEDDLGHARLIEKNIRRAGVNNEIIAFTDGTSALNYLFGDDK--SGRVSAGRAQLVLLDLNLPDMTGIDILKLV   81 (152)
T ss_dssp             -CEEEEECCCHHHHHHHHHHHHHTTCCCCEEEESSHHHHHHHHHCTTS--SSGGGTTCBEEEEECSBCSSSBHHHHHHHH
T ss_pred             CceEEEEeCCHHHHHHHHHHHHhCCCcceEEEeCCHHHHHHHHhcccc--ccccccCCCCEEEEeCCCCCCcHHHHHHHH
Confidence            58999999999999999999999998  89999999999999832110  000024679999999999999999999999


Q ss_pred             Hh--hCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEE
Q 023816          107 KV--TTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFI  184 (276)
Q Consensus       107 r~--~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l  184 (276)
                      |+  ..+                                             .+|||++|+........++++.|+++||
T Consensus        82 r~~~~~~---------------------------------------------~~pii~~t~~~~~~~~~~~~~~g~~~~l  116 (152)
T 3heb_A           82 KENPHTR---------------------------------------------RSPVVILTTTDDQREIQRCYDLGANVYI  116 (152)
T ss_dssp             HHSTTTT---------------------------------------------TSCEEEEESCCCHHHHHHHHHTTCSEEE
T ss_pred             Hhccccc---------------------------------------------CCCEEEEecCCCHHHHHHHHHCCCcEEE
Confidence            97  333                                             7999999999999999999999999999


Q ss_pred             eCCCCHHHHHHHHHHHHHhhh
Q 023816          185 VKPVKLSDVKRIKDYLTRDVN  205 (276)
Q Consensus       185 ~KPv~~~~L~~~~~~l~~~~~  205 (276)
                      .||++.++|...++.+.+.+.
T Consensus       117 ~KP~~~~~l~~~i~~~~~~~~  137 (152)
T 3heb_A          117 TKPVNYENFANAIRQLGLFFS  137 (152)
T ss_dssp             ECCSSHHHHHHHHHHHHHHHT
T ss_pred             eCCCCHHHHHHHHHHHHHHHH
Confidence            999999999888888765543

>1xhf_A DYE resistance, aerobic respiration control protein ARCA; two-component system, gene regulation, transcription factor, anoxic redox control; 2.15A {Escherichia coli} SCOP: c.23.1.1 PDB: 1xhe_A

Probab=99.87  E-value=4.1e-21  Score=146.99  Aligned_cols=118  Identities=22%  Similarity=0.405  Sum_probs=107.1

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHH
Q 023816           28 EEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIK  107 (276)
Q Consensus        28 ~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir  107 (276)
                      ...+||||||++..++.++..|+..||++..+.++.+|++.+           ....||+||+|+.||+++|++++++|+
T Consensus         2 ~~~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~~-----------~~~~~dlvi~D~~l~~~~g~~~~~~l~   70 (123)
T 1xhf_A            2 QTPHILIVEDELVTRNTLKSIFEAEGYDVFEATDGAEMHQIL-----------SEYDINLVIMDINLPGKNGLLLARELR   70 (123)
T ss_dssp             CCCEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHH-----------HHSCCSEEEECSSCSSSCHHHHHHHHH
T ss_pred             CCceEEEEeCCHHHHHHHHHHHhhCCcEEEEeCCHHHHHHHH-----------hcCCCCEEEEcCCCCCCCHHHHHHHHH
Confidence            356899999999999999999999999999999999999998           456799999999999999999999999


Q ss_pred             hhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCC
Q 023816          108 VTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKP  187 (276)
Q Consensus       108 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KP  187 (276)
                      +. +                                             .+|+|++|+........++++.|+++|+.||
T Consensus        71 ~~-~---------------------------------------------~~~ii~~s~~~~~~~~~~~~~~g~~~~l~KP  104 (123)
T 1xhf_A           71 EQ-A---------------------------------------------NVALMFLTGRDNEVDKILGLEIGADDYITKP  104 (123)
T ss_dssp             HH-C---------------------------------------------CCEEEEEESCCSHHHHHHHHHHTCSEEEESS
T ss_pred             hC-C---------------------------------------------CCcEEEEECCCChHHHHHHHhcCcceEEeCC
Confidence            75 4                                             6899999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHH
Q 023816          188 VKLSDVKRIKDYLTR  202 (276)
Q Consensus       188 v~~~~L~~~~~~l~~  202 (276)
                      ++.++|...+..+.+
T Consensus       105 ~~~~~l~~~i~~~~~  119 (123)
T 1xhf_A          105 FNPRELTIRARNLLS  119 (123)
T ss_dssp             CCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHH
Confidence            999999776665543

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

Probab=99.87  E-value=2.4e-21  Score=168.54  Aligned_cols=123  Identities=25%  Similarity=0.413  Sum_probs=112.2

Q ss_pred             CCCCccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHH
Q 023816           25 SDTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLK  104 (276)
Q Consensus        25 ~~~~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~  104 (276)
                      ..+++++||||||++..+..++.+|+..||+|..+.++++|++.+           ....||+||+|+.||+++|+++++
T Consensus        19 ~~~~~~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~-----------~~~~~dlvllD~~lp~~~g~~~~~   87 (250)
T 3r0j_A           19 NTTPEARVLVVDDEANIVELLSVSLKFQGFEVYTATNGAQALDRA-----------RETRPDAVILDVXMPGMDGFGVLR   87 (250)
T ss_dssp             -CCSSCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHH-----------HHHCCSEEEEESCCSSSCHHHHHH
T ss_pred             CCCCCceEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHH-----------HhCCCCEEEEeCCCCCCCHHHHHH
Confidence            345578999999999999999999999999999999999999998           556799999999999999999999


Q ss_pred             HHHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEE
Q 023816          105 KIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFI  184 (276)
Q Consensus       105 ~Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l  184 (276)
                      +||+..+                                             .+|||++|+..+.....++++.||+|||
T Consensus        88 ~lr~~~~---------------------------------------------~~~ii~lt~~~~~~~~~~~~~~Ga~~yl  122 (250)
T 3r0j_A           88 RLRADGI---------------------------------------------DAPALFLTARDSLQDKIAGLTLGGDDYV  122 (250)
T ss_dssp             HHHHTTC---------------------------------------------CCCEEEEECSTTHHHHHHHHTSTTCEEE
T ss_pred             HHHhcCC---------------------------------------------CCCEEEEECCCCHHHHHHHHHcCCcEEE
Confidence            9998666                                             7999999999999999999999999999


Q ss_pred             eCCCCHHHHHHHHHHHHHh
Q 023816          185 VKPVKLSDVKRIKDYLTRD  203 (276)
Q Consensus       185 ~KPv~~~~L~~~~~~l~~~  203 (276)
                      .||++.++|...+..+.+.
T Consensus       123 ~Kp~~~~~L~~~i~~~~~~  141 (250)
T 3r0j_A          123 TKPFSLEEVVARLRVILRR  141 (250)
T ss_dssp             ESSCCHHHHHHHHHHHHHH
T ss_pred             eCCCCHHHHHHHHHHHHHh
Confidence            9999999997777766554

>1zgz_A Torcad operon transcriptional regulatory protein; two-component system, gene regulation, transcription factor, respiratory system; 1.80A {Escherichia coli} SCOP: c.23.1.1

Probab=99.87  E-value=5.6e-21  Score=146.04  Aligned_cols=116  Identities=22%  Similarity=0.353  Sum_probs=106.1

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhh
Q 023816           30 VHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVT  109 (276)
Q Consensus        30 ~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~  109 (276)
                      .+||||||++..+..++..|+..||.+..+.++.++++.+           ....||+||+|+.||+++|++++++||+ 
T Consensus         3 ~~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~-----------~~~~~dlvi~d~~l~~~~g~~~~~~l~~-   70 (122)
T 1zgz_A            3 HHIVIVEDEPVTQARLQSYFTQEGYTVSVTASGAGLREIM-----------QNQSVDLILLDINLPDENGLMLTRALRE-   70 (122)
T ss_dssp             CEEEEECSSHHHHHHHHHHHHHTTCEEEEESSHHHHHHHH-----------HHSCCSEEEEESCCSSSCHHHHHHHHHT-
T ss_pred             cEEEEEECCHHHHHHHHHHHHHCCCeEEEecCHHHHHHHH-----------hcCCCCEEEEeCCCCCCChHHHHHHHHh-
Confidence            5899999999999999999999999999999999999988           4567999999999999999999999996 


Q ss_pred             CCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCC
Q 023816          110 TPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVK  189 (276)
Q Consensus       110 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~  189 (276)
                      .+                                             .+|||++|+........++++.|+++|+.||++
T Consensus        71 ~~---------------------------------------------~~~ii~~s~~~~~~~~~~~~~~ga~~~l~Kp~~  105 (122)
T 1zgz_A           71 RS---------------------------------------------TVGIILVTGRSDRIDRIVGLEMGADDYVTKPLE  105 (122)
T ss_dssp             TC---------------------------------------------CCEEEEEESSCCHHHHHHHHHHTCSEEEESSCC
T ss_pred             cC---------------------------------------------CCCEEEEECCCChhhHHHHHHhCHHHHccCCCC
Confidence            44                                             689999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHH
Q 023816          190 LSDVKRIKDYLTR  202 (276)
Q Consensus       190 ~~~L~~~~~~l~~  202 (276)
                      .+++...+..+.+
T Consensus       106 ~~~l~~~i~~~~~  118 (122)
T 1zgz_A          106 LRELVVRVKNLLW  118 (122)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            9999777666544

>1tmy_A CHEY protein, TMY; chemotaxis, phosphoryl transfer, signal transduction; 1.90A {Thermotoga maritima} SCOP: c.23.1.1 PDB: 2tmy_A 3tmy_A 4tmy_A 1u0s_Y

Probab=99.87  E-value=2.4e-21  Score=147.67  Aligned_cols=116  Identities=28%  Similarity=0.444  Sum_probs=105.4

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhCCCE-EEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHH
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTISSCK-VTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIK  107 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~g~~-v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir  107 (276)
                      +.+||||||++..+..++..|+..||+ +..+.++.+|++.+           ....||+||+|+.||+++|++++++|+
T Consensus         2 ~~~ilivdd~~~~~~~l~~~l~~~g~~vv~~~~~~~~a~~~~-----------~~~~~dlil~D~~l~~~~g~~~~~~l~   70 (120)
T 1tmy_A            2 GKRVLIVDDAAFMRMMLKDIITKAGYEVAGEATNGREAVEKY-----------KELKPDIVTMDITMPEMNGIDAIKEIM   70 (120)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHH-----------HHHCCSEEEEECSCGGGCHHHHHHHHH
T ss_pred             CceEEEEcCcHHHHHHHHHHHhhcCcEEEEEECCHHHHHHHH-----------HhcCCCEEEEeCCCCCCcHHHHHHHHH
Confidence            368999999999999999999999999 55799999999998           455799999999999999999999999


Q ss_pred             hhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCC
Q 023816          108 VTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKP  187 (276)
Q Consensus       108 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KP  187 (276)
                      +..|                                             .+|||++|+........++++.|+++|+.||
T Consensus        71 ~~~~---------------------------------------------~~~ii~~s~~~~~~~~~~~~~~g~~~~l~KP  105 (120)
T 1tmy_A           71 KIDP---------------------------------------------NAKIIVCSAMGQQAMVIEAIKAGAKDFIVKP  105 (120)
T ss_dssp             HHCT---------------------------------------------TCCEEEEECTTCHHHHHHHHHTTCCEEEESS
T ss_pred             hhCC---------------------------------------------CCeEEEEeCCCCHHHHHHHHHhCcceeEeCC
Confidence            8766                                             7899999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHH
Q 023816          188 VKLSDVKRIKDYL  200 (276)
Q Consensus       188 v~~~~L~~~~~~l  200 (276)
                      ++.++|...+..+
T Consensus       106 ~~~~~l~~~i~~~  118 (120)
T 1tmy_A          106 FQPSRVVEALNKV  118 (120)
T ss_dssp             CCHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHH
Confidence            9999997666543

>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=99.87  E-value=7.8e-22  Score=152.19  Aligned_cols=120  Identities=18%  Similarity=0.228  Sum_probs=105.6

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHH
Q 023816           27 TEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKI  106 (276)
Q Consensus        27 ~~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~I  106 (276)
                      |.+.+||||||++..++.++.+|+..||++..+.++++|++.+           ....||+||+|+.||+++|++++++|
T Consensus         1 M~~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l-----------~~~~~dlii~D~~l~~~~g~~~~~~l   69 (127)
T 3i42_A            1 MSLQQALIVEDYQAAAETFKELLEMLGFQADYVMSGTDALHAM-----------STRGYDAVFIDLNLPDTSGLALVKQL   69 (127)
T ss_dssp             -CCEEEEEECSCHHHHHHHHHHHHHTTEEEEEESSHHHHHHHH-----------HHSCCSEEEEESBCSSSBHHHHHHHH
T ss_pred             CCcceEEEEcCCHHHHHHHHHHHHHcCCCEEEECCHHHHHHHH-----------HhcCCCEEEEeCCCCCCCHHHHHHHH
Confidence            3468999999999999999999999999999999999999999           55679999999999999999999999


Q ss_pred             HhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeC
Q 023816          107 KVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVK  186 (276)
Q Consensus       107 r~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~K  186 (276)
                      |+...                                           ...+|||++|+...... .+++..|+++||.|
T Consensus        70 ~~~~~-------------------------------------------~~~~~ii~~s~~~~~~~-~~~~~~g~~~~l~K  105 (127)
T 3i42_A           70 RALPM-------------------------------------------EKTSKFVAVSGFAKNDL-GKEACELFDFYLEK  105 (127)
T ss_dssp             HHSCC-------------------------------------------SSCCEEEEEECC-CTTC-CHHHHHHCSEEEES
T ss_pred             Hhhhc-------------------------------------------cCCCCEEEEECCcchhH-HHHHHHhhHHheeC
Confidence            98511                                           22799999999988887 88999999999999


Q ss_pred             CCCHHHHHHHHHHHH
Q 023816          187 PVKLSDVKRIKDYLT  201 (276)
Q Consensus       187 Pv~~~~L~~~~~~l~  201 (276)
                      |++.++|.+.+..+.
T Consensus       106 P~~~~~L~~~i~~~~  120 (127)
T 3i42_A          106 PIDIASLEPILQSIE  120 (127)
T ss_dssp             SCCHHHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHhh
Confidence            999999976665544

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

Probab=99.87  E-value=1.9e-21  Score=153.50  Aligned_cols=126  Identities=21%  Similarity=0.277  Sum_probs=109.3

Q ss_pred             CCCCCCCccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHH
Q 023816           22 LSPSDTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYE  101 (276)
Q Consensus        22 ~~~~~~~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~e  101 (276)
                      |+......++||||||++..+..++..|+..||+|..+.++.+|++.+           ....||+||+|+.||+++|++
T Consensus         1 M~~~~~~~~~iLivd~~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l-----------~~~~~dlii~d~~l~~~~g~~   69 (147)
T 2zay_A            1 MSLAEGKWWRIMLVDTQLPALAASISALSQEGFDIIQCGNAIEAVPVA-----------VKTHPHLIITEANMPKISGMD   69 (147)
T ss_dssp             -------CEEEEEECTTGGGGHHHHHHHHHHTEEEEEESSHHHHHHHH-----------HHHCCSEEEEESCCSSSCHHH
T ss_pred             CCcccCCCceEEEEeCCHHHHHHHHHHHHHcCCeEEEeCCHHHHHHHH-----------HcCCCCEEEEcCCCCCCCHHH
Confidence            455667789999999999999999999999999999999999999998           455799999999999999999


Q ss_pred             HHHHHHh--hCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcC
Q 023816          102 LLKKIKV--TTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDG  179 (276)
Q Consensus       102 ll~~Ir~--~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~G  179 (276)
                      ++++|++  ..+                                             .+|||++|+........++++.|
T Consensus        70 ~~~~l~~~~~~~---------------------------------------------~~pii~ls~~~~~~~~~~~~~~g  104 (147)
T 2zay_A           70 LFNSLKKNPQTA---------------------------------------------SIPVIALSGRATAKEEAQLLDMG  104 (147)
T ss_dssp             HHHHHHTSTTTT---------------------------------------------TSCEEEEESSCCHHHHHHHHHHT
T ss_pred             HHHHHHcCcccC---------------------------------------------CCCEEEEeCCCCHHHHHHHHhCC
Confidence            9999997  333                                             79999999999999999999999


Q ss_pred             CCeEEeCCCCHHHHHHHHHHHHHh
Q 023816          180 AEDFIVKPVKLSDVKRIKDYLTRD  203 (276)
Q Consensus       180 a~d~l~KPv~~~~L~~~~~~l~~~  203 (276)
                      +++||.||++.++|...+..+.+.
T Consensus       105 ~~~~l~kp~~~~~L~~~i~~~~~~  128 (147)
T 2zay_A          105 FIDFIAKPVNAIRLSARIKRVLKL  128 (147)
T ss_dssp             CSEEEESSCCHHHHHHHHHHHHHH
T ss_pred             CCEEEeCCCCHHHHHHHHHHHHHH
Confidence            999999999999997777666544

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

Probab=99.87  E-value=1.6e-21  Score=153.10  Aligned_cols=118  Identities=19%  Similarity=0.287  Sum_probs=109.7

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhh-CCCEEEEECCHHHHHHHhcccccccccCCCC-CceeEEEEecCCC-CCCHHHHHHH
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTI-SSCKVTAVDSGRRALQFLGLDEEQSINGFDG-LKVDLIITDYCMP-GMTGYELLKK  105 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~-~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~-~~~DlIL~D~~mp-~~~G~ell~~  105 (276)
                      +.+||||||++..+..++.+|+. .||++..+.++.+|++.+           .. ..||+||+|+.|| +++|++++++
T Consensus         4 ~~~ilivdd~~~~~~~l~~~L~~~~~~~v~~~~~~~~a~~~l-----------~~~~~~dlvi~D~~l~~~~~g~~~~~~   72 (140)
T 3lua_A            4 DGTVLLIDYFEYEREKTKIIFDNIGEYDFIEVENLKKFYSIF-----------KDLDSITLIIMDIAFPVEKEGLEVLSA   72 (140)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHHCCCEEEEECSHHHHHTTT-----------TTCCCCSEEEECSCSSSHHHHHHHHHH
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHhccCccEEEECCHHHHHHHH-----------hcCCCCcEEEEeCCCCCCCcHHHHHHH
Confidence            67999999999999999999999 999999999999999998           66 7899999999999 9999999999


Q ss_pred             HHh--hCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeE
Q 023816          106 IKV--TTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDF  183 (276)
Q Consensus       106 Ir~--~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~  183 (276)
                      ||+  ..+                                             .+|||++|+....+...++++.|+++|
T Consensus        73 l~~~~~~~---------------------------------------------~~~ii~ls~~~~~~~~~~~~~~g~~~~  107 (140)
T 3lua_A           73 IRNNSRTA---------------------------------------------NTPVIIATKSDNPGYRHAALKFKVSDY  107 (140)
T ss_dssp             HHHSGGGT---------------------------------------------TCCEEEEESCCCHHHHHHHHHSCCSEE
T ss_pred             HHhCcccC---------------------------------------------CCCEEEEeCCCCHHHHHHHHHcCCCEE
Confidence            997  444                                             899999999999999999999999999


Q ss_pred             EeCCCCHHHHHHHHHHHHH
Q 023816          184 IVKPVKLSDVKRIKDYLTR  202 (276)
Q Consensus       184 l~KPv~~~~L~~~~~~l~~  202 (276)
                      |.||++.++|...+..+.+
T Consensus       108 l~KP~~~~~l~~~i~~~~~  126 (140)
T 3lua_A          108 ILKPYPTKRLENSVRSVLK  126 (140)
T ss_dssp             EESSCCTTHHHHHHHHHHC
T ss_pred             EECCCCHHHHHHHHHHHHH
Confidence            9999999999777776654

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

Probab=99.87  E-value=6.6e-21  Score=152.03  Aligned_cols=123  Identities=24%  Similarity=0.385  Sum_probs=110.6

Q ss_pred             CCCCccEEEEEeCCHHHHHHHHHHHhhCC--CEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHH
Q 023816           25 SDTEEVHVLAVDDSFVDRKVIERLLTISS--CKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYEL  102 (276)
Q Consensus        25 ~~~~~~~VLIVdD~~~~~~~L~~~L~~~g--~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~el  102 (276)
                      ....+++||||||++..++.++.+|+..|  +.+..+.++++|++.+           ....||+||+|+.||+++|+++
T Consensus        16 ~~~~m~~iLivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~al~~l-----------~~~~~dlii~D~~l~~~~g~~~   84 (150)
T 4e7p_A           16 PRGSHMKVLVAEDQSMLRDAMCQLLTLQPDVESVLQAKNGQEAIQLL-----------EKESVDIAILDVEMPVKTGLEV   84 (150)
T ss_dssp             ----CEEEEEECSCHHHHHHHHHHHHTSTTEEEEEEESSHHHHHHHH-----------TTSCCSEEEECSSCSSSCHHHH
T ss_pred             CCCCccEEEEEcCCHHHHHHHHHHHHhCCCcEEEEEECCHHHHHHHh-----------hccCCCEEEEeCCCCCCcHHHH
Confidence            44557899999999999999999999887  7899999999999999           6778999999999999999999


Q ss_pred             HHHHHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCe
Q 023816          103 LKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAED  182 (276)
Q Consensus       103 l~~Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d  182 (276)
                      ++.||+..+                                             .+|||++|+..+.+...++++.|+++
T Consensus        85 ~~~l~~~~~---------------------------------------------~~~ii~ls~~~~~~~~~~~~~~g~~~  119 (150)
T 4e7p_A           85 LEWIRSEKL---------------------------------------------ETKVVVVTTFKRAGYFERAVKAGVDA  119 (150)
T ss_dssp             HHHHHHTTC---------------------------------------------SCEEEEEESCCCHHHHHHHHHTTCSE
T ss_pred             HHHHHHhCC---------------------------------------------CCeEEEEeCCCCHHHHHHHHHCCCcE
Confidence            999998666                                             79999999999999999999999999


Q ss_pred             EEeCCCCHHHHHHHHHHHHHh
Q 023816          183 FIVKPVKLSDVKRIKDYLTRD  203 (276)
Q Consensus       183 ~l~KPv~~~~L~~~~~~l~~~  203 (276)
                      ||.||++.++|...+..+.+.
T Consensus       120 ~l~Kp~~~~~l~~~i~~~~~~  140 (150)
T 4e7p_A          120 YVLKERSIADLMQTLHTVLEG  140 (150)
T ss_dssp             EEETTSCHHHHHHHHHHHHTT
T ss_pred             EEecCCCHHHHHHHHHHHHcC
Confidence            999999999998777766643

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

Probab=99.87  E-value=1.5e-21  Score=153.01  Aligned_cols=121  Identities=13%  Similarity=0.212  Sum_probs=108.3

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHH
Q 023816           27 TEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKI  106 (276)
Q Consensus        27 ~~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~I  106 (276)
                      +.+.+||||||++..++.++.+|+..||++..+.++++|++.+           ....||+||+|+.||+++|++++++|
T Consensus         4 ~~~~~iLivdd~~~~~~~l~~~l~~~g~~v~~~~~~~~a~~~l-----------~~~~~dlvi~d~~l~~~~g~~~~~~l   72 (140)
T 3grc_A            4 APRPRILICEDDPDIARLLNLMLEKGGFDSDMVHSAAQALEQV-----------ARRPYAAMTVDLNLPDQDGVSLIRAL   72 (140)
T ss_dssp             -CCSEEEEECSCHHHHHHHHHHHHHTTCEEEEECSHHHHHHHH-----------HHSCCSEEEECSCCSSSCHHHHHHHH
T ss_pred             CCCCCEEEEcCCHHHHHHHHHHHHHCCCeEEEECCHHHHHHHH-----------HhCCCCEEEEeCCCCCCCHHHHHHHH
Confidence            4468999999999999999999999999999999999999999           56679999999999999999999999


Q ss_pred             Hh--hCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHH-HHHhcCCCeE
Q 023816          107 KV--TTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARID-RCLEDGAEDF  183 (276)
Q Consensus       107 r~--~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~-~al~~Ga~d~  183 (276)
                      |+  ..+                                             .+|||++|+........ ++++.|+++|
T Consensus        73 ~~~~~~~---------------------------------------------~~~ii~~s~~~~~~~~~~~~~~~g~~~~  107 (140)
T 3grc_A           73 RRDSRTR---------------------------------------------DLAIVVVSANAREGELEFNSQPLAVSTW  107 (140)
T ss_dssp             HTSGGGT---------------------------------------------TCEEEEECTTHHHHHHHHCCTTTCCCEE
T ss_pred             HhCcccC---------------------------------------------CCCEEEEecCCChHHHHHHhhhcCCCEE
Confidence            97  333                                             79999999988877777 8999999999


Q ss_pred             EeCCCCHHHHHHHHHHHHHh
Q 023816          184 IVKPVKLSDVKRIKDYLTRD  203 (276)
Q Consensus       184 l~KPv~~~~L~~~~~~l~~~  203 (276)
                      |.||++.++|...+..+.+.
T Consensus       108 l~kP~~~~~l~~~i~~~l~~  127 (140)
T 3grc_A          108 LEKPIDENLLILSLHRAIDN  127 (140)
T ss_dssp             ECSSCCHHHHHHHHHHHHHH
T ss_pred             EeCCCCHHHHHHHHHHHHHh
Confidence            99999999997777666544

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

Probab=99.87  E-value=3e-21  Score=151.11  Aligned_cols=118  Identities=18%  Similarity=0.382  Sum_probs=106.5

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhCC--CEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHH
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTISS--CKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKI  106 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~g--~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~I  106 (276)
                      +++||||||++..++.++.+|+..|  +.+..+.++.+|++.+           +...||+||+|+.||+++|++++++|
T Consensus         3 ~~~Ilivdd~~~~~~~l~~~l~~~~~~~~v~~~~~~~~al~~~-----------~~~~~dlvilD~~lp~~~g~~~~~~l   71 (133)
T 3b2n_A            3 LTSLIIAEDQNMLRQAMVQLIKLHGDFEILADTDNGLDAMKLI-----------EEYNPNVVILDIEMPGMTGLEVLAEI   71 (133)
T ss_dssp             CEEEEEECSCHHHHHHHHHHHHHHSSEEEEEEESCHHHHHHHH-----------HHHCCSEEEECSSCSSSCHHHHHHHH
T ss_pred             ceEEEEECCCHHHHHHHHHHHhhCCCcEEEEEcCCHHHHHHHH-----------hhcCCCEEEEecCCCCCCHHHHHHHH
Confidence            5789999999999999999999876  5667899999999998           45579999999999999999999999


Q ss_pred             HhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeC
Q 023816          107 KVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVK  186 (276)
Q Consensus       107 r~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~K  186 (276)
                      |+..|                                             .+|||++|+........++++.|+++||.|
T Consensus        72 ~~~~~---------------------------------------------~~~ii~ls~~~~~~~~~~~~~~ga~~~l~K  106 (133)
T 3b2n_A           72 RKKHL---------------------------------------------NIKVIIVTTFKRPGYFEKAVVNDVDAYVLK  106 (133)
T ss_dssp             HHTTC---------------------------------------------SCEEEEEESCCCHHHHHHHHHTTCSEEEET
T ss_pred             HHHCC---------------------------------------------CCcEEEEecCCCHHHHHHHHHcCCcEEEEC
Confidence            98666                                             799999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHH
Q 023816          187 PVKLSDVKRIKDYLTR  202 (276)
Q Consensus       187 Pv~~~~L~~~~~~l~~  202 (276)
                      |++.++|...++.+.+
T Consensus       107 p~~~~~L~~~i~~~~~  122 (133)
T 3b2n_A          107 ERSIEELVETINKVNN  122 (133)
T ss_dssp             TSCHHHHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHHc
Confidence            9999999777766554

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

Probab=99.87  E-value=9.2e-21  Score=151.43  Aligned_cols=122  Identities=25%  Similarity=0.354  Sum_probs=111.8

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHH
Q 023816           27 TEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKI  106 (276)
Q Consensus        27 ~~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~I  106 (276)
                      +.+++||||||++..++.++..|+..||++..+.++.+|++.+           ....||+||+|+.||+++|+++++.|
T Consensus         5 ~~~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l-----------~~~~~dlvi~d~~l~~~~g~~~~~~l   73 (154)
T 2rjn_A            5 YKNYTVMLVDDEQPILNSLKRLIKRLGCNIITFTSPLDALEAL-----------KGTSVQLVISDMRMPEMGGEVFLEQV   73 (154)
T ss_dssp             CSCCEEEEECSCHHHHHHHHHHHHTTTCEEEEESCHHHHHHHH-----------TTSCCSEEEEESSCSSSCHHHHHHHH
T ss_pred             CCCCeEEEEcCCHHHHHHHHHHHHHcCCeEEEeCCHHHHHHHH-----------hcCCCCEEEEecCCCCCCHHHHHHHH
Confidence            5678999999999999999999999999999999999999999           66789999999999999999999999


Q ss_pred             HhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcC-CCeEEe
Q 023816          107 KVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDG-AEDFIV  185 (276)
Q Consensus       107 r~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~G-a~d~l~  185 (276)
                      ++..|                                             .+|||++|+........++++.| +++||.
T Consensus        74 ~~~~~---------------------------------------------~~~ii~ls~~~~~~~~~~~~~~g~~~~~l~  108 (154)
T 2rjn_A           74 AKSYP---------------------------------------------DIERVVISGYADAQATIDAVNRGKISRFLL  108 (154)
T ss_dssp             HHHCT---------------------------------------------TSEEEEEECGGGHHHHHHHHHTTCCSEEEE
T ss_pred             HHhCC---------------------------------------------CCcEEEEecCCCHHHHHHHHhccchheeee
Confidence            98766                                             79999999999988999999998 999999


Q ss_pred             CCCCHHHHHHHHHHHHHhh
Q 023816          186 KPVKLSDVKRIKDYLTRDV  204 (276)
Q Consensus       186 KPv~~~~L~~~~~~l~~~~  204 (276)
                      ||++.++|...+..+.+..
T Consensus       109 kP~~~~~L~~~i~~~~~~~  127 (154)
T 2rjn_A          109 KPWEDEDVFKVVEKGLQLA  127 (154)
T ss_dssp             SSCCHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHH
Confidence            9999999977777665543

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

Probab=99.87  E-value=6.5e-21  Score=148.62  Aligned_cols=123  Identities=20%  Similarity=0.307  Sum_probs=108.2

Q ss_pred             CCCCccEEEEEeCCHHHHHHHHHHHhh-CCCE-EEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHH
Q 023816           25 SDTEEVHVLAVDDSFVDRKVIERLLTI-SSCK-VTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYEL  102 (276)
Q Consensus        25 ~~~~~~~VLIVdD~~~~~~~L~~~L~~-~g~~-v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~el  102 (276)
                      ..+.+++||||||++..++.++.+|+. .||+ +..+.++.+|++.+           +...||+||+|+.||+++|+++
T Consensus         4 ~~~~~~~iLivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~a~~~l-----------~~~~~dlii~d~~l~~~~g~~~   72 (143)
T 3cnb_A            4 NVKNDFSILIIEDDKEFADMLTQFLENLFPYAKIKIAYNPFDAGDLL-----------HTVKPDVVMLDLMMVGMDGFSI   72 (143)
T ss_dssp             -----CEEEEECSCHHHHHHHHHHHHHHCTTCEEEEECSHHHHHHHH-----------HHTCCSEEEEETTCTTSCHHHH
T ss_pred             cccCCceEEEEECCHHHHHHHHHHHHhccCccEEEEECCHHHHHHHH-----------HhcCCCEEEEecccCCCcHHHH
Confidence            345578999999999999999999998 9999 89999999999998           5567999999999999999999


Q ss_pred             HHHHHh--hCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCC
Q 023816          103 LKKIKV--TTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGA  180 (276)
Q Consensus       103 l~~Ir~--~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga  180 (276)
                      +++|++  ..+                                             .+|||++|+........++++.|+
T Consensus        73 ~~~l~~~~~~~---------------------------------------------~~~ii~~s~~~~~~~~~~~~~~g~  107 (143)
T 3cnb_A           73 CHRIKSTPATA---------------------------------------------NIIVIAMTGALTDDNVSRIVALGA  107 (143)
T ss_dssp             HHHHHTSTTTT---------------------------------------------TSEEEEEESSCCHHHHHHHHHTTC
T ss_pred             HHHHHhCcccc---------------------------------------------CCcEEEEeCCCCHHHHHHHHhcCC
Confidence            999997  333                                             799999999999999999999999


Q ss_pred             CeEEeCCCCHHHHHHHHHHHHHh
Q 023816          181 EDFIVKPVKLSDVKRIKDYLTRD  203 (276)
Q Consensus       181 ~d~l~KPv~~~~L~~~~~~l~~~  203 (276)
                      ++||.||++.++|...+..+.+.
T Consensus       108 ~~~l~kP~~~~~l~~~i~~~~~~  130 (143)
T 3cnb_A          108 ETCFGKPLNFTLLEKTIKQLVEQ  130 (143)
T ss_dssp             SEEEESSCCHHHHHHHHHHHHHT
T ss_pred             cEEEeCCCCHHHHHHHHHHHHHh
Confidence            99999999999997777766544

>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=99.87  E-value=6.7e-21  Score=150.29  Aligned_cols=122  Identities=26%  Similarity=0.380  Sum_probs=108.9

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhCCCE--EEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHH
Q 023816           28 EEVHVLAVDDSFVDRKVIERLLTISSCK--VTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKK  105 (276)
Q Consensus        28 ~~~~VLIVdD~~~~~~~L~~~L~~~g~~--v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~  105 (276)
                      .+++||||||++..++.++.+|+..|+.  +..+.++++|++.+           ....||+||+|+.||+++|++++++
T Consensus         4 ~~~~ILivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~a~~~l-----------~~~~~dlii~D~~l~~~~g~~~~~~   72 (144)
T 3kht_A            4 RSKRVLVVEDNPDDIALIRRVLDRKDIHCQLEFVDNGAKALYQV-----------QQAKYDLIILDIGLPIANGFEVMSA   72 (144)
T ss_dssp             -CEEEEEECCCHHHHHHHHHHHHHTTCCEEEEEESSHHHHHHHH-----------TTCCCSEEEECTTCGGGCHHHHHHH
T ss_pred             CCCEEEEEeCCHHHHHHHHHHHHhcCCCeeEEEECCHHHHHHHh-----------hcCCCCEEEEeCCCCCCCHHHHHHH
Confidence            4689999999999999999999999987  88899999999999           6778999999999999999999999


Q ss_pred             HHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEe
Q 023816          106 IKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIV  185 (276)
Q Consensus       106 Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~  185 (276)
                      ||+..                                           ....+|||++|+....+...++++.|+++||.
T Consensus        73 lr~~~-------------------------------------------~~~~~pii~~s~~~~~~~~~~~~~~ga~~~l~  109 (144)
T 3kht_A           73 VRKPG-------------------------------------------ANQHTPIVILTDNVSDDRAKQCMAAGASSVVD  109 (144)
T ss_dssp             HHSSS-------------------------------------------TTTTCCEEEEETTCCHHHHHHHHHTTCSEEEE
T ss_pred             HHhcc-------------------------------------------cccCCCEEEEeCCCCHHHHHHHHHcCCCEEEE
Confidence            99721                                           12279999999999999999999999999999


Q ss_pred             CCC-CHHHHHHHHHHHHHh
Q 023816          186 KPV-KLSDVKRIKDYLTRD  203 (276)
Q Consensus       186 KPv-~~~~L~~~~~~l~~~  203 (276)
                      ||+ +.++|.+.+..+.+.
T Consensus       110 Kp~~~~~~l~~~i~~~l~~  128 (144)
T 3kht_A          110 KSSNNVTDFYGRIYAIFSY  128 (144)
T ss_dssp             CCTTSHHHHHHHHHHHHHH
T ss_pred             CCCCcHHHHHHHHHHHHHH
Confidence            999 999997777666554

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

Probab=99.87  E-value=3.5e-21  Score=152.17  Aligned_cols=118  Identities=26%  Similarity=0.390  Sum_probs=108.0

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhh
Q 023816           30 VHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVT  109 (276)
Q Consensus        30 ~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~  109 (276)
                      .+||||||++..++.++.+|+..||+|..+.++.+|++.+           ....||+||+|+.||+++|++++++|++.
T Consensus         5 ~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l-----------~~~~~dlvllD~~l~~~~g~~l~~~l~~~   73 (137)
T 3cfy_A            5 PRVLLVEDSTSLAILYKQYVKDEPYDIFHVETGRDAIQFI-----------ERSKPQLIILDLKLPDMSGEDVLDWINQN   73 (137)
T ss_dssp             CEEEEECSCTTHHHHHHHHTTTSSSEEEEESSHHHHHHHH-----------HHHCCSEEEECSBCSSSBHHHHHHHHHHT
T ss_pred             ceEEEEeCCHHHHHHHHHHHHhcCceEEEeCCHHHHHHHH-----------HhcCCCEEEEecCCCCCCHHHHHHHHHhc
Confidence            4899999999999999999999999999999999999998           45579999999999999999999999986


Q ss_pred             CCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCC
Q 023816          110 TPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVK  189 (276)
Q Consensus       110 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~  189 (276)
                      .+                                             .+|||++|+........++++.|+++||.||++
T Consensus        74 ~~---------------------------------------------~~~ii~ls~~~~~~~~~~~~~~ga~~~l~KP~~  108 (137)
T 3cfy_A           74 DI---------------------------------------------PTSVIIATAHGSVDLAVNLIQKGAEDFLEKPIN  108 (137)
T ss_dssp             TC---------------------------------------------CCEEEEEESSCCHHHHHHHHHTTCSEEEESSCC
T ss_pred             CC---------------------------------------------CCCEEEEEecCcHHHHHHHHHCCccEEEeCCCC
Confidence            65                                             799999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHh
Q 023816          190 LSDVKRIKDYLTRD  203 (276)
Q Consensus       190 ~~~L~~~~~~l~~~  203 (276)
                      .++|...+..+.+.
T Consensus       109 ~~~L~~~i~~~~~~  122 (137)
T 3cfy_A          109 ADRLKTSVALHLKR  122 (137)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH
Confidence            99997777665543

>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=99.86  E-value=2.5e-21  Score=149.36  Aligned_cols=121  Identities=23%  Similarity=0.432  Sum_probs=107.5

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhCCC-EEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHH
Q 023816           28 EEVHVLAVDDSFVDRKVIERLLTISSC-KVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKI  106 (276)
Q Consensus        28 ~~~~VLIVdD~~~~~~~L~~~L~~~g~-~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~I  106 (276)
                      .+++||||||++..++.++.+|+..|+ .+..+.++++|++.+           ....||+||+|+.||+++|++++++|
T Consensus         5 ~~~~ilivdd~~~~~~~l~~~L~~~g~~~v~~~~~~~~a~~~~-----------~~~~~dlvl~D~~l~~~~g~~~~~~l   73 (129)
T 1p6q_A            5 EKIKVLIVDDQVTSRLLLGDALQQLGFKQITAAGDGEQGMKIM-----------AQNPHHLVISDFNMPKMDGLGLLQAV   73 (129)
T ss_dssp             SCCCEEEECSSHHHHHHHHHHHHTTTCSCEECCSSHHHHHHHH-----------HTSCCSEEEECSSSCSSCHHHHHHHH
T ss_pred             ccCeEEEEcCCHHHHHHHHHHHHHCCCcEEEecCCHHHHHHHH-----------HcCCCCEEEEeCCCCCCCHHHHHHHH
Confidence            457899999999999999999999999 788899999999998           56679999999999999999999999


Q ss_pred             HhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeC
Q 023816          107 KVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVK  186 (276)
Q Consensus       107 r~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~K  186 (276)
                      |+..                                           ....+|||++|+........++++.|+++|+.|
T Consensus        74 ~~~~-------------------------------------------~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~K  110 (129)
T 1p6q_A           74 RANP-------------------------------------------ATKKAAFIILTAQGDRALVQKAAALGANNVLAK  110 (129)
T ss_dssp             TTCT-------------------------------------------TSTTCEEEECCSCCCHHHHHHHHHHTCSCEECC
T ss_pred             hcCc-------------------------------------------cccCCCEEEEeCCCCHHHHHHHHHcCCCEEEEC
Confidence            9632                                           123789999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHH
Q 023816          187 PVKLSDVKRIKDYLTR  202 (276)
Q Consensus       187 Pv~~~~L~~~~~~l~~  202 (276)
                      |++.++|...+..+.+
T Consensus       111 P~~~~~l~~~i~~~~~  126 (129)
T 1p6q_A          111 PFTIEKMKAAIEAVFG  126 (129)
T ss_dssp             CSSHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHH
Confidence            9999999777766543

>3mm4_A Histidine kinase homolog; receiver domain, CKI1, cytokinin signaling, ROS fold, CHEY-like, transferase; 2.00A {Arabidopsis thaliana} PDB: 3mmn_A

Probab=99.86  E-value=2.9e-21  Score=164.83  Aligned_cols=135  Identities=25%  Similarity=0.377  Sum_probs=106.8

Q ss_pred             CCCccEEEEEeCCHHHHHHHHHHHhhCCC-EEEEECCHHHHHHHhcccc--cccccCCCCCceeEEEEecCCCCCCHHHH
Q 023816           26 DTEEVHVLAVDDSFVDRKVIERLLTISSC-KVTAVDSGRRALQFLGLDE--EQSINGFDGLKVDLIITDYCMPGMTGYEL  102 (276)
Q Consensus        26 ~~~~~~VLIVdD~~~~~~~L~~~L~~~g~-~v~~a~~g~~al~~l~~~~--~~~~~~~~~~~~DlIL~D~~mp~~~G~el  102 (276)
                      ...+.+||||||++.+++.++.+|+..|| .|..+.++++|++.+....  .+.........|||||+|+.||+++|+++
T Consensus        58 ~~~~~~ILiVdDd~~~~~~l~~~L~~~g~~~v~~a~~~~eal~~l~~~~~~~~~~~~~~~~~~dlillD~~lp~~~G~el  137 (206)
T 3mm4_A           58 FLRGKRVLVVDDNFISRKVATGKLKKMGVSEVEQCDSGKEALRLVTEGLTQREEQGSVDKLPFDYIFMDCQMPEMDGYEA  137 (206)
T ss_dssp             TTTTCEEEEECSCHHHHHHHHHHHHHTTCSEEEEESSHHHHHHHHHHHHHHHHHHTCSSCCSCSEEEEESCCSSSCHHHH
T ss_pred             ccCCCEEEEEeCCHHHHHHHHHHHHHcCCCeeeeeCCHHHHHHHHHhhcccccccccccCCCCCEEEEcCCCCCCCHHHH
Confidence            34567999999999999999999999999 8999999999999984310  00000112347999999999999999999


Q ss_pred             HHHHHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCC-CHHHHHHHHhcCCC
Q 023816          103 LKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSEN-ILARIDRCLEDGAE  181 (276)
Q Consensus       103 l~~Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~-~~~~~~~al~~Ga~  181 (276)
                      +++||+...                                         .....+|||++|++. ......++++.|++
T Consensus       138 ~~~lr~~~~-----------------------------------------~~~~~~piI~ls~~~~~~~~~~~~~~~Ga~  176 (206)
T 3mm4_A          138 TREIRKVEK-----------------------------------------SYGVRTPIIAVSGHDPGSEEARETIQAGMD  176 (206)
T ss_dssp             HHHHHHHHH-----------------------------------------TTTCCCCEEEEESSCCCHHHHHHHHHHTCS
T ss_pred             HHHHHhhhh-----------------------------------------hcCCCCcEEEEECCCCcHHHHHHHHhCCCC
Confidence            999997411                                         001279999999998 77889999999999


Q ss_pred             eEEeCCCCHHHHHHHHHHHHHh
Q 023816          182 DFIVKPVKLSDVKRIKDYLTRD  203 (276)
Q Consensus       182 d~l~KPv~~~~L~~~~~~l~~~  203 (276)
                      +||.||++  +|.+.+..+.+.
T Consensus       177 ~~l~KP~~--~L~~~i~~~l~~  196 (206)
T 3mm4_A          177 AFLDKSLN--QLANVIREIESK  196 (206)
T ss_dssp             EEEETTCT--THHHHHHHHC--
T ss_pred             EEEcCcHH--HHHHHHHHHHhh
Confidence            99999998  776666655543

>3hdg_A Uncharacterized protein; two-component sensor activity, response regulator, PSI-II, 11227F, NYSGXRC, structural genomics; 2.27A {Wolinella succinogenes} SCOP: c.23.1.0

Probab=99.86  E-value=2.7e-21  Score=150.99  Aligned_cols=121  Identities=21%  Similarity=0.295  Sum_probs=111.6

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHH
Q 023816           28 EEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIK  107 (276)
Q Consensus        28 ~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir  107 (276)
                      .+++||||||++..++.++++|+..|+.+..+.++++|++.+           +...||+||+|+.||+++|+++++.||
T Consensus         6 ~~~~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~a~~~l-----------~~~~~dlvi~d~~l~~~~g~~~~~~l~   74 (137)
T 3hdg_A            6 VALKILIVEDDTDAREWLSTIISNHFPEVWSAGDGEEGERLF-----------GLHAPDVIITDIRMPKLGGLEMLDRIK   74 (137)
T ss_dssp             -CCCEEEECSCHHHHHHHHHHHHTTCSCEEEESSHHHHHHHH-----------HHHCCSEEEECSSCSSSCHHHHHHHHH
T ss_pred             cccEEEEEeCCHHHHHHHHHHHHhcCcEEEEECCHHHHHHHH-----------hccCCCEEEEeCCCCCCCHHHHHHHHH
Confidence            368999999999999999999999999999999999999998           456799999999999999999999999


Q ss_pred             hhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCC
Q 023816          108 VTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKP  187 (276)
Q Consensus       108 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KP  187 (276)
                      +..+                                             .+|||++|+....+...++++.|+++||.||
T Consensus        75 ~~~~---------------------------------------------~~~ii~~s~~~~~~~~~~~~~~g~~~~l~kP  109 (137)
T 3hdg_A           75 AGGA---------------------------------------------KPYVIVISAFSEMKYFIKAIELGVHLFLPKP  109 (137)
T ss_dssp             HTTC---------------------------------------------CCEEEECCCCCCHHHHHHHHHHCCSEECCSS
T ss_pred             hcCC---------------------------------------------CCcEEEEecCcChHHHHHHHhCCcceeEcCC
Confidence            8766                                             7999999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHHHhh
Q 023816          188 VKLSDVKRIKDYLTRDV  204 (276)
Q Consensus       188 v~~~~L~~~~~~l~~~~  204 (276)
                      ++.++|...+..+.+..
T Consensus       110 ~~~~~l~~~i~~~~~~~  126 (137)
T 3hdg_A          110 IEPGRLMETLEDFRHIK  126 (137)
T ss_dssp             CCHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHH
Confidence            99999988887777653

>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=99.86  E-value=4.4e-21  Score=170.29  Aligned_cols=123  Identities=23%  Similarity=0.368  Sum_probs=109.3

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCC-ceeEEEEecCCCCCCHHHHHHHH
Q 023816           28 EEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGL-KVDLIITDYCMPGMTGYELLKKI  106 (276)
Q Consensus        28 ~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~-~~DlIL~D~~mp~~~G~ell~~I  106 (276)
                      .+++||||||++..++.+...|+..|+.+..+.+|++|++.+           ... .||+||+|++||++||++++++|
T Consensus       123 ~~~~ILivDD~~~~~~~l~~~L~~~~~~v~~a~~~~eal~~l-----------~~~~~~dlvllD~~mP~~dG~~l~~~l  191 (259)
T 3luf_A          123 QQIEVLVVDDSRTSRHRTMAQLRKQLLQVHEASHAREALATL-----------EQHPAIRLVLVDYYMPEIDGISLVRML  191 (259)
T ss_dssp             TTCEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHH-----------HHCTTEEEEEECSCCSSSCHHHHHHHH
T ss_pred             CCCcEEEEeCCHHHHHHHHHHHHHcCcEEEEeCCHHHHHHHH-----------hcCCCCCEEEEcCCCCCCCHHHHHHHH
Confidence            368999999999999999999999999999999999999998           333 49999999999999999999999


Q ss_pred             HhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeC
Q 023816          107 KVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVK  186 (276)
Q Consensus       107 r~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~K  186 (276)
                      |+..+                                           ...+|||++|+........+|++.||+|||.|
T Consensus       192 r~~~~-------------------------------------------~~~~~ii~~s~~~~~~~~~~a~~~Ga~~yl~K  228 (259)
T 3luf_A          192 RERYS-------------------------------------------KQQLAIIGISVSDKRGLSARYLKQGANDFLNQ  228 (259)
T ss_dssp             HHHCC-------------------------------------------TTTSEEEEEECSSSSSHHHHHHHTTCSEEEES
T ss_pred             HhccC-------------------------------------------CCCCeEEEEEccCCHHHHHHHHhcChhheEcC
Confidence            98654                                           22689999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHhh
Q 023816          187 PVKLSDVKRIKDYLTRDV  204 (276)
Q Consensus       187 Pv~~~~L~~~~~~l~~~~  204 (276)
                      |++.++|...+..+.+..
T Consensus       229 P~~~~~L~~~i~~~l~~~  246 (259)
T 3luf_A          229 PFEPEELQCRVSHNLEAL  246 (259)
T ss_dssp             SCCHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHhH
Confidence            999999976666555443

>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=99.86  E-value=3e-21  Score=170.32  Aligned_cols=122  Identities=26%  Similarity=0.523  Sum_probs=111.9

