Citrus Sinensis ID: 042079

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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---
Protein Sequence
MDACGVASSSSSSSSSNPKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLIN
Secondary Structure (PSIPRED)
cccccccccccccccccccccEEEEEcccHHHHHHHHHHHHHcccEEEEEccHHHHHHHHccccHHHHHHccccccccccEEEEEcccccccHHHHHHHHHcccccccccEEEEEccccHHHHHHHHHHcccccccccccHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccEEEEEcccHHHHHHHHHHHHHcccEEEEEccHHHHHHHHHHccccHHHHHHHHHcccccEEEEEcccccccHHHHHHHHHHccccccccEEEEEcccccHHHHHHHHcccccEccccccHHHHHHHHHHHHc
Coil and Loop (DISEMBL)
mdacgvasssssssssnpkpphvlavddsivDRKIVENLLKNSACKVTTAENGMRALEFLGLVdeqeqqnnlnsngtkVNLVITdycmpgmtGYELLKKIKESSVMKEVPVVVvsseniptRINECLEEGAqmfmlkplkpsdvkkltghlin
Flexible Loop (DISEMBL)
mdacgvasssssssssnpkpphvlavddsIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQnnlnsngtkvnLVITDYCMPGMTGYELLKKIKESSVMKEVPvvvvsseniptRINECLEEGAQMfmlkplkpsdvkkltghlin
Low Complexity Region (SEG)
MDACGVAsssssssssNPKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKIKessvmkevpvvvvsseNIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLIN
Disordered region (IsUnstruct)
**********************VLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVD**********NGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFML*****************
Disordered Region (DISOPRED)
**********************VLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLIN
Disordered Region (DISEMBL)
*********************HVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLIN
Disordered Region (DISPRO)
******************KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLIN
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDACGVASSSSSSSSSNPKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLIN
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	153	2.2.26 [Sep-21-2011]
Q9FPR6	153	Two-component response re	yes	no	0.960	0.960	0.677	5e-51
Q9SHC2	164	Two-component response re	no	no	0.862	0.804	0.689	3e-49
O82798	259	Two-component response re	no	no	0.830	0.490	0.638	4e-43
Q9ZWS9	231	Two-component response re	no	no	0.830	0.549	0.623	5e-43
Q9SB04	184	Two-component response re	no	no	0.928	0.771	0.569	3e-42
Q9ZWS6	186	Two-component response re	no	no	0.908	0.747	0.584	2e-41
O80366	234	Two-component response re	no	no	0.843	0.551	0.55	7e-41
O80365	225	Two-component response re	no	no	0.862	0.586	0.547	8e-41
Q9ZWS7	206	Two-component response re	no	no	0.803	0.597	0.634	4e-40
Q7G8V2	206	Two-component response re	no	no	0.803	0.597	0.634	5e-40

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

 Score =  199 bits (506), Expect = 5e-51,   Method: Compositional matrix adjust.
 Identities = 101/149 (67%), Positives = 121/149 (81%), Gaps = 2/149 (1%)

Query: 5   GVASSSSSSSSSNPKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVD 64
           G  S S S  SS  +  HVLAVDD+++DRK+VE +LK S+CKVTTAENG+RALE+LGL D
Sbjct: 4   GCGSGSDSCLSSMEEELHVLAVDDNLIDRKLVERILKISSCKVTTAENGLRALEYLGLGD 63

Query: 65  EQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRIN 124
            Q  Q +  +N  KVNL+ITDYCMPGMTG+ELLKK+KESS +KEVPVV++SSENIPTRIN
Sbjct: 64  PQ--QTDSLTNVMKVNLIITDYCMPGMTGFELLKKVKESSNLKEVPVVILSSENIPTRIN 121

Query: 125 ECLEEGAQMFMLKPLKPSDVKKLTGHLIN 153
           +CL  GAQMFM KPLK SDV+KL  HL+N
Sbjct: 122 KCLASGAQMFMQKPLKLSDVEKLKCHLLN 150

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 =  193 bits (491), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 91/132 (68%), Positives = 112/132 (84%)

Query: 22  HVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNL 81
           HVLAVDD+++DRK+VE LLK S CKVTTAEN +RALE+LGL D+ +  + L  N  KV+L
Sbjct: 30  HVLAVDDNLIDRKLVERLLKISCCKVTTAENALRALEYLGLGDQNQHIDALTCNVMKVSL 89

Query: 82  VITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKP 141
           +ITDYCMPGMTG+ELLKK+KESS ++EVPVV++SSENIPTRIN+CL  GAQMFM KPLK 
Sbjct: 90  IITDYCMPGMTGFELLKKVKESSNLREVPVVIMSSENIPTRINKCLASGAQMFMQKPLKL 149

Query: 142 SDVKKLTGHLIN 153
           +DV+KL  HL+N
Sbjct: 150 ADVEKLKCHLMN 161

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 =  173 bits (438), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 83/130 (63%), Positives = 105/130 (80%), Gaps = 3/130 (2%)

Query: 22  HVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNL 81
           HVLAVDDS+VDR ++E LL+ ++CKVT  ++G RALEFLGL +E+        +  KV+L
Sbjct: 35  HVLAVDDSLVDRIVIERLLRITSCKVTAVDSGWRALEFLGLDNEKASAE---FDRLKVDL 91

Query: 82  VITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKP 141
           +ITDYCMPGMTGYELLKKIKESS  +EVPVV++SSEN+ TRI+ CLEEGAQ F+LKP+K 
Sbjct: 92  IITDYCMPGMTGYELLKKIKESSNFREVPVVIMSSENVLTRIDRCLEEGAQDFLLKPVKL 151

Query: 142 SDVKKLTGHL 151
           +DVK+L  HL
Sbjct: 152 ADVKRLRSHL 161

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 =  172 bits (437), Expect = 5e-43,   Method: Compositional matrix adjust.
 Identities = 81/130 (62%), Positives = 106/130 (81%), Gaps = 3/130 (2%)

Query: 22  HVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNL 81
           HVLAVDDS+VDR ++E LL+ ++CKVT  ++G RALEFLGL D++     +  +  KV+L
Sbjct: 34  HVLAVDDSLVDRIVIERLLRITSCKVTAVDSGWRALEFLGLDDDKAA---VEFDRLKVDL 90

Query: 82  VITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKP 141
           +ITDYCMPGMTGYELLKKIKES+  KEVPVV++SSEN+ TRI+ CLEEGA+ F+LKP+K 
Sbjct: 91  IITDYCMPGMTGYELLKKIKESTSFKEVPVVIMSSENVMTRIDRCLEEGAEDFLLKPVKL 150

Query: 142 SDVKKLTGHL 151
           +DVK+L  +L
Sbjct: 151 ADVKRLRSYL 160

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 =  170 bits (430), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 82/144 (56%), Positives = 112/144 (77%), Gaps = 2/144 (1%)

Query: 9   SSSSSSSSNPKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQ 68
           S+ +SS ++PK  HVLAVDDS+VDRK +E LL+ S+CKVT  ++  RAL++LGL  + E 
Sbjct: 13  SNDTSSLASPKLLHVLAVDDSMVDRKFIERLLRVSSCKVTVVDSATRALQYLGL--DGEN 70

Query: 69  QNNLNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLE 128
            +++     K+NL++TDY MPGMTGYELLKKIKESS  +E+PVV++SSENI  RI+ CLE
Sbjct: 71  NSSVGFEDLKINLIMTDYSMPGMTGYELLKKIKESSAFREIPVVIMSSENILPRIDRCLE 130

Query: 129 EGAQMFMLKPLKPSDVKKLTGHLI 152
           EGA+ F+LKP+K +DVK+L   L+
Sbjct: 131 EGAEDFLLKPVKLADVKRLRDSLM 154

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

 Score =  167 bits (424), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 83/142 (58%), Positives = 106/142 (74%), Gaps = 3/142 (2%)

Query: 12  SSSSSNPKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNN 71
           SS   +P P HVLAVDDS VDRK +E LL+ S+CKVT  ++  RAL++LGL     ++ +
Sbjct: 16  SSKFGSPDPLHVLAVDDSHVDRKFIERLLRVSSCKVTVVDSATRALQYLGL---DVEEKS 72

Query: 72  LNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGA 131
           +     KVNL++TDY MPGMTGYELLKKIKESS  +EVPVV++SSENI  RI+ CLEEGA
Sbjct: 73  VGFEDLKVNLIMTDYSMPGMTGYELLKKIKESSAFREVPVVIMSSENILPRIDRCLEEGA 132

Query: 132 QMFMLKPLKPSDVKKLTGHLIN 153
           + F+LKP+K SDVK+L   L+ 
Sbjct: 133 EDFLLKPVKLSDVKRLRDSLMK 154

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 =  166 bits (419), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 77/140 (55%), Positives = 106/140 (75%), Gaps = 11/140 (7%)

Query: 22  HVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNN---------L 72
           HVLAVDDS+ DRK++E LL+ S+C+VTT ++G +ALEFLGL   Q   +N         +
Sbjct: 10  HVLAVDDSLFDRKLIERLLQKSSCQVTTVDSGSKALEFLGL--RQSTDSNDPNAFSKAPV 67

Query: 73  NSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQ 132
           N    +VNL+ITDYCMPGMTGY+LLKK+KESS  +++PVV++SSEN+P RI+ CLEEGA+
Sbjct: 68  NHQVVEVNLIITDYCMPGMTGYDLLKKVKESSAFRDIPVVIMSSENVPARISRCLEEGAE 127

Query: 133 MFMLKPLKPSDVKKLTGHLI 152
            F LKP++ +D+ KL  H++
Sbjct: 128 EFFLKPVRLADLNKLKPHMM 147

Functions as response regulator involved in His-to-Asp phosphorelay signal transduction system. Phosphorylation of the Asp residue in the receiver domain activates the ability of the protein to promote the transcription of target genes. Type-A response regulators seem to act as negative regulators of the cytokinin signaling.

Arabidopsis thaliana (taxid: 3702)

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

 Score =  165 bits (418), Expect = 8e-41,   Method: Compositional matrix adjust.
 Identities = 75/137 (54%), Positives = 106/137 (77%), Gaps = 5/137 (3%)

Query: 22  HVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSN-----G 76
           HVLAVDDS+ DRK++E LL+ S+C+VTT ++G +ALEFLGL  +    N L+++      
Sbjct: 10  HVLAVDDSLFDRKMIERLLQKSSCQVTTVDSGSKALEFLGLRVDDNDPNALSTSPQIHQE 69

Query: 77  TKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFML 136
            ++NL+ITDYCMPGMTGY+LLKK+KES+  + +PVV++SSEN+P RI+ CLEEGA+ F L
Sbjct: 70  VEINLIITDYCMPGMTGYDLLKKVKESAAFRSIPVVIMSSENVPARISRCLEEGAEEFFL 129

Query: 137 KPLKPSDVKKLTGHLIN 153
           KP+K +D+ KL  H++ 
Sbjct: 130 KPVKLADLTKLKPHMMK 146

Functions as response regulator involved in His-to-Asp phosphorelay signal transduction system. Phosphorylation of the Asp residue in the receiver domain activates the ability of the protein to promote the transcription of target genes. Type-A response regulators seem to act as negative regulators of the cytokinin signaling.

Arabidopsis thaliana (taxid: 3702)

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

 Score =  163 bits (412), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 80/126 (63%), Positives = 104/126 (82%), Gaps = 3/126 (2%)

Query: 22  HVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNL 81
           HVLAVDDSIVDRK++E LL+ S+CKVTT E+G RAL++LGL D  +  +NL     KVNL
Sbjct: 25  HVLAVDDSIVDRKVIERLLRISSCKVTTVESGTRALQYLGL-DGGKGASNLKD--LKVNL 81

Query: 82  VITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKP 141
           ++TDY MPG++GY+LLKKIKESS  +EVPVV++SSENI  RI ECL+EGA+ F+LKP+K 
Sbjct: 82  IVTDYSMPGLSGYDLLKKIKESSAFREVPVVIMSSENILPRIQECLKEGAEEFLLKPVKL 141

Query: 142 SDVKKL 147
           +DVK++
Sbjct: 142 ADVKRI 147

Functions as response regulator involved in His-to-Asp phosphorelay signal transduction system. Phosphorylation of the Asp residue in the receiver domain activates the ability of the protein to promote the transcription of target genes. Type-A response regulators seem to act as negative regulators of the cytokinin signaling.

Arabidopsis thaliana (taxid: 3702)

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

 Score =  162 bits (411), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 80/126 (63%), Positives = 101/126 (80%), Gaps = 3/126 (2%)

Query: 22  HVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNL 81
           HVLAVDDS VDRK++E LLK SACKVTT E+G RAL++LGL D     + L     KVNL
Sbjct: 19  HVLAVDDSFVDRKVIERLLKISACKVTTVESGTRALQYLGL-DGDNGSSGLKD--LKVNL 75

Query: 82  VITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKP 141
           ++TDY MPG+TGYELLKKIKESS ++E+PVV++SSENI  RI +C+ EGA+ F+LKP+K 
Sbjct: 76  IVTDYSMPGLTGYELLKKIKESSALREIPVVIMSSENIQPRIEQCMIEGAEEFLLKPVKL 135

Query: 142 SDVKKL 147
           +DVK+L
Sbjct: 136 ADVKRL 141

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	153
224144996	154	type-a response regulator [Populus trich	0.986	0.980	0.692	9e-54
255559713	155	two-component system sensor histidine ki	0.960	0.948	0.718	1e-53
370988689	158	type-A response regulator [Petunia x hyb	0.928	0.898	0.701	2e-53
309951240	154	putative A-type response regulator 8 [Po	0.986	0.980	0.686	3e-53
351724591	146	uncharacterized protein LOC100499827 [Gl	0.941	0.986	0.727	7e-53
225448707	153	PREDICTED: two-component response regula	0.973	0.973	0.655	1e-51
359807455	146	uncharacterized protein LOC100778707 [Gl	0.941	0.986	0.721	2e-51
297736479	141	unnamed protein product [Vitis vinifera]	0.843	0.914	0.725	1e-50
441415444	141	type-A response regulator [Torenia fourn	0.856	0.929	0.732	1e-50
18410485	153	two-component response regulator ARR17 [	0.960	0.960	0.677	3e-49

>gi|224144996|ref|XP_002325489.1| type-a response regulator [Populus trichocarpa] gi|222862364|gb|EEE99870.1| type-a response regulator [Populus trichocarpa]

 Score =  214 bits (545), Expect = 9e-54,   Method: Compositional matrix adjust.
 Identities = 106/153 (69%), Positives = 128/153 (83%), Gaps = 2/153 (1%)

Query: 1   MDACGVASSSSSSSSSNPKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFL 60
           MD  G +  +     +  + PHVLAVDDS+VDRK+VE LLKNS+CKVTTAENG+RALE+L
Sbjct: 1   MDGGGGSRENVMVGGAYTEEPHVLAVDDSLVDRKLVERLLKNSSCKVTTAENGLRALEYL 60

Query: 61  GLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIP 120
           GL DE+  + +L  N +KVNL+ITDYCMPGMTGYELLKKIKESS++KE+PVV++SSENIP
Sbjct: 61  GLGDEK--RTSLEDNVSKVNLIITDYCMPGMTGYELLKKIKESSMLKEIPVVIMSSENIP 118

Query: 121 TRINECLEEGAQMFMLKPLKPSDVKKLTGHLIN 153
           TRIN+CLEEGAQMFMLKPLK SDV KL  +L+N
Sbjct: 119 TRINKCLEEGAQMFMLKPLKQSDVVKLRCNLMN 151

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255559713|ref|XP_002520876.1| two-component system sensor histidine kinase/response regulator, putative [Ricinus communis] gi|223540007|gb|EEF41585.1| two-component system sensor histidine kinase/response regulator, putative [Ricinus communis]

 Score =  214 bits (544), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 107/149 (71%), Positives = 123/149 (82%), Gaps = 2/149 (1%)

Query: 5   GVASSSSSSSSSNPKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVD 64
           G  SS           PHVLAVDD+++DRK+VE LLKNS CKVTTAENG+RALE+LGL D
Sbjct: 6   GTCSSMEKVLGDYGDQPHVLAVDDNLIDRKLVEKLLKNSCCKVTTAENGLRALEYLGLGD 65

Query: 65  EQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRIN 124
           +   +N L +N +KVNL+ITDYCMPGMTGYELLKKIKESS+MKEVPVV+VSSENIPTRIN
Sbjct: 66  DD--RNCLENNVSKVNLIITDYCMPGMTGYELLKKIKESSIMKEVPVVIVSSENIPTRIN 123

Query: 125 ECLEEGAQMFMLKPLKPSDVKKLTGHLIN 153
           +CLEEGAQMFMLKPLK SDVKKL   ++N
Sbjct: 124 KCLEEGAQMFMLKPLKLSDVKKLRCDIMN 152

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|370988689|dbj|BAL43558.1| type-A response regulator [Petunia x hybrida]

 Score =  213 bits (542), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 101/144 (70%), Positives = 121/144 (84%), Gaps = 2/144 (1%)

Query: 10  SSSSSSSNPKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQ 69
           S     +    PHVLAVDD++VDRK+VE LLK S+CKVTTAENG+RALE+LGL  +QE  
Sbjct: 12  SRGMGETTADEPHVLAVDDNLVDRKLVERLLKKSSCKVTTAENGLRALEYLGLGGDQEHS 71

Query: 70  NNLNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEE 129
            N   NG+KVN++ITDYCMPGMTGYELLKKIKESS++K+VPVV++SSENIPTRI++C+EE
Sbjct: 72  TN--GNGSKVNMIITDYCMPGMTGYELLKKIKESSILKDVPVVIMSSENIPTRIDQCMEE 129

Query: 130 GAQMFMLKPLKPSDVKKLTGHLIN 153
           GAQMFMLKPLK SDVK+L   LIN
Sbjct: 130 GAQMFMLKPLKHSDVKRLRCQLIN 153

Source: Petunia x hybrida

Species: Petunia x hybrida

Genus: Petunia

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|309951240|emb|CBX43990.1| putative A-type response regulator 8 [Populus x canadensis]

 Score =  212 bits (540), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 105/153 (68%), Positives = 128/153 (83%), Gaps = 2/153 (1%)

Query: 1   MDACGVASSSSSSSSSNPKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFL 60
           MD  G +  +     +  + PHVLAVDDS+VDRK+VE LLKNS+CKVTTAENG+RALE+L
Sbjct: 1   MDGGGGSRENVMVGGAYTEEPHVLAVDDSLVDRKLVERLLKNSSCKVTTAENGLRALEYL 60

Query: 61  GLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIP 120
           GL DE+  + +L  N +KVNL+ITDYCMPGMTGYELLKKIKESS++K++PVV++SSENIP
Sbjct: 61  GLGDEK--RTSLEDNVSKVNLIITDYCMPGMTGYELLKKIKESSMLKKIPVVIMSSENIP 118

Query: 121 TRINECLEEGAQMFMLKPLKPSDVKKLTGHLIN 153
           TRIN+CLEEGAQMFMLKPLK SDV KL  +L+N
Sbjct: 119 TRINKCLEEGAQMFMLKPLKQSDVVKLRCNLMN 151

Source: Populus x canadensis

Species: Populus x canadensis

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|351724591|ref|NP_001236551.1| uncharacterized protein LOC100499827 [Glycine max] gi|255626955|gb|ACU13822.1| unknown [Glycine max]

 Score =  211 bits (537), Expect = 7e-53,   Method: Compositional matrix adjust.
 Identities = 107/147 (72%), Positives = 125/147 (85%), Gaps = 3/147 (2%)

Query: 7   ASSSSSSSSSNPKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQ 66
           ASSSS+    +   PHVLAVDD+++DRK+VE LL+NS+CKVTTAENG RALE LGL    
Sbjct: 3   ASSSSNWVMESGDVPHVLAVDDNLIDRKLVEKLLRNSSCKVTTAENGPRALELLGLTSGG 62

Query: 67  EQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINEC 126
             QNN+N   +KVN++ITDYCMPGMTGYELLKKIKESSVMKEVPVV++SSENIPTRIN+C
Sbjct: 63  --QNNMNGR-SKVNMIITDYCMPGMTGYELLKKIKESSVMKEVPVVIMSSENIPTRINKC 119

Query: 127 LEEGAQMFMLKPLKPSDVKKLTGHLIN 153
           LEEGAQMF+LKPLK SDV+KLT  L+N
Sbjct: 120 LEEGAQMFILKPLKQSDVRKLTCQLMN 146

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225448707|ref|XP_002280746.1| PREDICTED: two-component response regulator ARR17 [Vitis vinifera]

 Score =  207 bits (527), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 99/151 (65%), Positives = 125/151 (82%), Gaps = 2/151 (1%)

Query: 1   MDACGVASSSSSSSSSNPKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFL 60
           MDA   +S++          PHVLAVDD+++DRK++E LLKN +C+VTTAENG+RALE+L
Sbjct: 1   MDAASSSSANDMMVMDYGDEPHVLAVDDNLIDRKLIEKLLKNFSCRVTTAENGLRALEYL 60

Query: 61  GLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIP 120
           GL D Q  Q +  ++ +KVNL+ITDYCMPGMTGYELLK++K+SS++KEVPVV++SSENIP
Sbjct: 61  GLGDNQ--QTSHKASVSKVNLIITDYCMPGMTGYELLKRVKQSSILKEVPVVIMSSENIP 118

Query: 121 TRINECLEEGAQMFMLKPLKPSDVKKLTGHL 151
           TRIN+CLEEGAQMFMLKPLK SDVKKL  +L
Sbjct: 119 TRINKCLEEGAQMFMLKPLKQSDVKKLRCYL 149

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359807455|ref|NP_001241393.1| uncharacterized protein LOC100778707 [Glycine max] gi|255637322|gb|ACU18991.1| unknown [Glycine max]

 Score =  206 bits (525), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 106/147 (72%), Positives = 122/147 (82%), Gaps = 3/147 (2%)

Query: 7   ASSSSSSSSSNPKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQ 66
           A SSS+    +   PHVLAVDD+++DRK+VE LL+NS+CKVTTAENG RALE LGL    
Sbjct: 3   AGSSSNWVMESGDVPHVLAVDDNLIDRKLVEKLLRNSSCKVTTAENGPRALELLGLTSGG 62

Query: 67  EQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINEC 126
             QN +N   +KVN+VITDYCMPGMTGYELLKKIKESSV KEVPVV++SSENIPTRIN+C
Sbjct: 63  --QNTMNGR-SKVNMVITDYCMPGMTGYELLKKIKESSVTKEVPVVIMSSENIPTRINKC 119

Query: 127 LEEGAQMFMLKPLKPSDVKKLTGHLIN 153
           LEEGAQMF+LKPLK SDVKKLT  L+N
Sbjct: 120 LEEGAQMFILKPLKQSDVKKLTCQLMN 146

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297736479|emb|CBI25350.3| unnamed protein product [Vitis vinifera]

 Score =  204 bits (519), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 95/131 (72%), Positives = 118/131 (90%), Gaps = 2/131 (1%)

Query: 21  PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVN 80
           PHVLAVDD+++DRK++E LLKN +C+VTTAENG+RALE+LGL D Q  Q +  ++ +KVN
Sbjct: 9   PHVLAVDDNLIDRKLIEKLLKNFSCRVTTAENGLRALEYLGLGDNQ--QTSHKASVSKVN 66

Query: 81  LVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLK 140
           L+ITDYCMPGMTGYELLK++K+SS++KEVPVV++SSENIPTRIN+CLEEGAQMFMLKPLK
Sbjct: 67  LIITDYCMPGMTGYELLKRVKQSSILKEVPVVIMSSENIPTRINKCLEEGAQMFMLKPLK 126

Query: 141 PSDVKKLTGHL 151
            SDVKKL  +L
Sbjct: 127 QSDVKKLRCYL 137

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|441415444|dbj|BAM74646.1| type-A response regulator [Torenia fournieri]

 Score =  204 bits (518), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 96/131 (73%), Positives = 116/131 (88%)

Query: 22  HVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNL 81
           HVLAVDD+++DR IVE LLKNS+CKVTT ENG RALE+LGL D+Q   ++ N+  +KVN+
Sbjct: 9   HVLAVDDNLIDRTIVEKLLKNSSCKVTTVENGRRALEYLGLGDDQNISSDDNAAASKVNM 68

Query: 82  VITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKP 141
           +ITDYCMPGMTGYELLKKIKESSVMK+VPVV++SSEN+PTRIN+CLEEGA+MFMLKPLK 
Sbjct: 69  IITDYCMPGMTGYELLKKIKESSVMKDVPVVIMSSENVPTRINKCLEEGAEMFMLKPLKH 128

Query: 142 SDVKKLTGHLI 152
           SD+KKL   L+
Sbjct: 129 SDMKKLKCQLL 139

Source: Torenia fournieri

Species: Torenia fournieri

Genus: Torenia

Family: Linderniaceae

Order: Lamiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18410485|ref|NP_567037.1| two-component response regulator ARR17 [Arabidopsis thaliana] gi|51316089|sp|Q9FPR6.1|ARR17_ARATH RecName: Full=Two-component response regulator ARR17 gi|11870071|gb|AAG40613.1|AF305722_1 response regulator 17 [Arabidopsis thaliana] gi|332645994|gb|AEE79515.1| two-component response regulator ARR17 [Arabidopsis thaliana]

 Score =  199 bits (506), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 101/149 (67%), Positives = 121/149 (81%), Gaps = 2/149 (1%)

Query: 5   GVASSSSSSSSSNPKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVD 64
           G  S S S  SS  +  HVLAVDD+++DRK+VE +LK S+CKVTTAENG+RALE+LGL D
Sbjct: 4   GCGSGSDSCLSSMEEELHVLAVDDNLIDRKLVERILKISSCKVTTAENGLRALEYLGLGD 63

Query: 65  EQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRIN 124
            Q  Q +  +N  KVNL+ITDYCMPGMTG+ELLKK+KESS +KEVPVV++SSENIPTRIN
Sbjct: 64  PQ--QTDSLTNVMKVNLIITDYCMPGMTGFELLKKVKESSNLKEVPVVILSSENIPTRIN 121

Query: 125 ECLEEGAQMFMLKPLKPSDVKKLTGHLIN 153
           +CL  GAQMFM KPLK SDV+KL  HL+N
Sbjct: 122 KCLASGAQMFMQKPLKLSDVEKLKCHLLN 150

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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	153
TAIR|locus:2102509	153	RR17 "response regulator 17" [	0.849	0.849	0.636	7.8e-39
UNIPROTKB|Q4GZK2	201	rr9 "Type A response regulator	0.869	0.661	0.533	8.5e-33
UNIPROTKB|Q4GZK7	232	rr4 "Type A response regulator	0.856	0.564	0.510	8.5e-33
TAIR|locus:2194584	259	ARR4 "response regulator 4" [A	0.830	0.490	0.553	2.9e-32
TAIR|locus:2025911	231	ARR3 "response regulator 3" [A	0.830	0.549	0.538	9.8e-32
TAIR|locus:2040282	225	RR3 "response regulator 3" [Ar	0.856	0.582	0.492	9.8e-32
TAIR|locus:2080590	234	ARR9 "response regulator 9" [A	0.856	0.559	0.485	6.9e-31
TAIR|locus:2170723	186	ARR6 "response regulator 6" [A	0.869	0.715	0.529	1.1e-30
TAIR|locus:2011286	206	ARR7 "response regulator 7" [A	0.803	0.597	0.547	1.4e-30
TAIR|locus:2027237	206	ARR15 "response regulator 15"	0.803	0.597	0.555	1.4e-30

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

 Score = 415 (151.1 bits), Expect = 7.8e-39, P = 7.8e-39
 Identities = 84/132 (63%), Positives = 101/132 (76%)

Query:    22 HVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNL 81
             HVLAVDD+++DRK+VE +LK S+CKVTTAENG+RALE+LGL D Q Q ++L +N  KVNL
Sbjct:    21 HVLAVDDNLIDRKLVERILKISSCKVTTAENGLRALEYLGLGDPQ-QTDSL-TNVMKVNL 78

Query:    82 VITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLKPLKP 141
             +ITDYCMPGMTG+ELLKK+K                NIPTRIN+CL  GAQMFM KPLK 
Sbjct:    79 IITDYCMPGMTGFELLKKVKESSNLKEVPVVILSSENIPTRINKCLASGAQMFMQKPLKL 138

Query:   142 SDVKKLTGHLIN 153
             SDV+KL  HL+N
Sbjct:   139 SDVEKLKCHLLN 150

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

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

 Score = 358 (131.1 bits), Expect = 8.5e-33, P = 8.5e-33
 Identities = 72/135 (53%), Positives = 93/135 (68%)

Query:    20 PPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKV 79
             P HVLAVDDS+ DRK++E LLK S+ +VTT ++G +ALEFLGL D ++   +  S+  +V
Sbjct:     8 PFHVLAVDDSLPDRKLIERLLKTSSFQVTTVDSGSKALEFLGLHDHEDSPISTQSDQQEV 67

Query:    80 --NLVITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLK 137
               NL+ITDYCMPGMTGY+LLKKIK                NIP+RIN CLEEGA  F LK
Sbjct:    68 AVNLIITDYCMPGMTGYDLLKKIKESSYLRDIPVVIMSSDNIPSRINRCLEEGADEFFLK 127

Query:   138 PLKPSDVKKLTGHLI 152
             P++ SD+ KL  H++
Sbjct:   128 PVRLSDMSKLKPHIL 142

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

UNIPROTKB|Q4GZK7 rr4 "Type A response regulator 4" [Oryza sativa Indica Group (taxid:39946)]

 Score = 358 (131.1 bits), Expect = 8.5e-33, P = 8.5e-33
 Identities = 70/137 (51%), Positives = 95/137 (69%)

Query:    22 HVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTK--- 78
             HVLAVDDS++DRK++E LLKNS+ +VTT ++G +ALE LGL DE +  ++  S+ +    
Sbjct:    11 HVLAVDDSLIDRKLIEMLLKNSSYQVTTVDSGSKALELLGLRDEGDDSSSSPSSSSPDHQ 70

Query:    79 ---VNLVITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFM 135
                VNL+ITDYCMPGMTGY+LLK++K                N+P RIN CLE+GA+ F 
Sbjct:    71 EIDVNLIITDYCMPGMTGYDLLKRVKGSSSLKDIPVVIMSSENVPARINRCLEDGAEEFF 130

Query:   136 LKPLKPSDVKKLTGHLI 152
             LKP+K +D+KKL  HL+
Sbjct:   131 LKPVKLADMKKLKSHLL 147

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

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

 Score = 353 (129.3 bits), Expect = 2.9e-32, P = 2.9e-32
 Identities = 72/130 (55%), Positives = 92/130 (70%)

Query:    22 HVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNL 81
             HVLAVDDS+VDR ++E LL+ ++CKVT  ++G RALEFLGL +E+    +   +  KV+L
Sbjct:    35 HVLAVDDSLVDRIVIERLLRITSCKVTAVDSGWRALEFLGLDNEKA---SAEFDRLKVDL 91

Query:    82 VITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLKPLKP 141
             +ITDYCMPGMTGYELLKKIK                N+ TRI+ CLEEGAQ F+LKP+K 
Sbjct:    92 IITDYCMPGMTGYELLKKIKESSNFREVPVVIMSSENVLTRIDRCLEEGAQDFLLKPVKL 151

Query:   142 SDVKKLTGHL 151
             +DVK+L  HL
Sbjct:   152 ADVKRLRSHL 161

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

 Score = 348 (127.6 bits), Expect = 9.8e-32, P = 9.8e-32
 Identities = 70/130 (53%), Positives = 92/130 (70%)

Query:    22 HVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNL 81
             HVLAVDDS+VDR ++E LL+ ++CKVT  ++G RALEFLGL D++     +  +  KV+L
Sbjct:    34 HVLAVDDSLVDRIVIERLLRITSCKVTAVDSGWRALEFLGLDDDKAA---VEFDRLKVDL 90

Query:    82 VITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLKPLKP 141
             +ITDYCMPGMTGYELLKKIK                N+ TRI+ CLEEGA+ F+LKP+K 
Sbjct:    91 IITDYCMPGMTGYELLKKIKESTSFKEVPVVIMSSENVMTRIDRCLEEGAEDFLLKPVKL 150

Query:   142 SDVKKLTGHL 151
             +DVK+L  +L
Sbjct:   151 ADVKRLRSYL 160

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

 Score = 348 (127.6 bits), Expect = 9.8e-32, P = 9.8e-32
 Identities = 67/136 (49%), Positives = 93/136 (68%)

Query:    22 HVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNG----- 76
             HVLAVDDS+ DRK++E LL+ S+C+VTT ++G +ALEFLGL  +    N L+++      
Sbjct:    10 HVLAVDDSLFDRKMIERLLQKSSCQVTTVDSGSKALEFLGLRVDDNDPNALSTSPQIHQE 69

Query:    77 TKVNLVITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFML 136
              ++NL+ITDYCMPGMTGY+LLKK+K                N+P RI+ CLEEGA+ F L
Sbjct:    70 VEINLIITDYCMPGMTGYDLLKKVKESAAFRSIPVVIMSSENVPARISRCLEEGAEEFFL 129

Query:   137 KPLKPSDVKKLTGHLI 152
             KP+K +D+ KL  H++
Sbjct:   130 KPVKLADLTKLKPHMM 145

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

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

 Score = 340 (124.7 bits), Expect = 6.9e-31, P = 6.9e-31
 Identities = 67/138 (48%), Positives = 92/138 (66%)

Query:    22 HVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQN-N------LNS 74
             HVLAVDDS+ DRK++E LL+ S+C+VTT ++G +ALEFLGL    +  + N      +N 
Sbjct:    10 HVLAVDDSLFDRKLIERLLQKSSCQVTTVDSGSKALEFLGLRQSTDSNDPNAFSKAPVNH 69

Query:    75 NGTKVNLVITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMF 134
                +VNL+ITDYCMPGMTGY+LLKK+K                N+P RI+ CLEEGA+ F
Sbjct:    70 QVVEVNLIITDYCMPGMTGYDLLKKVKESSAFRDIPVVIMSSENVPARISRCLEEGAEEF 129

Query:   135 MLKPLKPSDVKKLTGHLI 152
              LKP++ +D+ KL  H++
Sbjct:   130 FLKPVRLADLNKLKPHMM 147

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

 Score = 338 (124.0 bits), Expect = 1.1e-30, P = 1.1e-30
 Identities = 72/136 (52%), Positives = 92/136 (67%)

Query:    17 NPKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNG 76
             +P P HVLAVDDS VDRK +E LL+ S+CKVT  ++  RAL++LGL D +E+  ++    
Sbjct:    21 SPDPLHVLAVDDSHVDRKFIERLLRVSSCKVTVVDSATRALQYLGL-DVEEK--SVGFED 77

Query:    77 TKVNLVITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFML 136
              KVNL++TDY MPGMTGYELLKKIK                NI  RI+ CLEEGA+ F+L
Sbjct:    78 LKVNLIMTDYSMPGMTGYELLKKIKESSAFREVPVVIMSSENILPRIDRCLEEGAEDFLL 137

Query:   137 KPLKPSDVKKLTGHLI 152
             KP+K SDVK+L   L+
Sbjct:   138 KPVKLSDVKRLRDSLM 153

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

 Score = 337 (123.7 bits), Expect = 1.4e-30, P = 1.4e-30
 Identities = 69/126 (54%), Positives = 90/126 (71%)

Query:    22 HVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNL 81
             HVLAVDDSIVDRK++E LL+ S+CKVTT E+G RAL++LGL D  +  +NL     KVNL
Sbjct:    25 HVLAVDDSIVDRKVIERLLRISSCKVTTVESGTRALQYLGL-DGGKGASNLKD--LKVNL 81

Query:    82 VITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLKPLKP 141
             ++TDY MPG++GY+LLKKIK                NI  RI ECL+EGA+ F+LKP+K 
Sbjct:    82 IVTDYSMPGLSGYDLLKKIKESSAFREVPVVIMSSENILPRIQECLKEGAEEFLLKPVKL 141

Query:   142 SDVKKL 147
             +DVK++
Sbjct:   142 ADVKRI 147

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

 Score = 337 (123.7 bits), Expect = 1.4e-30, P = 1.4e-30
 Identities = 70/126 (55%), Positives = 86/126 (68%)

Query:    22 HVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNL 81
             HVLAVDDS VDRK++E LLK SACKVTT E+G RAL++LGL D     + L     KVNL
Sbjct:    19 HVLAVDDSFVDRKVIERLLKISACKVTTVESGTRALQYLGL-DGDNGSSGLKD--LKVNL 75

Query:    82 VITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLKPLKP 141
             ++TDY MPG+TGYELLKKIK                NI  RI +C+ EGA+ F+LKP+K 
Sbjct:    76 IVTDYSMPGLTGYELLKKIKESSALREIPVVIMSSENIQPRIEQCMIEGAEEFLLKPVKL 135

Query:   142 SDVKKL 147
             +DVK+L
Sbjct:   136 ADVKRL 141

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

---

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)
Q9FPR6	ARR17_ARATH	No assigned EC number	0.6778	0.9607	0.9607	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:
	gw1.XIX.1648.1	type-a response regulator (136 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	eugene3.151650001	Predicted protein (347 aa)	•			•	•	•	•		0.868
	eugene3.106630001	Predicted protein (434 aa)	•			•			•		0.762
	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

---

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	153
PLN03029	222	PLN03029, PLN03029, type-a response regulator prot	2e-49
cd00156	113	cd00156, REC, Signal receiver domain; originally t	3e-23
COG0784	130	COG0784, CheY, FOG: CheY-like receiver [Signal tra	4e-22
pfam00072	111	pfam00072, Response_reg, Response regulator receiv	7e-21
COG2204	464	COG2204, AtoC, Response regulator containing CheY-	2e-15
COG3706	435	COG3706, PleD, Response regulator containing a Che	7e-15
COG3437	360	COG3437, COG3437, Response regulator containing a	4e-14
PRK10610	129	PRK10610, PRK10610, chemotaxis regulatory protein	3e-12
COG4753	475	COG4753, COG4753, Response regulator containing Ch	3e-11
PRK09581	457	PRK09581, pleD, response regulator PleD; Reviewed	4e-11
CHL00148	240	CHL00148, orf27, Ycf27; Reviewed	7e-10
COG2197	211	COG2197, CitB, Response regulator containing a Che	2e-09
COG0745	229	COG0745, OmpR, Response regulators consisting of a	3e-09
PRK15347	921	PRK15347, PRK15347, two component system sensor ki	7e-09
TIGR01818	463	TIGR01818, ntrC, nitrogen regulation protein NR(I)	7e-08
smart00448	55	smart00448, REC, cheY-homologous receiver domain	4e-07
PRK10841	924	PRK10841, PRK10841, hybrid sensory kinase in two-c	6e-07
COG2201	350	COG2201, CheB, Chemotaxis response regulator conta	9e-07
TIGR02154	226	TIGR02154, PhoB, phosphate regulon transcriptional	2e-06
PRK10161	229	PRK10161, PRK10161, transcriptional regulator PhoB	5e-06
PRK10693	303	PRK10693, PRK10693, response regulator of RpoS; Pr	5e-06
PRK10651	216	PRK10651, PRK10651, transcriptional regulator NarL	5e-06
PRK09390	202	PRK09390, fixJ, response regulator FixJ; Provision	7e-06
COG3947	361	COG3947, COG3947, Response regulator containing Ch	1e-05
PRK10365	441	PRK10365, PRK10365, transcriptional regulatory pro	2e-05
PRK00742	354	PRK00742, PRK00742, chemotaxis-specific methyleste	2e-05
PRK15115	444	PRK15115, PRK15115, response regulator GlrR; Provi	5e-05
PRK11107	919	PRK11107, PRK11107, hybrid sensory histidine kinas	6e-05
PRK11091	779	PRK11091, PRK11091, aerobic respiration control se	7e-05
PRK10923	469	PRK10923, glnG, nitrogen regulation protein NR(I);	8e-05
PRK13856	241	PRK13856, PRK13856, two-component response regulat	2e-04
PRK10529	225	PRK10529, PRK10529, DNA-binding transcriptional ac	3e-04
TIGR01387	218	TIGR01387, cztR_silR_copR, heavy metal response re	4e-04
PRK11361	457	PRK11361, PRK11361, acetoacetate metabolism regula	5e-04
COG4566	202	COG4566, TtrR, Response regulator [Signal transduc	0.001
PRK10360	196	PRK10360, PRK10360, DNA-binding transcriptional ac	0.001
PRK11083	228	PRK11083, PRK11083, DNA-binding response regulator	0.001
PRK10403	215	PRK10403, PRK10403, transcriptional regulator NarP	0.003
TIGR02956	968	TIGR02956, TMAO_torS, TMAO reductase sytem sensor	0.003
PRK11173	237	PRK11173, PRK11173, two-component response regulat	0.003
PRK10766	221	PRK10766, PRK10766, DNA-binding transcriptional re	0.004

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

 Score =  157 bits (399), Expect = 2e-49
 Identities = 74/137 (54%), Positives = 105/137 (76%), Gaps = 6/137 (4%)

Query: 22  HVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNL------NSN 75
           HVLAVDDS++DRK++E LLK S+ +VTT ++G +AL+FLGL ++     +       +  
Sbjct: 10  HVLAVDDSLIDRKLIEKLLKTSSYQVTTVDSGSKALKFLGLHEDDRSNPDTPSVSPNSHQ 69

Query: 76  GTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFM 135
             +VNL+ITDYCMPGMTGY+LLKKIKESS ++ +PVV++SSEN+P+RI  CLEEGA+ F 
Sbjct: 70  EVEVNLIITDYCMPGMTGYDLLKKIKESSSLRNIPVVIMSSENVPSRITRCLEEGAEEFF 129

Query: 136 LKPLKPSDVKKLTGHLI 152
           LKP++ SD+ +L  H++
Sbjct: 130 LKPVQLSDLNRLKPHMM 146

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 = 87.2 bits (217), Expect = 3e-23
 Identities = 34/123 (27%), Positives = 60/123 (48%), Gaps = 16/123 (13%)

Query: 24  LAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVI 83
           L VDD  + R+++  LL+    +V  AE+G  AL  L                 K +L++
Sbjct: 1   LIVDDDPLIRELLRRLLEKEGYEVVEAEDGEEALALL--------------AEEKPDLIL 46

Query: 84  TDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSD 143
            D  MPGM G ELL++I++     ++P++ +++        E L+ GA  ++ KP  P +
Sbjct: 47  LDIMMPGMDGLELLRRIRKR--GPDIPIIFLTAHGDDEDAVEALKAGADDYLTKPFSPEE 104

Query: 144 VKK 146
           +  
Sbjct: 105 LLA 107

Length = 113

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

 Score = 85.3 bits (211), Expect = 4e-22
 Identities = 34/128 (26%), Positives = 61/128 (47%), Gaps = 14/128 (10%)

Query: 17  NPKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNG 76
                 VL VDD  V+R++++ LL++   +V  A +G    E L L+ E  Q        
Sbjct: 2   LLSGLRVLVVDDEPVNRRLLKRLLEDLGYEVVEAADGE--EEALELLRELPQ-------- 51

Query: 77  TKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFML 136
              +L++ D  MPGM G ELL++++       +PV+++++          L  GA  ++ 
Sbjct: 52  --PDLILLDINMPGMDGIELLRRLRAR--GPNIPVILLTAYADEADRERALAAGADDYLT 107

Query: 137 KPLKPSDV 144
           KP+   + 
Sbjct: 108 KPIFLEEE 115

Length = 130

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

 Score = 81.5 bits (202), Expect = 7e-21
 Identities = 38/124 (30%), Positives = 62/124 (50%), Gaps = 16/124 (12%)

Query: 23  VLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLV 82
           VL VDD  + R+++  LL+     V  A++G  ALE L     +E+         + +L+
Sbjct: 1   VLIVDDDPLIRELLRQLLEKEGYVVAEADDGEEALELL-----KEK---------RPDLI 46

Query: 83  ITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPS 142
           + D  MPGM G ELL++I+        PV+V+++        E L+ GA  F+ KP  P 
Sbjct: 47  LLDIRMPGMDGLELLRRIRRRP--PTTPVIVLTAHGDEEDAVEALKAGANDFLSKPFDPE 104

Query: 143 DVKK 146
           ++  
Sbjct: 105 ELVA 108

This domain receives the signal from the sensor partner in bacterial two-component systems. It is usually found N-terminal to a DNA binding effector domain. Length = 111

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

 Score = 71.6 bits (176), Expect = 2e-15
 Identities = 41/121 (33%), Positives = 61/121 (50%), Gaps = 18/121 (14%)

Query: 22  HVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNL 81
            +L VDD    R+++E  L+ +  +V TAE+   ALE    + E              +L
Sbjct: 6   RILVVDDDPDIRELLEQALELAGYEVVTAESAEEALE---ALSESP-----------FDL 51

Query: 82  VITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSE-NIPTRINECLEEGAQMFMLKPLK 140
           V+ D  MPGM G ELLK+IK      ++PV+V++   +I T + E L  GA  F+ KP  
Sbjct: 52  VLLDIRMPGMDGLELLKEIKSRD--PDLPVIVMTGHGDIDTAV-EALRLGAFDFLEKPFD 108

Query: 141 P 141
            
Sbjct: 109 L 109

Length = 464

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

 Score = 70.0 bits (172), Expect = 7e-15
 Identities = 30/131 (22%), Positives = 57/131 (43%), Gaps = 14/131 (10%)

Query: 11  SSSSSSNPKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQN 70
            S       P  +L VDD    R+ +  +L+    +V  A +G  AL  L          
Sbjct: 123 VSPLLPEDAPKKILVVDDDATQRERLRRILQVEGFRVVEATDGEEALLQL---------- 172

Query: 71  NLNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEG 130
                    +LV+ D  MP M G EL  ++++    +++P++++SS++    +    E G
Sbjct: 173 ----AELPPDLVLLDANMPDMDGLELCTRLRQLERTRDIPIILLSSKDDDELVVRAFELG 228

Query: 131 AQMFMLKPLKP 141
              ++ KP++ 
Sbjct: 229 VNDYITKPIEE 239

Length = 435

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

 Score = 67.8 bits (166), Expect = 4e-14
 Identities = 38/137 (27%), Positives = 64/137 (46%), Gaps = 15/137 (10%)

Query: 10  SSSSSSSNPKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQ 69
           S    +   +   VL VDD   + + +  LL+    +V  AENG  AL+   L+ E+   
Sbjct: 4   SMQGKNEPDEKLTVLLVDDEPDNLEALRQLLRMIGYRVIEAENGEEALK---LLQEE--- 57

Query: 70  NNLNSNGTKVNLVITDYCMPGMTGYELLKKIKESS-VMKEVPVVVVSSENIPTRINECLE 128
                     +LV+ D  MP M G E+L K+K  S   + +PV+++++          LE
Sbjct: 58  --------PPDLVLLDVRMPEMDGAEVLNKLKAMSPSTRRIPVILLTAYADSEDRQRALE 109

Query: 129 EGAQMFMLKPLKPSDVK 145
            GA  ++ KP+ P ++ 
Sbjct: 110 AGADDYLSKPISPKELV 126

Length = 360

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

 Score = 59.6 bits (144), Expect = 3e-12
 Identities = 42/117 (35%), Positives = 58/117 (49%), Gaps = 15/117 (12%)

Query: 24  LAVDDSIVDRKIVENLLKNSAC-KVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLV 82
           L VDD    R+IV NLLK      V  AE+G+ AL            N L + G     V
Sbjct: 9   LVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDAL------------NKLQAGG--FGFV 54

Query: 83  ITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPL 139
           I+D+ MP M G ELLK I+    M  +PV++V++E     I    + GA  +++KP 
Sbjct: 55  ISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPF 111

Length = 129

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

 Score = 59.7 bits (145), Expect = 3e-11
 Identities = 40/134 (29%), Positives = 69/134 (51%), Gaps = 19/134 (14%)

Query: 23  VLAVDDSIVDRKIVENLLKNSACK---VTTAENGMRALEFLGLVDEQEQQNNLNSNGTKV 79
           VL VDD  + R+ +++L+   A     V TA NG  ALE +     QE Q          
Sbjct: 4   VLIVDDEPLIREGLKSLIDWEALGIEVVGTAANGKEALELI-----QETQ---------P 49

Query: 80  NLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPL 139
           ++VITD  MPGM G +L+K IKE S   +   +++S  +      + ++ G + ++LKP+
Sbjct: 50  DIVITDINMPGMDGLDLIKAIKEQS--PDTEFIILSGYDEFEYAKKAMKLGVKDYLLKPV 107

Query: 140 KPSDVKKLTGHLIN 153
             +++++    +I 
Sbjct: 108 DKAELEEALKKIIG 121

Length = 475

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

 Score = 59.1 bits (144), Expect = 4e-11
 Identities = 39/130 (30%), Positives = 63/130 (48%), Gaps = 18/130 (13%)

Query: 23  VLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLV 82
           +L VDD   + K++E  L      V TA +G  A+       E+EQ           +++
Sbjct: 5   ILVVDDIPANVKLLEAKLLAEYYTVLTASSGAEAIAIC----EREQ----------PDII 50

Query: 83  ITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKP- 141
           + D  MPGM G+E+ +++K       +PVV+V++ + P      LE GA  F+ KP+   
Sbjct: 51  LLDVMMPGMDGFEVCRRLKSDPATTHIPVVMVTALDDPEDRVRGLEAGADDFLTKPINDV 110

Query: 142 ---SDVKKLT 148
              + VK LT
Sbjct: 111 ALFARVKSLT 120

Length = 457

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

 Score = 55.1 bits (133), Expect = 7e-10
 Identities = 38/121 (31%), Positives = 63/121 (52%), Gaps = 19/121 (15%)

Query: 22  HVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNL 81
            +L VDD    RKI+E  L     +V TA +G  AL+       +EQ           +L
Sbjct: 8   KILVVDDEAYIRKILETRLSIIGYEVITASDGEEALKLF----RKEQ----------PDL 53

Query: 82  VITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSS-ENIPTRINECLEEGAQMFMLKPLK 140
           VI D  MP + GY + ++I++ S   +VP++++++  ++  RI   LE GA  +++KP  
Sbjct: 54  VILDVMMPKLDGYGVCQEIRKES---DVPIIMLTALGDVSDRITG-LELGADDYVVKPFS 109

Query: 141 P 141
           P
Sbjct: 110 P 110

Length = 240

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

 Score = 53.8 bits (130), Expect = 2e-09
 Identities = 35/124 (28%), Positives = 56/124 (45%), Gaps = 18/124 (14%)

Query: 22  HVLAVDDSIVDRKIVENLL-KNSACKVT-TAENGMRALEFLGLVDEQEQQNNLNSNGTKV 79
            VL VDD  + R+ +  LL      +V   A NG  AL+                   K 
Sbjct: 2   KVLIVDDHPLVREGLRQLLELEPDLEVVGEASNGEEALDLA--------------RELKP 47

Query: 80  NLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPL 139
           ++V+ D  MPGM G E LK+++      ++ VVV+++ + P  +   L  GA  ++LK  
Sbjct: 48  DVVLLDLSMPGMDGLEALKQLRAR--GPDIKVVVLTAHDDPAYVIRALRAGADGYLLKDA 105

Query: 140 KPSD 143
            P +
Sbjct: 106 SPEE 109

Length = 211

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

 Score = 53.1 bits (128), Expect = 3e-09
 Identities = 29/122 (23%), Positives = 56/122 (45%), Gaps = 18/122 (14%)

Query: 21  PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVN 80
             +L V+D     ++++  L+    +V  A +G  ALE      EQ             +
Sbjct: 1   MRILLVEDDPELAELLKEYLEEEGYEVDVAADGEEALE---AAREQ------------PD 45

Query: 81  LVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSS-ENIPTRINECLEEGAQMFMLKPL 139
           LV+ D  +P + G EL ++++        P++V+++ ++   R+   LE GA  ++ KP 
Sbjct: 46  LVLLDLMLPDLDGLELCRRLRAKKGSG-PPIIVLTARDDEEDRV-LGLEAGADDYLTKPF 103

Query: 140 KP 141
            P
Sbjct: 104 SP 105

Length = 229

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

 Score = 53.1 bits (128), Expect = 7e-09
 Identities = 35/135 (25%), Positives = 61/135 (45%), Gaps = 19/135 (14%)

Query: 14  SSSNPKPP---HVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQN 70
             + P  P    +L VDD   +R I+  +L     +VTTA +G  ALE LG      Q  
Sbjct: 681 VINLPLQPWQLQILLVDDVETNRDIIGMMLVELGQQVTTAASGTEALE-LG-----RQH- 733

Query: 71  NLNSNGTKVNLVITDYCMPGMTGYELLKKIKESS--VMKEVPVVVVSSENIPTRINECLE 128
                  + +LV+ D  MPG+ G E  +  ++    +  +  +V +++   P  I+ C +
Sbjct: 734 -------RFDLVLMDIRMPGLDGLETTQLWRDDPNNLDPDCMIVALTANAAPEEIHRCKK 786

Query: 129 EGAQMFMLKPLKPSD 143
            G   ++ KP+  + 
Sbjct: 787 AGMNHYLTKPVTLAQ 801

Length = 921

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

 Score = 49.7 bits (119), Expect = 7e-08
 Identities = 33/125 (26%), Positives = 54/125 (43%), Gaps = 19/125 (15%)

Query: 23  VLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLV 82
           V  VDD    R ++E  L  +  +V T  N    L  L     + Q +          L+
Sbjct: 1   VWVVDDDRSIRWVLEKALSRAGYEVRTFGNAASVLRALA----RGQPD----------LL 46

Query: 83  ITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPS 142
           ITD  MPG  G +LL +IK      ++PV+V+++ +         + GA  ++ KP    
Sbjct: 47  ITDVRMPGEDGLDLLPQIK--KRHPQLPVIVMTAHSDLDTAVAAYQRGAFEYLPKPF--- 101

Query: 143 DVKKL 147
           D+ + 
Sbjct: 102 DLDEA 106

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|214668 smart00448, REC, cheY-homologous receiver domain

 Score = 44.1 bits (105), Expect = 4e-07
 Identities = 19/69 (27%), Positives = 31/69 (44%), Gaps = 14/69 (20%)

Query: 21 PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVN 80
            +L VDD  + R++++ LL+    +V  A +G  ALE L                 K +
Sbjct: 1  MRILVVDDDPLLRELLKALLEKEGYEVDEATDGEEALELL--------------KEEKPD 46

Query: 81 LVITDYCMP 89
          L++ D  MP
Sbjct: 47 LILLDIMMP 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|182772 PRK10841, PRK10841, hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional

 Score = 47.3 bits (113), Expect = 6e-07
 Identities = 31/132 (23%), Positives = 63/132 (47%), Gaps = 23/132 (17%)

Query: 6   VASSSSSSSSSNPKPP-------HVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALE 58
           + S  S+++  +            +L VDD  ++R+++ + L +   +  TA +G+ AL 
Sbjct: 780 LESDDSANALPSTDKAVSDNDDMMILVVDDHPINRRLLADQLGSLGYQCKTANDGVDALN 839

Query: 59  FLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSEN 118
            L        +N+       +++V+TD  MP M GY L +++++      +PV+ V++  
Sbjct: 840 VL-------SKNH-------IDIVLTDVNMPNMDGYRLTQRLRQLG--LTLPVIGVTANA 883

Query: 119 IPTRINECLEEG 130
           +      CLE G
Sbjct: 884 LAEEKQRCLEAG 895

Length = 924

>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 = 46.5 bits (111), Expect = 9e-07
 Identities = 44/139 (31%), Positives = 64/139 (46%), Gaps = 36/139 (25%)

Query: 23  VLAVDDSIVDRKIVENLLKNSACK---VTTAENGMRALEFLGLVDEQEQQNNLNSNGTKV 79
           VL VDDS + RK++ ++L NS      V TA NG  A++ +                 K 
Sbjct: 4   VLVVDDSALMRKVISDIL-NSDPDIEVVGTARNGREAIDKVK--------------KLKP 48

Query: 80  NLVITDYCMPGMTGYELLKKIKESSVMKE--VPVVVVSSENIPTR----INECLEEGAQM 133
           +++  D  MP M G E L+KI     M+   +PV++VSS  +         E LE GA  
Sbjct: 49  DVITLDVEMPVMDGLEALRKI-----MRLRPLPVIMVSS--LTEEGAEATLEALELGAVD 101

Query: 134 FMLKP-----LKPSDVKKL 147
           F+ KP     L   +V +L
Sbjct: 102 FIAKPSGGISLGLDEVAEL 120

Length = 350

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

 Score = 45.0 bits (107), Expect = 2e-06
 Identities = 26/121 (21%), Positives = 54/121 (44%), Gaps = 14/121 (11%)

Query: 21  PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVN 80
             +L V+D    R+++   L+ +   V  A +G             E    +N  G    
Sbjct: 3   RRILVVEDEPAIRELIAYNLEKAGYDVVEAGDG------------DEALTLINERGPD-- 48

Query: 81  LVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLK 140
           L++ D+ +PG +G EL ++++     + +P++++++          LE GA  ++ KP  
Sbjct: 49  LILLDWMLPGTSGIELCRRLRRRPETRAIPIIMLTARGEEEDRVRGLETGADDYITKPFS 108

Query: 141 P 141
           P
Sbjct: 109 P 109

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|182277 PRK10161, PRK10161, transcriptional regulator PhoB; Provisional

 Score = 44.3 bits (104), Expect = 5e-06
 Identities = 30/122 (24%), Positives = 59/122 (48%), Gaps = 14/122 (11%)

Query: 23  VLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLV 82
           +L V+D    R++V  +L+ +  +   AE            D     N LN      +L+
Sbjct: 5   ILVVEDEAPIREMVCFVLEQNGFQPVEAE------------DYDSAVNQLNEPWP--DLI 50

Query: 83  ITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPS 142
           + D+ +PG +G + +K +K  S+ +++PVV++++          LE GA  ++ KP  P 
Sbjct: 51  LLDWMLPGGSGIQFIKHLKRESMTRDIPVVMLTARGEEEDRVRGLETGADDYITKPFSPK 110

Query: 143 DV 144
           ++
Sbjct: 111 EL 112

Length = 229

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

 Score = 44.2 bits (105), Expect = 5e-06
 Identities = 29/91 (31%), Positives = 43/91 (47%), Gaps = 16/91 (17%)

Query: 50  AENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEV 109
           A NG+ ALE LG              G   +L+I D  MP M G E ++ ++      + 
Sbjct: 3   AANGVDALELLG--------------GFTPDLIICDLAMPRMNGIEFVEHLRNRGD--QT 46

Query: 110 PVVVVSSENIPTRINECLEEGAQMFMLKPLK 140
           PV+V+S+      I + L  G Q  +LKP+K
Sbjct: 47  PVLVISATENMADIAKALRLGVQDVLLKPVK 77

Length = 303

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

 Score = 43.9 bits (104), Expect = 5e-06
 Identities = 38/130 (29%), Positives = 61/130 (46%), Gaps = 18/130 (13%)

Query: 16  SNPKPPHVLAVDDSIVDRKIVENLLKNSA--CKVTTAENGMRALEFLGLVDEQEQQNNLN 73
           SN +P  +L +DD  + R  V+ L+  +     V  A NG + +E    +D         
Sbjct: 2   SNQEPATILLIDDHPMLRTGVKQLISMAPDITVVGEASNGEQGIELAESLDP-------- 53

Query: 74  SNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQM 133
                 +L++ D  MPGM G E L K++E S+   + V  VS  N    +   L+ GA  
Sbjct: 54  ------DLILLDLNMPGMNGLETLDKLREKSLSGRIVVFSVS--NHEEDVVTALKRGADG 105

Query: 134 FMLKPLKPSD 143
           ++LK ++P D
Sbjct: 106 YLLKDMEPED 115

Length = 216

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

 Score = 43.5 bits (103), Expect = 7e-06
 Identities = 33/119 (27%), Positives = 55/119 (46%), Gaps = 18/119 (15%)

Query: 21  PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVN 80
             V  VDD    R  +  LL ++  +V   E+    L+ L  +            G    
Sbjct: 4   GVVHVVDDDEAMRDSLAFLLDSAGFEVRLFESAQAFLDALPGL----------RFGC--- 50

Query: 81  LVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSE-NIPTRINECLEEGAQMFMLKP 138
            V+TD  MPG+ G ELL+++K       +PV+V++   ++P  + E ++ GA  F+ KP
Sbjct: 51  -VVTDVRMPGIDGIELLRRLKARGSP--LPVIVMTGHGDVPLAV-EAMKLGAVDFIEKP 105

Length = 202

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

 Score = 43.3 bits (102), Expect = 1e-05
 Identities = 22/96 (22%), Positives = 45/96 (46%), Gaps = 16/96 (16%)

Query: 21  PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVN 80
           P ++ VDD     K++  +L  +  +V +  + + AL+ L        +        K +
Sbjct: 1   PRIIIVDDDAAIVKLLSVILSRAGHEVRSCSHPVEALDLL--------EVF------KPD 46

Query: 81  LVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSS 116
           L+  D  MP M G E  +++++  +   VP++ +SS
Sbjct: 47  LIFLDIVMPYMNGIEFAEQVRD--IESAVPIIFISS 80

Length = 361

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

 Score = 42.7 bits (100), Expect = 2e-05
 Identities = 33/117 (28%), Positives = 55/117 (47%), Gaps = 16/117 (13%)

Query: 23  VLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLV 82
           +L VDD I    I++ LL+     V  A +G +ALE                     +LV
Sbjct: 8   ILVVDDDISHCTILQALLRGWGYNVALANSGRQALE--------------QVREQVFDLV 53

Query: 83  ITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPL 139
           + D  M  M G   LK+IK  ++   +PV+++++ +      E L+ GA  +++KPL
Sbjct: 54  LCDVRMAEMDGIATLKEIK--ALNPAIPVLIMTAYSSVETAVEALKTGALDYLIKPL 108

Length = 441

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

 Score = 42.4 bits (101), Expect = 2e-05
 Identities = 41/125 (32%), Positives = 55/125 (44%), Gaps = 31/125 (24%)

Query: 23  VLAVDDSIVDRKIVENLLKNSACK---VTTAENGMRALEFLGLVDEQEQQNNLNSNGTKV 79
           VL VDDS   R+++  +L NS      V TA +G+ A E    + +              
Sbjct: 6   VLVVDDSAFMRRLISEIL-NSDPDIEVVGTAPDGLEARE---KIKKLNPD---------- 51

Query: 80  NLVIT-DYCMPGMTGYELLKKIKESSVMKE--VPVVVVSS---ENIPTRINECLEEGAQM 133
             VIT D  MP M G + L+KI     M+    PVV+VSS         +   LE GA  
Sbjct: 52  --VITLDVEMPVMDGLDALEKI-----MRLRPTPVVMVSSLTERGAEITL-RALELGAVD 103

Query: 134 FMLKP 138
           F+ KP
Sbjct: 104 FVTKP 108

Length = 354

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

 Score = 41.7 bits (98), Expect = 5e-05
 Identities = 38/122 (31%), Positives = 61/122 (50%), Gaps = 18/122 (14%)

Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTK 78
           KP H+L VDD     K++   L +    V TAE+G  AL  L              N  K
Sbjct: 4   KPAHLLLVDDDPGLLKLLGMRLTSEGYSVVTAESGQEALRVL--------------NREK 49

Query: 79  VNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSE-NIPTRINECLEEGAQMFMLK 137
           V+LVI+D  M  M G +L  +I++  V   +PV+++++  +IP  +    ++G   F+ K
Sbjct: 50  VDLVISDLRMDEMDGMQLFAEIQK--VQPGMPVIILTAHGSIPDAV-AATQQGVFSFLTK 106

Query: 138 PL 139
           P+
Sbjct: 107 PV 108

Length = 444

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

 Score = 41.4 bits (98), Expect = 6e-05
 Identities = 24/92 (26%), Positives = 44/92 (47%), Gaps = 14/92 (15%)

Query: 23  VLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLV 82
           V+AVDD+  + K++  LL+     V   ++G +A+       EQ +Q          +L+
Sbjct: 670 VMAVDDNPANLKLIGALLEEQVEHVVLCDSGHQAV-------EQAKQRPF-------DLI 715

Query: 83  ITDYCMPGMTGYELLKKIKESSVMKEVPVVVV 114
           + D  MPGM G    + I++    +  P++ V
Sbjct: 716 LMDIQMPGMDGIRACELIRQLPHNQNTPIIAV 747

Length = 919

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

 Score = 41.5 bits (98), Expect = 7e-05
 Identities = 36/131 (27%), Positives = 57/131 (43%), Gaps = 25/131 (19%)

Query: 22  HVLAVDD----SIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
           ++L V+D     IV R ++E L       V  A  G  ALE     D  E          
Sbjct: 527 NILLVEDIELNVIVARSVLEKL----GNSVDVAMTGKEALEM---FDPDEYD-------- 571

Query: 78  KVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLK 137
              LV+ D  +P MTG ++ ++++E    +++P +V  + N+     E L+ G    + K
Sbjct: 572 ---LVLLDIQLPDMTGLDIARELRERYPREDLPPLVALTANVLKDKKEYLDAGMDDVLSK 628

Query: 138 PLKPSDVKKLT 148
           PL    V  LT
Sbjct: 629 PLS---VPALT 636

Length = 779

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

 Score = 41.0 bits (96), Expect = 8e-05
 Identities = 35/116 (30%), Positives = 54/116 (46%), Gaps = 16/116 (13%)

Query: 23  VLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLV 82
           V  VDD    R ++E  L  +    TT ENG   LE             L S    V  +
Sbjct: 6   VWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLE------------ALASKTPDV--L 51

Query: 83  ITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKP 138
           ++D  MPGM G  LLK+IK+   M  +PV+++++ +         ++GA  ++ KP
Sbjct: 52  LSDIRMPGMDGLALLKQIKQRHPM--LPVIIMTAHSDLDAAVSAYQQGAFDYLPKP 105

Length = 469

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

 Score = 40.2 bits (94), Expect = 2e-04
 Identities = 32/122 (26%), Positives = 57/122 (46%), Gaps = 26/122 (21%)

Query: 22  HVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNL 81
           HVL +DD +  R ++   L   A KVT   +              +Q N + ++ T V++
Sbjct: 3   HVLVIDDDVAMRHLIVEYLTIHAFKVTAVADS-------------QQFNRVLASET-VDV 48

Query: 82  VITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINEC-----LEEGAQMFML 136
           V+ D  +    G E+++ +   S   +VP++++S +    R+ E      LE GA  F+ 
Sbjct: 49  VVVDLNLGREDGLEIVRSLATKS---DVPIIIISGD----RLEEADKVVALELGATDFIA 101

Query: 137 KP 138
           KP
Sbjct: 102 KP 103

Length = 241

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

 Score = 39.0 bits (91), Expect = 3e-04
 Identities = 29/116 (25%), Positives = 52/116 (44%), Gaps = 17/116 (14%)

Query: 23  VLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLV 82
           VL V+D    R+ +   L+    +V  AE   R L              L +   K +L+
Sbjct: 4   VLIVEDEQAIRRFLRTALEGDGMRVFEAETLQRGL--------------LEAATRKPDLI 49

Query: 83  ITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKP 138
           I D  +P   G E ++ +++ S    +PV+V+S+ +  +     L+ GA  ++ KP
Sbjct: 50  ILDLGLPDGDGIEFIRDLRQWSA---IPVIVLSARSEESDKIAALDAGADDYLSKP 102

Length = 225

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

 Score = 38.6 bits (90), Expect = 4e-04
 Identities = 26/100 (26%), Positives = 54/100 (54%), Gaps = 16/100 (16%)

Query: 51  ENGMRALEFL--GLVDEQEQQNNLNSNG---------TKVNLVITDYCMPGMTGYELLKK 99
           E+  +  E+L  GL  E     +  SNG            +L+I D  +PGM G+++L+ 
Sbjct: 5   EDEQKTAEYLQQGLS-ESGYVVDAASNGRDGLHLALKDDYDLIILDVMLPGMDGWQILQT 63

Query: 100 IKESSVMKEVPVVVVSS-ENIPTRINECLEEGAQMFMLKP 138
           ++ S   K+ PV+ +++ +++  ++ + L+ GA  +++KP
Sbjct: 64  LRRSG--KQTPVLFLTARDSVADKV-KGLDLGADDYLVKP 100

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

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

 Score = 38.7 bits (90), Expect = 5e-04
 Identities = 27/128 (21%), Positives = 53/128 (41%), Gaps = 18/128 (14%)

Query: 23  VLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLV 82
           +L VDD    R+++         +   A NG  AL     +                ++V
Sbjct: 7   ILIVDDEDNVRRMLSTAFALQGFETHCANNGRTALHLFADI--------------HPDVV 52

Query: 83  ITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSS-ENIPTRINECLEEGAQMFMLKPLKP 141
           + D  MP M G + LK+++        PV+++++   + T + E L  GA  +++KP   
Sbjct: 53  LMDIRMPEMDGIKALKEMRSHE--TRTPVILMTAYAEVETAV-EALRCGAFDYVIKPFDL 109

Query: 142 SDVKKLTG 149
            ++  +  
Sbjct: 110 DELNLIVQ 117

Length = 457

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

 Score = 37.3 bits (87), Expect = 0.001
 Identities = 34/129 (26%), Positives = 58/129 (44%), Gaps = 18/129 (13%)

Query: 17  NPKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNG 76
            P+ P V  VDD    R  +  LL+++  +V    +     EFL           L+  G
Sbjct: 1   MPREPLVHVVDDDESVRDALAFLLESAGFQVKCFASAE---EFLA-------AAPLDRPG 50

Query: 77  TKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSE-NIPTRINECLEEGAQMFM 135
                ++ D  MPGM+G EL  ++ E  +    PV+ ++   +IP  + + ++ GA  F+
Sbjct: 51  ----CLLLDVRMPGMSGLELQDRLAERGIRL--PVIFLTGHGDIPMAV-QAMKAGAVDFL 103

Query: 136 LKPLKPSDV 144
            KP    D+
Sbjct: 104 EKPFSEQDL 112

Length = 202

>gnl|CDD|182408 PRK10360, PRK10360, DNA-binding transcriptional activator UhpA; Provisional

 Score = 37.3 bits (86), Expect = 0.001
 Identities = 19/69 (27%), Positives = 35/69 (50%), Gaps = 5/69 (7%)

Query: 76  GTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFM 135
           G  V + I D  MP ++G ELL ++      K +  +++S  + P  + + L  GA+ F+
Sbjct: 45  GRGVQVCICDISMPDISGLELLSQLP-----KGMATIMLSVHDSPALVEQALNAGARGFL 99

Query: 136 LKPLKPSDV 144
            K   P ++
Sbjct: 100 SKRCSPDEL 108

Length = 196

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

 Score = 37.2 bits (87), Expect = 0.001
 Identities = 35/128 (27%), Positives = 61/128 (47%), Gaps = 24/128 (18%)

Query: 21  PHVLAVDD--SIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTK 78
           P +L V+D  +I D  +    L++    V   E G+ AL      D+  QQ         
Sbjct: 4   PTILLVEDEQAIADTLVY--ALQSEGFTVEWFERGLPAL------DKLRQQ--------P 47

Query: 79  VNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVS--SENIPTRINECLEEGAQMFML 136
            +LVI D  +P ++G+EL +++        +PV+ ++  S+ +  R+   LE GA  ++ 
Sbjct: 48  PDLVILDVGLPDISGFELCRQLLAFH--PALPVIFLTARSDEV-DRL-VGLEIGADDYVA 103

Query: 137 KPLKPSDV 144
           KP  P +V
Sbjct: 104 KPFSPREV 111

Length = 228

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

 Score = 36.4 bits (84), Expect = 0.003
 Identities = 29/124 (23%), Positives = 55/124 (44%), Gaps = 18/124 (14%)

Query: 20  PPHVLAVDDSIVDRKIVENLLKNSACKVTTAE--NGMRALEFLGLVDEQEQQNNLNSNGT 77
           P  VL VDD  + R+ V  LL+        AE  +G  A++               +N  
Sbjct: 6   PFQVLIVDDHPLMRRGVRQLLELDPGFEVVAEAGDGASAIDL--------------ANRL 51

Query: 78  KVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLK 137
             ++++ D  M GM+G + L  ++   V  ++ ++ VS  +  + +   ++ GA  ++LK
Sbjct: 52  DPDVILLDLNMKGMSGLDTLNALRRDGVTAQIIILTVS--DASSDVFALIDAGADGYLLK 109

Query: 138 PLKP 141
              P
Sbjct: 110 DSDP 113

Length = 215

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

 Score = 36.7 bits (85), Expect = 0.003
 Identities = 34/154 (22%), Positives = 63/154 (40%), Gaps = 15/154 (9%)

Query: 1   MDACGVASSSSSSSSSNPKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFL 60
           +     A  S++ +  +  P  VL V+D+ V++ + +  L     KVT AE+G  ALE  
Sbjct: 683 LTRGKPAEDSATLTVIDLPPQRVLLVEDNEVNQMVAQGFLTRLGHKVTLAESGQSALECF 742

Query: 61  GLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMK-EVPVVVVSSENI 119
                Q             +L + D  +P   G  LL++++     K EV  +  S+   
Sbjct: 743 ----HQHA----------FDLALLDINLPDGDGVTLLQQLRAIYGAKNEVKFIAFSAHVF 788

Query: 120 PTRINECLEEGAQMFMLKPLKPSDVKKLTGHLIN 153
              + + L  G   F+ KP+    +  +   ++ 
Sbjct: 789 NEDVAQYLAAGFDGFLAKPVVEEQLTAMIAVILA 822

This protein, TorS, is part of a regulatory system for the torCAD operon that encodes the pterin molybdenum cofactor-containing enzyme trimethylamine-N-oxide (TMAO) reductase (TorA), a cognate chaperone (TorD), and a penta-haem cytochrome (TorC). TorS works together with the inducer-binding protein TorT and the response regulator TorR. TorS contains histidine kinase ATPase (pfam02518), HAMP (pfam00672), phosphoacceptor (pfam00512), and phosphotransfer (pfam01627) domains and a response regulator receiver domain (pfam00072) [Signal transduction, Two-component systems]. Length = 968

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

 Score = 36.1 bits (84), Expect = 0.003
 Identities = 32/126 (25%), Positives = 56/126 (44%), Gaps = 27/126 (21%)

Query: 21  PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVN 80
           PH+L V+D +V R  ++++ +     V  A +G              + + + S    +N
Sbjct: 4   PHILIVEDELVTRNTLKSIFEAEGYDVFEATDG-------------AEMHQILSEND-IN 49

Query: 81  LVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINEC-----LEEGAQMFM 135
           LVI D  +PG  G  L ++++E      V ++ ++      R NE      LE GA  ++
Sbjct: 50  LVIMDINLPGKNGLLLARELREQ---ANVALMFLTG-----RDNEVDKILGLEIGADDYI 101

Query: 136 LKPLKP 141
            KP  P
Sbjct: 102 TKPFNP 107

Length = 237

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

 Score = 35.8 bits (83), Expect = 0.004
 Identities = 32/134 (23%), Positives = 63/134 (47%), Gaps = 25/134 (18%)

Query: 20  PPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKV 79
             H+L V+D  V R  ++   +     V+ A +G       G+ +  + Q+        V
Sbjct: 2   SYHILVVEDEPVTRARLQGYFEQEGYTVSEAASGA------GMREIMQNQH--------V 47

Query: 80  NLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVS--SENIPTRINECLEEGAQMFMLK 137
           +L++ D  +PG  G  L ++++  S    V +++V+  +++I   +   LE GA  ++ K
Sbjct: 48  DLILLDINLPGEDGLMLTRELRSRS---TVGIILVTGRTDSIDRIVG--LEMGADDYVTK 102

Query: 138 PLKPSD----VKKL 147
           PL+  +    VK L
Sbjct: 103 PLELRELLVRVKNL 116

Length = 221

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	153
COG0745	229	OmpR Response regulators consisting of a CheY-like	99.91
PF00072	112	Response_reg: Response regulator receiver domain;	99.87
COG2204	464	AtoC Response regulator containing CheY-like recei	99.86
COG4566	202	TtrR Response regulator [Signal transduction mecha	99.85
COG4753	475	Response regulator containing CheY-like receiver d	99.84
COG4565	224	CitB Response regulator of citrate/malate metaboli	99.82
COG3437	360	Response regulator containing a CheY-like receiver	99.81
KOG0519	786	consensus Sensory transduction histidine kinase [S	99.8
PLN03029	222	type-a response regulator protein; Provisional	99.79
COG2197	211	CitB Response regulator containing a CheY-like rec	99.77
COG0784	130	CheY FOG: CheY-like receiver [Signal transduction	99.77
PRK10046	225	dpiA two-component response regulator DpiA; Provis	99.77
COG3706	435	PleD Response regulator containing a CheY-like rec	99.76
PRK11107	919	hybrid sensory histidine kinase BarA; Provisional	99.75
PRK10161	229	transcriptional regulator PhoB; Provisional	99.74
PRK11173	237	two-component response regulator; Provisional	99.74
PRK10816	223	DNA-binding transcriptional regulator PhoP; Provis	99.74
PRK09836	227	DNA-binding transcriptional activator CusR; Provis	99.74
TIGR02154	226	PhoB phosphate regulon transcriptional regulatory	99.74
PRK10529	225	DNA-binding transcriptional activator KdpE; Provis	99.74
COG3947	361	Response regulator containing CheY-like receiver a	99.73
PRK10841	924	hybrid sensory kinase in two-component regulatory	99.73
PRK10840	216	transcriptional regulator RcsB; Provisional	99.73
PRK10643	222	DNA-binding transcriptional regulator BasR; Provis	99.73
PRK09468	239	ompR osmolarity response regulator; Provisional	99.72
PRK10336	219	DNA-binding transcriptional regulator QseB; Provis	99.72
PRK10766	221	DNA-binding transcriptional regulator TorR; Provis	99.72
PRK11083	228	DNA-binding response regulator CreB; Provisional	99.72
PRK15347	921	two component system sensor kinase SsrA; Provision	99.72
PRK11466	914	hybrid sensory histidine kinase TorS; Provisional	99.71
COG4567	182	Response regulator consisting of a CheY-like recei	99.71
TIGR02956	968	TMAO_torS TMAO reductase sytem sensor TorS. This p	99.71
TIGR03787	227	marine_sort_RR proteobacterial dedicated sortase s	99.7
PRK10955	232	DNA-binding transcriptional regulator CpxR; Provis	99.7
PRK13856	241	two-component response regulator VirG; Provisional	99.7
PRK10701	240	DNA-binding transcriptional regulator RstA; Provis	99.7
PRK11517	223	transcriptional regulatory protein YedW; Provision	99.7
CHL00148	240	orf27 Ycf27; Reviewed	99.69
PRK09958	204	DNA-binding transcriptional activator EvgA; Provis	99.69
PRK10430	239	DNA-binding transcriptional activator DcuR; Provis	99.69
PRK11091	779	aerobic respiration control sensor protein ArcB; P	99.69
TIGR02875	262	spore_0_A sporulation transcription factor Spo0A.	99.69
TIGR01387	218	cztR_silR_copR heavy metal response regulator. Mem	99.68
PRK10923	469	glnG nitrogen regulation protein NR(I); Provisiona	99.67
PRK15115	444	response regulator GlrR; Provisional	99.67
PRK11361	457	acetoacetate metabolism regulatory protein AtoC; P	99.67
PRK09935	210	transcriptional regulator FimZ; Provisional	99.67
PRK09581	457	pleD response regulator PleD; Reviewed	99.67
PRK09483	217	response regulator; Provisional	99.66
PRK10365	441	transcriptional regulatory protein ZraR; Provision	99.66
PRK14084	246	two-component response regulator; Provisional	99.65
PRK09959	1197	hybrid sensory histidine kinase in two-component r	99.65
TIGR02915	445	PEP_resp_reg putative PEP-CTERM system response re	99.64
PRK10710	240	DNA-binding transcriptional regulator BaeR; Provis	99.63
PRK10360	196	DNA-binding transcriptional activator UhpA; Provis	99.63
PRK09581	457	pleD response regulator PleD; Reviewed	99.63
PRK09390	202	fixJ response regulator FixJ; Provisional	99.63
TIGR01818	463	ntrC nitrogen regulation protein NR(I). This model	99.63
PRK15479	221	transcriptional regulatory protein TctD; Provision	99.62
PRK11697	238	putative two-component response-regulatory protein	99.61
PRK10610	129	chemotaxis regulatory protein CheY; Provisional	99.61
PRK13558	665	bacterio-opsin activator; Provisional	99.57
PRK10100	216	DNA-binding transcriptional regulator CsgD; Provis	99.57
PRK12555	337	chemotaxis-specific methylesterase; Provisional	99.56
PRK10403	215	transcriptional regulator NarP; Provisional	99.56
PRK13435	145	response regulator; Provisional	99.55
PRK10651	216	transcriptional regulator NarL; Provisional	99.55
PRK15369	211	two component system sensor kinase SsrB; Provision	99.54
PRK11475	207	DNA-binding transcriptional activator BglJ; Provis	99.52
PRK00742	354	chemotaxis-specific methylesterase; Provisional	99.52
PRK09191	261	two-component response regulator; Provisional	99.49
PRK15411	207	rcsA colanic acid capsular biosynthesis activation	99.48
PRK13837	828	two-component VirA-like sensor kinase; Provisional	99.48
COG2201	350	CheB Chemotaxis response regulator containing a Ch	99.47
cd00156	113	REC Signal receiver domain; originally thought to	99.43
COG3707	194	AmiR Response regulator with putative antiterminat	99.41
PRK13557	540	histidine kinase; Provisional	99.41
PRK10693	303	response regulator of RpoS; Provisional	99.36
PRK15029	755	arginine decarboxylase; Provisional	99.19
COG3279	244	LytT Response regulator of the LytR/AlgR family [T	99.06
PRK11107	919	hybrid sensory histidine kinase BarA; Provisional	98.75
PF06490	109	FleQ: Flagellar regulatory protein FleQ; InterPro:	98.34
COG3706	435	PleD Response regulator containing a CheY-like rec	98.25
smart00448	55	REC cheY-homologous receiver domain. CheY regulate	97.8
cd02071	122	MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 bin	97.61
PRK02261	137	methylaspartate mutase subunit S; Provisional	97.57
PF03709	115	OKR_DC_1_N: Orn/Lys/Arg decarboxylase, N-terminal	97.17
TIGR00640	132	acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal	97.07
COG4999	140	Uncharacterized domain of BarA-like signal transdu	96.91
cd02067	119	B12-binding B12 binding domain (B12-BD). This doma	96.76
PRK10618	894	phosphotransfer intermediate protein in two-compon	96.44
TIGR01501	134	MthylAspMutase methylaspartate mutase, S subunit.	96.35
PRK15399	713	lysine decarboxylase LdcC; Provisional	96.13
cd02070	201	corrinoid_protein_B12-BD B12 binding domain of cor	96.07
PRK15400	714	lysine decarboxylase CadA; Provisional	95.8
TIGR03815	322	CpaE_hom_Actino helicase/secretion neighborhood Cp	95.45
cd02069	213	methionine_synthase_B12_BD B12 binding domain of m	95.32
PF10087	97	DUF2325: Uncharacterized protein conserved in bact	95.22
cd02072	128	Glm_B12_BD B12 binding domain of glutamate mutase	95.22
PF02310	121	B12-binding: B12 binding domain; InterPro: IPR0061	95.08
TIGR02370	197	pyl_corrinoid methyltransferase cognate corrinoid	94.74
PRK10558	256	alpha-dehydro-beta-deoxy-D-glucarate aldolase; Pro	94.33
cd04728	248	ThiG Thiazole synthase (ThiG) is the tetrameric en	94.0
TIGR02311	249	HpaI 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldola	93.88
PRK00208	250	thiG thiazole synthase; Reviewed	93.35
COG0512	191	PabA Anthranilate/para-aminobenzoate synthases com	93.08
TIGR03239	249	GarL 2-dehydro-3-deoxyglucarate aldolase. In E. co	92.17
PRK09426	714	methylmalonyl-CoA mutase; Reviewed	91.95
PRK10128	267	2-keto-3-deoxy-L-rhamnonate aldolase; Provisional	90.88
PLN02591	250	tryptophan synthase	90.66
PRK13111	258	trpA tryptophan synthase subunit alpha; Provisiona	90.61
PRK05749	425	3-deoxy-D-manno-octulosonic-acid transferase; Revi	90.56
PRK00043	212	thiE thiamine-phosphate pyrophosphorylase; Reviewe	90.47
PF02581	180	TMP-TENI: Thiamine monophosphate synthase/TENI; In	90.27
COG2185	143	Sbm Methylmalonyl-CoA mutase, C-terminal domain/su	90.26
TIGR00262	256	trpA tryptophan synthase, alpha subunit. Tryptopha	90.24
cd04724	242	Tryptophan_synthase_alpha Ttryptophan synthase (TR	89.9
PRK07896	289	nicotinate-nucleotide pyrophosphorylase; Provision	89.64
TIGR01334	277	modD putative molybdenum utilization protein ModD.	89.53
PF07688	283	KaiA: KaiA domain; InterPro: IPR011648 KaiA is a c	88.74
TIGR00693	196	thiE thiamine-phosphate pyrophosphorylase. This mo	88.45
cd02068	127	radical_SAM_B12_BD B12 binding domain_like associa	88.43
PRK01130	221	N-acetylmannosamine-6-phosphate 2-epimerase; Provi	87.27
PRK08007	187	para-aminobenzoate synthase component II; Provisio	87.19
PRK07428	288	nicotinate-nucleotide pyrophosphorylase; Provision	87.18
TIGR03151	307	enACPred_II putative enoyl-(acyl-carrier-protein)	87.16
CHL00200	263	trpA tryptophan synthase alpha subunit; Provisiona	86.74
cd05212	140	NAD_bind_m-THF_DH_Cyclohyd_like NAD(P) binding dom	86.67
TIGR00138	181	gidB 16S rRNA methyltransferase GidB. GidB (glucos	86.48
cd00452	190	KDPG_aldolase KDPG and KHG aldolase. This family b	86.24
cd02065	125	B12-binding_like B12 binding domain (B12-BD). Most	85.43
PRK03659	601	glutathione-regulated potassium-efflux system prot	85.27
PRK03958	176	tRNA 2'-O-methylase; Reviewed	85.26
TIGR00566	188	trpG_papA glutamine amidotransferase of anthranila	85.03
PRK05848	273	nicotinate-nucleotide pyrophosphorylase; Provision	84.9
PF03602	183	Cons_hypoth95: Conserved hypothetical protein 95;	84.85
cd01573	272	modD_like ModD; Quinolinate phosphoribosyl transfe	84.73
PRK08385	278	nicotinate-nucleotide pyrophosphorylase; Provision	84.63
TIGR02026	497	BchE magnesium-protoporphyrin IX monomethyl ester	84.26
PF03328	221	HpcH_HpaI: HpcH/HpaI aldolase/citrate lyase family	84.19
PF01081	196	Aldolase: KDPG and KHG aldolase; InterPro: IPR0008	84.18
cd04727	283	pdxS PdxS is a subunit of the pyridoxal 5'-phospha	84.13
COG0352	211	ThiE Thiamine monophosphate synthase [Coenzyme met	83.59
PRK07649	195	para-aminobenzoate/anthranilate synthase glutamine	83.32
PRK06843	404	inosine 5-monophosphate dehydrogenase; Validated	83.22
COG0159	265	TrpA Tryptophan synthase alpha chain [Amino acid t	83.0
PRK06774	191	para-aminobenzoate synthase component II; Provisio	82.91
KOG1562	337	consensus Spermidine synthase [Amino acid transpor	82.87
PF01729	169	QRPTase_C: Quinolinate phosphoribosyl transferase,	82.73
KOG4175	268	consensus Tryptophan synthase alpha chain [Amino a	82.55
PRK06015	201	keto-hydroxyglutarate-aldolase/keto-deoxy-phosphog	82.13
cd04729	219	NanE N-acetylmannosamine-6-phosphate epimerase (Na	82.05
TIGR00343	287	pyridoxal 5'-phosphate synthase, synthase subunit	81.94
PRK05458	326	guanosine 5'-monophosphate oxidoreductase; Provisi	81.94
PRK06096	284	molybdenum transport protein ModD; Provisional	81.8
PF00290	259	Trp_syntA: Tryptophan synthase alpha chain; InterP	81.19
TIGR01579	414	MiaB-like-C MiaB-like tRNA modifying enzyme. This	81.11
PLN02335	222	anthranilate synthase	80.96
PRK09490	1229	metH B12-dependent methionine synthase; Provisiona	80.49
cd00564	196	TMP_TenI Thiamine monophosphate synthase (TMP synt	80.11
TIGR02082	1178	metH 5-methyltetrahydrofolate--homocysteine methyl	80.03

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

Probab=99.91  E-value=4.7e-23  Score=151.80  Aligned_cols=114  Identities=23%  Similarity=0.381  Sum_probs=104.5

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKI  100 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~l  100 (153)
                      ++||+|||++.....+...|+..||.+..+.++.+++..+.              .. ||+|++|+.||+++|+++++++
T Consensus         1 ~~ILiveDd~~i~~~l~~~L~~~g~~v~~~~~~~~a~~~~~--------------~~-~dlviLD~~lP~~dG~~~~~~i   65 (229)
T COG0745           1 MRILLVEDDPELAELLKEYLEEEGYEVDVAADGEEALEAAR--------------EQ-PDLVLLDLMLPDLDGLELCRRL   65 (229)
T ss_pred             CeEEEEcCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHh--------------cC-CCEEEEECCCCCCCHHHHHHHH
Confidence            47999999999999999999999999999999999999883              45 9999999999999999999999


Q ss_pred             HhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhh
Q 042079          101 KESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGH  150 (153)
Q Consensus       101 r~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~  150 (153)
                      |+. ....+|||++|+..+......+++.|||||++|||++.||...+.-
T Consensus        66 R~~-~~~~~PIi~Lta~~~~~d~v~gl~~GADDYl~KPf~~~EL~ARi~a  114 (229)
T COG0745          66 RAK-KGSGPPIIVLTARDDEEDRVLGLEAGADDYLTKPFSPRELLARLRA  114 (229)
T ss_pred             Hhh-cCCCCcEEEEECCCcHHHHHHHHhCcCCeeeeCCCCHHHHHHHHHH
Confidence            965 4467899999999999999999999999999999999999865554

>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=99.87  E-value=9.7e-21  Score=123.95  Aligned_cols=111  Identities=33%  Similarity=0.586  Sum_probs=103.5

Q ss_pred             EEEEeCCHHHHHHHHHHHHhcCc-EEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHHH
Q 042079           23 VLAVDDSIVDRKIVENLLKNSAC-KVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKIK  101 (153)
Q Consensus        23 iLiidd~~~~~~~l~~~l~~~~~-~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~lr  101 (153)
                      |||+|+++..+..++..|+..|+ .+..+.+..+++..+.              .+.||++++|+.+++.+|.++++.|+
T Consensus         1 Ilivd~~~~~~~~l~~~l~~~~~~~v~~~~~~~~~~~~~~--------------~~~~d~iiid~~~~~~~~~~~~~~i~   66 (112)
T PF00072_consen    1 ILIVDDDPEIRELLEKLLERAGYEEVTTASSGEEALELLK--------------KHPPDLIIIDLELPDGDGLELLEQIR   66 (112)
T ss_dssp             EEEEESSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHH--------------HSTESEEEEESSSSSSBHHHHHHHHH
T ss_pred             cEEEECCHHHHHHHHHHHHhCCCCEEEEECCHHHHHHHhc--------------ccCceEEEEEeeeccccccccccccc
Confidence            79999999999999999999999 9999999999999884              35699999999999999999999999


Q ss_pred             hccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHh
Q 042079          102 ESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTG  149 (153)
Q Consensus       102 ~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~  149 (153)
                      +..  +.+|+|+++...+.....++++.|+++|+.||++.+++.+.++
T Consensus        67 ~~~--~~~~ii~~t~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~i~  112 (112)
T PF00072_consen   67 QIN--PSIPIIVVTDEDDSDEVQEALRAGADDYLSKPFSPEELRAAIN  112 (112)
T ss_dssp             HHT--TTSEEEEEESSTSHHHHHHHHHTTESEEEESSSSHHHHHHHHH
T ss_pred             ccc--ccccEEEecCCCCHHHHHHHHHCCCCEEEECCCCHHHHHHhhC
Confidence            866  6899999999999999999999999999999999999998764

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 ....

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

Probab=99.86  E-value=1.2e-20  Score=149.71  Aligned_cols=117  Identities=33%  Similarity=0.470  Sum_probs=108.8

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKK   99 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~   99 (153)
                      ..+||||||+...+..+...|+..||.|..+.++.+++..+.              ...||+|++|+.||+++|+++++.
T Consensus         4 ~~~iLvVDDd~~ir~~l~~~L~~~G~~v~~a~~~~~al~~i~--------------~~~~~lvl~Di~mp~~~Gl~ll~~   69 (464)
T COG2204           4 MARILVVDDDPDIRELLEQALELAGYEVVTAESAEEALEALS--------------ESPFDLVLLDIRMPGMDGLELLKE   69 (464)
T ss_pred             cCCEEEEeCCHHHHHHHHHHHHHcCCeEEEeCCHHHHHHHHh--------------cCCCCEEEEecCCCCCchHHHHHH
Confidence            456999999999999999999999999999999999999984              336999999999999999999999


Q ss_pred             HHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079          100 IKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus       100 lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      +++..  +.+|+|++|++.+.+.+.+|++.||.||+.||++++++...+.+.+
T Consensus        70 i~~~~--~~~pVI~~Tg~g~i~~AV~A~k~GA~Dfl~KP~~~~~L~~~v~ral  120 (464)
T COG2204          70 IKSRD--PDLPVIVMTGHGDIDTAVEALRLGAFDFLEKPFDLDRLLAIVERAL  120 (464)
T ss_pred             HHhhC--CCCCEEEEeCCCCHHHHHHHHhcCcceeeeCCCCHHHHHHHHHHHH
Confidence            99865  7899999999999999999999999999999999999998888753

>COG4566 TtrR Response regulator [Signal transduction mechanisms]

Probab=99.85  E-value=3.6e-20  Score=129.88  Aligned_cols=117  Identities=23%  Similarity=0.333  Sum_probs=106.5

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      ..+.|.|+|||...++.+..+|+..||.+..+.++.+.+...              ....+-++++|+.||+++|+++.+
T Consensus         3 ~~~~V~vVDDD~~vr~al~~Ll~s~G~~v~~~~s~~~fL~~~--------------~~~~pGclllDvrMPg~sGlelq~   68 (202)
T COG4566           3 REPLVHVVDDDESVRDALAFLLESAGFQVKCFASAEEFLAAA--------------PLDRPGCLLLDVRMPGMSGLELQD   68 (202)
T ss_pred             CCCeEEEEcCcHHHHHHHHHHHHhCCceeeeecCHHHHHhhc--------------cCCCCCeEEEecCCCCCchHHHHH
Confidence            457799999999999999999999999999999999887764              235688999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      +|.+..  ...|||++|+..+.....+|++.||.|||.||++.+.+.+.+.+.
T Consensus        69 ~L~~~~--~~~PVIfiTGhgDIpmaV~AmK~GAvDFLeKP~~~q~Lldav~~A  119 (202)
T COG4566          69 RLAERG--IRLPVIFLTGHGDIPMAVQAMKAGAVDFLEKPFSEQDLLDAVERA  119 (202)
T ss_pred             HHHhcC--CCCCEEEEeCCCChHHHHHHHHcchhhHHhCCCchHHHHHHHHHH
Confidence            999866  689999999999999999999999999999999999999887764

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

Probab=99.84  E-value=2.6e-20  Score=147.62  Aligned_cols=115  Identities=32%  Similarity=0.507  Sum_probs=105.1

Q ss_pred             eEEEEeCCHHHHHHHHHHHHh--cCcE-EEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           22 HVLAVDDSIVDRKIVENLLKN--SACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        22 ~iLiidd~~~~~~~l~~~l~~--~~~~-v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      +||||||.+..++.|+.++..  .|++ |..+.+|.+|++.+.              ..+||++|+|+.||.++|+++++
T Consensus         3 kVlIVDDE~lIr~GLk~lI~w~~~g~eiVgtA~NG~eAleli~--------------e~~pDiviTDI~MP~mdGLdLI~   68 (475)
T COG4753           3 KVLIVDDEPLIREGLKSLIDWEALGIEVVGTAANGKEALELIQ--------------ETQPDIVITDINMPGMDGLDLIK   68 (475)
T ss_pred             eEEEecChHHHHHHHHHhCChhhcCCeEEEecccHHHHHHHHH--------------hcCCCEEEEecCCCCCcHHHHHH
Confidence            699999999999999999885  4665 568999999999983              56899999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      .+++..  |.+.+|++|+.++-+.+.+|++.|+.+||.||++.++|.+++.++.
T Consensus        69 ~ike~~--p~~~~IILSGy~eFeYak~Am~lGV~dYLLKP~~k~eL~~~L~ki~  120 (475)
T COG4753          69 AIKEQS--PDTEFIILSGYDEFEYAKKAMKLGVKDYLLKPVDKAELEEALKKII  120 (475)
T ss_pred             HHHHhC--CCceEEEEeccchhHHHHHHHhcCchhheeCcCCHHHHHHHHHHHH
Confidence            999854  7899999999999999999999999999999999999999888753

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

Probab=99.82  E-value=2.6e-19  Score=127.79  Aligned_cols=114  Identities=24%  Similarity=0.327  Sum_probs=101.7

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhc-CcE-EEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNS-ACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~-~~~-v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      .++|||+|++...+.-+.++++. ||. |..+.+..+|...+.              ..+||+|++|+.||+.+|++++.
T Consensus         1 i~VLIiEDD~mVaeih~~yv~~~~gF~~vg~A~~~~ea~~~i~--------------~~~pDLILLDiYmPd~~Gi~lL~   66 (224)
T COG4565           1 INVLIIEDDPMVAEIHRRYVKQIPGFSVVGTAGTLEEAKMIIE--------------EFKPDLILLDIYMPDGNGIELLP   66 (224)
T ss_pred             CcEEEEcCchHHHHHHHHHHHhCCCceEEEeeccHHHHHHHHH--------------hhCCCEEEEeeccCCCccHHHHH
Confidence            36999999999999999999975 665 568999999998883              45689999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhh
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGH  150 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~  150 (153)
                      .+|+..  ..+-||++|+..+.+-+.++++.|+.|||.|||..+.+.+.+.+
T Consensus        67 ~ir~~~--~~~DVI~iTAA~d~~tI~~alr~Gv~DYLiKPf~~eRl~~aL~~  116 (224)
T COG4565          67 ELRSQH--YPVDVIVITAASDMETIKEALRYGVVDYLIKPFTFERLQQALTR  116 (224)
T ss_pred             HHHhcC--CCCCEEEEeccchHHHHHHHHhcCchhheecceeHHHHHHHHHH
Confidence            999865  47788999998899999999999999999999999999988765

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

Probab=99.81  E-value=6.1e-19  Score=134.39  Aligned_cols=117  Identities=31%  Similarity=0.468  Sum_probs=106.3

Q ss_pred             CCCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHH
Q 042079           18 PKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELL   97 (153)
Q Consensus        18 ~~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~   97 (153)
                      ....++|++||++..+..++.+|+..+|.+..++++.++++...              +.++|++++|+.||.|+|.+++
T Consensus        12 ~~~~~vl~vDD~~~~~~~~~~lL~~~~y~v~~ae~g~~a~kl~~--------------~~~~dlvllD~~mp~mdg~ev~   77 (360)
T COG3437          12 DEKLTVLLVDDEPDNLEALRQLLRMIGYRVIEAENGEEALKLLQ--------------EEPPDLVLLDVRMPEMDGAEVL   77 (360)
T ss_pred             cccceEEEecCchhHHHHHHHHHHhcccceeeecCchHHHHHhc--------------ccCCceEEeeccCCCccHHHHH
Confidence            35578999999999999999999999999999999999988773              4569999999999999999999


Q ss_pred             HHHHh-ccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHH
Q 042079           98 KKIKE-SSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLT  148 (153)
Q Consensus        98 ~~lr~-~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~  148 (153)
                      ++|+. .+...++|++++|+..+.+...+++..|+++|+.||+++.++....
T Consensus        78 ~~lk~~~p~t~~ip~i~lT~~~d~~~~~~~~~~g~~dyl~KP~~~~~l~~rv  129 (360)
T COG3437          78 NKLKAMSPSTRRIPVILLTAYADSEDRQRALEAGADDYLSKPISPKELVARV  129 (360)
T ss_pred             HHHHhcCCcccccceEEEeecCChHHHHHHHHhhHHHHhcCCCCHHHHHHHH
Confidence            99998 5555678999999999999999999999999999999999988655

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

Probab=99.80  E-value=7.2e-19  Score=148.77  Aligned_cols=121  Identities=29%  Similarity=0.529  Sum_probs=111.5

Q ss_pred             CCCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHH
Q 042079           18 PKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELL   97 (153)
Q Consensus        18 ~~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~   97 (153)
                      .+..+||++||+...+++...+|+..|.++..+.++.+|+..+.             ..+.||+||||++||.+||+++.
T Consensus       664 l~g~~iLlvddn~vn~~Va~~~l~~~g~~~~~~~sg~e~l~~~~-------------~~~~y~~ifmD~qMP~mDG~e~~  730 (786)
T KOG0519|consen  664 LTGPKILLVDDNPVNRKVATGMLKKLGAEVTEVNSGQEALDKLK-------------PPHSYDVIFMDLQMPEMDGYEAT  730 (786)
T ss_pred             ccCCceEEEecccchHHHHHHHHHHhCCeeEeecCcHHHHHhcC-------------CCCcccEEEEEcCCcccchHHHH
Confidence            35689999999999999999999999999999999999999984             35789999999999999999999


Q ss_pred             HHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079           98 KKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus        98 ~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      +++|+... .++|||++|+...++...+|++.|.|+||.||++.+.+...+.+.+
T Consensus       731 ~~irk~~~-~~~pIvAlTa~~~~~~~~~c~~~Gmd~yl~KP~~~~~l~~~l~~~~  784 (786)
T KOG0519|consen  731 REIRKKER-WHLPIVALTADADPSTEEECLEVGMDGYLSKPFTLEKLVKILREFL  784 (786)
T ss_pred             HHHHHhhc-CCCCEEEEecCCcHHHHHHHHHhCCceEEcccccHHHHHHHHHHHh
Confidence            99998654 7899999999999999999999999999999999999998887754

>PLN03029 type-a response regulator protein; Provisional

Probab=99.79  E-value=1.1e-17  Score=123.00  Aligned_cols=134  Identities=55%  Similarity=0.944  Sum_probs=108.1

Q ss_pred             CCCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHh------hhhcccCCCcccEEEEeCCCCCC
Q 042079           18 PKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQ------QNNLNSNGTKVNLVITDYCMPGM   91 (153)
Q Consensus        18 ~~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~------~~~~~~~~~~~dlii~D~~~~~~   91 (153)
                      ....+||++||+...+..+..+|+..||.+..+.++.+++..+........      ...-......+|+||+|+.||++
T Consensus         6 ~~~~~VLiVdd~~~~~~~l~~~L~~~g~~v~~a~sg~~al~~l~~~~~d~~~p~~~~~~~~~~~~~~~dlVllD~~mp~~   85 (222)
T PLN03029          6 ESQFHVLAVDDSLIDRKLIEKLLKTSSYQVTTVDSGSKALKFLGLHEDDRSNPDTPSVSPNSHQEVEVNLIITDYCMPGM   85 (222)
T ss_pred             CCCccEEEEeCCHHHHHHHHHHHHHcCceEEEECCHHHHHHHHHhccccccccccccccccccccccCCEEEEcCCCCCC
Confidence            356889999999999999999999999999999999999988742110000      00000012357899999999999


Q ss_pred             CHHHHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           92 TGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        92 ~g~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      +|+++++.+++......+|+|++++........++++.|+++|+.||++..+|..+..++
T Consensus        86 ~G~e~l~~ir~~~~~~~ipvIils~~~~~~~~~~al~~Ga~dyl~KP~~~~~L~~l~~~~  145 (222)
T PLN03029         86 TGYDLLKKIKESSSLRNIPVVIMSSENVPSRITRCLEEGAEEFFLKPVQLSDLNRLKPHM  145 (222)
T ss_pred             CHHHHHHHHHhccccCCCcEEEEeCCCCHHHHHHHHHhCchheEECCCCHHHHHHHHHHH
Confidence            999999999976544578999999988888889999999999999999999998877664

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

Probab=99.77  E-value=2.3e-17  Score=120.37  Aligned_cols=114  Identities=31%  Similarity=0.496  Sum_probs=102.2

Q ss_pred             eEEEEeCCHHHHHHHHHHHHhcC-cE-EEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHH
Q 042079           22 HVLAVDDSIVDRKIVENLLKNSA-CK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKK   99 (153)
Q Consensus        22 ~iLiidd~~~~~~~l~~~l~~~~-~~-v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~   99 (153)
                      +|+|+||++..+..++.+|+..+ ++ +..+.++.+++..+              ...+||++++|+.||+++|++++++
T Consensus         2 ~vlivDDh~l~r~gl~~~L~~~~~~~vv~~a~~~~~~l~~~--------------~~~~pdvvl~Dl~mP~~~G~e~~~~   67 (211)
T COG2197           2 KVLIVDDHPLVREGLRQLLELEPDLEVVGEASNGEEALDLA--------------RELKPDVVLLDLSMPGMDGLEALKQ   67 (211)
T ss_pred             eEEEECCcHHHHHHHHHHHhhCCCCEEEEEeCCHHHHHHHh--------------hhcCCCEEEEcCCCCCCChHHHHHH
Confidence            69999999999999999998765 66 45677799999876              3567999999999999999999999


Q ss_pred             HHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          100 IKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       100 lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      |++..  ++++++++|...+.....++++.|+++|+.|..+++++.+.+...
T Consensus        68 l~~~~--p~~~vvvlt~~~~~~~v~~al~~Ga~Gyl~K~~~~~~l~~ai~~v  117 (211)
T COG2197          68 LRARG--PDIKVVVLTAHDDPAYVIRALRAGADGYLLKDASPEELVEAIRAV  117 (211)
T ss_pred             HHHHC--CCCcEEEEeccCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHH
Confidence            99654  688999999999999999999999999999999999999888765

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

Probab=99.77  E-value=4.5e-17  Score=109.02  Aligned_cols=118  Identities=29%  Similarity=0.489  Sum_probs=100.0

Q ss_pred             CCCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHH-HHHHHhchhhhHHhhhhcccCCC-cccEEEEeCCCCCCCHHH
Q 042079           18 PKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGM-RALEFLGLVDEQEQQNNLNSNGT-KVNLVITDYCMPGMTGYE   95 (153)
Q Consensus        18 ~~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~-~a~~~l~~~~~~~~~~~~~~~~~-~~dlii~D~~~~~~~g~~   95 (153)
                      .+..+||++||++..+..++..|...|+.+..+.++. +++..+.              .. .||++++|+.||.++|++
T Consensus         3 ~~~~~vLivdD~~~~~~~~~~~l~~~g~~v~~a~~g~~~al~~~~--------------~~~~~dlii~D~~mp~~~G~~   68 (130)
T COG0784           3 LSGLRVLVVDDEPVNRRLLKRLLEDLGYEVVEAADGEEEALELLR--------------ELPQPDLILLDINMPGMDGIE   68 (130)
T ss_pred             CCCcEEEEEcCCHHHHHHHHHHHHHcCCeEEEeCChHHHHHHHHH--------------hCCCCCEEEEeCCCCCCCHHH
Confidence            3568899999999999999999999999999999995 9999883              34 499999999999999999


Q ss_pred             HHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhH-HHHHHhhh
Q 042079           96 LLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSD-VKKLTGHL  151 (153)
Q Consensus        96 ~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~-l~~~~~~~  151 (153)
                      +++++++.  .+.+|++++|+.........+++.|+++|+.||+...+ +...+.+.
T Consensus        69 ~~~~l~~~--~~~~pvv~~t~~~~~~~~~~~~~~g~~~~l~kP~~~~~~l~~~i~~~  123 (130)
T COG0784          69 LLRRLRAR--GPNIPVILLTAYADEADRERALAAGADDYLTKPIFLEEELLAALRRL  123 (130)
T ss_pred             HHHHHHhC--CCCCCEEEEEcCcCHHHHHHHHHcCCCeEEcCCCCcHHHHHHHHHHH
Confidence            99999986  24678888888777766677899999999999977776 66665543

>PRK10046 dpiA two-component response regulator DpiA; Provisional

Probab=99.77  E-value=3.2e-17  Score=120.37  Aligned_cols=117  Identities=17%  Similarity=0.267  Sum_probs=102.8

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHh-cCc-EEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKN-SAC-KVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYEL   96 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~-~~~-~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~   96 (153)
                      +..+|||+||++..+..+...|+. .++ .+..+.++.+++..+.              ...||++++|+.||+++|+++
T Consensus         3 ~~~~ilivdd~~~~~~~l~~~L~~~~~~~~v~~a~~~~~al~~~~--------------~~~pdlvllD~~mp~~~gle~   68 (225)
T PRK10046          3 APLTLLIVEDETPLAEMHAEYIRHIPGFSQILLAGNLAQARMMIE--------------RFKPGLILLDNYLPDGRGINL   68 (225)
T ss_pred             CcceEEEECCCHHHHHHHHHHHHhCCCcEEEEEECCHHHHHHHHH--------------hcCCCEEEEeCCCCCCcHHHH
Confidence            347899999999999999999986 467 4778999999998873              457999999999999999999


Q ss_pred             HHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           97 LKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        97 ~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      ++.+++..  +..++|++|+..+.....++++.|+++|+.||++.+++...+.++
T Consensus        69 ~~~l~~~~--~~~~iivls~~~~~~~~~~al~~Ga~~yl~Kp~~~~~L~~~i~~~  121 (225)
T PRK10046         69 LHELVQAH--YPGDVVFTTAASDMETVSEAVRCGVFDYLIKPIAYERLGQTLTRF  121 (225)
T ss_pred             HHHHHhcC--CCCCEEEEEcCCCHHHHHHHHHcCccEEEECCcCHHHHHHHHHHH
Confidence            99998743  467899999988888899999999999999999999998877653

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

Probab=99.76  E-value=2e-17  Score=130.49  Aligned_cols=118  Identities=25%  Similarity=0.460  Sum_probs=107.9

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      ...+||++||+...+..++++|...|+.+..+.++.+|+..+.              +.+||+||.|+.||+++|+++++
T Consensus       131 ~~~kILvvdD~~~~~~~l~~~L~~~g~~v~~a~~~~~Al~~~~--------------e~~~dlil~d~~mp~~dg~el~~  196 (435)
T COG3706         131 APKKILVVDDDATQRERLRRILQVEGFRVVEATDGEEALLQLA--------------ELPPDLVLLDANMPDMDGLELCT  196 (435)
T ss_pred             cCceEEEEcCcHHHHHHHHHHHHhccceeeeecCHHHHHHHHh--------------cCCCcEEEEecCCCccCHHHHHH
Confidence            4578999999999999999999999999999999999999883              45899999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhh
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGH  150 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~  150 (153)
                      ++|+......+|+|++++..+.....+|++.|++||+.||+++.++..-+.+
T Consensus       197 ~lr~~~~t~~ipii~~~~~~d~~~~~~Af~~G~~Dyi~kPi~~~~l~~Rl~~  248 (435)
T COG3706         197 RLRQLERTRDIPIILLSSKDDDELVVRAFELGVNDYITKPIEEGELRARLRR  248 (435)
T ss_pred             HHhcccccccccEEEEecccchHHHHHHHHcCCcceEecCCCHHHHHHHHHH
Confidence            9998776678999999999999999999999999999999998888755544

>PRK11107 hybrid sensory histidine kinase BarA; Provisional

Probab=99.75  E-value=7.4e-17  Score=138.45  Aligned_cols=119  Identities=24%  Similarity=0.409  Sum_probs=108.4

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      ...+|||+||++..+..+..+|+..|+.+..+.++.+++..+.              ...||+||+|+.||+++|+++++
T Consensus       666 ~~~~vLivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~al~~~~--------------~~~~dlil~D~~mp~~~g~~~~~  731 (919)
T PRK11107        666 LPLTVMAVDDNPANLKLIGALLEEQVEHVVLCDSGHQAVEQAK--------------QRPFDLILMDIQMPGMDGIRACE  731 (919)
T ss_pred             CCCeEEEEeCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHH--------------hCCCCEEEEeCCCCCCcHHHHHH
Confidence            3578999999999999999999999999999999999999873              46799999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      .||+....+.+|+|++|+........++++.|+++|+.||++..++...+.+.
T Consensus       732 ~lr~~~~~~~~pii~lt~~~~~~~~~~~~~~G~~~~l~KP~~~~~L~~~l~~~  784 (919)
T PRK11107        732 LIRQLPHNQNTPIIAVTAHAMAGERERLLSAGMDDYLAKPIDEAMLKQVLLRY  784 (919)
T ss_pred             HHHhcccCCCCCEEEEeCCCCHHHHHHHHHcCCCeEeeCCCCHHHHHHHHHHH
Confidence            99975444678999999998899999999999999999999999999888765

>PRK10161 transcriptional regulator PhoB; Provisional

Probab=99.74  E-value=1.5e-16  Score=116.09  Aligned_cols=118  Identities=24%  Similarity=0.418  Sum_probs=104.2

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKK   99 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~   99 (153)
                      ..+||++||++..+..+...|+..|+.+..+.++.+++..+.              ...||++++|+.+++.+|.++++.
T Consensus         2 ~~~Ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~~~~~~~--------------~~~~dlvild~~l~~~~g~~~~~~   67 (229)
T PRK10161          2 ARRILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLN--------------EPWPDLILLDWMLPGGSGIQFIKH   67 (229)
T ss_pred             CCeEEEEcCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHh--------------ccCCCEEEEeCCCCCCCHHHHHHH
Confidence            367999999999999999999988999999999999988772              456999999999999999999999


Q ss_pred             HHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          100 IKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       100 lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      +++....+.+|+|+++...+.....++++.|+++|+.||++..++...+..+
T Consensus        68 l~~~~~~~~~pvi~ls~~~~~~~~~~~~~~Ga~~~l~kp~~~~~L~~~i~~~  119 (229)
T PRK10161         68 LKRESMTRDIPVVMLTARGEEEDRVRGLETGADDYITKPFSPKELVARIKAV  119 (229)
T ss_pred             HHhccccCCCCEEEEECCCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHH
Confidence            9875433578999999988888889999999999999999999998776654

>PRK11173 two-component response regulator; Provisional

Probab=99.74  E-value=1.3e-16  Score=117.29  Aligned_cols=115  Identities=26%  Similarity=0.493  Sum_probs=102.2

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKK   99 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~   99 (153)
                      ..+||+++|++..+..+...|+..|+.+..+.++.+++..+.              ...||++++|+.||+++|+++++.
T Consensus         3 ~~~iLiv~dd~~~~~~l~~~L~~~g~~v~~~~~~~~~~~~~~--------------~~~~dlvild~~l~~~~g~~~~~~   68 (237)
T PRK11173          3 TPHILIVEDELVTRNTLKSIFEAEGYDVFEATDGAEMHQILS--------------ENDINLVIMDINLPGKNGLLLARE   68 (237)
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHh--------------hCCCCEEEEcCCCCCCCHHHHHHH
Confidence            468999999999999999999999999999999999988773              356999999999999999999999


Q ss_pred             HHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          100 IKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       100 lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      +++.   +.+|+|++++..+......+++.|+++|+.||++..++...+..+
T Consensus        69 lr~~---~~~pii~lt~~~~~~~~~~~~~~ga~d~l~kP~~~~eL~~~i~~~  117 (237)
T PRK11173         69 LREQ---ANVALMFLTGRDNEVDKILGLEIGADDYITKPFNPRELTIRARNL  117 (237)
T ss_pred             HhcC---CCCCEEEEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHH
Confidence            9864   368999999988888888999999999999999999997655543

>PRK10816 DNA-binding transcriptional regulator PhoP; Provisional

Probab=99.74  E-value=1.4e-16  Score=115.79  Aligned_cols=115  Identities=23%  Similarity=0.364  Sum_probs=103.0

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKI  100 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~l  100 (153)
                      ++||++++++..+..+...|+..|+.+..+.++.+++..+.              ...||++++|+.+|+++|+++++.+
T Consensus         1 m~iLlv~d~~~~~~~l~~~L~~~g~~v~~~~~~~~~l~~~~--------------~~~~dlvild~~l~~~~g~~l~~~l   66 (223)
T PRK10816          1 MRVLVVEDNALLRHHLKVQLQDAGHQVDAAEDAKEADYYLN--------------EHLPDIAIVDLGLPDEDGLSLIRRW   66 (223)
T ss_pred             CeEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHh--------------hCCCCEEEEECCCCCCCHHHHHHHH
Confidence            37999999999999999999999999999999999988762              4569999999999999999999999


Q ss_pred             HhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          101 KESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       101 r~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      ++..  +.+|+|++++..+.....++++.|+++|+.||++..++...+..+
T Consensus        67 r~~~--~~~pii~ls~~~~~~~~~~~l~~Ga~d~l~kp~~~~eL~~~i~~~  115 (223)
T PRK10816         67 RSND--VSLPILVLTARESWQDKVEVLSAGADDYVTKPFHIEEVMARMQAL  115 (223)
T ss_pred             HhcC--CCCCEEEEEcCCCHHHHHHHHHcCCCeeEeCCCCHHHHHHHHHHH
Confidence            8754  578999999998888889999999999999999999998766553

>PRK09836 DNA-binding transcriptional activator CusR; Provisional

Probab=99.74  E-value=1.8e-16  Score=115.46  Aligned_cols=115  Identities=19%  Similarity=0.374  Sum_probs=102.6

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKI  100 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~l  100 (153)
                      ++||++++++..+..+...|+..|+.+..+.++.+++..+.              ...||++++|+.+|+.+|+++++.+
T Consensus         1 m~iliv~d~~~~~~~l~~~L~~~g~~v~~~~~~~~~~~~~~--------------~~~~dlvild~~~~~~~g~~~~~~l   66 (227)
T PRK09836          1 MKLLIVEDEKKTGEYLTKGLTEAGFVVDLADNGLNGYHLAM--------------TGDYDLIILDIMLPDVNGWDIVRML   66 (227)
T ss_pred             CeEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHh--------------hCCCCEEEEECCCCCCCHHHHHHHH
Confidence            37999999999999999999988999999999999988662              3569999999999999999999999


Q ss_pred             HhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          101 KESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       101 r~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      ++..  +.+|+|+++...+.....++++.|+++|+.||++..++...+..+
T Consensus        67 r~~~--~~~pii~ls~~~~~~~~~~~~~~Ga~~~l~kp~~~~~l~~~i~~~  115 (227)
T PRK09836         67 RSAN--KGMPILLLTALGTIEHRVKGLELGADDYLVKPFAFAELLARVRTL  115 (227)
T ss_pred             HhcC--CCCCEEEEEcCCCHHHHHHHHhCCCCEEEeCCCCHHHHHHHHHHH
Confidence            9754  578999999988889899999999999999999999998766553

>TIGR02154 PhoB phosphate regulon transcriptional regulatory protein PhoB

Probab=99.74  E-value=2.4e-16  Score=114.09  Aligned_cols=118  Identities=21%  Similarity=0.452  Sum_probs=103.8

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKK   99 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~   99 (153)
                      ..+||++||++..+..+...|+..++.+..+.+..+++..+.              ...||++++|+.+|+.+|+++++.
T Consensus         2 ~~~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~~--------------~~~~d~vi~d~~~~~~~g~~~~~~   67 (226)
T TIGR02154         2 TRRILVVEDEPAIRELIAYNLEKAGYDVVEAGDGDEALTLIN--------------ERGPDLILLDWMLPGTSGIELCRR   67 (226)
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHHCCCEEEEEcCHHHHHHHHH--------------hcCCCEEEEECCCCCCcHHHHHHH
Confidence            367999999999999999999988999989999999988762              356999999999999999999999


Q ss_pred             HHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          100 IKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       100 lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      ++.....+.+|+|++++..+.....++++.|+++|+.||++.+++...+..+
T Consensus        68 l~~~~~~~~~~ii~ls~~~~~~~~~~~~~~Ga~~~l~kp~~~~~l~~~i~~~  119 (226)
T TIGR02154        68 LRRRPETRAIPIIMLTARGEEEDRVRGLETGADDYITKPFSPRELLARIKAV  119 (226)
T ss_pred             HHccccCCCCCEEEEecCCCHHHHHHHHhcCcceEEeCCCCHHHHHHHHHHH
Confidence            9875433578999999988888888999999999999999999998777654

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.

