Citrus Sinensis ID: 048660

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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---
Protein Sequence
MNMKQYLQIFEPICVQFKPYKSQKSCSTTLNSPPRPQCTGAPTQRFPFAYSLTQTHNILTKTHQRLVKEKKFKETNRGFPFWAMATVAECSKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD
Secondary Structure (PSIPRED)
cccEEEEEEEEcEEEEEEEccccccEEEEEccccccccccccccEEEEEEEcccccHHHHHHHHHHHHHHHcccccccccccccHHHHccccccEEEEEcccHHHHHHHHHHHHHcccEEEEEccHHHHHHHHHccccccccccccccccEEEEEcccccccHHHHHHHHHcccccccccEEEEEccccHHcHHHHHHHcccccccccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHcHHHHHcccHHccccccEccccccccEEcccccccccHHHHHHHHHHHHHcHHHHHHHHcccccccccccccccccccccccccEEEEEcccHHHHHHHHHHHHHcccEEEEEccHHHHHHHHHHccccccccHccccccEEEEEcccccccHHHHHHHHHcccccccccEEEEEccccHHHHHHHHHccccEEEEccccccc
Coil and Loop (DISEMBL)
MNMKQYLQIFEPicvqfkpyksqkscsttlnspprpqctgaptqrfpfaysltqtHNILTKTHQRLVKEKkfketnrgfpfwAMATVAECSKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYlgldgeqsnvgfdalKVNLIItdytmpgmtGYELLKKIkessvfrevpVVIMSSEDVLTQIDSCLEEgaeeyivkpvklsd
Flexible Loop (DISEMBL)
MNMKQYLQIFEPICVQFKPYKSQKSCSTTLNSPPRPQCTGAPTQRFPFAYSLTQTHNILTKTHQRLVKEKKFKETNRGFPFWAMATVAECSKELHVLAVDDSYVDRKLIERLLqissckvtavESGTRALQYLgldgeqsnvgfDALKVNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCleegaeeyivkpvklsd
Low Complexity Region (SEG)
MNMKQYLQIFEPICVQFKPYKSQKSCSTTLNSPPRPQCTGAPTQRFPFAYSLTQTHNILTKTHQRLVKEKKFKETNRGFPFWAMATVAECSKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD
Disordered region (IsUnstruct)
*****YLQIFEPICVQFKPY***********************QRFPFAYSLTQTHNILTKTHQRLVKEKKFKETNRGFPFWAMATVAECSKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIV*******
Disordered Region (DISOPRED)
**MKQYLQIFEPICVQFKPYK***************************AYSLTQ*****************************************VLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKL**
Disordered Region (DISEMBL)
MNMKQYLQIFEPICVQFKP******************CTGAPTQRFPFAYSLTQTHNILTKTHQRLVKEKKFKETNRGFPFWAMATVAECSKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD
Disordered Region (DISPRO)
*NMKQYLQIFEPICVQFKPYKSQKSCSTTLNSPPRPQCTGAPTQRFPFAYSLTQTHNILTKTHQRLVKEKK*******************SKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPV****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MNMKQYLQIFEPICVQFKPYKSQKSCSTTLNSPPRPQCTGAPTQRFPFAYSLTQTHNILTKTHQRLVKEKKFKETNRGFPFWAMATVAECSKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD
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	213	2.2.26 [Sep-21-2011]
Q9ZWS6	186	Two-component response re	yes	no	0.563	0.645	0.791	2e-51
Q9SB04	184	Two-component response re	no	no	0.572	0.663	0.772	5e-51
Q7G8V2	206	Two-component response re	no	no	0.568	0.587	0.735	2e-48
Q9ZWS7	206	Two-component response re	no	no	0.568	0.587	0.752	2e-48
O82798	259	Two-component response re	no	no	0.568	0.467	0.760	2e-48
Q9ZWS9	231	Two-component response re	no	no	0.577	0.532	0.731	7e-48
Q9FPR6	153	Two-component response re	no	no	0.647	0.901	0.582	5e-41
O80366	234	Two-component response re	no	no	0.600	0.547	0.607	2e-40
O80365	225	Two-component response re	no	no	0.596	0.564	0.585	3e-39
Q9SHC2	164	Two-component response re	no	no	0.563	0.731	0.645	1e-38

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

 Score =  202 bits (513), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 95/120 (79%), Positives = 111/120 (92%)

Query: 94  LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLII 153
           LHVLAVDDS+VDRK IERLL++SSCKVT V+S TRALQYLGLD E+ +VGF+ LKVNLI+
Sbjct: 25  LHVLAVDDSHVDRKFIERLLRVSSCKVTVVDSATRALQYLGLDVEEKSVGFEDLKVNLIM 84

Query: 154 TDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD 213
           TDY+MPGMTGYELLKKIKESS FREVPVVIMSSE++L +ID CLEEGAE++++KPVKLSD
Sbjct: 85  TDYSMPGMTGYELLKKIKESSAFREVPVVIMSSENILPRIDRCLEEGAEDFLLKPVKLSD 144

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 =  200 bits (509), Expect = 5e-51,   Method: Compositional matrix adjust.
 Identities = 95/123 (77%), Positives = 112/123 (91%), Gaps = 1/123 (0%)

Query: 92  KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQ-SNVGFDALKVN 150
           K LHVLAVDDS VDRK IERLL++SSCKVT V+S TRALQYLGLDGE  S+VGF+ LK+N
Sbjct: 23  KLLHVLAVDDSMVDRKFIERLLRVSSCKVTVVDSATRALQYLGLDGENNSSVGFEDLKIN 82

Query: 151 LIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVK 210
           LI+TDY+MPGMTGYELLKKIKESS FRE+PVVIMSSE++L +ID CLEEGAE++++KPVK
Sbjct: 83  LIMTDYSMPGMTGYELLKKIKESSAFREIPVVIMSSENILPRIDRCLEEGAEDFLLKPVK 142

Query: 211 LSD 213
           L+D
Sbjct: 143 LAD 145

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 =  192 bits (488), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 89/121 (73%), Positives = 108/121 (89%)

Query: 93  ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLI 152
           ELHVLAVDDS+VDRK+IERLL+IS+CKVT VESGTRALQYLGLDG+  + G   LKVNLI
Sbjct: 17  ELHVLAVDDSFVDRKVIERLLKISACKVTTVESGTRALQYLGLDGDNGSSGLKDLKVNLI 76

Query: 153 ITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS 212
           +TDY+MPG+TGYELLKKIKESS  RE+PVVIMSSE++  +I+ C+ EGAEE+++KPVKL+
Sbjct: 77  VTDYSMPGLTGYELLKKIKESSALREIPVVIMSSENIQPRIEQCMIEGAEEFLLKPVKLA 136

Query: 213 D 213
           D
Sbjct: 137 D 137

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 =  192 bits (487), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 91/121 (75%), Positives = 107/121 (88%)

Query: 93  ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLI 152
           ELHVLAVDDS VDRK+IERLL+ISSCKVT VESGTRALQYLGLDG +       LKVNLI
Sbjct: 23  ELHVLAVDDSIVDRKVIERLLRISSCKVTTVESGTRALQYLGLDGGKGASNLKDLKVNLI 82

Query: 153 ITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS 212
           +TDY+MPG++GY+LLKKIKESS FREVPVVIMSSE++L +I  CL+EGAEE+++KPVKL+
Sbjct: 83  VTDYSMPGLSGYDLLKKIKESSAFREVPVVIMSSENILPRIQECLKEGAEEFLLKPVKLA 142

Query: 213 D 213
           D
Sbjct: 143 D 143

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 =  191 bits (486), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 92/121 (76%), Positives = 111/121 (91%)

Query: 93  ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLI 152
           E+HVLAVDDS VDR +IERLL+I+SCKVTAV+SG RAL++LGLD E+++  FD LKV+LI
Sbjct: 33  EVHVLAVDDSLVDRIVIERLLRITSCKVTAVDSGWRALEFLGLDNEKASAEFDRLKVDLI 92

Query: 153 ITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS 212
           ITDY MPGMTGYELLKKIKESS FREVPVVIMSSE+VLT+ID CLEEGA+++++KPVKL+
Sbjct: 93  ITDYCMPGMTGYELLKKIKESSNFREVPVVIMSSENVLTRIDRCLEEGAQDFLLKPVKLA 152

Query: 213 D 213
           D
Sbjct: 153 D 153

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

 Score =  190 bits (482), Expect = 7e-48,   Method: Compositional matrix adjust.
 Identities = 90/123 (73%), Positives = 112/123 (91%)

Query: 91  SKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVN 150
           S ++HVLAVDDS VDR +IERLL+I+SCKVTAV+SG RAL++LGLD +++ V FD LKV+
Sbjct: 30  SDQVHVLAVDDSLVDRIVIERLLRITSCKVTAVDSGWRALEFLGLDDDKAAVEFDRLKVD 89

Query: 151 LIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVK 210
           LIITDY MPGMTGYELLKKIKES+ F+EVPVVIMSSE+V+T+ID CLEEGAE++++KPVK
Sbjct: 90  LIITDYCMPGMTGYELLKKIKESTSFKEVPVVIMSSENVMTRIDRCLEEGAEDFLLKPVK 149

Query: 211 LSD 213
           L+D
Sbjct: 150 LAD 152

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 =  167 bits (423), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 81/139 (58%), Positives = 111/139 (79%), Gaps = 1/139 (0%)

Query: 76  NRGFPFWAMATVAECSKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGL 135
           N+G    + + ++   +ELHVLAVDD+ +DRKL+ER+L+ISSCKVT  E+G RAL+YLGL
Sbjct: 2   NKGCGSGSDSCLSSMEEELHVLAVDDNLIDRKLVERILKISSCKVTTAENGLRALEYLGL 61

Query: 136 -DGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQID 194
            D +Q++   + +KVNLIITDY MPGMTG+ELLKK+KESS  +EVPVVI+SSE++ T+I+
Sbjct: 62  GDPQQTDSLTNVMKVNLIITDYCMPGMTGFELLKKVKESSNLKEVPVVILSSENIPTRIN 121

Query: 195 SCLEEGAEEYIVKPVKLSD 213
            CL  GA+ ++ KP+KLSD
Sbjct: 122 KCLASGAQMFMQKPLKLSD 140

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 =  165 bits (418), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 85/140 (60%), Positives = 104/140 (74%), Gaps = 12/140 (8%)

Query: 84  MATVAECSKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGL----DGEQ 139
           M   AE   + HVLAVDDS  DRKLIERLLQ SSC+VT V+SG++AL++LGL    D   
Sbjct: 1   MGMAAES--QFHVLAVDDSLFDRKLIERLLQKSSCQVTTVDSGSKALEFLGLRQSTDSND 58

Query: 140 SN------VGFDALKVNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQI 193
            N      V    ++VNLIITDY MPGMTGY+LLKK+KESS FR++PVVIMSSE+V  +I
Sbjct: 59  PNAFSKAPVNHQVVEVNLIITDYCMPGMTGYDLLKKVKESSAFRDIPVVIMSSENVPARI 118

Query: 194 DSCLEEGAEEYIVKPVKLSD 213
             CLEEGAEE+ +KPV+L+D
Sbjct: 119 SRCLEEGAEEFFLKPVRLAD 138

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 =  161 bits (408), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 79/135 (58%), Positives = 102/135 (75%), Gaps = 8/135 (5%)

Query: 87  VAECSKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVG--- 143
           V E   + HVLAVDDS  DRK+IERLLQ SSC+VT V+SG++AL++LGL  + ++     
Sbjct: 2   VMETESKFHVLAVDDSLFDRKMIERLLQKSSCQVTTVDSGSKALEFLGLRVDDNDPNALS 61

Query: 144 -----FDALKVNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLE 198
                   +++NLIITDY MPGMTGY+LLKK+KES+ FR +PVVIMSSE+V  +I  CLE
Sbjct: 62  TSPQIHQEVEINLIITDYCMPGMTGYDLLKKVKESAAFRSIPVVIMSSENVPARISRCLE 121

Query: 199 EGAEEYIVKPVKLSD 213
           EGAEE+ +KPVKL+D
Sbjct: 122 EGAEEFFLKPVKLAD 136

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 =  159 bits (402), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 82/127 (64%), Positives = 102/127 (80%), Gaps = 7/127 (5%)

Query: 92  KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDAL---- 147
           +ELHVLAVDD+ +DRKL+ERLL+IS CKVT  E+  RAL+YLGL G+Q N   DAL    
Sbjct: 27  EELHVLAVDDNLIDRKLVERLLKISCCKVTTAENALRALEYLGL-GDQ-NQHIDALTCNV 84

Query: 148 -KVNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIV 206
            KV+LIITDY MPGMTG+ELLKK+KESS  REVPVVIMSSE++ T+I+ CL  GA+ ++ 
Sbjct: 85  MKVSLIITDYCMPGMTGFELLKKVKESSNLREVPVVIMSSENIPTRINKCLASGAQMFMQ 144

Query: 207 KPVKLSD 213
           KP+KL+D
Sbjct: 145 KPLKLAD 151

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	213
255540813	221	two-component sensor protein histidine p	0.577	0.556	0.853	2e-55
224135721	223	type-a response regulator [Populus trich	0.577	0.551	0.829	1e-54
224135725	192	type-a arp3-like response regulator [Pop	0.577	0.640	0.829	1e-54
148608693	194	type A response regulator, partial [Malu	0.558	0.613	0.865	2e-54
297733851	296	unnamed protein product [Vitis vinifera]	0.591	0.425	0.801	6e-54
225457164	222	PREDICTED: two-component response regula	0.582	0.558	0.814	7e-54
356516718	204	PREDICTED: two-component response regula	0.568	0.593	0.826	7e-54
351725781	201	uncharacterized protein LOC100306152 [Gl	0.568	0.601	0.826	1e-53
33330864	254	type-A response regulator [Catharanthus	0.577	0.484	0.821	2e-53
356562779	206	PREDICTED: two-component response regula	0.568	0.587	0.826	7e-53

>gi|255540813|ref|XP_002511471.1| two-component sensor protein histidine protein kinase, putative [Ricinus communis] gi|223550586|gb|EEF52073.1| two-component sensor protein histidine protein kinase, putative [Ricinus communis]

 Score =  221 bits (562), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 105/123 (85%), Positives = 119/123 (96%)

Query: 91  SKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVN 150
           S+ELHVLAVDDS VDRK+IERLL+ISSCKVTAV+SGTRALQYLGLDGE+S+VGF+ LKVN
Sbjct: 24  SEELHVLAVDDSLVDRKVIERLLKISSCKVTAVDSGTRALQYLGLDGEKSSVGFNDLKVN 83

Query: 151 LIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVK 210
           LI+TDY+MPGMTGYELLKKIKESS FRE+PVVIMSSE++LT+ID CLEEGAEE+IVKPVK
Sbjct: 84  LIMTDYSMPGMTGYELLKKIKESSAFREIPVVIMSSENILTRIDRCLEEGAEEFIVKPVK 143

Query: 211 LSD 213
           LSD
Sbjct: 144 LSD 146

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

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 =  218 bits (556), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 102/123 (82%), Positives = 118/123 (95%)

Query: 91  SKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVN 150
           S+ELHVLAVDDS+VDRK+IERLL+ISSCKVT VESG+RALQYLGLDGE+S+VGF+ LK+N
Sbjct: 26  SEELHVLAVDDSFVDRKVIERLLKISSCKVTVVESGSRALQYLGLDGEKSSVGFNDLKIN 85

Query: 151 LIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVK 210
           LI+TDY+MPGMTGYELLKKIKESS FRE+PVVIMSSE++L +ID CLEEGAEEYI+KPVK
Sbjct: 86  LIMTDYSMPGMTGYELLKKIKESSAFREIPVVIMSSENILARIDRCLEEGAEEYILKPVK 145

Query: 211 LSD 213
           LSD
Sbjct: 146 LSD 148

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224135725|ref|XP_002322145.1| type-a arp3-like response regulator [Populus trichocarpa] gi|222869141|gb|EEF06272.1| type-a arp3-like response regulator [Populus trichocarpa]

 Score =  218 bits (556), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 102/123 (82%), Positives = 118/123 (95%)

Query: 91  SKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVN 150
           S+ELHVLAVDDS+VDRK+IERLL+ISSCKVT VESG+RALQYLGLDGE+S+VGF+ LK+N
Sbjct: 26  SEELHVLAVDDSFVDRKVIERLLKISSCKVTVVESGSRALQYLGLDGEKSSVGFNDLKIN 85

Query: 151 LIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVK 210
           LI+TDY+MPGMTGYELLKKIKESS FRE+PVVIMSSE++L +ID CLEEGAEEYI+KPVK
Sbjct: 86  LIMTDYSMPGMTGYELLKKIKESSAFREIPVVIMSSENILARIDRCLEEGAEEYILKPVK 145

Query: 211 LSD 213
           LSD
Sbjct: 146 LSD 148

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|148608693|gb|ABQ95670.1| type A response regulator, partial [Malus x domestica]

 Score =  218 bits (554), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 103/119 (86%), Positives = 115/119 (96%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
           HV AVDDS+VDRK+IERLL+ISSCKVTAV+SGTRAL+YLGLDGE+S+VGFD +KVNLIIT
Sbjct: 1   HVFAVDDSHVDRKVIERLLKISSCKVTAVDSGTRALEYLGLDGEKSSVGFDNMKVNLIIT 60

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD 213
           DY+MPGMTGYELLKKIKESS FREVPVVIMSSE++LT+ID CLEEGAEEYIVKPVKLSD
Sbjct: 61  DYSMPGMTGYELLKKIKESSAFREVPVVIMSSENILTRIDRCLEEGAEEYIVKPVKLSD 119

Source: Malus x domestica

Species: Malus x domestica

Genus: Malus

Family: Rosaceae

Order: Rosales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297733851|emb|CBI15098.3| unnamed protein product [Vitis vinifera]

 Score =  216 bits (549), Expect = 6e-54,   Method: Compositional matrix adjust.
 Identities = 101/126 (80%), Positives = 118/126 (93%)

Query: 88  AECSKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDAL 147
           +    ELHVLAVDDS+VDRK+IERLL+ISSCKVTAVESGTRALQ+LGLDGE+++VGFD L
Sbjct: 97  SAAGSELHVLAVDDSHVDRKVIERLLKISSCKVTAVESGTRALQFLGLDGEENSVGFDGL 156

Query: 148 KVNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVK 207
           KVNLI+TDY+MPGMTGYELLKKIKES  FR++PVVIMSSE++LT+ID CLEEGAEE+IVK
Sbjct: 157 KVNLIMTDYSMPGMTGYELLKKIKESKAFRKIPVVIMSSENILTRIDRCLEEGAEEFIVK 216

Query: 208 PVKLSD 213
           PVKL+D
Sbjct: 217 PVKLAD 222

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225457164|ref|XP_002283787.1| PREDICTED: two-component response regulator ARR5-like [Vitis vinifera]

 Score =  216 bits (549), Expect = 7e-54,   Method: Compositional matrix adjust.
 Identities = 101/124 (81%), Positives = 117/124 (94%)

Query: 90  CSKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKV 149
              ELHVLAVDDS+VDRK+IERLL+ISSCKVTAVESGTRALQ+LGLDGE+++VGFD LKV
Sbjct: 25  AGSELHVLAVDDSHVDRKVIERLLKISSCKVTAVESGTRALQFLGLDGEENSVGFDGLKV 84

Query: 150 NLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPV 209
           NLI+TDY+MPGMTGYELLKKIKES  FR++PVVIMSSE++LT+ID CLEEGAEE+IVKPV
Sbjct: 85  NLIMTDYSMPGMTGYELLKKIKESKAFRKIPVVIMSSENILTRIDRCLEEGAEEFIVKPV 144

Query: 210 KLSD 213
           KL+D
Sbjct: 145 KLAD 148

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356516718|ref|XP_003527040.1| PREDICTED: two-component response regulator ARR6-like [Glycine max]

 Score =  216 bits (549), Expect = 7e-54,   Method: Compositional matrix adjust.
 Identities = 100/121 (82%), Positives = 119/121 (98%)

Query: 93  ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLI 152
           +LHVLAVDDS+VDRK+IERLL+ISSCKVT VESG+RALQYLGLDGE+S++GFD++ VNLI
Sbjct: 20  KLHVLAVDDSHVDRKVIERLLKISSCKVTVVESGSRALQYLGLDGEKSSIGFDSVDVNLI 79

Query: 153 ITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS 212
           +TDY+MPGMTGYELLKKIKESSVFREVPVV+MSSE++LT+IDSCLEEGAEE+++KPVKLS
Sbjct: 80  MTDYSMPGMTGYELLKKIKESSVFREVPVVVMSSENILTRIDSCLEEGAEEFLLKPVKLS 139

Query: 213 D 213
           D
Sbjct: 140 D 140

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351725781|ref|NP_001238384.1| uncharacterized protein LOC100306152 [Glycine max] gi|255627697|gb|ACU14193.1| unknown [Glycine max]

 Score =  214 bits (546), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 100/121 (82%), Positives = 119/121 (98%)

Query: 93  ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLI 152
           +LHVLAVDDS+VDRK+IERLL+ISSCKVT VESG+RALQYLGLDGE+S++G D++KVNLI
Sbjct: 20  KLHVLAVDDSHVDRKVIERLLKISSCKVTVVESGSRALQYLGLDGEKSSIGLDSVKVNLI 79

Query: 153 ITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS 212
           +TDY+MPGMTGYELLKKIKESSVFREVPVV+MSSE++LT+IDSCLEEGAEE+++KPVKLS
Sbjct: 80  MTDYSMPGMTGYELLKKIKESSVFREVPVVVMSSENILTRIDSCLEEGAEEFLLKPVKLS 139

Query: 213 D 213
           D
Sbjct: 140 D 140

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|33330864|gb|AAQ10675.1| type-A response regulator [Catharanthus roseus]

 Score =  214 bits (544), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 101/123 (82%), Positives = 114/123 (92%)

Query: 91  SKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVN 150
           +KELHVLAVDDS VDRK+IERLL+IS CKVTAVESG RALQYLGLDGE+S VGFD LKVN
Sbjct: 11  AKELHVLAVDDSLVDRKVIERLLKISCCKVTAVESGRRALQYLGLDGEKSTVGFDGLKVN 70

Query: 151 LIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVK 210
           LI+TDY+MPGMTGYELLKKIK SS  +E+PVVIMSSE++LT+ID CLEEGAEE++VKPVK
Sbjct: 71  LILTDYSMPGMTGYELLKKIKGSSTLKEIPVVIMSSENILTRIDRCLEEGAEEFLVKPVK 130

Query: 211 LSD 213
           LSD
Sbjct: 131 LSD 133

Source: Catharanthus roseus

Species: Catharanthus roseus

Genus: Catharanthus

Family: Apocynaceae

Order: Gentianales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356562779|ref|XP_003549646.1| PREDICTED: two-component response regulator ARR5-like isoform 1 [Glycine max]

 Score =  212 bits (540), Expect = 7e-53,   Method: Compositional matrix adjust.
 Identities = 100/121 (82%), Positives = 116/121 (95%)

Query: 93  ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLI 152
           ELHVLAVDDS VDRK+IERLL+ISSCKVT VESGTRALQYLGL+GE  ++GFD++KVNLI
Sbjct: 25  ELHVLAVDDSLVDRKVIERLLKISSCKVTVVESGTRALQYLGLEGENGSLGFDSVKVNLI 84

Query: 153 ITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS 212
           +TDY+MPGMTGYELLKKIKESSVFRE+PVVIMSSE+VLT+ID CLEEGAE++++KPVKLS
Sbjct: 85  MTDYSMPGMTGYELLKKIKESSVFREIPVVIMSSENVLTRIDRCLEEGAEDFLLKPVKLS 144

Query: 213 D 213
           D
Sbjct: 145 D 145

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	213
TAIR|locus:2170723	186	ARR6 "response regulator 6" [A	0.563	0.645	0.791	5.4e-47
TAIR|locus:2097870	184	RR5 "response regulator 5" [Ar	0.572	0.663	0.772	1.4e-46
TAIR|locus:2027237	206	ARR15 "response regulator 15"	0.577	0.597	0.731	9.1e-45
TAIR|locus:2194584	259	ARR4 "response regulator 4" [A	0.568	0.467	0.760	1.9e-44
TAIR|locus:2011286	206	ARR7 "response regulator 7" [A	0.568	0.587	0.752	3.9e-44
TAIR|locus:2025911	231	ARR3 "response regulator 3" [A	0.577	0.532	0.731	1e-43
TAIR|locus:2102509	153	RR17 "response regulator 17" [	0.647	0.901	0.582	2.6e-38
TAIR|locus:2080590	234	ARR9 "response regulator 9" [A	0.600	0.547	0.607	6.3e-37
TAIR|locus:2040282	225	RR3 "response regulator 3" [Ar	0.596	0.564	0.592	2.7e-36
UNIPROTKB|Q4GZK2	201	rr9 "Type A response regulator	0.600	0.636	0.6	5.1e-35

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

 Score = 492 (178.3 bits), Expect = 5.4e-47, P = 5.4e-47
 Identities = 95/120 (79%), Positives = 111/120 (92%)

Query:    94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLII 153
             LHVLAVDDS+VDRK IERLL++SSCKVT V+S TRALQYLGLD E+ +VGF+ LKVNLI+
Sbjct:    25 LHVLAVDDSHVDRKFIERLLRVSSCKVTVVDSATRALQYLGLDVEEKSVGFEDLKVNLIM 84

Query:   154 TDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD 213
             TDY+MPGMTGYELLKKIKESS FREVPVVIMSSE++L +ID CLEEGAE++++KPVKLSD
Sbjct:    85 TDYSMPGMTGYELLKKIKESSAFREVPVVIMSSENILPRIDRCLEEGAEDFLLKPVKLSD 144

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 = 488 (176.8 bits), Expect = 1.4e-46, P = 1.4e-46
 Identities = 95/123 (77%), Positives = 112/123 (91%)

Query:    92 KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQ-SNVGFDALKVN 150
             K LHVLAVDDS VDRK IERLL++SSCKVT V+S TRALQYLGLDGE  S+VGF+ LK+N
Sbjct:    23 KLLHVLAVDDSMVDRKFIERLLRVSSCKVTVVDSATRALQYLGLDGENNSSVGFEDLKIN 82

Query:   151 LIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVK 210
             LI+TDY+MPGMTGYELLKKIKESS FRE+PVVIMSSE++L +ID CLEEGAE++++KPVK
Sbjct:    83 LIMTDYSMPGMTGYELLKKIKESSAFREIPVVIMSSENILPRIDRCLEEGAEDFLLKPVK 142

Query:   211 LSD 213
             L+D
Sbjct:   143 LAD 145

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 = 471 (170.9 bits), Expect = 9.1e-45, P = 9.1e-45
 Identities = 90/123 (73%), Positives = 109/123 (88%)

Query:    91 SKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVN 150
             S ELHVLAVDDS+VDRK+IERLL+IS+CKVT VESGTRALQYLGLDG+  + G   LKVN
Sbjct:    15 SPELHVLAVDDSFVDRKVIERLLKISACKVTTVESGTRALQYLGLDGDNGSSGLKDLKVN 74

Query:   151 LIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVK 210
             LI+TDY+MPG+TGYELLKKIKESS  RE+PVVIMSSE++  +I+ C+ EGAEE+++KPVK
Sbjct:    75 LIVTDYSMPGLTGYELLKKIKESSALREIPVVIMSSENIQPRIEQCMIEGAEEFLLKPVK 134

Query:   211 LSD 213
             L+D
Sbjct:   135 LAD 137

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

 Score = 468 (169.8 bits), Expect = 1.9e-44, P = 1.9e-44
 Identities = 92/121 (76%), Positives = 111/121 (91%)

Query:    93 ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLI 152
             E+HVLAVDDS VDR +IERLL+I+SCKVTAV+SG RAL++LGLD E+++  FD LKV+LI
Sbjct:    33 EVHVLAVDDSLVDRIVIERLLRITSCKVTAVDSGWRALEFLGLDNEKASAEFDRLKVDLI 92

Query:   153 ITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS 212
             ITDY MPGMTGYELLKKIKESS FREVPVVIMSSE+VLT+ID CLEEGA+++++KPVKL+
Sbjct:    93 ITDYCMPGMTGYELLKKIKESSNFREVPVVIMSSENVLTRIDRCLEEGAQDFLLKPVKLA 152

Query:   213 D 213
             D
Sbjct:   153 D 153

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

 Score = 465 (168.7 bits), Expect = 3.9e-44, P = 3.9e-44
 Identities = 91/121 (75%), Positives = 107/121 (88%)

Query:    93 ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLI 152
             ELHVLAVDDS VDRK+IERLL+ISSCKVT VESGTRALQYLGLDG +       LKVNLI
Sbjct:    23 ELHVLAVDDSIVDRKVIERLLRISSCKVTTVESGTRALQYLGLDGGKGASNLKDLKVNLI 82

Query:   153 ITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS 212
             +TDY+MPG++GY+LLKKIKESS FREVPVVIMSSE++L +I  CL+EGAEE+++KPVKL+
Sbjct:    83 VTDYSMPGLSGYDLLKKIKESSAFREVPVVIMSSENILPRIQECLKEGAEEFLLKPVKLA 142

Query:   213 D 213
             D
Sbjct:   143 D 143

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

 Score = 461 (167.3 bits), Expect = 1.0e-43, P = 1.0e-43
 Identities = 90/123 (73%), Positives = 112/123 (91%)

Query:    91 SKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVN 150
             S ++HVLAVDDS VDR +IERLL+I+SCKVTAV+SG RAL++LGLD +++ V FD LKV+
Sbjct:    30 SDQVHVLAVDDSLVDRIVIERLLRITSCKVTAVDSGWRALEFLGLDDDKAAVEFDRLKVD 89

Query:   151 LIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVK 210
             LIITDY MPGMTGYELLKKIKES+ F+EVPVVIMSSE+V+T+ID CLEEGAE++++KPVK
Sbjct:    90 LIITDYCMPGMTGYELLKKIKESTSFKEVPVVIMSSENVMTRIDRCLEEGAEDFLLKPVK 149

Query:   211 LSD 213
             L+D
Sbjct:   150 LAD 152

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

 Score = 410 (149.4 bits), Expect = 2.6e-38, P = 2.6e-38
 Identities = 81/139 (58%), Positives = 111/139 (79%)

Query:    76 NRGFPFWAMATVAECSKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGL 135
             N+G    + + ++   +ELHVLAVDD+ +DRKL+ER+L+ISSCKVT  E+G RAL+YLGL
Sbjct:     2 NKGCGSGSDSCLSSMEEELHVLAVDDNLIDRKLVERILKISSCKVTTAENGLRALEYLGL 61

Query:   136 -DGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQID 194
              D +Q++   + +KVNLIITDY MPGMTG+ELLKK+KESS  +EVPVVI+SSE++ T+I+
Sbjct:    62 GDPQQTDSLTNVMKVNLIITDYCMPGMTGFELLKKVKESSNLKEVPVVILSSENIPTRIN 121

Query:   195 SCLEEGAEEYIVKPVKLSD 213
              CL  GA+ ++ KP+KLSD
Sbjct:   122 KCLASGAQMFMQKPLKLSD 140

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 = 397 (144.8 bits), Expect = 6.3e-37, P = 6.3e-37
 Identities = 85/140 (60%), Positives = 104/140 (74%)

Query:    84 MATVAECSKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGL----DGEQ 139
             M   AE   + HVLAVDDS  DRKLIERLLQ SSC+VT V+SG++AL++LGL    D   
Sbjct:     1 MGMAAE--SQFHVLAVDDSLFDRKLIERLLQKSSCQVTTVDSGSKALEFLGLRQSTDSND 58

Query:   140 SN------VGFDALKVNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQI 193
              N      V    ++VNLIITDY MPGMTGY+LLKK+KESS FR++PVVIMSSE+V  +I
Sbjct:    59 PNAFSKAPVNHQVVEVNLIITDYCMPGMTGYDLLKKVKESSAFRDIPVVIMSSENVPARI 118

Query:   194 DSCLEEGAEEYIVKPVKLSD 213
               CLEEGAEE+ +KPV+L+D
Sbjct:   119 SRCLEEGAEEFFLKPVRLAD 138

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 = 391 (142.7 bits), Expect = 2.7e-36, P = 2.7e-36
 Identities = 80/135 (59%), Positives = 103/135 (76%)

Query:    87 VAECSKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGL---DGEQSNVG 143
             V E   + HVLAVDDS  DRK+IERLLQ SSC+VT V+SG++AL++LGL   D + + + 
Sbjct:     2 VMETESKFHVLAVDDSLFDRKMIERLLQKSSCQVTTVDSGSKALEFLGLRVDDNDPNALS 61

Query:   144 -----FDALKVNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLE 198
                     +++NLIITDY MPGMTGY+LLKK+KES+ FR +PVVIMSSE+V  +I  CLE
Sbjct:    62 TSPQIHQEVEINLIITDYCMPGMTGYDLLKKVKESAAFRSIPVVIMSSENVPARISRCLE 121

Query:   199 EGAEEYIVKPVKLSD 213
             EGAEE+ +KPVKL+D
Sbjct:   122 EGAEEFFLKPVKLAD 136

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 = 379 (138.5 bits), Expect = 5.1e-35, P = 5.1e-35
 Identities = 81/135 (60%), Positives = 104/135 (77%)

Query:    84 MATVAECSKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGL-DGEQSNV 142
             MA   E     HVLAVDDS  DRKLIERLL+ SS +VT V+SG++AL++LGL D E S +
Sbjct:     1 MAVAIEAP--FHVLAVDDSLPDRKLIERLLKTSSFQVTTVDSGSKALEFLGLHDHEDSPI 58

Query:   143 GFDA----LKVNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLE 198
                +    + VNLIITDY MPGMTGY+LLKKIKESS  R++PVVIMSS+++ ++I+ CLE
Sbjct:    59 STQSDQQEVAVNLIITDYCMPGMTGYDLLKKIKESSYLRDIPVVIMSSDNIPSRINRCLE 118

Query:   199 EGAEEYIVKPVKLSD 213
             EGA+E+ +KPV+LSD
Sbjct:   119 EGADEFFLKPVRLSD 133

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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9ZWS6	ARR6_ARATH	No assigned EC number	0.7916	0.5633	0.6451	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	ARR3	type-a response regulator (193 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	GA2ox7	gibberellin 2-oxidase (322 aa)							•		0.510
	eugene3.00140701	response regulator (144 aa)							•		0.508
	GA2ox5	gibberellin 2-oxidase (306 aa)							•		0.508
	GA2ox2	gibberellin 2-oxidase (322 aa)							•		0.507
	GA2ox4	gibberellin 2-oxidase (322 aa)							•		0.506
	GA2ox3	gibberellin 2-oxidase (332 aa)							•		0.506
	GA2ox1	hypothetical protein (332 aa)							•		0.504
	GA2ox6	gibberellin 2-oxidase (332 aa)							•		0.504
	gw1.XIII.1446.1	serine/threonine protein kinase (574 aa)							•		0.502
	eugene3.00180913	serine/threonine protein kinase (637 aa)							•		0.502

---

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	213
PLN03029	222	PLN03029, PLN03029, type-a response regulator prot	1e-48
cd00156	113	cd00156, REC, Signal receiver domain; originally t	7e-24
COG0784	130	COG0784, CheY, FOG: CheY-like receiver [Signal tra	2e-23
pfam00072	111	pfam00072, Response_reg, Response regulator receiv	8e-22
COG3706	435	COG3706, PleD, Response regulator containing a Che	2e-18
COG2204	464	COG2204, AtoC, Response regulator containing CheY-	5e-14
COG0745	229	COG0745, OmpR, Response regulators consisting of a	5e-13
PRK10610	129	PRK10610, PRK10610, chemotaxis regulatory protein	1e-12
COG2197	211	COG2197, CitB, Response regulator containing a Che	3e-12
COG3437	360	COG3437, COG3437, Response regulator containing a	6e-12
PRK15347	921	PRK15347, PRK15347, two component system sensor ki	1e-11
TIGR01818	463	TIGR01818, ntrC, nitrogen regulation protein NR(I)	4e-11
CHL00148	240	CHL00148, orf27, Ycf27; Reviewed	2e-10
COG4753	475	COG4753, COG4753, Response regulator containing Ch	3e-09
PRK09581	457	PRK09581, pleD, response regulator PleD; Reviewed	1e-08
PRK13856	241	PRK13856, PRK13856, two-component response regulat	5e-08
PRK10923	469	PRK10923, glnG, nitrogen regulation protein NR(I);	6e-08
PRK09390	202	PRK09390, fixJ, response regulator FixJ; Provision	2e-07
TIGR02154	226	TIGR02154, PhoB, phosphate regulon transcriptional	3e-07
smart00448	55	smart00448, REC, cheY-homologous receiver domain	4e-07
PRK10651	216	PRK10651, PRK10651, transcriptional regulator NarL	6e-07
PRK10336	219	PRK10336, PRK10336, DNA-binding transcriptional re	6e-07
TIGR01387	218	TIGR01387, cztR_silR_copR, heavy metal response re	7e-07
PRK11361	457	PRK11361, PRK11361, acetoacetate metabolism regula	8e-07
PRK11517	223	PRK11517, PRK11517, transcriptional regulatory pro	1e-06
PRK11107	919	PRK11107, PRK11107, hybrid sensory histidine kinas	1e-06
COG2201	350	COG2201, CheB, Chemotaxis response regulator conta	2e-06
PRK10161	229	PRK10161, PRK10161, transcriptional regulator PhoB	2e-06
PRK10693	303	PRK10693, PRK10693, response regulator of RpoS; Pr	2e-06
COG3947	361	COG3947, COG3947, Response regulator containing Ch	4e-06
PRK00742	354	PRK00742, PRK00742, chemotaxis-specific methyleste	6e-06
PRK10643	222	PRK10643, PRK10643, DNA-binding transcriptional re	9e-06
PRK10841	924	PRK10841, PRK10841, hybrid sensory kinase in two-c	9e-06
PRK10766	221	PRK10766, PRK10766, DNA-binding transcriptional re	4e-05
PRK15115	444	PRK15115, PRK15115, response regulator GlrR; Provi	8e-05
PRK10403	215	PRK10403, PRK10403, transcriptional regulator NarP	1e-04
PRK11091	779	PRK11091, PRK11091, aerobic respiration control se	2e-04
PRK10529	225	PRK10529, PRK10529, DNA-binding transcriptional ac	2e-04
PRK10365	441	PRK10365, PRK10365, transcriptional regulatory pro	3e-04
PRK09959	1197	PRK09959, PRK09959, hybrid sensory histidine kinas	3e-04
PRK11083	228	PRK11083, PRK11083, DNA-binding response regulator	3e-04
PRK10955	232	PRK10955, PRK10955, DNA-binding transcriptional re	3e-04
PRK10710	240	PRK10710, PRK10710, DNA-binding transcriptional re	4e-04
PRK09836	227	PRK09836, PRK09836, DNA-binding transcriptional ac	0.002
PRK09468	239	PRK09468, ompR, osmolarity response regulator; Pro	0.002
COG4566	202	COG4566, TtrR, Response regulator [Signal transduc	0.002
TIGR02875	262	TIGR02875, spore_0_A, sporulation transcription fa	0.002
PRK11173	237	PRK11173, PRK11173, two-component response regulat	0.003
COG4565	224	COG4565, CitB, Response regulator of citrate/malat	0.003
PRK15479	221	PRK15479, PRK15479, transcriptional regulatory pro	0.003

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

 Score =  158 bits (400), Expect = 1e-48
 Identities = 79/130 (60%), Positives = 102/130 (78%), Gaps = 9/130 (6%)

Query: 93  ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGL-DGEQSNV--------G 143
           + HVLAVDDS +DRKLIE+LL+ SS +VT V+SG++AL++LGL + ++SN          
Sbjct: 8   QFHVLAVDDSLIDRKLIEKLLKTSSYQVTTVDSGSKALKFLGLHEDDRSNPDTPSVSPNS 67

Query: 144 FDALKVNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEE 203
              ++VNLIITDY MPGMTGY+LLKKIKESS  R +PVVIMSSE+V ++I  CLEEGAEE
Sbjct: 68  HQEVEVNLIITDYCMPGMTGYDLLKKIKESSSLRNIPVVIMSSENVPSRITRCLEEGAEE 127

Query: 204 YIVKPVKLSD 213
           + +KPV+LSD
Sbjct: 128 FFLKPVQLSD 137

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 = 91.1 bits (227), Expect = 7e-24
 Identities = 35/117 (29%), Positives = 58/117 (49%), Gaps = 13/117 (11%)

Query: 97  LAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDY 156
           L VDD  + R+L+ RLL+    +V   E G  AL  L              K +LI+ D 
Sbjct: 1   LIVDDDPLIRELLRRLLEKEGYEVVEAEDGEEALALL-----------AEEKPDLILLDI 49

Query: 157 TMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD 213
            MPGM G ELL++I++     ++P++ +++          L+ GA++Y+ KP    +
Sbjct: 50  MMPGMDGLELLRRIRKR--GPDIPIIFLTAHGDDEDAVEALKAGADDYLTKPFSPEE 104

Length = 113

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

 Score = 90.3 bits (224), Expect = 2e-23
 Identities = 36/119 (30%), Positives = 62/119 (52%), Gaps = 13/119 (10%)

Query: 92  KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTR-ALQYLGLDGEQSNVGFDALKVN 150
             L VL VDD  V+R+L++RLL+    +V     G   AL+ L           +  + +
Sbjct: 4   SGLRVLVVDDEPVNRRLLKRLLEDLGYEVVEAADGEEEALELLR----------ELPQPD 53

Query: 151 LIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPV 209
           LI+ D  MPGM G ELL++++       +PV+++++       +  L  GA++Y+ KP+
Sbjct: 54  LILLDINMPGMDGIELLRRLRAR--GPNIPVILLTAYADEADRERALAAGADDYLTKPI 110

Length = 130

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

 Score = 85.7 bits (213), Expect = 8e-22
 Identities = 33/118 (27%), Positives = 56/118 (47%), Gaps = 13/118 (11%)

Query: 96  VLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITD 155
           VL VDD  + R+L+ +LL+     V   + G  AL+ L              + +LI+ D
Sbjct: 1   VLIVDDDPLIRELLRQLLEKEGYVVAEADDGEEALELL-----------KEKRPDLILLD 49

Query: 156 YTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD 213
             MPGM G ELL++I+        PV+++++          L+ GA +++ KP    +
Sbjct: 50  IRMPGMDGLELLRRIRRRPP--TTPVIVLTAHGDEEDAVEALKAGANDFLSKPFDPEE 105

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 = 82.0 bits (203), Expect = 2e-18
 Identities = 33/114 (28%), Positives = 56/114 (49%), Gaps = 11/114 (9%)

Query: 96  VLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITD 155
           +L VDD    R+ + R+LQ+   +V     G  AL  L             L  +L++ D
Sbjct: 135 ILVVDDDATQRERLRRILQVEGFRVVEATDGEEALLQL-----------AELPPDLVLLD 183

Query: 156 YTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPV 209
             MP M G EL  ++++    R++P++++SS+D    +    E G  +YI KP+
Sbjct: 184 ANMPDMDGLELCTRLRQLERTRDIPIILLSSKDDDELVVRAFELGVNDYITKPI 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 = 69.6 bits (171), Expect = 5e-14
 Identities = 40/123 (32%), Positives = 64/123 (52%), Gaps = 15/123 (12%)

Query: 90  CSKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKV 149
                 +L VDD    R+L+E+ L+++  +V   ES   AL+ L          FD    
Sbjct: 1   MMMMARILVVDDDPDIRELLEQALELAGYEVVTAESAEEALEALSESP------FD---- 50

Query: 150 NLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSE-DVLTQIDSCLEEGAEEYIVKP 208
            L++ D  MPGM G ELLK+IK      ++PV++M+   D+ T +++ L  GA +++ KP
Sbjct: 51  -LVLLDIRMPGMDGLELLKEIKSRDP--DLPVIVMTGHGDIDTAVEA-LRLGAFDFLEKP 106

Query: 209 VKL 211
             L
Sbjct: 107 FDL 109

Length = 464

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

 Score = 65.0 bits (159), Expect = 5e-13
 Identities = 25/115 (21%), Positives = 50/115 (43%), Gaps = 13/115 (11%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
            +L V+D     +L++  L+    +V     G  AL+             D     L++ 
Sbjct: 2   RILLVEDDPELAELLKEYLEEEGYEVDVAADGEEALEAA-------REQPD-----LVLL 49

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPV 209
           D  +P + G EL ++++        P++++++ D        LE GA++Y+ KP 
Sbjct: 50  DLMLPDLDGLELCRRLRAKK-GSGPPIIVLTARDDEEDRVLGLEAGADDYLTKPF 103

Length = 229

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

 Score = 62.3 bits (151), Expect = 1e-12
 Identities = 39/118 (33%), Positives = 57/118 (48%), Gaps = 12/118 (10%)

Query: 92  KELHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVN 150
           KEL  L VDD    R+++  LL ++    V   E G  AL  L         GF      
Sbjct: 4   KELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKL------QAGGFG----- 52

Query: 151 LIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
            +I+D+ MP M G ELLK I+       +PV+++++E     I +  + GA  Y+VKP
Sbjct: 53  FVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKP 110

Length = 129

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

 Score = 62.7 bits (153), Expect = 3e-12
 Identities = 31/117 (26%), Positives = 55/117 (47%), Gaps = 15/117 (12%)

Query: 95  HVLAVDDSYVDRKLIERLL-QISSCKVTAV-ESGTRALQYLGLDGEQSNVGFDALKVNLI 152
            VL VDD  + R+ + +LL      +V     +G  AL                LK +++
Sbjct: 2   KVLIVDDHPLVREGLRQLLELEPDLEVVGEASNGEEALDLA-----------RELKPDVV 50

Query: 153 ITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPV 209
           + D +MPGM G E LK+++      ++ VV++++ D    +   L  GA+ Y++K  
Sbjct: 51  LLDLSMPGMDGLEALKQLRAR--GPDIKVVVLTAHDDPAYVIRALRAGADGYLLKDA 105

Length = 211

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

 Score = 63.5 bits (155), Expect = 6e-12
 Identities = 38/131 (29%), Positives = 65/131 (49%), Gaps = 12/131 (9%)

Query: 84  MATVAECSKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVG 143
           M    E  ++L VL VDD   + + + +LL++   +V   E+G  AL+ L     Q    
Sbjct: 5   MQGKNEPDEKLTVLLVDDEPDNLEALRQLLRMIGYRVIEAENGEEALKLL-----QEEP- 58

Query: 144 FDALKVNLIITDYTMPGMTGYELLKKIKESS-VFREVPVVIMSSEDVLTQIDSCLEEGAE 202
                 +L++ D  MP M G E+L K+K  S   R +PV+++++          LE GA+
Sbjct: 59  -----PDLVLLDVRMPEMDGAEVLNKLKAMSPSTRRIPVILLTAYADSEDRQRALEAGAD 113

Query: 203 EYIVKPVKLSD 213
           +Y+ KP+   +
Sbjct: 114 DYLSKPISPKE 124

Length = 360

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

 Score = 63.1 bits (154), Expect = 1e-11
 Identities = 35/122 (28%), Positives = 57/122 (46%), Gaps = 13/122 (10%)

Query: 94  LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLII 153
           L +L VDD   +R +I  +L     +VT   SGT AL+     G Q    FD     L++
Sbjct: 691 LQILLVDDVETNRDIIGMMLVELGQQVTTAASGTEALEL----GRQHR--FD-----LVL 739

Query: 154 TDYTMPGMTGYELLKKIKESS--VFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKL 211
            D  MPG+ G E  +  ++    +  +  +V +++     +I  C + G   Y+ KPV L
Sbjct: 740 MDIRMPGLDGLETTQLWRDDPNNLDPDCMIVALTANAAPEEIHRCKKAGMNHYLTKPVTL 799

Query: 212 SD 213
           + 
Sbjct: 800 AQ 801

Length = 921

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

 Score = 60.9 bits (148), Expect = 4e-11
 Identities = 34/118 (28%), Positives = 56/118 (47%), Gaps = 13/118 (11%)

Query: 96  VLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITD 155
           V  VDD    R ++E+ L  +  +V    +    L+ L   G+           +L+ITD
Sbjct: 1   VWVVDDDRSIRWVLEKALSRAGYEVRTFGNAASVLRALA-RGQP----------DLLITD 49

Query: 156 YTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD 213
             MPG  G +LL +IK      ++PV++M++   L    +  + GA EY+ KP  L +
Sbjct: 50  VRMPGEDGLDLLPQIK--KRHPQLPVIVMTAHSDLDTAVAAYQRGAFEYLPKPFDLDE 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|214376 CHL00148, orf27, Ycf27; Reviewed

 Score = 57.8 bits (140), Expect = 2e-10
 Identities = 39/119 (32%), Positives = 65/119 (54%), Gaps = 17/119 (14%)

Query: 91  SKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVN 150
           SKE  +L VDD    RK++E  L I   +V     G  AL+            F   + +
Sbjct: 5   SKE-KILVVDDEAYIRKILETRLSIIGYEVITASDGEEALKL-----------FRKEQPD 52

Query: 151 LIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSS-EDVLTQIDSCLEEGAEEYIVKP 208
           L+I D  MP + GY + ++I++ S   +VP++++++  DV  +I + LE GA++Y+VKP
Sbjct: 53  LVILDVMMPKLDGYGVCQEIRKES---DVPIIMLTALGDVSDRI-TGLELGADDYVVKP 107

Length = 240

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

 Score = 55.4 bits (134), Expect = 3e-09
 Identities = 32/118 (27%), Positives = 56/118 (47%), Gaps = 16/118 (13%)

Query: 96  VLAVDDSYVDRKLIERLLQISSCKVTAV---ESGTRALQYLGLDGEQSNVGFDALKVNLI 152
           VL VDD  + R+ ++ L+   +  +  V    +G  AL+                + +++
Sbjct: 4   VLIVDDEPLIREGLKSLIDWEALGIEVVGTAANGKEALEL-----------IQETQPDIV 52

Query: 153 ITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVK 210
           ITD  MPGM G +L+K IKE     +   +I+S  D        ++ G ++Y++KPV 
Sbjct: 53  ITDINMPGMDGLDLIKAIKE--QSPDTEFIILSGYDEFEYAKKAMKLGVKDYLLKPVD 108

Length = 475

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

 Score = 53.8 bits (130), Expect = 1e-08
 Identities = 33/119 (27%), Positives = 60/119 (50%), Gaps = 19/119 (15%)

Query: 96  VLAVDDSYVDRKLIE-RLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
           +L VDD   + KL+E +LL      +TA  SG  A+              +  + ++I+ 
Sbjct: 5   ILVVDDIPANVKLLEAKLLAEYYTVLTA-SSGAEAIAIC-----------EREQPDIILL 52

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDS---CLEEGAEEYIVKPVK 210
           D  MPGM G+E+ +++K       +PVV++++   L   +     LE GA++++ KP+ 
Sbjct: 53  DVMMPGMDGFEVCRRLKSDPATTHIPVVMVTA---LDDPEDRVRGLEAGADDFLTKPIN 108

Length = 457

>gnl|CDD|172377 PRK13856, PRK13856, two-component response regulator VirG; Provisional

 Score = 51.4 bits (123), Expect = 5e-08
 Identities = 37/116 (31%), Positives = 57/116 (49%), Gaps = 17/116 (14%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
           HVL +DD    R LI   L I + KVTAV            D +Q N    +  V++++ 
Sbjct: 3   HVLVIDDDVAMRHLIVEYLTIHAFKVTAVA-----------DSQQFNRVLASETVDVVVV 51

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDS--CLEEGAEEYIVKP 208
           D  +    G E+++ +   S   +VP++I+S  D L + D    LE GA ++I KP
Sbjct: 52  DLNLGREDGLEIVRSLATKS---DVPIIIISG-DRLEEADKVVALELGATDFIAKP 103

Length = 241

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

 Score = 51.8 bits (124), Expect = 6e-08
 Identities = 35/118 (29%), Positives = 57/118 (48%), Gaps = 13/118 (11%)

Query: 96  VLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITD 155
           V  VDD    R ++ER L  +    T  E+G   L+ L                +++++D
Sbjct: 6   VWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLEALASKTP-----------DVLLSD 54

Query: 156 YTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD 213
             MPGM G  LLK+IK+      +PV+IM++   L    S  ++GA +Y+ KP  + +
Sbjct: 55  IRMPGMDGLALLKQIKQRHPM--LPVIIMTAHSDLDAAVSAYQQGAFDYLPKPFDIDE 110

Length = 469

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

 Score = 48.8 bits (117), Expect = 2e-07
 Identities = 34/119 (28%), Positives = 56/119 (47%), Gaps = 15/119 (12%)

Query: 91  SKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVN 150
           S +  V  VDD    R  +  LL  +  +V   ES    L  L             L+  
Sbjct: 1   SDKGVVHVVDDDEAMRDSLAFLLDSAGFEVRLFESAQAFLDALP-----------GLRFG 49

Query: 151 LIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSE-DVLTQIDSCLEEGAEEYIVKP 208
            ++TD  MPG+ G ELL+++K       +PV++M+   DV   +++ ++ GA ++I KP
Sbjct: 50  CVVTDVRMPGIDGIELLRRLKARGS--PLPVIVMTGHGDVPLAVEA-MKLGAVDFIEKP 105

Length = 202

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

 Score = 48.9 bits (117), Expect = 3e-07
 Identities = 20/73 (27%), Positives = 42/73 (57%)

Query: 136 DGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDS 195
           DG+++    +    +LI+ D+ +PG +G EL ++++     R +P++++++         
Sbjct: 34  DGDEALTLINERGPDLILLDWMLPGTSGIELCRRLRRRPETRAIPIIMLTARGEEEDRVR 93

Query: 196 CLEEGAEEYIVKP 208
            LE GA++YI KP
Sbjct: 94  GLETGADDYITKP 106

PhoB is a DNA-binding response regulator protein acting with PhoR in a 2-component system responding to phosphate ion. PhoB acts as a positive regulator of gene expression for phosphate-related genes such as phoA, phoS, phoE and ugpAB as well as itself. It is often found proximal to genes for the high-affinity phosphate ABC transporter (pstSCAB; GenProp0190) and presumably regulates these as well [Regulatory functions, DNA interactions, Signal transduction, Two-component systems]. Length = 226

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

 Score = 45.3 bits (108), Expect = 4e-07
 Identities = 19/66 (28%), Positives = 30/66 (45%), Gaps = 11/66 (16%)

Query: 94  LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLII 153
           + +L VDD  + R+L++ LL+    +V     G  AL+ L              K +LI+
Sbjct: 1   MRILVVDDDPLLRELLKALLEKEGYEVDEATDGEEALELL-----------KEEKPDLIL 49

Query: 154 TDYTMP 159
            D  MP
Sbjct: 50  LDIMMP 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|182619 PRK10651, PRK10651, transcriptional regulator NarL; Provisional

 Score = 48.1 bits (115), Expect = 6e-07
 Identities = 34/114 (29%), Positives = 59/114 (51%), Gaps = 15/114 (13%)

Query: 96  VLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITD 155
           +L +DD  + R  +++L+ ++       E+          +GEQ     ++L  +LI+ D
Sbjct: 9   ILLIDDHPMLRTGVKQLISMAPDITVVGEAS---------NGEQGIELAESLDPDLILLD 59

Query: 156 YTMPGMTGYELLKKIKESSVFREVPVVIMS--SEDVLTQIDSCLEEGAEEYIVK 207
             MPGM G E L K++E S+   + V  +S   EDV+T     L+ GA+ Y++K
Sbjct: 60  LNMPGMNGLETLDKLREKSLSGRIVVFSVSNHEEDVVT----ALKRGADGYLLK 109

Length = 216

>gnl|CDD|182387 PRK10336, PRK10336, DNA-binding transcriptional regulator QseB; Provisional

 Score = 48.0 bits (114), Expect = 6e-07
 Identities = 23/76 (30%), Positives = 41/76 (53%), Gaps = 2/76 (2%)

Query: 136 DGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDS 195
            G Q      +   + +I D T+PGM G ++L++ +E    +  PV+I+++ D L +   
Sbjct: 32  QGRQGKEALYSAPYDAVILDLTLPGMDGRDILREWREKG--QREPVLILTARDALAERVE 89

Query: 196 CLEEGAEEYIVKPVKL 211
            L  GA++Y+ KP  L
Sbjct: 90  GLRLGADDYLCKPFAL 105

Length = 219

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

 Score = 47.9 bits (114), Expect = 7e-07
 Identities = 21/63 (33%), Positives = 40/63 (63%), Gaps = 2/63 (3%)

Query: 151 LIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVK 210
           LII D  +PGM G+++L+ ++ S   ++ PV+ +++ D +      L+ GA++Y+VKP  
Sbjct: 45  LIILDVMLPGMDGWQILQTLRRSG--KQTPVLFLTARDSVADKVKGLDLGADDYLVKPFS 102

Query: 211 LSD 213
            S+
Sbjct: 103 FSE 105

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

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

 Score = 48.3 bits (115), Expect = 8e-07
 Identities = 27/119 (22%), Positives = 55/119 (46%), Gaps = 15/119 (12%)

Query: 96  VLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITD 155
           +L VDD    R+++     +   +     +G  AL                +  ++++ D
Sbjct: 7   ILIVDDEDNVRRMLSTAFALQGFETHCANNGRTALHLFAD-----------IHPDVVLMD 55

Query: 156 YTMPGMTGYELLKKIKESSVFREVPVVIMSS-EDVLTQIDSCLEEGAEEYIVKPVKLSD 213
             MP M G + LK+++        PV++M++  +V T +++ L  GA +Y++KP  L +
Sbjct: 56  IRMPEMDGIKALKEMRSHE--TRTPVILMTAYAEVETAVEA-LRCGAFDYVIKPFDLDE 111

Length = 457

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

 Score = 47.2 bits (112), Expect = 1e-06
 Identities = 30/120 (25%), Positives = 62/120 (51%), Gaps = 14/120 (11%)

Query: 94  LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLII 153
           + +L ++D+   ++ + + L  +   + AV  G   L YL L  + +          LII
Sbjct: 1   MKILLIEDNQRTQEWVTQGLSEAGYVIDAVSDGRDGL-YLALKDDYA----------LII 49

Query: 154 TDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD 213
            D  +PGM G+++L+ ++ +   ++ PV+ +++ D +      L+ GA +Y+VKP   S+
Sbjct: 50  LDIMLPGMDGWQILQTLRTA---KQTPVICLTARDSVDDRVRGLDSGANDYLVKPFSFSE 106

Length = 223

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

 Score = 47.9 bits (115), Expect = 1e-06
 Identities = 32/116 (27%), Positives = 58/116 (50%), Gaps = 11/116 (9%)

Query: 94  LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLII 153
           L V+AVDD+  + KLI  LL+     V   +SG +A++       +    FD     LI+
Sbjct: 668 LTVMAVDDNPANLKLIGALLEEQVEHVVLCDSGHQAVEQ-----AKQRP-FD-----LIL 716

Query: 154 TDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPV 209
            D  MPGM G    + I++    +  P++ +++  +  + +  L  G ++Y+ KP+
Sbjct: 717 MDIQMPGMDGIRACELIRQLPHNQNTPIIAVTAHAMAGERERLLSAGMDDYLAKPI 772

Length = 919

>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 = 47.3 bits (113), Expect = 2e-06
 Identities = 39/118 (33%), Positives = 56/118 (47%), Gaps = 20/118 (16%)

Query: 96  VLAVDDSYVDRKLIERLLQISSCKVTAV---ESGTRALQYLGLDGEQSNVGFDALKVNLI 152
           VL VDDS + RK+I  +L  S   +  V    +G  A+  +             LK ++I
Sbjct: 4   VLVVDDSALMRKVISDILN-SDPDIEVVGTARNGREAIDKVK-----------KLKPDVI 51

Query: 153 ITDYTMPGMTGYELLKKIKESSVFREVPVVIMSS--EDVLTQIDSCLEEGAEEYIVKP 208
             D  MP M G E L+KI      R +PV+++SS  E+        LE GA ++I KP
Sbjct: 52  TLDVEMPVMDGLEALRKIMRL---RPLPVIMVSSLTEEGAEATLEALELGAVDFIAKP 106

Length = 350

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

 Score = 46.2 bits (109), Expect = 2e-06
 Identities = 21/59 (35%), Positives = 38/59 (64%)

Query: 150 NLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
           +LI+ D+ +PG +G + +K +K  S+ R++PVV++++          LE GA++YI KP
Sbjct: 48  DLILLDWMLPGGSGIQFIKHLKRESMTRDIPVVMLTARGEEEDRVRGLETGADDYITKP 106

Length = 229

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

 Score = 46.5 bits (111), Expect = 2e-06
 Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 2/79 (2%)

Query: 132 YLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLT 191
            L  +G  +         +LII D  MP M G E ++ ++      + PV+++S+ + + 
Sbjct: 1   VLAANGVDALELLGGFTPDLIICDLAMPRMNGIEFVEHLRNRGD--QTPVLVISATENMA 58

Query: 192 QIDSCLEEGAEEYIVKPVK 210
            I   L  G ++ ++KPVK
Sbjct: 59  DIAKALRLGVQDVLLKPVK 77

Length = 303

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

 Score = 46.4 bits (110), Expect = 4e-06
 Identities = 28/114 (24%), Positives = 49/114 (42%), Gaps = 15/114 (13%)

Query: 96  VLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITD 155
           ++ VDD     KL+  +L  +  +V +      AL  L           +  K +LI  D
Sbjct: 3   IIIVDDDAAIVKLLSVILSRAGHEVRSCSHPVEALDLL-----------EVFKPDLIFLD 51

Query: 156 YTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPV 209
             MP M G E  +++++  +   VP++ +SS       D       ++Y+ KPV
Sbjct: 52  IVMPYMNGIEFAEQVRD--IESAVPIIFISSHAEYA--DDSFGMNLDDYLPKPV 101

Length = 361

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

 Score = 45.5 bits (109), Expect = 6e-06
 Identities = 37/121 (30%), Positives = 53/121 (43%), Gaps = 26/121 (21%)

Query: 96  VLAVDDSYVDRKLIERLL-QISSCKVTAVES-GTRALQYLGLDGEQSNVGFDALKVNLII 153
           VL VDDS   R+LI  +L      +V      G  A + +             L  ++I 
Sbjct: 6   VLVVDDSAFMRRLISEILNSDPDIEVVGTAPDGLEAREKI-----------KKLNPDVIT 54

Query: 154 TDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQ------IDSCLEEGAEEYIVK 207
            D  MP M G + L+KI      R  PVV++SS   LT+      +   LE GA +++ K
Sbjct: 55  LDVEMPVMDGLDALEKIMRL---RPTPVVMVSS---LTERGAEITLR-ALELGAVDFVTK 107

Query: 208 P 208
           P
Sbjct: 108 P 108

Length = 354

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

 Score = 44.6 bits (106), Expect = 9e-06
 Identities = 19/63 (30%), Positives = 37/63 (58%), Gaps = 2/63 (3%)

Query: 151 LIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVK 210
           L++ D  +P   G  LL++ ++      +PV+I+++ D L    + L+ GA++Y+VKP  
Sbjct: 47  LVVLDLGLPDEDGLHLLRRWRQKKY--TLPVLILTARDTLEDRVAGLDVGADDYLVKPFA 104

Query: 211 LSD 213
           L +
Sbjct: 105 LEE 107

Length = 222

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

 Score = 45.3 bits (108), Expect = 9e-06
 Identities = 36/137 (26%), Positives = 64/137 (46%), Gaps = 29/137 (21%)

Query: 83  AMATVAECSKELHVLAVDDSYVDRKLIERLL--QISSCKVTAVESGTRALQYLGLDGEQS 140
           +       + ++ +L VDD  ++R    RLL  Q+ S               LG   + +
Sbjct: 791 STDKAVSDNDDMMILVVDDHPINR----RLLADQLGS---------------LGYQCKTA 831

Query: 141 NVGFDALKV------NLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQID 194
           N G DAL V      ++++TD  MP M GY L +++++      +PV+ +++  +  +  
Sbjct: 832 NDGVDALNVLSKNHIDIVLTDVNMPNMDGYRLTQRLRQLG--LTLPVIGVTANALAEEKQ 889

Query: 195 SCLEEGAEEYIVKPVKL 211
            CLE G +  + KPV L
Sbjct: 890 RCLEAGMDSCLSKPVTL 906

Length = 924

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

 Score = 42.7 bits (101), Expect = 4e-05
 Identities = 28/119 (23%), Positives = 51/119 (42%), Gaps = 18/119 (15%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
           H+L V+D  V R  ++   +     V+               G           V+LI+ 
Sbjct: 4   HILVVEDEPVTRARLQGYFEQEGYTVSEAA-----------SGAGMREIMQNQHVDLILL 52

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSC--LEEGAEEYIVKPVKL 211
           D  +PG  G  L ++++  S    V +++++       ID    LE GA++Y+ KP++L
Sbjct: 53  DINLPGEDGLMLTRELRSRS---TVGIILVTGRT--DSIDRIVGLEMGADDYVTKPLEL 106

Length = 221

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

 Score = 42.5 bits (100), Expect = 8e-05
 Identities = 33/118 (27%), Positives = 55/118 (46%), Gaps = 13/118 (11%)

Query: 92  KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNL 151
           K  H+L VDD     KL+   L      V   ESG  AL+ L  +           KV+L
Sbjct: 4   KPAHLLLVDDDPGLLKLLGMRLTSEGYSVVTAESGQEALRVLNRE-----------KVDL 52

Query: 152 IITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPV 209
           +I+D  M  M G +L  +I++      +PV+I+++   +    +  ++G   ++ KPV
Sbjct: 53  VISDLRMDEMDGMQLFAEIQKVQ--PGMPVIILTAHGSIPDAVAATQQGVFSFLTKPV 108

Length = 444

>gnl|CDD|182431 PRK10403, PRK10403, transcriptional regulator NarP; Provisional

 Score = 41.4 bits (97), Expect = 1e-04
 Identities = 31/115 (26%), Positives = 56/115 (48%), Gaps = 15/115 (13%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
            VL VDD  + R+ + +LL++        E+G         DG  +    + L  ++I+ 
Sbjct: 8   QVLIVDDHPLMRRGVRQLLELDPGFEVVAEAG---------DGASAIDLANRLDPDVILL 58

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMS--SEDVLTQIDSCLEEGAEEYIVK 207
           D  M GM+G + L  ++   V  ++ ++ +S  S DV   ID+    GA+ Y++K
Sbjct: 59  DLNMKGMSGLDTLNALRRDGVTAQIIILTVSDASSDVFALIDA----GADGYLLK 109

Length = 215

>gnl|CDD|236842 PRK11091, PRK11091, aerobic respiration control sensor protein ArcB; Provisional

 Score = 41.5 bits (98), Expect = 2e-04
 Identities = 28/123 (22%), Positives = 59/123 (47%), Gaps = 19/123 (15%)

Query: 94  LHVLAVDD----SYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKV 149
           L++L V+D      V R ++E+L       V    +G  AL+            FD  + 
Sbjct: 526 LNILLVEDIELNVIVARSVLEKL----GNSVDVAMTGKEALE-----------MFDPDEY 570

Query: 150 NLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPV 209
           +L++ D  +P MTG ++ ++++E     ++P ++  + +VL      L+ G ++ + KP+
Sbjct: 571 DLVLLDIQLPDMTGLDIARELRERYPREDLPPLVALTANVLKDKKEYLDAGMDDVLSKPL 630

Query: 210 KLS 212
            + 
Sbjct: 631 SVP 633

Length = 779

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

 Score = 40.6 bits (95), Expect = 2e-04
 Identities = 28/118 (23%), Positives = 54/118 (45%), Gaps = 14/118 (11%)

Query: 96  VLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITD 155
           VL V+D    R+ +   L+    +V   E+  R L                 K +LII D
Sbjct: 4   VLIVEDEQAIRRFLRTALEGDGMRVFEAETLQRGLLEAA-----------TRKPDLIILD 52

Query: 156 YTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD 213
             +P   G E ++ +++ S    +PV+++S+    +   + L+ GA++Y+ KP  + +
Sbjct: 53  LGLPDGDGIEFIRDLRQWSA---IPVIVLSARSEESDKIAALDAGADDYLSKPFGIGE 107

Length = 225

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

 Score = 40.8 bits (95), Expect = 3e-04
 Identities = 33/119 (27%), Positives = 58/119 (48%), Gaps = 13/119 (10%)

Query: 91  SKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVN 150
              + +L VDD      +++ LL+     V    SG +AL+ +     +  V FD     
Sbjct: 3   HDNIDILVVDDDISHCTILQALLRGWGYNVALANSGRQALEQV-----REQV-FD----- 51

Query: 151 LIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPV 209
           L++ D  M  M G   LK+IK  ++   +PV+IM++   +      L+ GA +Y++KP+
Sbjct: 52  LVLCDVRMAEMDGIATLKEIK--ALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPL 108

Length = 441

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

 Score = 41.3 bits (96), Expect = 3e-04
 Identities = 30/120 (25%), Positives = 56/120 (46%), Gaps = 13/120 (10%)

Query: 92   KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNL 151
            ++L +L  DD   +R L++R L +    V     G +AL  + +              +L
Sbjct: 957  EKLSILIADDHPTNRLLLKRQLNLLGYDVDEATDGVQALHKVSMQ-----------HYDL 1005

Query: 152  IITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKL 211
            +ITD  MP M G+EL +K++E +    +P+  +++     + +  L  G    + KP+ L
Sbjct: 1006 LITDVNMPNMDGFELTRKLREQN--SSLPIWGLTANAQANEREKGLSCGMNLCLFKPLTL 1063

Length = 1197

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

 Score = 39.9 bits (94), Expect = 3e-04
 Identities = 28/116 (24%), Positives = 50/116 (43%), Gaps = 17/116 (14%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
            +L V+D       +   LQ     V   E G  AL  L                +L+I 
Sbjct: 5   TILLVEDEQAIADTLVYALQSEGFTVEWFERGLPALDKLRQQP-----------PDLVIL 53

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSC--LEEGAEEYIVKP 208
           D  +P ++G+EL +++        +PV+ +++     ++D    LE GA++Y+ KP
Sbjct: 54  DVGLPDISGFELCRQLLAFH--PALPVIFLTARS--DEVDRLVGLEIGADDYVAKP 105

Length = 228

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

 Score = 40.2 bits (94), Expect = 3e-04
 Identities = 30/115 (26%), Positives = 58/115 (50%), Gaps = 19/115 (16%)

Query: 96  VLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITD 155
           +L VDD      L++ LL++    V     G +AL  L           D   ++L++ D
Sbjct: 4   ILLVDDDRELTSLLKELLEMEGFNVIVAHDGEQALDLL-----------DD-SIDLLLLD 51

Query: 156 YTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSC--LEEGAEEYIVKP 208
             MP   G + LK+++++    + PV+++++    +++D    LE GA++Y+ KP
Sbjct: 52  VMMPKKNGIDTLKELRQT---HQTPVIMLTARG--SELDRVLGLELGADDYLPKP 101

Length = 232

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

 Score = 39.7 bits (93), Expect = 4e-04
 Identities = 21/61 (34%), Positives = 39/61 (63%), Gaps = 7/61 (11%)

Query: 150 NLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCL--EEGAEEYIVK 207
           +LI+ D  +PG  G  L ++I+    F ++P+V+++++  + +ID  L  E GA++YI K
Sbjct: 56  DLILLDLMLPGTDGLTLCREIRR---FSDIPIVMVTAK--IEEIDRLLGLEIGADDYICK 110

Query: 208 P 208
           P
Sbjct: 111 P 111

Length = 240

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

 Score = 38.0 bits (88), Expect = 0.002
 Identities = 15/64 (23%), Positives = 41/64 (64%), Gaps = 2/64 (3%)

Query: 150 NLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPV 209
           +LII D  +P + G+++++ ++ ++  + +P++++++   +      LE GA++Y+VKP 
Sbjct: 46  DLIILDIMLPDVNGWDIVRMLRSAN--KGMPILLLTALGTIEHRVKGLELGADDYLVKPF 103

Query: 210 KLSD 213
             ++
Sbjct: 104 AFAE 107

Length = 227

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

 Score = 38.0 bits (89), Expect = 0.002
 Identities = 27/116 (23%), Positives = 54/116 (46%), Gaps = 17/116 (14%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
            +L VDD    R L+ER L     +V +             + EQ +        +L++ 
Sbjct: 7   KILVVDDDMRLRALLERYLTEQGFQVRSAA-----------NAEQMDRLLTRESFHLMVL 55

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSS--EDVLTQIDSCLEEGAEEYIVKP 208
           D  +PG  G  + ++++  +     P++++++  E+V   +   LE GA++Y+ KP
Sbjct: 56  DLMLPGEDGLSICRRLRSQN--NPTPIIMLTAKGEEVDRIVG--LEIGADDYLPKP 107

Length = 239

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

 Score = 37.7 bits (88), Expect = 0.002
 Identities = 17/63 (26%), Positives = 35/63 (55%), Gaps = 4/63 (6%)

Query: 152 IITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSE-DVLTQIDSCLEEGAEEYIVKPVK 210
           ++ D  MPGM+G EL  ++ E  +   +PV+ ++   D+   + + ++ GA +++ KP  
Sbjct: 52  LLLDVRMPGMSGLELQDRLAERGI--RLPVIFLTGHGDIPMAVQA-MKAGAVDFLEKPFS 108

Query: 211 LSD 213
             D
Sbjct: 109 EQD 111

Length = 202

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

 Score = 37.9 bits (88), Expect = 0.002
 Identities = 21/78 (26%), Positives = 43/78 (55%), Gaps = 10/78 (12%)

Query: 143 GFDALKV------NLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSS--EDVLTQID 194
           G DAL++      ++++ D  MP + G  +L+K+ E  +     V+++S+  ++ +TQ  
Sbjct: 37  GVDALELIKEQQPDVVVLDIIMPHLDGIGVLEKLNEIELSARPRVIMLSAFGQEKITQ-- 94

Query: 195 SCLEEGAEEYIVKPVKLS 212
             +  GA+ Y++KP  L 
Sbjct: 95  RAVALGADYYVLKPFDLE 112

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

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

 Score = 37.3 bits (87), Expect = 0.003
 Identities = 29/116 (25%), Positives = 52/116 (44%), Gaps = 18/116 (15%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
           H+L V+D  V R  ++ + +     V               DG + +       +NL+I 
Sbjct: 5   HILIVEDELVTRNTLKSIFEAEGYDVFEAT-----------DGAEMHQILSENDINLVIM 53

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSC--LEEGAEEYIVKP 208
           D  +PG  G  L ++++E      V ++ ++  D   ++D    LE GA++YI KP
Sbjct: 54  DINLPGKNGLLLARELREQ---ANVALMFLTGRD--NEVDKILGLEIGADDYITKP 104

Length = 237

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

 Score = 36.8 bits (86), Expect = 0.003
 Identities = 18/64 (28%), Positives = 32/64 (50%), Gaps = 2/64 (3%)

Query: 147 LKVNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIV 206
            K +LI+ D  MP   G ELL +++       V V+++++   +  I   L  G  +Y++
Sbjct: 45  FKPDLILLDIYMPDGNGIELLPELRSQ--HYPVDVIVITAASDMETIKEALRYGVVDYLI 102

Query: 207 KPVK 210
           KP  
Sbjct: 103 KPFT 106

Length = 224

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

 Score = 37.0 bits (86), Expect = 0.003
 Identities = 18/63 (28%), Positives = 38/63 (60%), Gaps = 2/63 (3%)

Query: 151 LIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVK 210
           L + D  MPGM G E+L+++++    + +PV+++++   +      L  GA++Y+ KP +
Sbjct: 47  LAVLDINMPGMDGLEVLQRLRKRG--QTLPVLLLTARSAVADRVKGLNVGADDYLPKPFE 104

Query: 211 LSD 213
           L +
Sbjct: 105 LEE 107

Length = 221

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	213
COG0745	229	OmpR Response regulators consisting of a CheY-like	99.91
KOG0519	786	consensus Sensory transduction histidine kinase [S	99.85
COG4753	475	Response regulator containing CheY-like receiver d	99.84
COG2204	464	AtoC Response regulator containing CheY-like recei	99.84
PF00072	112	Response_reg: Response regulator receiver domain;	99.83
COG3437	360	Response regulator containing a CheY-like receiver	99.83
COG4566	202	TtrR Response regulator [Signal transduction mecha	99.81
COG4565	224	CitB Response regulator of citrate/malate metaboli	99.81
COG0784	130	CheY FOG: CheY-like receiver [Signal transduction	99.8
COG2197	211	CitB Response regulator containing a CheY-like rec	99.78
COG3706	435	PleD Response regulator containing a CheY-like rec	99.77
PLN03029	222	type-a response regulator protein; Provisional	99.77
PRK11466	914	hybrid sensory histidine kinase TorS; Provisional	99.75
PRK10046	225	dpiA two-component response regulator DpiA; Provis	99.75
TIGR02956	968	TMAO_torS TMAO reductase sytem sensor TorS. This p	99.74
PRK10841	924	hybrid sensory kinase in two-component regulatory	99.74
PRK11091	779	aerobic respiration control sensor protein ArcB; P	99.73
PRK11107	919	hybrid sensory histidine kinase BarA; Provisional	99.73
PRK10816	223	DNA-binding transcriptional regulator PhoP; Provis	99.71
PRK15347	921	two component system sensor kinase SsrA; Provision	99.71
PRK09836	227	DNA-binding transcriptional activator CusR; Provis	99.71
PRK10529	225	DNA-binding transcriptional activator KdpE; Provis	99.7
PRK11173	237	two-component response regulator; Provisional	99.7
PRK10161	229	transcriptional regulator PhoB; Provisional	99.7
PRK10643	222	DNA-binding transcriptional regulator BasR; Provis	99.69
PRK09468	239	ompR osmolarity response regulator; Provisional	99.69
TIGR02154	226	PhoB phosphate regulon transcriptional regulatory	99.69
COG4567	182	Response regulator consisting of a CheY-like recei	99.69
PRK09959	1197	hybrid sensory histidine kinase in two-component r	99.68
PRK10766	221	DNA-binding transcriptional regulator TorR; Provis	99.68
PRK10336	219	DNA-binding transcriptional regulator QseB; Provis	99.68
PRK10430	239	DNA-binding transcriptional activator DcuR; Provis	99.68
PRK11083	228	DNA-binding response regulator CreB; Provisional	99.67
TIGR02875	262	spore_0_A sporulation transcription factor Spo0A.	99.67
PRK10955	232	DNA-binding transcriptional regulator CpxR; Provis	99.66
TIGR03787	227	marine_sort_RR proteobacterial dedicated sortase s	99.66
PRK10701	240	DNA-binding transcriptional regulator RstA; Provis	99.66
PRK13856	241	two-component response regulator VirG; Provisional	99.66
PRK10840	216	transcriptional regulator RcsB; Provisional	99.66
PRK09581	457	pleD response regulator PleD; Reviewed	99.66
PRK11517	223	transcriptional regulatory protein YedW; Provision	99.65
COG3947	361	Response regulator containing CheY-like receiver a	99.65
TIGR01387	218	cztR_silR_copR heavy metal response regulator. Mem	99.64
PRK10923	469	glnG nitrogen regulation protein NR(I); Provisiona	99.63
PRK15115	444	response regulator GlrR; Provisional	99.63
CHL00148	240	orf27 Ycf27; Reviewed	99.63
PRK09958	204	DNA-binding transcriptional activator EvgA; Provis	99.63
PRK11361	457	acetoacetate metabolism regulatory protein AtoC; P	99.63
PRK10365	441	transcriptional regulatory protein ZraR; Provision	99.63
PRK09483	217	response regulator; Provisional	99.61
PRK14084	246	two-component response regulator; Provisional	99.6
TIGR02915	445	PEP_resp_reg putative PEP-CTERM system response re	99.6
PRK09935	210	transcriptional regulator FimZ; Provisional	99.59
TIGR01818	463	ntrC nitrogen regulation protein NR(I). This model	99.59
PRK12555	337	chemotaxis-specific methylesterase; Provisional	99.57
PRK10710	240	DNA-binding transcriptional regulator BaeR; Provis	99.57
PRK15479	221	transcriptional regulatory protein TctD; Provision	99.57
PRK13558	665	bacterio-opsin activator; Provisional	99.56
COG2201	350	CheB Chemotaxis response regulator containing a Ch	99.56
PRK10360	196	DNA-binding transcriptional activator UhpA; Provis	99.56
PRK00742	354	chemotaxis-specific methylesterase; Provisional	99.55
PRK09390	202	fixJ response regulator FixJ; Provisional	99.55
PRK09581	457	pleD response regulator PleD; Reviewed	99.55
PRK13837	828	two-component VirA-like sensor kinase; Provisional	99.55
PRK11697	238	putative two-component response-regulatory protein	99.55
PRK10610	129	chemotaxis regulatory protein CheY; Provisional	99.52
PRK10100	216	DNA-binding transcriptional regulator CsgD; Provis	99.51
PRK10651	216	transcriptional regulator NarL; Provisional	99.48
PRK11475	207	DNA-binding transcriptional activator BglJ; Provis	99.48
PRK10403	215	transcriptional regulator NarP; Provisional	99.47
PRK15369	211	two component system sensor kinase SsrB; Provision	99.47
PRK13435	145	response regulator; Provisional	99.45
COG3707	194	AmiR Response regulator with putative antiterminat	99.45
PRK15411	207	rcsA colanic acid capsular biosynthesis activation	99.43
PRK13557	540	histidine kinase; Provisional	99.43
PRK09191	261	two-component response regulator; Provisional	99.37
cd00156	113	REC Signal receiver domain; originally thought to	99.29
PRK10693	303	response regulator of RpoS; Provisional	99.27
PRK15029	755	arginine decarboxylase; Provisional	99.26
COG3279	244	LytT Response regulator of the LytR/AlgR family [T	99.0
PRK11107	919	hybrid sensory histidine kinase BarA; Provisional	98.91
COG3706	435	PleD Response regulator containing a CheY-like rec	98.45
smart00448	55	REC cheY-homologous receiver domain. CheY regulate	97.98
PRK10618	894	phosphotransfer intermediate protein in two-compon	97.96
PF06490	109	FleQ: Flagellar regulatory protein FleQ; InterPro:	97.57
cd02071	122	MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 bin	97.42
cd02067	119	B12-binding B12 binding domain (B12-BD). This doma	97.04
TIGR00640	132	acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal	96.88
PF03709	115	OKR_DC_1_N: Orn/Lys/Arg decarboxylase, N-terminal	96.8
PRK02261	137	methylaspartate mutase subunit S; Provisional	96.65
cd02070	201	corrinoid_protein_B12-BD B12 binding domain of cor	95.99
PF02310	121	B12-binding: B12 binding domain; InterPro: IPR0061	95.94
cd02069	213	methionine_synthase_B12_BD B12 binding domain of m	95.16
PRK15399	713	lysine decarboxylase LdcC; Provisional	95.12
COG2185	143	Sbm Methylmalonyl-CoA mutase, C-terminal domain/su	94.88
PRK15400	714	lysine decarboxylase CadA; Provisional	94.55
cd04728	248	ThiG Thiazole synthase (ThiG) is the tetrameric en	93.9
TIGR02370	197	pyl_corrinoid methyltransferase cognate corrinoid	93.86
COG0512	191	PabA Anthranilate/para-aminobenzoate synthases com	93.57
cd02072	128	Glm_B12_BD B12 binding domain of glutamate mutase	93.51
TIGR01501	134	MthylAspMutase methylaspartate mutase, S subunit.	93.28
PRK00208	250	thiG thiazole synthase; Reviewed	93.11
COG4999	140	Uncharacterized domain of BarA-like signal transdu	93.05
TIGR03815	322	CpaE_hom_Actino helicase/secretion neighborhood Cp	92.55
PF01596	205	Methyltransf_3: O-methyltransferase; InterPro: IPR	92.28
PRK09426	714	methylmalonyl-CoA mutase; Reviewed	91.78
PRK03958	176	tRNA 2'-O-methylase; Reviewed	90.98
PRK08385	278	nicotinate-nucleotide pyrophosphorylase; Provision	90.3
COG4122	219	Predicted O-methyltransferase [General function pr	89.97
PF02254	116	TrkA_N: TrkA-N domain; InterPro: IPR003148 The reg	89.56
cd02065	125	B12-binding_like B12 binding domain (B12-BD). Most	89.23
PRK10558	256	alpha-dehydro-beta-deoxy-D-glucarate aldolase; Pro	88.93
TIGR00566	188	trpG_papA glutamine amidotransferase of anthranila	88.59
PRK01130	221	N-acetylmannosamine-6-phosphate 2-epimerase; Provi	88.38
PF10087	97	DUF2325: Uncharacterized protein conserved in bact	88.05
PRK10128	267	2-keto-3-deoxy-L-rhamnonate aldolase; Provisional	87.81
PRK00043	212	thiE thiamine-phosphate pyrophosphorylase; Reviewe	87.33
cd05212	140	NAD_bind_m-THF_DH_Cyclohyd_like NAD(P) binding dom	87.0
PRK13125	244	trpA tryptophan synthase subunit alpha; Provisiona	86.93
smart00052	241	EAL Putative diguanylate phosphodiesterase. Putati	86.21
cd04729	219	NanE N-acetylmannosamine-6-phosphate epimerase (Na	85.8
PRK06543	281	nicotinate-nucleotide pyrophosphorylase; Provision	85.73
cd01948	240	EAL EAL domain. This domain is found in diverse ba	85.7
TIGR03239	249	GarL 2-dehydro-3-deoxyglucarate aldolase. In E. co	85.52
PF01729	169	QRPTase_C: Quinolinate phosphoribosyl transferase,	85.38
PRK03659	601	glutathione-regulated potassium-efflux system prot	84.79
PF03602	183	Cons_hypoth95: Conserved hypothetical protein 95;	84.35
TIGR00693	196	thiE thiamine-phosphate pyrophosphorylase. This mo	84.2
TIGR01334	277	modD putative molybdenum utilization protein ModD.	84.11
PRK07649	195	para-aminobenzoate/anthranilate synthase glutamine	83.56
cd02068	127	radical_SAM_B12_BD B12 binding domain_like associa	83.41
PF07688	283	KaiA: KaiA domain; InterPro: IPR011648 KaiA is a c	83.28
TIGR00007	230	phosphoribosylformimino-5-aminoimidazole carboxami	83.15
PRK11840	326	bifunctional sulfur carrier protein/thiazole synth	82.49
PRK06774	191	para-aminobenzoate synthase component II; Provisio	82.38
PRK08007	187	para-aminobenzoate synthase component II; Provisio	82.37
PF05690	247	ThiG: Thiazole biosynthesis protein ThiG; InterPro	82.07
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	81.93
TIGR00736	231	nifR3_rel_arch TIM-barrel protein, putative. Membe	81.46
cd00452	190	KDPG_aldolase KDPG and KHG aldolase. This family b	81.14
PRK13566	720	anthranilate synthase; Provisional	80.64
PRK00811	283	spermidine synthase; Provisional	80.6
PRK05458	326	guanosine 5'-monophosphate oxidoreductase; Provisi	80.47
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	80.45
KOG2335	358	consensus tRNA-dihydrouridine synthase [Translatio	80.43
PLN02476	278	O-methyltransferase	80.42
PRK05670	189	anthranilate synthase component II; Provisional	80.23

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

Probab=99.91  E-value=9.6e-24  Score=173.10  Aligned_cols=107  Identities=22%  Similarity=0.425  Sum_probs=100.3

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhc
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKES  173 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~  173 (213)
                      .+||||||++..+..+...|+..||.|..+.+|.+|++.+           ... ||+||+|++||++||+++|++||+.
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            3799999999999999999999999999999999999998           555 9999999999999999999999975


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD  213 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~e  213 (213)
                       .....|||++|+..+..+...++++|||||+.|||++.|
T Consensus        69 -~~~~~PIi~Lta~~~~~d~v~gl~~GADDYl~KPf~~~E  107 (229)
T COG0745          69 -KGSGPPIIVLTARDDEEDRVLGLEAGADDYLTKPFSPRE  107 (229)
T ss_pred             -cCCCCcEEEEECCCcHHHHHHHHhCcCCeeeeCCCCHHH
Confidence             467889999999999999999999999999999998754

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

Probab=99.85  E-value=4.4e-21  Score=181.30  Aligned_cols=111  Identities=32%  Similarity=0.535  Sum_probs=103.3

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHH
Q 048660           91 SKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKI  170 (213)
Q Consensus        91 ~~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~i  170 (213)
                      ..+.+|||||||..+++....+|++.|+.++.+.+|.||++.+.          ....||+||||++||.|||++++++|
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            45789999999999999999999999999999999999999994          35689999999999999999999999


Q ss_pred             HhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          171 KESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       171 r~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      |+... .++|||++|++......++|++.|+|+||.|||+.+
T Consensus       734 rk~~~-~~~pIvAlTa~~~~~~~~~c~~~Gmd~yl~KP~~~~  774 (786)
T KOG0519|consen  734 RKKER-WHLPIVALTADADPSTEEECLEVGMDGYLSKPFTLE  774 (786)
T ss_pred             HHhhc-CCCCEEEEecCCcHHHHHHHHHhCCceEEcccccHH
Confidence            98653 789999999999999999999999999999999853

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

Probab=99.84  E-value=5.9e-21  Score=168.68  Aligned_cols=106  Identities=30%  Similarity=0.530  Sum_probs=98.4

Q ss_pred             cEEEEEeCCHHHHHHHHHHHh--hcCCE-EEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHH
Q 048660           94 LHVLAVDDSYVDRKLIERLLQ--ISSCK-VTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKI  170 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~--~~g~~-v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~i  170 (213)
                      .+||||||++.+|++|+.++.  .+|+. |.+|.||.+|++.+           ....|||||+|+.||+|||+++++.+
T Consensus         2 ykVlIVDDE~lIr~GLk~lI~w~~~g~eiVgtA~NG~eAleli-----------~e~~pDiviTDI~MP~mdGLdLI~~i   70 (475)
T COG4753           2 YKVLIVDDEPLIREGLKSLIDWEALGIEVVGTAANGKEALELI-----------QETQPDIVITDINMPGMDGLDLIKAI   70 (475)
T ss_pred             eeEEEecChHHHHHHHHHhCChhhcCCeEEEecccHHHHHHHH-----------HhcCCCEEEEecCCCCCcHHHHHHHH
Confidence            589999999999999999984  66885 56999999999999           66789999999999999999999999


Q ss_pred             HhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          171 KESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       171 r~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      ++.  .|.+.+|++||+++-+.+.+|++.|+.+||.||++.+
T Consensus        71 ke~--~p~~~~IILSGy~eFeYak~Am~lGV~dYLLKP~~k~  110 (475)
T COG4753          71 KEQ--SPDTEFIILSGYDEFEYAKKAMKLGVKDYLLKPVDKA  110 (475)
T ss_pred             HHh--CCCceEEEEeccchhHHHHHHHhcCchhheeCcCCHH
Confidence            986  7899999999999999999999999999999999854

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

Probab=99.84  E-value=1.5e-20  Score=166.22  Aligned_cols=107  Identities=34%  Similarity=0.537  Sum_probs=100.9

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHh
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKE  172 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~  172 (213)
                      ..+||||||+...|..+...|+..||.|..+.++.+|++.+.           ...||+||+|+.||++||+++++.|++
T Consensus         4 ~~~iLvVDDd~~ir~~l~~~L~~~G~~v~~a~~~~~al~~i~-----------~~~~~lvl~Di~mp~~~Gl~ll~~i~~   72 (464)
T COG2204           4 MARILVVDDDPDIRELLEQALELAGYEVVTAESAEEALEALS-----------ESPFDLVLLDIRMPGMDGLELLKEIKS   72 (464)
T ss_pred             cCCEEEEeCCHHHHHHHHHHHHHcCCeEEEeCCHHHHHHHHh-----------cCCCCEEEEecCCCCCchHHHHHHHHh
Confidence            357999999999999999999999999999999999999994           347999999999999999999999998


Q ss_pred             cCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          173 SSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       173 ~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      .  .+.+|||++|++.+.+....+++.||.|||.|||+.+
T Consensus        73 ~--~~~~pVI~~Tg~g~i~~AV~A~k~GA~Dfl~KP~~~~  110 (464)
T COG2204          73 R--DPDLPVIVMTGHGDIDTAVEALRLGAFDFLEKPFDLD  110 (464)
T ss_pred             h--CCCCCEEEEeCCCCHHHHHHHHhcCcceeeeCCCCHH
Confidence            7  5899999999999999999999999999999999865

>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=99.83  E-value=4.9e-20  Score=133.40  Aligned_cols=104  Identities=34%  Similarity=0.586  Sum_probs=98.1

Q ss_pred             EEEEeCCHHHHHHHHHHHhhcCC-EEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhcC
Q 048660           96 VLAVDDSYVDRKLIERLLQISSC-KVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKESS  174 (213)
Q Consensus        96 ILvVdD~~~~~~~l~~~L~~~g~-~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~~  174 (213)
                      ||||||++..+..++..|+..|+ .+..+.++.+|++.+           ....||++++|+.||+++|.++++.||+. 
T Consensus         1 Ilivd~~~~~~~~l~~~l~~~~~~~v~~~~~~~~~~~~~-----------~~~~~d~iiid~~~~~~~~~~~~~~i~~~-   68 (112)
T PF00072_consen    1 ILIVDDDPEIRELLEKLLERAGYEEVTTASSGEEALELL-----------KKHPPDLIIIDLELPDGDGLELLEQIRQI-   68 (112)
T ss_dssp             EEEEESSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHH-----------HHSTESEEEEESSSSSSBHHHHHHHHHHH-
T ss_pred             cEEEECCHHHHHHHHHHHHhCCCCEEEEECCHHHHHHHh-----------cccCceEEEEEeeeccccccccccccccc-
Confidence            79999999999999999999999 999999999999999           44579999999999999999999999987 


Q ss_pred             CCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          175 VFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       175 ~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                       .+.+|+|++|...+.....+++++|+++||.||++.+
T Consensus        69 -~~~~~ii~~t~~~~~~~~~~~~~~g~~~~l~kp~~~~  105 (112)
T PF00072_consen   69 -NPSIPIIVVTDEDDSDEVQEALRAGADDYLSKPFSPE  105 (112)
T ss_dssp             -TTTSEEEEEESSTSHHHHHHHHHTTESEEEESSSSHH
T ss_pred             -cccccEEEecCCCCHHHHHHHHHCCCCEEEECCCCHH
Confidence             4799999999999999999999999999999999864

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 ....

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

Probab=99.83  E-value=2.6e-20  Score=157.84  Aligned_cols=111  Identities=32%  Similarity=0.534  Sum_probs=103.7

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHH
Q 048660           91 SKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKI  170 (213)
Q Consensus        91 ~~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~i  170 (213)
                      ...++||+|||++.++..++.+|+..||.+..+++|++|++..           ....+|++|+|++||+|||++++++|
T Consensus        12 ~~~~~vl~vDD~~~~~~~~~~lL~~~~y~v~~ae~g~~a~kl~-----------~~~~~dlvllD~~mp~mdg~ev~~~l   80 (360)
T COG3437          12 DEKLTVLLVDDEPDNLEALRQLLRMIGYRVIEAENGEEALKLL-----------QEEPPDLVLLDVRMPEMDGAEVLNKL   80 (360)
T ss_pred             cccceEEEecCchhHHHHHHHHHHhcccceeeecCchHHHHHh-----------cccCCceEEeeccCCCccHHHHHHHH
Confidence            3467999999999999999999999999999999999999988           45569999999999999999999999


Q ss_pred             Hh-cCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          171 KE-SSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       171 r~-~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      +. .+....+|++++|+..+.+...+++.+|+++||.||+++.
T Consensus        81 k~~~p~t~~ip~i~lT~~~d~~~~~~~~~~g~~dyl~KP~~~~  123 (360)
T COG3437          81 KAMSPSTRRIPVILLTAYADSEDRQRALEAGADDYLSKPISPK  123 (360)
T ss_pred             HhcCCcccccceEEEeecCChHHHHHHHHhhHHHHhcCCCCHH
Confidence            98 7777889999999999999999999999999999999854

>COG4566 TtrR Response regulator [Signal transduction mechanisms]

Probab=99.81  E-value=2.2e-19  Score=139.94  Aligned_cols=107  Identities=24%  Similarity=0.354  Sum_probs=99.2

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHh
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKE  172 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~  172 (213)
                      ..-|-|||||..+|+.+..+|+..||.+.+..++.+.+...           ....|-++|+|+.||+++|.++-+.+.+
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            35689999999999999999999999999999999999875           4457889999999999999999999998


Q ss_pred             cCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          173 SSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       173 ~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      .  ....|||++|++.+..-..+++++||.|||.|||+.+
T Consensus        73 ~--~~~~PVIfiTGhgDIpmaV~AmK~GAvDFLeKP~~~q  110 (202)
T COG4566          73 R--GIRLPVIFLTGHGDIPMAVQAMKAGAVDFLEKPFSEQ  110 (202)
T ss_pred             c--CCCCCEEEEeCCCChHHHHHHHHcchhhHHhCCCchH
Confidence            7  5789999999999999999999999999999999853

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

Probab=99.81  E-value=2.8e-19  Score=141.88  Aligned_cols=106  Identities=23%  Similarity=0.420  Sum_probs=96.7

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhc-CCE-EEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           94 LHVLAVDDSYVDRKLIERLLQIS-SCK-VTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~-g~~-v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      ++|||||||+.+.+.-+.++++. ||+ |.+|.++++|...+           ....|||||+|+.||+.+|++++..||
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            47999999999999999999976 775 56899999999999           556789999999999999999999999


Q ss_pred             hcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          172 ESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      +.  ...+-||++|+.++.+.+.+++++|+.|||.|||..+
T Consensus        70 ~~--~~~~DVI~iTAA~d~~tI~~alr~Gv~DYLiKPf~~e  108 (224)
T COG4565          70 SQ--HYPVDVIVITAASDMETIKEALRYGVVDYLIKPFTFE  108 (224)
T ss_pred             hc--CCCCCEEEEeccchHHHHHHHHhcCchhheecceeHH
Confidence            87  5678899999999999999999999999999999754

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

Probab=99.80  E-value=1.7e-18  Score=128.35  Aligned_cols=107  Identities=36%  Similarity=0.632  Sum_probs=96.6

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHH-HHHHHhhhcCCCCCCCCCCC-ceeEEEEeCCCCCCCHHHHHHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGT-RALQYLGLDGEQSNVGFDAL-KVNLIITDYTMPGMTGYELLKK  169 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~-eal~~l~~~~~~~~~~~~~~-~~dlil~D~~mp~~~G~e~~~~  169 (213)
                      ...+||+|||++.++..+...|...|+.+..+.+|. +|++.+           ... .||+|++|+.||++||+++++.
T Consensus         4 ~~~~vLivdD~~~~~~~~~~~l~~~g~~v~~a~~g~~~al~~~-----------~~~~~~dlii~D~~mp~~~G~~~~~~   72 (130)
T COG0784           4 SGLRVLVVDDEPVNRRLLKRLLEDLGYEVVEAADGEEEALELL-----------RELPQPDLILLDINMPGMDGIELLRR   72 (130)
T ss_pred             CCcEEEEEcCCHHHHHHHHHHHHHcCCeEEEeCChHHHHHHHH-----------HhCCCCCEEEEeCCCCCCCHHHHHHH
Confidence            357999999999999999999999999999999995 999998           444 4999999999999999999999


Q ss_pred             HHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCC
Q 048660          170 IKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKL  211 (213)
Q Consensus       170 ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~  211 (213)
                      +|+.  .+.+|+|++|++........++..|+++|+.||+..
T Consensus        73 l~~~--~~~~pvv~~t~~~~~~~~~~~~~~g~~~~l~kP~~~  112 (130)
T COG0784          73 LRAR--GPNIPVILLTAYADEADRERALAAGADDYLTKPIFL  112 (130)
T ss_pred             HHhC--CCCCCEEEEEcCcCHHHHHHHHHcCCCeEEcCCCCc
Confidence            9986  567888999999988877888999999999999754

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

Probab=99.78  E-value=2.9e-18  Score=139.20  Aligned_cols=105  Identities=30%  Similarity=0.502  Sum_probs=95.9

Q ss_pred             EEEEEeCCHHHHHHHHHHHhhcC-CE-EEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHh
Q 048660           95 HVLAVDDSYVDRKLIERLLQISS-CK-VTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKE  172 (213)
Q Consensus        95 ~ILvVdD~~~~~~~l~~~L~~~g-~~-v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~  172 (213)
                      +|||+||++.+|..++.+|+..+ +. +..+.+|.++++.+           ....||++|+|+.||+++|+++++.|++
T Consensus         2 ~vlivDDh~l~r~gl~~~L~~~~~~~vv~~a~~~~~~l~~~-----------~~~~pdvvl~Dl~mP~~~G~e~~~~l~~   70 (211)
T COG2197           2 KVLIVDDHPLVREGLRQLLELEPDLEVVGEASNGEEALDLA-----------RELKPDVVLLDLSMPGMDGLEALKQLRA   70 (211)
T ss_pred             eEEEECCcHHHHHHHHHHHhhCCCCEEEEEeCCHHHHHHHh-----------hhcCCCEEEEcCCCCCCChHHHHHHHHH
Confidence            69999999999999999998776 66 45778899999987           5668999999999999999999999996


Q ss_pred             cCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          173 SSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       173 ~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      .  .++++|+++|.+.+.....+++++|+++|+.|..+.+
T Consensus        71 ~--~p~~~vvvlt~~~~~~~v~~al~~Ga~Gyl~K~~~~~  108 (211)
T COG2197          71 R--GPDIKVVVLTAHDDPAYVIRALRAGADGYLLKDASPE  108 (211)
T ss_pred             H--CCCCcEEEEeccCCHHHHHHHHHcCCCEEEeCCCCHH
Confidence            6  7889999999999999999999999999999997654

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

Probab=99.77  E-value=5.9e-18  Score=148.82  Aligned_cols=109  Identities=30%  Similarity=0.547  Sum_probs=103.3

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      ...+||+|||+...+..++.+|...||.+..+.++.+|+..+           .+.+||+||+|+.||++||+++|+++|
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            467999999999999999999999999999999999999998           556899999999999999999999999


Q ss_pred             hcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCC
Q 048660          172 ESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKL  211 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~  211 (213)
                      +......+|||++++..+.....++++.|++||+.||++.
T Consensus       200 ~~~~t~~ipii~~~~~~d~~~~~~Af~~G~~Dyi~kPi~~  239 (435)
T COG3706         200 QLERTRDIPIILLSSKDDDELVVRAFELGVNDYITKPIEE  239 (435)
T ss_pred             cccccccccEEEEecccchHHHHHHHHcCCcceEecCCCH
Confidence            9877789999999999999999999999999999999873

>PLN03029 type-a response regulator protein; Provisional

Probab=99.77  E-value=7.1e-18  Score=137.86  Aligned_cols=121  Identities=64%  Similarity=1.000  Sum_probs=101.3

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCC---------CCCCCCCCceeEEEEeCCCCCCC
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQ---------SNVGFDALKVNLIITDYTMPGMT  162 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~---------~~~~~~~~~~dlil~D~~mp~~~  162 (213)
                      ...+||||||+...+..+..+|+..||.+..+.++.+|++.+......         ....-....+|+||+|+.||+++
T Consensus         7 ~~~~VLiVdd~~~~~~~l~~~L~~~g~~v~~a~sg~~al~~l~~~~~d~~~p~~~~~~~~~~~~~~~dlVllD~~mp~~~   86 (222)
T PLN03029          7 SQFHVLAVDDSLIDRKLIEKLLKTSSYQVTTVDSGSKALKFLGLHEDDRSNPDTPSVSPNSHQEVEVNLIITDYCMPGMT   86 (222)
T ss_pred             CCccEEEEeCCHHHHHHHHHHHHHcCceEEEECCHHHHHHHHHhccccccccccccccccccccccCCEEEEcCCCCCCC
Confidence            457999999999999999999999999999999999999988532100         00000223578999999999999


Q ss_pred             HHHHHHHHHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          163 GYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       163 G~e~~~~ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      |+++++.|++......+|||++|+........+++++|+++||.||++..
T Consensus        87 G~e~l~~ir~~~~~~~ipvIils~~~~~~~~~~al~~Ga~dyl~KP~~~~  136 (222)
T PLN03029         87 GYDLLKKIKESSSLRNIPVVIMSSENVPSRITRCLEEGAEEFFLKPVQLS  136 (222)
T ss_pred             HHHHHHHHHhccccCCCcEEEEeCCCCHHHHHHHHHhCchheEECCCCHH
Confidence            99999999986445689999999999999999999999999999998753

>PRK11466 hybrid sensory histidine kinase TorS; Provisional

Probab=99.75  E-value=1.4e-17  Score=160.25  Aligned_cols=108  Identities=19%  Similarity=0.333  Sum_probs=99.4

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHh
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKE  172 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~  172 (213)
                      +.+||||||++.++..+..+|+..||.+..+.++.+|++.+.          ....||+||+|+.||+++|+++++.||+
T Consensus       681 ~~~vLivdD~~~~~~~l~~~L~~~g~~v~~a~~~~~al~~~~----------~~~~~Dlvl~D~~mp~~~G~~~~~~lr~  750 (914)
T PRK11466        681 GLRLLLIEDNPLTQRITAEMLNTSGAQVVAVGNAAQALETLQ----------NSEPFAAALVDFDLPDYDGITLARQLAQ  750 (914)
T ss_pred             CcceEEEeCCHHHHHHHHHHHHhcCCceEEeCCHHHHHHHHH----------cCCCCCEEEEeCCCCCCCHHHHHHHHHh
Confidence            568999999999999999999999999999999999999873          2346899999999999999999999998


Q ss_pred             cCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          173 SSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       173 ~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      .  .+.+|||++|++.......+++.+|+++||.||++.+
T Consensus       751 ~--~~~~~ii~~t~~~~~~~~~~~~~~g~~~~l~KP~~~~  788 (914)
T PRK11466        751 Q--YPSLVLIGFSAHVIDETLRQRTSSLFRGIIPKPVPRE  788 (914)
T ss_pred             h--CCCCCEEEEeCCCchhhHHHHHhcCcCCEEeCCCCHH
Confidence            6  5789999999999999999999999999999999864

>PRK10046 dpiA two-component response regulator DpiA; Provisional

Probab=99.75  E-value=2.6e-17  Score=134.33  Aligned_cols=107  Identities=18%  Similarity=0.310  Sum_probs=96.5

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhc-CC-EEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHH
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQIS-SC-KVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKI  170 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~-g~-~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~i  170 (213)
                      .++||||||++..+..+..+|+.. |+ .+..+.++.+|++.+           ....||+||+|+.||+++|+++++.|
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            478999999999999999999864 77 477899999999998           45579999999999999999999999


Q ss_pred             HhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          171 KESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       171 r~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      ++.  .+..+||++|+..+.....+++++|+++||.||++.+
T Consensus        73 ~~~--~~~~~iivls~~~~~~~~~~al~~Ga~~yl~Kp~~~~  112 (225)
T PRK10046         73 VQA--HYPGDVVFTTAASDMETVSEAVRCGVFDYLIKPIAYE  112 (225)
T ss_pred             Hhc--CCCCCEEEEEcCCCHHHHHHHHHcCccEEEECCcCHH
Confidence            975  4568999999999999999999999999999998754

>TIGR02956 TMAO_torS TMAO reductase sytem sensor TorS

Probab=99.74  E-value=2.1e-17  Score=159.67  Aligned_cols=109  Identities=25%  Similarity=0.369  Sum_probs=99.7

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHh
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKE  172 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~  172 (213)
                      ..+||||||++.++..+..+|+..||.|..+.+|.+|++.+           ....||+||+|+.||+++|+++++.||+
T Consensus       702 ~~~iLvvdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l-----------~~~~~dlvl~D~~mp~~~g~~~~~~ir~  770 (968)
T TIGR02956       702 PQRVLLVEDNEVNQMVAQGFLTRLGHKVTLAESGQSALECF-----------HQHAFDLALLDINLPDGDGVTLLQQLRA  770 (968)
T ss_pred             ccceEEEcCcHHHHHHHHHHHHHcCCEEEEECCHHHHHHHH-----------HCCCCCEEEECCCCCCCCHHHHHHHHHh
Confidence            45899999999999999999999999999999999999998           4467999999999999999999999998


Q ss_pred             cCCCCC-CcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          173 SSVFRE-VPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       173 ~~~~~~-~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      ...... +|||++|+........+++++|+++||.||++.+
T Consensus       771 ~~~~~~~~pii~lta~~~~~~~~~~~~~G~~~~l~KP~~~~  811 (968)
T TIGR02956       771 IYGAKNEVKFIAFSAHVFNEDVAQYLAAGFDGFLAKPVVEE  811 (968)
T ss_pred             CccccCCCeEEEEECCCCHHHHHHHHHCCCCEEEeCCCCHH
Confidence            643333 8999999999999999999999999999999854

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).