Q ss_pred             CCCccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHH
Q 023816           26 DTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKK  105 (276)
Q Consensus        26 ~~~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~  105 (276)
                      ....++||||||++.+++.+..+|+..||+|..+.++.+|++.+           +...||+||+|++||+++|++++++
T Consensus       126 ~~~~~~ILivdd~~~~~~~l~~~L~~~g~~v~~a~~~~eal~~l-----------~~~~~dlvl~D~~mp~~~G~~l~~~  194 (254)
T 2ayx_A          126 DNDDMMILVVDDHPINRRLLADQLGSLGYQCKTANDGVDALNVL-----------SKNHIDIVLSDVNMPNMDGYRLTQR  194 (254)
T ss_dssp             CCCCCEEEEEESSHHHHHHHHHHHHHHTSEEEEECCSHHHHHHH-----------HHSCCSEEEEEESSCSSCCHHHHHH
T ss_pred             CCCCCEEEEEeCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHH-----------HhCCCCEEEEcCCCCCCCHHHHHHH
Confidence            44568999999999999999999999999999999999999999           5567999999999999999999999


Q ss_pred             HHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEe
Q 023816          106 IKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIV  185 (276)
Q Consensus       106 Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~  185 (276)
                      ||+..+                                             .+|||++|+....+...++++.|+++||.
T Consensus       195 ir~~~~---------------------------------------------~~piI~lt~~~~~~~~~~~~~~G~~~~l~  229 (254)
T 2ayx_A          195 IRQLGL---------------------------------------------TLPVIGVTANALAEEKQRCLESGMDSCLS  229 (254)
T ss_dssp             HHHHHC---------------------------------------------CSCEEEEESSTTSHHHHHHHHCCCEEEEE
T ss_pred             HHhcCC---------------------------------------------CCcEEEEECCCCHHHHHHHHHcCCceEEE
Confidence            998655                                             79999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHh
Q 023816          186 KPVKLSDVKRIKDYLTRD  203 (276)
Q Consensus       186 KPv~~~~L~~~~~~l~~~  203 (276)
                      ||++.++|.+.+..+.+.
T Consensus       230 KP~~~~~L~~~l~~~~~~  247 (254)
T 2ayx_A          230 KPVTLDVIKQTLTLYAER  247 (254)
T ss_dssp             SSCCHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHH
Confidence            999999998777766554

>3ilh_A Two component response regulator; NYSGXRC, PSI-II, protein S initiative, structural genomics; 2.59A {Cytophaga hutchinsonii}

Probab=99.86  E-value=8.1e-21  Score=148.54  Aligned_cols=128  Identities=19%  Similarity=0.252  Sum_probs=109.4

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhCCC--EEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHH
Q 023816           28 EEVHVLAVDDSFVDRKVIERLLTISSC--KVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKK  105 (276)
Q Consensus        28 ~~~~VLIVdD~~~~~~~L~~~L~~~g~--~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~  105 (276)
                      .+++||||||++..+..++.+|+..|+  .+..+.++++|++.+.....      .+..||+||+|+.||+++|++++++
T Consensus         8 ~~~~iLivdd~~~~~~~l~~~l~~~~~~~~v~~~~~~~~a~~~l~~~~~------~~~~~dlvi~D~~l~~~~g~~~~~~   81 (146)
T 3ilh_A            8 KIDSVLLIDDDDIVNFLNTTIIRMTHRVEEIQSVTSGNAAINKLNELYA------AGRWPSIICIDINMPGINGWELIDL   81 (146)
T ss_dssp             CEEEEEEECSCHHHHHHHHHHHHTTCCEEEEEEESSHHHHHHHHHHHHT------SSCCCSEEEEESSCSSSCHHHHHHH
T ss_pred             ccceEEEEeCCHHHHHHHHHHHHhcCCCeeeeecCCHHHHHHHHHHhhc------cCCCCCEEEEcCCCCCCCHHHHHHH
Confidence            468999999999999999999999999  89999999999999832110      1268999999999999999999999


Q ss_pred             HHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcC-CCeEE
Q 023816          106 IKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDG-AEDFI  184 (276)
Q Consensus       106 Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~G-a~d~l  184 (276)
                      ||+..+                                         .....+|||++|+........++++.| +++||
T Consensus        82 l~~~~~-----------------------------------------~~~~~~~ii~~t~~~~~~~~~~~~~~g~~~~~l  120 (146)
T 3ilh_A           82 FKQHFQ-----------------------------------------PMKNKSIVCLLSSSLDPRDQAKAEASDWVDYYV  120 (146)
T ss_dssp             HHHHCG-----------------------------------------GGTTTCEEEEECSSCCHHHHHHHHHCSSCCEEE
T ss_pred             HHHhhh-----------------------------------------hccCCCeEEEEeCCCChHHHHHHHhcCCcceee
Confidence            998320                                         011279999999999999999999999 99999


Q ss_pred             eCCCCHHHHHHHHHHHHH
Q 023816          185 VKPVKLSDVKRIKDYLTR  202 (276)
Q Consensus       185 ~KPv~~~~L~~~~~~l~~  202 (276)
                      .||++.++|.+.+.....
T Consensus       121 ~KP~~~~~L~~~i~~~~~  138 (146)
T 3ilh_A          121 SKPLTANALNNLYNKVLN  138 (146)
T ss_dssp             CSSCCHHHHHHHHHHHHC
T ss_pred             eCCCCHHHHHHHHHHHHH
Confidence            999999999777766553

>1k68_A Phytochrome response regulator RCPA; phosphorylated aspartate, CHEY homologue, homodimer, (beta/alpha)5, signaling protein; HET: PHD; 1.90A {Tolypothrix SP} SCOP: c.23.1.1

Probab=99.86  E-value=1.9e-20  Score=144.73  Aligned_cols=128  Identities=26%  Similarity=0.373  Sum_probs=108.9

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhCCC--EEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHH
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTISSC--KVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKI  106 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~g~--~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~I  106 (276)
                      +.+||||||++..++.++..|+..|+  .+..+.++.+|++.+....+..    ....||+||+|+.||+++|++++++|
T Consensus         2 ~~~ilivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~a~~~l~~~~~~~----~~~~~dlvi~d~~~~~~~g~~~~~~l   77 (140)
T 1k68_A            2 HKKIFLVEDNKADIRLIQEALANSTVPHEVVTVRDGMEAMAYLRQEGEYA----NASRPDLILLXLNLPKKDGREVLAEI   77 (140)
T ss_dssp             CCEEEEECCCHHHHHHHHHHHHTCSSCCEEEEECSHHHHHHHHTTCGGGG----SCCCCSEEEECSSCSSSCHHHHHHHH
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCCceEEEECCHHHHHHHHHcccccc----cCCCCcEEEEecCCCcccHHHHHHHH
Confidence            56899999999999999999999998  9999999999999993100000    01689999999999999999999999


Q ss_pred             HhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeC
Q 023816          107 KVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVK  186 (276)
Q Consensus       107 r~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~K  186 (276)
                      |+...                                           ...+|||++|+....+...++++.|+++|+.|
T Consensus        78 ~~~~~-------------------------------------------~~~~pii~ls~~~~~~~~~~~~~~g~~~~l~k  114 (140)
T 1k68_A           78 KSDPT-------------------------------------------LKRIPVVVLSTSINEDDIFHSYDLHVNCYITK  114 (140)
T ss_dssp             HHSTT-------------------------------------------GGGSCEEEEESCCCHHHHHHHHHTTCSEEEEC
T ss_pred             HcCcc-------------------------------------------cccccEEEEecCCcHHHHHHHHHhchhheecC
Confidence            97441                                           12689999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHh
Q 023816          187 PVKLSDVKRIKDYLTRD  203 (276)
Q Consensus       187 Pv~~~~L~~~~~~l~~~  203 (276)
                      |++.++|...+..+.+.
T Consensus       115 P~~~~~l~~~i~~~~~~  131 (140)
T 1k68_A          115 SANLSQLFQIVKGIEEF  131 (140)
T ss_dssp             CSSHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHH
Confidence            99999997777766544

>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=99.86  E-value=9e-21  Score=147.82  Aligned_cols=121  Identities=22%  Similarity=0.375  Sum_probs=107.9

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHH
Q 023816           28 EEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIK  107 (276)
Q Consensus        28 ~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir  107 (276)
                      .+.+||||||++..++.++.+|+..||++..+.++.+|+..+.          ....||+||+|+.||+++|++++++||
T Consensus         6 ~~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~~~----------~~~~~dlvi~D~~l~~~~g~~~~~~l~   75 (136)
T 3hdv_A            6 ARPLVLVVDDNAVNREALILYLKSRGIDAVGADGAEEARLYLH----------YQKRIGLMITDLRMQPESGLDLIRTIR   75 (136)
T ss_dssp             -CCEEEEECSCHHHHHHHHHHHHHTTCCEEEESSHHHHHHHHH----------HCTTEEEEEECSCCSSSCHHHHHHHHH
T ss_pred             CCCeEEEECCCHHHHHHHHHHHHHcCceEEEeCCHHHHHHHHH----------hCCCCcEEEEeccCCCCCHHHHHHHHH
Confidence            4689999999999999999999999999999999999999882          223499999999999999999999999


Q ss_pred             hh-CCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeC
Q 023816          108 VT-TPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVK  186 (276)
Q Consensus       108 ~~-~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~K  186 (276)
                      +. .+                                             .+|||++|+........++++.|+++||.|
T Consensus        76 ~~~~~---------------------------------------------~~~ii~~s~~~~~~~~~~~~~~g~~~~l~K  110 (136)
T 3hdv_A           76 ASERA---------------------------------------------ALSIIVVSGDTDVEEAVDVMHLGVVDFLLK  110 (136)
T ss_dssp             TSTTT---------------------------------------------TCEEEEEESSCCHHHHHHHHHTTCSEEEES
T ss_pred             hcCCC---------------------------------------------CCCEEEEeCCCChHHHHHHHhCCcceEEeC
Confidence            75 34                                             799999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHh
Q 023816          187 PVKLSDVKRIKDYLTRD  203 (276)
Q Consensus       187 Pv~~~~L~~~~~~l~~~  203 (276)
                      |++.++|...++.+...
T Consensus       111 P~~~~~l~~~i~~~~~~  127 (136)
T 3hdv_A          111 PVDLGKLLELVNKELKI  127 (136)
T ss_dssp             SCCHHHHHHHHHHHHC-
T ss_pred             CCCHHHHHHHHHHHhcC
Confidence            99999997777766543

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

Probab=99.86  E-value=5.7e-22  Score=155.25  Aligned_cols=118  Identities=12%  Similarity=0.110  Sum_probs=108.5

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhCC-CEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHH
Q 023816           27 TEEVHVLAVDDSFVDRKVIERLLTISS-CKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKK  105 (276)
Q Consensus        27 ~~~~~VLIVdD~~~~~~~L~~~L~~~g-~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~  105 (276)
                      ....+||||||++..+..++.+|+..| |++..+.++++|++.+           ....||+||+|+.||+++|++++++
T Consensus        12 ~~~~~ilivdd~~~~~~~l~~~L~~~g~~~v~~~~~~~~a~~~l-----------~~~~~dlvi~D~~l~~~~g~~~~~~   80 (135)
T 3snk_A           12 TKRKQVALFSSDPNFKRDVATRLDALAIYDVRVSETDDFLKGPP-----------ADTRPGIVILDLGGGDLLGKPGIVE   80 (135)
T ss_dssp             -CCEEEEEECSCHHHHHHHHHHHHHTSSEEEEEECGGGGGGCCC-----------TTCCCSEEEEEEETTGGGGSTTHHH
T ss_pred             CCCcEEEEEcCCHHHHHHHHHHHhhcCCeEEEEeccHHHHHHHH-----------hccCCCEEEEeCCCCCchHHHHHHH
Confidence            346799999999999999999999999 9999999999999888           6778999999999999999999999


Q ss_pred             HHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEe
Q 023816          106 IKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIV  185 (276)
Q Consensus       106 Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~  185 (276)
                      ||+..+                                             .+|||++|+....+...++++.|+++||.
T Consensus        81 l~~~~~---------------------------------------------~~~ii~~s~~~~~~~~~~~~~~g~~~~l~  115 (135)
T 3snk_A           81 ARALWA---------------------------------------------TVPLIAVSDELTSEQTRVLVRMNASDWLH  115 (135)
T ss_dssp             HHGGGT---------------------------------------------TCCEEEEESCCCHHHHHHHHHTTCSEEEE
T ss_pred             HHhhCC---------------------------------------------CCcEEEEeCCCCHHHHHHHHHcCcHhhcc
Confidence            998666                                             79999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHH
Q 023816          186 KPVKLSDVKRIKDYL  200 (276)
Q Consensus       186 KPv~~~~L~~~~~~l  200 (276)
                      ||++.++|...+..+
T Consensus       116 KP~~~~~L~~~i~~~  130 (135)
T 3snk_A          116 KPLDGKELLNAVTFH  130 (135)
T ss_dssp             SSCCHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHHHH
Confidence            999999997666554

>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=99.86  E-value=7e-21  Score=144.33  Aligned_cols=115  Identities=27%  Similarity=0.400  Sum_probs=104.9

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhh
Q 023816           30 VHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVT  109 (276)
Q Consensus        30 ~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~  109 (276)
                      .+||||||++..++.++..|+..||++..+.++.+|++.+           ....||+||+|+.||+++|++++++|++.
T Consensus         2 ~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~~-----------~~~~~dlvl~D~~l~~~~g~~~~~~l~~~   70 (120)
T 2a9o_A            2 KKILIVDDEKPISDIIKFNMTKEGYEVVTAFNGREALEQF-----------EAEQPDIIILDLMLPEIDGLEVAKTIRKT   70 (120)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHH-----------HHHCCSEEEECSSCSSSCHHHHHHHHHHH
T ss_pred             ceEEEEcCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHH-----------HhCCCCEEEEeccCCCCCHHHHHHHHHhC
Confidence            4899999999999999999999999999999999999988           45579999999999999999999999963


Q ss_pred             CCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCC
Q 023816          110 TPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVK  189 (276)
Q Consensus       110 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~  189 (276)
                       +                                             .+|||++|+........++++.|+++|+.||++
T Consensus        71 -~---------------------------------------------~~~ii~~s~~~~~~~~~~~~~~g~~~~l~Kp~~  104 (120)
T 2a9o_A           71 -S---------------------------------------------SVPILMLSAKDSEFDKVIGLELGADDYVTKPFS  104 (120)
T ss_dssp             -C---------------------------------------------CCCEEEEESCCSHHHHHHHHHHTCSEEEESSCC
T ss_pred             -C---------------------------------------------CCCEEEEecCCchHHHHHHHhCCHhheEeCCCC
Confidence             3                                             689999999999988999999999999999999


Q ss_pred             HHHHHHHHHHHH
Q 023816          190 LSDVKRIKDYLT  201 (276)
Q Consensus       190 ~~~L~~~~~~l~  201 (276)
                      .++|...+..+.
T Consensus       105 ~~~l~~~i~~~~  116 (120)
T 2a9o_A          105 NRELQARVKALL  116 (120)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            999977666554

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

Probab=99.86  E-value=2.7e-21  Score=152.87  Aligned_cols=128  Identities=11%  Similarity=0.152  Sum_probs=113.9

Q ss_pred             CCCCCCCCccEEEEEeCCHHHHHHHHHHHhhCC-CEEEEECCHHHHHHHhcccccccccCCCC-CceeEEEEecCCCCCC
Q 023816           21 DLSPSDTEEVHVLAVDDSFVDRKVIERLLTISS-CKVTAVDSGRRALQFLGLDEEQSINGFDG-LKVDLIITDYCMPGMT   98 (276)
Q Consensus        21 ~~~~~~~~~~~VLIVdD~~~~~~~L~~~L~~~g-~~v~~a~~g~~al~~l~~~~~~~~~~~~~-~~~DlIL~D~~mp~~~   98 (276)
                      ...+......+||||||++..+..++.+|+..| |++..+.++.+++..+.          +. ..||+||+|+.||+++
T Consensus        12 ~~~~~~~~~~~ilivdd~~~~~~~l~~~L~~~g~~~v~~~~~~~~~~~~~~----------~~~~~~dlvi~D~~l~~~~   81 (146)
T 4dad_A           12 HENLYFQGMINILVASEDASRLAHLARLVGDAGRYRVTRTVGRAAQIVQRT----------DGLDAFDILMIDGAALDTA   81 (146)
T ss_dssp             -CCCCCGGGCEEEEECSCHHHHHHHHHHHHHHCSCEEEEECCCHHHHTTCH----------HHHTTCSEEEEECTTCCHH
T ss_pred             CCCCCcCCCCeEEEEeCCHHHHHHHHHHHhhCCCeEEEEeCCHHHHHHHHH----------hcCCCCCEEEEeCCCCCcc
Confidence            344566778999999999999999999999999 99999999999988762          23 6899999999999999


Q ss_pred             HHHHHHHHHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhc
Q 023816           99 GYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLED  178 (276)
Q Consensus        99 G~ell~~Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~  178 (276)
                      |++++++||+..|                                             .+|||++|+....+...++++.
T Consensus        82 g~~~~~~l~~~~~---------------------------------------------~~~ii~lt~~~~~~~~~~~~~~  116 (146)
T 4dad_A           82 ELAAIEKLSRLHP---------------------------------------------GLTCLLVTTDASSQTLLDAMRA  116 (146)
T ss_dssp             HHHHHHHHHHHCT---------------------------------------------TCEEEEEESCCCHHHHHHHHTT
T ss_pred             HHHHHHHHHHhCC---------------------------------------------CCcEEEEeCCCCHHHHHHHHHh
Confidence            9999999998777                                             7999999999999999999999


Q ss_pred             CCCeEEeCCCCHHHHHHHHHHHHHh
Q 023816          179 GAEDFIVKPVKLSDVKRIKDYLTRD  203 (276)
Q Consensus       179 Ga~d~l~KPv~~~~L~~~~~~l~~~  203 (276)
                      |+++||.||++.++|...+..+.+.
T Consensus       117 ga~~~l~Kp~~~~~L~~~i~~~~~~  141 (146)
T 4dad_A          117 GVRDVLRWPLEPRALDDALKRAAAQ  141 (146)
T ss_dssp             TEEEEEESSCCHHHHHHHHHHHHHT
T ss_pred             CCceeEcCCCCHHHHHHHHHHHHhh
Confidence            9999999999999998777766543

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

Probab=99.86  E-value=1.9e-20  Score=146.31  Aligned_cols=124  Identities=24%  Similarity=0.448  Sum_probs=105.2

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHH
Q 023816           27 TEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKI  106 (276)
Q Consensus        27 ~~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~I  106 (276)
                      ..+++||||||++..++.++.+|+..|++|..+.++.+|++.+           .... |+||+|+.||+++|++++++|
T Consensus         5 ~~~~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~~-----------~~~~-dlvllD~~lp~~~g~~~~~~l   72 (136)
T 1dcf_A            5 FTGLKVLVMDENGVSRMVTKGLLVHLGCEVTTVSSNEECLRVV-----------SHEH-KVVFMDVCMPGVENYQIALRI   72 (136)
T ss_dssp             CTTCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHC-----------CTTC-SEEEEECCSSTTTTTHHHHHH
T ss_pred             cCCCeEEEEeCCHHHHHHHHHHHHHcCCeEEEeCCHHHHHHHH-----------hccC-CEEEEeCCCCCCcHHHHHHHH
Confidence            4568999999999999999999999999999999999999988           4444 999999999999999999999


Q ss_pred             HhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeC
Q 023816          107 KVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVK  186 (276)
Q Consensus       107 r~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~K  186 (276)
                      ++..+                                        .......+||++|+........++++.|+++||.|
T Consensus        73 ~~~~~----------------------------------------~~~~~~~~ii~~s~~~~~~~~~~~~~~ga~~~l~K  112 (136)
T 1dcf_A           73 HEKFT----------------------------------------KQRHQRPLLVALSGNTDKSTKEKCMSFGLDGVLLK  112 (136)
T ss_dssp             HHHHC-----------------------------------------CCSCCCEEEEEESCCSHHHHHHHHHTTCCEEEES
T ss_pred             HHhhh----------------------------------------hccCCCceEEEEeCCCCHHHHHHHHHcCCCeEEEC
Confidence            85322                                        00011246888999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHH
Q 023816          187 PVKLSDVKRIKDYLTR  202 (276)
Q Consensus       187 Pv~~~~L~~~~~~l~~  202 (276)
                      |++.++|...+..+.+
T Consensus       113 P~~~~~L~~~l~~~~~  128 (136)
T 1dcf_A          113 PVSLDNIRDVLSDLLE  128 (136)
T ss_dssp             SCCHHHHHHHHHHHHS
T ss_pred             CCCHHHHHHHHHHHhc
Confidence            9999999777766543

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

Probab=99.86  E-value=1.8e-21  Score=151.03  Aligned_cols=119  Identities=21%  Similarity=0.362  Sum_probs=106.8

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhCCCEEE-EECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHH
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTISSCKVT-AVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIK  107 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~g~~v~-~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir  107 (276)
                      +++||||||++..++.++.+|+..|+.+. .+.++++|++.+           ....||+||+|+.||+++|++++++||
T Consensus         1 ~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~~a~~~~-----------~~~~~dlii~d~~l~~~~g~~~~~~l~   69 (134)
T 3f6c_A            1 SLNAIIIDDHPLAIAAIRNLLIKNDIEILAELTEGGSAVQRV-----------ETLKPDIVIIDVDIPGVNGIQVLETLR   69 (134)
T ss_dssp             CEEEEEECCCHHHHHHHHHHHHHTTEEEEEEESSSTTHHHHH-----------HHHCCSEEEEETTCSSSCHHHHHHHHH
T ss_pred             CeEEEEEcCCHHHHHHHHHHHhhCCcEEEEEcCCHHHHHHHH-----------HhcCCCEEEEecCCCCCChHHHHHHHH
Confidence            37999999999999999999999999998 799999999998           556799999999999999999999999


Q ss_pred             hhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCC
Q 023816          108 VTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKP  187 (276)
Q Consensus       108 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KP  187 (276)
                      +..|                                             .+|||++|+..+.....++++.|+++|+.||
T Consensus        70 ~~~~---------------------------------------------~~~ii~~s~~~~~~~~~~~~~~g~~~~l~kp  104 (134)
T 3f6c_A           70 KRQY---------------------------------------------SGIIIIVSAKNDHFYGKHCADAGANGFVSKK  104 (134)
T ss_dssp             HTTC---------------------------------------------CSEEEEEECC---CTHHHHHHTTCSEEEEGG
T ss_pred             hcCC---------------------------------------------CCeEEEEeCCCChHHHHHHHHhCCCEEEeCC
Confidence            8766                                             7999999999998899999999999999999


Q ss_pred             CCHHHHHHHHHHHHHh
Q 023816          188 VKLSDVKRIKDYLTRD  203 (276)
Q Consensus       188 v~~~~L~~~~~~l~~~  203 (276)
                      ++.++|.+.+..+.+.
T Consensus       105 ~~~~~l~~~i~~~~~~  120 (134)
T 3f6c_A          105 EGMNNIIAAIEAAKNG  120 (134)
T ss_dssp             GCTHHHHHHHHHHHTT
T ss_pred             CCHHHHHHHHHHHHCC
Confidence            9999998777776654

>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=99.86  E-value=1e-20  Score=151.28  Aligned_cols=122  Identities=26%  Similarity=0.428  Sum_probs=111.4

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHh
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKV  108 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~  108 (276)
                      +.+||||||++..+..+...|+..||+|..+.++.+|++.+           ....||+||+|+.||+++|+++++.|++
T Consensus         3 ~~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l-----------~~~~~dliild~~l~~~~g~~~~~~l~~   71 (155)
T 1qkk_A            3 APSVFLIDDDRDLRKAMQQTLELAGFTVSSFASATEALAGL-----------SADFAGIVISDIRMPGMDGLALFRKILA   71 (155)
T ss_dssp             -CEEEEECSCHHHHHHHHHHHHHTTCEEEEESCHHHHHHTC-----------CTTCCSEEEEESCCSSSCHHHHHHHHHH
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHHcCcEEEEECCHHHHHHHH-----------HhCCCCEEEEeCCCCCCCHHHHHHHHHh
Confidence            57899999999999999999999999999999999999998           6678999999999999999999999998


Q ss_pred             hCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCC
Q 023816          109 TTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPV  188 (276)
Q Consensus       109 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv  188 (276)
                      ..|                                             .+|||++|+........++++.|+++||.||+
T Consensus        72 ~~~---------------------------------------------~~pii~ls~~~~~~~~~~~~~~g~~~~l~kP~  106 (155)
T 1qkk_A           72 LDP---------------------------------------------DLPMILVTGHGDIPMAVQAIQDGAYDFIAKPF  106 (155)
T ss_dssp             HCT---------------------------------------------TSCEEEEECGGGHHHHHHHHHTTCCEEEESSC
T ss_pred             hCC---------------------------------------------CCCEEEEECCCChHHHHHHHhcCCCeEEeCCC
Confidence            766                                             79999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHhhhc
Q 023816          189 KLSDVKRIKDYLTRDVNL  206 (276)
Q Consensus       189 ~~~~L~~~~~~l~~~~~~  206 (276)
                      +.++|...+..+.+....
T Consensus       107 ~~~~L~~~i~~~~~~~~~  124 (155)
T 1qkk_A          107 AADRLVQSARRAEEKRRL  124 (155)
T ss_dssp             CHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHH
Confidence            999998777776655444

>3hzh_A Chemotaxis response regulator (CHEY-3); phosphatase, complex, response regulator, receiver domain, two-component signal transduction; HET: BFD; 1.96A {Borrelia burgdorferi}

Probab=99.86  E-value=6.2e-21  Score=153.99  Aligned_cols=120  Identities=24%  Similarity=0.351  Sum_probs=109.4

Q ss_pred             CCCCccEEEEEeCCHHHHHHHHHHHhhCCCEEE-EECCHHHHHHHhcccccccccCCCCC--ceeEEEEecCCCCCCHHH
Q 023816           25 SDTEEVHVLAVDDSFVDRKVIERLLTISSCKVT-AVDSGRRALQFLGLDEEQSINGFDGL--KVDLIITDYCMPGMTGYE  101 (276)
Q Consensus        25 ~~~~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~-~a~~g~~al~~l~~~~~~~~~~~~~~--~~DlIL~D~~mp~~~G~e  101 (276)
                      ....+++||||||++..++.++.+|+..||++. .+.++++|++.+           ...  .||+||+|+.||+++|++
T Consensus        32 ~~~~~~~Ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~~al~~l-----------~~~~~~~dliilD~~l~~~~g~~  100 (157)
T 3hzh_A           32 DTGIPFNVLIVDDSVFTVKQLTQIFTSEGFNIIDTAADGEEAVIKY-----------KNHYPNIDIVTLXITMPKMDGIT  100 (157)
T ss_dssp             TTTEECEEEEECSCHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHH-----------HHHGGGCCEEEECSSCSSSCHHH
T ss_pred             CCCCceEEEEEeCCHHHHHHHHHHHHhCCCeEEEEECCHHHHHHHH-----------HhcCCCCCEEEEeccCCCccHHH
Confidence            344568999999999999999999999999998 899999999999           444  789999999999999999


Q ss_pred             HHHHHHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCC
Q 023816          102 LLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAE  181 (276)
Q Consensus       102 ll~~Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~  181 (276)
                      ++++||+..+                                             .+|||++|+..+.+...++++.|++
T Consensus       101 ~~~~lr~~~~---------------------------------------------~~~ii~ls~~~~~~~~~~~~~~g~~  135 (157)
T 3hzh_A          101 CLSNIMEFDK---------------------------------------------NARVIMISALGKEQLVKDCLIKGAK  135 (157)
T ss_dssp             HHHHHHHHCT---------------------------------------------TCCEEEEESCCCHHHHHHHHHTTCS
T ss_pred             HHHHHHhhCC---------------------------------------------CCcEEEEeccCcHHHHHHHHHcCCC
Confidence            9999998777                                             7999999999999999999999999


Q ss_pred             eEEeCCCCHHHHHHHHHHH
Q 023816          182 DFIVKPVKLSDVKRIKDYL  200 (276)
Q Consensus       182 d~l~KPv~~~~L~~~~~~l  200 (276)
                      +||.||++.++|.+.+..+
T Consensus       136 ~~l~KP~~~~~l~~~i~~~  154 (157)
T 3hzh_A          136 TFIVKPLDRAKVLQRVMSV  154 (157)
T ss_dssp             EEEESSCCHHHHHHHHHHT
T ss_pred             EEEeCCCCHHHHHHHHHHH
Confidence            9999999999997666543

>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=99.86  E-value=1.4e-20  Score=147.20  Aligned_cols=131  Identities=27%  Similarity=0.401  Sum_probs=109.8

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhCCC--EEEEECCHHHHHHHhcccccccccCCCC--CceeEEEEecCCCCCCHHHH
Q 023816           27 TEEVHVLAVDDSFVDRKVIERLLTISSC--KVTAVDSGRRALQFLGLDEEQSINGFDG--LKVDLIITDYCMPGMTGYEL  102 (276)
Q Consensus        27 ~~~~~VLIVdD~~~~~~~L~~~L~~~g~--~v~~a~~g~~al~~l~~~~~~~~~~~~~--~~~DlIL~D~~mp~~~G~el  102 (276)
                      +.+.+||||||++..++.++..|+..|+  .+..+.++.+|++.+....+.   +-..  ..||+||+|+.||+++|+++
T Consensus         4 ~~~~~iLivdd~~~~~~~l~~~L~~~g~~~~v~~~~~~~~al~~l~~~~~~---~~~~~~~~~dlvi~D~~l~~~~g~~~   80 (149)
T 1k66_A            4 NATQPLLVVEDSDEDFSTFQRLLQREGVVNPIYRCITGDQALDFLYQTGSY---CNPDIAPRPAVILLDLNLPGTDGREV   80 (149)
T ss_dssp             CTTSCEEEECCCHHHHHHHHHHHHHTTBCSCEEEECSHHHHHHHHHTCCSS---SCGGGCCCCSEEEECSCCSSSCHHHH
T ss_pred             CCCccEEEEECCHHHHHHHHHHHHHcCCCceEEEECCHHHHHHHHHhcccc---cCcccCCCCcEEEEECCCCCCCHHHH
Confidence            4578999999999999999999999998  899999999999998321000   0001  68999999999999999999


Q ss_pred             HHHHHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCe
Q 023816          103 LKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAED  182 (276)
Q Consensus       103 l~~Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d  182 (276)
                      +++||+...                                           ...+|||++|+........++++.|+++
T Consensus        81 ~~~l~~~~~-------------------------------------------~~~~~ii~~t~~~~~~~~~~~~~~g~~~  117 (149)
T 1k66_A           81 LQEIKQDEV-------------------------------------------LKKIPVVIMTTSSNPKDIEICYSYSISS  117 (149)
T ss_dssp             HHHHTTSTT-------------------------------------------GGGSCEEEEESCCCHHHHHHHHHTTCSE
T ss_pred             HHHHHhCcc-------------------------------------------cCCCeEEEEeCCCCHHHHHHHHHCCCCE
Confidence            999997431                                           1278999999999999999999999999


Q ss_pred             EEeCCCCHHHHHHHHHHHHHh
Q 023816          183 FIVKPVKLSDVKRIKDYLTRD  203 (276)
Q Consensus       183 ~l~KPv~~~~L~~~~~~l~~~  203 (276)
                      ||.||++.++|...+..+.+.
T Consensus       118 ~l~kP~~~~~l~~~i~~~~~~  138 (149)
T 1k66_A          118 YIVKPLEIDRLTETVQTFIKY  138 (149)
T ss_dssp             EEECCSSHHHHHHHHHHHHHH
T ss_pred             EEeCCCCHHHHHHHHHHHHHH
Confidence            999999999997777666543

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

Probab=99.85  E-value=1.2e-20  Score=148.87  Aligned_cols=118  Identities=22%  Similarity=0.308  Sum_probs=107.0

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHh
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKV  108 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~  108 (276)
                      .++||||||++..++.++.+|+..|+.+..+.++.+|++.+           ....||+||+|+.||+++|++++++|++
T Consensus         4 ~~~Ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~-----------~~~~~dlvllD~~l~~~~g~~l~~~l~~   72 (136)
T 2qzj_A            4 QTKILIIDGDKDNCQKLKGFLEEKGISIDLAYNCEEAIGKI-----------FSNKYDLIFLEIILSDGDGWTLCKKIRN   72 (136)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHH-----------HHCCCSEEEEESEETTEEHHHHHHHHHT
T ss_pred             CCeEEEEcCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHH-----------HhcCCCEEEEeCCCCCCCHHHHHHHHcc
Confidence            57999999999999999999999999999999999999998           4567999999999999999999999995


Q ss_pred             hCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCC
Q 023816          109 TTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPV  188 (276)
Q Consensus       109 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv  188 (276)
                      ..                                              .+|||++|+........++++.|+++||.||+
T Consensus        73 ~~----------------------------------------------~~~ii~ls~~~~~~~~~~~~~~ga~~~l~KP~  106 (136)
T 2qzj_A           73 VT----------------------------------------------TCPIVYMTYINEDQSILNALNSGGDDYLIKPL  106 (136)
T ss_dssp             TC----------------------------------------------CCCEEEEESCCCHHHHHHHHHTTCCEEEESSC
T ss_pred             CC----------------------------------------------CCCEEEEEcCCCHHHHHHHHHcCCcEEEECCC
Confidence            21                                              58999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHh
Q 023816          189 KLSDVKRIKDYLTRD  203 (276)
Q Consensus       189 ~~~~L~~~~~~l~~~  203 (276)
                      +.++|...+..+.+.
T Consensus       107 ~~~~L~~~l~~~~~~  121 (136)
T 2qzj_A          107 NLEILYAKVKAILRR  121 (136)
T ss_dssp             CHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHH
Confidence            999997777665543

>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=99.85  E-value=1e-20  Score=147.16  Aligned_cols=118  Identities=25%  Similarity=0.353  Sum_probs=107.2

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHh
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKV  108 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~  108 (276)
                      +.+||||||++..+..+...|+..||.+..+.++.+|++.+           ....||+||+|+.||+++|++++++|++
T Consensus         3 ~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~~-----------~~~~~dlvl~D~~l~~~~g~~~~~~l~~   71 (136)
T 1mvo_A            3 NKKILVVDDEESIVTLLQYNLERSGYDVITASDGEEALKKA-----------ETEKPDLIVLDVMLPKLDGIEVCKQLRQ   71 (136)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHH-----------HHHCCSEEEEESSCSSSCHHHHHHHHHH
T ss_pred             CCEEEEEECCHHHHHHHHHHHHHCCcEEEEecCHHHHHHHH-----------hhcCCCEEEEecCCCCCCHHHHHHHHHc
Confidence            36899999999999999999999999999999999999988           4557999999999999999999999998


Q ss_pred             hCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCC
Q 023816          109 TTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPV  188 (276)
Q Consensus       109 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv  188 (276)
                      ..+                                             .+|||++|+........++++.|+++||.||+
T Consensus        72 ~~~---------------------------------------------~~~ii~~s~~~~~~~~~~~~~~g~~~~l~KP~  106 (136)
T 1mvo_A           72 QKL---------------------------------------------MFPILMLTAKDEEFDKVLGLELGADDYMTKPF  106 (136)
T ss_dssp             TTC---------------------------------------------CCCEEEEECTTCCCCHHHHHHTTCCEEEESSC
T ss_pred             CCC---------------------------------------------CCCEEEEECCCCHHHHHHHHhCCCCEEEECCC
Confidence            655                                             78999999998888888999999999999999


Q ss_pred             CHHHHHHHHHHHHH
Q 023816          189 KLSDVKRIKDYLTR  202 (276)
Q Consensus       189 ~~~~L~~~~~~l~~  202 (276)
                      +.++|...+..+.+
T Consensus       107 ~~~~l~~~i~~~~~  120 (136)
T 1mvo_A          107 SPREVNARVKAILR  120 (136)
T ss_dssp             CHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHH
Confidence            99999777766554

>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=99.85  E-value=9.3e-21  Score=158.77  Aligned_cols=119  Identities=23%  Similarity=0.362  Sum_probs=108.7

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHH
Q 023816           28 EEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIK  107 (276)
Q Consensus        28 ~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir  107 (276)
                      ...+||||||++..+..++.+|+..||+|..+.++.+|++.+           ....||+||+|+.||+++|++++++|+
T Consensus         3 ~~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~-----------~~~~~dlvl~D~~lp~~~g~~~~~~l~   71 (208)
T 1yio_A            3 AKPTVFVVDDDMSVREGLRNLLRSAGFEVETFDCASTFLEHR-----------RPEQHGCLVLDMRMPGMSGIELQEQLT   71 (208)
T ss_dssp             CCCEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHC-----------CTTSCEEEEEESCCSSSCHHHHHHHHH
T ss_pred             CCCEEEEEcCCHHHHHHHHHHHHhCCceEEEcCCHHHHHHhh-----------hccCCCEEEEeCCCCCCCHHHHHHHHH
Confidence            356899999999999999999999999999999999999998           667899999999999999999999999


Q ss_pred             hhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCC
Q 023816          108 VTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKP  187 (276)
Q Consensus       108 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KP  187 (276)
                      +..|                                             .+|||++|+..+.....++++.||+||+.||
T Consensus        72 ~~~~---------------------------------------------~~~ii~ls~~~~~~~~~~a~~~Ga~~~l~Kp  106 (208)
T 1yio_A           72 AISD---------------------------------------------GIPIVFITAHGDIPMTVRAMKAGAIEFLPKP  106 (208)
T ss_dssp             HTTC---------------------------------------------CCCEEEEESCTTSCCCHHHHHTTEEEEEESS
T ss_pred             hcCC---------------------------------------------CCCEEEEeCCCCHHHHHHHHHCCCcEEEeCC
Confidence            8666                                             7999999999998889999999999999999


Q ss_pred             CCHHHHHHHHHHHHH
Q 023816          188 VKLSDVKRIKDYLTR  202 (276)
Q Consensus       188 v~~~~L~~~~~~l~~  202 (276)
                      ++.++|...+..+.+
T Consensus       107 ~~~~~L~~~i~~~~~  121 (208)
T 1yio_A          107 FEEQALLDAIEQGLQ  121 (208)
T ss_dssp             CCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHh
Confidence            999999666655443

>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=99.85  E-value=4.2e-21  Score=147.29  Aligned_cols=119  Identities=24%  Similarity=0.369  Sum_probs=106.8

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhh
Q 023816           30 VHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVT  109 (276)
Q Consensus        30 ~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~  109 (276)
                      .+||||||++..++.++..|+..|+++..+.++.+|++.+           ....||+||+|+.||+++|++++++||+.
T Consensus         3 ~~ilivdd~~~~~~~l~~~l~~~g~~v~~~~~~~~a~~~~-----------~~~~~dlvi~D~~l~~~~g~~~~~~l~~~   71 (127)
T 2jba_A            3 RRILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQL-----------NEPWPDLILLAWMLPGGSGIQFIKHLRRE   71 (127)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEECSHHHHHTTC-----------SSSCCSEEEEESEETTEEHHHHHHHHHTS
T ss_pred             cEEEEEcCCHHHHHHHHHHHHHCCceEEEeCCHHHHHHHH-----------hccCCCEEEEecCCCCCCHHHHHHHHHhC
Confidence            5899999999999999999999999999999999999988           66789999999999999999999999964


Q ss_pred             CCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCC
Q 023816          110 TPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVK  189 (276)
Q Consensus       110 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~  189 (276)
                      .                                           ..+.+|||++|+........++++.|+++|+.||++
T Consensus        72 ~-------------------------------------------~~~~~~ii~~s~~~~~~~~~~~~~~ga~~~l~Kp~~  108 (127)
T 2jba_A           72 S-------------------------------------------MTRDIPVVMLTARGEEEDRVRGLETGADDCITKPFS  108 (127)
T ss_dssp             T-------------------------------------------TTTTSCEEEEEETTHHHHHHTTCCCSCSEEEEESCC
T ss_pred             c-------------------------------------------ccCCCCEEEEeCCCCHHHHHHHHhcCCCeEEeCCCC
Confidence            3                                           112799999999998888999999999999999999


Q ss_pred             HHHHHHHHHHHHH
Q 023816          190 LSDVKRIKDYLTR  202 (276)
Q Consensus       190 ~~~L~~~~~~l~~  202 (276)
                      .++|...+..+.+
T Consensus       109 ~~~l~~~i~~~~~  121 (127)
T 2jba_A          109 PKELVARIKAVMR  121 (127)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHh
Confidence            9999777666543

>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=99.85  E-value=6.6e-21  Score=145.60  Aligned_cols=118  Identities=28%  Similarity=0.392  Sum_probs=99.9

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhh
Q 023816           30 VHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVT  109 (276)
Q Consensus        30 ~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~  109 (276)
                      .+||||||++..++.++.+|+..|+++..+.++.+|++.+           ....||+||+|+.||+++|++++++||+.
T Consensus         2 ~~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~a~~~~-----------~~~~~dlvi~D~~l~~~~g~~~~~~l~~~   70 (124)
T 1mb3_A            2 KKVLIVEDNELNMKLFHDLLEAQGYETLQTREGLSALSIA-----------RENKPDLILMDIQLPEISGLEVTKWLKED   70 (124)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESCHHHHHHHH-----------HHHCCSEEEEESBCSSSBHHHHHHHHHHS
T ss_pred             cEEEEEcCCHHHHHHHHHHHHHcCcEEEEeCCHHHHHHHH-----------hcCCCCEEEEeCCCCCCCHHHHHHHHHcC
Confidence            4799999999999999999999999999999999999988           45579999999999999999999999973


Q ss_pred             CCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCC
Q 023816          110 TPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVK  189 (276)
Q Consensus       110 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~  189 (276)
                      ..                                           ...+|||++|+........++++.|+++||.||++
T Consensus        71 ~~-------------------------------------------~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~KP~~  107 (124)
T 1mb3_A           71 DD-------------------------------------------LAHIPVVAVTAFAMKGDEERIREGGCEAYISKPIS  107 (124)
T ss_dssp             TT-------------------------------------------TTTSCEEEEC------CHHHHHHHTCSEEECSSCC
T ss_pred             cc-------------------------------------------ccCCcEEEEECCCCHHHHHHHHhCCCCEEEeCCCC
Confidence            21                                           22689999999988888899999999999999999


Q ss_pred             HHHHHHHHHHHH
Q 023816          190 LSDVKRIKDYLT  201 (276)
Q Consensus       190 ~~~L~~~~~~l~  201 (276)
                      .++|...+..+.
T Consensus       108 ~~~l~~~i~~~~  119 (124)
T 1mb3_A          108 VVHFLETIKRLL  119 (124)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            999977666554

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

Probab=99.85  E-value=1.7e-20  Score=146.10  Aligned_cols=119  Identities=22%  Similarity=0.249  Sum_probs=108.9

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCC-----CCCHHHH
Q 023816           28 EEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMP-----GMTGYEL  102 (276)
Q Consensus        28 ~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp-----~~~G~el  102 (276)
                      .+++||||||++..+..++..|+..|+++..+.++.+|++.+           ....||+||+|+.||     +++|+++
T Consensus         2 ~~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l-----------~~~~~dlvi~d~~~~~~~~~~~~g~~~   70 (140)
T 2qr3_A            2 SLGTIIIVDDNKGVLTAVQLLLKNHFSKVITLSSPVSLSTVL-----------REENPEVVLLDMNFTSGINNGNEGLFW   70 (140)
T ss_dssp             CCCEEEEECSCHHHHHHHHHHHTTTSSEEEEECCHHHHHHHH-----------HHSCEEEEEEETTTTC-----CCHHHH
T ss_pred             CCceEEEEeCCHHHHHHHHHHHHhCCcEEEEeCCHHHHHHHH-----------HcCCCCEEEEeCCcCCCCCCCccHHHH
Confidence            468999999999999999999999999999999999999999           556799999999999     9999999


Q ss_pred             HHHHHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCe
Q 023816          103 LKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAED  182 (276)
Q Consensus       103 l~~Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d  182 (276)
                      +++|++..+                                             .+|||++|+........++++.|+++
T Consensus        71 ~~~l~~~~~---------------------------------------------~~~ii~ls~~~~~~~~~~~~~~g~~~  105 (140)
T 2qr3_A           71 LHEIKRQYR---------------------------------------------DLPVVLFTAYADIDLAVRGIKEGASD  105 (140)
T ss_dssp             HHHHHHHCT---------------------------------------------TCCEEEEEEGGGHHHHHHHHHTTCCE
T ss_pred             HHHHHhhCc---------------------------------------------CCCEEEEECCCCHHHHHHHHHcCchh
Confidence            999998766                                             79999999999999999999999999


Q ss_pred             EEeCCCCHHHHHHHHHHHHH
Q 023816          183 FIVKPVKLSDVKRIKDYLTR  202 (276)
Q Consensus       183 ~l~KPv~~~~L~~~~~~l~~  202 (276)
                      |+.||++.++|...+..+.+
T Consensus       106 ~l~kp~~~~~l~~~l~~~~~  125 (140)
T 2qr3_A          106 FVVKPWDNQKLLETLLNAAS  125 (140)
T ss_dssp             EEEESCCHHHHHHHHHHHHT
T ss_pred             eeeCCCCHHHHHHHHHHHHH
Confidence            99999999999777766654

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

Probab=99.85  E-value=6.5e-21  Score=150.44  Aligned_cols=119  Identities=23%  Similarity=0.296  Sum_probs=106.9

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCC-CceeEEEEecCCCC-CCHHHHHHH
Q 023816           28 EEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDG-LKVDLIITDYCMPG-MTGYELLKK  105 (276)
Q Consensus        28 ~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~-~~~DlIL~D~~mp~-~~G~ell~~  105 (276)
                      .+.+||||||++..++.++.+|+..||++..+.++.+|++.+           .. ..||+||+|+.||+ ++|++++++
T Consensus         4 ~~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l-----------~~~~~~dlvi~D~~l~~~~~g~~~~~~   72 (140)
T 3h5i_A            4 KDKKILIVEDSKFQAKTIANILNKYGYTVEIALTGEAAVEKV-----------SGGWYPDLILMDIELGEGMDGVQTALA   72 (140)
T ss_dssp             --CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHH-----------HTTCCCSEEEEESSCSSSCCHHHHHHH
T ss_pred             CCcEEEEEeCCHHHHHHHHHHHHHcCCEEEEecChHHHHHHH-----------hcCCCCCEEEEeccCCCCCCHHHHHHH
Confidence            467999999999999999999999999999999999999998           44 68999999999995 999999999


Q ss_pred             HHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEe
Q 023816          106 IKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIV  185 (276)
Q Consensus       106 Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~  185 (276)
                      ||+. +                                             .+|||++|+..+.....++++.|+++||.
T Consensus        73 l~~~-~---------------------------------------------~~~ii~ls~~~~~~~~~~~~~~g~~~~l~  106 (140)
T 3h5i_A           73 IQQI-S---------------------------------------------ELPVVFLTAHTEPAVVEKIRSVTAYGYVM  106 (140)
T ss_dssp             HHHH-C---------------------------------------------CCCEEEEESSSSCCCCGGGGGSCEEEEEE
T ss_pred             HHhC-C---------------------------------------------CCCEEEEECCCCHHHHHHHHhCCCcEEEe
Confidence            9975 4                                             79999999999888888999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHh
Q 023816          186 KPVKLSDVKRIKDYLTRD  203 (276)
Q Consensus       186 KPv~~~~L~~~~~~l~~~  203 (276)
                      ||++.++|...+..+.+.
T Consensus       107 KP~~~~~l~~~i~~~l~~  124 (140)
T 3h5i_A          107 KSATEQVLITIVEMALRL  124 (140)
T ss_dssp             TTCCHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHH
Confidence            999999997777766554

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

Probab=99.85  E-value=1.4e-20  Score=148.19  Aligned_cols=120  Identities=25%  Similarity=0.365  Sum_probs=103.9

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHh
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKV  108 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~  108 (276)
                      .++||||||++..++.++.+|+..||.+..+.++.+|++.+           ....||+||+|+.||+++|++++++|++
T Consensus         3 ~~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l-----------~~~~~dlvi~D~~l~~~~g~~~~~~l~~   71 (138)
T 3c3m_A            3 LYTILVVDDSPMIVDVFVTMLERGGYRPITAFSGEECLEAL-----------NATPPDLVLLDIMMEPMDGWETLERIKT   71 (138)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHH-----------HHSCCSEEEEESCCSSSCHHHHHHHHHH
T ss_pred             cceEEEEeCCHHHHHHHHHHHHHcCceEEEeCCHHHHHHHH-----------hccCCCEEEEeCCCCCCCHHHHHHHHHc
Confidence            57999999999999999999999999999999999999998           4567999999999999999999999996


Q ss_pred             hCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCC
Q 023816          109 TTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPV  188 (276)
Q Consensus       109 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv  188 (276)
                      ..+                                           ...+|||++|+.........++.+|+++||.||+
T Consensus        72 ~~~-------------------------------------------~~~~~ii~ls~~~~~~~~~~~~~~~~~~~l~KP~  108 (138)
T 3c3m_A           72 DPA-------------------------------------------TRDIPVLMLTAKPLTPEEANEYGSYIEDYILKPT  108 (138)
T ss_dssp             STT-------------------------------------------TTTSCEEEEESSCCCHHHHHHTTTTCSEEEECCC
T ss_pred             Ccc-------------------------------------------cCCCCEEEEECCCChHHHHHHhhcCHhheEeCCC
Confidence            321                                           2368999999987766666667778899999999


Q ss_pred             CHHHHHHHHHHHHH
Q 023816          189 KLSDVKRIKDYLTR  202 (276)
Q Consensus       189 ~~~~L~~~~~~l~~  202 (276)
                      +.++|...+..+.+
T Consensus       109 ~~~~L~~~i~~~~~  122 (138)
T 3c3m_A          109 THHQLYEAIEHVLA  122 (138)
T ss_dssp             HHHHHHHHHHHHHS
T ss_pred             CHHHHHHHHHHHHH
Confidence            99999777766543