>PRK10529 DNA-binding transcriptional activator KdpE; Provisional

Probab=99.74  E-value=2.2e-16  Score=114.78  Aligned_cols=114  Identities=24%  Similarity=0.371  Sum_probs=101.5

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKI  100 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~l  100 (153)
                      .+||++||++..+..+...|+..|+.+..+.++.+++..+.              ...||++|+|+.||+++|+++++.+
T Consensus         2 ~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~~~~~~~--------------~~~~dlvild~~l~~~~g~~~~~~l   67 (225)
T PRK10529          2 TNVLIVEDEQAIRRFLRTALEGDGMRVFEAETLQRGLLEAA--------------TRKPDLIILDLGLPDGDGIEFIRDL   67 (225)
T ss_pred             CEEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHh--------------cCCCCEEEEeCCCCCCCHHHHHHHH
Confidence            47999999999999999999989999999999999887662              3569999999999999999999999


Q ss_pred             HhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          101 KESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       101 r~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      ++.   +.+|+|++++..+.....++++.|+++|+.||++..++...+..+
T Consensus        68 r~~---~~~pvi~lt~~~~~~~~~~~~~~ga~~~l~kP~~~~~l~~~i~~~  115 (225)
T PRK10529         68 RQW---SAIPVIVLSARSEESDKIAALDAGADDYLSKPFGIGELQARLRVA  115 (225)
T ss_pred             HcC---CCCCEEEEECCCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHH
Confidence            863   468999999988888889999999999999999999998776653

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

Probab=99.73  E-value=2.1e-17  Score=122.94  Aligned_cols=113  Identities=22%  Similarity=0.442  Sum_probs=101.1

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKI  100 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~l  100 (153)
                      ++++|+||+......+..+|++.|..+..++...+++.++.              ..+||+||+|+.||+++|.+|++++
T Consensus         1 ~~~iiVDdd~a~~~~l~~iLs~~~~~~~~~~~~~eal~~Le--------------~~kpDLifldI~mp~~ngiefaeQv   66 (361)
T COG3947           1 PRIIIVDDDAAIVKLLSVILSRAGHEVRSCSHPVEALDLLE--------------VFKPDLIFLDIVMPYMNGIEFAEQV   66 (361)
T ss_pred             CcEEEEcchHHHHHHHHHHHHhccchhhccCCHHHHHHHHH--------------hcCCCEEEEEeecCCccHHHHHHHH
Confidence            47999999999999999999999988899999999999983              5789999999999999999999999


Q ss_pred             HhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          101 KESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       101 r~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      |...  +.+|||++|++.  +.....+....++|+.||++++.|-+++.+.
T Consensus        67 r~i~--~~v~iifIssh~--eya~dsf~~n~~dYl~KPvt~ekLnraIdr~  113 (361)
T COG3947          67 RDIE--SAVPIIFISSHA--EYADDSFGMNLDDYLPKPVTPEKLNRAIDRR  113 (361)
T ss_pred             HHhh--ccCcEEEEecch--hhhhhhcccchHhhccCCCCHHHHHHHHHHH
Confidence            9865  689999999864  4555677777899999999999999888875

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

Probab=99.73  E-value=1.8e-16  Score=136.65  Aligned_cols=117  Identities=26%  Similarity=0.506  Sum_probs=107.3

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      ...+||++||++..+..+...|+..|+.+..+.++.+++..+.              ...||+||+|+.||+++|+++++
T Consensus       800 ~~~~ILvVdD~~~~~~~l~~~L~~~G~~v~~a~~g~eal~~l~--------------~~~~DlVl~D~~mP~mdG~el~~  865 (924)
T PRK10841        800 DDMMILVVDDHPINRRLLADQLGSLGYQCKTANDGVDALNVLS--------------KNHIDIVLTDVNMPNMDGYRLTQ  865 (924)
T ss_pred             CCCEEEEECCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHH--------------hCCCCEEEEcCCCCCCCHHHHHH
Confidence            4468999999999999999999999999999999999999883              45799999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      .+|+..  +.+|||++|+....+...++++.|+++|+.||++.+++.+.+.+.
T Consensus       866 ~ir~~~--~~~pII~lTa~~~~~~~~~~~~aG~d~~L~KPv~~~~L~~~L~~~  916 (924)
T PRK10841        866 RLRQLG--LTLPVIGVTANALAEEKQRCLEAGMDSCLSKPVTLDVLKQTLTVY  916 (924)
T ss_pred             HHHhcC--CCCCEEEEECCCCHHHHHHHHHCCCCEEEeCCCCHHHHHHHHHHH
Confidence            999864  578999999998888899999999999999999999999888764

>PRK10840 transcriptional regulator RcsB; Provisional

Probab=99.73  E-value=2.4e-16  Score=114.80  Aligned_cols=117  Identities=24%  Similarity=0.320  Sum_probs=101.4

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCc-E-EEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCC---CCH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSAC-K-VTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPG---MTG   93 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~-~-v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~---~~g   93 (153)
                      ++.+|+|+||++..+..++..|+..++ . +..+.++.+++..+.              ...||++++|+.+|+   .+|
T Consensus         2 ~~~~Ilivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~~~~~~~--------------~~~~DlvllD~~l~~~~~~~g   67 (216)
T PRK10840          2 NNMNVIIADDHPIVLFGIRKSLEQIEWVNVVGEFEDSTALINNLP--------------KLDAHVLITDLSMPGDKYGDG   67 (216)
T ss_pred             CceEEEEECCcHHHHHHHHHHHhcCCCCEEEEEECCHHHHHHHHH--------------hCCCCEEEEeCcCCCCCCCCH
Confidence            347899999999999999999987554 3 667899999988762              356999999999999   499


Q ss_pred             HHHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           94 YELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        94 ~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      .++++++++..  +.+|+|+++...+.....++++.|+++|+.||.+++++.+.+..+
T Consensus        68 ~~~~~~l~~~~--~~~~iIvls~~~~~~~~~~a~~~Ga~~yl~K~~~~~~l~~ai~~v  123 (216)
T PRK10840         68 ITLIKYIKRHF--PSLSIIVLTMNNNPAILSAVLDLDIEGIVLKQGAPTDLPKALAAL  123 (216)
T ss_pred             HHHHHHHHHHC--CCCcEEEEEecCCHHHHHHHHHCCCeEEEECCCCHHHHHHHHHHH
Confidence            99999998753  678999999988888889999999999999999999999887764

>PRK10643 DNA-binding transcriptional regulator BasR; Provisional

Probab=99.73  E-value=3.9e-16  Score=112.78  Aligned_cols=115  Identities=19%  Similarity=0.311  Sum_probs=102.2

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKI  100 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~l  100 (153)
                      ++|+++||++..+..+...|+..|+.+..+.+..+++..+.              ...||++++|+.+|+++|+++++.+
T Consensus         1 ~~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~~--------------~~~~d~illd~~~~~~~g~~~~~~l   66 (222)
T PRK10643          1 MKILIVEDDTLLLQGLILALQTEGYACDCASTAREAEALLE--------------SGHYSLVVLDLGLPDEDGLHLLRRW   66 (222)
T ss_pred             CEEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHH--------------hCCCCEEEEECCCCCCCHHHHHHHH
Confidence            36999999999999999999988999989999999888762              3568999999999999999999999


Q ss_pred             HhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          101 KESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       101 r~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      +...  +.+|+|+++...+.....++++.|+++|+.||++.+++...+..+
T Consensus        67 ~~~~--~~~pii~ls~~~~~~~~~~~~~~ga~~~l~kp~~~~~l~~~i~~~  115 (222)
T PRK10643         67 RQKK--YTLPVLILTARDTLEDRVAGLDVGADDYLVKPFALEELHARIRAL  115 (222)
T ss_pred             HhcC--CCCcEEEEECCCCHHHHHHHHhcCCCeEEeCCCCHHHHHHHHHHH
Confidence            8754  578999999988888889999999999999999999998766653

>PRK09468 ompR osmolarity response regulator; Provisional

Probab=99.72  E-value=5e-16  Score=114.05  Aligned_cols=116  Identities=21%  Similarity=0.397  Sum_probs=103.8

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKK   99 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~   99 (153)
                      ..+||++++++..+..+...|+..|+.+..+.++.+++..+.              ...||++|+|+.+|+++|+++++.
T Consensus         5 ~~~iLiv~d~~~~~~~l~~~L~~~g~~v~~~~~~~~~~~~~~--------------~~~~dlvild~~l~~~~g~~~~~~   70 (239)
T PRK09468          5 NYKILVVDDDMRLRALLERYLTEQGFQVRSAANAEQMDRLLT--------------RESFHLMVLDLMLPGEDGLSICRR   70 (239)
T ss_pred             CCeEEEEcCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHh--------------cCCCCEEEEeCCCCCCCHHHHHHH
Confidence            467999999999999999999999999999999999888762              457999999999999999999999


Q ss_pred             HHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          100 IKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       100 lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      +++..  +.+|+|++++..+......+++.|+++|+.||++.+++...+..+
T Consensus        71 lr~~~--~~~pii~ls~~~~~~~~~~~l~~Ga~~~l~kP~~~~~L~~~i~~~  120 (239)
T PRK09468         71 LRSQN--NPTPIIMLTAKGEEVDRIVGLEIGADDYLPKPFNPRELLARIRAV  120 (239)
T ss_pred             HHhcC--CCCCEEEEECCCcHHHHHHHHhcCCCeEEECCCCHHHHHHHHHHH
Confidence            99753  578999999988888888999999999999999999998776654

>PRK10336 DNA-binding transcriptional regulator QseB; Provisional

Probab=99.72  E-value=4.6e-16  Score=112.32  Aligned_cols=115  Identities=23%  Similarity=0.346  Sum_probs=101.8

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKI  100 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~l  100 (153)
                      ++|+++||++..+..+...|+..++.+..+.+..+++..+.              ...||++++|+.+++.+|.++++.+
T Consensus         1 ~~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~~--------------~~~~dlvild~~l~~~~g~~~~~~i   66 (219)
T PRK10336          1 MRILLIEDDMLIGDGIKTGLSKMGFSVDWFTQGRQGKEALY--------------SAPYDAVILDLTLPGMDGRDILREW   66 (219)
T ss_pred             CeEEEEcCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHh--------------hCCCCEEEEECCCCCCCHHHHHHHH
Confidence            36999999999999999999988999989999998888762              3568999999999999999999999


Q ss_pred             HhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          101 KESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       101 r~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      ++..  +.+|+|+++...+.....++++.|+++|+.||++..++...+..+
T Consensus        67 ~~~~--~~~~ii~lt~~~~~~~~~~~~~~ga~~~i~kp~~~~~l~~~i~~~  115 (219)
T PRK10336         67 REKG--QREPVLILTARDALAERVEGLRLGADDYLCKPFALIEVAARLEAL  115 (219)
T ss_pred             HhcC--CCCcEEEEECCCCHHHHHHHHhCCCCeEEECCCCHHHHHHHHHHH
Confidence            9743  578999999988888888999999999999999999998766553

>PRK10766 DNA-binding transcriptional regulator TorR; Provisional

Probab=99.72  E-value=5.4e-16  Score=112.43  Aligned_cols=114  Identities=23%  Similarity=0.383  Sum_probs=101.6

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKK   99 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~   99 (153)
                      ..+||++++++.....+...|...|+.+..+.++.+++..+.              ...||++++|+.+|+++|.++++.
T Consensus         2 ~~~iLlv~d~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~--------------~~~~dlvild~~l~~~~g~~~~~~   67 (221)
T PRK10766          2 SYHILVVEDEPVTRARLQGYFEQEGYTVSEAASGAGMREIMQ--------------NQHVDLILLDINLPGEDGLMLTRE   67 (221)
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHh--------------cCCCCEEEEeCCCCCCCHHHHHHH
Confidence            357999999999999999999999999999999999988762              356999999999999999999999


Q ss_pred             HHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhh
Q 042079          100 IKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGH  150 (153)
Q Consensus       100 lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~  150 (153)
                      +++.   +.+|+|++++..+.....++++.|+++|+.||++..++...+..
T Consensus        68 lr~~---~~~~ii~l~~~~~~~~~~~~l~~Ga~d~l~kP~~~~~L~~~i~~  115 (221)
T PRK10766         68 LRSR---STVGIILVTGRTDSIDRIVGLEMGADDYVTKPLELRELLVRVKN  115 (221)
T ss_pred             HHhC---CCCCEEEEECCCcHHHHHHHHHcCCCcEEeCCCCHHHHHHHHHH
Confidence            9874   36899999998888888899999999999999999999766554

>PRK11083 DNA-binding response regulator CreB; Provisional

Probab=99.72  E-value=5.8e-16  Score=112.32  Aligned_cols=116  Identities=25%  Similarity=0.387  Sum_probs=102.5

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKK   99 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~   99 (153)
                      .++||++||++..+..+...|...++.+..+.+..+++..+.              ...||++++|+.+|+.+|+++++.
T Consensus         3 ~~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~--------------~~~~dlvl~d~~~~~~~g~~~~~~   68 (228)
T PRK11083          3 QPTILLVEDEQAIADTLVYALQSEGFTVEWFERGLPALDKLR--------------QQPPDLVILDVGLPDISGFELCRQ   68 (228)
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHHCCCEEEEEcCHHHHHHHHh--------------cCCCCEEEEeCCCCCCCHHHHHHH
Confidence            468999999999999999999988999988999998887762              456999999999999999999999


Q ss_pred             HHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          100 IKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       100 lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      +++..  +.+|+|+++...+......+++.|+++|+.||++..++...+...
T Consensus        69 l~~~~--~~~~ii~ls~~~~~~~~~~a~~~Ga~~~l~kp~~~~~l~~~i~~~  118 (228)
T PRK11083         69 LLAFH--PALPVIFLTARSDEVDRLVGLEIGADDYVAKPFSPREVAARVRTI  118 (228)
T ss_pred             HHhhC--CCCCEEEEEcCCcHHHHHHHhhcCCCeEEECCCCHHHHHHHHHHH
Confidence            99754  578999999988888888999999999999999999998776653

>PRK15347 two component system sensor kinase SsrA; Provisional

Probab=99.72  E-value=2.7e-16  Score=135.08  Aligned_cols=118  Identities=25%  Similarity=0.444  Sum_probs=106.0

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKK   99 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~   99 (153)
                      .++|||+||++..+..+...|+..|+.+..+.++.+++..+.              ...||+|++|+.||+++|+++++.
T Consensus       690 ~~~iLivdd~~~~~~~l~~~L~~~g~~v~~a~~~~~al~~~~--------------~~~~dlil~D~~mp~~~G~~~~~~  755 (921)
T PRK15347        690 QLQILLVDDVETNRDIIGMMLVELGQQVTTAASGTEALELGR--------------QHRFDLVLMDIRMPGLDGLETTQL  755 (921)
T ss_pred             cCCEEEEeCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHh--------------cCCCCEEEEeCCCCCCCHHHHHHH
Confidence            468999999999999999999999999999999999998873              467999999999999999999999


Q ss_pred             HHhcc--CCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          100 IKESS--VMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       100 lr~~~--~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      +|+..  ..+.+|||++|+..+.....++++.|+++|+.||++..+|...+.++
T Consensus       756 ir~~~~~~~~~~pii~lt~~~~~~~~~~~~~~G~~~~l~KP~~~~~L~~~l~~~  809 (921)
T PRK15347        756 WRDDPNNLDPDCMIVALTANAAPEEIHRCKKAGMNHYLTKPVTLAQLARALELA  809 (921)
T ss_pred             HHhchhhcCCCCcEEEEeCCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHH
Confidence            98632  22578999999998888899999999999999999999999887653

>PRK11466 hybrid sensory histidine kinase TorS; Provisional

Probab=99.71  E-value=3.8e-16  Score=134.26  Aligned_cols=118  Identities=19%  Similarity=0.313  Sum_probs=106.4

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      +..+|||+||++..+..+..+|+..|+.+..+.++.+++..+.             ...+||+||+|+.||+++|+++++
T Consensus       680 ~~~~vLivdD~~~~~~~l~~~L~~~g~~v~~a~~~~~al~~~~-------------~~~~~Dlvl~D~~mp~~~G~~~~~  746 (914)
T PRK11466        680 DGLRLLLIEDNPLTQRITAEMLNTSGAQVVAVGNAAQALETLQ-------------NSEPFAAALVDFDLPDYDGITLAR  746 (914)
T ss_pred             CCcceEEEeCCHHHHHHHHHHHHhcCCceEEeCCHHHHHHHHH-------------cCCCCCEEEEeCCCCCCCHHHHHH
Confidence            3568999999999999999999999999999999999998773             234689999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      .+++..  +.+|+|++|.........++++.|+++|+.||++.+++...+.++
T Consensus       747 ~lr~~~--~~~~ii~~t~~~~~~~~~~~~~~g~~~~l~KP~~~~~L~~~i~~~  797 (914)
T PRK11466        747 QLAQQY--PSLVLIGFSAHVIDETLRQRTSSLFRGIIPKPVPREVLGQLLAHY  797 (914)
T ss_pred             HHHhhC--CCCCEEEEeCCCchhhHHHHHhcCcCCEEeCCCCHHHHHHHHHHH
Confidence            999754  689999999998888888999999999999999999999888775

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

Probab=99.71  E-value=4.8e-16  Score=105.55  Aligned_cols=114  Identities=18%  Similarity=0.224  Sum_probs=104.5

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKK   99 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~   99 (153)
                      ...+||+|||..+...+...++..||.+..+.+..+++..+.              ...|...++|+.+.+.+|+.+++.
T Consensus         9 d~~lllvdDD~~f~~~LaRa~e~RGf~v~~a~~~~eal~~ar--------------t~~PayAvvDlkL~~gsGL~~i~~   74 (182)
T COG4567           9 DKSLLLVDDDTPFLRTLARAMERRGFAVVTAESVEEALAAAR--------------TAPPAYAVVDLKLGDGSGLAVIEA   74 (182)
T ss_pred             CceeEEecCChHHHHHHHHHHhccCceeEeeccHHHHHHHHh--------------cCCCceEEEEeeecCCCchHHHHH
Confidence            347999999999999999999999999999999999999883              567999999999999999999999


Q ss_pred             HHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHh
Q 042079          100 IKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTG  149 (153)
Q Consensus       100 lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~  149 (153)
                      |++..  +...+|++|++.+-.-..+|.+.|+++||.||-+.+.+...+.
T Consensus        75 lr~~~--~d~rivvLTGy~sIATAV~AvKlGA~~YLaKPAdaDdi~aAl~  122 (182)
T COG4567          75 LRERR--ADMRIVVLTGYASIATAVEAVKLGACDYLAKPADADDILAALL  122 (182)
T ss_pred             HHhcC--CcceEEEEecchHHHHHHHHHHhhhhhhcCCCCChHHHHHHHh
Confidence            99865  6889999999999999999999999999999999999876654

>TIGR02956 TMAO_torS TMAO reductase sytem sensor TorS

Probab=99.71  E-value=3.8e-16  Score=134.84  Aligned_cols=120  Identities=25%  Similarity=0.406  Sum_probs=107.5

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      +..+|||+||++..+..+...|+..|+.+..+.++.+++..+.              ...||+||+|+.||+++|+++++
T Consensus       701 ~~~~iLvvdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~--------------~~~~dlvl~D~~mp~~~g~~~~~  766 (968)
T TIGR02956       701 PPQRVLLVEDNEVNQMVAQGFLTRLGHKVTLAESGQSALECFH--------------QHAFDLALLDINLPDGDGVTLLQ  766 (968)
T ss_pred             cccceEEEcCcHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHH--------------CCCCCEEEECCCCCCCCHHHHHH
Confidence            3457999999999999999999999999999999999999883              46799999999999999999999


Q ss_pred             HHHhccCCCC-CcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079           99 KIKESSVMKE-VPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus        99 ~lr~~~~~~~-~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      .+++...... +|+|++|+.........+++.|+++|+.||++..+|...+.+++
T Consensus       767 ~ir~~~~~~~~~pii~lta~~~~~~~~~~~~~G~~~~l~KP~~~~~L~~~l~~~~  821 (968)
T TIGR02956       767 QLRAIYGAKNEVKFIAFSAHVFNEDVAQYLAAGFDGFLAKPVVEEQLTAMIAVIL  821 (968)
T ss_pred             HHHhCccccCCCeEEEEECCCCHHHHHHHHHCCCCEEEeCCCCHHHHHHHHHHHh
Confidence            9997543223 89999999988998999999999999999999999999887753

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).

>TIGR03787 marine_sort_RR proteobacterial dedicated sortase system response regulator

Probab=99.70  E-value=1.1e-15  Score=111.15  Aligned_cols=114  Identities=18%  Similarity=0.247  Sum_probs=100.6

Q ss_pred             eEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCC--CCHHHHHHH
Q 042079           22 HVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPG--MTGYELLKK   99 (153)
Q Consensus        22 ~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~--~~g~~~~~~   99 (153)
                      +||++||+...+..+...|+..|+.+..+.++.+++..+.              ...||++++|+.+|+  .+|+++++.
T Consensus         2 ~iLivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~~--------------~~~~dlvild~~l~~~~~~g~~~~~~   67 (227)
T TIGR03787         2 RIAIVEDEAAIRENYADALKRQGYQVTTYADRPSAMQAFR--------------QRLPDLAIIDIGLGEEIDGGFMLCQD   67 (227)
T ss_pred             eEEEEeCCHHHHHHHHHHHHHCCcEEEEecCHHHHHHHHH--------------hCCCCEEEEECCCCCCCCCHHHHHHH
Confidence            6999999999999999999988999988999999888762              356999999999997  489999999


Q ss_pred             HHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          100 IKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       100 lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      ++...  +.+|+|++++..+......+++.|+++|+.||++..++...+..+
T Consensus        68 i~~~~--~~~pii~ls~~~~~~~~~~~~~~Ga~~~l~kp~~~~~l~~~i~~~  117 (227)
T TIGR03787        68 LRSLS--ATLPIIFLTARDSDFDTVSGLRLGADDYLTKDISLPHLLARITAL  117 (227)
T ss_pred             HHhcC--CCCCEEEEECCCCHHHHHHHHhcCCCEEEECCCCHHHHHHHHHHH
Confidence            98753  568999999988888889999999999999999999998766553

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.

>PRK10955 DNA-binding transcriptional regulator CpxR; Provisional

Probab=99.70  E-value=1.3e-15  Score=110.90  Aligned_cols=113  Identities=24%  Similarity=0.424  Sum_probs=100.0

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKI  100 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~l  100 (153)
                      .+||++||++..+..+...|+..|+.+..+.++.+++..+.               ..||++++|+.+|+++|+++++.+
T Consensus         2 ~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~---------------~~~d~vl~d~~~~~~~g~~~~~~l   66 (232)
T PRK10955          2 NKILLVDDDRELTSLLKELLEMEGFNVIVAHDGEQALDLLD---------------DSIDLLLLDVMMPKKNGIDTLKEL   66 (232)
T ss_pred             ceEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHhh---------------cCCCEEEEeCCCCCCcHHHHHHHH
Confidence            37999999999999999999988999999999999988662               358999999999999999999999


Q ss_pred             HhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          101 KESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       101 r~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      ++..   .+|+|+++...+.....++++.|+++|+.||++.+++...+..+
T Consensus        67 ~~~~---~~~ii~lt~~~~~~~~~~~~~~ga~~~l~kp~~~~~l~~~i~~~  114 (232)
T PRK10955         67 RQTH---QTPVIMLTARGSELDRVLGLELGADDYLPKPFNDRELVARIRAI  114 (232)
T ss_pred             HhcC---CCcEEEEECCCCHHHHHHHHHcCCCEEEcCCCCHHHHHHHHHHH
Confidence            9754   38999999988888888999999999999999999998766653

>PRK13856 two-component response regulator VirG; Provisional

Probab=99.70  E-value=1.2e-15  Score=112.48  Aligned_cols=113  Identities=24%  Similarity=0.389  Sum_probs=98.6

Q ss_pred             eEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHHH
Q 042079           22 HVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKIK  101 (153)
Q Consensus        22 ~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~lr  101 (153)
                      +||+++|++..+..+...|+..|+.+..+.++.+++..+.              ...||++++|+.+|+.+|+++++.++
T Consensus         3 ~ILived~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~~--------------~~~~dlvi~d~~l~~~~g~~l~~~i~   68 (241)
T PRK13856          3 HVLVIDDDVAMRHLIVEYLTIHAFKVTAVADSQQFNRVLA--------------SETVDVVVVDLNLGREDGLEIVRSLA   68 (241)
T ss_pred             eEEEEeCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHh--------------hCCCCEEEEeCCCCCCCHHHHHHHHH
Confidence            7999999999999999999989999999999999988762              45799999999999999999999998


Q ss_pred             hccCCCCCcEEEEeCC-CChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          102 ESSVMKEVPVVVVSSE-NIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       102 ~~~~~~~~pii~~t~~-~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      +.   ..+|+|++++. ........+++.|+++|+.||++..++...+..+
T Consensus        69 ~~---~~~pii~lt~~~~~~~~~~~~l~~Ga~~yl~kP~~~~eL~~~i~~~  116 (241)
T PRK13856         69 TK---SDVPIIIISGDRLEEADKVVALELGATDFIAKPFGTREFLARIRVA  116 (241)
T ss_pred             hc---CCCcEEEEECCCCcHHHHHHHHhcCcCeEEeCCCCHHHHHHHHHHH
Confidence            64   36899999974 3556677899999999999999999998766543

>PRK10701 DNA-binding transcriptional regulator RstA; Provisional

Probab=99.70  E-value=1.4e-15  Score=111.77  Aligned_cols=113  Identities=21%  Similarity=0.287  Sum_probs=100.4

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKI  100 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~l  100 (153)
                      .+||+++|++..+..+...|+..|+.+..+.++.+++..+.              ...||++++|+.+|+.+|+++++.+
T Consensus         2 ~~iLivedd~~~~~~l~~~L~~~g~~v~~~~~~~~~l~~~~--------------~~~~dlvild~~l~~~~g~~~~~~i   67 (240)
T PRK10701          2 NKIVFVEDDAEVGSLIAAYLAKHDIDVTVEPRGDRAEATIL--------------REQPDLVLLDIMLPGKDGMTICRDL   67 (240)
T ss_pred             ceEEEEeCCHHHHHHHHHHHHHcCCEEEEeCCHHHHHHHHh--------------hCCCCEEEEeCCCCCCCHHHHHHHH
Confidence            37999999999999999999999999999999999988773              4569999999999999999999999


Q ss_pred             HhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhh
Q 042079          101 KESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGH  150 (153)
Q Consensus       101 r~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~  150 (153)
                      ++.   ...|+|+++...+.....++++.|+++|+.||++..++...+..
T Consensus        68 r~~---~~~pii~l~~~~~~~~~~~~~~~Ga~d~l~kP~~~~~l~~~i~~  114 (240)
T PRK10701         68 RPK---WQGPIVLLTSLDSDMNHILALEMGACDYILKTTPPAVLLARLRL  114 (240)
T ss_pred             Hhc---CCCCEEEEECCCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHH
Confidence            973   35799999988888878899999999999999999999876654

>PRK11517 transcriptional regulatory protein YedW; Provisional

Probab=99.70  E-value=1.7e-15  Score=109.69  Aligned_cols=114  Identities=20%  Similarity=0.387  Sum_probs=101.6

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKI  100 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~l  100 (153)
                      ++||++++++..+..+...|+..|+.+..+.+..+++..+.              ...||++++|+.+|+++|+++++.+
T Consensus         1 m~iliv~~~~~~~~~l~~~L~~~~~~v~~~~~~~~~l~~~~--------------~~~~dlvi~d~~~~~~~g~~~~~~l   66 (223)
T PRK11517          1 MKILLIEDNQRTQEWVTQGLSEAGYVIDAVSDGRDGLYLAL--------------KDDYALIILDIMLPGMDGWQILQTL   66 (223)
T ss_pred             CEEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHh--------------cCCCCEEEEECCCCCCCHHHHHHHH
Confidence            36999999999999999999988999999999999988762              4569999999999999999999999


Q ss_pred             HhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          101 KESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       101 r~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      +..   +.+|+|+++...+.....++++.|+++|+.||++..++...+...
T Consensus        67 ~~~---~~~~ii~ls~~~~~~~~~~a~~~Ga~~~l~kp~~~~~l~~~i~~~  114 (223)
T PRK11517         67 RTA---KQTPVICLTARDSVDDRVRGLDSGANDYLVKPFSFSELLARVRAQ  114 (223)
T ss_pred             HcC---CCCCEEEEECCCCHHHHHHHHhcCCCEEEECCCCHHHHHHHHHHH
Confidence            864   368999999988888899999999999999999999998776653

>CHL00148 orf27 Ycf27; Reviewed

Probab=99.69  E-value=2.3e-15  Score=110.17  Aligned_cols=116  Identities=28%  Similarity=0.471  Sum_probs=102.5

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      +.++|+++||++.....+...|...++.+..+.+..+++..+.              ...||++++|+.+|+.+|+++++
T Consensus         5 ~~~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~~l~~~~--------------~~~~d~illd~~~~~~~g~~~~~   70 (240)
T CHL00148          5 SKEKILVVDDEAYIRKILETRLSIIGYEVITASDGEEALKLFR--------------KEQPDLVILDVMMPKLDGYGVCQ   70 (240)
T ss_pred             CCceEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHH--------------hcCCCEEEEeCCCCCCCHHHHHH
Confidence            4568999999999999999999988999988899999888762              35699999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      .++..   +.+|+|++++..+.....++++.|+++|+.||++..++...+..+
T Consensus        71 ~l~~~---~~~~ii~ls~~~~~~~~~~~~~~Ga~~~l~kp~~~~~L~~~i~~~  120 (240)
T CHL00148         71 EIRKE---SDVPIIMLTALGDVSDRITGLELGADDYVVKPFSPKELEARIRSV  120 (240)
T ss_pred             HHHhc---CCCcEEEEECCCCHHhHHHHHHCCCCEEEeCCCCHHHHHHHHHHH
Confidence            99863   478999999988888888999999999999999999998776553

>PRK09958 DNA-binding transcriptional activator EvgA; Provisional

Probab=99.69  E-value=1.9e-15  Score=108.20  Aligned_cols=115  Identities=20%  Similarity=0.305  Sum_probs=101.6

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEE-EecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVT-TAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKK   99 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~-~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~   99 (153)
                      ++|+++|+++..+..+...|+..|+.+. .+.+..+++..+.              ...||++++|+.+|+.+|.++++.
T Consensus         1 m~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~~~--------------~~~~dlvi~d~~~~~~~g~~~~~~   66 (204)
T PRK09958          1 MNAIIIDDHPLAIAAIRNLLIKNDIEILAELTEGGSAVQRVE--------------TLKPDIVIIDVDIPGVNGIQVLET   66 (204)
T ss_pred             CcEEEECCcHHHHHHHHHHHhcCCCEEEEEeCCHHHHHHHHH--------------ccCCCEEEEeCCCCCCCHHHHHHH
Confidence            4799999999999999999998899886 6899999988773              456999999999999999999999


Q ss_pred             HHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          100 IKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       100 lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      ++...  +..|+|++++..+.....++++.|+++|+.||++.+++...+...
T Consensus        67 l~~~~--~~~~ii~ls~~~~~~~~~~~~~~ga~~~i~kp~~~~~l~~~i~~~  116 (204)
T PRK09958         67 LRKRQ--YSGIIIIVSAKNDHFYGKHCADAGANGFVSKKEGMNNIIAAIEAA  116 (204)
T ss_pred             HHhhC--CCCeEEEEeCCCCHHHHHHHHHCCCCEEEecCCCHHHHHHHHHHH
Confidence            98753  467899999988888888999999999999999999999887764

>PRK10430 DNA-binding transcriptional activator DcuR; Provisional

Probab=99.69  E-value=1.5e-15  Score=112.32  Aligned_cols=116  Identities=23%  Similarity=0.327  Sum_probs=99.0

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHh-cCcE-EEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKN-SACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~-~~~~-v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      .+|||+||++..+..+..+|.. .++. +..+.++.+++..+..            ....||++|+|+.||+++|+++++
T Consensus         2 ~~VLivdd~~~~~~~l~~~L~~~~~~~~~~~~~~~~~a~~~~~~------------~~~~~DlvilD~~~p~~~G~eli~   69 (239)
T PRK10430          2 INVLIVDDDAMVAELNRRYVAQIPGFQCCGTASTLEQAKEIIFN------------SDTPIDLILLDIYMQQENGLDLLP   69 (239)
T ss_pred             eeEEEEcCCHHHHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHh------------cCCCCCEEEEecCCCCCCcHHHHH
Confidence            4799999999999999999976 3565 4477888888776621            124689999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhh
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGH  150 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~  150 (153)
                      .+++..  +.+|+|++++..+.....++++.|+++|+.||++.+++.+.+.+
T Consensus        70 ~l~~~~--~~~~vI~ls~~~~~~~~~~al~~Ga~~yl~Kp~~~~~l~~~i~~  119 (239)
T PRK10430         70 VLHEAG--CKSDVIVISSAADAATIKDSLHYGVVDYLIKPFQASRFEEALTG  119 (239)
T ss_pred             HHHhhC--CCCCEEEEECCCcHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHH
Confidence            998754  57899999999888889999999999999999999999887764

>PRK11091 aerobic respiration control sensor protein ArcB; Provisional

Probab=99.69  E-value=1.2e-15  Score=129.41  Aligned_cols=119  Identities=22%  Similarity=0.393  Sum_probs=102.9

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      +..+|||+||++..+..+..+|+..|+.+..+.++.+++..+.              ...||+||+|+.||+++|+++++
T Consensus       524 ~~~~ILivdD~~~~~~~l~~~L~~~g~~v~~a~~~~eal~~~~--------------~~~~Dlvl~D~~mp~~~G~e~~~  589 (779)
T PRK11091        524 PALNILLVEDIELNVIVARSVLEKLGNSVDVAMTGKEALEMFD--------------PDEYDLVLLDIQLPDMTGLDIAR  589 (779)
T ss_pred             cccceEEEcCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHhh--------------cCCCCEEEEcCCCCCCCHHHHHH
Confidence            3478999999999999999999999999999999999999873              45799999999999999999999


Q ss_pred             HHHhccCCCC-CcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079           99 KIKESSVMKE-VPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus        99 ~lr~~~~~~~-~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      .||+....+. .|+|++++.... ...++++.|+++|+.||++..++...+.+++
T Consensus       590 ~ir~~~~~~~~~~ii~~ta~~~~-~~~~~~~~G~~~~l~KP~~~~~L~~~l~~~~  643 (779)
T PRK11091        590 ELRERYPREDLPPLVALTANVLK-DKKEYLDAGMDDVLSKPLSVPALTAMIKKFW  643 (779)
T ss_pred             HHHhccccCCCCcEEEEECCchH-hHHHHHHCCCCEEEECCCCHHHHHHHHHHHh
Confidence            9997543234 488888886544 4578899999999999999999999887753

>TIGR02875 spore_0_A sporulation transcription factor Spo0A

Probab=99.69  E-value=2e-15  Score=112.89  Aligned_cols=118  Identities=22%  Similarity=0.343  Sum_probs=101.0

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhc-CcE-EEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNS-ACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELL   97 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~-~~~-v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~   97 (153)
                      ..+||++||++..+..+...|... ++. +..+.++.+++..+.              ...||+|++|+.||+++|++++
T Consensus         2 ~~~vLivdd~~~~~~~l~~~L~~~~~~~~~~~a~~~~eal~~l~--------------~~~~DlvllD~~mp~~dG~~~l   67 (262)
T TIGR02875         2 KIRIVIADDNKEFCNLLKEYLAAQPDMEVVGVAHNGVDALELIK--------------EQQPDVVVLDIIMPHLDGIGVL   67 (262)
T ss_pred             CcEEEEEcCCHHHHHHHHHHHhcCCCeEEEEEeCCHHHHHHHHH--------------hcCCCEEEEeCCCCCCCHHHHH
Confidence            468999999999999999999853 444 447899999998873              4569999999999999999999


Q ss_pred             HHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           98 KKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        98 ~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      +.+++......+|+|++++........++++.|+++|+.||++.+++...+.++
T Consensus        68 ~~i~~~~~~~~~~iI~lt~~~~~~~~~~~~~~G~~~~l~KP~~~~~L~~~i~~~  121 (262)
T TIGR02875        68 EKLNEIELSARPRVIMLSAFGQEKITQRAVALGADYYVLKPFDLEILAARIRQL  121 (262)
T ss_pred             HHHHhhccccCCeEEEEeCCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHH
Confidence            999975533347899999988888889999999999999999999998877765

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.

>TIGR01387 cztR_silR_copR heavy metal response regulator

Probab=99.68  E-value=2.7e-15  Score=108.12  Aligned_cols=113  Identities=26%  Similarity=0.445  Sum_probs=100.9

Q ss_pred             EEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHHHh
Q 042079           23 VLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKIKE  102 (153)
Q Consensus        23 iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~lr~  102 (153)
                      |+++|+++..+..+...|...|+.+..+.+..+++..+.              ...||++++|+.+|+.+|.++++.++.
T Consensus         1 iliidd~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~--------------~~~~dlvl~d~~~~~~~g~~~~~~l~~   66 (218)
T TIGR01387         1 ILVVEDEQKTAEYLQQGLSESGYVVDAASNGRDGLHLAL--------------KDDYDLIILDVMLPGMDGWQILQTLRR   66 (218)
T ss_pred             CEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHh--------------cCCCCEEEEeCCCCCCCHHHHHHHHHc
Confidence            589999999999999999988999999999999988762              456999999999999999999999986


Q ss_pred             ccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          103 SSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       103 ~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      ..  +.+|+|+++...+.....++++.|+++|+.||++..++...+..+
T Consensus        67 ~~--~~~~iivls~~~~~~~~~~~~~~Ga~~~l~kp~~~~~l~~~i~~~  113 (218)
T TIGR01387        67 SG--KQTPVLFLTARDSVADKVKGLDLGADDYLVKPFSFSELLARVRTL  113 (218)
T ss_pred             cC--CCCcEEEEEcCCCHHHHHHHHHcCCCeEEECCCCHHHHHHHHHHH
Confidence            53  578999999988888889999999999999999999998776653

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=99.67  E-value=2.4e-15  Score=121.22  Aligned_cols=116  Identities=28%  Similarity=0.414  Sum_probs=104.9

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKK   99 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~   99 (153)
                      ..+|||+||++..+..+...|+..|+.+..+.++.+++..+.              ...||++|+|+.||+++|+++++.
T Consensus         3 ~~~ILiVdd~~~~~~~L~~~L~~~g~~v~~~~s~~~al~~l~--------------~~~~DlvllD~~lp~~dgl~~l~~   68 (469)
T PRK10923          3 RGIVWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLEALA--------------SKTPDVLLSDIRMPGMDGLALLKQ   68 (469)
T ss_pred             CCeEEEEECCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHh--------------cCCCCEEEECCCCCCCCHHHHHHH
Confidence            368999999999999999999999999999999999998873              457999999999999999999999


Q ss_pred             HHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          100 IKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       100 lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      ++...  +.+|+|++++..+......+++.|+++|+.||++..++...+.+.
T Consensus        69 ir~~~--~~~pvIvlt~~~~~~~~~~a~~~Ga~~~l~KP~~~~~L~~~i~~~  118 (469)
T PRK10923         69 IKQRH--PMLPVIIMTAHSDLDAAVSAYQQGAFDYLPKPFDIDEAVALVERA  118 (469)
T ss_pred             HHhhC--CCCeEEEEECCCCHHHHHHHHhcCcceEEecCCcHHHHHHHHHHH
Confidence            98754  578999999988888889999999999999999999998877654

>PRK15115 response regulator GlrR; Provisional

Probab=99.67  E-value=2.3e-15  Score=120.51  Aligned_cols=116  Identities=29%  Similarity=0.433  Sum_probs=104.7

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKK   99 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~   99 (153)
                      ..+|||+||++..+..+...++..|+.+..+.++.+++..+.              ...||+||+|+.||+++|+++++.
T Consensus         5 ~~~vLiVdd~~~~~~~l~~~L~~~g~~v~~~~~~~eal~~l~--------------~~~~dlvilD~~lp~~~g~~ll~~   70 (444)
T PRK15115          5 PAHLLLVDDDPGLLKLLGMRLTSEGYSVVTAESGQEALRVLN--------------REKVDLVISDLRMDEMDGMQLFAE   70 (444)
T ss_pred             CCeEEEEECCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHh--------------cCCCCEEEEcCCCCCCCHHHHHHH
Confidence            478999999999999999999999999999999999988773              456999999999999999999999


Q ss_pred             HHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          100 IKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       100 lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      +++..  +.+|+|++++..+.....++++.|+++|+.||++..++...+.++
T Consensus        71 l~~~~--~~~pvIvlt~~~~~~~~~~a~~~Ga~~~l~KP~~~~~L~~~l~~~  120 (444)
T PRK15115         71 IQKVQ--PGMPVIILTAHGSIPDAVAATQQGVFSFLTKPVDRDALYKAIDDA  120 (444)
T ss_pred             HHhcC--CCCcEEEEECCCCHHHHHHHHhcChhhhccCCCCHHHHHHHHHHH
Confidence            98753  678999999988888889999999999999999999998877654

>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional

Probab=99.67  E-value=3.4e-15  Score=119.86  Aligned_cols=117  Identities=22%  Similarity=0.369  Sum_probs=105.0

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      +..+|||+||++..+..+...|+..|+.+..+.+..+++..+.              ...||+|++|+.||+++|+++++
T Consensus         3 ~~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~--------------~~~~dlillD~~~p~~~g~~ll~   68 (457)
T PRK11361          3 AINRILIVDDEDNVRRMLSTAFALQGFETHCANNGRTALHLFA--------------DIHPDVVLMDIRMPEMDGIKALK   68 (457)
T ss_pred             CCCeEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHh--------------cCCCCEEEEeCCCCCCCHHHHHH
Confidence            3568999999999999999999999999999999999988773              45699999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      .++...  +.+|+|++|+..+.....++++.|+++|+.||++.+++...+.+.
T Consensus        69 ~i~~~~--~~~pvI~lt~~~~~~~~~~a~~~Ga~d~l~KP~~~~~L~~~i~~~  119 (457)
T PRK11361         69 EMRSHE--TRTPVILMTAYAEVETAVEALRCGAFDYVIKPFDLDELNLIVQRA  119 (457)
T ss_pred             HHHhcC--CCCCEEEEeCCCCHHHHHHHHHCCccEEEecccCHHHHHHHHhhh
Confidence            998754  578999999988888899999999999999999999998877654

>PRK09935 transcriptional regulator FimZ; Provisional

Probab=99.67  E-value=6.5e-15  Score=105.54  Aligned_cols=117  Identities=25%  Similarity=0.401  Sum_probs=100.6

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhc-CcEEE-EecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNS-ACKVT-TAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYEL   96 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~-~~~v~-~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~   96 (153)
                      +..+|+++++++..+..+...+... ++.+. .+.++.+++..+.              ...||++++|+.+|+.+|.++
T Consensus         2 ~~~~iliv~d~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~--------------~~~~dlvild~~l~~~~g~~~   67 (210)
T PRK09935          2 KPASVIIMDTHPIIRMSIEVLLQKNSELQIVLKTDDYRITIDYLR--------------TRPVDLIIMDIDLPGTDGFTF   67 (210)
T ss_pred             CcceEEEECCcHHHHHHHHHHHhhCCCceEEEEeCCHHHHHHHHH--------------hcCCCEEEEeCCCCCCCHHHH
Confidence            4567999999999999999999865 56664 6788888877662              356999999999999999999


Q ss_pred             HHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           97 LKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        97 ~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      ++.++...  +.+|+|++++..+.....++++.|+++|+.||++.+++...+..+
T Consensus        68 ~~~l~~~~--~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~i~~~  120 (210)
T PRK09935         68 LKRIKQIQ--STVKVLFLSSKSECFYAGRAIQAGANGFVSKCNDQNDIFHAVQMI  120 (210)
T ss_pred             HHHHHHhC--CCCcEEEEECCCcHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHH
Confidence            99999743  578999999988888888999999999999999999999877664

>PRK09581 pleD response regulator PleD; Reviewed

Probab=99.67  E-value=1.6e-15  Score=120.47  Aligned_cols=117  Identities=20%  Similarity=0.342  Sum_probs=102.7

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      ...+||++||++..+..+...+.. .+.+..+.++.+++..+              ...+||+|++|+.||.++|+++++
T Consensus       154 ~~~~vlivdd~~~~~~~l~~~l~~-~~~~~~~~~~~~a~~~~--------------~~~~~d~vi~d~~~p~~~g~~l~~  218 (457)
T PRK09581        154 EDGRILLVDDDVSQAERIANILKE-EFRVVVVSDPSEALFNA--------------AETNYDLVIVSANFENYDPLRLCS  218 (457)
T ss_pred             cCceEEEEecccchHHHHHHHHhh-cceeeeecChHHHHHhc--------------ccCCCCEEEecCCCCCchHhHHHH
Confidence            457899999999999999999965 46677889999998876              346799999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhh
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGH  150 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~  150 (153)
                      .+++....+.+|+|++|+..+.....++++.|+++|+.||++++++...+..
T Consensus       219 ~i~~~~~~~~~~ii~ls~~~~~~~~~~a~~~Ga~d~l~kp~~~~~l~~~i~~  270 (457)
T PRK09581        219 QLRSKERTRYVPILLLVDEDDDPRLVKALELGVNDYLMRPIDKNELLARVRT  270 (457)
T ss_pred             HHHhccccCCCcEEEEeCCCChHHHHHHHHccchhhhhCCCcHHHHHHHHHH
Confidence            9997544468999999999999999999999999999999999999866543

>PRK09483 response regulator; Provisional

Probab=99.66  E-value=5.9e-15  Score=106.57  Aligned_cols=115  Identities=24%  Similarity=0.364  Sum_probs=100.8

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhc-CcEEE-EecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNS-ACKVT-TAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~-~~~v~-~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      .+|+|+|+++..+..+..+|+.. ++.+. .+.+..+++..+.              ...||++++|+.+++.+|.++++
T Consensus         2 ~~ilivd~~~~~~~~l~~~L~~~~~~~~v~~~~~~~~~~~~~~--------------~~~~dlvi~d~~~~~~~g~~~~~   67 (217)
T PRK09483          2 INVLLVDDHELVRAGIRRILEDIKGIKVVGEACCGEDAVKWCR--------------TNAVDVVLMDMNMPGIGGLEATR   67 (217)
T ss_pred             eEEEEECCcHHHHHHHHHHHccCCCCEEEEEeCCHHHHHHHHH--------------hcCCCEEEEeCCCCCCCHHHHHH
Confidence            47999999999999999999864 77765 7889998888763              35699999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      .+++..  +.+|+|+++...+......++..|+++|+.||++.+++...+.++
T Consensus        68 ~l~~~~--~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~k~~~~~~l~~~i~~~  118 (217)
T PRK09483         68 KILRYT--PDVKIIMLTVHTENPLPAKVMQAGAAGYLSKGAAPQEVVSAIRSV  118 (217)
T ss_pred             HHHHHC--CCCeEEEEeCCCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHH
Confidence            998754  578999999988888888999999999999999999999887764

>PRK10365 transcriptional regulatory protein ZraR; Provisional

Probab=99.66  E-value=4.1e-15  Score=118.84  Aligned_cols=116  Identities=28%  Similarity=0.419  Sum_probs=104.3

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKK   99 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~   99 (153)
                      ..+|+||||++..+..+...|+..|+.+..+.++.+++..+.              ...||++|+|+.||+++|+++++.
T Consensus         5 ~~~Ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~--------------~~~~DlvilD~~m~~~~G~~~~~~   70 (441)
T PRK10365          5 NIDILVVDDDISHCTILQALLRGWGYNVALANSGRQALEQVR--------------EQVFDLVLCDVRMAEMDGIATLKE   70 (441)
T ss_pred             cceEEEEECCHHHHHHHHHHHHHCCCeEEEeCCHHHHHHHHh--------------cCCCCEEEEeCCCCCCCHHHHHHH
Confidence            478999999999999999999999999999999999988773              456899999999999999999999


Q ss_pred             HHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          100 IKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       100 lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      +++..  +.+|+|++|+..+.....++++.|+.+|+.||++.+++...+.+.
T Consensus        71 ir~~~--~~~~vi~lt~~~~~~~~~~a~~~ga~~~l~Kp~~~~~L~~~l~~~  120 (441)
T PRK10365         71 IKALN--PAIPVLIMTAYSSVETAVEALKTGALDYLIKPLDFDNLQATLEKA  120 (441)
T ss_pred             HHhhC--CCCeEEEEECCCCHHHHHHHHHhhhHHHhcCCCCHHHHHHHHHHH
Confidence            98754  678999999988888899999999999999999999998777653

>PRK14084 two-component response regulator; Provisional

Probab=99.65  E-value=6.4e-15  Score=109.06  Aligned_cols=113  Identities=21%  Similarity=0.321  Sum_probs=94.7

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcC-c-EEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSA-C-KVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~-~-~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      ++|+|+||++..+..+...|...+ + .+..+.++.+++..+.              ...||++++|+.||+++|+++++
T Consensus         1 ~~ilivdd~~~~~~~l~~~l~~~~~~~~v~~~~~~~~~l~~~~--------------~~~~dlv~lDi~m~~~~G~~~~~   66 (246)
T PRK14084          1 MKALIVDDEPLARNELTYLLNEIGGFEEINEAENVKETLEALL--------------INQYDIIFLDINLMDESGIELAA   66 (246)
T ss_pred             CEEEEECCCHHHHHHHHHHHHhCCCceEEEEECCHHHHHHHHH--------------hcCCCEEEEeCCCCCCCHHHHHH
Confidence            469999999999999999998754 4 4677899999888763              35699999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      .+++..  +..++|++|+..  ....++++.|+.+|+.||++.+++.+.+.++
T Consensus        67 ~i~~~~--~~~~iI~~t~~~--~~~~~~~~~~~~~yl~KP~~~~~l~~~l~~~  115 (246)
T PRK14084         67 KIQKMK--EPPAIIFATAHD--QFAVKAFELNATDYILKPFEQKRIEQAVNKV  115 (246)
T ss_pred             HHHhcC--CCCEEEEEecCh--HHHHHHHhcCCcEEEECCCCHHHHHHHHHHH
Confidence            999754  456777777653  4567899999999999999999999888775

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

Probab=99.65  E-value=5.6e-15  Score=130.24  Aligned_cols=116  Identities=26%  Similarity=0.423  Sum_probs=105.3

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKK   99 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~   99 (153)
                      ..+|||+||++..+..+...|+..|+.+..+.++.+++..+.              ...||+||+|+.||+++|+++++.
T Consensus       958 ~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~--------------~~~~dlil~D~~mp~~~g~~~~~~ 1023 (1197)
T PRK09959        958 KLSILIADDHPTNRLLLKRQLNLLGYDVDEATDGVQALHKVS--------------MQHYDLLITDVNMPNMDGFELTRK 1023 (1197)
T ss_pred             CceEEEcCCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHhh--------------cCCCCEEEEeCCCCCCCHHHHHHH
Confidence            468999999999999999999999999999999999998873              467999999999999999999999


Q ss_pred             HHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          100 IKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       100 lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      +++..  +.+|+|++|+........++++.|+++|+.||++.++|...+.++
T Consensus      1024 i~~~~--~~~pii~lt~~~~~~~~~~~~~~G~~~~l~KP~~~~~L~~~l~~~ 1073 (1197)
T PRK09959       1024 LREQN--SSLPIWGLTANAQANEREKGLSCGMNLCLFKPLTLDVLKTHLSQL 1073 (1197)
T ss_pred             HHhcC--CCCCEEEEECCCCHHHHHHHHHCCCCEEEeCCCCHHHHHHHHHHH
Confidence            99754  578999999998888889999999999999999999998877653

>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator

Probab=99.64  E-value=6.6e-15  Score=117.91  Aligned_cols=111  Identities=19%  Similarity=0.298  Sum_probs=98.7

Q ss_pred             EEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCC-----CCHHHHH
Q 042079           23 VLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPG-----MTGYELL   97 (153)
Q Consensus        23 iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~-----~~g~~~~   97 (153)
                      |||+||++..+..+...+  .+|.+..+.++.+++..+.              ...||+|++|+.||+     ++|++++
T Consensus         1 ILivddd~~~~~~l~~~l--~~~~v~~a~~~~~al~~l~--------------~~~~dlvllD~~mp~~~~~~~~g~~~l   64 (445)
T TIGR02915         1 LLIVEDDLGLQKQLKWSF--ADYELAVAADRESAIALVR--------------RHEPAVVTLDLGLPPDADGASEGLAAL   64 (445)
T ss_pred             CEEEECCHHHHHHHHHHh--CCCeEEEeCCHHHHHHHHh--------------hCCCCEEEEeCCCCCCcCCCCCHHHHH
Confidence            589999999999999888  6899999999999999873              357999999999996     7999999


Q ss_pred             HHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           98 KKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        98 ~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      +.+++..  +.+|+|++|+..+.+...++++.|+++|+.||++.+++...+.+.
T Consensus        65 ~~i~~~~--~~~piI~lt~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~  116 (445)
T TIGR02915        65 QQILAIA--PDTKVIVITGNDDRENAVKAIGLGAYDFYQKPIDPDVLKLIVDRA  116 (445)
T ss_pred             HHHHhhC--CCCCEEEEecCCCHHHHHHHHHCCccEEEeCCCCHHHHHHHHhhh
Confidence            9998754  678999999998889999999999999999999999998777553

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).

>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional

Probab=99.63  E-value=3.2e-14  Score=104.10  Aligned_cols=114  Identities=24%  Similarity=0.415  Sum_probs=100.9

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKI  100 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~l  100 (153)
                      .+|+++|+++.....+...|...++.+..+.++.+++..+.              ...||++++|+.+|+.+|.++++.+
T Consensus        11 ~~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~~--------------~~~~dlvl~d~~~~~~~g~~~~~~l   76 (240)
T PRK10710         11 PRILIVEDEPKLGQLLIDYLQAASYATTLLSHGDEVLPYVR--------------QTPPDLILLDLMLPGTDGLTLCREI   76 (240)
T ss_pred             CeEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHh--------------hCCCCEEEEeCCCCCCCHHHHHHHH
Confidence            48999999999999999999988999999999999988773              3568999999999999999999999


Q ss_pred             HhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          101 KESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       101 r~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      +..   +.+|+++++..........+++.|+++|+.||++..++...+..+
T Consensus        77 ~~~---~~~pii~l~~~~~~~~~~~~~~~ga~~~l~kp~~~~~L~~~i~~~  124 (240)
T PRK10710         77 RRF---SDIPIVMVTAKIEEIDRLLGLEIGADDYICKPYSPREVVARVKTI  124 (240)
T ss_pred             Hhc---CCCCEEEEEcCCCHHHHHHHHhcCCCeEEECCCCHHHHHHHHHHH
Confidence            863   468999999888888888899999999999999999998766553

>PRK10360 DNA-binding transcriptional activator UhpA; Provisional

Probab=99.63  E-value=1.9e-14  Score=102.38  Aligned_cols=113  Identities=26%  Similarity=0.406  Sum_probs=97.6

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhc-CcE-EEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNS-ACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~-~~~-v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      .+|+|+|+++..+..+...|... ++. +..+.++.+++..+.              ...||++++|+.+++.+|.++++
T Consensus         2 ~~ilivd~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~l~~~~--------------~~~~dlvi~d~~~~~~~g~~~~~   67 (196)
T PRK10360          2 ITVALIDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALAGLP--------------GRGVQVCICDISMPDISGLELLS   67 (196)
T ss_pred             eEEEEECCcHHHHHHHHHHHccCCCcEEEEEECCHHHHHHHHh--------------cCCCCEEEEeCCCCCCCHHHHHH
Confidence            47999999999999999999754 554 567889999988772              45699999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      .++.     ..|+++++...+......+++.|+++|+.||++.+++...+.++.
T Consensus        68 ~l~~-----~~~vi~~s~~~~~~~~~~~~~~ga~~~i~kp~~~~~l~~~i~~~~  116 (196)
T PRK10360         68 QLPK-----GMATIMLSVHDSPALVEQALNAGARGFLSKRCSPDELIAAVHTVA  116 (196)
T ss_pred             HHcc-----CCCEEEEECCCCHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHH
Confidence            8863     468999999888888899999999999999999999998887653

>PRK09581 pleD response regulator PleD; Reviewed

Probab=99.63  E-value=1.7e-14  Score=114.66  Aligned_cols=117  Identities=28%  Similarity=0.459  Sum_probs=104.2

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKI  100 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~l  100 (153)
                      .+||++++++..+..+...|...++.+..+.+..+++..+.              ...||+|++|+.+|+.+|.++++.+
T Consensus         3 ~~ilii~~~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~--------------~~~~dlvi~d~~~~~~~g~~l~~~i   68 (457)
T PRK09581          3 ARILVVDDIPANVKLLEAKLLAEYYTVLTASSGAEAIAICE--------------REQPDIILLDVMMPGMDGFEVCRRL   68 (457)
T ss_pred             CeEEEEeCCHHHHHHHHHHHHhCCCEEEEeCCHHHHHHHHh--------------hcCCCEEEEeCCCCCCCHHHHHHHH
Confidence            47999999999999999999888999999999999998873              3569999999999999999999999


Q ss_pred             HhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          101 KESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       101 r~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      ++....+.+|+|++++..+.....++++.|+++|+.||++.+++...+.++
T Consensus        69 ~~~~~~~~~~ii~~s~~~~~~~~~~~~~~ga~~~l~kp~~~~~l~~~i~~~  119 (457)
T PRK09581         69 KSDPATTHIPVVMVTALDDPEDRVRGLEAGADDFLTKPINDVALFARVKSL  119 (457)
T ss_pred             HcCcccCCCCEEEEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHH
Confidence            875433578999999988888899999999999999999999998777654

>PRK09390 fixJ response regulator FixJ; Provisional

Probab=99.63  E-value=2.5e-14  Score=101.26  Aligned_cols=116  Identities=28%  Similarity=0.383  Sum_probs=102.0

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      +..+|+++++++.....+...|...++.+..+.++.+++..+.              ...||++++|+.+++++|+++++
T Consensus         2 ~~~~iliv~~~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~--------------~~~~d~ii~d~~~~~~~~~~~~~   67 (202)
T PRK09390          2 DKGVVHVVDDDEAMRDSLAFLLDSAGFEVRLFESAQAFLDALP--------------GLRFGCVVTDVRMPGIDGIELLR   67 (202)
T ss_pred             CCCEEEEEeCCHHHHHHHHHHHHHCCCeEEEeCCHHHHHHHhc--------------cCCCCEEEEeCCCCCCcHHHHHH
Confidence            3478999999999999999999988999999999998887762              45699999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhh
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGH  150 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~  150 (153)
                      .+++..  +.+|+|+++...+......+++.|+.+|+.||++..++...+..
T Consensus        68 ~l~~~~--~~~~ii~l~~~~~~~~~~~~~~~g~~~~l~~p~~~~~l~~~l~~  117 (202)
T PRK09390         68 RLKARG--SPLPVIVMTGHGDVPLAVEAMKLGAVDFIEKPFEDERLIGAIER  117 (202)
T ss_pred             HHHhcC--CCCCEEEEECCCCHHHHHHHHHcChHHHhhCCCCHHHHHHHHHH
Confidence            998754  57899999998888888899999999999999999988766554

>TIGR01818 ntrC nitrogen regulation protein NR(I)

Probab=99.63  E-value=1.1e-14  Score=117.20  Aligned_cols=113  Identities=28%  Similarity=0.409  Sum_probs=101.7

Q ss_pred             EEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHHHh
Q 042079           23 VLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKIKE  102 (153)
Q Consensus        23 iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~lr~  102 (153)
                      |||+||++..+..+...|+..|+.+..+.++.+++..+.              ...||+|++|+.||+++|+++++.++.
T Consensus         1 ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~--------------~~~~DlVllD~~~p~~~g~~ll~~l~~   66 (463)
T TIGR01818         1 VWVVDDDRSIRWVLEKALSRAGYEVRTFGNAASVLRALA--------------RGQPDLLITDVRMPGEDGLDLLPQIKK   66 (463)
T ss_pred             CEEEECCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHh--------------cCCCCEEEEcCCCCCCCHHHHHHHHHH
Confidence            589999999999999999999999999999999988773              356999999999999999999999987


Q ss_pred             ccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          103 SSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       103 ~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      ..  +.+|+|++++..+.....++++.|+++|+.||++.+++...+.+.
T Consensus        67 ~~--~~~~vIvlt~~~~~~~~~~a~~~Ga~~~l~KP~~~~~L~~~i~~~  113 (463)
T TIGR01818        67 RH--PQLPVIVMTAHSDLDTAVAAYQRGAFEYLPKPFDLDEAVTLVERA  113 (463)
T ss_pred             hC--CCCeEEEEeCCCCHHHHHHHHHcCcceeecCCCCHHHHHHHHHHH
Confidence            53  578999999988888889999999999999999999998877664

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.

>PRK15479 transcriptional regulatory protein TctD; Provisional

Probab=99.62  E-value=4e-14  Score=102.15  Aligned_cols=115  Identities=22%  Similarity=0.364  Sum_probs=100.7

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKI  100 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~l  100 (153)
                      ++|+++|+++.....+...+...++.+..+.++.+++..+.              ...||++++|+.+|+.+|+++++.+
T Consensus         1 ~~ilivd~~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~--------------~~~~d~vild~~~~~~~~~~~~~~i   66 (221)
T PRK15479          1 MRLLLAEDNRELAHWLEKALVQNGFAVDCVFDGLAADHLLQ--------------SEMYALAVLDINMPGMDGLEVLQRL   66 (221)
T ss_pred             CeEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHh--------------hCCCCEEEEeCCCCCCcHHHHHHHH
Confidence            36999999999999999999988998888999998877662              3569999999999999999999999


Q ss_pred             HhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          101 KESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       101 r~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      +...  +.+|+|+++...+.....++++.|+++|+.||++..++...+..+
T Consensus        67 ~~~~--~~~~ii~lt~~~~~~~~~~~~~~g~~~~i~kp~~~~~l~~~i~~~  115 (221)
T PRK15479         67 RKRG--QTLPVLLLTARSAVADRVKGLNVGADDYLPKPFELEELDARLRAL  115 (221)
T ss_pred             HhcC--CCCCEEEEECCCCHHHHHHHHHcCCCeeEeCCCCHHHHHHHHHHH
Confidence            8754  578999999888888888999999999999999999998766553

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

Probab=99.61  E-value=2.4e-14  Score=105.32  Aligned_cols=112  Identities=27%  Similarity=0.399  Sum_probs=92.0

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcC-cE-EEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSA-CK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~-~~-v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      .+|+|+||++..+..+...|+..+ +. +..+.++.+++..+.              ...||++|+|+.||+++|+++++
T Consensus         2 ~~IlIvdd~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~l~~~~--------------~~~~dlv~lDi~~~~~~G~~~~~   67 (238)
T PRK11697          2 IKVLIVDDEPLAREELRELLQEEGDIEIVGECSNAIEAIGAIH--------------RLKPDVVFLDIQMPRISGLELVG   67 (238)
T ss_pred             cEEEEECCCHHHHHHHHHHHhhCCCcEEEEEeCCHHHHHHHHH--------------hcCCCEEEEeCCCCCCCHHHHHH
Confidence            579999999999999999998776 33 456889998887762              34689999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      .++..   ...++|++|+..  +...++++.|+.+|+.||++.+++...+.++
T Consensus        68 ~l~~~---~~~~ii~vt~~~--~~~~~a~~~~~~~yl~KP~~~~~l~~~l~~~  115 (238)
T PRK11697         68 MLDPE---HMPYIVFVTAFD--EYAIKAFEEHAFDYLLKPIDPARLAKTLARL  115 (238)
T ss_pred             Hhccc---CCCEEEEEeccH--HHHHHHHhcCCcEEEECCCCHHHHHHHHHHH
Confidence            98642   234677777653  4567899999999999999999998887765

>PRK10610 chemotaxis regulatory protein CheY; Provisional

Probab=99.61  E-value=1.3e-13  Score=89.97  Aligned_cols=119  Identities=34%  Similarity=0.537  Sum_probs=101.4

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcE-EEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELL   97 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~-v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~   97 (153)
                      +..+++++++++.....+...+...++. +..+.+..+++..+.              ...+|++++|..+++.+|++++
T Consensus         4 ~~~~il~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~--------------~~~~di~l~d~~~~~~~~~~~~   69 (129)
T PRK10610          4 KELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQ--------------AGGFGFVISDWNMPNMDGLELL   69 (129)
T ss_pred             ccceEEEEcCCHHHHHHHHHHHHHcCCCeEEEeCCHHHHHHHhh--------------ccCCCEEEEcCCCCCCCHHHHH
Confidence            4578999999999999999999988884 777888888877662              3568999999999999999999


Q ss_pred             HHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           98 KKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        98 ~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      +.+++....+.+|+++++..........+++.|+++|+.||++..++...+.++
T Consensus        70 ~~l~~~~~~~~~~~i~~~~~~~~~~~~~~~~~g~~~~i~~p~~~~~l~~~l~~~  123 (129)
T PRK10610         70 KTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKI  123 (129)
T ss_pred             HHHHhCCCcCCCcEEEEECCCCHHHHHHHHHhCCCeEEECCCCHHHHHHHHHHH
Confidence            999875444568899998877778888899999999999999999998777664

>PRK13558 bacterio-opsin activator; Provisional

Probab=99.57  E-value=6.5e-14  Score=117.10  Aligned_cols=107  Identities=19%  Similarity=0.228  Sum_probs=95.9

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      +.++||++||++..+..+..+|...++.+..+.++.+++..+.              ...||+||+|+.||+++|+++++
T Consensus         6 ~~~~ILivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~al~~~~--------------~~~~Dlvl~d~~lp~~~g~~~l~   71 (665)
T PRK13558          6 PTRGVLFVGDDPEAGPVDCDLDEDGRLDVTQIRDFVAARDRVE--------------AGEIDCVVADHEPDGFDGLALLE   71 (665)
T ss_pred             cceeEEEEccCcchHHHHHHHhhccCcceEeeCCHHHHHHHhh--------------ccCCCEEEEeccCCCCcHHHHHH
Confidence            4578999999999999999999888999999999999988773              45699999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCCh
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKP  141 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~  141 (153)
                      .++...  +.+|+|++++..+.....+++..|+.+|+.||.+.
T Consensus        72 ~l~~~~--~~~piI~lt~~~~~~~~~~al~~Ga~dyl~k~~~~  112 (665)
T PRK13558         72 AVRQTT--AVPPVVVVPTAGDEAVARRAVDADAAAYVPAVSDD  112 (665)
T ss_pred             HHHhcC--CCCCEEEEECCCCHHHHHHHHhcCcceEEeccchh
Confidence            998744  57899999999888899999999999999999764

>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional

Probab=99.57  E-value=1.2e-13  Score=101.15  Aligned_cols=114  Identities=9%  Similarity=0.067  Sum_probs=90.7

Q ss_pred             CCCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHH
Q 042079           18 PKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELL   97 (153)
Q Consensus        18 ~~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~   97 (153)
                      +...+++++||++.....++.+|+..--.+..+.++.+++..+                .+||++++|+.||+.+|++++
T Consensus         8 ~~~~~~~~v~~~~l~~~~l~~~L~~~~~v~~~~~~~~~~~~~~----------------~~~DvvllDi~~p~~~G~~~~   71 (216)
T PRK10100          8 SHGHTLLLITKPSLQATALLQHLKQSLAITGKLHNIQRSLDDI----------------SSGSIILLDMMEADKKLIHYW   71 (216)
T ss_pred             ccCceEEEEeChHhhhHHHHHHHHHhCCCeEEEcCHHHhhccC----------------CCCCEEEEECCCCCccHHHHH
Confidence            3456799999999999999999984333355677888887654                248999999999999999997


Q ss_pred             -HHHHhccCCCCCcEEEEeCCCChhhHHHHHH--hcCcccccCCCChhHHHHHHhhh
Q 042079           98 -KKIKESSVMKEVPVVVVSSENIPTRINECLE--EGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        98 -~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~--~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                       +.++...  +.++||++|...+  ....++.  .|+.+|+.|+.+.++|.+.+...
T Consensus        72 ~~~i~~~~--p~~~vvvlt~~~~--~~~~~~~~~~Ga~G~l~K~~~~~~L~~aI~~v  124 (216)
T PRK10100         72 QDTLSRKN--NNIKILLLNTPED--YPYREIENWPHINGVFYAMEDQERVVNGLQGV  124 (216)
T ss_pred             HHHHHHhC--CCCcEEEEECCch--hHHHHHHHhcCCeEEEECCCCHHHHHHHHHHH
Confidence             5577644  5789999998765  3344555  49999999999999999887654

>PRK12555 chemotaxis-specific methylesterase; Provisional

Probab=99.56  E-value=1.4e-13  Score=106.87  Aligned_cols=102  Identities=24%  Similarity=0.350  Sum_probs=86.8

Q ss_pred             CeEEEEeCCHHHHHHHHHHHH-hcCcEEE-EecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLK-NSACKVT-TAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~-~~~~~v~-~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      ++||++||++..+..+..+|. ..++.+. .+.++.+++..+.              ...||+|++|+.||+++|+++++
T Consensus         1 ~~VLvVdd~~~~~~~l~~~L~~~~~~~vv~~a~~~~eal~~l~--------------~~~pDlVllD~~mp~~~G~e~l~   66 (337)
T PRK12555          1 MRIGIVNDSPLAVEALRRALARDPDHEVVWVATDGAQAVERCA--------------AQPPDVILMDLEMPRMDGVEATR   66 (337)
T ss_pred             CEEEEEeCCHHHHHHHHHHHhhCCCCEEEEEECCHHHHHHHHh--------------ccCCCEEEEcCCCCCCCHHHHHH
Confidence            379999999999999999994 5677765 7899999998873              45799999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCC--hhhHHHHHHhcCcccccCCC
Q 042079           99 KIKESSVMKEVPVVVVSSENI--PTRINECLEEGAQMFMLKPL  139 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~--~~~~~~a~~~ga~~~l~KP~  139 (153)
                      ++++..   .+|+++++....  .....++++.|+++|+.||+
T Consensus        67 ~l~~~~---~~pvivvs~~~~~~~~~~~~al~~Ga~d~l~KP~  106 (337)
T PRK12555         67 RIMAER---PCPILIVTSLTERNASRVFEAMGAGALDAVDTPT  106 (337)
T ss_pred             HHHHHC---CCcEEEEeCCCCcCHHHHHHHHhcCceEEEECCC
Confidence            998743   579999987643  45566899999999999999

>PRK10403 transcriptional regulator NarP; Provisional

Probab=99.56  E-value=3.1e-13  Score=96.78  Aligned_cols=116  Identities=22%  Similarity=0.387  Sum_probs=98.6

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHh-cCcEEE-EecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKN-SACKVT-TAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELL   97 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~-~~~~v~-~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~   97 (153)
                      ..+||++++++.....+...++. .++.+. .+.+..+++..+.              ...||++++|+.+++++|.+++
T Consensus         6 ~~~ilii~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~--------------~~~~dlvi~d~~~~~~~~~~~~   71 (215)
T PRK10403          6 PFQVLIVDDHPLMRRGVRQLLELDPGFEVVAEAGDGASAIDLAN--------------RLDPDVILLDLNMKGMSGLDTL   71 (215)
T ss_pred             eEEEEEEcCCHHHHHHHHHHHhcCCCCEEEEEeCCHHHHHHHHH--------------hcCCCEEEEecCCCCCcHHHHH
Confidence            46899999999999999999975 466664 6888888887662              3569999999999999999999


Q ss_pred             HHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           98 KKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        98 ~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      +.+++..  +..|+++++..........+++.|+++|+.||++..++...+.+.
T Consensus        72 ~~l~~~~--~~~~ii~l~~~~~~~~~~~~~~~g~~~~i~kp~~~~~l~~~i~~~  123 (215)
T PRK10403         72 NALRRDG--VTAQIIILTVSDASSDVFALIDAGADGYLLKDSDPEVLLEAIRAG  123 (215)
T ss_pred             HHHHHhC--CCCeEEEEeCCCChHHHHHHHHcCCCeEEecCCCHHHHHHHHHHH
Confidence            9998754  467899999888888888899999999999999999998777653

>PRK13435 response regulator; Provisional

Probab=99.55  E-value=3e-13  Score=92.36  Aligned_cols=113  Identities=21%  Similarity=0.270  Sum_probs=94.3

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcEEE-EecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCC-CCCHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACKVT-TAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMP-GMTGYEL   96 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~v~-~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~-~~~g~~~   96 (153)
                      ...+||+++++......+...++..++.+. .+.+..+++..+.              ...||++++|+.++ +.+|.++
T Consensus         4 ~~~~iliid~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~--------------~~~~dliivd~~~~~~~~~~~~   69 (145)
T PRK13435          4 RQLKVLIVEDEALIALELEKLVEEAGHEVVGIAMSSEQAIALGR--------------RRQPDVALVDVHLADGPTGVEV   69 (145)
T ss_pred             ccceEEEEcCcHHHHHHHHHHHHhcCCeEEEeeCCHHHHHHHhh--------------hcCCCEEEEeeecCCCCcHHHH
Confidence            457899999999999999999998888876 6888888887662              34689999999998 4799999


Q ss_pred             HHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           97 LKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        97 ~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      ++.+++.   +.+|+|+++...+   ...+...|+++|+.||++..++.+.+.++
T Consensus        70 ~~~l~~~---~~~pii~ls~~~~---~~~~~~~ga~~~l~kp~~~~~l~~~i~~~  118 (145)
T PRK13435         70 ARRLSAD---GGVEVVFMTGNPE---RVPHDFAGALGVIAKPYSPRGVARALSYL  118 (145)
T ss_pred             HHHHHhC---CCCCEEEEeCCHH---HHHHHhcCcceeEeCCCCHHHHHHHHHHH
Confidence            9998763   3689999987532   24677899999999999999999988775

>PRK10651 transcriptional regulator NarL; Provisional

Probab=99.55  E-value=4.9e-13  Score=95.90  Aligned_cols=117  Identities=31%  Similarity=0.474  Sum_probs=99.7

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhc-CcE-EEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNS-ACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYEL   96 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~-~~~-v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~   96 (153)
                      ...+|+++++++..+..+..+|... ++. +..+.+..+++..+.              ...||++++|+.+++.+|+++
T Consensus         5 ~~~~iliv~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~--------------~~~~dlvl~d~~l~~~~~~~~   70 (216)
T PRK10651          5 EPATILLIDDHPMLRTGVKQLISMAPDITVVGEASNGEQGIELAE--------------SLDPDLILLDLNMPGMNGLET   70 (216)
T ss_pred             cceEEEEECCCHHHHHHHHHHHccCCCcEEEEEeCCHHHHHHHHH--------------hCCCCEEEEeCCCCCCcHHHH
Confidence            4478999999999999999999764 454 446889898888762              356999999999999999999


Q ss_pred             HHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           97 LKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        97 ~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      ++.+++..  +..|+++++...+......+++.|+++|+.||++..++...+.++
T Consensus        71 ~~~l~~~~--~~~~vi~l~~~~~~~~~~~~~~~g~~~~i~k~~~~~~l~~~i~~~  123 (216)
T PRK10651         71 LDKLREKS--LSGRIVVFSVSNHEEDVVTALKRGADGYLLKDMEPEDLLKALQQA  123 (216)
T ss_pred             HHHHHHhC--CCCcEEEEeCCCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHH
Confidence            99998754  567999999888888888999999999999999999998877664

>PRK15369 two component system sensor kinase SsrB; Provisional

Probab=99.54  E-value=5.7e-13  Score=94.76  Aligned_cols=117  Identities=20%  Similarity=0.305  Sum_probs=98.9

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhc-CcEE-EEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNS-ACKV-TTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYEL   96 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~-~~~v-~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~   96 (153)
                      +..+||++++++..+..+...|... ++.+ ..+.+..+++..+.              ...||++++|+.+++.+|+++
T Consensus         2 ~~~~iliv~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~--------------~~~~dlvl~d~~~~~~~~~~~   67 (211)
T PRK15369          2 KNYKILLVDDHELIINGIKNMLAPYPRYKIVGQVDNGLEVYNACR--------------QLEPDIVILDLGLPGMNGLDV   67 (211)
T ss_pred             CccEEEEECCcHHHHHHHHHHHccCCCcEEEEEECCHHHHHHHHH--------------hcCCCEEEEeCCCCCCCHHHH
Confidence            4578999999999999999999865 4554 47788888877652              356999999999999999999


Q ss_pred             HHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           97 LKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        97 ~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      ++.+++..  +..|+++++...+......+++.|+++|+.||++..++...+...
T Consensus        68 ~~~l~~~~--~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~i~~~  120 (211)
T PRK15369         68 IPQLHQRW--PAMNILVLTARQEEHMASRTLAAGALGYVLKKSPQQILLAAIQTV  120 (211)
T ss_pred             HHHHHHHC--CCCcEEEEeCCCCHHHHHHHHHhCCCEEEeCCCCHHHHHHHHHHH
Confidence            99998754  568999999888888888999999999999999999998777653

>PRK11475 DNA-binding transcriptional activator BglJ; Provisional

Probab=99.52  E-value=3.4e-13  Score=98.08  Aligned_cols=103  Identities=13%  Similarity=0.096  Sum_probs=83.9

Q ss_pred             HHHHHHHHHh---cCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEE---EeCCCCCCCHHHHHHHHHhccCC
Q 042079           33 RKIVENLLKN---SACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVI---TDYCMPGMTGYELLKKIKESSVM  106 (153)
Q Consensus        33 ~~~l~~~l~~---~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii---~D~~~~~~~g~~~~~~lr~~~~~  106 (153)
                      +..++.+|..   .++.+..+.++.+++..+.              ...||+++   +|+.||+++|++++++|++..  
T Consensus         3 r~gi~~lL~~~~~~~~~v~~~~~~~~~l~~~~--------------~~~pd~vl~dl~d~~mp~~~Gl~~~~~l~~~~--   66 (207)
T PRK11475          3 SIGIESLFRKFPGNPYKLHTFSSQSSFQDAMS--------------RISFSAVIFSLSAMRSERREGLSCLTELAIKF--   66 (207)
T ss_pred             hHHHHHHHhcCCCCeeEEEEeCCHHHHHHHhc--------------cCCCCEEEeeccccCCCCCCHHHHHHHHHHHC--
Confidence            5677788864   3566778999999988772              45689998   688889999999999998754  


Q ss_pred             CCCcEEEEeCCCChhhHHHHH-HhcCcccccCCCChhHHHHHHhhh
Q 042079          107 KEVPVVVVSSENIPTRINECL-EEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       107 ~~~pii~~t~~~~~~~~~~a~-~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      +.+|||++|...++.....++ +.|+++|+.||.+++++.+.+...
T Consensus        67 p~~~iIvlt~~~~~~~~~~~~~~~Ga~gyl~K~~~~~eL~~aI~~v  112 (207)
T PRK11475         67 PRMRRLVIADDDIEARLIGSLSPSPLDGVLSKASTLEILQQELFLS  112 (207)
T ss_pred             CCCCEEEEeCCCCHHHHHHHHHHcCCeEEEecCCCHHHHHHHHHHH
Confidence            689999999876665555554 799999999999999999888764

>PRK00742 chemotaxis-specific methylesterase; Provisional

Probab=99.52  E-value=7e-13  Score=103.51  Aligned_cols=105  Identities=33%  Similarity=0.418  Sum_probs=88.7

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhc-CcEEE-EecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNS-ACKVT-TAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYEL   96 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~-~~~v~-~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~   96 (153)
                      +..+||++||+...+..+...|... ++.+. .+.++.+++..+.              ...||++++|+.||+++|+++
T Consensus         2 ~~~~ILiVdd~~~~~~~L~~~L~~~~~~~vv~~a~~~~~al~~~~--------------~~~~DlVllD~~mp~~dgle~   67 (354)
T PRK00742          2 MKIRVLVVDDSAFMRRLISEILNSDPDIEVVGTAPDGLEAREKIK--------------KLNPDVITLDVEMPVMDGLDA   67 (354)
T ss_pred             CccEEEEECCCHHHHHHHHHHHhhCCCCEEEEEECCHHHHHHHHh--------------hhCCCEEEEeCCCCCCChHHH
Confidence            3578999999999999999999865 77766 7899999988772              456999999999999999999


Q ss_pred             HHHHHhccCCCCCcEEEEeCCC--ChhhHHHHHHhcCcccccCCCC
Q 042079           97 LKKIKESSVMKEVPVVVVSSEN--IPTRINECLEEGAQMFMLKPLK  140 (153)
Q Consensus        97 ~~~lr~~~~~~~~pii~~t~~~--~~~~~~~a~~~ga~~~l~KP~~  140 (153)
                      ++.+++..  + +|+|+++...  ......++++.|+++|+.||+.
T Consensus        68 l~~i~~~~--~-~piIvls~~~~~~~~~~~~al~~Ga~d~l~kP~~  110 (354)
T PRK00742         68 LEKIMRLR--P-TPVVMVSSLTERGAEITLRALELGAVDFVTKPFL  110 (354)
T ss_pred             HHHHHHhC--C-CCEEEEecCCCCCHHHHHHHHhCCCcEEEeCCcc
Confidence            99998754  3 8999998753  3355678999999999999994

>PRK09191 two-component response regulator; Provisional

Probab=99.49  E-value=2.1e-12  Score=96.23  Aligned_cols=113  Identities=19%  Similarity=0.311  Sum_probs=94.1

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCcEEE-EecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCC-CCHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSACKVT-TAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPG-MTGYELL   97 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~~~v~-~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~-~~g~~~~   97 (153)
                      ..+++|+|+++..+..+...|+..|+.+. .+.++.+++..+.              ...||++|+|+.+|+ .+|++++
T Consensus       137 ~~~~liidd~~~~~~~l~~~L~~~~~~~~~~~~~~~~~l~~l~--------------~~~~dlvi~d~~~~~~~~g~e~l  202 (261)
T PRK09191        137 ATRVLIIEDEPIIAMDLEQLVESLGHRVTGIARTRAEAVALAK--------------KTRPGLILADIQLADGSSGIDAV  202 (261)
T ss_pred             CCeEEEEcCcHHHHHHHHHHHhcCCCEEEEEECCHHHHHHHHh--------------ccCCCEEEEecCCCCCCCHHHHH
Confidence            46799999999999999999998888877 6888888888772              356999999999995 7999999


Q ss_pred             HHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           98 KKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        98 ~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      +.++...   .+|+|++++..+...  .+...++.+|+.||++.+++...+.++
T Consensus       203 ~~l~~~~---~~pii~ls~~~~~~~--~~~~~~~~~~l~kP~~~~~l~~~i~~~  251 (261)
T PRK09191        203 NDILKTF---DVPVIFITAFPERLL--TGERPEPAFLITKPFQPDTVKAAISQA  251 (261)
T ss_pred             HHHHHhC---CCCEEEEeCCCcHHH--HHHhcccCceEECCCCHHHHHHHHHHH
Confidence            9998743   689999998655443  344567889999999999999988875

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

Probab=99.48  E-value=1.9e-12  Score=94.18  Aligned_cols=114  Identities=13%  Similarity=0.096  Sum_probs=90.4

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCc---EEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCC--CCCCCHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSAC---KVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYC--MPGMTGYE   95 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~---~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~--~~~~~g~~   95 (153)
                      +.|+|+||++..+..++.+|+..++   .+..+.++.+++..+.              ..+||++++|+.  ++..+|.+
T Consensus         1 ~~~lIvDD~~~~~~gl~~~L~~~~~~~~vv~~~~~~~~~~~~~~--------------~~~pDlvLlDl~~~l~~~~g~~   66 (207)
T PRK15411          1 MSTIIMDLCSYTRLGLTGYLLSRGVKKREINDIETVDDLAIACD--------------SLRPSVVFINEDCFIHDASNSQ   66 (207)
T ss_pred             CCEEEEcCCHHHHHHHHHHHHhCCCcceEEEecCCHHHHHHHHh--------------ccCCCEEEEeCcccCCCCChHH
Confidence            3589999999999999999986542   4567899999888762              356899999965  88889999


Q ss_pred             HHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcc-cccCCCChhHHHHHHhhh
Q 042079           96 LLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQM-FMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        96 ~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~-~l~KP~~~~~l~~~~~~~  151 (153)
                      +++.|++..  +.+++|++|...+.... .++..|+.. |+.|+.+++++.+.++..
T Consensus        67 ~i~~i~~~~--p~~~iivlt~~~~~~~~-~~~~~~~~~~~~~K~~~~~~L~~aI~~v  120 (207)
T PRK15411         67 RIKQIINQH--PNTLFIVFMAIANIHFD-EYLLVRKNLLISSKSIKPESLDDLLGDI  120 (207)
T ss_pred             HHHHHHHHC--CCCeEEEEECCCchhHH-HHHHHHhhceeeeccCCHHHHHHHHHHH
Confidence            999998754  57899999987665543 355555544 889999999999888764

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

Probab=99.48  E-value=2.4e-12  Score=110.33  Aligned_cols=116  Identities=10%  Similarity=0.099  Sum_probs=101.9

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKK   99 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~   99 (153)
                      ..+||++||++..+..+...|...||.+..+.++.+++..+..            ....||+||+  .+|.++|.++++.
T Consensus       697 ~~~ILvVddd~~~~~~l~~~L~~~G~~v~~~~s~~~al~~l~~------------~~~~~DlVll--~~~~~~g~~l~~~  762 (828)
T PRK13837        697 GETVLLVEPDDATLERYEEKLAALGYEPVGFSTLAAAIAWISK------------GPERFDLVLV--DDRLLDEEQAAAA  762 (828)
T ss_pred             CCEEEEEcCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHHh------------CCCCceEEEE--CCCCCCHHHHHHH
Confidence            4589999999999999999999999999999999999987731            1234899999  6999999999999


Q ss_pred             HHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079          100 IKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus       100 lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      ++...  +.+|||+++.........+++..| ++|+.||++..++..++.+.+
T Consensus       763 l~~~~--~~ipIIvls~~~~~~~~~~~~~~G-~d~L~KP~~~~~L~~~l~~~l  812 (828)
T PRK13837        763 LHAAA--PTLPIILGGNSKTMALSPDLLASV-AEILAKPISSRTLAYALRTAL  812 (828)
T ss_pred             HHhhC--CCCCEEEEeCCCchhhhhhHhhcc-CcEEeCCCCHHHHHHHHHHHH
Confidence            98754  678999999988888888999999 999999999999998887753

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

Probab=99.47  E-value=9.8e-13  Score=101.36  Aligned_cols=103  Identities=37%  Similarity=0.476  Sum_probs=90.5

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcC--cEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSA--CKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~--~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      ++||+|||....|..++.+|...+  ..+..+.++.++++.+.              ...||+|.+|+.||.++|+++++
T Consensus         2 irVlvVddsal~R~~i~~~l~~~~~i~vv~~a~ng~~a~~~~~--------------~~~PDVi~ld~emp~mdgl~~l~   67 (350)
T COG2201           2 IRVLVVDDSALMRKVISDILNSDPDIEVVGTARNGREAIDKVK--------------KLKPDVITLDVEMPVMDGLEALR   67 (350)
T ss_pred             cEEEEEcCcHHHHHHHHHHHhcCCCeEEEEecCCHHHHHHHHH--------------hcCCCEEEEecccccccHHHHHH
Confidence            689999999999999999999887  56778999999999883              56799999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCC--hhhHHHHHHhcCcccccCCCC
Q 042079           99 KIKESSVMKEVPVVVVSSENI--PTRINECLEEGAQMFMLKPLK  140 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~--~~~~~~a~~~ga~~~l~KP~~  140 (153)
                      .+.+.   ..+|||++++...  .+...++++.|+.||+.||..
T Consensus        68 ~im~~---~p~pVimvsslt~~g~~~t~~al~~gAvD~i~kp~~  108 (350)
T COG2201          68 KIMRL---RPLPVIMVSSLTEEGAEATLEALELGAVDFIAKPSG  108 (350)
T ss_pred             HHhcC---CCCcEEEEeccccccHHHHHHHHhcCcceeecCCCc
Confidence            98764   4789999987543  566688999999999999974

>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=99.43  E-value=9.7e-12  Score=77.87  Aligned_cols=112  Identities=31%  Similarity=0.578  Sum_probs=95.8

Q ss_pred             EEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHHHhc
Q 042079           24 LAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKIKES  103 (153)
Q Consensus        24 Liidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~lr~~  103 (153)
                      +++++++..+..+...+...++.+..+.+..+++..+.              ...+|++++|..++..++.++++.++..
T Consensus         1 l~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~--------------~~~~~~ii~~~~~~~~~~~~~~~~l~~~   66 (113)
T cd00156           1 LIVDDDPLIRELLRRLLEKEGYEVVEAEDGEEALALLA--------------EEKPDLILLDIMMPGMDGLELLRRIRKR   66 (113)
T ss_pred             CeecCcHHHHHHHHHHHhhcCceEEEecCHHHHHHHHH--------------hCCCCEEEEecCCCCCchHHHHHHHHHh
Confidence            47899999999999999888988888888888877662              3568999999999999999999999875


Q ss_pred             cCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          104 SVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       104 ~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      .  +.+|+++++..........++..|+.+|+.||++..++...+.+.
T Consensus        67 ~--~~~~~i~~~~~~~~~~~~~~~~~~~~~~i~~p~~~~~l~~~l~~~  112 (113)
T cd00156          67 G--PDIPIIFLTAHGDDEDAVEALKAGADDYLTKPFSPEELLARIRAL  112 (113)
T ss_pred             C--CCCCEEEEEecccHHHHHHHHHcChhhHccCCCCHHHHHHHHHhh
Confidence            2  568999888776677778889999999999999999998887654

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

Probab=99.41  E-value=3e-12  Score=90.53  Aligned_cols=114  Identities=25%  Similarity=0.334  Sum_probs=92.0

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcEE-EEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACKV-TTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELL   97 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~v-~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~   97 (153)
                      ...++|+++|.+..+..+...|...||.+ ..+.++.++....              ..+.||+||+|+.+|..+-.+-+
T Consensus         4 ~~lrvlv~~d~~i~~~~i~~~l~eag~~~Vg~~~~~~~~~~~~--------------~~~~pDvVildie~p~rd~~e~~   69 (194)
T COG3707           4 MLLRVLVADDEALTRMDIREGLLEAGYQRVGEAADGLEAVEVC--------------ERLQPDVVILDIEMPRRDIIEAL   69 (194)
T ss_pred             cccceeeccccccchhhHHHHHHHcCCeEeeeecccccchhHH--------------HhcCCCEEEEecCCCCccHHHHH
Confidence            45789999999999999999999899864 4566666655544              35789999999999999844444


Q ss_pred             HHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHh
Q 042079           98 KKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTG  149 (153)
Q Consensus        98 ~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~  149 (153)
                      .+..+ .  ...|+|++|.+.++..+..+.+.|+.+|+.||+++..+...+.
T Consensus        70 ~~~~~-~--~~~piv~lt~~s~p~~i~~a~~~Gv~ayivkpi~~~rl~p~L~  118 (194)
T COG3707          70 LLASE-N--VARPIVALTAYSDPALIEAAIEAGVMAYIVKPLDESRLLPILD  118 (194)
T ss_pred             HHhhc-C--CCCCEEEEEccCChHHHHHHHHcCCeEEEecCcchhhhhHHHH
Confidence            33333 2  4679999999999999999999999999999999999886553

>PRK13557 histidine kinase; Provisional

Probab=99.41  E-value=1.5e-11  Score=99.76  Aligned_cols=118  Identities=21%  Similarity=0.328  Sum_probs=102.7

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCC-CCHHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPG-MTGYELLK   98 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~-~~g~~~~~   98 (153)
                      ..+||++++++..+..+...|+..++.+..+.+..+++..+.             ....||++++|..+++ ++|+++++
T Consensus       415 ~~~iliv~~~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~-------------~~~~~d~vi~d~~~~~~~~~~~~~~  481 (540)
T PRK13557        415 TETILIVDDRPDVAELARMILEDFGYRTLVASNGREALEILD-------------SHPEVDLLFTDLIMPGGMNGVMLAR  481 (540)
T ss_pred             CceEEEEcCcHHHHHHHHHHHHhcCCeEEEeCCHHHHHHHHh-------------cCCCceEEEEeccCCCCCCHHHHHH
Confidence            468999999999999999999989999999999999988762             1235999999999997 89999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      .++...  +.+|+++++..........++..|+.+|+.||++.+++...+.++.
T Consensus       482 ~l~~~~--~~~~ii~~~~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~l~~~~  533 (540)
T PRK13557        482 EARRRQ--PKIKVLLTTGYAEASIERTDAGGSEFDILNKPYRRAELARRVRMVL  533 (540)
T ss_pred             HHHHhC--CCCcEEEEcCCCchhhhhhhccccCCceeeCCCCHHHHHHHHHHHh
Confidence            999754  5789999998877777778889999999999999999998887753

>PRK10693 response regulator of RpoS; Provisional

Probab=99.36  E-value=8.8e-12  Score=95.57  Aligned_cols=86  Identities=33%  Similarity=0.576  Sum_probs=73.4

Q ss_pred             EecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHH
Q 042079           49 TAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLE  128 (153)
Q Consensus        49 ~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~  128 (153)
                      .+.++.+++..+.              ...||+|++|+.||+++|+++++.+++..  +.+|+|++++..+.+...++++
T Consensus         2 ~a~~g~~al~~l~--------------~~~pDlVL~D~~mp~~~Gle~~~~ir~~~--~~ipiI~lt~~~~~~~~~~al~   65 (303)
T PRK10693          2 LAANGVDALELLG--------------GFTPDLIICDLAMPRMNGIEFVEHLRNRG--DQTPVLVISATENMADIAKALR   65 (303)
T ss_pred             EeCCHHHHHHHHh--------------cCCCCEEEEeCCCCCCCHHHHHHHHHhcC--CCCcEEEEECCCCHHHHHHHHH
Confidence            3567788877762              35699999999999999999999999754  5789999999988888999999


Q ss_pred             hcCcccccCCC-ChhHHHHHHhh
Q 042079          129 EGAQMFMLKPL-KPSDVKKLTGH  150 (153)
Q Consensus       129 ~ga~~~l~KP~-~~~~l~~~~~~  150 (153)
                      .|+++|+.||+ +.+++...+.+
T Consensus        66 ~Ga~dyl~KP~~~~~~L~~~i~~   88 (303)
T PRK10693         66 LGVQDVLLKPVKDLNRLREMVFA   88 (303)
T ss_pred             CCCcEEEECCCCcHHHHHHHHHH
Confidence            99999999999 48888776554

>PRK15029 arginine decarboxylase; Provisional

Probab=99.19  E-value=1.9e-10  Score=97.01  Aligned_cols=104  Identities=16%  Similarity=0.221  Sum_probs=81.7

Q ss_pred             CeEEEEeCCHH--------HHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCC
Q 042079           21 PHVLAVDDSIV--------DRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMT   92 (153)
Q Consensus        21 ~~iLiidd~~~--------~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~   92 (153)
                      ++||||||+..        ..+.+...|+..||++..+.++.+++..+.             ....||+||+|+.||+++
T Consensus         1 MkILIVDDD~~~~~~~~~~i~~~L~~~Le~~G~eV~~a~s~~dAl~~l~-------------~~~~~DlVLLD~~LPd~d   67 (755)
T PRK15029          1 MKVLIVESEFLHQDTWVGNAVERLADALSQQNVTVIKSTSFDDGFAILS-------------SNEAIDCLMFSYQMEHPD   67 (755)
T ss_pred             CeEEEEeCCcccccchhHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHH-------------hcCCCcEEEEECCCCCCc
Confidence            36999999995        688999999999999999999999999883             124799999999999999


Q ss_pred             HH----HHHHHHHhccCCCCCcEEEEeCCCC--hhhHHHHHHhcCcccccCCCC
Q 042079           93 GY----ELLKKIKESSVMKEVPVVVVSSENI--PTRINECLEEGAQMFMLKPLK  140 (153)
Q Consensus        93 g~----~~~~~lr~~~~~~~~pii~~t~~~~--~~~~~~a~~~ga~~~l~KP~~  140 (153)
                      |+    ++++++|+..  .++|||++|+..+  .......+ .-++.|+.+--+
T Consensus        68 G~~~~~ell~~IR~~~--~~iPIIlLTar~~~~~~~~~~~~-~~~~~~~~~~~~  118 (755)
T PRK15029         68 EHQNVRQLIGKLHERQ--QNVPVFLLGDREKALAAMDRDLL-ELVDEFAWILED  118 (755)
T ss_pred             cchhHHHHHHHHHhhC--CCCCEEEEEcCCcccccCCHHHH-HhhheEEEecCC
Confidence            97    8999999743  5899999998875  33323322 235666666433

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

Probab=99.06  E-value=2.4e-09  Score=79.81  Aligned_cols=113  Identities=30%  Similarity=0.461  Sum_probs=91.9

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcC-cE-EEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSA-CK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~-~~-v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      ++++++||++..+..+..++.... .+ +..+.+..++++.+.              ...+|++|+|+.||+++|+++.+
T Consensus         2 ~~i~i~dd~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~--------------~~~~~~~fldI~~~~~~G~ela~   67 (244)
T COG3279           2 LKVLIVDDEPLAREELRRILNEIPDIEIVGEAENGEEALQLLQ--------------GLRPDLVFLDIAMPDINGIELAA   67 (244)
T ss_pred             CcEEEecCCHHHHHHHHHHHHhhhhcCeeeeeccchhhHHHHh--------------ccCCCeEEEeeccCccchHHHHH
Confidence            579999999999999999988322 22 236888888888773              34799999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      .++...  +..+|+++|+.  .+....+++..+.+|+.||++.+++...+.++
T Consensus        68 ~i~~~~--~~~~Ivfvt~~--~~~a~~afev~a~d~i~kp~~~~~l~~~l~~~  116 (244)
T COG3279          68 RIRKGD--PRPAIVFVTAH--DEYAVAAFEVEALDYLLKPISEERLAKTLERL  116 (244)
T ss_pred             HhcccC--CCCeEEEEEeh--HHHHHHHHhHHHHhhhcCcchHHHHHHHHHHH
Confidence            999753  46678888865  45666788999999999999999999887653

>PRK11107 hybrid sensory histidine kinase BarA; Provisional

Probab=98.75  E-value=3.9e-07  Score=78.79  Aligned_cols=114  Identities=11%  Similarity=0.075  Sum_probs=90.3

Q ss_pred             CCCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHH
Q 042079           18 PKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELL   97 (153)
Q Consensus        18 ~~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~   97 (153)
                      ..+.+|+++|+++..+..+..+|+..|+.+..+.+..+    +              ....||++++|..+|+..+...+
T Consensus       534 ~~g~~ili~d~~~~~~~~l~~~L~~~g~~v~~~~~~~~----l--------------~~~~~d~il~~~~~~~~~~~~~~  595 (919)
T PRK11107        534 LAGKRLLYVEPNSAAAQATLDILSETPLEVTYSPTLSQ----L--------------PEAHYDILLLGLPVTFREPLTML  595 (919)
T ss_pred             cCCCeEEEEeCCHHHHHHHHHHHHHCCCEEEEcCCHHH----h--------------ccCCCCEEEecccCCCCCCHHHH
Confidence            35678999999999999999999999999998888776    2              13469999999999987766554


Q ss_pred             HHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHh
Q 042079           98 KKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTG  149 (153)
Q Consensus        98 ~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~  149 (153)
                      ............+++++++.........+.+.|+++|+.||++..++...+.
T Consensus       596 ~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~l~  647 (919)
T PRK11107        596 HERLAKAKSMTDFLILALPCHEQVLAEQLKQDGADACLSKPLSHTRLLPALL  647 (919)
T ss_pred             HHHHHhhhhcCCcEEEEeCCcchhhHHHHhhCCCceEECCCCCHHHHHHHHH
Confidence            4433222223456777787777888888999999999999999999877664

>PF06490 FleQ: Flagellar regulatory protein FleQ; InterPro: IPR010518 This domain is found at the N terminus of a subset of sigma54-dependent transcriptional activators that are involved in regulation of flagellar motility e

Probab=98.34  E-value=9.4e-06  Score=53.22  Aligned_cols=108  Identities=13%  Similarity=0.126  Sum_probs=76.3

Q ss_pred             eEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHHH
Q 042079           22 HVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKIK  101 (153)
Q Consensus        22 ~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~lr  101 (153)
                      +|||||||...+..+..+|+-.|+.+..+.+..- ....              .....+.+++-..-.. ...+.++.+.
T Consensus         1 kILvIddd~~R~~~L~~ILeFlGe~~~~~~~~~~-~~~~--------------~~~~~~~~~v~~g~~~-~~~~~l~~l~   64 (109)
T PF06490_consen    1 KILVIDDDAERRQRLSTILEFLGEQCEAVSSSDW-SQAD--------------WSSPWEACAVILGSCS-KLAELLKELL   64 (109)
T ss_pred             CEEEECCcHHHHHhhhhhhhhcCCCeEEecHHHH-HHhh--------------hhcCCcEEEEEecCch-hHHHHHHHHH
Confidence            5899999999999999999999998888776443 1211              1233455544433333 5567778776


Q ss_pred             hccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079          102 ESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus       102 ~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      +..  +.+|++++.........     ..+.+-|..|++..+|.+++.|+.
T Consensus        65 ~~~--~~~Pvlllg~~~~~~~~-----~nvvg~Le~Pl~Y~qLt~~L~~cQ  108 (109)
T PF06490_consen   65 KWA--PHIPVLLLGEHDSPEEL-----PNVVGELEEPLNYPQLTDALHRCQ  108 (109)
T ss_pred             hhC--CCCCEEEECCCCccccc-----cCeeEecCCCCCHHHHHHHHHHhc
Confidence            644  68999999876555111     126667899999999999998864

g. FleQ in Pseudomonas aeruginosa. It is clearly related to IPR001789 from INTERPRO, but lacks the conserved aspartate residue that undergoes phosphorylation in the classic two-component system response regulator (IPR001789 from INTERPRO).

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

Probab=98.25  E-value=2.3e-06  Score=68.31  Aligned_cols=85  Identities=32%  Similarity=0.477  Sum_probs=70.9

Q ss_pred             EEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHHHhccCCCCCcEEEEeCCCChhhHHH
Q 042079           46 KVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINE  125 (153)
Q Consensus        46 ~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~  125 (153)
                      ++..+..+..++..+              ..+++|++++|..||+++|++++++++....    ++++++.........+
T Consensus        14 ~v~~a~~g~~~l~~~--------------~~~~~~~~lld~~m~~~~~~~~~~~lk~~~~----~~v~~t~~~~~~~~~~   75 (435)
T COG3706          14 EVATAKKGLIALAIL--------------LDHKPDYKLLDVMMPGMDGFELCRRLKAEPA----TVVMVTALDDSAPRVR   75 (435)
T ss_pred             hhhhccchHHHHHHH--------------hcCCCCeEEeecccCCcCchhHHHHHhcCCc----ceEEEEecCCCCcchh
Confidence            455577788877766              3678999999999999999999999997542    3788888888888889


Q ss_pred             HHHhcCcccccCCCChhHHHHHH
Q 042079          126 CLEEGAQMFMLKPLKPSDVKKLT  148 (153)
Q Consensus       126 a~~~ga~~~l~KP~~~~~l~~~~  148 (153)
                      ..+.|++.|++||++...+....
T Consensus        76 ~~~~~~~~~l~~~~~~~~~~~r~   98 (435)
T COG3706          76 GLKAGADDFLTKPVNDSQLFLRA   98 (435)
T ss_pred             HHhhhhhhhccCCCChHHHHHhh
Confidence            99999999999999998887543

>smart00448 REC cheY-homologous receiver domain

Probab=97.80  E-value=0.00028  Score=37.41  Aligned_cols=54  Identities=35%  Similarity=0.572  Sum_probs=45.0

Q ss_pred             eEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCC
Q 042079           22 HVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMP   89 (153)
Q Consensus        22 ~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~   89 (153)
                      +++++++++.....+...+...++.+..+.+...+...+.              ...++++++|+.++
T Consensus         2 ~i~i~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~--------------~~~~~~vi~~~~~~   55 (55)
T smart00448        2 RILVVDDDPLLRELLKALLEREGYEVDEATDGEEALELLK--------------EEKPDLILLDIMMP   55 (55)
T ss_pred             eEEEEcCCHHHHHHHHHHHhhcCcEEEEeCCHHHHHHHHH--------------hcCCCEEEEeccCC
Confidence            6899999999999999999888999888888888877662              34689999997653

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

>cd02071 MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 binding domain

Probab=97.61  E-value=0.0046  Score=41.15  Aligned_cols=106  Identities=13%  Similarity=0.051  Sum_probs=72.5

Q ss_pred             eCCHHHHHHHHHHHHhcCcEEEEecC---HHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCC--CHHHHHHHHH
Q 042079           27 DDSIVDRKIVENLLKNSACKVTTAEN---GMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGM--TGYELLKKIK  101 (153)
Q Consensus        27 dd~~~~~~~l~~~l~~~~~~v~~~~~---~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~--~g~~~~~~lr  101 (153)
                      |.|..-...+..+|+..||++.....   .++.++.+.              ..++|+|.+...++..  ..-++++.|+
T Consensus        10 d~H~lG~~~~~~~l~~~G~~vi~lG~~vp~e~~~~~a~--------------~~~~d~V~iS~~~~~~~~~~~~~~~~L~   75 (122)
T cd02071          10 DGHDRGAKVIARALRDAGFEVIYTGLRQTPEEIVEAAI--------------QEDVDVIGLSSLSGGHMTLFPEVIELLR   75 (122)
T ss_pred             ChhHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHH--------------HcCCCEEEEcccchhhHHHHHHHHHHHH
Confidence            55667777888889999999876443   445555542              4679999998877643  3456677787


Q ss_pred             hccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHH
Q 042079          102 ESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLT  148 (153)
Q Consensus       102 ~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~  148 (153)
                      +... +. +.+++.+....+...++.+.|++.|+..=-+.+++..-+
T Consensus        76 ~~~~-~~-i~i~~GG~~~~~~~~~~~~~G~d~~~~~~~~~~~~~~~~  120 (122)
T cd02071          76 ELGA-GD-ILVVGGGIIPPEDYELLKEMGVAEIFGPGTSIEEIIDKI  120 (122)
T ss_pred             hcCC-CC-CEEEEECCCCHHHHHHHHHCCCCEEECCCCCHHHHHHHH
Confidence            7542 23 445566555566677888999999998777776665433

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

>PRK02261 methylaspartate mutase subunit S; Provisional

Probab=97.57  E-value=0.01  Score=40.44  Aligned_cols=117  Identities=14%  Similarity=0.073  Sum_probs=82.4

Q ss_pred             CCCeEEEE----eCCHHHHHHHHHHHHhcCcEEEEec---CHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCC
Q 042079           19 KPPHVLAV----DDSIVDRKIVENLLKNSACKVTTAE---NGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGM   91 (153)
Q Consensus        19 ~~~~iLii----dd~~~~~~~l~~~l~~~~~~v~~~~---~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~   91 (153)
                      +.+++++.    |.|..-...+..+|+..||++....   ..++.++.+.              ...+|+|.+.+.+...
T Consensus         2 ~~~~vl~~~~~gD~H~lG~~iv~~~lr~~G~eVi~LG~~vp~e~i~~~a~--------------~~~~d~V~lS~~~~~~   67 (137)
T PRK02261          2 KKKTVVLGVIGADCHAVGNKILDRALTEAGFEVINLGVMTSQEEFIDAAI--------------ETDADAILVSSLYGHG   67 (137)
T ss_pred             CCCEEEEEeCCCChhHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHH--------------HcCCCEEEEcCccccC
Confidence            45677777    7788888888999999999987644   3455555542              4579999999877753


Q ss_pred             --CHHHHHHHHHhccCCCCCcEEEEeCCC------ChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           92 --TGYELLKKIKESSVMKEVPVVVVSSEN------IPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        92 --~g~~~~~~lr~~~~~~~~pii~~t~~~------~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                        ...++++.|++... +.++++ +.+..      ......++.+.|++.++....+.+++..-+.+.
T Consensus        68 ~~~~~~~~~~L~~~~~-~~~~i~-vGG~~~~~~~~~~~~~~~l~~~G~~~vf~~~~~~~~i~~~l~~~  133 (137)
T PRK02261         68 EIDCRGLREKCIEAGL-GDILLY-VGGNLVVGKHDFEEVEKKFKEMGFDRVFPPGTDPEEAIDDLKKD  133 (137)
T ss_pred             HHHHHHHHHHHHhcCC-CCCeEE-EECCCCCCccChHHHHHHHHHcCCCEEECcCCCHHHHHHHHHHH
Confidence              35677788887542 355544 44432      234456788999999988888888887766653

>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=97.17  E-value=0.0044  Score=40.88  Aligned_cols=93  Identities=17%  Similarity=0.214  Sum_probs=66.0

Q ss_pred             HHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCC--CCHHHHHHHHHhccCCCCCc
Q 042079           33 RKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPG--MTGYELLKKIKESSVMKEVP  110 (153)
Q Consensus        33 ~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~--~~g~~~~~~lr~~~~~~~~p  110 (153)
                      ...+...|++.|+++..+.+..+++..+.             ....+.+|+++|. +.  ....++++.++.++  ..+|
T Consensus         6 ~~~l~~~L~~~~~~vv~~~~~dd~~~~i~-------------~~~~i~avvi~~d-~~~~~~~~~ll~~i~~~~--~~iP   69 (115)
T PF03709_consen    6 SRELAEALEQRGREVVDADSTDDALAIIE-------------SFTDIAAVVISWD-GEEEDEAQELLDKIRERN--FGIP   69 (115)
T ss_dssp             HHHHHHHHHHTTTEEEEESSHHHHHHHHH-------------CTTTEEEEEEECH-HHHHHHHHHHHHHHHHHS--TT-E
T ss_pred             HHHHHHHHHHCCCEEEEeCChHHHHHHHH-------------hCCCeeEEEEEcc-cccchhHHHHHHHHHHhC--CCCC
Confidence            45677778888999999999999999885             3467899999986 21  23567889998876  6899


Q ss_pred             EEEEeCCCChhhHHHHHHhcCcccccCCCCh
Q 042079          111 VVVVSSENIPTRINECLEEGAQMFMLKPLKP  141 (153)
Q Consensus       111 ii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~  141 (153)
                      |++++.....+..-.-.-..+++|+-..-+.
T Consensus        70 VFl~~~~~~~~~l~~~~l~~v~~~i~l~~~t  100 (115)
T PF03709_consen   70 VFLLAERDTTEDLPAEVLGEVDGFIWLFEDT  100 (115)
T ss_dssp             EEEEESCCHHHCCCHHHHCCESEEEETTTTT
T ss_pred             EEEEecCCCcccCCHHHHhhccEEEEecCCC
Confidence            9999986544433333334466676554433

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

>TIGR00640 acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal domain

Probab=97.07  E-value=0.025  Score=38.26  Aligned_cols=108  Identities=14%  Similarity=0.056  Sum_probs=73.2

Q ss_pred             eCCHHHHHHHHHHHHhcCcEEEEe---cCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCC--CHHHHHHHHH
Q 042079           27 DDSIVDRKIVENLLKNSACKVTTA---ENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGM--TGYELLKKIK  101 (153)
Q Consensus        27 dd~~~~~~~l~~~l~~~~~~v~~~---~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~--~g~~~~~~lr  101 (153)
                      |.|..-.+.+..+|+..||+|...   .+.++.++...              .+.+|+|.+...+...  ..-++++.|+
T Consensus        13 D~Hd~g~~iv~~~l~~~GfeVi~lg~~~s~e~~v~aa~--------------e~~adii~iSsl~~~~~~~~~~~~~~L~   78 (132)
T TIGR00640        13 DGHDRGAKVIATAYADLGFDVDVGPLFQTPEEIARQAV--------------EADVHVVGVSSLAGGHLTLVPALRKELD   78 (132)
T ss_pred             CccHHHHHHHHHHHHhCCcEEEECCCCCCHHHHHHHHH--------------HcCCCEEEEcCchhhhHHHHHHHHHHHH
Confidence            567777788999999999998753   35666666552              3578999887655432  2345667777


Q ss_pred             hccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhh
Q 042079          102 ESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGH  150 (153)
Q Consensus       102 ~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~  150 (153)
                      +... ..++ +++.+....+...+..+.|++.|+..=-+..++.+.+.+
T Consensus        79 ~~g~-~~i~-vivGG~~~~~~~~~l~~~Gvd~~~~~gt~~~~i~~~l~~  125 (132)
T TIGR00640        79 KLGR-PDIL-VVVGGVIPPQDFDELKEMGVAEIFGPGTPIPESAIFLLK  125 (132)
T ss_pred             hcCC-CCCE-EEEeCCCChHhHHHHHHCCCCEEECCCCCHHHHHHHHHH
Confidence            7542 2344 445544455667788999999999877777777655443

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

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

Probab=96.91  E-value=0.011  Score=39.06  Aligned_cols=109  Identities=11%  Similarity=0.190  Sum_probs=73.4

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      .+.+++.|+.|.....-..++|.+.+.+|....+..+    +              -.+.||++++.+-.+-.+.+.+..
T Consensus        10 ~gk~LayiEpNstAA~~t~~iL~~tpleVtyr~t~~~----l--------------p~~hYD~~Ll~vavtfr~n~tm~~   71 (140)
T COG4999          10 AGKRLAYIEPNSTAAQCTLDILSETPLEVTYRPTFSA----L--------------PPAHYDMMLLGVAVTFRENLTMQH   71 (140)
T ss_pred             ccceeEEecCccHHHHHHHHHHhcCCceEEecccccc----c--------------ChhhhceeeecccccccCCchHHH
Confidence            4578999999999888888999999998887665443    2              124589999998776554444332


Q ss_pred             -HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHH
Q 042079           99 -KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKK  146 (153)
Q Consensus        99 -~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~  146 (153)
                       ++.+.-.+.+- +|+--.....-...+.+..|+.++|.||++..++..
T Consensus        72 ~~l~~Al~mtd~-vilalPs~~qv~AeqLkQ~g~~~CllKPls~~rLlp  119 (140)
T COG4999          72 ERLAKALSMTDF-VILALPSHAQVNAEQLKQDGAGACLLKPLSSTRLLP  119 (140)
T ss_pred             HHHHHHHhhhcc-eEEecCcHHHHhHHHHhhcchHhHhhCcchhhhhHH
Confidence             22221111222 332223334455567889999999999999998876

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

Probab=96.76  E-value=0.052  Score=35.68  Aligned_cols=95  Identities=15%  Similarity=0.208  Sum_probs=62.2

Q ss_pred             eCCHHHHHHHHHHHHhcCcEEEEec---CHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCC--CHHHHHHHHH
Q 042079           27 DDSIVDRKIVENLLKNSACKVTTAE---NGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGM--TGYELLKKIK  101 (153)
Q Consensus        27 dd~~~~~~~l~~~l~~~~~~v~~~~---~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~--~g~~~~~~lr  101 (153)
                      |.|..-...+..+|+..||++....   ..++.++.+.              ..+||+|.+...+...  ...++++.+|
T Consensus        10 e~H~lG~~~~~~~l~~~G~~V~~lg~~~~~~~l~~~~~--------------~~~pdvV~iS~~~~~~~~~~~~~i~~l~   75 (119)
T cd02067          10 DGHDIGKNIVARALRDAGFEVIDLGVDVPPEEIVEAAK--------------EEDADAIGLSGLLTTHMTLMKEVIEELK   75 (119)
T ss_pred             chhhHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHH--------------HcCCCEEEEeccccccHHHHHHHHHHHH
Confidence            4566666788889999999986533   3444445442              4579999998875543  4567778888


Q ss_pred             hccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccC
Q 042079          102 ESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLK  137 (153)
Q Consensus       102 ~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~K  137 (153)
                      +... ..++| ++.+.........+.+.|+|.|+..
T Consensus        76 ~~~~-~~~~i-~vGG~~~~~~~~~~~~~G~D~~~~~  109 (119)
T cd02067          76 EAGL-DDIPV-LVGGAIVTRDFKFLKEIGVDAYFGP  109 (119)
T ss_pred             HcCC-CCCeE-EEECCCCChhHHHHHHcCCeEEECC
Confidence            7542 25554 4555444443457889999888753

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.