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

Probab=99.74  E-value=2e-17  Score=159.58  Aligned_cols=108  Identities=27%  Similarity=0.548  Sum_probs=101.0

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      ...+||||||++.++..+..+|+..||.+..+.+|.+|++.+           ....||+||+|+.||+|+|+++++.||
T Consensus       800 ~~~~ILvVdD~~~~~~~l~~~L~~~G~~v~~a~~g~eal~~l-----------~~~~~DlVl~D~~mP~mdG~el~~~ir  868 (924)
T PRK10841        800 DDMMILVVDDHPINRRLLADQLGSLGYQCKTANDGVDALNVL-----------SKNHIDIVLTDVNMPNMDGYRLTQRLR  868 (924)
T ss_pred             CCCEEEEECCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHH-----------HhCCCCEEEEcCCCCCCCHHHHHHHHH
Confidence            567999999999999999999999999999999999999998           445799999999999999999999999


Q ss_pred             hcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          172 ESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      +.  .+.+|||++|+....+...+++++|+++||.||++.+
T Consensus       869 ~~--~~~~pII~lTa~~~~~~~~~~~~aG~d~~L~KPv~~~  907 (924)
T PRK10841        869 QL--GLTLPVIGVTANALAEEKQRCLEAGMDSCLSKPVTLD  907 (924)
T ss_pred             hc--CCCCCEEEEECCCCHHHHHHHHHCCCCEEEeCCCCHH
Confidence            86  4679999999999999999999999999999999864

>PRK11091 aerobic respiration control sensor protein ArcB; Provisional

Probab=99.73  E-value=3.1e-17  Score=155.56  Aligned_cols=109  Identities=21%  Similarity=0.426  Sum_probs=96.4

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      .+.+||||||++.++..+..+|+..||.+..+.++.+|++.+           ....||+||+|+.||+++|+++++.||
T Consensus       524 ~~~~ILivdD~~~~~~~l~~~L~~~g~~v~~a~~~~eal~~~-----------~~~~~Dlvl~D~~mp~~~G~e~~~~ir  592 (779)
T PRK11091        524 PALNILLVEDIELNVIVARSVLEKLGNSVDVAMTGKEALEMF-----------DPDEYDLVLLDIQLPDMTGLDIARELR  592 (779)
T ss_pred             cccceEEEcCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHh-----------hcCCCCEEEEcCCCCCCCHHHHHHHHH
Confidence            357899999999999999999999999999999999999998           455799999999999999999999999


Q ss_pred             hcCCCCC-CcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          172 ESSVFRE-VPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       172 ~~~~~~~-~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      +....+. .|||++|++... ....++++|+++||.||++.+
T Consensus       593 ~~~~~~~~~~ii~~ta~~~~-~~~~~~~~G~~~~l~KP~~~~  633 (779)
T PRK11091        593 ERYPREDLPPLVALTANVLK-DKKEYLDAGMDDVLSKPLSVP  633 (779)
T ss_pred             hccccCCCCcEEEEECCchH-hHHHHHHCCCCEEEECCCCHH
Confidence            8643355 489999998754 467899999999999999753

>PRK11107 hybrid sensory histidine kinase BarA; Provisional

Probab=99.73  E-value=3.4e-17  Score=157.20  Aligned_cols=110  Identities=27%  Similarity=0.459  Sum_probs=102.0

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      ..++||||||++.++..++.+|+..|+.+..+.++.+|++.+           ....||+||+|+.||+++|+++++.||
T Consensus       666 ~~~~vLivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~al~~~-----------~~~~~dlil~D~~mp~~~g~~~~~~lr  734 (919)
T PRK11107        666 LPLTVMAVDDNPANLKLIGALLEEQVEHVVLCDSGHQAVEQA-----------KQRPFDLILMDIQMPGMDGIRACELIR  734 (919)
T ss_pred             CCCeEEEEeCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHH-----------HhCCCCEEEEeCCCCCCcHHHHHHHHH
Confidence            357999999999999999999999999999999999999998           456799999999999999999999999


Q ss_pred             hcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          172 ESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      +....+.+|||++|+........+++++|+++||.||++.+
T Consensus       735 ~~~~~~~~pii~lt~~~~~~~~~~~~~~G~~~~l~KP~~~~  775 (919)
T PRK11107        735 QLPHNQNTPIIAVTAHAMAGERERLLSAGMDDYLAKPIDEA  775 (919)
T ss_pred             hcccCCCCCEEEEeCCCCHHHHHHHHHcCCCeEeeCCCCHH
Confidence            86556789999999999999999999999999999999753

>PRK10816 DNA-binding transcriptional regulator PhoP; Provisional

Probab=99.71  E-value=1.5e-16  Score=128.30  Aligned_cols=105  Identities=24%  Similarity=0.442  Sum_probs=97.6

Q ss_pred             EEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhcC
Q 048660           95 HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKESS  174 (213)
Q Consensus        95 ~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~~  174 (213)
                      +||+|||++..+..+...|+..|+.+..+.++.+|+..+           ....||++++|+.||+++|+++++.+++. 
T Consensus         2 ~iLlv~d~~~~~~~l~~~L~~~g~~v~~~~~~~~~l~~~-----------~~~~~dlvild~~l~~~~g~~l~~~lr~~-   69 (223)
T PRK10816          2 RVLVVEDNALLRHHLKVQLQDAGHQVDAAEDAKEADYYL-----------NEHLPDIAIVDLGLPDEDGLSLIRRWRSN-   69 (223)
T ss_pred             eEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHH-----------hhCCCCEEEEECCCCCCCHHHHHHHHHhc-
Confidence            799999999999999999999999999999999999987           44579999999999999999999999975 


Q ss_pred             CCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          175 VFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       175 ~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                       .+.+|+|++|+..+......+++.|+++|+.||++.+
T Consensus        70 -~~~~pii~ls~~~~~~~~~~~l~~Ga~d~l~kp~~~~  106 (223)
T PRK10816         70 -DVSLPILVLTARESWQDKVEVLSAGADDYVTKPFHIE  106 (223)
T ss_pred             -CCCCCEEEEEcCCCHHHHHHHHHcCCCeeEeCCCCHH
Confidence             4689999999999999999999999999999999754

>PRK15347 two component system sensor kinase SsrA; Provisional

Probab=99.71  E-value=7e-17  Score=155.20  Aligned_cols=110  Identities=28%  Similarity=0.487  Sum_probs=100.4

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      .+++||||||++.++..+..+|+..|+.+..+.+|.+|++.+           ....||+||+|+.||+++|+++++.||
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            356899999999999999999999999999999999999988           456799999999999999999999999


Q ss_pred             hcC--CCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          172 ESS--VFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       172 ~~~--~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      +..  ..+.+|||++|+..+.....+++++|+++||.||++.+
T Consensus       758 ~~~~~~~~~~pii~lt~~~~~~~~~~~~~~G~~~~l~KP~~~~  800 (921)
T PRK15347        758 DDPNNLDPDCMIVALTANAAPEEIHRCKKAGMNHYLTKPVTLA  800 (921)
T ss_pred             hchhhcCCCCcEEEEeCCCCHHHHHHHHHCCCCEEEECCCCHH
Confidence            742  23679999999999999999999999999999999754

>PRK09836 DNA-binding transcriptional activator CusR; Provisional

Probab=99.71  E-value=2.3e-16  Score=127.54  Aligned_cols=105  Identities=20%  Similarity=0.432  Sum_probs=97.2

Q ss_pred             EEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhcC
Q 048660           95 HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKESS  174 (213)
Q Consensus        95 ~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~~  174 (213)
                      +||++||++..+..+...|+..|+.+..+.++.++++.+           ....||++++|+.||+++|+++++.+++. 
T Consensus         2 ~iliv~d~~~~~~~l~~~L~~~g~~v~~~~~~~~~~~~~-----------~~~~~dlvild~~~~~~~g~~~~~~lr~~-   69 (227)
T PRK09836          2 KLLIVEDEKKTGEYLTKGLTEAGFVVDLADNGLNGYHLA-----------MTGDYDLIILDIMLPDVNGWDIVRMLRSA-   69 (227)
T ss_pred             eEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHH-----------hhCCCCEEEEECCCCCCCHHHHHHHHHhc-
Confidence            799999999999999999999999999999999999887           44579999999999999999999999975 


Q ss_pred             CCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          175 VFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       175 ~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                       .+.+|+|++|+..+......++++|+++|+.||++.+
T Consensus        70 -~~~~pii~ls~~~~~~~~~~~~~~Ga~~~l~kp~~~~  106 (227)
T PRK09836         70 -NKGMPILLLTALGTIEHRVKGLELGADDYLVKPFAFA  106 (227)
T ss_pred             -CCCCCEEEEEcCCCHHHHHHHHhCCCCEEEeCCCCHH
Confidence             4689999999999999999999999999999999864

>PRK10529 DNA-binding transcriptional activator KdpE; Provisional

Probab=99.70  E-value=2.9e-16  Score=126.66  Aligned_cols=105  Identities=26%  Similarity=0.450  Sum_probs=96.5

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhc
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKES  173 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~  173 (213)
                      .+||+|||++..+..+...|+..|+.+..+.++.+++..+           ....||+|++|+.||+++|+++++.+++.
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            4799999999999999999999999999999999999877           44579999999999999999999999963


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                         +.+|+|++|+..+......++++|+++|+.||++.+
T Consensus        71 ---~~~pvi~lt~~~~~~~~~~~~~~ga~~~l~kP~~~~  106 (225)
T PRK10529         71 ---SAIPVIVLSARSEESDKIAALDAGADDYLSKPFGIG  106 (225)
T ss_pred             ---CCCCEEEEECCCCHHHHHHHHHcCCCEEEeCCCCHH
Confidence               478999999999999999999999999999999864

>PRK11173 two-component response regulator; Provisional

Probab=99.70  E-value=3.2e-16  Score=127.92  Aligned_cols=105  Identities=28%  Similarity=0.482  Sum_probs=97.0

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhc
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKES  173 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~  173 (213)
                      .+||+|||++..+..+...|+..|+.+..+.++.++++.+           ....||+|++|+.||+++|+++++.+++.
T Consensus         4 ~~iLiv~dd~~~~~~l~~~L~~~g~~v~~~~~~~~~~~~~-----------~~~~~dlvild~~l~~~~g~~~~~~lr~~   72 (237)
T PRK11173          4 PHILIVEDELVTRNTLKSIFEAEGYDVFEATDGAEMHQIL-----------SENDINLVIMDINLPGKNGLLLARELREQ   72 (237)
T ss_pred             CeEEEEeCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHH-----------hhCCCCEEEEcCCCCCCCHHHHHHHHhcC
Confidence            5899999999999999999999999999999999999988           44579999999999999999999999974


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                         +.+|+|++|+..+......+++.|+++|+.||++.+
T Consensus        73 ---~~~pii~lt~~~~~~~~~~~~~~ga~d~l~kP~~~~  108 (237)
T PRK11173         73 ---ANVALMFLTGRDNEVDKILGLEIGADDYITKPFNPR  108 (237)
T ss_pred             ---CCCCEEEEECCCCHHHHHHHHHCCCCEEEECCCCHH
Confidence               468999999999988899999999999999999854

>PRK10161 transcriptional regulator PhoB; Provisional

Probab=99.70  E-value=4.1e-16  Score=126.27  Aligned_cols=108  Identities=27%  Similarity=0.451  Sum_probs=98.7

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhc
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKES  173 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~  173 (213)
                      .+||+|||++..+..+...|+..|+.+..+.++.++++.+           ....||++++|+.||+++|+++++.+++.
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            5799999999999999999999999999999999999987           44579999999999999999999999975


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      ...+.+|+|++|+..+.....+++++|+++|+.||++.+
T Consensus        72 ~~~~~~pvi~ls~~~~~~~~~~~~~~Ga~~~l~kp~~~~  110 (229)
T PRK10161         72 SMTRDIPVVMLTARGEEEDRVRGLETGADDYITKPFSPK  110 (229)
T ss_pred             cccCCCCEEEEECCCCHHHHHHHHHcCCCEEEECCCCHH
Confidence            434689999999999999999999999999999998754

>PRK10643 DNA-binding transcriptional regulator BasR; Provisional

Probab=99.69  E-value=4.7e-16  Score=124.58  Aligned_cols=106  Identities=25%  Similarity=0.426  Sum_probs=97.3

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhc
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKES  173 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~  173 (213)
                      ++||+|||++..+..+...|+..|+.+..+.++.++++.+           ....||+|++|+.||+++|+++++.+++.
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            3799999999999999999999999999999999999987           44568999999999999999999999975


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                        .+.+|+|++|+..+......++++|+++|+.||++.+
T Consensus        70 --~~~~pii~ls~~~~~~~~~~~~~~ga~~~l~kp~~~~  106 (222)
T PRK10643         70 --KYTLPVLILTARDTLEDRVAGLDVGADDYLVKPFALE  106 (222)
T ss_pred             --CCCCcEEEEECCCCHHHHHHHHhcCCCeEEeCCCCHH
Confidence              4678999999999999999999999999999999764

>PRK09468 ompR osmolarity response regulator; Provisional

Probab=99.69  E-value=4.9e-16  Score=126.72  Aligned_cols=107  Identities=22%  Similarity=0.420  Sum_probs=98.7

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHh
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKE  172 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~  172 (213)
                      ..+||++||++..+..+...|+..|+.+..+.++.++++.+           ....||+|++|+.||+++|+++++.+|+
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            46899999999999999999999999999999999999987           4557999999999999999999999997


Q ss_pred             cCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          173 SSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       173 ~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      .  .+.+|||++++..+......++.+|+++|+.||++.+
T Consensus        74 ~--~~~~pii~ls~~~~~~~~~~~l~~Ga~~~l~kP~~~~  111 (239)
T PRK09468         74 Q--NNPTPIIMLTAKGEEVDRIVGLEIGADDYLPKPFNPR  111 (239)
T ss_pred             c--CCCCCEEEEECCCcHHHHHHHHhcCCCeEEECCCCHH
Confidence            5  4689999999999999999999999999999999854

>TIGR02154 PhoB phosphate regulon transcriptional regulatory protein PhoB

Probab=99.69  E-value=5.1e-16  Score=124.56  Aligned_cols=108  Identities=27%  Similarity=0.490  Sum_probs=98.4

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhc
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKES  173 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~  173 (213)
                      .+||++||++..+..+...|+..|+.+..+.++.+++..+           ....||++++|+.||+++|+++++.+++.
T Consensus         3 ~~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~-----------~~~~~d~vi~d~~~~~~~g~~~~~~l~~~   71 (226)
T TIGR02154         3 RRILVVEDEPAIRELIAYNLEKAGYDVVEAGDGDEALTLI-----------NERGPDLILLDWMLPGTSGIELCRRLRRR   71 (226)
T ss_pred             CeEEEEeCCHHHHHHHHHHHHHCCCEEEEEcCHHHHHHHH-----------HhcCCCEEEEECCCCCCcHHHHHHHHHcc
Confidence            5799999999999999999999999999999999999988           44579999999999999999999999975


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      ...+.+|||++|+..+......++++|+++|+.||++.+
T Consensus        72 ~~~~~~~ii~ls~~~~~~~~~~~~~~Ga~~~l~kp~~~~  110 (226)
T TIGR02154        72 PETRAIPIIMLTARGEEEDRVRGLETGADDYITKPFSPR  110 (226)
T ss_pred             ccCCCCCEEEEecCCCHHHHHHHHhcCcceEEeCCCCHH
Confidence            445679999999999999999999999999999998754

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.

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

Probab=99.69  E-value=2.3e-16  Score=118.86  Aligned_cols=105  Identities=18%  Similarity=0.288  Sum_probs=99.2

Q ss_pred             EEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhcC
Q 048660           95 HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKESS  174 (213)
Q Consensus        95 ~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~~  174 (213)
                      ..|+||||..+...|.+.+++-||.|.++.+.++++..+           +...|...++|+.|.+.+|+++++.||+. 
T Consensus        11 ~lllvdDD~~f~~~LaRa~e~RGf~v~~a~~~~eal~~a-----------rt~~PayAvvDlkL~~gsGL~~i~~lr~~-   78 (182)
T COG4567          11 SLLLVDDDTPFLRTLARAMERRGFAVVTAESVEEALAAA-----------RTAPPAYAVVDLKLGDGSGLAVIEALRER-   78 (182)
T ss_pred             eeEEecCChHHHHHHHHHHhccCceeEeeccHHHHHHHH-----------hcCCCceEEEEeeecCCCchHHHHHHHhc-
Confidence            799999999999999999999999999999999999998           55678999999999999999999999987 


Q ss_pred             CCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          175 VFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       175 ~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                       .++..||++|++.+-.....+.+.|+++||.||-+.+
T Consensus        79 -~~d~rivvLTGy~sIATAV~AvKlGA~~YLaKPAdaD  115 (182)
T COG4567          79 -RADMRIVVLTGYASIATAVEAVKLGACDYLAKPADAD  115 (182)
T ss_pred             -CCcceEEEEecchHHHHHHHHHHhhhhhhcCCCCChH
Confidence             6789999999999999999999999999999998754

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

Probab=99.68  E-value=3e-16  Score=154.86  Aligned_cols=108  Identities=28%  Similarity=0.488  Sum_probs=100.3

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      ...+||||||++.++..+..+|+..|+.+..+.++.+|++.+           ....||+||+|+.||+++|+++++.||
T Consensus       957 ~~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~-----------~~~~~dlil~D~~mp~~~g~~~~~~i~ 1025 (1197)
T PRK09959        957 EKLSILIADDHPTNRLLLKRQLNLLGYDVDEATDGVQALHKV-----------SMQHYDLLITDVNMPNMDGFELTRKLR 1025 (1197)
T ss_pred             cCceEEEcCCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHh-----------hcCCCCEEEEeCCCCCCCHHHHHHHHH
Confidence            356899999999999999999999999999999999999998           556799999999999999999999999


Q ss_pred             hcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          172 ESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      +.  .+.+|||++|+........+++++|+++||.||++.+
T Consensus      1026 ~~--~~~~pii~lt~~~~~~~~~~~~~~G~~~~l~KP~~~~ 1064 (1197)
T PRK09959       1026 EQ--NSSLPIWGLTANAQANEREKGLSCGMNLCLFKPLTLD 1064 (1197)
T ss_pred             hc--CCCCCEEEEECCCCHHHHHHHHHCCCCEEEeCCCCHH
Confidence            76  5689999999999999999999999999999999754

>PRK10766 DNA-binding transcriptional regulator TorR; Provisional

Probab=99.68  E-value=7e-16  Score=124.10  Aligned_cols=105  Identities=25%  Similarity=0.465  Sum_probs=96.9

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhc
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKES  173 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~  173 (213)
                      .+||+|||+...+..+...|...|+.+..+.++.++++.+           ....||++++|+.||+++|+++++.+++.
T Consensus         3 ~~iLlv~d~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~-----------~~~~~dlvild~~l~~~~g~~~~~~lr~~   71 (221)
T PRK10766          3 YHILVVEDEPVTRARLQGYFEQEGYTVSEAASGAGMREIM-----------QNQHVDLILLDINLPGEDGLMLTRELRSR   71 (221)
T ss_pred             CEEEEEeCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHH-----------hcCCCCEEEEeCCCCCCCHHHHHHHHHhC
Confidence            5899999999999999999999999999999999999987           44579999999999999999999999974


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                         +.+|+|++++..+......++++|+++|+.||++.+
T Consensus        72 ---~~~~ii~l~~~~~~~~~~~~l~~Ga~d~l~kP~~~~  107 (221)
T PRK10766         72 ---STVGIILVTGRTDSIDRIVGLEMGADDYVTKPLELR  107 (221)
T ss_pred             ---CCCCEEEEECCCcHHHHHHHHHcCCCcEEeCCCCHH
Confidence               478999999999999999999999999999999754

>PRK10336 DNA-binding transcriptional regulator QseB; Provisional

Probab=99.68  E-value=7.6e-16  Score=123.27  Aligned_cols=106  Identities=26%  Similarity=0.436  Sum_probs=97.1

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhc
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKES  173 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~  173 (213)
                      ++||+|||++..+..+...|+..|+.+..+.++.+++..+           ....||++++|+.||+++|+++++.+++.
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            3799999999999999999999999999999999999987           44578999999999999999999999975


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                        .+.+|+|++|+..+......++++|+++|+.||++.+
T Consensus        70 --~~~~~ii~lt~~~~~~~~~~~~~~ga~~~i~kp~~~~  106 (219)
T PRK10336         70 --GQREPVLILTARDALAERVEGLRLGADDYLCKPFALI  106 (219)
T ss_pred             --CCCCcEEEEECCCCHHHHHHHHhCCCCeEEECCCCHH
Confidence              5688999999999999999999999999999998754

>PRK10430 DNA-binding transcriptional activator DcuR; Provisional

Probab=99.68  E-value=8.7e-16  Score=126.36  Aligned_cols=108  Identities=24%  Similarity=0.330  Sum_probs=94.6

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhc-CCEE-EEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           94 LHVLAVDDSYVDRKLIERLLQIS-SCKV-TAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~-g~~v-~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      ++||||||++..+..+..+|... |+.+ ..+.++.++++.+..         ....||+||+|+.||+++|+++++.++
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            58999999999999999999864 6764 578999999988731         124699999999999999999999999


Q ss_pred             hcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          172 ESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      +.  .+.+|||++|+..+......++..|+++|+.||++.+
T Consensus        73 ~~--~~~~~vI~ls~~~~~~~~~~al~~Ga~~yl~Kp~~~~  111 (239)
T PRK10430         73 EA--GCKSDVIVISSAADAATIKDSLHYGVVDYLIKPFQAS  111 (239)
T ss_pred             hh--CCCCCEEEEECCCcHHHHHHHHHcCCCEEEeCCCCHH
Confidence            76  5689999999999999999999999999999998754

>PRK11083 DNA-binding response regulator CreB; Provisional

Probab=99.67  E-value=1.6e-15  Score=121.97  Aligned_cols=106  Identities=25%  Similarity=0.373  Sum_probs=97.2

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhc
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKES  173 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~  173 (213)
                      .+||+|||++..+..+...|...|+.+..+.++.+++..+           ....||++++|+.||+.+|+++++.+++.
T Consensus         4 ~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~-----------~~~~~dlvl~d~~~~~~~g~~~~~~l~~~   72 (228)
T PRK11083          4 PTILLVEDEQAIADTLVYALQSEGFTVEWFERGLPALDKL-----------RQQPPDLVILDVGLPDISGFELCRQLLAF   72 (228)
T ss_pred             CEEEEEeCCHHHHHHHHHHHHHCCCEEEEEcCHHHHHHHH-----------hcCCCCEEEEeCCCCCCCHHHHHHHHHhh
Confidence            5899999999999999999999999999999999999887           44579999999999999999999999986


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                        .+.+|+|++|+..+......+++.|+++|+.||++.+
T Consensus        73 --~~~~~ii~ls~~~~~~~~~~a~~~Ga~~~l~kp~~~~  109 (228)
T PRK11083         73 --HPALPVIFLTARSDEVDRLVGLEIGADDYVAKPFSPR  109 (228)
T ss_pred             --CCCCCEEEEEcCCcHHHHHHHhhcCCCeEEECCCCHH
Confidence              4689999999999888889999999999999998754

>TIGR02875 spore_0_A sporulation transcription factor Spo0A

Probab=99.67  E-value=1.1e-15  Score=127.09  Aligned_cols=109  Identities=21%  Similarity=0.386  Sum_probs=95.5

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhc-CCEE-EEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHH
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQIS-SCKV-TAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKI  170 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~-g~~v-~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~i  170 (213)
                      .++||+|||++..+..+...|... ++.+ ..+.++.++++.+           ....||+||+|+.||+++|+++++.+
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            468999999999999999999864 5554 4789999999988           44579999999999999999999999


Q ss_pred             HhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          171 KESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       171 r~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      ++.......|+|++|+.........+++.|+++|+.||++.+
T Consensus        71 ~~~~~~~~~~iI~lt~~~~~~~~~~~~~~G~~~~l~KP~~~~  112 (262)
T TIGR02875        71 NEIELSARPRVIMLSAFGQEKITQRAVALGADYYVLKPFDLE  112 (262)
T ss_pred             HhhccccCCeEEEEeCCCCHHHHHHHHHCCCCEEEECCCCHH
Confidence            986433458999999999999999999999999999999754

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.

>PRK10955 DNA-binding transcriptional regulator CpxR; Provisional

Probab=99.66  E-value=1.6e-15  Score=122.67  Aligned_cols=104  Identities=28%  Similarity=0.485  Sum_probs=94.8

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhc
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKES  173 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~  173 (213)
                      .+||+|||++..+..+...|+..|+.+..+.++.++++.+           . ..||++++|+.||+++|+++++.+++.
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            3799999999999999999999999999999999999976           3 269999999999999999999999985


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                        .+ +|+|++|+..+......++++|+++|+.||++.+
T Consensus        70 --~~-~~ii~lt~~~~~~~~~~~~~~ga~~~l~kp~~~~  105 (232)
T PRK10955         70 --HQ-TPVIMLTARGSELDRVLGLELGADDYLPKPFNDR  105 (232)
T ss_pred             --CC-CcEEEEECCCCHHHHHHHHHcCCCEEEcCCCCHH
Confidence              33 8999999999888889999999999999999754

>TIGR03787 marine_sort_RR proteobacterial dedicated sortase system response regulator

Probab=99.66  E-value=1.6e-15  Score=122.51  Aligned_cols=105  Identities=21%  Similarity=0.302  Sum_probs=95.9

Q ss_pred             EEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCC--CCHHHHHHHHHh
Q 048660           95 HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPG--MTGYELLKKIKE  172 (213)
Q Consensus        95 ~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~--~~G~e~~~~ir~  172 (213)
                      +||++||+...+..+...|+..|+.+..+.++.+++..+           ....||++++|+.||+  .+|+++++.+++
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            699999999999999999999999999999999999987           4457999999999998  589999999997


Q ss_pred             cCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          173 SSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       173 ~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      .  .+.+|+|++|+..+......++++|+++|+.||++.+
T Consensus        71 ~--~~~~pii~ls~~~~~~~~~~~~~~Ga~~~l~kp~~~~  108 (227)
T TIGR03787        71 L--SATLPIIFLTARDSDFDTVSGLRLGADDYLTKDISLP  108 (227)
T ss_pred             c--CCCCCEEEEECCCCHHHHHHHHhcCCCEEEECCCCHH
Confidence            5  4678999999999999999999999999999999753

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.

>PRK10701 DNA-binding transcriptional regulator RstA; Provisional

Probab=99.66  E-value=1.6e-15  Score=123.86  Aligned_cols=104  Identities=25%  Similarity=0.346  Sum_probs=95.6

Q ss_pred             EEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhcC
Q 048660           95 HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKESS  174 (213)
Q Consensus        95 ~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~~  174 (213)
                      +||+|||++..+..+...|+..|+.+..+.++.++++.+           ....||++++|+.||+++|+++++.+++. 
T Consensus         3 ~iLivedd~~~~~~l~~~L~~~g~~v~~~~~~~~~l~~~-----------~~~~~dlvild~~l~~~~g~~~~~~ir~~-   70 (240)
T PRK10701          3 KIVFVEDDAEVGSLIAAYLAKHDIDVTVEPRGDRAEATI-----------LREQPDLVLLDIMLPGKDGMTICRDLRPK-   70 (240)
T ss_pred             eEEEEeCCHHHHHHHHHHHHHcCCEEEEeCCHHHHHHHH-----------hhCCCCEEEEeCCCCCCCHHHHHHHHHhc-
Confidence            799999999999999999999999999999999999988           44579999999999999999999999974 


Q ss_pred             CCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          175 VFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       175 ~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                        ...|+|++++.........++++|+++|+.||++.+
T Consensus        71 --~~~pii~l~~~~~~~~~~~~~~~Ga~d~l~kP~~~~  106 (240)
T PRK10701         71 --WQGPIVLLTSLDSDMNHILALEMGACDYILKTTPPA  106 (240)
T ss_pred             --CCCCEEEEECCCCHHHHHHHHHcCCCEEEECCCCHH
Confidence              357999999998888888999999999999999753

>PRK13856 two-component response regulator VirG; Provisional

Probab=99.66  E-value=1.7e-15  Score=124.10  Aligned_cols=104  Identities=30%  Similarity=0.483  Sum_probs=93.9

Q ss_pred             EEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhcC
Q 048660           95 HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKESS  174 (213)
Q Consensus        95 ~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~~  174 (213)
                      +||+|||++..+..+...|+..||.+..+.++.++++.+           ....||+|++|+.||+++|+++++.+++. 
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            799999999999999999999999999999999999987           45579999999999999999999999974 


Q ss_pred             CCCCCcEEEEecCC-CHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          175 VFREVPVVIMSSED-VLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       175 ~~~~~pII~lt~~~-~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                        ..+|+|++|+.. .......++++|+++|+.||++.+
T Consensus        71 --~~~pii~lt~~~~~~~~~~~~l~~Ga~~yl~kP~~~~  107 (241)
T PRK13856         71 --SDVPIIIISGDRLEEADKVVALELGATDFIAKPFGTR  107 (241)
T ss_pred             --CCCcEEEEECCCCcHHHHHHHHhcCcCeEEeCCCCHH
Confidence              468999999854 566778899999999999999864

>PRK10840 transcriptional regulator RcsB; Provisional

Probab=99.66  E-value=1.8e-15  Score=122.46  Aligned_cols=107  Identities=23%  Similarity=0.365  Sum_probs=95.2

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCC-E-EEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCC---CCHHHHH
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSC-K-VTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPG---MTGYELL  167 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~-~-v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~---~~G~e~~  167 (213)
                      .++||||||++..+..++..|+..++ . +..+.++.++++.+           ....||++|+|+.||+   .+|++++
T Consensus         3 ~~~Ilivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~~~~~~-----------~~~~~DlvllD~~l~~~~~~~g~~~~   71 (216)
T PRK10840          3 NMNVIIADDHPIVLFGIRKSLEQIEWVNVVGEFEDSTALINNL-----------PKLDAHVLITDLSMPGDKYGDGITLI   71 (216)
T ss_pred             ceEEEEECCcHHHHHHHHHHHhcCCCCEEEEEECCHHHHHHHH-----------HhCCCCEEEEeCcCCCCCCCCHHHHH
Confidence            36899999999999999999987765 3 66889999999988           4457999999999999   5999999


Q ss_pred             HHHHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          168 KKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       168 ~~ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      +.|++.  .+.+|||++|+..+......+++.|+++|+.||++.+
T Consensus        72 ~~l~~~--~~~~~iIvls~~~~~~~~~~a~~~Ga~~yl~K~~~~~  114 (216)
T PRK10840         72 KYIKRH--FPSLSIIVLTMNNNPAILSAVLDLDIEGIVLKQGAPT  114 (216)
T ss_pred             HHHHHH--CCCCcEEEEEecCCHHHHHHHHHCCCeEEEECCCCHH
Confidence            999976  5789999999999999999999999999999998754

>PRK09581 pleD response regulator PleD; Reviewed

Probab=99.66  E-value=4.6e-16  Score=137.72  Aligned_cols=111  Identities=21%  Similarity=0.364  Sum_probs=100.0

Q ss_pred             cCCccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHH
Q 048660           90 CSKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKK  169 (213)
Q Consensus        90 ~~~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~  169 (213)
                      .....+||+|||++..+..+..+|. +++.+..+.++.+|+..+           ....||+|++|+.||+++|+++++.
T Consensus       152 ~~~~~~vlivdd~~~~~~~l~~~l~-~~~~~~~~~~~~~a~~~~-----------~~~~~d~vi~d~~~p~~~g~~l~~~  219 (457)
T PRK09581        152 KDEDGRILLVDDDVSQAERIANILK-EEFRVVVVSDPSEALFNA-----------AETNYDLVIVSANFENYDPLRLCSQ  219 (457)
T ss_pred             cccCceEEEEecccchHHHHHHHHh-hcceeeeecChHHHHHhc-----------ccCCCCEEEecCCCCCchHhHHHHH
Confidence            3456789999999999999999996 567778899999999987           5568999999999999999999999


Q ss_pred             HHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          170 IKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       170 ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      +|+....+.+|+|++|++.+.+...++++.|+++||.||++.+
T Consensus       220 i~~~~~~~~~~ii~ls~~~~~~~~~~a~~~Ga~d~l~kp~~~~  262 (457)
T PRK09581        220 LRSKERTRYVPILLLVDEDDDPRLVKALELGVNDYLMRPIDKN  262 (457)
T ss_pred             HHhccccCCCcEEEEeCCCChHHHHHHHHccchhhhhCCCcHH
Confidence            9985445799999999999999999999999999999999764

>PRK11517 transcriptional regulatory protein YedW; Provisional

Probab=99.65  E-value=2.5e-15  Score=120.71  Aligned_cols=104  Identities=26%  Similarity=0.509  Sum_probs=96.0

Q ss_pred             EEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhcC
Q 048660           95 HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKESS  174 (213)
Q Consensus        95 ~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~~  174 (213)
                      +||+|||++..+..+...|+..|+.+..+.++.+++..+           ....||++++|+.||+++|+++++.+++. 
T Consensus         2 ~iliv~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~l~~~-----------~~~~~dlvi~d~~~~~~~g~~~~~~l~~~-   69 (223)
T PRK11517          2 KILLIEDNQRTQEWVTQGLSEAGYVIDAVSDGRDGLYLA-----------LKDDYALIILDIMLPGMDGWQILQTLRTA-   69 (223)
T ss_pred             EEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHH-----------hcCCCCEEEEECCCCCCCHHHHHHHHHcC-
Confidence            799999999999999999999999999999999999987           44579999999999999999999999974 


Q ss_pred             CCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          175 VFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       175 ~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                        ..+|+|++|+..+......++++|+++|+.||++.+
T Consensus        70 --~~~~ii~ls~~~~~~~~~~a~~~Ga~~~l~kp~~~~  105 (223)
T PRK11517         70 --KQTPVICLTARDSVDDRVRGLDSGANDYLVKPFSFS  105 (223)
T ss_pred             --CCCCEEEEECCCCHHHHHHHHhcCCCEEEECCCCHH
Confidence              468999999999999999999999999999998754

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

Probab=99.65  E-value=3.6e-16  Score=129.36  Aligned_cols=104  Identities=27%  Similarity=0.439  Sum_probs=93.6

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhc
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKES  173 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~  173 (213)
                      ++|+||||+......|..+|++.|+.+..++...+|++.+           ....||||++|+.||+|+|+++++++|..
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            3799999999999999999999999999999999999999           66789999999999999999999999987


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                        .+.+|||++|++..  .....+..-.+|||.|||+.+
T Consensus        70 --~~~v~iifIssh~e--ya~dsf~~n~~dYl~KPvt~e  104 (361)
T COG3947          70 --ESAVPIIFISSHAE--YADDSFGMNLDDYLPKPVTPE  104 (361)
T ss_pred             --hccCcEEEEecchh--hhhhhcccchHhhccCCCCHH
Confidence              58999999999864  455566666799999999864

>TIGR01387 cztR_silR_copR heavy metal response regulator

Probab=99.64  E-value=3.8e-15  Score=118.99  Aligned_cols=104  Identities=29%  Similarity=0.514  Sum_probs=95.9

Q ss_pred             EEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhcCC
Q 048660           96 VLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKESSV  175 (213)
Q Consensus        96 ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~~~  175 (213)
                      ||++||++..+..+...|+..|+.+..+.++.++++.+           ....||++++|+.||+++|+++++.+++.  
T Consensus         1 iliidd~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~-----------~~~~~dlvl~d~~~~~~~g~~~~~~l~~~--   67 (218)
T TIGR01387         1 ILVVEDEQKTAEYLQQGLSESGYVVDAASNGRDGLHLA-----------LKDDYDLIILDVMLPGMDGWQILQTLRRS--   67 (218)
T ss_pred             CEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHH-----------hcCCCCEEEEeCCCCCCCHHHHHHHHHcc--
Confidence            58999999999999999999999999999999999988           44579999999999999999999999975  


Q ss_pred             CCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          176 FREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       176 ~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      .+.+|+|++|+..+......++++|+++|+.||++.+
T Consensus        68 ~~~~~iivls~~~~~~~~~~~~~~Ga~~~l~kp~~~~  104 (218)
T TIGR01387        68 GKQTPVLFLTARDSVADKVKGLDLGADDYLVKPFSFS  104 (218)
T ss_pred             CCCCcEEEEEcCCCHHHHHHHHHcCCCeEEECCCCHH
Confidence            4688999999999999999999999999999998754

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.

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

Probab=99.63  E-value=3.7e-15  Score=133.97  Aligned_cols=106  Identities=33%  Similarity=0.504  Sum_probs=98.7

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhc
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKES  173 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~  173 (213)
                      .+||||||++..+..+...|+..||.+..+.++.+|+..+           ....||+||+|+.||+++|+++++.+++.
T Consensus         4 ~~ILiVdd~~~~~~~L~~~L~~~g~~v~~~~s~~~al~~l-----------~~~~~DlvllD~~lp~~dgl~~l~~ir~~   72 (469)
T PRK10923          4 GIVWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLEAL-----------ASKTPDVLLSDIRMPGMDGLALLKQIKQR   72 (469)
T ss_pred             CeEEEEECCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHH-----------hcCCCCEEEECCCCCCCCHHHHHHHHHhh
Confidence            5899999999999999999999999999999999999998           45579999999999999999999999976


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                        .+.+|+|++|+..+......++++|+++|+.||++.+
T Consensus        73 --~~~~pvIvlt~~~~~~~~~~a~~~Ga~~~l~KP~~~~  109 (469)
T PRK10923         73 --HPMLPVIIMTAHSDLDAAVSAYQQGAFDYLPKPFDID  109 (469)
T ss_pred             --CCCCeEEEEECCCCHHHHHHHHhcCcceEEecCCcHH
Confidence              5689999999999999999999999999999998753

>PRK15115 response regulator GlrR; Provisional

Probab=99.63  E-value=2.9e-15  Score=133.77  Aligned_cols=107  Identities=30%  Similarity=0.454  Sum_probs=99.0

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHh
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKE  172 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~  172 (213)
                      ..+||||||++..+..+...|+..||.+..+.++.+|++.+           ....||+||+|+.||+++|+++++.+++
T Consensus         5 ~~~vLiVdd~~~~~~~l~~~L~~~g~~v~~~~~~~eal~~l-----------~~~~~dlvilD~~lp~~~g~~ll~~l~~   73 (444)
T PRK15115          5 PAHLLLVDDDPGLLKLLGMRLTSEGYSVVTAESGQEALRVL-----------NREKVDLVISDLRMDEMDGMQLFAEIQK   73 (444)
T ss_pred             CCeEEEEECCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHH-----------hcCCCCEEEEcCCCCCCCHHHHHHHHHh
Confidence            47899999999999999999999999999999999999988           4457999999999999999999999997


Q ss_pred             cCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          173 SSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       173 ~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      .  .+.+|||++|+..+.....+++++|+++|+.||++.+
T Consensus        74 ~--~~~~pvIvlt~~~~~~~~~~a~~~Ga~~~l~KP~~~~  111 (444)
T PRK15115         74 V--QPGMPVIILTAHGSIPDAVAATQQGVFSFLTKPVDRD  111 (444)
T ss_pred             c--CCCCcEEEEECCCCHHHHHHHHhcChhhhccCCCCHH
Confidence            6  5789999999999999999999999999999998753

>CHL00148 orf27 Ycf27; Reviewed

Probab=99.63  E-value=6.5e-15  Score=119.62  Aligned_cols=106  Identities=29%  Similarity=0.525  Sum_probs=96.9

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHh
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKE  172 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~  172 (213)
                      ..+||++||++..+..+...|...|+.+..+.++.+++..+           ....||++++|+.||+++|+++++.+++
T Consensus         6 ~~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~~l~~~-----------~~~~~d~illd~~~~~~~g~~~~~~l~~   74 (240)
T CHL00148          6 KEKILVVDDEAYIRKILETRLSIIGYEVITASDGEEALKLF-----------RKEQPDLVILDVMMPKLDGYGVCQEIRK   74 (240)
T ss_pred             CceEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHH-----------HhcCCCEEEEeCCCCCCCHHHHHHHHHh
Confidence            46899999999999999999999999999999999999987           4457999999999999999999999997


Q ss_pred             cCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          173 SSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       173 ~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      .   +.+|+|++|+..+......++++|+++|+.||++.+
T Consensus        75 ~---~~~~ii~ls~~~~~~~~~~~~~~Ga~~~l~kp~~~~  111 (240)
T CHL00148         75 E---SDVPIIMLTALGDVSDRITGLELGADDYVVKPFSPK  111 (240)
T ss_pred             c---CCCcEEEEECCCCHHhHHHHHHCCCCEEEeCCCCHH
Confidence            4   478999999999988889999999999999998754

>PRK09958 DNA-binding transcriptional activator EvgA; Provisional

Probab=99.63  E-value=5.5e-15  Score=117.31  Aligned_cols=106  Identities=21%  Similarity=0.412  Sum_probs=96.1

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEE-EEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHh
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVT-AVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKE  172 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~-~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~  172 (213)
                      ++||++||++..+..+...|+..|+.+. .+.++.++++.+           ....||++++|+.+|+++|+++++.+++
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            3799999999999999999999999987 699999999988           4457999999999999999999999997


Q ss_pred             cCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          173 SSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       173 ~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      .  .+..|+|++|+..+......++++|+++|+.||++.+
T Consensus        70 ~--~~~~~ii~ls~~~~~~~~~~~~~~ga~~~i~kp~~~~  107 (204)
T PRK09958         70 R--QYSGIIIIVSAKNDHFYGKHCADAGANGFVSKKEGMN  107 (204)
T ss_pred             h--CCCCeEEEEeCCCCHHHHHHHHHCCCCEEEecCCCHH
Confidence            5  4678999999999989999999999999999999754

>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional

Probab=99.63  E-value=4.8e-15  Score=132.70  Aligned_cols=107  Identities=23%  Similarity=0.448  Sum_probs=98.9

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHh
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKE  172 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~  172 (213)
                      ..+||||||++..+..+...|+..||.+..+.++.+|+..+           ....||+||+|+.||+++|+++++.+++
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            45899999999999999999999999999999999999988           4557999999999999999999999997


Q ss_pred             cCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          173 SSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       173 ~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      .  .+.+|+|++|+..+......+++.|+++|+.||++.+
T Consensus        73 ~--~~~~pvI~lt~~~~~~~~~~a~~~Ga~d~l~KP~~~~  110 (457)
T PRK11361         73 H--ETRTPVILMTAYAEVETAVEALRCGAFDYVIKPFDLD  110 (457)
T ss_pred             c--CCCCCEEEEeCCCCHHHHHHHHHCCccEEEecccCHH
Confidence            6  5689999999999999999999999999999998753

>PRK10365 transcriptional regulatory protein ZraR; Provisional

Probab=99.63  E-value=3e-15  Score=133.38  Aligned_cols=108  Identities=28%  Similarity=0.471  Sum_probs=99.5

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      ..++||||||++..+..+...|+..|+.+..+.++.+++..+           ....||+||+|+.||+++|+++++.++
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            357999999999999999999999999999999999999988           445799999999999999999999999


Q ss_pred             hcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          172 ESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      +.  .+.+|||++|++.+......+++.|+.+|+.||++.+
T Consensus        73 ~~--~~~~~vi~lt~~~~~~~~~~a~~~ga~~~l~Kp~~~~  111 (441)
T PRK10365         73 AL--NPAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFD  111 (441)
T ss_pred             hh--CCCCeEEEEECCCCHHHHHHHHHhhhHHHhcCCCCHH
Confidence            86  5789999999999999999999999999999998753

>PRK09483 response regulator; Provisional

Probab=99.61  E-value=1.1e-14  Score=116.75  Aligned_cols=106  Identities=25%  Similarity=0.391  Sum_probs=95.5

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhc-CCEEE-EEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           94 LHVLAVDDSYVDRKLIERLLQIS-SCKVT-AVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~-g~~v~-~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      ++|||+||++..+..+..+|+.. |+.+. .+.++.++++.+           ....||++|+|+.+|+++|+++++.++
T Consensus         2 ~~ilivd~~~~~~~~l~~~L~~~~~~~~v~~~~~~~~~~~~~-----------~~~~~dlvi~d~~~~~~~g~~~~~~l~   70 (217)
T PRK09483          2 INVLLVDDHELVRAGIRRILEDIKGIKVVGEACCGEDAVKWC-----------RTNAVDVVLMDMNMPGIGGLEATRKIL   70 (217)
T ss_pred             eEEEEECCcHHHHHHHHHHHccCCCCEEEEEeCCHHHHHHHH-----------HhcCCCEEEEeCCCCCCCHHHHHHHHH
Confidence            58999999999999999999875 78775 789999999988           445799999999999999999999998


Q ss_pred             hcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          172 ESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      +.  .+.+|+|++|...+......++..|+++|+.||++.+
T Consensus        71 ~~--~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~k~~~~~  109 (217)
T PRK09483         71 RY--TPDVKIIMLTVHTENPLPAKVMQAGAAGYLSKGAAPQ  109 (217)
T ss_pred             HH--CCCCeEEEEeCCCCHHHHHHHHHcCCCEEEeCCCCHH
Confidence            76  5789999999999999999999999999999998753

>PRK14084 two-component response regulator; Provisional

Probab=99.60  E-value=1.2e-14  Score=119.54  Aligned_cols=104  Identities=23%  Similarity=0.330  Sum_probs=89.2

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcC-C-EEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISS-C-KVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g-~-~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      ++||++||++..+..+..+|+..+ + .+..+.++.+++..+           ....||++++|+.||+++|+++++.|+
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            479999999999999999999866 4 567899999999988           345799999999999999999999999


Q ss_pred             hcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          172 ESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      +.  .+..+||++|++.  ....++++.|+.+||.||++.+
T Consensus        70 ~~--~~~~~iI~~t~~~--~~~~~~~~~~~~~yl~KP~~~~  106 (246)
T PRK14084         70 KM--KEPPAIIFATAHD--QFAVKAFELNATDYILKPFEQK  106 (246)
T ss_pred             hc--CCCCEEEEEecCh--HHHHHHHhcCCcEEEECCCCHH
Confidence            85  4567788888865  3567889999999999998743

>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator

Probab=99.60  E-value=1e-14  Score=130.30  Aligned_cols=102  Identities=16%  Similarity=0.272  Sum_probs=93.9

Q ss_pred             EEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCC-----CCHHHHHHHH
Q 048660           96 VLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPG-----MTGYELLKKI  170 (213)
Q Consensus        96 ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~-----~~G~e~~~~i  170 (213)
                      ||||||++..+..+...|  .||.+..+.++.+|++.+           ....||+||+|+.||+     ++|+++++.+
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            689999999999999988  799999999999999998           4457999999999996     8999999999


Q ss_pred             HhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          171 KESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       171 r~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      ++.  .+.+|||++|+..+.+...+++++|+++||.||++.+
T Consensus        68 ~~~--~~~~piI~lt~~~~~~~~~~a~~~Ga~dyl~KP~~~~  107 (445)
T TIGR02915        68 LAI--APDTKVIVITGNDDRENAVKAIGLGAYDFYQKPIDPD  107 (445)
T ss_pred             Hhh--CCCCCEEEEecCCCHHHHHHHHHCCccEEEeCCCCHH
Confidence            986  5789999999999999999999999999999999864

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).

>PRK09935 transcriptional regulator FimZ; Provisional

Probab=99.59  E-value=2.5e-14  Score=113.57  Aligned_cols=107  Identities=27%  Similarity=0.403  Sum_probs=95.0

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhc-CCEEE-EEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHH
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQIS-SCKVT-AVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKI  170 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~-g~~v~-~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~i  170 (213)
                      ..+|||+||++..+..+...|+.. ++.+. .+.++.++++.+           ....||++++|+.||+++|.++++.+
T Consensus         3 ~~~iliv~d~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~dlvild~~l~~~~g~~~~~~l   71 (210)
T PRK09935          3 PASVIIMDTHPIIRMSIEVLLQKNSELQIVLKTDDYRITIDYL-----------RTRPVDLIIMDIDLPGTDGFTFLKRI   71 (210)
T ss_pred             cceEEEECCcHHHHHHHHHHHhhCCCceEEEEeCCHHHHHHHH-----------HhcCCCEEEEeCCCCCCCHHHHHHHH
Confidence            468999999999999999999877 57765 688999999887           44579999999999999999999999


Q ss_pred             HhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          171 KESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       171 r~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      ++.  .+.+|||++|+.........++..|+++|+.||++.+
T Consensus        72 ~~~--~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~kp~~~~  111 (210)
T PRK09935         72 KQI--QSTVKVLFLSSKSECFYAGRAIQAGANGFVSKCNDQN  111 (210)
T ss_pred             HHh--CCCCcEEEEECCCcHHHHHHHHHcCCCEEEeCCCCHH
Confidence            975  5679999999999888999999999999999998753

>TIGR01818 ntrC nitrogen regulation protein NR(I)

Probab=99.59  E-value=1.3e-14  Score=130.20  Aligned_cols=104  Identities=32%  Similarity=0.497  Sum_probs=96.3

Q ss_pred             EEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhcCC
Q 048660           96 VLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKESSV  175 (213)
Q Consensus        96 ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~~~  175 (213)
                      ||||||++..+..+...|+..|+.+..+.++.+|+..+           ....||+||+|+.||+++|+++++.+++.  
T Consensus         1 ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~-----------~~~~~DlVllD~~~p~~~g~~ll~~l~~~--   67 (463)
T TIGR01818         1 VWVVDDDRSIRWVLEKALSRAGYEVRTFGNAASVLRAL-----------ARGQPDLLITDVRMPGEDGLDLLPQIKKR--   67 (463)
T ss_pred             CEEEECCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHH-----------hcCCCCEEEEcCCCCCCCHHHHHHHHHHh--
Confidence            68999999999999999999999999999999999988           44579999999999999999999999986  


Q ss_pred             CCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          176 FREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       176 ~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      .+.+|+|++|+........+++++|+++|+.||++.+
T Consensus        68 ~~~~~vIvlt~~~~~~~~~~a~~~Ga~~~l~KP~~~~  104 (463)
T TIGR01818        68 HPQLPVIVMTAHSDLDTAVAAYQRGAFEYLPKPFDLD  104 (463)
T ss_pred             CCCCeEEEEeCCCCHHHHHHHHHcCcceeecCCCCHH
Confidence            5688999999999999999999999999999998753

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=99.57  E-value=4.2e-14  Score=122.23  Aligned_cols=102  Identities=24%  Similarity=0.382  Sum_probs=89.4

Q ss_pred             cEEEEEeCCHHHHHHHHHHH-hhcCCEEE-EEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           94 LHVLAVDDSYVDRKLIERLL-QISSCKVT-AVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L-~~~g~~v~-~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      ++||||||++..+..+..+| +..++.+. .+.++.+|++.+           ....||+|++|+.||+|+|+++++.|+
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            37999999999999999999 46688775 789999999998           455799999999999999999999998


Q ss_pred             hcCCCCCCcEEEEecCCC--HHHHHHHHHcCCCeeeeCCC
Q 048660          172 ESSVFREVPVVIMSSEDV--LTQIDSCLEEGAEEYIVKPV  209 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~--~~~~~~~~~~G~~~~L~KP~  209 (213)
                      +.   ..+|+|++++...  .....++++.|+++|+.||+
T Consensus        70 ~~---~~~pvivvs~~~~~~~~~~~~al~~Ga~d~l~KP~  106 (337)
T PRK12555         70 AE---RPCPILIVTSLTERNASRVFEAMGAGALDAVDTPT  106 (337)
T ss_pred             HH---CCCcEEEEeCCCCcCHHHHHHHHhcCceEEEECCC
Confidence            74   3589999998754  45667899999999999998

>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional

Probab=99.57  E-value=5.7e-14  Score=114.03  Aligned_cols=105  Identities=28%  Similarity=0.431  Sum_probs=95.9

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhc
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKES  173 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~  173 (213)
                      .+||++||++..+..+...|...|+.+..+.++.+++..+           ....||++++|+.||+++|+++++.+++.
T Consensus        11 ~~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~-----------~~~~~dlvl~d~~~~~~~g~~~~~~l~~~   79 (240)
T PRK10710         11 PRILIVEDEPKLGQLLIDYLQAASYATTLLSHGDEVLPYV-----------RQTPPDLILLDLMLPGTDGLTLCREIRRF   79 (240)
T ss_pred             CeEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHH-----------hhCCCCEEEEeCCCCCCCHHHHHHHHHhc
Confidence            3899999999999999999999999999999999999988           44579999999999999999999999963


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                         +.+|+|++++.........+++.|+++|+.||++.+
T Consensus        80 ---~~~pii~l~~~~~~~~~~~~~~~ga~~~l~kp~~~~  115 (240)
T PRK10710         80 ---SDIPIVMVTAKIEEIDRLLGLEIGADDYICKPYSPR  115 (240)
T ss_pred             ---CCCCEEEEEcCCCHHHHHHHHhcCCCeEEECCCCHH
Confidence               478999999998888889999999999999998754

>PRK15479 transcriptional regulatory protein TctD; Provisional

Probab=99.57  E-value=6.3e-14  Score=112.12  Aligned_cols=105  Identities=26%  Similarity=0.445  Sum_probs=96.0

Q ss_pred             EEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhcC
Q 048660           95 HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKESS  174 (213)
Q Consensus        95 ~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~~  174 (213)
                      +||++||++..+..+...|...|+.+..+.++.++++.+           ....||++++|+.+|+++|+++++.+++. 
T Consensus         2 ~ilivd~~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~-----------~~~~~d~vild~~~~~~~~~~~~~~i~~~-   69 (221)
T PRK15479          2 RLLLAEDNRELAHWLEKALVQNGFAVDCVFDGLAADHLL-----------QSEMYALAVLDINMPGMDGLEVLQRLRKR-   69 (221)
T ss_pred             eEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHH-----------hhCCCCEEEEeCCCCCCcHHHHHHHHHhc-
Confidence            699999999999999999999999999999999999877           44579999999999999999999999976 


Q ss_pred             CCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          175 VFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       175 ~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                       .+.+|+|++|+..+.....++++.|+++|+.||++.+
T Consensus        70 -~~~~~ii~lt~~~~~~~~~~~~~~g~~~~i~kp~~~~  106 (221)
T PRK15479         70 -GQTLPVLLLTARSAVADRVKGLNVGADDYLPKPFELE  106 (221)
T ss_pred             -CCCCCEEEEECCCCHHHHHHHHHcCCCeeEeCCCCHH
Confidence             4678999999999888889999999999999998753

>PRK13558 bacterio-opsin activator; Provisional

Probab=99.56  E-value=3.1e-14  Score=132.96  Aligned_cols=105  Identities=18%  Similarity=0.208  Sum_probs=97.3

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHh
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKE  172 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~  172 (213)
                      ..+||||||++.++..+..+|...||.+..+.++.+++..+           ....||+||+|+.||+++|+++++.|++
T Consensus         7 ~~~ILivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~al~~~-----------~~~~~Dlvl~d~~lp~~~g~~~l~~l~~   75 (665)
T PRK13558          7 TRGVLFVGDDPEAGPVDCDLDEDGRLDVTQIRDFVAARDRV-----------EAGEIDCVVADHEPDGFDGLALLEAVRQ   75 (665)
T ss_pred             ceeEEEEccCcchHHHHHHHhhccCcceEeeCCHHHHHHHh-----------hccCCCEEEEeccCCCCcHHHHHHHHHh
Confidence            47899999999999999999999999999999999999988           4457999999999999999999999997


Q ss_pred             cCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCC
Q 048660          173 SSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVK  210 (213)
Q Consensus       173 ~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~  210 (213)
                      .  .+.+|||++|+..+.....+++..|+.+|+.||.+
T Consensus        76 ~--~~~~piI~lt~~~~~~~~~~al~~Ga~dyl~k~~~  111 (665)
T PRK13558         76 T--TAVPPVVVVPTAGDEAVARRAVDADAAAYVPAVSD  111 (665)
T ss_pred             c--CCCCCEEEEECCCCHHHHHHHHhcCcceEEeccch
Confidence            5  57899999999999999999999999999999964

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

Probab=99.56  E-value=4.5e-14  Score=121.02  Aligned_cols=103  Identities=36%  Similarity=0.498  Sum_probs=92.2

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcC--CEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISS--CKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g--~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      +|||||||+...|..++.+|...|  ..|..+.||.+|++.+           ....||+|++|+.||.|||+++++.|-
T Consensus         2 irVlvVddsal~R~~i~~~l~~~~~i~vv~~a~ng~~a~~~~-----------~~~~PDVi~ld~emp~mdgl~~l~~im   70 (350)
T COG2201           2 IRVLVVDDSALMRKVISDILNSDPDIEVVGTARNGREAIDKV-----------KKLKPDVITLDVEMPVMDGLEALRKIM   70 (350)
T ss_pred             cEEEEEcCcHHHHHHHHHHHhcCCCeEEEEecCCHHHHHHHH-----------HhcCCCEEEEecccccccHHHHHHHHh
Confidence            589999999999999999999998  5678999999999999           566899999999999999999999998


Q ss_pred             hcCCCCCCcEEEEecCCC--HHHHHHHHHcCCCeeeeCCCC
Q 048660          172 ESSVFREVPVVIMSSEDV--LTQIDSCLEEGAEEYIVKPVK  210 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~--~~~~~~~~~~G~~~~L~KP~~  210 (213)
                      +.   ..+|||++++-..  .+...++++.|+.||+.||..
T Consensus        71 ~~---~p~pVimvsslt~~g~~~t~~al~~gAvD~i~kp~~  108 (350)
T COG2201          71 RL---RPLPVIMVSSLTEEGAEATLEALELGAVDFIAKPSG  108 (350)
T ss_pred             cC---CCCcEEEEeccccccHHHHHHHHhcCcceeecCCCc
Confidence            74   5899999987543  467788999999999999974

>PRK10360 DNA-binding transcriptional activator UhpA; Provisional

Probab=99.56  E-value=7.4e-14  Score=110.12  Aligned_cols=103  Identities=26%  Similarity=0.442  Sum_probs=91.1

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhc-CCE-EEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           94 LHVLAVDDSYVDRKLIERLLQIS-SCK-VTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~-g~~-v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      .+||+|||++..+..+...|... ++. +..+.++.++++.+           ....||+|++|+.||+++|+++++.++
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            47999999999999999999754 565 56889999999988           445799999999999999999999986


Q ss_pred             hcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          172 ESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      .     .+|+|++|...+......+++.|+++|+.||++.+
T Consensus        71 ~-----~~~vi~~s~~~~~~~~~~~~~~ga~~~i~kp~~~~  106 (196)
T PRK10360         71 K-----GMATIMLSVHDSPALVEQALNAGARGFLSKRCSPD  106 (196)
T ss_pred             c-----CCCEEEEECCCCHHHHHHHHHcCCcEEEECCCCHH
Confidence            3     47899999999999999999999999999998754

>PRK00742 chemotaxis-specific methylesterase; Provisional

Probab=99.55  E-value=9.4e-14  Score=120.80  Aligned_cols=104  Identities=33%  Similarity=0.450  Sum_probs=91.1

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhc-CCEEE-EEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHH
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQIS-SCKVT-AVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKI  170 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~-g~~v~-~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~i  170 (213)
                      .++||||||+..++..+...|... |+.+. .+.++.++++.+           ....||+|++|+.||+++|+++++.|
T Consensus         3 ~~~ILiVdd~~~~~~~L~~~L~~~~~~~vv~~a~~~~~al~~~-----------~~~~~DlVllD~~mp~~dgle~l~~i   71 (354)
T PRK00742          3 KIRVLVVDDSAFMRRLISEILNSDPDIEVVGTAPDGLEAREKI-----------KKLNPDVITLDVEMPVMDGLDALEKI   71 (354)
T ss_pred             ccEEEEECCCHHHHHHHHHHHhhCCCCEEEEEECCHHHHHHHH-----------hhhCCCEEEEeCCCCCCChHHHHHHH
Confidence            469999999999999999999876 78776 899999999988           44579999999999999999999999


Q ss_pred             HhcCCCCCCcEEEEecCC--CHHHHHHHHHcCCCeeeeCCCC
Q 048660          171 KESSVFREVPVVIMSSED--VLTQIDSCLEEGAEEYIVKPVK  210 (213)
Q Consensus       171 r~~~~~~~~pII~lt~~~--~~~~~~~~~~~G~~~~L~KP~~  210 (213)
                      ++..  + +|+|++|+..  ......++++.|+++||.||++
T Consensus        72 ~~~~--~-~piIvls~~~~~~~~~~~~al~~Ga~d~l~kP~~  110 (354)
T PRK00742         72 MRLR--P-TPVVMVSSLTERGAEITLRALELGAVDFVTKPFL  110 (354)
T ss_pred             HHhC--C-CCEEEEecCCCCCHHHHHHHHhCCCcEEEeCCcc
Confidence            9863  3 8999999754  3456778999999999999984

>PRK09390 fixJ response regulator FixJ; Provisional

Probab=99.55  E-value=9.8e-14  Score=108.74  Aligned_cols=106  Identities=29%  Similarity=0.428  Sum_probs=97.3

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHh
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKE  172 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~  172 (213)
                      +.+||++||++..+..+...|...|+.+..+.++.++++.+           ....||++++|+.+|+++|+++++.+++
T Consensus         3 ~~~iliv~~~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~-----------~~~~~d~ii~d~~~~~~~~~~~~~~l~~   71 (202)
T PRK09390          3 KGVVHVVDDDEAMRDSLAFLLDSAGFEVRLFESAQAFLDAL-----------PGLRFGCVVTDVRMPGIDGIELLRRLKA   71 (202)
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHHCCCeEEEeCCHHHHHHHh-----------ccCCCCEEEEeCCCCCCcHHHHHHHHHh
Confidence            46899999999999999999999999999999999999887           4557999999999999999999999997


Q ss_pred             cCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCC
Q 048660          173 SSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKL  211 (213)
Q Consensus       173 ~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~  211 (213)
                      .  .+.+|+|++|+..+......++..|+.+|+.||++.
T Consensus        72 ~--~~~~~ii~l~~~~~~~~~~~~~~~g~~~~l~~p~~~  108 (202)
T PRK09390         72 R--GSPLPVIVMTGHGDVPLAVEAMKLGAVDFIEKPFED  108 (202)
T ss_pred             c--CCCCCEEEEECCCCHHHHHHHHHcChHHHhhCCCCH
Confidence            5  578999999999998999999999999999999874

>PRK09581 pleD response regulator PleD; Reviewed

Probab=99.55  E-value=7.1e-14  Score=123.74  Aligned_cols=108  Identities=29%  Similarity=0.483  Sum_probs=98.7

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhc
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKES  173 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~  173 (213)
                      .+||+|||++..+..+...|...|+.+..+.++.++++.+           ....||+|++|+.||+++|.++++.+++.
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            3799999999999999999998999999999999999988           44579999999999999999999999975


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      ...+.+|||++|+..+.....+++..|+++|+.||++.+
T Consensus        72 ~~~~~~~ii~~s~~~~~~~~~~~~~~ga~~~l~kp~~~~  110 (457)
T PRK09581         72 PATTHIPVVMVTALDDPEDRVRGLEAGADDFLTKPINDV  110 (457)
T ss_pred             cccCCCCEEEEECCCCHHHHHHHHHCCCCEEEECCCCHH
Confidence            444679999999999999999999999999999999754

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

Probab=99.55  E-value=7.3e-14  Score=133.70  Aligned_cols=107  Identities=11%  Similarity=0.162  Sum_probs=95.8

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      .+.+||||||++..+..+...|...||.+..+.++.++++.+..         ....||+||+  .||+++|+++++.|+
T Consensus       696 ~~~~ILvVddd~~~~~~l~~~L~~~G~~v~~~~s~~~al~~l~~---------~~~~~DlVll--~~~~~~g~~l~~~l~  764 (828)
T PRK13837        696 RGETVLLVEPDDATLERYEEKLAALGYEPVGFSTLAAAIAWISK---------GPERFDLVLV--DDRLLDEEQAAAALH  764 (828)
T ss_pred             CCCEEEEEcCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHHh---------CCCCceEEEE--CCCCCCHHHHHHHHH
Confidence            34689999999999999999999999999999999999998842         1235899999  799999999999999


Q ss_pred             hcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          172 ESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      +.  .+.+|||++|+........+++..| ++||.||++.+
T Consensus       765 ~~--~~~ipIIvls~~~~~~~~~~~~~~G-~d~L~KP~~~~  802 (828)
T PRK13837        765 AA--APTLPIILGGNSKTMALSPDLLASV-AEILAKPISSR  802 (828)
T ss_pred             hh--CCCCCEEEEeCCCchhhhhhHhhcc-CcEEeCCCCHH
Confidence            76  5789999999999999999999999 99999999864

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

Probab=99.55  E-value=5.8e-14  Score=114.72  Aligned_cols=103  Identities=26%  Similarity=0.408  Sum_probs=86.8

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCC-E-EEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSC-K-VTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~-~-v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      ++|||+||++..+..+..+|+..|. . +..+.++.++++.+           ....||++|+|+.||+++|+++++.++
T Consensus         2 ~~IlIvdd~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~l~~~-----------~~~~~dlv~lDi~~~~~~G~~~~~~l~   70 (238)
T PRK11697          2 IKVLIVDDEPLAREELRELLQEEGDIEIVGECSNAIEAIGAI-----------HRLKPDVVFLDIQMPRISGLELVGMLD   70 (238)
T ss_pred             cEEEEECCCHHHHHHHHHHHhhCCCcEEEEEeCCHHHHHHHH-----------HhcCCCEEEEeCCCCCCCHHHHHHHhc
Confidence            5899999999999999999998874 3 45789999999987           344799999999999999999999996


Q ss_pred             hcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          172 ESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      ..   ...+||++|+..  +...++++.|+.+||.||++.+
T Consensus        71 ~~---~~~~ii~vt~~~--~~~~~a~~~~~~~yl~KP~~~~  106 (238)
T PRK11697         71 PE---HMPYIVFVTAFD--EYAIKAFEEHAFDYLLKPIDPA  106 (238)
T ss_pred             cc---CCCEEEEEeccH--HHHHHHHhcCCcEEEECCCCHH
Confidence            42   244688888765  4667899999999999998753

>PRK10610 chemotaxis regulatory protein CheY; Provisional

Probab=99.52  E-value=6.3e-13  Score=95.64  Aligned_cols=110  Identities=35%  Similarity=0.562  Sum_probs=96.9

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCC-EEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSC-KVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKI  170 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~-~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~i  170 (213)
                      +..+||++++++.....+...|+..|+ .+..+.++.+++..+           ....+|++++|..+++++|+++++.+
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            346899999999999999999999898 477889999999887           44578999999999999999999999


Q ss_pred             HhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          171 KESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       171 r~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      ++....+.+|+++++..........+++.|+++|+.||++.+
T Consensus        73 ~~~~~~~~~~~i~~~~~~~~~~~~~~~~~g~~~~i~~p~~~~  114 (129)
T PRK10610         73 RADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAA  114 (129)
T ss_pred             HhCCCcCCCcEEEEECCCCHHHHHHHHHhCCCeEEECCCCHH
Confidence            986445678999999988888889999999999999998754

>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional

Probab=99.51  E-value=1.4e-13  Score=112.10  Aligned_cols=104  Identities=8%  Similarity=0.073  Sum_probs=84.6

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHH-HHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELL-KKI  170 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~-~~i  170 (213)
                      ...++++|||++..+..|+.+|...-..+..+.++.++++.+           .  .||+||+|+.||+++|++++ +.|
T Consensus         9 ~~~~~~~v~~~~l~~~~l~~~L~~~~~v~~~~~~~~~~~~~~-----------~--~~DvvllDi~~p~~~G~~~~~~~i   75 (216)
T PRK10100          9 HGHTLLLITKPSLQATALLQHLKQSLAITGKLHNIQRSLDDI-----------S--SGSIILLDMMEADKKLIHYWQDTL   75 (216)
T ss_pred             cCceEEEEeChHhhhHHHHHHHHHhCCCeEEEcCHHHhhccC-----------C--CCCEEEEECCCCCccHHHHHHHHH
Confidence            456899999999999999999984333456788999998865           3  38999999999999999997 567


Q ss_pred             HhcCCCCCCcEEEEecCCCHHHHHHHHH--cCCCeeeeCCCCCC
Q 048660          171 KESSVFREVPVVIMSSEDVLTQIDSCLE--EGAEEYIVKPVKLS  212 (213)
Q Consensus       171 r~~~~~~~~pII~lt~~~~~~~~~~~~~--~G~~~~L~KP~~~~  212 (213)
                      ++.  .+.++||++|+..+.  ...++.  +|+.+|+.|+.+.+
T Consensus        76 ~~~--~p~~~vvvlt~~~~~--~~~~~~~~~Ga~G~l~K~~~~~  115 (216)
T PRK10100         76 SRK--NNNIKILLLNTPEDY--PYREIENWPHINGVFYAMEDQE  115 (216)
T ss_pred             HHh--CCCCcEEEEECCchh--HHHHHHHhcCCeEEEECCCCHH
Confidence            865  678999999998763  334444  59999999987654

>PRK10651 transcriptional regulator NarL; Provisional

Probab=99.48  E-value=8.5e-13  Score=104.90  Aligned_cols=108  Identities=25%  Similarity=0.470  Sum_probs=94.7

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhc-CCEE-EEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQIS-SCKV-TAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKK  169 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~-g~~v-~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~  169 (213)
                      ...+||+|||++..+..+...|... ++.+ ..+.++.+++..+           ....||++++|+.+|+++|+++++.
T Consensus         5 ~~~~iliv~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~dlvl~d~~l~~~~~~~~~~~   73 (216)
T PRK10651          5 EPATILLIDDHPMLRTGVKQLISMAPDITVVGEASNGEQGIELA-----------ESLDPDLILLDLNMPGMNGLETLDK   73 (216)
T ss_pred             cceEEEEECCCHHHHHHHHHHHccCCCcEEEEEeCCHHHHHHHH-----------HhCCCCEEEEeCCCCCCcHHHHHHH
Confidence            4578999999999999999999865 5654 4689999999988           4457999999999999999999999


Q ss_pred             HHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          170 IKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       170 ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      +++.  .+..|+|+++...+......+++.|+++|+.||++.+
T Consensus        74 l~~~--~~~~~vi~l~~~~~~~~~~~~~~~g~~~~i~k~~~~~  114 (216)
T PRK10651         74 LREK--SLSGRIVVFSVSNHEEDVVTALKRGADGYLLKDMEPE  114 (216)
T ss_pred             HHHh--CCCCcEEEEeCCCCHHHHHHHHHcCCCEEEeCCCCHH
Confidence            9986  4678999999999999999999999999999998753

>PRK11475 DNA-binding transcriptional activator BglJ; Provisional

Probab=99.48  E-value=3.2e-13  Score=109.29  Aligned_cols=95  Identities=14%  Similarity=0.223  Sum_probs=79.3

Q ss_pred             HHHHHHHHHhh---cCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEE---EeCCCCCCCHHHHHHHHHhcCCCCC
Q 048660          105 DRKLIERLLQI---SSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLII---TDYTMPGMTGYELLKKIKESSVFRE  178 (213)
Q Consensus       105 ~~~~l~~~L~~---~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil---~D~~mp~~~G~e~~~~ir~~~~~~~  178 (213)
                      .|..++.+|+.   .|+.+..+.++.++++.+           ....||++|   +|+.||+++|++++++|++.  .+.
T Consensus         2 ~r~gi~~lL~~~~~~~~~v~~~~~~~~~l~~~-----------~~~~pd~vl~dl~d~~mp~~~Gl~~~~~l~~~--~p~   68 (207)
T PRK11475          2 SSIGIESLFRKFPGNPYKLHTFSSQSSFQDAM-----------SRISFSAVIFSLSAMRSERREGLSCLTELAIK--FPR   68 (207)
T ss_pred             chHHHHHHHhcCCCCeeEEEEeCCHHHHHHHh-----------ccCCCCEEEeeccccCCCCCCHHHHHHHHHHH--CCC
Confidence            36788888865   366678999999999987           455789998   68899999999999999986  678


Q ss_pred             CcEEEEecCCCHHHHHHHH-HcCCCeeeeCCCCCC
Q 048660          179 VPVVIMSSEDVLTQIDSCL-EEGAEEYIVKPVKLS  212 (213)
Q Consensus       179 ~pII~lt~~~~~~~~~~~~-~~G~~~~L~KP~~~~  212 (213)
                      +|||++|+..+......++ ++|+++||.||++.+
T Consensus        69 ~~iIvlt~~~~~~~~~~~~~~~Ga~gyl~K~~~~~  103 (207)
T PRK11475         69 MRRLVIADDDIEARLIGSLSPSPLDGVLSKASTLE  103 (207)
T ss_pred             CCEEEEeCCCCHHHHHHHHHHcCCeEEEecCCCHH
Confidence            9999999987776555555 799999999998764

>PRK10403 transcriptional regulator NarP; Provisional

Probab=99.47  E-value=9e-13  Score=104.54  Aligned_cols=106  Identities=24%  Similarity=0.461  Sum_probs=93.7

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhh-cCCEEE-EEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHH
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQI-SSCKVT-AVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKI  170 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~-~g~~v~-~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~i  170 (213)
                      ..+||++||++..+..+...|+. .++.+. .+.++.++++.+           ....||++++|+.+|+++|.++++.+
T Consensus         6 ~~~ilii~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~dlvi~d~~~~~~~~~~~~~~l   74 (215)
T PRK10403          6 PFQVLIVDDHPLMRRGVRQLLELDPGFEVVAEAGDGASAIDLA-----------NRLDPDVILLDLNMKGMSGLDTLNAL   74 (215)
T ss_pred             eEEEEEEcCCHHHHHHHHHHHhcCCCCEEEEEeCCHHHHHHHH-----------HhcCCCEEEEecCCCCCcHHHHHHHH
Confidence            46899999999999999999975 577765 689999999887           44579999999999999999999999


Q ss_pred             HhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCC
Q 048660          171 KESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKL  211 (213)
Q Consensus       171 r~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~  211 (213)
                      ++.  .+..|+++++..........+++.|+++|+.||++.
T Consensus        75 ~~~--~~~~~ii~l~~~~~~~~~~~~~~~g~~~~i~kp~~~  113 (215)
T PRK10403         75 RRD--GVTAQIIILTVSDASSDVFALIDAGADGYLLKDSDP  113 (215)
T ss_pred             HHh--CCCCeEEEEeCCCChHHHHHHHHcCCCeEEecCCCH
Confidence            976  467899999998888888999999999999999874

>PRK15369 two component system sensor kinase SsrB; Provisional

Probab=99.47  E-value=2e-12  Score=101.79  Aligned_cols=106  Identities=20%  Similarity=0.386  Sum_probs=93.7

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhc-CCEE-EEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHH
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQIS-SCKV-TAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKI  170 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~-g~~v-~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~i  170 (213)
                      ..+||++||++..+..+...|... ++.+ ..+.++.++++.+           ....||+|++|+.+++++|+++++.+
T Consensus         3 ~~~iliv~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~dlvl~d~~~~~~~~~~~~~~l   71 (211)
T PRK15369          3 NYKILLVDDHELIINGIKNMLAPYPRYKIVGQVDNGLEVYNAC-----------RQLEPDIVILDLGLPGMNGLDVIPQL   71 (211)
T ss_pred             ccEEEEECCcHHHHHHHHHHHccCCCcEEEEEECCHHHHHHHH-----------HhcCCCEEEEeCCCCCCCHHHHHHHH
Confidence            468999999999999999999876 4654 4789999999877           44579999999999999999999999


Q ss_pred             HhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCC
Q 048660          171 KESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKL  211 (213)
Q Consensus       171 r~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~  211 (213)
                      ++.  .+..|+|++|+..+......++..|+++|+.||++.
T Consensus        72 ~~~--~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~kp~~~  110 (211)
T PRK15369         72 HQR--WPAMNILVLTARQEEHMASRTLAAGALGYVLKKSPQ  110 (211)
T ss_pred             HHH--CCCCcEEEEeCCCCHHHHHHHHHhCCCEEEeCCCCH
Confidence            986  467899999999999999999999999999999874

>PRK13435 response regulator; Provisional

Probab=99.45  E-value=1.3e-12  Score=98.92  Aligned_cols=103  Identities=23%  Similarity=0.273  Sum_probs=88.3

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCEEE-EEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCC-CCCHHHHHHHH
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCKVT-AVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMP-GMTGYELLKKI  170 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~v~-~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp-~~~G~e~~~~i  170 (213)
                      ..+|||+|++......+...|+..|+.+. .++++.++++.+           ....||++++|+.++ +.+|.++++.+
T Consensus         5 ~~~iliid~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~-----------~~~~~dliivd~~~~~~~~~~~~~~~l   73 (145)
T PRK13435          5 QLKVLIVEDEALIALELEKLVEEAGHEVVGIAMSSEQAIALG-----------RRRQPDVALVDVHLADGPTGVEVARRL   73 (145)
T ss_pred             cceEEEEcCcHHHHHHHHHHHHhcCCeEEEeeCCHHHHHHHh-----------hhcCCCEEEEeeecCCCCcHHHHHHHH
Confidence            57899999999999999999998899876 789999999887           344799999999998 58999999999


Q ss_pred             HhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          171 KESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       171 r~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      ++.   +.+|+|++++..+   ...++..|+++|+.||++.+
T Consensus        74 ~~~---~~~pii~ls~~~~---~~~~~~~ga~~~l~kp~~~~  109 (145)
T PRK13435         74 SAD---GGVEVVFMTGNPE---RVPHDFAGALGVIAKPYSPR  109 (145)
T ss_pred             HhC---CCCCEEEEeCCHH---HHHHHhcCcceeEeCCCCHH
Confidence            863   4789999997643   34678899999999999754

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

Probab=99.45  E-value=4.7e-13  Score=105.11  Aligned_cols=107  Identities=27%  Similarity=0.327  Sum_probs=89.9

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCCE-EEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSCK-VTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKI  170 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~~-v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~i  170 (213)
                      ..++||++||++..+..+...|...||. |.++.++.++.+..           ....||+||+|+.||..|-.+.....
T Consensus         4 ~~lrvlv~~d~~i~~~~i~~~l~eag~~~Vg~~~~~~~~~~~~-----------~~~~pDvVildie~p~rd~~e~~~~~   72 (194)
T COG3707           4 MLLRVLVADDEALTRMDIREGLLEAGYQRVGEAADGLEAVEVC-----------ERLQPDVVILDIEMPRRDIIEALLLA   72 (194)
T ss_pred             cccceeeccccccchhhHHHHHHHcCCeEeeeecccccchhHH-----------HhcCCCEEEEecCCCCccHHHHHHHh
Confidence            3579999999999999999999999995 55778888888877           55689999999999999933333222


Q ss_pred             HhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          171 KESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       171 r~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      .   .....|||++|++++++..+.+.++|+.+|+.||++..
T Consensus        73 ~---~~~~~piv~lt~~s~p~~i~~a~~~Gv~ayivkpi~~~  111 (194)
T COG3707          73 S---ENVARPIVALTAYSDPALIEAAIEAGVMAYIVKPLDES  111 (194)
T ss_pred             h---cCCCCCEEEEEccCChHHHHHHHHcCCeEEEecCcchh
Confidence            2   24678999999999999999999999999999999753

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

Probab=99.43  E-value=1.3e-12  Score=105.71  Aligned_cols=104  Identities=11%  Similarity=0.095  Sum_probs=85.2

Q ss_pred             EEEEEeCCHHHHHHHHHHHhhcCC---EEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCC--CCCCCHHHHHHH
Q 048660           95 HVLAVDDSYVDRKLIERLLQISSC---KVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYT--MPGMTGYELLKK  169 (213)
Q Consensus        95 ~ILvVdD~~~~~~~l~~~L~~~g~---~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~--mp~~~G~e~~~~  169 (213)
                      .||||||++..+..++.+|+..++   .+..+.++.++++.+           ....||++|+|+.  +++++|.++++.
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            589999999999999999986553   456789999999987           4457999999966  888899999999


Q ss_pred             HHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCe-eeeCCCCCC
Q 048660          170 IKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEE-YIVKPVKLS  212 (213)
Q Consensus       170 ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~-~L~KP~~~~  212 (213)
                      |++.  .+.++||++|+..+..... ++..|... |+.|+.+.+
T Consensus        71 i~~~--~p~~~iivlt~~~~~~~~~-~~~~~~~~~~~~K~~~~~  111 (207)
T PRK15411         71 IINQ--HPNTLFIVFMAIANIHFDE-YLLVRKNLLISSKSIKPE  111 (207)
T ss_pred             HHHH--CCCCeEEEEECCCchhHHH-HHHHHhhceeeeccCCHH
Confidence            9976  6789999999987766543 55556554 889987754

>PRK13557 histidine kinase; Provisional

Probab=99.43  E-value=2.3e-12  Score=116.43  Aligned_cols=108  Identities=21%  Similarity=0.286  Sum_probs=96.6

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCC-CCHHHHHHHHH
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPG-MTGYELLKKIK  171 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~-~~G~e~~~~ir  171 (213)
                      ..+||+++|++..+..+..+|+..||.+..+.++.++++.+.          ....||++++|..||+ ++|+++++.|+
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            458999999999999999999999999999999999999873          2235999999999997 99999999999


Q ss_pred             hcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          172 ESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      +.  .+.+|+|++|..........++..|+.+|+.||++.+
T Consensus       485 ~~--~~~~~ii~~~~~~~~~~~~~~~~~g~~~~l~kp~~~~  523 (540)
T PRK13557        485 RR--QPKIKVLLTTGYAEASIERTDAGGSEFDILNKPYRRA  523 (540)
T ss_pred             Hh--CCCCcEEEEcCCCchhhhhhhccccCCceeeCCCCHH
Confidence            86  4678999999998888888899999999999999754

>PRK09191 two-component response regulator; Provisional

Probab=99.37  E-value=7.8e-12  Score=103.47  Aligned_cols=105  Identities=19%  Similarity=0.283  Sum_probs=88.8

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCCEEE-EEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCC-CCHHHHHHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSCKVT-AVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPG-MTGYELLKK  169 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~-~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~-~~G~e~~~~  169 (213)
                      -..+||++||++..+..+...|+..|+.+. .+.++.++++.+           ....||+|++|+.||+ ++|+++++.
T Consensus       136 ~~~~~liidd~~~~~~~l~~~L~~~~~~~~~~~~~~~~~l~~l-----------~~~~~dlvi~d~~~~~~~~g~e~l~~  204 (261)
T PRK09191        136 VATRVLIIEDEPIIAMDLEQLVESLGHRVTGIARTRAEAVALA-----------KKTRPGLILADIQLADGSSGIDAVND  204 (261)
T ss_pred             CCCeEEEEcCcHHHHHHHHHHHhcCCCEEEEEECCHHHHHHHH-----------hccCCCEEEEecCCCCCCCHHHHHHH
Confidence            345899999999999999999999999887 789999999988           4457999999999995 899999999


Q ss_pred             HHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          170 IKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       170 ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      +++.  . .+|+|++|+.......  ....|+.+|+.||++.+
T Consensus       205 l~~~--~-~~pii~ls~~~~~~~~--~~~~~~~~~l~kP~~~~  242 (261)
T PRK09191        205 ILKT--F-DVPVIFITAFPERLLT--GERPEPAFLITKPFQPD  242 (261)
T ss_pred             HHHh--C-CCCEEEEeCCCcHHHH--HHhcccCceEECCCCHH
Confidence            9976  3 7899999997665433  34567889999999854

>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=99.29  E-value=7.5e-11  Score=81.14  Aligned_cols=102  Identities=34%  Similarity=0.590  Sum_probs=91.0

Q ss_pred             EEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhcCCC
Q 048660           97 LAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKESSVF  176 (213)
Q Consensus        97 LvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~~~~  176 (213)
                      |++++++..+..+...|...|+.+..+.+..+++..+           ....+|++++|..+++.+|.++++.+++.  .
T Consensus         1 l~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~-----------~~~~~~~ii~~~~~~~~~~~~~~~~l~~~--~   67 (113)
T cd00156           1 LIVDDDPLIRELLRRLLEKEGYEVVEAEDGEEALALL-----------AEEKPDLILLDIMMPGMDGLELLRRIRKR--G   67 (113)
T ss_pred             CeecCcHHHHHHHHHHHhhcCceEEEecCHHHHHHHH-----------HhCCCCEEEEecCCCCCchHHHHHHHHHh--C
Confidence            4789999999999999999999999999999999887           34578999999999999999999999986  5


Q ss_pred             CCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCC
Q 048660          177 REVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKL  211 (213)
Q Consensus       177 ~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~  211 (213)
                      +.+|+++++..........++..|+.+|+.||++.
T Consensus        68 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~i~~p~~~  102 (113)
T cd00156          68 PDIPIIFLTAHGDDEDAVEALKAGADDYLTKPFSP  102 (113)
T ss_pred             CCCCEEEEEecccHHHHHHHHHcChhhHccCCCCH
Confidence            67899999988777788889999999999999874

>PRK10693 response regulator of RpoS; Provisional

Probab=99.27  E-value=2.8e-11  Score=103.34  Aligned_cols=76  Identities=30%  Similarity=0.595  Sum_probs=69.3

Q ss_pred             EEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhcCCCCCCcEEEEecCCCHHHHHHHHHcCC
Q 048660          122 AVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGA  201 (213)
Q Consensus       122 ~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~  201 (213)
                      .+.++.+|++.+           ....||+||+|+.||+++|+++++.+++.  .+.+|||++|+..+.+...+++++|+
T Consensus         2 ~a~~g~~al~~l-----------~~~~pDlVL~D~~mp~~~Gle~~~~ir~~--~~~ipiI~lt~~~~~~~~~~al~~Ga   68 (303)
T PRK10693          2 LAANGVDALELL-----------GGFTPDLIICDLAMPRMNGIEFVEHLRNR--GDQTPVLVISATENMADIAKALRLGV   68 (303)
T ss_pred             EeCCHHHHHHHH-----------hcCCCCEEEEeCCCCCCCHHHHHHHHHhc--CCCCcEEEEECCCCHHHHHHHHHCCC
Confidence            478899999988           44579999999999999999999999986  46799999999999999999999999


Q ss_pred             CeeeeCCCC
Q 048660          202 EEYIVKPVK  210 (213)
Q Consensus       202 ~~~L~KP~~  210 (213)
                      ++|+.||++
T Consensus        69 ~dyl~KP~~   77 (303)
T PRK10693         69 QDVLLKPVK   77 (303)
T ss_pred             cEEEECCCC
Confidence            999999984

>PRK15029 arginine decarboxylase; Provisional

Probab=99.26  E-value=3.5e-11  Score=113.07  Aligned_cols=82  Identities=18%  Similarity=0.311  Sum_probs=74.6

Q ss_pred             EEEEEeCCHH--------HHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCC-CceeEEEEeCCCCCCCHH-
Q 048660           95 HVLAVDDSYV--------DRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDA-LKVNLIITDYTMPGMTGY-  164 (213)
Q Consensus        95 ~ILvVdD~~~--------~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~-~~~dlil~D~~mp~~~G~-  164 (213)
                      +||||||+..        .++.++..|+..||.|..+.++.+|++.+           .. ..||+||+|+.||+++|+ 
T Consensus         2 kILIVDDD~~~~~~~~~~i~~~L~~~Le~~G~eV~~a~s~~dAl~~l-----------~~~~~~DlVLLD~~LPd~dG~~   70 (755)
T PRK15029          2 KVLIVESEFLHQDTWVGNAVERLADALSQQNVTVIKSTSFDDGFAIL-----------SSNEAIDCLMFSYQMEHPDEHQ   70 (755)
T ss_pred             eEEEEeCCcccccchhHHHHHHHHHHHHHCCCEEEEECCHHHHHHHH-----------HhcCCCcEEEEECCCCCCccch
Confidence            6999999995        69999999999999999999999999998           33 479999999999999997 


Q ss_pred             ---HHHHHHHhcCCCCCCcEEEEecCCC
Q 048660          165 ---ELLKKIKESSVFREVPVVIMSSEDV  189 (213)
Q Consensus       165 ---e~~~~ir~~~~~~~~pII~lt~~~~  189 (213)
                         ++++.||+.  ..++|||++|+..+
T Consensus        71 ~~~ell~~IR~~--~~~iPIIlLTar~~   96 (755)
T PRK15029         71 NVRQLIGKLHER--QQNVPVFLLGDREK   96 (755)
T ss_pred             hHHHHHHHHHhh--CCCCCEEEEEcCCc
Confidence               899999975  46899999999885

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

Probab=99.00  E-value=1.8e-09  Score=89.53  Aligned_cols=104  Identities=31%  Similarity=0.494  Sum_probs=86.8

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhc-CC-EEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           94 LHVLAVDDSYVDRKLIERLLQIS-SC-KVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~-g~-~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      ++|+++||++..++.+..++... .+ .+..+.++.++++.+           ....+|++++|+.||+++|+++.+.|+
T Consensus         2 ~~i~i~dd~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~~~~fldI~~~~~~G~ela~~i~   70 (244)
T COG3279           2 LKVLIVDDEPLAREELRRILNEIPDIEIVGEAENGEEALQLL-----------QGLRPDLVFLDIAMPDINGIELAARIR   70 (244)
T ss_pred             CcEEEecCCHHHHHHHHHHHHhhhhcCeeeeeccchhhHHHH-----------hccCCCeEEEeeccCccchHHHHHHhc
Confidence            57999999999999999999843 22 233788999999988           445899999999999999999999999


Q ss_pred             hcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          172 ESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      ..  .+..+|+++|++.  +....+++..+-+|+.||++.+
T Consensus        71 ~~--~~~~~Ivfvt~~~--~~a~~afev~a~d~i~kp~~~~  107 (244)
T COG3279          71 KG--DPRPAIVFVTAHD--EYAVAAFEVEALDYLLKPISEE  107 (244)
T ss_pred             cc--CCCCeEEEEEehH--HHHHHHHhHHHHhhhcCcchHH
Confidence            85  5677899999985  4566677888999999998643

>PRK11107 hybrid sensory histidine kinase BarA; Provisional

Probab=98.91  E-value=9.4e-09  Score=99.11  Aligned_cols=105  Identities=10%  Similarity=0.097  Sum_probs=87.0

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      .+.+||++||++..+..+..+|+.+|+.+..+.++.+    +           ....||++++|+.||++++...+....
T Consensus       535 ~g~~ili~d~~~~~~~~l~~~L~~~g~~v~~~~~~~~----l-----------~~~~~d~il~~~~~~~~~~~~~~~~~~  599 (919)
T PRK11107        535 AGKRLLYVEPNSAAAQATLDILSETPLEVTYSPTLSQ----L-----------PEAHYDILLLGLPVTFREPLTMLHERL  599 (919)
T ss_pred             CCCeEEEEeCCHHHHHHHHHHHHHCCCEEEEcCCHHH----h-----------ccCCCCEEEecccCCCCCCHHHHHHHH
Confidence            4579999999999999999999999999999999877    2           334699999999999887776555444


Q ss_pred             hcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCC
Q 048660          172 ESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKL  211 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~  211 (213)
                      ........++++++..........+.+.|+++|+.||++.
T Consensus       600 ~~~~~~~~~~i~~~~~~~~~~~~~~~~~g~~~~l~kp~~~  639 (919)
T PRK11107        600 AKAKSMTDFLILALPCHEQVLAEQLKQDGADACLSKPLSH  639 (919)
T ss_pred             HhhhhcCCcEEEEeCCcchhhHHHHhhCCCceEECCCCCH
Confidence            3322345578888888888889999999999999999875

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

Probab=98.45  E-value=1.7e-07  Score=83.08  Aligned_cols=79  Identities=30%  Similarity=0.470  Sum_probs=70.5

Q ss_pred             CEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhcCCCCCCcEEEEecCCCHHHHHHHH
Q 048660          118 CKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCL  197 (213)
Q Consensus       118 ~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~~~~~~~pII~lt~~~~~~~~~~~~  197 (213)
                      +.|..+.+|.+|+..+           ....+|.+++|+.||+++|+++++.+++...    .++++|.........+.+
T Consensus        13 ~~v~~a~~g~~~l~~~-----------~~~~~~~~lld~~m~~~~~~~~~~~lk~~~~----~~v~~t~~~~~~~~~~~~   77 (435)
T COG3706          13 KEVATAKKGLIALAIL-----------LDHKPDYKLLDVMMPGMDGFELCRRLKAEPA----TVVMVTALDDSAPRVRGL   77 (435)
T ss_pred             hhhhhccchHHHHHHH-----------hcCCCCeEEeecccCCcCchhHHHHHhcCCc----ceEEEEecCCCCcchhHH
Confidence            4666799999999988           5678999999999999999999999998642    288899999999999999


Q ss_pred             HcCCCeeeeCCCCC
Q 048660          198 EEGAEEYIVKPVKL  211 (213)
Q Consensus       198 ~~G~~~~L~KP~~~  211 (213)
                      ++|++++|+||++.
T Consensus        78 ~~~~~~~l~~~~~~   91 (435)
T COG3706          78 KAGADDFLTKPVND   91 (435)
T ss_pred             hhhhhhhccCCCCh
Confidence            99999999999874

>smart00448 REC cheY-homologous receiver domain

Probab=97.98  E-value=6.1e-05  Score=44.19  Aligned_cols=54  Identities=35%  Similarity=0.536  Sum_probs=47.4

Q ss_pred             EEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCC
Q 048660           95 HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMP  159 (213)
Q Consensus        95 ~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp  159 (213)
                      +++++++++..+..+...+...|+.+..+.++.+++..+           ....++++++|+.++
T Consensus         2 ~i~i~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~-----------~~~~~~~vi~~~~~~   55 (55)
T smart00448        2 RILVVDDDPLLRELLKALLEREGYEVDEATDGEEALELL-----------KEEKPDLILLDIMMP   55 (55)
T ss_pred             eEEEEcCCHHHHHHHHHHHhhcCcEEEEeCCHHHHHHHH-----------HhcCCCEEEEeccCC
Confidence            689999999999999999999999999999999999887           334689999998654

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

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

Probab=97.96  E-value=1.2e-05  Score=78.06  Aligned_cols=50  Identities=20%  Similarity=0.175  Sum_probs=43.0

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCC
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTM  158 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~m  158 (213)
                      .+.+||||||++.++..+..+|+++|+.|..+.++      .           ....||+||+|+.+
T Consensus       688 ~g~~vLlvdD~~~~r~~l~~~L~~~G~~v~~a~~~------~-----------~~~~~Dlvl~D~~~  737 (894)
T PRK10618        688 DGVTVLLDITSEEVRKIVTRQLENWGATCITPDER------L-----------ISQEYDIFLTDNPS  737 (894)
T ss_pred             CCCEEEEEeCCHHHHHHHHHHHHHCCCEEEEcCcc------c-----------cCCCCCEEEECCCC
Confidence            45799999999999999999999999999988763      1           33469999999984

>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=97.57  E-value=0.0006  Score=49.52  Aligned_cols=96  Identities=18%  Similarity=0.196  Sum_probs=64.2

Q ss_pred             EEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCcee-EEEEeCCCCCCCHHHHHHHHHhc
Q 048660           95 HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVN-LIITDYTMPGMTGYELLKKIKES  173 (213)
Q Consensus        95 ~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~d-lil~D~~mp~~~G~e~~~~ir~~  173 (213)
                      ||||||||...+..|..+|+=.|+.+..+.+.+- ....           .....+ +++.....+  ...+.++.+.+.
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            6999999999999999999999999888876443 2222           112233 334333333  456677777766


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKL  211 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~  211 (213)
                        .+.+|++++..........     .+-+-|..|++.
T Consensus        67 --~~~~Pvlllg~~~~~~~~~-----nvvg~Le~Pl~Y   97 (109)
T PF06490_consen   67 --APHIPVLLLGEHDSPEELP-----NVVGELEEPLNY   97 (109)
T ss_pred             --CCCCCEEEECCCCcccccc-----CeeEecCCCCCH
Confidence              6899999998876551111     155667777763

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).

>cd02071 MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 binding domain

Probab=97.42  E-value=0.0032  Score=46.51  Aligned_cols=95  Identities=16%  Similarity=0.045  Sum_probs=68.8

Q ss_pred             eCCHHHHHHHHHHHhhcCCEEEEEc---CHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCC--CHHHHHHHHHhcC
Q 048660          100 DDSYVDRKLIERLLQISSCKVTAVE---SGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGM--TGYELLKKIKESS  174 (213)
Q Consensus       100 dD~~~~~~~l~~~L~~~g~~v~~a~---~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~--~G~e~~~~ir~~~  174 (213)
                      |.+..=..++..+|+..||+|....   ..++.++.+           ....+|+|.+-..++..  .-.++++.+++..
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            5666667778888999999988653   466777776           44579999998877642  2345677777753


Q ss_pred             CCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeC
Q 048660          175 VFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVK  207 (213)
Q Consensus       175 ~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~K  207 (213)
                        +....+++.+....+...++.++|+++|+..
T Consensus        79 --~~~i~i~~GG~~~~~~~~~~~~~G~d~~~~~  109 (122)
T cd02071          79 --AGDILVVGGGIIPPEDYELLKEMGVAEIFGP  109 (122)
T ss_pred             --CCCCEEEEECCCCHHHHHHHHHCCCCEEECC
Confidence              3234466776666777889999999999865

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.

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

Probab=97.04  E-value=0.012  Score=42.90  Aligned_cols=94  Identities=15%  Similarity=0.230  Sum_probs=66.5

Q ss_pred             eCCHHHHHHHHHHHhhcCCEEEEE---cCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCC--CCHHHHHHHHHhcC
Q 048660          100 DDSYVDRKLIERLLQISSCKVTAV---ESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPG--MTGYELLKKIKESS  174 (213)
Q Consensus       100 dD~~~~~~~l~~~L~~~g~~v~~a---~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~--~~G~e~~~~ir~~~  174 (213)
                      |.+..-..++..+|+..||+|...   ...++.++.+           .+..||+|.+-..+..  ....++++.+|+..
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            556666788899999999998654   3456666766           4568999999887654  34567888888763


Q ss_pred             CCCCCcEEEEecCCCHHHHHHHHHcCCCeeee
Q 048660          175 VFREVPVVIMSSEDVLTQIDSCLEEGAEEYIV  206 (213)
Q Consensus       175 ~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~  206 (213)
                      . .+++ |++.+.........+.+.|+|.|+.
T Consensus        79 ~-~~~~-i~vGG~~~~~~~~~~~~~G~D~~~~  108 (119)
T cd02067          79 L-DDIP-VLVGGAIVTRDFKFLKEIGVDAYFG  108 (119)
T ss_pred             C-CCCe-EEEECCCCChhHHHHHHcCCeEEEC
Confidence            1 2555 5566655555556788999988765

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=96.88  E-value=0.023  Score=42.66  Aligned_cols=101  Identities=15%  Similarity=0.088  Sum_probs=69.9

Q ss_pred             cEEEEE----eCCHHHHHHHHHHHhhcCCEEEEE---cCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCC-CC-HH
Q 048660           94 LHVLAV----DDSYVDRKLIERLLQISSCKVTAV---ESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPG-MT-GY  164 (213)
Q Consensus        94 ~~ILvV----dD~~~~~~~l~~~L~~~g~~v~~a---~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~-~~-G~  164 (213)
                      .||++.    |-+..-...+..+|+..||+|...   .+.++.++.+           .+..+|+|.+...+.. +. --
T Consensus         3 ~~v~~a~~g~D~Hd~g~~iv~~~l~~~GfeVi~lg~~~s~e~~v~aa-----------~e~~adii~iSsl~~~~~~~~~   71 (132)
T TIGR00640         3 PRILVAKMGQDGHDRGAKVIATAYADLGFDVDVGPLFQTPEEIARQA-----------VEADVHVVGVSSLAGGHLTLVP   71 (132)
T ss_pred             CEEEEEeeCCCccHHHHHHHHHHHHhCCcEEEECCCCCCHHHHHHHH-----------HHcCCCEEEEcCchhhhHHHHH
Confidence            455555    456666778888999999998754   4577777777           4457889888766643 22 34


Q ss_pred             HHHHHHHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeC
Q 048660          165 ELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVK  207 (213)
Q Consensus       165 e~~~~ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~K  207 (213)
                      ++++.|++.. ...++ |++.+....++...+.++|+++|+..
T Consensus        72 ~~~~~L~~~g-~~~i~-vivGG~~~~~~~~~l~~~Gvd~~~~~  112 (132)
T TIGR00640        72 ALRKELDKLG-RPDIL-VVVGGVIPPQDFDELKEMGVAEIFGP  112 (132)
T ss_pred             HHHHHHHhcC-CCCCE-EEEeCCCChHhHHHHHHCCCCEEECC
Confidence            4677777753 23444 55566566777888999999999864

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.

>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=96.80  E-value=0.0071  Score=44.25  Aligned_cols=89  Identities=17%  Similarity=0.262  Sum_probs=65.6

Q ss_pred             HHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCC--CCHHHHHHHHHhcCCCCCCcEEE
Q 048660          106 RKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPG--MTGYELLKKIKESSVFREVPVVI  183 (213)
Q Consensus       106 ~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~--~~G~e~~~~ir~~~~~~~~pII~  183 (213)
                      ...|...|++.|+.|+.+.+.++++..++          ....+..|++|+. ++  ....++++.||+.  ...+||.+
T Consensus         6 ~~~l~~~L~~~~~~vv~~~~~dd~~~~i~----------~~~~i~avvi~~d-~~~~~~~~~ll~~i~~~--~~~iPVFl   72 (115)
T PF03709_consen    6 SRELAEALEQRGREVVDADSTDDALAIIE----------SFTDIAAVVISWD-GEEEDEAQELLDKIRER--NFGIPVFL   72 (115)
T ss_dssp             HHHHHHHHHHTTTEEEEESSHHHHHHHHH----------CTTTEEEEEEECH-HHHHHHHHHHHHHHHHH--STT-EEEE
T ss_pred             HHHHHHHHHHCCCEEEEeCChHHHHHHHH----------hCCCeeEEEEEcc-cccchhHHHHHHHHHHh--CCCCCEEE
Confidence            34577778889999999999999999996          3457899999986 22  2356789999987  67999999


Q ss_pred             EecCCCHHHHHHHHHcCCCeeeeC
Q 048660          184 MSSEDVLTQIDSCLEEGAEEYIVK  207 (213)
Q Consensus       184 lt~~~~~~~~~~~~~~G~~~~L~K  207 (213)
                      ++.....+......-..+++|+..
T Consensus        73 ~~~~~~~~~l~~~~l~~v~~~i~l   96 (115)
T PF03709_consen   73 LAERDTTEDLPAEVLGEVDGFIWL   96 (115)
T ss_dssp             EESCCHHHCCCHHHHCCESEEEET
T ss_pred             EecCCCcccCCHHHHhhccEEEEe
Confidence            998764444444444456666654

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=96.65  E-value=0.045  Score=41.36  Aligned_cols=104  Identities=13%  Similarity=0.073  Sum_probs=74.6

Q ss_pred             ccEEEEE----eCCHHHHHHHHHHHhhcCCEEEEE---cCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCC--CH
Q 048660           93 ELHVLAV----DDSYVDRKLIERLLQISSCKVTAV---ESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGM--TG  163 (213)
Q Consensus        93 ~~~ILvV----dD~~~~~~~l~~~L~~~g~~v~~a---~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~--~G  163 (213)
                      +.+||+.    |.+..-...+..+|+..||+|+..   ...++.++.+           .+..+|+|.+...+...  ..
T Consensus         3 ~~~vl~~~~~gD~H~lG~~iv~~~lr~~G~eVi~LG~~vp~e~i~~~a-----------~~~~~d~V~lS~~~~~~~~~~   71 (137)
T PRK02261          3 KKTVVLGVIGADCHAVGNKILDRALTEAGFEVINLGVMTSQEEFIDAA-----------IETDADAILVSSLYGHGEIDC   71 (137)
T ss_pred             CCEEEEEeCCCChhHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHH-----------HHcCCCEEEEcCccccCHHHH
Confidence            4578887    778888888999999999998865   3466777766           45689999999888753  35


Q ss_pred             HHHHHHHHhcCCCCCCcEEEEecCC------CHHHHHHHHHcCCCeeeeCCC
Q 048660          164 YELLKKIKESSVFREVPVVIMSSED------VLTQIDSCLEEGAEEYIVKPV  209 (213)
Q Consensus       164 ~e~~~~ir~~~~~~~~pII~lt~~~------~~~~~~~~~~~G~~~~L~KP~  209 (213)
                      .++++.+++.. .++++ |++.+..      ..+...++.+.|++.+....-
T Consensus        72 ~~~~~~L~~~~-~~~~~-i~vGG~~~~~~~~~~~~~~~l~~~G~~~vf~~~~  121 (137)
T PRK02261         72 RGLREKCIEAG-LGDIL-LYVGGNLVVGKHDFEEVEKKFKEMGFDRVFPPGT  121 (137)
T ss_pred             HHHHHHHHhcC-CCCCe-EEEECCCCCCccChHHHHHHHHHcCCCEEECcCC
Confidence            56788888763 33554 4455543      345667899999988776543

>cd02070 corrinoid_protein_B12-BD B12 binding domain of corrinoid proteins

Probab=95.99  E-value=0.11  Score=41.69  Aligned_cols=99  Identities=17%  Similarity=0.210  Sum_probs=69.4

Q ss_pred             ccEEEEE----eCCHHHHHHHHHHHhhcCCEEEEE---cCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCC--CH
Q 048660           93 ELHVLAV----DDSYVDRKLIERLLQISSCKVTAV---ESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGM--TG  163 (213)
Q Consensus        93 ~~~ILvV----dD~~~~~~~l~~~L~~~g~~v~~a---~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~--~G  163 (213)
                      ..+||+.    |-+..=..++..+|+..||+|...   ...++.++.+           ....||+|-+...|...  ..
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            4578777    667777888999999999998753   3466777777           45689999999977653  35


Q ss_pred             HHHHHHHHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeee
Q 048660          164 YELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYI  205 (213)
Q Consensus       164 ~e~~~~ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L  205 (213)
                      .++++.+|+.+...+++|++ .+..-...  -+...|+|.|-
T Consensus       151 ~~~i~~lr~~~~~~~~~i~v-GG~~~~~~--~~~~~GaD~~~  189 (201)
T cd02070         151 KEVIEALKEAGLRDKVKVMV-GGAPVNQE--FADEIGADGYA  189 (201)
T ss_pred             HHHHHHHHHCCCCcCCeEEE-ECCcCCHH--HHHHcCCcEEE
Confidence            56788888864333666654 44333332  46677998874

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.

>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=95.94  E-value=0.12  Score=37.50  Aligned_cols=92  Identities=14%  Similarity=0.202  Sum_probs=61.0

Q ss_pred             CCHHHHHHHHHHHhhcCCEEEEE---cCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeC-CCCCC-CHHHHHHHHHhcCC
Q 048660          101 DSYVDRKLIERLLQISSCKVTAV---ESGTRALQYLGLDGEQSNVGFDALKVNLIITDY-TMPGM-TGYELLKKIKESSV  175 (213)
Q Consensus       101 D~~~~~~~l~~~L~~~g~~v~~a---~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~-~mp~~-~G~e~~~~ir~~~~  175 (213)
                      -.+.-...+..+|++.||+|...   .+.++..+.+           ...+||+|.+.. ..+.. ...++++.+|+.  
T Consensus        12 ~~~lGl~~la~~l~~~G~~v~~~d~~~~~~~l~~~~-----------~~~~pd~V~iS~~~~~~~~~~~~l~~~~k~~--   78 (121)
T PF02310_consen   12 VHPLGLLYLAAYLRKAGHEVDILDANVPPEELVEAL-----------RAERPDVVGISVSMTPNLPEAKRLARAIKER--   78 (121)
T ss_dssp             STSHHHHHHHHHHHHTTBEEEEEESSB-HHHHHHHH-----------HHTTCSEEEEEESSSTHHHHHHHHHHHHHTT--
T ss_pred             chhHHHHHHHHHHHHCCCeEEEECCCCCHHHHHHHH-----------hcCCCcEEEEEccCcCcHHHHHHHHHHHHhc--
Confidence            34666788999999999999876   3346666666           345799999998 44443 356677777765  


Q ss_pred             CCCCcEEEEecCCCHHHHHHHHH--cCCCeeee
Q 048660          176 FREVPVVIMSSEDVLTQIDSCLE--EGAEEYIV  206 (213)
Q Consensus       176 ~~~~pII~lt~~~~~~~~~~~~~--~G~~~~L~  206 (213)
                      .++++++ +.+.........+++  .|+|..+.
T Consensus        79 ~p~~~iv-~GG~~~t~~~~~~l~~~~~~D~vv~  110 (121)
T PF02310_consen   79 NPNIPIV-VGGPHATADPEEILREYPGIDYVVR  110 (121)
T ss_dssp             CTTSEEE-EEESSSGHHHHHHHHHHHTSEEEEE
T ss_pred             CCCCEEE-EECCchhcChHHHhccCcCcceecC
Confidence            4566655 555444444555555  68876554

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 ....

>cd02069 methionine_synthase_B12_BD B12 binding domain of methionine synthase

Probab=95.16  E-value=0.25  Score=40.11  Aligned_cols=100  Identities=12%  Similarity=0.145  Sum_probs=68.2

Q ss_pred             ccEEEEE----eCCHHHHHHHHHHHhhcCCEEEEEc---CHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCC-C-CH
Q 048660           93 ELHVLAV----DDSYVDRKLIERLLQISSCKVTAVE---SGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPG-M-TG  163 (213)
Q Consensus        93 ~~~ILvV----dD~~~~~~~l~~~L~~~g~~v~~a~---~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~-~-~G  163 (213)
                      ..+|++.    |.+..=..++..+|+..||+|.-..   ..++.++.+           .+.++|+|.+...|+. + .-
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            4577777    7777778888889999999998653   466777777           4568999999998865 2 34


Q ss_pred             HHHHHHHHhcCCCCCCcEEEEecCCCHHHHHH---HHHcCCCeee
Q 048660          164 YELLKKIKESSVFREVPVVIMSSEDVLTQIDS---CLEEGAEEYI  205 (213)
Q Consensus       164 ~e~~~~ir~~~~~~~~pII~lt~~~~~~~~~~---~~~~G~~~~L  205 (213)
                      .++++.|++.  ..+++|++=.+..+.+....   +-..|+|.|-
T Consensus       157 ~~~i~~L~~~--~~~~~i~vGG~~~~~~~~~~~~~~~~~gad~y~  199 (213)
T cd02069         157 VEVAEEMNRR--GIKIPLLIGGAATSRKHTAVKIAPEYDGPVVYV  199 (213)
T ss_pred             HHHHHHHHhc--CCCCeEEEEChhcCHHHHhhhhccccCCCceEe
Confidence            5578888876  34666664443333333322   2356888773

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

>PRK15399 lysine decarboxylase LdcC; Provisional

Probab=95.12  E-value=0.18  Score=47.98  Aligned_cols=79  Identities=15%  Similarity=0.198  Sum_probs=59.2

Q ss_pred             EEEEEeCCH-HH-----HHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHH
Q 048660           95 HVLAVDDSY-VD-----RKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLK  168 (213)
Q Consensus        95 ~ILvVdD~~-~~-----~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~  168 (213)
                      +|++|+++- .+     .+.|..-|++.|+.|..+.+..+++..++          .....+++++|+.-.   ..++++
T Consensus         2 ~~~~i~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~----------~~~~~~~~~~~~~~~---~~~~~~   68 (713)
T PRK15399          2 NIIAIMGPHGVFYKDEPIKELESALQAQGFQTIWPQNSVDLLKFIE----------HNPRICGVIFDWDEY---SLDLCS   68 (713)
T ss_pred             cEEEEecccccccccHHHHHHHHHHHHCCcEEEEecCHHHHHHHHh----------cccceeEEEEecccc---hHHHHH
Confidence            577787663 11     34566678889999999999999999885          334678999995332   355889


Q ss_pred             HHHhcCCCCCCcEEEEecCC
Q 048660          169 KIKESSVFREVPVVIMSSED  188 (213)
Q Consensus       169 ~ir~~~~~~~~pII~lt~~~  188 (213)
                      .+|+.  ...+||+++....
T Consensus        69 ~~~~~--~~~~Pv~~~~~~~   86 (713)
T PRK15399         69 DINQL--NEYLPLYAFINTH   86 (713)
T ss_pred             HHHHh--CCCCCEEEEcCcc
Confidence            99987  5799999998743

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

Probab=94.88  E-value=0.45  Score=36.14  Aligned_cols=103  Identities=17%  Similarity=0.141  Sum_probs=72.7

Q ss_pred             CccEEEEE----eCCHHHHHHHHHHHhhcCCEEEE---EcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCC--CC
Q 048660           92 KELHVLAV----DDSYVDRKLIERLLQISSCKVTA---VESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPG--MT  162 (213)
Q Consensus        92 ~~~~ILvV----dD~~~~~~~l~~~L~~~g~~v~~---a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~--~~  162 (213)
                      .+.|||+.    |-+..-.+.+.+.|+..||+|..   ..+.+|+.+..           -+...|+|.+...-..  ..
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            46788776    67777889999999999999875   56788888776           3446777776543222  12


Q ss_pred             HHHHHHHHHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeC
Q 048660          163 GYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVK  207 (213)
Q Consensus       163 G~e~~~~ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~K  207 (213)
                      .-++.+.+|+.+ ..++. +++.+.-..++..+..+.|++.++.-
T Consensus        80 ~~~lve~lre~G-~~~i~-v~~GGvip~~d~~~l~~~G~~~if~p  122 (143)
T COG2185          80 VPGLVEALREAG-VEDIL-VVVGGVIPPGDYQELKEMGVDRIFGP  122 (143)
T ss_pred             HHHHHHHHHHhC-CcceE-EeecCccCchhHHHHHHhCcceeeCC
Confidence            344566666653 23333 46777778888889999999998764

>PRK15400 lysine decarboxylase CadA; Provisional

Probab=94.55  E-value=0.25  Score=47.04  Aligned_cols=79  Identities=15%  Similarity=0.239  Sum_probs=58.3

Q ss_pred             EEEEEeCCH-H-----HHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHH
Q 048660           95 HVLAVDDSY-V-----DRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLK  168 (213)
Q Consensus        95 ~ILvVdD~~-~-----~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~  168 (213)
                      +||+|+++. .     -.+.|..-|++.|+.|..+.+..+++..+.          ......++++|+.-   ....+++
T Consensus         2 ~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~----------~~~~~~~~~~~~~~---~~~~~~~   68 (714)
T PRK15400          2 NVIAILNHMGVYFKEEPIRELHRALERLNFQIVYPNDRDDLLKLIE----------NNARLCGVIFDWDK---YNLELCE   68 (714)
T ss_pred             cEEEEccccccccccHHHHHHHHHHHHCCcEEEEeCCHHHHHHHHh----------cccceeEEEEecch---hhHHHHH
Confidence            567776652 1     144566678889999999999999999885          23467889999532   2255889


Q ss_pred             HHHhcCCCCCCcEEEEecCC
Q 048660          169 KIKESSVFREVPVVIMSSED  188 (213)
Q Consensus       169 ~ir~~~~~~~~pII~lt~~~  188 (213)
                      .+|+.  ...+||+++....
T Consensus        69 ~~~~~--~~~~Pv~~~~~~~   86 (714)
T PRK15400         69 EISKM--NENLPLYAFANTY   86 (714)
T ss_pred             HHHHh--CCCCCEEEEcccc
Confidence            99986  5799999998743

>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=93.90  E-value=0.64  Score=38.54  Aligned_cols=93  Identities=17%  Similarity=0.239  Sum_probs=60.8

Q ss_pred             cEEEEEeCCHHHHH----HHHH--HHhhcCCEEE--EEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCC------
Q 048660           94 LHVLAVDDSYVDRK----LIER--LLQISSCKVT--AVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMP------  159 (213)
Q Consensus        94 ~~ILvVdD~~~~~~----~l~~--~L~~~g~~v~--~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp------  159 (213)
                      +++=|+.|+.....    .++.  .|-+.|+.+.  ++.|...|-....            ..+++|     ||      
T Consensus        94 iKlEVi~d~~~Llpd~~~tv~aa~~L~~~Gf~vlpyc~dd~~~ar~l~~------------~G~~~v-----mPlg~pIG  156 (248)
T cd04728          94 IKLEVIGDDKTLLPDPIETLKAAEILVKEGFTVLPYCTDDPVLAKRLED------------AGCAAV-----MPLGSPIG  156 (248)
T ss_pred             EEEEEecCccccccCHHHHHHHHHHHHHCCCEEEEEeCCCHHHHHHHHH------------cCCCEe-----CCCCcCCC
Confidence            45666665532222    2221  2334699876  5566666655542            245555     55      


Q ss_pred             ---CCCHHHHHHHHHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeee
Q 048660          160 ---GMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIV  206 (213)
Q Consensus       160 ---~~~G~e~~~~ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~  206 (213)
                         +..-.++++.|++.   .++|||+=.+-...++..++++.|+++++.
T Consensus       157 sg~Gi~~~~~I~~I~e~---~~vpVI~egGI~tpeda~~AmelGAdgVlV  203 (248)
T cd04728         157 SGQGLLNPYNLRIIIER---ADVPVIVDAGIGTPSDAAQAMELGADAVLL  203 (248)
T ss_pred             CCCCCCCHHHHHHHHHh---CCCcEEEeCCCCCHHHHHHHHHcCCCEEEE
Confidence               22226788888875   478999888899999999999999999874

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).