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

Probab=99.85  E-value=1.1e-20  Score=150.81  Aligned_cols=120  Identities=25%  Similarity=0.452  Sum_probs=108.5

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCc-eeEEEEecCCCCCCHHHHHHHHH
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLK-VDLIITDYCMPGMTGYELLKKIK  107 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~-~DlIL~D~~mp~~~G~ell~~Ir  107 (276)
                      +.+||||||++..++.++.+|+. |+++..+.++.+|++.+           .... ||+||+|+.||+++|++++++||
T Consensus         4 ~~~ILivdd~~~~~~~l~~~L~~-~~~v~~~~~~~~a~~~l-----------~~~~~~dlvi~D~~l~~~~g~~~~~~l~   71 (151)
T 3kcn_A            4 NERILLVDDDYSLLNTLKRNLSF-DFEVTTCESGPEALACI-----------KKSDPFSVIMVDMRMPGMEGTEVIQKAR   71 (151)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHTT-TSEEEEESSHHHHHHHH-----------HHSCCCSEEEEESCCSSSCHHHHHHHHH
T ss_pred             CCeEEEEeCCHHHHHHHHHHhcc-CceEEEeCCHHHHHHHH-----------HcCCCCCEEEEeCCCCCCcHHHHHHHHH
Confidence            57999999999999999999985 99999999999999998           3444 69999999999999999999999


Q ss_pred             hhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcC-CCeEEeC
Q 023816          108 VTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDG-AEDFIVK  186 (276)
Q Consensus       108 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~G-a~d~l~K  186 (276)
                      +..|                                             .+|||++|+..+.....++++.| +++||.|
T Consensus        72 ~~~~---------------------------------------------~~~ii~~s~~~~~~~~~~~~~~g~~~~~l~K  106 (151)
T 3kcn_A           72 LISP---------------------------------------------NSVYLMLTGNQDLTTAMEAVNEGQVFRFLNK  106 (151)
T ss_dssp             HHCS---------------------------------------------SCEEEEEECGGGHHHHHHHHHHTCCSEEEES
T ss_pred             hcCC---------------------------------------------CcEEEEEECCCCHHHHHHHHHcCCeeEEEcC
Confidence            8777                                             79999999999999999999999 9999999


Q ss_pred             CCCHHHHHHHHHHHHHhhh
Q 023816          187 PVKLSDVKRIKDYLTRDVN  205 (276)
Q Consensus       187 Pv~~~~L~~~~~~l~~~~~  205 (276)
                      |++.++|...+..+.+...
T Consensus       107 P~~~~~L~~~i~~~l~~~~  125 (151)
T 3kcn_A          107 PCQMSDIKAAINAGIKQYD  125 (151)
T ss_dssp             SCCHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHH
Confidence            9999999777776665443

>3n0r_A Response regulator; sigma factor, receiver, two-component SI transduction, signaling protein; HET: MSE GOL; 1.25A {Caulobacter vibrioides} PDB: 3t0y_A

Probab=99.85  E-value=1.6e-21  Score=177.14  Aligned_cols=116  Identities=22%  Similarity=0.229  Sum_probs=104.4

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhCCCEEE-EECCHHHHHHHhcccccccccCCCCCceeEEEEecCCC-CCCHHHHHHHH
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTISSCKVT-AVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMP-GMTGYELLKKI  106 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~g~~v~-~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp-~~~G~ell~~I  106 (276)
                      ..+||+|||++.++..++.+|+..||+|. .+.||++|++.+           ....|||||+|++|| +|||+++++.|
T Consensus       160 ~~rILvVdD~~~~~~~l~~~L~~~g~~v~~~a~~g~eAl~~~-----------~~~~~dlvl~D~~MPd~mdG~e~~~~i  228 (286)
T 3n0r_A          160 ATEVLIIEDEPVIAADIEALVRELGHDVTDIAATRGEALEAV-----------TRRTPGLVLADIQLADGSSGIDAVKDI  228 (286)
T ss_dssp             CCEEEEECCSHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHH-----------HHCCCSEEEEESCCTTSCCTTTTTHHH
T ss_pred             CCcEEEEcCCHHHHHHHHHHhhccCceEEEEeCCHHHHHHHH-----------HhCCCCEEEEcCCCCCCCCHHHHHHHH
Confidence            45899999999999999999999999999 899999999999           556799999999999 89999999999


Q ss_pred             HhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeC
Q 023816          107 KVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVK  186 (276)
Q Consensus       107 r~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~K  186 (276)
                      |+..                                              .+|||++|++.  +...+|+++|++|||.|
T Consensus       229 r~~~----------------------------------------------~~piI~lT~~~--~~~~~~~~~G~~~~l~K  260 (286)
T 3n0r_A          229 LGRM----------------------------------------------DVPVIFITAFP--ERLLTGERPEPTFLITK  260 (286)
T ss_dssp             HHHT----------------------------------------------TCCEEEEESCG--GGGCCSSSCCCSSEEES
T ss_pred             HhcC----------------------------------------------CCCEEEEeCCH--HHHHHHHhCCCcEEEeC
Confidence            9632                                              69999999985  35678999999999999


Q ss_pred             CCCHHHHHHHHHHHHHh
Q 023816          187 PVKLSDVKRIKDYLTRD  203 (276)
Q Consensus       187 Pv~~~~L~~~~~~l~~~  203 (276)
                      |++.++|...+..+...
T Consensus       261 P~~~~~L~~~i~~~l~~  277 (286)
T 3n0r_A          261 PFQPETVKAAIGQALFF  277 (286)
T ss_dssp             SCCHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHh
Confidence            99999998777776654

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

Probab=99.85  E-value=1.3e-20  Score=146.17  Aligned_cols=116  Identities=20%  Similarity=0.361  Sum_probs=104.3

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhC-CCEEE-EECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHH
Q 023816           30 VHVLAVDDSFVDRKVIERLLTIS-SCKVT-AVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIK  107 (276)
Q Consensus        30 ~~VLIVdD~~~~~~~L~~~L~~~-g~~v~-~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir  107 (276)
                      ++||||||++..++.++.+|+.. |+.+. .+.++.+|++.+           ....||+||+|+.||+++|++++++|+
T Consensus         3 ~~ilivdd~~~~~~~l~~~l~~~~~~~~~~~~~~~~~a~~~~-----------~~~~~dlvllD~~l~~~~g~~~~~~l~   71 (130)
T 1dz3_A            3 IKVCIADDNRELVSLLDEYISSQPDMEVIGTAYNGQDCLQML-----------EEKRPDILLLDIIMPHLDGLAVLERIR   71 (130)
T ss_dssp             EEEEEECSCHHHHHHHHHHHHTSTTEEEEEEESSHHHHHHHH-----------HHHCCSEEEEESCCSSSCHHHHHHHHH
T ss_pred             eEEEEEcCCHHHHHHHHHHHHhCCCceEEEEeCCHHHHHHHH-----------hcCCCCEEEEecCCCCCCHHHHHHHHH
Confidence            68999999999999999999987 88876 799999999998           455799999999999999999999999


Q ss_pred             hh-CCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeC
Q 023816          108 VT-TPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVK  186 (276)
Q Consensus       108 ~~-~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~K  186 (276)
                      +. .+                                             .+|||++|+........++++.|+++||.|
T Consensus        72 ~~~~~---------------------------------------------~~~ii~ls~~~~~~~~~~~~~~ga~~~l~K  106 (130)
T 1dz3_A           72 AGFEH---------------------------------------------QPNVIMLTAFGQEDVTKKAVELGASYFILK  106 (130)
T ss_dssp             HHCSS---------------------------------------------CCEEEEEEETTCHHHHHHHHHTTCEEEEEC
T ss_pred             hcCCC---------------------------------------------CCcEEEEecCCCHHHHHHHHHcCCCEEEeC
Confidence            74 33                                             689999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHH
Q 023816          187 PVKLSDVKRIKDYLT  201 (276)
Q Consensus       187 Pv~~~~L~~~~~~l~  201 (276)
                      |++.++|...+..+.
T Consensus       107 P~~~~~l~~~i~~~~  121 (130)
T 1dz3_A          107 PFDMENLAHHIRQVY  121 (130)
T ss_dssp             SSCCTTHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHh
Confidence            999999977766654

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

Probab=99.85  E-value=2.9e-20  Score=145.90  Aligned_cols=117  Identities=23%  Similarity=0.348  Sum_probs=109.0

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHh
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKV  108 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~  108 (276)
                      +.+||||||++..++.++..|+..||++..+.++.+|++.+           +...||+||+|+ ||+++|+++++.|++
T Consensus         4 ~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l-----------~~~~~dlvi~d~-~~~~~g~~~~~~l~~   71 (142)
T 2qxy_A            4 TPTVMVVDESRITFLAVKNALEKDGFNVIWAKNEQEAFTFL-----------RREKIDLVFVDV-FEGEESLNLIRRIRE   71 (142)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHGGGTCEEEEESSHHHHHHHH-----------TTSCCSEEEEEC-TTTHHHHHHHHHHHH
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHhCCCEEEEECCHHHHHHHH-----------hccCCCEEEEeC-CCCCcHHHHHHHHHH
Confidence            57999999999999999999999999999999999999999           667899999999 999999999999998


Q ss_pred             hCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCC
Q 023816          109 TTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPV  188 (276)
Q Consensus       109 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv  188 (276)
                      ..+                                             .+|||++|+........++++.|+++|+.||+
T Consensus        72 ~~~---------------------------------------------~~pii~ls~~~~~~~~~~~~~~g~~~~l~kP~  106 (142)
T 2qxy_A           72 EFP---------------------------------------------DTKVAVLSAYVDKDLIINSVKAGAVDYILKPF  106 (142)
T ss_dssp             HCT---------------------------------------------TCEEEEEESCCCHHHHHHHHHHTCSCEEESSC
T ss_pred             HCC---------------------------------------------CCCEEEEECCCCHHHHHHHHHCCcceeEeCCC
Confidence            766                                             79999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHH
Q 023816          189 KLSDVKRIKDYLTR  202 (276)
Q Consensus       189 ~~~~L~~~~~~l~~  202 (276)
                      +.++|...+..+.+
T Consensus       107 ~~~~l~~~i~~~~~  120 (142)
T 2qxy_A          107 RLDYLLERVKKIIS  120 (142)
T ss_dssp             CHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHh
Confidence            99999777766654

>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=99.85  E-value=1.5e-20  Score=142.68  Aligned_cols=116  Identities=24%  Similarity=0.380  Sum_probs=105.1

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhh
Q 023816           30 VHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVT  109 (276)
Q Consensus        30 ~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~  109 (276)
                      ++||||||++..++.++..|+..|+.+..+.++.+++..+           ....||+||+|+.||+++|++++++|++ 
T Consensus         2 ~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~-----------~~~~~dlvi~D~~l~~~~g~~~~~~l~~-   69 (121)
T 1zh2_A            2 TNVLIVEDEQAIRRFLRTALEGDGMRVFEAETLQRGLLEA-----------ATRKPDLIILDLGLPDGDGIEFIRDLRQ-   69 (121)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHH-----------HHHCCSEEEEESEETTEEHHHHHHHHHT-
T ss_pred             cEEEEEeCCHHHHHHHHHHHhcCCCEEEEeCCHHHHHHHH-----------hcCCCCEEEEeCCCCCCcHHHHHHHHHh-
Confidence            5899999999999999999999999999999999999887           4457999999999999999999999994 


Q ss_pred             CCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCC
Q 023816          110 TPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVK  189 (276)
Q Consensus       110 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~  189 (276)
                      .+                                             .+|+|++|+........++++.|+++|+.||++
T Consensus        70 ~~---------------------------------------------~~~ii~~s~~~~~~~~~~~~~~g~~~~l~Kp~~  104 (121)
T 1zh2_A           70 WS---------------------------------------------AVPVIVLSARSEESDKIAALDAGADDYLSKPFG  104 (121)
T ss_dssp             TC---------------------------------------------CCCEEEEESCCSHHHHHHHHHHTCSEEEESSCC
T ss_pred             CC---------------------------------------------CCcEEEEECCCCHHHHHHHHhcCCCeEEeCCcC
Confidence            34                                             689999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHH
Q 023816          190 LSDVKRIKDYLTR  202 (276)
Q Consensus       190 ~~~L~~~~~~l~~  202 (276)
                      .++|...+..+.+
T Consensus       105 ~~~l~~~i~~~~~  117 (121)
T 1zh2_A          105 IGELQARLRVALR  117 (121)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            9999776665543

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

Probab=99.85  E-value=3.2e-20  Score=144.57  Aligned_cols=120  Identities=18%  Similarity=0.297  Sum_probs=108.8

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhCCCEEE-EECCHHHHHHHhcccccccccCCCCCceeEEEEecCCC-CCCHHHHHH
Q 023816           27 TEEVHVLAVDDSFVDRKVIERLLTISSCKVT-AVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMP-GMTGYELLK  104 (276)
Q Consensus        27 ~~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~-~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp-~~~G~ell~  104 (276)
                      ..+++||||||++..++.++..|+..||++. .+.++.+|++.+           ....||+||+|+.|| +++|+++++
T Consensus         7 ~~~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~~a~~~~-----------~~~~~dlii~d~~~~~~~~g~~~~~   75 (140)
T 3cg0_A            7 DDLPGVLIVEDGRLAAATLRIQLESLGYDVLGVFDNGEEAVRCA-----------PDLRPDIALVDIMLCGALDGVETAA   75 (140)
T ss_dssp             -CCCEEEEECCBHHHHHHHHHHHHHHTCEEEEEESSHHHHHHHH-----------HHHCCSEEEEESSCCSSSCHHHHHH
T ss_pred             CCCceEEEEECCHHHHHHHHHHHHHCCCeeEEEECCHHHHHHHH-----------HhCCCCEEEEecCCCCCCCHHHHHH
Confidence            4578999999999999999999999999999 499999999998           455799999999999 799999999


Q ss_pred             HHHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEE
Q 023816          105 KIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFI  184 (276)
Q Consensus       105 ~Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l  184 (276)
                      +|++. +                                             .+|||++|+........++++.|+++||
T Consensus        76 ~l~~~-~---------------------------------------------~~~ii~ls~~~~~~~~~~~~~~g~~~~l  109 (140)
T 3cg0_A           76 RLAAG-C---------------------------------------------NLPIIFITSSQDVETFQRAKRVNPFGYL  109 (140)
T ss_dssp             HHHHH-S---------------------------------------------CCCEEEEECCCCHHHHHHHHTTCCSEEE
T ss_pred             HHHhC-C---------------------------------------------CCCEEEEecCCCHHHHHHHHhcCCCEEE
Confidence            99976 5                                             7999999999999999999999999999


Q ss_pred             eCCCCHHHHHHHHHHHHHh
Q 023816          185 VKPVKLSDVKRIKDYLTRD  203 (276)
Q Consensus       185 ~KPv~~~~L~~~~~~l~~~  203 (276)
                      .||++.++|...+..+.+.
T Consensus       110 ~kp~~~~~l~~~i~~~~~~  128 (140)
T 3cg0_A          110 AKPVAADTLHRSIEMAIHK  128 (140)
T ss_dssp             EESCCHHHHHHHHHHHHHH
T ss_pred             eCCCCHHHHHHHHHHHHhc
Confidence            9999999997777766544

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

Probab=99.85  E-value=2.3e-20  Score=144.59  Aligned_cols=119  Identities=26%  Similarity=0.360  Sum_probs=101.6

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHh
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKV  108 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~  108 (276)
                      ..+||||||++..+..++.+|+ .|+++..+.++.+|++.+           ....||+||+|+.||+++|++++++||+
T Consensus         4 ~~~ilivdd~~~~~~~l~~~l~-~~~~v~~~~~~~~a~~~l-----------~~~~~dlvi~d~~l~~~~g~~~~~~l~~   71 (133)
T 3nhm_A            4 KPKVLIVENSWTMRETLRLLLS-GEFDCTTAADGASGLQQA-----------LAHPPDVLISDVNMDGMDGYALCGHFRS   71 (133)
T ss_dssp             -CEEEEECSCHHHHHHHHHHHT-TTSEEEEESSHHHHHHHH-----------HHSCCSEEEECSSCSSSCHHHHHHHHHH
T ss_pred             CCEEEEEcCCHHHHHHHHHHHh-CCcEEEEECCHHHHHHHH-----------hcCCCCEEEEeCCCCCCCHHHHHHHHHh
Confidence            5799999999999999999999 899999999999999998           5567999999999999999999999997


Q ss_pred             hCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCC
Q 023816          109 TTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPV  188 (276)
Q Consensus       109 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv  188 (276)
                      ..+                                           .+.+|||++|+...... .++++.|+++||.||+
T Consensus        72 ~~~-------------------------------------------~~~~pii~~s~~~~~~~-~~~~~~g~~~~l~KP~  107 (133)
T 3nhm_A           72 EPT-------------------------------------------LKHIPVIFVSGYAPRTE-GPADQPVPDAYLVKPV  107 (133)
T ss_dssp             STT-------------------------------------------TTTCCEEEEESCCC------TTSCCCSEEEESSC
T ss_pred             CCc-------------------------------------------cCCCCEEEEeCCCcHhH-HHHhhcCCceEEeccC
Confidence            421                                           23789999999988777 8999999999999999


Q ss_pred             CHHHHHHHHHHHHHh
Q 023816          189 KLSDVKRIKDYLTRD  203 (276)
Q Consensus       189 ~~~~L~~~~~~l~~~  203 (276)
                      +.++|...+..+.+.
T Consensus       108 ~~~~l~~~i~~~l~~  122 (133)
T 3nhm_A          108 KPPVLIAQLHALLAR  122 (133)
T ss_dssp             CHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHhh
Confidence            999997777666544

>1a04_A Nitrate/nitrite response regulator protein NARL; signal transduction protein, response regulators, two- component systems; 2.20A {Escherichia coli} SCOP: a.4.6.2 c.23.1.1 PDB: 1rnl_A

Probab=99.85  E-value=2.4e-20  Score=157.35  Aligned_cols=121  Identities=24%  Similarity=0.428  Sum_probs=108.7

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhCC-CEE-EEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHH
Q 023816           27 TEEVHVLAVDDSFVDRKVIERLLTISS-CKV-TAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLK  104 (276)
Q Consensus        27 ~~~~~VLIVdD~~~~~~~L~~~L~~~g-~~v-~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~  104 (276)
                      ..+++||||||++..+..++.+|+..+ +.+ ..+.++.+|++.+           ....||+||+|+.||+++|+++++
T Consensus         3 ~~~~~ilivdd~~~~~~~l~~~L~~~~~~~vv~~~~~~~~al~~~-----------~~~~~dlvllD~~lp~~~g~~~~~   71 (215)
T 1a04_A            3 QEPATILLIDDHPMLRTGVKQLISMAPDITVVGEASNGEQGIELA-----------ESLDPDLILLDLNMPGMNGLETLD   71 (215)
T ss_dssp             -CCEEEEEECSCHHHHHHHHHHHTTCTTEEEEEEESSHHHHHHHH-----------HHHCCSEEEEETTSTTSCHHHHHH
T ss_pred             CCceEEEEECCCHHHHHHHHHHHhcCCCcEEEEEeCCHHHHHHHH-----------HhcCCCEEEEeCCCCCCcHHHHHH
Confidence            346899999999999999999999874 887 6799999999998           455799999999999999999999


Q ss_pred             HHHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEE
Q 023816          105 KIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFI  184 (276)
Q Consensus       105 ~Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l  184 (276)
                      +||+..|                                             .+|||++|+....+...++++.|+++||
T Consensus        72 ~lr~~~~---------------------------------------------~~~ii~ls~~~~~~~~~~~~~~Ga~~~l  106 (215)
T 1a04_A           72 KLREKSL---------------------------------------------SGRIVVFSVSNHEEDVVTALKRGADGYL  106 (215)
T ss_dssp             HHHHSCC---------------------------------------------CSEEEEEECCCCHHHHHHHHHTTCSEEE
T ss_pred             HHHHhCC---------------------------------------------CCcEEEEECCCCHHHHHHHHHcCCcEEE
Confidence            9998666                                             7999999999999999999999999999


Q ss_pred             eCCCCHHHHHHHHHHHHHh
Q 023816          185 VKPVKLSDVKRIKDYLTRD  203 (276)
Q Consensus       185 ~KPv~~~~L~~~~~~l~~~  203 (276)
                      .||++.++|...+..+.+.
T Consensus       107 ~Kp~~~~~L~~~i~~~~~~  125 (215)
T 1a04_A          107 LKDMEPEDLLKALHQAAAG  125 (215)
T ss_dssp             ETTCCHHHHHHHHHHHHHS
T ss_pred             eCCCCHHHHHHHHHHHHcC
Confidence            9999999997777766553

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

Probab=99.84  E-value=1.2e-20  Score=147.80  Aligned_cols=121  Identities=21%  Similarity=0.350  Sum_probs=109.1

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHH
Q 023816           27 TEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKI  106 (276)
Q Consensus        27 ~~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~I  106 (276)
                      +.+++||||||++..++.++..|+..||+|..+.++++|++.+           +...||+||+|+.||+++|++++++|
T Consensus         5 ~~~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l-----------~~~~~dlii~d~~l~~~~g~~~~~~l   73 (142)
T 3cg4_A            5 EHKGDVMIVDDDAHVRIAVKTILSDAGFHIISADSGGQCIDLL-----------KKGFSGVVLLDIMMPGMDGWDTIRAI   73 (142)
T ss_dssp             -CCCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHH-----------HTCCCEEEEEESCCSSSCHHHHHHHH
T ss_pred             CCCCeEEEEcCCHHHHHHHHHHHHHCCeEEEEeCCHHHHHHHH-----------HhcCCCEEEEeCCCCCCCHHHHHHHH
Confidence            4578999999999999999999999999999999999999999           56679999999999999999999999


Q ss_pred             Hh--hCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEE
Q 023816          107 KV--TTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFI  184 (276)
Q Consensus       107 r~--~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l  184 (276)
                      ++  ..+                                             .+|||++|+........++++.|+++||
T Consensus        74 ~~~~~~~---------------------------------------------~~pii~~s~~~~~~~~~~~~~~g~~~~l  108 (142)
T 3cg4_A           74 LDNSLEQ---------------------------------------------GIAIVMLTAKNAPDAKMIGLQEYVVDYI  108 (142)
T ss_dssp             HHTTCCT---------------------------------------------TEEEEEEECTTCCCCSSTTGGGGEEEEE
T ss_pred             HhhcccC---------------------------------------------CCCEEEEECCCCHHHHHHHHhcCccEEE
Confidence            97  344                                             7999999999888888899999999999


Q ss_pred             eCCCCHHHHHHHHHHHHHh
Q 023816          185 VKPVKLSDVKRIKDYLTRD  203 (276)
Q Consensus       185 ~KPv~~~~L~~~~~~l~~~  203 (276)
                      .||++.++|...+..+.+.
T Consensus       109 ~kp~~~~~l~~~i~~~~~~  127 (142)
T 3cg4_A          109 TKPFDNEDLIEKTTFFMGF  127 (142)
T ss_dssp             ESSCCHHHHHHHHHHHHHH
T ss_pred             eCCCCHHHHHHHHHHHHHH
Confidence            9999999997777665543

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

Probab=99.84  E-value=3.8e-20  Score=147.53  Aligned_cols=125  Identities=25%  Similarity=0.374  Sum_probs=108.9

Q ss_pred             CCCCCCccEEEEEeCCHHHHHHHHHHHhhCCCE--EEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHH
Q 023816           23 SPSDTEEVHVLAVDDSFVDRKVIERLLTISSCK--VTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGY  100 (276)
Q Consensus        23 ~~~~~~~~~VLIVdD~~~~~~~L~~~L~~~g~~--v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~  100 (276)
                      .+....+.+||||||++..++.++.+|+..|+.  +..+.++.+|++.+           ....||+||+|+.||+++|+
T Consensus         9 ~~~~~~~~~iLivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~a~~~l-----------~~~~~dlii~d~~l~~~~g~   77 (152)
T 3eul_A            9 SNPQPEKVRVVVGDDHPLFREGVVRALSLSGSVNVVGEADDGAAALELI-----------KAHLPDVALLDYRMPGMDGA   77 (152)
T ss_dssp             -----CCEEEEEECSSHHHHHHHHHHHHHHSSEEEEEEESSHHHHHHHH-----------HHHCCSEEEEETTCSSSCHH
T ss_pred             CCCCCceEEEEEEcCCHHHHHHHHHHHhhCCCeEEEEEeCCHHHHHHHH-----------HhcCCCEEEEeCCCCCCCHH
Confidence            344566889999999999999999999999854  55799999999998           55679999999999999999


Q ss_pred             HHHHHHHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCC
Q 023816          101 ELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGA  180 (276)
Q Consensus       101 ell~~Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga  180 (276)
                      +++++||+..|                                             .+|||++|+..+.....++++.|+
T Consensus        78 ~~~~~l~~~~~---------------------------------------------~~~ii~~s~~~~~~~~~~~~~~g~  112 (152)
T 3eul_A           78 QVAAAVRSYEL---------------------------------------------PTRVLLISAHDEPAIVYQALQQGA  112 (152)
T ss_dssp             HHHHHHHHTTC---------------------------------------------SCEEEEEESCCCHHHHHHHHHTTC
T ss_pred             HHHHHHHhcCC---------------------------------------------CCeEEEEEccCCHHHHHHHHHcCC
Confidence            99999998766                                             799999999999999999999999


Q ss_pred             CeEEeCCCCHHHHHHHHHHHHHh
Q 023816          181 EDFIVKPVKLSDVKRIKDYLTRD  203 (276)
Q Consensus       181 ~d~l~KPv~~~~L~~~~~~l~~~  203 (276)
                      ++||.||++.++|...+..+.+.
T Consensus       113 ~~~l~Kp~~~~~l~~~i~~~~~~  135 (152)
T 3eul_A          113 AGFLLKDSTRTEIVKAVLDCAKG  135 (152)
T ss_dssp             SEEEETTCCHHHHHHHHHHHHHC
T ss_pred             CEEEecCCCHHHHHHHHHHHHcC
Confidence            99999999999997777666543

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

Probab=99.84  E-value=3.5e-20  Score=143.42  Aligned_cols=121  Identities=19%  Similarity=0.342  Sum_probs=101.9

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHH
Q 023816           27 TEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKI  106 (276)
Q Consensus        27 ~~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~I  106 (276)
                      ..+.+||||||++..+..++.+|+..||.+..+.++.+|++.+           ....||+||+|+.||+++|++++++|
T Consensus         4 ~~~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l-----------~~~~~dlii~d~~l~~~~g~~~~~~l   72 (132)
T 3lte_A            4 KQSKRILVVDDDQAMAAAIERVLKRDHWQVEIAHNGFDAGIKL-----------STFEPAIMTLDLSMPKLDGLDVIRSL   72 (132)
T ss_dssp             ---CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHH-----------HHTCCSEEEEESCBTTBCHHHHHHHH
T ss_pred             CCCccEEEEECCHHHHHHHHHHHHHCCcEEEEeCCHHHHHHHH-----------HhcCCCEEEEecCCCCCCHHHHHHHH
Confidence            3468999999999999999999999999999999999999998           56689999999999999999999999


Q ss_pred             HhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeC
Q 023816          107 KVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVK  186 (276)
Q Consensus       107 r~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~K  186 (276)
                      |+..+                                           ...++||++++.... ...++++.|+++||.|
T Consensus        73 ~~~~~-------------------------------------------~~~~~ii~~~~~~~~-~~~~~~~~g~~~~l~k  108 (132)
T 3lte_A           73 RQNKV-------------------------------------------ANQPKILVVSGLDKA-KLQQAVTEGADDYLEK  108 (132)
T ss_dssp             HTTTC-------------------------------------------SSCCEEEEECCSCSH-HHHHHHHHTCCEEECS
T ss_pred             HhcCc-------------------------------------------cCCCeEEEEeCCChH-HHHHHHHhChHHHhhC
Confidence            97542                                           114566666665554 7889999999999999


Q ss_pred             CCCHHHHHHHHHHHHH
Q 023816          187 PVKLSDVKRIKDYLTR  202 (276)
Q Consensus       187 Pv~~~~L~~~~~~l~~  202 (276)
                      |++.++|...+.....
T Consensus       109 P~~~~~l~~~i~~~~~  124 (132)
T 3lte_A          109 PFDNDALLDRIHDLVN  124 (132)
T ss_dssp             SCCHHHHHHHHHHHHC
T ss_pred             CCCHHHHHHHHHHHcC
Confidence            9999999766665543

>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=99.84  E-value=6.9e-21  Score=149.55  Aligned_cols=122  Identities=23%  Similarity=0.335  Sum_probs=98.7

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHH
Q 023816           28 EEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIK  107 (276)
Q Consensus        28 ~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir  107 (276)
                      .+.+||||||++..+..++.+|+.. +.+..+.++.+|++.+           ....||+||+|+.||+++|++++++||
T Consensus         2 ~~~~iLivdd~~~~~~~l~~~l~~~-~~v~~~~~~~~a~~~~-----------~~~~~dlvi~D~~l~~~~g~~~~~~l~   69 (140)
T 3n53_A            2 SLKKILIIDQQDFSRIELKNFLDSE-YLVIESKNEKEALEQI-----------DHHHPDLVILDMDIIGENSPNLCLKLK   69 (140)
T ss_dssp             -CCEEEEECSCHHHHHHHHHHHTTT-SEEEEESSHHHHHHHH-----------HHHCCSEEEEETTC------CHHHHHH
T ss_pred             CCCEEEEEeCCHHHHHHHHHHHHhc-ceEEEeCCHHHHHHHH-----------hcCCCCEEEEeCCCCCCcHHHHHHHHH
Confidence            4679999999999999999999988 9999999999999998           556799999999999999999999999


Q ss_pred             hhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCC
Q 023816          108 VTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKP  187 (276)
Q Consensus       108 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KP  187 (276)
                      +..                                           ....+|||++|+....+...++++.|+++||.||
T Consensus        70 ~~~-------------------------------------------~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~KP  106 (140)
T 3n53_A           70 RSK-------------------------------------------GLKNVPLILLFSSEHKEAIVNGLHSGADDYLTKP  106 (140)
T ss_dssp             TST-------------------------------------------TCTTCCEEEEECC----CTTTTTTCCCSEEEESS
T ss_pred             cCc-------------------------------------------ccCCCCEEEEecCCCHHHHHHHHhcCCCeeeeCC
Confidence            754                                           1127999999999988888999999999999999


Q ss_pred             CCHHHHHHHHHHHHHhh
Q 023816          188 VKLSDVKRIKDYLTRDV  204 (276)
Q Consensus       188 v~~~~L~~~~~~l~~~~  204 (276)
                      ++.++|...+..+.+..
T Consensus       107 ~~~~~l~~~i~~~~~~~  123 (140)
T 3n53_A          107 FNRNDLLSRIEIHLRTQ  123 (140)
T ss_dssp             CCHHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhhH
Confidence            99999977777665543

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

Probab=99.84  E-value=1.4e-20  Score=142.67  Aligned_cols=113  Identities=21%  Similarity=0.368  Sum_probs=101.4

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhh
Q 023816           30 VHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVT  109 (276)
Q Consensus        30 ~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~  109 (276)
                      .+||||||++..++.++..|+..|+.+..+.++.+|++.+           ....||+||+|+.||+++|++++++||+.
T Consensus         2 ~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~~-----------~~~~~dlvl~D~~l~~~~g~~~~~~l~~~   70 (116)
T 3a10_A            2 KRILVVDDEPNIRELLKEELQEEGYEIDTAENGEEALKKF-----------FSGNYDLVILDIEMPGISGLEVAGEIRKK   70 (116)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHH-----------HHSCCSEEEECSCCSSSCHHHHHHHHHHH
T ss_pred             cEEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHH-----------hcCCCCEEEEECCCCCCCHHHHHHHHHcc
Confidence            4899999999999999999999999999999999999998           45679999999999999999999999987


Q ss_pred             CCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCC
Q 023816          110 TPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVK  189 (276)
Q Consensus       110 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~  189 (276)
                      .|                                             .+|||++|+.....  .++++.|+++|+.||++
T Consensus        71 ~~---------------------------------------------~~~ii~~s~~~~~~--~~~~~~g~~~~l~Kp~~  103 (116)
T 3a10_A           71 KK---------------------------------------------DAKIILLTAYSHYR--SDMSSWAADEYVVKSFN  103 (116)
T ss_dssp             CT---------------------------------------------TCCEEEEESCGGGG--GCGGGGGSSEEEECCSS
T ss_pred             CC---------------------------------------------CCeEEEEECCcchH--HHHHhccccceEECCCC
Confidence            66                                             78999999876654  67889999999999999


Q ss_pred             HHHHHHHHHHH
Q 023816          190 LSDVKRIKDYL  200 (276)
Q Consensus       190 ~~~L~~~~~~l  200 (276)
                      .++|...+..+
T Consensus       104 ~~~l~~~i~~~  114 (116)
T 3a10_A          104 FDELKEKVKKL  114 (116)
T ss_dssp             THHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99996665543

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

Probab=99.84  E-value=3.6e-21  Score=178.75  Aligned_cols=117  Identities=28%  Similarity=0.485  Sum_probs=103.8

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHh
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKV  108 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~  108 (276)
                      +.+||||||++.+++.++.+|+..||+|..+.++++|++.+           +...||+||+|+.||++||++++++||+
T Consensus         5 ~~~iLivdD~~~~~~~l~~~L~~~g~~v~~a~~~~~al~~~-----------~~~~~dlvllD~~mp~~~G~~~~~~lr~   73 (394)
T 3eq2_A            5 SATLLIIDDDEVVRESLAAYLEDSNFKVLQALNGLQGLQIF-----------ESEQPDLVICDLRMPQIDGLELIRRIRQ   73 (394)
T ss_dssp             EEEEEEECSCHHHHHHHHHHHHHTTEEEEECSSHHHHHHHH-----------HHSCCSEEEECCCSSSSCTHHHHHHHHH
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHhCCCEEEEECCHHHHHHHH-----------hhCCCCEEEEcCCCCCCCHHHHHHHHHh
Confidence            67999999999999999999999999999999999999998           5567999999999999999999999998


Q ss_pred             hCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCC
Q 023816          109 TTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPV  188 (276)
Q Consensus       109 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv  188 (276)
                      ..+                                             .+|||++|+..+.+...+|++.|++|||.||+
T Consensus        74 ~~~---------------------------------------------~~pii~lt~~~~~~~~~~a~~~ga~~yl~KP~  108 (394)
T 3eq2_A           74 TAS---------------------------------------------ETPIIVLSGAGVMSDAVEALRLGAADYLIKPL  108 (394)
T ss_dssp             TTC---------------------------------------------CCCEEEC---CHHHHHHHHHHHTCSEECCSSC
T ss_pred             hCC---------------------------------------------CCcEEEEEcCCCHHHHHHHHhcChhhEEECCC
Confidence            766                                             79999999999999999999999999999999


Q ss_pred             -CHHHHHHHHHHHH
Q 023816          189 -KLSDVKRIKDYLT  201 (276)
Q Consensus       189 -~~~~L~~~~~~l~  201 (276)
                       ..+.|.+.+..+.
T Consensus       109 ~~~~~l~~~i~~~~  122 (394)
T 3eq2_A          109 EDLAVLEHSVRRAL  122 (394)
T ss_dssp             SCTHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHH
Confidence             5777765555443

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

Probab=99.84  E-value=2.2e-20  Score=148.30  Aligned_cols=118  Identities=23%  Similarity=0.295  Sum_probs=100.5

Q ss_pred             cEEEEEeCCHHHHHHHHHHHh--hCCCEEE-EECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHH
Q 023816           30 VHVLAVDDSFVDRKVIERLLT--ISSCKVT-AVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKI  106 (276)
Q Consensus        30 ~~VLIVdD~~~~~~~L~~~L~--~~g~~v~-~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~I  106 (276)
                      ++||||||++..++.+...|.  ..|+.+. .+.++.+|++.+           ....||+||+|+.||+++|++++++|
T Consensus         3 ~~ILivdd~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~al~~~-----------~~~~~dlvllD~~lp~~~g~~l~~~l   71 (141)
T 3cu5_A            3 LRILIVDDEKLTRDGLIANINWKALSFDQIDQADDGINAIQIA-----------LKHPPNVLLTDVRMPRMDGIELVDNI   71 (141)
T ss_dssp             CEEEEECSCHHHHHHHHHHCCGGGSCCSEEEEESSHHHHHHHH-----------TTSCCSEEEEESCCSSSCHHHHHHHH
T ss_pred             ceEEEEeCCHHHHHHHHHHHHHccCCcEEeeecccHHHHHHHH-----------hcCCCCEEEEeCCCCCCCHHHHHHHH
Confidence            689999999999999999997  3688877 899999999998           66789999999999999999999999


Q ss_pred             HhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeC
Q 023816          107 KVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVK  186 (276)
Q Consensus       107 r~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~K  186 (276)
                      ++..|                                             .+|||++|+........++++.|+++||.|
T Consensus        72 ~~~~~---------------------------------------------~~~ii~ls~~~~~~~~~~~~~~ga~~~l~K  106 (141)
T 3cu5_A           72 LKLYP---------------------------------------------DCSVIFMSGYSDKEYLKAAIKFRAIRYVEK  106 (141)
T ss_dssp             HHHCT---------------------------------------------TCEEEEECCSTTTCCC------CCCEEECS
T ss_pred             HhhCC---------------------------------------------CCcEEEEeCCCcHHHHHHHHhCCccEEEeC
Confidence            98766                                             799999999988888889999999999999


Q ss_pred             CCCHHHHHHHHHHHHHh
Q 023816          187 PVKLSDVKRIKDYLTRD  203 (276)
Q Consensus       187 Pv~~~~L~~~~~~l~~~  203 (276)
                      |++.++|...+..+.+.
T Consensus       107 P~~~~~L~~~i~~~~~~  123 (141)
T 3cu5_A          107 PIDPSEIMDALKQSIQT  123 (141)
T ss_dssp             SCCHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHH
Confidence            99999997776665543

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

Probab=99.84  E-value=2.1e-20  Score=144.41  Aligned_cols=118  Identities=18%  Similarity=0.229  Sum_probs=105.7

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHH
Q 023816           28 EEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIK  107 (276)
Q Consensus        28 ~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir  107 (276)
                      .+.+||||||++..++.++.+|+..++.+..+.+++++++.+           ... ||+||+|+.||+++|++++++||
T Consensus         2 ~~~~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~-----------~~~-~dlvi~D~~l~~~~g~~~~~~l~   69 (135)
T 3eqz_A            2 SLNRVFIVDDDTLTCNLLKTIVEPIFGNVEAFQHPRAFLTLS-----------LNK-QDIIILDLMMPDMDGIEVIRHLA   69 (135)
T ss_dssp             -CCEEEEECSCHHHHHHHHHHHTTTCSCEEEESCHHHHTTSC-----------CCT-TEEEEEECCTTTTHHHHHHHHHH
T ss_pred             CcceEEEEeCCHHHHHHHHHHHHhhcceeeeecCHHHHHHhh-----------ccC-CCEEEEeCCCCCCCHHHHHHHHH
Confidence            468999999999999999999998888999999999999877           555 99999999999999999999999


Q ss_pred             hhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCH-----HHHHHHHhcCCCe
Q 023816          108 VTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENIL-----ARIDRCLEDGAED  182 (276)
Q Consensus       108 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~-----~~~~~al~~Ga~d  182 (276)
                      +..+                                             .+|||++|+....     ....++++.|+++
T Consensus        70 ~~~~---------------------------------------------~~~ii~~s~~~~~~~~~~~~~~~~~~~g~~~  104 (135)
T 3eqz_A           70 EHKS---------------------------------------------PASLILISGYDSGVLHSAETLALSCGLNVIN  104 (135)
T ss_dssp             HTTC---------------------------------------------CCEEEEEESSCHHHHHHHHHHHHHTTCEEEE
T ss_pred             hCCC---------------------------------------------CCCEEEEEeccchhHHHHHHHHHHcCCCcce
Confidence            8766                                             7999999998875     6677899999999


Q ss_pred             EEeCCCCHHHHHHHHHHHHH
Q 023816          183 FIVKPVKLSDVKRIKDYLTR  202 (276)
Q Consensus       183 ~l~KPv~~~~L~~~~~~l~~  202 (276)
                      ||.||++.++|...+..+..
T Consensus       105 ~l~KP~~~~~l~~~l~~~~~  124 (135)
T 3eqz_A          105 TFTKPINTEVLTCFLTSLSN  124 (135)
T ss_dssp             EEESSCCHHHHHHHHHHHSC
T ss_pred             eeCCCCCHHHHHHHHHHHHh
Confidence            99999999999777766553

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

Probab=99.84  E-value=5.3e-20  Score=144.68  Aligned_cols=118  Identities=24%  Similarity=0.312  Sum_probs=104.5

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhh
Q 023816           30 VHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVT  109 (276)
Q Consensus        30 ~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~  109 (276)
                      .+||||||++..+..++.+|+.. |.+..+.++.+|++.+           ....||+||+|+.||+++|++++++|++.
T Consensus         2 ~~Ilivdd~~~~~~~l~~~l~~~-~~v~~~~~~~~a~~~~-----------~~~~~dlvl~D~~lp~~~g~~~~~~l~~~   69 (139)
T 2jk1_A            2 PAILLVDDEPHSLAAMKLALEDD-FDVLTAQGAEAAIAIL-----------EEEWVQVIICDQRMPGRTGVDFLTEVRER   69 (139)
T ss_dssp             CEEEEECSSHHHHHHHHHHHTTT-SCEEEESSHHHHHHHH-----------HHSCEEEEEEESCCSSSCHHHHHHHHHHH
T ss_pred             CeEEEEcCCHHHHHHHHHHhhcC-ceEEEcCCHHHHHHHH-----------hcCCCCEEEEeCCCCCCcHHHHHHHHHHh
Confidence            37999999999999999999875 9999999999999998           45679999999999999999999999987


Q ss_pred             CCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhc-CCCeEEeCCC
Q 023816          110 TPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLED-GAEDFIVKPV  188 (276)
Q Consensus       110 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~-Ga~d~l~KPv  188 (276)
                      .|                                             .+|+|++|+..+.....++++. |+++||.||+
T Consensus        70 ~~---------------------------------------------~~~ii~~s~~~~~~~~~~~~~~~ga~~~l~KP~  104 (139)
T 2jk1_A           70 WP---------------------------------------------ETVRIIITGYTDSASMMAAINDAGIHQFLTKPW  104 (139)
T ss_dssp             CT---------------------------------------------TSEEEEEESCTTCHHHHHHHHHTTCCEEEESSC
T ss_pred             CC---------------------------------------------CCcEEEEeCCCChHHHHHHHHhhchhhhccCCC
Confidence            66                                             7899999999888888888875 6999999999


Q ss_pred             CHHHHHHHHHHHHHhh
Q 023816          189 KLSDVKRIKDYLTRDV  204 (276)
Q Consensus       189 ~~~~L~~~~~~l~~~~  204 (276)
                      +.++|...+..+.+..
T Consensus       105 ~~~~L~~~i~~~~~~~  120 (139)
T 2jk1_A          105 HPEQLLSSARNAARMF  120 (139)
T ss_dssp             CHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHH
Confidence            9999977776655443

>1kgs_A DRRD, DNA binding response regulator D; DNA-binding protein, ALPH-beta sandwich, winged-helix, helix helix, DNA binding protein; HET: DNA MSE; 1.50A {Thermotoga maritima} SCOP: a.4.6.1 c.23.1.1 PDB: 3nnn_A*

Probab=99.84  E-value=4.2e-20  Score=156.19  Aligned_cols=119  Identities=24%  Similarity=0.345  Sum_probs=109.6

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHh
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKV  108 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~  108 (276)
                      +++||||||++..+..++.+|+..|++|..+.++.+|++.+           ....||+||+|+.||+++|++++++||+
T Consensus         2 ~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~~-----------~~~~~dlvllD~~l~~~~g~~~~~~lr~   70 (225)
T 1kgs_A            2 NVRVLVVEDERDLADLITEALKKEMFTVDVCYDGEEGMYMA-----------LNEPFDVVILDIMLPVHDGWEILKSMRE   70 (225)
T ss_dssp             CCEEEEECSSHHHHHHHHHHHHHTTCEEEEESSHHHHHHHH-----------HHSCCSEEEEESCCSSSCHHHHHHHHHH
T ss_pred             CceEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHH-----------hcCCCCEEEEeCCCCCCCHHHHHHHHHh
Confidence            47999999999999999999999999999999999999988           5567999999999999999999999998


Q ss_pred             hCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCC
Q 023816          109 TTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPV  188 (276)
Q Consensus       109 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv  188 (276)
                      ..|                                             .+|||++|+........++++.|+++|+.||+
T Consensus        71 ~~~---------------------------------------------~~~ii~ls~~~~~~~~~~~~~~ga~~~l~Kp~  105 (225)
T 1kgs_A           71 SGV---------------------------------------------NTPVLMLTALSDVEYRVKGLNMGADDYLPKPF  105 (225)
T ss_dssp             TTC---------------------------------------------CCCEEEEESSCHHHHHHHTCCCCCSEEEESSC
T ss_pred             cCC---------------------------------------------CCCEEEEeCCCCHHHHHHHHhCCccEEEeCCC
Confidence            666                                             79999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHh
Q 023816          189 KLSDVKRIKDYLTRD  203 (276)
Q Consensus       189 ~~~~L~~~~~~l~~~  203 (276)
                      +.++|...+..+.+.
T Consensus       106 ~~~~l~~~i~~~~~~  120 (225)
T 1kgs_A          106 DLRELIARVRALIRR  120 (225)
T ss_dssp             CHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHhh
Confidence            999997777766554

>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=99.84  E-value=1.3e-20  Score=177.30  Aligned_cols=118  Identities=19%  Similarity=0.282  Sum_probs=109.8

Q ss_pred             EEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhhC
Q 023816           31 HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVTT  110 (276)
Q Consensus        31 ~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~~  110 (276)
                      +||||||++..+..++.+|+..||.+..+.++++|++.+           ....||+||+|+.||+|||++++++||+..
T Consensus         2 ~ILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~eal~~l-----------~~~~~DlvllDi~mP~~dG~ell~~lr~~~   70 (368)
T 3dzd_A            2 RVLVVDDEESITSSLSAILEEEGYHPDTAKTLREAEKKI-----------KELFFPVIVLDVWMPDGDGVNFIDFIKENS   70 (368)
T ss_dssp             EEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHH-----------HHBCCSEEEEESEETTEETTTHHHHHHHHC
T ss_pred             EEEEEeCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHH-----------HhCCCCEEEEeCCCCCCCHHHHHHHHHhhC
Confidence            799999999999999999999999999999999999999           566899999999999999999999999877


Q ss_pred             CCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCCH
Q 023816          111 PFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKL  190 (276)
Q Consensus       111 p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~~  190 (276)
                      |                                             .+|||++|++.+.+...+|++.||+|||.||++.
T Consensus        71 ~---------------------------------------------~~pvI~lT~~~~~~~~~~a~~~Ga~~yl~KP~~~  105 (368)
T 3dzd_A           71 P---------------------------------------------DSVVIVITGHGSVDTAVKAIKKGAYEFLEKPFSV  105 (368)
T ss_dssp             T---------------------------------------------TCEEEEEECSSCCHHHHHHHHHTCCEEEESSCCH
T ss_pred             C---------------------------------------------CCeEEEEeCCCCHHHHHHHHhcCcceEEeCCCCH
Confidence            7                                             7999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhh
Q 023816          191 SDVKRIKDYLTRDV  204 (276)
Q Consensus       191 ~~L~~~~~~l~~~~  204 (276)
                      ++|...+..+....
T Consensus       106 ~~L~~~i~~~l~~~  119 (368)
T 3dzd_A          106 ERFLLTIKHAFEEY  119 (368)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHh
Confidence            99977777665543

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

Probab=99.84  E-value=2.2e-20  Score=163.98  Aligned_cols=121  Identities=21%  Similarity=0.354  Sum_probs=109.0

Q ss_pred             CCCccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHH
Q 023816           26 DTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKK  105 (276)
Q Consensus        26 ~~~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~  105 (276)
                      .+.+++||||||++..+..++.+|+..|+.|..+.++.+|++.+           ....||+||+|+.||+++|++++++
T Consensus        34 ~m~~~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~-----------~~~~~DlvllD~~lp~~~G~~l~~~  102 (249)
T 3q9s_A           34 RMNEQRILVIEDDHDIANVLRMDLTDAGYVVDHADSAMNGLIKA-----------REDHPDLILLDLGLPDFDGGDVVQR  102 (249)
T ss_dssp             ---CCEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHH-----------HHSCCSEEEEECCSCHHHHHHHHHH
T ss_pred             CCCCCEEEEEECCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHH-----------hcCCCCEEEEcCCCCCCCHHHHHHH
Confidence            35568999999999999999999999999999999999999998           5567999999999999999999999


Q ss_pred             HHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEe
Q 023816          106 IKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIV  185 (276)
Q Consensus       106 Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~  185 (276)
                      ||+ .|                                             .+|||++|+..+.+...+|++.||++||.
T Consensus       103 lr~-~~---------------------------------------------~~~iI~lt~~~~~~~~~~a~~~Ga~~yl~  136 (249)
T 3q9s_A          103 LRK-NS---------------------------------------------ALPIIVLTARDTVEEKVRLLGLGADDYLI  136 (249)
T ss_dssp             HHT-TC---------------------------------------------CCCEEEEESCCSHHHHHHHHHHTCSEEEE
T ss_pred             HHc-CC---------------------------------------------CCCEEEEECCCCHHHHHHHHHCCCcEEEE
Confidence            996 44                                             78999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHh
Q 023816          186 KPVKLSDVKRIKDYLTRD  203 (276)
Q Consensus       186 KPv~~~~L~~~~~~l~~~  203 (276)
                      ||++.++|...+..+.+.
T Consensus       137 Kp~~~~~L~~~i~~~l~~  154 (249)
T 3q9s_A          137 KPFHPDELLARVKVQLRQ  154 (249)
T ss_dssp             SSCCHHHHHHHHHHHHCC
T ss_pred             CCCCHHHHHHHHHHHHhh
Confidence            999999997777766543

