Psyllid ID: psy11008

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90------
Protein Sequence
MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVENSNQLVTLIPDQIAS
Secondary Structure (PSIPRED)
cHHHHHHHcccHHHHHHHHHHHHHcccccEEEcccccEEEEcHHHHHHHHHHHHHHcccccHHHHHHHHccccccHHHHHHHccccEEEccccccc
Secondary Structure Prediction (SSPRO)
cHHHHHHccccHHHHHHHHHHHHHcccEEEEEcccccEEEEcHHHHHHHHHHHHHcccccHHHHHHHHHHcccccHHHHHHHHccHEccccccccc
Coil and Loop (DISEMBL)
MEDLAALFRMKTQSVIDRIVELQKtgaltgviddrgKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVENSNQLVTLIPDQIAS
Flexible Loop (DISEMBL)
MEDLAALFRMKTQSVIDRIVElqktgaltgvidDRGKFIYISQEELNSVATFIKQRGREELNSVATfikqkgrvsvselvensnqlvtlipdqias
Low Complexity Region (SEG)
MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVENSNQLVTLIPDQIAS
Disordered region (IsUnstruct)
*****ALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELV*****LVTL*******
Disordered Region (DISOPRED)
*EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVENSNQLV**I******
Disordered Region (DISEMBL)
MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVENSNQLVTLIPDQIAS
Disordered Region (DISPRO)
MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVENSNQLVTLIP*****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVENSNQLVTLIPDQIAS
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	96	2.2.26 [Sep-21-2011]
B0WIW5	287	DDRGK domain-containing p	N/A	N/A	0.791	0.264	0.615	2e-25
C3Y431	298	DDRGK domain-containing p	yes	N/A	0.802	0.258	0.597	1e-23
C0KYB6	289	DDRGK domain-containing p	N/A	N/A	0.791	0.262	0.593	2e-23
B4PQC4	312	DDRGK domain-containing p	N/A	N/A	0.791	0.243	0.582	5e-23
B3P045	312	DDRGK domain-containing p	N/A	N/A	0.791	0.243	0.582	6e-23
B4NKL1	307	DDRGK domain-containing p	N/A	N/A	0.843	0.263	0.572	7e-23
B4LYB9	307	DDRGK domain-containing p	N/A	N/A	0.791	0.247	0.560	6e-22
B3MTS7	304	DDRGK domain-containing p	N/A	N/A	0.791	0.25	0.549	3e-21
Q9VDD1	309	DDRGK domain-containing p	yes	N/A	0.791	0.245	0.560	4e-21
Q295B1	309	DDRGK domain-containing p	yes	N/A	0.791	0.245	0.549	1e-20

>sp|B0WIW5|DDRGK_CULQU DDRGK domain-containing protein 1 OS=Culex quinquefasciatus GN=CPIJ007479 PE=3 SV=1

 Score =  114 bits (285), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 56/91 (61%), Positives = 67/91 (73%), Gaps = 15/91 (16%)

Query: 1   MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREE 60
           +EDLA  F++KTQ+ IDRIVELQK G L+GVIDDRGKFIYIS+EELN+VA FIKQR    
Sbjct: 208 LEDLAVQFKLKTQAAIDRIVELQKDGRLSGVIDDRGKFIYISEEELNAVAKFIKQR---- 263

Query: 61  LNSVATFIKQKGRVSVSELVENSNQLVTLIP 91
                      GRVS++EL ENSN L+ L+P
Sbjct: 264 -----------GRVSITELAENSNNLINLVP 283

Culex quinquefasciatus (taxid: 7176)

>sp|C3Y431|DDRGK_BRAFL DDRGK domain-containing protein 1 OS=Branchiostoma floridae GN=BRAFLDRAFT_114851 PE=3 SV=1

 Score =  108 bits (269), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 55/92 (59%), Positives = 66/92 (71%), Gaps = 15/92 (16%)

Query: 1   MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREE 60
           +EDLAA F M+TQ  I R+ EL++ G LTGVIDDRGKFIYISQEEL +VA FIKQR    
Sbjct: 212 LEDLAAQFNMRTQDCIQRVQELREQGRLTGVIDDRGKFIYISQEELQAVAKFIKQR---- 267

Query: 61  LNSVATFIKQKGRVSVSELVENSNQLVTLIPD 92
                      GRVS+++LVE+SNQL+ LIPD
Sbjct: 268 -----------GRVSITDLVESSNQLIHLIPD 288

Branchiostoma floridae (taxid: 7739)

>sp|C0KYB6|DDRGK_BOMMO DDRGK domain-containing protein 1 OS=Bombyx mori PE=2 SV=1

 Score =  107 bits (268), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 54/91 (59%), Positives = 63/91 (69%), Gaps = 15/91 (16%)