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

Probab=96.44  E-value=0.0065  Score=53.32  Aligned_cols=51  Identities=24%  Similarity=0.158  Sum_probs=42.4

Q ss_pred             CCCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCC
Q 042079           18 PKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCM   88 (153)
Q Consensus        18 ~~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~   88 (153)
                      ....+||++||++..+..+..+|++.|+.|..+.+..                    ....||+|++|+.+
T Consensus       687 l~g~~vLlvdD~~~~r~~l~~~L~~~G~~v~~a~~~~--------------------~~~~~Dlvl~D~~~  737 (894)
T PRK10618        687 LDGVTVLLDITSEEVRKIVTRQLENWGATCITPDERL--------------------ISQEYDIFLTDNPS  737 (894)
T ss_pred             CCCCEEEEEeCCHHHHHHHHHHHHHCCCEEEEcCccc--------------------cCCCCCEEEECCCC
Confidence            3457899999999999999999999999998877521                    13469999999983

>TIGR01501 MthylAspMutase methylaspartate mutase, S subunit

Probab=96.35  E-value=0.18  Score=34.29  Aligned_cols=110  Identities=15%  Similarity=0.057  Sum_probs=73.1

Q ss_pred             eCCHHHHHHHHHHHHhcCcEEEEe---cCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCC--HHHHHHHHH
Q 042079           27 DDSIVDRKIVENLLKNSACKVTTA---ENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMT--GYELLKKIK  101 (153)
Q Consensus        27 dd~~~~~~~l~~~l~~~~~~v~~~---~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~--g~~~~~~lr  101 (153)
                      |-|..-.+.+..+|+..||+|...   .+.++.++...              .+.+|+|-+...+...-  .-++.+.|+
T Consensus        12 D~HdiGk~iv~~~l~~~GfeVi~LG~~v~~e~~v~aa~--------------~~~adiVglS~l~~~~~~~~~~~~~~l~   77 (134)
T TIGR01501        12 DCHAVGNKILDHAFTNAGFNVVNLGVLSPQEEFIKAAI--------------ETKADAILVSSLYGHGEIDCKGLRQKCD   77 (134)
T ss_pred             ChhhHhHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHH--------------HcCCCEEEEecccccCHHHHHHHHHHHH
Confidence            335555677888999999988753   45566666552              35799999887775432  455677788


Q ss_pred             hccCCCCCcEEEEeCCC--Chh----hHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079          102 ESSVMKEVPVVVVSSEN--IPT----RINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus       102 ~~~~~~~~pii~~t~~~--~~~----~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      +... .. +.+++.+..  .++    ...++.+.|++..+...-.++++..-+.+.+
T Consensus        78 ~~gl-~~-~~vivGG~~vi~~~d~~~~~~~l~~~Gv~~vF~pgt~~~~iv~~l~~~~  132 (134)
T TIGR01501        78 EAGL-EG-ILLYVGGNLVVGKQDFPDVEKRFKEMGFDRVFAPGTPPEVVIADLKKDL  132 (134)
T ss_pred             HCCC-CC-CEEEecCCcCcChhhhHHHHHHHHHcCCCEEECcCCCHHHHHHHHHHHh
Confidence            7653 34 345565531  122    2346889999998888888888887777644

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.

>PRK15399 lysine decarboxylase LdcC; Provisional

Probab=96.13  E-value=0.06  Score=46.12  Aligned_cols=80  Identities=18%  Similarity=0.260  Sum_probs=59.4

Q ss_pred             CeEEEEeCCH-H-----HHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHH
Q 042079           21 PHVLAVDDSI-V-----DRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGY   94 (153)
Q Consensus        21 ~~iLiidd~~-~-----~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~   94 (153)
                      ++++||+++- .     ..+.+...|++.|+++..+.+..+++..+.             ......++++++...   ..
T Consensus         1 ~~~~~i~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~-------------~~~~~~~~~~~~~~~---~~   64 (713)
T PRK15399          1 MNIIAIMGPHGVFYKDEPIKELESALQAQGFQTIWPQNSVDLLKFIE-------------HNPRICGVIFDWDEY---SL   64 (713)
T ss_pred             CcEEEEecccccccccHHHHHHHHHHHHCCcEEEEecCHHHHHHHHh-------------cccceeEEEEecccc---hH
Confidence            3577777663 1     135566778889999999999999988774             345689999996443   35


Q ss_pred             HHHHHHHhccCCCCCcEEEEeCCC
Q 042079           95 ELLKKIKESSVMKEVPVVVVSSEN  118 (153)
Q Consensus        95 ~~~~~lr~~~~~~~~pii~~t~~~  118 (153)
                      ++++.+|++.  ..+||+++....
T Consensus        65 ~~~~~~~~~~--~~~Pv~~~~~~~   86 (713)
T PRK15399         65 DLCSDINQLN--EYLPLYAFINTH   86 (713)
T ss_pred             HHHHHHHHhC--CCCCEEEEcCcc
Confidence            5888888765  589999987643

>cd02070 corrinoid_protein_B12-BD B12 binding domain of corrinoid proteins

Probab=96.07  E-value=0.17  Score=36.53  Aligned_cols=100  Identities=17%  Similarity=0.137  Sum_probs=67.1

Q ss_pred             CCeEEEE----eCCHHHHHHHHHHHHhcCcEEEEec---CHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCC-
Q 042079           20 PPHVLAV----DDSIVDRKIVENLLKNSACKVTTAE---NGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGM-   91 (153)
Q Consensus        20 ~~~iLii----dd~~~~~~~l~~~l~~~~~~v~~~~---~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~-   91 (153)
                      ..++++.    |-|..=...+..+|+..||+|....   ..++.++.+              ...+||+|-+.+.++.. 
T Consensus        82 ~~~vl~~~~~gd~H~lG~~~v~~~l~~~G~~vi~lG~~~p~~~l~~~~--------------~~~~~d~v~lS~~~~~~~  147 (201)
T cd02070          82 KGKVVIGTVEGDIHDIGKNLVATMLEANGFEVIDLGRDVPPEEFVEAV--------------KEHKPDILGLSALMTTTM  147 (201)
T ss_pred             CCeEEEEecCCccchHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHH--------------HHcCCCEEEEeccccccH
Confidence            4567777    7777778889999999999987532   344555555              24679999999877654 


Q ss_pred             -CHHHHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCccccc
Q 042079           92 -TGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFML  136 (153)
Q Consensus        92 -~g~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~  136 (153)
                       ...++++.+|+.....+++|++=...-+.+   -+...|+|.|-.
T Consensus       148 ~~~~~~i~~lr~~~~~~~~~i~vGG~~~~~~---~~~~~GaD~~~~  190 (201)
T cd02070         148 GGMKEVIEALKEAGLRDKVKVMVGGAPVNQE---FADEIGADGYAE  190 (201)
T ss_pred             HHHHHHHHHHHHCCCCcCCeEEEECCcCCHH---HHHHcCCcEEEC
Confidence             456677888876432356665443333332   356779998854

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.

>PRK15400 lysine decarboxylase CadA; Provisional

Probab=95.80  E-value=0.087  Score=45.17  Aligned_cols=80  Identities=15%  Similarity=0.233  Sum_probs=58.8

Q ss_pred             CeEEEEeCCH------HHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHH
Q 042079           21 PHVLAVDDSI------VDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGY   94 (153)
Q Consensus        21 ~~iLiidd~~------~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~   94 (153)
                      +++++|+++.      ...+.+...|++.|++|..+.+..+++..+.             ......++++++...   ..
T Consensus         1 ~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~-------------~~~~~~~~~~~~~~~---~~   64 (714)
T PRK15400          1 MNVIAILNHMGVYFKEEPIRELHRALERLNFQIVYPNDRDDLLKLIE-------------NNARLCGVIFDWDKY---NL   64 (714)
T ss_pred             CcEEEEccccccccccHHHHHHHHHHHHCCcEEEEeCCHHHHHHHHh-------------cccceeEEEEecchh---hH
Confidence            3566776652      1245666778889999999999999988774             345688999996442   35


Q ss_pred             HHHHHHHhccCCCCCcEEEEeCCC
Q 042079           95 ELLKKIKESSVMKEVPVVVVSSEN  118 (153)
Q Consensus        95 ~~~~~lr~~~~~~~~pii~~t~~~  118 (153)
                      .+++.+|++.  ..+||+++....
T Consensus        65 ~~~~~~~~~~--~~~Pv~~~~~~~   86 (714)
T PRK15400         65 ELCEEISKMN--ENLPLYAFANTY   86 (714)
T ss_pred             HHHHHHHHhC--CCCCEEEEcccc
Confidence            5888888765  589999988743

>TIGR03815 CpaE_hom_Actino helicase/secretion neighborhood CpaE-like protein

Probab=95.45  E-value=0.093  Score=40.60  Aligned_cols=67  Identities=19%  Similarity=0.134  Sum_probs=45.1

Q ss_pred             CcccEEEEeCCCCCCCHHHHHHHHHhccCCCCCcEEEEeC-CCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           77 TKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSS-ENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        77 ~~~dlii~D~~~~~~~g~~~~~~lr~~~~~~~~pii~~t~-~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      ....++++|..+-.    ..+...-  .  ++..+++++. ..+.+....+++.|+.+|+.+|.+..++.+.+.+.
T Consensus        18 ~~~~~v~~~~~~~~----~~~~~~~--p--~~~~vv~v~~~~~~~~~~~~a~~~Ga~~~l~~P~~~~~l~~~l~~~   85 (322)
T TIGR03815        18 ARAPLVLVDADMAE----ACAAAGL--P--RRRRVVLVGGGEPGGALWRAAAAVGAEHVAVLPEAEGWLVELLADL   85 (322)
T ss_pred             ccCCeEEECchhhh----HHHhccC--C--CCCCEEEEeCCCCCHHHHHHHHHhChhheeeCCCCHHHHHHHHHhh
Confidence            44678998864411    1111111  1  2334554544 55688889999999999999999999998887664

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.

>cd02069 methionine_synthase_B12_BD B12 binding domain of methionine synthase

Probab=95.32  E-value=0.41  Score=35.06  Aligned_cols=101  Identities=11%  Similarity=0.142  Sum_probs=66.5

Q ss_pred             CCeEEEE----eCCHHHHHHHHHHHHhcCcEEEEec---CHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCC-
Q 042079           20 PPHVLAV----DDSIVDRKIVENLLKNSACKVTTAE---NGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGM-   91 (153)
Q Consensus        20 ~~~iLii----dd~~~~~~~l~~~l~~~~~~v~~~~---~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~-   91 (153)
                      ..++++.    |.|..=...+..+|+..||+|....   ...+.++.+              ...++|+|.+...|+.. 
T Consensus        88 ~~~vvl~t~~gd~HdiG~~iv~~~l~~~G~~Vi~LG~~vp~e~~v~~~--------------~~~~~~~V~lS~~~~~~~  153 (213)
T cd02069          88 KGKIVLATVKGDVHDIGKNLVGVILSNNGYEVIDLGVMVPIEKILEAA--------------KEHKADIIGLSGLLVPSL  153 (213)
T ss_pred             CCeEEEEeCCCchhHHHHHHHHHHHHhCCCEEEECCCCCCHHHHHHHH--------------HHcCCCEEEEccchhccH
Confidence            4567777    7788888888999999999987644   244444444              24679999999888754 


Q ss_pred             -CHHHHHHHHHhccCCCCCcEEEEeCCCChhhHHH---HHHhcCccccc
Q 042079           92 -TGYELLKKIKESSVMKEVPVVVVSSENIPTRINE---CLEEGAQMFML  136 (153)
Q Consensus        92 -~g~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~---a~~~ga~~~l~  136 (153)
                       ...++++.|++..  .+++|++=....+.+...+   +-..|+|.|-.
T Consensus       154 ~~~~~~i~~L~~~~--~~~~i~vGG~~~~~~~~~~~~~~~~~gad~y~~  200 (213)
T cd02069         154 DEMVEVAEEMNRRG--IKIPLLIGGAATSRKHTAVKIAPEYDGPVVYVK  200 (213)
T ss_pred             HHHHHHHHHHHhcC--CCCeEEEEChhcCHHHHhhhhccccCCCceEec
Confidence             4566778888754  3666654443334443322   13468887753

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

>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=95.22  E-value=0.44  Score=30.23  Aligned_cols=88  Identities=19%  Similarity=0.147  Sum_probs=57.9

Q ss_pred             eEEEEeCCHHHHHHHHHHHHhcCcEEEEe------cCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHH
Q 042079           22 HVLAVDDSIVDRKIVENLLKNSACKVTTA------ENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYE   95 (153)
Q Consensus        22 ~iLiidd~~~~~~~l~~~l~~~~~~v~~~------~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~   95 (153)
                      +||||...+.....++..+++.|+.....      .....-++..               -.+.|+||+=...-.-+...
T Consensus         1 ~vliVGG~~~~~~~~~~~~~~~G~~~~~hg~~~~~~~~~~~l~~~---------------i~~aD~VIv~t~~vsH~~~~   65 (97)
T PF10087_consen    1 SVLIVGGREDRERRYKRILEKYGGKLIHHGRDGGDEKKASRLPSK---------------IKKADLVIVFTDYVSHNAMW   65 (97)
T ss_pred             CEEEEcCCcccHHHHHHHHHHcCCEEEEEecCCCCccchhHHHHh---------------cCCCCEEEEEeCCcChHHHH
Confidence            48999998888899999999999987777      2222113321               24579998866666666666


Q ss_pred             HHHHHHhccCCCCCcEEEEeCCCChhhHHHHHH
Q 042079           96 LLKKIKESSVMKEVPVVVVSSENIPTRINECLE  128 (153)
Q Consensus        96 ~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~  128 (153)
                      .++..-+.   ..+|+++.-+ .+.....+++.
T Consensus        66 ~vk~~akk---~~ip~~~~~~-~~~~~l~~~l~   94 (97)
T PF10087_consen   66 KVKKAAKK---YGIPIIYSRS-RGVSSLERALE   94 (97)
T ss_pred             HHHHHHHH---cCCcEEEECC-CCHHHHHHHHH
Confidence            66665443   3678885543 45555555543

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

Probab=95.22  E-value=0.57  Score=31.55  Aligned_cols=106  Identities=13%  Similarity=0.080  Sum_probs=70.2

Q ss_pred             eCCHHHHHHHHHHHHhcCcEEEE---ecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCC--CHHHHHHHHH
Q 042079           27 DDSIVDRKIVENLLKNSACKVTT---AENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGM--TGYELLKKIK  101 (153)
Q Consensus        27 dd~~~~~~~l~~~l~~~~~~v~~---~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~--~g~~~~~~lr  101 (153)
                      |-|..-.+.+..+|+..||+|.-   ..+.++.++...              .+++|+|.+..-|...  ..-++++.|+
T Consensus        10 D~HdiGkniv~~~L~~~GfeVidLG~~v~~e~~v~aa~--------------~~~adiVglS~L~t~~~~~~~~~~~~l~   75 (128)
T cd02072          10 DCHAVGNKILDHAFTEAGFNVVNLGVLSPQEEFIDAAI--------------ETDADAILVSSLYGHGEIDCKGLREKCD   75 (128)
T ss_pred             chhHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHH--------------HcCCCEEEEeccccCCHHHHHHHHHHHH
Confidence            33555567888899999998864   345555555542              3579999988777653  3456777888


Q ss_pred             hccCCCCCcEEEEeCCC--C----hhhHHHHHHhcCcccccCCCChhHHHHHH
Q 042079          102 ESSVMKEVPVVVVSSEN--I----PTRINECLEEGAQMFMLKPLKPSDVKKLT  148 (153)
Q Consensus       102 ~~~~~~~~pii~~t~~~--~----~~~~~~a~~~ga~~~l~KP~~~~~l~~~~  148 (153)
                      +... ..++++ +.+..  .    .+...++.+.|++..+...-+++++.+-+
T Consensus        76 ~~gl-~~v~vi-vGG~~~i~~~d~~~~~~~L~~~Gv~~vf~pgt~~~~i~~~l  126 (128)
T cd02072          76 EAGL-KDILLY-VGGNLVVGKQDFEDVEKRFKEMGFDRVFAPGTPPEEAIADL  126 (128)
T ss_pred             HCCC-CCCeEE-EECCCCCChhhhHHHHHHHHHcCCCEEECcCCCHHHHHHHH
Confidence            7653 355544 44432  1    33446688999999988777777776544

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.

>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=95.08  E-value=0.33  Score=31.63  Aligned_cols=92  Identities=18%  Similarity=0.273  Sum_probs=56.1

Q ss_pred             CHHHHHHHHHHHHhcCcEEEEec---CHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCC-CCC-CHHHHHHHHHhc
Q 042079           29 SIVDRKIVENLLKNSACKVTTAE---NGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCM-PGM-TGYELLKKIKES  103 (153)
Q Consensus        29 ~~~~~~~l~~~l~~~~~~v~~~~---~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~-~~~-~g~~~~~~lr~~  103 (153)
                      ++.-...+..+|++.|+++....   +..+..+.+.              ..+||+|.+...+ +.. ...++++.+|+.
T Consensus        13 ~~lGl~~la~~l~~~G~~v~~~d~~~~~~~l~~~~~--------------~~~pd~V~iS~~~~~~~~~~~~l~~~~k~~   78 (121)
T PF02310_consen   13 HPLGLLYLAAYLRKAGHEVDILDANVPPEELVEALR--------------AERPDVVGISVSMTPNLPEAKRLARAIKER   78 (121)
T ss_dssp             TSHHHHHHHHHHHHTTBEEEEEESSB-HHHHHHHHH--------------HTTCSEEEEEESSSTHHHHHHHHHHHHHTT
T ss_pred             hhHHHHHHHHHHHHCCCeEEEECCCCCHHHHHHHHh--------------cCCCcEEEEEccCcCcHHHHHHHHHHHHhc
Confidence            44556788899999999987663   2344444442              3579999998843 333 456677777764


Q ss_pred             cCCCCCcEEEEeCCCChhhHHHHHH--hcCcccccC
Q 042079          104 SVMKEVPVVVVSSENIPTRINECLE--EGAQMFMLK  137 (153)
Q Consensus       104 ~~~~~~pii~~t~~~~~~~~~~a~~--~ga~~~l~K  137 (153)
                      .  ++++++ +.+........++++  .|+|..+.-
T Consensus        79 ~--p~~~iv-~GG~~~t~~~~~~l~~~~~~D~vv~G  111 (121)
T PF02310_consen   79 N--PNIPIV-VGGPHATADPEEILREYPGIDYVVRG  111 (121)
T ss_dssp             C--TTSEEE-EEESSSGHHHHHHHHHHHTSEEEEEE
T ss_pred             C--CCCEEE-EECCchhcChHHHhccCcCcceecCC
Confidence            3  466555 444443444455555  677765543

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 ....

>TIGR02370 pyl_corrinoid methyltransferase cognate corrinoid proteins, Methanosarcina family

Probab=94.74  E-value=0.54  Score=33.92  Aligned_cols=92  Identities=15%  Similarity=0.136  Sum_probs=59.1

Q ss_pred             CCHHHHHHHHHHHHhcCcEEEEec---CHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCC--CHHHHHHHHHh
Q 042079           28 DSIVDRKIVENLLKNSACKVTTAE---NGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGM--TGYELLKKIKE  102 (153)
Q Consensus        28 d~~~~~~~l~~~l~~~~~~v~~~~---~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~--~g~~~~~~lr~  102 (153)
                      .|..-...+..+|+..||+|....   ..++.++.+              ...+||+|.+.+.++..  .-.++++.+++
T Consensus        96 ~H~lG~~~v~~~l~~~G~~vi~LG~~vp~e~~v~~~--------------~~~~pd~v~lS~~~~~~~~~~~~~i~~l~~  161 (197)
T TIGR02370        96 VHDIGKNIVVTMLRANGFDVIDLGRDVPIDTVVEKV--------------KKEKPLMLTGSALMTTTMYGQKDINDKLKE  161 (197)
T ss_pred             hhHHHHHHHHHHHHhCCcEEEECCCCCCHHHHHHHH--------------HHcCCCEEEEccccccCHHHHHHHHHHHHH
Confidence            455666778888999999987543   334444444              24679999999887754  34567778887


Q ss_pred             ccCCCCCcEEEEeCCCChhhHHHHHHhcCccccc
Q 042079          103 SSVMKEVPVVVVSSENIPTRINECLEEGAQMFML  136 (153)
Q Consensus       103 ~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~  136 (153)
                      ....+.++|+ +.+..-..  .-+.+.|+|.|-.
T Consensus       162 ~~~~~~v~i~-vGG~~~~~--~~~~~~gad~~~~  192 (197)
T TIGR02370       162 EGYRDSVKFM-VGGAPVTQ--DWADKIGADVYGE  192 (197)
T ss_pred             cCCCCCCEEE-EEChhcCH--HHHHHhCCcEEeC
Confidence            6443345554 54433222  2356789998854

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.

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

Probab=94.33  E-value=0.84  Score=34.41  Aligned_cols=103  Identities=14%  Similarity=0.098  Sum_probs=67.2

Q ss_pred             HHHHHHHHhcCcE--EEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHHHhccCCCCCcE
Q 042079           34 KIVENLLKNSACK--VTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPV  111 (153)
Q Consensus        34 ~~l~~~l~~~~~~--v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~lr~~~~~~~~pi  111 (153)
                      +.+++.|+.....  ++.......+.+.+.              ...||.+++|+.-...+--++...++.... ..++.
T Consensus         8 n~lk~~l~~g~~~~g~~~~~~sp~~~e~~a--------------~~G~D~v~iD~EHg~~~~~~~~~~i~a~~~-~g~~~   72 (256)
T PRK10558          8 NKFKAALAAKQVQIGCWSALANPITTEVLG--------------LAGFDWLVLDGEHAPNDVSTFIPQLMALKG-SASAP   72 (256)
T ss_pred             HHHHHHHHcCCceEEEEEcCCCcHHHHHHH--------------hcCCCEEEEccccCCCCHHHHHHHHHHHhh-cCCCc
Confidence            3466666654322  223233334556553              346999999999988887777776664332 34555


Q ss_pred             EEEeCCCChhhHHHHHHhcCcccccC-CCChhHHHHHHhhh
Q 042079          112 VVVSSENIPTRINECLEEGAQMFMLK-PLKPSDVKKLTGHL  151 (153)
Q Consensus       112 i~~t~~~~~~~~~~a~~~ga~~~l~K-P~~~~~l~~~~~~~  151 (153)
                      ++=.+..++..+.++++.|++.++.. --+.++.++++..+
T Consensus        73 lVRvp~~~~~~i~r~LD~Ga~giivP~v~tae~a~~~v~a~  113 (256)
T PRK10558         73 VVRVPTNEPVIIKRLLDIGFYNFLIPFVETAEEARRAVAST  113 (256)
T ss_pred             EEECCCCCHHHHHHHhCCCCCeeeecCcCCHHHHHHHHHHc
Confidence            55666678899999999999998654 35666777766543

>cd04728 ThiG Thiazole synthase (ThiG) is the tetrameric enzyme that is involved in the formation of the thiazole moiety of thiamin pyrophosphate, an essential ubiquitous cofactor that plays an important role in carbohydrate and amino acid metabolism

Probab=94.00  E-value=0.86  Score=34.10  Aligned_cols=40  Identities=30%  Similarity=0.414  Sum_probs=33.7

Q ss_pred             HHHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCccccc
Q 042079           94 YELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFML  136 (153)
Q Consensus        94 ~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~  136 (153)
                      .++++.+++.   ..+|+|+=..-.++++..++++.|++..+.
T Consensus       164 ~~~I~~I~e~---~~vpVI~egGI~tpeda~~AmelGAdgVlV  203 (248)
T cd04728         164 PYNLRIIIER---ADVPVIVDAGIGTPSDAAQAMELGADAVLL  203 (248)
T ss_pred             HHHHHHHHHh---CCCcEEEeCCCCCHHHHHHHHHcCCCEEEE
Confidence            6888888874   368998888888999999999999998753

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).

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

Probab=93.88  E-value=1.2  Score=33.40  Aligned_cols=74  Identities=14%  Similarity=0.081  Sum_probs=55.5

Q ss_pred             CcccEEEEeCCCCCCCHHHHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCccc-ccCCCChhHHHHHHhhh
Q 042079           77 TKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMF-MLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        77 ~~~dlii~D~~~~~~~g~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~-l~KP~~~~~l~~~~~~~  151 (153)
                      ..||.|++|+.-...+.-++...++.... .....++=.+..+...+.++++.|++++ +.|--+.+++++++..+
T Consensus        32 ~g~D~v~iDlEH~~~~~~~~~~~~~a~~~-~g~~~~VRv~~~~~~~i~~~Ld~Ga~gIivP~v~s~e~a~~~v~~~  106 (249)
T TIGR02311        32 AGFDWLLIDGEHAPNDVRTILSQLQALAP-YPSSPVVRPAIGDPVLIKQLLDIGAQTLLVPMIETAEQAEAAVAAT  106 (249)
T ss_pred             cCCCEEEEeccCCCCCHHHHHHHHHHHHh-cCCCcEEECCCCCHHHHHHHhCCCCCEEEecCcCCHHHHHHHHHHc
Confidence            46999999998888887777777765322 2345555566667778899999999986 56677888888877654

This model represents the aldolase which performs the final step unique to the 4-hydroxyphenylacetic acid catabolism pathway in which 2,4-dihydroxyhept-2-ene-1,7-dioic acid is split into pyruvate and succinate-semialdehyde. The gene for enzyme is generally found adjacent to other genes for this pathway organized into an operon.

>PRK00208 thiG thiazole synthase; Reviewed

Probab=93.35  E-value=1.2  Score=33.35  Aligned_cols=51  Identities=24%  Similarity=0.318  Sum_probs=38.6

Q ss_pred             HHHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccc-----cCCCChhHHHHH
Q 042079           94 YELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFM-----LKPLKPSDVKKL  147 (153)
Q Consensus        94 ~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l-----~KP~~~~~l~~~  147 (153)
                      .++++.+++.   ..+|+|+=..-..+++..++++.|++..+     .|.-++..+-+.
T Consensus       164 ~~~i~~i~e~---~~vpVIveaGI~tpeda~~AmelGAdgVlV~SAItka~dP~~ma~a  219 (250)
T PRK00208        164 PYNLRIIIEQ---ADVPVIVDAGIGTPSDAAQAMELGADAVLLNTAIAVAGDPVAMARA  219 (250)
T ss_pred             HHHHHHHHHh---cCCeEEEeCCCCCHHHHHHHHHcCCCEEEEChHhhCCCCHHHHHHH
Confidence            6788888874   36899988888899999999999999874     453344554433

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

Probab=93.08  E-value=0.57  Score=33.68  Aligned_cols=77  Identities=18%  Similarity=0.251  Sum_probs=51.9

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCC--CCCC--HHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCM--PGMT--GYEL   96 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~--~~~~--g~~~   96 (153)
                      ++||+||+...+--.|.+++++.|.++....+.......+              ...+||.|++.-..  |...  ..++
T Consensus         2 ~~IL~IDNyDSFtyNLv~yl~~lg~~v~V~rnd~~~~~~~--------------~~~~pd~iviSPGPG~P~d~G~~~~~   67 (191)
T COG0512           2 MMILLIDNYDSFTYNLVQYLRELGAEVTVVRNDDISLELI--------------EALKPDAIVISPGPGTPKDAGISLEL   67 (191)
T ss_pred             ceEEEEECccchHHHHHHHHHHcCCceEEEECCccCHHHH--------------hhcCCCEEEEcCCCCChHHcchHHHH
Confidence            5799999999898899999999998877776653222322              13458999987544  3322  3445


Q ss_pred             HHHHHhccCCCCCcEEEEeC
Q 042079           97 LKKIKESSVMKEVPVVVVSS  116 (153)
Q Consensus        97 ~~~lr~~~~~~~~pii~~t~  116 (153)
                      ++++.     .++||+-+.-
T Consensus        68 i~~~~-----~~~PiLGVCL   82 (191)
T COG0512          68 IRRFA-----GRIPILGVCL   82 (191)
T ss_pred             HHHhc-----CCCCEEEECc
Confidence            55442     3689987763

>TIGR03239 GarL 2-dehydro-3-deoxyglucarate aldolase

Probab=92.17  E-value=3.3  Score=31.07  Aligned_cols=73  Identities=12%  Similarity=0.104  Sum_probs=53.4

Q ss_pred             CcccEEEEeCCCCCCCHHHHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccC-CCChhHHHHHHhh
Q 042079           77 TKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLK-PLKPSDVKKLTGH  150 (153)
Q Consensus        77 ~~~dlii~D~~~~~~~g~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~K-P~~~~~l~~~~~~  150 (153)
                      ..||.+++|+.-...+--++...++.... ..++.++=.+..++..+.++++.|++.++.. --+.++.++++..
T Consensus        32 ~G~D~v~iD~EHg~~~~~~~~~~~~a~~~-~g~~~~VRvp~~~~~~i~r~LD~Ga~gIivP~v~taeea~~~v~a  105 (249)
T TIGR03239        32 AGFDWLLLDGEHAPNDVLTFIPQLMALKG-SASAPVVRPPWNEPVIIKRLLDIGFYNFLIPFVESAEEAERAVAA  105 (249)
T ss_pred             cCCCEEEEecccCCCCHHHHHHHHHHHhh-cCCCcEEECCCCCHHHHHHHhcCCCCEEEecCcCCHHHHHHHHHH
Confidence            45999999999988887777777764332 3455555666678888999999999998654 3466666666654

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

>PRK09426 methylmalonyl-CoA mutase; Reviewed

Probab=91.95  E-value=3.3  Score=35.87  Aligned_cols=106  Identities=15%  Similarity=0.085  Sum_probs=69.3

Q ss_pred             eCCHHHHHHHHHHHHhcCcEEEEe---cCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCC--CHHHHHHHHH
Q 042079           27 DDSIVDRKIVENLLKNSACKVTTA---ENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGM--TGYELLKKIK  101 (153)
Q Consensus        27 dd~~~~~~~l~~~l~~~~~~v~~~---~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~--~g~~~~~~lr  101 (153)
                      |.|..-...+..+|...|++|...   .+.++.++...              ...+|+|++-..+...  ..-.+++.|+
T Consensus       593 d~H~~ra~fv~~~l~~~GfeV~~~~~~~s~e~~v~aa~--------------~~~a~ivvlcs~d~~~~e~~~~l~~~Lk  658 (714)
T PRK09426        593 DGHDRGAKVIATAFADLGFDVDIGPLFQTPEEAARQAV--------------ENDVHVVGVSSLAAGHKTLVPALIEALK  658 (714)
T ss_pred             cchhHhHHHHHHHHHhCCeeEecCCCCCCHHHHHHHHH--------------HcCCCEEEEeccchhhHHHHHHHHHHHH
Confidence            346666788889999999998643   35666666552              3568888876555432  3567788888


Q ss_pred             hccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHH
Q 042079          102 ESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLT  148 (153)
Q Consensus       102 ~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~  148 (153)
                      +.+. .++++ ++.+...+.....+.+.|+|.|+..=.+..++.+.+
T Consensus       659 ~~G~-~~v~v-l~GG~~~~~~~~~l~~aGvD~~i~~g~d~~~~L~~l  703 (714)
T PRK09426        659 KLGR-EDIMV-VVGGVIPPQDYDFLYEAGVAAIFGPGTVIADAAIDL  703 (714)
T ss_pred             hcCC-CCcEE-EEeCCCChhhHHHHHhCCCCEEECCCCCHHHHHHHH
Confidence            7641 23434 355432344446678899999998777777665443

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

Probab=90.88  E-value=3.8  Score=31.16  Aligned_cols=73  Identities=14%  Similarity=0.176  Sum_probs=51.8

Q ss_pred             CcccEEEEeCCCCCCCHHHHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCC-ChhHHHHHHhh
Q 042079           77 TKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPL-KPSDVKKLTGH  150 (153)
Q Consensus        77 ~~~dlii~D~~~~~~~g~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~-~~~~l~~~~~~  150 (153)
                      ..||.+++|+.-...+--++...++.... ..++.++=....+...+.++++.|+++.+..=+ +.++.++++..
T Consensus        38 ~GfD~v~iD~EHg~~~~~~l~~~i~a~~~-~g~~~lVRvp~~~~~~i~r~LD~GA~GIivP~V~saeeA~~~V~a  111 (267)
T PRK10128         38 SGYDWLLIDGEHAPNTIQDLYHQLQAIAP-YASQPVIRPVEGSKPLIKQVLDIGAQTLLIPMVDTAEQARQVVSA  111 (267)
T ss_pred             cCCCEEEEccccCCCCHHHHHHHHHHHHh-cCCCeEEECCCCCHHHHHHHhCCCCCeeEecCcCCHHHHHHHHHh
Confidence            45999999999988887777666664332 344445566667888899999999999876544 44555555543

>PLN02591 tryptophan synthase

Probab=90.66  E-value=0.82  Score=34.35  Aligned_cols=57  Identities=16%  Similarity=0.230  Sum_probs=42.7

Q ss_pred             CHHHHHHHHHhccCCCCCcEEEEeCCCC------hhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           92 TGYELLKKIKESSVMKEVPVVVVSSENI------PTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        92 ~g~~~~~~lr~~~~~~~~pii~~t~~~~------~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      +.+++++++|+.   .++|+++++-.+.      +....+|.+.|+++.|.-.+.+++..+....+
T Consensus        65 ~~~~~~~~~r~~---~~~p~ilm~Y~N~i~~~G~~~F~~~~~~aGv~GviipDLP~ee~~~~~~~~  127 (250)
T PLN02591         65 SVISMLKEVAPQ---LSCPIVLFTYYNPILKRGIDKFMATIKEAGVHGLVVPDLPLEETEALRAEA  127 (250)
T ss_pred             HHHHHHHHHhcC---CCCCEEEEecccHHHHhHHHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHH
Confidence            457777777743   4689888887543      44567888999999999999988888776654

>PRK13111 trpA tryptophan synthase subunit alpha; Provisional

Probab=90.61  E-value=1.3  Score=33.36  Aligned_cols=58  Identities=21%  Similarity=0.456  Sum_probs=42.8

Q ss_pred             CHHHHHHHHHhccCCCCCcEEEEeCCC------ChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           92 TGYELLKKIKESSVMKEVPVVVVSSEN------IPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        92 ~g~~~~~~lr~~~~~~~~pii~~t~~~------~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      ..+++++++|+..  .++|+++++-.+      .+....++.+.|+++.+.-.+.+++..+....+
T Consensus        75 ~~~~~~~~~r~~~--~~~p~vlm~Y~N~i~~~G~e~f~~~~~~aGvdGviipDLp~ee~~~~~~~~  138 (258)
T PRK13111         75 DVFELVREIREKD--PTIPIVLMTYYNPIFQYGVERFAADAAEAGVDGLIIPDLPPEEAEELRAAA  138 (258)
T ss_pred             HHHHHHHHHHhcC--CCCCEEEEecccHHhhcCHHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHH
Confidence            3467777777433  578998888543      245578899999999999888888887776554

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

Probab=90.56  E-value=7.1  Score=31.13  Aligned_cols=67  Identities=16%  Similarity=0.073  Sum_probs=35.3

Q ss_pred             ccEEEEeCCCCCCCHHHHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079           79 VNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus        79 ~dlii~D~~~~~~~g~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      .|++++--+....-|..+++.+.-     ..|+|.-..........+...  ..+++..|-+.+++.+.+.+++
T Consensus       320 aDi~~v~~S~~e~~g~~~lEAma~-----G~PVI~g~~~~~~~e~~~~~~--~~g~~~~~~d~~~La~~l~~ll  386 (425)
T PRK05749        320 ADIAFVGGSLVKRGGHNPLEPAAF-----GVPVISGPHTFNFKEIFERLL--QAGAAIQVEDAEDLAKAVTYLL  386 (425)
T ss_pred             CCEEEECCCcCCCCCCCHHHHHHh-----CCCEEECCCccCHHHHHHHHH--HCCCeEEECCHHHHHHHHHHHh
Confidence            477666433322334455555442     568874222122233322221  2356667888888887777654

>PRK00043 thiE thiamine-phosphate pyrophosphorylase; Reviewed

Probab=90.47  E-value=5  Score=28.73  Aligned_cols=56  Identities=25%  Similarity=0.391  Sum_probs=41.0

Q ss_pred             CcccEEEEeCCCCCC--------CHHHHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccc
Q 042079           77 TKVNLVITDYCMPGM--------TGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFM  135 (153)
Q Consensus        77 ~~~dlii~D~~~~~~--------~g~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l  135 (153)
                      ..+|+|.+.-..|..        .|++.++++++..  +++||++..+- +.+.+.++++.|++.+.
T Consensus       123 ~gaD~v~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~--~~~~v~a~GGI-~~~~i~~~~~~Ga~gv~  186 (212)
T PRK00043        123 AGADYVGVGPIFPTPTKKDAKAPQGLEGLREIRAAV--GDIPIVAIGGI-TPENAPEVLEAGADGVA  186 (212)
T ss_pred             cCCCEEEECCccCCCCCCCCCCCCCHHHHHHHHHhc--CCCCEEEECCc-CHHHHHHHHHcCCCEEE
Confidence            468999887545432        3588899988743  34888877665 67888899999998875

>PF02581 TMP-TENI: Thiamine monophosphate synthase/TENI; InterPro: IPR003733 Thiamine monophosphate synthase (TMP) (2

Probab=90.27  E-value=4.8  Score=28.39  Aligned_cols=78  Identities=23%  Similarity=0.235  Sum_probs=51.6

Q ss_pred             HHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCC-------CHHHHHHHHHhccCCCCCc
Q 042079           38 NLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGM-------TGYELLKKIKESSVMKEVP  110 (153)
Q Consensus        38 ~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~-------~g~~~~~~lr~~~~~~~~p  110 (153)
                      ..+....+.-.++++..++....               ...+|.+++.--.|..       -|++.++++.+..   ++|
T Consensus        90 ~~~~~~~~ig~S~h~~~e~~~a~---------------~~g~dYv~~gpvf~T~sk~~~~~~g~~~l~~~~~~~---~~p  151 (180)
T PF02581_consen   90 KLLGPDKIIGASCHSLEEAREAE---------------ELGADYVFLGPVFPTSSKPGAPPLGLDGLREIARAS---PIP  151 (180)
T ss_dssp             HHHTTTSEEEEEESSHHHHHHHH---------------HCTTSEEEEETSS--SSSSS-TTCHHHHHHHHHHHT---SSC
T ss_pred             hhcccceEEEeecCcHHHHHHhh---------------hcCCCEEEECCccCCCCCccccccCHHHHHHHHHhC---CCC
Confidence            33433334455788888865544               2457999998765443       3888888887653   589


Q ss_pred             EEEEeCCCChhhHHHHHHhcCccc
Q 042079          111 VVVVSSENIPTRINECLEEGAQMF  134 (153)
Q Consensus       111 ii~~t~~~~~~~~~~a~~~ga~~~  134 (153)
                      ++++.+- +.+...++.+.|++++
T Consensus       152 v~AlGGI-~~~~i~~l~~~Ga~gv  174 (180)
T PF02581_consen  152 VYALGGI-TPENIPELREAGADGV  174 (180)
T ss_dssp             EEEESS---TTTHHHHHHTT-SEE
T ss_pred             EEEEcCC-CHHHHHHHHHcCCCEE
Confidence            9988875 5666778899999875

5.1.3 from EC) catalyzes the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5- (beta-hydroxyethyl)thiazole phosphate to yield thiamine phosphate in the thiamine biosynthesis pathway []. TENI, a protein from Bacillus subtilis that regulates the production of several extracellular enzymes by reducing alkaline protease production belongs to this group [].; GO: 0004789 thiamine-phosphate diphosphorylase activity, 0009228 thiamine biosynthetic process; PDB: 3NL5_A 3NL2_A 3NM1_A 3NM3_C 3NL6_B 3NL3_A 3CEU_A 3O63_B 3QH2_C 1YAD_D ....

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

Probab=90.26  E-value=4.4  Score=27.81  Aligned_cols=111  Identities=18%  Similarity=0.180  Sum_probs=73.3

Q ss_pred             CCCeEEE----EeCCHHHHHHHHHHHHhcCcEEEE---ecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCC-
Q 042079           19 KPPHVLA----VDDSIVDRKIVENLLKNSACKVTT---AENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPG-   90 (153)
Q Consensus        19 ~~~~iLi----idd~~~~~~~l~~~l~~~~~~v~~---~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~-   90 (153)
                      ..++|++    .|.|..-.+.+.+.|+..|++|..   ..+..|++...-              .+..|+|.+...... 
T Consensus        11 ~rprvlvak~GlDgHd~gakvia~~l~d~GfeVi~~g~~~tp~e~v~aA~--------------~~dv~vIgvSsl~g~h   76 (143)
T COG2185          11 ARPRVLVAKLGLDGHDRGAKVIARALADAGFEVINLGLFQTPEEAVRAAV--------------EEDVDVIGVSSLDGGH   76 (143)
T ss_pred             CCceEEEeccCccccccchHHHHHHHHhCCceEEecCCcCCHHHHHHHHH--------------hcCCCEEEEEeccchH
Confidence            3455555    477888889999999999998764   667788777652              245788876543322 


Q ss_pred             -CCHHHHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHH
Q 042079           91 -MTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVK  145 (153)
Q Consensus        91 -~~g~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~  145 (153)
                       ....++++.+|+... .++. ++..+.-.++...+..+.|++.++.--....+..
T Consensus        77 ~~l~~~lve~lre~G~-~~i~-v~~GGvip~~d~~~l~~~G~~~if~pgt~~~~~~  130 (143)
T COG2185          77 LTLVPGLVEALREAGV-EDIL-VVVGGVIPPGDYQELKEMGVDRIFGPGTPIEEAL  130 (143)
T ss_pred             HHHHHHHHHHHHHhCC-cceE-EeecCccCchhHHHHHHhCcceeeCCCCCHHHHH
Confidence             134556677787653 3333 3445444566677788899999986655555544

>TIGR00262 trpA tryptophan synthase, alpha subunit

Probab=90.24  E-value=1.2  Score=33.48  Aligned_cols=58  Identities=21%  Similarity=0.377  Sum_probs=39.4

Q ss_pred             CHHHHHHHHHhccCCCCCcEEEEeCCCC------hhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           92 TGYELLKKIKESSVMKEVPVVVVSSENI------PTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        92 ~g~~~~~~lr~~~~~~~~pii~~t~~~~------~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      ..+++++.+|+..  .++|+++++-.+.      +....++.+.|++.++......++..+.+..+
T Consensus        73 ~~~~~v~~ir~~~--~~~plv~m~Y~Npi~~~G~e~f~~~~~~aGvdgviipDlp~ee~~~~~~~~  136 (256)
T TIGR00262        73 KCFELLKKVRQKH--PNIPIGLLTYYNLIFRKGVEEFYAKCKEVGVDGVLVADLPLEESGDLVEAA  136 (256)
T ss_pred             HHHHHHHHHHhcC--CCCCEEEEEeccHHhhhhHHHHHHHHHHcCCCEEEECCCChHHHHHHHHHH
Confidence            3456677776532  3678777766544      56677888889988888777777776665543

Tryptophan synthase catalyzes the last step in the biosynthesis of tryptophan. The alpha chain is responsible for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3-phosphate. In bacteria and plants each domain is found on a separate subunit (alpha and beta chains), while in fungi the two domains are fused together on a single multifunctional protein. The signature pattern for trpA contains three conserved acidic residues. [LIVM]-E-[LIVM]-G-x(2)-[FYC]-[ST]-[DE]-[PA]-[LIVMY]-[AGLI]-[DE]-G and this is located between residues 43-58 of the model. The Sulfolobus solfataricus trpA is known to be quite divergent from other known trpA sequences.

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

Probab=89.90  E-value=1.4  Score=32.90  Aligned_cols=57  Identities=19%  Similarity=0.389  Sum_probs=38.8

Q ss_pred             CHHHHHHHHHhccCCCCCcEEEEeCCCC------hhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           92 TGYELLKKIKESSVMKEVPVVVVSSENI------PTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        92 ~g~~~~~~lr~~~~~~~~pii~~t~~~~------~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      .++++++.+|+..   ++|+++++..+.      +.....+.+.|++..+.-.+.++++.+++.++
T Consensus        63 ~~~~~~~~vr~~~---~~pv~lm~y~n~~~~~G~~~fi~~~~~aG~~giiipDl~~ee~~~~~~~~  125 (242)
T cd04724          63 DVLELVKEIRKKN---TIPIVLMGYYNPILQYGLERFLRDAKEAGVDGLIIPDLPPEEAEEFREAA  125 (242)
T ss_pred             HHHHHHHHHhhcC---CCCEEEEEecCHHHHhCHHHHHHHHHHCCCcEEEECCCCHHHHHHHHHHH
Confidence            3566777777542   578777766432      55677788899998888666677776666554

TPRS is a bifunctional tetrameric enzyme (2 alpha and 2 beta subunits) that catalyzes the last two steps of L-tryptophan biosynthesis. Alpha and beta subunit catalyze two distinct reactions which are both strongly stimulated by the formation of the complex. The alpha subunit catalyzes the cleavage of indole 3-glycerol phosphate (IGP) to indole and d-glyceraldehyde 3-phosphate (G3P). Indole is then channeled to the active site of the beta subunit, a PLP-dependent enzyme that catalyzes a replacement reaction to convert L-serine into L-tryptophan.

>PRK07896 nicotinate-nucleotide pyrophosphorylase; Provisional

Probab=89.64  E-value=2.1  Score=32.88  Aligned_cols=94  Identities=16%  Similarity=0.141  Sum_probs=58.1

Q ss_pred             eEEEEeCCHHHHHHHHHHHH----hcC--cEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHH
Q 042079           22 HVLAVDDSIVDRKIVENLLK----NSA--CKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYE   95 (153)
Q Consensus        22 ~iLiidd~~~~~~~l~~~l~----~~~--~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~   95 (153)
                      .|||-|+|......+...++    ..+  .....+++.+++.+.+.               ..+|+|++|- |+...--+
T Consensus       172 ~ilIkdNHi~~~G~i~~ai~~~r~~~~~~kIeVEv~tl~ea~eal~---------------~gaDiI~LDn-m~~e~vk~  235 (289)
T PRK07896        172 AALIKDNHVAAAGSVVAALRAVRAAAPDLPCEVEVDSLEQLDEVLA---------------EGAELVLLDN-FPVWQTQE  235 (289)
T ss_pred             eeeecHHHHHHhCcHHHHHHHHHHhCCCCCEEEEcCCHHHHHHHHH---------------cCCCEEEeCC-CCHHHHHH
Confidence            47777777655433333333    222  23556788899888872               4589999993 33323333


Q ss_pred             HHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCccc
Q 042079           96 LLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMF  134 (153)
Q Consensus        96 ~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~  134 (153)
                      .++.++...  +++ .+..++.-+.+.+.+....|+|-+
T Consensus       236 av~~~~~~~--~~v-~ieaSGGI~~~ni~~yA~tGvD~I  271 (289)
T PRK07896        236 AVQRRDARA--PTV-LLESSGGLTLDTAAAYAETGVDYL  271 (289)
T ss_pred             HHHHHhccC--CCE-EEEEECCCCHHHHHHHHhcCCCEE
Confidence            444444332  333 566777778888888888998765

>TIGR01334 modD putative molybdenum utilization protein ModD

Probab=89.53  E-value=3.1  Score=31.78  Aligned_cols=95  Identities=15%  Similarity=0.157  Sum_probs=59.8

Q ss_pred             eEEEEeCCHHHHH---HHHHHHH---hc---CcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCC
Q 042079           22 HVLAVDDSIVDRK---IVENLLK---NS---ACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMT   92 (153)
Q Consensus        22 ~iLiidd~~~~~~---~l~~~l~---~~---~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~   92 (153)
                      .|||-|+|.....   .+...++   +.   ......+.+.+++.+.+.               ..+|+|++| .|+..+
T Consensus       158 ~ilikdnHi~~~g~~~~i~~av~~~r~~~~~~kIeVEv~tleea~ea~~---------------~GaDiI~lD-n~~~e~  221 (277)
T TIGR01334       158 TLLVFANHRTFLNDNFDWGGAIGRLKQTAPERKITVEADTIEQALTVLQ---------------ASPDILQLD-KFTPQQ  221 (277)
T ss_pred             hheehHHHHHHhCCcccHHHHHHHHHHhCCCCCEEEECCCHHHHHHHHH---------------cCcCEEEEC-CCCHHH
Confidence            4778888766543   3333332   21   123456778888888772               458999999 344444


Q ss_pred             HHHHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccc
Q 042079           93 GYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFM  135 (153)
Q Consensus        93 g~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l  135 (153)
                      -.+.++.+++..  ++ ..+..++.-+.+.+.+....|+|-+.
T Consensus       222 l~~~v~~l~~~~--~~-~~leasGGI~~~ni~~ya~~GvD~is  261 (277)
T TIGR01334       222 LHHLHERLKFFD--HI-PTLAAAGGINPENIADYIEAGIDLFI  261 (277)
T ss_pred             HHHHHHHHhccC--CC-EEEEEECCCCHHHHHHHHhcCCCEEE
Confidence            455555555322  23 35667777788888888889987653

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.

>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=88.74  E-value=8.5  Score=29.14  Aligned_cols=77  Identities=14%  Similarity=0.213  Sum_probs=53.6

Q ss_pred             EEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHHHh
Q 042079           23 VLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKIKE  102 (153)
Q Consensus        23 iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~lr~  102 (153)
                      |-+.-.++.....+.++|....|.+..+.+..+.++.+..            .++.+|++++......   ..++..|.+
T Consensus         3 I~~~v~s~~Laqsl~~~L~~dRY~l~~~~s~~ef~~~le~------------~~e~iDCLvle~~~~~---~~~~~~L~e   67 (283)
T PF07688_consen    3 ICLLVSSPALAQSLRQWLPGDRYELVQVDSPEEFLEFLEQ------------HREQIDCLVLEQSPLL---PPLFNQLYE   67 (283)
T ss_dssp             EEEE-S-HHHHHHHHHHT-STTEEEEEESSCHHHHHHHCC------------TTTT-SEEEEETTSTT---HHHHHHHHH
T ss_pred             EEEEeCCHHHHHHHHHHcccCceEEEEcCcHHHHHHHHHh------------chhccCEEEEecCCCc---HHHHHHHHH
Confidence            4455567778888999998888999999999998888842            4568999999876554   567788887


Q ss_pred             ccCCCCCcEEEEeC
Q 042079          103 SSVMKEVPVVVVSS  116 (153)
Q Consensus       103 ~~~~~~~pii~~t~  116 (153)
                      .+.  -.|+|++..
T Consensus        68 ~g~--LLPaVil~~   79 (283)
T PF07688_consen   68 QGI--LLPAVILGS   79 (283)
T ss_dssp             CT------EEEES-
T ss_pred             cCc--cccEEEEec
Confidence            653  468888866

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.

>TIGR00693 thiE thiamine-phosphate pyrophosphorylase

Probab=88.45  E-value=7.1  Score=27.69  Aligned_cols=55  Identities=24%  Similarity=0.349  Sum_probs=39.0

Q ss_pred             CcccEEEEeCCCCC--------CCHHHHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCccc
Q 042079           77 TKVNLVITDYCMPG--------MTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMF  134 (153)
Q Consensus        77 ~~~dlii~D~~~~~--------~~g~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~  134 (153)
                      ..+|++.++-..+.        ..|++.++++.+..  +++|++++.+- +.+...++.+.|++.+
T Consensus       115 ~g~dyi~~~~v~~t~~k~~~~~~~g~~~l~~~~~~~--~~~pv~a~GGI-~~~~~~~~~~~G~~gv  177 (196)
T TIGR00693       115 EGADYIGFGPIFPTPTKKDPAPPAGVELLREIAATS--IDIPIVAIGGI-TLENAAEVLAAGADGV  177 (196)
T ss_pred             cCCCEEEECCccCCCCCCCCCCCCCHHHHHHHHHhc--CCCCEEEECCc-CHHHHHHHHHcCCCEE
Confidence            46899987654442        23788888887532  35888877655 5777888889998775

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

>cd02068 radical_SAM_B12_BD B12 binding domain_like associated with radical SAM domain

Probab=88.43  E-value=5.3  Score=26.28  Aligned_cols=103  Identities=21%  Similarity=0.142  Sum_probs=55.9

Q ss_pred             HHHHHHHHHhcCcEEEEec--CHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCC-CHHHHHHHHHhccCCCCC
Q 042079           33 RKIVENLLKNSACKVTTAE--NGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGM-TGYELLKKIKESSVMKEV  109 (153)
Q Consensus        33 ~~~l~~~l~~~~~~v~~~~--~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~-~g~~~~~~lr~~~~~~~~  109 (153)
                      ...+..++++.|+.+....  ...+.++.+.             ....||+|.+.+..+.. ....+++.+|+..  +++
T Consensus         5 l~~~aa~l~~~g~~v~~~~~~~~~~~~~~~~-------------~~~~pdiv~~S~~~~~~~~~~~~~~~ik~~~--p~~   69 (127)
T cd02068           5 LAYLAAVLEDAGFIVAEHDVLSADDIVEDIK-------------ELLKPDVVGISLMTSAIYEALELAKIAKEVL--PNV   69 (127)
T ss_pred             HHHHHHHHHHCCCeeeecCCCCHHHHHHHHH-------------HhcCCCEEEEeeccccHHHHHHHHHHHHHHC--CCC
Confidence            3456777888787655433  3333344331             11579999999865554 4677888888865  466


Q ss_pred             cEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          110 PVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       110 pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      ++++-....+ ......+.....||+.+=--..-+.++++++
T Consensus        70 ~iv~GG~~~t-~~p~~~~~~~~~D~vv~GEgE~~~~~l~~~l  110 (127)
T cd02068          70 IVVVGGPHAT-FFPEEILEEPGVDFVVIGEGEETFLKLLEEL  110 (127)
T ss_pred             EEEECCcchh-hCHHHHhcCCCCCEEEECCcHHHHHHHHHHH
Confidence            6654433322 2223323333345655432233444555443

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.

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

Probab=87.27  E-value=9.3  Score=27.77  Aligned_cols=82  Identities=18%  Similarity=0.262  Sum_probs=51.9

Q ss_pred             HHHHHh-cCcEE-EEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCC-------CCCCCHHHHHHHHHhccCCC
Q 042079           37 ENLLKN-SACKV-TTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYC-------MPGMTGYELLKKIKESSVMK  107 (153)
Q Consensus        37 ~~~l~~-~~~~v-~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~-------~~~~~g~~~~~~lr~~~~~~  107 (153)
                      ....++ .+..+ ..+.+.+++....               ...+|++.+...       ......+++++++++..   
T Consensus       111 i~~~~~~~~i~vi~~v~t~ee~~~a~---------------~~G~d~i~~~~~g~t~~~~~~~~~~~~~i~~i~~~~---  172 (221)
T PRK01130        111 VKRIKEYPGQLLMADCSTLEEGLAAQ---------------KLGFDFIGTTLSGYTEETKKPEEPDFALLKELLKAV---  172 (221)
T ss_pred             HHHHHhCCCCeEEEeCCCHHHHHHHH---------------HcCCCEEEcCCceeecCCCCCCCcCHHHHHHHHHhC---
Confidence            333444 44433 3456666664433               235788865321       11223478888888743   


Q ss_pred             CCcEEEEeCCCChhhHHHHHHhcCccccc
Q 042079          108 EVPVVVVSSENIPTRINECLEEGAQMFML  136 (153)
Q Consensus       108 ~~pii~~t~~~~~~~~~~a~~~ga~~~l~  136 (153)
                      ++|++...+-.+.+.+.++++.|++.++.
T Consensus       173 ~iPvia~GGI~t~~~~~~~l~~GadgV~i  201 (221)
T PRK01130        173 GCPVIAEGRINTPEQAKKALELGAHAVVV  201 (221)
T ss_pred             CCCEEEECCCCCHHHHHHHHHCCCCEEEE
Confidence            68998877777889999999999988643

>PRK08007 para-aminobenzoate synthase component II; Provisional

Probab=87.19  E-value=1.7  Score=30.94  Aligned_cols=76  Identities=16%  Similarity=0.145  Sum_probs=46.3

Q ss_pred             EEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCC--CCCCHHHHHHHH
Q 042079           23 VLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCM--PGMTGYELLKKI  100 (153)
Q Consensus        23 iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~--~~~~g~~~~~~l  100 (153)
                      ||+||....+-..+.++|++.|+.+..+.+....++.+.              ...||.||+--..  |...+. ..+.+
T Consensus         2 il~idn~Dsft~nl~~~l~~~g~~v~v~~~~~~~~~~~~--------------~~~~d~iils~GPg~p~~~~~-~~~~~   66 (187)
T PRK08007          2 ILLIDNYDSFTWNLYQYFCELGADVLVKRNDALTLADID--------------ALKPQKIVISPGPCTPDEAGI-SLDVI   66 (187)
T ss_pred             EEEEECCCccHHHHHHHHHHCCCcEEEEeCCCCCHHHHH--------------hcCCCEEEEcCCCCChHHCCc-cHHHH
Confidence            899999999999999999998888777665432222221              1247888875433  222222 12223


Q ss_pred             HhccCCCCCcEEEEe
Q 042079          101 KESSVMKEVPVVVVS  115 (153)
Q Consensus       101 r~~~~~~~~pii~~t  115 (153)
                      +..  ...+|++-+.
T Consensus        67 ~~~--~~~~PiLGIC   79 (187)
T PRK08007         67 RHY--AGRLPILGVC   79 (187)
T ss_pred             HHh--cCCCCEEEEC
Confidence            321  1467987776

>PRK07428 nicotinate-nucleotide pyrophosphorylase; Provisional

Probab=87.18  E-value=4.8  Score=30.96  Aligned_cols=94  Identities=16%  Similarity=0.162  Sum_probs=57.4

Q ss_pred             eEEEEeCCHHHHHHHHHHHH----hcC--cE-EEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHH
Q 042079           22 HVLAVDDSIVDRKIVENLLK----NSA--CK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGY   94 (153)
Q Consensus        22 ~iLiidd~~~~~~~l~~~l~----~~~--~~-v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~   94 (153)
                      .|||-|+|......+...+.    ..+  .. -..+++.+|+.+.+.               ..+|+|.+|- |+...--
T Consensus       168 ~ilikdNHi~~~g~i~~av~~~r~~~~~~~~I~VEv~tleea~eA~~---------------~GaD~I~LDn-~~~e~l~  231 (288)
T PRK07428        168 AVMIKDNHIQAAGGIGEAITRIRQRIPYPLTIEVETETLEQVQEALE---------------YGADIIMLDN-MPVDLMQ  231 (288)
T ss_pred             eeeecHHHHHHhCCHHHHHHHHHHhCCCCCEEEEECCCHHHHHHHHH---------------cCCCEEEECC-CCHHHHH
Confidence            58888888665543444332    233  22 346788999988772               4689999993 3222223


Q ss_pred             HHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCccc
Q 042079           95 ELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMF  134 (153)
Q Consensus        95 ~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~  134 (153)
                      +.++.++...  +++|+. .++.-+.+.+.+....|+|.+
T Consensus       232 ~av~~~~~~~--~~i~le-AsGGIt~~ni~~ya~tGvD~I  268 (288)
T PRK07428        232 QAVQLIRQQN--PRVKIE-ASGNITLETIRAVAETGVDYI  268 (288)
T ss_pred             HHHHHHHhcC--CCeEEE-EECCCCHHHHHHHHHcCCCEE
Confidence            3344444322  455544 555567888888889998865

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

Probab=87.16  E-value=12  Score=28.94  Aligned_cols=82  Identities=16%  Similarity=0.177  Sum_probs=54.9

Q ss_pred             HHHHHHhcCcEEE-EecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCC-----CCCCCHHHHHHHHHhccCCCCC
Q 042079           36 VENLLKNSACKVT-TAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYC-----MPGMTGYELLKKIKESSVMKEV  109 (153)
Q Consensus        36 l~~~l~~~~~~v~-~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~-----~~~~~g~~~~~~lr~~~~~~~~  109 (153)
                      +-..++..|..+. .+.+..++....               ...+|.|++.-.     ......+.+++++++..   ++
T Consensus       101 ~i~~lk~~g~~v~~~v~s~~~a~~a~---------------~~GaD~Ivv~g~eagGh~g~~~~~~ll~~v~~~~---~i  162 (307)
T TIGR03151       101 YIPRLKENGVKVIPVVASVALAKRME---------------KAGADAVIAEGMESGGHIGELTTMALVPQVVDAV---SI  162 (307)
T ss_pred             HHHHHHHcCCEEEEEcCCHHHHHHHH---------------HcCCCEEEEECcccCCCCCCCcHHHHHHHHHHHh---CC
Confidence            3344555666543 466777665544               235899987432     12234588888888643   68


Q ss_pred             cEEEEeCCCChhhHHHHHHhcCcccc
Q 042079          110 PVVVVSSENIPTRINECLEEGAQMFM  135 (153)
Q Consensus       110 pii~~t~~~~~~~~~~a~~~ga~~~l  135 (153)
                      |||.-.+-.+...+.+++..|++...
T Consensus       163 PviaaGGI~~~~~~~~al~~GA~gV~  188 (307)
T TIGR03151       163 PVIAAGGIADGRGMAAAFALGAEAVQ  188 (307)
T ss_pred             CEEEECCCCCHHHHHHHHHcCCCEee
Confidence            99887777788889999999998764

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

>CHL00200 trpA tryptophan synthase alpha subunit; Provisional

Probab=86.74  E-value=2.1  Score=32.43  Aligned_cols=56  Identities=14%  Similarity=0.203  Sum_probs=40.9

Q ss_pred             HHHHHHHHHhccCCCCCcEEEEeCCCC------hhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           93 GYELLKKIKESSVMKEVPVVVVSSENI------PTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        93 g~~~~~~lr~~~~~~~~pii~~t~~~~------~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      .+++++++|+.   .++|+++++-.+.      +....+|.+.|++.++.-.+.+++..+....+
T Consensus        79 ~~~~~~~~r~~---~~~p~vlm~Y~N~i~~~G~e~F~~~~~~aGvdgviipDLP~ee~~~~~~~~  140 (263)
T CHL00200         79 ILSILSEVNGE---IKAPIVIFTYYNPVLHYGINKFIKKISQAGVKGLIIPDLPYEESDYLISVC  140 (263)
T ss_pred             HHHHHHHHhcC---CCCCEEEEecccHHHHhCHHHHHHHHHHcCCeEEEecCCCHHHHHHHHHHH
Confidence            46667777642   4789888877542      45578888999999999888888877766544

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

Probab=86.67  E-value=6.7  Score=26.73  Aligned_cols=54  Identities=17%  Similarity=0.181  Sum_probs=44.2

Q ss_pred             CCCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEec----CHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCC
Q 042079           18 PKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAE----NGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPG   90 (153)
Q Consensus        18 ~~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~----~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~   90 (153)
                      .+..++.|++.+....+-+..+|.+.|..+..++    +..++++                   ..|+|++-..-+.
T Consensus        26 ~~gk~v~VvGrs~~vG~pla~lL~~~gatV~~~~~~t~~l~~~v~-------------------~ADIVvsAtg~~~   83 (140)
T cd05212          26 LDGKKVLVVGRSGIVGAPLQCLLQRDGATVYSCDWKTIQLQSKVH-------------------DADVVVVGSPKPE   83 (140)
T ss_pred             CCCCEEEEECCCchHHHHHHHHHHHCCCEEEEeCCCCcCHHHHHh-------------------hCCEEEEecCCCC
Confidence            4678999999999999999999999999999888    4444333                   3699999887664

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

>TIGR00138 gidB 16S rRNA methyltransferase GidB

Probab=86.48  E-value=9.3  Score=27.04  Aligned_cols=102  Identities=8%  Similarity=0.068  Sum_probs=56.6

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCc-EEEEe-cCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSAC-KVTTA-ENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYEL   96 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~-~v~~~-~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~   96 (153)
                      +..++..+|-++.....++...++.++ .+... .+..+ +  .              ...+||+|+++. +..  -.++
T Consensus        65 ~~~~V~~iD~s~~~~~~a~~~~~~~~~~~i~~i~~d~~~-~--~--------------~~~~fD~I~s~~-~~~--~~~~  124 (181)
T TIGR00138        65 PELKLTLLESNHKKVAFLREVKAELGLNNVEIVNGRAED-F--Q--------------HEEQFDVITSRA-LAS--LNVL  124 (181)
T ss_pred             CCCeEEEEeCcHHHHHHHHHHHHHhCCCCeEEEecchhh-c--c--------------ccCCccEEEehh-hhC--HHHH
Confidence            346799999999888777777776654 23322 23222 1  1              124799999986 322  2344


Q ss_pred             HHHHHhccCCCCCcEEEEeCCCChhhHHHHHH----hcCcccccCCCCh
Q 042079           97 LKKIKESSVMKEVPVVVVSSENIPTRINECLE----EGAQMFMLKPLKP  141 (153)
Q Consensus        97 ~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~----~ga~~~l~KP~~~  141 (153)
                      ++.+.+. ..+...+++.-..........+.+    .|..-.=.||++.
T Consensus       125 ~~~~~~~-LkpgG~lvi~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~  172 (181)
T TIGR00138       125 LELTLNL-LKVGGYFLAYKGKKYLDEIEEAKRKCQVLGVEPLEVPPLTG  172 (181)
T ss_pred             HHHHHHh-cCCCCEEEEEcCCCcHHHHHHHHHhhhhcCceEeeccccCC
Confidence            5555432 224555666655555555444433    3555444455543

GidB (glucose-inhibited division protein B) appears to be present and in a single copy in nearly all complete eubacterial genomes. It is missing only from some obligate intracellular species of various lineages (Chlamydiae, Ehrlichia, Wolbachia, Anaplasma, Buchnera, etc.). GidB shows a methytransferase fold in its the crystal structure, and acts as a 7-methylguanosine (m(7)G) methyltransferase, apparently specific to 16S rRNA.

>cd00452 KDPG_aldolase KDPG and KHG aldolase

Probab=86.24  E-value=4.8  Score=28.65  Aligned_cols=67  Identities=13%  Similarity=0.117  Sum_probs=48.3

Q ss_pred             EEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHHHhccCCCCCcEEEEeCCCChhhHHHHH
Q 042079           48 TTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECL  127 (153)
Q Consensus        48 ~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~  127 (153)
                      ..+.+.+|+....               ...+|+|-++-. +. .|.++++.++..  .+++|++.+.+- +.+...+.+
T Consensus       102 ~gv~t~~e~~~A~---------------~~Gad~i~~~p~-~~-~g~~~~~~l~~~--~~~~p~~a~GGI-~~~n~~~~~  161 (190)
T cd00452         102 PGVATPTEIMQAL---------------ELGADIVKLFPA-EA-VGPAYIKALKGP--FPQVRFMPTGGV-SLDNAAEWL  161 (190)
T ss_pred             CCcCCHHHHHHHH---------------HCCCCEEEEcCC-cc-cCHHHHHHHHhh--CCCCeEEEeCCC-CHHHHHHHH
Confidence            3566888877765               245899987532 22 389999999863  246888866665 788889999


Q ss_pred             HhcCccc
Q 042079          128 EEGAQMF  134 (153)
Q Consensus       128 ~~ga~~~  134 (153)
                      +.|++.+
T Consensus       162 ~~G~~~v  168 (190)
T cd00452         162 AAGVVAV  168 (190)
T ss_pred             HCCCEEE
Confidence            9998775

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.

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

Probab=85.43  E-value=6.9  Score=25.31  Aligned_cols=73  Identities=16%  Similarity=0.157  Sum_probs=46.7

Q ss_pred             eCCHHHHHHHHHHHHhcCcEEEEec---CHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCC-CHHHHHHHHHh
Q 042079           27 DDSIVDRKIVENLLKNSACKVTTAE---NGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGM-TGYELLKKIKE  102 (153)
Q Consensus        27 dd~~~~~~~l~~~l~~~~~~v~~~~---~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~-~g~~~~~~lr~  102 (153)
                      +.++.....+..++++.|+++....   ...+.++.+              ...+||+|.+.+..... .....+..+++
T Consensus        10 ~~h~lg~~~~~~~l~~~G~~v~~l~~~~~~~~~~~~i--------------~~~~pdiV~iS~~~~~~~~~~~~~~~~~~   75 (125)
T cd02065          10 DVHDIGKNIVAIALRDNGFEVIDLGVDVPPEEIVEAA--------------KEEDADVVGLSALSTTHMEAMKLVIEALK   75 (125)
T ss_pred             chhhHHHHHHHHHHHHCCCEEEEcCCCCCHHHHHHHH--------------HHcCCCEEEEecchHhHHHHHHHHHHHHH
Confidence            4566667788888999999887654   333344433              13579999998877654 34555666666


Q ss_pred             ccCCC-CCcEEEEe
Q 042079          103 SSVMK-EVPVVVVS  115 (153)
Q Consensus       103 ~~~~~-~~pii~~t  115 (153)
                      ..  + ++++++-.
T Consensus        76 ~~--p~~~~ivvGG   87 (125)
T cd02065          76 EL--GIDIPVVVGG   87 (125)
T ss_pred             hc--CCCCeEEEeC
Confidence            44  3 56665443

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.

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

Probab=85.27  E-value=11  Score=31.88  Aligned_cols=55  Identities=11%  Similarity=0.186  Sum_probs=35.9

Q ss_pred             CcccEEEEeCCCCCCCHHHHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCccccc
Q 042079           77 TKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFML  136 (153)
Q Consensus        77 ~~~dlii~D~~~~~~~g~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~  136 (153)
                      .+.+++++-...+. ....++...|+..  ++.+|++-+.  +.+......+.|++..+.
T Consensus       463 ~~A~~vv~~~~d~~-~n~~i~~~~r~~~--p~~~IiaRa~--~~~~~~~L~~~Ga~~vv~  517 (601)
T PRK03659        463 EKAEAIVITCNEPE-DTMKIVELCQQHF--PHLHILARAR--GRVEAHELLQAGVTQFSR  517 (601)
T ss_pred             ccCCEEEEEeCCHH-HHHHHHHHHHHHC--CCCeEEEEeC--CHHHHHHHHhCCCCEEEc
Confidence            34666666544432 3455666777654  6778876663  567777888999997753

>PRK03958 tRNA 2'-O-methylase; Reviewed

Probab=85.26  E-value=11  Score=26.78  Aligned_cols=58  Identities=10%  Similarity=0.146  Sum_probs=47.5

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcC--cEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCC
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSA--CKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPG   90 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~--~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~   90 (153)
                      .+++|+.+++..+..++.+++.+|  |.+....+..++++... .           ....+.+++.+....+
T Consensus        32 ~~~yiv~~~~~q~~~v~~I~~~WGg~fnv~~~~s~~~~i~~~k-~-----------~G~vvhLtmyga~~~~   91 (176)
T PRK03958         32 DKIILASNDEHVKESVEDIVERWGGPFEVEVTKSWKKEIREWK-D-----------GGIVVHLTMYGENIQD   91 (176)
T ss_pred             ceEEEecCcHHHHHHHHHHHHhcCCceEEEEcCCHHHHHHHHH-h-----------CCcEEEEEEecCCccc
Confidence            578999999999999999999876  67899999999988773 1           2456888888877765

>TIGR00566 trpG_papA glutamine amidotransferase of anthranilate synthase or aminodeoxychorismate synthase

Probab=85.03  E-value=4.9  Score=28.61  Aligned_cols=30  Identities=17%  Similarity=0.096  Sum_probs=25.9

Q ss_pred             EEEEeCCHHHHHHHHHHHHhcCcEEEEecC
Q 042079           23 VLAVDDSIVDRKIVENLLKNSACKVTTAEN   52 (153)
Q Consensus        23 iLiidd~~~~~~~l~~~l~~~~~~v~~~~~   52 (153)
                      ||+||....+...+..+|++.|+.+....+
T Consensus         2 il~id~~dsft~~~~~~l~~~g~~v~v~~~   31 (188)
T TIGR00566         2 VLMIDNYDSFTYNLVQYFCELGAEVVVKRN   31 (188)
T ss_pred             EEEEECCcCHHHHHHHHHHHcCCceEEEEC
Confidence            899999999999999999988888776653

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.

>PRK05848 nicotinate-nucleotide pyrophosphorylase; Provisional

Probab=84.90  E-value=13  Score=28.35  Aligned_cols=95  Identities=14%  Similarity=0.117  Sum_probs=56.7

Q ss_pred             eEEEEeCCHHHHHHHHHHHH----hcCc---EEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHH
Q 042079           22 HVLAVDDSIVDRKIVENLLK----NSAC---KVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGY   94 (153)
Q Consensus        22 ~iLiidd~~~~~~~l~~~l~----~~~~---~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~   94 (153)
                      .|||-|+|......+...++    ..+.   ....+++.+++.+.+.               ..+|+|++|-..| ..--
T Consensus       154 ~vlikdnHi~~~g~i~~~v~~~k~~~p~~~~I~VEv~tleea~~A~~---------------~GaDiI~LDn~~~-e~l~  217 (273)
T PRK05848        154 CLMLKDTHLKHIKDLKEFIQHARKNIPFTAKIEIECESLEEAKNAMN---------------AGADIVMCDNMSV-EEIK  217 (273)
T ss_pred             hhCcCHHHHHHHCcHHHHHHHHHHhCCCCceEEEEeCCHHHHHHHHH---------------cCCCEEEECCCCH-HHHH
Confidence            47777777665544444443    2332   2446889999988773               4589999885211 1112


Q ss_pred             HHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccc
Q 042079           95 ELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFM  135 (153)
Q Consensus        95 ~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l  135 (153)
                      +.++.++..  .+++ .+..++.-+++.+.+..+.|+|.+.
T Consensus       218 ~~v~~~~~~--~~~~-~ieAsGgIt~~ni~~ya~~GvD~Is  255 (273)
T PRK05848        218 EVVAYRNAN--YPHV-LLEASGNITLENINAYAKSGVDAIS  255 (273)
T ss_pred             HHHHHhhcc--CCCe-EEEEECCCCHHHHHHHHHcCCCEEE
Confidence            222222211  1333 4556666788999999999998653

>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=84.85  E-value=7.9  Score=27.56  Aligned_cols=70  Identities=23%  Similarity=0.304  Sum_probs=43.6

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcE---EEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCH---H
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACK---VTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTG---Y   94 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~---v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g---~   94 (153)
                      .++..||.++.....++.-++..+..   .....+...++.....            ...+||+|++|  .|-..+   .
T Consensus        66 ~~v~fVE~~~~a~~~i~~N~~~l~~~~~~~v~~~d~~~~l~~~~~------------~~~~fDiIflD--PPY~~~~~~~  131 (183)
T PF03602_consen   66 KSVVFVEKNRKAIKIIKKNLEKLGLEDKIRVIKGDAFKFLLKLAK------------KGEKFDIIFLD--PPYAKGLYYE  131 (183)
T ss_dssp             SEEEEEES-HHHHHHHHHHHHHHT-GGGEEEEESSHHHHHHHHHH------------CTS-EEEEEE----STTSCHHHH
T ss_pred             CeEEEEECCHHHHHHHHHHHHHhCCCcceeeeccCHHHHHHhhcc------------cCCCceEEEEC--CCcccchHHH
Confidence            57999999999999999888876632   3345565555554411            24679999999  344333   4


Q ss_pred             HHHHHHHhcc
Q 042079           95 ELLKKIKESS  104 (153)
Q Consensus        95 ~~~~~lr~~~  104 (153)
                      ++++.|.+..
T Consensus       132 ~~l~~l~~~~  141 (183)
T PF03602_consen  132 ELLELLAENN  141 (183)
T ss_dssp             HHHHHHHHTT
T ss_pred             HHHHHHHHCC
Confidence            5777776433

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.

>cd01573 modD_like ModD; Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase) present in some modABC operons in bacteria, which are involved in molybdate transport

Probab=84.73  E-value=12  Score=28.39  Aligned_cols=94  Identities=14%  Similarity=0.094  Sum_probs=56.7

Q ss_pred             EEEEeCCHHHHHH------HHHHHHhcC--cEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHH
Q 042079           23 VLAVDDSIVDRKI------VENLLKNSA--CKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGY   94 (153)
Q Consensus        23 iLiidd~~~~~~~------l~~~l~~~~--~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~   94 (153)
                      |||-|+|......      +...-+..+  .....+++..++.+.+.               ..+|+|.+|-..|. +--
T Consensus       155 vlikdnH~~~~g~~~~~~av~~~R~~~~~~~IgVev~t~eea~~A~~---------------~gaD~I~ld~~~p~-~l~  218 (272)
T cd01573         155 ILVFAEHRAFLGGPEPLKALARLRATAPEKKIVVEVDSLEEALAAAE---------------AGADILQLDKFSPE-ELA  218 (272)
T ss_pred             eEeehhHHHHhCCchHHHHHHHHHHhCCCCeEEEEcCCHHHHHHHHH---------------cCCCEEEECCCCHH-HHH
Confidence            7888877544322      222221111  23456888888877652               45799999965443 223


Q ss_pred             HHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccc
Q 042079           95 ELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFM  135 (153)
Q Consensus        95 ~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l  135 (153)
                      ++++.++...  +++|+++.. .-+.+.+.+..+.|++.+.
T Consensus       219 ~~~~~~~~~~--~~i~i~AsG-GI~~~ni~~~~~~Gvd~I~  256 (272)
T cd01573         219 ELVPKLRSLA--PPVLLAAAG-GINIENAAAYAAAGADILV  256 (272)
T ss_pred             HHHHHHhccC--CCceEEEEC-CCCHHHHHHHHHcCCcEEE
Confidence            4444454321  467776554 4577888899999998764

In general, QPRTases are part of the de novo synthesis pathway of NAD in both prokaryotes and eukaryotes. They catalyse the reaction of quinolinic acid (QA) with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to produce nicotinic acid mononucleotide (NAMN), pyrophosphate and carbon dioxide.

>PRK08385 nicotinate-nucleotide pyrophosphorylase; Provisional

Probab=84.63  E-value=16  Score=27.99  Aligned_cols=94  Identities=16%  Similarity=0.204  Sum_probs=60.2

Q ss_pred             EEEEeCCHHHHHHHHHHHHh---cC---cEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHH
Q 042079           23 VLAVDDSIVDRKIVENLLKN---SA---CKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYEL   96 (153)
Q Consensus        23 iLiidd~~~~~~~l~~~l~~---~~---~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~   96 (153)
                      |||-|+|.... .+...++.   ..   .....+++..++.+.+.               ..+|+|++|-..|. .--+.
T Consensus       157 vLikdnHi~~~-~i~~av~~~r~~~~~~kIeVEv~~leea~~a~~---------------agaDiI~LDn~~~e-~l~~~  219 (278)
T PRK08385        157 ILIKDNHLALV-PLEEAIRRAKEFSVYKVVEVEVESLEDALKAAK---------------AGADIIMLDNMTPE-EIREV  219 (278)
T ss_pred             EEEccCHHHHH-HHHHHHHHHHHhCCCCcEEEEeCCHHHHHHHHH---------------cCcCEEEECCCCHH-HHHHH
Confidence            89999997665 45554442   11   12446889999888773               45899999965433 33344


Q ss_pred             HHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCccc
Q 042079           97 LKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMF  134 (153)
Q Consensus        97 ~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~  134 (153)
                      .+.++.....++ ..+..++.-+.+.+.+..+.|+|-+
T Consensus       220 v~~l~~~~~~~~-~~leaSGGI~~~ni~~yA~tGvD~I  256 (278)
T PRK08385        220 IEALKREGLRER-VKIEVSGGITPENIEEYAKLDVDVI  256 (278)
T ss_pred             HHHHHhcCcCCC-EEEEEECCCCHHHHHHHHHcCCCEE
Confidence            444554321123 3566677778888888889998765

>TIGR02026 BchE magnesium-protoporphyrin IX monomethyl ester anaerobic oxidative cyclase

Probab=84.26  E-value=22  Score=29.37  Aligned_cols=105  Identities=17%  Similarity=0.132  Sum_probs=57.9

Q ss_pred             CHHHHHHHHHHHHhcC-cEEEEecCH------HHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCC-CHHHHHHHH
Q 042079           29 SIVDRKIVENLLKNSA-CKVTTAENG------MRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGM-TGYELLKKI  100 (153)
Q Consensus        29 ~~~~~~~l~~~l~~~~-~~v~~~~~~------~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~-~g~~~~~~l  100 (153)
                      .|.-...+...|++.| ++|...+..      .+..+.+              ....||+|.+....+.. ...++++.+
T Consensus        21 pPlgl~~lAa~L~~~G~~~V~iiD~~~~~~~~~~~~~~l--------------~~~~pdvVgis~~t~~~~~a~~~~~~~   86 (497)
T TIGR02026        21 PPLWVAYIGGALLDAGYHDVTFLDAMTGPLTDEKLVERL--------------RAHCPDLVLITAITPAIYIACETLKFA   86 (497)
T ss_pred             CCHHHHHHHHHHHhcCCcceEEecccccCCCHHHHHHHH--------------HhcCcCEEEEecCcccHHHHHHHHHHH
Confidence            4555667888898888 577665422      1222222              13569999997655543 356777778


Q ss_pred             HhccCCCCCcEEEEeCCCChhhHHHHHH-hcCcccccCCCChhHHHHHHhh
Q 042079          101 KESSVMKEVPVVVVSSENIPTRINECLE-EGAQMFMLKPLKPSDVKKLTGH  150 (153)
Q Consensus       101 r~~~~~~~~pii~~t~~~~~~~~~~a~~-~ga~~~l~KP~~~~~l~~~~~~  150 (153)
                      |+..  ++++|| +.+........+++. ....||+..==-..-+.++++.
T Consensus        87 k~~~--P~~~iV-~GG~h~t~~~~~~l~~~p~vD~Vv~GEGE~~~~~Ll~~  134 (497)
T TIGR02026        87 RERL--PNAIIV-LGGIHPTFMFHQVLTEAPWIDFIVRGEGEETVVKLIAA  134 (497)
T ss_pred             HHHC--CCCEEE-EcCCCcCcCHHHHHhcCCCccEEEeCCcHHHHHHHHHH
Confidence            8754  566665 444322223344554 3334565553333444455544

This model respresents the cobalamin-dependent oxidative cyclase responsible for forming the distinctive E-ring of the chlorin ring system under anaerobic conditions. This step is essential in the biosynthesis of both bacteriochlorophyll and chlorophyll under anaerobic conditions (a separate enzyme, AcsF, acts under aerobic conditions). This model identifies two clades of sequences, one from photosynthetic, non-cyanobacterial bacteria and another including Synechocystis and several non-photosynthetic bacteria. The function of the Synechocystis gene is supported by gene clustering with other photosynthetic genes, so the purpose of the gene in the non-photosynthetic bacteria is uncertain. Note that homologs of this gene are not found in plants which rely solely on the aerobic cyclase.

>PF03328 HpcH_HpaI: HpcH/HpaI aldolase/citrate lyase family; InterPro: IPR005000 This family includes 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase (4

Probab=84.19  E-value=14  Score=26.91  Aligned_cols=75  Identities=19%  Similarity=0.191  Sum_probs=47.0

Q ss_pred             CCcccEEEEeCCCCC---------CCHHHHHHHHHhccCCCCCcEEEEeCCCChhhHHH---HHHhcCcccc-cCCCChh
Q 042079           76 GTKVNLVITDYCMPG---------MTGYELLKKIKESSVMKEVPVVVVSSENIPTRINE---CLEEGAQMFM-LKPLKPS  142 (153)
Q Consensus        76 ~~~~dlii~D~~~~~---------~~g~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~---a~~~ga~~~l-~KP~~~~  142 (153)
                      ...+|.|++|+.-..         .+-.++++.++.... ....+++=.+..+.....+   +++.|++.++ .|=-+.+
T Consensus        19 ~~g~D~vilDlEd~~~~~~K~~ar~~~~~~~~~~~~~~~-~~~~~~VRvn~~~~~~~~~Dl~~l~~g~~gI~lP~ves~~   97 (221)
T PF03328_consen   19 ASGADFVILDLEDGVPPDEKDEAREDLAEALRSIRAARA-AGSEIIVRVNSLDSPHIERDLEALDAGADGIVLPKVESAE   97 (221)
T ss_dssp             TTCSSEEEEESSTTSSGGGHHHHHHHHHHHHHHHHHHTT-SSSEEEEE-SSTTCHHHHHHHHHHHTTSSEEEETT--SHH
T ss_pred             hcCCCEEEEeCcccCCcccchhhHHHHHHHHHhhccccc-ccccceecCCCCCcchhhhhhhhcccCCCeeeccccCcHH
Confidence            357999999998876         444555555554221 2345665566556556666   8999999864 4445677


Q ss_pred             HHHHHHhhh
Q 042079          143 DVKKLTGHL  151 (153)
Q Consensus       143 ~l~~~~~~~  151 (153)
                      +++++...+
T Consensus        98 ~~~~~~~~~  106 (221)
T PF03328_consen   98 DARQAVAAL  106 (221)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            777766543

1.2 from EC) and 4-hydroxy-2-oxovalerate aldolase (4.1.2 from EC). ; GO: 0016830 carbon-carbon lyase activity, 0006725 cellular aromatic compound metabolic process; PDB: 1DXF_B 1DXE_A 3QZ6_A 3QLL_C 3QQW_F 3OYZ_A 3PUG_A 3OYX_A 1IZC_A 2V5K_B ....

>PF01081 Aldolase: KDPG and KHG aldolase; InterPro: IPR000887 4-Hydroxy-2-oxoglutarate aldolase (4

Probab=84.18  E-value=6  Score=28.66  Aligned_cols=63  Identities=13%  Similarity=0.232  Sum_probs=39.8

Q ss_pred             EEEeCCCCCCCHHHHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHH
Q 042079           82 VITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLT  148 (153)
Q Consensus        82 ii~D~~~~~~~g~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~  148 (153)
                      =++++.+...++++.++.+++..  +++ +|-...-.+.+...+|.+.|++ |+..|....++.+..
T Consensus        35 ~~iEiT~~t~~a~~~I~~l~~~~--p~~-~vGAGTV~~~e~a~~a~~aGA~-FivSP~~~~~v~~~~   97 (196)
T PF01081_consen   35 RAIEITLRTPNALEAIEALRKEF--PDL-LVGAGTVLTAEQAEAAIAAGAQ-FIVSPGFDPEVIEYA   97 (196)
T ss_dssp             -EEEEETTSTTHHHHHHHHHHHH--TTS-EEEEES--SHHHHHHHHHHT-S-EEEESS--HHHHHHH
T ss_pred             CEEEEecCCccHHHHHHHHHHHC--CCC-eeEEEeccCHHHHHHHHHcCCC-EEECCCCCHHHHHHH
Confidence            34566666677899999888754  443 4444445578888899999997 777776666665443

1.3.16 from EC) (KHG-aldolase) catalyzes the interconversion of 4-hydroxy-2-oxoglutarate into pyruvate and glyoxylate. Phospho-2-dehydro-3-deoxygluconate aldolase (4.1.2.14 from EC) (KDPG-aldolase) catalyzes the interconversion of 6-phospho-2-dehydro-3-deoxy-D-gluconate into pyruvate and glyceraldehyde 3-phosphate. These two enzymes are structurally and functionally related []. They are both homotrimeric proteins of approximately 220 amino-acid residues. They are class I aldolases whose catalytic mechanism involves the formation of a Schiff-base intermediate between the substrate and the epsilon-amino group of a lysine residue. In both enzymes, an arginine is required for catalytic activity.; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 3VCR_A 1FQ0_A 1EUN_A 1EUA_B 1FWR_A 2C0A_B 1WBH_A 1WAU_A 2YW3_B 2YW4_A ....

>cd04727 pdxS PdxS is a subunit of the pyridoxal 5'-phosphate (PLP) synthase, an important enzyme in deoxyxylulose 5-phosphate (DXP)-independent pathway for de novo biosynthesis of PLP, present in some eubacteria, in archaea, fungi, plants, plasmodia, and some metazoa

Probab=84.13  E-value=7.2  Score=29.88  Aligned_cols=41  Identities=24%  Similarity=0.382  Sum_probs=32.4

Q ss_pred             CHHHHHHHHHhccCCCCCcEE--EEeCCCChhhHHHHHHhcCcccc
Q 042079           92 TGYELLKKIKESSVMKEVPVV--VVSSENIPTRINECLEEGAQMFM  135 (153)
Q Consensus        92 ~g~~~~~~lr~~~~~~~~pii--~~t~~~~~~~~~~a~~~ga~~~l  135 (153)
                      .++++++.+++..   .+|+|  ....-.+++....+++.|++.++
T Consensus       181 ~d~elLk~l~~~~---~iPVV~iAeGGI~Tpena~~v~e~GAdgVa  223 (283)
T cd04727         181 APYELVKETAKLG---RLPVVNFAAGGVATPADAALMMQLGADGVF  223 (283)
T ss_pred             CCHHHHHHHHHhc---CCCeEEEEeCCCCCHHHHHHHHHcCCCEEE
Confidence            4788899988743   58997  55555589999999999998874

Together with PdxT, PdxS forms the PLP synthase, a heteromeric glutamine amidotransferase (GATase), whereby PdxT produces ammonia from glutamine and PdxS combines ammonia with five- and three-carbon phosphosugars to form PLP. PLP is the biologically active form of vitamin B6, an essential cofactor in many biochemical processes. PdxS subunits form two hexameric rings.

>COG0352 ThiE Thiamine monophosphate synthase [Coenzyme metabolism]

Probab=83.59  E-value=15  Score=26.91  Aligned_cols=68  Identities=26%  Similarity=0.268  Sum_probs=50.0

Q ss_pred             EEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCC-------CCCHHHHHHHHHhccCCCCCcEEEEeCCCCh
Q 042079           48 TTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMP-------GMTGYELLKKIKESSVMKEVPVVVVSSENIP  120 (153)
Q Consensus        48 ~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~-------~~~g~~~~~~lr~~~~~~~~pii~~t~~~~~  120 (153)
                      .++++.+++.+...               ..+|.|.+.--.|       ...|++.++++++..   .+|++.+.+- +.
T Consensus       109 ~S~h~~eea~~A~~---------------~g~DYv~~GpifpT~tK~~~~~~G~~~l~~~~~~~---~iP~vAIGGi-~~  169 (211)
T COG0352         109 LSTHDLEEALEAEE---------------LGADYVGLGPIFPTSTKPDAPPLGLEGLREIRELV---NIPVVAIGGI-NL  169 (211)
T ss_pred             eecCCHHHHHHHHh---------------cCCCEEEECCcCCCCCCCCCCccCHHHHHHHHHhC---CCCEEEEcCC-CH
Confidence            35667777766542               3489999875443       346899999998753   4899988875 67


Q ss_pred             hhHHHHHHhcCccc
Q 042079          121 TRINECLEEGAQMF  134 (153)
Q Consensus       121 ~~~~~a~~~ga~~~  134 (153)
                      +.+.+.++.|++..
T Consensus       170 ~nv~~v~~~Ga~gV  183 (211)
T COG0352         170 ENVPEVLEAGADGV  183 (211)
T ss_pred             HHHHHHHHhCCCeE
Confidence            77889999998764

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

Probab=83.32  E-value=1.8  Score=31.11  Aligned_cols=31  Identities=13%  Similarity=0.090  Sum_probs=27.4

Q ss_pred             EEEEeCCHHHHHHHHHHHHhcCcEEEEecCH
Q 042079           23 VLAVDDSIVDRKIVENLLKNSACKVTTAENG   53 (153)
Q Consensus        23 iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~   53 (153)
                      ||+||.+..+-..+..+|++.|+++......
T Consensus         2 il~idn~dsft~nl~~~l~~~g~~v~v~~~~   32 (195)
T PRK07649          2 ILMIDNYDSFTFNLVQFLGELGQELVVKRND   32 (195)
T ss_pred             EEEEeCCCccHHHHHHHHHHCCCcEEEEeCC
Confidence            8999999999999999999999888777655

>PRK06843 inosine 5-monophosphate dehydrogenase; Validated

Probab=83.22  E-value=5.1  Score=32.31  Aligned_cols=56  Identities=18%  Similarity=0.222  Sum_probs=42.3

Q ss_pred             CcccEEEEeCCCCC-CCHHHHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccc
Q 042079           77 TKVNLVITDYCMPG-MTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFM  135 (153)
Q Consensus        77 ~~~dlii~D~~~~~-~~g~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l  135 (153)
                      ..+|+|.+|...+. ..-.++++++|+..  +++++| +..-.+.+....+.+.|+|...
T Consensus       164 aGvDvI~iD~a~g~~~~~~~~v~~ik~~~--p~~~vi-~g~V~T~e~a~~l~~aGaD~I~  220 (404)
T PRK06843        164 AHVDILVIDSAHGHSTRIIELVKKIKTKY--PNLDLI-AGNIVTKEAALDLISVGADCLK  220 (404)
T ss_pred             cCCCEEEEECCCCCChhHHHHHHHHHhhC--CCCcEE-EEecCCHHHHHHHHHcCCCEEE
Confidence            46899999998874 45678899998754  566644 5455678888899999998764

>COG0159 TrpA Tryptophan synthase alpha chain [Amino acid transport and metabolism]

Probab=83.00  E-value=5.4  Score=30.27  Aligned_cols=53  Identities=21%  Similarity=0.393  Sum_probs=35.1

Q ss_pred             CHHHHHHHHHhccCCCCCcEEEEeCCCC------hhhHHHHHHhcCcccccCCCChhHHHH
Q 042079           92 TGYELLKKIKESSVMKEVPVVVVSSENI------PTRINECLEEGAQMFMLKPLKPSDVKK  146 (153)
Q Consensus        92 ~g~~~~~~lr~~~~~~~~pii~~t~~~~------~~~~~~a~~~ga~~~l~KP~~~~~l~~  146 (153)
                      +-+++++.+|+..  ..+|+++++-.+.      +....++.+.|++++|.-.+.+++-.+
T Consensus        80 ~~lel~~~~r~~~--~~~Pivlm~Y~Npi~~~Gie~F~~~~~~~GvdGlivpDLP~ee~~~  138 (265)
T COG0159          80 DTLELVEEIRAKG--VKVPIVLMTYYNPIFNYGIEKFLRRAKEAGVDGLLVPDLPPEESDE  138 (265)
T ss_pred             HHHHHHHHHHhcC--CCCCEEEEEeccHHHHhhHHHHHHHHHHcCCCEEEeCCCChHHHHH
Confidence            3456666677544  5788888876542      334567788888888887666666544

>PRK06774 para-aminobenzoate synthase component II; Provisional

Probab=82.91  E-value=3.4  Score=29.40  Aligned_cols=31  Identities=13%  Similarity=0.045  Sum_probs=27.1

Q ss_pred             EEEEeCCHHHHHHHHHHHHhcCcEEEEecCH
Q 042079           23 VLAVDDSIVDRKIVENLLKNSACKVTTAENG   53 (153)
Q Consensus        23 iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~   53 (153)
                      ||+||....+-..+..+|+..|+++..+.+.
T Consensus         2 il~id~~dsf~~nl~~~l~~~~~~~~v~~~~   32 (191)
T PRK06774          2 LLLIDNYDSFTYNLYQYFCELGTEVMVKRND   32 (191)
T ss_pred             EEEEECCCchHHHHHHHHHHCCCcEEEEeCC
Confidence            8999999999999999999989888877754

>KOG1562 consensus Spermidine synthase [Amino acid transport and metabolism]

Probab=82.87  E-value=11  Score=29.29  Aligned_cols=64  Identities=17%  Similarity=0.148  Sum_probs=46.3

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhc--CcE----EEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNS--ACK----VTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGY   94 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~--~~~----v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~   94 (153)
                      -.|++++-+....+.-.+++...  ||+    .....++...++.+              ...++|+||+|.+-|.+.+.
T Consensus       146 e~i~~~eiD~~Vie~sk~y~p~la~gy~~~~v~l~iGDG~~fl~~~--------------~~~~~dVii~dssdpvgpa~  211 (337)
T KOG1562|consen  146 ENILLCEIDENVIESSKQYLPTLACGYEGKKVKLLIGDGFLFLEDL--------------KENPFDVIITDSSDPVGPAC  211 (337)
T ss_pred             cceeeehhhHHHHHHHHHHhHHHhcccCCCceEEEeccHHHHHHHh--------------ccCCceEEEEecCCccchHH
Confidence            46899999988888877777753  442    23444777666655              24679999999999998887


Q ss_pred             HHHH
Q 042079           95 ELLK   98 (153)
Q Consensus        95 ~~~~   98 (153)
                      .+..
T Consensus       212 ~lf~  215 (337)
T KOG1562|consen  212 ALFQ  215 (337)
T ss_pred             HHHH
Confidence            6554

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

Probab=82.73  E-value=14  Score=25.99  Aligned_cols=95  Identities=19%  Similarity=0.162  Sum_probs=60.0

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHh----cC--c-EEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKN----SA--C-KVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTG   93 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~----~~--~-~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g   93 (153)
                      ..+||-|+|......+...++.    .+  . ....+++.+++.+.+.               ..+|+|++|-..| .+-
T Consensus        51 d~ili~~nHi~~~g~i~~av~~~~~~~~~~~~I~VEv~~~ee~~ea~~---------------~g~d~I~lD~~~~-~~~  114 (169)
T PF01729_consen   51 DMILIKDNHIAFFGGIEEAVKAARQAAPEKKKIEVEVENLEEAEEALE---------------AGADIIMLDNMSP-EDL  114 (169)
T ss_dssp             SSEEE-HHHHHHHSSHHHHHHHHHHHSTTTSEEEEEESSHHHHHHHHH---------------TT-SEEEEES-CH-HHH
T ss_pred             CcEEehHHHHHHhCCHHHHHHHHHHhCCCCceEEEEcCCHHHHHHHHH---------------hCCCEEEecCcCH-HHH
Confidence            3478888887766545544432    22  2 3456888888888773               4589999997544 233


Q ss_pred             HHHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCccc
Q 042079           94 YELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMF  134 (153)
Q Consensus        94 ~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~  134 (153)
                      -++++.++...  ++ ..|.+++.-+.+.+.+..+.|+|.+
T Consensus       115 ~~~v~~l~~~~--~~-v~ie~SGGI~~~ni~~ya~~gvD~i  152 (169)
T PF01729_consen  115 KEAVEELRELN--PR-VKIEASGGITLENIAEYAKTGVDVI  152 (169)
T ss_dssp             HHHHHHHHHHT--TT-SEEEEESSSSTTTHHHHHHTT-SEE
T ss_pred             HHHHHHHhhcC--Cc-EEEEEECCCCHHHHHHHHhcCCCEE
Confidence            44555555543  34 5667888788888888889998765

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 ....

>KOG4175 consensus Tryptophan synthase alpha chain [Amino acid transport and metabolism]

Probab=82.55  E-value=4.8  Score=29.46  Aligned_cols=43  Identities=21%  Similarity=0.420  Sum_probs=33.8

Q ss_pred             CCCcEEEEeCCC------ChhhHHHHHHhcCcccccCCCChhHHHHHHh
Q 042079          107 KEVPVVVVSSEN------IPTRINECLEEGAQMFMLKPLKPSDVKKLTG  149 (153)
Q Consensus       107 ~~~pii~~t~~~------~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~  149 (153)
                      -.+|||+++-+.      ....++.+.+.|+++|+.-.+.++|-..+=+
T Consensus        94 vt~PIiLmgYYNPIl~yG~e~~iq~ak~aGanGfiivDlPpEEa~~~Rn  142 (268)
T KOG4175|consen   94 VTCPIILMGYYNPILRYGVENYIQVAKNAGANGFIIVDLPPEEAETLRN  142 (268)
T ss_pred             cccceeeeecccHHHhhhHHHHHHHHHhcCCCceEeccCChHHHHHHHH
Confidence            468999987653      4667788999999999999888888765433

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

Probab=82.13  E-value=11  Score=27.33  Aligned_cols=61  Identities=8%  Similarity=0.231  Sum_probs=33.7

Q ss_pred             EEeCCCCCCCHHHHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHH
Q 042079           83 ITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKL  147 (153)
Q Consensus        83 i~D~~~~~~~g~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~  147 (153)
                      .+++.+.....++.++++++..  ++ -+|=...-.+.+...++.+.|++ |+..|....++.+.
T Consensus        32 ~iEit~~tp~a~~~I~~l~~~~--~~-~~vGAGTVl~~e~a~~ai~aGA~-FivSP~~~~~vi~~   92 (201)
T PRK06015         32 AIEITLRTPAALDAIRAVAAEV--EE-AIVGAGTILNAKQFEDAAKAGSR-FIVSPGTTQELLAA   92 (201)
T ss_pred             EEEEeCCCccHHHHHHHHHHHC--CC-CEEeeEeCcCHHHHHHHHHcCCC-EEECCCCCHHHHHH
Confidence            3444445555677777776543  23 12223333456666777777776 66666555555443

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

Probab=82.05  E-value=17  Score=26.39  Aligned_cols=71  Identities=21%  Similarity=0.303  Sum_probs=48.1

Q ss_pred             EEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCC-------CCCCCHHHHHHHHHhccCCCCCcEEEEeCCCCh
Q 042079           48 TTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYC-------MPGMTGYELLKKIKESSVMKEVPVVVVSSENIP  120 (153)
Q Consensus        48 ~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~-------~~~~~g~~~~~~lr~~~~~~~~pii~~t~~~~~  120 (153)
                      ..+.+..++....               ...+|++.+...       ......++.++.+++..   ++|++...+-.+.
T Consensus       128 v~v~t~~ea~~a~---------------~~G~d~i~~~~~g~t~~~~~~~~~~~~~l~~i~~~~---~ipvia~GGI~~~  189 (219)
T cd04729         128 ADISTLEEALNAA---------------KLGFDIIGTTLSGYTEETAKTEDPDFELLKELRKAL---GIPVIAEGRINSP  189 (219)
T ss_pred             EECCCHHHHHHHH---------------HcCCCEEEccCccccccccCCCCCCHHHHHHHHHhc---CCCEEEeCCCCCH
Confidence            3556677765544               235788765321       11223578889888743   6899887777788


Q ss_pred             hhHHHHHHhcCccccc
Q 042079          121 TRINECLEEGAQMFML  136 (153)
Q Consensus       121 ~~~~~a~~~ga~~~l~  136 (153)
                      +...++++.|++.++.
T Consensus       190 ~~~~~~l~~GadgV~v  205 (219)
T cd04729         190 EQAAKALELGADAVVV  205 (219)
T ss_pred             HHHHHHHHCCCCEEEE
Confidence            9999999999988754

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.

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

Probab=81.94  E-value=9.1  Score=29.39  Aligned_cols=51  Identities=22%  Similarity=0.335  Sum_probs=37.2

Q ss_pred             CHHHHHHHHHhccCCCCCcEE--EEeCCCChhhHHHHHHhcCcccc-----cCCCChhHHH
Q 042079           92 TGYELLKKIKESSVMKEVPVV--VVSSENIPTRINECLEEGAQMFM-----LKPLKPSDVK  145 (153)
Q Consensus        92 ~g~~~~~~lr~~~~~~~~pii--~~t~~~~~~~~~~a~~~ga~~~l-----~KP~~~~~l~  145 (153)
                      .++++++++++..   .+|+|  ...+-.+++....+++.|++.++     .|.-++.+..
T Consensus       184 ~~~elLkei~~~~---~iPVV~fAiGGI~TPedAa~~melGAdGVaVGSaI~ks~dP~~~a  241 (287)
T TIGR00343       184 VPVELLLEVLKLG---KLPVVNFAAGGVATPADAALMMQLGADGVFVGSGIFKSSNPEKLA  241 (287)
T ss_pred             CCHHHHHHHHHhC---CCCEEEeccCCCCCHHHHHHHHHcCCCEEEEhHHhhcCCCHHHHH
Confidence            5789999988743   68998  55555689999999999998873     3433455543

This protein had been believed to be a singlet oxygen resistance protein. Subsequent work showed that it is a protein of pyridoxine (vitamin B6) biosynthesis, and that pyridoxine quenches the highly toxic singlet form of oxygen produced by light in the presence of certain chemicals.

>PRK05458 guanosine 5'-monophosphate oxidoreductase; Provisional

Probab=81.94  E-value=5.1  Score=31.36  Aligned_cols=55  Identities=16%  Similarity=0.203  Sum_probs=40.9

Q ss_pred             cccEEEEeCCCCCC-CHHHHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccc
Q 042079           78 KVNLVITDYCMPGM-TGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFM  135 (153)
Q Consensus        78 ~~dlii~D~~~~~~-~g~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l  135 (153)
                      .+|+|.+|+..+.. ...+++++||+..  +.+|+|. ..-.+.+....+.+.|++...
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 TPEYITIDIAHGHSDSVINMIQHIKKHL--PETFVIA-GNVGTPEAVRELENAGADATK  166 (326)
T ss_pred             CCCEEEEECCCCchHHHHHHHHHHHhhC--CCCeEEE-EecCCHHHHHHHHHcCcCEEE
Confidence            35999999988754 4678899998754  4566654 223477888899999999864

>PRK06096 molybdenum transport protein ModD; Provisional

Probab=81.80  E-value=11  Score=29.03  Aligned_cols=95  Identities=11%  Similarity=0.127  Sum_probs=58.1

Q ss_pred             eEEEEeCCHHHHH-------HHHHHHHhcC--cEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCC
Q 042079           22 HVLAVDDSIVDRK-------IVENLLKNSA--CKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMT   92 (153)
Q Consensus        22 ~iLiidd~~~~~~-------~l~~~l~~~~--~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~   92 (153)
                      .+||-|+|.....       .++.+-+..+  .....+.+.+++.+.+.               ..+|+|++|- |+...
T Consensus       159 ~vLikdNHi~~~g~~~~i~~av~~~r~~~~~~kIeVEv~tleqa~ea~~---------------agaDiI~LDn-~~~e~  222 (284)
T PRK06096        159 TILLFANHRHFLHDPQDWSGAINQLRRHAPEKKIVVEADTPKEAIAALR---------------AQPDVLQLDK-FSPQQ  222 (284)
T ss_pred             hhhhHHHHHHHhCCcccHHHHHHHHHHhCCCCCEEEECCCHHHHHHHHH---------------cCCCEEEECC-CCHHH
Confidence            3677777765443       2222222222  23456789999888873               4589999994 43333


Q ss_pred             HHHHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccc
Q 042079           93 GYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFM  135 (153)
Q Consensus        93 g~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l  135 (153)
                      --+..+.+++..  ++ ..+-.++.-+.+.+.+....|+|-+.
T Consensus       223 l~~av~~~~~~~--~~-~~leaSGGI~~~ni~~yA~tGvD~Is  262 (284)
T PRK06096        223 ATEIAQIAPSLA--PH-CTLSLAGGINLNTLKNYADCGIRLFI  262 (284)
T ss_pred             HHHHHHHhhccC--CC-eEEEEECCCCHHHHHHHHhcCCCEEE
Confidence            344455554322  23 35667777788888888889987653

>PF00290 Trp_syntA: Tryptophan synthase alpha chain; InterPro: IPR002028 Tryptophan synthase (4

Probab=81.19  E-value=3.6  Score=31.10  Aligned_cols=55  Identities=24%  Similarity=0.457  Sum_probs=38.7

Q ss_pred             HHHHHHHHHhccCCCCCcEEEEeCCCC------hhhHHHHHHhcCcccccCCCChhHHHHHHh
Q 042079           93 GYELLKKIKESSVMKEVPVVVVSSENI------PTRINECLEEGAQMFMLKPLKPSDVKKLTG  149 (153)
Q Consensus        93 g~~~~~~lr~~~~~~~~pii~~t~~~~------~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~  149 (153)
                      .+++++++|+..  .++|+++++-.+.      +....+|.+.|+++++.-.+.+++-.+...
T Consensus        74 ~~~~~~~ir~~~--~~~pivlm~Y~N~i~~~G~e~F~~~~~~aGvdGlIipDLP~ee~~~~~~  134 (259)
T PF00290_consen   74 IFELVKEIRKKE--PDIPIVLMTYYNPIFQYGIERFFKEAKEAGVDGLIIPDLPPEESEELRE  134 (259)
T ss_dssp             HHHHHHHHHHHC--TSSEEEEEE-HHHHHHH-HHHHHHHHHHHTEEEEEETTSBGGGHHHHHH
T ss_pred             HHHHHHHHhccC--CCCCEEEEeeccHHhccchHHHHHHHHHcCCCEEEEcCCChHHHHHHHH
Confidence            466777888433  5889999987432      345677888999999998877776655443

2.1.20 from EC) catalyzes the last step in the biosynthesis of tryptophan [, ]: L-serine + 1-(indol-3-yl)glycerol 3-phosphate = L-tryptophan + glyceraldehyde 3-phosphate + H2O It has two functional domains, each found in bacteria and plants on a separate subunit. In Escherichia coli, the 2 subunits, A and B, are encoded by the trpA and trpB genes respectively. The alpha chain is for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3-phosphate and the beta chain IPR006653 from INTERPRO is for the synthesis of tryptophan from indole and serine. In fungi the two domains are fused together in a single multifunctional protein, in the order: (NH2-A-B-COOH) [, ]. The two domains of the Neurospora crassa polypeptide are linked by a connector of 54-amino acid residues that has less than 25% identity to the 45-residue connector of the Saccharomyces cerevisiae (Baker's yeast) polypeptide. Two acidic residues are believed to serve as proton donors/acceptors in the enzyme's catalytic mechanism.; GO: 0004834 tryptophan synthase activity, 0006568 tryptophan metabolic process; PDB: 1TJR_B 1RD5_B 1K8X_A 1QOQ_A 1KFE_A 1KFB_A 2CLO_A 1TTP_A 2RH9_A 1K7F_A ....

>TIGR01579 MiaB-like-C MiaB-like tRNA modifying enzyme

Probab=81.11  E-value=23  Score=28.46  Aligned_cols=70  Identities=11%  Similarity=0.192  Sum_probs=41.5

Q ss_pred             cccEEEEeCCCCCC----CHHHHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhh
Q 042079           78 KVNLVITDYCMPGM----TGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGH  150 (153)
Q Consensus        78 ~~dlii~D~~~~~~----~g~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~  150 (153)
                      .+|+|++.......    ...+.++++++..  +..+|| +++........++.+....+++..+-....+.+++..
T Consensus        33 ~aD~v~intctv~~~a~~~~~~~i~~~k~~~--p~~~vv-vgGc~a~~~~ee~~~~~~vD~vv~~e~~~~~~~ll~~  106 (414)
T TIGR01579        33 KADVYIINTCTVTAKADSKARRAIRRARRQN--PTAKII-VTGCYAQSNPKELADLKDVDLVLGNKEKDKINKLLSL  106 (414)
T ss_pred             cCCEEEEeccccchHHHHHHHHHHHHHHhhC--CCcEEE-EECCccccCHHHHhcCCCCcEEECCCCHHHHHHHHHH
Confidence            47999998655443    3677788887643  455554 5443333333444455455677777666666666543

This clade is a member of a subfamily (TIGR00089) and spans low GC Gram positive bacteria, alpha and epsilon proteobacteria, Campylobacter, Porphyromonas, Aquifex, Thermotoga, Chlamydia, Treponema and Fusobacterium.

>PLN02335 anthranilate synthase

Probab=80.96  E-value=12  Score=27.46  Aligned_cols=81  Identities=16%  Similarity=0.123  Sum_probs=47.1

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCC--CCCCHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCM--PGMTGYEL   96 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~--~~~~g~~~   96 (153)
                      .+.+||+||........+.++|++.|+.+..+......++.+.              ...||.||+--..  |...+ ..
T Consensus        17 ~~~~ilviD~~dsft~~i~~~L~~~g~~~~v~~~~~~~~~~~~--------------~~~~d~iVisgGPg~p~d~~-~~   81 (222)
T PLN02335         17 QNGPIIVIDNYDSFTYNLCQYMGELGCHFEVYRNDELTVEELK--------------RKNPRGVLISPGPGTPQDSG-IS   81 (222)
T ss_pred             ccCcEEEEECCCCHHHHHHHHHHHCCCcEEEEECCCCCHHHHH--------------hcCCCEEEEcCCCCChhhcc-ch
Confidence            4568999998777778889999988987776654211122121              1246777764322  22122 12


Q ss_pred             HHHHHhccCCCCCcEEEEeC
Q 042079           97 LKKIKESSVMKEVPVVVVSS  116 (153)
Q Consensus        97 ~~~lr~~~~~~~~pii~~t~  116 (153)
                      .+.++...  ..+|++-+.-
T Consensus        82 ~~~~~~~~--~~~PiLGICl   99 (222)
T PLN02335         82 LQTVLELG--PLVPLFGVCM   99 (222)
T ss_pred             HHHHHHhC--CCCCEEEecH
Confidence            44444322  3679877763

>PRK09490 metH B12-dependent methionine synthase; Provisional

Probab=80.49  E-value=21  Score=33.08  Aligned_cols=85  Identities=12%  Similarity=0.151  Sum_probs=58.7

Q ss_pred             CCeEEEE----eCCHHHHHHHHHHHHhcCcEEEEec---CHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCC-
Q 042079           20 PPHVLAV----DDSIVDRKIVENLLKNSACKVTTAE---NGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGM-   91 (153)
Q Consensus        20 ~~~iLii----dd~~~~~~~l~~~l~~~~~~v~~~~---~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~-   91 (153)
                      ..+|++.    |-|..=.+.+..+|+..||+|.-..   ..++.++.+              ..+++|+|.+...|... 
T Consensus       751 ~gkvvlaTv~GDvHDIGkniV~~~L~~~GfeVIdLG~~vp~e~iv~aa--------------~e~~~diVgLS~L~t~s~  816 (1229)
T PRK09490        751 NGKILMATVKGDVHDIGKNIVGVVLQCNNYEVIDLGVMVPAEKILETA--------------KEENADIIGLSGLITPSL  816 (1229)
T ss_pred             CCeEEEEeCCCCcchHHHHHHHHHHHhCCCEEEECCCCCCHHHHHHHH--------------HHhCCCEEEEcCcchhhH
Confidence            4567777    7788878888888999999987544   334444444              24679999998877643 


Q ss_pred             -CHHHHHHHHHhccCCCCCcEEEEeCCCCh
Q 042079           92 -TGYELLKKIKESSVMKEVPVVVVSSENIP  120 (153)
Q Consensus        92 -~g~~~~~~lr~~~~~~~~pii~~t~~~~~  120 (153)
                       ...++++.|++..  ..+||++-.+..+.
T Consensus       817 ~~m~~~i~~L~~~g--~~v~v~vGGa~~s~  844 (1229)
T PRK09490        817 DEMVHVAKEMERQG--FTIPLLIGGATTSK  844 (1229)
T ss_pred             HHHHHHHHHHHhcC--CCCeEEEEeeccch
Confidence             3566788888764  47787765554444

>cd00564 TMP_TenI Thiamine monophosphate synthase (TMP synthase)/TenI

Probab=80.11  E-value=17  Score=25.25  Aligned_cols=55  Identities=31%  Similarity=0.398  Sum_probs=39.5

Q ss_pred             CcccEEEEeCCCCC--------CCHHHHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccc
Q 042079           77 TKVNLVITDYCMPG--------MTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFM  135 (153)
Q Consensus        77 ~~~dlii~D~~~~~--------~~g~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l  135 (153)
                      ..+|+|++....|.        ..+++.++++++.   .++|+++..+- +.+.+.++...|++.+.
T Consensus       114 ~g~d~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~pv~a~GGi-~~~~i~~~~~~Ga~~i~  176 (196)
T cd00564         114 LGADYVGFGPVFPTPTKPGAGPPLGLELLREIAEL---VEIPVVAIGGI-TPENAAEVLAAGADGVA  176 (196)
T ss_pred             cCCCEEEECCccCCCCCCCCCCCCCHHHHHHHHHh---CCCCEEEECCC-CHHHHHHHHHcCCCEEE
Confidence            35899988754432        3467888888764   36888877665 56778889999998763

TMP synthase catalyzes an important step in the thiamine biosynthesis pathway, the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5- (beta-hydroxyethyl) thiazole phosphate to yield thiamine phosphate. TenI is a enzymatically inactive regulatory protein involved in the regulation of several extracellular enzymes. This superfamily also contains other enzymatically inactive proteins with unknown functions.

