Citrus Sinensis ID: 042991

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90---
Protein Sequence
LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQSANGFDVRTIYSREIPVVIMSPEIILVRIDRYLEDGAEDSETCQMWARLRD
Secondary Structure (PSIPRED)
cccHHHHHHHHHHHHHHcccccEEEEccHHHHHHHHcccccccccHHHHHHHHHccccEEEEcccccHHHHHHHHHcccccHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccccHHHHHHHHHHHHHccccEEEEEccHHHHHHHHccccccccccccEEccccccccEEEEEccccHHHHHHHHHccccccHHHHHHHHHcc
Coil and Loop (DISEMBL)
LNDSFVDRKVIERLLTISSsrdlycscsgrralqflgldeeqsangfdvrtiysreipvvimspeIILVRIDRyledgaedseTCQMWARLRD
Flexible Loop (DISEMBL)
LNDSFVDRKVIERLltisssrdlycSCSGRRALQflgldeeqsangfdvrtiysreipvvimspeIILVRIDRYledgaedsetcqmwarlrd
Low Complexity Region (SEG)
LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQSANGFDVRTIYSREIPVVIMSPEIILVRIDRYLEDGAEDSETCQMWARLRD
Disordered region (IsUnstruct)
*****VDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQSANGFDVRTIYSREIPVVIMSPEIILVRIDRYLEDG***************
Disordered Region (DISOPRED)
LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQSANGFDVRTIYSREIPVVIMSPEIILVRIDRYLEDGAEDSETCQMWARLR*
Disordered Region (DISEMBL)
LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQSANGFDVRTIYSREIPVVIMSPEIILVRIDRYLEDGAEDSETCQMWARLRD
Disordered Region (DISPRO)
**DSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQSANGFDVRTIYSREIPVVIMSPEIILVRIDRYLEDGAEDSETCQMWARLR*
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQSANGFDVRTIYSREIPVVIMSPEIILVRIDRYLEDGAEDSETCQMWARLRD
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	93	2.2.26 [Sep-21-2011]
Q9ZWS6	186	Two-component response re	yes	no	0.860	0.430	0.462	2e-12
Q9SB04	184	Two-component response re	no	no	0.860	0.434	0.476	6e-12
O82798	259	Two-component response re	no	no	0.860	0.308	0.443	3e-11
Q9ZWS9	231	Two-component response re	no	no	0.860	0.346	0.433	3e-11
Q7G8V2	206	Two-component response re	no	no	0.860	0.388	0.424	3e-10
Q9ZWS7	206	Two-component response re	no	no	0.860	0.388	0.433	5e-10
O80366	234	Two-component response re	no	no	0.860	0.341	0.344	3e-06
O80365	225	Two-component response re	no	no	0.860	0.355	0.359	5e-06
Q9FPR6	153	Two-component response re	no	no	0.849	0.516	0.320	6e-06
Q9SHC2	164	Two-component response re	no	no	0.849	0.481	0.333	2e-05

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

 Score = 71.2 bits (173), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 49/106 (46%), Positives = 61/106 (57%), Gaps = 26/106 (24%)

Query: 1   LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQSANGFD------VRTIYS 54
           ++DS VDRK IERLL +SS + +    S  RALQ+LGLD E+ + GF+      + T YS
Sbjct: 30  VDDSHVDRKFIERLLRVSSCK-VTVVDSATRALQYLGLDVEEKSVGFEDLKVNLIMTDYS 88

Query: 55  -------------------REIPVVIMSPEIILVRIDRYLEDGAED 81
                              RE+PVVIMS E IL RIDR LE+GAED
Sbjct: 89  MPGMTGYELLKKIKESSAFREVPVVIMSSENILPRIDRCLEEGAED 134

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 = 69.3 bits (168), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 51/107 (47%), Positives = 61/107 (57%), Gaps = 27/107 (25%)

Query: 1   LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLD-EEQSANGFD------VRTIY 53
           ++DS VDRK IERLL +SS + +    S  RALQ+LGLD E  S+ GF+      + T Y
Sbjct: 30  VDDSMVDRKFIERLLRVSSCK-VTVVDSATRALQYLGLDGENNSSVGFEDLKINLIMTDY 88

Query: 54  S-------------------REIPVVIMSPEIILVRIDRYLEDGAED 81
           S                   REIPVVIMS E IL RIDR LE+GAED
Sbjct: 89  SMPGMTGYELLKKIKESSAFREIPVVIMSSENILPRIDRCLEEGAED 135

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 = 67.4 bits (163), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 47/106 (44%), Positives = 61/106 (57%), Gaps = 26/106 (24%)

Query: 1   LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQSANGFD------VRTIYS 54
           ++DS VDR VIERLL I+S + +    SG RAL+FLGLD E+++  FD      + T Y 
Sbjct: 39  VDDSLVDRIVIERLLRITSCK-VTAVDSGWRALEFLGLDNEKASAEFDRLKVDLIITDYC 97

Query: 55  -------------------REIPVVIMSPEIILVRIDRYLEDGAED 81
                              RE+PVVIMS E +L RIDR LE+GA+D
Sbjct: 98  MPGMTGYELLKKIKESSNFREVPVVIMSSENVLTRIDRCLEEGAQD 143

Functions as response regulator involved in His-to-Asp phosphorelay signal transduction system. Phosphorylation of the Asp residue in the receiver domain activates the ability of the protein to promote the transcription of target genes. Type-A response regulators seem to act as negative regulators of the cytokinin signaling. 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 = 67.0 bits (162), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 46/106 (43%), Positives = 62/106 (58%), Gaps = 26/106 (24%)

Query: 1   LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQSANGFD------VRTIYS 54
           ++DS VDR VIERLL I+S + +    SG RAL+FLGLD++++A  FD      + T Y 
Sbjct: 38  VDDSLVDRIVIERLLRITSCK-VTAVDSGWRALEFLGLDDDKAAVEFDRLKVDLIITDYC 96

Query: 55  -------------------REIPVVIMSPEIILVRIDRYLEDGAED 81
                              +E+PVVIMS E ++ RIDR LE+GAED
Sbjct: 97  MPGMTGYELLKKIKESTSFKEVPVVIMSSENVMTRIDRCLEEGAED 142

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 = 63.9 bits (154), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 45/106 (42%), Positives = 60/106 (56%), Gaps = 26/106 (24%)

Query: 1   LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQSANGFD------VRTIYS 54
           ++DSFVDRKVIERLL IS+ + +    SG RALQ+LGLD +  ++G        + T YS
Sbjct: 23  VDDSFVDRKVIERLLKISACK-VTTVESGTRALQYLGLDGDNGSSGLKDLKVNLIVTDYS 81

Query: 55  -------------------REIPVVIMSPEIILVRIDRYLEDGAED 81
                              REIPVVIMS E I  RI++ + +GAE+
Sbjct: 82  MPGLTGYELLKKIKESSALREIPVVIMSSENIQPRIEQCMIEGAEE 127

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 = 63.2 bits (152), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 46/106 (43%), Positives = 58/106 (54%), Gaps = 26/106 (24%)

Query: 1   LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQSANGFD------VRTIYS 54
           ++DS VDRKVIERLL ISS + +    SG RALQ+LGLD  + A+         + T YS
Sbjct: 29  VDDSIVDRKVIERLLRISSCK-VTTVESGTRALQYLGLDGGKGASNLKDLKVNLIVTDYS 87

Query: 55  -------------------REIPVVIMSPEIILVRIDRYLEDGAED 81
                              RE+PVVIMS E IL RI   L++GAE+
Sbjct: 88  MPGLSGYDLLKKIKESSAFREVPVVIMSSENILPRIQECLKEGAEE 133

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 = 50.8 bits (120), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 40/116 (34%), Positives = 56/116 (48%), Gaps = 36/116 (31%)

Query: 1   LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQSAN--------------- 45
           ++DS  DRK+IERLL  SS + +    SG +AL+FLGL +   +N               
Sbjct: 14  VDDSLFDRKLIERLLQKSSCQ-VTTVDSGSKALEFLGLRQSTDSNDPNAFSKAPVNHQVV 72

Query: 46  ---------------GFDV-----RTIYSREIPVVIMSPEIILVRIDRYLEDGAED 81
                          G+D+      +   R+IPVVIMS E +  RI R LE+GAE+
Sbjct: 73  EVNLIITDYCMPGMTGYDLLKKVKESSAFRDIPVVIMSSENVPARISRCLEEGAEE 128

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 = 49.7 bits (117), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 41/114 (35%), Positives = 56/114 (49%), Gaps = 34/114 (29%)

Query: 1   LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGL---DEEQSA------------- 44
           ++DS  DRK+IERLL  SS + +    SG +AL+FLGL   D + +A             
Sbjct: 14  VDDSLFDRKMIERLLQKSSCQ-VTTVDSGSKALEFLGLRVDDNDPNALSTSPQIHQEVEI 72

Query: 45  ------------NGFDV-----RTIYSREIPVVIMSPEIILVRIDRYLEDGAED 81
                        G+D+      +   R IPVVIMS E +  RI R LE+GAE+
Sbjct: 73  NLIITDYCMPGMTGYDLLKKVKESAAFRSIPVVIMSSENVPARISRCLEEGAEE 126

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

Arabidopsis thaliana (taxid: 3702)

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

 Score = 49.7 bits (117), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 34/106 (32%), Positives = 55/106 (51%), Gaps = 27/106 (25%)

Query: 1   LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQSA----NGFDVRTIYS-- 54
           ++D+ +DRK++ER+L ISS + +  + +G RAL++LGL + Q      N   V  I +  
Sbjct: 25  VDDNLIDRKLVERILKISSCK-VTTAENGLRALEYLGLGDPQQTDSLTNVMKVNLIITDY 83

Query: 55  --------------------REIPVVIMSPEIILVRIDRYLEDGAE 80
                               +E+PVVI+S E I  RI++ L  GA+
Sbjct: 84  CMPGMTGFELLKKVKESSNLKEVPVVILSSENIPTRINKCLASGAQ 129

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 = 47.4 bits (111), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 36/108 (33%), Positives = 55/108 (50%), Gaps = 29/108 (26%)

Query: 1   LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGL-DEEQ-----SANGFDVRTIYS 54
           ++D+ +DRK++ERLL IS  + +  + +  RAL++LGL D+ Q     + N   V  I +
Sbjct: 34  VDDNLIDRKLVERLLKISCCK-VTTAENALRALEYLGLGDQNQHIDALTCNVMKVSLIIT 92

Query: 55  ----------------------REIPVVIMSPEIILVRIDRYLEDGAE 80
                                 RE+PVVIMS E I  RI++ L  GA+
Sbjct: 93  DYCMPGMTGFELLKKVKESSNLREVPVVIMSSENIPTRINKCLASGAQ 140


  Database: swissprot
    Posted date:  Mar 23, 2013  2:32 AM
  Number of letters in database: 191,569,459
  Number of sequences in database:  539,616
  
Lambda     K      H
   0.323    0.138    0.402 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 33,019,510
Number of Sequences: 539616
Number of extensions: 1139501
Number of successful extensions: 2137
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 2109
Number of HSP's gapped (non-prelim): 15
length of query: 93
length of database: 191,569,459
effective HSP length: 63
effective length of query: 30
effective length of database: 157,573,651
effective search space: 4727209530
effective search space used: 4727209530
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 55 (25.8 bits)

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	93
297733851	296	unnamed protein product [Vitis vinifera]	0.860	0.270	0.5	7e-14
224135725	192	type-a arp3-like response regulator [Pop	0.860	0.416	0.509	9e-14
224135721	223	type-a response regulator [Populus trich	0.860	0.358	0.509	9e-14
296086487	221	unnamed protein product [Vitis vinifera]	0.860	0.361	0.509	1e-13
147768948	210	hypothetical protein VITISV_026384 [Viti	0.860	0.380	0.509	1e-13
33330864	254	type-A response regulator [Catharanthus	0.860	0.314	0.5	2e-13
255558348	258	two-component sensor protein histidine p	0.860	0.310	0.495	3e-13
255540813	221	two-component sensor protein histidine p	0.860	0.361	0.5	3e-13
225457164	222	PREDICTED: two-component response regula	0.860	0.360	0.5	6e-13
357477303	214	Two-component response regulator ARR5 [M	0.860	0.373	0.509	8e-13

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

 Score = 81.3 bits (199), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 53/106 (50%), Positives = 64/106 (60%), Gaps = 26/106 (24%)

Query: 1   LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQSANGFD------VRTIYS 54
           ++DS VDRKVIERLL ISS + +    SG RALQFLGLD E+++ GFD      + T YS
Sbjct: 108 VDDSHVDRKVIERLLKISSCK-VTAVESGTRALQFLGLDGEENSVGFDGLKVNLIMTDYS 166

Query: 55  -------------------REIPVVIMSPEIILVRIDRYLEDGAED 81
                              R+IPVVIMS E IL RIDR LE+GAE+
Sbjct: 167 MPGMTGYELLKKIKESKAFRKIPVVIMSSENILTRIDRCLEEGAEE 212

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score = 80.9 bits (198), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 54/106 (50%), Positives = 65/106 (61%), Gaps = 26/106 (24%)

Query: 1   LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQSANGFD------VRTIYS 54
           ++DSFVDRKVIERLL ISS + +    SG RALQ+LGLD E+S+ GF+      + T YS
Sbjct: 34  VDDSFVDRKVIERLLKISSCK-VTVVESGSRALQYLGLDGEKSSVGFNDLKINLIMTDYS 92

Query: 55  -------------------REIPVVIMSPEIILVRIDRYLEDGAED 81
                              REIPVVIMS E IL RIDR LE+GAE+
Sbjct: 93  MPGMTGYELLKKIKESSAFREIPVVIMSSENILARIDRCLEEGAEE 138

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score = 80.9 bits (198), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 54/106 (50%), Positives = 65/106 (61%), Gaps = 26/106 (24%)

Query: 1   LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQSANGFD------VRTIYS 54
           ++DSFVDRKVIERLL ISS + +    SG RALQ+LGLD E+S+ GF+      + T YS
Sbjct: 34  VDDSFVDRKVIERLLKISSCK-VTVVESGSRALQYLGLDGEKSSVGFNDLKINLIMTDYS 92

Query: 55  -------------------REIPVVIMSPEIILVRIDRYLEDGAED 81
                              REIPVVIMS E IL RIDR LE+GAE+
Sbjct: 93  MPGMTGYELLKKIKESSAFREIPVVIMSSENILARIDRCLEEGAEE 138

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score = 80.1 bits (196), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 54/106 (50%), Positives = 63/106 (59%), Gaps = 26/106 (24%)

Query: 1   LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQSANGFD------VRTIYS 54
           ++DS VDRKVIERLL ISS + +    SGRRALQFLGLDEE+++ G D      + T Y 
Sbjct: 35  VDDSLVDRKVIERLLKISSCK-VTAVDSGRRALQFLGLDEEKNSAGLDGLKVDLIITDYC 93

Query: 55  -------------------REIPVVIMSPEIILVRIDRYLEDGAED 81
                              RE PVVIMS E IL RIDR LE+GAED
Sbjct: 94  MPGMTGYELLKKIKESSTFRETPVVIMSSENILTRIDRCLEEGAED 139

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score = 80.1 bits (196), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 54/106 (50%), Positives = 63/106 (59%), Gaps = 26/106 (24%)

Query: 1   LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQSANGFD------VRTIYS 54
           ++DS VDRKVIERLL ISS + +    SGRRALQFLGLDEE+++ G D      + T Y 
Sbjct: 24  VDDSLVDRKVIERLLKISSCK-VTAVDSGRRALQFLGLDEEKNSAGLDGLKVDLIITDYC 82

Query: 55  -------------------REIPVVIMSPEIILVRIDRYLEDGAED 81
                              RE PVVIMS E IL RIDR LE+GAED
Sbjct: 83  MPGMTGYELLKKIKESSTFRETPVVIMSSENILTRIDRCLEEGAED 128

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score = 79.7 bits (195), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 53/106 (50%), Positives = 63/106 (59%), Gaps = 26/106 (24%)

Query: 1   LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQSANGFD------VRTIYS 54
           ++DS VDRKVIERLL IS  + +    SGRRALQ+LGLD E+S  GFD      + T YS
Sbjct: 19  VDDSLVDRKVIERLLKISCCK-VTAVESGRRALQYLGLDGEKSTVGFDGLKVNLILTDYS 77

Query: 55  -------------------REIPVVIMSPEIILVRIDRYLEDGAED 81
                              +EIPVVIMS E IL RIDR LE+GAE+
Sbjct: 78  MPGMTGYELLKKIKGSSTLKEIPVVIMSSENILTRIDRCLEEGAEE 123

Source: Catharanthus roseus

Species: Catharanthus roseus

Genus: Catharanthus

Family: Apocynaceae

Order: Gentianales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score = 79.3 bits (194), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 52/105 (49%), Positives = 63/105 (60%), Gaps = 25/105 (23%)

Query: 1   LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQSAN--GFDVRTIYS---- 54
           ++DS VDRKVIERLL I+S + +    SGRRALQFLGLDEE+S +  G  V  I +    
Sbjct: 34  VDDSLVDRKVIERLLKITSCK-VTAVDSGRRALQFLGLDEEKSTSIQGLKVDLIITDYCM 92

Query: 55  ------------------REIPVVIMSPEIILVRIDRYLEDGAED 81
                             REIPVVIMS E ++ RIDR LE+GAED
Sbjct: 93  PGMTGYELLKKIKESSTFREIPVVIMSSENVMARIDRCLEEGAED 137

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score = 79.0 bits (193), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 53/106 (50%), Positives = 64/106 (60%), Gaps = 26/106 (24%)

Query: 1   LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQSANGFD------VRTIYS 54
           ++DS VDRKVIERLL ISS + +    SG RALQ+LGLD E+S+ GF+      + T YS
Sbjct: 32  VDDSLVDRKVIERLLKISSCK-VTAVDSGTRALQYLGLDGEKSSVGFNDLKVNLIMTDYS 90

Query: 55  -------------------REIPVVIMSPEIILVRIDRYLEDGAED 81
                              REIPVVIMS E IL RIDR LE+GAE+
Sbjct: 91  MPGMTGYELLKKIKESSAFREIPVVIMSSENILTRIDRCLEEGAEE 136

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score = 78.2 bits (191), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 53/106 (50%), Positives = 64/106 (60%), Gaps = 26/106 (24%)

Query: 1   LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQSANGFD------VRTIYS 54
           ++DS VDRKVIERLL ISS + +    SG RALQFLGLD E+++ GFD      + T YS
Sbjct: 34  VDDSHVDRKVIERLLKISSCK-VTAVESGTRALQFLGLDGEENSVGFDGLKVNLIMTDYS 92

Query: 55  -------------------REIPVVIMSPEIILVRIDRYLEDGAED 81
                              R+IPVVIMS E IL RIDR LE+GAE+
Sbjct: 93  MPGMTGYELLKKIKESKAFRKIPVVIMSSENILTRIDRCLEEGAEE 138

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357477303|ref|XP_003608937.1| Two-component response regulator ARR5 [Medicago truncatula] gi|355509992|gb|AES91134.1| Two-component response regulator ARR5 [Medicago truncatula]

 Score = 77.8 bits (190), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 54/106 (50%), Positives = 60/106 (56%), Gaps = 26/106 (24%)

Query: 1   LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQSANGFD------VRTIYS 54
           ++DS VDRKVIERLL ISS +      S RRALQFLGLD E S   FD      + T YS
Sbjct: 31  VDDSLVDRKVIERLLKISSCKVTVVE-SARRALQFLGLDGENSDVAFDAVKVNLIMTDYS 89

Query: 55  -------------------REIPVVIMSPEIILVRIDRYLEDGAED 81
                              REIPVVIMS E +L RIDR LE+GAED
Sbjct: 90  MPGMTGYELLKKIKESSVFREIPVVIMSSENVLTRIDRCLEEGAED 135

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	93
TAIR|locus:2170723	186	ARR6 "response regulator 6" [A	0.505	0.252	0.520	2.8e-15
TAIR|locus:2097870	184	RR5 "response regulator 5" [Ar	0.505	0.255	0.530	6.7e-15
TAIR|locus:2025911	231	ARR3 "response regulator 3" [A	0.505	0.203	0.541	3.4e-14
TAIR|locus:2194584	259	ARR4 "response regulator 4" [A	0.505	0.181	0.541	4.8e-14
TAIR|locus:2027237	206	ARR15 "response regulator 15"	0.483	0.218	0.565	7.3e-13
TAIR|locus:2011286	206	ARR7 "response regulator 7" [A	0.473	0.213	0.577	1.4e-12
UNIPROTKB|Q4GZK2	201	rr9 "Type A response regulator	0.451	0.208	0.522	3.9e-10
TAIR|locus:2080590	234	ARR9 "response regulator 9" [A	0.473	0.188	0.466	5.8e-10
TAIR|locus:2102509	153	RR17 "response regulator 17" [	0.473	0.287	0.4	1.4e-09
UNIPROTKB|Q4GZK7	232	rr4 "Type A response regulator	0.290	0.116	0.629	2e-09

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

 Score = 109 (43.4 bits), Expect = 2.8e-15, Sum P(2) = 2.8e-15
 Identities = 25/48 (52%), Positives = 33/48 (68%)

Query:     1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQSANGFD 48
             ++DS VDRK IERLL +SS +      S  RALQ+LGLD E+ + GF+
Sbjct:    30 VDDSHVDRKFIERLLRVSSCKVTVVD-SATRALQYLGLDVEEKSVGFE 76

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

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

GO:0005634 "nucleus" evidence=ISM;IDA

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

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

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

GO:0005515 "protein binding" evidence=IPI

GO:0007623 "circadian rhythm" evidence=RCA

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

 Score = 105 (42.0 bits), Expect = 6.7e-15, Sum P(2) = 6.7e-15
 Identities = 26/49 (53%), Positives = 33/49 (67%)

Query:     1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLD-EEQSANGFD 48
             ++DS VDRK IERLL +SS +      S  RALQ+LGLD E  S+ GF+
Sbjct:    30 VDDSMVDRKFIERLLRVSSCKVTVVD-SATRALQYLGLDGENNSSVGFE 77

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

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

GO:0005634 "nucleus" evidence=ISM;IDA

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

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

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

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

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

GO:0005515 "protein binding" evidence=IPI

GO:0005737 "cytoplasm" evidence=IDA

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

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

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

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

 Score = 109 (43.4 bits), Expect = 3.4e-14, Sum P(2) = 3.4e-14
 Identities = 26/48 (54%), Positives = 36/48 (75%)

Query:     1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQSANGFD 48
             ++DS VDR VIERLL I+S + +    SG RAL+FLGLD++++A  FD
Sbjct:    38 VDDSLVDRIVIERLLRITSCK-VTAVDSGWRALEFLGLDDDKAAVEFD 84

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

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

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

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

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

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

GO:0007623 "circadian rhythm" evidence=IMP

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

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

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

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

 Score = 108 (43.1 bits), Expect = 4.8e-14, Sum P(2) = 4.8e-14
 Identities = 26/48 (54%), Positives = 35/48 (72%)

Query:     1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQSANGFD 48
             ++DS VDR VIERLL I+S + +    SG RAL+FLGLD E+++  FD
Sbjct:    39 VDDSLVDRIVIERLLRITSCK-VTAVDSGWRALEFLGLDNEKASAEFD 85

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

 Score = 115 (45.5 bits), Expect = 7.3e-13, Sum P(2) = 7.3e-13
 Identities = 26/46 (56%), Positives = 34/46 (73%)

Query:     1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQSANG 46
             ++DSFVDRKVIERLL IS+ +      SG RALQ+LGLD +  ++G
Sbjct:    23 VDDSFVDRKVIERLLKISACKVTTVE-SGTRALQYLGLDGDNGSSG 67

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

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

GO:0005634 "nucleus" evidence=ISM;IDA

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

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

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

GO:0005515 "protein binding" evidence=IPI

GO:0005737 "cytoplasm" evidence=IDA

GO:0007623 "circadian rhythm" evidence=RCA

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

 Score = 106 (42.4 bits), Expect = 1.4e-12, Sum P(2) = 1.4e-12
 Identities = 26/45 (57%), Positives = 32/45 (71%)

Query:     1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQSAN 45
             ++DS VDRKVIERLL ISS +      SG RALQ+LGLD  + A+
Sbjct:    29 VDDSIVDRKVIERLLRISSCKVTTVE-SGTRALQYLGLDGGKGAS 72

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

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

 Score = 85 (35.0 bits), Expect = 3.9e-10, Sum P(2) = 3.9e-10
 Identities = 23/44 (52%), Positives = 29/44 (65%)

Query:     1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGL-DEEQS 43
             ++DS  DRK+IERLL  SS +      SG +AL+FLGL D E S
Sbjct:    14 VDDSLPDRKLIERLLKTSSFQVTTVD-SGSKALEFLGLHDHEDS 56

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

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

 Score = 85 (35.0 bits), Expect = 5.8e-10, Sum P(2) = 5.8e-10
 Identities = 21/45 (46%), Positives = 29/45 (64%)

Query:     1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQSAN 45
             ++DS  DRK+IERLL  SS +      SG +AL+FLGL +   +N
Sbjct:    14 VDDSLFDRKLIERLLQKSSCQVTTVD-SGSKALEFLGLRQSTDSN 57

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

 Score = 89 (36.4 bits), Expect = 1.4e-09, Sum P(2) = 1.4e-09
 Identities = 18/45 (40%), Positives = 33/45 (73%)

Query:     1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQSAN 45
             ++D+ +DRK++ER+L ISS + +  + +G RAL++LGL + Q  +
Sbjct:    25 VDDNLIDRKLVERILKISSCK-VTTAENGLRALEYLGLGDPQQTD 68

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

 Score = 82 (33.9 bits), Expect = 2.0e-09, Sum P(2) = 2.0e-09
 Identities = 17/27 (62%), Positives = 22/27 (81%)

Query:    55 REIPVVIMSPEIILVRIDRYLEDGAED 81
             ++IPVVIMS E +  RI+R LEDGAE+
Sbjct:   102 KDIPVVIMSSENVPARINRCLEDGAEE 128

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	93
PLN03029	222	PLN03029, PLN03029, type-a response regulator prot	3e-12

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

 Score = 59.3 bits (143), Expect = 3e-12
 Identities = 40/115 (34%), Positives = 57/115 (49%), Gaps = 35/115 (30%)

Query: 1   LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQSAN--------------- 45
           ++DS +DRK+IE+LL  SS + +    SG +AL+FLGL E+  +N               
Sbjct: 14  VDDSLIDRKLIEKLLKTSSYQ-VTTVDSGSKALKFLGLHEDDRSNPDTPSVSPNSHQEVE 72

Query: 46  --------------GFDV-----RTIYSREIPVVIMSPEIILVRIDRYLEDGAED 81
                         G+D+      +   R IPVVIMS E +  RI R LE+GAE+
Sbjct: 73  VNLIITDYCMPGMTGYDLLKKIKESSSLRNIPVVIMSSENVPSRITRCLEEGAEE 127

Length = 222

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	93
COG0745	229	OmpR Response regulators consisting of a CheY-like	99.76
COG4566	202	TtrR Response regulator [Signal transduction mecha	99.74
COG2204	464	AtoC Response regulator containing CheY-like recei	99.64
COG4567	182	Response regulator consisting of a CheY-like recei	99.54
PF00072	112	Response_reg: Response regulator receiver domain;	99.54
COG4753	475	Response regulator containing CheY-like receiver d	99.5
COG3437	360	Response regulator containing a CheY-like receiver	99.44
COG4565	224	CitB Response regulator of citrate/malate metaboli	99.42
COG3706	435	PleD Response regulator containing a CheY-like rec	99.35
PRK09836	227	DNA-binding transcriptional activator CusR; Provis	99.28
PRK10816	223	DNA-binding transcriptional regulator PhoP; Provis	99.27
PRK10529	225	DNA-binding transcriptional activator KdpE; Provis	99.26
PRK11173	237	two-component response regulator; Provisional	99.25
PRK10766	221	DNA-binding transcriptional regulator TorR; Provis	99.25
PLN03029	222	type-a response regulator protein; Provisional	99.24
PRK10841	924	hybrid sensory kinase in two-component regulatory	99.22
PRK09468	239	ompR osmolarity response regulator; Provisional	99.21
COG2197	211	CitB Response regulator containing a CheY-like rec	99.21
KOG0519	786	consensus Sensory transduction histidine kinase [S	99.2
PRK10046	225	dpiA two-component response regulator DpiA; Provis	99.2
PRK10701	240	DNA-binding transcriptional regulator RstA; Provis	99.19
PRK10161	229	transcriptional regulator PhoB; Provisional	99.19
PRK11107	919	hybrid sensory histidine kinase BarA; Provisional	99.18
COG0784	130	CheY FOG: CheY-like receiver [Signal transduction	99.18
PRK10336	219	DNA-binding transcriptional regulator QseB; Provis	99.18
PRK13856	241	two-component response regulator VirG; Provisional	99.18
TIGR03787	227	marine_sort_RR proteobacterial dedicated sortase s	99.18
PRK10643	222	DNA-binding transcriptional regulator BasR; Provis	99.17
PRK15347	921	two component system sensor kinase SsrA; Provision	99.16
TIGR01387	218	cztR_silR_copR heavy metal response regulator. Mem	99.15
PRK11083	228	DNA-binding response regulator CreB; Provisional	99.14
TIGR02154	226	PhoB phosphate regulon transcriptional regulatory	99.13
PRK11517	223	transcriptional regulatory protein YedW; Provision	99.13
TIGR02956	968	TMAO_torS TMAO reductase sytem sensor TorS. This p	99.12
PRK10955	232	DNA-binding transcriptional regulator CpxR; Provis	99.1
TIGR02915	445	PEP_resp_reg putative PEP-CTERM system response re	99.1
PRK15115	444	response regulator GlrR; Provisional	99.09
CHL00148	240	orf27 Ycf27; Reviewed	99.09
PRK10923	469	glnG nitrogen regulation protein NR(I); Provisiona	99.09
PRK11466	914	hybrid sensory histidine kinase TorS; Provisional	99.09
PRK09959	1197	hybrid sensory histidine kinase in two-component r	99.08
PRK11361	457	acetoacetate metabolism regulatory protein AtoC; P	99.08
PRK09958	204	DNA-binding transcriptional activator EvgA; Provis	99.07
PRK10360	196	DNA-binding transcriptional activator UhpA; Provis	99.04
PRK10840	216	transcriptional regulator RcsB; Provisional	99.03
TIGR01818	463	ntrC nitrogen regulation protein NR(I). This model	99.03
PRK10365	441	transcriptional regulatory protein ZraR; Provision	99.02
PRK10430	239	DNA-binding transcriptional activator DcuR; Provis	99.02
PRK10710	240	DNA-binding transcriptional regulator BaeR; Provis	98.98
PRK09581	457	pleD response regulator PleD; Reviewed	98.95
PRK13558	665	bacterio-opsin activator; Provisional	98.95
PRK09483	217	response regulator; Provisional	98.94
PRK15479	221	transcriptional regulatory protein TctD; Provision	98.94
PRK09581	457	pleD response regulator PleD; Reviewed	98.94
COG3947	361	Response regulator containing CheY-like receiver a	98.94
PRK11091	779	aerobic respiration control sensor protein ArcB; P	98.93
PRK09935	210	transcriptional regulator FimZ; Provisional	98.87
TIGR02875	262	spore_0_A sporulation transcription factor Spo0A.	98.85
PRK09390	202	fixJ response regulator FixJ; Provisional	98.84
PRK13837	828	two-component VirA-like sensor kinase; Provisional	98.83
PRK12555	337	chemotaxis-specific methylesterase; Provisional	98.8
PRK11475	207	DNA-binding transcriptional activator BglJ; Provis	98.78
PRK14084	246	two-component response regulator; Provisional	98.78
COG3707	194	AmiR Response regulator with putative antiterminat	98.7
COG2201	350	CheB Chemotaxis response regulator containing a Ch	98.69
PRK00742	354	chemotaxis-specific methylesterase; Provisional	98.68
PRK11697	238	putative two-component response-regulatory protein	98.65
PRK10610	129	chemotaxis regulatory protein CheY; Provisional	98.62
PRK10651	216	transcriptional regulator NarL; Provisional	98.61
PRK15369	211	two component system sensor kinase SsrB; Provision	98.6
PRK10403	215	transcriptional regulator NarP; Provisional	98.58
PRK13435	145	response regulator; Provisional	98.51
PRK10693	303	response regulator of RpoS; Provisional	98.47
cd00156	113	REC Signal receiver domain; originally thought to	98.46
PRK13557	540	histidine kinase; Provisional	98.37
PRK10100	216	DNA-binding transcriptional regulator CsgD; Provis	98.27
PRK09191	261	two-component response regulator; Provisional	98.24
PRK15411	207	rcsA colanic acid capsular biosynthesis activation	98.04
PRK15029	755	arginine decarboxylase; Provisional	97.6
COG3279	244	LytT Response regulator of the LytR/AlgR family [T	97.1
PRK11107	919	hybrid sensory histidine kinase BarA; Provisional	96.63
PF03709	115	OKR_DC_1_N: Orn/Lys/Arg decarboxylase, N-terminal	93.55
TIGR03815	322	CpaE_hom_Actino helicase/secretion neighborhood Cp	91.91
smart00448	55	REC cheY-homologous receiver domain. CheY regulate	91.1
COG3706	435	PleD Response regulator containing a CheY-like rec	90.79
cd04728	248	ThiG Thiazole synthase (ThiG) is the tetrameric en	90.76
PRK11840	326	bifunctional sulfur carrier protein/thiazole synth	90.45
PRK00208	250	thiG thiazole synthase; Reviewed	89.05
PF06490	109	FleQ: Flagellar regulatory protein FleQ; InterPro:	87.34
cd02071	122	MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 bin	86.09
COG0134	254	TrpC Indole-3-glycerol phosphate synthase [Amino a	84.51
PRK12704	520	phosphodiesterase; Provisional	84.5
PF05690	247	ThiG: Thiazole biosynthesis protein ThiG; InterPro	81.13

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

Probab=99.76  E-value=1.4e-17  Score=102.09  Aligned_cols=86  Identities=15%  Similarity=0.144  Sum_probs=74.6

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhhh----cCCcEEEEcCCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIYS----REIPVVIMSPEII   67 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~~----~~~pii~lt~~~~   67 (93)
                      |||++..+..+..+|+..||+ +.++.++.+|++.+... ++         +++|++++..+.    ..+|||++|+.++
T Consensus         6 veDd~~i~~~l~~~L~~~g~~-v~~~~~~~~a~~~~~~~-~dlviLD~~lP~~dG~~~~~~iR~~~~~~~PIi~Lta~~~   83 (229)
T COG0745           6 VEDDPELAELLKEYLEEEGYE-VDVAADGEEALEAAREQ-PDLVLLDLMLPDLDGLELCRRLRAKKGSGPPIIVLTARDD   83 (229)
T ss_pred             EcCCHHHHHHHHHHHHHCCCE-EEEECCHHHHHHHHhcC-CCEEEEECCCCCCCHHHHHHHHHhhcCCCCcEEEEECCCc
Confidence            689999999999999999999 99999999999998754 32         345666644333    7789999999999


Q ss_pred             HHHHHHHHHcCCcceeeccch
Q 042991           68 LVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        68 ~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      ..+.+.+++.|||||++|||+
T Consensus        84 ~~d~v~gl~~GADDYl~KPf~  104 (229)
T COG0745          84 EEDRVLGLEAGADDYLTKPFS  104 (229)
T ss_pred             HHHHHHHHhCcCCeeeeCCCC
Confidence            999999999999999999998

>COG4566 TtrR Response regulator [Signal transduction mechanisms]

Probab=99.74  E-value=2.2e-17  Score=97.23  Aligned_cols=89  Identities=17%  Similarity=0.189  Sum_probs=76.5

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCcc---------cCCCchHH---HhhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEE---------QSANGFDV---RTIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~---------~~~~~~d~---l~~~~~~~pii~lt~~~~~   68 (93)
                      ||||...++.+..+|+..||+ +..+.|+++.+.......+         ++++|+++   +......+|||++|++++.
T Consensus        10 VDDD~~vr~al~~Ll~s~G~~-v~~~~s~~~fL~~~~~~~pGclllDvrMPg~sGlelq~~L~~~~~~~PVIfiTGhgDI   88 (202)
T COG4566          10 VDDDESVRDALAFLLESAGFQ-VKCFASAEEFLAAAPLDRPGCLLLDVRMPGMSGLELQDRLAERGIRLPVIFLTGHGDI   88 (202)
T ss_pred             EcCcHHHHHHHHHHHHhCCce-eeeecCHHHHHhhccCCCCCeEEEecCCCCCchHHHHHHHHhcCCCCCEEEEeCCCCh
Confidence            689999999999999999999 9999999999988643332         24567776   5555599999999999999


Q ss_pred             HHHHHHHHcCCcceeeccchhh
Q 042991           69 VRIDRYLEDGAEDSETCQMWAR   90 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~~~   90 (93)
                      ...++++++||.|||.||++.+
T Consensus        89 pmaV~AmK~GAvDFLeKP~~~q  110 (202)
T COG4566          89 PMAVQAMKAGAVDFLEKPFSEQ  110 (202)
T ss_pred             HHHHHHHHcchhhHHhCCCchH
Confidence            9999999999999999999743

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

Probab=99.64  E-value=2.7e-15  Score=99.11  Aligned_cols=88  Identities=18%  Similarity=0.168  Sum_probs=76.2

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCcc---------cCCCchHHHh---hhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEE---------QSANGFDVRT---IYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~---------~~~~~~d~l~---~~~~~~pii~lt~~~~~   68 (93)
                      |||+...+..+...|+..||. +..+.++.+|+..+.....         ++++|++++.   ...+++|||++|++++.
T Consensus        10 VDDd~~ir~~l~~~L~~~G~~-v~~a~~~~~al~~i~~~~~~lvl~Di~mp~~~Gl~ll~~i~~~~~~~pVI~~Tg~g~i   88 (464)
T COG2204          10 VDDDPDIRELLEQALELAGYE-VVTAESAEEALEALSESPFDLVLLDIRMPGMDGLELLKEIKSRDPDLPVIVMTGHGDI   88 (464)
T ss_pred             EeCCHHHHHHHHHHHHHcCCe-EEEeCCHHHHHHHHhcCCCCEEEEecCCCCCchHHHHHHHHhhCCCCCEEEEeCCCCH
Confidence            689999999999999999999 9999999999999976632         1345666643   33389999999999999


Q ss_pred             HHHHHHHHcCCcceeeccchh
Q 042991           69 VRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      +..++|++.||.||+.||++.
T Consensus        89 ~~AV~A~k~GA~Dfl~KP~~~  109 (464)
T COG2204          89 DTAVEALRLGAFDFLEKPFDL  109 (464)
T ss_pred             HHHHHHHhcCcceeeeCCCCH
Confidence            999999999999999999973

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

Probab=99.54  E-value=6.8e-14  Score=80.15  Aligned_cols=87  Identities=13%  Similarity=0.051  Sum_probs=75.6

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHH---HhhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDV---RTIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~---l~~~~~~~pii~lt~~~~~   68 (93)
                      ||||......|++.+++.||. +..+.+.++++..++...+.         +-+|+++   +++...++.||++|++.+-
T Consensus        15 vdDD~~f~~~LaRa~e~RGf~-v~~a~~~~eal~~art~~PayAvvDlkL~~gsGL~~i~~lr~~~~d~rivvLTGy~sI   93 (182)
T COG4567          15 VDDDTPFLRTLARAMERRGFA-VVTAESVEEALAAARTAPPAYAVVDLKLGDGSGLAVIEALRERRADMRIVVLTGYASI   93 (182)
T ss_pred             ecCChHHHHHHHHHHhccCce-eEeeccHHHHHHHHhcCCCceEEEEeeecCCCchHHHHHHHhcCCcceEEEEecchHH
Confidence            689999999999999999999 99999999999998754431         2267776   5555599999999999999


Q ss_pred             HHHHHHHHcCCcceeeccch
Q 042991           69 VRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~   88 (93)
                      ...++|.+.||.+||.||-+
T Consensus        94 ATAV~AvKlGA~~YLaKPAd  113 (182)
T COG4567          94 ATAVEAVKLGACDYLAKPAD  113 (182)
T ss_pred             HHHHHHHHhhhhhhcCCCCC
Confidence            99999999999999999976

>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=99.54  E-value=1.2e-13  Score=75.55  Aligned_cols=88  Identities=20%  Similarity=0.322  Sum_probs=73.4

Q ss_pred             CCCcHHHHHHHHHHHhhcCC-CceEEeCCHHHHHHHhccCccc---------CCCchHH---HhhhhcCCcEEEEcCCCC
Q 042991            1 LNDSFVDRKVIERLLTISSS-RDLYCSCSGRRALQFLGLDEEQ---------SANGFDV---RTIYSREIPVVIMSPEII   67 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~-~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~---l~~~~~~~pii~lt~~~~   67 (93)
                      +||++..+..+..+|+..|+ . +..+.++.++++.+....++         +..++++   +....+.+|+|++|+..+
T Consensus         4 vd~~~~~~~~l~~~l~~~~~~~-v~~~~~~~~~~~~~~~~~~d~iiid~~~~~~~~~~~~~~i~~~~~~~~ii~~t~~~~   82 (112)
T PF00072_consen    4 VDDDPEIRELLEKLLERAGYEE-VTTASSGEEALELLKKHPPDLIIIDLELPDGDGLELLEQIRQINPSIPIIVVTDEDD   82 (112)
T ss_dssp             EESSHHHHHHHHHHHHHTTEEE-EEEESSHHHHHHHHHHSTESEEEEESSSSSSBHHHHHHHHHHHTTTSEEEEEESSTS
T ss_pred             EECCHHHHHHHHHHHHhCCCCE-EEEECCHHHHHHHhcccCceEEEEEeeeccccccccccccccccccccEEEecCCCC
Confidence            57899999999999999999 7 99999999999999655432         2344554   333338999999999999


Q ss_pred             HHHHHHHHHcCCcceeeccchh
Q 042991           68 LVRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        68 ~~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      .....+++++|+++|+.||++.
T Consensus        83 ~~~~~~~~~~g~~~~l~kp~~~  104 (112)
T PF00072_consen   83 SDEVQEALRAGADDYLSKPFSP  104 (112)
T ss_dssp             HHHHHHHHHTTESEEEESSSSH
T ss_pred             HHHHHHHHHCCCCEEEECCCCH
Confidence            9999999999999999999863

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 ....

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

Probab=99.50  E-value=1.4e-13  Score=91.13  Aligned_cols=88  Identities=15%  Similarity=0.166  Sum_probs=75.5

Q ss_pred             CCCcHHHHHHHHHHHh--hcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHH---hhhhcCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLT--ISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYSREIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~--~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~~~~pii~lt~~~   66 (93)
                      |||++..|+.|+.++.  +.|++.|-.|.||.+|++.++..+++         .+.|+|++   ....+.+.+|++|+..
T Consensus         7 VDDE~lIr~GLk~lI~w~~~g~eiVgtA~NG~eAleli~e~~pDiviTDI~MP~mdGLdLI~~ike~~p~~~~IILSGy~   86 (475)
T COG4753           7 VDDEPLIREGLKSLIDWEALGIEVVGTAANGKEALELIQETQPDIVITDINMPGMDGLDLIKAIKEQSPDTEFIILSGYD   86 (475)
T ss_pred             ecChHHHHHHHHHhCChhhcCCeEEEecccHHHHHHHHHhcCCCEEEEecCCCCCcHHHHHHHHHHhCCCceEEEEeccc
Confidence            6999999999999996  56787789999999999999765542         34667763   3444999999999999


Q ss_pred             CHHHHHHHHHcCCcceeeccch
Q 042991           67 ILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      +-+.+.+|+++|+.|||+||++
T Consensus        87 eFeYak~Am~lGV~dYLLKP~~  108 (475)
T COG4753          87 EFEYAKKAMKLGVKDYLLKPVD  108 (475)
T ss_pred             hhHHHHHHHhcCchhheeCcCC
Confidence            9999999999999999999987

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

Probab=99.44  E-value=5.6e-13  Score=85.17  Aligned_cols=89  Identities=22%  Similarity=0.321  Sum_probs=74.2

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhhh------cCCcEEEEcCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIYS------REIPVVIMSPE   65 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~~------~~~pii~lt~~   65 (93)
                      |||.+..+..+..+|+..+|+ +..+.+|++|++.......+         .+.|.+++..+.      ..+|++++|+.
T Consensus        20 vDD~~~~~~~~~~lL~~~~y~-v~~ae~g~~a~kl~~~~~~dlvllD~~mp~mdg~ev~~~lk~~~p~t~~ip~i~lT~~   98 (360)
T COG3437          20 VDDEPDNLEALRQLLRMIGYR-VIEAENGEEALKLLQEEPPDLVLLDVRMPEMDGAEVLNKLKAMSPSTRRIPVILLTAY   98 (360)
T ss_pred             ecCchhHHHHHHHHHHhcccc-eeeecCchHHHHHhcccCCceEEeeccCCCccHHHHHHHHHhcCCcccccceEEEeec
Confidence            689999999999999999999 99999999999998654321         234555533222      78999999999


Q ss_pred             CCHHHHHHHHHcCCcceeeccchhh
Q 042991           66 IILVRIDRYLEDGAEDSETCQMWAR   90 (93)
Q Consensus        66 ~~~~~~~~~~~~ga~d~l~kP~~~~   90 (93)
                      .+.+...++++.|+++|+.||++..
T Consensus        99 ~d~~~~~~~~~~g~~dyl~KP~~~~  123 (360)
T COG3437          99 ADSEDRQRALEAGADDYLSKPISPK  123 (360)
T ss_pred             CChHHHHHHHHhhHHHHhcCCCCHH
Confidence            9999999999999999999999844

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

Probab=99.42  E-value=2.4e-12  Score=77.43  Aligned_cols=88  Identities=11%  Similarity=0.081  Sum_probs=72.9

Q ss_pred             CCCcHHHHHHHHHHHhh-cCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhhh---cCCcEEEEcCCCC
Q 042991            1 LNDSFVDRKVIERLLTI-SSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIYS---REIPVVIMSPEII   67 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~-~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~~---~~~pii~lt~~~~   67 (93)
                      ||||+...+.-+.+++. .||+.|-.+.++++|...++...++         +-.|++++....   ..+-||++|+.++
T Consensus         6 iEDD~mVaeih~~yv~~~~gF~~vg~A~~~~ea~~~i~~~~pDLILLDiYmPd~~Gi~lL~~ir~~~~~~DVI~iTAA~d   85 (224)
T COG4565           6 IEDDPMVAEIHRRYVKQIPGFSVVGTAGTLEEAKMIIEEFKPDLILLDIYMPDGNGIELLPELRSQHYPVDVIVITAASD   85 (224)
T ss_pred             EcCchHHHHHHHHHHHhCCCceEEEeeccHHHHHHHHHhhCCCEEEEeeccCCCccHHHHHHHHhcCCCCCEEEEeccch
Confidence            68999999999999986 5787788999999999999754431         235666644433   7778999999999


Q ss_pred             HHHHHHHHHcCCcceeeccch
Q 042991           68 LVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        68 ~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      .+.+.+++.+|+.|||.|||.
T Consensus        86 ~~tI~~alr~Gv~DYLiKPf~  106 (224)
T COG4565          86 METIKEALRYGVVDYLIKPFT  106 (224)
T ss_pred             HHHHHHHHhcCchhheeccee
Confidence            999999999999999999996

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

Probab=99.35  E-value=1.2e-11  Score=81.55  Aligned_cols=87  Identities=23%  Similarity=0.306  Sum_probs=72.8

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhhh-----cCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIYS-----REIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~~-----~~~pii~lt~~~   66 (93)
                      |||+...+..+..+|...||. +..+.++++|+..+.+..+.         .+.|+++...+.     ..+|||++++..
T Consensus       138 vdD~~~~~~~l~~~L~~~g~~-v~~a~~~~~Al~~~~e~~~dlil~d~~mp~~dg~el~~~lr~~~~t~~ipii~~~~~~  216 (435)
T COG3706         138 VDDDATQRERLRRILQVEGFR-VVEATDGEEALLQLAELPPDLVLLDANMPDMDGLELCTRLRQLERTRDIPIILLSSKD  216 (435)
T ss_pred             EcCcHHHHHHHHHHHHhccce-eeeecCHHHHHHHHhcCCCcEEEEecCCCccCHHHHHHHHhcccccccccEEEEeccc
Confidence            578889999999999999999 99999999999999755321         234555433222     799999999999


Q ss_pred             CHHHHHHHHHcCCcceeeccch
Q 042991           67 ILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      +.....+|++.|++||++||+.
T Consensus       217 d~~~~~~Af~~G~~Dyi~kPi~  238 (435)
T COG3706         217 DDELVVRAFELGVNDYITKPIE  238 (435)
T ss_pred             chHHHHHHHHcCCcceEecCCC
Confidence            9999999999999999999986

>PRK09836 DNA-binding transcriptional activator CusR; Provisional

Probab=99.28  E-value=8.6e-11  Score=71.12  Aligned_cols=88  Identities=15%  Similarity=0.151  Sum_probs=70.2

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHH---hhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~~~~pii~lt~~~~~   68 (93)
                      ++|++..+..+...|+..|+. +..+.++.+++..+....++         +..|++++   ....+.+|+|++|+..+.
T Consensus         6 v~d~~~~~~~l~~~L~~~g~~-v~~~~~~~~~~~~~~~~~~dlvild~~~~~~~g~~~~~~lr~~~~~~pii~ls~~~~~   84 (227)
T PRK09836          6 VEDEKKTGEYLTKGLTEAGFV-VDLADNGLNGYHLAMTGDYDLIILDIMLPDVNGWDIVRMLRSANKGMPILLLTALGTI   84 (227)
T ss_pred             EeCCHHHHHHHHHHHHHCCCE-EEEECCHHHHHHHHhhCCCCEEEEECCCCCCCHHHHHHHHHhcCCCCCEEEEEcCCCH
Confidence            478889999999999988998 99999999999877543321         22344443   222368999999999999


Q ss_pred             HHHHHHHHcCCcceeeccchh
Q 042991           69 VRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      ....++++.|+++|+.||++.
T Consensus        85 ~~~~~~~~~Ga~~~l~kp~~~  105 (227)
T PRK09836         85 EHRVKGLELGADDYLVKPFAF  105 (227)
T ss_pred             HHHHHHHhCCCCEEEeCCCCH
Confidence            999999999999999999873

>PRK10816 DNA-binding transcriptional regulator PhoP; Provisional

Probab=99.27  E-value=9.2e-11  Score=70.82  Aligned_cols=88  Identities=14%  Similarity=0.179  Sum_probs=70.5

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHh---hhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRT---IYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~---~~~~~~pii~lt~~~~~   68 (93)
                      ++|++..+..+...|+..|+. +..+.++.+++..+....++         +..|++++.   ...+.+|+|++|+..+.
T Consensus         6 v~d~~~~~~~l~~~L~~~g~~-v~~~~~~~~~l~~~~~~~~dlvild~~l~~~~g~~l~~~lr~~~~~~pii~ls~~~~~   84 (223)
T PRK10816          6 VEDNALLRHHLKVQLQDAGHQ-VDAAEDAKEADYYLNEHLPDIAIVDLGLPDEDGLSLIRRWRSNDVSLPILVLTARESW   84 (223)
T ss_pred             EeCCHHHHHHHHHHHHHCCCE-EEEECCHHHHHHHHhhCCCCEEEEECCCCCCCHHHHHHHHHhcCCCCCEEEEEcCCCH
Confidence            478888999999999999999 99999999999887644321         223444432   22368999999999999


Q ss_pred             HHHHHHHHcCCcceeeccchh
Q 042991           69 VRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      .....+++.|+++|+.||++.
T Consensus        85 ~~~~~~l~~Ga~d~l~kp~~~  105 (223)
T PRK10816         85 QDKVEVLSAGADDYVTKPFHI  105 (223)
T ss_pred             HHHHHHHHcCCCeeEeCCCCH
Confidence            999999999999999999863

>PRK10529 DNA-binding transcriptional activator KdpE; Provisional

Probab=99.26  E-value=1.4e-10  Score=70.08  Aligned_cols=88  Identities=17%  Similarity=0.171  Sum_probs=69.8

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhh--hcCCcEEEEcCCCCHH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIY--SREIPVVIMSPEIILV   69 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~--~~~~pii~lt~~~~~~   69 (93)
                      +||++..+..+...|+..|+. +..+.++.+++..+....++         +..|++++...  ...+|+|++|+..+..
T Consensus         7 vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~~~~~~~~~~~~dlvild~~l~~~~g~~~~~~lr~~~~~pvi~lt~~~~~~   85 (225)
T PRK10529          7 VEDEQAIRRFLRTALEGDGMR-VFEAETLQRGLLEAATRKPDLIILDLGLPDGDGIEFIRDLRQWSAIPVIVLSARSEES   85 (225)
T ss_pred             EeCCHHHHHHHHHHHHHCCCE-EEEeCCHHHHHHHHhcCCCCEEEEeCCCCCCCHHHHHHHHHcCCCCCEEEEECCCCHH
Confidence            578899999999999988998 99999999998877543321         22344442222  2678999999999999


Q ss_pred             HHHHHHHcCCcceeeccchh
Q 042991           70 RIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        70 ~~~~~~~~ga~d~l~kP~~~   89 (93)
                      ...++++.|+++|+.||+..
T Consensus        86 ~~~~~~~~ga~~~l~kP~~~  105 (225)
T PRK10529         86 DKIAALDAGADDYLSKPFGI  105 (225)
T ss_pred             HHHHHHHcCCCEEEeCCCCH
Confidence            99999999999999999873

>PRK11173 two-component response regulator; Provisional

Probab=99.25  E-value=1.5e-10  Score=70.67  Aligned_cols=87  Identities=17%  Similarity=0.210  Sum_probs=69.9

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhh--hcCCcEEEEcCCCCHH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIY--SREIPVVIMSPEIILV   69 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~--~~~~pii~lt~~~~~~   69 (93)
                      ++|++..+..+...|+..|+. +..+.++.+++..+....++         +..|++++...  ...+|+|++|+..+..
T Consensus         9 v~dd~~~~~~l~~~L~~~g~~-v~~~~~~~~~~~~~~~~~~dlvild~~l~~~~g~~~~~~lr~~~~~pii~lt~~~~~~   87 (237)
T PRK11173          9 VEDELVTRNTLKSIFEAEGYD-VFEATDGAEMHQILSENDINLVIMDINLPGKNGLLLARELREQANVALMFLTGRDNEV   87 (237)
T ss_pred             EeCCHHHHHHHHHHHHHcCCE-EEEECCHHHHHHHHhhCCCCEEEEcCCCCCCCHHHHHHHHhcCCCCCEEEEECCCCHH
Confidence            478899999999999989999 99999999999888644321         22344442222  1678999999999988


Q ss_pred             HHHHHHHcCCcceeeccch
Q 042991           70 RIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        70 ~~~~~~~~ga~d~l~kP~~   88 (93)
                      ....+++.|+++|+.||++
T Consensus        88 ~~~~~~~~ga~d~l~kP~~  106 (237)
T PRK11173         88 DKILGLEIGADDYITKPFN  106 (237)
T ss_pred             HHHHHHHCCCCEEEECCCC
Confidence            8889999999999999986

>PRK10766 DNA-binding transcriptional regulator TorR; Provisional

Probab=99.25  E-value=1.8e-10  Score=69.38  Aligned_cols=88  Identities=14%  Similarity=0.127  Sum_probs=69.7

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhh--hcCCcEEEEcCCCCHH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIY--SREIPVVIMSPEIILV   69 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~--~~~~pii~lt~~~~~~   69 (93)
                      ++|++.....+...|+..|+. +..+.++.+++..+....++         ++.|++++...  ...+|+|++++..+..
T Consensus         8 v~d~~~~~~~l~~~l~~~~~~-v~~~~~~~~~~~~~~~~~~dlvild~~l~~~~g~~~~~~lr~~~~~~ii~l~~~~~~~   86 (221)
T PRK10766          8 VEDEPVTRARLQGYFEQEGYT-VSEAASGAGMREIMQNQHVDLILLDINLPGEDGLMLTRELRSRSTVGIILVTGRTDSI   86 (221)
T ss_pred             EeCCHHHHHHHHHHHHHcCCE-EEEECCHHHHHHHHhcCCCCEEEEeCCCCCCCHHHHHHHHHhCCCCCEEEEECCCcHH
Confidence            478888899999999988999 99999999999887644321         22344442222  1678999999999998


Q ss_pred             HHHHHHHcCCcceeeccchh
Q 042991           70 RIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        70 ~~~~~~~~ga~d~l~kP~~~   89 (93)
                      ...++++.|+++|+.||+..
T Consensus        87 ~~~~~l~~Ga~d~l~kP~~~  106 (221)
T PRK10766         87 DRIVGLEMGADDYVTKPLEL  106 (221)
T ss_pred             HHHHHHHcCCCcEEeCCCCH
Confidence            88899999999999999873

>PLN03029 type-a response regulator protein; Provisional

Probab=99.24  E-value=1.6e-10  Score=70.65  Aligned_cols=87  Identities=45%  Similarity=0.647  Sum_probs=69.1

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCcc-------------------c----------CCCchHHHh
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEE-------------------Q----------SANGFDVRT   51 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~-------------------~----------~~~~~d~l~   51 (93)
                      |+|+...+..+..+|+..||. +..+.++.+++..+.....                   .          .+.|++++.
T Consensus        14 Vdd~~~~~~~l~~~L~~~g~~-v~~a~sg~~al~~l~~~~~d~~~p~~~~~~~~~~~~~~~dlVllD~~mp~~~G~e~l~   92 (222)
T PLN03029         14 VDDSLIDRKLIEKLLKTSSYQ-VTTVDSGSKALKFLGLHEDDRSNPDTPSVSPNSHQEVEVNLIITDYCMPGMTGYDLLK   92 (222)
T ss_pred             EeCCHHHHHHHHHHHHHcCce-EEEECCHHHHHHHHHhccccccccccccccccccccccCCEEEEcCCCCCCCHHHHHH
Confidence            578899999999999999999 9999999999998742210                   1          223444432


Q ss_pred             hhh-----cCCcEEEEcCCCCHHHHHHHHHcCCcceeeccch
Q 042991           52 IYS-----REIPVVIMSPEIILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        52 ~~~-----~~~pii~lt~~~~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      .+.     ..+|+|++|+........++++.|+++|+.||+.
T Consensus        93 ~ir~~~~~~~ipvIils~~~~~~~~~~al~~Ga~dyl~KP~~  134 (222)
T PLN03029         93 KIKESSSLRNIPVVIMSSENVPSRITRCLEEGAEEFFLKPVQ  134 (222)
T ss_pred             HHHhccccCCCcEEEEeCCCCHHHHHHHHHhCchheEECCCC
Confidence            221     5789999999999999999999999999999986

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

Probab=99.22  E-value=1.5e-10  Score=82.67  Aligned_cols=87  Identities=16%  Similarity=0.263  Sum_probs=73.3

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHH---HhhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDV---RTIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~---l~~~~~~~pii~lt~~~~~   68 (93)
                      |||++..+..+..+|++.||. +..+.++.+|++.+....++         .++|+++   ++...+.+|||++|+....
T Consensus       807 VdD~~~~~~~l~~~L~~~G~~-v~~a~~g~eal~~l~~~~~DlVl~D~~mP~mdG~el~~~ir~~~~~~pII~lTa~~~~  885 (924)
T PRK10841        807 VDDHPINRRLLADQLGSLGYQ-CKTANDGVDALNVLSKNHIDIVLTDVNMPNMDGYRLTQRLRQLGLTLPVIGVTANALA  885 (924)
T ss_pred             ECCCHHHHHHHHHHHHHcCCE-EEEECCHHHHHHHHHhCCCCEEEEcCCCCCCCHHHHHHHHHhcCCCCCEEEEECCCCH
Confidence            589999999999999999999 99999999999998654432         2345555   3333478999999999999


Q ss_pred             HHHHHHHHcCCcceeeccch
Q 042991           69 VRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~   88 (93)
                      +...++++.|+++|+.||++
T Consensus       886 ~~~~~~~~aG~d~~L~KPv~  905 (924)
T PRK10841        886 EEKQRCLEAGMDSCLSKPVT  905 (924)
T ss_pred             HHHHHHHHCCCCEEEeCCCC
Confidence            99999999999999999997

>PRK09468 ompR osmolarity response regulator; Provisional

Probab=99.21  E-value=3e-10  Score=69.25  Aligned_cols=87  Identities=17%  Similarity=0.203  Sum_probs=69.8

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHH---hhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~~~~pii~lt~~~~~   68 (93)
                      ++|++..+..+...|+..||. +..+.++.+++..+....++         ...|++++   ....+.+|+|++++..+.
T Consensus        11 v~d~~~~~~~l~~~L~~~g~~-v~~~~~~~~~~~~~~~~~~dlvild~~l~~~~g~~~~~~lr~~~~~~pii~ls~~~~~   89 (239)
T PRK09468         11 VDDDMRLRALLERYLTEQGFQ-VRSAANAEQMDRLLTRESFHLMVLDLMLPGEDGLSICRRLRSQNNPTPIIMLTAKGEE   89 (239)
T ss_pred             EcCCHHHHHHHHHHHHHCCCE-EEEECCHHHHHHHHhcCCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCCEEEEECCCcH
Confidence            478888999999999999999 99999999999887643321         22344443   222268899999999999


Q ss_pred             HHHHHHHHcCCcceeeccch
Q 042991           69 VRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~   88 (93)
                      .....+++.|+++|+.||+.
T Consensus        90 ~~~~~~l~~Ga~~~l~kP~~  109 (239)
T PRK09468         90 VDRIVGLEIGADDYLPKPFN  109 (239)
T ss_pred             HHHHHHHhcCCCeEEECCCC
Confidence            88889999999999999987

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

Probab=99.21  E-value=3.5e-10  Score=68.81  Aligned_cols=89  Identities=17%  Similarity=0.178  Sum_probs=72.1