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

Probab=99.83  E-value=8.1e-20  Score=145.79  Aligned_cols=120  Identities=18%  Similarity=0.282  Sum_probs=109.8

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhh-CCCEEE-EECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHH
Q 023816           28 EEVHVLAVDDSFVDRKVIERLLTI-SSCKVT-AVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKK  105 (276)
Q Consensus        28 ~~~~VLIVdD~~~~~~~L~~~L~~-~g~~v~-~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~  105 (276)
                      .+++||||||++..++.++.+|+. .|+.+. .+.++.+|++.+           ....||+||+|+.||+++|++++++
T Consensus         4 ~~~~ILivdd~~~~~~~l~~~L~~~~~~~v~~~~~~~~~a~~~l-----------~~~~~dlii~D~~l~~~~g~~~~~~   72 (153)
T 3cz5_A            4 STARIMLVDDHPIVREGYRRLIERRPGYAVVAEAADAGEAYRLY-----------RETTPDIVVMDLTLPGPGGIEATRH   72 (153)
T ss_dssp             CCEEEEEECSCHHHHHHHHHHHTTSTTEEEEEEESSHHHHHHHH-----------HTTCCSEEEECSCCSSSCHHHHHHH
T ss_pred             cccEEEEECCcHHHHHHHHHHHhhCCCcEEEEEeCCHHHHHHHH-----------hcCCCCEEEEecCCCCCCHHHHHHH
Confidence            468999999999999999999998 799998 799999999998           5667999999999999999999999


Q ss_pred             HHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEe
Q 023816          106 IKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIV  185 (276)
Q Consensus       106 Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~  185 (276)
                      |++..+                                             .+|||++|+........++++.|+++||.
T Consensus        73 l~~~~~---------------------------------------------~~~ii~ls~~~~~~~~~~~~~~g~~~~l~  107 (153)
T 3cz5_A           73 IRQWDG---------------------------------------------AARILIFTMHQGSAFALKAFEAGASGYVT  107 (153)
T ss_dssp             HHHHCT---------------------------------------------TCCEEEEESCCSHHHHHHHHHTTCSEEEE
T ss_pred             HHHhCC---------------------------------------------CCeEEEEECCCCHHHHHHHHHCCCcEEEe
Confidence            998766                                             79999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHh
Q 023816          186 KPVKLSDVKRIKDYLTRD  203 (276)
Q Consensus       186 KPv~~~~L~~~~~~l~~~  203 (276)
                      ||++.++|...+..+.+.
T Consensus       108 kp~~~~~L~~~i~~~~~~  125 (153)
T 3cz5_A          108 KSSDPAELVQAIEAILAG  125 (153)
T ss_dssp             TTSCTTHHHHHHHHHTTT
T ss_pred             cCCCHHHHHHHHHHHHhC
Confidence            999999997777666543

>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=99.83  E-value=3.5e-20  Score=157.41  Aligned_cols=121  Identities=27%  Similarity=0.390  Sum_probs=109.5

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHH
Q 023816           27 TEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKI  106 (276)
Q Consensus        27 ~~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~I  106 (276)
                      +..++||||||++..+..+..+|+..||+|..+.++.+|++.+           ....||+||+|+.||+++|+++++.|
T Consensus         5 ~~~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~~-----------~~~~~dlvllD~~l~~~~g~~~~~~l   73 (233)
T 1ys7_A            5 VTSPRVLVVDDDSDVLASLERGLRLSGFEVATAVDGAEALRSA-----------TENRPDAIVLDINMPVLDGVSVVTAL   73 (233)
T ss_dssp             --CCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHH-----------HHSCCSEEEEESSCSSSCHHHHHHHH
T ss_pred             CCCCeEEEEeCCHHHHHHHHHHHHhCCCEEEEECCHHHHHHHH-----------HhCCCCEEEEeCCCCCCCHHHHHHHH
Confidence            3467999999999999999999999999999999999999998           55679999999999999999999999


Q ss_pred             HhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeC
Q 023816          107 KVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVK  186 (276)
Q Consensus       107 r~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~K  186 (276)
                      ++..|                                             .+|||++|+........++++.||++||.|
T Consensus        74 ~~~~~---------------------------------------------~~~ii~lt~~~~~~~~~~~~~~ga~~~l~K  108 (233)
T 1ys7_A           74 RAMDN---------------------------------------------DVPVCVLSARSSVDDRVAGLEAGADDYLVK  108 (233)
T ss_dssp             HHTTC---------------------------------------------CCCEEEEECCCTTTCCCTTTTTTCSEEEES
T ss_pred             HhcCC---------------------------------------------CCCEEEEEcCCCHHHHHHHHHcCCCEEEeC
Confidence            98666                                             799999999999888889999999999999


Q ss_pred             CCCHHHHHHHHHHHHHh
Q 023816          187 PVKLSDVKRIKDYLTRD  203 (276)
Q Consensus       187 Pv~~~~L~~~~~~l~~~  203 (276)
                      |++.++|...+..+.+.
T Consensus       109 p~~~~~L~~~i~~~~~~  125 (233)
T 1ys7_A          109 PFVLAELVARVKALLRR  125 (233)
T ss_dssp             SCCHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHhh
Confidence            99999997777766554

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

Probab=99.83  E-value=1.3e-19  Score=142.06  Aligned_cols=124  Identities=22%  Similarity=0.361  Sum_probs=105.4

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhCCC--EEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHH
Q 023816           28 EEVHVLAVDDSFVDRKVIERLLTISSC--KVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKK  105 (276)
Q Consensus        28 ~~~~VLIVdD~~~~~~~L~~~L~~~g~--~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~  105 (276)
                      .+++||||||++..++.++..|+..|+  .+..+.++.+|++.+......     ....||+||+|+.||+++|++++++
T Consensus         6 ~~~~ILivdd~~~~~~~l~~~L~~~g~~~~v~~~~~~~~a~~~l~~~~~~-----~~~~~dlii~D~~l~~~~g~~~~~~   80 (143)
T 2qvg_A            6 DKVDILYLEDDEVDIQSVERVFHKISSLIKIEIAKSGNQALDMLYGRNKE-----NKIHPKLILLDINIPKMNGIEFLKE   80 (143)
T ss_dssp             -CCSEEEECCCHHHHHHHHHHHHHHCTTCCEEEESSHHHHHHHHHTCTTC-----CCCCCSEEEEETTCTTSCHHHHHHH
T ss_pred             CCCeEEEEeCCHHHHHHHHHHHHHhCCCceEEEECCHHHHHHHHHhcccc-----cCCCCCEEEEecCCCCCCHHHHHHH
Confidence            467899999999999999999999998  999999999999998311000     0267999999999999999999999


Q ss_pred             HHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEe
Q 023816          106 IKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIV  185 (276)
Q Consensus       106 Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~  185 (276)
                      ||+..                                           ....+|||++|+....+...++++.|+++||.
T Consensus        81 l~~~~-------------------------------------------~~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~  117 (143)
T 2qvg_A           81 LRDDS-------------------------------------------SFTDIEVFVLTAAYTSKDKLAFESLNIRGHLI  117 (143)
T ss_dssp             HTTSG-------------------------------------------GGTTCEEEEEESCCCHHHHHHHTTTTCCEEEE
T ss_pred             HHcCc-------------------------------------------cccCCcEEEEeCCCCHHHHHHHHhcCCCeEEE
Confidence            99643                                           11279999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHH
Q 023816          186 KPVKLSDVKRIKDY  199 (276)
Q Consensus       186 KPv~~~~L~~~~~~  199 (276)
                      ||++.++|.+.+..
T Consensus       118 kP~~~~~L~~~~~~  131 (143)
T 2qvg_A          118 KPLDYGEAIKLFWI  131 (143)
T ss_dssp             SSCCHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHH
Confidence            99999999666443

>2gkg_A Response regulator homolog; social motility, receiver domain, signalling, high resolutio signaling protein; 1.00A {Myxococcus xanthus} PDB: 2i6f_A 2nt4_A 2nt3_A

Probab=99.83  E-value=6e-20  Score=139.64  Aligned_cols=118  Identities=19%  Similarity=0.315  Sum_probs=104.7

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCC-CCCHHHHHHHHH
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMP-GMTGYELLKKIK  107 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp-~~~G~ell~~Ir  107 (276)
                      .++||||||++..++.++..|+..||++..+.++.+|++.+           ....||+||+|+.|| +++|++++++||
T Consensus         5 ~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~~-----------~~~~~dlvi~d~~~~~~~~g~~~~~~l~   73 (127)
T 2gkg_A            5 SKKILIVESDTALSATLRSALEGRGFTVDETTDGKGSVEQI-----------RRDRPDLVVLAVDLSAGQNGYLICGKLK   73 (127)
T ss_dssp             -CEEEEECSCHHHHHHHHHHHHHHTCEEEEECCHHHHHHHH-----------HHHCCSEEEEESBCGGGCBHHHHHHHHH
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCceEEEecCHHHHHHHH-----------HhcCCCEEEEeCCCCCCCCHHHHHHHHh
Confidence            46999999999999999999999999999999999999998           455799999999999 999999999999


Q ss_pred             hhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCC
Q 023816          108 VTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKP  187 (276)
Q Consensus       108 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KP  187 (276)
                      +..                                           ....+|||++ +........++++.|+++|+.||
T Consensus        74 ~~~-------------------------------------------~~~~~~ii~~-~~~~~~~~~~~~~~g~~~~l~kp  109 (127)
T 2gkg_A           74 KDD-------------------------------------------DLKNVPIVII-GNPDGFAQHRKLKAHADEYVAKP  109 (127)
T ss_dssp             HST-------------------------------------------TTTTSCEEEE-ECGGGHHHHHHSTTCCSEEEESS
T ss_pred             cCc-------------------------------------------cccCCCEEEE-ecCCchhHHHHHHhCcchheeCC
Confidence            751                                           1127899999 88888888999999999999999


Q ss_pred             CCHHHHHHHHHHHH
Q 023816          188 VKLSDVKRIKDYLT  201 (276)
Q Consensus       188 v~~~~L~~~~~~l~  201 (276)
                      ++.++|...+..+.
T Consensus       110 ~~~~~l~~~i~~~~  123 (127)
T 2gkg_A          110 VDADQLVERAGALI  123 (127)
T ss_dssp             CCHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH
Confidence            99999977766554

>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=99.83  E-value=7.2e-20  Score=153.76  Aligned_cols=116  Identities=22%  Similarity=0.363  Sum_probs=105.0

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhCCCEEE-EECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHH
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTISSCKVT-AVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIK  107 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~g~~v~-~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir  107 (276)
                      +.+||||||++..+..+..+|+..||++. .+.++.+|++.+           ....||+||+|+.||+++|++++++|+
T Consensus        13 ~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~~al~~~-----------~~~~~dlvi~D~~~p~~~g~~~~~~l~   81 (205)
T 1s8n_A           13 PRRVLIAEDEALIRMDLAEMLREEGYEIVGEAGDGQEAVELA-----------ELHKPDLVIMDVKMPRRDGIDAASEIA   81 (205)
T ss_dssp             CCEEEEECSSHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHH-----------HHHCCSEEEEESSCSSSCHHHHHHHHH
T ss_pred             CccEEEEECCHHHHHHHHHHHHHCCCEEEEEeCCHHHHHHHH-----------hhcCCCEEEEeCCCCCCChHHHHHHHH
Confidence            46999999999999999999999999998 899999999998           456799999999999999999999999


Q ss_pred             hhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCC
Q 023816          108 VTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKP  187 (276)
Q Consensus       108 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KP  187 (276)
                      +..+                                              .|||++|++.......++++.|+++||.||
T Consensus        82 ~~~~----------------------------------------------~pii~lt~~~~~~~~~~~~~~ga~~~l~KP  115 (205)
T 1s8n_A           82 SKRI----------------------------------------------APIVVLTAFSQRDLVERARDAGAMAYLVKP  115 (205)
T ss_dssp             HTTC----------------------------------------------SCEEEEEEGGGHHHHHTTGGGSCEEEEEES
T ss_pred             hcCC----------------------------------------------CCEEEEecCCCHHHHHHHHhcCCcEEEeCC
Confidence            7443                                              599999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHH
Q 023816          188 VKLSDVKRIKDYLT  201 (276)
Q Consensus       188 v~~~~L~~~~~~l~  201 (276)
                      ++.++|...+..+.
T Consensus       116 ~~~~~L~~~i~~~~  129 (205)
T 1s8n_A          116 FSISDLIPAIELAV  129 (205)
T ss_dssp             CCHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH
Confidence            99999966665544

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

Probab=99.82  E-value=7.9e-20  Score=145.62  Aligned_cols=120  Identities=28%  Similarity=0.339  Sum_probs=98.4

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhC-CC-EEEEECCHHHHHHHhcccccccccCCCC-CceeEEEEecCCCCCCHHHHHH
Q 023816           28 EEVHVLAVDDSFVDRKVIERLLTIS-SC-KVTAVDSGRRALQFLGLDEEQSINGFDG-LKVDLIITDYCMPGMTGYELLK  104 (276)
Q Consensus        28 ~~~~VLIVdD~~~~~~~L~~~L~~~-g~-~v~~a~~g~~al~~l~~~~~~~~~~~~~-~~~DlIL~D~~mp~~~G~ell~  104 (276)
                      ..++||||||++..+..++..|+.. |+ .+..+.++.+|++.+           .. ..||+||+|+.||+++|+++++
T Consensus         2 ~~~~iLivdd~~~~~~~l~~~L~~~~g~~~v~~~~~~~~a~~~l-----------~~~~~~dlvi~d~~l~~~~g~~~~~   70 (154)
T 2qsj_A            2 SLTVVLIVDDHHLIRAGAKNLLEGAFSGMRVEGAETVSDALAFL-----------EADNTVDLILLDVNLPDAEAIDGLV   70 (154)
T ss_dssp             -CEEEEEECSCHHHHHHHHHHHHHHCTTEEEEEESSHHHHHHHH-----------HTTCCCSEEEECC------CHHHHH
T ss_pred             CccEEEEEcCCHHHHHHHHHHHHhCCCceEEEEecCHHHHHHHH-----------hccCCCCEEEEeCCCCCCchHHHHH
Confidence            4689999999999999999999987 88 688899999999999           55 6899999999999999999999


Q ss_pred             HHHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEE
Q 023816          105 KIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFI  184 (276)
Q Consensus       105 ~Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l  184 (276)
                      +|++..|                                             .+|||++|+........++++.|+++|+
T Consensus        71 ~l~~~~~---------------------------------------------~~~ii~ls~~~~~~~~~~~~~~g~~~~l  105 (154)
T 2qsj_A           71 RLKRFDP---------------------------------------------SNAVALISGETDHELIRAALEAGADGFI  105 (154)
T ss_dssp             HHHHHCT---------------------------------------------TSEEEEC-----CHHHHHHHHTTCCBBC
T ss_pred             HHHHhCC---------------------------------------------CCeEEEEeCCCCHHHHHHHHHccCCEEE
Confidence            9998776                                             7999999999988899999999999999


Q ss_pred             eCCCCHHHHHHHHHHHHHh
Q 023816          185 VKPVKLSDVKRIKDYLTRD  203 (276)
Q Consensus       185 ~KPv~~~~L~~~~~~l~~~  203 (276)
                      .||++.++|...+..+.+.
T Consensus       106 ~kp~~~~~L~~~l~~~~~~  124 (154)
T 2qsj_A          106 PKSADPQVLIHAVSLILEG  124 (154)
T ss_dssp             CTTSCHHHHHHHHHHHHTT
T ss_pred             eCCCCHHHHHHHHHHHHcC
Confidence            9999999998777766654

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

Probab=99.82  E-value=3.3e-19  Score=137.53  Aligned_cols=119  Identities=24%  Similarity=0.316  Sum_probs=106.6

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCC-ceeEEEEecCCCC-CCHHHHHH
Q 023816           27 TEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGL-KVDLIITDYCMPG-MTGYELLK  104 (276)
Q Consensus        27 ~~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~-~~DlIL~D~~mp~-~~G~ell~  104 (276)
                      +.+++||||||++..++.++..|+..||++..+.++.+|++.+           ... .||+||+|+.||+ ++|+++++
T Consensus         3 m~~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l-----------~~~~~~dlvi~d~~l~~~~~g~~~~~   71 (132)
T 2rdm_A            3 LEAVTILLADDEAILLLDFESTLTDAGFLVTAVSSGAKAIEML-----------KSGAAIDGVVTDIRFCQPPDGWQVAR   71 (132)
T ss_dssp             CSSCEEEEECSSHHHHHHHHHHHHHTTCEEEEESSHHHHHHHH-----------HTTCCCCEEEEESCCSSSSCHHHHHH
T ss_pred             CCCceEEEEcCcHHHHHHHHHHHHHcCCEEEEECCHHHHHHHH-----------HcCCCCCEEEEeeeCCCCCCHHHHHH
Confidence            4578999999999999999999999999999999999999998           555 7999999999997 99999999


Q ss_pred             HHHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEE
Q 023816          105 KIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFI  184 (276)
Q Consensus       105 ~Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l  184 (276)
                      +|++..+                                             .+|||++|+........++++.|  +|+
T Consensus        72 ~l~~~~~---------------------------------------------~~~ii~~s~~~~~~~~~~~~~~~--~~l  104 (132)
T 2rdm_A           72 VAREIDP---------------------------------------------NMPIVYISGHAALEWASNGVPDS--IIL  104 (132)
T ss_dssp             HHHHHCT---------------------------------------------TCCEEEEESSCCTTHHHHSCTTC--EEE
T ss_pred             HHHhcCC---------------------------------------------CCCEEEEeCCccHHHHHhhcCCc--ceE
Confidence            9998766                                             79999999999888888888776  899


Q ss_pred             eCCCCHHHHHHHHHHHHHh
Q 023816          185 VKPVKLSDVKRIKDYLTRD  203 (276)
Q Consensus       185 ~KPv~~~~L~~~~~~l~~~  203 (276)
                      .||++.++|...++.+.+.
T Consensus       105 ~kP~~~~~l~~~i~~~~~~  123 (132)
T 2rdm_A          105 EKPFTSAQLITAVSQLLNA  123 (132)
T ss_dssp             ESSCCHHHHHHHHHHHHHT
T ss_pred             eCCCCHHHHHHHHHHHHhc
Confidence            9999999997777666543

>1ny5_A Transcriptional regulator (NTRC family); AAA+ ATPase, sigma54 activator, bacterial transcription, DIM transcription; HET: ADP; 2.40A {Aquifex aeolicus} SCOP: c.23.1.1 c.37.1.20 PDB: 1ny6_A* 3m0e_A* 1zy2_A*

Probab=99.82  E-value=9.2e-20  Score=172.12  Aligned_cols=119  Identities=25%  Similarity=0.479  Sum_probs=109.8

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhh
Q 023816           30 VHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVT  109 (276)
Q Consensus        30 ~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~  109 (276)
                      ++||||||++..+..++.+|+..||+|..+.++.+|++.+           ....||+||+|+.||+++|++++++|++.
T Consensus         1 m~ILIVDDd~~~~~~l~~~L~~~g~~v~~a~~~~eal~~l-----------~~~~~DlvllD~~mp~~dG~ell~~lr~~   69 (387)
T 1ny5_A            1 MNVLVIEDDKVFRGLLEEYLSMKGIKVESAERGKEAYKLL-----------SEKHFNVVLLDLLLPDVNGLEILKWIKER   69 (387)
T ss_dssp             CEEEEECCCHHHHHHHHHHHHHHTCEEEEESSHHHHHHHH-----------HHSCCSEEEEESBCSSSBHHHHHHHHHHH
T ss_pred             CEEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHH-----------HhCCCCEEEEeCCCCCCCHHHHHHHHHhh
Confidence            4799999999999999999999999999999999999998           55679999999999999999999999987


Q ss_pred             CCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCC
Q 023816          110 TPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVK  189 (276)
Q Consensus       110 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~  189 (276)
                      .|                                             .+|||++|++...+...+|++.||+|||.||++
T Consensus        70 ~~---------------------------------------------~~pvIvlT~~~~~~~~~~a~~~Ga~dyl~KP~~  104 (387)
T 1ny5_A           70 SP---------------------------------------------ETEVIVITGHGTIKTAVEAMKMGAYDFLTKPCM  104 (387)
T ss_dssp             CT---------------------------------------------TSEEEEEEETTCHHHHHHHHTTTCCEEEEESCC
T ss_pred             CC---------------------------------------------CCcEEEEeCCCCHHHHHHHHhcCceEEecCCCC
Confidence            77                                             799999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhh
Q 023816          190 LSDVKRIKDYLTRDV  204 (276)
Q Consensus       190 ~~~L~~~~~~l~~~~  204 (276)
                      .++|...+..+.+..
T Consensus       105 ~~~L~~~i~~~l~~~  119 (387)
T 1ny5_A          105 LEEIELTINKAIEHR  119 (387)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHH
Confidence            999977776665443

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

Probab=99.81  E-value=7.7e-20  Score=144.68  Aligned_cols=114  Identities=29%  Similarity=0.374  Sum_probs=95.1

Q ss_pred             CCCCCCccEEEEEeCCHHHHHHHHHHHhhC-CCEEE-EECCHHHHHHHhcccccccccCCCCC-ceeEEEEecCCCCCCH
Q 023816           23 SPSDTEEVHVLAVDDSFVDRKVIERLLTIS-SCKVT-AVDSGRRALQFLGLDEEQSINGFDGL-KVDLIITDYCMPGMTG   99 (276)
Q Consensus        23 ~~~~~~~~~VLIVdD~~~~~~~L~~~L~~~-g~~v~-~a~~g~~al~~l~~~~~~~~~~~~~~-~~DlIL~D~~mp~~~G   99 (276)
                      ++...++.+||||||++..+..++.+|+.. |+.++ .+.++++|++.+           ... .||+||+|+.||+++|
T Consensus         7 ~~~~~~~~~vlivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~al~~l-----------~~~~~~dlvilD~~l~~~~g   75 (145)
T 3kyj_B            7 HHHHGSPYNVMIVDDAAMMRLYIASFIKTLPDFKVVAQAANGQEALDKL-----------AAQPNVDLILLDIEMPVMDG   75 (145)
T ss_dssp             ----CCSEEEEEECSCHHHHHHHHHHHTTCTTEEEEEEESSHHHHHHHH-----------HHCTTCCEEEECTTSCCCTT
T ss_pred             CCCCCCCCeEEEEcCCHHHHHHHHHHHHhCCCceEEEEECCHHHHHHHH-----------hcCCCCCEEEEeCCCCCCCH
Confidence            345566889999999999999999999988 88865 799999999998           445 7999999999999999


Q ss_pred             HHHHHHHHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEec--CCCHHHHHHHHh
Q 023816          100 YELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSS--ENILARIDRCLE  177 (276)
Q Consensus       100 ~ell~~Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~--~~~~~~~~~al~  177 (276)
                      ++++++||+..                                              +.|++++++  ........++++
T Consensus        76 ~~~~~~lr~~~----------------------------------------------~~~iiil~~~~~~~~~~~~~~~~  109 (145)
T 3kyj_B           76 MEFLRHAKLKT----------------------------------------------RAKICMLSSVAVSGSPHAARARE  109 (145)
T ss_dssp             CHHHHHHHHHC----------------------------------------------CCEEC-CBSSCSTTSSHHHHHHH
T ss_pred             HHHHHHHHhcC----------------------------------------------CCCeEEEEEeccCChHHHHHHHh
Confidence            99999999754                                              378888887  555667889999


Q ss_pred             cCCCeEEeCCCCHHHH
Q 023816          178 DGAEDFIVKPVKLSDV  193 (276)
Q Consensus       178 ~Ga~d~l~KPv~~~~L  193 (276)
                      .|+++||.||++..+|
T Consensus       110 ~ga~~~l~KP~~~~~l  125 (145)
T 3kyj_B          110 LGADGVVAKPSGTVSH  125 (145)
T ss_dssp             TTCSCCCBCCCSCC--
T ss_pred             CCCCEEEeCCCCHHHH
Confidence            9999999999996665

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

Probab=99.81  E-value=3.8e-20  Score=158.28  Aligned_cols=122  Identities=10%  Similarity=0.077  Sum_probs=105.8

Q ss_pred             CCCccEEEEEeCCHHHHHHHHHHHh-hCCCEEEE-ECCHHHHHHH-hcccccccccCCCCCceeEEEEecCCCCCCHHHH
Q 023816           26 DTEEVHVLAVDDSFVDRKVIERLLT-ISSCKVTA-VDSGRRALQF-LGLDEEQSINGFDGLKVDLIITDYCMPGMTGYEL  102 (276)
Q Consensus        26 ~~~~~~VLIVdD~~~~~~~L~~~L~-~~g~~v~~-a~~g~~al~~-l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~el  102 (276)
                      ...+++||||||++..+..++.+|+ ..|+.+.. +.++.+++.. +           ....||+||+|+.||+++|+++
T Consensus         4 ~~~~~~IlivdD~~~~~~~l~~~L~~~~~~~v~~~~~~~~~~~~~~~-----------~~~~~dlvllD~~mp~~~G~~~   72 (225)
T 3klo_A            4 DENKLNVRMLSDVCMQSRLLKEALESKLPLALEITPFSELWLEENKP-----------ESRSIQMLVIDYSRISDDVLTD   72 (225)
T ss_dssp             CCSSEEEEEESCCSHHHHHHHHHHHHHSSEEEEEECGGGHHHHTTCS-----------GGGGCCEEEEEGGGCCHHHHHH
T ss_pred             CCCceEEEEEcCcHHHHHHHHHHHhhCCCceEEEEeCCcHHHHHHHh-----------hccCCCEEEEeCCCCCCCHHHH
Confidence            3457899999999999999999998 56898865 4566666654 4           4567999999999999999999


Q ss_pred             HHHHHh-hCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCC
Q 023816          103 LKKIKV-TTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAE  181 (276)
Q Consensus       103 l~~Ir~-~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~  181 (276)
                      +++||+ ..|                                             .+|||++|+..+......+++.||+
T Consensus        73 ~~~lr~~~~~---------------------------------------------~~~ii~lt~~~~~~~~~~~~~~Ga~  107 (225)
T 3klo_A           73 YSSFKHISCP---------------------------------------------DAKEVIINCPQDIEHKLLFKWNNLA  107 (225)
T ss_dssp             HHHHHHHHCT---------------------------------------------TCEEEEEEECTTCCHHHHTTSTTEE
T ss_pred             HHHHHHhhCC---------------------------------------------CCcEEEEECCcchhHHHHHHHhCCC
Confidence            999998 677                                             7999999999998899999999999


Q ss_pred             eEEeCCCCHHHHHHHHHHHHHh
Q 023816          182 DFIVKPVKLSDVKRIKDYLTRD  203 (276)
Q Consensus       182 d~l~KPv~~~~L~~~~~~l~~~  203 (276)
                      |||.||++.++|...+..+.+.
T Consensus       108 ~~l~Kp~~~~~L~~~i~~~~~~  129 (225)
T 3klo_A          108 GVFYIDDDMDTLIKGMSKILQD  129 (225)
T ss_dssp             EEEETTCCHHHHHHHHHHHHTT
T ss_pred             EEEecCCCHHHHHHHHHHHHCC
Confidence            9999999999998777776654

>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=99.81  E-value=2.8e-19  Score=168.22  Aligned_cols=120  Identities=31%  Similarity=0.410  Sum_probs=107.6

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhh
Q 023816           30 VHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVT  109 (276)
Q Consensus        30 ~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~  109 (276)
                      .+||||||++..+..++.+|+..|+.|..+.+|.+|++.+           ....||+||+|+.||+++|++++++||+.
T Consensus         2 ~~iLivdD~~~~~~~l~~~L~~~~~~v~~a~~~~~al~~~-----------~~~~~dlvllD~~mp~~~G~~~~~~l~~~   70 (459)
T 1w25_A            2 ARILVVDDIEANVRLLEAKLTAEYYEVSTAMDGPTALAMA-----------ARDLPDIILLDVMMPGMDGFTVCRKLKDD   70 (459)
T ss_dssp             CEEEEECSSTTHHHHHHHHHHHTTCEEEEESSHHHHHHHH-----------HHHCCSEEEEESCCSSSCHHHHHHHHHHS
T ss_pred             CeEEEEeCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHH-----------hcCCCCEEEEcCCCCCCCHHHHHHHHhcC
Confidence            4799999999999999999999999999999999999998           45579999999999999999999999973


Q ss_pred             CCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCC
Q 023816          110 TPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVK  189 (276)
Q Consensus       110 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~  189 (276)
                      .                                           ....+|||++|+..+.....++++.||+|||.||++
T Consensus        71 ~-------------------------------------------~~~~~pii~lt~~~~~~~~~~a~~~Ga~~~l~KP~~  107 (459)
T 1w25_A           71 P-------------------------------------------TTRHIPVVLITALDGRGDRIQGLESGASDFLTKPID  107 (459)
T ss_dssp             T-------------------------------------------TTTTSCEEEEECSSCHHHHHHHHHHTCCEEEESSCC
T ss_pred             c-------------------------------------------ccCCCCEEEEECCCCHHHHHHHHHcCCCEEEeCCCC
Confidence            2                                           123799999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHh
Q 023816          190 LSDVKRIKDYLTRD  203 (276)
Q Consensus       190 ~~~L~~~~~~l~~~  203 (276)
                      .++|...+..+.+.
T Consensus       108 ~~~l~~~i~~~~~~  121 (459)
T 1w25_A          108 DVMLFARVRSLTRF  121 (459)
T ss_dssp             HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH
Confidence            99997766665543

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

Probab=99.81  E-value=6.6e-19  Score=138.28  Aligned_cols=119  Identities=25%  Similarity=0.374  Sum_probs=101.6

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhC-CCEEE-EECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHH
Q 023816           28 EEVHVLAVDDSFVDRKVIERLLTIS-SCKVT-AVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKK  105 (276)
Q Consensus        28 ~~~~VLIVdD~~~~~~~L~~~L~~~-g~~v~-~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~  105 (276)
                      .+++||||||++..++.++..|+.. |+.+. .+.++.+|++.+           ....||+||+|+.||+++|++++++
T Consensus         8 ~~~~iLivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~al~~l-----------~~~~~dlvi~d~~l~~~~g~~~~~~   76 (143)
T 2qv0_A            8 EKMKVIIVEDEFLAQQELSWLINTHSQMEIVGSFDDGLDVLKFL-----------QHNKVDAIFLDINIPSLDGVLLAQN   76 (143)
T ss_dssp             --CEEEEECSCHHHHHHHHHHHHHHSCCEEEEEESCHHHHHHHH-----------HHCCCSEEEECSSCSSSCHHHHHHH
T ss_pred             CceEEEEEcCCHHHHHHHHHHHHhCCCceEEEEeCCHHHHHHHH-----------HhCCCCEEEEecCCCCCCHHHHHHH
Confidence            3689999999999999999999876 88854 799999999998           4567999999999999999999999


Q ss_pred             HHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEe
Q 023816          106 IKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIV  185 (276)
Q Consensus       106 Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~  185 (276)
                      |++..+                                             ..|||++|+...  ...++++.|+++||.
T Consensus        77 l~~~~~---------------------------------------------~~~ii~~s~~~~--~~~~~~~~g~~~~l~  109 (143)
T 2qv0_A           77 ISQFAH---------------------------------------------KPFIVFITAWKE--HAVEAFELEAFDYIL  109 (143)
T ss_dssp             HTTSTT---------------------------------------------CCEEEEEESCCT--THHHHHHTTCSEEEE
T ss_pred             HHccCC---------------------------------------------CceEEEEeCCHH--HHHHHHhCCcceEEe
Confidence            997544                                             678899988743  677899999999999


Q ss_pred             CCCCHHHHHHHHHHHHHhh
Q 023816          186 KPVKLSDVKRIKDYLTRDV  204 (276)
Q Consensus       186 KPv~~~~L~~~~~~l~~~~  204 (276)
                      ||++.++|...+..+.+..
T Consensus       110 KP~~~~~l~~~i~~~~~~~  128 (143)
T 2qv0_A          110 KPYQESRIINMLQKLTTAW  128 (143)
T ss_dssp             SSCCHHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHH
Confidence            9999999977777665543

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

Probab=99.81  E-value=1.9e-19  Score=141.60  Aligned_cols=120  Identities=21%  Similarity=0.326  Sum_probs=100.2

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHh
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKV  108 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~  108 (276)
                      .++||||||++..+..++.+|+..|+.+..+.++.+|++.+           ....||+||+|+.||+++|++++++|++
T Consensus        10 ~~~iLivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~al~~l-----------~~~~~dlvllD~~lp~~~g~~~~~~l~~   78 (140)
T 3c97_A           10 PLSVLIAEDNDICRLVAAKALEKCTNDITVVTNGLQALQAY-----------QNRQFDVIIMDIQMPVMDGLEAVSEIRN   78 (140)
T ss_dssp             CCEEEEECCCHHHHHHHHHHHTTTCSEEEEESSHHHHHHHH-----------HHSCCSEEEECTTCCSSCHHHHHHHHHH
T ss_pred             CceEEEEcCCHHHHHHHHHHHHHcCCceEEECCHHHHHHHH-----------hcCCCCEEEEeCCCCCCcHHHHHHHHHh
Confidence            46999999999999999999999999999999999999998           4567999999999999999999999996


Q ss_pred             hCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCC
Q 023816          109 TTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPV  188 (276)
Q Consensus       109 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv  188 (276)
                      ...                                        ......+||+++|+.......   .++|+++||.||+
T Consensus        79 ~~~----------------------------------------~~~~~~~~ii~~s~~~~~~~~---~~~g~~~~l~KP~  115 (140)
T 3c97_A           79 YER----------------------------------------THNTKRASIIAITADTIDDDR---PGAELDEYVSKPL  115 (140)
T ss_dssp             HHH----------------------------------------HHTCCCCCCEEEESSCCSCCC---CCSSCSEEEESSC
T ss_pred             hhh----------------------------------------hcCCCceEEEEEeCccchhHH---HhCChhheEeCCC
Confidence            310                                        001126899999987654433   2789999999999


Q ss_pred             CHHHHHHHHHHHHH
Q 023816          189 KLSDVKRIKDYLTR  202 (276)
Q Consensus       189 ~~~~L~~~~~~l~~  202 (276)
                      +.++|...+..+..
T Consensus       116 ~~~~L~~~i~~~~~  129 (140)
T 3c97_A          116 NPNQLRDVVLTCHS  129 (140)
T ss_dssp             CHHHHHHHHHHHHC
T ss_pred             CHHHHHHHHHHHhC
Confidence            99999777766553

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

Probab=99.80  E-value=2.1e-19  Score=162.84  Aligned_cols=119  Identities=24%  Similarity=0.386  Sum_probs=104.5

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHh-hCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHH
Q 023816           28 EEVHVLAVDDSFVDRKVIERLLT-ISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKI  106 (276)
Q Consensus        28 ~~~~VLIVdD~~~~~~~L~~~L~-~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~I  106 (276)
                      ...+||||||++..++.++.+|. ..|++|..+.+|.+|++.+           ....||+||+|+.||++||++++++|
T Consensus        17 ~~~~ilivdD~~~~~~~l~~~l~~~~~~~v~~~~~~~~al~~~-----------~~~~~dlvl~D~~mp~~~G~~~~~~l   85 (358)
T 3bre_A           17 GAVMVLLVDDQAMIGEAVRRSLASEAGIDFHFCSDPQQAVAVA-----------NQIKPTVILQDLVMPGVDGLTLLAAY   85 (358)
T ss_dssp             -CEEEEEECSCTTHHHHHHTTSSSCTTEEEEEECCHHHHHHHH-----------HHHCCSEEEEESBCSSSBHHHHHHHH
T ss_pred             cCceEEEEECCHHHHHHHHHHHHhccCcEEEEeCCHHHHHHHH-----------HhCCCCEEEEeCCCCCCCHHHHHHHH
Confidence            35689999999999999999996 4689999999999999998           45579999999999999999999999


Q ss_pred             HhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeC
Q 023816          107 KVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVK  186 (276)
Q Consensus       107 r~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~K  186 (276)
                      |+..                                           ....+|||++|+..+.....+|++.|++|||.|
T Consensus        86 ~~~~-------------------------------------------~~~~~~ii~~s~~~~~~~~~~a~~~Ga~~~l~K  122 (358)
T 3bre_A           86 RGNP-------------------------------------------ATRDIPIIVLSTKEEPTVKSAAFAAGANDYLVK  122 (358)
T ss_dssp             TTST-------------------------------------------TTTTSCEEEEESSCCHHHHHHHHHTTCSEEEES
T ss_pred             hcCc-------------------------------------------ccCCCcEEEEeCCCCHHHHHHHHhcChheEeec
Confidence            9631                                           123799999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHH
Q 023816          187 PVKLSDVKRIKDYL  200 (276)
Q Consensus       187 Pv~~~~L~~~~~~l  200 (276)
                      |++.++|...+..+
T Consensus       123 p~~~~~l~~~v~~~  136 (358)
T 3bre_A          123 LPDAIELVARIRYH  136 (358)
T ss_dssp             CCCHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHH
Confidence            99999986655544

>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=99.80  E-value=3.4e-19  Score=151.45  Aligned_cols=118  Identities=25%  Similarity=0.384  Sum_probs=107.7

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHh
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKV  108 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~  108 (276)
                      +++||||||++..+..+..+|+..|++|..+.++.+|++.+           ....||+||+|+.||+++|++++++|++
T Consensus         4 ~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~-----------~~~~~dlvllD~~l~~~~g~~~~~~l~~   72 (230)
T 2oqr_A            4 ATSVLIVEDEESLADPLAFLLRKEGFEATVVTDGPAALAEF-----------DRAGADIVLLDLMLPGMSGTDVCKQLRA   72 (230)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEECSHHHHHHHH-----------HHHCCSEEEEESSCSSSCHHHHHHHHHH
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHH-----------hccCCCEEEEECCCCCCCHHHHHHHHHc
Confidence            37999999999999999999999999999999999999998           4557999999999999999999999997


Q ss_pred             hCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCC
Q 023816          109 TTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPV  188 (276)
Q Consensus       109 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv  188 (276)
                      . |                                             .+|||++|+........++++.||++|+.||+
T Consensus        73 ~-~---------------------------------------------~~~ii~lt~~~~~~~~~~~~~~ga~~~l~Kp~  106 (230)
T 2oqr_A           73 R-S---------------------------------------------SVPVIMVTARDSEIDKVVGLELGADDYVTKPY  106 (230)
T ss_dssp             H-C---------------------------------------------SCSEEEEECCHHHHHHHHHHHHCCSCCCCSSC
T ss_pred             C-C---------------------------------------------CCCEEEEeCCCcHHHHHHHHHcCCCEEEeCCC
Confidence            4 5                                             79999999998888899999999999999999


Q ss_pred             CHHHHHHHHHHHHHh
Q 023816          189 KLSDVKRIKDYLTRD  203 (276)
Q Consensus       189 ~~~~L~~~~~~l~~~  203 (276)
                      +.++|...+..+.+.
T Consensus       107 ~~~~l~~~i~~~~~~  121 (230)
T 2oqr_A          107 SARELIARIRAVLRR  121 (230)
T ss_dssp             CHHHHHHHHHHHHTT
T ss_pred             CHHHHHHHHHHHHhh
Confidence            999997777766543

>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=99.79  E-value=6.8e-21  Score=144.77  Aligned_cols=119  Identities=30%  Similarity=0.457  Sum_probs=107.7

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHH
Q 023816           28 EEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIK  107 (276)
Q Consensus        28 ~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir  107 (276)
                      ...+||||||++..+..++..|+..|+.+..+.++.++++.+           ....||+||+|+.||+++|++++++|+
T Consensus         2 ~~~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~-----------~~~~~dlvi~d~~~~~~~g~~~~~~l~   70 (124)
T 1dc7_A            2 QRGIVWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLAAL-----------ASKTPDVLLSDIRMPGMDGLALLKQIK   70 (124)
T ss_dssp             CCCCCEEECSSSSHHHHHHHHHTTTTCCCEECCCTTHHHHHS-----------SSCCCSCEEECSCSSHHHHCSTHHHHH
T ss_pred             CccEEEEEeCCHHHHHHHHHHHHhCCcEEEEeCCHHHHHHHH-----------hcCCCCEEEEeeecCCCCHHHHHHHHH
Confidence            456899999999999999999999999999999999999998           566899999999999999999999999


Q ss_pred             hhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCC
Q 023816          108 VTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKP  187 (276)
Q Consensus       108 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KP  187 (276)
                      +..|                                             .+|+|++|+........++++.|+++|+.||
T Consensus        71 ~~~~---------------------------------------------~~~ii~~s~~~~~~~~~~~~~~g~~~~l~kp  105 (124)
T 1dc7_A           71 QRHP---------------------------------------------MLPVIIMTAHSDLDAAVSAYQQGAFDYLPKP  105 (124)
T ss_dssp             HHCT---------------------------------------------TSCCCCBCCSTTSTTTTSSCTTCCCCCBCSS
T ss_pred             hhCC---------------------------------------------CCCEEEEecCCCHHHHHHHHhcCcceEeeCC
Confidence            8766                                             7899999999888888899999999999999


Q ss_pred             CCHHHHHHHHHHHHH
Q 023816          188 VKLSDVKRIKDYLTR  202 (276)
Q Consensus       188 v~~~~L~~~~~~l~~  202 (276)
                      ++.++|...+..+.+
T Consensus       106 ~~~~~l~~~i~~~~~  120 (124)
T 1dc7_A          106 FDIDEAVALVERAIS  120 (124)
T ss_dssp             CCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHH
Confidence            999999776665543

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

Probab=99.79  E-value=4.6e-19  Score=166.31  Aligned_cols=120  Identities=21%  Similarity=0.315  Sum_probs=105.0

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhh-CCCEEEEECCHHHHHHHhcccccccccCCCC-CceeEEEEecCCCCCCHHHHHHH
Q 023816           28 EEVHVLAVDDSFVDRKVIERLLTI-SSCKVTAVDSGRRALQFLGLDEEQSINGFDG-LKVDLIITDYCMPGMTGYELLKK  105 (276)
Q Consensus        28 ~~~~VLIVdD~~~~~~~L~~~L~~-~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~-~~~DlIL~D~~mp~~~G~ell~~  105 (276)
                      .+++||||||++..++.++.+|+. .|+.|..+.||++|++.+           +. ..||+||+|+.||+|||++++++
T Consensus         2 ~~~~ILivDD~~~~~~~l~~~L~~~~~~~v~~a~~g~eal~~l-----------~~~~~~DlvllDi~mP~~dG~ell~~   70 (400)
T 3sy8_A            2 NDLNVLVLEDEPFQRLVAVTALKKVVPGSILEAADGKEAVAIL-----------ESCGHVDIAICDLQMSGMDGLAFLRH   70 (400)
T ss_dssp             CCEEEEEECSSHHHHHHHHHHHHHHCSEEEEEESSHHHHHHHH-----------HHHSCEEEEEECSSCSSSCHHHHHHH
T ss_pred             CCceEEEEcCCHHHHHHHHHHHHhcCCcEEEEecCHHHHHHHH-----------hhCCCCCEEEEeCCCCCCCHHHHHHH
Confidence            458999999999999999999997 678999999999999998           44 47999999999999999999999


Q ss_pred             HHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCH-----HHHHHHHhcCC
Q 023816          106 IKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENIL-----ARIDRCLEDGA  180 (276)
Q Consensus       106 Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~-----~~~~~al~~Ga  180 (276)
                      ||+..+                                             .++||++|+....     ....+|++.||
T Consensus        71 l~~~~~---------------------------------------------~~~ii~~s~~~~~~~~~~~~~~~a~~~ga  105 (400)
T 3sy8_A           71 ASLSGK---------------------------------------------VHSVILSSEVDPILRQATISMIECLGLNF  105 (400)
T ss_dssp             HHHHTC---------------------------------------------EEEEEESCCCCGGGHHHHHHHHHTTTCEE
T ss_pred             HHhcCC---------------------------------------------CceEEEEcCchHHHHHHHHHHHHHcCCee
Confidence            998766                                             5677777777665     56778999999


Q ss_pred             CeEEeCCCCHHHHHHHHHHHHHh
Q 023816          181 EDFIVKPVKLSDVKRIKDYLTRD  203 (276)
Q Consensus       181 ~d~l~KPv~~~~L~~~~~~l~~~  203 (276)
                      ++||.||++.++|...+..+.+.
T Consensus       106 ~~yl~KP~~~~~L~~~i~~~~~~  128 (400)
T 3sy8_A          106 LGDLGKPFSLERITALLTRYNAR  128 (400)
T ss_dssp             EEECCSSCCHHHHHHHHHHHHHH
T ss_pred             ccCcCCCcCHHHHHHHHHHHHHh
Confidence            99999999999998777766554

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

Probab=99.79  E-value=2.7e-18  Score=145.28  Aligned_cols=116  Identities=22%  Similarity=0.270  Sum_probs=106.0

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHh
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKV  108 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~  108 (276)
                      +++||||||++..+..++.+|+..| .+..+.++.+|++.+             ..||+||+|+.||+++|++++++|++
T Consensus         2 m~~ilivdd~~~~~~~l~~~L~~~~-~v~~~~~~~~al~~~-------------~~~dlvllD~~lp~~~g~~~~~~lr~   67 (220)
T 1p2f_A            2 MWKIAVVDDDKNILKKVSEKLQQLG-RVKTFLTGEDFLNDE-------------EAFHVVVLDVMLPDYSGYEICRMIKE   67 (220)
T ss_dssp             CEEEEEECSCHHHHHHHHHHHTTTE-EEEEESSHHHHHHCC-------------SCCSEEEEESBCSSSBHHHHHHHHHH
T ss_pred             CceEEEEeCCHHHHHHHHHHHHhCC-CEEEECCHHHHHHhc-------------CCCCEEEEeCCCCCCCHHHHHHHHHh
Confidence            4689999999999999999999989 899999999999854             36999999999999999999999998


Q ss_pred             hCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCC
Q 023816          109 TTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPV  188 (276)
Q Consensus       109 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv  188 (276)
                      ..|                                             .+|||++|+..+.....++++.|+++||.||+
T Consensus        68 ~~~---------------------------------------------~~~ii~lt~~~~~~~~~~~~~~ga~~~l~Kp~  102 (220)
T 1p2f_A           68 TRP---------------------------------------------ETWVILLTLLSDDESVLKGFEAGADDYVTKPF  102 (220)
T ss_dssp             HCT---------------------------------------------TSEEEEEESCCSHHHHHHHHHHTCSEEEESSC
T ss_pred             cCC---------------------------------------------CCcEEEEEcCCCHHHHHHHHHcCCCEEEECCC
Confidence            766                                             79999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHh
Q 023816          189 KLSDVKRIKDYLTRD  203 (276)
Q Consensus       189 ~~~~L~~~~~~l~~~  203 (276)
                      +.++|...+..+.+.
T Consensus       103 ~~~~L~~~i~~~~~~  117 (220)
T 1p2f_A          103 NPEILLARVKRFLER  117 (220)
T ss_dssp             CHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHcc
Confidence            999997777766554

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

Probab=99.79  E-value=1.1e-19  Score=155.98  Aligned_cols=119  Identities=23%  Similarity=0.294  Sum_probs=107.9

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhCC-CEEE-EECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHH
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTISS-CKVT-AVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKI  106 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~g-~~v~-~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~I  106 (276)
                      +++||||||++..++.++.+|+..| +.++ .+.++.+|++.+           ....||+||+|+.||+++|++++++|
T Consensus         1 m~~ILivdd~~~~~~~l~~~L~~~~~~~vv~~~~~~~~al~~l-----------~~~~~dlvllD~~lp~~~g~~~~~~l   69 (225)
T 3c3w_A            1 MVKVFLVDDHEVVRRGLVDLLGADPELDVVGEAGSVAEAMARV-----------PAARPDVAVLDVRLPDGNGIELCRDL   69 (225)
T ss_dssp             CEEEEEECSCHHHHHHHHHHHHTCTTEEEEEEESSHHHHHHHH-----------HHHCCSEEEECSEETTEEHHHHHHHH
T ss_pred             CcEEEEEcCCHHHHHHHHHHHhcCCCcEEEEEECCHHHHHHHH-----------hhcCCCEEEEeCCCCCCCHHHHHHHH
Confidence            3789999999999999999999887 8855 699999999998           45579999999999999999999999


Q ss_pred             HhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeC
Q 023816          107 KVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVK  186 (276)
Q Consensus       107 r~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~K  186 (276)
                      |+..|                                             .+|||++|+..+.+...++++.|+++||.|
T Consensus        70 r~~~~---------------------------------------------~~~ii~lt~~~~~~~~~~~~~~Ga~~~l~K  104 (225)
T 3c3w_A           70 LSRMP---------------------------------------------DLRCLILTSYTSDEAMLDAILAGASGYVVK  104 (225)
T ss_dssp             HHHCT---------------------------------------------TCEEEEGGGSSSHHHHHHHHHHTCCCHHHH
T ss_pred             HHhCC---------------------------------------------CCcEEEEECCCCHHHHHHHHHCCCCEEEEC
Confidence            98777                                             799999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHh
Q 023816          187 PVKLSDVKRIKDYLTRD  203 (276)
Q Consensus       187 Pv~~~~L~~~~~~l~~~  203 (276)
                      |++.++|...+..+.+.
T Consensus       105 p~~~~~L~~~i~~~~~~  121 (225)
T 3c3w_A          105 DIKGMELARAVKDVGAG  121 (225)
T ss_dssp             HHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHcC
Confidence            99999997777766554