>TIGR02082 metH 5-methyltetrahydrofolate--homocysteine methyltransferase

Probab=80.03  E-value=31  Score=31.91  Aligned_cols=100  Identities=11%  Similarity=0.147  Sum_probs=65.3

Q ss_pred             CCeEEEE----eCCHHHHHHHHHHHHhcCcEEEEec---CHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCC-
Q 042079           20 PPHVLAV----DDSIVDRKIVENLLKNSACKVTTAE---NGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGM-   91 (153)
Q Consensus        20 ~~~iLii----dd~~~~~~~l~~~l~~~~~~v~~~~---~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~-   91 (153)
                      ..+|++.    |-|.+=.+.+..+|+..||+|.-..   ..++.++.+              ..+++|+|-+...|... 
T Consensus       732 ~gkVvlaTV~GDvHDIGKnIV~~~L~~~GfeVIdLG~dVp~e~iv~aa--------------~e~~~diVgLS~Lmt~t~  797 (1178)
T TIGR02082       732 KGKIVLATVKGDVHDIGKNIVGVVLSCNGYEVVDLGVMVPIEKILEAA--------------KDHNADVIGLSGLITPSL  797 (1178)
T ss_pred             CCeEEEEecCCCccHHHHHHHHHHHHhCCCEEEECCCCCCHHHHHHHH--------------HHhCCCEEEEcCcccccH
Confidence            4567777    6677777888888999999987544   234444444              24679999998877643 


Q ss_pred             -CHHHHHHHHHhccCCCCCcEEEEeCCCChhhHHHH---HHhcCcccc
Q 042079           92 -TGYELLKKIKESSVMKEVPVVVVSSENIPTRINEC---LEEGAQMFM  135 (153)
Q Consensus        92 -~g~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a---~~~ga~~~l  135 (153)
                       ...+.++.|++..  .++||++=....+......-   ...|++.|-
T Consensus       798 ~~m~~vi~~L~~~g--~~v~v~vGGa~~s~~~~~~~i~~~~~gad~y~  843 (1178)
T TIGR02082       798 DEMKEVAEEMNRRG--ITIPLLIGGAATSKTHTAVKIAPIYKGPVVYV  843 (1178)
T ss_pred             HHHHHHHHHHHhcC--CCceEEEeccccchhHHHhhhhhhccCCeEEe
Confidence             3466788888765  46777765555455544321   122777664

S-methyltransferase (MetE, EC 2.1.1.14, the cobalamin-independent methionine synthase) and betaine-homocysteine methyltransferase.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	153
3dge_C	122	Structure Of A Histidine Kinase-response Regulator		2e-07
3myy_A	128	Structure Of E. Coli Chey Mutant A113p Bound To Ber		2e-06
3gl9_A	122	The Structure Of A Histidine Kinase-Response Regula		2e-06
3oo0_A	129	Structure Of Apo Chey A113p Length = 129		2e-06
1ymv_A	129	Signal Transduction Protein Chey Mutant With Phe 14		5e-06
3fgz_A	128	Crystal Structure Of Chey Triple Mutant F14e, N59m,		6e-06
3f7n_A	128	Crystal Structure Of Chey Triple Mutant F14e, N59m,		6e-06
1ymu_A	130	Signal Transduction Protein Chey Mutant With Met 17		7e-06
1udr_A	129	Chey Mutant With Lys 91 Replaced By Asp, Lys 92 Rep		8e-06
3to5_A	134	High Resolution Structure Of Chey3 From Vibrio Chol		8e-06
3ffw_A	128	Crystal Structure Of Chey Triple Mutant F14q, N59k,		9e-06
3ffx_A	128	Crystal Structure Of Chey Triple Mutant F14e, N59r,		1e-05
3fft_A	128	Crystal Structure Of Chey Double Mutant F14e, E89r		1e-05
1jbe_A	128	1.08 A Structure Of Apo-Chey Reveals Meta-Active Co		1e-05
3rvj_A	132	Structure Of The Chey-Bef3 Complex With Substitutio		1e-05
1ab6_A	125	Structure Of Chey Mutant F14n, V86t Length = 125		1e-05
3rvn_A	132	Structure Of The Chey-Bef3 Complex With Substitutio		1e-05
2fka_A	129	Crystal Structure Of Mg(2+) And Bef(3)(-)-Bound Che		1e-05
3rvl_A	132	Structure Of The Chey-Bef3 Complex With Substitutio		1e-05
1mih_A	129	A Role For Chey Glu 89 In Chez-Mediated Dephosphory		1e-05
1eay_A	128	Chey-Binding (P2) Domain Of Chea In Complex With Ch		1e-05
3rvp_A	132	Structure Of The Chey-Bef3 Complex With Substitutio		1e-05
1cye_A	129	Three Dimensional Structure Of Chemotactic Che Y Pr		2e-05
2che_A	128	Structure Of The Mg2+-Bound Form Of Chey And Mechan		2e-05
1cey_A	128	Assignments, Secondary Structure, Global Fold, And		2e-05
1djm_A	129	Solution Structure Of Bef3-Activated Chey From Esch		2e-05
5chy_A	128	Structure Of Chemotaxis Protein Chey Length = 128		2e-05
3olx_A	129	Structural And Functional Effects Of Substitution A		2e-05
3olw_A	129	Structural And Functional Effects Of Substitution A		2e-05
3oly_A	129	Structural And Functional Effects Of Substitution A		2e-05
1vlz_A	128	Uncoupled Phosphorylation And Activation In Bacteri		2e-05
3olv_A	129	Structural And Functional Effects Of Substitution A		2e-05
6chy_A	128	Structure Of Chemotaxis Protein Chey Length = 128		2e-05
3gt7_A	154	Crystal Structure Of Signal Receiver Domain Of Sign		2e-05
1d4z_A	128	Crystal Structure Of Chey-95iv, A Hyperactive Chey		2e-05
3h1g_A	129	Crystal Structure Of Chey Mutant T84a Of Helicobact		3e-05
3gwg_A	129	Crystal Structure Of Chey Of Helicobacter Pylori Le		4e-05
2chy_A	128	Three-Dimensional Structure Of Chey, The Response R		4e-05
1ab5_A	125	Structure Of Chey Mutant F14n, V21t Length = 125		5e-05
1ehc_A	128	Structure Of Signal Transduction Protein Chey Lengt		1e-04
1c4w_A	128	1.9 A Structure Of A-Thiophosphonate Modified Chey		1e-04
1zdm_A	129	Crystal Structure Of Activated Chey Bound To Xe Len		1e-04
1e6m_A	128	Two-Component Signal Transduction System D57a Mutan		1e-04
1e6k_A	130	Two-Component Signal Transduction System D12a Mutan		1e-04
1e6l_A	127	Two-Component Signal Transduction System D13a Mutan		1e-04
2id7_A	128	1.75 A Structure Of T87i Phosphono-Chey Length = 12		1e-04
2id9_A	128	1.85 A Structure Of T87iY106W PHOSPHONO-Chey Length		2e-04
3h1f_A	129	Crystal Structure Of Chey Mutant D53a Of Helicobact		3e-04

>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 = 51.2 bits (121), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 44/131 (33%), Positives = 56/131 (42%), Gaps = 14/131 (10%)
Query: 23  VLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLV 82
           VL VDDS V RKIV   LK    +V  AENG  ALE L             S  T  +L+
Sbjct: 5   VLLVDDSAVLRKIVSFNLKKEGYEVIEAENGQIALEKL-------------SEFTP-DLI 50
Query: 83  ITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLKPLKPS 142
           + D  MP M G+ +LKK++                      +  L  GA+  M KP  PS
Sbjct: 51  VLDIMMPVMDGFTVLKKLQEKEEWKRIPVIVLTAKGGEEDESLALSLGARKVMRKPFSPS 110
Query: 143 DVKKLTGHLIN 153
              +   HL+N
Sbjct: 111 QFIEEVKHLLN 121

>pdb|3MYY|A Chain A, Structure Of E. Coli Chey Mutant A113p Bound To Beryllium Fluoride Length = 128

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 39/129 (30%), Positives = 54/129 (41%), Gaps = 15/129 (11%)
Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
           K    L VDD    R+IV NLLK      V  AE+G+ AL            N L + G 
Sbjct: 3   KELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDAL------------NKLQAGG- 49
Query: 78  KVNLVITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLK 137
               VI+D+ MP M G ELLK I+                     I    + GA  +++K
Sbjct: 50  -YGFVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVK 108
Query: 138 PLKPSDVKK 146
           P  P+ +++
Sbjct: 109 PFTPATLEE 117

>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 = 48.1 bits (113), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 43/131 (32%), Positives = 55/131 (41%), Gaps = 14/131 (10%)
Query: 23  VLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLV 82
           VL VDDS V RKIV   LK    +V  AENG  ALE L             S  T  +L+
Sbjct: 5   VLLVDDSAVLRKIVSFNLKKEGYEVIEAENGQIALEKL-------------SEFTP-DLI 50
Query: 83  ITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLKPLKPS 142
           +    MP M G+ +LKK++                      +  L  GA+  M KP  PS
Sbjct: 51  VLXIMMPVMDGFTVLKKLQEKEEWKRIPVIVLTAKGGEEDESLALSLGARKVMRKPFSPS 110
Query: 143 DVKKLTGHLIN 153
              +   HL+N
Sbjct: 111 QFIEEVKHLLN 121

>pdb|3OO0|A Chain A, Structure Of Apo Chey A113p Length = 129

Iteration: 1
 Score = 48.1 bits (113), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 39/129 (30%), Positives = 54/129 (41%), Gaps = 15/129 (11%)
Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
           K    L VDD    R+IV NLLK      V  AE+G+ AL            N L + G 
Sbjct: 4   KELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDAL------------NKLQAGG- 50
Query: 78  KVNLVITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLK 137
               VI+D+ MP M G ELLK I+                     I    + GA  +++K
Sbjct: 51  -YGFVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVK 109
Query: 138 PLKPSDVKK 146
           P  P+ +++
Sbjct: 110 PFTPATLEE 118

>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 = 46.6 bits (109), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 38/129 (29%), Positives = 53/129 (41%), Gaps = 15/129 (11%)
Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
           K    L VDD    R+IV NLLK      V  AE+G+ AL            N L + G 
Sbjct: 4   KELKFLVVDDGGTGRRIVRNLLKELGFNNVEEAEDGVDAL------------NKLQAGG- 50
Query: 78  KVNLVITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLK 137
               VI+D+ MP M G ELLK I+                     I    + GA  +++K
Sbjct: 51  -YGFVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVK 109
Query: 138 PLKPSDVKK 146
           P   + +++
Sbjct: 110 PFTAATLEE 118

>pdb|3FGZ|A Chain A, Crystal Structure Of Chey Triple Mutant F14e, N59m, E89r Complexed With Bef3- And Mn2+ Length = 128

Iteration: 1
 Score = 46.6 bits (109), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 38/129 (29%), Positives = 53/129 (41%), Gaps = 15/129 (11%)
Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
           K    L VDD    R+IV NLLK      V  AE+G+ AL            N L + G 
Sbjct: 3   KELKFLVVDDESTMRRIVRNLLKELGFNNVEEAEDGVDAL------------NKLQAGG- 49
Query: 78  KVNLVITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLK 137
               VI+D+ MP M G ELLK I+                     I    + GA  +++K
Sbjct: 50  -YGFVISDWMMPNMDGLELLKTIRADGAMSALPVLMVTARAKKENIIAAAQAGASGYVVK 108
Query: 138 PLKPSDVKK 146
           P   + +++
Sbjct: 109 PFTAATLEE 117

>pdb|3F7N|A Chain A, Crystal Structure Of Chey Triple Mutant F14e, N59m, E89l Complexed With Bef3- And Mn2+ Length = 128

Iteration: 1
 Score = 46.6 bits (109), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 38/129 (29%), Positives = 53/129 (41%), Gaps = 15/129 (11%)
Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
           K    L VDD    R+IV NLLK      V  AE+G+ AL            N L + G 
Sbjct: 3   KELKFLVVDDESTMRRIVRNLLKELGFNNVEEAEDGVDAL------------NKLQAGG- 49
Query: 78  KVNLVITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLK 137
               VI+D+ MP M G ELLK I+                     I    + GA  +++K
Sbjct: 50  -YGFVISDWMMPNMDGLELLKTIRADGAMSALPVLMVTALAKKENIIAAAQAGASGYVVK 108
Query: 138 PLKPSDVKK 146
           P   + +++
Sbjct: 109 PFTAATLEE 117

>pdb|1YMU|A Chain A, Signal Transduction Protein Chey Mutant With Met 17 Replaced By Gly (M17g) Length = 130

Iteration: 1
 Score = 46.2 bits (108), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 38/129 (29%), Positives = 53/129 (41%), Gaps = 15/129 (11%)
Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
           K    L VDD    R+IV NLLK      V  AE+G+ AL            N L + G 
Sbjct: 5   KELKFLVVDDFSTGRRIVRNLLKELGFNNVEEAEDGVDAL------------NKLQAGG- 51
Query: 78  KVNLVITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLK 137
               VI+D+ MP M G ELLK I+                     I    + GA  +++K
Sbjct: 52  -YGFVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVK 110
Query: 138 PLKPSDVKK 146
           P   + +++
Sbjct: 111 PFTAATLEE 119

>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 = 46.2 bits (108), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 38/129 (29%), Positives = 53/129 (41%), Gaps = 15/129 (11%)
Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
           K    L VDD    R+IV NLLK      V  AE+G+ AL            N L + G 
Sbjct: 4   KELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDAL------------NKLQAGG- 50
Query: 78  KVNLVITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLK 137
               VI+D+ MP M G ELLK I+                     I    + GA  +++K
Sbjct: 51  -YGFVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEADAENIKALAQAGASGYVVK 109
Query: 138 PLKPSDVKK 146
           P   + +++
Sbjct: 110 PFTAATLEE 118

>pdb|3TO5|A Chain A, High Resolution Structure Of Chey3 From Vibrio Cholerae Length = 134

Iteration: 1
 Score = 45.8 bits (107), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 35/125 (28%), Positives = 56/125 (44%), Gaps = 15/125 (12%)
Query: 23  VLAVDDSIVDRKIVENLLKNSACKVTT-AENGMRALEFLGLVDEQEQQNNLNSNGTKVNL 81
           +L VDD    R+IV+NLL++     T  A++G+ AL  L   D               + 
Sbjct: 15  ILIVDDFSTMRRIVKNLLRDLGFNNTQEADDGLTALPMLKKGD--------------FDF 60
Query: 82  VITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLKPLKP 141
           V+TD+ MPGM G +LLK I+                    +I E  + G   +++KP   
Sbjct: 61  VVTDWNMPGMQGIDLLKNIRADEELKHLPVLMITAEAKREQIIEAAQAGVNGYIVKPFTA 120
Query: 142 SDVKK 146
           + +K+
Sbjct: 121 ATLKE 125

>pdb|3FFW|A Chain A, Crystal Structure Of Chey Triple Mutant F14q, N59k, E89y Complexed With Bef3- And Mn2+ Length = 128

Iteration: 1
 Score = 45.8 bits (107), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 38/125 (30%), Positives = 50/125 (40%), Gaps = 15/125 (12%)
Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
           K    L VDD    R+IV NLLK      V  AE+G+ AL            N L + G 
Sbjct: 3   KELKFLVVDDQSTMRRIVRNLLKELGFNNVEEAEDGVDAL------------NKLQAGG- 49
Query: 78  KVNLVITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLK 137
               VI+D+ MP M G ELLK I+                     I    + GA  +++K
Sbjct: 50  -YGFVISDWKMPNMDGLELLKTIRADGAMSALPVLMVTAYAKKENIIAAAQAGASGYVVK 108
Query: 138 PLKPS 142
           P   +
Sbjct: 109 PFTAA 113

>pdb|3FFX|A Chain A, Crystal Structure Of Chey Triple Mutant F14e, N59r, E89h Complexed With Bef3- And Mn2+ Length = 128

Iteration: 1
 Score = 45.8 bits (107), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 38/129 (29%), Positives = 53/129 (41%), Gaps = 15/129 (11%)
Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
           K    L VDD    R+IV NLLK      V  AE+G+ AL            N L + G 
Sbjct: 3   KELKFLVVDDESTMRRIVRNLLKELGFNNVEEAEDGVDAL------------NKLQAGG- 49
Query: 78  KVNLVITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLK 137
               VI+D+ MP M G ELLK I+                     I    + GA  +++K
Sbjct: 50  -YGFVISDWRMPNMDGLELLKTIRADGAMSALPVLMVTAHAKKENIIAAAQAGASGYVVK 108
Query: 138 PLKPSDVKK 146
           P   + +++
Sbjct: 109 PFTAATLEE 117

>pdb|3FFT|A Chain A, Crystal Structure Of Chey Double Mutant F14e, E89r Complexed With Bef3- And Mn2+ Length = 128

Iteration: 1
 Score = 45.8 bits (107), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 38/129 (29%), Positives = 53/129 (41%), Gaps = 15/129 (11%)
Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
           K    L VDD    R+IV NLLK      V  AE+G+ AL            N L + G 
Sbjct: 3   KELKFLVVDDESTMRRIVRNLLKELGFNNVEEAEDGVDAL------------NKLQAGG- 49
Query: 78  KVNLVITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLK 137
               VI+D+ MP M G ELLK I+                     I    + GA  +++K
Sbjct: 50  -YGFVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTARAKKENIIAAAQAGASGYVVK 108
Query: 138 PLKPSDVKK 146
           P   + +++
Sbjct: 109 PFTAATLEE 117

>pdb|1JBE|A Chain A, 1.08 A Structure Of Apo-Chey Reveals Meta-Active Conformation Length = 128

Iteration: 1
 Score = 45.4 bits (106), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 40/129 (31%), Positives = 55/129 (42%), Gaps = 15/129 (11%)
Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
           K    L VDD    R+IV NLLK      V  AE+G+ AL            N L + G 
Sbjct: 3   KELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDAL------------NKLQAGG- 49
Query: 78  KVNLVITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLK 137
               VI+D+ MP M G ELLK I+                     I    + GA  +++K
Sbjct: 50  -YGFVISDWNMPNMDGLELLKTIRAXXAMSALPVLMVTAEAKKENIIAAAQAGASGYVVK 108
Query: 138 PLKPSDVKK 146
           P   + +++
Sbjct: 109 PFTAATLEE 117

>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 = 45.4 bits (106), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 38/129 (29%), Positives = 53/129 (41%), Gaps = 15/129 (11%)
Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
           K    L VDD    R+IV NLLK      V  AE+G+ AL            N L + G 
Sbjct: 7   KELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDAL------------NKLQAGG- 53
Query: 78  KVNLVITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLK 137
               VI+D+ MP M G ELLK I+                     I    + GA  +++K
Sbjct: 54  -YGFVISDWDMPNMDGLELLKTIRADGAMSALPVLMVTAQAKKENIIAAAQAGASGYVVK 112
Query: 138 PLKPSDVKK 146
           P   + +++
Sbjct: 113 PFTAATLEE 121

>pdb|1AB6|A Chain A, Structure Of Chey Mutant F14n, V86t Length = 125

Iteration: 1
 Score = 45.4 bits (106), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 37/124 (29%), Positives = 53/124 (42%), Gaps = 15/124 (12%)
Query: 24  LAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLV 82
           L VDD+   R+IV NLLK      V  AE+G+ AL            N L + G     V
Sbjct: 5   LVVDDNSTMRRIVRNLLKELGFNNVEEAEDGVDAL------------NKLQAGG--YGFV 50
Query: 83  ITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLKPLKPS 142
           I+D+ MP M G ELLK I+                     I    + GA  +++KP   +
Sbjct: 51  ISDWNMPNMDGLELLKTIRADGAMSALPVLMTTAEAKKENIIAAAQAGASGYVVKPFTAA 110
Query: 143 DVKK 146
            +++
Sbjct: 111 TLEE 114

>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 = 45.4 bits (106), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 38/129 (29%), Positives = 53/129 (41%), Gaps = 15/129 (11%)
Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
           K    L VDD    R+IV NLLK      V  AE+G+ AL            N L + G 
Sbjct: 7   KELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDAL------------NKLQAGG- 53
Query: 78  KVNLVITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLK 137
               VI+D+ MP M G ELLK I+                     I    + GA  +++K
Sbjct: 54  -YGFVISDWDMPNMDGLELLKTIRADGAMSALPVLMVTAYAKKENIIAAAQAGASGYVVK 112
Query: 138 PLKPSDVKK 146
           P   + +++
Sbjct: 113 PFTAATLEE 121

>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 = 45.4 bits (106), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 37/129 (28%), Positives = 53/129 (41%), Gaps = 15/129 (11%)
Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
           K    L VDD    R+IV NLLK      V  AE+G+ AL            N L + G 
Sbjct: 4   KELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDAL------------NKLQAGG- 50
Query: 78  KVNLVITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLK 137
               +I+D+ MP M G ELLK I+                     I    + GA  +++K
Sbjct: 51  -FGFIISDWNMPNMDGLELLKTIRADSAMSALPVLMVTAEAKKENIIAAAQAGASGYVVK 109
Query: 138 PLKPSDVKK 146
           P   + +++
Sbjct: 110 PFTAATLEE 118

>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 = 45.4 bits (106), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 38/129 (29%), Positives = 53/129 (41%), Gaps = 15/129 (11%)
Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
           K    L VDD    R+IV NLLK      V  AE+G+ AL            N L + G 
Sbjct: 7   KELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDAL------------NKLQAGG- 53
Query: 78  KVNLVITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLK 137
               VI+D+ MP M G ELLK I+                     I    + GA  +++K
Sbjct: 54  -YGFVISDWDMPNMDGLELLKTIRADGAMSALPVLMVTARAKKENIIAAAQAGASGYVVK 112
Query: 138 PLKPSDVKK 146
           P   + +++
Sbjct: 113 PFTAATLEE 121

>pdb|1MIH|A Chain A, A Role For Chey Glu 89 In Chez-Mediated Dephosphorylation Of The E. Coli Chemotaxis Response Regulator Chey Length = 129

Iteration: 1
 Score = 45.4 bits (106), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 38/129 (29%), Positives = 53/129 (41%), Gaps = 15/129 (11%)
Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
           K    L VDD    R+IV NLLK      V  AE+G+ AL            N L + G 
Sbjct: 4   KELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDAL------------NKLQAGG- 50
Query: 78  KVNLVITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLK 137
               VI+D+ MP M G ELLK I+                     I    + GA  +++K
Sbjct: 51  -YGFVISDWRMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVK 109
Query: 138 PLKPSDVKK 146
           P   + +++
Sbjct: 110 PFTAATLEE 118

>pdb|1EAY|A Chain A, Chey-Binding (P2) Domain Of Chea In Complex With Chey From Escherichia Coli Length = 128

Iteration: 1
 Score = 45.4 bits (106), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 38/129 (29%), Positives = 53/129 (41%), Gaps = 15/129 (11%)
Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
           K    L VDD    R+IV NLLK      V  AE+G+ AL            N L + G 
Sbjct: 3   KELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDAL------------NKLQAGG- 49
Query: 78  KVNLVITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLK 137
               VI+D+ MP M G ELLK I+                     I    + GA  +++K
Sbjct: 50  -YGFVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVK 108
Query: 138 PLKPSDVKK 146
           P   + +++
Sbjct: 109 PFTAATLEE 117

>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 = 45.1 bits (105), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 38/125 (30%), Positives = 50/125 (40%), Gaps = 15/125 (12%)
Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
           K    L VDD    R+IV NLLK      V  AE+G+ AL            N L + G 
Sbjct: 7   KELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDAL------------NKLQAGG- 53
Query: 78  KVNLVITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLK 137
               VI+D+ MP M G ELLK I+                     I    + GA  +++K
Sbjct: 54  -YGFVISDWDMPNMDGLELLKTIRADGAMSALPVLMVTAKAKKENIIAAAQAGASGYVVK 112
Query: 138 PLKPS 142
           P   +
Sbjct: 113 PFTAA 117

>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 = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 38/129 (29%), Positives = 53/129 (41%), Gaps = 15/129 (11%)
Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
           K    L VDD    R+IV NLLK      V  AE+G+ AL            N L + G 
Sbjct: 4   KELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDAL------------NKLQAGG- 50
Query: 78  KVNLVITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLK 137
               VI+D+ MP M G ELLK I+                     I    + GA  +++K
Sbjct: 51  -YGFVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVK 109
Query: 138 PLKPSDVKK 146
           P   + +++
Sbjct: 110 PFTAATLEE 118

>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 = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 37/129 (28%), Positives = 53/129 (41%), Gaps = 15/129 (11%)
Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
           K    L VDD    R+IV NLLK      V  AE+G+ AL            N L + G 
Sbjct: 3   KELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDAL------------NKLQAGG- 49
Query: 78  KVNLVITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLK 137
               +I+D+ MP M G ELLK I+                     I    + GA  +++K
Sbjct: 50  -FGFIISDWNMPNMDGLELLKTIRADSAMSALPVLMVTAEAKKENIIAAAQAGASGYVVK 108
Query: 138 PLKPSDVKK 146
           P   + +++
Sbjct: 109 PFTAATLEE 117

>pdb|1CEY|A Chain A, Assignments, Secondary Structure, Global Fold, And Dynamics Of Chemotaxis Y Protein Using Three-And Four-Dimensional Heteronuclear (13c,15n) Nmr Spectroscopy Length = 128

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 38/129 (29%), Positives = 53/129 (41%), Gaps = 15/129 (11%)
Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
           K    L VDD    R+IV NLLK      V  AE+G+ AL            N L + G 
Sbjct: 3   KELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDAL------------NKLQAGG- 49
Query: 78  KVNLVITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLK 137
               VI+D+ MP M G ELLK I+                     I    + GA  +++K
Sbjct: 50  -YGFVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVK 108
Query: 138 PLKPSDVKK 146
           P   + +++
Sbjct: 109 PFTAATLEE 117

>pdb|1DJM|A Chain A, Solution Structure Of Bef3-Activated Chey From Escherichia Coli Length = 129

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 38/129 (29%), Positives = 53/129 (41%), Gaps = 15/129 (11%)
Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
           K    L VDD    R+IV NLLK      V  AE+G+ AL            N L + G 
Sbjct: 4   KELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDAL------------NKLQAGG- 50
Query: 78  KVNLVITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLK 137
               VI+D+ MP M G ELLK I+                     I    + GA  +++K
Sbjct: 51  -YGFVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVK 109
Query: 138 PLKPSDVKK 146
           P   + +++
Sbjct: 110 PFTAATLEE 118

>pdb|5CHY|A Chain A, Structure Of Chemotaxis Protein Chey Length = 128

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 38/129 (29%), Positives = 53/129 (41%), Gaps = 15/129 (11%)
Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
           K    L VDD    R+IV NLLK      V  AE+G+ AL            N L + G 
Sbjct: 3   KELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDAL------------NKLQAGG- 49
Query: 78  KVNLVITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLK 137
               VI+D+ MP M G ELLK I+                     I    + GA  +++K
Sbjct: 50  -YGFVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGWVVK 108
Query: 138 PLKPSDVKK 146
           P   + +++
Sbjct: 109 PFTAATLEE 117

>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 = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 38/129 (29%), Positives = 53/129 (41%), Gaps = 15/129 (11%)
Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
           K    L VDD    R+IV NLLK      V  AE+G+ AL            N L + G 
Sbjct: 4   KELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDAL------------NKLQAGG- 50
Query: 78  KVNLVITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLK 137
               VI+D+ MP M G ELLK I+                     I    + GA  +++K
Sbjct: 51  -YGFVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTSEAKKENIIAAAQAGASGYVVK 109
Query: 138 PLKPSDVKK 146
           P   + +++
Sbjct: 110 PFTAATLEE 118

>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 = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 38/129 (29%), Positives = 53/129 (41%), Gaps = 15/129 (11%)
Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
           K    L VDD    R+IV NLLK      V  AE+G+ AL            N L + G 
Sbjct: 4   KELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDAL------------NKLQAGG- 50
Query: 78  KVNLVITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLK 137
               VI+D+ MP M G ELLK I+                     I    + GA  +++K
Sbjct: 51  -YGFVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTTEAKKENIIAAAQAGASGYVVK 109
Query: 138 PLKPSDVKK 146
           P   + +++
Sbjct: 110 PFTAATLEE 118

>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 = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 38/129 (29%), Positives = 53/129 (41%), Gaps = 15/129 (11%)
Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
           K    L VDD    R+IV NLLK      V  AE+G+ AL            N L + G 
Sbjct: 4   KELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDAL------------NKLQAGG- 50
Query: 78  KVNLVITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLK 137
               VI+D+ MP M G ELLK I+                     I    + GA  +++K
Sbjct: 51  -YGFVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTMEAKKENIIAAAQAGASGYVVK 109
Query: 138 PLKPSDVKK 146
           P   + +++
Sbjct: 110 PFTAATLEE 118

>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 = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 38/129 (29%), Positives = 53/129 (41%), Gaps = 15/129 (11%)
Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
           K    L VDD    R+IV NLLK      V  AE+G+ AL            N L + G 
Sbjct: 3   KELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDAL------------NKLQAGG- 49
Query: 78  KVNLVITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLK 137
               VI+D+ MP M G ELLK I+                     I    + GA  +++K
Sbjct: 50  -YGFVISDWNMPNMDGLELLKTIRADGAMSALPVLMVIAEAKKENIIAAAQAGASGYVVK 108
Query: 138 PLKPSDVKK 146
           P   + +++
Sbjct: 109 PFTAATLEE 117

>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 = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 38/129 (29%), Positives = 53/129 (41%), Gaps = 15/129 (11%)
Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
           K    L VDD    R+IV NLLK      V  AE+G+ AL            N L + G 
Sbjct: 4   KELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDAL------------NKLQAGG- 50
Query: 78  KVNLVITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLK 137
               VI+D+ MP M G ELLK I+                     I    + GA  +++K
Sbjct: 51  -YGFVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTVEAKKENIIAAAQAGASGYVVK 109
Query: 138 PLKPSDVKK 146
           P   + +++
Sbjct: 110 PFTAATLEE 118

>pdb|6CHY|A Chain A, Structure Of Chemotaxis Protein Chey Length = 128

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 38/129 (29%), Positives = 53/129 (41%), Gaps = 15/129 (11%)
Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
           K    L VDD    R+IV NLLK      V  AE+G+ AL            N L + G 
Sbjct: 3   KELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDAL------------NKLQAGG- 49
Query: 78  KVNLVITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLK 137
               VI+D+ MP M G ELLK I+                     I    + GA  +++K
Sbjct: 50  -YGFVISDWNMPNMDGLELLKTIRADGAMSALPVLMVIAEAKKENIIAAAQAGASGWVVK 108
Query: 138 PLKPSDVKK 146
           P   + +++
Sbjct: 109 PFTAATLEE 117

>pdb|3GT7|A Chain A, Crystal Structure Of Signal Receiver Domain Of Signal Transduction Histidine Kinase From Syntrophus Aciditrophicus Length = 154

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 35/129 (27%), Positives = 56/129 (43%), Gaps = 18/129 (13%)
Query: 23  VLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLV 82
           +L V+DS    + ++++L+ +  +     NG  A+ FL L              T+ +L+
Sbjct: 10  ILIVEDSPTQAEHLKHILEETGYQTEHVRNGREAVRFLSL--------------TRPDLI 55
Query: 83  ITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLKPLK-- 140
           I+D  MP M GY L + +K                + P  +   LE GA  F+ KP K  
Sbjct: 56  ISDVLMPEMDGYALCRWLKGQPDLRTIPVILLTILSDPRDVVRSLECGADDFITKPCKDV 115
Query: 141 --PSDVKKL 147
              S VK+L
Sbjct: 116 VLASHVKRL 124

>pdb|1D4Z|A Chain A, Crystal Structure Of Chey-95iv, A Hyperactive Chey Mutant Length = 128

Iteration: 1
 Score = 44.7 bits (104), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 37/129 (28%), Positives = 53/129 (41%), Gaps = 15/129 (11%)
Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
           K    L VDD    R+IV NLLK      V  AE+G+ AL            N L + G 
Sbjct: 3   KELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDAL------------NKLQAGG- 49
Query: 78  KVNLVITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLK 137
               VI+D+ MP M G ELLK I+                     +    + GA  +++K
Sbjct: 50  -YGFVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENVIAAAQAGASGYVVK 108
Query: 138 PLKPSDVKK 146
           P   + +++
Sbjct: 109 PFTAATLEE 117

>pdb|3H1G|A Chain A, Crystal Structure Of Chey Mutant T84a Of Helicobacter Pylori Length = 129

Iteration: 1
 Score = 43.9 bits (102), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 36/126 (28%), Positives = 58/126 (46%), Gaps = 16/126 (12%)
Query: 23  VLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNG-TKVN 80
           +L VDDS   R+I++N L     + V  AE+G+ A E             L++N  TKV 
Sbjct: 8   LLVVDDSSTMRRIIKNTLSRLGYEDVLEAEHGVEAWE------------KLDANADTKV- 54
Query: 81  LVITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLKPLK 140
            +ITD+ MP M G +L+KK++                     +   L+ G   +++KP  
Sbjct: 55  -LITDWNMPEMNGLDLVKKVRSDSRFKEIPIIMITAEGGKAEVITALKAGVNNYIVKPFT 113
Query: 141 PSDVKK 146
           P  +K+
Sbjct: 114 PQVLKE 119

>pdb|3GWG|A Chain A, Crystal Structure Of Chey Of Helicobacter Pylori Length = 129

Iteration: 1
 Score = 43.9 bits (102), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 36/126 (28%), Positives = 58/126 (46%), Gaps = 16/126 (12%)
Query: 23  VLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNG-TKVN 80
           +L VDDS   R+I++N L     + V  AE+G+ A E             L++N  TKV 
Sbjct: 8   LLVVDDSSTMRRIIKNTLSRLGYEDVLEAEHGVEAWE------------KLDANADTKV- 54
Query: 81  LVITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLKPLK 140
            +ITD+ MP M G +L+KK++                     +   L+ G   +++KP  
Sbjct: 55  -LITDWNMPEMNGLDLVKKVRSDSRFKEIPIIMITTEGGKAEVITALKAGVNNYIVKPFT 113
Query: 141 PSDVKK 146
           P  +K+
Sbjct: 114 PQVLKE 119

>pdb|2CHY|A Chain A, Three-Dimensional Structure Of Chey, The Response Regulator Of Bacterial Chemotaxis Length = 128

Iteration: 1
 Score = 43.9 bits (102), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 37/129 (28%), Positives = 52/129 (40%), Gaps = 15/129 (11%)
Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
           K    L VDD    R+IV NLLK      V  AE+G+ AL            N L + G 
Sbjct: 3   KELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDAL------------NKLQAGG- 49
Query: 78  KVNLVITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLK 137
               +I D+ MP M G ELLK I+                     I    + GA  +++K
Sbjct: 50  -FGFIICDWNMPNMDGLELLKTIRADSAMSALPVLMVTAEAKKENIIAAAQAGASGYVVK 108
Query: 138 PLKPSDVKK 146
           P   + +++
Sbjct: 109 PFTAATLEE 117

>pdb|1AB5|A Chain A, Structure Of Chey Mutant F14n, V21t Length = 125

Iteration: 1
 Score = 43.5 bits (101), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 36/124 (29%), Positives = 52/124 (41%), Gaps = 15/124 (12%)
Query: 24  LAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLV 82
           L VDD+   R+I  NLLK      V  AE+G+ AL            N L + G     V
Sbjct: 5   LVVDDNSTMRRITRNLLKELGFNNVEEAEDGVDAL------------NKLQAGG--YGFV 50
Query: 83  ITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLKPLKPS 142
           I+D+ MP M G ELLK I+                     I    + GA  +++KP   +
Sbjct: 51  ISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAA 110
Query: 143 DVKK 146
            +++
Sbjct: 111 TLEE 114

>pdb|1EHC|A Chain A, Structure Of Signal Transduction Protein Chey Length = 128

Iteration: 1
 Score = 42.4 bits (98), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 37/129 (28%), Positives = 52/129 (40%), Gaps = 15/129 (11%)
Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
           K    L VD     R+IV NLLK      V  AE+G+ AL            N L + G 
Sbjct: 3   KELKFLVVDKFSTMRRIVRNLLKELGFNNVEEAEDGVDAL------------NKLQAGG- 49
Query: 78  KVNLVITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLK 137
               VI+D+ MP M G ELLK I+                     I    + GA  +++K
Sbjct: 50  -YGFVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVK 108
Query: 138 PLKPSDVKK 146
           P   + +++
Sbjct: 109 PFTAATLEE 117

>pdb|1C4W|A Chain A, 1.9 A Structure Of A-Thiophosphonate Modified Chey D57c Length = 128

Iteration: 1
 Score = 42.4 bits (98), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 37/129 (28%), Positives = 52/129 (40%), Gaps = 15/129 (11%)
Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
           K    L VDD    R+IV NLLK      V  AE+G+ AL            N L + G 
Sbjct: 3   KELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDAL------------NKLQAGG- 49
Query: 78  KVNLVITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLK 137
               VI+ + MP M G ELLK I+                     I    + GA  +++K
Sbjct: 50  -YGFVISXWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVK 108
Query: 138 PLKPSDVKK 146
           P   + +++
Sbjct: 109 PFTAATLEE 117

>pdb|1ZDM|A Chain A, Crystal Structure Of Activated Chey Bound To Xe Length = 129

Iteration: 1
 Score = 42.4 bits (98), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 37/129 (28%), Positives = 52/129 (40%), Gaps = 15/129 (11%)
Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
           K    L VDD    R+IV NLLK      V  AE+G+ AL            N L + G 
Sbjct: 4   KELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDAL------------NKLQAGG- 50
Query: 78  KVNLVITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLK 137
               VI+ + MP M G ELLK I+                     I    + GA  +++K
Sbjct: 51  -YGFVISXWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVK 109
Query: 138 PLKPSDVKK 146
           P   + +++
Sbjct: 110 PFTAATLEE 118

>pdb|1E6M|A Chain A, Two-Component Signal Transduction System D57a Mutant Of Chey Length = 128

Iteration: 1
 Score = 42.4 bits (98), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 37/129 (28%), Positives = 52/129 (40%), Gaps = 15/129 (11%)
Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
           K    L VDD    R+IV NLLK      V  AE+G+ AL            N L + G 
Sbjct: 3   KELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDAL------------NKLQAGG- 49
Query: 78  KVNLVITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLK 137
               VI+ + MP M G ELLK I+                     I    + GA  +++K
Sbjct: 50  -YGFVISAWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVK 108
Query: 138 PLKPSDVKK 146
           P   + +++
Sbjct: 109 PFTAATLEE 117

>pdb|1E6K|A Chain A, Two-Component Signal Transduction System D12a Mutant Of Chey Length = 130

Iteration: 1
 Score = 42.0 bits (97), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 37/129 (28%), Positives = 52/129 (40%), Gaps = 15/129 (11%)
Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
           K    L V D    R+IV NLLK      V  AE+G+ AL            N L + G 
Sbjct: 5   KELKFLVVADFSTMRRIVRNLLKELGFNNVEEAEDGVDAL------------NKLQAGG- 51
Query: 78  KVNLVITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLK 137
               VI+D+ MP M G ELLK I+                     I    + GA  +++K
Sbjct: 52  -YGFVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVK 110
Query: 138 PLKPSDVKK 146
           P   + +++
Sbjct: 111 PFTAATLEE 119

>pdb|1E6L|A Chain A, Two-Component Signal Transduction System D13a Mutant Of Chey Length = 127

Iteration: 1
 Score = 42.0 bits (97), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 37/129 (28%), Positives = 52/129 (40%), Gaps = 15/129 (11%)
Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
           K    L VD     R+IV NLLK      V  AE+G+ AL            N L + G 
Sbjct: 2   KELKFLVVDAFSTMRRIVRNLLKELGFNNVEEAEDGVDAL------------NKLQAGG- 48
Query: 78  KVNLVITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLK 137
               VI+D+ MP M G ELLK I+                     I    + GA  +++K
Sbjct: 49  -YGFVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQAGASGYVVK 107
Query: 138 PLKPSDVKK 146
           P   + +++
Sbjct: 108 PFTAATLEE 116

>pdb|2ID7|A Chain A, 1.75 A Structure Of T87i Phosphono-Chey Length = 128

Iteration: 1
 Score = 42.0 bits (97), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 37/129 (28%), Positives = 52/129 (40%), Gaps = 15/129 (11%)
Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
           K    L VDD    R+IV NLLK      V  AE+G+ AL            N L + G 
Sbjct: 3   KELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDAL------------NKLQAGG- 49
Query: 78  KVNLVITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLK 137
               VI+ + MP M G ELLK I+                     I    + GA  +++K
Sbjct: 50  -YGFVISXWNMPNMDGLELLKTIRADGAMSALPVLMVIAEAKKENIIAAAQAGASGYVVK 108
Query: 138 PLKPSDVKK 146
           P   + +++
Sbjct: 109 PFTAATLEE 117

>pdb|2ID9|A Chain A, 1.85 A Structure Of T87iY106W PHOSPHONO-Chey Length = 128

Iteration: 1
 Score = 42.0 bits (97), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 37/129 (28%), Positives = 52/129 (40%), Gaps = 15/129 (11%)
Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
           K    L VDD    R+IV NLLK      V  AE+G+ AL            N L + G 
Sbjct: 3   KELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDAL------------NKLQAGG- 49
Query: 78  KVNLVITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLK 137
               VI+ + MP M G ELLK I+                     I    + GA  +++K
Sbjct: 50  -YGFVISXWNMPNMDGLELLKTIRADGAMSALPVLMVIAEAKKENIIAAAQAGASGWVVK 108
Query: 138 PLKPSDVKK 146
           P   + +++
Sbjct: 109 PFTAATLEE 117

>pdb|3H1F|A Chain A, Crystal Structure Of Chey Mutant D53a Of Helicobacter Pylori Length = 129

Iteration: 1
 Score = 40.8 bits (94), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 35/126 (27%), Positives = 57/126 (45%), Gaps = 16/126 (12%)
Query: 23  VLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNG-TKVN 80
           +L VDDS   R+I++N L     + V  AE+G+ A E             L++N  TKV 
Sbjct: 8   LLVVDDSSTMRRIIKNTLSRLGYEDVLEAEHGVEAWE------------KLDANADTKV- 54
Query: 81  LVITDYCMPGMTGYELLKKIKXXXXXXXXXXXXXXXXNIPTRINECLEEGAQMFMLKPLK 140
            +IT + MP M G +L+KK++                     +   L+ G   +++KP  
Sbjct: 55  -LITAWNMPEMNGLDLVKKVRSDSRFKEIPIIMITTEGGKAEVITALKAGVNNYIVKPFT 113
Query: 141 PSDVKK 146
           P  +K+
Sbjct: 114 PQVLKE 119

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	153
3eq2_A	394	Probable two-component response regulator; adaptor	1e-26
3bre_A	358	Probable two-component response regulator; protein	6e-26
3luf_A	259	Two-component system response regulator/ggdef doma	7e-25
3luf_A	259	Two-component system response regulator/ggdef doma	6e-21
1k66_A	149	Phytochrome response regulator RCPB; CHEY homologu	2e-24
2qvg_A	143	Two component response regulator; NYSGXRC, PSI-2,	1e-23
1w25_A	459	Stalked-cell differentiation controlling protein;	1e-23
1w25_A	459	Stalked-cell differentiation controlling protein;	4e-18
1jbe_A	128	Chemotaxis protein CHEY; signaling protein; 1.08A	8e-23
1i3c_A	149	Response regulator RCP1; phytochrome, signaling pr	1e-22
3heb_A	152	Response regulator receiver domain protein (CHEY);	1e-22
3ilh_A	146	Two component response regulator; NYSGXRC, PSI-II,	6e-22
1p6q_A	129	CHEY2; chemotaxis, signal transduction, response r	2e-20
3hdv_A	136	Response regulator; PSI-II, structural genomics, P	7e-20
3cfy_A	137	Putative LUXO repressor protein; structural genomi	8e-20
3hdg_A	137	Uncharacterized protein; two-component sensor acti	2e-19
2rjn_A	154	Response regulator receiver:metal-dependent phosph	2e-19
3h1g_A	129	Chemotaxis protein CHEY homolog; sulfate-bound CHE	2e-19
3hv2_A	153	Response regulator/HD domain protein; PSI-2, NYSGX	4e-19
3jte_A	143	Response regulator receiver protein; structural ge	4e-19
1srr_A	124	SPO0F, sporulation response regulatory protein; as	1e-18
2qxy_A	142	Response regulator; regulation of transcription, N	3e-18
1k68_A	140	Phytochrome response regulator RCPA; phosphorylate	6e-18
3cnb_A	143	DNA-binding response regulator, MERR family; signa	2e-17
3grc_A	140	Sensor protein, kinase; protein structure initiati	1e-16
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	1e-16
1dc7_A	124	NTRC, nitrogen regulation protein; receiver domain	4e-16
1qkk_A	155	DCTD, C4-dicarboxylate transport transcriptional r	4e-16
3i42_A	127	Response regulator receiver domain protein (CHEY-	5e-16
3lua_A	140	Response regulator receiver protein; two-component	5e-16
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	8e-16
3nhm_A	133	Response regulator; protein structure initiative I	8e-16
2jk1_A	139	HUPR, hydrogenase transcriptional regulatory prote	2e-15
1tmy_A	120	CHEY protein, TMY; chemotaxis, phosphoryl transfer	4e-15
3gt7_A	154	Sensor protein; structural genomics, signal receiv	6e-15
3kcn_A	151	Adenylate cyclase homolog; SGX, PSI 2, structural	2e-14
3eod_A	130	Protein HNR; response regulator, phosphoprotein, t	2e-14
3m6m_D	143	Sensory/regulatory protein RPFC; RPFF, REC, enoyl-	2e-14
2ayx_A	254	Sensor kinase protein RCSC; two independent struct	3e-14
2zay_A	147	Response regulator receiver protein; structural ge	7e-14
3hzh_A	157	Chemotaxis response regulator (CHEY-3); phosphatas	9e-14
3kyj_B	145	CHEY6 protein, putative histidine protein kinase;	2e-13
2rdm_A	132	Response regulator receiver protein; structural ge	2e-13
1a2o_A	349	CHEB methylesterase; bacterial chemotaxis, adaptat	3e-13
1mb3_A	124	Cell division response regulator DIVK; signal tran	4e-13
3n53_A	140	Response regulator receiver modulated diguanylate;	4e-13
2qr3_A	140	Two-component system response regulator; structura	4e-13
3gl9_A	122	Response regulator; beta-sheet, surrounded by alph	5e-13
3kht_A	144	Response regulator; PSI-II, 11023K, structural gen	6e-13
2j48_A	119	Two-component sensor kinase; pseudo-receiver, circ	9e-13
1s8n_A	205	Putative antiterminator; RV1626, structural genomi	1e-12
3crn_A	132	Response regulator receiver domain protein, CHEY-;	1e-12
1yio_A	208	Response regulatory protein; transcription regulat	2e-12
3c3m_A	138	Response regulator receiver protein; structural ge	2e-12
3snk_A	135	Response regulator CHEY-like protein; P-loop conta	2e-12
4dad_A	146	Putative pilus assembly-related protein; response	3e-12
3cg4_A	142	Response regulator receiver domain protein (CHEY-;	3e-12
3t8y_A	164	CHEB, chemotaxis response regulator protein-glutam	4e-12
1xhf_A	123	DYE resistance, aerobic respiration control protei	4e-12
3h5i_A	140	Response regulator/sensory box protein/ggdef domai	4e-12
3eqz_A	135	Response regulator; structural genomics, unknown f	5e-12
3rqi_A	184	Response regulator protein; structural genomics, s	5e-12
1dbw_A	126	Transcriptional regulatory protein FIXJ; doubly wo	5e-12
3cu5_A	141	Two component transcriptional regulator, ARAC FAM;	1e-11
1dcf_A	136	ETR1 protein; beta-alpha five sandwich, transferas	3e-11
1zgz_A	122	Torcad operon transcriptional regulatory protein;	8e-11
3t6k_A	136	Response regulator receiver; flavodoxin-like, stru	1e-10
3r0j_A	250	Possible two component system response transcript	2e-10
3cg0_A	140	Response regulator receiver modulated diguanylate	2e-10
1zh2_A	121	KDP operon transcriptional regulatory protein KDPE	3e-10
2a9o_A	120	Response regulator; essential protein, YYCF/YYCG h	3e-10
3f6p_A	120	Transcriptional regulatory protein YYCF; unphospho	4e-10
2b4a_A	138	BH3024; flavodoxin-like fold, structural genomics,	6e-10
3mm4_A	206	Histidine kinase homolog; receiver domain, CKI1, c	7e-10
3lte_A	132	Response regulator; structural genomics, PSI, prot	8e-10
2qzj_A	136	Two-component response regulator; 11017X, PSI-II,	9e-10
2oqr_A	230	Sensory transduction protein REGX3; response regul	1e-09
2jba_A	127	Phosphate regulon transcriptional regulatory PROT;	2e-09
3c97_A	140	Signal transduction histidine kinase; structural g	3e-09
2gwr_A	238	DNA-binding response regulator MTRA; two-component	4e-09
2gkg_A	127	Response regulator homolog; social motility, recei	4e-09
1mvo_A	136	PHOP response regulator; phosphate regulon, transc	7e-09
2r25_B	133	Osmosensing histidine protein kinase SLN1; alpha5-	1e-08
3kto_A	136	Response regulator receiver protein; PSI-II,struct	1e-08
3a10_A	116	Response regulator; phosphoacceptor, signaling pro	1e-08
1p2f_A	220	Response regulator; DRRB, OMPR/PHOB, transcription	2e-08
1qo0_D	196	AMIR; binding protein, gene regulator, receptor; 2	6e-08
2qv0_A	143	Protein MRKE; structural genomics, transcription,	7e-08
3q9s_A	249	DNA-binding response regulator; DNA binding protei	1e-07
2qsj_A	154	DNA-binding response regulator, LUXR family; struc	1e-07
1ys7_A	233	Transcriptional regulatory protein PRRA; response	8e-07
3b2n_A	133	Uncharacterized protein Q99UF4; structural genomic	3e-06
3sy8_A	400	ROCR; TIM barrel phosphodiesterase-A, transcriptio	5e-06
3f6c_A	134	Positive transcription regulator EVGA; structural	1e-05
3klo_A	225	Transcriptional regulator VPST; REC domain, HTH do	3e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-05
2pl1_A	121	Transcriptional regulatory protein PHOP; CHEY-like	5e-05
1kgs_A	225	DRRD, DNA binding response regulator D; DNA-bindin	2e-04
4e7p_A	150	Response regulator; DNA binding, cytosol, transcri	3e-04
1dz3_A	130	Stage 0 sporulation protein A; response regulator,	4e-04

>3eq2_A Probable two-component response regulator; adaptor sigmas, signaling protein; 3.40A {Pseudomonas aeruginosa} PDB: 3f7a_A Length = 394

 Score =  101 bits (254), Expect = 1e-26
 Identities = 35/128 (27%), Positives = 64/128 (50%), Gaps = 16/128 (12%)

Query: 17  NPKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNG 76
           +     +L +DD  V R+ +   L++S  KV  A NG++ L+                  
Sbjct: 2   HKVSATLLIIDDDEVVRESLAAYLEDSNFKVLQALNGLQGLQIF--------------ES 47

Query: 77  TKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFML 136
            + +LVI D  MP + G EL+++I++++   E P++V+S   + +   E L  GA  +++
Sbjct: 48  EQPDLVICDLRMPQIDGLELIRRIRQTA--SETPIIVLSGAGVMSDAVEALRLGAADYLI 105

Query: 137 KPLKPSDV 144
           KPL+   V
Sbjct: 106 KPLEDLAV 113

>3bre_A Probable two-component response regulator; protein-nucleotide complex, signaling protein; HET: C2E; 2.40A {Pseudomonas aeruginosa} PDB: 3i5a_A* Length = 358

 Score = 99.4 bits (248), Expect = 6e-26
 Identities = 27/140 (19%), Positives = 55/140 (39%), Gaps = 15/140 (10%)

Query: 7   ASSSSSSSSSNPKPPHVLAVDDSIVDRKIVENLLKNSA-CKVTTAENGMRALEFLGLVDE 65
             S +   +       VL VDD  +  + V   L + A        +  +A+        
Sbjct: 5   HESKTDLGAPLDGAVMVLLVDDQAMIGEAVRRSLASEAGIDFHFCSDPQQAVAVA----- 59

Query: 66  QEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINE 125
                    N  K  +++ D  MPG+ G  LL   + +   +++P++V+S++  PT  + 
Sbjct: 60  ---------NQIKPTVILQDLVMPGVDGLTLLAAYRGNPATRDIPIIVLSTKEEPTVKSA 110

Query: 126 CLEEGAQMFMLKPLKPSDVK 145
               GA  +++K     ++ 
Sbjct: 111 AFAAGANDYLVKLPDAIELV 130

>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 = 95.0 bits (237), Expect = 7e-25
 Identities = 30/136 (22%), Positives = 57/136 (41%), Gaps = 13/136 (9%)

Query: 18  PKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
            +   VL VDDS   R      L+    +V  A +   AL  L                 
Sbjct: 122 NQQIEVLVVDDSRTSRHRTMAQLRKQLLQVHEASHAREALATL-------------EQHP 168

Query: 78  KVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLK 137
            + LV+ DY MP + G  L++ ++E    +++ ++ +S  +        L++GA  F+ +
Sbjct: 169 AIRLVLVDYYMPEIDGISLVRMLRERYSKQQLAIIGISVSDKRGLSARYLKQGANDFLNQ 228

Query: 138 PLKPSDVKKLTGHLIN 153
           P +P +++    H + 
Sbjct: 229 PFEPEELQCRVSHNLE 244

>3luf_A Two-component system response regulator/ggdef domain protein; structural genomics, ASA_2441, PSI-2, protein structure initiative; HET: MSE; 1.76A {Aeromonas salmonicida} PDB: 3mf4_A* Length = 259

 Score = 84.6 bits (210), Expect = 6e-21
 Identities = 20/123 (16%), Positives = 47/123 (38%), Gaps = 18/123 (14%)

Query: 20  PPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKV 79
              +L V+DS+  R+++   +         A + +                     G + 
Sbjct: 4   KQKILIVEDSMTIRRMLIQAIAQQTGLEIDAFDTLEGARHC--------------QGDEY 49

Query: 80  NLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPL 139
            + + D  +P     E +K + E    + +PVV+++++    +    LE G   +++K  
Sbjct: 50  VVALVDLTLPDAPSGEAVKVLLE----RGLPVVILTADISEDKREAWLEAGVLDYVMKDS 105

Query: 140 KPS 142
           + S
Sbjct: 106 RHS 108

>1k66_A Phytochrome response regulator RCPB; CHEY homologue, homodimer, APO-protein, (beta/alpha)5, signaling protein; 1.75A {Tolypothrix SP} SCOP: c.23.1.1 Length = 149

 Score = 91.2 bits (227), Expect = 2e-24
 Identities = 32/131 (24%), Positives = 61/131 (46%), Gaps = 6/131 (4%)

Query: 15  SSNPKPPHVLAVDDSIVDRKIVENLLKNS--ACKVTTAENGMRALEFLGLVDEQEQQNNL 72
           +       +L V+DS  D    + LL+       +     G +AL+FL     Q      
Sbjct: 1   AVGNATQPLLVVEDSDEDFSTFQRLLQREGVVNPIYRCITGDQALDFL----YQTGSYCN 56

Query: 73  NSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQ 132
                +  +++ D  +PG  G E+L++IK+  V+K++PVV++++ + P  I  C      
Sbjct: 57  PDIAPRPAVILLDLNLPGTDGREVLQEIKQDEVLKKIPVVIMTTSSNPKDIEICYSYSIS 116

Query: 133 MFMLKPLKPSD 143
            +++KPL+   
Sbjct: 117 SYIVKPLEIDR 127

>2qvg_A Two component response regulator; NYSGXRC, PSI-2, structural genomics, protein structure initiative; 1.50A {Legionella pneumophila subsp} Length = 143

 Score = 88.8 bits (221), Expect = 1e-23
 Identities = 30/135 (22%), Positives = 61/135 (45%), Gaps = 10/135 (7%)

Query: 15  SSNPKPPHVLAVDDSIVDRKIVENLLK--NSACKVTTAENGMRALEFLGLVDEQEQQNNL 72
           S       +L ++D  VD + VE +    +S  K+  A++G +AL+ L   +++ +    
Sbjct: 2   SLAADKVDILYLEDDEVDIQSVERVFHKISSLIKIEIAKSGNQALDMLYGRNKENK---- 57

Query: 73  NSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQ 132
                   L++ D  +P M G E LK++++ S   ++ V V+++               +
Sbjct: 58  ----IHPKLILLDINIPKMNGIEFLKELRDDSSFTDIEVFVLTAAYTSKDKLAFESLNIR 113

Query: 133 MFMLKPLKPSDVKKL 147
             ++KPL   +  KL
Sbjct: 114 GHLIKPLDYGEAIKL 128

>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 = 94.1 bits (234), Expect = 1e-23
 Identities = 30/123 (24%), Positives = 58/123 (47%), Gaps = 14/123 (11%)

Query: 23  VLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLV 82
           +L VDD   + +++E  L     +V+TA +G  AL                      +++
Sbjct: 4   ILVVDDIEANVRLLEAKLTAEYYEVSTAMDGPTALAMA-----ARDL---------PDII 49

Query: 83  ITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPS 142
           + D  MPGM G+ + +K+K+    + +PVV++++ +      + LE GA  F+ KP+   
Sbjct: 50  LLDVMMPGMDGFTVCRKLKDDPTTRHIPVVLITALDGRGDRIQGLESGASDFLTKPIDDV 109

Query: 143 DVK 145
            + 
Sbjct: 110 MLF 112

>1w25_A Stalked-cell differentiation controlling protein; two-component system, ggdef domain, cyclic dinucleotide, cyclic-digmp; HET: C2E; 2.70A {Caulobacter vibrioides} SCOP: c.23.1.1 c.23.1.1 d.58.29.2 PDB: 2v0n_A* 2wb4_A* Length = 459

 Score = 78.7 bits (194), Expect = 4e-18
 Identities = 23/129 (17%), Positives = 45/129 (34%), Gaps = 16/129 (12%)

Query: 17  NPKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNG 76
           +     VL VDD+    + V   L      V  ++     +   G VD            
Sbjct: 149 DGLGGRVLIVDDNERQAQRVAAELGVEHRPVIESDPEKAKISAGGPVD------------ 196

Query: 77  TKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFML 136
               LVI +       G      ++     +++PV+ +   +   R+ + LE G    + 
Sbjct: 197 ----LVIVNAAAKNFDGLRFTAALRSEERTRQLPVLAMVDPDDRGRMVKALEIGVNDILS 252

Query: 137 KPLKPSDVK 145
           +P+ P ++ 
Sbjct: 253 RPIDPQELS 261

>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 = 86.1 bits (214), Expect = 8e-23
 Identities = 41/125 (32%), Positives = 56/125 (44%), Gaps = 15/125 (12%)

Query: 18  PKPPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNG 76
            K    L VDD    R+IV NLLK      V  AE+G+ AL  L                
Sbjct: 2   DKELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKL--------------QA 47

Query: 77  TKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFML 136
                VI+D+ MP M G ELLK I+    M  +PV++V++E     I    + GA  +++
Sbjct: 48  GGYGFVISDWNMPNMDGLELLKTIRAXXAMSALPVLMVTAEAKKENIIAAAQAGASGYVV 107

Query: 137 KPLKP 141
           KP   
Sbjct: 108 KPFTA 112

>1i3c_A Response regulator RCP1; phytochrome, signaling protein; 1.90A {Synechocystis SP} SCOP: c.23.1.1 PDB: 1jlk_A Length = 149

 Score = 86.6 bits (215), Expect = 1e-22
 Identities = 35/132 (26%), Positives = 64/132 (48%), Gaps = 9/132 (6%)

Query: 14  SSSNPKPPHVLAVDDSIVDRKIVENLLKNS--ACKVTTAENGMRALEFLGLVDEQEQQNN 71
           S  +  P  +L V+DS  D ++V+ +LK S    ++    +G+ A+ FL       QQ  
Sbjct: 2   SDESNPPKVILLVEDSKADSRLVQEVLKTSTIDHELIILRDGLAAMAFL-------QQQG 54

Query: 72  LNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGA 131
              N  + NL++ D  +P   G E+L +IK++  +K +PVVV+++ +    +    E   
Sbjct: 55  EYENSPRPNLILLDLNLPKKDGREVLAEIKQNPDLKRIPVVVLTTSHNEDDVIASYELHV 114

Query: 132 QMFMLKPLKPSD 143
             ++ K     D
Sbjct: 115 NCYLTKSRNLKD 126

>3heb_A Response regulator receiver domain protein (CHEY); NYSGXRC, PSI-II, respose regulator, structure initiative, structural genomics; 2.40A {Rhodospirillum rubrum} Length = 152

 Score = 86.2 bits (214), Expect = 1e-22
 Identities = 27/126 (21%), Positives = 64/126 (50%), Gaps = 7/126 (5%)

Query: 20  PPHVLAVDDSIVDRKIVENLLKNS--ACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
              ++ ++D +   +++E  ++ +    ++    +G  AL +L   D+  + +       
Sbjct: 4   SVTIVMIEDDLGHARLIEKNIRRAGVNNEIIAFTDGTSALNYLFGDDKSGRVSA-----G 58

Query: 78  KVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLK 137
           +  LV+ D  +P MTG ++LK +KE+   +  PVV++++ +    I  C + GA +++ K
Sbjct: 59  RAQLVLLDLNLPDMTGIDILKLVKENPHTRRSPVVILTTTDDQREIQRCYDLGANVYITK 118

Query: 138 PLKPSD 143
           P+   +
Sbjct: 119 PVNYEN 124

>3ilh_A Two component response regulator; NYSGXRC, PSI-II, protein S initiative, structural genomics; 2.59A {Cytophaga hutchinsonii} Length = 146

 Score = 84.7 bits (210), Expect = 6e-22
 Identities = 27/138 (19%), Positives = 58/138 (42%), Gaps = 14/138 (10%)

Query: 13  SSSSNPKPPHVLAVDDSIVDRKIVENLLKNSAC--KVTTAENGMRALEFLGLVDEQEQQN 70
           S +   K   VL +DD  +   +   +++ +    ++ +  +G  A+  L         N
Sbjct: 2   SLADTRKIDSVLLIDDDDIVNFLNTTIIRMTHRVEEIQSVTSGNAAINKL---------N 52

Query: 71  NLNSNGTKVNLVITDYCMPGMTGYELLKKIKESS--VMKEVPVVVVSSENIPT-RINECL 127
            L + G   +++  D  MPG+ G+EL+   K+    +  +  V ++SS   P  +     
Sbjct: 53  ELYAAGRWPSIICIDINMPGINGWELIDLFKQHFQPMKNKSIVCLLSSSLDPRDQAKAEA 112

Query: 128 EEGAQMFMLKPLKPSDVK 145
            +    ++ KPL  + + 
Sbjct: 113 SDWVDYYVSKPLTANALN 130

>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 = 80.2 bits (199), Expect = 2e-20
 Identities = 26/124 (20%), Positives = 55/124 (44%), Gaps = 15/124 (12%)

Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
           +   VL VDD +  R ++ + L+    K +T A +G + ++ +                 
Sbjct: 5   EKIKVLIVDDQVTSRLLLGDALQQLGFKQITAAGDGEQGMKIM--------------AQN 50

Query: 78  KVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLK 137
             +LVI+D+ MP M G  LL+ ++ +   K+   ++++++     + +    GA   + K
Sbjct: 51  PHHLVISDFNMPKMDGLGLLQAVRANPATKKAAFIILTAQGDRALVQKAAALGANNVLAK 110

Query: 138 PLKP 141
           P   
Sbjct: 111 PFTI 114

>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 = 79.2 bits (196), Expect = 7e-20
 Identities = 32/134 (23%), Positives = 59/134 (44%), Gaps = 16/134 (11%)

Query: 15  SSNPKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNS 74
           S     P VL VDD+ V+R+ +   LK+       A+    A  +L              
Sbjct: 2   SLVAARPLVLVVDDNAVNREALILYLKSRGIDAVGADGAEEARLYL-------------H 48

Query: 75  NGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSS-ENIPTRINECLEEGAQM 133
              ++ L+ITD  M   +G +L++ I+ S     + ++VVS   ++   + + +  G   
Sbjct: 49  YQKRIGLMITDLRMQPESGLDLIRTIRASE-RAALSIIVVSGDTDVEEAV-DVMHLGVVD 106

Query: 134 FMLKPLKPSDVKKL 147
           F+LKP+    + +L
Sbjct: 107 FLLKPVDLGKLLEL 120

>3cfy_A Putative LUXO repressor protein; structural genomics, unknown function, uncharacterized protein, signal receiver domain; 2.50A {Vibrio parahaemolyticus rimd 2210633} Length = 137

 Score = 78.7 bits (195), Expect = 8e-20
 Identities = 27/126 (21%), Positives = 58/126 (46%), Gaps = 18/126 (14%)

Query: 21  PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVN 80
           P VL V+DS     + +  +K+    +   E G  A++F+                +K  
Sbjct: 5   PRVLLVEDSTSLAILYKQYVKDEPYDIFHVETGRDAIQFI--------------ERSKPQ 50

Query: 81  LVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSE-NIPTRINECLEEGAQMFMLKPL 139
           L+I D  +P M+G ++L  I ++       V++ ++  ++   +   +++GA+ F+ KP+
Sbjct: 51  LIILDLKLPDMSGEDVLDWINQND--IPTSVIIATAHGSVDLAV-NLIQKGAEDFLEKPI 107

Query: 140 KPSDVK 145
               +K
Sbjct: 108 NADRLK 113

>3hdg_A Uncharacterized protein; two-component sensor activity, response regulator, PSI-II, 11227F, NYSGXRC, structural genomics; 2.27A {Wolinella succinogenes} Length = 137

 Score = 78.0 bits (193), Expect = 2e-19
 Identities = 30/133 (22%), Positives = 58/133 (43%), Gaps = 18/133 (13%)

Query: 15  SSNPKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNS 74
           S       +L V+D    R+ +  ++ N   +V +A +G        L            
Sbjct: 2   SLREVALKILIVEDDTDAREWLSTIISNHFPEVWSAGDGEEGER---LFGLH-------- 50

Query: 75  NGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSS-ENIPTRINECLEEGAQM 133
                +++ITD  MP + G E+L +IK      +  V+V+S+   +   I + +E G  +
Sbjct: 51  ---APDVIITDIRMPKLGGLEMLDRIKAGG--AKPYVIVISAFSEMKYFI-KAIELGVHL 104

Query: 134 FMLKPLKPSDVKK 146
           F+ KP++P  + +
Sbjct: 105 FLPKPIEPGRLME 117

>2rjn_A Response regulator receiver:metal-dependent phosphohydrolase, HD subdomain; structural genomics, oceanospirillum SP. MED92; 2.10A {Neptuniibacter caesariensis} Length = 154

 Score = 78.4 bits (194), Expect = 2e-19
 Identities = 37/133 (27%), Positives = 58/133 (43%), Gaps = 19/133 (14%)

Query: 15  SSNPKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNS 74
           S N K   V+ VDD       ++ L+K   C + T  + + ALE L    +         
Sbjct: 2   SLNYKNYTVMLVDDEQPILNSLKRLIKRLGCNIITFTSPLDALEAL----KGTS------ 51

Query: 75  NGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSS-ENIPTRINECLEEGAQ- 132
               V LVI+D  MP M G   L+++ +S    ++  VV+S   +    I + +  G   
Sbjct: 52  ----VQLVISDMRMPEMGGEVFLEQVAKSY--PDIERVVISGYADAQATI-DAVNRGKIS 104

Query: 133 MFMLKPLKPSDVK 145
            F+LKP +  DV 
Sbjct: 105 RFLLKPWEDEDVF 117

>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 = 77.5 bits (192), Expect = 2e-19
 Identities = 36/121 (29%), Positives = 62/121 (51%), Gaps = 14/121 (11%)

Query: 22  HVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVN 80
            +L VDDS   R+I++N L     + V  AE+G+ A E L                    
Sbjct: 7   KLLVVDDSSTMRRIIKNTLSRLGYEDVLEAEHGVEAWEKL-------------DANADTK 53

Query: 81  LVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLK 140
           ++ITD+ MP M G +L+KK++  S  KE+P++++++E     +   L+ G   +++KP  
Sbjct: 54  VLITDWNMPEMNGLDLVKKVRSDSRFKEIPIIMITAEGGKAEVITALKAGVNNYIVKPFT 113

Query: 141 P 141
           P
Sbjct: 114 P 114

>3hv2_A Response regulator/HD domain protein; PSI-2, NYSGXRC, structural genomics, protein structure initiative; 1.50A {Pseudomonas fluorescens pf-5} Length = 153

 Score = 77.6 bits (192), Expect = 4e-19
 Identities = 26/140 (18%), Positives = 56/140 (40%), Gaps = 19/140 (13%)

Query: 8   SSSSSSSSSNPKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQE 67
           S    + ++  + P +L VD   V  + ++ LL      +  A +  +AL+ L       
Sbjct: 2   SLGELNVATVTRRPEILLVDSQEVILQRLQQLLSPLPYTLHFARDATQALQLL----ASR 57

Query: 68  QQNNLNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSS-ENIPTRINEC 126
           +          V+LVI+   +P M G  LL +I +         ++++   ++     + 
Sbjct: 58  E----------VDLVISAAHLPQMDGPTLLARIHQQY--PSTTRILLTGDPDLKLIA-KA 104

Query: 127 LEEGAQM-FMLKPLKPSDVK 145
           + EG    ++ KP    ++ 
Sbjct: 105 INEGEIYRYLSKPWDDQELL 124

>3jte_A Response regulator receiver protein; structural genomics, nysgrc, response regulator receiver domain, target 11226E, PSI-2; 1.90A {Clostridium thermocellum atcc 27405} Length = 143

 Score = 77.2 bits (191), Expect = 4e-19
 Identities = 28/126 (22%), Positives = 60/126 (47%), Gaps = 16/126 (12%)

Query: 21  PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVN 80
             +L +DD     + ++ LL+    +V TA +    L                 N   ++
Sbjct: 4   AKILVIDDESTILQNIKFLLEIDGNEVLTASSSTEGLRIF------------TENCNSID 51

Query: 81  LVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSE-NIPTRINECLEEGAQMFMLKPL 139
           +VITD  MP ++G ++L++IK+ +    + V++++   ++   I   ++EGA  ++ KP+
Sbjct: 52  VVITDMKMPKLSGMDILREIKKIT--PHMAVIILTGHGDLDNAI-LAMKEGAFEYLRKPV 108

Query: 140 KPSDVK 145
              D+ 
Sbjct: 109 TAQDLS 114

>1srr_A SPO0F, sporulation response regulatory protein; aspartate pocket, two component system; 1.90A {Bacillus subtilis} SCOP: c.23.1.1 PDB: 1pey_A 3q15_C 2ftk_E* 1fsp_A 1nat_A 1pux_A 2fsp_A 2jvj_A 2jvk_A 2jvi_A 1f51_E Length = 124

 Score = 75.6 bits (187), Expect = 1e-18
 Identities = 29/126 (23%), Positives = 58/126 (46%), Gaps = 18/126 (14%)

Query: 21  PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVN 80
             +L VDD    R ++  +      +   A NG++AL+   +V ++           + +
Sbjct: 4   EKILIVDDQSGIRILLNEVFNKEGYQTFQAANGLQALD---IVTKE-----------RPD 49

Query: 81  LVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSE-NIPTRINECLEEGAQMFMLKPL 139
           LV+ D  +PGM G E+LK++K     + + V+++++   +     E  E GA     KP 
Sbjct: 50  LVLLDMKIPGMDGIEILKRMKVID--ENIRVIIMTAYGELDMIQ-ESKELGALTHFAKPF 106

Query: 140 KPSDVK 145
              +++
Sbjct: 107 DIDEIR 112

>2qxy_A Response regulator; regulation of transcription, NYSGXRC, protein structure initiative II (PSI II), structural genomics; 1.95A {Thermotoga maritima} Length = 142

 Score = 74.9 bits (185), Expect = 3e-18
 Identities = 31/124 (25%), Positives = 52/124 (41%), Gaps = 19/124 (15%)

Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTK 78
             P V+ VD+S +    V+N L+     V  A+N   A  FL                 K
Sbjct: 3   LTPTVMVVDESRITFLAVKNALEKDGFNVIWAKNEQEAFTFL--------------RREK 48

Query: 79  VNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSE-NIPTRINECLEEGAQMFMLK 137
           ++LV  D    G     L+++I+E     +  V V+S+  +    I   ++ GA  ++LK
Sbjct: 49  IDLVFVDV-FEGEESLNLIRRIREEF--PDTKVAVLSAYVDKDLII-NSVKAGAVDYILK 104

Query: 138 PLKP 141
           P + 
Sbjct: 105 PFRL 108

>1k68_A Phytochrome response regulator RCPA; phosphorylated aspartate, CHEY homologue, homodimer, (beta/alpha)5, signaling protein; HET: PHD; 1.90A {Tolypothrix SP} SCOP: c.23.1.1 Length = 140

 Score = 74.2 bits (182), Expect = 6e-18
 Identities = 30/123 (24%), Positives = 58/123 (47%), Gaps = 9/123 (7%)

Query: 23  VLAVDDSIVDRKIVENLLKNS--ACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVN 80
           +  V+D+  D ++++  L NS    +V T  +GM A+ +L       +Q    +N ++ +
Sbjct: 5   IFLVEDNKADIRLIQEALANSTVPHEVVTVRDGMEAMAYL-------RQEGEYANASRPD 57

Query: 81  LVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLK 140
           L++    +P   G E+L +IK    +K +PVVV+S+      I    +     ++ K   
Sbjct: 58  LILLXLNLPKKDGREVLAEIKSDPTLKRIPVVVLSTSINEDDIFHSYDLHVNCYITKSAN 117

Query: 141 PSD 143
            S 
Sbjct: 118 LSQ 120

>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 = 73.0 bits (180), Expect = 2e-17
 Identities = 25/134 (18%), Positives = 53/134 (39%), Gaps = 16/134 (11%)

Query: 14  SSSNPKPPHVLAVDDSIVDRKIVENLLKNSAC--KVTTAENGMRALEFLGLVDEQEQQNN 71
           S +      +L ++D      ++   L+N     K+  A N   A +   L+        
Sbjct: 2   SLNVKNDFSILIIEDDKEFADMLTQFLENLFPYAKIKIAYNPFDAGD---LLHTV----- 53

Query: 72  LNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGA 131
                 K ++V+ D  M GM G+ +  +IK +     + V+ ++       ++  +  GA
Sbjct: 54  ------KPDVVMLDLMMVGMDGFSICHRIKSTPATANIIVIAMTGALTDDNVSRIVALGA 107

Query: 132 QMFMLKPLKPSDVK 145
           +    KPL  + ++
Sbjct: 108 ETCFGKPLNFTLLE 121

>3grc_A Sensor protein, kinase; protein structure initiative II(PSI II), NYSGXRC, 11025B, structural genomics; 2.21A {Polaromonas SP} Length = 140

 Score = 71.1 bits (175), Expect = 1e-16
 Identities = 20/128 (15%), Positives = 44/128 (34%), Gaps = 17/128 (13%)

Query: 16  SNPKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSN 75
           S    P +L  +D     +++  +L+          +  +ALE    V  +         
Sbjct: 2   SLAPRPRILICEDDPDIARLLNLMLEKGGFDSDMVHSAAQALE---QVARR--------- 49

Query: 76  GTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVS--SENIPTRINECLEEGAQM 133
                 +  D  +P   G  L++ ++  S  +++ +VVVS  +                 
Sbjct: 50  --PYAAMTVDLNLPDQDGVSLIRALRRDSRTRDLAIVVVSANAREGELEF-NSQPLAVST 106

Query: 134 FMLKPLKP 141
           ++ KP+  
Sbjct: 107 WLEKPIDE 114

>1ny5_A Transcriptional regulator (NTRC family); AAA+ ATPase, sigma54 activator, bacterial transcription, DIM transcription; HET: ADP; 2.40A {Aquifex aeolicus} SCOP: c.23.1.1 c.37.1.20 PDB: 1ny6_A* 3m0e_A* 1zy2_A* Length = 387

 Score = 74.0 bits (183), Expect = 1e-16
 Identities = 37/127 (29%), Positives = 61/127 (48%), Gaps = 18/127 (14%)

Query: 22  HVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNL 81
           +VL ++D  V R ++E  L     KV +AE G  A + L     ++            N+
Sbjct: 2   NVLVIEDDKVFRGLLEEYLSMKGIKVESAERGKEAYKLL----SEKH----------FNV 47

Query: 82  VITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSE-NIPTRINECLEEGAQMFMLKPLK 140
           V+ D  +P + G E+LK IKE S   E  V+V++    I T + E ++ GA  F+ KP  
Sbjct: 48  VLLDLLLPDVNGLEILKWIKERS--PETEVIVITGHGTIKTAV-EAMKMGAYDFLTKPCM 104

Query: 141 PSDVKKL 147
             +++  
Sbjct: 105 LEEIELT 111

>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 = 69.1 bits (170), Expect = 4e-16
 Identities = 34/132 (25%), Positives = 59/132 (44%), Gaps = 22/132 (16%)

Query: 19  KPPHVLAVDD--SIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNG 76
           +   V  VDD  SI  R ++E  L  +    TT ENG   L  L                
Sbjct: 2   QRGIVWVVDDDSSI--RWVLERALAGAGLTCTTFENGNEVLAAL--------------AS 45

Query: 77  TKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSE-NIPTRINECLEEGAQMFM 135
              +++++D  MPGM G  LLK+IK+      +PV+++++  ++   +    ++GA  ++
Sbjct: 46  KTPDVLLSDIRMPGMDGLALLKQIKQRH--PMLPVIIMTAHSDLDAAV-SAYQQGAFDYL 102

Query: 136 LKPLKPSDVKKL 147
            KP    +   L
Sbjct: 103 PKPFDIDEAVAL 114

>1qkk_A DCTD, C4-dicarboxylate transport transcriptional regulatory protein; receiver domain, 2-component signal transduction; 1.7A {Sinorhizobium meliloti} SCOP: c.23.1.1 PDB: 1l5z_A 1l5y_A Length = 155

 Score = 69.9 bits (172), Expect = 4e-16
 Identities = 31/127 (24%), Positives = 58/127 (45%), Gaps = 22/127 (17%)

Query: 21  PHVLAVDD--SIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTK 78
           P V  +DD   +  RK ++  L+ +   V++  +   AL  L              +   
Sbjct: 4   PSVFLIDDDRDL--RKAMQQTLELAGFTVSSFASATEALAGL--------------SADF 47

Query: 79  VNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSE-NIPTRINECLEEGAQMFMLK 137
             +VI+D  MPGM G  L +KI       ++P+++V+   +IP  + + +++GA  F+ K
Sbjct: 48  AGIVISDIRMPGMDGLALFRKILALD--PDLPMILVTGHGDIPMAV-QAIQDGAYDFIAK 104

Query: 138 PLKPSDV 144
           P     +
Sbjct: 105 PFAADRL 111

>3i42_A Response regulator receiver domain protein (CHEY- like); structural genomics, PSI-2, protein structure initiative; 2.15A {Methylobacillus flagellatus KT} Length = 127

 Score = 68.7 bits (169), Expect = 5e-16
 Identities = 23/134 (17%), Positives = 47/134 (35%), Gaps = 19/134 (14%)

Query: 21  PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVN 80
              L V+D     +  + LL+    +     +G  AL     +  +             +
Sbjct: 4   QQALIVEDYQAAAETFKELLEMLGFQADYVMSGTDALH---AMSTR-----------GYD 49

Query: 81  LVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLK 140
            V  D  +P  +G  L+K+++   + K    V VS         +   E    ++ KP+ 
Sbjct: 50  AVFIDLNLPDTSGLALVKQLRALPMEKTSKFVAVSGFAKNDLG-KEACELFDFYLEKPID 108

Query: 141 PSD----VKKLTGH 150
            +     ++ + GH
Sbjct: 109 IASLEPILQSIEGH 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 = 69.2 bits (170), Expect = 5e-16
 Identities = 23/121 (19%), Positives = 43/121 (35%), Gaps = 15/121 (12%)

Query: 23  VLAVDDSIVDRKIVENLLKNSAC-KVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNL 81
           VL +D    +R+  + +  N         EN  +                   +   + L
Sbjct: 7   VLLIDYFEYEREKTKIIFDNIGEYDFIEVENLKKFYSIF-------------KDLDSITL 53

Query: 82  VITDYCMP-GMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLK 140
           +I D   P    G E+L  I+ +S     PV++ +  + P   +  L+     ++LKP  
Sbjct: 54  IIMDIAFPVEKEGLEVLSAIRNNSRTANTPVIIATKSDNPGYRHAALKFKVSDYILKPYP 113

Query: 141 P 141
            
Sbjct: 114 T 114

>3dzd_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+ ATPase, response regulator, transcriptional activator, ATP-binding; HET: ADP; 2.40A {Aquifex aeolicus} PDB: 1zit_A 2jrl_A Length = 368

 Score = 72.1 bits (178), Expect = 8e-16
 Identities = 25/126 (19%), Positives = 50/126 (39%), Gaps = 18/126 (14%)

Query: 23  VLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLV 82
           VL VDD       +  +L+       TA+    A + +    ++              ++
Sbjct: 3   VLVVDDEESITSSLSAILEEEGYHPDTAKTLREAEKKI----KELF----------FPVI 48

Query: 83  ITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSE-NIPTRINECLEEGAQMFMLKPLKP 141
           + D  MP   G   +  IKE+S   +  V+V++   ++ T + + +++GA  F+ KP   
Sbjct: 49  VLDVWMPDGDGVNFIDFIKENS--PDSVVIVITGHGSVDTAV-KAIKKGAYEFLEKPFSV 105

Query: 142 SDVKKL 147
                 
Sbjct: 106 ERFLLT 111

>3nhm_A Response regulator; protein structure initiative II(PSI II), NYSGXRC, structural genomics; 2.19A {Myxococcus xanthus} Length = 133

 Score = 68.4 bits (168), Expect = 8e-16
 Identities = 31/125 (24%), Positives = 51/125 (40%), Gaps = 16/125 (12%)

Query: 21  PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVN 80
           P VL V++S   R+ +  LL       TTA +G   L+                     +
Sbjct: 5   PKVLIVENSWTMRETLRLLLSGE-FDCTTAADGASGLQ---QALAH-----------PPD 49

Query: 81  LVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLK 140
           ++I+D  M GM GY L    +    +K +PV+ VS     T      +     +++KP+K
Sbjct: 50  VLISDVNMDGMDGYALCGHFRSEPTLKHIPVIFVSGYAPRTEG-PADQPVPDAYLVKPVK 108

Query: 141 PSDVK 145
           P  + 
Sbjct: 109 PPVLI 113

>2jk1_A HUPR, hydrogenase transcriptional regulatory protein HU; nucleotide-binding, transcription regulation; 2.10A {Rhodobacter capsulatus} PDB: 2vui_B 2vuh_B Length = 139

 Score = 67.6 bits (166), Expect = 2e-15
 Identities = 32/129 (24%), Positives = 55/129 (42%), Gaps = 24/129 (18%)

Query: 21  PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVN 80
           P +L VDD       ++  L++    V TA+    A+  L    E+E           V 
Sbjct: 2   PAILLVDDEPHSLAAMKLALEDD-FDVLTAQGAEAAIAIL----EEEW----------VQ 46

Query: 81  LVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVS----SENIPTRINECLEEGAQMFML 136
           ++I D  MPG TG + L +++E     E   ++++    S ++   IN+    G   F+ 
Sbjct: 47  VIICDQRMPGRTGVDFLTEVRERW--PETVRIIITGYTDSASMMAAINDA---GIHQFLT 101

Query: 137 KPLKPSDVK 145
           KP  P  + 
Sbjct: 102 KPWHPEQLL 110

>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 = 66.4 bits (163), Expect = 4e-15
 Identities = 33/123 (26%), Positives = 59/123 (47%), Gaps = 17/123 (13%)

Query: 23  VLAVDDSIVDRKIVENLLKNSACKVT-TAENGMRALEFLGLVDEQEQQNNLNSNGTKVNL 81
           VL VDD+   R ++++++  +  +V   A NG  A+E      E            K ++
Sbjct: 5   VLIVDDAAFMRMMLKDIITKAGYEVAGEATNGREAVE---KYKE-----------LKPDI 50

Query: 82  VITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKP 141
           V  D  MP M G + +K+I +        ++V S+      + E ++ GA+ F++KP +P
Sbjct: 51  VTMDITMPEMNGIDAIKEIMKID--PNAKIIVCSAMGQQAMVIEAIKAGAKDFIVKPFQP 108

Query: 142 SDV 144
           S V
Sbjct: 109 SRV 111

>3gt7_A Sensor protein; structural genomics, signal receiver domain, kinase, PSI-2, protein structure initiative; 2.30A {Syntrophus aciditrophicus SB} Length = 154

 Score = 66.5 bits (163), Expect = 6e-15
 Identities = 30/127 (23%), Positives = 60/127 (47%), Gaps = 14/127 (11%)

Query: 15  SSNPKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNS 74
           S + +   +L V+DS    + ++++L+ +  +     NG  A+     +           
Sbjct: 2   SLSNRAGEILIVEDSPTQAEHLKHILEETGYQTEHVRNGREAVR---FLSLT-------- 50

Query: 75  NGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMF 134
              + +L+I+D  MP M GY L + +K    ++ +PV++++  + P  +   LE GA  F
Sbjct: 51  ---RPDLIISDVLMPEMDGYALCRWLKGQPDLRTIPVILLTILSDPRDVVRSLECGADDF 107

Query: 135 MLKPLKP 141
           + KP K 
Sbjct: 108 ITKPCKD 114

>3kcn_A Adenylate cyclase homolog; SGX, PSI 2, structural genomics, protein structure initiative; 2.45A {Rhodopirellula baltica} Length = 151

 Score = 64.9 bits (159), Expect = 2e-14
 Identities = 31/130 (23%), Positives = 56/130 (43%), Gaps = 19/130 (14%)

Query: 18  PKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
                +L VDD       ++  L     +VTT E+G  AL  +                 
Sbjct: 2   SLNERILLVDDDYSLLNTLKRNLSFD-FEVTTCESGPEALACI-------------KKSD 47

Query: 78  KVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSE-NIPTRINECLEEG-AQMFM 135
             ++++ D  MPGM G E+++K +  S       ++++   ++ T + E + EG    F+
Sbjct: 48  PFSVIMVDMRMPGMEGTEVIQKARLIS--PNSVYLMLTGNQDLTTAM-EAVNEGQVFRFL 104

Query: 136 LKPLKPSDVK 145
            KP + SD+K
Sbjct: 105 NKPCQMSDIK 114

>3eod_A Protein HNR; response regulator, phosphoprotein, two-component regulatory system, signaling protein; 1.75A {Escherichia coli K12} Length = 130

 Score = 64.5 bits (158), Expect = 2e-14
 Identities = 34/123 (27%), Positives = 58/123 (47%), Gaps = 18/123 (14%)

Query: 22  HVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNL 81
            +L V+D  V R ++++   +       A +G+ ALE L               G   +L
Sbjct: 9   QILIVEDEQVFRSLLDSWFSSLGATTVLAADGVDALELL--------------GGFTPDL 54

Query: 82  VITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSS-ENIPTRINECLEEGAQMFMLKPLK 140
           +I D  MP M G +LL+ I+      + PV+V+S+ EN+     + L  G +  +LKP+K
Sbjct: 55  MICDIAMPRMNGLKLLEHIRNRG--DQTPVLVISATENMADIA-KALRLGVEDVLLKPVK 111

Query: 141 PSD 143
             +
Sbjct: 112 DLN 114

>3m6m_D Sensory/regulatory protein RPFC; RPFF, REC, enoyl-COA hydratase, lyase-transferase COMP; 2.50A {Xanthomonas campestris PV} Length = 143

 Score = 64.9 bits (159), Expect = 2e-14
 Identities = 35/138 (25%), Positives = 64/138 (46%), Gaps = 16/138 (11%)

Query: 8   SSSSSSSSSNPKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQE 67
           S+      +  +   +L  DD   +R +++ LL+ +  KV       + L+ +       
Sbjct: 2   SNPFLRHRARVRSMRMLVADDHEANRMVLQRLLEKAGHKVLCVNGAEQVLDAMA------ 55

Query: 68  QQNNLNSNGTKVNLVITDYCMPGMTGYELLKKI--KESSVMKEVPVVVVSSENIPTRINE 125
                       + VI D  MPGM G ++LK++   ++S M+  PVVV+S++  P  I  
Sbjct: 56  --------EEDYDAVIVDLHMPGMNGLDMLKQLRVMQASGMRYTPVVVLSADVTPEAIRA 107

Query: 126 CLEEGAQMFMLKPLKPSD 143
           C + GA+ F+ KP+  + 
Sbjct: 108 CEQAGARAFLAKPVVAAK 125

>2ayx_A Sensor kinase protein RCSC; two independent structural domains, transferase; NMR {Escherichia coli} SCOP: c.23.1.1 c.23.1.6 PDB: 2ayz_A 2ayy_A Length = 254

 Score = 66.7 bits (163), Expect = 3e-14
 Identities = 33/137 (24%), Positives = 64/137 (46%), Gaps = 16/137 (11%)

Query: 7   ASSSSSSSSSNPKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQ 66
           A  S+  + S+     +L VDD  ++R+++ + L +   +  TA +G+ AL  L      
Sbjct: 116 ALPSTDKAVSDNDDMMILVVDDHPINRRLLADQLGSLGYQCKTANDGVDALNVL-----S 170

Query: 67  EQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINEC 126
           +           +++V++D  MP M GY L ++I++      +PV+ V++  +      C
Sbjct: 171 KNH---------IDIVLSDVNMPNMDGYRLTQRIRQLG--LTLPVIGVTANALAEEKQRC 219

Query: 127 LEEGAQMFMLKPLKPSD 143
           LE G    + KP+    
Sbjct: 220 LESGMDSCLSKPVTLDV 236

>2zay_A Response regulator receiver protein; structural genomics, NYSGXRC, target 11006U, protein structure initiative; 2.00A {Desulfuromonas acetoxidans} Length = 147

 Score = 63.8 bits (156), Expect = 7e-14
 Identities = 23/128 (17%), Positives = 49/128 (38%), Gaps = 14/128 (10%)

Query: 14  SSSNPKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLN 73
           S +  K   ++ VD  +       + L      +    N + A+    +  +        
Sbjct: 2   SLAEGKWWRIMLVDTQLPALAASISALSQEGFDIIQCGNAIEAVP---VAVKT------- 51

Query: 74  SNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQM 133
                 +L+IT+  MP ++G +L   +K++     +PV+ +S         + L+ G   
Sbjct: 52  ----HPHLIITEANMPKISGMDLFNSLKKNPQTASIPVIALSGRATAKEEAQLLDMGFID 107

Query: 134 FMLKPLKP 141
           F+ KP+  
Sbjct: 108 FIAKPVNA 115

>3hzh_A Chemotaxis response regulator (CHEY-3); phosphatase, complex, response regulator, receiver domain, two-component signal transduction; HET: BFD; 1.96A {Borrelia burgdorferi} Length = 157

 Score = 63.8 bits (155), Expect = 9e-14
 Identities = 33/139 (23%), Positives = 57/139 (41%), Gaps = 15/139 (10%)

Query: 7   ASSSSSSSSSNPKPPHVLAVDDSIVDRKIVENLLKNSACKVT-TAENGMRALEFLGLVDE 65
           +S     +     P +VL VDDS+   K +  +  +    +  TA +G  A+        
Sbjct: 23  SSKPRGINYDTGIPFNVLIVDDSVFTVKQLTQIFTSEGFNIIDTAADGEEAVI---KYKN 79

Query: 66  QEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINE 125
                        +++V     MP M G   L  I E    K   V+++S+      + +
Sbjct: 80  HYPN---------IDIVTLXITMPKMDGITCLSNIMEFD--KNARVIMISALGKEQLVKD 128

Query: 126 CLEEGAQMFMLKPLKPSDV 144
           CL +GA+ F++KPL  + V
Sbjct: 129 CLIKGAKTFIVKPLDRAKV 147

>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 = 62.6 bits (153), Expect = 2e-13
 Identities = 33/135 (24%), Positives = 51/135 (37%), Gaps = 22/135 (16%)

Query: 9   SSSSSSSSNPKPPHVLAVDDSIVDRKIVENLL-KNSACKVT-TAENGMRALEFLGLVDEQ 66
             S     +  P +V+ VDD+ + R  + + +      KV   A NG  AL+ L      
Sbjct: 2   RGSHHHHHHGSPYNVMIVDDAAMMRLYIASFIKTLPDFKVVAQAANGQEALDKL------ 55

Query: 67  EQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSS---ENIPTRI 123
                  +    V+L++ D  MP M G E L+  K         + ++SS      P   
Sbjct: 56  -------AAQPNVDLILLDIEMPVMDGMEFLRHAKLK---TRAKICMLSSVAVSGSPHAA 105

Query: 124 NECLEEGAQMFMLKP 138
               E GA   + KP
Sbjct: 106 -RARELGADGVVAKP 119

>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 = 2e-13
 Identities = 22/128 (17%), Positives = 49/128 (38%), Gaps = 22/128 (17%)

Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTK 78
           +   +L  DD  +     E+ L ++   VT   +G +A+E L              +G  
Sbjct: 4   EAVTILLADDEAILLLDFESTLTDAGFLVTAVSSGAKAIEML-------------KSGAA 50

Query: 79  VNLVITDYCMP-GMTGYELLKKIKESSVMKEVPVVVVS--SENIPTRINECLEEGAQMFM 135
           ++ V+TD        G+++ +  +E  +   +P+V +S  +          + +     +
Sbjct: 51  IDGVVTDIRFCQPPDGWQVARVARE--IDPNMPIVYISGHAALEWAS--NGVPDSI--IL 104

Query: 136 LKPLKPSD 143
            KP   + 
Sbjct: 105 EKPFTSAQ 112

>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 = 64.5 bits (158), Expect = 3e-13
 Identities = 34/123 (27%), Positives = 60/123 (48%), Gaps = 27/123 (21%)

Query: 23  VLAVDDSIVDRKIVENLL-KNSACKVT-TAENGMRALEFLGLVDEQEQQNNLNSNGTKVN 80
           VL+VDDS + R+I+  ++  +S  ++  TA + + A +   L+ +              +
Sbjct: 6   VLSVDDSALMRQIMTEIINSHSDMEMVATAPDPLVARD---LIKKF-----------NPD 51

Query: 81  LVITDYCMPGMTGYELLKKIKESSVMKE--VPVVVVSS---ENIPTRINECLEEGAQMFM 135
           ++  D  MP M G + L+K+     M+   +PVV+VSS   +     +   LE GA  F+
Sbjct: 52  VLTLDVEMPRMDGLDFLEKL-----MRLRPMPVVMVSSLTGKGSEVTL-RALELGAIDFV 105

Query: 136 LKP 138
            KP
Sbjct: 106 TKP 108

>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 = 61.0 bits (149), Expect = 4e-13
 Identities = 27/121 (22%), Positives = 55/121 (45%), Gaps = 14/121 (11%)

Query: 23  VLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLV 82
           VL V+D+ ++ K+  +LL+    +      G+ AL        +E +          +L+
Sbjct: 4   VLIVEDNELNMKLFHDLLEAQGYETLQTREGLSALSIA-----RENK---------PDLI 49

Query: 83  ITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPS 142
           + D  +P ++G E+ K +KE   +  +PVV V++  +        E G + ++ KP+   
Sbjct: 50  LMDIQLPEISGLEVTKWLKEDDDLAHIPVVAVTAFAMKGDEERIREGGCEAYISKPISVV 109

Query: 143 D 143
            
Sbjct: 110 H 110

>3n53_A Response regulator receiver modulated diguanylate; diguanylate cyclase, protein structure I II(PSI II), NYSGXRC, structural genomics; 2.20A {Pelobacter carbinolicus} Length = 140

 Score = 61.4 bits (150), Expect = 4e-13
 Identities = 30/121 (24%), Positives = 48/121 (39%), Gaps = 15/121 (12%)

Query: 21  PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVN 80
             +L +D     R  ++N L +    V  ++N   ALE    +D               +
Sbjct: 4   KKILIIDQQDFSRIELKNFLDSE-YLVIESKNEKEALE---QIDHH-----------HPD 48

Query: 81  LVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLK 140
           LVI D  + G     L  K+K S  +K VP++++ S      I   L  GA  ++ KP  
Sbjct: 49  LVILDMDIIGENSPNLCLKLKRSKGLKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFN 108

Query: 141 P 141
            
Sbjct: 109 R 109

>2qr3_A Two-component system response regulator; structural genomics, signal receiver, PSI-2, protein structu initiative; 1.80A {Bacteroides fragilis} Length = 140

 Score = 61.4 bits (150), Expect = 4e-13
 Identities = 29/127 (22%), Positives = 50/127 (39%), Gaps = 23/127 (18%)

Query: 21  PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVN 80
             ++ VDD+      V+ LLKN   KV T  + +     L                    
Sbjct: 4   GTIIIVDDNKGVLTAVQLLLKNHFSKVITLSSPVSLSTVL--------------REENPE 49

Query: 81  LVITDYCMP-----GMTGYELLKKIKESSVMKEVPVVVVSSE-NIPTRINECLEEGAQMF 134
           +V+ D         G  G   L +IK     +++PVV+ ++  +I   +   ++EGA  F
Sbjct: 50  VVLLDMNFTSGINNGNEGLFWLHEIKRQY--RDLPVVLFTAYADIDLAV-RGIKEGASDF 106

Query: 135 MLKPLKP 141
           ++KP   
Sbjct: 107 VVKPWDN 113

>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 = 60.9 bits (148), Expect = 5e-13
 Identities = 43/125 (34%), Positives = 60/125 (48%), Gaps = 14/125 (11%)

Query: 20  PPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKV 79
              VL VDDS V RKIV   LK    +V  AENG  ALE    + E              
Sbjct: 2   SKKVLLVDDSAVLRKIVSFNLKKEGYEVIEAENGQIALE---KLSEF-----------TP 47

Query: 80  NLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPL 139
           +L++    MP M G+ +LKK++E    K +PV+V++++      +  L  GA+  M KP 
Sbjct: 48  DLIVLXIMMPVMDGFTVLKKLQEKEEWKRIPVIVLTAKGGEEDESLALSLGARKVMRKPF 107

Query: 140 KPSDV 144
            PS  
Sbjct: 108 SPSQF 112

>3kht_A Response regulator; PSI-II, 11023K, structural genomics, Pro structure initiative, NEW YORK SGX research center for STRU genomics, nysgxrc; 2.10A {Hahella chejuensis} Length = 144

 Score = 61.1 bits (149), Expect = 6e-13
 Identities = 27/127 (21%), Positives = 55/127 (43%), Gaps = 16/127 (12%)

Query: 19  KPPHVLAVDDSIVDRKIVENLLKNS--ACKVTTAENGMRALEFLGLVDEQEQQNNLNSNG 76
           +   VL V+D+  D  ++  +L      C++   +NG +AL  +       QQ       
Sbjct: 4   RSKRVLVVEDNPDDIALIRRVLDRKDIHCQLEFVDNGAKALYQV-------QQA------ 50

Query: 77  TKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFML 136
            K +L+I D  +P   G+E++  +++    +  P+V+++      R  +C+  GA   + 
Sbjct: 51  -KYDLIILDIGLPIANGFEVMSAVRKPGANQHTPIVILTDNVSDDRAKQCMAAGASSVVD 109

Query: 137 KPLKPSD 143
           K      
Sbjct: 110 KSSNNVT 116

>2j48_A Two-component sensor kinase; pseudo-receiver, circadian clock, transferase, response regulator, histidine protein kinase; NMR {Synechococcus elongatus} Length = 119

 Score = 60.2 bits (147), Expect = 9e-13
 Identities = 23/120 (19%), Positives = 45/120 (37%), Gaps = 17/120 (14%)

Query: 22  HVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNL 81
           H+L +++      +V  +L  +  KV    +G  AL+    +D             +  +
Sbjct: 3   HILLLEEEDEAATVVCEMLTAAGFKVIWLVDGSTALD---QLDLL-----------QPIV 48

Query: 82  VITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKP 141
           ++  +  P  +   LL+ ++E       P+V+   E         L   A   + KPL P
Sbjct: 49  ILMAWPPPDQSCLLLLQHLREHQADPHPPLVLFLGEPPVDP---LLTAQASAILSKPLDP 105

>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 = 61.6 bits (150), Expect = 1e-12
 Identities = 29/138 (21%), Positives = 58/138 (42%), Gaps = 18/138 (13%)

Query: 9   SSSSSSSSNPKPPHVLAVDDSIVDRKIVENLLKNSACKVT-TAENGMRALEFLGLVDEQE 67
           +  ++ +    P  VL  +D  + R  +  +L+    ++   A +G  A+E   L +   
Sbjct: 2   TGPTTDADAAVPRRVLIAEDEALIRMDLAEMLREEGYEIVGEAGDGQEAVE---LAEL-- 56

Query: 68  QQNNLNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECL 127
                     K +LVI D  MP   G +   +I      +  P+VV+++ +    +    
Sbjct: 57  ---------HKPDLVIMDVKMPRRDGIDAASEIASK---RIAPIVVLTAFSQRDLVERAR 104

Query: 128 EEGAQMFMLKPLKPSDVK 145
           + GA  +++KP   SD+ 
Sbjct: 105 DAGAMAYLVKPFSISDLI 122

>3crn_A Response regulator receiver domain protein, CHEY-; structural genomics, signal regulator receiver domain; HET: PHD; 1.58A {Methanospirillum hungatei jf-1} Length = 132

 Score = 59.8 bits (145), Expect = 1e-12
 Identities = 25/125 (20%), Positives = 44/125 (35%), Gaps = 16/125 (12%)

Query: 21  PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVN 80
             +L VDD        + +L+    +V  A      L  +                   N
Sbjct: 4   KRILIVDDDTAILDSTKQILEFEGYEVEIAATAGEGLAKI--------------ENEFFN 49

Query: 81  LVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLK 140
           L +    +P M G ELL+K  +      +  ++V+           L  GA  +++KP+ 
Sbjct: 50  LALFXIKLPDMEGTELLEKAHKLR--PGMKKIMVTGYASLENSVFSLNAGADAYIMKPVN 107

Query: 141 PSDVK 145
           P D+ 
Sbjct: 108 PRDLL 112

>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 = 61.2 bits (149), Expect = 2e-12
 Identities = 32/127 (25%), Positives = 58/127 (45%), Gaps = 18/127 (14%)

Query: 18  PKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
              P V  VDD +  R+ + NLL+++  +V T +    A  FL     ++          
Sbjct: 2   TAKPTVFVVDDDMSVREGLRNLLRSAGFEVETFDC---ASTFLEHRRPEQ---------- 48

Query: 78  KVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVS-SENIPTRINECLEEGAQMFML 136
               ++ D  MPGM+G EL +++   S    +P+V ++   +IP  +   ++ GA  F+ 
Sbjct: 49  -HGCLVLDMRMPGMSGIELQEQLTAISD--GIPIVFITAHGDIPMTV-RAMKAGAIEFLP 104

Query: 137 KPLKPSD 143
           KP +   
Sbjct: 105 KPFEEQA 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 = 59.5 bits (145), Expect = 2e-12
 Identities = 29/123 (23%), Positives = 53/123 (43%), Gaps = 18/123 (14%)

Query: 21  PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVN 80
             +L VDDS +   +   +L+    +  TA +G   LE    ++               +
Sbjct: 4   YTILVVDDSPMIVDVFVTMLERGGYRPITAFSGEECLE---ALNAT-----------PPD 49

Query: 81  LVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVS--SENIPTRINECLEEGAQMFMLKP 138
           LV+ D  M  M G+E L++IK     +++PV++++      P   NE      + ++LKP
Sbjct: 50  LVLLDIMMEPMDGWETLERIKTDPATRDIPVLMLTAKPL-TPEEANE-YGSYIEDYILKP 107

Query: 139 LKP 141
              
Sbjct: 108 TTH 110

>3snk_A Response regulator CHEY-like protein; P-loop containing nucleoside triphosphate hydrolases, struct genomics; 2.02A {Mesorhizobium loti} Length = 135

 Score = 59.2 bits (144), Expect = 2e-12
 Identities = 20/137 (14%), Positives = 39/137 (28%), Gaps = 23/137 (16%)

Query: 9   SSSSSSSSNPKPPHVLAVDDSIVDRKIVE----NLLKNSACKVTTAENGMRALEFLGLVD 64
           ++ ++  +  K   V        D          L   +   V  +E             
Sbjct: 3   NAINTKVTPTKRKQVALFSS---DPNFKRDVATRLDALAIYDVRVSETDDFLKGPPA--- 56

Query: 65  EQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRIN 124
                       T+  +VI D     + G   + + +       VP++ VS E    +  
Sbjct: 57  -----------DTRPGIVILDLGGGDLLGKPGIVEARAL--WATVPLIAVSDELTSEQTR 103

Query: 125 ECLEEGAQMFMLKPLKP 141
             +   A  ++ KPL  
Sbjct: 104 VLVRMNASDWLHKPLDG 120

>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 = 59.3 bits (144), Expect = 3e-12
 Identities = 13/127 (10%), Positives = 40/127 (31%), Gaps = 15/127 (11%)

Query: 22  HVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNL 81
           ++L   +       +  L+ ++     T   G  A                       ++
Sbjct: 22  NILVASEDASRLAHLARLVGDAGRYRVTRTVGRAAQIVQRTDGLDA-----------FDI 70

Query: 82  VITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSS-ENIPTRINECLEEGAQMFMLKPLK 140
           ++ D           ++K+        +  ++V++  +  T + + +  G +  +  PL+
Sbjct: 71  LMIDGAALDTAELAAIEKLSRLHP--GLTCLLVTTDASSQTLL-DAMRAGVRDVLRWPLE 127

Query: 141 PSDVKKL 147
           P  +   
Sbjct: 128 PRALDDA 134

>3cg4_A Response regulator receiver domain protein (CHEY-; structural genomics, unknown function; HET: MSE; 1.61A {Methanospirillum hungatei jf-1} Length = 142

 Score = 59.1 bits (144), Expect = 3e-12
 Identities = 21/98 (21%), Positives = 47/98 (47%), Gaps = 14/98 (14%)

Query: 15  SSNPKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNS 74
           S       V+ VDD    R  V+ +L ++   + +A++G + ++   L+ +         
Sbjct: 2   SLAEHKGDVMIVDDDAHVRIAVKTILSDAGFHIISADSGGQCID---LLKKG-------- 50

Query: 75  NGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVV 112
                 +V+ D  MPGM G++ ++ I ++S+ + + +V
Sbjct: 51  ---FSGVVLLDIMMPGMDGWDTIRAILDNSLEQGIAIV 85

>3t8y_A CHEB, chemotaxis response regulator protein-glutamate methylesterase; CHEA, hydrolase; 1.90A {Thermotoga maritima} Length = 164

 Score = 59.6 bits (145), Expect = 4e-12
 Identities = 39/139 (28%), Positives = 59/139 (42%), Gaps = 27/139 (19%)

Query: 7   ASSSSSSSSSNPKPPHVLAVDDSIVDRKIVENLL-KNSACKVT-TAENGMRALEFLGLVD 64
           +      S    +   VL VDDS   R ++++++      KV   A++G+ A+E      
Sbjct: 12  SGLVPRGSHMTDRVIRVLVVDDSAFMRMVLKDIIDSQPDMKVVGFAKDGLEAVE---KAI 68

Query: 65  EQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKE--VPVVVVSS---ENI 119
           E            K +++  D  MP + G E LK I     MK+    V++VSS   E  
Sbjct: 69  EL-----------KPDVITMDIEMPNLNGIEALKLI-----MKKAPTRVIMVSSLTEEGA 112

Query: 120 PTRINECLEEGAQMFMLKP 138
              I E L  GA  F+ KP
Sbjct: 113 AITI-EALRNGAVDFITKP 130

>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 = 58.2 bits (142), Expect = 4e-12
 Identities = 22/95 (23%), Positives = 44/95 (46%), Gaps = 17/95 (17%)

Query: 21  PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVN 80
           PH+L V+D +V R  ++++ +     V  A +G    + L              +   +N
Sbjct: 4   PHILIVEDELVTRNTLKSIFEAEGYDVFEATDGAEMHQIL--------------SEYDIN 49

Query: 81  LVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVS 115
           LVI D  +PG  G  L ++++E +    V ++ ++
Sbjct: 50  LVIMDINLPGKNGLLLARELREQA---NVALMFLT 81

>3h5i_A Response regulator/sensory box protein/ggdef domain protein; structural genomics, transcription, PSI-2; 1.90A {Carboxydothermus hydrogenoformans z-2901} Length = 140

 Score = 58.7 bits (143), Expect = 4e-12
 Identities = 28/127 (22%), Positives = 51/127 (40%), Gaps = 17/127 (13%)

Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTK 78
           K   +L V+DS    K + N+L      V  A  G  A+E +             S G  
Sbjct: 4   KDKKILIVEDSKFQAKTIANILNKYGYTVEIALTGEAAVEKV-------------SGGWY 50

Query: 79  VNLVITDYCMPG-MTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLK 137
            +L++ D  +   M G +    I++ S   E+PVV +++   P  + +     A  +++K
Sbjct: 51  PDLILMDIELGEGMDGVQTALAIQQIS---ELPVVFLTAHTEPAVVEKIRSVTAYGYVMK 107

Query: 138 PLKPSDV 144
                 +
Sbjct: 108 SATEQVL 114

>3eqz_A Response regulator; structural genomics, unknown function, PSI-2, protein struct initiative; 2.15A {Colwellia psychrerythraea} Length = 135

 Score = 58.8 bits (143), Expect = 5e-12
 Identities = 22/127 (17%), Positives = 43/127 (33%), Gaps = 24/127 (18%)

Query: 21  PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVN 80
             V  VDD  +   +++ +++     V  A    RA   L              +  K +
Sbjct: 4   NRVFIVDDDTLTCNLLKTIVEPIFGNVE-AFQHPRAFLTL--------------SLNKQD 48

Query: 81  LVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVS------SENIPTRINECLEEGAQMF 134
           ++I D  MP M G E+++ + E        ++++S        +  T             
Sbjct: 49  IIILDLMMPDMDGIEVIRHLAEHK--SPASLILISGYDSGVLHSAETLALS-CGLNVINT 105

Query: 135 MLKPLKP 141
             KP+  
Sbjct: 106 FTKPINT 112

>3rqi_A Response regulator protein; structural genomics, seattle structural genomics center for infectious disease, ssgcid; HET: PHD CIT; 1.70A {Burkholderia pseudomallei} Length = 184

 Score = 59.6 bits (145), Expect = 5e-12
 Identities = 20/128 (15%), Positives = 45/128 (35%), Gaps = 24/128 (18%)

Query: 21  PHVLAVDDSIVDRKIVENL---LKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
            + L +DD   +      L   L+     V  A N   AL+                   
Sbjct: 8   KNFLVIDD---NEVFAGTLARGLERRGYAVRQAHNKDEALKLA--------------GAE 50

Query: 78  KVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSE-NIPTRINECLEEGAQMFML 136
           K   +     +   +G  L+  + +     +  ++V++   +I T + + +++GA  ++ 
Sbjct: 51  KFEFITVXLHLGNDSGLSLIAPLCDLQ--PDARILVLTGYASIATAV-QAVKDGADNYLA 107

Query: 137 KPLKPSDV 144
           KP     +
Sbjct: 108 KPANVESI 115

>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 = 58.3 bits (142), Expect = 5e-12
 Identities = 28/125 (22%), Positives = 54/125 (43%), Gaps = 18/125 (14%)

Query: 20  PPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKV 79
              V  VDD    RK +  +L  +   V   ++    L F                  + 
Sbjct: 3   DYTVHIVDDEEPVRKSLAFMLTMNGFAVKMHQSAEAFLAFA--------------PDVRN 48

Query: 80  NLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSE-NIPTRINECLEEGAQMFMLKP 138
            +++TD  MP M+G ELL+ + +  +   +P +V++   ++P  + E ++ GA  F+ KP
Sbjct: 49  GVLVTDLRMPDMSGVELLRNLGDLKI--NIPSIVITGHGDVPMAV-EAMKAGAVDFIEKP 105

Query: 139 LKPSD 143
            + + 
Sbjct: 106 FEDTV 110

>3cu5_A Two component transcriptional regulator, ARAC FAM; structural genomics, protein structure initiative; 2.60A {Clostridium phytofermentans isdg} Length = 141

 Score = 57.5 bits (140), Expect = 1e-11
 Identities = 27/131 (20%), Positives = 54/131 (41%), Gaps = 27/131 (20%)

Query: 23  VLAVDDSIVDRKIVENLLKNSACK---VTTAENGMRALEFLGLVDEQEQQNNLNSNGTKV 79
           +L VDD  + R  +   +   A     +  A++G+ A++       +             
Sbjct: 5   ILIVDDEKLTRDGLIANINWKALSFDQIDQADDGINAIQIA----LKH----------PP 50

Query: 80  NLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSS----ENIPTRINECLEEGAQMFM 135
           N+++TD  MP M G EL+  I +     +  V+ +S     E     +   ++  A  ++
Sbjct: 51  NVLLTDVRMPRMDGIELVDNILKLY--PDCSVIFMSGYSDKEY----LKAAIKFRAIRYV 104

Query: 136 LKPLKPSDVKK 146
            KP+ PS++  
Sbjct: 105 EKPIDPSEIMD 115

>1dcf_A ETR1 protein; beta-alpha five sandwich, transferase; 2.50A {Arabidopsis thaliana} SCOP: c.23.1.2 Length = 136

 Score = 56.4 bits (137), Expect = 3e-11
 Identities = 28/130 (21%), Positives = 55/130 (42%), Gaps = 22/130 (16%)

Query: 22  HVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNL 81
            VL +D++ V R + + LL +  C+VTT  +    L  +                 +  +
Sbjct: 9   KVLVMDENGVSRMVTKGLLVHLGCEVTTVSSNEECLRVV---------------SHEHKV 53

Query: 82  VITDYCMPGMTGYELLKKIKE---SSVMKEVPVVVVSSENIPTRINECLEEGAQM--FML 136
           V  D CMPG+  Y++  +I E       +   +V +S     +   +C+  G  +   +L
Sbjct: 54  VFMDVCMPGVENYQIALRIHEKFTKQRHQRPLLVALSGNTDKSTKEKCMSFG--LDGVLL 111

Query: 137 KPLKPSDVKK 146
           KP+   +++ 
Sbjct: 112 KPVSLDNIRD 121

>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 = 55.2 bits (134), Expect = 8e-11
 Identities = 29/124 (23%), Positives = 54/124 (43%), Gaps = 21/124 (16%)

Query: 20  PPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKV 79
           P H++ V+D  V +  +++        V+   +G    E +                  V
Sbjct: 2   PHHIVIVEDEPVTQARLQSYFTQEGYTVSVTASGAGLREIM--------------QNQSV 47

Query: 80  NLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVS--SENIPTRINECLEEGAQMFMLK 137
           +L++ D  +P   G  L + ++E S    V +++V+  S+ I  RI   LE GA  ++ K
Sbjct: 48  DLILLDINLPDENGLMLTRALRERS---TVGIILVTGRSDRI-DRI-VGLEMGADDYVTK 102

Query: 138 PLKP 141
           PL+ 
Sbjct: 103 PLEL 106

>3t6k_A Response regulator receiver; flavodoxin-like, structural genomics, joint center for struc genomics, JCSG, protein structure initiative; HET: MSE; 1.86A {Chloroflexus aurantiacus} Length = 136

 Score = 54.9 bits (133), Expect = 1e-10
 Identities = 25/97 (25%), Positives = 46/97 (47%), Gaps = 20/97 (20%)

Query: 19  KPPHVLAVDDSIVDRKIVENL---LKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSN 75
           KP  +L VDD   D  + E L   L+ +  +V  A +G  AL+    + +          
Sbjct: 3   KPHTLLIVDD---DDTVAEMLELVLRGAGYEVRRAASGEEALQ---QIYKN--------- 47

Query: 76  GTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVV 112
               + +I D  +PG+ GY L K++++  + K +P++
Sbjct: 48  --LPDALICDVLLPGIDGYTLCKRVRQHPLTKTLPIL 82

>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 = 56.3 bits (135), Expect = 2e-10
 Identities = 34/141 (24%), Positives = 59/141 (41%), Gaps = 22/141 (15%)

Query: 7   ASSSSSSSSSNPKPPHVLAVDDSIVDRKIVENL---LKNSACKVTTAENGMRALEFLGLV 63
             ++ +   +      VL VDD   +  IVE L   LK    +V TA NG +AL+     
Sbjct: 10  LVTAGTPGENTTPEARVLVVDD---EANIVELLSVSLKFQGFEVYTATNGAQALD---RA 63

Query: 64  DEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRI 123
            E              + VI D  MPGM G+ +L++++   +  + P + +++ +     
Sbjct: 64  RETR-----------PDAVILDVXMPGMDGFGVLRRLRADGI--DAPALFLTARDSLQDK 110

Query: 124 NECLEEGAQMFMLKPLKPSDV 144
              L  G   ++ KP    +V
Sbjct: 111 IAGLTLGGDDYVTKPFSLEEV 131

>3cg0_A Response regulator receiver modulated diguanylate with PAS/PAC sensor; signal receiver domain, diguanylate cyclase; 2.15A {Desulfovibrio desulfuricans subsp} Length = 140

 Score = 54.1 bits (131), Expect = 2e-10
 Identities = 19/135 (14%), Positives = 47/135 (34%), Gaps = 19/135 (14%)

Query: 13  SSSSNPKPPHVLAVDDSIVDRKIVENLLKNSACKVT-TAENGMRALEFLGLVDEQEQQNN 71
           S +++   P VL V+D  +    +   L++    V    +NG  A+       +      
Sbjct: 2   SLTASDDLPGVLIVEDGRLAAATLRIQLESLGYDVLGVFDNGEEAVR---CAPD------ 52

Query: 72  LNSNGTKVNLVITDYCMPG-MTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEG 130
                 + ++ + D  + G + G E   ++        +P++ ++S              
Sbjct: 53  -----LRPDIALVDIMLCGALDGVETAARLAAGC---NLPIIFITSSQDVETFQRAKRVN 104

Query: 131 AQMFMLKPLKPSDVK 145
              ++ KP+    + 
Sbjct: 105 PFGYLAKPVAADTLH 119

>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 = 53.6 bits (130), Expect = 3e-10
 Identities = 32/125 (25%), Positives = 54/125 (43%), Gaps = 31/125 (24%)

Query: 21  PHVLAVDD--SIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTK 78
            +VL V+D  +I  R+ +   L+    +V  AE   R L        +           K
Sbjct: 2   TNVLIVEDEQAI--RRFLRTALEGDGMRVFEAETLQRGLL---EAATR-----------K 45

Query: 79  VNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINEC-----LEEGAQM 133
            +L+I D  +P   G E ++ +++ S    VPV+V+S+     R  E      L+ GA  
Sbjct: 46  PDLIILDLGLPDGDGIEFIRDLRQWS---AVPVIVLSA-----RSEESDKIAALDAGADD 97

Query: 134 FMLKP 138
           ++ KP
Sbjct: 98  YLSKP 102

>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 = 53.2 bits (129), Expect = 3e-10
 Identities = 24/94 (25%), Positives = 45/94 (47%), Gaps = 17/94 (18%)

Query: 22  HVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNL 81
            +L VDD      I++  +     +V TA NG  ALE     + +           + ++
Sbjct: 3   KILIVDDEKPISDIIKFNMTKEGYEVVTAFNGREALE---QFEAE-----------QPDI 48

Query: 82  VITDYCMPGMTGYELLKKIKESSVMKEVPVVVVS 115
           +I D  +P + G E+ K I+++S    VP++++S
Sbjct: 49  IILDLMLPEIDGLEVAKTIRKTS---SVPILMLS 79

>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 = 53.2 bits (129), Expect = 4e-10
 Identities = 22/98 (22%), Positives = 48/98 (48%), Gaps = 21/98 (21%)

Query: 20  PPHVLAVDD--SIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
              +L VDD   I D  I+E  L+    +V  A +G  A+E   +V+E            
Sbjct: 2   DKKILVVDDEKPIAD--ILEFNLRKEGYEVHCAHDGNEAVE---MVEEL----------- 45

Query: 78  KVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVS 115
           + +L++ D  +P   G E+ +++++     ++P+++++
Sbjct: 46  QPDLILLDIMLPNKDGVEVCREVRKKY---DMPIIMLT 80

>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 = 53.0 bits (128), Expect = 6e-10
 Identities = 16/97 (16%), Positives = 38/97 (39%), Gaps = 15/97 (15%)

Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTK 78
           +P  V  V+D      +++  L     +VT   +G    +    +               
Sbjct: 14  QPFRVTLVEDEPSHATLIQYHLNQLGAEVTVHPSGSAFFQHRSQLS-------------T 60

Query: 79  VNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVS 115
            +L+I    +  ++ + LL  +KE +  K+  V++++
Sbjct: 61  CDLLIVSDQLVDLSIFSLLDIVKEQT--KQPSVLILT 95

>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 = 54.0 bits (130), Expect = 7e-10
 Identities = 34/143 (23%), Positives = 54/143 (37%), Gaps = 13/143 (9%)

Query: 7   ASSSSSSSSSNPKPPHVLAVDDSIVDRKIVENLLKNSAC-KVTTAENGMRALEFLGLVDE 65
             +S  S     +   VL VDD+ + RK+    LK     +V   ++G  AL  +     
Sbjct: 48  QETSKPSDDEFLRGKRVLVVDDNFISRKVATGKLKKMGVSEVEQCDSGKEALRLVTEGLT 107