Q ss_pred             CCCcHHHHHHHHHHHhhcC-CCceEEeCCHHHHHHHhccCccc---------CCCchHH---HhhhhcCCcEEEEcCCCC
Q 042991            1 LNDSFVDRKVIERLLTISS-SRDLYCSCSGRRALQFLGLDEEQ---------SANGFDV---RTIYSREIPVVIMSPEII   67 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~-~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~---l~~~~~~~pii~lt~~~~   67 (93)
                      +||++..+..++.+|...+ ++.+..+.++.++++.+....++         +++|+++   +....++++++++|...+
T Consensus         6 vDDh~l~r~gl~~~L~~~~~~~vv~~a~~~~~~l~~~~~~~pdvvl~Dl~mP~~~G~e~~~~l~~~~p~~~vvvlt~~~~   85 (211)
T COG2197           6 VDDHPLVREGLRQLLELEPDLEVVGEASNGEEALDLARELKPDVVLLDLSMPGMDGLEALKQLRARGPDIKVVVLTAHDD   85 (211)
T ss_pred             ECCcHHHHHHHHHHHhhCCCCEEEEEeCCHHHHHHHhhhcCCCEEEEcCCCCCCChHHHHHHHHHHCCCCcEEEEeccCC
Confidence            5899999999999998665 66677888899999987544432         2456665   343349999999999999


Q ss_pred             HHHHHHHHHcCCcceeeccchh
Q 042991           68 LVRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        68 ~~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      +....++++.||++|+.|....
T Consensus        86 ~~~v~~al~~Ga~Gyl~K~~~~  107 (211)
T COG2197          86 PAYVIRALRAGADGYLLKDASP  107 (211)
T ss_pred             HHHHHHHHHcCCCEEEeCCCCH
Confidence            9999999999999999998653

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

Probab=99.20  E-value=4.1e-11  Score=84.27  Aligned_cols=88  Identities=19%  Similarity=0.231  Sum_probs=72.6

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCcccC----------CCchHH---Hhhh-hcCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQS----------ANGFDV---RTIY-SREIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~~----------~~~~d~---l~~~-~~~~pii~lt~~~   66 (93)
                      |||+...+.....+|+++|.. +..+.++.+|++.++..++++          ++|+++   ++.. ..++|||++|+..
T Consensus       672 vddn~vn~~Va~~~l~~~g~~-~~~~~sg~e~l~~~~~~~~y~~ifmD~qMP~mDG~e~~~~irk~~~~~~pIvAlTa~~  750 (786)
T KOG0519|consen  672 VDDNPVNRKVATGMLKKLGAE-VTEVNSGQEALDKLKPPHSYDVIFMDLQMPEMDGYEATREIRKKERWHLPIVALTADA  750 (786)
T ss_pred             EecccchHHHHHHHHHHhCCe-eEeecCcHHHHHhcCCCCcccEEEEEcCCcccchHHHHHHHHHhhcCCCCEEEEecCC
Confidence            588899999999999999999 888889999999998444432          234443   2222 1699999999999


Q ss_pred             CHHHHHHHHHcCCcceeeccchh
Q 042991           67 ILVRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      .+....++++.|.|+||.||+.-
T Consensus       751 ~~~~~~~c~~~Gmd~yl~KP~~~  773 (786)
T KOG0519|consen  751 DPSTEEECLEVGMDGYLSKPFTL  773 (786)
T ss_pred             cHHHHHHHHHhCCceEEcccccH
Confidence            99999999999999999999973

>PRK10046 dpiA two-component response regulator DpiA; Provisional

Probab=99.20  E-value=3.8e-10  Score=68.90  Aligned_cols=88  Identities=8%  Similarity=-0.014  Sum_probs=69.0

Q ss_pred             CCCcHHHHHHHHHHHhh-cCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhh---hcCCcEEEEcCCCC
Q 042991            1 LNDSFVDRKVIERLLTI-SSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIY---SREIPVVIMSPEII   67 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~-~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~---~~~~pii~lt~~~~   67 (93)
                      +||++..+..+...|+. .++..+..+.++.++++.+....++         ++.|++++...   .+..|||++|+..+
T Consensus        10 vdd~~~~~~~l~~~L~~~~~~~~v~~a~~~~~al~~~~~~~pdlvllD~~mp~~~gle~~~~l~~~~~~~~iivls~~~~   89 (225)
T PRK10046         10 VEDETPLAEMHAEYIRHIPGFSQILLAGNLAQARMMIERFKPGLILLDNYLPDGRGINLLHELVQAHYPGDVVFTTAASD   89 (225)
T ss_pred             ECCCHHHHHHHHHHHHhCCCcEEEEEECCHHHHHHHHHhcCCCEEEEeCCCCCCcHHHHHHHHHhcCCCCCEEEEEcCCC
Confidence            58899999999999986 4674378899999999998644321         23455543322   25678999999999


Q ss_pred             HHHHHHHHHcCCcceeeccch
Q 042991           68 LVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        68 ~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      .....++++.|+++|+.||++
T Consensus        90 ~~~~~~al~~Ga~~yl~Kp~~  110 (225)
T PRK10046         90 METVSEAVRCGVFDYLIKPIA  110 (225)
T ss_pred             HHHHHHHHHcCccEEEECCcC
Confidence            999999999999999999986

>PRK10701 DNA-binding transcriptional regulator RstA; Provisional

Probab=99.19  E-value=4.8e-10  Score=68.49  Aligned_cols=87  Identities=16%  Similarity=0.066  Sum_probs=69.1

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhh--hcCCcEEEEcCCCCHH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIY--SREIPVVIMSPEIILV   69 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~--~~~~pii~lt~~~~~~   69 (93)
                      ++|++..+..+...|+..|+. +..+.++.+++..+....++         ...|++++..+  ....|+|++++..+..
T Consensus         7 vedd~~~~~~l~~~L~~~g~~-v~~~~~~~~~l~~~~~~~~dlvild~~l~~~~g~~~~~~ir~~~~~pii~l~~~~~~~   85 (240)
T PRK10701          7 VEDDAEVGSLIAAYLAKHDID-VTVEPRGDRAEATILREQPDLVLLDIMLPGKDGMTICRDLRPKWQGPIVLLTSLDSDM   85 (240)
T ss_pred             EeCCHHHHHHHHHHHHHcCCE-EEEeCCHHHHHHHHhhCCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCEEEEECCCCHH
Confidence            578899999999999999999 99999999999988644321         23445542222  2567999999988888


Q ss_pred             HHHHHHHcCCcceeeccch
Q 042991           70 RIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        70 ~~~~~~~~ga~d~l~kP~~   88 (93)
                      ....+++.|+++|+.||+.
T Consensus        86 ~~~~~~~~Ga~d~l~kP~~  104 (240)
T PRK10701         86 NHILALEMGACDYILKTTP  104 (240)
T ss_pred             HHHHHHHcCCCEEEECCCC
Confidence            8889999999999999986

>PRK10161 transcriptional regulator PhoB; Provisional

Probab=99.19  E-value=5.4e-10  Score=67.69  Aligned_cols=87  Identities=21%  Similarity=0.135  Sum_probs=69.1

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhhh-----cCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIYS-----REIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~~-----~~~pii~lt~~~   66 (93)
                      +||++..+..+...|+..|+. +..+.++.+++..+....++         +..+++++..+.     +.+|+|++|+..
T Consensus         8 vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~~~~~~~~~~~~dlvild~~l~~~~g~~~~~~l~~~~~~~~~pvi~ls~~~   86 (229)
T PRK10161          8 VEDEAPIREMVCFVLEQNGFQ-PVEAEDYDSAVNQLNEPWPDLILLDWMLPGGSGIQFIKHLKRESMTRDIPVVMLTARG   86 (229)
T ss_pred             EcCCHHHHHHHHHHHHHCCCE-EEEECCHHHHHHHHhccCCCEEEEeCCCCCCCHHHHHHHHHhccccCCCCEEEEECCC
Confidence            578889999999999988999 88999999999887644321         123444432221     578999999999


Q ss_pred             CHHHHHHHHHcCCcceeeccch
Q 042991           67 ILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      +.....++++.|+++|+.||++
T Consensus        87 ~~~~~~~~~~~Ga~~~l~kp~~  108 (229)
T PRK10161         87 EEEDRVRGLETGADDYITKPFS  108 (229)
T ss_pred             CHHHHHHHHHcCCCEEEECCCC
Confidence            9999999999999999999986

>PRK11107 hybrid sensory histidine kinase BarA; Provisional

Probab=99.18  E-value=3e-10  Score=80.41  Aligned_cols=88  Identities=16%  Similarity=0.229  Sum_probs=72.2

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhh-----hcCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIY-----SREIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~-----~~~~pii~lt~~~   66 (93)
                      |||++..+..++.+|+..|+. +..+.++.+|++.+....++         .++|++++..+     .+.+|||++|+..
T Consensus       673 vdd~~~~~~~l~~~L~~~~~~-v~~~~~~~~al~~~~~~~~dlil~D~~mp~~~g~~~~~~lr~~~~~~~~pii~lt~~~  751 (919)
T PRK11107        673 VDDNPANLKLIGALLEEQVEH-VVLCDSGHQAVEQAKQRPFDLILMDIQMPGMDGIRACELIRQLPHNQNTPIIAVTAHA  751 (919)
T ss_pred             EeCCHHHHHHHHHHHHHcCCE-EEEECCHHHHHHHHHhCCCCEEEEeCCCCCCcHHHHHHHHHhcccCCCCCEEEEeCCC
Confidence            589999999999999999999 99999999999998654432         23455542222     2679999999999


Q ss_pred             CHHHHHHHHHcCCcceeeccchh
Q 042991           67 ILVRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      ......++++.|+++|+.||+..
T Consensus       752 ~~~~~~~~~~~G~~~~l~KP~~~  774 (919)
T PRK11107        752 MAGERERLLSAGMDDYLAKPIDE  774 (919)
T ss_pred             CHHHHHHHHHcCCCeEeeCCCCH
Confidence            99999999999999999999973

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

Probab=99.18  E-value=6.5e-10  Score=61.97  Aligned_cols=87  Identities=23%  Similarity=0.350  Sum_probs=69.2

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHH-HHHHHhccCc-cc---------CCCchHHHhhhh---cCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGR-RALQFLGLDE-EQ---------SANGFDVRTIYS---REIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~-~a~~~~~~~~-~~---------~~~~~d~l~~~~---~~~pii~lt~~~   66 (93)
                      +||++..+..+...|...|+. +..+.++. +|+..++... .+         .++|++++..+.   +.+|++++|+..
T Consensus        11 vdD~~~~~~~~~~~l~~~g~~-v~~a~~g~~~al~~~~~~~~~dlii~D~~mp~~~G~~~~~~l~~~~~~~pvv~~t~~~   89 (130)
T COG0784          11 VDDEPVNRRLLKRLLEDLGYE-VVEAADGEEEALELLRELPQPDLILLDINMPGMDGIELLRRLRARGPNIPVILLTAYA   89 (130)
T ss_pred             EcCCHHHHHHHHHHHHHcCCe-EEEeCChHHHHHHHHHhCCCCCEEEEeCCCCCCCHHHHHHHHHhCCCCCCEEEEEcCc
Confidence            589999999999999999999 99999995 9999997542 21         234555544333   578888899988


Q ss_pred             CHHHHHHHHHcCCcceeeccch
Q 042991           67 ILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      .......+++.|+++|+.||+.
T Consensus        90 ~~~~~~~~~~~g~~~~l~kP~~  111 (130)
T COG0784          90 DEADRERALAAGADDYLTKPIF  111 (130)
T ss_pred             CHHHHHHHHHcCCCeEEcCCCC
Confidence            8877677889999999999964

>PRK10336 DNA-binding transcriptional regulator QseB; Provisional

Probab=99.18  E-value=5.9e-10  Score=66.83  Aligned_cols=87  Identities=18%  Similarity=0.119  Sum_probs=69.1

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHH---hhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~~~~pii~lt~~~~~   68 (93)
                      +||++..+..+...|+..++. +..+.++.+++..+....++         +..|++++   ....+.+|+|++|+..+.
T Consensus         6 vdd~~~~~~~l~~~L~~~~~~-v~~~~~~~~~~~~~~~~~~dlvild~~l~~~~g~~~~~~i~~~~~~~~ii~lt~~~~~   84 (219)
T PRK10336          6 IEDDMLIGDGIKTGLSKMGFS-VDWFTQGRQGKEALYSAPYDAVILDLTLPGMDGRDILREWREKGQREPVLILTARDAL   84 (219)
T ss_pred             EcCCHHHHHHHHHHHHHCCCE-EEEeCCHHHHHHHHhhCCCCEEEEECCCCCCCHHHHHHHHHhcCCCCcEEEEECCCCH
Confidence            578889999999999988998 88999999999887543321         22344442   232378899999999998


Q ss_pred             HHHHHHHHcCCcceeeccch
Q 042991           69 VRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~   88 (93)
                      ....++++.|+++|+.||++
T Consensus        85 ~~~~~~~~~ga~~~i~kp~~  104 (219)
T PRK10336         85 AERVEGLRLGADDYLCKPFA  104 (219)
T ss_pred             HHHHHHHhCCCCeEEECCCC
Confidence            88889999999999999986

>PRK13856 two-component response regulator VirG; Provisional

Probab=99.18  E-value=5.6e-10  Score=68.41  Aligned_cols=87  Identities=18%  Similarity=0.269  Sum_probs=67.4

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhhh--cCCcEEEEcCC-CCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIYS--REIPVVIMSPE-IIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~~--~~~pii~lt~~-~~~   68 (93)
                      ++|++..+..+...|+..||. +..+.++.+++..+....++         +.+|++++....  ..+|++++|+. .+.
T Consensus         7 ved~~~~~~~l~~~L~~~~~~-v~~~~~~~~~~~~~~~~~~dlvi~d~~l~~~~g~~l~~~i~~~~~~pii~lt~~~~~~   85 (241)
T PRK13856          7 IDDDVAMRHLIVEYLTIHAFK-VTAVADSQQFNRVLASETVDVVVVDLNLGREDGLEIVRSLATKSDVPIIIISGDRLEE   85 (241)
T ss_pred             EeCCHHHHHHHHHHHHHcCCE-EEEECCHHHHHHHHhhCCCCEEEEeCCCCCCCHHHHHHHHHhcCCCcEEEEECCCCcH
Confidence            578899999999999988999 99999999999887544321         234455433221  67899999985 466


Q ss_pred             HHHHHHHHcCCcceeeccch
Q 042991           69 VRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~   88 (93)
                      ....++++.|+++|+.||++
T Consensus        86 ~~~~~~l~~Ga~~yl~kP~~  105 (241)
T PRK13856         86 ADKVVALELGATDFIAKPFG  105 (241)
T ss_pred             HHHHHHHhcCcCeEEeCCCC
Confidence            66778999999999999997

>TIGR03787 marine_sort_RR proteobacterial dedicated sortase system response regulator

Probab=99.18  E-value=5.6e-10  Score=67.48  Aligned_cols=87  Identities=16%  Similarity=0.110  Sum_probs=69.3

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc------CC-----CchHHHhhh---hcCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ------SA-----NGFDVRTIY---SREIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~------~~-----~~~d~l~~~---~~~~pii~lt~~~   66 (93)
                      +||+...+..+...|+..||. +..+.++.+++..+....++      .+     .|++++..+   .+.+|+|++|+..
T Consensus         6 vdd~~~~~~~l~~~L~~~~~~-v~~~~~~~~~~~~~~~~~~dlvild~~l~~~~~~g~~~~~~i~~~~~~~pii~ls~~~   84 (227)
T TIGR03787         6 VEDEAAIRENYADALKRQGYQ-VTTYADRPSAMQAFRQRLPDLAIIDIGLGEEIDGGFMLCQDLRSLSATLPIIFLTARD   84 (227)
T ss_pred             EeCCHHHHHHHHHHHHHCCcE-EEEecCHHHHHHHHHhCCCCEEEEECCCCCCCCCHHHHHHHHHhcCCCCCEEEEECCC
Confidence            578889999999999988998 88899999999887543321      11     244543222   2678999999999


Q ss_pred             CHHHHHHHHHcCCcceeeccch
Q 042991           67 ILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      +......+++.|+++|+.||+.
T Consensus        85 ~~~~~~~~~~~Ga~~~l~kp~~  106 (227)
T TIGR03787        85 SDFDTVSGLRLGADDYLTKDIS  106 (227)
T ss_pred             CHHHHHHHHhcCCCEEEECCCC
Confidence            9999999999999999999986

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.

>PRK10643 DNA-binding transcriptional regulator BasR; Provisional

Probab=99.17  E-value=6e-10  Score=66.88  Aligned_cols=87  Identities=17%  Similarity=0.159  Sum_probs=69.4

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhh---hhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTI---YSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~---~~~~~pii~lt~~~~~   68 (93)
                      ++|++..+..+...|+..|+. +..+.++.+++..+....++         +..|++++..   ..+.+|+|++|+..+.
T Consensus         6 vdd~~~~~~~l~~~L~~~~~~-v~~~~~~~~~~~~~~~~~~d~illd~~~~~~~g~~~~~~l~~~~~~~pii~ls~~~~~   84 (222)
T PRK10643          6 VEDDTLLLQGLILALQTEGYA-CDCASTAREAEALLESGHYSLVVLDLGLPDEDGLHLLRRWRQKKYTLPVLILTARDTL   84 (222)
T ss_pred             EeCCHHHHHHHHHHHHHCCCE-EEEeCCHHHHHHHHHhCCCCEEEEECCCCCCCHHHHHHHHHhcCCCCcEEEEECCCCH
Confidence            578889999999999988998 99999999999887543321         2234444322   2267899999999999


Q ss_pred             HHHHHHHHcCCcceeeccch
Q 042991           69 VRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~   88 (93)
                      ....++++.|+++|+.||+.
T Consensus        85 ~~~~~~~~~ga~~~l~kp~~  104 (222)
T PRK10643         85 EDRVAGLDVGADDYLVKPFA  104 (222)
T ss_pred             HHHHHHHhcCCCeEEeCCCC
Confidence            99999999999999999986

>PRK15347 two component system sensor kinase SsrA; Provisional

Probab=99.16  E-value=4.9e-10  Score=79.42  Aligned_cols=87  Identities=16%  Similarity=0.240  Sum_probs=71.7

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhh-------hcCCcEEEEcC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIY-------SREIPVVIMSP   64 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~-------~~~~pii~lt~   64 (93)
                      |||++..+..+..+|+..|+. +..+.++.+|++.+....++         .++|++++..+       .+.+|||++|+
T Consensus       696 vdd~~~~~~~l~~~L~~~g~~-v~~a~~~~~al~~~~~~~~dlil~D~~mp~~~G~~~~~~ir~~~~~~~~~~pii~lt~  774 (921)
T PRK15347        696 VDDVETNRDIIGMMLVELGQQ-VTTAASGTEALELGRQHRFDLVLMDIRMPGLDGLETTQLWRDDPNNLDPDCMIVALTA  774 (921)
T ss_pred             EeCCHHHHHHHHHHHHHcCCE-EEEECCHHHHHHHHhcCCCCEEEEeCCCCCCCHHHHHHHHHhchhhcCCCCcEEEEeC
Confidence            589999999999999999999 99999999999998654431         23455553221       26789999999


Q ss_pred             CCCHHHHHHHHHcCCcceeeccch
Q 042991           65 EIILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        65 ~~~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      ........++++.|+++|+.||+.
T Consensus       775 ~~~~~~~~~~~~~G~~~~l~KP~~  798 (921)
T PRK15347        775 NAAPEEIHRCKKAGMNHYLTKPVT  798 (921)
T ss_pred             CCCHHHHHHHHHCCCCEEEECCCC
Confidence            999999999999999999999986

>TIGR01387 cztR_silR_copR heavy metal response regulator

Probab=99.15  E-value=9.4e-10  Score=65.85  Aligned_cols=87  Identities=16%  Similarity=0.224  Sum_probs=69.6

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhh---hhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTI---YSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~---~~~~~pii~lt~~~~~   68 (93)
                      ++|++..+..+...|+..|+. +..+.++.+++..+....++         +..+++++..   ..+.+|+|++++..+.
T Consensus         4 idd~~~~~~~l~~~l~~~~~~-v~~~~~~~~~~~~~~~~~~dlvl~d~~~~~~~g~~~~~~l~~~~~~~~iivls~~~~~   82 (218)
T TIGR01387         4 VEDEQKTAEYLQQGLSESGYV-VDAASNGRDGLHLALKDDYDLIILDVMLPGMDGWQILQTLRRSGKQTPVLFLTARDSV   82 (218)
T ss_pred             EECCHHHHHHHHHHHHHCCCE-EEEECCHHHHHHHHhcCCCCEEEEeCCCCCCCHHHHHHHHHccCCCCcEEEEEcCCCH
Confidence            478888999999999988998 99999999999887544321         2234444322   2378899999999999


Q ss_pred             HHHHHHHHcCCcceeeccch
Q 042991           69 VRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~   88 (93)
                      ....++++.|+++|+.||+.
T Consensus        83 ~~~~~~~~~Ga~~~l~kp~~  102 (218)
T TIGR01387        83 ADKVKGLDLGADDYLVKPFS  102 (218)
T ss_pred             HHHHHHHHcCCCeEEECCCC
Confidence            99999999999999999986

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.

>PRK11083 DNA-binding response regulator CreB; Provisional

Probab=99.14  E-value=9.7e-10  Score=66.19  Aligned_cols=88  Identities=18%  Similarity=0.142  Sum_probs=69.1

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHH---hhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~~~~pii~lt~~~~~   68 (93)
                      +||++..+..+...|...++. +..+.++.+++..+....++         +..+++++   ....+.+|+|++|+..+.
T Consensus         9 vdd~~~~~~~l~~~l~~~~~~-v~~~~~~~~~~~~~~~~~~dlvl~d~~~~~~~g~~~~~~l~~~~~~~~ii~ls~~~~~   87 (228)
T PRK11083          9 VEDEQAIADTLVYALQSEGFT-VEWFERGLPALDKLRQQPPDLVILDVGLPDISGFELCRQLLAFHPALPVIFLTARSDE   87 (228)
T ss_pred             EeCCHHHHHHHHHHHHHCCCE-EEEEcCHHHHHHHHhcCCCCEEEEeCCCCCCCHHHHHHHHHhhCCCCCEEEEEcCCcH
Confidence            478888999999999888998 88999999999887543321         22344442   222378999999999888


Q ss_pred             HHHHHHHHcCCcceeeccchh
Q 042991           69 VRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      .....+++.|+++|+.||+..
T Consensus        88 ~~~~~a~~~Ga~~~l~kp~~~  108 (228)
T PRK11083         88 VDRLVGLEIGADDYVAKPFSP  108 (228)
T ss_pred             HHHHHHhhcCCCeEEECCCCH
Confidence            888899999999999999863

>TIGR02154 PhoB phosphate regulon transcriptional regulatory protein PhoB

Probab=99.13  E-value=1.2e-09  Score=65.70  Aligned_cols=88  Identities=20%  Similarity=0.235  Sum_probs=69.2

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhh-----hcCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIY-----SREIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~-----~~~~pii~lt~~~   66 (93)
                      +||++..+..+...|+..++. +..+.++.+++..+....++         +..|++++...     .+.+|++++|+..
T Consensus         8 vdd~~~~~~~l~~~L~~~~~~-v~~~~~~~~~~~~~~~~~~d~vi~d~~~~~~~g~~~~~~l~~~~~~~~~~ii~ls~~~   86 (226)
T TIGR02154         8 VEDEPAIRELIAYNLEKAGYD-VVEAGDGDEALTLINERGPDLILLDWMLPGTSGIELCRRLRRRPETRAIPIIMLTARG   86 (226)
T ss_pred             EeCCHHHHHHHHHHHHHCCCE-EEEEcCHHHHHHHHHhcCCCEEEEECCCCCCcHHHHHHHHHccccCCCCCEEEEecCC
Confidence            478889999999999888888 88999999999888644321         22344443222     1578999999999


Q ss_pred             CHHHHHHHHHcCCcceeeccchh
Q 042991           67 ILVRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      +.....++++.|+++|+.||+..
T Consensus        87 ~~~~~~~~~~~Ga~~~l~kp~~~  109 (226)
T TIGR02154        87 EEEDRVRGLETGADDYITKPFSP  109 (226)
T ss_pred             CHHHHHHHHhcCcceEEeCCCCH
Confidence            98888899999999999999863

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.

>PRK11517 transcriptional regulatory protein YedW; Provisional

Probab=99.13  E-value=1.4e-09  Score=65.50  Aligned_cols=87  Identities=16%  Similarity=0.213  Sum_probs=68.9

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhh--hcCCcEEEEcCCCCHH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIY--SREIPVVIMSPEIILV   69 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~--~~~~pii~lt~~~~~~   69 (93)
                      ++|++..+..+...|+..|+. +..+.++.+++..+....++         +..+++++...  ...+|++++++..+..
T Consensus         6 v~~~~~~~~~l~~~L~~~~~~-v~~~~~~~~~l~~~~~~~~dlvi~d~~~~~~~g~~~~~~l~~~~~~~ii~ls~~~~~~   84 (223)
T PRK11517          6 IEDNQRTQEWVTQGLSEAGYV-IDAVSDGRDGLYLALKDDYALIILDIMLPGMDGWQILQTLRTAKQTPVICLTARDSVD   84 (223)
T ss_pred             EeCCHHHHHHHHHHHHHCCCE-EEEECCHHHHHHHHhcCCCCEEEEECCCCCCCHHHHHHHHHcCCCCCEEEEECCCCHH
Confidence            478888999999999988988 99999999999887543321         22344443222  1578999999999999


Q ss_pred             HHHHHHHcCCcceeeccch
Q 042991           70 RIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        70 ~~~~~~~~ga~d~l~kP~~   88 (93)
                      ...++++.|+++|+.||+.
T Consensus        85 ~~~~a~~~Ga~~~l~kp~~  103 (223)
T PRK11517         85 DRVRGLDSGANDYLVKPFS  103 (223)
T ss_pred             HHHHHHhcCCCEEEECCCC
Confidence            9999999999999999986

>TIGR02956 TMAO_torS TMAO reductase sytem sensor TorS

Probab=99.12  E-value=8.3e-10  Score=78.67  Aligned_cols=87  Identities=16%  Similarity=0.223  Sum_probs=71.1

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHH---hhhhcC---CcEEEEcCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYSRE---IPVVIMSPE   65 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~~~---~pii~lt~~   65 (93)
                      |||++..+..+..+|+..||. +..+.++.+|++.+....++         ++.|++++   +...+.   +|||++|+.
T Consensus       708 vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~~a~~~l~~~~~dlvl~D~~mp~~~g~~~~~~ir~~~~~~~~~pii~lta~  786 (968)
T TIGR02956       708 VEDNEVNQMVAQGFLTRLGHK-VTLAESGQSALECFHQHAFDLALLDINLPDGDGVTLLQQLRAIYGAKNEVKFIAFSAH  786 (968)
T ss_pred             EcCcHHHHHHHHHHHHHcCCE-EEEECCHHHHHHHHHCCCCCEEEECCCCCCCCHHHHHHHHHhCccccCCCeEEEEECC
Confidence            589999999999999999999 99999999999998654332         23444442   222233   899999999


Q ss_pred             CCHHHHHHHHHcCCcceeeccch
Q 042991           66 IILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        66 ~~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      .......++++.|+++|+.||+.
T Consensus       787 ~~~~~~~~~~~~G~~~~l~KP~~  809 (968)
T TIGR02956       787 VFNEDVAQYLAAGFDGFLAKPVV  809 (968)
T ss_pred             CCHHHHHHHHHCCCCEEEeCCCC
Confidence            99999999999999999999997

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).

>PRK10955 DNA-binding transcriptional regulator CpxR; Provisional

Probab=99.10  E-value=2e-09  Score=65.16  Aligned_cols=86  Identities=20%  Similarity=0.226  Sum_probs=67.6

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhhh--cCCcEEEEcCCCCHH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIYS--REIPVVIMSPEIILV   69 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~~--~~~pii~lt~~~~~~   69 (93)
                      +||++..+..+...|+..|+. +..+.++.+++..+.. .++         +..|++++..+.  ..+|+|++|+..+..
T Consensus         7 vdd~~~~~~~l~~~l~~~~~~-v~~~~~~~~~~~~~~~-~~d~vl~d~~~~~~~g~~~~~~l~~~~~~~ii~lt~~~~~~   84 (232)
T PRK10955          7 VDDDRELTSLLKELLEMEGFN-VIVAHDGEQALDLLDD-SIDLLLLDVMMPKKNGIDTLKELRQTHQTPVIMLTARGSEL   84 (232)
T ss_pred             EeCCHHHHHHHHHHHHHCCCE-EEEeCCHHHHHHHhhc-CCCEEEEeCCCCCCcHHHHHHHHHhcCCCcEEEEECCCCHH
Confidence            578999999999999988898 8899999999988753 221         223444422221  338999999998888


Q ss_pred             HHHHHHHcCCcceeeccch
Q 042991           70 RIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        70 ~~~~~~~~ga~d~l~kP~~   88 (93)
                      ...++++.|+++|+.||++
T Consensus        85 ~~~~~~~~ga~~~l~kp~~  103 (232)
T PRK10955         85 DRVLGLELGADDYLPKPFN  103 (232)
T ss_pred             HHHHHHHcCCCEEEcCCCC
Confidence            8889999999999999986

>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator

Probab=99.10  E-value=1.3e-09  Score=72.26  Aligned_cols=86  Identities=12%  Similarity=0.096  Sum_probs=68.3

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc------C--------CCchHHH---hhhhcCCcEEEEc
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ------S--------ANGFDVR---TIYSREIPVVIMS   63 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~------~--------~~~~d~l---~~~~~~~pii~lt   63 (93)
                      +||++..+..+...+  .+|. +..+.++.+|++.+....++      .        ++|++++   ....+.+|||++|
T Consensus         4 vddd~~~~~~l~~~l--~~~~-v~~a~~~~~al~~l~~~~~dlvllD~~mp~~~~~~~~g~~~l~~i~~~~~~~piI~lt   80 (445)
T TIGR02915         4 VEDDLGLQKQLKWSF--ADYE-LAVAADRESAIALVRRHEPAVVTLDLGLPPDADGASEGLAALQQILAIAPDTKVIVIT   80 (445)
T ss_pred             EECCHHHHHHHHHHh--CCCe-EEEeCCHHHHHHHHhhCCCCEEEEeCCCCCCcCCCCCHHHHHHHHHhhCCCCCEEEEe
Confidence            578888888888888  6898 99999999999998644321      1        2344443   2333789999999


Q ss_pred             CCCCHHHHHHHHHcCCcceeeccchh
Q 042991           64 PEIILVRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        64 ~~~~~~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      +..+.+...++++.|+++|+.||++.
T Consensus        81 ~~~~~~~~~~a~~~Ga~dyl~KP~~~  106 (445)
T TIGR02915        81 GNDDRENAVKAIGLGAYDFYQKPIDP  106 (445)
T ss_pred             cCCCHHHHHHHHHCCccEEEeCCCCH
Confidence            99999999999999999999999873

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).

>PRK15115 response regulator GlrR; Provisional

Probab=99.09  E-value=1e-09  Score=72.83  Aligned_cols=87  Identities=17%  Similarity=0.148  Sum_probs=71.1

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHh---hhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRT---IYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~---~~~~~~pii~lt~~~~~   68 (93)
                      |||++..+..+...|+..||. +..+.++.+|+..+....++         ++.|++++.   ...+.+|+|++|+..+.
T Consensus        11 Vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~eal~~l~~~~~dlvilD~~lp~~~g~~ll~~l~~~~~~~pvIvlt~~~~~   89 (444)
T PRK15115         11 VDDDPGLLKLLGMRLTSEGYS-VVTAESGQEALRVLNREKVDLVISDLRMDEMDGMQLFAEIQKVQPGMPVIILTAHGSI   89 (444)
T ss_pred             EECCHHHHHHHHHHHHHCCCE-EEEeCCHHHHHHHHhcCCCCEEEEcCCCCCCCHHHHHHHHHhcCCCCcEEEEECCCCH
Confidence            578999999999999999998 99999999999988644321         234455432   22378999999999998


Q ss_pred             HHHHHHHHcCCcceeeccch
Q 042991           69 VRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~   88 (93)
                      ....++++.|+++|+.||+.
T Consensus        90 ~~~~~a~~~Ga~~~l~KP~~  109 (444)
T PRK15115         90 PDAVAATQQGVFSFLTKPVD  109 (444)
T ss_pred             HHHHHHHhcChhhhccCCCC
Confidence            88999999999999999986

>CHL00148 orf27 Ycf27; Reviewed

Probab=99.09  E-value=2.4e-09  Score=65.08  Aligned_cols=86  Identities=20%  Similarity=0.283  Sum_probs=68.5

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHH---HhhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDV---RTIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~---l~~~~~~~pii~lt~~~~~   68 (93)
                      ++|++.....+...|...++. +..+.++.+++..+....++         +..|+++   +... +.+|+|++|+..+.
T Consensus        12 vdd~~~~~~~l~~~l~~~~~~-v~~~~~~~~~l~~~~~~~~d~illd~~~~~~~g~~~~~~l~~~-~~~~ii~ls~~~~~   89 (240)
T CHL00148         12 VDDEAYIRKILETRLSIIGYE-VITASDGEEALKLFRKEQPDLVILDVMMPKLDGYGVCQEIRKE-SDVPIIMLTALGDV   89 (240)
T ss_pred             EeCCHHHHHHHHHHHHHCCCE-EEEeCCHHHHHHHHHhcCCCEEEEeCCCCCCCHHHHHHHHHhc-CCCcEEEEECCCCH
Confidence            478888899999999988888 88899999999887543321         2234444   2222 68999999999998


Q ss_pred             HHHHHHHHcCCcceeeccch
Q 042991           69 VRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~   88 (93)
                      .....+++.|+++|+.||++
T Consensus        90 ~~~~~~~~~Ga~~~l~kp~~  109 (240)
T CHL00148         90 SDRITGLELGADDYVVKPFS  109 (240)
T ss_pred             HhHHHHHHCCCCEEEeCCCC
Confidence            88889999999999999986

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

Probab=99.09  E-value=1.5e-09  Score=72.50  Aligned_cols=87  Identities=21%  Similarity=0.160  Sum_probs=71.3

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHH---hhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~~~~pii~lt~~~~~   68 (93)
                      |||++..+..+...|+..||. +..+.++.+++..+....++         ++.|++++   ....+.+|+|++|+..+.
T Consensus         9 Vdd~~~~~~~L~~~L~~~g~~-v~~~~s~~~al~~l~~~~~DlvllD~~lp~~dgl~~l~~ir~~~~~~pvIvlt~~~~~   87 (469)
T PRK10923          9 VDDDSSIRWVLERALAGAGLT-CTTFENGNEVLEALASKTPDVLLSDIRMPGMDGLALLKQIKQRHPMLPVIIMTAHSDL   87 (469)
T ss_pred             EECCHHHHHHHHHHHHHcCCE-EEEECCHHHHHHHHhcCCCCEEEECCCCCCCCHHHHHHHHHhhCCCCeEEEEECCCCH
Confidence            578999999999999999999 99999999999998644321         23445542   333378899999999999


Q ss_pred             HHHHHHHHcCCcceeeccch
Q 042991           69 VRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~   88 (93)
                      .....+++.|+.+|+.||+.
T Consensus        88 ~~~~~a~~~Ga~~~l~KP~~  107 (469)
T PRK10923         88 DAAVSAYQQGAFDYLPKPFD  107 (469)
T ss_pred             HHHHHHHhcCcceEEecCCc
Confidence            88899999999999999986

>PRK11466 hybrid sensory histidine kinase TorS; Provisional

Probab=99.09  E-value=1.4e-09  Score=77.20  Aligned_cols=87  Identities=11%  Similarity=0.107  Sum_probs=71.3

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc----------CCCchHH---HhhhhcCCcEEEEcCCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ----------SANGFDV---RTIYSREIPVVIMSPEII   67 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~----------~~~~~d~---l~~~~~~~pii~lt~~~~   67 (93)
                      +||++..+..+..+|+..||. +..+.++.+|+..+.....+          +++|+++   +....+.+|+|++|+...
T Consensus       687 vdD~~~~~~~l~~~L~~~g~~-v~~a~~~~~al~~~~~~~~~Dlvl~D~~mp~~~G~~~~~~lr~~~~~~~ii~~t~~~~  765 (914)
T PRK11466        687 IEDNPLTQRITAEMLNTSGAQ-VVAVGNAAQALETLQNSEPFAAALVDFDLPDYDGITLARQLAQQYPSLVLIGFSAHVI  765 (914)
T ss_pred             EeCCHHHHHHHHHHHHhcCCc-eEEeCCHHHHHHHHHcCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCCCCEEEEeCCCc
Confidence            588999999999999999999 99999999999987532222          2345555   333337899999999999


Q ss_pred             HHHHHHHHHcCCcceeeccch
Q 042991           68 LVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        68 ~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      .....++++.|+++|+.||+.
T Consensus       766 ~~~~~~~~~~g~~~~l~KP~~  786 (914)
T PRK11466        766 DETLRQRTSSLFRGIIPKPVP  786 (914)
T ss_pred             hhhHHHHHhcCcCCEEeCCCC
Confidence            988889999999999999996

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

Probab=99.08  E-value=1.8e-09  Score=78.61  Aligned_cols=88  Identities=14%  Similarity=0.178  Sum_probs=72.7

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHH---hhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~~~~pii~lt~~~~~   68 (93)
                      |||++..+..+..+|+..|++ +..+.++.+|+..+...+++         +++|++++   ....+.+|+|++|+....
T Consensus       964 vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~~al~~~~~~~~dlil~D~~mp~~~g~~~~~~i~~~~~~~pii~lt~~~~~ 1042 (1197)
T PRK09959        964 ADDHPTNRLLLKRQLNLLGYD-VDEATDGVQALHKVSMQHYDLLITDVNMPNMDGFELTRKLREQNSSLPIWGLTANAQA 1042 (1197)
T ss_pred             cCCCHHHHHHHHHHHHHcCCE-EEEECCHHHHHHHhhcCCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCCEEEEECCCCH
Confidence            689999999999999999999 99999999999998644321         23455543   333378999999999999


Q ss_pred             HHHHHHHHcCCcceeeccchh
Q 042991           69 VRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      ....++++.|+++|+.||+..
T Consensus      1043 ~~~~~~~~~G~~~~l~KP~~~ 1063 (1197)
T PRK09959       1043 NEREKGLSCGMNLCLFKPLTL 1063 (1197)
T ss_pred             HHHHHHHHCCCCEEEeCCCCH
Confidence            999999999999999999863

>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional

Probab=99.08  E-value=1.8e-09  Score=71.80  Aligned_cols=87  Identities=17%  Similarity=0.202  Sum_probs=70.6

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHH---hhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~~~~pii~lt~~~~~   68 (93)
                      ++|++..+..+...|+..||. +..+.++.+++..+....++         ++.|++++   ....+.+|+|++|+..+.
T Consensus        10 vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~~al~~l~~~~~dlillD~~~p~~~g~~ll~~i~~~~~~~pvI~lt~~~~~   88 (457)
T PRK11361         10 VDDEDNVRRMLSTAFALQGFE-THCANNGRTALHLFADIHPDVVLMDIRMPEMDGIKALKEMRSHETRTPVILMTAYAEV   88 (457)
T ss_pred             EECCHHHHHHHHHHHHHCCCE-EEEECCHHHHHHHHhcCCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCCEEEEeCCCCH
Confidence            578889999999999988999 99999999999988644321         22344442   223378999999999999


Q ss_pred             HHHHHHHHcCCcceeeccch
Q 042991           69 VRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~   88 (93)
                      ....++++.|+++|+.||+.
T Consensus        89 ~~~~~a~~~Ga~d~l~KP~~  108 (457)
T PRK11361         89 ETAVEALRCGAFDYVIKPFD  108 (457)
T ss_pred             HHHHHHHHCCccEEEecccC
Confidence            99999999999999999986

>PRK09958 DNA-binding transcriptional activator EvgA; Provisional

Probab=99.07  E-value=4e-09  Score=62.76  Aligned_cols=87  Identities=16%  Similarity=0.086  Sum_probs=68.1

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceE-EeCCHHHHHHHhccCccc---------CCCchHHHh---hhhcCCcEEEEcCCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLY-CSCSGRRALQFLGLDEEQ---------SANGFDVRT---IYSREIPVVIMSPEII   67 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~-~~~~~~~a~~~~~~~~~~---------~~~~~d~l~---~~~~~~pii~lt~~~~   67 (93)
                      ++|++..+..+...|+..|+. +. .+.++.+++..+....++         +..|++++.   ...+..|+|++++..+
T Consensus         6 vdd~~~~~~~l~~~L~~~~~~-v~~~~~~~~~~~~~~~~~~~dlvi~d~~~~~~~g~~~~~~l~~~~~~~~ii~ls~~~~   84 (204)
T PRK09958          6 IDDHPLAIAAIRNLLIKNDIE-ILAELTEGGSAVQRVETLKPDIVIIDVDIPGVNGIQVLETLRKRQYSGIIIIVSAKND   84 (204)
T ss_pred             ECCcHHHHHHHHHHHhcCCCE-EEEEeCCHHHHHHHHHccCCCEEEEeCCCCCCCHHHHHHHHHhhCCCCeEEEEeCCCC
Confidence            578888999999999888888 76 699999999888644321         223444432   2226789999999989


Q ss_pred             HHHHHHHHHcCCcceeeccch
Q 042991           68 LVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        68 ~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      .....++++.|+++|+.||++
T Consensus        85 ~~~~~~~~~~ga~~~i~kp~~  105 (204)
T PRK09958         85 HFYGKHCADAGANGFVSKKEG  105 (204)
T ss_pred             HHHHHHHHHCCCCEEEecCCC
Confidence            888889999999999999986

>PRK10360 DNA-binding transcriptional activator UhpA; Provisional

Probab=99.04  E-value=5.9e-09  Score=61.66  Aligned_cols=89  Identities=18%  Similarity=0.198  Sum_probs=67.5

Q ss_pred             CCCcHHHHHHHHHHHhhc-CCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhhhcCCcEEEEcCCCCHHH
Q 042991            1 LNDSFVDRKVIERLLTIS-SSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIYSREIPVVIMSPEIILVR   70 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~-~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~~~~~pii~lt~~~~~~~   70 (93)
                      ++|++..+..+...|+.. ++..+..+.++.+++..+....++         +..|++++....+.+|+++++...+...
T Consensus         7 vd~~~~~~~~l~~~L~~~~~~~~~~~~~~~~~~l~~~~~~~~dlvi~d~~~~~~~g~~~~~~l~~~~~vi~~s~~~~~~~   86 (196)
T PRK10360          7 IDDHLIVRSGFAQLLGLEPDLQVVAEFGSGREALAGLPGRGVQVCICDISMPDISGLELLSQLPKGMATIMLSVHDSPAL   86 (196)
T ss_pred             ECCcHHHHHHHHHHHccCCCcEEEEEECCHHHHHHHHhcCCCCEEEEeCCCCCCCHHHHHHHHccCCCEEEEECCCCHHH
Confidence            578888999999999754 554356889999999988644321         1223333444446789999999999988


Q ss_pred             HHHHHHcCCcceeeccchh
Q 042991           71 IDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        71 ~~~~~~~ga~d~l~kP~~~   89 (93)
                      ..++++.|+++|+.||+..
T Consensus        87 ~~~~~~~ga~~~i~kp~~~  105 (196)
T PRK10360         87 VEQALNAGARGFLSKRCSP  105 (196)
T ss_pred             HHHHHHcCCcEEEECCCCH
Confidence            8899999999999999874

>PRK10840 transcriptional regulator RcsB; Provisional

Probab=99.03  E-value=6.7e-09  Score=62.89  Aligned_cols=88  Identities=9%  Similarity=-0.060  Sum_probs=67.6

Q ss_pred             CCCcHHHHHHHHHHHhhcCC-CceEEeCCHHHHHHHhccCccc---------C---CCchHHHh---hhhcCCcEEEEcC
Q 042991            1 LNDSFVDRKVIERLLTISSS-RDLYCSCSGRRALQFLGLDEEQ---------S---ANGFDVRT---IYSREIPVVIMSP   64 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~-~~v~~~~~~~~a~~~~~~~~~~---------~---~~~~d~l~---~~~~~~pii~lt~   64 (93)
                      +||++..+..++.+|+..++ ..+..+.++.+++..+....++         +   ..|++++.   ...+.+|||++|.
T Consensus         9 vdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~~~~~~~~~~~DlvllD~~l~~~~~~~g~~~~~~l~~~~~~~~iIvls~   88 (216)
T PRK10840          9 ADDHPIVLFGIRKSLEQIEWVNVVGEFEDSTALINNLPKLDAHVLITDLSMPGDKYGDGITLIKYIKRHFPSLSIIVLTM   88 (216)
T ss_pred             ECCcHHHHHHHHHHHhcCCCCEEEEEECCHHHHHHHHHhCCCCEEEEeCcCCCCCCCCHHHHHHHHHHHCCCCcEEEEEe
Confidence            57889999999999987654 3367789999999887543321         1   13455432   2237889999999


Q ss_pred             CCCHHHHHHHHHcCCcceeeccch
Q 042991           65 EIILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        65 ~~~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      ..+......+++.|+++|+.||..
T Consensus        89 ~~~~~~~~~a~~~Ga~~yl~K~~~  112 (216)
T PRK10840         89 NNNPAILSAVLDLDIEGIVLKQGA  112 (216)
T ss_pred             cCCHHHHHHHHHCCCeEEEECCCC
Confidence            999888889999999999999986

>TIGR01818 ntrC nitrogen regulation protein NR(I)

Probab=99.03  E-value=3.6e-09  Score=70.51  Aligned_cols=87  Identities=17%  Similarity=0.176  Sum_probs=70.4

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHH---HhhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDV---RTIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~---l~~~~~~~pii~lt~~~~~   68 (93)
                      +||++..+..+...|+..||. +..+.++.+|+..+....++         ++.|+++   +....+.+|+|++|+..+.
T Consensus         4 vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~~al~~~~~~~~DlVllD~~~p~~~g~~ll~~l~~~~~~~~vIvlt~~~~~   82 (463)
T TIGR01818         4 VDDDRSIRWVLEKALSRAGYE-VRTFGNAASVLRALARGQPDLLITDVRMPGEDGLDLLPQIKKRHPQLPVIVMTAHSDL   82 (463)
T ss_pred             EECCHHHHHHHHHHHHHcCCE-EEEECCHHHHHHHHhcCCCCEEEEcCCCCCCCHHHHHHHHHHhCCCCeEEEEeCCCCH
Confidence            578899999999999989999 99999999999888644321         2234444   2233378899999999998


Q ss_pred             HHHHHHHHcCCcceeeccch
Q 042991           69 VRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~   88 (93)
                      ....++++.|+++|+.||+.
T Consensus        83 ~~~~~a~~~Ga~~~l~KP~~  102 (463)
T TIGR01818        83 DTAVAAYQRGAFEYLPKPFD  102 (463)
T ss_pred             HHHHHHHHcCcceeecCCCC
Confidence            88899999999999999986

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.

>PRK10365 transcriptional regulatory protein ZraR; Provisional

Probab=99.02  E-value=2.2e-09  Score=71.03  Aligned_cols=87  Identities=21%  Similarity=0.198  Sum_probs=70.9

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHH---HhhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDV---RTIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~---l~~~~~~~pii~lt~~~~~   68 (93)
                      +||++..+..+...|+..|+. +..+.++.+++..+....++         ++.|+++   +....+.+|+|++|+..+.
T Consensus        11 vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~~al~~l~~~~~DlvilD~~m~~~~G~~~~~~ir~~~~~~~vi~lt~~~~~   89 (441)
T PRK10365         11 VDDDISHCTILQALLRGWGYN-VALANSGRQALEQVREQVFDLVLCDVRMAEMDGIATLKEIKALNPAIPVLIMTAYSSV   89 (441)
T ss_pred             EECCHHHHHHHHHHHHHCCCe-EEEeCCHHHHHHHHhcCCCCEEEEeCCCCCCCHHHHHHHHHhhCCCCeEEEEECCCCH
Confidence            578899999999999999999 99999999999888644321         2345554   3333378999999999988


Q ss_pred             HHHHHHHHcCCcceeeccch
Q 042991           69 VRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~   88 (93)
                      ....++++.|+.+|+.||+.
T Consensus        90 ~~~~~a~~~ga~~~l~Kp~~  109 (441)
T PRK10365         90 ETAVEALKTGALDYLIKPLD  109 (441)
T ss_pred             HHHHHHHHhhhHHHhcCCCC
Confidence            89999999999999999986

>PRK10430 DNA-binding transcriptional activator DcuR; Provisional

Probab=99.02  E-value=8.5e-09  Score=63.43  Aligned_cols=89  Identities=15%  Similarity=0.080  Sum_probs=67.5

Q ss_pred             CCCcHHHHHHHHHHHhh-cCCCceEEeCCHHHHHHHhcc--Cccc---------CCCchHHHh---hhhcCCcEEEEcCC
Q 042991            1 LNDSFVDRKVIERLLTI-SSSRDLYCSCSGRRALQFLGL--DEEQ---------SANGFDVRT---IYSREIPVVIMSPE   65 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~-~~~~~v~~~~~~~~a~~~~~~--~~~~---------~~~~~d~l~---~~~~~~pii~lt~~   65 (93)
                      +||++..+..+..+|.. .++..+..+.++.+++..+..  ..++         +++|++++.   ...+.+|+|++|+.
T Consensus         7 vdd~~~~~~~l~~~L~~~~~~~~~~~~~~~~~a~~~~~~~~~~~DlvilD~~~p~~~G~eli~~l~~~~~~~~vI~ls~~   86 (239)
T PRK10430          7 VDDDAMVAELNRRYVAQIPGFQCCGTASTLEQAKEIIFNSDTPIDLILLDIYMQQENGLDLLPVLHEAGCKSDVIVISSA   86 (239)
T ss_pred             EcCCHHHHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhcCCCCCEEEEecCCCCCCcHHHHHHHHhhCCCCCEEEEECC
Confidence            58899999999999975 356534578899999888742  2211         234555533   33378999999999


Q ss_pred             CCHHHHHHHHHcCCcceeeccchh
Q 042991           66 IILVRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        66 ~~~~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      .+.....++++.|+++|+.||++.
T Consensus        87 ~~~~~~~~al~~Ga~~yl~Kp~~~  110 (239)
T PRK10430         87 ADAATIKDSLHYGVVDYLIKPFQA  110 (239)
T ss_pred             CcHHHHHHHHHcCCCEEEeCCCCH
Confidence            999999999999999999999863

>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional

Probab=98.98  E-value=1.2e-08  Score=61.94  Aligned_cols=87  Identities=17%  Similarity=0.163  Sum_probs=68.6

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhh--hcCCcEEEEcCCCCHH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIY--SREIPVVIMSPEIILV   69 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~--~~~~pii~lt~~~~~~   69 (93)
                      +++++.....+...|...++. +..+.++.+++..+....++         +..+++++...  ...+|++++++.....
T Consensus        16 vdd~~~~~~~l~~~L~~~~~~-v~~~~~~~~~~~~~~~~~~dlvl~d~~~~~~~g~~~~~~l~~~~~~pii~l~~~~~~~   94 (240)
T PRK10710         16 VEDEPKLGQLLIDYLQAASYA-TTLLSHGDEVLPYVRQTPPDLILLDLMLPGTDGLTLCREIRRFSDIPIVMVTAKIEEI   94 (240)
T ss_pred             EeCCHHHHHHHHHHHHHCCCE-EEEeCCHHHHHHHHhhCCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCEEEEEcCCCHH
Confidence            478888999999999988998 88999999999888644321         22344442222  2678999999988888


Q ss_pred             HHHHHHHcCCcceeeccch
Q 042991           70 RIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        70 ~~~~~~~~ga~d~l~kP~~   88 (93)
                      ....+++.|+++|+.||+.
T Consensus        95 ~~~~~~~~ga~~~l~kp~~  113 (240)
T PRK10710         95 DRLLGLEIGADDYICKPYS  113 (240)
T ss_pred             HHHHHHhcCCCeEEECCCC
Confidence            8888999999999999986

>PRK09581 pleD response regulator PleD; Reviewed

Probab=98.95  E-value=4e-09  Score=69.39  Aligned_cols=87  Identities=16%  Similarity=0.138  Sum_probs=67.3

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhhh-----cCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIYS-----REIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~~-----~~~pii~lt~~~   66 (93)
                      +||++..+..+...+.. .+. +..+.++.+|+..+....++         .+.|++++....     +.+|+|++|+..
T Consensus       161 vdd~~~~~~~l~~~l~~-~~~-~~~~~~~~~a~~~~~~~~~d~vi~d~~~p~~~g~~l~~~i~~~~~~~~~~ii~ls~~~  238 (457)
T PRK09581        161 VDDDVSQAERIANILKE-EFR-VVVVSDPSEALFNAAETNYDLVIVSANFENYDPLRLCSQLRSKERTRYVPILLLVDED  238 (457)
T ss_pred             EecccchHHHHHHHHhh-cce-eeeecChHHHHHhcccCCCCEEEecCCCCCchHhHHHHHHHhccccCCCcEEEEeCCC
Confidence            47888889999999964 466 77899999999987543321         224445433221     789999999999


Q ss_pred             CHHHHHHHHHcCCcceeeccchh
Q 042991           67 ILVRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      +.....++++.|++||+.||+..
T Consensus       239 ~~~~~~~a~~~Ga~d~l~kp~~~  261 (457)
T PRK09581        239 DDPRLVKALELGVNDYLMRPIDK  261 (457)
T ss_pred             ChHHHHHHHHccchhhhhCCCcH
Confidence            99999999999999999999863

>PRK13558 bacterio-opsin activator; Provisional

Probab=98.95  E-value=8.2e-09  Score=71.42  Aligned_cols=87  Identities=13%  Similarity=-0.076  Sum_probs=69.7

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHH---hhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~~~~pii~lt~~~~~   68 (93)
                      |||++..+..+..+|...+|. +..+.++.+++..+....++         ++.|++++   ....+.+|+|++|+..+.
T Consensus        13 vdd~~~~~~~l~~~l~~~~~~-v~~~~~~~~al~~~~~~~~Dlvl~d~~lp~~~g~~~l~~l~~~~~~~piI~lt~~~~~   91 (665)
T PRK13558         13 VGDDPEAGPVDCDLDEDGRLD-VTQIRDFVAARDRVEAGEIDCVVADHEPDGFDGLALLEAVRQTTAVPPVVVVPTAGDE   91 (665)
T ss_pred             EccCcchHHHHHHHhhccCcc-eEeeCCHHHHHHHhhccCCCEEEEeccCCCCcHHHHHHHHHhcCCCCCEEEEECCCCH
Confidence            578888999999999888998 99999999999987643321         22344443   232378999999999999


Q ss_pred             HHHHHHHHcCCcceeeccch
Q 042991           69 VRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~   88 (93)
                      ....++++.|+.+|+.||..
T Consensus        92 ~~~~~al~~Ga~dyl~k~~~  111 (665)
T PRK13558         92 AVARRAVDADAAAYVPAVSD  111 (665)
T ss_pred             HHHHHHHhcCcceEEeccch
Confidence            99999999999999999965

>PRK09483 response regulator; Provisional

Probab=98.94  E-value=2.3e-08  Score=60.02  Aligned_cols=89  Identities=13%  Similarity=0.217  Sum_probs=67.8

Q ss_pred             CCCcHHHHHHHHHHHhhc-CCCceEEeCCHHHHHHHhccCccc---------CCCchHHH---hhhhcCCcEEEEcCCCC
Q 042991            1 LNDSFVDRKVIERLLTIS-SSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYSREIPVVIMSPEII   67 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~-~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~~~~pii~lt~~~~   67 (93)
                      +|+++..+..+..+|+.. ++..+..+.++.+++..+....++         +..|++++   ....+.+|++++|...+
T Consensus         7 vd~~~~~~~~l~~~L~~~~~~~~v~~~~~~~~~~~~~~~~~~dlvi~d~~~~~~~g~~~~~~l~~~~~~~~ii~ls~~~~   86 (217)
T PRK09483          7 VDDHELVRAGIRRILEDIKGIKVVGEACCGEDAVKWCRTNAVDVVLMDMNMPGIGGLEATRKILRYTPDVKIIMLTVHTE   86 (217)
T ss_pred             ECCcHHHHHHHHHHHccCCCCEEEEEeCCHHHHHHHHHhcCCCEEEEeCCCCCCCHHHHHHHHHHHCCCCeEEEEeCCCC
Confidence            578889999999999864 677234789999999888644321         22344442   23337899999999999


Q ss_pred             HHHHHHHHHcCCcceeeccchh
Q 042991           68 LVRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        68 ~~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      .....+++..|+++|+.||...
T Consensus        87 ~~~~~~~~~~g~~~~l~k~~~~  108 (217)
T PRK09483         87 NPLPAKVMQAGAAGYLSKGAAP  108 (217)
T ss_pred             HHHHHHHHHcCCCEEEeCCCCH
Confidence            8888899999999999999863

>PRK15479 transcriptional regulatory protein TctD; Provisional

Probab=98.94  E-value=2.4e-08  Score=59.88  Aligned_cols=88  Identities=17%  Similarity=0.190  Sum_probs=67.8

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHH---hhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~~~~pii~lt~~~~~   68 (93)
                      +++++.....+...++..++. +..+.++.++...+....++         +..+++.+   ....+.+|++++++..+.
T Consensus         6 vd~~~~~~~~l~~~l~~~~~~-v~~~~~~~~~~~~~~~~~~d~vild~~~~~~~~~~~~~~i~~~~~~~~ii~lt~~~~~   84 (221)
T PRK15479          6 AEDNRELAHWLEKALVQNGFA-VDCVFDGLAADHLLQSEMYALAVLDINMPGMDGLEVLQRLRKRGQTLPVLLLTARSAV   84 (221)
T ss_pred             EeCCHHHHHHHHHHHHHCCCE-EEEeCCHHHHHHHHhhCCCCEEEEeCCCCCCcHHHHHHHHHhcCCCCCEEEEECCCCH
Confidence            477888888999999888888 88999999998777543321         22334432   222268899999999888


Q ss_pred             HHHHHHHHcCCcceeeccchh
Q 042991           69 VRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      ....++++.|+++|+.||+..
T Consensus        85 ~~~~~~~~~g~~~~i~kp~~~  105 (221)
T PRK15479         85 ADRVKGLNVGADDYLPKPFEL  105 (221)
T ss_pred             HHHHHHHHcCCCeeEeCCCCH
Confidence            888899999999999999863

>PRK09581 pleD response regulator PleD; Reviewed

Probab=98.94  E-value=1.9e-08  Score=66.18  Aligned_cols=87  Identities=24%  Similarity=0.255  Sum_probs=68.8

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhhh-----cCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIYS-----REIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~~-----~~~pii~lt~~~   66 (93)
                      +++++..+..+...|...++. +..+.++.+++..+....+.         +..|++++....     +.+|+|++|+..
T Consensus         8 i~~~~~~~~~l~~~l~~~~~~-v~~~~~~~~~~~~~~~~~~dlvi~d~~~~~~~g~~l~~~i~~~~~~~~~~ii~~s~~~   86 (457)
T PRK09581          8 VDDIPANVKLLEAKLLAEYYT-VLTASSGAEAIAICEREQPDIILLDVMMPGMDGFEVCRRLKSDPATTHIPVVMVTALD   86 (457)
T ss_pred             EeCCHHHHHHHHHHHHhCCCE-EEEeCCHHHHHHHHhhcCCCEEEEeCCCCCCCHHHHHHHHHcCcccCCCCEEEEECCC
Confidence            478888889999999888899 99999999999998644321         223444433221     468999999999


Q ss_pred             CHHHHHHHHHcCCcceeeccch
Q 042991           67 ILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      +.....++++.|+++|+.||++
T Consensus        87 ~~~~~~~~~~~ga~~~l~kp~~  108 (457)
T PRK09581         87 DPEDRVRGLEAGADDFLTKPIN  108 (457)
T ss_pred             CHHHHHHHHHCCCCEEEECCCC
Confidence            9989999999999999999986

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

Probab=98.94  E-value=2.4e-09  Score=67.54  Aligned_cols=86  Identities=13%  Similarity=0.161  Sum_probs=67.7

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHH---HhhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDV---RTIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~---l~~~~~~~pii~lt~~~~~   68 (93)
                      |||+......|..+|++.+.. +..|++..+|+..+....++         ++.|+|+   +++..+.+|||++|++...
T Consensus         6 VDdd~a~~~~l~~iLs~~~~~-~~~~~~~~eal~~Le~~kpDLifldI~mp~~ngiefaeQvr~i~~~v~iifIssh~ey   84 (361)
T COG3947           6 VDDDAAIVKLLSVILSRAGHE-VRSCSHPVEALDLLEVFKPDLIFLDIVMPYMNGIEFAEQVRDIESAVPIIFISSHAEY   84 (361)
T ss_pred             EcchHHHHHHHHHHHHhccch-hhccCCHHHHHHHHHhcCCCEEEEEeecCCccHHHHHHHHHHhhccCcEEEEecchhh
Confidence            688899999999999998877 99999999999999754432         2346666   4555699999999987665


Q ss_pred             HHHHHHHHcCCcceeeccchh
Q 042991           69 VRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      ..  .++..-+.||++||+..
T Consensus        85 a~--dsf~~n~~dYl~KPvt~  103 (361)
T COG3947          85 AD--DSFGMNLDDYLPKPVTP  103 (361)
T ss_pred             hh--hhcccchHhhccCCCCH
Confidence            44  35556679999999973

>PRK11091 aerobic respiration control sensor protein ArcB; Provisional

Probab=98.93  E-value=1.5e-08  Score=71.15  Aligned_cols=86  Identities=19%  Similarity=0.330  Sum_probs=66.2

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHH---hhhh--cC-CcEEEEcCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYS--RE-IPVVIMSPE   65 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~--~~-~pii~lt~~   65 (93)
                      +||++..+..+..+|+..||. +..+.++.+|++.+....++         +++|++++   +...  .. +|+|++|+.
T Consensus       531 vdD~~~~~~~l~~~L~~~g~~-v~~a~~~~eal~~~~~~~~Dlvl~D~~mp~~~G~e~~~~ir~~~~~~~~~~ii~~ta~  609 (779)
T PRK11091        531 VEDIELNVIVARSVLEKLGNS-VDVAMTGKEALEMFDPDEYDLVLLDIQLPDMTGLDIARELRERYPREDLPPLVALTAN  609 (779)
T ss_pred             EcCCHHHHHHHHHHHHHcCCE-EEEECCHHHHHHHhhcCCCCEEEEcCCCCCCCHHHHHHHHHhccccCCCCcEEEEECC
Confidence            589999999999999999999 99999999999998644321         23455543   2221  34 488988887


Q ss_pred             CCHHHHHHHHHcCCcceeeccch
Q 042991           66 IILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        66 ~~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      ... ...++++.|+++|+.||+.
T Consensus       610 ~~~-~~~~~~~~G~~~~l~KP~~  631 (779)
T PRK11091        610 VLK-DKKEYLDAGMDDVLSKPLS  631 (779)
T ss_pred             chH-hHHHHHHCCCCEEEECCCC
Confidence            654 4567899999999999986

>PRK09935 transcriptional regulator FimZ; Provisional

Probab=98.87  E-value=7.1e-08  Score=57.38  Aligned_cols=87  Identities=16%  Similarity=0.155  Sum_probs=65.1

Q ss_pred             CCCcHHHHHHHHHHHhhc-CCCceE-EeCCHHHHHHHhccCccc---------CCCchHHH---hhhhcCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTIS-SSRDLY-CSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYSREIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~-~~~~v~-~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~~~~pii~lt~~~   66 (93)
                      ++|++..+..+...++.. ++. +. .+.++.+++..+....++         ...|++++   ....+.+|+|++|+..
T Consensus         9 v~d~~~~~~~l~~~l~~~~~~~-~~~~~~~~~~~~~~~~~~~~dlvild~~l~~~~g~~~~~~l~~~~~~~~ii~ls~~~   87 (210)
T PRK09935          9 MDTHPIIRMSIEVLLQKNSELQ-IVLKTDDYRITIDYLRTRPVDLIIMDIDLPGTDGFTFLKRIKQIQSTVKVLFLSSKS   87 (210)
T ss_pred             ECCcHHHHHHHHHHHhhCCCce-EEEEeCCHHHHHHHHHhcCCCEEEEeCCCCCCCHHHHHHHHHHhCCCCcEEEEECCC
Confidence            478888889999999865 466 54 688999998887543321         12334432   2222678999999998


Q ss_pred             CHHHHHHHHHcCCcceeeccch
Q 042991           67 ILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      +.....++++.|+++|+.||+.
T Consensus        88 ~~~~~~~~~~~g~~~~l~kp~~  109 (210)
T PRK09935         88 ECFYAGRAIQAGANGFVSKCND  109 (210)
T ss_pred             cHHHHHHHHHcCCCEEEeCCCC
Confidence            8888889999999999999986

>TIGR02875 spore_0_A sporulation transcription factor Spo0A

Probab=98.85  E-value=5.2e-08  Score=60.54  Aligned_cols=89  Identities=13%  Similarity=0.052  Sum_probs=66.0

Q ss_pred             CCCcHHHHHHHHHHHhhc-CCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhh---hc--CCcEEEEcCC
Q 042991            1 LNDSFVDRKVIERLLTIS-SSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIY---SR--EIPVVIMSPE   65 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~-~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~---~~--~~pii~lt~~   65 (93)
                      +||++..+..+...|+.. ++..+..+.++.+++..+....++         .+.|++++..+   ..  .+|+|++|+.
T Consensus         8 vdd~~~~~~~l~~~L~~~~~~~~~~~a~~~~eal~~l~~~~~DlvllD~~mp~~dG~~~l~~i~~~~~~~~~~iI~lt~~   87 (262)
T TIGR02875         8 ADDNKEFCNLLKEYLAAQPDMEVVGVAHNGVDALELIKEQQPDVVVLDIIMPHLDGIGVLEKLNEIELSARPRVIMLSAF   87 (262)
T ss_pred             EcCCHHHHHHHHHHHhcCCCeEEEEEeCCHHHHHHHHHhcCCCEEEEeCCCCCCCHHHHHHHHHhhccccCCeEEEEeCC
Confidence            578889999999999754 445245789999999988644321         22344442222   12  3899999999


Q ss_pred             CCHHHHHHHHHcCCcceeeccchh
Q 042991           66 IILVRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        66 ~~~~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      .......++++.|+++|+.||+..
T Consensus        88 ~~~~~~~~~~~~G~~~~l~KP~~~  111 (262)
T TIGR02875        88 GQEKITQRAVALGADYYVLKPFDL  111 (262)
T ss_pred             CCHHHHHHHHHCCCCEEEECCCCH
Confidence            999888899999999999999863

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.