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

Probab=99.78  E-value=1e-18  Score=130.24  Aligned_cols=113  Identities=21%  Similarity=0.232  Sum_probs=100.1

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhh
Q 023816           30 VHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVT  109 (276)
Q Consensus        30 ~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~  109 (276)
                      .+||||||++..++.+...|+..|+++..+.++.++++.+           ....||+||+|+.||+++|+++++.|++.
T Consensus         2 ~~iliv~~~~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~l-----------~~~~~dlii~d~~~~~~~~~~~~~~l~~~   70 (119)
T 2j48_A            2 GHILLLEEEDEAATVVCEMLTAAGFKVIWLVDGSTALDQL-----------DLLQPIVILMAWPPPDQSCLLLLQHLREH   70 (119)
T ss_dssp             CEEEEECCCHHHHHHHHHHHHHTTCEEEEESCHHHHHHHH-----------HHHCCSEEEEECSTTCCTHHHHHHHHHHT
T ss_pred             CEEEEEeCCHHHHHHHHHHHHhCCcEEEEecCHHHHHHHH-----------HhcCCCEEEEecCCCCCCHHHHHHHHHhc
Confidence            5899999999999999999999999999999999999998           45579999999999999999999999975


Q ss_pred             CCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCC
Q 023816          110 TPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVK  189 (276)
Q Consensus       110 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~  189 (276)
                      ..                                           ...+|||++|+.....   ++++.|+++|+.||++
T Consensus        71 ~~-------------------------------------------~~~~~ii~~~~~~~~~---~~~~~g~~~~l~kp~~  104 (119)
T 2j48_A           71 QA-------------------------------------------DPHPPLVLFLGEPPVD---PLLTAQASAILSKPLD  104 (119)
T ss_dssp             CC-------------------------------------------CSSCCCEEEESSCCSS---HHHHHHCSEECSSCST
T ss_pred             cc-------------------------------------------cCCCCEEEEeCCCCch---hhhhcCHHHhccCCCC
Confidence            41                                           1278999999987765   8999999999999999


Q ss_pred             HHHHHHHHHH
Q 023816          190 LSDVKRIKDY  199 (276)
Q Consensus       190 ~~~L~~~~~~  199 (276)
                      .++|...+..
T Consensus       105 ~~~l~~~l~~  114 (119)
T 2j48_A          105 PQLLLTTLQG  114 (119)
T ss_dssp             THHHHHHHHT
T ss_pred             HHHHHHHHHH
Confidence            9998665543

>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=99.78  E-value=8.9e-19  Score=137.12  Aligned_cols=116  Identities=22%  Similarity=0.284  Sum_probs=99.3

Q ss_pred             CCCCccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCC-CceeEEEEecCCCCCCHHHHH
Q 023816           25 SDTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDG-LKVDLIITDYCMPGMTGYELL  103 (276)
Q Consensus        25 ~~~~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~-~~~DlIL~D~~mp~~~G~ell  103 (276)
                      ...++.+||||||++..++.++..|+..||++..+.++.+|++.+           .. ..||+||+|+.||+++|++++
T Consensus        11 ~~~~~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l-----------~~~~~~dlvilD~~l~~~~g~~~~   79 (138)
T 2b4a_A           11 HHMQPFRVTLVEDEPSHATLIQYHLNQLGAEVTVHPSGSAFFQHR-----------SQLSTCDLLIVSDQLVDLSIFSLL   79 (138)
T ss_dssp             ---CCCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHTG-----------GGGGSCSEEEEETTCTTSCHHHHH
T ss_pred             CCCCCCeEEEECCCHHHHHHHHHHHHHcCCEEEEeCCHHHHHHHH-----------HhCCCCCEEEEeCCCCCCCHHHHH
Confidence            456688999999999999999999999999999999999999988           55 679999999999999999999


Q ss_pred             HHHHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEe-cCCCHHHHHHHHhcCCCe
Q 023816          104 KKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMS-SENILARIDRCLEDGAED  182 (276)
Q Consensus       104 ~~Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls-~~~~~~~~~~al~~Ga~d  182 (276)
                      ++|++..+                                             .+|||++| +...... .+++   +++
T Consensus        80 ~~l~~~~~---------------------------------------------~~~ii~ls~~~~~~~~-~~~~---~~~  110 (138)
T 2b4a_A           80 DIVKEQTK---------------------------------------------QPSVLILTTGRHELIE-SSEH---NLS  110 (138)
T ss_dssp             HHHTTSSS---------------------------------------------CCEEEEEESCC--CCC-CSSS---CEE
T ss_pred             HHHHhhCC---------------------------------------------CCCEEEEECCCCCHHH-HHHH---HHh
Confidence            99997555                                             79999999 8776665 5666   999


Q ss_pred             EEeCCCCHHHHHHHHHHH
Q 023816          183 FIVKPVKLSDVKRIKDYL  200 (276)
Q Consensus       183 ~l~KPv~~~~L~~~~~~l  200 (276)
                      |+.||++.++|...+..+
T Consensus       111 ~l~KP~~~~~L~~~i~~~  128 (138)
T 2b4a_A          111 YLQKPFAISELRAAIDYH  128 (138)
T ss_dssp             EEESSCCHHHHHHHHHHT
T ss_pred             eeeCCCCHHHHHHHHHHH
Confidence            999999999997666544

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

Probab=99.78  E-value=1.3e-18  Score=149.89  Aligned_cols=117  Identities=24%  Similarity=0.440  Sum_probs=105.9

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHh
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKV  108 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~  108 (276)
                      +++||||||++..+..++.+|+..||+|..+.++.+|++.+           ....||+||+|+.||+++|++++++|++
T Consensus         5 ~~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l-----------~~~~~dlvilD~~l~~~~g~~~~~~lr~   73 (238)
T 2gwr_A            5 RQRILVVDDDASLAEMLTIVLRGEGFDTAVIGDGTQALTAV-----------RELRPDLVLLDLMLPGMNGIDVCRVLRA   73 (238)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEECCGGGHHHHH-----------HHHCCSEEEEESSCSSSCHHHHHHHHHT
T ss_pred             cCeEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHH-----------HhCCCCEEEEeCCCCCCCHHHHHHHHHh
Confidence            36999999999999999999999999999999999999988           4557999999999999999999999995


Q ss_pred             hCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCC
Q 023816          109 TTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPV  188 (276)
Q Consensus       109 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv  188 (276)
                      . +                                             .+|||++|+........++++.||++||.||+
T Consensus        74 ~-~---------------------------------------------~~~ii~lt~~~~~~~~~~~~~~Ga~~~l~Kp~  107 (238)
T 2gwr_A           74 D-S---------------------------------------------GVPIVMLTAKTDTVDVVLGLESGADDYIMKPF  107 (238)
T ss_dssp             T-C---------------------------------------------CCCEEEEEETTCCSCHHHHHHTTCCEEEEESC
T ss_pred             C-C---------------------------------------------CCcEEEEeCCCCHHHHHHHHHCCCCEEEeCCC
Confidence            2 2                                             68999999999988899999999999999999


Q ss_pred             CHHHHHHHHHHHHH
Q 023816          189 KLSDVKRIKDYLTR  202 (276)
Q Consensus       189 ~~~~L~~~~~~l~~  202 (276)
                      +.++|...+..+.+
T Consensus       108 ~~~~L~~~i~~~~~  121 (238)
T 2gwr_A          108 KPKELVARVRARLR  121 (238)
T ss_dssp             CHHHHHHHHHHHCC
T ss_pred             CHHHHHHHHHHHHh
Confidence            99999777665543

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

Probab=99.78  E-value=3.4e-18  Score=139.48  Aligned_cols=109  Identities=33%  Similarity=0.396  Sum_probs=93.9

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhCC-CE-EEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHH
Q 023816           28 EEVHVLAVDDSFVDRKVIERLLTISS-CK-VTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKK  105 (276)
Q Consensus        28 ~~~~VLIVdD~~~~~~~L~~~L~~~g-~~-v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~  105 (276)
                      .+++||||||++..+..++.+|+..| +. +..+.++.+|++.+           ....||+||+|+.||+++|++++++
T Consensus        24 ~~~~ILivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~al~~l-----------~~~~~dlvilD~~l~~~~g~~l~~~   92 (164)
T 3t8y_A           24 RVIRVLVVDDSAFMRMVLKDIIDSQPDMKVVGFAKDGLEAVEKA-----------IELKPDVITMDIEMPNLNGIEALKL   92 (164)
T ss_dssp             CCEEEEEECSCHHHHHHHHHHHHTSTTEEEEEEESSHHHHHHHH-----------HHHCCSEEEECSSCSSSCHHHHHHH
T ss_pred             CccEEEEEcCCHHHHHHHHHHHhcCCCeEEEEecCCHHHHHHHh-----------ccCCCCEEEEeCCCCCCCHHHHHHH
Confidence            46899999999999999999999875 44 44799999999998           4567999999999999999999999


Q ss_pred             HHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHH--HHHHHHhcCCCeE
Q 023816          106 IKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILA--RIDRCLEDGAEDF  183 (276)
Q Consensus       106 Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~--~~~~al~~Ga~d~  183 (276)
                      ||+..+                                              +|||++|+.....  ...++++.|+++|
T Consensus        93 lr~~~~----------------------------------------------~~ii~~s~~~~~~~~~~~~~~~~ga~~~  126 (164)
T 3t8y_A           93 IMKKAP----------------------------------------------TRVIMVSSLTEEGAAITIEALRNGAVDF  126 (164)
T ss_dssp             HHHHSC----------------------------------------------CEEEEEESSCCTTCHHHHHHHHTTCCEE
T ss_pred             HHhcCC----------------------------------------------ceEEEEecCCccchHHHHHHHHcCcCEE
Confidence            997543                                              7999999877644  6779999999999


Q ss_pred             EeCCCCHHHH
Q 023816          184 IVKPVKLSDV  193 (276)
Q Consensus       184 l~KPv~~~~L  193 (276)
                      |.||++.++|
T Consensus       127 l~KP~~~~~l  136 (164)
T 3t8y_A          127 ITKPHGSISL  136 (164)
T ss_dssp             EECSSSSSCG
T ss_pred             EeCCCCHHHH
Confidence            9999994443

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

Probab=99.77  E-value=8.9e-18  Score=131.24  Aligned_cols=118  Identities=19%  Similarity=0.236  Sum_probs=104.3

Q ss_pred             CCCCCccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHH
Q 023816           24 PSDTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELL  103 (276)
Q Consensus        24 ~~~~~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell  103 (276)
                      +......+||||||++..+..++.+|+..||++..+.++.+|++.+           ....||+||    ||+++|++++
T Consensus        13 ~~~~~~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l-----------~~~~~dlvi----~~~~~g~~~~   77 (137)
T 2pln_A           13 LVPRGSMRVLLIEKNSVLGGEIEKGLNVKGFMADVTESLEDGEYLM-----------DIRNYDLVM----VSDKNALSFV   77 (137)
T ss_dssp             --CTTCSEEEEECSCHHHHHHHHHHHHHTTCEEEEESCHHHHHHHH-----------HHSCCSEEE----ECSTTHHHHH
T ss_pred             ccCCCCCeEEEEeCCHHHHHHHHHHHHHcCcEEEEeCCHHHHHHHH-----------HcCCCCEEE----EcCccHHHHH
Confidence            3455678999999999999999999999999999999999999998           556799999    8999999999


Q ss_pred             HHHHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeE
Q 023816          104 KKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDF  183 (276)
Q Consensus       104 ~~Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~  183 (276)
                      ++|++. +                                            ..+|||++|+........++++.|+++|
T Consensus        78 ~~l~~~-~--------------------------------------------~~~~ii~ls~~~~~~~~~~~~~~g~~~~  112 (137)
T 2pln_A           78 SRIKEK-H--------------------------------------------SSIVVLVSSDNPTSEEEVHAFEQGADDY  112 (137)
T ss_dssp             HHHHHH-S--------------------------------------------TTSEEEEEESSCCHHHHHHHHHTTCSEE
T ss_pred             HHHHhc-C--------------------------------------------CCccEEEEeCCCCHHHHHHHHHcCCcee
Confidence            999963 2                                            1589999999999999999999999999


Q ss_pred             EeCCC-CHHHHHHHHHHHH
Q 023816          184 IVKPV-KLSDVKRIKDYLT  201 (276)
Q Consensus       184 l~KPv-~~~~L~~~~~~l~  201 (276)
                      +.||+ +.++|...+..+.
T Consensus       113 l~kP~~~~~~l~~~i~~~~  131 (137)
T 2pln_A          113 IAKPYRSIKALVARIEARL  131 (137)
T ss_dssp             EESSCSCHHHHHHHHHHHT
T ss_pred             eeCCCCCHHHHHHHHHHHH
Confidence            99999 9999977666554

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

Probab=99.75  E-value=2.8e-18  Score=143.10  Aligned_cols=113  Identities=16%  Similarity=0.157  Sum_probs=98.4

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHH
Q 023816           27 TEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKI  106 (276)
Q Consensus        27 ~~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~I  106 (276)
                      ..+++||||||++..+..+...|+..||.+..+.++.+|+               ...||+||+|+.||+++|. +++.+
T Consensus        10 ~~~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al---------------~~~~dlvl~D~~mp~~~g~-l~~~~   73 (196)
T 1qo0_D           10 LRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAF---------------DVPVDVVFTSIFQNRHHDE-IAALL   73 (196)
T ss_dssp             GGGCEEEEESCTTHHHHHHHHHHHHHTCEEEEECSCCSSC---------------SSCCSEEEEECCSSTHHHH-HHHHH
T ss_pred             hcCCeEEEEcCChhHHHHHHHHHHHcCCeEEEecCchhhC---------------CCCCCEEEEeCCCCccchH-HHHHH
Confidence            3467999999999999999999999999999888776543               2369999999999999998 88888


Q ss_pred             HhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeC
Q 023816          107 KVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVK  186 (276)
Q Consensus       107 r~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~K  186 (276)
                      +...+                                             .+|||++|++.+.+...++++.|+++||.|
T Consensus        74 ~~~~~---------------------------------------------~~~ii~lt~~~~~~~~~~a~~~ga~~~l~K  108 (196)
T 1qo0_D           74 AAGTP---------------------------------------------RTTLVALVEYESPAVLSQIIELECHGVITQ  108 (196)
T ss_dssp             HHSCT---------------------------------------------TCEEEEEECCCSHHHHHHHHHHTCSEEEES
T ss_pred             hccCC---------------------------------------------CCCEEEEEcCCChHHHHHHHHcCCCeeEec
Confidence            86434                                             799999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHH
Q 023816          187 PVKLSDVKRIKDYL  200 (276)
Q Consensus       187 Pv~~~~L~~~~~~l  200 (276)
                      |++.++|...+..+
T Consensus       109 P~~~~~L~~~l~~~  122 (196)
T 1qo0_D          109 PLDAHRVLPVLVSA  122 (196)
T ss_dssp             SCCGGGHHHHHHHH
T ss_pred             CcCHHHHHHHHHHH
Confidence            99999986655543

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

Probab=99.75  E-value=2.8e-17  Score=139.30  Aligned_cols=114  Identities=20%  Similarity=0.259  Sum_probs=103.9

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhh
Q 023816           30 VHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVT  109 (276)
Q Consensus        30 ~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~  109 (276)
                      ++||||||++..+..+..+|+..||.|..+.++.+|++.+           ....||+||    ||+++|++++++|++.
T Consensus         1 m~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l-----------~~~~~dlvi----lp~~~g~~~~~~lr~~   65 (223)
T 2hqr_A            1 MRVLLIEKNSVLGGEIEKGLNVKGFMADVTESLEDGEYLM-----------DIRNYDLVM----VSDKNALSFVSRIKEK   65 (223)
T ss_dssp             CCEEEECSCHHHHHHHHHHHGGGTCCEEEESSHHHHHHHH-----------TTSCCSEEE----ECCTTHHHHHHHHHHH
T ss_pred             CEEEEEcCCHHHHHHHHHHHHHCCcEEEEECCHHHHHHHH-----------hcCCCCEEE----eCCCCHHHHHHHHHhC
Confidence            4799999999999999999999999999999999999999           667899999    9999999999999975


Q ss_pred             CCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCC-
Q 023816          110 TPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPV-  188 (276)
Q Consensus       110 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv-  188 (276)
                       +                                            ..+|||++|+..+.....++++.||++||.||+ 
T Consensus        66 -~--------------------------------------------~~~~ii~lt~~~~~~~~~~~~~~Ga~~~l~Kp~~  100 (223)
T 2hqr_A           66 -H--------------------------------------------SSIVVLVSSDNPTSEEEVHAFEQGADDYIAKPYR  100 (223)
T ss_dssp             -C--------------------------------------------TTSEEEEEESSCCHHHHHHHHHHTCSEEEETTCS
T ss_pred             -C--------------------------------------------CCCcEEEEECCCCHHHHHHHHHcCCCEEEECCCC
Confidence             2                                            168999999999999999999999999999999 


Q ss_pred             CHHHHHHHHHHHHHh
Q 023816          189 KLSDVKRIKDYLTRD  203 (276)
Q Consensus       189 ~~~~L~~~~~~l~~~  203 (276)
                      +.++|...+..+.+.
T Consensus       101 ~~~~L~~~i~~~~~~  115 (223)
T 2hqr_A          101 SIKALVARIEARLRF  115 (223)
T ss_dssp             CTHHHHHHHHHHTSS
T ss_pred             CHHHHHHHHHHHhcc
Confidence            999997777666543

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

Probab=99.72  E-value=6.3e-17  Score=151.54  Aligned_cols=105  Identities=30%  Similarity=0.428  Sum_probs=93.9

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhC-CCE-EEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHH
Q 023816           28 EEVHVLAVDDSFVDRKVIERLLTIS-SCK-VTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKK  105 (276)
Q Consensus        28 ~~~~VLIVdD~~~~~~~L~~~L~~~-g~~-v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~  105 (276)
                      .+++||||||++..++.++.+|+.. |++ +..+.++.+|++.+           ....||+||+|+.||++||++++++
T Consensus         2 ~~~rVLIVDD~~~~r~~L~~~L~~~~g~~vv~~a~~~~eAl~~l-----------~~~~pDlVllDi~mp~~dGlell~~   70 (349)
T 1a2o_A            2 SKIRVLSVDDSALMRQIMTEIINSHSDMEMVATAPDPLVARDLI-----------KKFNPDVLTLDVEMPRMDGLDFLEK   70 (349)
T ss_dssp             CCEEEEEECSCHHHHHHHHHHHHTSTTEEEEEEESSHHHHHHHH-----------HHHCCSEEEEECCCSSSCHHHHHHH
T ss_pred             CCCEEEEEECCHHHHHHHHHHHhcCCCcEEEEEeCCHHHHHHHH-----------hccCCCEEEEECCCCCCCHHHHHHH
Confidence            4689999999999999999999986 898 55899999999998           4567999999999999999999999


Q ss_pred             HHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCH--HHHHHHHhcCCCeE
Q 023816          106 IKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENIL--ARIDRCLEDGAEDF  183 (276)
Q Consensus       106 Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~--~~~~~al~~Ga~d~  183 (276)
                      |++..                                              ++|||++|+....  +...++++.|++||
T Consensus        71 l~~~~----------------------------------------------p~pVIvlS~~~~~~~~~~~~al~~Ga~d~  104 (349)
T 1a2o_A           71 LMRLR----------------------------------------------PMPVVMVSSLTGKGSEVTLRALELGAIDF  104 (349)
T ss_dssp             HHHSS----------------------------------------------CCCEEEEECCTHHHHHHHHHHHHHTCCEE
T ss_pred             HHhcC----------------------------------------------CCcEEEEECCCcccHHHHHHHHhCCceEE
Confidence            99743                                              3899999998775  34789999999999


Q ss_pred             EeCCCC
Q 023816          184 IVKPVK  189 (276)
Q Consensus       184 l~KPv~  189 (276)
                      |.||++
T Consensus       105 l~KP~~  110 (349)
T 1a2o_A          105 VTKPQL  110 (349)
T ss_dssp             EECSSS
T ss_pred             EECCCC
Confidence            999998

>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=99.71  E-value=3e-17  Score=145.54  Aligned_cols=104  Identities=21%  Similarity=0.348  Sum_probs=87.8

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhh-CCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHH
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTI-SSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIK  107 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~-~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir  107 (276)
                      ..+||||||++..++.+...|.. .|+.+.+++ +.+++..+           ....||+||+|+.||++||++++++||
T Consensus         4 ~~~ILiVdD~~~~~~~l~~~L~~~~~~~v~~~~-~~~~~~~~-----------~~~~~dlvllD~~mP~~~G~~~~~~lr   71 (259)
T 3luf_A            4 KQKILIVEDSMTIRRMLIQAIAQQTGLEIDAFD-TLEGARHC-----------QGDEYVVALVDLTLPDAPSGEAVKVLL   71 (259)
T ss_dssp             CCEEEEECCCHHHHHHHHHHHHHHHCCEEEEES-STGGGTTC-----------CTTTEEEEEEESCBTTBTTSHHHHHHH
T ss_pred             CCeEEEEECCHHHHHHHHHHHHhcCCeEEEEeC-hHHHHHHh-----------hcCCCcEEEEeCCCCCCCHHHHHHHHH
Confidence            35899999999999999999975 478886554 44555544           456899999999999999999999999


Q ss_pred             hhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCC
Q 023816          108 VTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKP  187 (276)
Q Consensus       108 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KP  187 (276)
                      +.                                               .+|||++|++...+.+.+|+++||+|||.||
T Consensus        72 ~~-----------------------------------------------~~pvi~lt~~~~~~~~~~a~~~Ga~dyl~Kp  104 (259)
T 3luf_A           72 ER-----------------------------------------------GLPVVILTADISEDKREAWLEAGVLDYVMKD  104 (259)
T ss_dssp             HT-----------------------------------------------TCCEEEEECC-CHHHHHHHHHTTCCEEEECS
T ss_pred             hC-----------------------------------------------CCCEEEEEccCCHHHHHHHHHCCCcEEEeCC
Confidence            51                                               4799999999999999999999999999999


Q ss_pred             CCHH
Q 023816          188 VKLS  191 (276)
Q Consensus       188 v~~~  191 (276)
                      +..+
T Consensus       105 ~~~~  108 (259)
T 3luf_A          105 SRHS  108 (259)
T ss_dssp             SHHH
T ss_pred             chhH
Confidence            7543

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

Probab=99.65  E-value=2.4e-16  Score=160.96  Aligned_cols=118  Identities=21%  Similarity=0.292  Sum_probs=105.8

Q ss_pred             cEEEEEeCCH-HH-------HHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCC-ceeEEEEecCCCC----
Q 023816           30 VHVLAVDDSF-VD-------RKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGL-KVDLIITDYCMPG----   96 (276)
Q Consensus        30 ~~VLIVdD~~-~~-------~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~-~~DlIL~D~~mp~----   96 (276)
                      ++||||||++ ..       ++.|...|+..||+|..+.|+++|+..+           +.. .+|+||+|+.||+    
T Consensus         1 m~ILiVdDd~~~~~~~~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~~-----------~~~~~~d~vilDi~lp~~~~~   69 (755)
T 2vyc_A            1 MKVLIVESEFLHQDTWVGNAVERLADALSQQNVTVIKSTSFDDGFAIL-----------SSNEAIDCLMFSYQMEHPDEH   69 (755)
T ss_dssp             CEEEEECCTTSTTSHHHHHHHHHHHHHHHHTTCEEEEESSHHHHHHHH-----------TTTCCCSEEEEECCCCSHHHH
T ss_pred             CeEEEEeCCccccccccHHHHHHHHHHHHhCCCEEEEECCHHHHHHHH-----------hcCCCCcEEEEeCCCCccccc
Confidence            3899999999 88       9999999999999999999999999999           554 5999999999999    


Q ss_pred             CCHHHHHHHHHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCC-HHHHHHH
Q 023816           97 MTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENI-LARIDRC  175 (276)
Q Consensus        97 ~~G~ell~~Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~-~~~~~~a  175 (276)
                      ++|++++++||+..+                                             .+||+++|+... .++....
T Consensus        70 ~~G~~ll~~iR~~~~---------------------------------------------~iPIi~lTa~~~~~~d~~~~  104 (755)
T 2vyc_A           70 QNVRQLIGKLHERQQ---------------------------------------------NVPVFLLGDREKALAAMDRD  104 (755)
T ss_dssp             HHHHHHHHHHHHHST---------------------------------------------TCCEEEEECHHHHHHTCSHH
T ss_pred             ccHHHHHHHHHHhCC---------------------------------------------CCCEEEEecCCcchhhccHh
Confidence            999999999998765                                             799999999877 7788889


Q ss_pred             HhcCCCeEEeCCCCHHH-H-HHHHHHHHHh
Q 023816          176 LEDGAEDFIVKPVKLSD-V-KRIKDYLTRD  203 (276)
Q Consensus       176 l~~Ga~d~l~KPv~~~~-L-~~~~~~l~~~  203 (276)
                      +..|++||+.||++..+ | .|+...+.|.
T Consensus       105 l~~gaddyi~kpf~~~efl~~ri~a~~rr~  134 (755)
T 2vyc_A          105 LLELVDEFAWILEDTADFIAGRAVAAMTRY  134 (755)
T ss_dssp             HHHHCSEEEETTTSCHHHHHHHHHHHHHHH
T ss_pred             HhhcCCceEeCCCCCHHHHHHHHHHHHHHh
Confidence            99999999999999999 5 5666666553

>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=99.22  E-value=2.6e-10  Score=107.06  Aligned_cols=118  Identities=19%  Similarity=0.273  Sum_probs=96.6

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHH
Q 023816           28 EEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIK  107 (276)
Q Consensus        28 ~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir  107 (276)
                      ...+|++|||+...++.+...|.. .+.+....++.+++. .           ....||+|++|+.||+|+|+++++.||
T Consensus       151 ~~~~ilivdd~~~~~~~i~~~L~~-~~~~~~~~~~~~~~~-~-----------~~~~~dlil~D~~mp~~dG~~~~~~ir  217 (459)
T 1w25_A          151 LGGRVLIVDDNERQAQRVAAELGV-EHRPVIESDPEKAKI-S-----------AGGPVDLVIVNAAAKNFDGLRFTAALR  217 (459)
T ss_dssp             CSCEEEEECSCHHHHHHHHHHHTT-TSEEEEECCHHHHHH-H-----------HHSSCSEEEEETTCSSSCHHHHHHHHH
T ss_pred             CCCeEEEECCchhhHHHHHHHHhc-ccceeeccCHHHHhh-h-----------ccCCCCEEEEecCCCCCcHHHHHHHHH
Confidence            456899999999999988888865 466777888888753 2           234689999999999999999999999


Q ss_pred             hhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCC
Q 023816          108 VTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKP  187 (276)
Q Consensus       108 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KP  187 (276)
                      ...                                           ....+|++++|+........++++.|++||+.||
T Consensus       218 ~~~-------------------------------------------~~~~~pii~lt~~~~~~~~~~~l~~Ga~d~~~kp  254 (459)
T 1w25_A          218 SEE-------------------------------------------RTRQLPVLAMVDPDDRGRMVKALEIGVNDILSRP  254 (459)
T ss_dssp             TSG-------------------------------------------GGTTCCEEEEECTTCHHHHHHHHHTTCCEEEESS
T ss_pred             hCc-------------------------------------------cccCCcEEEEcCCCchHHHHHHHhccccccccCC
Confidence            522                                           2347899999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHH
Q 023816          188 VKLSDVKRIKDYLT  201 (276)
Q Consensus       188 v~~~~L~~~~~~l~  201 (276)
                      +...++...+..+.
T Consensus       255 ~~~~~l~~~v~~~~  268 (459)
T 1w25_A          255 IDPQELSARVKTQI  268 (459)
T ss_dssp             CCHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH
Confidence            99998855444443

>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=99.20  E-value=7.7e-12  Score=105.61  Aligned_cols=87  Identities=28%  Similarity=0.431  Sum_probs=70.6

Q ss_pred             CEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhhCCCCcccchheehhhhhhhhhhhh
Q 023816           54 CKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFIL  133 (276)
Q Consensus        54 ~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~~p~~~~~~~~~~~~~~~~~~~~~~  133 (276)
                      +.|..+.++.+|++.+           +...||+||+|+.||+++|++++++||+..+                      
T Consensus         6 ~~v~~~~~~~~a~~~~-----------~~~~~dlvl~D~~~p~~~g~~~~~~l~~~~~----------------------   52 (237)
T 3cwo_X            6 LIVDDATNGREAVEKY-----------KELKPDIVTMDITMPEMNGIDAIKEIMKIDP----------------------   52 (237)
T ss_dssp             EEEECCCSSSTTHHHH-----------HHHCCSCEEEECCSTTSSHHHHHHHHHHHSS----------------------
T ss_pred             EEEEECCCHHHHHHHH-----------HhcCCCEEEEeCCCCCCCHHHHHHHHHHhCC----------------------
Confidence            4455588999999988           4557999999999999999999999998665                      


Q ss_pred             hccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCC--CCHHHHHHH
Q 023816          134 SICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKP--VKLSDVKRI  196 (276)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KP--v~~~~L~~~  196 (276)
                                             ..++++++.....+...++++.|+++|+.||  ++..++...
T Consensus        53 -----------------------~~~i~vi~~~~~~~~~~~~~~~Ga~~~l~kp~~~~~~~l~~~   94 (237)
T 3cwo_X           53 -----------------------NAKIIVCSAMGQQAMVIEAIKAGAKDFIVNTAAVENPSLITQ   94 (237)
T ss_dssp             -----------------------SCCEEEECCSSTHHHHHHHHHTTCCEEEESHHHHHCTHHHHH
T ss_pred             -----------------------CCCEEEEECCCCHHHHHHHHHCCHHheEeCCcccChHHHHHH
Confidence                                   4556666666668889999999999999999  665566433

>2ayx_A Sensor kinase protein RCSC; two independent structural domains, transferase; NMR {Escherichia coli} SCOP: c.23.1.1 c.23.1.6 PDB: 2ayz_A 2ayy_A

Probab=97.58  E-value=0.00032  Score=61.19  Aligned_cols=57  Identities=16%  Similarity=0.048  Sum_probs=47.2

Q ss_pred             CCCCccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCH
Q 023816           25 SDTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTG   99 (276)
Q Consensus        25 ~~~~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G   99 (276)
                      ..-.+.+||||||+...++.+++.|...|+++..+.+       .           ....+|++|+|+.+|...+
T Consensus         7 ~~l~~~~vlvv~d~~~~~~~l~~~L~~~g~~v~~~~~-------~-----------~~~~~~~ii~d~~~~~~~~   63 (254)
T 2ayx_A            7 EGLSGKRCWLAVRNASLCQFLETSLQRSGIVVTTYEG-------Q-----------EPTPEDVLITDEVVSKKWQ   63 (254)
T ss_dssp             CTTTTEEEEEECCCHHHHHHHHHHHTTTTEEEEECSS-------C-----------CCCTTCEEEEESSCSCCCC
T ss_pred             cccCCCEEEEEcCCHHHHHHHHHHHHHCCCEEEEecC-------C-----------CCCcCcEEEEcCCCccccc
Confidence            3455779999999999999999999999999988764       1           2346899999999987543

>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=97.42  E-value=0.0002  Score=73.42  Aligned_cols=94  Identities=11%  Similarity=0.104  Sum_probs=73.7

Q ss_pred             HHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhhCCCCcccchhee
Q 023816           42 RKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIV  121 (276)
Q Consensus        42 ~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~~p~~~~~~~~~~  121 (276)
                      .+.|.+.|+..||+|..+.++++|+..+.          ....+++||+|+.++   +.+++++||+..+          
T Consensus        19 i~~L~~~Le~~g~~V~~a~s~~Da~~~i~----------~~~~i~avIld~d~~---~~~ll~~Ir~~~~----------   75 (715)
T 3n75_A           19 IRELHRALERLNFQIVYPNDRDDLLKLIE----------NNARLCGVIFDWDKY---NLELCEEISKMNE----------   75 (715)
T ss_dssp             HHHHHHHHHHTTCEEECCSSHHHHHHHHH----------HCTTEEEEEEEHHHH---HHHHHHHHHHHCT----------
T ss_pred             HHHHHHHHHHCCcEEEEeCCHHHHHHHHH----------hCCCceEEEEecccc---HHHHHHHHHHhCC----------
Confidence            34566888899999999999999999994          334699999999986   7899999999877          


Q ss_pred             hhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCCHHHH
Q 023816          122 FLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSDV  193 (276)
Q Consensus       122 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~~~~L  193 (276)
                                                         ++||.+++.......+.-....++++|+.+..+..+.
T Consensus        76 -----------------------------------~iPVFl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  112 (715)
T 3n75_A           76 -----------------------------------NLPLYAFANTYSTLDVSLNDLRLQISFFEYALGAAED  112 (715)
T ss_dssp             -----------------------------------TCEEEEECCTTCCCCGGGTTSCCEEEEECCCTTCHHH
T ss_pred             -----------------------------------CCCEEEEecCCcccccchhhhhccCeEEEeCCCCHHH
Confidence                                               8999999988543333222245789999998755554

>2yxb_A Coenzyme B12-dependent mutase; alpha/beta, structural genomics, NPPSFA, national project on structural and functional analyses; 1.80A {Aeropyrum pernix}

Probab=96.12  E-value=0.12  Score=43.05  Aligned_cols=118  Identities=17%  Similarity=0.168  Sum_probs=78.6

Q ss_pred             CccEEEEE----eCCHHHHHHHHHHHhhCCCEEEE---ECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCC-C-C
Q 023816           28 EEVHVLAV----DDSFVDRKVIERLLTISSCKVTA---VDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPG-M-T   98 (276)
Q Consensus        28 ~~~~VLIV----dD~~~~~~~L~~~L~~~g~~v~~---a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~-~-~   98 (276)
                      ...+|++.    |-...-...+..+|+..||+|..   ....++.++.+           .+.++|+|.+...+.. + .
T Consensus        17 ~~~~vlla~~~gd~HdiG~~~va~~l~~~G~eVi~lG~~~p~e~lv~aa-----------~~~~~diV~lS~~~~~~~~~   85 (161)
T 2yxb_A           17 RRYKVLVAKMGLDGHDRGAKVVARALRDAGFEVVYTGLRQTPEQVAMAA-----------VQEDVDVIGVSILNGAHLHL   85 (161)
T ss_dssp             CSCEEEEEEESSSSCCHHHHHHHHHHHHTTCEEECCCSBCCHHHHHHHH-----------HHTTCSEEEEEESSSCHHHH
T ss_pred             CCCEEEEEeCCCCccHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHH-----------HhcCCCEEEEEeechhhHHH
Confidence            35677777    67778888899999999999996   34677777777           5678999999887653 1 2


Q ss_pred             HHHHHHHHHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhc
Q 023816           99 GYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLED  178 (276)
Q Consensus        99 G~ell~~Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~  178 (276)
                      -.++++.||+..+                                            ++++|+ +-+.....+...+.+.
T Consensus        86 ~~~~i~~L~~~g~--------------------------------------------~~i~v~-vGG~~~~~~~~~l~~~  120 (161)
T 2yxb_A           86 MKRLMAKLRELGA--------------------------------------------DDIPVV-LGGTIPIPDLEPLRSL  120 (161)
T ss_dssp             HHHHHHHHHHTTC--------------------------------------------TTSCEE-EEECCCHHHHHHHHHT
T ss_pred             HHHHHHHHHhcCC--------------------------------------------CCCEEE-EeCCCchhcHHHHHHC
Confidence            2346666665321                                            245544 4555555566667789


Q ss_pred             CCCeEEeCCCCHHHHHHHHHHHH
Q 023816          179 GAEDFIVKPVKLSDVKRIKDYLT  201 (276)
Q Consensus       179 Ga~d~l~KPv~~~~L~~~~~~l~  201 (276)
                      |++.++..-.+..+....+..+.
T Consensus       121 G~d~v~~~~~~~~~~~~~~~~~~  143 (161)
T 2yxb_A          121 GIREIFLPGTSLGEIIEKVRKLA  143 (161)
T ss_dssp             TCCEEECTTCCHHHHHHHHHHHH
T ss_pred             CCcEEECCCCCHHHHHHHHHHHH
Confidence            99887765555555544444333

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

Probab=95.78  E-value=0.021  Score=47.49  Aligned_cols=40  Identities=10%  Similarity=0.338  Sum_probs=35.3

Q ss_pred             CCeEEEEecCCCHHHHHHHHhcCCCeEE------eCCCCHHHHHHH
Q 023816          157 EIPVVIMSSENILARIDRCLEDGAEDFI------VKPVKLSDVKRI  196 (276)
Q Consensus       157 ~ipiV~ls~~~~~~~~~~al~~Ga~d~l------~KPv~~~~L~~~  196 (276)
                      .+|||++++....++..++++.|+++++      .+|++..++.+.
T Consensus       174 ~~Pvia~~g~~~~~~~~~~~~~G~~~~~vg~a~~~~~~~~~~~~~~  219 (237)
T 3cwo_X          174 TLPIIASGGAGKMEHFLEAFLAGADAALAASVFHFREIDVRELKEY  219 (237)
T ss_dssp             CSCEEEESCCCSHHHHHHHHHHTCSEEEESHHHHTTSSCHHHHHHH
T ss_pred             CCCEEecCCCCCHHHHHHHHHcCcHHHhhhHHHHcCCCCHHHHHHH
Confidence            6899999999999999999999999995      688888887553

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

Probab=94.58  E-value=0.73  Score=37.22  Aligned_cols=107  Identities=17%  Similarity=0.195  Sum_probs=79.0

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHh
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKV  108 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~  108 (276)
                      +-+||.|-.+-..--.+++++....|+++......                 ++..-|+|+|.|-+-..+       |..
T Consensus        12 ~~~iL~VtEd~~ls~QlKel~~~~eY~~~is~~~~-----------------~e~~AdlIfCEYlLLPe~-------ifS   67 (121)
T 3q7r_A           12 PKHVLLVSEHWDLFFQTKELLNPEEYRCTIGQQYK-----------------QELSADLVVCEYSLLPRE-------IRS   67 (121)
T ss_dssp             CEEEEEECSCHHHHHHHHHHSCTTTEEEEEESSCC-----------------CCTTEEEEEEEGGGSCTT-------CCC
T ss_pred             CcEEEEEecCchhhHHHHHhcCCcceeEEeccccC-----------------CcccceeEEEeeecChHH-------hcC
Confidence            55789998888888889999988889988765311                 456789999999652211       110


Q ss_pred             hCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCC
Q 023816          109 TTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPV  188 (276)
Q Consensus       109 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv  188 (276)
                                                                 ....++.-+|++-.--+.+.+.+.+..||. |+..|+
T Consensus        68 -------------------------------------------~k~~~~~dliVLfD~F~EEa~v~vLd~Ga~-yLlrPI  103 (121)
T 3q7r_A           68 -------------------------------------------PKSLEGSFVLVLLDFFDEETSVDLLDRGFW-YLIRPI  103 (121)
T ss_dssp             -------------------------------------------CTTCCSCEEEEEESSCCHHHHHHHHHTTCE-EEESCC
T ss_pred             -------------------------------------------CCCCCcccEEEEehhhchHHHHHHHhCCce-eEeccC
Confidence                                                       112235567777777788899999999999 999999


Q ss_pred             CHHHHHHHHHHHHHh
Q 023816          189 KLSDVKRIKDYLTRD  203 (276)
Q Consensus       189 ~~~~L~~~~~~l~~~  203 (276)
                      +..-+..++....+.
T Consensus       104 T~kvldAvIraFLrq  118 (121)
T 3q7r_A          104 TPRILKSAISLFLSQ  118 (121)
T ss_dssp             CHHHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHhc
Confidence            998887777766654

>1ccw_A Protein (glutamate mutase); coenzyme B12, radical reaction, TIM-barrel rossman-fold, isomerase; HET: CNC TAR; 1.60A {Clostridium cochlearium} SCOP: c.23.6.1 PDB: 1cb7_A* 1b1a_A 1i9c_A* 1be1_A 1fmf_A 1id8_A*

Probab=93.28  E-value=1.2  Score=35.86  Aligned_cols=62  Identities=16%  Similarity=0.087  Sum_probs=44.5

Q ss_pred             eCCHHHHHHHHHHHhhCCCEEEE---ECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCC-C-HHHHHHHHHh
Q 023816           36 DDSFVDRKVIERLLTISSCKVTA---VDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGM-T-GYELLKKIKV  108 (276)
Q Consensus        36 dD~~~~~~~L~~~L~~~g~~v~~---a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~-~-G~ell~~Ir~  108 (276)
                      |-+..-.+.+..+|+..||+|..   ....++.++.+           .+.++|+|.+...+... . --++++.+++
T Consensus        14 d~HdiG~~~v~~~l~~~G~~Vi~lG~~~p~e~~v~~a-----------~~~~~d~v~lS~~~~~~~~~~~~~i~~l~~   80 (137)
T 1ccw_A           14 DCHAVGNKILDHAFTNAGFNVVNIGVLSPQELFIKAA-----------IETKADAILVSSLYGQGEIDCKGLRQKCDE   80 (137)
T ss_dssp             CCCCHHHHHHHHHHHHTTCEEEEEEEEECHHHHHHHH-----------HHHTCSEEEEEECSSTHHHHHTTHHHHHHH
T ss_pred             chhHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHH-----------HhcCCCEEEEEecCcCcHHHHHHHHHHHHh
Confidence            44556667788999999999984   55778888877           55689999999877431 1 2246666765

>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=91.31  E-value=1.3  Score=38.79  Aligned_cols=88  Identities=15%  Similarity=0.122  Sum_probs=61.1

Q ss_pred             HHHHHHHHHHHhhCCCEEEE-ECCHHHHHHHhcccccccccCCCCCceeEEEEecC------CCCCCHHHHHHHHHhhCC
Q 023816           39 FVDRKVIERLLTISSCKVTA-VDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYC------MPGMTGYELLKKIKVTTP  111 (276)
Q Consensus        39 ~~~~~~L~~~L~~~g~~v~~-a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~------mp~~~G~ell~~Ir~~~p  111 (276)
                      +...+.+.+.++..|..+.. +.+.+++.+..            +..+|.|.+...      .+...++++++++++.  
T Consensus       115 p~~l~~~i~~~~~~g~~v~~~v~t~eea~~a~------------~~Gad~Ig~~~~g~t~~~~~~~~~~~li~~l~~~--  180 (229)
T 3q58_A          115 PVDIDSLLTRIRLHGLLAMADCSTVNEGISCH------------QKGIEFIGTTLSGYTGPITPVEPDLAMVTQLSHA--  180 (229)
T ss_dssp             SSCHHHHHHHHHHTTCEEEEECSSHHHHHHHH------------HTTCSEEECTTTTSSSSCCCSSCCHHHHHHHHTT--
T ss_pred             hHHHHHHHHHHHHCCCEEEEecCCHHHHHHHH------------hCCCCEEEecCccCCCCCcCCCCCHHHHHHHHHc--
Confidence            33444455555667877665 77877776654            345777753221      2234567888888741  


Q ss_pred             CCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEe
Q 023816          112 FNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIV  185 (276)
Q Consensus       112 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~  185 (276)
                                                                   ++|||.-.+-...+++.++++.||+.++.
T Consensus       181 ---------------------------------------------~ipvIA~GGI~t~~d~~~~~~~GadgV~V  209 (229)
T 3q58_A          181 ---------------------------------------------GCRVIAEGRYNTPALAANAIEHGAWAVTV  209 (229)
T ss_dssp             ---------------------------------------------TCCEEEESSCCSHHHHHHHHHTTCSEEEE
T ss_pred             ---------------------------------------------CCCEEEECCCCCHHHHHHHHHcCCCEEEE
Confidence                                                         58999888888899999999999999986

>1wv2_A Thiazole moeity, thiazole biosynthesis protein THIG; structural genomics, protein structure initiative, PSI; 2.90A {Pseudomonas aeruginosa} SCOP: c.1.31.1

Probab=90.93  E-value=1.2  Score=40.92  Aligned_cols=90  Identities=16%  Similarity=0.096  Sum_probs=62.5

Q ss_pred             eCCHHHHHHHHHHHhhCCCEEE--EECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCC-----CCHHHHHHHHHh
Q 023816           36 DDSFVDRKVIERLLTISSCKVT--AVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPG-----MTGYELLKKIKV  108 (276)
Q Consensus        36 dD~~~~~~~L~~~L~~~g~~v~--~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~-----~~G~ell~~Ir~  108 (276)
                      -|.....+..+ .|.+.||+|.  ++++...|-+..            ..+++.| +.+..|.     ....++++.|++
T Consensus       119 pD~~~tv~aa~-~L~~~Gf~Vlpy~~dd~~~akrl~------------~~G~~aV-mPlg~pIGsG~Gi~~~~lI~~I~e  184 (265)
T 1wv2_A          119 PNVVETLKAAE-QLVKDGFDVMVYTSDDPIIARQLA------------EIGCIAV-MPLAGLIGSGLGICNPYNLRIILE  184 (265)
T ss_dssp             BCHHHHHHHHH-HHHTTTCEEEEEECSCHHHHHHHH------------HSCCSEE-EECSSSTTCCCCCSCHHHHHHHHH
T ss_pred             cCHHHHHHHHH-HHHHCCCEEEEEeCCCHHHHHHHH------------HhCCCEE-EeCCccCCCCCCcCCHHHHHHHHh
Confidence            34444444443 5567899988  466766665443            3457777 6655542     234788999987


Q ss_pred             hCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEe
Q 023816          109 TTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIV  185 (276)
Q Consensus       109 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~  185 (276)
                      . +                                             .+|||+=-+-..+++...|++.||+..++
T Consensus       185 ~-~---------------------------------------------~vPVI~eGGI~TPsDAa~AmeLGAdgVlV  215 (265)
T 1wv2_A          185 E-A---------------------------------------------KVPVLVDAGVGTASDAAIAMELGCEAVLM  215 (265)
T ss_dssp             H-C---------------------------------------------SSCBEEESCCCSHHHHHHHHHHTCSEEEE
T ss_pred             c-C---------------------------------------------CCCEEEeCCCCCHHHHHHHHHcCCCEEEE
Confidence            3 3                                             68999877778899999999999999875

>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=89.53  E-value=2.5  Score=37.07  Aligned_cols=88  Identities=19%  Similarity=0.098  Sum_probs=60.1

Q ss_pred             HHHHHHHHHHHhhCCCEEEE-ECCHHHHHHHhcccccccccCCCCCceeEEEEecC------CCCCCHHHHHHHHHhhCC
Q 023816           39 FVDRKVIERLLTISSCKVTA-VDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYC------MPGMTGYELLKKIKVTTP  111 (276)
Q Consensus        39 ~~~~~~L~~~L~~~g~~v~~-a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~------mp~~~G~ell~~Ir~~~p  111 (276)
                      +...+.+.+.++..|..+.. +.+.+++.+..            ...+|.|.+...      -+...++++++++++.  
T Consensus       115 p~~l~~~i~~~~~~g~~v~~~v~t~eea~~a~------------~~Gad~Ig~~~~g~t~~~~~~~~~~~~i~~l~~~--  180 (232)
T 3igs_A          115 PVAVEALLARIHHHHLLTMADCSSVDDGLACQ------------RLGADIIGTTMSGYTTPDTPEEPDLPLVKALHDA--  180 (232)
T ss_dssp             SSCHHHHHHHHHHTTCEEEEECCSHHHHHHHH------------HTTCSEEECTTTTSSSSSCCSSCCHHHHHHHHHT--
T ss_pred             HHHHHHHHHHHHHCCCEEEEeCCCHHHHHHHH------------hCCCCEEEEcCccCCCCCCCCCCCHHHHHHHHhc--
Confidence            33444455555667877665 67777776554            335777753221      1233467888888752  


Q ss_pred             CCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEe
Q 023816          112 FNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIV  185 (276)
Q Consensus       112 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~  185 (276)
                                                                   ++|||.-.+-...+++.++++.||+.++.
T Consensus       181 ---------------------------------------------~ipvIA~GGI~t~~d~~~~~~~GadgV~V  209 (232)
T 3igs_A          181 ---------------------------------------------GCRVIAEGRYNSPALAAEAIRYGAWAVTV  209 (232)
T ss_dssp             ---------------------------------------------TCCEEEESCCCSHHHHHHHHHTTCSEEEE
T ss_pred             ---------------------------------------------CCcEEEECCCCCHHHHHHHHHcCCCEEEE
Confidence                                                         58999888878899999999999999986

>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=88.20  E-value=1.4  Score=39.24  Aligned_cols=47  Identities=21%  Similarity=0.328  Sum_probs=35.3

Q ss_pred             CCeEEEEecCCC------HHHHHHHHhcCCCeEEeCCCCHHHHHHHHHHHHHh
Q 023816          157 EIPVVIMSSENI------LARIDRCLEDGAEDFIVKPVKLSDVKRIKDYLTRD  203 (276)
Q Consensus       157 ~ipiV~ls~~~~------~~~~~~al~~Ga~d~l~KPv~~~~L~~~~~~l~~~  203 (276)
                      .+|+++|+-.+.      ......|.++|++.++.-.+..+++...++.+.+.
T Consensus        94 ~~Pi~~m~y~n~v~~~g~~~f~~~~~~aG~dgvii~dl~~ee~~~~~~~~~~~  146 (262)
T 2ekc_A           94 DIPFLLMTYYNPIFRIGLEKFCRLSREKGIDGFIVPDLPPEEAEELKAVMKKY  146 (262)
T ss_dssp             TSCEEEECCHHHHHHHCHHHHHHHHHHTTCCEEECTTCCHHHHHHHHHHHHHT
T ss_pred             CCCEEEEecCcHHHHhhHHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHHHc
Confidence            689999864432      35667899999999999888888877776666543