Query: 66  QEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKI--KESSVMKEVPVV-----VVSSEN 118
           Q ++          + +  D  MP M GYE  ++I   E S     P++        SE 
Sbjct: 108 QREEQGSVDKLP-FDYIFMDCQMPEMDGYEATREIRKVEKSYGVRTPIIAVSGHDPGSE- 165

Query: 119 IPTRINECLEEGAQMFMLKPLKP 141
                 E ++ G   F+ K L  
Sbjct: 166 ---EARETIQAGMDAFLDKSLNQ 185

>3lte_A Response regulator; structural genomics, PSI, protein structure initiative, NYSG YORK structural genomix research consortium, nysgxrc; 2.00A {Bermanella marisrubri} Length = 132

 Score = 52.6 bits (127), Expect = 8e-10
 Identities = 26/130 (20%), Positives = 52/130 (40%), Gaps = 23/130 (17%)

Query: 16  SNPKPPHVLAVDDSIVDRKIVENL---LKNSACKVTTAENGMRALEFLGLVDEQEQQNNL 72
           S  +   +L VDD   D+ +   +   LK    +V  A NG  A      +         
Sbjct: 2   SLKQSKRILVVDD---DQAMAAAIERVLKRDHWQVEIAHNGFDAGI---KLSTF------ 49

Query: 73  NSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSS-ENIPTRINECLEEGA 131
                +  ++  D  MP + G ++++ ++++ V    P ++V S  +      + + EGA
Sbjct: 50  -----EPAIMTLDLSMPKLDGLDVIRSLRQNKVAN-QPKILVVSGLDKAKLQ-QAVTEGA 102

Query: 132 QMFMLKPLKP 141
             ++ KP   
Sbjct: 103 DDYLEKPFDN 112

>2qzj_A Two-component response regulator; 11017X, PSI-II, structural genomics; 2.89A {Clostridium difficile} Length = 136

 Score = 52.5 bits (127), Expect = 9e-10
 Identities = 15/94 (15%), Positives = 35/94 (37%), Gaps = 17/94 (18%)

Query: 22  HVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNL 81
            +L +D    + + ++  L+     +  A N   A+     +              K +L
Sbjct: 6   KILIIDGDKDNCQKLKGFLEEKGISIDLAYNCEEAIG---KIFSN-----------KYDL 51

Query: 82  VITDYCMPGMTGYELLKKIKESSVMKEVPVVVVS 115
           +  +  +    G+ L KKI+  +     P+V ++
Sbjct: 52  IFLEIILSDGDGWTLCKKIRNVT---TCPIVYMT 82

>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 = 53.7 bits (130), Expect = 1e-09
 Identities = 23/99 (23%), Positives = 43/99 (43%), Gaps = 23/99 (23%)

Query: 20  PPHVLAVDDSIVDRKIVENL---LKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNG 76
              VL V+D   +  + + L   L+    + T   +G  AL      D            
Sbjct: 4   ATSVLIVED---EESLADPLAFLLRKEGFEATVVTDGPAALA---EFDRA---------- 47

Query: 77  TKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVS 115
              ++V+ D  +PGM+G ++ K+++  S    VPV++V+
Sbjct: 48  -GADIVLLDLMLPGMSGTDVCKQLRARS---SVPVIMVT 82

>2jba_A Phosphate regulon transcriptional regulatory PROT; transcription factor, sensory transduction, phosphate regula transcription regulation; 1.45A {Escherichia coli} PDB: 2jba_B 1b00_A 2iyn_A 2jb9_A 1zes_A Length = 127

 Score = 51.7 bits (125), Expect = 2e-09
 Identities = 19/96 (19%), Positives = 44/96 (45%), Gaps = 20/96 (20%)

Query: 20  PPHVLAVDDSIVDRKIVENL---LKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNG 76
              +L V+D   +  I E +   L+ +  +   AE+   A+     ++E           
Sbjct: 2   ARRILVVED---EAPIREMVCFVLEQNGFQPVEAEDYDSAVN---QLNEP---------- 45

Query: 77  TKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVV 112
              +L++  + +PG +G + +K ++  S+ +++PVV
Sbjct: 46  -WPDLILLAWMLPGGSGIQFIKHLRRESMTRDIPVV 80

>3c97_A Signal transduction histidine kinase; structural genomics, signaling, PSI-2, protein structure initiative; 1.70A {Aspergillus oryzae RIB40} Length = 140

 Score = 51.4 bits (124), Expect = 3e-09
 Identities = 24/104 (23%), Positives = 43/104 (41%), Gaps = 17/104 (16%)

Query: 12  SSSSSNPKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNN 71
           S   S   P  VL  +D+ + R +    L+     +T   NG++AL+       Q +Q  
Sbjct: 2   SLEPSQIMPLSVLIAEDNDICRLVAAKALEKCTNDITVVTNGLQALQAY-----QNRQ-- 54

Query: 72  LNSNGTKVNLVITDYCMPGMTGYELLKKIKE---SSVMKEVPVV 112
                   +++I D  MP M G E + +I+    +   K   ++
Sbjct: 55  -------FDVIIMDIQMPVMDGLEAVSEIRNYERTHNTKRASII 91

>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 = 52.5 bits (127), Expect = 4e-09
 Identities = 32/130 (24%), Positives = 56/130 (43%), Gaps = 33/130 (25%)

Query: 20  PPHVLAVDDSIVDRKIVENL---LKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNG 76
              +L VDD   D  + E L   L+          +G +AL     V E           
Sbjct: 5   RQRILVVDD---DASLAEMLTIVLRGEGFDTAVIGDGTQALT---AVREL---------- 48

Query: 77  TKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINEC-----LEEGA 131
            + +LV+ D  +PGM G ++ + ++  S    VP+V++++     + +       LE GA
Sbjct: 49  -RPDLVLLDLMLPGMNGIDVCRVLRADS---GVPIVMLTA-----KTDTVDVVLGLESGA 99

Query: 132 QMFMLKPLKP 141
             +++KP KP
Sbjct: 100 DDYIMKPFKP 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 = 50.6 bits (122), Expect = 4e-09
 Identities = 23/126 (18%), Positives = 49/126 (38%), Gaps = 22/126 (17%)

Query: 20  PPHVLAVDDSIVDRKIVENL---LKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNG 76
              +L V+    D  +   L   L+     V    +G  ++E    +             
Sbjct: 5   SKKILIVES---DTALSATLRSALEGRGFTVDETTDGKGSVE---QIRRD---------- 48

Query: 77  TKVNLVITDYCM-PGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFM 135
            + +LV+    +  G  GY +  K+K+   +K VP+V++ + +   +    L+  A  ++
Sbjct: 49  -RPDLVVLAVDLSAGQNGYLICGKLKKDDDLKNVPIVIIGNPDGFAQH-RKLKAHADEYV 106

Query: 136 LKPLKP 141
            KP+  
Sbjct: 107 AKPVDA 112

>1mvo_A PHOP response regulator; phosphate regulon, transcriptional regulatory protein, alpha/beta doubly wound fold, phosphorylation; 1.60A {Bacillus subtilis} SCOP: c.23.1.1 Length = 136

 Score = 50.2 bits (121), Expect = 7e-09
 Identities = 20/96 (20%), Positives = 44/96 (45%), Gaps = 16/96 (16%)

Query: 20  PPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKV 79
              +L VDD      +++  L+ S   V TA +G  AL+     + +           K 
Sbjct: 3   NKKILVVDDEESIVTLLQYNLERSGYDVITASDGEEALK---KAETE-----------KP 48

Query: 80  NLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVS 115
           +L++ D  +P + G E+ K++++       P+++++
Sbjct: 49  DLIVLDVMLPKLDGIEVCKQLRQQK--LMFPILMLT 82

>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 = 49.8 bits (120), Expect = 1e-08
 Identities = 28/126 (22%), Positives = 58/126 (46%), Gaps = 11/126 (8%)

Query: 22  HVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVN 80
            +L V+D+ V++++++ +L     + +  A +G  A + +  +  + +           N
Sbjct: 4   KILVVEDNHVNQEVIKRMLNLEGIENIELACDGQEAFDKVKELTSKGEN---------YN 54

Query: 81  LVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLK 140
           ++  D  MP + G    K I+        P+V +++    + I ECLE G   F+ KP+K
Sbjct: 55  MIFMDVQMPKVDGLLSTKMIRRDLG-YTSPIVALTAFADDSNIKECLESGMNGFLSKPIK 113

Query: 141 PSDVKK 146
              +K 
Sbjct: 114 RPKLKT 119

>3kto_A Response regulator receiver protein; PSI-II,structural genomics, protein structure initiative; 1.98A {Pseudoalteromonas atlantica T6C} Length = 136

 Score = 49.9 bits (120), Expect = 1e-08
 Identities = 23/128 (17%), Positives = 44/128 (34%), Gaps = 24/128 (18%)

Query: 21  PHVLAVDD--SIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTK 78
           P +  VD       R  +  LL      +    +   A  F+      +           
Sbjct: 7   PIIYLVDHQKDA--RAALSKLLSPLDVTIQCFAS---AESFMRQQISDDA---------- 51

Query: 79  VNLVITDYCMPGM--TGYELLKKIKESSVMKEVPVVVVSSE-NIPTRINECLEEGAQMFM 135
              +I +  +     +G ELL+ + +      +P +V++S  +IPT +   +   A  F+
Sbjct: 52  -IGMIIEAHLEDKKDSGIELLETLVKRGF--HLPTIVMASSSDIPTAV-RAMRASAADFI 107

Query: 136 LKPLKPSD 143
            KP     
Sbjct: 108 EKPFIEHV 115

>3a10_A Response regulator; phosphoacceptor, signaling protein; HET: MSE PG4; 1.63A {Thermotoga maritima} PDB: 3a0r_B* 3a0u_A* Length = 116

 Score = 49.4 bits (119), Expect = 1e-08
 Identities = 24/94 (25%), Positives = 46/94 (48%), Gaps = 16/94 (17%)

Query: 22  HVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNL 81
            +L VDD    R++++  L+    ++ TAENG  AL+                     +L
Sbjct: 3   RILVVDDEPNIRELLKEELQEEGYEIDTAENGEEALK---KFFSG-----------NYDL 48

Query: 82  VITDYCMPGMTGYELLKKIKESSVMKEVPVVVVS 115
           VI D  MPG++G E+  +I++    K+  +++++
Sbjct: 49  VILDIEMPGISGLEVAGEIRKKK--KDAKIILLT 80

>1p2f_A Response regulator; DRRB, OMPR/PHOB, transcription; HET: MSE; 1.80A {Thermotoga maritima} SCOP: a.4.6.1 c.23.1.1 PDB: 3nns_A* Length = 220

 Score = 50.5 bits (122), Expect = 2e-08
 Identities = 23/97 (23%), Positives = 41/97 (42%), Gaps = 23/97 (23%)

Query: 21  PHVLAVDD--SIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTK 78
             +  VDD  +I   K V   L+    +V T   G   L       ++E           
Sbjct: 3   WKIAVVDDDKNI--LKKVSEKLQQLG-RVKTFLTGEDFLN------DEE----------A 43

Query: 79  VNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVS 115
            ++V+ D  +P  +GYE+ + IKE+    E  V++++
Sbjct: 44  FHVVVLDVMLPDYSGYEICRMIKETR--PETWVILLT 78

>1qo0_D AMIR; binding protein, gene regulator, receptor; 2.25A {Pseudomonas aeruginosa} SCOP: c.23.1.3 Length = 196

 Score = 48.9 bits (116), Expect = 6e-08
 Identities = 15/123 (12%), Positives = 30/123 (24%), Gaps = 21/123 (17%)

Query: 22  HVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNL 81
            VL ++        +   L    C V        A +                    V++
Sbjct: 14  QVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAFD------------------VPVDV 55

Query: 82  VITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKP 141
           V T                  +       +V +     P  +++ +E      + +PL  
Sbjct: 56  VFTSIFQNRHHDEIAALLAAGTP---RTTLVALVEYESPAVLSQIIELECHGVITQPLDA 112

Query: 142 SDV 144
             V
Sbjct: 113 HRV 115

>2qv0_A Protein MRKE; structural genomics, transcription, PSI-2, protein structure initiative; 2.40A {Klebsiella pneumoniae} Length = 143

 Score = 47.6 bits (114), Expect = 7e-08
 Identities = 18/99 (18%), Positives = 42/99 (42%), Gaps = 19/99 (19%)

Query: 17  NPKPPHVLAVDDSIVDRKIVENLL-KNSACKVT-TAENGMRALEFLGLVDEQEQQNNLNS 74
           + +   V+ V+D  + ++ +  L+  +S  ++  + ++G+  L+FL              
Sbjct: 6   SGEKMKVIIVEDEFLAQQELSWLINTHSQMEIVGSFDDGLDVLKFL-------------- 51

Query: 75  NGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVV 113
              KV+ +  D  +P + G  L + I +       P +V
Sbjct: 52  QHNKVDAIFLDINIPSLDGVLLAQNISQ---FAHKPFIV 87

>3q9s_A DNA-binding response regulator; DNA binding protein; 2.40A {Deinococcus radiodurans} Length = 249

 Score = 48.3 bits (116), Expect = 1e-07
 Identities = 20/113 (17%), Positives = 47/113 (41%), Gaps = 23/113 (20%)

Query: 6   VASSSSSSSSSNPKPPHVLAVDDSIVDRKIVENL---LKNSACKVTTAENGMRALEFLGL 62
           +AS +            +L ++D   D  I   L   L ++   V  A++ M  L     
Sbjct: 23  MASMTGGQQMGRMNEQRILVIED---DHDIANVLRMDLTDAGYVVDHADSAMNGLI---K 76

Query: 63  VDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVS 115
             E              +L++ D  +P   G +++++++++S    +P++V++
Sbjct: 77  AREDH-----------PDLILLDLGLPDFDGGDVVQRLRKNS---ALPIIVLT 115

>2qsj_A DNA-binding response regulator, LUXR family; structural genomics, PSI-2, protein structure initiative; 2.10A {Silicibacter pomeroyi dss-3} Length = 154

 Score = 47.2 bits (113), Expect = 1e-07
 Identities = 32/121 (26%), Positives = 47/121 (38%), Gaps = 17/121 (14%)

Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSA--CKVTTAENGMRALEFLGLVDEQEQQNNLNSNG 76
               VL VDD  + R   +NLL+ +    +V  AE    AL FL                
Sbjct: 2   SLTVVLIVDDHHLIRAGAKNLLEGAFSGMRVEGAETVSDALAFL-------------EAD 48

Query: 77  TKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFML 136
             V+L++ D  +P     + L ++K         V ++S E     I   LE GA  F+ 
Sbjct: 49  NTVDLILLDVNLPDAEAIDGLVRLKRFD--PSNAVALISGETDHELIRAALEAGADGFIP 106

Query: 137 K 137
           K
Sbjct: 107 K 107

>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 = 45.9 bits (110), Expect = 8e-07
 Identities = 33/128 (25%), Positives = 57/128 (44%), Gaps = 24/128 (18%)

Query: 15  SSNPKPPHVLAVDDSIVDRKIVENL---LKNSACKVTTAENGMRALEFLGLVDEQEQQNN 71
            +    P VL VDD   D  ++ +L   L+ S  +V TA +G  AL       E      
Sbjct: 2   DTGVTSPRVLVVDD---DSDVLASLERGLRLSGFEVATAVDGAEALR---SATENR---- 51

Query: 72  LNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSS-ENIPTRINECLEEG 130
                   + ++ D  MP + G  ++  ++      +VPV V+S+  ++  R+   LE G
Sbjct: 52  -------PDAIVLDINMPVLDGVSVVTALRAMD--NDVPVCVLSARSSVDDRV-AGLEAG 101

Query: 131 AQMFMLKP 138
           A  +++KP
Sbjct: 102 ADDYLVKP 109

>3b2n_A Uncharacterized protein Q99UF4; structural genomics, PSI-2, protein structure initiative, NE SGX research center for structural genomics; 2.04A {Staphylococcus aureus} Length = 133

 Score = 42.9 bits (102), Expect = 3e-06
 Identities = 23/91 (25%), Positives = 44/91 (48%), Gaps = 16/91 (17%)

Query: 47  VTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVM 106
           +   +NG+ A++   L++E              N+VI D  MPGMTG E+L +I++    
Sbjct: 32  LADTDNGLDAMK---LIEE-----------YNPNVVILDIEMPGMTGLEVLAEIRKKH-- 75

Query: 107 KEVPVVVVSSENIPTRINECLEEGAQMFMLK 137
             + V++V++   P    + +      ++LK
Sbjct: 76  LNIKVIIVTTFKRPGYFEKAVVNDVDAYVLK 106

>3sy8_A ROCR; TIM barrel phosphodiesterase-A, transcription regulator; HET: EPE; 2.50A {Pseudomonas aeruginosa} Length = 400

 Score = 43.9 bits (104), Expect = 5e-06
 Identities = 20/100 (20%), Positives = 35/100 (35%), Gaps = 16/100 (16%)

Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
              +VL ++D    R +    LK      +  A +G    E + +++             
Sbjct: 2   NDLNVLVLEDEPFQRLVAVTALKKVVPGSILEAADG---KEAVAILESCGH--------- 49

Query: 78  KVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSE 117
            V++ I D  M GM G   L+    S       V++ S  
Sbjct: 50  -VDIAICDLQMSGMDGLAFLRHASLSGK--VHSVILSSEV 86

>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 = 41.3 bits (98), Expect = 1e-05
 Identities = 24/116 (20%), Positives = 51/116 (43%), Gaps = 17/116 (14%)

Query: 23  VLAVDDSIVDRKIVENLLKNSACKVT-TAENGMRALEFLGLVDEQEQQNNLNSNGTKVNL 81
            + +DD  +    + NLL  +  ++      G  A++    V+             K ++
Sbjct: 4   AIIIDDHPLAIAAIRNLLIKNDIEILAELTEGGSAVQ---RVET-----------LKPDI 49

Query: 82  VITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLK 137
           VI D  +PG+ G ++L+ +++        +++VS++N       C + GA  F+ K
Sbjct: 50  VIIDVDIPGVNGIQVLETLRKRQ--YSGIIIIVSAKNDHFYGKHCADAGANGFVSK 103

>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 = 41.1 bits (97), Expect = 3e-05
 Identities = 9/125 (7%), Positives = 30/125 (24%), Gaps = 18/125 (14%)

Query: 16  SNPKPPHVLAVDDSIVDRKIVENLLKNSAC---KVTTAENGMRALEFLGLVDEQEQQNNL 72
            +    +V  + D  +  ++++  L++      ++T               +        
Sbjct: 3   KDENKLNVRMLSDVCMQSRLLKEALESKLPLALEITPFSELWLEEN---KPES------- 52

Query: 73  NSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQ 132
                 + +++ DY              K  S   +   V+++                 
Sbjct: 53  ----RSIQMLVIDYSRISDDVLTDYSSFKHISC-PDAKEVIINCPQDIEHKLLFKWNNLA 107

Query: 133 MFMLK 137
                
Sbjct: 108 GVFYI 112

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 41.4 bits (96), Expect = 4e-05
 Identities = 28/150 (18%), Positives = 55/150 (36%), Gaps = 42/150 (28%)

Query: 21  PHVLAVDDSIVDRKIVENLLKNSACK--VTTAENGMRALEFLGLVDEQEQQNNLNSNGTK 78
            + L V  ++ + K       N +CK  +TT     R   F  + D       L++  T 
Sbjct: 244 ENCLLVLLNVQNAKAWNAF--NLSCKILLTT-----R---FKQVTDF------LSAATTT 287

Query: 79  VNLVITDYCMPGMT---GYELLKK---IKESSVMKEV----PVVV-VSSENI---PTRIN 124
              +  D+    +T      LL K    +   + +EV    P  + + +E+I       +
Sbjct: 288 H--ISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWD 345

Query: 125 -------ECLEEGAQMFMLKPLKPSDVKKL 147
                  + L    +   L  L+P++ +K+
Sbjct: 346 NWKHVNCDKLTTIIESS-LNVLEPAEYRKM 374

>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 = 39.3 bits (93), Expect = 5e-05
 Identities = 26/121 (21%), Positives = 56/121 (46%), Gaps = 24/121 (19%)

Query: 22  HVLAVDDSIVDRKIVENL---LKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTK 78
            VL V+D   +  +  +L   ++++  +V  AE+   A  +L              N   
Sbjct: 2   RVLVVED---NALLRHHLKVQIQDAGHQVDDAEDAKEADYYL--------------NEHI 44

Query: 79  VNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSS-ENIPTRINECLEEGAQMFMLK 137
            ++ I D  +P   G  L+++ + + V   +P++V+++ E+   ++ E L  GA  ++ K
Sbjct: 45  PDIAIVDLGLPDEDGLSLIRRWRSNDV--SLPILVLTARESWQDKV-EVLSAGADDYVTK 101

Query: 138 P 138
           P
Sbjct: 102 P 102

>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 = 39.3 bits (93), Expect = 2e-04
 Identities = 22/93 (23%), Positives = 38/93 (40%), Gaps = 22/93 (23%)

Query: 22  HVLAVDDSIVDRKIVENL---LKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTK 78
            VL V+D   +R + + +   LK     V    +G   +    +   +            
Sbjct: 4   RVLVVED---ERDLADLITEALKKEMFTVDVCYDGEEGMY---MALNEP----------- 46

Query: 79  VNLVITDYCMPGMTGYELLKKIKESSVMKEVPV 111
            ++VI D  +P   G+E+LK ++ES V    PV
Sbjct: 47  FDVVILDIMLPVHDGWEILKSMRESGV--NTPV 77

>4e7p_A Response regulator; DNA binding, cytosol, transcription regulator; 1.89A {Streptococcus pneumoniae} PDB: 4e7o_A Length = 150

 Score = 37.9 bits (89), Expect = 3e-04
 Identities = 34/147 (23%), Positives = 57/147 (38%), Gaps = 22/147 (14%)

Query: 1   MDACGVASSSSSSSSSNPKPPHVLAVDDSIVDRKIVENLLKNSACK----VTTAENGMRA 56
           M +       SS          VL  +D  + R  +  LL  +       V  A+NG  A
Sbjct: 1   MGSSHHHHHHSSGLVPRGSHMKVLVAEDQSMLRDAMCQLL--TLQPDVESVLQAKNGQEA 58

Query: 57  LEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSS 116
           ++   L+++             V++ I D  MP  TG E+L+ I+      E  VVVV++
Sbjct: 59  IQ---LLEK-----------ESVDIAILDVEMPVKTGLEVLEWIRSEK--LETKVVVVTT 102

Query: 117 ENIPTRINECLEEGAQMFMLKPLKPSD 143
                     ++ G   ++LK    +D
Sbjct: 103 FKRAGYFERAVKAGVDAYVLKERSIAD 129

>1dz3_A Stage 0 sporulation protein A; response regulator, domain swapping; 1.65A {Bacillus stearothermophilus} SCOP: c.23.1.1 PDB: 1qmp_A* Length = 130

 Score = 37.1 bits (87), Expect = 4e-04
 Identities = 24/126 (19%), Positives = 56/126 (44%), Gaps = 21/126 (16%)

Query: 23  VLAVDDSIVDRKIVENLLKNSACK----VTTAENGMRALEFLGLVDEQEQQNNLNSNGTK 78
           V   DD+     +++  +  S+      + TA NG   L+   +++E            +
Sbjct: 5   VCIADDNRELVSLLDEYI--SSQPDMEVIGTAYNGQDCLQ---MLEE-----------KR 48

Query: 79  VNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKP 138
            ++++ D  MP + G  +L++I+      +  V+++++        + +E GA  F+LKP
Sbjct: 49  PDILLLDIIMPHLDGLAVLERIRAGFE-HQPNVIMLTAFGQEDVTKKAVELGASYFILKP 107

Query: 139 LKPSDV 144
               ++
Sbjct: 108 FDMENL 113

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	153
3to5_A	134	CHEY homolog; alpha(5)beta(5), chemotaxis, FLIM, p	99.96
3gl9_A	122	Response regulator; beta-sheet, surrounded by alph	99.93
3t6k_A	136	Response regulator receiver; flavodoxin-like, stru	99.92
2lpm_A	123	Two-component response regulator; transcription re	99.91
3h1g_A	129	Chemotaxis protein CHEY homolog; sulfate-bound CHE	99.91
3f6p_A	120	Transcriptional regulatory protein YYCF; unphospho	99.91
3m6m_D	143	Sensory/regulatory protein RPFC; RPFF, REC, enoyl-	99.9
2r25_B	133	Osmosensing histidine protein kinase SLN1; alpha5-	99.9
3rqi_A	184	Response regulator protein; structural genomics, s	99.9
1dbw_A	126	Transcriptional regulatory protein FIXJ; doubly wo	99.9
3gt7_A	154	Sensor protein; structural genomics, signal receiv	99.9
3eod_A	130	Protein HNR; response regulator, phosphoprotein, t	99.9
1srr_A	124	SPO0F, sporulation response regulatory protein; as	99.89
1jbe_A	128	Chemotaxis protein CHEY; signaling protein; 1.08A	99.89
3lua_A	140	Response regulator receiver protein; two-component	99.89
3hv2_A	153	Response regulator/HD domain protein; PSI-2, NYSGX	99.89
3crn_A	132	Response regulator receiver domain protein, CHEY-;	99.89
3kto_A	136	Response regulator receiver protein; PSI-II,struct	99.89
3snk_A	135	Response regulator CHEY-like protein; P-loop conta	99.89
1tmy_A	120	CHEY protein, TMY; chemotaxis, phosphoryl transfer	99.89
1mb3_A	124	Cell division response regulator DIVK; signal tran	99.88
1i3c_A	149	Response regulator RCP1; phytochrome, signaling pr	99.88
1p6q_A	129	CHEY2; chemotaxis, signal transduction, response r	99.88
3i42_A	127	Response regulator receiver domain protein (CHEY-	99.88
3jte_A	143	Response regulator receiver protein; structural ge	99.88
4e7p_A	150	Response regulator; DNA binding, cytosol, transcri	99.88
2pl1_A	121	Transcriptional regulatory protein PHOP; CHEY-like	99.88
3hzh_A	157	Chemotaxis response regulator (CHEY-3); phosphatas	99.88
3kht_A	144	Response regulator; PSI-II, 11023K, structural gen	99.88
3heb_A	152	Response regulator receiver domain protein (CHEY);	99.88
3hdv_A	136	Response regulator; PSI-II, structural genomics, P	99.88
1xhf_A	123	DYE resistance, aerobic respiration control protei	99.88
3r0j_A	250	Possible two component system response transcript	99.88
1k68_A	140	Phytochrome response regulator RCPA; phosphorylate	99.88
3b2n_A	133	Uncharacterized protein Q99UF4; structural genomic	99.88
3luf_A	259	Two-component system response regulator/ggdef doma	99.88
3grc_A	140	Sensor protein, kinase; protein structure initiati	99.88
3hdg_A	137	Uncharacterized protein; two-component sensor acti	99.88
1zgz_A	122	Torcad operon transcriptional regulatory protein;	99.88
3ilh_A	146	Two component response regulator; NYSGXRC, PSI-II,	99.87
3lte_A	132	Response regulator; structural genomics, PSI, prot	99.87
3nhm_A	133	Response regulator; protein structure initiative I	99.87
4dad_A	146	Putative pilus assembly-related protein; response	99.87
3mm4_A	206	Histidine kinase homolog; receiver domain, CKI1, c	99.87
3cfy_A	137	Putative LUXO repressor protein; structural genomi	99.87
2jba_A	127	Phosphate regulon transcriptional regulatory PROT;	99.87
3c3m_A	138	Response regulator receiver protein; structural ge	99.87
1dcf_A	136	ETR1 protein; beta-alpha five sandwich, transferas	99.87
3cnb_A	143	DNA-binding response regulator, MERR family; signa	99.87
3q9s_A	249	DNA-binding response regulator; DNA binding protei	99.87
1yio_A	208	Response regulatory protein; transcription regulat	99.87
1k66_A	149	Phytochrome response regulator RCPB; CHEY homologu	99.87
3eul_A	152	Possible nitrate/nitrite response transcriptional	99.87
3f6c_A	134	Positive transcription regulator EVGA; structural	99.87
2a9o_A	120	Response regulator; essential protein, YYCF/YYCG h	99.87
2qzj_A	136	Two-component response regulator; 11017X, PSI-II,	99.87
1mvo_A	136	PHOP response regulator; phosphate regulon, transc	99.86
2zay_A	147	Response regulator receiver protein; structural ge	99.86
2ayx_A	254	Sensor kinase protein RCSC; two independent struct	99.86
2rjn_A	154	Response regulator receiver:metal-dependent phosph	99.86
2qxy_A	142	Response regulator; regulation of transcription, N	99.86
3n0r_A	286	Response regulator; sigma factor, receiver, two-co	99.86
3h5i_A	140	Response regulator/sensory box protein/ggdef domai	99.86
2qr3_A	140	Two-component system response regulator; structura	99.86
1dz3_A	130	Stage 0 sporulation protein A; response regulator,	99.86
3cg4_A	142	Response regulator receiver domain protein (CHEY-;	99.86
3a10_A	116	Response regulator; phosphoacceptor, signaling pro	99.85
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	99.85
3kcn_A	151	Adenylate cyclase homolog; SGX, PSI 2, structural	99.85
3n53_A	140	Response regulator receiver modulated diguanylate;	99.85
1qkk_A	155	DCTD, C4-dicarboxylate transport transcriptional r	99.85
3eqz_A	135	Response regulator; structural genomics, unknown f	99.85
1a04_A	215	Nitrate/nitrite response regulator protein NARL; s	99.85
3cg0_A	140	Response regulator receiver modulated diguanylate	99.85
3cz5_A	153	Two-component response regulator, LUXR family; str	99.85
1s8n_A	205	Putative antiterminator; RV1626, structural genomi	99.85
2gkg_A	127	Response regulator homolog; social motility, recei	99.85
1zh2_A	121	KDP operon transcriptional regulatory protein KDPE	99.85
3cu5_A	141	Two component transcriptional regulator, ARAC FAM;	99.85
2qvg_A	143	Two component response regulator; NYSGXRC, PSI-2,	99.84
1kgs_A	225	DRRD, DNA binding response regulator D; DNA-bindin	99.84
3eq2_A	394	Probable two-component response regulator; adaptor	99.84
2jk1_A	139	HUPR, hydrogenase transcriptional regulatory prote	99.84
2qsj_A	154	DNA-binding response regulator, LUXR family; struc	99.84
1w25_A	459	Stalked-cell differentiation controlling protein;	99.84
2j48_A	119	Two-component sensor kinase; pseudo-receiver, circ	99.83
3kyj_B	145	CHEY6 protein, putative histidine protein kinase;	99.83
1ys7_A	233	Transcriptional regulatory protein PRRA; response	99.83
2pln_A	137	HP1043, response regulator; signaling protein; 1.8	99.83
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	99.83
2b4a_A	138	BH3024; flavodoxin-like fold, structural genomics,	99.83
2oqr_A	230	Sensory transduction protein REGX3; response regul	99.82
2gwr_A	238	DNA-binding response regulator MTRA; two-component	99.82
2rdm_A	132	Response regulator receiver protein; structural ge	99.82
2qv0_A	143	Protein MRKE; structural genomics, transcription,	99.81
3bre_A	358	Probable two-component response regulator; protein	99.81
1p2f_A	220	Response regulator; DRRB, OMPR/PHOB, transcription	99.81
1dc7_A	124	NTRC, nitrogen regulation protein; receiver domain	99.81
3t8y_A	164	CHEB, chemotaxis response regulator protein-glutam	99.8
3c97_A	140	Signal transduction histidine kinase; structural g	99.8
3c3w_A	225	Two component transcriptional regulatory protein;	99.8
3klo_A	225	Transcriptional regulator VPST; REC domain, HTH do	99.8
3sy8_A	400	ROCR; TIM barrel phosphodiesterase-A, transcriptio	99.8
2hqr_A	223	Putative transcriptional regulator; phosporylation	99.78
1qo0_D	196	AMIR; binding protein, gene regulator, receptor; 2	99.77
1a2o_A	349	CHEB methylesterase; bacterial chemotaxis, adaptat	99.73
3luf_A	259	Two-component system response regulator/ggdef doma	99.73
2vyc_A	755	Biodegradative arginine decarboxylase; pyridoxal p	99.68
1w25_A	459	Stalked-cell differentiation controlling protein;	99.22
3cwo_X	237	Beta/alpha-barrel protein based on 1THF and 1TMY;	99.17
3q7r_A	121	Transcriptional regulatory protein; CHXR, receiver	98.09
2ayx_A	254	Sensor kinase protein RCSC; two independent struct	97.63
3n75_A	715	LDC, lysine decarboxylase, inducible; pyridoxal-5'	97.45
2yxb_A	161	Coenzyme B12-dependent mutase; alpha/beta, structu	97.17
3cwo_X	237	Beta/alpha-barrel protein based on 1THF and 1TMY;	96.85
1ccw_A	137	Protein (glutamate mutase); coenzyme B12, radical	95.38
1wv2_A	265	Thiazole moeity, thiazole biosynthesis protein THI	94.97
1y80_A	210	Predicted cobalamin binding protein; corrinoid, fa	94.81
3ezx_A	215	MMCP 1, monomethylamine corrinoid protein 1; N ter	94.8
3q58_A	229	N-acetylmannosamine-6-phosphate 2-epimerase; TIM b	94.17
3igs_A	232	N-acetylmannosamine-6-phosphate 2-epimerase 2; ene	93.31
2i2x_B	258	MTAC, methyltransferase 1; TIM barrel and helix bu	93.3
3o63_A	243	Probable thiamine-phosphate pyrophosphorylase; thi	90.77
2htm_A	268	Thiazole biosynthesis protein THIG; thiamin biosyn	90.58
1xrs_B	262	D-lysine 5,6-aminomutase beta subunit; TIM barrel,	90.1
2ekc_A	262	AQ_1548, tryptophan synthase alpha chain; structur	89.74
2xij_A	762	Methylmalonyl-COA mutase, mitochondrial; isomerase	89.69
3qja_A	272	IGPS, indole-3-glycerol phosphate synthase; struct	89.51
3qz6_A	261	HPCH/HPAI aldolase; structural genomics, PSI-biolo	89.16
2v5j_A	287	2,4-dihydroxyhept-2-ENE-1,7-dioic acid aldolase; l	88.9
1geq_A	248	Tryptophan synthase alpha-subunit; hyperthermophIl	88.47
3vnd_A	267	TSA, tryptophan synthase alpha chain; psychrophili	88.29
1req_A	727	Methylmalonyl-COA mutase; isomerase, intramolecula	87.9
3nav_A	271	Tryptophan synthase alpha chain; alpha subunit, st	86.48
2vws_A	267	YFAU, 2-keto-3-deoxy sugar aldolase; lyase, escher	86.05
3kp1_A	763	D-ornithine aminomutase E component; 5 aminomutase	84.9
1yad_A	221	Regulatory protein TENI; TIM barrel, transcription	84.17
3rht_A	259	(gatase1)-like protein; structural genomics, PSI-b	83.65
3fkq_A	373	NTRC-like two-domain protein; RER070207001320, str	83.37
1qop_A	268	Tryptophan synthase alpha chain; lyase, carbon-oxy	82.89
3lab_A	217	Putative KDPG (2-keto-3-deoxy-6-phosphogluconate)	82.36
1ujp_A	271	Tryptophan synthase alpha chain; riken structural	82.0
3bul_A	579	Methionine synthase; transferase, reactivation con	81.59
1xi3_A	215	Thiamine phosphate pyrophosphorylase; structural g	80.94
3tfw_A	248	Putative O-methyltransferase; PSI-biology, nysgrc,	80.44

>3to5_A CHEY homolog; alpha(5)beta(5), chemotaxis, FLIM, phosphorylation, motor AC signaling protein; 1.65A {Vibrio cholerae}

Probab=99.96  E-value=1.2e-28  Score=167.02  Aligned_cols=121  Identities=31%  Similarity=0.576  Sum_probs=110.4

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcE-EEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELL   97 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~-v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~   97 (153)
                      ++++||||||++..+..++.+|+..||. +..+.++.+|++.+.              .+.||+||+|+.||+++|++++
T Consensus        11 k~~rILiVDD~~~~r~~l~~~L~~~G~~~v~~a~~g~~al~~~~--------------~~~~DlillD~~MP~mdG~el~   76 (134)
T 3to5_A           11 KNMKILIVDDFSTMRRIVKNLLRDLGFNNTQEADDGLTALPMLK--------------KGDFDFVVTDWNMPGMQGIDLL   76 (134)
T ss_dssp             TTCCEEEECSCHHHHHHHHHHHHHTTCCCEEEESSHHHHHHHHH--------------HHCCSEEEEESCCSSSCHHHHH
T ss_pred             CCCEEEEEeCCHHHHHHHHHHHHHcCCcEEEEECCHHHHHHHHH--------------hCCCCEEEEcCCCCCCCHHHHH
Confidence            4578999999999999999999999985 778999999999884              3469999999999999999999


Q ss_pred             HHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhcC
Q 042079           98 KKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLIN  153 (153)
Q Consensus        98 ~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~~  153 (153)
                      ++||+....+++|||++|+..+.+...++++.|+++||.||+++++|.+.+.++++
T Consensus        77 ~~ir~~~~~~~ipvI~lTa~~~~~~~~~~~~~Ga~~yl~KP~~~~~L~~~i~~~l~  132 (134)
T 3to5_A           77 KNIRADEELKHLPVLMITAEAKREQIIEAAQAGVNGYIVKPFTAATLKEKLDKIFE  132 (134)
T ss_dssp             HHHHHSTTTTTCCEEEEESSCCHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHHCC
T ss_pred             HHHHhCCCCCCCeEEEEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHh
Confidence            99998666678999999999999999999999999999999999999998888653

>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=99.93  E-value=1.7e-24  Score=143.12  Aligned_cols=118  Identities=38%  Similarity=0.503  Sum_probs=108.7

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKI  100 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~l  100 (153)
                      .+|||+||++..+..+...|+..||.+..+.++.++++.+.              ...||+||+|+.||+++|+++++++
T Consensus         3 ~~ILivdd~~~~~~~l~~~l~~~g~~v~~~~~~~~al~~l~--------------~~~~dlvllD~~~p~~~g~~~~~~l   68 (122)
T 3gl9_A            3 KKVLLVDDSAVLRKIVSFNLKKEGYEVIEAENGQIALEKLS--------------EFTPDLIVLXIMMPVMDGFTVLKKL   68 (122)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHT--------------TBCCSEEEECSCCSSSCHHHHHHHH
T ss_pred             ceEEEEeCCHHHHHHHHHHHHHCCcEEEEeCCHHHHHHHHH--------------hcCCCEEEEeccCCCCcHHHHHHHH
Confidence            58999999999999999999999999999999999999883              4579999999999999999999999


Q ss_pred             HhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079          101 KESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus       101 r~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      |+....+.+|+|++|+..+.....++++.|+++|+.||++++++...+.+++
T Consensus        69 ~~~~~~~~~pii~~s~~~~~~~~~~~~~~Ga~~~l~KP~~~~~L~~~i~~~l  120 (122)
T 3gl9_A           69 QEKEEWKRIPVIVLTAKGGEEDESLALSLGARKVMRKPFSPSQFIEEVKHLL  120 (122)
T ss_dssp             HTSTTTTTSCEEEEESCCSHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHH
T ss_pred             HhcccccCCCEEEEecCCchHHHHHHHhcChhhhccCCCCHHHHHHHHHHHh
Confidence            9765456899999999999999999999999999999999999999888765

>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=99.92  E-value=8.9e-24  Score=142.06  Aligned_cols=119  Identities=24%  Similarity=0.459  Sum_probs=107.9

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      +..+|||+||++..+..+..+|+..||.+..+.++.++++.+.              ...||+||+|+.||+++|+++++
T Consensus         3 ~~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~--------------~~~~dlvl~D~~lp~~~g~~~~~   68 (136)
T 3t6k_A            3 KPHTLLIVDDDDTVAEMLELVLRGAGYEVRRAASGEEALQQIY--------------KNLPDALICDVLLPGIDGYTLCK   68 (136)
T ss_dssp             CCCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--------------HSCCSEEEEESCCSSSCHHHHHH
T ss_pred             CCCEEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHH--------------hCCCCEEEEeCCCCCCCHHHHHH
Confidence            4578999999999999999999999999999999999999873              35699999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      ++|+....+.+|+|++|+..+.....++++.|+++|+.||++.++|...+.++
T Consensus        69 ~lr~~~~~~~~pii~~t~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~i~~~  121 (136)
T 3t6k_A           69 RVRQHPLTKTLPILMLTAQGDISAKIAGFEAGANDYLAKPFEPQELVYRVKNI  121 (136)
T ss_dssp             HHHHSGGGTTCCEEEEECTTCHHHHHHHHHHTCSEEEETTCCHHHHHHHHHHH
T ss_pred             HHHcCCCcCCccEEEEecCCCHHHHHHHHhcCcceEEeCCCCHHHHHHHHHHH
Confidence            99975444678999999998888889999999999999999999999887765

>2lpm_A Two-component response regulator; transcription regulator; NMR {Sinorhizobium meliloti}

Probab=99.91  E-value=1.1e-25  Score=150.20  Aligned_cols=113  Identities=19%  Similarity=0.250  Sum_probs=99.2

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcEEE-EecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACKVT-TAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELL   97 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~v~-~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~   97 (153)
                      +.++||||||++..+..++.+|+..||++. .+.++.+|++.+.              .++||+||+|+.||+++|++++
T Consensus         7 r~~rILiVdD~~~~~~~l~~~L~~~G~~v~~~a~~g~eAl~~~~--------------~~~~DlvllDi~mP~~~G~el~   72 (123)
T 2lpm_A            7 RRLRVLVVEDESMIAMLIEDTLCELGHEVAATASRMQEALDIAR--------------KGQFDIAIIDVNLDGEPSYPVA   72 (123)
T ss_dssp             CCCCEEEESSSTTTSHHHHHHHHHHCCCCCBCSCCHHHHHHHHH--------------HCCSSEEEECSSSSSCCSHHHH
T ss_pred             CCCEEEEEeCCHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHH--------------hCCCCEEEEecCCCCCCHHHHH
Confidence            457899999999999999999999999975 7899999999883              3579999999999999999999


Q ss_pred             HHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079           98 KKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus        98 ~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      +++|+.    ++|||++|+..+...   +.+.|+++||.||+++++|...+.++.
T Consensus        73 ~~lr~~----~ipvI~lTa~~~~~~---~~~~g~~~yl~KP~~~~~L~~~l~~~~  120 (123)
T 2lpm_A           73 DILAER----NVPFIFATGYGSKGL---DTRYSNIPLLTKPFLDSELEAVLVQIS  120 (123)
T ss_dssp             HHHHHT----CCSSCCBCTTCTTSC---CSSSCSCSCBCSSSSHHHHHHHHSTTC
T ss_pred             HHHHcC----CCCEEEEecCccHHH---HHhCCCCcEEECCCCHHHHHHHHHHHH
Confidence            999973    589999998765543   346799999999999999999998864

>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=99.91  E-value=6.7e-23  Score=136.37  Aligned_cols=120  Identities=31%  Similarity=0.553  Sum_probs=106.6

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCcE-EEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~~~-v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      .++|||+||++..+..++.+|+..|+. +..+.++.+++..+.             ....||+||+|+.||+++|+++++
T Consensus         5 ~~~iLivdd~~~~~~~l~~~L~~~g~~~v~~~~~~~~a~~~~~-------------~~~~~dlvi~D~~~p~~~g~~~~~   71 (129)
T 3h1g_A            5 SMKLLVVDDSSTMRRIIKNTLSRLGYEDVLEAEHGVEAWEKLD-------------ANADTKVLITDWNMPEMNGLDLVK   71 (129)
T ss_dssp             -CCEEEECSCHHHHHHHHHHHHHTTCCCEEEESSHHHHHHHHH-------------HCTTCCEEEECSCCSSSCHHHHHH
T ss_pred             CcEEEEEeCCHHHHHHHHHHHHHcCCcEEEEeCCHHHHHHHHH-------------hCCCCCEEEEeCCCCCCCHHHHHH
Confidence            468999999999999999999999985 889999999988763             123689999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      ++|+....+.+|+|++|+..+.....++++.|+++|+.||++++++...+..++
T Consensus        72 ~lr~~~~~~~~pii~~s~~~~~~~~~~~~~~g~~~~l~KP~~~~~L~~~l~~~l  125 (129)
T 3h1g_A           72 KVRSDSRFKEIPIIMITAEGGKAEVITALKAGVNNYIVKPFTPQVLKEKLEVVL  125 (129)
T ss_dssp             HHHTSTTCTTCCEEEEESCCSHHHHHHHHHHTCCEEEESCCCHHHHHHHHHHHH
T ss_pred             HHHhcCCCCCCeEEEEeCCCChHHHHHHHHcCccEEEeCCCCHHHHHHHHHHHh
Confidence            999755446899999999999999999999999999999999999999888754

>3f6p_A Transcriptional regulatory protein YYCF; unphosphorelated, receiver domain, cytoplasm, DNA-binding, phosphoprotein, transcription regulation; 1.95A {Bacillus subtilis} SCOP: c.23.1.1 PDB: 2zwm_A

Probab=99.91  E-value=4.9e-23  Score=135.51  Aligned_cols=116  Identities=21%  Similarity=0.372  Sum_probs=105.5

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKK   99 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~   99 (153)
                      ..+|||+||++..+..+...|+..||.+..+.++.++++.+.              ..+||+||+|+.||+++|++++++
T Consensus         2 ~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~--------------~~~~dlii~D~~~p~~~g~~~~~~   67 (120)
T 3f6p_A            2 DKKILVVDDEKPIADILEFNLRKEGYEVHCAHDGNEAVEMVE--------------ELQPDLILLDIMLPNKDGVEVCRE   67 (120)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--------------TTCCSEEEEETTSTTTHHHHHHHH
T ss_pred             CCeEEEEECCHHHHHHHHHHHHhCCEEEEEeCCHHHHHHHHh--------------hCCCCEEEEeCCCCCCCHHHHHHH
Confidence            358999999999999999999999999999999999999873              457999999999999999999999


Q ss_pred             HHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079          100 IKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus       100 lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      +|+.   ..+|+|++|+..+.....++++.|+++|+.||++.+++...+.+.+
T Consensus        68 lr~~---~~~~ii~~t~~~~~~~~~~~~~~ga~~~l~KP~~~~~l~~~i~~~l  117 (120)
T 3f6p_A           68 VRKK---YDMPIIMLTAKDSEIDKVIGLEIGADDYVTKPFSTRELLARVKANL  117 (120)
T ss_dssp             HHTT---CCSCEEEEEESSCHHHHHHHHHTTCCEEEEESCCHHHHHHHHHHHH
T ss_pred             HHhc---CCCCEEEEECCCChHHHHHHHhCCcceeEcCCCCHHHHHHHHHHHH
Confidence            9974   3689999999988888899999999999999999999998887753

>3m6m_D Sensory/regulatory protein RPFC; RPFF, REC, enoyl-COA hydratase, lyase-transferase COMP; 2.50A {Xanthomonas campestris PV}

Probab=99.90  E-value=8.9e-23  Score=138.35  Aligned_cols=121  Identities=29%  Similarity=0.512  Sum_probs=104.1

Q ss_pred             CCCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHH
Q 042079           18 PKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELL   97 (153)
Q Consensus        18 ~~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~   97 (153)
                      .+.++|||+||++..+..++.+|+..|+.+..+.++.++++.+.              ...||+||+|+.||+++|++++
T Consensus        12 ~~~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~--------------~~~~dlvl~D~~mp~~~g~~~~   77 (143)
T 3m6m_D           12 VRSMRMLVADDHEANRMVLQRLLEKAGHKVLCVNGAEQVLDAMA--------------EEDYDAVIVDLHMPGMNGLDML   77 (143)
T ss_dssp             ---CEEEEECSSHHHHHHHHHHHHC--CEEEEESSHHHHHHHHH--------------HSCCSEEEEESCCSSSCHHHHH
T ss_pred             cccceEEEEeCCHHHHHHHHHHHHHcCCeEEEeCCHHHHHHHHh--------------cCCCCEEEEeCCCCCCCHHHHH
Confidence            45579999999999999999999999999999999999998873              3569999999999999999999


Q ss_pred             HHHHhc--cCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079           98 KKIKES--SVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus        98 ~~lr~~--~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      +++|+.  ...+.+|+|++|+..+.+...++++.|+++||.||++.++|...+.++.
T Consensus        78 ~~lr~~~~~~~~~~pii~~s~~~~~~~~~~~~~~Ga~~~l~KP~~~~~L~~~l~~~~  134 (143)
T 3m6m_D           78 KQLRVMQASGMRYTPVVVLSADVTPEAIRACEQAGARAFLAKPVVAAKLLDTLADLA  134 (143)
T ss_dssp             HHHHHHHHTTCCCCCEEEEESCCCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHC
T ss_pred             HHHHhchhccCCCCeEEEEeCCCCHHHHHHHHHcChhheeeCCCCHHHHHHHHHHHH
Confidence            999853  2235689999999989999999999999999999999999999887753

>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=99.90  E-value=1.4e-22  Score=135.67  Aligned_cols=123  Identities=24%  Similarity=0.422  Sum_probs=105.4

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCc-EEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSAC-KVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~~-~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      ..+|||+||++..+..++.+|+..|+ .+..+.++.+++..+.....         ....||+||+|+.||+++|+++++
T Consensus         2 ~~~ILivdD~~~~~~~l~~~L~~~g~~~v~~~~~~~~al~~~~~~~~---------~~~~~dlvllD~~mp~~~G~~~~~   72 (133)
T 2r25_B            2 SVKILVVEDNHVNQEVIKRMLNLEGIENIELACDGQEAFDKVKELTS---------KGENYNMIFMDVQMPKVDGLLSTK   72 (133)
T ss_dssp             CSCEEEECSCHHHHHHHHHHHHHTTCCCEEEESSHHHHHHHHHHHHH---------HTCCCSEEEECSCCSSSCHHHHHH
T ss_pred             CceEEEEcCCHHHHHHHHHHHHHcCCceEEEECCHHHHHHHHHHHHh---------cCCCCCEEEEeCCCCCCChHHHHH
Confidence            35799999999999999999998887 58889999999987742110         124699999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      .+|+.. .+.+|+|++|+..+.....++++.|+++|+.||++.+++.+.+.+++
T Consensus        73 ~lr~~~-~~~~~ii~lt~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~l~~~~  125 (133)
T 2r25_B           73 MIRRDL-GYTSPIVALTAFADDSNIKECLESGMNGFLSKPIKRPKLKTILTEFC  125 (133)
T ss_dssp             HHHHHS-CCCSCEEEEESCCSHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHC
T ss_pred             HHHhhc-CCCCCEEEEECCCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHH
Confidence            999632 24689999999988888999999999999999999999999888754

>3rqi_A Response regulator protein; structural genomics, seattle structural genomics center for infectious disease, ssgcid; HET: PHD CIT; 1.70A {Burkholderia pseudomallei}

Probab=99.90  E-value=4.8e-23  Score=145.33  Aligned_cols=118  Identities=16%  Similarity=0.237  Sum_probs=107.3

Q ss_pred             CCCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHH
Q 042079           18 PKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELL   97 (153)
Q Consensus        18 ~~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~   97 (153)
                      ++..+||||||++..+..+..+|+..||.+..+.++.++++.+.              ...||+||+|+.||+++|++++
T Consensus         5 m~~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~--------------~~~~dlvl~D~~lp~~~g~~~~   70 (184)
T 3rqi_A            5 MSDKNFLVIDDNEVFAGTLARGLERRGYAVRQAHNKDEALKLAG--------------AEKFEFITVXLHLGNDSGLSLI   70 (184)
T ss_dssp             --CCEEEEECSCHHHHHHHHHHHHHTTCEEEEECSHHHHHHHHT--------------TSCCSEEEECSEETTEESHHHH
T ss_pred             CCCCeEEEEcCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHh--------------hCCCCEEEEeccCCCccHHHHH
Confidence            35678999999999999999999999999999999999999883              4679999999999999999999


Q ss_pred             HHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           98 KKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        98 ~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      +++++..  +.+|||++|+..+.+...++++.|+++|+.||++.++|...+.++
T Consensus        71 ~~l~~~~--~~~~ii~lt~~~~~~~~~~a~~~Ga~~~l~KP~~~~~L~~~i~~~  122 (184)
T 3rqi_A           71 APLCDLQ--PDARILVLTGYASIATAVQAVKDGADNYLAKPANVESILAALQTN  122 (184)
T ss_dssp             HHHHHHC--TTCEEEEEESSCCHHHHHHHHHHTCSEEEESSCCHHHHHHHTSTT
T ss_pred             HHHHhcC--CCCCEEEEeCCCCHHHHHHHHHhCHHHheeCCCCHHHHHHHHHHH
Confidence            9999864  689999999999999999999999999999999999999877654

>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=99.90  E-value=4.4e-22  Score=131.64  Aligned_cols=117  Identities=23%  Similarity=0.332  Sum_probs=106.2

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      +..+|||+||++..+..+...|+..|+.+..+.++.+++..+.              ...||++|+|+.||+++|+++++
T Consensus         2 ~~~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~--------------~~~~dlvi~D~~l~~~~g~~~~~   67 (126)
T 1dbw_A            2 QDYTVHIVDDEEPVRKSLAFMLTMNGFAVKMHQSAEAFLAFAP--------------DVRNGVLVTDLRMPDMSGVELLR   67 (126)
T ss_dssp             CCCEEEEEESSHHHHHHHHHHHHHTTCEEEEESCHHHHHHHGG--------------GCCSEEEEEECCSTTSCHHHHHH
T ss_pred             CCCEEEEEcCCHHHHHHHHHHHHhCCcEEEEeCCHHHHHHHHh--------------cCCCCEEEEECCCCCCCHHHHHH
Confidence            3568999999999999999999988999999999999998773              35689999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      ++++..  +.+|+|++|+..+.....++++.|+++|+.||++.+++...+.++
T Consensus        68 ~l~~~~--~~~~ii~~s~~~~~~~~~~~~~~ga~~~l~Kp~~~~~l~~~i~~~  118 (126)
T 1dbw_A           68 NLGDLK--INIPSIVITGHGDVPMAVEAMKAGAVDFIEKPFEDTVIIEAIERA  118 (126)
T ss_dssp             HHHHTT--CCCCEEEEECTTCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHH
T ss_pred             HHHhcC--CCCCEEEEECCCCHHHHHHHHHhCHHHheeCCCCHHHHHHHHHHH
Confidence            999754  678999999998888899999999999999999999999888765

>3gt7_A Sensor protein; structural genomics, signal receiver domain, kinase, PSI-2, protein structure initiative; 2.30A {Syntrophus aciditrophicus SB}

Probab=99.90  E-value=4.5e-22  Score=136.33  Aligned_cols=119  Identities=28%  Similarity=0.474  Sum_probs=108.7

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      +..+|||+||++..+..+..+|+..||.+..+.++.+++..+.              ..+||+||+|+.||+++|+++++
T Consensus         6 ~~~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~--------------~~~~dlii~D~~l~~~~g~~~~~   71 (154)
T 3gt7_A            6 RAGEILIVEDSPTQAEHLKHILEETGYQTEHVRNGREAVRFLS--------------LTRPDLIISDVLMPEMDGYALCR   71 (154)
T ss_dssp             -CCEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHT--------------TCCCSEEEEESCCSSSCHHHHHH
T ss_pred             CCCcEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHH--------------hCCCCEEEEeCCCCCCCHHHHHH
Confidence            3578999999999999999999999999999999999999883              46799999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      .|++....+.+|+|++++..+.....++++.|+++|+.||++.+++...+.++
T Consensus        72 ~lr~~~~~~~~pii~~s~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~  124 (154)
T 3gt7_A           72 WLKGQPDLRTIPVILLTILSDPRDVVRSLECGADDFITKPCKDVVLASHVKRL  124 (154)
T ss_dssp             HHHHSTTTTTSCEEEEECCCSHHHHHHHHHHCCSEEEESSCCHHHHHHHHHHH
T ss_pred             HHHhCCCcCCCCEEEEECCCChHHHHHHHHCCCCEEEeCCCCHHHHHHHHHHH
Confidence            99986544689999999999999999999999999999999999999888765

>3eod_A Protein HNR; response regulator, phosphoprotein, two-component regulatory system, signaling protein; 1.75A {Escherichia coli K12}

Probab=99.90  E-value=4.2e-22  Score=132.24  Aligned_cols=119  Identities=28%  Similarity=0.483  Sum_probs=102.2

Q ss_pred             CCCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHH
Q 042079           18 PKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELL   97 (153)
Q Consensus        18 ~~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~   97 (153)
                      .+..+|||+||++..+..+..+|+..|+.+..+.++.+++..+.              ..+||+||+|+.+|+.+|++++
T Consensus         5 ~~~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~--------------~~~~dlvi~d~~l~~~~g~~~~   70 (130)
T 3eod_A            5 LVGKQILIVEDEQVFRSLLDSWFSSLGATTVLAADGVDALELLG--------------GFTPDLMICDIAMPRMNGLKLL   70 (130)
T ss_dssp             TTTCEEEEECSCHHHHHHHHHHHHHTTCEEEEESCHHHHHHHHT--------------TCCCSEEEECCC-----CHHHH
T ss_pred             CCCCeEEEEeCCHHHHHHHHHHHHhCCceEEEeCCHHHHHHHHh--------------cCCCCEEEEecCCCCCCHHHHH
Confidence            35679999999999999999999999999999999999999883              4679999999999999999999


Q ss_pred             HHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCC-ChhHHHHHHhhhc
Q 042079           98 KKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPL-KPSDVKKLTGHLI  152 (153)
Q Consensus        98 ~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~-~~~~l~~~~~~~~  152 (153)
                      +.+++..  +.+|+|++|+..+.....++++.|+++|+.||+ +.+++.+.+.+++
T Consensus        71 ~~l~~~~--~~~~ii~~t~~~~~~~~~~~~~~g~~~~l~KP~~~~~~l~~~i~~~l  124 (130)
T 3eod_A           71 EHIRNRG--DQTPVLVISATENMADIAKALRLGVEDVLLKPVKDLNRLREMVFACL  124 (130)
T ss_dssp             HHHHHTT--CCCCEEEEECCCCHHHHHHHHHHCCSEEEESCC---CHHHHHHHHHH
T ss_pred             HHHHhcC--CCCCEEEEEcCCCHHHHHHHHHcCCCEEEeCCCCcHHHHHHHHHHHh
Confidence            9999854  689999999999999889999999999999999 8999999888764

>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=99.89  E-value=3.9e-22  Score=131.38  Aligned_cols=117  Identities=25%  Similarity=0.440  Sum_probs=106.0

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKK   99 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~   99 (153)
                      ..+|||+||++..+..++..|+..|+.+..+.++.+++..+.              ...||++|+|+.||+++|+++++.
T Consensus         3 ~~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~~~--------------~~~~dlvl~D~~l~~~~g~~~~~~   68 (124)
T 1srr_A            3 NEKILIVDDQSGIRILLNEVFNKEGYQTFQAANGLQALDIVT--------------KERPDLVLLDMKIPGMDGIEILKR   68 (124)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHH--------------HHCCSEEEEESCCTTCCHHHHHHH
T ss_pred             CceEEEEeCCHHHHHHHHHHHHHCCcEEEEeCCHHHHHHHHh--------------ccCCCEEEEecCCCCCCHHHHHHH
Confidence            468999999999999999999998999999999999998873              235899999999999999999999


Q ss_pred             HHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079          100 IKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus       100 lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      +++..  +.+|+|++|+..+.....++++.|+++|+.||++.+++...+.+++
T Consensus        69 l~~~~--~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~~  119 (124)
T 1srr_A           69 MKVID--ENIRVIIMTAYGELDMIQESKELGALTHFAKPFDIDEIRDAVKKYL  119 (124)
T ss_dssp             HHHHC--TTCEEEEEESSCCHHHHHHHHHHTCCCEEESSCCHHHHHHHHHHHS
T ss_pred             HHHhC--CCCCEEEEEccCchHHHHHHHhcChHhhccCCCCHHHHHHHHHHHh
Confidence            99754  5789999999888888899999999999999999999999888754

>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=99.89  E-value=1.4e-21  Score=129.31  Aligned_cols=119  Identities=34%  Similarity=0.534  Sum_probs=105.6

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCc-EEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSAC-KVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELL   97 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~-~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~   97 (153)
                      +.++|||+||++..+..++..|+..|+ .+..+.++.+++..+.              ...||++++|+.||+++|++++
T Consensus         3 ~~~~ilivdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~--------------~~~~dlvi~D~~l~~~~g~~l~   68 (128)
T 1jbe_A            3 KELKFLVVDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQ--------------AGGYGFVISDWNMPNMDGLELL   68 (128)
T ss_dssp             TTCCEEEECSCHHHHHHHHHHHHHTTCCCEEEESSHHHHHHHHT--------------TCCCCEEEEESCCSSSCHHHHH
T ss_pred             CccEEEEECCCHHHHHHHHHHHHHcCCcEEEeeCCHHHHHHHHH--------------hcCCCEEEEeCCCCCCCHHHHH
Confidence            456899999999999999999998888 7899999999998873              4569999999999999999999


Q ss_pred             HHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           98 KKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        98 ~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      +.+++....+.+|+|++++..+.....++++.|+++|+.||++.+++...+.++
T Consensus        69 ~~l~~~~~~~~~~ii~~s~~~~~~~~~~~~~~ga~~~l~KP~~~~~l~~~i~~~  122 (128)
T 1jbe_A           69 KTIRAXXAMSALPVLMVTAEAKKENIIAAAQAGASGYVVKPFTAATLEEKLNKI  122 (128)
T ss_dssp             HHHHC--CCTTCCEEEEESSCCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHH
T ss_pred             HHHHhhcccCCCcEEEEecCccHHHHHHHHHhCcCceeecCCCHHHHHHHHHHH
Confidence            999974444678999999998888899999999999999999999999888764

>3lua_A Response regulator receiver protein; two-component signal transduction system, histidine kinase, phosphorelay, receiver domain, nysgxrc; 2.40A {Clostridium thermocellum}

Probab=99.89  E-value=3.7e-22  Score=134.22  Aligned_cols=120  Identities=19%  Similarity=0.320  Sum_probs=109.0

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHh-cCcEEEEecCHHHHHHHhchhhhHHhhhhcccCC-CcccEEEEeCCCC-CCCHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKN-SACKVTTAENGMRALEFLGLVDEQEQQNNLNSNG-TKVNLVITDYCMP-GMTGYE   95 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~-~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~-~~~dlii~D~~~~-~~~g~~   95 (153)
                      +..+|||+||++..+..++.+|+. .|+.+..+.++.+++..+.              . ..||+||+|+.|| +++|++
T Consensus         3 ~~~~ilivdd~~~~~~~l~~~L~~~~~~~v~~~~~~~~a~~~l~--------------~~~~~dlvi~D~~l~~~~~g~~   68 (140)
T 3lua_A            3 LDGTVLLIDYFEYEREKTKIIFDNIGEYDFIEVENLKKFYSIFK--------------DLDSITLIIMDIAFPVEKEGLE   68 (140)
T ss_dssp             CCCEEEEECSCHHHHHHHHHHHHHHCCCEEEEECSHHHHHTTTT--------------TCCCCSEEEECSCSSSHHHHHH
T ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhccCccEEEECCHHHHHHHHh--------------cCCCCcEEEEeCCCCCCCcHHH
Confidence            357899999999999999999998 8999999999999998873              4 6799999999999 999999


Q ss_pred             HHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079           96 LLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus        96 ~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      +++.||+....+.+|+|++|+..+.....++++.|+++||.||++.++|...+.+++
T Consensus        69 ~~~~l~~~~~~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~~  125 (140)
T 3lua_A           69 VLSAIRNNSRTANTPVIIATKSDNPGYRHAALKFKVSDYILKPYPTKRLENSVRSVL  125 (140)
T ss_dssp             HHHHHHHSGGGTTCCEEEEESCCCHHHHHHHHHSCCSEEEESSCCTTHHHHHHHHHH
T ss_pred             HHHHHHhCcccCCCCEEEEeCCCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHH
Confidence            999999833346899999999999999999999999999999999999999888764

>3hv2_A Response regulator/HD domain protein; PSI-2, NYSGXRC, structural genomics, protein structure initiative; 1.50A {Pseudomonas fluorescens pf-5}

Probab=99.89  E-value=1.2e-21  Score=133.80  Aligned_cols=119  Identities=22%  Similarity=0.356  Sum_probs=108.3

Q ss_pred             CCCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHH
Q 042079           18 PKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELL   97 (153)
Q Consensus        18 ~~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~   97 (153)
                      .+..+|||+||++..+..+..+|+..||.+..+.++.+++..+.              ...||+||+|+.+|+++|++++
T Consensus        12 ~~~~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~--------------~~~~dlvi~D~~l~~~~g~~~~   77 (153)
T 3hv2_A           12 TRRPEILLVDSQEVILQRLQQLLSPLPYTLHFARDATQALQLLA--------------SREVDLVISAAHLPQMDGPTLL   77 (153)
T ss_dssp             CSCCEEEEECSCHHHHHHHHHHHTTSSCEEEEESSHHHHHHHHH--------------HSCCSEEEEESCCSSSCHHHHH
T ss_pred             cCCceEEEECCCHHHHHHHHHHhcccCcEEEEECCHHHHHHHHH--------------cCCCCEEEEeCCCCcCcHHHHH
Confidence            34679999999999999999999999999999999999999883              3569999999999999999999


Q ss_pred             HHHHhccCCCCCcEEEEeCCCChhhHHHHHHhc-CcccccCCCChhHHHHHHhhhc
Q 042079           98 KKIKESSVMKEVPVVVVSSENIPTRINECLEEG-AQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus        98 ~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~g-a~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      +.|++..  +.+|+|++++..+.....++++.| +++||.||++.++|...+.+++
T Consensus        78 ~~l~~~~--~~~~ii~~s~~~~~~~~~~~~~~g~~~~~l~KP~~~~~l~~~i~~~l  131 (153)
T 3hv2_A           78 ARIHQQY--PSTTRILLTGDPDLKLIAKAINEGEIYRYLSKPWDDQELLLALRQAL  131 (153)
T ss_dssp             HHHHHHC--TTSEEEEECCCCCHHHHHHHHHTTCCSEEECSSCCHHHHHHHHHHHH
T ss_pred             HHHHhHC--CCCeEEEEECCCCHHHHHHHHhCCCcceEEeCCCCHHHHHHHHHHHH
Confidence            9999854  689999999999999999999999 9999999999999998887753

>3crn_A Response regulator receiver domain protein, CHEY-; structural genomics, signal regulator receiver domain; HET: PHD; 1.58A {Methanospirillum hungatei jf-1}

Probab=99.89  E-value=7.5e-22  Score=131.74  Aligned_cols=116  Identities=22%  Similarity=0.287  Sum_probs=105.5

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKK   99 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~   99 (153)
                      ..+|||+||++..+..++.+|+..|+.+..+.++.+++..+.              ...||++|+|+.||+++|+++++.
T Consensus         3 ~~~Ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~--------------~~~~dlvl~D~~l~~~~g~~~~~~   68 (132)
T 3crn_A            3 LKRILIVDDDTAILDSTKQILEFEGYEVEIAATAGEGLAKIE--------------NEFFNLALFXIKLPDMEGTELLEK   68 (132)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--------------HSCCSEEEECSBCSSSBHHHHHHH
T ss_pred             ccEEEEEeCCHHHHHHHHHHHHHCCceEEEeCCHHHHHHHHh--------------cCCCCEEEEecCCCCCchHHHHHH
Confidence            468999999999999999999988999999999999998873              246899999999999999999999


Q ss_pred             HHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          100 IKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       100 lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      +++..  +.+|+|++|+..+.....++++.|+++|+.||++.+++...+.++
T Consensus        69 l~~~~--~~~~ii~~s~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~i~~~  118 (132)
T 3crn_A           69 AHKLR--PGMKKIMVTGYASLENSVFSLNAGADAYIMKPVNPRDLLEKIKEK  118 (132)
T ss_dssp             HHHHC--TTSEEEEEESCCCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHH
T ss_pred             HHhhC--CCCcEEEEeccccHHHHHHHHhccchhhccCCCCHHHHHHHHHHH
Confidence            99754  578999999998888889999999999999999999999887764

>3kto_A Response regulator receiver protein; PSI-II,structural genomics, protein structure initiative; 1.98A {Pseudoalteromonas atlantica T6C} SCOP: c.23.1.0

Probab=99.89  E-value=3.5e-22  Score=134.00  Aligned_cols=118  Identities=16%  Similarity=0.183  Sum_probs=107.2

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCC--CCHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPG--MTGYEL   96 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~--~~g~~~   96 (153)
                      +..+|||+||++..+..+..+|+..||.+..+.++.+++..+.              ...||+||+|+.+|+  ++|+++
T Consensus         5 ~~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~--------------~~~~dlvi~D~~l~~~~~~g~~~   70 (136)
T 3kto_A            5 HHPIIYLVDHQKDARAALSKLLSPLDVTIQCFASAESFMRQQI--------------SDDAIGMIIEAHLEDKKDSGIEL   70 (136)
T ss_dssp             --CEEEEECSCHHHHHHHHHHHTTSSSEEEEESSHHHHTTSCC--------------CTTEEEEEEETTGGGBTTHHHHH
T ss_pred             CCCeEEEEcCCHHHHHHHHHHHHHCCcEEEEeCCHHHHHHHHh--------------ccCCCEEEEeCcCCCCCccHHHH
Confidence            4578999999999999999999999999999999999988773              467999999999999  999999


Q ss_pred             HHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079           97 LKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus        97 ~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      ++++++..  +.+|+|++|+..+.....++++.|+++||.||++.++|...+.++.
T Consensus        71 ~~~l~~~~--~~~~ii~~s~~~~~~~~~~~~~~ga~~~l~KP~~~~~l~~~i~~~~  124 (136)
T 3kto_A           71 LETLVKRG--FHLPTIVMASSSDIPTAVRAMRASAADFIEKPFIEHVLVHDVQQII  124 (136)
T ss_dssp             HHHHHHTT--CCCCEEEEESSCCHHHHHHHHHTTCSEEEESSBCHHHHHHHHHHHH
T ss_pred             HHHHHhCC--CCCCEEEEEcCCCHHHHHHHHHcChHHheeCCCCHHHHHHHHHHHH
Confidence            99999864  6899999999999999999999999999999999999999888753

>3snk_A Response regulator CHEY-like protein; P-loop containing nucleoside triphosphate hydrolases, struct genomics; 2.02A {Mesorhizobium loti}

Probab=99.89  E-value=7e-23  Score=137.15  Aligned_cols=118  Identities=18%  Similarity=0.114  Sum_probs=108.0

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcC-cEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSA-CKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELL   97 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~-~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~   97 (153)
                      +..+|||+||++..+..++.+|+..| |.+..+.++.+++..+              ....||+||+|+.+|+++|++++
T Consensus        13 ~~~~ilivdd~~~~~~~l~~~L~~~g~~~v~~~~~~~~a~~~l--------------~~~~~dlvi~D~~l~~~~g~~~~   78 (135)
T 3snk_A           13 KRKQVALFSSDPNFKRDVATRLDALAIYDVRVSETDDFLKGPP--------------ADTRPGIVILDLGGGDLLGKPGI   78 (135)
T ss_dssp             CCEEEEEECSCHHHHHHHHHHHHHTSSEEEEEECGGGGGGCCC--------------TTCCCSEEEEEEETTGGGGSTTH
T ss_pred             CCcEEEEEcCCHHHHHHHHHHHhhcCCeEEEEeccHHHHHHHH--------------hccCCCEEEEeCCCCCchHHHHH
Confidence            44689999999999999999999999 9999999999998877              34679999999999999999999


Q ss_pred             HHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079           98 KKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus        98 ~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      +.+|+..  +.+|+|++|+..+.....++++.|+++|+.||++.++|...+.+++
T Consensus        79 ~~l~~~~--~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~KP~~~~~L~~~i~~~~  131 (135)
T 3snk_A           79 VEARALW--ATVPLIAVSDELTSEQTRVLVRMNASDWLHKPLDGKELLNAVTFHD  131 (135)
T ss_dssp             HHHHGGG--TTCCEEEEESCCCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHTC
T ss_pred             HHHHhhC--CCCcEEEEeCCCCHHHHHHHHHcCcHhhccCCCCHHHHHHHHHHHh
Confidence            9999865  5899999999999999999999999999999999999999988764

>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=99.89  E-value=7.3e-22  Score=129.25  Aligned_cols=117  Identities=26%  Similarity=0.434  Sum_probs=105.2

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCcE-EEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~~~-v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      ..+|||+||++..+..++..|+..|+. +..+.++.+++..+.              ...||++++|+.||+++|+++++
T Consensus         2 ~~~ilivdd~~~~~~~l~~~l~~~g~~vv~~~~~~~~a~~~~~--------------~~~~dlil~D~~l~~~~g~~~~~   67 (120)
T 1tmy_A            2 GKRVLIVDDAAFMRMMLKDIITKAGYEVAGEATNGREAVEKYK--------------ELKPDIVTMDITMPEMNGIDAIK   67 (120)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHH--------------HHCCSEEEEECSCGGGCHHHHHH
T ss_pred             CceEEEEcCcHHHHHHHHHHHhhcCcEEEEEECCHHHHHHHHH--------------hcCCCEEEEeCCCCCCcHHHHHH
Confidence            368999999999999999999988998 568999999998873              23589999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      ++++..  +.+|+|++++..+.....++++.|+++|+.||++.+++...+.+++
T Consensus        68 ~l~~~~--~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~~  119 (120)
T 1tmy_A           68 EIMKID--PNAKIIVCSAMGQQAMVIEAIKAGAKDFIVKPFQPSRVVEALNKVS  119 (120)
T ss_dssp             HHHHHC--TTCCEEEEECTTCHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHHC
T ss_pred             HHHhhC--CCCeEEEEeCCCCHHHHHHHHHhCcceeEeCCCCHHHHHHHHHHHh
Confidence            999754  5789999999988888899999999999999999999999988764

>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=99.88  E-value=6.1e-22  Score=130.20  Aligned_cols=118  Identities=24%  Similarity=0.417  Sum_probs=100.5

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKI  100 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~l  100 (153)
                      .+|||+||++..+..++..|+..|+.+..+.++.+++..+.              ...||++|+|+.||+++|+++++.+
T Consensus         2 ~~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~a~~~~~--------------~~~~dlvi~D~~l~~~~g~~~~~~l   67 (124)
T 1mb3_A            2 KKVLIVEDNELNMKLFHDLLEAQGYETLQTREGLSALSIAR--------------ENKPDLILMDIQLPEISGLEVTKWL   67 (124)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESCHHHHHHHHH--------------HHCCSEEEEESBCSSSBHHHHHHHH
T ss_pred             cEEEEEcCCHHHHHHHHHHHHHcCcEEEEeCCHHHHHHHHh--------------cCCCCEEEEeCCCCCCCHHHHHHHH
Confidence            47999999999999999999999999999999999988773              2358999999999999999999999


Q ss_pred             HhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079          101 KESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus       101 r~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      ++....+.+|+|++|+..+.....++++.|+++|+.||++.+++...+.+++
T Consensus        68 ~~~~~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~~  119 (124)
T 1mb3_A           68 KEDDDLAHIPVVAVTAFAMKGDEERIREGGCEAYISKPISVVHFLETIKRLL  119 (124)
T ss_dssp             HHSTTTTTSCEEEEC------CHHHHHHHTCSEEECSSCCHHHHHHHHHHHH
T ss_pred             HcCccccCCcEEEEECCCCHHHHHHHHhCCCCEEEeCCCCHHHHHHHHHHHH
Confidence            9854346789999999888888889999999999999999999998887754

>1i3c_A Response regulator RCP1; phytochrome, signaling protein; 1.90A {Synechocystis SP} SCOP: c.23.1.1 PDB: 1jlk_A

Probab=99.88  E-value=2.3e-21  Score=131.92  Aligned_cols=126  Identities=27%  Similarity=0.455  Sum_probs=106.3

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCc--EEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSAC--KVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYEL   96 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~--~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~   96 (153)
                      +..+|||+||++..+..++..|+..|+  .+..+.++.+++..+.....       ..+...||+||+|+.||+++|+++
T Consensus         7 ~~~~ILivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~al~~l~~~~~-------~~~~~~~dlillD~~lp~~~g~~l   79 (149)
T 1i3c_A            7 PPKVILLVEDSKADSRLVQEVLKTSTIDHELIILRDGLAAMAFLQQQGE-------YENSPRPNLILLDLNLPKKDGREV   79 (149)
T ss_dssp             CCEEEEEECCCHHHHHHHHHHHHSCCSCEEEEEECSHHHHHHHHTTCGG-------GTTCCCCSEEEECSCCSSSCHHHH
T ss_pred             CCCeEEEEECCHHHHHHHHHHHHhcCCCccEEEeCCHHHHHHHHHhccc-------cccCCCCCEEEEeCCCCCCcHHHH
Confidence            346899999999999999999998776  78899999999988731000       000246999999999999999999


Q ss_pred             HHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           97 LKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        97 ~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      ++.|++....+.+|+|++|+..+.....++++.|+++|+.||++.+++...+.++
T Consensus        80 ~~~l~~~~~~~~~piiils~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~i~~~  134 (149)
T 1i3c_A           80 LAEIKQNPDLKRIPVVVLTTSHNEDDVIASYELHVNCYLTKSRNLKDLFKMVQGI  134 (149)
T ss_dssp             HHHHHHCTTTTTSCEEEEESCCCHHHHHHHHHTTCSEEEECCSSHHHHHHHHHHH
T ss_pred             HHHHHhCcCcCCCeEEEEECCCChHHHHHHHHcCCcEEEECCCCHHHHHHHHHHH
Confidence            9999985434578999999988888889999999999999999999999887764

>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=99.88  E-value=1e-21  Score=130.12  Aligned_cols=118  Identities=22%  Similarity=0.424  Sum_probs=105.7

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCc-EEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSAC-KVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~~-~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      ..+|||+||++..+..+...|+..|+ .+..+.++.+++..+.              ...||++|+|+.||+++|+++++
T Consensus         6 ~~~ilivdd~~~~~~~l~~~L~~~g~~~v~~~~~~~~a~~~~~--------------~~~~dlvl~D~~l~~~~g~~~~~   71 (129)
T 1p6q_A            6 KIKVLIVDDQVTSRLLLGDALQQLGFKQITAAGDGEQGMKIMA--------------QNPHHLVISDFNMPKMDGLGLLQ   71 (129)
T ss_dssp             CCCEEEECSSHHHHHHHHHHHHTTTCSCEECCSSHHHHHHHHH--------------TSCCSEEEECSSSCSSCHHHHHH
T ss_pred             cCeEEEEcCCHHHHHHHHHHHHHCCCcEEEecCCHHHHHHHHH--------------cCCCCEEEEeCCCCCCCHHHHHH
Confidence            46899999999999999999998888 7889999999998873              35699999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      .+++....+.+|+|++|+..+.....++++.|+++|+.||++.+++...+.++
T Consensus        72 ~l~~~~~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~  124 (129)
T 1p6q_A           72 AVRANPATKKAAFIILTAQGDRALVQKAAALGANNVLAKPFTIEKMKAAIEAV  124 (129)
T ss_dssp             HHTTCTTSTTCEEEECCSCCCHHHHHHHHHHTCSCEECCCSSHHHHHHHHHHH
T ss_pred             HHhcCccccCCCEEEEeCCCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHH
Confidence            99975434678999999988888889999999999999999999999888764

>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=99.88  E-value=4.7e-22  Score=131.50  Aligned_cols=118  Identities=18%  Similarity=0.236  Sum_probs=105.3

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      +..+|||+||++..+..+..+|+..|+.+..+.++.+++..+.              ...||+||+|+.+|+++|+++++
T Consensus         2 ~~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~--------------~~~~dlii~D~~l~~~~g~~~~~   67 (127)
T 3i42_A            2 SLQQALIVEDYQAAAETFKELLEMLGFQADYVMSGTDALHAMS--------------TRGYDAVFIDLNLPDTSGLALVK   67 (127)
T ss_dssp             CCEEEEEECSCHHHHHHHHHHHHHTTEEEEEESSHHHHHHHHH--------------HSCCSEEEEESBCSSSBHHHHHH
T ss_pred             CcceEEEEcCCHHHHHHHHHHHHHcCCCEEEECCHHHHHHHHH--------------hcCCCEEEEeCCCCCCCHHHHHH
Confidence            3568999999999999999999999999999999999999883              35699999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      .+|+....+.+|+|++++..+... .+++..|+++|+.||++.++|.+.+.+.
T Consensus        68 ~l~~~~~~~~~~ii~~s~~~~~~~-~~~~~~g~~~~l~KP~~~~~L~~~i~~~  119 (127)
T 3i42_A           68 QLRALPMEKTSKFVAVSGFAKNDL-GKEACELFDFYLEKPIDIASLEPILQSI  119 (127)
T ss_dssp             HHHHSCCSSCCEEEEEECC-CTTC-CHHHHHHCSEEEESSCCHHHHHHHHHHH
T ss_pred             HHHhhhccCCCCEEEEECCcchhH-HHHHHHhhHHheeCCCCHHHHHHHHHHh
Confidence            999864346899999999887777 7899999999999999999999888764

>3jte_A Response regulator receiver protein; structural genomics, nysgrc, response regulator receiver DOM target 11226E, PSI-2; 1.90A {Clostridium thermocellum atcc 27405}

Probab=99.88  E-value=2.1e-21  Score=130.78  Aligned_cols=119  Identities=23%  Similarity=0.371  Sum_probs=107.3

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      +..+|||+||++..+..++.+|+..|+.+..+.+..+++..+..            ....||+||+|+.+|+.+|+++++
T Consensus         2 ~~~~ilivdd~~~~~~~l~~~l~~~g~~v~~~~~~~~a~~~~~~------------~~~~~dlvi~d~~l~~~~g~~~~~   69 (143)
T 3jte_A            2 SLAKILVIDDESTILQNIKFLLEIDGNEVLTASSSTEGLRIFTE------------NCNSIDVVITDMKMPKLSGMDILR   69 (143)
T ss_dssp             -CCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHHH------------TTTTCCEEEEESCCSSSCHHHHHH
T ss_pred             CCCEEEEEcCCHHHHHHHHHHHHhCCceEEEeCCHHHHHHHHHh------------CCCCCCEEEEeCCCCCCcHHHHHH
Confidence            45789999999999999999999999999999999999988731            135799999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      .+++..  +.+|+|++++..+.....++++.|+++|+.||++.+++...+.++
T Consensus        70 ~l~~~~--~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~l~~~  120 (143)
T 3jte_A           70 EIKKIT--PHMAVIILTGHGDLDNAILAMKEGAFEYLRKPVTAQDLSIAINNA  120 (143)
T ss_dssp             HHHHHC--TTCEEEEEECTTCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHH
T ss_pred             HHHHhC--CCCeEEEEECCCCHHHHHHHHHhCcceeEeCCCCHHHHHHHHHHH
Confidence            999864  689999999998888899999999999999999999999888765

>4e7p_A Response regulator; DNA binding, cytosol, transcription regulator; 1.89A {Streptococcus pneumoniae} PDB: 4e7o_A

Probab=99.88  E-value=2.1e-21  Score=132.21  Aligned_cols=118  Identities=26%  Similarity=0.347  Sum_probs=107.2

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcC--cEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSA--CKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYEL   96 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~--~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~   96 (153)
                      ..++|||+||++..+..+..+|+..+  +.+..+.++.+++..+.              ...||+||+|+.+|+.+|+++
T Consensus        19 ~m~~iLivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~al~~l~--------------~~~~dlii~D~~l~~~~g~~~   84 (150)
T 4e7p_A           19 SHMKVLVAEDQSMLRDAMCQLLTLQPDVESVLQAKNGQEAIQLLE--------------KESVDIAILDVEMPVKTGLEV   84 (150)
T ss_dssp             -CEEEEEECSCHHHHHHHHHHHHTSTTEEEEEEESSHHHHHHHHT--------------TSCCSEEEECSSCSSSCHHHH
T ss_pred             CccEEEEEcCCHHHHHHHHHHHHhCCCcEEEEEECCHHHHHHHhh--------------ccCCCEEEEeCCCCCCcHHHH
Confidence            44789999999999999999999877  78999999999999883              467999999999999999999


Q ss_pred             HHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079           97 LKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus        97 ~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      ++.|++..  +.+|+|++++..+.....++++.|+++|+.||++.+++...+.+++
T Consensus        85 ~~~l~~~~--~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~Kp~~~~~l~~~i~~~~  138 (150)
T 4e7p_A           85 LEWIRSEK--LETKVVVVTTFKRAGYFERAVKAGVDAYVLKERSIADLMQTLHTVL  138 (150)
T ss_dssp             HHHHHHTT--CSCEEEEEESCCCHHHHHHHHHTTCSEEEETTSCHHHHHHHHHHHH
T ss_pred             HHHHHHhC--CCCeEEEEeCCCCHHHHHHHHHCCCcEEEecCCCHHHHHHHHHHHH
Confidence            99999854  6899999999999999999999999999999999999999888764

>2pl1_A Transcriptional regulatory protein PHOP; CHEY-like fold, response regulator, beryllium fluoride, transcription factor, activated, virulence; 1.90A {Escherichia coli} SCOP: c.23.1.1 PDB: 2pkx_A

Probab=99.88  E-value=2e-21  Score=127.14  Aligned_cols=115  Identities=22%  Similarity=0.359  Sum_probs=104.4

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKI  100 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~l  100 (153)
                      ++|||+||++..+..+...|+..|+.+..+.++.+++..+.              ...||++++|+.||+++|+++++.+
T Consensus         1 ~~ilivdd~~~~~~~l~~~l~~~g~~v~~~~~~~~a~~~~~--------------~~~~dlil~D~~l~~~~g~~~~~~l   66 (121)
T 2pl1_A            1 MRVLVVEDNALLRHHLKVQIQDAGHQVDDAEDAKEADYYLN--------------EHIPDIAIVDLGLPDEDGLSLIRRW   66 (121)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--------------HSCCSEEEECSCCSSSCHHHHHHHH
T ss_pred             CeEEEEeCcHHHHHHHHHHHhhcCCEEEEeCCHHHHHHHHh--------------ccCCCEEEEecCCCCCCHHHHHHHH
Confidence            37999999999999999999999999999999999998873              3468999999999999999999999


Q ss_pred             HhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          101 KESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       101 r~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      ++..  +.+|+|++++..+.....++++.|+++|+.||++.+++...+.++
T Consensus        67 ~~~~--~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~i~~~  115 (121)
T 2pl1_A           67 RSND--VSLPILVLTARESWQDKVEVLSAGADDYVTKPFHIEEVMARMQAL  115 (121)
T ss_dssp             HHTT--CCSCEEEEESCCCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHH
T ss_pred             HhcC--CCCCEEEEecCCCHHHHHHHHHcCccceEECCCCHHHHHHHHHHH
Confidence            9754  578999999998888889999999999999999999999887764

>3hzh_A Chemotaxis response regulator (CHEY-3); phosphatase, complex, response regulator, receiver domain, two-component signal transduction; HET: BFD; 1.96A {Borrelia burgdorferi}

Probab=99.88  E-value=1e-21  Score=134.92  Aligned_cols=120  Identities=27%  Similarity=0.403  Sum_probs=107.9

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcEEE-EecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACKVT-TAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELL   97 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~v~-~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~   97 (153)
                      +..+|||+||++..+..+..+|+..|+.+. .+.+..+++..+...            ...||+||+|+.||+++|++++
T Consensus        35 ~~~~Ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~~al~~l~~~------------~~~~dliilD~~l~~~~g~~~~  102 (157)
T 3hzh_A           35 IPFNVLIVDDSVFTVKQLTQIFTSEGFNIIDTAADGEEAVIKYKNH------------YPNIDIVTLXITMPKMDGITCL  102 (157)
T ss_dssp             EECEEEEECSCHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHHHH------------GGGCCEEEECSSCSSSCHHHHH
T ss_pred             CceEEEEEeCCHHHHHHHHHHHHhCCCeEEEEECCHHHHHHHHHhc------------CCCCCEEEEeccCCCccHHHHH
Confidence            346899999999999999999999999988 999999999988421            1158999999999999999999


Q ss_pred             HHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079           98 KKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus        98 ~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      +.|++..  +.+|+|++++..+.....++++.|+++||.||++.++|...+.+++
T Consensus       103 ~~lr~~~--~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~l  155 (157)
T 3hzh_A          103 SNIMEFD--KNARVIMISALGKEQLVKDCLIKGAKTFIVKPLDRAKVLQRVMSVF  155 (157)
T ss_dssp             HHHHHHC--TTCCEEEEESCCCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHTT
T ss_pred             HHHHhhC--CCCcEEEEeccCcHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHh
Confidence            9999865  6899999999999999999999999999999999999999998865

>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=99.88  E-value=1.7e-21  Score=131.57  Aligned_cols=120  Identities=21%  Similarity=0.389  Sum_probs=107.9

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcE--EEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACK--VTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYEL   96 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~--v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~   96 (153)
                      +..+|||+||++..+..+..+|+..|+.  +..+.++.+++..+.              ...||+||+|+.+|+++|+++
T Consensus         4 ~~~~ILivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~a~~~l~--------------~~~~dlii~D~~l~~~~g~~~   69 (144)
T 3kht_A            4 RSKRVLVVEDNPDDIALIRRVLDRKDIHCQLEFVDNGAKALYQVQ--------------QAKYDLIILDIGLPIANGFEV   69 (144)
T ss_dssp             -CEEEEEECCCHHHHHHHHHHHHHTTCCEEEEEESSHHHHHHHHT--------------TCCCSEEEECTTCGGGCHHHH
T ss_pred             CCCEEEEEeCCHHHHHHHHHHHHhcCCCeeEEEECCHHHHHHHhh--------------cCCCCEEEEeCCCCCCCHHHH
Confidence            4578999999999999999999998887  889999999999883              467999999999999999999


Q ss_pred             HHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCC-ChhHHHHHHhhhc
Q 042079           97 LKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPL-KPSDVKKLTGHLI  152 (153)
Q Consensus        97 ~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~-~~~~l~~~~~~~~  152 (153)
                      ++.||+....+.+|+|++++..+.....++++.|+++|+.||+ +.+++...+.+++
T Consensus        70 ~~~lr~~~~~~~~pii~~s~~~~~~~~~~~~~~ga~~~l~Kp~~~~~~l~~~i~~~l  126 (144)
T 3kht_A           70 MSAVRKPGANQHTPIVILTDNVSDDRAKQCMAAGASSVVDKSSNNVTDFYGRIYAIF  126 (144)
T ss_dssp             HHHHHSSSTTTTCCEEEEETTCCHHHHHHHHHTTCSEEEECCTTSHHHHHHHHHHHH
T ss_pred             HHHHHhcccccCCCEEEEeCCCCHHHHHHHHHcCCCEEEECCCCcHHHHHHHHHHHH
Confidence            9999984444789999999999999999999999999999999 9999998887753

>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=99.88  E-value=2e-21  Score=132.42  Aligned_cols=127  Identities=22%  Similarity=0.463  Sum_probs=108.1

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCc--EEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSAC--KVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELL   97 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~~--~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~   97 (153)
                      ..+|||+||++..+..+...|+..|+  .+..+.++.+++..+.....     ........||+||+|+.||+++|++++
T Consensus         4 ~~~ILivddd~~~~~~l~~~L~~~g~~~~v~~~~~~~~al~~l~~~~~-----~~~~~~~~~dliilD~~l~~~~g~~~~   78 (152)
T 3heb_A            4 SVTIVMIEDDLGHARLIEKNIRRAGVNNEIIAFTDGTSALNYLFGDDK-----SGRVSAGRAQLVLLDLNLPDMTGIDIL   78 (152)
T ss_dssp             -CEEEEECCCHHHHHHHHHHHHHTTCCCCEEEESSHHHHHHHHHCTTS-----SSGGGTTCBEEEEECSBCSSSBHHHHH
T ss_pred             CceEEEEeCCHHHHHHHHHHHHhCCCcceEEEeCCHHHHHHHHhcccc-----ccccccCCCCEEEEeCCCCCCcHHHHH
Confidence            47899999999999999999999988  89999999999998731100     000013579999999999999999999


Q ss_pred             HHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           98 KKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        98 ~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      +.||+....+.+|+|++|+..+.....++++.|+++||.||++.++|...+.++
T Consensus        79 ~~lr~~~~~~~~pii~~t~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~  132 (152)
T 3heb_A           79 KLVKENPHTRRSPVVILTTTDDQREIQRCYDLGANVYITKPVNYENFANAIRQL  132 (152)
T ss_dssp             HHHHHSTTTTTSCEEEEESCCCHHHHHHHHHTTCSEEEECCSSHHHHHHHHHHH
T ss_pred             HHHHhcccccCCCEEEEecCCCHHHHHHHHHCCCcEEEeCCCCHHHHHHHHHHH
Confidence            999985445789999999999988899999999999999999999999988775

>3hdv_A Response regulator; PSI-II, structural genomics, Pro structure initiative, NEW YORK SGX research center for STRU genomics, nysgxrc; 2.09A {Pseudomonas putida} SCOP: c.23.1.0

Probab=99.88  E-value=2.4e-21  Score=129.50  Aligned_cols=120  Identities=26%  Similarity=0.404  Sum_probs=107.4

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      +..+|||+||++..+..++.+|+..|+.+..+.+..+++..+..             ...||+||+|+.+|+.+|+++++
T Consensus         6 ~~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~~~~-------------~~~~dlvi~D~~l~~~~g~~~~~   72 (136)
T 3hdv_A            6 ARPLVLVVDDNAVNREALILYLKSRGIDAVGADGAEEARLYLHY-------------QKRIGLMITDLRMQPESGLDLIR   72 (136)
T ss_dssp             -CCEEEEECSCHHHHHHHHHHHHHTTCCEEEESSHHHHHHHHHH-------------CTTEEEEEECSCCSSSCHHHHHH
T ss_pred             CCCeEEEECCCHHHHHHHHHHHHHcCceEEEeCCHHHHHHHHHh-------------CCCCcEEEEeccCCCCCHHHHHH
Confidence            45789999999999999999999999999999999999887731             23499999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      .|++.. .+.+|+|++++..+.....++++.|+++|+.||++.++|...+.+..
T Consensus        73 ~l~~~~-~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~~  125 (136)
T 3hdv_A           73 TIRASE-RAALSIIVVSGDTDVEEAVDVMHLGVVDFLLKPVDLGKLLELVNKEL  125 (136)
T ss_dssp             HHHTST-TTTCEEEEEESSCCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHH
T ss_pred             HHHhcC-CCCCCEEEEeCCCChHHHHHHHhCCcceEEeCCCCHHHHHHHHHHHh
Confidence            999853 36899999999999989999999999999999999999999888753

>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=99.88  E-value=3e-21  Score=126.84  Aligned_cols=115  Identities=26%  Similarity=0.486  Sum_probs=104.2

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKK   99 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~   99 (153)
                      ..+|||+||++..+..++..|+..|+.+..+.++.+++..+.              ...||++|+|+.||+++|+++++.
T Consensus         3 ~~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~~~--------------~~~~dlvi~D~~l~~~~g~~~~~~   68 (123)
T 1xhf_A            3 TPHILIVEDELVTRNTLKSIFEAEGYDVFEATDGAEMHQILS--------------EYDINLVIMDINLPGKNGLLLARE   68 (123)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHH--------------HSCCSEEEECSSCSSSCHHHHHHH
T ss_pred             CceEEEEeCCHHHHHHHHHHHhhCCcEEEEeCCHHHHHHHHh--------------cCCCCEEEEcCCCCCCCHHHHHHH
Confidence            468999999999999999999988999999999999998873              346999999999999999999999


Q ss_pred             HHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          100 IKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       100 lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      +++.   +.+|+|++++..+.....++++.|+++|+.||++.+++...+.++
T Consensus        69 l~~~---~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~  117 (123)
T 1xhf_A           69 LREQ---ANVALMFLTGRDNEVDKILGLEIGADDYITKPFNPRELTIRARNL  117 (123)
T ss_dssp             HHHH---CCCEEEEEESCCSHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHH
T ss_pred             HHhC---CCCcEEEEECCCChHHHHHHHhcCcceEEeCCCCHHHHHHHHHHH
Confidence            9975   478999999988888889999999999999999999998877664

>3r0j_A Possible two component system response transcript positive regulator PHOP; beta-alpha fold, winged helix-turn-helix; 2.50A {Mycobacterium tuberculosis}

Probab=99.88  E-value=1.2e-21  Score=144.25  Aligned_cols=118  Identities=25%  Similarity=0.376  Sum_probs=107.4

Q ss_pred             CCCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHH
Q 042079           18 PKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELL   97 (153)
Q Consensus        18 ~~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~   97 (153)
                      .+.++|||+||++..+..+..+|+..||.+..+.++.++++.+.              ...||+||+|+.||+++|++++
T Consensus        21 ~~~~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~--------------~~~~dlvllD~~lp~~~g~~~~   86 (250)
T 3r0j_A           21 TPEARVLVVDDEANIVELLSVSLKFQGFEVYTATNGAQALDRAR--------------ETRPDAVILDVXMPGMDGFGVL   86 (250)
T ss_dssp             CSSCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--------------HHCCSEEEEESCCSSSCHHHHH
T ss_pred             CCCceEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHH--------------hCCCCEEEEeCCCCCCCHHHHH
Confidence            35689999999999999999999999999999999999999873              2469999999999999999999


Q ss_pred             HHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           98 KKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        98 ~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      ++||+..  +.+|+|++|+..+.....++++.|+++|+.||++.++|...+..+
T Consensus        87 ~~lr~~~--~~~~ii~lt~~~~~~~~~~~~~~Ga~~yl~Kp~~~~~L~~~i~~~  138 (250)
T 3r0j_A           87 RRLRADG--IDAPALFLTARDSLQDKIAGLTLGGDDYVTKPFSLEEVVARLRVI  138 (250)
T ss_dssp             HHHHHTT--CCCCEEEEECSTTHHHHHHHHTSTTCEEEESSCCHHHHHHHHHHH
T ss_pred             HHHHhcC--CCCCEEEEECCCCHHHHHHHHHcCCcEEEeCCCCHHHHHHHHHHH
Confidence            9999864  578999999999999999999999999999999999998877664

>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=99.88  E-value=4.7e-21  Score=127.98  Aligned_cols=125  Identities=24%  Similarity=0.418  Sum_probs=107.2

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCc--EEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSAC--KVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELL   97 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~~--~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~   97 (153)
                      .++|||+||++..+..+...|+..|+  .+..+.++.+++..+.....       ......||+||+|+.+|+++|++++
T Consensus         2 ~~~ilivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~a~~~l~~~~~-------~~~~~~~dlvi~d~~~~~~~g~~~~   74 (140)
T 1k68_A            2 HKKIFLVEDNKADIRLIQEALANSTVPHEVVTVRDGMEAMAYLRQEGE-------YANASRPDLILLXLNLPKKDGREVL   74 (140)
T ss_dssp             CCEEEEECCCHHHHHHHHHHHHTCSSCCEEEEECSHHHHHHHHTTCGG-------GGSCCCCSEEEECSSCSSSCHHHHH
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCCCceEEEECCHHHHHHHHHcccc-------cccCCCCcEEEEecCCCcccHHHHH
Confidence            46899999999999999999999888  89999999999998831000       0001579999999999999999999


Q ss_pred             HHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           98 KKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        98 ~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      +.+++....+.+|+|++++..+.....++++.|+++|+.||++.+++...+.++
T Consensus        75 ~~l~~~~~~~~~pii~ls~~~~~~~~~~~~~~g~~~~l~kP~~~~~l~~~i~~~  128 (140)
T 1k68_A           75 AEIKSDPTLKRIPVVVLSTSINEDDIFHSYDLHVNCYITKSANLSQLFQIVKGI  128 (140)
T ss_dssp             HHHHHSTTGGGSCEEEEESCCCHHHHHHHHHTTCSEEEECCSSHHHHHHHHHHH
T ss_pred             HHHHcCcccccccEEEEecCCcHHHHHHHHHhchhheecCCCCHHHHHHHHHHH
Confidence            999985433578999999998888899999999999999999999999888765

>3b2n_A Uncharacterized protein Q99UF4; structural genomics, PSI-2, protein structure initiative, NE SGX research center for structural genomics; 2.04A {Staphylococcus aureus}

Probab=99.88  E-value=1.4e-21  Score=130.50  Aligned_cols=117  Identities=21%  Similarity=0.378  Sum_probs=103.9

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcC--cEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSA--CKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELL   97 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~--~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~   97 (153)
                      ..+|||+||++..+..+..+|+..+  +.+..+.++.+++..+.              ...||++|+|+.||+++|++++
T Consensus         3 ~~~Ilivdd~~~~~~~l~~~l~~~~~~~~v~~~~~~~~al~~~~--------------~~~~dlvilD~~lp~~~g~~~~   68 (133)
T 3b2n_A            3 LTSLIIAEDQNMLRQAMVQLIKLHGDFEILADTDNGLDAMKLIE--------------EYNPNVVILDIEMPGMTGLEVL   68 (133)
T ss_dssp             CEEEEEECSCHHHHHHHHHHHHHHSSEEEEEEESCHHHHHHHHH--------------HHCCSEEEECSSCSSSCHHHHH
T ss_pred             ceEEEEECCCHHHHHHHHHHHhhCCCcEEEEEcCCHHHHHHHHh--------------hcCCCEEEEecCCCCCCHHHHH
Confidence            3579999999999999999999776  56778999999998873              2358999999999999999999


Q ss_pred             HHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079           98 KKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus        98 ~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      +.+++..  +.+|+|++|+..+.....++++.|+++|+.||++.+++...+.+++
T Consensus        69 ~~l~~~~--~~~~ii~ls~~~~~~~~~~~~~~ga~~~l~Kp~~~~~L~~~i~~~~  121 (133)
T 3b2n_A           69 AEIRKKH--LNIKVIIVTTFKRPGYFEKAVVNDVDAYVLKERSIEELVETINKVN  121 (133)
T ss_dssp             HHHHHTT--CSCEEEEEESCCCHHHHHHHHHTTCSEEEETTSCHHHHHHHHHHHH
T ss_pred             HHHHHHC--CCCcEEEEecCCCHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHHH
Confidence            9999753  6899999999988888999999999999999999999999887753

>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=99.88  E-value=1.8e-21  Score=144.57  Aligned_cols=120  Identities=25%  Similarity=0.400  Sum_probs=107.1

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      +..+|||+||++..+..+...|+..|+.+..+.++.++++.+..             ...||+||+|+.||+++|+++++
T Consensus       123 ~~~~ILivDD~~~~~~~l~~~L~~~~~~v~~a~~~~eal~~l~~-------------~~~~dlvllD~~mP~~dG~~l~~  189 (259)
T 3luf_A          123 QQIEVLVVDDSRTSRHRTMAQLRKQLLQVHEASHAREALATLEQ-------------HPAIRLVLVDYYMPEIDGISLVR  189 (259)
T ss_dssp             TTCEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHHH-------------CTTEEEEEECSCCSSSCHHHHHH
T ss_pred             CCCcEEEEeCCHHHHHHHHHHHHHcCcEEEEeCCHHHHHHHHhc-------------CCCCCEEEEcCCCCCCCHHHHHH
Confidence            35789999999999999999999999999999999999998731             22489999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      +||+......+|||++|+..+.....++++.|+++||.||+++++|...+.++
T Consensus       190 ~lr~~~~~~~~~ii~~s~~~~~~~~~~a~~~Ga~~yl~KP~~~~~L~~~i~~~  242 (259)
T 3luf_A          190 MLRERYSKQQLAIIGISVSDKRGLSARYLKQGANDFLNQPFEPEELQCRVSHN  242 (259)
T ss_dssp             HHHHHCCTTTSEEEEEECSSSSSHHHHHHHTTCSEEEESSCCHHHHHHHHHHH
T ss_pred             HHHhccCCCCCeEEEEEccCCHHHHHHHHhcChhheEcCCCCHHHHHHHHHHH
Confidence            99986544578999999998888889999999999999999999998877764

>3grc_A Sensor protein, kinase; protein structure initiative II(PSI II), NYSGXRC, 11025B, structural genomics; 2.21A {Polaromonas SP}

Probab=99.88  E-value=4.3e-22  Score=133.81  Aligned_cols=120  Identities=16%  Similarity=0.273  Sum_probs=106.2

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      +..+|||+||++..+..+..+|+..|+.+..+.++.+++..+.              ...||+||+|+.||+++|+++++
T Consensus         5 ~~~~iLivdd~~~~~~~l~~~l~~~g~~v~~~~~~~~a~~~l~--------------~~~~dlvi~d~~l~~~~g~~~~~   70 (140)
T 3grc_A            5 PRPRILICEDDPDIARLLNLMLEKGGFDSDMVHSAAQALEQVA--------------RRPYAAMTVDLNLPDQDGVSLIR   70 (140)
T ss_dssp             CCSEEEEECSCHHHHHHHHHHHHHTTCEEEEECSHHHHHHHHH--------------HSCCSEEEECSCCSSSCHHHHHH
T ss_pred             CCCCEEEEcCCHHHHHHHHHHHHHCCCeEEEECCHHHHHHHHH--------------hCCCCEEEEeCCCCCCCHHHHHH
Confidence            4578999999999999999999999999999999999999883              35699999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHH-HHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRIN-ECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~-~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      .|++....+.+|+|++++..+..... ++++.|+++|+.||++.++|...+.+++
T Consensus        71 ~l~~~~~~~~~~ii~~s~~~~~~~~~~~~~~~g~~~~l~kP~~~~~l~~~i~~~l  125 (140)
T 3grc_A           71 ALRRDSRTRDLAIVVVSANAREGELEFNSQPLAVSTWLEKPIDENLLILSLHRAI  125 (140)
T ss_dssp             HHHTSGGGTTCEEEEECTTHHHHHHHHCCTTTCCCEEECSSCCHHHHHHHHHHHH
T ss_pred             HHHhCcccCCCCEEEEecCCChHHHHHHhhhcCCCEEEeCCCCHHHHHHHHHHHH
Confidence            99974334689999999876666666 7899999999999999999998887753

>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=99.88  E-value=1.2e-21  Score=131.10  Aligned_cols=118  Identities=24%  Similarity=0.383  Sum_probs=107.4

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      +..+|||+||++..+..+..+|+..++.+..+.++.+++..+.              ...||+||+|+.+|+.+|+++++
T Consensus         6 ~~~~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~a~~~l~--------------~~~~dlvi~d~~l~~~~g~~~~~   71 (137)
T 3hdg_A            6 VALKILIVEDDTDAREWLSTIISNHFPEVWSAGDGEEGERLFG--------------LHAPDVIITDIRMPKLGGLEMLD   71 (137)
T ss_dssp             -CCCEEEECSCHHHHHHHHHHHHTTCSCEEEESSHHHHHHHHH--------------HHCCSEEEECSSCSSSCHHHHHH
T ss_pred             cccEEEEEeCCHHHHHHHHHHHHhcCcEEEEECCHHHHHHHHh--------------ccCCCEEEEeCCCCCCCHHHHHH
Confidence            3578999999999999999999998999999999999999884              24699999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      .|++..  +.+|+|++++..+.....++++.|+++|+.||++.++|.+.+.+++
T Consensus        72 ~l~~~~--~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~kP~~~~~l~~~i~~~~  123 (137)
T 3hdg_A           72 RIKAGG--AKPYVIVISAFSEMKYFIKAIELGVHLFLPKPIEPGRLMETLEDFR  123 (137)
T ss_dssp             HHHHTT--CCCEEEECCCCCCHHHHHHHHHHCCSEECCSSCCHHHHHHHHHHHH
T ss_pred             HHHhcC--CCCcEEEEecCcChHHHHHHHhCCcceeEcCCCCHHHHHHHHHHHH
Confidence            999864  6889999999988889999999999999999999999999888764

>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=99.88  E-value=4.5e-21  Score=125.81  Aligned_cols=114  Identities=21%  Similarity=0.357  Sum_probs=103.4

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKI  100 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~l  100 (153)
                      .+|||+||++..+..+...|+..|+.+..+.++.+++..+.              ...||++|+|+.||+++|+++++.+
T Consensus         3 ~~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~~--------------~~~~dlvi~d~~l~~~~g~~~~~~l   68 (122)
T 1zgz_A            3 HHIVIVEDEPVTQARLQSYFTQEGYTVSVTASGAGLREIMQ--------------NQSVDLILLDINLPDENGLMLTRAL   68 (122)
T ss_dssp             CEEEEECSSHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--------------HSCCSEEEEESCCSSSCHHHHHHHH
T ss_pred             cEEEEEECCHHHHHHHHHHHHHCCCeEEEecCHHHHHHHHh--------------cCCCCEEEEeCCCCCCChHHHHHHH
Confidence            57999999999999999999988999999999999988773              2468999999999999999999999


Q ss_pred             HhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          101 KESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       101 r~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      ++ .  +.+|+|++++..+.....++++.|+++|+.||++.+++...+.++
T Consensus        69 ~~-~--~~~~ii~~s~~~~~~~~~~~~~~ga~~~l~Kp~~~~~l~~~i~~~  116 (122)
T 1zgz_A           69 RE-R--STVGIILVTGRSDRIDRIVGLEMGADDYVTKPLELRELVVRVKNL  116 (122)
T ss_dssp             HT-T--CCCEEEEEESSCCHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHH
T ss_pred             Hh-c--CCCCEEEEECCCChhhHHHHHHhCHHHHccCCCCHHHHHHHHHHH
Confidence            97 3  578999999988888889999999999999999999999877764

>3ilh_A Two component response regulator; NYSGXRC, PSI-II, protein S initiative, structural genomics; 2.59A {Cytophaga hutchinsonii}

Probab=99.87  E-value=3.3e-21  Score=129.89  Aligned_cols=124  Identities=20%  Similarity=0.329  Sum_probs=108.3

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCc--EEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSAC--KVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYEL   96 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~--~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~   96 (153)
                      +..+|||+||++..+..+..+|+..|+  .+..+.++.+++..+....         .....||+||+|+.||+++|+++
T Consensus         8 ~~~~iLivdd~~~~~~~l~~~l~~~~~~~~v~~~~~~~~a~~~l~~~~---------~~~~~~dlvi~D~~l~~~~g~~~   78 (146)
T 3ilh_A            8 KIDSVLLIDDDDIVNFLNTTIIRMTHRVEEIQSVTSGNAAINKLNELY---------AAGRWPSIICIDINMPGINGWEL   78 (146)
T ss_dssp             CEEEEEEECSCHHHHHHHHHHHHTTCCEEEEEEESSHHHHHHHHHHHH---------TSSCCCSEEEEESSCSSSCHHHH
T ss_pred             ccceEEEEeCCHHHHHHHHHHHHhcCCCeeeeecCCHHHHHHHHHHhh---------ccCCCCCEEEEcCCCCCCCHHHH
Confidence            457899999999999999999999998  8999999999999884210         11257999999999999999999


Q ss_pred             HHHHHhcc--CCCCCcEEEEeCCCChhhHHHHHHhc-CcccccCCCChhHHHHHHhhh
Q 042079           97 LKKIKESS--VMKEVPVVVVSSENIPTRINECLEEG-AQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        97 ~~~lr~~~--~~~~~pii~~t~~~~~~~~~~a~~~g-a~~~l~KP~~~~~l~~~~~~~  151 (153)
                      ++.|++..  ..+.+|+|++++..+.....+++..| +++||.||++.++|...+.+.
T Consensus        79 ~~~l~~~~~~~~~~~~ii~~t~~~~~~~~~~~~~~g~~~~~l~KP~~~~~L~~~i~~~  136 (146)
T 3ilh_A           79 IDLFKQHFQPMKNKSIVCLLSSSLDPRDQAKAEASDWVDYYVSKPLTANALNNLYNKV  136 (146)
T ss_dssp             HHHHHHHCGGGTTTCEEEEECSSCCHHHHHHHHHCSSCCEEECSSCCHHHHHHHHHHH
T ss_pred             HHHHHHhhhhccCCCeEEEEeCCCChHHHHHHHhcCCcceeeeCCCCHHHHHHHHHHH
Confidence            99999832  33688999999999999999999999 999999999999999998875

>3lte_A Response regulator; structural genomics, PSI, protein structure initiative, NYSG YORK structural genomix research consortium, nysgxrc; 2.00A {Bermanella marisrubri}

Probab=99.87  E-value=6.1e-21  Score=126.78  Aligned_cols=118  Identities=23%  Similarity=0.404  Sum_probs=100.1

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      +..+|||+||++..+..+..+|++.|+.+..+.++.+++..+.              ...||+||+|+.+|+++|+++++
T Consensus         5 ~~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~--------------~~~~dlii~d~~l~~~~g~~~~~   70 (132)
T 3lte_A            5 QSKRILVVDDDQAMAAAIERVLKRDHWQVEIAHNGFDAGIKLS--------------TFEPAIMTLDLSMPKLDGLDVIR   70 (132)
T ss_dssp             --CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--------------HTCCSEEEEESCBTTBCHHHHHH
T ss_pred             CCccEEEEECCHHHHHHHHHHHHHCCcEEEEeCCHHHHHHHHH--------------hcCCCEEEEecCCCCCCHHHHHH
Confidence            4578999999999999999999999999999999999998873              35699999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      .+|+....+..+|++++... .....++++.|+++|+.||++.+++...+.+.
T Consensus        71 ~l~~~~~~~~~~ii~~~~~~-~~~~~~~~~~g~~~~l~kP~~~~~l~~~i~~~  122 (132)
T 3lte_A           71 SLRQNKVANQPKILVVSGLD-KAKLQQAVTEGADDYLEKPFDNDALLDRIHDL  122 (132)
T ss_dssp             HHHTTTCSSCCEEEEECCSC-SHHHHHHHHHTCCEEECSSCCHHHHHHHHHHH
T ss_pred             HHHhcCccCCCeEEEEeCCC-hHHHHHHHHhChHHHhhCCCCHHHHHHHHHHH
Confidence            99975432345565555544 44778899999999999999999999888774

>3nhm_A Response regulator; protein structure initiative II(PSI II), NYSGXRC, structural genomics; 2.19A {Myxococcus xanthus}

Probab=99.87  E-value=2e-21  Score=129.34  Aligned_cols=118  Identities=27%  Similarity=0.404  Sum_probs=100.8

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      +..+|||+||++..+..++.+|+ .++.+..+.++.+++..+.              ..+||+||+|+.+|+++|+++++
T Consensus         3 ~~~~ilivdd~~~~~~~l~~~l~-~~~~v~~~~~~~~a~~~l~--------------~~~~dlvi~d~~l~~~~g~~~~~   67 (133)
T 3nhm_A            3 LKPKVLIVENSWTMRETLRLLLS-GEFDCTTAADGASGLQQAL--------------AHPPDVLISDVNMDGMDGYALCG   67 (133)
T ss_dssp             --CEEEEECSCHHHHHHHHHHHT-TTSEEEEESSHHHHHHHHH--------------HSCCSEEEECSSCSSSCHHHHHH
T ss_pred             CCCEEEEEcCCHHHHHHHHHHHh-CCcEEEEECCHHHHHHHHh--------------cCCCCEEEEeCCCCCCCHHHHHH
Confidence            35789999999999999999998 7899999999999999873              35699999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      .+++....+.+|+|++++..+... .++++.|+++|+.||++.++|...+.+++
T Consensus        68 ~l~~~~~~~~~pii~~s~~~~~~~-~~~~~~g~~~~l~KP~~~~~l~~~i~~~l  120 (133)
T 3nhm_A           68 HFRSEPTLKHIPVIFVSGYAPRTE-GPADQPVPDAYLVKPVKPPVLIAQLHALL  120 (133)
T ss_dssp             HHHHSTTTTTCCEEEEESCCC------TTSCCCSEEEESSCCHHHHHHHHHHHH
T ss_pred             HHHhCCccCCCCEEEEeCCCcHhH-HHHhhcCCceEEeccCCHHHHHHHHHHHH
Confidence            999865446899999999877766 78999999999999999999999888754

>4dad_A Putative pilus assembly-related protein; response regulator receiver domain, CHEY-related protein, ST genomics; 2.50A {Burkholderia pseudomallei} PDB: 4dn6_A

Probab=99.87  E-value=9.1e-22  Score=133.20  Aligned_cols=123  Identities=10%  Similarity=0.168  Sum_probs=108.3

Q ss_pred             CCCCCCCeEEEEeCCHHHHHHHHHHHHhcC-cEEEEecCHHHHHHHhchhhhHHhhhhcccCC-CcccEEEEeCCCCCCC
Q 042079           15 SSNPKPPHVLAVDDSIVDRKIVENLLKNSA-CKVTTAENGMRALEFLGLVDEQEQQNNLNSNG-TKVNLVITDYCMPGMT   92 (153)
Q Consensus        15 ~~~~~~~~iLiidd~~~~~~~l~~~l~~~~-~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~-~~~dlii~D~~~~~~~   92 (153)
                      ....+..+|||+||++..+..+..+|+..| |.+..+.++.+++..+.             .. ..||+||+|+.||+++
T Consensus        15 ~~~~~~~~ilivdd~~~~~~~l~~~L~~~g~~~v~~~~~~~~~~~~~~-------------~~~~~~dlvi~D~~l~~~~   81 (146)
T 4dad_A           15 LYFQGMINILVASEDASRLAHLARLVGDAGRYRVTRTVGRAAQIVQRT-------------DGLDAFDILMIDGAALDTA   81 (146)
T ss_dssp             CCCGGGCEEEEECSCHHHHHHHHHHHHHHCSCEEEEECCCHHHHTTCH-------------HHHTTCSEEEEECTTCCHH
T ss_pred             CCcCCCCeEEEEeCCHHHHHHHHHHHhhCCCeEEEEeCCHHHHHHHHH-------------hcCCCCCEEEEeCCCCCcc
Confidence            333456899999999999999999999988 99999999998877652             12 4699999999999999


Q ss_pred             HHHHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079           93 GYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus        93 g~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      |+++++.+++..  +.+|+|++++..+.....++++.|+++||.||++.++|...+.+++
T Consensus        82 g~~~~~~l~~~~--~~~~ii~lt~~~~~~~~~~~~~~ga~~~l~Kp~~~~~L~~~i~~~~  139 (146)
T 4dad_A           82 ELAAIEKLSRLH--PGLTCLLVTTDASSQTLLDAMRAGVRDVLRWPLEPRALDDALKRAA  139 (146)
T ss_dssp             HHHHHHHHHHHC--TTCEEEEEESCCCHHHHHHHHTTTEEEEEESSCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhC--CCCcEEEEeCCCCHHHHHHHHHhCCceeEcCCCCHHHHHHHHHHHH
Confidence            999999999865  6899999999999999999999999999999999999999887753