>TIGR02370 pyl_corrinoid methyltransferase cognate corrinoid proteins, Methanosarcina family

Probab=93.86  E-value=0.68  Score=37.06  Aligned_cols=99  Identities=15%  Similarity=0.137  Sum_probs=66.6

Q ss_pred             cEEEEE----eCCHHHHHHHHHHHhhcCCEEEEE---cCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCC-C-HH
Q 048660           94 LHVLAV----DDSYVDRKLIERLLQISSCKVTAV---ESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGM-T-GY  164 (213)
Q Consensus        94 ~~ILvV----dD~~~~~~~l~~~L~~~g~~v~~a---~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~-~-G~  164 (213)
                      .+|++.    |.+..=..++..+|+..||+|...   ...++.++.+           ....||+|.+.+.|... . -.
T Consensus        85 ~~vv~~t~~gd~H~lG~~~v~~~l~~~G~~vi~LG~~vp~e~~v~~~-----------~~~~pd~v~lS~~~~~~~~~~~  153 (197)
T TIGR02370        85 GKVVCGVAEGDVHDIGKNIVVTMLRANGFDVIDLGRDVPIDTVVEKV-----------KKEKPLMLTGSALMTTTMYGQK  153 (197)
T ss_pred             CeEEEEeCCCchhHHHHHHHHHHHHhCCcEEEECCCCCCHHHHHHHH-----------HHcCCCEEEEccccccCHHHHH
Confidence            466655    456666777888899999999854   3456777777           45689999999887652 2 34


Q ss_pred             HHHHHHHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeee
Q 048660          165 ELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIV  206 (213)
Q Consensus       165 e~~~~ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~  206 (213)
                      ++++.+|+....++++|+ +.+..-..  .-+.+.|+|.|-.
T Consensus       154 ~~i~~l~~~~~~~~v~i~-vGG~~~~~--~~~~~~gad~~~~  192 (197)
T TIGR02370       154 DINDKLKEEGYRDSVKFM-VGGAPVTQ--DWADKIGADVYGE  192 (197)
T ss_pred             HHHHHHHHcCCCCCCEEE-EEChhcCH--HHHHHhCCcEEeC
Confidence            577888876433455554 55544332  3456789998854

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.

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

Probab=93.57  E-value=0.29  Score=38.98  Aligned_cols=79  Identities=18%  Similarity=0.174  Sum_probs=53.4

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCC-CHHHHHHHHHh
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGM-TGYELLKKIKE  172 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~-~G~e~~~~ir~  172 (213)
                      .+||+||+...+--.|..+|++.|+.+.+..|....+..+           +...||.|++.=.-..- +.--....|++
T Consensus         2 ~~IL~IDNyDSFtyNLv~yl~~lg~~v~V~rnd~~~~~~~-----------~~~~pd~iviSPGPG~P~d~G~~~~~i~~   70 (191)
T COG0512           2 MMILLIDNYDSFTYNLVQYLRELGAEVTVVRNDDISLELI-----------EALKPDAIVISPGPGTPKDAGISLELIRR   70 (191)
T ss_pred             ceEEEEECccchHHHHHHHHHHcCCceEEEECCccCHHHH-----------hhcCCCEEEEcCCCCChHHcchHHHHHHH
Confidence            5799999999999999999999999888887763333333           34468999987432111 11123444444


Q ss_pred             cCCCCCCcEEEEe
Q 048660          173 SSVFREVPVVIMS  185 (213)
Q Consensus       173 ~~~~~~~pII~lt  185 (213)
                      .  ..++||+.+.
T Consensus        71 ~--~~~~PiLGVC   81 (191)
T COG0512          71 F--AGRIPILGVC   81 (191)
T ss_pred             h--cCCCCEEEEC
Confidence            3  3578998775

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

Probab=93.51  E-value=0.96  Score=33.77  Aligned_cols=94  Identities=10%  Similarity=0.070  Sum_probs=64.3

Q ss_pred             CHHHHHHHHHHHhhcCCEEEEE---cCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCC-CC-HHHHHHHHHhcCCC
Q 048660          102 SYVDRKLIERLLQISSCKVTAV---ESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPG-MT-GYELLKKIKESSVF  176 (213)
Q Consensus       102 ~~~~~~~l~~~L~~~g~~v~~a---~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~-~~-G~e~~~~ir~~~~~  176 (213)
                      +..-...+..+|+..||+|.-.   ...++.++.+           .+..+|+|.+...|.. +. .-++.+.+++.. .
T Consensus        12 HdiGkniv~~~L~~~GfeVidLG~~v~~e~~v~aa-----------~~~~adiVglS~L~t~~~~~~~~~~~~l~~~g-l   79 (128)
T cd02072          12 HAVGNKILDHAFTEAGFNVVNLGVLSPQEEFIDAA-----------IETDADAILVSSLYGHGEIDCKGLREKCDEAG-L   79 (128)
T ss_pred             hHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHH-----------HHcCCCEEEEeccccCCHHHHHHHHHHHHHCC-C
Confidence            4455678888999999998753   5667777776           4457899999887755 33 456788888764 3


Q ss_pred             CCCcEEEEecCC--C----HHHHHHHHHcCCCeeeeCC
Q 048660          177 REVPVVIMSSED--V----LTQIDSCLEEGAEEYIVKP  208 (213)
Q Consensus       177 ~~~pII~lt~~~--~----~~~~~~~~~~G~~~~L~KP  208 (213)
                      .+++ |++.+..  .    .++..++.+.|++..+...
T Consensus        80 ~~v~-vivGG~~~i~~~d~~~~~~~L~~~Gv~~vf~pg  116 (128)
T cd02072          80 KDIL-LYVGGNLVVGKQDFEDVEKRFKEMGFDRVFAPG  116 (128)
T ss_pred             CCCe-EEEECCCCCChhhhHHHHHHHHHcCCCEEECcC
Confidence            3544 4455542  2    2345678899999887643

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.

>TIGR01501 MthylAspMutase methylaspartate mutase, S subunit

Probab=93.28  E-value=1  Score=33.88  Aligned_cols=94  Identities=11%  Similarity=0.055  Sum_probs=63.2

Q ss_pred             CHHHHHHHHHHHhhcCCEEEEE---cCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCC--HHHHHHHHHhcCCC
Q 048660          102 SYVDRKLIERLLQISSCKVTAV---ESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMT--GYELLKKIKESSVF  176 (213)
Q Consensus       102 ~~~~~~~l~~~L~~~g~~v~~a---~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~--G~e~~~~ir~~~~~  176 (213)
                      +..-...+..+|+..||+|.-.   ...++.++.+           .+..+|+|-+...|...-  --++.+.+++.. .
T Consensus        14 HdiGk~iv~~~l~~~GfeVi~LG~~v~~e~~v~aa-----------~~~~adiVglS~l~~~~~~~~~~~~~~l~~~g-l   81 (134)
T TIGR01501        14 HAVGNKILDHAFTNAGFNVVNLGVLSPQEEFIKAA-----------IETKADAILVSSLYGHGEIDCKGLRQKCDEAG-L   81 (134)
T ss_pred             hhHhHHHHHHHHHHCCCEEEECCCCCCHHHHHHHH-----------HHcCCCEEEEecccccCHHHHHHHHHHHHHCC-C
Confidence            4555677888999999998754   5677777777           445789999988775422  445777888764 2


Q ss_pred             CCCcEEEEecCC--CHH----HHHHHHHcCCCeeeeCC
Q 048660          177 REVPVVIMSSED--VLT----QIDSCLEEGAEEYIVKP  208 (213)
Q Consensus       177 ~~~pII~lt~~~--~~~----~~~~~~~~G~~~~L~KP  208 (213)
                      .. +.+++.+..  ..+    ...++.+.|++..+...
T Consensus        82 ~~-~~vivGG~~vi~~~d~~~~~~~l~~~Gv~~vF~pg  118 (134)
T TIGR01501        82 EG-ILLYVGGNLVVGKQDFPDVEKRFKEMGFDRVFAPG  118 (134)
T ss_pred             CC-CEEEecCCcCcChhhhHHHHHHHHHcCCCEEECcC
Confidence            34 446666631  122    24568899998877643

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=93.11  E-value=1.4  Score=36.64  Aligned_cols=93  Identities=17%  Similarity=0.248  Sum_probs=61.1

Q ss_pred             cEEEEEeCCHH----HHHHHHH--HHhhcCCEEE--EEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCC------
Q 048660           94 LHVLAVDDSYV----DRKLIER--LLQISSCKVT--AVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMP------  159 (213)
Q Consensus        94 ~~ILvVdD~~~----~~~~l~~--~L~~~g~~v~--~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp------  159 (213)
                      +++=|+.|+..    ..+.++.  .|-+.|+.+.  ++.|...|-....            ..+++|     ||      
T Consensus        94 iKlEVi~d~~~llpd~~~tv~aa~~L~~~Gf~vlpyc~~d~~~ak~l~~------------~G~~~v-----mPlg~pIG  156 (250)
T PRK00208         94 IKLEVIGDDKTLLPDPIETLKAAEILVKEGFVVLPYCTDDPVLAKRLEE------------AGCAAV-----MPLGAPIG  156 (250)
T ss_pred             EEEEEecCCCCCCcCHHHHHHHHHHHHHCCCEEEEEeCCCHHHHHHHHH------------cCCCEe-----CCCCcCCC
Confidence            46666665532    2222222  2334699876  5566666655542            245555     55      


Q ss_pred             ---CCCHHHHHHHHHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeee
Q 048660          160 ---GMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIV  206 (213)
Q Consensus       160 ---~~~G~e~~~~ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~  206 (213)
                         +..-.++++.|++.   .++|||+=.+-...++..++++.|+++++.
T Consensus       157 sg~gi~~~~~i~~i~e~---~~vpVIveaGI~tpeda~~AmelGAdgVlV  203 (250)
T PRK00208        157 SGLGLLNPYNLRIIIEQ---ADVPVIVDAGIGTPSDAAQAMELGADAVLL  203 (250)
T ss_pred             CCCCCCCHHHHHHHHHh---cCCeEEEeCCCCCHHHHHHHHHcCCCEEEE
Confidence               22226778888875   478999999999999999999999999874

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

Probab=93.05  E-value=0.44  Score=35.09  Aligned_cols=103  Identities=11%  Similarity=0.142  Sum_probs=68.8

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHH--HH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELL--KK  169 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~--~~  169 (213)
                      .+.|.+.||-|..-.......|..-+..|+.-...    ..+           -...||.+|+.+-.+-.+...+-  +.
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            46789999999999999999999999888754432    222           23479999999877654433221  11


Q ss_pred             HHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCC
Q 048660          170 IKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKL  211 (213)
Q Consensus       170 ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~  211 (213)
                      .+... ..+--|+++-... ....++..+.|+.++|.||++.
T Consensus        75 ~~Al~-mtd~vilalPs~~-qv~AeqLkQ~g~~~CllKPls~  114 (140)
T COG4999          75 AKALS-MTDFVILALPSHA-QVNAEQLKQDGAGACLLKPLSS  114 (140)
T ss_pred             HHHHh-hhcceEEecCcHH-HHhHHHHhhcchHhHhhCcchh
Confidence            22211 2233344444333 3467788999999999999975

>TIGR03815 CpaE_hom_Actino helicase/secretion neighborhood CpaE-like protein

Probab=92.55  E-value=0.25  Score=42.36  Aligned_cols=75  Identities=19%  Similarity=0.150  Sum_probs=46.4

Q ss_pred             CCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhcCCCCCCcEEEEec-CCCHHHHHH
Q 048660          117 SCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSS-EDVLTQIDS  195 (213)
Q Consensus       117 g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~~~~~~~pII~lt~-~~~~~~~~~  195 (213)
                      |..+..+.+..++-..+.             .-.+||+|..+-     .  ..+.... .+...++++++ ..+.+....
T Consensus         1 ~~~~~~~~~~~~~~~~~~-------------~~~~v~~~~~~~-----~--~~~~~~~-p~~~~vv~v~~~~~~~~~~~~   59 (322)
T TIGR03815         1 GVELDVAPDPEAARRAWA-------------RAPLVLVDADMA-----E--ACAAAGL-PRRRRVVLVGGGEPGGALWRA   59 (322)
T ss_pred             CCceEEccCchhhhhccc-------------cCCeEEECchhh-----h--HHHhccC-CCCCCEEEEeCCCCCHHHHHH
Confidence            456677777666655442             346899986431     1  1122211 12223554444 556888999


Q ss_pred             HHHcCCCeeeeCCCCCC
Q 048660          196 CLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       196 ~~~~G~~~~L~KP~~~~  212 (213)
                      ++++|+.+||.+|++.+
T Consensus        60 a~~~Ga~~~l~~P~~~~   76 (322)
T TIGR03815        60 AAAVGAEHVAVLPEAEG   76 (322)
T ss_pred             HHHhChhheeeCCCCHH
Confidence            99999999999998753

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.

>PF01596 Methyltransf_3: O-methyltransferase; InterPro: IPR002935 Members of this family are O-methyltransferases

Probab=92.28  E-value=2.9  Score=33.71  Aligned_cols=86  Identities=12%  Similarity=0.149  Sum_probs=58.4

Q ss_pred             HHHhhhhhhcccCCCcchhhhhhhhcCCccEEEEEeCCHHHHHHHHHHHhhcCC--EEE-EEcCHHHHHHHhhhcCCCCC
Q 048660           65 RLVKEKKFKETNRGFPFWAMATVAECSKELHVLAVDDSYVDRKLIERLLQISSC--KVT-AVESGTRALQYLGLDGEQSN  141 (213)
Q Consensus        65 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ILvVdD~~~~~~~l~~~L~~~g~--~v~-~a~~g~eal~~l~~~~~~~~  141 (213)
                      +..+.+..-+.+.+....+..........-+|.-+|-++...+..+..+++.|+  ++. ...++.+.+..+....    
T Consensus        42 ~~~~~k~vLEIGt~~GySal~la~~l~~~g~i~tiE~~~~~~~~A~~~~~~ag~~~~I~~~~gda~~~l~~l~~~~----  117 (205)
T PF01596_consen   42 RLTRPKRVLEIGTFTGYSALWLAEALPEDGKITTIEIDPERAEIARENFRKAGLDDRIEVIEGDALEVLPELANDG----  117 (205)
T ss_dssp             HHHT-SEEEEESTTTSHHHHHHHHTSTTTSEEEEEESSHHHHHHHHHHHHHTTGGGGEEEEES-HHHHHHHHHHTT----
T ss_pred             HhcCCceEEEeccccccHHHHHHHhhcccceEEEecCcHHHHHHHHHHHHhcCCCCcEEEEEeccHhhHHHHHhcc----
Confidence            344556666666665544444443344567999999999999999999998886  444 4577888887764321    


Q ss_pred             CCCCCCceeEEEEeCC
Q 048660          142 VGFDALKVNLIITDYT  157 (213)
Q Consensus       142 ~~~~~~~~dlil~D~~  157 (213)
                         ....||+||+|..
T Consensus       118 ---~~~~fD~VFiDa~  130 (205)
T PF01596_consen  118 ---EEGQFDFVFIDAD  130 (205)
T ss_dssp             ---TTTSEEEEEEEST
T ss_pred             ---CCCceeEEEEccc
Confidence               1347999999984

The family includes also bacterial O-methyltransferases that may be involved in antibiotic production [].; GO: 0008171 O-methyltransferase activity; PDB: 1SUI_C 1SUS_D 3CBG_A 2GPY_B 3TR6_A 2AVD_A 3DUL_B 3DUW_B 2ZTH_A 1VID_A ....

>PRK09426 methylmalonyl-CoA mutase; Reviewed

Probab=91.78  E-value=2.1  Score=41.00  Aligned_cols=104  Identities=13%  Similarity=0.089  Sum_probs=70.0

Q ss_pred             CCccEEEEE----eCCHHHHHHHHHHHhhcCCEEEEE---cCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCC--
Q 048660           91 SKELHVLAV----DDSYVDRKLIERLLQISSCKVTAV---ESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGM--  161 (213)
Q Consensus        91 ~~~~~ILvV----dD~~~~~~~l~~~L~~~g~~v~~a---~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~--  161 (213)
                      .+..+|++.    |.+..-...+..+|+..||.|..-   .+.+++.+..           ....+|+|.+-..+...  
T Consensus       580 g~rpkV~LatlG~d~H~~ra~fv~~~l~~~GfeV~~~~~~~s~e~~v~aa-----------~~~~a~ivvlcs~d~~~~e  648 (714)
T PRK09426        580 GRRPRILVAKMGQDGHDRGAKVIATAFADLGFDVDIGPLFQTPEEAARQA-----------VENDVHVVGVSSLAAGHKT  648 (714)
T ss_pred             CCCceEEEEecCCcchhHhHHHHHHHHHhCCeeEecCCCCCCHHHHHHHH-----------HHcCCCEEEEeccchhhHH
Confidence            456677766    455666677888899999999643   3567777777           33467888876655442  


Q ss_pred             CHHHHHHHHHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeC
Q 048660          162 TGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVK  207 (213)
Q Consensus       162 ~G~e~~~~ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~K  207 (213)
                      ..-.+++.|++.+ ..+++ |++.+...+++...+.++|+|+|+..
T Consensus       649 ~~~~l~~~Lk~~G-~~~v~-vl~GG~~~~~~~~~l~~aGvD~~i~~  692 (714)
T PRK09426        649 LVPALIEALKKLG-REDIM-VVVGGVIPPQDYDFLYEAGVAAIFGP  692 (714)
T ss_pred             HHHHHHHHHHhcC-CCCcE-EEEeCCCChhhHHHHHhCCCCEEECC
Confidence            3556888888763 22333 44665534555677889999999864

>PRK03958 tRNA 2'-O-methylase; Reviewed

Probab=90.98  E-value=4.3  Score=31.98  Aligned_cols=80  Identities=11%  Similarity=0.154  Sum_probs=58.1

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcC--CEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISS--CKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKK  169 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g--~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~  169 (213)
                      .--++.++.+++..++.++.++..||  |.|....+-+++++.++.         ....+.|+..+....+     ....
T Consensus        30 Ga~~~yiv~~~~~q~~~v~~I~~~WGg~fnv~~~~s~~~~i~~~k~---------~G~vvhLtmyga~~~~-----~~~~   95 (176)
T PRK03958         30 GADKIILASNDEHVKESVEDIVERWGGPFEVEVTKSWKKEIREWKD---------GGIVVHLTMYGENIQD-----VEPE   95 (176)
T ss_pred             CCceEEEecCcHHHHHHHHHHHHhcCCceEEEEcCCHHHHHHHHHh---------CCcEEEEEEecCCccc-----hHHH
Confidence            34579999999999999999999997  679999999999998852         2246788888887765     4444


Q ss_pred             HHhcCCCCCCcEEEEec
Q 048660          170 IKESSVFREVPVVIMSS  186 (213)
Q Consensus       170 ir~~~~~~~~pII~lt~  186 (213)
                      ||+.... .-|++++-+
T Consensus        96 ir~~~~~-~~p~LIvvG  111 (176)
T PRK03958         96 IREAHRK-GEPLLIVVG  111 (176)
T ss_pred             HHHhhcc-CCcEEEEEc
Confidence            5542111 335555544

>PRK08385 nicotinate-nucleotide pyrophosphorylase; Provisional

Probab=90.30  E-value=5.6  Score=33.71  Aligned_cols=94  Identities=18%  Similarity=0.149  Sum_probs=62.3

Q ss_pred             EEEEeCCHHHHHHHHHHHhh---c-C-C-EEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHH
Q 048660           96 VLAVDDSYVDRKLIERLLQI---S-S-C-KVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKK  169 (213)
Q Consensus        96 ILvVdD~~~~~~~l~~~L~~---~-g-~-~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~  169 (213)
                      |||-|++-... .+...++.   . + . ..+.+++.++|.+.+.            ...|+|++|=..|. +--++.+.
T Consensus       157 vLikdnHi~~~-~i~~av~~~r~~~~~~kIeVEv~~leea~~a~~------------agaDiI~LDn~~~e-~l~~~v~~  222 (278)
T PRK08385        157 ILIKDNHLALV-PLEEAIRRAKEFSVYKVVEVEVESLEDALKAAK------------AGADIIMLDNMTPE-EIREVIEA  222 (278)
T ss_pred             EEEccCHHHHH-HHHHHHHHHHHhCCCCcEEEEeCCHHHHHHHHH------------cCcCEEEECCCCHH-HHHHHHHH
Confidence            78888886554 45554432   1 2 2 4457899999999883            25799999954333 34445555


Q ss_pred             HHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCee
Q 048660          170 IKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEY  204 (213)
Q Consensus       170 ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~  204 (213)
                      +++... ..-..+..|+.-+.+...+..+.|+|.+
T Consensus       223 l~~~~~-~~~~~leaSGGI~~~ni~~yA~tGvD~I  256 (278)
T PRK08385        223 LKREGL-RERVKIEVSGGITPENIEEYAKLDVDVI  256 (278)
T ss_pred             HHhcCc-CCCEEEEEECCCCHHHHHHHHHcCCCEE
Confidence            555321 2234677888889999999999999765

>COG4122 Predicted O-methyltransferase [General function prediction only]

Probab=89.97  E-value=2.2  Score=34.91  Aligned_cols=84  Identities=11%  Similarity=0.086  Sum_probs=54.8

Q ss_pred             hhhhhhcccCCCcchhhhhhhhcCCccEEEEEeCCHHHHHHHHHHHhhcCC--EEEEEcCHHHHHHHhhhcCCCCCCCCC
Q 048660           68 KEKKFKETNRGFPFWAMATVAECSKELHVLAVDDSYVDRKLIERLLQISSC--KVTAVESGTRALQYLGLDGEQSNVGFD  145 (213)
Q Consensus        68 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ILvVdD~~~~~~~l~~~L~~~g~--~v~~a~~g~eal~~l~~~~~~~~~~~~  145 (213)
                      ..+..-+.+.+...............-++.-+|-|+...+..++.+++.|.  ++..... .+|++.+...        .
T Consensus        59 ~~k~iLEiGT~~GySal~mA~~l~~~g~l~tiE~~~e~~~~A~~n~~~ag~~~~i~~~~~-gdal~~l~~~--------~  129 (219)
T COG4122          59 GPKRILEIGTAIGYSALWMALALPDDGRLTTIERDEERAEIARENLAEAGVDDRIELLLG-GDALDVLSRL--------L  129 (219)
T ss_pred             CCceEEEeecccCHHHHHHHhhCCCCCeEEEEeCCHHHHHHHHHHHHHcCCcceEEEEec-CcHHHHHHhc--------c
Confidence            445555556554444444444444355899999999999999999999986  3444442 3445544320        3


Q ss_pred             CCceeEEEEeCCCCC
Q 048660          146 ALKVNLIITDYTMPG  160 (213)
Q Consensus       146 ~~~~dlil~D~~mp~  160 (213)
                      ...||+||+|..=+.
T Consensus       130 ~~~fDliFIDadK~~  144 (219)
T COG4122         130 DGSFDLVFIDADKAD  144 (219)
T ss_pred             CCCccEEEEeCChhh
Confidence            468999999985443

>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=89.56  E-value=5.8  Score=28.12  Aligned_cols=93  Identities=11%  Similarity=0.095  Sum_probs=59.4

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCH-HHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHh
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESG-TRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKE  172 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g-~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~  172 (213)
                      .+|.++|.++...+    .+...|+.+...+-. .+.++.+           .-...+.+++...-. .....++..+|+
T Consensus        22 ~~vvvid~d~~~~~----~~~~~~~~~i~gd~~~~~~l~~a-----------~i~~a~~vv~~~~~d-~~n~~~~~~~r~   85 (116)
T PF02254_consen   22 IDVVVIDRDPERVE----ELREEGVEVIYGDATDPEVLERA-----------GIEKADAVVILTDDD-EENLLIALLARE   85 (116)
T ss_dssp             SEEEEEESSHHHHH----HHHHTTSEEEES-TTSHHHHHHT-----------TGGCESEEEEESSSH-HHHHHHHHHHHH
T ss_pred             CEEEEEECCcHHHH----HHHhcccccccccchhhhHHhhc-----------CccccCEEEEccCCH-HHHHHHHHHHHH
Confidence            58999999987643    334456776654332 4455555           334677888876522 345677888887


Q ss_pred             cCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeee
Q 048660          173 SSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIV  206 (213)
Q Consensus       173 ~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~  206 (213)
                      .  .+..+|++....  ......+.+.|++..+.
T Consensus        86 ~--~~~~~ii~~~~~--~~~~~~l~~~g~d~vi~  115 (116)
T PF02254_consen   86 L--NPDIRIIARVND--PENAELLRQAGADHVIS  115 (116)
T ss_dssp             H--TTTSEEEEEESS--HHHHHHHHHTT-SEEEE
T ss_pred             H--CCCCeEEEEECC--HHHHHHHHHCCcCEEEC
Confidence            6  466777766654  55667778899987664

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 ....

>cd02065 B12-binding_like B12 binding domain (B12-BD)

Probab=89.23  E-value=2.8  Score=30.16  Aligned_cols=72  Identities=10%  Similarity=0.148  Sum_probs=50.1

Q ss_pred             eCCHHHHHHHHHHHhhcCCEEEEEc---CHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCC-CHHHHHHHHHhcCC
Q 048660          100 DDSYVDRKLIERLLQISSCKVTAVE---SGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGM-TGYELLKKIKESSV  175 (213)
Q Consensus       100 dD~~~~~~~l~~~L~~~g~~v~~a~---~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~-~G~e~~~~ir~~~~  175 (213)
                      |.+......+..+|++.|+.+....   ...+.++.+           ....||+|.+.+.+... ..+..+..+++.  
T Consensus        10 ~~h~lg~~~~~~~l~~~G~~v~~l~~~~~~~~~~~~i-----------~~~~pdiV~iS~~~~~~~~~~~~~~~~~~~--   76 (125)
T cd02065          10 DVHDIGKNIVAIALRDNGFEVIDLGVDVPPEEIVEAA-----------KEEDADVVGLSALSTTHMEAMKLVIEALKE--   76 (125)
T ss_pred             chhhHHHHHHHHHHHHCCCEEEEcCCCCCHHHHHHHH-----------HHcCCCEEEEecchHhHHHHHHHHHHHHHh--
Confidence            5566777888999999999988653   445555555           34579999999877653 356667777765  


Q ss_pred             CC-CCcEEEE
Q 048660          176 FR-EVPVVIM  184 (213)
Q Consensus       176 ~~-~~pII~l  184 (213)
                      .+ ++++++=
T Consensus        77 ~p~~~~ivvG   86 (125)
T cd02065          77 LGIDIPVVVG   86 (125)
T ss_pred             cCCCCeEEEe
Confidence            34 6666543

Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain 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. Not all members of this family contain the conserved binding motif.

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

Probab=88.93  E-value=3.3  Score=34.56  Aligned_cols=90  Identities=11%  Similarity=0.100  Sum_probs=60.0

Q ss_pred             HHHHHHHhhcCCE--EEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhcCCCCCCcEEEE
Q 048660          107 KLIERLLQISSCK--VTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIM  184 (213)
Q Consensus       107 ~~l~~~L~~~g~~--v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~~~~~~~pII~l  184 (213)
                      ..++..|..-...  .+.....-.+.+.+.           ...||.|++|+.....|--++...++......-.|+|=+
T Consensus         8 n~lk~~l~~g~~~~g~~~~~~sp~~~e~~a-----------~~G~D~v~iD~EHg~~~~~~~~~~i~a~~~~g~~~lVRv   76 (256)
T PRK10558          8 NKFKAALAAKQVQIGCWSALANPITTEVLG-----------LAGFDWLVLDGEHAPNDVSTFIPQLMALKGSASAPVVRV   76 (256)
T ss_pred             HHHHHHHHcCCceEEEEEcCCCcHHHHHHH-----------hcCCCEEEEccccCCCCHHHHHHHHHHHhhcCCCcEEEC
Confidence            3466666643332  223333345666663           335999999999999988888888886543334444444


Q ss_pred             ecCCCHHHHHHHHHcCCCeeeeCC
Q 048660          185 SSEDVLTQIDSCLEEGAEEYIVKP  208 (213)
Q Consensus       185 t~~~~~~~~~~~~~~G~~~~L~KP  208 (213)
                       ...+.....+++++|+++++.--
T Consensus        77 -p~~~~~~i~r~LD~Ga~giivP~   99 (256)
T PRK10558         77 -PTNEPVIIKRLLDIGFYNFLIPF   99 (256)
T ss_pred             -CCCCHHHHHHHhCCCCCeeeecC
Confidence             45567889999999999987643

>TIGR00566 trpG_papA glutamine amidotransferase of anthranilate synthase or aminodeoxychorismate synthase

Probab=88.59  E-value=1.4  Score=34.90  Aligned_cols=77  Identities=19%  Similarity=0.205  Sum_probs=47.2

Q ss_pred             EEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEE-eCC-CCCCCHHHHHHHHHhc
Q 048660           96 VLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT-DYT-MPGMTGYELLKKIKES  173 (213)
Q Consensus        96 ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~-D~~-mp~~~G~e~~~~ir~~  173 (213)
                      ||+||....+-..+.++|++.|+.+....+....++.+           ....||.|++ .=- -|.-++.+ .+.+++.
T Consensus         2 il~id~~dsft~~~~~~l~~~g~~v~v~~~~~~~~~~~-----------~~~~~d~iilsgGpg~p~~~~~~-~~~i~~~   69 (188)
T TIGR00566         2 VLMIDNYDSFTYNLVQYFCELGAEVVVKRNDSLTLQEI-----------EALLPLLIVISPGPCTPNEAGIS-LEAIRHF   69 (188)
T ss_pred             EEEEECCcCHHHHHHHHHHHcCCceEEEECCCCCHHHH-----------HhcCCCEEEEcCCCCChhhcchh-HHHHHHh
Confidence            89999999999999999999999888776433223333           1225775555 221 11112222 3444443


Q ss_pred             CCCCCCcEEEEec
Q 048660          174 SVFREVPVVIMSS  186 (213)
Q Consensus       174 ~~~~~~pII~lt~  186 (213)
                        ...+||+.+.-
T Consensus        70 --~~~~PvLGIC~   80 (188)
T TIGR00566        70 --AGKLPILGVCL   80 (188)
T ss_pred             --ccCCCEEEECH
Confidence              24688887763

This model describes the glutamine amidotransferase domain or peptide of the tryptophan-biosynthetic pathway enzyme anthranilate synthase or of the folate biosynthetic pathway enzyme para-aminobenzoate synthase. In at least one case, a single polypeptide from Bacillus subtilis was shown to have both functions. This model covers a subset of the sequences described by the pfam model GATase.

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

Probab=88.38  E-value=7.7  Score=31.28  Aligned_cols=83  Identities=19%  Similarity=0.244  Sum_probs=54.4

Q ss_pred             HHHHHhh-cCCEEE-EEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCC-------CCCCCHHHHHHHHHhcCCCCCC
Q 048660          109 IERLLQI-SSCKVT-AVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYT-------MPGMTGYELLKKIKESSVFREV  179 (213)
Q Consensus       109 l~~~L~~-~g~~v~-~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~-------mp~~~G~e~~~~ir~~~~~~~~  179 (213)
                      +....++ .+..+. .+.+.+++.....            ..+|++.+...       .....++++++++++.   -++
T Consensus       110 ~i~~~~~~~~i~vi~~v~t~ee~~~a~~------------~G~d~i~~~~~g~t~~~~~~~~~~~~~i~~i~~~---~~i  174 (221)
T PRK01130        110 LVKRIKEYPGQLLMADCSTLEEGLAAQK------------LGFDFIGTTLSGYTEETKKPEEPDFALLKELLKA---VGC  174 (221)
T ss_pred             HHHHHHhCCCCeEEEeCCCHHHHHHHHH------------cCCCEEEcCCceeecCCCCCCCcCHHHHHHHHHh---CCC
Confidence            3334444 565443 4567777755432            24676654311       1223457889999875   268


Q ss_pred             cEEEEecCCCHHHHHHHHHcCCCeeee
Q 048660          180 PVVIMSSEDVLTQIDSCLEEGAEEYIV  206 (213)
Q Consensus       180 pII~lt~~~~~~~~~~~~~~G~~~~L~  206 (213)
                      |+++..+-.+.++..++++.|+++++.
T Consensus       175 Pvia~GGI~t~~~~~~~l~~GadgV~i  201 (221)
T PRK01130        175 PVIAEGRINTPEQAKKALELGAHAVVV  201 (221)
T ss_pred             CEEEECCCCCHHHHHHHHHCCCCEEEE
Confidence            999888888899999999999998754

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

Probab=88.05  E-value=7.1  Score=27.24  Aligned_cols=88  Identities=19%  Similarity=0.199  Sum_probs=53.7

Q ss_pred             EEEEEeCCHHHHHHHHHHHhhcCCEEEEE------cCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHH
Q 048660           95 HVLAVDDSYVDRKLIERLLQISSCKVTAV------ESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLK  168 (213)
Q Consensus        95 ~ILvVdD~~~~~~~l~~~L~~~g~~v~~a------~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~  168 (213)
                      +||||...+.....++..+++.|+.....      ......++..            -...|+||+=...=.-+....++
T Consensus         1 ~vliVGG~~~~~~~~~~~~~~~G~~~~~hg~~~~~~~~~~~l~~~------------i~~aD~VIv~t~~vsH~~~~~vk   68 (97)
T PF10087_consen    1 SVLIVGGREDRERRYKRILEKYGGKLIHHGRDGGDEKKASRLPSK------------IKKADLVIVFTDYVSHNAMWKVK   68 (97)
T ss_pred             CEEEEcCCcccHHHHHHHHHHcCCEEEEEecCCCCccchhHHHHh------------cCCCCEEEEEeCCcChHHHHHHH
Confidence            48999998888999999999999998888      2222123321            12568887655444434444444


Q ss_pred             HHHhcCCCCCCcEEEEecCCCHHHHHHHHH
Q 048660          169 KIKESSVFREVPVVIMSSEDVLTQIDSCLE  198 (213)
Q Consensus       169 ~ir~~~~~~~~pII~lt~~~~~~~~~~~~~  198 (213)
                      ..-+   ..++|++..-..+ .....+++.
T Consensus        69 ~~ak---k~~ip~~~~~~~~-~~~l~~~l~   94 (97)
T PF10087_consen   69 KAAK---KYGIPIIYSRSRG-VSSLERALE   94 (97)
T ss_pred             HHHH---HcCCcEEEECCCC-HHHHHHHHH
Confidence            4333   3578888665333 444554443

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

Probab=87.81  E-value=4.5  Score=34.05  Aligned_cols=91  Identities=13%  Similarity=0.156  Sum_probs=59.9

Q ss_pred             HHHHHHhhcCCE--EEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhcCCCCCCcEEEEe
Q 048660          108 LIERLLQISSCK--VTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMS  185 (213)
Q Consensus       108 ~l~~~L~~~g~~--v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~~~~~~~pII~lt  185 (213)
                      .++..|+.-...  .+.....-.+.+.+.           ...||.|++|+.....|--++...++......-.|++ =.
T Consensus         8 ~lk~~L~~G~~~~G~~~~~~sp~~~E~~a-----------~~GfD~v~iD~EHg~~~~~~l~~~i~a~~~~g~~~lV-Rv   75 (267)
T PRK10128          8 PFKEGLRKGEVQIGLWLSSTTSYMAEIAA-----------TSGYDWLLIDGEHAPNTIQDLYHQLQAIAPYASQPVI-RP   75 (267)
T ss_pred             HHHHHHHcCCceEEEEecCCCcHHHHHHH-----------HcCCCEEEEccccCCCCHHHHHHHHHHHHhcCCCeEE-EC
Confidence            455666543222  223333345666653           2359999999999988888888788765433444544 44


Q ss_pred             cCCCHHHHHHHHHcCCCeeeeCCCC
Q 048660          186 SEDVLTQIDSCLEEGAEEYIVKPVK  210 (213)
Q Consensus       186 ~~~~~~~~~~~~~~G~~~~L~KP~~  210 (213)
                      ...+.....+++++|+++.+.--++
T Consensus        76 p~~~~~~i~r~LD~GA~GIivP~V~  100 (267)
T PRK10128         76 VEGSKPLIKQVLDIGAQTLLIPMVD  100 (267)
T ss_pred             CCCCHHHHHHHhCCCCCeeEecCcC
Confidence            5556788899999999999875443

>PRK00043 thiE thiamine-phosphate pyrophosphorylase; Reviewed

Probab=87.33  E-value=6.9  Score=31.03  Aligned_cols=76  Identities=18%  Similarity=0.271  Sum_probs=51.4

Q ss_pred             cCCEEE-EEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCC--------CHHHHHHHHHhcCCCCCCcEEEEec
Q 048660          116 SSCKVT-AVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGM--------TGYELLKKIKESSVFREVPVVIMSS  186 (213)
Q Consensus       116 ~g~~v~-~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~--------~G~e~~~~ir~~~~~~~~pII~lt~  186 (213)
                      .+..+. .+.+..++.+...            ...|.|.+.-..|..        .|++.++.+++.  .+++||++..+
T Consensus       103 ~~~~~g~~~~t~~e~~~a~~------------~gaD~v~~~~~~~~~~~~~~~~~~g~~~~~~~~~~--~~~~~v~a~GG  168 (212)
T PRK00043        103 PDAIIGLSTHTLEEAAAALA------------AGADYVGVGPIFPTPTKKDAKAPQGLEGLREIRAA--VGDIPIVAIGG  168 (212)
T ss_pred             CCCEEEEeCCCHHHHHHHhH------------cCCCEEEECCccCCCCCCCCCCCCCHHHHHHHHHh--cCCCCEEEECC
Confidence            444444 3345566666542            257888876544432        358899999875  34589887776


Q ss_pred             CCCHHHHHHHHHcCCCeeee
Q 048660          187 EDVLTQIDSCLEEGAEEYIV  206 (213)
Q Consensus       187 ~~~~~~~~~~~~~G~~~~L~  206 (213)
                      - +.+....++++|++++..
T Consensus       169 I-~~~~i~~~~~~Ga~gv~~  187 (212)
T PRK00043        169 I-TPENAPEVLEAGADGVAV  187 (212)
T ss_pred             c-CHHHHHHHHHcCCCEEEE
Confidence            6 578888999999998853

>cd05212 NAD_bind_m-THF_DH_Cyclohyd_like NAD(P) binding domain of methylene-tetrahydrofolate dehydrogenase and methylene-tetrahydrofolate dehydrogenase/cyclohydrolase

Probab=87.00  E-value=3  Score=31.57  Aligned_cols=53  Identities=17%  Similarity=0.193  Sum_probs=43.4

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEc----CHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCC
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSCKVTAVE----SGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPG  160 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~----~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~  160 (213)
                      .+.+|+|+..+..+.+-+..+|.+.|+.|..+.    +.+++++.                -|+|+.-..-+.
T Consensus        27 ~gk~v~VvGrs~~vG~pla~lL~~~gatV~~~~~~t~~l~~~v~~----------------ADIVvsAtg~~~   83 (140)
T cd05212          27 DGKKVLVVGRSGIVGAPLQCLLQRDGATVYSCDWKTIQLQSKVHD----------------ADVVVVGSPKPE   83 (140)
T ss_pred             CCCEEEEECCCchHHHHHHHHHHHCCCEEEEeCCCCcCHHHHHhh----------------CCEEEEecCCCC
Confidence            467999999999999999999999999999987    55555443                478888876664

NAD(P) binding domains of methylene-tetrahydrofolate dehydrogenase (m-THF DH) and m-THF DH/cyclohydrolase bifunctional enzymes (m-THF DH/cyclohydrolase). M-THF is a versatile carrier of activated one-carbon units. The major one-carbon folate donors are N-5 methyltetrahydrofolate, N5,N10-m-THF, and N10-formayltetrahydrofolate. The oxidation of metabolic intermediate m-THF to m-THF requires the enzyme m-THF DH. In addition, most DHs also have an associated cyclohydrolase activity which catalyzes its hydrolysis to N10-formyltetrahydrofolate. m-THF DH is typically found as part of a multifunctional protein in eukaryotes. NADP-dependent m-THF DH in mammals, birds and yeast are components of a trifunctional enzyme with DH, cyclohydrolase, and synthetase activities. Certain eukaryotic cells also contain homodimeric bifunctional

>PRK13125 trpA tryptophan synthase subunit alpha; Provisional

Probab=86.93  E-value=10  Score=31.28  Aligned_cols=88  Identities=16%  Similarity=0.123  Sum_probs=54.0

Q ss_pred             HHHHHHHHHhhcCCEEEEEcCH---HHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCC------CHHHHHHHHHhcCC
Q 048660          105 DRKLIERLLQISSCKVTAVESG---TRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGM------TGYELLKKIKESSV  175 (213)
Q Consensus       105 ~~~~l~~~L~~~g~~v~~a~~g---~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~------~G~e~~~~ir~~~~  175 (213)
                      ....+...+++.|..+..+-+.   .+.++.+.           .....+++| -.+|+.      +..+.++++|+.  
T Consensus       117 ~~~~~~~~~~~~Gl~~~~~v~p~T~~e~l~~~~-----------~~~~~~l~m-sv~~~~g~~~~~~~~~~i~~lr~~--  182 (244)
T PRK13125        117 DLEKYVEIIKNKGLKPVFFTSPKFPDLLIHRLS-----------KLSPLFIYY-GLRPATGVPLPVSVERNIKRVRNL--  182 (244)
T ss_pred             HHHHHHHHHHHcCCCEEEEECCCCCHHHHHHHH-----------HhCCCEEEE-EeCCCCCCCchHHHHHHHHHHHHh--
Confidence            3445667778889877655443   33444432           123456767 445552      234577777765  


Q ss_pred             CCCCcEEEEecCCCHHHHHHHHHcCCCeeee
Q 048660          176 FREVPVVIMSSEDVLTQIDSCLEEGAEEYIV  206 (213)
Q Consensus       176 ~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~  206 (213)
                      .+..||++=.+-.+.++...+.++|+|+++.
T Consensus       183 ~~~~~i~v~gGI~~~e~i~~~~~~gaD~vvv  213 (244)
T PRK13125        183 VGNKYLVVGFGLDSPEDARDALSAGADGVVV  213 (244)
T ss_pred             cCCCCEEEeCCcCCHHHHHHHHHcCCCEEEE
Confidence            3346655434444788888889999999875

>smart00052 EAL Putative diguanylate phosphodiesterase

Probab=86.21  E-value=6.4  Score=31.42  Aligned_cols=94  Identities=19%  Similarity=0.268  Sum_probs=60.8

Q ss_pred             HHHHHHhhcCCEEEE--EcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCC-----CCHHHHHHHHHhcCCCCCCc
Q 048660          108 LIERLLQISSCKVTA--VESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPG-----MTGYELLKKIKESSVFREVP  180 (213)
Q Consensus       108 ~l~~~L~~~g~~v~~--a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~-----~~G~e~~~~ir~~~~~~~~p  180 (213)
                      .....|++.|+.+..  +..+..-+..+           ....||.|=+|..+-.     .....+++.+........+.
T Consensus       137 ~~i~~l~~~G~~ialddfg~~~~~~~~l-----------~~l~~d~iKld~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~  205 (241)
T smart00052      137 ATLQRLRELGVRIALDDFGTGYSSLSYL-----------KRLPVDLLKIDKSFVRDLQTDPEDEAIVQSIIELAQKLGLQ  205 (241)
T ss_pred             HHHHHHHHCCCEEEEeCCCCcHHHHHHH-----------HhCCCCeEEECHHHHhhhccChhHHHHHHHHHHHHHHCCCe
Confidence            344556788987765  34555666666           3447899999965421     12334555555432223444


Q ss_pred             EEEEecCCCHHHHHHHHHcCCC---e-eeeCCCCCCC
Q 048660          181 VVIMSSEDVLTQIDSCLEEGAE---E-YIVKPVKLSD  213 (213)
Q Consensus       181 II~lt~~~~~~~~~~~~~~G~~---~-~L~KP~~~~e  213 (213)
                       ++.++-.+.+....+.+.|++   | |+.||...+|
T Consensus       206 -via~gVe~~~~~~~l~~~Gi~~~QG~~~~~p~~~~~  241 (241)
T smart00052      206 -VVAEGVETPEQLDLLRSLGCDYGQGYLFSRPLPLDD  241 (241)
T ss_pred             -EEEecCCCHHHHHHHHHcCCCEEeeceeccCCCCCC
Confidence             457788889999999999985   3 5788887764

Putative diguanylate phosphodiesterase, present in a variety of bacteria.

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

Probab=85.80  E-value=17  Score=29.29  Aligned_cols=87  Identities=24%  Similarity=0.361  Sum_probs=55.1

Q ss_pred             HHHHHHHHHHhhcC-CEE-EEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeC-C------CCCCCHHHHHHHHHhcC
Q 048660          104 VDRKLIERLLQISS-CKV-TAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDY-T------MPGMTGYELLKKIKESS  174 (213)
Q Consensus       104 ~~~~~l~~~L~~~g-~~v-~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~-~------mp~~~G~e~~~~ir~~~  174 (213)
                      ...+.++.. ++.| ..+ ..+.+.+++.....            ..+|.+.... .      .....++++++.+++. 
T Consensus       110 ~~~~~i~~~-~~~g~~~iiv~v~t~~ea~~a~~------------~G~d~i~~~~~g~t~~~~~~~~~~~~~l~~i~~~-  175 (219)
T cd04729         110 TLAELIKRI-HEEYNCLLMADISTLEEALNAAK------------LGFDIIGTTLSGYTEETAKTEDPDFELLKELRKA-  175 (219)
T ss_pred             CHHHHHHHH-HHHhCCeEEEECCCHHHHHHHHH------------cCCCEEEccCccccccccCCCCCCHHHHHHHHHh-
Confidence            334444333 3344 433 34567777766542            2366664321 0      1223457889999875 


Q ss_pred             CCCCCcEEEEecCCCHHHHHHHHHcCCCeeee
Q 048660          175 VFREVPVVIMSSEDVLTQIDSCLEEGAEEYIV  206 (213)
Q Consensus       175 ~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~  206 (213)
                       . ++|+++..+-.+.++..++++.|+++++.
T Consensus       176 -~-~ipvia~GGI~~~~~~~~~l~~GadgV~v  205 (219)
T cd04729         176 -L-GIPVIAEGRINSPEQAAKALELGADAVVV  205 (219)
T ss_pred             -c-CCCEEEeCCCCCHHHHHHHHHCCCCEEEE
Confidence             2 68999888888899999999999998764

This reaction is part of the pathway that allows the usage of sialic acid as a carbohydrate source. Sialic acids are a family of related sugars that are found as a component of glycoproteins, gangliosides, and other sialoglycoconjugates.

>PRK06543 nicotinate-nucleotide pyrophosphorylase; Provisional

Probab=85.73  E-value=9.4  Score=32.42  Aligned_cols=91  Identities=14%  Similarity=0.092  Sum_probs=59.7

Q ss_pred             EEEEEeCCHHHH--------HHHHHHHhhcCC---EEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCH
Q 048660           95 HVLAVDDSYVDR--------KLIERLLQISSC---KVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTG  163 (213)
Q Consensus        95 ~ILvVdD~~~~~--------~~l~~~L~~~g~---~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G  163 (213)
                      .|||-|++-...        ..++.+-+..++   ..+.+++.+++.+.+.            ..+|+|++| +|+--+-
T Consensus       161 ~vLikdNHi~~~~~g~~~i~~av~~~r~~~~~~~kIeVEv~slee~~ea~~------------~gaDiImLD-n~s~e~l  227 (281)
T PRK06543        161 AVMAKDNHLAALAAQGLDLTEALRHVRAQLGHTTHVEVEVDRLDQIEPVLA------------AGVDTIMLD-NFSLDDL  227 (281)
T ss_pred             eEEEeHHHHHHHhCCchHHHHHHHHHHHhCCCCCcEEEEeCCHHHHHHHHh------------cCCCEEEEC-CCCHHHH
Confidence            477777775532        333333334453   3467899999999873            257999999 3333233


Q ss_pred             HHHHHHHHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCee
Q 048660          164 YELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEY  204 (213)
Q Consensus       164 ~e~~~~ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~  204 (213)
                      -+++..++.      ..++-.|+.-+.+........|+|-.
T Consensus       228 ~~av~~~~~------~~~leaSGgI~~~ni~~yA~tGVD~I  262 (281)
T PRK06543        228 REGVELVDG------RAIVEASGNVNLNTVGAIASTGVDVI  262 (281)
T ss_pred             HHHHHHhCC------CeEEEEECCCCHHHHHHHHhcCCCEE
Confidence            344444432      23788899999999999999999654

>cd01948 EAL EAL domain

Probab=85.70  E-value=4.5  Score=32.31  Aligned_cols=93  Identities=16%  Similarity=0.237  Sum_probs=60.8

Q ss_pred             HHHHHhhcCCEEEEE--cCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCC-----CCHHHHHHHHHhcCCCCCCcE
Q 048660          109 IERLLQISSCKVTAV--ESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPG-----MTGYELLKKIKESSVFREVPV  181 (213)
Q Consensus       109 l~~~L~~~g~~v~~a--~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~-----~~G~e~~~~ir~~~~~~~~pI  181 (213)
                      ....|++.|+.+..-  ..+...++.+           ....||.|=+|..+-.     .....+++.+........++ 
T Consensus       137 ~~~~l~~~G~~l~ld~~g~~~~~~~~l-----------~~~~~d~iKld~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~-  204 (240)
T cd01948         137 TLRRLRALGVRIALDDFGTGYSSLSYL-----------KRLPVDYLKIDRSFVRDIETDPEDRAIVRAIIALAHSLGLK-  204 (240)
T ss_pred             HHHHHHHCCCeEEEeCCCCcHhhHHHH-----------HhCCCCEEEECHHHHHhHhcChhhHHHHHHHHHHHHHCCCe-
Confidence            444567789987764  4566666666           3446899999965421     23345555555432223444 


Q ss_pred             EEEecCCCHHHHHHHHHcCCC---e-eeeCCCCCCC
Q 048660          182 VIMSSEDVLTQIDSCLEEGAE---E-YIVKPVKLSD  213 (213)
Q Consensus       182 I~lt~~~~~~~~~~~~~~G~~---~-~L~KP~~~~e  213 (213)
                      ++.++-.+.+....+.+.|++   | |+.||...++
T Consensus       205 via~gVe~~~~~~~~~~~gi~~~QG~~~~~p~~~~~  240 (240)
T cd01948         205 VVAEGVETEEQLELLRELGCDYVQGYLFSRPLPAEE  240 (240)
T ss_pred             EEEEecCCHHHHHHHHHcCCCeeeeceeccCCCCCC
Confidence            557888889999999999984   3 5778887764

This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second messenger, cyclic di-GMP, and is a good candidate for a diguanylate phosphodiesterase function. Together with the GGDEF domain, EAL might be involved in regulating cell surface adhesiveness in bacteria.

>TIGR03239 GarL 2-dehydro-3-deoxyglucarate aldolase

Probab=85.52  E-value=8  Score=32.16  Aligned_cols=62  Identities=13%  Similarity=0.087  Sum_probs=47.0

Q ss_pred             CceeEEEEeCCCCCCCHHHHHHHHHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCC
Q 048660          147 LKVNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPV  209 (213)
Q Consensus       147 ~~~dlil~D~~mp~~~G~e~~~~ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~  209 (213)
                      ..||.|++|+....+|--++...++......-.|+|=+ ...+.....+++++|+++++.-=+
T Consensus        32 ~G~D~v~iD~EHg~~~~~~~~~~~~a~~~~g~~~~VRv-p~~~~~~i~r~LD~Ga~gIivP~v   93 (249)
T TIGR03239        32 AGFDWLLLDGEHAPNDVLTFIPQLMALKGSASAPVVRP-PWNEPVIIKRLLDIGFYNFLIPFV   93 (249)
T ss_pred             cCCCEEEEecccCCCCHHHHHHHHHHHhhcCCCcEEEC-CCCCHHHHHHHhcCCCCEEEecCc
Confidence            35999999999999988888888886543333455544 555678899999999999876433

In E. coli this enzyme (GarL, ) 2-dehydro-3-deoxyglucarate aldolase acts in the catabolism of several sugars including D-galactarate, D-glucarate and L-idarate. In fact, 5-dehydro-4-deoxy-D-glucarate aldolase is a synonym for this enzyme as it is unclear in the literature whether the enzyme acts on only one of these or, as seems likely, has no preference. (Despite the apparent large difference in substrate stucture indicated by their names, 2-DH-3DO- and 5-DH-4DO-glucarate differ only by the chirality of most central hydroxyl-bearing carbon and is alternately named 2-DH-3DO-galactarate.) The reported product of D-galactarate dehydratase (4.2.1.42) is the 5DH-4DO-glucarate isomer and this enzyme is found proximal to the aldolase in many genomes (GenProp0714) where no epimerase is known. Similarly, the product of D-glucarate dehydratase (4.2.1.40) is again the 5-DH-4DO isomer, so the provenance of the 2-DH-3DO-glucarate isomer for which

>PF01729 QRPTase_C: Quinolinate phosphoribosyl transferase, C-terminal domain; InterPro: IPR002638 Quinolinate phosphoribosyl transferase (QPRTase) or nicotinate-nucleotide pyrophosphorylase 2

Probab=85.38  E-value=4.3  Score=31.72  Aligned_cols=94  Identities=19%  Similarity=0.125  Sum_probs=59.2

Q ss_pred             EEEEEeCCHHHHHHHHHHH----hhcCC---EEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHH
Q 048660           95 HVLAVDDSYVDRKLIERLL----QISSC---KVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELL  167 (213)
Q Consensus        95 ~ILvVdD~~~~~~~l~~~L----~~~g~---~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~  167 (213)
                      .|||-|++-...-.+...+    +..+.   ..+.+++.+++.+.++            ..+|.|.+|-.-| -+--+++
T Consensus        52 ~ili~~nHi~~~g~i~~av~~~~~~~~~~~~I~VEv~~~ee~~ea~~------------~g~d~I~lD~~~~-~~~~~~v  118 (169)
T PF01729_consen   52 MILIKDNHIAFFGGIEEAVKAARQAAPEKKKIEVEVENLEEAEEALE------------AGADIIMLDNMSP-EDLKEAV  118 (169)
T ss_dssp             SEEE-HHHHHHHSSHHHHHHHHHHHSTTTSEEEEEESSHHHHHHHHH------------TT-SEEEEES-CH-HHHHHHH
T ss_pred             cEEehHHHHHHhCCHHHHHHHHHHhCCCCceEEEEcCCHHHHHHHHH------------hCCCEEEecCcCH-HHHHHHH
Confidence            4666666544333333333    22232   3457889999999884            2489999996544 2444456


Q ss_pred             HHHHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCee
Q 048660          168 KKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEY  204 (213)
Q Consensus       168 ~~ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~  204 (213)
                      +.++..  .++ ..|..++.-+.+...+..+.|+|.+
T Consensus       119 ~~l~~~--~~~-v~ie~SGGI~~~ni~~ya~~gvD~i  152 (169)
T PF01729_consen  119 EELREL--NPR-VKIEASGGITLENIAEYAKTGVDVI  152 (169)
T ss_dssp             HHHHHH--TTT-SEEEEESSSSTTTHHHHHHTT-SEE
T ss_pred             HHHhhc--CCc-EEEEEECCCCHHHHHHHHhcCCCEE
Confidence            666555  233 6778899988999999999998765

4.2.19 from EC is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to give rise to nicotinic acid mononucleotide (NaMN), pyrophosphate and carbon dioxide [, ]. Unlike IPR004393 from INTERPRO, this domain also includes the molybdenum transport system protein ModD.; GO: 0004514 nicotinate-nucleotide diphosphorylase (carboxylating) activity, 0009435 NAD biosynthetic process; PDB: 3C2O_A 3C2F_A 3C2E_A 3C2R_A 3C2V_A 1QPN_E 1QPO_A 1QPQ_F 1QPR_E 2I14_D ....

>PRK03659 glutathione-regulated potassium-efflux system protein KefB; Provisional

Probab=84.79  E-value=12  Score=35.09  Aligned_cols=94  Identities=12%  Similarity=0.197  Sum_probs=56.0

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcC-HHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCKVTAVES-GTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~-g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      +..++++|.|+...+.+    ++.|+.+...+- -.+.++..           .-.+.|+++.-..-+ .+-..++..+|
T Consensus       423 g~~vvvID~d~~~v~~~----~~~g~~v~~GDat~~~~L~~a-----------gi~~A~~vv~~~~d~-~~n~~i~~~~r  486 (601)
T PRK03659        423 KMRITVLERDISAVNLM----RKYGYKVYYGDATQLELLRAA-----------GAEKAEAIVITCNEP-EDTMKIVELCQ  486 (601)
T ss_pred             CCCEEEEECCHHHHHHH----HhCCCeEEEeeCCCHHHHHhc-----------CCccCCEEEEEeCCH-HHHHHHHHHHH
Confidence            45677777776544333    335666555432 22344433           223456676655433 23456777888


Q ss_pred             hcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeee
Q 048660          172 ESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIV  206 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~  206 (213)
                      +.  .++.+|++-+.+  .+......++|++..+.
T Consensus       487 ~~--~p~~~IiaRa~~--~~~~~~L~~~Ga~~vv~  517 (601)
T PRK03659        487 QH--FPHLHILARARG--RVEAHELLQAGVTQFSR  517 (601)
T ss_pred             HH--CCCCeEEEEeCC--HHHHHHHHhCCCCEEEc
Confidence            76  578888765543  56778888999987653

>PF03602 Cons_hypoth95: Conserved hypothetical protein 95; InterPro: IPR004398 This entry contains Ribosomal RNA small subunit methyltransferase D as well as the putative rRNA methyltransferase YlbH

Probab=84.35  E-value=12  Score=29.58  Aligned_cols=69  Identities=23%  Similarity=0.214  Sum_probs=46.5

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCC---EEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCH---HHHH
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSC---KVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTG---YELL  167 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~---~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G---~e~~  167 (213)
                      .+|..||-+......+++-++..+.   ..+...|...++..+..         ....||+|++|=  |-..+   .+++
T Consensus        66 ~~v~fVE~~~~a~~~i~~N~~~l~~~~~~~v~~~d~~~~l~~~~~---------~~~~fDiIflDP--PY~~~~~~~~~l  134 (183)
T PF03602_consen   66 KSVVFVEKNRKAIKIIKKNLEKLGLEDKIRVIKGDAFKFLLKLAK---------KGEKFDIIFLDP--PYAKGLYYEELL  134 (183)
T ss_dssp             SEEEEEES-HHHHHHHHHHHHHHT-GGGEEEEESSHHHHHHHHHH---------CTS-EEEEEE----STTSCHHHHHHH
T ss_pred             CeEEEEECCHHHHHHHHHHHHHhCCCcceeeeccCHHHHHHhhcc---------cCCCceEEEECC--CcccchHHHHHH
Confidence            5899999999999999999998874   23456777777766532         345899999994  43322   4577


Q ss_pred             HHHHhc
Q 048660          168 KKIKES  173 (213)
Q Consensus       168 ~~ir~~  173 (213)
                      +.|.+.
T Consensus       135 ~~l~~~  140 (183)
T PF03602_consen  135 ELLAEN  140 (183)
T ss_dssp             HHHHHT
T ss_pred             HHHHHC
Confidence            777653

They methylate the guanosine in position 966 of 16S rRNA in the assembled 30S particle [].; GO: 0008168 methyltransferase activity, 0031167 rRNA methylation; PDB: 3P9N_A 2ESR_B 2IFT_A 1WS6_A 2FPO_B 2FHP_A.

>TIGR00693 thiE thiamine-phosphate pyrophosphorylase

Probab=84.20  E-value=11  Score=29.59  Aligned_cols=55  Identities=24%  Similarity=0.356  Sum_probs=39.7

Q ss_pred             ceeEEEEeCCCCC--------CCHHHHHHHHHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeee
Q 048660          148 KVNLIITDYTMPG--------MTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYI  205 (213)
Q Consensus       148 ~~dlil~D~~mp~--------~~G~e~~~~ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L  205 (213)
                      ..|.|.++-..|.        ..|++.++.+.+.  .+++||+++.+- +.+...++.+.|++++.
T Consensus       116 g~dyi~~~~v~~t~~k~~~~~~~g~~~l~~~~~~--~~~~pv~a~GGI-~~~~~~~~~~~G~~gva  178 (196)
T TIGR00693       116 GADYIGFGPIFPTPTKKDPAPPAGVELLREIAAT--SIDIPIVAIGGI-TLENAAEVLAAGADGVA  178 (196)
T ss_pred             CCCEEEECCccCCCCCCCCCCCCCHHHHHHHHHh--cCCCCEEEECCc-CHHHHHHHHHcCCCEEE
Confidence            5788887654432        2378888888764  346898887666 47788889999998864

This model includes ThiE from Bacillus subtilis but excludes its paralog, the regulatory protein TenI, and neighbors of TenI.

>TIGR01334 modD putative molybdenum utilization protein ModD

Probab=84.11  E-value=17  Score=30.85  Aligned_cols=94  Identities=16%  Similarity=0.149  Sum_probs=60.6

Q ss_pred             EEEEEeCCHHH-------HHHHHHHHhhcC--CEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHH
Q 048660           95 HVLAVDDSYVD-------RKLIERLLQISS--CKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYE  165 (213)
Q Consensus        95 ~ILvVdD~~~~-------~~~l~~~L~~~g--~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e  165 (213)
                      .|||-|++-..       ...+...=+..+  ...+.+.+.++|.+.+.            ..+|+|++| +|+.-+-.+
T Consensus       158 ~ilikdnHi~~~g~~~~i~~av~~~r~~~~~~kIeVEv~tleea~ea~~------------~GaDiI~lD-n~~~e~l~~  224 (277)
T TIGR01334       158 TLLVFANHRTFLNDNFDWGGAIGRLKQTAPERKITVEADTIEQALTVLQ------------ASPDILQLD-KFTPQQLHH  224 (277)
T ss_pred             hheehHHHHHHhCCcccHHHHHHHHHHhCCCCCEEEECCCHHHHHHHHH------------cCcCEEEEC-CCCHHHHHH
Confidence            36666665433       333333333322  24467789999999883            248999999 444444455


Q ss_pred             HHHHHHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCee
Q 048660          166 LLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEY  204 (213)
Q Consensus       166 ~~~~ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~  204 (213)
                      +.+.+++.  .+ -.++..|+.-+.+........|+|-+
T Consensus       225 ~v~~l~~~--~~-~~~leasGGI~~~ni~~ya~~GvD~i  260 (277)
T TIGR01334       225 LHERLKFF--DH-IPTLAAAGGINPENIADYIEAGIDLF  260 (277)
T ss_pred             HHHHHhcc--CC-CEEEEEECCCCHHHHHHHHhcCCCEE
Confidence            55555532  22 34677899999999999999998764

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

>PRK07649 para-aminobenzoate/anthranilate synthase glutamine amidotransferase component II; Validated

Probab=83.56  E-value=1.4  Score=35.12  Aligned_cols=75  Identities=11%  Similarity=0.160  Sum_probs=47.8

Q ss_pred             EEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHH---HHHHHHh
Q 048660           96 VLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYE---LLKKIKE  172 (213)
Q Consensus        96 ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e---~~~~ir~  172 (213)
                      |||||....+-..+...|++.|+.+.+..+.+..++.+           ....||.|++-=. | ++-.+   ....++.
T Consensus         2 il~idn~dsft~nl~~~l~~~g~~v~v~~~~~~~~~~~-----------~~~~~d~iIlsgG-P-~~p~~~~~~~~~i~~   68 (195)
T PRK07649          2 ILMIDNYDSFTFNLVQFLGELGQELVVKRNDEVTISDI-----------ENMKPDFLMISPG-P-CSPNEAGISMEVIRY   68 (195)
T ss_pred             EEEEeCCCccHHHHHHHHHHCCCcEEEEeCCCCCHHHH-----------hhCCCCEEEECCC-C-CChHhCCCchHHHHH
Confidence            89999999999999999999999888877654333333           2235777776422 1 12111   2233333


Q ss_pred             cCCCCCCcEEEEe
Q 048660          173 SSVFREVPVVIMS  185 (213)
Q Consensus       173 ~~~~~~~pII~lt  185 (213)
                      .  ...+|++.+.
T Consensus        69 ~--~~~~PvLGIC   79 (195)
T PRK07649         69 F--AGKIPIFGVC   79 (195)
T ss_pred             h--cCCCCEEEEc
Confidence            2  2467888776

>cd02068 radical_SAM_B12_BD B12 binding domain_like associated with radical SAM domain

Probab=83.41  E-value=7.8  Score=28.24  Aligned_cols=71  Identities=18%  Similarity=0.216  Sum_probs=46.7

Q ss_pred             HHHHHHHHHhhcCCEEEEEc--CHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCC-CHHHHHHHHHhcCCCCCCcE
Q 048660          105 DRKLIERLLQISSCKVTAVE--SGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGM-TGYELLKKIKESSVFREVPV  181 (213)
Q Consensus       105 ~~~~l~~~L~~~g~~v~~a~--~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~-~G~e~~~~ir~~~~~~~~pI  181 (213)
                      -...+..+|++.|+.+....  .-++.++.+.          ...+||+|.+.+.-... ...++++.+|+.  .++++|
T Consensus         4 gl~~~aa~l~~~g~~v~~~~~~~~~~~~~~~~----------~~~~pdiv~~S~~~~~~~~~~~~~~~ik~~--~p~~~i   71 (127)
T cd02068           4 GLAYLAAVLEDAGFIVAEHDVLSADDIVEDIK----------ELLKPDVVGISLMTSAIYEALELAKIAKEV--LPNVIV   71 (127)
T ss_pred             hHHHHHHHHHHCCCeeeecCCCCHHHHHHHHH----------HhcCCCEEEEeeccccHHHHHHHHHHHHHH--CCCCEE
Confidence            34577888988888766543  3444555552          11579999999855553 467789999986  566666


Q ss_pred             EEEecC
Q 048660          182 VIMSSE  187 (213)
Q Consensus       182 I~lt~~  187 (213)
                      |+=...
T Consensus        72 v~GG~~   77 (127)
T cd02068          72 VVGGPH   77 (127)
T ss_pred             EECCcc
Confidence            644333

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.

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

Probab=83.28  E-value=11  Score=31.50  Aligned_cols=78  Identities=15%  Similarity=0.170  Sum_probs=53.7

Q ss_pred             EEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhcCC
Q 048660           96 VLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKESSV  175 (213)
Q Consensus        96 ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~~~  175 (213)
                      |-+.=-++.....+..+|...-|.+....++++.++.+..         ....+|++++....   .-..+...+++.  
T Consensus         3 I~~~v~s~~Laqsl~~~L~~dRY~l~~~~s~~ef~~~le~---------~~e~iDCLvle~~~---~~~~~~~~L~e~--   68 (283)
T PF07688_consen    3 ICLLVSSPALAQSLRQWLPGDRYELVQVDSPEEFLEFLEQ---------HREQIDCLVLEQSP---LLPPLFNQLYEQ--   68 (283)
T ss_dssp             EEEE-S-HHHHHHHHHHT-STTEEEEEESSCHHHHHHHCC---------TTTT-SEEEEETTS---TTHHHHHHHHHC--
T ss_pred             EEEEeCCHHHHHHHHHHcccCceEEEEcCcHHHHHHHHHh---------chhccCEEEEecCC---CcHHHHHHHHHc--
Confidence            4455556777888999999888999999999999999964         34579999998643   446678888876  


Q ss_pred             CCCCcEEEEecC
Q 048660          176 FREVPVVIMSSE  187 (213)
Q Consensus       176 ~~~~pII~lt~~  187 (213)
                      .--+|+|++...
T Consensus        69 g~LLPaVil~~~   80 (283)
T PF07688_consen   69 GILLPAVILGSS   80 (283)
T ss_dssp             T----EEEES--
T ss_pred             CccccEEEEecC
Confidence            457899998663

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

>TIGR00007 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase

Probab=83.15  E-value=9  Score=30.99  Aligned_cols=55  Identities=24%  Similarity=0.378  Sum_probs=42.1

Q ss_pred             ee-EEEEeCCCCCC-C--HHHHHHHHHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeee
Q 048660          149 VN-LIITDYTMPGM-T--GYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIV  206 (213)
Q Consensus       149 ~d-lil~D~~mp~~-~--G~e~~~~ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~  206 (213)
                      .+ +++.|+.--++ .  -+++++.+++.   .++|+++-.+-.+.++..++++.|+++++.
T Consensus       159 ~~~ii~~~~~~~g~~~g~~~~~i~~i~~~---~~ipvia~GGi~~~~di~~~~~~Gadgv~i  217 (230)
T TIGR00007       159 LEGIIYTDISRDGTLSGPNFELTKELVKA---VNVPVIASGGVSSIDDLIALKKLGVYGVIV  217 (230)
T ss_pred             CCEEEEEeecCCCCcCCCCHHHHHHHHHh---CCCCEEEeCCCCCHHHHHHHHHCCCCEEEE
Confidence            44 77788754332 2  26788888874   478999999899999999999999998764

Examples of this enzyme in Actinobacteria have been found to be bifunctional, also possessing phosphoribosylanthranilate isomerase activity ; the trusted cutoff here has now been raised to 275.0 to exclude the bifunctional group, now represented by model TIGR01919. HisA from Lactococcus lactis was reported to be inactive (MEDLINE:93322317).

>PRK11840 bifunctional sulfur carrier protein/thiazole synthase protein; Provisional

Probab=82.49  E-value=12  Score=32.36  Aligned_cols=76  Identities=13%  Similarity=0.168  Sum_probs=52.7

Q ss_pred             hcCCEE--EEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCC-----CCHHHHHHHHHhcCCCCCCcEEEEecC
Q 048660          115 ISSCKV--TAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPG-----MTGYELLKKIKESSVFREVPVVIMSSE  187 (213)
Q Consensus       115 ~~g~~v--~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~-----~~G~e~~~~ir~~~~~~~~pII~lt~~  187 (213)
                      +.|+.+  +++.|...|-+....            .+ +.+|-+.-|-     ....+.++.+.+.   +.+|||+=.+-
T Consensus       195 ~~Gf~v~~yc~~d~~~a~~l~~~------------g~-~avmPl~~pIGsg~gv~~p~~i~~~~e~---~~vpVivdAGI  258 (326)
T PRK11840        195 KEGFQVMVYCSDDPIAAKRLEDA------------GA-VAVMPLGAPIGSGLGIQNPYTIRLIVEG---ATVPVLVDAGV  258 (326)
T ss_pred             HCCCEEEEEeCCCHHHHHHHHhc------------CC-EEEeeccccccCCCCCCCHHHHHHHHHc---CCCcEEEeCCC
Confidence            459977  566777776665521            22 4444433232     2245667777764   57999999999


Q ss_pred             CCHHHHHHHHHcCCCeeee
Q 048660          188 DVLTQIDSCLEEGAEEYIV  206 (213)
Q Consensus       188 ~~~~~~~~~~~~G~~~~L~  206 (213)
                      ...++...+++.|+|+.|.
T Consensus       259 g~~sda~~AmelGadgVL~  277 (326)
T PRK11840        259 GTASDAAVAMELGCDGVLM  277 (326)
T ss_pred             CCHHHHHHHHHcCCCEEEE
Confidence            9999999999999999875

>PRK06774 para-aminobenzoate synthase component II; Provisional

Probab=82.38  E-value=1.7  Score=34.33  Aligned_cols=77  Identities=13%  Similarity=0.134  Sum_probs=47.2

Q ss_pred             EEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeC-CC-CCCCHHHHHHHHHhc
Q 048660           96 VLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDY-TM-PGMTGYELLKKIKES  173 (213)
Q Consensus        96 ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~-~m-p~~~G~e~~~~ir~~  173 (213)
                      ||+||....+-..|..+|++.|+.+..+.+..--++.+           ....||.|++.= -| |..++. ....++..
T Consensus         2 il~id~~dsf~~nl~~~l~~~~~~~~v~~~~~~~~~~~-----------~~~~~~~iilsgGP~~~~~~~~-~~~~i~~~   69 (191)
T PRK06774          2 LLLIDNYDSFTYNLYQYFCELGTEVMVKRNDELQLTDI-----------EQLAPSHLVISPGPCTPNEAGI-SLAVIRHF   69 (191)
T ss_pred             EEEEECCCchHHHHHHHHHHCCCcEEEEeCCCCCHHHH-----------HhcCCCeEEEcCCCCChHhCCC-chHHHHHh
Confidence            89999999999999999999999998887653222333           222566666532 11 111222 22333332


Q ss_pred             CCCCCCcEEEEec
Q 048660          174 SVFREVPVVIMSS  186 (213)
Q Consensus       174 ~~~~~~pII~lt~  186 (213)
                        ...+||+.+.-
T Consensus        70 --~~~~PiLGIC~   80 (191)
T PRK06774         70 --ADKLPILGVCL   80 (191)
T ss_pred             --cCCCCEEEECH
Confidence              24688887763

>PRK08007 para-aminobenzoate synthase component II; Provisional

Probab=82.37  E-value=2.9  Score=33.04  Aligned_cols=88  Identities=17%  Similarity=0.139  Sum_probs=52.5

Q ss_pred             EEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCC--CCCCHHHHHHHHHhc
Q 048660           96 VLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTM--PGMTGYELLKKIKES  173 (213)
Q Consensus        96 ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~m--p~~~G~e~~~~ir~~  173 (213)
                      ||+||....+--.|..+|++.|+.+.+..+.+..++.+           ....||.|++-=.-  |.-++. ..+.++..
T Consensus         2 il~idn~Dsft~nl~~~l~~~g~~v~v~~~~~~~~~~~-----------~~~~~d~iils~GPg~p~~~~~-~~~~~~~~   69 (187)
T PRK08007          2 ILLIDNYDSFTWNLYQYFCELGADVLVKRNDALTLADI-----------DALKPQKIVISPGPCTPDEAGI-SLDVIRHY   69 (187)
T ss_pred             EEEEECCCccHHHHHHHHHHCCCcEEEEeCCCCCHHHH-----------HhcCCCEEEEcCCCCChHHCCc-cHHHHHHh
Confidence            89999999999999999999999888876653223333           12257766664321  111222 22333332


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHcCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEEGA  201 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~G~  201 (213)
                        ...+||+.+.-    ....-+...|+
T Consensus        70 --~~~~PiLGICl----G~Q~la~a~Gg   91 (187)
T PRK08007         70 --AGRLPILGVCL----GHQAMAQAFGG   91 (187)
T ss_pred             --cCCCCEEEECH----HHHHHHHHcCC
Confidence              34688887763    33334444454

>PF05690 ThiG: Thiazole biosynthesis protein ThiG; InterPro: IPR008867 This family consists of several bacterial thiazole biosynthesis protein G sequences

Probab=82.07  E-value=19  Score=29.84  Aligned_cols=97  Identities=18%  Similarity=0.186  Sum_probs=57.4

Q ss_pred             cEEEEEeCC----HHHHHHHH--HHHhhcCCEEEEE--cCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHH-
Q 048660           94 LHVLAVDDS----YVDRKLIE--RLLQISSCKVTAV--ESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGY-  164 (213)
Q Consensus        94 ~~ILvVdD~----~~~~~~l~--~~L~~~g~~v~~a--~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~-  164 (213)
                      +++=|+.|+    |+..+.++  +.|-+.||.|.-.  .|.--|-+.. ..+            -..+|-+.-|-.+|. 
T Consensus        94 IKLEVi~D~~~L~PD~~etl~Aae~Lv~eGF~VlPY~~~D~v~akrL~-d~G------------caavMPlgsPIGSg~G  160 (247)
T PF05690_consen   94 IKLEVIGDDKTLLPDPIETLKAAEILVKEGFVVLPYCTDDPVLAKRLE-DAG------------CAAVMPLGSPIGSGRG  160 (247)
T ss_dssp             EEE--BS-TTT--B-HHHHHHHHHHHHHTT-EEEEEE-S-HHHHHHHH-HTT-------------SEBEEBSSSTTT---
T ss_pred             EEEEEeCCCCCcCCChhHHHHHHHHHHHCCCEEeecCCCCHHHHHHHH-HCC------------CCEEEecccccccCcC
Confidence            456566555    33344433  4467889998744  4444444433 211            136777777766543 


Q ss_pred             ----HHHHHHHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeee
Q 048660          165 ----ELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIV  206 (213)
Q Consensus       165 ----e~~~~ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~  206 (213)
                          ..++.|++.   .++|+|+=.+-..+.+...+++.|+|+.|.
T Consensus       161 i~n~~~l~~i~~~---~~vPvIvDAGiG~pSdaa~AMElG~daVLv  203 (247)
T PF05690_consen  161 IQNPYNLRIIIER---ADVPVIVDAGIGTPSDAAQAMELGADAVLV  203 (247)
T ss_dssp             SSTHHHHHHHHHH---GSSSBEEES---SHHHHHHHHHTT-SEEEE
T ss_pred             CCCHHHHHHHHHh---cCCcEEEeCCCCCHHHHHHHHHcCCceeeh
Confidence                467888875   389999999999999999999999999985

ThiG, together with ThiF and ThiH, is proposed to be involved in the synthesis of 4-methyl-5-(b-hydroxyethyl)thiazole (THZ) which is an intermediate in the thiazole production pathway [].; GO: 0009228 thiamine biosynthetic process; PDB: 1WV2_B 1TYG_C 1XM3_B 2HTM_C 2YZR_C.

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=81.93  E-value=22  Score=32.10  Aligned_cols=100  Identities=13%  Similarity=0.092  Sum_probs=55.0

Q ss_pred             CccEEEEEeCCHH---HHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCC--HHHH
Q 048660           92 KELHVLAVDDSYV---DRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMT--GYEL  166 (213)
Q Consensus        92 ~~~~ILvVdD~~~---~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~--G~e~  166 (213)
                      .+.+|++++-|..   ....++.+....|..+..+.+..++.+.+           ....+|+||+|.  ++..  ..+.
T Consensus       251 ~G~~V~Lit~Dt~R~aA~eQLk~yAe~lgvp~~~~~~~~~l~~~l-----------~~~~~D~VLIDT--aGr~~rd~~~  317 (432)
T PRK12724        251 MGKSVSLYTTDNYRIAAIEQLKRYADTMGMPFYPVKDIKKFKETL-----------ARDGSELILIDT--AGYSHRNLEQ  317 (432)
T ss_pred             cCCeEEEecccchhhhHHHHHHHHHHhcCCCeeehHHHHHHHHHH-----------HhCCCCEEEEeC--CCCCccCHHH
Confidence            3568888887752   12234444445566666565666666666           234689999997  3321  1233


Q ss_pred             HHHHHh---c-C-CCCCCcEEEEecCCCHHHHHHHHH----cCCCee
Q 048660          167 LKKIKE---S-S-VFREVPVVIMSSEDVLTQIDSCLE----EGAEEY  204 (213)
Q Consensus       167 ~~~ir~---~-~-~~~~~pII~lt~~~~~~~~~~~~~----~G~~~~  204 (213)
                      ++.+.+   . . ..+.-.++++++.....+.....+    .|.+++
T Consensus       318 l~eL~~~~~~~~~~~~~e~~LVLsAt~~~~~~~~~~~~f~~~~~~gl  364 (432)
T PRK12724        318 LERMQSFYSCFGEKDSVENLLVLSSTSSYHHTLTVLKAYESLNYRRI  364 (432)
T ss_pred             HHHHHHHHHhhcCCCCCeEEEEEeCCCCHHHHHHHHHHhcCCCCCEE
Confidence            333332   1 1 113346778888776655544443    455554

>TIGR00736 nifR3_rel_arch TIM-barrel protein, putative

Probab=81.46  E-value=9.9  Score=31.29  Aligned_cols=56  Identities=25%  Similarity=0.308  Sum_probs=44.6

Q ss_pred             ceeEEEEeCCCCCC--CHHHHHHHHHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeee
Q 048660          148 KVNLIITDYTMPGM--TGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYI  205 (213)
Q Consensus       148 ~~dlil~D~~mp~~--~G~e~~~~ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L  205 (213)
                      ..|.|-+|...++.  -.++.++.+++.  .+.+|||..-+-.+.++..+.++.|++++.
T Consensus       161 Gad~i~Vd~~~~g~~~a~~~~I~~i~~~--~~~ipIIgNGgI~s~eda~e~l~~GAd~Vm  218 (231)
T TIGR00736       161 GFDGIHVDAMYPGKPYADMDLLKILSEE--FNDKIIIGNNSIDDIESAKEMLKAGADFVS  218 (231)
T ss_pred             CCCEEEEeeCCCCCchhhHHHHHHHHHh--cCCCcEEEECCcCCHHHHHHHHHhCCCeEE
Confidence            46777778766664  258889999885  335999999999999999999999999874

Members of this family show a distant relationship by PSI-BLAST to alpha/beta (TIM) barrel enzymes such as dihydroorotate dehydrogenase and glycolate oxidase. At least two closely related but well-separable families among the bacteria, the nifR3/yhdG family and the yjbN family, share a more distant relationship to this family of shorter, exclusively archaeal proteins.

>cd00452 KDPG_aldolase KDPG and KHG aldolase

Probab=81.14  E-value=15  Score=28.84  Aligned_cols=68  Identities=19%  Similarity=0.233  Sum_probs=49.7

Q ss_pred             EEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhcCCCCCCcEEEEecCCCHHHHHHHHHc
Q 048660          120 VTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEE  199 (213)
Q Consensus       120 v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~~~~~~~pII~lt~~~~~~~~~~~~~~  199 (213)
                      +.-+.+.+|+.+.++            ...|.|-++- .+.. |.++++.+++.  .+++|+++..+- +.+....++++
T Consensus       101 i~gv~t~~e~~~A~~------------~Gad~i~~~p-~~~~-g~~~~~~l~~~--~~~~p~~a~GGI-~~~n~~~~~~~  163 (190)
T cd00452         101 LPGVATPTEIMQALE------------LGADIVKLFP-AEAV-GPAYIKALKGP--FPQVRFMPTGGV-SLDNAAEWLAA  163 (190)
T ss_pred             ECCcCCHHHHHHHHH------------CCCCEEEEcC-Cccc-CHHHHHHHHhh--CCCCeEEEeCCC-CHHHHHHHHHC
Confidence            345668888888763            2467777753 3333 89999999865  556888876666 78899999999


Q ss_pred             CCCee
Q 048660          200 GAEEY  204 (213)
Q Consensus       200 G~~~~  204 (213)
                      |++.+
T Consensus       164 G~~~v  168 (190)
T cd00452         164 GVVAV  168 (190)
T ss_pred             CCEEE
Confidence            98775

This family belongs to the class I adolases whose reaction mechanism involves Schiff base formation between a substrate carbonyl and lysine residue in the active site. 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase, is best known for its role in the Entner-Doudoroff pathway of bacteria, where it catalyzes the reversible cleavage of KDPG to pyruvate and glyceraldehyde-3-phosphate. 2-keto-4-hydroxyglutarate (KHG) aldolase, which has enzymatic specificity toward glyoxylate, forming KHG in the presence of pyruvate, and is capable of regulating glyoxylate levels in the glyoxylate bypass, an alternate pathway when bacteria are grown on acetate carbon sources.

>PRK13566 anthranilate synthase; Provisional

Probab=80.64  E-value=5.3  Score=38.45  Aligned_cols=82  Identities=17%  Similarity=0.223  Sum_probs=51.9

Q ss_pred             hcCCccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCC--CCC-CCHHH
Q 048660           89 ECSKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYT--MPG-MTGYE  165 (213)
Q Consensus        89 ~~~~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~--mp~-~~G~e  165 (213)
                      ....+.+|||||....+-..+.++|++.|+.|..+..... .+.+           ....||.||+-=.  .|. .+-.+
T Consensus       522 ~~~~g~~IlvID~~dsf~~~l~~~Lr~~G~~v~vv~~~~~-~~~~-----------~~~~~DgVVLsgGpgsp~d~~~~~  589 (720)
T PRK13566        522 AVGEGKRVLLVDHEDSFVHTLANYFRQTGAEVTTVRYGFA-EEML-----------DRVNPDLVVLSPGPGRPSDFDCKA  589 (720)
T ss_pred             CCCCCCEEEEEECCCchHHHHHHHHHHCCCEEEEEECCCC-hhHh-----------hhcCCCEEEECCCCCChhhCCcHH
Confidence            3456789999999988899999999999999988766432 1222           2235788776211  111 12233


Q ss_pred             HHHHHHhcCCCCCCcEEEEec
Q 048660          166 LLKKIKESSVFREVPVVIMSS  186 (213)
Q Consensus       166 ~~~~ir~~~~~~~~pII~lt~  186 (213)
                      +++.+.+    .++||+.+.-
T Consensus       590 lI~~a~~----~~iPILGICl  606 (720)
T PRK13566        590 TIDAALA----RNLPIFGVCL  606 (720)
T ss_pred             HHHHHHH----CCCcEEEEeh
Confidence            4444332    3688888764

>PRK00811 spermidine synthase; Provisional

Probab=80.60  E-value=23  Score=29.90  Aligned_cols=69  Identities=16%  Similarity=0.125  Sum_probs=45.8

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcC------CEE-EEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCC---
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISS------CKV-TAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMT---  162 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g------~~v-~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~---  162 (213)
                      ..+|.+||=++.+.+..++.+...+      -++ ....|+.+.+..            ....||+|++|..-|...   
T Consensus       100 ~~~V~~VEid~~vv~~a~~~~~~~~~~~~~d~rv~v~~~Da~~~l~~------------~~~~yDvIi~D~~dp~~~~~~  167 (283)
T PRK00811        100 VEKITLVEIDERVVEVCRKYLPEIAGGAYDDPRVELVIGDGIKFVAE------------TENSFDVIIVDSTDPVGPAEG  167 (283)
T ss_pred             CCEEEEEeCCHHHHHHHHHHhHHhccccccCCceEEEECchHHHHhh------------CCCcccEEEECCCCCCCchhh
Confidence            3589999999999999999886432      233 345666554432            234799999998666422   


Q ss_pred             --HHHHHHHHHhc
Q 048660          163 --GYELLKKIKES  173 (213)
Q Consensus       163 --G~e~~~~ir~~  173 (213)
                        .-++.+.+++.
T Consensus       168 l~t~ef~~~~~~~  180 (283)
T PRK00811        168 LFTKEFYENCKRA  180 (283)
T ss_pred             hhHHHHHHHHHHh
Confidence              24556666654

>PRK05458 guanosine 5'-monophosphate oxidoreductase; Provisional

Probab=80.47  E-value=5.3  Score=34.64  Aligned_cols=55  Identities=15%  Similarity=0.127  Sum_probs=41.6

Q ss_pred             ceeEEEEeCCCCCCC-HHHHHHHHHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeee
Q 048660          148 KVNLIITDYTMPGMT-GYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYI  205 (213)
Q Consensus       148 ~~dlil~D~~mp~~~-G~e~~~~ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L  205 (213)
                      .+|+|.+|+..+..+ -.+++++||+.  ++++|||+= .-.+.+....+.++|+|...
T Consensus       111 ~~d~i~iD~a~gh~~~~~e~I~~ir~~--~p~~~vi~g-~V~t~e~a~~l~~aGad~i~  166 (326)
T PRK05458        111 TPEYITIDIAHGHSDSVINMIQHIKKH--LPETFVIAG-NVGTPEAVRELENAGADATK  166 (326)
T ss_pred             CCCEEEEECCCCchHHHHHHHHHHHhh--CCCCeEEEE-ecCCHHHHHHHHHcCcCEEE
Confidence            359999999997644 56689999986  667776652 23367888999999998864

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=80.45  E-value=27  Score=31.38  Aligned_cols=93  Identities=15%  Similarity=0.074  Sum_probs=52.6

Q ss_pred             CccEEEEEeCCHHH---HHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCC-----H
Q 048660           92 KELHVLAVDDSYVD---RKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMT-----G  163 (213)
Q Consensus        92 ~~~~ILvVdD~~~~---~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~-----G  163 (213)
                      .+.+|.+|+-|+.-   .+.+..+-+..|..+..+.+..+....+..          ...+|+||+|.  |+..     .
T Consensus       250 ~g~~V~li~~D~~r~~a~eqL~~~a~~~~vp~~~~~~~~~l~~~l~~----------~~~~DlVlIDt--~G~~~~d~~~  317 (424)
T PRK05703        250 GKKKVALITLDTYRIGAVEQLKTYAKIMGIPVEVVYDPKELAKALEQ----------LRDCDVILIDT--AGRSQRDKRL  317 (424)
T ss_pred             CCCeEEEEECCccHHHHHHHHHHHHHHhCCceEccCCHHhHHHHHHH----------hCCCCEEEEeC--CCCCCCCHHH
Confidence            45789999877632   233444445567777777777666655532          22589999997  3332     2


Q ss_pred             HHHHHHHHhcCCCCCCcEEEEecCCCHHHHHHH
Q 048660          164 YELLKKIKESSVFREVPVVIMSSEDVLTQIDSC  196 (213)
Q Consensus       164 ~e~~~~ir~~~~~~~~pII~lt~~~~~~~~~~~  196 (213)
                      .+.+..+-+....+.-..+++++.....+..+.
T Consensus       318 ~~~L~~ll~~~~~~~~~~LVl~a~~~~~~l~~~  350 (424)
T PRK05703        318 IEELKALIEFSGEPIDVYLVLSATTKYEDLKDI  350 (424)
T ss_pred             HHHHHHHHhccCCCCeEEEEEECCCCHHHHHHH
Confidence            223333322111233346778887766555443

>KOG2335 consensus tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]

Probab=80.43  E-value=23  Score=31.00  Aligned_cols=104  Identities=14%  Similarity=0.286  Sum_probs=70.6

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCC----EEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCC------
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSC----KVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMT------  162 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~----~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~------  162 (213)
                      +.-..+.++-+.+.+++..+=...+.    ++.+..|.++-++.++..        .....+++.+--.-+...      
T Consensus       117 ~yGa~L~~~~eLv~e~V~~v~~~l~~pVs~KIRI~~d~~kTvd~ak~~--------e~aG~~~ltVHGRtr~~kg~~~~p  188 (358)
T KOG2335|consen  117 GYGAFLMDNPELVGEMVSAVRANLNVPVSVKIRIFVDLEKTVDYAKML--------EDAGVSLLTVHGRTREQKGLKTGP  188 (358)
T ss_pred             CccceeccCHHHHHHHHHHHHhhcCCCeEEEEEecCcHHHHHHHHHHH--------HhCCCcEEEEecccHHhcCCCCCC
Confidence            34467777777777777777666653    445567777766665422        112334455444433333      


Q ss_pred             -HHHHHHHHHhcCCCCCCcEEEEecCCCHHHHHHHHH-cCCCeeee
Q 048660          163 -GYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLE-EGAEEYIV  206 (213)
Q Consensus       163 -G~e~~~~ir~~~~~~~~pII~lt~~~~~~~~~~~~~-~G~~~~L~  206 (213)
                       -++.++.||++  .+++|+|+-.+-...++..++++ .|+++.+.
T Consensus       189 ad~~~i~~v~~~--~~~ipviaNGnI~~~~d~~~~~~~tG~dGVM~  232 (358)
T KOG2335|consen  189 ADWEAIKAVREN--VPDIPVIANGNILSLEDVERCLKYTGADGVMS  232 (358)
T ss_pred             cCHHHHHHHHHh--CcCCcEEeeCCcCcHHHHHHHHHHhCCceEEe
Confidence             37899999987  56699998888788889999998 99999865

>PLN02476 O-methyltransferase

Probab=80.42  E-value=25  Score=29.85  Aligned_cols=59  Identities=10%  Similarity=0.173  Sum_probs=41.9

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCCE--EE-EEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCC
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSCK--VT-AVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYT  157 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~~--v~-~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~  157 (213)
                      ..-+|.-+|-++...+..+..+++.|+.  +. ...+..+.+..+..+.       ....||+||+|..
T Consensus       142 ~~G~V~TiE~d~e~~~~Ar~n~~~aGl~~~I~li~GdA~e~L~~l~~~~-------~~~~FD~VFIDa~  203 (278)
T PLN02476        142 ESGCLVACERDSNSLEVAKRYYELAGVSHKVNVKHGLAAESLKSMIQNG-------EGSSYDFAFVDAD  203 (278)
T ss_pred             CCCEEEEEECCHHHHHHHHHHHHHcCCCCcEEEEEcCHHHHHHHHHhcc-------cCCCCCEEEECCC
Confidence            3457999999999999999999998873  43 3456566665442111       1347999999975

>PRK05670 anthranilate synthase component II; Provisional

Probab=80.23  E-value=5.2  Score=31.47  Aligned_cols=31  Identities=13%  Similarity=0.076  Sum_probs=27.0

Q ss_pred             EEEEeCCHHHHHHHHHHHhhcCCEEEEEcCH
Q 048660           96 VLAVDDSYVDRKLIERLLQISSCKVTAVESG  126 (213)
Q Consensus        96 ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g  126 (213)
                      |||+|.....-..+.+.|++.|+.+......
T Consensus         2 iliid~~d~f~~~i~~~l~~~g~~~~v~~~~   32 (189)
T PRK05670          2 ILLIDNYDSFTYNLVQYLGELGAEVVVYRND   32 (189)
T ss_pred             EEEEECCCchHHHHHHHHHHCCCcEEEEECC
Confidence            8999999999999999999999988777553

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	213
2fka_A	129	Crystal Structure Of Mg(2+) And Bef(3)(-)-Bound Che		1e-11
2che_A	128	Structure Of The Mg2+-Bound Form Of Chey And Mechan		1e-11
3h1g_A	129	Crystal Structure Of Chey Mutant T84a Of Helicobact		2e-11
3gwg_A	129	Crystal Structure Of Chey Of Helicobacter Pylori Le		2e-11
1ymv_A	129	Signal Transduction Protein Chey Mutant With Phe 14		2e-11
2chy_A	128	Three-Dimensional Structure Of Chey, The Response R		4e-11
3olx_A	129	Structural And Functional Effects Of Substitution A		5e-11
1ymu_A	130	Signal Transduction Protein Chey Mutant With Met 17		5e-11
3heb_A	152	Crystal Structure Of Response Regulator Receiver Do		7e-11
1udr_A	129	Chey Mutant With Lys 91 Replaced By Asp, Lys 92 Rep		7e-11
3myy_A	128	Structure Of E. Coli Chey Mutant A113p Bound To Ber		8e-11
3oo0_A	129	Structure Of Apo Chey A113p Length = 129		8e-11
1eay_A	128	Chey-Binding (P2) Domain Of Chea In Complex With Ch		9e-11
1djm_A	129	Solution Structure Of Bef3-Activated Chey From Esch		9e-11
3olw_A	129	Structural And Functional Effects Of Substitution A		1e-10
1cye_A	129	Three Dimensional Structure Of Chemotactic Che Y Pr		1e-10
1jbe_A	128	1.08 A Structure Of Apo-Chey Reveals Meta-Active Co		1e-10
1cey_A	128	Assignments, Secondary Structure, Global Fold, And		1e-10
1d4z_A	128	Crystal Structure Of Chey-95iv, A Hyperactive Chey		1e-10
3h1f_A	129	Crystal Structure Of Chey Mutant D53a Of Helicobact		1e-10
1mih_A	129	A Role For Chey Glu 89 In Chez-Mediated Dephosphory		1e-10
5chy_A	128	Structure Of Chemotaxis Protein Chey Length = 128		2e-10
3oly_A	129	Structural And Functional Effects Of Substitution A		2e-10
3fft_A	128	Crystal Structure Of Chey Double Mutant F14e, E89r		2e-10
1ab6_A	125	Structure Of Chey Mutant F14n, V86t Length = 125		2e-10
3olv_A	129	Structural And Functional Effects Of Substitution A		3e-10
1vlz_A	128	Uncoupled Phosphorylation And Activation In Bacteri		3e-10
3ffx_A	128	Crystal Structure Of Chey Triple Mutant F14e, N59r,		3e-10
3fgz_A	128	Crystal Structure Of Chey Triple Mutant F14e, N59m,		3e-10
3m6m_D	143	Crystal Structure Of Rpff Complexed With Rec Domain		3e-10
3rvj_A	132	Structure Of The Chey-Bef3 Complex With Substitutio		3e-10
1ab5_A	125	Structure Of Chey Mutant F14n, V21t Length = 125		4e-10
3rvp_A	132	Structure Of The Chey-Bef3 Complex With Substitutio		5e-10
6chy_A	128	Structure Of Chemotaxis Protein Chey Length = 128		5e-10
3rvl_A	132	Structure Of The Chey-Bef3 Complex With Substitutio		5e-10
3ffw_A	128	Crystal Structure Of Chey Triple Mutant F14q, N59k,		6e-10
1ehc_A	128	Structure Of Signal Transduction Protein Chey Lengt		6e-10
3f7n_A	128	Crystal Structure Of Chey Triple Mutant F14e, N59m,		7e-10
1zdm_A	129	Crystal Structure Of Activated Chey Bound To Xe Len		7e-10
1c4w_A	128	1.9 A Structure Of A-Thiophosphonate Modified Chey		8e-10
1e6k_A	130	Two-Component Signal Transduction System D12a Mutan		1e-09
3rvn_A	132	Structure Of The Chey-Bef3 Complex With Substitutio		1e-09
1e6m_A	128	Two-Component Signal Transduction System D57a Mutan		1e-09
1e6l_A	127	Two-Component Signal Transduction System D13a Mutan		1e-09
3to5_A	134	High Resolution Structure Of Chey3 From Vibrio Chol		1e-09
2id7_A	128	1.75 A Structure Of T87i Phosphono-Chey Length = 12		2e-09
2id9_A	128	1.85 A Structure Of T87iY106W PHOSPHONO-Chey Length		4e-09
1k66_A	149	Crystal Structure Of The Cyanobacterial Phytochrome		4e-09
1hey_A	128	Investigating The Structural Determinants Of The P2		4e-09
3f7a_A	394	Structure Of Orthorhombic Crystal Form Of Pseudomon		7e-08
1u8t_A	128	Crystal Structure Of Chey D13k Y106w Alone And In C		8e-08
3eq2_A	394	Structure Of Hexagonal Crystal Form Of Pseudomonas		2e-07
1dc7_A	124	Structure Of A Transiently Phosphorylated "switch"		2e-07
1j56_A	124	Minimized Average Structure Of Beryllofluoride-Acti		3e-07
2ayx_A	254	Solution Structure Of The E.Coli Rcsc C-Terminus (R		3e-07
1krw_A	124	Solution Structure And Backbone Dynamics Of Beryllo		3e-07
2wb4_A	459	Activated Diguanylate Cyclase Pled In Complex With		3e-07
1w25_A	459	Response Regulator Pled In Complex With C-digmp Len		3e-07
3gt7_A	154	Crystal Structure Of Signal Receiver Domain Of Sign		5e-07
3dge_C	122	Structure Of A Histidine Kinase-response Regulator		6e-07
2ayz_A	133	Solution Structure Of The E.Coli Rcsc C-Terminus (R		7e-07
3eod_A	130	Crystal Structure Of N-Terminal Domain Of E. Coli R		7e-07
1jlk_A	147	Crystal Structure Of The Mn(2+)-Bound Form Of Respo		8e-07
1i3c_A	149	Response Regulator For Cyanobacterial Phytochrome,		2e-06
1dc8_A	124	Structure Of A Transiently Phosphorylated "switch"		2e-06
1zes_A	125	Bef3- Activated Phob Receiver Domain Length = 125		2e-06
1b00_A	127	Phob Receiver Domain From Escherichia Coli Length =		2e-06
3jte_A	143	Crystal Structure Of Response Regulator Receiver Do		4e-06
1l5y_A	155	Crystal Structure Of Mg2+ / Bef3-bound Receiver Dom		5e-06
1qkk_A	155	Crystal Structure Of The Receiver Domain And Linker		5e-06
3gl9_A	122	The Structure Of A Histidine Kinase-Response Regula		6e-06
3t6k_A	136	Crystal Structure Of A Hypothetical Response Regula		9e-06
2jb9_A	127	Phob Response Regulator Receiver Domain Constitutiv		9e-06
2oqr_A	230	The Structure Of The Response Regulator Regx3 From		1e-05
3nhz_A	125	Structure Of N-Terminal Domain Of Mtra Length = 125		1e-05
3mm4_A	206	Crystal Structure Of The Receiver Domain Of The His		2e-05
1p6u_A	129	Nmr Structure Of The Bef3-Activated Structure Of Th		6e-05
3bre_A	358	Crystal Structure Of P.Aeruginosa Pa3702 Length = 3		7e-05
1xhe_A	123	Crystal Structure Of The Receiver Domain Of Redox R		8e-05
1xhf_A	123	Crystal Structure Of The Bef3-Activated Receiver Do		9e-05
3i5a_A	334	Crystal Structure Of Full-Length Wpsr From Pseudomo		9e-05
1zy2_A	150	Crystal Structure Of The Phosphorylated Receiver Do		9e-05
1oxb_B	134	Complex Between Ypd1 And Sln1 Response Regulator Do		1e-04
2r25_B	133	Complex Of Ypd1 And Sln1-R1 With Bound Mg2+ And Bef		1e-04
1nxo_A	120	Micarec Ph7.0 Length = 120		2e-04
1m5t_A	124	Crystal Structure Of The Response Regulator Divk Le		2e-04
2jba_B	127	Phob Response Regulator Receiver Domain Constitutiv		3e-04
2jba_A	127	Phob Response Regulator Receiver Domain Constitutiv		5e-04
1zh2_A	121	Crystal Structure Of The Calcium-Bound Receiver Dom		5e-04
2zay_A	147	Crystal Structure Of Response Regulator From Desulf		6e-04
3kht_A	144	Crystal Structure Of Response Regulator From Hahell		9e-04

>pdb|2FKA|A Chain A, Crystal Structure Of Mg(2+) And Bef(3)(-)-Bound Chey In Complex With Chez(200-214) Solved From A F432 Crystal Grown In Caps (Ph 10.5) Length = 129

Iteration: 1
 Score = 65.9 bits (159), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 41/120 (34%), Positives = 59/120 (49%), Gaps = 12/120 (10%)
Query: 90  CSKELHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALK 148
             KEL  L VDD    R+++  LL ++    V   E G  AL  L    +    GF    
Sbjct: 2   ADKELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKL----QAGGFGF---- 53
Query: 149 VNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
              II+D+ MP M G ELLK I+  S    +PV+++++E     I +  + GA  Y+VKP
Sbjct: 54  ---IISDWNMPNMDGLELLKTIRADSAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKP 110

>pdb|2CHE|A Chain A, Structure Of The Mg2+-Bound Form Of Chey And Mechanism Of Phosphoryl Transfer In Bacterial Chemotaxis Length = 128

Iteration: 1
 Score = 65.9 bits (159), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 41/120 (34%), Positives = 59/120 (49%), Gaps = 12/120 (10%)
Query: 90  CSKELHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALK 148
             KEL  L VDD    R+++  LL ++    V   E G  AL  L    +    GF    
Sbjct: 1   ADKELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKL----QAGGFGF---- 52
Query: 149 VNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
              II+D+ MP M G ELLK I+  S    +PV+++++E     I +  + GA  Y+VKP
Sbjct: 53  ---IISDWNMPNMDGLELLKTIRADSAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKP 109

>pdb|3H1G|A Chain A, Crystal Structure Of Chey Mutant T84a Of Helicobacter Pylori Length = 129

Iteration: 1
 Score = 65.9 bits (159), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 35/116 (30%), Positives = 64/116 (55%), Gaps = 11/116 (9%)
Query: 94  LHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLI 152
           + +L VDDS   R++I+  L ++    V   E G  A + L  + +            ++
Sbjct: 6   MKLLVVDDSSTMRRIIKNTLSRLGYEDVLEAEHGVEAWEKLDANADTK----------VL 55
Query: 153 ITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
           ITD+ MP M G +L+KK++  S F+E+P++++++E    ++ + L+ G   YIVKP
Sbjct: 56  ITDWNMPEMNGLDLVKKVRSDSRFKEIPIIMITAEGGKAEVITALKAGVNNYIVKP 111

>pdb|3GWG|A Chain A, Crystal Structure Of Chey Of Helicobacter Pylori Length = 129

Iteration: 1
 Score = 65.9 bits (159), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 35/116 (30%), Positives = 64/116 (55%), Gaps = 11/116 (9%)
Query: 94  LHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLI 152
           + +L VDDS   R++I+  L ++    V   E G  A + L  + +            ++
Sbjct: 6   MKLLVVDDSSTMRRIIKNTLSRLGYEDVLEAEHGVEAWEKLDANADTK----------VL 55
Query: 153 ITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
           ITD+ MP M G +L+KK++  S F+E+P++++++E    ++ + L+ G   YIVKP
Sbjct: 56  ITDWNMPEMNGLDLVKKVRSDSRFKEIPIIMITTEGGKAEVITALKAGVNNYIVKP 111

>pdb|1YMV|A Chain A, Signal Transduction Protein Chey Mutant With Phe 14 Replaced By Gly, Ser 15 Replaced By Gly, And Met 17 Replaced By Gly Length = 129

Iteration: 1
 Score = 65.5 bits (158), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 39/120 (32%), Positives = 58/120 (48%), Gaps = 12/120 (10%)
Query: 90  CSKELHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALK 148
             KEL  L VDD    R+++  LL ++    V   E G  AL  L    +    GF    
Sbjct: 2   SDKELKFLVVDDGGTGRRIVRNLLKELGFNNVEEAEDGVDALNKL----QAGGYGF---- 53
Query: 149 VNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
              +I+D+ MP M G ELLK I+       +PV+++++E     I +  + GA  Y+VKP
Sbjct: 54  ---VISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKP 110

>pdb|2CHY|A Chain A, Three-Dimensional Structure Of Chey, The Response Regulator Of Bacterial Chemotaxis Length = 128

Iteration: 1
 Score = 64.3 bits (155), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 41/120 (34%), Positives = 58/120 (48%), Gaps = 12/120 (10%)
Query: 90  CSKELHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALK 148
             KEL  L VDD    R+++  LL ++    V   E G  AL  L    +    GF    
Sbjct: 1   ADKELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKL----QAGGFGF---- 52
Query: 149 VNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
              II D+ MP M G ELLK I+  S    +PV+++++E     I +  + GA  Y+VKP
Sbjct: 53  ---IICDWNMPNMDGLELLKTIRADSAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKP 109

>pdb|3OLX|A Chain A, Structural And Functional Effects Of Substitution At Position T+1 In Chey: Cheya88s-Bef3-Mn Complex Length = 129

Iteration: 1
 Score = 64.3 bits (155), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 40/120 (33%), Positives = 58/120 (48%), Gaps = 12/120 (10%)
Query: 90  CSKELHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALK 148
             KEL  L VDD    R+++  LL ++    V   E G  AL  L    +    GF    
Sbjct: 2   ADKELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKL----QAGGYGF---- 53
Query: 149 VNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
              +I+D+ MP M G ELLK I+       +PV++++SE     I +  + GA  Y+VKP
Sbjct: 54  ---VISDWNMPNMDGLELLKTIRADGAMSALPVLMVTSEAKKENIIAAAQAGASGYVVKP 110

>pdb|1YMU|A Chain A, Signal Transduction Protein Chey Mutant With Met 17 Replaced By Gly (M17g) Length = 130