>PRK09390 fixJ response regulator FixJ; Provisional

Probab=98.84  E-value=4.5e-08  Score=57.57  Aligned_cols=88  Identities=16%  Similarity=0.060  Sum_probs=69.0

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHH---hhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~~~~pii~lt~~~~~   68 (93)
                      +++++.....+...|...++. +..+.++.+++..+....+.         ...+++.+   ....+.+|++++++..+.
T Consensus         9 v~~~~~~~~~l~~~l~~~~~~-v~~~~~~~~~~~~~~~~~~d~ii~d~~~~~~~~~~~~~~l~~~~~~~~ii~l~~~~~~   87 (202)
T PRK09390          9 VDDDEAMRDSLAFLLDSAGFE-VRLFESAQAFLDALPGLRFGCVVTDVRMPGIDGIELLRRLKARGSPLPVIVMTGHGDV   87 (202)
T ss_pred             EeCCHHHHHHHHHHHHHCCCe-EEEeCCHHHHHHHhccCCCCEEEEeCCCCCCcHHHHHHHHHhcCCCCCEEEEECCCCH
Confidence            478888889999999888998 88999999998887544321         22344442   222378999999999888


Q ss_pred             HHHHHHHHcCCcceeeccchh
Q 042991           69 VRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      .....+++.|+.+|+.||+..
T Consensus        88 ~~~~~~~~~g~~~~l~~p~~~  108 (202)
T PRK09390         88 PLAVEAMKLGAVDFIEKPFED  108 (202)
T ss_pred             HHHHHHHHcChHHHhhCCCCH
Confidence            888899999999999999863

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

Probab=98.83  E-value=4.3e-08  Score=69.57  Aligned_cols=87  Identities=6%  Similarity=-0.037  Sum_probs=69.5

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCc-cc--------CCCchHH---HhhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDE-EQ--------SANGFDV---RTIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~-~~--------~~~~~d~---l~~~~~~~pii~lt~~~~~   68 (93)
                      +||++..+..+...|+..||. +..+.++.+++..+.... .+        .+.++++   +....+.+|||++++....
T Consensus       703 Vddd~~~~~~l~~~L~~~G~~-v~~~~s~~~al~~l~~~~~~~DlVll~~~~~~g~~l~~~l~~~~~~ipIIvls~~~~~  781 (828)
T PRK13837        703 VEPDDATLERYEEKLAALGYE-PVGFSTLAAAIAWISKGPERFDLVLVDDRLLDEEQAAAALHAAAPTLPIILGGNSKTM  781 (828)
T ss_pred             EcCCHHHHHHHHHHHHHCCCE-EEEeCCHHHHHHHHHhCCCCceEEEECCCCCCHHHHHHHHHhhCCCCCEEEEeCCCch
Confidence            578999999999999999999 999999999999985322 11        1233443   2233388999999999888


Q ss_pred             HHHHHHHHcCCcceeeccchh
Q 042991           69 VRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      ....++++.| ++|+.||++.
T Consensus       782 ~~~~~~~~~G-~d~L~KP~~~  801 (828)
T PRK13837        782 ALSPDLLASV-AEILAKPISS  801 (828)
T ss_pred             hhhhhHhhcc-CcEEeCCCCH
Confidence            8888899999 9999999973

>PRK12555 chemotaxis-specific methylesterase; Provisional

Probab=98.80  E-value=9.6e-08  Score=61.64  Aligned_cols=87  Identities=17%  Similarity=0.252  Sum_probs=63.4

Q ss_pred             CCCcHHHHHHHHHHHh-hcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhh--hcCCcEEEEcCCCC-
Q 042991            1 LNDSFVDRKVIERLLT-ISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIY--SREIPVVIMSPEII-   67 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~-~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~--~~~~pii~lt~~~~-   67 (93)
                      +||++..+..+..+|+ ..++..+..+.++.++++.+....++         .+.|++++...  ...+|++++++... 
T Consensus         6 Vdd~~~~~~~l~~~L~~~~~~~vv~~a~~~~eal~~l~~~~pDlVllD~~mp~~~G~e~l~~l~~~~~~pvivvs~~~~~   85 (337)
T PRK12555          6 VNDSPLAVEALRRALARDPDHEVVWVATDGAQAVERCAAQPPDVILMDLEMPRMDGVEATRRIMAERPCPILIVTSLTER   85 (337)
T ss_pred             EeCCHHHHHHHHHHHhhCCCCEEEEEECCHHHHHHHHhccCCCEEEEcCCCCCCCHHHHHHHHHHHCCCcEEEEeCCCCc
Confidence            5889999999999995 55677234789999999998644321         23444542222  25689999998643 


Q ss_pred             -HHHHHHHHHcCCcceeeccc
Q 042991           68 -LVRIDRYLEDGAEDSETCQM   87 (93)
Q Consensus        68 -~~~~~~~~~~ga~d~l~kP~   87 (93)
                       .....++++.|+++|+.||+
T Consensus        86 ~~~~~~~al~~Ga~d~l~KP~  106 (337)
T PRK12555         86 NASRVFEAMGAGALDAVDTPT  106 (337)
T ss_pred             CHHHHHHHHhcCceEEEECCC
Confidence             45566889999999999998

>PRK11475 DNA-binding transcriptional activator BglJ; Provisional

Probab=98.78  E-value=1.1e-07  Score=57.78  Aligned_cols=81  Identities=14%  Similarity=0.021  Sum_probs=57.4

Q ss_pred             HHHHHHHHhh---cCCCceEEeCCHHHHHHHhccCccc------------CCCchHHHh---hhhcCCcEEEEcCCCCHH
Q 042991            8 RKVIERLLTI---SSSRDLYCSCSGRRALQFLGLDEEQ------------SANGFDVRT---IYSREIPVVIMSPEIILV   69 (93)
Q Consensus         8 ~~~l~~~l~~---~~~~~v~~~~~~~~a~~~~~~~~~~------------~~~~~d~l~---~~~~~~pii~lt~~~~~~   69 (93)
                      |..+..+|+.   .++. +..+.++.++++.+....++            +++|++++.   ...+.+|||++|+..++.
T Consensus         3 r~gi~~lL~~~~~~~~~-v~~~~~~~~~l~~~~~~~pd~vl~dl~d~~mp~~~Gl~~~~~l~~~~p~~~iIvlt~~~~~~   81 (207)
T PRK11475          3 SIGIESLFRKFPGNPYK-LHTFSSQSSFQDAMSRISFSAVIFSLSAMRSERREGLSCLTELAIKFPRMRRLVIADDDIEA   81 (207)
T ss_pred             hHHHHHHHhcCCCCeeE-EEEeCCHHHHHHHhccCCCCEEEeeccccCCCCCCHHHHHHHHHHHCCCCCEEEEeCCCCHH
Confidence            5667778864   3444 67899999999988643321            224455533   333899999999987776


Q ss_pred             HHHHHH-HcCCcceeeccchh
Q 042991           70 RIDRYL-EDGAEDSETCQMWA   89 (93)
Q Consensus        70 ~~~~~~-~~ga~d~l~kP~~~   89 (93)
                      ...+++ +.||.+|+.||.+.
T Consensus        82 ~~~~~~~~~Ga~gyl~K~~~~  102 (207)
T PRK11475         82 RLIGSLSPSPLDGVLSKASTL  102 (207)
T ss_pred             HHHHHHHHcCCeEEEecCCCH
Confidence            666655 79999999999863

>PRK14084 two-component response regulator; Provisional

Probab=98.78  E-value=9.3e-08  Score=58.79  Aligned_cols=86  Identities=12%  Similarity=0.088  Sum_probs=62.3

Q ss_pred             CCCcHHHHHHHHHHHhhcC-CCceEEeCCHHHHHHHhccCccc---------CCCchHH---HhhhhcCCcEEEEcCCCC
Q 042991            1 LNDSFVDRKVIERLLTISS-SRDLYCSCSGRRALQFLGLDEEQ---------SANGFDV---RTIYSREIPVVIMSPEII   67 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~-~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~---l~~~~~~~pii~lt~~~~   67 (93)
                      +||++..+..+..+++..+ +..+..+.++.+++..+....++         ++.|+++   +....+..++|++|+...
T Consensus         6 vdd~~~~~~~l~~~l~~~~~~~~v~~~~~~~~~l~~~~~~~~dlv~lDi~m~~~~G~~~~~~i~~~~~~~~iI~~t~~~~   85 (246)
T PRK14084          6 VDDEPLARNELTYLLNEIGGFEEINEAENVKETLEALLINQYDIIFLDINLMDESGIELAAKIQKMKEPPAIIFATAHDQ   85 (246)
T ss_pred             ECCCHHHHHHHHHHHHhCCCceEEEEECCHHHHHHHHHhcCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCEEEEEecChH
Confidence            5788999999999998755 43377899999999887543321         2345555   333335667888887643


Q ss_pred             HHHHHHHHHcCCcceeeccch
Q 042991           68 LVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        68 ~~~~~~~~~~ga~d~l~kP~~   88 (93)
                        ...++++.|+.+|+.||+.
T Consensus        86 --~~~~~~~~~~~~yl~KP~~  104 (246)
T PRK14084         86 --FAVKAFELNATDYILKPFE  104 (246)
T ss_pred             --HHHHHHhcCCcEEEECCCC
Confidence              4567899999999999986

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

Probab=98.70  E-value=2.9e-08  Score=59.17  Aligned_cols=86  Identities=14%  Similarity=0.064  Sum_probs=62.7

Q ss_pred             CCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCcccCCCchHH----------Hhhh--hcCCcEEEEcCCCCHH
Q 042991            2 NDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQSANGFDV----------RTIY--SREIPVVIMSPEIILV   69 (93)
Q Consensus         2 dd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~~~~~~d~----------l~~~--~~~~pii~lt~~~~~~   69 (93)
                      +|.+..+-.+...|...||+.|..+.++..+.......+ +++..+|+          +.-.  ....|||++|+++++.
T Consensus        12 ~d~~i~~~~i~~~l~eag~~~Vg~~~~~~~~~~~~~~~~-pDvVildie~p~rd~~e~~~~~~~~~~~piv~lt~~s~p~   90 (194)
T COG3707          12 DDEALTRMDIREGLLEAGYQRVGEAADGLEAVEVCERLQ-PDVVILDIEMPRRDIIEALLLASENVARPIVALTAYSDPA   90 (194)
T ss_pred             cccccchhhHHHHHHHcCCeEeeeecccccchhHHHhcC-CCEEEEecCCCCccHHHHHHHhhcCCCCCEEEEEccCChH
Confidence            455666777888888889986777777777766654333 22222222          1111  1577899999999999


Q ss_pred             HHHHHHHcCCcceeeccch
Q 042991           70 RIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        70 ~~~~~~~~ga~d~l~kP~~   88 (93)
                      .+..+.++|+..|+.||+.
T Consensus        91 ~i~~a~~~Gv~ayivkpi~  109 (194)
T COG3707          91 LIEAAIEAGVMAYIVKPLD  109 (194)
T ss_pred             HHHHHHHcCCeEEEecCcc
Confidence            9999999999999999997

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

Probab=98.69  E-value=2.3e-07  Score=60.10  Aligned_cols=88  Identities=23%  Similarity=0.197  Sum_probs=67.5

Q ss_pred             CCCcHHHHHHHHHHHhhcC-CCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhhh--cCCcEEEEcCCCC-
Q 042991            1 LNDSFVDRKVIERLLTISS-SRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIYS--REIPVVIMSPEII-   67 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~-~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~~--~~~pii~lt~~~~-   67 (93)
                      |||+...|..++.+|...+ .+.+..+.|+.+|++.+..-.++         .++|++.+...+  ..+|||++++.+. 
T Consensus         7 Vddsal~R~~i~~~l~~~~~i~vv~~a~ng~~a~~~~~~~~PDVi~ld~emp~mdgl~~l~~im~~~p~pVimvsslt~~   86 (350)
T COG2201           7 VDDSALMRKVISDILNSDPDIEVVGTARNGREAIDKVKKLKPDVITLDVEMPVMDGLEALRKIMRLRPLPVIMVSSLTEE   86 (350)
T ss_pred             EcCcHHHHHHHHHHHhcCCCeEEEEecCCHHHHHHHHHhcCCCEEEEecccccccHHHHHHHHhcCCCCcEEEEeccccc
Confidence            6899999999999999888 33488999999999998644322         234555433332  7899999997544 


Q ss_pred             -HHHHHHHHHcCCcceeeccch
Q 042991           68 -LVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        68 -~~~~~~~~~~ga~d~l~kP~~   88 (93)
                       .+...++++.||.||+.||..
T Consensus        87 g~~~t~~al~~gAvD~i~kp~~  108 (350)
T COG2201          87 GAEATLEALELGAVDFIAKPSG  108 (350)
T ss_pred             cHHHHHHHHhcCcceeecCCCc
Confidence             455567899999999999984

>PRK00742 chemotaxis-specific methylesterase; Provisional

Probab=98.68  E-value=3.4e-07  Score=59.41  Aligned_cols=87  Identities=24%  Similarity=0.198  Sum_probs=62.8

Q ss_pred             CCCcHHHHHHHHHHHhhc-CCCceE-EeCCHHHHHHHhccCccc---------CCCchHHHhhhh--cCCcEEEEcCCC-
Q 042991            1 LNDSFVDRKVIERLLTIS-SSRDLY-CSCSGRRALQFLGLDEEQ---------SANGFDVRTIYS--REIPVVIMSPEI-   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~-~~~~v~-~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~~--~~~pii~lt~~~-   66 (93)
                      ++|+...+..+..+|... ++. +. .+.++.+++..+....++         .+.|++++..+.  ..+|+|++|+.. 
T Consensus         9 Vdd~~~~~~~L~~~L~~~~~~~-vv~~a~~~~~al~~~~~~~~DlVllD~~mp~~dgle~l~~i~~~~~~piIvls~~~~   87 (354)
T PRK00742          9 VDDSAFMRRLISEILNSDPDIE-VVGTAPDGLEAREKIKKLNPDVITLDVEMPVMDGLDALEKIMRLRPTPVVMVSSLTE   87 (354)
T ss_pred             ECCCHHHHHHHHHHHhhCCCCE-EEEEECCHHHHHHHHhhhCCCEEEEeCCCCCCChHHHHHHHHHhCCCCEEEEecCCC
Confidence            578889999999999865 677 55 789999999887644321         223444432221  339999999753 


Q ss_pred             -CHHHHHHHHHcCCcceeeccch
Q 042991           67 -ILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        67 -~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                       ......++++.|+++|+.||+.
T Consensus        88 ~~~~~~~~al~~Ga~d~l~kP~~  110 (354)
T PRK00742         88 RGAEITLRALELGAVDFVTKPFL  110 (354)
T ss_pred             CCHHHHHHHHhCCCcEEEeCCcc
Confidence             3455668899999999999983

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

Probab=98.65  E-value=5.6e-07  Score=54.99  Aligned_cols=86  Identities=12%  Similarity=0.041  Sum_probs=60.2

Q ss_pred             CCCcHHHHHHHHHHHhhcCC-CceEEeCCHHHHHHHhccCccc---------CCCchHHHhhhh--cCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSS-RDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIYS--REIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~-~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~~--~~~pii~lt~~~~~   68 (93)
                      +||++..+..+..+|+..+. ..+..+.++.+++..+....++         ++.|+++.....  ...++|++|+..  
T Consensus         7 vdd~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~dlv~lDi~~~~~~G~~~~~~l~~~~~~~ii~vt~~~--   84 (238)
T PRK11697          7 VDDEPLAREELRELLQEEGDIEIVGECSNAIEAIGAIHRLKPDVVFLDIQMPRISGLELVGMLDPEHMPYIVFVTAFD--   84 (238)
T ss_pred             ECCCHHHHHHHHHHHhhCCCcEEEEEeCCHHHHHHHHHhcCCCEEEEeCCCCCCCHHHHHHHhcccCCCEEEEEeccH--
Confidence            58899999999999987763 3245788999999887543321         234555433222  234677777654  


Q ss_pred             HHHHHHHHcCCcceeeccch
Q 042991           69 VRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~   88 (93)
                      +...++++.|+.+|+.||+.
T Consensus        85 ~~~~~a~~~~~~~yl~KP~~  104 (238)
T PRK11697         85 EYAIKAFEEHAFDYLLKPID  104 (238)
T ss_pred             HHHHHHHhcCCcEEEECCCC
Confidence            45678899999999999986

>PRK10610 chemotaxis regulatory protein CheY; Provisional

Probab=98.62  E-value=2.1e-06  Score=46.47  Aligned_cols=88  Identities=17%  Similarity=0.173  Sum_probs=63.9

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhhh-----cCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIYS-----REIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~~-----~~~pii~lt~~~   66 (93)
                      +++++.....+...++..+++.+..+.++.+++..+......         ...+++++....     +.+|+++++...
T Consensus        11 ~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~di~l~d~~~~~~~~~~~~~~l~~~~~~~~~~~i~~~~~~   90 (129)
T PRK10610         11 VDDFSTMRRIVRNLLKELGFNNVEEAEDGVDALNKLQAGGFGFVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEA   90 (129)
T ss_pred             EcCCHHHHHHHHHHHHHcCCCeEEEeCCHHHHHHHhhccCCCEEEEcCCCCCCCHHHHHHHHHhCCCcCCCcEEEEECCC
Confidence            367778888898999888874366788999988877533321         122333322221     567999999888


Q ss_pred             CHHHHHHHHHcCCcceeeccch
Q 042991           67 ILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      ......++++.|+++|+.||+.
T Consensus        91 ~~~~~~~~~~~g~~~~i~~p~~  112 (129)
T PRK10610         91 KKENIIAAAQAGASGYVVKPFT  112 (129)
T ss_pred             CHHHHHHHHHhCCCeEEECCCC
Confidence            8888888999999999999986

>PRK10651 transcriptional regulator NarL; Provisional

Probab=98.61  E-value=1.2e-06  Score=52.08  Aligned_cols=88  Identities=15%  Similarity=0.140  Sum_probs=64.8

Q ss_pred             CCCcHHHHHHHHHHHhhc-CCCceEEeCCHHHHHHHhccCccc---------CCCchHH---HhhhhcCCcEEEEcCCCC
Q 042991            1 LNDSFVDRKVIERLLTIS-SSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDV---RTIYSREIPVVIMSPEII   67 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~-~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~---l~~~~~~~pii~lt~~~~   67 (93)
                      +++++..+..+...|+.. ++..+..+.++.+++..+....++         +.++++.   +....+..|+++++....
T Consensus        12 v~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~dlvl~d~~l~~~~~~~~~~~l~~~~~~~~vi~l~~~~~   91 (216)
T PRK10651         12 IDDHPMLRTGVKQLISMAPDITVVGEASNGEQGIELAESLDPDLILLDLNMPGMNGLETLDKLREKSLSGRIVVFSVSNH   91 (216)
T ss_pred             ECCCHHHHHHHHHHHccCCCcEEEEEeCCHHHHHHHHHhCCCCEEEEeCCCCCCcHHHHHHHHHHhCCCCcEEEEeCCCC
Confidence            478888888899988764 455244688999999887543321         1233443   222236789999999888


Q ss_pred             HHHHHHHHHcCCcceeeccch
Q 042991           68 LVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        68 ~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      ......+++.|+++|+.||+.
T Consensus        92 ~~~~~~~~~~g~~~~i~k~~~  112 (216)
T PRK10651         92 EEDVVTALKRGADGYLLKDME  112 (216)
T ss_pred             HHHHHHHHHcCCCEEEeCCCC
Confidence            888889999999999999986

>PRK15369 two component system sensor kinase SsrB; Provisional

Probab=98.60  E-value=1.3e-06  Score=51.60  Aligned_cols=89  Identities=15%  Similarity=0.029  Sum_probs=65.0

Q ss_pred             CCCcHHHHHHHHHHHhhc-CCCceEEeCCHHHHHHHhccCccc---------CCCchHH---HhhhhcCCcEEEEcCCCC
Q 042991            1 LNDSFVDRKVIERLLTIS-SSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDV---RTIYSREIPVVIMSPEII   67 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~-~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~---l~~~~~~~pii~lt~~~~   67 (93)
                      +++++..+..+...|... ++..+..+.++.+++..+....++         +..|+++   +....+..|++++|+...
T Consensus         9 v~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~dlvl~d~~~~~~~~~~~~~~l~~~~~~~~ii~ls~~~~   88 (211)
T PRK15369          9 VDDHELIINGIKNMLAPYPRYKIVGQVDNGLEVYNACRQLEPDIVILDLGLPGMNGLDVIPQLHQRWPAMNILVLTARQE   88 (211)
T ss_pred             ECCcHHHHHHHHHHHccCCCcEEEEEECCHHHHHHHHHhcCCCEEEEeCCCCCCCHHHHHHHHHHHCCCCcEEEEeCCCC
Confidence            477888889999999765 355244788999988776533321         2234444   222237789999999999


Q ss_pred             HHHHHHHHHcCCcceeeccchh
Q 042991           68 LVRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        68 ~~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      ......+++.|+++|+.||+..
T Consensus        89 ~~~~~~~~~~g~~~~l~kp~~~  110 (211)
T PRK15369         89 EHMASRTLAAGALGYVLKKSPQ  110 (211)
T ss_pred             HHHHHHHHHhCCCEEEeCCCCH
Confidence            8888899999999999999863

>PRK10403 transcriptional regulator NarP; Provisional

Probab=98.58  E-value=1.5e-06  Score=51.64  Aligned_cols=87  Identities=13%  Similarity=0.148  Sum_probs=63.7

Q ss_pred             CCCcHHHHHHHHHHHhh-cCCCceE-EeCCHHHHHHHhccCccc---------CCCchHHH---hhhhcCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTI-SSSRDLY-CSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYSREIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~-~~~~~v~-~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~~~~pii~lt~~~   66 (93)
                      +++++..+..+...|+. .++. +. .+.++.+++..+....++         ...+++++   ....+..|+++++...
T Consensus        12 i~~~~~~~~~l~~~l~~~~~~~-~~~~~~~~~~~~~~~~~~~~dlvi~d~~~~~~~~~~~~~~l~~~~~~~~ii~l~~~~   90 (215)
T PRK10403         12 VDDHPLMRRGVRQLLELDPGFE-VVAEAGDGASAIDLANRLDPDVILLDLNMKGMSGLDTLNALRRDGVTAQIIILTVSD   90 (215)
T ss_pred             EcCCHHHHHHHHHHHhcCCCCE-EEEEeCCHHHHHHHHHhcCCCEEEEecCCCCCcHHHHHHHHHHhCCCCeEEEEeCCC
Confidence            46788888888888874 4666 54 688999999877543321         12334432   2222678999999888


Q ss_pred             CHHHHHHHHHcCCcceeeccch
Q 042991           67 ILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      .......+++.|+++|+.||+.
T Consensus        91 ~~~~~~~~~~~g~~~~i~kp~~  112 (215)
T PRK10403         91 ASSDVFALIDAGADGYLLKDSD  112 (215)
T ss_pred             ChHHHHHHHHcCCCeEEecCCC
Confidence            8888888999999999999986

>PRK13435 response regulator; Provisional

Probab=98.51  E-value=2.6e-06  Score=48.40  Aligned_cols=85  Identities=14%  Similarity=0.074  Sum_probs=59.3

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceE-EeCCHHHHHHHhccCccc----------CCCchHHHhhh--hcCCcEEEEcCCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLY-CSCSGRRALQFLGLDEEQ----------SANGFDVRTIY--SREIPVVIMSPEII   67 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~-~~~~~~~a~~~~~~~~~~----------~~~~~d~l~~~--~~~~pii~lt~~~~   67 (93)
                      ++++......+...|+..|+. +. .+.++.+++..+....++          ...+++.+...  ...+|+|++++..+
T Consensus        11 id~~~~~~~~l~~~l~~~~~~-~~~~~~~~~~~~~~~~~~~~dliivd~~~~~~~~~~~~~~~l~~~~~~pii~ls~~~~   89 (145)
T PRK13435         11 VEDEALIALELEKLVEEAGHE-VVGIAMSSEQAIALGRRRQPDVALVDVHLADGPTGVEVARRLSADGGVEVVFMTGNPE   89 (145)
T ss_pred             EcCcHHHHHHHHHHHHhcCCe-EEEeeCCHHHHHHHhhhcCCCEEEEeeecCCCCcHHHHHHHHHhCCCCCEEEEeCCHH
Confidence            467778888899999888888 65 789999998887533221          11233332222  16789999987543


Q ss_pred             HHHHHHHHHcCCcceeeccchh
Q 042991           68 LVRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        68 ~~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      .   ..++..|+++|+.||++.
T Consensus        90 ~---~~~~~~ga~~~l~kp~~~  108 (145)
T PRK13435         90 R---VPHDFAGALGVIAKPYSP  108 (145)
T ss_pred             H---HHHHhcCcceeEeCCCCH
Confidence            2   457789999999999863

>PRK10693 response regulator of RpoS; Provisional

Probab=98.47  E-value=1.1e-06  Score=56.10  Aligned_cols=64  Identities=22%  Similarity=0.260  Sum_probs=47.1

Q ss_pred             EeCCHHHHHHHhccCcc---------cCCCchHHH---hhhhcCCcEEEEcCCCCHHHHHHHHHcCCcceeeccch
Q 042991           25 CSCSGRRALQFLGLDEE---------QSANGFDVR---TIYSREIPVVIMSPEIILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        25 ~~~~~~~a~~~~~~~~~---------~~~~~~d~l---~~~~~~~pii~lt~~~~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      .+.++.+|++.+....+         +++.|++++   ....+.+|+|++|+..+.+...++++.|+++|+.||+.
T Consensus         2 ~a~~g~~al~~l~~~~pDlVL~D~~mp~~~Gle~~~~ir~~~~~ipiI~lt~~~~~~~~~~al~~Ga~dyl~KP~~   77 (303)
T PRK10693          2 LAANGVDALELLGGFTPDLIICDLAMPRMNGIEFVEHLRNRGDQTPVLVISATENMADIAKALRLGVQDVLLKPVK   77 (303)
T ss_pred             EeCCHHHHHHHHhcCCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCcEEEEECCCCHHHHHHHHHCCCcEEEECCCC
Confidence            35677788777754332         123455543   22237799999999999999999999999999999984

>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=98.46  E-value=5.3e-06  Score=43.06  Aligned_cols=88  Identities=19%  Similarity=0.271  Sum_probs=64.3

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHH---HhhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDV---RTIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~---l~~~~~~~pii~lt~~~~~   68 (93)
                      +++++..+..+...+...|+. +..+.+..+++..+......         ...+.+.   +....+.+|+++++.....
T Consensus         3 ~~~~~~~~~~l~~~l~~~~~~-~~~~~~~~~~~~~~~~~~~~~ii~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~~~~~   81 (113)
T cd00156           3 VDDDPLIRELLRRLLEKEGYE-VVEAEDGEEALALLAEEKPDLILLDIMMPGMDGLELLRRIRKRGPDIPIIFLTAHGDD   81 (113)
T ss_pred             ecCcHHHHHHHHHHHhhcCce-EEEecCHHHHHHHHHhCCCCEEEEecCCCCCchHHHHHHHHHhCCCCCEEEEEecccH
Confidence            366777888899989888888 88999999988877533221         1122332   2222367899999887777


Q ss_pred             HHHHHHHHcCCcceeeccchh
Q 042991           69 VRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      ....++++.|+.+|+.||+..
T Consensus        82 ~~~~~~~~~~~~~~i~~p~~~  102 (113)
T cd00156          82 EDAVEALKAGADDYLTKPFSP  102 (113)
T ss_pred             HHHHHHHHcChhhHccCCCCH
Confidence            777788899999999999873

>PRK13557 histidine kinase; Provisional

Probab=98.37  E-value=4.9e-06  Score=55.94  Aligned_cols=87  Identities=15%  Similarity=0.055  Sum_probs=67.2

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCc-cc---------C-CCchHHH---hhhhcCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDE-EQ---------S-ANGFDVR---TIYSREIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~-~~---------~-~~~~d~l---~~~~~~~pii~lt~~~   66 (93)
                      +++++..+..+..+|+..||. +..+.++.+++..+.... ++         + ..+++++   ....+.+|+++++...
T Consensus       421 v~~~~~~~~~l~~~l~~~~~~-v~~~~~~~~~~~~~~~~~~~d~vi~d~~~~~~~~~~~~~~~l~~~~~~~~ii~~~~~~  499 (540)
T PRK13557        421 VDDRPDVAELARMILEDFGYR-TLVASNGREALEILDSHPEVDLLFTDLIMPGGMNGVMLAREARRRQPKIKVLLTTGYA  499 (540)
T ss_pred             EcCcHHHHHHHHHHHHhcCCe-EEEeCCHHHHHHHHhcCCCceEEEEeccCCCCCCHHHHHHHHHHhCCCCcEEEEcCCC
Confidence            467888889999999989999 999999999999885332 11         1 2344442   2223779999999988


Q ss_pred             CHHHHHHHHHcCCcceeeccch
Q 042991           67 ILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      .......++..|+.+|+.||+.
T Consensus       500 ~~~~~~~~~~~g~~~~l~kp~~  521 (540)
T PRK13557        500 EASIERTDAGGSEFDILNKPYR  521 (540)
T ss_pred             chhhhhhhccccCCceeeCCCC
Confidence            8887778889999999999987

>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional

Probab=98.27  E-value=1.1e-05  Score=49.35  Aligned_cols=85  Identities=8%  Similarity=-0.069  Sum_probs=59.0

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCcc-------cCCCchHHHh----hhhcCCcEEEEcCCCCHH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEE-------QSANGFDVRT----IYSREIPVVIMSPEIILV   69 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~-------~~~~~~d~l~----~~~~~~pii~lt~~~~~~   69 (93)
                      ++|++..+..++.+|. .++..+..+.++.+++..+...+.       ++.+|++.+.    ...+.++||++|+..+. 
T Consensus        16 v~~~~l~~~~l~~~L~-~~~~v~~~~~~~~~~~~~~~~~DvvllDi~~p~~~G~~~~~~~i~~~~p~~~vvvlt~~~~~-   93 (216)
T PRK10100         16 ITKPSLQATALLQHLK-QSLAITGKLHNIQRSLDDISSGSIILLDMMEADKKLIHYWQDTLSRKNNNIKILLLNTPEDY-   93 (216)
T ss_pred             EeChHhhhHHHHHHHH-HhCCCeEEEcCHHHhhccCCCCCEEEEECCCCCccHHHHHHHHHHHhCCCCcEEEEECCchh-
Confidence            5789999999999998 344436678899999887653121       1234555432    22378999999998763 


Q ss_pred             HHHHHHH--cCCcceeeccch
Q 042991           70 RIDRYLE--DGAEDSETCQMW   88 (93)
Q Consensus        70 ~~~~~~~--~ga~d~l~kP~~   88 (93)
                       ...++.  .||.+|+.|+.+
T Consensus        94 -~~~~~~~~~Ga~G~l~K~~~  113 (216)
T PRK10100         94 -PYREIENWPHINGVFYAMED  113 (216)
T ss_pred             -HHHHHHHhcCCeEEEECCCC
Confidence             334455  599999999875

>PRK09191 two-component response regulator; Provisional

Probab=98.24  E-value=2.4e-05  Score=48.38  Aligned_cols=86  Identities=12%  Similarity=0.042  Sum_probs=60.0

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceE-EeCCHHHHHHHhccCccc------C----CCchHHHhhhh--cCCcEEEEcCCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLY-CSCSGRRALQFLGLDEEQ------S----ANGFDVRTIYS--REIPVVIMSPEII   67 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~-~~~~~~~a~~~~~~~~~~------~----~~~~d~l~~~~--~~~pii~lt~~~~   67 (93)
                      +++++..+..+...|+..|+. +. .+.++.+++..+.....+      .    ..|++.+....  ..+|+|++|+..+
T Consensus       143 idd~~~~~~~l~~~L~~~~~~-~~~~~~~~~~~l~~l~~~~~dlvi~d~~~~~~~~g~e~l~~l~~~~~~pii~ls~~~~  221 (261)
T PRK09191        143 IEDEPIIAMDLEQLVESLGHR-VTGIARTRAEAVALAKKTRPGLILADIQLADGSSGIDAVNDILKTFDVPVIFITAFPE  221 (261)
T ss_pred             EcCcHHHHHHHHHHHhcCCCE-EEEEECCHHHHHHHHhccCCCEEEEecCCCCCCCHHHHHHHHHHhCCCCEEEEeCCCc
Confidence            478888888999999888888 66 788999999887643321      1    22344432221  3799999998766


Q ss_pred             HHHHHHHHHcCCcceeeccchh
Q 042991           68 LVRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        68 ~~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      ....  ....|+.+|+.||++.
T Consensus       222 ~~~~--~~~~~~~~~l~kP~~~  241 (261)
T PRK09191        222 RLLT--GERPEPAFLITKPFQP  241 (261)
T ss_pred             HHHH--HHhcccCceEECCCCH
Confidence            5443  3346788999999963

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

Probab=98.04  E-value=6.1e-05  Score=45.77  Aligned_cols=88  Identities=6%  Similarity=-0.136  Sum_probs=59.7

Q ss_pred             CCCcHHHHHHHHHHHhhcCC--CceEEeCCHHHHHHHhccCccc----C----C---CchHHHh---hhhcCCcEEEEcC
Q 042991            1 LNDSFVDRKVIERLLTISSS--RDLYCSCSGRRALQFLGLDEEQ----S----A---NGFDVRT---IYSREIPVVIMSP   64 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~--~~v~~~~~~~~a~~~~~~~~~~----~----~---~~~d~l~---~~~~~~pii~lt~   64 (93)
                      +||++..+..++.+|...++  ..+..+.++.+++..++...++    +    +   .|.+++.   ...+++++|++|+
T Consensus         6 vDD~~~~~~gl~~~L~~~~~~~~vv~~~~~~~~~~~~~~~~~pDlvLlDl~~~l~~~~g~~~i~~i~~~~p~~~iivlt~   85 (207)
T PRK15411          6 MDLCSYTRLGLTGYLLSRGVKKREINDIETVDDLAIACDSLRPSVVFINEDCFIHDASNSQRIKQIINQHPNTLFIVFMA   85 (207)
T ss_pred             EcCCHHHHHHHHHHHHhCCCcceEEEecCCHHHHHHHHhccCCCEEEEeCcccCCCCChHHHHHHHHHHCCCCeEEEEEC
Confidence            58999999999999986553  3367889999999887543321    2    2   2333322   2237899999998


Q ss_pred             CCCHHHHHHHHHcCCcc-eeeccchh
Q 042991           65 EIILVRIDRYLEDGAED-SETCQMWA   89 (93)
Q Consensus        65 ~~~~~~~~~~~~~ga~d-~l~kP~~~   89 (93)
                      ..+.... .++..|+.. |+.|+.+.
T Consensus        86 ~~~~~~~-~~~~~~~~~~~~~K~~~~  110 (207)
T PRK15411         86 IANIHFD-EYLLVRKNLLISSKSIKP  110 (207)
T ss_pred             CCchhHH-HHHHHHhhceeeeccCCH
Confidence            8776553 345555544 78998763

>PRK15029 arginine decarboxylase; Provisional

Probab=97.60  E-value=0.00032  Score=50.03  Aligned_cols=60  Identities=10%  Similarity=0.106  Sum_probs=45.2

Q ss_pred             HHHHHHHHHhhcCCCceEEeCCHHHHHHHhccC-ccc---------CCCch----HHH---hhhhcCCcEEEEcCCCC
Q 042991            7 DRKVIERLLTISSSRDLYCSCSGRRALQFLGLD-EEQ---------SANGF----DVR---TIYSREIPVVIMSPEII   67 (93)
Q Consensus         7 ~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~-~~~---------~~~~~----d~l---~~~~~~~pii~lt~~~~   67 (93)
                      .++.++..|+..||+ +.++.++.+|+..+... ..+         +++|+    +++   +....++|||++|+..+
T Consensus        20 i~~~L~~~Le~~G~e-V~~a~s~~dAl~~l~~~~~~DlVLLD~~LPd~dG~~~~~ell~~IR~~~~~iPIIlLTar~~   96 (755)
T PRK15029         20 AVERLADALSQQNVT-VIKSTSFDDGFAILSSNEAIDCLMFSYQMEHPDEHQNVRQLIGKLHERQQNVPVFLLGDREK   96 (755)
T ss_pred             HHHHHHHHHHHCCCE-EEEECCHHHHHHHHHhcCCCcEEEEECCCCCCccchhHHHHHHHHHhhCCCCCEEEEEcCCc
Confidence            688999999999999 99999999999999642 321         23344    342   22236899999999885

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

Probab=97.10  E-value=0.0018  Score=40.47  Aligned_cols=86  Identities=17%  Similarity=0.097  Sum_probs=59.2

Q ss_pred             CCCcHHHHHHHHHHHhhcC-CCceEEeCCHHHHHHHhccCccc---------CCCchHH---HhhhhcCCcEEEEcCCCC
Q 042991            1 LNDSFVDRKVIERLLTISS-SRDLYCSCSGRRALQFLGLDEEQ---------SANGFDV---RTIYSREIPVVIMSPEII   67 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~-~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~---l~~~~~~~pii~lt~~~~   67 (93)
                      +||++..+..+..++.... .+.+..+.++.++++.++.....         +++|+++   ++...+..+|+++|++..
T Consensus         7 ~dd~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fldI~~~~~~G~ela~~i~~~~~~~~Ivfvt~~~~   86 (244)
T COG3279           7 VDDEPLAREELRRILNEIPDIEIVGEAENGEEALQLLQGLRPDLVFLDIAMPDINGIELAARIRKGDPRPAIVFVTAHDE   86 (244)
T ss_pred             ecCCHHHHHHHHHHHHhhhhcCeeeeeccchhhHHHHhccCCCeEEEeeccCccchHHHHHHhcccCCCCeEEEEEehHH
Confidence            4788999999999888433 23233788888888888644211         2345554   333336778999998655


Q ss_pred             HHHHHHHHHcCCcceeeccch
Q 042991           68 LVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        68 ~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      -.  ..+++..+-||+.||+.
T Consensus        87 ~a--~~afev~a~d~i~kp~~  105 (244)
T COG3279          87 YA--VAAFEVEALDYLLKPIS  105 (244)
T ss_pred             HH--HHHHhHHHHhhhcCcch
Confidence            44  45678889999999994

>PRK11107 hybrid sensory histidine kinase BarA; Provisional

Probab=96.63  E-value=0.0084  Score=43.27  Aligned_cols=83  Identities=11%  Similarity=0.023  Sum_probs=58.2

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCcccCC----------CchHH----Hhhh-hcCCcEEEEcCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQSA----------NGFDV----RTIY-SREIPVVIMSPE   65 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~~~----------~~~d~----l~~~-~~~~pii~lt~~   65 (93)
                      +++++..+..+..+|...|+. +..+.++.+ +   .... +++          .+...    +... ....+++++++.
T Consensus       542 ~d~~~~~~~~l~~~L~~~g~~-v~~~~~~~~-l---~~~~-~d~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~  615 (919)
T PRK11107        542 VEPNSAAAQATLDILSETPLE-VTYSPTLSQ-L---PEAH-YDILLLGLPVTFREPLTMLHERLAKAKSMTDFLILALPC  615 (919)
T ss_pred             EeCCHHHHHHHHHHHHHCCCE-EEEcCCHHH-h---ccCC-CCEEEecccCCCCCCHHHHHHHHHhhhhcCCcEEEEeCC
Confidence            367888999999999999999 988888887 2   1111 111          11111    1111 144567778888


Q ss_pred             CCHHHHHHHHHcCCcceeeccchh
Q 042991           66 IILVRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        66 ~~~~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      ........+.+.|+++|+.||+..
T Consensus       616 ~~~~~~~~~~~~g~~~~l~kp~~~  639 (919)
T PRK11107        616 HEQVLAEQLKQDGADACLSKPLSH  639 (919)
T ss_pred             cchhhHHHHhhCCCceEECCCCCH
Confidence            888888888999999999999863

>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=93.55  E-value=0.19  Score=27.77  Aligned_cols=76  Identities=12%  Similarity=0.041  Sum_probs=46.5

Q ss_pred             HHHHHHHhhcCCCceEEeCCHHHHHHHhccCcccCC--CchH---------H---HhhhhcCCcEEEEcCCCCHHHHHHH
Q 042991            9 KVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQSA--NGFD---------V---RTIYSREIPVVIMSPEIILVRIDRY   74 (93)
Q Consensus         9 ~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~~~--~~~d---------~---l~~~~~~~pii~lt~~~~~~~~~~~   74 (93)
                      ..+...|.+.|++ +..+.+..+++..++.......  ..+|         +   +......+||.+++.....+.+...
T Consensus         7 ~~l~~~L~~~~~~-vv~~~~~dd~~~~i~~~~~i~avvi~~d~~~~~~~~~ll~~i~~~~~~iPVFl~~~~~~~~~l~~~   85 (115)
T PF03709_consen    7 RELAEALEQRGRE-VVDADSTDDALAIIESFTDIAAVVISWDGEEEDEAQELLDKIRERNFGIPVFLLAERDTTEDLPAE   85 (115)
T ss_dssp             HHHHHHHHHTTTE-EEEESSHHHHHHHHHCTTTEEEEEEECHHHHHHHHHHHHHHHHHHSTT-EEEEEESCCHHHCCCHH
T ss_pred             HHHHHHHHHCCCE-EEEeCChHHHHHHHHhCCCeeEEEEEcccccchhHHHHHHHHHHhCCCCCEEEEecCCCcccCCHH
Confidence            4566777778999 9999999999999974432211  1122         1   3334499999999986644333222


Q ss_pred             HHcCCcceeec
Q 042991           75 LEDGAEDSETC   85 (93)
Q Consensus        75 ~~~ga~d~l~k   85 (93)
                      .=..+++|+-.
T Consensus        86 ~l~~v~~~i~l   96 (115)
T PF03709_consen   86 VLGEVDGFIWL   96 (115)
T ss_dssp             HHCCESEEEET
T ss_pred             HHhhccEEEEe
Confidence            22235555544

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.

>TIGR03815 CpaE_hom_Actino helicase/secretion neighborhood CpaE-like protein

Probab=91.91  E-value=0.26  Score=31.93  Aligned_cols=35  Identities=20%  Similarity=-0.021  Sum_probs=26.4

Q ss_pred             cCCcEEEEcC-CCCHHHHHHHHHcCCcceeeccchh
Q 042991           55 REIPVVIMSP-EIILVRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        55 ~~~pii~lt~-~~~~~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      ++..++++.+ ..+.....+++..|+.+|+.+|...
T Consensus        40 ~~~~vv~v~~~~~~~~~~~~a~~~Ga~~~l~~P~~~   75 (322)
T TIGR03815        40 RRRRVVLVGGGEPGGALWRAAAAVGAEHVAVLPEAE   75 (322)
T ss_pred             CCCCEEEEeCCCCCHHHHHHHHHhChhheeeCCCCH
Confidence            4444665555 5567777789999999999999873

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.

>smart00448 REC cheY-homologous receiver domain

Probab=91.10  E-value=0.66  Score=19.70  Aligned_cols=35  Identities=23%  Similarity=0.331  Sum_probs=28.8

Q ss_pred             CCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhc
Q 042991            2 NDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLG   37 (93)
Q Consensus         2 dd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~   37 (93)
                      ++++.....+...+...+++ +..+.+..+++..+.
T Consensus         7 ~~~~~~~~~~~~~l~~~~~~-~~~~~~~~~~~~~~~   41 (55)
T smart00448        7 DDDPLLRELLKALLEREGYE-VDEATDGEEALELLK   41 (55)
T ss_pred             cCCHHHHHHHHHHHhhcCcE-EEEeCCHHHHHHHHH
Confidence            56777778888888888888 889999999887774

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

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

Probab=90.79  E-value=0.31  Score=33.20  Aligned_cols=68  Identities=21%  Similarity=0.136  Sum_probs=46.0

Q ss_pred             CCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhhh-cCCcEEEEcCCCCHHHHHHHHHcCCcceeeccch
Q 042991           20 SRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIYS-REIPVVIMSPEIILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        20 ~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~~-~~~pii~lt~~~~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      +. +..+.++..+++........         ++.|+++..... -..+++++|.........+.+++|++++++||..
T Consensus        13 ~~-v~~a~~g~~~l~~~~~~~~~~~lld~~m~~~~~~~~~~~lk~~~~~~v~~t~~~~~~~~~~~~~~~~~~~l~~~~~   90 (435)
T COG3706          13 KE-VATAKKGLIALAILLDHKPDYKLLDVMMPGMDGFELCRRLKAEPATVVMVTALDDSAPRVRGLKAGADDFLTKPVN   90 (435)
T ss_pred             hh-hhhccchHHHHHHHhcCCCCeEEeecccCCcCchhHHHHHhcCCcceEEEEecCCCCcchhHHhhhhhhhccCCCC
Confidence            34 66688899988887433221         223344322221 2223788888888888889999999999999986

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

Probab=90.76  E-value=2.9  Score=26.53  Aligned_cols=69  Identities=14%  Similarity=0.028  Sum_probs=45.0

Q ss_pred             hcCCCce-EEeCCHHHHHHHhccCcc---c---------CCCchHHHhhhh--cCCcEEEEcCCCCHHHHHHHHHcCCcc
Q 042991           17 ISSSRDL-YCSCSGRRALQFLGLDEE---Q---------SANGFDVRTIYS--REIPVVIMSPEIILVRIDRYLEDGAED   81 (93)
Q Consensus        17 ~~~~~~v-~~~~~~~~a~~~~~~~~~---~---------~~~~~d~l~~~~--~~~pii~lt~~~~~~~~~~~~~~ga~d   81 (93)
                      +.||.++ +..+|...|.+.......   +         .+...+.+..+.  ..+|||+=.+-.++++..++++.|++.
T Consensus       121 ~~Gf~vlpyc~dd~~~ar~l~~~G~~~vmPlg~pIGsg~Gi~~~~~I~~I~e~~~vpVI~egGI~tpeda~~AmelGAdg  200 (248)
T cd04728         121 KEGFTVLPYCTDDPVLAKRLEDAGCAAVMPLGSPIGSGQGLLNPYNLRIIIERADVPVIVDAGIGTPSDAAQAMELGADA  200 (248)
T ss_pred             HCCCEEEEEeCCCHHHHHHHHHcCCCEeCCCCcCCCCCCCCCCHHHHHHHHHhCCCcEEEeCCCCCHHHHHHHHHcCCCE
Confidence            4698844 566677777666532211   0         111233333222  578999888889999999999999999


Q ss_pred             eeec
Q 042991           82 SETC   85 (93)
Q Consensus        82 ~l~k   85 (93)
                      ++.-
T Consensus       201 VlV~  204 (248)
T cd04728         201 VLLN  204 (248)
T ss_pred             EEEC
Confidence            8753

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).

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

Probab=90.45  E-value=3.7  Score=27.16  Aligned_cols=69  Identities=12%  Similarity=0.032  Sum_probs=46.0

Q ss_pred             hcCCCc-eEEeCCHHHHHHHhccCcc-----c-------CCCchHHHhhhh--cCCcEEEEcCCCCHHHHHHHHHcCCcc
Q 042991           17 ISSSRD-LYCSCSGRRALQFLGLDEE-----Q-------SANGFDVRTIYS--REIPVVIMSPEIILVRIDRYLEDGAED   81 (93)
Q Consensus        17 ~~~~~~-v~~~~~~~~a~~~~~~~~~-----~-------~~~~~d~l~~~~--~~~pii~lt~~~~~~~~~~~~~~ga~d   81 (93)
                      +.||.+ +++.+|...|.+.......     .       .+...+.+....  ..+|+|+=.+=..+++...+++.|++.
T Consensus       195 ~~Gf~v~~yc~~d~~~a~~l~~~g~~avmPl~~pIGsg~gv~~p~~i~~~~e~~~vpVivdAGIg~~sda~~AmelGadg  274 (326)
T PRK11840        195 KEGFQVMVYCSDDPIAAKRLEDAGAVAVMPLGAPIGSGLGIQNPYTIRLIVEGATVPVLVDAGVGTASDAAVAMELGCDG  274 (326)
T ss_pred             HCCCEEEEEeCCCHHHHHHHHhcCCEEEeeccccccCCCCCCCHHHHHHHHHcCCCcEEEeCCCCCHHHHHHHHHcCCCE
Confidence            469984 5667777777666532221     1       111223222211  779999888889999999999999999


Q ss_pred             eeec
Q 042991           82 SETC   85 (93)
Q Consensus        82 ~l~k   85 (93)
                      .+..
T Consensus       275 VL~n  278 (326)
T PRK11840        275 VLMN  278 (326)
T ss_pred             EEEc
Confidence            8864

>PRK00208 thiG thiazole synthase; Reviewed

Probab=89.05  E-value=4.2  Score=25.86  Aligned_cols=68  Identities=13%  Similarity=-0.017  Sum_probs=44.9

Q ss_pred             hcCCCce-EEeCCHHHHHHHhccCcc---c---------CCCchHH---HhhhhcCCcEEEEcCCCCHHHHHHHHHcCCc
Q 042991           17 ISSSRDL-YCSCSGRRALQFLGLDEE---Q---------SANGFDV---RTIYSREIPVVIMSPEIILVRIDRYLEDGAE   80 (93)
Q Consensus        17 ~~~~~~v-~~~~~~~~a~~~~~~~~~---~---------~~~~~d~---l~~~~~~~pii~lt~~~~~~~~~~~~~~ga~   80 (93)
                      +.||.++ +..+|...|.+.......   +         .+...+.   +... ..+|||+=.+-..+++..++++.|++
T Consensus       121 ~~Gf~vlpyc~~d~~~ak~l~~~G~~~vmPlg~pIGsg~gi~~~~~i~~i~e~-~~vpVIveaGI~tpeda~~AmelGAd  199 (250)
T PRK00208        121 KEGFVVLPYCTDDPVLAKRLEEAGCAAVMPLGAPIGSGLGLLNPYNLRIIIEQ-ADVPVIVDAGIGTPSDAAQAMELGAD  199 (250)
T ss_pred             HCCCEEEEEeCCCHHHHHHHHHcCCCEeCCCCcCCCCCCCCCCHHHHHHHHHh-cCCeEEEeCCCCCHHHHHHHHHcCCC
Confidence            4699844 566777777666532211   0         1112333   2232 67899988888999999999999999


Q ss_pred             ceeec
Q 042991           81 DSETC   85 (93)
Q Consensus        81 d~l~k   85 (93)
                      .++.-
T Consensus       200 gVlV~  204 (250)
T PRK00208        200 AVLLN  204 (250)
T ss_pred             EEEEC
Confidence            98753

>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=87.34  E-value=3.3  Score=22.66  Aligned_cols=82  Identities=11%  Similarity=0.078  Sum_probs=48.2

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc------CCCc-hHH---HhhhhcCCcEEEEcCCCCHHH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ------SANG-FDV---RTIYSREIPVVIMSPEIILVR   70 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~------~~~~-~d~---l~~~~~~~pii~lt~~~~~~~   70 (93)
                      |||+...+..+..+|+-.|++ +..+.+..-...........      ...+ .+.   +....+++|++++........
T Consensus         5 Iddd~~R~~~L~~ILeFlGe~-~~~~~~~~~~~~~~~~~~~~~~v~~g~~~~~~~~l~~l~~~~~~~Pvlllg~~~~~~~   83 (109)
T PF06490_consen    5 IDDDAERRQRLSTILEFLGEQ-CEAVSSSDWSQADWSSPWEACAVILGSCSKLAELLKELLKWAPHIPVLLLGEHDSPEE   83 (109)
T ss_pred             ECCcHHHHHhhhhhhhhcCCC-eEEecHHHHHHhhhhcCCcEEEEEecCchhHHHHHHHHHhhCCCCCEEEECCCCcccc
Confidence            589999999999999988988 88877644411111111111      0110 111   223339999999987766622


Q ss_pred             HHHHHHcCCcceeeccch
Q 042991           71 IDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        71 ~~~~~~~ga~d~l~kP~~   88 (93)
                      ..     .+.+-|..|+.
T Consensus        84 ~~-----nvvg~Le~Pl~   96 (109)
T PF06490_consen   84 LP-----NVVGELEEPLN   96 (109)
T ss_pred             cc-----CeeEecCCCCC
Confidence            11     14455666664

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

>cd02071 MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 binding domain

Probab=86.09  E-value=4.2  Score=22.58  Aligned_cols=78  Identities=13%  Similarity=-0.015  Sum_probs=44.0

Q ss_pred             HHHHHHHHhhcCCCceEEeCC---HHHHHHHhccCccc--CCCchH---------H---HhhhhcCCcEEEEcCCCCHHH
Q 042991            8 RKVIERLLTISSSRDLYCSCS---GRRALQFLGLDEEQ--SANGFD---------V---RTIYSREIPVVIMSPEIILVR   70 (93)
Q Consensus         8 ~~~l~~~l~~~~~~~v~~~~~---~~~a~~~~~~~~~~--~~~~~d---------~---l~~~~~~~pii~lt~~~~~~~   70 (93)
                      ...+..+|+..||+ +.....   .++..+.+......  .++..+         +   +....+.-+.+++.+...++.
T Consensus        16 ~~~~~~~l~~~G~~-vi~lG~~vp~e~~~~~a~~~~~d~V~iS~~~~~~~~~~~~~~~~L~~~~~~~i~i~~GG~~~~~~   94 (122)
T cd02071          16 AKVIARALRDAGFE-VIYTGLRQTPEEIVEAAIQEDVDVIGLSSLSGGHMTLFPEVIELLRELGAGDILVVGGGIIPPED   94 (122)
T ss_pred             HHHHHHHHHHCCCE-EEECCCCCCHHHHHHHHHHcCCCEEEEcccchhhHHHHHHHHHHHHhcCCCCCEEEEECCCCHHH
Confidence            35667788889999 665553   56666665433321  111111         1   111113233444565555666


Q ss_pred             HHHHHHcCCcceeecc
Q 042991           71 IDRYLEDGAEDSETCQ   86 (93)
Q Consensus        71 ~~~~~~~ga~d~l~kP   86 (93)
                      ..++.++|++.|+..-
T Consensus        95 ~~~~~~~G~d~~~~~~  110 (122)
T cd02071          95 YELLKEMGVAEIFGPG  110 (122)
T ss_pred             HHHHHHCCCCEEECCC
Confidence            6777899999998763

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.