>3mm4_A Histidine kinase homolog; receiver domain, CKI1, cytokinin signaling, ROS fold, CHEY-like, transferase; 2.00A {Arabidopsis thaliana} PDB: 3mmn_A

Probab=99.87  E-value=3.1e-21  Score=138.57  Aligned_cols=132  Identities=23%  Similarity=0.376  Sum_probs=105.7

Q ss_pred             CCCCeEEEEeCCHHHHHHHHHHHHhcCc-EEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHH
Q 042079           18 PKPPHVLAVDDSIVDRKIVENLLKNSAC-KVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYEL   96 (153)
Q Consensus        18 ~~~~~iLiidd~~~~~~~l~~~l~~~~~-~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~   96 (153)
                      ....+||||||++..+..+..+|+..|+ .+..+.++.++++.+.......+ .........||+||+|+.||+++|+++
T Consensus        59 ~~~~~ILiVdDd~~~~~~l~~~L~~~g~~~v~~a~~~~eal~~l~~~~~~~~-~~~~~~~~~~dlillD~~lp~~~G~el  137 (206)
T 3mm4_A           59 LRGKRVLVVDDNFISRKVATGKLKKMGVSEVEQCDSGKEALRLVTEGLTQRE-EQGSVDKLPFDYIFMDCQMPEMDGYEA  137 (206)
T ss_dssp             TTTCEEEEECSCHHHHHHHHHHHHHTTCSEEEEESSHHHHHHHHHHHHHHHH-HHTCSSCCSCSEEEEESCCSSSCHHHH
T ss_pred             cCCCEEEEEeCCHHHHHHHHHHHHHcCCCeeeeeCCHHHHHHHHHhhccccc-ccccccCCCCCEEEEcCCCCCCCHHHH
Confidence            3557999999999999999999999998 89999999999998842100000 000011246999999999999999999


Q ss_pred             HHHHHhccC--CCCCcEEEEeCCC-ChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079           97 LKKIKESSV--MKEVPVVVVSSEN-IPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus        97 ~~~lr~~~~--~~~~pii~~t~~~-~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      +++||+...  .+.+|||++|+.. +.....++++.|+++||.||++  +|...+.+++
T Consensus       138 ~~~lr~~~~~~~~~~piI~ls~~~~~~~~~~~~~~~Ga~~~l~KP~~--~L~~~i~~~l  194 (206)
T 3mm4_A          138 TREIRKVEKSYGVRTPIIAVSGHDPGSEEARETIQAGMDAFLDKSLN--QLANVIREIE  194 (206)
T ss_dssp             HHHHHHHHHTTTCCCCEEEEESSCCCHHHHHHHHHHTCSEEEETTCT--THHHHHHHHC
T ss_pred             HHHHHhhhhhcCCCCcEEEEECCCCcHHHHHHHHhCCCCEEEcCcHH--HHHHHHHHHH
Confidence            999997421  2578999999987 7788889999999999999999  8888877754

>3cfy_A Putative LUXO repressor protein; structural genomics, unknown function, uncharacterized protein, signal receiver domain; 2.50A {Vibrio parahaemolyticus rimd 2210633}

Probab=99.87  E-value=2.8e-21  Score=129.91  Aligned_cols=115  Identities=23%  Similarity=0.407  Sum_probs=104.5

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKI  100 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~l  100 (153)
                      .+|||+||++..+..++.+|+..||.+..+.++.+++..+.              ...||++|+|+.||+++|+++++.|
T Consensus         5 ~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~--------------~~~~dlvllD~~l~~~~g~~l~~~l   70 (137)
T 3cfy_A            5 PRVLLVEDSTSLAILYKQYVKDEPYDIFHVETGRDAIQFIE--------------RSKPQLIILDLKLPDMSGEDVLDWI   70 (137)
T ss_dssp             CEEEEECSCTTHHHHHHHHTTTSSSEEEEESSHHHHHHHHH--------------HHCCSEEEECSBCSSSBHHHHHHHH
T ss_pred             ceEEEEeCCHHHHHHHHHHHHhcCceEEEeCCHHHHHHHHH--------------hcCCCEEEEecCCCCCCHHHHHHHH
Confidence            48999999999999999999988999999999999998873              2368999999999999999999999


Q ss_pred             HhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          101 KESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       101 r~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      ++..  +.+|+|++++..+.....++++.|+++|+.||++.+++...+.++
T Consensus        71 ~~~~--~~~~ii~ls~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~i~~~  119 (137)
T 3cfy_A           71 NQND--IPTSVIIATAHGSVDLAVNLIQKGAEDFLEKPINADRLKTSVALH  119 (137)
T ss_dssp             HHTT--CCCEEEEEESSCCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHH
T ss_pred             HhcC--CCCCEEEEEecCcHHHHHHHHHCCccEEEeCCCCHHHHHHHHHHH
Confidence            9754  578999999988888889999999999999999999999887764

>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=99.87  E-value=8.7e-22  Score=129.96  Aligned_cols=117  Identities=22%  Similarity=0.389  Sum_probs=105.1

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKI  100 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~l  100 (153)
                      .+|||+||++..+..+...|+..|+.+..+.++.+++..+.              ...||++|+|+.+|+++|+++++++
T Consensus         3 ~~ilivdd~~~~~~~l~~~l~~~g~~v~~~~~~~~a~~~~~--------------~~~~dlvi~D~~l~~~~g~~~~~~l   68 (127)
T 2jba_A            3 RRILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLN--------------EPWPDLILLAWMLPGGSGIQFIKHL   68 (127)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEECSHHHHHTTCS--------------SSCCSEEEEESEETTEEHHHHHHHH
T ss_pred             cEEEEEcCCHHHHHHHHHHHHHCCceEEEeCCHHHHHHHHh--------------ccCCCEEEEecCCCCCCHHHHHHHH
Confidence            58999999999999999999989999999999999988772              4569999999999999999999999


Q ss_pred             HhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          101 KESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       101 r~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      ++....+.+|+|++|+..+.....++++.|+++|+.||++.+++...+.++
T Consensus        69 ~~~~~~~~~~ii~~s~~~~~~~~~~~~~~ga~~~l~Kp~~~~~l~~~i~~~  119 (127)
T 2jba_A           69 RRESMTRDIPVVMLTARGEEEDRVRGLETGADDCITKPFSPKELVARIKAV  119 (127)
T ss_dssp             HTSTTTTTSCEEEEEETTHHHHHHTTCCCSCSEEEEESCCHHHHHHHHHHH
T ss_pred             HhCcccCCCCEEEEeCCCCHHHHHHHHhcCCCeEEeCCCCHHHHHHHHHHH
Confidence            975434678999999988888888899999999999999999999887764

>3c3m_A Response regulator receiver protein; structural genomics, unknown function, PSI-2, protein struct initiative; HET: MSE; 1.70A {Methanoculleus marisnigri JR1}

Probab=99.87  E-value=4.5e-21  Score=128.81  Aligned_cols=119  Identities=24%  Similarity=0.384  Sum_probs=101.4

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKK   99 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~   99 (153)
                      ..+|||+||++..+..+..+|+..|+.+..+.++.+++..+.              ...||+||+|+.||+++|+++++.
T Consensus         3 ~~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~--------------~~~~dlvi~D~~l~~~~g~~~~~~   68 (138)
T 3c3m_A            3 LYTILVVDDSPMIVDVFVTMLERGGYRPITAFSGEECLEALN--------------ATPPDLVLLDIMMEPMDGWETLER   68 (138)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--------------HSCCSEEEEESCCSSSCHHHHHHH
T ss_pred             cceEEEEeCCHHHHHHHHHHHHHcCceEEEeCCHHHHHHHHh--------------ccCCCEEEEeCCCCCCCHHHHHHH
Confidence            368999999999999999999999999999999999998873              246899999999999999999999


Q ss_pred             HHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079          100 IKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus       100 lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      |++....+.+|+|++|+.........++..|+++|+.||++.+++...+.+++
T Consensus        69 l~~~~~~~~~~ii~ls~~~~~~~~~~~~~~~~~~~l~KP~~~~~L~~~i~~~~  121 (138)
T 3c3m_A           69 IKTDPATRDIPVLMLTAKPLTPEEANEYGSYIEDYILKPTTHHQLYEAIEHVL  121 (138)
T ss_dssp             HHHSTTTTTSCEEEEESSCCCHHHHHHTTTTCSEEEECCCHHHHHHHHHHHHH
T ss_pred             HHcCcccCCCCEEEEECCCChHHHHHHhhcCHhheEeCCCCHHHHHHHHHHHH
Confidence            99754345789999998765554445556668999999999999998887653

>1dcf_A ETR1 protein; beta-alpha five sandwich, transferase; 2.50A {Arabidopsis thaliana} SCOP: c.23.1.2

Probab=99.87  E-value=1.5e-20  Score=125.65  Aligned_cols=120  Identities=24%  Similarity=0.453  Sum_probs=102.5

Q ss_pred             CCCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHH
Q 042079           18 PKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELL   97 (153)
Q Consensus        18 ~~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~   97 (153)
                      .+..+|||+||++..+..+..+|+..|+.+..+.++.+++..+.              ... |++++|+.||+++|++++
T Consensus         5 ~~~~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~~~--------------~~~-dlvllD~~lp~~~g~~~~   69 (136)
T 1dcf_A            5 FTGLKVLVMDENGVSRMVTKGLLVHLGCEVTTVSSNEECLRVVS--------------HEH-KVVFMDVCMPGVENYQIA   69 (136)
T ss_dssp             CTTCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHCC--------------TTC-SEEEEECCSSTTTTTHHH
T ss_pred             cCCCeEEEEeCCHHHHHHHHHHHHHcCCeEEEeCCHHHHHHHHh--------------ccC-CEEEEeCCCCCCcHHHHH
Confidence            34678999999999999999999999999999999999998773              233 999999999999999999


Q ss_pred             HHHHhccCC--CCC-cEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079           98 KKIKESSVM--KEV-PVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus        98 ~~lr~~~~~--~~~-pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      +.+++....  ... ++|++|+..+.....++++.|+++|+.||++.+++...+.+++
T Consensus        70 ~~l~~~~~~~~~~~~~ii~~s~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~l~~~~  127 (136)
T 1dcf_A           70 LRIHEKFTKQRHQRPLLVALSGNTDKSTKEKCMSFGLDGVLLKPVSLDNIRDVLSDLL  127 (136)
T ss_dssp             HHHHHHHC-CCSCCCEEEEEESCCSHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHHH
T ss_pred             HHHHHhhhhccCCCceEEEEeCCCCHHHHHHHHHcCCCeEEECCCCHHHHHHHHHHHh
Confidence            999843211  123 5778898888888889999999999999999999998887753

>3cnb_A DNA-binding response regulator, MERR family; signal receiver domain, DNA binding protein, protein structu initiative, PSI-2; 2.00A {Colwellia psychrerythraea}

Probab=99.87  E-value=8.6e-21  Score=127.41  Aligned_cols=120  Identities=21%  Similarity=0.325  Sum_probs=106.9

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHh-cCcE-EEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKN-SACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYEL   96 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~-~~~~-v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~   96 (153)
                      +..+|||+|+++..+..+...|+. .|+. +..+.++.+++..+.              ...||+||+|+.+|+.+|+++
T Consensus         7 ~~~~iLivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~a~~~l~--------------~~~~dlii~d~~l~~~~g~~~   72 (143)
T 3cnb_A            7 NDFSILIIEDDKEFADMLTQFLENLFPYAKIKIAYNPFDAGDLLH--------------TVKPDVVMLDLMMVGMDGFSI   72 (143)
T ss_dssp             --CEEEEECSCHHHHHHHHHHHHHHCTTCEEEEECSHHHHHHHHH--------------HTCCSEEEEETTCTTSCHHHH
T ss_pred             CCceEEEEECCHHHHHHHHHHHHhccCccEEEEECCHHHHHHHHH--------------hcCCCEEEEecccCCCcHHHH
Confidence            457899999999999999999998 8999 999999999998873              346999999999999999999


Q ss_pred             HHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079           97 LKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus        97 ~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      ++.+++....+.+|+|++++..+.....++++.|+++|+.||++.+++...+.+++
T Consensus        73 ~~~l~~~~~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~kP~~~~~l~~~i~~~~  128 (143)
T 3cnb_A           73 CHRIKSTPATANIIVIAMTGALTDDNVSRIVALGAETCFGKPLNFTLLEKTIKQLV  128 (143)
T ss_dssp             HHHHHTSTTTTTSEEEEEESSCCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHH
T ss_pred             HHHHHhCccccCCcEEEEeCCCCHHHHHHHHhcCCcEEEeCCCCHHHHHHHHHHHH
Confidence            99999843446899999999988888899999999999999999999998887753

>3q9s_A DNA-binding response regulator; DNA binding protein; 2.40A {Deinococcus radiodurans}

Probab=99.87  E-value=2.6e-21  Score=142.79  Aligned_cols=118  Identities=16%  Similarity=0.350  Sum_probs=106.3

Q ss_pred             CCCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHH
Q 042079           18 PKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELL   97 (153)
Q Consensus        18 ~~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~   97 (153)
                      ++..+|||+||++..+..+..+|+..|+.+..+.++.+++..+.              ...||+||+|+.||+++|++++
T Consensus        35 m~~~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~--------------~~~~DlvllD~~lp~~~G~~l~  100 (249)
T 3q9s_A           35 MNEQRILVIEDDHDIANVLRMDLTDAGYVVDHADSAMNGLIKAR--------------EDHPDLILLDLGLPDFDGGDVV  100 (249)
T ss_dssp             --CCEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHH--------------HSCCSEEEEECCSCHHHHHHHH
T ss_pred             CCCCEEEEEECCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHh--------------cCCCCEEEEcCCCCCCCHHHHH
Confidence            34578999999999999999999999999999999999998873              3469999999999999999999


Q ss_pred             HHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079           98 KKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus        98 ~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      ++|++ .  +.+|||++|+..+.....++++.|+++||.||+++++|...+..++
T Consensus       101 ~~lr~-~--~~~~iI~lt~~~~~~~~~~a~~~Ga~~yl~Kp~~~~~L~~~i~~~l  152 (249)
T 3q9s_A          101 QRLRK-N--SALPIIVLTARDTVEEKVRLLGLGADDYLIKPFHPDELLARVKVQL  152 (249)
T ss_dssp             HHHHT-T--CCCCEEEEESCCSHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHH
T ss_pred             HHHHc-C--CCCCEEEEECCCCHHHHHHHHHCCCcEEEECCCCHHHHHHHHHHHH
Confidence            99997 3  5789999999999999999999999999999999999998887653

>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=99.87  E-value=5.3e-21  Score=136.71  Aligned_cols=117  Identities=25%  Similarity=0.380  Sum_probs=106.2

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      +..+|||+||++..+..+..+|+..|+.+..+.++.+++..+.              ...||+||+|+.||+++|+++++
T Consensus         3 ~~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~--------------~~~~dlvl~D~~lp~~~g~~~~~   68 (208)
T 1yio_A            3 AKPTVFVVDDDMSVREGLRNLLRSAGFEVETFDCASTFLEHRR--------------PEQHGCLVLDMRMPGMSGIELQE   68 (208)
T ss_dssp             CCCEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHCC--------------TTSCEEEEEESCCSSSCHHHHHH
T ss_pred             CCCEEEEEcCCHHHHHHHHHHHHhCCceEEEcCCHHHHHHhhh--------------ccCCCEEEEeCCCCCCCHHHHHH
Confidence            3568999999999999999999999999999999999998873              45799999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      .+++..  +.+|+|++|+..+.....++++.|+++|+.||++.+++...+.++
T Consensus        69 ~l~~~~--~~~~ii~ls~~~~~~~~~~a~~~Ga~~~l~Kp~~~~~L~~~i~~~  119 (208)
T 1yio_A           69 QLTAIS--DGIPIVFITAHGDIPMTVRAMKAGAIEFLPKPFEEQALLDAIEQG  119 (208)
T ss_dssp             HHHHTT--CCCCEEEEESCTTSCCCHHHHHTTEEEEEESSCCHHHHHHHHHHH
T ss_pred             HHHhcC--CCCCEEEEeCCCCHHHHHHHHHCCCcEEEeCCCCHHHHHHHHHHH
Confidence            999854  689999999988888889999999999999999999998877664

>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=99.87  E-value=7.3e-21  Score=128.44  Aligned_cols=124  Identities=26%  Similarity=0.469  Sum_probs=107.5

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCc--EEEEecCHHHHHHHhchhhhHHhhhhcccC---C--CcccEEEEeCCCCCC
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSAC--KVTTAENGMRALEFLGLVDEQEQQNNLNSN---G--TKVNLVITDYCMPGM   91 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~--~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~---~--~~~dlii~D~~~~~~   91 (153)
                      +..+|||+||++..+..++..|+..|+  .+..+.++.+++..+....         ..   .  ..||+||+|+.+|++
T Consensus         5 ~~~~iLivdd~~~~~~~l~~~L~~~g~~~~v~~~~~~~~al~~l~~~~---------~~~~~~~~~~~dlvi~D~~l~~~   75 (149)
T 1k66_A            5 ATQPLLVVEDSDEDFSTFQRLLQREGVVNPIYRCITGDQALDFLYQTG---------SYCNPDIAPRPAVILLDLNLPGT   75 (149)
T ss_dssp             TTSCEEEECCCHHHHHHHHHHHHHTTBCSCEEEECSHHHHHHHHHTCC---------SSSCGGGCCCCSEEEECSCCSSS
T ss_pred             CCccEEEEECCHHHHHHHHHHHHHcCCCceEEEECCHHHHHHHHHhcc---------cccCcccCCCCcEEEEECCCCCC
Confidence            457899999999999999999999888  8999999999999883100         00   0  579999999999999


Q ss_pred             CHHHHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           92 TGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        92 ~g~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      +|+++++.+++....+.+|+|++++..+.....++++.|+++|+.||++.+++...+.++
T Consensus        76 ~g~~~~~~l~~~~~~~~~~ii~~t~~~~~~~~~~~~~~g~~~~l~kP~~~~~l~~~i~~~  135 (149)
T 1k66_A           76 DGREVLQEIKQDEVLKKIPVVIMTTSSNPKDIEICYSYSISSYIVKPLEIDRLTETVQTF  135 (149)
T ss_dssp             CHHHHHHHHTTSTTGGGSCEEEEESCCCHHHHHHHHHTTCSEEEECCSSHHHHHHHHHHH
T ss_pred             CHHHHHHHHHhCcccCCCeEEEEeCCCCHHHHHHHHHCCCCEEEeCCCCHHHHHHHHHHH
Confidence            999999999975433578999999998888899999999999999999999999888775

>3eul_A Possible nitrate/nitrite response transcriptional regulatory protein NARL (DNA-binding...; central beta strand flanked by alpha helices; 1.90A {Mycobacterium tuberculosis}

Probab=99.87  E-value=5.1e-21  Score=130.41  Aligned_cols=122  Identities=26%  Similarity=0.391  Sum_probs=105.3

Q ss_pred             CCCCCCCCeEEEEeCCHHHHHHHHHHHHhcCcE--EEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCC
Q 042079           14 SSSNPKPPHVLAVDDSIVDRKIVENLLKNSACK--VTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGM   91 (153)
Q Consensus        14 ~~~~~~~~~iLiidd~~~~~~~l~~~l~~~~~~--v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~   91 (153)
                      .....+..+|||+||++..+..+..+|+..|+.  +..+.++.+++..+.              ...||+||+|+.+|++
T Consensus         9 ~~~~~~~~~iLivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~a~~~l~--------------~~~~dlii~d~~l~~~   74 (152)
T 3eul_A            9 SNPQPEKVRVVVGDDHPLFREGVVRALSLSGSVNVVGEADDGAAALELIK--------------AHLPDVALLDYRMPGM   74 (152)
T ss_dssp             -----CCEEEEEECSSHHHHHHHHHHHHHHSSEEEEEEESSHHHHHHHHH--------------HHCCSEEEEETTCSSS
T ss_pred             CCCCCceEEEEEEcCCHHHHHHHHHHHhhCCCeEEEEEeCCHHHHHHHHH--------------hcCCCEEEEeCCCCCC
Confidence            333456689999999999999999999988843  568999999999874              2469999999999999


Q ss_pred             CHHHHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           92 TGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        92 ~g~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      +|+++++.+++..  +.+|+|++++..+.....++++.|+++|+.||++.+++...+.++
T Consensus        75 ~g~~~~~~l~~~~--~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~Kp~~~~~l~~~i~~~  132 (152)
T 3eul_A           75 DGAQVAAAVRSYE--LPTRVLLISAHDEPAIVYQALQQGAAGFLLKDSTRTEIVKAVLDC  132 (152)
T ss_dssp             CHHHHHHHHHHTT--CSCEEEEEESCCCHHHHHHHHHTTCSEEEETTCCHHHHHHHHHHH
T ss_pred             CHHHHHHHHHhcC--CCCeEEEEEccCCHHHHHHHHHcCCCEEEecCCCHHHHHHHHHHH
Confidence            9999999999864  688999999999999999999999999999999999999888765

>3f6c_A Positive transcription regulator EVGA; structural genomics, PSI-2, protein structure initiative, PO transcription regulator EVGA; 1.45A {Escherichia coli k-12}

Probab=99.87  E-value=1.5e-21  Score=130.14  Aligned_cols=116  Identities=20%  Similarity=0.296  Sum_probs=102.8

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEE-EecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVT-TAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKK   99 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~-~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~   99 (153)
                      .+|||+||++..+..++.+|++.|+.+. .+.++.+++..+.              ...||+||+|+.+|+++|+++++.
T Consensus         2 ~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~~a~~~~~--------------~~~~dlii~d~~l~~~~g~~~~~~   67 (134)
T 3f6c_A            2 LNAIIIDDHPLAIAAIRNLLIKNDIEILAELTEGGSAVQRVE--------------TLKPDIVIIDVDIPGVNGIQVLET   67 (134)
T ss_dssp             EEEEEECCCHHHHHHHHHHHHHTTEEEEEEESSSTTHHHHHH--------------HHCCSEEEEETTCSSSCHHHHHHH
T ss_pred             eEEEEEcCCHHHHHHHHHHHhhCCcEEEEEcCCHHHHHHHHH--------------hcCCCEEEEecCCCCCChHHHHHH
Confidence            5799999999999999999999999887 8999999998873              246999999999999999999999


Q ss_pred             HHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079          100 IKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus       100 lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      +|+..  +.+|+|++|+..+.....++++.|+++|+.||++.+++...+.+++
T Consensus        68 l~~~~--~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~i~~~~  118 (134)
T 3f6c_A           68 LRKRQ--YSGIIIIVSAKNDHFYGKHCADAGANGFVSKKEGMNNIIAAIEAAK  118 (134)
T ss_dssp             HHHTT--CCSEEEEEECC---CTHHHHHHTTCSEEEEGGGCTHHHHHHHHHHH
T ss_pred             HHhcC--CCCeEEEEeCCCChHHHHHHHHhCCCEEEeCCCCHHHHHHHHHHHH
Confidence            99864  6899999999988888899999999999999999999999888754

>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=99.87  E-value=9e-21  Score=123.74  Aligned_cols=114  Identities=26%  Similarity=0.406  Sum_probs=103.2

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKI  100 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~l  100 (153)
                      .+|||+||++..+..+...|+..|+.+..+.++.+++..+.              ...||++|+|+.||+++|+++++++
T Consensus         2 ~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~~~--------------~~~~dlvl~D~~l~~~~g~~~~~~l   67 (120)
T 2a9o_A            2 KKILIVDDEKPISDIIKFNMTKEGYEVVTAFNGREALEQFE--------------AEQPDIIILDLMLPEIDGLEVAKTI   67 (120)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--------------HHCCSEEEECSSCSSSCHHHHHHHH
T ss_pred             ceEEEEcCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHHH--------------hCCCCEEEEeccCCCCCHHHHHHHH
Confidence            47999999999999999999999999999999999998773              2358999999999999999999999


Q ss_pred             HhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          101 KESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       101 r~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      ++.   +.+|+|++++..+.....++++.|+++|+.||++.+++...+.++
T Consensus        68 ~~~---~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~Kp~~~~~l~~~i~~~  115 (120)
T 2a9o_A           68 RKT---SSVPILMLSAKDSEFDKVIGLELGADDYVTKPFSNRELQARVKAL  115 (120)
T ss_dssp             HHH---CCCCEEEEESCCSHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHH
T ss_pred             HhC---CCCCEEEEecCCchHHHHHHHhCCHhheEeCCCCHHHHHHHHHHH
Confidence            973   478999999988888888999999999999999999999888764

>2qzj_A Two-component response regulator; 11017X, PSI-II, structural genomics; 2.89A {Clostridium difficile}

Probab=99.87  E-value=5.4e-21  Score=128.34  Aligned_cols=115  Identities=19%  Similarity=0.303  Sum_probs=104.3

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKK   99 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~   99 (153)
                      ..+|||+||++..+..+..+|+..|+.+..+.++.+++..+.              ...||++|+|+.||+++|+++++.
T Consensus         4 ~~~Ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~--------------~~~~dlvllD~~l~~~~g~~l~~~   69 (136)
T 2qzj_A            4 QTKILIIDGDKDNCQKLKGFLEEKGISIDLAYNCEEAIGKIF--------------SNKYDLIFLEIILSDGDGWTLCKK   69 (136)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHH--------------HCCCSEEEEESEETTEEHHHHHHH
T ss_pred             CCeEEEEcCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHH--------------hcCCCEEEEeCCCCCCCHHHHHHH
Confidence            468999999999999999999988999999999999998873              246899999999999999999999


Q ss_pred             HHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          100 IKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       100 lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      |++..   .+|+|++++..+.....++++.|+++|+.||++.+++...+.++
T Consensus        70 l~~~~---~~~ii~ls~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~l~~~  118 (136)
T 2qzj_A           70 IRNVT---TCPIVYMTYINEDQSILNALNSGGDDYLIKPLNLEILYAKVKAI  118 (136)
T ss_dssp             HHTTC---CCCEEEEESCCCHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHH
T ss_pred             HccCC---CCCEEEEEcCCCHHHHHHHHHcCCcEEEECCCCHHHHHHHHHHH
Confidence            99742   68999999988888889999999999999999999999877764

>1mvo_A PHOP response regulator; phosphate regulon, transcriptional regulatory protein, alpha/beta doubly wound fold, phosphorylation; 1.60A {Bacillus subtilis} SCOP: c.23.1.1

Probab=99.86  E-value=6.8e-21  Score=127.15  Aligned_cols=116  Identities=25%  Similarity=0.386  Sum_probs=104.4

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKK   99 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~   99 (153)
                      ..+|||+||++..+..+...|+..|+.+..+.++.+++..+.              ...||++|+|+.||+++|+++++.
T Consensus         3 ~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~~~--------------~~~~dlvl~D~~l~~~~g~~~~~~   68 (136)
T 1mvo_A            3 NKKILVVDDEESIVTLLQYNLERSGYDVITASDGEEALKKAE--------------TEKPDLIVLDVMLPKLDGIEVCKQ   68 (136)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--------------HHCCSEEEEESSCSSSCHHHHHHH
T ss_pred             CCEEEEEECCHHHHHHHHHHHHHCCcEEEEecCHHHHHHHHh--------------hcCCCEEEEecCCCCCCHHHHHHH
Confidence            468999999999999999999999999999999999998773              235899999999999999999999


Q ss_pred             HHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          100 IKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       100 lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      +++..  +.+|+|++++..+......+++.|+++|+.||++.+++...+.++
T Consensus        69 l~~~~--~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~  118 (136)
T 1mvo_A           69 LRQQK--LMFPILMLTAKDEEFDKVLGLELGADDYMTKPFSPREVNARVKAI  118 (136)
T ss_dssp             HHHTT--CCCCEEEEECTTCCCCHHHHHHTTCCEEEESSCCHHHHHHHHHHH
T ss_pred             HHcCC--CCCCEEEEECCCCHHHHHHHHhCCCCEEEECCCCHHHHHHHHHHH
Confidence            99854  578999999988888888999999999999999999999887764

>2zay_A Response regulator receiver protein; structural genomics, NYSGXRC, target 11006U, protein structure initiative; 2.00A {Desulfuromonas acetoxidans}

Probab=99.86  E-value=4.9e-21  Score=129.59  Aligned_cols=119  Identities=19%  Similarity=0.304  Sum_probs=106.9

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      +..+|||+|+++..+..+...|+..|+.+..+.++.+++..+.              ...||+||+|+.+|+++|+++++
T Consensus         7 ~~~~iLivd~~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~--------------~~~~dlii~d~~l~~~~g~~~~~   72 (147)
T 2zay_A            7 KWWRIMLVDTQLPALAASISALSQEGFDIIQCGNAIEAVPVAV--------------KTHPHLIITEANMPKISGMDLFN   72 (147)
T ss_dssp             -CEEEEEECTTGGGGHHHHHHHHHHTEEEEEESSHHHHHHHHH--------------HHCCSEEEEESCCSSSCHHHHHH
T ss_pred             CCceEEEEeCCHHHHHHHHHHHHHcCCeEEEeCCHHHHHHHHH--------------cCCCCEEEEcCCCCCCCHHHHHH
Confidence            4578999999999999999999999999999999999998873              23699999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      .|++....+.+|+|++++..+.....++++.|+++|+.||++.++|...+.++
T Consensus        73 ~l~~~~~~~~~pii~ls~~~~~~~~~~~~~~g~~~~l~kp~~~~~L~~~i~~~  125 (147)
T 2zay_A           73 SLKKNPQTASIPVIALSGRATAKEEAQLLDMGFIDFIAKPVNAIRLSARIKRV  125 (147)
T ss_dssp             HHHTSTTTTTSCEEEEESSCCHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHH
T ss_pred             HHHcCcccCCCCEEEEeCCCCHHHHHHHHhCCCCEEEeCCCCHHHHHHHHHHH
Confidence            99974334689999999998888889999999999999999999999888765

>2ayx_A Sensor kinase protein RCSC; two independent structural domains, transferase; NMR {Escherichia coli} SCOP: c.23.1.1 c.23.1.6 PDB: 2ayz_A 2ayy_A

Probab=99.86  E-value=7e-21  Score=140.92  Aligned_cols=117  Identities=26%  Similarity=0.511  Sum_probs=107.1

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      ...+|||+||++..+..+..+|+..||.+..+.++.+++..+.              ...||+||+|+.||+++|+++++
T Consensus       128 ~~~~ILivdd~~~~~~~l~~~L~~~g~~v~~a~~~~eal~~l~--------------~~~~dlvl~D~~mp~~~G~~l~~  193 (254)
T 2ayx_A          128 DDMMILVVDDHPINRRLLADQLGSLGYQCKTANDGVDALNVLS--------------KNHIDIVLSDVNMPNMDGYRLTQ  193 (254)
T ss_dssp             CCCEEEEEESSHHHHHHHHHHHHHHTSEEEEECCSHHHHHHHH--------------HSCCSEEEEEESSCSSCCHHHHH
T ss_pred             CCCEEEEEeCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHH--------------hCCCCEEEEcCCCCCCCHHHHHH
Confidence            4578999999999999999999999999999999999999883              24699999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      +||+..  +.+|||++|+........++++.|+++|+.||++.++|...+.++
T Consensus       194 ~ir~~~--~~~piI~lt~~~~~~~~~~~~~~G~~~~l~KP~~~~~L~~~l~~~  244 (254)
T 2ayx_A          194 RIRQLG--LTLPVIGVTANALAEEKQRCLESGMDSCLSKPVTLDVIKQTLTLY  244 (254)
T ss_dssp             HHHHHH--CCSCEEEEESSTTSHHHHHHHHCCCEEEEESSCCHHHHHHHHHHH
T ss_pred             HHHhcC--CCCcEEEEECCCCHHHHHHHHHcCCceEEECCCCHHHHHHHHHHH
Confidence            999865  579999999998888889999999999999999999999888764

>2rjn_A Response regulator receiver:metal-dependent phosphohydrolase, HD subdomain; structural genomics, oceanospirillum SP. MED92; 2.10A {Neptuniibacter caesariensis}

Probab=99.86  E-value=2.4e-20  Score=127.31  Aligned_cols=118  Identities=31%  Similarity=0.411  Sum_probs=106.9

Q ss_pred             CCCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHH
Q 042079           18 PKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELL   97 (153)
Q Consensus        18 ~~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~   97 (153)
                      .+..+|||+|+++..+..+...|+..|+.+..+.++.+++..+.              ...||+||+|+.+|+.+|++++
T Consensus         5 ~~~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~--------------~~~~dlvi~d~~l~~~~g~~~~   70 (154)
T 2rjn_A            5 YKNYTVMLVDDEQPILNSLKRLIKRLGCNIITFTSPLDALEALK--------------GTSVQLVISDMRMPEMGGEVFL   70 (154)
T ss_dssp             CSCCEEEEECSCHHHHHHHHHHHHTTTCEEEEESCHHHHHHHHT--------------TSCCSEEEEESSCSSSCHHHHH
T ss_pred             CCCCeEEEEcCCHHHHHHHHHHHHHcCCeEEEeCCHHHHHHHHh--------------cCCCCEEEEecCCCCCCHHHHH
Confidence            45688999999999999999999999999999999999999883              4569999999999999999999


Q ss_pred             HHHHhccCCCCCcEEEEeCCCChhhHHHHHHhc-CcccccCCCChhHHHHHHhhh
Q 042079           98 KKIKESSVMKEVPVVVVSSENIPTRINECLEEG-AQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        98 ~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~g-a~~~l~KP~~~~~l~~~~~~~  151 (153)
                      +.+++..  +.+|+|++++..+.....++++.| +++|+.||++.+++...+.++
T Consensus        71 ~~l~~~~--~~~~ii~ls~~~~~~~~~~~~~~g~~~~~l~kP~~~~~L~~~i~~~  123 (154)
T 2rjn_A           71 EQVAKSY--PDIERVVISGYADAQATIDAVNRGKISRFLLKPWEDEDVFKVVEKG  123 (154)
T ss_dssp             HHHHHHC--TTSEEEEEECGGGHHHHHHHHHTTCCSEEEESSCCHHHHHHHHHHH
T ss_pred             HHHHHhC--CCCcEEEEecCCCHHHHHHHHhccchheeeeCCCCHHHHHHHHHHH
Confidence            9999854  589999999988888888999998 999999999999999887764

>2qxy_A Response regulator; regulation of transcription, NYSGXRC, protein structure initiative II (PSI II), structural genomics; 1.95A {Thermotoga maritima}

Probab=99.86  E-value=1.8e-20  Score=126.10  Aligned_cols=116  Identities=27%  Similarity=0.387  Sum_probs=106.1

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      +..+|||+||++..+..+...|+..||.+..+.++.+++..+.              ...||+||+|+ +|+.+|+++++
T Consensus         3 ~~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~--------------~~~~dlvi~d~-~~~~~g~~~~~   67 (142)
T 2qxy_A            3 LTPTVMVVDESRITFLAVKNALEKDGFNVIWAKNEQEAFTFLR--------------REKIDLVFVDV-FEGEESLNLIR   67 (142)
T ss_dssp             CCCEEEEECSCHHHHHHHHHHHGGGTCEEEEESSHHHHHHHHT--------------TSCCSEEEEEC-TTTHHHHHHHH
T ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhCCCEEEEECCHHHHHHHHh--------------ccCCCEEEEeC-CCCCcHHHHHH
Confidence            3568999999999999999999999999999999999999883              45799999999 99999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      .+++..  +.+|+|++++..+.....++++.|+++|+.||++.+++...+.++
T Consensus        68 ~l~~~~--~~~pii~ls~~~~~~~~~~~~~~g~~~~l~kP~~~~~l~~~i~~~  118 (142)
T 2qxy_A           68 RIREEF--PDTKVAVLSAYVDKDLIINSVKAGAVDYILKPFRLDYLLERVKKI  118 (142)
T ss_dssp             HHHHHC--TTCEEEEEESCCCHHHHHHHHHHTCSCEEESSCCHHHHHHHHHHH
T ss_pred             HHHHHC--CCCCEEEEECCCCHHHHHHHHHCCcceeEeCCCCHHHHHHHHHHH
Confidence            999764  579999999998888899999999999999999999999888775

>3n0r_A Response regulator; sigma factor, receiver, two-component SI transduction, signaling protein; HET: MSE GOL; 1.25A {Caulobacter vibrioides} PDB: 3t0y_A

Probab=99.86  E-value=5.2e-22  Score=149.68  Aligned_cols=114  Identities=25%  Similarity=0.379  Sum_probs=102.6

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCcEEE-EecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCC-CCCHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSACKVT-TAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMP-GMTGYELL   97 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~~~v~-~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~-~~~g~~~~   97 (153)
                      ..+||++||++..+..+..+|+..||.+. .+.++.+|++.+.              ...||+||+|+.|| +++|++++
T Consensus       160 ~~rILvVdD~~~~~~~l~~~L~~~g~~v~~~a~~g~eAl~~~~--------------~~~~dlvl~D~~MPd~mdG~e~~  225 (286)
T 3n0r_A          160 ATEVLIIEDEPVIAADIEALVRELGHDVTDIAATRGEALEAVT--------------RRTPGLVLADIQLADGSSGIDAV  225 (286)
T ss_dssp             CCEEEEECCSHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHH--------------HCCCSEEEEESCCTTSCCTTTTT
T ss_pred             CCcEEEEcCCHHHHHHHHHHhhccCceEEEEeCCHHHHHHHHH--------------hCCCCEEEEcCCCCCCCCHHHHH
Confidence            46899999999999999999999999999 9999999999884              35699999999999 79999999


Q ss_pred             HHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079           98 KKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus        98 ~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      +.||+..   .+|||++|+..  +...++++.|+++||.||+++++|...+.+++
T Consensus       226 ~~ir~~~---~~piI~lT~~~--~~~~~~~~~G~~~~l~KP~~~~~L~~~i~~~l  275 (286)
T 3n0r_A          226 KDILGRM---DVPVIFITAFP--ERLLTGERPEPTFLITKPFQPETVKAAIGQAL  275 (286)
T ss_dssp             HHHHHHT---TCCEEEEESCG--GGGCCSSSCCCSSEEESSCCHHHHHHHHHHHH
T ss_pred             HHHHhcC---CCCEEEEeCCH--HHHHHHHhCCCcEEEeCCCCHHHHHHHHHHHH
Confidence            9999864   89999999974  34667899999999999999999999888754

>3h5i_A Response regulator/sensory box protein/ggdef domain protein; structural genomics, transcription, PSI-2; 1.90A {Carboxydothermus hydrogenoformans z-2901}

Probab=99.86  E-value=3.1e-21  Score=129.92  Aligned_cols=118  Identities=22%  Similarity=0.312  Sum_probs=104.7

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCC-CCHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPG-MTGYELL   97 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~-~~g~~~~   97 (153)
                      +..+|||+||++..+..+..+|+..|+.+..+.++.+++..+.             ....||+||+|+.||+ ++|++++
T Consensus         4 ~~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~-------------~~~~~dlvi~D~~l~~~~~g~~~~   70 (140)
T 3h5i_A            4 KDKKILIVEDSKFQAKTIANILNKYGYTVEIALTGEAAVEKVS-------------GGWYPDLILMDIELGEGMDGVQTA   70 (140)
T ss_dssp             --CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH-------------TTCCCSEEEEESSCSSSCCHHHHH
T ss_pred             CCcEEEEEeCCHHHHHHHHHHHHHcCCEEEEecChHHHHHHHh-------------cCCCCCEEEEeccCCCCCCHHHHH
Confidence            4578999999999999999999999999999999999999873             2257999999999995 9999999


Q ss_pred             HHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079           98 KKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus        98 ~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      +.+++.   +.+|+|++++..+.....++++.|+++|+.||++.++|...+.+++
T Consensus        71 ~~l~~~---~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~l  122 (140)
T 3h5i_A           71 LAIQQI---SELPVVFLTAHTEPAVVEKIRSVTAYGYVMKSATEQVLITIVEMAL  122 (140)
T ss_dssp             HHHHHH---CCCCEEEEESSSSCCCCGGGGGSCEEEEEETTCCHHHHHHHHHHHH
T ss_pred             HHHHhC---CCCCEEEEECCCCHHHHHHHHhCCCcEEEeCCCCHHHHHHHHHHHH
Confidence            999974   5789999999888877888999999999999999999998887753

>2qr3_A Two-component system response regulator; structural genomics, signal receiver, PSI-2, protein structu initiative; 1.80A {Bacteroides fragilis}

Probab=99.86  E-value=1.1e-20  Score=126.59  Aligned_cols=118  Identities=24%  Similarity=0.261  Sum_probs=106.0

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCC-----CCCH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMP-----GMTG   93 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~-----~~~g   93 (153)
                      +..+|||+|+++..+..+...|+..|+.+..+.+..+++..+.              ...||+||+|+.++     +.+|
T Consensus         2 ~~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~--------------~~~~dlvi~d~~~~~~~~~~~~g   67 (140)
T 2qr3_A            2 SLGTIIIVDDNKGVLTAVQLLLKNHFSKVITLSSPVSLSTVLR--------------EENPEVVLLDMNFTSGINNGNEG   67 (140)
T ss_dssp             CCCEEEEECSCHHHHHHHHHHHTTTSSEEEEECCHHHHHHHHH--------------HSCEEEEEEETTTTC-----CCH
T ss_pred             CCceEEEEeCCHHHHHHHHHHHHhCCcEEEEeCCHHHHHHHHH--------------cCCCCEEEEeCCcCCCCCCCccH
Confidence            4578999999999999999999999999999999999998873              34699999999999     9999


Q ss_pred             HHHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079           94 YELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus        94 ~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      +++++.+++..  +.+|+|++++..+.....++++.|+++|+.||++.+++...+.+++
T Consensus        68 ~~~~~~l~~~~--~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~l~~~~  124 (140)
T 2qr3_A           68 LFWLHEIKRQY--RDLPVVLFTAYADIDLAVRGIKEGASDFVVKPWDNQKLLETLLNAA  124 (140)
T ss_dssp             HHHHHHHHHHC--TTCCEEEEEEGGGHHHHHHHHHTTCCEEEEESCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHhhC--cCCCEEEEECCCCHHHHHHHHHcCchheeeCCCCHHHHHHHHHHHH
Confidence            99999999864  6899999999888888899999999999999999999999888754

>1dz3_A Stage 0 sporulation protein A; response regulator, domain swapping; 1.65A {Bacillus stearothermophilus} SCOP: c.23.1.1 PDB: 1qmp_A*

Probab=99.86  E-value=8.3e-21  Score=126.07  Aligned_cols=116  Identities=21%  Similarity=0.363  Sum_probs=102.2

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhc-CcEEE-EecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNS-ACKVT-TAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~-~~~v~-~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      .+|||+||++..+..++.+|+.. |+.+. .+.++.+++..+.              ...||++|+|+.||+++|+++++
T Consensus         3 ~~ilivdd~~~~~~~l~~~l~~~~~~~~~~~~~~~~~a~~~~~--------------~~~~dlvllD~~l~~~~g~~~~~   68 (130)
T 1dz3_A            3 IKVCIADDNRELVSLLDEYISSQPDMEVIGTAYNGQDCLQMLE--------------EKRPDILLLDIIMPHLDGLAVLE   68 (130)
T ss_dssp             EEEEEECSCHHHHHHHHHHHHTSTTEEEEEEESSHHHHHHHHH--------------HHCCSEEEEESCCSSSCHHHHHH
T ss_pred             eEEEEEcCCHHHHHHHHHHHHhCCCceEEEEeCCHHHHHHHHh--------------cCCCCEEEEecCCCCCCHHHHHH
Confidence            57999999999999999999976 78765 7899999998873              23589999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      ++++.. .+.+|+|++|+..+.....++++.|+++|+.||++.+++...+.++
T Consensus        69 ~l~~~~-~~~~~ii~ls~~~~~~~~~~~~~~ga~~~l~KP~~~~~l~~~i~~~  120 (130)
T 1dz3_A           69 RIRAGF-EHQPNVIMLTAFGQEDVTKKAVELGASYFILKPFDMENLAHHIRQV  120 (130)
T ss_dssp             HHHHHC-SSCCEEEEEEETTCHHHHHHHHHTTCEEEEECSSCCTTHHHHHHHH
T ss_pred             HHHhcC-CCCCcEEEEecCCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHH
Confidence            999742 2567899999988888889999999999999999999999888764

>3cg4_A Response regulator receiver domain protein (CHEY-; structural genomics, unknown function; HET: MSE; 1.61A {Methanospirillum hungatei jf-1}

Probab=99.86  E-value=5.1e-21  Score=128.67  Aligned_cols=120  Identities=23%  Similarity=0.428  Sum_probs=107.4

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      +..+|||+|+++..+..+...|+..|+.+..+.+..+++..+.              ...||+||+|+.+|+++|+++++
T Consensus         6 ~~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~--------------~~~~dlii~d~~l~~~~g~~~~~   71 (142)
T 3cg4_A            6 HKGDVMIVDDDAHVRIAVKTILSDAGFHIISADSGGQCIDLLK--------------KGFSGVVLLDIMMPGMDGWDTIR   71 (142)
T ss_dssp             CCCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--------------TCCCEEEEEESCCSSSCHHHHHH
T ss_pred             CCCeEEEEcCCHHHHHHHHHHHHHCCeEEEEeCCHHHHHHHHH--------------hcCCCEEEEeCCCCCCCHHHHHH
Confidence            5678999999999999999999999999999999999999883              35699999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      .+++....+.+|+|++++..+.....++++.|+++|+.||++.++|...+.+++
T Consensus        72 ~l~~~~~~~~~pii~~s~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~i~~~~  125 (142)
T 3cg4_A           72 AILDNSLEQGIAIVMLTAKNAPDAKMIGLQEYVVDYITKPFDNEDLIEKTTFFM  125 (142)
T ss_dssp             HHHHTTCCTTEEEEEEECTTCCCCSSTTGGGGEEEEEESSCCHHHHHHHHHHHH
T ss_pred             HHHhhcccCCCCEEEEECCCCHHHHHHHHhcCccEEEeCCCCHHHHHHHHHHHH
Confidence            999843346899999999887777788999999999999999999998887753

>3a10_A Response regulator; phosphoacceptor, signaling protein; HET: MSE PG4; 1.63A {Thermotoga maritima} PDB: 3a0r_B* 3a0u_A*

Probab=99.85  E-value=8.6e-21  Score=123.40  Aligned_cols=114  Identities=25%  Similarity=0.405  Sum_probs=101.0

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKI  100 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~l  100 (153)
                      .+|||+||++..+..+...|+..|+.+..+.++.+++..+.              ...||++++|+.||+++|+++++.+
T Consensus         2 ~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~~~--------------~~~~dlvl~D~~l~~~~g~~~~~~l   67 (116)
T 3a10_A            2 KRILVVDDEPNIRELLKEELQEEGYEIDTAENGEEALKKFF--------------SGNYDLVILDIEMPGISGLEVAGEI   67 (116)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--------------HSCCSEEEECSCCSSSCHHHHHHHH
T ss_pred             cEEEEEeCCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHh--------------cCCCCEEEEECCCCCCCHHHHHHHH
Confidence            47999999999999999999999999999999999998873              2469999999999999999999999


Q ss_pred             HhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079          101 KESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus       101 r~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      ++..  +.+|+|++++..+..  .++++.|+++|+.||++.+++...+.+++
T Consensus        68 ~~~~--~~~~ii~~s~~~~~~--~~~~~~g~~~~l~Kp~~~~~l~~~i~~~~  115 (116)
T 3a10_A           68 RKKK--KDAKIILLTAYSHYR--SDMSSWAADEYVVKSFNFDELKEKVKKLL  115 (116)
T ss_dssp             HHHC--TTCCEEEEESCGGGG--GCGGGGGSSEEEECCSSTHHHHHHHHHHT
T ss_pred             HccC--CCCeEEEEECCcchH--HHHHhccccceEECCCCHHHHHHHHHHHh
Confidence            9764  578999999875544  67889999999999999999999888764

>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=99.85  E-value=2.7e-21  Score=150.40  Aligned_cols=115  Identities=22%  Similarity=0.265  Sum_probs=105.9

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKI  100 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~l  100 (153)
                      .+||||||++..+..+..+|+..||.+..+.++.++++.+.              ...||+||+|+.||+++|+++++++
T Consensus         1 ~~ILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~eal~~l~--------------~~~~DlvllDi~mP~~dG~ell~~l   66 (368)
T 3dzd_A            1 KRVLVVDDEESITSSLSAILEEEGYHPDTAKTLREAEKKIK--------------ELFFPVIVLDVWMPDGDGVNFIDFI   66 (368)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--------------HBCCSEEEEESEETTEETTTHHHHH
T ss_pred             CEEEEEeCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHH--------------hCCCCEEEEeCCCCCCCHHHHHHHH
Confidence            37999999999999999999999999999999999999883              3469999999999999999999999


Q ss_pred             HhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          101 KESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       101 r~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      ++..  +.+|||++|+..+.+...++++.|+++|+.||++.+++...+.++
T Consensus        67 r~~~--~~~pvI~lT~~~~~~~~~~a~~~Ga~~yl~KP~~~~~L~~~i~~~  115 (368)
T 3dzd_A           67 KENS--PDSVVIVITGHGSVDTAVKAIKKGAYEFLEKPFSVERFLLTIKHA  115 (368)
T ss_dssp             HHHC--TTCEEEEEECSSCCHHHHHHHHHTCCEEEESSCCHHHHHHHHHHH
T ss_pred             HhhC--CCCeEEEEeCCCCHHHHHHHHhcCcceEEeCCCCHHHHHHHHHHH
Confidence            9865  688999999998888999999999999999999999999888764

>3kcn_A Adenylate cyclase homolog; SGX, PSI 2, structural genomics, protein structure initiative; 2.45A {Rhodopirellula baltica}

Probab=99.85  E-value=2.6e-20  Score=126.85  Aligned_cols=117  Identities=26%  Similarity=0.332  Sum_probs=104.5

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      +..+|||+||++..+..+..+|+. ++.+..+.++.+++..+..             ..+||+||+|+.+|+++|+++++
T Consensus         3 ~~~~ILivdd~~~~~~~l~~~L~~-~~~v~~~~~~~~a~~~l~~-------------~~~~dlvi~D~~l~~~~g~~~~~   68 (151)
T 3kcn_A            3 LNERILLVDDDYSLLNTLKRNLSF-DFEVTTCESGPEALACIKK-------------SDPFSVIMVDMRMPGMEGTEVIQ   68 (151)
T ss_dssp             CCCEEEEECSCHHHHHHHHHHHTT-TSEEEEESSHHHHHHHHHH-------------SCCCSEEEEESCCSSSCHHHHHH
T ss_pred             CCCeEEEEeCCHHHHHHHHHHhcc-CceEEEeCCHHHHHHHHHc-------------CCCCCEEEEeCCCCCCcHHHHHH
Confidence            457899999999999999999976 8999999999999998841             23479999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhc-CcccccCCCChhHHHHHHhhh
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEG-AQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~g-a~~~l~KP~~~~~l~~~~~~~  151 (153)
                      .+++..  +.+|+|++++..+.....+++..| +++|+.||++.+++...+.++
T Consensus        69 ~l~~~~--~~~~ii~~s~~~~~~~~~~~~~~g~~~~~l~KP~~~~~L~~~i~~~  120 (151)
T 3kcn_A           69 KARLIS--PNSVYLMLTGNQDLTTAMEAVNEGQVFRFLNKPCQMSDIKAAINAG  120 (151)
T ss_dssp             HHHHHC--SSCEEEEEECGGGHHHHHHHHHHTCCSEEEESSCCHHHHHHHHHHH
T ss_pred             HHHhcC--CCcEEEEEECCCCHHHHHHHHHcCCeeEEEcCCCCHHHHHHHHHHH
Confidence            999765  688999999988888889999999 999999999999999888765

>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=99.85  E-value=2e-21  Score=130.67  Aligned_cols=119  Identities=25%  Similarity=0.329  Sum_probs=96.7

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      +..+|||+||++..+..+..+|+.. +.+..+.++.+++..+.              ...||+||+|+.+|+++|+++++
T Consensus         2 ~~~~iLivdd~~~~~~~l~~~l~~~-~~v~~~~~~~~a~~~~~--------------~~~~dlvi~D~~l~~~~g~~~~~   66 (140)
T 3n53_A            2 SLKKILIIDQQDFSRIELKNFLDSE-YLVIESKNEKEALEQID--------------HHHPDLVILDMDIIGENSPNLCL   66 (140)
T ss_dssp             -CCEEEEECSCHHHHHHHHHHHTTT-SEEEEESSHHHHHHHHH--------------HHCCSEEEEETTC------CHHH
T ss_pred             CCCEEEEEeCCHHHHHHHHHHHHhc-ceEEEeCCHHHHHHHHh--------------cCCCCEEEEeCCCCCCcHHHHHH
Confidence            3578999999999999999999987 99999999999999883              24689999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      .+++....+.+|+|++++..+.+...++++.|+++|+.||++.+++...+.+++
T Consensus        67 ~l~~~~~~~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~~  120 (140)
T 3n53_A           67 KLKRSKGLKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHL  120 (140)
T ss_dssp             HHHTSTTCTTCCEEEEECC----CTTTTTTCCCSEEEESSCCHHHHHHHHHHHH
T ss_pred             HHHcCcccCCCCEEEEecCCCHHHHHHHHhcCCCeeeeCCCCHHHHHHHHHHHH
Confidence            999865446899999999888888888999999999999999999998887753

>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=99.85  E-value=3.7e-20  Score=126.49  Aligned_cols=116  Identities=25%  Similarity=0.400  Sum_probs=105.5

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKK   99 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~   99 (153)
                      .++|||+|+++..+..+...|...||.+..+.++.+++..+.              ...||+||+|+.+|+.+|+++++.
T Consensus         3 ~~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~--------------~~~~dliild~~l~~~~g~~~~~~   68 (155)
T 1qkk_A            3 APSVFLIDDDRDLRKAMQQTLELAGFTVSSFASATEALAGLS--------------ADFAGIVISDIRMPGMDGLALFRK   68 (155)
T ss_dssp             -CEEEEECSCHHHHHHHHHHHHHTTCEEEEESCHHHHHHTCC--------------TTCCSEEEEESCCSSSCHHHHHHH
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHHcCcEEEEECCHHHHHHHHH--------------hCCCCEEEEeCCCCCCCHHHHHHH
Confidence            468999999999999999999999999999999999998873              457999999999999999999999


Q ss_pred             HHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          100 IKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       100 lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      +++..  +.+|+|++++..+.....++++.|+++|+.||++.+++...+.++
T Consensus        69 l~~~~--~~~pii~ls~~~~~~~~~~~~~~g~~~~l~kP~~~~~L~~~i~~~  118 (155)
T 1qkk_A           69 ILALD--PDLPMILVTGHGDIPMAVQAIQDGAYDFIAKPFAADRLVQSARRA  118 (155)
T ss_dssp             HHHHC--TTSCEEEEECGGGHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHH
T ss_pred             HHhhC--CCCCEEEEECCCChHHHHHHHhcCCCeEEeCCCCHHHHHHHHHHH
Confidence            99764  689999999988888889999999999999999999999888764

>3eqz_A Response regulator; structural genomics, unknown function, PSI-2, protein struct initiative; 2.15A {Colwellia psychrerythraea} SCOP: c.23.1.0

Probab=99.85  E-value=9.3e-21  Score=126.08  Aligned_cols=117  Identities=15%  Similarity=0.239  Sum_probs=103.1

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      +..+|||+||++..+..++.+|+..++.+..+.+..+++..+              ... ||+||+|+.+|+.+|+++++
T Consensus         2 ~~~~ilivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~~~~~~--------------~~~-~dlvi~D~~l~~~~g~~~~~   66 (135)
T 3eqz_A            2 SLNRVFIVDDDTLTCNLLKTIVEPIFGNVEAFQHPRAFLTLS--------------LNK-QDIIILDLMMPDMDGIEVIR   66 (135)
T ss_dssp             -CCEEEEECSCHHHHHHHHHHHTTTCSCEEEESCHHHHTTSC--------------CCT-TEEEEEECCTTTTHHHHHHH
T ss_pred             CcceEEEEeCCHHHHHHHHHHHHhhcceeeeecCHHHHHHhh--------------ccC-CCEEEEeCCCCCCCHHHHHH
Confidence            457899999999999999999998888999999999988766              234 99999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCCh-----hhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079           99 KIKESSVMKEVPVVVVSSENIP-----TRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~-----~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      .+++..  +.+|+|++++..+.     ....+++..|+++|+.||++.+++...+.++.
T Consensus        67 ~l~~~~--~~~~ii~~s~~~~~~~~~~~~~~~~~~~g~~~~l~KP~~~~~l~~~l~~~~  123 (135)
T 3eqz_A           67 HLAEHK--SPASLILISGYDSGVLHSAETLALSCGLNVINTFTKPINTEVLTCFLTSLS  123 (135)
T ss_dssp             HHHHTT--CCCEEEEEESSCHHHHHHHHHHHHHTTCEEEEEEESSCCHHHHHHHHHHHS
T ss_pred             HHHhCC--CCCCEEEEEeccchhHHHHHHHHHHcCCCcceeeCCCCCHHHHHHHHHHHH
Confidence            999855  67899999987764     56667889999999999999999999998864

>1a04_A Nitrate/nitrite response regulator protein NARL; signal transduction protein, response regulators, two- component systems; 2.20A {Escherichia coli} SCOP: a.4.6.2 c.23.1.1 PDB: 1rnl_A

Probab=99.85  E-value=1.8e-20  Score=134.67  Aligned_cols=117  Identities=31%  Similarity=0.473  Sum_probs=104.3

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhc-CcEE-EEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNS-ACKV-TTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYEL   96 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~-~~~v-~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~   96 (153)
                      +..+|||+||++..+..+..+|+.. ++.+ ..+.++.+++..+.              ...||+||+|+.||+++|+++
T Consensus         4 ~~~~ilivdd~~~~~~~l~~~L~~~~~~~vv~~~~~~~~al~~~~--------------~~~~dlvllD~~lp~~~g~~~   69 (215)
T 1a04_A            4 EPATILLIDDHPMLRTGVKQLISMAPDITVVGEASNGEQGIELAE--------------SLDPDLILLDLNMPGMNGLET   69 (215)
T ss_dssp             CCEEEEEECSCHHHHHHHHHHHTTCTTEEEEEEESSHHHHHHHHH--------------HHCCSEEEEETTSTTSCHHHH
T ss_pred             CceEEEEECCCHHHHHHHHHHHhcCCCcEEEEEeCCHHHHHHHHH--------------hcCCCEEEEeCCCCCCcHHHH
Confidence            3468999999999999999999876 4777 78999999998873              245899999999999999999


Q ss_pred             HHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           97 LKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        97 ~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      ++.+++..  +.+|+|++|...+.+...++++.|+++|+.||++++++...+.++
T Consensus        70 ~~~lr~~~--~~~~ii~ls~~~~~~~~~~~~~~Ga~~~l~Kp~~~~~L~~~i~~~  122 (215)
T 1a04_A           70 LDKLREKS--LSGRIVVFSVSNHEEDVVTALKRGADGYLLKDMEPEDLLKALHQA  122 (215)
T ss_dssp             HHHHHHSC--CCSEEEEEECCCCHHHHHHHHHTTCSEEEETTCCHHHHHHHHHHH
T ss_pred             HHHHHHhC--CCCcEEEEECCCCHHHHHHHHHcCCcEEEeCCCCHHHHHHHHHHH
Confidence            99999854  578999999998999999999999999999999999999888764

>3cg0_A Response regulator receiver modulated diguanylate with PAS/PAC sensor; signal receiver domain, diguanylate cyclase; 2.15A {Desulfovibrio desulfuricans subsp}

Probab=99.85  E-value=1.9e-20  Score=125.36  Aligned_cols=118  Identities=15%  Similarity=0.259  Sum_probs=105.7

Q ss_pred             CCCCeEEEEeCCHHHHHHHHHHHHhcCcEEE-EecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCC-CCCHHH
Q 042079           18 PKPPHVLAVDDSIVDRKIVENLLKNSACKVT-TAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMP-GMTGYE   95 (153)
Q Consensus        18 ~~~~~iLiidd~~~~~~~l~~~l~~~~~~v~-~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~-~~~g~~   95 (153)
                      .+..+|||+|+++..+..+...|+..|+.+. .+.++.+++..+.              ...||+||+|+.+| +.+|++
T Consensus         7 ~~~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~~a~~~~~--------------~~~~dlii~d~~~~~~~~g~~   72 (140)
T 3cg0_A            7 DDLPGVLIVEDGRLAAATLRIQLESLGYDVLGVFDNGEEAVRCAP--------------DLRPDIALVDIMLCGALDGVE   72 (140)
T ss_dssp             -CCCEEEEECCBHHHHHHHHHHHHHHTCEEEEEESSHHHHHHHHH--------------HHCCSEEEEESSCCSSSCHHH
T ss_pred             CCCceEEEEECCHHHHHHHHHHHHHCCCeeEEEECCHHHHHHHHH--------------hCCCCEEEEecCCCCCCCHHH
Confidence            3467899999999999999999999999998 5999999998873              23599999999998 799999


Q ss_pred             HHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079           96 LLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus        96 ~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      +++.+++.   +.+|+|++++..+.....++++.|+++|+.||++.+++...+.+++
T Consensus        73 ~~~~l~~~---~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~i~~~~  126 (140)
T 3cg0_A           73 TAARLAAG---CNLPIIFITSSQDVETFQRAKRVNPFGYLAKPVAADTLHRSIEMAI  126 (140)
T ss_dssp             HHHHHHHH---SCCCEEEEECCCCHHHHHHHHTTCCSEEEEESCCHHHHHHHHHHHH
T ss_pred             HHHHHHhC---CCCCEEEEecCCCHHHHHHHHhcCCCEEEeCCCCHHHHHHHHHHHH
Confidence            99999985   5789999999988888899999999999999999999998887753

>3cz5_A Two-component response regulator, LUXR family; structural genomics, protein structure initiative; 2.70A {Aurantimonas SP}

Probab=99.85  E-value=4.4e-20  Score=125.84  Aligned_cols=118  Identities=18%  Similarity=0.316  Sum_probs=106.5

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHh-cCcEEE-EecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKN-SACKVT-TAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYEL   96 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~-~~~~v~-~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~   96 (153)
                      +..+|||+||++..+..+...|+. .|+.+. .+.++.+++..+.              ...||+||+|+.+++.+|+++
T Consensus         4 ~~~~ILivdd~~~~~~~l~~~L~~~~~~~v~~~~~~~~~a~~~l~--------------~~~~dlii~D~~l~~~~g~~~   69 (153)
T 3cz5_A            4 STARIMLVDDHPIVREGYRRLIERRPGYAVVAEAADAGEAYRLYR--------------ETTPDIVVMDLTLPGPGGIEA   69 (153)
T ss_dssp             CCEEEEEECSCHHHHHHHHHHHTTSTTEEEEEEESSHHHHHHHHH--------------TTCCSEEEECSCCSSSCHHHH
T ss_pred             cccEEEEECCcHHHHHHHHHHHhhCCCcEEEEEeCCHHHHHHHHh--------------cCCCCEEEEecCCCCCCHHHH
Confidence            346899999999999999999998 789887 8999999998873              356999999999999999999


Q ss_pred             HHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079           97 LKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus        97 ~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      ++++++..  +.+|+|++++..+.....++++.|+++|+.||++.++|...+.+++
T Consensus        70 ~~~l~~~~--~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~kp~~~~~L~~~i~~~~  123 (153)
T 3cz5_A           70 TRHIRQWD--GAARILIFTMHQGSAFALKAFEAGASGYVTKSSDPAELVQAIEAIL  123 (153)
T ss_dssp             HHHHHHHC--TTCCEEEEESCCSHHHHHHHHHTTCSEEEETTSCTTHHHHHHHHHT
T ss_pred             HHHHHHhC--CCCeEEEEECCCCHHHHHHHHHCCCcEEEecCCCHHHHHHHHHHHH
Confidence            99999864  5789999999988888999999999999999999999999888754

>1s8n_A Putative antiterminator; RV1626, structural genomics, transcriptional antiterminator, component system, PSI; 1.48A {Mycobacterium tuberculosis} SCOP: c.23.1.1 PDB: 1sd5_A

Probab=99.85  E-value=6.5e-21  Score=136.18  Aligned_cols=117  Identities=24%  Similarity=0.364  Sum_probs=104.0

Q ss_pred             CCCCeEEEEeCCHHHHHHHHHHHHhcCcEEE-EecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHH
Q 042079           18 PKPPHVLAVDDSIVDRKIVENLLKNSACKVT-TAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYEL   96 (153)
Q Consensus        18 ~~~~~iLiidd~~~~~~~l~~~l~~~~~~v~-~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~   96 (153)
                      .+..+|||+||++..+..+...|...||.+. .+.++.+++..+.              ...||+||+|+.||+++|+++
T Consensus        11 ~m~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~~al~~~~--------------~~~~dlvi~D~~~p~~~g~~~   76 (205)
T 1s8n_A           11 AVPRRVLIAEDEALIRMDLAEMLREEGYEIVGEAGDGQEAVELAE--------------LHKPDLVIMDVKMPRRDGIDA   76 (205)
T ss_dssp             CCCCEEEEECSSHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHH--------------HHCCSEEEEESSCSSSCHHHH
T ss_pred             CCCccEEEEECCHHHHHHHHHHHHHCCCEEEEEeCCHHHHHHHHh--------------hcCCCEEEEeCCCCCCChHHH
Confidence            3457899999999999999999999999987 8999999998873              245999999999999999999


Q ss_pred             HHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           97 LKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        97 ~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      ++.+++..   ..|+|++|+..+.....++++.|+++|+.||++.++|...+.++
T Consensus        77 ~~~l~~~~---~~pii~lt~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~i~~~  128 (205)
T 1s8n_A           77 ASEIASKR---IAPIVVLTAFSQRDLVERARDAGAMAYLVKPFSISDLIPAIELA  128 (205)
T ss_dssp             HHHHHHTT---CSCEEEEEEGGGHHHHHTTGGGSCEEEEEESCCHHHHHHHHHHH
T ss_pred             HHHHHhcC---CCCEEEEecCCCHHHHHHHHhcCCcEEEeCCCCHHHHHHHHHHH
Confidence            99999754   35999999988888888999999999999999999998877664

>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=99.85  E-value=1.1e-20  Score=124.15  Aligned_cols=119  Identities=20%  Similarity=0.350  Sum_probs=104.7

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCC-CCCHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMP-GMTGYELL   97 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~-~~~g~~~~   97 (153)
                      +..+|||+|+++..+..+...|+..|+.+..+.++.+++..+.              ...||++|+|+.+| +.+|++++
T Consensus         4 m~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~~~--------------~~~~dlvi~d~~~~~~~~g~~~~   69 (127)
T 2gkg_A            4 MSKKILIVESDTALSATLRSALEGRGFTVDETTDGKGSVEQIR--------------RDRPDLVVLAVDLSAGQNGYLIC   69 (127)
T ss_dssp             --CEEEEECSCHHHHHHHHHHHHHHTCEEEEECCHHHHHHHHH--------------HHCCSEEEEESBCGGGCBHHHHH
T ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCceEEEecCHHHHHHHHH--------------hcCCCEEEEeCCCCCCCCHHHHH
Confidence            3468999999999999999999999999999999999998873              24589999999999 99999999


Q ss_pred             HHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079           98 KKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus        98 ~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      +.+++....+.+|+|++ +..+.....++++.|+++|+.||++.+++...+.+++
T Consensus        70 ~~l~~~~~~~~~~ii~~-~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~i~~~~  123 (127)
T 2gkg_A           70 GKLKKDDDLKNVPIVII-GNPDGFAQHRKLKAHADEYVAKPVDADQLVERAGALI  123 (127)
T ss_dssp             HHHHHSTTTTTSCEEEE-ECGGGHHHHHHSTTCCSEEEESSCCHHHHHHHHHHHH
T ss_pred             HHHhcCccccCCCEEEE-ecCCchhHHHHHHhCcchheeCCCCHHHHHHHHHHHH
Confidence            99998643468899999 7777778888999999999999999999999888754

>1zh2_A KDP operon transcriptional regulatory protein KDPE; two-component system, gene regulation, transcription factor, KDP potassium transport system; 2.00A {Escherichia coli} SCOP: c.23.1.1 PDB: 1zh4_A

Probab=99.85  E-value=2.2e-20  Score=122.08  Aligned_cols=114  Identities=25%  Similarity=0.371  Sum_probs=102.6

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKI  100 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~l  100 (153)
                      ++|||+||++..+..+...|+..|+.+..+.++.+++..+.              ...||++|+|+.||+++|+++++.+
T Consensus         2 ~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~--------------~~~~dlvi~D~~l~~~~g~~~~~~l   67 (121)
T 1zh2_A            2 TNVLIVEDEQAIRRFLRTALEGDGMRVFEAETLQRGLLEAA--------------TRKPDLIILDLGLPDGDGIEFIRDL   67 (121)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHH--------------HHCCSEEEEESEETTEEHHHHHHHH
T ss_pred             cEEEEEeCCHHHHHHHHHHHhcCCCEEEEeCCHHHHHHHHh--------------cCCCCEEEEeCCCCCCcHHHHHHHH
Confidence            47999999999999999999988999999999999988763              2358999999999999999999999


Q ss_pred             HhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          101 KESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       101 r~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      ++ .  +.+|+|++++..+.....++++.|+++|+.||++.+++...+.++
T Consensus        68 ~~-~--~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~Kp~~~~~l~~~i~~~  115 (121)
T 1zh2_A           68 RQ-W--SAVPVIVLSARSEESDKIAALDAGADDYLSKPFGIGELQARLRVA  115 (121)
T ss_dssp             HT-T--CCCCEEEEESCCSHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHH
T ss_pred             Hh-C--CCCcEEEEECCCCHHHHHHHHhcCCCeEEeCCcCHHHHHHHHHHH
Confidence            94 2  578999999998888889999999999999999999999887764

>3cu5_A Two component transcriptional regulator, ARAC FAM; structural genomics, protein structure initiative; 2.60A {Clostridium phytofermentans isdg}

Probab=99.85  E-value=1.8e-20  Score=126.47  Aligned_cols=115  Identities=22%  Similarity=0.309  Sum_probs=95.9

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHh--cCcEEE-EecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKN--SACKVT-TAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELL   97 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~--~~~~v~-~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~   97 (153)
                      .+|||+||++..+..+...|..  .++.+. .+.++.+++..+.              ...||++|+|+.||+++|++++
T Consensus         3 ~~ILivdd~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~al~~~~--------------~~~~dlvllD~~lp~~~g~~l~   68 (141)
T 3cu5_A            3 LRILIVDDEKLTRDGLIANINWKALSFDQIDQADDGINAIQIAL--------------KHPPNVLLTDVRMPRMDGIELV   68 (141)
T ss_dssp             CEEEEECSCHHHHHHHHHHCCGGGSCCSEEEEESSHHHHHHHHT--------------TSCCSEEEEESCCSSSCHHHHH
T ss_pred             ceEEEEeCCHHHHHHHHHHHHHccCCcEEeeecccHHHHHHHHh--------------cCCCCEEEEeCCCCCCCHHHHH
Confidence            5799999999999999999973  577766 8999999998873              4569999999999999999999


Q ss_pred             HHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           98 KKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        98 ~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      ++|++..  +.+|+|++|+..+.....++++.|+++|+.||++.+++...+.++
T Consensus        69 ~~l~~~~--~~~~ii~ls~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~i~~~  120 (141)
T 3cu5_A           69 DNILKLY--PDCSVIFMSGYSDKEYLKAAIKFRAIRYVEKPIDPSEIMDALKQS  120 (141)
T ss_dssp             HHHHHHC--TTCEEEEECCSTTTCCC------CCCEEECSSCCHHHHHHHHHHH
T ss_pred             HHHHhhC--CCCcEEEEeCCCcHHHHHHHHhCCccEEEeCCCCHHHHHHHHHHH
Confidence            9999754  578999999988877888999999999999999999999887764

>2qvg_A Two component response regulator; NYSGXRC, PSI-2, structural genomics, protein structure initiative; 1.50A {Legionella pneumophila subsp}

Probab=99.84  E-value=4.8e-20  Score=123.98  Aligned_cols=124  Identities=23%  Similarity=0.345  Sum_probs=105.5

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCc--EEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSAC--KVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYEL   96 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~--~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~   96 (153)
                      +..+|||+||++..+..+...|+..|+  .+..+.++.+++..+....        ......||+||+|+.+|+.+|+++
T Consensus         6 ~~~~ILivdd~~~~~~~l~~~L~~~g~~~~v~~~~~~~~a~~~l~~~~--------~~~~~~~dlii~D~~l~~~~g~~~   77 (143)
T 2qvg_A            6 DKVDILYLEDDEVDIQSVERVFHKISSLIKIEIAKSGNQALDMLYGRN--------KENKIHPKLILLDINIPKMNGIEF   77 (143)
T ss_dssp             -CCSEEEECCCHHHHHHHHHHHHHHCTTCCEEEESSHHHHHHHHHTCT--------TCCCCCCSEEEEETTCTTSCHHHH
T ss_pred             CCCeEEEEeCCHHHHHHHHHHHHHhCCCceEEEECCHHHHHHHHHhcc--------cccCCCCCEEEEecCCCCCCHHHH
Confidence            356899999999999999999998887  8999999999998873100        000257999999999999999999


Q ss_pred             HHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhh
Q 042079           97 LKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGH  150 (153)
Q Consensus        97 ~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~  150 (153)
                      ++.+++....+.+|+|+++...+.....++++.|+++|+.||++.+++.+.+.+
T Consensus        78 ~~~l~~~~~~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~kP~~~~~L~~~~~~  131 (143)
T 2qvg_A           78 LKELRDDSSFTDIEVFVLTAAYTSKDKLAFESLNIRGHLIKPLDYGEAIKLFWI  131 (143)
T ss_dssp             HHHHTTSGGGTTCEEEEEESCCCHHHHHHHTTTTCCEEEESSCCHHHHHHHHHH
T ss_pred             HHHHHcCccccCCcEEEEeCCCCHHHHHHHHhcCCCeEEECCCCHHHHHHHHHH
Confidence            999997543357899999999888888999999999999999999999887654

>1kgs_A DRRD, DNA binding response regulator D; DNA-binding protein, ALPH-beta sandwich, winged-helix, helix helix, DNA binding protein; HET: DNA MSE; 1.50A {Thermotoga maritima} SCOP: a.4.6.1 c.23.1.1 PDB: 3nnn_A*

Probab=99.84  E-value=2.7e-20  Score=134.41  Aligned_cols=116  Identities=22%  Similarity=0.318  Sum_probs=105.5

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKK   99 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~   99 (153)
                      .++|||+||++..+..+...|+..|+.+..+.++.+++..+.              ...||++|+|+.||+++|+++++.
T Consensus         2 ~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~~~--------------~~~~dlvllD~~l~~~~g~~~~~~   67 (225)
T 1kgs_A            2 NVRVLVVEDERDLADLITEALKKEMFTVDVCYDGEEGMYMAL--------------NEPFDVVILDIMLPVHDGWEILKS   67 (225)
T ss_dssp             CCEEEEECSSHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--------------HSCCSEEEEESCCSSSCHHHHHHH
T ss_pred             CceEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHh--------------cCCCCEEEEeCCCCCCCHHHHHHH
Confidence            368999999999999999999999999999999999998773              346999999999999999999999


Q ss_pred             HHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          100 IKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       100 lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      +++..  +.+|+|++|+..+.....++++.|+++|+.||++++++...+.++
T Consensus        68 lr~~~--~~~~ii~ls~~~~~~~~~~~~~~ga~~~l~Kp~~~~~l~~~i~~~  117 (225)
T 1kgs_A           68 MRESG--VNTPVLMLTALSDVEYRVKGLNMGADDYLPKPFDLRELIARVRAL  117 (225)
T ss_dssp             HHHTT--CCCCEEEEESSCHHHHHHHTCCCCCSEEEESSCCHHHHHHHHHHH
T ss_pred             HHhcC--CCCCEEEEeCCCCHHHHHHHHhCCccEEEeCCCCHHHHHHHHHHH
Confidence            99854  689999999988888889999999999999999999999887764

>3eq2_A Probable two-component response regulator; adaptor sigmas, signaling protein; 3.40A {Pseudomonas aeruginosa} PDB: 3f7a_A

Probab=99.84  E-value=1.6e-20  Score=146.72  Aligned_cols=116  Identities=29%  Similarity=0.514  Sum_probs=101.6

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKK   99 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~   99 (153)
                      ..+||||||++..+..++.+|+..||.+..+.++.++++.+.              ...||+||+|+.||+++|++++++
T Consensus         5 ~~~iLivdD~~~~~~~l~~~L~~~g~~v~~a~~~~~al~~~~--------------~~~~dlvllD~~mp~~~G~~~~~~   70 (394)
T 3eq2_A            5 SATLLIIDDDEVVRESLAAYLEDSNFKVLQALNGLQGLQIFE--------------SEQPDLVICDLRMPQIDGLELIRR   70 (394)
T ss_dssp             EEEEEEECSCHHHHHHHHHHHHHTTEEEEECSSHHHHHHHHH--------------HSCCSEEEECCCSSSSCTHHHHHH
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHhCCCEEEEECCHHHHHHHHh--------------hCCCCEEEEcCCCCCCCHHHHHHH
Confidence            468999999999999999999999999999999999999873              356999999999999999999999


Q ss_pred             HHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCC-ChhHHHHHHhhh
Q 042079          100 IKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPL-KPSDVKKLTGHL  151 (153)
Q Consensus       100 lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~-~~~~l~~~~~~~  151 (153)
                      ||+..  +.+|+|++|+..+.+...++++.|+++||.||+ +.+++...+.++
T Consensus        71 lr~~~--~~~pii~lt~~~~~~~~~~a~~~ga~~yl~KP~~~~~~l~~~i~~~  121 (394)
T 3eq2_A           71 IRQTA--SETPIIVLSGAGVMSDAVEALRLGAADYLIKPLEDLAVLEHSVRRA  121 (394)
T ss_dssp             HHHTT--CCCCEEEC---CHHHHHHHHHHHTCSEECCSSCSCTHHHHHHHHHH
T ss_pred             HHhhC--CCCcEEEEEcCCCHHHHHHHHhcChhhEEECCCChHHHHHHHHHHH
Confidence            99864  689999999998889999999999999999999 578777766553

>2jk1_A HUPR, hydrogenase transcriptional regulatory protein HU; nucleotide-binding, transcription regulation; 2.10A {Rhodobacter capsulatus} PDB: 2vui_B 2vuh_B

Probab=99.84  E-value=7.8e-20  Score=122.75  Aligned_cols=114  Identities=24%  Similarity=0.393  Sum_probs=99.7

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKI  100 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~l  100 (153)
                      .+|||+||++..+..+...|+.. +.+..+.++.+++..+.              ...||++|+|+.||+++|+++++.|
T Consensus         2 ~~Ilivdd~~~~~~~l~~~l~~~-~~v~~~~~~~~a~~~~~--------------~~~~dlvl~D~~lp~~~g~~~~~~l   66 (139)
T 2jk1_A            2 PAILLVDDEPHSLAAMKLALEDD-FDVLTAQGAEAAIAILE--------------EEWVQVIICDQRMPGRTGVDFLTEV   66 (139)
T ss_dssp             CEEEEECSSHHHHHHHHHHHTTT-SCEEEESSHHHHHHHHH--------------HSCEEEEEEESCCSSSCHHHHHHHH
T ss_pred             CeEEEEcCCHHHHHHHHHHhhcC-ceEEEcCCHHHHHHHHh--------------cCCCCEEEEeCCCCCCcHHHHHHHH
Confidence            47999999999999999999875 88999999999998873              2469999999999999999999999


Q ss_pred             HhccCCCCCcEEEEeCCCChhhHHHHHHh-cCcccccCCCChhHHHHHHhhh
Q 042079          101 KESSVMKEVPVVVVSSENIPTRINECLEE-GAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       101 r~~~~~~~~pii~~t~~~~~~~~~~a~~~-ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      ++..  +.+|+|++++..+.....+++.. |+++|+.||++.+++...+.++
T Consensus        67 ~~~~--~~~~ii~~s~~~~~~~~~~~~~~~ga~~~l~KP~~~~~L~~~i~~~  116 (139)
T 2jk1_A           67 RERW--PETVRIIITGYTDSASMMAAINDAGIHQFLTKPWHPEQLLSSARNA  116 (139)
T ss_dssp             HHHC--TTSEEEEEESCTTCHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHH
T ss_pred             HHhC--CCCcEEEEeCCCChHHHHHHHHhhchhhhccCCCCHHHHHHHHHHH
Confidence            9754  57899999998777777788876 5999999999999999877664

>2qsj_A DNA-binding response regulator, LUXR family; structural genomics, PSI-2, protein structure initiative; 2.10A {Silicibacter pomeroyi dss-3}

Probab=99.84  E-value=4.4e-20  Score=125.87  Aligned_cols=118  Identities=28%  Similarity=0.355  Sum_probs=95.1

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhc-Cc-EEEEecCHHHHHHHhchhhhHHhhhhcccCC-CcccEEEEeCCCCCCCHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNS-AC-KVTTAENGMRALEFLGLVDEQEQQNNLNSNG-TKVNLVITDYCMPGMTGYE   95 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~-~~-~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~-~~~dlii~D~~~~~~~g~~   95 (153)
                      +.++|||+|+++..+..+...|+.. |+ .+..+.+..+++..+.              . ..||+||+|+.+|+.+|++
T Consensus         2 ~~~~iLivdd~~~~~~~l~~~L~~~~g~~~v~~~~~~~~a~~~l~--------------~~~~~dlvi~d~~l~~~~g~~   67 (154)
T 2qsj_A            2 SLTVVLIVDDHHLIRAGAKNLLEGAFSGMRVEGAETVSDALAFLE--------------ADNTVDLILLDVNLPDAEAID   67 (154)
T ss_dssp             -CEEEEEECSCHHHHHHHHHHHHHHCTTEEEEEESSHHHHHHHHH--------------TTCCCSEEEECC------CHH
T ss_pred             CccEEEEEcCCHHHHHHHHHHHHhCCCceEEEEecCHHHHHHHHh--------------ccCCCCEEEEeCCCCCCchHH
Confidence            3468999999999999999999987 77 6889999999999883              3 5799999999999999999


Q ss_pred             HHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079           96 LLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus        96 ~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      +++.+++..  +.+|+|++++..+.....++++.|+++|+.||++.++|...+.+++
T Consensus        68 ~~~~l~~~~--~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~kp~~~~~L~~~l~~~~  122 (154)
T 2qsj_A           68 GLVRLKRFD--PSNAVALISGETDHELIRAALEAGADGFIPKSADPQVLIHAVSLIL  122 (154)
T ss_dssp             HHHHHHHHC--TTSEEEEC-----CHHHHHHHHTTCCBBCCTTSCHHHHHHHHHHHH
T ss_pred             HHHHHHHhC--CCCeEEEEeCCCCHHHHHHHHHccCCEEEeCCCCHHHHHHHHHHHH
Confidence            999999864  5789999999888888899999999999999999999999888753

>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=99.84  E-value=4.7e-20  Score=146.35  Aligned_cols=117  Identities=26%  Similarity=0.434  Sum_probs=105.7

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKI  100 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~l  100 (153)
                      .+||||||++..+..+..+|+..|+.+..+.++.+++..+.              ...||+||+|+.||+++|+++++.|
T Consensus         2 ~~iLivdD~~~~~~~l~~~L~~~~~~v~~a~~~~~al~~~~--------------~~~~dlvllD~~mp~~~G~~~~~~l   67 (459)
T 1w25_A            2 ARILVVDDIEANVRLLEAKLTAEYYEVSTAMDGPTALAMAA--------------RDLPDIILLDVMMPGMDGFTVCRKL   67 (459)
T ss_dssp             CEEEEECSSTTHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--------------HHCCSEEEEESCCSSSCHHHHHHHH
T ss_pred             CeEEEEeCCHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHh--------------cCCCCEEEEcCCCCCCCHHHHHHHH
Confidence            47999999999999999999999999999999999999873              2468999999999999999999999


Q ss_pred             HhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          101 KESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       101 r~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      ++....+.+|||++|+..+.....++++.|+++||.||++.++|...+.++
T Consensus        68 ~~~~~~~~~pii~lt~~~~~~~~~~a~~~Ga~~~l~KP~~~~~l~~~i~~~  118 (459)
T 1w25_A           68 KDDPTTRHIPVVLITALDGRGDRIQGLESGASDFLTKPIDDVMLFARVRSL  118 (459)
T ss_dssp             HHSTTTTTSCEEEEECSSCHHHHHHHHHHTCCEEEESSCCHHHHHHHHHHH
T ss_pred             hcCcccCCCCEEEEECCCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHH
Confidence            975444679999999999999999999999999999999999998877654

>2j48_A Two-component sensor kinase; pseudo-receiver, circadian clock, transferase, response regulator, histidine protein kinase; NMR {Synechococcus elongatus}

Probab=99.83  E-value=1.1e-19  Score=117.57  Aligned_cols=115  Identities=21%  Similarity=0.254  Sum_probs=102.2

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKI  100 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~l  100 (153)
                      ++||++|+++..+..+...|+..|+.+..+.+..+++..+.              ...||++|+|+.+++.+|+++++.+
T Consensus         2 ~~iliv~~~~~~~~~l~~~l~~~g~~v~~~~~~~~~~~~l~--------------~~~~dlii~d~~~~~~~~~~~~~~l   67 (119)
T 2j48_A            2 GHILLLEEEDEAATVVCEMLTAAGFKVIWLVDGSTALDQLD--------------LLQPIVILMAWPPPDQSCLLLLQHL   67 (119)
T ss_dssp             CEEEEECCCHHHHHHHHHHHHHTTCEEEEESCHHHHHHHHH--------------HHCCSEEEEECSTTCCTHHHHHHHH
T ss_pred             CEEEEEeCCHHHHHHHHHHHHhCCcEEEEecCHHHHHHHHH--------------hcCCCEEEEecCCCCCCHHHHHHHH
Confidence            57999999999999999999999999999999999998873              2368999999999999999999999


Q ss_pred             HhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079          101 KESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus       101 r~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      ++....+.+|+|++++..+..   .+++.|+++|+.||++.+++...+.+++
T Consensus        68 ~~~~~~~~~~ii~~~~~~~~~---~~~~~g~~~~l~kp~~~~~l~~~l~~~~  116 (119)
T 2j48_A           68 REHQADPHPPLVLFLGEPPVD---PLLTAQASAILSKPLDPQLLLTTLQGLC  116 (119)
T ss_dssp             HHTCCCSSCCCEEEESSCCSS---HHHHHHCSEECSSCSTTHHHHHHHHTTC
T ss_pred             HhccccCCCCEEEEeCCCCch---hhhhcCHHHhccCCCCHHHHHHHHHHHh
Confidence            986434678999999876655   8899999999999999999999888754

>3kyj_B CHEY6 protein, putative histidine protein kinase; protein-protein interaction, histidine kinase, response regulator, phosphorylation; 1.40A {Rhodobacter sphaeroides} PDB: 3kyi_B*

Probab=99.83  E-value=4.8e-20  Score=124.61  Aligned_cols=110  Identities=29%  Similarity=0.392  Sum_probs=92.5

Q ss_pred             CCCCeEEEEeCCHHHHHHHHHHHHhc-CcEE-EEecCHHHHHHHhchhhhHHhhhhcccCCC-cccEEEEeCCCCCCCHH
Q 042079           18 PKPPHVLAVDDSIVDRKIVENLLKNS-ACKV-TTAENGMRALEFLGLVDEQEQQNNLNSNGT-KVNLVITDYCMPGMTGY   94 (153)
Q Consensus        18 ~~~~~iLiidd~~~~~~~l~~~l~~~-~~~v-~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~-~~dlii~D~~~~~~~g~   94 (153)
                      .+..+|||+||++..+..++.+|++. |+.+ ..+.++.+++..+.              .. .||+||+|+.||+++|+
T Consensus        11 ~~~~~vlivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~al~~l~--------------~~~~~dlvilD~~l~~~~g~   76 (145)
T 3kyj_B           11 GSPYNVMIVDDAAMMRLYIASFIKTLPDFKVVAQAANGQEALDKLA--------------AQPNVDLILLDIEMPVMDGM   76 (145)
T ss_dssp             CCSEEEEEECSCHHHHHHHHHHHTTCTTEEEEEEESSHHHHHHHHH--------------HCTTCCEEEECTTSCCCTTC
T ss_pred             CCCCeEEEEcCCHHHHHHHHHHHHhCCCceEEEEECCHHHHHHHHh--------------cCCCCCEEEEeCCCCCCCHH
Confidence            45688999999999999999999987 8875 48999999998873              23 69999999999999999


Q ss_pred             HHHHHHHhccCCCCCcEEEEeC--CCChhhHHHHHHhcCcccccCCCChhHH
Q 042079           95 ELLKKIKESSVMKEVPVVVVSS--ENIPTRINECLEEGAQMFMLKPLKPSDV  144 (153)
Q Consensus        95 ~~~~~lr~~~~~~~~pii~~t~--~~~~~~~~~a~~~ga~~~l~KP~~~~~l  144 (153)
                      ++++++|+..   ..|+++++.  ..+.....++++.|+++|+.||+++.++
T Consensus        77 ~~~~~lr~~~---~~~iiil~~~~~~~~~~~~~~~~~ga~~~l~KP~~~~~l  125 (145)
T 3kyj_B           77 EFLRHAKLKT---RAKICMLSSVAVSGSPHAARARELGADGVVAKPSGTVSH  125 (145)
T ss_dssp             HHHHHHHHHC---CCEEC-CBSSCSTTSSHHHHHHHTTCSCCCBCCCSCC--
T ss_pred             HHHHHHHhcC---CCCeEEEEEeccCChHHHHHHHhCCCCEEEeCCCCHHHH
Confidence            9999999754   378888887  4556667889999999999999995543

>1ys7_A Transcriptional regulatory protein PRRA; response regulator, DNA binding domain, phosphorylation; 1.58A {Mycobacterium tuberculosis} SCOP: a.4.6.1 c.23.1.1 PDB: 1ys6_A

Probab=99.83  E-value=3.8e-20  Score=134.26  Aligned_cols=117  Identities=26%  Similarity=0.372  Sum_probs=105.4

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      ..++|||+||++..+..+...|+..|+.+..+.++.+++..+.              ...||++|+|+.||+++|+++++
T Consensus         6 ~~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~~~--------------~~~~dlvllD~~l~~~~g~~~~~   71 (233)
T 1ys7_A            6 TSPRVLVVDDDSDVLASLERGLRLSGFEVATAVDGAEALRSAT--------------ENRPDAIVLDINMPVLDGVSVVT   71 (233)
T ss_dssp             -CCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--------------HSCCSEEEEESSCSSSCHHHHHH
T ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhCCCEEEEECCHHHHHHHHH--------------hCCCCEEEEeCCCCCCCHHHHHH
Confidence            3478999999999999999999999999999999999998773              34699999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      .+++..  +.+|+|++|+..+.....++++.|+++|+.||++.+++...+.++
T Consensus        72 ~l~~~~--~~~~ii~lt~~~~~~~~~~~~~~ga~~~l~Kp~~~~~L~~~i~~~  122 (233)
T 1ys7_A           72 ALRAMD--NDVPVCVLSARSSVDDRVAGLEAGADDYLVKPFVLAELVARVKAL  122 (233)
T ss_dssp             HHHHTT--CCCCEEEEECCCTTTCCCTTTTTTCSEEEESSCCHHHHHHHHHHH
T ss_pred             HHHhcC--CCCCEEEEEcCCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHH
Confidence            999754  689999999988888888899999999999999999999887765

>2pln_A HP1043, response regulator; signaling protein; 1.80A {Helicobacter pylori} PDB: 2hqo_A

Probab=99.83  E-value=3.1e-19  Score=119.44  Aligned_cols=117  Identities=16%  Similarity=0.175  Sum_probs=103.7

Q ss_pred             CCCCCCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHH
Q 042079           15 SSNPKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGY   94 (153)
Q Consensus        15 ~~~~~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~   94 (153)
                      ....+..+|||+||++..+..+...|+..|+.+..+.++.+++..+.              ...||+||    +|+++|+
T Consensus        13 ~~~~~~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~--------------~~~~dlvi----~~~~~g~   74 (137)
T 2pln_A           13 LVPRGSMRVLLIEKNSVLGGEIEKGLNVKGFMADVTESLEDGEYLMD--------------IRNYDLVM----VSDKNAL   74 (137)
T ss_dssp             --CTTCSEEEEECSCHHHHHHHHHHHHHTTCEEEEESCHHHHHHHHH--------------HSCCSEEE----ECSTTHH
T ss_pred             ccCCCCCeEEEEeCCHHHHHHHHHHHHHcCcEEEEeCCHHHHHHHHH--------------cCCCCEEE----EcCccHH
Confidence            33346689999999999999999999999999999999999998873              34689999    8999999


Q ss_pred             HHHHHHHhccCCC-CCcEEEEeCCCChhhHHHHHHhcCcccccCCC-ChhHHHHHHhhhc
Q 042079           95 ELLKKIKESSVMK-EVPVVVVSSENIPTRINECLEEGAQMFMLKPL-KPSDVKKLTGHLI  152 (153)
Q Consensus        95 ~~~~~lr~~~~~~-~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~-~~~~l~~~~~~~~  152 (153)
                      ++++.|++.   + .+|+|++++..+.....++++.|+++|+.||+ +.+++...+.+++
T Consensus        75 ~~~~~l~~~---~~~~~ii~ls~~~~~~~~~~~~~~g~~~~l~kP~~~~~~l~~~i~~~~  131 (137)
T 2pln_A           75 SFVSRIKEK---HSSIVVLVSSDNPTSEEEVHAFEQGADDYIAKPYRSIKALVARIEARL  131 (137)
T ss_dssp             HHHHHHHHH---STTSEEEEEESSCCHHHHHHHHHTTCSEEEESSCSCHHHHHHHHHHHT
T ss_pred             HHHHHHHhc---CCCccEEEEeCCCCHHHHHHHHHcCCceeeeCCCCCHHHHHHHHHHHH
Confidence            999999985   5 78999999998888899999999999999999 9999999888754

>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=99.83  E-value=6.5e-20  Score=143.48  Aligned_cols=115  Identities=30%  Similarity=0.445  Sum_probs=105.4

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKI  100 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~l  100 (153)
                      ++||||||++..+..+..+|+..||.+..+.++.+++..+.              ...||+||+|+.||+++|+++++++
T Consensus         1 m~ILIVDDd~~~~~~l~~~L~~~g~~v~~a~~~~eal~~l~--------------~~~~DlvllD~~mp~~dG~ell~~l   66 (387)
T 1ny5_A            1 MNVLVIEDDKVFRGLLEEYLSMKGIKVESAERGKEAYKLLS--------------EKHFNVVLLDLLLPDVNGLEILKWI   66 (387)
T ss_dssp             CEEEEECCCHHHHHHHHHHHHHHTCEEEEESSHHHHHHHHH--------------HSCCSEEEEESBCSSSBHHHHHHHH
T ss_pred             CEEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHH--------------hCCCCEEEEeCCCCCCCHHHHHHHH
Confidence            47999999999999999999988999999999999999873              3469999999999999999999999


Q ss_pred             HhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          101 KESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       101 r~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      ++..  +.+|+|++|+..+.+...++++.|+++|+.||++.+++...+.++
T Consensus        67 r~~~--~~~pvIvlT~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~  115 (387)
T 1ny5_A           67 KERS--PETEVIVITGHGTIKTAVEAMKMGAYDFLTKPCMLEEIELTINKA  115 (387)
T ss_dssp             HHHC--TTSEEEEEEETTCHHHHHHHHTTTCCEEEEESCCHHHHHHHHHHH
T ss_pred             HhhC--CCCcEEEEeCCCCHHHHHHHHhcCceEEecCCCCHHHHHHHHHHH
Confidence            9754  689999999999999999999999999999999999999887764

>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=99.83  E-value=6e-20  Score=123.06  Aligned_cols=123  Identities=15%  Similarity=0.229  Sum_probs=99.1

Q ss_pred             CCCCCCCCCCCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCC-CcccEEEEeCCC
Q 042079           10 SSSSSSSNPKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNG-TKVNLVITDYCM   88 (153)
Q Consensus        10 ~~~~~~~~~~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~-~~~dlii~D~~~   88 (153)
                      +........+..+|||+||++..+..+...|+..|+.+..+.++.+++..+.              . ..||++|+|+.|
T Consensus         5 ~~~~~~~~~~~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~--------------~~~~~dlvilD~~l   70 (138)
T 2b4a_A            5 KIHHHHHHMQPFRVTLVEDEPSHATLIQYHLNQLGAEVTVHPSGSAFFQHRS--------------QLSTCDLLIVSDQL   70 (138)
T ss_dssp             ---------CCCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHTGG--------------GGGSCSEEEEETTC
T ss_pred             hhhhccCCCCCCeEEEECCCHHHHHHHHHHHHHcCCEEEEeCCHHHHHHHHH--------------hCCCCCEEEEeCCC
Confidence            3344444556789999999999999999999999999999999999998873              3 469999999999


Q ss_pred             CCCCHHHHHHHHHhccCCCCCcEEEEe-CCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079           89 PGMTGYELLKKIKESSVMKEVPVVVVS-SENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus        89 ~~~~g~~~~~~lr~~~~~~~~pii~~t-~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      |+++|+++++.+++..  +.+|+|+++ +..+... .+++   +++|+.||++.+++...+.+++
T Consensus        71 ~~~~g~~~~~~l~~~~--~~~~ii~ls~~~~~~~~-~~~~---~~~~l~KP~~~~~L~~~i~~~~  129 (138)
T 2b4a_A           71 VDLSIFSLLDIVKEQT--KQPSVLILTTGRHELIE-SSEH---NLSYLQKPFAISELRAAIDYHK  129 (138)
T ss_dssp             TTSCHHHHHHHHTTSS--SCCEEEEEESCC--CCC-CSSS---CEEEEESSCCHHHHHHHHHHTC
T ss_pred             CCCCHHHHHHHHHhhC--CCCCEEEEECCCCCHHH-HHHH---HHheeeCCCCHHHHHHHHHHHH
Confidence            9999999999999743  689999999 7766555 5555   9999999999999999888754

>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=99.82  E-value=1.5e-19  Score=130.98  Aligned_cols=116  Identities=23%  Similarity=0.378  Sum_probs=104.8

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKK   99 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~   99 (153)
                      ..+|||+||++..+..+..+|+..|+.+..+.++.+++..+.              ...||++|+|+.||+++|+++++.
T Consensus         4 ~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~~~--------------~~~~dlvllD~~l~~~~g~~~~~~   69 (230)
T 2oqr_A            4 ATSVLIVEDEESLADPLAFLLRKEGFEATVVTDGPAALAEFD--------------RAGADIVLLDLMLPGMSGTDVCKQ   69 (230)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEECSHHHHHHHHH--------------HHCCSEEEEESSCSSSCHHHHHHH
T ss_pred             CCeEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHh--------------ccCCCEEEEECCCCCCCHHHHHHH
Confidence            368999999999999999999999999999999999998773              235899999999999999999999


Q ss_pred             HHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079          100 IKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus       100 lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      +++.   +.+|+|++|+..+.....++++.|+++|+.||++.+++...+.+++
T Consensus        70 l~~~---~~~~ii~lt~~~~~~~~~~~~~~ga~~~l~Kp~~~~~l~~~i~~~~  119 (230)
T 2oqr_A           70 LRAR---SSVPVIMVTARDSEIDKVVGLELGADDYVTKPYSARELIARIRAVL  119 (230)
T ss_dssp             HHHH---CSCSEEEEECCHHHHHHHHHHHHCCSCCCCSSCCHHHHHHHHHHHH
T ss_pred             HHcC---CCCCEEEEeCCCcHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHH
Confidence            9974   4789999999888888889999999999999999999998887753

>2gwr_A DNA-binding response regulator MTRA; two-component regulatory system, transcription regulation, phosphorylation, OMPR family; 2.10A {Mycobacterium tuberculosis} PDB: 3nhz_A

Probab=99.82  E-value=1.5e-19  Score=131.99  Aligned_cols=116  Identities=22%  Similarity=0.446  Sum_probs=105.0

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKK   99 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~   99 (153)
                      ..+|||+||++..+..+...|+..|+.+..+.++.+++..+.              ...||+||+|+.||+++|+++++.
T Consensus         5 ~~~ILivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~--------------~~~~dlvilD~~l~~~~g~~~~~~   70 (238)
T 2gwr_A            5 RQRILVVDDDASLAEMLTIVLRGEGFDTAVIGDGTQALTAVR--------------ELRPDLVLLDLMLPGMNGIDVCRV   70 (238)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEECCGGGHHHHHH--------------HHCCSEEEEESSCSSSCHHHHHHH
T ss_pred             cCeEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHH--------------hCCCCEEEEeCCCCCCCHHHHHHH
Confidence            368999999999999999999999999999999999998773              235899999999999999999999


Q ss_pred             HHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079          100 IKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus       100 lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      +++.   +.+|+|++|+..+.....++++.|+++|+.||+++++|...+.+++
T Consensus        71 lr~~---~~~~ii~lt~~~~~~~~~~~~~~Ga~~~l~Kp~~~~~L~~~i~~~~  120 (238)
T 2gwr_A           71 LRAD---SGVPIVMLTAKTDTVDVVLGLESGADDYIMKPFKPKELVARVRARL  120 (238)
T ss_dssp             HHTT---CCCCEEEEEETTCCSCHHHHHHTTCCEEEEESCCHHHHHHHHHHHC
T ss_pred             HHhC---CCCcEEEEeCCCCHHHHHHHHHCCCCEEEeCCCCHHHHHHHHHHHH
Confidence            9974   3789999999888888899999999999999999999998887754

>2rdm_A Response regulator receiver protein; structural genomics, unknown function, PSI-2, protein struct initiative; HET: MSE; 1.76A {Sinorhizobium medicae}

Probab=99.82  E-value=4.9e-19  Score=117.37  Aligned_cols=116  Identities=19%  Similarity=0.309  Sum_probs=101.3

Q ss_pred             CCCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCC-cccEEEEeCCCCC-CCHHH
Q 042079           18 PKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGT-KVNLVITDYCMPG-MTGYE   95 (153)
Q Consensus        18 ~~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~-~~dlii~D~~~~~-~~g~~   95 (153)
                      ++..+|||+|+++..+..+...|+..|+.+..+.++.+++..+.              .. .||++|+|+.+|+ .+|++
T Consensus         3 m~~~~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~a~~~l~--------------~~~~~dlvi~d~~l~~~~~g~~   68 (132)
T 2rdm_A            3 LEAVTILLADDEAILLLDFESTLTDAGFLVTAVSSGAKAIEMLK--------------SGAAIDGVVTDIRFCQPPDGWQ   68 (132)
T ss_dssp             CSSCEEEEECSSHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--------------TTCCCCEEEEESCCSSSSCHHH
T ss_pred             CCCceEEEEcCcHHHHHHHHHHHHHcCCEEEEECCHHHHHHHHH--------------cCCCCCEEEEeeeCCCCCCHHH
Confidence            34578999999999999999999999999999999999998873              33 6999999999997 99999


Q ss_pred             HHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           96 LLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        96 ~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      +++.+++..  +.+|+|++++..+.....+++..|  +|+.||++.+++...+.++
T Consensus        69 ~~~~l~~~~--~~~~ii~~s~~~~~~~~~~~~~~~--~~l~kP~~~~~l~~~i~~~  120 (132)
T 2rdm_A           69 VARVAREID--PNMPIVYISGHAALEWASNGVPDS--IILEKPFTSAQLITAVSQL  120 (132)
T ss_dssp             HHHHHHHHC--TTCCEEEEESSCCTTHHHHSCTTC--EEEESSCCHHHHHHHHHHH
T ss_pred             HHHHHHhcC--CCCCEEEEeCCccHHHHHhhcCCc--ceEeCCCCHHHHHHHHHHH
Confidence            999999864  589999999988777766666654  7999999999999888775

>2qv0_A Protein MRKE; structural genomics, transcription, PSI-2, protein structure initiative; 2.40A {Klebsiella pneumoniae}

Probab=99.81  E-value=5.5e-19  Score=118.89  Aligned_cols=116  Identities=22%  Similarity=0.372  Sum_probs=98.2

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhc-CcE-EEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNS-ACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYEL   96 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~-~~~-v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~   96 (153)
                      +..+|||+||++..+..+...|+.. ++. +..+.++.+++..+.              ...||+||+|+.+|+.+|+++
T Consensus         8 ~~~~iLivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~al~~l~--------------~~~~dlvi~d~~l~~~~g~~~   73 (143)
T 2qv0_A            8 EKMKVIIVEDEFLAQQELSWLINTHSQMEIVGSFDDGLDVLKFLQ--------------HNKVDAIFLDINIPSLDGVLL   73 (143)
T ss_dssp             --CEEEEECSCHHHHHHHHHHHHHHSCCEEEEEESCHHHHHHHHH--------------HCCCSEEEECSSCSSSCHHHH
T ss_pred             CceEEEEEcCCHHHHHHHHHHHHhCCCceEEEEeCCHHHHHHHHH--------------hCCCCEEEEecCCCCCCHHHH
Confidence            3578999999999999999999875 787 458999999998873              346999999999999999999


Q ss_pred             HHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079           97 LKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus        97 ~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      ++.+++..  +..|+|++++..  +...++++.|+++|+.||++.+++...+.+++
T Consensus        74 ~~~l~~~~--~~~~ii~~s~~~--~~~~~~~~~g~~~~l~KP~~~~~l~~~i~~~~  125 (143)
T 2qv0_A           74 AQNISQFA--HKPFIVFITAWK--EHAVEAFELEAFDYILKPYQESRIINMLQKLT  125 (143)
T ss_dssp             HHHHTTST--TCCEEEEEESCC--TTHHHHHHTTCSEEEESSCCHHHHHHHHHHHH
T ss_pred             HHHHHccC--CCceEEEEeCCH--HHHHHHHhCCcceEEeCCCCHHHHHHHHHHHH
Confidence            99999753  466788888763  45678999999999999999999998887753

>3bre_A Probable two-component response regulator; protein-nucleotide complex, signaling protein; HET: C2E; 2.40A {Pseudomonas aeruginosa} PDB: 3i5a_A*

Probab=99.81  E-value=1.3e-19  Score=139.35  Aligned_cols=117  Identities=21%  Similarity=0.349  Sum_probs=103.4

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHH-hcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLK-NSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~-~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      ..+||||||++..+..+...|. ..|+.+..+.++.++++.+.              ...||+||+|+.||+++|+++++
T Consensus        18 ~~~ilivdD~~~~~~~l~~~l~~~~~~~v~~~~~~~~al~~~~--------------~~~~dlvl~D~~mp~~~G~~~~~   83 (358)
T 3bre_A           18 AVMVLLVDDQAMIGEAVRRSLASEAGIDFHFCSDPQQAVAVAN--------------QIKPTVILQDLVMPGVDGLTLLA   83 (358)
T ss_dssp             CEEEEEECSCTTHHHHHHTTSSSCTTEEEEEECCHHHHHHHHH--------------HHCCSEEEEESBCSSSBHHHHHH
T ss_pred             CceEEEEECCHHHHHHHHHHHHhccCcEEEEeCCHHHHHHHHH--------------hCCCCEEEEeCCCCCCCHHHHHH
Confidence            3579999999999999999996 45899999999999999873              24689999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhh
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGH  150 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~  150 (153)
                      .+++....+.+|+|++|+..+.....++++.|+++||.||++..++...+..
T Consensus        84 ~l~~~~~~~~~~ii~~s~~~~~~~~~~a~~~Ga~~~l~Kp~~~~~l~~~v~~  135 (358)
T 3bre_A           84 AYRGNPATRDIPIIVLSTKEEPTVKSAAFAAGANDYLVKLPDAIELVARIRY  135 (358)
T ss_dssp             HHTTSTTTTTSCEEEEESSCCHHHHHHHHHTTCSEEEESCCCHHHHHHHHHH
T ss_pred             HHhcCcccCCCcEEEEeCCCCHHHHHHHHhcChheEeeccCCHHHHHHHHHH
Confidence            9997543467999999999999989999999999999999999999876654

>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=99.81  E-value=7.1e-19  Score=126.69  Aligned_cols=112  Identities=24%  Similarity=0.304  Sum_probs=102.3

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKI  100 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~l  100 (153)
                      .+|||+||++..+..+...|+..| .+..+.++.+++..+                ..||++|+|+.||+++|+++++.+
T Consensus         3 ~~ilivdd~~~~~~~l~~~L~~~~-~v~~~~~~~~al~~~----------------~~~dlvllD~~lp~~~g~~~~~~l   65 (220)
T 1p2f_A            3 WKIAVVDDDKNILKKVSEKLQQLG-RVKTFLTGEDFLNDE----------------EAFHVVVLDVMLPDYSGYEICRMI   65 (220)
T ss_dssp             EEEEEECSCHHHHHHHHHHHTTTE-EEEEESSHHHHHHCC----------------SCCSEEEEESBCSSSBHHHHHHHH
T ss_pred             ceEEEEeCCHHHHHHHHHHHHhCC-CEEEECCHHHHHHhc----------------CCCCEEEEeCCCCCCCHHHHHHHH
Confidence            589999999999999999999888 899999999988754                358999999999999999999999


Q ss_pred             HhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          101 KESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       101 r~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      ++..  +.+|+|++|+..+.....++++.|+++|+.||++.+++...+.++
T Consensus        66 r~~~--~~~~ii~lt~~~~~~~~~~~~~~ga~~~l~Kp~~~~~L~~~i~~~  114 (220)
T 1p2f_A           66 KETR--PETWVILLTLLSDDESVLKGFEAGADDYVTKPFNPEILLARVKRF  114 (220)
T ss_dssp             HHHC--TTSEEEEEESCCSHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHH
T ss_pred             HhcC--CCCcEEEEEcCCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHH
Confidence            9864  589999999998988999999999999999999999999888765

>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=99.81  E-value=4.5e-21  Score=125.71  Aligned_cols=116  Identities=28%  Similarity=0.404  Sum_probs=103.8

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKK   99 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~   99 (153)
                      ..+|||+||++..+..+...|+..|+.+..+.++.+++..+.              ...||++++|+.+|+++|+++++.
T Consensus         3 ~~~ilivdd~~~~~~~l~~~l~~~~~~v~~~~~~~~~~~~~~--------------~~~~dlvi~d~~~~~~~g~~~~~~   68 (124)
T 1dc7_A            3 RGIVWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLAALA--------------SKTPDVLLSDIRMPGMDGLALLKQ   68 (124)
T ss_dssp             CCCCEEECSSSSHHHHHHHHHTTTTCCCEECCCTTHHHHHSS--------------SCCCSCEEECSCSSHHHHCSTHHH
T ss_pred             ccEEEEEeCCHHHHHHHHHHHHhCCcEEEEeCCHHHHHHHHh--------------cCCCCEEEEeeecCCCCHHHHHHH
Confidence            467999999999999999999988999999999999998873              456999999999999999999999


Q ss_pred             HHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          100 IKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       100 lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      +++..  +.+|+|++++..+.....++++.|+++|+.||++.+++...+.++
T Consensus        69 l~~~~--~~~~ii~~s~~~~~~~~~~~~~~g~~~~l~kp~~~~~l~~~i~~~  118 (124)
T 1dc7_A           69 IKQRH--PMLPVIIMTAHSDLDAAVSAYQQGAFDYLPKPFDIDEAVALVERA  118 (124)
T ss_dssp             HHHHC--TTSCCCCBCCSTTSTTTTSSCTTCCCCCBCSSCCHHHHHHHHHHH
T ss_pred             HHhhC--CCCCEEEEecCCCHHHHHHHHhcCcceEeeCCCCHHHHHHHHHHH
Confidence            98754  578999999887777778899999999999999999999888764

>3t8y_A CHEB, chemotaxis response regulator protein-glutamate methylesterase; CHEA, hydrolase; 1.90A {Thermotoga maritima}

Probab=99.80  E-value=1.1e-18  Score=120.66  Aligned_cols=115  Identities=28%  Similarity=0.345  Sum_probs=95.3

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcC-c-EEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSA-C-KVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELL   97 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~-~-~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~   97 (153)
                      ..+|||+||++..+..++.+|+..+ + .+..+.++.+++..+.              ...||+||+|+.||+++|++++
T Consensus        25 ~~~ILivdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~al~~l~--------------~~~~dlvilD~~l~~~~g~~l~   90 (164)
T 3t8y_A           25 VIRVLVVDDSAFMRMVLKDIIDSQPDMKVVGFAKDGLEAVEKAI--------------ELKPDVITMDIEMPNLNGIEAL   90 (164)
T ss_dssp             CEEEEEECSCHHHHHHHHHHHHTSTTEEEEEEESSHHHHHHHHH--------------HHCCSEEEECSSCSSSCHHHHH
T ss_pred             ccEEEEEcCCHHHHHHHHHHHhcCCCeEEEEecCCHHHHHHHhc--------------cCCCCEEEEeCCCCCCCHHHHH
Confidence            4689999999999999999999764 3 3557999999998873              2459999999999999999999


Q ss_pred             HHHHhccCCCCCcEEEEeCCCChh--hHHHHHHhcCcccccCCCC---------hhHHHHHHhhh
Q 042079           98 KKIKESSVMKEVPVVVVSSENIPT--RINECLEEGAQMFMLKPLK---------PSDVKKLTGHL  151 (153)
Q Consensus        98 ~~lr~~~~~~~~pii~~t~~~~~~--~~~~a~~~ga~~~l~KP~~---------~~~l~~~~~~~  151 (153)
                      +.|++..  + +|+|+++...+..  ...++++.|+++||.||++         ..++.+.+.+.
T Consensus        91 ~~lr~~~--~-~~ii~~s~~~~~~~~~~~~~~~~ga~~~l~KP~~~~~l~~r~~~~~l~~~i~~~  152 (164)
T 3t8y_A           91 KLIMKKA--P-TRVIMVSSLTEEGAAITIEALRNGAVDFITKPHGSISLTFRQVAPELLEKIRQA  152 (164)
T ss_dssp             HHHHHHS--C-CEEEEEESSCCTTCHHHHHHHHTTCCEEEECSSSSSCGGGGGGHHHHHHHHHHH
T ss_pred             HHHHhcC--C-ceEEEEecCCccchHHHHHHHHcCcCEEEeCCCCHHHHHHHhhhHHHHHHHHHH
Confidence            9999864  3 7999999866543  5678999999999999999         45665555543

>3c97_A Signal transduction histidine kinase; structural genomics, signaling, PSI-2, protein structure initiative; 1.70A {Aspergillus oryzae RIB40}

Probab=99.80  E-value=4.1e-19  Score=119.33  Aligned_cols=116  Identities=22%  Similarity=0.395  Sum_probs=97.9

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKK   99 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~   99 (153)
                      ..+|||+||++..+..+..+|+..|+.+..+.++.+++..+.              ...||++|+|+.||+++|+++++.
T Consensus        10 ~~~iLivdd~~~~~~~l~~~L~~~~~~v~~~~~~~~al~~l~--------------~~~~dlvllD~~lp~~~g~~~~~~   75 (140)
T 3c97_A           10 PLSVLIAEDNDICRLVAAKALEKCTNDITVVTNGLQALQAYQ--------------NRQFDVIIMDIQMPVMDGLEAVSE   75 (140)
T ss_dssp             CCEEEEECCCHHHHHHHHHHHTTTCSEEEEESSHHHHHHHHH--------------HSCCSEEEECTTCCSSCHHHHHHH
T ss_pred             CceEEEEcCCHHHHHHHHHHHHHcCCceEEECCHHHHHHHHh--------------cCCCCEEEEeCCCCCCcHHHHHHH
Confidence            368999999999999999999988999999999999998873              246899999999999999999999


Q ss_pred             HHhcc---CCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079          100 IKESS---VMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus       100 lr~~~---~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      |++..   ..+.+|++++++........   ..|+++|+.||++.++|...+.+++
T Consensus        76 l~~~~~~~~~~~~~ii~~s~~~~~~~~~---~~g~~~~l~KP~~~~~L~~~i~~~~  128 (140)
T 3c97_A           76 IRNYERTHNTKRASIIAITADTIDDDRP---GAELDEYVSKPLNPNQLRDVVLTCH  128 (140)
T ss_dssp             HHHHHHHHTCCCCCCEEEESSCCSCCCC---CSSCSEEEESSCCHHHHHHHHHHHH
T ss_pred             HHhhhhhcCCCceEEEEEeCccchhHHH---hCChhheEeCCCCHHHHHHHHHHHh
Confidence            98631   12568899998865444322   6899999999999999998887753

>3c3w_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 2.20A {Mycobacterium tuberculosis}

Probab=99.80  E-value=8.5e-20  Score=132.49  Aligned_cols=115  Identities=18%  Similarity=0.281  Sum_probs=102.8

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcC-cE-EEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSA-CK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~-~~-v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      ++|||+||++..+..+..+|+..+ +. +..+.++.+++..+.              ...||+||+|+.||+++|+++++
T Consensus         2 ~~ILivdd~~~~~~~l~~~L~~~~~~~vv~~~~~~~~al~~l~--------------~~~~dlvllD~~lp~~~g~~~~~   67 (225)
T 3c3w_A            2 VKVFLVDDHEVVRRGLVDLLGADPELDVVGEAGSVAEAMARVP--------------AARPDVAVLDVRLPDGNGIELCR   67 (225)
T ss_dssp             EEEEEECSCHHHHHHHHHHHHTCTTEEEEEEESSHHHHHHHHH--------------HHCCSEEEECSEETTEEHHHHHH
T ss_pred             cEEEEEcCCHHHHHHHHHHHhcCCCcEEEEEECCHHHHHHHHh--------------hcCCCEEEEeCCCCCCCHHHHHH
Confidence            479999999999999999999876 87 457999999998873              23589999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      .+++..  +.+|+|++|+..+.....++++.|+++|+.||++.+++...+.++
T Consensus        68 ~lr~~~--~~~~ii~lt~~~~~~~~~~~~~~Ga~~~l~Kp~~~~~L~~~i~~~  118 (225)
T 3c3w_A           68 DLLSRM--PDLRCLILTSYTSDEAMLDAILAGASGYVVKDIKGMELARAVKDV  118 (225)
T ss_dssp             HHHHHC--TTCEEEEGGGSSSHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhC--CCCcEEEEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHH
Confidence            999854  689999999998999999999999999999999999999877764

>3klo_A Transcriptional regulator VPST; REC domain, HTH domain, DNA-binding, transcription regulation; HET: C2E TAR; 2.80A {Vibrio cholerae} PDB: 3kln_A*

Probab=99.80  E-value=7.8e-20  Score=132.50  Aligned_cols=118  Identities=8%  Similarity=0.036  Sum_probs=99.2