Iteration: 1
 Score = 63.9 bits (154), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 39/120 (32%), Positives = 58/120 (48%), Gaps = 12/120 (10%)
Query: 90  CSKELHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALK 148
             KEL  L VDD    R+++  LL ++    V   E G  AL  L    +    GF    
Sbjct: 3   SDKELKFLVVDDFSTGRRIVRNLLKELGFNNVEEAEDGVDALNKL----QAGGYGF---- 54
Query: 149 VNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
              +I+D+ MP M G ELLK I+       +PV+++++E     I +  + GA  Y+VKP
Sbjct: 55  ---VISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKP 111

>pdb|3HEB|A Chain A, Crystal Structure Of Response Regulator Receiver Domain From Rhodospirillum Rubrum Length = 152

Iteration: 1
 Score = 63.9 bits (154), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 39/122 (31%), Positives = 65/122 (53%), Gaps = 4/122 (3%)
Query: 91  SKELHVLAVDDSYVDRKLIERLLQISSC--KVTAVESGTRALQYLGLDGEQSNVGFDALK 148
           S  + ++ ++D     +LIE+ ++ +    ++ A   GT AL YL  D +   V   A +
Sbjct: 2   SLSVTIVXIEDDLGHARLIEKNIRRAGVNNEIIAFTDGTSALNYLFGDDKSGRVS--AGR 59
Query: 149 VNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
             L++ D  +P  TG ++LK +KE+   R  PVVI+++ D   +I  C + GA  YI KP
Sbjct: 60  AQLVLLDLNLPDXTGIDILKLVKENPHTRRSPVVILTTTDDQREIQRCYDLGANVYITKP 119
Query: 209 VK 210
           V 
Sbjct: 120 VN 121

>pdb|1UDR|A Chain A, Chey Mutant With Lys 91 Replaced By Asp, Lys 92 Replaced By Ala, Ile 96 Replaced By Lys And Ala 98 Replaced By Leu (Stabilizing Mutations In Helix 4) Length = 129

Iteration: 1
 Score = 63.9 bits (154), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 39/119 (32%), Positives = 58/119 (48%), Gaps = 12/119 (10%)
Query: 91  SKELHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKV 149
            KEL  L VDD    R+++  LL ++    V   E G  AL  L    +    GF     
Sbjct: 3   DKELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKL----QAGGYGF----- 53
Query: 150 NLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
             +I+D+ MP M G ELLK I+       +PV+++++E     I +  + GA  Y+VKP
Sbjct: 54  --VISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEADAENIKALAQAGASGYVVKP 110

>pdb|3MYY|A Chain A, Structure Of E. Coli Chey Mutant A113p Bound To Beryllium Fluoride Length = 128

Iteration: 1
 Score = 63.5 bits (153), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 39/120 (32%), Positives = 58/120 (48%), Gaps = 12/120 (10%)
Query: 90  CSKELHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALK 148
             KEL  L VDD    R+++  LL ++    V   E G  AL  L    +    GF    
Sbjct: 1   ADKELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKL----QAGGYGF---- 52
Query: 149 VNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
              +I+D+ MP M G ELLK I+       +PV+++++E     I +  + GA  Y+VKP
Sbjct: 53  ---VISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKP 109

>pdb|3OO0|A Chain A, Structure Of Apo Chey A113p Length = 129

Iteration: 1
 Score = 63.5 bits (153), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 39/120 (32%), Positives = 58/120 (48%), Gaps = 12/120 (10%)
Query: 90  CSKELHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALK 148
             KEL  L VDD    R+++  LL ++    V   E G  AL  L    +    GF    
Sbjct: 2   ADKELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKL----QAGGYGF---- 53
Query: 149 VNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
              +I+D+ MP M G ELLK I+       +PV+++++E     I +  + GA  Y+VKP
Sbjct: 54  ---VISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKP 110

>pdb|1EAY|A Chain A, Chey-Binding (P2) Domain Of Chea In Complex With Chey From Escherichia Coli Length = 128

Iteration: 1
 Score = 63.5 bits (153), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 39/120 (32%), Positives = 58/120 (48%), Gaps = 12/120 (10%)
Query: 90  CSKELHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALK 148
             KEL  L VDD    R+++  LL ++    V   E G  AL  L    +    GF    
Sbjct: 1   ADKELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKL----QAGGYGF---- 52
Query: 149 VNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
              +I+D+ MP M G ELLK I+       +PV+++++E     I +  + GA  Y+VKP
Sbjct: 53  ---VISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKP 109

>pdb|1DJM|A Chain A, Solution Structure Of Bef3-Activated Chey From Escherichia Coli Length = 129

Iteration: 1
 Score = 63.5 bits (153), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 39/120 (32%), Positives = 58/120 (48%), Gaps = 12/120 (10%)
Query: 90  CSKELHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALK 148
             KEL  L VDD    R+++  LL ++    V   E G  AL  L    +    GF    
Sbjct: 2   ADKELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKL----QAGGYGF---- 53
Query: 149 VNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
              +I+D+ MP M G ELLK I+       +PV+++++E     I +  + GA  Y+VKP
Sbjct: 54  ---VISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKP 110

>pdb|3OLW|A Chain A, Structural And Functional Effects Of Substitution At Position T+1 In Chey: Cheya88t-Bef3-Mn Complex Length = 129

Iteration: 1
 Score = 63.2 bits (152), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 39/120 (32%), Positives = 58/120 (48%), Gaps = 12/120 (10%)
Query: 90  CSKELHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALK 148
             KEL  L VDD    R+++  LL ++    V   E G  AL  L    +    GF    
Sbjct: 2   ADKELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKL----QAGGYGF---- 53
Query: 149 VNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
              +I+D+ MP M G ELLK I+       +PV+++++E     I +  + GA  Y+VKP
Sbjct: 54  ---VISDWNMPNMDGLELLKTIRADGAMSALPVLMVTTEAKKENIIAAAQAGASGYVVKP 110

>pdb|1CYE|A Chain A, Three Dimensional Structure Of Chemotactic Che Y Protein In Aqueous Solution By Nuclear Magnetic Resonance Methods Length = 129

Iteration: 1
 Score = 63.2 bits (152), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 39/120 (32%), Positives = 58/120 (48%), Gaps = 12/120 (10%)
Query: 90  CSKELHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALK 148
             KEL  L VDD    R+++  LL ++    V   E G  AL  L    +    GF    
Sbjct: 2   SDKELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKL----QAGGYGF---- 53
Query: 149 VNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
              +I+D+ MP M G ELLK I+       +PV+++++E     I +  + GA  Y+VKP
Sbjct: 54  ---VISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKP 110

>pdb|1JBE|A Chain A, 1.08 A Structure Of Apo-Chey Reveals Meta-Active Conformation Length = 128

Iteration: 1
 Score = 62.8 bits (151), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 39/120 (32%), Positives = 58/120 (48%), Gaps = 12/120 (10%)
Query: 90  CSKELHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALK 148
             KEL  L VDD    R+++  LL ++    V   E G  AL  L    +    GF    
Sbjct: 1   ADKELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKL----QAGGYGF---- 52
Query: 149 VNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
              +I+D+ MP M G ELLK I+       +PV+++++E     I +  + GA  Y+VKP
Sbjct: 53  ---VISDWNMPNMDGLELLKTIRAXXAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKP 109

>pdb|1CEY|A Chain A, Assignments, Secondary Structure, Global Fold, And Dynamics Of Chemotaxis Y Protein Using Three-And Four-Dimensional Heteronuclear (13c,15n) Nmr Spectroscopy Length = 128

Iteration: 1
 Score = 62.8 bits (151), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 39/119 (32%), Positives = 58/119 (48%), Gaps = 12/119 (10%)
Query: 91  SKELHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKV 149
            KEL  L VDD    R+++  LL ++    V   E G  AL  L    +    GF     
Sbjct: 2   DKELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKL----QAGGYGF----- 52
Query: 150 NLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
             +I+D+ MP M G ELLK I+       +PV+++++E     I +  + GA  Y+VKP
Sbjct: 53  --VISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKP 109

>pdb|1D4Z|A Chain A, Crystal Structure Of Chey-95iv, A Hyperactive Chey Mutant Length = 128

Iteration: 1
 Score = 62.8 bits (151), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 38/120 (31%), Positives = 58/120 (48%), Gaps = 12/120 (10%)
Query: 90  CSKELHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALK 148
             KEL  L VDD    R+++  LL ++    V   E G  AL  L    +    GF    
Sbjct: 1   ADKELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKL----QAGGYGF---- 52
Query: 149 VNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
              +I+D+ MP M G ELLK I+       +PV+++++E     + +  + GA  Y+VKP
Sbjct: 53  ---VISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENVIAAAQAGASGYVVKP 109

>pdb|3H1F|A Chain A, Crystal Structure Of Chey Mutant D53a Of Helicobacter Pylori Length = 129

Iteration: 1
 Score = 62.8 bits (151), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 34/116 (29%), Positives = 63/116 (54%), Gaps = 11/116 (9%)
Query: 94  LHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLI 152
           + +L VDDS   R++I+  L ++    V   E G  A + L  + +            ++
Sbjct: 6   MKLLVVDDSSTMRRIIKNTLSRLGYEDVLEAEHGVEAWEKLDANADTK----------VL 55
Query: 153 ITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
           IT + MP M G +L+KK++  S F+E+P++++++E    ++ + L+ G   YIVKP
Sbjct: 56  ITAWNMPEMNGLDLVKKVRSDSRFKEIPIIMITTEGGKAEVITALKAGVNNYIVKP 111

>pdb|1MIH|A Chain A, A Role For Chey Glu 89 In Chez-Mediated Dephosphorylation Of The E. Coli Chemotaxis Response Regulator Chey Length = 129

Iteration: 1
 Score = 62.8 bits (151), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 39/120 (32%), Positives = 58/120 (48%), Gaps = 12/120 (10%)
Query: 90  CSKELHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALK 148
             KEL  L VDD    R+++  LL ++    V   E G  AL  L    +    GF    
Sbjct: 2   ADKELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKL----QAGGYGF---- 53
Query: 149 VNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
              +I+D+ MP M G ELLK I+       +PV+++++E     I +  + GA  Y+VKP
Sbjct: 54  ---VISDWRMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKP 110

>pdb|5CHY|A Chain A, Structure Of Chemotaxis Protein Chey Length = 128

Iteration: 1
 Score = 62.4 bits (150), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 38/120 (31%), Positives = 58/120 (48%), Gaps = 12/120 (10%)
Query: 90  CSKELHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALK 148
             KEL  L VDD    R+++  LL ++    V   E G  AL  L    +    GF    
Sbjct: 1   ADKELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKL----QAGGYGF---- 52
Query: 149 VNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
              +I+D+ MP M G ELLK I+       +PV+++++E     I +  + GA  ++VKP
Sbjct: 53  ---VISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGWVVKP 109

>pdb|3OLY|A Chain A, Structural And Functional Effects Of Substitution At Position T+1 In Chey: Cheya88m-Bef3-Mn Complex Length = 129

Iteration: 1
 Score = 62.0 bits (149), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 39/120 (32%), Positives = 57/120 (47%), Gaps = 12/120 (10%)
Query: 90  CSKELHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALK 148
             KEL  L VDD    R+++  LL ++    V   E G  AL  L    +    GF    
Sbjct: 2   ADKELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKL----QAGGYGF---- 53
Query: 149 VNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
              +I+D+ MP M G ELLK I+       +PV++++ E     I +  + GA  Y+VKP
Sbjct: 54  ---VISDWNMPNMDGLELLKTIRADGAMSALPVLMVTMEAKKENIIAAAQAGASGYVVKP 110

>pdb|3FFT|A Chain A, Crystal Structure Of Chey Double Mutant F14e, E89r Complexed With Bef3- And Mn2+ Length = 128

Iteration: 1
 Score = 62.0 bits (149), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 38/120 (31%), Positives = 57/120 (47%), Gaps = 12/120 (10%)
Query: 90  CSKELHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALK 148
             KEL  L VDD    R+++  LL ++    V   E G  AL  L    +    GF    
Sbjct: 1   ADKELKFLVVDDESTMRRIVRNLLKELGFNNVEEAEDGVDALNKL----QAGGYGF---- 52
Query: 149 VNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
              +I+D+ MP M G ELLK I+       +PV+++++      I +  + GA  Y+VKP
Sbjct: 53  ---VISDWNMPNMDGLELLKTIRADGAMSALPVLMVTARAKKENIIAAAQAGASGYVVKP 109

>pdb|1AB6|A Chain A, Structure Of Chey Mutant F14n, V86t Length = 125

Iteration: 1
 Score = 62.0 bits (149), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 38/117 (32%), Positives = 57/117 (48%), Gaps = 12/117 (10%)
Query: 93  ELHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNL 151
           EL  L VDD+   R+++  LL ++    V   E G  AL  L    +    GF       
Sbjct: 1   ELKFLVVDDNSTMRRIVRNLLKELGFNNVEEAEDGVDALNKL----QAGGYGF------- 49
Query: 152 IITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
           +I+D+ MP M G ELLK I+       +PV++ ++E     I +  + GA  Y+VKP
Sbjct: 50  VISDWNMPNMDGLELLKTIRADGAMSALPVLMTTAEAKKENIIAAAQAGASGYVVKP 106

>pdb|3OLV|A Chain A, Structural And Functional Effects Of Substitution At Position T+1 In Chey: Cheya88v-Bef3-Mg Complex Length = 129

Iteration: 1
 Score = 62.0 bits (149), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 39/120 (32%), Positives = 57/120 (47%), Gaps = 12/120 (10%)
Query: 90  CSKELHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALK 148
             KEL  L VDD    R+++  LL ++    V   E G  AL  L    +    GF    
Sbjct: 2   ADKELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKL----QAGGYGF---- 53
Query: 149 VNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
              +I+D+ MP M G ELLK I+       +PV++++ E     I +  + GA  Y+VKP
Sbjct: 54  ---VISDWNMPNMDGLELLKTIRADGAMSALPVLMVTVEAKKENIIAAAQAGASGYVVKP 110

>pdb|1VLZ|A Chain A, Uncoupled Phosphorylation And Activation In Bacterial Chemotaxis: The 2.1 Angstrom Structure Of A Threonine To Isoleucine Mutant At Position 87 Of Chey Length = 128

Iteration: 1
 Score = 62.0 bits (149), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 39/120 (32%), Positives = 57/120 (47%), Gaps = 12/120 (10%)
Query: 90  CSKELHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALK 148
             KEL  L VDD    R+++  LL ++    V   E G  AL  L    +    GF    
Sbjct: 1   ADKELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKL----QAGGYGF---- 52
Query: 149 VNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
              +I+D+ MP M G ELLK I+       +PV+++ +E     I +  + GA  Y+VKP
Sbjct: 53  ---VISDWNMPNMDGLELLKTIRADGAMSALPVLMVIAEAKKENIIAAAQAGASGYVVKP 109

>pdb|3FFX|A Chain A, Crystal Structure Of Chey Triple Mutant F14e, N59r, E89h Complexed With Bef3- And Mn2+ Length = 128

Iteration: 1
 Score = 61.6 bits (148), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 38/120 (31%), Positives = 57/120 (47%), Gaps = 12/120 (10%)
Query: 90  CSKELHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALK 148
             KEL  L VDD    R+++  LL ++    V   E G  AL  L    +    GF    
Sbjct: 1   ADKELKFLVVDDESTMRRIVRNLLKELGFNNVEEAEDGVDALNKL----QAGGYGF---- 52
Query: 149 VNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
              +I+D+ MP M G ELLK I+       +PV+++++      I +  + GA  Y+VKP
Sbjct: 53  ---VISDWRMPNMDGLELLKTIRADGAMSALPVLMVTAHAKKENIIAAAQAGASGYVVKP 109

>pdb|3FGZ|A Chain A, Crystal Structure Of Chey Triple Mutant F14e, N59m, E89r Complexed With Bef3- And Mn2+ Length = 128

Iteration: 1
 Score = 61.6 bits (148), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 38/120 (31%), Positives = 57/120 (47%), Gaps = 12/120 (10%)
Query: 90  CSKELHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALK 148
             KEL  L VDD    R+++  LL ++    V   E G  AL  L    +    GF    
Sbjct: 1   ADKELKFLVVDDESTMRRIVRNLLKELGFNNVEEAEDGVDALNKL----QAGGYGF---- 52
Query: 149 VNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
              +I+D+ MP M G ELLK I+       +PV+++++      I +  + GA  Y+VKP
Sbjct: 53  ---VISDWMMPNMDGLELLKTIRADGAMSALPVLMVTARAKKENIIAAAQAGASGYVVKP 109

>pdb|3M6M|D Chain D, Crystal Structure Of Rpff Complexed With Rec Domain Of Rpfc Length = 143

Iteration: 1
 Score = 61.6 bits (148), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 35/120 (29%), Positives = 64/120 (53%), Gaps = 13/120 (10%)
Query: 92  KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNL 151
           + + +L  DD   +R +++RLL+ +  KV  V    + L  +      +   +DA     
Sbjct: 13  RSMRMLVADDHEANRMVLQRLLEKAGHKVLCVNGAEQVLDAM------AEEDYDA----- 61
Query: 152 IITDYTMPGMTGYELLKKIK--ESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPV 209
           +I D  MPGM G ++LK+++  ++S  R  PVV++S++     I +C + GA  ++ KPV
Sbjct: 62  VIVDLHMPGMNGLDMLKQLRVMQASGMRYTPVVVLSADVTPEAIRACEQAGARAFLAKPV 121

>pdb|3RVJ|A Chain A, Structure Of The Chey-Bef3 Complex With Substitutions At 59 And 89: N59d And E89q Length = 132

Iteration: 1
 Score = 61.6 bits (148), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 38/120 (31%), Positives = 58/120 (48%), Gaps = 12/120 (10%)
Query: 90  CSKELHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALK 148
             KEL  L VDD    R+++  LL ++    V   E G  AL  L    +    GF    
Sbjct: 5   ADKELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKL----QAGGYGF---- 56
Query: 149 VNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
              +I+D+ MP M G ELLK I+       +PV++++++     I +  + GA  Y+VKP
Sbjct: 57  ---VISDWDMPNMDGLELLKTIRADGAMSALPVLMVTAQAKKENIIAAAQAGASGYVVKP 113

>pdb|1AB5|A Chain A, Structure Of Chey Mutant F14n, V21t Length = 125

Iteration: 1
 Score = 61.2 bits (147), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 38/117 (32%), Positives = 57/117 (48%), Gaps = 12/117 (10%)
Query: 93  ELHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNL 151
           EL  L VDD+   R++   LL ++    V   E G  AL  L    +    GF       
Sbjct: 1   ELKFLVVDDNSTMRRITRNLLKELGFNNVEEAEDGVDALNKL----QAGGYGF------- 49
Query: 152 IITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
           +I+D+ MP M G ELLK I+       +PV+++++E     I +  + GA  Y+VKP
Sbjct: 50  VISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKP 106

>pdb|3RVP|A Chain A, Structure Of The Chey-Bef3 Complex With Substitutions At 59 And 89: N59d And E89k Length = 132

Iteration: 1
 Score = 60.8 bits (146), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 38/120 (31%), Positives = 58/120 (48%), Gaps = 12/120 (10%)
Query: 90  CSKELHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALK 148
             KEL  L VDD    R+++  LL ++    V   E G  AL  L    +    GF    
Sbjct: 5   ADKELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKL----QAGGYGF---- 56
Query: 149 VNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
              +I+D+ MP M G ELLK I+       +PV++++++     I +  + GA  Y+VKP
Sbjct: 57  ---VISDWDMPNMDGLELLKTIRADGAMSALPVLMVTAKAKKENIIAAAQAGASGYVVKP 113

>pdb|6CHY|A Chain A, Structure Of Chemotaxis Protein Chey Length = 128

Iteration: 1
 Score = 60.8 bits (146), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 38/120 (31%), Positives = 57/120 (47%), Gaps = 12/120 (10%)
Query: 90  CSKELHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALK 148
             KEL  L VDD    R+++  LL ++    V   E G  AL  L    +    GF    
Sbjct: 1   ADKELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKL----QAGGYGF---- 52
Query: 149 VNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
              +I+D+ MP M G ELLK I+       +PV+++ +E     I +  + GA  ++VKP
Sbjct: 53  ---VISDWNMPNMDGLELLKTIRADGAMSALPVLMVIAEAKKENIIAAAQAGASGWVVKP 109

>pdb|3RVL|A Chain A, Structure Of The Chey-Bef3 Complex With Substitutions At 59 And 89: N59d And E89r Length = 132

Iteration: 1
 Score = 60.8 bits (146), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 38/120 (31%), Positives = 57/120 (47%), Gaps = 12/120 (10%)
Query: 90  CSKELHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALK 148
             KEL  L VDD    R+++  LL ++    V   E G  AL  L    +    GF    
Sbjct: 5   ADKELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKL----QAGGYGF---- 56
Query: 149 VNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
              +I+D+ MP M G ELLK I+       +PV+++++      I +  + GA  Y+VKP
Sbjct: 57  ---VISDWDMPNMDGLELLKTIRADGAMSALPVLMVTARAKKENIIAAAQAGASGYVVKP 113

>pdb|3FFW|A Chain A, Crystal Structure Of Chey Triple Mutant F14q, N59k, E89y Complexed With Bef3- And Mn2+ Length = 128

Iteration: 1
 Score = 60.8 bits (146), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 38/120 (31%), Positives = 57/120 (47%), Gaps = 12/120 (10%)
Query: 90  CSKELHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALK 148
             KEL  L VDD    R+++  LL ++    V   E G  AL  L    +    GF    
Sbjct: 1   ADKELKFLVVDDQSTMRRIVRNLLKELGFNNVEEAEDGVDALNKL----QAGGYGF---- 52
Query: 149 VNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
              +I+D+ MP M G ELLK I+       +PV+++++      I +  + GA  Y+VKP
Sbjct: 53  ---VISDWKMPNMDGLELLKTIRADGAMSALPVLMVTAYAKKENIIAAAQAGASGYVVKP 109

>pdb|1EHC|A Chain A, Structure Of Signal Transduction Protein Chey Length = 128

Iteration: 1
 Score = 60.5 bits (145), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 38/120 (31%), Positives = 57/120 (47%), Gaps = 12/120 (10%)
Query: 90  CSKELHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALK 148
             KEL  L VD     R+++  LL ++    V   E G  AL  L    +    GF    
Sbjct: 1   ADKELKFLVVDKFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKL----QAGGYGF---- 52
Query: 149 VNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
              +I+D+ MP M G ELLK I+       +PV+++++E     I +  + GA  Y+VKP
Sbjct: 53  ---VISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKP 109

>pdb|3F7N|A Chain A, Crystal Structure Of Chey Triple Mutant F14e, N59m, E89l Complexed With Bef3- And Mn2+ Length = 128

Iteration: 1
 Score = 60.5 bits (145), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 38/120 (31%), Positives = 57/120 (47%), Gaps = 12/120 (10%)
Query: 90  CSKELHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALK 148
             KEL  L VDD    R+++  LL ++    V   E G  AL  L    +    GF    
Sbjct: 1   ADKELKFLVVDDESTMRRIVRNLLKELGFNNVEEAEDGVDALNKL----QAGGYGF---- 52
Query: 149 VNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
              +I+D+ MP M G ELLK I+       +PV+++++      I +  + GA  Y+VKP
Sbjct: 53  ---VISDWMMPNMDGLELLKTIRADGAMSALPVLMVTALAKKENIIAAAQAGASGYVVKP 109

>pdb|1ZDM|A Chain A, Crystal Structure Of Activated Chey Bound To Xe Length = 129

Iteration: 1
 Score = 60.5 bits (145), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 38/120 (31%), Positives = 57/120 (47%), Gaps = 12/120 (10%)
Query: 90  CSKELHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALK 148
             KEL  L VDD    R+++  LL ++    V   E G  AL  L    +    GF    
Sbjct: 2   ADKELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKL----QAGGYGF---- 53
Query: 149 VNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
              +I+ + MP M G ELLK I+       +PV+++++E     I +  + GA  Y+VKP
Sbjct: 54  ---VISXWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKP 110

>pdb|1C4W|A Chain A, 1.9 A Structure Of A-Thiophosphonate Modified Chey D57c Length = 128

Iteration: 1
 Score = 60.5 bits (145), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 38/120 (31%), Positives = 57/120 (47%), Gaps = 12/120 (10%)
Query: 90  CSKELHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALK 148
             KEL  L VDD    R+++  LL ++    V   E G  AL  L    +    GF    
Sbjct: 1   ADKELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKL----QAGGYGF---- 52
Query: 149 VNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
              +I+ + MP M G ELLK I+       +PV+++++E     I +  + GA  Y+VKP
Sbjct: 53  ---VISXWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKP 109

>pdb|1E6K|A Chain A, Two-Component Signal Transduction System D12a Mutant Of Chey Length = 130

Iteration: 1
 Score = 59.7 bits (143), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 38/120 (31%), Positives = 57/120 (47%), Gaps = 12/120 (10%)
Query: 90  CSKELHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALK 148
             KEL  L V D    R+++  LL ++    V   E G  AL  L    +    GF    
Sbjct: 3   SDKELKFLVVADFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKL----QAGGYGF---- 54
Query: 149 VNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
              +I+D+ MP M G ELLK I+       +PV+++++E     I +  + GA  Y+VKP
Sbjct: 55  ---VISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKP 111

>pdb|3RVN|A Chain A, Structure Of The Chey-Bef3 Complex With Substitutions At 59 And 89: N59d And E89y Length = 132

Iteration: 1
 Score = 59.7 bits (143), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 38/120 (31%), Positives = 57/120 (47%), Gaps = 12/120 (10%)
Query: 90  CSKELHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALK 148
             KEL  L VDD    R+++  LL ++    V   E G  AL  L    +    GF    
Sbjct: 5   ADKELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKL----QAGGYGF---- 56
Query: 149 VNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
              +I+D+ MP M G ELLK I+       +PV+++++      I +  + GA  Y+VKP
Sbjct: 57  ---VISDWDMPNMDGLELLKTIRADGAMSALPVLMVTAYAKKENIIAAAQAGASGYVVKP 113

>pdb|1E6M|A Chain A, Two-Component Signal Transduction System D57a Mutant Of Chey Length = 128

Iteration: 1
 Score = 59.7 bits (143), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 38/120 (31%), Positives = 57/120 (47%), Gaps = 12/120 (10%)
Query: 90  CSKELHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALK 148
             KEL  L VDD    R+++  LL ++    V   E G  AL  L    +    GF    
Sbjct: 1   SDKELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKL----QAGGYGF---- 52
Query: 149 VNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
              +I+ + MP M G ELLK I+       +PV+++++E     I +  + GA  Y+VKP
Sbjct: 53  ---VISAWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKP 109

>pdb|1E6L|A Chain A, Two-Component Signal Transduction System D13a Mutant Of Chey Length = 127

Iteration: 1
 Score = 59.7 bits (143), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 38/118 (32%), Positives = 57/118 (48%), Gaps = 12/118 (10%)
Query: 92  KELHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVN 150
           KEL  L VD     R+++  LL ++    V   E G  AL  L    +    GF      
Sbjct: 2   KELKFLVVDAFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKL----QAGGYGF------ 51
Query: 151 LIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
            +I+D+ MP M G ELLK I+       +PV+++++E     I +  + GA  Y+VKP
Sbjct: 52  -VISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKP 108

>pdb|3TO5|A Chain A, High Resolution Structure Of Chey3 From Vibrio Cholerae Length = 134

Iteration: 1
 Score = 59.7 bits (143), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 36/122 (29%), Positives = 62/122 (50%), Gaps = 12/122 (9%)
Query: 88  AECSKELHVLAVDDSYVDRKLIERLLQ-ISSCKVTAVESGTRALQYLGLDGEQSNVGFDA 146
           A  +K + +L VDD    R++++ LL+ +        + G  AL  L    ++ +  F  
Sbjct: 7   AILNKNMKILIVDDFSTMRRIVKNLLRDLGFNNTQEADDGLTALPML----KKGDFDF-- 60
Query: 147 LKVNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIV 206
                ++TD+ MPGM G +LLK I+     + +PV+++++E    QI    + G   YIV
Sbjct: 61  -----VVTDWNMPGMQGIDLLKNIRADEELKHLPVLMITAEAKREQIIEAAQAGVNGYIV 115
Query: 207 KP 208
           KP
Sbjct: 116 KP 117

>pdb|2ID7|A Chain A, 1.75 A Structure Of T87i Phosphono-Chey Length = 128

Iteration: 1
 Score = 58.5 bits (140), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 38/120 (31%), Positives = 56/120 (46%), Gaps = 12/120 (10%)
Query: 90  CSKELHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALK 148
             KEL  L VDD    R+++  LL ++    V   E G  AL  L    +    GF    
Sbjct: 1   ADKELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKL----QAGGYGF---- 52
Query: 149 VNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
              +I+ + MP M G ELLK I+       +PV+++ +E     I +  + GA  Y+VKP
Sbjct: 53  ---VISXWNMPNMDGLELLKTIRADGAMSALPVLMVIAEAKKENIIAAAQAGASGYVVKP 109

>pdb|2ID9|A Chain A, 1.85 A Structure Of T87iY106W PHOSPHONO-Chey Length = 128

Iteration: 1
 Score = 57.8 bits (138), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 37/120 (30%), Positives = 56/120 (46%), Gaps = 12/120 (10%)
Query: 90  CSKELHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALK 148
             KEL  L VDD    R+++  LL ++    V   E G  AL  L    +    GF    
Sbjct: 1   ADKELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKL----QAGGYGF---- 52
Query: 149 VNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
              +I+ + MP M G ELLK I+       +PV+++ +E     I +  + GA  ++VKP
Sbjct: 53  ---VISXWNMPNMDGLELLKTIRADGAMSALPVLMVIAEAKKENIIAAAQAGASGWVVKP 109

>pdb|1K66|A Chain A, Crystal Structure Of The Cyanobacterial Phytochrome Response Regulator, Rcpb Length = 149

Iteration: 1
 Score = 57.8 bits (138), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 38/119 (31%), Positives = 62/119 (52%), Gaps = 3/119 (2%)
Query: 96  VLAVDDSYVDRKLIERLLQISSC--KVTAVESGTRALQYLGLDGEQSNVGFDALKVNLII 153
           +L V+DS  D    +RLLQ       +    +G +AL +L   G   N    A +  +I+
Sbjct: 9   LLVVEDSDEDFSTFQRLLQREGVVNPIYRCITGDQALDFLYQTGSYCNPDI-APRPAVIL 67
Query: 154 TDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS 212
            D  +PG  G E+L++IK+  V +++PVVIM++      I+ C       YIVKP+++ 
Sbjct: 68  LDLNLPGTDGREVLQEIKQDEVLKKIPVVIMTTSSNPKDIEICYSYSISSYIVKPLEID 126

>pdb|1HEY|A Chain A, Investigating The Structural Determinants Of The P21-Like Triphosphate And Mg2+ Binding Site Length = 128

Iteration: 1
 Score = 57.8 bits (138), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 36/120 (30%), Positives = 55/120 (45%), Gaps = 12/120 (10%)
Query: 90  CSKELHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALK 148
             KEL  L V +    +  +  LL ++    V   E G  AL  L    +    GF    
Sbjct: 1   ADKELKFLVVGNGGTGKSTVRNLLKELGFNNVEDAEDGVDALNKL----QAGGYGF---- 52
Query: 149 VNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
              +I+D+ MP M G ELLK I+       +PV+++++E     I +  + GA  Y+VKP
Sbjct: 53  ---VISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKP 109

>pdb|3F7A|A Chain A, Structure Of Orthorhombic Crystal Form Of Pseudomonas Aeruginosa Rssb Length = 394

Iteration: 1
 Score = 53.9 bits (128), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 31/115 (26%), Positives = 63/115 (54%), Gaps = 13/115 (11%)
Query: 96  VLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITD 155
           +L +DD  V R+ +   L+ S+ KV    +G + LQ            F++ + +L+I D
Sbjct: 8   LLIIDDDEVVRESLAAYLEDSNFKVLQALNGLQGLQI-----------FESEQPDLVICD 56
Query: 156 YTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVK 210
              P + G EL+++I++++   E P++++S   V++     L  GA +Y++KP++
Sbjct: 57  LRXPQIDGLELIRRIRQTA--SETPIIVLSGAGVMSDAVEALRLGAADYLIKPLE 109

>pdb|1U8T|A Chain A, Crystal Structure Of Chey D13k Y106w Alone And In Complex With A Flim Peptide Length = 128

Iteration: 1
 Score = 53.5 bits (127), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 35/120 (29%), Positives = 54/120 (45%), Gaps = 12/120 (10%)
Query: 90  CSKELHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALK 148
             KEL  L VD     R+++  LL ++    V   E G  AL  L    +    GF    
Sbjct: 1   ADKELKFLVVDKFSTXRRIVRNLLKELGFNNVEEAEDGVDALNKL----QAGGYGF---- 52
Query: 149 VNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
              +I+D+  P   G ELLK I+       +PV+ +++E     I +  + GA  ++VKP
Sbjct: 53  ---VISDWNXPNXDGLELLKTIRADGAXSALPVLXVTAEAKKENIIAAAQAGASGWVVKP 109

>pdb|3EQ2|A Chain A, Structure Of Hexagonal Crystal Form Of Pseudomonas Aeruginosa Rssb Length = 394

Iteration: 1
 Score = 52.8 bits (125), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 31/115 (26%), Positives = 62/115 (53%), Gaps = 13/115 (11%)
Query: 96  VLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITD 155
           +L +DD  V R+ +   L+ S+ KV    +G + LQ            F++ + +L+I D
Sbjct: 8   LLIIDDDEVVRESLAAYLEDSNFKVLQALNGLQGLQI-----------FESEQPDLVICD 56
Query: 156 YTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVK 210
              P + G EL+++I++++   E P++++S   V +     L  GA +Y++KP++
Sbjct: 57  LRXPQIDGLELIRRIRQTA--SETPIIVLSGAGVXSDAVEALRLGAADYLIKPLE 109

>pdb|1DC7|A Chain A, Structure Of A Transiently Phosphorylated "switch" In Bacterial Signal Transduction Length = 124

Iteration: 1
 Score = 52.0 bits (123), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 35/118 (29%), Positives = 57/118 (48%), Gaps = 13/118 (11%)
Query: 96  VLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITD 155
           V  VDD    R ++ER L  +    T  E+G   L  L            +   +++++D
Sbjct: 6   VWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLAALA-----------SKTPDVLLSD 54
Query: 156 YTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD 213
             MPGM G  LLK+IK+      +PV+IM++   L    S  ++GA +Y+ KP  + +
Sbjct: 55  IRMPGMDGLALLKQIKQRHPM--LPVIIMTAHSDLDAAVSAYQQGAFDYLPKPFDIDE 110

>pdb|1J56|A Chain A, Minimized Average Structure Of Beryllofluoride-Activated Ntrc Receiver Domain: Model Structure Incorporating Active Site Contacts Length = 124

Iteration: 1
 Score = 52.0 bits (123), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 35/118 (29%), Positives = 57/118 (48%), Gaps = 13/118 (11%)
Query: 96  VLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITD 155
           V  VDD    R ++ER L  +    T  E+G   L  L            +   +++++D
Sbjct: 6   VWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLAALA-----------SKTPDVLLSD 54
Query: 156 YTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD 213
             MPGM G  LLK+IK+      +PV+IM++   L    S  ++GA +Y+ KP  + +
Sbjct: 55  IRMPGMDGLALLKQIKQRHPM--LPVIIMTAHSDLDAAVSAYQQGAFDYLPKPFDIDE 110

>pdb|2AYX|A Chain A, Solution Structure Of The E.Coli Rcsc C-Terminus (Residues 700-949) Containing Linker Region And Phosphoreceiver Domain Length = 254

Iteration: 1
 Score = 52.0 bits (123), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 40/180 (22%), Positives = 80/180 (44%), Gaps = 29/180 (16%)
Query: 40  GAPTQRFP--FAYSLTQTHNILTKTHQRLVKEKKFKETNRGFPFWAMATVAECSKELHVL 97
           G P ++ P  + +S+   H +     +  + E +  +     P  +       + ++ +L
Sbjct: 76  GIPLEKAPGEWVHSVAAPHELPALLARIYLIEMESDDPANALP--STDKAVSDNDDMMIL 133
Query: 98  AVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKV------NL 151
            VDD  ++R+L+                    L  LG   + +N G DAL V      ++
Sbjct: 134 VVDDHPINRRLL-----------------ADQLGSLGYQCKTANDGVDALNVLSKNHIDI 176
Query: 152 IITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKL 211
           +++D  MP M GY L ++I++  +   +PV+ +++  +  +   CLE G +  + KPV L
Sbjct: 177 VLSDVNMPNMDGYRLTQRIRQLGL--TLPVIGVTANALAEEKQRCLESGMDSCLSKPVTL 234

>pdb|1KRW|A Chain A, Solution Structure And Backbone Dynamics Of Beryllofluoride- Activated Ntrc Receiver Domain Length = 124

Iteration: 1
 Score = 51.6 bits (122), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 35/118 (29%), Positives = 57/118 (48%), Gaps = 13/118 (11%)
Query: 96  VLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITD 155
           V  VDD    R ++ER L  +    T  E+G   L  L            +   +++++D
Sbjct: 6   VWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLAALA-----------SKTPDVLLSD 54
Query: 156 YTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD 213
             MPGM G  LLK+IK+      +PV+IM++   L    S  ++GA +Y+ KP  + +
Sbjct: 55  IRMPGMDGLALLKQIKQRHPM--LPVIIMTAHSDLDAAVSAYQQGAFDYLPKPFDIDE 110

>pdb|2WB4|A Chain A, Activated Diguanylate Cyclase Pled In Complex With C-Di-Gmp Length = 459

Iteration: 1
 Score = 51.6 bits (122), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 32/114 (28%), Positives = 55/114 (48%), Gaps = 11/114 (9%)
Query: 96  VLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITD 155
           +L VDD   + +L+E  L     +V+    G  AL     D             ++I+ D
Sbjct: 5   ILVVDDIEANVRLLEAKLTAEYYEVSTAMDGPTALAMAARD-----------LPDIILLD 53
Query: 156 YTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPV 209
             MPGM G+ + +K+K+    R +PVV++++ D        LE GA +++ KP+
Sbjct: 54  VMMPGMDGFTVCRKLKDDPTTRHIPVVLITALDGRGDRIQGLESGASDFLTKPI 107

>pdb|1W25|A Chain A, Response Regulator Pled In Complex With C-digmp Length = 459

Iteration: 1
 Score = 51.6 bits (122), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 32/115 (27%), Positives = 55/115 (47%), Gaps = 11/115 (9%)
Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
            +L VDD   + +L+E  L     +V+    G  AL     D             ++I+ 
Sbjct: 3   RILVVDDIEANVRLLEAKLTAEYYEVSTAMDGPTALAMAARD-----------LPDIILL 51
Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPV 209
           D  MPGM G+ + +K+K+    R +PVV++++ D        LE GA +++ KP+
Sbjct: 52  DVMMPGMDGFTVCRKLKDDPTTRHIPVVLITALDGRGDRIQGLESGASDFLTKPI 106

>pdb|3GT7|A Chain A, Crystal Structure Of Signal Receiver Domain Of Signal Transduction Histidine Kinase From Syntrophus Aciditrophicus Length = 154

Iteration: 1
 Score = 50.8 bits (120), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 32/115 (27%), Positives = 59/115 (51%), Gaps = 11/115 (9%)
Query: 96  VLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITD 155
           +L V+DS    + ++ +L+ +  +   V +G  A+++L L            + +LII+D
Sbjct: 10  ILIVEDSPTQAEHLKHILEETGYQTEHVRNGREAVRFLSLT-----------RPDLIISD 58
Query: 156 YTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVK 210
             MP M GY L + +K     R +PV++++       +   LE GA+++I KP K
Sbjct: 59  VLMPEMDGYALCRWLKGQPDLRTIPVILLTILSDPRDVVRSLECGADDFITKPCK 113

>pdb|3DGE|C Chain C, Structure Of A Histidine Kinase-response Regulator Complex Reveals Insights Into Two-component Signaling And A Novel Cis- Autophosphorylation Mechanism Length = 122

Iteration: 1
 Score = 50.4 bits (119), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 34/113 (30%), Positives = 57/113 (50%), Gaps = 11/113 (9%)
Query: 96  VLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITD 155
           VL VDDS V RK++   L+    +V   E+G  AL+ L                +LI+ D
Sbjct: 5   VLLVDDSAVLRKIVSFNLKKEGYEVIEAENGQIALEKLS-----------EFTPDLIVLD 53
Query: 156 YTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
             MP M G+ +LKK++E   ++ +PV++++++         L  GA + + KP
Sbjct: 54  IMMPVMDGFTVLKKLQEKEEWKRIPVIVLTAKGGEEDESLALSLGARKVMRKP 106

>pdb|2AYZ|A Chain A, Solution Structure Of The E.Coli Rcsc C-Terminus (Residues 817-949) Containing Phosphoreceiver Domain Length = 133

Iteration: 1
 Score = 50.4 bits (119), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 33/128 (25%), Positives = 62/128 (48%), Gaps = 25/128 (19%)
Query: 91  SKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKV- 149
           + ++ +L VDD  ++R+L+                    L  LG   + +N G DAL V 
Sbjct: 6   NDDMMILVVDDHPINRRLL-----------------ADQLGSLGYQCKTANDGVDALNVL 48
Query: 150 -----NLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEY 204
                +++++D  MP M GY L ++I++  +   +PV+ +++  +  +   CLE G +  
Sbjct: 49  SKNHIDIVLSDVNMPNMDGYRLTQRIRQLGL--TLPVIGVTANALAEEKQRCLESGMDSC 106
Query: 205 IVKPVKLS 212
           + KPV L 
Sbjct: 107 LSKPVTLD 114

>pdb|3EOD|A Chain A, Crystal Structure Of N-Terminal Domain Of E. Coli Rssb Length = 130

Iteration: 1
 Score = 50.4 bits (119), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 34/116 (29%), Positives = 54/116 (46%), Gaps = 13/116 (11%)
Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
            +L V+D  V R L++               G  AL+ LG        GF     +L+I 
Sbjct: 9   QILIVEDEQVFRSLLDSWFSSLGATTVLAADGVDALELLG--------GFTP---DLMIC 57
Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVK 210
           D  MP M G +LL+ I+      + PV+++S+ + +  I   L  G E+ ++KPVK
Sbjct: 58  DIAMPRMNGLKLLEHIRNRG--DQTPVLVISATENMADIAKALRLGVEDVLLKPVK 111

>pdb|1JLK|A Chain A, Crystal Structure Of The Mn(2+)-Bound Form Of Response Regulator Rcp1 Length = 147

Iteration: 1
 Score = 50.1 bits (118), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 32/120 (26%), Positives = 62/120 (51%), Gaps = 6/120 (5%)
Query: 96  VLAVDDSYVDRKLIERLLQISSC--KVTAVESGTRALQYLGLDGEQSNVGFDALKVNLII 153
           +L V+DS  D +L++ +L+ S+   ++  +  G  A+ +L   GE  N    + + NLI+
Sbjct: 11  ILLVEDSKADSRLVQEVLKTSTIDHELIILRDGLAAMAFLQQQGEYEN----SPRPNLIL 66
Query: 154 TDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD 213
            D  +P   G E+L +IK++   + +PVV++++      + +  E     Y+ K   L D
Sbjct: 67  LDLNLPKKDGREVLAEIKQNPDLKRIPVVVLTTSHNEDDVIASYELHVNCYLTKSRNLKD 126

>pdb|1I3C|A Chain A, Response Regulator For Cyanobacterial Phytochrome, Rcp1 Length = 149

Iteration: 1
 Score = 49.3 bits (116), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 32/120 (26%), Positives = 61/120 (50%), Gaps = 6/120 (5%)
Query: 96  VLAVDDSYVDRKLIERLLQISSC--KVTAVESGTRALQYLGLDGEQSNVGFDALKVNLII 153
           +L V+DS  D +L++ +L+ S+   ++  +  G  A  +L   GE  N    + + NLI+
Sbjct: 11  ILLVEDSKADSRLVQEVLKTSTIDHELIILRDGLAAXAFLQQQGEYEN----SPRPNLIL 66
Query: 154 TDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD 213
            D  +P   G E+L +IK++   + +PVV++++      + +  E     Y+ K   L D
Sbjct: 67  LDLNLPKKDGREVLAEIKQNPDLKRIPVVVLTTSHNEDDVIASYELHVNCYLTKSRNLKD 126

>pdb|1DC8|A Chain A, Structure Of A Transiently Phosphorylated "switch" In Bacterial Signal Transduction Length = 124

Iteration: 1
 Score = 48.9 bits (115), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 34/118 (28%), Positives = 56/118 (47%), Gaps = 13/118 (11%)
Query: 96  VLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITD 155
           V  VDD    R ++ER L  +    T  E+G   L  L            +   +++++ 
Sbjct: 6   VWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLAALA-----------SKTPDVLLSX 54
Query: 156 YTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD 213
             MPGM G  LLK+IK+      +PV+IM++   L    S  ++GA +Y+ KP  + +
Sbjct: 55  IRMPGMDGLALLKQIKQRHPM--LPVIIMTAHSDLDAAVSAYQQGAFDYLPKPFDIDE 110

>pdb|1ZES|A Chain A, Bef3- Activated Phob Receiver Domain Length = 125

Iteration: 1
 Score = 48.9 bits (115), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 21/59 (35%), Positives = 38/59 (64%)
Query: 150 NLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
           +LI+ D+ +PG +G + +K +K  S+ R++PVV++++          LE GA++YI KP
Sbjct: 48  DLILLDWMLPGGSGIQFIKHLKRESMTRDIPVVMLTARGEEEDRVRGLETGADDYITKP 106

>pdb|1B00|A Chain A, Phob Receiver Domain From Escherichia Coli Length = 127

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 21/59 (35%), Positives = 38/59 (64%)
Query: 150 NLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
           +LI+ D+ +PG +G + +K +K  S+ R++PVV++++          LE GA++YI KP
Sbjct: 48  DLILLDWMLPGGSGIQFIKHLKRESMTRDIPVVMLTARGEEEDRVRGLETGADDYITKP 106

>pdb|3JTE|A Chain A, Crystal Structure Of Response Regulator Receiver Domain Protein From Clostridium Thermocellum Length = 143

Iteration: 1
 Score = 47.8 bits (112), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 34/118 (28%), Positives = 60/118 (50%), Gaps = 11/118 (9%)
Query: 96  VLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITD 155
           +L +DD     + I+ LL+I   +V    S T  L+      E  N       ++++ITD
Sbjct: 6   ILVIDDESTILQNIKFLLEIDGNEVLTASSSTEGLRIFT---ENCN------SIDVVITD 56
Query: 156 YTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD 213
             MP ++G ++L++IK+  +   + V+I++    L      ++EGA EY+ KPV   D
Sbjct: 57  MKMPKLSGMDILREIKK--ITPHMAVIILTGHGDLDNAILAMKEGAFEYLRKPVTAQD 112

>pdb|1L5Y|A Chain A, Crystal Structure Of Mg2+ / Bef3-bound Receiver Domain Of Sinorhizobium Meliloti Dctd Length = 155

Iteration: 1
 Score = 47.8 bits (112), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 29/113 (25%), Positives = 57/113 (50%), Gaps = 13/113 (11%)
Query: 96  VLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITD 155
           V  +DD    RK +++ L+++   V++  S T AL            G  A    ++I+D
Sbjct: 6   VFLIDDDRDLRKAMQQTLELAGFTVSSFASATEAL-----------AGLSADFAGIVISD 54
Query: 156 YTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
             MPGM G  L +KI   ++  ++P+++++    +      +++GA ++I KP
Sbjct: 55  IRMPGMDGLALFRKIL--ALDPDLPMILVTGHGDIPMAVQAIQDGAYDFIAKP 105

>pdb|1QKK|A Chain A, Crystal Structure Of The Receiver Domain And Linker Region Of Dctd From Sinorhizobium Meliloti Length = 155

Iteration: 1
 Score = 47.8 bits (112), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 29/113 (25%), Positives = 57/113 (50%), Gaps = 13/113 (11%)
Query: 96  VLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITD 155
           V  +DD    RK +++ L+++   V++  S T AL            G  A    ++I+D
Sbjct: 6   VFLIDDDRDLRKAMQQTLELAGFTVSSFASATEAL-----------AGLSADFAGIVISD 54
Query: 156 YTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
             MPGM G  L +KI   ++  ++P+++++    +      +++GA ++I KP
Sbjct: 55  IRMPGMDGLALFRKIL--ALDPDLPMILVTGHGDIPMAVQAIQDGAYDFIAKP 105

>pdb|3GL9|A Chain A, The Structure Of A Histidine Kinase-Response Regulator Complex Sheds Light Into Two-Component Signaling And Reveals A Novel Cis Autophosphorylation Mechanism Length = 122

Iteration: 1
 Score = 47.4 bits (111), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 33/113 (29%), Positives = 56/113 (49%), Gaps = 11/113 (9%)
Query: 96  VLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITD 155
           VL VDDS V RK++   L+    +V   E+G  AL+ L                +LI+  
Sbjct: 5   VLLVDDSAVLRKIVSFNLKKEGYEVIEAENGQIALEKLS-----------EFTPDLIVLX 53
Query: 156 YTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
             MP M G+ +LKK++E   ++ +PV++++++         L  GA + + KP
Sbjct: 54  IMMPVMDGFTVLKKLQEKEEWKRIPVIVLTAKGGEEDESLALSLGARKVMRKP 106

>pdb|3T6K|A Chain A, Crystal Structure Of A Hypothetical Response Regulator (Caur_3799) From Chloroflexus Aurantiacus J-10-Fl At 1.86 A Resolution Length = 136

Iteration: 1
 Score = 47.0 bits (110), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 31/113 (27%), Positives = 60/113 (53%), Gaps = 11/113 (9%)
Query: 96  VLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITD 155
           +L VDD     + +E +L+ +  +V    SG  ALQ +       N+  DAL     I D
Sbjct: 7   LLIVDDDDTVAEXLELVLRGAGYEVRRAASGEEALQQI-----YKNLP-DAL-----ICD 55
Query: 156 YTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
             +PG+ GY L K++++  + + +P++ ++++  ++   +  E GA +Y+ KP
Sbjct: 56  VLLPGIDGYTLCKRVRQHPLTKTLPILXLTAQGDISAKIAGFEAGANDYLAKP 108

>pdb|2JB9|A Chain A, Phob Response Regulator Receiver Domain Constitutively- Active Double Mutant D10a And D53e. Length = 127

Iteration: 1
 Score = 46.6 bits (109), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 20/59 (33%), Positives = 38/59 (64%)
Query: 150 NLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
           +LI+ ++ +PG +G + +K +K  S+ R++PVV++++          LE GA++YI KP
Sbjct: 48  DLILLEWMLPGGSGIQFIKHLKRESMTRDIPVVMLTARGEEEDRVRGLETGADDYITKP 106

>pdb|2OQR|A Chain A, The Structure Of The Response Regulator Regx3 From Mycobacterium Tuberculosis Length = 230

Iteration: 1
 Score = 46.6 bits (109), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 46/75 (61%), Gaps = 7/75 (9%)
Query: 136 DGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDS 195
           DG  +   FD    ++++ D  +PGM+G ++ K+++  S    VPV+++++ D  ++ID 
Sbjct: 36  DGPAALAEFDRAGADIVLLDLMLPGMSGTDVCKQLRARS---SVPVIMVTARD--SEIDK 90
Query: 196 C--LEEGAEEYIVKP 208
              LE GA++Y+ KP
Sbjct: 91  VVGLELGADDYVTKP 105

>pdb|3NHZ|A Chain A, Structure Of N-Terminal Domain Of Mtra Length = 125

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 23/75 (30%), Positives = 44/75 (58%), Gaps = 3/75 (4%)
Query: 136 DGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDS 195
           DG Q+      L+ +L++ D  +PGM G ++ + ++  S    VP+V+++++     +  
Sbjct: 37  DGTQALTAVRELRPDLVLLDLMLPGMNGIDVCRVLRADS---GVPIVMLTAKTDTVDVVL 93
Query: 196 CLEEGAEEYIVKPVK 210
            LE GA++YI+KP K
Sbjct: 94  GLESGADDYIMKPFK 108

>pdb|3MM4|A Chain A, Crystal Structure Of The Receiver Domain Of The Histidine Kinase Cki1 From Arabidopsis Thaliana Length = 206

Iteration: 1
 Score = 45.8 bits (107), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 31/99 (31%), Positives = 50/99 (50%), Gaps = 5/99 (5%)
Query: 95  HVLAVDDSYVDRKL-IERLLQISSCKVTAVESGTRALQYL--GLDGEQSNVGFDALKVNL 151
            VL VDD+++ RK+   +L ++   +V   +SG  AL+ +  GL   +     D L  + 
Sbjct: 63  RVLVVDDNFISRKVATGKLKKMGVSEVEQCDSGKEALRLVTEGLTQREEQGSVDKLPFDY 122
Query: 152 IITDYTMPGMTGYELLKKIK--ESSVFREVPVVIMSSED 188
           I  D  MP M GYE  ++I+  E S     P++ +S  D
Sbjct: 123 IFMDCQMPEMDGYEATREIRKVEKSYGVRTPIIAVSGHD 161

>pdb|1P6U|A Chain A, Nmr Structure Of The Bef3-Activated Structure Of The Response Regulator Chey2-Mg2+ From Sinorhizobium Meliloti Length = 129

Iteration: 1
 Score = 43.9 bits (102), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 26/120 (21%), Positives = 57/120 (47%), Gaps = 12/120 (10%)
Query: 90  CSKELHVLAVDDSYVDRKLI-ERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALK 148
            ++++ VL VDD    R L+ + L Q+   ++TA   G + ++ +  +            
Sbjct: 3   LAEKIKVLIVDDQVTSRLLLGDALQQLGFKQITAAGDGEQGMKIMAQNPH---------- 52
Query: 149 VNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
            +L+I+D+ MP M G  LL+ ++ +   ++   +I++++     +      GA   + KP
Sbjct: 53  -HLVISDFNMPKMDGLGLLQAVRANPATKKAAFIILTAQGDRALVQKAAALGANNVLAKP 111

>pdb|3BRE|A Chain A, Crystal Structure Of P.Aeruginosa Pa3702 Length = 358

Iteration: 1
 Score = 43.5 bits (101), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 20/72 (27%), Positives = 41/72 (56%)
Query: 136 DGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDS 195
           D +Q+    + +K  +I+ D  MPG+ G  LL   + +   R++P++++S+++  T   +
Sbjct: 51  DPQQAVAVANQIKPTVILQDLVMPGVDGLTLLAAYRGNPATRDIPIIVLSTKEEPTVKSA 110
Query: 196 CLEEGAEEYIVK 207
               GA +Y+VK
Sbjct: 111 AFAAGANDYLVK 122

>pdb|1XHE|A Chain A, Crystal Structure Of The Receiver Domain Of Redox Response Regulator Arca Length = 123

Iteration: 1
 Score = 43.5 bits (101), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 30/116 (25%), Positives = 52/116 (44%), Gaps = 18/116 (15%)
Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
           H+L V+D  V R  ++ + +     V     G    Q L               +NL+I 
Sbjct: 5   HILIVEDELVTRNTLKSIFEAEGYDVFEATDGAEMHQILS-----------EYDINLVIM 53
Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSC--LEEGAEEYIVKP 208
           D  +PG  G  L ++++E +    V ++ ++  D   ++D    LE GA++YI KP
Sbjct: 54  DINLPGKNGLLLARELREQA---NVALMFLTGRD--NEVDKILGLEIGADDYITKP 104

>pdb|1XHF|A Chain A, Crystal Structure Of The Bef3-Activated Receiver Domain Of Redox Response Regulator Arca Length = 123

Iteration: 1
 Score = 43.5 bits (101), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 30/116 (25%), Positives = 51/116 (43%), Gaps = 18/116 (15%)
Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
           H+L V+D  V R  ++ + +     V     G    Q L               +NL+I 
Sbjct: 5   HILIVEDELVTRNTLKSIFEAEGYDVFEATDGAEXHQILS-----------EYDINLVIX 53
Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSC--LEEGAEEYIVKP 208
           D  +PG  G  L ++++E +    V +  ++  D   ++D    LE GA++YI KP
Sbjct: 54  DINLPGKNGLLLARELREQA---NVALXFLTGRD--NEVDKILGLEIGADDYITKP 104

>pdb|3I5A|A Chain A, Crystal Structure Of Full-Length Wpsr From Pseudomonas Syringae Length = 334

Iteration: 1
 Score = 43.5 bits (101), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 19/62 (30%), Positives = 40/62 (64%), Gaps = 2/62 (3%)
Query: 147 LKVNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSS-EDVLTQIDSCLEEGAEEYI 205
           +K  +I+ D  MPG+ G  L+++ + + + R++P++++S+ ED L +  +    GA +Y+
Sbjct: 60  IKPTVILQDLVMPGLDGLTLVREYRSNPLTRDIPIIVLSTKEDPLIK-SAAFAAGANDYL 118
Query: 206 VK 207
           VK
Sbjct: 119 VK 120

>pdb|1ZY2|A Chain A, Crystal Structure Of The Phosphorylated Receiver Domain Of The Transcription Regulator Ntrc1 From Aquifex Aeolicus Length = 150

Iteration: 1
 Score = 43.5 bits (101), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 33/120 (27%), Positives = 58/120 (48%), Gaps = 13/120 (10%)
Query: 94  LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLII 153
           ++VL ++D  V R L+E  L +   KV + E G  A + L      S   F     N+++
Sbjct: 1   MNVLVIEDDKVFRGLLEEYLSMKGIKVESAERGKEAYKLL------SEKHF-----NVVL 49
Query: 154 TDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD 213
               +P + G E+LK IKE S   E  V++++    +      ++ GA +++ KP  L +
Sbjct: 50  LXLLLPDVNGLEILKWIKERSP--ETEVIVITGHGTIKTAVEAMKMGAYDFLTKPCMLEE 107

>pdb|1OXB|B Chain B, Complex Between Ypd1 And Sln1 Response Regulator Domain In Space Group P2(1)2(1)2(1) Length = 134

Iteration: 1
 Score = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 32/125 (25%), Positives = 62/125 (49%), Gaps = 22/125 (17%)
Query: 94  LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALK----- 148
           + +L V+D++V++++I+R+L +    +  +E        L  DG+++   FD +K     
Sbjct: 2   VKILVVEDNHVNQEVIKRMLNLEG--IENIE--------LACDGQEA---FDKVKELTSK 48
Query: 149 ---VNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYI 205
               N+I  D  MP + G    K I+    +   P+V +++    + I  CLE G   ++
Sbjct: 49  GENYNMIFMDVQMPKVDGLLSTKMIRRDLGYTS-PIVALTAFADDSNIKECLESGMNGFL 107
Query: 206 VKPVK 210
            KP+K
Sbjct: 108 SKPIK 112

>pdb|2R25|B Chain B, Complex Of Ypd1 And Sln1-R1 With Bound Mg2+ And Bef3- Length = 133

Iteration: 1
 Score = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 32/125 (25%), Positives = 62/125 (49%), Gaps = 22/125 (17%)
Query: 94  LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALK----- 148
           + +L V+D++V++++I+R+L +    +  +E        L  DG+++   FD +K     
Sbjct: 3   VKILVVEDNHVNQEVIKRMLNLEG--IENIE--------LACDGQEA---FDKVKELTSK 49
Query: 149 ---VNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYI 205
               N+I  D  MP + G    K I+    +   P+V +++    + I  CLE G   ++
Sbjct: 50  GENYNMIFMDVQMPKVDGLLSTKMIRRDLGYTS-PIVALTAFADDSNIKECLESGMNGFL 108
Query: 206 VKPVK 210
            KP+K
Sbjct: 109 SKPIK 113

>pdb|1NXO|A Chain A, Micarec Ph7.0 Length = 120

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/77 (31%), Positives = 48/77 (62%), Gaps = 7/77 (9%)
Query: 134 GLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQI 193
             +G ++   F+A + ++II D  +P + G E+ K I+++S    VP++++S++D  ++ 
Sbjct: 31  AFNGREALEQFEAEQPDIIILDLMLPEIDGLEVAKTIRKTS---SVPILMLSAKD--SEF 85
Query: 194 DSC--LEEGAEEYIVKP 208
           D    LE GA++Y+ KP
Sbjct: 86  DKVIGLELGADDYVTKP 102

>pdb|1M5T|A Chain A, Crystal Structure Of The Response Regulator Divk Length = 124

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 32/114 (28%), Positives = 53/114 (46%), Gaps = 11/114 (9%)
Query: 96  VLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITD 155
           VL V+D+ ++ KL   LL+    +      G  AL        + N      K +LI+ D
Sbjct: 4   VLIVEDNELNMKLFHDLLEAQGYETLQTREGLSALSI-----AREN------KPDLILMD 52
Query: 156 YTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPV 209
             +P ++G E+ K +KE      +PVV +++  +    +   E G E YI KP+
Sbjct: 53  IQLPEISGLEVTKWLKEDDDLAHIPVVAVTAFAMKGDEERIREGGCEAYISKPI 106

>pdb|2JBA|B Chain B, Phob Response Regulator Receiver Domain Constitutively- Active Double Mutant D53a And Y102c Length = 127

Iteration: 1
 Score = 41.6 bits (96), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 19/59 (32%), Positives = 36/59 (61%)
Query: 150 NLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
           +LI+  + +PG +G + +K +K  S+ R++PVV++++          LE GA++ I KP
Sbjct: 48  DLILLAWMLPGGSGIQFIKHLKRESMTRDIPVVMLTARGEEEDRVRGLETGADDCITKP 106

>pdb|2JBA|A Chain A, Phob Response Regulator Receiver Domain Constitutively- Active Double Mutant D53a And Y102c Length = 127

Iteration: 1
 Score = 40.8 bits (94), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 18/59 (30%), Positives = 36/59 (61%)
Query: 150 NLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
           +LI+  + +PG +G + +K ++  S+ R++PVV++++          LE GA++ I KP
Sbjct: 48  DLILLAWMLPGGSGIQFIKHLRRESMTRDIPVVMLTARGEEEDRVRGLETGADDCITKP 106

>pdb|1ZH2|A Chain A, Crystal Structure Of The Calcium-Bound Receiver Domain Of Kdp Potassium Transport System Response Regulator Kdpe Length = 121

Iteration: 1
 Score = 40.8 bits (94), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 29/119 (24%), Positives = 55/119 (46%), Gaps = 14/119 (11%)
Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
           +VL V+D    R+ +   L+    +V   E+  R L                 K +LII 
Sbjct: 3   NVLIVEDEQAIRRFLRTALEGDGMRVFEAETLQRGLLEAA-----------TRKPDLIIL 51
Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD 213
           D  +P   G E ++ +++ S    VPV+++S+    +   + L+ GA++Y+ KP  + +
Sbjct: 52  DLGLPDGDGIEFIRDLRQWSA---VPVIVLSARSEESDKIAALDAGADDYLSKPFGIGE 107

>pdb|2ZAY|A Chain A, Crystal Structure Of Response Regulator From Desulfuromonas Acetoxidans Length = 147

Iteration: 1
 Score = 40.8 bits (94), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 26/103 (25%), Positives = 49/103 (47%), Gaps = 6/103 (5%)
Query: 113 LQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKV------NLIITDYTMPGMTGYEL 166
           + +   ++ A+ +   AL   G D  Q     +A+ V      +LIIT+  MP ++G +L
Sbjct: 11  IMLVDTQLPALAASISALSQEGFDIIQCGNAIEAVPVAVKTHPHLIITEANMPKISGMDL 70
Query: 167 LKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPV 209
              +K++     +PV+ +S      +    L+ G  ++I KPV
Sbjct: 71  FNSLKKNPQTASIPVIALSGRATAKEEAQLLDMGFIDFIAKPV 113

>pdb|3KHT|A Chain A, Crystal Structure Of Response Regulator From Hahella Chejuensis Length = 144

Iteration: 1
 Score = 40.0 bits (92), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 30/114 (26%), Positives = 54/114 (47%), Gaps = 13/114 (11%)
Query: 96  VLAVDDSYVDRKLIERLLQISS--CKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLII 153
           VL V+D+  D  LI R+L      C++  V++G +AL  +    +Q+       K +LII
Sbjct: 8   VLVVEDNPDDIALIRRVLDRKDIHCQLEFVDNGAKALYQV----QQA-------KYDLII 56
Query: 154 TDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVK 207
            D  +P   G+E+   +++    +  P+VI++      +   C   GA   + K
Sbjct: 57  LDIGLPIANGFEVXSAVRKPGANQHTPIVILTDNVSDDRAKQCXAAGASSVVDK 110

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	213
3luf_A	259	Two-component system response regulator/ggdef doma	2e-27
3luf_A	259	Two-component system response regulator/ggdef doma	7e-22
3heb_A	152	Response regulator receiver domain protein (CHEY);	4e-26
1k66_A	149	Phytochrome response regulator RCPB; CHEY homologu	8e-26
2qvg_A	143	Two component response regulator; NYSGXRC, PSI-2,	1e-25
1i3c_A	149	Response regulator RCP1; phytochrome, signaling pr	9e-25
1jbe_A	128	Chemotaxis protein CHEY; signaling protein; 1.08A	6e-24
1w25_A	459	Stalked-cell differentiation controlling protein;	3e-23
1w25_A	459	Stalked-cell differentiation controlling protein;	9e-19
3bre_A	358	Probable two-component response regulator; protein	4e-23
3eq2_A	394	Probable two-component response regulator; adaptor	4e-23
1p6q_A	129	CHEY2; chemotaxis, signal transduction, response r	2e-22
3ilh_A	146	Two component response regulator; NYSGXRC, PSI-II,	3e-22
3i42_A	127	Response regulator receiver domain protein (CHEY-	3e-21
3h1g_A	129	Chemotaxis protein CHEY homolog; sulfate-bound CHE	6e-21
1srr_A	124	SPO0F, sporulation response regulatory protein; as	9e-20
3hdv_A	136	Response regulator; PSI-II, structural genomics, P	2e-19
1k68_A	140	Phytochrome response regulator RCPA; phosphorylate	4e-19
3hdg_A	137	Uncharacterized protein; two-component sensor acti	5e-19
1dc7_A	124	NTRC, nitrogen regulation protein; receiver domain	7e-19
3jte_A	143	Response regulator receiver protein; structural ge	2e-18
2qxy_A	142	Response regulator; regulation of transcription, N	2e-18
2rjn_A	154	Response regulator receiver:metal-dependent phosph	3e-18
3grc_A	140	Sensor protein, kinase; protein structure initiati	4e-18
3m6m_D	143	Sensory/regulatory protein RPFC; RPFF, REC, enoyl-	4e-18
3cfy_A	137	Putative LUXO repressor protein; structural genomi	7e-18
3cnb_A	143	DNA-binding response regulator, MERR family; signa	9e-18
1qkk_A	155	DCTD, C4-dicarboxylate transport transcriptional r	9e-18
3hv2_A	153	Response regulator/HD domain protein; PSI-2, NYSGX	2e-17
3lua_A	140	Response regulator receiver protein; two-component	3e-17
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	6e-17
2ayx_A	254	Sensor kinase protein RCSC; two independent struct	2e-16
3nhm_A	133	Response regulator; protein structure initiative I	2e-16
4dad_A	146	Putative pilus assembly-related protein; response	2e-16
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	3e-16
1mb3_A	124	Cell division response regulator DIVK; signal tran	3e-16
3gt7_A	154	Sensor protein; structural genomics, signal receiv	7e-16
3eqz_A	135	Response regulator; structural genomics, unknown f	1e-15
2j48_A	119	Two-component sensor kinase; pseudo-receiver, circ	1e-15
3eod_A	130	Protein HNR; response regulator, phosphoprotein, t	2e-15
2jk1_A	139	HUPR, hydrogenase transcriptional regulatory prote	3e-15
3kht_A	144	Response regulator; PSI-II, 11023K, structural gen	5e-15
1dcf_A	136	ETR1 protein; beta-alpha five sandwich, transferas	2e-14
2zay_A	147	Response regulator receiver protein; structural ge	2e-14
3kcn_A	151	Adenylate cyclase homolog; SGX, PSI 2, structural	2e-14
3cg4_A	142	Response regulator receiver domain protein (CHEY-;	2e-14
3c3m_A	138	Response regulator receiver protein; structural ge	2e-14
1xhf_A	123	DYE resistance, aerobic respiration control protei	3e-14
3n53_A	140	Response regulator receiver modulated diguanylate;	3e-14
2qr3_A	140	Two-component system response regulator; structura	5e-14
3kyj_B	145	CHEY6 protein, putative histidine protein kinase;	9e-14
1zgz_A	122	Torcad operon transcriptional regulatory protein;	1e-13
1yio_A	208	Response regulatory protein; transcription regulat	1e-13
3snk_A	135	Response regulator CHEY-like protein; P-loop conta	1e-13
2b4a_A	138	BH3024; flavodoxin-like fold, structural genomics,	3e-13
3h5i_A	140	Response regulator/sensory box protein/ggdef domai	4e-13
1a2o_A	349	CHEB methylesterase; bacterial chemotaxis, adaptat	4e-13
1tmy_A	120	CHEY protein, TMY; chemotaxis, phosphoryl transfer	5e-13
3cu5_A	141	Two component transcriptional regulator, ARAC FAM;	6e-13
3t8y_A	164	CHEB, chemotaxis response regulator protein-glutam	7e-13
2qzj_A	136	Two-component response regulator; 11017X, PSI-II,	7e-13
2rdm_A	132	Response regulator receiver protein; structural ge	9e-13
3f6p_A	120	Transcriptional regulatory protein YYCF; unphospho	1e-12
2a9o_A	120	Response regulator; essential protein, YYCF/YYCG h	2e-12
1dbw_A	126	Transcriptional regulatory protein FIXJ; doubly wo	2e-12
3crn_A	132	Response regulator receiver domain protein, CHEY-;	2e-12
1zh2_A	121	KDP operon transcriptional regulatory protein KDPE	2e-12
3t6k_A	136	Response regulator receiver; flavodoxin-like, stru	3e-12
2jba_A	127	Phosphate regulon transcriptional regulatory PROT;	5e-12
3hzh_A	157	Chemotaxis response regulator (CHEY-3); phosphatas	6e-12
3lte_A	132	Response regulator; structural genomics, PSI, prot	7e-12
2gkg_A	127	Response regulator homolog; social motility, recei	8e-12
2oqr_A	230	Sensory transduction protein REGX3; response regul	8e-12
2gwr_A	238	DNA-binding response regulator MTRA; two-component	2e-11
1mvo_A	136	PHOP response regulator; phosphate regulon, transc	3e-11
3a10_A	116	Response regulator; phosphoacceptor, signaling pro	4e-11
3rqi_A	184	Response regulator protein; structural genomics, s	4e-11
2r25_B	133	Osmosensing histidine protein kinase SLN1; alpha5-	6e-11
3gl9_A	122	Response regulator; beta-sheet, surrounded by alph	6e-11
3kto_A	136	Response regulator receiver protein; PSI-II,struct	8e-11
3r0j_A	250	Possible two component system response transcript	1e-10
1s8n_A	205	Putative antiterminator; RV1626, structural genomi	5e-10
3mm4_A	206	Histidine kinase homolog; receiver domain, CKI1, c	5e-10
3cg0_A	140	Response regulator receiver modulated diguanylate	5e-10
1p2f_A	220	Response regulator; DRRB, OMPR/PHOB, transcription	1e-09
3c97_A	140	Signal transduction histidine kinase; structural g	1e-09
1kgs_A	225	DRRD, DNA binding response regulator D; DNA-bindin	2e-09
1ys7_A	233	Transcriptional regulatory protein PRRA; response	2e-09
3n0r_A	286	Response regulator; sigma factor, receiver, two-co	4e-09
2pl1_A	121	Transcriptional regulatory protein PHOP; CHEY-like	5e-09
1qo0_D	196	AMIR; binding protein, gene regulator, receptor; 2	6e-09
3q9s_A	249	DNA-binding response regulator; DNA binding protei	8e-09
2qv0_A	143	Protein MRKE; structural genomics, transcription,	1e-08
3sy8_A	400	ROCR; TIM barrel phosphodiesterase-A, transcriptio	2e-07
2hqr_A	223	Putative transcriptional regulator; phosporylation	2e-07
2qsj_A	154	DNA-binding response regulator, LUXR family; struc	2e-07
2pln_A	137	HP1043, response regulator; signaling protein; 1.8	1e-06
3klo_A	225	Transcriptional regulator VPST; REC domain, HTH do	2e-06
3f6c_A	134	Positive transcription regulator EVGA; structural	7e-05
3b2n_A	133	Uncharacterized protein Q99UF4; structural genomic	8e-05

>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 =  103 bits (260), Expect = 2e-27
 Identities = 26/118 (22%), Positives = 52/118 (44%), Gaps = 10/118 (8%)

Query: 92  KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNL 151
           +++ VL VDDS   R      L+    +V        AL  L     + +         L
Sbjct: 123 QQIEVLVVDDSRTSRHRTMAQLRKQLLQVHEASHAREALATL-----EQHPAIR-----L 172

Query: 152 IITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPV 209
           ++ DY MP + G  L++ ++E    +++ ++ +S  D        L++GA +++ +P 
Sbjct: 173 VLVDYYMPEIDGISLVRMLRERYSKQQLAIIGISVSDKRGLSARYLKQGANDFLNQPF 230

>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 = 88.9 bits (221), Expect = 7e-22
 Identities = 22/118 (18%), Positives = 50/118 (42%), Gaps = 15/118 (12%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
            +L V+DS   R+++ + +   +             ++           +      + + 
Sbjct: 6   KILIVEDSMTIRRMLIQAIAQQTGLEIDAFDTLEGARHC------QGDEYV-----VALV 54

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS 212
           D T+P     E +K + E    R +PVVI++++    + ++ LE G  +Y++K  + S
Sbjct: 55  DLTLPDAPSGEAVKVLLE----RGLPVVILTADISEDKREAWLEAGVLDYVMKDSRHS 108

>3heb_A Response regulator receiver domain protein (CHEY); NYSGXRC, PSI-II, respose regulator, structure initiative, structural genomics; 2.40A {Rhodospirillum rubrum} Length = 152

 Score = 97.4 bits (243), Expect = 4e-26
 Identities = 40/125 (32%), Positives = 68/125 (54%), Gaps = 4/125 (3%)

Query: 91  SKELHVLAVDDSYVDRKLIERLLQIS--SCKVTAVESGTRALQYLGLDGEQSNVGFDALK 148
           S  + ++ ++D     +LIE+ ++ +  + ++ A   GT AL YL  D +   V   A +
Sbjct: 2   SLSVTIVMIEDDLGHARLIEKNIRRAGVNNEIIAFTDGTSALNYLFGDDKSGRV--SAGR 59

Query: 149 VNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
             L++ D  +P MTG ++LK +KE+   R  PVVI+++ D   +I  C + GA  YI KP
Sbjct: 60  AQLVLLDLNLPDMTGIDILKLVKENPHTRRSPVVILTTTDDQREIQRCYDLGANVYITKP 119

Query: 209 VKLSD 213
           V   +
Sbjct: 120 VNYEN 124

>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 = 96.6 bits (241), Expect = 8e-26
 Identities = 38/121 (31%), Positives = 62/121 (51%), Gaps = 3/121 (2%)

Query: 95  HVLAVDDSYVDRKLIERLLQIS--SCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLI 152
            +L V+DS  D    +RLLQ       +    +G +AL +L   G   N    A +  +I
Sbjct: 8   PLLVVEDSDEDFSTFQRLLQREGVVNPIYRCITGDQALDFLYQTGSYCNPD-IAPRPAVI 66

Query: 153 ITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS 212
           + D  +PG  G E+L++IK+  V +++PVVIM++      I+ C       YIVKP+++ 
Sbjct: 67  LLDLNLPGTDGREVLQEIKQDEVLKKIPVVIMTTSSNPKDIEICYSYSISSYIVKPLEID 126

Query: 213 D 213
            
Sbjct: 127 R 127

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

 Score = 96.1 bits (240), Expect = 1e-25
 Identities = 26/123 (21%), Positives = 59/123 (47%), Gaps = 7/123 (5%)

Query: 91  SKELHVLAVDDSYVDRKLIERLLQIS--SCKVTAVESGTRALQYLGLDGEQSNVGFDALK 148
           + ++ +L ++D  VD + +ER+        K+   +SG +AL  L    +++ +      
Sbjct: 5   ADKVDILYLEDDEVDIQSVERVFHKISSLIKIEIAKSGNQALDMLYGRNKENKIHPK--- 61

Query: 149 VNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
             LI+ D  +P M G E LK++++ S F ++ V ++++        +        +++KP
Sbjct: 62  --LILLDINIPKMNGIEFLKELRDDSSFTDIEVFVLTAAYTSKDKLAFESLNIRGHLIKP 119

Query: 209 VKL 211
           +  
Sbjct: 120 LDY 122

>1i3c_A Response regulator RCP1; phytochrome, signaling protein; 1.90A {Synechocystis SP} SCOP: c.23.1.1 PDB: 1jlk_A Length = 149

 Score = 93.9 bits (234), Expect = 9e-25
 Identities = 31/127 (24%), Positives = 63/127 (49%), Gaps = 6/127 (4%)

Query: 89  ECSKELHVLAVDDSYVDRKLIERLLQIS--SCKVTAVESGTRALQYLGLDGEQSNVGFDA 146
           E +    +L V+DS  D +L++ +L+ S    ++  +  G  A+ +L    +Q     ++
Sbjct: 4   ESNPPKVILLVEDSKADSRLVQEVLKTSTIDHELIILRDGLAAMAFL----QQQGEYENS 59

Query: 147 LKVNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIV 206
            + NLI+ D  +P   G E+L +IK++   + +PVV++++      + +  E     Y+ 
Sbjct: 60  PRPNLILLDLNLPKKDGREVLAEIKQNPDLKRIPVVVLTTSHNEDDVIASYELHVNCYLT 119

Query: 207 KPVKLSD 213
           K   L D
Sbjct: 120 KSRNLKD 126

>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 = 91.1 bits (227), Expect = 6e-24
 Identities = 38/118 (32%), Positives = 56/118 (47%), Gaps = 12/118 (10%)

Query: 92  KELHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVN 150
           KEL  L VDD    R+++  LL ++    V   E G  AL  L            A    
Sbjct: 3   KELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKL-----------QAGGYG 51

Query: 151 LIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
            +I+D+ MP M G ELLK I+       +PV+++++E     I +  + GA  Y+VKP
Sbjct: 52  FVISDWNMPNMDGLELLKTIRAXXAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKP 109

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

 Score = 95.6 bits (238), Expect = 3e-23
 Identities = 31/115 (26%), Positives = 54/115 (46%), Gaps = 11/115 (9%)

Query: 96  VLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITD 155
           +L VDD   + +L+E  L     +V+    G  AL                   ++I+ D
Sbjct: 4   ILVVDDIEANVRLLEAKLTAEYYEVSTAMDGPTALAMA-----------ARDLPDIILLD 52

Query: 156 YTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVK 210
             MPGM G+ + +K+K+    R +PVV++++ D        LE GA +++ KP+ 
Sbjct: 53  VMMPGMDGFTVCRKLKDDPTTRHIPVVLITALDGRGDRIQGLESGASDFLTKPID 107

>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 = 82.5 bits (204), Expect = 9e-19
 Identities = 25/156 (16%), Positives = 51/156 (32%), Gaps = 16/156 (10%)

Query: 54  QTHNILTKTHQRLVKEKKFKETNRGFPFWAMATVAECSKELHVLAVDDSYVDRKLIERLL 113
           ++          L   ++ + + R     A A          VL VDD+    + +   L
Sbjct: 116 RSLTRFKLVIDEL---RQREASGRRMGVIAGAAARLDGLGGRVLIVDDNERQAQRVAAEL 172

Query: 114 QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKES 173
            +    V   +     +   G              V+L+I +       G      ++  
Sbjct: 173 GVEHRPVIESDPEKAKISAGG-------------PVDLVIVNAAAKNFDGLRFTAALRSE 219

Query: 174 SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPV 209
              R++PV+ M   D   ++   LE G  + + +P+
Sbjct: 220 ERTRQLPVLAMVDPDDRGRMVKALEIGVNDILSRPI 255

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

 Score = 94.0 bits (234), Expect = 4e-23
 Identities = 26/117 (22%), Positives = 51/117 (43%), Gaps = 12/117 (10%)

Query: 95  HVLAVDDSYVDRKLIERLLQ-ISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLII 153
            VL VDD  +  + + R L   +           +A+              + +K  +I+
Sbjct: 20  MVLLVDDQAMIGEAVRRSLASEAGIDFHFCSDPQQAVAVA-----------NQIKPTVIL 68

Query: 154 TDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVK 210
            D  MPG+ G  LL   + +   R++P++++S+++  T   +    GA +Y+VK   
Sbjct: 69  QDLVMPGVDGLTLLAAYRGNPATRDIPIIVLSTKEEPTVKSAAFAAGANDYLVKLPD 125

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

 Score = 94.6 bits (235), Expect = 4e-23
 Identities = 31/116 (26%), Positives = 62/116 (53%), Gaps = 13/116 (11%)

Query: 94  LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLII 153
             +L +DD  V R+ +   L+ S+ KV    +G + LQ             ++ + +L+I
Sbjct: 6   ATLLIIDDDEVVRESLAAYLEDSNFKVLQALNGLQGLQIF-----------ESEQPDLVI 54

Query: 154 TDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPV 209
            D  MP + G EL+++I++++   E P++++S   V++     L  GA +Y++KP+
Sbjct: 55  CDLRMPQIDGLELIRRIRQTA--SETPIIVLSGAGVMSDAVEALRLGAADYLIKPL 108

>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 = 87.2 bits (217), Expect = 2e-22
 Identities = 27/119 (22%), Positives = 54/119 (45%), Gaps = 12/119 (10%)

Query: 91  SKELHVLAVDDSYVDRKLIERLLQISSCK-VTAVESGTRALQYLGLDGEQSNVGFDALKV 149
           ++++ VL VDD    R L+   LQ    K +TA   G + ++ +                
Sbjct: 4   AEKIKVLIVDDQVTSRLLLGDALQQLGFKQITAAGDGEQGMKIM-----------AQNPH 52

Query: 150 NLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
           +L+I+D+ MP M G  LL+ ++ +   ++   +I++++     +      GA   + KP
Sbjct: 53  HLVISDFNMPKMDGLGLLQAVRANPATKKAAFIILTAQGDRALVQKAAALGANNVLAKP 111

>3ilh_A Two component response regulator; NYSGXRC, PSI-II, protein S initiative, structural genomics; 2.59A {Cytophaga hutchinsonii} Length = 146

 Score = 87.4 bits (217), Expect = 3e-22
 Identities = 29/129 (22%), Positives = 59/129 (45%), Gaps = 11/129 (8%)

Query: 86  TVAECSKELHVLAVDDSYVDRKLIERLLQISSC--KVTAVESGTRALQYLGLDGEQSNVG 143
           ++A+  K   VL +DD  +   L   +++++    ++ +V SG  A+  L  +   +   
Sbjct: 2   SLADTRKIDSVLLIDDDDIVNFLNTTIIRMTHRVEEIQSVTSGNAAINKLN-ELYAAGRW 60

Query: 144 FDALKVNLIITDYTMPGMTGYELLKKIKESS--VFREVPVVIMSS-EDVLTQIDSCLEEG 200
                  +I  D  MPG+ G+EL+   K+    +  +  V ++SS  D   Q  +   + 
Sbjct: 61  PS-----IICIDINMPGINGWELIDLFKQHFQPMKNKSIVCLLSSSLDPRDQAKAEASDW 115

Query: 201 AEEYIVKPV 209
            + Y+ KP+
Sbjct: 116 VDYYVSKPL 124

>3i42_A Response regulator receiver domain protein (CHEY- like); structural genomics, PSI-2, protein structure initiative; 2.15A {Methylobacillus flagellatus KT} Length = 127

 Score = 84.1 bits (209), Expect = 3e-21
 Identities = 26/122 (21%), Positives = 50/122 (40%), Gaps = 18/122 (14%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
             L V+D     +  + LL++   +   V SGT AL  +      S  G+D      +  
Sbjct: 5   QALIVEDYQAAAETFKELLEMLGFQADYVMSGTDALHAM------STRGYD-----AVFI 53

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMS---SEDVLTQIDSCLEEGAEEYIVKPVKL 211
           D  +P  +G  L+K+++   + +    V +S     D+         E  + Y+ KP+ +
Sbjct: 54  DLNLPDTSGLALVKQLRALPMEKTSKFVAVSGFAKNDL----GKEACELFDFYLEKPIDI 109

Query: 212 SD 213
           + 
Sbjct: 110 AS 111

>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 = 83.3 bits (207), Expect = 6e-21
 Identities = 36/118 (30%), Positives = 63/118 (53%), Gaps = 11/118 (9%)

Query: 92  KELHVLAVDDSYVDRKLIERLLQISSCK-VTAVESGTRALQYLGLDGEQSNVGFDALKVN 150
             + +L VDDS   R++I+  L     + V   E G  A + L      +N         
Sbjct: 4   GSMKLLVVDDSSTMRRIIKNTLSRLGYEDVLEAEHGVEAWEKL-----DANADTK----- 53

Query: 151 LIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
           ++ITD+ MP M G +L+KK++  S F+E+P++++++E    ++ + L+ G   YIVKP
Sbjct: 54  VLITDWNMPEMNGLDLVKKVRSDSRFKEIPIIMITAEGGKAEVITALKAGVNNYIVKP 111

>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 = 80.2 bits (199), Expect = 9e-20
 Identities = 27/118 (22%), Positives = 51/118 (43%), Gaps = 15/118 (12%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
            +L VDD    R L+  +      +     +G +AL  +              + +L++ 
Sbjct: 5   KILIVDDQSGIRILLNEVFNKEGYQTFQAANGLQALDIV-----------TKERPDLVLL 53

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSSE-DVLTQIDSCLEEGAEEYIVKPVKL 211
           D  +PGM G E+LK++K       + V+IM++  ++    +   E GA  +  KP  +
Sbjct: 54  DMKIPGMDGIEILKRMKVID--ENIRVIIMTAYGELDMIQE-SKELGALTHFAKPFDI 108

>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 = 79.6 bits (197), Expect = 2e-19
 Identities = 29/122 (23%), Positives = 53/122 (43%), Gaps = 13/122 (10%)

Query: 91  SKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVN 150
           +    VL VDD+ V+R+ +   L+         +    A  YL                 
Sbjct: 5   AARPLVLVVDDNAVNREALILYLKSRGIDAVGADGAEEARLYL-----HYQKRIG----- 54

Query: 151 LIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSS-EDVLTQIDSCLEEGAEEYIVKPV 209
           L+ITD  M   +G +L++ I+ S     + ++++S   DV   +D  +  G  ++++KPV
Sbjct: 55  LMITDLRMQPESGLDLIRTIRASE-RAALSIIVVSGDTDVEEAVD-VMHLGVVDFLLKPV 112

Query: 210 KL 211
            L
Sbjct: 113 DL 114

>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 = 78.8 bits (194), Expect = 4e-19
 Identities = 34/120 (28%), Positives = 56/120 (46%), Gaps = 6/120 (5%)

Query: 96  VLAVDDSYVDRKLIERLLQIS--SCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLII 153
           +  V+D+  D +LI+  L  S    +V  V  G  A+ YL  +GE +    +A + +LI+
Sbjct: 5   IFLVEDNKADIRLIQEALANSTVPHEVVTVRDGMEAMAYLRQEGEYA----NASRPDLIL 60

Query: 154 TDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD 213
               +P   G E+L +IK     + +PVV++S+      I    +     YI K   LS 
Sbjct: 61  LXLNLPKKDGREVLAEIKSDPTLKRIPVVVLSTSINEDDIFHSYDLHVNCYITKSANLSQ 120

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

 Score = 78.8 bits (195), Expect = 5e-19
 Identities = 26/123 (21%), Positives = 52/123 (42%), Gaps = 15/123 (12%)

Query: 92  KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNL 151
             L +L V+D    R+ +  ++     +V +   G    +            F     ++
Sbjct: 6   VALKILIVEDDTDAREWLSTIISNHFPEVWSAGDGEEGERL-----------FGLHAPDV 54

Query: 152 IITDYTMPGMTGYELLKKIKESSVFREVPVVIMSS-EDVLTQIDSCLEEGAEEYIVKPVK 210
           IITD  MP + G E+L +IK      +  V+++S+  ++   I   +E G   ++ KP++
Sbjct: 55  IITDIRMPKLGGLEMLDRIKAGG--AKPYVIVISAFSEMKYFIK-AIELGVHLFLPKPIE 111

Query: 211 LSD 213
              
Sbjct: 112 PGR 114

>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 = 77.9 bits (193), Expect = 7e-19
 Identities = 34/118 (28%), Positives = 57/118 (48%), Gaps = 15/118 (12%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
            V  VDD    R ++ER L  +    T  E+G   L  L                +++++
Sbjct: 5   IVWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLAALASK-----------TPDVLLS 53

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSSE-DVLTQIDSCLEEGAEEYIVKPVKL 211
           D  MPGM G  LLK+IK+      +PV+IM++  D+   + +  ++GA +Y+ KP  +
Sbjct: 54  DIRMPGMDGLALLKQIKQR--HPMLPVIIMTAHSDLDAAVSA-YQQGAFDYLPKPFDI 108

>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 = 77.6 bits (192), Expect = 2e-18
 Identities = 33/118 (27%), Positives = 60/118 (50%), Gaps = 13/118 (11%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
            +L +DD     + I+ LL+I   +V    S T  L+       ++    D     ++IT
Sbjct: 5   KILVIDDESTILQNIKFLLEIDGNEVLTASSSTEGLRIF----TENCNSID-----VVIT 55

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSSE-DVLTQIDSCLEEGAEEYIVKPVKL 211
           D  MP ++G ++L++IK+ +    + V+I++   D+   I   ++EGA EY+ KPV  
Sbjct: 56  DMKMPKLSGMDILREIKKIT--PHMAVIILTGHGDLDNAIL-AMKEGAFEYLRKPVTA 110

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

 Score = 77.2 bits (191), Expect = 2e-18
 Identities = 27/121 (22%), Positives = 53/121 (43%), Gaps = 14/121 (11%)

Query: 91  SKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVN 150
           S    V+ VD+S +    ++  L+     V   ++   A  +L              K++
Sbjct: 2   SLTPTVMVVDESRITFLAVKNALEKDGFNVIWAKNEQEAFTFL-----------RREKID 50

Query: 151 LIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVK 210
           L+  D    G     L+++I+E   F +  V ++S+      I + ++ GA +YI+KP +
Sbjct: 51  LVFVDV-FEGEESLNLIRRIREE--FPDTKVAVLSAYVDKDLIINSVKAGAVDYILKPFR 107

Query: 211 L 211
           L
Sbjct: 108 L 108

>2rjn_A Response regulator receiver:metal-dependent phosphohydrolase, HD subdomain; structural genomics, oceanospirillum SP. MED92; 2.10A {Neptuniibacter caesariensis} Length = 154

 Score = 76.9 bits (190), Expect = 3e-18
 Identities = 30/124 (24%), Positives = 53/124 (42%), Gaps = 16/124 (12%)

Query: 92  KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNL 151
           K   V+ VDD       ++RL++   C +    S   AL+ L               V L
Sbjct: 6   KNYTVMLVDDEQPILNSLKRLIKRLGCNIITFTSPLDALEAL-----------KGTSVQL 54

Query: 152 IITDYTMPGMTGYELLKKIKESSVFREVPVVIMSS-EDVLTQIDSCLEEGA-EEYIVKPV 209
           +I+D  MP M G   L+++ +   + ++  V++S   D    ID  +  G    +++KP 
Sbjct: 55  VISDMRMPEMGGEVFLEQVAK--SYPDIERVVISGYADAQATID-AVNRGKISRFLLKPW 111

Query: 210 KLSD 213
           +  D
Sbjct: 112 EDED 115

>3grc_A Sensor protein, kinase; protein structure initiative II(PSI II), NYSGXRC, 11025B, structural genomics; 2.21A {Polaromonas SP} Length = 140

 Score = 76.5 bits (189), Expect = 4e-18
 Identities = 18/116 (15%), Positives = 44/116 (37%), Gaps = 14/116 (12%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
            +L  +D     +L+  +L+        V S  +AL+ +                  +  
Sbjct: 8   RILICEDDPDIARLLNLMLEKGGFDSDMVHSAAQALEQV-----------ARRPYAAMTV 56

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMS--SEDVLTQIDSCLEEGAEEYIVKP 208
           D  +P   G  L++ ++  S  R++ +V++S  + +   +  +        ++ KP
Sbjct: 57  DLNLPDQDGVSLIRALRRDSRTRDLAIVVVSANAREGELEF-NSQPLAVSTWLEKP 111

>3m6m_D Sensory/regulatory protein RPFC; RPFF, REC, enoyl-COA hydratase, lyase-transferase COMP; 2.50A {Xanthomonas campestris PV} Length = 143

 Score = 76.5 bits (189), Expect = 4e-18
 Identities = 35/126 (27%), Positives = 61/126 (48%), Gaps = 21/126 (16%)

Query: 94  LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLII 153
           + +L  DD   +R +++RLL+ +  KV  V    + L  +      +   +D      +I
Sbjct: 15  MRMLVADDHEANRMVLQRLLEKAGHKVLCVNGAEQVLDAM------AEEDYD-----AVI 63

Query: 154 TDYTMPGMTGYELLKKI--KESSVFREVPVVIMS----SEDVLTQIDSCLEEGAEEYIVK 207
            D  MPGM G ++LK++   ++S  R  PVV++S     E     I +C + GA  ++ K
Sbjct: 64  VDLHMPGMNGLDMLKQLRVMQASGMRYTPVVVLSADVTPEA----IRACEQAGARAFLAK 119

Query: 208 PVKLSD 213
           PV  + 
Sbjct: 120 PVVAAK 125

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

 Score = 75.6 bits (187), Expect = 7e-18
 Identities = 29/118 (24%), Positives = 59/118 (50%), Gaps = 15/118 (12%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
            VL V+DS     L ++ ++     +  VE+G  A+Q++           +  K  LII 
Sbjct: 6   RVLLVEDSTSLAILYKQYVKDEPYDIFHVETGRDAIQFI-----------ERSKPQLIIL 54

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSSE-DVLTQIDSCLEEGAEEYIVKPVKL 211
           D  +P M+G ++L  I ++ +     V+I ++   V   ++  +++GAE+++ KP+  
Sbjct: 55  DLKLPDMSGEDVLDWINQNDI--PTSVIIATAHGSVDLAVN-LIQKGAEDFLEKPINA 109

>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 = 75.7 bits (187), Expect = 9e-18
 Identities = 21/121 (17%), Positives = 46/121 (38%), Gaps = 13/121 (10%)

Query: 91  SKELHVLAVDDSYVDRKLIERLLQ--ISSCKVTAVESGTRALQYLGLDGEQSNVGFDALK 148
             +  +L ++D      ++ + L+      K+    +   A   L             +K
Sbjct: 6   KNDFSILIIEDDKEFADMLTQFLENLFPYAKIKIAYNPFDAGDLL-----------HTVK 54

Query: 149 VNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
            ++++ D  M GM G+ +  +IK +     + V+ M+       +   +  GAE    KP
Sbjct: 55  PDVVMLDLMMVGMDGFSICHRIKSTPATANIIVIAMTGALTDDNVSRIVALGAETCFGKP 114

Query: 209 V 209
           +
Sbjct: 115 L 115

>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 = 75.7 bits (187), Expect = 9e-18
 Identities = 31/122 (25%), Positives = 58/122 (47%), Gaps = 15/122 (12%)

Query: 91  SKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVN 150
           S    V  +DD    RK +++ L+++   V++  S T AL  L  D              
Sbjct: 1   SAAPSVFLIDDDRDLRKAMQQTLELAGFTVSSFASATEALAGLSAD-----------FAG 49

Query: 151 LIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSE-DVLTQIDSCLEEGAEEYIVKPV 209
           ++I+D  MPGM G  L +KI       ++P+++++   D+   +   +++GA ++I KP 
Sbjct: 50  IVISDIRMPGMDGLALFRKILALD--PDLPMILVTGHGDIPMAV-QAIQDGAYDFIAKPF 106

Query: 210 KL 211
             
Sbjct: 107 AA 108

>3hv2_A Response regulator/HD domain protein; PSI-2, NYSGXRC, structural genomics, protein structure initiative; 1.50A {Pseudomonas fluorescens pf-5} Length = 153

 Score = 74.9 bits (185), Expect = 2e-17
 Identities = 28/130 (21%), Positives = 54/130 (41%), Gaps = 16/130 (12%)

Query: 86  TVAECSKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFD 145
            VA  ++   +L VD   V  + +++LL      +      T+ALQ L            
Sbjct: 7   NVATVTRRPEILLVDSQEVILQRLQQLLSPLPYTLHFARDATQALQLL-----------A 55

Query: 146 ALKVNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSS-EDVLTQIDSCLEEGAE-E 203
           + +V+L+I+   +P M G  LL +I +   +     ++++   D+       + EG    
Sbjct: 56  SREVDLVISAAHLPQMDGPTLLARIHQ--QYPSTTRILLTGDPDLKLIAK-AINEGEIYR 112

Query: 204 YIVKPVKLSD 213
           Y+ KP    +
Sbjct: 113 YLSKPWDDQE 122

>3lua_A Response regulator receiver protein; two-component signal transduction system, histidine kinase, phosphorelay, receiver domain, nysgxrc; 2.40A {Clostridium thermocellum} Length = 140

 Score = 74.2 bits (183), Expect = 3e-17
 Identities = 26/115 (22%), Positives = 43/115 (37%), Gaps = 12/115 (10%)

Query: 96  VLAVDDSYVDRKLIERLLQISSC-KVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
           VL +D    +R+  + +           VE+  +                D   + LII 
Sbjct: 7   VLLIDYFEYEREKTKIIFDNIGEYDFIEVENLKKFYSIF----------KDLDSITLIIM 56

Query: 155 DYTMP-GMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
           D   P    G E+L  I+ +S     PV+I +  D      + L+    +YI+KP
Sbjct: 57  DIAFPVEKEGLEVLSAIRNNSRTANTPVIIATKSDNPGYRHAALKFKVSDYILKP 111

>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 = 77.1 bits (191), Expect = 6e-17
 Identities = 34/119 (28%), Positives = 61/119 (51%), Gaps = 15/119 (12%)

Query: 94  LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLII 153
           ++VL ++D  V R L+E  L +   KV + E G  A + L      S   F+     +++
Sbjct: 1   MNVLVIEDDKVFRGLLEEYLSMKGIKVESAERGKEAYKLL------SEKHFN-----VVL 49

Query: 154 TDYTMPGMTGYELLKKIKESSVFREVPVVIMSSE-DVLTQIDSCLEEGAEEYIVKPVKL 211
            D  +P + G E+LK IKE S   E  V++++    + T ++  ++ GA +++ KP  L
Sbjct: 50  LDLLLPDVNGLEILKWIKERS--PETEVIVITGHGTIKTAVE-AMKMGAYDFLTKPCML 105

>2ayx_A Sensor kinase protein RCSC; two independent structural domains, transferase; NMR {Escherichia coli} SCOP: c.23.1.1 c.23.1.6 PDB: 2ayz_A 2ayy_A Length = 254

 Score = 74.8 bits (184), Expect = 2e-16
 Identities = 32/135 (23%), Positives = 58/135 (42%), Gaps = 21/135 (15%)

Query: 83  AMATVAECSKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNV 142
           +       + ++ +L VDD  ++R+L+   L     +      G  AL  L      S  
Sbjct: 119 STDKAVSDNDDMMILVVDDHPINRRLLADQLGSLGYQCKTANDGVDALNVL------SKN 172

Query: 143 GFDALKVNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMS----SEDVLTQIDSCLE 198
             D     ++++D  MP M GY L ++I++      +PV+ ++    +E+       CLE
Sbjct: 173 HID-----IVLSDVNMPNMDGYRLTQRIRQLG--LTLPVIGVTANALAEE----KQRCLE 221

Query: 199 EGAEEYIVKPVKLSD 213
            G +  + KPV L  
Sbjct: 222 SGMDSCLSKPVTLDV 236

>3nhm_A Response regulator; protein structure initiative II(PSI II), NYSGXRC, structural genomics; 2.19A {Myxococcus xanthus} Length = 133

 Score = 71.5 bits (176), Expect = 2e-16
 Identities = 30/115 (26%), Positives = 49/115 (42%), Gaps = 13/115 (11%)

Query: 96  VLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITD 155
           VL V++S+  R+ +  LL       T    G   LQ              A   +++I+D
Sbjct: 7   VLIVENSWTMRETLRLLLS-GEFDCTTAADGASGLQQA-----------LAHPPDVLISD 54

Query: 156 YTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVK 210
             M GM GY L    +     + +PV+ +S     T+  +  +   + Y+VKPVK
Sbjct: 55  VNMDGMDGYALCGHFRSEPTLKHIPVIFVSGYAPRTEGPA-DQPVPDAYLVKPVK 108

>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 = 72.1 bits (177), Expect = 2e-16
 Identities = 15/117 (12%), Positives = 41/117 (35%), Gaps = 12/117 (10%)

Query: 94  LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLII 153
           +++L   +       + RL+  +         G  A      DG  +   FD     +++
Sbjct: 21  INILVASEDASRLAHLARLVGDAGRYRVTRTVGRAAQIVQRTDGLDA---FD-----ILM 72

Query: 154 TDYTMPGMTGYELLKKIKESSVFREVPVVIMSS-EDVLTQIDSCLEEGAEEYIVKPV 209
            D           ++K+        +  +++++     T +D+ +  G  + +  P+
Sbjct: 73  IDGAALDTAELAAIEKLSRL--HPGLTCLLVTTDASSQTLLDA-MRAGVRDVLRWPL 126

>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 = 75.2 bits (186), Expect = 3e-16
 Identities = 24/117 (20%), Positives = 47/117 (40%), Gaps = 15/117 (12%)

Query: 96  VLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITD 155
           VL VDD       +  +L+         ++   A + +        + F      +I+ D
Sbjct: 3   VLVVDDEESITSSLSAILEEEGYHPDTAKTLREAEKKI------KELFFP-----VIVLD 51

Query: 156 YTMPGMTGYELLKKIKESSVFREVPVVIMSSE-DVLTQIDSCLEEGAEEYIVKPVKL 211
             MP   G   +  IKE     +  V++++    V T +   +++GA E++ KP  +
Sbjct: 52  VWMPDGDGVNFIDFIKE--NSPDSVVIVITGHGSVDTAVK-AIKKGAYEFLEKPFSV 105

>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 = 71.0 bits (175), Expect = 3e-16
 Identities = 32/122 (26%), Positives = 50/122 (40%), Gaps = 19/122 (15%)

Query: 96  VLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITD 155
           VL V+D+ ++ KL   LL+    +      G  AL              D     LI+ D
Sbjct: 4   VLIVEDNELNMKLFHDLLEAQGYETLQTREGLSALSIA------RENKPD-----LILMD 52

Query: 156 YTMPGMTGYELLKKIKESSVFREVPVVIMS----SEDVLTQIDSCLEEGAEEYIVKPVKL 211
             +P ++G E+ K +KE      +PVV ++      D     +   E G E YI KP+ +
Sbjct: 53  IQLPEISGLEVTKWLKEDDDLAHIPVVAVTAFAMKGD----EERIREGGCEAYISKPISV 108

Query: 212 SD 213
             
Sbjct: 109 VH 110

>3gt7_A Sensor protein; structural genomics, signal receiver domain, kinase, PSI-2, protein structure initiative; 2.30A {Syntrophus aciditrophicus SB} Length = 154

 Score = 70.8 bits (174), Expect = 7e-16
 Identities = 32/121 (26%), Positives = 61/121 (50%), Gaps = 13/121 (10%)

Query: 91  SKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVN 150
           ++   +L V+DS    + ++ +L+ +  +   V +G  A+++               + +
Sbjct: 5   NRAGEILIVEDSPTQAEHLKHILEETGYQTEHVRNGREAVRF-----------LSLTRPD 53

Query: 151 LIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSS-EDVLTQIDSCLEEGAEEYIVKPV 209
           LII+D  MP M GY L + +K     R +PV++++   D    + S LE GA+++I KP 
Sbjct: 54  LIISDVLMPEMDGYALCRWLKGQPDLRTIPVILLTILSDPRDVVRS-LECGADDFITKPC 112

Query: 210 K 210
           K
Sbjct: 113 K 113

>3eqz_A Response regulator; structural genomics, unknown function, PSI-2, protein struct initiative; 2.15A {Colwellia psychrerythraea} Length = 135

 Score = 69.6 bits (171), Expect = 1e-15
 Identities = 24/119 (20%), Positives = 42/119 (35%), Gaps = 19/119 (15%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
            V  VDD  +   L++ +++     V A     RA                  K ++II 
Sbjct: 5   RVFIVDDDTLTCNLLKTIVEPIFGNVEA-FQHPRAFLT-----------LSLNKQDIIIL 52

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMS--SEDVLTQIDSC---LEEGAEEYIVKP 208
           D  MP M G E+++ + E        ++++S     VL   ++              KP
Sbjct: 53  DLMMPDMDGIEVIRHLAEHKS--PASLILISGYDSGVLHSAETLALSCGLNVINTFTKP 109

>2j48_A Two-component sensor kinase; pseudo-receiver, circadian clock, transferase, response regulator, histidine protein kinase; NMR {Synechococcus elongatus} Length = 119

 Score = 69.0 bits (170), Expect = 1e-15
 Identities = 23/114 (20%), Positives = 45/114 (39%), Gaps = 14/114 (12%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
           H+L +++      ++  +L  +  KV  +  G+ AL              D L+  +I+ 
Sbjct: 3   HILLLEEEDEAATVVCEMLTAAGFKVIWLVDGSTALDQ-----------LDLLQPIVILM 51

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
            +  P  +   LL+ ++E       P+V+   E     +D  L   A   + KP
Sbjct: 52  AWPPPDQSCLLLLQHLREHQADPHPPLVLFLGEP---PVDPLLTAQASAILSKP 102

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

 Score = 69.1 bits (170), Expect = 2e-15
 Identities = 28/114 (24%), Positives = 48/114 (42%), Gaps = 13/114 (11%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
            +L V+D  V R L++               G  AL+                  +L+I 
Sbjct: 9   QILIVEDEQVFRSLLDSWFSSLGATTVLAADGVDALEL-----------LGGFTPDLMIC 57

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
           D  MP M G +LL+ I+      + PV+++S+ + +  I   L  G E+ ++KP
Sbjct: 58  DIAMPRMNGLKLLEHIRNRG--DQTPVLVISATENMADIAKALRLGVEDVLLKP 109

>2jk1_A HUPR, hydrogenase transcriptional regulatory protein HU; nucleotide-binding, transcription regulation; 2.10A {Rhodobacter capsulatus} PDB: 2vui_B 2vuh_B Length = 139

 Score = 68.7 bits (169), Expect = 3e-15
 Identities = 25/119 (21%), Positives = 48/119 (40%), Gaps = 15/119 (12%)

Query: 96  VLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITD 155
           +L VDD       ++  L+     V   +    A+  L           +   V +II D
Sbjct: 4   ILLVDDEPHSLAAMKLALE-DDFDVLTAQGAEAAIAIL-----------EEEWVQVIICD 51

Query: 156 YTMPGMTGYELLKKIKESSVFREVPVVIMSS-EDVLTQIDSCLEEGAEEYIVKPVKLSD 213
             MPG TG + L +++E   + E   +I++   D  + + +  + G  +++ KP     
Sbjct: 52  QRMPGRTGVDFLTEVRE--RWPETVRIIITGYTDSASMMAAINDAGIHQFLTKPWHPEQ 108

>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 = 68.0 bits (167), Expect = 5e-15
 Identities = 31/125 (24%), Positives = 57/125 (45%), Gaps = 21/125 (16%)

Query: 92  KELHVLAVDDSYVDRKLIERLLQIS--SCKVTAVESGTRALQYLGLDGEQSNVGFDALKV 149
           +   VL V+D+  D  LI R+L      C++  V++G +AL  +    +Q+   +D    
Sbjct: 4   RSKRVLVVEDNPDDIALIRRVLDRKDIHCQLEFVDNGAKALYQV----QQAK--YD---- 53

Query: 150 NLIITDYTMPGMTGYELLKKIKESSVFREVPVVIM----SSEDVLTQIDSCLEEGAEEYI 205
            LII D  +P   G+E++  +++    +  P+VI+    S +        C+  GA   +
Sbjct: 54  -LIILDIGLPIANGFEVMSAVRKPGANQHTPIVILTDNVSDDR----AKQCMAAGASSVV 108

Query: 206 VKPVK 210
            K   
Sbjct: 109 DKSSN 113

>1dcf_A ETR1 protein; beta-alpha five sandwich, transferase; 2.50A {Arabidopsis thaliana} SCOP: c.23.1.2 Length = 136

 Score = 66.8 bits (164), Expect = 2e-14
 Identities = 29/127 (22%), Positives = 53/127 (41%), Gaps = 23/127 (18%)

Query: 94  LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLII 153
           L VL +D++ V R + + LL    C+VT V S    L+ +  +              ++ 
Sbjct: 8   LKVLVMDENGVSRMVTKGLLVHLGCEVTTVSSNEECLRVVSHE-------HK-----VVF 55

Query: 154 TDYTMPGMTGYELLKKIKE---SSVFREVPVVIMS----SEDVLTQIDSCLEEGAEEYIV 206
            D  MPG+  Y++  +I E       +   +V +S            + C+  G +  ++
Sbjct: 56  MDVCMPGVENYQIALRIHEKFTKQRHQRPLLVALSGNTDKST----KEKCMSFGLDGVLL 111

Query: 207 KPVKLSD 213
           KPV L +
Sbjct: 112 KPVSLDN 118

>2zay_A Response regulator receiver protein; structural genomics, NYSGXRC, target 11006U, protein structure initiative; 2.00A {Desulfuromonas acetoxidans} Length = 147

 Score = 66.8 bits (164), Expect = 2e-14
 Identities = 22/118 (18%), Positives = 41/118 (34%), Gaps = 17/118 (14%)

Query: 96  VLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITD 155
           ++ VD            L      +    +   A+                   +LIIT+
Sbjct: 11  IMLVDTQLPALAASISALSQEGFDIIQCGNAIEAVPV-----------AVKTHPHLIITE 59

Query: 156 YTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSC---LEEGAEEYIVKPVK 210
             MP ++G +L   +K++     +PV+ +S              L+ G  ++I KPV 
Sbjct: 60  ANMPKISGMDLFNSLKKNPQTASIPVIALSG---RATAKEEAQLLDMGFIDFIAKPVN 114

>3kcn_A Adenylate cyclase homolog; SGX, PSI 2, structural genomics, protein structure initiative; 2.45A {Rhodopirellula baltica} Length = 151

 Score = 66.9 bits (164), Expect = 2e-14
 Identities = 31/124 (25%), Positives = 56/124 (45%), Gaps = 14/124 (11%)

Query: 91  SKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVN 150
           S    +L VDD Y     ++R L     +VT  ESG  AL  +                +
Sbjct: 2   SLNERILLVDDDYSLLNTLKRNLS-FDFEVTTCESGPEALACIKKSDP----------FS 50