>2htm_A Thiazole biosynthesis protein THIG; thiamin biosynthesis, THIG, thermus thermophilus HB8, structural genomics, NPPSFA; 2.30A {Thermus thermophilus}

Probab=86.66  E-value=2.4  Score=38.87  Aligned_cols=90  Identities=19%  Similarity=0.157  Sum_probs=59.6

Q ss_pred             CCHHHHHHHHHHHhhCCCEEE--EECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCH-----HHHHHHHHhh
Q 023816           37 DSFVDRKVIERLLTISSCKVT--AVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTG-----YELLKKIKVT  109 (276)
Q Consensus        37 D~~~~~~~L~~~L~~~g~~v~--~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G-----~ell~~Ir~~  109 (276)
                      |.....+..+ .|.+.||.|.  ..+|...|-+..            ...++.| +.+-.|..+|     .++++.|++.
T Consensus       109 D~~~tv~aa~-~L~k~Gf~Vlpy~~~D~~~ak~l~------------~~G~~aV-mPlg~pIGsG~Gi~~~~~L~~i~~~  174 (268)
T 2htm_A          109 DPLETLKAAE-RLIEEDFLVLPYMGPDLVLAKRLA------------ALGTATV-MPLAAPIGSGWGVRTRALLELFARE  174 (268)
T ss_dssp             CHHHHHHHHH-HHHHTTCEECCEECSCHHHHHHHH------------HHTCSCB-EEBSSSTTTCCCSTTHHHHHHHHHT
T ss_pred             CHHHHHHHHH-HHHHCCCEEeeccCCCHHHHHHHH------------hcCCCEE-EecCccCcCCcccCCHHHHHHHHHh
Confidence            4444444444 3445799877  345664443332            2356666 7766553333     5678888864


Q ss_pred             CCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCC-CeEEEEecCCCHHHHHHHHhcCCCeEEe
Q 023816          110 TPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALRE-IPVVIMSSENILARIDRCLEDGAEDFIV  185 (276)
Q Consensus       110 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-ipiV~ls~~~~~~~~~~al~~Ga~d~l~  185 (276)
                      .+                                             + +|||+=-+-..+++...|++.||+..++
T Consensus       175 ~~---------------------------------------------~~vPVI~~GGI~tpsDAa~AmeLGAdgVlV  206 (268)
T 2htm_A          175 KA---------------------------------------------SLPPVVVDAGLGLPSHAAEVMELGLDAVLV  206 (268)
T ss_dssp             TT---------------------------------------------TSSCBEEESCCCSHHHHHHHHHTTCCEEEE
T ss_pred             cC---------------------------------------------CCCeEEEeCCCCCHHHHHHHHHcCCCEEEE
Confidence            44                                             6 8999877778899999999999999875

>3vnd_A TSA, tryptophan synthase alpha chain; psychrophilic enzyme, cold adaptation; HET: PE8; 2.60A {Shewanella frigidimarina}

Probab=86.48  E-value=1.2  Score=40.28  Aligned_cols=46  Identities=9%  Similarity=0.233  Sum_probs=36.2

Q ss_pred             CCeEEEEecCCC------HHHHHHHHhcCCCeEEeCCCCHHHHHHHHHHHHH
Q 023816          157 EIPVVIMSSENI------LARIDRCLEDGAEDFIVKPVKLSDVKRIKDYLTR  202 (276)
Q Consensus       157 ~ipiV~ls~~~~------~~~~~~al~~Ga~d~l~KPv~~~~L~~~~~~l~~  202 (276)
                      ++|+++|+-.+.      .....+|.++|++..|.-....++..+.+..+..
T Consensus        95 ~~Pivlm~Y~npv~~~g~e~f~~~~~~aGvdgvii~Dlp~ee~~~~~~~~~~  146 (267)
T 3vnd_A           95 DMPIGLLLYANLVFANGIDEFYTKAQAAGVDSVLIADVPVEESAPFSKAAKA  146 (267)
T ss_dssp             TCCEEEEECHHHHHHHCHHHHHHHHHHHTCCEEEETTSCGGGCHHHHHHHHH
T ss_pred             CCCEEEEecCcHHHHhhHHHHHHHHHHcCCCEEEeCCCCHhhHHHHHHHHHH
Confidence            789999975442      5678899999999999988888877666666654

>1req_A Methylmalonyl-COA mutase; isomerase, intramolecular transferase; HET: B12 DCA; 2.00A {Propionibacterium freudenreichii subspshermanii} SCOP: c.1.19.1 c.23.6.1 PDB: 2req_A* 3req_A* 4req_A* 6req_A* 7req_A* 5req_A* 1e1c_A*

Probab=85.35  E-value=7.3  Score=40.18  Aligned_cols=116  Identities=14%  Similarity=0.080  Sum_probs=76.1

Q ss_pred             ccEEEEE----eCCHHHHHHHHHHHhhCCCEEEEE---CCHHHHHHHhcccccccccCCCCCceeEEEEecCCCC-C-CH
Q 023816           29 EVHVLAV----DDSFVDRKVIERLLTISSCKVTAV---DSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPG-M-TG   99 (276)
Q Consensus        29 ~~~VLIV----dD~~~~~~~L~~~L~~~g~~v~~a---~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~-~-~G   99 (276)
                      ..+|++.    |-+..-.+.+..+|+..||+|...   .+.++.++.+           .+.++|+|.+..-|.. + ..
T Consensus       596 r~kVvlatvg~D~HdiG~~iVa~~l~~~GfeVi~lG~~v~~eeiv~aA-----------~e~~adiVglSsl~~~~~~~~  664 (727)
T 1req_A          596 RPRILLAKMGQDGHDRGQKVIATAYADLGFDVDVGPLFQTPEETARQA-----------VEADVHVVGVSSLAGGHLTLV  664 (727)
T ss_dssp             CCEEEEECBTTCCCCHHHHHHHHHHHHHTCEEEECCTTBCHHHHHHHH-----------HHTTCSEEEEEECSSCHHHHH
T ss_pred             CCEEEEEeCCcchhHHHHHHHHHHHHhCCeEEEeCCCCCCHHHHHHHH-----------HHcCCCEEEEeeecHhHHHHH
Confidence            4567765    455556667788999999999873   3567888877           5668999998876653 2 23


Q ss_pred             HHHHHHHHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcC
Q 023816          100 YELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDG  179 (276)
Q Consensus       100 ~ell~~Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~G  179 (276)
                      -++++.|++...                                            ++++ |++-+-.-..+...+.+.|
T Consensus       665 ~~vi~~L~~~G~--------------------------------------------~~i~-VivGG~~p~~d~~~l~~~G  699 (727)
T 1req_A          665 PALRKELDKLGR--------------------------------------------PDIL-ITVGGVIPEQDFDELRKDG  699 (727)
T ss_dssp             HHHHHHHHHTTC--------------------------------------------TTSE-EEEEESCCGGGHHHHHHTT
T ss_pred             HHHHHHHHhcCC--------------------------------------------CCCE-EEEcCCCccccHHHHHhCC
Confidence            467777876332                                            2333 3344323333556678999


Q ss_pred             CCeEEeCCCCHHHH-HHHHHHH
Q 023816          180 AEDFIVKPVKLSDV-KRIKDYL  200 (276)
Q Consensus       180 a~d~l~KPv~~~~L-~~~~~~l  200 (276)
                      ++.|+..-.+..++ ..+++.+
T Consensus       700 aD~~f~~gt~~~e~a~~l~~~l  721 (727)
T 1req_A          700 AVEIYTPGTVIPESAISLVKKL  721 (727)
T ss_dssp             EEEEECTTCCHHHHHHHHHHHH
T ss_pred             CCEEEcCCccHHHHHHHHHHHH
Confidence            99999876677666 3444444

>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=84.89  E-value=1.9  Score=38.22  Aligned_cols=47  Identities=23%  Similarity=0.378  Sum_probs=35.1

Q ss_pred             CCeEEEEecCC------CHHHHHHHHhcCCCeEEeCCCCHHHHHHHHHHHHHh
Q 023816          157 EIPVVIMSSEN------ILARIDRCLEDGAEDFIVKPVKLSDVKRIKDYLTRD  203 (276)
Q Consensus       157 ~ipiV~ls~~~------~~~~~~~al~~Ga~d~l~KPv~~~~L~~~~~~l~~~  203 (276)
                      ++||++|+-.+      .......+.++|++.++.-....+++.+.++.+.+.
T Consensus        94 ~~Pv~lm~y~n~v~~~g~~~~~~~~~~aGadgii~~d~~~e~~~~~~~~~~~~  146 (268)
T 1qop_A           94 TIPIGLLMYANLVFNNGIDAFYARCEQVGVDSVLVADVPVEESAPFRQAALRH  146 (268)
T ss_dssp             SSCEEEEECHHHHHTTCHHHHHHHHHHHTCCEEEETTCCGGGCHHHHHHHHHT
T ss_pred             CCCEEEEEcccHHHHhhHHHHHHHHHHcCCCEEEEcCCCHHHHHHHHHHHHHc
Confidence            58888886332      246788899999999999888877777766666543

>2i2x_B MTAC, methyltransferase 1; TIM barrel and helix bundle (MTAB), rossman fold and helix B (MTAC); HET: B13; 2.50A {Methanosarcina barkeri}

Probab=84.67  E-value=9.4  Score=33.65  Aligned_cols=72  Identities=14%  Similarity=0.084  Sum_probs=52.0

Q ss_pred             ccEEEEE----eCCHHHHHHHHHHHhhCCCEEEE---ECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCC-CCH-
Q 023816           29 EVHVLAV----DDSFVDRKVIERLLTISSCKVTA---VDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPG-MTG-   99 (276)
Q Consensus        29 ~~~VLIV----dD~~~~~~~L~~~L~~~g~~v~~---a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~-~~G-   99 (276)
                      .-+||+.    |-+..-...+..+|+..||+|..   -...++.++.+           ...++|+|.+...+.. +.. 
T Consensus       123 ~~~vlla~~~gd~HdiG~~iva~~L~~~G~~Vi~LG~~vp~e~l~~~~-----------~~~~~d~V~lS~l~~~~~~~~  191 (258)
T 2i2x_B          123 KGTVVCHVAEGDVHDIGKNIVTALLRANGYNVVDLGRDVPAEEVLAAV-----------QKEKPIMLTGTALMTTTMYAF  191 (258)
T ss_dssp             SCEEEEEECTTCCCCHHHHHHHHHHHHTTCEEEEEEEECCSHHHHHHH-----------HHHCCSEEEEECCCTTTTTHH
T ss_pred             CCeEEEEeCCCCccHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHH-----------HHcCCCEEEEEeeccCCHHHH
Confidence            4567776    56667788899999999999875   23556666666           5568999999987764 333 


Q ss_pred             HHHHHHHHhhCC
Q 023816          100 YELLKKIKVTTP  111 (276)
Q Consensus       100 ~ell~~Ir~~~p  111 (276)
                      -++++.+|+..+
T Consensus       192 ~~~i~~l~~~~~  203 (258)
T 2i2x_B          192 KEVNDMLLENGI  203 (258)
T ss_dssp             HHHHHHHHTTTC
T ss_pred             HHHHHHHHhcCC
Confidence            357788886444

>2xij_A Methylmalonyl-COA mutase, mitochondrial; isomerase, organic aciduria, vitamin B12; HET: B12 5AD BTB; 1.95A {Homo sapiens} PDB: 2xiq_A* 3bic_A

Probab=84.63  E-value=11  Score=39.09  Aligned_cols=114  Identities=15%  Similarity=0.046  Sum_probs=74.5

Q ss_pred             ccEEEEE----eCCHHHHHHHHHHHhhCCCEEEEE---CCHHHHHHHhcccccccccCCCCCceeEEEEecCCCC-C-CH
Q 023816           29 EVHVLAV----DDSFVDRKVIERLLTISSCKVTAV---DSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPG-M-TG   99 (276)
Q Consensus        29 ~~~VLIV----dD~~~~~~~L~~~L~~~g~~v~~a---~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~-~-~G   99 (276)
                      ..+|++.    |-+.+-.+.+..+|+..||+|...   .+.++.++.+           .+.++|+|.+..-|.. + ..
T Consensus       604 r~kVvlatvg~D~HdiG~~iVa~~l~~~GfeVi~lG~~v~~eeiv~aA-----------~e~~adiVglSsl~~~~~~~~  672 (762)
T 2xij_A          604 RPRLLVAKMGQDGHDRGAKVIATGFADLGFDVDIGPLFQTPREVAQQA-----------VDADVHAVGVSTLAAGHKTLV  672 (762)
T ss_dssp             CCEEEEECCSSCCCCHHHHHHHHHHHHTTCEEEECCTTCCHHHHHHHH-----------HHTTCSEEEEEECSSCHHHHH
T ss_pred             CCEEEEEecCcchhhHHHHHHHHHHHhCCeEEeeCCCCCCHHHHHHHH-----------HHcCCCEEEEeeecHHHHHHH
Confidence            4567765    445556667788999999999873   3567888777           5668999998876643 2 23


Q ss_pred             HHHHHHHHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcC
Q 023816          100 YELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDG  179 (276)
Q Consensus       100 ~ell~~Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~G  179 (276)
                      -++++.|++...                                            ++++| ++-+-.-..+...+.+.|
T Consensus       673 ~~vi~~Lr~~G~--------------------------------------------~dv~V-ivGG~~P~~d~~~l~~~G  707 (762)
T 2xij_A          673 PELIKELNSLGR--------------------------------------------PDILV-MCGGVIPPQDYEFLFEVG  707 (762)
T ss_dssp             HHHHHHHHHTTC--------------------------------------------TTSEE-EEEESCCGGGHHHHHHHT
T ss_pred             HHHHHHHHhcCC--------------------------------------------CCCEE-EEeCCCCcccHHHHHhCC
Confidence            467777776332                                            24333 333323333456678999


Q ss_pred             CCeEEeCCCCHHHHHHHHH
Q 023816          180 AEDFIVKPVKLSDVKRIKD  198 (276)
Q Consensus       180 a~d~l~KPv~~~~L~~~~~  198 (276)
                      ++.|+..--+..++...+.
T Consensus       708 aD~~f~pgtd~~e~~~~i~  726 (762)
T 2xij_A          708 VSNVFGPGTRIPKAAVQVL  726 (762)
T ss_dssp             CCEEECTTCCHHHHHHHHH
T ss_pred             CCEEeCCCCCHHHHHHHHH
Confidence            9999986667777643333

>1geq_A Tryptophan synthase alpha-subunit; hyperthermophIle, pyrococ furiosus, X-RAY analysis, stability, calorimetry, lyase; 2.00A {Pyrococcus furiosus} SCOP: c.1.2.4 PDB: 1wdw_A* 2dzu_A 2dzp_A 2e09_A 2dzw_A 2dzs_A 2dzv_A 2dzt_A 2dzx_A

Probab=84.56  E-value=3  Score=35.75  Aligned_cols=45  Identities=16%  Similarity=0.263  Sum_probs=31.5

Q ss_pred             CCeEEEEecCCC------HHHHHHHHhcCCCeEEeCCCCHHHHHHHHHHHH
Q 023816          157 EIPVVIMSSENI------LARIDRCLEDGAEDFIVKPVKLSDVKRIKDYLT  201 (276)
Q Consensus       157 ~ipiV~ls~~~~------~~~~~~al~~Ga~d~l~KPv~~~~L~~~~~~l~  201 (276)
                      ++||++++..+.      .+.+..++++||+..+.-.....+..++++.+.
T Consensus        80 ~~pv~~~~~~~~~~~~~~~~~~~~~~~~Gad~v~~~~~~~~~~~~~~~~~~  130 (248)
T 1geq_A           80 STPIVLMTYYNPIYRAGVRNFLAEAKASGVDGILVVDLPVFHAKEFTEIAR  130 (248)
T ss_dssp             CCCEEEEECHHHHHHHCHHHHHHHHHHHTCCEEEETTCCGGGHHHHHHHHH
T ss_pred             CCCEEEEeccchhhhcCHHHHHHHHHHCCCCEEEECCCChhhHHHHHHHHH
Confidence            468888874333      578889999999999987665555555544444

>3f4w_A Putative hexulose 6 phosphate synthase; humps, malonate, lyase; 1.65A {Salmonella typhimurium} SCOP: c.1.2.0

Probab=82.20  E-value=6.8  Score=32.58  Aligned_cols=28  Identities=11%  Similarity=0.096  Sum_probs=21.1

Q ss_pred             CCeEEEEecCCCHHHHHHHHhcCCCeEEe
Q 023816          157 EIPVVIMSSENILARIDRCLEDGAEDFIV  185 (276)
Q Consensus       157 ~ipiV~ls~~~~~~~~~~al~~Ga~d~l~  185 (276)
                      ++||++-.+= ..+.+.+++++||+.++.
T Consensus       159 ~~~i~~~gGI-~~~~~~~~~~~Gad~vvv  186 (211)
T 3f4w_A          159 KARIAVAGGI-SSQTVKDYALLGPDVVIV  186 (211)
T ss_dssp             SCEEEEESSC-CTTTHHHHHTTCCSEEEE
T ss_pred             CCcEEEECCC-CHHHHHHHHHcCCCEEEE
Confidence            5777655444 478888999999998875

>3nav_A Tryptophan synthase alpha chain; alpha subunit, structural genomics, CSG center for structural genomics of infectious diseases; 2.10A {Vibrio cholerae o1 biovar el tor} SCOP: c.1.2.4

Probab=81.15  E-value=2.3  Score=38.49  Aligned_cols=46  Identities=15%  Similarity=0.313  Sum_probs=35.5

Q ss_pred             CCeEEEEecC------CCHHHHHHHHhcCCCeEEeCCCCHHHHHHHHHHHHH
Q 023816          157 EIPVVIMSSE------NILARIDRCLEDGAEDFIVKPVKLSDVKRIKDYLTR  202 (276)
Q Consensus       157 ~ipiV~ls~~------~~~~~~~~al~~Ga~d~l~KPv~~~~L~~~~~~l~~  202 (276)
                      ++|+|+|+-.      .......+|.++|++.+|.--+..++....+..+..
T Consensus        97 ~~Pivlm~Y~n~v~~~g~~~f~~~~~~aGvdGvIipDlp~ee~~~~~~~~~~  148 (271)
T 3nav_A           97 ETPIGLLMYANLVYARGIDDFYQRCQKAGVDSVLIADVPTNESQPFVAAAEK  148 (271)
T ss_dssp             TSCEEEEECHHHHHHTCHHHHHHHHHHHTCCEEEETTSCGGGCHHHHHHHHH
T ss_pred             CCCEEEEecCcHHHHHhHHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHH
Confidence            7899999743      335678899999999999987877776666665554

>3qja_A IGPS, indole-3-glycerol phosphate synthase; structural genomics, T structural genomics consortium, TBSGC, lyase; 1.29A {Mycobacterium tuberculosis} PDB: 3t40_A* 3t44_A* 3t55_A* 3t78_A* 4fb7_A*

Probab=80.88  E-value=17  Score=32.57  Aligned_cols=30  Identities=17%  Similarity=0.095  Sum_probs=26.6

Q ss_pred             CCeEEEEecCCCHHHHHHHHhcCCCeEEeC
Q 023816          157 EIPVVIMSSENILARIDRCLEDGAEDFIVK  186 (276)
Q Consensus       157 ~ipiV~ls~~~~~~~~~~al~~Ga~d~l~K  186 (276)
                      ++|+|+.++-...+++.++.+.|++.+++=
T Consensus       213 ~~pvVaegGI~t~edv~~l~~~GadgvlVG  242 (272)
T 3qja_A          213 SVIRIAESGVRGTADLLAYAGAGADAVLVG  242 (272)
T ss_dssp             TSEEEEESCCCSHHHHHHHHHTTCSEEEEC
T ss_pred             cCEEEEECCCCCHHHHHHHHHcCCCEEEEc
Confidence            588998888888999999999999999983

>1y80_A Predicted cobalamin binding protein; corrinoid, factor IIIM, methyl transferase, structural genomics, PSI, protein structure initiative; HET: B1M; 1.70A {Moorella thermoacetica}

Probab=80.62  E-value=6.1  Score=33.34  Aligned_cols=70  Identities=7%  Similarity=0.075  Sum_probs=50.2

Q ss_pred             ccEEEEE----eCCHHHHHHHHHHHhhCCCEEEEEC---CHHHHHHHhcccccccccCCCCCceeEEEEecCCCC-CC-H
Q 023816           29 EVHVLAV----DDSFVDRKVIERLLTISSCKVTAVD---SGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPG-MT-G   99 (276)
Q Consensus        29 ~~~VLIV----dD~~~~~~~L~~~L~~~g~~v~~a~---~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~-~~-G   99 (276)
                      .-+||+.    |-+..-...+..+|+..||+|....   ..++.++.+           ...++|+|.+...+.. +. -
T Consensus        88 ~~~vll~~~~gd~H~iG~~~va~~l~~~G~~v~~LG~~vp~~~l~~~~-----------~~~~~d~v~lS~~~~~~~~~~  156 (210)
T 1y80_A           88 VGKIVLGTVKGDLHDIGKNLVAMMLESGGFTVYNLGVDIEPGKFVEAV-----------KKYQPDIVGMSALLTTTMMNM  156 (210)
T ss_dssp             CCEEEEEEBTTCCCCHHHHHHHHHHHHTTCEEEECCSSBCHHHHHHHH-----------HHHCCSEEEEECCSGGGTHHH
T ss_pred             CCEEEEEeCCCcccHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHH-----------HHcCCCEEEEeccccccHHHH
Confidence            4477777    6667788889999999999999733   456666666           4568999999987653 22 2


Q ss_pred             HHHHHHHHhh
Q 023816          100 YELLKKIKVT  109 (276)
Q Consensus       100 ~ell~~Ir~~  109 (276)
                      .++++.+|+.
T Consensus       157 ~~~i~~l~~~  166 (210)
T 1y80_A          157 KSTIDALIAA  166 (210)
T ss_dssp             HHHHHHHHHT
T ss_pred             HHHHHHHHhc
Confidence            3566777753

---

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	276
d1dcfa_	134	c.23.1.2 (A:) Receiver domain of the ethylene rece	1e-14
d1zesa1	121	c.23.1.1 (A:3-123) PhoB receiver domain {Escherich	2e-13
d1k68a_	140	c.23.1.1 (A:) Response regulator for cyanobacteria	4e-13
d1peya_	119	c.23.1.1 (A:) Sporulation response regulator Spo0F	5e-13
d2ayxa1	133	c.23.1.1 (A:817-949) Sensor kinase protein RcsC, C	2e-12
d2r25b1	128	c.23.1.1 (B:1087-1214) Response regulator Sin1 {Ba	2e-12
d1i3ca_	144	c.23.1.1 (A:) Response regulator for cyanobacteria	2e-12
d1dz3a_	123	c.23.1.1 (A:) Sporulation response regulator Spo0A	2e-12
d2b4aa1	118	c.23.1.1 (A:2-119) Hypothetical protein BH3024 {Ba	2e-12
d1k66a_	149	c.23.1.1 (A:) Response regulator for cyanobacteria	5e-12
d1mb3a_	123	c.23.1.1 (A:) Cell division response regulator Div	7e-12
d1a04a2	138	c.23.1.1 (A:5-142) Nitrate/nitrite response regula	1e-11
d1jbea_	128	c.23.1.1 (A:) CheY protein {Escherichia coli [TaxI	2e-11
d1krwa_	123	c.23.1.1 (A:) NTRC receiver domain {Salmonella typ	3e-11
d1u0sy_	118	c.23.1.1 (Y:) CheY protein {Thermotoga maritima [T	6e-11
d1p6qa_	129	c.23.1.1 (A:) CheY protein {Sinorhizobium meliloti	1e-10
d1a2oa1	140	c.23.1.1 (A:1-140) Methylesterase CheB, N-terminal	2e-10
d2a9pa1	117	c.23.1.1 (A:2-118) DNA-binding response regulator	5e-10
d1qkka_	140	c.23.1.1 (A:) Transcriptional regulatory protein D	8e-10
d1s8na_	190	c.23.1.1 (A:) Probable two-component system transc	3e-09
d1yioa2	128	c.23.1.1 (A:3-130) Response regulatory protein Sty	3e-09
d1zgza1	120	c.23.1.1 (A:2-121) TorCAD operon transcriptional r	4e-09
d1xhfa1	121	c.23.1.1 (A:2-122) Aerobic respiration control pro	6e-09
d1dbwa_	123	c.23.1.1 (A:) Transcriptional regulatory protein F	2e-08
d1mvoa_	121	c.23.1.1 (A:) PhoP receiver domain {Bacillus subti	1e-07
d1ys7a2	121	c.23.1.1 (A:7-127) Transcriptional regulatory prot	1e-07
d1zh2a1	119	c.23.1.1 (A:2-120) Transcriptional regulatory prot	4e-07
d1qo0d_	189	c.23.1.3 (D:) Positive regulator of the amidase op	4e-07
d2pl1a1	119	c.23.1.1 (A:1-119) PhoP receiver domain {Escherich	6e-07
d1ny5a1	137	c.23.1.1 (A:1-137) Transcriptional activator sigm5	6e-07
d1p2fa2	120	c.23.1.1 (A:1-120) Response regulator DrrB {Thermo	1e-06
d1w25a2	153	c.23.1.1 (A:141-293) Response regulator PleD, rece	2e-06
d1kgsa2	122	c.23.1.1 (A:2-123) PhoB receiver domain {Thermotog	6e-06
d1w25a1	139	c.23.1.1 (A:2-140) Response regulator PleD, receiv	2e-05

>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 = 66.9 bits (163), Expect = 1e-14
 Identities = 32/179 (17%), Positives = 60/179 (33%), Gaps = 53/179 (29%)

Query: 25  SDTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLK 84
           S+   + VL +D++ V R V + LL    C+VT V S    L+   +   +         
Sbjct: 3   SNFTGLKVLVMDENGVSRMVTKGLLVHLGCEVTTVSSNEECLR---VVSHE--------- 50

Query: 85  VDLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFP 144
             ++  D CMPG+  Y++  +I                                      
Sbjct: 51  HKVVFMDVCMPGVENYQIALRIHEKFT--------------------------------- 77

Query: 145 SNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSD-VKRIKDYLTR 202
                      +   +V +S     +  ++C+  G +  ++KPV L +    + D L  
Sbjct: 78  -------KQRHQRPLLVALSGNTDKSTKEKCMSFGLDGVLLKPVSLDNIRDVLSDLLEP 129

>d1zesa1 c.23.1.1 (A:3-123) PhoB receiver domain {Escherichia coli [TaxId: 562]} Length = 121

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: PhoB receiver domain
species: Escherichia coli [TaxId: 562]

 Score = 63.4 bits (154), Expect = 2e-13
 Identities = 36/172 (20%), Positives = 62/172 (36%), Gaps = 55/172 (31%)

Query: 32  VLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITD 91
           +L V+D    R+++  +L  +  +    +    A+  L                DLI+ D
Sbjct: 3   ILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLNEPWP-----------DLILLD 51

Query: 92  YCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQD 151
           + +PG +G + +K +K                                            
Sbjct: 52  WMLPGGSGIQFIKHLK-------------------------------------------R 68

Query: 152 SSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSD-VKRIKDYLTR 202
            S  R+IPVV++++        R LE GA+D+I KP    + V RIK  + R
Sbjct: 69  ESMTRDIPVVMLTARGEEEDRVRGLETGADDYITKPFSPKELVARIKAVMRR 120

>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 = 63.2 bits (153), Expect = 4e-13
 Identities = 36/181 (19%), Positives = 63/181 (34%), Gaps = 53/181 (29%)

Query: 32  VLAVDDSFVDRKVIERLLTIS--SCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLII 89
           +  V+D+  D ++I+  L  S    +V  V  G  A+ +L  + E +    +  + DLI+
Sbjct: 5   IFLVEDNKADIRLIQEALANSTVPHEVVTVRDGMEAMAYLRQEGEYA----NASRPDLIL 60

Query: 90  TDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLE 149
            D  +P   G E+L +I                                           
Sbjct: 61  LDLNLPKKDGREVLAEI------------------------------------------- 77

Query: 150 QDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSD----VKRIKDYLTRDVN 205
           +    L+ IPVV++S+      I    +     +I K   LS     VK I+++      
Sbjct: 78  KSDPTLKRIPVVVLSTSINEDDIFHSYDLHVNCYITKSANLSQLFQIVKGIEEFWLSTAT 137

Query: 206 L 206
           L
Sbjct: 138 L 138

>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 = 62.3 bits (151), Expect = 5e-13
 Identities = 34/170 (20%), Positives = 55/170 (32%), Gaps = 57/170 (33%)

Query: 32  VLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITD 91
           +L VDD    R ++  +      +     +G +AL  +              + DL++ D
Sbjct: 4   ILIVDDQSGIRILLNEVFNKEGYQTFQAANGLQALDIV-----------TKERPDLVLLD 52

Query: 92  YCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQD 151
             +PGM G E+LK++KV                                           
Sbjct: 53  MKIPGMDGIEILKRMKVIDE---------------------------------------- 72

Query: 152 SSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSD-VKRIKDYL 200
                 I V+IM++   L  I    E GA     KP  + +    +K YL
Sbjct: 73  -----NIRVIIMTAYGELDMIQESKELGALTHFAKPFDIDEIRDAVKKYL 117

>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 = 2e-12
 Identities = 37/198 (18%), Positives = 70/198 (35%), Gaps = 69/198 (34%)

Query: 25  SDTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLK 84
           SD +++ +L VDD  ++R+++   L     +    + G             ++N      
Sbjct: 4   SDNDDMMILVVDDHPINRRLLADQLGSLGYQCKTANDG-----------VDALNVLSKNH 52

Query: 85  VDLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFP 144
           +D++++D  MP M GY L ++I+                                     
Sbjct: 53  IDIVLSDVNMPNMDGYRLTQRIRQLGLT-------------------------------- 80

Query: 145 SNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSDVK-RIKDYLTRD 203
                        +PV+ +++  +     RCLE G +  + KPV L  +K  +  Y  R 
Sbjct: 81  -------------LPVIGVTANALAEEKQRCLESGMDSCLSKPVTLDVIKQTLTLYAER- 126

Query: 204 VNLGNEGRGINKRKARES 221
                       RK+R+S
Sbjct: 127 -----------VRKSRDS 133

>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 = 61.2 bits (148), Expect = 2e-12
 Identities = 31/175 (17%), Positives = 60/175 (34%), Gaps = 52/175 (29%)

Query: 30  VHVLAVDDSFVDRKVIERLLTISSCK-VTAVDSGRRALQFLGLDEEQSINGFDGLKVDLI 88
           V +L V+D+ V+++VI+R+L +   + +     G+ A   +     +  N       ++I
Sbjct: 2   VKILVVEDNHVNQEVIKRMLNLEGIENIELACDGQEAFDKVKELTSKGEN------YNMI 55

Query: 89  ITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNL 148
             D  MP + G    K I+                                         
Sbjct: 56  FMDVQMPKVDGLLSTKMIR----------------------------------------- 74

Query: 149 EQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSDVK-RIKDYLTR 202
                     P+V +++    + I  CLE G   F+ KP+K   +K  + ++   
Sbjct: 75  ---RDLGYTSPIVALTAFADDSNIKECLESGMNGFLSKPIKRPKLKTILTEFCAA 126

>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 = 61.3 bits (148), Expect = 2e-12
 Identities = 34/182 (18%), Positives = 66/182 (36%), Gaps = 53/182 (29%)

Query: 31  HVLAVDDSFVDRKVIERLLTIS--SCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLI 88
            +L V+DS  D ++++ +L  S    ++  +  G  A+ FL    +Q     +  + +LI
Sbjct: 5   VILLVEDSKADSRLVQEVLKTSTIDHELIILRDGLAAMAFL----QQQGEYENSPRPNLI 60

Query: 89  ITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNL 148
           + D  +P   G E+L +IK                                         
Sbjct: 61  LLDLNLPKKDGREVLAEIK----------------------------------------- 79

Query: 149 EQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSD----VKRIKDYLTRDV 204
              +  L+ IPVV++++ +    +    E     ++ K   L D    V+ I+ +    V
Sbjct: 80  --QNPDLKRIPVVVLTTSHNEDDVIASYELHVNCYLTKSRNLKDLFKMVQGIESFWLETV 137

Query: 205 NL 206
            L
Sbjct: 138 TL 139

>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 = 60.6 bits (147), Expect = 2e-12
 Identities = 23/176 (13%), Positives = 56/176 (31%), Gaps = 58/176 (32%)

Query: 30  VHVLAVDDSFVDRKVIERLLTISSCK--VTAVDSGRRALQFLGLDEEQSINGFDGLKVDL 87
           + V   DD+     +++  ++       +    +G+  LQ L           +  + D+
Sbjct: 2   IKVCIADDNRELVSLLDEYISSQPDMEVIGTAYNGQDCLQML-----------EEKRPDI 50

Query: 88  IITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNN 147
           ++ D  MP + G  +L++I+                                        
Sbjct: 51  LLLDIIMPHLDGLAVLERIRAGFE------------------------------------ 74

Query: 148 LEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSD-VKRIKDYLTR 202
                    +  V+++++        + +E GA  FI+KP  + +    I+    +
Sbjct: 75  --------HQPNVIMLTAFGQEDVTKKAVELGASYFILKPFDMENLAHHIRQVYGK 122

>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 = 60.3 bits (146), Expect = 2e-12
 Identities = 24/174 (13%), Positives = 46/174 (26%), Gaps = 59/174 (33%)

Query: 28  EEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDL 87
           +   V  V+D      +I+  L     +VT   SG    Q                  DL
Sbjct: 1   QPFRVTLVEDEPSHATLIQYHLNQLGAEVTVHPSGSAFFQHR----------SQLSTCDL 50

Query: 88  IITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNN 147
           +I    +  ++ + LL  +K  T                                     
Sbjct: 51  LIVSDQLVDLSIFSLLDIVKEQTK------------------------------------ 74

Query: 148 LEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSD-VKRIKDYL 200
                    +  V+I+++      +    E     ++ KP  +S+    I  + 
Sbjct: 75  ---------QPSVLILTTGR--HELIESSEHNL-SYLQKPFAISELRAAIDYHK 116

>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 = 60.2 bits (145), Expect = 5e-12
 Identities = 35/173 (20%), Positives = 63/173 (36%), Gaps = 47/173 (27%)

Query: 31  HVLAVDDSFVDRKVIERLLTIS--SCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLI 88
            +L V+DS  D    +RLL        +    +G +AL F         N     +  +I
Sbjct: 8   PLLVVEDSDEDFSTFQRLLQREGVVNPIYRCITGDQALDF-LYQTGSYCNPDIAPRPAVI 66

Query: 89  ITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNL 148
           + D  +PG  G E+L++IK                                         
Sbjct: 67  LLDLNLPGTDGREVLQEIK----------------------------------------- 85

Query: 149 EQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSD-VKRIKDYL 200
                 L++IPVVIM++ +    I+ C       +IVKP+++    + ++ ++
Sbjct: 86  --QDEVLKKIPVVIMTTSSNPKDIEICYSYSISSYIVKPLEIDRLTETVQTFI 136

>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 = 59.3 bits (143), Expect = 7e-12
 Identities = 36/172 (20%), Positives = 59/172 (34%), Gaps = 55/172 (31%)

Query: 32  VLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITD 91
           VL V+D+ ++ K+   LL     +      G  AL                 K DLI+ D
Sbjct: 4   VLIVEDNELNMKLFHDLLEAQGYETLQTREGLSALSIA-----------RENKPDLILMD 52

Query: 92  YCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQD 151
             +P ++G E+ K +K                                           +
Sbjct: 53  IQLPEISGLEVTKWLK-------------------------------------------E 69

Query: 152 SSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSD-VKRIKDYLTR 202
              L  IPVV +++  +    +R  E G E +I KP+ +   ++ IK  L R
Sbjct: 70  DDDLAHIPVVAVTAFAMKGDEERIREGGCEAYISKPISVVHFLETIKRLLER 121

>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 = 59.1 bits (143), Expect = 1e-11
 Identities = 30/180 (16%), Positives = 63/180 (35%), Gaps = 59/180 (32%)

Query: 28  EEVHVLAVDDSFVDRKVIERLLTISS--CKVTAVDSGRRALQFLGLDEEQSINGFDGLKV 85
           E   +L +DD  + R  +++L++++     V    +G + ++             + L  
Sbjct: 1   EPATILLIDDHPMLRTGVKQLISMAPDITVVGEASNGEQGIELA-----------ESLDP 49

Query: 86  DLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPS 145
           DLI+ D  MPGM G E L K++  +                                   
Sbjct: 50  DLILLDLNMPGMNGLETLDKLREKSL---------------------------------- 75

Query: 146 NNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSD-VKRIKDYLTRDV 204
                         +V+ S  N    +   L+ GA+ +++K ++  D +K +      ++
Sbjct: 76  -----------SGRIVVFSVSNHEEDVVTALKRGADGYLLKDMEPEDLLKALHQAAAGEM 124

>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 = 57.4 bits (138), Expect = 3e-11
 Identities = 37/173 (21%), Positives = 60/173 (34%), Gaps = 57/173 (32%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
            V  VDD    R V+ER L  +    T  ++G   L  L                D++++
Sbjct: 5   IVWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLAALASKTP-----------DVLLS 53

Query: 91  DYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQ 150
           D  MPGM G  LLK+IK   P                                       
Sbjct: 54  DIRMPGMDGLALLKQIKQRHP--------------------------------------- 74

Query: 151 DSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSD-VKRIKDYLTR 202
                  +PV+IM++ + L       + GA D++ KP  + + V  ++  ++ 
Sbjct: 75  ------MLPVIIMTAHSDLDAAVSAYQQGAFDYLPKPFDIDEAVALVERAISH 121

>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 = 56.5 bits (136), Expect = 6e-11
 Identities = 33/169 (19%), Positives = 61/169 (36%), Gaps = 58/169 (34%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCK-VTAVDSGRRALQFLGLDEEQSINGFDGLKVDLII 89
            VL VDD+   R +++ ++T +  +      +GR A++            +  LK D++ 
Sbjct: 3   RVLIVDDAAFMRMMLKDIITKAGYEVAGEATNGREAVEK-----------YKELKPDIVT 51

Query: 90  TDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLE 149
            D  MP M G + +K+I    P                                      
Sbjct: 52  MDITMPEMNGIDAIKEIMKIDP-------------------------------------- 73

Query: 150 QDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSD-VKRIK 197
                     +++ S+    A +   ++ GA+DFIVKP + S  V+ + 
Sbjct: 74  -------NAKIIVCSAMGQQAMVIEAIKAGAKDFIVKPFQPSRVVEALN 115

>d1p6qa_ c.23.1.1 (A:) CheY protein {Sinorhizobium meliloti, CheY2 [TaxId: 382]} Length = 129

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: CheY protein
species: Sinorhizobium meliloti, CheY2 [TaxId: 382]

 Score = 56.1 bits (135), Expect = 1e-10
 Identities = 30/180 (16%), Positives = 60/180 (33%), Gaps = 56/180 (31%)

Query: 25  SDTEEVHVLAVDDSFVDRKVIERLLTISSCK-VTAVDSGRRALQFLGLDEEQSINGFDGL 83
           S  E++ VL VDD    R ++   L     K +TA   G + ++ +  +           
Sbjct: 2   SLAEKIKVLIVDDQVTSRLLLGDALQQLGFKQITAAGDGEQGMKIMAQNPH--------- 52

Query: 84  KVDLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFF 143
              L+I+D+ MP M G  LL+ ++                                    
Sbjct: 53  --HLVISDFNMPKMDGLGLLQAVR------------------------------------ 74

Query: 144 PSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSD-VKRIKDYLTR 202
                   + A ++   +I++++   A + +    GA + + KP  +      I+     
Sbjct: 75  -------ANPATKKAAFIILTAQGDRALVQKAAALGANNVLAKPFTIEKMKAAIEAVFGA 127

>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 = 55.7 bits (134), Expect = 2e-10
 Identities = 29/163 (17%), Positives = 50/163 (30%), Gaps = 57/163 (34%)

Query: 28  EEVHVLAVDDSFVDRKVIERLLTISS--CKVTAVDSGRRALQFLGLDEEQSINGFDGLKV 85
            ++ VL+VDDS + R+++  ++   S    V        A   +                
Sbjct: 2   SKIRVLSVDDSALMRQIMTEIINSHSDMEMVATAPDPLVARDLI-----------KKFNP 50

Query: 86  DLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPS 145
           D++  D  MP M G + L+K+    P                                  
Sbjct: 51  DVLTLDVEMPRMDGLDFLEKLMRLRPM--------------------------------- 77

Query: 146 NNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPV 188
                       + V  ++ +     + R LE GA DF+ KP 
Sbjct: 78  ----------PVVMVSSLTGKGSEVTL-RALELGAIDFVTKPQ 109

>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 = 53.8 bits (129), Expect = 5e-10
 Identities = 33/172 (19%), Positives = 60/172 (34%), Gaps = 58/172 (33%)

Query: 32  VLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITD 91
           +L VDD      +I+  +T    +V    +GR AL+             +  + D+II D
Sbjct: 3   ILIVDDEKPISDIIKFNMTKEGYEVVTAFNGREALEQF-----------EAEQPDIIILD 51

Query: 92  YCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQD 151
             +P + G E+ K I+                                            
Sbjct: 52  LMLPEIDGLEVAKTIR-------------------------------------------- 67

Query: 152 SSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSD-VKRIKDYLTR 202
                 +P++++S+++        LE GA+D++ KP    +   R+K  L R
Sbjct: 68  --KTSSVPILMLSAKDSEFDKVIGLELGADDYVTKPFSNRELQARVKALLRR 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 = 53.9 bits (129), Expect = 8e-10
 Identities = 30/173 (17%), Positives = 59/173 (34%), Gaps = 57/173 (32%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
            V  +DD    RK +++ L ++   V++  S             +++ G       ++I+
Sbjct: 2   SVFLIDDDRDLRKAMQQTLELAGFTVSSFASA-----------TEALAGLSADFAGIVIS 50

Query: 91  DYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQ 150
           D  MPGM G  L +KI    P                                       
Sbjct: 51  DIRMPGMDGLALFRKILALDP--------------------------------------- 71

Query: 151 DSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSD-VKRIKDYLTR 202
                 ++P+++++    +    + ++DGA DFI KP      V+  +    +
Sbjct: 72  ------DLPMILVTGHGDIPMAVQAIQDGAYDFIAKPFAADRLVQSARRAEEK 118

>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 = 53.3 bits (127), Expect = 3e-09
 Identities = 29/174 (16%), Positives = 59/174 (33%), Gaps = 59/174 (33%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAV-DSGRRALQFLGLDEEQSINGFDGLKVDLII 89
            VL  +D  + R  +  +L     ++      G+ A++             +  K DL+I
Sbjct: 5   RVLIAEDEALIRMDLAEMLREEGYEIVGEAGDGQEAVEL-----------AELHKPDLVI 53

Query: 90  TDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLE 149
            D  MP   G +   +I                                           
Sbjct: 54  MDVKMPRRDGIDAASEIA------------------------------------------ 71

Query: 150 QDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSD-VKRIKDYLTR 202
               + R  P+V++++ +    ++R  + GA  ++VKP  +SD +  I+  ++R
Sbjct: 72  ----SKRIAPIVVLTAFSQRDLVERARDAGAMAYLVKPFSISDLIPAIELAVSR 121

>d1yioa2 c.23.1.1 (A:3-130) Response regulatory protein StyR, N-terminal domain {Pseudomonas fluorescens [TaxId: 294]} Length = 128

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulatory protein StyR, N-terminal domain
species: Pseudomonas fluorescens [TaxId: 294]

 Score = 51.6 bits (123), Expect = 3e-09
 Identities = 29/173 (16%), Positives = 55/173 (31%), Gaps = 57/173 (32%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
            V  VDD    R+ +  LL  +  +V   D     L+    ++              ++ 
Sbjct: 4   TVFVVDDDMSVREGLRNLLRSAGFEVETFDCASTFLEHRRPEQH-----------GCLVL 52

Query: 91  DYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQ 150
           D  MPGM+G EL +++   +                                        
Sbjct: 53  DMRMPGMSGIELQEQLTAISD--------------------------------------- 73

Query: 151 DSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSD-VKRIKDYLTR 202
                  IP+V +++   +    R ++ GA +F+ KP +    +  I+  L  
Sbjct: 74  ------GIPIVFITAHGDIPMTVRAMKAGAIEFLPKPFEEQALLDAIEQGLQL 120

>d1zgza1 c.23.1.1 (A:2-121) TorCAD operon transcriptional regulator TorD, N-terminal domain {Escherichia coli [TaxId: 562]} Length = 120

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: TorCAD operon transcriptional regulator TorD, N-terminal domain
species: Escherichia coli [TaxId: 562]

 Score = 51.5 bits (123), Expect = 4e-09
 Identities = 29/173 (16%), Positives = 58/173 (33%), Gaps = 58/173 (33%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
           H++ V+D  V +  ++   T     V+   SG    + +               VDLI+ 
Sbjct: 3   HIVIVEDEPVTQARLQSYFTQEGYTVSVTASGAGLREIM-----------QNQSVDLILL 51

Query: 91  DYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQ 150
           D  +P   G  L + ++  +                                        
Sbjct: 52  DINLPDENGLMLTRALRERSTV-------------------------------------- 73

Query: 151 DSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSD-VKRIKDYLTR 202
                    +++++  +        LE GA+D++ KP++L + V R+K+ L R
Sbjct: 74  --------GIILVTGRSDRIDRIVGLEMGADDYVTKPLELRELVVRVKNLLWR 118

>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 = 50.8 bits (121), Expect = 6e-09
 Identities = 28/173 (16%), Positives = 53/173 (30%), Gaps = 58/173 (33%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
           H+L V+D  V R  ++ +       V     G    Q L               ++L+I 
Sbjct: 4   HILIVEDELVTRNTLKSIFEAEGYDVFEATDGAEMHQIL-----------SEYDINLVIM 52

Query: 91  DYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQ 150
           D  +PG  G  L ++++                                           
Sbjct: 53  DINLPGKNGLLLARELR------------------------------------------- 69

Query: 151 DSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSD-VKRIKDYLTR 202
                  + ++ ++  +        LE GA+D+I KP    +   R ++ L+R
Sbjct: 70  ---EQANVALMFLTGRDNEVDKILGLEIGADDYITKPFNPRELTIRARNLLSR 119

>d1dbwa_ c.23.1.1 (A:) Transcriptional regulatory protein FixJ, receiver domain {Rhizobium meliloti [TaxId: 382]} Length = 123

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Transcriptional regulatory protein FixJ, receiver domain
species: Rhizobium meliloti [TaxId: 382]

 Score = 49.6 bits (118), Expect = 2e-08
 Identities = 29/176 (16%), Positives = 55/176 (31%), Gaps = 57/176 (32%)

Query: 28  EEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDL 87
           ++  V  VDD    RK +  +LT++   V    S    L F              ++  +
Sbjct: 2   QDYTVHIVDDEEPVRKSLAFMLTMNGFAVKMHQSAEAFLAFA-----------PDVRNGV 50

Query: 88  IITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNN 147
           ++TD  MP M+G ELL+ +                                         
Sbjct: 51  LVTDLRMPDMSGVELLRNLGDLKINIP--------------------------------- 77

Query: 148 LEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSD-VKRIKDYLTR 202
                        ++++    +      ++ GA DFI KP + +  ++ I+     
Sbjct: 78  ------------SIVITGHGDVPMAVEAMKAGAVDFIEKPFEDTVIIEAIERASEH 121

>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 = 47.4 bits (112), Expect = 1e-07
 Identities = 30/173 (17%), Positives = 56/173 (32%), Gaps = 57/173 (32%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
            +L VDD      +++  L  S   V     G  AL+             +  K DLI+ 
Sbjct: 4   KILVVDDEESIVTLLQYNLERSGYDVITASDGEEALKK-----------AETEKPDLIVL 52

Query: 91  DYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQ 150
           D  +P + G E+ K+++                                           
Sbjct: 53  DVMLPKLDGIEVCKQLRQQKLMFP------------------------------------ 76

Query: 151 DSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSD-VKRIKDYLTR 202
                    ++++++++        LE GA+D++ KP    +   R+K  L R
Sbjct: 77  ---------ILMLTAKDEEFDKVLGLELGADDYMTKPFSPREVNARVKAILRR 120

>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 = 47.3 bits (112), Expect = 1e-07
 Identities = 36/173 (20%), Positives = 60/173 (34%), Gaps = 57/173 (32%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
            VL VDD       +ER L +S  +V     G  AL+    +           + D I+ 
Sbjct: 3   RVLVVDDDSDVLASLERGLRLSGFEVATAVDGAEALRSATEN-----------RPDAIVL 51

Query: 91  DYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQ 150
           D  MP + G  ++  ++                                           
Sbjct: 52  DINMPVLDGVSVVTALRAMDND-------------------------------------- 73

Query: 151 DSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSD-VKRIKDYLTR 202
                  +PV ++S+ + +      LE GA+D++VKP  L++ V R+K  L R
Sbjct: 74  -------VPVCVLSARSSVDDRVAGLEAGADDYLVKPFVLAELVARVKALLRR 119

>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 = 45.9 bits (108), Expect = 4e-07
 Identities = 30/172 (17%), Positives = 57/172 (33%), Gaps = 58/172 (33%)

Query: 32  VLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITD 91
           VL V+D    R+ +   L     +V   ++ +R L                 K DLII D
Sbjct: 3   VLIVEDEQAIRRFLRTALEGDGMRVFEAETLQRGLLEA-----------ATRKPDLIILD 51