>COG0134 TrpC Indole-3-glycerol phosphate synthase [Amino acid transport and metabolism]

Probab=84.51  E-value=8.3  Score=24.64  Aligned_cols=73  Identities=11%  Similarity=0.013  Sum_probs=45.1

Q ss_pred             HHHhhcCCCceEEeCCHHHHHHHhccCcc-c-----CCCchHH----Hhhhh----cCCcEEEEcCCCCHHHHHHHHHcC
Q 042991           13 RLLTISSSRDLYCSCSGRRALQFLGLDEE-Q-----SANGFDV----RTIYS----REIPVVIMSPEIILVRIDRYLEDG   78 (93)
Q Consensus        13 ~~l~~~~~~~v~~~~~~~~a~~~~~~~~~-~-----~~~~~d~----l~~~~----~~~pii~lt~~~~~~~~~~~~~~g   78 (93)
                      .+-++.|...++.+.|.++.-..++.... .     ++..+.+    ...+.    .+.-+|.-|+=.+++++.+..+.|
T Consensus       150 ~~A~~LGm~~LVEVh~~eEl~rAl~~ga~iIGINnRdL~tf~vdl~~t~~la~~~p~~~~~IsESGI~~~~dv~~l~~~g  229 (254)
T COG0134         150 DRAHELGMEVLVEVHNEEELERALKLGAKIIGINNRDLTTLEVDLETTEKLAPLIPKDVILISESGISTPEDVRRLAKAG  229 (254)
T ss_pred             HHHHHcCCeeEEEECCHHHHHHHHhCCCCEEEEeCCCcchheecHHHHHHHHhhCCCCcEEEecCCCCCHHHHHHHHHcC
Confidence            33345777768889999998877752221 0     1111111    11112    334455556667799999999999


Q ss_pred             Ccceeec
Q 042991           79 AEDSETC   85 (93)
Q Consensus        79 a~d~l~k   85 (93)
                      ++.||.-
T Consensus       230 a~a~LVG  236 (254)
T COG0134         230 ADAFLVG  236 (254)
T ss_pred             CCEEEec
Confidence            9999864

>PRK12704 phosphodiesterase; Provisional

Probab=84.50  E-value=0.48  Score=33.05  Aligned_cols=35  Identities=17%  Similarity=-0.037  Sum_probs=28.4

Q ss_pred             cCCcEEEEcCCCCHH--HHHHHHHcCCcceeeccchh
Q 042991           55 REIPVVIMSPEIILV--RIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        55 ~~~pii~lt~~~~~~--~~~~~~~~ga~d~l~kP~~~   89 (93)
                      ....+|++|+.+...  ....+++.|+.|+..||+..
T Consensus       248 dtp~~v~ls~~~~~rre~a~~~l~~l~~dg~i~P~~i  284 (520)
T PRK12704        248 DTPEAVILSGFDPIRREIARLALEKLVQDGRIHPARI  284 (520)
T ss_pred             CCCCeEEEecCChhhHHHHHHHHHHHHhcCCcCCCCH
Confidence            445678899988766  67788999999999999863

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

Probab=81.13  E-value=3  Score=26.40  Aligned_cols=31  Identities=16%  Similarity=0.152  Sum_probs=24.9

Q ss_pred             cCCcEEEEcCCCCHHHHHHHHHcCCcceeec
Q 042991           55 REIPVVIMSPEIILVRIDRYLEDGAEDSETC   85 (93)
Q Consensus        55 ~~~pii~lt~~~~~~~~~~~~~~ga~d~l~k   85 (93)
                      ..+|+|+=.+-+.+.+...+++.|+|..|..
T Consensus       174 ~~vPvIvDAGiG~pSdaa~AMElG~daVLvN  204 (247)
T PF05690_consen  174 ADVPVIVDAGIGTPSDAAQAMELGADAVLVN  204 (247)
T ss_dssp             GSSSBEEES---SHHHHHHHHHTT-SEEEES
T ss_pred             cCCcEEEeCCCCCHHHHHHHHHcCCceeehh
Confidence            6999999999999999999999999999875

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

No hit with e-value below 0.005

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	93
3to5_A	134	CHEY homolog; alpha(5)beta(5), chemotaxis, FLIM, p	99.82
3gl9_A	122	Response regulator; beta-sheet, surrounded by alph	99.69
3t6k_A	136	Response regulator receiver; flavodoxin-like, stru	99.65
3rqi_A	184	Response regulator protein; structural genomics, s	99.64
3f6p_A	120	Transcriptional regulatory protein YYCF; unphospho	99.64
2r25_B	133	Osmosensing histidine protein kinase SLN1; alpha5-	99.6
3h1g_A	129	Chemotaxis protein CHEY homolog; sulfate-bound CHE	99.6
1dbw_A	126	Transcriptional regulatory protein FIXJ; doubly wo	99.59
3m6m_D	143	Sensory/regulatory protein RPFC; RPFF, REC, enoyl-	99.59
3kto_A	136	Response regulator receiver protein; PSI-II,struct	99.58
3crn_A	132	Response regulator receiver domain protein, CHEY-;	99.58
2lpm_A	123	Two-component response regulator; transcription re	99.58
2pl1_A	121	Transcriptional regulatory protein PHOP; CHEY-like	99.58
3eod_A	130	Protein HNR; response regulator, phosphoprotein, t	99.57
1srr_A	124	SPO0F, sporulation response regulatory protein; as	99.57
3gt7_A	154	Sensor protein; structural genomics, signal receiv	99.57
3dzd_A	368	Transcriptional regulator (NTRC family); sigma43 a	99.56
3r0j_A	250	Possible two component system response transcript	99.56
3snk_A	135	Response regulator CHEY-like protein; P-loop conta	99.55
3lua_A	140	Response regulator receiver protein; two-component	99.54
3mm4_A	206	Histidine kinase homolog; receiver domain, CKI1, c	99.54
1zgz_A	122	Torcad operon transcriptional regulatory protein;	99.54
2a9o_A	120	Response regulator; essential protein, YYCF/YYCG h	99.54
1tmy_A	120	CHEY protein, TMY; chemotaxis, phosphoryl transfer	99.53
1jbe_A	128	Chemotaxis protein CHEY; signaling protein; 1.08A	99.53
3n0r_A	286	Response regulator; sigma factor, receiver, two-co	99.53
1xhf_A	123	DYE resistance, aerobic respiration control protei	99.53
3hv2_A	153	Response regulator/HD domain protein; PSI-2, NYSGX	99.53
2qzj_A	136	Two-component response regulator; 11017X, PSI-II,	99.53
3jte_A	143	Response regulator receiver protein; structural ge	99.52
3cfy_A	137	Putative LUXO repressor protein; structural genomi	99.52
3hdg_A	137	Uncharacterized protein; two-component sensor acti	99.52
3luf_A	259	Two-component system response regulator/ggdef doma	99.52
3eq2_A	394	Probable two-component response regulator; adaptor	99.52
1p6q_A	129	CHEY2; chemotaxis, signal transduction, response r	99.51
3heb_A	152	Response regulator receiver domain protein (CHEY);	99.51
1mb3_A	124	Cell division response regulator DIVK; signal tran	99.51
3hzh_A	157	Chemotaxis response regulator (CHEY-3); phosphatas	99.51
2ayx_A	254	Sensor kinase protein RCSC; two independent struct	99.51
3hdv_A	136	Response regulator; PSI-II, structural genomics, P	99.51
1yio_A	208	Response regulatory protein; transcription regulat	99.5
4e7p_A	150	Response regulator; DNA binding, cytosol, transcri	99.5
3b2n_A	133	Uncharacterized protein Q99UF4; structural genomic	99.5
1i3c_A	149	Response regulator RCP1; phytochrome, signaling pr	99.5
3kht_A	144	Response regulator; PSI-II, 11023K, structural gen	99.49
1ny5_A	387	Transcriptional regulator (NTRC family); AAA+ ATPa	99.49
3f6c_A	134	Positive transcription regulator EVGA; structural	99.49
3i42_A	127	Response regulator receiver domain protein (CHEY-	99.48
3q9s_A	249	DNA-binding response regulator; DNA binding protei	99.48
1mvo_A	136	PHOP response regulator; phosphate regulon, transc	99.48
1zh2_A	121	KDP operon transcriptional regulatory protein KDPE	99.48
1k68_A	140	Phytochrome response regulator RCPA; phosphorylate	99.48
3grc_A	140	Sensor protein, kinase; protein structure initiati	99.48
1dcf_A	136	ETR1 protein; beta-alpha five sandwich, transferas	99.48
1qkk_A	155	DCTD, C4-dicarboxylate transport transcriptional r	99.48
1w25_A	459	Stalked-cell differentiation controlling protein;	99.47
2jba_A	127	Phosphate regulon transcriptional regulatory PROT;	99.47
1k66_A	149	Phytochrome response regulator RCPB; CHEY homologu	99.46
3ilh_A	146	Two component response regulator; NYSGXRC, PSI-II,	99.46
1kgs_A	225	DRRD, DNA binding response regulator D; DNA-bindin	99.46
2hqr_A	223	Putative transcriptional regulator; phosporylation	99.46
2rjn_A	154	Response regulator receiver:metal-dependent phosph	99.46
1dz3_A	130	Stage 0 sporulation protein A; response regulator,	99.45
2pln_A	137	HP1043, response regulator; signaling protein; 1.8	99.45
2qxy_A	142	Response regulator; regulation of transcription, N	99.45
3c3m_A	138	Response regulator receiver protein; structural ge	99.45
2qr3_A	140	Two-component system response regulator; structura	99.44
3cnb_A	143	DNA-binding response regulator, MERR family; signa	99.44
3h5i_A	140	Response regulator/sensory box protein/ggdef domai	99.44
3lte_A	132	Response regulator; structural genomics, PSI, prot	99.44
1a04_A	215	Nitrate/nitrite response regulator protein NARL; s	99.43
2qvg_A	143	Two component response regulator; NYSGXRC, PSI-2,	99.43
3a10_A	116	Response regulator; phosphoacceptor, signaling pro	99.43
3eul_A	152	Possible nitrate/nitrite response transcriptional	99.43
2zay_A	147	Response regulator receiver protein; structural ge	99.43
1s8n_A	205	Putative antiterminator; RV1626, structural genomi	99.43
3cz5_A	153	Two-component response regulator, LUXR family; str	99.42
3nhm_A	133	Response regulator; protein structure initiative I	99.42
4dad_A	146	Putative pilus assembly-related protein; response	99.41
3kcn_A	151	Adenylate cyclase homolog; SGX, PSI 2, structural	99.41
2oqr_A	230	Sensory transduction protein REGX3; response regul	99.41
3cg0_A	140	Response regulator receiver modulated diguanylate	99.41
3cu5_A	141	Two component transcriptional regulator, ARAC FAM;	99.4
1ys7_A	233	Transcriptional regulatory protein PRRA; response	99.4
2jk1_A	139	HUPR, hydrogenase transcriptional regulatory prote	99.39
2gwr_A	238	DNA-binding response regulator MTRA; two-component	99.38
3cg4_A	142	Response regulator receiver domain protein (CHEY-;	99.37
3n53_A	140	Response regulator receiver modulated diguanylate;	99.37
2qsj_A	154	DNA-binding response regulator, LUXR family; struc	99.36
3kyj_B	145	CHEY6 protein, putative histidine protein kinase;	99.35
3bre_A	358	Probable two-component response regulator; protein	99.35
3c3w_A	225	Two component transcriptional regulatory protein;	99.35
2gkg_A	127	Response regulator homolog; social motility, recei	99.35
3luf_A	259	Two-component system response regulator/ggdef doma	99.34
3eqz_A	135	Response regulator; structural genomics, unknown f	99.32
1p2f_A	220	Response regulator; DRRB, OMPR/PHOB, transcription	99.32
2j48_A	119	Two-component sensor kinase; pseudo-receiver, circ	99.27
1dc7_A	124	NTRC, nitrogen regulation protein; receiver domain	99.26
3t8y_A	164	CHEB, chemotaxis response regulator protein-glutam	99.26
2rdm_A	132	Response regulator receiver protein; structural ge	99.23
2qv0_A	143	Protein MRKE; structural genomics, transcription,	99.22
3sy8_A	400	ROCR; TIM barrel phosphodiesterase-A, transcriptio	99.21
3c97_A	140	Signal transduction histidine kinase; structural g	99.18
1a2o_A	349	CHEB methylesterase; bacterial chemotaxis, adaptat	99.18
3klo_A	225	Transcriptional regulator VPST; REC domain, HTH do	99.15
2vyc_A	755	Biodegradative arginine decarboxylase; pyridoxal p	99.15
1qo0_D	196	AMIR; binding protein, gene regulator, receptor; 2	99.14
2b4a_A	138	BH3024; flavodoxin-like fold, structural genomics,	99.12
3cwo_X	237	Beta/alpha-barrel protein based on 1THF and 1TMY;	97.95
1w25_A	459	Stalked-cell differentiation controlling protein;	97.67
3q7r_A	121	Transcriptional regulatory protein; CHXR, receiver	96.08
3n75_A	715	LDC, lysine decarboxylase, inducible; pyridoxal-5'	95.63
3cwo_X	237	Beta/alpha-barrel protein based on 1THF and 1TMY;	93.06
1wv2_A	265	Thiazole moeity, thiazole biosynthesis protein THI	90.02
3tsm_A	272	IGPS, indole-3-glycerol phosphate synthase; struct	89.17

>3to5_A CHEY homolog; alpha(5)beta(5), chemotaxis, FLIM, phosphorylation, motor AC signaling protein; 1.65A {Vibrio cholerae}

Probab=99.82  E-value=1.8e-19  Score=101.73  Aligned_cols=89  Identities=18%  Similarity=0.192  Sum_probs=75.0

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCcc---------cCCCchHHHhhh-----hcCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEE---------QSANGFDVRTIY-----SREIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~---------~~~~~~d~l~~~-----~~~~pii~lt~~~   66 (93)
                      |||++..+..++.+|+..||+.+..+.+|.+|++.++..++         ++++|++++..+     .+++|||++|+..
T Consensus        18 VDD~~~~r~~l~~~L~~~G~~~v~~a~~g~~al~~~~~~~~DlillD~~MP~mdG~el~~~ir~~~~~~~ipvI~lTa~~   97 (134)
T 3to5_A           18 VDDFSTMRRIVKNLLRDLGFNNTQEADDGLTALPMLKKGDFDFVVTDWNMPGMQGIDLLKNIRADEELKHLPVLMITAEA   97 (134)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCCCEEEESSHHHHHHHHHHHCCSEEEEESCCSSSCHHHHHHHHHHSTTTTTCCEEEEESSC
T ss_pred             EeCCHHHHHHHHHHHHHcCCcEEEEECCHHHHHHHHHhCCCCEEEEcCCCCCCCHHHHHHHHHhCCCCCCCeEEEEECCC
Confidence            68999999999999999998647789999999999875443         245677764332     2789999999999


Q ss_pred             CHHHHHHHHHcCCcceeeccchh
Q 042991           67 ILVRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      +.+...+++++|+++|+.||++.
T Consensus        98 ~~~~~~~~~~~Ga~~yl~KP~~~  120 (134)
T 3to5_A           98 KREQIIEAAQAGVNGYIVKPFTA  120 (134)
T ss_dssp             CHHHHHHHHHTTCCEEEESSCCH
T ss_pred             CHHHHHHHHHCCCCEEEECCCCH
Confidence            99999999999999999999973

>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=99.69  E-value=5.9e-16  Score=85.11  Aligned_cols=88  Identities=22%  Similarity=0.169  Sum_probs=73.6

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhh-----hcCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIY-----SREIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~-----~~~~pii~lt~~~   66 (93)
                      +||++..+..++.+|+..||+ +..+.++.+|++.++...++         +++|++++..+     .+.+|||++|+..
T Consensus         8 vdd~~~~~~~l~~~l~~~g~~-v~~~~~~~~al~~l~~~~~dlvllD~~~p~~~g~~~~~~l~~~~~~~~~pii~~s~~~   86 (122)
T 3gl9_A            8 VDDSAVLRKIVSFNLKKEGYE-VIEAENGQIALEKLSEFTPDLIVLXIMMPVMDGFTVLKKLQEKEEWKRIPVIVLTAKG   86 (122)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCE-EEEESSHHHHHHHHTTBCCSEEEECSCCSSSCHHHHHHHHHTSTTTTTSCEEEEESCC
T ss_pred             EeCCHHHHHHHHHHHHHCCcE-EEEeCCHHHHHHHHHhcCCCEEEEeccCCCCcHHHHHHHHHhcccccCCCEEEEecCC
Confidence            589999999999999999999 99999999999999754432         33566664333     1679999999999


Q ss_pred             CHHHHHHHHHcCCcceeeccchh
Q 042991           67 ILVRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      +.....++++.|+++|+.||++.
T Consensus        87 ~~~~~~~~~~~Ga~~~l~KP~~~  109 (122)
T 3gl9_A           87 GEEDESLALSLGARKVMRKPFSP  109 (122)
T ss_dssp             SHHHHHHHHHTTCSEEEESSCCH
T ss_pred             chHHHHHHHhcChhhhccCCCCH
Confidence            99999999999999999999973

>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=99.65  E-value=2.6e-15  Score=83.89  Aligned_cols=88  Identities=16%  Similarity=0.199  Sum_probs=73.1

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhh-----hcCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIY-----SREIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~-----~~~~pii~lt~~~   66 (93)
                      +||++..+..++.+|+..||. +..+.++.+|++.+....++         +++|++++..+     .+.+|||++|+..
T Consensus        10 vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~~al~~~~~~~~dlvl~D~~lp~~~g~~~~~~lr~~~~~~~~pii~~t~~~   88 (136)
T 3t6k_A           10 VDDDDTVAEMLELVLRGAGYE-VRRAASGEEALQQIYKNLPDALICDVLLPGIDGYTLCKRVRQHPLTKTLPILMLTAQG   88 (136)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCE-EEEESSHHHHHHHHHHSCCSEEEEESCCSSSCHHHHHHHHHHSGGGTTCCEEEEECTT
T ss_pred             EeCCHHHHHHHHHHHHHCCCE-EEEeCCHHHHHHHHHhCCCCEEEEeCCCCCCCHHHHHHHHHcCCCcCCccEEEEecCC
Confidence            589999999999999999999 99999999999998644321         33566653322     2689999999999


Q ss_pred             CHHHHHHHHHcCCcceeeccchh
Q 042991           67 ILVRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      +.....++++.|+++|+.||+..
T Consensus        89 ~~~~~~~~~~~ga~~~l~KP~~~  111 (136)
T 3t6k_A           89 DISAKIAGFEAGANDYLAKPFEP  111 (136)
T ss_dssp             CHHHHHHHHHHTCSEEEETTCCH
T ss_pred             CHHHHHHHHhcCcceEEeCCCCH
Confidence            99999999999999999999973

>3rqi_A Response regulator protein; structural genomics, seattle structural genomics center for infectious disease, ssgcid; HET: PHD CIT; 1.70A {Burkholderia pseudomallei}

Probab=99.64  E-value=2.2e-15  Score=88.17  Aligned_cols=88  Identities=13%  Similarity=0.151  Sum_probs=74.2

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHH---hhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~~~~pii~lt~~~~~   68 (93)
                      |||++..+..+..+|+..||. +..+.++.+|++.+....++         +++|++++   ....+.+|||++|+..+.
T Consensus        13 vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~~al~~~~~~~~dlvl~D~~lp~~~g~~~~~~l~~~~~~~~ii~lt~~~~~   91 (184)
T 3rqi_A           13 IDDNEVFAGTLARGLERRGYA-VRQAHNKDEALKLAGAEKFEFITVXLHLGNDSGLSLIAPLCDLQPDARILVLTGYASI   91 (184)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCE-EEEECSHHHHHHHHTTSCCSEEEECSEETTEESHHHHHHHHHHCTTCEEEEEESSCCH
T ss_pred             EcCCHHHHHHHHHHHHHCCCE-EEEeCCHHHHHHHHhhCCCCEEEEeccCCCccHHHHHHHHHhcCCCCCEEEEeCCCCH
Confidence            589999999999999999999 99999999999999755432         23456653   333388999999999999


Q ss_pred             HHHHHHHHcCCcceeeccchh
Q 042991           69 VRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      ....++++.|+++|+.||+..
T Consensus        92 ~~~~~a~~~Ga~~~l~KP~~~  112 (184)
T 3rqi_A           92 ATAVQAVKDGADNYLAKPANV  112 (184)
T ss_dssp             HHHHHHHHHTCSEEEESSCCH
T ss_pred             HHHHHHHHhCHHHheeCCCCH
Confidence            999999999999999999873

>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=99.64  E-value=2.4e-15  Score=82.38  Aligned_cols=88  Identities=17%  Similarity=0.226  Sum_probs=71.7

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhh--hcCCcEEEEcCCCCHH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIY--SREIPVVIMSPEIILV   69 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~--~~~~pii~lt~~~~~~   69 (93)
                      +||++..+..++.+|++.||. +..+.++.+|++.++...++         +.+|++++..+  ...+|+|++|+..+..
T Consensus         8 vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~~al~~~~~~~~dlii~D~~~p~~~g~~~~~~lr~~~~~~ii~~t~~~~~~   86 (120)
T 3f6p_A            8 VDDEKPIADILEFNLRKEGYE-VHCAHDGNEAVEMVEELQPDLILLDIMLPNKDGVEVCREVRKKYDMPIIMLTAKDSEI   86 (120)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCE-EEEESSHHHHHHHHHTTCCSEEEEETTSTTTHHHHHHHHHHTTCCSCEEEEEESSCHH
T ss_pred             EECCHHHHHHHHHHHHhCCEE-EEEeCCHHHHHHHHhhCCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCEEEEECCCChH
Confidence            589999999999999999999 99999999999998654432         22344443222  2678999999999999


Q ss_pred             HHHHHHHcCCcceeeccchh
Q 042991           70 RIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        70 ~~~~~~~~ga~d~l~kP~~~   89 (93)
                      ...++++.|+++|+.||++.
T Consensus        87 ~~~~~~~~ga~~~l~KP~~~  106 (120)
T 3f6p_A           87 DKVIGLEIGADDYVTKPFST  106 (120)
T ss_dssp             HHHHHHHTTCCEEEEESCCH
T ss_pred             HHHHHHhCCcceeEcCCCCH
Confidence            88999999999999999973

>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=99.60  E-value=2.2e-14  Score=79.80  Aligned_cols=88  Identities=18%  Similarity=0.317  Sum_probs=70.8

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhcc-----Cccc---------CCCchHHHhhh----hcCCcEEEE
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGL-----DEEQ---------SANGFDVRTIY----SREIPVVIM   62 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~-----~~~~---------~~~~~d~l~~~----~~~~pii~l   62 (93)
                      |||++..+..++.+|+..|+..+..+.++.+|++.+..     ..++         +++|++++..+    .+.+|||++
T Consensus         8 vdD~~~~~~~l~~~L~~~g~~~v~~~~~~~~al~~~~~~~~~~~~~dlvllD~~mp~~~G~~~~~~lr~~~~~~~~ii~l   87 (133)
T 2r25_B            8 VEDNHVNQEVIKRMLNLEGIENIELACDGQEAFDKVKELTSKGENYNMIFMDVQMPKVDGLLSTKMIRRDLGYTSPIVAL   87 (133)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCCCEEEESSHHHHHHHHHHHHHHTCCCSEEEECSCCSSSCHHHHHHHHHHHSCCCSCEEEE
T ss_pred             EcCCHHHHHHHHHHHHHcCCceEEEECCHHHHHHHHHHHHhcCCCCCEEEEeCCCCCCChHHHHHHHHhhcCCCCCEEEE
Confidence            58999999999999998887438889999999998854     2221         33566653322    257899999


Q ss_pred             cCCCCHHHHHHHHHcCCcceeeccch
Q 042991           63 SPEIILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        63 t~~~~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      |+..+.....++++.|+++|+.||++
T Consensus        88 t~~~~~~~~~~~~~~ga~~~l~KP~~  113 (133)
T 2r25_B           88 TAFADDSNIKECLESGMNGFLSKPIK  113 (133)
T ss_dssp             ESCCSHHHHHHHHHTTCSEEEESSCC
T ss_pred             ECCCCHHHHHHHHHcCCCEEEeCCCC
Confidence            99999999999999999999999986

>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=99.60  E-value=2.2e-14  Score=79.33  Aligned_cols=89  Identities=20%  Similarity=0.275  Sum_probs=71.7

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccC-cc---------cCCCchHHHhhhh-----cCCcEEEEcCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLD-EE---------QSANGFDVRTIYS-----REIPVVIMSPE   65 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~-~~---------~~~~~~d~l~~~~-----~~~pii~lt~~   65 (93)
                      +||++..+..++.+|++.||..+..+.++.+|+..+... .+         ++++|++++..+.     +.+|||++|+.
T Consensus        11 vdd~~~~~~~l~~~L~~~g~~~v~~~~~~~~a~~~~~~~~~~dlvi~D~~~p~~~g~~~~~~lr~~~~~~~~pii~~s~~   90 (129)
T 3h1g_A           11 VDDSSTMRRIIKNTLSRLGYEDVLEAEHGVEAWEKLDANADTKVLITDWNMPEMNGLDLVKKVRSDSRFKEIPIIMITAE   90 (129)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCCCEEEESSHHHHHHHHHHCTTCCEEEECSCCSSSCHHHHHHHHHTSTTCTTCCEEEEESC
T ss_pred             EeCCHHHHHHHHHHHHHcCCcEEEEeCCHHHHHHHHHhCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCCCeEEEEeCC
Confidence            589999999999999999985488999999999887533 22         1335666533221     67899999999


Q ss_pred             CCHHHHHHHHHcCCcceeeccchh
Q 042991           66 IILVRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        66 ~~~~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      .+.....++++.|+++|+.||+..
T Consensus        91 ~~~~~~~~~~~~g~~~~l~KP~~~  114 (129)
T 3h1g_A           91 GGKAEVITALKAGVNNYIVKPFTP  114 (129)
T ss_dssp             CSHHHHHHHHHHTCCEEEESCCCH
T ss_pred             CChHHHHHHHHcCccEEEeCCCCH
Confidence            999999999999999999999973

>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=99.59  E-value=2.5e-14  Score=78.61  Aligned_cols=88  Identities=16%  Similarity=0.100  Sum_probs=72.5

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHH---hhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~~~~pii~lt~~~~~   68 (93)
                      +||++..+..++.+|+..||. +..+.++.++++.+....++         +.+|++++   ....+.+|+|++|+..+.
T Consensus         9 vdd~~~~~~~l~~~l~~~~~~-v~~~~~~~~~~~~~~~~~~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~ii~~s~~~~~   87 (126)
T 1dbw_A            9 VDDEEPVRKSLAFMLTMNGFA-VKMHQSAEAFLAFAPDVRNGVLVTDLRMPDMSGVELLRNLGDLKINIPSIVITGHGDV   87 (126)
T ss_dssp             EESSHHHHHHHHHHHHHTTCE-EEEESCHHHHHHHGGGCCSEEEEEECCSTTSCHHHHHHHHHHTTCCCCEEEEECTTCH
T ss_pred             EcCCHHHHHHHHHHHHhCCcE-EEEeCCHHHHHHHHhcCCCCEEEEECCCCCCCHHHHHHHHHhcCCCCCEEEEECCCCH
Confidence            578999999999999988999 99999999999988644321         23556653   333378999999999999


Q ss_pred             HHHHHHHHcCCcceeeccchh
Q 042991           69 VRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      ....++++.|+++|+.||++.
T Consensus        88 ~~~~~~~~~ga~~~l~Kp~~~  108 (126)
T 1dbw_A           88 PMAVEAMKAGAVDFIEKPFED  108 (126)
T ss_dssp             HHHHHHHHTTCSEEEESSCCH
T ss_pred             HHHHHHHHhCHHHheeCCCCH
Confidence            899999999999999999863

>3m6m_D Sensory/regulatory protein RPFC; RPFF, REC, enoyl-COA hydratase, lyase-transferase COMP; 2.50A {Xanthomonas campestris PV}

Probab=99.59  E-value=2.5e-14  Score=80.52  Aligned_cols=87  Identities=22%  Similarity=0.345  Sum_probs=70.1

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhhh-------cCCcEEEEcC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIYS-------REIPVVIMSP   64 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~~-------~~~pii~lt~   64 (93)
                      +||++..+..++.+|++.||. +..+.++++|++.+....++         +++|++++..+.       +.+|+|++|+
T Consensus        20 vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~~al~~~~~~~~dlvl~D~~mp~~~g~~~~~~lr~~~~~~~~~~pii~~s~   98 (143)
T 3m6m_D           20 ADDHEANRMVLQRLLEKAGHK-VLCVNGAEQVLDAMAEEDYDAVIVDLHMPGMNGLDMLKQLRVMQASGMRYTPVVVLSA   98 (143)
T ss_dssp             ECSSHHHHHHHHHHHHC--CE-EEEESSHHHHHHHHHHSCCSEEEEESCCSSSCHHHHHHHHHHHHHTTCCCCCEEEEES
T ss_pred             EeCCHHHHHHHHHHHHHcCCe-EEEeCCHHHHHHHHhcCCCCEEEEeCCCCCCCHHHHHHHHHhchhccCCCCeEEEEeC
Confidence            589999999999999999999 99999999999988644321         345666533221       5689999999


Q ss_pred             CCCHHHHHHHHHcCCcceeeccch
Q 042991           65 EIILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        65 ~~~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      ..+.....++++.|+++|+.||+.
T Consensus        99 ~~~~~~~~~~~~~Ga~~~l~KP~~  122 (143)
T 3m6m_D           99 DVTPEAIRACEQAGARAFLAKPVV  122 (143)
T ss_dssp             CCCHHHHHHHHHTTCSEEEESSCC
T ss_pred             CCCHHHHHHHHHcChhheeeCCCC
Confidence            999999999999999999999997

>3kto_A Response regulator receiver protein; PSI-II,structural genomics, protein structure initiative; 1.98A {Pseudoalteromonas atlantica T6C} SCOP: c.23.1.0

Probab=99.58  E-value=1.1e-14  Score=81.23  Aligned_cols=88  Identities=14%  Similarity=0.173  Sum_probs=72.6

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------C--CCchHHH---hhhhcCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------S--ANGFDVR---TIYSREIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~--~~~~d~l---~~~~~~~pii~lt~~~   66 (93)
                      +||++..+..++.+|+..||+ +..+.++.+|++.++...++         +  ..|++++   +...+.+|||++|+..
T Consensus        12 vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~~a~~~l~~~~~dlvi~D~~l~~~~~~g~~~~~~l~~~~~~~~ii~~s~~~   90 (136)
T 3kto_A           12 VDHQKDARAALSKLLSPLDVT-IQCFASAESFMRQQISDDAIGMIIEAHLEDKKDSGIELLETLVKRGFHLPTIVMASSS   90 (136)
T ss_dssp             ECSCHHHHHHHHHHHTTSSSE-EEEESSHHHHTTSCCCTTEEEEEEETTGGGBTTHHHHHHHHHHHTTCCCCEEEEESSC
T ss_pred             EcCCHHHHHHHHHHHHHCCcE-EEEeCCHHHHHHHHhccCCCEEEEeCcCCCCCccHHHHHHHHHhCCCCCCEEEEEcCC
Confidence            589999999999999999999 99999999999988654431         2  3344443   3333789999999999


Q ss_pred             CHHHHHHHHHcCCcceeeccchh
Q 042991           67 ILVRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      +.....++++.|+++|+.||+..
T Consensus        91 ~~~~~~~~~~~ga~~~l~KP~~~  113 (136)
T 3kto_A           91 DIPTAVRAMRASAADFIEKPFIE  113 (136)
T ss_dssp             CHHHHHHHHHTTCSEEEESSBCH
T ss_pred             CHHHHHHHHHcChHHheeCCCCH
Confidence            99999999999999999999863

>3crn_A Response regulator receiver domain protein, CHEY-; structural genomics, signal regulator receiver domain; HET: PHD; 1.58A {Methanospirillum hungatei jf-1}

Probab=99.58  E-value=3e-14  Score=79.06  Aligned_cols=87  Identities=9%  Similarity=0.040  Sum_probs=72.0

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHh---hhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRT---IYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~---~~~~~~pii~lt~~~~~   68 (93)
                      +||++..+..++.+|+..||. +..+.++.++++.+....++         +++|++++.   ...+.+|+|++|+..+.
T Consensus         9 vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~~al~~~~~~~~dlvl~D~~l~~~~g~~~~~~l~~~~~~~~ii~~s~~~~~   87 (132)
T 3crn_A            9 VDDDTAILDSTKQILEFEGYE-VEIAATAGEGLAKIENEFFNLALFXIKLPDMEGTELLEKAHKLRPGMKKIMVTGYASL   87 (132)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCE-EEEESSHHHHHHHHHHSCCSEEEECSBCSSSBHHHHHHHHHHHCTTSEEEEEESCCCH
T ss_pred             EeCCHHHHHHHHHHHHHCCce-EEEeCCHHHHHHHHhcCCCCEEEEecCCCCCchHHHHHHHHhhCCCCcEEEEeccccH
Confidence            589999999999999988999 99999999999988644321         234565533   33378999999999999


Q ss_pred             HHHHHHHHcCCcceeeccch
Q 042991           69 VRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~   88 (93)
                      ....++++.|+++|+.||++
T Consensus        88 ~~~~~~~~~ga~~~l~KP~~  107 (132)
T 3crn_A           88 ENSVFSLNAGADAYIMKPVN  107 (132)
T ss_dssp             HHHHHHHHTTCSEEEESSCC
T ss_pred             HHHHHHHhccchhhccCCCC
Confidence            89899999999999999986

>2lpm_A Two-component response regulator; transcription regulator; NMR {Sinorhizobium meliloti}

Probab=99.58  E-value=1.7e-16  Score=88.36  Aligned_cols=85  Identities=13%  Similarity=0.041  Sum_probs=67.1

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceE-EeCCHHHHHHHhccCccc---------CCCchHHHhhhh-cCCcEEEEcCCCCHH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLY-CSCSGRRALQFLGLDEEQ---------SANGFDVRTIYS-REIPVVIMSPEIILV   69 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~-~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~~-~~~pii~lt~~~~~~   69 (93)
                      |||++..+..++.+|+..||+ +. .+.|+++|++.++..+++         +++|++++..+. .++|||++|++.+..
T Consensus        14 VdD~~~~~~~l~~~L~~~G~~-v~~~a~~g~eAl~~~~~~~~DlvllDi~mP~~~G~el~~~lr~~~ipvI~lTa~~~~~   92 (123)
T 2lpm_A           14 VEDESMIAMLIEDTLCELGHE-VAATASRMQEALDIARKGQFDIAIIDVNLDGEPSYPVADILAERNVPFIFATGYGSKG   92 (123)
T ss_dssp             ESSSTTTSHHHHHHHHHHCCC-CCBCSCCHHHHHHHHHHCCSSEEEECSSSSSCCSHHHHHHHHHTCCSSCCBCTTCTTS
T ss_pred             EeCCHHHHHHHHHHHHHCCCE-EEEEECCHHHHHHHHHhCCCCEEEEecCCCCCCHHHHHHHHHcCCCCEEEEecCccHH
Confidence            689999999999999999999 64 789999999999755432         346666633322 789999999987654


Q ss_pred             HHHHHHHcCCcceeeccchh
Q 042991           70 RIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        70 ~~~~~~~~ga~d~l~kP~~~   89 (93)
                      .   +.++|+.+||.||+..
T Consensus        93 ~---~~~~g~~~yl~KP~~~  109 (123)
T 2lpm_A           93 L---DTRYSNIPLLTKPFLD  109 (123)
T ss_dssp             C---CSSSCSCSCBCSSSSH
T ss_pred             H---HHhCCCCcEEECCCCH
Confidence            3   3468999999999973

>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=99.58  E-value=4.8e-14  Score=76.76  Aligned_cols=88  Identities=13%  Similarity=0.161  Sum_probs=72.1

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHH---hhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~~~~pii~lt~~~~~   68 (93)
                      +||++..+..++..|+..||. +..+.++.+|+..+....++         +.+|++++   ....+.+|+|++|+..+.
T Consensus         6 vdd~~~~~~~l~~~l~~~g~~-v~~~~~~~~a~~~~~~~~~dlil~D~~l~~~~g~~~~~~l~~~~~~~~ii~~s~~~~~   84 (121)
T 2pl1_A            6 VEDNALLRHHLKVQIQDAGHQ-VDDAEDAKEADYYLNEHIPDIAIVDLGLPDEDGLSLIRRWRSNDVSLPILVLTARESW   84 (121)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCE-EEEESSHHHHHHHHHHSCCSEEEECSCCSSSCHHHHHHHHHHTTCCSCEEEEESCCCH
T ss_pred             EeCcHHHHHHHHHHHhhcCCE-EEEeCCHHHHHHHHhccCCCEEEEecCCCCCCHHHHHHHHHhcCCCCCEEEEecCCCH
Confidence            588999999999999999999 99999999999988644321         23455553   333378999999999999


Q ss_pred             HHHHHHHHcCCcceeeccchh
Q 042991           69 VRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      ....++++.|+++|+.||++.
T Consensus        85 ~~~~~~~~~g~~~~l~kp~~~  105 (121)
T 2pl1_A           85 QDKVEVLSAGADDYVTKPFHI  105 (121)
T ss_dssp             HHHHHHHHTTCSEEEESSCCH
T ss_pred             HHHHHHHHcCccceEECCCCH
Confidence            888999999999999999863

>3eod_A Protein HNR; response regulator, phosphoprotein, two-component regulatory system, signaling protein; 1.75A {Escherichia coli K12}

Probab=99.57  E-value=5.3e-14  Score=77.62  Aligned_cols=86  Identities=21%  Similarity=0.271  Sum_probs=70.9

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHH---hhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~~~~pii~lt~~~~~   68 (93)
                      +||++..+..++.+|+..||. +..+.++.+|++.++...++         +..|++++   +...+.+|+|++|+..+.
T Consensus        13 vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~~a~~~l~~~~~dlvi~d~~l~~~~g~~~~~~l~~~~~~~~ii~~t~~~~~   91 (130)
T 3eod_A           13 VEDEQVFRSLLDSWFSSLGAT-TVLAADGVDALELLGGFTPDLMICDIAMPRMNGLKLLEHIRNRGDQTPVLVISATENM   91 (130)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCE-EEEESCHHHHHHHHTTCCCSEEEECCC-----CHHHHHHHHHTTCCCCEEEEECCCCH
T ss_pred             EeCCHHHHHHHHHHHHhCCce-EEEeCCHHHHHHHHhcCCCCEEEEecCCCCCCHHHHHHHHHhcCCCCCEEEEEcCCCH
Confidence            588999999999999999999 99999999999998655432         22355543   333378999999999999


Q ss_pred             HHHHHHHHcCCcceeeccc
Q 042991           69 VRIDRYLEDGAEDSETCQM   87 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~   87 (93)
                      ....++++.|+++|+.||+
T Consensus        92 ~~~~~~~~~g~~~~l~KP~  110 (130)
T 3eod_A           92 ADIAKALRLGVEDVLLKPV  110 (130)
T ss_dssp             HHHHHHHHHCCSEEEESCC
T ss_pred             HHHHHHHHcCCCEEEeCCC
Confidence            9989999999999999998

>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=99.57  E-value=3.5e-14  Score=77.81  Aligned_cols=88  Identities=17%  Similarity=0.202  Sum_probs=72.1

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHH---hhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~~~~pii~lt~~~~~   68 (93)
                      +||++..+..++.+|+..||. +..+.++.+|+..+....++         +.+|++++   ....+.+|+|++|+..+.
T Consensus         9 vdd~~~~~~~l~~~l~~~~~~-v~~~~~~~~a~~~~~~~~~dlvl~D~~l~~~~g~~~~~~l~~~~~~~~ii~~s~~~~~   87 (124)
T 1srr_A            9 VDDQSGIRILLNEVFNKEGYQ-TFQAANGLQALDIVTKERPDLVLLDMKIPGMDGIEILKRMKVIDENIRVIIMTAYGEL   87 (124)
T ss_dssp             ECSCHHHHHHHHHHHHTTTCE-EEEESSHHHHHHHHHHHCCSEEEEESCCTTCCHHHHHHHHHHHCTTCEEEEEESSCCH
T ss_pred             EeCCHHHHHHHHHHHHHCCcE-EEEeCCHHHHHHHHhccCCCEEEEecCCCCCCHHHHHHHHHHhCCCCCEEEEEccCch
Confidence            589999999999999988999 99999999999988643321         23455553   333378999999999998


Q ss_pred             HHHHHHHHcCCcceeeccchh
Q 042991           69 VRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      ....++++.|+++|+.||++.
T Consensus        88 ~~~~~~~~~g~~~~l~KP~~~  108 (124)
T 1srr_A           88 DMIQESKELGALTHFAKPFDI  108 (124)
T ss_dssp             HHHHHHHHHTCCCEEESSCCH
T ss_pred             HHHHHHHhcChHhhccCCCCH
Confidence            888899999999999999873

>3gt7_A Sensor protein; structural genomics, signal receiver domain, kinase, PSI-2, protein structure initiative; 2.30A {Syntrophus aciditrophicus SB}

Probab=99.57  E-value=6.4e-14  Score=79.64  Aligned_cols=88  Identities=24%  Similarity=0.294  Sum_probs=73.1

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhh-----hcCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIY-----SREIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~-----~~~~pii~lt~~~   66 (93)
                      +||++..+..++.+|+..||. +..+.++.+|++.+....++         +..|++++..+     .+.+|||++|+..
T Consensus        13 vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~~al~~l~~~~~dlii~D~~l~~~~g~~~~~~lr~~~~~~~~pii~~s~~~   91 (154)
T 3gt7_A           13 VEDSPTQAEHLKHILEETGYQ-TEHVRNGREAVRFLSLTRPDLIISDVLMPEMDGYALCRWLKGQPDLRTIPVILLTILS   91 (154)
T ss_dssp             ECSCHHHHHHHHHHHHTTTCE-EEEESSHHHHHHHHTTCCCSEEEEESCCSSSCHHHHHHHHHHSTTTTTSCEEEEECCC
T ss_pred             EeCCHHHHHHHHHHHHHCCCE-EEEeCCHHHHHHHHHhCCCCEEEEeCCCCCCCHHHHHHHHHhCCCcCCCCEEEEECCC
Confidence            589999999999999999999 99999999999998754432         23455553322     1688999999999


Q ss_pred             CHHHHHHHHHcCCcceeeccchh
Q 042991           67 ILVRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      +.....++++.|+++|+.||+..
T Consensus        92 ~~~~~~~~~~~g~~~~l~KP~~~  114 (154)
T 3gt7_A           92 DPRDVVRSLECGADDFITKPCKD  114 (154)
T ss_dssp             SHHHHHHHHHHCCSEEEESSCCH
T ss_pred             ChHHHHHHHHCCCCEEEeCCCCH
Confidence            99999999999999999999873

>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=99.56  E-value=1.3e-14  Score=93.34  Aligned_cols=88  Identities=10%  Similarity=-0.015  Sum_probs=74.0

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHH---hhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~~~~pii~lt~~~~~   68 (93)
                      |||++..+..++.+|+..||. +..+.++.+|++.+....++         +++|++++   ....+.+|||++|++.+.
T Consensus         6 VDDd~~~~~~l~~~L~~~g~~-v~~a~~~~eal~~l~~~~~DlvllDi~mP~~dG~ell~~lr~~~~~~pvI~lT~~~~~   84 (368)
T 3dzd_A            6 VDDEESITSSLSAILEEEGYH-PDTAKTLREAEKKIKELFFPVIVLDVWMPDGDGVNFIDFIKENSPDSVVIVITGHGSV   84 (368)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCE-EEEESSHHHHHHHHHHBCCSEEEEESEETTEETTTHHHHHHHHCTTCEEEEEECSSCC
T ss_pred             EeCCHHHHHHHHHHHHHcCCE-EEEECCHHHHHHHHHhCCCCEEEEeCCCCCCCHHHHHHHHHhhCCCCeEEEEeCCCCH
Confidence            689999999999999999999 99999999999998644432         23455553   333488999999999999


Q ss_pred             HHHHHHHHcCCcceeeccchh
Q 042991           69 VRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      +...++++.||++|+.||++.
T Consensus        85 ~~~~~a~~~Ga~~yl~KP~~~  105 (368)
T 3dzd_A           85 DTAVKAIKKGAYEFLEKPFSV  105 (368)
T ss_dssp             HHHHHHHHHTCCEEEESSCCH
T ss_pred             HHHHHHHhcCcceEEeCCCCH
Confidence            999999999999999999973

>3r0j_A Possible two component system response transcript positive regulator PHOP; beta-alpha fold, winged helix-turn-helix; 2.50A {Mycobacterium tuberculosis}

Probab=99.56  E-value=3.1e-14  Score=86.74  Aligned_cols=88  Identities=17%  Similarity=0.167  Sum_probs=73.5

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHH---hhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~~~~pii~lt~~~~~   68 (93)
                      |||++..+..++.+|+..||+ +..+.++.+|++.+....++         +++|++++   +...+.+|||++|+..+.
T Consensus        29 vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~~al~~~~~~~~dlvllD~~lp~~~g~~~~~~lr~~~~~~~ii~lt~~~~~  107 (250)
T 3r0j_A           29 VDDEANIVELLSVSLKFQGFE-VYTATNGAQALDRARETRPDAVILDVXMPGMDGFGVLRRLRADGIDAPALFLTARDSL  107 (250)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCE-EEEESSHHHHHHHHHHHCCSEEEEESCCSSSCHHHHHHHHHHTTCCCCEEEEECSTTH
T ss_pred             EECCHHHHHHHHHHHHHCCCE-EEEECCHHHHHHHHHhCCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCCEEEEECCCCH
Confidence            589999999999999999999 99999999999998644321         33566653   333378999999999999


Q ss_pred             HHHHHHHHcCCcceeeccchh
Q 042991           69 VRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      ....++++.||++|+.||++.
T Consensus       108 ~~~~~~~~~Ga~~yl~Kp~~~  128 (250)
T 3r0j_A          108 QDKIAGLTLGGDDYVTKPFSL  128 (250)
T ss_dssp             HHHHHHHTSTTCEEEESSCCH
T ss_pred             HHHHHHHHcCCcEEEeCCCCH
Confidence            999999999999999999973

>3snk_A Response regulator CHEY-like protein; P-loop containing nucleoside triphosphate hydrolases, struct genomics; 2.02A {Mesorhizobium loti}

Probab=99.55  E-value=1.1e-14  Score=81.11  Aligned_cols=88  Identities=9%  Similarity=-0.062  Sum_probs=72.2

Q ss_pred             CCCcHHHHHHHHHHHhhcC-CCceEEeCCHHHHHHHhccCccc---------CCCchHH---HhhhhcCCcEEEEcCCCC
Q 042991            1 LNDSFVDRKVIERLLTISS-SRDLYCSCSGRRALQFLGLDEEQ---------SANGFDV---RTIYSREIPVVIMSPEII   67 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~-~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~---l~~~~~~~pii~lt~~~~   67 (93)
                      +||++..+..++.+|+..| |+ +..+.++.+|++.+....++         +..|+++   ++...+.+|+|++|+..+
T Consensus        20 vdd~~~~~~~l~~~L~~~g~~~-v~~~~~~~~a~~~l~~~~~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~ii~~s~~~~   98 (135)
T 3snk_A           20 FSSDPNFKRDVATRLDALAIYD-VRVSETDDFLKGPPADTRPGIVILDLGGGDLLGKPGIVEARALWATVPLIAVSDELT   98 (135)
T ss_dssp             ECSCHHHHHHHHHHHHHTSSEE-EEEECGGGGGGCCCTTCCCSEEEEEEETTGGGGSTTHHHHHGGGTTCCEEEEESCCC
T ss_pred             EcCCHHHHHHHHHHHhhcCCeE-EEEeccHHHHHHHHhccCCCEEEEeCCCCCchHHHHHHHHHhhCCCCcEEEEeCCCC
Confidence            5899999999999999999 99 99999999999888644432         1234444   333337899999999999


Q ss_pred             HHHHHHHHHcCCcceeeccchh
Q 042991           68 LVRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        68 ~~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      .....++++.|+++|+.||+..
T Consensus        99 ~~~~~~~~~~g~~~~l~KP~~~  120 (135)
T 3snk_A           99 SEQTRVLVRMNASDWLHKPLDG  120 (135)
T ss_dssp             HHHHHHHHHTTCSEEEESSCCH
T ss_pred             HHHHHHHHHcCcHhhccCCCCH
Confidence            9999999999999999999873

>3lua_A Response regulator receiver protein; two-component signal transduction system, histidine kinase, phosphorelay, receiver domain, nysgxrc; 2.40A {Clostridium thermocellum}

Probab=99.54  E-value=5.3e-14  Score=78.59  Aligned_cols=87  Identities=10%  Similarity=-0.032  Sum_probs=72.6

Q ss_pred             CCCcHHHHHHHHHHHhh-cCCCceEEeCCHHHHHHHhcc-Cccc------CCC----chHH---Hhh--hhcCCcEEEEc
Q 042991            1 LNDSFVDRKVIERLLTI-SSSRDLYCSCSGRRALQFLGL-DEEQ------SAN----GFDV---RTI--YSREIPVVIMS   63 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~-~~~~~v~~~~~~~~a~~~~~~-~~~~------~~~----~~d~---l~~--~~~~~pii~lt   63 (93)
                      +||++..+..++.+|+. .||+ +..+.++.+|++.+.. ..++      .++    |+++   ++.  ..+.+|||++|
T Consensus        10 vdd~~~~~~~l~~~L~~~~~~~-v~~~~~~~~a~~~l~~~~~~dlvi~D~~l~~~~~g~~~~~~l~~~~~~~~~~ii~ls   88 (140)
T 3lua_A           10 IDYFEYEREKTKIIFDNIGEYD-FIEVENLKKFYSIFKDLDSITLIIMDIAFPVEKEGLEVLSAIRNNSRTANTPVIIAT   88 (140)
T ss_dssp             ECSCHHHHHHHHHHHHHHCCCE-EEEECSHHHHHTTTTTCCCCSEEEECSCSSSHHHHHHHHHHHHHSGGGTTCCEEEEE
T ss_pred             EeCCHHHHHHHHHHHHhccCcc-EEEECCHHHHHHHHhcCCCCcEEEEeCCCCCCCcHHHHHHHHHhCcccCCCCEEEEe
Confidence            58999999999999998 8999 9999999999999876 4432      233    3343   333  34899999999


Q ss_pred             CCCCHHHHHHHHHcCCcceeeccch
Q 042991           64 PEIILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        64 ~~~~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      +..+.....++++.|+++|+.||+.
T Consensus        89 ~~~~~~~~~~~~~~g~~~~l~KP~~  113 (140)
T 3lua_A           89 KSDNPGYRHAALKFKVSDYILKPYP  113 (140)
T ss_dssp             SCCCHHHHHHHHHSCCSEEEESSCC
T ss_pred             CCCCHHHHHHHHHcCCCEEEECCCC
Confidence            9999999999999999999999986

>3mm4_A Histidine kinase homolog; receiver domain, CKI1, cytokinin signaling, ROS fold, CHEY-like, transferase; 2.00A {Arabidopsis thaliana} PDB: 3mmn_A

Probab=99.54  E-value=7.5e-14  Score=83.12  Aligned_cols=89  Identities=17%  Similarity=0.222  Sum_probs=72.3

Q ss_pred             CCCcHHHHHHHHHHHhhcCC-CceEEeCCHHHHHHHhccC-------------ccc---------CCCchHHH---hhh-
Q 042991            1 LNDSFVDRKVIERLLTISSS-RDLYCSCSGRRALQFLGLD-------------EEQ---------SANGFDVR---TIY-   53 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~-~~v~~~~~~~~a~~~~~~~-------------~~~---------~~~~~d~l---~~~-   53 (93)
                      |||++..+..+..+|+..|| . +..+.++.+|++.+...             .++         +++|++++   +.. 
T Consensus        67 VdDd~~~~~~l~~~L~~~g~~~-v~~a~~~~eal~~l~~~~~~~~~~~~~~~~~~dlillD~~lp~~~G~el~~~lr~~~  145 (206)
T 3mm4_A           67 VDDNFISRKVATGKLKKMGVSE-VEQCDSGKEALRLVTEGLTQREEQGSVDKLPFDYIFMDCQMPEMDGYEATREIRKVE  145 (206)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCSE-EEEESSHHHHHHHHHHHHHHHHHHTCSSCCSCSEEEEESCCSSSCHHHHHHHHHHHH
T ss_pred             EeCCHHHHHHHHHHHHHcCCCe-eeeeCCHHHHHHHHHhhcccccccccccCCCCCEEEEcCCCCCCCHHHHHHHHHhhh
Confidence            58999999999999999998 7 99999999999998642             221         33566653   332 


Q ss_pred             ---hcCCcEEEEcCCC-CHHHHHHHHHcCCcceeeccchhhh
Q 042991           54 ---SREIPVVIMSPEI-ILVRIDRYLEDGAEDSETCQMWARL   91 (93)
Q Consensus        54 ---~~~~pii~lt~~~-~~~~~~~~~~~ga~d~l~kP~~~~~   91 (93)
                         .+.+|||++|+.. +.....++++.|+++||.||+. .|
T Consensus       146 ~~~~~~~piI~ls~~~~~~~~~~~~~~~Ga~~~l~KP~~-~L  186 (206)
T 3mm4_A          146 KSYGVRTPIIAVSGHDPGSEEARETIQAGMDAFLDKSLN-QL  186 (206)
T ss_dssp             HTTTCCCCEEEEESSCCCHHHHHHHHHHTCSEEEETTCT-TH
T ss_pred             hhcCCCCcEEEEECCCCcHHHHHHHHhCCCCEEEcCcHH-HH
Confidence               3789999999988 7788888999999999999998 44

>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=99.54  E-value=1.3e-13  Score=75.18  Aligned_cols=88  Identities=15%  Similarity=0.147  Sum_probs=71.6

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhh--hcCCcEEEEcCCCCHH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIY--SREIPVVIMSPEIILV   69 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~--~~~~pii~lt~~~~~~   69 (93)
                      +||++..+..++.+|+..||. +..+.++.++++.+....++         +.+|++++..+  .+.+|+|++|+..+..
T Consensus         8 vdd~~~~~~~l~~~L~~~~~~-v~~~~~~~~~~~~~~~~~~dlvi~d~~l~~~~g~~~~~~l~~~~~~~ii~~s~~~~~~   86 (122)
T 1zgz_A            8 VEDEPVTQARLQSYFTQEGYT-VSVTASGAGLREIMQNQSVDLILLDINLPDENGLMLTRALRERSTVGIILVTGRSDRI   86 (122)
T ss_dssp             ECSSHHHHHHHHHHHHHTTCE-EEEESSHHHHHHHHHHSCCSEEEEESCCSSSCHHHHHHHHHTTCCCEEEEEESSCCHH
T ss_pred             EECCHHHHHHHHHHHHHCCCe-EEEecCHHHHHHHHhcCCCCEEEEeCCCCCCChHHHHHHHHhcCCCCEEEEECCCChh
Confidence            588999999999999988999 99999999999888643321         23455553322  3789999999999998


Q ss_pred             HHHHHHHcCCcceeeccchh
Q 042991           70 RIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        70 ~~~~~~~~ga~d~l~kP~~~   89 (93)
                      ...++++.|+++|+.||++.
T Consensus        87 ~~~~~~~~ga~~~l~Kp~~~  106 (122)
T 1zgz_A           87 DRIVGLEMGADDYVTKPLEL  106 (122)
T ss_dssp             HHHHHHHHTCSEEEESSCCH
T ss_pred             hHHHHHHhCHHHHccCCCCH
Confidence            88899999999999999863

>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=99.54  E-value=1.2e-13  Score=74.98  Aligned_cols=88  Identities=19%  Similarity=0.238  Sum_probs=71.4

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhh--hcCCcEEEEcCCCCHH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIY--SREIPVVIMSPEIILV   69 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~--~~~~pii~lt~~~~~~   69 (93)
                      +||++..+..++..|+..||. +..+.++.++++.+....++         +..|++++..+  .+.+|+|++|+..+..
T Consensus         7 vdd~~~~~~~l~~~l~~~~~~-v~~~~~~~~a~~~~~~~~~dlvl~D~~l~~~~g~~~~~~l~~~~~~~ii~~s~~~~~~   85 (120)
T 2a9o_A            7 VDDEKPISDIIKFNMTKEGYE-VVTAFNGREALEQFEAEQPDIIILDLMLPEIDGLEVAKTIRKTSSVPILMLSAKDSEF   85 (120)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCE-EEEESSHHHHHHHHHHHCCSEEEECSSCSSSCHHHHHHHHHHHCCCCEEEEESCCSHH
T ss_pred             EcCCHHHHHHHHHHHHhcCcE-EEEecCHHHHHHHHHhCCCCEEEEeccCCCCCHHHHHHHHHhCCCCCEEEEecCCchH
Confidence            588999999999999988999 99999999999988543321         23455553222  2789999999999988


Q ss_pred             HHHHHHHcCCcceeeccchh
Q 042991           70 RIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        70 ~~~~~~~~ga~d~l~kP~~~   89 (93)
                      ...++++.|+++|+.||+..
T Consensus        86 ~~~~~~~~g~~~~l~Kp~~~  105 (120)
T 2a9o_A           86 DKVIGLELGADDYVTKPFSN  105 (120)
T ss_dssp             HHHHHHHHTCSEEEESSCCH
T ss_pred             HHHHHHhCCHhheEeCCCCH
Confidence            88899999999999999863

>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=99.53  E-value=1e-13  Score=75.39  Aligned_cols=88  Identities=15%  Similarity=0.128  Sum_probs=70.5

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHh---hhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRT---IYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~---~~~~~~pii~lt~~~~~   68 (93)
                      +||++..+..++..|+..||..+..+.++.+|++.+....++         +.+|++++.   ...+.+|+|++|+..+.
T Consensus         8 vdd~~~~~~~l~~~l~~~g~~vv~~~~~~~~a~~~~~~~~~dlil~D~~l~~~~g~~~~~~l~~~~~~~~ii~~s~~~~~   87 (120)
T 1tmy_A            8 VDDAAFMRMMLKDIITKAGYEVAGEATNGREAVEKYKELKPDIVTMDITMPEMNGIDAIKEIMKIDPNAKIIVCSAMGQQ   87 (120)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHHHHCCSEEEEECSCGGGCHHHHHHHHHHHCTTCCEEEEECTTCH
T ss_pred             EcCcHHHHHHHHHHHhhcCcEEEEEECCHHHHHHHHHhcCCCEEEEeCCCCCCcHHHHHHHHHhhCCCCeEEEEeCCCCH
Confidence            588999999999999988988345799999999988643321         234555533   33378999999999999


Q ss_pred             HHHHHHHHcCCcceeeccch
Q 042991           69 VRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~   88 (93)
                      ....++++.|+++|+.||++
T Consensus        88 ~~~~~~~~~g~~~~l~KP~~  107 (120)
T 1tmy_A           88 AMVIEAIKAGAKDFIVKPFQ  107 (120)
T ss_dssp             HHHHHHHHTTCCEEEESSCC
T ss_pred             HHHHHHHHhCcceeEeCCCC
Confidence            98899999999999999986

>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=99.53  E-value=3.2e-13  Score=74.21  Aligned_cols=88  Identities=18%  Similarity=0.174  Sum_probs=71.4

Q ss_pred             CCCcHHHHHHHHHHHhhcCC-CceEEeCCHHHHHHHhccCccc---------CCCchHHHhhh-----hcCCcEEEEcCC
Q 042991            1 LNDSFVDRKVIERLLTISSS-RDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIY-----SREIPVVIMSPE   65 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~-~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~-----~~~~pii~lt~~   65 (93)
                      +||++..+..++.+|+..|| . +..+.++.++++.+....++         +++|++++..+     .+.+|+|++|+.
T Consensus        10 vdd~~~~~~~l~~~l~~~~~~~-v~~~~~~~~a~~~~~~~~~dlvi~D~~l~~~~g~~l~~~l~~~~~~~~~~ii~~s~~   88 (128)
T 1jbe_A           10 VDDFSTMRRIVRNLLKELGFNN-VEEAEDGVDALNKLQAGGYGFVISDWNMPNMDGLELLKTIRAXXAMSALPVLMVTAE   88 (128)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCCC-EEEESSHHHHHHHHTTCCCCEEEEESCCSSSCHHHHHHHHHC--CCTTCCEEEEESS
T ss_pred             ECCCHHHHHHHHHHHHHcCCcE-EEeeCCHHHHHHHHHhcCCCEEEEeCCCCCCCHHHHHHHHHhhcccCCCcEEEEecC
Confidence            57899999999999998898 6 99999999999998644321         23455553322     257899999999


Q ss_pred             CCHHHHHHHHHcCCcceeeccchh
Q 042991           66 IILVRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        66 ~~~~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      .+.....++++.|+++|+.||++.
T Consensus        89 ~~~~~~~~~~~~ga~~~l~KP~~~  112 (128)
T 1jbe_A           89 AKKENIIAAAQAGASGYVVKPFTA  112 (128)
T ss_dssp             CCHHHHHHHHHTTCSEEEESSCCH
T ss_pred             ccHHHHHHHHHhCcCceeecCCCH
Confidence            999999999999999999999873

>3n0r_A Response regulator; sigma factor, receiver, two-component SI transduction, signaling protein; HET: MSE GOL; 1.25A {Caulobacter vibrioides} PDB: 3t0y_A

Probab=99.53  E-value=6.9e-15  Score=91.79  Aligned_cols=85  Identities=15%  Similarity=0.064  Sum_probs=68.8

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceE-EeCCHHHHHHHhccCcc---------c-CCCchHH---HhhhhcCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLY-CSCSGRRALQFLGLDEE---------Q-SANGFDV---RTIYSREIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~-~~~~~~~a~~~~~~~~~---------~-~~~~~d~---l~~~~~~~pii~lt~~~   66 (93)
                      +||++..+..++.+|+..||. +. .+.|+.+|++.+....+         + .++|+++   ++.. .++|||++|+..
T Consensus       166 VdD~~~~~~~l~~~L~~~g~~-v~~~a~~g~eAl~~~~~~~~dlvl~D~~MPd~mdG~e~~~~ir~~-~~~piI~lT~~~  243 (286)
T 3n0r_A          166 IEDEPVIAADIEALVRELGHD-VTDIAATRGEALEAVTRRTPGLVLADIQLADGSSGIDAVKDILGR-MDVPVIFITAFP  243 (286)
T ss_dssp             ECCSHHHHHHHHHHHHHTTCE-EEEEESSHHHHHHHHHHCCCSEEEEESCCTTSCCTTTTTHHHHHH-TTCCEEEEESCG
T ss_pred             EcCCHHHHHHHHHHhhccCce-EEEEeCCHHHHHHHHHhCCCCEEEEcCCCCCCCCHHHHHHHHHhc-CCCCEEEEeCCH
Confidence            589999999999999999999 88 99999999999975443         2 2445554   4444 499999999985


Q ss_pred             CHHHHHHHHHcCCcceeeccchh
Q 042991           67 ILVRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      +  ...++++.|+++||.||+..
T Consensus       244 ~--~~~~~~~~G~~~~l~KP~~~  264 (286)
T 3n0r_A          244 E--RLLTGERPEPTFLITKPFQP  264 (286)
T ss_dssp             G--GGCCSSSCCCSSEEESSCCH
T ss_pred             H--HHHHHHhCCCcEEEeCCCCH
Confidence            3  45568899999999999973

>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=99.53  E-value=1.7e-13  Score=74.84  Aligned_cols=88  Identities=17%  Similarity=0.189  Sum_probs=71.5

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhhh--cCCcEEEEcCCCCHH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIYS--REIPVVIMSPEIILV   69 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~~--~~~pii~lt~~~~~~   69 (93)
                      +||++..+..++..|+..||. +..+.++.++++.+....++         +.+|++++..+.  +.+|+|++|+..+..
T Consensus         9 vdd~~~~~~~l~~~l~~~~~~-v~~~~~~~~a~~~~~~~~~dlvi~D~~l~~~~g~~~~~~l~~~~~~~ii~~s~~~~~~   87 (123)
T 1xhf_A            9 VEDELVTRNTLKSIFEAEGYD-VFEATDGAEMHQILSEYDINLVIMDINLPGKNGLLLARELREQANVALMFLTGRDNEV   87 (123)
T ss_dssp             ECSCHHHHHHHHHHHHTTTCE-EEEESSHHHHHHHHHHSCCSEEEECSSCSSSCHHHHHHHHHHHCCCEEEEEESCCSHH
T ss_pred             EeCCHHHHHHHHHHHhhCCcE-EEEeCCHHHHHHHHhcCCCCEEEEcCCCCCCCHHHHHHHHHhCCCCcEEEEECCCChH
Confidence            588999999999999988999 99999999999988644321         234555533221  789999999999988


Q ss_pred             HHHHHHHcCCcceeeccchh
Q 042991           70 RIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        70 ~~~~~~~~ga~d~l~kP~~~   89 (93)
                      ...++++.|+++|+.||++.
T Consensus        88 ~~~~~~~~g~~~~l~KP~~~  107 (123)
T 1xhf_A           88 DKILGLEIGADDYITKPFNP  107 (123)
T ss_dssp             HHHHHHHHTCSEEEESSCCH
T ss_pred             HHHHHHhcCcceEEeCCCCH
Confidence            88899999999999999863

>3hv2_A Response regulator/HD domain protein; PSI-2, NYSGXRC, structural genomics, protein structure initiative; 1.50A {Pseudomonas fluorescens pf-5}

Probab=99.53  E-value=1.4e-13  Score=78.06  Aligned_cols=87  Identities=15%  Similarity=0.101  Sum_probs=72.9