Query: 151 LIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSE-DVLTQIDSCLEEGAEEYIVKPV 209
           +I+ D  MPGM G E+++K +   +      ++++   D+ T +++  E     ++ KP 
Sbjct: 51  VIMVDMRMPGMEGTEVIQKARL--ISPNSVYLMLTGNQDLTTAMEAVNEGQVFRFLNKPC 108

Query: 210 KLSD 213
           ++SD
Sbjct: 109 QMSD 112

>3cg4_A Response regulator receiver domain protein (CHEY-; structural genomics, unknown function; HET: MSE; 1.61A {Methanospirillum hungatei jf-1} Length = 142

 Score = 66.4 bits (163), Expect = 2e-14
 Identities = 23/118 (19%), Positives = 52/118 (44%), Gaps = 19/118 (16%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
            V+ VDD    R  ++ +L  +   + + +SG + +                    +++ 
Sbjct: 9   DVMIVDDDAHVRIAVKTILSDAGFHIISADSGGQCIDL-----------LKKGFSGVVLL 57

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMS--SEDVLTQIDSC--LEEGAEEYIVKP 208
           D  MPGM G++ ++ I ++S+ + + +V+++  +            L+E   +YI KP
Sbjct: 58  DIMMPGMDGWDTIRAILDNSLEQGIAIVMLTAKNAP----DAKMIGLQEYVVDYITKP 111

>3c3m_A Response regulator receiver protein; structural genomics, unknown function, PSI-2, protein struct initiative; HET: MSE; 1.70A {Methanoculleus marisnigri JR1} Length = 138

 Score = 66.4 bits (163), Expect = 2e-14
 Identities = 27/117 (23%), Positives = 52/117 (44%), Gaps = 19/117 (16%)

Query: 96  VLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITD 155
           +L VDDS +   +   +L+    +     SG   L+             +A   +L++ D
Sbjct: 6   ILVVDDSPMIVDVFVTMLERGGYRPITAFSGEECLEA-----------LNATPPDLVLLD 54

Query: 156 YTMPGMTGYELLKKIKESSVFREVPVVIMS----SEDVLTQIDSCLEEGAEEYIVKP 208
             M  M G+E L++IK     R++PV++++    + +   +         E+YI+KP
Sbjct: 55  IMMEPMDGWETLERIKTDPATRDIPVLMLTAKPLTPEEANE----YGSYIEDYILKP 107

>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 = 65.5 bits (161), Expect = 3e-14
 Identities = 30/120 (25%), Positives = 50/120 (41%), Gaps = 26/120 (21%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
           H+L V+D  V R  ++ + +     V     G    Q                 +NL+I 
Sbjct: 5   HILIVEDELVTRNTLKSIFEAEGYDVFEATDGAEMHQI-----------LSEYDINLVIM 53

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLT----QID--SCLEEGAEEYIVKP 208
           D  +PG  G  L ++++E +    V  ++      LT    ++D    LE GA++YI KP
Sbjct: 54  DINLPGKNGLLLARELREQA---NVA-LMF-----LTGRDNEVDKILGLEIGADDYITKP 104

>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 = 66.0 bits (162), Expect = 3e-14
 Identities = 27/115 (23%), Positives = 48/115 (41%), Gaps = 14/115 (12%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
            +L +D     R  ++  L  S   V   ++   AL+             D    +L+I 
Sbjct: 5   KILIIDQQDFSRIELKNFLD-SEYLVIESKNEKEALEQ-----------IDHHHPDLVIL 52

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSS-EDVLTQIDSCLEEGAEEYIVKP 208
           D  + G     L  K+K S   + VP++++ S E     ++  L  GA++Y+ KP
Sbjct: 53  DMDIIGENSPNLCLKLKRSKGLKNVPLILLFSSEHKEAIVNG-LHSGADDYLTKP 106

>2qr3_A Two-component system response regulator; structural genomics, signal receiver, PSI-2, protein structu initiative; 1.80A {Bacteroides fragilis} Length = 140

 Score = 65.7 bits (161), Expect = 5e-14
 Identities = 26/120 (21%), Positives = 50/120 (41%), Gaps = 20/120 (16%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
            ++ VDD+      ++ LL+    KV  + S       L                 +++ 
Sbjct: 5   TIIIVDDNKGVLTAVQLLLKNHFSKVITLSSPVSLSTVL-----------REENPEVVLL 53

Query: 155 DYTMP-----GMTGYELLKKIKESSVFREVPVVIMSSE-DVLTQIDSCLEEGAEEYIVKP 208
           D         G  G   L +IK    +R++PVV+ ++  D+   +   ++EGA +++VKP
Sbjct: 54  DMNFTSGINNGNEGLFWLHEIKRQ--YRDLPVVLFTAYADIDLAVRG-IKEGASDFVVKP 110

>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 = 64.9 bits (159), Expect = 9e-14
 Identities = 32/120 (26%), Positives = 47/120 (39%), Gaps = 23/120 (19%)

Query: 96  VLAVDDSYVDRKLIERLL-QISSCKVTAV-ESGTRALQYLGLDGEQSNVGFDALKVNLII 153
           V+ VDD+ + R  I   +  +   KV A   +G  AL  L               V+LI+
Sbjct: 16  VMIVDDAAMMRLYIASFIKTLPDFKVVAQAANGQEALDKLAAQ----------PNVDLIL 65

Query: 154 TDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDS-----CLEEGAEEYIVKP 208
            D  MP M G E L+  K         + ++SS   +    S       E GA+  + KP
Sbjct: 66  LDIEMPVMDGMEFLRHAKLK---TRAKICMLSS---VAVSGSPHAARARELGADGVVAKP 119

>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 = 64.0 bits (157), Expect = 1e-13
 Identities = 28/120 (23%), Positives = 49/120 (40%), Gaps = 26/120 (21%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
           H++ V+D  V +  ++         V+   SG    +                 V+LI+ 
Sbjct: 4   HIVIVEDEPVTQARLQSYFTQEGYTVSVTASGAGLREI-----------MQNQSVDLILL 52

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLT----QID--SCLEEGAEEYIVKP 208
           D  +P   G  L + ++E S    V  +I+     +T    +ID    LE GA++Y+ KP
Sbjct: 53  DINLPDENGLMLTRALRERS---TVG-IIL-----VTGRSDRIDRIVGLEMGADDYVTKP 103

>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 = 66.2 bits (162), Expect = 1e-13
 Identities = 25/119 (21%), Positives = 53/119 (44%), Gaps = 13/119 (10%)

Query: 91  SKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVN 150
           + +  V  VDD    R+ +  LL+ +  +V   +  +  L++               +  
Sbjct: 2   TAKPTVFVVDDDMSVREGLRNLLRSAGFEVETFDCASTFLEHR-----------RPEQHG 50

Query: 151 LIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPV 209
            ++ D  MPGM+G EL +++   S    +P+V +++   +      ++ GA E++ KP 
Sbjct: 51  CLVLDMRMPGMSGIELQEQLTAISD--GIPIVFITAHGDIPMTVRAMKAGAIEFLPKPF 107

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

 Score = 64.6 bits (158), Expect = 1e-13
 Identities = 18/127 (14%), Positives = 42/127 (33%), Gaps = 14/127 (11%)

Query: 83  AMATVAECSKELHVLAVDDSYVDRKLIERLLQ-ISSCKVTAVESGTRALQYLGLDGEQSN 141
           A+ T    +K   V         ++ +   L  ++   V   E+              ++
Sbjct: 4   AINTKVTPTKRKQVALFSSDPNFKRDVATRLDALAIYDVRVSETDDFLKGPP------AD 57

Query: 142 VGFDALKVNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGA 201
                    ++I D     + G   + + +    +  VP++ +S E    Q    +   A
Sbjct: 58  TRPG-----IVILDLGGGDLLGKPGIVEARAL--WATVPLIAVSDELTSEQTRVLVRMNA 110

Query: 202 EEYIVKP 208
            +++ KP
Sbjct: 111 SDWLHKP 117

>2b4a_A BH3024; flavodoxin-like fold, structural genomics, joint center for structural genomics, JCSG, protein structure initiative; 2.42A {Bacillus halodurans} SCOP: c.23.1.1 Length = 138

 Score = 63.4 bits (155), Expect = 3e-13
 Identities = 24/116 (20%), Positives = 45/116 (38%), Gaps = 19/116 (16%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
            V  V+D      LI+  L     +VT   SG+   Q+            D     L+I 
Sbjct: 17  RVTLVEDEPSHATLIQYHLNQLGAEVTVHPSGSAFFQHRSQLS-----TCD-----LLIV 66

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMS--SEDVLTQIDSCLEEGAEEYIVKP 208
              +  ++ + LL  +KE +  ++  V+I++    +++        E    Y+ KP
Sbjct: 67  SDQLVDLSIFSLLDIVKEQT--KQPSVLILTTGRHELIE-----SSEHNLSYLQKP 115

>3h5i_A Response regulator/sensory box protein/ggdef domain protein; structural genomics, transcription, PSI-2; 1.90A {Carboxydothermus hydrogenoformans z-2901} Length = 140

 Score = 63.4 bits (155), Expect = 4e-13
 Identities = 26/122 (21%), Positives = 49/122 (40%), Gaps = 18/122 (14%)

Query: 92  KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNL 151
           K+  +L V+DS    K I  +L      V    +G  A++ +                +L
Sbjct: 4   KDKKILIVEDSKFQAKTIANILNKYGYTVEIALTGEAAVEKV----------SGGWYPDL 53

Query: 152 IITDYTMPG-MTGYELLKKIKESSVFREVPVVIMS--SEDVLTQIDSCLEEGAEEYIVKP 208
           I+ D  +   M G +    I++ S   E+PVV ++  +E  +  ++      A  Y++K 
Sbjct: 54  ILMDIELGEGMDGVQTALAIQQIS---ELPVVFLTAHTEPAV--VEKIRSVTAYGYVMKS 108

Query: 209 VK 210
             
Sbjct: 109 AT 110

>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 = 66.0 bits (162), Expect = 4e-13
 Identities = 32/120 (26%), Positives = 54/120 (45%), Gaps = 24/120 (20%)

Query: 96  VLAVDDSYVDRKLIERLL-QISSCKVTAV-ESGTRALQYLGLDGEQSNVGFDALKVNLII 153
           VL+VDDS + R+++  ++   S  ++ A       A   +                +++ 
Sbjct: 6   VLSVDDSALMRQIMTEIINSHSDMEMVATAPDPLVARDLI-----------KKFNPDVLT 54

Query: 154 TDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDS-----CLEEGAEEYIVKP 208
            D  MP M G + L+K+      R +PVV++SS   LT   S      LE GA +++ KP
Sbjct: 55  LDVEMPRMDGLDFLEKLMRL---RPMPVVMVSS---LTGKGSEVTLRALELGAIDFVTKP 108

>1tmy_A CHEY protein, TMY; chemotaxis, phosphoryl transfer, signal transduction; 1.90A {Thermotoga maritima} SCOP: c.23.1.1 PDB: 2tmy_A 3tmy_A 4tmy_A 1u0s_Y Length = 120

 Score = 62.1 bits (152), Expect = 5e-13
 Identities = 27/119 (22%), Positives = 58/119 (48%), Gaps = 14/119 (11%)

Query: 96  VLAVDDSYVDRKLIERLLQISSCKVTAV-ESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
           VL VDD+   R +++ ++  +  +V     +G  A++            +  LK +++  
Sbjct: 5   VLIVDDAAFMRMMLKDIITKAGYEVAGEATNGREAVEK-----------YKELKPDIVTM 53

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD 213
           D TMP M G + +K+I +  +     +++ S+      +   ++ GA+++IVKP + S 
Sbjct: 54  DITMPEMNGIDAIKEIMK--IDPNAKIIVCSAMGQQAMVIEAIKAGAKDFIVKPFQPSR 110

>3cu5_A Two component transcriptional regulator, ARAC FAM; structural genomics, protein structure initiative; 2.60A {Clostridium phytofermentans isdg} Length = 141

 Score = 62.6 bits (153), Expect = 6e-13
 Identities = 27/126 (21%), Positives = 49/126 (38%), Gaps = 26/126 (20%)

Query: 96  VLAVDDSYVDRKLIERLLQISSCKVTAV---ESGTRALQYLGLDGEQSNVGFDALKVNLI 152
           +L VDD  + R  +   +   +     +   + G  A+Q                  N++
Sbjct: 5   ILIVDDEKLTRDGLIANINWKALSFDQIDQADDGINAIQIA-----------LKHPPNVL 53

Query: 153 ITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQID-----SCLEEGAEEYIVK 207
           +TD  MP M G EL+  I +   + +  V+ MS        D     + ++  A  Y+ K
Sbjct: 54  LTDVRMPRMDGIELVDNILKL--YPDCSVIFMSGYS-----DKEYLKAAIKFRAIRYVEK 106

Query: 208 PVKLSD 213
           P+  S+
Sbjct: 107 PIDPSE 112

>3t8y_A CHEB, chemotaxis response regulator protein-glutamate methylesterase; CHEA, hydrolase; 1.90A {Thermotoga maritima} Length = 164

 Score = 63.1 bits (154), Expect = 7e-13
 Identities = 33/120 (27%), Positives = 52/120 (43%), Gaps = 24/120 (20%)

Query: 96  VLAVDDSYVDRKLIERLL-QISSCKVTAV-ESGTRALQYLGLDGEQSNVGFDALKVNLII 153
           VL VDDS   R +++ ++      KV    + G  A++               LK ++I 
Sbjct: 28  VLVVDDSAFMRMVLKDIIDSQPDMKVVGFAKDGLEAVEKA-----------IELKPDVIT 76

Query: 154 TDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDS-----CLEEGAEEYIVKP 208
            D  MP + G E LK I +        V+++SS   LT+  +      L  GA ++I KP
Sbjct: 77  MDIEMPNLNGIEALKLIMKK---APTRVIMVSS---LTEEGAAITIEALRNGAVDFITKP 130

>2qzj_A Two-component response regulator; 11017X, PSI-II, structural genomics; 2.89A {Clostridium difficile} Length = 136

 Score = 62.1 bits (152), Expect = 7e-13
 Identities = 22/118 (18%), Positives = 47/118 (39%), Gaps = 22/118 (18%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
            +L +D    + + ++  L+     +    +   A+               + K +LI  
Sbjct: 6   KILIIDGDKDNCQKLKGFLEEKGISIDLAYNCEEAIGK-----------IFSNKYDLIFL 54

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMS--SEDVLTQID--SCLEEGAEEYIVKP 208
           +  +    G+ L KKI+  +     P+V M+  +ED        + L  G ++Y++KP
Sbjct: 55  EIILSDGDGWTLCKKIRNVT---TCPIVYMTYINED----QSILNALNSGGDDYLIKP 105

>2rdm_A Response regulator receiver protein; structural genomics, unknown function, PSI-2, protein struct initiative; HET: MSE; 1.76A {Sinorhizobium medicae} Length = 132

 Score = 61.8 bits (151), Expect = 9e-13
 Identities = 25/124 (20%), Positives = 50/124 (40%), Gaps = 15/124 (12%)

Query: 91  SKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVN 150
            + + +L  DD  +     E  L  +   VTAV SG +A++ L     +S    D     
Sbjct: 3   LEAVTILLADDEAILLLDFESTLTDAGFLVTAVSSGAKAIEML-----KSGAAID----- 52

Query: 151 LIITDYTMP-GMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPV 209
            ++TD        G+++ +  +E  +   +P+V +S    L    + + +     + KP 
Sbjct: 53  GVVTDIRFCQPPDGWQVARVARE--IDPNMPIVYISGHAALEWASNGVPDSI--ILEKPF 108

Query: 210 KLSD 213
             + 
Sbjct: 109 TSAQ 112

>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 = 60.9 bits (149), Expect = 1e-12
 Identities = 30/120 (25%), Positives = 55/120 (45%), Gaps = 26/120 (21%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
            +L VDD      ++E  L+    +V     G  A++             + L+ +LI+ 
Sbjct: 4   KILVVDDEKPIADILEFNLRKEGYEVHCAHDGNEAVEM-----------VEELQPDLILL 52

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLT----QID--SCLEEGAEEYIVKP 208
           D  +P   G E+ +++++     ++P +IM     LT    +ID    LE GA++Y+ KP
Sbjct: 53  DIMLPNKDGVEVCREVRKKY---DMP-IIM-----LTAKDSEIDKVIGLEIGADDYVTKP 103

>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 = 60.9 bits (149), Expect = 2e-12
 Identities = 31/118 (26%), Positives = 56/118 (47%), Gaps = 22/118 (18%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
            +L VDD      +I+  +     +V    +G  AL+            F+A + ++II 
Sbjct: 3   KILIVDDEKPISDIIKFNMTKEGYEVVTAFNGREALEQ-----------FEAEQPDIIIL 51

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMS--SEDVLTQID--SCLEEGAEEYIVKP 208
           D  +P + G E+ K I+++S    VP++++S    +     D    LE GA++Y+ KP
Sbjct: 52  DLMLPEIDGLEVAKTIRKTS---SVPILMLSAKDSE----FDKVIGLELGADDYVTKP 102

>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 = 61.0 bits (149), Expect = 2e-12
 Identities = 27/119 (22%), Positives = 56/119 (47%), Gaps = 15/119 (12%)

Query: 93  ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLI 152
           +  V  VDD    RK +  +L ++   V   +S    L +               +  ++
Sbjct: 3   DYTVHIVDDEEPVRKSLAFMLTMNGFAVKMHQSAEAFLAFAPDV-----------RNGVL 51

Query: 153 ITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSE-DVLTQIDSCLEEGAEEYIVKPVK 210
           +TD  MP M+G ELL+ + +  +   +P ++++   DV   +++ ++ GA ++I KP +
Sbjct: 52  VTDLRMPDMSGVELLRNLGDLKI--NIPSIVITGHGDVPMAVEA-MKAGAVDFIEKPFE 107

>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 = 60.9 bits (148), Expect = 2e-12
 Identities = 26/117 (22%), Positives = 46/117 (39%), Gaps = 13/117 (11%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
            +L VDD        +++L+    +V    +    L  +       N  F+     L + 
Sbjct: 5   RILIVDDDTAILDSTKQILEFEGYEVEIAATAGEGLAKI------ENEFFN-----LALF 53

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKL 211
              +P M G ELL+K  +      +  ++++    L      L  GA+ YI+KPV  
Sbjct: 54  XIKLPDMEGTELLEKAHKLR--PGMKKIMVTGYASLENSVFSLNAGADAYIMKPVNP 108

>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 = 60.5 bits (148), Expect = 2e-12
 Identities = 30/116 (25%), Positives = 54/116 (46%), Gaps = 18/116 (15%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
           +VL V+D    R+ +   L+    +V   E+  R L                 K +LII 
Sbjct: 3   NVLIVEDEQAIRRFLRTALEGDGMRVFEAETLQRGLLE-----------AATRKPDLIIL 51

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQID--SCLEEGAEEYIVKP 208
           D  +P   G E ++ +++ S    VPV+++S+     + D  + L+ GA++Y+ KP
Sbjct: 52  DLGLPDGDGIEFIRDLRQWS---AVPVIVLSARS--EESDKIAALDAGADDYLSKP 102

>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 = 60.6 bits (148), Expect = 3e-12
 Identities = 30/120 (25%), Positives = 53/120 (44%), Gaps = 23/120 (19%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
            +L VDD     +++E +L+ +  +V    SG  ALQ                  + +I 
Sbjct: 6   TLLIVDDDDTVAEMLELVLRGAGYEVRRAASGEEALQQ-----------IYKNLPDALIC 54

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLT----QIDSC--LEEGAEEYIVKP 208
           D  +PG+ GY L K++++  + + +P ++M     LT            E GA +Y+ KP
Sbjct: 55  DVLLPGIDGYTLCKRVRQHPLTKTLP-ILM-----LTAQGDISAKIAGFEAGANDYLAKP 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 = 59.8 bits (146), Expect = 5e-12
 Identities = 28/120 (23%), Positives = 55/120 (45%), Gaps = 23/120 (19%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
            +L V+D    R+++  +L+ +  +    E    A+              +    +LI+ 
Sbjct: 4   RILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQ-----------LNEPWPDLILL 52

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLT----QIDSC--LEEGAEEYIVKP 208
            + +PG +G + +K ++  S+ R++P V+M     LT    + D    LE GA++ I KP
Sbjct: 53  AWMLPGGSGIQFIKHLRRESMTRDIP-VVM-----LTARGEEEDRVRGLETGADDCITKP 106

>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 = 60.3 bits (146), Expect = 6e-12
 Identities = 28/129 (21%), Positives = 49/129 (37%), Gaps = 12/129 (9%)

Query: 86  TVAECSKELHVLAVDDSYVDRKLIERLLQISSCKVTAV-ESGTRALQYLGLDGEQSNVGF 144
              +     +VL VDDS    K + ++       +      G  A+       +      
Sbjct: 29  INYDTGIPFNVLIVDDSVFTVKQLTQIFTSEGFNIIDTAADGEEAVIKY----KNHYPNI 84

Query: 145 DALKVNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEY 204
           D     ++    TMP M G   L  I E    +   V+++S+      +  CL +GA+ +
Sbjct: 85  D-----IVTLXITMPKMDGITCLSNIMEFD--KNARVIMISALGKEQLVKDCLIKGAKTF 137

Query: 205 IVKPVKLSD 213
           IVKP+  + 
Sbjct: 138 IVKPLDRAK 146

>3lte_A Response regulator; structural genomics, PSI, protein structure initiative, NYSG YORK structural genomix research consortium, nysgxrc; 2.00A {Bermanella marisrubri} Length = 132

 Score = 59.5 bits (145), Expect = 7e-12
 Identities = 23/116 (19%), Positives = 49/116 (42%), Gaps = 16/116 (13%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
            +L VDD       IER+L+    +V    +G  A                  +  ++  
Sbjct: 8   RILVVDDDQAMAAAIERVLKRDHWQVEIAHNGFDAGIK-----------LSTFEPAIMTL 56

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQID--SCLEEGAEEYIVKP 208
           D +MP + G ++++ ++++      P +++ S     +      + EGA++Y+ KP
Sbjct: 57  DLSMPKLDGLDVIRSLRQNK-VANQPKILVVSGL--DKAKLQQAVTEGADDYLEKP 109

>2gkg_A Response regulator homolog; social motility, receiver domain, signalling, high resolutio signaling protein; 1.00A {Myxococcus xanthus} PDB: 2i6f_A 2nt4_A 2nt3_A Length = 127

 Score = 59.4 bits (145), Expect = 8e-12
 Identities = 23/115 (20%), Positives = 45/115 (39%), Gaps = 13/115 (11%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
            +L V+        +   L+     V     G  +++                + +L++ 
Sbjct: 7   KILIVESDTALSATLRSALEGRGFTVDETTDGKGSVEQ-----------IRRDRPDLVVL 55

Query: 155 DYTM-PGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
              +  G  GY +  K+K+    + VP+VI+ + D   Q    L+  A+EY+ KP
Sbjct: 56  AVDLSAGQNGYLICGKLKKDDDLKNVPIVIIGNPDGFAQHRK-LKAHADEYVAKP 109

>2oqr_A Sensory transduction protein REGX3; response regulator, winged-helix-turn-helix, DNA-binding, 3D swapping, two component system; 2.03A {Mycobacterium tuberculosis H37RV} Length = 230

 Score = 61.4 bits (150), Expect = 8e-12
 Identities = 33/116 (28%), Positives = 58/116 (50%), Gaps = 18/116 (15%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
            VL V+D       +  LL+    + T V  G  AL             FD    ++++ 
Sbjct: 6   SVLIVEDEESLADPLAFLLRKEGFEATVVTDGPAALAE-----------FDRAGADIVLL 54

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQID--SCLEEGAEEYIVKP 208
           D  +PGM+G ++ K+++  S    VPV+++++ D  ++ID    LE GA++Y+ KP
Sbjct: 55  DLMLPGMSGTDVCKQLRARS---SVPVIMVTARD--SEIDKVVGLELGADDYVTKP 105

>2gwr_A DNA-binding response regulator MTRA; two-component regulatory system, transcription regulation, phosphorylation, OMPR family; 2.10A {Mycobacterium tuberculosis} PDB: 3nhz_A Length = 238

 Score = 60.2 bits (147), Expect = 2e-11
 Identities = 29/116 (25%), Positives = 57/116 (49%), Gaps = 18/116 (15%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
            +L VDD     +++  +L+        +  GT+AL                L+ +L++ 
Sbjct: 7   RILVVDDDASLAEMLTIVLRGEGFDTAVIGDGTQALTA-----------VRELRPDLVLL 55

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSC--LEEGAEEYIVKP 208
           D  +PGM G ++ + ++  S    VP+V+++++     +D    LE GA++YI+KP
Sbjct: 56  DLMLPGMNGIDVCRVLRADS---GVPIVMLTAKT--DTVDVVLGLESGADDYIMKP 106

>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 = 57.9 bits (141), Expect = 3e-11
 Identities = 31/120 (25%), Positives = 52/120 (43%), Gaps = 25/120 (20%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
            +L VDD      L++  L+ S   V     G  AL+             +  K +LI+ 
Sbjct: 5   KILVVDDEESIVTLLQYNLERSGYDVITASDGEEALKK-----------AETEKPDLIVL 53

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLT----QIDSC--LEEGAEEYIVKP 208
           D  +P + G E+ K++++       P ++M     LT    + D    LE GA++Y+ KP
Sbjct: 54  DVMLPKLDGIEVCKQLRQQK--LMFP-ILM-----LTAKDEEFDKVLGLELGADDYMTKP 105

>3a10_A Response regulator; phosphoacceptor, signaling protein; HET: MSE PG4; 1.63A {Thermotoga maritima} PDB: 3a0r_B* 3a0u_A* Length = 116

 Score = 57.1 bits (139), Expect = 4e-11
 Identities = 27/114 (23%), Positives = 54/114 (47%), Gaps = 15/114 (13%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
            +L VDD    R+L++  LQ    ++   E+G  AL+            F +   +L+I 
Sbjct: 3   RILVVDDEPNIRELLKEELQEEGYEIDTAENGEEALKK-----------FFSGNYDLVIL 51

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
           D  MPG++G E+  +I++    ++  ++++++              A+EY+VK 
Sbjct: 52  DIEMPGISGLEVAGEIRKKK--KDAKIILLTAYS--HYRSDMSSWAADEYVVKS 101

>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 = 58.5 bits (142), Expect = 4e-11
 Identities = 19/120 (15%), Positives = 47/120 (39%), Gaps = 15/120 (12%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
           + L +DD+ V    + R L+     V    +   AL+            F+      I  
Sbjct: 9   NFLVIDDNEVFAGTLARGLERRGYAVRQAHNKDEALKLA------GAEKFE-----FITV 57

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSSED-VLTQIDSCLEEGAEEYIVKPVKLSD 213
              +   +G  L+  + +     +  +++++    + T + + +++GA+ Y+ KP  +  
Sbjct: 58  XLHLGNDSGLSLIAPLCDLQ--PDARILVLTGYASIATAVQA-VKDGADNYLAKPANVES 114

>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 = 57.2 bits (139), Expect = 6e-11
 Identities = 26/125 (20%), Positives = 55/125 (44%), Gaps = 16/125 (12%)

Query: 94  LHVLAVDDSYVDRKLIERLLQISSCK-VTAVESGTRALQYLGLDGEQSNVGFDALKVNLI 152
           + +L V+D++V++++I+R+L +   + +     G  A   +     +    ++     +I
Sbjct: 3   VKILVVEDNHVNQEVIKRMLNLEGIENIELACDGQEAFDKVKELTSKGE-NYN-----MI 56

Query: 153 ITDYTMPGMTGYELLKKIKESSVFREVPVVIMS----SEDVLTQIDSCLEEGAEEYIVKP 208
             D  MP + G    K I+    +   P+V ++      +    I  CLE G   ++ KP
Sbjct: 57  FMDVQMPKVDGLLSTKMIRRDLGYT-SPIVALTAFADDSN----IKECLESGMNGFLSKP 111

Query: 209 VKLSD 213
           +K   
Sbjct: 112 IKRPK 116

>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 = 56.7 bits (137), Expect = 6e-11
 Identities = 32/116 (27%), Positives = 55/116 (47%), Gaps = 11/116 (9%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
            VL VDDS V RK++   L+    +V   E+G  AL+                  +LI+ 
Sbjct: 4   KVLLVDDSAVLRKIVSFNLKKEGYEVIEAENGQIALEK-----------LSEFTPDLIVL 52

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVK 210
              MP M G+ +LKK++E   ++ +PV++++++         L  GA + + KP  
Sbjct: 53  XIMMPVMDGFTVLKKLQEKEEWKRIPVIVLTAKGGEEDESLALSLGARKVMRKPFS 108

>3kto_A Response regulator receiver protein; PSI-II,structural genomics, protein structure initiative; 1.98A {Pseudoalteromonas atlantica T6C} Length = 136

 Score = 56.8 bits (138), Expect = 8e-11
 Identities = 21/123 (17%), Positives = 45/123 (36%), Gaps = 17/123 (13%)

Query: 91  SKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVN 150
           +    +  VD     R  + +LL      +    S    ++    D              
Sbjct: 4   NHHPIIYLVDHQKDARAALSKLLSPLDVTIQCFASAESFMRQQISDDA-----------I 52

Query: 151 LIITDYTMPGM--TGYELLKKIKESSVFREVPVVIMSSE-DVLTQIDSCLEEGAEEYIVK 207
            +I +  +     +G ELL+ + +      +P ++M+S  D+ T + + +   A ++I K
Sbjct: 53  GMIIEAHLEDKKDSGIELLETLVKRGF--HLPTIVMASSSDIPTAVRA-MRASAADFIEK 109

Query: 208 PVK 210
           P  
Sbjct: 110 PFI 112

>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 = 58.6 bits (141), Expect = 1e-10
 Identities = 31/134 (23%), Positives = 56/134 (41%), Gaps = 13/134 (9%)

Query: 80  PFWAMATVAECSKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQ 139
              A       + E  VL VDD     +L+   L+    +V    +G +AL         
Sbjct: 10  LVTAGTPGENTTPEARVLVVDDEANIVELLSVSLKFQGFEVYTATNGAQALDRA------ 63

Query: 140 SNVGFDALKVNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEE 199
                D      +I D  MPGM G+ +L++++   +  + P + +++ D L    + L  
Sbjct: 64  RETRPD-----AVILDVXMPGMDGFGVLRRLRADGI--DAPALFLTARDSLQDKIAGLTL 116

Query: 200 GAEEYIVKPVKLSD 213
           G ++Y+ KP  L +
Sbjct: 117 GGDDYVTKPFSLEE 130

>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 = 56.2 bits (136), Expect = 5e-10
 Identities = 28/130 (21%), Positives = 54/130 (41%), Gaps = 15/130 (11%)

Query: 85  ATVAECSKELHVLAVDDSYVDRKLIERLLQISSCKVTA-VESGTRALQYLGLDGEQSNVG 143
            T A+ +    VL  +D  + R  +  +L+    ++      G  A++            
Sbjct: 5   TTDADAAVPRRVLIAEDEALIRMDLAEMLREEGYEIVGEAGDGQEAVELA---------- 54

Query: 144 FDALKVNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEE 203
            +  K +L+I D  MP   G +   +I      R  P+V++++      ++   + GA  
Sbjct: 55  -ELHKPDLVIMDVKMPRRDGIDAASEIASK---RIAPIVVLTAFSQRDLVERARDAGAMA 110

Query: 204 YIVKPVKLSD 213
           Y+VKP  +SD
Sbjct: 111 YLVKPFSISD 120

>3mm4_A Histidine kinase homolog; receiver domain, CKI1, cytokinin signaling, ROS fold, CHEY-like, transferase; 2.00A {Arabidopsis thaliana} PDB: 3mmn_A Length = 206

 Score = 55.9 bits (135), Expect = 5e-10
 Identities = 35/138 (25%), Positives = 61/138 (44%), Gaps = 14/138 (10%)

Query: 83  AMATVAECSKELHVLAVDDSYVDRKLIERLLQISSC-KVTAVESGTRALQYL--GLDGEQ 139
           +  +  E  +   VL VDD+++ RK+    L+     +V   +SG  AL+ +  GL   +
Sbjct: 51  SKPSDDEFLRGKRVLVVDDNFISRKVATGKLKKMGVSEVEQCDSGKEALRLVTEGLTQRE 110

Query: 140 SNVGFDALKVNLIITDYTMPGMTGYELLKKI--KESSVFREVPVVIMS-----SEDVLTQ 192
                D L  + I  D  MP M GYE  ++I   E S     P++ +S     SE+    
Sbjct: 111 EQGSVDKLPFDYIFMDCQMPEMDGYEATREIRKVEKSYGVRTPIIAVSGHDPGSEE---- 166

Query: 193 IDSCLEEGAEEYIVKPVK 210
               ++ G + ++ K + 
Sbjct: 167 ARETIQAGMDAFLDKSLN 184

>3cg0_A Response regulator receiver modulated diguanylate with PAS/PAC sensor; signal receiver domain, diguanylate cyclase; 2.15A {Desulfovibrio desulfuricans subsp} Length = 140

 Score = 54.9 bits (133), Expect = 5e-10
 Identities = 20/130 (15%), Positives = 45/130 (34%), Gaps = 16/130 (12%)

Query: 86  TVAECSKELHVLAVDDSYVDRKLIERLLQISSCKVTAV-ESGTRALQYLGLDGEQSNVGF 144
           ++        VL V+D  +    +   L+     V  V ++G  A++             
Sbjct: 2   SLTASDDLPGVLIVEDGRLAAATLRIQLESLGYDVLGVFDNGEEAVRC-----------A 50

Query: 145 DALKVNLIITDYTMPG-MTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEE 203
             L+ ++ + D  + G + G E   ++        +P++ ++S   +             
Sbjct: 51  PDLRPDIALVDIMLCGALDGVETAARLAAGC---NLPIIFITSSQDVETFQRAKRVNPFG 107

Query: 204 YIVKPVKLSD 213
           Y+ KPV    
Sbjct: 108 YLAKPVAADT 117

>1p2f_A Response regulator; DRRB, OMPR/PHOB, transcription; HET: MSE; 1.80A {Thermotoga maritima} SCOP: a.4.6.1 c.23.1.1 PDB: 3nns_A* Length = 220

 Score = 55.2 bits (134), Expect = 1e-09
 Identities = 28/118 (23%), Positives = 49/118 (41%), Gaps = 24/118 (20%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
            +  VDD     K +   LQ    +V    +G   L              D    ++++ 
Sbjct: 4   KIAVVDDDKNILKKVSEKLQ-QLGRVKTFLTGEDFLN-------------DEEAFHVVVL 49

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMS--SEDVLTQIDSC--LEEGAEEYIVKP 208
           D  +P  +GYE+ + IKE+    E  V++++  S+D           E GA++Y+ KP
Sbjct: 50  DVMLPDYSGYEICRMIKETR--PETWVILLTLLSDD----ESVLKGFEAGADDYVTKP 101

>3c97_A Signal transduction histidine kinase; structural genomics, signaling, PSI-2, protein structure initiative; 1.70A {Aspergillus oryzae RIB40} Length = 140

 Score = 53.7 bits (130), Expect = 1e-09
 Identities = 29/127 (22%), Positives = 54/127 (42%), Gaps = 25/127 (19%)

Query: 94  LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLII 153
           L VL  +D+ + R +  + L+  +  +T V +G +ALQ         N  FD     +II
Sbjct: 11  LSVLIAEDNDICRLVAAKALEKCTNDITVVTNGLQALQAY------QNRQFD-----VII 59

Query: 154 TDYTMPGMTGYELLKKIKE---SSVFREVPVVIMS----SEDVLTQIDSCLEEGAEEYIV 206
            D  MP M G E + +I+    +   +   ++ ++     +D             +EY+ 
Sbjct: 60  MDIQMPVMDGLEAVSEIRNYERTHNTKRASIIAITADTIDDD-------RPGAELDEYVS 112

Query: 207 KPVKLSD 213
           KP+  + 
Sbjct: 113 KPLNPNQ 119

>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 = 54.8 bits (133), Expect = 2e-09
 Identities = 31/117 (26%), Positives = 53/117 (45%), Gaps = 19/117 (16%)

Query: 95  HVLAVDDSYVDRKL---IERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNL 151
            VL V+D   +R L   I   L+     V     G   + Y+ L+       FD     +
Sbjct: 4   RVLVVED---ERDLADLITEALKKEMFTVDVCYDGEEGM-YMALNEP-----FD-----V 49

Query: 152 IITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
           +I D  +P   G+E+LK ++ES      PV+++++   +      L  GA++Y+ KP
Sbjct: 50  VILDIMLPVHDGWEILKSMRESG--VNTPVLMLTALSDVEYRVKGLNMGADDYLPKP 104

>1ys7_A Transcriptional regulatory protein PRRA; response regulator, DNA binding domain, phosphorylation; 1.58A {Mycobacterium tuberculosis} SCOP: a.4.6.1 c.23.1.1 PDB: 1ys6_A Length = 233

 Score = 54.4 bits (132), Expect = 2e-09
 Identities = 31/114 (27%), Positives = 52/114 (45%), Gaps = 13/114 (11%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
            VL VDD       +ER L++S  +V     G  AL+        +    D      I+ 
Sbjct: 9   RVLVVDDDSDVLASLERGLRLSGFEVATAVDGAEALRSA------TENRPD-----AIVL 57

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
           D  MP + G  ++  ++      +VPV ++S+   +    + LE GA++Y+VKP
Sbjct: 58  DINMPVLDGVSVVTALRAMDN--DVPVCVLSARSSVDDRVAGLEAGADDYLVKP 109

>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 = 54.0 bits (130), Expect = 4e-09
 Identities = 26/135 (19%), Positives = 46/135 (34%), Gaps = 22/135 (16%)

Query: 83  AMATVAECSKELHVLAVDDSYVDRKLIERLLQISSCKVTAV-ESGTRALQYLGLDGEQSN 141
                 +      VL ++D  V    IE L++     VT +  +   AL+          
Sbjct: 150 DAQAEIDAELATEVLIIEDEPVIAADIEALVRELGHDVTDIAATRGEALEA--------- 200

Query: 142 VGFDALKVNLIITDYTMP-GMTGYELLKKIKESSVFREVPVVIMS--SEDVLTQIDSCLE 198
                    L++ D  +  G +G + +K I       +VPV+ ++   E +LT       
Sbjct: 201 --VTRRTPGLVLADIQLADGSSGIDAVKDILGRM---DVPVIFITAFPERLLTG----ER 251

Query: 199 EGAEEYIVKPVKLSD 213
                 I KP +   
Sbjct: 252 PEPTFLITKPFQPET 266

>2pl1_A Transcriptional regulatory protein PHOP; CHEY-like fold, response regulator, beryllium fluoride, transcription factor, activated, virulence; 1.90A {Escherichia coli} SCOP: c.23.1.1 PDB: 2pkx_A Length = 121

 Score = 51.3 bits (124), Expect = 5e-09
 Identities = 24/114 (21%), Positives = 51/114 (44%), Gaps = 13/114 (11%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
            VL V+D+ + R  ++  +Q +  +V   E    A  YL      +    D     + I 
Sbjct: 2   RVLVVEDNALLRHHLKVQIQDAGHQVDDAEDAKEADYYL------NEHIPD-----IAIV 50

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
           D  +P   G  L+++ + +     +P++++++ +        L  GA++Y+ KP
Sbjct: 51  DLGLPDEDGLSLIRRWRSND--VSLPILVLTARESWQDKVEVLSAGADDYVTKP 102

>1qo0_D AMIR; binding protein, gene regulator, receptor; 2.25A {Pseudomonas aeruginosa} SCOP: c.23.1.3 Length = 196

 Score = 52.8 bits (126), Expect = 6e-09
 Identities = 14/122 (11%), Positives = 30/122 (24%), Gaps = 18/122 (14%)

Query: 92  KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNL 151
           +EL VL ++        +   L    C V        A                 + V++
Sbjct: 11  RELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAF---------------DVPVDV 55

Query: 152 IITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKL 211
           + T                  +       +V +   +    +   +E      I +P+  
Sbjct: 56  VFTSIFQNRHHDEIAALLAAGT---PRTTLVALVEYESPAVLSQIIELECHGVITQPLDA 112

Query: 212 SD 213
             
Sbjct: 113 HR 114

>3q9s_A DNA-binding response regulator; DNA binding protein; 2.40A {Deinococcus radiodurans} Length = 249

 Score = 52.9 bits (128), Expect = 8e-09
 Identities = 24/132 (18%), Positives = 56/132 (42%), Gaps = 21/132 (15%)

Query: 77  RGFPFWAMATVAECSKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLD 136
            G     M        E  +L ++D +    ++   L  +   V   +S    L      
Sbjct: 28  GGQQMGRMN-------EQRILVIEDDHDIANVLRMDLTDAGYVVDHADSAMNGLIKA--- 77

Query: 137 GEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSC 196
                   D     LI+ D  +P   G +++++++++S    +P++++++ D + +    
Sbjct: 78  ---REDHPD-----LILLDLGLPDFDGGDVVQRLRKNS---ALPIIVLTARDTVEEKVRL 126

Query: 197 LEEGAEEYIVKP 208
           L  GA++Y++KP
Sbjct: 127 LGLGADDYLIKP 138

>2qv0_A Protein MRKE; structural genomics, transcription, PSI-2, protein structure initiative; 2.40A {Klebsiella pneumoniae} Length = 143

 Score = 51.1 bits (123), Expect = 1e-08
 Identities = 25/126 (19%), Positives = 54/126 (42%), Gaps = 27/126 (21%)

Query: 91  SKELHVLAVDDSYVDRKLIERLL-QISSCKVTA-VESGTRALQYLGLDGEQSNVGFDALK 148
            +++ V+ V+D ++ ++ +  L+   S  ++    + G   L++L              K
Sbjct: 7   GEKMKVIIVEDEFLAQQELSWLINTHSQMEIVGSFDDGLDVLKFL-----------QHNK 55

Query: 149 VNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQ-----IDSCLEEGAEE 203
           V+ I  D  +P + G  L + I +   F   P ++      +T      +++  E  A +
Sbjct: 56  VDAIFLDINIPSLDGVLLAQNISQ---FAHKPFIVF-----ITAWKEHAVEA-FELEAFD 106

Query: 204 YIVKPV 209
           YI+KP 
Sbjct: 107 YILKPY 112

>3sy8_A ROCR; TIM barrel phosphodiesterase-A, transcription regulator; HET: EPE; 2.50A {Pseudomonas aeruginosa} Length = 400

 Score = 49.6 bits (119), Expect = 2e-07
 Identities = 21/100 (21%), Positives = 37/100 (37%), Gaps = 13/100 (13%)

Query: 92  KELHVLAVDDSYVDRKLIERLL-QISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVN 150
            +L+VL ++D    R +    L ++    +     G  A+  L               V+
Sbjct: 2   NDLNVLVLEDEPFQRLVAVTALKKVVPGSILEAADGKEAVAILE----------SCGHVD 51

Query: 151 LIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVL 190
           + I D  M GM G   L+    S   +   V++ S  D +
Sbjct: 52  IAICDLQMSGMDGLAFLRHASLSG--KVHSVILSSEVDPI 89

>2hqr_A Putative transcriptional regulator; phosporylation-independent response regulator, H. pylori, SY dimer, signaling protein; NMR {Helicobacter pylori} Length = 223

 Score = 49.0 bits (118), Expect = 2e-07
 Identities = 24/117 (20%), Positives = 42/117 (35%), Gaps = 23/117 (19%)

Query: 95  HVLAVDDSYVDRKL---IERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNL 151
            VL ++    +  L   IE+ L +        ES      YL          +D     L
Sbjct: 2   RVLLIEK---NSVLGGEIEKGLNVKGFMADVTESLEDGE-YLMDIRN-----YD-----L 47

Query: 152 IITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
           ++    +        + +IKE      + V++ S      +     E+GA++YI KP
Sbjct: 48  VM----VSDKNALSFVSRIKEKH--SSIVVLVSSDNPTSEEEVHAFEQGADDYIAKP 98

>2qsj_A DNA-binding response regulator, LUXR family; structural genomics, PSI-2, protein structure initiative; 2.10A {Silicibacter pomeroyi dss-3} Length = 154

 Score = 48.0 bits (115), Expect = 2e-07
 Identities = 31/114 (27%), Positives = 51/114 (44%), Gaps = 14/114 (12%)

Query: 96  VLAVDDSYVDRKLIERLLQISS--CKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLII 153
           VL VDD ++ R   + LL+ +    +V   E+ + AL +L  D            V+LI+
Sbjct: 6   VLIVDDHHLIRAGAKNLLEGAFSGMRVEGAETVSDALAFLEAD----------NTVDLIL 55

Query: 154 TDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVK 207
            D  +P     + L ++K         V ++S E     I + LE GA+ +I K
Sbjct: 56  LDVNLPDAEAIDGLVRLKRF--DPSNAVALISGETDHELIRAALEAGADGFIPK 107

>2pln_A HP1043, response regulator; signaling protein; 1.80A {Helicobacter pylori} PDB: 2hqo_A Length = 137

 Score = 45.2 bits (108), Expect = 1e-06
 Identities = 22/116 (18%), Positives = 41/116 (35%), Gaps = 23/116 (19%)

Query: 96  VLAVDDSYVDRKL---IERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLI 152
           VL ++    +  L   IE+ L +        ES       +          +D     L+
Sbjct: 21  VLLIEK---NSVLGGEIEKGLNVKGFMADVTESLEDGEYLM------DIRNYD-----LV 66

Query: 153 ITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
           +    +        + +IKE      + V++ S      +     E+GA++YI KP
Sbjct: 67  M----VSDKNALSFVSRIKEKH--SSIVVLVSSDNPTSEEEVHAFEQGADDYIAKP 116

>3klo_A Transcriptional regulator VPST; REC domain, HTH domain, DNA-binding, transcription regulation; HET: C2E TAR; 2.80A {Vibrio cholerae} PDB: 3kln_A* Length = 225

 Score = 45.7 bits (109), Expect = 2e-06
 Identities = 11/118 (9%), Positives = 32/118 (27%), Gaps = 11/118 (9%)

Query: 91  SKELHVLAVDDSYVDRKLIERLLQISS-CKVTAVESGTRALQYLGLDGEQSNVGFDALKV 149
             +L+V  + D  +  +L++  L+      +               +        ++  +
Sbjct: 5   ENKLNVRMLSDVCMQSRLLKEALESKLPLALEITPFS---------ELWLEENKPESRSI 55

Query: 150 NLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVK 207
            +++ DY+             K  S   +   VI++    +                 
Sbjct: 56  QMLVIDYSRISDDVLTDYSSFKHIS-CPDAKEVIINCPQDIEHKLLFKWNNLAGVFYI 112

>3f6c_A Positive transcription regulator EVGA; structural genomics, PSI-2, protein structure initiative, PO transcription regulator EVGA; 1.45A {Escherichia coli k-12} Length = 134

 Score = 40.1 bits (95), Expect = 7e-05
 Identities = 22/112 (19%), Positives = 51/112 (45%), Gaps = 12/112 (10%)

Query: 96  VLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITD 155
            + +DD  +    I  LL  +  ++ A E           +G  +    + LK +++I D
Sbjct: 4   AIIIDDHPLAIAAIRNLLIKNDIEILA-ELT---------EGGSAVQRVETLKPDIVIID 53

Query: 156 YTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVK 207
             +PG+ G ++L+ +++        ++I+S+++       C + GA  ++ K
Sbjct: 54  VDIPGVNGIQVLETLRKR--QYSGIIIIVSAKNDHFYGKHCADAGANGFVSK 103

>3b2n_A Uncharacterized protein Q99UF4; structural genomics, PSI-2, protein structure initiative, NE SGX research center for structural genomics; 2.04A {Staphylococcus aureus} Length = 133

 Score = 40.2 bits (95), Expect = 8e-05
 Identities = 22/114 (19%), Positives = 56/114 (49%), Gaps = 15/114 (13%)

Query: 96  VLAVDDSYVDRKLIERLLQI-SSCKVTA-VESGTRALQYLGLDGEQSNVGFDALKVNLII 153
           ++  +D  + R+ + +L+++    ++ A  ++G  A++ +           +    N++I
Sbjct: 6   LIIAEDQNMLRQAMVQLIKLHGDFEILADTDNGLDAMKLI-----------EEYNPNVVI 54

Query: 154 TDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVK 207
            D  MPGMTG E+L +I++      + V+I+++       +  +    + Y++K
Sbjct: 55  LDIEMPGMTGLEVLAEIRKK--HLNIKVIIVTTFKRPGYFEKAVVNDVDAYVLK 106

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	213
3to5_A	134	CHEY homolog; alpha(5)beta(5), chemotaxis, FLIM, p	99.96
3gl9_A	122	Response regulator; beta-sheet, surrounded by alph	99.92
2lpm_A	123	Two-component response regulator; transcription re	99.91
3t6k_A	136	Response regulator receiver; flavodoxin-like, stru	99.9
3mm4_A	206	Histidine kinase homolog; receiver domain, CKI1, c	99.9
3h1g_A	129	Chemotaxis protein CHEY homolog; sulfate-bound CHE	99.89
2r25_B	133	Osmosensing histidine protein kinase SLN1; alpha5-	99.89
3f6p_A	120	Transcriptional regulatory protein YYCF; unphospho	99.89
3rqi_A	184	Response regulator protein; structural genomics, s	99.89
3m6m_D	143	Sensory/regulatory protein RPFC; RPFF, REC, enoyl-	99.88
3gt7_A	154	Sensor protein; structural genomics, signal receiv	99.88
1dbw_A	126	Transcriptional regulatory protein FIXJ; doubly wo	99.87
3eod_A	130	Protein HNR; response regulator, phosphoprotein, t	99.87
3lua_A	140	Response regulator receiver protein; two-component	99.87
3luf_A	259	Two-component system response regulator/ggdef doma	99.87
1jbe_A	128	Chemotaxis protein CHEY; signaling protein; 1.08A	99.87
3heb_A	152	Response regulator receiver domain protein (CHEY);	99.87
3crn_A	132	Response regulator receiver domain protein, CHEY-;	99.87
1srr_A	124	SPO0F, sporulation response regulatory protein; as	99.87
1i3c_A	149	Response regulator RCP1; phytochrome, signaling pr	99.87
3n0r_A	286	Response regulator; sigma factor, receiver, two-co	99.87
2pl1_A	121	Transcriptional regulatory protein PHOP; CHEY-like	99.86
3kto_A	136	Response regulator receiver protein; PSI-II,struct	99.86
1mb3_A	124	Cell division response regulator DIVK; signal tran	99.86
3i42_A	127	Response regulator receiver domain protein (CHEY-	99.86
1p6q_A	129	CHEY2; chemotaxis, signal transduction, response r	99.86
3hv2_A	153	Response regulator/HD domain protein; PSI-2, NYSGX	99.86
3hdv_A	136	Response regulator; PSI-II, structural genomics, P	99.86
3r0j_A	250	Possible two component system response transcript	99.86
3ilh_A	146	Two component response regulator; NYSGXRC, PSI-II,	99.86
1tmy_A	120	CHEY protein, TMY; chemotaxis, phosphoryl transfer	99.86
3kht_A	144	Response regulator; PSI-II, 11023K, structural gen	99.86
4e7p_A	150	Response regulator; DNA binding, cytosol, transcri	99.85
1k68_A	140	Phytochrome response regulator RCPA; phosphorylate	99.85
1xhf_A	123	DYE resistance, aerobic respiration control protei	99.85
3grc_A	140	Sensor protein, kinase; protein structure initiati	99.85
3jte_A	143	Response regulator receiver protein; structural ge	99.85
1zgz_A	122	Torcad operon transcriptional regulatory protein;	99.85
3hdg_A	137	Uncharacterized protein; two-component sensor acti	99.85
1dz3_A	130	Stage 0 sporulation protein A; response regulator,	99.85
3snk_A	135	Response regulator CHEY-like protein; P-loop conta	99.85
3b2n_A	133	Uncharacterized protein Q99UF4; structural genomic	99.85
3cfy_A	137	Putative LUXO repressor protein; structural genomi	99.85
2ayx_A	254	Sensor kinase protein RCSC; two independent struct	99.85
3hzh_A	157	Chemotaxis response regulator (CHEY-3); phosphatas	99.85
3f6c_A	134	Positive transcription regulator EVGA; structural	99.84
3nhm_A	133	Response regulator; protein structure initiative I	99.84
2qzj_A	136	Two-component response regulator; 11017X, PSI-II,	99.84
1yio_A	208	Response regulatory protein; transcription regulat	99.84
3lte_A	132	Response regulator; structural genomics, PSI, prot	99.84
3c3m_A	138	Response regulator receiver protein; structural ge	99.84
2a9o_A	120	Response regulator; essential protein, YYCF/YYCG h	99.84
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	99.84
3cnb_A	143	DNA-binding response regulator, MERR family; signa	99.84
2jba_A	127	Phosphate regulon transcriptional regulatory PROT;	99.84
1k66_A	149	Phytochrome response regulator RCPB; CHEY homologu	99.84
1dcf_A	136	ETR1 protein; beta-alpha five sandwich, transferas	99.84
1mvo_A	136	PHOP response regulator; phosphate regulon, transc	99.84
4dad_A	146	Putative pilus assembly-related protein; response	99.84
2qxy_A	142	Response regulator; regulation of transcription, N	99.84
3eul_A	152	Possible nitrate/nitrite response transcriptional	99.84
2zay_A	147	Response regulator receiver protein; structural ge	99.84
2rjn_A	154	Response regulator receiver:metal-dependent phosph	99.83
3a10_A	116	Response regulator; phosphoacceptor, signaling pro	99.83
2qvg_A	143	Two component response regulator; NYSGXRC, PSI-2,	99.83
1a04_A	215	Nitrate/nitrite response regulator protein NARL; s	99.83
3cg4_A	142	Response regulator receiver domain protein (CHEY-;	99.83
3eq2_A	394	Probable two-component response regulator; adaptor	99.83
1qkk_A	155	DCTD, C4-dicarboxylate transport transcriptional r	99.83
1zh2_A	121	KDP operon transcriptional regulatory protein KDPE	99.83
3h5i_A	140	Response regulator/sensory box protein/ggdef domai	99.83
3q9s_A	249	DNA-binding response regulator; DNA binding protei	99.82
1w25_A	459	Stalked-cell differentiation controlling protein;	99.82
3cz5_A	153	Two-component response regulator, LUXR family; str	99.82
3kyj_B	145	CHEY6 protein, putative histidine protein kinase;	99.82
2qr3_A	140	Two-component system response regulator; structura	99.82
3cg0_A	140	Response regulator receiver modulated diguanylate	99.82
3kcn_A	151	Adenylate cyclase homolog; SGX, PSI 2, structural	99.82
3t8y_A	164	CHEB, chemotaxis response regulator protein-glutam	99.82
3cu5_A	141	Two component transcriptional regulator, ARAC FAM;	99.82
3n53_A	140	Response regulator receiver modulated diguanylate;	99.82
1kgs_A	225	DRRD, DNA binding response regulator D; DNA-bindin	99.82
2jk1_A	139	HUPR, hydrogenase transcriptional regulatory prote	99.81
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	99.81
1ys7_A	233	Transcriptional regulatory protein PRRA; response	99.81
1s8n_A	205	Putative antiterminator; RV1626, structural genomi	99.81
2gkg_A	127	Response regulator homolog; social motility, recei	99.8
3eqz_A	135	Response regulator; structural genomics, unknown f	99.8
3bre_A	358	Probable two-component response regulator; protein	99.8
2j48_A	119	Two-component sensor kinase; pseudo-receiver, circ	99.79
2qsj_A	154	DNA-binding response regulator, LUXR family; struc	99.79
2oqr_A	230	Sensory transduction protein REGX3; response regul	99.78
2qv0_A	143	Protein MRKE; structural genomics, transcription,	99.78
2gwr_A	238	DNA-binding response regulator MTRA; two-component	99.78
2pln_A	137	HP1043, response regulator; signaling protein; 1.8	99.78
2rdm_A	132	Response regulator receiver protein; structural ge	99.78
3c97_A	140	Signal transduction histidine kinase; structural g	99.77
3c3w_A	225	Two component transcriptional regulatory protein;	99.77
3luf_A	259	Two-component system response regulator/ggdef doma	99.77
3klo_A	225	Transcriptional regulator VPST; REC domain, HTH do	99.77
3sy8_A	400	ROCR; TIM barrel phosphodiesterase-A, transcriptio	99.77
1p2f_A	220	Response regulator; DRRB, OMPR/PHOB, transcription	99.76
2b4a_A	138	BH3024; flavodoxin-like fold, structural genomics,	99.76
1dc7_A	124	NTRC, nitrogen regulation protein; receiver domain	99.75
2hqr_A	223	Putative transcriptional regulator; phosporylation	99.75
1qo0_D	196	AMIR; binding protein, gene regulator, receptor; 2	99.75
1a2o_A	349	CHEB methylesterase; bacterial chemotaxis, adaptat	99.72
2vyc_A	755	Biodegradative arginine decarboxylase; pyridoxal p	99.68
1w25_A	459	Stalked-cell differentiation controlling protein;	99.25
3cwo_X	237	Beta/alpha-barrel protein based on 1THF and 1TMY;	99.17
3n75_A	715	LDC, lysine decarboxylase, inducible; pyridoxal-5'	97.37
2ayx_A	254	Sensor kinase protein RCSC; two independent struct	97.36
3cwo_X	237	Beta/alpha-barrel protein based on 1THF and 1TMY;	96.59
2yxb_A	161	Coenzyme B12-dependent mutase; alpha/beta, structu	96.15
3q7r_A	121	Transcriptional regulatory protein; CHXR, receiver	95.68
1ccw_A	137	Protein (glutamate mutase); coenzyme B12, radical	95.03
1wv2_A	265	Thiazole moeity, thiazole biosynthesis protein THI	95.01
1y80_A	210	Predicted cobalamin binding protein; corrinoid, fa	94.2
3ezx_A	215	MMCP 1, monomethylamine corrinoid protein 1; N ter	93.93
2i2x_B	258	MTAC, methyltransferase 1; TIM barrel and helix bu	92.68
3q58_A	229	N-acetylmannosamine-6-phosphate 2-epimerase; TIM b	92.57
2htm_A	268	Thiazole biosynthesis protein THIG; thiamin biosyn	92.31
3igs_A	232	N-acetylmannosamine-6-phosphate 2-epimerase 2; ene	91.33
2xij_A	762	Methylmalonyl-COA mutase, mitochondrial; isomerase	89.69
1req_A	727	Methylmalonyl-COA mutase; isomerase, intramolecula	89.28
3qja_A	272	IGPS, indole-3-glycerol phosphate synthase; struct	88.58
3ffs_A	400	Inosine-5-monophosphate dehydrogenase; beta-alpha	88.2
1xrs_B	262	D-lysine 5,6-aminomutase beta subunit; TIM barrel,	87.23
1r8j_A	289	KAIA; circadian clock protein; 2.03A {Synechococcu	85.19
3fkq_A	373	NTRC-like two-domain protein; RER070207001320, str	83.28
3rht_A	259	(gatase1)-like protein; structural genomics, PSI-b	82.23
3f4w_A	211	Putative hexulose 6 phosphate synthase; humps, mal	81.73
3ovp_A	228	Ribulose-phosphate 3-epimerase; iron binding, isom	81.73
3o63_A	243	Probable thiamine-phosphate pyrophosphorylase; thi	81.56
1yad_A	221	Regulatory protein TENI; TIM barrel, transcription	81.5
3fwz_A	140	Inner membrane protein YBAL; TRKA-N domain, E.coli	81.18
3kp1_A	763	D-ornithine aminomutase E component; 5 aminomutase	80.61
2oo3_A	283	Protein involved in catabolism of external DNA; st	80.28

>3to5_A CHEY homolog; alpha(5)beta(5), chemotaxis, FLIM, phosphorylation, motor AC signaling protein; 1.65A {Vibrio cholerae}

Probab=99.96  E-value=1.5e-29  Score=190.40  Aligned_cols=111  Identities=31%  Similarity=0.560  Sum_probs=102.9

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhcCCE-EEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHH
Q 048660           91 SKELHVLAVDDSYVDRKLIERLLQISSCK-VTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKK  169 (213)
Q Consensus        91 ~~~~~ILvVdD~~~~~~~l~~~L~~~g~~-v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~  169 (213)
                      ++.+|||||||++.+|..++.+|+.+||. +..|.||.+|++.++           ...||+||+|+.||+|||++++++
T Consensus        10 ~k~~rILiVDD~~~~r~~l~~~L~~~G~~~v~~a~~g~~al~~~~-----------~~~~DlillD~~MP~mdG~el~~~   78 (134)
T 3to5_A           10 NKNMKILIVDDFSTMRRIVKNLLRDLGFNNTQEADDGLTALPMLK-----------KGDFDFVVTDWNMPGMQGIDLLKN   78 (134)
T ss_dssp             CTTCCEEEECSCHHHHHHHHHHHHHTTCCCEEEESSHHHHHHHHH-----------HHCCSEEEEESCCSSSCHHHHHHH
T ss_pred             CCCCEEEEEeCCHHHHHHHHHHHHHcCCcEEEEECCHHHHHHHHH-----------hCCCCEEEEcCCCCCCCHHHHHHH
Confidence            45689999999999999999999999996 778999999999984           457999999999999999999999


Q ss_pred             HHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          170 IKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       170 ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      ||+....+++|||++|++.+.+...+++++|+++||.|||+.+
T Consensus        79 ir~~~~~~~ipvI~lTa~~~~~~~~~~~~~Ga~~yl~KP~~~~  121 (134)
T 3to5_A           79 IRADEELKHLPVLMITAEAKREQIIEAAQAGVNGYIVKPFTAA  121 (134)
T ss_dssp             HHHSTTTTTCCEEEEESSCCHHHHHHHHHTTCCEEEESSCCHH
T ss_pred             HHhCCCCCCCeEEEEECCCCHHHHHHHHHCCCCEEEECCCCHH
Confidence            9987667899999999999999999999999999999999864

>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=99.92  E-value=4.3e-24  Score=156.16  Aligned_cols=108  Identities=31%  Similarity=0.473  Sum_probs=101.1

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhc
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKES  173 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~  173 (213)
                      .+||||||++..+..++.+|+..||.+..+.++.+|++.+           ....||+||+|+.||+++|+++++.+|+.
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            4899999999999999999999999999999999999998           55679999999999999999999999986


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      ...+.+|||++|+..+.....++++.|+++||.||++.+
T Consensus        72 ~~~~~~pii~~s~~~~~~~~~~~~~~Ga~~~l~KP~~~~  110 (122)
T 3gl9_A           72 EEWKRIPVIVLTAKGGEEDESLALSLGARKVMRKPFSPS  110 (122)
T ss_dssp             TTTTTSCEEEEESCCSHHHHHHHHHTTCSEEEESSCCHH
T ss_pred             ccccCCCEEEEecCCchHHHHHHHhcChhhhccCCCCHH
Confidence            556789999999999999999999999999999999864

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

Probab=99.91  E-value=2.1e-26  Score=170.67  Aligned_cols=104  Identities=21%  Similarity=0.228  Sum_probs=92.0

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhcCCEEE-EEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHH
Q 048660           91 SKELHVLAVDDSYVDRKLIERLLQISSCKVT-AVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKK  169 (213)
Q Consensus        91 ~~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~-~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~  169 (213)
                      .+++|||||||++.++..++.+|+.+||.|. .|.||.+|++.+           ...+||+||+|++||+|||+++++.
T Consensus         6 ~r~~rILiVdD~~~~~~~l~~~L~~~G~~v~~~a~~g~eAl~~~-----------~~~~~DlvllDi~mP~~~G~el~~~   74 (123)
T 2lpm_A            6 ERRLRVLVVEDESMIAMLIEDTLCELGHEVAATASRMQEALDIA-----------RKGQFDIAIIDVNLDGEPSYPVADI   74 (123)
T ss_dssp             CCCCCEEEESSSTTTSHHHHHHHHHHCCCCCBCSCCHHHHHHHH-----------HHCCSSEEEECSSSSSCCSHHHHHH
T ss_pred             CCCCEEEEEeCCHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHH-----------HhCCCCEEEEecCCCCCCHHHHHHH
Confidence            3467999999999999999999999999985 799999999999           4457999999999999999999999


Q ss_pred             HHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          170 IKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       170 ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      ||+.    ++|||++|++.+...   +.++|+++||.|||+.+
T Consensus        75 lr~~----~ipvI~lTa~~~~~~---~~~~g~~~yl~KP~~~~  110 (123)
T 2lpm_A           75 LAER----NVPFIFATGYGSKGL---DTRYSNIPLLTKPFLDS  110 (123)
T ss_dssp             HHHT----CCSSCCBCTTCTTSC---CSSSCSCSCBCSSSSHH
T ss_pred             HHcC----CCCEEEEecCccHHH---HHhCCCCcEEECCCCHH
Confidence            9973    689999999876543   34679999999999864

>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=1.9e-23  Score=155.47  Aligned_cols=109  Identities=25%  Similarity=0.466  Sum_probs=100.8

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHh
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKE  172 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~  172 (213)
                      ..+||||||++..+..+..+|+..||.|..+.++.+|++.+.           ...||+||+|+.||+++|+++++.||+
T Consensus         4 ~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~-----------~~~~dlvl~D~~lp~~~g~~~~~~lr~   72 (136)
T 3t6k_A            4 PHTLLIVDDDDTVAEMLELVLRGAGYEVRRAASGEEALQQIY-----------KNLPDALICDVLLPGIDGYTLCKRVRQ   72 (136)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH-----------HSCCSEEEEESCCSSSCHHHHHHHHHH
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHH-----------hCCCCEEEEeCCCCCCCHHHHHHHHHc
Confidence            468999999999999999999999999999999999999983           457999999999999999999999998


Q ss_pred             cCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          173 SSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       173 ~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      ....+.+|||++|+..+.....+++++|+++||.||++.+
T Consensus        73 ~~~~~~~pii~~t~~~~~~~~~~~~~~ga~~~l~KP~~~~  112 (136)
T 3t6k_A           73 HPLTKTLPILMLTAQGDISAKIAGFEAGANDYLAKPFEPQ  112 (136)
T ss_dssp             SGGGTTCCEEEEECTTCHHHHHHHHHHTCSEEEETTCCHH
T ss_pred             CCCcCCccEEEEecCCCHHHHHHHHhcCcceEEeCCCCHH
Confidence            6445789999999999999999999999999999999854

>3mm4_A Histidine kinase homolog; receiver domain, CKI1, cytokinin signaling, ROS fold, CHEY-like, transferase; 2.00A {Arabidopsis thaliana} PDB: 3mmn_A

Probab=99.90  E-value=4.7e-23  Score=164.59  Aligned_cols=119  Identities=24%  Similarity=0.419  Sum_probs=99.4

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCC-EEEEEcCHHHHHHHhhhcCC--CCCCCCCCCceeEEEEeCCCCCCCHHHHHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSC-KVTAVESGTRALQYLGLDGE--QSNVGFDALKVNLIITDYTMPGMTGYELLK  168 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~-~v~~a~~g~eal~~l~~~~~--~~~~~~~~~~~dlil~D~~mp~~~G~e~~~  168 (213)
                      .+.+||||||++.++..+..+|+..|| .|..+.++.+|++.+.....  ..........||+||+|+.||+++|+++++
T Consensus        60 ~~~~ILiVdDd~~~~~~l~~~L~~~g~~~v~~a~~~~eal~~l~~~~~~~~~~~~~~~~~~dlillD~~lp~~~G~el~~  139 (206)
T 3mm4_A           60 RGKRVLVVDDNFISRKVATGKLKKMGVSEVEQCDSGKEALRLVTEGLTQREEQGSVDKLPFDYIFMDCQMPEMDGYEATR  139 (206)
T ss_dssp             TTCEEEEECSCHHHHHHHHHHHHHTTCSEEEEESSHHHHHHHHHHHHHHHHHHTCSSCCSCSEEEEESCCSSSCHHHHHH
T ss_pred             CCCEEEEEeCCHHHHHHHHHHHHHcCCCeeeeeCCHHHHHHHHHhhcccccccccccCCCCCEEEEcCCCCCCCHHHHHH
Confidence            457999999999999999999999999 89999999999999853200  000000123799999999999999999999


Q ss_pred             HHHhcCC--CCCCcEEEEecCC-CHHHHHHHHHcCCCeeeeCCCC
Q 048660          169 KIKESSV--FREVPVVIMSSED-VLTQIDSCLEEGAEEYIVKPVK  210 (213)
Q Consensus       169 ~ir~~~~--~~~~pII~lt~~~-~~~~~~~~~~~G~~~~L~KP~~  210 (213)
                      .||+...  .+.+|||++|+.. +.....+++++|+++||.||++
T Consensus       140 ~lr~~~~~~~~~~piI~ls~~~~~~~~~~~~~~~Ga~~~l~KP~~  184 (206)
T 3mm4_A          140 EIRKVEKSYGVRTPIIAVSGHDPGSEEARETIQAGMDAFLDKSLN  184 (206)
T ss_dssp             HHHHHHHTTTCCCCEEEEESSCCCHHHHHHHHHHTCSEEEETTCT
T ss_pred             HHHhhhhhcCCCCcEEEEECCCCcHHHHHHHHhCCCCEEEcCcHH
Confidence            9997421  3789999999998 7788899999999999999987

>3h1g_A Chemotaxis protein CHEY homolog; sulfate-bound CHEY, cytoplasm, flagellar rotatio magnesium, metal-binding, phosphoprotein; 1.70A {Helicobacter pylori} SCOP: c.23.1.1 PDB: 3gwg_A 3h1e_A 3h1f_A

Probab=99.89  E-value=1.2e-22  Score=149.53  Aligned_cols=110  Identities=32%  Similarity=0.587  Sum_probs=99.5

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCE-EEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCK-VTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~-v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      .++||||||++..+..++.+|++.||. +..+.++.+|++.+..          ...||+||+|+.||+++|+++++.||
T Consensus         5 ~~~iLivdd~~~~~~~l~~~L~~~g~~~v~~~~~~~~a~~~~~~----------~~~~dlvi~D~~~p~~~g~~~~~~lr   74 (129)
T 3h1g_A            5 SMKLLVVDDSSTMRRIIKNTLSRLGYEDVLEAEHGVEAWEKLDA----------NADTKVLITDWNMPEMNGLDLVKKVR   74 (129)
T ss_dssp             -CCEEEECSCHHHHHHHHHHHHHTTCCCEEEESSHHHHHHHHHH----------CTTCCEEEECSCCSSSCHHHHHHHHH
T ss_pred             CcEEEEEeCCHHHHHHHHHHHHHcCCcEEEEeCCHHHHHHHHHh----------CCCCCEEEEeCCCCCCCHHHHHHHHH
Confidence            468999999999999999999999995 8899999999998742          23689999999999999999999999


Q ss_pred             hcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          172 ESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      +....+.+|||++|+..+.....+++++|+++||.||++.+
T Consensus        75 ~~~~~~~~pii~~s~~~~~~~~~~~~~~g~~~~l~KP~~~~  115 (129)
T 3h1g_A           75 SDSRFKEIPIIMITAEGGKAEVITALKAGVNNYIVKPFTPQ  115 (129)
T ss_dssp             TSTTCTTCCEEEEESCCSHHHHHHHHHHTCCEEEESCCCHH
T ss_pred             hcCCCCCCeEEEEeCCCChHHHHHHHHcCccEEEeCCCCHH
Confidence            86556789999999999999999999999999999999864

>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=1.1e-22  Score=150.83  Aligned_cols=113  Identities=24%  Similarity=0.411  Sum_probs=97.7

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCC-EEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSC-KVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~-~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      ..+||||||++..+..++.+|+..|+ .+..+.++.+|++.+.....      ....||+||+|+.||+++|+++++.||
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            35899999999999999999999997 58899999999998842100      014699999999999999999999999


Q ss_pred             hcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          172 ESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      +.. .+.+|||++|+..+.....++++.|+++||.||++.+
T Consensus        76 ~~~-~~~~~ii~lt~~~~~~~~~~~~~~ga~~~l~KP~~~~  115 (133)
T 2r25_B           76 RDL-GYTSPIVALTAFADDSNIKECLESGMNGFLSKPIKRP  115 (133)
T ss_dssp             HHS-CCCSCEEEEESCCSHHHHHHHHHTTCSEEEESSCCHH
T ss_pred             hhc-CCCCCEEEEECCCCHHHHHHHHHcCCCEEEeCCCCHH
Confidence            742 3468999999999999999999999999999999754

>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=1.3e-22  Score=147.62  Aligned_cols=105  Identities=24%  Similarity=0.468  Sum_probs=97.8

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhc
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKES  173 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~  173 (213)
                      .+||||||++..+..++..|++.||.+..+.++.+|++.+           ....||+||+|+.||+++|+++++.+|+.
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            4899999999999999999999999999999999999998           44579999999999999999999999974


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                         ..+|||++|+..+.....++++.|+++||.||++.+
T Consensus        72 ---~~~~ii~~t~~~~~~~~~~~~~~ga~~~l~KP~~~~  107 (120)
T 3f6p_A           72 ---YDMPIIMLTAKDSEIDKVIGLEIGADDYVTKPFSTR  107 (120)
T ss_dssp             ---CCSCEEEEEESSCHHHHHHHHHTTCCEEEEESCCHH
T ss_pred             ---CCCCEEEEECCCChHHHHHHHhCCcceeEcCCCCHH
Confidence               378999999999999999999999999999999854

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

Probab=99.89  E-value=6.9e-23  Score=160.40  Aligned_cols=107  Identities=18%  Similarity=0.318  Sum_probs=100.9

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHh
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKE  172 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~  172 (213)
                      ..+||||||++..+..++.+|+..||.|..+.++.+|++.+           ....||+||+|+.||+++|+++++.||+
T Consensus         7 ~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~-----------~~~~~dlvl~D~~lp~~~g~~~~~~l~~   75 (184)
T 3rqi_A            7 DKNFLVIDDNEVFAGTLARGLERRGYAVRQAHNKDEALKLA-----------GAEKFEFITVXLHLGNDSGLSLIAPLCD   75 (184)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEECSHHHHHHHH-----------TTSCCSEEEECSEETTEESHHHHHHHHH
T ss_pred             CCeEEEEcCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHH-----------hhCCCCEEEEeccCCCccHHHHHHHHHh
Confidence            57999999999999999999999999999999999999998           5567999999999999999999999998


Q ss_pred             cCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          173 SSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       173 ~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      .  .+.+|||++|+..+.+...++++.|+++||.||++.+
T Consensus        76 ~--~~~~~ii~lt~~~~~~~~~~a~~~Ga~~~l~KP~~~~  113 (184)
T 3rqi_A           76 L--QPDARILVLTGYASIATAVQAVKDGADNYLAKPANVE  113 (184)
T ss_dssp             H--CTTCEEEEEESSCCHHHHHHHHHHTCSEEEESSCCHH
T ss_pred             c--CCCCCEEEEeCCCCHHHHHHHHHhCHHHheeCCCCHH
Confidence            6  5789999999999999999999999999999999854

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

Probab=99.88  E-value=2.3e-22  Score=150.99  Aligned_cols=110  Identities=30%  Similarity=0.562  Sum_probs=96.9

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      ..++||||||++..+..++.+|++.||.+..+.++.+|++.+.           ...||+||+|+.||+++|+++++.||
T Consensus        13 ~~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~-----------~~~~dlvl~D~~mp~~~g~~~~~~lr   81 (143)
T 3m6m_D           13 RSMRMLVADDHEANRMVLQRLLEKAGHKVLCVNGAEQVLDAMA-----------EEDYDAVIVDLHMPGMNGLDMLKQLR   81 (143)
T ss_dssp             --CEEEEECSSHHHHHHHHHHHHC--CEEEEESSHHHHHHHHH-----------HSCCSEEEEESCCSSSCHHHHHHHHH
T ss_pred             ccceEEEEeCCHHHHHHHHHHHHHcCCeEEEeCCHHHHHHHHh-----------cCCCCEEEEeCCCCCCCHHHHHHHHH
Confidence            4579999999999999999999999999999999999999983           45799999999999999999999999


Q ss_pred             hc--CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          172 ES--SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       172 ~~--~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      +.  ...+.+|||++|+..+.+...+++++|+++||.||++.+
T Consensus        82 ~~~~~~~~~~pii~~s~~~~~~~~~~~~~~Ga~~~l~KP~~~~  124 (143)
T 3m6m_D           82 VMQASGMRYTPVVVLSADVTPEAIRACEQAGARAFLAKPVVAA  124 (143)
T ss_dssp             HHHHTTCCCCCEEEEESCCCHHHHHHHHHTTCSEEEESSCCHH
T ss_pred             hchhccCCCCeEEEEeCCCCHHHHHHHHHcChhheeeCCCCHH
Confidence            53  224678999999999999999999999999999999854

>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=8.2e-22  Score=149.59  Aligned_cols=110  Identities=28%  Similarity=0.498  Sum_probs=101.9

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      ...+||||||++..+..++.+|+..||.|..+.++.+|++.+           ....||+||+|+.||+++|+++++.||
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            357999999999999999999999999999999999999999           556799999999999999999999999


Q ss_pred             hcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          172 ESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      +....+.+|||++|+..+.....+++++|+++||.||++.+
T Consensus        75 ~~~~~~~~pii~~s~~~~~~~~~~~~~~g~~~~l~KP~~~~  115 (154)
T 3gt7_A           75 GQPDLRTIPVILLTILSDPRDVVRSLECGADDFITKPCKDV  115 (154)
T ss_dssp             HSTTTTTSCEEEEECCCSHHHHHHHHHHCCSEEEESSCCHH
T ss_pred             hCCCcCCCCEEEEECCCChHHHHHHHHCCCCEEEeCCCCHH
Confidence            87555789999999999999999999999999999999753

>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=99.87  E-value=1.7e-21  Score=142.46  Aligned_cols=107  Identities=23%  Similarity=0.413  Sum_probs=99.2

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHh
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKE  172 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~  172 (213)
                      ..+||||||++..+..++..|+..||.+..+.++.++++.+           ....||++|+|+.||+++|+++++.+|+
T Consensus         3 ~~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~-----------~~~~~dlvi~D~~l~~~~g~~~~~~l~~   71 (126)
T 1dbw_A            3 DYTVHIVDDEEPVRKSLAFMLTMNGFAVKMHQSAEAFLAFA-----------PDVRNGVLVTDLRMPDMSGVELLRNLGD   71 (126)
T ss_dssp             CCEEEEEESSHHHHHHHHHHHHHTTCEEEEESCHHHHHHHG-----------GGCCSEEEEEECCSTTSCHHHHHHHHHH
T ss_pred             CCEEEEEcCCHHHHHHHHHHHHhCCcEEEEeCCHHHHHHHH-----------hcCCCCEEEEECCCCCCCHHHHHHHHHh
Confidence            46899999999999999999999999999999999999988           4457999999999999999999999998


Q ss_pred             cCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          173 SSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       173 ~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      .  .+.+|||++|+..+.....++++.|+++||.||++.+
T Consensus        72 ~--~~~~~ii~~s~~~~~~~~~~~~~~ga~~~l~Kp~~~~  109 (126)
T 1dbw_A           72 L--KINIPSIVITGHGDVPMAVEAMKAGAVDFIEKPFEDT  109 (126)
T ss_dssp             T--TCCCCEEEEECTTCHHHHHHHHHTTCSEEEESSCCHH
T ss_pred             c--CCCCCEEEEECCCCHHHHHHHHHhCHHHheeCCCCHH
Confidence            6  5789999999999999999999999999999999754

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

Probab=99.87  E-value=1.8e-21  Score=142.85  Aligned_cols=108  Identities=29%  Similarity=0.509  Sum_probs=94.6

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      .+.+||||||++..+..+..+|+..||.+..+.++.+|++.+           ....||+||+|+.||+++|+++++.+|
T Consensus         6 ~~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l-----------~~~~~dlvi~d~~l~~~~g~~~~~~l~   74 (130)
T 3eod_A            6 VGKQILIVEDEQVFRSLLDSWFSSLGATTVLAADGVDALELL-----------GGFTPDLMICDIAMPRMNGLKLLEHIR   74 (130)
T ss_dssp             TTCEEEEECSCHHHHHHHHHHHHHTTCEEEEESCHHHHHHHH-----------TTCCCSEEEECCC-----CHHHHHHHH
T ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhCCceEEEeCCHHHHHHHH-----------hcCCCCEEEEecCCCCCCHHHHHHHHH
Confidence            457999999999999999999999999999999999999998           556799999999999999999999999


Q ss_pred             hcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCC-CCC
Q 048660          172 ESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPV-KLS  212 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~-~~~  212 (213)
                      +.  .+.+|||++|+..+.....++++.|+++||.||+ +.+
T Consensus        75 ~~--~~~~~ii~~t~~~~~~~~~~~~~~g~~~~l~KP~~~~~  114 (130)
T 3eod_A           75 NR--GDQTPVLVISATENMADIAKALRLGVEDVLLKPVKDLN  114 (130)
T ss_dssp             HT--TCCCCEEEEECCCCHHHHHHHHHHCCSEEEESCC---C
T ss_pred             hc--CCCCCEEEEEcCCCHHHHHHHHHcCCCEEEeCCCCcHH
Confidence            86  5789999999999999999999999999999999 544

>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=7.8e-22  Score=146.80  Aligned_cols=109  Identities=23%  Similarity=0.313  Sum_probs=101.6

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhh-cCCEEEEEcCHHHHHHHhhhcCCCCCCCCCC-CceeEEEEeCCCC-CCCHHHHHHH
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQI-SSCKVTAVESGTRALQYLGLDGEQSNVGFDA-LKVNLIITDYTMP-GMTGYELLKK  169 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~-~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~-~~~dlil~D~~mp-~~~G~e~~~~  169 (213)
                      ..+||||||++..+..++.+|+. .||.+..+.++.+|++.+           .. ..||+||+|+.|| +++|+++++.
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            57999999999999999999999 999999999999999988           55 6899999999999 9999999999


Q ss_pred             HHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          170 IKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       170 ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      ||+....+.+|||++|+..+.+...+++++|+++||.||++.+
T Consensus        73 l~~~~~~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~KP~~~~  115 (140)
T 3lua_A           73 IRNNSRTANTPVIIATKSDNPGYRHAALKFKVSDYILKPYPTK  115 (140)
T ss_dssp             HHHSGGGTTCCEEEEESCCCHHHHHHHHHSCCSEEEESSCCTT
T ss_pred             HHhCcccCCCCEEEEeCCCCHHHHHHHHHcCCCEEEECCCCHH
Confidence            9984336899999999999999999999999999999999875

>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=99.87  E-value=7.9e-22  Score=163.06  Aligned_cols=112  Identities=23%  Similarity=0.381  Sum_probs=101.9

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHH
Q 048660           91 SKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKI  170 (213)
Q Consensus        91 ~~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~i  170 (213)
                      ....+||||||++..+..+...|+..|+.+..+.++.+|++.+..          ...||+||+|+.||++||+++++.|
T Consensus       122 ~~~~~ILivDD~~~~~~~l~~~L~~~~~~v~~a~~~~eal~~l~~----------~~~~dlvllD~~mP~~dG~~l~~~l  191 (259)
T 3luf_A          122 NQQIEVLVVDDSRTSRHRTMAQLRKQLLQVHEASHAREALATLEQ----------HPAIRLVLVDYYMPEIDGISLVRML  191 (259)
T ss_dssp             HTTCEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHHH----------CTTEEEEEECSCCSSSCHHHHHHHH
T ss_pred             cCCCcEEEEeCCHHHHHHHHHHHHHcCcEEEEeCCHHHHHHHHhc----------CCCCCEEEEcCCCCCCCHHHHHHHH
Confidence            356799999999999999999999999999999999999999842          2248999999999999999999999


Q ss_pred             HhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          171 KESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       171 r~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      |+......+|||++|+..+.....+++++|+++||.||++.+
T Consensus       192 r~~~~~~~~~ii~~s~~~~~~~~~~a~~~Ga~~yl~KP~~~~  233 (259)
T 3luf_A          192 RERYSKQQLAIIGISVSDKRGLSARYLKQGANDFLNQPFEPE  233 (259)
T ss_dssp             HHHCCTTTSEEEEEECSSSSSHHHHHHHTTCSEEEESSCCHH
T ss_pred             HhccCCCCCeEEEEEccCCHHHHHHHHhcChhheEcCCCCHH
Confidence            987655689999999999999999999999999999999864

>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=2.7e-21  Score=141.41  Aligned_cols=109  Identities=34%  Similarity=0.555  Sum_probs=99.0

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCC-EEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSC-KVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~-~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      ..+||||||++..+..++.+|+..|| .+..+.++.+|++.+           ....||++|+|+.||+++|+++++.+|
T Consensus         4 ~~~ilivdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~-----------~~~~~dlvi~D~~l~~~~g~~l~~~l~   72 (128)
T 1jbe_A            4 ELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKL-----------QAGGYGFVISDWNMPNMDGLELLKTIR   72 (128)
T ss_dssp             TCCEEEECSCHHHHHHHHHHHHHTTCCCEEEESSHHHHHHHH-----------TTCCCCEEEEESCCSSSCHHHHHHHHH
T ss_pred             ccEEEEECCCHHHHHHHHHHHHHcCCcEEEeeCCHHHHHHHH-----------HhcCCCEEEEeCCCCCCCHHHHHHHHH
Confidence            46899999999999999999999999 799999999999998           445799999999999999999999999


Q ss_pred             hcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          172 ESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      +....+.+|||++|+..+.....++++.|+++|+.||++.+
T Consensus        73 ~~~~~~~~~ii~~s~~~~~~~~~~~~~~ga~~~l~KP~~~~  113 (128)
T 1jbe_A           73 AXXAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAA  113 (128)
T ss_dssp             C--CCTTCCEEEEESSCCHHHHHHHHHTTCSEEEESSCCHH
T ss_pred             hhcccCCCcEEEEecCccHHHHHHHHHhCcCceeecCCCHH
Confidence            85446789999999999999999999999999999999754

>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=2.1e-21  Score=146.50  Aligned_cols=118  Identities=32%  Similarity=0.552  Sum_probs=101.7

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCC--EEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHH
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSC--KVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKI  170 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~--~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~i  170 (213)
                      .++||||||++..+..++.+|+..|+  .+..+.++.+|++.++.....  .......||+||+|+.||+++|+++++.|
T Consensus         4 ~~~ILivddd~~~~~~l~~~L~~~g~~~~v~~~~~~~~al~~l~~~~~~--~~~~~~~~dliilD~~l~~~~g~~~~~~l   81 (152)
T 3heb_A            4 SVTIVMIEDDLGHARLIEKNIRRAGVNNEIIAFTDGTSALNYLFGDDKS--GRVSAGRAQLVLLDLNLPDMTGIDILKLV   81 (152)
T ss_dssp             -CEEEEECCCHHHHHHHHHHHHHTTCCCCEEEESSHHHHHHHHHCTTSS--SGGGTTCBEEEEECSBCSSSBHHHHHHHH
T ss_pred             CceEEEEeCCHHHHHHHHHHHHhCCCcceEEEeCCHHHHHHHHhccccc--cccccCCCCEEEEeCCCCCCcHHHHHHHH
Confidence            57999999999999999999999998  899999999999998521100  00023579999999999999999999999


Q ss_pred             HhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          171 KESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       171 r~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      |+....+.+|||++|+..+.....++++.|+++||.||++.+
T Consensus        82 r~~~~~~~~pii~~t~~~~~~~~~~~~~~g~~~~l~KP~~~~  123 (152)
T 3heb_A           82 KENPHTRRSPVVILTTTDDQREIQRCYDLGANVYITKPVNYE  123 (152)
T ss_dssp             HHSTTTTTSCEEEEESCCCHHHHHHHHHTTCSEEEECCSSHH
T ss_pred             HhcccccCCCEEEEecCCCHHHHHHHHHCCCcEEEeCCCCHH
Confidence            985557899999999999999999999999999999999854

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

Probab=99.87  E-value=1.9e-21  Score=143.59  Aligned_cols=107  Identities=23%  Similarity=0.318  Sum_probs=98.9

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHh
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKE  172 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~  172 (213)
                      ..+||||||++..+..++.+|+..||.+..+.++.+|++.+.           ...||+||+|+.||+++|+++++.+++
T Consensus         3 ~~~Ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~-----------~~~~dlvl~D~~l~~~~g~~~~~~l~~   71 (132)
T 3crn_A            3 LKRILIVDDDTAILDSTKQILEFEGYEVEIAATAGEGLAKIE-----------NEFFNLALFXIKLPDMEGTELLEKAHK   71 (132)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH-----------HSCCSEEEECSBCSSSBHHHHHHHHHH
T ss_pred             ccEEEEEeCCHHHHHHHHHHHHHCCceEEEeCCHHHHHHHHh-----------cCCCCEEEEecCCCCCchHHHHHHHHh
Confidence            358999999999999999999999999999999999999984           347999999999999999999999998


Q ss_pred             cCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          173 SSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       173 ~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      .  .+.+|+|++|+..+.....+++++|+++||.||++.+
T Consensus        72 ~--~~~~~ii~~s~~~~~~~~~~~~~~ga~~~l~KP~~~~  109 (132)
T 3crn_A           72 L--RPGMKKIMVTGYASLENSVFSLNAGADAYIMKPVNPR  109 (132)
T ss_dssp             H--CTTSEEEEEESCCCHHHHHHHHHTTCSEEEESSCCHH
T ss_pred             h--CCCCcEEEEeccccHHHHHHHHhccchhhccCCCCHH
Confidence            6  4689999999999999999999999999999999754

>1srr_A SPO0F, sporulation response regulatory protein; aspartate pocket, two component system; 1.90A {Bacillus subtilis} SCOP: c.23.1.1 PDB: 1pey_A 3q15_C 2ftk_E* 1fsp_A 1nat_A 1pux_A 2fsp_A 2jvj_A 2jvk_A 2jvi_A 1f51_E

Probab=99.87  E-value=1.8e-21  Score=141.71  Aligned_cols=106  Identities=27%  Similarity=0.417  Sum_probs=98.5

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhc
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKES  173 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~  173 (213)
                      .+||||||++..+..++..|+..||.+..+.++.+|++.+.           ...||++|+|+.||+++|+++++.+|+.
T Consensus         4 ~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~~~-----------~~~~dlvl~D~~l~~~~g~~~~~~l~~~   72 (124)
T 1srr_A            4 EKILIVDDQSGIRILLNEVFNKEGYQTFQAANGLQALDIVT-----------KERPDLVLLDMKIPGMDGIEILKRMKVI   72 (124)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHH-----------HHCCSEEEEESCCTTCCHHHHHHHHHHH
T ss_pred             ceEEEEeCCHHHHHHHHHHHHHCCcEEEEeCCHHHHHHHHh-----------ccCCCEEEEecCCCCCCHHHHHHHHHHh
Confidence            58999999999999999999999999999999999999884           3469999999999999999999999986


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                        .+.+|||++|+..+.....++++.|+++||.||++.+
T Consensus        73 --~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~KP~~~~  109 (124)
T 1srr_A           73 --DENIRVIIMTAYGELDMIQESKELGALTHFAKPFDID  109 (124)
T ss_dssp             --CTTCEEEEEESSCCHHHHHHHHHHTCCCEEESSCCHH
T ss_pred             --CCCCCEEEEEccCchHHHHHHHhcChHhhccCCCCHH
Confidence              5789999999999999999999999999999999754

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

Probab=99.87  E-value=4.1e-21  Score=144.80  Aligned_cols=116  Identities=26%  Similarity=0.447  Sum_probs=99.8

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCC--EEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHH
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSC--KVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKI  170 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~--~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~i  170 (213)
                      ..+||||||++..+..++.+|+..|+  .+..+.++.+|++.+.....    ......||+||+|+.||+++|+++++.|
T Consensus         8 ~~~ILivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~al~~l~~~~~----~~~~~~~dlillD~~lp~~~g~~l~~~l   83 (149)
T 1i3c_A            8 PKVILLVEDSKADSRLVQEVLKTSTIDHELIILRDGLAAMAFLQQQGE----YENSPRPNLILLDLNLPKKDGREVLAEI   83 (149)
T ss_dssp             CEEEEEECCCHHHHHHHHHHHHSCCSCEEEEEECSHHHHHHHHTTCGG----GTTCCCCSEEEECSCCSSSCHHHHHHHH
T ss_pred             CCeEEEEECCHHHHHHHHHHHHhcCCCccEEEeCCHHHHHHHHHhccc----cccCCCCCEEEEeCCCCCCcHHHHHHHH
Confidence            46899999999999999999998887  88999999999999842100    0002469999999999999999999999


Q ss_pred             HhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          171 KESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       171 r~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      |+....+.+|||++|+..+.....++++.|+++||.||++.+
T Consensus        84 ~~~~~~~~~piiils~~~~~~~~~~~~~~ga~~~l~KP~~~~  125 (149)
T 1i3c_A           84 KQNPDLKRIPVVVLTTSHNEDDVIASYELHVNCYLTKSRNLK  125 (149)
T ss_dssp             HHCTTTTTSCEEEEESCCCHHHHHHHHHTTCSEEEECCSSHH
T ss_pred             HhCcCcCCCeEEEEECCCChHHHHHHHHcCCcEEEECCCCHH
Confidence            986444789999999999999999999999999999999754

>3n0r_A Response regulator; sigma factor, receiver, two-component SI transduction, signaling protein; HET: MSE GOL; 1.25A {Caulobacter vibrioides} PDB: 3t0y_A

Probab=99.87  E-value=6.8e-23  Score=172.14  Aligned_cols=105  Identities=22%  Similarity=0.279  Sum_probs=95.5

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCCEEE-EEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCC-CCCHHHHHHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSCKVT-AVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMP-GMTGYELLKK  169 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~-~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp-~~~G~e~~~~  169 (213)
                      ...+||||||++.++..++.+|+..||.|. .+.||.+|++.+.           ...|||||+|+.|| +|||+++++.
T Consensus       159 l~~rILvVdD~~~~~~~l~~~L~~~g~~v~~~a~~g~eAl~~~~-----------~~~~dlvl~D~~MPd~mdG~e~~~~  227 (286)
T 3n0r_A          159 LATEVLIIEDEPVIAADIEALVRELGHDVTDIAATRGEALEAVT-----------RRTPGLVLADIQLADGSSGIDAVKD  227 (286)
T ss_dssp             CCCEEEEECCSHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHH-----------HCCCSEEEEESCCTTSCCTTTTTHH
T ss_pred             CCCcEEEEcCCHHHHHHHHHHhhccCceEEEEeCCHHHHHHHHH-----------hCCCCEEEEcCCCCCCCCHHHHHHH
Confidence            346899999999999999999999999999 9999999999994           45799999999999 8999999999


Q ss_pred             HHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          170 IKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       170 ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      ||+..   ++|||++|+..  +...+++++|+++||.|||+.+
T Consensus       228 ir~~~---~~piI~lT~~~--~~~~~~~~~G~~~~l~KP~~~~  265 (286)
T 3n0r_A          228 ILGRM---DVPVIFITAFP--ERLLTGERPEPTFLITKPFQPE  265 (286)
T ss_dssp             HHHHT---TCCEEEEESCG--GGGCCSSSCCCSSEEESSCCHH
T ss_pred             HHhcC---CCCEEEEeCCH--HHHHHHHhCCCcEEEeCCCCHH
Confidence            99973   89999999985  4567789999999999999864

>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=99.86  E-value=2.8e-21  Score=139.75  Aligned_cols=106  Identities=22%  Similarity=0.429  Sum_probs=98.1

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhc
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKES  173 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~  173 (213)
                      ++||||||++..+..+...|+..||.+..+.++.+|++.+.           ...||++|+|+.||+++|+++++.+++.
T Consensus         1 ~~ilivdd~~~~~~~l~~~l~~~g~~v~~~~~~~~a~~~~~-----------~~~~dlil~D~~l~~~~g~~~~~~l~~~   69 (121)
T 2pl1_A            1 MRVLVVEDNALLRHHLKVQIQDAGHQVDDAEDAKEADYYLN-----------EHIPDIAIVDLGLPDEDGLSLIRRWRSN   69 (121)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH-----------HSCCSEEEECSCCSSSCHHHHHHHHHHT
T ss_pred             CeEEEEeCcHHHHHHHHHHHhhcCCEEEEeCCHHHHHHHHh-----------ccCCCEEEEecCCCCCCHHHHHHHHHhc
Confidence            37999999999999999999999999999999999999983           3479999999999999999999999976


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                        .+.+|+|++|+..+.....++++.|+++|+.||++.+
T Consensus        70 --~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~kp~~~~  106 (121)
T 2pl1_A           70 --DVSLPILVLTARESWQDKVEVLSAGADDYVTKPFHIE  106 (121)
T ss_dssp             --TCCSCEEEEESCCCHHHHHHHHHTTCSEEEESSCCHH
T ss_pred             --CCCCCEEEEecCCCHHHHHHHHHcCccceEECCCCHH
Confidence              5689999999999999999999999999999999754

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

Probab=99.86  E-value=1e-21  Score=145.73  Aligned_cols=107  Identities=17%  Similarity=0.213  Sum_probs=99.8

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCC--CCHHHHHHHH
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPG--MTGYELLKKI  170 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~--~~G~e~~~~i  170 (213)
                      ..+||||||++..+..++.+|+..||.+..+.++.+|++.+           ....||+||+|+.||+  ++|+++++.|
T Consensus         6 ~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l-----------~~~~~dlvi~D~~l~~~~~~g~~~~~~l   74 (136)
T 3kto_A            6 HPIIYLVDHQKDARAALSKLLSPLDVTIQCFASAESFMRQQ-----------ISDDAIGMIIEAHLEDKKDSGIELLETL   74 (136)
T ss_dssp             -CEEEEECSCHHHHHHHHHHHTTSSSEEEEESSHHHHTTSC-----------CCTTEEEEEEETTGGGBTTHHHHHHHHH
T ss_pred             CCeEEEEcCCHHHHHHHHHHHHHCCcEEEEeCCHHHHHHHH-----------hccCCCEEEEeCcCCCCCccHHHHHHHH
Confidence            46999999999999999999999999999999999999987           5567999999999999  9999999999


Q ss_pred             HhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          171 KESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       171 r~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      |+.  .+.+|||++|+..+.....++++.|+++||.||++.+
T Consensus        75 ~~~--~~~~~ii~~s~~~~~~~~~~~~~~ga~~~l~KP~~~~  114 (136)
T 3kto_A           75 VKR--GFHLPTIVMASSSDIPTAVRAMRASAADFIEKPFIEH  114 (136)
T ss_dssp             HHT--TCCCCEEEEESSCCHHHHHHHHHTTCSEEEESSBCHH
T ss_pred             HhC--CCCCCEEEEEcCCCHHHHHHHHHcChHHheeCCCCHH
Confidence            987  5789999999999999999999999999999999754

>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=99.86  E-value=1.3e-21  Score=142.21  Aligned_cols=108  Identities=29%  Similarity=0.441  Sum_probs=93.3

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhc
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKES  173 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~  173 (213)
                      .+||||||++..+..++.+|+..||.+..+.++.+|++.+.           ...||++|+|+.||+++|+++++.||+.
T Consensus         2 ~~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~a~~~~~-----------~~~~dlvi~D~~l~~~~g~~~~~~l~~~   70 (124)
T 1mb3_A            2 KKVLIVEDNELNMKLFHDLLEAQGYETLQTREGLSALSIAR-----------ENKPDLILMDIQLPEISGLEVTKWLKED   70 (124)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESCHHHHHHHHH-----------HHCCSEEEEESBCSSSBHHHHHHHHHHS
T ss_pred             cEEEEEcCCHHHHHHHHHHHHHcCcEEEEeCCHHHHHHHHh-----------cCCCCEEEEeCCCCCCCHHHHHHHHHcC
Confidence            47999999999999999999999999999999999999884           3469999999999999999999999986


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      ...+.+|||++|+..+......+++.|+++||.||++.+
T Consensus        71 ~~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~KP~~~~  109 (124)
T 1mb3_A           71 DDLAHIPVVAVTAFAMKGDEERIREGGCEAYISKPISVV  109 (124)
T ss_dssp             TTTTTSCEEEEC------CHHHHHHHTCSEEECSSCCHH
T ss_pred             ccccCCcEEEEECCCCHHHHHHHHhCCCCEEEeCCCCHH
Confidence            445789999999998888889999999999999999754

>3i42_A Response regulator receiver domain protein (CHEY- like); structural genomics, PSI-2, protein structure initiative; 2.15A {Methylobacillus flagellatus KT} SCOP: c.23.1.0

Probab=99.86  E-value=9.2e-22  Score=143.88  Aligned_cols=108  Identities=20%  Similarity=0.274  Sum_probs=98.5

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHh
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKE  172 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~  172 (213)
                      ..+||||||++..+..++.+|++.||.|..+.++.+|++.+.           ...||+||+|+.||+++|+++++.||+
T Consensus         3 ~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~-----------~~~~dlii~D~~l~~~~g~~~~~~l~~   71 (127)
T 3i42_A            3 LQQALIVEDYQAAAETFKELLEMLGFQADYVMSGTDALHAMS-----------TRGYDAVFIDLNLPDTSGLALVKQLRA   71 (127)
T ss_dssp             CEEEEEECSCHHHHHHHHHHHHHTTEEEEEESSHHHHHHHHH-----------HSCCSEEEEESBCSSSBHHHHHHHHHH
T ss_pred             cceEEEEcCCHHHHHHHHHHHHHcCCCEEEECCHHHHHHHHH-----------hcCCCEEEEeCCCCCCCHHHHHHHHHh
Confidence            468999999999999999999999999999999999999984           457999999999999999999999998


Q ss_pred             cCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          173 SSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       173 ~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      ....+.+|||++|+..+... ..++..|+++||.||++.+
T Consensus        72 ~~~~~~~~ii~~s~~~~~~~-~~~~~~g~~~~l~KP~~~~  110 (127)
T 3i42_A           72 LPMEKTSKFVAVSGFAKNDL-GKEACELFDFYLEKPIDIA  110 (127)
T ss_dssp             SCCSSCCEEEEEECC-CTTC-CHHHHHHCSEEEESSCCHH
T ss_pred             hhccCCCCEEEEECCcchhH-HHHHHHhhHHheeCCCCHH
Confidence            75567899999999988887 8899999999999999864

>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=1.7e-21  Score=142.60  Aligned_cols=109  Identities=24%  Similarity=0.460  Sum_probs=99.7

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCC-EEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSC-KVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~-~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      ..+||||||++..+..++.+|+..|| .+..+.++.+|++.+           ....||+||+|+.||+++|+++++.+|
T Consensus         6 ~~~ilivdd~~~~~~~l~~~L~~~g~~~v~~~~~~~~a~~~~-----------~~~~~dlvl~D~~l~~~~g~~~~~~l~   74 (129)
T 1p6q_A            6 KIKVLIVDDQVTSRLLLGDALQQLGFKQITAAGDGEQGMKIM-----------AQNPHHLVISDFNMPKMDGLGLLQAVR   74 (129)
T ss_dssp             CCCEEEECSSHHHHHHHHHHHHTTTCSCEECCSSHHHHHHHH-----------HTSCCSEEEECSSSCSSCHHHHHHHHT
T ss_pred             cCeEEEEcCCHHHHHHHHHHHHHCCCcEEEecCCHHHHHHHH-----------HcCCCCEEEEeCCCCCCCHHHHHHHHh
Confidence            46899999999999999999999999 889999999999998           345799999999999999999999999


Q ss_pred             hcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          172 ESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      +....+.+|||++|+..+.....++++.|+++||.||++.+
T Consensus        75 ~~~~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~KP~~~~  115 (129)
T 1p6q_A           75 ANPATKKAAFIILTAQGDRALVQKAAALGANNVLAKPFTIE  115 (129)
T ss_dssp             TCTTSTTCEEEECCSCCCHHHHHHHHHHTCSCEECCCSSHH
T ss_pred             cCccccCCCEEEEeCCCCHHHHHHHHHcCCCEEEECCCCHH
Confidence            86445789999999999999999999999999999999854

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

Probab=99.86  E-value=3.2e-21  Score=145.88  Aligned_cols=109  Identities=25%  Similarity=0.408  Sum_probs=101.3

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHH
Q 048660           91 SKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKI  170 (213)
Q Consensus        91 ~~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~i  170 (213)
                      ....+||||||++..+..+..+|+..||.|..+.++.+|++.+.           ...||+||+|+.||+++|+++++.|
T Consensus        12 ~~~~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~-----------~~~~dlvi~D~~l~~~~g~~~~~~l   80 (153)
T 3hv2_A           12 TRRPEILLVDSQEVILQRLQQLLSPLPYTLHFARDATQALQLLA-----------SREVDLVISAAHLPQMDGPTLLARI   80 (153)
T ss_dssp             CSCCEEEEECSCHHHHHHHHHHHTTSSCEEEEESSHHHHHHHHH-----------HSCCSEEEEESCCSSSCHHHHHHHH
T ss_pred             cCCceEEEECCCHHHHHHHHHHhcccCcEEEEECCHHHHHHHHH-----------cCCCCEEEEeCCCCcCcHHHHHHHH
Confidence            45679999999999999999999999999999999999999984           4579999999999999999999999


Q ss_pred             HhcCCCCCCcEEEEecCCCHHHHHHHHHcC-CCeeeeCCCCCC
Q 048660          171 KESSVFREVPVVIMSSEDVLTQIDSCLEEG-AEEYIVKPVKLS  212 (213)
Q Consensus       171 r~~~~~~~~pII~lt~~~~~~~~~~~~~~G-~~~~L~KP~~~~  212 (213)
                      |+.  .+.+|||++|+..+.....++++.| +++||.||++.+
T Consensus        81 ~~~--~~~~~ii~~s~~~~~~~~~~~~~~g~~~~~l~KP~~~~  121 (153)
T 3hv2_A           81 HQQ--YPSTTRILLTGDPDLKLIAKAINEGEIYRYLSKPWDDQ  121 (153)
T ss_dssp             HHH--CTTSEEEEECCCCCHHHHHHHHHTTCCSEEECSSCCHH
T ss_pred             HhH--CCCCeEEEEECCCCHHHHHHHHhCCCcceEEeCCCCHH
Confidence            986  5789999999999999999999999 999999999754

>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=5e-21  Score=141.56  Aligned_cols=110  Identities=24%  Similarity=0.425  Sum_probs=99.9

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      ...+||||||++..+..++.+|+..||.+..+.++.+|+..+..          ...||+||+|+.||+++|+++++.||
T Consensus         6 ~~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~~~~----------~~~~dlvi~D~~l~~~~g~~~~~~l~   75 (136)
T 3hdv_A            6 ARPLVLVVDDNAVNREALILYLKSRGIDAVGADGAEEARLYLHY----------QKRIGLMITDLRMQPESGLDLIRTIR   75 (136)
T ss_dssp             -CCEEEEECSCHHHHHHHHHHHHHTTCCEEEESSHHHHHHHHHH----------CTTEEEEEECSCCSSSCHHHHHHHHH
T ss_pred             CCCeEEEECCCHHHHHHHHHHHHHcCceEEEeCCHHHHHHHHHh----------CCCCcEEEEeccCCCCCHHHHHHHHH
Confidence            35799999999999999999999999999999999999998842          22499999999999999999999999


Q ss_pred             hcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          172 ESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      +.. .+.+|||++|+..+.....++++.|+++||.||++.+
T Consensus        76 ~~~-~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~KP~~~~  115 (136)
T 3hdv_A           76 ASE-RAALSIIVVSGDTDVEEAVDVMHLGVVDFLLKPVDLG  115 (136)
T ss_dssp             TST-TTTCEEEEEESSCCHHHHHHHHHTTCSEEEESSCCHH
T ss_pred             hcC-CCCCCEEEEeCCCChHHHHHHHhCCcceEEeCCCCHH
Confidence            864 5789999999999999999999999999999999754

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

Probab=99.86  E-value=2.2e-21  Score=158.73  Aligned_cols=108  Identities=27%  Similarity=0.463  Sum_probs=100.7

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      ...+||||||++..+..+..+|+..||.|..+.++.+|++.+.           ...||+||+|+.||+++|+++++.||
T Consensus        22 ~~~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~-----------~~~~dlvllD~~lp~~~g~~~~~~lr   90 (250)
T 3r0j_A           22 PEARVLVVDDEANIVELLSVSLKFQGFEVYTATNGAQALDRAR-----------ETRPDAVILDVXMPGMDGFGVLRRLR   90 (250)
T ss_dssp             SSCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH-----------HHCCSEEEEESCCSSSCHHHHHHHHH
T ss_pred             CCceEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHH-----------hCCCCEEEEeCCCCCCCHHHHHHHHH
Confidence            4579999999999999999999999999999999999999984           34799999999999999999999999


Q ss_pred             hcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          172 ESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      +.  .+.+|||++|+..+.....+++++|+++||.||++.+
T Consensus        91 ~~--~~~~~ii~lt~~~~~~~~~~~~~~Ga~~yl~Kp~~~~  129 (250)
T 3r0j_A           91 AD--GIDAPALFLTARDSLQDKIAGLTLGGDDYVTKPFSLE  129 (250)
T ss_dssp             HT--TCCCCEEEEECSTTHHHHHHHHTSTTCEEEESSCCHH
T ss_pred             hc--CCCCCEEEEECCCCHHHHHHHHHcCCcEEEeCCCCHH
Confidence            86  5689999999999999999999999999999999864

>3ilh_A Two component response regulator; NYSGXRC, PSI-II, protein S initiative, structural genomics; 2.59A {Cytophaga hutchinsonii}

Probab=99.86  E-value=4.3e-21  Score=143.04  Aligned_cols=116  Identities=22%  Similarity=0.291  Sum_probs=102.4

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhcCC--EEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHH
Q 048660           91 SKELHVLAVDDSYVDRKLIERLLQISSC--KVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLK  168 (213)
Q Consensus        91 ~~~~~ILvVdD~~~~~~~l~~~L~~~g~--~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~  168 (213)
                      .+..+||||||++..+..+..+|+..|+  .+..+.++.+|++.+.....      ....||+||+|+.||+++|+++++
T Consensus         7 ~~~~~iLivdd~~~~~~~l~~~l~~~~~~~~v~~~~~~~~a~~~l~~~~~------~~~~~dlvi~D~~l~~~~g~~~~~   80 (146)
T 3ilh_A            7 RKIDSVLLIDDDDIVNFLNTTIIRMTHRVEEIQSVTSGNAAINKLNELYA------AGRWPSIICIDINMPGINGWELID   80 (146)
T ss_dssp             CCEEEEEEECSCHHHHHHHHHHHHTTCCEEEEEEESSHHHHHHHHHHHHT------SSCCCSEEEEESSCSSSCHHHHHH
T ss_pred             CccceEEEEeCCHHHHHHHHHHHHhcCCCeeeeecCCHHHHHHHHHHhhc------cCCCCCEEEEcCCCCCCCHHHHHH
Confidence            3567999999999999999999999999  89999999999999853111      125799999999999999999999