Query: 92  YCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQD 151
             +P   G E ++ ++  +                                         
Sbjct: 52  LGLPDGDGIEFIRDLRQWSAV--------------------------------------- 72

Query: 152 SSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSD-VKRIKDYLTR 202
                  PV+++S+ +  +     L+ GA+D++ KP  + +   R++  L R
Sbjct: 73  -------PVIVLSARSEESDKIAALDAGADDYLSKPFGIGELQARLRVALRR 117

>d1qo0d_ c.23.1.3 (D:) Positive regulator of the amidase operon AmiR {Pseudomonas aeruginosa [TaxId: 287]} Length = 189

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: Positive regulator of the amidase operon AmiR
domain: Positive regulator of the amidase operon AmiR
species: Pseudomonas aeruginosa [TaxId: 287]

 Score = 46.9 bits (110), Expect = 4e-07
 Identities = 15/163 (9%), Positives = 27/163 (16%), Gaps = 61/163 (37%)

Query: 25  SDTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLK 84
               E+ VL ++        +   L    C V        A                   
Sbjct: 7   GSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAFDVP--------------- 51

Query: 85  VDLIITDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFP 144
           VD++ T                                                      
Sbjct: 52  VDVVFTSIFQNRHHDEIAALLAA------------------------------------- 74

Query: 145 SNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKP 187
                          +V +      A + + +E      I +P
Sbjct: 75  ---------GTPRTTLVALVEYESPAVLSQIIELECHGVITQP 108

>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 = 45.1 bits (106), Expect = 6e-07
 Identities = 22/172 (12%), Positives = 55/172 (31%), Gaps = 57/172 (33%)

Query: 32  VLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITD 91
           VL V+D+ + R  ++  +  +  +V   +  + A  +L           +    D+ I D
Sbjct: 3   VLVVEDNALLRHHLKVQIQDAGHQVDDAEDAKEADYYL-----------NEHIPDIAIVD 51

Query: 92  YCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQD 151
             +P   G  L+++ +                                            
Sbjct: 52  LGLPDEDGLSLIRRWRSNDVSLP------------------------------------- 74

Query: 152 SSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSD-VKRIKDYLTR 202
                   ++++++          L  GA+D++ KP  + + + R++  + R
Sbjct: 75  --------ILVLTARESWQDKVEVLSAGADDYVTKPFHIEEVMARMQALMRR 118

>d1ny5a1 c.23.1.1 (A:1-137) Transcriptional activator sigm54 (NtrC1), N-terminal domain {Aquifex aeolicus [TaxId: 63363]} Length = 137

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Transcriptional activator sigm54 (NtrC1), N-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

 Score = 45.8 bits (108), Expect = 6e-07
 Identities = 31/173 (17%), Positives = 60/173 (34%), Gaps = 57/173 (32%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
           +VL ++D  V R ++E  L++   KV + + G+ A + L                ++++ 
Sbjct: 2   NVLVIEDDKVFRGLLEEYLSMKGIKVESAERGKEAYKLLSEKHF-----------NVVLL 50

Query: 91  DYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQ 150
           D  +P + G E+LK IK  +P                                       
Sbjct: 51  DLLLPDVNGLEILKWIKERSP--------------------------------------- 71

Query: 151 DSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSD-VKRIKDYLTR 202
                 E  V++++    +      ++ GA DF+ KP  L +    I   +  
Sbjct: 72  ------ETEVIVITGHGTIKTAVEAMKMGAYDFLTKPCMLEEIELTINKAIEH 118

>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 = 44.6 bits (105), Expect = 1e-06
 Identities = 29/173 (16%), Positives = 56/173 (32%), Gaps = 60/173 (34%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
            +  VDD     K +   L     +V    +G   L      +E++          +++ 
Sbjct: 4   KIAVVDDDKNILKKVSEKLQ-QLGRVKTFLTGEDFLN-----DEEAF--------HVVVL 49

Query: 91  DYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQ 150
           D  +P  +GYE+ + IK T P                                       
Sbjct: 50  DVMLPDYSGYEICRMIKETRPET------------------------------------- 72

Query: 151 DSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSD-VKRIKDYLTR 202
                    V++++  +    + +  E GA+D++ KP      + R+K +L R
Sbjct: 73  --------WVILLTLLSDDESVLKGFEAGADDYVTKPFNPEILLARVKRFLER 117

>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 = 44.3 bits (104), Expect = 2e-06
 Identities = 27/173 (15%), Positives = 49/173 (28%), Gaps = 57/173 (32%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
            VL VDD+    + +   L +    V   D  +  +               G  VDL+I 
Sbjct: 15  RVLIVDDNERQAQRVAAELGVEHRPVIESDPEKAKI-------------SAGGPVDLVIV 61

Query: 91  DYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQ 150
           +       G      ++                                           
Sbjct: 62  NAAAKNFDGLRFTAALR------------------------------------------- 78

Query: 151 DSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSD-VKRIKDYLTR 202
                R++PV+ M   +   R+ + LE G  D + +P+   +   R+K  + R
Sbjct: 79  SEERTRQLPVLAMVDPDDRGRMVKALEIGVNDILSRPIDPQELSARVKTQIQR 131

>d1kgsa2 c.23.1.1 (A:2-123) PhoB receiver domain {Thermotoga maritima [TaxId: 2336]} Length = 122

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: PhoB receiver domain
species: Thermotoga maritima [TaxId: 2336]

 Score = 42.4 bits (99), Expect = 6e-06
 Identities = 28/174 (16%), Positives = 55/174 (31%), Gaps = 57/174 (32%)

Query: 30  VHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLII 89
           V VL V+D      +I   L      V     G   +                   D++I
Sbjct: 2   VRVLVVEDERDLADLITEALKKEMFTVDVCYDGEEGMYMA-----------LNEPFDVVI 50

Query: 90  TDYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLE 149
            D  +P   G+E+LK ++                                          
Sbjct: 51  LDIMLPVHDGWEILKSMR------------------------------------------ 68

Query: 150 QDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSD-VKRIKDYLTR 202
               +    PV+++++ + +    + L  GA+D++ KP  L + + R++  + R
Sbjct: 69  ---ESGVNTPVLMLTALSDVEYRVKGLNMGADDYLPKPFDLRELIARVRALIRR 119

>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 = 41.4 bits (96), Expect = 2e-05
 Identities = 35/173 (20%), Positives = 59/173 (34%), Gaps = 55/173 (31%)

Query: 31  HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIIT 90
            +L VDD   + +++E  LT    +V+    G  AL                   D+I+ 
Sbjct: 3   RILVVDDIEANVRLLEAKLTAEYYEVSTAMDGPTALAM-----------AARDLPDIILL 51

Query: 91  DYCMPGMTGYELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQ 150
           D  MPGM G+ + +K+                                           +
Sbjct: 52  DVMMPGMDGFTVCRKL-------------------------------------------K 68

Query: 151 DSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKLSD-VKRIKDYLTR 202
           D    R IPVV++++ +      + LE GA DF+ KP+       R++     
Sbjct: 69  DDPTTRHIPVVLITALDGRGDRIQGLESGASDFLTKPIDDVMLFARVRSLTRF 121

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	276
d2pl1a1	119	PhoP receiver domain {Escherichia coli [TaxId: 562	99.95
d1dbwa_	123	Transcriptional regulatory protein FixJ, receiver	99.95
d1qkka_	140	Transcriptional regulatory protein DctD, receiver	99.95
d2ayxa1	133	Sensor kinase protein RcsC, C-terminal domain {Esc	99.95
d1ny5a1	137	Transcriptional activator sigm54 (NtrC1), N-termin	99.95
d1peya_	119	Sporulation response regulator Spo0F {Bacillus sub	99.94
d1kgsa2	122	PhoB receiver domain {Thermotoga maritima [TaxId:	99.94
d1ys7a2	121	Transcriptional regulatory protein PrrA, N-termina	99.94
d1zesa1	121	PhoB receiver domain {Escherichia coli [TaxId: 562	99.94
d1krwa_	123	NTRC receiver domain {Salmonella typhimurium [TaxI	99.94
d1dcfa_	134	Receiver domain of the ethylene receptor {Thale cr	99.94
d1mvoa_	121	PhoP receiver domain {Bacillus subtilis [TaxId: 14	99.94
d1zh2a1	119	Transcriptional regulatory protein KdpE, N-termina	99.94
d1i3ca_	144	Response regulator for cyanobacterial phytochrome	99.94
d2r25b1	128	Response regulator Sin1 {Baker's yeast (Saccharomy	99.94
d1mb3a_	123	Cell division response regulator DivK {Caulobacter	99.94
d1zgza1	120	TorCAD operon transcriptional regulator TorD, N-te	99.94
d1k68a_	140	Response regulator for cyanobacterial phytochrome	99.93
d1jbea_	128	CheY protein {Escherichia coli [TaxId: 562]}	99.93
d1u0sy_	118	CheY protein {Thermotoga maritima [TaxId: 2336]}	99.93
d2a9pa1	117	DNA-binding response regulator MicA, N-terminal do	99.93
d1s8na_	190	Probable two-component system transcriptional regu	99.93
d1yioa2	128	Response regulatory protein StyR, N-terminal domai	99.93
d1w25a1	139	Response regulator PleD, receiver domain {Caulobac	99.93
d1p6qa_	129	CheY protein {Sinorhizobium meliloti, CheY2 [TaxId	99.93
d1xhfa1	121	Aerobic respiration control protein ArcA, N-termin	99.93
d1a04a2	138	Nitrate/nitrite response regulator (NarL), receive	99.93
d1dz3a_	123	Sporulation response regulator Spo0A {Bacillus ste	99.92
d1p2fa2	120	Response regulator DrrB {Thermotoga maritima [TaxI	99.92
d1k66a_	149	Response regulator for cyanobacterial phytochrome	99.92
d1w25a2	153	Response regulator PleD, receiver domain {Caulobac	99.91
d2b4aa1	118	Hypothetical protein BH3024 {Bacillus halodurans [	99.9
d1a2oa1	140	Methylesterase CheB, N-terminal domain {Salmonella	99.9
d1qo0d_	189	Positive regulator of the amidase operon AmiR {Pse	99.85
d7reqa2	168	Methylmalonyl-CoA mutase alpha subunit, C-terminal	94.26
d1ccwa_	137	Glutamate mutase, small subunit {Clostridium cochl	91.43
d1xrsb1	160	D-lysine 5,6-aminomutase beta subunit KamE, C-term	85.82

>d2pl1a1 c.23.1.1 (A:1-119) PhoP receiver domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: PhoP receiver domain
species: Escherichia coli [TaxId: 562]

Probab=99.95  E-value=3.2e-27  Score=188.07  Aligned_cols=117  Identities=21%  Similarity=0.400  Sum_probs=109.3

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhh
Q 023816           30 VHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVT  109 (276)
Q Consensus        30 ~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~  109 (276)
                      +|||||||++..++.++.+|+..||+|..+.+|++|++.+           ++..||+||+|+.||++||++++++||+.
T Consensus         1 mrILvVDDd~~~~~~l~~~L~~~G~~v~~a~~g~eal~~l-----------~~~~~dliilD~~mP~~~G~e~~~~i~~~   69 (119)
T d2pl1a1           1 MRVLVVEDNALLRHHLKVQIQDAGHQVDDAEDAKEADYYL-----------NEHIPDIAIVDLGLPDEDGLSLIRRWRSN   69 (119)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHH-----------HHSCCSEEEECSCCSSSCHHHHHHHHHHT
T ss_pred             CEEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHH-----------HhcccceeehhccCCCchhHHHHHHHHhc
Confidence            6899999999999999999999999999999999999999           56789999999999999999999999986


Q ss_pred             CCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCC
Q 023816          110 TPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVK  189 (276)
Q Consensus       110 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~  189 (276)
                      .+                                             .+|||++|+....+...+|++.||+|||.||++
T Consensus        70 ~~---------------------------------------------~~pvi~lt~~~~~~~~~~a~~~Ga~~yl~KP~~  104 (119)
T d2pl1a1          70 DV---------------------------------------------SLPILVLTARESWQDKVEVLSAGADDYVTKPFH  104 (119)
T ss_dssp             TC---------------------------------------------CSCEEEEESCCCHHHHHHHHHTTCSEEEESSCC
T ss_pred             Cc---------------------------------------------ccceEeeeccCCHHHHHHHHHcCCCEEEECCCC
Confidence            65                                             799999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHH
Q 023816          190 LSDVKRIKDYLTR  202 (276)
Q Consensus       190 ~~~L~~~~~~l~~  202 (276)
                      .++|...++.+.+
T Consensus       105 ~~~L~~~v~~~lr  117 (119)
T d2pl1a1         105 IEEVMARMQALMR  117 (119)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHc
Confidence            9999766666554

>d1dbwa_ c.23.1.1 (A:) Transcriptional regulatory protein FixJ, receiver domain {Rhizobium meliloti [TaxId: 382]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Transcriptional regulatory protein FixJ, receiver domain
species: Rhizobium meliloti [TaxId: 382]

Probab=99.95  E-value=5.7e-27  Score=187.58  Aligned_cols=119  Identities=25%  Similarity=0.374  Sum_probs=110.8

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHH
Q 023816           27 TEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKI  106 (276)
Q Consensus        27 ~~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~I  106 (276)
                      |...+||||||++..++.++.+|+..||+|..+.+|++|++.+           +...||+||+|+.||++||++++++|
T Consensus         1 M~~~~ILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~~al~~~-----------~~~~~dlvi~D~~mp~~~G~e~~~~l   69 (123)
T d1dbwa_           1 MQDYTVHIVDDEEPVRKSLAFMLTMNGFAVKMHQSAEAFLAFA-----------PDVRNGVLVTDLRMPDMSGVELLRNL   69 (123)
T ss_dssp             CCCCEEEEEESSHHHHHHHHHHHHHTTCEEEEESCHHHHHHHG-----------GGCCSEEEEEECCSTTSCHHHHHHHH
T ss_pred             CCCCEEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHH-----------hhcCCcEEEEeccCccccchHHHHHH
Confidence            4578999999999999999999999999999999999999999           66789999999999999999999999


Q ss_pred             HhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeC
Q 023816          107 KVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVK  186 (276)
Q Consensus       107 r~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~K  186 (276)
                      |+..|                                             ++|||++|++.+.+...+|++.||+|||.|
T Consensus        70 r~~~~---------------------------------------------~~~iI~lt~~~~~~~~~~a~~~Ga~~yl~K  104 (123)
T d1dbwa_          70 GDLKI---------------------------------------------NIPSIVITGHGDVPMAVEAMKAGAVDFIEK  104 (123)
T ss_dssp             HHTTC---------------------------------------------CCCEEEEECTTCHHHHHHHHHTTCSEEEES
T ss_pred             HhcCC---------------------------------------------CCeEEEEEeeCCHHHHHHHHHCCCCEEEEC
Confidence            98777                                             899999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHH
Q 023816          187 PVKLSDVKRIKDYLT  201 (276)
Q Consensus       187 Pv~~~~L~~~~~~l~  201 (276)
                      |++.++|...+++..
T Consensus       105 P~~~~~L~~~i~~a~  119 (123)
T d1dbwa_         105 PFEDTVIIEAIERAS  119 (123)
T ss_dssp             SCCHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHH
Confidence            999999976665543

>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=99.95  E-value=2.7e-27  Score=193.32  Aligned_cols=123  Identities=27%  Similarity=0.424  Sum_probs=112.7

Q ss_pred             EEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhhC
Q 023816           31 HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVTT  110 (276)
Q Consensus        31 ~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~~  110 (276)
                      +||||||++.++..++.+|+..||++..+.||++|++.+           +...||+||+|+.||+|||++++++||+..
T Consensus         2 ~ILiVDDd~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l-----------~~~~~dlil~D~~mP~~~G~el~~~lr~~~   70 (140)
T d1qkka_           2 SVFLIDDDRDLRKAMQQTLELAGFTVSSFASATEALAGL-----------SADFAGIVISDIRMPGMDGLALFRKILALD   70 (140)
T ss_dssp             EEEEECSCHHHHHHHHHHHHHTTCEEEEESCHHHHHHTC-----------CTTCCSEEEEESCCSSSCHHHHHHHHHHHC
T ss_pred             EEEEEECCHHHHHHHHHHHHHCCCEEEEeCChHHHHHHH-----------hccCcchHHHhhccCCCCHHHHHHHHHHhC
Confidence            799999999999999999999999999999999999999           778999999999999999999999999987


Q ss_pred             CCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCCH
Q 023816          111 PFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKL  190 (276)
Q Consensus       111 p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~~  190 (276)
                      |                                             ++|||++|++.+.+...+|++.||+|||.||++.
T Consensus        71 ~---------------------------------------------~~pvI~lT~~~~~~~~~~a~~~Ga~dyl~KP~~~  105 (140)
T d1qkka_          71 P---------------------------------------------DLPMILVTGHGDIPMAVQAIQDGAYDFIAKPFAA  105 (140)
T ss_dssp             T---------------------------------------------TSCEEEEECGGGHHHHHHHHHTTCCEEEESSCCH
T ss_pred             C---------------------------------------------CCcEEEEECCCCHHHHHHHHHcCCCEeecCCCCH
Confidence            7                                             8999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhhhcccc
Q 023816          191 SDVKRIKDYLTRDVNLGNE  209 (276)
Q Consensus       191 ~~L~~~~~~l~~~~~~~~~  209 (276)
                      ++|...+....+...+..+
T Consensus       106 ~~L~~~i~~~~~~~~~~~e  124 (140)
T d1qkka_         106 DRLVQSARRAEEKRRLVME  124 (140)
T ss_dssp             HHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHH
Confidence            9997666665554444433

>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=99.95  E-value=2.5e-27  Score=192.02  Aligned_cols=124  Identities=27%  Similarity=0.516  Sum_probs=114.6

Q ss_pred             CCCCCccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHH
Q 023816           24 PSDTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELL  103 (276)
Q Consensus        24 ~~~~~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell  103 (276)
                      .++...++||||||++.+++.+.++|+..||+|..+.+|.+|++.+           ....||+||+|++||++||++++
T Consensus         3 ~~~~~~~~ILiVDD~~~~~~~l~~~L~~~g~~v~~a~~g~ea~~~~-----------~~~~~dlillD~~mP~~dG~el~   71 (133)
T d2ayxa1           3 VSDNDDMMILVVDDHPINRRLLADQLGSLGYQCKTANDGVDALNVL-----------SKNHIDIVLSDVNMPNMDGYRLT   71 (133)
T ss_dssp             CCCCCCCEEEEEESSHHHHHHHHHHHHHHTSEEEEECCSHHHHHHH-----------HHSCCSEEEEEESSCSSCCHHHH
T ss_pred             CCCCCCCEEEEEECCHHHHHHHHHHHHHcCCEEEEECcHHHHHHHH-----------hccCceEEEEeccCCCCCHHHHH
Confidence            4566789999999999999999999999999999999999999999           56789999999999999999999


Q ss_pred             HHHHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeE
Q 023816          104 KKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDF  183 (276)
Q Consensus       104 ~~Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~  183 (276)
                      ++||+..+                                             .+|||++|++...+...+|++.|++||
T Consensus        72 ~~ir~~~~---------------------------------------------~~pii~lt~~~~~~~~~~~~~~G~~~~  106 (133)
T d2ayxa1          72 QRIRQLGL---------------------------------------------TLPVIGVTANALAEEKQRCLESGMDSC  106 (133)
T ss_dssp             HHHHHHHC---------------------------------------------CSCEEEEESSTTSHHHHHHHHCCCEEE
T ss_pred             HHHHHhCC---------------------------------------------CCCEEEEeccCCHHHHHHHHHcCCCEE
Confidence            99998666                                             789999999999999999999999999


Q ss_pred             EeCCCCHHHHHHHHHHHHHh
Q 023816          184 IVKPVKLSDVKRIKDYLTRD  203 (276)
Q Consensus       184 l~KPv~~~~L~~~~~~l~~~  203 (276)
                      |.||++.++|.+.+..+.+.
T Consensus       107 l~KP~~~~~L~~~l~~~~~r  126 (133)
T d2ayxa1         107 LSKPVTLDVIKQTLTLYAER  126 (133)
T ss_dssp             EESSCCHHHHHHHHHHHHHH
T ss_pred             EECCCCHHHHHHHHHHHHHH
Confidence            99999999998777766543

>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=99.95  E-value=2.7e-27  Score=192.39  Aligned_cols=122  Identities=25%  Similarity=0.477  Sum_probs=112.5

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhh
Q 023816           30 VHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVT  109 (276)
Q Consensus        30 ~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~  109 (276)
                      +|||||||++..++.++.+|+..||+|..+.+|++|++.+           ....||+||+|+.||+++|++++++||+.
T Consensus         1 mkILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~eAl~~l-----------~~~~~dlvilD~~mp~~~G~e~~~~lr~~   69 (137)
T d1ny5a1           1 MNVLVIEDDKVFRGLLEEYLSMKGIKVESAERGKEAYKLL-----------SEKHFNVVLLDLLLPDVNGLEILKWIKER   69 (137)
T ss_dssp             CEEEEECCCHHHHHHHHHHHHHHTCEEEEESSHHHHHHHH-----------HHSCCSEEEEESBCSSSBHHHHHHHHHHH
T ss_pred             CEEEEEecCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHh-----------hccccccchHHHhhhhhhHHHHHHHHHHh
Confidence            6899999999999999999999999999999999999999           56789999999999999999999999988


Q ss_pred             CCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCC
Q 023816          110 TPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVK  189 (276)
Q Consensus       110 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~  189 (276)
                      .|                                             .+|||++|++.+.+...+|++.||+|||.||++
T Consensus        70 ~~---------------------------------------------~~piI~lT~~~~~~~~~~a~~~Ga~dyl~KP~~  104 (137)
T d1ny5a1          70 SP---------------------------------------------ETEVIVITGHGTIKTAVEAMKMGAYDFLTKPCM  104 (137)
T ss_dssp             CT---------------------------------------------TSEEEEEEETTCHHHHHHHHTTTCCEEEEESCC
T ss_pred             CC---------------------------------------------CCCEEEEECCCCHHHHHHHHHcCCCEEEeCCCC
Confidence            77                                             899999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhhhcc
Q 023816          190 LSDVKRIKDYLTRDVNLG  207 (276)
Q Consensus       190 ~~~L~~~~~~l~~~~~~~  207 (276)
                      .++|...+..+.+...+.
T Consensus       105 ~~~L~~~i~~~l~~~~~~  122 (137)
T d1ny5a1         105 LEEIELTINKAIEHRKLR  122 (137)
T ss_dssp             HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHH
Confidence            999977776665544443

>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=99.94  E-value=8.9e-27  Score=185.49  Aligned_cols=114  Identities=27%  Similarity=0.431  Sum_probs=107.2

Q ss_pred             EEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhhC
Q 023816           31 HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVTT  110 (276)
Q Consensus        31 ~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~~  110 (276)
                      |||||||++.+++.++++|+..||+|..+.||++|++.+           ++..||+||+|+.||++||+|++++||+..
T Consensus         3 rILvVDD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~~-----------~~~~~dlillD~~mP~~~G~el~~~lr~~~   71 (119)
T d1peya_           3 KILIVDDQSGIRILLNEVFNKEGYQTFQAANGLQALDIV-----------TKERPDLVLLDMKIPGMDGIEILKRMKVID   71 (119)
T ss_dssp             EEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHH-----------HHHCCSEEEEESCCTTCCHHHHHHHHHHHC
T ss_pred             EEEEEeCCHHHHHHHHHHHHHcCCEEEEeCCHHHHHHHH-----------HhCCCCEEEEeccCCCCCHHHHHHHHHHhC
Confidence            799999999999999999999999999999999999999           566899999999999999999999999877


Q ss_pred             CCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCCH
Q 023816          111 PFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKL  190 (276)
Q Consensus       111 p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~~  190 (276)
                      +                                             .+|||++|++...+...+|++.||+|||.||++.
T Consensus        72 ~---------------------------------------------~~pvi~lt~~~~~~~~~~a~~~Ga~~yl~KP~~~  106 (119)
T d1peya_          72 E---------------------------------------------NIRVIIMTAYGELDMIQESKELGALTHFAKPFDI  106 (119)
T ss_dssp             T---------------------------------------------TCEEEEEESSCCHHHHHHHHHTTCCEEEESSCCH
T ss_pred             C---------------------------------------------CCcEEEEecCCCHHHHHHHHHCCCCEEEECCCCH
Confidence            7                                             7999999999999999999999999999999999


Q ss_pred             HHHHHHHHHH
Q 023816          191 SDVKRIKDYL  200 (276)
Q Consensus       191 ~~L~~~~~~l  200 (276)
                      ++|...++++
T Consensus       107 ~~L~~~v~~~  116 (119)
T d1peya_         107 DEIRDAVKKY  116 (119)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9997666543

>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=99.94  E-value=7.8e-27  Score=185.98  Aligned_cols=119  Identities=24%  Similarity=0.345  Sum_probs=110.2

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHh
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKV  108 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~  108 (276)
                      .+|||||||++..++.++++|+..||+|..+.+|++|++.+           ....||+||+|+.||+++|++++++||.
T Consensus         1 nirILiVdDd~~~~~~l~~~L~~~g~~v~~a~~~~~al~~l-----------~~~~~dlillD~~mp~~~g~~~~~~lr~   69 (122)
T d1kgsa2           1 NVRVLVVEDERDLADLITEALKKEMFTVDVCYDGEEGMYMA-----------LNEPFDVVILDIMLPVHDGWEILKSMRE   69 (122)
T ss_dssp             CCEEEEECSSHHHHHHHHHHHHHTTCEEEEESSHHHHHHHH-----------HHSCCSEEEEESCCSSSCHHHHHHHHHH
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHHCCCEEEEEcchHHHHHHH-----------HhhCccccccccccccchhHHHHHHHHh
Confidence            37999999999999999999999999999999999999999           5678999999999999999999999998


Q ss_pred             hCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCC
Q 023816          109 TTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPV  188 (276)
Q Consensus       109 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv  188 (276)
                      ..+                                             .+|||++|++.+.+...+|++.||+|||.||+
T Consensus        70 ~~~---------------------------------------------~~piI~lt~~~~~~~~~~~~~~Ga~~yl~KP~  104 (122)
T d1kgsa2          70 SGV---------------------------------------------NTPVLMLTALSDVEYRVKGLNMGADDYLPKPF  104 (122)
T ss_dssp             TTC---------------------------------------------CCCEEEEESSCHHHHHHHTCCCCCSEEEESSC
T ss_pred             cCC---------------------------------------------CCcEEEEcCCCCHHHHHHHHHcCCceeecCCC
Confidence            665                                             78999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHh
Q 023816          189 KLSDVKRIKDYLTRD  203 (276)
Q Consensus       189 ~~~~L~~~~~~l~~~  203 (276)
                      +.++|...++.+.++
T Consensus       105 ~~~~L~~~i~~~l~r  119 (122)
T d1kgsa2         105 DLRELIARVRALIRR  119 (122)
T ss_dssp             CHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHH
Confidence            999997666665543

>d1ys7a2 c.23.1.1 (A:7-127) Transcriptional regulatory protein PrrA, N-terminal domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Transcriptional regulatory protein PrrA, N-terminal domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=99.94  E-value=4.1e-27  Score=188.22  Aligned_cols=117  Identities=28%  Similarity=0.408  Sum_probs=109.0

Q ss_pred             EEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhhC
Q 023816           31 HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVTT  110 (276)
Q Consensus        31 ~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~~  110 (276)
                      |||||||++..++.+.++|+..||+|..+.||++|++.+           +...||+||+|++||++||++++++||+..
T Consensus         3 kILiVDD~~~~~~~l~~~L~~~g~~v~~a~~~~eal~~~-----------~~~~~dlvl~D~~mP~~~G~el~~~ir~~~   71 (121)
T d1ys7a2           3 RVLVVDDDSDVLASLERGLRLSGFEVATAVDGAEALRSA-----------TENRPDAIVLDINMPVLDGVSVVTALRAMD   71 (121)
T ss_dssp             EEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHH-----------HHSCCSEEEEESSCSSSCHHHHHHHHHHTT
T ss_pred             EEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHH-----------HhCCCCEEEEEeeccCcccHHHHHHHHhcC
Confidence            899999999999999999999999999999999999999           567899999999999999999999999866


Q ss_pred             CCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCCH
Q 023816          111 PFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKL  190 (276)
Q Consensus       111 p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~~  190 (276)
                      +                                             .+|||++|+..+.+...+|+++||+|||.||++.
T Consensus        72 ~---------------------------------------------~~piI~lt~~~~~~~~~~a~~~Ga~dyl~KP~~~  106 (121)
T d1ys7a2          72 N---------------------------------------------DVPVCVLSARSSVDDRVAGLEAGADDYLVKPFVL  106 (121)
T ss_dssp             C---------------------------------------------CCCEEEEECCCTTTCCCTTTTTTCSEEEESSCCH
T ss_pred             C---------------------------------------------CCEEEEEEeeCCHHHHHHHHHCCCCEEEECCCCH
Confidence            5                                             7999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHh
Q 023816          191 SDVKRIKDYLTRD  203 (276)
Q Consensus       191 ~~L~~~~~~l~~~  203 (276)
                      ++|...++.+.++
T Consensus       107 ~~L~~~i~~~l~r  119 (121)
T d1ys7a2         107 AELVARVKALLRR  119 (121)
T ss_dssp             HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHc
Confidence            9997766665543

>d1zesa1 c.23.1.1 (A:3-123) PhoB receiver domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: PhoB receiver domain
species: Escherichia coli [TaxId: 562]

Probab=99.94  E-value=3.3e-26  Score=182.08  Aligned_cols=118  Identities=27%  Similarity=0.412  Sum_probs=108.4

Q ss_pred             EEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhhC
Q 023816           31 HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVTT  110 (276)
Q Consensus        31 ~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~~  110 (276)
                      |||||||++..++.+..+|+..||+|..+.+|++|++.+           ....||+||+|++||++||++++++||+. 
T Consensus         2 kILiVDD~~~~~~~l~~~L~~~g~~v~~a~~~~~al~~l-----------~~~~~dlil~D~~mp~~~G~~l~~~lr~~-   69 (121)
T d1zesa1           2 RILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQL-----------NEPWPDLILLDWMLPGGSGIQFIKHLKRE-   69 (121)
T ss_dssp             EEEEECSCHHHHHHHHHHHHHTTCEEEEECSHHHHHHHS-----------SSSCCSEEEECSSCTTSCHHHHHHHHHHS-
T ss_pred             EEEEEeCCHHHHHHHHHHHHHCCCEEEEECChHHHHHHH-----------HccCCCEEEeecCCCCCCHHHHHHHHHhC-
Confidence            799999999999999999999999999999999999999           67789999999999999999999999973 


Q ss_pred             CCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCCH
Q 023816          111 PFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKL  190 (276)
Q Consensus       111 p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~~  190 (276)
                                                                ...+.+|||++|++.+.....+|++.||+||+.||++.
T Consensus        70 ------------------------------------------~~~~~~pvi~lt~~~~~~~~~~~~~~G~~d~l~KP~~~  107 (121)
T d1zesa1          70 ------------------------------------------SMTRDIPVVMLTARGEEEDRVRGLETGADDYITKPFSP  107 (121)
T ss_dssp             ------------------------------------------TTTTTSCEEEEESCCSHHHHHHHHHHTCSEEEESSCCH
T ss_pred             ------------------------------------------ccCCCCeEEEEECCCCHHHHHHHHHCCCCEEEECCCCH
Confidence                                                      23457999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHH
Q 023816          191 SDVKRIKDYLTR  202 (276)
Q Consensus       191 ~~L~~~~~~l~~  202 (276)
                      ++|...++.+.+
T Consensus       108 ~~L~~~v~~~lr  119 (121)
T d1zesa1         108 KELVARIKAVMR  119 (121)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHc
Confidence            999766665544

>d1krwa_ c.23.1.1 (A:) NTRC receiver domain {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: NTRC receiver domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=99.94  E-value=7.7e-27  Score=186.53  Aligned_cols=120  Identities=30%  Similarity=0.452  Sum_probs=111.0

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHH
Q 023816           27 TEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKI  106 (276)
Q Consensus        27 ~~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~I  106 (276)
                      |.+-+||||||++..++.++++|+..||+|..+.||++|++.+           ++..||+||+|+.||++||++++++|
T Consensus         1 M~k~~ILIVDDd~~~~~~l~~~L~~~g~~v~~a~~~~~a~~~l-----------~~~~~dlii~D~~mp~~~G~el~~~l   69 (123)
T d1krwa_           1 MQRGIVWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLAAL-----------ASKTPDVLLSDIRMPGMDGLALLKQI   69 (123)
T ss_dssp             CCCCEEEEESSSHHHHHHHHHHHHHTTCEEEEESSSHHHHHHH-----------TTCCCSEEEECCSSSSSTTHHHHHHH
T ss_pred             CCCCEEEEEECCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHH-----------HhCCCCEEEehhhcCCchHHHHHHHH
Confidence            3456899999999999999999999999999999999999999           77889999999999999999999999


Q ss_pred             HhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeC
Q 023816          107 KVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVK  186 (276)
Q Consensus       107 r~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~K  186 (276)
                      |+..|                                             .+|||++|++.+.+.+.+|++.|++|||.|
T Consensus        70 ~~~~~---------------------------------------------~~piI~~t~~~~~~~~~~a~~~Ga~dyl~K  104 (123)
T d1krwa_          70 KQRHP---------------------------------------------MLPVIIMTAHSDLDAAVSAYQQGAFDYLPK  104 (123)
T ss_dssp             HHHSS---------------------------------------------SCCEEESCCCSCHHHHHHHHHHTEEEECSS
T ss_pred             HHhCC---------------------------------------------CCeEEEEecCCCHHHHHHHHHcCCCeEEeC
Confidence            98777                                             799999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHH
Q 023816          187 PVKLSDVKRIKDYLTR  202 (276)
Q Consensus       187 Pv~~~~L~~~~~~l~~  202 (276)
                      |++.++|...++++.+
T Consensus       105 P~~~~eL~~~i~~~l~  120 (123)
T d1krwa_         105 PFDIDEAVALVERAIS  120 (123)
T ss_dssp             CCHHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHH
Confidence            9999999666665443

>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=99.94  E-value=3.4e-26  Score=185.46  Aligned_cols=126  Identities=25%  Similarity=0.455  Sum_probs=111.5

Q ss_pred             CCCCccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHH
Q 023816           25 SDTEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLK  104 (276)
Q Consensus        25 ~~~~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~  104 (276)
                      ++-.++|||||||++.+++.++++|+..||++..+.||++|++.+           + ..||+||+|++||++||+++++
T Consensus         3 ~d~~g~rILvVDD~~~~~~~l~~~L~~~G~~v~~a~~g~eal~~l-----------~-~~~dlillD~~mP~~dG~el~~   70 (134)
T d1dcfa_           3 SNFTGLKVLVMDENGVSRMVTKGLLVHLGCEVTTVSSNEECLRVV-----------S-HEHKVVFMDVCMPGVENYQIAL   70 (134)
T ss_dssp             CCCTTCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHC-----------C-TTCSEEEEECCSSTTTTTHHHH
T ss_pred             CCCCCCEEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHh-----------h-cCCCeEEEEeccCCCchHHHHH
Confidence            344679999999999999999999999999999999999999977           3 3699999999999999999999


Q ss_pred             HHHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEE
Q 023816          105 KIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFI  184 (276)
Q Consensus       105 ~Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l  184 (276)
                      +||+...                                        ......+|||++|++...+...+|+++|+++||
T Consensus        71 ~ir~~~~----------------------------------------~~~~~~~~ii~lT~~~~~~~~~~~~~~G~~~~l  110 (134)
T d1dcfa_          71 RIHEKFT----------------------------------------KQRHQRPLLVALSGNTDKSTKEKCMSFGLDGVL  110 (134)
T ss_dssp             HHHHHHC-----------------------------------------CCSCCCEEEEEESCCSHHHHHHHHHTTCCEEE
T ss_pred             HHHHhcc----------------------------------------cccCCCCeEEEEeCCCCHHHHHHHHHcCCCEEE
Confidence            9997433                                        233446899999999999999999999999999


Q ss_pred             eCCCCHHHHHHHHHHHHH
Q 023816          185 VKPVKLSDVKRIKDYLTR  202 (276)
Q Consensus       185 ~KPv~~~~L~~~~~~l~~  202 (276)
                      .||++.++|.+++..+.+
T Consensus       111 ~KP~~~~~L~~~l~~~l~  128 (134)
T d1dcfa_         111 LKPVSLDNIRDVLSDLLE  128 (134)
T ss_dssp             ESSCCHHHHHHHHHHHHS
T ss_pred             ECCCCHHHHHHHHHHHhh
Confidence            999999999887776654

>d1mvoa_ c.23.1.1 (A:) PhoP receiver domain {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: PhoP receiver domain
species: Bacillus subtilis [TaxId: 1423]

Probab=99.94  E-value=2.4e-26  Score=182.61  Aligned_cols=116  Identities=25%  Similarity=0.361  Sum_probs=107.8

Q ss_pred             EEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhhC
Q 023816           31 HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVTT  110 (276)
Q Consensus        31 ~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~~  110 (276)
                      |||||||++.+++.++.+|+..||+|..+.+|++|++.+           +...||+||+|+.||+++|+++++++|...
T Consensus         4 rILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~~al~~l-----------~~~~~dlillD~~mp~~~G~~~~~~~r~~~   72 (121)
T d1mvoa_           4 KILVVDDEESIVTLLQYNLERSGYDVITASDGEEALKKA-----------ETEKPDLIVLDVMLPKLDGIEVCKQLRQQK   72 (121)
T ss_dssp             EEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHH-----------HHHCCSEEEEESSCSSSCHHHHHHHHHHTT
T ss_pred             CEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHH-----------hcccccEEEecccccCCCCchhhhhhhccC
Confidence            899999999999999999999999999999999999999           566899999999999999999999999866


Q ss_pred             CCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCCH
Q 023816          111 PFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKL  190 (276)
Q Consensus       111 p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~~  190 (276)
                      +                                             .+|||++|+........+|++.||+|||.||++.
T Consensus        73 ~---------------------------------------------~~~ii~lt~~~~~~~~~~~~~~Ga~~yl~KP~~~  107 (121)
T d1mvoa_          73 L---------------------------------------------MFPILMLTAKDEEFDKVLGLELGADDYMTKPFSP  107 (121)
T ss_dssp             C---------------------------------------------CCCEEEEECTTCCCCHHHHHHTTCCEEEESSCCH
T ss_pred             C---------------------------------------------CCEEEEEEeeCCHHHHHHHHHCCCCEEEECCCCH
Confidence            6                                             7899999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHH
Q 023816          191 SDVKRIKDYLTR  202 (276)
Q Consensus       191 ~~L~~~~~~l~~  202 (276)
                      ++|...++.+.+
T Consensus       108 ~~L~~~i~~~lr  119 (121)
T d1mvoa_         108 REVNARVKAILR  119 (121)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHc
Confidence            999766665544

>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=99.94  E-value=2.1e-26  Score=183.06  Aligned_cols=115  Identities=24%  Similarity=0.386  Sum_probs=106.2

Q ss_pred             EEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhhC
Q 023816           31 HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVTT  110 (276)
Q Consensus        31 ~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~~  110 (276)
                      +||||||++.+++.++.+|+..||+|..+.||++|++.+           ++..||+||+|++||++||++++++||+..
T Consensus         2 nILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~eal~~l-----------~~~~~dliilD~~mP~~~G~e~~~~ir~~~   70 (119)
T d1zh2a1           2 NVLIVEDEQAIRRFLRTALEGDGMRVFEAETLQRGLLEA-----------ATRKPDLIILDLGLPDGDGIEFIRDLRQWS   70 (119)
T ss_dssp             EEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHH-----------HHHCCSEEEEESEETTEEHHHHHHHHHTTC
T ss_pred             EEEEEECCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHH-----------HhcCCCEEEeccccCCCCCchHHHHHHhcc
Confidence            799999999999999999999999999999999999999           566899999999999999999999999632


Q ss_pred             CCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCCH
Q 023816          111 PFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKL  190 (276)
Q Consensus       111 p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~~  190 (276)
                                                                    ++|||++|+....+...+|++.||+|||.||++.
T Consensus        71 ----------------------------------------------~~piI~lt~~~~~~~~~~a~~~Ga~dyl~KP~~~  104 (119)
T d1zh2a1          71 ----------------------------------------------AVPVIVLSARSEESDKIAALDAGADDYLSKPFGI  104 (119)
T ss_dssp             ----------------------------------------------CCCEEEEESCCSHHHHHHHHHHTCSEEEESSCCH
T ss_pred             ----------------------------------------------CCcEEEEeccCCHHHHHHHHHcCCCEEEECCCCH
Confidence                                                          5799999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHH
Q 023816          191 SDVKRIKDYLTR  202 (276)
Q Consensus       191 ~~L~~~~~~l~~  202 (276)
                      ++|...++.+.+
T Consensus       105 ~~L~~~i~~~lr  116 (119)
T d1zh2a1         105 GELQARLRVALR  116 (119)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHh
Confidence            999766665544

>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=99.94  E-value=1.4e-25  Score=183.84  Aligned_cols=129  Identities=23%  Similarity=0.366  Sum_probs=111.3

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhCC--CEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHH
Q 023816           28 EEVHVLAVDDSFVDRKVIERLLTISS--CKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKK  105 (276)
Q Consensus        28 ~~~~VLIVdD~~~~~~~L~~~L~~~g--~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~  105 (276)
                      ++-+||||||++.+++.++++|+..|  ++|..+.||++|++++....+..    ....||+||+|+.||++||+|++++
T Consensus         2 ppk~ILiVdD~~~~~~~l~~~L~~~g~~~~v~~a~~g~~Al~~l~~~~~~~----~~~~pdlIllD~~mP~~~G~el~~~   77 (144)
T d1i3ca_           2 PPKVILLVEDSKADSRLVQEVLKTSTIDHELIILRDGLAAMAFLQQQGEYE----NSPRPNLILLDLNLPKKDGREVLAE   77 (144)
T ss_dssp             CCEEEEEECCCHHHHHHHHHHHHSCCSCEEEEEECSHHHHHHHHTTCGGGT----TCCCCSEEEECSCCSSSCHHHHHHH
T ss_pred             CCCEEEEEECCHHHHHHHHHHHHHcCCCeEEEEECCHHHHHHHHHhchhhh----ccCCCCEEEEECccccccchHHHHH
Confidence            56799999999999999999999876  58889999999999995332211    3446999999999999999999999


Q ss_pred             HHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEe
Q 023816          106 IKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIV  185 (276)
Q Consensus       106 Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~  185 (276)
                      ||+.                                           ...+.+|||++|++.+.+...+|++.||++||.
T Consensus        78 ir~~-------------------------------------------~~~~~iPvi~lT~~~~~~~~~~a~~~Ga~~yl~  114 (144)
T d1i3ca_          78 IKQN-------------------------------------------PDLKRIPVVVLTTSHNEDDVIASYELHVNCYLT  114 (144)
T ss_dssp             HHHC-------------------------------------------TTTTTSCEEEEESCCCHHHHHHHHHTTCSEEEE
T ss_pred             HHhC-------------------------------------------cccCCCeEEEEECCCCHHHHHHHHHCCCCEEEE
Confidence            9962                                           334589999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHHh
Q 023816          186 KPVKLSDVKRIKDYLTRD  203 (276)
Q Consensus       186 KPv~~~~L~~~~~~l~~~  203 (276)
                      ||++.++|.+.++.+.+.
T Consensus       115 KP~~~~~L~~~i~~l~~~  132 (144)
T d1i3ca_         115 KSRNLKDLFKMVQGIESF  132 (144)
T ss_dssp             CCSSHHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHH
Confidence            999999997777766654

>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=99.94  E-value=5e-26  Score=183.68  Aligned_cols=122  Identities=26%  Similarity=0.427  Sum_probs=107.5

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhCCCE-EEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHh
Q 023816           30 VHVLAVDDSFVDRKVIERLLTISSCK-VTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKV  108 (276)
Q Consensus        30 ~~VLIVdD~~~~~~~L~~~L~~~g~~-v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~  108 (276)
                      +|||||||++.+++.++++|+..||+ |..+.||++|++.+.....      .+..||+||+|++||++||++++++||+
T Consensus         2 irVLvVDD~~~~~~~l~~~L~~~g~~~v~~a~~g~eAl~~l~~~~~------~~~~~dlillD~~mP~~dG~el~~~ir~   75 (128)
T d2r25b1           2 VKILVVEDNHVNQEVIKRMLNLEGIENIELACDGQEAFDKVKELTS------KGENYNMIFMDVQMPKVDGLLSTKMIRR   75 (128)
T ss_dssp             SCEEEECSCHHHHHHHHHHHHHTTCCCEEEESSHHHHHHHHHHHHH------HTCCCSEEEECSCCSSSCHHHHHHHHHH
T ss_pred             eEEEEEeCCHHHHHHHHHHHHHcCCeEEEEEcChHHHHHHHHhhhh------ccCCCCEEEEEeCCCCCCHHHHHHHHHH
Confidence            79999999999999999999999996 7889999999998843221      2457999999999999999999999996


Q ss_pred             hCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCC
Q 023816          109 TTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPV  188 (276)
Q Consensus       109 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv  188 (276)
                      ...                                            ..+|||++|++...+...+|++.|+++||.||+
T Consensus        76 ~~~--------------------------------------------~~~piI~lT~~~~~~~~~~~~~~G~~~~l~KP~  111 (128)
T d2r25b1          76 DLG--------------------------------------------YTSPIVALTAFADDSNIKECLESGMNGFLSKPI  111 (128)
T ss_dssp             HSC--------------------------------------------CCSCEEEEESCCSHHHHHHHHHTTCSEEEESSC
T ss_pred             ccC--------------------------------------------CCCeEEEEECCCCHHHHHHHHHcCCCEEEECCC
Confidence            322                                            268999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHH
Q 023816          189 KLSDVKRIKDYLT  201 (276)
Q Consensus       189 ~~~~L~~~~~~l~  201 (276)
                      +.++|.+++..+.
T Consensus       112 ~~~~L~~~l~~~~  124 (128)
T d2r25b1         112 KRPKLKTILTEFC  124 (128)
T ss_dssp             CHHHHHHHHHHHC
T ss_pred             CHHHHHHHHHHHH
Confidence            9999988776653

>d1mb3a_ c.23.1.1 (A:) Cell division response regulator DivK {Caulobacter crescentus [TaxId: 155892]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Cell division response regulator DivK
species: Caulobacter crescentus [TaxId: 155892]

Probab=99.94  E-value=2.3e-26  Score=182.93  Aligned_cols=118  Identities=28%  Similarity=0.399  Sum_probs=102.1

Q ss_pred             EEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhhC
Q 023816           31 HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVTT  110 (276)
Q Consensus        31 ~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~~  110 (276)
                      |||||||++.+++.++.+|+..||+|..+.+|.+|++.+           ++..||+||+|+.||++||++++++||+..
T Consensus         3 rILiVDD~~~~~~~l~~~L~~~g~~v~~a~~~~~al~~~-----------~~~~~dlil~D~~mp~~dG~el~~~ir~~~   71 (123)
T d1mb3a_           3 KVLIVEDNELNMKLFHDLLEAQGYETLQTREGLSALSIA-----------RENKPDLILMDIQLPEISGLEVTKWLKEDD   71 (123)
T ss_dssp             EEEEECSCHHHHHHHHHHHHHTTCEEEEESCHHHHHHHH-----------HHHCCSEEEEESBCSSSBHHHHHHHHHHST
T ss_pred             eEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHH-----------HhCCCCEEEEEeccCCCcHHHHHHHHHhCC
Confidence            799999999999999999999999999999999999999           556899999999999999999999999732


Q ss_pred             CCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCCH
Q 023816          111 PFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKL  190 (276)
Q Consensus       111 p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~~  190 (276)
                                                                 ....+|||++|+....+...+++++|+++||.||++.
T Consensus        72 -------------------------------------------~~~~iPii~lt~~~~~~~~~~~~~~G~~~~l~KP~~~  108 (123)
T d1mb3a_          72 -------------------------------------------DLAHIPVVAVTAFAMKGDEERIREGGCEAYISKPISV  108 (123)
T ss_dssp             -------------------------------------------TTTTSCEEEEC------CHHHHHHHTCSEEECSSCCH
T ss_pred             -------------------------------------------CcCCCCeEEEEEecCHHHHHHHHHcCCCEEEECCCCH
Confidence                                                       3457999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHH
Q 023816          191 SDVKRIKDYLTR  202 (276)
Q Consensus       191 ~~L~~~~~~l~~  202 (276)
                      ++|.+.+..+.+
T Consensus       109 ~~L~~~i~~~l~  120 (123)
T d1mb3a_         109 VHFLETIKRLLE  120 (123)
T ss_dssp             HHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHh
Confidence            999776666553

>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=99.94  E-value=8.7e-26  Score=178.82  Aligned_cols=118  Identities=21%  Similarity=0.348  Sum_probs=108.3

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHh
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKV  108 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~  108 (276)
                      |.|||||||++.+++.++.+|+..||+|..+.+|++|++.+           +...||+||+|+.||++||+++++.+|.
T Consensus         1 P~rILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~~a~~~~-----------~~~~~dliilD~~mp~~~g~~~~~~~~~   69 (120)
T d1zgza1           1 PHHIVIVEDEPVTQARLQSYFTQEGYTVSVTASGAGLREIM-----------QNQSVDLILLDINLPDENGLMLTRALRE   69 (120)
T ss_dssp             CCEEEEECSSHHHHHHHHHHHHHTTCEEEEESSHHHHHHHH-----------HHSCCSEEEEESCCSSSCHHHHHHHHHT
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHH-----------HhcCCCEEeeehhhccchhHHHHHHHhc
Confidence            57999999999999999999999999999999999999999           6678999999999999999999999885