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHH---hhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~~~~pii~lt~~~~~   68 (93)
                      +||++..+..+..+|+..||. +..+.++.+|++.+....++         +..|++++   ....+.+|||++|+..+.
T Consensus        20 vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~~a~~~l~~~~~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~ii~~s~~~~~   98 (153)
T 3hv2_A           20 VDSQEVILQRLQQLLSPLPYT-LHFARDATQALQLLASREVDLVISAAHLPQMDGPTLLARIHQQYPSTTRILLTGDPDL   98 (153)
T ss_dssp             ECSCHHHHHHHHHHHTTSSCE-EEEESSHHHHHHHHHHSCCSEEEEESCCSSSCHHHHHHHHHHHCTTSEEEEECCCCCH
T ss_pred             ECCCHHHHHHHHHHhcccCcE-EEEECCHHHHHHHHHcCCCCEEEEeCCCCcCcHHHHHHHHHhHCCCCeEEEEECCCCH
Confidence            588999999999999999999 99999999999998654421         23455553   333388999999999999


Q ss_pred             HHHHHHHHcC-Ccceeeccch
Q 042991           69 VRIDRYLEDG-AEDSETCQMW   88 (93)
Q Consensus        69 ~~~~~~~~~g-a~d~l~kP~~   88 (93)
                      ....++++.| +++|+.||+.
T Consensus        99 ~~~~~~~~~g~~~~~l~KP~~  119 (153)
T 3hv2_A           99 KLIAKAINEGEIYRYLSKPWD  119 (153)
T ss_dssp             HHHHHHHHTTCCSEEECSSCC
T ss_pred             HHHHHHHhCCCcceEEeCCCC
Confidence            9999999999 9999999986

>2qzj_A Two-component response regulator; 11017X, PSI-II, structural genomics; 2.89A {Clostridium difficile}

Probab=99.53  E-value=1.4e-13  Score=76.85  Aligned_cols=87  Identities=11%  Similarity=0.081  Sum_probs=71.0

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhhh--cCCcEEEEcCCCCHH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIYS--REIPVVIMSPEIILV   69 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~~--~~~pii~lt~~~~~~   69 (93)
                      +||++..+..++.+|+..||. +..+.++.++++.+....++         +..|++++..+.  ..+|+|++|+..+..
T Consensus        10 vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~~al~~~~~~~~dlvllD~~l~~~~g~~l~~~l~~~~~~~ii~ls~~~~~~   88 (136)
T 2qzj_A           10 IDGDKDNCQKLKGFLEEKGIS-IDLAYNCEEAIGKIFSNKYDLIFLEIILSDGDGWTLCKKIRNVTTCPIVYMTYINEDQ   88 (136)
T ss_dssp             ECSCHHHHHHHHHHHHTTTCE-EEEESSHHHHHHHHHHCCCSEEEEESEETTEEHHHHHHHHHTTCCCCEEEEESCCCHH
T ss_pred             EcCCHHHHHHHHHHHHHCCCE-EEEECCHHHHHHHHHhcCCCEEEEeCCCCCCCHHHHHHHHccCCCCCEEEEEcCCCHH
Confidence            589999999999999988999 99999999999988644321         224555533322  478999999999998


Q ss_pred             HHHHHHHcCCcceeeccch
Q 042991           70 RIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        70 ~~~~~~~~ga~d~l~kP~~   88 (93)
                      ...++++.|+++|+.||++
T Consensus        89 ~~~~~~~~ga~~~l~KP~~  107 (136)
T 2qzj_A           89 SILNALNSGGDDYLIKPLN  107 (136)
T ss_dssp             HHHHHHHTTCCEEEESSCC
T ss_pred             HHHHHHHcCCcEEEECCCC
Confidence            9999999999999999986

>3jte_A Response regulator receiver protein; structural genomics, nysgrc, response regulator receiver DOM target 11226E, PSI-2; 1.90A {Clostridium thermocellum atcc 27405}

Probab=99.52  E-value=2.2e-13  Score=76.22  Aligned_cols=87  Identities=16%  Similarity=0.173  Sum_probs=72.0

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhcc--Cccc---------CCCchHHH---hhhhcCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGL--DEEQ---------SANGFDVR---TIYSREIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~--~~~~---------~~~~~d~l---~~~~~~~pii~lt~~~   66 (93)
                      +||++..+..++.+|+..||. +..+.++.+|++.+..  ..++         +..|++++   ....+.+|||++|+..
T Consensus         9 vdd~~~~~~~l~~~l~~~g~~-v~~~~~~~~a~~~~~~~~~~~dlvi~d~~l~~~~g~~~~~~l~~~~~~~~ii~ls~~~   87 (143)
T 3jte_A            9 IDDESTILQNIKFLLEIDGNE-VLTASSSTEGLRIFTENCNSIDVVITDMKMPKLSGMDILREIKKITPHMAVIILTGHG   87 (143)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCE-EEEESSHHHHHHHHHHTTTTCCEEEEESCCSSSCHHHHHHHHHHHCTTCEEEEEECTT
T ss_pred             EcCCHHHHHHHHHHHHhCCce-EEEeCCHHHHHHHHHhCCCCCCEEEEeCCCCCCcHHHHHHHHHHhCCCCeEEEEECCC
Confidence            588999999999999999999 9999999999999862  2221         23455553   3333789999999999


Q ss_pred             CHHHHHHHHHcCCcceeeccch
Q 042991           67 ILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      +.....++++.|+++|+.||+.
T Consensus        88 ~~~~~~~~~~~g~~~~l~kp~~  109 (143)
T 3jte_A           88 DLDNAILAMKEGAFEYLRKPVT  109 (143)
T ss_dssp             CHHHHHHHHHTTCSEEEESSCC
T ss_pred             CHHHHHHHHHhCcceeEeCCCC
Confidence            9999999999999999999986

>3cfy_A Putative LUXO repressor protein; structural genomics, unknown function, uncharacterized protein, signal receiver domain; 2.50A {Vibrio parahaemolyticus rimd 2210633}

Probab=99.52  E-value=7.1e-14  Score=78.10  Aligned_cols=87  Identities=20%  Similarity=0.190  Sum_probs=71.2

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHH---hhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~~~~pii~lt~~~~~   68 (93)
                      +||++..+..++.+|+..||. +..+.++.+|++.+....++         +..|++++   ....+.+|+|++|+..+.
T Consensus        10 vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~~a~~~l~~~~~dlvllD~~l~~~~g~~l~~~l~~~~~~~~ii~ls~~~~~   88 (137)
T 3cfy_A           10 VEDSTSLAILYKQYVKDEPYD-IFHVETGRDAIQFIERSKPQLIILDLKLPDMSGEDVLDWINQNDIPTSVIIATAHGSV   88 (137)
T ss_dssp             ECSCTTHHHHHHHHTTTSSSE-EEEESSHHHHHHHHHHHCCSEEEECSBCSSSBHHHHHHHHHHTTCCCEEEEEESSCCH
T ss_pred             EeCCHHHHHHHHHHHHhcCce-EEEeCCHHHHHHHHHhcCCCEEEEecCCCCCCHHHHHHHHHhcCCCCCEEEEEecCcH
Confidence            578889999999999988999 99999999999988643321         23455553   333378999999999999


Q ss_pred             HHHHHHHHcCCcceeeccch
Q 042991           69 VRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~   88 (93)
                      ....++++.|+++|+.||++
T Consensus        89 ~~~~~~~~~ga~~~l~KP~~  108 (137)
T 3cfy_A           89 DLAVNLIQKGAEDFLEKPIN  108 (137)
T ss_dssp             HHHHHHHHTTCSEEEESSCC
T ss_pred             HHHHHHHHCCccEEEeCCCC
Confidence            89899999999999999986

>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=99.52  E-value=1.3e-13  Score=76.72  Aligned_cols=87  Identities=11%  Similarity=0.145  Sum_probs=72.1

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHH---hhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~~~~pii~lt~~~~~   68 (93)
                      +||++..+..++.+|+..++. +..+.++.+|++.++...++         +..|++++   +...+.+|||++|+..+.
T Consensus        13 vdd~~~~~~~l~~~L~~~~~~-v~~~~~~~~a~~~l~~~~~dlvi~d~~l~~~~g~~~~~~l~~~~~~~~ii~~s~~~~~   91 (137)
T 3hdg_A           13 VEDDTDAREWLSTIISNHFPE-VWSAGDGEEGERLFGLHAPDVIITDIRMPKLGGLEMLDRIKAGGAKPYVIVISAFSEM   91 (137)
T ss_dssp             ECSCHHHHHHHHHHHHTTCSC-EEEESSHHHHHHHHHHHCCSEEEECSSCSSSCHHHHHHHHHHTTCCCEEEECCCCCCH
T ss_pred             EeCCHHHHHHHHHHHHhcCcE-EEEECCHHHHHHHHhccCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCcEEEEecCcCh
Confidence            588999999999999998888 99999999999998644321         23455553   333378999999999999


Q ss_pred             HHHHHHHHcCCcceeeccch
Q 042991           69 VRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~   88 (93)
                      ....++++.|+++|+.||+.
T Consensus        92 ~~~~~~~~~g~~~~l~kP~~  111 (137)
T 3hdg_A           92 KYFIKAIELGVHLFLPKPIE  111 (137)
T ss_dssp             HHHHHHHHHCCSEECCSSCC
T ss_pred             HHHHHHHhCCcceeEcCCCC
Confidence            99999999999999999986

>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=99.52  E-value=8e-14  Score=85.71  Aligned_cols=88  Identities=18%  Similarity=0.160  Sum_probs=72.4

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCc-c---------cCCCchHHHhhhh-----cCCcEEEEcCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDE-E---------QSANGFDVRTIYS-----REIPVVIMSPE   65 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~-~---------~~~~~~d~l~~~~-----~~~pii~lt~~   65 (93)
                      |||++..+..+...|+..++. +..+.++.+|++.++... +         ++++|++++..+.     ..+|||++|+.
T Consensus       130 vDD~~~~~~~l~~~L~~~~~~-v~~a~~~~eal~~l~~~~~~dlvllD~~mP~~dG~~l~~~lr~~~~~~~~~ii~~s~~  208 (259)
T 3luf_A          130 VDDSRTSRHRTMAQLRKQLLQ-VHEASHAREALATLEQHPAIRLVLVDYYMPEIDGISLVRMLRERYSKQQLAIIGISVS  208 (259)
T ss_dssp             ECSCHHHHHHHHHHHHTTTCE-EEEESSHHHHHHHHHHCTTEEEEEECSCCSSSCHHHHHHHHHHHCCTTTSEEEEEECS
T ss_pred             EeCCHHHHHHHHHHHHHcCcE-EEEeCCHHHHHHHHhcCCCCCEEEEcCCCCCCCHHHHHHHHHhccCCCCCeEEEEEcc
Confidence            589999999999999999999 999999999999986442 2         1345666643322     46899999999


Q ss_pred             CCHHHHHHHHHcCCcceeeccchh
Q 042991           66 IILVRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        66 ~~~~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      .+.....++++.||++|+.||++.
T Consensus       209 ~~~~~~~~a~~~Ga~~yl~KP~~~  232 (259)
T 3luf_A          209 DKRGLSARYLKQGANDFLNQPFEP  232 (259)
T ss_dssp             SSSSHHHHHHHTTCSEEEESSCCH
T ss_pred             CCHHHHHHHHhcChhheEcCCCCH
Confidence            998888999999999999999973

>3eq2_A Probable two-component response regulator; adaptor sigmas, signaling protein; 3.40A {Pseudomonas aeruginosa} PDB: 3f7a_A

Probab=99.52  E-value=4.3e-14  Score=91.09  Aligned_cols=87  Identities=18%  Similarity=0.256  Sum_probs=70.8

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHH---hhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~~~~pii~lt~~~~~   68 (93)
                      |||++..+..++.+|+..||+ +..+.++.+|++.+....++         +++|++++   +...+++|||++|+..+.
T Consensus        11 vdD~~~~~~~l~~~L~~~g~~-v~~a~~~~~al~~~~~~~~dlvllD~~mp~~~G~~~~~~lr~~~~~~pii~lt~~~~~   89 (394)
T 3eq2_A           11 IDDDEVVRESLAAYLEDSNFK-VLQALNGLQGLQIFESEQPDLVICDLRMPQIDGLELIRRIRQTASETPIIVLSGAGVM   89 (394)
T ss_dssp             ECSCHHHHHHHHHHHHHTTEE-EEECSSHHHHHHHHHHSCCSEEEECCCSSSSCTHHHHHHHHHTTCCCCEEEC---CHH
T ss_pred             EeCCHHHHHHHHHHHHhCCCE-EEEECCHHHHHHHHhhCCCCEEEEcCCCCCCCHHHHHHHHHhhCCCCcEEEEEcCCCH
Confidence            589999999999999999999 99999999999998654431         34566663   333488999999999999


Q ss_pred             HHHHHHHHcCCcceeeccch
Q 042991           69 VRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~   88 (93)
                      +...++++.|+++|+.||+.
T Consensus        90 ~~~~~a~~~ga~~yl~KP~~  109 (394)
T 3eq2_A           90 SDAVEALRLGAADYLIKPLE  109 (394)
T ss_dssp             HHHHHHHHHTCSEECCSSCS
T ss_pred             HHHHHHHhcChhhEEECCCC
Confidence            99999999999999999983

>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=99.51  E-value=2e-13  Score=75.09  Aligned_cols=88  Identities=9%  Similarity=0.192  Sum_probs=71.2

Q ss_pred             CCCcHHHHHHHHHHHhhcCC-CceEEeCCHHHHHHHhccCccc---------CCCchHHHhhh-----hcCCcEEEEcCC
Q 042991            1 LNDSFVDRKVIERLLTISSS-RDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIY-----SREIPVVIMSPE   65 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~-~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~-----~~~~pii~lt~~   65 (93)
                      +||++..+..++.+|+..|| . +..+.++.++++.+....++         +.+|++++..+     .+.+|+|++|+.
T Consensus        12 vdd~~~~~~~l~~~L~~~g~~~-v~~~~~~~~a~~~~~~~~~dlvl~D~~l~~~~g~~~~~~l~~~~~~~~~~ii~~s~~   90 (129)
T 1p6q_A           12 VDDQVTSRLLLGDALQQLGFKQ-ITAAGDGEQGMKIMAQNPHHLVISDFNMPKMDGLGLLQAVRANPATKKAAFIILTAQ   90 (129)
T ss_dssp             ECSSHHHHHHHHHHHHTTTCSC-EECCSSHHHHHHHHHTSCCSEEEECSSSCSSCHHHHHHHHTTCTTSTTCEEEECCSC
T ss_pred             EcCCHHHHHHHHHHHHHCCCcE-EEecCCHHHHHHHHHcCCCCEEEEeCCCCCCCHHHHHHHHhcCccccCCCEEEEeCC
Confidence            58899999999999998898 6 88999999999988644321         23456653322     267899999999


Q ss_pred             CCHHHHHHHHHcCCcceeeccchh
Q 042991           66 IILVRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        66 ~~~~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      .+.....++++.|+++|+.||++.
T Consensus        91 ~~~~~~~~~~~~g~~~~l~KP~~~  114 (129)
T 1p6q_A           91 GDRALVQKAAALGANNVLAKPFTI  114 (129)
T ss_dssp             CCHHHHHHHHHHTCSCEECCCSSH
T ss_pred             CCHHHHHHHHHcCCCEEEECCCCH
Confidence            999888899999999999999863

>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=99.51  E-value=4.3e-13  Score=75.86  Aligned_cols=88  Identities=23%  Similarity=0.268  Sum_probs=71.8

Q ss_pred             CCCcHHHHHHHHHHHhhcCC--CceEEeCCHHHHHHHhc---------cCccc---------CCCchHH---Hhh--hhc
Q 042991            1 LNDSFVDRKVIERLLTISSS--RDLYCSCSGRRALQFLG---------LDEEQ---------SANGFDV---RTI--YSR   55 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~--~~v~~~~~~~~a~~~~~---------~~~~~---------~~~~~d~---l~~--~~~   55 (93)
                      |||++..+..++.+|+..|+  . +..+.++.+|++.++         ...++         +..|+++   ++.  ..+
T Consensus        10 vddd~~~~~~l~~~L~~~g~~~~-v~~~~~~~~al~~l~~~~~~~~~~~~~~dliilD~~l~~~~g~~~~~~lr~~~~~~   88 (152)
T 3heb_A           10 IEDDLGHARLIEKNIRRAGVNNE-IIAFTDGTSALNYLFGDDKSGRVSAGRAQLVLLDLNLPDMTGIDILKLVKENPHTR   88 (152)
T ss_dssp             ECCCHHHHHHHHHHHHHTTCCCC-EEEESSHHHHHHHHHCTTSSSGGGTTCBEEEEECSBCSSSBHHHHHHHHHHSTTTT
T ss_pred             EeCCHHHHHHHHHHHHhCCCcce-EEEeCCHHHHHHHHhccccccccccCCCCEEEEeCCCCCCcHHHHHHHHHhccccc
Confidence            58999999999999999998  6 999999999999984         22211         2345665   333  237


Q ss_pred             CCcEEEEcCCCCHHHHHHHHHcCCcceeeccchh
Q 042991           56 EIPVVIMSPEIILVRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        56 ~~pii~lt~~~~~~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      .+|||++|+..+.....++++.|+++|+.||+..
T Consensus        89 ~~pii~~t~~~~~~~~~~~~~~g~~~~l~KP~~~  122 (152)
T 3heb_A           89 RSPVVILTTTDDQREIQRCYDLGANVYITKPVNY  122 (152)
T ss_dssp             TSCEEEEESCCCHHHHHHHHHTTCSEEEECCSSH
T ss_pred             CCCEEEEecCCCHHHHHHHHHCCCcEEEeCCCCH
Confidence            8999999999999999999999999999999873

>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=99.51  E-value=9.8e-14  Score=75.82  Aligned_cols=87  Identities=20%  Similarity=0.225  Sum_probs=65.3

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhh-----hcCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIY-----SREIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~-----~~~~pii~lt~~~   66 (93)
                      +||++..+..++.+|+..||. +..+.++.+|+..++...++         +++|++++..+     .+.+|+|++|+..
T Consensus         7 vdd~~~~~~~l~~~L~~~~~~-v~~~~~~~~a~~~~~~~~~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~~~ii~~s~~~   85 (124)
T 1mb3_A            7 VEDNELNMKLFHDLLEAQGYE-TLQTREGLSALSIARENKPDLILMDIQLPEISGLEVTKWLKEDDDLAHIPVVAVTAFA   85 (124)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCE-EEEESCHHHHHHHHHHHCCSEEEEESBCSSSBHHHHHHHHHHSTTTTTSCEEEEC---
T ss_pred             EcCCHHHHHHHHHHHHHcCcE-EEEeCCHHHHHHHHhcCCCCEEEEeCCCCCCCHHHHHHHHHcCccccCCcEEEEECCC
Confidence            589999999999999999999 99999999999988543321         23456653322     2578999999988


Q ss_pred             CHHHHHHHHHcCCcceeeccch
Q 042991           67 ILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      +.....++++.|+++|+.||++
T Consensus        86 ~~~~~~~~~~~g~~~~l~KP~~  107 (124)
T 1mb3_A           86 MKGDEERIREGGCEAYISKPIS  107 (124)
T ss_dssp             ---CHHHHHHHTCSEEECSSCC
T ss_pred             CHHHHHHHHhCCCCEEEeCCCC
Confidence            8888888999999999999986

>3hzh_A Chemotaxis response regulator (CHEY-3); phosphatase, complex, response regulator, receiver domain, two-component signal transduction; HET: BFD; 1.96A {Borrelia burgdorferi}

Probab=99.51  E-value=2.3e-13  Score=77.59  Aligned_cols=87  Identities=14%  Similarity=0.144  Sum_probs=72.3

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceE-EeCCHHHHHHHhccC--ccc---------CCCchHH---HhhhhcCCcEEEEcCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLY-CSCSGRRALQFLGLD--EEQ---------SANGFDV---RTIYSREIPVVIMSPE   65 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~-~~~~~~~a~~~~~~~--~~~---------~~~~~d~---l~~~~~~~pii~lt~~   65 (93)
                      +||++..+..++.+|+..||. +. .+.++.+|++.+...  .++         +..|+++   ++...+.+|||++|+.
T Consensus        42 vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~~~al~~l~~~~~~~dliilD~~l~~~~g~~~~~~lr~~~~~~~ii~ls~~  120 (157)
T 3hzh_A           42 VDDSVFTVKQLTQIFTSEGFN-IIDTAADGEEAVIKYKNHYPNIDIVTLXITMPKMDGITCLSNIMEFDKNARVIMISAL  120 (157)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCE-EEEEESSHHHHHHHHHHHGGGCCEEEECSSCSSSCHHHHHHHHHHHCTTCCEEEEESC
T ss_pred             EeCCHHHHHHHHHHHHhCCCe-EEEEECCHHHHHHHHHhcCCCCCEEEEeccCCCccHHHHHHHHHhhCCCCcEEEEecc
Confidence            588999999999999999999 77 999999999998644  221         2345555   3333488999999999


Q ss_pred             CCHHHHHHHHHcCCcceeeccch
Q 042991           66 IILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        66 ~~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      .+.....++++.|+++|+.||+.
T Consensus       121 ~~~~~~~~~~~~g~~~~l~KP~~  143 (157)
T 3hzh_A          121 GKEQLVKDCLIKGAKTFIVKPLD  143 (157)
T ss_dssp             CCHHHHHHHHHTTCSEEEESSCC
T ss_pred             CcHHHHHHHHHcCCCEEEeCCCC
Confidence            99999999999999999999986

>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=99.51  E-value=7.8e-14  Score=85.47  Aligned_cols=87  Identities=16%  Similarity=0.265  Sum_probs=73.3

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHH---HhhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDV---RTIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~---l~~~~~~~pii~lt~~~~~   68 (93)
                      +||++..+..+..+|++.||+ +..+.++.+|++.++...++         +++|+++   ++...+.+|||++|+....
T Consensus       135 vdd~~~~~~~l~~~L~~~g~~-v~~a~~~~eal~~l~~~~~dlvl~D~~mp~~~G~~l~~~ir~~~~~~piI~lt~~~~~  213 (254)
T 2ayx_A          135 VDDHPINRRLLADQLGSLGYQ-CKTANDGVDALNVLSKNHIDIVLSDVNMPNMDGYRLTQRIRQLGLTLPVIGVTANALA  213 (254)
T ss_dssp             EESSHHHHHHHHHHHHHHTSE-EEEECCSHHHHHHHHHSCCSEEEEEESSCSSCCHHHHHHHHHHHCCSCEEEEESSTTS
T ss_pred             EeCCHHHHHHHHHHHHHcCCE-EEEECCHHHHHHHHHhCCCCEEEEcCCCCCCCHHHHHHHHHhcCCCCcEEEEECCCCH
Confidence            589999999999999999999 99999999999998654321         3456665   3333478999999999998


Q ss_pred             HHHHHHHHcCCcceeeccch
Q 042991           69 VRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~   88 (93)
                      ....++++.|+++|+.||+.
T Consensus       214 ~~~~~~~~~G~~~~l~KP~~  233 (254)
T 2ayx_A          214 EEKQRCLESGMDSCLSKPVT  233 (254)
T ss_dssp             HHHHHHHHCCCEEEEESSCC
T ss_pred             HHHHHHHHcCCceEEECCCC
Confidence            88899999999999999986

>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=99.51  E-value=3.4e-13  Score=74.86  Aligned_cols=88  Identities=13%  Similarity=0.115  Sum_probs=72.3

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCc-cc---------CCCchHHH---hhh-hcCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDE-EQ---------SANGFDVR---TIY-SREIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~-~~---------~~~~~d~l---~~~-~~~~pii~lt~~~   66 (93)
                      +||++..+..++.+|+..||+ +..+.++.+++..+.... ++         +..|++++   +.. .+.+|+|++|+..
T Consensus        13 vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~~a~~~~~~~~~~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~~ii~~s~~~   91 (136)
T 3hdv_A           13 VDDNAVNREALILYLKSRGID-AVGADGAEEARLYLHYQKRIGLMITDLRMQPESGLDLIRTIRASERAALSIIVVSGDT   91 (136)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCC-EEEESSHHHHHHHHHHCTTEEEEEECSCCSSSCHHHHHHHHHTSTTTTCEEEEEESSC
T ss_pred             ECCCHHHHHHHHHHHHHcCce-EEEeCCHHHHHHHHHhCCCCcEEEEeccCCCCCHHHHHHHHHhcCCCCCCEEEEeCCC
Confidence            588999999999999999999 999999999999886443 21         23455553   333 3778999999999


Q ss_pred             CHHHHHHHHHcCCcceeeccchh
Q 042991           67 ILVRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      +.....++++.|+++|+.||+..
T Consensus        92 ~~~~~~~~~~~g~~~~l~KP~~~  114 (136)
T 3hdv_A           92 DVEEAVDVMHLGVVDFLLKPVDL  114 (136)
T ss_dssp             CHHHHHHHHHTTCSEEEESSCCH
T ss_pred             ChHHHHHHHhCCcceEEeCCCCH
Confidence            99999999999999999999863

>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=99.50  E-value=7.1e-14  Score=82.78  Aligned_cols=88  Identities=16%  Similarity=0.169  Sum_probs=72.8

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHH---hhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~~~~pii~lt~~~~~   68 (93)
                      +||++..+..+..+|+..||. +..+.++.+|++.+....++         +++|++++   ....+.+|||++|+..+.
T Consensus        10 vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~~al~~~~~~~~dlvl~D~~lp~~~g~~~~~~l~~~~~~~~ii~ls~~~~~   88 (208)
T 1yio_A           10 VDDDMSVREGLRNLLRSAGFE-VETFDCASTFLEHRRPEQHGCLVLDMRMPGMSGIELQEQLTAISDGIPIVFITAHGDI   88 (208)
T ss_dssp             ECSCHHHHHHHHHHHHTTTCE-EEEESSHHHHHHHCCTTSCEEEEEESCCSSSCHHHHHHHHHHTTCCCCEEEEESCTTS
T ss_pred             EcCCHHHHHHHHHHHHhCCce-EEEcCCHHHHHHhhhccCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCCEEEEeCCCCH
Confidence            589999999999999988999 99999999999998654321         33566653   333378999999999888


Q ss_pred             HHHHHHHHcCCcceeeccchh
Q 042991           69 VRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      ....++++.|+++|+.||+..
T Consensus        89 ~~~~~a~~~Ga~~~l~Kp~~~  109 (208)
T 1yio_A           89 PMTVRAMKAGAIEFLPKPFEE  109 (208)
T ss_dssp             CCCHHHHHTTEEEEEESSCCH
T ss_pred             HHHHHHHHCCCcEEEeCCCCH
Confidence            888899999999999999863

>4e7p_A Response regulator; DNA binding, cytosol, transcription regulator; 1.89A {Streptococcus pneumoniae} PDB: 4e7o_A

Probab=99.50  E-value=3.7e-13  Score=76.03  Aligned_cols=87  Identities=18%  Similarity=0.201  Sum_probs=71.9

Q ss_pred             CCCcHHHHHHHHHHHhhcC--CCceEEeCCHHHHHHHhccCccc---------CCCchHHH---hhhhcCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTISS--SRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYSREIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~--~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~~~~pii~lt~~~   66 (93)
                      +||++..+..+..+|+..+  +. +..+.++.+|++.+....++         +..|++++   +...+.+|||++|+..
T Consensus        26 vdd~~~~~~~l~~~L~~~~~~~~-v~~~~~~~~al~~l~~~~~dlii~D~~l~~~~g~~~~~~l~~~~~~~~ii~ls~~~  104 (150)
T 4e7p_A           26 AEDQSMLRDAMCQLLTLQPDVES-VLQAKNGQEAIQLLEKESVDIAILDVEMPVKTGLEVLEWIRSEKLETKVVVVTTFK  104 (150)
T ss_dssp             ECSCHHHHHHHHHHHHTSTTEEE-EEEESSHHHHHHHHTTSCCSEEEECSSCSSSCHHHHHHHHHHTTCSCEEEEEESCC
T ss_pred             EcCCHHHHHHHHHHHHhCCCcEE-EEEECCHHHHHHHhhccCCCEEEEeCCCCCCcHHHHHHHHHHhCCCCeEEEEeCCC
Confidence            5889999999999999876  66 99999999999998755432         23455553   3333889999999999


Q ss_pred             CHHHHHHHHHcCCcceeeccch
Q 042991           67 ILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      +.....++++.|+++|+.||+.
T Consensus       105 ~~~~~~~~~~~g~~~~l~Kp~~  126 (150)
T 4e7p_A          105 RAGYFERAVKAGVDAYVLKERS  126 (150)
T ss_dssp             CHHHHHHHHHTTCSEEEETTSC
T ss_pred             CHHHHHHHHHCCCcEEEecCCC
Confidence            9999999999999999999986

>3b2n_A Uncharacterized protein Q99UF4; structural genomics, PSI-2, protein structure initiative, NE SGX research center for structural genomics; 2.04A {Staphylococcus aureus}

Probab=99.50  E-value=1.8e-13  Score=75.90  Aligned_cols=87  Identities=13%  Similarity=0.114  Sum_probs=70.0

Q ss_pred             CCCcHHHHHHHHHHHhhcC--CCceEEeCCHHHHHHHhccCccc---------CCCchHHH---hhhhcCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTISS--SRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYSREIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~--~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~~~~pii~lt~~~   66 (93)
                      +||++..+..++.+|+..+  +. +..+.++.++++.+....++         +++|++++   +...+.+|||++|+..
T Consensus         9 vdd~~~~~~~l~~~l~~~~~~~~-v~~~~~~~~al~~~~~~~~dlvilD~~lp~~~g~~~~~~l~~~~~~~~ii~ls~~~   87 (133)
T 3b2n_A            9 AEDQNMLRQAMVQLIKLHGDFEI-LADTDNGLDAMKLIEEYNPNVVILDIEMPGMTGLEVLAEIRKKHLNIKVIIVTTFK   87 (133)
T ss_dssp             ECSCHHHHHHHHHHHHHHSSEEE-EEEESCHHHHHHHHHHHCCSEEEECSSCSSSCHHHHHHHHHHTTCSCEEEEEESCC
T ss_pred             ECCCHHHHHHHHHHHhhCCCcEE-EEEcCCHHHHHHHHhhcCCCEEEEecCCCCCCHHHHHHHHHHHCCCCcEEEEecCC
Confidence            5889999999999999776  45 78899999999988543321         23456653   3333789999999999


Q ss_pred             CHHHHHHHHHcCCcceeeccch
Q 042991           67 ILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      +.....++++.|+++|+.||++
T Consensus        88 ~~~~~~~~~~~ga~~~l~Kp~~  109 (133)
T 3b2n_A           88 RPGYFEKAVVNDVDAYVLKERS  109 (133)
T ss_dssp             CHHHHHHHHHTTCSEEEETTSC
T ss_pred             CHHHHHHHHHcCCcEEEECCCC
Confidence            9999999999999999999986

>1i3c_A Response regulator RCP1; phytochrome, signaling protein; 1.90A {Synechocystis SP} SCOP: c.23.1.1 PDB: 1jlk_A

Probab=99.50  E-value=5.6e-13  Score=75.30  Aligned_cols=88  Identities=20%  Similarity=0.203  Sum_probs=70.3

Q ss_pred             CCCcHHHHHHHHHHHhhcCCC-ceEEeCCHHHHHHHhcc-------Cccc---------CCCchHHHhhhh-----cCCc
Q 042991            1 LNDSFVDRKVIERLLTISSSR-DLYCSCSGRRALQFLGL-------DEEQ---------SANGFDVRTIYS-----REIP   58 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~-~v~~~~~~~~a~~~~~~-------~~~~---------~~~~~d~l~~~~-----~~~p   58 (93)
                      +||++..+..++.+|+..|+. .+..+.++.+|++.++.       ..++         +++|++++..+.     +.+|
T Consensus        14 vdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~al~~l~~~~~~~~~~~~dlillD~~lp~~~g~~l~~~l~~~~~~~~~p   93 (149)
T 1i3c_A           14 VEDSKADSRLVQEVLKTSTIDHELIILRDGLAAMAFLQQQGEYENSPRPNLILLDLNLPKKDGREVLAEIKQNPDLKRIP   93 (149)
T ss_dssp             ECCCHHHHHHHHHHHHSCCSCEEEEEECSHHHHHHHHTTCGGGTTCCCCSEEEECSCCSSSCHHHHHHHHHHCTTTTTSC
T ss_pred             EECCHHHHHHHHHHHHhcCCCccEEEeCCHHHHHHHHHhccccccCCCCCEEEEeCCCCCCcHHHHHHHHHhCcCcCCCe
Confidence            589999999999999988872 28999999999999864       1221         234566533221     5789


Q ss_pred             EEEEcCCCCHHHHHHHHHcCCcceeeccch
Q 042991           59 VVIMSPEIILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        59 ii~lt~~~~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      ||++|+..+.....++++.|+++|+.||++
T Consensus        94 iiils~~~~~~~~~~~~~~ga~~~l~KP~~  123 (149)
T 1i3c_A           94 VVVLTTSHNEDDVIASYELHVNCYLTKSRN  123 (149)
T ss_dssp             EEEEESCCCHHHHHHHHHTTCSEEEECCSS
T ss_pred             EEEEECCCChHHHHHHHHcCCcEEEECCCC
Confidence            999999999888899999999999999986

>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=99.49  E-value=7.3e-13  Score=74.20  Aligned_cols=88  Identities=23%  Similarity=0.260  Sum_probs=71.7

Q ss_pred             CCCcHHHHHHHHHHHhhcCCC-ceEEeCCHHHHHHHhccCccc---------CCCchHH---Hhh--hhcCCcEEEEcCC
Q 042991            1 LNDSFVDRKVIERLLTISSSR-DLYCSCSGRRALQFLGLDEEQ---------SANGFDV---RTI--YSREIPVVIMSPE   65 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~-~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~---l~~--~~~~~pii~lt~~   65 (93)
                      +||++..+..++.+|+..|+. .+..+.++.+|++.+....++         +..|+++   ++.  ..+.+|||++|+.
T Consensus        11 vdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~a~~~l~~~~~dlii~D~~l~~~~g~~~~~~lr~~~~~~~~pii~~s~~   90 (144)
T 3kht_A           11 VEDNPDDIALIRRVLDRKDIHCQLEFVDNGAKALYQVQQAKYDLIILDIGLPIANGFEVMSAVRKPGANQHTPIVILTDN   90 (144)
T ss_dssp             ECCCHHHHHHHHHHHHHTTCCEEEEEESSHHHHHHHHTTCCCSEEEECTTCGGGCHHHHHHHHHSSSTTTTCCEEEEETT
T ss_pred             EeCCHHHHHHHHHHHHhcCCCeeEEEECCHHHHHHHhhcCCCCEEEEeCCCCCCCHHHHHHHHHhcccccCCCEEEEeCC
Confidence            588999999999999988876 488899999999998754432         2234554   333  2378999999999


Q ss_pred             CCHHHHHHHHHcCCcceeeccc-h
Q 042991           66 IILVRIDRYLEDGAEDSETCQM-W   88 (93)
Q Consensus        66 ~~~~~~~~~~~~ga~d~l~kP~-~   88 (93)
                      .+.....++++.|+++|+.||+ .
T Consensus        91 ~~~~~~~~~~~~ga~~~l~Kp~~~  114 (144)
T 3kht_A           91 VSDDRAKQCMAAGASSVVDKSSNN  114 (144)
T ss_dssp             CCHHHHHHHHHTTCSEEEECCTTS
T ss_pred             CCHHHHHHHHHcCCCEEEECCCCc
Confidence            9999999999999999999998 5

>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=99.49  E-value=1.3e-13  Score=89.17  Aligned_cols=87  Identities=20%  Similarity=0.235  Sum_probs=73.4

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHH---hhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~~~~pii~lt~~~~~   68 (93)
                      |||++..+..++.+|+..||. +..+.++.+|++.+....++         +++|++++   ....+++|||++|+..+.
T Consensus         6 VDDd~~~~~~l~~~L~~~g~~-v~~a~~~~eal~~l~~~~~DlvllD~~mp~~dG~ell~~lr~~~~~~pvIvlT~~~~~   84 (387)
T 1ny5_A            6 IEDDKVFRGLLEEYLSMKGIK-VESAERGKEAYKLLSEKHFNVVLLDLLLPDVNGLEILKWIKERSPETEVIVITGHGTI   84 (387)
T ss_dssp             ECCCHHHHHHHHHHHHHHTCE-EEEESSHHHHHHHHHHSCCSEEEEESBCSSSBHHHHHHHHHHHCTTSEEEEEEETTCH
T ss_pred             EECCHHHHHHHHHHHHHCCCE-EEEECCHHHHHHHHHhCCCCEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEeCCCCH
Confidence            589999999999999988999 99999999999998644321         33566653   333488999999999999


Q ss_pred             HHHHHHHHcCCcceeeccch
Q 042991           69 VRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~   88 (93)
                      +...++++.||++|+.||++
T Consensus        85 ~~~~~a~~~Ga~dyl~KP~~  104 (387)
T 1ny5_A           85 KTAVEAMKMGAYDFLTKPCM  104 (387)
T ss_dssp             HHHHHHHTTTCCEEEEESCC
T ss_pred             HHHHHHHhcCceEEecCCCC
Confidence            99999999999999999986

>3f6c_A Positive transcription regulator EVGA; structural genomics, PSI-2, protein structure initiative, PO transcription regulator EVGA; 1.45A {Escherichia coli k-12}

Probab=99.49  E-value=6.2e-14  Score=77.63  Aligned_cols=87  Identities=16%  Similarity=0.086  Sum_probs=68.6

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceE-EeCCHHHHHHHhccCccc---------CCCchHHH---hhhhcCCcEEEEcCCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLY-CSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYSREIPVVIMSPEII   67 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~-~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~~~~pii~lt~~~~   67 (93)
                      +||++..+..++.+|++.||. +. .+.++.+|++.++...++         +..|++++   +...+.+|+|++|+..+
T Consensus         7 vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~~~a~~~~~~~~~dlii~d~~l~~~~g~~~~~~l~~~~~~~~ii~~s~~~~   85 (134)
T 3f6c_A            7 IDDHPLAIAAIRNLLIKNDIE-ILAELTEGGSAVQRVETLKPDIVIIDVDIPGVNGIQVLETLRKRQYSGIIIIVSAKND   85 (134)
T ss_dssp             ECCCHHHHHHHHHHHHHTTEE-EEEEESSSTTHHHHHHHHCCSEEEEETTCSSSCHHHHHHHHHHTTCCSEEEEEECC--
T ss_pred             EcCCHHHHHHHHHHHhhCCcE-EEEEcCCHHHHHHHHHhcCCCEEEEecCCCCCChHHHHHHHHhcCCCCeEEEEeCCCC
Confidence            588999999999999999988 76 899999999988644321         23455553   33348899999999999


Q ss_pred             HHHHHHHHHcCCcceeeccch
Q 042991           68 LVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        68 ~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      .....++++.|+++|+.||+.
T Consensus        86 ~~~~~~~~~~g~~~~l~kp~~  106 (134)
T 3f6c_A           86 HFYGKHCADAGANGFVSKKEG  106 (134)
T ss_dssp             -CTHHHHHHTTCSEEEEGGGC
T ss_pred             hHHHHHHHHhCCCEEEeCCCC
Confidence            888889999999999999986

>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=99.48  E-value=6.9e-14  Score=76.89  Aligned_cols=87  Identities=11%  Similarity=-0.006  Sum_probs=70.1

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHH---hhh--hcCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVR---TIY--SREIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~--~~~~pii~lt~~~   66 (93)
                      +||++..+..++.+|+..||. +..+.++.+|++.++...++         +..|++++   +..  .+.+|+|++|+..
T Consensus         9 vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~~a~~~l~~~~~dlii~D~~l~~~~g~~~~~~l~~~~~~~~~~ii~~s~~~   87 (127)
T 3i42_A            9 VEDYQAAAETFKELLEMLGFQ-ADYVMSGTDALHAMSTRGYDAVFIDLNLPDTSGLALVKQLRALPMEKTSKFVAVSGFA   87 (127)
T ss_dssp             ECSCHHHHHHHHHHHHHTTEE-EEEESSHHHHHHHHHHSCCSEEEEESBCSSSBHHHHHHHHHHSCCSSCCEEEEEECC-
T ss_pred             EcCCHHHHHHHHHHHHHcCCC-EEEECCHHHHHHHHHhcCCCEEEEeCCCCCCCHHHHHHHHHhhhccCCCCEEEEECCc
Confidence            588999999999999999998 99999999999998654421         23455553   333  3789999999988


Q ss_pred             CHHHHHHHHHcCCcceeeccchh
Q 042991           67 ILVRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      +... .+++..|+++|+.||++.
T Consensus        88 ~~~~-~~~~~~g~~~~l~KP~~~  109 (127)
T 3i42_A           88 KNDL-GKEACELFDFYLEKPIDI  109 (127)
T ss_dssp             CTTC-CHHHHHHCSEEEESSCCH
T ss_pred             chhH-HHHHHHhhHHheeCCCCH
Confidence            8877 788999999999999973

>3q9s_A DNA-binding response regulator; DNA binding protein; 2.40A {Deinococcus radiodurans}

Probab=99.48  E-value=2e-13  Score=83.42  Aligned_cols=88  Identities=18%  Similarity=0.139  Sum_probs=71.9

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc------CC---CchHHHhhh--hcCCcEEEEcCCCCHH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ------SA---NGFDVRTIY--SREIPVVIMSPEIILV   69 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~------~~---~~~d~l~~~--~~~~pii~lt~~~~~~   69 (93)
                      |||++..+..++.+|+..||. +..+.++.+|++.+....++      .+   +|++++..+  .+.+|||++|+..+..
T Consensus        43 vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~~al~~~~~~~~DlvllD~~lp~~~G~~l~~~lr~~~~~~iI~lt~~~~~~  121 (249)
T 3q9s_A           43 IEDDHDIANVLRMDLTDAGYV-VDHADSAMNGLIKAREDHPDLILLDLGLPDFDGGDVVQRLRKNSALPIIVLTARDTVE  121 (249)
T ss_dssp             ECSCHHHHHHHHHHHHTTTCE-EEEESSHHHHHHHHHHSCCSEEEEECCSCHHHHHHHHHHHHTTCCCCEEEEESCCSHH
T ss_pred             EECCHHHHHHHHHHHHHCCCE-EEEeCCHHHHHHHHhcCCCCEEEEcCCCCCCCHHHHHHHHHcCCCCCEEEEECCCCHH
Confidence            589999999999999999998 99999999999998644422      12   334442222  2789999999999999


Q ss_pred             HHHHHHHcCCcceeeccchh
Q 042991           70 RIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        70 ~~~~~~~~ga~d~l~kP~~~   89 (93)
                      ...+++++||++|+.||+..
T Consensus       122 ~~~~a~~~Ga~~yl~Kp~~~  141 (249)
T 3q9s_A          122 EKVRLLGLGADDYLIKPFHP  141 (249)
T ss_dssp             HHHHHHHHTCSEEEESSCCH
T ss_pred             HHHHHHHCCCcEEEECCCCH
Confidence            99999999999999999873

>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=99.48  E-value=2.1e-13  Score=75.60  Aligned_cols=87  Identities=17%  Similarity=0.143  Sum_probs=70.6

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHH---hhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~~~~pii~lt~~~~~   68 (93)
                      +||++..+..+...|+..||. +..+.++.+++..+....++         +..|++++   ....+.+|+|++|+..+.
T Consensus         9 vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~~a~~~~~~~~~dlvl~D~~l~~~~g~~~~~~l~~~~~~~~ii~~s~~~~~   87 (136)
T 1mvo_A            9 VDDEESIVTLLQYNLERSGYD-VITASDGEEALKKAETEKPDLIVLDVMLPKLDGIEVCKQLRQQKLMFPILMLTAKDEE   87 (136)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCE-EEEESSHHHHHHHHHHHCCSEEEEESSCSSSCHHHHHHHHHHTTCCCCEEEEECTTCC
T ss_pred             EECCHHHHHHHHHHHHHCCcE-EEEecCHHHHHHHHhhcCCCEEEEecCCCCCCHHHHHHHHHcCCCCCCEEEEECCCCH
Confidence            588999999999999988999 99999999999988543321         23455553   333378999999998888


Q ss_pred             HHHHHHHHcCCcceeeccch
Q 042991           69 VRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~   88 (93)
                      ....++++.|+++|+.||++
T Consensus        88 ~~~~~~~~~g~~~~l~KP~~  107 (136)
T 1mvo_A           88 FDKVLGLELGADDYMTKPFS  107 (136)
T ss_dssp             CCHHHHHHTTCCEEEESSCC
T ss_pred             HHHHHHHhCCCCEEEECCCC
Confidence            88888999999999999986

>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=99.48  E-value=3.9e-13  Score=73.04  Aligned_cols=87  Identities=16%  Similarity=0.172  Sum_probs=70.2

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhh--hcCCcEEEEcCCCCHH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIY--SREIPVVIMSPEIILV   69 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~--~~~~pii~lt~~~~~~   69 (93)
                      +||++..+..++..|+..||. +..+.++.+++..+....++         +..|++++...  .+.+|+|++|+..+..
T Consensus         7 vdd~~~~~~~l~~~l~~~~~~-v~~~~~~~~~~~~~~~~~~dlvi~D~~l~~~~g~~~~~~l~~~~~~~ii~~s~~~~~~   85 (121)
T 1zh2_A            7 VEDEQAIRRFLRTALEGDGMR-VFEAETLQRGLLEAATRKPDLIILDLGLPDGDGIEFIRDLRQWSAVPVIVLSARSEES   85 (121)
T ss_dssp             ECSCHHHHHHHHHHHHTTTCE-EEEESSHHHHHHHHHHHCCSEEEEESEETTEEHHHHHHHHHTTCCCCEEEEESCCSHH
T ss_pred             EeCCHHHHHHHHHHHhcCCCE-EEEeCCHHHHHHHHhcCCCCEEEEeCCCCCCcHHHHHHHHHhCCCCcEEEEECCCCHH
Confidence            588999999999999988999 99999999999887533221         22455553222  2789999999999998


Q ss_pred             HHHHHHHcCCcceeeccch
Q 042991           70 RIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        70 ~~~~~~~~ga~d~l~kP~~   88 (93)
                      ...++++.|+++|+.||++
T Consensus        86 ~~~~~~~~g~~~~l~Kp~~  104 (121)
T 1zh2_A           86 DKIAALDAGADDYLSKPFG  104 (121)
T ss_dssp             HHHHHHHHTCSEEEESSCC
T ss_pred             HHHHHHhcCCCeEEeCCcC
Confidence            8889999999999999986

>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=99.48  E-value=7.6e-13  Score=73.34  Aligned_cols=87  Identities=21%  Similarity=0.202  Sum_probs=71.3

Q ss_pred             CCCcHHHHHHHHHHHhhcCC--CceEEeCCHHHHHHHhcc-------Cccc---------CCCchHHHh---hhh--cCC
Q 042991            1 LNDSFVDRKVIERLLTISSS--RDLYCSCSGRRALQFLGL-------DEEQ---------SANGFDVRT---IYS--REI   57 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~--~~v~~~~~~~~a~~~~~~-------~~~~---------~~~~~d~l~---~~~--~~~   57 (93)
                      +||++..+..++.+|+..|+  . +..+.++.+|++.+..       ..++         +..|++++.   ...  +.+
T Consensus         8 vdd~~~~~~~l~~~L~~~~~~~~-v~~~~~~~~a~~~l~~~~~~~~~~~~dlvi~d~~~~~~~g~~~~~~l~~~~~~~~~   86 (140)
T 1k68_A            8 VEDNKADIRLIQEALANSTVPHE-VVTVRDGMEAMAYLRQEGEYANASRPDLILLXLNLPKKDGREVLAEIKSDPTLKRI   86 (140)
T ss_dssp             ECCCHHHHHHHHHHHHTCSSCCE-EEEECSHHHHHHHHTTCGGGGSCCCCSEEEECSSCSSSCHHHHHHHHHHSTTGGGS
T ss_pred             EeCCHHHHHHHHHHHHhcCCCce-EEEECCHHHHHHHHHcccccccCCCCcEEEEecCCCcccHHHHHHHHHcCcccccc
Confidence            58899999999999999888  6 9999999999999875       2221         234555533   322  678


Q ss_pred             cEEEEcCCCCHHHHHHHHHcCCcceeeccch
Q 042991           58 PVVIMSPEIILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        58 pii~lt~~~~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      |+|++|+..+.....++++.|+++|+.||++
T Consensus        87 pii~ls~~~~~~~~~~~~~~g~~~~l~kP~~  117 (140)
T 1k68_A           87 PVVVLSTSINEDDIFHSYDLHVNCYITKSAN  117 (140)
T ss_dssp             CEEEEESCCCHHHHHHHHHTTCSEEEECCSS
T ss_pred             cEEEEecCCcHHHHHHHHHhchhheecCCCC
Confidence            9999999999999999999999999999986

>3grc_A Sensor protein, kinase; protein structure initiative II(PSI II), NYSGXRC, 11025B, structural genomics; 2.21A {Polaromonas SP}

Probab=99.48  E-value=1.1e-13  Score=77.28  Aligned_cols=87  Identities=10%  Similarity=0.035  Sum_probs=71.1

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHH---Hhh--hhcCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDV---RTI--YSREIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~---l~~--~~~~~pii~lt~~~   66 (93)
                      +||++..+..++.+|++.||. +..+.++.+|++.+....++         +..|+++   ++.  ..+.+|||++|+..
T Consensus        12 vdd~~~~~~~l~~~l~~~g~~-v~~~~~~~~a~~~l~~~~~dlvi~d~~l~~~~g~~~~~~l~~~~~~~~~~ii~~s~~~   90 (140)
T 3grc_A           12 CEDDPDIARLLNLMLEKGGFD-SDMVHSAAQALEQVARRPYAAMTVDLNLPDQDGVSLIRALRRDSRTRDLAIVVVSANA   90 (140)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCE-EEEECSHHHHHHHHHHSCCSEEEECSCCSSSCHHHHHHHHHTSGGGTTCEEEEECTTH
T ss_pred             EcCCHHHHHHHHHHHHHCCCe-EEEECCHHHHHHHHHhCCCCEEEEeCCCCCCCHHHHHHHHHhCcccCCCCEEEEecCC
Confidence            589999999999999999999 99999999999998654431         2345565   333  23789999999988


Q ss_pred             CHHHHH-HHHHcCCcceeeccch
Q 042991           67 ILVRID-RYLEDGAEDSETCQMW   88 (93)
Q Consensus        67 ~~~~~~-~~~~~ga~d~l~kP~~   88 (93)
                      +..... .+++.|+++|+.||+.
T Consensus        91 ~~~~~~~~~~~~g~~~~l~kP~~  113 (140)
T 3grc_A           91 REGELEFNSQPLAVSTWLEKPID  113 (140)
T ss_dssp             HHHHHHHCCTTTCCCEEECSSCC
T ss_pred             ChHHHHHHhhhcCCCEEEeCCCC
Confidence            877766 7889999999999986

>1dcf_A ETR1 protein; beta-alpha five sandwich, transferase; 2.50A {Arabidopsis thaliana} SCOP: c.23.1.2

Probab=99.48  E-value=8.8e-13  Score=73.24  Aligned_cols=87  Identities=11%  Similarity=0.132  Sum_probs=68.3

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCcc--------cCCCchHHHhhhh---c----CC-cEEEEcC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEE--------QSANGFDVRTIYS---R----EI-PVVIMSP   64 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~--------~~~~~~d~l~~~~---~----~~-pii~lt~   64 (93)
                      +||++..+..++.+|+..||. +..+.++.+|++.+.....        ++.+|++++..+.   +    .. |||++|+
T Consensus        13 vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~~a~~~~~~~~dlvllD~~lp~~~g~~~~~~l~~~~~~~~~~~~~ii~~s~   91 (136)
T 1dcf_A           13 MDENGVSRMVTKGLLVHLGCE-VTTVSSNEECLRVVSHEHKVVFMDVCMPGVENYQIALRIHEKFTKQRHQRPLLVALSG   91 (136)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCE-EEEESSHHHHHHHCCTTCSEEEEECCSSTTTTTHHHHHHHHHHC-CCSCCCEEEEEES
T ss_pred             EeCCHHHHHHHHHHHHHcCCe-EEEeCCHHHHHHHHhccCCEEEEeCCCCCCcHHHHHHHHHHhhhhccCCCceEEEEeC
Confidence            589999999999999988999 9999999999998864321        1234555533221   2    23 5788999


Q ss_pred             CCCHHHHHHHHHcCCcceeeccch
Q 042991           65 EIILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        65 ~~~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      ..+.....++++.|+++|+.||++
T Consensus        92 ~~~~~~~~~~~~~ga~~~l~KP~~  115 (136)
T 1dcf_A           92 NTDKSTKEKCMSFGLDGVLLKPVS  115 (136)
T ss_dssp             CCSHHHHHHHHHTTCCEEEESSCC
T ss_pred             CCCHHHHHHHHHcCCCeEEECCCC
Confidence            999888889999999999999986

>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=99.48  E-value=6.1e-13  Score=75.43  Aligned_cols=87  Identities=17%  Similarity=0.186  Sum_probs=71.9

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHH---hhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~~~~pii~lt~~~~~   68 (93)
                      +||++..+..+..+|+..||. +..+.++.+|+..+....++         +..|++++   ....+.+|||++|+..+.
T Consensus         9 vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~~a~~~l~~~~~dliild~~l~~~~g~~~~~~l~~~~~~~pii~ls~~~~~   87 (155)
T 1qkk_A            9 IDDDRDLRKAMQQTLELAGFT-VSSFASATEALAGLSADFAGIVISDIRMPGMDGLALFRKILALDPDLPMILVTGHGDI   87 (155)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCE-EEEESCHHHHHHTCCTTCCSEEEEESCCSSSCHHHHHHHHHHHCTTSCEEEEECGGGH
T ss_pred             EeCCHHHHHHHHHHHHHcCcE-EEEECCHHHHHHHHHhCCCCEEEEeCCCCCCCHHHHHHHHHhhCCCCCEEEEECCCCh
Confidence            588999999999999999999 99999999999998654321         22455543   333378999999999998


Q ss_pred             HHHHHHHHcCCcceeeccch
Q 042991           69 VRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~   88 (93)
                      ....++++.|+++|+.||+.
T Consensus        88 ~~~~~~~~~g~~~~l~kP~~  107 (155)
T 1qkk_A           88 PMAVQAIQDGAYDFIAKPFA  107 (155)
T ss_dssp             HHHHHHHHTTCCEEEESSCC
T ss_pred             HHHHHHHhcCCCeEEeCCCC
Confidence            88899999999999999986

>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=99.47  E-value=2.2e-13  Score=89.12  Aligned_cols=87  Identities=25%  Similarity=0.231  Sum_probs=72.5

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCcc---------cCCCchHHHhhh-----hcCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEE---------QSANGFDVRTIY-----SREIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~---------~~~~~~d~l~~~-----~~~~pii~lt~~~   66 (93)
                      |||++..+..+..+|+..||. +..+.++.+|++.+....+         ++++|++++..+     .+.+|||++|+..
T Consensus         7 vdD~~~~~~~l~~~L~~~~~~-v~~a~~~~~al~~~~~~~~dlvllD~~mp~~~G~~~~~~l~~~~~~~~~pii~lt~~~   85 (459)
T 1w25_A            7 VDDIEANVRLLEAKLTAEYYE-VSTAMDGPTALAMAARDLPDIILLDVMMPGMDGFTVCRKLKDDPTTRHIPVVLITALD   85 (459)
T ss_dssp             ECSSTTHHHHHHHHHHHTTCE-EEEESSHHHHHHHHHHHCCSEEEEESCCSSSCHHHHHHHHHHSTTTTTSCEEEEECSS
T ss_pred             EeCCHHHHHHHHHHHHHcCCE-EEEECCHHHHHHHHhcCCCCEEEEcCCCCCCCHHHHHHHHhcCcccCCCCEEEEECCC
Confidence            589999999999999988999 9999999999998864332         134566663322     2578999999999


Q ss_pred             CHHHHHHHHHcCCcceeeccch
Q 042991           67 ILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      +.....++++.||++||.||+.
T Consensus        86 ~~~~~~~a~~~Ga~~~l~KP~~  107 (459)
T 1w25_A           86 GRGDRIQGLESGASDFLTKPID  107 (459)
T ss_dssp             CHHHHHHHHHHTCCEEEESSCC
T ss_pred             CHHHHHHHHHcCCCEEEeCCCC
Confidence            9999999999999999999986

>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=99.47  E-value=8.5e-14  Score=76.36  Aligned_cols=87  Identities=22%  Similarity=0.150  Sum_probs=70.4

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhh---h--cCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIY---S--REIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~---~--~~~pii~lt~~~   66 (93)
                      +||++..+..++.+|+..||. +..+.++.++++.+....++         +.+|++++..+   .  +.+|+|++|+..
T Consensus         8 vdd~~~~~~~l~~~l~~~g~~-v~~~~~~~~a~~~~~~~~~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~~~ii~~s~~~   86 (127)
T 2jba_A            8 VEDEAPIREMVCFVLEQNGFQ-PVEAEDYDSAVNQLNEPWPDLILLAWMLPGGSGIQFIKHLRRESMTRDIPVVMLTARG   86 (127)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCE-EEEECSHHHHHTTCSSSCCSEEEEESEETTEEHHHHHHHHHTSTTTTTSCEEEEEETT
T ss_pred             EcCCHHHHHHHHHHHHHCCce-EEEeCCHHHHHHHHhccCCCEEEEecCCCCCCHHHHHHHHHhCcccCCCCEEEEeCCC
Confidence            589999999999999988999 99999999999888654321         22345543322   2  678999999998


Q ss_pred             CHHHHHHHHHcCCcceeeccch
Q 042991           67 ILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      +.....++++.|+++|+.||++
T Consensus        87 ~~~~~~~~~~~ga~~~l~Kp~~  108 (127)
T 2jba_A           87 EEEDRVRGLETGADDCITKPFS  108 (127)
T ss_dssp             HHHHHHTTCCCSCSEEEEESCC
T ss_pred             CHHHHHHHHhcCCCeEEeCCCC
Confidence            8888888999999999999986

>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=99.46  E-value=9.9e-13  Score=73.64  Aligned_cols=88  Identities=24%  Similarity=0.257  Sum_probs=71.4

Q ss_pred             CCCcHHHHHHHHHHHhhcCC--CceEEeCCHHHHHHHhcc----------Cccc---------CCCchHHHhhh---h--
Q 042991            1 LNDSFVDRKVIERLLTISSS--RDLYCSCSGRRALQFLGL----------DEEQ---------SANGFDVRTIY---S--   54 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~--~~v~~~~~~~~a~~~~~~----------~~~~---------~~~~~d~l~~~---~--   54 (93)
                      +||++..+..++.+|+..|+  . +..+.++.+|++.+..          ..++         +..|++++..+   .  
T Consensus        12 vdd~~~~~~~l~~~L~~~g~~~~-v~~~~~~~~al~~l~~~~~~~~~~~~~~~dlvi~D~~l~~~~g~~~~~~l~~~~~~   90 (149)
T 1k66_A           12 VEDSDEDFSTFQRLLQREGVVNP-IYRCITGDQALDFLYQTGSYCNPDIAPRPAVILLDLNLPGTDGREVLQEIKQDEVL   90 (149)
T ss_dssp             ECCCHHHHHHHHHHHHHTTBCSC-EEEECSHHHHHHHHHTCCSSSCGGGCCCCSEEEECSCCSSSCHHHHHHHHTTSTTG
T ss_pred             EECCHHHHHHHHHHHHHcCCCce-EEEECCHHHHHHHHHhcccccCcccCCCCcEEEEECCCCCCCHHHHHHHHHhCccc
Confidence            58899999999999999988  6 9999999999999864          2221         23455553322   2  


Q ss_pred             cCCcEEEEcCCCCHHHHHHHHHcCCcceeeccchh
Q 042991           55 REIPVVIMSPEIILVRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        55 ~~~pii~lt~~~~~~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      +.+|+|++|+..+.....++++.|+++|+.||++.
T Consensus        91 ~~~~ii~~t~~~~~~~~~~~~~~g~~~~l~kP~~~  125 (149)
T 1k66_A           91 KKIPVVIMTTSSNPKDIEICYSYSISSYIVKPLEI  125 (149)
T ss_dssp             GGSCEEEEESCCCHHHHHHHHHTTCSEEEECCSSH
T ss_pred             CCCeEEEEeCCCCHHHHHHHHHCCCCEEEeCCCCH
Confidence            67899999999999999999999999999999863

>3ilh_A Two component response regulator; NYSGXRC, PSI-II, protein S initiative, structural genomics; 2.59A {Cytophaga hutchinsonii}

Probab=99.46  E-value=1.2e-12  Score=73.12  Aligned_cols=87  Identities=10%  Similarity=0.098  Sum_probs=72.2

Q ss_pred             CCCcHHHHHHHHHHHhhcCC--CceEEeCCHHHHHHHhcc-----Cccc---------CCCchHH---Hhh----hhcCC
Q 042991            1 LNDSFVDRKVIERLLTISSS--RDLYCSCSGRRALQFLGL-----DEEQ---------SANGFDV---RTI----YSREI   57 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~--~~v~~~~~~~~a~~~~~~-----~~~~---------~~~~~d~---l~~----~~~~~   57 (93)
                      +||++..+..++.+|+..|+  . +..+.++.+|++.+..     ..++         +..|+++   ++.    ..+.+
T Consensus        15 vdd~~~~~~~l~~~l~~~~~~~~-v~~~~~~~~a~~~l~~~~~~~~~~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~~~~   93 (146)
T 3ilh_A           15 IDDDDIVNFLNTTIIRMTHRVEE-IQSVTSGNAAINKLNELYAAGRWPSIICIDINMPGINGWELIDLFKQHFQPMKNKS   93 (146)
T ss_dssp             ECSCHHHHHHHHHHHHTTCCEEE-EEEESSHHHHHHHHHHHHTSSCCCSEEEEESSCSSSCHHHHHHHHHHHCGGGTTTC
T ss_pred             EeCCHHHHHHHHHHHHhcCCCee-eeecCCHHHHHHHHHHhhccCCCCCEEEEcCCCCCCCHHHHHHHHHHhhhhccCCC
Confidence            58899999999999999998  7 9999999999999865     3321         2345665   333    33789