Q ss_pred             HHHhcC--CCCCCcEEEEecCCCHHHHHHHHHcC-CCeeeeCCCCCC
Q 048660          169 KIKESS--VFREVPVVIMSSEDVLTQIDSCLEEG-AEEYIVKPVKLS  212 (213)
Q Consensus       169 ~ir~~~--~~~~~pII~lt~~~~~~~~~~~~~~G-~~~~L~KP~~~~  212 (213)
                      .||+..  ..+.+|||++|+..+.....+++..| +++||.||++.+
T Consensus        81 ~l~~~~~~~~~~~~ii~~t~~~~~~~~~~~~~~g~~~~~l~KP~~~~  127 (146)
T 3ilh_A           81 LFKQHFQPMKNKSIVCLLSSSLDPRDQAKAEASDWVDYYVSKPLTAN  127 (146)
T ss_dssp             HHHHHCGGGTTTCEEEEECSSCCHHHHHHHHHCSSCCEEECSSCCHH
T ss_pred             HHHHhhhhccCCCeEEEEeCCCChHHHHHHHhcCCcceeeeCCCCHH
Confidence            999842  36789999999999999999999999 999999999854

>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=99.86  E-value=3.3e-21  Score=139.41  Aligned_cols=106  Identities=25%  Similarity=0.420  Sum_probs=97.4

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCE-EEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHh
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCK-VTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKE  172 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~-v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~  172 (213)
                      .+||||||++..+..++..|+..||. +..+.++.+|++.+.           ...||+||+|+.||+++|+++++.+|+
T Consensus         3 ~~ilivdd~~~~~~~l~~~l~~~g~~vv~~~~~~~~a~~~~~-----------~~~~dlil~D~~l~~~~g~~~~~~l~~   71 (120)
T 1tmy_A            3 KRVLIVDDAAFMRMMLKDIITKAGYEVAGEATNGREAVEKYK-----------ELKPDIVTMDITMPEMNGIDAIKEIMK   71 (120)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHH-----------HHCCSEEEEECSCGGGCHHHHHHHHHH
T ss_pred             ceEEEEcCcHHHHHHHHHHHhhcCcEEEEEECCHHHHHHHHH-----------hcCCCEEEEeCCCCCCcHHHHHHHHHh
Confidence            58999999999999999999999999 568999999999984           346999999999999999999999998


Q ss_pred             cCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          173 SSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       173 ~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      .  .+.+|+|++|+..+.....++++.|+++||.||++.+
T Consensus        72 ~--~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~KP~~~~  109 (120)
T 1tmy_A           72 I--DPNAKIIVCSAMGQQAMVIEAIKAGAKDFIVKPFQPS  109 (120)
T ss_dssp             H--CTTCCEEEEECTTCHHHHHHHHHTTCCEEEESSCCHH
T ss_pred             h--CCCCeEEEEeCCCCHHHHHHHHHhCcceeEeCCCCHH
Confidence            6  4689999999999999999999999999999999754

>3kht_A Response regulator; PSI-II, 11023K, structural genomics, Pro structure initiative, NEW YORK SGX research center for STRU genomics, nysgxrc; 2.10A {Hahella chejuensis} SCOP: c.23.1.0

Probab=99.86  E-value=5.9e-21  Score=142.63  Aligned_cols=109  Identities=26%  Similarity=0.459  Sum_probs=100.5

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCCE--EEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSCK--VTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKK  169 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~~--v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~  169 (213)
                      ...+||||||++..+..+..+|+..|+.  +..+.++.+|++.+           ....||+||+|+.||+++|+++++.
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            3579999999999999999999999987  88999999999999           5567999999999999999999999


Q ss_pred             HHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCC-CC
Q 048660          170 IKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPV-KL  211 (213)
Q Consensus       170 ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~-~~  211 (213)
                      ||+....+.+|||++|+..+.....+++++|+++||.||+ +.
T Consensus        73 lr~~~~~~~~pii~~s~~~~~~~~~~~~~~ga~~~l~Kp~~~~  115 (144)
T 3kht_A           73 VRKPGANQHTPIVILTDNVSDDRAKQCMAAGASSVVDKSSNNV  115 (144)
T ss_dssp             HHSSSTTTTCCEEEEETTCCHHHHHHHHHTTCSEEEECCTTSH
T ss_pred             HHhcccccCCCEEEEeCCCCHHHHHHHHHcCCCEEEECCCCcH
Confidence            9985447899999999999999999999999999999999 64

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

Probab=99.85  E-value=9.7e-21  Score=142.72  Aligned_cols=109  Identities=25%  Similarity=0.405  Sum_probs=100.1

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhcC--CEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHH
Q 048660           91 SKELHVLAVDDSYVDRKLIERLLQISS--CKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLK  168 (213)
Q Consensus        91 ~~~~~ILvVdD~~~~~~~l~~~L~~~g--~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~  168 (213)
                      ...++||||||++..+..+..+|+..|  +.+..+.++.+|++.+           ....||+||+|+.||+++|+++++
T Consensus        18 ~~m~~iLivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~al~~l-----------~~~~~dlii~D~~l~~~~g~~~~~   86 (150)
T 4e7p_A           18 GSHMKVLVAEDQSMLRDAMCQLLTLQPDVESVLQAKNGQEAIQLL-----------EKESVDIAILDVEMPVKTGLEVLE   86 (150)
T ss_dssp             --CEEEEEECSCHHHHHHHHHHHHTSTTEEEEEEESSHHHHHHHH-----------TTSCCSEEEECSSCSSSCHHHHHH
T ss_pred             CCccEEEEEcCCHHHHHHHHHHHHhCCCcEEEEEECCHHHHHHHh-----------hccCCCEEEEeCCCCCCcHHHHHH
Confidence            346799999999999999999999887  7899999999999998           556799999999999999999999


Q ss_pred             HHHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          169 KIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       169 ~ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      .||+.  .+.+|||++|+..+.....++++.|+++||.||++.+
T Consensus        87 ~l~~~--~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~Kp~~~~  128 (150)
T 4e7p_A           87 WIRSE--KLETKVVVVTTFKRAGYFERAVKAGVDAYVLKERSIA  128 (150)
T ss_dssp             HHHHT--TCSCEEEEEESCCCHHHHHHHHHTTCSEEEETTSCHH
T ss_pred             HHHHh--CCCCeEEEEeCCCCHHHHHHHHHCCCcEEEecCCCHH
Confidence            99986  5789999999999999999999999999999999754

>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=99.85  E-value=1e-20  Score=139.62  Aligned_cols=116  Identities=29%  Similarity=0.471  Sum_probs=100.6

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCC--EEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHH
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSC--KVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKI  170 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~--~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~i  170 (213)
                      +.+||||||++..+..+...|+..|+  .+..+.++.+|++.+......+    ....||+||+|+.||+++|+++++.|
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            46899999999999999999999998  9999999999999984210000    01579999999999999999999999


Q ss_pred             HhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          171 KESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       171 r~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      |+....+.+|||++|+..+.+...++++.|+++||.||++.+
T Consensus        78 ~~~~~~~~~pii~ls~~~~~~~~~~~~~~g~~~~l~kP~~~~  119 (140)
T 1k68_A           78 KSDPTLKRIPVVVLSTSINEDDIFHSYDLHVNCYITKSANLS  119 (140)
T ss_dssp             HHSTTGGGSCEEEEESCCCHHHHHHHHHTTCSEEEECCSSHH
T ss_pred             HcCcccccccEEEEecCCcHHHHHHHHHhchhheecCCCCHH
Confidence            986434789999999999999999999999999999999754

>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=99.85  E-value=9e-21  Score=137.65  Aligned_cols=106  Identities=27%  Similarity=0.486  Sum_probs=97.8

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHh
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKE  172 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~  172 (213)
                      ..+||||||++..+..++..|+..||.+..+.++.+|++.+.           ...||++|+|+.||+++|+++++.+|+
T Consensus         3 ~~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~~~-----------~~~~dlvi~D~~l~~~~g~~~~~~l~~   71 (123)
T 1xhf_A            3 TPHILIVEDELVTRNTLKSIFEAEGYDVFEATDGAEMHQILS-----------EYDINLVIMDINLPGKNGLLLARELRE   71 (123)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHH-----------HSCCSEEEECSSCSSSCHHHHHHHHHH
T ss_pred             CceEEEEeCCHHHHHHHHHHHhhCCcEEEEeCCHHHHHHHHh-----------cCCCCEEEEcCCCCCCCHHHHHHHHHh
Confidence            358999999999999999999999999999999999999983           347999999999999999999999998


Q ss_pred             cCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          173 SSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       173 ~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      .   +.+|+|++|+..+.....+++++|+++||.||++.+
T Consensus        72 ~---~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~KP~~~~  108 (123)
T 1xhf_A           72 Q---ANVALMFLTGRDNEVDKILGLEIGADDYITKPFNPR  108 (123)
T ss_dssp             H---CCCEEEEEESCCSHHHHHHHHHHTCSEEEESSCCHH
T ss_pred             C---CCCcEEEEECCCChHHHHHHHhcCcceEEeCCCCHH
Confidence            5   478999999999999999999999999999999854

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

Probab=99.85  E-value=1.2e-21  Score=145.51  Aligned_cols=110  Identities=16%  Similarity=0.312  Sum_probs=99.3

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      ...+||||||++..+..++.+|++.||.+..+.++.+|++.+.           ...||+||+|+.||+++|+++++.||
T Consensus         5 ~~~~iLivdd~~~~~~~l~~~l~~~g~~v~~~~~~~~a~~~l~-----------~~~~dlvi~d~~l~~~~g~~~~~~l~   73 (140)
T 3grc_A            5 PRPRILICEDDPDIARLLNLMLEKGGFDSDMVHSAAQALEQVA-----------RRPYAAMTVDLNLPDQDGVSLIRALR   73 (140)
T ss_dssp             CCSEEEEECSCHHHHHHHHHHHHHTTCEEEEECSHHHHHHHHH-----------HSCCSEEEECSCCSSSCHHHHHHHHH
T ss_pred             CCCCEEEEcCCHHHHHHHHHHHHHCCCeEEEECCHHHHHHHHH-----------hCCCCEEEEeCCCCCCCHHHHHHHHH
Confidence            3579999999999999999999999999999999999999984           45799999999999999999999999


Q ss_pred             hcCCCCCCcEEEEecCCCHHHHH-HHHHcCCCeeeeCCCCCC
Q 048660          172 ESSVFREVPVVIMSSEDVLTQID-SCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~~~~~~-~~~~~G~~~~L~KP~~~~  212 (213)
                      +....+.+|||++|+..+..... .+++.|+++||.||++.+
T Consensus        74 ~~~~~~~~~ii~~s~~~~~~~~~~~~~~~g~~~~l~kP~~~~  115 (140)
T 3grc_A           74 RDSRTRDLAIVVVSANAREGELEFNSQPLAVSTWLEKPIDEN  115 (140)
T ss_dssp             TSGGGTTCEEEEECTTHHHHHHHHCCTTTCCCEEECSSCCHH
T ss_pred             hCcccCCCCEEEEecCCChHHHHHHhhhcCCCEEEeCCCCHH
Confidence            84446899999999988777766 889999999999999754

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

Probab=99.85  E-value=1.3e-20  Score=140.45  Aligned_cols=109  Identities=28%  Similarity=0.448  Sum_probs=100.5

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHh
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKE  172 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~  172 (213)
                      ..+||||||++..+..++.+|+..||.+..+.++.+|++.+..         ....||+||+|+.||+++|+++++.||+
T Consensus         3 ~~~ilivdd~~~~~~~l~~~l~~~g~~v~~~~~~~~a~~~~~~---------~~~~~dlvi~d~~l~~~~g~~~~~~l~~   73 (143)
T 3jte_A            3 LAKILVIDDESTILQNIKFLLEIDGNEVLTASSSTEGLRIFTE---------NCNSIDVVITDMKMPKLSGMDILREIKK   73 (143)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHH---------TTTTCCEEEEESCCSSSCHHHHHHHHHH
T ss_pred             CCEEEEEcCCHHHHHHHHHHHHhCCceEEEeCCHHHHHHHHHh---------CCCCCCEEEEeCCCCCCcHHHHHHHHHH
Confidence            4689999999999999999999999999999999999999842         1457999999999999999999999998


Q ss_pred             cCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          173 SSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       173 ~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      .  .+.+|||++|+..+.....++++.|+++||.||++.+
T Consensus        74 ~--~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~kp~~~~  111 (143)
T 3jte_A           74 I--TPHMAVIILTGHGDLDNAILAMKEGAFEYLRKPVTAQ  111 (143)
T ss_dssp             H--CTTCEEEEEECTTCHHHHHHHHHTTCSEEEESSCCHH
T ss_pred             h--CCCCeEEEEECCCCHHHHHHHHHhCcceeEeCCCCHH
Confidence            7  5789999999999999999999999999999998754

>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=99.85  E-value=1.2e-20  Score=136.82  Aligned_cols=105  Identities=23%  Similarity=0.406  Sum_probs=97.0

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhc
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKES  173 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~  173 (213)
                      .+||||||++..+..+...|+..||.+..+.++.++++.+.           ...||++|+|+.||+++|+++++.+|+ 
T Consensus         3 ~~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~~-----------~~~~dlvi~d~~l~~~~g~~~~~~l~~-   70 (122)
T 1zgz_A            3 HHIVIVEDEPVTQARLQSYFTQEGYTVSVTASGAGLREIMQ-----------NQSVDLILLDINLPDENGLMLTRALRE-   70 (122)
T ss_dssp             CEEEEECSSHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH-----------HSCCSEEEEESCCSSSCHHHHHHHHHT-
T ss_pred             cEEEEEECCHHHHHHHHHHHHHCCCeEEEecCHHHHHHHHh-----------cCCCCEEEEeCCCCCCChHHHHHHHHh-
Confidence            48999999999999999999999999999999999999883           346999999999999999999999997 


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                        .+.+|+|++|+..+.....++++.|+++|+.||++.+
T Consensus        71 --~~~~~ii~~s~~~~~~~~~~~~~~ga~~~l~Kp~~~~  107 (122)
T 1zgz_A           71 --RSTVGIILVTGRSDRIDRIVGLEMGADDYVTKPLELR  107 (122)
T ss_dssp             --TCCCEEEEEESSCCHHHHHHHHHHTCSEEEESSCCHH
T ss_pred             --cCCCCEEEEECCCChhhHHHHHHhCHHHHccCCCCHH
Confidence              3579999999999999999999999999999999754

>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=99.85  E-value=3.6e-21  Score=142.51  Aligned_cols=108  Identities=23%  Similarity=0.363  Sum_probs=99.9

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      ..++||||||++..+..+..+|+..|+.+..+.++.+|++.++           ...||+||+|+.||+++|+++++.||
T Consensus         6 ~~~~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~a~~~l~-----------~~~~dlvi~d~~l~~~~g~~~~~~l~   74 (137)
T 3hdg_A            6 VALKILIVEDDTDAREWLSTIISNHFPEVWSAGDGEEGERLFG-----------LHAPDVIITDIRMPKLGGLEMLDRIK   74 (137)
T ss_dssp             -CCCEEEECSCHHHHHHHHHHHHTTCSCEEEESSHHHHHHHHH-----------HHCCSEEEECSSCSSSCHHHHHHHHH
T ss_pred             cccEEEEEeCCHHHHHHHHHHHHhcCcEEEEECCHHHHHHHHh-----------ccCCCEEEEeCCCCCCCHHHHHHHHH
Confidence            3579999999999999999999999999999999999999984           34799999999999999999999999


Q ss_pred             hcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          172 ESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      +.  .+.+|||++|+..+.+...+++++|+++||.||++.+
T Consensus        75 ~~--~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~kP~~~~  113 (137)
T 3hdg_A           75 AG--GAKPYVIVISAFSEMKYFIKAIELGVHLFLPKPIEPG  113 (137)
T ss_dssp             HT--TCCCEEEECCCCCCHHHHHHHHHHCCSEECCSSCCHH
T ss_pred             hc--CCCCcEEEEecCcChHHHHHHHhCCcceeEcCCCCHH
Confidence            87  5789999999999999999999999999999999754

>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=1.4e-20  Score=138.16  Aligned_cols=108  Identities=20%  Similarity=0.367  Sum_probs=97.2

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhc-CCEEE-EEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           94 LHVLAVDDSYVDRKLIERLLQIS-SCKVT-AVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~-g~~v~-~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      .+||||||++..+..++.+|+.. |+.+. .+.++.+|++.+.           ...||+||+|+.||+++|+++++.||
T Consensus         3 ~~ilivdd~~~~~~~l~~~l~~~~~~~~~~~~~~~~~a~~~~~-----------~~~~dlvllD~~l~~~~g~~~~~~l~   71 (130)
T 1dz3_A            3 IKVCIADDNRELVSLLDEYISSQPDMEVIGTAYNGQDCLQMLE-----------EKRPDILLLDIIMPHLDGLAVLERIR   71 (130)
T ss_dssp             EEEEEECSCHHHHHHHHHHHHTSTTEEEEEEESSHHHHHHHHH-----------HHCCSEEEEESCCSSSCHHHHHHHHH
T ss_pred             eEEEEEcCCHHHHHHHHHHHHhCCCceEEEEeCCHHHHHHHHh-----------cCCCCEEEEecCCCCCCHHHHHHHHH
Confidence            58999999999999999999987 88865 7999999999984           34689999999999999999999999


Q ss_pred             hcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCCC
Q 048660          172 ESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD  213 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~e  213 (213)
                      +.. .+..|||++|+..+.....++++.|+++||.||++.++
T Consensus        72 ~~~-~~~~~ii~ls~~~~~~~~~~~~~~ga~~~l~KP~~~~~  112 (130)
T 1dz3_A           72 AGF-EHQPNVIMLTAFGQEDVTKKAVELGASYFILKPFDMEN  112 (130)
T ss_dssp             HHC-SSCCEEEEEEETTCHHHHHHHHHTTCEEEEECSSCCTT
T ss_pred             hcC-CCCCcEEEEecCCCHHHHHHHHHcCCCEEEeCCCCHHH
Confidence            842 35789999999999999999999999999999998764

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

Probab=99.85  E-value=5.2e-22  Score=147.02  Aligned_cols=108  Identities=15%  Similarity=0.137  Sum_probs=100.4

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcC-CEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISS-CKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKI  170 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g-~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~i  170 (213)
                      ...+||||||++..+..++.+|+..| |.+..+.++.+|++.+           ....||+||+|+.||+++|+++++.|
T Consensus        13 ~~~~ilivdd~~~~~~~l~~~L~~~g~~~v~~~~~~~~a~~~l-----------~~~~~dlvi~D~~l~~~~g~~~~~~l   81 (135)
T 3snk_A           13 KRKQVALFSSDPNFKRDVATRLDALAIYDVRVSETDDFLKGPP-----------ADTRPGIVILDLGGGDLLGKPGIVEA   81 (135)
T ss_dssp             CCEEEEEECSCHHHHHHHHHHHHHTSSEEEEEECGGGGGGCCC-----------TTCCCSEEEEEEETTGGGGSTTHHHH
T ss_pred             CCcEEEEEcCCHHHHHHHHHHHhhcCCeEEEEeccHHHHHHHH-----------hccCCCEEEEeCCCCCchHHHHHHHH
Confidence            45799999999999999999999999 9999999999999887           55679999999999999999999999


Q ss_pred             HhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          171 KESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       171 r~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      |+.  .+.+|||++|+..+.+...++++.|+++||.||++.+
T Consensus        82 ~~~--~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~KP~~~~  121 (135)
T 3snk_A           82 RAL--WATVPLIAVSDELTSEQTRVLVRMNASDWLHKPLDGK  121 (135)
T ss_dssp             HGG--GTTCCEEEEESCCCHHHHHHHHHTTCSEEEESSCCHH
T ss_pred             Hhh--CCCCcEEEEeCCCCHHHHHHHHHcCcHhhccCCCCHH
Confidence            987  4589999999999999999999999999999999854

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

Probab=99.85  E-value=6.4e-21  Score=140.90  Aligned_cols=106  Identities=20%  Similarity=0.421  Sum_probs=96.9

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcC--CEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISS--CKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g--~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      .+|||+||++..+..++.+|+..|  +.+..+.++.+|++.+.           ...||+||+|+.||+++|+++++.||
T Consensus         4 ~~Ilivdd~~~~~~~l~~~l~~~~~~~~v~~~~~~~~al~~~~-----------~~~~dlvilD~~lp~~~g~~~~~~l~   72 (133)
T 3b2n_A            4 TSLIIAEDQNMLRQAMVQLIKLHGDFEILADTDNGLDAMKLIE-----------EYNPNVVILDIEMPGMTGLEVLAEIR   72 (133)
T ss_dssp             EEEEEECSCHHHHHHHHHHHHHHSSEEEEEEESCHHHHHHHHH-----------HHCCSEEEECSSCSSSCHHHHHHHHH
T ss_pred             eEEEEECCCHHHHHHHHHHHhhCCCcEEEEEcCCHHHHHHHHh-----------hcCCCEEEEecCCCCCCHHHHHHHHH
Confidence            589999999999999999999887  56788999999999884           34689999999999999999999999


Q ss_pred             hcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          172 ESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      +.  .+.+|||++|+..+.....++++.|+++||.||++.+
T Consensus        73 ~~--~~~~~ii~ls~~~~~~~~~~~~~~ga~~~l~Kp~~~~  111 (133)
T 3b2n_A           73 KK--HLNIKVIIVTTFKRPGYFEKAVVNDVDAYVLKERSIE  111 (133)
T ss_dssp             HT--TCSCEEEEEESCCCHHHHHHHHHTTCSEEEETTSCHH
T ss_pred             HH--CCCCcEEEEecCCCHHHHHHHHHcCCcEEEECCCCHH
Confidence            85  5789999999999999999999999999999999754

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

Probab=99.85  E-value=5.6e-21  Score=142.24  Aligned_cols=106  Identities=26%  Similarity=0.421  Sum_probs=98.2

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhc
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKES  173 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~  173 (213)
                      .+||||||++..+..++.+|+..||.|..+.++.+|++.+.           ...||+||+|+.||+++|+++++.||+.
T Consensus         5 ~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~-----------~~~~dlvllD~~l~~~~g~~l~~~l~~~   73 (137)
T 3cfy_A            5 PRVLLVEDSTSLAILYKQYVKDEPYDIFHVETGRDAIQFIE-----------RSKPQLIILDLKLPDMSGEDVLDWINQN   73 (137)
T ss_dssp             CEEEEECSCTTHHHHHHHHTTTSSSEEEEESSHHHHHHHHH-----------HHCCSEEEECSBCSSSBHHHHHHHHHHT
T ss_pred             ceEEEEeCCHHHHHHHHHHHHhcCceEEEeCCHHHHHHHHH-----------hcCCCEEEEecCCCCCCHHHHHHHHHhc
Confidence            48999999999999999999999999999999999999984           3469999999999999999999999986


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                        .+.+|||++|+..+.....++++.|+++||.||++.+
T Consensus        74 --~~~~~ii~ls~~~~~~~~~~~~~~ga~~~l~KP~~~~  110 (137)
T 3cfy_A           74 --DIPTSVIIATAHGSVDLAVNLIQKGAEDFLEKPINAD  110 (137)
T ss_dssp             --TCCCEEEEEESSCCHHHHHHHHHTTCSEEEESSCCHH
T ss_pred             --CCCCCEEEEEecCcHHHHHHHHHCCccEEEeCCCCHH
Confidence              5789999999999999999999999999999999754

>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=99.85  E-value=2.3e-21  Score=159.69  Aligned_cols=109  Identities=27%  Similarity=0.546  Sum_probs=100.8

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHH
Q 048660           91 SKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKI  170 (213)
Q Consensus        91 ~~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~i  170 (213)
                      ....+||||||++.++..+..+|+..||.|..+.++.+|++.+.           ...||+||+|+.||+++|+++++.|
T Consensus       127 ~~~~~ILivdd~~~~~~~l~~~L~~~g~~v~~a~~~~eal~~l~-----------~~~~dlvl~D~~mp~~~G~~l~~~i  195 (254)
T 2ayx_A          127 NDDMMILVVDDHPINRRLLADQLGSLGYQCKTANDGVDALNVLS-----------KNHIDIVLSDVNMPNMDGYRLTQRI  195 (254)
T ss_dssp             CCCCEEEEEESSHHHHHHHHHHHHHHTSEEEEECCSHHHHHHHH-----------HSCCSEEEEEESSCSSCCHHHHHHH
T ss_pred             CCCCEEEEEeCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHH-----------hCCCCEEEEcCCCCCCCHHHHHHHH
Confidence            45679999999999999999999999999999999999999984           3469999999999999999999999


Q ss_pred             HhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          171 KESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       171 r~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      |+.  .+.+|||++|+....+...+++++|+++||.||++.+
T Consensus       196 r~~--~~~~piI~lt~~~~~~~~~~~~~~G~~~~l~KP~~~~  235 (254)
T 2ayx_A          196 RQL--GLTLPVIGVTANALAEEKQRCLESGMDSCLSKPVTLD  235 (254)
T ss_dssp             HHH--HCCSCEEEEESSTTSHHHHHHHHCCCEEEEESSCCHH
T ss_pred             Hhc--CCCCcEEEEECCCCHHHHHHHHHcCCceEEECCCCHH
Confidence            987  4589999999999999999999999999999999754

>3hzh_A Chemotaxis response regulator (CHEY-3); phosphatase, complex, response regulator, receiver domain, two-component signal transduction; HET: BFD; 1.96A {Borrelia burgdorferi}

Probab=99.85  E-value=1e-20  Score=143.89  Aligned_cols=110  Identities=25%  Similarity=0.390  Sum_probs=100.1

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCCEEE-EEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSCKVT-AVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKI  170 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~-~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~i  170 (213)
                      ...+||||||++..+..++.+|++.||.+. .+.++.+|++.+...         ...||+||+|+.||+++|+++++.|
T Consensus        35 ~~~~Ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~~al~~l~~~---------~~~~dliilD~~l~~~~g~~~~~~l  105 (157)
T 3hzh_A           35 IPFNVLIVDDSVFTVKQLTQIFTSEGFNIIDTAADGEEAVIKYKNH---------YPNIDIVTLXITMPKMDGITCLSNI  105 (157)
T ss_dssp             EECEEEEECSCHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHHHH---------GGGCCEEEECSSCSSSCHHHHHHHH
T ss_pred             CceEEEEEeCCHHHHHHHHHHHHhCCCeEEEEECCHHHHHHHHHhc---------CCCCCEEEEeccCCCccHHHHHHHH
Confidence            457999999999999999999999999988 999999999998431         1168999999999999999999999


Q ss_pred             HhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          171 KESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       171 r~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      |+.  .+.+|||++|+..+.....+++++|+++||.||++.+
T Consensus       106 r~~--~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~KP~~~~  145 (157)
T 3hzh_A          106 MEF--DKNARVIMISALGKEQLVKDCLIKGAKTFIVKPLDRA  145 (157)
T ss_dssp             HHH--CTTCCEEEEESCCCHHHHHHHHHTTCSEEEESSCCHH
T ss_pred             Hhh--CCCCcEEEEeccCcHHHHHHHHHcCCCEEEeCCCCHH
Confidence            987  5789999999999999999999999999999999753

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

Probab=99.84  E-value=3.2e-21  Score=142.07  Aligned_cols=106  Identities=22%  Similarity=0.405  Sum_probs=95.8

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEE-EEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHh
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVT-AVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKE  172 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~-~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~  172 (213)
                      ++||||||++..+..++.+|++.||.+. .+.++.+|++.+.           ...||+||+|+.||+++|+++++.||+
T Consensus         2 ~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~~a~~~~~-----------~~~~dlii~d~~l~~~~g~~~~~~l~~   70 (134)
T 3f6c_A            2 LNAIIIDDHPLAIAAIRNLLIKNDIEILAELTEGGSAVQRVE-----------TLKPDIVIIDVDIPGVNGIQVLETLRK   70 (134)
T ss_dssp             EEEEEECCCHHHHHHHHHHHHHTTEEEEEEESSSTTHHHHHH-----------HHCCSEEEEETTCSSSCHHHHHHHHHH
T ss_pred             eEEEEEcCCHHHHHHHHHHHhhCCcEEEEEcCCHHHHHHHHH-----------hcCCCEEEEecCCCCCChHHHHHHHHh
Confidence            6899999999999999999999999987 8999999999984           447999999999999999999999998


Q ss_pred             cCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          173 SSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       173 ~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      .  .+.+|||++|+..+.....++++.|+++||.||++.+
T Consensus        71 ~--~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~kp~~~~  108 (134)
T 3f6c_A           71 R--QYSGIIIIVSAKNDHFYGKHCADAGANGFVSKKEGMN  108 (134)
T ss_dssp             T--TCCSEEEEEECC---CTHHHHHHTTCSEEEEGGGCTH
T ss_pred             c--CCCCeEEEEeCCCChHHHHHHHHhCCCEEEeCCCCHH
Confidence            6  5789999999999988999999999999999999864

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

Probab=99.84  E-value=5.9e-21  Score=140.45  Aligned_cols=107  Identities=28%  Similarity=0.451  Sum_probs=93.5

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHh
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKE  172 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~  172 (213)
                      ..+||||||++..+..++.+|+ .||.+..+.++.+|++.+.           ...||+||+|+.||+++|+++++.||+
T Consensus         4 ~~~ilivdd~~~~~~~l~~~l~-~~~~v~~~~~~~~a~~~l~-----------~~~~dlvi~d~~l~~~~g~~~~~~l~~   71 (133)
T 3nhm_A            4 KPKVLIVENSWTMRETLRLLLS-GEFDCTTAADGASGLQQAL-----------AHPPDVLISDVNMDGMDGYALCGHFRS   71 (133)
T ss_dssp             -CEEEEECSCHHHHHHHHHHHT-TTSEEEEESSHHHHHHHHH-----------HSCCSEEEECSSCSSSCHHHHHHHHHH
T ss_pred             CCEEEEEcCCHHHHHHHHHHHh-CCcEEEEECCHHHHHHHHh-----------cCCCCEEEEeCCCCCCCHHHHHHHHHh
Confidence            4699999999999999999999 8999999999999999984           457999999999999999999999998


Q ss_pred             cCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          173 SSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       173 ~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      ....+.+|||++|+..+... ..+++.|+++||.||++.+
T Consensus        72 ~~~~~~~pii~~s~~~~~~~-~~~~~~g~~~~l~KP~~~~  110 (133)
T 3nhm_A           72 EPTLKHIPVIFVSGYAPRTE-GPADQPVPDAYLVKPVKPP  110 (133)
T ss_dssp             STTTTTCCEEEEESCCC------TTSCCCSEEEESSCCHH
T ss_pred             CCccCCCCEEEEeCCCcHhH-HHHhhcCCceEEeccCCHH
Confidence            75567899999999987777 8899999999999999854

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

Probab=99.84  E-value=8.9e-21  Score=140.94  Aligned_cols=106  Identities=21%  Similarity=0.354  Sum_probs=97.8

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHh
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKE  172 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~  172 (213)
                      ..+||||||++..+..+..+|+..||.+..+.++.+|++.+.           ...||+||+|+.||+++|+++++.||+
T Consensus         4 ~~~Ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~-----------~~~~dlvllD~~l~~~~g~~l~~~l~~   72 (136)
T 2qzj_A            4 QTKILIIDGDKDNCQKLKGFLEEKGISIDLAYNCEEAIGKIF-----------SNKYDLIFLEIILSDGDGWTLCKKIRN   72 (136)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHH-----------HCCCSEEEEESEETTEEHHHHHHHHHT
T ss_pred             CCeEEEEcCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHH-----------hcCCCEEEEeCCCCCCCHHHHHHHHcc
Confidence            468999999999999999999999999999999999999983           347999999999999999999999997


Q ss_pred             cCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          173 SSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       173 ~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      .  . .+|||++|+..+.....++++.|+++||.||++.+
T Consensus        73 ~--~-~~~ii~ls~~~~~~~~~~~~~~ga~~~l~KP~~~~  109 (136)
T 2qzj_A           73 V--T-TCPIVYMTYINEDQSILNALNSGGDDYLIKPLNLE  109 (136)
T ss_dssp             T--C-CCCEEEEESCCCHHHHHHHHHTTCCEEEESSCCHH
T ss_pred             C--C-CCCEEEEEcCCCHHHHHHHHHcCCcEEEECCCCHH
Confidence            5  2 78999999999999999999999999999999754

>1yio_A Response regulatory protein; transcription regulation, DNA binding protein; 2.20A {Pseudomonas fluorescens} SCOP: a.4.6.2 c.23.1.1 PDB: 1zn2_A

Probab=99.84  E-value=6.5e-21  Score=151.16  Aligned_cols=107  Identities=22%  Similarity=0.391  Sum_probs=99.5

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHh
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKE  172 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~  172 (213)
                      ..+||||||++..+..+..+|+..||.|..+.++.+|++.+           ....||+||+|+.||+++|+++++.||+
T Consensus         4 ~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~-----------~~~~~dlvl~D~~lp~~~g~~~~~~l~~   72 (208)
T 1yio_A            4 KPTVFVVDDDMSVREGLRNLLRSAGFEVETFDCASTFLEHR-----------RPEQHGCLVLDMRMPGMSGIELQEQLTA   72 (208)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHC-----------CTTSCEEEEEESCCSSSCHHHHHHHHHH
T ss_pred             CCEEEEEcCCHHHHHHHHHHHHhCCceEEEcCCHHHHHHhh-----------hccCCCEEEEeCCCCCCCHHHHHHHHHh
Confidence            46899999999999999999999999999999999999988           5567999999999999999999999998


Q ss_pred             cCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          173 SSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       173 ~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      .  .+.+|||++|+..+.....++++.|+++||.||++.+
T Consensus        73 ~--~~~~~ii~ls~~~~~~~~~~a~~~Ga~~~l~Kp~~~~  110 (208)
T 1yio_A           73 I--SDGIPIVFITAHGDIPMTVRAMKAGAIEFLPKPFEEQ  110 (208)
T ss_dssp             T--TCCCCEEEEESCTTSCCCHHHHHTTEEEEEESSCCHH
T ss_pred             c--CCCCCEEEEeCCCCHHHHHHHHHCCCcEEEeCCCCHH
Confidence            6  5789999999999888899999999999999999754

>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=1.5e-20  Score=138.17  Aligned_cols=109  Identities=23%  Similarity=0.439  Sum_probs=94.4

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      ...+||||||++..+..++.+|++.||.+..+.++.+|++.+           ....||+||+|+.||+++|+++++.||
T Consensus         5 ~~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l-----------~~~~~dlii~d~~l~~~~g~~~~~~l~   73 (132)
T 3lte_A            5 QSKRILVVDDDQAMAAAIERVLKRDHWQVEIAHNGFDAGIKL-----------STFEPAIMTLDLSMPKLDGLDVIRSLR   73 (132)
T ss_dssp             --CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHH-----------HHTCCSEEEEESCBTTBCHHHHHHHHH
T ss_pred             CCccEEEEECCHHHHHHHHHHHHHCCcEEEEeCCHHHHHHHH-----------HhcCCCEEEEecCCCCCCHHHHHHHHH
Confidence            357999999999999999999999999999999999999998           345799999999999999999999999


Q ss_pred             hcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          172 ESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      +....+..+||++++.... ...+++++|+++||.||++.+
T Consensus        74 ~~~~~~~~~ii~~~~~~~~-~~~~~~~~g~~~~l~kP~~~~  113 (132)
T 3lte_A           74 QNKVANQPKILVVSGLDKA-KLQQAVTEGADDYLEKPFDND  113 (132)
T ss_dssp             TTTCSSCCEEEEECCSCSH-HHHHHHHHTCCEEECSSCCHH
T ss_pred             hcCccCCCeEEEEeCCChH-HHHHHHHhChHHHhhCCCCHH
Confidence            8643356667766666555 788999999999999999854

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

Probab=99.84  E-value=1e-20  Score=140.64  Aligned_cols=108  Identities=26%  Similarity=0.418  Sum_probs=95.3

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhc
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKES  173 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~  173 (213)
                      .+||||||++..+..+..+|+..||.+..+.++.+|++.+.           ...||+||+|+.||+++|+++++.||+.
T Consensus         4 ~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~-----------~~~~dlvi~D~~l~~~~g~~~~~~l~~~   72 (138)
T 3c3m_A            4 YTILVVDDSPMIVDVFVTMLERGGYRPITAFSGEECLEALN-----------ATPPDLVLLDIMMEPMDGWETLERIKTD   72 (138)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH-----------HSCCSEEEEESCCSSSCHHHHHHHHHHS
T ss_pred             ceEEEEeCCHHHHHHHHHHHHHcCceEEEeCCHHHHHHHHh-----------ccCCCEEEEeCCCCCCCHHHHHHHHHcC
Confidence            58999999999999999999999999999999999999984           3469999999999999999999999986


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      ...+.+|||++|+.........+..+|+++||.||++.+
T Consensus        73 ~~~~~~~ii~ls~~~~~~~~~~~~~~~~~~~l~KP~~~~  111 (138)
T 3c3m_A           73 PATRDIPVLMLTAKPLTPEEANEYGSYIEDYILKPTTHH  111 (138)
T ss_dssp             TTTTTSCEEEEESSCCCHHHHHHTTTTCSEEEECCCHHH
T ss_pred             cccCCCCEEEEECCCChHHHHHHhhcCHhheEeCCCCHH
Confidence            445689999999987666666666777899999998753

>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=99.84  E-value=1.8e-20  Score=135.19  Aligned_cols=105  Identities=28%  Similarity=0.429  Sum_probs=96.7

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhc
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKES  173 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~  173 (213)
                      .+||||||++..+..++..|+..||.+..+.++.+|++.+.           ...||++|+|+.||+++|+++++.+|+.
T Consensus         2 ~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~~~-----------~~~~dlvl~D~~l~~~~g~~~~~~l~~~   70 (120)
T 2a9o_A            2 KKILIVDDEKPISDIIKFNMTKEGYEVVTAFNGREALEQFE-----------AEQPDIIILDLMLPEIDGLEVAKTIRKT   70 (120)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH-----------HHCCSEEEECSSCSSSCHHHHHHHHHHH
T ss_pred             ceEEEEcCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHHH-----------hCCCCEEEEeccCCCCCHHHHHHHHHhC
Confidence            37999999999999999999999999999999999999884           3469999999999999999999999974


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                         +.+|+|++|+..+......+++.|+++||.||++.+
T Consensus        71 ---~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~Kp~~~~  106 (120)
T 2a9o_A           71 ---SSVPILMLSAKDSEFDKVIGLELGADDYVTKPFSNR  106 (120)
T ss_dssp             ---CCCCEEEEESCCSHHHHHHHHHHTCSEEEESSCCHH
T ss_pred             ---CCCCEEEEecCCchHHHHHHHhCCHhheEeCCCCHH
Confidence               578999999999998899999999999999999754

>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=2.6e-21  Score=167.86  Aligned_cols=105  Identities=21%  Similarity=0.310  Sum_probs=98.9

Q ss_pred             EEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhcC
Q 048660           95 HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKESS  174 (213)
Q Consensus        95 ~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~~  174 (213)
                      +||||||++.++..++.+|+..||.|..+.++.+|++.+.           ...||+||+|+.||+|||+++++.||+. 
T Consensus         2 ~ILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~eal~~l~-----------~~~~DlvllDi~mP~~dG~ell~~lr~~-   69 (368)
T 3dzd_A            2 RVLVVDDEESITSSLSAILEEEGYHPDTAKTLREAEKKIK-----------ELFFPVIVLDVWMPDGDGVNFIDFIKEN-   69 (368)
T ss_dssp             EEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH-----------HBCCSEEEEESEETTEETTTHHHHHHHH-
T ss_pred             EEEEEeCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHH-----------hCCCCEEEEeCCCCCCCHHHHHHHHHhh-
Confidence            7999999999999999999999999999999999999984           4579999999999999999999999987 


Q ss_pred             CCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          175 VFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       175 ~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                       .+.+|||++|++.+.+...++++.|+++||.||++.+
T Consensus        70 -~~~~pvI~lT~~~~~~~~~~a~~~Ga~~yl~KP~~~~  106 (368)
T 3dzd_A           70 -SPDSVVIVITGHGSVDTAVKAIKKGAYEFLEKPFSVE  106 (368)
T ss_dssp             -CTTCEEEEEECSSCCHHHHHHHHHTCCEEEESSCCHH
T ss_pred             -CCCCeEEEEeCCCCHHHHHHHHhcCcceEEeCCCCHH
Confidence             5789999999999999999999999999999999854

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

Probab=99.84  E-value=2.5e-20  Score=138.35  Aligned_cols=110  Identities=18%  Similarity=0.327  Sum_probs=99.9

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhh-cCCE-EEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQI-SSCK-VTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKK  169 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~-~g~~-v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~  169 (213)
                      ...+||||||++..+..++.+|+. .||. +..+.++.+|++.+.           ...||+||+|+.||+++|+++++.
T Consensus         7 ~~~~iLivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~a~~~l~-----------~~~~dlii~d~~l~~~~g~~~~~~   75 (143)
T 3cnb_A            7 NDFSILIIEDDKEFADMLTQFLENLFPYAKIKIAYNPFDAGDLLH-----------TVKPDVVMLDLMMVGMDGFSICHR   75 (143)
T ss_dssp             --CEEEEECSCHHHHHHHHHHHHHHCTTCEEEEECSHHHHHHHHH-----------HTCCSEEEEETTCTTSCHHHHHHH
T ss_pred             CCceEEEEECCHHHHHHHHHHHHhccCccEEEEECCHHHHHHHHH-----------hcCCCEEEEecccCCCcHHHHHHH
Confidence            457999999999999999999999 8999 999999999999984           446999999999999999999999


Q ss_pred             HHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          170 IKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       170 ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      ||+....+.+|||++|+..+.....++++.|+++||.||++.+
T Consensus        76 l~~~~~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~kP~~~~  118 (143)
T 3cnb_A           76 IKSTPATANIIVIAMTGALTDDNVSRIVALGAETCFGKPLNFT  118 (143)
T ss_dssp             HHTSTTTTTSEEEEEESSCCHHHHHHHHHTTCSEEEESSCCHH
T ss_pred             HHhCccccCCcEEEEeCCCCHHHHHHHHhcCCcEEEeCCCCHH
Confidence            9985446889999999999999999999999999999999754

>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=99.84  E-value=2.7e-21  Score=141.05  Aligned_cols=108  Identities=24%  Similarity=0.408  Sum_probs=99.1

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhc
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKES  173 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~  173 (213)
                      .+||||||++..+..+...|+..||.+..+.++.+|++.+           ....||++|+|+.||+++|+++++.+|+.
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            5899999999999999999999999999999999999887           45579999999999999999999999986


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      ...+.+|||++|+..+.....++++.|+++||.||++.+
T Consensus        72 ~~~~~~~ii~~s~~~~~~~~~~~~~~ga~~~l~Kp~~~~  110 (127)
T 2jba_A           72 SMTRDIPVVMLTARGEEEDRVRGLETGADDCITKPFSPK  110 (127)
T ss_dssp             TTTTTSCEEEEEETTHHHHHHTTCCCSCSEEEEESCCHH
T ss_pred             cccCCCCEEEEeCCCCHHHHHHHHhcCCCeEEeCCCCHH
Confidence            444789999999999888889999999999999999754

>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=99.84  E-value=1.7e-20  Score=140.08  Aligned_cols=118  Identities=31%  Similarity=0.533  Sum_probs=101.5

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCC--EEEEEcCHHHHHHHhhhcCCCCCCCCCC--CceeEEEEeCCCCCCCHHHHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSC--KVTAVESGTRALQYLGLDGEQSNVGFDA--LKVNLIITDYTMPGMTGYELL  167 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~--~v~~a~~g~eal~~l~~~~~~~~~~~~~--~~~dlil~D~~mp~~~G~e~~  167 (213)
                      ...+||||||++..+..++.+|+..|+  .+..+.++.+|++.+......+.   ..  ..||+||+|+.||+++|++++
T Consensus         5 ~~~~iLivdd~~~~~~~l~~~L~~~g~~~~v~~~~~~~~al~~l~~~~~~~~---~~~~~~~dlvi~D~~l~~~~g~~~~   81 (149)
T 1k66_A            5 ATQPLLVVEDSDEDFSTFQRLLQREGVVNPIYRCITGDQALDFLYQTGSYCN---PDIAPRPAVILLDLNLPGTDGREVL   81 (149)
T ss_dssp             TTSCEEEECCCHHHHHHHHHHHHHTTBCSCEEEECSHHHHHHHHHTCCSSSC---GGGCCCCSEEEECSCCSSSCHHHHH
T ss_pred             CCccEEEEECCHHHHHHHHHHHHHcCCCceEEEECCHHHHHHHHHhcccccC---cccCCCCcEEEEECCCCCCCHHHHH
Confidence            457899999999999999999999998  89999999999999853211000   01  579999999999999999999


Q ss_pred             HHHHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          168 KKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       168 ~~ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      +.||+....+.+|||++|+..+......+++.|+++||.||++.+
T Consensus        82 ~~l~~~~~~~~~~ii~~t~~~~~~~~~~~~~~g~~~~l~kP~~~~  126 (149)
T 1k66_A           82 QEIKQDEVLKKIPVVIMTTSSNPKDIEICYSYSISSYIVKPLEID  126 (149)
T ss_dssp             HHHTTSTTGGGSCEEEEESCCCHHHHHHHHHTTCSEEEECCSSHH
T ss_pred             HHHHhCcccCCCeEEEEeCCCCHHHHHHHHHCCCCEEEeCCCCHH
Confidence            999986433789999999999999999999999999999999754

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

Probab=99.84  E-value=2.6e-20  Score=137.85  Aligned_cols=109  Identities=27%  Similarity=0.453  Sum_probs=94.6

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      .+.+||||||++..+..+..+|+..||.|..+.++.+|++.+           .... |+||+|+.||+++|+++++.|+
T Consensus         6 ~~~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~~-----------~~~~-dlvllD~~lp~~~g~~~~~~l~   73 (136)
T 1dcf_A            6 TGLKVLVMDENGVSRMVTKGLLVHLGCEVTTVSSNEECLRVV-----------SHEH-KVVFMDVCMPGVENYQIALRIH   73 (136)
T ss_dssp             TTCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHC-----------CTTC-SEEEEECCSSTTTTTHHHHHHH
T ss_pred             CCCeEEEEeCCHHHHHHHHHHHHHcCCeEEEeCCHHHHHHHH-----------hccC-CEEEEeCCCCCCcHHHHHHHHH
Confidence            357899999999999999999999999999999999999987           3334 9999999999999999999998


Q ss_pred             hcCCC---CCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          172 ESSVF---REVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       172 ~~~~~---~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      +....   ...+||++|+..+.....++++.|+++||.||++.+
T Consensus        74 ~~~~~~~~~~~~ii~~s~~~~~~~~~~~~~~ga~~~l~KP~~~~  117 (136)
T 1dcf_A           74 EKFTKQRHQRPLLVALSGNTDKSTKEKCMSFGLDGVLLKPVSLD  117 (136)
T ss_dssp             HHHC-CCSCCCEEEEEESCCSHHHHHHHHHTTCCEEEESSCCHH
T ss_pred             HhhhhccCCCceEEEEeCCCCHHHHHHHHHcCCCeEEECCCCHH
Confidence            53211   223588899999999999999999999999999754

>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=99.84  E-value=1.5e-20  Score=138.84  Aligned_cols=107  Identities=26%  Similarity=0.390  Sum_probs=97.9

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHh
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKE  172 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~  172 (213)
                      ..+||||||++..+..+...|+..||.+..+.++.+|++.+.           ...||+||+|+.||+++|+++++.||+
T Consensus         3 ~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~~~-----------~~~~dlvl~D~~l~~~~g~~~~~~l~~   71 (136)
T 1mvo_A            3 NKKILVVDDEESIVTLLQYNLERSGYDVITASDGEEALKKAE-----------TEKPDLIVLDVMLPKLDGIEVCKQLRQ   71 (136)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH-----------HHCCSEEEEESSCSSSCHHHHHHHHHH
T ss_pred             CCEEEEEECCHHHHHHHHHHHHHCCcEEEEecCHHHHHHHHh-----------hcCCCEEEEecCCCCCCHHHHHHHHHc
Confidence            358999999999999999999999999999999999999883           346899999999999999999999998


Q ss_pred             cCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          173 SSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       173 ~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      .  .+.+|||++|+..+......+++.|+++||.||++.+
T Consensus        72 ~--~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~KP~~~~  109 (136)
T 1mvo_A           72 Q--KLMFPILMLTAKDEEFDKVLGLELGADDYMTKPFSPR  109 (136)
T ss_dssp             T--TCCCCEEEEECTTCCCCHHHHHHTTCCEEEESSCCHH
T ss_pred             C--CCCCCEEEEECCCCHHHHHHHHhCCCCEEEECCCCHH
Confidence            6  4679999999998888888999999999999999753

>4dad_A Putative pilus assembly-related protein; response regulator receiver domain, CHEY-related protein, ST genomics; 2.50A {Burkholderia pseudomallei} PDB: 4dn6_A

Probab=99.84  E-value=3.5e-21  Score=144.25  Aligned_cols=110  Identities=9%  Similarity=0.173  Sum_probs=100.1

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhcC-CEEEEEcCHHHHHHHhhhcCCCCCCCCCC-CceeEEEEeCCCCCCCHHHHHH
Q 048660           91 SKELHVLAVDDSYVDRKLIERLLQISS-CKVTAVESGTRALQYLGLDGEQSNVGFDA-LKVNLIITDYTMPGMTGYELLK  168 (213)
Q Consensus        91 ~~~~~ILvVdD~~~~~~~l~~~L~~~g-~~v~~a~~g~eal~~l~~~~~~~~~~~~~-~~~dlil~D~~mp~~~G~e~~~  168 (213)
                      ....+||||||++..+..+..+|+..| |.+..+.++.+++..+.          .. ..||+||+|+.||+++|+++++
T Consensus        18 ~~~~~ilivdd~~~~~~~l~~~L~~~g~~~v~~~~~~~~~~~~~~----------~~~~~~dlvi~D~~l~~~~g~~~~~   87 (146)
T 4dad_A           18 QGMINILVASEDASRLAHLARLVGDAGRYRVTRTVGRAAQIVQRT----------DGLDAFDILMIDGAALDTAELAAIE   87 (146)
T ss_dssp             GGGCEEEEECSCHHHHHHHHHHHHHHCSCEEEEECCCHHHHTTCH----------HHHTTCSEEEEECTTCCHHHHHHHH
T ss_pred             CCCCeEEEEeCCHHHHHHHHHHHhhCCCeEEEEeCCHHHHHHHHH----------hcCCCCCEEEEeCCCCCccHHHHHH
Confidence            346799999999999999999999999 99999999999887763          22 5799999999999999999999


Q ss_pred             HHHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          169 KIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       169 ~ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      .||+.  .+.+|||++|+..+.+...+++++|+++||.||++.+
T Consensus        88 ~l~~~--~~~~~ii~lt~~~~~~~~~~~~~~ga~~~l~Kp~~~~  129 (146)
T 4dad_A           88 KLSRL--HPGLTCLLVTTDASSQTLLDAMRAGVRDVLRWPLEPR  129 (146)
T ss_dssp             HHHHH--CTTCEEEEEESCCCHHHHHHHHTTTEEEEEESSCCHH
T ss_pred             HHHHh--CCCCcEEEEeCCCCHHHHHHHHHhCCceeEcCCCCHH
Confidence            99987  5789999999999999999999999999999999754

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

Probab=99.84  E-value=3.2e-20  Score=138.15  Aligned_cols=106  Identities=25%  Similarity=0.423  Sum_probs=99.1

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHh
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKE  172 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~  172 (213)
                      ..+||||||++..+..++..|+..||.+..+.++.+|++.+           ....||+||+|+ ||+++|+++++.||+
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            56899999999999999999999999999999999999999           556799999999 999999999999998


Q ss_pred             cCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          173 SSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       173 ~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      .  .+.+|||++|+..+.....++++.|+++||.||++.+
T Consensus        72 ~--~~~~pii~ls~~~~~~~~~~~~~~g~~~~l~kP~~~~  109 (142)
T 2qxy_A           72 E--FPDTKVAVLSAYVDKDLIINSVKAGAVDYILKPFRLD  109 (142)
T ss_dssp             H--CTTCEEEEEESCCCHHHHHHHHHHTCSCEEESSCCHH
T ss_pred             H--CCCCCEEEEECCCCHHHHHHHHHCCcceeEeCCCCHH
Confidence            7  5689999999999999999999999999999999754

>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=2.7e-20  Score=140.45  Aligned_cols=109  Identities=24%  Similarity=0.387  Sum_probs=98.8

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhcCCE--EEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHH
Q 048660           91 SKELHVLAVDDSYVDRKLIERLLQISSCK--VTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLK  168 (213)
Q Consensus        91 ~~~~~ILvVdD~~~~~~~l~~~L~~~g~~--v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~  168 (213)
                      ..+.+||||||++..+..+..+|++.|+.  +..+.++.+|++.+.           ...||+||+|+.||+++|+++++
T Consensus        13 ~~~~~iLivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~a~~~l~-----------~~~~dlii~d~~l~~~~g~~~~~   81 (152)
T 3eul_A           13 PEKVRVVVGDDHPLFREGVVRALSLSGSVNVVGEADDGAAALELIK-----------AHLPDVALLDYRMPGMDGAQVAA   81 (152)
T ss_dssp             -CCEEEEEECSSHHHHHHHHHHHHHHSSEEEEEEESSHHHHHHHHH-----------HHCCSEEEEETTCSSSCHHHHHH
T ss_pred             CceEEEEEEcCCHHHHHHHHHHHhhCCCeEEEEEeCCHHHHHHHHH-----------hcCCCEEEEeCCCCCCCHHHHHH
Confidence            45689999999999999999999999964  568999999999984           34799999999999999999999


Q ss_pred             HHHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          169 KIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       169 ~ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      .||+.  .+.+|||++|+..+.....+++++|+++||.||++.+
T Consensus        82 ~l~~~--~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~Kp~~~~  123 (152)
T 3eul_A           82 AVRSY--ELPTRVLLISAHDEPAIVYQALQQGAAGFLLKDSTRT  123 (152)
T ss_dssp             HHHHT--TCSCEEEEEESCCCHHHHHHHHHTTCSEEEETTCCHH
T ss_pred             HHHhc--CCCCeEEEEEccCCHHHHHHHHHcCCCEEEecCCCHH
Confidence            99987  5789999999999999999999999999999999753

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

Probab=99.84  E-value=1.5e-20  Score=140.73  Aligned_cols=110  Identities=21%  Similarity=0.308  Sum_probs=100.6

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      ...+||||||++..+..+...|+..||.|..+.++.+|++.+.           ...||+||+|+.||+++|+++++.||
T Consensus         7 ~~~~iLivd~~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~-----------~~~~dlii~d~~l~~~~g~~~~~~l~   75 (147)
T 2zay_A            7 KWWRIMLVDTQLPALAASISALSQEGFDIIQCGNAIEAVPVAV-----------KTHPHLIITEANMPKISGMDLFNSLK   75 (147)
T ss_dssp             -CEEEEEECTTGGGGHHHHHHHHHHTEEEEEESSHHHHHHHHH-----------HHCCSEEEEESCCSSSCHHHHHHHHH
T ss_pred             CCceEEEEeCCHHHHHHHHHHHHHcCCeEEEeCCHHHHHHHHH-----------cCCCCEEEEcCCCCCCCHHHHHHHHH
Confidence            4579999999999999999999999999999999999999984           34699999999999999999999999


Q ss_pred             hcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          172 ESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      +....+.+|||++|+..+.....++++.|+++||.||++.+
T Consensus        76 ~~~~~~~~pii~ls~~~~~~~~~~~~~~g~~~~l~kp~~~~  116 (147)
T 2zay_A           76 KNPQTASIPVIALSGRATAKEEAQLLDMGFIDFIAKPVNAI  116 (147)
T ss_dssp             TSTTTTTSCEEEEESSCCHHHHHHHHHHTCSEEEESSCCHH
T ss_pred             cCcccCCCCEEEEeCCCCHHHHHHHHhCCCCEEEeCCCCHH
Confidence            84446789999999999999999999999999999999754

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

Probab=99.83  E-value=6.7e-20  Score=138.51  Aligned_cols=108  Identities=25%  Similarity=0.413  Sum_probs=100.0

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      +..+||||||++..+..+...|+..||.+..+.++.+|++.+           ....||+||+|+.||+++|+++++.|+
T Consensus         6 ~~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l-----------~~~~~dlvi~d~~l~~~~g~~~~~~l~   74 (154)
T 2rjn_A            6 KNYTVMLVDDEQPILNSLKRLIKRLGCNIITFTSPLDALEAL-----------KGTSVQLVISDMRMPEMGGEVFLEQVA   74 (154)
T ss_dssp             SCCEEEEECSCHHHHHHHHHHHHTTTCEEEEESCHHHHHHHH-----------TTSCCSEEEEESSCSSSCHHHHHHHHH
T ss_pred             CCCeEEEEcCCHHHHHHHHHHHHHcCCeEEEeCCHHHHHHHH-----------hcCCCCEEEEecCCCCCCHHHHHHHHH
Confidence            467999999999999999999999999999999999999998           455799999999999999999999999


Q ss_pred             hcCCCCCCcEEEEecCCCHHHHHHHHHcC-CCeeeeCCCCCC
Q 048660          172 ESSVFREVPVVIMSSEDVLTQIDSCLEEG-AEEYIVKPVKLS  212 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~~~~~~~~~~~G-~~~~L~KP~~~~  212 (213)
                      +.  .+.+|||++|+..+......+++.| +++||.||++.+
T Consensus        75 ~~--~~~~~ii~ls~~~~~~~~~~~~~~g~~~~~l~kP~~~~  114 (154)
T 2rjn_A           75 KS--YPDIERVVISGYADAQATIDAVNRGKISRFLLKPWEDE  114 (154)
T ss_dssp             HH--CTTSEEEEEECGGGHHHHHHHHHTTCCSEEEESSCCHH
T ss_pred             Hh--CCCCcEEEEecCCCHHHHHHHHhccchheeeeCCCCHH
Confidence            86  5789999999999888999999998 999999999753

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

Probab=99.83  E-value=1.8e-20  Score=134.70  Aligned_cols=104  Identities=25%  Similarity=0.430  Sum_probs=93.9

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhc
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKES  173 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~  173 (213)
                      .+||||||++..+..++..|+..||.+..+.++.+|++.+.           ...||++|+|+.||+++|+++++.+|+.
T Consensus         2 ~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~~~-----------~~~~dlvl~D~~l~~~~g~~~~~~l~~~   70 (116)
T 3a10_A            2 KRILVVDDEPNIRELLKEELQEEGYEIDTAENGEEALKKFF-----------SGNYDLVILDIEMPGISGLEVAGEIRKK   70 (116)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH-----------HSCCSEEEECSCCSSSCHHHHHHHHHHH
T ss_pred             cEEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHh-----------cCCCCEEEEECCCCCCCHHHHHHHHHcc
Confidence            37999999999999999999999999999999999999884           3469999999999999999999999986


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                        .+.+|+|++|+..+..  ..+++.|+++||.||++.+
T Consensus        71 --~~~~~ii~~s~~~~~~--~~~~~~g~~~~l~Kp~~~~  105 (116)
T 3a10_A           71 --KKDAKIILLTAYSHYR--SDMSSWAADEYVVKSFNFD  105 (116)
T ss_dssp             --CTTCCEEEEESCGGGG--GCGGGGGSSEEEECCSSTH
T ss_pred             --CCCCeEEEEECCcchH--HHHHhccccceEECCCCHH
Confidence              4689999999986554  6788999999999999864

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

Probab=99.83  E-value=2.5e-20  Score=138.75  Aligned_cols=116  Identities=23%  Similarity=0.421  Sum_probs=100.8

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCC--EEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSC--KVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKK  169 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~--~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~  169 (213)
                      +..+||||||++..+..++..|++.|+  .+..+.++.+|++.+......     ....||+||+|+.||+++|+++++.
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            357899999999999999999999998  999999999999998531100     0257999999999999999999999


Q ss_pred             HHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          170 IKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       170 ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      ||+....+.+|||++|+..+.....++++.|+++||.||++.+
T Consensus        81 l~~~~~~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~kP~~~~  123 (143)
T 2qvg_A           81 LRDDSSFTDIEVFVLTAAYTSKDKLAFESLNIRGHLIKPLDYG  123 (143)
T ss_dssp             HTTSGGGTTCEEEEEESCCCHHHHHHHTTTTCCEEEESSCCHH
T ss_pred             HHcCccccCCcEEEEeCCCCHHHHHHHHhcCCCeEEECCCCHH
Confidence            9986433789999999999999999999999999999999854

>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=99.83  E-value=3.4e-20  Score=147.85  Aligned_cols=107  Identities=25%  Similarity=0.460  Sum_probs=97.7

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcC-CEE-EEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHH
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISS-CKV-TAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKI  170 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g-~~v-~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~i  170 (213)
                      ..+||||||++..+..+..+|+..| +.+ ..+.++.+|++.+.           ...||+||+|+.||+++|+++++.|
T Consensus         5 ~~~ilivdd~~~~~~~l~~~L~~~~~~~vv~~~~~~~~al~~~~-----------~~~~dlvllD~~lp~~~g~~~~~~l   73 (215)
T 1a04_A            5 PATILLIDDHPMLRTGVKQLISMAPDITVVGEASNGEQGIELAE-----------SLDPDLILLDLNMPGMNGLETLDKL   73 (215)
T ss_dssp             CEEEEEECSCHHHHHHHHHHHTTCTTEEEEEEESSHHHHHHHHH-----------HHCCSEEEEETTSTTSCHHHHHHHH
T ss_pred             ceEEEEECCCHHHHHHHHHHHhcCCCcEEEEEeCCHHHHHHHHH-----------hcCCCEEEEeCCCCCCcHHHHHHHH
Confidence            4689999999999999999999874 877 78999999999884           3469999999999999999999999


Q ss_pred             HhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          171 KESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       171 r~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      |+.  .+.+|||++|+..+.+....+++.|+++||.||++.+
T Consensus        74 r~~--~~~~~ii~ls~~~~~~~~~~~~~~Ga~~~l~Kp~~~~  113 (215)
T 1a04_A           74 REK--SLSGRIVVFSVSNHEEDVVTALKRGADGYLLKDMEPE  113 (215)
T ss_dssp             HHS--CCCSEEEEEECCCCHHHHHHHHHTTCSEEEETTCCHH
T ss_pred             HHh--CCCCcEEEEECCCCHHHHHHHHHcCCcEEEeCCCCHH
Confidence            986  5789999999999999999999999999999999754

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

Probab=99.83  E-value=1e-20  Score=140.64  Aligned_cols=110  Identities=22%  Similarity=0.388  Sum_probs=100.5

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      ...+||||||++..+..+..+|+..||.|..+.++.+|++.+           ....||+||+|+.||+++|+++++.||
T Consensus         6 ~~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l-----------~~~~~dlii~d~~l~~~~g~~~~~~l~   74 (142)
T 3cg4_A            6 HKGDVMIVDDDAHVRIAVKTILSDAGFHIISADSGGQCIDLL-----------KKGFSGVVLLDIMMPGMDGWDTIRAIL   74 (142)
T ss_dssp             CCCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHH-----------HTCCCEEEEEESCCSSSCHHHHHHHHH
T ss_pred             CCCeEEEEcCCHHHHHHHHHHHHHCCeEEEEeCCHHHHHHHH-----------HhcCCCEEEEeCCCCCCCHHHHHHHHH
Confidence            467999999999999999999999999999999999999998           445799999999999999999999999


Q ss_pred             hcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          172 ESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      +....+.+|||++|+..+......++++|+++||.||++.+
T Consensus        75 ~~~~~~~~pii~~s~~~~~~~~~~~~~~g~~~~l~kp~~~~  115 (142)
T 3cg4_A           75 DNSLEQGIAIVMLTAKNAPDAKMIGLQEYVVDYITKPFDNE  115 (142)
T ss_dssp             HTTCCTTEEEEEEECTTCCCCSSTTGGGGEEEEEESSCCHH
T ss_pred             hhcccCCCCEEEEECCCCHHHHHHHHhcCccEEEeCCCCHH
Confidence            84446789999999998888888899999999999999754

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

Probab=99.83  E-value=1.9e-20  Score=162.96  Aligned_cols=105  Identities=30%  Similarity=0.551  Sum_probs=95.9

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHh
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKE  172 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~  172 (213)
                      ..+||||||++.++..++.+|+..||.|..+.++.+|++.+.           ...||+||+|+.||++||+++++.||+
T Consensus         5 ~~~iLivdD~~~~~~~l~~~L~~~g~~v~~a~~~~~al~~~~-----------~~~~dlvllD~~mp~~~G~~~~~~lr~   73 (394)
T 3eq2_A            5 SATLLIIDDDEVVRESLAAYLEDSNFKVLQALNGLQGLQIFE-----------SEQPDLVICDLRMPQIDGLELIRRIRQ   73 (394)
T ss_dssp             EEEEEEECSCHHHHHHHHHHHHHTTEEEEECSSHHHHHHHHH-----------HSCCSEEEECCCSSSSCTHHHHHHHHH
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHhCCCEEEEECCHHHHHHHHh-----------hCCCCEEEEcCCCCCCCHHHHHHHHHh
Confidence            579999999999999999999999999999999999999983           457999999999999999999999998


Q ss_pred             cCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCC
Q 048660          173 SSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVK  210 (213)
Q Consensus       173 ~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~  210 (213)
                      .  .+++|||++|+..+.+...++++.|+++||.||++
T Consensus        74 ~--~~~~pii~lt~~~~~~~~~~a~~~ga~~yl~KP~~  109 (394)
T 3eq2_A           74 T--ASETPIIVLSGAGVMSDAVEALRLGAADYLIKPLE  109 (394)
T ss_dssp             T--TCCCCEEEC---CHHHHHHHHHHHTCSEECCSSCS
T ss_pred             h--CCCCcEEEEEcCCCHHHHHHHHhcChhhEEECCCC
Confidence            6  57899999999999999999999999999999994

>1qkk_A DCTD, C4-dicarboxylate transport transcriptional regulatory protein; receiver domain, 2-component signal transduction; 1.7A {Sinorhizobium meliloti} SCOP: c.23.1.1 PDB: 1l5z_A 1l5y_A

Probab=99.83  E-value=6.9e-20  Score=138.60  Aligned_cols=107  Identities=27%  Similarity=0.456  Sum_probs=99.2

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHh
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKE  172 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~  172 (213)
                      +.+||||||++..+..+..+|+..||.|..+.++.+|++.+           ....||+||+|+.||+++|+++++.|++
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            46899999999999999999999999999999999999988           5567999999999999999999999998


Q ss_pred             cCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          173 SSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       173 ~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      .  .+.+|||++|+..+......+++.|+++||.||++.+
T Consensus        72 ~--~~~~pii~ls~~~~~~~~~~~~~~g~~~~l~kP~~~~  109 (155)
T 1qkk_A           72 L--DPDLPMILVTGHGDIPMAVQAIQDGAYDFIAKPFAAD  109 (155)
T ss_dssp             H--CTTSCEEEEECGGGHHHHHHHHHTTCCEEEESSCCHH
T ss_pred             h--CCCCCEEEEECCCChHHHHHHHhcCCCeEEeCCCCHH
Confidence            7  5789999999999888999999999999999999753

>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=99.83  E-value=3.8e-20  Score=133.62  Aligned_cols=105  Identities=27%  Similarity=0.476  Sum_probs=96.5

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhc
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKES  173 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~  173 (213)
                      .+||||||++..+..+...|+..||.+..+.++.+++..+.           ...||++|+|+.||+++|+++++.+|+ 
T Consensus         2 ~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~-----------~~~~dlvi~D~~l~~~~g~~~~~~l~~-   69 (121)
T 1zh2_A            2 TNVLIVEDEQAIRRFLRTALEGDGMRVFEAETLQRGLLEAA-----------TRKPDLIILDLGLPDGDGIEFIRDLRQ-   69 (121)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHH-----------HHCCSEEEEESEETTEEHHHHHHHHHT-
T ss_pred             cEEEEEeCCHHHHHHHHHHHhcCCCEEEEeCCHHHHHHHHh-----------cCCCCEEEEeCCCCCCcHHHHHHHHHh-
Confidence            47999999999999999999999999999999999998873           346899999999999999999999994 


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                        .+.+|+|++|+..+.....++++.|+++|+.||++.+
T Consensus        70 --~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~Kp~~~~  106 (121)
T 1zh2_A           70 --WSAVPVIVLSARSEESDKIAALDAGADDYLSKPFGIG  106 (121)
T ss_dssp             --TCCCCEEEEESCCSHHHHHHHHHHTCSEEEESSCCHH
T ss_pred             --CCCCcEEEEECCCCHHHHHHHHhcCCCeEEeCCcCHH
Confidence              4679999999999999999999999999999999754

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

Probab=99.83  E-value=1.2e-20  Score=140.63  Aligned_cols=107  Identities=21%  Similarity=0.313  Sum_probs=97.1

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCC-CCHHHHHHHHH
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPG-MTGYELLKKIK  171 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~-~~G~e~~~~ir  171 (213)
                      ..+||||||++..+..++.+|+..||.+..+.++.+|++.+.          ....||+||+|+.||+ ++|+++++.||
T Consensus         5 ~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~----------~~~~~dlvi~D~~l~~~~~g~~~~~~l~   74 (140)
T 3h5i_A            5 DKKILIVEDSKFQAKTIANILNKYGYTVEIALTGEAAVEKVS----------GGWYPDLILMDIELGEGMDGVQTALAIQ   74 (140)
T ss_dssp             -CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH----------TTCCCSEEEEESSCSSSCCHHHHHHHHH
T ss_pred             CcEEEEEeCCHHHHHHHHHHHHHcCCEEEEecChHHHHHHHh----------cCCCCCEEEEeccCCCCCCHHHHHHHHH
Confidence            569999999999999999999999999999999999999984          2257999999999995 99999999999


Q ss_pred             hcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          172 ESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      +.   +.+|||++|+..+.....+++++|+++||.||++.+
T Consensus        75 ~~---~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~KP~~~~  112 (140)
T 3h5i_A           75 QI---SELPVVFLTAHTEPAVVEKIRSVTAYGYVMKSATEQ  112 (140)
T ss_dssp             HH---CCCCEEEEESSSSCCCCGGGGGSCEEEEEETTCCHH
T ss_pred             hC---CCCCEEEEECCCCHHHHHHHHhCCCcEEEeCCCCHH
Confidence            75   689999999999888888999999999999999754

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

Probab=99.82  E-value=2.9e-20  Score=152.53  Aligned_cols=106  Identities=19%  Similarity=0.378  Sum_probs=98.8

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHh
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKE  172 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~  172 (213)
                      ..+||||||++..+..+..+|+..||.|..+.++.+|++.+.           ...||+||+|+.||+++|+++++.||+
T Consensus        37 ~~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~-----------~~~~DlvllD~~lp~~~G~~l~~~lr~  105 (249)
T 3q9s_A           37 EQRILVIEDDHDIANVLRMDLTDAGYVVDHADSAMNGLIKAR-----------EDHPDLILLDLGLPDFDGGDVVQRLRK  105 (249)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHH-----------HSCCSEEEEECCSCHHHHHHHHHHHHT
T ss_pred             CCEEEEEECCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHh-----------cCCCCEEEEcCCCCCCCHHHHHHHHHc
Confidence            468999999999999999999999999999999999999983           457999999999999999999999997


Q ss_pred             cCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          173 SSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       173 ~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                         .+.+|||++|+..+.....+++++|+++||.||++.+
T Consensus       106 ---~~~~~iI~lt~~~~~~~~~~a~~~Ga~~yl~Kp~~~~  142 (249)
T 3q9s_A          106 ---NSALPIIVLTARDTVEEKVRLLGLGADDYLIKPFHPD  142 (249)
T ss_dssp             ---TCCCCEEEEESCCSHHHHHHHHHHTCSEEEESSCCHH
T ss_pred             ---CCCCCEEEEECCCCHHHHHHHHHCCCcEEEECCCCHH
Confidence               3679999999999999999999999999999999854

>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=99.82  E-value=3.2e-20  Score=164.31  Aligned_cols=108  Identities=29%  Similarity=0.471  Sum_probs=99.8

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhc
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKES  173 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~  173 (213)
                      .+||||||++..+..+..+|+..||.|..+.+|.+|++.+.           ...||+||+|+.||+++|+++++.||+.
T Consensus         2 ~~iLivdD~~~~~~~l~~~L~~~~~~v~~a~~~~~al~~~~-----------~~~~dlvllD~~mp~~~G~~~~~~l~~~   70 (459)
T 1w25_A            2 ARILVVDDIEANVRLLEAKLTAEYYEVSTAMDGPTALAMAA-----------RDLPDIILLDVMMPGMDGFTVCRKLKDD   70 (459)
T ss_dssp             CEEEEECSSTTHHHHHHHHHHHTTCEEEEESSHHHHHHHHH-----------HHCCSEEEEESCCSSSCHHHHHHHHHHS
T ss_pred             CeEEEEeCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHh-----------cCCCCEEEEcCCCCCCCHHHHHHHHhcC
Confidence            47999999999999999999999999999999999999984           3469999999999999999999999986


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      ...+.+|||++|+..+.....+++++|+++||.||++.+
T Consensus        71 ~~~~~~pii~lt~~~~~~~~~~a~~~Ga~~~l~KP~~~~  109 (459)
T 1w25_A           71 PTTRHIPVVLITALDGRGDRIQGLESGASDFLTKPIDDV  109 (459)
T ss_dssp             TTTTTSCEEEEECSSCHHHHHHHHHHTCCEEEESSCCHH
T ss_pred             cccCCCCEEEEECCCCHHHHHHHHHcCCCEEEeCCCCHH
Confidence            445789999999999999999999999999999999753

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

Probab=99.82  E-value=1.7e-19  Score=136.18  Aligned_cols=107  Identities=20%  Similarity=0.305  Sum_probs=99.4

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhh-cCCEEE-EEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHH
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQI-SSCKVT-AVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKI  170 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~-~g~~v~-~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~i  170 (213)
                      ..+||||||++..+..+..+|+. .||.+. .+.++.+|++.+           ....||+||+|+.||+++|+++++.|
T Consensus         5 ~~~ILivdd~~~~~~~l~~~L~~~~~~~v~~~~~~~~~a~~~l-----------~~~~~dlii~D~~l~~~~g~~~~~~l   73 (153)
T 3cz5_A            5 TARIMLVDDHPIVREGYRRLIERRPGYAVVAEAADAGEAYRLY-----------RETTPDIVVMDLTLPGPGGIEATRHI   73 (153)
T ss_dssp             CEEEEEECSCHHHHHHHHHHHTTSTTEEEEEEESSHHHHHHHH-----------HTTCCSEEEECSCCSSSCHHHHHHHH
T ss_pred             ccEEEEECCcHHHHHHHHHHHhhCCCcEEEEEeCCHHHHHHHH-----------hcCCCCEEEEecCCCCCCHHHHHHHH
Confidence            57899999999999999999998 799988 899999999998           44579999999999999999999999


Q ss_pred             HhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          171 KESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       171 r~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      |+.  .+.+|||++|+..+.....++++.|+++||.||++.+
T Consensus        74 ~~~--~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~kp~~~~  113 (153)
T 3cz5_A           74 RQW--DGAARILIFTMHQGSAFALKAFEAGASGYVTKSSDPA  113 (153)
T ss_dssp             HHH--CTTCCEEEEESCCSHHHHHHHHHTTCSEEEETTSCTT
T ss_pred             HHh--CCCCeEEEEECCCCHHHHHHHHHCCCcEEEecCCCHH
Confidence            987  5789999999999999999999999999999999875

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

Probab=99.82  E-value=3.5e-20  Score=138.76  Aligned_cols=108  Identities=29%  Similarity=0.400  Sum_probs=94.3

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhc-CCEEE-EEcCHHHHHHHhhhcCCCCCCCCCCC-ceeEEEEeCCCCCCCHHHHH
Q 048660           91 SKELHVLAVDDSYVDRKLIERLLQIS-SCKVT-AVESGTRALQYLGLDGEQSNVGFDAL-KVNLIITDYTMPGMTGYELL  167 (213)
Q Consensus        91 ~~~~~ILvVdD~~~~~~~l~~~L~~~-g~~v~-~a~~g~eal~~l~~~~~~~~~~~~~~-~~dlil~D~~mp~~~G~e~~  167 (213)
                      ....+||||||++..+..++.+|++. |+.+. .+.++.+|++.+.           .. .||+||+|+.||+++|++++
T Consensus        11 ~~~~~vlivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~al~~l~-----------~~~~~dlvilD~~l~~~~g~~~~   79 (145)
T 3kyj_B           11 GSPYNVMIVDDAAMMRLYIASFIKTLPDFKVVAQAANGQEALDKLA-----------AQPNVDLILLDIEMPVMDGMEFL   79 (145)
T ss_dssp             CCSEEEEEECSCHHHHHHHHHHHTTCTTEEEEEEESSHHHHHHHHH-----------HCTTCCEEEECTTSCCCTTCHHH
T ss_pred             CCCCeEEEEcCCHHHHHHHHHHHHhCCCceEEEEECCHHHHHHHHh-----------cCCCCCEEEEeCCCCCCCHHHHH
Confidence            45679999999999999999999988 88864 8999999999984           34 69999999999999999999


Q ss_pred             HHHHhcCCCCCCcEEEEec--CCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          168 KKIKESSVFREVPVVIMSS--EDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       168 ~~ir~~~~~~~~pII~lt~--~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      +.||+..   ..|++++++  ..+.....++++.|+++||.||++.+
T Consensus        80 ~~lr~~~---~~~iiil~~~~~~~~~~~~~~~~~ga~~~l~KP~~~~  123 (145)
T 3kyj_B           80 RHAKLKT---RAKICMLSSVAVSGSPHAARARELGADGVVAKPSGTV  123 (145)
T ss_dssp             HHHHHHC---CCEEC-CBSSCSTTSSHHHHHHHTTCSCCCBCCCSCC
T ss_pred             HHHHhcC---CCCeEEEEEeccCChHHHHHHHhCCCCEEEeCCCCHH
Confidence            9999863   389999987  55566788999999999999999864

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

Probab=99.82  E-value=7.2e-20  Score=135.56  Aligned_cols=107  Identities=23%  Similarity=0.331  Sum_probs=98.4

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCC-----CCCHHHHH
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMP-----GMTGYELL  167 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp-----~~~G~e~~  167 (213)
                      ..+||||||++..+..++..|+..||.+..+.++.+|++.+.           ...||+||+|+.||     +++|++++
T Consensus         3 ~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~-----------~~~~dlvi~d~~~~~~~~~~~~g~~~~   71 (140)
T 2qr3_A            3 LGTIIIVDDNKGVLTAVQLLLKNHFSKVITLSSPVSLSTVLR-----------EENPEVVLLDMNFTSGINNGNEGLFWL   71 (140)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHTTTSSEEEEECCHHHHHHHHH-----------HSCEEEEEEETTTTC-----CCHHHHH
T ss_pred             CceEEEEeCCHHHHHHHHHHHHhCCcEEEEeCCHHHHHHHHH-----------cCCCCEEEEeCCcCCCCCCCccHHHHH
Confidence            468999999999999999999999999999999999999984           44799999999999     99999999


Q ss_pred             HHHHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          168 KKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       168 ~~ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      +.||+.  .+.+|||++|+..+.....++++.|+++||.||++.+
T Consensus        72 ~~l~~~--~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~kp~~~~  114 (140)
T 2qr3_A           72 HEIKRQ--YRDLPVVLFTAYADIDLAVRGIKEGASDFVVKPWDNQ  114 (140)
T ss_dssp             HHHHHH--CTTCCEEEEEEGGGHHHHHHHHHTTCCEEEEESCCHH
T ss_pred             HHHHhh--CcCCCEEEEECCCCHHHHHHHHHcCchheeeCCCCHH
Confidence            999987  5789999999999888999999999999999999753

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

Probab=99.82  E-value=5.3e-20  Score=136.31  Aligned_cols=108  Identities=17%  Similarity=0.297  Sum_probs=98.4

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhcCCEEE-EEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCC-CCCHHHHHH
Q 048660           91 SKELHVLAVDDSYVDRKLIERLLQISSCKVT-AVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMP-GMTGYELLK  168 (213)
Q Consensus        91 ~~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~-~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp-~~~G~e~~~  168 (213)
                      ....+||||||++..+..++..|+..||.+. .+.++.+|++.+.           ...||+||+|+.|| +++|+++++
T Consensus         7 ~~~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~~a~~~~~-----------~~~~dlii~d~~~~~~~~g~~~~~   75 (140)
T 3cg0_A            7 DDLPGVLIVEDGRLAAATLRIQLESLGYDVLGVFDNGEEAVRCAP-----------DLRPDIALVDIMLCGALDGVETAA   75 (140)
T ss_dssp             -CCCEEEEECCBHHHHHHHHHHHHHHTCEEEEEESSHHHHHHHHH-----------HHCCSEEEEESSCCSSSCHHHHHH
T ss_pred             CCCceEEEEECCHHHHHHHHHHHHHCCCeeEEEECCHHHHHHHHH-----------hCCCCEEEEecCCCCCCCHHHHHH
Confidence            3467999999999999999999999999999 5999999999984           34699999999998 799999999


Q ss_pred             HHHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          169 KIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       169 ~ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      .||+.   +.+|||++|+..+......+++.|+++||.||++.+
T Consensus        76 ~l~~~---~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~kp~~~~  116 (140)
T 3cg0_A           76 RLAAG---CNLPIIFITSSQDVETFQRAKRVNPFGYLAKPVAAD  116 (140)
T ss_dssp             HHHHH---SCCCEEEEECCCCHHHHHHHHTTCCSEEEEESCCHH
T ss_pred             HHHhC---CCCCEEEEecCCCHHHHHHHHhcCCCEEEeCCCCHH
Confidence            99986   689999999999999999999999999999999754

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

Probab=99.82  E-value=8.4e-20  Score=137.70  Aligned_cols=107  Identities=28%  Similarity=0.435  Sum_probs=97.4

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHh
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKE  172 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~  172 (213)
                      ..+||||||++..+..+..+|+. ||.+..+.++.+|++.+..          ...||+||+|+.||+++|+++++.||+
T Consensus         4 ~~~ILivdd~~~~~~~l~~~L~~-~~~v~~~~~~~~a~~~l~~----------~~~~dlvi~D~~l~~~~g~~~~~~l~~   72 (151)
T 3kcn_A            4 NERILLVDDDYSLLNTLKRNLSF-DFEVTTCESGPEALACIKK----------SDPFSVIMVDMRMPGMEGTEVIQKARL   72 (151)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHTT-TSEEEEESSHHHHHHHHHH----------SCCCSEEEEESCCSSSCHHHHHHHHHH
T ss_pred             CCeEEEEeCCHHHHHHHHHHhcc-CceEEEeCCHHHHHHHHHc----------CCCCCEEEEeCCCCCCcHHHHHHHHHh
Confidence            56999999999999999999985 9999999999999999842          224699999999999999999999998


Q ss_pred             cCCCCCCcEEEEecCCCHHHHHHHHHcC-CCeeeeCCCCCC
Q 048660          173 SSVFREVPVVIMSSEDVLTQIDSCLEEG-AEEYIVKPVKLS  212 (213)
Q Consensus       173 ~~~~~~~pII~lt~~~~~~~~~~~~~~G-~~~~L~KP~~~~  212 (213)
                      .  .+.+|||++|+..+.....++++.| +++||.||++.+
T Consensus        73 ~--~~~~~ii~~s~~~~~~~~~~~~~~g~~~~~l~KP~~~~  111 (151)
T 3kcn_A           73 I--SPNSVYLMLTGNQDLTTAMEAVNEGQVFRFLNKPCQMS  111 (151)
T ss_dssp             H--CSSCEEEEEECGGGHHHHHHHHHHTCCSEEEESSCCHH
T ss_pred             c--CCCcEEEEEECCCCHHHHHHHHHcCCeeEEEcCCCCHH
Confidence            7  5789999999999999999999999 999999999754

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

Probab=99.82  E-value=1.6e-19  Score=138.53  Aligned_cols=108  Identities=28%  Similarity=0.350  Sum_probs=93.4

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhcC-C-EEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHH
Q 048660           91 SKELHVLAVDDSYVDRKLIERLLQISS-C-KVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLK  168 (213)
Q Consensus        91 ~~~~~ILvVdD~~~~~~~l~~~L~~~g-~-~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~  168 (213)
                      ....+||||||++..+..++.+|+..| + .+..+.++.+|++.+.           ...||+||+|+.||+++|+++++
T Consensus        23 ~~~~~ILivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~al~~l~-----------~~~~dlvilD~~l~~~~g~~l~~   91 (164)
T 3t8y_A           23 DRVIRVLVVDDSAFMRMVLKDIIDSQPDMKVVGFAKDGLEAVEKAI-----------ELKPDVITMDIEMPNLNGIEALK   91 (164)
T ss_dssp             -CCEEEEEECSCHHHHHHHHHHHHTSTTEEEEEEESSHHHHHHHHH-----------HHCCSEEEECSSCSSSCHHHHHH
T ss_pred             cCccEEEEEcCCHHHHHHHHHHHhcCCCeEEEEecCCHHHHHHHhc-----------cCCCCEEEEeCCCCCCCHHHHHH
Confidence            456899999999999999999999875 3 3457999999999984           34699999999999999999999


Q ss_pred             HHHhcCCCCCCcEEEEecCCCHH--HHHHHHHcCCCeeeeCCCCCC
Q 048660          169 KIKESSVFREVPVVIMSSEDVLT--QIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       169 ~ir~~~~~~~~pII~lt~~~~~~--~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      .||+.  .+ +|+|++|+..+..  ...+++++|+++||.||++.+
T Consensus        92 ~lr~~--~~-~~ii~~s~~~~~~~~~~~~~~~~ga~~~l~KP~~~~  134 (164)
T 3t8y_A           92 LIMKK--AP-TRVIMVSSLTEEGAAITIEALRNGAVDFITKPHGSI  134 (164)
T ss_dssp             HHHHH--SC-CEEEEEESSCCTTCHHHHHHHHTTCCEEEECSSSSS
T ss_pred             HHHhc--CC-ceEEEEecCCccchHHHHHHHHcCcCEEEeCCCCHH
Confidence            99987  34 8999999977654  677899999999999999854

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

Probab=99.82  E-value=3.7e-20  Score=138.40  Aligned_cols=106  Identities=26%  Similarity=0.372  Sum_probs=90.3

Q ss_pred             cEEEEEeCCHHHHHHHHHHHh--hcCCEEE-EEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHH
Q 048660           94 LHVLAVDDSYVDRKLIERLLQ--ISSCKVT-AVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKI  170 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~--~~g~~v~-~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~i  170 (213)
                      .+||||||++..+..+...|.  ..|+.+. .+.++.+|++.+           ....||+||+|+.||+++|+++++.|
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            589999999999999999997  3688777 899999999998           45579999999999999999999999


Q ss_pred             HhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          171 KESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       171 r~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      |+.  .+.+|||++|+..+.....++++.|+++||.||++.+
T Consensus        72 ~~~--~~~~~ii~ls~~~~~~~~~~~~~~ga~~~l~KP~~~~  111 (141)
T 3cu5_A           72 LKL--YPDCSVIFMSGYSDKEYLKAAIKFRAIRYVEKPIDPS  111 (141)
T ss_dssp             HHH--CTTCEEEEECCSTTTCCC------CCCEEECSSCCHH
T ss_pred             Hhh--CCCCcEEEEeCCCcHHHHHHHHhCCccEEEeCCCCHH
Confidence            986  5789999999998888888999999999999999754

>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=99.82  E-value=1.2e-20  Score=140.28  Aligned_cols=108  Identities=23%  Similarity=0.366  Sum_probs=89.4

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHh
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKE  172 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~  172 (213)
                      ..+||||||++..+..+..+|+.. |.+..+.++.+|++.+.           ...||+||+|+.||+++|+++++.||+
T Consensus         3 ~~~iLivdd~~~~~~~l~~~l~~~-~~v~~~~~~~~a~~~~~-----------~~~~dlvi~D~~l~~~~g~~~~~~l~~   70 (140)
T 3n53_A            3 LKKILIIDQQDFSRIELKNFLDSE-YLVIESKNEKEALEQID-----------HHHPDLVILDMDIIGENSPNLCLKLKR   70 (140)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHTTT-SEEEEESSHHHHHHHHH-----------HHCCSEEEEETTC------CHHHHHHT
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHhc-ceEEEeCCHHHHHHHHh-----------cCCCCEEEEeCCCCCCcHHHHHHHHHc
Confidence            468999999999999999999988 99999999999999984           347999999999999999999999998


Q ss_pred             cCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          173 SSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       173 ~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      ....+.+|||++|+..+.+...+++++|+++||.||++.+
T Consensus        71 ~~~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~KP~~~~  110 (140)
T 3n53_A           71 SKGLKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRN  110 (140)
T ss_dssp             STTCTTCCEEEEECC----CTTTTTTCCCSEEEESSCCHH
T ss_pred             CcccCCCCEEEEecCCCHHHHHHHHhcCCCeeeeCCCCHH
Confidence            7544899999999999888888999999999999999754

>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=99.82  E-value=5e-20  Score=147.58  Aligned_cols=106  Identities=25%  Similarity=0.375  Sum_probs=98.7

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhc
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKES  173 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~  173 (213)
                      ++||||||++..+..+..+|+..||.|..+.++.+|++.+.           ...||+||+|+.||+++|+++++.||+.
T Consensus         3 ~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~~~-----------~~~~dlvllD~~l~~~~g~~~~~~lr~~   71 (225)
T 1kgs_A            3 VRVLVVEDERDLADLITEALKKEMFTVDVCYDGEEGMYMAL-----------NEPFDVVILDIMLPVHDGWEILKSMRES   71 (225)
T ss_dssp             CEEEEECSSHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH-----------HSCCSEEEEESCCSSSCHHHHHHHHHHT
T ss_pred             ceEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHh-----------cCCCCEEEEeCCCCCCCHHHHHHHHHhc
Confidence            58999999999999999999999999999999999999883           4479999999999999999999999986


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                        .+.+|||++|+..+......++++|+++||.||++.+
T Consensus        72 --~~~~~ii~ls~~~~~~~~~~~~~~ga~~~l~Kp~~~~  108 (225)
T 1kgs_A           72 --GVNTPVLMLTALSDVEYRVKGLNMGADDYLPKPFDLR  108 (225)
T ss_dssp             --TCCCCEEEEESSCHHHHHHHTCCCCCSEEEESSCCHH
T ss_pred             --CCCCCEEEEeCCCCHHHHHHHHhCCccEEEeCCCCHH
Confidence              5789999999999888999999999999999999754

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

Probab=99.81  E-value=1.5e-19  Score=134.31  Aligned_cols=105  Identities=23%  Similarity=0.360  Sum_probs=93.9

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhc
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKES  173 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~  173 (213)
                      .+||||||++..+..+..+|+.. |.+..+.++.+|++.+.           ...||+||+|+.||+++|+++++.||+.
T Consensus         2 ~~Ilivdd~~~~~~~l~~~l~~~-~~v~~~~~~~~a~~~~~-----------~~~~dlvl~D~~lp~~~g~~~~~~l~~~   69 (139)
T 2jk1_A            2 PAILLVDDEPHSLAAMKLALEDD-FDVLTAQGAEAAIAILE-----------EEWVQVIICDQRMPGRTGVDFLTEVRER   69 (139)
T ss_dssp             CEEEEECSSHHHHHHHHHHHTTT-SCEEEESSHHHHHHHHH-----------HSCEEEEEEESCCSSSCHHHHHHHHHHH
T ss_pred             CeEEEEcCCHHHHHHHHHHhhcC-ceEEEcCCHHHHHHHHh-----------cCCCCEEEEeCCCCCCcHHHHHHHHHHh
Confidence            37999999999999999999875 99999999999999884           3469999999999999999999999986


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHc-CCCeeeeCCCCCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEE-GAEEYIVKPVKLS  212 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~-G~~~~L~KP~~~~  212 (213)
                        .+.+|+|++|+..+......++.. |+++||.||++.+
T Consensus        70 --~~~~~ii~~s~~~~~~~~~~~~~~~ga~~~l~KP~~~~  107 (139)
T 2jk1_A           70 --WPETVRIIITGYTDSASMMAAINDAGIHQFLTKPWHPE  107 (139)
T ss_dssp             --CTTSEEEEEESCTTCHHHHHHHHHTTCCEEEESSCCHH
T ss_pred             --CCCCcEEEEeCCCChHHHHHHHHhhchhhhccCCCCHH
Confidence              568999999999887778888876 5999999999754

>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=99.81  E-value=8.6e-20  Score=159.28  Aligned_cols=106  Identities=29%  Similarity=0.519  Sum_probs=99.0

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhc
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKES  173 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~  173 (213)
                      ++||||||++..+..++.+|+..||.|..+.++.+|++.+.           ...||+||+|+.||+++|+++++.|++.
T Consensus         1 m~ILIVDDd~~~~~~l~~~L~~~g~~v~~a~~~~eal~~l~-----------~~~~DlvllD~~mp~~dG~ell~~lr~~   69 (387)
T 1ny5_A            1 MNVLVIEDDKVFRGLLEEYLSMKGIKVESAERGKEAYKLLS-----------EKHFNVVLLDLLLPDVNGLEILKWIKER   69 (387)
T ss_dssp             CEEEEECCCHHHHHHHHHHHHHHTCEEEEESSHHHHHHHHH-----------HSCCSEEEEESBCSSSBHHHHHHHHHHH
T ss_pred             CEEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHH-----------hCCCCEEEEeCCCCCCCHHHHHHHHHhh
Confidence            37999999999999999999999999999999999999983           4579999999999999999999999986


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                        .+.+|||++|++.+.+...++++.|+++||.||++.+
T Consensus        70 --~~~~pvIvlT~~~~~~~~~~a~~~Ga~dyl~KP~~~~  106 (387)
T 1ny5_A           70 --SPETEVIVITGHGTIKTAVEAMKMGAYDFLTKPCMLE  106 (387)
T ss_dssp             --CTTSEEEEEEETTCHHHHHHHHTTTCCEEEEESCCHH
T ss_pred             --CCCCcEEEEeCCCCHHHHHHHHhcCceEEecCCCCHH
Confidence              5789999999999999999999999999999999754

>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=99.81  E-value=4.2e-20  Score=148.73  Aligned_cols=107  Identities=29%  Similarity=0.443  Sum_probs=98.9

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHh
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKE  172 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~  172 (213)
                      .++||||||++..+..+..+|+..||.|..+.++.+|++.+.           ...||+||+|+.||+++|+++++.||+
T Consensus         7 ~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~~~-----------~~~~dlvllD~~l~~~~g~~~~~~l~~   75 (233)
T 1ys7_A            7 SPRVLVVDDDSDVLASLERGLRLSGFEVATAVDGAEALRSAT-----------ENRPDAIVLDINMPVLDGVSVVTALRA   75 (233)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH-----------HSCCSEEEEESSCSSSCHHHHHHHHHH
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHhCCCEEEEECCHHHHHHHHH-----------hCCCCEEEEeCCCCCCCHHHHHHHHHh
Confidence            468999999999999999999999999999999999999883           447999999999999999999999998


Q ss_pred             cCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          173 SSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       173 ~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      .  .+.+|||++|+..+......++++|+++||.||++.+
T Consensus        76 ~--~~~~~ii~lt~~~~~~~~~~~~~~ga~~~l~Kp~~~~  113 (233)
T 1ys7_A           76 M--DNDVPVCVLSARSSVDDRVAGLEAGADDYLVKPFVLA  113 (233)
T ss_dssp             T--TCCCCEEEEECCCTTTCCCTTTTTTCSEEEESSCCHH
T ss_pred             c--CCCCCEEEEEcCCCHHHHHHHHHcCCCEEEeCCCCHH
Confidence            6  4789999999999888888999999999999999754

>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=99.81  E-value=5.9e-20  Score=145.57  Aligned_cols=106  Identities=23%  Similarity=0.382  Sum_probs=96.6

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCEEE-EEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCKVT-AVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~v~-~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      ..+||||||++..+..+..+|+..||.+. .+.++.+|++.+.           ...||+||+|+.||+++|+++++.|+
T Consensus        13 ~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~~al~~~~-----------~~~~dlvi~D~~~p~~~g~~~~~~l~   81 (205)
T 1s8n_A           13 PRRVLIAEDEALIRMDLAEMLREEGYEIVGEAGDGQEAVELAE-----------LHKPDLVIMDVKMPRRDGIDAASEIA   81 (205)
T ss_dssp             CCEEEEECSSHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHH-----------HHCCSEEEEESSCSSSCHHHHHHHHH
T ss_pred             CccEEEEECCHHHHHHHHHHHHHCCCEEEEEeCCHHHHHHHHh-----------hcCCCEEEEeCCCCCCChHHHHHHHH
Confidence            36899999999999999999999999988 8999999999884           34699999999999999999999999


Q ss_pred             hcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          172 ESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      +..   ..|||++|+..+......+++.|+++||.||++.+
T Consensus        82 ~~~---~~pii~lt~~~~~~~~~~~~~~ga~~~l~KP~~~~  119 (205)
T 1s8n_A           82 SKR---IAPIVVLTAFSQRDLVERARDAGAMAYLVKPFSIS  119 (205)
T ss_dssp             HTT---CSCEEEEEEGGGHHHHHTTGGGSCEEEEEESCCHH
T ss_pred             hcC---CCCEEEEecCCCHHHHHHHHhcCCcEEEeCCCCHH
Confidence            863   34999999999999999999999999999999754

>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=99.80  E-value=1e-19  Score=132.05  Aligned_cols=107  Identities=21%  Similarity=0.344  Sum_probs=97.7

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCC-CCCHHHHHHHHHh
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMP-GMTGYELLKKIKE  172 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp-~~~G~e~~~~ir~  172 (213)
                      .+||||||++..+..+...|++.||.+..+.++.+|++.+.           ...||+||+|+.|| +++|+++++.+|+
T Consensus         6 ~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~~~-----------~~~~dlvi~d~~~~~~~~g~~~~~~l~~   74 (127)
T 2gkg_A            6 KKILIVESDTALSATLRSALEGRGFTVDETTDGKGSVEQIR-----------RDRPDLVVLAVDLSAGQNGYLICGKLKK   74 (127)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHHTCEEEEECCHHHHHHHHH-----------HHCCSEEEEESBCGGGCBHHHHHHHHHH
T ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCceEEEecCHHHHHHHHH-----------hcCCCEEEEeCCCCCCCCHHHHHHHHhc
Confidence            58999999999999999999999999999999999999984           34699999999999 9999999999998


Q ss_pred             cCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          173 SSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       173 ~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      ....+.+|||++ +..+......+++.|+++|+.||++.+
T Consensus        75 ~~~~~~~~ii~~-~~~~~~~~~~~~~~g~~~~l~kp~~~~  113 (127)
T 2gkg_A           75 DDDLKNVPIVII-GNPDGFAQHRKLKAHADEYVAKPVDAD  113 (127)
T ss_dssp             STTTTTSCEEEE-ECGGGHHHHHHSTTCCSEEEESSCCHH
T ss_pred             CccccCCCEEEE-ecCCchhHHHHHHhCcchheeCCCCHH
Confidence            654578999999 888788888999999999999999754

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

Probab=99.80  E-value=6.3e-20  Score=134.89  Aligned_cols=106  Identities=20%  Similarity=0.258  Sum_probs=95.8

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHh
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKE  172 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~  172 (213)
                      ..+||||||++..+..++.+|+..++.+..+.++.++++.+           ... ||+||+|+.||+++|+++++.||+
T Consensus         3 ~~~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~-----------~~~-~dlvi~D~~l~~~~g~~~~~~l~~   70 (135)
T 3eqz_A            3 LNRVFIVDDDTLTCNLLKTIVEPIFGNVEAFQHPRAFLTLS-----------LNK-QDIIILDLMMPDMDGIEVIRHLAE   70 (135)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHTTTCSCEEEESCHHHHTTSC-----------CCT-TEEEEEECCTTTTHHHHHHHHHHH
T ss_pred             cceEEEEeCCHHHHHHHHHHHHhhcceeeeecCHHHHHHhh-----------ccC-CCEEEEeCCCCCCCHHHHHHHHHh
Confidence            46899999999999999999999888999999999999876           445 999999999999999999999998


Q ss_pred             cCCCCCCcEEEEecCCCH-----HHHHHHHHcCCCeeeeCCCCCC
Q 048660          173 SSVFREVPVVIMSSEDVL-----TQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       173 ~~~~~~~pII~lt~~~~~-----~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      .  .+.+|||++|+..+.     ....+++..|+++||.||++.+
T Consensus        71 ~--~~~~~ii~~s~~~~~~~~~~~~~~~~~~~g~~~~l~KP~~~~  113 (135)
T 3eqz_A           71 H--KSPASLILISGYDSGVLHSAETLALSCGLNVINTFTKPINTE  113 (135)
T ss_dssp             T--TCCCEEEEEESSCHHHHHHHHHHHHHTTCEEEEEEESSCCHH
T ss_pred             C--CCCCCEEEEEeccchhHHHHHHHHHHcCCCcceeeCCCCCHH
Confidence            6  578999999999875     6677788999999999999854

>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=6.5e-20  Score=157.00  Aligned_cols=109  Identities=24%  Similarity=0.412  Sum_probs=99.0

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHh-hcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQ-ISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~-~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      ..+||||||++..+..++.+|. ..||.|..+.+|.+|++.+.           ...||+||+|+.||+++|+++++.||
T Consensus        18 ~~~ilivdD~~~~~~~l~~~l~~~~~~~v~~~~~~~~al~~~~-----------~~~~dlvl~D~~mp~~~G~~~~~~l~   86 (358)
T 3bre_A           18 AVMVLLVDDQAMIGEAVRRSLASEAGIDFHFCSDPQQAVAVAN-----------QIKPTVILQDLVMPGVDGLTLLAAYR   86 (358)
T ss_dssp             CEEEEEECSCTTHHHHHHTTSSSCTTEEEEEECCHHHHHHHHH-----------HHCCSEEEEESBCSSSBHHHHHHHHT
T ss_pred             CceEEEEECCHHHHHHHHHHHHhccCcEEEEeCCHHHHHHHHH-----------hCCCCEEEEeCCCCCCCHHHHHHHHh
Confidence            4679999999999999999996 46899999999999999984           34699999999999999999999999


Q ss_pred             hcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          172 ESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      +....+.+|||++|+..+.....++++.|+++||.||++.+
T Consensus        87 ~~~~~~~~~ii~~s~~~~~~~~~~a~~~Ga~~~l~Kp~~~~  127 (358)
T 3bre_A           87 GNPATRDIPIIVLSTKEEPTVKSAAFAAGANDYLVKLPDAI  127 (358)
T ss_dssp             TSTTTTTSCEEEEESSCCHHHHHHHHHTTCSEEEESCCCHH
T ss_pred             cCcccCCCcEEEEeCCCCHHHHHHHHhcChheEeeccCCHH
Confidence            86546789999999999999999999999999999999753

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

Probab=99.79  E-value=3.9e-19  Score=126.94  Aligned_cols=105  Identities=21%  Similarity=0.315  Sum_probs=95.3

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhc
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKES  173 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~  173 (213)
                      .+||||||++..+..+...|+..||.+..+.++.++++.+.           ...||++|+|+.||+++|+++++.+|+.
T Consensus         2 ~~iliv~~~~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~l~-----------~~~~dlii~d~~~~~~~~~~~~~~l~~~   70 (119)
T 2j48_A            2 GHILLLEEEDEAATVVCEMLTAAGFKVIWLVDGSTALDQLD-----------LLQPIVILMAWPPPDQSCLLLLQHLREH   70 (119)
T ss_dssp             CEEEEECCCHHHHHHHHHHHHHTTCEEEEESCHHHHHHHHH-----------HHCCSEEEEECSTTCCTHHHHHHHHHHT
T ss_pred             CEEEEEeCCHHHHHHHHHHHHhCCcEEEEecCHHHHHHHHH-----------hcCCCEEEEecCCCCCCHHHHHHHHHhc
Confidence            48999999999999999999999999999999999999984           3469999999999999999999999987


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      ...+.+|+|++|+..+..   .+++.|+++|+.||++.+
T Consensus        71 ~~~~~~~ii~~~~~~~~~---~~~~~g~~~~l~kp~~~~  106 (119)
T 2j48_A           71 QADPHPPLVLFLGEPPVD---PLLTAQASAILSKPLDPQ  106 (119)
T ss_dssp             CCCSSCCCEEEESSCCSS---HHHHHHCSEECSSCSTTH
T ss_pred             cccCCCCEEEEeCCCCch---hhhhcCHHHhccCCCCHH
Confidence            544789999999987765   889999999999999864

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

Probab=99.79  E-value=3e-19  Score=134.79  Aligned_cols=107  Identities=30%  Similarity=0.343  Sum_probs=87.6

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhc-CC-EEEEEcCHHHHHHHhhhcCCCCCCCCCC-CceeEEEEeCCCCCCCHHHHHHH
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQIS-SC-KVTAVESGTRALQYLGLDGEQSNVGFDA-LKVNLIITDYTMPGMTGYELLKK  169 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~-g~-~v~~a~~g~eal~~l~~~~~~~~~~~~~-~~~dlil~D~~mp~~~G~e~~~~  169 (213)
                      ..+||||||++..+..+..+|+.. |+ .+..+.++.+|++.+.           . ..||+||+|+.||+++|+++++.
T Consensus         3 ~~~iLivdd~~~~~~~l~~~L~~~~g~~~v~~~~~~~~a~~~l~-----------~~~~~dlvi~d~~l~~~~g~~~~~~   71 (154)
T 2qsj_A            3 LTVVLIVDDHHLIRAGAKNLLEGAFSGMRVEGAETVSDALAFLE-----------ADNTVDLILLDVNLPDAEAIDGLVR   71 (154)
T ss_dssp             CEEEEEECSCHHHHHHHHHHHHHHCTTEEEEEESSHHHHHHHHH-----------TTCCCSEEEECC------CHHHHHH
T ss_pred             ccEEEEEcCCHHHHHHHHHHHHhCCCceEEEEecCHHHHHHHHh-----------ccCCCCEEEEeCCCCCCchHHHHHH
Confidence            468999999999999999999988 88 7889999999999983           4 57999999999999999999999


Q ss_pred             HHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          170 IKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       170 ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      ||+.  .+.+|||++|+..+......+++.|+++||.||++.+
T Consensus        72 l~~~--~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~kp~~~~  112 (154)
T 2qsj_A           72 LKRF--DPSNAVALISGETDHELIRAALEAGADGFIPKSADPQ  112 (154)
T ss_dssp             HHHH--CTTSEEEEC-----CHHHHHHHHTTCCBBCCTTSCHH
T ss_pred             HHHh--CCCCeEEEEeCCCCHHHHHHHHHccCCEEEeCCCCHH
Confidence            9987  5789999999998888899999999999999999753

>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=99.78  E-value=4.4e-19  Score=142.62  Aligned_cols=105  Identities=27%  Similarity=0.445  Sum_probs=97.3

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhc
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKES  173 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~  173 (213)
                      .+||||||++..+..+..+|+..||.|..+.++.+|++.+.           ...||+||+|+.||+++|+++++.||+.
T Consensus         5 ~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~-----------~~~~dlvllD~~l~~~~g~~~~~~l~~~   73 (230)
T 2oqr_A            5 TSVLIVEDEESLADPLAFLLRKEGFEATVVTDGPAALAEFD-----------RAGADIVLLDLMLPGMSGTDVCKQLRAR   73 (230)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEECSHHHHHHHHH-----------HHCCSEEEEESSCSSSCHHHHHHHHHHH
T ss_pred             CeEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHh-----------ccCCCEEEEECCCCCCCHHHHHHHHHcC
Confidence            58999999999999999999999999999999999999884           3469999999999999999999999984


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                         +.+|||++|+..+......+++.|+++||.||++.+
T Consensus        74 ---~~~~ii~lt~~~~~~~~~~~~~~ga~~~l~Kp~~~~  109 (230)
T 2oqr_A           74 ---SSVPVIMVTARDSEIDKVVGLELGADDYVTKPYSAR  109 (230)
T ss_dssp             ---CSCSEEEEECCHHHHHHHHHHHHCCSCCCCSSCCHH
T ss_pred             ---CCCCEEEEeCCCcHHHHHHHHHcCCCEEEeCCCCHH
Confidence               579999999998888899999999999999999754

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

Probab=99.78  E-value=9.6e-19  Score=130.22  Aligned_cols=106  Identities=23%  Similarity=0.401  Sum_probs=91.5

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhc-CCE-EEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQIS-SCK-VTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKK  169 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~-g~~-v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~  169 (213)
                      ...+||||||++..+..+...|+.. |+. +..+.++.+|++.+.           ...||+||+|+.||+++|+++++.
T Consensus         8 ~~~~iLivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~al~~l~-----------~~~~dlvi~d~~l~~~~g~~~~~~   76 (143)
T 2qv0_A            8 EKMKVIIVEDEFLAQQELSWLINTHSQMEIVGSFDDGLDVLKFLQ-----------HNKVDAIFLDINIPSLDGVLLAQN   76 (143)
T ss_dssp             --CEEEEECSCHHHHHHHHHHHHHHSCCEEEEEESCHHHHHHHHH-----------HCCCSEEEECSSCSSSCHHHHHHH
T ss_pred             CceEEEEEcCCHHHHHHHHHHHHhCCCceEEEEeCCHHHHHHHHH-----------hCCCCEEEEecCCCCCCHHHHHHH
Confidence            3579999999999999999999986 888 458999999999984           346999999999999999999999


Q ss_pred             HHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          170 IKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       170 ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      ||+.  .+..|||++|+..  +...++++.|+++||.||++.+
T Consensus        77 l~~~--~~~~~ii~~s~~~--~~~~~~~~~g~~~~l~KP~~~~  115 (143)
T 2qv0_A           77 ISQF--AHKPFIVFITAWK--EHAVEAFELEAFDYILKPYQES  115 (143)
T ss_dssp             HTTS--TTCCEEEEEESCC--TTHHHHHHTTCSEEEESSCCHH
T ss_pred             HHcc--CCCceEEEEeCCH--HHHHHHHhCCcceEEeCCCCHH
Confidence            9985  4677899999874  3577899999999999999753

>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=3.5e-19  Score=144.45  Aligned_cols=106  Identities=26%  Similarity=0.510  Sum_probs=97.6

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHh
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKE  172 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~  172 (213)
                      ..+||||||++..+..+..+|+..||.|..+.++.+|++.+.           ...||+||+|+.||+++|+++++.||+
T Consensus         5 ~~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~-----------~~~~dlvilD~~l~~~~g~~~~~~lr~   73 (238)
T 2gwr_A            5 RQRILVVDDDASLAEMLTIVLRGEGFDTAVIGDGTQALTAVR-----------ELRPDLVLLDLMLPGMNGIDVCRVLRA   73 (238)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEECCGGGHHHHHH-----------HHCCSEEEEESSCSSSCHHHHHHHHHT
T ss_pred             cCeEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHH-----------hCCCCEEEEeCCCCCCCHHHHHHHHHh
Confidence            358999999999999999999999999999999999999884           346999999999999999999999997