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHh-cCcEEEE-ecCHHHHHHH-hchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKN-SACKVTT-AENGMRALEF-LGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYE   95 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~-~~~~v~~-~~~~~~a~~~-l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~   95 (153)
                      +..+||||||++..+..+..+|+. .|+.+.. +.++.+++.. +              ....||+||+|+.||+++|++
T Consensus         6 ~~~~IlivdD~~~~~~~l~~~L~~~~~~~v~~~~~~~~~~~~~~~--------------~~~~~dlvllD~~mp~~~G~~   71 (225)
T 3klo_A            6 NKLNVRMLSDVCMQSRLLKEALESKLPLALEITPFSELWLEENKP--------------ESRSIQMLVIDYSRISDDVLT   71 (225)
T ss_dssp             SSEEEEEESCCSHHHHHHHHHHHHHSSEEEEEECGGGHHHHTTCS--------------GGGGCCEEEEEGGGCCHHHHH
T ss_pred             CceEEEEEcCcHHHHHHHHHHHhhCCCceEEEEeCCcHHHHHHHh--------------hccCCCEEEEeCCCCCCCHHH
Confidence            357899999999999999999984 6887754 4555555543 3              135699999999999999999


Q ss_pred             HHHHHHh-ccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079           96 LLKKIKE-SSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus        96 ~~~~lr~-~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      +++++++ ..  +.+|+|++|+..+......+++.|+++|+.||++++++...+.+++
T Consensus        72 ~~~~lr~~~~--~~~~ii~lt~~~~~~~~~~~~~~Ga~~~l~Kp~~~~~L~~~i~~~~  127 (225)
T 3klo_A           72 DYSSFKHISC--PDAKEVIINCPQDIEHKLLFKWNNLAGVFYIDDDMDTLIKGMSKIL  127 (225)
T ss_dssp             HHHHHHHHHC--TTCEEEEEEECTTCCHHHHTTSTTEEEEEETTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHhhC--CCCcEEEEECCcchhHHHHHHHhCCCEEEecCCCHHHHHHHHHHHH
Confidence            9999997 44  6899999999888888889999999999999999999998887653

>3sy8_A ROCR; TIM barrel phosphodiesterase-A, transcription regulator; HET: EPE; 2.50A {Pseudomonas aeruginosa}

Probab=99.80  E-value=2.4e-19  Score=140.54  Aligned_cols=117  Identities=24%  Similarity=0.298  Sum_probs=99.7

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHh-cCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKN-SACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~-~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      ..+||||||++..+..+..+|+. .++.+..+.++.++++.+..             ...||+||+|+.||+++|+++++
T Consensus         3 ~~~ILivDD~~~~~~~l~~~L~~~~~~~v~~a~~g~eal~~l~~-------------~~~~DlvllDi~mP~~dG~ell~   69 (400)
T 3sy8_A            3 DLNVLVLEDEPFQRLVAVTALKKVVPGSILEAADGKEAVAILES-------------CGHVDIAICDLQMSGMDGLAFLR   69 (400)
T ss_dssp             CEEEEEECSSHHHHHHHHHHHHHHCSEEEEEESSHHHHHHHHHH-------------HSCEEEEEECSSCSSSCHHHHHH
T ss_pred             CceEEEEcCCHHHHHHHHHHHHhcCCcEEEEecCHHHHHHHHhh-------------CCCCCEEEEeCCCCCCCHHHHHH
Confidence            46899999999999999999997 57899999999999998831             13699999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCCh-----hhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           99 KIKESSVMKEVPVVVVSSENIP-----TRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~-----~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      ++++..  +..|||++|.....     ....+++..|+++|+.||++.+++...+.++
T Consensus        70 ~l~~~~--~~~~ii~~s~~~~~~~~~~~~~~~a~~~ga~~yl~KP~~~~~L~~~i~~~  125 (400)
T 3sy8_A           70 HASLSG--KVHSVILSSEVDPILRQATISMIECLGLNFLGDLGKPFSLERITALLTRY  125 (400)
T ss_dssp             HHHHHT--CEEEEEESCCCCGGGHHHHHHHHHTTTCEEEEECCSSCCHHHHHHHHHHH
T ss_pred             HHHhcC--CCceEEEEcCchHHHHHHHHHHHHHcCCeeccCcCCCcCHHHHHHHHHHH
Confidence            999764  45667766666555     4567788999999999999999999888765

>2hqr_A Putative transcriptional regulator; phosporylation-independent response regulator, H. pylori, SY dimer, signaling protein; NMR {Helicobacter pylori}

Probab=99.78  E-value=6e-18  Score=122.05  Aligned_cols=112  Identities=17%  Similarity=0.194  Sum_probs=101.6

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKI  100 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~l  100 (153)
                      ++|||+||++..+..+..+|+..|+.+..+.++.+++..+.              ...||++|    ||+++|+++++.+
T Consensus         1 m~ilivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~--------------~~~~dlvi----lp~~~g~~~~~~l   62 (223)
T 2hqr_A            1 MRVLLIEKNSVLGGEIEKGLNVKGFMADVTESLEDGEYLMD--------------IRNYDLVM----VSDKNALSFVSRI   62 (223)
T ss_dssp             CCEEEECSCHHHHHHHHHHHGGGTCCEEEESSHHHHHHHHT--------------TSCCSEEE----ECCTTHHHHHHHH
T ss_pred             CEEEEEcCCHHHHHHHHHHHHHCCcEEEEECCHHHHHHHHh--------------cCCCCEEE----eCCCCHHHHHHHH
Confidence            36999999999999999999999999999999999999883              45799999    8999999999999


Q ss_pred             HhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCC-ChhHHHHHHhhhc
Q 042079          101 KESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPL-KPSDVKKLTGHLI  152 (153)
Q Consensus       101 r~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~-~~~~l~~~~~~~~  152 (153)
                      ++.  ...+|+|++|+..+.....++++.|+++|+.||+ +.+++...+.+++
T Consensus        63 r~~--~~~~~ii~lt~~~~~~~~~~~~~~Ga~~~l~Kp~~~~~~L~~~i~~~~  113 (223)
T 2hqr_A           63 KEK--HSSIVVLVSSDNPTSEEEVHAFEQGADDYIAKPYRSIKALVARIEARL  113 (223)
T ss_dssp             HHH--CTTSEEEEEESSCCHHHHHHHHHHTCSEEEETTCSCTHHHHHHHHHHT
T ss_pred             HhC--CCCCcEEEEECCCCHHHHHHHHHcCCCEEEECCCCCHHHHHHHHHHHh
Confidence            975  1378999999999999999999999999999999 9999999887754

>1qo0_D AMIR; binding protein, gene regulator, receptor; 2.25A {Pseudomonas aeruginosa} SCOP: c.23.1.3

Probab=99.77  E-value=1.2e-18  Score=123.55  Aligned_cols=112  Identities=13%  Similarity=0.133  Sum_probs=97.7

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      +..+|||+||++..+..+...|...||.+..+.++.+++                  ...||+||+|+.||+++|. +++
T Consensus        11 ~~~~iLivdd~~~~~~~l~~~L~~~g~~v~~~~~~~~al------------------~~~~dlvl~D~~mp~~~g~-l~~   71 (196)
T 1qo0_D           11 RELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAF------------------DVPVDVVFTSIFQNRHHDE-IAA   71 (196)
T ss_dssp             GGCEEEEESCTTHHHHHHHHHHHHHTCEEEEECSCCSSC------------------SSCCSEEEEECCSSTHHHH-HHH
T ss_pred             cCCeEEEEcCChhHHHHHHHHHHHcCCeEEEecCchhhC------------------CCCCCEEEEeCCCCccchH-HHH
Confidence            457899999999999999999998899998887766543                  1368999999999999998 888


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      .++...  +.+|+|++|+..+.+...++++.|+++||.||++..++...+.++
T Consensus        72 ~~~~~~--~~~~ii~lt~~~~~~~~~~a~~~ga~~~l~KP~~~~~L~~~l~~~  122 (196)
T 1qo0_D           72 LLAAGT--PRTTLVALVEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSA  122 (196)
T ss_dssp             HHHHSC--TTCEEEEEECCCSHHHHHHHHHHTCSEEEESSCCGGGHHHHHHHH
T ss_pred             HHhccC--CCCCEEEEEcCCChHHHHHHHHcCCCeeEecCcCHHHHHHHHHHH
Confidence            888753  578999999999999999999999999999999999998877653

>1a2o_A CHEB methylesterase; bacterial chemotaxis, adaptation, serine hydrolase; 2.40A {Salmonella typhimurium} SCOP: c.23.1.1 c.40.1.1

Probab=99.73  E-value=4.3e-17  Score=125.98  Aligned_cols=105  Identities=30%  Similarity=0.394  Sum_probs=91.6

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhc-CcE-EEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNS-ACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELL   97 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~-~~~-v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~   97 (153)
                      ..+|||+||++..+..+..+|+.. ++. +..+.++.++++.+.              ...||++++|+.||+++|++++
T Consensus         3 ~~rVLIVDD~~~~r~~L~~~L~~~~g~~vv~~a~~~~eAl~~l~--------------~~~pDlVllDi~mp~~dGlell   68 (349)
T 1a2o_A            3 KIRVLSVDDSALMRQIMTEIINSHSDMEMVATAPDPLVARDLIK--------------KFNPDVLTLDVEMPRMDGLDFL   68 (349)
T ss_dssp             CEEEEEECSCHHHHHHHHHHHHTSTTEEEEEEESSHHHHHHHHH--------------HHCCSEEEEECCCSSSCHHHHH
T ss_pred             CCEEEEEECCHHHHHHHHHHHhcCCCcEEEEEeCCHHHHHHHHh--------------ccCCCEEEEECCCCCCCHHHHH
Confidence            468999999999999999999985 888 668999999998873              2358999999999999999999


Q ss_pred             HHHHhccCCCCCcEEEEeCCCCh--hhHHHHHHhcCcccccCCCCh
Q 042079           98 KKIKESSVMKEVPVVVVSSENIP--TRINECLEEGAQMFMLKPLKP  141 (153)
Q Consensus        98 ~~lr~~~~~~~~pii~~t~~~~~--~~~~~a~~~ga~~~l~KP~~~  141 (153)
                      ++|++..  + +|+|++|+..+.  +...++++.|+++|+.||++.
T Consensus        69 ~~l~~~~--p-~pVIvlS~~~~~~~~~~~~al~~Ga~d~l~KP~~~  111 (349)
T 1a2o_A           69 EKLMRLR--P-MPVVMVSSLTGKGSEVTLRALELGAIDFVTKPQLG  111 (349)
T ss_dssp             HHHHHSS--C-CCEEEEECCTHHHHHHHHHHHHHTCCEEEECSSSS
T ss_pred             HHHHhcC--C-CcEEEEECCCcccHHHHHHHHhCCceEEEECCCCc
Confidence            9999754  3 899999987664  347889999999999999984

>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=99.73  E-value=1.6e-17  Score=123.21  Aligned_cols=104  Identities=18%  Similarity=0.353  Sum_probs=85.6

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHh-cCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKN-SACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~-~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      ..+||||||++..+..+...|.. .|+.+..++ +.+++..+              ....||+|++|+.||+++|+++++
T Consensus         4 ~~~ILiVdD~~~~~~~l~~~L~~~~~~~v~~~~-~~~~~~~~--------------~~~~~dlvllD~~mP~~~G~~~~~   68 (259)
T 3luf_A            4 KQKILIVEDSMTIRRMLIQAIAQQTGLEIDAFD-TLEGARHC--------------QGDEYVVALVDLTLPDAPSGEAVK   68 (259)
T ss_dssp             CCEEEEECCCHHHHHHHHHHHHHHHCCEEEEES-STGGGTTC--------------CTTTEEEEEEESCBTTBTTSHHHH
T ss_pred             CCeEEEEECCHHHHHHHHHHHHhcCCeEEEEeC-hHHHHHHh--------------hcCCCcEEEEeCCCCCCCHHHHHH
Confidence            35899999999999999999875 477775544 44444433              235799999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChh
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPS  142 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~  142 (153)
                      ++|+.    .+|||++|+..+.+...++++.||++|+.||....
T Consensus        69 ~lr~~----~~pvi~lt~~~~~~~~~~a~~~Ga~dyl~Kp~~~~  108 (259)
T 3luf_A           69 VLLER----GLPVVILTADISEDKREAWLEAGVLDYVMKDSRHS  108 (259)
T ss_dssp             HHHHT----TCCEEEEECC-CHHHHHHHHHTTCCEEEECSSHHH
T ss_pred             HHHhC----CCCEEEEEccCCHHHHHHHHHCCCcEEEeCCchhH
Confidence            99973    57999999999999999999999999999996543

>2vyc_A Biodegradative arginine decarboxylase; pyridoxal phosphate, PLP-dependent E lyase, acid resistance; HET: LLP; 2.4A {Escherichia coli}

Probab=99.68  E-value=1.3e-16  Score=133.97  Aligned_cols=110  Identities=16%  Similarity=0.227  Sum_probs=97.5

Q ss_pred             CeEEEEeCCH-HH-------HHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCC--
Q 042079           21 PHVLAVDDSI-VD-------RKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPG--   90 (153)
Q Consensus        21 ~~iLiidd~~-~~-------~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~--   90 (153)
                      ++||||||+. ..       ++.+...|++.||+|..+.++.+++..+.             ....||+||+|+.||+  
T Consensus         1 m~ILiVdDd~~~~~~~~~~~~~~L~~~L~~~g~~v~~a~~g~~al~~~~-------------~~~~~d~vilDi~lp~~~   67 (755)
T 2vyc_A            1 MKVLIVESEFLHQDTWVGNAVERLADALSQQNVTVIKSTSFDDGFAILS-------------SNEAIDCLMFSYQMEHPD   67 (755)
T ss_dssp             CEEEEECCTTSTTSHHHHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHT-------------TTCCCSEEEEECCCCSHH
T ss_pred             CeEEEEeCCccccccccHHHHHHHHHHHHhCCCEEEEECCHHHHHHHHh-------------cCCCCcEEEEeCCCCccc
Confidence            3799999999 88       89999999999999999999999999883             1235999999999999  


Q ss_pred             --CCHHHHHHHHHhccCCCCCcEEEEeCCCC-hhhHHHHHHhcCcccccCCCChhH-HH
Q 042079           91 --MTGYELLKKIKESSVMKEVPVVVVSSENI-PTRINECLEEGAQMFMLKPLKPSD-VK  145 (153)
Q Consensus        91 --~~g~~~~~~lr~~~~~~~~pii~~t~~~~-~~~~~~a~~~ga~~~l~KP~~~~~-l~  145 (153)
                        ++|++++++||+..  +.+|||++|+..+ .+.....+..|+++|+.||++..+ +.
T Consensus        68 ~~~~G~~ll~~iR~~~--~~iPIi~lTa~~~~~~d~~~~l~~gaddyi~kpf~~~efl~  124 (755)
T 2vyc_A           68 EHQNVRQLIGKLHERQ--QNVPVFLLGDREKALAAMDRDLLELVDEFAWILEDTADFIA  124 (755)
T ss_dssp             HHHHHHHHHHHHHHHS--TTCCEEEEECHHHHHHTCSHHHHHHCSEEEETTTSCHHHHH
T ss_pred             ccccHHHHHHHHHHhC--CCCCEEEEecCCcchhhccHhHhhcCCceEeCCCCCHHHHH
Confidence              99999999999865  5799999998766 666778899999999999999999 54

>1w25_A Stalked-cell differentiation controlling protein; two-component system, ggdef domain, cyclic dinucleotide, cyclic-digmp; HET: C2E; 2.70A {Caulobacter vibrioides} SCOP: c.23.1.1 c.23.1.1 d.58.29.2 PDB: 2v0n_A* 2wb4_A*

Probab=99.22  E-value=5.3e-10  Score=88.46  Aligned_cols=115  Identities=19%  Similarity=0.277  Sum_probs=93.9

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      ...++++++++......+...+.. .+.+....+..++....               ...||++++|+.||.++|+++++
T Consensus       151 ~~~~ilivdd~~~~~~~i~~~L~~-~~~~~~~~~~~~~~~~~---------------~~~~dlil~D~~mp~~dG~~~~~  214 (459)
T 1w25_A          151 LGGRVLIVDDNERQAQRVAAELGV-EHRPVIESDPEKAKISA---------------GGPVDLVIVNAAAKNFDGLRFTA  214 (459)
T ss_dssp             CSCEEEEECSCHHHHHHHHHHHTT-TSEEEEECCHHHHHHHH---------------HSSCSEEEEETTCSSSCHHHHHH
T ss_pred             CCCeEEEECCchhhHHHHHHHHhc-ccceeeccCHHHHhhhc---------------cCCCCEEEEecCCCCCcHHHHHH
Confidence            346899999999888888777764 45666777777764221               24589999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHh
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTG  149 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~  149 (153)
                      .+|.......+|+++++..........+++.|+++|+.||++..++...+.
T Consensus       215 ~ir~~~~~~~~pii~lt~~~~~~~~~~~l~~Ga~d~~~kp~~~~~l~~~v~  265 (459)
T 1w25_A          215 ALRSEERTRQLPVLAMVDPDDRGRMVKALEIGVNDILSRPIDPQELSARVK  265 (459)
T ss_dssp             HHHTSGGGTTCCEEEEECTTCHHHHHHHHHTTCCEEEESSCCHHHHHHHHH
T ss_pred             HHHhCccccCCcEEEEcCCCchHHHHHHHhccccccccCCCCHHHHHHHHH
Confidence            999765556789999999988888889999999999999999988765443

>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=1.1e-11  Score=89.37  Aligned_cols=90  Identities=23%  Similarity=0.357  Sum_probs=69.8

Q ss_pred             cEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHHHhccCCCCCcEEEEeCCCChhhHH
Q 042079           45 CKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRIN  124 (153)
Q Consensus        45 ~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~  124 (153)
                      +.|..+.++.++++.+.              ...||++|+|+.||+++|+++++.+++..  +..++++++.....+...
T Consensus         6 ~~v~~~~~~~~a~~~~~--------------~~~~dlvl~D~~~p~~~g~~~~~~l~~~~--~~~~i~vi~~~~~~~~~~   69 (237)
T 3cwo_X            6 LIVDDATNGREAVEKYK--------------ELKPDIVTMDITMPEMNGIDAIKEIMKID--PNAKIIVCSAMGQQAMVI   69 (237)
T ss_dssp             EEEECCCSSSTTHHHHH--------------HHCCSCEEEECCSTTSSHHHHHHHHHHHS--SSCCEEEECCSSTHHHHH
T ss_pred             EEEEECCCHHHHHHHHH--------------hcCCCEEEEeCCCCCCCHHHHHHHHHHhC--CCCCEEEEECCCCHHHHH
Confidence            45666888888888773              23589999999999999999999999754  344555566555578888


Q ss_pred             HHHHhcCcccccCC--CChhHHHHHHhh
Q 042079          125 ECLEEGAQMFMLKP--LKPSDVKKLTGH  150 (153)
Q Consensus       125 ~a~~~ga~~~l~KP--~~~~~l~~~~~~  150 (153)
                      ++++.|+++|+.||  ++..++...+.+
T Consensus        70 ~~~~~Ga~~~l~kp~~~~~~~l~~~i~~   97 (237)
T 3cwo_X           70 EAIKAGAKDFIVNTAAVENPSLITQIAQ   97 (237)
T ss_dssp             HHHHTTCCEEEESHHHHHCTHHHHHHHH
T ss_pred             HHHHCCHHheEeCCcccChHHHHHHHHH
Confidence            99999999999999  676676654443

>3q7r_A Transcriptional regulatory protein; CHXR, receiver domain, transcription factor, OMPR, chlamydia transcription; 1.60A {Chlamydia trachomatis} PDB: 3q7s_A* 3q7t_A

Probab=98.09  E-value=3.6e-05  Score=48.31  Aligned_cols=105  Identities=18%  Similarity=0.246  Sum_probs=78.1

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      .+..||++..|-....+++.++....|.+.......                    .+...|+|+|++.+-..+      
T Consensus        11 ~~~~iL~VtEd~~ls~QlKel~~~~eY~~~is~~~~--------------------~e~~AdlIfCEYlLLPe~------   64 (121)
T 3q7r_A           11 GPKHVLLVSEHWDLFFQTKELLNPEEYRCTIGQQYK--------------------QELSADLVVCEYSLLPRE------   64 (121)
T ss_dssp             CCEEEEEECSCHHHHHHHHHHSCTTTEEEEEESSCC--------------------CCTTEEEEEEEGGGSCTT------
T ss_pred             CCcEEEEEecCchhhHHHHHhcCCcceeEEeccccC--------------------CcccceeEEEeeecChHH------
Confidence            346799999999999999999977778887765422                    235679999998654322      


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                       +...+.....-+|++-.-=+++...+.++.|+. ||.+|+++.-++.+++..
T Consensus        65 -ifS~k~~~~~dliVLfD~F~EEa~v~vLd~Ga~-yLlrPIT~kvldAvIraF  115 (121)
T 3q7r_A           65 -IRSPKSLEGSFVLVLLDFFDEETSVDLLDRGFW-YLIRPITPRILKSAISLF  115 (121)
T ss_dssp             -CCCCTTCCSCEEEEEESSCCHHHHHHHHHTTCE-EEESCCCHHHHHHHHHHH
T ss_pred             -hcCCCCCCcccEEEEehhhchHHHHHHHhCCce-eEeccCcHHHHHHHHHHH
Confidence             122222234456667666678888999999999 999999999999988763

>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=97.63  E-value=0.00019  Score=52.29  Aligned_cols=95  Identities=19%  Similarity=0.146  Sum_probs=67.0

Q ss_pred             CCCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHH
Q 042079           18 PKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELL   97 (153)
Q Consensus        18 ~~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~   97 (153)
                      ....+|||++|+...+..+..+|...|+.+..+.+       .              ....+|++++|+.++...+.   
T Consensus         9 l~~~~vlvv~d~~~~~~~l~~~L~~~g~~v~~~~~-------~--------------~~~~~~~ii~d~~~~~~~~~---   64 (254)
T 2ayx_A            9 LSGKRCWLAVRNASLCQFLETSLQRSGIVVTTYEG-------Q--------------EPTPEDVLITDEVVSKKWQG---   64 (254)
T ss_dssp             TTTEEEEEECCCHHHHHHHHHHHTTTTEEEEECSS-------C--------------CCCTTCEEEEESSCSCCCCS---
T ss_pred             cCCCEEEEEcCCHHHHHHHHHHHHHCCCEEEEecC-------C--------------CCCcCcEEEEcCCCcccccc---
Confidence            45689999999999999999999999999988764       1              12468999999999875321   


Q ss_pred             HHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           98 KKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        98 ~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                                 ..++.++.......    ...+...|+.+|+.+.++..++.++
T Consensus        65 -----------~~~i~~~~~~~~~~----~~~~~~~~~~~~~~~~~l~~~l~~~  103 (254)
T 2ayx_A           65 -----------RAVVTFCRRHIGIP----LEKAPGEWVHSVAAPHELPALLARI  103 (254)
T ss_dssp             -----------SEEEEECSSCCCSC----CTTSTTEEEECSSCCSHHHHHHHHH
T ss_pred             -----------ceEEEEecccCCCc----ccccCCceeccccchHHHHHHHHHH
Confidence                       12444444321110    1223457888999988888777654

>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=97.45  E-value=8.3e-05  Score=62.22  Aligned_cols=94  Identities=12%  Similarity=0.109  Sum_probs=69.7

Q ss_pred             HHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHHHhccCCCCCcEE
Q 042079           33 RKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVV  112 (153)
Q Consensus        33 ~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~lr~~~~~~~~pii  112 (153)
                      .+.|...|++.||+|..+.+..+++..+..             ...+++|++|+.++   +.+++++||+++  .++||+
T Consensus        19 i~~L~~~Le~~g~~V~~a~s~~Da~~~i~~-------------~~~i~avIld~d~~---~~~ll~~Ir~~~--~~iPVF   80 (715)
T 3n75_A           19 IRELHRALERLNFQIVYPNDRDDLLKLIEN-------------NARLCGVIFDWDKY---NLELCEEISKMN--ENLPLY   80 (715)
T ss_dssp             HHHHHHHHHHTTCEEECCSSHHHHHHHHHH-------------CTTEEEEEEEHHHH---HHHHHHHHHHHC--TTCEEE
T ss_pred             HHHHHHHHHHCCcEEEEeCCHHHHHHHHHh-------------CCCceEEEEecccc---HHHHHHHHHHhC--CCCCEE
Confidence            355667788899999999999999998842             34689999999885   688999999876  689999


Q ss_pred             EEeCCCChhhHHHHHHhcCcccccCCCChhHH
Q 042079          113 VVSSENIPTRINECLEEGAQMFMLKPLKPSDV  144 (153)
Q Consensus       113 ~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l  144 (153)
                      +++...+.....-..-.++++|+.+..+..++
T Consensus        81 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  112 (715)
T 3n75_A           81 AFANTYSTLDVSLNDLRLQISFFEYALGAAED  112 (715)
T ss_dssp             EECCTTCCCCGGGTTSCCEEEEECCCTTCHHH
T ss_pred             EEecCCcccccchhhhhccCeEEEeCCCCHHH
Confidence            99987543322111124677888876654444

>2yxb_A Coenzyme B12-dependent mutase; alpha/beta, structural genomics, NPPSFA, national project on structural and functional analyses; 1.80A {Aeropyrum pernix}

Probab=97.17  E-value=0.014  Score=39.74  Aligned_cols=116  Identities=14%  Similarity=0.139  Sum_probs=76.7

Q ss_pred             CCCeEEEE----eCCHHHHHHHHHHHHhcCcEEEEe---cCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCC
Q 042079           19 KPPHVLAV----DDSIVDRKIVENLLKNSACKVTTA---ENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGM   91 (153)
Q Consensus        19 ~~~~iLii----dd~~~~~~~l~~~l~~~~~~v~~~---~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~   91 (153)
                      ..++|++.    |.|..-...+..+|+..||+|...   .+.++.++.+.              ...+|+|.+...+...
T Consensus        17 ~~~~vlla~~~gd~HdiG~~~va~~l~~~G~eVi~lG~~~p~e~lv~aa~--------------~~~~diV~lS~~~~~~   82 (161)
T 2yxb_A           17 RRYKVLVAKMGLDGHDRGAKVVARALRDAGFEVVYTGLRQTPEQVAMAAV--------------QEDVDVIGVSILNGAH   82 (161)
T ss_dssp             CSCEEEEEEESSSSCCHHHHHHHHHHHHTTCEEECCCSBCCHHHHHHHHH--------------HTTCSEEEEEESSSCH
T ss_pred             CCCEEEEEeCCCCccHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHH--------------hcCCCEEEEEeechhh
Confidence            35678877    778888899999999999998753   35556666552              3578999998776642


Q ss_pred             --CHHHHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhh
Q 042079           92 --TGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGH  150 (153)
Q Consensus        92 --~g~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~  150 (153)
                        ...++++.|++... ++++|+ +.+.........+.+.|++.++..--+..+..+.+.+
T Consensus        83 ~~~~~~~i~~L~~~g~-~~i~v~-vGG~~~~~~~~~l~~~G~d~v~~~~~~~~~~~~~~~~  141 (161)
T 2yxb_A           83 LHLMKRLMAKLRELGA-DDIPVV-LGGTIPIPDLEPLRSLGIREIFLPGTSLGEIIEKVRK  141 (161)
T ss_dssp             HHHHHHHHHHHHHTTC-TTSCEE-EEECCCHHHHHHHHHTTCCEEECTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhcCC-CCCEEE-EeCCCchhcHHHHHHCCCcEEECCCCCHHHHHHHHHH
Confidence              34566777877542 356665 4554445555567789999755443444455444443

>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=96.85  E-value=0.0029  Score=44.79  Aligned_cols=69  Identities=12%  Similarity=0.231  Sum_probs=53.5

Q ss_pred             ccEEEEeC-CCCCCCH--HHHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCccc------ccCCCChhHHHHHHh
Q 042079           79 VNLVITDY-CMPGMTG--YELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMF------MLKPLKPSDVKKLTG  149 (153)
Q Consensus        79 ~dlii~D~-~~~~~~g--~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~------l~KP~~~~~l~~~~~  149 (153)
                      .++++.+. .++.++|  .+.+++++..   .+.|+|.+++....+...++++.|++++      ..+|+++.++.+.+.
T Consensus       145 ~~vli~~~~~~g~~~g~~~~~i~~~~~~---~~~Pvia~~g~~~~~~~~~~~~~G~~~~~vg~a~~~~~~~~~~~~~~l~  221 (237)
T 3cwo_X          145 GEILLTSIDRDGTKSGYDTEMIRFVRPL---TTLPIIASGGAGKMEHFLEAFLAGADAALAASVFHFREIDVRELKEYLK  221 (237)
T ss_dssp             SEEEEEETTTTTCCSCCCHHHHHHHGGG---CCSCEEEESCCCSHHHHHHHHHHTCSEEEESHHHHTTSSCHHHHHHHHH
T ss_pred             CeEEEEecCCCCccccccHHHHHHHHHh---cCCCEEecCCCCCHHHHHHHHHcCcHHHhhhHHHHcCCCCHHHHHHHHH
Confidence            45888886 5565666  4456666553   4789999999999999999999999997      489999999987664


Q ss_pred             h
Q 042079          150 H  150 (153)
Q Consensus       150 ~  150 (153)
                      .
T Consensus       222 ~  222 (237)
T 3cwo_X          222 K  222 (237)
T ss_dssp             T
T ss_pred             H
Confidence            3

>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=95.38  E-value=0.21  Score=32.82  Aligned_cols=104  Identities=13%  Similarity=0.074  Sum_probs=67.1

Q ss_pred             eCCHHHHHHHHHHHHhcCcEEE---EecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCC--CHHHHHHHHH
Q 042079           27 DDSIVDRKIVENLLKNSACKVT---TAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGM--TGYELLKKIK  101 (153)
Q Consensus        27 dd~~~~~~~l~~~l~~~~~~v~---~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~--~g~~~~~~lr  101 (153)
                      |-|..-...+..+|+..||+|.   ...+.++.++...              ...+|+|.+...+...  ...++++.|+
T Consensus        14 d~HdiG~~~v~~~l~~~G~~Vi~lG~~~p~e~~v~~a~--------------~~~~d~v~lS~~~~~~~~~~~~~i~~l~   79 (137)
T 1ccw_A           14 DCHAVGNKILDHAFTNAGFNVVNIGVLSPQELFIKAAI--------------ETKADAILVSSLYGQGEIDCKGLRQKCD   79 (137)
T ss_dssp             CCCCHHHHHHHHHHHHTTCEEEEEEEEECHHHHHHHHH--------------HHTCSEEEEEECSSTHHHHHTTHHHHHH
T ss_pred             chhHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHH--------------hcCCCEEEEEecCcCcHHHHHHHHHHHH
Confidence            3466667788899999999877   4456777666663              2468999998877542  2345677787


Q ss_pred             hccCCCCCcEEEEeCCC-C-hh----hHHHHHHhcCcccccCCCChhHHHH
Q 042079          102 ESSVMKEVPVVVVSSEN-I-PT----RINECLEEGAQMFMLKPLKPSDVKK  146 (153)
Q Consensus       102 ~~~~~~~~pii~~t~~~-~-~~----~~~~a~~~ga~~~l~KP~~~~~l~~  146 (153)
                      +... ++++++ +.+.. . .+    ....+.+.|++.|+.---+..++.+
T Consensus        80 ~~g~-~~i~v~-vGG~~~~~~~~~~~~~~~~~~~G~d~~~~~g~~~~~~~~  128 (137)
T 1ccw_A           80 EAGL-EGILLY-VGGNIVVGKQHWPDVEKRFKDMGYDRVYAPGTPPEVGIA  128 (137)
T ss_dssp             HTTC-TTCEEE-EEESCSSSSCCHHHHHHHHHHTTCSEECCTTCCHHHHHH
T ss_pred             hcCC-CCCEEE-EECCCcCchHhhhhhHHHHHHCCCCEEECCCCCHHHHHH
Confidence            7542 356665 44432 1 11    1345789999998865555555543

>1wv2_A Thiazole moeity, thiazole biosynthesis protein THIG; structural genomics, protein structure initiative, PSI; 2.90A {Pseudomonas aeruginosa} SCOP: c.1.31.1

Probab=94.97  E-value=0.41  Score=35.12  Aligned_cols=81  Identities=19%  Similarity=0.203  Sum_probs=55.3

Q ss_pred             HHHHHhcCcEEE--EecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCC-----CCCHHHHHHHHHhccCCCCC
Q 042079           37 ENLLKNSACKVT--TAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMP-----GMTGYELLKKIKESSVMKEV  109 (153)
Q Consensus        37 ~~~l~~~~~~v~--~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~-----~~~g~~~~~~lr~~~~~~~~  109 (153)
                      .+.|.+.|+.+.  +..+...+-....               -.+++| +.+..|     +...+++++.+++.   .++
T Consensus       128 a~~L~~~Gf~Vlpy~~dd~~~akrl~~---------------~G~~aV-mPlg~pIGsG~Gi~~~~lI~~I~e~---~~v  188 (265)
T 1wv2_A          128 AEQLVKDGFDVMVYTSDDPIIARQLAE---------------IGCIAV-MPLAGLIGSGLGICNPYNLRIILEE---AKV  188 (265)
T ss_dssp             HHHHHTTTCEEEEEECSCHHHHHHHHH---------------SCCSEE-EECSSSTTCCCCCSCHHHHHHHHHH---CSS
T ss_pred             HHHHHHCCCEEEEEeCCCHHHHHHHHH---------------hCCCEE-EeCCccCCCCCCcCCHHHHHHHHhc---CCC
Confidence            344556788766  5666666544431               346777 443332     12347899999874   478


Q ss_pred             cEEEEeCCCChhhHHHHHHhcCccccc
Q 042079          110 PVVVVSSENIPTRINECLEEGAQMFML  136 (153)
Q Consensus       110 pii~~t~~~~~~~~~~a~~~ga~~~l~  136 (153)
                      |||.=.+-.++++...+++.|++..+.
T Consensus       189 PVI~eGGI~TPsDAa~AmeLGAdgVlV  215 (265)
T 1wv2_A          189 PVLVDAGVGTASDAAIAMELGCEAVLM  215 (265)
T ss_dssp             CBEEESCCCSHHHHHHHHHHTCSEEEE
T ss_pred             CEEEeCCCCCHHHHHHHHHcCCCEEEE
Confidence            999877778899999999999999753

>1y80_A Predicted cobalamin binding protein; corrinoid, factor IIIM, methyl transferase, structural genomics, PSI, protein structure initiative; HET: B1M; 1.70A {Moorella thermoacetica}

Probab=94.81  E-value=0.27  Score=34.51  Aligned_cols=100  Identities=12%  Similarity=0.069  Sum_probs=65.1

Q ss_pred             CCeEEEE----eCCHHHHHHHHHHHHhcCcEEEEec---CHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCC-
Q 042079           20 PPHVLAV----DDSIVDRKIVENLLKNSACKVTTAE---NGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGM-   91 (153)
Q Consensus        20 ~~~iLii----dd~~~~~~~l~~~l~~~~~~v~~~~---~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~-   91 (153)
                      ..+|++.    |-|..-...+..+|+..||+|....   ...+.++.+.              ..+||+|.+-..++.. 
T Consensus        88 ~~~vll~~~~gd~H~iG~~~va~~l~~~G~~v~~LG~~vp~~~l~~~~~--------------~~~~d~v~lS~~~~~~~  153 (210)
T 1y80_A           88 VGKIVLGTVKGDLHDIGKNLVAMMLESGGFTVYNLGVDIEPGKFVEAVK--------------KYQPDIVGMSALLTTTM  153 (210)
T ss_dssp             CCEEEEEEBTTCCCCHHHHHHHHHHHHTTCEEEECCSSBCHHHHHHHHH--------------HHCCSEEEEECCSGGGT
T ss_pred             CCEEEEEeCCCcccHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHH--------------HcCCCEEEEeccccccH
Confidence            4567777    6677888899999999999988543   3344444442              2468999998876643 


Q ss_pred             -CHHHHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCccccc
Q 042079           92 -TGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFML  136 (153)
Q Consensus        92 -~g~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~  136 (153)
                       ...++++.+|+....+++|+++-....+.+.   +.+.|++.|-.
T Consensus       154 ~~~~~~i~~l~~~~~~~~~~v~vGG~~~~~~~---~~~~gad~~~~  196 (210)
T 1y80_A          154 MNMKSTIDALIAAGLRDRVKVIVGGAPLSQDF---ADEIGADGYAP  196 (210)
T ss_dssp             HHHHHHHHHHHHTTCGGGCEEEEESTTCCHHH---HHHHTCSEECS
T ss_pred             HHHHHHHHHHHhcCCCCCCeEEEECCCCCHHH---HHHcCCeEEEC
Confidence             2456677787754323577765544444332   35679987753

>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=94.80  E-value=0.19  Score=35.71  Aligned_cols=101  Identities=14%  Similarity=0.114  Sum_probs=66.6

Q ss_pred             CCCeEEEE----eCCHHHHHHHHHHHHhcCcEEEEec---CHHHHHHHhchhhhHHhhhhcccCCCcccEEEE--eCCCC
Q 042079           19 KPPHVLAV----DDSIVDRKIVENLLKNSACKVTTAE---NGMRALEFLGLVDEQEQQNNLNSNGTKVNLVIT--DYCMP   89 (153)
Q Consensus        19 ~~~~iLii----dd~~~~~~~l~~~l~~~~~~v~~~~---~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~--D~~~~   89 (153)
                      +..++++.    |-|..=...+..+|+..||+|....   ...+.++.+.              .+++|+|.+  ...+.
T Consensus        91 ~~~~vll~~v~gd~HdiG~~iv~~~l~~~G~~Vi~LG~~vp~e~iv~~~~--------------~~~~d~v~l~~S~l~~  156 (215)
T 3ezx_A           91 EAGLAITFVAEGDIHDIGHRLVTTMLGANGFQIVDLGVDVLNENVVEEAA--------------KHKGEKVLLVGSALMT  156 (215)
T ss_dssp             -CCEEEEEECTTCCCCHHHHHHHHHHHHTSCEEEECCSSCCHHHHHHHHH--------------HTTTSCEEEEEECSSH
T ss_pred             CCCeEEEEeCCCChhHHHHHHHHHHHHHCCCeEEEcCCCCCHHHHHHHHH--------------HcCCCEEEEEchhccc
Confidence            34677776    6688888889999999999987543   4455555552              357899999  77665


Q ss_pred             C-C-CHHHHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCccccc
Q 042079           90 G-M-TGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFML  136 (153)
Q Consensus        90 ~-~-~g~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~  136 (153)
                      . + ...++++.+++.....++|+++-....+++   -+.+.|+|.|-.
T Consensus       157 ~~~~~~~~~i~~l~~~~~~~~v~v~vGG~~~~~~---~a~~iGad~~~~  202 (215)
T 3ezx_A          157 TSMLGQKDLMDRLNEEKLRDSVKCMFGGAPVSDK---WIEEIGADATAE  202 (215)
T ss_dssp             HHHTHHHHHHHHHHHTTCGGGSEEEEESSSCCHH---HHHHHTCCBCCS
T ss_pred             CcHHHHHHHHHHHHHcCCCCCCEEEEECCCCCHH---HHHHhCCeEEEC
Confidence            3 2 245677788876532357776544444443   344679998853

>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=94.17  E-value=0.71  Score=33.08  Aligned_cols=86  Identities=10%  Similarity=0.144  Sum_probs=58.5

Q ss_pred             HHHHHHHHHHhcCcEE-EEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCC------CCCCCHHHHHHHHHhcc
Q 042079           32 DRKIVENLLKNSACKV-TTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYC------MPGMTGYELLKKIKESS  104 (153)
Q Consensus        32 ~~~~l~~~l~~~~~~v-~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~------~~~~~g~~~~~~lr~~~  104 (153)
                      ....+-..+++.|..+ ..+.+.+++.....               ..+|+|.+...      .+...++++++++++. 
T Consensus       117 ~l~~~i~~~~~~g~~v~~~v~t~eea~~a~~---------------~Gad~Ig~~~~g~t~~~~~~~~~~~li~~l~~~-  180 (229)
T 3q58_A          117 DIDSLLTRIRLHGLLAMADCSTVNEGISCHQ---------------KGIEFIGTTLSGYTGPITPVEPDLAMVTQLSHA-  180 (229)
T ss_dssp             CHHHHHHHHHHTTCEEEEECSSHHHHHHHHH---------------TTCSEEECTTTTSSSSCCCSSCCHHHHHHHHTT-
T ss_pred             HHHHHHHHHHHCCCEEEEecCCHHHHHHHHh---------------CCCCEEEecCccCCCCCcCCCCCHHHHHHHHHc-
Confidence            3334444455556544 46778888766552               35888864321      1234568888988862 


Q ss_pred             CCCCCcEEEEeCCCChhhHHHHHHhcCccccc
Q 042079          105 VMKEVPVVVVSSENIPTRINECLEEGAQMFML  136 (153)
Q Consensus       105 ~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~  136 (153)
                         ++|+|.-.+-.+.+...++++.|++.++.
T Consensus       181 ---~ipvIA~GGI~t~~d~~~~~~~GadgV~V  209 (229)
T 3q58_A          181 ---GCRVIAEGRYNTPALAANAIEHGAWAVTV  209 (229)
T ss_dssp             ---TCCEEEESSCCSHHHHHHHHHTTCSEEEE
T ss_pred             ---CCCEEEECCCCCHHHHHHHHHcCCCEEEE
Confidence               68999888877899999999999998753

>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=93.31  E-value=1.3  Score=31.81  Aligned_cols=86  Identities=13%  Similarity=0.132  Sum_probs=57.9

Q ss_pred             HHHHHHHHHHhcCcEE-EEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCC------CCCCCHHHHHHHHHhcc
Q 042079           32 DRKIVENLLKNSACKV-TTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYC------MPGMTGYELLKKIKESS  104 (153)
Q Consensus        32 ~~~~l~~~l~~~~~~v-~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~------~~~~~g~~~~~~lr~~~  104 (153)
                      ....+...+++.|..+ ..+.+..++.....               ..+|+|.+...      ......+++++++++. 
T Consensus       117 ~l~~~i~~~~~~g~~v~~~v~t~eea~~a~~---------------~Gad~Ig~~~~g~t~~~~~~~~~~~~i~~l~~~-  180 (232)
T 3igs_A          117 AVEALLARIHHHHLLTMADCSSVDDGLACQR---------------LGADIIGTTMSGYTTPDTPEEPDLPLVKALHDA-  180 (232)
T ss_dssp             CHHHHHHHHHHTTCEEEEECCSHHHHHHHHH---------------TTCSEEECTTTTSSSSSCCSSCCHHHHHHHHHT-
T ss_pred             HHHHHHHHHHHCCCEEEEeCCCHHHHHHHHh---------------CCCCEEEEcCccCCCCCCCCCCCHHHHHHHHhc-
Confidence            3334444455556544 45778877766542               35788864321      1223468889998863 


Q ss_pred             CCCCCcEEEEeCCCChhhHHHHHHhcCccccc
Q 042079          105 VMKEVPVVVVSSENIPTRINECLEEGAQMFML  136 (153)
Q Consensus       105 ~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~  136 (153)
                         ++|+|.-.+-.+.+...++++.|++.++.
T Consensus       181 ---~ipvIA~GGI~t~~d~~~~~~~GadgV~V  209 (232)
T 3igs_A          181 ---GCRVIAEGRYNSPALAAEAIRYGAWAVTV  209 (232)
T ss_dssp             ---TCCEEEESCCCSHHHHHHHHHTTCSEEEE
T ss_pred             ---CCcEEEECCCCCHHHHHHHHHcCCCEEEE
Confidence               68999888777899999999999998753

>2i2x_B MTAC, methyltransferase 1; TIM barrel and helix bundle (MTAB), rossman fold and helix B (MTAC); HET: B13; 2.50A {Methanosarcina barkeri}

Probab=93.30  E-value=1.4  Score=31.93  Aligned_cols=101  Identities=13%  Similarity=0.070  Sum_probs=65.3

Q ss_pred             CCCeEEEE----eCCHHHHHHHHHHHHhcCcEEEEe---cCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCC
Q 042079           19 KPPHVLAV----DDSIVDRKIVENLLKNSACKVTTA---ENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGM   91 (153)
Q Consensus        19 ~~~~iLii----dd~~~~~~~l~~~l~~~~~~v~~~---~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~   91 (153)
                      ...+|++.    |-|..-...+..+|+..||+|...   -...+.++.+.              ...+|+|.+-..++..
T Consensus       122 ~~~~vlla~~~gd~HdiG~~iva~~L~~~G~~Vi~LG~~vp~e~l~~~~~--------------~~~~d~V~lS~l~~~~  187 (258)
T 2i2x_B          122 TKGTVVCHVAEGDVHDIGKNIVTALLRANGYNVVDLGRDVPAEEVLAAVQ--------------KEKPIMLTGTALMTTT  187 (258)
T ss_dssp             CSCEEEEEECTTCCCCHHHHHHHHHHHHTTCEEEEEEEECCSHHHHHHHH--------------HHCCSEEEEECCCTTT
T ss_pred             CCCeEEEEeCCCCccHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHH--------------HcCCCEEEEEeeccCC
Confidence            34667777    567788888999999999987532   34444445442              2468999998876643


Q ss_pred             --CHHHHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCC
Q 042079           92 --TGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKP  138 (153)
Q Consensus        92 --~g~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP  138 (153)
                        ...++++.|++..  .++||++-....+.+.   +...|++.|-.-.
T Consensus       188 ~~~~~~~i~~l~~~~--~~~~v~vGG~~~~~~~---~~~igad~~~~da  231 (258)
T 2i2x_B          188 MYAFKEVNDMLLENG--IKIPFACGGGAVNQDF---VSQFALGVYGEEA  231 (258)
T ss_dssp             TTHHHHHHHHHHTTT--CCCCEEEESTTCCHHH---HHTSTTEEECSST
T ss_pred             HHHHHHHHHHHHhcC--CCCcEEEECccCCHHH---HHHcCCeEEECCH
Confidence              2456778888754  3577765444434332   2367887775433

>3o63_A Probable thiamine-phosphate pyrophosphorylase; thiamin biosynthesis, TIM barrel, transferase; 2.35A {Mycobacterium tuberculosis}

Probab=90.77  E-value=2  Score=31.04  Aligned_cols=71  Identities=14%  Similarity=0.243  Sum_probs=49.9

Q ss_pred             EEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCC-------CCHHHHHHHHHhccCCCCCcEEEEeCCCCh
Q 042079           48 TTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPG-------MTGYELLKKIKESSVMKEVPVVVVSSENIP  120 (153)
Q Consensus        48 ~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~-------~~g~~~~~~lr~~~~~~~~pii~~t~~~~~  120 (153)
                      .++.+..|+.....               ..+|+|.+.-..|.       .-|++.++++++.. ..++|++.+.+- +.
T Consensus       140 ~S~ht~~Ea~~A~~---------------~GaDyI~vgpvf~T~tK~~~~~~gl~~l~~~~~~~-~~~iPvvAiGGI-~~  202 (243)
T 3o63_A          140 RSTHDPDQVAAAAA---------------GDADYFCVGPCWPTPTKPGRAAPGLGLVRVAAELG-GDDKPWFAIGGI-NA  202 (243)
T ss_dssp             EEECSHHHHHHHHH---------------SSCSEEEECCSSCCCC-----CCCHHHHHHHHTC----CCCEEEESSC-CT
T ss_pred             EeCCCHHHHHHHhh---------------CCCCEEEEcCccCCCCCCCcchhhHHHHHHHHHhc-cCCCCEEEecCC-CH
Confidence            36788888766542               35899998764443       23688888887631 137899988776 67


Q ss_pred             hhHHHHHHhcCcccc
Q 042079          121 TRINECLEEGAQMFM  135 (153)
Q Consensus       121 ~~~~~a~~~ga~~~l  135 (153)
                      +.+.++++.|++.+.
T Consensus       203 ~ni~~~~~aGa~gva  217 (243)
T 3o63_A          203 QRLPAVLDAGARRIV  217 (243)
T ss_dssp             TTHHHHHHTTCCCEE
T ss_pred             HHHHHHHHcCCCEEE
Confidence            778899999998864

>2htm_A Thiazole biosynthesis protein THIG; thiamin biosynthesis, THIG, thermus thermophilus HB8, structural genomics, NPPSFA; 2.30A {Thermus thermophilus}

Probab=90.58  E-value=0.75  Score=33.82  Aligned_cols=79  Identities=19%  Similarity=0.196  Sum_probs=51.1

Q ss_pred             HHhcCcEEE--EecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCC-----HHHHHHHHHhccCCCC-CcE
Q 042079           40 LKNSACKVT--TAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMT-----GYELLKKIKESSVMKE-VPV  111 (153)
Q Consensus        40 l~~~~~~v~--~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~-----g~~~~~~lr~~~~~~~-~pi  111 (153)
                      |.+.||.+.  +..+...+-.+..               -.+++| +.+..|-..     ..++++.+++..  .+ +||
T Consensus       120 L~k~Gf~Vlpy~~~D~~~ak~l~~---------------~G~~aV-mPlg~pIGsG~Gi~~~~~L~~i~~~~--~~~vPV  181 (268)
T 2htm_A          120 LIEEDFLVLPYMGPDLVLAKRLAA---------------LGTATV-MPLAAPIGSGWGVRTRALLELFAREK--ASLPPV  181 (268)
T ss_dssp             HHHTTCEECCEECSCHHHHHHHHH---------------HTCSCB-EEBSSSTTTCCCSTTHHHHHHHHHTT--TTSSCB
T ss_pred             HHHCCCEEeeccCCCHHHHHHHHh---------------cCCCEE-EecCccCcCCcccCCHHHHHHHHHhc--CCCCeE
Confidence            445688755  4456654433321               235666 565444222     356788888732  36 899


Q ss_pred             EEEeCCCChhhHHHHHHhcCccccc
Q 042079          112 VVVSSENIPTRINECLEEGAQMFML  136 (153)
Q Consensus       112 i~~t~~~~~~~~~~a~~~ga~~~l~  136 (153)
                      |.=..-.+++++..+++.|++..+.
T Consensus       182 I~~GGI~tpsDAa~AmeLGAdgVlV  206 (268)
T 2htm_A          182 VVDAGLGLPSHAAEVMELGLDAVLV  206 (268)
T ss_dssp             EEESCCCSHHHHHHHHHTTCCEEEE
T ss_pred             EEeCCCCCHHHHHHHHHcCCCEEEE
Confidence            9877778899999999999999753

>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=90.10  E-value=3.1  Score=30.45  Aligned_cols=108  Identities=10%  Similarity=0.042  Sum_probs=66.6

Q ss_pred             CeEEEE----eCCHHHHHHHHHH--------HHhc-CcEEEEe---cCHHHHHHHhchhhhHHhhhhcccCCCcccEEEE
Q 042079           21 PHVLAV----DDSIVDRKIVENL--------LKNS-ACKVTTA---ENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVIT   84 (153)
Q Consensus        21 ~~iLii----dd~~~~~~~l~~~--------l~~~-~~~v~~~---~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~   84 (153)
                      .+|++.    |-|..=.+.+..+        |+.. ||+|...   -..++.++...              ..++|+|.+
T Consensus       121 ~~Vvlatv~gD~HdiG~~iv~~~k~~~~~~~L~~~~G~eVi~LG~~vp~e~iv~aa~--------------e~~~d~Vgl  186 (262)
T 1xrs_B          121 IVVVGASTGTDAHTVGIDAIMNMKGYAGHYGLERYEMIDAYNLGSQVANEDFIKKAV--------------ELEADVLLV  186 (262)
T ss_dssp             EEEEEEEBTTCCCCHHHHHHHSTTCBTTBCCGGGCTTEEEEECCSSBCHHHHHHHHH--------------HTTCSEEEE
T ss_pred             CEEEEEeCCCCCchHHHHHHhhhhcccchHHHHhcCCcEEEECCCCCCHHHHHHHHH--------------HcCCCEEEE
Confidence            455554    5676666777777        8888 9998642   34555555542              357999999


Q ss_pred             eCCCCCC-----CHHHHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHH
Q 042079           85 DYCMPGM-----TGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVK  145 (153)
Q Consensus        85 D~~~~~~-----~g~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~  145 (153)
                      ...+...     .-.++++.|++.....+++++ +.+....  ..-+.+.|++.|..--....++.
T Consensus       187 S~l~t~~~~~~~~~~~~i~~L~~~g~~~~i~vi-vGG~~~~--~~~a~~iGad~~~~da~~~~~~a  249 (262)
T 1xrs_B          187 SQTVTQKNVHIQNMTHLIELLEAEGLRDRFVLL-CGGPRIN--NEIAKELGYDAGFGPGRFADDVA  249 (262)
T ss_dssp             ECCCCTTSHHHHHHHHHHHHHHHTTCGGGSEEE-EECTTCC--HHHHHTTTCSEEECTTCCHHHHH
T ss_pred             EeecCCccchHHHHHHHHHHHHhcCCCCCCEEE-EECCcCC--HHHHHHcCCeEEECCchHHHHHH
Confidence            9888762     233466777765432236654 4443322  23366889998876555555543

>2ekc_A AQ_1548, tryptophan synthase alpha chain; structural genomics, lyase, NPPSFA, national project on PROT structural and functional analyses; 2.00A {Aquifex aeolicus}

Probab=89.74  E-value=1.8  Score=31.54  Aligned_cols=72  Identities=14%  Similarity=0.270  Sum_probs=48.5

Q ss_pred             CcccEEEEeCCCCC--CC--------------------HHHHHHHHHhccCCCCCcEEEEeCCCC------hhhHHHHHH
Q 042079           77 TKVNLVITDYCMPG--MT--------------------GYELLKKIKESSVMKEVPVVVVSSENI------PTRINECLE  128 (153)
Q Consensus        77 ~~~dlii~D~~~~~--~~--------------------g~~~~~~lr~~~~~~~~pii~~t~~~~------~~~~~~a~~  128 (153)
                      ...|+|.+++-..+  .+                    .+++++.+|+..  +.+|+++++..+.      ......+.+
T Consensus        43 ~G~D~IElG~P~sdP~adgp~i~~a~~~al~~G~~~~~~~~~v~~ir~~~--~~~Pi~~m~y~n~v~~~g~~~f~~~~~~  120 (262)
T 2ekc_A           43 NGTDILEIGFPFSDPVADGPTIQVAHEVALKNGIRFEDVLELSETLRKEF--PDIPFLLMTYYNPIFRIGLEKFCRLSRE  120 (262)
T ss_dssp             TTCSEEEEECCCSCCTTSCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC--TTSCEEEECCHHHHHHHCHHHHHHHHHH
T ss_pred             cCCCEEEECCCCCCcccccHHHHHHHHHHHHcCCCHHHHHHHHHHHHhhc--CCCCEEEEecCcHHHHhhHHHHHHHHHH
Confidence            35899998874432  22                    345677787642  3789998753321      355577889


Q ss_pred             hcCcccccCCCChhHHHHHHhh
Q 042079          129 EGAQMFMLKPLKPSDVKKLTGH  150 (153)
Q Consensus       129 ~ga~~~l~KP~~~~~l~~~~~~  150 (153)
                      .|++.++.-.+..+++.+....
T Consensus       121 aG~dgvii~dl~~ee~~~~~~~  142 (262)
T 2ekc_A          121 KGIDGFIVPDLPPEEAEELKAV  142 (262)
T ss_dssp             TTCCEEECTTCCHHHHHHHHHH
T ss_pred             cCCCEEEECCCCHHHHHHHHHH
Confidence            9999999888888877665543

>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=4.8  Score=34.01  Aligned_cols=113  Identities=13%  Similarity=0.087  Sum_probs=72.4

Q ss_pred             CCeEEEE----eCCHHHHHHHHHHHHhcCcEEEEec---CHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCC-
Q 042079           20 PPHVLAV----DDSIVDRKIVENLLKNSACKVTTAE---NGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGM-   91 (153)
Q Consensus        20 ~~~iLii----dd~~~~~~~l~~~l~~~~~~v~~~~---~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~-   91 (153)
                      .++|++.    |.|..-.+.+..+|+..||+|....   +.++.++...              ...+|+|.+...+... 
T Consensus       604 r~kVvlatvg~D~HdiG~~iVa~~l~~~GfeVi~lG~~v~~eeiv~aA~--------------e~~adiVglSsl~~~~~  669 (762)
T 2xij_A          604 RPRLLVAKMGQDGHDRGAKVIATGFADLGFDVDIGPLFQTPREVAQQAV--------------DADVHAVGVSTLAAGHK  669 (762)
T ss_dssp             CCEEEEECCSSCCCCHHHHHHHHHHHHTTCEEEECCTTCCHHHHHHHHH--------------HTTCSEEEEEECSSCHH
T ss_pred             CCEEEEEecCcchhhHHHHHHHHHHHhCCeEEeeCCCCCCHHHHHHHHH--------------HcCCCEEEEeeecHHHH
Confidence            4566665    3466667788889999999987543   4566666552              3568999887766542 


Q ss_pred             -CHHHHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHH
Q 042079           92 -TGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLT  148 (153)
Q Consensus        92 -~g~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~  148 (153)
                       ...++++.|++... ..++| ++.+-........+.+.|++.|+..=-+..+..+.+
T Consensus       670 ~~~~~vi~~Lr~~G~-~dv~V-ivGG~~P~~d~~~l~~~GaD~~f~pgtd~~e~~~~i  725 (762)
T 2xij_A          670 TLVPELIKELNSLGR-PDILV-MCGGVIPPQDYEFLFEVGVSNVFGPGTRIPKAAVQV  725 (762)
T ss_dssp             HHHHHHHHHHHHTTC-TTSEE-EEEESCCGGGHHHHHHHTCCEEECTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCC-CCCEE-EEeCCCCcccHHHHHhCCCCEEeCCCCCHHHHHHHH
Confidence             35667788887653 34444 344322233455678999999987444655555433

>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=89.51  E-value=4.9  Score=29.47  Aligned_cols=88  Identities=8%  Similarity=-0.036  Sum_probs=56.8

Q ss_pred             HHHHHHHHHhcCcEEE-EecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCC-C-CCHHHHHHHHHhccCCCCC
Q 042079           33 RKIVENLLKNSACKVT-TAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMP-G-MTGYELLKKIKESSVMKEV  109 (153)
Q Consensus        33 ~~~l~~~l~~~~~~v~-~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~-~-~~g~~~~~~lr~~~~~~~~  109 (153)
                      ...+....+..|..+. .+++..++...+.               ..+|+|-+.-... . ..+++.+++|.+.. ...+
T Consensus       151 l~~l~~~a~~lGl~~lvev~t~ee~~~A~~---------------~Gad~IGv~~r~l~~~~~dl~~~~~l~~~v-~~~~  214 (272)
T 3qja_A          151 LVSMLDRTESLGMTALVEVHTEQEADRALK---------------AGAKVIGVNARDLMTLDVDRDCFARIAPGL-PSSV  214 (272)
T ss_dssp             HHHHHHHHHHTTCEEEEEESSHHHHHHHHH---------------HTCSEEEEESBCTTTCCBCTTHHHHHGGGS-CTTS
T ss_pred             HHHHHHHHHHCCCcEEEEcCCHHHHHHHHH---------------CCCCEEEECCCcccccccCHHHHHHHHHhC-cccC
Confidence            3344455556787644 5778877655441               2478888763221 1 12356667776542 1268


Q ss_pred             cEEEEeCCCChhhHHHHHHhcCccccc
Q 042079          110 PVVVVSSENIPTRINECLEEGAQMFML  136 (153)
Q Consensus       110 pii~~t~~~~~~~~~~a~~~ga~~~l~  136 (153)
                      |+|..++-.+.+.+.++.+.|++.++.
T Consensus       215 pvVaegGI~t~edv~~l~~~GadgvlV  241 (272)
T 3qja_A          215 IRIAESGVRGTADLLAYAGAGADAVLV  241 (272)
T ss_dssp             EEEEESCCCSHHHHHHHHHTTCSEEEE
T ss_pred             EEEEECCCCCHHHHHHHHHcCCCEEEE
Confidence            888888877899999999999999865

>3qz6_A HPCH/HPAI aldolase; structural genomics, PSI-biology, protein structure initiati midwest center for structural genomics, MCSG; 2.00A {Desulfitobacterium hafniense} SCOP: c.1.12.0

Probab=89.16  E-value=3.2  Score=30.21  Aligned_cols=74  Identities=15%  Similarity=0.123  Sum_probs=52.1

Q ss_pred             CcccEEEEeCCCCCCCHHHHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCccc-ccCCCChhHHHHHHhhh
Q 042079           77 TKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMF-MLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        77 ~~~dlii~D~~~~~~~g~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~-l~KP~~~~~l~~~~~~~  151 (153)
                      ..+|.|++|+.-...+.-.+...++.... ...++++=.+..+...+..+++.|++.. ++|--+.++++++...+
T Consensus        36 ~g~D~vilDlEhav~~~~k~~~~l~a~~~-~~~~~~VRVn~~~~~di~~~ld~G~~gI~lP~v~saed~~~~~~~~  110 (261)
T 3qz6_A           36 AGLDYFIVDCEHAAYTFREINHLVSVAKN-AGVSVLVRIPQVDRAHVQRLLDIGAEGFMIPGVQSAETMRETVRLA  110 (261)
T ss_dssp             TTCSEEEEESSSSCCCHHHHHHHHHHHHH-HTCEEEEECSSCCHHHHHHHHHHTCCEEEETTCCSHHHHHHHHHHH
T ss_pred             CCcCEEEEeccCCCCCHHHHHHHHHHHhh-cCCeEEEEeCCCCHHHHHHHHhcCCCEEEECCcCCHHHHHHHHHHh
Confidence            46999999998887776666666553221 2345565666667778899999999875 55566788888776554

>2v5j_A 2,4-dihydroxyhept-2-ENE-1,7-dioic acid aldolase; lyase, class II aldolase, homoprotocatechuate, aromatic DEGR aromatic hydrocarbons catabolism; 1.60A {Escherichia coli} PDB: 2v5k_A

Probab=88.90  E-value=5.6  Score=29.37  Aligned_cols=74  Identities=15%  Similarity=0.132  Sum_probs=52.5

Q ss_pred             CcccEEEEeCCCCCCCHHHHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCccc-ccCCCChhHHHHHHhhh
Q 042079           77 TKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMF-MLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        77 ~~~dlii~D~~~~~~~g~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~-l~KP~~~~~l~~~~~~~  151 (153)
                      ..+|.+++|+.-...+--.+...++.... ...++++=+...+...+..+++.|++.. +.|--+.++++++...+
T Consensus        59 ~GaD~v~lDlEh~~~~~~~~~~~l~a~~~-~~~~~~VRv~~~d~~di~~~ld~ga~~ImlP~V~saeea~~~~~~~  133 (287)
T 2v5j_A           59 AGFDWLLIDGEHAPNNVQTVLTQLQAIAP-YPSQPVVRPSWNDPVQIKQLLDVGTQTLLVPMVQNADEAREAVRAT  133 (287)
T ss_dssp             SCCSEEEEESSSSSCCHHHHHHHHHHHTT-SSSEEEEECSSSCHHHHHHHHHTTCCEEEESCCCSHHHHHHHHHHT
T ss_pred             CCCCEEEEeCCCccchHHHHHHHHHHHHh-cCCCEEEEECCCCHHHHHHHHhCCCCEEEeCCCCCHHHHHHHHHHh
Confidence            46999999997766665555555554322 2567777777777888899999999875 55556788888776543

>1geq_A Tryptophan synthase alpha-subunit; hyperthermophIle, pyrococ furiosus, X-RAY analysis, stability, calorimetry, lyase; 2.00A {Pyrococcus furiosus} SCOP: c.1.2.4 PDB: 1wdw_A* 2dzu_A 2dzp_A 2e09_A 2dzw_A 2dzs_A 2dzv_A 2dzt_A 2dzx_A

Probab=88.47  E-value=1.4  Score=31.46  Aligned_cols=52  Identities=19%  Similarity=0.311  Sum_probs=35.9

Q ss_pred             HHHHHHHHhccCCCCCcEEEEeCCCC------hhhHHHHHHhcCcccccCCCChhHHHHHH
Q 042079           94 YELLKKIKESSVMKEVPVVVVSSENI------PTRINECLEEGAQMFMLKPLKPSDVKKLT  148 (153)
Q Consensus        94 ~~~~~~lr~~~~~~~~pii~~t~~~~------~~~~~~a~~~ga~~~l~KP~~~~~l~~~~  148 (153)
                      +++++.+|+..   ++|+.+++..+.      .+....+.+.|++.++.-.....+..+++
T Consensus        69 ~~~i~~i~~~~---~~pv~~~~~~~~~~~~~~~~~~~~~~~~Gad~v~~~~~~~~~~~~~~  126 (248)
T 1geq_A           69 FWIVKEFRRHS---STPIVLMTYYNPIYRAGVRNFLAEAKASGVDGILVVDLPVFHAKEFT  126 (248)
T ss_dssp             HHHHHHHHTTC---CCCEEEEECHHHHHHHCHHHHHHHHHHHTCCEEEETTCCGGGHHHHH
T ss_pred             HHHHHHHHhhC---CCCEEEEeccchhhhcCHHHHHHHHHHCCCCEEEECCCChhhHHHHH
Confidence            67788888642   578887774222      46777889999999887666555555443

>3vnd_A TSA, tryptophan synthase alpha chain; psychrophilic enzyme, cold adaptation; HET: PE8; 2.60A {Shewanella frigidimarina}

Probab=88.29  E-value=0.59  Score=34.40  Aligned_cols=55  Identities=7%  Similarity=0.295  Sum_probs=39.2

Q ss_pred             HHHHHHHHhccCCCCCcEEEEeCCCC------hhhHHHHHHhcCcccccCCCChhHHHHHHhh
Q 042079           94 YELLKKIKESSVMKEVPVVVVSSENI------PTRINECLEEGAQMFMLKPLKPSDVKKLTGH  150 (153)
Q Consensus        94 ~~~~~~lr~~~~~~~~pii~~t~~~~------~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~  150 (153)
                      +++++.+|+..  .++|+++++-.+.      +....++.+.|++.++.-.+.+++..+....
T Consensus        83 ~~~v~~ir~~~--~~~Pivlm~Y~npv~~~g~e~f~~~~~~aGvdgvii~Dlp~ee~~~~~~~  143 (267)
T 3vnd_A           83 FDIITKVRAQH--PDMPIGLLLYANLVFANGIDEFYTKAQAAGVDSVLIADVPVEESAPFSKA  143 (267)
T ss_dssp             HHHHHHHHHHC--TTCCEEEEECHHHHHHHCHHHHHHHHHHHTCCEEEETTSCGGGCHHHHHH
T ss_pred             HHHHHHHHhcC--CCCCEEEEecCcHHHHhhHHHHHHHHHHcCCCEEEeCCCCHhhHHHHHHH
Confidence            56677777642  3689998875322      5567888999999998888887776655443

>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=87.90  E-value=5.4  Score=33.52  Aligned_cols=110  Identities=13%  Similarity=0.089  Sum_probs=71.6

Q ss_pred             CCeEEEE----eCCHHHHHHHHHHHHhcCcEEEEec---CHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCC-
Q 042079           20 PPHVLAV----DDSIVDRKIVENLLKNSACKVTTAE---NGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGM-   91 (153)
Q Consensus        20 ~~~iLii----dd~~~~~~~l~~~l~~~~~~v~~~~---~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~-   91 (153)
                      .++|++.    |.|..-.+.+..+|+..||+|....   +.++.++...              ...+|+|.+...+... 
T Consensus       596 r~kVvlatvg~D~HdiG~~iVa~~l~~~GfeVi~lG~~v~~eeiv~aA~--------------e~~adiVglSsl~~~~~  661 (727)
T 1req_A          596 RPRILLAKMGQDGHDRGQKVIATAYADLGFDVDVGPLFQTPEETARQAV--------------EADVHVVGVSSLAGGHL  661 (727)
T ss_dssp             CCEEEEECBTTCCCCHHHHHHHHHHHHHTCEEEECCTTBCHHHHHHHHH--------------HTTCSEEEEEECSSCHH
T ss_pred             CCEEEEEeCCcchhHHHHHHHHHHHHhCCeEEEeCCCCCCHHHHHHHHH--------------HcCCCEEEEeeecHhHH
Confidence            4566665    4566667888889999999987643   4566666552              3568999887766542 


Q ss_pred             -CHHHHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHH
Q 042079           92 -TGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVK  145 (153)
Q Consensus        92 -~g~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~  145 (153)
                       ...++++.|++... ..++| ++.+-........+.+.|++.|+..=.+..++.
T Consensus       662 ~~~~~vi~~L~~~G~-~~i~V-ivGG~~p~~d~~~l~~~GaD~~f~~gt~~~e~a  714 (727)
T 1req_A          662 TLVPALRKELDKLGR-PDILI-TVGGVIPEQDFDELRKDGAVEIYTPGTVIPESA  714 (727)
T ss_dssp             HHHHHHHHHHHHTTC-TTSEE-EEEESCCGGGHHHHHHTTEEEEECTTCCHHHHH
T ss_pred             HHHHHHHHHHHhcCC-CCCEE-EEcCCCccccHHHHHhCCCCEEEcCCccHHHHH
Confidence             35667788887653 34444 444422333455678999999986545555543

>3nav_A Tryptophan synthase alpha chain; alpha subunit, structural genomics, CSG center for structural genomics of infectious diseases; 2.10A {Vibrio cholerae o1 biovar el tor} SCOP: c.1.2.4

Probab=86.48  E-value=1.4  Score=32.43  Aligned_cols=54  Identities=15%  Similarity=0.401  Sum_probs=38.7

Q ss_pred             HHHHHHHHhccCCCCCcEEEEeCC------CChhhHHHHHHhcCcccccCCCChhHHHHHHh
Q 042079           94 YELLKKIKESSVMKEVPVVVVSSE------NIPTRINECLEEGAQMFMLKPLKPSDVKKLTG  149 (153)
Q Consensus        94 ~~~~~~lr~~~~~~~~pii~~t~~------~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~  149 (153)
                      +++++++|+..  .++|+++++-.      .......++.+.|++.++.-.+.+++..+...
T Consensus        85 ~~~v~~~r~~~--~~~Pivlm~Y~n~v~~~g~~~f~~~~~~aGvdGvIipDlp~ee~~~~~~  144 (271)
T 3nav_A           85 FELIAQIRARN--PETPIGLLMYANLVYARGIDDFYQRCQKAGVDSVLIADVPTNESQPFVA  144 (271)
T ss_dssp             HHHHHHHHHHC--TTSCEEEEECHHHHHHTCHHHHHHHHHHHTCCEEEETTSCGGGCHHHHH
T ss_pred             HHHHHHHHhcC--CCCCEEEEecCcHHHHHhHHHHHHHHHHCCCCEEEECCCCHHHHHHHHH
Confidence            56777777643  47899998743      23556788899999999888787777655443

>2vws_A YFAU, 2-keto-3-deoxy sugar aldolase; lyase, escherichia coli K-12 protein YFAU, 2-keto-3-deoxy SU aldolase, degradation of homoprotocatechuate; 1.39A {Escherichia coli} PDB: 2vwt_A

Probab=86.05  E-value=8  Score=28.09  Aligned_cols=74  Identities=14%  Similarity=0.120  Sum_probs=51.8

Q ss_pred             CcccEEEEeCCCCCCCHHHHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCccc-ccCCCChhHHHHHHhhh
Q 042079           77 TKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMF-MLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        77 ~~~dlii~D~~~~~~~g~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~-l~KP~~~~~l~~~~~~~  151 (153)
                      ..+|.+++|+.-...+.-.+...++.... ...++++=+...++..+..+++.|++.. +.|=-+.++++++...+
T Consensus        38 ~GaD~v~lDlE~~~~~~~~~~~~~~a~~~-~~~~~~VRv~~~~~~~i~~~l~~g~~~I~~P~V~s~ee~~~~~~~~  112 (267)
T 2vws_A           38 SGYDWLLIDGEHAPNTIQDLYHQLQAVAP-YASQPVIRPVEGSKPLIKQVLDIGAQTLLIPMVDTAEQARQVVSAT  112 (267)
T ss_dssp             TCCSEEEEETTTSCCCHHHHHHHHHHHTT-SSSEEEEECSSCCHHHHHHHHHTTCCEEEECCCCSHHHHHHHHHHT
T ss_pred             CCCCEEEEcCCCCCCCHHHHHHHHHHHHh-CCCcEEEEeCCCCHHHHHHHHHhCCCEEEeCCCCCHHHHHHHHHHH
Confidence            46999999997766665555555554222 2456777777777888889999999874 55556788888776544

>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=84.90  E-value=8.3  Score=32.15  Aligned_cols=109  Identities=11%  Similarity=0.101  Sum_probs=67.2

Q ss_pred             CCeEEEE----eCCHHHHHHH----HHHHHhcCcEEEEec---CHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCC
Q 042079           20 PPHVLAV----DDSIVDRKIV----ENLLKNSACKVTTAE---NGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCM   88 (153)
Q Consensus        20 ~~~iLii----dd~~~~~~~l----~~~l~~~~~~v~~~~---~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~   88 (153)
                      ..+|++.    |-|..=.+.+    ..+|+..||+|....   +.++.++.+.              ...+|+|.+...+
T Consensus       602 kGKVVIATVgGD~HDIGKklVaNIVa~~LE~aGFEVIDLGvdVPpEeIVeAA~--------------EedADVVGLSsLL  667 (763)
T 3kp1_A          602 PLKIVAATVGEDEHSVGLREVIDIKHGGIEKYGVEVHYLGTSVPVEKLVDAAI--------------ELKADAILASTII  667 (763)
T ss_dssp             CCEEEEEEBTTCCCCHHHHHTTSTTTTCGGGGTCEEEECCSSBCHHHHHHHHH--------------HTTCSEEEEECCC
T ss_pred             CCEEEEEeCCCChhhhhhHHHHHHHHHHHHhCCCEEEECCCCCCHHHHHHHHH--------------HcCCCEEEEeccc
Confidence            3567776    4455444333    467888999987433   5566666552              3579999999888


Q ss_pred             CC----CC-HHHHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHH
Q 042079           89 PG----MT-GYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVK  145 (153)
Q Consensus        89 ~~----~~-g~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~  145 (153)
                      ..    +. --++++.|++......++|++=....+.+   -+.+.|++.|........++.
T Consensus       668 Tt~dihL~~MkevIelLrE~GlrDkIkVIVGGa~~tqd---~AkeIGADa~f~DATeAVeVA  726 (763)
T 3kp1_A          668 SHDDIHYKNMKRIHELAVEKGIRDKIMIGCGGTQVTPE---VAVKQGVDAGFGRGSKGIHVA  726 (763)
T ss_dssp             CGGGHHHHHHHHHHHHHHHTTCTTTSEEEEECTTCCHH---HHHTTTCSEEECTTCCHHHHH
T ss_pred             cCchhhHHHHHHHHHHHHhcCCCCCCEEEEECCCCCHH---HHHHcCCcEEECCcchHHHHH
Confidence            76    22 34567778876542235555333233333   345899999887666555553

>1yad_A Regulatory protein TENI; TIM barrel, transcription; 2.10A {Bacillus subtilis} PDB: 3qh2_A*

Probab=84.17  E-value=8.5  Score=26.76  Aligned_cols=67  Identities=19%  Similarity=0.313  Sum_probs=45.9

Q ss_pred             EecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCC-------CCHHHHHHHHHhccCCCCCcEEEEeCCCChh
Q 042079           49 TAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPG-------MTGYELLKKIKESSVMKEVPVVVVSSENIPT  121 (153)
Q Consensus        49 ~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~-------~~g~~~~~~lr~~~~~~~~pii~~t~~~~~~  121 (153)
                      .+.+..++.....               ...|.|+++...+.       ..+++.++.+++..   ++|+++..+- +.+
T Consensus       116 sv~t~~~~~~a~~---------------~gaD~i~~~~~f~~~~~~g~~~~~~~~l~~~~~~~---~~pvia~GGI-~~~  176 (221)
T 1yad_A          116 SVHSLEEAVQAEK---------------EDADYVLFGHVFETDCKKGLEGRGVSLLSDIKQRI---SIPVIAIGGM-TPD  176 (221)
T ss_dssp             EECSHHHHHHHHH---------------TTCSEEEEECCC----------CHHHHHHHHHHHC---CSCEEEESSC-CGG
T ss_pred             EcCCHHHHHHHHh---------------CCCCEEEECCccccCCCCCCCCCCHHHHHHHHHhC---CCCEEEECCC-CHH
Confidence            5667777655441               34799998764332       23678888887642   6888877666 788


Q ss_pred             hHHHHHHhcCccc
Q 042079          122 RINECLEEGAQMF  134 (153)
Q Consensus       122 ~~~~a~~~ga~~~  134 (153)
                      .+.++++.|++.+
T Consensus       177 nv~~~~~~Ga~gv  189 (221)
T 1yad_A          177 RLRDVKQAGADGI  189 (221)
T ss_dssp             GHHHHHHTTCSEE
T ss_pred             HHHHHHHcCCCEE
Confidence            8999999999865

>3rht_A (gatase1)-like protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, unknown function; HET: MSE; 1.83A {Planctomyces limnophilus}

Probab=83.65  E-value=0.72  Score=33.78  Aligned_cols=32  Identities=13%  Similarity=0.120  Sum_probs=25.4

Q ss_pred             CeEEEEeCC--HHHHHHHHHHHHhcCcEEEEecC
Q 042079           21 PHVLAVDDS--IVDRKIVENLLKNSACKVTTAEN   52 (153)
Q Consensus        21 ~~iLiidd~--~~~~~~l~~~l~~~~~~v~~~~~   52 (153)
                      +++|||+++  +.-...+...|+..|+.|.....
T Consensus         5 ~~vLiV~g~~~~~~a~~l~~aL~~~g~~V~~i~~   38 (259)
T 3rht_A            5 TRVLYCGDTSLETAAGYLAGLMTSWQWEFDYIPS   38 (259)
T ss_dssp             -CEEEEESSCTTTTHHHHHHHHHHTTCCCEEECT
T ss_pred             ceEEEECCCCchhHHHHHHHHHHhCCceEEEecc
Confidence            579999988  55677888899999998887664

>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=83.37  E-value=3.1  Score=31.66  Aligned_cols=58  Identities=10%  Similarity=0.084  Sum_probs=47.0

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhc---CcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCC
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNS---ACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPG   90 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~---~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~   90 (153)
                      ...++.|+|.++...+.+..++.+.   .+.+..+++.+...+...              ++++|++++|-.+..
T Consensus        20 ~~i~l~i~d~d~~Y~~~l~~y~~~~~~~~~~v~~ft~~e~~~~~~~--------------~~~~dilli~e~~~~   80 (373)
T 3fkq_A           20 MKIKVALLDKDKEYLDRLTGVFNTKYADKLEVYSFTDEKNAIESVK--------------EYRIDVLIAEEDFNI   80 (373)
T ss_dssp             CCEEEEEECSCHHHHHHHHHHHHHHTTTTEEEEEESCHHHHHHHHH--------------HHTCSEEEEETTCCC
T ss_pred             ceEEEEEEeCCHHHHHHHHHHHhhccCCceEEEEECCHHHHHHHHh--------------cCCCCEEEEcchhhh
Confidence            4578999999999999999998753   578999999998888763              246899999876644

>1qop_A Tryptophan synthase alpha chain; lyase, carbon-oxygen lyase, tryptophan biosynthesis, pyridoxal phosphate; HET: IPL PLP; 1.4A {Salmonella typhimurium} SCOP: c.1.2.4 PDB: 1k8x_A* 1wbj_A* 2clk_A* 2j9z_A* 3cep_A* 1k8y_A* 1a5s_A* 1a50_A* 1c29_A* 1c8v_A* 1c9d_A* 1bks_A* 1cx9_A* 1fuy_A* 1cw2_A* 1k7e_A* 1k7f_A* 1k7x_A* 1k3u_A* 1k8z_A* ...

Probab=82.89  E-value=1.7  Score=31.73  Aligned_cols=72  Identities=13%  Similarity=0.210  Sum_probs=47.5

Q ss_pred             CcccEEEEeCCCC--CCC--------------------HHHHHHHHHhccCCCCCcEEEEeCCC------ChhhHHHHHH
Q 042079           77 TKVNLVITDYCMP--GMT--------------------GYELLKKIKESSVMKEVPVVVVSSEN------IPTRINECLE  128 (153)
Q Consensus        77 ~~~dlii~D~~~~--~~~--------------------g~~~~~~lr~~~~~~~~pii~~t~~~------~~~~~~~a~~  128 (153)
                      ...|.|-+++-..  -++                    ++++++.+|+..  .++|+++++...      .......+.+
T Consensus        43 ~GaD~ieig~P~sdp~~DG~~i~~a~~~al~~G~~~~~~~~~v~~ir~~~--~~~Pv~lm~y~n~v~~~g~~~~~~~~~~  120 (268)
T 1qop_A           43 AGADALELGVPFSDPLADGPTIQNANLRAFAAGVTPAQCFEMLAIIREKH--PTIPIGLLMYANLVFNNGIDAFYARCEQ  120 (268)
T ss_dssp             TTCSSEEEECCCSCCTTCCHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC--SSSCEEEEECHHHHHTTCHHHHHHHHHH
T ss_pred             CCCCEEEECCCCCCccCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHhcC--CCCCEEEEEcccHHHHhhHHHHHHHHHH
Confidence            3478888887442  222                    346678888752  367888775321      1466777899


Q ss_pred             hcCcccccCCCChhHHHHHHhh
Q 042079          129 EGAQMFMLKPLKPSDVKKLTGH  150 (153)
Q Consensus       129 ~ga~~~l~KP~~~~~l~~~~~~  150 (153)
                      .|++.++.-....+++.+.+..
T Consensus       121 aGadgii~~d~~~e~~~~~~~~  142 (268)
T 1qop_A          121 VGVDSVLVADVPVEESAPFRQA  142 (268)
T ss_dssp             HTCCEEEETTCCGGGCHHHHHH
T ss_pred             cCCCEEEEcCCCHHHHHHHHHH
Confidence            9999988877777666555443

>1ujp_A Tryptophan synthase alpha chain; riken structural genomics/P initiative, RSGI, structural genomics, lyase; HET: CIT; 1.34A {Thermus thermophilus} SCOP: c.1.2.4 PDB: 1wxj_A*

Probab=82.00  E-value=2.7  Score=30.79  Aligned_cols=68  Identities=18%  Similarity=0.227  Sum_probs=45.8

Q ss_pred             ccEEEEeCCCCC--CC--------------------HHHHHHHHHhccCCCCCcEEEEeCCC------ChhhHHHHHHhc
Q 042079           79 VNLVITDYCMPG--MT--------------------GYELLKKIKESSVMKEVPVVVVSSEN------IPTRINECLEEG  130 (153)
Q Consensus        79 ~dlii~D~~~~~--~~--------------------g~~~~~~lr~~~~~~~~pii~~t~~~------~~~~~~~a~~~g  130 (153)
                      .|+|.+++-..+  .+                    .++.++.+|+.   .++|+++++..+      .......+.+.|
T Consensus        43 aD~IElG~PfsdP~adGp~Iq~a~~~Al~~G~~~~~~~~~v~~ir~~---~~~Pii~m~y~n~v~~~g~~~f~~~~~~aG  119 (271)
T 1ujp_A           43 ADLLEIGLPYSDPLGDGPVIQRASELALRKGMSVQGALELVREVRAL---TEKPLFLMTYLNPVLAWGPERFFGLFKQAG  119 (271)
T ss_dssp             CSSEEEECCCCC----CHHHHHHHHHHHHTTCCHHHHHHHHHHHHHH---CCSCEEEECCHHHHHHHCHHHHHHHHHHHT
T ss_pred             CCEEEECCCCCCcccccHHHHHHHHHHHHcCCCHHHHHHHHHHHHhc---CCCCEEEEecCcHHHHhhHHHHHHHHHHcC
Confidence            899999864432  12                    35667788764   368999875322      244566788999


Q ss_pred             CcccccCCCChhHHHHHHh
Q 042079          131 AQMFMLKPLKPSDVKKLTG  149 (153)
Q Consensus       131 a~~~l~KP~~~~~l~~~~~  149 (153)
                      +++++.-.+..++..+...
T Consensus       120 ~dGviv~Dl~~ee~~~~~~  138 (271)
T 1ujp_A          120 ATGVILPDLPPDEDPGLVR  138 (271)
T ss_dssp             CCEEECTTCCGGGCHHHHH
T ss_pred             CCEEEecCCCHHHHHHHHH
Confidence            9999887777776655443

>3bul_A Methionine synthase; transferase, reactivation conformation, cobalamin, intermodular interactions, amino-acid biosynthesis, cobalt; HET: B12; 2.30A {Escherichia coli} SCOP: a.46.1.1 c.23.6.1 d.173.1.1 PDB: 3iv9_A* 3iva_A* 1k7y_A* 1k98_A* 1bmt_A*

Probab=81.59  E-value=11  Score=30.83  Aligned_cols=99  Identities=9%  Similarity=0.154  Sum_probs=63.0

Q ss_pred             CCeEEEE----eCCHHHHHHHHHHHHhcCcEEEEe---cCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCC-
Q 042079           20 PPHVLAV----DDSIVDRKIVENLLKNSACKVTTA---ENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGM-   91 (153)
Q Consensus        20 ~~~iLii----dd~~~~~~~l~~~l~~~~~~v~~~---~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~-   91 (153)
                      ..+|++.    |-|..-...+..+|+..||+|...   -...+.+..+.              ...+|+|.+...+... 
T Consensus        98 ~~kVLlatv~GD~HdiG~~iva~~L~~~G~eVi~LG~~vP~e~iv~aa~--------------~~~~diVgLS~l~t~~~  163 (579)
T 3bul_A           98 NGKMVIATVKGDVHDIGKNIVGVVLQCNNYEIVDLGVMVPAEKILRTAK--------------EVNADLIGLSGLITPSL  163 (579)
T ss_dssp             SCEEEEEEBTTCCCCHHHHHHHHHHHTTTCEEEECCSSBCHHHHHHHHH--------------HHTCSEEEEECCSTHHH
T ss_pred             CCeEEEEECCCCCchHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHH--------------HcCCCEEEEEecCCCCH
Confidence            4567776    567777888899999999998753   34455555442              2468999998877532 


Q ss_pred             -CHHHHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHh-----cCccccc
Q 042079           92 -TGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEE-----GAQMFML  136 (153)
Q Consensus        92 -~g~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~-----ga~~~l~  136 (153)
                       ...++++.|++..  .++||++-....+....  .-+.     |++.|-.
T Consensus       164 ~~m~~~i~~Lr~~g--~~i~ViVGGa~~~~~~a--~~~i~p~~~GAD~ya~  210 (579)
T 3bul_A          164 DEMVNVAKEMERQG--FTIPLLIGGATTSKAHT--AVKIEQNYSGPTVYVQ  210 (579)
T ss_dssp             HHHHHHHHHHHHTT--CCSCEEEESTTCCHHHH--HHHTGGGCSSCEEECC
T ss_pred             HHHHHHHHHHHHcC--CCCeEEEEccccchhhh--hhhhhhcccCCeEEEC
Confidence             2345677787754  47887654444444432  1133     7877743

>1xi3_A Thiamine phosphate pyrophosphorylase; structural genomics, southeast collaboratory for structural genomics, hyperthermophIle; 1.70A {Pyrococcus furiosus} SCOP: c.1.3.1

Probab=80.94  E-value=6.9  Score=26.86  Aligned_cols=53  Identities=28%  Similarity=0.416  Sum_probs=38.2

Q ss_pred             cccEEEEeCCCCC-------CCHHHHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCccc
Q 042079           78 KVNLVITDYCMPG-------MTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMF  134 (153)
Q Consensus        78 ~~dlii~D~~~~~-------~~g~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~  134 (153)
                      .+|.++++...|.       ..+++.++++++..   ++|+++..+-. .+.+.++.+.|++.+
T Consensus       128 g~d~i~~~~~~~~~~~~~~~~~~~~~l~~l~~~~---~~pvia~GGI~-~~nv~~~~~~Ga~gv  187 (215)
T 1xi3_A          128 GADYLGAGSVFPTKTKEDARVIGLEGLRKIVESV---KIPVVAIGGIN-KDNAREVLKTGVDGI  187 (215)
T ss_dssp             TCSEEEEECSSCC----CCCCCHHHHHHHHHHHC---SSCEEEESSCC-TTTHHHHHTTTCSEE
T ss_pred             CCCEEEEcCCccCCCCCCCCCcCHHHHHHHHHhC---CCCEEEECCcC-HHHHHHHHHcCCCEE
Confidence            4799998753442       34788888887643   67888766554 777888888998876

>3tfw_A Putative O-methyltransferase; PSI-biology, nysgrc, structural genomics, NEW YORK structura genomics research consortium; 1.88A {Klebsiella pneumoniae subsp}

Probab=80.44  E-value=7.8  Score=27.43  Aligned_cols=79  Identities=15%  Similarity=0.192  Sum_probs=49.3

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCcE--EE-EecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSACK--VT-TAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYEL   96 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~~~--v~-~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~   96 (153)
                      ..++..+|-++......+..+...+..  +. ...+..+.+..+.             ....||+|++|...  .+-..+
T Consensus        88 ~~~v~~vD~s~~~~~~a~~~~~~~g~~~~v~~~~~d~~~~l~~~~-------------~~~~fD~V~~d~~~--~~~~~~  152 (248)
T 3tfw_A           88 DGQLLTLEADAHHAQVARENLQLAGVDQRVTLREGPALQSLESLG-------------ECPAFDLIFIDADK--PNNPHY  152 (248)
T ss_dssp             TCEEEEEECCHHHHHHHHHHHHHTTCTTTEEEEESCHHHHHHTCC-------------SCCCCSEEEECSCG--GGHHHH
T ss_pred             CCEEEEEECCHHHHHHHHHHHHHcCCCCcEEEEEcCHHHHHHhcC-------------CCCCeEEEEECCch--HHHHHH
Confidence            578999999999998888888766542  33 4555555444331             12479999998742  233456


Q ss_pred             HHHHHhccCCCCCcEEEEe
Q 042079           97 LKKIKESSVMKEVPVVVVS  115 (153)
Q Consensus        97 ~~~lr~~~~~~~~pii~~t  115 (153)
                      ++.+.+.- .+.. ++++.
T Consensus       153 l~~~~~~L-kpGG-~lv~~  169 (248)
T 3tfw_A          153 LRWALRYS-RPGT-LIIGD  169 (248)
T ss_dssp             HHHHHHTC-CTTC-EEEEE
T ss_pred             HHHHHHhc-CCCe-EEEEe
Confidence            66665432 2333 44443

---

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	153
d1i3ca_	144	c.23.1.1 (A:) Response regulator for cyanobacteria	2e-20
d1zesa1	121	c.23.1.1 (A:3-123) PhoB receiver domain {Escherich	8e-20
d1k68a_	140	c.23.1.1 (A:) Response regulator for cyanobacteria	4e-19
d2r25b1	128	c.23.1.1 (B:1087-1214) Response regulator Sin1 {Ba	1e-18
d1mb3a_	123	c.23.1.1 (A:) Cell division response regulator Div	2e-18
d1k66a_	149	c.23.1.1 (A:) Response regulator for cyanobacteria	3e-18
d1jbea_	128	c.23.1.1 (A:) CheY protein {Escherichia coli [TaxI	4e-18
d1a04a2	138	c.23.1.1 (A:5-142) Nitrate/nitrite response regula	4e-18
d1dcfa_	134	c.23.1.2 (A:) Receiver domain of the ethylene rece	5e-18
d1a2oa1	140	c.23.1.1 (A:1-140) Methylesterase CheB, N-terminal	6e-18
d1dz3a_	123	c.23.1.1 (A:) Sporulation response regulator Spo0A	7e-18
d2b4aa1	118	c.23.1.1 (A:2-119) Hypothetical protein BH3024 {Ba	3e-17
d1peya_	119	c.23.1.1 (A:) Sporulation response regulator Spo0F	3e-17
d1u0sy_	118	c.23.1.1 (Y:) CheY protein {Thermotoga maritima [T	5e-17
d1krwa_	123	c.23.1.1 (A:) NTRC receiver domain {Salmonella typ	7e-16
d1p6qa_	129	c.23.1.1 (A:) CheY protein {Sinorhizobium meliloti	8e-16
d1xhfa1	121	c.23.1.1 (A:2-122) Aerobic respiration control pro	1e-15
d2ayxa1	133	c.23.1.1 (A:817-949) Sensor kinase protein RcsC, C	6e-15
d2a9pa1	117	c.23.1.1 (A:2-118) DNA-binding response regulator	7e-15
d1qkka_	140	c.23.1.1 (A:) Transcriptional regulatory protein D	2e-14
d1s8na_	190	c.23.1.1 (A:) Probable two-component system transc	2e-14
d1zgza1	120	c.23.1.1 (A:2-121) TorCAD operon transcriptional r	3e-14
d1dbwa_	123	c.23.1.1 (A:) Transcriptional regulatory protein F	1e-13
d1yioa2	128	c.23.1.1 (A:3-130) Response regulatory protein Sty	1e-13
d1ys7a2	121	c.23.1.1 (A:7-127) Transcriptional regulatory prot	1e-13
d1w25a1	139	c.23.1.1 (A:2-140) Response regulator PleD, receiv	4e-13
d1qo0d_	189	c.23.1.3 (D:) Positive regulator of the amidase op	2e-12
d1w25a2	153	c.23.1.1 (A:141-293) Response regulator PleD, rece	5e-12
d1zh2a1	119	c.23.1.1 (A:2-120) Transcriptional regulatory prot	6e-12
d2pl1a1	119	c.23.1.1 (A:1-119) PhoP receiver domain {Escherich	2e-11
d1kgsa2	122	c.23.1.1 (A:2-123) PhoB receiver domain {Thermotog	4e-11
d1ny5a1	137	c.23.1.1 (A:1-137) Transcriptional activator sigm5	5e-11
d1mvoa_	121	c.23.1.1 (A:) PhoP receiver domain {Bacillus subti	8e-11
d1p2fa2	120	c.23.1.1 (A:1-120) Response regulator DrrB {Thermo	2e-09

>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 = 2e-20
 Identities = 37/132 (28%), Positives = 66/132 (50%), Gaps = 10/132 (7%)

Query: 17  NPKPPHVLAVDDSIVDRKIVENLLKNS--ACKVTTAENGMRALEFLGLVDEQEQQNNLNS 74
           NP P  +L V+DS  D ++V+ +LK S    ++    +G+ A+ FL       QQ     
Sbjct: 1   NP-PKVILLVEDSKADSRLVQEVLKTSTIDHELIILRDGLAAMAFL-------QQQGEYE 52

Query: 75  NGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMF 134
           N  + NL++ D  +P   G E+L +IK++  +K +PVVV+++ +    +    E     +
Sbjct: 53  NSPRPNLILLDLNLPKKDGREVLAEIKQNPDLKRIPVVVLTTSHNEDDVIASYELHVNCY 112

Query: 135 MLKPLKPSDVKK 146
           + K     D+ K
Sbjct: 113 LTKSRNLKDLFK 124

>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 = 77.3 bits (190), Expect = 8e-20
 Identities = 29/122 (23%), Positives = 60/122 (49%), Gaps = 14/122 (11%)

Query: 23  VLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLV 82
           +L V+D    R++V  +L+ +  +   AE+   A+  L              N    +L+
Sbjct: 3   ILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQL--------------NEPWPDLI 48

Query: 83  ITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPS 142
           + D+ +PG +G + +K +K  S+ +++PVV++++          LE GA  ++ KP  P 
Sbjct: 49  LLDWMLPGGSGIQFIKHLKRESMTRDIPVVMLTARGEEEDRVRGLETGADDYITKPFSPK 108

Query: 143 DV 144
           ++
Sbjct: 109 EL 110

>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 = 76.3 bits (187), Expect = 4e-19
 Identities = 31/124 (25%), Positives = 60/124 (48%), Gaps = 9/124 (7%)

Query: 23  VLAVDDSIVDRKIVENLLKNS--ACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVN 80
           +  V+D+  D ++++  L NS    +V T  +GM A+ +L       +Q    +N ++ +
Sbjct: 5   IFLVEDNKADIRLIQEALANSTVPHEVVTVRDGMEAMAYL-------RQEGEYANASRPD 57

Query: 81  LVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLK 140
           L++ D  +P   G E+L +IK    +K +PVVV+S+      I    +     ++ K   
Sbjct: 58  LILLDLNLPKKDGREVLAEIKSDPTLKRIPVVVLSTSINEDDIFHSYDLHVNCYITKSAN 117

Query: 141 PSDV 144
            S +
Sbjct: 118 LSQL 121

>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 = 74.3 bits (182), Expect = 1e-18
 Identities = 31/126 (24%), Positives = 59/126 (46%), Gaps = 11/126 (8%)

Query: 23  VLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNL 81
           +L V+D+ V++++++ +L     + +  A +G  A + +           L S G   N+
Sbjct: 4   ILVVEDNHVNQEVIKRMLNLEGIENIELACDGQEAFDKV---------KELTSKGENYNM 54

Query: 82  VITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKP 141
           +  D  MP + G    K I+        P+V +++    + I ECLE G   F+ KP+K 
Sbjct: 55  IFMDVQMPKVDGLLSTKMIRRDL-GYTSPIVALTAFADDSNIKECLESGMNGFLSKPIKR 113

Query: 142 SDVKKL 147
             +K +
Sbjct: 114 PKLKTI 119

>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 = 73.9 bits (181), Expect = 2e-18
 Identities = 27/122 (22%), Positives = 53/122 (43%), Gaps = 14/122 (11%)

Query: 23  VLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLV 82
           VL V+D+ ++ K+  +LL+    +      G+ AL                    K +L+
Sbjct: 4   VLIVEDNELNMKLFHDLLEAQGYETLQTREGLSALSIA--------------RENKPDLI 49

Query: 83  ITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPS 142
           + D  +P ++G E+ K +KE   +  +PVV V++  +        E G + ++ KP+   
Sbjct: 50  LMDIQLPEISGLEVTKWLKEDDDLAHIPVVAVTAFAMKGDEERIREGGCEAYISKPISVV 109

Query: 143 DV 144
             
Sbjct: 110 HF 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 = 74.1 bits (181), Expect = 3e-18
 Identities = 31/127 (24%), Positives = 61/127 (48%), Gaps = 6/127 (4%)

Query: 22  HVLAVDDSIVDRKIVENLLKNS--ACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKV 79
            +L V+DS  D    + LL+       +     G +AL+F      Q           + 
Sbjct: 8   PLLVVEDSDEDFSTFQRLLQREGVVNPIYRCITGDQALDF----LYQTGSYCNPDIAPRP 63

Query: 80  NLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPL 139
            +++ D  +PG  G E+L++IK+  V+K++PVV++++ + P  I  C       +++KPL
Sbjct: 64  AVILLDLNLPGTDGREVLQEIKQDEVLKKIPVVIMTTSSNPKDIEICYSYSISSYIVKPL 123

Query: 140 KPSDVKK 146
           +   + +
Sbjct: 124 EIDRLTE 130

>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 = 4e-18
 Identities = 36/129 (27%), Positives = 57/129 (44%), Gaps = 18/129 (13%)

Query: 20  PPHVLAVDDSIVDRKIVENLLKNS--ACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGT 77
           P  +L +DD  + R  V+ L+  +     V  A NG + +E                   
Sbjct: 2   PATILLIDDHPMLRTGVKQLISMAPDITVVGEASNGEQGIELA--------------ESL 47

Query: 78  KVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLK 137
             +L++ D  MPGM G E L K++E S      +VV S  N    +   L+ GA  ++LK
Sbjct: 48  DPDLILLDLNMPGMNGLETLDKLREKS--LSGRIVVFSVSNHEEDVVTALKRGADGYLLK 105

Query: 138 PLKPSDVKK 146
            ++P D+ K
Sbjct: 106 DMEPEDLLK 114

>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 = 73.1 bits (179), Expect = 5e-18
 Identities = 29/134 (21%), Positives = 56/134 (41%), Gaps = 18/134 (13%)

Query: 22  HVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNL 81
            VL +D++ V R + + LL +  C+VTT  +    L                    +  +
Sbjct: 9   KVLVMDENGVSRMVTKGLLVHLGCEVTTVSSNEECLRV---------------VSHEHKV 53

Query: 82  VITDYCMPGMTGYELLKKIKE---SSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKP 138
           V  D CMPG+  Y++  +I E       +   +V +S     +   +C+  G    +LKP
Sbjct: 54  VFMDVCMPGVENYQIALRIHEKFTKQRHQRPLLVALSGNTDKSTKEKCMSFGLDGVLLKP 113

Query: 139 LKPSDVKKLTGHLI 152
           +   +++ +   L+
Sbjct: 114 VSLDNIRDVLSDLL 127

>d1a2oa1 c.23.1.1 (A:1-140) Methylesterase CheB, N-terminal domain {Salmonella typhimurium [TaxId: 90371]} Length = 140

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Methylesterase CheB, N-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

 Score = 73.1 bits (179), Expect = 6e-18
 Identities = 29/123 (23%), Positives = 51/123 (41%), Gaps = 17/123 (13%)

Query: 23  VLAVDDSIVDRKIVENLLK--NSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVN 80
           VL+VDDS + R+I+  ++   +    V TA + + A + +                   +
Sbjct: 6   VLSVDDSALMRQIMTEIINSHSDMEMVATAPDPLVARDLI--------------KKFNPD 51

Query: 81  LVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLK 140
           ++  D  MP M G + L+K+     M  V V  ++ +     +   LE GA  F+ KP  
Sbjct: 52  VLTLDVEMPRMDGLDFLEKLMRLRPMPVVMVSSLTGKGSEVTL-RALELGAIDFVTKPQL 110

Query: 141 PSD 143
              
Sbjct: 111 GIR 113

>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 = 72.5 bits (178), Expect = 7e-18
 Identities = 23/125 (18%), Positives = 52/125 (41%), Gaps = 17/125 (13%)

Query: 22  HVLAVDDSIVDRKIVENLLKNSACK--VTTAENGMRALEFLGLVDEQEQQNNLNSNGTKV 79
            V   DD+     +++  + +      + TA NG   L+ L                 + 
Sbjct: 3   KVCIADDNRELVSLLDEYISSQPDMEVIGTAYNGQDCLQML--------------EEKRP 48

Query: 80  NLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPL 139
           ++++ D  MP + G  +L++I+      +  V+++++        + +E GA  F+LKP 
Sbjct: 49  DILLLDIIMPHLDGLAVLERIRAGF-EHQPNVIMLTAFGQEDVTKKAVELGASYFILKPF 107

Query: 140 KPSDV 144
              ++
Sbjct: 108 DMENL 112

>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 = 70.7 bits (173), Expect = 3e-17
 Identities = 22/126 (17%), Positives = 50/126 (39%), Gaps = 18/126 (14%)

Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTK 78
           +P  V  V+D      +++  L     +VT   +G    +               S  + 
Sbjct: 1   QPFRVTLVEDEPSHATLIQYHLNQLGAEVTVHPSGSAFFQHR-------------SQLST 47

Query: 79  VNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKP 138
            +L+I    +  ++ + LL  +KE +  K+  V+++++      + E  E     ++ KP
Sbjct: 48  CDLLIVSDQLVDLSIFSLLDIVKEQT--KQPSVLILTTGR--HELIESSEHNLS-YLQKP 102

Query: 139 LKPSDV 144
              S++
Sbjct: 103 FAISEL 108

>d1peya_ c.23.1.1 (A:) Sporulation response regulator Spo0F {Bacillus subtilis [TaxId: 1423]} Length = 119

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Sporulation response regulator Spo0F
species: Bacillus subtilis [TaxId: 1423]

 Score = 70.7 bits (173), Expect = 3e-17
 Identities = 29/122 (23%), Positives = 54/122 (44%), Gaps = 16/122 (13%)

Query: 23  VLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLV 82
           +L VDD    R ++  +      +   A NG++AL+ +                 + +LV
Sbjct: 4   ILIVDDQSGIRILLNEVFNKEGYQTFQAANGLQALDIV--------------TKERPDLV 49

Query: 83  ITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPS 142
           + D  +PGM G E+LK++K     + + V+++++      I E  E GA     KP    
Sbjct: 50  LLDMKIPGMDGIEILKRMKVID--ENIRVIIMTAYGELDMIQESKELGALTHFAKPFDID 107

Query: 143 DV 144
           ++
Sbjct: 108 EI 109

>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 = 69.9 bits (171), Expect = 5e-17
 Identities = 31/124 (25%), Positives = 57/124 (45%), Gaps = 17/124 (13%)

Query: 22  HVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVN 80
            VL VDD+   R ++++++  +  +    A NG  A+E                   K +
Sbjct: 3   RVLIVDDAAFMRMMLKDIITKAGYEVAGEATNGREAVEKY--------------KELKPD 48

Query: 81  LVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLK 140
           +V  D  MP M G + +K+I +        ++V S+      + E ++ GA+ F++KP +
Sbjct: 49  IVTMDITMPEMNGIDAIKEIMKID--PNAKIIVCSAMGQQAMVIEAIKAGAKDFIVKPFQ 106

Query: 141 PSDV 144
           PS V
Sbjct: 107 PSRV 110

>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 = 7e-16
 Identities = 31/124 (25%), Positives = 53/124 (42%), Gaps = 16/124 (12%)

Query: 21  PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVN 80
             V  VDD    R ++E  L  +    TT ENG   L  L                   +
Sbjct: 4   GIVWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLAAL--------------ASKTPD 49

Query: 81  LVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLK 140
           ++++D  MPGM G  LLK+IK+      +PV+++++ +         ++GA  ++ KP  
Sbjct: 50  VLLSDIRMPGMDGLALLKQIKQR--HPMLPVIIMTAHSDLDAAVSAYQQGAFDYLPKPFD 107

Query: 141 PSDV 144
             + 
Sbjct: 108 IDEA 111

>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 = 67.3 bits (164), Expect = 8e-16
 Identities = 29/141 (20%), Positives = 61/141 (43%), Gaps = 19/141 (13%)

Query: 16  SNPKPPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNS 74
           S  +   VL VDD +  R ++ + L+    K +T A +G + ++ +              
Sbjct: 2   SLAEKIKVLIVDDQVTSRLLLGDALQQLGFKQITAAGDGEQGMKIM-------------- 47

Query: 75  NGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMF 134
                +LVI+D+ MP M G  LL+ ++ +   K+   ++++++     + +    GA   
Sbjct: 48  AQNPHHLVISDFNMPKMDGLGLLQAVRANPATKKAAFIILTAQGDRALVQKAAALGANNV 107

Query: 135 MLKPLKPSD----VKKLTGHL 151
           + KP         ++ + G L
Sbjct: 108 LAKPFTIEKMKAAIEAVFGAL 128

>d1xhfa1 c.23.1.1 (A:2-122) Aerobic respiration control protein ArcA, N-terminal domain {Escherichia coli [TaxId: 562]} Length = 121

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Aerobic respiration control protein ArcA, N-terminal domain
species: Escherichia coli [TaxId: 562]

 Score = 66.6 bits (162), Expect = 1e-15
 Identities = 29/124 (23%), Positives = 55/124 (44%), Gaps = 17/124 (13%)

Query: 21  PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVN 80
           PH+L V+D +V R  ++++ +     V  A +G    + L              +   +N
Sbjct: 3   PHILIVEDELVTRNTLKSIFEAEGYDVFEATDGAEMHQIL--------------SEYDIN 48

Query: 81  LVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLK 140
           LVI D  +PG  G  L ++++E      V ++ ++  +        LE GA  ++ KP  
Sbjct: 49  LVIMDINLPGKNGLLLARELRE---QANVALMFLTGRDNEVDKILGLEIGADDYITKPFN 105

Query: 141 PSDV 144
           P ++
Sbjct: 106 PREL 109

>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 = 65.1 bits (158), Expect = 6e-15
 Identities = 31/131 (23%), Positives = 62/131 (47%), Gaps = 16/131 (12%)

Query: 16  SNPKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSN 75
           S+     +L VDD  ++R+++ + L +   +  TA +G+ AL                 +
Sbjct: 4   SDNDDMMILVVDDHPINRRLLADQLGSLGYQCKTANDGVDALNV--------------LS 49

Query: 76  GTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFM 135
              +++V++D  MP M GY L ++I++      +PV+ V++  +      CLE G    +
Sbjct: 50  KNHIDIVLSDVNMPNMDGYRLTQRIRQL--GLTLPVIGVTANALAEEKQRCLESGMDSCL 107

Query: 136 LKPLKPSDVKK 146
            KP+    +K+
Sbjct: 108 SKPVTLDVIKQ 118

>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 = 64.6 bits (157), Expect = 7e-15
 Identities = 29/122 (23%), Positives = 54/122 (44%), Gaps = 17/122 (13%)

Query: 23  VLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLV 82
           +L VDD      I++  +     +V TA NG  ALE                   + +++
Sbjct: 3   ILIVDDEKPISDIIKFNMTKEGYEVVTAFNGREALEQF--------------EAEQPDII 48

Query: 83  ITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPS 142
           I D  +P + G E+ K I++      VP++++S+++        LE GA  ++ KP    
Sbjct: 49  ILDLMLPEIDGLEVAKTIRK---TSSVPILMLSAKDSEFDKVIGLELGADDYVTKPFSNR 105

Query: 143 DV 144
           ++
Sbjct: 106 EL 107

>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 = 63.9 bits (155), Expect = 2e-14
 Identities = 29/124 (23%), Positives = 53/124 (42%), Gaps = 16/124 (12%)

Query: 21  PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVN 80
           P V  +DD    RK ++  L+ +   V++  +   AL  L              +     
Sbjct: 1   PSVFLIDDDRDLRKAMQQTLELAGFTVSSFASATEALAGL--------------SADFAG 46

Query: 81  LVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLK 140
           +VI+D  MPGM G  L +KI       ++P+++V+         + +++GA  F+ KP  
Sbjct: 47  IVISDIRMPGMDGLALFRKILALD--PDLPMILVTGHGDIPMAVQAIQDGAYDFIAKPFA 104

Query: 141 PSDV 144
              +
Sbjct: 105 ADRL 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 = 65.3 bits (158), Expect = 2e-14
 Identities = 28/125 (22%), Positives = 51/125 (40%), Gaps = 18/125 (14%)

Query: 20  PPHVLAVDDSIVDRKIVENLLKNSACKVT-TAENGMRALEFLGLVDEQEQQNNLNSNGTK 78
           P  VL  +D  + R  +  +L+    ++   A +G  A+E                   K
Sbjct: 3   PRRVLIAEDEALIRMDLAEMLREEGYEIVGEAGDGQEAVELA--------------ELHK 48

Query: 79  VNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKP 138
            +LVI D  MP   G +   +I      +  P+VV+++ +    +    + GA  +++KP
Sbjct: 49  PDLVIMDVKMPRRDGIDAASEIAS---KRIAPIVVLTAFSQRDLVERARDAGAMAYLVKP 105

Query: 139 LKPSD 143
              SD
Sbjct: 106 FSISD 110

>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 = 62.7 bits (152), Expect = 3e-14
 Identities = 24/125 (19%), Positives = 52/125 (41%), Gaps = 17/125 (13%)

Query: 20  PPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKV 79
           P H++ V+D  V +  +++        V+   +G    E +                  V
Sbjct: 1   PHHIVIVEDEPVTQARLQSYFTQEGYTVSVTASGAGLREIM--------------QNQSV 46

Query: 80  NLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPL 139
           +L++ D  +P   G  L + ++E S +    +++V+  +        LE GA  ++ KPL
Sbjct: 47  DLILLDINLPDENGLMLTRALRERSTV---GIILVTGRSDRIDRIVGLEMGADDYVTKPL 103

Query: 140 KPSDV 144
           +  ++
Sbjct: 104 ELREL 108

>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 = 61.6 bits (149), Expect = 1e-13
 Identities = 29/138 (21%), Positives = 57/138 (41%), Gaps = 20/138 (14%)

Query: 19  KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTK 78
           +   V  VDD    RK +  +L  +   V   ++    L F                  +
Sbjct: 2   QDYTVHIVDDEEPVRKSLAFMLTMNGFAVKMHQSAEAFLAFA--------------PDVR 47

Query: 79  VNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKP 138
             +++TD  MP M+G ELL+ + +  +    P +V++         E ++ GA  F+ KP
Sbjct: 48  NGVLVTDLRMPDMSGVELLRNLGDLKINI--PSIVITGHGDVPMAVEAMKAGAVDFIEKP 105

Query: 139 LKPSD----VKKLTGHLI 152
            + +     +++ + HL+
Sbjct: 106 FEDTVIIEAIERASEHLV 123

>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 = 61.6 bits (149), Expect = 1e-13
 Identities = 29/124 (23%), Positives = 54/124 (43%), Gaps = 16/124 (12%)

Query: 21  PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVN 80
           P V  VDD +  R+ + NLL+++  +V T +     LE                   +  
Sbjct: 3   PTVFVVDDDMSVREGLRNLLRSAGFEVETFDCASTFLEHR--------------RPEQHG 48

Query: 81  LVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLK 140
            ++ D  MPGM+G EL +++   S    +P+V +++          ++ GA  F+ KP +
Sbjct: 49  CLVLDMRMPGMSGIELQEQLTAIS--DGIPIVFITAHGDIPMTVRAMKAGAIEFLPKPFE 106

Query: 141 PSDV 144
              +
Sbjct: 107 EQAL 110

>d1ys7a2 c.23.1.1 (A:7-127) Transcriptional regulatory protein PrrA, N-terminal domain {Mycobacterium tuberculosis [TaxId: 1773]} Length = 121

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Transcriptional regulatory protein PrrA, N-terminal domain
species: Mycobacterium tuberculosis [TaxId: 1773]

 Score = 61.2 bits (148), Expect = 1e-13
 Identities = 30/124 (24%), Positives = 53/124 (42%), Gaps = 16/124 (12%)

Query: 21  PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVN 80
           P VL VDD       +E  L+ S  +V TA +G  AL                    + +
Sbjct: 2   PRVLVVDDDSDVLASLERGLRLSGFEVATAVDGAEALRSA--------------TENRPD 47

Query: 81  LVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLK 140
            ++ D  MP + G  ++  ++      +VPV V+S+ +        LE GA  +++KP  
Sbjct: 48  AIVLDINMPVLDGVSVVTALRAMD--NDVPVCVLSARSSVDDRVAGLEAGADDYLVKPFV 105

Query: 141 PSDV 144
            +++
Sbjct: 106 LAEL 109

>d1w25a1 c.23.1.1 (A:2-140) Response regulator PleD, receiver domain {Caulobacter crescentus [TaxId: 155892]} Length = 139

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Response regulator PleD, receiver domain
species: Caulobacter crescentus [TaxId: 155892]

 Score = 60.6 bits (146), Expect = 4e-13
 Identities = 30/123 (24%), Positives = 59/123 (47%), Gaps = 14/123 (11%)

Query: 22  HVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNL 81
            +L VDD   + +++E  L     +V+TA +G  AL                +     ++
Sbjct: 3   RILVVDDIEANVRLLEAKLTAEYYEVSTAMDGPTALAM--------------AARDLPDI 48

Query: 82  VITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKP 141
           ++ D  MPGM G+ + +K+K+    + +PVV++++ +      + LE GA  F+ KP+  
Sbjct: 49  ILLDVMMPGMDGFTVCRKLKDDPTTRHIPVVLITALDGRGDRIQGLESGASDFLTKPIDD 108

Query: 142 SDV 144
             +
Sbjct: 109 VML 111

>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 = 59.6 bits (143), Expect = 2e-12
 Identities = 15/129 (11%), Positives = 34/129 (26%), Gaps = 21/129 (16%)

Query: 10  SSSSSSSNPKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQ 69
           S++S   + +   VL ++        +   L    C V        A +           
Sbjct: 1   SANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAFDVP--------- 51

Query: 70  NNLNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEE 129
                    V++V T                  +       +V +     P  +++ +E 
Sbjct: 52  ---------VDVVFTSIFQNRHHDEIAALLAAGTP---RTTLVALVEYESPAVLSQIIEL 99

Query: 130 GAQMFMLKP 138
                + +P
Sbjct: 100 ECHGVITQP 108

>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 = 57.8 bits (139), Expect = 5e-12
 Identities = 23/135 (17%), Positives = 49/135 (36%), Gaps = 16/135 (11%)

Query: 10  SSSSSSSNPKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQ 69
           + +++  +     VL VDD+    + V   L      V  ++     +   G VD     
Sbjct: 3   AGAAARLDGLGGRVLIVDDNERQAQRVAAELGVEHRPVIESDPEKAKISAGGPVD----- 57

Query: 70  NNLNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEE 129
                      LVI +       G      ++     +++PV+ +   +   R+ + LE 
Sbjct: 58  -----------LVIVNAAAKNFDGLRFTAALRSEERTRQLPVLAMVDPDDRGRMVKALEI 106

Query: 130 GAQMFMLKPLKPSDV 144
           G    + +P+ P ++
Sbjct: 107 GVNDILSRPIDPQEL 121

>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 = 57.0 bits (137), Expect = 6e-12
 Identities = 28/122 (22%), Positives = 51/122 (41%), Gaps = 17/122 (13%)

Query: 23  VLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLV 82
           VL V+D    R+ +   L+    +V  AE   R L                    K +L+
Sbjct: 3   VLIVEDEQAIRRFLRTALEGDGMRVFEAETLQRGLLEA--------------ATRKPDLI 48

Query: 83  ITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPS 142
           I D  +P   G E ++ +++      VPV+V+S+ +  +     L+ GA  ++ KP    
Sbjct: 49  ILDLGLPDGDGIEFIRDLRQ---WSAVPVIVLSARSEESDKIAALDAGADDYLSKPFGIG 105

Query: 143 DV 144
           ++
Sbjct: 106 EL 107

>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 = 55.9 bits (134), Expect = 2e-11
 Identities = 26/122 (21%), Positives = 54/122 (44%), Gaps = 16/122 (13%)

Query: 23  VLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLV 82
           VL V+D+ + R  ++  ++++  +V  AE+   A  +L              N    ++ 
Sbjct: 3   VLVVEDNALLRHHLKVQIQDAGHQVDDAEDAKEADYYL--------------NEHIPDIA 48

Query: 83  ITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPS 142
           I D  +P   G  L+++ + + V    P++V+++        E L  GA  ++ KP    
Sbjct: 49  IVDLGLPDEDGLSLIRRWRSNDVSL--PILVLTARESWQDKVEVLSAGADDYVTKPFHIE 106

Query: 143 DV 144
           +V
Sbjct: 107 EV 108

>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 = 54.7 bits (131), Expect = 4e-11
 Identities = 26/122 (21%), Positives = 49/122 (40%), Gaps = 16/122 (13%)