Q ss_pred             cEEEEcCCCCHHHHHHHHHcC-Ccceeeccch
Q 042991           58 PVVIMSPEIILVRIDRYLEDG-AEDSETCQMW   88 (93)
Q Consensus        58 pii~lt~~~~~~~~~~~~~~g-a~d~l~kP~~   88 (93)
                      |+|++|+..+.....++++.| +++|+.||+.
T Consensus        94 ~ii~~t~~~~~~~~~~~~~~g~~~~~l~KP~~  125 (146)
T 3ilh_A           94 IVCLLSSSLDPRDQAKAEASDWVDYYVSKPLT  125 (146)
T ss_dssp             EEEEECSSCCHHHHHHHHHCSSCCEEECSSCC
T ss_pred             eEEEEeCCCChHHHHHHHhcCCcceeeeCCCC
Confidence            999999999999999999999 9999999997

>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=99.46  E-value=3e-13  Score=80.82  Aligned_cols=88  Identities=13%  Similarity=0.068  Sum_probs=72.5

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHH---hhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~~~~pii~lt~~~~~   68 (93)
                      +||++..+..+..+|+..||. +..+.++.+|+..+....++         +.+|++++   ....+.+|||++|+..+.
T Consensus         8 vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~~a~~~~~~~~~dlvllD~~l~~~~g~~~~~~lr~~~~~~~ii~ls~~~~~   86 (225)
T 1kgs_A            8 VEDERDLADLITEALKKEMFT-VDVCYDGEEGMYMALNEPFDVVILDIMLPVHDGWEILKSMRESGVNTPVLMLTALSDV   86 (225)
T ss_dssp             ECSSHHHHHHHHHHHHHTTCE-EEEESSHHHHHHHHHHSCCSEEEEESCCSSSCHHHHHHHHHHTTCCCCEEEEESSCHH
T ss_pred             EeCCHHHHHHHHHHHHHCCCE-EEEECCHHHHHHHHhcCCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCCEEEEeCCCCH
Confidence            589999999999999998999 99999999999988644321         23456653   333378999999999988


Q ss_pred             HHHHHHHHcCCcceeeccchh
Q 042991           69 VRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      ....++++.|+++|+.||++.
T Consensus        87 ~~~~~~~~~ga~~~l~Kp~~~  107 (225)
T 1kgs_A           87 EYRVKGLNMGADDYLPKPFDL  107 (225)
T ss_dssp             HHHHHTCCCCCSEEEESSCCH
T ss_pred             HHHHHHHhCCccEEEeCCCCH
Confidence            888899999999999999863

>2hqr_A Putative transcriptional regulator; phosporylation-independent response regulator, H. pylori, SY dimer, signaling protein; NMR {Helicobacter pylori}

Probab=99.46  E-value=1.4e-12  Score=78.02  Aligned_cols=86  Identities=15%  Similarity=0.050  Sum_probs=72.8

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCcc-----cCCCchHHH---hhhhc-CCcEEEEcCCCCHHHH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEE-----QSANGFDVR---TIYSR-EIPVVIMSPEIILVRI   71 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~-----~~~~~~d~l---~~~~~-~~pii~lt~~~~~~~~   71 (93)
                      +||++..+..+..+|+..||. +..+.++.+|++.+....+     ++++|++++   ... + .+|||++|+..+....
T Consensus         6 vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~~al~~l~~~~~dlvilp~~~g~~~~~~lr~~-~~~~~ii~lt~~~~~~~~   83 (223)
T 2hqr_A            6 IEKNSVLGGEIEKGLNVKGFM-ADVTESLEDGEYLMDIRNYDLVMVSDKNALSFVSRIKEK-HSSIVVLVSSDNPTSEEE   83 (223)
T ss_dssp             ECSCHHHHHHHHHHHGGGTCC-EEEESSHHHHHHHHTTSCCSEEEECCTTHHHHHHHHHHH-CTTSEEEEEESSCCHHHH
T ss_pred             EcCCHHHHHHHHHHHHHCCcE-EEEECCHHHHHHHHhcCCCCEEEeCCCCHHHHHHHHHhC-CCCCcEEEEECCCCHHHH
Confidence            589999999999999999999 9999999999999875432     234566653   333 5 8999999999999999


Q ss_pred             HHHHHcCCcceeeccc-h
Q 042991           72 DRYLEDGAEDSETCQM-W   88 (93)
Q Consensus        72 ~~~~~~ga~d~l~kP~-~   88 (93)
                      .++++.|+++|+.||+ +
T Consensus        84 ~~~~~~Ga~~~l~Kp~~~  101 (223)
T 2hqr_A           84 VHAFEQGADDYIAKPYRS  101 (223)
T ss_dssp             HHHHHHTCSEEEETTCSC
T ss_pred             HHHHHcCCCEEEECCCCC
Confidence            9999999999999998 5

>2rjn_A Response regulator receiver:metal-dependent phosphohydrolase, HD subdomain; structural genomics, oceanospirillum SP. MED92; 2.10A {Neptuniibacter caesariensis}

Probab=99.46  E-value=1.3e-12  Score=74.06  Aligned_cols=87  Identities=15%  Similarity=-0.026  Sum_probs=71.7

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHH---hhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~~~~pii~lt~~~~~   68 (93)
                      +||++..+..+..+|+..||. +..+.++.+|+..+....++         +..|++++   ....+.+|||++|+..+.
T Consensus        13 vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~~a~~~l~~~~~dlvi~d~~l~~~~g~~~~~~l~~~~~~~~ii~ls~~~~~   91 (154)
T 2rjn_A           13 VDDEQPILNSLKRLIKRLGCN-IITFTSPLDALEALKGTSVQLVISDMRMPEMGGEVFLEQVAKSYPDIERVVISGYADA   91 (154)
T ss_dssp             ECSCHHHHHHHHHHHHTTTCE-EEEESCHHHHHHHHTTSCCSEEEEESSCSSSCHHHHHHHHHHHCTTSEEEEEECGGGH
T ss_pred             EcCCHHHHHHHHHHHHHcCCe-EEEeCCHHHHHHHHhcCCCCEEEEecCCCCCCHHHHHHHHHHhCCCCcEEEEecCCCH
Confidence            588999999999999999999 99999999999998754421         23455553   333378999999999998


Q ss_pred             HHHHHHHHcC-Ccceeeccch
Q 042991           69 VRIDRYLEDG-AEDSETCQMW   88 (93)
Q Consensus        69 ~~~~~~~~~g-a~d~l~kP~~   88 (93)
                      ....++++.| +++|+.||+.
T Consensus        92 ~~~~~~~~~g~~~~~l~kP~~  112 (154)
T 2rjn_A           92 QATIDAVNRGKISRFLLKPWE  112 (154)
T ss_dssp             HHHHHHHHTTCCSEEEESSCC
T ss_pred             HHHHHHHhccchheeeeCCCC
Confidence            8888999998 9999999986

>1dz3_A Stage 0 sporulation protein A; response regulator, domain swapping; 1.65A {Bacillus stearothermophilus} SCOP: c.23.1.1 PDB: 1qmp_A*

Probab=99.45  E-value=5.5e-13  Score=73.57  Aligned_cols=87  Identities=13%  Similarity=0.081  Sum_probs=69.2

Q ss_pred             CCCcHHHHHHHHHHHhhc-CCCceE-EeCCHHHHHHHhccCccc---------CCCchHHH---hhh-hcCCcEEEEcCC
Q 042991            1 LNDSFVDRKVIERLLTIS-SSRDLY-CSCSGRRALQFLGLDEEQ---------SANGFDVR---TIY-SREIPVVIMSPE   65 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~-~~~~v~-~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~-~~~~pii~lt~~   65 (93)
                      +||++..+..++.+|+.. ||. +. .+.++.+|++.+....++         +.+|++++   ... .+.+|+|++|+.
T Consensus         8 vdd~~~~~~~l~~~l~~~~~~~-~~~~~~~~~~a~~~~~~~~~dlvllD~~l~~~~g~~~~~~l~~~~~~~~~ii~ls~~   86 (130)
T 1dz3_A            8 ADDNRELVSLLDEYISSQPDME-VIGTAYNGQDCLQMLEEKRPDILLLDIIMPHLDGLAVLERIRAGFEHQPNVIMLTAF   86 (130)
T ss_dssp             ECSCHHHHHHHHHHHHTSTTEE-EEEEESSHHHHHHHHHHHCCSEEEEESCCSSSCHHHHHHHHHHHCSSCCEEEEEEET
T ss_pred             EcCCHHHHHHHHHHHHhCCCce-EEEEeCCHHHHHHHHhcCCCCEEEEecCCCCCCHHHHHHHHHhcCCCCCcEEEEecC
Confidence            589999999999999876 777 54 899999999988643321         23566653   332 267889999999


Q ss_pred             CCHHHHHHHHHcCCcceeeccch
Q 042991           66 IILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        66 ~~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      .+.....++++.|+++|+.||++
T Consensus        87 ~~~~~~~~~~~~ga~~~l~KP~~  109 (130)
T 1dz3_A           87 GQEDVTKKAVELGASYFILKPFD  109 (130)
T ss_dssp             TCHHHHHHHHHTTCEEEEECSSC
T ss_pred             CCHHHHHHHHHcCCCEEEeCCCC
Confidence            99989899999999999999986

>2pln_A HP1043, response regulator; signaling protein; 1.80A {Helicobacter pylori} PDB: 2hqo_A

Probab=99.45  E-value=1.5e-12  Score=72.39  Aligned_cols=86  Identities=15%  Similarity=0.052  Sum_probs=71.9

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc-----CCCchHH---Hhhhhc-CCcEEEEcCCCCHHHH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ-----SANGFDV---RTIYSR-EIPVVIMSPEIILVRI   71 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~-----~~~~~d~---l~~~~~-~~pii~lt~~~~~~~~   71 (93)
                      +||++..+..++.+|+..||. +..+.++.+++..+....++     +..|+++   +... + .+|||++|+..+....
T Consensus        24 vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~~al~~l~~~~~dlvi~~~~~g~~~~~~l~~~-~~~~~ii~ls~~~~~~~~  101 (137)
T 2pln_A           24 IEKNSVLGGEIEKGLNVKGFM-ADVTESLEDGEYLMDIRNYDLVMVSDKNALSFVSRIKEK-HSSIVVLVSSDNPTSEEE  101 (137)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCE-EEEESCHHHHHHHHHHSCCSEEEECSTTHHHHHHHHHHH-STTSEEEEEESSCCHHHH
T ss_pred             EeCCHHHHHHHHHHHHHcCcE-EEEeCCHHHHHHHHHcCCCCEEEEcCccHHHHHHHHHhc-CCCccEEEEeCCCCHHHH
Confidence            589999999999999999999 99999999999988644321     2345565   3333 6 8999999999999999


Q ss_pred             HHHHHcCCcceeeccc-h
Q 042991           72 DRYLEDGAEDSETCQM-W   88 (93)
Q Consensus        72 ~~~~~~ga~d~l~kP~-~   88 (93)
                      .++++.|+++|+.||+ .
T Consensus       102 ~~~~~~g~~~~l~kP~~~  119 (137)
T 2pln_A          102 VHAFEQGADDYIAKPYRS  119 (137)
T ss_dssp             HHHHHTTCSEEEESSCSC
T ss_pred             HHHHHcCCceeeeCCCCC
Confidence            9999999999999998 5

>2qxy_A Response regulator; regulation of transcription, NYSGXRC, protein structure initiative II (PSI II), structural genomics; 1.95A {Thermotoga maritima}

Probab=99.45  E-value=1.1e-12  Score=73.18  Aligned_cols=87  Identities=13%  Similarity=0.089  Sum_probs=70.6

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc----C-C---CchHHH---hhhhcCCcEEEEcCCCCHH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ----S-A---NGFDVR---TIYSREIPVVIMSPEIILV   69 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~----~-~---~~~d~l---~~~~~~~pii~lt~~~~~~   69 (93)
                      +||++..+..++.+|+..||+ +..+.++.+|++.+....++    + +   .|++++   ....+.+|+|++|+..+..
T Consensus        10 vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~~a~~~l~~~~~dlvi~d~~~~~~g~~~~~~l~~~~~~~pii~ls~~~~~~   88 (142)
T 2qxy_A           10 VDESRITFLAVKNALEKDGFN-VIWAKNEQEAFTFLRREKIDLVFVDVFEGEESLNLIRRIREEFPDTKVAVLSAYVDKD   88 (142)
T ss_dssp             ECSCHHHHHHHHHHHGGGTCE-EEEESSHHHHHHHHTTSCCSEEEEECTTTHHHHHHHHHHHHHCTTCEEEEEESCCCHH
T ss_pred             EeCCHHHHHHHHHHHHhCCCE-EEEECCHHHHHHHHhccCCCEEEEeCCCCCcHHHHHHHHHHHCCCCCEEEEECCCCHH
Confidence            588999999999999999999 99999999999998754421    1 1   123332   2223789999999999998


Q ss_pred             HHHHHHHcCCcceeeccch
Q 042991           70 RIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        70 ~~~~~~~~ga~d~l~kP~~   88 (93)
                      ...++++.|+++|+.||+.
T Consensus        89 ~~~~~~~~g~~~~l~kP~~  107 (142)
T 2qxy_A           89 LIINSVKAGAVDYILKPFR  107 (142)
T ss_dssp             HHHHHHHHTCSCEEESSCC
T ss_pred             HHHHHHHCCcceeEeCCCC
Confidence            8999999999999999986

>3c3m_A Response regulator receiver protein; structural genomics, unknown function, PSI-2, protein struct initiative; HET: MSE; 1.70A {Methanoculleus marisnigri JR1}

Probab=99.45  E-value=1e-12  Score=73.25  Aligned_cols=88  Identities=18%  Similarity=0.198  Sum_probs=67.7

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhh-----hcCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIY-----SREIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~-----~~~~pii~lt~~~   66 (93)
                      +||++..+..++.+|+..||. +..+.++.+|++.+....++         +.+|++++..+     .+.+|||++|+..
T Consensus         9 vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~~al~~l~~~~~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~~~ii~ls~~~   87 (138)
T 3c3m_A            9 VDDSPMIVDVFVTMLERGGYR-PITAFSGEECLEALNATPPDLVLLDIMMEPMDGWETLERIKTDPATRDIPVLMLTAKP   87 (138)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCE-EEEESSHHHHHHHHHHSCCSEEEEESCCSSSCHHHHHHHHHHSTTTTTSCEEEEESSC
T ss_pred             EeCCHHHHHHHHHHHHHcCce-EEEeCCHHHHHHHHhccCCCEEEEeCCCCCCCHHHHHHHHHcCcccCCCCEEEEECCC
Confidence            589999999999999999999 99999999999988644321         23466653322     1578999999987


Q ss_pred             CHHHHHHHHHcCCcceeeccchh
Q 042991           67 ILVRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      .......+...|+++|+.||+..
T Consensus        88 ~~~~~~~~~~~~~~~~l~KP~~~  110 (138)
T 3c3m_A           88 LTPEEANEYGSYIEDYILKPTTH  110 (138)
T ss_dssp             CCHHHHHHTTTTCSEEEECCCHH
T ss_pred             ChHHHHHHhhcCHhheEeCCCCH
Confidence            66555555667789999999873

>2qr3_A Two-component system response regulator; structural genomics, signal receiver, PSI-2, protein structu initiative; 1.80A {Bacteroides fragilis}

Probab=99.44  E-value=8.1e-13  Score=73.48  Aligned_cols=87  Identities=17%  Similarity=0.102  Sum_probs=71.0

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc--------------CCCchHHH---hhhhcCCcEEEEc
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ--------------SANGFDVR---TIYSREIPVVIMS   63 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~--------------~~~~~d~l---~~~~~~~pii~lt   63 (93)
                      +||++..+..++.+|+..||. +..+.++.+|++.+....++              +..|++++   ....+.+|||++|
T Consensus         9 vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~~a~~~l~~~~~dlvi~d~~~~~~~~~~~~g~~~~~~l~~~~~~~~ii~ls   87 (140)
T 2qr3_A            9 VDDNKGVLTAVQLLLKNHFSK-VITLSSPVSLSTVLREENPEVVLLDMNFTSGINNGNEGLFWLHEIKRQYRDLPVVLFT   87 (140)
T ss_dssp             ECSCHHHHHHHHHHHTTTSSE-EEEECCHHHHHHHHHHSCEEEEEEETTTTC-----CCHHHHHHHHHHHCTTCCEEEEE
T ss_pred             EeCCHHHHHHHHHHHHhCCcE-EEEeCCHHHHHHHHHcCCCCEEEEeCCcCCCCCCCccHHHHHHHHHhhCcCCCEEEEE
Confidence            588999999999999999999 99999999999998644321              22344443   3333789999999


Q ss_pred             CCCCHHHHHHHHHcCCcceeeccch
Q 042991           64 PEIILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        64 ~~~~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      +..+.....++++.|+++|+.||+.
T Consensus        88 ~~~~~~~~~~~~~~g~~~~l~kp~~  112 (140)
T 2qr3_A           88 AYADIDLAVRGIKEGASDFVVKPWD  112 (140)
T ss_dssp             EGGGHHHHHHHHHTTCCEEEEESCC
T ss_pred             CCCCHHHHHHHHHcCchheeeCCCC
Confidence            9999888899999999999999986

>3cnb_A DNA-binding response regulator, MERR family; signal receiver domain, DNA binding protein, protein structu initiative, PSI-2; 2.00A {Colwellia psychrerythraea}

Probab=99.44  E-value=2.5e-12  Score=71.64  Aligned_cols=88  Identities=15%  Similarity=0.121  Sum_probs=71.4

Q ss_pred             CCCcHHHHHHHHHHHhh-cCCCceEEeCCHHHHHHHhccCccc---------CCCchHH---Hhh--hhcCCcEEEEcCC
Q 042991            1 LNDSFVDRKVIERLLTI-SSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDV---RTI--YSREIPVVIMSPE   65 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~-~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~---l~~--~~~~~pii~lt~~   65 (93)
                      +||++..+..++.+|+. .||..+..+.++.+|++.++...++         +..|+++   +..  ..+.+|+|++|+.
T Consensus        14 vdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~a~~~l~~~~~dlii~d~~l~~~~g~~~~~~l~~~~~~~~~~ii~~s~~   93 (143)
T 3cnb_A           14 IEDDKEFADMLTQFLENLFPYAKIKIAYNPFDAGDLLHTVKPDVVMLDLMMVGMDGFSICHRIKSTPATANIIVIAMTGA   93 (143)
T ss_dssp             ECSCHHHHHHHHHHHHHHCTTCEEEEECSHHHHHHHHHHTCCSEEEEETTCTTSCHHHHHHHHHTSTTTTTSEEEEEESS
T ss_pred             EECCHHHHHHHHHHHHhccCccEEEEECCHHHHHHHHHhcCCCEEEEecccCCCcHHHHHHHHHhCccccCCcEEEEeCC
Confidence            58899999999999998 8887578899999999998644321         2345555   333  2378999999999


Q ss_pred             CCHHHHHHHHHcCCcceeeccch
Q 042991           66 IILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        66 ~~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      .+.....++++.|+++|+.||+.
T Consensus        94 ~~~~~~~~~~~~g~~~~l~kP~~  116 (143)
T 3cnb_A           94 LTDDNVSRIVALGAETCFGKPLN  116 (143)
T ss_dssp             CCHHHHHHHHHTTCSEEEESSCC
T ss_pred             CCHHHHHHHHhcCCcEEEeCCCC
Confidence            99998899999999999999986

>3h5i_A Response regulator/sensory box protein/ggdef domain protein; structural genomics, transcription, PSI-2; 1.90A {Carboxydothermus hydrogenoformans z-2901}

Probab=99.44  E-value=2e-13  Score=76.37  Aligned_cols=86  Identities=15%  Similarity=0.111  Sum_probs=70.9

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhcc-Cccc----------CCCchHH---HhhhhcCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGL-DEEQ----------SANGFDV---RTIYSREIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~-~~~~----------~~~~~d~---l~~~~~~~pii~lt~~~   66 (93)
                      +||++..+..++.+|+..||. +..+.++.+|++.+.. ..++          +..|+++   +... +.+|+|++|+..
T Consensus        11 vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~~a~~~l~~~~~~dlvi~D~~l~~~~~g~~~~~~l~~~-~~~~ii~ls~~~   88 (140)
T 3h5i_A           11 VEDSKFQAKTIANILNKYGYT-VEIALTGEAAVEKVSGGWYPDLILMDIELGEGMDGVQTALAIQQI-SELPVVFLTAHT   88 (140)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCE-EEEESSHHHHHHHHHTTCCCSEEEEESSCSSSCCHHHHHHHHHHH-CCCCEEEEESSS
T ss_pred             EeCCHHHHHHHHHHHHHcCCE-EEEecChHHHHHHHhcCCCCCEEEEeccCCCCCCHHHHHHHHHhC-CCCCEEEEECCC
Confidence            589999999999999999999 9999999999999864 2221          1345555   3333 899999999998


Q ss_pred             CHHHHHHHHHcCCcceeeccch
Q 042991           67 ILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      +.....++++.|+++|+.||+.
T Consensus        89 ~~~~~~~~~~~g~~~~l~KP~~  110 (140)
T 3h5i_A           89 EPAVVEKIRSVTAYGYVMKSAT  110 (140)
T ss_dssp             SCCCCGGGGGSCEEEEEETTCC
T ss_pred             CHHHHHHHHhCCCcEEEeCCCC
Confidence            8877778899999999999986

>3lte_A Response regulator; structural genomics, PSI, protein structure initiative, NYSG YORK structural genomix research consortium, nysgxrc; 2.00A {Bermanella marisrubri}

Probab=99.44  E-value=1.9e-12  Score=71.42  Aligned_cols=87  Identities=18%  Similarity=0.156  Sum_probs=65.3

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhhh-----cCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIYS-----REIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~~-----~~~pii~lt~~~   66 (93)
                      +||++..+..++.+|++.||. +..+.++.+|++.++...++         +..|++++..+.     ..++|+++++..
T Consensus        12 vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~~a~~~l~~~~~dlii~d~~l~~~~g~~~~~~l~~~~~~~~~~ii~~~~~~   90 (132)
T 3lte_A           12 VDDDQAMAAAIERVLKRDHWQ-VEIAHNGFDAGIKLSTFEPAIMTLDLSMPKLDGLDVIRSLRQNKVANQPKILVVSGLD   90 (132)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCE-EEEESSHHHHHHHHHHTCCSEEEEESCBTTBCHHHHHHHHHTTTCSSCCEEEEECCSC
T ss_pred             EECCHHHHHHHHHHHHHCCcE-EEEeCCHHHHHHHHHhcCCCEEEEecCCCCCCHHHHHHHHHhcCccCCCeEEEEeCCC
Confidence            588999999999999999999 99999999999998644421         234555533322     345566555555


Q ss_pred             CHHHHHHHHHcCCcceeeccchh
Q 042991           67 ILVRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      .. ...++++.|+++|+.||+..
T Consensus        91 ~~-~~~~~~~~g~~~~l~kP~~~  112 (132)
T 3lte_A           91 KA-KLQQAVTEGADDYLEKPFDN  112 (132)
T ss_dssp             SH-HHHHHHHHTCCEEECSSCCH
T ss_pred             hH-HHHHHHHhChHHHhhCCCCH
Confidence            44 77789999999999999873

>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=99.43  E-value=9.1e-13  Score=78.38  Aligned_cols=88  Identities=15%  Similarity=0.152  Sum_probs=70.7

Q ss_pred             CCCcHHHHHHHHHHHhhcC-CCce-EEeCCHHHHHHHhccCccc---------CCCchHHHh---hhhcCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTISS-SRDL-YCSCSGRRALQFLGLDEEQ---------SANGFDVRT---IYSREIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~-~~~v-~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~---~~~~~~pii~lt~~~   66 (93)
                      +||++..+..++.+|+..+ |. + ..+.++.+|++.+....++         +++|++++.   ...+.+|||++|+..
T Consensus        11 vdd~~~~~~~l~~~L~~~~~~~-vv~~~~~~~~al~~~~~~~~dlvllD~~lp~~~g~~~~~~lr~~~~~~~ii~ls~~~   89 (215)
T 1a04_A           11 IDDHPMLRTGVKQLISMAPDIT-VVGEASNGEQGIELAESLDPDLILLDLNMPGMNGLETLDKLREKSLSGRIVVFSVSN   89 (215)
T ss_dssp             ECSCHHHHHHHHHHHTTCTTEE-EEEEESSHHHHHHHHHHHCCSEEEEETTSTTSCHHHHHHHHHHSCCCSEEEEEECCC
T ss_pred             ECCCHHHHHHHHHHHhcCCCcE-EEEEeCCHHHHHHHHHhcCCCEEEEeCCCCCCcHHHHHHHHHHhCCCCcEEEEECCC
Confidence            5899999999999999764 77 5 7899999999988643321         234566533   333789999999999


Q ss_pred             CHHHHHHHHHcCCcceeeccchh
Q 042991           67 ILVRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      +.....++++.|+++|+.||++.
T Consensus        90 ~~~~~~~~~~~Ga~~~l~Kp~~~  112 (215)
T 1a04_A           90 HEEDVVTALKRGADGYLLKDMEP  112 (215)
T ss_dssp             CHHHHHHHHHTTCSEEEETTCCH
T ss_pred             CHHHHHHHHHcCCcEEEeCCCCH
Confidence            99999999999999999999863

>2qvg_A Two component response regulator; NYSGXRC, PSI-2, structural genomics, protein structure initiative; 1.50A {Legionella pneumophila subsp}

Probab=99.43  E-value=1.7e-12  Score=72.52  Aligned_cols=88  Identities=20%  Similarity=0.158  Sum_probs=71.0

Q ss_pred             CCCcHHHHHHHHHHHhhcCC--CceEEeCCHHHHHHHhcc------Cccc---------CCCchHHHhh---hh--cCCc
Q 042991            1 LNDSFVDRKVIERLLTISSS--RDLYCSCSGRRALQFLGL------DEEQ---------SANGFDVRTI---YS--REIP   58 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~--~~v~~~~~~~~a~~~~~~------~~~~---------~~~~~d~l~~---~~--~~~p   58 (93)
                      +||++..+..++.+|+..|+  . +..+.++.+|++.++.      ..++         +..|++++..   ..  +.+|
T Consensus        13 vdd~~~~~~~l~~~L~~~g~~~~-v~~~~~~~~a~~~l~~~~~~~~~~~dlii~D~~l~~~~g~~~~~~l~~~~~~~~~~   91 (143)
T 2qvg_A           13 LEDDEVDIQSVERVFHKISSLIK-IEIAKSGNQALDMLYGRNKENKIHPKLILLDINIPKMNGIEFLKELRDDSSFTDIE   91 (143)
T ss_dssp             ECCCHHHHHHHHHHHHHHCTTCC-EEEESSHHHHHHHHHTCTTCCCCCCSEEEEETTCTTSCHHHHHHHHTTSGGGTTCE
T ss_pred             EeCCHHHHHHHHHHHHHhCCCce-EEEECCHHHHHHHHHhcccccCCCCCEEEEecCCCCCCHHHHHHHHHcCccccCCc
Confidence            58899999999999998888  7 9999999999999864      2221         2245555332   22  6889


Q ss_pred             EEEEcCCCCHHHHHHHHHcCCcceeeccchh
Q 042991           59 VVIMSPEIILVRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        59 ii~lt~~~~~~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      +|++|+..+.....++++.|+++|+.||++.
T Consensus        92 ii~ls~~~~~~~~~~~~~~g~~~~l~kP~~~  122 (143)
T 2qvg_A           92 VFVLTAAYTSKDKLAFESLNIRGHLIKPLDY  122 (143)
T ss_dssp             EEEEESCCCHHHHHHHTTTTCCEEEESSCCH
T ss_pred             EEEEeCCCCHHHHHHHHhcCCCeEEECCCCH
Confidence            9999999999898999999999999999963

>3a10_A Response regulator; phosphoacceptor, signaling protein; HET: MSE PG4; 1.63A {Thermotoga maritima} PDB: 3a0r_B* 3a0u_A*

Probab=99.43  E-value=3.8e-13  Score=72.73  Aligned_cols=86  Identities=10%  Similarity=0.091  Sum_probs=67.8

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHH---hhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~~~~pii~lt~~~~~   68 (93)
                      +||++..+..++..|+..||. +..+.++.++++.+....++         +.+|++++   +...+.+|+|++|+..+.
T Consensus         7 vdd~~~~~~~l~~~l~~~~~~-v~~~~~~~~a~~~~~~~~~dlvl~D~~l~~~~g~~~~~~l~~~~~~~~ii~~s~~~~~   85 (116)
T 3a10_A            7 VDDEPNIRELLKEELQEEGYE-IDTAENGEEALKKFFSGNYDLVILDIEMPGISGLEVAGEIRKKKKDAKIILLTAYSHY   85 (116)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCE-EEEESSHHHHHHHHHHSCCSEEEECSCCSSSCHHHHHHHHHHHCTTCCEEEEESCGGG
T ss_pred             EeCCHHHHHHHHHHHHHCCCE-EEEeCCHHHHHHHHhcCCCCEEEEECCCCCCCHHHHHHHHHccCCCCeEEEEECCcch
Confidence            589999999999999999999 99999999999988644321         23455553   333378999999987665


Q ss_pred             HHHHHHHHcCCcceeeccchh
Q 042991           69 VRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      .  .++.+.|+++|+.||+..
T Consensus        86 ~--~~~~~~g~~~~l~Kp~~~  104 (116)
T 3a10_A           86 R--SDMSSWAADEYVVKSFNF  104 (116)
T ss_dssp             G--GCGGGGGSSEEEECCSST
T ss_pred             H--HHHHhccccceEECCCCH
Confidence            4  567889999999999863

>3eul_A Possible nitrate/nitrite response transcriptional regulatory protein NARL (DNA-binding...; central beta strand flanked by alpha helices; 1.90A {Mycobacterium tuberculosis}

Probab=99.43  E-value=1.4e-12  Score=73.72  Aligned_cols=88  Identities=19%  Similarity=0.131  Sum_probs=70.6

Q ss_pred             CCCcHHHHHHHHHHHhhcCCC-ceEEeCCHHHHHHHhccCccc---------CCCchHHH---hhhhcCCcEEEEcCCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSR-DLYCSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYSREIPVVIMSPEII   67 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~-~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~~~~pii~lt~~~~   67 (93)
                      +||++..+..++.+|+..|+. .+..+.++.+|++.++...++         +..|++++   ....+.+|||++|+..+
T Consensus        21 vdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~a~~~l~~~~~dlii~d~~l~~~~g~~~~~~l~~~~~~~~ii~~s~~~~  100 (152)
T 3eul_A           21 GDDHPLFREGVVRALSLSGSVNVVGEADDGAAALELIKAHLPDVALLDYRMPGMDGAQVAAAVRSYELPTRVLLISAHDE  100 (152)
T ss_dssp             ECSSHHHHHHHHHHHHHHSSEEEEEEESSHHHHHHHHHHHCCSEEEEETTCSSSCHHHHHHHHHHTTCSCEEEEEESCCC
T ss_pred             EcCCHHHHHHHHHHHhhCCCeEEEEEeCCHHHHHHHHHhcCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCeEEEEEccCC
Confidence            589999999999999988843 356899999999998644321         23455553   33348899999999999


Q ss_pred             HHHHHHHHHcCCcceeeccch
Q 042991           68 LVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        68 ~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      .....++++.|+++|+.||+.
T Consensus       101 ~~~~~~~~~~g~~~~l~Kp~~  121 (152)
T 3eul_A          101 PAIVYQALQQGAAGFLLKDST  121 (152)
T ss_dssp             HHHHHHHHHTTCSEEEETTCC
T ss_pred             HHHHHHHHHcCCCEEEecCCC
Confidence            999999999999999999986

>2zay_A Response regulator receiver protein; structural genomics, NYSGXRC, target 11006U, protein structure initiative; 2.00A {Desulfuromonas acetoxidans}

Probab=99.43  E-value=5e-13  Score=75.04  Aligned_cols=87  Identities=13%  Similarity=0.073  Sum_probs=71.1

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHH---Hhh--hhcCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDV---RTI--YSREIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~---l~~--~~~~~pii~lt~~~   66 (93)
                      +||++..+..+...|+..||+ +..+.++.+++..+....++         +..|+++   +..  ..+.+|||++|+..
T Consensus        14 vd~~~~~~~~l~~~L~~~g~~-v~~~~~~~~a~~~l~~~~~dlii~d~~l~~~~g~~~~~~l~~~~~~~~~pii~ls~~~   92 (147)
T 2zay_A           14 VDTQLPALAASISALSQEGFD-IIQCGNAIEAVPVAVKTHPHLIITEANMPKISGMDLFNSLKKNPQTASIPVIALSGRA   92 (147)
T ss_dssp             ECTTGGGGHHHHHHHHHHTEE-EEEESSHHHHHHHHHHHCCSEEEEESCCSSSCHHHHHHHHHTSTTTTTSCEEEEESSC
T ss_pred             EeCCHHHHHHHHHHHHHcCCe-EEEeCCHHHHHHHHHcCCCCEEEEcCCCCCCCHHHHHHHHHcCcccCCCCEEEEeCCC
Confidence            478888899999999999999 99999999999988643321         2345555   333  23789999999999


Q ss_pred             CHHHHHHHHHcCCcceeeccch
Q 042991           67 ILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      +.....++++.|+++|+.||+.
T Consensus        93 ~~~~~~~~~~~g~~~~l~kp~~  114 (147)
T 2zay_A           93 TAKEEAQLLDMGFIDFIAKPVN  114 (147)
T ss_dssp             CHHHHHHHHHHTCSEEEESSCC
T ss_pred             CHHHHHHHHhCCCCEEEeCCCC
Confidence            9999999999999999999986

>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=99.43  E-value=4.2e-13  Score=79.40  Aligned_cols=87  Identities=16%  Similarity=0.201  Sum_probs=70.1

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceE-EeCCHHHHHHHhccCccc---------CCCchHHHhhhh--cCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLY-CSCSGRRALQFLGLDEEQ---------SANGFDVRTIYS--REIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~-~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~~--~~~pii~lt~~~~~   68 (93)
                      |||++..+..+..+|+..||. +. .+.++.+|++.+....++         +++|++++..+.  ...|||++|+..+.
T Consensus        19 vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~~~al~~~~~~~~dlvi~D~~~p~~~g~~~~~~l~~~~~~pii~lt~~~~~   97 (205)
T 1s8n_A           19 AEDEALIRMDLAEMLREEGYE-IVGEAGDGQEAVELAELHKPDLVIMDVKMPRRDGIDAASEIASKRIAPIVVLTAFSQR   97 (205)
T ss_dssp             ECSSHHHHHHHHHHHHHTTCE-EEEEESSHHHHHHHHHHHCCSEEEEESSCSSSCHHHHHHHHHHTTCSCEEEEEEGGGH
T ss_pred             EECCHHHHHHHHHHHHHCCCE-EEEEeCCHHHHHHHHhhcCCCEEEEeCCCCCCChHHHHHHHHhcCCCCEEEEecCCCH
Confidence            589999999999999998999 77 899999999988643321         235566533221  34599999999998


Q ss_pred             HHHHHHHHcCCcceeeccch
Q 042991           69 VRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~   88 (93)
                      ....++++.|+++|+.||++
T Consensus        98 ~~~~~~~~~ga~~~l~KP~~  117 (205)
T 1s8n_A           98 DLVERARDAGAMAYLVKPFS  117 (205)
T ss_dssp             HHHHTTGGGSCEEEEEESCC
T ss_pred             HHHHHHHhcCCcEEEeCCCC
Confidence            88889999999999999986

>3cz5_A Two-component response regulator, LUXR family; structural genomics, protein structure initiative; 2.70A {Aurantimonas SP}

Probab=99.42  E-value=2.5e-12  Score=72.73  Aligned_cols=87  Identities=13%  Similarity=0.101  Sum_probs=70.8

Q ss_pred             CCCcHHHHHHHHHHHhh-cCCCceE-EeCCHHHHHHHhccCccc---------CCCchHHH---hhhhcCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTI-SSSRDLY-CSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYSREIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~-~~~~~v~-~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~~~~pii~lt~~~   66 (93)
                      +||++..+..++.+|+. .||. +. .+.++.+|++.+....++         +..|++++   ....+.+|||++|+..
T Consensus        11 vdd~~~~~~~l~~~L~~~~~~~-v~~~~~~~~~a~~~l~~~~~dlii~D~~l~~~~g~~~~~~l~~~~~~~~ii~ls~~~   89 (153)
T 3cz5_A           11 VDDHPIVREGYRRLIERRPGYA-VVAEAADAGEAYRLYRETTPDIVVMDLTLPGPGGIEATRHIRQWDGAARILIFTMHQ   89 (153)
T ss_dssp             ECSCHHHHHHHHHHHTTSTTEE-EEEEESSHHHHHHHHHTTCCSEEEECSCCSSSCHHHHHHHHHHHCTTCCEEEEESCC
T ss_pred             ECCcHHHHHHHHHHHhhCCCcE-EEEEeCCHHHHHHHHhcCCCCEEEEecCCCCCCHHHHHHHHHHhCCCCeEEEEECCC
Confidence            58899999999999997 7888 76 899999999998654321         22455553   3333789999999999


Q ss_pred             CHHHHHHHHHcCCcceeeccch
Q 042991           67 ILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      +.....++++.|+++|+.||+.
T Consensus        90 ~~~~~~~~~~~g~~~~l~kp~~  111 (153)
T 3cz5_A           90 GSAFALKAFEAGASGYVTKSSD  111 (153)
T ss_dssp             SHHHHHHHHHTTCSEEEETTSC
T ss_pred             CHHHHHHHHHCCCcEEEecCCC
Confidence            9999999999999999999986

>3nhm_A Response regulator; protein structure initiative II(PSI II), NYSGXRC, structural genomics; 2.19A {Myxococcus xanthus}

Probab=99.42  E-value=8.8e-13  Score=72.84  Aligned_cols=86  Identities=14%  Similarity=0.117  Sum_probs=64.9

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHh---hh--hcCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRT---IY--SREIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~---~~--~~~~pii~lt~~~   66 (93)
                      +||++..+..++.+|+ .+|. +..+.++.+|++.+....++         +..|++++.   ..  .+.+|||++|+..
T Consensus        10 vdd~~~~~~~l~~~l~-~~~~-v~~~~~~~~a~~~l~~~~~dlvi~d~~l~~~~g~~~~~~l~~~~~~~~~pii~~s~~~   87 (133)
T 3nhm_A           10 VENSWTMRETLRLLLS-GEFD-CTTAADGASGLQQALAHPPDVLISDVNMDGMDGYALCGHFRSEPTLKHIPVIFVSGYA   87 (133)
T ss_dssp             ECSCHHHHHHHHHHHT-TTSE-EEEESSHHHHHHHHHHSCCSEEEECSSCSSSCHHHHHHHHHHSTTTTTCCEEEEESCC
T ss_pred             EcCCHHHHHHHHHHHh-CCcE-EEEECCHHHHHHHHhcCCCCEEEEeCCCCCCCHHHHHHHHHhCCccCCCCEEEEeCCC
Confidence            5889999999999998 7899 99999999999998644431         234555533   22  2589999999988


Q ss_pred             CHHHHHHHHHcCCcceeeccchh
Q 042991           67 ILVRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      +... .++++.|+++|+.||+..
T Consensus        88 ~~~~-~~~~~~g~~~~l~KP~~~  109 (133)
T 3nhm_A           88 PRTE-GPADQPVPDAYLVKPVKP  109 (133)
T ss_dssp             C------TTSCCCSEEEESSCCH
T ss_pred             cHhH-HHHhhcCCceEEeccCCH
Confidence            7777 788999999999999873

>4dad_A Putative pilus assembly-related protein; response regulator receiver domain, CHEY-related protein, ST genomics; 2.50A {Burkholderia pseudomallei} PDB: 4dn6_A

Probab=99.41  E-value=3.8e-13  Score=75.55  Aligned_cols=87  Identities=8%  Similarity=0.033  Sum_probs=69.5

Q ss_pred             CCCcHHHHHHHHHHHhhcC-CCceEEeCCHHHHHHHhcc--Cccc------CC---CchHHH---hhhhcCCcEEEEcCC
Q 042991            1 LNDSFVDRKVIERLLTISS-SRDLYCSCSGRRALQFLGL--DEEQ------SA---NGFDVR---TIYSREIPVVIMSPE   65 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~-~~~v~~~~~~~~a~~~~~~--~~~~------~~---~~~d~l---~~~~~~~pii~lt~~   65 (93)
                      +||++..+..++.+|+..| |. +..+.++.+++..+..  ..++      .+   .|++++   +...+.+|||++|+.
T Consensus        26 vdd~~~~~~~l~~~L~~~g~~~-v~~~~~~~~~~~~~~~~~~~~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~ii~lt~~  104 (146)
T 4dad_A           26 ASEDASRLAHLARLVGDAGRYR-VTRTVGRAAQIVQRTDGLDAFDILMIDGAALDTAELAAIEKLSRLHPGLTCLLVTTD  104 (146)
T ss_dssp             ECSCHHHHHHHHHHHHHHCSCE-EEEECCCHHHHTTCHHHHTTCSEEEEECTTCCHHHHHHHHHHHHHCTTCEEEEEESC
T ss_pred             EeCCHHHHHHHHHHHhhCCCeE-EEEeCCHHHHHHHHHhcCCCCCEEEEeCCCCCccHHHHHHHHHHhCCCCcEEEEeCC
Confidence            5899999999999999988 99 9999999988877643  2221      11   234442   333378999999999


Q ss_pred             CCHHHHHHHHHcCCcceeeccch
Q 042991           66 IILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        66 ~~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      .+.....++++.|+++|+.||+.
T Consensus       105 ~~~~~~~~~~~~ga~~~l~Kp~~  127 (146)
T 4dad_A          105 ASSQTLLDAMRAGVRDVLRWPLE  127 (146)
T ss_dssp             CCHHHHHHHHTTTEEEEEESSCC
T ss_pred             CCHHHHHHHHHhCCceeEcCCCC
Confidence            99999999999999999999986

>3kcn_A Adenylate cyclase homolog; SGX, PSI 2, structural genomics, protein structure initiative; 2.45A {Rhodopirellula baltica}

Probab=99.41  E-value=2.2e-12  Score=72.91  Aligned_cols=86  Identities=14%  Similarity=0.136  Sum_probs=70.7

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc----------CCCchHH---HhhhhcCCcEEEEcCCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ----------SANGFDV---RTIYSREIPVVIMSPEII   67 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~----------~~~~~d~---l~~~~~~~pii~lt~~~~   67 (93)
                      +||++..+..+..+|+. +|. +..+.++.+|++.+....+.          +..|+++   +....+.+|||++|+..+
T Consensus        10 vdd~~~~~~~l~~~L~~-~~~-v~~~~~~~~a~~~l~~~~~~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~ii~~s~~~~   87 (151)
T 3kcn_A           10 VDDDYSLLNTLKRNLSF-DFE-VTTCESGPEALACIKKSDPFSVIMVDMRMPGMEGTEVIQKARLISPNSVYLMLTGNQD   87 (151)
T ss_dssp             ECSCHHHHHHHHHHHTT-TSE-EEEESSHHHHHHHHHHSCCCSEEEEESCCSSSCHHHHHHHHHHHCSSCEEEEEECGGG
T ss_pred             EeCCHHHHHHHHHHhcc-Cce-EEEeCCHHHHHHHHHcCCCCCEEEEeCCCCCCcHHHHHHHHHhcCCCcEEEEEECCCC
Confidence            58899999999999975 889 99999999999998654321          2345555   333348899999999999


Q ss_pred             HHHHHHHHHcC-Ccceeeccch
Q 042991           68 LVRIDRYLEDG-AEDSETCQMW   88 (93)
Q Consensus        68 ~~~~~~~~~~g-a~d~l~kP~~   88 (93)
                      .....++++.| +++|+.||+.
T Consensus        88 ~~~~~~~~~~g~~~~~l~KP~~  109 (151)
T 3kcn_A           88 LTTAMEAVNEGQVFRFLNKPCQ  109 (151)
T ss_dssp             HHHHHHHHHHTCCSEEEESSCC
T ss_pred             HHHHHHHHHcCCeeEEEcCCCC
Confidence            99999999999 9999999986

>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=99.41  E-value=1.1e-12  Score=78.67  Aligned_cols=86  Identities=20%  Similarity=0.120  Sum_probs=71.3

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHH---HhhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDV---RTIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~---l~~~~~~~pii~lt~~~~~   68 (93)
                      +||++..+..+..+|+..||. +..+.++.+|++.+....++         +.+|+++   +... +.+|||++|+..+.
T Consensus        10 vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~~al~~~~~~~~dlvllD~~l~~~~g~~~~~~l~~~-~~~~ii~lt~~~~~   87 (230)
T 2oqr_A           10 VEDEESLADPLAFLLRKEGFE-ATVVTDGPAALAEFDRAGADIVLLDLMLPGMSGTDVCKQLRAR-SSVPVIMVTARDSE   87 (230)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCE-EEEECSHHHHHHHHHHHCCSEEEEESSCSSSCHHHHHHHHHHH-CSCSEEEEECCHHH
T ss_pred             EeCCHHHHHHHHHHHHHCCCE-EEEECCHHHHHHHHhccCCCEEEEECCCCCCCHHHHHHHHHcC-CCCCEEEEeCCCcH
Confidence            589999999999999988999 99999999999988543321         2345555   3332 78999999999888


Q ss_pred             HHHHHHHHcCCcceeeccch
Q 042991           69 VRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~   88 (93)
                      ....++++.|+++|+.||++
T Consensus        88 ~~~~~~~~~ga~~~l~Kp~~  107 (230)
T 2oqr_A           88 IDKVVGLELGADDYVTKPYS  107 (230)
T ss_dssp             HHHHHHHHHCCSCCCCSSCC
T ss_pred             HHHHHHHHcCCCEEEeCCCC
Confidence            88889999999999999986

>3cg0_A Response regulator receiver modulated diguanylate with PAS/PAC sensor; signal receiver domain, diguanylate cyclase; 2.15A {Desulfovibrio desulfuricans subsp}

Probab=99.41  E-value=2.3e-12  Score=71.61  Aligned_cols=86  Identities=8%  Similarity=0.038  Sum_probs=70.7

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceE-EeCCHHHHHHHhccCccc----------CCCchHH---HhhhhcCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLY-CSCSGRRALQFLGLDEEQ----------SANGFDV---RTIYSREIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~-~~~~~~~a~~~~~~~~~~----------~~~~~d~---l~~~~~~~pii~lt~~~   66 (93)
                      +||++..+..++..|+..||+ +. .+.++.+|++.+....++          +..|+++   +... +.+|||++|+..
T Consensus        15 vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~~~a~~~~~~~~~dlii~d~~~~~~~~g~~~~~~l~~~-~~~~ii~ls~~~   92 (140)
T 3cg0_A           15 VEDGRLAAATLRIQLESLGYD-VLGVFDNGEEAVRCAPDLRPDIALVDIMLCGALDGVETAARLAAG-CNLPIIFITSSQ   92 (140)
T ss_dssp             ECCBHHHHHHHHHHHHHHTCE-EEEEESSHHHHHHHHHHHCCSEEEEESSCCSSSCHHHHHHHHHHH-SCCCEEEEECCC
T ss_pred             EECCHHHHHHHHHHHHHCCCe-eEEEECCHHHHHHHHHhCCCCEEEEecCCCCCCCHHHHHHHHHhC-CCCCEEEEecCC
Confidence            578999999999999999999 88 599999999988643321          2345555   3333 789999999999


Q ss_pred             CHHHHHHHHHcCCcceeeccch
Q 042991           67 ILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      +.....++++.|+++|+.||+.
T Consensus        93 ~~~~~~~~~~~g~~~~l~kp~~  114 (140)
T 3cg0_A           93 DVETFQRAKRVNPFGYLAKPVA  114 (140)
T ss_dssp             CHHHHHHHHTTCCSEEEEESCC
T ss_pred             CHHHHHHHHhcCCCEEEeCCCC
Confidence            9998889999999999999986

>3cu5_A Two component transcriptional regulator, ARAC FAM; structural genomics, protein structure initiative; 2.60A {Clostridium phytofermentans isdg}

Probab=99.40  E-value=9.9e-13  Score=73.70  Aligned_cols=88  Identities=13%  Similarity=-0.003  Sum_probs=64.1

Q ss_pred             CCCcHHHHHHHHHHHhh--cCCCceE-EeCCHHHHHHHhccCccc---------CCCchHHH---hhhhcCCcEEEEcCC
Q 042991            1 LNDSFVDRKVIERLLTI--SSSRDLY-CSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYSREIPVVIMSPE   65 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~--~~~~~v~-~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~~~~pii~lt~~   65 (93)
                      +||++..+..+...|..  .+|. +. .+.++.++++.+....++         +++|++++   ....+.+|||++|+.
T Consensus         8 vdd~~~~~~~l~~~L~~~~~~~~-~~~~~~~~~~al~~~~~~~~dlvllD~~lp~~~g~~l~~~l~~~~~~~~ii~ls~~   86 (141)
T 3cu5_A            8 VDDEKLTRDGLIANINWKALSFD-QIDQADDGINAIQIALKHPPNVLLTDVRMPRMDGIELVDNILKLYPDCSVIFMSGY   86 (141)
T ss_dssp             ECSCHHHHHHHHHHCCGGGSCCS-EEEEESSHHHHHHHHTTSCCSEEEEESCCSSSCHHHHHHHHHHHCTTCEEEEECCS
T ss_pred             EeCCHHHHHHHHHHHHHccCCcE-EeeecccHHHHHHHHhcCCCCEEEEeCCCCCCCHHHHHHHHHhhCCCCcEEEEeCC
Confidence            58999999999999973  5787 66 999999999988654321         23556653   333378999999998


Q ss_pred             CCHHHHHHHHHcCCcceeeccchh
Q 042991           66 IILVRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        66 ~~~~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      .+.....++++.|+++|+.||++.
T Consensus        87 ~~~~~~~~~~~~ga~~~l~KP~~~  110 (141)
T 3cu5_A           87 SDKEYLKAAIKFRAIRYVEKPIDP  110 (141)
T ss_dssp             TTTCCC------CCCEEECSSCCH
T ss_pred             CcHHHHHHHHhCCccEEEeCCCCH
Confidence            888788889999999999999863

>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=99.40  E-value=3.7e-13  Score=80.81  Aligned_cols=87  Identities=21%  Similarity=0.211  Sum_probs=71.6

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHH---hhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~~~~pii~lt~~~~~   68 (93)
                      +||++..+..+..+|+..||. +..+.++.+|++.+....++         +.+|++++   ....+.+|||++|+..+.
T Consensus        13 vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~~a~~~~~~~~~dlvllD~~l~~~~g~~~~~~l~~~~~~~~ii~lt~~~~~   91 (233)
T 1ys7_A           13 VDDDSDVLASLERGLRLSGFE-VATAVDGAEALRSATENRPDAIVLDINMPVLDGVSVVTALRAMDNDVPVCVLSARSSV   91 (233)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCE-EEEESSHHHHHHHHHHSCCSEEEEESSCSSSCHHHHHHHHHHTTCCCCEEEEECCCTT
T ss_pred             EeCCHHHHHHHHHHHHhCCCE-EEEECCHHHHHHHHHhCCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCCEEEEEcCCCH
Confidence            589999999999999998999 99999999999988644321         23456653   333378999999999888


Q ss_pred             HHHHHHHHcCCcceeeccch
Q 042991           69 VRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~   88 (93)
                      ....++++.|+++|+.||++
T Consensus        92 ~~~~~~~~~ga~~~l~Kp~~  111 (233)
T 1ys7_A           92 DDRVAGLEAGADDYLVKPFV  111 (233)
T ss_dssp             TCCCTTTTTTCSEEEESSCC
T ss_pred             HHHHHHHHcCCCEEEeCCCC
Confidence            88888999999999999986

>2jk1_A HUPR, hydrogenase transcriptional regulatory protein HU; nucleotide-binding, transcription regulation; 2.10A {Rhodobacter capsulatus} PDB: 2vui_B 2vuh_B

Probab=99.39  E-value=4.3e-12  Score=70.74  Aligned_cols=86  Identities=14%  Similarity=0.040  Sum_probs=67.9

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHH---hhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~~~~pii~lt~~~~~   68 (93)
                      +||++..+..++.+|+.. |. +..+.++.++++.+....++         +++|++++   ....+.+|+|++|+..+.
T Consensus         7 vdd~~~~~~~l~~~l~~~-~~-v~~~~~~~~a~~~~~~~~~dlvl~D~~lp~~~g~~~~~~l~~~~~~~~ii~~s~~~~~   84 (139)
T 2jk1_A            7 VDDEPHSLAAMKLALEDD-FD-VLTAQGAEAAIAILEEEWVQVIICDQRMPGRTGVDFLTEVRERWPETVRIIITGYTDS   84 (139)
T ss_dssp             ECSSHHHHHHHHHHHTTT-SC-EEEESSHHHHHHHHHHSCEEEEEEESCCSSSCHHHHHHHHHHHCTTSEEEEEESCTTC
T ss_pred             EcCCHHHHHHHHHHhhcC-ce-EEEcCCHHHHHHHHhcCCCCEEEEeCCCCCCcHHHHHHHHHHhCCCCcEEEEeCCCCh
Confidence            589999999999999865 88 99999999999988644321         33566653   333378899999998887


Q ss_pred             HHHHHHHHc-CCcceeeccch
Q 042991           69 VRIDRYLED-GAEDSETCQMW   88 (93)
Q Consensus        69 ~~~~~~~~~-ga~d~l~kP~~   88 (93)
                      ....++++. |+++|+.||+.
T Consensus        85 ~~~~~~~~~~ga~~~l~KP~~  105 (139)
T 2jk1_A           85 ASMMAAINDAGIHQFLTKPWH  105 (139)
T ss_dssp             HHHHHHHHHTTCCEEEESSCC
T ss_pred             HHHHHHHHhhchhhhccCCCC
Confidence            787888876 59999999986

>2gwr_A DNA-binding response regulator MTRA; two-component regulatory system, transcription regulation, phosphorylation, OMPR family; 2.10A {Mycobacterium tuberculosis} PDB: 3nhz_A

Probab=99.38  E-value=1e-12  Score=79.48  Aligned_cols=88  Identities=19%  Similarity=0.204  Sum_probs=71.4

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhhh--cCCcEEEEcCCCCHH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIYS--REIPVVIMSPEIILV   69 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~~--~~~pii~lt~~~~~~   69 (93)
                      +||++..+..++.+|+..||. +..+.++.+|++.+....++         +.+|++++..+.  ..+|||++|+..+..
T Consensus        11 vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~~al~~l~~~~~dlvilD~~l~~~~g~~~~~~lr~~~~~~ii~lt~~~~~~   89 (238)
T 2gwr_A           11 VDDDASLAEMLTIVLRGEGFD-TAVIGDGTQALTAVRELRPDLVLLDLMLPGMNGIDVCRVLRADSGVPIVMLTAKTDTV   89 (238)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCE-EEEECCGGGHHHHHHHHCCSEEEEESSCSSSCHHHHHHHHHTTCCCCEEEEEETTCCS
T ss_pred             EeCCHHHHHHHHHHHHHCCCE-EEEECCHHHHHHHHHhCCCCEEEEeCCCCCCCHHHHHHHHHhCCCCcEEEEeCCCCHH
Confidence            589999999999999988999 99999999999988543321         234555533222  589999999998888


Q ss_pred             HHHHHHHcCCcceeeccchh
Q 042991           70 RIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        70 ~~~~~~~~ga~d~l~kP~~~   89 (93)
                      ...++++.|+++|+.||++.
T Consensus        90 ~~~~~~~~Ga~~~l~Kp~~~  109 (238)
T 2gwr_A           90 DVVLGLESGADDYIMKPFKP  109 (238)
T ss_dssp             CHHHHHHTTCCEEEEESCCH
T ss_pred             HHHHHHHCCCCEEEeCCCCH
Confidence            88899999999999999863

>3cg4_A Response regulator receiver domain protein (CHEY-; structural genomics, unknown function; HET: MSE; 1.61A {Methanospirillum hungatei jf-1}

Probab=99.37  E-value=3.4e-13  Score=75.29  Aligned_cols=87  Identities=15%  Similarity=0.122  Sum_probs=71.1

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHH---Hhh--hhcCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDV---RTI--YSREIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~---l~~--~~~~~pii~lt~~~   66 (93)
                      +||++..+..+..+|+..||+ +..+.++.+|++.++...++         +..|+++   +..  ..+.+|||++|+..
T Consensus        13 vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~~a~~~l~~~~~dlii~d~~l~~~~g~~~~~~l~~~~~~~~~pii~~s~~~   91 (142)
T 3cg4_A           13 VDDDAHVRIAVKTILSDAGFH-IISADSGGQCIDLLKKGFSGVVLLDIMMPGMDGWDTIRAILDNSLEQGIAIVMLTAKN   91 (142)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCE-EEEESSHHHHHHHHHTCCCEEEEEESCCSSSCHHHHHHHHHHTTCCTTEEEEEEECTT
T ss_pred             EcCCHHHHHHHHHHHHHCCeE-EEEeCCHHHHHHHHHhcCCCEEEEeCCCCCCCHHHHHHHHHhhcccCCCCEEEEECCC
Confidence            588999999999999999999 99999999999998654321         2345555   333  23788999999988


Q ss_pred             CHHHHHHHHHcCCcceeeccch
Q 042991           67 ILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      +.....++++.|+++|+.||+.
T Consensus        92 ~~~~~~~~~~~g~~~~l~kp~~  113 (142)
T 3cg4_A           92 APDAKMIGLQEYVVDYITKPFD  113 (142)
T ss_dssp             CCCCSSTTGGGGEEEEEESSCC
T ss_pred             CHHHHHHHHhcCccEEEeCCCC
Confidence            8777778899999999999986

>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=99.37  E-value=6e-13  Score=74.25  Aligned_cols=86  Identities=15%  Similarity=0.153  Sum_probs=64.0

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHH---hhhh--cCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYS--REIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~--~~~pii~lt~~~   66 (93)
                      +||++..+..+..+|+.. |. +..+.++.+|++.+....++         +..|++++   +...  +.+|+|++|+..
T Consensus         9 vdd~~~~~~~l~~~l~~~-~~-v~~~~~~~~a~~~~~~~~~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~~~ii~~s~~~   86 (140)
T 3n53_A            9 IDQQDFSRIELKNFLDSE-YL-VIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILLFSSE   86 (140)
T ss_dssp             ECSCHHHHHHHHHHHTTT-SE-EEEESSHHHHHHHHHHHCCSEEEEETTC------CHHHHHHTSTTCTTCCEEEEECC-
T ss_pred             EeCCHHHHHHHHHHHHhc-ce-EEEeCCHHHHHHHHhcCCCCEEEEeCCCCCCcHHHHHHHHHcCcccCCCCEEEEecCC
Confidence            588999999999999877 88 99999999999998644321         12344442   3322  789999999998


Q ss_pred             CHHHHHHHHHcCCcceeeccch
Q 042991           67 ILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      +.....++++.|+++|+.||+.
T Consensus        87 ~~~~~~~~~~~g~~~~l~KP~~  108 (140)
T 3n53_A           87 HKEAIVNGLHSGADDYLTKPFN  108 (140)
T ss_dssp             ---CTTTTTTCCCSEEEESSCC
T ss_pred             CHHHHHHHHhcCCCeeeeCCCC
Confidence            8888888999999999999986

>2qsj_A DNA-binding response regulator, LUXR family; structural genomics, PSI-2, protein structure initiative; 2.10A {Silicibacter pomeroyi dss-3}

Probab=99.36  E-value=4e-12  Score=71.88  Aligned_cols=88  Identities=22%  Similarity=0.137  Sum_probs=64.8

Q ss_pred             CCCcHHHHHHHHHHHhhc-CCCceEEeCCHHHHHHHhcc-Cccc---------CCCchHHH---hhhhcCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTIS-SSRDLYCSCSGRRALQFLGL-DEEQ---------SANGFDVR---TIYSREIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~-~~~~v~~~~~~~~a~~~~~~-~~~~---------~~~~~d~l---~~~~~~~pii~lt~~~   66 (93)
                      +||++..+..++.+|+.. |+..+..+.++.+|+..++. ..++         +..|++++   ....+.+|||++|+..
T Consensus         9 vdd~~~~~~~l~~~L~~~~g~~~v~~~~~~~~a~~~l~~~~~~dlvi~d~~l~~~~g~~~~~~l~~~~~~~~ii~ls~~~   88 (154)
T 2qsj_A            9 VDDHHLIRAGAKNLLEGAFSGMRVEGAETVSDALAFLEADNTVDLILLDVNLPDAEAIDGLVRLKRFDPSNAVALISGET   88 (154)
T ss_dssp             ECSCHHHHHHHHHHHHHHCTTEEEEEESSHHHHHHHHHTTCCCSEEEECC------CHHHHHHHHHHCTTSEEEEC----
T ss_pred             EcCCHHHHHHHHHHHHhCCCceEEEEecCHHHHHHHHhccCCCCEEEEeCCCCCCchHHHHHHHHHhCCCCeEEEEeCCC
Confidence            588999999999999987 77328899999999999875 3321         12344443   3333789999999998


Q ss_pred             CHHHHHHHHHcCCcceeeccch
Q 042991           67 ILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      +.....++++.|+++|+.||+.
T Consensus        89 ~~~~~~~~~~~g~~~~l~kp~~  110 (154)
T 2qsj_A           89 DHELIRAALEAGADGFIPKSAD  110 (154)
T ss_dssp             -CHHHHHHHHTTCCBBCCTTSC
T ss_pred             CHHHHHHHHHccCCEEEeCCCC
Confidence            8888889999999999999986

>3kyj_B CHEY6 protein, putative histidine protein kinase; protein-protein interaction, histidine kinase, response regulator, phosphorylation; 1.40A {Rhodobacter sphaeroides} PDB: 3kyi_B*

Probab=99.35  E-value=2.2e-12  Score=72.38  Aligned_cols=88  Identities=15%  Similarity=0.117  Sum_probs=65.7