Q ss_pred             cCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          173 SSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       173 ~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      .   +.+|||++|+..+......++++|+++||.||++.+
T Consensus        74 ~---~~~~ii~lt~~~~~~~~~~~~~~Ga~~~l~Kp~~~~  110 (238)
T 2gwr_A           74 D---SGVPIVMLTAKTDTVDVVLGLESGADDYIMKPFKPK  110 (238)
T ss_dssp             T---CCCCEEEEEETTCCSCHHHHHHTTCCEEEEESCCHH
T ss_pred             C---CCCcEEEEeCCCCHHHHHHHHHCCCCEEEeCCCCHH
Confidence            5   379999999999888899999999999999999754

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

Probab=99.78  E-value=1.7e-18  Score=128.04  Aligned_cols=104  Identities=20%  Similarity=0.314  Sum_probs=95.5

Q ss_pred             cCCccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHH
Q 048660           90 CSKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKK  169 (213)
Q Consensus        90 ~~~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~  169 (213)
                      .....+||||||++..+..+..+|+..||.+..+.++.+|++.+.           ...||+||    ||+++|+++++.
T Consensus        15 ~~~~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~-----------~~~~dlvi----~~~~~g~~~~~~   79 (137)
T 2pln_A           15 PRGSMRVLLIEKNSVLGGEIEKGLNVKGFMADVTESLEDGEYLMD-----------IRNYDLVM----VSDKNALSFVSR   79 (137)
T ss_dssp             CTTCSEEEEECSCHHHHHHHHHHHHHTTCEEEEESCHHHHHHHHH-----------HSCCSEEE----ECSTTHHHHHHH
T ss_pred             CCCCCeEEEEeCCHHHHHHHHHHHHHcCcEEEEeCCHHHHHHHHH-----------cCCCCEEE----EcCccHHHHHHH
Confidence            345679999999999999999999999999999999999999984           34799999    899999999999


Q ss_pred             HHhcCCCC-CCcEEEEecCCCHHHHHHHHHcCCCeeeeCCC-CC
Q 048660          170 IKESSVFR-EVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPV-KL  211 (213)
Q Consensus       170 ir~~~~~~-~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~-~~  211 (213)
                      ||+.   + .+|||++|+..+.....++++.|+++||.||+ +.
T Consensus        80 l~~~---~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~kP~~~~  120 (137)
T 2pln_A           80 IKEK---HSSIVVLVSSDNPTSEEEVHAFEQGADDYIAKPYRSI  120 (137)
T ss_dssp             HHHH---STTSEEEEEESSCCHHHHHHHHHTTCSEEEESSCSCH
T ss_pred             HHhc---CCCccEEEEeCCCCHHHHHHHHHcCCceeeeCCCCCH
Confidence            9986   5 89999999999999999999999999999999 64

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

Probab=99.78  E-value=1.4e-18  Score=127.25  Aligned_cols=106  Identities=22%  Similarity=0.292  Sum_probs=94.5

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCC-ceeEEEEeCCCCC-CCHHHHHHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDAL-KVNLIITDYTMPG-MTGYELLKK  169 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~-~~dlil~D~~mp~-~~G~e~~~~  169 (213)
                      ...+||||||++..+..+...|+..||.+..+.++.+|++.+.           .. .||+||+|+.||+ ++|+++++.
T Consensus         4 ~~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~-----------~~~~~dlvi~d~~l~~~~~g~~~~~~   72 (132)
T 2rdm_A            4 EAVTILLADDEAILLLDFESTLTDAGFLVTAVSSGAKAIEMLK-----------SGAAIDGVVTDIRFCQPPDGWQVARV   72 (132)
T ss_dssp             SSCEEEEECSSHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH-----------TTCCCCEEEEESCCSSSSCHHHHHHH
T ss_pred             CCceEEEEcCcHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHH-----------cCCCCCEEEEeeeCCCCCCHHHHHHH
Confidence            3578999999999999999999999999999999999999983           44 7999999999997 999999999


Q ss_pred             HHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          170 IKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       170 ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      ||+.  .+.+|||++|+..+......++..|  +||.||++.+
T Consensus        73 l~~~--~~~~~ii~~s~~~~~~~~~~~~~~~--~~l~kP~~~~  111 (132)
T 2rdm_A           73 AREI--DPNMPIVYISGHAALEWASNGVPDS--IILEKPFTSA  111 (132)
T ss_dssp             HHHH--CTTCCEEEEESSCCTTHHHHSCTTC--EEEESSCCHH
T ss_pred             HHhc--CCCCCEEEEeCCccHHHHHhhcCCc--ceEeCCCCHH
Confidence            9987  5689999999998887777776665  7999999754

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

Probab=99.77  E-value=4.1e-19  Score=132.07  Aligned_cols=106  Identities=24%  Similarity=0.401  Sum_probs=91.3

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHh
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKE  172 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~  172 (213)
                      ..+||||||++..+..++.+|+..|+.+..+.++.+|++.+.           ...||+||+|+.||+++|+++++.||+
T Consensus        10 ~~~iLivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~al~~l~-----------~~~~dlvllD~~lp~~~g~~~~~~l~~   78 (140)
T 3c97_A           10 PLSVLIAEDNDICRLVAAKALEKCTNDITVVTNGLQALQAYQ-----------NRQFDVIIMDIQMPVMDGLEAVSEIRN   78 (140)
T ss_dssp             CCEEEEECCCHHHHHHHHHHHTTTCSEEEEESSHHHHHHHHH-----------HSCCSEEEECTTCCSSCHHHHHHHHHH
T ss_pred             CceEEEEcCCHHHHHHHHHHHHHcCCceEEECCHHHHHHHHh-----------cCCCCEEEEeCCCCCCcHHHHHHHHHh
Confidence            358999999999999999999999999999999999999983           347999999999999999999999997


Q ss_pred             cC---CCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          173 SS---VFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       173 ~~---~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      ..   ..+.+|||++|+........   .+|+++||.||++.+
T Consensus        79 ~~~~~~~~~~~ii~~s~~~~~~~~~---~~g~~~~l~KP~~~~  118 (140)
T 3c97_A           79 YERTHNTKRASIIAITADTIDDDRP---GAELDEYVSKPLNPN  118 (140)
T ss_dssp             HHHHHTCCCCCCEEEESSCCSCCCC---CSSCSEEEESSCCHH
T ss_pred             hhhhcCCCceEEEEEeCccchhHHH---hCChhheEeCCCCHH
Confidence            42   24678999999876554332   789999999999754

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

Probab=99.77  E-value=9.5e-20  Score=146.88  Aligned_cols=106  Identities=24%  Similarity=0.314  Sum_probs=96.6

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcC-CEE-EEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISS-CKV-TAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g-~~v-~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      ++||||||++..+..+..+|+..| |.+ ..+.++.+|++.+.           ...||+||+|+.||+++|+++++.||
T Consensus         2 ~~ILivdd~~~~~~~l~~~L~~~~~~~vv~~~~~~~~al~~l~-----------~~~~dlvllD~~lp~~~g~~~~~~lr   70 (225)
T 3c3w_A            2 VKVFLVDDHEVVRRGLVDLLGADPELDVVGEAGSVAEAMARVP-----------AARPDVAVLDVRLPDGNGIELCRDLL   70 (225)
T ss_dssp             EEEEEECSCHHHHHHHHHHHHTCTTEEEEEEESSHHHHHHHHH-----------HHCCSEEEECSEETTEEHHHHHHHHH
T ss_pred             cEEEEEcCCHHHHHHHHHHHhcCCCcEEEEEECCHHHHHHHHh-----------hcCCCEEEEeCCCCCCCHHHHHHHHH
Confidence            589999999999999999999887 874 57999999999984           34699999999999999999999999


Q ss_pred             hcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          172 ESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      +.  .+.+|||++|+..+.....++++.|+++||.||++.+
T Consensus        71 ~~--~~~~~ii~lt~~~~~~~~~~~~~~Ga~~~l~Kp~~~~  109 (225)
T 3c3w_A           71 SR--MPDLRCLILTSYTSDEAMLDAILAGASGYVVKDIKGM  109 (225)
T ss_dssp             HH--CTTCEEEEGGGSSSHHHHHHHHHHTCCCHHHHHHHHH
T ss_pred             Hh--CCCCcEEEEECCCCHHHHHHHHHCCCCEEEECCCCHH
Confidence            87  5789999999999999999999999999999998653

>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=99.77  E-value=4.9e-19  Score=146.25  Aligned_cols=101  Identities=21%  Similarity=0.330  Sum_probs=86.4

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhh-cCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHh
Q 048660           94 LHVLAVDDSYVDRKLIERLLQI-SSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKE  172 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~-~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~  172 (213)
                      .+||||||++.++..+...|.. .|+.+.. .++.+++..+           ....||+||+|+.||++||+++++.+|+
T Consensus         5 ~~ILiVdD~~~~~~~l~~~L~~~~~~~v~~-~~~~~~~~~~-----------~~~~~dlvllD~~mP~~~G~~~~~~lr~   72 (259)
T 3luf_A            5 QKILIVEDSMTIRRMLIQAIAQQTGLEIDA-FDTLEGARHC-----------QGDEYVVALVDLTLPDAPSGEAVKVLLE   72 (259)
T ss_dssp             CEEEEECCCHHHHHHHHHHHHHHHCCEEEE-ESSTGGGTTC-----------CTTTEEEEEEESCBTTBTTSHHHHHHHH
T ss_pred             CeEEEEECCHHHHHHHHHHHHhcCCeEEEE-eChHHHHHHh-----------hcCCCcEEEEeCCCCCCCHHHHHHHHHh
Confidence            5899999999999999999976 4777754 4555555544           4457999999999999999999999997


Q ss_pred             cCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCC
Q 048660          173 SSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVK  210 (213)
Q Consensus       173 ~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~  210 (213)
                      .    .+|||++|+..+.+...+++++|+++||.||+.
T Consensus        73 ~----~~pvi~lt~~~~~~~~~~a~~~Ga~dyl~Kp~~  106 (259)
T 3luf_A           73 R----GLPVVILTADISEDKREAWLEAGVLDYVMKDSR  106 (259)
T ss_dssp             T----TCCEEEEECC-CHHHHHHHHHTTCCEEEECSSH
T ss_pred             C----CCCEEEEEccCCHHHHHHHHHCCCcEEEeCCch
Confidence            4    589999999999999999999999999999964

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

Probab=99.77  E-value=9.9e-20  Score=146.54  Aligned_cols=108  Identities=11%  Similarity=0.081  Sum_probs=93.4

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhh-cCCEEEE-EcCHHHHHHH-hhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQI-SSCKVTA-VESGTRALQY-LGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLK  168 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~-~g~~v~~-a~~g~eal~~-l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~  168 (213)
                      ...+||||||++..+..++.+|+. .|+.+.. +.++.+++.. +           ....||+||+|+.||+++|+++++
T Consensus         6 ~~~~IlivdD~~~~~~~l~~~L~~~~~~~v~~~~~~~~~~~~~~~-----------~~~~~dlvllD~~mp~~~G~~~~~   74 (225)
T 3klo_A            6 NKLNVRMLSDVCMQSRLLKEALESKLPLALEITPFSELWLEENKP-----------ESRSIQMLVIDYSRISDDVLTDYS   74 (225)
T ss_dssp             SSEEEEEESCCSHHHHHHHHHHHHHSSEEEEEECGGGHHHHTTCS-----------GGGGCCEEEEEGGGCCHHHHHHHH
T ss_pred             CceEEEEEcCcHHHHHHHHHHHhhCCCceEEEEeCCcHHHHHHHh-----------hccCCCEEEEeCCCCCCCHHHHHH
Confidence            357999999999999999999994 6888754 4566666653 4           445799999999999999999999


Q ss_pred             HHHh-cCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          169 KIKE-SSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       169 ~ir~-~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      .||+ .  .+.+|||++|+..+......++++|+++||.||++.+
T Consensus        75 ~lr~~~--~~~~~ii~lt~~~~~~~~~~~~~~Ga~~~l~Kp~~~~  117 (225)
T 3klo_A           75 SFKHIS--CPDAKEVIINCPQDIEHKLLFKWNNLAGVFYIDDDMD  117 (225)
T ss_dssp             HHHHHH--CTTCEEEEEEECTTCCHHHHTTSTTEEEEEETTCCHH
T ss_pred             HHHHhh--CCCCcEEEEECCcchhHHHHHHHhCCCEEEecCCCHH
Confidence            9998 5  5789999999999888899999999999999999764

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

Probab=99.77  E-value=3.8e-19  Score=155.48  Aligned_cols=108  Identities=24%  Similarity=0.327  Sum_probs=93.7

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhh-cCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQI-SSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~-~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      ..+||||||++.++..+..+|+. .|+.|..+.+|.+|++.++.          ...||+||+|+.||+|||+++++.+|
T Consensus         3 ~~~ILivDD~~~~~~~l~~~L~~~~~~~v~~a~~g~eal~~l~~----------~~~~DlvllDi~mP~~dG~ell~~l~   72 (400)
T 3sy8_A            3 DLNVLVLEDEPFQRLVAVTALKKVVPGSILEAADGKEAVAILES----------CGHVDIAICDLQMSGMDGLAFLRHAS   72 (400)
T ss_dssp             CEEEEEECSSHHHHHHHHHHHHHHCSEEEEEESSHHHHHHHHHH----------HSCEEEEEECSSCSSSCHHHHHHHHH
T ss_pred             CceEEEEcCCHHHHHHHHHHHHhcCCcEEEEecCHHHHHHHHhh----------CCCCCEEEEeCCCCCCCHHHHHHHHH
Confidence            36899999999999999999998 57899999999999999842          13799999999999999999999999


Q ss_pred             hcCCCCCCcEEEEecCCCH-----HHHHHHHHcCCCeeeeCCCCCC
Q 048660          172 ESSVFREVPVVIMSSEDVL-----TQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~~-----~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      +.  .+..+||++|+....     ....+++..|+++||.||++.+
T Consensus        73 ~~--~~~~~ii~~s~~~~~~~~~~~~~~~a~~~ga~~yl~KP~~~~  116 (400)
T 3sy8_A           73 LS--GKVHSVILSSEVDPILRQATISMIECLGLNFLGDLGKPFSLE  116 (400)
T ss_dssp             HH--TCEEEEEESCCCCGGGHHHHHHHHHTTTCEEEEECCSSCCHH
T ss_pred             hc--CCCceEEEEcCchHHHHHHHHHHHHHcCCeeccCcCCCcCHH
Confidence            87  456777777777765     5677889999999999999854

>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=99.76  E-value=3.6e-18  Score=136.48  Aligned_cols=103  Identities=24%  Similarity=0.346  Sum_probs=95.6

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhc
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKES  173 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~  173 (213)
                      .+||||||++..+..+..+|+..| .+..+.++.+|++.+             ..||+||+|+.||+++|+++++.||+.
T Consensus         3 ~~ilivdd~~~~~~~l~~~L~~~~-~v~~~~~~~~al~~~-------------~~~dlvllD~~lp~~~g~~~~~~lr~~   68 (220)
T 1p2f_A            3 WKIAVVDDDKNILKKVSEKLQQLG-RVKTFLTGEDFLNDE-------------EAFHVVVLDVMLPDYSGYEICRMIKET   68 (220)
T ss_dssp             EEEEEECSCHHHHHHHHHHHTTTE-EEEEESSHHHHHHCC-------------SCCSEEEEESBCSSSBHHHHHHHHHHH
T ss_pred             ceEEEEeCCHHHHHHHHHHHHhCC-CEEEECCHHHHHHhc-------------CCCCEEEEeCCCCCCCHHHHHHHHHhc
Confidence            589999999999999999999989 899999999999854             368999999999999999999999987


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                        .+.+|||++|+..+.....+++++|+++||.||++.+
T Consensus        69 --~~~~~ii~lt~~~~~~~~~~~~~~ga~~~l~Kp~~~~  105 (220)
T 1p2f_A           69 --RPETWVILLTLLSDDESVLKGFEAGADDYVTKPFNPE  105 (220)
T ss_dssp             --CTTSEEEEEESCCSHHHHHHHHHHTCSEEEESSCCHH
T ss_pred             --CCCCcEEEEEcCCCHHHHHHHHHcCCCEEEECCCCHH
Confidence              4789999999999999999999999999999999754

>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=99.76  E-value=9.9e-19  Score=129.54  Aligned_cols=105  Identities=24%  Similarity=0.318  Sum_probs=91.3

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCC-CceeEEEEeCCCCCCCHHHHHHH
Q 048660           91 SKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDA-LKVNLIITDYTMPGMTGYELLKK  169 (213)
Q Consensus        91 ~~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~-~~~dlil~D~~mp~~~G~e~~~~  169 (213)
                      ....+||||||++..+..+..+|+..||.+..+.++.+|++.+           .. ..||+||+|+.||+++|+++++.
T Consensus        13 ~~~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l-----------~~~~~~dlvilD~~l~~~~g~~~~~~   81 (138)
T 2b4a_A           13 MQPFRVTLVEDEPSHATLIQYHLNQLGAEVTVHPSGSAFFQHR-----------SQLSTCDLLIVSDQLVDLSIFSLLDI   81 (138)
T ss_dssp             -CCCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHTG-----------GGGGSCSEEEEETTCTTSCHHHHHHH
T ss_pred             CCCCeEEEECCCHHHHHHHHHHHHHcCCEEEEeCCHHHHHHHH-----------HhCCCCCEEEEeCCCCCCCHHHHHHH
Confidence            4567999999999999999999999999999999999999988           44 57999999999999999999999


Q ss_pred             HHhcCCCCCCcEEEEe-cCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          170 IKESSVFREVPVVIMS-SEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       170 ir~~~~~~~~pII~lt-~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      ||+.  .+.+|||++| +..+... .+++   +++||.||++.+
T Consensus        82 l~~~--~~~~~ii~ls~~~~~~~~-~~~~---~~~~l~KP~~~~  119 (138)
T 2b4a_A           82 VKEQ--TKQPSVLILTTGRHELIE-SSEH---NLSYLQKPFAIS  119 (138)
T ss_dssp             HTTS--SSCCEEEEEESCC--CCC-CSSS---CEEEEESSCCHH
T ss_pred             HHhh--CCCCCEEEEECCCCCHHH-HHHH---HHheeeCCCCHH
Confidence            9985  5789999999 8776655 5555   999999999754

>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=99.75  E-value=1.9e-20  Score=135.54  Aligned_cols=107  Identities=33%  Similarity=0.494  Sum_probs=97.9

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHh
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKE  172 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~  172 (213)
                      ..+|||+||++..+..+...|+..||.+..+.++.++++.+           ....||++|+|+.||+++|+++++.+++
T Consensus         3 ~~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~-----------~~~~~dlvi~d~~~~~~~g~~~~~~l~~   71 (124)
T 1dc7_A            3 RGIVWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLAAL-----------ASKTPDVLLSDIRMPGMDGLALLKQIKQ   71 (124)
T ss_dssp             CCCCEEECSSSSHHHHHHHHHTTTTCCCEECCCTTHHHHHS-----------SSCCCSCEEECSCSSHHHHCSTHHHHHH
T ss_pred             ccEEEEEeCCHHHHHHHHHHHHhCCcEEEEeCCHHHHHHHH-----------hcCCCCEEEEeeecCCCCHHHHHHHHHh
Confidence            35799999999999999999999999999999999999988           4557999999999999999999999998


Q ss_pred             cCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          173 SSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       173 ~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      .  .+.+|+|++|+..+.....++++.|+++|+.||++.+
T Consensus        72 ~--~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~kp~~~~  109 (124)
T 1dc7_A           72 R--HPMLPVIIMTAHSDLDAAVSAYQQGAFDYLPKPFDID  109 (124)
T ss_dssp             H--CTTSCCCCBCCSTTSTTTTSSCTTCCCCCBCSSCCHH
T ss_pred             h--CCCCCEEEEecCCCHHHHHHHHhcCcceEeeCCCCHH
Confidence            6  5789999999998888888999999999999999754

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

Probab=99.75  E-value=1.1e-17  Score=134.00  Aligned_cols=102  Identities=22%  Similarity=0.346  Sum_probs=94.3

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhc
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKES  173 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~  173 (213)
                      ++||||||++..+..+..+|+..||.|..+.++.+|++.+           ....||+||    ||+++|+++++.||+.
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            3799999999999999999999999999999999999998           556799999    8999999999999986


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCC-CCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPV-KLS  212 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~-~~~  212 (213)
                        ...+|||++|+..+......++++|+++||.||+ +.+
T Consensus        66 --~~~~~ii~lt~~~~~~~~~~~~~~Ga~~~l~Kp~~~~~  103 (223)
T 2hqr_A           66 --HSSIVVLVSSDNPTSEEEVHAFEQGADDYIAKPYRSIK  103 (223)
T ss_dssp             --CTTSEEEEEESSCCHHHHHHHHHHTCSEEEETTCSCTH
T ss_pred             --CCCCcEEEEECCCCHHHHHHHHHcCCCEEEECCCCCHH
Confidence              3389999999999999999999999999999999 764

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

Probab=99.75  E-value=1.8e-18  Score=136.04  Aligned_cols=103  Identities=14%  Similarity=0.156  Sum_probs=92.0

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      ...+||||||++..+..+..+|...||.+..+.++.+|+               ...||+||+|+.||+++|+ +++.++
T Consensus        11 ~~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al---------------~~~~dlvl~D~~mp~~~g~-l~~~~~   74 (196)
T 1qo0_D           11 RELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAF---------------DVPVDVVFTSIFQNRHHDE-IAALLA   74 (196)
T ss_dssp             GGCEEEEESCTTHHHHHHHHHHHHHTCEEEEECSCCSSC---------------SSCCSEEEEECCSSTHHHH-HHHHHH
T ss_pred             cCCeEEEEcCChhHHHHHHHHHHHcCCeEEEecCchhhC---------------CCCCCEEEEeCCCCccchH-HHHHHh
Confidence            357999999999999999999999999999888876644               1369999999999999998 899888


Q ss_pred             hcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          172 ESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      +.  .+.+|||++|+..+.+...++++.|+++||.||++.+
T Consensus        75 ~~--~~~~~ii~lt~~~~~~~~~~a~~~ga~~~l~KP~~~~  113 (196)
T 1qo0_D           75 AG--TPRTTLVALVEYESPAVLSQIIELECHGVITQPLDAH  113 (196)
T ss_dssp             HS--CTTCEEEEEECCCSHHHHHHHHHHTCSEEEESSCCGG
T ss_pred             cc--CCCCCEEEEEcCCChHHHHHHHHcCCCeeEecCcCHH
Confidence            75  2789999999999999999999999999999999865

>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=3.7e-17  Score=140.81  Aligned_cols=104  Identities=26%  Similarity=0.396  Sum_probs=93.1

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhc-CCE-EEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHH
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQIS-SCK-VTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKI  170 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~-g~~-v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~i  170 (213)
                      ..+||||||++..+..+..+|+.. ||. +..+.++.+|++.+.           ...||+|++|+.||+++|+++++.|
T Consensus         3 ~~rVLIVDD~~~~r~~L~~~L~~~~g~~vv~~a~~~~eAl~~l~-----------~~~pDlVllDi~mp~~dGlell~~l   71 (349)
T 1a2o_A            3 KIRVLSVDDSALMRQIMTEIINSHSDMEMVATAPDPLVARDLIK-----------KFNPDVLTLDVEMPRMDGLDFLEKL   71 (349)
T ss_dssp             CEEEEEECSCHHHHHHHHHHHHTSTTEEEEEEESSHHHHHHHHH-----------HHCCSEEEEECCCSSSCHHHHHHHH
T ss_pred             CCEEEEEECCHHHHHHHHHHHhcCCCcEEEEEeCCHHHHHHHHh-----------ccCCCEEEEECCCCCCCHHHHHHHH
Confidence            468999999999999999999986 888 569999999999984           3469999999999999999999999


Q ss_pred             HhcCCCCCCcEEEEecCCCH--HHHHHHHHcCCCeeeeCCCC
Q 048660          171 KESSVFREVPVVIMSSEDVL--TQIDSCLEEGAEEYIVKPVK  210 (213)
Q Consensus       171 r~~~~~~~~pII~lt~~~~~--~~~~~~~~~G~~~~L~KP~~  210 (213)
                      ++.  .+ +|||++|+..+.  +...++++.|+++||.||++
T Consensus        72 ~~~--~p-~pVIvlS~~~~~~~~~~~~al~~Ga~d~l~KP~~  110 (349)
T 1a2o_A           72 MRL--RP-MPVVMVSSLTGKGSEVTLRALELGAIDFVTKPQL  110 (349)
T ss_dssp             HHS--SC-CCEEEEECCTHHHHHHHHHHHHHTCCEEEECSSS
T ss_pred             Hhc--CC-CcEEEEECCCcccHHHHHHHHhCCceEEEECCCC
Confidence            986  34 999999998765  44788999999999999997

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

Probab=99.68  E-value=3.2e-17  Score=153.94  Aligned_cols=105  Identities=19%  Similarity=0.268  Sum_probs=96.7

Q ss_pred             EEEEEeCCH-HH-------HHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCC-ceeEEEEeCCCCC----C
Q 048660           95 HVLAVDDSY-VD-------RKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDAL-KVNLIITDYTMPG----M  161 (213)
Q Consensus        95 ~ILvVdD~~-~~-------~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~-~~dlil~D~~mp~----~  161 (213)
                      +||||||+. ..       ++.|+..|++.||.|..+.++++|+..+           ... .||+||+|++||+    +
T Consensus         2 ~ILiVdDd~~~~~~~~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~~-----------~~~~~~d~vilDi~lp~~~~~~   70 (755)
T 2vyc_A            2 KVLIVESEFLHQDTWVGNAVERLADALSQQNVTVIKSTSFDDGFAIL-----------SSNEAIDCLMFSYQMEHPDEHQ   70 (755)
T ss_dssp             EEEEECCTTSTTSHHHHHHHHHHHHHHHHTTCEEEEESSHHHHHHHH-----------TTTCCCSEEEEECCCCSHHHHH
T ss_pred             eEEEEeCCccccccccHHHHHHHHHHHHhCCCEEEEECCHHHHHHHH-----------hcCCCCcEEEEeCCCCcccccc
Confidence            799999999 88       9999999999999999999999999998           433 5999999999999    9


Q ss_pred             CHHHHHHHHHhcCCCCCCcEEEEecCCC-HHHHHHHHHcCCCeeeeCCCCCC
Q 048660          162 TGYELLKKIKESSVFREVPVVIMSSEDV-LTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       162 ~G~e~~~~ir~~~~~~~~pII~lt~~~~-~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      +|++++++||+.  ...+||+++|+... .++....+..|+|||+.||++..
T Consensus        71 ~G~~ll~~iR~~--~~~iPIi~lTa~~~~~~d~~~~l~~gaddyi~kpf~~~  120 (755)
T 2vyc_A           71 NVRQLIGKLHER--QQNVPVFLLGDREKALAAMDRDLLELVDEFAWILEDTA  120 (755)
T ss_dssp             HHHHHHHHHHHH--STTCCEEEEECHHHHHHTCSHHHHHHCSEEEETTTSCH
T ss_pred             cHHHHHHHHHHh--CCCCCEEEEecCCcchhhccHhHhhcCCceEeCCCCCH
Confidence            999999999987  46899999999877 77888899999999999999865

>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=99.25  E-value=8e-11  Score=103.81  Aligned_cols=107  Identities=19%  Similarity=0.261  Sum_probs=91.9

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      ...+|++|||+..++..+...|.. .+.+....++.+++..            ....||++++|+.||+|+|+++++.+|
T Consensus       151 ~~~~ilivdd~~~~~~~i~~~L~~-~~~~~~~~~~~~~~~~------------~~~~~dlil~D~~mp~~dG~~~~~~ir  217 (459)
T 1w25_A          151 LGGRVLIVDDNERQAQRVAAELGV-EHRPVIESDPEKAKIS------------AGGPVDLVIVNAAAKNFDGLRFTAALR  217 (459)
T ss_dssp             CSCEEEEECSCHHHHHHHHHHHTT-TSEEEEECCHHHHHHH------------HHSSCSEEEEETTCSSSCHHHHHHHHH
T ss_pred             CCCeEEEECCchhhHHHHHHHHhc-ccceeeccCHHHHhhh------------ccCCCCEEEEecCCCCCcHHHHHHHHH
Confidence            356899999999998888888865 4667778888887632            123689999999999999999999999


Q ss_pred             hcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCC
Q 048660          172 ESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKL  211 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~  211 (213)
                      +......+|++++|+.........+++.|+++|+.||++.
T Consensus       218 ~~~~~~~~pii~lt~~~~~~~~~~~l~~Ga~d~~~kp~~~  257 (459)
T 1w25_A          218 SEERTRQLPVLAMVDPDDRGRMVKALEIGVNDILSRPIDP  257 (459)
T ss_dssp             TSGGGTTCCEEEEECTTCHHHHHHHHHTTCCEEEESSCCH
T ss_pred             hCccccCCcEEEEcCCCchHHHHHHHhccccccccCCCCH
Confidence            8765678999999999999999999999999999999874

>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=99.17  E-value=7.6e-12  Score=100.17  Aligned_cols=78  Identities=23%  Similarity=0.419  Sum_probs=65.4

Q ss_pred             CEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhcCCCCCCcEEEEecCCCHHHHHHHH
Q 048660          118 CKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCL  197 (213)
Q Consensus       118 ~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~~~~~~~pII~lt~~~~~~~~~~~~  197 (213)
                      +.|..+.++.+|++.+.           ...||++|+|+.||+++|+++++.||+..  +..++++++.....+...+++
T Consensus         6 ~~v~~~~~~~~a~~~~~-----------~~~~dlvl~D~~~p~~~g~~~~~~l~~~~--~~~~i~vi~~~~~~~~~~~~~   72 (237)
T 3cwo_X            6 LIVDDATNGREAVEKYK-----------ELKPDIVTMDITMPEMNGIDAIKEIMKID--PNAKIIVCSAMGQQAMVIEAI   72 (237)
T ss_dssp             EEEECCCSSSTTHHHHH-----------HHCCSCEEEECCSTTSSHHHHHHHHHHHS--SSCCEEEECCSSTHHHHHHHH
T ss_pred             EEEEECCCHHHHHHHHH-----------hcCCCEEEEeCCCCCCCHHHHHHHHHHhC--CCCCEEEEECCCCHHHHHHHH
Confidence            45566889999999884           34689999999999999999999999863  445666666666688899999


Q ss_pred             HcCCCeeeeCC
Q 048660          198 EEGAEEYIVKP  208 (213)
Q Consensus       198 ~~G~~~~L~KP  208 (213)
                      +.|+++|+.||
T Consensus        73 ~~Ga~~~l~kp   83 (237)
T 3cwo_X           73 KAGAKDFIVNT   83 (237)
T ss_dssp             HTTCCEEEESH
T ss_pred             HCCHHheEeCC
Confidence            99999999998

>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=97.37  E-value=8.6e-05  Score=69.20  Aligned_cols=90  Identities=10%  Similarity=0.097  Sum_probs=68.4

Q ss_pred             HHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhcCCCCCCcEEEEe
Q 048660          106 RKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMS  185 (213)
Q Consensus       106 ~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~~~~~~~pII~lt  185 (213)
                      .+.|...|++.||.|..+.++++|+..++.+          ..+++|++|+.++   +.+++++||+.  ..++||++++
T Consensus        19 i~~L~~~Le~~g~~V~~a~s~~Da~~~i~~~----------~~i~avIld~d~~---~~~ll~~Ir~~--~~~iPVFl~~   83 (715)
T 3n75_A           19 IRELHRALERLNFQIVYPNDRDDLLKLIENN----------ARLCGVIFDWDKY---NLELCEEISKM--NENLPLYAFA   83 (715)
T ss_dssp             HHHHHHHHHHTTCEEECCSSHHHHHHHHHHC----------TTEEEEEEEHHHH---HHHHHHHHHHH--CTTCEEEEEC
T ss_pred             HHHHHHHHHHCCcEEEEeCCHHHHHHHHHhC----------CCceEEEEecccc---HHHHHHHHHHh--CCCCCEEEEe
Confidence            3456688889999999999999999999643          3589999999886   78999999987  6799999999


Q ss_pred             cCCCHHHHHHHHHcCCCeeeeCCCC
Q 048660          186 SEDVLTQIDSCLEEGAEEYIVKPVK  210 (213)
Q Consensus       186 ~~~~~~~~~~~~~~G~~~~L~KP~~  210 (213)
                      ............-.++++|+.+..+
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~  108 (715)
T 3n75_A           84 NTYSTLDVSLNDLRLQISFFEYALG  108 (715)
T ss_dssp             CTTCCCCGGGTTSCCEEEEECCCTT
T ss_pred             cCCcccccchhhhhccCeEEEeCCC
Confidence            8754332221123456777766543

>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=97.36  E-value=0.00026  Score=57.31  Aligned_cols=53  Identities=19%  Similarity=0.092  Sum_probs=45.1

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCC
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMT  162 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~  162 (213)
                      .+.+||||||+...+..+...|..+|+.+..+.+       .           ....||++++|+.+|...
T Consensus        10 ~~~~vlvv~d~~~~~~~l~~~L~~~g~~v~~~~~-------~-----------~~~~~~~ii~d~~~~~~~   62 (254)
T 2ayx_A           10 SGKRCWLAVRNASLCQFLETSLQRSGIVVTTYEG-------Q-----------EPTPEDVLITDEVVSKKW   62 (254)
T ss_dssp             TTEEEEEECCCHHHHHHHHHHHTTTTEEEEECSS-------C-----------CCCTTCEEEEESSCSCCC
T ss_pred             CCCEEEEEcCCHHHHHHHHHHHHHCCCEEEEecC-------C-----------CCCcCcEEEEcCCCcccc
Confidence            4679999999999999999999999999988764       1           224689999999998754

>3cwo_X Beta/alpha-barrel protein based on 1THF and 1TMY; XRAY, CHEY, HISF, half barrel, de novo protein; 3.10A {Thermotoga maritima} PDB: 2lle_A

Probab=96.59  E-value=0.0036  Score=49.03  Aligned_cols=69  Identities=9%  Similarity=0.173  Sum_probs=50.7

Q ss_pred             cCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeC-CCCCCCHHH--HHHHHHhcCCCCCCcEEEEecCCCHHHHHHHHHcC
Q 048660          124 ESGTRALQYLGLDGEQSNVGFDALKVNLIITDY-TMPGMTGYE--LLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEG  200 (213)
Q Consensus       124 ~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~-~mp~~~G~e--~~~~ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G  200 (213)
                      .+..+.++.+...          ...+++++++ .++.++|+.  .+++++.   ..++|+|++++....++..++++.|
T Consensus       130 ~~~~~~i~~~~~~----------~~~~vli~~~~~~g~~~g~~~~~i~~~~~---~~~~Pvia~~g~~~~~~~~~~~~~G  196 (237)
T 3cwo_X          130 ILLRDWVVEVEKR----------GAGEILLTSIDRDGTKSGYDTEMIRFVRP---LTTLPIIASGGAGKMEHFLEAFLAG  196 (237)
T ss_dssp             EEHHHHHHHHHHH----------TCSEEEEEETTTTTCCSCCCHHHHHHHGG---GCCSCEEEESCCCSHHHHHHHHHHT
T ss_pred             cCHHHHHHHHhhc----------CCCeEEEEecCCCCccccccHHHHHHHHH---hcCCCEEecCCCCCHHHHHHHHHcC
Confidence            3455666655422          2346889987 667777755  4555554   4589999999999999999999999


Q ss_pred             CCeee
Q 048660          201 AEEYI  205 (213)
Q Consensus       201 ~~~~L  205 (213)
                      +++++
T Consensus       197 ~~~~~  201 (237)
T 3cwo_X          197 ADAAL  201 (237)
T ss_dssp             CSEEE
T ss_pred             cHHHh
Confidence            99985

>2yxb_A Coenzyme B12-dependent mutase; alpha/beta, structural genomics, NPPSFA, national project on structural and functional analyses; 1.80A {Aeropyrum pernix}

Probab=96.15  E-value=0.055  Score=40.81  Aligned_cols=102  Identities=17%  Similarity=0.215  Sum_probs=73.7

Q ss_pred             CccEEEEE----eCCHHHHHHHHHHHhhcCCEEEEE---cCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCC-C-C
Q 048660           92 KELHVLAV----DDSYVDRKLIERLLQISSCKVTAV---ESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPG-M-T  162 (213)
Q Consensus        92 ~~~~ILvV----dD~~~~~~~l~~~L~~~g~~v~~a---~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~-~-~  162 (213)
                      .+.+|++.    |-+..-...+..+|+..||+|...   ...++.++.+           ....+|+|.+-..+.. + .
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            35688888    778888899999999999999853   4677777777           4457899999887754 2 2


Q ss_pred             HHHHHHHHHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeee
Q 048660          163 GYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIV  206 (213)
Q Consensus       163 G~e~~~~ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~  206 (213)
                      -.++++.||+.. .++++|+ +.+.....+...+.+.|+|.++.
T Consensus        86 ~~~~i~~L~~~g-~~~i~v~-vGG~~~~~~~~~l~~~G~d~v~~  127 (161)
T 2yxb_A           86 MKRLMAKLRELG-ADDIPVV-LGGTIPIPDLEPLRSLGIREIFL  127 (161)
T ss_dssp             HHHHHHHHHHTT-CTTSCEE-EEECCCHHHHHHHHHTTCCEEEC
T ss_pred             HHHHHHHHHhcC-CCCCEEE-EeCCCchhcHHHHHHCCCcEEEC
Confidence            445777888753 2456655 56666666666678999997553

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

Probab=95.68  E-value=0.15  Score=35.41  Aligned_cols=94  Identities=18%  Similarity=0.262  Sum_probs=72.2

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCC-CCCCHHHHHHHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTM-PGMTGYELLKKI  170 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~m-p~~~G~e~~~~i  170 (213)
                      ....||+|..|-.....++.++....|+++.....       .          .+..-|+|++...+ |.        .|
T Consensus        11 ~~~~iL~VtEd~~ls~QlKel~~~~eY~~~is~~~-------~----------~e~~AdlIfCEYlLLPe--------~i   65 (121)
T 3q7r_A           11 GPKHVLLVSEHWDLFFQTKELLNPEEYRCTIGQQY-------K----------QELSADLVVCEYSLLPR--------EI   65 (121)
T ss_dssp             CCEEEEEECSCHHHHHHHHHHSCTTTEEEEEESSC-------C----------CCTTEEEEEEEGGGSCT--------TC
T ss_pred             CCcEEEEEecCchhhHHHHHhcCCcceeEEecccc-------C----------CcccceeEEEeeecChH--------Hh
Confidence            35689999999999999999998888998876542       0          34467999999866 43        23


Q ss_pred             HhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCC
Q 048660          171 KESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKL  211 (213)
Q Consensus       171 r~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~  211 (213)
                      .........-+|++=..-+.+...+.+..|+. ||..|++.
T Consensus        66 fS~k~~~~~dliVLfD~F~EEa~v~vLd~Ga~-yLlrPIT~  105 (121)
T 3q7r_A           66 RSPKSLEGSFVLVLLDFFDEETSVDLLDRGFW-YLIRPITP  105 (121)
T ss_dssp             CCCTTCCSCEEEEEESSCCHHHHHHHHHTTCE-EEESCCCH
T ss_pred             cCCCCCCcccEEEEehhhchHHHHHHHhCCce-eEeccCcH
Confidence            43333455667777777788899999999998 99999874

>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=95.03  E-value=0.19  Score=36.62  Aligned_cols=100  Identities=10%  Similarity=0.058  Sum_probs=67.1

Q ss_pred             cEEEEE----eCCHHHHHHHHHHHhhcCCEEE---EEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCC-CC-HH
Q 048660           94 LHVLAV----DDSYVDRKLIERLLQISSCKVT---AVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPG-MT-GY  164 (213)
Q Consensus        94 ~~ILvV----dD~~~~~~~l~~~L~~~g~~v~---~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~-~~-G~  164 (213)
                      .+|++.    |-+..-...+..+|+..||+|.   .....++.++.+.           +..+|+|.+...+.. +. ..
T Consensus         4 ~~vvla~~~~d~HdiG~~~v~~~l~~~G~~Vi~lG~~~p~e~~v~~a~-----------~~~~d~v~lS~~~~~~~~~~~   72 (137)
T 1ccw_A            4 KTIVLGVIGSDCHAVGNKILDHAFTNAGFNVVNIGVLSPQELFIKAAI-----------ETKADAILVSSLYGQGEIDCK   72 (137)
T ss_dssp             CEEEEEEETTCCCCHHHHHHHHHHHHTTCEEEEEEEEECHHHHHHHHH-----------HHTCSEEEEEECSSTHHHHHT
T ss_pred             CEEEEEeCCCchhHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHH-----------hcCCCEEEEEecCcCcHHHHH
Confidence            355555    4566667788899999999887   4567888888773           347899999887754 22 33


Q ss_pred             HHHHHHHhcCCCCCCcEEEEecCC-----CH-HHHHHHHHcCCCeeee
Q 048660          165 ELLKKIKESSVFREVPVVIMSSED-----VL-TQIDSCLEEGAEEYIV  206 (213)
Q Consensus       165 e~~~~ir~~~~~~~~pII~lt~~~-----~~-~~~~~~~~~G~~~~L~  206 (213)
                      ++++.+++.. .++++|+ +.+..     +. .....+.+.|++.|..
T Consensus        73 ~~i~~l~~~g-~~~i~v~-vGG~~~~~~~~~~~~~~~~~~~G~d~~~~  118 (137)
T 1ccw_A           73 GLRQKCDEAG-LEGILLY-VGGNIVVGKQHWPDVEKRFKDMGYDRVYA  118 (137)
T ss_dssp             THHHHHHHTT-CTTCEEE-EEESCSSSSCCHHHHHHHHHHTTCSEECC
T ss_pred             HHHHHHHhcC-CCCCEEE-EECCCcCchHhhhhhHHHHHHCCCCEEEC
Confidence            4677888753 2356654 45532     11 1245688999988864

>1wv2_A Thiazole moeity, thiazole biosynthesis protein THIG; structural genomics, protein structure initiative, PSI; 2.90A {Pseudomonas aeruginosa} SCOP: c.1.31.1

Probab=95.01  E-value=0.2  Score=40.76  Aligned_cols=82  Identities=16%  Similarity=0.114  Sum_probs=58.8

Q ss_pred             HHHHHhhcCCEEE--EEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCC-----CCHHHHHHHHHhcCCCCCCcE
Q 048660          109 IERLLQISSCKVT--AVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPG-----MTGYELLKKIKESSVFREVPV  181 (213)
Q Consensus       109 l~~~L~~~g~~v~--~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~-----~~G~e~~~~ir~~~~~~~~pI  181 (213)
                      ..+.|.+.|+.|.  ++.|...|-....            ..+++| +.+..|.     ...+++++.|++.   .++||
T Consensus       127 aa~~L~~~Gf~Vlpy~~dd~~~akrl~~------------~G~~aV-mPlg~pIGsG~Gi~~~~lI~~I~e~---~~vPV  190 (265)
T 1wv2_A          127 AAEQLVKDGFDVMVYTSDDPIIARQLAE------------IGCIAV-MPLAGLIGSGLGICNPYNLRIILEE---AKVPV  190 (265)
T ss_dssp             HHHHHHTTTCEEEEEECSCHHHHHHHHH------------SCCSEE-EECSSSTTCCCCCSCHHHHHHHHHH---CSSCB
T ss_pred             HHHHHHHCCCEEEEEeCCCHHHHHHHHH------------hCCCEE-EeCCccCCCCCCcCCHHHHHHHHhc---CCCCE
Confidence            4445667899877  5666666555432            245655 6655542     2247889999984   57999


Q ss_pred             EEEecCCCHHHHHHHHHcCCCeeee
Q 048660          182 VIMSSEDVLTQIDSCLEEGAEEYIV  206 (213)
Q Consensus       182 I~lt~~~~~~~~~~~~~~G~~~~L~  206 (213)
                      |+=.+-..+++...+++.|+++++.
T Consensus       191 I~eGGI~TPsDAa~AmeLGAdgVlV  215 (265)
T 1wv2_A          191 LVDAGVGTASDAAIAMELGCEAVLM  215 (265)
T ss_dssp             EEESCCCSHHHHHHHHHHTCSEEEE
T ss_pred             EEeCCCCCHHHHHHHHHcCCCEEEE
Confidence            9877888999999999999999874

>1y80_A Predicted cobalamin binding protein; corrinoid, factor IIIM, methyl transferase, structural genomics, PSI, protein structure initiative; HET: B1M; 1.70A {Moorella thermoacetica}

Probab=94.20  E-value=0.27  Score=38.27  Aligned_cols=99  Identities=11%  Similarity=0.113  Sum_probs=67.4

Q ss_pred             ccEEEEE----eCCHHHHHHHHHHHhhcCCEEEEEc---CHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCC-CC-H
Q 048660           93 ELHVLAV----DDSYVDRKLIERLLQISSCKVTAVE---SGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPG-MT-G  163 (213)
Q Consensus        93 ~~~ILvV----dD~~~~~~~l~~~L~~~g~~v~~a~---~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~-~~-G  163 (213)
                      ..+||+.    |-+..-...+..+|+..||.|....   ..++.++.+           ....||+|.+-..+.. +. -
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            4578888    6677888899999999999998643   456666666           3347899999987754 33 3


Q ss_pred             HHHHHHHHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeee
Q 048660          164 YELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYI  205 (213)
Q Consensus       164 ~e~~~~ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L  205 (213)
                      .++++.+|+....+++||++--...+.+.   +.+.|+|.|-
T Consensus       157 ~~~i~~l~~~~~~~~~~v~vGG~~~~~~~---~~~~gad~~~  195 (210)
T 1y80_A          157 KSTIDALIAAGLRDRVKVIVGGAPLSQDF---ADEIGADGYA  195 (210)
T ss_dssp             HHHHHHHHHTTCGGGCEEEEESTTCCHHH---HHHHTCSEEC
T ss_pred             HHHHHHHHhcCCCCCCeEEEECCCCCHHH---HHHcCCeEEE
Confidence            45778888753334677665544444332   3567998764

>3ezx_A MMCP 1, monomethylamine corrinoid protein 1; N terminal all helical bundle C terminal rossmann fold, cobalt, metal-binding; HET: HCB; 2.56A {Methanosarcina barkeri}

Probab=93.93  E-value=0.28  Score=38.70  Aligned_cols=99  Identities=12%  Similarity=0.116  Sum_probs=68.2

Q ss_pred             ccEEEEE----eCCHHHHHHHHHHHhhcCCEEEEE---cCHHHHHHHhhhcCCCCCCCCCCCceeEEEE--eCCCCC-CC
Q 048660           93 ELHVLAV----DDSYVDRKLIERLLQISSCKVTAV---ESGTRALQYLGLDGEQSNVGFDALKVNLIIT--DYTMPG-MT  162 (213)
Q Consensus        93 ~~~ILvV----dD~~~~~~~l~~~L~~~g~~v~~a---~~g~eal~~l~~~~~~~~~~~~~~~~dlil~--D~~mp~-~~  162 (213)
                      ..+||+.    |-+..-..++..+|+..||+|...   ...++.++.+           .+.++|+|.+  ...|.. +.
T Consensus        92 ~~~vll~~v~gd~HdiG~~iv~~~l~~~G~~Vi~LG~~vp~e~iv~~~-----------~~~~~d~v~l~~S~l~~~~~~  160 (215)
T 3ezx_A           92 AGLAITFVAEGDIHDIGHRLVTTMLGANGFQIVDLGVDVLNENVVEEA-----------AKHKGEKVLLVGSALMTTSML  160 (215)
T ss_dssp             CCEEEEEECTTCCCCHHHHHHHHHHHHTSCEEEECCSSCCHHHHHHHH-----------HHTTTSCEEEEEECSSHHHHT
T ss_pred             CCeEEEEeCCCChhHHHHHHHHHHHHHCCCeEEEcCCCCCHHHHHHHH-----------HHcCCCEEEEEchhcccCcHH
Confidence            4578877    667788888999999999998754   3566777777           4457899999  877743 33


Q ss_pred             -HHHHHHHHHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeee
Q 048660          163 -GYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYI  205 (213)
Q Consensus       163 -G~e~~~~ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L  205 (213)
                       -.++++.+++.....++||++=.+..+.+   -+.+.|+|.|-
T Consensus       161 ~~~~~i~~l~~~~~~~~v~v~vGG~~~~~~---~a~~iGad~~~  201 (215)
T 3ezx_A          161 GQKDLMDRLNEEKLRDSVKCMFGGAPVSDK---WIEEIGADATA  201 (215)
T ss_dssp             HHHHHHHHHHHTTCGGGSEEEEESSSCCHH---HHHHHTCCBCC
T ss_pred             HHHHHHHHHHHcCCCCCCEEEEECCCCCHH---HHHHhCCeEEE
Confidence             45578888876422367766544444433   34567998874

>2i2x_B MTAC, methyltransferase 1; TIM barrel and helix bundle (MTAB), rossman fold and helix B (MTAC); HET: B13; 2.50A {Methanosarcina barkeri}

Probab=92.68  E-value=0.92  Score=36.57  Aligned_cols=98  Identities=13%  Similarity=0.075  Sum_probs=66.6

Q ss_pred             CccEEEEE----eCCHHHHHHHHHHHhhcCCEEEEE---cCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCC-CC-
Q 048660           92 KELHVLAV----DDSYVDRKLIERLLQISSCKVTAV---ESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPG-MT-  162 (213)
Q Consensus        92 ~~~~ILvV----dD~~~~~~~l~~~L~~~g~~v~~a---~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~-~~-  162 (213)
                      ...+||+.    |-+..-..++..+|+..||.|...   ...++.++.+           ....+|+|.+-..+.. +. 
T Consensus       122 ~~~~vlla~~~gd~HdiG~~iva~~L~~~G~~Vi~LG~~vp~e~l~~~~-----------~~~~~d~V~lS~l~~~~~~~  190 (258)
T 2i2x_B          122 TKGTVVCHVAEGDVHDIGKNIVTALLRANGYNVVDLGRDVPAEEVLAAV-----------QKEKPIMLTGTALMTTTMYA  190 (258)
T ss_dssp             CSCEEEEEECTTCCCCHHHHHHHHHHHHTTCEEEEEEEECCSHHHHHHH-----------HHHCCSEEEEECCCTTTTTH
T ss_pred             CCCeEEEEeCCCCccHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHH-----------HHcCCCEEEEEeeccCCHHH
Confidence            35678888    667788889999999999988532   4566666666           3347899999987754 44 


Q ss_pred             HHHHHHHHHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeee
Q 048660          163 GYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYI  205 (213)
Q Consensus       163 G~e~~~~ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L  205 (213)
                      -.++++.+|+.  ...+||++--.....+ .  +...|++.|-
T Consensus       191 ~~~~i~~l~~~--~~~~~v~vGG~~~~~~-~--~~~igad~~~  228 (258)
T 2i2x_B          191 FKEVNDMLLEN--GIKIPFACGGGAVNQD-F--VSQFALGVYG  228 (258)
T ss_dssp             HHHHHHHHHTT--TCCCCEEEESTTCCHH-H--HHTSTTEEEC
T ss_pred             HHHHHHHHHhc--CCCCcEEEECccCCHH-H--HHHcCCeEEE
Confidence            44578888876  3457766544444433 2  3367887664

>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=92.57  E-value=0.84  Score=36.23  Aligned_cols=84  Identities=10%  Similarity=0.117  Sum_probs=58.8

Q ss_pred             HHHHHHHhhcCCEEE-EEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCC------CCCCCHHHHHHHHHhcCCCCCC
Q 048660          107 KLIERLLQISSCKVT-AVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYT------MPGMTGYELLKKIKESSVFREV  179 (213)
Q Consensus       107 ~~l~~~L~~~g~~v~-~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~------mp~~~G~e~~~~ir~~~~~~~~  179 (213)
                      ..+.+.+++.|..+. .+.+.+++....+            ..+|+|.+...      .+...++++++++++.    ++
T Consensus       119 ~~~i~~~~~~g~~v~~~v~t~eea~~a~~------------~Gad~Ig~~~~g~t~~~~~~~~~~~li~~l~~~----~i  182 (229)
T 3q58_A          119 DSLLTRIRLHGLLAMADCSTVNEGISCHQ------------KGIEFIGTTLSGYTGPITPVEPDLAMVTQLSHA----GC  182 (229)
T ss_dssp             HHHHHHHHHTTCEEEEECSSHHHHHHHHH------------TTCSEEECTTTTSSSSCCCSSCCHHHHHHHHTT----TC
T ss_pred             HHHHHHHHHCCCEEEEecCCHHHHHHHHh------------CCCCEEEecCccCCCCCcCCCCCHHHHHHHHHc----CC
Confidence            334444456677654 5678888877653            24666753221      2234578899999863    78


Q ss_pred             cEEEEecCCCHHHHHHHHHcCCCeeee
Q 048660          180 PVVIMSSEDVLTQIDSCLEEGAEEYIV  206 (213)
Q Consensus       180 pII~lt~~~~~~~~~~~~~~G~~~~L~  206 (213)
                      |+|+-.+-.+.++..+++++|+++++.
T Consensus       183 pvIA~GGI~t~~d~~~~~~~GadgV~V  209 (229)
T 3q58_A          183 RVIAEGRYNTPALAANAIEHGAWAVTV  209 (229)
T ss_dssp             CEEEESSCCSHHHHHHHHHTTCSEEEE
T ss_pred             CEEEECCCCCHHHHHHHHHcCCCEEEE
Confidence            999999998999999999999999864

>2htm_A Thiazole biosynthesis protein THIG; thiamin biosynthesis, THIG, thermus thermophilus HB8, structural genomics, NPPSFA; 2.30A {Thermus thermophilus}

Probab=92.31  E-value=0.22  Score=40.55  Aligned_cols=81  Identities=17%  Similarity=0.130  Sum_probs=55.3

Q ss_pred             HHHhhcCCEEE--EEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCH-----HHHHHHHHhcCCCCC-CcEE
Q 048660          111 RLLQISSCKVT--AVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTG-----YELLKKIKESSVFRE-VPVV  182 (213)
Q Consensus       111 ~~L~~~g~~v~--~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G-----~e~~~~ir~~~~~~~-~pII  182 (213)
                      +.|.+.||.|.  +..|...|-....            ..++.| +.+..|-.+|     .++++.+++.  ..+ +|||
T Consensus       118 ~~L~k~Gf~Vlpy~~~D~~~ak~l~~------------~G~~aV-mPlg~pIGsG~Gi~~~~~L~~i~~~--~~~~vPVI  182 (268)
T 2htm_A          118 ERLIEEDFLVLPYMGPDLVLAKRLAA------------LGTATV-MPLAAPIGSGWGVRTRALLELFARE--KASLPPVV  182 (268)
T ss_dssp             HHHHHTTCEECCEECSCHHHHHHHHH------------HTCSCB-EEBSSSTTTCCCSTTHHHHHHHHHT--TTTSSCBE
T ss_pred             HHHHHCCCEEeeccCCCHHHHHHHHh------------cCCCEE-EecCccCcCCcccCCHHHHHHHHHh--cCCCCeEE
Confidence            34556799876  5566644443331            134555 7766554333     5668888873  245 8999


Q ss_pred             EEecCCCHHHHHHHHHcCCCeeee
Q 048660          183 IMSSEDVLTQIDSCLEEGAEEYIV  206 (213)
Q Consensus       183 ~lt~~~~~~~~~~~~~~G~~~~L~  206 (213)
                      +=.+-...++...+++.|+++.+.
T Consensus       183 ~~GGI~tpsDAa~AmeLGAdgVlV  206 (268)
T 2htm_A          183 VDAGLGLPSHAAEVMELGLDAVLV  206 (268)
T ss_dssp             EESCCCSHHHHHHHHHTTCCEEEE
T ss_pred             EeCCCCCHHHHHHHHHcCCCEEEE
Confidence            888888999999999999999864

>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=91.33  E-value=1.4  Score=34.92  Aligned_cols=84  Identities=14%  Similarity=0.117  Sum_probs=58.3

Q ss_pred             HHHHHHHhhcCCEEE-EEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCC------CCCCCHHHHHHHHHhcCCCCCC
Q 048660          107 KLIERLLQISSCKVT-AVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYT------MPGMTGYELLKKIKESSVFREV  179 (213)
Q Consensus       107 ~~l~~~L~~~g~~v~-~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~------mp~~~G~e~~~~ir~~~~~~~~  179 (213)
                      ..+...+++.|..+. .+.+.+++....+            ...|+|.+...      .....++++++++++.    ++
T Consensus       119 ~~~i~~~~~~g~~v~~~v~t~eea~~a~~------------~Gad~Ig~~~~g~t~~~~~~~~~~~~i~~l~~~----~i  182 (232)
T 3igs_A          119 EALLARIHHHHLLTMADCSSVDDGLACQR------------LGADIIGTTMSGYTTPDTPEEPDLPLVKALHDA----GC  182 (232)
T ss_dssp             HHHHHHHHHTTCEEEEECCSHHHHHHHHH------------TTCSEEECTTTTSSSSSCCSSCCHHHHHHHHHT----TC
T ss_pred             HHHHHHHHHCCCEEEEeCCCHHHHHHHHh------------CCCCEEEEcCccCCCCCCCCCCCHHHHHHHHhc----CC
Confidence            334444456677654 5677778776653            24566653211      1233568899999863    78


Q ss_pred             cEEEEecCCCHHHHHHHHHcCCCeeee
Q 048660          180 PVVIMSSEDVLTQIDSCLEEGAEEYIV  206 (213)
Q Consensus       180 pII~lt~~~~~~~~~~~~~~G~~~~L~  206 (213)
                      |+|+-.+-.+.++..+++++|+++++.
T Consensus       183 pvIA~GGI~t~~d~~~~~~~GadgV~V  209 (232)
T 3igs_A          183 RVIAEGRYNSPALAAEAIRYGAWAVTV  209 (232)
T ss_dssp             CEEEESCCCSHHHHHHHHHTTCSEEEE
T ss_pred             cEEEECCCCCHHHHHHHHHcCCCEEEE
Confidence            999999988999999999999999864

>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=89.69  E-value=2.7  Score=39.21  Aligned_cols=103  Identities=14%  Similarity=0.063  Sum_probs=71.8

Q ss_pred             CCccEEEEE----eCCHHHHHHHHHHHhhcCCEEEEE---cCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCC-C-
Q 048660           91 SKELHVLAV----DDSYVDRKLIERLLQISSCKVTAV---ESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPG-M-  161 (213)
Q Consensus        91 ~~~~~ILvV----dD~~~~~~~l~~~L~~~g~~v~~a---~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~-~-  161 (213)
                      ..+.+|++.    |.+..-...+..+|+..||+|...   ...++.++.+           .+..+|+|.+...|.. + 
T Consensus       602 g~r~kVvlatvg~D~HdiG~~iVa~~l~~~GfeVi~lG~~v~~eeiv~aA-----------~e~~adiVglSsl~~~~~~  670 (762)
T 2xij_A          602 GRRPRLLVAKMGQDGHDRGAKVIATGFADLGFDVDIGPLFQTPREVAQQA-----------VDADVHAVGVSTLAAGHKT  670 (762)
T ss_dssp             SSCCEEEEECCSSCCCCHHHHHHHHHHHHTTCEEEECCTTCCHHHHHHHH-----------HHTTCSEEEEEECSSCHHH
T ss_pred             CCCCEEEEEecCcchhhHHHHHHHHHHHhCCeEEeeCCCCCCHHHHHHHH-----------HHcCCCEEEEeeecHHHHH
Confidence            456788887    556666777888999999999864   3567777777           3446899988877654 2 


Q ss_pred             CHHHHHHHHHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeee
Q 048660          162 TGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIV  206 (213)
Q Consensus       162 ~G~e~~~~ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~  206 (213)
                      ...++++.|++.+ ..+++ |++.+.....+...+.+.|+++|..
T Consensus       671 ~~~~vi~~Lr~~G-~~dv~-VivGG~~P~~d~~~l~~~GaD~~f~  713 (762)
T 2xij_A          671 LVPELIKELNSLG-RPDIL-VMCGGVIPPQDYEFLFEVGVSNVFG  713 (762)
T ss_dssp             HHHHHHHHHHHTT-CTTSE-EEEEESCCGGGHHHHHHHTCCEEEC
T ss_pred             HHHHHHHHHHhcC-CCCCE-EEEeCCCCcccHHHHHhCCCCEEeC
Confidence            3566788888864 23444 4455534444566788999999876

>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=89.28  E-value=2.1  Score=39.83  Aligned_cols=103  Identities=13%  Similarity=0.094  Sum_probs=72.4

Q ss_pred             CCccEEEEE----eCCHHHHHHHHHHHhhcCCEEEEE---cCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCC-C-
Q 048660           91 SKELHVLAV----DDSYVDRKLIERLLQISSCKVTAV---ESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPG-M-  161 (213)
Q Consensus        91 ~~~~~ILvV----dD~~~~~~~l~~~L~~~g~~v~~a---~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~-~-  161 (213)
                      ..+.+|++.    |.+..-...+..+|+..||+|...   ...++.++.+           .+..+|+|.+...|.. + 
T Consensus       594 g~r~kVvlatvg~D~HdiG~~iVa~~l~~~GfeVi~lG~~v~~eeiv~aA-----------~e~~adiVglSsl~~~~~~  662 (727)
T 1req_A          594 GRRPRILLAKMGQDGHDRGQKVIATAYADLGFDVDVGPLFQTPEETARQA-----------VEADVHVVGVSSLAGGHLT  662 (727)
T ss_dssp             SSCCEEEEECBTTCCCCHHHHHHHHHHHHHTCEEEECCTTBCHHHHHHHH-----------HHTTCSEEEEEECSSCHHH
T ss_pred             CCCCEEEEEeCCcchhHHHHHHHHHHHHhCCeEEEeCCCCCCHHHHHHHH-----------HHcCCCEEEEeeecHhHHH
Confidence            456788887    556667777888999999999764   3567777777           3447899998877654 2 


Q ss_pred             CHHHHHHHHHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeee
Q 048660          162 TGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIV  206 (213)
Q Consensus       162 ~G~e~~~~ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~  206 (213)
                      ...++++.|++.+ ..+++ |++.+..-..+...+.+.|+++|..
T Consensus       663 ~~~~vi~~L~~~G-~~~i~-VivGG~~p~~d~~~l~~~GaD~~f~  705 (727)
T 1req_A          663 LVPALRKELDKLG-RPDIL-ITVGGVIPEQDFDELRKDGAVEIYT  705 (727)
T ss_dssp             HHHHHHHHHHHTT-CTTSE-EEEEESCCGGGHHHHHHTTEEEEEC
T ss_pred             HHHHHHHHHHhcC-CCCCE-EEEcCCCccccHHHHHhCCCCEEEc
Confidence            3566888888864 23444 4455544455567788999999875

>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=88.58  E-value=4  Score=33.16  Aligned_cols=98  Identities=11%  Similarity=-0.003  Sum_probs=61.9

Q ss_pred             EEEEEeC--CHHHHHHHHHHHhhcCCEEE-EEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCC---CCCCCHHHHHH
Q 048660           95 HVLAVDD--SYVDRKLIERLLQISSCKVT-AVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYT---MPGMTGYELLK  168 (213)
Q Consensus        95 ~ILvVdD--~~~~~~~l~~~L~~~g~~v~-~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~---mp~~~G~e~~~  168 (213)
                      .|++...  +......+....+++|..+. .+.+.+++...+..            ..|+|-+.-.   ... -+++.+.
T Consensus       138 ~VlLi~a~l~~~~l~~l~~~a~~lGl~~lvev~t~ee~~~A~~~------------Gad~IGv~~r~l~~~~-~dl~~~~  204 (272)
T 3qja_A          138 MLLLIVAALEQSVLVSMLDRTESLGMTALVEVHTEQEADRALKA------------GAKVIGVNARDLMTLD-VDRDCFA  204 (272)
T ss_dssp             EEEEEGGGSCHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHHH------------TCSEEEEESBCTTTCC-BCTTHHH
T ss_pred             EEEEecccCCHHHHHHHHHHHHHCCCcEEEEcCCHHHHHHHHHC------------CCCEEEECCCcccccc-cCHHHHH
Confidence            4665432  22223334445566788654 56788776655531            3566655421   111 2356677


Q ss_pred             HHHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeee
Q 048660          169 KIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIV  206 (213)
Q Consensus       169 ~ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~  206 (213)
                      .+.+.- ..++|+|+-++-.+.++..++.++|+++++.
T Consensus       205 ~l~~~v-~~~~pvVaegGI~t~edv~~l~~~GadgvlV  241 (272)
T 3qja_A          205 RIAPGL-PSSVIRIAESGVRGTADLLAYAGAGADAVLV  241 (272)
T ss_dssp             HHGGGS-CTTSEEEEESCCCSHHHHHHHHHTTCSEEEE
T ss_pred             HHHHhC-cccCEEEEECCCCCHHHHHHHHHcCCCEEEE
Confidence            777642 2378999999988899999999999999875

>3ffs_A Inosine-5-monophosphate dehydrogenase; beta-alpha barrel, TIM fold, oxidoreductase; 3.19A {Cryptosporidium parvum}

Probab=88.20  E-value=10  Score=32.57  Aligned_cols=101  Identities=13%  Similarity=0.119  Sum_probs=66.1

Q ss_pred             ccEEEEEe----CCHHHHHHHHHHHhhcCCEEE--EEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCC---------
Q 048660           93 ELHVLAVD----DSYVDRKLIERLLQISSCKVT--AVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYT---------  157 (213)
Q Consensus        93 ~~~ILvVd----D~~~~~~~l~~~L~~~g~~v~--~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~---------  157 (213)
                      +..++++|    +.....+.++.+-+..+..|.  .+.+.++|....+            ...|.|.+...         
T Consensus       156 GvdvIvldta~G~~~~~~e~I~~ik~~~~i~Vi~g~V~t~e~A~~a~~------------aGAD~I~vG~g~Gs~~~tr~  223 (400)
T 3ffs_A          156 GVDVIVLDSAHGHSLNIIRTLKEIKSKMNIDVIVGNVVTEEATKELIE------------NGADGIKVGIGPGSICTTRI  223 (400)
T ss_dssp             TCSEEEECCSCCSBHHHHHHHHHHHTTCCCEEEEEEECSHHHHHHHHH------------TTCSEEEECC---------C
T ss_pred             CCCEEEEeCCCCCcccHHHHHHHHHhcCCCeEEEeecCCHHHHHHHHH------------cCCCEEEEeCCCCcCccccc
Confidence            35677764    233445566665555576655  5788888887763            24577776321         


Q ss_pred             --CCCCCHHHHHHHHHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeee
Q 048660          158 --MPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYI  205 (213)
Q Consensus       158 --mp~~~G~e~~~~ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L  205 (213)
                        -.+...++++..+.+.....++|||+-.+-.+..+..+++.+|++...
T Consensus       224 ~~g~g~p~~~al~~v~~~~~~~~IPVIA~GGI~~~~di~kalalGAd~V~  273 (400)
T 3ffs_A          224 VAGVGVPQITAIEKCSSVASKFGIPIIADGGIRYSGDIGKALAVGASSVM  273 (400)
T ss_dssp             CSCBCCCHHHHHHHHHHHHTTTTCCEEEESCCCSHHHHHHHHTTTCSEEE
T ss_pred             ccccchhHHHHHHHHHHHHHhcCCCEEecCCCCCHHHHHHHHHcCCCEEE
Confidence              011245667777765322347999998888889999999999999864

>1xrs_B D-lysine 5,6-aminomutase beta subunit; TIM barrel, rossmann domain, PLP, cobalamin, 5'-deoxyad radical, adenosylcobalamin; HET: B12 PLP 5AD; 2.80A {Clostridium sticklandii} SCOP: c.23.6.1 d.230.4.1

Probab=87.23  E-value=2.3  Score=34.49  Aligned_cols=100  Identities=10%  Similarity=0.123  Sum_probs=65.2

Q ss_pred             ccEEEEE----eCCHHHHHHHHHH--------Hhhc-CCEEEEE---cCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeC
Q 048660           93 ELHVLAV----DDSYVDRKLIERL--------LQIS-SCKVTAV---ESGTRALQYLGLDGEQSNVGFDALKVNLIITDY  156 (213)
Q Consensus        93 ~~~ILvV----dD~~~~~~~l~~~--------L~~~-g~~v~~a---~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~  156 (213)
                      ..+|++.    |-+..-...+..+        |+.. ||+|+-.   ...++.++.+           .+..+|+|.+..
T Consensus       120 ~~~Vvlatv~gD~HdiG~~iv~~~k~~~~~~~L~~~~G~eVi~LG~~vp~e~iv~aa-----------~e~~~d~VglS~  188 (262)
T 1xrs_B          120 KIVVVGASTGTDAHTVGIDAIMNMKGYAGHYGLERYEMIDAYNLGSQVANEDFIKKA-----------VELEADVLLVSQ  188 (262)
T ss_dssp             CEEEEEEEBTTCCCCHHHHHHHSTTCBTTBCCGGGCTTEEEEECCSSBCHHHHHHHH-----------HHTTCSEEEEEC
T ss_pred             CCEEEEEeCCCCCchHHHHHHhhhhcccchHHHHhcCCcEEEECCCCCCHHHHHHHH-----------HHcCCCEEEEEe
Confidence            4577665    5566666667777        9999 9998753   4567777776           445799999999


Q ss_pred             CCCC----CCH-HHHHHHHHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeee
Q 048660          157 TMPG----MTG-YELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIV  206 (213)
Q Consensus       157 ~mp~----~~G-~e~~~~ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~  206 (213)
                      .+..    +.. .++++.+++.....+++|+ +.+....  ...+.+.|++.|..
T Consensus       189 l~t~~~~~~~~~~~~i~~L~~~g~~~~i~vi-vGG~~~~--~~~a~~iGad~~~~  240 (262)
T 1xrs_B          189 TVTQKNVHIQNMTHLIELLEAEGLRDRFVLL-CGGPRIN--NEIAKELGYDAGFG  240 (262)
T ss_dssp             CCCTTSHHHHHHHHHHHHHHHTTCGGGSEEE-EECTTCC--HHHHHTTTCSEEEC
T ss_pred             ecCCccchHHHHHHHHHHHHhcCCCCCCEEE-EECCcCC--HHHHHHcCCeEEEC
Confidence            8875    222 3467777765323346654 4444332  33467889988754

>1r8j_A KAIA; circadian clock protein; 2.03A {Synechococcus elongatus pcc 7942} SCOP: a.186.1.1 c.23.1.5 PDB: 1m2e_A 1m2f_A

Probab=85.19  E-value=13  Score=30.29  Aligned_cols=83  Identities=13%  Similarity=0.132  Sum_probs=67.0

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      ..+.|-+.--++.....+..+|...-|.+..+.++.+.++.++.         ...++|++++...  +..-..+...++
T Consensus         8 ~~LsI~~~~~s~~l~~~~~~~L~~dRY~l~~~~s~~~f~~~le~---------~~e~iDcLvle~~--~~~~~~~~~~L~   76 (289)
T 1r8j_A            8 SQIAICIWVESTAILQDCQRALSADRYQLQVCESGEMLLEYAQT---------HRDQIDCLILVAA--NPSFRAVVQQLC   76 (289)
T ss_dssp             CCEEEEEECCCHHHHHHHHHHTCSTTEEEEEECSHHHHHHHHHH---------STTSCSEEEEETT--STTHHHHHHHHH
T ss_pred             cceeEEEEeCCHHHHHHHHHhcccCceEEEEcCcHHHHHHHHHh---------ccccCCEEEEEeC--CCccHHHHHHHH
Confidence            45788888889999999999999888999999999999999865         4457999998752  334667888888


Q ss_pred             hcCCCCCCcEEEEecC
Q 048660          172 ESSVFREVPVVIMSSE  187 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~  187 (213)
                      +.  .--+|+|++...
T Consensus        77 ~~--g~lLP~vil~~~   90 (289)
T 1r8j_A           77 FE--GVVVPAIVVGDR   90 (289)
T ss_dssp             HT--TCCCCEEEESCC
T ss_pred             Hc--CccccEEEeccC
Confidence            76  457899988664

>3fkq_A NTRC-like two-domain protein; RER070207001320, structural GE joint center for structural genomics, JCSG, protein structu initiative, PSI-2; HET: ATP 2PE; 2.10A {Eubacterium rectale}

Probab=83.28  E-value=2.3  Score=35.87  Aligned_cols=59  Identities=8%  Similarity=0.166  Sum_probs=47.7

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhh---cCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCC
Q 048660           91 SKELHVLAVDDSYVDRKLIERLLQI---SSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPG  160 (213)
Q Consensus        91 ~~~~~ILvVdD~~~~~~~l~~~L~~---~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~  160 (213)
                      ...+++.|+|.|....+.|..+|.+   ..+.+..+++.+.+.+.++           +..+|++|+|-.+..
T Consensus        19 ~~~i~l~i~d~d~~Y~~~l~~y~~~~~~~~~~v~~ft~~e~~~~~~~-----------~~~~dilli~e~~~~   80 (373)
T 3fkq_A           19 GMKIKVALLDKDKEYLDRLTGVFNTKYADKLEVYSFTDEKNAIESVK-----------EYRIDVLIAEEDFNI   80 (373)
T ss_dssp             -CCEEEEEECSCHHHHHHHHHHHHHHTTTTEEEEEESCHHHHHHHHH-----------HHTCSEEEEETTCCC
T ss_pred             CceEEEEEEeCCHHHHHHHHHHHhhccCCceEEEEECCHHHHHHHHh-----------cCCCCEEEEcchhhh
Confidence            3468999999999999999999864   3689999999999999884           346788888876643

>3rht_A (gatase1)-like protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, unknown function; HET: MSE; 1.83A {Planctomyces limnophilus}

Probab=82.23  E-value=0.58  Score=38.00  Aligned_cols=50  Identities=18%  Similarity=0.153  Sum_probs=35.6

Q ss_pred             ccEEEEEeCC--HHHHHHHHHHHhhcCCEEEEEcCHHH--HHHHhhhcCCCCCCCCCCCceeEEEEe
Q 048660           93 ELHVLAVDDS--YVDRKLIERLLQISSCKVTAVESGTR--ALQYLGLDGEQSNVGFDALKVNLIITD  155 (213)
Q Consensus        93 ~~~ILvVdD~--~~~~~~l~~~L~~~g~~v~~a~~g~e--al~~l~~~~~~~~~~~~~~~~dlil~D  155 (213)
                      ..+||+|+++  +.-...+...|+..|+.|.......-  -.+.+             ..||+||++
T Consensus         4 m~~vLiV~g~~~~~~a~~l~~aL~~~g~~V~~i~~~~~~~~~~~L-------------~~yDvIIl~   57 (259)
T 3rht_A            4 MTRVLYCGDTSLETAAGYLAGLMTSWQWEFDYIPSHVGLDVGELL-------------AKQDLVILS   57 (259)
T ss_dssp             --CEEEEESSCTTTTHHHHHHHHHHTTCCCEEECTTSCBCSSHHH-------------HTCSEEEEE
T ss_pred             CceEEEECCCCchhHHHHHHHHHHhCCceEEEecccccccChhHH-------------hcCCEEEEc
Confidence            3589999988  66778899999999999988765321  01222             268999887

>3f4w_A Putative hexulose 6 phosphate synthase; humps, malonate, lyase; 1.65A {Salmonella typhimurium} SCOP: c.1.2.0

Probab=81.73  E-value=6.7  Score=29.92  Aligned_cols=98  Identities=10%  Similarity=0.053  Sum_probs=56.6

Q ss_pred             EEEEEeCCH--HHHHHHHHHHhhcCCEEEEE----cCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCC----CCCHH
Q 048660           95 HVLAVDDSY--VDRKLIERLLQISSCKVTAV----ESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMP----GMTGY  164 (213)
Q Consensus        95 ~ILvVdD~~--~~~~~l~~~L~~~g~~v~~a----~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp----~~~G~  164 (213)
                      ..+++-+..  .....+...+++.|..+...    .+..+.++.+..           ...|.|-++....    ...++
T Consensus        79 d~v~v~~~~~~~~~~~~~~~~~~~g~~~~v~~~~~~t~~~~~~~~~~-----------~g~d~i~v~~g~~g~~~~~~~~  147 (211)
T 3f4w_A           79 DYVTVLGVTDVLTIQSCIRAAKEAGKQVVVDMICVDDLPARVRLLEE-----------AGADMLAVHTGTDQQAAGRKPI  147 (211)
T ss_dssp             SEEEEETTSCHHHHHHHHHHHHHHTCEEEEECTTCSSHHHHHHHHHH-----------HTCCEEEEECCHHHHHTTCCSH
T ss_pred             CEEEEeCCCChhHHHHHHHHHHHcCCeEEEEecCCCCHHHHHHHHHH-----------cCCCEEEEcCCCcccccCCCCH
Confidence            344444433  33345556666778776642    333333333321           1356666652100    11357


Q ss_pred             HHHHHHHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeee
Q 048660          165 ELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIV  206 (213)
Q Consensus       165 e~~~~ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~  206 (213)
                      +.++++++.  .+++|+++-.+- +.+...++.++|++.++.
T Consensus       148 ~~i~~l~~~--~~~~~i~~~gGI-~~~~~~~~~~~Gad~vvv  186 (211)
T 3f4w_A          148 DDLITMLKV--RRKARIAVAGGI-SSQTVKDYALLGPDVVIV  186 (211)
T ss_dssp             HHHHHHHHH--CSSCEEEEESSC-CTTTHHHHHTTCCSEEEE
T ss_pred             HHHHHHHHH--cCCCcEEEECCC-CHHHHHHHHHcCCCEEEE
Confidence            888888875  346888765555 478888999999998754

>3ovp_A Ribulose-phosphate 3-epimerase; iron binding, isomerase; HET: XPE; 1.70A {Homo sapiens} SCOP: c.1.2.0 PDB: 3ovq_A* 3ovr_A* 3qc3_A

Probab=81.73  E-value=4.3  Score=32.05  Aligned_cols=56  Identities=14%  Similarity=0.332  Sum_probs=40.4

Q ss_pred             ceeEEEEeCCCCCCCH-------HHHHHHHHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeee
Q 048660          148 KVNLIITDYTMPGMTG-------YELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIV  206 (213)
Q Consensus       148 ~~dlil~D~~mp~~~G-------~e~~~~ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~  206 (213)
                      ..|.|++....|+.+|       ++-++++|+.  ..+.+ |.+.+.-+.+....+.++|+|.++.
T Consensus       134 ~~D~Vl~msv~pGf~Gq~f~~~~l~ki~~lr~~--~~~~~-I~VdGGI~~~t~~~~~~aGAd~~Vv  196 (228)
T 3ovp_A          134 QIDMALVMTVEPGFGGQKFMEDMMPKVHWLRTQ--FPSLD-IEVDGGVGPDTVHKCAEAGANMIVS  196 (228)
T ss_dssp             GCSEEEEESSCTTTCSCCCCGGGHHHHHHHHHH--CTTCE-EEEESSCSTTTHHHHHHHTCCEEEE
T ss_pred             cCCeEEEeeecCCCCCcccCHHHHHHHHHHHHh--cCCCC-EEEeCCcCHHHHHHHHHcCCCEEEE
Confidence            4688887777787655       4557777765  34555 4566666788899999999998764

>3o63_A Probable thiamine-phosphate pyrophosphorylase; thiamin biosynthesis, TIM barrel, transferase; 2.35A {Mycobacterium tuberculosis}

Probab=81.56  E-value=9.1  Score=30.46  Aligned_cols=71  Identities=13%  Similarity=0.165  Sum_probs=50.0

Q ss_pred             EEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCC-------CCHHHHHHHHHhcCCCCCCcEEEEecCCCHHHHH
Q 048660          122 AVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPG-------MTGYELLKKIKESSVFREVPVVIMSSEDVLTQID  194 (213)
Q Consensus       122 ~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~-------~~G~e~~~~ir~~~~~~~~pII~lt~~~~~~~~~  194 (213)
                      .+.+.+|+.+...            ...|.|.+.-..|.       .-|++.++++++.. ..++|++++.+- +.+...
T Consensus       141 S~ht~~Ea~~A~~------------~GaDyI~vgpvf~T~tK~~~~~~gl~~l~~~~~~~-~~~iPvvAiGGI-~~~ni~  206 (243)
T 3o63_A          141 STHDPDQVAAAAA------------GDADYFCVGPCWPTPTKPGRAAPGLGLVRVAAELG-GDDKPWFAIGGI-NAQRLP  206 (243)
T ss_dssp             EECSHHHHHHHHH------------SSCSEEEECCSSCCCC-----CCCHHHHHHHHTC----CCCEEEESSC-CTTTHH
T ss_pred             eCCCHHHHHHHhh------------CCCCEEEEcCccCCCCCCCcchhhHHHHHHHHHhc-cCCCCEEEecCC-CHHHHH
Confidence            5688888777652            24788887543332       23788888888641 147999999887 577888


Q ss_pred             HHHHcCCCeeee
Q 048660          195 SCLEEGAEEYIV  206 (213)
Q Consensus       195 ~~~~~G~~~~L~  206 (213)
                      .++++|++++..
T Consensus       207 ~~~~aGa~gvav  218 (243)
T 3o63_A          207 AVLDAGARRIVV  218 (243)
T ss_dssp             HHHHTTCCCEEE
T ss_pred             HHHHcCCCEEEE
Confidence            999999998753

>1yad_A Regulatory protein TENI; TIM barrel, transcription; 2.10A {Bacillus subtilis} PDB: 3qh2_A*

Probab=81.50  E-value=16  Score=28.02  Aligned_cols=73  Identities=18%  Similarity=0.245  Sum_probs=49.8

Q ss_pred             CCEE-EEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCC-------CCHHHHHHHHHhcCCCCCCcEEEEecCC
Q 048660          117 SCKV-TAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPG-------MTGYELLKKIKESSVFREVPVVIMSSED  188 (213)
Q Consensus       117 g~~v-~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~-------~~G~e~~~~ir~~~~~~~~pII~lt~~~  188 (213)
                      |..+ ..+.+..++.+...            ...|.|+++-..+.       ..|++.++.+++.   .++|+++..+- 
T Consensus       110 ~~~ig~sv~t~~~~~~a~~------------~gaD~i~~~~~f~~~~~~g~~~~~~~~l~~~~~~---~~~pvia~GGI-  173 (221)
T 1yad_A          110 HLHIGRSVHSLEEAVQAEK------------EDADYVLFGHVFETDCKKGLEGRGVSLLSDIKQR---ISIPVIAIGGM-  173 (221)
T ss_dssp             TCEEEEEECSHHHHHHHHH------------TTCSEEEEECCC----------CHHHHHHHHHHH---CCSCEEEESSC-
T ss_pred             CCEEEEEcCCHHHHHHHHh------------CCCCEEEECCccccCCCCCCCCCCHHHHHHHHHh---CCCCEEEECCC-
Confidence            5443 35567777766542            24688888654322       2367888888764   27898877777 


Q ss_pred             CHHHHHHHHHcCCCeee
Q 048660          189 VLTQIDSCLEEGAEEYI  205 (213)
Q Consensus       189 ~~~~~~~~~~~G~~~~L  205 (213)
                      +.+...+++++|++++.
T Consensus       174 ~~~nv~~~~~~Ga~gv~  190 (221)
T 1yad_A          174 TPDRLRDVKQAGADGIA  190 (221)
T ss_dssp             CGGGHHHHHHTTCSEEE
T ss_pred             CHHHHHHHHHcCCCEEE
Confidence            78889999999998864

>3fwz_A Inner membrane protein YBAL; TRKA-N domain, E.coli, structural genomics, PSI-2, Pro structure initiative; HET: MSE AMP; 1.79A {Escherichia coli k-12}

Probab=81.18  E-value=12  Score=26.40  Aligned_cols=94  Identities=7%  Similarity=0.111  Sum_probs=55.7

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcC-HHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCKVTAVES-GTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~-g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      +..|.++|.++...+.++    ..|+.+..... -.+.++.+           .-...|++++-+.-.. .-..++..+|
T Consensus        30 g~~v~vid~~~~~~~~~~----~~g~~~i~gd~~~~~~l~~a-----------~i~~ad~vi~~~~~~~-~n~~~~~~a~   93 (140)
T 3fwz_A           30 DIPLVVIETSRTRVDELR----ERGVRAVLGNAANEEIMQLA-----------HLECAKWLILTIPNGY-EAGEIVASAR   93 (140)
T ss_dssp             TCCEEEEESCHHHHHHHH----HTTCEEEESCTTSHHHHHHT-----------TGGGCSEEEECCSCHH-HHHHHHHHHH
T ss_pred             CCCEEEEECCHHHHHHHH----HcCCCEEECCCCCHHHHHhc-----------CcccCCEEEEECCChH-HHHHHHHHHH
Confidence            457888888876554433    35776654432 23344443           2235788887553221 2334566677


Q ss_pred             hcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeee
Q 048660          172 ESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIV  206 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~  206 (213)
                      +.  .+..+||+.+.+  .+....+.+.|++..+.
T Consensus        94 ~~--~~~~~iiar~~~--~~~~~~l~~~G~d~vi~  124 (140)
T 3fwz_A           94 AK--NPDIEIIARAHY--DDEVAYITERGANQVVM  124 (140)
T ss_dssp             HH--CSSSEEEEEESS--HHHHHHHHHTTCSEEEE
T ss_pred             HH--CCCCeEEEEECC--HHHHHHHHHCCCCEEEC
Confidence            65  456777766643  55667778899987653

>3kp1_A D-ornithine aminomutase E component; 5 aminomutase (OAM), metal binding protein; HET: PLP B12 5AD; 2.01A {Clostridium sticklandii} PDB: 3kow_A* 3koy_A* 3koz_A* 3kp0_A* 3kox_A*

Probab=80.61  E-value=4.3  Score=37.27  Aligned_cols=100  Identities=10%  Similarity=0.105  Sum_probs=64.8

Q ss_pred             ccEEEEE---eCCHHHHH-HH----HHHHhhcCCEEEEE---cCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCC-
Q 048660           93 ELHVLAV---DDSYVDRK-LI----ERLLQISSCKVTAV---ESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPG-  160 (213)
Q Consensus        93 ~~~ILvV---dD~~~~~~-~l----~~~L~~~g~~v~~a---~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~-  160 (213)
                      +.+||+.   .|-..+.. .+    ..+|+..||+|+-.   ...++.++.+           .+..+|+|.+...|.. 
T Consensus       602 kGKVVIATVgGD~HDIGKklVaNIVa~~LE~aGFEVIDLGvdVPpEeIVeAA-----------~EedADVVGLSsLLTt~  670 (763)
T 3kp1_A          602 PLKIVAATVGEDEHSVGLREVIDIKHGGIEKYGVEVHYLGTSVPVEKLVDAA-----------IELKADAILASTIISHD  670 (763)
T ss_dssp             CCEEEEEEBTTCCCCHHHHHTTSTTTTCGGGGTCEEEECCSSBCHHHHHHHH-----------HHTTCSEEEEECCCCGG
T ss_pred             CCEEEEEeCCCChhhhhhHHHHHHHHHHHHhCCCEEEECCCCCCHHHHHHHH-----------HHcCCCEEEEeccccCc
Confidence            5678887   24333333 22    57899999999754   4678888877           4457999999988876 


Q ss_pred             ---CCH-HHHHHHHHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeee
Q 048660          161 ---MTG-YELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIV  206 (213)
Q Consensus       161 ---~~G-~e~~~~ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~  206 (213)
                         +.. -++++.+++.+....++|+ +.+..-..+  -+.+.|++.|..
T Consensus       671 dihL~~MkevIelLrE~GlrDkIkVI-VGGa~~tqd--~AkeIGADa~f~  717 (763)
T 3kp1_A          671 DIHYKNMKRIHELAVEKGIRDKIMIG-CGGTQVTPE--VAVKQGVDAGFG  717 (763)
T ss_dssp             GHHHHHHHHHHHHHHHTTCTTTSEEE-EECTTCCHH--HHHTTTCSEEEC
T ss_pred             hhhHHHHHHHHHHHHhcCCCCCCEEE-EECCCCCHH--HHHHcCCcEEEC
Confidence               333 3477888876533345655 444433332  345899988764

>2oo3_A Protein involved in catabolism of external DNA; structural genomics, unknown function, PSI-2, protein structure initiative; 2.00A {Legionella pneumophila subsp} SCOP: c.66.1.59

Probab=80.28  E-value=4.9  Score=32.94  Aligned_cols=86  Identities=14%  Similarity=0.051  Sum_probs=55.0

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCC-CCHHHHHHHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPG-MTGYELLKKI  170 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~-~~G~e~~~~i  170 (213)
                      ..-++..||-++.....|+..++..+-..+...|+.+++..+..         ...++|+||+|=--.. .+.-.+++.|
T Consensus       112 ~~d~~vfvE~~~~a~~~L~~Nl~~~~~~~V~~~D~~~~L~~l~~---------~~~~fdLVfiDPPYe~k~~~~~vl~~L  182 (283)
T 2oo3_A          112 SQDRLYLCELHPTEYNFLLKLPHFNKKVYVNHTDGVSKLNALLP---------PPEKRGLIFIDPSYERKEEYKEIPYAI  182 (283)
T ss_dssp             TTSEEEEECCSHHHHHHHTTSCCTTSCEEEECSCHHHHHHHHCS---------CTTSCEEEEECCCCCSTTHHHHHHHHH
T ss_pred             CCCeEEEEeCCHHHHHHHHHHhCcCCcEEEEeCcHHHHHHHhcC---------CCCCccEEEECCCCCCCcHHHHHHHHH
Confidence            44789999999999999999998654444566888888887632         2236999999952221 2344455555


Q ss_pred             HhcCC-CCCCcEEEEec
Q 048660          171 KESSV-FREVPVVIMSS  186 (213)
Q Consensus       171 r~~~~-~~~~pII~lt~  186 (213)
                      .+... ++.--+++.-.
T Consensus       183 ~~~~~r~~~Gi~v~WYP  199 (283)
T 2oo3_A          183 KNAYSKFSTGLYCVWYP  199 (283)
T ss_dssp             HHHHHHCTTSEEEEEEE
T ss_pred             HHhCccCCCeEEEEEEe
Confidence            54211 33444444444

---

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	213
d1zesa1	121	c.23.1.1 (A:3-123) PhoB receiver domain {Escherich	3e-20
d1jbea_	128	c.23.1.1 (A:) CheY protein {Escherichia coli [TaxI	4e-20
d1i3ca_	144	c.23.1.1 (A:) Response regulator for cyanobacteria	1e-19
d1k68a_	140	c.23.1.1 (A:) Response regulator for cyanobacteria	5e-19
d1peya_	119	c.23.1.1 (A:) Sporulation response regulator Spo0F	2e-18
d1dz3a_	123	c.23.1.1 (A:) Sporulation response regulator Spo0A	4e-18
d1k66a_	149	c.23.1.1 (A:) Response regulator for cyanobacteria	5e-18
d2b4aa1	118	c.23.1.1 (A:2-119) Hypothetical protein BH3024 {Ba	5e-18
d1a2oa1	140	c.23.1.1 (A:1-140) Methylesterase CheB, N-terminal	6e-18
d1dcfa_	134	c.23.1.2 (A:) Receiver domain of the ethylene rece	8e-18
d1u0sy_	118	c.23.1.1 (Y:) CheY protein {Thermotoga maritima [T	9e-18
d1mb3a_	123	c.23.1.1 (A:) Cell division response regulator Div	1e-17
d1a04a2	138	c.23.1.1 (A:5-142) Nitrate/nitrite response regula	2e-17
d2r25b1	128	c.23.1.1 (B:1087-1214) Response regulator Sin1 {Ba	2e-17
d1p6qa_	129	c.23.1.1 (A:) CheY protein {Sinorhizobium meliloti	1e-16
d2ayxa1	133	c.23.1.1 (A:817-949) Sensor kinase protein RcsC, C	3e-15
d1krwa_	123	c.23.1.1 (A:) NTRC receiver domain {Salmonella typ	4e-15
d2a9pa1	117	c.23.1.1 (A:2-118) DNA-binding response regulator	2e-14
d1qkka_	140	c.23.1.1 (A:) Transcriptional regulatory protein D	4e-14
d1dbwa_	123	c.23.1.1 (A:) Transcriptional regulatory protein F	1e-13
d1xhfa1	121	c.23.1.1 (A:2-122) Aerobic respiration control pro	3e-13
d1s8na_	190	c.23.1.1 (A:) Probable two-component system transc	1e-12
d1qo0d_	189	c.23.1.3 (D:) Positive regulator of the amidase op	1e-12
d1yioa2	128	c.23.1.1 (A:3-130) Response regulatory protein Sty	1e-12
d1zgza1	120	c.23.1.1 (A:2-121) TorCAD operon transcriptional r	2e-12
d1ys7a2	121	c.23.1.1 (A:7-127) Transcriptional regulatory prot	4e-12
d2pl1a1	119	c.23.1.1 (A:1-119) PhoP receiver domain {Escherich	7e-12
d1mvoa_	121	c.23.1.1 (A:) PhoP receiver domain {Bacillus subti	8e-12
d1zh2a1	119	c.23.1.1 (A:2-120) Transcriptional regulatory prot	1e-11
d1w25a1	139	c.23.1.1 (A:2-140) Response regulator PleD, receiv	2e-11
d1ny5a1	137	c.23.1.1 (A:1-137) Transcriptional activator sigm5	2e-11
d1w25a2	153	c.23.1.1 (A:141-293) Response regulator PleD, rece	2e-11
d1kgsa2	122	c.23.1.1 (A:2-123) PhoB receiver domain {Thermotog	6e-11
d1p2fa2	120	c.23.1.1 (A:1-120) Response regulator DrrB {Thermo	8e-10

>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 = 80.3 bits (198), Expect = 3e-20
 Identities = 29/118 (24%), Positives = 58/118 (49%), Gaps = 11/118 (9%)

Query: 96  VLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITD 155
           +L V+D    R+++  +L+ +  +    E    A+  L           +    +LI+ D
Sbjct: 3   ILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQL-----------NEPWPDLILLD 51

Query: 156 YTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD 213
           + +PG +G + +K +K  S+ R++PVV++++          LE GA++YI KP    +
Sbjct: 52  WMLPGGSGIQFIKHLKRESMTRDIPVVMLTARGEEEDRVRGLETGADDYITKPFSPKE 109

>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 = 79.4 bits (195), Expect = 1e-19
 Identities = 30/121 (24%), Positives = 61/121 (50%), Gaps = 6/121 (4%)

Query: 95  HVLAVDDSYVDRKLIERLLQIS--SCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLI 152
            +L V+DS  D +L++ +L+ S    ++  +  G  A+ +L    +Q     ++ + NLI
Sbjct: 5   VILLVEDSKADSRLVQEVLKTSTIDHELIILRDGLAAMAFL----QQQGEYENSPRPNLI 60

Query: 153 ITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS 212
           + D  +P   G E+L +IK++   + +PVV++++      + +  E     Y+ K   L 
Sbjct: 61  LLDLNLPKKDGREVLAEIKQNPDLKRIPVVVLTTSHNEDDVIASYELHVNCYLTKSRNLK 120

Query: 213 D 213
           D
Sbjct: 121 D 121

>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 = 77.4 bits (190), Expect = 5e-19
 Identities = 36/120 (30%), Positives = 57/120 (47%), Gaps = 6/120 (5%)

Query: 96  VLAVDDSYVDRKLIERLLQIS--SCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLII 153
           +  V+D+  D +LI+  L  S    +V  V  G  A+ YL  +GE +N    A + +LI+
Sbjct: 5   IFLVEDNKADIRLIQEALANSTVPHEVVTVRDGMEAMAYLRQEGEYAN----ASRPDLIL 60

Query: 154 TDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD 213
            D  +P   G E+L +IK     + +PVV++S+      I    +     YI K   LS 
Sbjct: 61  LDLNLPKKDGREVLAEIKSDPTLKRIPVVVLSTSINEDDIFHSYDLHVNCYITKSANLSQ 120

>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 = 75.4 bits (185), Expect = 2e-18
 Identities = 29/118 (24%), Positives = 51/118 (43%), Gaps = 13/118 (11%)

Query: 96  VLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITD 155
           +L VDD    R L+  +      +     +G +AL  +              + +L++ D
Sbjct: 4   ILIVDDQSGIRILLNEVFNKEGYQTFQAANGLQALDIV-----------TKERPDLVLLD 52

Query: 156 YTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD 213
             +PGM G E+LK++K       + V+IM++   L  I    E GA  +  KP  + +
Sbjct: 53  MKIPGMDGIEILKRMKVID--ENIRVIIMTAYGELDMIQESKELGALTHFAKPFDIDE 108

>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 = 74.8 bits (184), Expect = 4e-18
 Identities = 21/122 (17%), Positives = 50/122 (40%), Gaps = 14/122 (11%)

Query: 94  LHVLAVDDSYVDRKLIERLLQISSCK--VTAVESGTRALQYLGLDGEQSNVGFDALKVNL 151
           + V   DD+     L++  +        +    +G   LQ L           +  + ++
Sbjct: 2   IKVCIADDNRELVSLLDEYISSQPDMEVIGTAYNGQDCLQML-----------EEKRPDI 50

Query: 152 IITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKL 211
           ++ D  MP + G  +L++I+      +  V+++++          +E GA  +I+KP  +
Sbjct: 51  LLLDIIMPHLDGLAVLERIRAGF-EHQPNVIMLTAFGQEDVTKKAVELGASYFILKPFDM 109

Query: 212 SD 213
            +
Sbjct: 110 EN 111

>d1k66a_ c.23.1.1 (A:) Response regulator for cyanobacterial phytochrome {Calothrix sp. pcc 7601, RcpB [TaxId: 1188]} Length = 149

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulator for cyanobacterial phytochrome
species: Calothrix sp. pcc 7601, RcpB [TaxId: 1188]

 Score = 75.2 bits (184), Expect = 5e-18
 Identities = 38/121 (31%), Positives = 62/121 (51%), Gaps = 3/121 (2%)

Query: 95  HVLAVDDSYVDRKLIERLLQIS--SCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLI 152
            +L V+DS  D    +RLLQ       +    +G +AL +L   G   N    A +  +I
Sbjct: 8   PLLVVEDSDEDFSTFQRLLQREGVVNPIYRCITGDQALDFLYQTGSYCNP-DIAPRPAVI 66

Query: 153 ITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS 212
           + D  +PG  G E+L++IK+  V +++PVVIM++      I+ C       YIVKP+++ 
Sbjct: 67  LLDLNLPGTDGREVLQEIKQDEVLKKIPVVIMTTSSNPKDIEICYSYSISSYIVKPLEID 126

Query: 213 D 213
            
Sbjct: 127 R 127

>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 = 74.5 bits (183), Expect = 5e-18
 Identities = 24/122 (19%), Positives = 49/122 (40%), Gaps = 15/122 (12%)

Query: 92  KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNL 151
           +   V  V+D      LI+  L     +VT   SG+   Q+                 +L
Sbjct: 1   QPFRVTLVEDEPSHATLIQYHLNQLGAEVTVHPSGSAFFQHR----------SQLSTCDL 50

Query: 152 IITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKL 211
           +I    +  ++ + LL  +KE +  ++  V+I+++     ++    E     Y+ KP  +
Sbjct: 51  LIVSDQLVDLSIFSLLDIVKEQT--KQPSVLILTTGR--HELIESSEHNL-SYLQKPFAI 105

Query: 212 SD 213
           S+
Sbjct: 106 SE 107

>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 = 74.6 bits (183), Expect = 6e-18
 Identities = 25/120 (20%), Positives = 48/120 (40%), Gaps = 14/120 (11%)

Query: 92  KELHVLAVDDSYVDRKLIERLLQISS--CKVTAVESGTRALQYLGLDGEQSNVGFDALKV 149
            ++ VL+VDDS + R+++  ++   S    V        A   +                
Sbjct: 2   SKIRVLSVDDSALMRQIMTEIINSHSDMEMVATAPDPLVARDLI-----------KKFNP 50

Query: 150 NLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPV 209
           +++  D  MP M G + L+K+        V V  ++ +     +   LE GA +++ KP 
Sbjct: 51  DVLTLDVEMPRMDGLDFLEKLMRLRPMPVVMVSSLTGKGSEVTLR-ALELGAIDFVTKPQ 109

>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 = 74.3 bits (182), Expect = 8e-18
 Identities = 29/123 (23%), Positives = 54/123 (43%), Gaps = 15/123 (12%)

Query: 94  LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLII 153
           L VL +D++ V R + + LL    C+VT V S    L+              + +  ++ 
Sbjct: 8   LKVLVMDENGVSRMVTKGLLVHLGCEVTTVSSNEECLRV------------VSHEHKVVF 55

Query: 154 TDYTMPGMTGYELLKKIKE---SSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVK 210
            D  MPG+  Y++  +I E       +   +V +S     +  + C+  G +  ++KPV 
Sbjct: 56  MDVCMPGVENYQIALRIHEKFTKQRHQRPLLVALSGNTDKSTKEKCMSFGLDGVLLKPVS 115

Query: 211 LSD 213
           L +
Sbjct: 116 LDN 118

>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 = 73.8 bits (181), Expect = 9e-18
 Identities = 26/119 (21%), Positives = 57/119 (47%), Gaps = 12/119 (10%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
            VL VDD+   R +++ ++  +  +V    +          +G ++   +  LK +++  
Sbjct: 3   RVLIVDDAAFMRMMLKDIITKAGYEVAGEAT----------NGREAVEKYKELKPDIVTM 52

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD 213
           D TMP M G + +K+I +        +++ S+      +   ++ GA+++IVKP + S 
Sbjct: 53  DITMPEMNGIDAIKEIMKI--DPNAKIIVCSAMGQQAMVIEAIKAGAKDFIVKPFQPSR 109

>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 = 73.5 bits (180), Expect = 1e-17
 Identities = 31/118 (26%), Positives = 52/118 (44%), Gaps = 11/118 (9%)

Query: 96  VLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITD 155
           VL V+D+ ++ KL   LL+    +      G  AL                 K +LI+ D
Sbjct: 4   VLIVEDNELNMKLFHDLLEAQGYETLQTREGLSALSIA-----------RENKPDLILMD 52

Query: 156 YTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD 213
             +P ++G E+ K +KE      +PVV +++  +    +   E G E YI KP+ +  
Sbjct: 53  IQLPEISGLEVTKWLKEDDDLAHIPVVAVTAFAMKGDEERIREGGCEAYISKPISVVH 110

>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 = 73.4 bits (180), Expect = 2e-17
 Identities = 29/122 (23%), Positives = 59/122 (48%), Gaps = 15/122 (12%)

Query: 94  LHVLAVDDSYVDRKLIERLLQISS--CKVTAVESGTRALQYLGLDGEQSNVGFDALKVNL 151
             +L +DD  + R  +++L+ ++     V    +G + ++             ++L  +L
Sbjct: 3   ATILLIDDHPMLRTGVKQLISMAPDITVVGEASNGEQGIELA-----------ESLDPDL 51

Query: 152 IITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKL 211
           I+ D  MPGM G E L K++E S      +V+ S  +    + + L+ GA+ Y++K ++ 
Sbjct: 52  ILLDLNMPGMNGLETLDKLREKS--LSGRIVVFSVSNHEEDVVTALKRGADGYLLKDMEP 109

Query: 212 SD 213
            D
Sbjct: 110 ED 111

>d2r25b1 c.23.1.1 (B:1087-1214) Response regulator Sin1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 128

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulator Sin1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

 Score = 73.1 bits (179), Expect = 2e-17
 Identities = 27/119 (22%), Positives = 53/119 (44%), Gaps = 8/119 (6%)

Query: 96  VLAVDDSYVDRKLIERLLQISSCK-VTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
           +L V+D++V++++I+R+L +   + +     G  A   +     +          N+I  
Sbjct: 4   ILVVEDNHVNQEVIKRMLNLEGIENIELACDGQEAFDKVKELTSKGE------NYNMIFM 57

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD 213
           D  MP + G    K I+        P+V +++    + I  CLE G   ++ KP+K   
Sbjct: 58  DVQMPKVDGLLSTKMIRRDL-GYTSPIVALTAFADDSNIKECLESGMNGFLSKPIKRPK 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 = 70.8 bits (173), Expect = 1e-16
 Identities = 27/124 (21%), Positives = 55/124 (44%), Gaps = 12/124 (9%)

Query: 91  SKELHVLAVDDSYVDRKLIERLLQISSCK-VTAVESGTRALQYLGLDGEQSNVGFDALKV 149
           ++++ VL VDD    R L+   LQ    K +TA   G + ++ +                
Sbjct: 4   AEKIKVLIVDDQVTSRLLLGDALQQLGFKQITAAGDGEQGMKIM-----------AQNPH 52

Query: 150 NLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPV 209
           +L+I+D+ MP M G  LL+ ++ +   ++   +I++++     +      GA   + KP 
Sbjct: 53  HLVISDFNMPKMDGLGLLQAVRANPATKKAAFIILTAQGDRALVQKAAALGANNVLAKPF 112

Query: 210 KLSD 213
            +  
Sbjct: 113 TIEK 116

>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 = 67.4 bits (164), Expect = 3e-15
 Identities = 27/122 (22%), Positives = 55/122 (45%), Gaps = 13/122 (10%)

Query: 92  KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNL 151
            ++ +L VDD  ++R+L+   L     +                DG  +        +++
Sbjct: 7   DDMMILVVDDHPINRRLLADQLGSLGYQCKTAN-----------DGVDALNVLSKNHIDI 55

Query: 152 IITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKL 211
           +++D  MP M GY L ++I++      +PV+ +++  +  +   CLE G +  + KPV L
Sbjct: 56  VLSDVNMPNMDGYRLTQRIRQL--GLTLPVIGVTANALAEEKQRCLESGMDSCLSKPVTL 113

Query: 212 SD 213
             
Sbjct: 114 DV 115

>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 = 67.1 bits (163), Expect = 4e-15
 Identities = 35/119 (29%), Positives = 57/119 (47%), Gaps = 13/119 (10%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
            V  VDD    R ++ER L  +    T  E+G   L  L            +   +++++
Sbjct: 5   IVWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLAAL-----------ASKTPDVLLS 53

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD 213
           D  MPGM G  LLK+IK+      +PV+IM++   L    S  ++GA +Y+ KP  + +
Sbjct: 54  DIRMPGMDGLALLKQIKQR--HPMLPVIIMTAHSDLDAAVSAYQQGAFDYLPKPFDIDE 110

>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 = 65.0 bits (158), Expect = 2e-14
 Identities = 30/118 (25%), Positives = 57/118 (48%), Gaps = 14/118 (11%)

Query: 96  VLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITD 155
           +L VDD      +I+  +     +V    +G  AL+             +A + ++II D
Sbjct: 3   ILIVDDEKPISDIIKFNMTKEGYEVVTAFNGREALEQF-----------EAEQPDIIILD 51

Query: 156 YTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD 213
             +P + G E+ K I+++S    VP++++S++D        LE GA++Y+ KP    +
Sbjct: 52  LMLPEIDGLEVAKTIRKTS---SVPILMLSAKDSEFDKVIGLELGADDYVTKPFSNRE 106

>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 = 64.7 bits (157), Expect = 4e-14
 Identities = 25/115 (21%), Positives = 53/115 (46%), Gaps = 13/115 (11%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
            V  +DD    RK +++ L+++   V++                ++  G  A    ++I+
Sbjct: 2   SVFLIDDDRDLRKAMQQTLELAGFTVSSFA-----------SATEALAGLSADFAGIVIS 50

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPV 209
           D  MPGM G  L +KI       ++P+++++    +      +++GA ++I KP 
Sbjct: 51  DIRMPGMDGLALFRKILAL--DPDLPMILVTGHGDIPMAVQAIQDGAYDFIAKPF 103

>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 = 63.1 bits (153), Expect = 1e-13
 Identities = 25/122 (20%), Positives = 54/122 (44%), Gaps = 13/122 (10%)

Query: 92  KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNL 151
           ++  V  VDD    RK +  +L ++   V   +S    L +              ++  +
Sbjct: 2   QDYTVHIVDDEEPVRKSLAFMLTMNGFAVKMHQSAEAFLAFA-----------PDVRNGV 50

Query: 152 IITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKL 211
           ++TD  MP M+G ELL+ + +      +P ++++    +      ++ GA ++I KP + 
Sbjct: 51  LVTDLRMPDMSGVELLRNLGDLK--INIPSIVITGHGDVPMAVEAMKAGAVDFIEKPFED 108

Query: 212 SD 213
           + 
Sbjct: 109 TV 110

>d1xhfa1 c.23.1.1 (A:2-122) Aerobic respiration control protein ArcA, N-terminal domain {Escherichia coli [TaxId: 562]} Length = 121

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Aerobic respiration control protein ArcA, N-terminal domain
species: Escherichia coli [TaxId: 562]

 Score = 61.6 bits (149), Expect = 3e-13
 Identities = 29/119 (24%), Positives = 50/119 (42%), Gaps = 14/119 (11%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
           H+L V+D  V R  ++ + +     V     G    Q L               +NL+I 
Sbjct: 4   HILIVEDELVTRNTLKSIFEAEGYDVFEATDGAEMHQIL-----------SEYDINLVIM 52

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD 213
           D  +PG  G  L ++++E +    V ++ ++  D        LE GA++YI KP    +
Sbjct: 53  DINLPGKNGLLLARELREQA---NVALMFLTGRDNEVDKILGLEIGADDYITKPFNPRE 108

>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 = 61.8 bits (149), Expect = 1e-12
 Identities = 26/120 (21%), Positives = 50/120 (41%), Gaps = 15/120 (12%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAV-ESGTRALQYLGLDGEQSNVGFDALKVNLII 153
            VL  +D  + R  +  +L+    ++      G  A++             +  K +L+I
Sbjct: 5   RVLIAEDEALIRMDLAEMLREEGYEIVGEAGDGQEAVEL-----------AELHKPDLVI 53

Query: 154 TDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD 213
            D  MP   G +   +I      R  P+V++++      ++   + GA  Y+VKP  +SD
Sbjct: 54  MDVKMPRRDGIDAASEIASK---RIAPIVVLTAFSQRDLVERARDAGAMAYLVKPFSISD 110

>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 = 61.6 bits (148), Expect = 1e-12
 Identities = 14/117 (11%), Positives = 28/117 (23%), Gaps = 18/117 (15%)

Query: 92  KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNL 151
           +EL VL ++        +   L    C V        A                   V++
Sbjct: 10  RELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAFDVP---------------VDV 54

Query: 152 IITDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKP 208
           + T                  +       +V +   +    +   +E      I +P
Sbjct: 55  VFTSIFQNRHHDEIAALLAAGTP---RTTLVALVEYESPAVLSQIIELECHGVITQP 108

>d1yioa2 c.23.1.1 (A:3-130) Response regulatory protein StyR, N-terminal domain {Pseudomonas fluorescens [TaxId: 294]} Length = 128

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulatory protein StyR, N-terminal domain
species: Pseudomonas fluorescens [TaxId: 294]

 Score = 60.1 bits (145), Expect = 1e-12
 Identities = 25/119 (21%), Positives = 52/119 (43%), Gaps = 13/119 (10%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
            V  VDD    R+ +  LL+ +  +V   +  +  L++               +   ++ 
Sbjct: 4   TVFVVDDDMSVREGLRNLLRSAGFEVETFDCASTFLEHR-----------RPEQHGCLVL 52

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD 213
           D  MPGM+G EL +++   S    +P+V +++   +      ++ GA E++ KP +   
Sbjct: 53  DMRMPGMSGIELQEQLTAIS--DGIPIVFITAHGDIPMTVRAMKAGAIEFLPKPFEEQA 109