Query: 23  VLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLV 82
           VL V+D      ++   LK     V    +G   +                      ++V
Sbjct: 4   VLVVEDERDLADLITEALKKEMFTVDVCYDGEEGMYMA--------------LNEPFDVV 49

Query: 83  ITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPS 142
           I D  +P   G+E+LK ++ES V    PV+++++ +      + L  GA  ++ KP    
Sbjct: 50  ILDIMLPVHDGWEILKSMRESGVNT--PVLMLTALSDVEYRVKGLNMGADDYLPKPFDLR 107

Query: 143 DV 144
           ++
Sbjct: 108 EL 109

>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 = 55.0 bits (132), Expect = 5e-11
 Identities = 34/123 (27%), Positives = 55/123 (44%), Gaps = 16/123 (13%)

Query: 22  HVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNL 81
           +VL ++D  V R ++E  L     KV +AE G  A +                +    N+
Sbjct: 2   NVLVIEDDKVFRGLLEEYLSMKGIKVESAERGKEAYKL--------------LSEKHFNV 47

Query: 82  VITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKP 141
           V+ D  +P + G E+LK IKE S   E  V+V++         E ++ GA  F+ KP   
Sbjct: 48  VLLDLLLPDVNGLEILKWIKERS--PETEVIVITGHGTIKTAVEAMKMGAYDFLTKPCML 105

Query: 142 SDV 144
            ++
Sbjct: 106 EEI 108

>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 = 53.9 bits (129), Expect = 8e-11
 Identities = 29/123 (23%), Positives = 57/123 (46%), Gaps = 16/123 (13%)

Query: 22  HVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNL 81
            +L VDD      +++  L+ S   V TA +G  AL+               +   K +L
Sbjct: 4   KILVVDDEESIVTLLQYNLERSGYDVITASDGEEALKK--------------AETEKPDL 49

Query: 82  VITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKP 141
           ++ D  +P + G E+ K++++       P++++++++        LE GA  +M KP  P
Sbjct: 50  IVLDVMLPKLDGIEVCKQLRQQK--LMFPILMLTAKDEEFDKVLGLELGADDYMTKPFSP 107

Query: 142 SDV 144
            +V
Sbjct: 108 REV 110

>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 = 50.0 bits (119), Expect = 2e-09
 Identities = 27/124 (21%), Positives = 47/124 (37%), Gaps = 19/124 (15%)

Query: 21  PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVN 80
             +  VDD     K V   L+    +V T   G   L                       
Sbjct: 3   WKIAVVDDDKNILKKVSEKLQ-QLGRVKTFLTGEDFLNDEEAFH---------------- 45

Query: 81  LVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLK 140
           +V+ D  +P  +GYE+ + IKE+    E  V++++  +    + +  E GA  ++ KP  
Sbjct: 46  VVVLDVMLPDYSGYEICRMIKET--RPETWVILLTLLSDDESVLKGFEAGADDYVTKPFN 103

Query: 141 PSDV 144
           P  +
Sbjct: 104 PEIL 107

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	153
d1dbwa_	123	Transcriptional regulatory protein FixJ, receiver	99.96
d1zesa1	121	PhoB receiver domain {Escherichia coli [TaxId: 562	99.96
d1peya_	119	Sporulation response regulator Spo0F {Bacillus sub	99.96
d2pl1a1	119	PhoP receiver domain {Escherichia coli [TaxId: 562	99.96
d1krwa_	123	NTRC receiver domain {Salmonella typhimurium [TaxI	99.96
d1qkka_	140	Transcriptional regulatory protein DctD, receiver	99.95
d1mb3a_	123	Cell division response regulator DivK {Caulobacter	99.95
d1jbea_	128	CheY protein {Escherichia coli [TaxId: 562]}	99.95
d1ys7a2	121	Transcriptional regulatory protein PrrA, N-termina	99.95
d1mvoa_	121	PhoP receiver domain {Bacillus subtilis [TaxId: 14	99.95
d2a9pa1	117	DNA-binding response regulator MicA, N-terminal do	99.95
d1p6qa_	129	CheY protein {Sinorhizobium meliloti, CheY2 [TaxId	99.95
d2r25b1	128	Response regulator Sin1 {Baker's yeast (Saccharomy	99.95
d1kgsa2	122	PhoB receiver domain {Thermotoga maritima [TaxId:	99.95
d1xhfa1	121	Aerobic respiration control protein ArcA, N-termin	99.95
d1ny5a1	137	Transcriptional activator sigm54 (NtrC1), N-termin	99.95
d1u0sy_	118	CheY protein {Thermotoga maritima [TaxId: 2336]}	99.95
d2ayxa1	133	Sensor kinase protein RcsC, C-terminal domain {Esc	99.95
d1zh2a1	119	Transcriptional regulatory protein KdpE, N-termina	99.95
d1k68a_	140	Response regulator for cyanobacterial phytochrome	99.95
d1i3ca_	144	Response regulator for cyanobacterial phytochrome	99.95
d1yioa2	128	Response regulatory protein StyR, N-terminal domai	99.94
d1dcfa_	134	Receiver domain of the ethylene receptor {Thale cr	99.94
d1w25a1	139	Response regulator PleD, receiver domain {Caulobac	99.94
d1zgza1	120	TorCAD operon transcriptional regulator TorD, N-te	99.94
d1k66a_	149	Response regulator for cyanobacterial phytochrome	99.94
d1p2fa2	120	Response regulator DrrB {Thermotoga maritima [TaxI	99.93
d1a04a2	138	Nitrate/nitrite response regulator (NarL), receive	99.93
d1dz3a_	123	Sporulation response regulator Spo0A {Bacillus ste	99.93
d1w25a2	153	Response regulator PleD, receiver domain {Caulobac	99.93
d1s8na_	190	Probable two-component system transcriptional regu	99.93
d2b4aa1	118	Hypothetical protein BH3024 {Bacillus halodurans [	99.91
d1a2oa1	140	Methylesterase CheB, N-terminal domain {Salmonella	99.88
d1qo0d_	189	Positive regulator of the amidase operon AmiR {Pse	99.85
d1ccwa_	137	Glutamate mutase, small subunit {Clostridium cochl	96.89
d1dxea_	253	2-dehydro-3-deoxy-galactarate aldolase {Escherichi	94.63
d7reqa2	168	Methylmalonyl-CoA mutase alpha subunit, C-terminal	93.97
d1qpoa1	169	Quinolinic acid phosphoribosyltransferase (Nicotin	93.09
d1xrsb1	160	D-lysine 5,6-aminomutase beta subunit KamE, C-term	92.22
d1xi3a_	206	Thiamin phosphate synthase {Archaeon (Pyrococcus f	90.67
d1o4ua1	170	Quinolinic acid phosphoribosyltransferase (Nicotin	90.21
d1r8ja2	135	N-terminal domain of the circadian clock protein K	88.76
d3bula2	156	Methionine synthase, C-terminal domain {Escherichi	88.69
d1izca_	299	Macrophomate synthase {Macrophoma commelinae [TaxI	88.05
d1wa3a1	202	KDPG aldolase {Thermotoga maritima [TaxId: 2336]}	86.84
d1mxsa_	216	KDPG aldolase {Pseudomonas putida [TaxId: 303]}	85.15
d1wl8a1	188	GMP synthase subunit A, GuaAA {Archaeon Pyrococcus	84.87
d2esra1	152	Putative methyltransferase SPy1538 {Streptococcus	83.73
d2fpoa1	183	Methylase YhhF {Escherichia coli [TaxId: 562]}	83.52
d7reqb2	163	Methylmalonyl-CoA mutase beta subunit, C-terminal	83.07
d1id1a_	153	Rck domain from putative potassium channel Kch {Es	82.51
d1wbha1	213	KDPG aldolase {Escherichia coli [TaxId: 562]}	82.49
d1i7qb_	192	Anthranilate synthase GAT subunit, TrpG {Serratia	82.08
d1ujpa_	271	Trp synthase alpha-subunit {Thermus thermophilus [	81.27
d1vhca_	212	Hypothetical protein HI0047 {Haemophilus influenza	80.95
d1iy9a_	274	Spermidine synthase {Bacillus subtilis [TaxId: 142	80.78
d2ifta1	183	Putative methylase HI0767 {Haemophilus influenzae	80.75

>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=99.96  E-value=4e-28  Score=160.58  Aligned_cols=119  Identities=23%  Similarity=0.315  Sum_probs=109.9

Q ss_pred             CCCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHH
Q 042079           18 PKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELL   97 (153)
Q Consensus        18 ~~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~   97 (153)
                      ++..+||||||++..+..++.+|+..||.+..+.++.+++..+.              ..+||+||+|+.||+++|++++
T Consensus         1 M~~~~ILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~~al~~~~--------------~~~~dlvi~D~~mp~~~G~e~~   66 (123)
T d1dbwa_           1 MQDYTVHIVDDEEPVRKSLAFMLTMNGFAVKMHQSAEAFLAFAP--------------DVRNGVLVTDLRMPDMSGVELL   66 (123)
T ss_dssp             CCCCEEEEEESSHHHHHHHHHHHHHTTCEEEEESCHHHHHHHGG--------------GCCSEEEEEECCSTTSCHHHHH
T ss_pred             CCCCEEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHh--------------hcCCcEEEEeccCccccchHHH
Confidence            35679999999999999999999999999999999999999883              4579999999999999999999


Q ss_pred             HHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079           98 KKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus        98 ~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      +++|+..  +.+|+|++|+..+.+...+|++.|+++||.||+++++|.+.+.+.+
T Consensus        67 ~~lr~~~--~~~~iI~lt~~~~~~~~~~a~~~Ga~~yl~KP~~~~~L~~~i~~a~  119 (123)
T d1dbwa_          67 RNLGDLK--INIPSIVITGHGDVPMAVEAMKAGAVDFIEKPFEDTVIIEAIERAS  119 (123)
T ss_dssp             HHHHHTT--CCCCEEEEECTTCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHH
T ss_pred             HHHHhcC--CCCeEEEEEeeCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHH
Confidence            9999854  6899999999999999999999999999999999999998887754

>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=99.96  E-value=7.1e-28  Score=158.90  Aligned_cols=118  Identities=24%  Similarity=0.425  Sum_probs=109.6

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKI  100 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~l  100 (153)
                      .+||||||++..+..+..+|+..||++..+.++.+|++.+.              ...||+||+|+.||+++|+++++.|
T Consensus         1 KkILiVDD~~~~~~~l~~~L~~~g~~v~~a~~~~~al~~l~--------------~~~~dlil~D~~mp~~~G~~l~~~l   66 (121)
T d1zesa1           1 RRILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLN--------------EPWPDLILLDWMLPGGSGIQFIKHL   66 (121)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEECSHHHHHHHSS--------------SSCCSEEEECSSCTTSCHHHHHHHH
T ss_pred             CEEEEEeCCHHHHHHHHHHHHHCCCEEEEECChHHHHHHHH--------------ccCCCEEEeecCCCCCCHHHHHHHH
Confidence            47999999999999999999999999999999999999883              5679999999999999999999999


Q ss_pred             HhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079          101 KESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus       101 r~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      |+....+.+|+|++|+..+.....++++.|+++|+.||++.++|...+.+++
T Consensus        67 r~~~~~~~~pvi~lt~~~~~~~~~~~~~~G~~d~l~KP~~~~~L~~~v~~~l  118 (121)
T d1zesa1          67 KRESMTRDIPVVMLTARGEEEDRVRGLETGADDYITKPFSPKELVARIKAVM  118 (121)
T ss_dssp             HHSTTTTTSCEEEEESCCSHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHH
T ss_pred             HhCccCCCCeEEEEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHH
Confidence            9876667899999999999999999999999999999999999998777653

>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=99.96  E-value=3.2e-28  Score=160.16  Aligned_cols=117  Identities=25%  Similarity=0.440  Sum_probs=108.8

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKK   99 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~   99 (153)
                      +.+||||||++..+..++.+|+..||++..+.++.+|++.+.              .+.||+|++|+.||+++|++++++
T Consensus         1 NkrILvVDD~~~~~~~l~~~L~~~g~~v~~a~~g~eal~~~~--------------~~~~dlillD~~mP~~~G~el~~~   66 (119)
T d1peya_           1 NEKILIVDDQSGIRILLNEVFNKEGYQTFQAANGLQALDIVT--------------KERPDLVLLDMKIPGMDGIEILKR   66 (119)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--------------HHCCSEEEEESCCTTCCHHHHHHH
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHHcCCEEEEeCCHHHHHHHHH--------------hCCCCEEEEeccCCCCCHHHHHHH
Confidence            358999999999999999999999999999999999999884              346999999999999999999999


Q ss_pred             HHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079          100 IKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus       100 lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      +|+..  +.+|+|++|+..+.+...++++.|+++|+.||++.+++...+.+.+
T Consensus        67 lr~~~--~~~pvi~lt~~~~~~~~~~a~~~Ga~~yl~KP~~~~~L~~~v~~~L  117 (119)
T d1peya_          67 MKVID--ENIRVIIMTAYGELDMIQESKELGALTHFAKPFDIDEIRDAVKKYL  117 (119)
T ss_dssp             HHHHC--TTCEEEEEESSCCHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHHS
T ss_pred             HHHhC--CCCcEEEEecCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHC
Confidence            99865  6899999999999999999999999999999999999999998865

>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=99.96  E-value=5.3e-28  Score=159.09  Aligned_cols=116  Identities=22%  Similarity=0.363  Sum_probs=107.9

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKI  100 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~l  100 (153)
                      ++||||||++..+..++..|+..||+|..+.++.+|+..+.              ...||+||+|+.||+++|+++++++
T Consensus         1 mrILvVDDd~~~~~~l~~~L~~~G~~v~~a~~g~eal~~l~--------------~~~~dliilD~~mP~~~G~e~~~~i   66 (119)
T d2pl1a1           1 MRVLVVEDNALLRHHLKVQIQDAGHQVDDAEDAKEADYYLN--------------EHIPDIAIVDLGLPDEDGLSLIRRW   66 (119)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--------------HSCCSEEEECSCCSSSCHHHHHHHH
T ss_pred             CEEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHH--------------hcccceeehhccCCCchhHHHHHHH
Confidence            57999999999999999999999999999999999999884              3579999999999999999999999


Q ss_pred             HhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079          101 KESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus       101 r~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      ++..  +.+|+|++|+..+.+...++++.|+++|+.||++.++|...+++++
T Consensus        67 ~~~~--~~~pvi~lt~~~~~~~~~~a~~~Ga~~yl~KP~~~~~L~~~v~~~l  116 (119)
T d2pl1a1          67 RSND--VSLPILVLTARESWQDKVEVLSAGADDYVTKPFHIEEVMARMQALM  116 (119)
T ss_dssp             HHTT--CCSCEEEEESCCCHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHH
T ss_pred             HhcC--cccceEeeeccCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHH
Confidence            9865  5899999999999999999999999999999999999998887754

>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=99.96  E-value=3.8e-28  Score=160.64  Aligned_cols=118  Identities=28%  Similarity=0.412  Sum_probs=109.5

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      +..+||||||++..+..++.+|+..||+|..+.++.+|++.+.              .+.||+||+|+.||+++|+++++
T Consensus         2 ~k~~ILIVDDd~~~~~~l~~~L~~~g~~v~~a~~~~~a~~~l~--------------~~~~dlii~D~~mp~~~G~el~~   67 (123)
T d1krwa_           2 QRGIVWVVDDDSSIRWVLERALAGAGLTCTTFENGNEVLAALA--------------SKTPDVLLSDIRMPGMDGLALLK   67 (123)
T ss_dssp             CCCEEEEESSSHHHHHHHHHHHHHTTCEEEEESSSHHHHHHHT--------------TCCCSEEEECCSSSSSTTHHHHH
T ss_pred             CCCEEEEEECCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHH--------------hCCCCEEEehhhcCCchHHHHHH
Confidence            4568999999999999999999999999999999999999883              56799999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      ++++..  +.+|+|++|+..+.+...+|++.|+++||.||++.++|...+.+.+
T Consensus        68 ~l~~~~--~~~piI~~t~~~~~~~~~~a~~~Ga~dyl~KP~~~~eL~~~i~~~l  119 (123)
T d1krwa_          68 QIKQRH--PMLPVIIMTAHSDLDAAVSAYQQGAFDYLPKPFDIDEAVALVERAI  119 (123)
T ss_dssp             HHHHHS--SSCCEEESCCCSCHHHHHHHHHHTEEEECSSCCHHHHHHHHHHHHH
T ss_pred             HHHHhC--CCCeEEEEecCCCHHHHHHHHHcCCCeEEeCcCCHHHHHHHHHHHH
Confidence            999865  6899999999999999999999999999999999999998888754

>d1qkka_ c.23.1.1 (A:) Transcriptional regulatory protein DctD, receiver domain {Sinorhizobium meliloti [TaxId: 382]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Transcriptional regulatory protein DctD, receiver domain
species: Sinorhizobium meliloti [TaxId: 382]

Probab=99.95  E-value=1.6e-27  Score=160.93  Aligned_cols=115  Identities=25%  Similarity=0.404  Sum_probs=107.4

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKI  100 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~l  100 (153)
                      ++||||||++..+..+..+|+..||.+..+.++.+|+..+              ..+.||+||+|+.||+++|+++++++
T Consensus         1 P~ILiVDDd~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l--------------~~~~~dlil~D~~mP~~~G~el~~~l   66 (140)
T d1qkka_           1 PSVFLIDDDRDLRKAMQQTLELAGFTVSSFASATEALAGL--------------SADFAGIVISDIRMPGMDGLALFRKI   66 (140)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESCHHHHHHTC--------------CTTCCSEEEEESCCSSSCHHHHHHHH
T ss_pred             CEEEEEECCHHHHHHHHHHHHHCCCEEEEeCChHHHHHHH--------------hccCcchHHHhhccCCCCHHHHHHHH
Confidence            5899999999999999999999999999999999999988              35789999999999999999999999


Q ss_pred             HhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          101 KESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       101 r~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      |+..  +.+|||++|+..+.+...+|++.||++||.||++.++|...+++.
T Consensus        67 r~~~--~~~pvI~lT~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~  115 (140)
T d1qkka_          67 LALD--PDLPMILVTGHGDIPMAVQAIQDGAYDFIAKPFAADRLVQSARRA  115 (140)
T ss_dssp             HHHC--TTSCEEEEECGGGHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHH
T ss_pred             HHhC--CCCcEEEEECCCCHHHHHHHHHcCCCEeecCCCCHHHHHHHHHHH
Confidence            9865  689999999999999999999999999999999999998877664

>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=9.2e-28  Score=158.73  Aligned_cols=118  Identities=24%  Similarity=0.417  Sum_probs=104.1

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKI  100 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~l  100 (153)
                      .+||||||++..+..+..+|+..||++..+.++.+|++.+.              ..+||+||+|+.||+++|++++++|
T Consensus         2 krILiVDD~~~~~~~l~~~L~~~g~~v~~a~~~~~al~~~~--------------~~~~dlil~D~~mp~~dG~el~~~i   67 (123)
T d1mb3a_           2 KKVLIVEDNELNMKLFHDLLEAQGYETLQTREGLSALSIAR--------------ENKPDLILMDIQLPEISGLEVTKWL   67 (123)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESCHHHHHHHHH--------------HHCCSEEEEESBCSSSBHHHHHHHH
T ss_pred             ceEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHH--------------hCCCCEEEEEeccCCCcHHHHHHHH
Confidence            57999999999999999999999999999999999999884              2469999999999999999999999


Q ss_pred             HhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079          101 KESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus       101 r~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      |+......+|+|++|+........++++.|+++|+.||+++.+|.+.+.+++
T Consensus        68 r~~~~~~~iPii~lt~~~~~~~~~~~~~~G~~~~l~KP~~~~~L~~~i~~~l  119 (123)
T d1mb3a_          68 KEDDDLAHIPVVAVTAFAMKGDEERIREGGCEAYISKPISVVHFLETIKRLL  119 (123)
T ss_dssp             HHSTTTTTSCEEEEC------CHHHHHHHTCSEEECSSCCHHHHHHHHHHHH
T ss_pred             HhCCCcCCCCeEEEEEecCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHH
Confidence            9877667899999999888888899999999999999999999999888865

>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=4.3e-28  Score=159.98  Aligned_cols=116  Identities=27%  Similarity=0.382  Sum_probs=107.6

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKI  100 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~l  100 (153)
                      ++||||||++..+..+...|++.||+|..+.++.+|++.+.              ...||+|++|+.||+++|+++++++
T Consensus         2 PkILiVDD~~~~~~~l~~~L~~~g~~v~~a~~~~eal~~~~--------------~~~~dlvl~D~~mP~~~G~el~~~i   67 (121)
T d1ys7a2           2 PRVLVVDDDSDVLASLERGLRLSGFEVATAVDGAEALRSAT--------------ENRPDAIVLDINMPVLDGVSVVTAL   67 (121)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--------------HSCCSEEEEESSCSSSCHHHHHHHH
T ss_pred             CEEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHH--------------hCCCCEEEEEeeccCcccHHHHHHH
Confidence            58999999999999999999999999999999999999884              3579999999999999999999999


Q ss_pred             HhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079          101 KESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus       101 r~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      |+..  +.+|||++|+..+.+...++++.|+++||.||++.++|...+.+++
T Consensus        68 r~~~--~~~piI~lt~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~l  117 (121)
T d1ys7a2          68 RAMD--NDVPVCVLSARSSVDDRVAGLEAGADDYLVKPFVLAELVARVKALL  117 (121)
T ss_dssp             HHTT--CCCCEEEEECCCTTTCCCTTTTTTCSEEEESSCCHHHHHHHHHHHH
T ss_pred             HhcC--CCCEEEEEEeeCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHH
Confidence            9865  6899999999999998999999999999999999999998887654

>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=99.95  E-value=2.1e-27  Score=156.57  Aligned_cols=117  Identities=25%  Similarity=0.391  Sum_probs=107.3

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKK   99 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~   99 (153)
                      +.+||||||++..+..++.+|+..||+|..+.++.+|++.+.              ..+||+||+|+.||+++|++++++
T Consensus         2 ~krILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~~al~~l~--------------~~~~dlillD~~mp~~~G~~~~~~   67 (121)
T d1mvoa_           2 NKKILVVDDEESIVTLLQYNLERSGYDVITASDGEEALKKAE--------------TEKPDLIVLDVMLPKLDGIEVCKQ   67 (121)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--------------HHCCSEEEEESSCSSSCHHHHHHH
T ss_pred             CCCEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHh--------------cccccEEEecccccCCCCchhhhh
Confidence            368999999999999999999999999999999999999884              346999999999999999999999


Q ss_pred             HHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079          100 IKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus       100 lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      +|...  +..|||++|+..+.+...++++.|+++|+.||+++++|...+.+++
T Consensus        68 ~r~~~--~~~~ii~lt~~~~~~~~~~~~~~Ga~~yl~KP~~~~~L~~~i~~~l  118 (121)
T d1mvoa_          68 LRQQK--LMFPILMLTAKDEEFDKVLGLELGADDYMTKPFSPREVNARVKAIL  118 (121)
T ss_dssp             HHHTT--CCCCEEEEECTTCCCCHHHHHHTTCCEEEESSCCHHHHHHHHHHHH
T ss_pred             hhccC--CCCEEEEEEeeCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHH
Confidence            99865  5789999999988888999999999999999999999998877653

>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=3.1e-27  Score=154.97  Aligned_cols=115  Identities=26%  Similarity=0.411  Sum_probs=106.5

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKI  100 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~l  100 (153)
                      .+||||||++..+..+..+|+..||+|..+.++.+|++.+.              ..+||+|++|+.||+++|+++++++
T Consensus         1 KrILiVdDd~~~~~~l~~~L~~~g~~v~~a~~~~eal~~~~--------------~~~~dlillD~~mp~~~G~~~~~~i   66 (117)
T d2a9pa1           1 KKILIVDDEKPISDIIKFNMTKEGYEVVTAFNGREALEQFE--------------AEQPDIIILDLMLPEIDGLEVAKTI   66 (117)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--------------HHCCSEEEECSSCSSSCHHHHHHHH
T ss_pred             CEEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHH--------------hcCCCEEEeccccCCCCccHHHHHH
Confidence            47999999999999999999999999999999999999884              3569999999999999999999999


Q ss_pred             HhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079          101 KESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus       101 r~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      ++.   +++|+|++|+..+.+...++++.|+++|+.||+++++|...+.+++
T Consensus        67 ~~~---~~~pvI~lt~~~~~~~~~~a~~~Ga~d~l~KP~~~~~L~~~i~~~l  115 (117)
T d2a9pa1          67 RKT---SSVPILMLSAKDSEFDKVIGLELGADDYVTKPFSNRELQARVKALL  115 (117)
T ss_dssp             HTT---CCCCEEEEESCCSHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHH
T ss_pred             HhC---CCCCEEEEecCCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHh
Confidence            874   4789999999999999999999999999999999999998887754

>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=3.1e-27  Score=157.42  Aligned_cols=120  Identities=23%  Similarity=0.427  Sum_probs=109.5

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcE-EEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELL   97 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~-v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~   97 (153)
                      ...+||||||++..+..+...|++.||. +..+.++.+|++.+.              .++||+||+|+.||+++|++++
T Consensus         5 ~~~kILiVDD~~~~~~~l~~~L~~~g~~~v~~a~~~~~al~~l~--------------~~~~dlii~D~~mP~~~G~el~   70 (129)
T d1p6qa_           5 EKIKVLIVDDQVTSRLLLGDALQQLGFKQITAAGDGEQGMKIMA--------------QNPHHLVISDFNMPKMDGLGLL   70 (129)
T ss_dssp             SCCCEEEECSSHHHHHHHHHHHHTTTCSCEECCSSHHHHHHHHH--------------TSCCSEEEECSSSCSSCHHHHH
T ss_pred             CCCEEEEEECCHHHHHHHHHHHHHCCCeEEEEECCHHHHHHHHH--------------hCCCCeEEeeeecCCCChHHHH
Confidence            4568999999999999999999999995 788999999999883              4679999999999999999999


Q ss_pred             HHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079           98 KKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus        98 ~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      +.+|+....+.+|+|++|+..+.+...++++.|+++|+.||++.++|...+.+++
T Consensus        71 ~~lr~~~~~~~~pii~lt~~~~~~~~~~a~~~G~~~~l~KP~~~~~L~~~i~~vl  125 (129)
T d1p6qa_          71 QAVRANPATKKAAFIILTAQGDRALVQKAAALGANNVLAKPFTIEKMKAAIEAVF  125 (129)
T ss_dssp             HHHTTCTTSTTCEEEECCSCCCHHHHHHHHHHTCSCEECCCSSHHHHHHHHHHHH
T ss_pred             HHHHhCcccCCCeEEEEEecCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHH
Confidence            9999876667899999999999999999999999999999999999998887753

>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=6.7e-27  Score=155.62  Aligned_cols=122  Identities=24%  Similarity=0.426  Sum_probs=108.3

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcE-EEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKK   99 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~-v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~   99 (153)
                      .+||||||++..+..+..+|+..|+. +..+.++.+|++.+.....         ...+||+||+|+.||+++|++++++
T Consensus         2 irVLvVDD~~~~~~~l~~~L~~~g~~~v~~a~~g~eAl~~l~~~~~---------~~~~~dlillD~~mP~~dG~el~~~   72 (128)
T d2r25b1           2 VKILVVEDNHVNQEVIKRMLNLEGIENIELACDGQEAFDKVKELTS---------KGENYNMIFMDVQMPKVDGLLSTKM   72 (128)
T ss_dssp             SCEEEECSCHHHHHHHHHHHHHTTCCCEEEESSHHHHHHHHHHHHH---------HTCCCSEEEECSCCSSSCHHHHHHH
T ss_pred             eEEEEEeCCHHHHHHHHHHHHHcCCeEEEEEcChHHHHHHHHhhhh---------ccCCCCEEEEEeCCCCCCHHHHHHH
Confidence            47999999999999999999999985 7889999999998743211         2467999999999999999999999


Q ss_pred             HHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079          100 IKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus       100 lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      +|+... ..+|||++|+..+.....++++.|+++||.||++.++|.+.+.+++
T Consensus        73 ir~~~~-~~~piI~lT~~~~~~~~~~~~~~G~~~~l~KP~~~~~L~~~l~~~~  124 (128)
T d2r25b1          73 IRRDLG-YTSPIVALTAFADDSNIKECLESGMNGFLSKPIKRPKLKTILTEFC  124 (128)
T ss_dssp             HHHHSC-CCSCEEEEESCCSHHHHHHHHHTTCSEEEESSCCHHHHHHHHHHHC
T ss_pred             HHHccC-CCCeEEEEECCCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHH
Confidence            987543 5789999999999999999999999999999999999999998864

>d1kgsa2 c.23.1.1 (A:2-123) PhoB receiver domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: PhoB receiver domain
species: Thermotoga maritima [TaxId: 2336]

Probab=99.95  E-value=2.6e-27  Score=156.36  Aligned_cols=117  Identities=23%  Similarity=0.327  Sum_probs=107.9

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKK   99 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~   99 (153)
                      +.+||||||++..+..++.+|+..||.|..+.++.+|++.+.              ...||+|++|+.||+++|++++++
T Consensus         1 nirILiVdDd~~~~~~l~~~L~~~g~~v~~a~~~~~al~~l~--------------~~~~dlillD~~mp~~~g~~~~~~   66 (122)
T d1kgsa2           1 NVRVLVVEDERDLADLITEALKKEMFTVDVCYDGEEGMYMAL--------------NEPFDVVILDIMLPVHDGWEILKS   66 (122)
T ss_dssp             CCEEEEECSSHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--------------HSCCSEEEEESCCSSSCHHHHHHH
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHHCCCEEEEEcchHHHHHHHH--------------hhCccccccccccccchhHHHHHH
Confidence            468999999999999999999999999999999999999884              357999999999999999999999


Q ss_pred             HHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079          100 IKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus       100 lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      +|+..  +.+|+|++|+..+.+...++++.|+++||.||+++++|...+.+++
T Consensus        67 lr~~~--~~~piI~lt~~~~~~~~~~~~~~Ga~~yl~KP~~~~~L~~~i~~~l  117 (122)
T d1kgsa2          67 MRESG--VNTPVLMLTALSDVEYRVKGLNMGADDYLPKPFDLRELIARVRALI  117 (122)
T ss_dssp             HHHTT--CCCCEEEEESSCHHHHHHHTCCCCCSEEEESSCCHHHHHHHHHHHH
T ss_pred             HHhcC--CCCcEEEEcCCCCHHHHHHHHHcCCceeecCCCCHHHHHHHHHHHH
Confidence            99754  5789999999999999999999999999999999999988777653

>d1xhfa1 c.23.1.1 (A:2-122) Aerobic respiration control protein ArcA, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Aerobic respiration control protein ArcA, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=99.95  E-value=7.9e-27  Score=153.85  Aligned_cols=115  Identities=26%  Similarity=0.494  Sum_probs=106.5

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKI  100 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~l  100 (153)
                      ++||||||++..+..+..+|+..||++..+.++.++++.+.              ...||+|++|+.||+++|+++++++
T Consensus         3 p~ILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~~al~~l~--------------~~~~dlii~D~~mp~~~G~~~~~~~   68 (121)
T d1xhfa1           3 PHILIVEDELVTRNTLKSIFEAEGYDVFEATDGAEMHQILS--------------EYDINLVIMDINLPGKNGLLLAREL   68 (121)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHH--------------HSCCSEEEECSSCSSSCHHHHHHHH
T ss_pred             CEEEEEECCHHHHHHHHHHHHHCCCEEEEECChHHHHHHHH--------------hcCCCEEEeecccCCccCcHHHHHH
Confidence            58999999999999999999999999999999999999884              3579999999999999999999999


Q ss_pred             HhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079          101 KESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus       101 r~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      |+.   +++|+|++|+..+.....++++.|+++||.||+++++|...+.+++
T Consensus        69 r~~---~~~pii~lt~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~v~~~l  117 (121)
T d1xhfa1          69 REQ---ANVALMFLTGRDNEVDKILGLEIGADDYITKPFNPRELTIRARNLL  117 (121)
T ss_dssp             HHH---CCCEEEEEESCCSHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHH
T ss_pred             Hhc---CCCcEEEEECCCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHHH
Confidence            975   4799999999999999999999999999999999999987776653

>d1ny5a1 c.23.1.1 (A:1-137) Transcriptional activator sigm54 (NtrC1), N-terminal domain {Aquifex aeolicus [TaxId: 63363]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Transcriptional activator sigm54 (NtrC1), N-terminal domain
species: Aquifex aeolicus [TaxId: 63363]

Probab=99.95  E-value=2.8e-27  Score=159.15  Aligned_cols=115  Identities=30%  Similarity=0.445  Sum_probs=107.2

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKI  100 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~l  100 (153)
                      ++||||||++..+..++.+|+..||++..+.++.+|+..+.              .+.||+||+|+.||+++|+++++++
T Consensus         1 mkILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~eAl~~l~--------------~~~~dlvilD~~mp~~~G~e~~~~l   66 (137)
T d1ny5a1           1 MNVLVIEDDKVFRGLLEEYLSMKGIKVESAERGKEAYKLLS--------------EKHFNVVLLDLLLPDVNGLEILKWI   66 (137)
T ss_dssp             CEEEEECCCHHHHHHHHHHHHHHTCEEEEESSHHHHHHHHH--------------HSCCSEEEEESBCSSSBHHHHHHHH
T ss_pred             CEEEEEecCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHhh--------------ccccccchHHHhhhhhhHHHHHHHH
Confidence            57999999999999999999999999999999999999884              3579999999999999999999999


Q ss_pred             HhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          101 KESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       101 r~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      |+..  +.+|||++|+..+.+...+|++.||++||.||+++++|...+.+.
T Consensus        67 r~~~--~~~piI~lT~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~  115 (137)
T d1ny5a1          67 KERS--PETEVIVITGHGTIKTAVEAMKMGAYDFLTKPCMLEEIELTINKA  115 (137)
T ss_dssp             HHHC--TTSEEEEEEETTCHHHHHHHHTTTCCEEEEESCCHHHHHHHHHHH
T ss_pred             HHhC--CCCCEEEEECCCCHHHHHHHHHcCCCEEEeCCCCHHHHHHHHHHH
Confidence            9865  689999999999999999999999999999999999999877764

>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=5.4e-27  Score=154.01  Aligned_cols=115  Identities=28%  Similarity=0.466  Sum_probs=106.1

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEE-EecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVT-TAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKK   99 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~-~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~   99 (153)
                      .+||||||++..+..++.+|+..||++. .+.++.+|++.+.              ...||+||+|+.||+++|++++++
T Consensus         2 krILivDD~~~~~~~l~~~L~~~g~~v~~~a~~~~~al~~~~--------------~~~~dliilD~~mp~~~G~e~~~~   67 (118)
T d1u0sy_           2 KRVLIVDDAAFMRMMLKDIITKAGYEVAGEATNGREAVEKYK--------------ELKPDIVTMDITMPEMNGIDAIKE   67 (118)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHH--------------HHCCSEEEEECSCGGGCHHHHHHH
T ss_pred             CEEEEEeCCHHHHHHHHHHHHHcCCceEEEECCHHHHHHHHH--------------hccCCEEEEecCCCCCCHHHHHHH
Confidence            6899999999999999999999999876 6899999999884              246999999999999999999999


Q ss_pred             HHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          100 IKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       100 lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      +|+..  +++|+|++|+..+.+...++++.|+++||.||+++++|.+.++++
T Consensus        68 ir~~~--~~~pvi~ls~~~~~~~~~~a~~~Ga~~yl~KP~~~~~L~~~l~~v  117 (118)
T d1u0sy_          68 IMKID--PNAKIIVCSAMGQQAMVIEAIKAGAKDFIVKPFQPSRVVEALNKV  117 (118)
T ss_dssp             HHHHC--TTCCEEEEECTTCHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHH
T ss_pred             HHHhC--CCCcEEEEEccCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHh
Confidence            99765  689999999999999999999999999999999999999998774

>d2ayxa1 c.23.1.1 (A:817-949) Sensor kinase protein RcsC, C-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Sensor kinase protein RcsC, C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=99.95  E-value=3.3e-27  Score=158.10  Aligned_cols=118  Identities=26%  Similarity=0.504  Sum_probs=108.9

Q ss_pred             CCCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHH
Q 042079           18 PKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELL   97 (153)
Q Consensus        18 ~~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~   97 (153)
                      ....+||||||++..+..+..+|+..||.+..+.++.+|++.+.              ..+||+||+|+.||+++|++++
T Consensus         6 ~~~~~ILiVDD~~~~~~~l~~~L~~~g~~v~~a~~g~ea~~~~~--------------~~~~dlillD~~mP~~dG~el~   71 (133)
T d2ayxa1           6 NDDMMILVVDDHPINRRLLADQLGSLGYQCKTANDGVDALNVLS--------------KNHIDIVLSDVNMPNMDGYRLT   71 (133)
T ss_dssp             CCCCEEEEEESSHHHHHHHHHHHHHHTSEEEEECCSHHHHHHHH--------------HSCCSEEEEEESSCSSCCHHHH
T ss_pred             CCCCEEEEEECCHHHHHHHHHHHHHcCCEEEEECcHHHHHHHHh--------------ccCceEEEEeccCCCCCHHHHH
Confidence            35689999999999999999999999999999999999999884              3579999999999999999999


Q ss_pred             HHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           98 KKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        98 ~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      ++||+..  +.+||+++|+....+...++++.|+++||.||++.++|...+.+.
T Consensus        72 ~~ir~~~--~~~pii~lt~~~~~~~~~~~~~~G~~~~l~KP~~~~~L~~~l~~~  123 (133)
T d2ayxa1          72 QRIRQLG--LTLPVIGVTANALAEEKQRCLESGMDSCLSKPVTLDVIKQTLTLY  123 (133)
T ss_dssp             HHHHHHH--CCSCEEEEESSTTSHHHHHHHHCCCEEEEESSCCHHHHHHHHHHH
T ss_pred             HHHHHhC--CCCCEEEEeccCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHH
Confidence            9999876  578999999999999999999999999999999999999887764

>d1zh2a1 c.23.1.1 (A:2-120) Transcriptional regulatory protein KdpE, N-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Transcriptional regulatory protein KdpE, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=99.95  E-value=3.8e-27  Score=154.97  Aligned_cols=115  Identities=24%  Similarity=0.376  Sum_probs=106.0

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKI  100 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~l  100 (153)
                      .+||||||++..+..+..+|+..||++..+.++.+|++.+.              ...||+||+|+.||+++|+++++++
T Consensus         1 TnILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~eal~~l~--------------~~~~dliilD~~mP~~~G~e~~~~i   66 (119)
T d1zh2a1           1 TNVLIVEDEQAIRRFLRTALEGDGMRVFEAETLQRGLLEAA--------------TRKPDLIILDLGLPDGDGIEFIRDL   66 (119)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHHH--------------HHCCSEEEEESEETTEEHHHHHHHH
T ss_pred             CEEEEEECCHHHHHHHHHHHHHCCCEEEEeCCHHHHHHHHH--------------hcCCCEEEeccccCCCCCchHHHHH
Confidence            47999999999999999999999999999999999999884              3469999999999999999999999


Q ss_pred             HhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079          101 KESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus       101 r~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      |+.   +..|+|++|+..+.+...++++.|+++||.||+++++|...+.+++
T Consensus        67 r~~---~~~piI~lt~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~l  115 (119)
T d1zh2a1          67 RQW---SAVPVIVLSARSEESDKIAALDAGADDYLSKPFGIGELQARLRVAL  115 (119)
T ss_dssp             HTT---CCCCEEEEESCCSHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHH
T ss_pred             Hhc---cCCcEEEEeccCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHH
Confidence            974   4679999999999999999999999999999999999998887654

>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=99.95  E-value=1.4e-26  Score=156.29  Aligned_cols=125  Identities=24%  Similarity=0.409  Sum_probs=109.5

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcC--cEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSA--CKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELL   97 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~--~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~   97 (153)
                      +++||||||++..+..++..|++.|  +++..+.++.+|++.+....       ......+||+||+|+.||+++|++++
T Consensus         2 ~krILiVDD~~~~~~~l~~~L~~~g~~~~v~~a~~g~eAl~~l~~~~-------~~~~~~~pdlillD~~mP~~dG~el~   74 (140)
T d1k68a_           2 HKKIFLVEDNKADIRLIQEALANSTVPHEVVTVRDGMEAMAYLRQEG-------EYANASRPDLILLDLNLPKKDGREVL   74 (140)
T ss_dssp             CCEEEEECCCHHHHHHHHHHHHTCSSCCEEEEECSHHHHHHHHTTCG-------GGGSCCCCSEEEECSSCSSSCHHHHH
T ss_pred             CCcEEEEECCHHHHHHHHHHHHHcCCCeEEEEECCHHHHHHHHHHhH-------HhhccCCCCEEEEeeccccccChHHH
Confidence            4689999999999999999999765  68999999999999884321       11134679999999999999999999


Q ss_pred             HHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           98 KKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        98 ~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      +++|+......+|||++|+..+.+...++++.|+++|+.||++.++|.+.+..+
T Consensus        75 ~~ir~~~~~~~iPvI~ls~~~~~~~~~~a~~~Ga~~yl~KP~~~~~L~~~i~~i  128 (140)
T d1k68a_          75 AEIKSDPTLKRIPVVVLSTSINEDDIFHSYDLHVNCYITKSANLSQLFQIVKGI  128 (140)
T ss_dssp             HHHHHSTTGGGSCEEEEESCCCHHHHHHHHHTTCSEEEECCSSHHHHHHHHHHH
T ss_pred             HHHHhCcccCCCcEEEEeCCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHH
Confidence            999987666689999999999999999999999999999999999998887764

>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=99.95  E-value=2.5e-26  Score=155.66  Aligned_cols=125  Identities=26%  Similarity=0.443  Sum_probs=109.1

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcC--cEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSA--CKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELL   97 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~--~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~   97 (153)
                      ..+||||||++..+..++.+|++.|  +++..+.++.+|+..+....       .......||+||+|+.||+++|++++
T Consensus         3 pk~ILiVdD~~~~~~~l~~~L~~~g~~~~v~~a~~g~~Al~~l~~~~-------~~~~~~~pdlIllD~~mP~~~G~el~   75 (144)
T d1i3ca_           3 PKVILLVEDSKADSRLVQEVLKTSTIDHELIILRDGLAAMAFLQQQG-------EYENSPRPNLILLDLNLPKKDGREVL   75 (144)
T ss_dssp             CEEEEEECCCHHHHHHHHHHHHSCCSCEEEEEECSHHHHHHHHTTCG-------GGTTCCCCSEEEECSCCSSSCHHHHH
T ss_pred             CCEEEEEECCHHHHHHHHHHHHHcCCCeEEEEECCHHHHHHHHHhch-------hhhccCCCCEEEEECccccccchHHH
Confidence            4689999999999999999998765  57889999999999884321       11134569999999999999999999


Q ss_pred             HHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           98 KKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        98 ~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      ++||+......+|||++|+..+.+...+|++.|+++||.||++.++|.+.+.++
T Consensus        76 ~~ir~~~~~~~iPvi~lT~~~~~~~~~~a~~~Ga~~yl~KP~~~~~L~~~i~~l  129 (144)
T d1i3ca_          76 AEIKQNPDLKRIPVVVLTTSHNEDDVIASYELHVNCYLTKSRNLKDLFKMVQGI  129 (144)
T ss_dssp             HHHHHCTTTTTSCEEEEESCCCHHHHHHHHHTTCSEEEECCSSHHHHHHHHHHH
T ss_pred             HHHHhCcccCCCeEEEEECCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHH
Confidence            999987666789999999999999999999999999999999999998877664

>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=99.94  E-value=1.3e-26  Score=154.20  Aligned_cols=116  Identities=25%  Similarity=0.397  Sum_probs=107.6

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKI  100 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~l  100 (153)
                      ++||||||++..+..+..+|+..||.|..+.++.+++..+              ....||+||+|+.||+++|+++++++
T Consensus         3 P~ILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~~al~~~--------------~~~~~dliilD~~mp~~~G~~~~~~i   68 (128)
T d1yioa2           3 PTVFVVDDDMSVREGLRNLLRSAGFEVETFDCASTFLEHR--------------RPEQHGCLVLDMRMPGMSGIELQEQL   68 (128)
T ss_dssp             CEEEEECSCHHHHHHHHHHHHTTTCEEEEESSHHHHHHHC--------------CTTSCEEEEEESCCSSSCHHHHHHHH
T ss_pred             CEEEEEECCHHHHHHHHHHHHHcCCCccccccHHHHHHHH--------------HhcCCCEeehhhhcccchhHHHHHHH
Confidence            5899999999999999999999999999999999999988              35679999999999999999999999


Q ss_pred             HhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079          101 KESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus       101 r~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      ++..  +..|++++|+..+.+...++++.|+++||.||++.++|...+.+.+
T Consensus        69 ~~~~--~~~~ii~lt~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~l  118 (128)
T d1yioa2          69 TAIS--DGIPIVFITAHGDIPMTVRAMKAGAIEFLPKPFEEQALLDAIEQGL  118 (128)
T ss_dssp             HHTT--CCCCEEEEESCTTSCCCHHHHHTTEEEEEESSCCHHHHHHHHHHHH
T ss_pred             HhhC--CCCeEEEEEEECCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHH
Confidence            9865  6789999999988888899999999999999999999998887753

>d1dcfa_ c.23.1.2 (A:) Receiver domain of the ethylene receptor {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: Receiver domain of the ethylene receptor
domain: Receiver domain of the ethylene receptor
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.94  E-value=3.4e-26  Score=153.28  Aligned_cols=120  Identities=24%  Similarity=0.446  Sum_probs=107.8

Q ss_pred             CCCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHH
Q 042079           18 PKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELL   97 (153)
Q Consensus        18 ~~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~   97 (153)
                      -++.+||||||++..+..++.+|+..|+++..+.++.+|++.+.               +.||+||+|+.||+++|++++
T Consensus         5 ~~g~rILvVDD~~~~~~~l~~~L~~~G~~v~~a~~g~eal~~l~---------------~~~dlillD~~mP~~dG~el~   69 (134)
T d1dcfa_           5 FTGLKVLVMDENGVSRMVTKGLLVHLGCEVTTVSSNEECLRVVS---------------HEHKVVFMDVCMPGVENYQIA   69 (134)
T ss_dssp             CTTCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHHCC---------------TTCSEEEEECCSSTTTTTHHH
T ss_pred             CCCCEEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHhh---------------cCCCeEEEEeccCCCchHHHH
Confidence            35689999999999999999999999999999999999998772               469999999999999999999


Q ss_pred             HHHHhcc---CCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079           98 KKIKESS---VMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus        98 ~~lr~~~---~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      +++|+..   ..+.+|||++|+....+...++++.|+++|+.||++.++|.+.+.+++
T Consensus        70 ~~ir~~~~~~~~~~~~ii~lT~~~~~~~~~~~~~~G~~~~l~KP~~~~~L~~~l~~~l  127 (134)
T d1dcfa_          70 LRIHEKFTKQRHQRPLLVALSGNTDKSTKEKCMSFGLDGVLLKPVSLDNIRDVLSDLL  127 (134)
T ss_dssp             HHHHHHHC-CCSCCCEEEEEESCCSHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHHH
T ss_pred             HHHHHhcccccCCCCeEEEEeCCCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHHh
Confidence            9998532   234578999999989999999999999999999999999999988864

>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=1.2e-26  Score=156.41  Aligned_cols=117  Identities=26%  Similarity=0.434  Sum_probs=108.0

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKI  100 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~l  100 (153)
                      .+||||||++..++.++.+|+..||+|..+.++.+|++.+.              .+.||+|++|+.||+++|+++++.+
T Consensus         2 arILiVDD~~~~~~~l~~~L~~~g~~v~~a~~~~eal~~~~--------------~~~~dlil~D~~~p~~~G~~~~~~i   67 (139)
T d1w25a1           2 ARILVVDDIEANVRLLEAKLTAEYYEVSTAMDGPTALAMAA--------------RDLPDIILLDVMMPGMDGFTVCRKL   67 (139)
T ss_dssp             CEEEEECSSTTHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--------------HHCCSEEEEESCCSSSCHHHHHHHH
T ss_pred             CEEEEEECCHHHHHHHHHHHHHCCCEEEEEccchhhhhhhh--------------cccceeeeeeccccCCCchHHHHHh
Confidence            47999999999999999999999999999999999999884              3469999999999999999999999


Q ss_pred             HhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079          101 KESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus       101 r~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      |.......+|||++|+..+.....++++.|+++|+.||+++.+|...+..+
T Consensus        68 r~~~~~~~~piI~lt~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~  118 (139)
T d1w25a1          68 KDDPTTRHIPVVLITALDGRGDRIQGLESGASDFLTKPIDDVMLFARVRSL  118 (139)
T ss_dssp             HHSTTTTTSCEEEEECSSCHHHHHHHHHHTCCEEEESSCCHHHHHHHHHHH
T ss_pred             hhcccccCCCEEEEEcCCCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHH
Confidence            986666789999999999999999999999999999999999998766654

>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=3.4e-26  Score=150.49  Aligned_cols=115  Identities=21%  Similarity=0.362  Sum_probs=105.9

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKI  100 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~l  100 (153)
                      .+||||||++..+..+..+|+..||.|..+.++.++++.+.              .+.||+|++|+.||+++|+++++.+
T Consensus         2 ~rILiVDDd~~~~~~l~~~L~~~g~~v~~a~~~~~a~~~~~--------------~~~~dliilD~~mp~~~g~~~~~~~   67 (120)
T d1zgza1           2 HHIVIVEDEPVTQARLQSYFTQEGYTVSVTASGAGLREIMQ--------------NQSVDLILLDINLPDENGLMLTRAL   67 (120)
T ss_dssp             CEEEEECSSHHHHHHHHHHHHHTTCEEEEESSHHHHHHHHH--------------HSCCSEEEEESCCSSSCHHHHHHHH
T ss_pred             CEEEEEeCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHH--------------hcCCCEEeeehhhccchhHHHHHHH
Confidence            58999999999999999999999999999999999999883              3579999999999999999999998


Q ss_pred             HhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079          101 KESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus       101 r~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      +..   +.+|+|++|+..+.....+|++.||++|+.||++.++|...+++++
T Consensus        68 ~~~---~~~piI~lt~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~l  116 (120)
T d1zgza1          68 RER---STVGIILVTGRSDRIDRIVGLEMGADDYVTKPLELRELVVRVKNLL  116 (120)
T ss_dssp             HTT---CCCEEEEEESSCCHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHH
T ss_pred             hcc---CCCeEEEEEccCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHH
Confidence            864   4789999999999999999999999999999999999998777653

>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=5.2e-26  Score=154.93  Aligned_cols=128  Identities=25%  Similarity=0.440  Sum_probs=109.0

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCc--EEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSAC--KVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~--~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      .+||||||++..+..++.+|++.|+  .+..+.++.+|++.+.....    .........||+||+|+.||+++|+++++
T Consensus         7 ~~ILiVDD~~~~~~~l~~~L~~~g~~~~v~~a~~g~eAl~~l~~~~~----~~~~~~~~~pdlillD~~mP~~~G~el~~   82 (149)
T d1k66a_           7 QPLLVVEDSDEDFSTFQRLLQREGVVNPIYRCITGDQALDFLYQTGS----YCNPDIAPRPAVILLDLNLPGTDGREVLQ   82 (149)
T ss_dssp             SCEEEECCCHHHHHHHHHHHHHTTBCSCEEEECSHHHHHHHHHTCCS----SSCGGGCCCCSEEEECSCCSSSCHHHHHH
T ss_pred             CcEEEEECCHHHHHHHHHHHHHcCCceEEEEECChHHHHHHHHhhcc----ccccccccCCCeEEccccccCCCcHHHHH
Confidence            4699999999999999999999887  78999999999998842110    00001134699999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      +||+....+.+|||++|+..+.+...++++.|+++|+.||++.++|...+.+++
T Consensus        83 ~ir~~~~~~~ipiI~lT~~~~~~~~~~~~~~Ga~~~l~KP~~~~~L~~~i~~~l  136 (149)
T d1k66a_          83 EIKQDEVLKKIPVVIMTTSSNPKDIEICYSYSISSYIVKPLEIDRLTETVQTFI  136 (149)
T ss_dssp             HHTTSTTGGGSCEEEEESCCCHHHHHHHHHTTCSEEEECCSSHHHHHHHHHHHH
T ss_pred             HHHhccccCCCeEEEEeCCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHH
Confidence            999866567899999999999999999999999999999999999988777653

>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=8.3e-26  Score=148.69  Aligned_cols=113  Identities=24%  Similarity=0.301  Sum_probs=102.2

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKI  100 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~l  100 (153)
                      .+||||||++..+..++..|++.|+ +..+.++.+++..                .++||+||+|+.||+++|+++++++
T Consensus         3 ~kILiVDDd~~~~~~l~~~L~~~g~-v~~~~~~~~al~~----------------~~~~dlillD~~mP~~~G~~~~~~l   65 (120)
T d1p2fa2           3 WKIAVVDDDKNILKKVSEKLQQLGR-VKTFLTGEDFLND----------------EEAFHVVVLDVMLPDYSGYEICRMI   65 (120)
T ss_dssp             EEEEEECSCHHHHHHHHHHHTTTEE-EEEESSHHHHHHC----------------CSCCSEEEEESBCSSSBHHHHHHHH
T ss_pred             CEEEEEECCHHHHHHHHHHHHhCCE-EEEECCHHHHHhc----------------CCCCCEEEEeCcccccchhHHHHHH
Confidence            5899999999999999999998886 8889999988752                2469999999999999999999999


Q ss_pred             HhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079          101 KESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus       101 r~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      |+..  +.+|+|++|+..+.+...+|++.|+++|+.||+++++|...+.+++
T Consensus        66 r~~~--~~~~ii~it~~~~~~~~~~a~~~Ga~dyl~KP~~~~~L~~~i~~~l  115 (120)
T d1p2fa2          66 KETR--PETWVILLTLLSDDESVLKGFEAGADDYVTKPFNPEILLARVKRFL  115 (120)
T ss_dssp             HHHC--TTSEEEEEESCCSHHHHHHHHHHTCSEEEESSCCHHHHHHHHHHHH
T ss_pred             hhcC--CCCcEEEEecCCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHH
Confidence            9765  6899999999999999999999999999999999999998877753

>d1a04a2 c.23.1.1 (A:5-142) Nitrate/nitrite response regulator (NarL), receiver domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Nitrate/nitrite response regulator (NarL), receiver domain
species: Escherichia coli [TaxId: 562]

Probab=99.93  E-value=2.5e-25  Score=149.68  Aligned_cols=116  Identities=31%  Similarity=0.472  Sum_probs=105.0

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcC--cEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSA--CKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELL   97 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~--~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~   97 (153)
                      +.+||||||++..+..++.+|+..+  +.+..+.++.++++.+.              .+.||++++|+.||+++|++++
T Consensus         2 Pi~VLiVDD~~~~r~~l~~~L~~~~~~~~v~~a~~~~~al~~~~--------------~~~~DlvllD~~mP~~~G~el~   67 (138)
T d1a04a2           2 PATILLIDDHPMLRTGVKQLISMAPDITVVGEASNGEQGIELAE--------------SLDPDLILLDLNMPGMNGLETL   67 (138)
T ss_dssp             CEEEEEECSCHHHHHHHHHHHTTCTTEEEEEEESSHHHHHHHHH--------------HHCCSEEEEETTSTTSCHHHHH
T ss_pred             CCEEEEECCCHHHHHHHHHHHHhCCCcEEEEEECCHHHHHHHHH--------------hcCCCEEEEecCCCCCCHHHHH
Confidence            4689999999999999999998766  56778999999999884              3469999999999999999999


Q ss_pred             HHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           98 KKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        98 ~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      ++||+..  +.+|++++|...+.+...++++.|+++|+.||+++++|.+.+.+.
T Consensus        68 ~~ir~~~--~~~~vivlt~~~~~~~~~~a~~~Ga~~yl~Kp~~~~~L~~~i~~v  119 (138)
T d1a04a2          68 DKLREKS--LSGRIVVFSVSNHEEDVVTALKRGADGYLLKDMEPEDLLKALHQA  119 (138)
T ss_dssp             HHHHHSC--CCSEEEEEECCCCHHHHHHHHHTTCSEEEETTCCHHHHHHHHHHH
T ss_pred             HHHHhhC--CCCCEEEEEEECCHHHHHHHHHcCCCEEEECCCCHHHHHHHHHHH
Confidence            9999865  688999999999999999999999999999999999999888764

>d1dz3a_ c.23.1.1 (A:) Sporulation response regulator Spo0A {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Sporulation response regulator Spo0A
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=99.93  E-value=1.9e-25  Score=147.56  Aligned_cols=117  Identities=20%  Similarity=0.349  Sum_probs=102.7

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcC-c-EEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSA-C-KVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~-~-~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      .+|||+||++..+..++.+|+..+ + .+..+.++.+|++.+.              ...||+||+|+.||+++|+++++
T Consensus         2 irILivDD~~~~~~~l~~~L~~~~~~~~v~~a~~g~~al~~~~--------------~~~~dlillD~~mP~~dG~e~~~   67 (123)
T d1dz3a_           2 IKVCIADDNRELVSLLDEYISSQPDMEVIGTAYNGQDCLQMLE--------------EKRPDILLLDIIMPHLDGLAVLE   67 (123)
T ss_dssp             EEEEEECSCHHHHHHHHHHHHTSTTEEEEEEESSHHHHHHHHH--------------HHCCSEEEEESCCSSSCHHHHHH
T ss_pred             cEEEEEeCCHHHHHHHHHHHHhCCCcEEEEEECCHHHHHHHHH--------------hcCCCEEEEcCCCCCCCHHHHHH
Confidence            589999999999999999998765 3 3568999999999884              34699999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhhc
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHLI  152 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~~  152 (153)
                      ++|+... ...|||++|+..+.....++++.|+++|+.||+++++|.+.+++++
T Consensus        68 ~ir~~~~-~~~~ii~~t~~~~~~~~~~a~~~Ga~~~l~KP~~~~~L~~~i~~v~  120 (123)
T d1dz3a_          68 RIRAGFE-HQPNVIMLTAFGQEDVTKKAVELGASYFILKPFDMENLAHHIRQVY  120 (123)
T ss_dssp             HHHHHCS-SCCEEEEEEETTCHHHHHHHHHTTCEEEEECSSCCTTHHHHHHHHH
T ss_pred             HHHhcCC-CCCeEEEEECcCCHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHH
Confidence            9997542 3457999999999999999999999999999999999999888753

>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=3.3e-25  Score=151.53  Aligned_cols=117  Identities=19%  Similarity=0.276  Sum_probs=101.2

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      ...+||||||++..+..+...|+..||.+..  ++.++...+.              .++||+||+|+.||+++|+++++
T Consensus        12 ~~~rILiVDD~~~~~~~l~~~L~~~g~~v~~--~~~~~~~~~~--------------~~~~DlillD~~mP~~dG~el~~   75 (153)
T d1w25a2          12 LGGRVLIVDDNERQAQRVAAELGVEHRPVIE--SDPEKAKISA--------------GGPVDLVIVNAAAKNFDGLRFTA   75 (153)
T ss_dssp             CSCEEEEECSCHHHHHHHHHHHTTTSEEEEE--CCHHHHHHHH--------------HSSCSEEEEETTCSSSCHHHHHH
T ss_pred             CCCeEEEEeCCHHHHHHHHHHHHHCCCEEEE--ccHHHHHHHh--------------cCCCCEEEEECccccccchHHHH
Confidence            4578999999999999999999999988744  4455555542              35799999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      .||.....+.+|||++|+..+.....+|++.|+++||.||+++.+|...+...
T Consensus        76 ~ir~~~~~~~iPiI~lt~~~~~~~~~~a~~~Ga~d~l~KP~~~~~L~~~i~~~  128 (153)
T d1w25a2          76 ALRSEERTRQLPVLAMVDPDDRGRMVKALEIGVNDILSRPIDPQELSARVKTQ  128 (153)
T ss_dssp             HHHTSGGGTTCCEEEEECTTCHHHHHHHHHTTCCEEEESSCCHHHHHHHHHHH
T ss_pred             HHHhccccccceeEEeecCCCHHHHHHHHhcCcceEEECCCCHHHHHHHHHHH
Confidence            99976656789999999999999999999999999999999999998766553

>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=6.9e-26  Score=159.87  Aligned_cols=114  Identities=25%  Similarity=0.389  Sum_probs=104.2

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCcEEE-EecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSACKVT-TAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~~~v~-~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      +.+||||||++..+..+..+|+..||++. .+.++.+|++.+.              ...||+|++|+.||+++|+++++
T Consensus         3 p~kILiVDD~~~~r~~l~~~L~~~g~~vv~~a~~g~eal~~~~--------------~~~pDlvllDi~mP~~dG~e~~~   68 (190)
T d1s8na_           3 PRRVLIAEDEALIRMDLAEMLREEGYEIVGEAGDGQEAVELAE--------------LHKPDLVIMDVKMPRRDGIDAAS   68 (190)
T ss_dssp             CCEEEEECSSHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHH--------------HHCCSEEEEESSCSSSCHHHHHH
T ss_pred             CCEEEEEeCCHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHh--------------cCCCCEEEEeccccCcchHHHHH
Confidence            57899999999999999999999999865 7999999999884              34699999999999999999999


Q ss_pred             HHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhh
Q 042079           99 KIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGH  150 (153)
Q Consensus        99 ~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~  150 (153)
                      ++|+.   +.+|||++|+..+.+...+|++.||++|+.||++++++...+..
T Consensus        69 ~ir~~---~~~pIi~lTa~~~~~~~~~al~~Ga~~yl~KP~~~~~L~~~i~~  117 (190)
T d1s8na_          69 EIASK---RIAPIVVLTAFSQRDLVERARDAGAMAYLVKPFSISDLIPAIEL  117 (190)
T ss_dssp             HHHHT---TCSCEEEEEEGGGHHHHHTTGGGSCEEEEEESCCHHHHHHHHHH
T ss_pred             HHHhc---CCCCEEEEeCCCCHHHHHHHHHcCCCEeccCCCCHHHHHHHHHH
Confidence            99975   36899999999999999999999999999999999999877754

>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=3.7e-24  Score=140.32  Aligned_cols=113  Identities=19%  Similarity=0.283  Sum_probs=96.5

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKK   99 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~   99 (153)
                      +++||||||++..+..+..+|++.||++..+.++.++++.+.             ...+||+||+|+.||+++|++++++
T Consensus         2 p~rILvVdDd~~~~~~l~~~L~~~g~~v~~~~~~~~al~~l~-------------~~~~~dliilD~~lp~~~G~el~~~   68 (118)
T d2b4aa1           2 PFRVTLVEDEPSHATLIQYHLNQLGAEVTVHPSGSAFFQHRS-------------QLSTCDLLIVSDQLVDLSIFSLLDI   68 (118)
T ss_dssp             CCEEEEECSCHHHHHHHHHHHHHTTCEEEEESSHHHHHHTGG-------------GGGSCSEEEEETTCTTSCHHHHHHH
T ss_pred             CCEEEEEECCHHHHHHHHHHHHhcCCCeEEECCHHHHHHHHH-------------hcCCCCEEEEeCCCCCCCHHHHHHH
Confidence            478999999999999999999999999999999999998663             1236999999999999999999999


Q ss_pred             HHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhh
Q 042079          100 IKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGH  150 (153)
Q Consensus       100 lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~  150 (153)
                      +|+..  +.+|+|++|+..+..  .++...|+ +||.||+++++|...+.+
T Consensus        69 ir~~~--~~~pii~lt~~~~~~--~~~~~~~~-dyl~KP~~~~eL~~~i~~  114 (118)
T d2b4aa1          69 VKEQT--KQPSVLILTTGRHEL--IESSEHNL-SYLQKPFAISELRAAIDY  114 (118)
T ss_dssp             HTTSS--SCCEEEEEESCC--C--CCCSSSCE-EEEESSCCHHHHHHHHHH
T ss_pred             HHhcC--CCCcEEEEECCccHH--HHHhhcCC-CEEECCCCHHHHHHHHHH
Confidence            99764  579999999865433  34556676 799999999999887765

>d1a2oa1 c.23.1.1 (A:1-140) Methylesterase CheB, N-terminal domain {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: CheY-related
domain: Methylesterase CheB, N-terminal domain
species: Salmonella typhimurium [TaxId: 90371]

Probab=99.88  E-value=8.1e-23  Score=137.52  Aligned_cols=106  Identities=27%  Similarity=0.323  Sum_probs=87.8

Q ss_pred             CCCeEEEEeCCHHHHHHHHHHHHhcC--cEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHH
Q 042079           19 KPPHVLAVDDSIVDRKIVENLLKNSA--CKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYEL   96 (153)
Q Consensus        19 ~~~~iLiidd~~~~~~~l~~~l~~~~--~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~   96 (153)
                      +..+||||||++..+..++.+|+..|  +.|..+.++.+|++.+.              .+.||+||+|+.||+++|+++
T Consensus         2 ~kirVLiVDD~~~~r~~l~~~L~~~g~~~~v~~a~~g~~al~~~~--------------~~~pDlvllDi~MP~~dG~e~   67 (140)
T d1a2oa1           2 SKIRVLSVDDSALMRQIMTEIINSHSDMEMVATAPDPLVARDLIK--------------KFNPDVLTLDVEMPRMDGLDF   67 (140)
T ss_dssp             CCEEEEEECSCHHHHHHHHHHHHTSTTEEEEEEESSHHHHHHHHH--------------HHCCSEEEEECCCSSSCHHHH
T ss_pred             CCCEEEEEeCCHHHHHHHHHHHHhCCCeEEEEEECCHHHHHHHHH--------------hcCCCEEEEcCCCCCCCHHHH
Confidence            45789999999999999999999887  55778999999999884              346999999999999999999


Q ss_pred             HHHHHhccCCCCCcEEEEeCCC-ChhhHHHHHHhcCcccccCCCC
Q 042079           97 LKKIKESSVMKEVPVVVVSSEN-IPTRINECLEEGAQMFMLKPLK  140 (153)
Q Consensus        97 ~~~lr~~~~~~~~pii~~t~~~-~~~~~~~a~~~ga~~~l~KP~~  140 (153)
                      ++++|+..  +..++++++... ..+...+|++.|+++|+.||+.
T Consensus        68 ~~~ir~~~--~~~~i~i~~~~~~~~~~~~~al~~Ga~~yl~KP~~  110 (140)
T d1a2oa1          68 LEKLMRLR--PMPVVMVSSLTGKGSEVTLRALELGAIDFVTKPQL  110 (140)
T ss_dssp             HHHHHHSS--CCCEEEEECCTHHHHHHHHHHHHHTCCEEEECSSS
T ss_pred             HHHHHHhC--CCCcEEEEEecCCChHHHHHHHHcCCCEEEECCCC
Confidence            99999865  344455555432 2345678999999999999974

>d1qo0d_ c.23.1.3 (D:) Positive regulator of the amidase operon AmiR {Pseudomonas aeruginosa [TaxId: 287]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: CheY-like
family: Positive regulator of the amidase operon AmiR
domain: Positive regulator of the amidase operon AmiR
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=99.85  E-value=1.1e-21  Score=137.50  Aligned_cols=113  Identities=13%  Similarity=0.114  Sum_probs=98.4

Q ss_pred             CCCCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHH
Q 042079           18 PKPPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELL   97 (153)
Q Consensus        18 ~~~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~   97 (153)
                      .+..+|||+||++..+..+...|+..||+|..+.++.+++.                  ..||+||+|+.||+++|..+.
T Consensus         9 l~~~~iLvvdd~~~~~~~l~~~L~~~G~~v~~~~~~~~al~------------------~~~Dlvl~D~~mp~~~~~~~~   70 (189)
T d1qo0d_           9 LRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAFD------------------VPVDVVFTSIFQNRHHDEIAA   70 (189)
T ss_dssp             GGGCEEEEESCTTHHHHHHHHHHHHHTCEEEEECSCCSSCS------------------SCCSEEEEECCSSTHHHHHHH
T ss_pred             ccCCEEEEEeCCHHHHHHHHHHHHHcCCcceecCCHHHhcc------------------CCCCEEEEcCCCCCcHHHHHH
Confidence            35689999999999999999999999999999998887652                  469999999999998776655


Q ss_pred             HHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHhhh
Q 042079           98 KKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTGHL  151 (153)
Q Consensus        98 ~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~~  151 (153)
                      + ++...  +.+|||++|+..+.+...+|++.|+++||.||+++.++...+.+.
T Consensus        71 ~-~~~~~--p~~pvI~lta~~~~~~~~~al~~Ga~~yL~KP~~~~~L~~~i~~~  121 (189)
T d1qo0d_          71 L-LAAGT--PRTTLVALVEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSA  121 (189)
T ss_dssp             H-HHHSC--TTCEEEEEECCCSHHHHHHHHHHTCSEEEESSCCGGGHHHHHHHH
T ss_pred             H-HHHcC--CCCCEEEEeccchHHHHHHHHHcCCcEEEEecchhhHHHHHHhhc
Confidence            4 44433  689999999999999999999999999999999999999877653

>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=96.89  E-value=0.012  Score=37.55  Aligned_cols=116  Identities=13%  Similarity=0.062  Sum_probs=77.4

Q ss_pred             CCeEEE--E--eCCHHHHHHHHHHHHhcCcEEEE---ecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCC-
Q 042079           20 PPHVLA--V--DDSIVDRKIVENLLKNSACKVTT---AENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGM-   91 (153)
Q Consensus        20 ~~~iLi--i--dd~~~~~~~l~~~l~~~~~~v~~---~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~-   91 (153)
                      ..+|++  +  |-|..-...+..+|+..||+|..   ....++.++.+.              .+.+|+|.+...+... 
T Consensus         3 k~kVvi~~~~gD~H~lG~~mva~~l~~~G~~V~~LG~~~p~e~iv~a~~--------------~~~~d~v~lS~~~~~~~   68 (137)
T d1ccwa_           3 KKTIVLGVIGSDCHAVGNKILDHAFTNAGFNVVNIGVLSPQELFIKAAI--------------ETKADAILVSSLYGQGE   68 (137)
T ss_dssp             CCEEEEEEETTCCCCHHHHHHHHHHHHTTCEEEEEEEEECHHHHHHHHH--------------HHTCSEEEEEECSSTHH
T ss_pred             CCEEEEEecCCChhHHHHHHHHHHHHHCCCeEEecccccCHHHHHHHHH--------------hcCCCEEEEeeccccch
Confidence            345555  2  45667778889999999998763   346666666663              3468999999888764 


Q ss_pred             -CHHHHHHHHHhccCCCCCcEEEEeCCC-----ChhhHHHHHHhcCcccccCCCChhHHHHHHhh
Q 042079           92 -TGYELLKKIKESSVMKEVPVVVVSSEN-----IPTRINECLEEGAQMFMLKPLKPSDVKKLTGH  150 (153)
Q Consensus        92 -~g~~~~~~lr~~~~~~~~pii~~t~~~-----~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~  150 (153)
                       ...++++.||+.. ..++|+++=....     .+....+..+.|++..+....+++++.+-+.+
T Consensus        69 ~~~~~~~~~l~~~~-~~~i~iivGG~~~~~~~~~~~~~~~l~~~Gv~~if~~~t~~~~~~~~l~~  132 (137)
T d1ccwa_          69 IDCKGLRQKCDEAG-LEGILLYVGGNIVVGKQHWPDVEKRFKDMGYDRVYAPGTPPEVGIADLKK  132 (137)
T ss_dssp             HHHTTHHHHHHHTT-CTTCEEEEEESCSSSSCCHHHHHHHHHHTTCSEECCTTCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhc-cCCCEEEEeCCcCCCccccHHHHHHHHHcCCCEEECCCCCHHHHHHHHHH
Confidence             2234556677654 3467766433221     13344556788999888788888888776665

>d1dxea_ c.1.12.5 (A:) 2-dehydro-3-deoxy-galactarate aldolase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: Phosphoenolpyruvate/pyruvate domain
family: HpcH/HpaI aldolase
domain: 2-dehydro-3-deoxy-galactarate aldolase
species: Escherichia coli [TaxId: 562]

Probab=94.63  E-value=0.42  Score=33.13  Aligned_cols=102  Identities=14%  Similarity=0.083  Sum_probs=69.5

Q ss_pred             HHHHHHHhcCcE--EEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHHHhccCCCCCcEE
Q 042079           35 IVENLLKNSACK--VTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVV  112 (153)
Q Consensus        35 ~l~~~l~~~~~~--v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~lr~~~~~~~~pii  112 (153)
                      .+++.|++....  ++.........+.+.              ...||.+++|+.-...+--++...++.... ..++.+
T Consensus         6 ~lk~~l~~g~~~~G~~~~~~~p~~~ei~a--------------~~G~Dfv~iD~EHg~~~~~~~~~~i~a~~~-~g~~~~   70 (253)
T d1dxea_           6 KFKAALAAKQVQIGCWSALSNPISTEVLG--------------LAGFDWLVLDGEHAPNDISTFIPQLMALKG-SASAPV   70 (253)
T ss_dssp             HHHHHHHTTCCEEEEEECSCSHHHHHHHT--------------TSCCSEEEEESSSSSCCHHHHHHHHHHTTT-CSSEEE
T ss_pred             HHHHHHHCCCCEEEEEecCCCHHHHHHHH--------------cCCCCEEEEecccCCCChhHHHHHHHHHhc-cCCCce
Confidence            355666654322  333334444556663              456999999999988887777777775432 456666


Q ss_pred             EEeCCCChhhHHHHHHhcCcccccCCC-ChhHHHHHHhhh
Q 042079          113 VVSSENIPTRINECLEEGAQMFMLKPL-KPSDVKKLTGHL  151 (153)
Q Consensus       113 ~~t~~~~~~~~~~a~~~ga~~~l~KP~-~~~~l~~~~~~~  151 (153)
                      +=.+..++..+.++++.|+++.+.--+ +.++.++++..+
T Consensus        71 VRvp~~~~~~i~~~LD~Ga~GIivP~v~s~eea~~~v~~~  110 (253)
T d1dxea_          71 VRVPTNEPVIIKRLLDIGFYNFLIPFVETKEEAELAVAST  110 (253)
T ss_dssp             EECSSSCHHHHHHHHHTTCCEEEESCCCSHHHHHHHHHTT
T ss_pred             ecCCCCCHHHHHHHHhcCccEEEecccCCHHHHHHHHHhh
Confidence            677778999999999999999876544 556666666543

>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=93.97  E-value=0.43  Score=30.98  Aligned_cols=101  Identities=14%  Similarity=0.125  Sum_probs=67.8

Q ss_pred             CCeEEEE----eCCHHHHHHHHHHHHhcCcEEEEe---cCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCC-
Q 042079           20 PPHVLAV----DDSIVDRKIVENLLKNSACKVTTA---ENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGM-   91 (153)
Q Consensus        20 ~~~iLii----dd~~~~~~~l~~~l~~~~~~v~~~---~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~-   91 (153)
                      .++|++.    |-|..-...+..+|+..||+|...   .+.++.++...              .+.+|+|.+...+... 
T Consensus        37 ~pkVlla~~g~D~Hd~G~~~va~~l~~~G~eVi~lg~~~~~e~iv~aa~--------------~~~advI~iSs~~~~~~  102 (168)
T d7reqa2          37 RPRILLAKMGQDGHDRGQKVIATAYADLGFDVDVGPLFQTPEETARQAV--------------EADVHVVGVSSLAGGHL  102 (168)
T ss_dssp             CCEEEEECBTTCCCCHHHHHHHHHHHHTTCEEEECCTTBCHHHHHHHHH--------------HHTCSEEEEEECSSCHH
T ss_pred             CCeEEEEeCCccHHHHHHHHHHHHHHhCCcceecCCCcCcHHHHHHHHH--------------ccCCCEEEEecCcccch
Confidence            4567665    446677788899999999998764   36666666653              2468999988665542 


Q ss_pred             -CHHHHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCccccc
Q 042079           92 -TGYELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFML  136 (153)
Q Consensus        92 -~g~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~  136 (153)
                       ..-++++.|++.. ..+++|+ +.+.-.........+.|+++++.
T Consensus       103 ~~~~~l~~~L~~~g-~~~v~Vi-vGG~ip~~d~~~l~~~Gv~~iF~  146 (168)
T d7reqa2         103 TLVPALRKELDKLG-RPDILIT-VGGVIPEQDFDELRKDGAVEIYT  146 (168)
T ss_dssp             HHHHHHHHHHHHTT-CTTSEEE-EEESCCGGGHHHHHHHTEEEEEC
T ss_pred             HHHHHHHHHHHhcC-CCCeEEE-EeCCCCHHHHHHHHhCCCCEEEC
Confidence             3455667777764 2455554 54433456667788999998654

>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=93.09  E-value=0.22  Score=32.51  Aligned_cols=95  Identities=12%  Similarity=0.056  Sum_probs=63.6

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHh----cC--cEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKN----SA--CKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGY   94 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~----~~--~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~   94 (153)
                      -.+||-|+|-.....+...++.    ..  .....+.+.+++.+.+.               ..+|+|++|-..|. +--
T Consensus        51 d~ilikdNHi~~~g~i~~~i~~~k~~~~~~~I~VEv~s~~q~~~a~~---------------~~~diImLDN~sp~-~~k  114 (169)
T d1qpoa1          51 DAALIKDNHVAAAGSVVDALRAVRNAAPDLPCEVEVDSLEQLDAVLP---------------EKPELILLDNFAVW-QTQ  114 (169)
T ss_dssp             SSEEECHHHHHHHSSHHHHHHHHHHHCTTSCEEEEESSHHHHHHHGG---------------GCCSEEEEETCCHH-HHH
T ss_pred             ceEEeehhHHhHhcchhhhhhhhhhhcCCCceEEEeccHHHhhhhhh---------------cCCcEEEecCcChH-hHH
Confidence            3588888888776655555442    11  23557899999988773               45899999954332 334


Q ss_pred             HHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCccc
Q 042079           95 ELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMF  134 (153)
Q Consensus        95 ~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~  134 (153)
                      +.++.++...   .-.++-.++.-+.+.+.+....|+|-+
T Consensus       115 ~~v~~~~~~~---~~i~lEaSGgI~~~ni~~ya~~GvD~I  151 (169)
T d1qpoa1         115 TAVQRRDSRA---PTVMLESSGGLSLQTAATYAETGVDYL  151 (169)
T ss_dssp             HHHHHHHHHC---TTCEEEEESSCCTTTHHHHHHTTCSEE
T ss_pred             HHHHHhhccC---CeeEEEEeCCCCHHHHHHHHHcCCCEE
Confidence            5556665543   234666777778888888888998754

>d1xrsb1 c.23.6.1 (B:102-261) D-lysine 5,6-aminomutase beta subunit KamE, C-terminal domain {Clostridium sticklandii [TaxId: 1511]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: Cobalamin (vitamin B12)-binding domain
family: Cobalamin (vitamin B12)-binding domain
domain: D-lysine 5,6-aminomutase beta subunit KamE, C-terminal domain
species: Clostridium sticklandii [TaxId: 1511]

Probab=92.22  E-value=0.49  Score=30.42  Aligned_cols=106  Identities=8%  Similarity=0.030  Sum_probs=66.7

Q ss_pred             eCCHHHHHHHHHHHHhcC---------cEEEEe---cCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCH-
Q 042079           27 DDSIVDRKIVENLLKNSA---------CKVTTA---ENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTG-   93 (153)
Q Consensus        27 dd~~~~~~~l~~~l~~~~---------~~v~~~---~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g-   93 (153)
                      |-|..=.+.+..+|+..|         |+|...   .+.++.++.+.              .+.+|+|-+...|....+ 
T Consensus        30 D~HdiG~~iv~~~l~~~G~~~~~~~~~~eVi~LG~~vp~e~~v~~a~--------------e~~~d~VglS~l~t~~~~h   95 (160)
T d1xrsb1          30 DAHTVGIDAIMNMKGYAGHYGLERYEMIDAYNLGSQVANEDFIKKAV--------------ELEADVLLVSQTVTQKNVH   95 (160)
T ss_dssp             CCCCHHHHHHHSTTCBTTBCCGGGCTTEEEEECCSSBCHHHHHHHHH--------------HTTCSEEEEECCCCTTSHH
T ss_pred             cHHHHHHHHHHHHHHHcCCcccccccceEEEeCCCCCCHHHHHHHHH--------------hcCCCEEEEeecccccchh
Confidence            446666677888888888         777642   35555666552              367999999998876432 


Q ss_pred             ----HHHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHh
Q 042079           94 ----YELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTG  149 (153)
Q Consensus        94 ----~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~  149 (153)
                          -++++.+++......+|+ ++.+..-..  .-+.+.|++.|...=.+..++.+.+.
T Consensus        96 ~~~~~~~i~~l~~~g~~d~v~v-ivGG~~~~~--~~a~~~GaD~~f~~g~~a~~~a~~l~  152 (160)
T d1xrsb1          96 IQNMTHLIELLEAEGLRDRFVL-LCGGPRINN--EIAKELGYDAGFGPGRFADDVATFAV  152 (160)
T ss_dssp             HHHHHHHHHHHHHTTCGGGSEE-EEECTTCCH--HHHHTTTCSEEECTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCCceEE-EEcCCCCCH--HHHHHcCCCEEcCCCCCHHHHHHHHH
Confidence                356667776543223444 455433222  34568899999876666666654443

>d1xi3a_ c.1.3.1 (A:) Thiamin phosphate synthase {Archaeon (Pyrococcus furiosus) [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: Thiamin phosphate synthase
family: Thiamin phosphate synthase
domain: Thiamin phosphate synthase
species: Archaeon (Pyrococcus furiosus) [TaxId: 2261]

Probab=90.67  E-value=1.2  Score=29.44  Aligned_cols=84  Identities=20%  Similarity=0.183  Sum_probs=57.2

Q ss_pred             EEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCC-------CHHHHHHHHHhccCCCCCcEEEEeCCC
Q 042079           46 KVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGM-------TGYELLKKIKESSVMKEVPVVVVSSEN  118 (153)
Q Consensus        46 ~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~-------~g~~~~~~lr~~~~~~~~pii~~t~~~  118 (153)
                      ....+.+..++.....               ..+|.+.+.--.+..       -|++.++++.+.   .++|++++.+- 
T Consensus       102 ig~s~h~~~e~~~a~~---------------~g~DYi~~gpvf~T~tk~~~~~~g~~~l~~~~~~---~~~Pv~AiGGI-  162 (206)
T d1xi3a_         102 IGASVYSLEEALEAEK---------------KGADYLGAGSVFPTKTKEDARVIGLEGLRKIVES---VKIPVVAIGGI-  162 (206)
T ss_dssp             EEEEESSHHHHHHHHH---------------HTCSEEEEECSSCC----CCCCCHHHHHHHHHHH---CSSCEEEESSC-
T ss_pred             cccccCCHHHHHHHHh---------------cCCCEEEeccccccccccccccccHHHHHHHHHh---cCCCEEEECCC-
Confidence            3457778777655441               358999988655421       388999988764   36899988875 


Q ss_pred             ChhhHHHHHHhcCccc-----ccCCCChhHHHHHH
Q 042079          119 IPTRINECLEEGAQMF-----MLKPLKPSDVKKLT  148 (153)
Q Consensus       119 ~~~~~~~a~~~ga~~~-----l~KP~~~~~l~~~~  148 (153)
                      +.+...++++.|++.+     +...-++.+..+.+
T Consensus       163 ~~~ni~~~~~~Ga~gvAvis~I~~~~dp~~~~~~l  197 (206)
T d1xi3a_         163 NKDNAREVLKTGVDGIAVISAVMGAEDVRKATEEL  197 (206)
T ss_dssp             CTTTHHHHHTTTCSEEEESHHHHTSSSHHHHHHHH
T ss_pred             CHHHHHHHHHhCCCEEEEhHHHHCCCCHHHHHHHH
Confidence            5666888999999887     55544555444333

>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=90.21  E-value=0.13  Score=33.67  Aligned_cols=94  Identities=17%  Similarity=0.133  Sum_probs=60.5

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHh----cC---cEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKN----SA---CKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTG   93 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~----~~---~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g   93 (153)
                      -.|||-|+|......+...++.    .+   .....+++..++.+.+.               ..+|+|++|-..|. .-
T Consensus        49 d~ilikdNHi~~~g~~~~~~~~~~~~~~~~~~I~VEv~~~~e~~~a~~---------------~g~d~i~LDn~~pe-~~  112 (170)
T d1o4ua1          49 GCVMIKDNHLKMYGSAERAVQEVRKIIPFTTKIEVEVENLEDALRAVE---------------AGADIVMLDNLSPE-EV  112 (170)
T ss_dssp             -CEEECHHHHHHHSSHHHHHHHHHTTSCTTSCEEEEESSHHHHHHHHH---------------TTCSEEEEESCCHH-HH
T ss_pred             cceEEcccHHHHhccHHHHHHHHHhhCCCCceEEEEeCcHHHHHHHHh---------------cCccEEEEcCcChh-hH
Confidence            3488888888776655555543    22   23557889999888772               46899999953332 33


Q ss_pred             HHHHHHHHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcc
Q 042079           94 YELLKKIKESSVMKEVPVVVVSSENIPTRINECLEEGAQM  133 (153)
Q Consensus        94 ~~~~~~lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~  133 (153)
                      -++.+.++...  ++ ..+-.++.-+.+.+.+....|+|-
T Consensus       113 k~~~~~lk~~~--~~-i~lEaSGGI~~~ni~~~a~~GVD~  149 (170)
T d1o4ua1         113 KDISRRIKDIN--PN-VIVEVSGGITEENVSLYDFETVDV  149 (170)
T ss_dssp             HHHHHHHHHHC--TT-SEEEEEECCCTTTGGGGCCTTCCE
T ss_pred             hHHHHHHHhhC--Cc-EEEEEECCCCHHHHHHHHHcCCCE
Confidence            34556666543  34 455577766777777777788774

>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=88.76  E-value=1.7  Score=27.01  Aligned_cols=83  Identities=14%  Similarity=0.155  Sum_probs=61.6

Q ss_pred             CCeEEEEeCCHHHHHHHHHHHHhcCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHH
Q 042079           20 PPHVLAVDDSIVDRKIVENLLKNSACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKK   99 (153)
Q Consensus        20 ~~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~   99 (153)
                      ...|-+.-.++.....++++|....|.+..+.++.+.++++..            .++.+|++++--.  +.+-..++..
T Consensus         4 ~LtI~l~l~s~~L~q~~~q~L~~dRY~l~~~~s~~ef~~~le~------------~~e~iDcLVl~~~--~~~l~~l~~q   69 (135)
T d1r8ja2           4 QIAICIWVESTAILQDCQRALSADRYQLQVCESGEMLLEYAQT------------HRDQIDCLILVAA--NPSFRAVVQQ   69 (135)
T ss_dssp             CEEEEEECCCHHHHHHHHHHTCSTTEEEEEECSHHHHHHHHHH------------STTSCSEEEEETT--STTHHHHHHH
T ss_pred             eEEEEEEeCCHHHHHHHHHhcCCCceEEEEcCCHHHHHHHHHh------------CcccCCEEEEEec--CCccHHHHHH
Confidence            3567777788889999999998888999999999999888842            4578999986322  2334556678


Q ss_pred             HHhccCCCCCcEEEEeCCC
Q 042079          100 IKESSVMKEVPVVVVSSEN  118 (153)
Q Consensus       100 lr~~~~~~~~pii~~t~~~  118 (153)
                      |.+.+.  =.|.|++....
T Consensus        70 L~~~Gl--LlPaViv~~~~   86 (135)
T d1r8ja2          70 LCFEGV--VVPAIVVGDRD   86 (135)
T ss_dssp             HHHTTC--CCCEEEESCCC
T ss_pred             HHhcCc--cccEEEEecCC
Confidence            887663  46888886543

>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=88.69  E-value=1.9  Score=27.37  Aligned_cols=80  Identities=10%  Similarity=0.130  Sum_probs=54.1

Q ss_pred             eCCHHHHHHHHHHHHhcCcEEEEe---cCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCC--CHHHHHHHHH
Q 042079           27 DDSIVDRKIVENLLKNSACKVTTA---ENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGM--TGYELLKKIK  101 (153)
Q Consensus        27 dd~~~~~~~l~~~l~~~~~~v~~~---~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~--~g~~~~~~lr  101 (153)
                      |-|..=.+.+..+|+..||+|...   ...++.++.+.              .+++|+|.+...|+..  ...++++.++
T Consensus        17 D~HdiG~~iv~~~l~~~G~~Vi~LG~~~p~e~~~~~~~--------------~~~~d~i~lS~l~~~~~~~~~~~~~~l~   82 (156)
T d3bula2          17 DVHDIGKNIVGVVLQCNNYEIVDLGVMVPAEKILRTAK--------------EVNADLIGLSGLITPSLDEMVNVAKEME   82 (156)
T ss_dssp             CCCCHHHHHHHHHHHTTTCEEEECCSSBCHHHHHHHHH--------------HHTCSEEEEECCSTHHHHHHHHHHHHHH
T ss_pred             ChhhHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHH--------------hhCCCEEEEecccccchHHHHHHHHHHH
Confidence            556777788999999999998763   34555555552              3568999999988753  3455667777


Q ss_pred             hccCCCCCcEEEEeCCCChhh
Q 042079          102 ESSVMKEVPVVVVSSENIPTR  122 (153)
Q Consensus       102 ~~~~~~~~pii~~t~~~~~~~  122 (153)
                      +..  .++|+++-........
T Consensus        83 ~~g--~~~~vivGG~~~~~~~  101 (156)
T d3bula2          83 RQG--FTIPLLIGGATTSKAH  101 (156)
T ss_dssp             HTT--CCSCEEEESTTCCHHH
T ss_pred             hcc--ccceEEEecccccchH
Confidence            755  4677765554444443

>d1izca_ c.1.12.5 (A:) Macrophomate synthase {Macrophoma commelinae [TaxId: 108330]}

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: Phosphoenolpyruvate/pyruvate domain
family: HpcH/HpaI aldolase
domain: Macrophomate synthase
species: Macrophoma commelinae [TaxId: 108330]

Probab=88.05  E-value=3.1  Score=29.21  Aligned_cols=105  Identities=15%  Similarity=0.175  Sum_probs=65.2

Q ss_pred             HHHHHHHHHHhcC-c--EEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHH---HHhccC
Q 042079           32 DRKIVENLLKNSA-C--KVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKK---IKESSV  105 (153)
Q Consensus        32 ~~~~l~~~l~~~~-~--~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~---lr~~~~  105 (153)
                      .++.+++.+...+ .  -++..-......+.+.              ...||.|++|+.-...+--++...   ++....
T Consensus        27 ~r~~l~~~~~~~~~~~~G~~~~~~s~~~~e~~a--------------~~g~D~v~iD~EHg~~~~~~~~~~i~a~~~~~~   92 (299)
T d1izca_          27 LRQALKDAMADPSKTLMGVAHGIPSTFVTKVLA--------------ATKPDFVWIDVEHGMFNRLELHDAIHAAQHHSE   92 (299)
T ss_dssp             HHHHHHHHHHCGGGCEEEEEECSCCHHHHHHHH--------------HTCCSEEEEETTTSCCCHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHhhccCCceeeeeccCCCHHHHHHHH--------------cCCCCEEEEcCCCCCCCHHHHHHHHHHHHHhCC
Confidence            4566676665432 2  2333333344456553              356999999999887775555444   333221


Q ss_pred             CCCCcEEEEeCCCChhhHHHHHHhcCcccccCC-CChhHHHHHHhhh
Q 042079          106 MKEVPVVVVSSENIPTRINECLEEGAQMFMLKP-LKPSDVKKLTGHL  151 (153)
Q Consensus       106 ~~~~pii~~t~~~~~~~~~~a~~~ga~~~l~KP-~~~~~l~~~~~~~  151 (153)
                       ..++.++=.+..+...+.++++.|++..+.-= -+.++.++++..+
T Consensus        93 -~~~~~iVRvp~~~~~~I~~~LD~Ga~GIivP~V~s~eea~~~v~~~  138 (299)
T d1izca_          93 -GRSLVIVRVPKHDEVSLSTALDAGAAGIVIPHVETVEEVREFVKEM  138 (299)
T ss_dssp             -TCSEEEEECCTTCHHHHHHHHHHTCSEEEETTCCCHHHHHHHHHHH
T ss_pred             -CCCCeEEeCCCCChHHHHHHHHhCcCeeeccccccHHHHHHHHHhh
Confidence             23444555666788889999999999987644 3566677776654

>d1wa3a1 c.1.10.1 (A:2-203) KDPG aldolase {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: Aldolase
family: Class I aldolase
domain: KDPG aldolase
species: Thermotoga maritima [TaxId: 2336]

Probab=86.84  E-value=2.3  Score=28.13  Aligned_cols=95  Identities=17%  Similarity=0.188  Sum_probs=54.3

Q ss_pred             HHHHHhcCcE-EEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHHHhccCCCCCcEEEEe
Q 042079           37 ENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVS  115 (153)
Q Consensus        37 ~~~l~~~~~~-v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~lr~~~~~~~~pii~~t  115 (153)
                      .++|++.+.. +....+.+++........           ...+.  ++++.+-..++++.++.|++... +++ +|-..
T Consensus         3 ~~~l~~~~iipvlr~~~~~~a~~~~~al~-----------~~Gi~--~iEitlr~p~a~~~i~~l~~~~~-~~~-~vGaG   67 (202)
T d1wa3a1           3 EELFKKHKIVAVLRANSVEEAKEKALAVF-----------EGGVH--LIEITFTVPDADTVIKELSFLKE-KGA-IIGAG   67 (202)
T ss_dssp             HHHHHHHCEEEEECCSSHHHHHHHHHHHH-----------HTTCC--EEEEETTSTTHHHHHHHTHHHHH-TTC-EEEEE
T ss_pred             HHHHHhCCEEEEEECCCHHHHHHHHHHHH-----------HcCCC--EEEEecCCccHHHHHHHHHHhcC-CCc-EEEec
Confidence            4556655543 445666666666543221           12233  34445556678888888764321 232 34444


Q ss_pred             CCCChhhHHHHHHhcCcccccCCCChhHHHHH
Q 042079          116 SENIPTRINECLEEGAQMFMLKPLKPSDVKKL  147 (153)
Q Consensus       116 ~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~  147 (153)
                      .-.+.+...++.+.|++ |+..|-...++.+.
T Consensus        68 TV~~~~~~~~a~~aGa~-fivsP~~~~~v~~~   98 (202)
T d1wa3a1          68 TVTSVEQCRKAVESGAE-FIVSPHLDEEISQF   98 (202)
T ss_dssp             SCCSHHHHHHHHHHTCS-EEECSSCCHHHHHH
T ss_pred             ccccHHHHHHHHhhccc-EEeCCCCcHHHHHH
Confidence            45577888888999987 55667555555443

>d1mxsa_ c.1.10.1 (A:) KDPG aldolase {Pseudomonas putida [TaxId: 303]}

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: Aldolase
family: Class I aldolase
domain: KDPG aldolase
species: Pseudomonas putida [TaxId: 303]

Probab=85.15  E-value=3.8  Score=27.37  Aligned_cols=100  Identities=13%  Similarity=0.166  Sum_probs=65.2

Q ss_pred             HHHHHHHHHhcCc-EEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHHHhccCCCCCcE
Q 042079           33 RKIVENLLKNSAC-KVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPV  111 (153)
Q Consensus        33 ~~~l~~~l~~~~~-~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~lr~~~~~~~~pi  111 (153)
                      ...+..++++... -+....+.+++++......           ...+.+  +++.+.....++.++.+++..  +++ .
T Consensus         7 ~~~i~~~l~~~~iipvl~~~~~~~a~~~~~al~-----------~~Gi~~--iEitl~~p~a~~~i~~l~~~~--p~~-~   70 (216)
T d1mxsa_           7 AARIDAICEKARILPVITIAREEDILPLADALA-----------AGGIRT--LEVTLRSQHGLKAIQVLREQR--PEL-C   70 (216)
T ss_dssp             HHHHHHHHHHHSEEEEECCSCGGGHHHHHHHHH-----------HTTCCE--EEEESSSTHHHHHHHHHHHHC--TTS-E
T ss_pred             HHHHHHHHHhCCEEEEEECCCHHHHHHHHHHHH-----------HCCCCE--EEEeCCChhHHHHHHHHHHhC--CCc-c
Confidence            4456677776554 3455667777766553222           123444  444455556899999998754  453 4


Q ss_pred             EEEeCCCChhhHHHHHHhcCcccccCCCChhHHHHHHh
Q 042079          112 VVVSSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTG  149 (153)
Q Consensus       112 i~~t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~  149 (153)
                      |-...-.+.+...++.+.|++ |+..|....++.+...
T Consensus        71 vGaGTV~~~~~~~~a~~aGa~-FivsP~~~~~v~~~a~  107 (216)
T d1mxsa_          71 VGAGTVLDRSMFAAVEAAGAQ-FVVTPGITEDILEAGV  107 (216)
T ss_dssp             EEEECCCSHHHHHHHHHHTCS-SEECSSCCHHHHHHHH
T ss_pred             eeeeeeecHHHHHHHHhCCCC-EEECCCCcHHHHHHHH
Confidence            555556678889999999995 8888887777766543

>d1wl8a1 c.23.16.1 (A:1-188) GMP synthase subunit A, GuaAA {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: Class I glutamine amidotransferase-like
family: Class I glutamine amidotransferases (GAT)
domain: GMP synthase subunit A, GuaAA
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=84.87  E-value=1.5  Score=28.18  Aligned_cols=32  Identities=9%  Similarity=0.017  Sum_probs=25.5

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEEEecC
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVTTAEN   52 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~   52 (153)
                      +.|+|+|-...+...+.+.|+..|+.+.....
T Consensus         1 mmI~iiD~g~~~~~~i~~~L~~~G~~~~v~~~   32 (188)
T d1wl8a1           1 MMIVIMDNGGQYVHRIWRTLRYLGVETKIIPN   32 (188)
T ss_dssp             CEEEEEECSCTTHHHHHHHHHHTTCEEEEEET
T ss_pred             CEEEEEECCCcHHHHHHHHHHHCCCeEEEEeC
Confidence            45899998777777788899999998877654

>d2esra1 c.66.1.46 (A:28-179) Putative methyltransferase SPy1538 {Streptococcus pyogenes [TaxId: 1314]}

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 methyltransferase SPy1538
species: Streptococcus pyogenes [TaxId: 1314]

Probab=83.73  E-value=1.8  Score=26.90  Aligned_cols=66  Identities=17%  Similarity=0.232  Sum_probs=43.4

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCc--EEE-EecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCC--CHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSAC--KVT-TAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGM--TGYE   95 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~--~v~-~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~--~g~~   95 (153)
                      .++..+|-++...+.++.-++..+.  .+. ...+....+...               ..+||+|++|.  |-.  ....
T Consensus        38 ~~v~~ve~~~~a~~~~~~n~~~~~~~~~~~ii~~D~~~~l~~~---------------~~~fDiIf~DP--Py~~~~~~~  100 (152)
T d2esra1          38 SAAVLVEKNRKAQAIIQDNIIMTKAENRFTLLKMEAERAIDCL---------------TGRFDLVFLDP--PYAKETIVA  100 (152)
T ss_dssp             CEEEEECCCHHHHHHHHHHHHTTTCGGGEEEECSCHHHHHHHB---------------CSCEEEEEECC--SSHHHHHHH
T ss_pred             ceeeeehhchhhhhhhhhhhhhcccccchhhhccccccccccc---------------ccccceeEech--hhccchHHH
Confidence            5899999999999988888886653  233 334544444432               45799999983  422  2345


Q ss_pred             HHHHHHhc
Q 042079           96 LLKKIKES  103 (153)
Q Consensus        96 ~~~~lr~~  103 (153)
                      .++.|.+.
T Consensus       101 ~l~~i~~~  108 (152)
T d2esra1         101 TIEALAAK  108 (152)
T ss_dssp             HHHHHHHT
T ss_pred             HHHHHHHC
Confidence            66666543

>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=83.52  E-value=3.9  Score=26.17  Aligned_cols=68  Identities=16%  Similarity=0.143  Sum_probs=43.8

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCc-EEE-EecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSAC-KVT-TAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLK   98 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~-~v~-~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~   98 (153)
                      .++..||-++...+.++.-++..+. .+. ...+   ++..+..            ...+||+|++|-=-.......++.
T Consensus        67 ~~v~~VE~~~~a~~~~k~N~~~~~~~~~~ii~~d---~~~~l~~------------~~~~fDlIf~DPPY~~~~~~~~l~  131 (183)
T d2fpoa1          67 AGATLIEMDRAVSQQLIKNLATLKAGNARVVNSN---AMSFLAQ------------KGTPHNIVFVDPPFRRGLLEETIN  131 (183)
T ss_dssp             SEEEEECSCHHHHHHHHHHHHHTTCCSEEEECSC---HHHHHSS------------CCCCEEEEEECCSSSTTTHHHHHH
T ss_pred             ceeEEEEEeechhhHHHHHHhhccccceeeeeec---ccccccc------------cccccCEEEEcCccccchHHHHHH
Confidence            4799999999999988887776543 222 3333   3444421            246799999994222334567777


Q ss_pred             HHHhc
Q 042079           99 KIKES  103 (153)
Q Consensus        99 ~lr~~  103 (153)
                      .|.+.
T Consensus       132 ~l~~~  136 (183)
T d2fpoa1         132 LLEDN  136 (183)
T ss_dssp             HHHHT
T ss_pred             HHHHC
Confidence            77653

>d7reqb2 c.23.6.1 (B:476-638) Methylmalonyl-CoA mutase beta subunit, C-terminal domain {Propionibacterium freudenreichii, subsp. shermanii [TaxId: 1744]}

class: Alpha and beta proteins (a/b)
fold: Flavodoxin-like
superfamily: Cobalamin (vitamin B12)-binding domain
family: Cobalamin (vitamin B12)-binding domain
domain: Methylmalonyl-CoA mutase beta subunit, C-terminal domain
species: Propionibacterium freudenreichii, subsp. shermanii [TaxId: 1744]

Probab=83.07  E-value=0.99  Score=28.95  Aligned_cols=113  Identities=9%  Similarity=-0.037  Sum_probs=65.4

Q ss_pred             CCeEEEEeC-----CHHHHHHHHHHHHhcCcEEEEe--cCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCC-
Q 042079           20 PPHVLAVDD-----SIVDRKIVENLLKNSACKVTTA--ENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGM-   91 (153)
Q Consensus        20 ~~~iLiidd-----~~~~~~~l~~~l~~~~~~v~~~--~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~-   91 (153)
                      .++|+++-=     +..-.....++|...|+++...  -+..+..+...              ....|++.+-..+..- 
T Consensus        35 rP~v~la~lG~~a~h~ara~f~~n~f~~gGfev~~~~~~~~~e~v~aa~--------------~~~a~vvvicssd~~y~  100 (163)
T d7reqb2          35 RPKVFLACLGTRRDFGGREGFSSPVWHIAGIDTPQVEGGTTAEIVEAFK--------------KSGAQVADLCSSAKVYA  100 (163)
T ss_dssp             CCBCEEEECSCHHHHHHHHHHHHHHHHHTTCBCCEEESCCHHHHHHHHH--------------HHTCSEEEEECCHHHHH
T ss_pred             CCeEEEEcCCChhhhhhHHHHHHHHHHccCeeeccCCCCCcHHHHHHHH--------------hCCCCEEEEecCccchH
Confidence            355665432     2334466788888889876542  24455555442              2356777765443322 


Q ss_pred             -CHHHHHHHHHhccCCCCCcEEEEeCC-CChhhHHHHHHhcCcccccCCCChhHHH-HHHhh
Q 042079           92 -TGYELLKKIKESSVMKEVPVVVVSSE-NIPTRINECLEEGAQMFMLKPLKPSDVK-KLTGH  150 (153)
Q Consensus        92 -~g~~~~~~lr~~~~~~~~pii~~t~~-~~~~~~~~a~~~ga~~~l~KP~~~~~l~-~~~~~  150 (153)
                       -.-++++.||...  ..  .+++... ..........+.|+++|+..=.+.-+.. .++.+
T Consensus       101 ~~~~~~~~aLk~ag--~~--~~vlaGg~~~~~d~~~l~~aGVd~~i~~G~d~~~~l~~l~~~  158 (163)
T d7reqb2         101 QQGLEVAKALKAAG--AK--ALYLSGAFKEFGDDAAEAEKLIDGRLFMGMDVVDTLSSTLDI  158 (163)
T ss_dssp             HHHHHHHHHHHHTT--CS--EEEEESCGGGGGGGHHHHHHHCCEEECTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcc--cc--eeEEEecCCCcccHHHHHhCCCCeEecCCCcHHHHHHHHHHH
Confidence             2446888888754  23  3334443 3445556778999999997766655543 34433

>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=82.51  E-value=3.7  Score=25.19  Aligned_cols=96  Identities=10%  Similarity=0.043  Sum_probs=49.5

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCcEEEEecC-HHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSACKVTTAEN-GMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKK   99 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~~v~~~~~-~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~   99 (153)
                      ..+.+++.++.........+...++.+...+. ..+.++..              +-...+.+++-..... .-...+..
T Consensus        27 ~~v~vId~d~~~~~~~~~~~~~~~~~vi~Gd~~d~~~L~~a--------------~i~~a~~vi~~~~~d~-~n~~~~~~   91 (153)
T d1id1a_          27 QNVTVISNLPEDDIKQLEQRLGDNADVIPGDSNDSSVLKKA--------------GIDRCRAILALSDNDA-DNAFVVLS   91 (153)
T ss_dssp             CCEEEEECCCHHHHHHHHHHHCTTCEEEESCTTSHHHHHHH--------------TTTTCSEEEECSSCHH-HHHHHHHH
T ss_pred             CCEEEEeccchhHHHHHHHhhcCCcEEEEccCcchHHHHHh--------------ccccCCEEEEccccHH-HHHHHHHH
Confidence            34566666654332222223334565554332 22234433              2235677776543222 23344445


Q ss_pred             HHhccCCCCCcEEEEeCCCChhhHHHHHHhcCcccc
Q 042079          100 IKESSVMKEVPVVVVSSENIPTRINECLEEGAQMFM  135 (153)
Q Consensus       100 lr~~~~~~~~pii~~t~~~~~~~~~~a~~~ga~~~l  135 (153)
                      +|+..  +.+++|+.+.  +++......+.|++..+
T Consensus        92 ~r~~~--~~~~iia~~~--~~~~~~~l~~~Gad~vi  123 (153)
T d1id1a_          92 AKDMS--SDVKTVLAVS--DSKNLNKIKMVHPDIIL  123 (153)
T ss_dssp             HHHHT--SSSCEEEECS--SGGGHHHHHTTCCSEEE
T ss_pred             HHHhC--CCCceEEEEc--CHHHHHHHHHCCCCEEE
Confidence            56543  5677776664  45666667788998654

>d1wbha1 c.1.10.1 (A:1-213) KDPG aldolase {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: Aldolase
family: Class I aldolase
domain: KDPG aldolase
species: Escherichia coli [TaxId: 562]

Probab=82.49  E-value=3.2  Score=27.73  Aligned_cols=93  Identities=17%  Similarity=0.221  Sum_probs=55.7

Q ss_pred             HHHHhcCcE-EEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHHHhccCCCCCcEEEEeC
Q 042079           38 NLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVVSS  116 (153)
Q Consensus        38 ~~l~~~~~~-v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~lr~~~~~~~~pii~~t~  116 (153)
                      .+|+..+.. +....+.++++.......           ...+.  .+++.+.....++.++.++++.  +++ +|-...
T Consensus        10 ~~l~~~~iipvlr~~~~~~a~~~~~al~-----------~~Gi~--~iEitl~tp~a~~~I~~l~~~~--p~~-~vGaGT   73 (213)
T d1wbha1          10 SILTTGPVVPVIVVKKLEHAVPMAKALV-----------AGGVR--VLNVTLRTECAVDAIRAIAKEV--PEA-IVGAGT   73 (213)
T ss_dssp             HHHHSCSEEEEECCSSGGGHHHHHHHHH-----------HTTCC--EEEEESCSTTHHHHHHHHHHHC--TTS-EEEEES
T ss_pred             HHHHhCCEEEEEECCCHHHHHHHHHHHH-----------HCCCC--EEEEeCCChhHHHHHHHHHHHC--CCC-eeeccc
Confidence            445555442 445566666655543221           12233  4445555556888888888754  454 455555


Q ss_pred             CCChhhHHHHHHhcCcccccCCCChhHHHHH
Q 042079          117 ENIPTRINECLEEGAQMFMLKPLKPSDVKKL  147 (153)
Q Consensus       117 ~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~  147 (153)
                      -.+.+...++.+.|++ |+..|....++.+.
T Consensus        74 V~~~~~~~~a~~aGa~-FivSP~~~~~v~~~  103 (213)
T d1wbha1          74 VLNPQQLAEVTEAGAQ-FAISPGLTEPLLKA  103 (213)
T ss_dssp             CCSHHHHHHHHHHTCS-CEEESSCCHHHHHH
T ss_pred             cccHHHHHHHHHCCCc-EEECCCCCHHHHHH
Confidence            6678888889999987 66677655555443

>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=82.08  E-value=1.9  Score=28.01  Aligned_cols=30  Identities=17%  Similarity=0.118  Sum_probs=24.0

Q ss_pred             eEEEEeCCHHHHHHHHHHHHhcCcEEEEec
Q 042079           22 HVLAVDDSIVDRKIVENLLKNSACKVTTAE   51 (153)
Q Consensus        22 ~iLiidd~~~~~~~l~~~l~~~~~~v~~~~   51 (153)
                      +|||||....+...+.++|++.|+.+....
T Consensus         2 niliiD~~DSFt~ni~~~l~~lG~~~~v~~   31 (192)
T d1i7qb_           2 DILLLDNVDSFTYNLVDQLRASGHQVVIYR   31 (192)
T ss_dssp             EEEEEECSCSSHHHHHHHHHHTTCEEEEEE
T ss_pred             cEEEEECCCcHHHHHHHHHHHCCCeEEEEe
Confidence            699999866666677888999999887764

>d1ujpa_ c.1.2.4 (A:) Trp synthase alpha-subunit {Thermus thermophilus [TaxId: 274]}

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: Ribulose-phoshate binding barrel
family: Tryptophan biosynthesis enzymes
domain: Trp synthase alpha-subunit
species: Thermus thermophilus [TaxId: 274]

Probab=81.27  E-value=0.85  Score=31.87  Aligned_cols=55  Identities=20%  Similarity=0.277  Sum_probs=38.5

Q ss_pred             HHHHHHHHHhccCCCCCcEEEEeCCCC------hhhHHHHHHhcCcccccCCCChhHHHHHHhh
Q 042079           93 GYELLKKIKESSVMKEVPVVVVSSENI------PTRINECLEEGAQMFMLKPLKPSDVKKLTGH  150 (153)
Q Consensus        93 g~~~~~~lr~~~~~~~~pii~~t~~~~------~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~~  150 (153)
                      .+++++++|+.   ..+|+++++-.+.      +....+|.+.|+++++.-.+.+++-.+....
T Consensus        79 ~~~~~~~~r~~---~~~pivlm~Y~N~i~~~G~~~F~~~~~~aGvdGliipDLP~ee~~~~~~~  139 (271)
T d1ujpa_          79 ALELVREVRAL---TEKPLFLMTYLNPVLAWGPERFFGLFKQAGATGVILPDLPPDEDPGLVRL  139 (271)
T ss_dssp             HHHHHHHHHHH---CCSCEEEECCHHHHHHHCHHHHHHHHHHHTCCEEECTTCCGGGCHHHHHH
T ss_pred             HHHHHHHHhcc---cCCcEEEEeechhhhhCCchhHhHHHhhcCceeEeccchhhhhHHHHHHH
Confidence            34556666654   3689999987543      5567888999999999887777766554443

>d1vhca_ c.1.10.1 (A:) Hypothetical protein HI0047 {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: Aldolase
family: Class I aldolase
domain: Hypothetical protein HI0047
species: Haemophilus influenzae [TaxId: 727]

Probab=80.95  E-value=4.4  Score=26.98  Aligned_cols=97  Identities=10%  Similarity=0.199  Sum_probs=59.2

Q ss_pred             HHHHHHhcCcE-EEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHHHHHHHhccCCCCCcEEEE
Q 042079           36 VENLLKNSACK-VTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYELLKKIKESSVMKEVPVVVV  114 (153)
Q Consensus        36 l~~~l~~~~~~-v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~~~~lr~~~~~~~~pii~~  114 (153)
                      +-+.|++.+.. +....+..++........           ...+.  .+++.+.....++.++.+++..  +++ +|-.
T Consensus         7 ~~~~l~~~~iipvlr~~~~~~~~~~~~al~-----------~~Gi~--~iEitl~~~~a~~~I~~l~~~~--p~~-~vGa   70 (212)
T d1vhca_           7 IIEKLRELKIVPVIALDNADDILPLADTLA-----------KNGLS--VAEITFRSEAAADAIRLLRANR--PDF-LIAA   70 (212)
T ss_dssp             HHHHHHHHCEEEEECCSSGGGHHHHHHHHH-----------HTTCC--EEEEETTSTTHHHHHHHHHHHC--TTC-EEEE
T ss_pred             HHHHHHHCCEEEEEeCCCHHHHHHHHHHHH-----------HCCCC--EEEEeCCChhHHHHHHHHHhcC--CCc-eEee
Confidence            33445555543 445556666655443221           12333  4455555667899999998754  453 4555


Q ss_pred             eCCCChhhHHHHHHhcCcccccCCCChhHHHHHHh
Q 042079          115 SSENIPTRINECLEEGAQMFMLKPLKPSDVKKLTG  149 (153)
Q Consensus       115 t~~~~~~~~~~a~~~ga~~~l~KP~~~~~l~~~~~  149 (153)
                      ..-.+.+...++.+.|++ |+..|....++.+...
T Consensus        71 GTV~~~~~~~~a~~aGa~-FivSP~~~~~v~~~a~  104 (212)
T d1vhca_          71 GTVLTAEQVVLAKSSGAD-FVVTPGLNPKIVKLCQ  104 (212)
T ss_dssp             ESCCSHHHHHHHHHHTCS-EEECSSCCHHHHHHHH
T ss_pred             eecccHHHHHHHHhhCCc-EEECCCCCHHHHHHHH
Confidence            555678888999999997 7777876666655443

>d1iy9a_ c.66.1.17 (A:) Spermidine synthase {Bacillus subtilis [TaxId: 1423]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Spermidine synthase
domain: Spermidine synthase
species: Bacillus subtilis [TaxId: 1423]

Probab=80.78  E-value=2  Score=29.81  Aligned_cols=70  Identities=13%  Similarity=0.147  Sum_probs=46.3

Q ss_pred             CCCCeEEEEeCCHHHHHHHHHHHHh-------cCcEEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCC
Q 042079           18 PKPPHVLAVDDSIVDRKIVENLLKN-------SACKVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPG   90 (153)
Q Consensus        18 ~~~~~iLiidd~~~~~~~l~~~l~~-------~~~~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~   90 (153)
                      .+..+|-++|-|+...+..+.++..       ...++ ...++.+.+..               ...+||+||+|...|.
T Consensus        97 ~~~~~i~~VEID~~Vi~~a~~~~~~~~~~~~d~r~~i-~~~D~~~~l~~---------------~~~~yDvIi~D~~~p~  160 (274)
T d1iy9a_          97 PSVKKATLVDIDGKVIEYSKKFLPSIAGKLDDPRVDV-QVDDGFMHIAK---------------SENQYDVIMVDSTEPV  160 (274)
T ss_dssp             TTCSEEEEEESCHHHHHHHHHHCHHHHTTTTSTTEEE-EESCSHHHHHT---------------CCSCEEEEEESCSSCC
T ss_pred             CCcceEEEecCCHHHHHHHHHhChhhcccccCCCeEE-EechHHHHHhh---------------cCCCCCEEEEcCCCCC
Confidence            3456899999999999888887642       12223 44555555442               2457999999986654


Q ss_pred             C-----CHHHHHHHHHhc
Q 042079           91 M-----TGYELLKKIKES  103 (153)
Q Consensus        91 ~-----~g~~~~~~lr~~  103 (153)
                      .     -..+|.+.+++.
T Consensus       161 ~~~~~L~t~eFy~~~~~~  178 (274)
T d1iy9a_         161 GPAVNLFTKGFYAGIAKA  178 (274)
T ss_dssp             SCCCCCSTTHHHHHHHHH
T ss_pred             CcchhhccHHHHHHHHhh
Confidence            2     255677777653

>d2ifta1 c.66.1.46 (A:11-193) Putative methylase HI0767 {Haemophilus influenzae [TaxId: 727]}

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 HI0767
species: Haemophilus influenzae [TaxId: 727]

Probab=80.75  E-value=4.2  Score=25.99  Aligned_cols=70  Identities=11%  Similarity=0.074  Sum_probs=43.1

Q ss_pred             CeEEEEeCCHHHHHHHHHHHHhcCc----EEEEecCHHHHHHHhchhhhHHhhhhcccCCCcccEEEEeCCCCCCCHHHH
Q 042079           21 PHVLAVDDSIVDRKIVENLLKNSAC----KVTTAENGMRALEFLGLVDEQEQQNNLNSNGTKVNLVITDYCMPGMTGYEL   96 (153)
Q Consensus        21 ~~iLiidd~~~~~~~l~~~l~~~~~----~v~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~dlii~D~~~~~~~g~~~   96 (153)
                      ..+..||.+....+.++.-++..+.    ......+..+.+...             ....+||+|++|-=-......++
T Consensus        67 ~~v~fVE~~~~a~~~ik~Ni~~l~~~~~~~~~~~~d~~~~l~~~-------------~~~~~fDlIFlDPPY~~~~~~~~  133 (183)
T d2ifta1          67 KKVTFLELDKTVANQLKKNLQTLKCSSEQAEVINQSSLDFLKQP-------------QNQPHFDVVFLDPPFHFNLAEQA  133 (183)
T ss_dssp             SEEEEECSCHHHHHHHHHHHHHTTCCTTTEEEECSCHHHHTTSC-------------CSSCCEEEEEECCCSSSCHHHHH
T ss_pred             eeeEEeecccchhhhHhhHHhhhccccccccccccccccccccc-------------ccCCcccEEEechhHhhhhHHHH
Confidence            4789999999999999888776543    233444443333221             12456999999942112224566


Q ss_pred             HHHHHhc
Q 042079           97 LKKIKES  103 (153)
Q Consensus        97 ~~~lr~~  103 (153)
                      ++.|.+.
T Consensus       134 l~~l~~~  140 (183)
T d2ifta1         134 ISLLCEN  140 (183)
T ss_dssp             HHHHHHT
T ss_pred             HHHHHHh
Confidence            6776653