Q ss_pred             hCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCC
Q 023816          109 TTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPV  188 (276)
Q Consensus       109 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv  188 (276)
                      ..                                              .+|||++|+........+|+++||+|||.||+
T Consensus        70 ~~----------------------------------------------~~piI~lt~~~~~~~~~~a~~~Ga~dyl~KP~  103 (120)
T d1zgza1          70 RS----------------------------------------------TVGIILVTGRSDRIDRIVGLEMGADDYVTKPL  103 (120)
T ss_dssp             TC----------------------------------------------CCEEEEEESSCCHHHHHHHHHHTCSEEEESSC
T ss_pred             cC----------------------------------------------CCeEEEEEccCCHHHHHHHHHCCCCEEEECCC
Confidence            32                                              58999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHh
Q 023816          189 KLSDVKRIKDYLTRD  203 (276)
Q Consensus       189 ~~~~L~~~~~~l~~~  203 (276)
                      +.++|...+..+.++
T Consensus       104 ~~~~L~~~i~~~lrR  118 (120)
T d1zgza1         104 ELRELVVRVKNLLWR  118 (120)
T ss_dssp             CHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHcc
Confidence            999997666666554

>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=99.93  E-value=1.3e-25  Score=183.17  Aligned_cols=126  Identities=27%  Similarity=0.392  Sum_probs=109.7

Q ss_pred             EEEEEeCCHHHHHHHHHHHhhCC--CEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHh
Q 023816           31 HVLAVDDSFVDRKVIERLLTISS--CKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKV  108 (276)
Q Consensus        31 ~VLIVdD~~~~~~~L~~~L~~~g--~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~  108 (276)
                      |||||||++.+++.+++.|+..|  |+|..+.||++|++.+....+.+    ....||+||+|++||++||+|++++||.
T Consensus         4 rILiVDD~~~~~~~l~~~L~~~g~~~~v~~a~~g~eAl~~l~~~~~~~----~~~~pdlillD~~mP~~dG~el~~~ir~   79 (140)
T d1k68a_           4 KIFLVEDNKADIRLIQEALANSTVPHEVVTVRDGMEAMAYLRQEGEYA----NASRPDLILLDLNLPKKDGREVLAEIKS   79 (140)
T ss_dssp             EEEEECCCHHHHHHHHHHHHTCSSCCEEEEECSHHHHHHHHTTCGGGG----SCCCCSEEEECSSCSSSCHHHHHHHHHH
T ss_pred             cEEEEECCHHHHHHHHHHHHHcCCCeEEEEECCHHHHHHHHHHhHHhh----ccCCCCEEEEeeccccccChHHHHHHHh
Confidence            79999999999999999999876  68999999999999995433222    3457999999999999999999999996


Q ss_pred             hCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCC
Q 023816          109 TTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPV  188 (276)
Q Consensus       109 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv  188 (276)
                      .                                           +..+.+|||++|++.+.....+|++.||++||.||+
T Consensus        80 ~-------------------------------------------~~~~~iPvI~ls~~~~~~~~~~a~~~Ga~~yl~KP~  116 (140)
T d1k68a_          80 D-------------------------------------------PTLKRIPVVVLSTSINEDDIFHSYDLHVNCYITKSA  116 (140)
T ss_dssp             S-------------------------------------------TTGGGSCEEEEESCCCHHHHHHHHHTTCSEEEECCS
T ss_pred             C-------------------------------------------cccCCCcEEEEeCCCCHHHHHHHHHCCCCEEEECCC
Confidence            2                                           234479999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHHh
Q 023816          189 KLSDVKRIKDYLTRD  203 (276)
Q Consensus       189 ~~~~L~~~~~~l~~~  203 (276)
                      +.++|.+.++.+.+.
T Consensus       117 ~~~~L~~~i~~i~~~  131 (140)
T d1k68a_         117 NLSQLFQIVKGIEEF  131 (140)
T ss_dssp             SHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHH
Confidence            999997777666554

>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=99.93  E-value=6.2e-26  Score=180.32  Aligned_cols=115  Identities=30%  Similarity=0.464  Sum_probs=107.0

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhCCCEEE-EECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHh
Q 023816           30 VHVLAVDDSFVDRKVIERLLTISSCKVT-AVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKV  108 (276)
Q Consensus        30 ~~VLIVdD~~~~~~~L~~~L~~~g~~v~-~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~  108 (276)
                      -|||||||++..++.++.+|+..||+|. .+.||++|++.+           ++..||+||+|++||++||+|++++||+
T Consensus         2 krILivDD~~~~~~~l~~~L~~~g~~v~~~a~~~~~al~~~-----------~~~~~dliilD~~mp~~~G~e~~~~ir~   70 (118)
T d1u0sy_           2 KRVLIVDDAAFMRMMLKDIITKAGYEVAGEATNGREAVEKY-----------KELKPDIVTMDITMPEMNGIDAIKEIMK   70 (118)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHH-----------HHHCCSEEEEECSCGGGCHHHHHHHHHH
T ss_pred             CEEEEEeCCHHHHHHHHHHHHHcCCceEEEECCHHHHHHHH-----------HhccCCEEEEecCCCCCCHHHHHHHHHH
Confidence            4899999999999999999999999987 589999999999           5568999999999999999999999998


Q ss_pred             hCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCC
Q 023816          109 TTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPV  188 (276)
Q Consensus       109 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv  188 (276)
                      ..|                                             .+|||++|++...+...+|++.||+|||.||+
T Consensus        71 ~~~---------------------------------------------~~pvi~ls~~~~~~~~~~a~~~Ga~~yl~KP~  105 (118)
T d1u0sy_          71 IDP---------------------------------------------NAKIIVCSAMGQQAMVIEAIKAGAKDFIVKPF  105 (118)
T ss_dssp             HCT---------------------------------------------TCCEEEEECTTCHHHHHHHHHTTCCEEEESSC
T ss_pred             hCC---------------------------------------------CCcEEEEEccCCHHHHHHHHHcCCCEEEECCC
Confidence            777                                             79999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHH
Q 023816          189 KLSDVKRIKDYL  200 (276)
Q Consensus       189 ~~~~L~~~~~~l  200 (276)
                      +.++|.+.++++
T Consensus       106 ~~~~L~~~l~~v  117 (118)
T d1u0sy_         106 QPSRVVEALNKV  117 (118)
T ss_dssp             CHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHh
Confidence            999997766543

>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=99.93  E-value=6.4e-26  Score=179.72  Aligned_cols=114  Identities=27%  Similarity=0.408  Sum_probs=105.8

Q ss_pred             EEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhhC
Q 023816           31 HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVTT  110 (276)
Q Consensus        31 ~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~~  110 (276)
                      |||||||++..++.+..+|+..||+|..+.||++|++.+           +...||+||+|+.||+++|++++++|++. 
T Consensus         2 rILiVdDd~~~~~~l~~~L~~~g~~v~~a~~~~eal~~~-----------~~~~~dlillD~~mp~~~G~~~~~~i~~~-   69 (117)
T d2a9pa1           2 KILIVDDEKPISDIIKFNMTKEGYEVVTAFNGREALEQF-----------EAEQPDIIILDLMLPEIDGLEVAKTIRKT-   69 (117)
T ss_dssp             EEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHH-----------HHHCCSEEEECSSCSSSCHHHHHHHHHTT-
T ss_pred             EEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHH-----------HhcCCCEEEeccccCCCCccHHHHHHHhC-
Confidence            799999999999999999999999999999999999999           56789999999999999999999999852 


Q ss_pred             CCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCCH
Q 023816          111 PFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKL  190 (276)
Q Consensus       111 p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~~  190 (276)
                      +                                             ++|||++|+....+...+|++.||+|||.||++.
T Consensus        70 ~---------------------------------------------~~pvI~lt~~~~~~~~~~a~~~Ga~d~l~KP~~~  104 (117)
T d2a9pa1          70 S---------------------------------------------SVPILMLSAKDSEFDKVIGLELGADDYVTKPFSN  104 (117)
T ss_dssp             C---------------------------------------------CCCEEEEESCCSHHHHHHHHHHTCSEEEESSCCH
T ss_pred             C---------------------------------------------CCCEEEEecCCCHHHHHHHHHcCCCEEEECCCCH
Confidence            3                                             6899999999999999999999999999999999


Q ss_pred             HHHHHHHHHHH
Q 023816          191 SDVKRIKDYLT  201 (276)
Q Consensus       191 ~~L~~~~~~l~  201 (276)
                      ++|...++.+.
T Consensus       105 ~~L~~~i~~~l  115 (117)
T d2a9pa1         105 RELQARVKALL  115 (117)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHh
Confidence            99976666554

>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=99.93  E-value=3.3e-26  Score=193.64  Aligned_cols=114  Identities=23%  Similarity=0.370  Sum_probs=105.3

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhCCCEEE-EECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHH
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTISSCKVT-AVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIK  107 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~g~~v~-~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir  107 (276)
                      |+|||||||++.+|+.++.+|+..||+++ .|.||.+|++.+           +...|||||+|++||+|||+|++++||
T Consensus         3 p~kILiVDD~~~~r~~l~~~L~~~g~~vv~~a~~g~eal~~~-----------~~~~pDlvllDi~mP~~dG~e~~~~ir   71 (190)
T d1s8na_           3 PRRVLIAEDEALIRMDLAEMLREEGYEIVGEAGDGQEAVELA-----------ELHKPDLVIMDVKMPRRDGIDAASEIA   71 (190)
T ss_dssp             CCEEEEECSSHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHH-----------HHHCCSEEEEESSCSSSCHHHHHHHHH
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHH-----------hcCCCCEEEEeccccCcchHHHHHHHH
Confidence            78999999999999999999999999976 699999999999           667899999999999999999999999


Q ss_pred             hhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCC
Q 023816          108 VTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKP  187 (276)
Q Consensus       108 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KP  187 (276)
                      +. +                                             ++|||++|++.+.+...+|+++||+|||.||
T Consensus        72 ~~-~---------------------------------------------~~pIi~lTa~~~~~~~~~al~~Ga~~yl~KP  105 (190)
T d1s8na_          72 SK-R---------------------------------------------IAPIVVLTAFSQRDLVERARDAGAMAYLVKP  105 (190)
T ss_dssp             HT-T---------------------------------------------CSCEEEEEEGGGHHHHHTTGGGSCEEEEEES
T ss_pred             hc-C---------------------------------------------CCCEEEEeCCCCHHHHHHHHHcCCCEeccCC
Confidence            63 2                                             5899999999999999999999999999999


Q ss_pred             CCHHHHHHHHHH
Q 023816          188 VKLSDVKRIKDY  199 (276)
Q Consensus       188 v~~~~L~~~~~~  199 (276)
                      ++.++|...+..
T Consensus       106 ~~~~~L~~~i~~  117 (190)
T d1s8na_         106 FSISDLIPAIEL  117 (190)
T ss_dssp             CCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHH
Confidence            999998655543

>d1yioa2 c.23.1.1 (A:3-130) Response regulatory protein StyR, N-terminal domain {Pseudomonas fluorescens [TaxId: 294]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulatory protein StyR, N-terminal domain
species: Pseudomonas fluorescens [TaxId: 294]

Probab=99.93  E-value=4.8e-26  Score=182.48  Aligned_cols=116  Identities=23%  Similarity=0.373  Sum_probs=108.7

Q ss_pred             EEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhhC
Q 023816           31 HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVTT  110 (276)
Q Consensus        31 ~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~~  110 (276)
                      +|||||||+.+++.+..+|+..||+|..+.++++|++.+           +...||+||+|++||+++|+++++++++..
T Consensus         4 ~ILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~~al~~~-----------~~~~~dliilD~~mp~~~G~~~~~~i~~~~   72 (128)
T d1yioa2           4 TVFVVDDDMSVREGLRNLLRSAGFEVETFDCASTFLEHR-----------RPEQHGCLVLDMRMPGMSGIELQEQLTAIS   72 (128)
T ss_dssp             EEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHC-----------CTTSCEEEEEESCCSSSCHHHHHHHHHHTT
T ss_pred             EEEEEECCHHHHHHHHHHHHHcCCCccccccHHHHHHHH-----------HhcCCCEeehhhhcccchhHHHHHHHHhhC
Confidence            899999999999999999999999999999999999999           678899999999999999999999999877


Q ss_pred             CCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCCH
Q 023816          111 PFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKL  190 (276)
Q Consensus       111 p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~~  190 (276)
                      +                                             .+||+++|++.+.+...+|++.||+|||.||++.
T Consensus        73 ~---------------------------------------------~~~ii~lt~~~~~~~~~~a~~~Ga~dyl~KP~~~  107 (128)
T d1yioa2          73 D---------------------------------------------GIPIVFITAHGDIPMTVRAMKAGAIEFLPKPFEE  107 (128)
T ss_dssp             C---------------------------------------------CCCEEEEESCTTSCCCHHHHHTTEEEEEESSCCH
T ss_pred             C---------------------------------------------CCeEEEEEEECCHHHHHHHHHCCCCEEEECCCCH
Confidence            7                                             7899999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHH
Q 023816          191 SDVKRIKDYLTR  202 (276)
Q Consensus       191 ~~L~~~~~~l~~  202 (276)
                      ++|.+.+..+.+
T Consensus       108 ~~L~~~i~~~l~  119 (128)
T d1yioa2         108 QALLDAIEQGLQ  119 (128)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHH
Confidence            999776665544

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

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulator PleD, receiver domain
species: Caulobacter crescentus [TaxId: 155892]

Probab=99.93  E-value=4.5e-26  Score=185.54  Aligned_cols=121  Identities=31%  Similarity=0.402  Sum_probs=110.1

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhh
Q 023816           30 VHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVT  109 (276)
Q Consensus        30 ~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~  109 (276)
                      .|||||||++.+++.++.+|+..||+|..+.||++|++.+           ....|||||+|+.||+++|+++++.+|..
T Consensus         2 arILiVDD~~~~~~~l~~~L~~~g~~v~~a~~~~eal~~~-----------~~~~~dlil~D~~~p~~~G~~~~~~ir~~   70 (139)
T d1w25a1           2 ARILVVDDIEANVRLLEAKLTAEYYEVSTAMDGPTALAMA-----------ARDLPDIILLDVMMPGMDGFTVCRKLKDD   70 (139)
T ss_dssp             CEEEEECSSTTHHHHHHHHHHHTTCEEEEESSHHHHHHHH-----------HHHCCSEEEEESCCSSSCHHHHHHHHHHS
T ss_pred             CEEEEEECCHHHHHHHHHHHHHCCCEEEEEccchhhhhhh-----------hcccceeeeeeccccCCCchHHHHHhhhc
Confidence            4899999999999999999999999999999999999999           56689999999999999999999999973


Q ss_pred             CCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCC
Q 023816          110 TPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVK  189 (276)
Q Consensus       110 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~  189 (276)
                      .                                           ..+.+|||++|++...+...+|+++||+|||.||++
T Consensus        71 ~-------------------------------------------~~~~~piI~lt~~~~~~~~~~a~~~Ga~dyl~KP~~  107 (139)
T d1w25a1          71 P-------------------------------------------TTRHIPVVLITALDGRGDRIQGLESGASDFLTKPID  107 (139)
T ss_dssp             T-------------------------------------------TTTTSCEEEEECSSCHHHHHHHHHHTCCEEEESSCC
T ss_pred             c-------------------------------------------cccCCCEEEEEcCCCHHHHHHHHHcCCCEEEECCCC
Confidence            2                                           244799999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHhh
Q 023816          190 LSDVKRIKDYLTRDV  204 (276)
Q Consensus       190 ~~~L~~~~~~l~~~~  204 (276)
                      ..+|...+..+.+..
T Consensus       108 ~~~L~~~i~~~lr~~  122 (139)
T d1w25a1         108 DVMLFARVRSLTRFK  122 (139)
T ss_dssp             HHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHH
Confidence            999976666666544

>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=99.93  E-value=5.5e-26  Score=182.88  Aligned_cols=122  Identities=24%  Similarity=0.436  Sum_probs=110.3

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhCCCE-EEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHH
Q 023816           27 TEEVHVLAVDDSFVDRKVIERLLTISSCK-VTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKK  105 (276)
Q Consensus        27 ~~~~~VLIVdD~~~~~~~L~~~L~~~g~~-v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~  105 (276)
                      .+++|||||||++.+++.+.++|+..||. |..+.+|++|++.+           .+..||+||+|+.||++||++++++
T Consensus         4 ~~~~kILiVDD~~~~~~~l~~~L~~~g~~~v~~a~~~~~al~~l-----------~~~~~dlii~D~~mP~~~G~el~~~   72 (129)
T d1p6qa_           4 AEKIKVLIVDDQVTSRLLLGDALQQLGFKQITAAGDGEQGMKIM-----------AQNPHHLVISDFNMPKMDGLGLLQA   72 (129)
T ss_dssp             SSCCCEEEECSSHHHHHHHHHHHHTTTCSCEECCSSHHHHHHHH-----------HTSCCSEEEECSSSCSSCHHHHHHH
T ss_pred             CCCCEEEEEECCHHHHHHHHHHHHHCCCeEEEEECCHHHHHHHH-----------HhCCCCeEEeeeecCCCChHHHHHH
Confidence            46789999999999999999999999995 78899999999999           6678999999999999999999999


Q ss_pred             HHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEe
Q 023816          106 IKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIV  185 (276)
Q Consensus       106 Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~  185 (276)
                      ||+.                                           ...+.+|||++|++.+.+...+|++.|+++|+.
T Consensus        73 lr~~-------------------------------------------~~~~~~pii~lt~~~~~~~~~~a~~~G~~~~l~  109 (129)
T d1p6qa_          73 VRAN-------------------------------------------PATKKAAFIILTAQGDRALVQKAAALGANNVLA  109 (129)
T ss_dssp             HTTC-------------------------------------------TTSTTCEEEECCSCCCHHHHHHHHHHTCSCEEC
T ss_pred             HHhC-------------------------------------------cccCCCeEEEEEecCCHHHHHHHHHCCCCEEEE
Confidence            9962                                           234579999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHH
Q 023816          186 KPVKLSDVKRIKDYLTR  202 (276)
Q Consensus       186 KPv~~~~L~~~~~~l~~  202 (276)
                      ||++.++|.+.++.+..
T Consensus       110 KP~~~~~L~~~i~~vl~  126 (129)
T d1p6qa_         110 KPFTIEKMKAAIEAVFG  126 (129)
T ss_dssp             CCSSHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHH
Confidence            99999999777766543

>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=99.93  E-value=2.4e-25  Score=177.58  Aligned_cols=115  Identities=23%  Similarity=0.416  Sum_probs=106.7

Q ss_pred             EEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHhhC
Q 023816           31 HVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKVTT  110 (276)
Q Consensus        31 ~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~~~  110 (276)
                      +||||||++..++.+..+|+..||+|..+.||++|++.+           +...||+||+|+.||+++|+++++++|+. 
T Consensus         4 ~ILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~~al~~l-----------~~~~~dlii~D~~mp~~~G~~~~~~~r~~-   71 (121)
T d1xhfa1           4 HILIVEDELVTRNTLKSIFEAEGYDVFEATDGAEMHQIL-----------SEYDINLVIMDINLPGKNGLLLARELREQ-   71 (121)
T ss_dssp             EEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHH-----------HHSCCSEEEECSSCSSSCHHHHHHHHHHH-
T ss_pred             EEEEEECCHHHHHHHHHHHHHCCCEEEEECChHHHHHHH-----------HhcCCCEEEeecccCCccCcHHHHHHHhc-
Confidence            999999999999999999999999999999999999999           56789999999999999999999999963 


Q ss_pred             CCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCCCH
Q 023816          111 PFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPVKL  190 (276)
Q Consensus       111 p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv~~  190 (276)
                      +                                             ++|||++|++.+.....+|+++||+|||.||++.
T Consensus        72 ~---------------------------------------------~~pii~lt~~~~~~~~~~a~~~Ga~dyl~KP~~~  106 (121)
T d1xhfa1          72 A---------------------------------------------NVALMFLTGRDNEVDKILGLEIGADDYITKPFNP  106 (121)
T ss_dssp             C---------------------------------------------CCEEEEEESCCSHHHHHHHHHHTCSEEEESSCCH
T ss_pred             C---------------------------------------------CCcEEEEECCCCHHHHHHHHHcCCCEEEeCCCCH
Confidence            3                                             6999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHH
Q 023816          191 SDVKRIKDYLTR  202 (276)
Q Consensus       191 ~~L~~~~~~l~~  202 (276)
                      ++|...++.+.+
T Consensus       107 ~~L~~~v~~~l~  118 (121)
T d1xhfa1         107 RELTIRARNLLS  118 (121)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHh
Confidence            999666655543

>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=99.93  E-value=2.6e-25  Score=180.22  Aligned_cols=119  Identities=24%  Similarity=0.432  Sum_probs=109.1

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhCC--CEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHH
Q 023816           28 EEVHVLAVDDSFVDRKVIERLLTISS--CKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKK  105 (276)
Q Consensus        28 ~~~~VLIVdD~~~~~~~L~~~L~~~g--~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~  105 (276)
                      +|++||||||++..++.++.+|+..|  +.|..+.+|++|++.+           ++..||+||+|++||++||++++++
T Consensus         1 ePi~VLiVDD~~~~r~~l~~~L~~~~~~~~v~~a~~~~~al~~~-----------~~~~~DlvllD~~mP~~~G~el~~~   69 (138)
T d1a04a2           1 EPATILLIDDHPMLRTGVKQLISMAPDITVVGEASNGEQGIELA-----------ESLDPDLILLDLNMPGMNGLETLDK   69 (138)
T ss_dssp             CCEEEEEECSCHHHHHHHHHHHTTCTTEEEEEEESSHHHHHHHH-----------HHHCCSEEEEETTSTTSCHHHHHHH
T ss_pred             CCCEEEEECCCHHHHHHHHHHHHhCCCcEEEEEECCHHHHHHHH-----------HhcCCCEEEEecCCCCCCHHHHHHH
Confidence            47999999999999999999998877  4566799999999999           5668999999999999999999999


Q ss_pred             HHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEe
Q 023816          106 IKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIV  185 (276)
Q Consensus       106 Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~  185 (276)
                      ||+..|                                             .+|||++|++.+.+...+|+++||++||.
T Consensus        70 ir~~~~---------------------------------------------~~~vivlt~~~~~~~~~~a~~~Ga~~yl~  104 (138)
T d1a04a2          70 LREKSL---------------------------------------------SGRIVVFSVSNHEEDVVTALKRGADGYLL  104 (138)
T ss_dssp             HHHSCC---------------------------------------------CSEEEEEECCCCHHHHHHHHHTTCSEEEE
T ss_pred             HHhhCC---------------------------------------------CCCEEEEEEECCHHHHHHHHHcCCCEEEE
Confidence            998777                                             79999999999999999999999999999


Q ss_pred             CCCCHHHHHHHHHHHHH
Q 023816          186 KPVKLSDVKRIKDYLTR  202 (276)
Q Consensus       186 KPv~~~~L~~~~~~l~~  202 (276)
                      ||++.++|.+.+..+.+
T Consensus       105 Kp~~~~~L~~~i~~v~~  121 (138)
T d1a04a2         105 KDMEPEDLLKALHQAAA  121 (138)
T ss_dssp             TTCCHHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHC
Confidence            99999999777776654

>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=99.92  E-value=3.5e-25  Score=176.84  Aligned_cols=117  Identities=19%  Similarity=0.353  Sum_probs=104.0

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhCC-CE-EEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHH
Q 023816           30 VHVLAVDDSFVDRKVIERLLTISS-CK-VTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIK  107 (276)
Q Consensus        30 ~~VLIVdD~~~~~~~L~~~L~~~g-~~-v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir  107 (276)
                      +|||||||++..++.++++|+..| +. |..+.||++|++.+           +...||+||+|+.||+|||+|++++||
T Consensus         2 irILivDD~~~~~~~l~~~L~~~~~~~~v~~a~~g~~al~~~-----------~~~~~dlillD~~mP~~dG~e~~~~ir   70 (123)
T d1dz3a_           2 IKVCIADDNRELVSLLDEYISSQPDMEVIGTAYNGQDCLQML-----------EEKRPDILLLDIIMPHLDGLAVLERIR   70 (123)
T ss_dssp             EEEEEECSCHHHHHHHHHHHHTSTTEEEEEEESSHHHHHHHH-----------HHHCCSEEEEESCCSSSCHHHHHHHHH
T ss_pred             cEEEEEeCCHHHHHHHHHHHHhCCCcEEEEEECCHHHHHHHH-----------HhcCCCEEEEcCCCCCCCHHHHHHHHH
Confidence            799999999999999999999876 44 45799999999999           566899999999999999999999999


Q ss_pred             hhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCC
Q 023816          108 VTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKP  187 (276)
Q Consensus       108 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KP  187 (276)
                      +..+                                            ..+|||++|++...+...+|++.||++||.||
T Consensus        71 ~~~~--------------------------------------------~~~~ii~~t~~~~~~~~~~a~~~Ga~~~l~KP  106 (123)
T d1dz3a_          71 AGFE--------------------------------------------HQPNVIMLTAFGQEDVTKKAVELGASYFILKP  106 (123)
T ss_dssp             HHCS--------------------------------------------SCCEEEEEEETTCHHHHHHHHHTTCEEEEECS
T ss_pred             hcCC--------------------------------------------CCCeEEEEECcCCHHHHHHHHHCCCCEEEECC
Confidence            7544                                            14579999999999999999999999999999


Q ss_pred             CCHHHHHHHHHHHH
Q 023816          188 VKLSDVKRIKDYLT  201 (276)
Q Consensus       188 v~~~~L~~~~~~l~  201 (276)
                      ++.++|.+.++++.
T Consensus       107 ~~~~~L~~~i~~v~  120 (123)
T d1dz3a_         107 FDMENLAHHIRQVY  120 (123)
T ss_dssp             SCCTTHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHH
Confidence            99999977666554

>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=99.92  E-value=8.3e-25  Score=174.20  Aligned_cols=115  Identities=22%  Similarity=0.265  Sum_probs=104.1

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHh
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKV  108 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~  108 (276)
                      +.|||||||++..++.++.+|+..|+ +.++.+|++|++.             ...||+||+|+.||++||+++++++|.
T Consensus         2 M~kILiVDDd~~~~~~l~~~L~~~g~-v~~~~~~~~al~~-------------~~~~dlillD~~mP~~~G~~~~~~lr~   67 (120)
T d1p2fa2           2 MWKIAVVDDDKNILKKVSEKLQQLGR-VKTFLTGEDFLND-------------EEAFHVVVLDVMLPDYSGYEICRMIKE   67 (120)
T ss_dssp             CEEEEEECSCHHHHHHHHHHHTTTEE-EEEESSHHHHHHC-------------CSCCSEEEEESBCSSSBHHHHHHHHHH
T ss_pred             CCEEEEEECCHHHHHHHHHHHHhCCE-EEEECCHHHHHhc-------------CCCCCEEEEeCcccccchhHHHHHHhh
Confidence            46999999999999999999999986 8889999999762             346999999999999999999999998


Q ss_pred             hCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCC
Q 023816          109 TTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPV  188 (276)
Q Consensus       109 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv  188 (276)
                      ..|                                             .+|||++|+..+.+...+|++.||+|||.||+
T Consensus        68 ~~~---------------------------------------------~~~ii~it~~~~~~~~~~a~~~Ga~dyl~KP~  102 (120)
T d1p2fa2          68 TRP---------------------------------------------ETWVILLTLLSDDESVLKGFEAGADDYVTKPF  102 (120)
T ss_dssp             HCT---------------------------------------------TSEEEEEESCCSHHHHHHHHHHTCSEEEESSC
T ss_pred             cCC---------------------------------------------CCcEEEEecCCCHHHHHHHHHCCCCEEEECCC
Confidence            777                                             89999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHHH
Q 023816          189 KLSDVKRIKDYLTR  202 (276)
Q Consensus       189 ~~~~L~~~~~~l~~  202 (276)
                      +.++|...++.+.+
T Consensus       103 ~~~~L~~~i~~~l~  116 (120)
T d1p2fa2         103 NPEILLARVKRFLE  116 (120)
T ss_dssp             CHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHH
Confidence            99999666665543

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

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulator for cyanobacterial phytochrome
species: Calothrix sp. pcc 7601, RcpB [TaxId: 1188]

Probab=99.92  E-value=7.1e-25  Score=180.53  Aligned_cols=131  Identities=27%  Similarity=0.403  Sum_probs=109.7

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhCCC--EEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHH
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTISSC--KVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKI  106 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~g~--~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~I  106 (276)
                      .-+||||||++.++..++++|+..|+  +|..+.||++|++++...... .+......||+||+|++||+|||+|++++|
T Consensus         6 ~~~ILiVDD~~~~~~~l~~~L~~~g~~~~v~~a~~g~eAl~~l~~~~~~-~~~~~~~~pdlillD~~mP~~~G~el~~~i   84 (149)
T d1k66a_           6 TQPLLVVEDSDEDFSTFQRLLQREGVVNPIYRCITGDQALDFLYQTGSY-CNPDIAPRPAVILLDLNLPGTDGREVLQEI   84 (149)
T ss_dssp             TSCEEEECCCHHHHHHHHHHHHHTTBCSCEEEECSHHHHHHHHHTCCSS-SCGGGCCCCSEEEECSCCSSSCHHHHHHHH
T ss_pred             CCcEEEEECCHHHHHHHHHHHHHcCCceEEEEECChHHHHHHHHhhccc-cccccccCCCeEEccccccCCCcHHHHHHH
Confidence            34699999999999999999999997  789999999999999532211 011123479999999999999999999999


Q ss_pred             HhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeC
Q 023816          107 KVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVK  186 (276)
Q Consensus       107 r~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~K  186 (276)
                      |+.                                           ...+.+|||++|++...+.+.+|+++||++||.|
T Consensus        85 r~~-------------------------------------------~~~~~ipiI~lT~~~~~~~~~~~~~~Ga~~~l~K  121 (149)
T d1k66a_          85 KQD-------------------------------------------EVLKKIPVVIMTTSSNPKDIEICYSYSISSYIVK  121 (149)
T ss_dssp             TTS-------------------------------------------TTGGGSCEEEEESCCCHHHHHHHHHTTCSEEEEC
T ss_pred             Hhc-------------------------------------------cccCCCeEEEEeCCCCHHHHHHHHHCCCCEEEEC
Confidence            962                                           2345799999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHHHHh
Q 023816          187 PVKLSDVKRIKDYLTRD  203 (276)
Q Consensus       187 Pv~~~~L~~~~~~l~~~  203 (276)
                      |++..+|...+..+.+.
T Consensus       122 P~~~~~L~~~i~~~l~~  138 (149)
T d1k66a_         122 PLEIDRLTETVQTFIKY  138 (149)
T ss_dssp             CSSHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHH
Confidence            99999997666665543

>d1w25a2 c.23.1.1 (A:141-293) Response regulator PleD, receiver domain {Caulobacter crescentus [TaxId: 155892]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulator PleD, receiver domain
species: Caulobacter crescentus [TaxId: 155892]

Probab=99.91  E-value=5.8e-24  Score=176.22  Aligned_cols=117  Identities=21%  Similarity=0.298  Sum_probs=101.2

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHHh
Q 023816           29 EVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIKV  108 (276)
Q Consensus        29 ~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir~  108 (276)
                      +.|||||||++.+++.+..+|+..||.|..  ++.++++.+           ....|||||+|++||++||++++++||.
T Consensus        13 ~~rILiVDD~~~~~~~l~~~L~~~g~~v~~--~~~~~~~~~-----------~~~~~DlillD~~mP~~dG~el~~~ir~   79 (153)
T d1w25a2          13 GGRVLIVDDNERQAQRVAAELGVEHRPVIE--SDPEKAKIS-----------AGGPVDLVIVNAAAKNFDGLRFTAALRS   79 (153)
T ss_dssp             SCEEEEECSCHHHHHHHHHHHTTTSEEEEE--CCHHHHHHH-----------HHSSCSEEEEETTCSSSCHHHHHHHHHT
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHHCCCEEEE--ccHHHHHHH-----------hcCCCCEEEEECccccccchHHHHHHHh
Confidence            669999999999999999999999998754  456777766           5568999999999999999999999995


Q ss_pred             hCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCCC
Q 023816          109 TTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKPV  188 (276)
Q Consensus       109 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KPv  188 (276)
                      .                                           ...+++|||++|+..+.....+|++.||+|||.||+
T Consensus        80 ~-------------------------------------------~~~~~iPiI~lt~~~~~~~~~~a~~~Ga~d~l~KP~  116 (153)
T d1w25a2          80 E-------------------------------------------ERTRQLPVLAMVDPDDRGRMVKALEIGVNDILSRPI  116 (153)
T ss_dssp             S-------------------------------------------GGGTTCCEEEEECTTCHHHHHHHHHTTCCEEEESSC
T ss_pred             c-------------------------------------------cccccceeEEeecCCCHHHHHHHHhcCcceEEECCC
Confidence            2                                           234489999999999999999999999999999999


Q ss_pred             CHHHHHHHHHHHH
Q 023816          189 KLSDVKRIKDYLT  201 (276)
Q Consensus       189 ~~~~L~~~~~~l~  201 (276)
                      +..+|...+..+.
T Consensus       117 ~~~~L~~~i~~~l  129 (153)
T d1w25a2         117 DPQELSARVKTQI  129 (153)
T ss_dssp             CHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHH
Confidence            9999965444433

>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=99.90  E-value=6.7e-24  Score=169.15  Aligned_cols=113  Identities=21%  Similarity=0.272  Sum_probs=97.8

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHHH
Q 023816           28 EEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKIK  107 (276)
Q Consensus        28 ~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~Ir  107 (276)
                      ++++||||||++..++.++.+|+..||+|..+.+|++|++.+.          +...||+||+|+.||+++|++++++||
T Consensus         1 qp~rILvVdDd~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~----------~~~~~dliilD~~lp~~~G~el~~~ir   70 (118)
T d2b4aa1           1 QPFRVTLVEDEPSHATLIQYHLNQLGAEVTVHPSGSAFFQHRS----------QLSTCDLLIVSDQLVDLSIFSLLDIVK   70 (118)
T ss_dssp             CCCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHTGG----------GGGSCSEEEEETTCTTSCHHHHHHHHT
T ss_pred             CCCEEEEEECCHHHHHHHHHHHHhcCCCeEEECCHHHHHHHHH----------hcCCCCEEEEeCCCCCCCHHHHHHHHH
Confidence            3789999999999999999999999999999999999998772          334699999999999999999999999


Q ss_pred             hhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeCC
Q 023816          108 VTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVKP  187 (276)
Q Consensus       108 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~KP  187 (276)
                      +..+                                             .+|||++|++...  ..++...|+ |||.||
T Consensus        71 ~~~~---------------------------------------------~~pii~lt~~~~~--~~~~~~~~~-dyl~KP  102 (118)
T d2b4aa1          71 EQTK---------------------------------------------QPSVLILTTGRHE--LIESSEHNL-SYLQKP  102 (118)
T ss_dssp             TSSS---------------------------------------------CCEEEEEESCC----CCCCSSSCE-EEEESS
T ss_pred             hcCC---------------------------------------------CCcEEEEECCccH--HHHHhhcCC-CEEECC
Confidence            7655                                             7999999987653  445777787 899999


Q ss_pred             CCHHHHHHHHH
Q 023816          188 VKLSDVKRIKD  198 (276)
Q Consensus       188 v~~~~L~~~~~  198 (276)
                      ++.++|...++
T Consensus       103 ~~~~eL~~~i~  113 (118)
T d2b4aa1         103 FAISELRAAID  113 (118)
T ss_dssp             CCHHHHHHHHH
T ss_pred             CCHHHHHHHHH
Confidence            99999965554

>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=99.90  E-value=1.2e-23  Score=171.06  Aligned_cols=107  Identities=28%  Similarity=0.372  Sum_probs=91.8

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhCC--CEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHH
Q 023816           27 TEEVHVLAVDDSFVDRKVIERLLTISS--CKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLK  104 (276)
Q Consensus        27 ~~~~~VLIVdD~~~~~~~L~~~L~~~g--~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~  104 (276)
                      |..+|||||||++.+++.++++|+..|  +.|..+.||.+|++.+           +...||+||+|++||+|||+++++
T Consensus         1 M~kirVLiVDD~~~~r~~l~~~L~~~g~~~~v~~a~~g~~al~~~-----------~~~~pDlvllDi~MP~~dG~e~~~   69 (140)
T d1a2oa1           1 MSKIRVLSVDDSALMRQIMTEIINSHSDMEMVATAPDPLVARDLI-----------KKFNPDVLTLDVEMPRMDGLDFLE   69 (140)
T ss_dssp             CCCEEEEEECSCHHHHHHHHHHHHTSTTEEEEEEESSHHHHHHHH-----------HHHCCSEEEEECCCSSSCHHHHHH
T ss_pred             CCCCEEEEEeCCHHHHHHHHHHHHhCCCeEEEEEECCHHHHHHHH-----------HhcCCCEEEEcCCCCCCCHHHHHH
Confidence            457899999999999999999999998  4567799999999999           567899999999999999999999


Q ss_pred             HHHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCC-HHHHHHHHhcCCCeE
Q 023816          105 KIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENI-LARIDRCLEDGAEDF  183 (276)
Q Consensus       105 ~Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~-~~~~~~al~~Ga~d~  183 (276)
                      +||+..|                                             ..+|++++.+.. .+...+|++.||+||
T Consensus        70 ~ir~~~~---------------------------------------------~~~i~i~~~~~~~~~~~~~al~~Ga~~y  104 (140)
T d1a2oa1          70 KLMRLRP---------------------------------------------MPVVMVSSLTGKGSEVTLRALELGAIDF  104 (140)
T ss_dssp             HHHHSSC---------------------------------------------CCEEEEECCTHHHHHHHHHHHHHTCCEE
T ss_pred             HHHHhCC---------------------------------------------CCcEEEEEecCCChHHHHHHHHcCCCEE
Confidence            9998776                                             455666555432 356778999999999


Q ss_pred             EeCCCC
Q 023816          184 IVKPVK  189 (276)
Q Consensus       184 l~KPv~  189 (276)
                      |.||+.
T Consensus       105 l~KP~~  110 (140)
T d1a2oa1         105 VTKPQL  110 (140)
T ss_dssp             EECSSS
T ss_pred             EECCCC
Confidence            999964

>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=99.85  E-value=1.1e-21  Score=163.76  Aligned_cols=113  Identities=16%  Similarity=0.141  Sum_probs=98.6

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhCCCEEEEECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCCHHHHHHHH
Q 023816           27 TEEVHVLAVDDSFVDRKVIERLLTISSCKVTAVDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMTGYELLKKI  106 (276)
Q Consensus        27 ~~~~~VLIVdD~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~G~ell~~I  106 (276)
                      ...+|||||||++.+++.|+..|+..||+|..+.++.+|+.               ..||+||+|++||+++|..+. ++
T Consensus         9 l~~~~iLvvdd~~~~~~~l~~~L~~~G~~v~~~~~~~~al~---------------~~~Dlvl~D~~mp~~~~~~~~-~~   72 (189)
T d1qo0d_           9 LRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAFD---------------VPVDVVFTSIFQNRHHDEIAA-LL   72 (189)
T ss_dssp             GGGCEEEEESCTTHHHHHHHHHHHHHTCEEEEECSCCSSCS---------------SCCSEEEEECCSSTHHHHHHH-HH
T ss_pred             ccCCEEEEEeCCHHHHHHHHHHHHHcCCcceecCCHHHhcc---------------CCCCEEEEcCCCCCcHHHHHH-HH
Confidence            45789999999999999999999999999999999887652               369999999999998777665 45


Q ss_pred             HhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcCCCeEEeC
Q 023816          107 KVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDGAEDFIVK  186 (276)
Q Consensus       107 r~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~Ga~d~l~K  186 (276)
                      +...|                                             ++|||++|++.+.+.+.+|++.||+|||.|
T Consensus        73 ~~~~p---------------------------------------------~~pvI~lta~~~~~~~~~al~~Ga~~yL~K  107 (189)
T d1qo0d_          73 AAGTP---------------------------------------------RTTLVALVEYESPAVLSQIIELECHGVITQ  107 (189)
T ss_dssp             HHSCT---------------------------------------------TCEEEEEECCCSHHHHHHHHHHTCSEEEES
T ss_pred             HHcCC---------------------------------------------CCCEEEEeccchHHHHHHHHHcCCcEEEEe
Confidence            55555                                             799999999999999999999999999999


Q ss_pred             CCCHHHHHHHHHHH
Q 023816          187 PVKLSDVKRIKDYL  200 (276)
Q Consensus       187 Pv~~~~L~~~~~~l  200 (276)
                      |++.++|...+..+
T Consensus       108 P~~~~~L~~~i~~~  121 (189)
T d1qo0d_         108 PLDAHRVLPVLVSA  121 (189)
T ss_dssp             SCCGGGHHHHHHHH
T ss_pred             cchhhHHHHHHhhc
Confidence            99999986655543

>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=94.26  E-value=0.28  Score=39.72  Aligned_cols=118  Identities=14%  Similarity=0.063  Sum_probs=76.8

Q ss_pred             ccEEEEE----eCCHHHHHHHHHHHhhCCCEEEEE---CCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCC--CH
Q 023816           29 EVHVLAV----DDSFVDRKVIERLLTISSCKVTAV---DSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGM--TG   99 (276)
Q Consensus        29 ~~~VLIV----dD~~~~~~~L~~~L~~~g~~v~~a---~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~--~G   99 (276)
                      +.+||+.    |-+..-++.+..+|+..||+|...   .+.++.++.+           .+.++|+|.+...+...  .-
T Consensus        37 ~pkVlla~~g~D~Hd~G~~~va~~l~~~G~eVi~lg~~~~~e~iv~aa-----------~~~~advI~iSs~~~~~~~~~  105 (168)
T d7reqa2          37 RPRILLAKMGQDGHDRGQKVIATAYADLGFDVDVGPLFQTPEETARQA-----------VEADVHVVGVSSLAGGHLTLV  105 (168)
T ss_dssp             CCEEEEECBTTCCCCHHHHHHHHHHHHTTCEEEECCTTBCHHHHHHHH-----------HHHTCSEEEEEECSSCHHHHH
T ss_pred             CCeEEEEeCCccHHHHHHHHHHHHHHhCCcceecCCCcCcHHHHHHHH-----------HccCCCEEEEecCcccchHHH
Confidence            5678776    456677888999999999999883   4778888887           56689999998765441  22


Q ss_pred             HHHHHHHHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEecCCCHHHHHHHHhcC
Q 023816          100 YELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSSENILARIDRCLEDG  179 (276)
Q Consensus       100 ~ell~~Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~~~~~~~~~~al~~G  179 (276)
                      -++++.|++..                                            .++++|+ +-+.--..+.....+.|
T Consensus       106 ~~l~~~L~~~g--------------------------------------------~~~v~Vi-vGG~ip~~d~~~l~~~G  140 (168)
T d7reqa2         106 PALRKELDKLG--------------------------------------------RPDILIT-VGGVIPEQDFDELRKDG  140 (168)
T ss_dssp             HHHHHHHHHTT--------------------------------------------CTTSEEE-EEESCCGGGHHHHHHHT
T ss_pred             HHHHHHHHhcC--------------------------------------------CCCeEEE-EeCCCCHHHHHHHHhCC
Confidence            34556666421                                            2345553 44333455667778999


Q ss_pred             CCeEEeCCCCHHHH-HHHHHHHHH
Q 023816          180 AEDFIVKPVKLSDV-KRIKDYLTR  202 (276)
Q Consensus       180 a~d~l~KPv~~~~L-~~~~~~l~~  202 (276)
                      +++....--+..+. ..+++.+..
T Consensus       141 v~~iF~pgt~~~e~a~~~~~~~~~  164 (168)
T d7reqa2         141 AVEIYTPGTVIPESAISLVKKLRA  164 (168)
T ss_dssp             EEEEECTTCCHHHHHHHHHHHHHH
T ss_pred             CCEEECcCCCHHHHHHHHHHHHHH
Confidence            98866544444443 445555443

>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=91.43  E-value=1.4  Score=33.81  Aligned_cols=110  Identities=13%  Similarity=0.062  Sum_probs=72.1

Q ss_pred             ccEEEE--E--eCCHHHHHHHHHHHhhCCCEEEE---ECCHHHHHHHhcccccccccCCCCCceeEEEEecCCCCCC--H
Q 023816           29 EVHVLA--V--DDSFVDRKVIERLLTISSCKVTA---VDSGRRALQFLGLDEEQSINGFDGLKVDLIITDYCMPGMT--G   99 (276)
Q Consensus        29 ~~~VLI--V--dD~~~~~~~L~~~L~~~g~~v~~---a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~~mp~~~--G   99 (276)
                      +-+||+  +  |-+..-...+..+|+..||+|..   ....++.++.+           .+.++|+|.+...|....  -
T Consensus         3 k~kVvi~~~~gD~H~lG~~mva~~l~~~G~~V~~LG~~~p~e~iv~a~-----------~~~~~d~v~lS~~~~~~~~~~   71 (137)
T d1ccwa_           3 KKTIVLGVIGSDCHAVGNKILDHAFTNAGFNVVNIGVLSPQELFIKAA-----------IETKADAILVSSLYGQGEIDC   71 (137)
T ss_dssp             CCEEEEEEETTCCCCHHHHHHHHHHHHTTCEEEEEEEEECHHHHHHHH-----------HHHTCSEEEEEECSSTHHHHH
T ss_pred             CCEEEEEecCCChhHHHHHHHHHHHHHCCCeEEecccccCHHHHHHHH-----------HhcCCCEEEEeeccccchHHH
Confidence            345555  3  44556677889999999999986   34778888887           566899999999887531  1


Q ss_pred             HHHHHHHHhhCCCCcccchheehhhhhhhhhhhhhccccCCcCCCCCcccccccCCCCCeEEEEec----CCC-HHHHHH
Q 023816          100 YELLKKIKVTTPFNFLYSTIIVFLNLQNLFLFILSICFCFPFFFPSNNLEQDSSALREIPVVIMSS----ENI-LARIDR  174 (276)
Q Consensus       100 ~ell~~Ir~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ipiV~ls~----~~~-~~~~~~  174 (276)
                      .++++.+|+.                                            ...++||++=-+    ... .....+
T Consensus        72 ~~~~~~l~~~--------------------------------------------~~~~i~iivGG~~~~~~~~~~~~~~~  107 (137)
T d1ccwa_          72 KGLRQKCDEA--------------------------------------------GLEGILLYVGGNIVVGKQHWPDVEKR  107 (137)
T ss_dssp             TTHHHHHHHT--------------------------------------------TCTTCEEEEEESCSSSSCCHHHHHHH
T ss_pred             HHHHHHHHHh--------------------------------------------ccCCCEEEEeCCcCCCccccHHHHHH
Confidence            2345555542                                            233677654322    222 334555


Q ss_pred             HHhcCCCeEEeCCCCHHHH
Q 023816          175 CLEDGAEDFIVKPVKLSDV  193 (276)
Q Consensus       175 al~~Ga~d~l~KPv~~~~L  193 (276)
                      ..+.|++.......+.+++
T Consensus       108 l~~~Gv~~if~~~t~~~~~  126 (137)
T d1ccwa_         108 FKDMGYDRVYAPGTPPEVG  126 (137)
T ss_dssp             HHHTTCSEECCTTCCHHHH
T ss_pred             HHHcCCCEEECCCCCHHHH
Confidence            6688988887777666665

>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=85.82  E-value=2.4  Score=33.55  Aligned_cols=69  Identities=10%  Similarity=0.116  Sum_probs=48.1

Q ss_pred             ccEEEEE----eCCHHHHHHHHHHHhhCC---------CEEEE---ECCHHHHHHHhcccccccccCCCCCceeEEEEec
Q 023816           29 EVHVLAV----DDSFVDRKVIERLLTISS---------CKVTA---VDSGRRALQFLGLDEEQSINGFDGLKVDLIITDY   92 (276)
Q Consensus        29 ~~~VLIV----dD~~~~~~~L~~~L~~~g---------~~v~~---a~~g~~al~~l~~~~~~~~~~~~~~~~DlIL~D~   92 (276)
                      +.+|++.    |=+..=.+.+..+|+..|         |+|..   -.+.++.++.+           .+.++|+|-+..
T Consensus        19 ~~~vv~~~~g~D~HdiG~~iv~~~l~~~G~~~~~~~~~~eVi~LG~~vp~e~~v~~a-----------~e~~~d~VglS~   87 (160)
T d1xrsb1          19 KIVVVGASTGTDAHTVGIDAIMNMKGYAGHYGLERYEMIDAYNLGSQVANEDFIKKA-----------VELEADVLLVSQ   87 (160)
T ss_dssp             CEEEEEEEBTTCCCCHHHHHHHSTTCBTTBCCGGGCTTEEEEECCSSBCHHHHHHHH-----------HHTTCSEEEEEC
T ss_pred             CcEEEEEEeCCcHHHHHHHHHHHHHHHcCCcccccccceEEEeCCCCCCHHHHHHHH-----------HhcCCCEEEEee
Confidence            4455543    344556677888999999         77775   33677888887           667899999999


Q ss_pred             CCCCCCH-----HHHHHHHHh
Q 023816           93 CMPGMTG-----YELLKKIKV  108 (276)
Q Consensus        93 ~mp~~~G-----~ell~~Ir~  108 (276)
                      -|....+     -++++.+++
T Consensus        88 l~t~~~~h~~~~~~~i~~l~~  108 (160)
T d1xrsb1          88 TVTQKNVHIQNMTHLIELLEA  108 (160)
T ss_dssp             CCCTTSHHHHHHHHHHHHHHH
T ss_pred             cccccchhHHHHHHHHHHHHH
Confidence            8875443     245666665