Q ss_pred             CCCcHHHHHHHHHHHhhc-CCCceEEeCCHHHHHHHhccC-ccc---------CCCchHHHhhhh--cCCcEEEEcC--C
Q 042991            1 LNDSFVDRKVIERLLTIS-SSRDLYCSCSGRRALQFLGLD-EEQ---------SANGFDVRTIYS--REIPVVIMSP--E   65 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~-~~~~v~~~~~~~~a~~~~~~~-~~~---------~~~~~d~l~~~~--~~~pii~lt~--~   65 (93)
                      +||++..+..++.+|++. ||..+..+.++.+|++.+... .++         +..|++++..+.  ...|++++++  .
T Consensus        19 vdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~al~~l~~~~~~dlvilD~~l~~~~g~~~~~~lr~~~~~~iiil~~~~~   98 (145)
T 3kyj_B           19 VDDAAMMRLYIASFIKTLPDFKVVAQAANGQEALDKLAAQPNVDLILLDIEMPVMDGMEFLRHAKLKTRAKICMLSSVAV   98 (145)
T ss_dssp             ECSCHHHHHHHHHHHTTCTTEEEEEEESSHHHHHHHHHHCTTCCEEEECTTSCCCTTCHHHHHHHHHCCCEEC-CBSSCS
T ss_pred             EcCCHHHHHHHHHHHHhCCCceEEEEECCHHHHHHHHhcCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCeEEEEEecc
Confidence            589999999999999987 777345899999999988654 321         234555533222  4588999987  5


Q ss_pred             CCHHHHHHHHHcCCcceeeccch
Q 042991           66 IILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        66 ~~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      .+.....++++.|+++|+.||+.
T Consensus        99 ~~~~~~~~~~~~ga~~~l~KP~~  121 (145)
T 3kyj_B           99 SGSPHAARARELGADGVVAKPSG  121 (145)
T ss_dssp             TTSSHHHHHHHTTCSCCCBCCCS
T ss_pred             CChHHHHHHHhCCCCEEEeCCCC
Confidence            55666778999999999999986

>3bre_A Probable two-component response regulator; protein-nucleotide complex, signaling protein; HET: C2E; 2.40A {Pseudomonas aeruginosa} PDB: 3i5a_A*

Probab=99.35  E-value=1.4e-12  Score=82.78  Aligned_cols=87  Identities=15%  Similarity=0.201  Sum_probs=70.3

Q ss_pred             CCCcHHHHHHHHHHHh-hcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhh-----hcCCcEEEEcCC
Q 042991            1 LNDSFVDRKVIERLLT-ISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIY-----SREIPVVIMSPE   65 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~-~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~-----~~~~pii~lt~~   65 (93)
                      |||++..+..++.+|. ..||. +..+.++.+|++.+....++         +++|++++..+     .+.+|||++|+.
T Consensus        24 vdD~~~~~~~l~~~l~~~~~~~-v~~~~~~~~al~~~~~~~~dlvl~D~~mp~~~G~~~~~~l~~~~~~~~~~ii~~s~~  102 (358)
T 3bre_A           24 VDDQAMIGEAVRRSLASEAGID-FHFCSDPQQAVAVANQIKPTVILQDLVMPGVDGLTLLAAYRGNPATRDIPIIVLSTK  102 (358)
T ss_dssp             ECSCTTHHHHHHTTSSSCTTEE-EEEECCHHHHHHHHHHHCCSEEEEESBCSSSBHHHHHHHHTTSTTTTTSCEEEEESS
T ss_pred             EECCHHHHHHHHHHHHhccCcE-EEEeCCHHHHHHHHHhCCCCEEEEeCCCCCCCHHHHHHHHhcCcccCCCcEEEEeCC
Confidence            5889999999999996 45888 89999999999998643321         34566653332     257999999999


Q ss_pred             CCHHHHHHHHHcCCcceeeccch
Q 042991           66 IILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        66 ~~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      .+.....++++.|+++|+.||+.
T Consensus       103 ~~~~~~~~a~~~Ga~~~l~Kp~~  125 (358)
T 3bre_A          103 EEPTVKSAAFAAGANDYLVKLPD  125 (358)
T ss_dssp             CCHHHHHHHHHTTCSEEEESCCC
T ss_pred             CCHHHHHHHHhcChheEeeccCC
Confidence            99999999999999999999986

>3c3w_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 2.20A {Mycobacterium tuberculosis}

Probab=99.35  E-value=1e-12  Score=78.95  Aligned_cols=89  Identities=13%  Similarity=0.059  Sum_probs=70.6

Q ss_pred             CCCcHHHHHHHHHHHhhcC-CCceEEeCCHHHHHHHhccCccc---------CCCchHHH---hhhhcCCcEEEEcCCCC
Q 042991            1 LNDSFVDRKVIERLLTISS-SRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYSREIPVVIMSPEII   67 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~-~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~~~~pii~lt~~~~   67 (93)
                      |||++..+..++.+|+..+ |..+..+.++.+|++.+....++         +++|++++   ....+.+|||++|+..+
T Consensus         7 vdd~~~~~~~l~~~L~~~~~~~vv~~~~~~~~al~~l~~~~~dlvllD~~lp~~~g~~~~~~lr~~~~~~~ii~lt~~~~   86 (225)
T 3c3w_A            7 VDDHEVVRRGLVDLLGADPELDVVGEAGSVAEAMARVPAARPDVAVLDVRLPDGNGIELCRDLLSRMPDLRCLILTSYTS   86 (225)
T ss_dssp             ECSCHHHHHHHHHHHHTCTTEEEEEEESSHHHHHHHHHHHCCSEEEECSEETTEEHHHHHHHHHHHCTTCEEEEGGGSSS
T ss_pred             EcCCHHHHHHHHHHHhcCCCcEEEEEECCHHHHHHHHhhcCCCEEEEeCCCCCCCHHHHHHHHHHhCCCCcEEEEECCCC
Confidence            5899999999999999876 76244799999999988643321         22455553   33338899999999999


Q ss_pred             HHHHHHHHHcCCcceeeccchh
Q 042991           68 LVRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        68 ~~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      .....++++.|+++|+.||++.
T Consensus        87 ~~~~~~~~~~Ga~~~l~Kp~~~  108 (225)
T 3c3w_A           87 DEAMLDAILAGASGYVVKDIKG  108 (225)
T ss_dssp             HHHHHHHHHHTCCCHHHHHHHH
T ss_pred             HHHHHHHHHCCCCEEEECCCCH
Confidence            9999999999999999999863

>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=99.35  E-value=3.8e-12  Score=69.40  Aligned_cols=87  Identities=14%  Similarity=0.134  Sum_probs=69.0

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc----------CCCchHH---Hhhh--hcCCcEEEEcCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ----------SANGFDV---RTIY--SREIPVVIMSPE   65 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~----------~~~~~d~---l~~~--~~~~pii~lt~~   65 (93)
                      +||++..+..++..|+..||+ +..+.++.++++.++...++          +..|+++   ++..  .+.+|+|++ +.
T Consensus        11 vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~~a~~~~~~~~~dlvi~d~~~~~~~~g~~~~~~l~~~~~~~~~~ii~~-~~   88 (127)
T 2gkg_A           11 VESDTALSATLRSALEGRGFT-VDETTDGKGSVEQIRRDRPDLVVLAVDLSAGQNGYLICGKLKKDDDLKNVPIVII-GN   88 (127)
T ss_dssp             ECSCHHHHHHHHHHHHHHTCE-EEEECCHHHHHHHHHHHCCSEEEEESBCGGGCBHHHHHHHHHHSTTTTTSCEEEE-EC
T ss_pred             EeCCHHHHHHHHHHHHhcCce-EEEecCHHHHHHHHHhcCCCEEEEeCCCCCCCCHHHHHHHHhcCccccCCCEEEE-ec
Confidence            578999999999999999999 99999999999988643321          2234444   2332  378999999 88


Q ss_pred             CCHHHHHHHHHcCCcceeeccchh
Q 042991           66 IILVRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        66 ~~~~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      .+.....++++.|+++|+.||++.
T Consensus        89 ~~~~~~~~~~~~g~~~~l~kp~~~  112 (127)
T 2gkg_A           89 PDGFAQHRKLKAHADEYVAKPVDA  112 (127)
T ss_dssp             GGGHHHHHHSTTCCSEEEESSCCH
T ss_pred             CCchhHHHHHHhCcchheeCCCCH
Confidence            888888889999999999999863

>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=99.34  E-value=1.7e-12  Score=79.79  Aligned_cols=88  Identities=18%  Similarity=0.198  Sum_probs=63.3

Q ss_pred             CCCcHHHHHHHHHHHhhc-CCCceEEeCCHHHHHHHhccCcc---------cCCCchHHHhhhh-cCCcEEEEcCCCCHH
Q 042991            1 LNDSFVDRKVIERLLTIS-SSRDLYCSCSGRRALQFLGLDEE---------QSANGFDVRTIYS-REIPVVIMSPEIILV   69 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~-~~~~v~~~~~~~~a~~~~~~~~~---------~~~~~~d~l~~~~-~~~pii~lt~~~~~~   69 (93)
                      |||++..+..+...|... ++. +..+ ++.+++..+....+         ++++|++++.... ..+|||++|+..+.+
T Consensus        10 VdD~~~~~~~l~~~L~~~~~~~-v~~~-~~~~~~~~~~~~~~dlvllD~~mP~~~G~~~~~~lr~~~~pvi~lt~~~~~~   87 (259)
T 3luf_A           10 VEDSMTIRRMLIQAIAQQTGLE-IDAF-DTLEGARHCQGDEYVVALVDLTLPDAPSGEAVKVLLERGLPVVILTADISED   87 (259)
T ss_dssp             ECCCHHHHHHHHHHHHHHHCCE-EEEE-SSTGGGTTCCTTTEEEEEEESCBTTBTTSHHHHHHHHTTCCEEEEECC-CHH
T ss_pred             EECCHHHHHHHHHHHHhcCCeE-EEEe-ChHHHHHHhhcCCCcEEEEeCCCCCCCHHHHHHHHHhCCCCEEEEEccCCHH
Confidence            589999999999999764 666 6544 55555555443322         1345666543322 579999999999999


Q ss_pred             HHHHHHHcCCcceeeccchhh
Q 042991           70 RIDRYLEDGAEDSETCQMWAR   90 (93)
Q Consensus        70 ~~~~~~~~ga~d~l~kP~~~~   90 (93)
                      ...++++.||++|+.||....
T Consensus        88 ~~~~a~~~Ga~dyl~Kp~~~~  108 (259)
T 3luf_A           88 KREAWLEAGVLDYVMKDSRHS  108 (259)
T ss_dssp             HHHHHHHTTCCEEEECSSHHH
T ss_pred             HHHHHHHCCCcEEEeCCchhH
Confidence            999999999999999997643

>3eqz_A Response regulator; structural genomics, unknown function, PSI-2, protein struct initiative; 2.15A {Colwellia psychrerythraea} SCOP: c.23.1.0

Probab=99.32  E-value=3.7e-12  Score=70.28  Aligned_cols=87  Identities=8%  Similarity=-0.005  Sum_probs=67.8

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHH---HhhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDV---RTIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~---l~~~~~~~pii~lt~~~~~   68 (93)
                      +||++..+..++.+|+..++. +..+.++.+++..+... ++         +..|+++   +....+.+|+|++|+..+.
T Consensus         9 vdd~~~~~~~l~~~L~~~~~~-v~~~~~~~~~~~~~~~~-~dlvi~D~~l~~~~g~~~~~~l~~~~~~~~ii~~s~~~~~   86 (135)
T 3eqz_A            9 VDDDTLTCNLLKTIVEPIFGN-VEAFQHPRAFLTLSLNK-QDIIILDLMMPDMDGIEVIRHLAEHKSPASLILISGYDSG   86 (135)
T ss_dssp             ECSCHHHHHHHHHHHTTTCSC-EEEESCHHHHTTSCCCT-TEEEEEECCTTTTHHHHHHHHHHHTTCCCEEEEEESSCHH
T ss_pred             EeCCHHHHHHHHHHHHhhcce-eeeecCHHHHHHhhccC-CCEEEEeCCCCCCCHHHHHHHHHhCCCCCCEEEEEeccch
Confidence            589999999999999988778 99999999999887654 21         1234444   3333388999999998775


Q ss_pred             -----HHHHHHHHcCCcceeeccchh
Q 042991           69 -----VRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        69 -----~~~~~~~~~ga~d~l~kP~~~   89 (93)
                           ....++++.|+++|+.||+..
T Consensus        87 ~~~~~~~~~~~~~~g~~~~l~KP~~~  112 (135)
T 3eqz_A           87 VLHSAETLALSCGLNVINTFTKPINT  112 (135)
T ss_dssp             HHHHHHHHHHHTTCEEEEEEESSCCH
T ss_pred             hHHHHHHHHHHcCCCcceeeCCCCCH
Confidence                 566678899999999999973

>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=99.32  E-value=1.3e-11  Score=73.52  Aligned_cols=87  Identities=16%  Similarity=0.053  Sum_probs=70.0

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCcc-------cCCCchHHH---hhhhcCCcEEEEcCCCCHHH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEE-------QSANGFDVR---TIYSREIPVVIMSPEIILVR   70 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~-------~~~~~~d~l---~~~~~~~pii~lt~~~~~~~   70 (93)
                      +||++..+..+..+|+..| . +..+.++.+|++.+...+.       ++.+|++++   ....+.+|||++|+..+...
T Consensus         8 vdd~~~~~~~l~~~L~~~~-~-v~~~~~~~~al~~~~~~dlvllD~~lp~~~g~~~~~~lr~~~~~~~ii~lt~~~~~~~   85 (220)
T 1p2f_A            8 VDDDKNILKKVSEKLQQLG-R-VKTFLTGEDFLNDEEAFHVVVLDVMLPDYSGYEICRMIKETRPETWVILLTLLSDDES   85 (220)
T ss_dssp             ECSCHHHHHHHHHHHTTTE-E-EEEESSHHHHHHCCSCCSEEEEESBCSSSBHHHHHHHHHHHCTTSEEEEEESCCSHHH
T ss_pred             EeCCHHHHHHHHHHHHhCC-C-EEEECCHHHHHHhcCCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCcEEEEEcCCCHHH
Confidence            5899999999999999888 7 9999999999988721111       123456653   33337899999999999999


Q ss_pred             HHHHHHcCCcceeeccchh
Q 042991           71 IDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        71 ~~~~~~~ga~d~l~kP~~~   89 (93)
                      ..++++.|+++|+.||++.
T Consensus        86 ~~~~~~~ga~~~l~Kp~~~  104 (220)
T 1p2f_A           86 VLKGFEAGADDYVTKPFNP  104 (220)
T ss_dssp             HHHHHHHTCSEEEESSCCH
T ss_pred             HHHHHHcCCCEEEECCCCH
Confidence            9999999999999999863

>2j48_A Two-component sensor kinase; pseudo-receiver, circadian clock, transferase, response regulator, histidine protein kinase; NMR {Synechococcus elongatus}

Probab=99.27  E-value=1.1e-11  Score=66.54  Aligned_cols=84  Identities=17%  Similarity=0.091  Sum_probs=66.0

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHH---hhhh--cCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYS--REIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~--~~~pii~lt~~~   66 (93)
                      +++++..+..+...|+..||+ +..+.++.+++..++...++         +..+++++   ....  +.+|+|++|+..
T Consensus         7 v~~~~~~~~~l~~~l~~~g~~-v~~~~~~~~~~~~l~~~~~dlii~d~~~~~~~~~~~~~~l~~~~~~~~~~ii~~~~~~   85 (119)
T 2j48_A            7 LEEEDEAATVVCEMLTAAGFK-VIWLVDGSTALDQLDLLQPIVILMAWPPPDQSCLLLLQHLREHQADPHPPLVLFLGEP   85 (119)
T ss_dssp             ECCCHHHHHHHHHHHHHTTCE-EEEESCHHHHHHHHHHHCCSEEEEECSTTCCTHHHHHHHHHHTCCCSSCCCEEEESSC
T ss_pred             EeCCHHHHHHHHHHHHhCCcE-EEEecCHHHHHHHHHhcCCCEEEEecCCCCCCHHHHHHHHHhccccCCCCEEEEeCCC
Confidence            478899999999999999999 99999999999988643321         22344543   2222  688999999877


Q ss_pred             CHHHHHHHHHcCCcceeeccch
Q 042991           67 ILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      +..   .+++.|+++|+.||++
T Consensus        86 ~~~---~~~~~g~~~~l~kp~~  104 (119)
T 2j48_A           86 PVD---PLLTAQASAILSKPLD  104 (119)
T ss_dssp             CSS---HHHHHHCSEECSSCST
T ss_pred             Cch---hhhhcCHHHhccCCCC
Confidence            665   7889999999999986

>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=99.26  E-value=8.4e-13  Score=71.89  Aligned_cols=88  Identities=20%  Similarity=0.133  Sum_probs=68.4

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc------CCCc---hHH---HhhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ------SANG---FDV---RTIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~------~~~~---~d~---l~~~~~~~pii~lt~~~~~   68 (93)
                      +||++..+..++..|+..||. +..+.++.++++.+....++      .+++   +++   +....+.+|+|++|+..+.
T Consensus         9 vdd~~~~~~~l~~~l~~~~~~-v~~~~~~~~~~~~~~~~~~dlvi~d~~~~~~~g~~~~~~l~~~~~~~~ii~~s~~~~~   87 (124)
T 1dc7_A            9 VDDDSSIRWVLERALAGAGLT-CTTFENGNEVLAALASKTPDVLLSDIRMPGMDGLALLKQIKQRHPMLPVIIMTAHSDL   87 (124)
T ss_dssp             ECSSSSHHHHHHHHHTTTTCC-CEECCCTTHHHHHSSSCCCSCEEECSCSSHHHHCSTHHHHHHHCTTSCCCCBCCSTTS
T ss_pred             EeCCHHHHHHHHHHHHhCCcE-EEEeCCHHHHHHHHhcCCCCEEEEeeecCCCCHHHHHHHHHhhCCCCCEEEEecCCCH
Confidence            478888899999999988999 99999999999998654321      1122   222   2232378999999998888


Q ss_pred             HHHHHHHHcCCcceeeccchh
Q 042991           69 VRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      ....++++.|+++|+.||++.
T Consensus        88 ~~~~~~~~~g~~~~l~kp~~~  108 (124)
T 1dc7_A           88 DAAVSAYQQGAFDYLPKPFDI  108 (124)
T ss_dssp             TTTTSSCTTCCCCCBCSSCCH
T ss_pred             HHHHHHHhcCcceEeeCCCCH
Confidence            777788999999999999863

>3t8y_A CHEB, chemotaxis response regulator protein-glutamate methylesterase; CHEA, hydrolase; 1.90A {Thermotoga maritima}

Probab=99.26  E-value=3.5e-11  Score=68.99  Aligned_cols=88  Identities=17%  Similarity=0.080  Sum_probs=65.3

Q ss_pred             CCCcHHHHHHHHHHHhhcC-CCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhhh--cCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISS-SRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIYS--REIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~-~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~~--~~~pii~lt~~~~~   68 (93)
                      +||++..+..++.+|+..+ +..+..+.++.+|++.+....++         +..|++++..+.  ...|+|++|+..+.
T Consensus        31 vdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~al~~l~~~~~dlvilD~~l~~~~g~~l~~~lr~~~~~~ii~~s~~~~~  110 (164)
T 3t8y_A           31 VDDSAFMRMVLKDIIDSQPDMKVVGFAKDGLEAVEKAIELKPDVITMDIEMPNLNGIEALKLIMKKAPTRVIMVSSLTEE  110 (164)
T ss_dssp             ECSCHHHHHHHHHHHHTSTTEEEEEEESSHHHHHHHHHHHCCSEEEECSSCSSSCHHHHHHHHHHHSCCEEEEEESSCCT
T ss_pred             EcCCHHHHHHHHHHHhcCCCeEEEEecCCHHHHHHHhccCCCCEEEEeCCCCCCCHHHHHHHHHhcCCceEEEEecCCcc
Confidence            5899999999999999765 33355899999999988543321         234555533221  34899999987664


Q ss_pred             H--HHHHHHHcCCcceeeccch
Q 042991           69 V--RIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        69 ~--~~~~~~~~ga~d~l~kP~~   88 (93)
                      .  ...++++.|+++||.||+.
T Consensus       111 ~~~~~~~~~~~ga~~~l~KP~~  132 (164)
T 3t8y_A          111 GAAITIEALRNGAVDFITKPHG  132 (164)
T ss_dssp             TCHHHHHHHHTTCCEEEECSSS
T ss_pred             chHHHHHHHHcCcCEEEeCCCC
Confidence            3  5668999999999999987

>2rdm_A Response regulator receiver protein; structural genomics, unknown function, PSI-2, protein struct initiative; HET: MSE; 1.76A {Sinorhizobium medicae}

Probab=99.23  E-value=5.8e-11  Score=65.25  Aligned_cols=86  Identities=17%  Similarity=0.148  Sum_probs=66.7

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccC-ccc---------C-CCchHHH---hhhhcCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLD-EEQ---------S-ANGFDVR---TIYSREIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~-~~~---------~-~~~~d~l---~~~~~~~pii~lt~~~   66 (93)
                      +||++..+..++..|+..||+ +..+.++.++++.+... .++         + ..|++++   ....+.+|+|++|+..
T Consensus        11 vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~~a~~~l~~~~~~dlvi~d~~l~~~~~g~~~~~~l~~~~~~~~ii~~s~~~   89 (132)
T 2rdm_A           11 ADDEAILLLDFESTLTDAGFL-VTAVSSGAKAIEMLKSGAAIDGVVTDIRFCQPPDGWQVARVAREIDPNMPIVYISGHA   89 (132)
T ss_dssp             ECSSHHHHHHHHHHHHHTTCE-EEEESSHHHHHHHHHTTCCCCEEEEESCCSSSSCHHHHHHHHHHHCTTCCEEEEESSC
T ss_pred             EcCcHHHHHHHHHHHHHcCCE-EEEECCHHHHHHHHHcCCCCCEEEEeeeCCCCCCHHHHHHHHHhcCCCCCEEEEeCCc
Confidence            578999999999999988999 99999999999998654 321         2 3455553   3333789999999988


Q ss_pred             CHHHHHHHHHcCCcceeeccchh
Q 042991           67 ILVRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      +.....++++.|  +|+.||+..
T Consensus        90 ~~~~~~~~~~~~--~~l~kP~~~  110 (132)
T 2rdm_A           90 ALEWASNGVPDS--IILEKPFTS  110 (132)
T ss_dssp             CTTHHHHSCTTC--EEEESSCCH
T ss_pred             cHHHHHhhcCCc--ceEeCCCCH
Confidence            877776666665  799999863

>2qv0_A Protein MRKE; structural genomics, transcription, PSI-2, protein structure initiative; 2.40A {Klebsiella pneumoniae}

Probab=99.22  E-value=6.9e-11  Score=65.91  Aligned_cols=86  Identities=15%  Similarity=0.118  Sum_probs=63.8

Q ss_pred             CCCcHHHHHHHHHHHhhc-CCCceEEeCCHHHHHHHhccCccc---------CCCchHHHh---hhhcCCcEEEEcCCCC
Q 042991            1 LNDSFVDRKVIERLLTIS-SSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRT---IYSREIPVVIMSPEII   67 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~-~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~---~~~~~~pii~lt~~~~   67 (93)
                      +||++..+..+...|+.. ++..+..+.++.+|++.+....++         +..|++++.   ...+..|||++|+..+
T Consensus        15 vdd~~~~~~~l~~~L~~~~~~~~v~~~~~~~~al~~l~~~~~dlvi~d~~l~~~~g~~~~~~l~~~~~~~~ii~~s~~~~   94 (143)
T 2qv0_A           15 VEDEFLAQQELSWLINTHSQMEIVGSFDDGLDVLKFLQHNKVDAIFLDINIPSLDGVLLAQNISQFAHKPFIVFITAWKE   94 (143)
T ss_dssp             ECSCHHHHHHHHHHHHHHSCCEEEEEESCHHHHHHHHHHCCCSEEEECSSCSSSCHHHHHHHHTTSTTCCEEEEEESCCT
T ss_pred             EcCCHHHHHHHHHHHHhCCCceEEEEeCCHHHHHHHHHhCCCCEEEEecCCCCCCHHHHHHHHHccCCCceEEEEeCCHH
Confidence            588999999999999875 676345899999999988644321         234555533   3225677888888743


Q ss_pred             HHHHHHHHHcCCcceeeccch
Q 042991           68 LVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        68 ~~~~~~~~~~ga~d~l~kP~~   88 (93)
                        ...++++.|+++|+.||+.
T Consensus        95 --~~~~~~~~g~~~~l~KP~~  113 (143)
T 2qv0_A           95 --HAVEAFELEAFDYILKPYQ  113 (143)
T ss_dssp             --THHHHHHTTCSEEEESSCC
T ss_pred             --HHHHHHhCCcceEEeCCCC
Confidence              5667899999999999986

>3sy8_A ROCR; TIM barrel phosphodiesterase-A, transcription regulator; HET: EPE; 2.50A {Pseudomonas aeruginosa}

Probab=99.21  E-value=1.2e-11  Score=80.07  Aligned_cols=87  Identities=14%  Similarity=0.109  Sum_probs=66.8

Q ss_pred             CCCcHHHHHHHHHHHhh-cCCCceEEeCCHHHHHHHhcc-Cccc---------CCCchHHHh---hhhcCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTI-SSSRDLYCSCSGRRALQFLGL-DEEQ---------SANGFDVRT---IYSREIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~-~~~~~v~~~~~~~~a~~~~~~-~~~~---------~~~~~d~l~---~~~~~~pii~lt~~~   66 (93)
                      |||++..+..++.+|+. .++. +..+.++.+|++.+.. ..++         +++|++++.   ...+.+|||++|+..
T Consensus         9 vDD~~~~~~~l~~~L~~~~~~~-v~~a~~g~eal~~l~~~~~~DlvllDi~mP~~dG~ell~~l~~~~~~~~ii~~s~~~   87 (400)
T 3sy8_A            9 LEDEPFQRLVAVTALKKVVPGS-ILEAADGKEAVAILESCGHVDIAICDLQMSGMDGLAFLRHASLSGKVHSVILSSEVD   87 (400)
T ss_dssp             ECSSHHHHHHHHHHHHHHCSEE-EEEESSHHHHHHHHHHHSCEEEEEECSSCSSSCHHHHHHHHHHHTCEEEEEESCCCC
T ss_pred             EcCCHHHHHHHHHHHHhcCCcE-EEEecCHHHHHHHHhhCCCCCEEEEeCCCCCCCHHHHHHHHHhcCCCceEEEEcCch
Confidence            58999999999999997 5678 8999999999999864 2321         345666633   333666777777766


Q ss_pred             CH-----HHHHHHHHcCCcceeeccch
Q 042991           67 IL-----VRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        67 ~~-----~~~~~~~~~ga~d~l~kP~~   88 (93)
                      ..     ....++++.|+++|+.||++
T Consensus        88 ~~~~~~~~~~~~a~~~ga~~yl~KP~~  114 (400)
T 3sy8_A           88 PILRQATISMIECLGLNFLGDLGKPFS  114 (400)
T ss_dssp             GGGHHHHHHHHHTTTCEEEEECCSSCC
T ss_pred             HHHHHHHHHHHHHcCCeeccCcCCCcC
Confidence            65     56677889999999999996

>3c97_A Signal transduction histidine kinase; structural genomics, signaling, PSI-2, protein structure initiative; 1.70A {Aspergillus oryzae RIB40}

Probab=99.18  E-value=4e-11  Score=66.80  Aligned_cols=85  Identities=12%  Similarity=0.132  Sum_probs=64.1

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhh--------hcCCcEEEEc
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIY--------SREIPVVIMS   63 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~--------~~~~pii~lt   63 (93)
                      +||++..+..++.+|+..|+. +..+.++.+|++.+....++         +.+|++++..+        .+.+|++++|
T Consensus        16 vdd~~~~~~~l~~~L~~~~~~-v~~~~~~~~al~~l~~~~~dlvllD~~lp~~~g~~~~~~l~~~~~~~~~~~~~ii~~s   94 (140)
T 3c97_A           16 AEDNDICRLVAAKALEKCTND-ITVVTNGLQALQAYQNRQFDVIIMDIQMPVMDGLEAVSEIRNYERTHNTKRASIIAIT   94 (140)
T ss_dssp             ECCCHHHHHHHHHHHTTTCSE-EEEESSHHHHHHHHHHSCCSEEEECTTCCSSCHHHHHHHHHHHHHHHTCCCCCCEEEE
T ss_pred             EcCCHHHHHHHHHHHHHcCCc-eEEECCHHHHHHHHhcCCCCEEEEeCCCCCCcHHHHHHHHHhhhhhcCCCceEEEEEe
Confidence            588999999999999988898 99999999999988644321         23566653222        1578999999


Q ss_pred             CCCCHHHHHHHHHcCCcceeeccchh
Q 042991           64 PEIILVRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        64 ~~~~~~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      +........   +.|+++|+.||++.
T Consensus        95 ~~~~~~~~~---~~g~~~~l~KP~~~  117 (140)
T 3c97_A           95 ADTIDDDRP---GAELDEYVSKPLNP  117 (140)
T ss_dssp             SSCCSCCCC---CSSCSEEEESSCCH
T ss_pred             CccchhHHH---hCChhheEeCCCCH
Confidence            866544332   78999999999863

>1a2o_A CHEB methylesterase; bacterial chemotaxis, adaptation, serine hydrolase; 2.40A {Salmonella typhimurium} SCOP: c.23.1.1 c.40.1.1

Probab=99.18  E-value=1.1e-10  Score=74.74  Aligned_cols=88  Identities=20%  Similarity=0.153  Sum_probs=67.3

Q ss_pred             CCCcHHHHHHHHHHHhhc-CCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhhh--cCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTIS-SSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIYS--REIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~-~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~~--~~~pii~lt~~~~~   68 (93)
                      |||++..+..++.+|+.. +|+.+..+.++.+|++.++...++         +++|++++..+.  ..+|+|++|+..+.
T Consensus         9 VDD~~~~r~~L~~~L~~~~g~~vv~~a~~~~eAl~~l~~~~pDlVllDi~mp~~dGlell~~l~~~~p~pVIvlS~~~~~   88 (349)
T 1a2o_A            9 VDDSALMRQIMTEIINSHSDMEMVATAPDPLVARDLIKKFNPDVLTLDVEMPRMDGLDFLEKLMRLRPMPVVMVSSLTGK   88 (349)
T ss_dssp             ECSCHHHHHHHHHHHHTSTTEEEEEEESSHHHHHHHHHHHCCSEEEEECCCSSSCHHHHHHHHHHSSCCCEEEEECCTHH
T ss_pred             EECCHHHHHHHHHHHhcCCCcEEEEEeCCHHHHHHHHhccCCCEEEEECCCCCCCHHHHHHHHHhcCCCcEEEEECCCcc
Confidence            589999999999999975 777456999999999988643321         235666533322  33999999988775


Q ss_pred             --HHHHHHHHcCCcceeeccch
Q 042991           69 --VRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        69 --~~~~~~~~~ga~d~l~kP~~   88 (93)
                        +...++++.|+++|+.||+.
T Consensus        89 ~~~~~~~al~~Ga~d~l~KP~~  110 (349)
T 1a2o_A           89 GSEVTLRALELGAIDFVTKPQL  110 (349)
T ss_dssp             HHHHHHHHHHHTCCEEEECSSS
T ss_pred             cHHHHHHHHhCCceEEEECCCC
Confidence              34778999999999999986

>3klo_A Transcriptional regulator VPST; REC domain, HTH domain, DNA-binding, transcription regulation; HET: C2E TAR; 2.80A {Vibrio cholerae} PDB: 3kln_A*

Probab=99.15  E-value=1e-11  Score=74.51  Aligned_cols=88  Identities=10%  Similarity=-0.099  Sum_probs=63.9

Q ss_pred             CCCcHHHHHHHHHHHhh-cCCCceE-EeCCHHHHHHH-hccCccc---------CCCchHH---Hhh-hhcCCcEEEEcC
Q 042991            1 LNDSFVDRKVIERLLTI-SSSRDLY-CSCSGRRALQF-LGLDEEQ---------SANGFDV---RTI-YSREIPVVIMSP   64 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~-~~~~~v~-~~~~~~~a~~~-~~~~~~~---------~~~~~d~---l~~-~~~~~pii~lt~   64 (93)
                      |||++..+..++.+|+. .||. +. .+.++.+++.. +....++         +++|+++   +.. ..+++|||++|+
T Consensus        13 vdD~~~~~~~l~~~L~~~~~~~-v~~~~~~~~~~~~~~~~~~~~dlvllD~~mp~~~G~~~~~~lr~~~~~~~~ii~lt~   91 (225)
T 3klo_A           13 LSDVCMQSRLLKEALESKLPLA-LEITPFSELWLEENKPESRSIQMLVIDYSRISDDVLTDYSSFKHISCPDAKEVIINC   91 (225)
T ss_dssp             ESCCSHHHHHHHHHHHHHSSEE-EEEECGGGHHHHTTCSGGGGCCEEEEEGGGCCHHHHHHHHHHHHHHCTTCEEEEEEE
T ss_pred             EcCcHHHHHHHHHHHhhCCCce-EEEEeCCcHHHHHHHhhccCCCEEEEeCCCCCCCHHHHHHHHHHhhCCCCcEEEEEC
Confidence            58999999999999984 5777 54 34556665543 4433321         2234444   334 347899999999


Q ss_pred             CCCHHHHHHHHHcCCcceeeccchh
Q 042991           65 EIILVRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        65 ~~~~~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      ..+......+++.|+++|+.||+..
T Consensus        92 ~~~~~~~~~~~~~Ga~~~l~Kp~~~  116 (225)
T 3klo_A           92 PQDIEHKLLFKWNNLAGVFYIDDDM  116 (225)
T ss_dssp             CTTCCHHHHTTSTTEEEEEETTCCH
T ss_pred             CcchhHHHHHHHhCCCEEEecCCCH
Confidence            9888888889999999999999873

>2vyc_A Biodegradative arginine decarboxylase; pyridoxal phosphate, PLP-dependent E lyase, acid resistance; HET: LLP; 2.4A {Escherichia coli}

Probab=99.15  E-value=1.6e-11  Score=85.04  Aligned_cols=88  Identities=14%  Similarity=0.117  Sum_probs=69.3

Q ss_pred             CCCcH-HH-------HHHHHHHHhhcCCCceEEeCCHHHHHHHhccCc-cc------CCCc----hH---H---Hhhhhc
Q 042991            1 LNDSF-VD-------RKVIERLLTISSSRDLYCSCSGRRALQFLGLDE-EQ------SANG----FD---V---RTIYSR   55 (93)
Q Consensus         1 vdd~~-~~-------~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~-~~------~~~~----~d---~---l~~~~~   55 (93)
                      |||+. ..       ++.|+..|++.||+ |..+.++++|+..++... .+      ++++    .+   +   ++....
T Consensus         6 VdDd~~~~~~~~~~~~~~L~~~L~~~g~~-v~~a~~g~~al~~~~~~~~~d~vilDi~lp~~~~~~~G~~ll~~iR~~~~   84 (755)
T 2vyc_A            6 VESEFLHQDTWVGNAVERLADALSQQNVT-VIKSTSFDDGFAILSSNEAIDCLMFSYQMEHPDEHQNVRQLIGKLHERQQ   84 (755)
T ss_dssp             ECCTTSTTSHHHHHHHHHHHHHHHHTTCE-EEEESSHHHHHHHHTTTCCCSEEEEECCCCSHHHHHHHHHHHHHHHHHST
T ss_pred             EeCCccccccccHHHHHHHHHHHHhCCCE-EEEECCHHHHHHHHhcCCCCcEEEEeCCCCcccccccHHHHHHHHHHhCC
Confidence            46776 66       89999999999999 999999999999997543 21      2233    33   3   333336


Q ss_pred             CCcEEEEcCCCC-HHHHHHHHHcCCcceeeccchh
Q 042991           56 EIPVVIMSPEII-LVRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        56 ~~pii~lt~~~~-~~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      .+||+++|+..+ .++....+..|++||+.||++.
T Consensus        85 ~iPIi~lTa~~~~~~d~~~~l~~gaddyi~kpf~~  119 (755)
T 2vyc_A           85 NVPVFLLGDREKALAAMDRDLLELVDEFAWILEDT  119 (755)
T ss_dssp             TCCEEEEECHHHHHHTCSHHHHHHCSEEEETTTSC
T ss_pred             CCCEEEEecCCcchhhccHhHhhcCCceEeCCCCC
Confidence            899999999877 7778888999999999999963

>1qo0_D AMIR; binding protein, gene regulator, receptor; 2.25A {Pseudomonas aeruginosa} SCOP: c.23.1.3

Probab=99.14  E-value=7.5e-11  Score=69.22  Aligned_cols=84  Identities=11%  Similarity=-0.060  Sum_probs=64.0

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc------CCCchH--H---HhhhhcCCcEEEEcCCCCHH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ------SANGFD--V---RTIYSREIPVVIMSPEIILV   69 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~------~~~~~d--~---l~~~~~~~pii~lt~~~~~~   69 (93)
                      |||++..+..+..+|...||. +..+.++.+++   . ..++      .+++.+  +   +....+.+|||++|+..+..
T Consensus        18 vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~~al---~-~~~dlvl~D~~mp~~~g~l~~~~~~~~~~~~ii~lt~~~~~~   92 (196)
T 1qo0_D           18 LNPPGEVSDALVLQLIRIGCS-VRQCWPPPEAF---D-VPVDVVFTSIFQNRHHDEIAALLAAGTPRTTLVALVEYESPA   92 (196)
T ss_dssp             ESCTTHHHHHHHHHHHHHTCE-EEEECSCCSSC---S-SCCSEEEEECCSSTHHHHHHHHHHHSCTTCEEEEEECCCSHH
T ss_pred             EcCChhHHHHHHHHHHHcCCe-EEEecCchhhC---C-CCCCEEEEeCCCCccchHHHHHHhccCCCCCEEEEEcCCChH
Confidence            588999999999999988999 88888877765   2 1111      223332  2   11111789999999999999


Q ss_pred             HHHHHHHcCCcceeeccchh
Q 042991           70 RIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        70 ~~~~~~~~ga~d~l~kP~~~   89 (93)
                      ...++++.|+++|+.||+..
T Consensus        93 ~~~~a~~~ga~~~l~KP~~~  112 (196)
T 1qo0_D           93 VLSQIIELECHGVITQPLDA  112 (196)
T ss_dssp             HHHHHHHHTCSEEEESSCCG
T ss_pred             HHHHHHHcCCCeeEecCcCH
Confidence            99999999999999999863

>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=99.12  E-value=6e-11  Score=65.88  Aligned_cols=83  Identities=12%  Similarity=0.047  Sum_probs=62.9

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhcc-Cccc---------CCCchHHHh---hhhcCCcEEEEc-CCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGL-DEEQ---------SANGFDVRT---IYSREIPVVIMS-PEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~-~~~~---------~~~~~d~l~---~~~~~~pii~lt-~~~   66 (93)
                      +||++..+..++.+|+..||. +..+.++.+|++.++. ..++         +..|++++.   ...+.+|+|++| +..
T Consensus        21 vdd~~~~~~~l~~~L~~~g~~-v~~~~~~~~al~~l~~~~~~dlvilD~~l~~~~g~~~~~~l~~~~~~~~ii~ls~~~~   99 (138)
T 2b4a_A           21 VEDEPSHATLIQYHLNQLGAE-VTVHPSGSAFFQHRSQLSTCDLLIVSDQLVDLSIFSLLDIVKEQTKQPSVLILTTGRH   99 (138)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCE-EEEESSHHHHHHTGGGGGSCSEEEEETTCTTSCHHHHHHHHTTSSSCCEEEEEESCC-
T ss_pred             ECCCHHHHHHHHHHHHHcCCE-EEEeCCHHHHHHHHHhCCCCCEEEEeCCCCCCCHHHHHHHHHhhCCCCCEEEEECCCC
Confidence            588999999999999998998 9999999999999875 4321         224555433   323789999999 876


Q ss_pred             CHHHHHHHHHcCCcceeeccch
Q 042991           67 ILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      +... .+++   +++|+.||+.
T Consensus       100 ~~~~-~~~~---~~~~l~KP~~  117 (138)
T 2b4a_A          100 ELIE-SSEH---NLSYLQKPFA  117 (138)
T ss_dssp             -CCC-CSSS---CEEEEESSCC
T ss_pred             CHHH-HHHH---HHheeeCCCC
Confidence            6655 5555   9999999986

>3cwo_X Beta/alpha-barrel protein based on 1THF and 1TMY; XRAY, CHEY, HISF, half barrel, de novo protein; 3.10A {Thermotoga maritima} PDB: 2lle_A

Probab=97.95  E-value=5.6e-06  Score=49.31  Aligned_cols=64  Identities=16%  Similarity=0.119  Sum_probs=45.8

Q ss_pred             eEEeCCHHHHHHHhccCccc---------CCCchHHHhh---hhcCCcEEEEcCCCCHHHHHHHHHcCCcceeecc
Q 042991           23 LYCSCSGRRALQFLGLDEEQ---------SANGFDVRTI---YSREIPVVIMSPEIILVRIDRYLEDGAEDSETCQ   86 (93)
Q Consensus        23 v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~---~~~~~pii~lt~~~~~~~~~~~~~~ga~d~l~kP   86 (93)
                      +..+.++.+|++.+....++         +++|++++..   ..+..++++++.....+...++++.|+++|+.||
T Consensus         8 v~~~~~~~~a~~~~~~~~~dlvl~D~~~p~~~g~~~~~~l~~~~~~~~i~vi~~~~~~~~~~~~~~~Ga~~~l~kp   83 (237)
T 3cwo_X            8 VDDATNGREAVEKYKELKPDIVTMDITMPEMNGIDAIKEIMKIDPNAKIIVCSAMGQQAMVIEAIKAGAKDFIVNT   83 (237)
T ss_dssp             EECCCSSSTTHHHHHHHCCSCEEEECCSTTSSHHHHHHHHHHHSSSCCEEEECCSSTHHHHHHHHHTTCCEEEESH
T ss_pred             EEECCCHHHHHHHHHhcCCCEEEEeCCCCCCCHHHHHHHHHHhCCCCCEEEEECCCCHHHHHHHHHCCHHheEeCC
Confidence            77788899988887543321         2345555333   3356667777776678888899999999999999

>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=97.67  E-value=0.0008  Score=43.93  Aligned_cols=85  Identities=16%  Similarity=0.137  Sum_probs=57.0

Q ss_pred             CCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCcc---------cCCCchHHHhhh-----hcCCcEEEEcCCCC
Q 042991            2 NDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEE---------QSANGFDVRTIY-----SREIPVVIMSPEII   67 (93)
Q Consensus         2 dd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~---------~~~~~~d~l~~~-----~~~~pii~lt~~~~   67 (93)
                      +|+......+...+.. .+. +....++.+++.. ....+         +.+.|+++....     ...+|++++|+...
T Consensus       159 dd~~~~~~~i~~~L~~-~~~-~~~~~~~~~~~~~-~~~~~dlil~D~~mp~~dG~~~~~~ir~~~~~~~~pii~lt~~~~  235 (459)
T 1w25_A          159 DDNERQAQRVAAELGV-EHR-PVIESDPEKAKIS-AGGPVDLVIVNAAAKNFDGLRFTAALRSEERTRQLPVLAMVDPDD  235 (459)
T ss_dssp             CSCHHHHHHHHHHHTT-TSE-EEEECCHHHHHHH-HHSSCSEEEEETTCSSSCHHHHHHHHHTSGGGTTCCEEEEECTTC
T ss_pred             CCchhhHHHHHHHHhc-ccc-eeeccCHHHHhhh-ccCCCCEEEEecCCCCCcHHHHHHHHHhCccccCCcEEEEcCCCc
Confidence            4555566666666653 345 6677788777532 11111         123455542211     27889999999999


Q ss_pred             HHHHHHHHHcCCcceeeccchh
Q 042991           68 LVRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        68 ~~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      .....++++.|+++|+.||+..
T Consensus       236 ~~~~~~~l~~Ga~d~~~kp~~~  257 (459)
T 1w25_A          236 RGRMVKALEIGVNDILSRPIDP  257 (459)
T ss_dssp             HHHHHHHHHTTCCEEEESSCCH
T ss_pred             hHHHHHHHhccccccccCCCCH
Confidence            9888899999999999999863

>3q7r_A Transcriptional regulatory protein; CHXR, receiver domain, transcription factor, OMPR, chlamydia transcription; 1.60A {Chlamydia trachomatis} PDB: 3q7s_A* 3q7t_A

Probab=96.08  E-value=0.0088  Score=31.85  Aligned_cols=38  Identities=11%  Similarity=-0.089  Sum_probs=31.1

Q ss_pred             cCCcEEEEcCCCCHHHHHHHHHcCCcceeeccchhhhcC
Q 042991           55 REIPVVIMSPEIILVRIDRYLEDGAEDSETCQMWARLRD   93 (93)
Q Consensus        55 ~~~pii~lt~~~~~~~~~~~~~~ga~d~l~kP~~~~~~~   93 (93)
                      ...-+|++-..=+++..++.++.|+. |+..|+..++.|
T Consensus        72 ~~~dliVLfD~F~EEa~v~vLd~Ga~-yLlrPIT~kvld  109 (121)
T 3q7r_A           72 EGSFVLVLLDFFDEETSVDLLDRGFW-YLIRPITPRILK  109 (121)
T ss_dssp             CSCEEEEEESSCCHHHHHHHHHTTCE-EEESCCCHHHHH
T ss_pred             CcccEEEEehhhchHHHHHHHhCCce-eEeccCcHHHHH
Confidence            44557777777888888999999999 999999987653

>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=95.63  E-value=0.0049  Score=43.05  Aligned_cols=79  Identities=5%  Similarity=0.001  Sum_probs=50.2

Q ss_pred             HHHHHHHHhhcCCCceEEeCCHHHHHHHhccCcccCCCc-------hHH---HhhhhcCCcEEEEcCCCCHHHHHHHHHc
Q 042991            8 RKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQSANG-------FDV---RTIYSREIPVVIMSPEIILVRIDRYLED   77 (93)
Q Consensus         8 ~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~~~~~-------~d~---l~~~~~~~pii~lt~~~~~~~~~~~~~~   77 (93)
                      ...|...|++.||+ |..+.+..+|+..++......+..       .++   ++....++||.+++.......+....-.
T Consensus        19 i~~L~~~Le~~g~~-V~~a~s~~Da~~~i~~~~~i~avIld~d~~~~~ll~~Ir~~~~~iPVFl~~~~~~~~~~~~~~~~   97 (715)
T 3n75_A           19 IRELHRALERLNFQ-IVYPNDRDDLLKLIENNARLCGVIFDWDKYNLELCEEISKMNENLPLYAFANTYSTLDVSLNDLR   97 (715)
T ss_dssp             HHHHHHHHHHTTCE-EECCSSHHHHHHHHHHCTTEEEEEEEHHHHHHHHHHHHHHHCTTCEEEEECCTTCCCCGGGTTSC
T ss_pred             HHHHHHHHHHCCcE-EEEeCCHHHHHHHHHhCCCceEEEEeccccHHHHHHHHHHhCCCCCEEEEecCCcccccchhhhh
Confidence            34566788889999 999999999999997554322211       122   3444489999999987543332111123


Q ss_pred             CCcceeeccc
Q 042991           78 GAEDSETCQM   87 (93)
Q Consensus        78 ga~d~l~kP~   87 (93)
                      ++++|+-+..
T Consensus        98 ~~~~~~~~~~  107 (715)
T 3n75_A           98 LQISFFEYAL  107 (715)
T ss_dssp             CEEEEECCCT
T ss_pred             ccCeEEEeCC
Confidence            5666666543

>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=93.06  E-value=0.14  Score=30.03  Aligned_cols=29  Identities=10%  Similarity=0.135  Sum_probs=27.0

Q ss_pred             cCCcEEEEcCCCCHHHHHHHHHcCCccee
Q 042991           55 REIPVVIMSPEIILVRIDRYLEDGAEDSE   83 (93)
Q Consensus        55 ~~~pii~lt~~~~~~~~~~~~~~ga~d~l   83 (93)
                      .++|+|.+++...++...++++.|+++++
T Consensus       173 ~~~Pvia~~g~~~~~~~~~~~~~G~~~~~  201 (237)
T 3cwo_X          173 TTLPIIASGGAGKMEHFLEAFLAGADAAL  201 (237)
T ss_dssp             CCSCEEEESCCCSHHHHHHHHHHTCSEEE
T ss_pred             cCCCEEecCCCCCHHHHHHHHHcCcHHHh
Confidence            68999999999999999999999999986

>1wv2_A Thiazole moeity, thiazole biosynthesis protein THIG; structural genomics, protein structure initiative, PSI; 2.90A {Pseudomonas aeruginosa} SCOP: c.1.31.1

Probab=90.02  E-value=2.3  Score=26.40  Aligned_cols=74  Identities=15%  Similarity=-0.012  Sum_probs=47.4

Q ss_pred             HHHHhhcCCCce-EEeCCHHHHHHHhccCcc-----c-------CCCchHHHhhh--hcCCcEEEEcCCCCHHHHHHHHH
Q 042991           12 ERLLTISSSRDL-YCSCSGRRALQFLGLDEE-----Q-------SANGFDVRTIY--SREIPVVIMSPEIILVRIDRYLE   76 (93)
Q Consensus        12 ~~~l~~~~~~~v-~~~~~~~~a~~~~~~~~~-----~-------~~~~~d~l~~~--~~~~pii~lt~~~~~~~~~~~~~   76 (93)
                      .+.|.+.||..+ ++..+...|.........     .       .+..++++...  ...+|||.=.+-.++++...+++
T Consensus       128 a~~L~~~Gf~Vlpy~~dd~~~akrl~~~G~~aVmPlg~pIGsG~Gi~~~~lI~~I~e~~~vPVI~eGGI~TPsDAa~Ame  207 (265)
T 1wv2_A          128 AEQLVKDGFDVMVYTSDDPIIARQLAEIGCIAVMPLAGLIGSGLGICNPYNLRIILEEAKVPVLVDAGVGTASDAAIAME  207 (265)
T ss_dssp             HHHHHTTTCEEEEEECSCHHHHHHHHHSCCSEEEECSSSTTCCCCCSCHHHHHHHHHHCSSCBEEESCCCSHHHHHHHHH
T ss_pred             HHHHHHCCCEEEEEeCCCHHHHHHHHHhCCCEEEeCCccCCCCCCcCCHHHHHHHHhcCCCCEEEeCCCCCHHHHHHHHH
Confidence            344556799833 467777777665432211     0       11223443222  27899998667788999999999


Q ss_pred             cCCcceeec
Q 042991           77 DGAEDSETC   85 (93)
Q Consensus        77 ~ga~d~l~k   85 (93)
                      .|++.++.-
T Consensus       208 LGAdgVlVg  216 (265)
T 1wv2_A          208 LGCEAVLMN  216 (265)
T ss_dssp             HTCSEEEES
T ss_pred             cCCCEEEEC
Confidence            999998754

>3tsm_A IGPS, indole-3-glycerol phosphate synthase; structural genomics, ssgcid, seattle structural GE center for infectious disease, lyase; 2.15A {Brucella melitensis} SCOP: c.1.2.0

Probab=89.17  E-value=2.7  Score=26.07  Aligned_cols=75  Identities=11%  Similarity=-0.079  Sum_probs=47.9

Q ss_pred             HHHHHHhhcCCCceEEeCCHHHHHHHhccCcc-c-----CCCc--hHH-----Hhh-hhcCCcEEEEcCCCCHHHHHHHH
Q 042991           10 VIERLLTISSSRDLYCSCSGRRALQFLGLDEE-Q-----SANG--FDV-----RTI-YSREIPVVIMSPEIILVRIDRYL   75 (93)
Q Consensus        10 ~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~-~-----~~~~--~d~-----l~~-~~~~~pii~lt~~~~~~~~~~~~   75 (93)
                      .+....+..|...+..+.+.+++...+..... .     ++..  .|+     +.. ...++|+|.-++-.+++++.+..
T Consensus       160 ~l~~~a~~lGl~~lvevh~~eEl~~A~~~ga~iIGinnr~l~t~~~dl~~~~~L~~~ip~~~~vIaesGI~t~edv~~l~  239 (272)
T 3tsm_A          160 ELEDTAFALGMDALIEVHDEAEMERALKLSSRLLGVNNRNLRSFEVNLAVSERLAKMAPSDRLLVGESGIFTHEDCLRLE  239 (272)
T ss_dssp             HHHHHHHHTTCEEEEEECSHHHHHHHTTSCCSEEEEECBCTTTCCBCTHHHHHHHHHSCTTSEEEEESSCCSHHHHHHHH
T ss_pred             HHHHHHHHcCCeEEEEeCCHHHHHHHHhcCCCEEEECCCCCccCCCChHHHHHHHHhCCCCCcEEEECCCCCHHHHHHHH
Confidence            33344455676657778899998776643211 0     1111  111     111 11468889888888999999999


Q ss_pred             HcCCcceee
Q 042991           76 EDGAEDSET   84 (93)
Q Consensus        76 ~~ga~d~l~   84 (93)
                      ++|++.++.
T Consensus       240 ~~Ga~gvLV  248 (272)
T 3tsm_A          240 KSGIGTFLI  248 (272)
T ss_dssp             TTTCCEEEE
T ss_pred             HcCCCEEEE
Confidence            999999986

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	93
d1qkka_	140	Transcriptional regulatory protein DctD, receiver	99.83
d1dbwa_	123	Transcriptional regulatory protein FixJ, receiver	99.83
d2pl1a1	119	PhoP receiver domain {Escherichia coli [TaxId: 562	99.83
d2a9pa1	117	DNA-binding response regulator MicA, N-terminal do	99.82
d1peya_	119	Sporulation response regulator Spo0F {Bacillus sub	99.82
d1zesa1	121	PhoB receiver domain {Escherichia coli [TaxId: 562	99.82
d1xhfa1	121	Aerobic respiration control protein ArcA, N-termin	99.82
d1ny5a1	137	Transcriptional activator sigm54 (NtrC1), N-termin	99.81
d1krwa_	123	NTRC receiver domain {Salmonella typhimurium [TaxI	99.81
d1w25a1	139	Response regulator PleD, receiver domain {Caulobac	99.81
d1zh2a1	119	Transcriptional regulatory protein KdpE, N-termina	99.81
d1ys7a2	121	Transcriptional regulatory protein PrrA, N-termina	99.8
d1zgza1	120	TorCAD operon transcriptional regulator TorD, N-te	99.8
d1mvoa_	121	PhoP receiver domain {Bacillus subtilis [TaxId: 14	99.8
d1u0sy_	118	CheY protein {Thermotoga maritima [TaxId: 2336]}	99.79
d1kgsa2	122	PhoB receiver domain {Thermotoga maritima [TaxId:	99.79
d2ayxa1	133	Sensor kinase protein RcsC, C-terminal domain {Esc	99.78
d1jbea_	128	CheY protein {Escherichia coli [TaxId: 562]}	99.78
d1mb3a_	123	Cell division response regulator DivK {Caulobacter	99.77
d1yioa2	128	Response regulatory protein StyR, N-terminal domai	99.76
d1s8na_	190	Probable two-component system transcriptional regu	99.76
d2r25b1	128	Response regulator Sin1 {Baker's yeast (Saccharomy	99.76
d1p6qa_	129	CheY protein {Sinorhizobium meliloti, CheY2 [TaxId	99.76
d1dcfa_	134	Receiver domain of the ethylene receptor {Thale cr	99.75
d1i3ca_	144	Response regulator for cyanobacterial phytochrome	99.75
d1k66a_	149	Response regulator for cyanobacterial phytochrome	99.75
d1k68a_	140	Response regulator for cyanobacterial phytochrome	99.74
d1p2fa2	120	Response regulator DrrB {Thermotoga maritima [TaxI	99.7
d1a04a2	138	Nitrate/nitrite response regulator (NarL), receive	99.69
d1dz3a_	123	Sporulation response regulator Spo0A {Bacillus ste	99.68
d1w25a2	153	Response regulator PleD, receiver domain {Caulobac	99.66
d1a2oa1	140	Methylesterase CheB, N-terminal domain {Salmonella	99.6
d2b4aa1	118	Hypothetical protein BH3024 {Bacillus halodurans [	99.6
d1qo0d_	189	Positive regulator of the amidase operon AmiR {Pse	99.57
d1yxya1	230	Putative N-acetylmannosamine-6-phosphate 2-epimera	85.18
d1a53a_	247	Indole-3-glycerophosphate synthase, IPGS {Archaeon	80.33
d1y0ea_	222	Putative N-acetylmannosamine-6-phosphate 2-epimera	80.22

>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=99.83  E-value=3.7e-20  Score=103.84  Aligned_cols=87  Identities=17%  Similarity=0.189  Sum_probs=76.5

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHH---HhhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDV---RTIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~---l~~~~~~~pii~lt~~~~~   68 (93)
                      |||++..+..++.+|+..||. +..+.|+.+|++.++...++         +++|+++   ++...+++|||++|++++.
T Consensus         6 VDDd~~~~~~l~~~L~~~g~~-v~~~~~~~~al~~l~~~~~dlil~D~~mP~~~G~el~~~lr~~~~~~pvI~lT~~~~~   84 (140)
T d1qkka_           6 IDDDRDLRKAMQQTLELAGFT-VSSFASATEALAGLSADFAGIVISDIRMPGMDGLALFRKILALDPDLPMILVTGHGDI   84 (140)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCE-EEEESCHHHHHHTCCTTCCSEEEEESCCSSSCHHHHHHHHHHHCTTSCEEEEECGGGH
T ss_pred             EECCHHHHHHHHHHHHHCCCE-EEEeCChHHHHHHHhccCcchHHHhhccCCCCHHHHHHHHHHhCCCCcEEEEECCCCH
Confidence            689999999999999999999 99999999999999765432         4567776   3344489999999999999


Q ss_pred             HHHHHHHHcCCcceeeccch
Q 042991           69 VRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~   88 (93)
                      +...+|++.||+|||.||+.
T Consensus        85 ~~~~~a~~~Ga~dyl~KP~~  104 (140)
T d1qkka_          85 PMAVQAIQDGAYDFIAKPFA  104 (140)
T ss_dssp             HHHHHHHHTTCCEEEESSCC
T ss_pred             HHHHHHHHcCCCEeecCCCC
Confidence            99999999999999999986

>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=99.83  E-value=5.7e-20  Score=101.08  Aligned_cols=88  Identities=16%  Similarity=0.100  Sum_probs=76.7

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHH---HhhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDV---RTIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~---l~~~~~~~pii~lt~~~~~   68 (93)
                      |||++..+..++.+|+..||+ +..+.++++|++.++..+++         +++|+++   ++...+++|+|++|++.+.
T Consensus         9 VDDd~~~~~~l~~~L~~~g~~-v~~a~~~~~al~~~~~~~~dlvi~D~~mp~~~G~e~~~~lr~~~~~~~iI~lt~~~~~   87 (123)
T d1dbwa_           9 VDDEEPVRKSLAFMLTMNGFA-VKMHQSAEAFLAFAPDVRNGVLVTDLRMPDMSGVELLRNLGDLKINIPSIVITGHGDV   87 (123)
T ss_dssp             EESSHHHHHHHHHHHHHTTCE-EEEESCHHHHHHHGGGCCSEEEEEECCSTTSCHHHHHHHHHHTTCCCCEEEEECTTCH
T ss_pred             EECCHHHHHHHHHHHHHCCCE-EEEECCHHHHHHHHhhcCCcEEEEeccCccccchHHHHHHHhcCCCCeEEEEEeeCCH
Confidence            689999999999999999999 99999999999999755432         4567776   4444489999999999999


Q ss_pred             HHHHHHHHcCCcceeeccchh
Q 042991           69 VRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      +...++++.||++|+.||++.
T Consensus        88 ~~~~~a~~~Ga~~yl~KP~~~  108 (123)
T d1dbwa_          88 PMAVEAMKAGAVDFIEKPFED  108 (123)
T ss_dssp             HHHHHHHHTTCSEEEESSCCH
T ss_pred             HHHHHHHHCCCCEEEECCCCH
Confidence            999999999999999999973

>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=99.83  E-value=5.7e-20  Score=100.57  Aligned_cols=87  Identities=13%  Similarity=0.166  Sum_probs=76.0

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHh---hhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRT---IYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~---~~~~~~pii~lt~~~~~   68 (93)
                      |||++..+..++.+|+..||+ +..+.++.+|++.++...++         +++|++++.   ...+.+|+|++|+..+.
T Consensus         6 VDDd~~~~~~l~~~L~~~G~~-v~~a~~g~eal~~l~~~~~dliilD~~mP~~~G~e~~~~i~~~~~~~pvi~lt~~~~~   84 (119)
T d2pl1a1           6 VEDNALLRHHLKVQIQDAGHQ-VDDAEDAKEADYYLNEHIPDIAIVDLGLPDEDGLSLIRRWRSNDVSLPILVLTARESW   84 (119)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCE-EEEESSHHHHHHHHHHSCCSEEEECSCCSSSCHHHHHHHHHHTTCCSCEEEEESCCCH
T ss_pred             EeCCHHHHHHHHHHHHHCCCE-EEEECCHHHHHHHHHhcccceeehhccCCCchhHHHHHHHHhcCcccceEeeeccCCH
Confidence            689999999999999999999 99999999999999765432         446777633   33389999999999999


Q ss_pred             HHHHHHHHcCCcceeeccch
Q 042991           69 VRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~   88 (93)
                      +...++++.||++|+.||++
T Consensus        85 ~~~~~a~~~Ga~~yl~KP~~  104 (119)
T d2pl1a1          85 QDKVEVLSAGADDYVTKPFH  104 (119)
T ss_dssp             HHHHHHHHTTCSEEEESSCC
T ss_pred             HHHHHHHHcCCCEEEECCCC
Confidence            99999999999999999997

>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=99.82  E-value=5.3e-20  Score=100.40  Aligned_cols=87  Identities=20%  Similarity=0.242  Sum_probs=74.7