>d1zgza1 c.23.1.1 (A:2-121) TorCAD operon transcriptional regulator TorD, N-terminal domain {Escherichia coli [TaxId: 562]} Length = 120

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: TorCAD operon transcriptional regulator TorD, N-terminal domain
species: Escherichia coli [TaxId: 562]

 Score = 59.6 bits (144), Expect = 2e-12
 Identities = 24/120 (20%), Positives = 50/120 (41%), Gaps = 14/120 (11%)

Query: 94  LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLII 153
            H++ V+D  V +  ++         V+   SG    + +               V+LI+
Sbjct: 2   HHIVIVEDEPVTQARLQSYFTQEGYTVSVTASGAGLREIM-----------QNQSVDLIL 50

Query: 154 TDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD 213
            D  +P   G  L + ++E      V +++++           LE GA++Y+ KP++L +
Sbjct: 51  LDINLPDENGLMLTRALRE---RSTVGIILVTGRSDRIDRIVGLEMGADDYVTKPLELRE 107

>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 = 58.9 bits (142), Expect = 4e-12
 Identities = 31/119 (26%), Positives = 55/119 (46%), Gaps = 13/119 (10%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
            VL VDD       +ER L++S  +V     G  AL+                + + I+ 
Sbjct: 3   RVLVVDDDSDVLASLERGLRLSGFEVATAVDGAEALRSA-----------TENRPDAIVL 51

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD 213
           D  MP + G  ++  ++      +VPV ++S+   +    + LE GA++Y+VKP  L++
Sbjct: 52  DINMPVLDGVSVVTALRAMD--NDVPVCVLSARSSVDDRVAGLEAGADDYLVKPFVLAE 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 = 58.2 bits (140), Expect = 7e-12
 Identities = 23/120 (19%), Positives = 54/120 (45%), Gaps = 13/120 (10%)

Query: 94  LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLII 153
           + VL V+D+ + R  ++  +Q +  +V   E    A  YL           +    ++ I
Sbjct: 1   MRVLVVEDNALLRHHLKVQIQDAGHQVDDAEDAKEADYYL-----------NEHIPDIAI 49

Query: 154 TDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD 213
            D  +P   G  L+++ + +     +P++++++ +        L  GA++Y+ KP  + +
Sbjct: 50  VDLGLPDEDGLSLIRRWRSND--VSLPILVLTARESWQDKVEVLSAGADDYVTKPFHIEE 107

>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 = 58.2 bits (140), Expect = 8e-12
 Identities = 28/119 (23%), Positives = 54/119 (45%), Gaps = 13/119 (10%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
            +L VDD      L++  L+ S   V     G  AL+             +  K +LI+ 
Sbjct: 4   KILVVDDEESIVTLLQYNLERSGYDVITASDGEEALKK-----------AETEKPDLIVL 52

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD 213
           D  +P + G E+ K++++       P+++++++D        LE GA++Y+ KP    +
Sbjct: 53  DVMLPKLDGIEVCKQLRQQK--LMFPILMLTAKDEEFDKVLGLELGADDYMTKPFSPRE 109

>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 = 57.4 bits (138), Expect = 1e-11
 Identities = 28/118 (23%), Positives = 54/118 (45%), Gaps = 14/118 (11%)

Query: 96  VLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITD 155
           VL V+D    R+ +   L+    +V   E+  R L                 K +LII D
Sbjct: 3   VLIVEDEQAIRRFLRTALEGDGMRVFEAETLQRGLLEA-----------ATRKPDLIILD 51

Query: 156 YTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD 213
             +P   G E ++ +++   +  VPV+++S+    +   + L+ GA++Y+ KP  + +
Sbjct: 52  LGLPDGDGIEFIRDLRQ---WSAVPVIVLSARSEESDKIAALDAGADDYLSKPFGIGE 106

>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 = 57.6 bits (138), Expect = 2e-11
 Identities = 31/119 (26%), Positives = 54/119 (45%), Gaps = 11/119 (9%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
            +L VDD   + +L+E  L     +V+    G  AL                   ++I+ 
Sbjct: 3   RILVVDDIEANVRLLEAKLTAEYYEVSTAMDGPTALAM-----------AARDLPDIILL 51

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD 213
           D  MPGM G+ + +K+K+    R +PVV++++ D        LE GA +++ KP+    
Sbjct: 52  DVMMPGMDGFTVCRKLKDDPTTRHIPVVLITALDGRGDRIQGLESGASDFLTKPIDDVM 110

>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 = 57.0 bits (137), Expect = 2e-11
 Identities = 32/120 (26%), Positives = 57/120 (47%), Gaps = 13/120 (10%)

Query: 94  LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLII 153
           ++VL ++D  V R L+E  L +   KV + E G  A + L                N+++
Sbjct: 1   MNVLVIEDDKVFRGLLEEYLSMKGIKVESAERGKEAYKLLSEK-----------HFNVVL 49

Query: 154 TDYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD 213
            D  +P + G E+LK IKE S   E  V++++    +      ++ GA +++ KP  L +
Sbjct: 50  LDLLLPDVNGLEILKWIKERS--PETEVIVITGHGTIKTAVEAMKMGAYDFLTKPCMLEE 107

>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 = 57.4 bits (138), Expect = 2e-11
 Identities = 22/119 (18%), Positives = 43/119 (36%), Gaps = 13/119 (10%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
            VL VDD+    + +   L +    V  +ES     +                 V+L+I 
Sbjct: 15  RVLIVDDNERQAQRVAAELGVEHRPV--IESDPEKAKIS-----------AGGPVDLVIV 61

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD 213
           +       G      ++     R++PV+ M   D   ++   LE G  + + +P+   +
Sbjct: 62  NAAAKNFDGLRFTAALRSEERTRQLPVLAMVDPDDRGRMVKALEIGVNDILSRPIDPQE 120

>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 = 55.5 bits (133), Expect = 6e-11
 Identities = 27/118 (22%), Positives = 48/118 (40%), Gaps = 13/118 (11%)

Query: 96  VLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITD 155
           VL V+D      LI   L+     V     G   +                   +++I D
Sbjct: 4   VLVVEDERDLADLITEALKKEMFTVDVCYDGEEGMYMA-----------LNEPFDVVILD 52

Query: 156 YTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD 213
             +P   G+E+LK ++ES      PV+++++   +      L  GA++Y+ KP  L +
Sbjct: 53  IMLPVHDGWEILKSMRESG--VNTPVLMLTALSDVEYRVKGLNMGADDYLPKPFDLRE 108

>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 = 52.3 bits (125), Expect = 8e-10
 Identities = 27/119 (22%), Positives = 48/119 (40%), Gaps = 16/119 (13%)

Query: 95  HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIIT 154
            +  VDD     K +   LQ    +V    +G   L              D    ++++ 
Sbjct: 4   KIAVVDDDKNILKKVSEKLQ-QLGRVKTFLTGEDFLN-------------DEEAFHVVVL 49

Query: 155 DYTMPGMTGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD 213
           D  +P  +GYE+ + IKE+     V ++ + S+D    +    E GA++Y+ KP     
Sbjct: 50  DVMLPDYSGYEICRMIKETRPETWVILLTLLSDD--ESVLKGFEAGADDYVTKPFNPEI 106

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	213
d1zesa1	121	PhoB receiver domain {Escherichia coli [TaxId: 562	99.95
d2pl1a1	119	PhoP receiver domain {Escherichia coli [TaxId: 562	99.95
d1peya_	119	Sporulation response regulator Spo0F {Bacillus sub	99.95
d1dbwa_	123	Transcriptional regulatory protein FixJ, receiver	99.95
d2r25b1	128	Response regulator Sin1 {Baker's yeast (Saccharomy	99.95
d1mb3a_	123	Cell division response regulator DivK {Caulobacter	99.95
d1ys7a2	121	Transcriptional regulatory protein PrrA, N-termina	99.95
d1jbea_	128	CheY protein {Escherichia coli [TaxId: 562]}	99.95
d2a9pa1	117	DNA-binding response regulator MicA, N-terminal do	99.95
d1p6qa_	129	CheY protein {Sinorhizobium meliloti, CheY2 [TaxId	99.95
d1kgsa2	122	PhoB receiver domain {Thermotoga maritima [TaxId:	99.95
d1u0sy_	118	CheY protein {Thermotoga maritima [TaxId: 2336]}	99.95
d1krwa_	123	NTRC receiver domain {Salmonella typhimurium [TaxI	99.94
d1qkka_	140	Transcriptional regulatory protein DctD, receiver	99.94
d1mvoa_	121	PhoP receiver domain {Bacillus subtilis [TaxId: 14	99.94
d1ny5a1	137	Transcriptional activator sigm54 (NtrC1), N-termin	99.94
d1zh2a1	119	Transcriptional regulatory protein KdpE, N-termina	99.94
d1xhfa1	121	Aerobic respiration control protein ArcA, N-termin	99.94
d1i3ca_	144	Response regulator for cyanobacterial phytochrome	99.94
d2ayxa1	133	Sensor kinase protein RcsC, C-terminal domain {Esc	99.94
d1k68a_	140	Response regulator for cyanobacterial phytochrome	99.94
d1w25a1	139	Response regulator PleD, receiver domain {Caulobac	99.94
d1dcfa_	134	Receiver domain of the ethylene receptor {Thale cr	99.94
d1k66a_	149	Response regulator for cyanobacterial phytochrome	99.94
d1zgza1	120	TorCAD operon transcriptional regulator TorD, N-te	99.94
d1dz3a_	123	Sporulation response regulator Spo0A {Bacillus ste	99.94
d1s8na_	190	Probable two-component system transcriptional regu	99.93
d1yioa2	128	Response regulatory protein StyR, N-terminal domai	99.93
d1p2fa2	120	Response regulator DrrB {Thermotoga maritima [TaxI	99.93
d1a04a2	138	Nitrate/nitrite response regulator (NarL), receive	99.93
d1w25a2	153	Response regulator PleD, receiver domain {Caulobac	99.93
d1a2oa1	140	Methylesterase CheB, N-terminal domain {Salmonella	99.91
d2b4aa1	118	Hypothetical protein BH3024 {Bacillus halodurans [	99.91
d1qo0d_	189	Positive regulator of the amidase operon AmiR {Pse	99.87
d7reqa2	168	Methylmalonyl-CoA mutase alpha subunit, C-terminal	95.62
d1ccwa_	137	Glutamate mutase, small subunit {Clostridium cochl	95.47
d3bula2	156	Methionine synthase, C-terminal domain {Escherichi	91.11
d1qpoa1	169	Quinolinic acid phosphoribosyltransferase (Nicotin	90.81
d1dxea_	253	2-dehydro-3-deoxy-galactarate aldolase {Escherichi	90.13
d1xrsb1	160	D-lysine 5,6-aminomutase beta subunit KamE, C-term	89.36
d1r8ja2	135	N-terminal domain of the circadian clock protein K	88.78
d1susa1	227	Caffeoyl-CoA O-methyltransferase {Alfalfa (Medicag	88.42
d1id1a_	153	Rck domain from putative potassium channel Kch {Es	88.3
d2avda1	219	COMT domain-containing protein 1, COMTD1 {Human (H	88.03
d1kzyc2	106	53BP1 {Human (Homo sapiens) [TaxId: 9606]}	88.03
d2cl5a1	214	Catechol O-methyltransferase, COMT {Rat (Rattus no	88.02
d1o4ua1	170	Quinolinic acid phosphoribosyltransferase (Nicotin	85.46
d1i7qb_	192	Anthranilate synthase GAT subunit, TrpG {Serratia	84.41
d2fpoa1	183	Methylase YhhF {Escherichia coli [TaxId: 562]}	83.36
d1wv2a_	243	Thiazole biosynthesis protein ThiG {Pseudomonas ae	82.4
d2fhpa1	182	Putative methylase EF2452 {Enterococcus faecalis [	82.27
d1xm3a_	251	Thiazole biosynthesis protein ThiG {Bacillus subti	81.5

>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=99.95  E-value=2.7e-28  Score=178.52  Aligned_cols=107  Identities=27%  Similarity=0.462  Sum_probs=102.1

Q ss_pred             EEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhcC
Q 048660           95 HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKESS  174 (213)
Q Consensus        95 ~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~~  174 (213)
                      |||||||++.+++.+..+|+..||.|..+.+|.+|++.+           ....||+||+|+.||++||++++++||+..
T Consensus         2 kILiVDD~~~~~~~l~~~L~~~g~~v~~a~~~~~al~~l-----------~~~~~dlil~D~~mp~~~G~~l~~~lr~~~   70 (121)
T d1zesa1           2 RILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQL-----------NEPWPDLILLDWMLPGGSGIQFIKHLKRES   70 (121)
T ss_dssp             EEEEECSCHHHHHHHHHHHHHTTCEEEEECSHHHHHHHS-----------SSSCCSEEEECSSCTTSCHHHHHHHHHHST
T ss_pred             EEEEEeCCHHHHHHHHHHHHHCCCEEEEECChHHHHHHH-----------HccCCCEEEeecCCCCCCHHHHHHHHHhCc
Confidence            799999999999999999999999999999999999999           566899999999999999999999999877


Q ss_pred             CCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          175 VFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       175 ~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      ..+++|||++|+..+.....+++++|+++||.|||+.+
T Consensus        71 ~~~~~pvi~lt~~~~~~~~~~~~~~G~~d~l~KP~~~~  108 (121)
T d1zesa1          71 MTRDIPVVMLTARGEEEDRVRGLETGADDYITKPFSPK  108 (121)
T ss_dssp             TTTTSCEEEEESCCSHHHHHHHHHHTCSEEEESSCCHH
T ss_pred             cCCCCeEEEEECCCCHHHHHHHHHCCCCEEEECCCCHH
Confidence            77899999999999999999999999999999999864

>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=2e-28  Score=178.80  Aligned_cols=106  Identities=22%  Similarity=0.435  Sum_probs=100.2

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhc
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKES  173 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~  173 (213)
                      +|||||||++.++..++.+|+.+||.|..+.+|.+|++.+           ....||+||+|+.||++||++++++||+.
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            4899999999999999999999999999999999999999           44579999999999999999999999987


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                        .+.+|+|++|+..+.+...+++++|+++||.|||+.+
T Consensus        70 --~~~~pvi~lt~~~~~~~~~~a~~~Ga~~yl~KP~~~~  106 (119)
T d2pl1a1          70 --DVSLPILVLTARESWQDKVEVLSAGADDYVTKPFHIE  106 (119)
T ss_dssp             --TCCSCEEEEESCCCHHHHHHHHHTTCSEEEESSCCHH
T ss_pred             --CcccceEeeeccCCHHHHHHHHHcCCCEEEECCCCHH
Confidence              5689999999999999999999999999999999864

>d1peya_ c.23.1.1 (A:) Sporulation response regulator Spo0F {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Sporulation response regulator Spo0F
species: Bacillus subtilis [TaxId: 1423]

Probab=99.95  E-value=3.1e-28  Score=177.78  Aligned_cols=106  Identities=27%  Similarity=0.417  Sum_probs=99.9

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhc
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKES  173 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~  173 (213)
                      .|||||||++.++..++.+|+..||.|..+.+|.+|++.++           ..+||+||+|+.||++||++++++||+.
T Consensus         2 krILvVDD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~~~-----------~~~~dlillD~~mP~~~G~el~~~lr~~   70 (119)
T d1peya_           2 EKILIVDDQSGIRILLNEVFNKEGYQTFQAANGLQALDIVT-----------KERPDLVLLDMKIPGMDGIEILKRMKVI   70 (119)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH-----------HHCCSEEEEESCCTTCCHHHHHHHHHHH
T ss_pred             CEEEEEeCCHHHHHHHHHHHHHcCCEEEEeCCHHHHHHHHH-----------hCCCCEEEEeccCCCCCHHHHHHHHHHh
Confidence            48999999999999999999999999999999999999994           4579999999999999999999999987


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                        .+++|||++|++.+.+...+++++|+++||.|||+.+
T Consensus        71 --~~~~pvi~lt~~~~~~~~~~a~~~Ga~~yl~KP~~~~  107 (119)
T d1peya_          71 --DENIRVIIMTAYGELDMIQESKELGALTHFAKPFDID  107 (119)
T ss_dssp             --CTTCEEEEEESSCCHHHHHHHHHTTCCEEEESSCCHH
T ss_pred             --CCCCcEEEEecCCCHHHHHHHHHCCCCEEEECCCCHH
Confidence              5789999999999999999999999999999999864

>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=6.9e-28  Score=176.91  Aligned_cols=107  Identities=23%  Similarity=0.413  Sum_probs=101.2

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHh
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKE  172 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~  172 (213)
                      ..+||||||++.++..++.+|+..||.|..+.+|++|++.+           ....||+||+|+.||++||++++++||+
T Consensus         3 ~~~ILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~~al~~~-----------~~~~~dlvi~D~~mp~~~G~e~~~~lr~   71 (123)
T d1dbwa_           3 DYTVHIVDDEEPVRKSLAFMLTMNGFAVKMHQSAEAFLAFA-----------PDVRNGVLVTDLRMPDMSGVELLRNLGD   71 (123)
T ss_dssp             CCEEEEEESSHHHHHHHHHHHHHTTCEEEEESCHHHHHHHG-----------GGCCSEEEEEECCSTTSCHHHHHHHHHH
T ss_pred             CCEEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHH-----------hhcCCcEEEEeccCccccchHHHHHHHh
Confidence            46999999999999999999999999999999999999998           5568999999999999999999999998


Q ss_pred             cCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          173 SSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       173 ~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      .  .+++|+|++|++.+.+...+++++|+++||.||++.+
T Consensus        72 ~--~~~~~iI~lt~~~~~~~~~~a~~~Ga~~yl~KP~~~~  109 (123)
T d1dbwa_          72 L--KINIPSIVITGHGDVPMAVEAMKAGAVDFIEKPFEDT  109 (123)
T ss_dssp             T--TCCCCEEEEECTTCHHHHHHHHHTTCSEEEESSCCHH
T ss_pred             c--CCCCeEEEEEeeCCHHHHHHHHHCCCCEEEECCCCHH
Confidence            6  5789999999999999999999999999999999864

>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=99.95  E-value=5.8e-28  Score=178.56  Aligned_cols=112  Identities=24%  Similarity=0.415  Sum_probs=100.2

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCE-EEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHh
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCK-VTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKE  172 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~-v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~  172 (213)
                      +|||||||++.++..++.+|+++|+. |..|.||++|++.++....      ....||+||+|+.||++||++++++||+
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            68999999999999999999999995 7899999999998864211      2357999999999999999999999997


Q ss_pred             cCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          173 SSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       173 ~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      .. ...+|||++|++.+.+...+++++|+++||.|||+.+
T Consensus        76 ~~-~~~~piI~lT~~~~~~~~~~~~~~G~~~~l~KP~~~~  114 (128)
T d2r25b1          76 DL-GYTSPIVALTAFADDSNIKECLESGMNGFLSKPIKRP  114 (128)
T ss_dssp             HS-CCCSCEEEEESCCSHHHHHHHHHTTCSEEEESSCCHH
T ss_pred             cc-CCCCeEEEEECCCCHHHHHHHHHcCCCEEEECCCCHH
Confidence            64 4578999999999999999999999999999999854

>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=99.95  E-value=3.8e-28  Score=178.18  Aligned_cols=108  Identities=29%  Similarity=0.441  Sum_probs=96.0

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhc
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKES  173 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~  173 (213)
                      .|||||||++.++..+..+|+.+||.|..+.+|.+|++.++           ...||+||+|+.||++||++++++||+.
T Consensus         2 krILiVDD~~~~~~~l~~~L~~~g~~v~~a~~~~~al~~~~-----------~~~~dlil~D~~mp~~dG~el~~~ir~~   70 (123)
T d1mb3a_           2 KKVLIVEDNELNMKLFHDLLEAQGYETLQTREGLSALSIAR-----------ENKPDLILMDIQLPEISGLEVTKWLKED   70 (123)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESCHHHHHHHHH-----------HHCCSEEEEESBCSSSBHHHHHHHHHHS
T ss_pred             ceEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHH-----------hCCCCEEEEEeccCCCcHHHHHHHHHhC
Confidence            48999999999999999999999999999999999999994           4579999999999999999999999998


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      ....++|||++|+........+++++|+++||.|||+.+
T Consensus        71 ~~~~~iPii~lt~~~~~~~~~~~~~~G~~~~l~KP~~~~  109 (123)
T d1mb3a_          71 DDLAHIPVVAVTAFAMKGDEERIREGGCEAYISKPISVV  109 (123)
T ss_dssp             TTTTTSCEEEEC------CHHHHHHHTCSEEECSSCCHH
T ss_pred             CCcCCCCeEEEEEecCHHHHHHHHHcCCCEEEECCCCHH
Confidence            777899999999999999999999999999999999854

>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=99.95  E-value=1.7e-28  Score=179.70  Aligned_cols=106  Identities=29%  Similarity=0.450  Sum_probs=99.9

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhc
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKES  173 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~  173 (213)
                      .|||||||++.++..+..+|++.||.|..+.+|.+|++.+           ....||+||+|+.||+++|++++++||+.
T Consensus         2 PkILiVDD~~~~~~~l~~~L~~~g~~v~~a~~~~eal~~~-----------~~~~~dlvl~D~~mP~~~G~el~~~ir~~   70 (121)
T d1ys7a2           2 PRVLVVDDDSDVLASLERGLRLSGFEVATAVDGAEALRSA-----------TENRPDAIVLDINMPVLDGVSVVTALRAM   70 (121)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHH-----------HHSCCSEEEEESSCSSSCHHHHHHHHHHT
T ss_pred             CEEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHH-----------HhCCCCEEEEEeeccCcccHHHHHHHHhc
Confidence            4899999999999999999999999999999999999999           44579999999999999999999999986


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                        .+++|||++|+..+.+...+++++|+++||.|||+.+
T Consensus        71 --~~~~piI~lt~~~~~~~~~~a~~~Ga~dyl~KP~~~~  107 (121)
T d1ys7a2          71 --DNDVPVCVLSARSSVDDRVAGLEAGADDYLVKPFVLA  107 (121)
T ss_dssp             --TCCCCEEEEECCCTTTCCCTTTTTTCSEEEESSCCHH
T ss_pred             --CCCCEEEEEEeeCCHHHHHHHHHCCCCEEEECCCCHH
Confidence              5789999999999999999999999999999999864

>d2a9pa1 c.23.1.1 (A:2-118) DNA-binding response regulator MicA, N-terminal domain {Streptococcus pneumoniae [TaxId: 1313]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: DNA-binding response regulator MicA, N-terminal domain
species: Streptococcus pneumoniae [TaxId: 1313]

Probab=99.95  E-value=1.7e-27  Score=173.28  Aligned_cols=104  Identities=28%  Similarity=0.440  Sum_probs=98.3

Q ss_pred             EEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhcC
Q 048660           95 HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKESS  174 (213)
Q Consensus        95 ~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~~  174 (213)
                      |||||||++.++..+..+|+..||.|..+.||.+|++.++           ...||+||+|+.||+++|++++++|++. 
T Consensus         2 rILiVdDd~~~~~~l~~~L~~~g~~v~~a~~~~eal~~~~-----------~~~~dlillD~~mp~~~G~~~~~~i~~~-   69 (117)
T d2a9pa1           2 KILIVDDEKPISDIIKFNMTKEGYEVVTAFNGREALEQFE-----------AEQPDIIILDLMLPEIDGLEVAKTIRKT-   69 (117)
T ss_dssp             EEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH-----------HHCCSEEEECSSCSSSCHHHHHHHHHTT-
T ss_pred             EEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHH-----------hcCCCEEEeccccCCCCccHHHHHHHhC-
Confidence            7999999999999999999999999999999999999994           4579999999999999999999999974 


Q ss_pred             CCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          175 VFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       175 ~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                        +++|||++|+..+.....+++++|+++||.|||+.+
T Consensus        70 --~~~pvI~lt~~~~~~~~~~a~~~Ga~d~l~KP~~~~  105 (117)
T d2a9pa1          70 --SSVPILMLSAKDSEFDKVIGLELGADDYVTKPFSNR  105 (117)
T ss_dssp             --CCCCEEEEESCCSHHHHHHHHHHTCSEEEESSCCHH
T ss_pred             --CCCCEEEEecCCCHHHHHHHHHcCCCEEEECCCCHH
Confidence              579999999999999999999999999999999864

>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=99.95  E-value=1e-27  Score=177.39  Aligned_cols=110  Identities=25%  Similarity=0.464  Sum_probs=102.5

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCCE-EEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSCK-VTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKI  170 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~~-v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~i  170 (213)
                      .++|||||||++.++..++.+|++.||. |..+.+|++|++.+           .+..||+||+|+.||++||+++++.+
T Consensus         5 ~~~kILiVDD~~~~~~~l~~~L~~~g~~~v~~a~~~~~al~~l-----------~~~~~dlii~D~~mP~~~G~el~~~l   73 (129)
T d1p6qa_           5 EKIKVLIVDDQVTSRLLLGDALQQLGFKQITAAGDGEQGMKIM-----------AQNPHHLVISDFNMPKMDGLGLLQAV   73 (129)
T ss_dssp             SCCCEEEECSSHHHHHHHHHHHHTTTCSCEECCSSHHHHHHHH-----------HTSCCSEEEECSSSCSSCHHHHHHHH
T ss_pred             CCCEEEEEECCHHHHHHHHHHHHHCCCeEEEEECCHHHHHHHH-----------HhCCCCeEEeeeecCCCChHHHHHHH
Confidence            4679999999999999999999999995 78899999999999           45679999999999999999999999


Q ss_pred             HhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          171 KESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       171 r~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      |+.....++|||++|+..+.+...+++++|+++||.|||+.+
T Consensus        74 r~~~~~~~~pii~lt~~~~~~~~~~a~~~G~~~~l~KP~~~~  115 (129)
T d1p6qa_          74 RANPATKKAAFIILTAQGDRALVQKAAALGANNVLAKPFTIE  115 (129)
T ss_dssp             TTCTTSTTCEEEECCSCCCHHHHHHHHHHTCSCEECCCSSHH
T ss_pred             HhCcccCCCeEEEEEecCCHHHHHHHHHCCCCEEEECCCCHH
Confidence            987777899999999999999999999999999999999864

>d1kgsa2 c.23.1.1 (A:2-123) PhoB receiver domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: PhoB receiver domain
species: Thermotoga maritima [TaxId: 2336]

Probab=99.95  E-value=8.4e-28  Score=176.16  Aligned_cols=106  Identities=25%  Similarity=0.376  Sum_probs=100.2

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhc
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKES  173 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~  173 (213)
                      +|||||||++.++..++.+|+.+||.|..+.+|++|++.+           ....||+||+|+.||+++|+++++.+|+.
T Consensus         2 irILiVdDd~~~~~~l~~~L~~~g~~v~~a~~~~~al~~l-----------~~~~~dlillD~~mp~~~g~~~~~~lr~~   70 (122)
T d1kgsa2           2 VRVLVVEDERDLADLITEALKKEMFTVDVCYDGEEGMYMA-----------LNEPFDVVILDIMLPVHDGWEILKSMRES   70 (122)
T ss_dssp             CEEEEECSSHHHHHHHHHHHHHTTCEEEEESSHHHHHHHH-----------HHSCCSEEEEESCCSSSCHHHHHHHHHHT
T ss_pred             CEEEEEeCCHHHHHHHHHHHHHCCCEEEEEcchHHHHHHH-----------HhhCccccccccccccchhHHHHHHHHhc
Confidence            6899999999999999999999999999999999999999           44589999999999999999999999986


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                        .+.+|||++|+..+.....+++++|+++||.||++.+
T Consensus        71 --~~~~piI~lt~~~~~~~~~~~~~~Ga~~yl~KP~~~~  107 (122)
T d1kgsa2          71 --GVNTPVLMLTALSDVEYRVKGLNMGADDYLPKPFDLR  107 (122)
T ss_dssp             --TCCCCEEEEESSCHHHHHHHTCCCCCSEEEESSCCHH
T ss_pred             --CCCCcEEEEcCCCCHHHHHHHHHcCCceeecCCCCHH
Confidence              5689999999999999999999999999999999864

>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=99.95  E-value=1.5e-27  Score=173.88  Aligned_cols=107  Identities=25%  Similarity=0.429  Sum_probs=99.5

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCEEE-EEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCKVT-AVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~v~-~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      +.|||||||++.++..++.+|+++||.|. .|.+|.+|++.++           ...||+||+|+.||++||++++++||
T Consensus         1 GkrILivDD~~~~~~~l~~~L~~~g~~v~~~a~~~~~al~~~~-----------~~~~dliilD~~mp~~~G~e~~~~ir   69 (118)
T d1u0sy_           1 GKRVLIVDDAAFMRMMLKDIITKAGYEVAGEATNGREAVEKYK-----------ELKPDIVTMDITMPEMNGIDAIKEIM   69 (118)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHH-----------HHCCSEEEEECSCGGGCHHHHHHHHH
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHHcCCceEEEECCHHHHHHHHH-----------hccCCEEEEecCCCCCCHHHHHHHHH
Confidence            35899999999999999999999999876 6899999999994           45799999999999999999999999


Q ss_pred             hcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          172 ESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      +.  .+++|||++|++.+.+...++++.|+++||.|||+.+
T Consensus        70 ~~--~~~~pvi~ls~~~~~~~~~~a~~~Ga~~yl~KP~~~~  108 (118)
T d1u0sy_          70 KI--DPNAKIIVCSAMGQQAMVIEAIKAGAKDFIVKPFQPS  108 (118)
T ss_dssp             HH--CTTCCEEEEECTTCHHHHHHHHHTTCCEEEESSCCHH
T ss_pred             Hh--CCCCcEEEEEccCCHHHHHHHHHcCCCEEEECCCCHH
Confidence            87  5789999999999999999999999999999999864

>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=6.8e-28  Score=176.91  Aligned_cols=107  Identities=33%  Similarity=0.494  Sum_probs=101.1

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHh
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKE  172 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~  172 (213)
                      +.+|||||||+.++..++.+|+..||.|..+.+|.+|++.+           ....||+||+|+.||+++|++++++||+
T Consensus         3 k~~ILIVDDd~~~~~~l~~~L~~~g~~v~~a~~~~~a~~~l-----------~~~~~dlii~D~~mp~~~G~el~~~l~~   71 (123)
T d1krwa_           3 RGIVWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLAAL-----------ASKTPDVLLSDIRMPGMDGLALLKQIKQ   71 (123)
T ss_dssp             CCEEEEESSSHHHHHHHHHHHHHTTCEEEEESSSHHHHHHH-----------TTCCCSEEEECCSSSSSTTHHHHHHHHH
T ss_pred             CCEEEEEECCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHH-----------HhCCCCEEEehhhcCCchHHHHHHHHHH
Confidence            35799999999999999999999999999999999999999           5568999999999999999999999998


Q ss_pred             cCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          173 SSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       173 ~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      .  .+.+|||++|+..+.+...++++.|+++||.||++.+
T Consensus        72 ~--~~~~piI~~t~~~~~~~~~~a~~~Ga~dyl~KP~~~~  109 (123)
T d1krwa_          72 R--HPMLPVIIMTAHSDLDAAVSAYQQGAFDYLPKPFDID  109 (123)
T ss_dssp             H--SSSCCEEESCCCSCHHHHHHHHHHTEEEECSSCCHHH
T ss_pred             h--CCCCeEEEEecCCCHHHHHHHHHcCCCeEEeCcCCHH
Confidence            7  6789999999999999999999999999999999754

>d1qkka_ c.23.1.1 (A:) Transcriptional regulatory protein DctD, receiver domain {Sinorhizobium meliloti [TaxId: 382]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Transcriptional regulatory protein DctD, receiver domain
species: Sinorhizobium meliloti [TaxId: 382]

Probab=99.94  E-value=2.2e-27  Score=177.96  Aligned_cols=105  Identities=28%  Similarity=0.472  Sum_probs=100.2

Q ss_pred             EEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhcC
Q 048660           95 HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKESS  174 (213)
Q Consensus        95 ~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~~  174 (213)
                      +||||||++.++..++.+|+..||.+..+.||.+|++.+           ....||+||+|+.||+|||++++++||+. 
T Consensus         2 ~ILiVDDd~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l-----------~~~~~dlil~D~~mP~~~G~el~~~lr~~-   69 (140)
T d1qkka_           2 SVFLIDDDRDLRKAMQQTLELAGFTVSSFASATEALAGL-----------SADFAGIVISDIRMPGMDGLALFRKILAL-   69 (140)
T ss_dssp             EEEEECSCHHHHHHHHHHHHHTTCEEEEESCHHHHHHTC-----------CTTCCSEEEEESCCSSSCHHHHHHHHHHH-
T ss_pred             EEEEEECCHHHHHHHHHHHHHCCCEEEEeCChHHHHHHH-----------hccCcchHHHhhccCCCCHHHHHHHHHHh-
Confidence            799999999999999999999999999999999999998           56789999999999999999999999987 


Q ss_pred             CCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          175 VFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       175 ~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                       .+++|||++|++.+.+...+++++|+++||.||++.+
T Consensus        70 -~~~~pvI~lT~~~~~~~~~~a~~~Ga~dyl~KP~~~~  106 (140)
T d1qkka_          70 -DPDLPMILVTGHGDIPMAVQAIQDGAYDFIAKPFAAD  106 (140)
T ss_dssp             -CTTSCEEEEECGGGHHHHHHHHHTTCCEEEESSCCHH
T ss_pred             -CCCCcEEEEECCCCHHHHHHHHHcCCCEeecCCCCHH
Confidence             6789999999999999999999999999999999754

>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=1.4e-27  Score=174.61  Aligned_cols=106  Identities=26%  Similarity=0.391  Sum_probs=99.5

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhc
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKES  173 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~  173 (213)
                      .|||||||++.++..++.+|++.||.|..|.+|.+|++.+.           ...||+||+|+.||+++|+++++++|+.
T Consensus         3 krILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~~al~~l~-----------~~~~dlillD~~mp~~~G~~~~~~~r~~   71 (121)
T d1mvoa_           3 KKILVVDDEESIVTLLQYNLERSGYDVITASDGEEALKKAE-----------TEKPDLIVLDVMLPKLDGIEVCKQLRQQ   71 (121)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH-----------HHCCSEEEEESSCSSSCHHHHHHHHHHT
T ss_pred             CCEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHh-----------cccccEEEecccccCCCCchhhhhhhcc
Confidence            48999999999999999999999999999999999999994           4579999999999999999999999987


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                        .+.+|||++|+..+.+...+++++|+++||.|||+.+
T Consensus        72 --~~~~~ii~lt~~~~~~~~~~~~~~Ga~~yl~KP~~~~  108 (121)
T d1mvoa_          72 --KLMFPILMLTAKDEEFDKVLGLELGADDYMTKPFSPR  108 (121)
T ss_dssp             --TCCCCEEEEECTTCCCCHHHHHHTTCCEEEESSCCHH
T ss_pred             --CCCCEEEEEEeeCCHHHHHHHHHCCCCEEEECCCCHH
Confidence              5678999999999999999999999999999999864

>d1ny5a1 c.23.1.1 (A:1-137) Transcriptional activator sigm54 (NtrC1), N-terminal domain {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Transcriptional activator sigm54 (NtrC1), N-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

Probab=99.94  E-value=1.8e-27  Score=177.81  Aligned_cols=106  Identities=29%  Similarity=0.519  Sum_probs=100.2

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhc
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKES  173 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~  173 (213)
                      +|||||||++.++..++.+|+..||.|..|.+|.+|++.+.           ...||+||+|+.||+++|+++++.||+.
T Consensus         1 mkILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~eAl~~l~-----------~~~~dlvilD~~mp~~~G~e~~~~lr~~   69 (137)
T d1ny5a1           1 MNVLVIEDDKVFRGLLEEYLSMKGIKVESAERGKEAYKLLS-----------EKHFNVVLLDLLLPDVNGLEILKWIKER   69 (137)
T ss_dssp             CEEEEECCCHHHHHHHHHHHHHHTCEEEEESSHHHHHHHHH-----------HSCCSEEEEESBCSSSBHHHHHHHHHHH
T ss_pred             CEEEEEecCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHhh-----------ccccccchHHHhhhhhhHHHHHHHHHHh
Confidence            48999999999999999999999999999999999999994           4579999999999999999999999987


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                        .+++|||++|++.+.+...+++++|+++||.||++.+
T Consensus        70 --~~~~piI~lT~~~~~~~~~~a~~~Ga~dyl~KP~~~~  106 (137)
T d1ny5a1          70 --SPETEVIVITGHGTIKTAVEAMKMGAYDFLTKPCMLE  106 (137)
T ss_dssp             --CTTSEEEEEEETTCHHHHHHHHTTTCCEEEEESCCHH
T ss_pred             --CCCCCEEEEECCCCHHHHHHHHHcCCCEEEeCCCCHH
Confidence              6789999999999999999999999999999999854

>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=1.6e-27  Score=174.00  Aligned_cols=104  Identities=27%  Similarity=0.462  Sum_probs=98.0

Q ss_pred             EEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhcC
Q 048660           95 HVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKESS  174 (213)
Q Consensus        95 ~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~~  174 (213)
                      +||||||++.+++.++.+|+.+||+|..+.+|++|++.++           ...||+||+|+.||+++|+++++.||+. 
T Consensus         2 nILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~eal~~l~-----------~~~~dliilD~~mP~~~G~e~~~~ir~~-   69 (119)
T d1zh2a1           2 NVLIVEDEQAIRRFLRTALEGDGMRVFEAETLQRGLLEAA-----------TRKPDLIILDLGLPDGDGIEFIRDLRQW-   69 (119)
T ss_dssp             EEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHH-----------HHCCSEEEEESEETTEEHHHHHHHHHTT-
T ss_pred             EEEEEECCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHH-----------hcCCCEEEeccccCCCCCchHHHHHHhc-
Confidence            6999999999999999999999999999999999999994           4579999999999999999999999974 


Q ss_pred             CCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          175 VFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       175 ~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                        +..|||++|+..+.+...++++.|+++||.|||+.+
T Consensus        70 --~~~piI~lt~~~~~~~~~~a~~~Ga~dyl~KP~~~~  105 (119)
T d1zh2a1          70 --SAVPVIVLSARSEESDKIAALDAGADDYLSKPFGIG  105 (119)
T ss_dssp             --CCCCEEEEESCCSHHHHHHHHHHTCSEEEESSCCHH
T ss_pred             --cCCcEEEEeccCCHHHHHHHHHcCCCEEEECCCCHH
Confidence              568999999999999999999999999999999864

>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=99.94  E-value=4.8e-27  Score=171.87  Aligned_cols=105  Identities=28%  Similarity=0.491  Sum_probs=99.2

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhc
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKES  173 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~  173 (213)
                      .+||||||++.+++.+..+|+++||.|..+.+|++|++.+.           ...||+||+|+.||+++|+++++.+|+.
T Consensus         3 p~ILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~~al~~l~-----------~~~~dlii~D~~mp~~~G~~~~~~~r~~   71 (121)
T d1xhfa1           3 PHILIVEDELVTRNTLKSIFEAEGYDVFEATDGAEMHQILS-----------EYDINLVIMDINLPGKNGLLLARELREQ   71 (121)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHH-----------HSCCSEEEECSSCSSSCHHHHHHHHHHH
T ss_pred             CEEEEEECCHHHHHHHHHHHHHCCCEEEEECChHHHHHHHH-----------hcCCCEEEeecccCCccCcHHHHHHHhc
Confidence            48999999999999999999999999999999999999994           4579999999999999999999999985


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                         +++|||++|+..+.....+++++|+++||.|||+.+
T Consensus        72 ---~~~pii~lt~~~~~~~~~~a~~~Ga~dyl~KP~~~~  107 (121)
T d1xhfa1          72 ---ANVALMFLTGRDNEVDKILGLEIGADDYITKPFNPR  107 (121)
T ss_dssp             ---CCCEEEEEESCCSHHHHHHHHHHTCSEEEESSCCHH
T ss_pred             ---CCCcEEEEECCCCHHHHHHHHHcCCCEEEeCCCCHH
Confidence               579999999999999999999999999999999864

>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=9.3e-27  Score=175.28  Aligned_cols=116  Identities=26%  Similarity=0.447  Sum_probs=102.6

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcC--CEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHH
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISS--CKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKI  170 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g--~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~i  170 (213)
                      ..+||||||++.++..++.+|++.|  +.|..+.||.+|+++++....    ......||+||+|+.||++||++++++|
T Consensus         3 pk~ILiVdD~~~~~~~l~~~L~~~g~~~~v~~a~~g~~Al~~l~~~~~----~~~~~~pdlIllD~~mP~~~G~el~~~i   78 (144)
T d1i3ca_           3 PKVILLVEDSKADSRLVQEVLKTSTIDHELIILRDGLAAMAFLQQQGE----YENSPRPNLILLDLNLPKKDGREVLAEI   78 (144)
T ss_dssp             CEEEEEECCCHHHHHHHHHHHHSCCSCEEEEEECSHHHHHHHHTTCGG----GTTCCCCSEEEECSCCSSSCHHHHHHHH
T ss_pred             CCEEEEEECCHHHHHHHHHHHHHcCCCeEEEEECCHHHHHHHHHhchh----hhccCCCCEEEEECccccccchHHHHHH
Confidence            4689999999999999999998876  588999999999999964211    1123469999999999999999999999


Q ss_pred             HhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          171 KESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       171 r~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      |+.....++|||++|+..+.+...+++++|+++||.||++.+
T Consensus        79 r~~~~~~~iPvi~lT~~~~~~~~~~a~~~Ga~~yl~KP~~~~  120 (144)
T d1i3ca_          79 KQNPDLKRIPVVVLTTSHNEDDVIASYELHVNCYLTKSRNLK  120 (144)
T ss_dssp             HHCTTTTTSCEEEEESCCCHHHHHHHHHTTCSEEEECCSSHH
T ss_pred             HhCcccCCCeEEEEECCCCHHHHHHHHHCCCCEEEECCCCHH
Confidence            998777899999999999999999999999999999999864

>d2ayxa1 c.23.1.1 (A:817-949) Sensor kinase protein RcsC, C-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Sensor kinase protein RcsC, C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=99.94  E-value=1.2e-27  Score=177.84  Aligned_cols=108  Identities=27%  Similarity=0.549  Sum_probs=101.4

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      ..++||||||++.++..+..+|+.+||.|..+.+|.+|++.+           ....||+||+|+.||++||++++++||
T Consensus         7 ~~~~ILiVDD~~~~~~~l~~~L~~~g~~v~~a~~g~ea~~~~-----------~~~~~dlillD~~mP~~dG~el~~~ir   75 (133)
T d2ayxa1           7 DDMMILVVDDHPINRRLLADQLGSLGYQCKTANDGVDALNVL-----------SKNHIDIVLSDVNMPNMDGYRLTQRIR   75 (133)
T ss_dssp             CCCEEEEEESSHHHHHHHHHHHHHHTSEEEEECCSHHHHHHH-----------HHSCCSEEEEEESSCSSCCHHHHHHHH
T ss_pred             CCCEEEEEECCHHHHHHHHHHHHHcCCEEEEECcHHHHHHHH-----------hccCceEEEEeccCCCCCHHHHHHHHH
Confidence            468999999999999999999999999999999999999998           445799999999999999999999999


Q ss_pred             hcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          172 ESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      +.  .+.+|||++|+....+...++++.|+++||.|||+.+
T Consensus        76 ~~--~~~~pii~lt~~~~~~~~~~~~~~G~~~~l~KP~~~~  114 (133)
T d2ayxa1          76 QL--GLTLPVIGVTANALAEEKQRCLESGMDSCLSKPVTLD  114 (133)
T ss_dssp             HH--HCCSCEEEEESSTTSHHHHHHHHCCCEEEEESSCCHH
T ss_pred             Hh--CCCCCEEEEeccCCHHHHHHHHHcCCCEEEECCCCHH
Confidence            87  4689999999999999999999999999999999854

>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=99.94  E-value=7.6e-27  Score=174.96  Aligned_cols=115  Identities=30%  Similarity=0.473  Sum_probs=102.3

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcC--CEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISS--CKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g--~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      .|||||||++.++..++.+|++.|  |.|..+.||.+|++.++.....    .....||+||+|++||+|||++++++||
T Consensus         3 krILiVDD~~~~~~~l~~~L~~~g~~~~v~~a~~g~eAl~~l~~~~~~----~~~~~pdlillD~~mP~~dG~el~~~ir   78 (140)
T d1k68a_           3 KKIFLVEDNKADIRLIQEALANSTVPHEVVTVRDGMEAMAYLRQEGEY----ANASRPDLILLDLNLPKKDGREVLAEIK   78 (140)
T ss_dssp             CEEEEECCCHHHHHHHHHHHHTCSSCCEEEEECSHHHHHHHHTTCGGG----GSCCCCSEEEECSSCSSSCHHHHHHHHH
T ss_pred             CcEEEEECCHHHHHHHHHHHHHcCCCeEEEEECCHHHHHHHHHHhHHh----hccCCCCEEEEeeccccccChHHHHHHH
Confidence            589999999999999999999876  6899999999999999643211    1335699999999999999999999999


Q ss_pred             hcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          172 ESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      +....+++|||++|+..+.+...+++++|+++||.||++.+
T Consensus        79 ~~~~~~~iPvI~ls~~~~~~~~~~a~~~Ga~~yl~KP~~~~  119 (140)
T d1k68a_          79 SDPTLKRIPVVVLSTSINEDDIFHSYDLHVNCYITKSANLS  119 (140)
T ss_dssp             HSTTGGGSCEEEEESCCCHHHHHHHHHTTCSEEEECCSSHH
T ss_pred             hCcccCCCcEEEEeCCCCHHHHHHHHHCCCCEEEECCCCHH
Confidence            97767789999999999999999999999999999999864

>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=99.94  E-value=3.8e-27  Score=176.41  Aligned_cols=108  Identities=29%  Similarity=0.471  Sum_probs=101.9

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhc
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKES  173 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~  173 (213)
                      -|||||||++.+++.++.+|++.||.|..+.||.+|++.+.           ...||+||+|+.||+++|+++++.+|+.
T Consensus         2 arILiVDD~~~~~~~l~~~L~~~g~~v~~a~~~~eal~~~~-----------~~~~dlil~D~~~p~~~G~~~~~~ir~~   70 (139)
T d1w25a1           2 ARILVVDDIEANVRLLEAKLTAEYYEVSTAMDGPTALAMAA-----------RDLPDIILLDVMMPGMDGFTVCRKLKDD   70 (139)
T ss_dssp             CEEEEECSSTTHHHHHHHHHHHTTCEEEEESSHHHHHHHHH-----------HHCCSEEEEESCCSSSCHHHHHHHHHHS
T ss_pred             CEEEEEECCHHHHHHHHHHHHHCCCEEEEEccchhhhhhhh-----------cccceeeeeeccccCCCchHHHHHhhhc
Confidence            48999999999999999999999999999999999999994           4579999999999999999999999987


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      ....++|||++|+..+.....+++++|++|||.|||+.+
T Consensus        71 ~~~~~~piI~lt~~~~~~~~~~a~~~Ga~dyl~KP~~~~  109 (139)
T d1w25a1          71 PTTRHIPVVLITALDGRGDRIQGLESGASDFLTKPIDDV  109 (139)
T ss_dssp             TTTTTSCEEEEECSSCHHHHHHHHHHTCCEEEESSCCHH
T ss_pred             ccccCCCEEEEEcCCCHHHHHHHHHcCCCEEEECCCCHH
Confidence            767899999999999999999999999999999999854

>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=7.6e-27  Score=173.74  Aligned_cols=109  Identities=27%  Similarity=0.467  Sum_probs=99.3

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      .++|||||||++.++..++.+|+++||.+..+.||.+|++.+           . ..||+||+|+.||+|||++++++||
T Consensus         6 ~g~rILvVDD~~~~~~~l~~~L~~~G~~v~~a~~g~eal~~l-----------~-~~~dlillD~~mP~~dG~el~~~ir   73 (134)
T d1dcfa_           6 TGLKVLVMDENGVSRMVTKGLLVHLGCEVTTVSSNEECLRVV-----------S-HEHKVVFMDVCMPGVENYQIALRIH   73 (134)
T ss_dssp             TTCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHC-----------C-TTCSEEEEECCSSTTTTTHHHHHHH
T ss_pred             CCCEEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHh-----------h-cCCCeEEEEeccCCCchHHHHHHHH
Confidence            468999999999999999999999999999999999999987           2 3699999999999999999999999


Q ss_pred             hc---CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          172 ES---SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       172 ~~---~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      +.   ...+.+|||++|++.+.+...+++++|+++||.||++.+
T Consensus        74 ~~~~~~~~~~~~ii~lT~~~~~~~~~~~~~~G~~~~l~KP~~~~  117 (134)
T d1dcfa_          74 EKFTKQRHQRPLLVALSGNTDKSTKEKCMSFGLDGVLLKPVSLD  117 (134)
T ss_dssp             HHHC-CCSCCCEEEEEESCCSHHHHHHHHHTTCCEEEESSCCHH
T ss_pred             HhcccccCCCCeEEEEeCCCCHHHHHHHHHcCCCEEEECCCCHH
Confidence            63   234568899999999999999999999999999999854

>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=99.94  E-value=1.4e-26  Score=175.19  Aligned_cols=119  Identities=32%  Similarity=0.511  Sum_probs=103.7

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCC--EEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHH
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSC--KVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKI  170 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~--~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~i  170 (213)
                      ..+||||||++.++..++.+|++.|+  .|..+.||.+|++.+++....... .....||+||+|++||+|||++++++|
T Consensus         6 ~~~ILiVDD~~~~~~~l~~~L~~~g~~~~v~~a~~g~eAl~~l~~~~~~~~~-~~~~~pdlillD~~mP~~~G~el~~~i   84 (149)
T d1k66a_           6 TQPLLVVEDSDEDFSTFQRLLQREGVVNPIYRCITGDQALDFLYQTGSYCNP-DIAPRPAVILLDLNLPGTDGREVLQEI   84 (149)
T ss_dssp             TSCEEEECCCHHHHHHHHHHHHHTTBCSCEEEECSHHHHHHHHHTCCSSSCG-GGCCCCSEEEECSCCSSSCHHHHHHHH
T ss_pred             CCcEEEEECCHHHHHHHHHHHHHcCCceEEEEECChHHHHHHHHhhcccccc-ccccCCCeEEccccccCCCcHHHHHHH
Confidence            45799999999999999999999998  789999999999999653221100 123469999999999999999999999


Q ss_pred             HhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          171 KESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       171 r~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      |+....+++|||++|+..+.+...+++++|+++||.||++.+
T Consensus        85 r~~~~~~~ipiI~lT~~~~~~~~~~~~~~Ga~~~l~KP~~~~  126 (149)
T d1k66a_          85 KQDEVLKKIPVVIMTTSSNPKDIEICYSYSISSYIVKPLEID  126 (149)
T ss_dssp             TTSTTGGGSCEEEEESCCCHHHHHHHHHTTCSEEEECCSSHH
T ss_pred             HhccccCCCeEEEEeCCCCHHHHHHHHHCCCCEEEECCCCHH
Confidence            987767899999999999999999999999999999999754

>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=2.3e-26  Score=167.79  Aligned_cols=105  Identities=23%  Similarity=0.421  Sum_probs=98.5

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhc
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKES  173 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~  173 (213)
                      .|||||||++.++..+..+|++.||.|..+.++++|++.+           ....||+|++|+.||+++|+++++.+|..
T Consensus         2 ~rILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~~a~~~~-----------~~~~~dliilD~~mp~~~g~~~~~~~~~~   70 (120)
T d1zgza1           2 HHIVIVEDEPVTQARLQSYFTQEGYTVSVTASGAGLREIM-----------QNQSVDLILLDINLPDENGLMLTRALRER   70 (120)
T ss_dssp             CEEEEECSSHHHHHHHHHHHHHTTCEEEEESSHHHHHHHH-----------HHSCCSEEEEESCCSSSCHHHHHHHHHTT
T ss_pred             CEEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHH-----------HhcCCCEEeeehhhccchhHHHHHHHhcc
Confidence            4899999999999999999999999999999999999999           44579999999999999999999999864


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                         ..+|||++|+..+.....+++++|+++||.||++.+
T Consensus        71 ---~~~piI~lt~~~~~~~~~~a~~~Ga~dyl~KP~~~~  106 (120)
T d1zgza1          71 ---STVGIILVTGRSDRIDRIVGLEMGADDYVTKPLELR  106 (120)
T ss_dssp             ---CCCEEEEEESSCCHHHHHHHHHHTCSEEEESSCCHH
T ss_pred             ---CCCeEEEEEccCCHHHHHHHHHCCCCEEEECCCCHH
Confidence               578999999999999999999999999999999864

>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=99.94  E-value=2.8e-26  Score=168.17  Aligned_cols=108  Identities=19%  Similarity=0.362  Sum_probs=96.7

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcC-C-EEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISS-C-KVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g-~-~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      +|||||||++.++..++.+|+..| + .|..|.||.+|++.++           ...||+||+|+.||+|||++++++||
T Consensus         2 irILivDD~~~~~~~l~~~L~~~~~~~~v~~a~~g~~al~~~~-----------~~~~dlillD~~mP~~dG~e~~~~ir   70 (123)
T d1dz3a_           2 IKVCIADDNRELVSLLDEYISSQPDMEVIGTAYNGQDCLQMLE-----------EKRPDILLLDIIMPHLDGLAVLERIR   70 (123)
T ss_dssp             EEEEEECSCHHHHHHHHHHHHTSTTEEEEEEESSHHHHHHHHH-----------HHCCSEEEEESCCSSSCHHHHHHHHH
T ss_pred             cEEEEEeCCHHHHHHHHHHHHhCCCcEEEEEECCHHHHHHHHH-----------hcCCCEEEEcCCCCCCCHHHHHHHHH
Confidence            689999999999999999999876 3 4568999999999994           45799999999999999999999999


Q ss_pred             hcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCCC
Q 048660          172 ESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD  213 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~e  213 (213)
                      +... ...|||++|+..+.....+++++|+++||.||++.++
T Consensus        71 ~~~~-~~~~ii~~t~~~~~~~~~~a~~~Ga~~~l~KP~~~~~  111 (123)
T d1dz3a_          71 AGFE-HQPNVIMLTAFGQEDVTKKAVELGASYFILKPFDMEN  111 (123)
T ss_dssp             HHCS-SCCEEEEEEETTCHHHHHHHHHTTCEEEEECSSCCTT
T ss_pred             hcCC-CCCeEEEEECcCCHHHHHHHHHCCCCEEEECCCCHHH
Confidence            8642 3457999999999999999999999999999999875

>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=4.7e-27  Score=184.42  Aligned_cols=106  Identities=24%  Similarity=0.409  Sum_probs=98.6

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCEEE-EEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCKVT-AVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~v~-~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      ..|||||||++.+|..++.+|++.||.++ .|.||.+|++.+           ....||+||+|++||+|||+++++.||
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            47999999999999999999999999865 799999999999           445899999999999999999999999


Q ss_pred             hcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          172 ESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      +.   +.+|||++|++.+.+...+|+++|+++||.||++.+
T Consensus        72 ~~---~~~pIi~lTa~~~~~~~~~al~~Ga~~yl~KP~~~~  109 (190)
T d1s8na_          72 SK---RIAPIVVLTAFSQRDLVERARDAGAMAYLVKPFSIS  109 (190)
T ss_dssp             HT---TCSCEEEEEEGGGHHHHHTTGGGSCEEEEEESCCHH
T ss_pred             hc---CCCCEEEEeCCCCHHHHHHHHHcCCCEeccCCCCHH
Confidence            85   468999999999999999999999999999999864

>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=1.5e-26  Score=170.79  Aligned_cols=106  Identities=23%  Similarity=0.391  Sum_probs=100.1

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhc
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKES  173 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~  173 (213)
                      .+|||||||+.+++.+..+|+..||.|..+.++++|++.+           ....||+||+|+.||+++|+++++.+|+.
T Consensus         3 P~ILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~~al~~~-----------~~~~~dliilD~~mp~~~G~~~~~~i~~~   71 (128)
T d1yioa2           3 PTVFVVDDDMSVREGLRNLLRSAGFEVETFDCASTFLEHR-----------RPEQHGCLVLDMRMPGMSGIELQEQLTAI   71 (128)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHC-----------CTTSCEEEEEESCCSSSCHHHHHHHHHHT
T ss_pred             CEEEEEECCHHHHHHHHHHHHHcCCCccccccHHHHHHHH-----------HhcCCCEeehhhhcccchhHHHHHHHHhh
Confidence            4899999999999999999999999999999999999998           56689999999999999999999999987


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                        .+.+||+++|+..+.+...++++.|+++||.|||+.+
T Consensus        72 --~~~~~ii~lt~~~~~~~~~~a~~~Ga~dyl~KP~~~~  108 (128)
T d1yioa2          72 --SDGIPIVFITAHGDIPMTVRAMKAGAIEFLPKPFEEQ  108 (128)
T ss_dssp             --TCCCCEEEEESCTTSCCCHHHHHTTEEEEEESSCCHH
T ss_pred             --CCCCeEEEEEEECCHHHHHHHHHCCCCEEEECCCCHH
Confidence              5789999999999999999999999999999999864

>d1p2fa2 c.23.1.1 (A:1-120) Response regulator DrrB {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulator DrrB
species: Thermotoga maritima [TaxId: 2336]

Probab=99.93  E-value=9.1e-26  Score=164.78  Aligned_cols=103  Identities=24%  Similarity=0.339  Sum_probs=95.1

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhc
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKES  173 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~  173 (213)
                      .|||||||++.+++.++.+|++.|+ +.++.+|.+|++.             ...||+||+|+.||++||+++++++|+.
T Consensus         3 ~kILiVDDd~~~~~~l~~~L~~~g~-v~~~~~~~~al~~-------------~~~~dlillD~~mP~~~G~~~~~~lr~~   68 (120)
T d1p2fa2           3 WKIAVVDDDKNILKKVSEKLQQLGR-VKTFLTGEDFLND-------------EEAFHVVVLDVMLPDYSGYEICRMIKET   68 (120)
T ss_dssp             EEEEEECSCHHHHHHHHHHHTTTEE-EEEESSHHHHHHC-------------CSCCSEEEEESBCSSSBHHHHHHHHHHH
T ss_pred             CEEEEEECCHHHHHHHHHHHHhCCE-EEEECCHHHHHhc-------------CCCCCEEEEeCcccccchhHHHHHHhhc
Confidence            5899999999999999999999996 8889999999862             2369999999999999999999999987


Q ss_pred             CCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          174 SVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       174 ~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                        .+.+|||++|+..+.+...+++++|+++||.|||+.+
T Consensus        69 --~~~~~ii~it~~~~~~~~~~a~~~Ga~dyl~KP~~~~  105 (120)
T d1p2fa2          69 --RPETWVILLTLLSDDESVLKGFEAGADDYVTKPFNPE  105 (120)
T ss_dssp             --CTTSEEEEEESCCSHHHHHHHHHHTCSEEEESSCCHH
T ss_pred             --CCCCcEEEEecCCCHHHHHHHHHCCCCEEEECCCCHH
Confidence              5789999999999999999999999999999999864

>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=9.5e-26  Score=168.41  Aligned_cols=107  Identities=25%  Similarity=0.456  Sum_probs=98.5

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcC--CEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHH
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISS--CKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKI  170 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g--~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~i  170 (213)
                      .+|||||||++.+|..++.+|+..|  +.|..+.+|.+|++.++           ...||+||+|+.||++||++++++|
T Consensus         2 Pi~VLiVDD~~~~r~~l~~~L~~~~~~~~v~~a~~~~~al~~~~-----------~~~~DlvllD~~mP~~~G~el~~~i   70 (138)
T d1a04a2           2 PATILLIDDHPMLRTGVKQLISMAPDITVVGEASNGEQGIELAE-----------SLDPDLILLDLNMPGMNGLETLDKL   70 (138)
T ss_dssp             CEEEEEECSCHHHHHHHHHHHTTCTTEEEEEEESSHHHHHHHHH-----------HHCCSEEEEETTSTTSCHHHHHHHH
T ss_pred             CCEEEEECCCHHHHHHHHHHHHhCCCcEEEEEECCHHHHHHHHH-----------hcCCCEEEEecCCCCCCHHHHHHHH
Confidence            4699999999999999999999877  46778999999999984           4579999999999999999999999


Q ss_pred             HhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          171 KESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       171 r~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      |+.  .+.+|+|++|+..+.+...+++++|+++||.||++.+
T Consensus        71 r~~--~~~~~vivlt~~~~~~~~~~a~~~Ga~~yl~Kp~~~~  110 (138)
T d1a04a2          71 REK--SLSGRIVVFSVSNHEEDVVTALKRGADGYLLKDMEPE  110 (138)
T ss_dssp             HHS--CCCSEEEEEECCCCHHHHHHHHHTTCSEEEETTCCHH
T ss_pred             Hhh--CCCCCEEEEEEECCHHHHHHHHHcCCCEEEECCCCHH
Confidence            986  6789999999999999999999999999999999864

>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=99.93  E-value=6.7e-26  Score=172.23  Aligned_cols=108  Identities=20%  Similarity=0.284  Sum_probs=96.6

Q ss_pred             CccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           92 KELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        92 ~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      .+.|||||||++.++..+...|+..||.|.  .++.++++.+           ....||+||+|+.||++||+++++.||
T Consensus        12 ~~~rILiVDD~~~~~~~l~~~L~~~g~~v~--~~~~~~~~~~-----------~~~~~DlillD~~mP~~dG~el~~~ir   78 (153)
T d1w25a2          12 LGGRVLIVDDNERQAQRVAAELGVEHRPVI--ESDPEKAKIS-----------AGGPVDLVIVNAAAKNFDGLRFTAALR   78 (153)
T ss_dssp             CSCEEEEECSCHHHHHHHHHHHTTTSEEEE--ECCHHHHHHH-----------HHSSCSEEEEETTCSSSCHHHHHHHHH
T ss_pred             CCCeEEEEeCCHHHHHHHHHHHHHCCCEEE--EccHHHHHHH-----------hcCCCCEEEEECccccccchHHHHHHH
Confidence            356999999999999999999999999874  4556777766           345799999999999999999999999


Q ss_pred             hcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          172 ESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      +....+++|||++|+..+.....+++++|+++||.|||+.+
T Consensus        79 ~~~~~~~iPiI~lt~~~~~~~~~~a~~~Ga~d~l~KP~~~~  119 (153)
T d1w25a2          79 SEERTRQLPVLAMVDPDDRGRMVKALEIGVNDILSRPIDPQ  119 (153)
T ss_dssp             TSGGGTTCCEEEEECTTCHHHHHHHHHTTCCEEEESSCCHH
T ss_pred             hccccccceeEEeecCCCHHHHHHHHhcCcceEEECCCCHH
Confidence            87667899999999999999999999999999999999864

>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=99.91  E-value=1.6e-24  Score=162.08  Aligned_cols=105  Identities=24%  Similarity=0.323  Sum_probs=89.6

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcC--CEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHH
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISS--CKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKI  170 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g--~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~i  170 (213)
                      ++|||||||++.+++.++.+|+..|  +.|..+.||.+|++.+           ....||+||+|+.||+|||+++++.|
T Consensus         3 kirVLiVDD~~~~r~~l~~~L~~~g~~~~v~~a~~g~~al~~~-----------~~~~pDlvllDi~MP~~dG~e~~~~i   71 (140)
T d1a2oa1           3 KIRVLSVDDSALMRQIMTEIINSHSDMEMVATAPDPLVARDLI-----------KKFNPDVLTLDVEMPRMDGLDFLEKL   71 (140)
T ss_dssp             CEEEEEECSCHHHHHHHHHHHHTSTTEEEEEEESSHHHHHHHH-----------HHHCCSEEEEECCCSSSCHHHHHHHH
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHhCCCeEEEEEECCHHHHHHHH-----------HhcCCCEEEEcCCCCCCCHHHHHHHH
Confidence            5799999999999999999999998  4577899999999998           44579999999999999999999999


Q ss_pred             HhcCCCCCCcEEEEecCC-CHHHHHHHHHcCCCeeeeCCCC
Q 048660          171 KESSVFREVPVVIMSSED-VLTQIDSCLEEGAEEYIVKPVK  210 (213)
Q Consensus       171 r~~~~~~~~pII~lt~~~-~~~~~~~~~~~G~~~~L~KP~~  210 (213)
                      |+.  .+..+|++++... ..+...++++.|+++||.||+.
T Consensus        72 r~~--~~~~~i~i~~~~~~~~~~~~~al~~Ga~~yl~KP~~  110 (140)
T d1a2oa1          72 MRL--RPMPVVMVSSLTGKGSEVTLRALELGAIDFVTKPQL  110 (140)
T ss_dssp             HHS--SCCCEEEEECCTHHHHHHHHHHHHHTCCEEEECSSS
T ss_pred             HHh--CCCCcEEEEEecCCChHHHHHHHHcCCCEEEECCCC
Confidence            987  3455555555543 2356788999999999999975

>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=99.91  E-value=3e-25  Score=161.59  Aligned_cols=105  Identities=23%  Similarity=0.295  Sum_probs=90.7

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHh
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKE  172 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~  172 (213)
                      .+|||||||++.+++.+..+|+.+||.|..+.+|.+|++.+.          +...||+||+|+.||+++|++++++||+
T Consensus         2 p~rILvVdDd~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~----------~~~~~dliilD~~lp~~~G~el~~~ir~   71 (118)
T d2b4aa1           2 PFRVTLVEDEPSHATLIQYHLNQLGAEVTVHPSGSAFFQHRS----------QLSTCDLLIVSDQLVDLSIFSLLDIVKE   71 (118)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHTGG----------GGGSCSEEEEETTCTTSCHHHHHHHHTT
T ss_pred             CCEEEEEECCHHHHHHHHHHHHhcCCCeEEECCHHHHHHHHH----------hcCCCCEEEEeCCCCCCCHHHHHHHHHh
Confidence            479999999999999999999999999999999999999773          2346999999999999999999999998


Q ss_pred             cCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCC
Q 048660          173 SSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLS  212 (213)
Q Consensus       173 ~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~  212 (213)
                      .  .+++|||++|+..+..  .++...|+ |||.|||+.+
T Consensus        72 ~--~~~~pii~lt~~~~~~--~~~~~~~~-dyl~KP~~~~  106 (118)
T d2b4aa1          72 Q--TKQPSVLILTTGRHEL--IESSEHNL-SYLQKPFAIS  106 (118)
T ss_dssp             S--SSCCEEEEEESCC--C--CCCSSSCE-EEEESSCCHH
T ss_pred             c--CCCCcEEEEECCccHH--HHHhhcCC-CEEECCCCHH
Confidence            6  5789999999976543  34556666 8999999864

>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=99.87  E-value=7.4e-23  Score=159.55  Aligned_cols=105  Identities=13%  Similarity=0.107  Sum_probs=93.2

Q ss_pred             CCccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHH
Q 048660           91 SKELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKI  170 (213)
Q Consensus        91 ~~~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~i  170 (213)
                      .+.+|||||||++.++..+...|+++||.|..+.++.+|++               ..||+||+|++||+++|..+.+..
T Consensus         9 l~~~~iLvvdd~~~~~~~l~~~L~~~G~~v~~~~~~~~al~---------------~~~Dlvl~D~~mp~~~~~~~~~~~   73 (189)
T d1qo0d_           9 LRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAFD---------------VPVDVVFTSIFQNRHHDEIAALLA   73 (189)
T ss_dssp             GGGCEEEEESCTTHHHHHHHHHHHHHTCEEEEECSCCSSCS---------------SCCSEEEEECCSSTHHHHHHHHHH
T ss_pred             ccCCEEEEEeCCHHHHHHHHHHHHHcCCcceecCCHHHhcc---------------CCCCEEEEcCCCCCcHHHHHHHHH
Confidence            35689999999999999999999999999999999887763               269999999999998887666554


Q ss_pred             HhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeeeCCCCCCC
Q 048660          171 KESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIVKPVKLSD  213 (213)
Q Consensus       171 r~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~KP~~~~e  213 (213)
                      +.   .+.+|||++|++.+.+...++++.|+++||.|||+.++
T Consensus        74 ~~---~p~~pvI~lta~~~~~~~~~al~~Ga~~yL~KP~~~~~  113 (189)
T d1qo0d_          74 AG---TPRTTLVALVEYESPAVLSQIIELECHGVITQPLDAHR  113 (189)
T ss_dssp             HS---CTTCEEEEEECCCSHHHHHHHHHHTCSEEEESSCCGGG
T ss_pred             Hc---CCCCCEEEEeccchHHHHHHHHHcCCcEEEEecchhhH
Confidence            43   57899999999999999999999999999999998753

>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=95.62  E-value=0.044  Score=39.92  Aligned_cols=103  Identities=13%  Similarity=0.079  Sum_probs=74.8

Q ss_pred             CCccEEEEE----eCCHHHHHHHHHHHhhcCCEEEEE---cCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCC--
Q 048660           91 SKELHVLAV----DDSYVDRKLIERLLQISSCKVTAV---ESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGM--  161 (213)
Q Consensus        91 ~~~~~ILvV----dD~~~~~~~l~~~L~~~g~~v~~a---~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~--  161 (213)
                      .++.+||+.    |-+..-...+..+|+..||+|...   .+.++..+.+.           ...+|+|.+...+...  
T Consensus        35 gr~pkVlla~~g~D~Hd~G~~~va~~l~~~G~eVi~lg~~~~~e~iv~aa~-----------~~~advI~iSs~~~~~~~  103 (168)
T d7reqa2          35 GRRPRILLAKMGQDGHDRGQKVIATAYADLGFDVDVGPLFQTPEETARQAV-----------EADVHVVGVSSLAGGHLT  103 (168)
T ss_dssp             SSCCEEEEECBTTCCCCHHHHHHHHHHHHTTCEEEECCTTBCHHHHHHHHH-----------HHTCSEEEEEECSSCHHH
T ss_pred             CCCCeEEEEeCCccHHHHHHHHHHHHHHhCCcceecCCCcCcHHHHHHHHH-----------ccCCCEEEEecCcccchH
Confidence            456789888    557777889999999999999864   46788888773           4478999988766542  


Q ss_pred             CHHHHHHHHHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeee
Q 048660          162 TGYELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIV  206 (213)
Q Consensus       162 ~G~e~~~~ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~  206 (213)
                      .--++++.|++.. ..+++| ++.+....++...+.+.|+++++.
T Consensus       104 ~~~~l~~~L~~~g-~~~v~V-ivGG~ip~~d~~~l~~~Gv~~iF~  146 (168)
T d7reqa2         104 LVPALRKELDKLG-RPDILI-TVGGVIPEQDFDELRKDGAVEIYT  146 (168)
T ss_dssp             HHHHHHHHHHHTT-CTTSEE-EEEESCCGGGHHHHHHHTEEEEEC
T ss_pred             HHHHHHHHHHhcC-CCCeEE-EEeCCCCHHHHHHHHhCCCCEEEC
Confidence            3445677777764 345554 466665677788889999988653

>d1ccwa_ c.23.6.1 (A:) Glutamate mutase, small subunit {Clostridium cochlearium [TaxId: 1494]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: Cobalamin (vitamin B12)-binding domain
family: Cobalamin (vitamin B12)-binding domain
domain: Glutamate mutase, small subunit
species: Clostridium cochlearium [TaxId: 1494]

Probab=95.47  E-value=0.042  Score=38.62  Aligned_cols=103  Identities=10%  Similarity=0.068  Sum_probs=69.7

Q ss_pred             ccEEEE--E--eCCHHHHHHHHHHHhhcCCEEEE---EcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCC--H
Q 048660           93 ELHVLA--V--DDSYVDRKLIERLLQISSCKVTA---VESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMT--G  163 (213)
Q Consensus        93 ~~~ILv--V--dD~~~~~~~l~~~L~~~g~~v~~---a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~--G  163 (213)
                      +.+||+  +  |-+..-..++..+|+..||+|..   ....++.++.+           ....+|+|.+...|....  .
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            346766  3  45667778899999999998874   45788888887           345789999999887632  2


Q ss_pred             HHHHHHHHhcCCCCCCcEEEEecC----C-CHHHHHHHHHcCCCeeeeC
Q 048660          164 YELLKKIKESSVFREVPVVIMSSE----D-VLTQIDSCLEEGAEEYIVK  207 (213)
Q Consensus       164 ~e~~~~ir~~~~~~~~pII~lt~~----~-~~~~~~~~~~~G~~~~L~K  207 (213)
                      .++++.+|+.. ..++||++=-+-    . ......++.+.|++..+..
T Consensus        72 ~~~~~~l~~~~-~~~i~iivGG~~~~~~~~~~~~~~~l~~~Gv~~if~~  119 (137)
T d1ccwa_          72 KGLRQKCDEAG-LEGILLYVGGNIVVGKQHWPDVEKRFKDMGYDRVYAP  119 (137)
T ss_dssp             TTHHHHHHHTT-CTTCEEEEEESCSSSSCCHHHHHHHHHHTTCSEECCT
T ss_pred             HHHHHHHHHhc-cCCCEEEEeCCcCCCccccHHHHHHHHHcCCCEEECC
Confidence            23566777653 456776643322    1 2445666678899887643

>d3bula2 c.23.6.1 (A:741-896) Methionine synthase, C-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: Cobalamin (vitamin B12)-binding domain
family: Cobalamin (vitamin B12)-binding domain
domain: Methionine synthase, C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=91.11  E-value=0.74  Score=32.57  Aligned_cols=84  Identities=11%  Similarity=0.188  Sum_probs=59.0

Q ss_pred             EEEEE----eCCHHHHHHHHHHHhhcCCEEEEE---cCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCC-CC-HHH
Q 048660           95 HVLAV----DDSYVDRKLIERLLQISSCKVTAV---ESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPG-MT-GYE  165 (213)
Q Consensus        95 ~ILvV----dD~~~~~~~l~~~L~~~g~~v~~a---~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~-~~-G~e  165 (213)
                      +|++.    |-+..=..++..+|+..||+|...   ...++.++.+           ....+|+|.+...|.. +. -.+
T Consensus         8 kivi~tv~gD~HdiG~~iv~~~l~~~G~~Vi~LG~~~p~e~~~~~~-----------~~~~~d~i~lS~l~~~~~~~~~~   76 (156)
T d3bula2           8 KMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDLGVMVPAEKILRTA-----------KEVNADLIGLSGLITPSLDEMVN   76 (156)
T ss_dssp             EEEEEEBTTCCCCHHHHHHHHHHHTTTCEEEECCSSBCHHHHHHHH-----------HHHTCSEEEEECCSTHHHHHHHH
T ss_pred             EEEEEeeCCChhhHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHH-----------HhhCCCEEEEecccccchHHHHH
Confidence            56555    556777788899999999998864   4577788877           3457999999998875 33 345


Q ss_pred             HHHHHHhcCCCCCCcEEEEecCCCHH
Q 048660          166 LLKKIKESSVFREVPVVIMSSEDVLT  191 (213)
Q Consensus       166 ~~~~ir~~~~~~~~pII~lt~~~~~~  191 (213)
                      +++.+++.  ..+.|+++-.+.....
T Consensus        77 ~~~~l~~~--g~~~~vivGG~~~~~~  100 (156)
T d3bula2          77 VAKEMERQ--GFTIPLLIGGATTSKA  100 (156)
T ss_dssp             HHHHHHHT--TCCSCEEEESTTCCHH
T ss_pred             HHHHHHhc--cccceEEEecccccch
Confidence            67777776  3467766554444433

>d1qpoa1 c.1.17.1 (A:117-285) Quinolinic acid phosphoribosyltransferase (Nicotinate-nucleotide pyrophosphorylase, NadC), C-terminal domain {Mycobacterium tuberculosis [TaxId: 1773]}

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: Nicotinate/Quinolinate PRTase C-terminal domain-like
family: NadC C-terminal domain-like
domain: Quinolinic acid phosphoribosyltransferase (Nicotinate-nucleotide pyrophosphorylase, NadC), C-terminal domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=90.81  E-value=0.4  Score=34.60  Aligned_cols=94  Identities=15%  Similarity=0.072  Sum_probs=62.9

Q ss_pred             EEEEEeCCHHHHHHHHHHHh----hcC--CEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHH
Q 048660           95 HVLAVDDSYVDRKLIERLLQ----ISS--CKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLK  168 (213)
Q Consensus        95 ~ILvVdD~~~~~~~l~~~L~----~~g--~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~  168 (213)
                      .|||-|++-.....+...++    ...  ...+.+++.+++.+.+.            ..+|+|++| +|...+--++++
T Consensus        52 ~ilikdNHi~~~g~i~~~i~~~k~~~~~~~I~VEv~s~~q~~~a~~------------~~~diImLD-N~sp~~~k~~v~  118 (169)
T d1qpoa1          52 AALIKDNHVAAAGSVVDALRAVRNAAPDLPCEVEVDSLEQLDAVLP------------EKPELILLD-NFAVWQTQTAVQ  118 (169)
T ss_dssp             SEEECHHHHHHHSSHHHHHHHHHHHCTTSCEEEEESSHHHHHHHGG------------GCCSEEEEE-TCCHHHHHHHHH
T ss_pred             eEEeehhHHhHhcchhhhhhhhhhhcCCCceEEEeccHHHhhhhhh------------cCCcEEEec-CcChHhHHHHHH
Confidence            47777776555444444442    222  25567899999999873            257999999 343334445566


Q ss_pred             HHHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCee
Q 048660          169 KIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEY  204 (213)
Q Consensus       169 ~ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~  204 (213)
                      .++..   ....++-.|+.-+.+....+...|+|-.
T Consensus       119 ~~~~~---~~~i~lEaSGgI~~~ni~~ya~~GvD~I  151 (169)
T d1qpoa1         119 RRDSR---APTVMLESSGGLSLQTAATYAETGVDYL  151 (169)
T ss_dssp             HHHHH---CTTCEEEEESSCCTTTHHHHHHTTCSEE
T ss_pred             Hhhcc---CCeeEEEEeCCCCHHHHHHHHHcCCCEE
Confidence            66654   2335777899999999999999999754

>d1dxea_ c.1.12.5 (A:) 2-dehydro-3-deoxy-galactarate aldolase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: Phosphoenolpyruvate/pyruvate domain
family: HpcH/HpaI aldolase
domain: 2-dehydro-3-deoxy-galactarate aldolase
species: Escherichia coli [TaxId: 562]

Probab=90.13  E-value=2.3  Score=32.29  Aligned_cols=90  Identities=10%  Similarity=0.052  Sum_probs=62.0

Q ss_pred             HHHHHHhhcCCE--EEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHhcCCCCCCcEEEEe
Q 048660          108 LIERLLQISSCK--VTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKESSVFREVPVVIMS  185 (213)
Q Consensus       108 ~l~~~L~~~g~~--v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~~~~~~~~pII~lt  185 (213)
                      .++..|++-...  ++.........+.+           ....||.|++|+.....|--++...++.... ..++.++=.
T Consensus         6 ~lk~~l~~g~~~~G~~~~~~~p~~~ei~-----------a~~G~Dfv~iD~EHg~~~~~~~~~~i~a~~~-~g~~~~VRv   73 (253)
T d1dxea_           6 KFKAALAAKQVQIGCWSALSNPISTEVL-----------GLAGFDWLVLDGEHAPNDISTFIPQLMALKG-SASAPVVRV   73 (253)
T ss_dssp             HHHHHHHTTCCEEEEEECSCSHHHHHHH-----------TTSCCSEEEEESSSSSCCHHHHHHHHHHTTT-CSSEEEEEC
T ss_pred             HHHHHHHCCCCEEEEEecCCCHHHHHHH-----------HcCCCCEEEEecccCCCChhHHHHHHHHHhc-cCCCceecC
Confidence            355556543222  22333445566666           3446999999999988888888888887643 345555555


Q ss_pred             cCCCHHHHHHHHHcCCCeeeeCCC
Q 048660          186 SEDVLTQIDSCLEEGAEEYIVKPV  209 (213)
Q Consensus       186 ~~~~~~~~~~~~~~G~~~~L~KP~  209 (213)
                      ...+.....+++++|+++.+.--+
T Consensus        74 p~~~~~~i~~~LD~Ga~GIivP~v   97 (253)
T d1dxea_          74 PTNEPVIIKRLLDIGFYNFLIPFV   97 (253)
T ss_dssp             SSSCHHHHHHHHHTTCCEEEESCC
T ss_pred             CCCCHHHHHHHHhcCccEEEeccc
Confidence            567889999999999999987544

>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=89.36  E-value=0.89  Score=32.31  Aligned_cols=101  Identities=9%  Similarity=0.093  Sum_probs=66.1

Q ss_pred             CccEEEEE----eCCHHHHHHHHHHHhhcC---------CEEEE---EcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEe
Q 048660           92 KELHVLAV----DDSYVDRKLIERLLQISS---------CKVTA---VESGTRALQYLGLDGEQSNVGFDALKVNLIITD  155 (213)
Q Consensus        92 ~~~~ILvV----dD~~~~~~~l~~~L~~~g---------~~v~~---a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D  155 (213)
                      ++.+|++.    |-+..=.+.+..+|+..|         |+|.-   -...++.++.+           .+..+|+|-+.
T Consensus        18 r~~~vv~~~~g~D~HdiG~~iv~~~l~~~G~~~~~~~~~~eVi~LG~~vp~e~~v~~a-----------~e~~~d~VglS   86 (160)
T d1xrsb1          18 RKIVVVGASTGTDAHTVGIDAIMNMKGYAGHYGLERYEMIDAYNLGSQVANEDFIKKA-----------VELEADVLLVS   86 (160)
T ss_dssp             SCEEEEEEEBTTCCCCHHHHHHHSTTCBTTBCCGGGCTTEEEEECCSSBCHHHHHHHH-----------HHTTCSEEEEE
T ss_pred             CCcEEEEEEeCCcHHHHHHHHHHHHHHHcCCcccccccceEEEeCCCCCCHHHHHHHH-----------HhcCCCEEEEe
Confidence            34566655    446666777888898888         77763   34677888877           45689999999


Q ss_pred             CCCCCCCH-----HHHHHHHHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeee
Q 048660          156 YTMPGMTG-----YELLKKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIV  206 (213)
Q Consensus       156 ~~mp~~~G-----~e~~~~ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~  206 (213)
                      ..|....+     .++++.+++.....+++ |++-+..-.  ...+.+.|+|.|..
T Consensus        87 ~l~t~~~~h~~~~~~~i~~l~~~g~~d~v~-vivGG~~~~--~~~a~~~GaD~~f~  139 (160)
T d1xrsb1          87 QTVTQKNVHIQNMTHLIELLEAEGLRDRFV-LLCGGPRIN--NEIAKELGYDAGFG  139 (160)
T ss_dssp             CCCCTTSHHHHHHHHHHHHHHHTTCGGGSE-EEEECTTCC--HHHHHTTTCSEEEC
T ss_pred             ecccccchhHHHHHHHHHHHHHcCCCCceE-EEEcCCCCC--HHHHHHcCCCEEcC
Confidence            98876432     35677777754222344 445554332  23466889998864

>d1r8ja2 c.23.1.5 (A:1-135) N-terminal domain of the circadian clock protein KaiA {Synechococcus elongatus [TaxId: 32046]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: N-terminal domain of the circadian clock protein KaiA
domain: N-terminal domain of the circadian clock protein KaiA
species: Synechococcus elongatus [TaxId: 32046]

Probab=88.78  E-value=2.5  Score=29.00  Aligned_cols=82  Identities=13%  Similarity=0.133  Sum_probs=62.7

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHHh
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIKE  172 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~  172 (213)
                      .+.|-+.=-++.....++.+|...-|.+....++++.++.+++         ..+++|++++--.  +.+-..+..++++
T Consensus         4 ~LtI~l~l~s~~L~q~~~q~L~~dRY~l~~~~s~~ef~~~le~---------~~e~iDcLVl~~~--~~~l~~l~~qL~~   72 (135)
T d1r8ja2           4 QIAICIWVESTAILQDCQRALSADRYQLQVCESGEMLLEYAQT---------HRDQIDCLILVAA--NPSFRAVVQQLCF   72 (135)
T ss_dssp             CEEEEEECCCHHHHHHHHHHTCSTTEEEEEECSHHHHHHHHHH---------STTSCSEEEEETT--STTHHHHHHHHHH
T ss_pred             eEEEEEEeCCHHHHHHHHHhcCCCceEEEEcCCHHHHHHHHHh---------CcccCCEEEEEec--CCccHHHHHHHHh
Confidence            4567677778888999999999888999999999999999976         4557999876322  2344556778887


Q ss_pred             cCCCCCCcEEEEecC
Q 048660          173 SSVFREVPVVIMSSE  187 (213)
Q Consensus       173 ~~~~~~~pII~lt~~  187 (213)
                      .  .--.|+|++...
T Consensus        73 ~--GlLlPaViv~~~   85 (135)
T d1r8ja2          73 E--GVVVPAIVVGDR   85 (135)
T ss_dssp             T--TCCCCEEEESCC
T ss_pred             c--CccccEEEEecC
Confidence            6  457899988544

>d1susa1 c.66.1.1 (A:21-247) Caffeoyl-CoA O-methyltransferase {Alfalfa (Medicago sativa) [TaxId: 3879]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: COMT-like
domain: Caffeoyl-CoA O-methyltransferase
species: Alfalfa (Medicago sativa) [TaxId: 3879]

Probab=88.42  E-value=1.9  Score=32.24  Aligned_cols=101  Identities=14%  Similarity=0.080  Sum_probs=64.8

Q ss_pred             HHHHhhhhhhcccCCCcchhhhhhhhcCCccEEEEEeCCHHHHHHHHHHHhhcCC---EEEEEcCHHHHHHHhhhcCCCC
Q 048660           64 QRLVKEKKFKETNRGFPFWAMATVAECSKELHVLAVDDSYVDRKLIERLLQISSC---KVTAVESGTRALQYLGLDGEQS  140 (213)
Q Consensus        64 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ILvVdD~~~~~~~l~~~L~~~g~---~v~~a~~g~eal~~l~~~~~~~  140 (213)
                      .+..+++..-+.+.+....+..........-+|.-+|-++......+..+++.|+   ......+..+.+..+.....  
T Consensus        55 ~~~~~~k~iLEiGT~~GyStl~la~al~~~g~v~tie~~~~~~~~A~~~~~~~g~~~~i~~~~g~a~~~L~~l~~~~~--  132 (227)
T d1susa1          55 LKLINAKNTMEIGVYTGYSLLATALAIPEDGKILAMDINKENYELGLPVIKKAGVDHKIDFREGPALPVLDEMIKDEK--  132 (227)
T ss_dssp             HHHHTCCEEEEECCGGGHHHHHHHHHSCTTCEEEEEESCCHHHHHHHHHHHHTTCGGGEEEEESCHHHHHHHHHHCGG--
T ss_pred             HHhcCCCcEEEecchhhhhHHHHHhhCCCCcEEEEEeccchhHHHHHHHHHHhccccceeeeehHHHHHHHHHHhccc--
Confidence            3444555566666655444444333344456999999999999999999998887   33456788888876632211  


Q ss_pred             CCCCCCCceeEEEEeCCCCCCCHHHHHHHHHh
Q 048660          141 NVGFDALKVNLIITDYTMPGMTGYELLKKIKE  172 (213)
Q Consensus       141 ~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir~  172 (213)
                          ....||+|++|..=..  -....+.+..
T Consensus       133 ----~~~~fD~iFiDa~k~~--y~~~~e~~~~  158 (227)
T d1susa1         133 ----NHGSYDFIFVDADKDN--YLNYHKRLID  158 (227)
T ss_dssp             ----GTTCBSEEEECSCSTT--HHHHHHHHHH
T ss_pred             ----cCCceeEEEeccchhh--hHHHHHHHHh
Confidence                2347999999975433  3334444443

>d1id1a_ c.2.1.9 (A:) Rck domain from putative potassium channel Kch {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: NAD(P)-binding Rossmann-fold domains
superfamily: NAD(P)-binding Rossmann-fold domains
family: Potassium channel NAD-binding domain
domain: Rck domain from putative potassium channel Kch
species: Escherichia coli [TaxId: 562]

Probab=88.30  E-value=2.1  Score=29.37  Aligned_cols=98  Identities=9%  Similarity=-0.003  Sum_probs=59.3

Q ss_pred             ccEEEEEeCCHHHHHHHHHHHhhcCCEEEEEc-CHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           93 ELHVLAVDDSYVDRKLIERLLQISSCKVTAVE-SGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        93 ~~~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~-~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      +..|.|||.++.........+...|+.+.... .-.+.|+.+           .-...+.+++-..-. ..-..++..+|
T Consensus        26 ~~~v~vId~d~~~~~~~~~~~~~~~~~vi~Gd~~d~~~L~~a-----------~i~~a~~vi~~~~~d-~~n~~~~~~~r   93 (153)
T d1id1a_          26 GQNVTVISNLPEDDIKQLEQRLGDNADVIPGDSNDSSVLKKA-----------GIDRCRAILALSDND-ADNAFVVLSAK   93 (153)
T ss_dssp             TCCEEEEECCCHHHHHHHHHHHCTTCEEEESCTTSHHHHHHH-----------TTTTCSEEEECSSCH-HHHHHHHHHHH
T ss_pred             CCCEEEEeccchhHHHHHHHhhcCCcEEEEccCcchHHHHHh-----------ccccCCEEEEccccH-HHHHHHHHHHH
Confidence            45788888877554444444445688777543 234455555           223466777654322 23445566677


Q ss_pred             hcCCCCCCcEEEEecCCCHHHHHHHHHcCCCeeee
Q 048660          172 ESSVFREVPVVIMSSEDVLTQIDSCLEEGAEEYIV  206 (213)
Q Consensus       172 ~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~~L~  206 (213)
                      +.  .+..++|+.+..  .+....+.++|++..+.
T Consensus        94 ~~--~~~~~iia~~~~--~~~~~~l~~~Gad~vi~  124 (153)
T d1id1a_          94 DM--SSDVKTVLAVSD--SKNLNKIKMVHPDIILS  124 (153)
T ss_dssp             HH--TSSSCEEEECSS--GGGHHHHHTTCCSEEEC
T ss_pred             Hh--CCCCceEEEEcC--HHHHHHHHHCCCCEEEC
Confidence            65  567788877654  45666778899986654

>d2avda1 c.66.1.1 (A:44-262) COMT domain-containing protein 1, COMTD1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: COMT-like
domain: COMT domain-containing protein 1, COMTD1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.03  E-value=3.1  Score=30.68  Aligned_cols=88  Identities=17%  Similarity=0.157  Sum_probs=59.6

Q ss_pred             HHHHhhhhhhcccCCCcchhhhhhhhcCCccEEEEEeCCHHHHHHHHHHHhhcCC--EE-EEEcCHHHHHHHhhhcCCCC
Q 048660           64 QRLVKEKKFKETNRGFPFWAMATVAECSKELHVLAVDDSYVDRKLIERLLQISSC--KV-TAVESGTRALQYLGLDGEQS  140 (213)
Q Consensus        64 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ILvVdD~~~~~~~l~~~L~~~g~--~v-~~a~~g~eal~~l~~~~~~~  140 (213)
                      .+..+.+..-+.+.+....+..........-+|.-+|-++......+..+++.|+  .+ ....+..+.+..+....   
T Consensus        55 ~~~~~~k~vLEiGt~~GyStl~~a~al~~~g~i~tie~~~~~~~~A~~~~~~ag~~~~i~~~~Gda~e~l~~~~~~~---  131 (219)
T d2avda1          55 ARLIQAKKALDLGTFTGYSALALALALPADGRVVTCEVDAQPPELGRPLWRQAEAEHKIDLRLKPALETLDELLAAG---  131 (219)
T ss_dssp             HHHTTCCEEEEECCTTSHHHHHHHTTSCTTCEEEEEESCSHHHHHHHHHHHHTTCTTTEEEEESCHHHHHHHHHHTT---
T ss_pred             HHccCCCeEEEEechhhHHHHHHHHhCCCCceEEEEeechhHHHHHHHHHHhcCccceEEEEEeehhhcchhhhhhc---
Confidence            3444556666666665544444444444456999999999999999999998875  33 35578778776553322   


Q ss_pred             CCCCCCCceeEEEEeCCC
Q 048660          141 NVGFDALKVNLIITDYTM  158 (213)
Q Consensus       141 ~~~~~~~~~dlil~D~~m  158 (213)
                          ....||+|++|..=
T Consensus       132 ----~~~~fD~ifiD~dk  145 (219)
T d2avda1         132 ----EAGTFDVAVVDADK  145 (219)
T ss_dssp             ----CTTCEEEEEECSCS
T ss_pred             ----ccCCccEEEEeCCH
Confidence                34579999999743

>d1kzyc2 c.15.1.4 (C:1867-1972) 53BP1 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: BRCT domain
superfamily: BRCT domain
family: 53BP1
domain: 53BP1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.03  E-value=0.12  Score=34.38  Aligned_cols=71  Identities=24%  Similarity=0.299  Sum_probs=45.8

Q ss_pred             CccEEEEEeCCH-HHHHHHHHHHhhcCCEEEEE-cCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHH
Q 048660           92 KELHVLAVDDSY-VDRKLIERLLQISSCKVTAV-ESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKK  169 (213)
Q Consensus        92 ~~~~ILvVdD~~-~~~~~l~~~L~~~g~~v~~a-~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~  169 (213)
                      +++|||++-|.. .+++.-..+|...|..++.. ....            ...+.....+|++++|-.+|.    ++.+.
T Consensus         4 ~~l~vl~vs~~~~~F~e~Ws~IL~~~Ga~vV~~~~~~~------------~~sd~~~~~~DVvvTD~scp~----~vl~~   67 (106)
T d1kzyc2           4 QNLKVLLVSDQQQNFLELWSEILMTGGAASVKQHHSSA------------HNKDIALGVFDVVVTDPSCPA----SVLKC   67 (106)
T ss_dssp             TTCEEEEEESCTTTTHHHHHHHHHHTTCSEEEEEESSS------------SCCCSCGGGCSEEEECTTCCH----HHHHH
T ss_pred             cceEEEEEecccccHHHHHHHHHHhCCceEeeccccch------------hhccCccccccEEEeCCCCCH----HHHHH
Confidence            468999998854 57999999999999865432 2210            001113457999999998886    34444


Q ss_pred             HHhcCCCCCCcEE
Q 048660          170 IKESSVFREVPVV  182 (213)
Q Consensus       170 ir~~~~~~~~pII  182 (213)
                      ..+.    ++|++
T Consensus        68 a~~~----~ipvV   76 (106)
T d1kzyc2          68 AEAL----QLPVV   76 (106)
T ss_dssp             HHHH----TCCEE
T ss_pred             HHHc----CCcEe
Confidence            4332    56665

>d2cl5a1 c.66.1.1 (A:3-216) Catechol O-methyltransferase, COMT {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: COMT-like
domain: Catechol O-methyltransferase, COMT
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=88.02  E-value=1.7  Score=32.07  Aligned_cols=85  Identities=12%  Similarity=0.064  Sum_probs=56.5

Q ss_pred             HHHhhhhhhcccCCCcchhhhhhhhcCCccEEEEEeCCHHHHHHHHHHHhhcCC--EE-EEEcCHHHHHHHhhhcCCCCC
Q 048660           65 RLVKEKKFKETNRGFPFWAMATVAECSKELHVLAVDDSYVDRKLIERLLQISSC--KV-TAVESGTRALQYLGLDGEQSN  141 (213)
Q Consensus        65 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ILvVdD~~~~~~~l~~~L~~~g~--~v-~~a~~g~eal~~l~~~~~~~~  141 (213)
                      +..+++..-+.+.+....+..........-+|..+|-++...+..+..++..|+  .| ....+..+.+..+....    
T Consensus        53 ~~~kpk~ILEiGt~~G~Sti~la~al~~~g~v~sid~~~~~~~~a~~~~~~~gl~~~i~l~~Gd~~e~l~~l~~~~----  128 (214)
T d2cl5a1          53 REYSPSLVLELGAYCGYSAVRMARLLQPGARLLTMEMNPDYAAITQQMLNFAGLQDKVTILNGASQDLIPQLKKKY----  128 (214)
T ss_dssp             HHHCCSEEEEECCTTSHHHHHHHTTCCTTCEEEEEESCHHHHHHHHHHHHHHTCGGGEEEEESCHHHHGGGHHHHS----
T ss_pred             HhhCCCEEEEEccCchhHHHHHHHhCCCccEEEEEeccHHHHHHHHHHHHHcCCCccceeeeccccccccchhhcc----
Confidence            344555566666655444333333334557999999999999999999998886  23 45677777766553221    


Q ss_pred             CCCCCCceeEEEEeC
Q 048660          142 VGFDALKVNLIITDY  156 (213)
Q Consensus       142 ~~~~~~~~dlil~D~  156 (213)
                         ....+|+|++|.
T Consensus       129 ---~~~~~D~ifiD~  140 (214)
T d2cl5a1         129 ---DVDTLDMVFLDH  140 (214)
T ss_dssp             ---CCCCEEEEEECS
T ss_pred             ---cccccceeeecc
Confidence               234799999994

>d1o4ua1 c.1.17.1 (A:104-273) Quinolinic acid phosphoribosyltransferase (Nicotinate-nucleotide pyrophosphorylase, NadC), C-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: Nicotinate/Quinolinate PRTase C-terminal domain-like
family: NadC C-terminal domain-like
domain: Quinolinic acid phosphoribosyltransferase (Nicotinate-nucleotide pyrophosphorylase, NadC), C-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=85.46  E-value=0.38  Score=34.77  Aligned_cols=93  Identities=16%  Similarity=0.093  Sum_probs=61.6

Q ss_pred             EEEEEeCCHHHHHHHHHHHhh----cC---CEEEEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHH
Q 048660           95 HVLAVDDSYVDRKLIERLLQI----SS---CKVTAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELL  167 (213)
Q Consensus        95 ~ILvVdD~~~~~~~l~~~L~~----~g---~~v~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~  167 (213)
                      .|||-|++-.....+...++.    .+   ...+.+++.+++++.+.            ..+|+|++| +|..-+--++.
T Consensus        50 ~ilikdNHi~~~g~~~~~~~~~~~~~~~~~~I~VEv~~~~e~~~a~~------------~g~d~i~LD-n~~pe~~k~~~  116 (170)
T d1o4ua1          50 CVMIKDNHLKMYGSAERAVQEVRKIIPFTTKIEVEVENLEDALRAVE------------AGADIVMLD-NLSPEEVKDIS  116 (170)
T ss_dssp             CEEECHHHHHHHSSHHHHHHHHHTTSCTTSCEEEEESSHHHHHHHHH------------TTCSEEEEE-SCCHHHHHHHH
T ss_pred             ceEEcccHHHHhccHHHHHHHHHhhCCCCceEEEEeCcHHHHHHHHh------------cCccEEEEc-CcChhhHhHHH
Confidence            477777665554444444432    23   24568999999999873            257999999 33322334455


Q ss_pred             HHHHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCCe
Q 048660          168 KKIKESSVFREVPVVIMSSEDVLTQIDSCLEEGAEE  203 (213)
Q Consensus       168 ~~ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~~  203 (213)
                      +.++..  .+. ..+..++.-+.+....+.+.|+|-
T Consensus       117 ~~lk~~--~~~-i~lEaSGGI~~~ni~~~a~~GVD~  149 (170)
T d1o4ua1         117 RRIKDI--NPN-VIVEVSGGITEENVSLYDFETVDV  149 (170)
T ss_dssp             HHHHHH--CTT-SEEEEEECCCTTTGGGGCCTTCCE
T ss_pred             HHHHhh--CCc-EEEEEECCCCHHHHHHHHHcCCCE
Confidence            667665  233 567788888888888888899874

>d1i7qb_ c.23.16.1 (B:) Anthranilate synthase GAT subunit, TrpG {Serratia marcescens [TaxId: 615]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: Class I glutamine amidotransferase-like
family: Class I glutamine amidotransferases (GAT)
domain: Anthranilate synthase GAT subunit, TrpG
species: Serratia marcescens [TaxId: 615]

Probab=84.41  E-value=0.79  Score=33.23  Aligned_cols=90  Identities=11%  Similarity=0.153  Sum_probs=51.6

Q ss_pred             EEEEEeCCHHHHHHHHHHHhhcCCEEEEEcC---HHHHHHHhhhcCCCCCCCCCCCceeEEEEeCC--CCCCCHHHHHHH
Q 048660           95 HVLAVDDSYVDRKLIERLLQISSCKVTAVES---GTRALQYLGLDGEQSNVGFDALKVNLIITDYT--MPGMTGYELLKK  169 (213)
Q Consensus        95 ~ILvVdD~~~~~~~l~~~L~~~g~~v~~a~~---g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~--mp~~~G~e~~~~  169 (213)
                      +||+||....+--.+..+|++.|+.+.+..+   .....+.+           ....+|.|++-=.  .|....  ....
T Consensus         2 niliiD~~DSFt~ni~~~l~~lG~~~~v~~~~~~~~~~~~~l-----------~~~~~~~iils~Gpg~~~~~~--~~~~   68 (192)
T d1i7qb_           2 DILLLDNVDSFTYNLVDQLRASGHQVVIYRNQIGAEVIIERL-----------QHMEQPVLMLSPGPGTPSEAG--CMPE   68 (192)
T ss_dssp             EEEEEECSCSSHHHHHHHHHHTTCEEEEEETTSCHHHHHHHH-----------HHCSSEEEEECCCSSCGGGST--THHH
T ss_pred             cEEEEECCCcHHHHHHHHHHHCCCeEEEEeCCCcccccHHHH-----------HhcCCCeEEecCccccccccc--cchh
Confidence            7999997666666788889999999888753   33344444           2235788876421  111111  1112


Q ss_pred             HHhcCCCCCCcEEEEecCCCHHHHHHHHHcCCC
Q 048660          170 IKESSVFREVPVVIMSSEDVLTQIDSCLEEGAE  202 (213)
Q Consensus       170 ir~~~~~~~~pII~lt~~~~~~~~~~~~~~G~~  202 (213)
                      +++.- ...+||+.+.-    ....-+...|..
T Consensus        69 i~~~l-~~~iPiLGICl----G~Q~la~~~Gg~   96 (192)
T d1i7qb_          69 LLQRL-RGQLPIIGICL----GHQAIVEAYGGQ   96 (192)
T ss_dssp             HHHHH-BTTBCEEEETH----HHHHHHHHTTCE
T ss_pred             hHHhh-hcCccEEeeeH----HHHHHHHHCCCe
Confidence            22211 34789998863    334444555553

>d2fpoa1 c.66.1.46 (A:10-192) Methylase YhhF {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: YhhF-like
domain: Methylase YhhF
species: Escherichia coli [TaxId: 562]

Probab=83.36  E-value=2.1  Score=30.51  Aligned_cols=68  Identities=9%  Similarity=0.084  Sum_probs=46.7

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCC-EEE-EEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHHH
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSC-KVT-AVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKIK  171 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~-~v~-~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~ir  171 (213)
                      .+|..||-+....+.++.-++..+. .+. ...|   +++.+..         ....||+|++|---.....-+++..|.
T Consensus        67 ~~v~~VE~~~~a~~~~k~N~~~~~~~~~~ii~~d---~~~~l~~---------~~~~fDlIf~DPPY~~~~~~~~l~~l~  134 (183)
T d2fpoa1          67 AGATLIEMDRAVSQQLIKNLATLKAGNARVVNSN---AMSFLAQ---------KGTPHNIVFVDPPFRRGLLEETINLLE  134 (183)
T ss_dssp             SEEEEECSCHHHHHHHHHHHHHTTCCSEEEECSC---HHHHHSS---------CCCCEEEEEECCSSSTTTHHHHHHHHH
T ss_pred             ceeEEEEEeechhhHHHHHHhhccccceeeeeec---ccccccc---------cccccCEEEEcCccccchHHHHHHHHH
Confidence            4799999999999999999887654 232 2333   5565532         345799999995222344567777777


Q ss_pred             hc
Q 048660          172 ES  173 (213)
Q Consensus       172 ~~  173 (213)
                      +.
T Consensus       135 ~~  136 (183)
T d2fpoa1         135 DN  136 (183)
T ss_dssp             HT
T ss_pred             HC
Confidence            64

>d1wv2a_ c.1.31.1 (A:) Thiazole biosynthesis protein ThiG {Pseudomonas aeruginosa [TaxId: 287]}

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: ThiG-like
family: ThiG-like
domain: Thiazole biosynthesis protein ThiG
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=82.40  E-value=7.5  Score=29.19  Aligned_cols=81  Identities=17%  Similarity=0.137  Sum_probs=56.3

Q ss_pred             HHHhhcCCEEEEEcCHH-HHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCC-----CCHHHHHHHHHhcCCCCCCcEEEE
Q 048660          111 RLLQISSCKVTAVESGT-RALQYLGLDGEQSNVGFDALKVNLIITDYTMPG-----MTGYELLKKIKESSVFREVPVVIM  184 (213)
Q Consensus       111 ~~L~~~g~~v~~a~~g~-eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~-----~~G~e~~~~ir~~~~~~~~pII~l  184 (213)
                      ..|-+.||.|....+.+ ...+.+..-+            --++|-+.-|.     ..-...++.|++.   .++|+|+=
T Consensus       121 ~~Lv~egF~Vlpy~~~D~v~ak~le~~G------------c~~vMplgsPIGsg~Gi~n~~~l~~i~~~---~~vpvivd  185 (243)
T d1wv2a_         121 EQLVKDGFDVMVYTSDDPIIARQLAEIG------------CIAVMPLAGLIGSGLGICNPYNLRIILEE---AKVPVLVD  185 (243)
T ss_dssp             HHHHTTTCEEEEEECSCHHHHHHHHHSC------------CSEEEECSSSTTCCCCCSCHHHHHHHHHH---CSSCBEEE
T ss_pred             HHhhcCceEEEeccCCCHHHHhHHHHcC------------ceeeeecccccccccccccHHHHHhcccc---CCcceEee
Confidence            35667899887553332 3333332211            13677777783     3344567777764   58999999


Q ss_pred             ecCCCHHHHHHHHHcCCCeeee
Q 048660          185 SSEDVLTQIDSCLEEGAEEYIV  206 (213)
Q Consensus       185 t~~~~~~~~~~~~~~G~~~~L~  206 (213)
                      .+-....+...+++.|+|+.|.
T Consensus       186 AGIg~psdaa~AMElG~dgVLv  207 (243)
T d1wv2a_         186 AGVGTASDAAIAMELGCEAVLM  207 (243)
T ss_dssp             SCCCSHHHHHHHHHHTCSEEEE
T ss_pred             cccCCHHHHHHHHHccCCEEEe
Confidence            9999999999999999999885

>d2fhpa1 c.66.1.46 (A:1-182) Putative methylase EF2452 {Enterococcus faecalis [TaxId: 1351]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: YhhF-like
domain: Putative methylase EF2452
species: Enterococcus faecalis [TaxId: 1351]

Probab=82.27  E-value=6  Score=28.01  Aligned_cols=70  Identities=19%  Similarity=0.250  Sum_probs=50.7

Q ss_pred             cEEEEEeCCHHHHHHHHHHHhhcCC--EE-EEEcCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCCHHHHHHHH
Q 048660           94 LHVLAVDDSYVDRKLIERLLQISSC--KV-TAVESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMTGYELLKKI  170 (213)
Q Consensus        94 ~~ILvVdD~~~~~~~l~~~L~~~g~--~v-~~a~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~G~e~~~~i  170 (213)
                      .+|..||-+......++.-++..+.  .+ ....|..++++.+..         ....||+|++|---...+..+.+..|
T Consensus        65 ~~v~~ve~~~~a~~~~~~N~~~~~~~~~~~i~~~D~~~~l~~~~~---------~~~~fDlIflDPPY~~~~~~~~l~~i  135 (182)
T d2fhpa1          65 DKSICIEKNFAALKVIKENIAITKEPEKFEVRKMDANRALEQFYE---------EKLQFDLVLLDPPYAKQEIVSQLEKM  135 (182)
T ss_dssp             SEEEEEESCHHHHHHHHHHHHHHTCGGGEEEEESCHHHHHHHHHH---------TTCCEEEEEECCCGGGCCHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHhhhhhcccccccccccchhhhhhhcc---------cCCCcceEEechhhhhhHHHHHHHHH
Confidence            4799999999999999998886654  23 456788888876543         33479999999521134567778877


Q ss_pred             Hh
Q 048660          171 KE  172 (213)
Q Consensus       171 r~  172 (213)
                      .+
T Consensus       136 ~~  137 (182)
T d2fhpa1         136 LE  137 (182)
T ss_dssp             HH
T ss_pred             HH
Confidence            65

>d1xm3a_ c.1.31.1 (A:) Thiazole biosynthesis protein ThiG {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: ThiG-like
family: ThiG-like
domain: Thiazole biosynthesis protein ThiG
species: Bacillus subtilis [TaxId: 1423]

Probab=81.50  E-value=4.9  Score=30.31  Aligned_cols=80  Identities=19%  Similarity=0.081  Sum_probs=56.5

Q ss_pred             HHHhhcCCEEEEE--cCHHHHHHHhhhcCCCCCCCCCCCceeEEEEeCCCCCCC-----HHHHHHHHHhcCCCCCCcEEE
Q 048660          111 RLLQISSCKVTAV--ESGTRALQYLGLDGEQSNVGFDALKVNLIITDYTMPGMT-----GYELLKKIKESSVFREVPVVI  183 (213)
Q Consensus       111 ~~L~~~g~~v~~a--~~g~eal~~l~~~~~~~~~~~~~~~~dlil~D~~mp~~~-----G~e~~~~ir~~~~~~~~pII~  183 (213)
                      +.|-+.||.|...  .|..-|-+... -+          .  ..+|-+..|-.+     -...++.|++.   .++|||+
T Consensus       119 e~Lv~eGF~VlpY~~~D~v~ak~Le~-~G----------c--~avMPlgsPIGSg~Gl~n~~~l~~i~~~---~~vPvIv  182 (251)
T d1xm3a_         119 EQLLEEGFIVLPYTSDDVVLARKLEE-LG----------V--HAIMPGASPIGSGQGILNPLNLSFIIEQ---AKVPVIV  182 (251)
T ss_dssp             HHHHHTTCCEEEEECSCHHHHHHHHH-HT----------C--SCBEECSSSTTCCCCCSCHHHHHHHHHH---CSSCBEE
T ss_pred             HHHHhCCcEEEEecCCCHHHHHHHHH-cC----------C--hhHHHhhhhhhcCCCcCChHHHHHHHhc---CCccEEE
Confidence            3466789988644  44444444332 11          0  256777777544     34567888875   5899999


Q ss_pred             EecCCCHHHHHHHHHcCCCeeee
Q 048660          184 MSSEDVLTQIDSCLEEGAEEYIV  206 (213)
Q Consensus       184 lt~~~~~~~~~~~~~~G~~~~L~  206 (213)
                      =.+-..+.+...+++.|+|++|.
T Consensus       183 DAGIG~pSdAa~AMElG~daVLv  205 (251)
T d1xm3a_         183 DAGIGSPKDAAYAMELGADGVLL  205 (251)
T ss_dssp             ESCCCSHHHHHHHHHTTCSEEEE
T ss_pred             ecCCCCHHHHHHHHHccCCEEEe
Confidence            99999999999999999999985