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhh--hcCCcEEEEcCCCCHH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIY--SREIPVVIMSPEIILV   69 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~--~~~~pii~lt~~~~~~   69 (93)
                      |||++..+..++.+|+..||+ +..+.++++|++.++...++         +++|++++...  .+++|||++|+..+..
T Consensus         6 VdDd~~~~~~l~~~L~~~g~~-v~~a~~~~eal~~~~~~~~dlillD~~mp~~~G~~~~~~i~~~~~~pvI~lt~~~~~~   84 (117)
T d2a9pa1           6 VDDEKPISDIIKFNMTKEGYE-VVTAFNGREALEQFEAEQPDIIILDLMLPEIDGLEVAKTIRKTSSVPILMLSAKDSEF   84 (117)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCE-EEEESSHHHHHHHHHHHCCSEEEECSSCSSSCHHHHHHHHHTTCCCCEEEEESCCSHH
T ss_pred             EECCHHHHHHHHHHHHHCCCE-EEEECCHHHHHHHHHhcCCCEEEeccccCCCCccHHHHHHHhCCCCCEEEEecCCCHH
Confidence            689999999999999999999 99999999999999755432         34566653322  2889999999999999


Q ss_pred             HHHHHHHcCCcceeeccch
Q 042991           70 RIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        70 ~~~~~~~~ga~d~l~kP~~   88 (93)
                      ...++++.||++|+.||+.
T Consensus        85 ~~~~a~~~Ga~d~l~KP~~  103 (117)
T d2a9pa1          85 DKVIGLELGADDYVTKPFS  103 (117)
T ss_dssp             HHHHHHHHTCSEEEESSCC
T ss_pred             HHHHHHHcCCCEEEECCCC
Confidence            9999999999999999997

>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=99.82  E-value=6.5e-20  Score=100.33  Aligned_cols=88  Identities=17%  Similarity=0.202  Sum_probs=76.0

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHH---hhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~~~~pii~lt~~~~~   68 (93)
                      |||++..+..++.+|+..||+ +..+.++.+|++.++..+++         +++|++++   +...+++|||++|++.+.
T Consensus         7 VDD~~~~~~~l~~~L~~~g~~-v~~a~~g~eal~~~~~~~~dlillD~~mP~~~G~el~~~lr~~~~~~pvi~lt~~~~~   85 (119)
T d1peya_           7 VDDQSGIRILLNEVFNKEGYQ-TFQAANGLQALDIVTKERPDLVLLDMKIPGMDGIEILKRMKVIDENIRVIIMTAYGEL   85 (119)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCE-EEEESSHHHHHHHHHHHCCSEEEEESCCTTCCHHHHHHHHHHHCTTCEEEEEESSCCH
T ss_pred             EeCCHHHHHHHHHHHHHcCCE-EEEeCCHHHHHHHHHhCCCCEEEEeccCCCCCHHHHHHHHHHhCCCCcEEEEecCCCH
Confidence            689999999999999999999 99999999999999755432         44667763   333489999999999999


Q ss_pred             HHHHHHHHcCCcceeeccchh
Q 042991           69 VRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      +...+++++|+++|+.||++.
T Consensus        86 ~~~~~a~~~Ga~~yl~KP~~~  106 (119)
T d1peya_          86 DMIQESKELGALTHFAKPFDI  106 (119)
T ss_dssp             HHHHHHHHTTCCEEEESSCCH
T ss_pred             HHHHHHHHCCCCEEEECCCCH
Confidence            999999999999999999973

>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=99.82  E-value=1.1e-19  Score=99.56  Aligned_cols=88  Identities=20%  Similarity=0.140  Sum_probs=75.5

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhh-----hcCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIY-----SREIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~-----~~~~pii~lt~~~   66 (93)
                      |||++..+..+..+|+..||+ +..+.++++|++.++...++         +++|++++..+     .+++|+|++|+.+
T Consensus         6 VDD~~~~~~~l~~~L~~~g~~-v~~a~~~~~al~~l~~~~~dlil~D~~mp~~~G~~l~~~lr~~~~~~~~pvi~lt~~~   84 (121)
T d1zesa1           6 VEDEAPIREMVCFVLEQNGFQ-PVEAEDYDSAVNQLNEPWPDLILLDWMLPGGSGIQFIKHLKRESMTRDIPVVMLTARG   84 (121)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCE-EEEECSHHHHHHHSSSSCCSEEEECSSCTTSCHHHHHHHHHHSTTTTTSCEEEEESCC
T ss_pred             EeCCHHHHHHHHHHHHHCCCE-EEEECChHHHHHHHHccCCCEEEeecCCCCCCHHHHHHHHHhCccCCCCeEEEEECCC
Confidence            689999999999999999999 99999999999999765432         34566663322     2789999999999


Q ss_pred             CHHHHHHHHHcCCcceeeccchh
Q 042991           67 ILVRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      +.....++++.|+++|+.||+..
T Consensus        85 ~~~~~~~~~~~G~~d~l~KP~~~  107 (121)
T d1zesa1          85 EEEDRVRGLETGADDYITKPFSP  107 (121)
T ss_dssp             SHHHHHHHHHHTCSEEEESSCCH
T ss_pred             CHHHHHHHHHCCCCEEEECCCCH
Confidence            99999999999999999999973

>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=99.82  E-value=1.1e-19  Score=99.71  Aligned_cols=87  Identities=17%  Similarity=0.191  Sum_probs=74.8

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhh--hcCCcEEEEcCCCCHH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIY--SREIPVVIMSPEIILV   69 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~--~~~~pii~lt~~~~~~   69 (93)
                      |||++..+..+..+|++.||+ +..+.++++|++.+....++         +++|++++...  .+++|||++|+..+..
T Consensus         8 VDDd~~~~~~l~~~L~~~g~~-v~~a~~~~~al~~l~~~~~dlii~D~~mp~~~G~~~~~~~r~~~~~pii~lt~~~~~~   86 (121)
T d1xhfa1           8 VEDELVTRNTLKSIFEAEGYD-VFEATDGAEMHQILSEYDINLVIMDINLPGKNGLLLARELREQANVALMFLTGRDNEV   86 (121)
T ss_dssp             ECSCHHHHHHHHHHHHTTTCE-EEEESSHHHHHHHHHHSCCSEEEECSSCSSSCHHHHHHHHHHHCCCEEEEEESCCSHH
T ss_pred             EECCHHHHHHHHHHHHHCCCE-EEEECChHHHHHHHHhcCCCEEEeecccCCccCcHHHHHHHhcCCCcEEEEECCCCHH
Confidence            689999999999999999999 99999999999999755432         34566653322  2899999999999999


Q ss_pred             HHHHHHHcCCcceeeccch
Q 042991           70 RIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        70 ~~~~~~~~ga~d~l~kP~~   88 (93)
                      ...+++++|++|||.||++
T Consensus        87 ~~~~a~~~Ga~dyl~KP~~  105 (121)
T d1xhfa1          87 DKILGLEIGADDYITKPFN  105 (121)
T ss_dssp             HHHHHHHHTCSEEEESSCC
T ss_pred             HHHHHHHcCCCEEEeCCCC
Confidence            9999999999999999996

>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=99.81  E-value=5.2e-20  Score=102.88  Aligned_cols=87  Identities=20%  Similarity=0.234  Sum_probs=75.7

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHH---HhhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDV---RTIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~---l~~~~~~~pii~lt~~~~~   68 (93)
                      |||++..+..++.+|+..||+ +..+.++++|++.++..+++         +++|+++   ++...+++|||++|++.+.
T Consensus         6 VDDd~~~~~~l~~~L~~~g~~-v~~a~~~~eAl~~l~~~~~dlvilD~~mp~~~G~e~~~~lr~~~~~~piI~lT~~~~~   84 (137)
T d1ny5a1           6 IEDDKVFRGLLEEYLSMKGIK-VESAERGKEAYKLLSEKHFNVVLLDLLLPDVNGLEILKWIKERSPETEVIVITGHGTI   84 (137)
T ss_dssp             ECCCHHHHHHHHHHHHHHTCE-EEEESSHHHHHHHHHHSCCSEEEEESBCSSSBHHHHHHHHHHHCTTSEEEEEEETTCH
T ss_pred             EecCHHHHHHHHHHHHHCCCE-EEEECCHHHHHHHhhccccccchHHHhhhhhhHHHHHHHHHHhCCCCCEEEEECCCCH
Confidence            689999999999999999999 99999999999999755432         3456666   3344489999999999999


Q ss_pred             HHHHHHHHcCCcceeeccch
Q 042991           69 VRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~   88 (93)
                      +...+++++||+||+.||+.
T Consensus        85 ~~~~~a~~~Ga~dyl~KP~~  104 (137)
T d1ny5a1          85 KTAVEAMKMGAYDFLTKPCM  104 (137)
T ss_dssp             HHHHHHHTTTCCEEEEESCC
T ss_pred             HHHHHHHHcCCCEEEeCCCC
Confidence            99999999999999999986

>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=99.81  E-value=6.5e-20  Score=100.84  Aligned_cols=88  Identities=20%  Similarity=0.148  Sum_probs=76.7

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHH---hhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~~~~pii~lt~~~~~   68 (93)
                      |||++..+..++.+|+..||+ +..+.++.+|++.++..+++         +++|++++   +...+.+|||++|+..+.
T Consensus         9 VDDd~~~~~~l~~~L~~~g~~-v~~a~~~~~a~~~l~~~~~dlii~D~~mp~~~G~el~~~l~~~~~~~piI~~t~~~~~   87 (123)
T d1krwa_           9 VDDDSSIRWVLERALAGAGLT-CTTFENGNEVLAALASKTPDVLLSDIRMPGMDGLALLKQIKQRHPMLPVIIMTAHSDL   87 (123)
T ss_dssp             ESSSHHHHHHHHHHHHHTTCE-EEEESSSHHHHHHHTTCCCSEEEECCSSSSSTTHHHHHHHHHHSSSCCEEESCCCSCH
T ss_pred             EECCHHHHHHHHHHHHHCCCE-EEEeCCHHHHHHHHHhCCCCEEEehhhcCCchHHHHHHHHHHhCCCCeEEEEecCCCH
Confidence            689999999999999999999 99999999999999765532         34677763   333489999999999999


Q ss_pred             HHHHHHHHcCCcceeeccchh
Q 042991           69 VRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      +...++++.|+++|+.||++.
T Consensus        88 ~~~~~a~~~Ga~dyl~KP~~~  108 (123)
T d1krwa_          88 DAAVSAYQQGAFDYLPKPFDI  108 (123)
T ss_dssp             HHHHHHHHHTEEEECSSCCHH
T ss_pred             HHHHHHHHcCCCeEEeCcCCH
Confidence            999999999999999999973

>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=99.81  E-value=8.3e-20  Score=102.26  Aligned_cols=87  Identities=25%  Similarity=0.218  Sum_probs=74.0

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHh---hh--hcCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRT---IY--SREIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~---~~--~~~~pii~lt~~~   66 (93)
                      |||++..+..++.+|++.||+ |..+.|+.+|++.++...++         +++|++++.   ..  .+++|||++|+..
T Consensus         7 VDD~~~~~~~l~~~L~~~g~~-v~~a~~~~eal~~~~~~~~dlil~D~~~p~~~G~~~~~~ir~~~~~~~~piI~lt~~~   85 (139)
T d1w25a1           7 VDDIEANVRLLEAKLTAEYYE-VSTAMDGPTALAMAARDLPDIILLDVMMPGMDGFTVCRKLKDDPTTRHIPVVLITALD   85 (139)
T ss_dssp             ECSSTTHHHHHHHHHHHTTCE-EEEESSHHHHHHHHHHHCCSEEEEESCCSSSCHHHHHHHHHHSTTTTTSCEEEEECSS
T ss_pred             EECCHHHHHHHHHHHHHCCCE-EEEEccchhhhhhhhcccceeeeeeccccCCCchHHHHHhhhcccccCCCEEEEEcCC
Confidence            689999999999999999999 99999999999999754432         335565532   21  2789999999999


Q ss_pred             CHHHHHHHHHcCCcceeeccch
Q 042991           67 ILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      +.....+++++|++||+.||+.
T Consensus        86 ~~~~~~~a~~~Ga~dyl~KP~~  107 (139)
T d1w25a1          86 GRGDRIQGLESGASDFLTKPID  107 (139)
T ss_dssp             CHHHHHHHHHHTCCEEEESSCC
T ss_pred             CHHHHHHHHHcCCCEEEECCCC
Confidence            9999999999999999999997

>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=99.81  E-value=1.3e-19  Score=99.10  Aligned_cols=88  Identities=16%  Similarity=0.167  Sum_probs=74.7

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhh--hcCCcEEEEcCCCCHH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIY--SREIPVVIMSPEIILV   69 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~--~~~~pii~lt~~~~~~   69 (93)
                      |||++..+..++.+|+..||+ +..+.++++|++.++...++         +++|++++..+  .+..|+|++|+..+..
T Consensus         6 VDDd~~~~~~l~~~L~~~g~~-v~~a~~~~eal~~l~~~~~dliilD~~mP~~~G~e~~~~ir~~~~~piI~lt~~~~~~   84 (119)
T d1zh2a1           6 VEDEQAIRRFLRTALEGDGMR-VFEAETLQRGLLEAATRKPDLIILDLGLPDGDGIEFIRDLRQWSAVPVIVLSARSEES   84 (119)
T ss_dssp             ECSCHHHHHHHHHHHHTTTCE-EEEESSHHHHHHHHHHHCCSEEEEESEETTEEHHHHHHHHHTTCCCCEEEEESCCSHH
T ss_pred             EECCHHHHHHHHHHHHHCCCE-EEEeCCHHHHHHHHHhcCCCEEEeccccCCCCCchHHHHHHhccCCcEEEEeccCCHH
Confidence            699999999999999999999 99999999999999754432         34566653322  2788999999999999


Q ss_pred             HHHHHHHcCCcceeeccchh
Q 042991           70 RIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        70 ~~~~~~~~ga~d~l~kP~~~   89 (93)
                      ...++++.||++|+.||++.
T Consensus        85 ~~~~a~~~Ga~dyl~KP~~~  104 (119)
T d1zh2a1          85 DKIAALDAGADDYLSKPFGI  104 (119)
T ss_dssp             HHHHHHHHTCSEEEESSCCH
T ss_pred             HHHHHHHcCCCEEEECCCCH
Confidence            99999999999999999973

>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=99.80  E-value=2.9e-20  Score=102.03  Aligned_cols=88  Identities=20%  Similarity=0.203  Sum_probs=75.8

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHH---HhhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDV---RTIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~---l~~~~~~~pii~lt~~~~~   68 (93)
                      |||++..+..+..+|++.||+ |..+.++.+|++.++...++         +++|+++   ++...+++|||++|+..+.
T Consensus         7 VDD~~~~~~~l~~~L~~~g~~-v~~a~~~~eal~~~~~~~~dlvl~D~~mP~~~G~el~~~ir~~~~~~piI~lt~~~~~   85 (121)
T d1ys7a2           7 VDDDSDVLASLERGLRLSGFE-VATAVDGAEALRSATENRPDAIVLDINMPVLDGVSVVTALRAMDNDVPVCVLSARSSV   85 (121)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCE-EEEESSHHHHHHHHHHSCCSEEEEESSCSSSCHHHHHHHHHHTTCCCCEEEEECCCTT
T ss_pred             EECCHHHHHHHHHHHHHCCCE-EEEECCHHHHHHHHHhCCCCEEEEEeeccCcccHHHHHHHHhcCCCCEEEEEEeeCCH
Confidence            689999999999999999999 99999999999999755432         3456666   3443489999999999999


Q ss_pred             HHHHHHHHcCCcceeeccchh
Q 042991           69 VRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      +...++++.||++|+.||++.
T Consensus        86 ~~~~~a~~~Ga~dyl~KP~~~  106 (121)
T d1ys7a2          86 DDRVAGLEAGADDYLVKPFVL  106 (121)
T ss_dssp             TCCCTTTTTTCSEEEESSCCH
T ss_pred             HHHHHHHHCCCCEEEECCCCH
Confidence            999999999999999999973

>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=99.80  E-value=3.7e-19  Score=97.32  Aligned_cols=88  Identities=15%  Similarity=0.147  Sum_probs=74.5

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhh--hcCCcEEEEcCCCCHH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIY--SREIPVVIMSPEIILV   69 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~--~~~~pii~lt~~~~~~   69 (93)
                      |||++..+..++.+|++.||+ +..+.++++|++.++...+.         +++|++++...  ...+|||++|+..+..
T Consensus         7 VDDd~~~~~~l~~~L~~~g~~-v~~a~~~~~a~~~~~~~~~dliilD~~mp~~~g~~~~~~~~~~~~~piI~lt~~~~~~   85 (120)
T d1zgza1           7 VEDEPVTQARLQSYFTQEGYT-VSVTASGAGLREIMQNQSVDLILLDINLPDENGLMLTRALRERSTVGIILVTGRSDRI   85 (120)
T ss_dssp             ECSSHHHHHHHHHHHHHTTCE-EEEESSHHHHHHHHHHSCCSEEEEESCCSSSCHHHHHHHHHTTCCCEEEEEESSCCHH
T ss_pred             EeCCHHHHHHHHHHHHHCCCE-EEEECCHHHHHHHHHhcCCCEEeeehhhccchhHHHHHHHhccCCCeEEEEEccCCHH
Confidence            689999999999999999999 99999999999999755432         33455553322  2889999999999999


Q ss_pred             HHHHHHHcCCcceeeccchh
Q 042991           70 RIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        70 ~~~~~~~~ga~d~l~kP~~~   89 (93)
                      ...+++++||++|+.||+..
T Consensus        86 ~~~~a~~~Ga~dyl~KP~~~  105 (120)
T d1zgza1          86 DRIVGLEMGADDYVTKPLEL  105 (120)
T ss_dssp             HHHHHHHHTCSEEEESSCCH
T ss_pred             HHHHHHHCCCCEEEECCCCH
Confidence            99999999999999999973

>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=99.80  E-value=1.4e-19  Score=99.19  Aligned_cols=88  Identities=17%  Similarity=0.142  Sum_probs=75.0

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHH---HhhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDV---RTIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~---l~~~~~~~pii~lt~~~~~   68 (93)
                      |||++..+..++.+|++.||+ |..+.++++|++.++..+++         +++|+++   ++...+.+|||++|+..+.
T Consensus         8 VDDd~~~~~~l~~~L~~~g~~-v~~a~~~~~al~~l~~~~~dlillD~~mp~~~G~~~~~~~r~~~~~~~ii~lt~~~~~   86 (121)
T d1mvoa_           8 VDDEESIVTLLQYNLERSGYD-VITASDGEEALKKAETEKPDLIVLDVMLPKLDGIEVCKQLRQQKLMFPILMLTAKDEE   86 (121)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCE-EEEESSHHHHHHHHHHHCCSEEEEESSCSSSCHHHHHHHHHHTTCCCCEEEEECTTCC
T ss_pred             EECCHHHHHHHHHHHHHCCCE-EEEECCHHHHHHHHhcccccEEEecccccCCCCchhhhhhhccCCCCEEEEEEeeCCH
Confidence            689999999999999999999 99999999999999755432         3456665   3333488999999999998


Q ss_pred             HHHHHHHHcCCcceeeccchh
Q 042991           69 VRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      +...++++.|+++|+.||+..
T Consensus        87 ~~~~~~~~~Ga~~yl~KP~~~  107 (121)
T d1mvoa_          87 FDKVLGLELGADDYMTKPFSP  107 (121)
T ss_dssp             CCHHHHHHTTCCEEEESSCCH
T ss_pred             HHHHHHHHCCCCEEEECCCCH
Confidence            889999999999999999973

>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=99.79  E-value=4.1e-19  Score=96.97  Aligned_cols=87  Identities=15%  Similarity=0.156  Sum_probs=74.3

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceE-EeCCHHHHHHHhccCccc---------CCCchHHH---hhhhcCCcEEEEcCCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLY-CSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYSREIPVVIMSPEII   67 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~-~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~~~~pii~lt~~~~   67 (93)
                      |||++..+..++.+|++.||+ +. .+.++.+|++.++...++         +++|++++   +...+++|||++|++++
T Consensus         7 vDD~~~~~~~l~~~L~~~g~~-v~~~a~~~~~al~~~~~~~~dliilD~~mp~~~G~e~~~~ir~~~~~~pvi~ls~~~~   85 (118)
T d1u0sy_           7 VDDAAFMRMMLKDIITKAGYE-VAGEATNGREAVEKYKELKPDIVTMDITMPEMNGIDAIKEIMKIDPNAKIIVCSAMGQ   85 (118)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCE-EEEEESSHHHHHHHHHHHCCSEEEEECSCGGGCHHHHHHHHHHHCTTCCEEEEECTTC
T ss_pred             EeCCHHHHHHHHHHHHHcCCc-eEEEECCHHHHHHHHHhccCCEEEEecCCCCCCHHHHHHHHHHhCCCCcEEEEEccCC
Confidence            689999999999999999998 65 689999999999754432         34666763   34448999999999999


Q ss_pred             HHHHHHHHHcCCcceeeccch
Q 042991           68 LVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        68 ~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      .....++++.||++|+.||+.
T Consensus        86 ~~~~~~a~~~Ga~~yl~KP~~  106 (118)
T d1u0sy_          86 QAMVIEAIKAGAKDFIVKPFQ  106 (118)
T ss_dssp             HHHHHHHHHTTCCEEEESSCC
T ss_pred             HHHHHHHHHcCCCEEEECCCC
Confidence            999999999999999999996

>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=99.79  E-value=2e-19  Score=98.68  Aligned_cols=88  Identities=13%  Similarity=0.070  Sum_probs=75.4

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHH---HhhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDV---RTIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~---l~~~~~~~pii~lt~~~~~   68 (93)
                      |||++..+..++.+|++.||+ +..+.++++|++.++...++         +++|+++   ++...+.+|||++|+..+.
T Consensus         7 VdDd~~~~~~l~~~L~~~g~~-v~~a~~~~~al~~l~~~~~dlillD~~mp~~~g~~~~~~lr~~~~~~piI~lt~~~~~   85 (122)
T d1kgsa2           7 VEDERDLADLITEALKKEMFT-VDVCYDGEEGMYMALNEPFDVVILDIMLPVHDGWEILKSMRESGVNTPVLMLTALSDV   85 (122)
T ss_dssp             ECSSHHHHHHHHHHHHHTTCE-EEEESSHHHHHHHHHHSCCSEEEEESCCSSSCHHHHHHHHHHTTCCCCEEEEESSCHH
T ss_pred             EeCCHHHHHHHHHHHHHCCCE-EEEEcchHHHHHHHHhhCccccccccccccchhHHHHHHHHhcCCCCcEEEEcCCCCH
Confidence            689999999999999999999 99999999999999755432         3456665   3333388999999999999


Q ss_pred             HHHHHHHHcCCcceeeccchh
Q 042991           69 VRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      ....++++.|+++|+.||+..
T Consensus        86 ~~~~~~~~~Ga~~yl~KP~~~  106 (122)
T d1kgsa2          86 EYRVKGLNMGADDYLPKPFDL  106 (122)
T ss_dssp             HHHHHTCCCCCSEEEESSCCH
T ss_pred             HHHHHHHHcCCceeecCCCCH
Confidence            999999999999999999973

>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=99.78  E-value=5.4e-19  Score=98.28  Aligned_cols=87  Identities=16%  Similarity=0.265  Sum_probs=76.1

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHH---HhhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDV---RTIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~---l~~~~~~~pii~lt~~~~~   68 (93)
                      |||++..+..++.+|+..||+ +..+.++.+|++.+...+++         +++|+++   ++...+.+||+++|++...
T Consensus        14 VDD~~~~~~~l~~~L~~~g~~-v~~a~~g~ea~~~~~~~~~dlillD~~mP~~dG~el~~~ir~~~~~~pii~lt~~~~~   92 (133)
T d2ayxa1          14 VDDHPINRRLLADQLGSLGYQ-CKTANDGVDALNVLSKNHIDIVLSDVNMPNMDGYRLTQRIRQLGLTLPVIGVTANALA   92 (133)
T ss_dssp             EESSHHHHHHHHHHHHHHTSE-EEEECCSHHHHHHHHHSCCSEEEEEESSCSSCCHHHHHHHHHHHCCSCEEEEESSTTS
T ss_pred             EECCHHHHHHHHHHHHHcCCE-EEEECcHHHHHHHHhccCceEEEEeccCCCCCHHHHHHHHHHhCCCCCEEEEeccCCH
Confidence            689999999999999999999 99999999999998755432         4567776   4444588999999999999


Q ss_pred             HHHHHHHHcCCcceeeccch
Q 042991           69 VRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~   88 (93)
                      +...++++.|+++||.||+.
T Consensus        93 ~~~~~~~~~G~~~~l~KP~~  112 (133)
T d2ayxa1          93 EEKQRCLESGMDSCLSKPVT  112 (133)
T ss_dssp             HHHHHHHHCCCEEEEESSCC
T ss_pred             HHHHHHHHcCCCEEEECCCC
Confidence            99999999999999999996

>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=99.77  E-value=6.9e-19  Score=96.60  Aligned_cols=87  Identities=20%  Similarity=0.234  Sum_probs=68.8

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhhh-----cCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIYS-----REIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~~-----~~~pii~lt~~~   66 (93)
                      |||++..+..++.+|++.||+ +..+.++.+|++.++...++         +++|++++..+.     ..+|+|++|+..
T Consensus         7 VDD~~~~~~~l~~~L~~~g~~-v~~a~~~~~al~~~~~~~~dlil~D~~mp~~dG~el~~~ir~~~~~~~iPii~lt~~~   85 (123)
T d1mb3a_           7 VEDNELNMKLFHDLLEAQGYE-TLQTREGLSALSIARENKPDLILMDIQLPEISGLEVTKWLKEDDDLAHIPVVAVTAFA   85 (123)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCE-EEEESCHHHHHHHHHHHCCSEEEEESBCSSSBHHHHHHHHHHSTTTTTSCEEEEC---
T ss_pred             EECCHHHHHHHHHHHHHCCCE-EEEECCHHHHHHHHHhCCCCEEEEEeccCCCcHHHHHHHHHhCCCcCCCCeEEEEEec
Confidence            689999999999999999999 99999999999999754432         346777633322     788999999999


Q ss_pred             CHHHHHHHHHcCCcceeeccch
Q 042991           67 ILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      ......+++++|+++|+.||++
T Consensus        86 ~~~~~~~~~~~G~~~~l~KP~~  107 (123)
T d1mb3a_          86 MKGDEERIREGGCEAYISKPIS  107 (123)
T ss_dssp             ---CHHHHHHHTCSEEECSSCC
T ss_pred             CHHHHHHHHHcCCCEEEECCCC
Confidence            9988899999999999999996

>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=99.76  E-value=8.7e-19  Score=96.79  Aligned_cols=88  Identities=16%  Similarity=0.169  Sum_probs=75.0

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHH---hhhhcCCcEEEEcCCCCH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYSREIPVVIMSPEIIL   68 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~~~~pii~lt~~~~~   68 (93)
                      |||++..+..+..+|+..||. +..+.++++|++.++...++         +++|++++   ....+..||+++|+..+.
T Consensus         8 VDDd~~~~~~l~~~L~~~g~~-v~~a~~~~~al~~~~~~~~dliilD~~mp~~~G~~~~~~i~~~~~~~~ii~lt~~~~~   86 (128)
T d1yioa2           8 VDDDMSVREGLRNLLRSAGFE-VETFDCASTFLEHRRPEQHGCLVLDMRMPGMSGIELQEQLTAISDGIPIVFITAHGDI   86 (128)
T ss_dssp             ECSCHHHHHHHHHHHHTTTCE-EEEESSHHHHHHHCCTTSCEEEEEESCCSSSCHHHHHHHHHHTTCCCCEEEEESCTTS
T ss_pred             EECCHHHHHHHHHHHHHcCCC-ccccccHHHHHHHHHhcCCCEeehhhhcccchhHHHHHHHHhhCCCCeEEEEEEECCH
Confidence            689999999999999999999 99999999999999755432         34566653   333488999999999998


Q ss_pred             HHHHHHHHcCCcceeeccchh
Q 042991           69 VRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        69 ~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      +...++++.||++||.||+..
T Consensus        87 ~~~~~a~~~Ga~dyl~KP~~~  107 (128)
T d1yioa2          87 PMTVRAMKAGAIEFLPKPFEE  107 (128)
T ss_dssp             CCCHHHHHTTEEEEEESSCCH
T ss_pred             HHHHHHHHCCCCEEEECCCCH
Confidence            888999999999999999973

>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=99.76  E-value=5e-19  Score=103.39  Aligned_cols=89  Identities=16%  Similarity=0.165  Sum_probs=74.8

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhhh--cCCcEEEEcCCCCHH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIYS--REIPVVIMSPEIILV   69 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~~--~~~pii~lt~~~~~~   69 (93)
                      |||++..+..++.+|++.||+.+..+.|+.+|++.++...++         +++|++++....  +.+|||++|++.+.+
T Consensus         9 VDD~~~~r~~l~~~L~~~g~~vv~~a~~g~eal~~~~~~~pDlvllDi~mP~~dG~e~~~~ir~~~~~pIi~lTa~~~~~   88 (190)
T d1s8na_           9 AEDEALIRMDLAEMLREEGYEIVGEAGDGQEAVELAELHKPDLVIMDVKMPRRDGIDAASEIASKRIAPIVVLTAFSQRD   88 (190)
T ss_dssp             ECSSHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHHHHCCSEEEEESSCSSSCHHHHHHHHHHTTCSCEEEEEEGGGHH
T ss_pred             EeCCHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHhcCCCCEEEEeccccCcchHHHHHHHHhcCCCCEEEEeCCCCHH
Confidence            699999999999999999998334899999999998755432         456777643322  779999999999999


Q ss_pred             HHHHHHHcCCcceeeccchh
Q 042991           70 RIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        70 ~~~~~~~~ga~d~l~kP~~~   89 (93)
                      ...+|+++||++|++||+..
T Consensus        89 ~~~~al~~Ga~~yl~KP~~~  108 (190)
T d1s8na_          89 LVERARDAGAMAYLVKPFSI  108 (190)
T ss_dssp             HHHTTGGGSCEEEEEESCCH
T ss_pred             HHHHHHHcCCCEeccCCCCH
Confidence            99999999999999999974

>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=99.76  E-value=7e-18  Score=93.19  Aligned_cols=88  Identities=18%  Similarity=0.293  Sum_probs=72.5

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhcc-----Ccc---------cCCCchHHHh----hhhcCCcEEEE
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGL-----DEE---------QSANGFDVRT----IYSREIPVVIM   62 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~-----~~~---------~~~~~~d~l~----~~~~~~pii~l   62 (93)
                      |||++..+..++.+|++.|++.+..+.||++|++.++.     .++         ++++|++++.    +....+|||++
T Consensus         7 VDD~~~~~~~l~~~L~~~g~~~v~~a~~g~eAl~~l~~~~~~~~~~dlillD~~mP~~dG~el~~~ir~~~~~~~piI~l   86 (128)
T d2r25b1           7 VEDNHVNQEVIKRMLNLEGIENIELACDGQEAFDKVKELTSKGENYNMIFMDVQMPKVDGLLSTKMIRRDLGYTSPIVAL   86 (128)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCCCEEEESSHHHHHHHHHHHHHHTCCCSEEEECSCCSSSCHHHHHHHHHHHSCCCSCEEEE
T ss_pred             EeCCHHHHHHHHHHHHHcCCeEEEEEcChHHHHHHHHhhhhccCCCCEEEEEeCCCCCCHHHHHHHHHHccCCCCeEEEE
Confidence            68999999999999999998647889999999998852     121         1345666632    22367899999


Q ss_pred             cCCCCHHHHHHHHHcCCcceeeccch
Q 042991           63 SPEIILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        63 t~~~~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      |+..+.....+++++|+++|+.||++
T Consensus        87 T~~~~~~~~~~~~~~G~~~~l~KP~~  112 (128)
T d2r25b1          87 TAFADDSNIKECLESGMNGFLSKPIK  112 (128)
T ss_dssp             ESCCSHHHHHHHHHTTCSEEEESSCC
T ss_pred             ECCCCHHHHHHHHHcCCCEEEECCCC
Confidence            99999999999999999999999996

>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=99.76  E-value=4.8e-18  Score=93.91  Aligned_cols=88  Identities=9%  Similarity=0.203  Sum_probs=74.1

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc---------CCCchHHHhhh-----hcCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ---------SANGFDVRTIY-----SREIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l~~~-----~~~~pii~lt~~~   66 (93)
                      |||++..+..++.+|+..||..+..+.++++|++.++...++         +++|++++..+     .+++|||++|+..
T Consensus        12 VDD~~~~~~~l~~~L~~~g~~~v~~a~~~~~al~~l~~~~~dlii~D~~mP~~~G~el~~~lr~~~~~~~~pii~lt~~~   91 (129)
T d1p6qa_          12 VDDQVTSRLLLGDALQQLGFKQITAAGDGEQGMKIMAQNPHHLVISDFNMPKMDGLGLLQAVRANPATKKAAFIILTAQG   91 (129)
T ss_dssp             ECSSHHHHHHHHHHHHTTTCSCEECCSSHHHHHHHHHTSCCSEEEECSSSCSSCHHHHHHHHTTCTTSTTCEEEECCSCC
T ss_pred             EECCHHHHHHHHHHHHHCCCeEEEEECCHHHHHHHHHhCCCCeEEeeeecCCCChHHHHHHHHhCcccCCCeEEEEEecC
Confidence            689999999999999999995377899999999999765432         34566663322     2789999999999


Q ss_pred             CHHHHHHHHHcCCcceeeccch
Q 042991           67 ILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      +.....++++.|+++|+.||++
T Consensus        92 ~~~~~~~a~~~G~~~~l~KP~~  113 (129)
T d1p6qa_          92 DRALVQKAAALGANNVLAKPFT  113 (129)
T ss_dssp             CHHHHHHHHHHTCSCEECCCSS
T ss_pred             CHHHHHHHHHCCCCEEEECCCC
Confidence            9999999999999999999997

>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=99.75  E-value=1.2e-17  Score=92.83  Aligned_cols=88  Identities=11%  Similarity=0.126  Sum_probs=72.4

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCcc--------cCCCchHHHhhh--------hcCCcEEEEcC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEE--------QSANGFDVRTIY--------SREIPVVIMSP   64 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~--------~~~~~~d~l~~~--------~~~~pii~lt~   64 (93)
                      |||++..+..++.+|++.||+ +..+.|+.+|++.++....        ++++|++++...        .+.+|||++|+
T Consensus        13 VDD~~~~~~~l~~~L~~~G~~-v~~a~~g~eal~~l~~~~dlillD~~mP~~dG~el~~~ir~~~~~~~~~~~~ii~lT~   91 (134)
T d1dcfa_          13 MDENGVSRMVTKGLLVHLGCE-VTTVSSNEECLRVVSHEHKVVFMDVCMPGVENYQIALRIHEKFTKQRHQRPLLVALSG   91 (134)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCE-EEEESSHHHHHHHCCTTCSEEEEECCSSTTTTTHHHHHHHHHHC-CCSCCCEEEEEES
T ss_pred             EeCCHHHHHHHHHHHHHCCCE-EEEECCHHHHHHHhhcCCCeEEEEeccCCCchHHHHHHHHHhcccccCCCCeEEEEeC
Confidence            689999999999999999999 9999999999998864321        134566653222        15678999999


Q ss_pred             CCCHHHHHHHHHcCCcceeeccchh
Q 042991           65 EIILVRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        65 ~~~~~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      +...+...+++++|+++|+.||+..
T Consensus        92 ~~~~~~~~~~~~~G~~~~l~KP~~~  116 (134)
T d1dcfa_          92 NTDKSTKEKCMSFGLDGVLLKPVSL  116 (134)
T ss_dssp             CCSHHHHHHHHHTTCCEEEESSCCH
T ss_pred             CCCHHHHHHHHHcCCCEEEECCCCH
Confidence            9999999999999999999999973

>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=99.75  E-value=1.5e-17  Score=93.44  Aligned_cols=88  Identities=20%  Similarity=0.201  Sum_probs=72.2

Q ss_pred             CCCcHHHHHHHHHHHhhcCCC-ceEEeCCHHHHHHHhccCc-------c---------cCCCchHHHhhhh-----cCCc
Q 042991            1 LNDSFVDRKVIERLLTISSSR-DLYCSCSGRRALQFLGLDE-------E---------QSANGFDVRTIYS-----REIP   58 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~-~v~~~~~~~~a~~~~~~~~-------~---------~~~~~~d~l~~~~-----~~~p   58 (93)
                      |||++..+..++.+|++.|+. .+.++.|+.+|+++++...       +         ++++|++++..+.     .++|
T Consensus         9 VdD~~~~~~~l~~~L~~~g~~~~v~~a~~g~~Al~~l~~~~~~~~~~~pdlIllD~~mP~~~G~el~~~ir~~~~~~~iP   88 (144)
T d1i3ca_           9 VEDSKADSRLVQEVLKTSTIDHELIILRDGLAAMAFLQQQGEYENSPRPNLILLDLNLPKKDGREVLAEIKQNPDLKRIP   88 (144)
T ss_dssp             ECCCHHHHHHHHHHHHSCCSCEEEEEECSHHHHHHHHTTCGGGTTCCCCSEEEECSCCSSSCHHHHHHHHHHCTTTTTSC
T ss_pred             EECCHHHHHHHHHHHHHcCCCeEEEEECCHHHHHHHHHhchhhhccCCCCEEEEECccccccchHHHHHHHhCcccCCCe
Confidence            689999999999999987753 3899999999999986431       1         1345666633322     7899


Q ss_pred             EEEEcCCCCHHHHHHHHHcCCcceeeccch
Q 042991           59 VVIMSPEIILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        59 ii~lt~~~~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      ||++|+..+.+...+++++||++|+.||++
T Consensus        89 vi~lT~~~~~~~~~~a~~~Ga~~yl~KP~~  118 (144)
T d1i3ca_          89 VVVLTTSHNEDDVIASYELHVNCYLTKSRN  118 (144)
T ss_dssp             EEEEESCCCHHHHHHHHHTTCSEEEECCSS
T ss_pred             EEEEECCCCHHHHHHHHHCCCCEEEECCCC
Confidence            999999999999999999999999999986

>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=99.75  E-value=1.1e-17  Score=94.50  Aligned_cols=88  Identities=24%  Similarity=0.251  Sum_probs=72.8

Q ss_pred             CCCcHHHHHHHHHHHhhcCCC-ceEEeCCHHHHHHHhccCc----------c---------cCCCchHHHhhhh-----c
Q 042991            1 LNDSFVDRKVIERLLTISSSR-DLYCSCSGRRALQFLGLDE----------E---------QSANGFDVRTIYS-----R   55 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~-~v~~~~~~~~a~~~~~~~~----------~---------~~~~~~d~l~~~~-----~   55 (93)
                      |||++..+..++.+|++.||. .+..+.|+.+|+++++...          +         ++++|++++..+.     +
T Consensus        12 VDD~~~~~~~l~~~L~~~g~~~~v~~a~~g~eAl~~l~~~~~~~~~~~~~~pdlillD~~mP~~~G~el~~~ir~~~~~~   91 (149)
T d1k66a_          12 VEDSDEDFSTFQRLLQREGVVNPIYRCITGDQALDFLYQTGSYCNPDIAPRPAVILLDLNLPGTDGREVLQEIKQDEVLK   91 (149)
T ss_dssp             ECCCHHHHHHHHHHHHHTTBCSCEEEECSHHHHHHHHHTCCSSSCGGGCCCCSEEEECSCCSSSCHHHHHHHHTTSTTGG
T ss_pred             EECCHHHHHHHHHHHHHcCCceEEEEECChHHHHHHHHhhccccccccccCCCeEEccccccCCCcHHHHHHHHhccccC
Confidence            689999999999999999873 3899999999999985321          1         1345666643332     7


Q ss_pred             CCcEEEEcCCCCHHHHHHHHHcCCcceeeccch
Q 042991           56 EIPVVIMSPEIILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        56 ~~pii~lt~~~~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      .+|||++|+..+.+...+++++|+++|+.||++
T Consensus        92 ~ipiI~lT~~~~~~~~~~~~~~Ga~~~l~KP~~  124 (149)
T d1k66a_          92 KIPVVIMTTSSNPKDIEICYSYSISSYIVKPLE  124 (149)
T ss_dssp             GSCEEEEESCCCHHHHHHHHHTTCSEEEECCSS
T ss_pred             CCeEEEEeCCCCHHHHHHHHHCCCCEEEECCCC
Confidence            899999999999999999999999999999986

>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=99.74  E-value=1.8e-17  Score=92.72  Aligned_cols=87  Identities=21%  Similarity=0.208  Sum_probs=71.9

Q ss_pred             CCCcHHHHHHHHHHHhhcC--CCceEEeCCHHHHHHHhccCc-------c---------cCCCchHHHhhhh-----cCC
Q 042991            1 LNDSFVDRKVIERLLTISS--SRDLYCSCSGRRALQFLGLDE-------E---------QSANGFDVRTIYS-----REI   57 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~--~~~v~~~~~~~~a~~~~~~~~-------~---------~~~~~~d~l~~~~-----~~~   57 (93)
                      |||++..+..++.+|++.|  |+ +..+.+|.+|++.++...       +         ++++|++++..+.     +++
T Consensus         8 VDD~~~~~~~l~~~L~~~g~~~~-v~~a~~g~eAl~~l~~~~~~~~~~~pdlillD~~mP~~dG~el~~~ir~~~~~~~i   86 (140)
T d1k68a_           8 VEDNKADIRLIQEALANSTVPHE-VVTVRDGMEAMAYLRQEGEYANASRPDLILLDLNLPKKDGREVLAEIKSDPTLKRI   86 (140)
T ss_dssp             ECCCHHHHHHHHHHHHTCSSCCE-EEEECSHHHHHHHHTTCGGGGSCCCCSEEEECSSCSSSCHHHHHHHHHHSTTGGGS
T ss_pred             EECCHHHHHHHHHHHHHcCCCeE-EEEECCHHHHHHHHHHhHHhhccCCCCEEEEeeccccccChHHHHHHHhCcccCCC
Confidence            6899999999999999876  56 999999999999985321       1         1345677643221     689


Q ss_pred             cEEEEcCCCCHHHHHHHHHcCCcceeeccch
Q 042991           58 PVVIMSPEIILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        58 pii~lt~~~~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      |||++|+..+.+...+++++|+++|+.||+.
T Consensus        87 PvI~ls~~~~~~~~~~a~~~Ga~~yl~KP~~  117 (140)
T d1k68a_          87 PVVVLSTSINEDDIFHSYDLHVNCYITKSAN  117 (140)
T ss_dssp             CEEEEESCCCHHHHHHHHHTTCSEEEECCSS
T ss_pred             cEEEEeCCCCHHHHHHHHHCCCCEEEECCCC
Confidence            9999999999999999999999999999986

>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=99.70  E-value=5.8e-17  Score=88.53  Aligned_cols=87  Identities=16%  Similarity=0.053  Sum_probs=70.0

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCcc-------cCCCchHHH---hhhhcCCcEEEEcCCCCHHH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEE-------QSANGFDVR---TIYSREIPVVIMSPEIILVR   70 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~-------~~~~~~d~l---~~~~~~~pii~lt~~~~~~~   70 (93)
                      |||++..+..++.+|++.| . +..+.++.+|+...+..+-       ++++|++++   +...+.+|||++|+.++.+.
T Consensus         8 VDDd~~~~~~l~~~L~~~g-~-v~~~~~~~~al~~~~~~dlillD~~mP~~~G~~~~~~lr~~~~~~~ii~it~~~~~~~   85 (120)
T d1p2fa2           8 VDDDKNILKKVSEKLQQLG-R-VKTFLTGEDFLNDEEAFHVVVLDVMLPDYSGYEICRMIKETRPETWVILLTLLSDDES   85 (120)
T ss_dssp             ECSCHHHHHHHHHHHTTTE-E-EEEESSHHHHHHCCSCCSEEEEESBCSSSBHHHHHHHHHHHCTTSEEEEEESCCSHHH
T ss_pred             EECCHHHHHHHHHHHHhCC-E-EEEECCHHHHHhcCCCCCEEEEeCcccccchhHHHHHHhhcCCCCcEEEEecCCCHHH
Confidence            6899999999999999877 5 7789999999874322111       244666663   33348999999999999999


Q ss_pred             HHHHHHcCCcceeeccchh
Q 042991           71 IDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        71 ~~~~~~~ga~d~l~kP~~~   89 (93)
                      ..++++.||++|+.||++.
T Consensus        86 ~~~a~~~Ga~dyl~KP~~~  104 (120)
T d1p2fa2          86 VLKGFEAGADDYVTKPFNP  104 (120)
T ss_dssp             HHHHHHHTCSEEEESSCCH
T ss_pred             HHHHHHCCCCEEEECCCCH
Confidence            9999999999999999973

>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=99.69  E-value=9e-17  Score=89.57  Aligned_cols=88  Identities=15%  Similarity=0.148  Sum_probs=72.7

Q ss_pred             CCCcHHHHHHHHHHHhhcCC-CceEEeCCHHHHHHHhccCccc---------CCCchHHH---hhhhcCCcEEEEcCCCC
Q 042991            1 LNDSFVDRKVIERLLTISSS-RDLYCSCSGRRALQFLGLDEEQ---------SANGFDVR---TIYSREIPVVIMSPEII   67 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~-~~v~~~~~~~~a~~~~~~~~~~---------~~~~~d~l---~~~~~~~pii~lt~~~~   67 (93)
                      |||++..+..++.+|+..+. ..+..+.++.+|++.++..+++         +++|++++   +...+..|++++|+..+
T Consensus         8 VDD~~~~r~~l~~~L~~~~~~~~v~~a~~~~~al~~~~~~~~DlvllD~~mP~~~G~el~~~ir~~~~~~~vivlt~~~~   87 (138)
T d1a04a2           8 IDDHPMLRTGVKQLISMAPDITVVGEASNGEQGIELAESLDPDLILLDLNMPGMNGLETLDKLREKSLSGRIVVFSVSNH   87 (138)
T ss_dssp             ECSCHHHHHHHHHHHTTCTTEEEEEEESSHHHHHHHHHHHCCSEEEEETTSTTSCHHHHHHHHHHSCCCSEEEEEECCCC
T ss_pred             ECCCHHHHHHHHHHHHhCCCcEEEEEECCHHHHHHHHHhcCCCEEEEecCCCCCCHHHHHHHHHhhCCCCCEEEEEEECC
Confidence            68999999999999987662 2377899999999998754432         34677763   33348999999999999


Q ss_pred             HHHHHHHHHcCCcceeeccch
Q 042991           68 LVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        68 ~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      .+...+++++||++|+.||++
T Consensus        88 ~~~~~~a~~~Ga~~yl~Kp~~  108 (138)
T d1a04a2          88 EEDVVTALKRGADGYLLKDME  108 (138)
T ss_dssp             HHHHHHHHHTTCSEEEETTCC
T ss_pred             HHHHHHHHHcCCCEEEECCCC
Confidence            999999999999999999996

>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=99.68  E-value=1.2e-16  Score=87.60  Aligned_cols=88  Identities=13%  Similarity=0.061  Sum_probs=70.4

Q ss_pred             CCCcHHHHHHHHHHHhhcC-CCceEEeCCHHHHHHHhccCcc---------cCCCchHHHhhhh----cCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTISS-SRDLYCSCSGRRALQFLGLDEE---------QSANGFDVRTIYS----REIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~-~~~v~~~~~~~~a~~~~~~~~~---------~~~~~~d~l~~~~----~~~pii~lt~~~   66 (93)
                      |||++..+..++.+|+..+ +..+..+.||++|++.++...+         ++++|++++..+.    ..+||+++|+..
T Consensus         7 vDD~~~~~~~l~~~L~~~~~~~~v~~a~~g~~al~~~~~~~~dlillD~~mP~~dG~e~~~~ir~~~~~~~~ii~~t~~~   86 (123)
T d1dz3a_           7 ADDNRELVSLLDEYISSQPDMEVIGTAYNGQDCLQMLEEKRPDILLLDIIMPHLDGLAVLERIRAGFEHQPNVIMLTAFG   86 (123)
T ss_dssp             ECSCHHHHHHHHHHHHTSTTEEEEEEESSHHHHHHHHHHHCCSEEEEESCCSSSCHHHHHHHHHHHCSSCCEEEEEEETT
T ss_pred             EeCCHHHHHHHHHHHHhCCCcEEEEEECCHHHHHHHHHhcCCCEEEEcCCCCCCCHHHHHHHHHhcCCCCCeEEEEECcC
Confidence            6899999999999998766 3436689999999999975443         2456777633322    345799999999


Q ss_pred             CHHHHHHHHHcCCcceeeccch
Q 042991           67 ILVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~   88 (93)
                      +.....++++.||++|+.||++
T Consensus        87 ~~~~~~~a~~~Ga~~~l~KP~~  108 (123)
T d1dz3a_          87 QEDVTKKAVELGASYFILKPFD  108 (123)
T ss_dssp             CHHHHHHHHHTTCEEEEECSSC
T ss_pred             CHHHHHHHHHCCCCEEEECCCC
Confidence            9999999999999999999987

>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=99.66  E-value=1.7e-16  Score=89.89  Aligned_cols=86  Identities=15%  Similarity=0.140  Sum_probs=67.3

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCcc---------cCCCchHHHhhh-----hcCCcEEEEcCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEE---------QSANGFDVRTIY-----SREIPVVIMSPEI   66 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~---------~~~~~~d~l~~~-----~~~~pii~lt~~~   66 (93)
                      |||++..+..+...|+..||. +..  ++.++...+...++         ++++|++++..+     .+++|||++|+..
T Consensus        19 VDD~~~~~~~l~~~L~~~g~~-v~~--~~~~~~~~~~~~~~DlillD~~mP~~dG~el~~~ir~~~~~~~iPiI~lt~~~   95 (153)
T d1w25a2          19 VDDNERQAQRVAAELGVEHRP-VIE--SDPEKAKISAGGPVDLVIVNAAAKNFDGLRFTAALRSEERTRQLPVLAMVDPD   95 (153)
T ss_dssp             ECSCHHHHHHHHHHHTTTSEE-EEE--CCHHHHHHHHHSSCSEEEEETTCSSSCHHHHHHHHHTSGGGTTCCEEEEECTT
T ss_pred             EeCCHHHHHHHHHHHHHCCCE-EEE--ccHHHHHHHhcCCCCEEEEECccccccchHHHHHHHhccccccceeEEeecCC
Confidence            589999999999999988887 644  45566666543332         245677763322     2789999999999


Q ss_pred             CHHHHHHHHHcCCcceeeccchh
Q 042991           67 ILVRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        67 ~~~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      +.....++++.||+|||.||+..
T Consensus        96 ~~~~~~~a~~~Ga~d~l~KP~~~  118 (153)
T d1w25a2          96 DRGRMVKALEIGVNDILSRPIDP  118 (153)
T ss_dssp             CHHHHHHHHHTTCCEEEESSCCH
T ss_pred             CHHHHHHHHhcCcceEEECCCCH
Confidence            99999999999999999999973

>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=99.60  E-value=1.6e-15  Score=84.56  Aligned_cols=88  Identities=18%  Similarity=0.055  Sum_probs=65.6

Q ss_pred             CCCcHHHHHHHHHHHhhcCCC-ceEEeCCHHHHHHHhccCcc---------cCCCchHHHh---hhhcCCcEEEEcCCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSR-DLYCSCSGRRALQFLGLDEE---------QSANGFDVRT---IYSREIPVVIMSPEII   67 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~-~v~~~~~~~~a~~~~~~~~~---------~~~~~~d~l~---~~~~~~pii~lt~~~~   67 (93)
                      |||++..+..++.+|+..|+. .+..+.|+.+|++.++...+         ++++|++++.   ...+..++++++.+..
T Consensus         9 VDD~~~~r~~l~~~L~~~g~~~~v~~a~~g~~al~~~~~~~pDlvllDi~MP~~dG~e~~~~ir~~~~~~~i~i~~~~~~   88 (140)
T d1a2oa1           9 VDDSALMRQIMTEIINSHSDMEMVATAPDPLVARDLIKKFNPDVLTLDVEMPRMDGLDFLEKLMRLRPMPVVMVSSLTGK   88 (140)
T ss_dssp             ECSCHHHHHHHHHHHHTSTTEEEEEEESSHHHHHHHHHHHCCSEEEEECCCSSSCHHHHHHHHHHSSCCCEEEEECCTHH
T ss_pred             EeCCHHHHHHHHHHHHhCCCeEEEEEECCHHHHHHHHHhcCCCEEEEcCCCCCCCHHHHHHHHHHhCCCCcEEEEEecCC
Confidence            699999999999999988843 27789999999999865443         2456777643   3335555666665433


Q ss_pred             -HHHHHHHHHcCCcceeeccch
Q 042991           68 -LVRIDRYLEDGAEDSETCQMW   88 (93)
Q Consensus        68 -~~~~~~~~~~ga~d~l~kP~~   88 (93)
                       .+...++++.||++|+.||+.
T Consensus        89 ~~~~~~~al~~Ga~~yl~KP~~  110 (140)
T d1a2oa1          89 GSEVTLRALELGAIDFVTKPQL  110 (140)
T ss_dssp             HHHHHHHHHHHTCCEEEECSSS
T ss_pred             ChHHHHHHHHcCCCEEEECCCC
Confidence             345678999999999999974

>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=99.60  E-value=4.3e-16  Score=84.80  Aligned_cols=85  Identities=12%  Similarity=0.008  Sum_probs=64.8

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc----------CCCchHHH---hhhhcCCcEEEEcCCCC
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ----------SANGFDVR---TIYSREIPVVIMSPEII   67 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~----------~~~~~d~l---~~~~~~~pii~lt~~~~   67 (93)
                      |||++..+..++.+|+..||+ +..+.++.+|++.+.+...+          +++|++++   +...+++|||++|+..+
T Consensus         8 VdDd~~~~~~l~~~L~~~g~~-v~~~~~~~~al~~l~~~~~~dliilD~~lp~~~G~el~~~ir~~~~~~pii~lt~~~~   86 (118)
T d2b4aa1           8 VEDEPSHATLIQYHLNQLGAE-VTVHPSGSAFFQHRSQLSTCDLLIVSDQLVDLSIFSLLDIVKEQTKQPSVLILTTGRH   86 (118)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCE-EEEESSHHHHHHTGGGGGSCSEEEEETTCTTSCHHHHHHHHTTSSSCCEEEEEESCC-
T ss_pred             EECCHHHHHHHHHHHHhcCCC-eEEECCHHHHHHHHHhcCCCCEEEEeCCCCCCCHHHHHHHHHhcCCCCcEEEEECCcc
Confidence            689999999999999999999 99999999999877433222          34666663   33338899999998765


Q ss_pred             HHHHHHHHHcCCcceeeccchh
Q 042991           68 LVRIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        68 ~~~~~~~~~~ga~d~l~kP~~~   89 (93)
                      ..  .++...|+ ||+.||++.
T Consensus        87 ~~--~~~~~~~~-dyl~KP~~~  105 (118)
T d2b4aa1          87 EL--IESSEHNL-SYLQKPFAI  105 (118)
T ss_dssp             -C--CCCSSSCE-EEEESSCCH
T ss_pred             HH--HHHhhcCC-CEEECCCCH
Confidence            33  34566676 899999973

>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=99.57  E-value=3.9e-16  Score=90.60  Aligned_cols=84  Identities=11%  Similarity=-0.069  Sum_probs=68.0

Q ss_pred             CCCcHHHHHHHHHHHhhcCCCceEEeCCHHHHHHHhccCccc------CCCchHH-----HhhhhcCCcEEEEcCCCCHH
Q 042991            1 LNDSFVDRKVIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ------SANGFDV-----RTIYSREIPVVIMSPEIILV   69 (93)
Q Consensus         1 vdd~~~~~~~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~------~~~~~d~-----l~~~~~~~pii~lt~~~~~~   69 (93)
                      |||++..+..+...|++.||+ +..+.++.+|+..    .++      .+++.+.     +....+.+|||++|++.+.+
T Consensus        17 vdd~~~~~~~l~~~L~~~G~~-v~~~~~~~~al~~----~~Dlvl~D~~mp~~~~~~~~~~~~~~p~~pvI~lta~~~~~   91 (189)
T d1qo0d_          17 LNPPGEVSDALVLQLIRIGCS-VRQCWPPPEAFDV----PVDVVFTSIFQNRHHDEIAALLAAGTPRTTLVALVEYESPA   91 (189)
T ss_dssp             ESCTTHHHHHHHHHHHHHTCE-EEEECSCCSSCSS----CCSEEEEECCSSTHHHHHHHHHHHSCTTCEEEEEECCCSHH
T ss_pred             EeCCHHHHHHHHHHHHHcCCc-ceecCCHHHhccC----CCCEEEEcCCCCCcHHHHHHHHHHcCCCCCEEEEeccchHH
Confidence            589999999999999999999 9999999988732    211      2333332     11222899999999999999


Q ss_pred             HHHHHHHcCCcceeeccchh
Q 042991           70 RIDRYLEDGAEDSETCQMWA   89 (93)
Q Consensus        70 ~~~~~~~~ga~d~l~kP~~~   89 (93)
                      ...++++.|+++||.||+..
T Consensus        92 ~~~~al~~Ga~~yL~KP~~~  111 (189)
T d1qo0d_          92 VLSQIIELECHGVITQPLDA  111 (189)
T ss_dssp             HHHHHHHHTCSEEEESSCCG
T ss_pred             HHHHHHHcCCcEEEEecchh
Confidence            99999999999999999973

>d1yxya1 c.1.2.5 (A:4-233) Putative N-acetylmannosamine-6-phosphate 2-epimerase NanE {Streptococcus pyogenes [TaxId: 1314]}

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: Ribulose-phoshate binding barrel
family: NanE-like
domain: Putative N-acetylmannosamine-6-phosphate 2-epimerase NanE
species: Streptococcus pyogenes [TaxId: 1314]

Probab=85.18  E-value=0.63  Score=25.97  Aligned_cols=30  Identities=10%  Similarity=-0.037  Sum_probs=26.7

Q ss_pred             cCCcEEEEcCCCCHHHHHHHHHcCCcceee
Q 042991           55 REIPVVIMSPEIILVRIDRYLEDGAEDSET   84 (93)
Q Consensus        55 ~~~pii~lt~~~~~~~~~~~~~~ga~d~l~   84 (93)
                      .++|+|+-.+-.+.+++.+++++||+.++.
T Consensus       182 ~~ipvia~GGI~t~~d~~~al~~GAd~V~v  211 (230)
T d1yxya1         182 AGIAVIAEGKIHSPEEAKKINDLGVAGIVV  211 (230)
T ss_dssp             TTCCEEEESCCCSHHHHHHHHTTCCSEEEE
T ss_pred             CCCeEEEeCCCCCHHHHHHHHHcCCCEEEE
Confidence            789999988888899999999999999764

>d1a53a_ c.1.2.4 (A:) Indole-3-glycerophosphate synthase, IPGS {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: Ribulose-phoshate binding barrel
family: Tryptophan biosynthesis enzymes
domain: Indole-3-glycerophosphate synthase, IPGS
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=80.33  E-value=3.7  Score=23.73  Aligned_cols=76  Identities=8%  Similarity=-0.090  Sum_probs=48.7

Q ss_pred             HHHHHHhhcCCCceEEeCCHHHHHHHhccCccc------CCCchH--H-----H-hhhhcCCcEEEEcCCCCHHHHHHHH
Q 042991           10 VIERLLTISSSRDLYCSCSGRRALQFLGLDEEQ------SANGFD--V-----R-TIYSREIPVVIMSPEIILVRIDRYL   75 (93)
Q Consensus        10 ~l~~~l~~~~~~~v~~~~~~~~a~~~~~~~~~~------~~~~~d--~-----l-~~~~~~~pii~lt~~~~~~~~~~~~   75 (93)
                      .+..+-++.|.+.+..+.+.+++...+......      ++..+.  .     + .....+..+|.-++-.+.+++.+..
T Consensus       143 ~l~~~a~~lgl~~LvEvh~~~El~~a~~~~a~iIGINnRnL~t~~vd~~~~~~L~~~ip~~~~~IaESGI~t~~dv~~l~  222 (247)
T d1a53a_         143 SLLEYARSYGMEPLIEINDENDLDIALRIGARFIGINSRDLETLEINKENQRKLISMIPSNVVKVAESGISERNEIEELR  222 (247)
T ss_dssp             HHHHHHHTTTCCCEEEECSHHHHHHHHHTTCSEEEEESBCTTTCCBCHHHHHHHHHHSCTTSEEEEESCCCCHHHHHHHH
T ss_pred             HHHHHHHHHhhhHHhhcCCHHHHHHHHhCCCCeEeeeccChhhhhhhhhHHHHHHhhCCCCCeEEEecCCCCHHHHHHHH
Confidence            344444567766688899999987776432210      111111  1     1 1122577788888888899998888


Q ss_pred             HcCCcceeec
Q 042991           76 EDGAEDSETC   85 (93)
Q Consensus        76 ~~ga~d~l~k   85 (93)
                      ++|++.++.-
T Consensus       223 ~~G~davLIG  232 (247)
T d1a53a_         223 KLGVNAFLIG  232 (247)
T ss_dssp             HTTCCEEEEC
T ss_pred             HCCCCEEEEC
Confidence            9999999864

>d1y0ea_ c.1.2.5 (A:) Putative N-acetylmannosamine-6-phosphate 2-epimerase NanE {Staphylococcus aureus [TaxId: 1280]}

class: Alpha and beta proteins (a/b)
fold: TIM beta/alpha-barrel
superfamily: Ribulose-phoshate binding barrel
family: NanE-like
domain: Putative N-acetylmannosamine-6-phosphate 2-epimerase NanE
species: Staphylococcus aureus [TaxId: 1280]

Probab=80.22  E-value=1.4  Score=24.27  Aligned_cols=30  Identities=17%  Similarity=0.071  Sum_probs=26.2

Q ss_pred             cCCcEEEEcCCCCHHHHHHHHHcCCcceee
Q 042991           55 REIPVVIMSPEIILVRIDRYLEDGAEDSET   84 (93)
Q Consensus        55 ~~~pii~lt~~~~~~~~~~~~~~ga~d~l~   84 (93)
                      ..+|++.-.+=.+.+++.+++++||+.++.
T Consensus       174 ~~iPVia~GGI~t~~d~~~~~~~GAdgV~i  203 (222)
T d1y0ea_         174 VDAKVIAEGNVITPDMYKRVMDLGVHCSVV  203 (222)
T ss_dssp             CCSEEEEESSCCSHHHHHHHHHTTCSEEEE
T ss_pred             CCCcEEEeCCCCCHHHHHHHHHcCCCEEEE
Confidence            789999877777899999999999999765