Query: 1   MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREE 60
           +EDLAA F++KTQ+ IDRI ELQ +G LTGVIDDRGKFIYISQ EL S+A FIKQR    
Sbjct: 210 LEDLAAHFKLKTQAAIDRITELQASGELTGVIDDRGKFIYISQSELESIAKFIKQR---- 265

Query: 61  LNSVATFIKQKGRVSVSELVENSNQLVTLIP 91
                      GRVS++EL E SN L+ L P
Sbjct: 266 -----------GRVSIAELAECSNDLINLAP 285

Bombyx mori (taxid: 7091)

>sp|B4PQC4|DDRGK_DROYA DDRGK domain-containing protein 1 OS=Drosophila yakuba GN=GE25716 PE=3 SV=1

 Score =  105 bits (263), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 53/91 (58%), Positives = 64/91 (70%), Gaps = 15/91 (16%)

Query: 1   MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREE 60
           +EDLA  F++KTQ VIDRI ELQ  G LTGVIDDRGKFIY+S+EEL++VA FIKQR    
Sbjct: 227 LEDLAVAFKLKTQQVIDRIQELQADGTLTGVIDDRGKFIYVSEEELSAVAKFIKQR---- 282

Query: 61  LNSVATFIKQKGRVSVSELVENSNQLVTLIP 91
                      GRVS++EL E+SN L+ L P
Sbjct: 283 -----------GRVSIAELAESSNNLINLTP 302

Drosophila yakuba (taxid: 7245)

>sp|B3P045|DDRGK_DROER DDRGK domain-containing protein 1 OS=Drosophila erecta GN=GG24454 PE=3 SV=1

 Score =  105 bits (263), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 53/91 (58%), Positives = 64/91 (70%), Gaps = 15/91 (16%)

Query: 1   MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREE 60
           +EDLA  F++KTQ VIDRI ELQ  G LTGVIDDRGKFIY+S+EEL++VA FIKQR    
Sbjct: 227 LEDLAVAFKLKTQQVIDRIQELQADGTLTGVIDDRGKFIYVSEEELSAVAKFIKQR---- 282

Query: 61  LNSVATFIKQKGRVSVSELVENSNQLVTLIP 91
                      GRVS++EL E+SN L+ L P
Sbjct: 283 -----------GRVSITELAESSNNLINLTP 302

Drosophila erecta (taxid: 7220)

>sp|B4NKL1|DDRGK_DROWI DDRGK domain-containing protein 1 OS=Drosophila willistoni GN=GK14514 PE=3 SV=1

 Score =  105 bits (262), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 55/96 (57%), Positives = 66/96 (68%), Gaps = 15/96 (15%)

Query: 1   MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREE 60
           +EDLA  F++KTQ  I+RI ELQ  G+LTGVIDDRGKFIYISQEEL +VA FIKQR    
Sbjct: 223 LEDLAVAFKLKTQQAIERIQELQANGSLTGVIDDRGKFIYISQEELAAVAKFIKQR---- 278

Query: 61  LNSVATFIKQKGRVSVSELVENSNQLVTLIPDQIAS 96
                      GRVS++EL E+SN L+ L P Q A+
Sbjct: 279 -----------GRVSIAELAESSNNLINLTPVQSAA 303

Drosophila willistoni (taxid: 7260)

>sp|B4LYB9|DDRGK_DROVI DDRGK domain-containing protein 1 OS=Drosophila virilis GN=GJ23857 PE=3 SV=1

 Score =  102 bits (255), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 51/91 (56%), Positives = 62/91 (68%), Gaps = 15/91 (16%)

Query: 1   MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREE 60
           +EDLA  F++KTQ  IDRI ELQ+ G LTGVIDDRGKFIY+S+ EL +VA FIKQR    
Sbjct: 224 LEDLATAFKLKTQQAIDRIQELQENGTLTGVIDDRGKFIYVSEAELAAVAKFIKQR---- 279

Query: 61  LNSVATFIKQKGRVSVSELVENSNQLVTLIP 91
                      GRVS++EL E+SN L+ L P
Sbjct: 280 -----------GRVSIAELAESSNNLINLTP 299

Drosophila virilis (taxid: 7244)

>sp|B3MTS7|DDRGK_DROAN DDRGK domain-containing protein 1 OS=Drosophila ananassae GN=GF23066 PE=3 SV=1

 Score =  100 bits (248), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 50/91 (54%), Positives = 62/91 (68%), Gaps = 15/91 (16%)

Query: 1   MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREE 60
           +EDLA  F++KTQ  IDRI ELQ  G +TGVIDDRGKFIY+S+EEL +VA FIKQR    
Sbjct: 222 LEDLAVAFKLKTQQAIDRIQELQADGTITGVIDDRGKFIYVSEEELVAVAKFIKQR---- 277

Query: 61  LNSVATFIKQKGRVSVSELVENSNQLVTLIP 91
                      GRVS+++L E+SN L+ L P
Sbjct: 278 -----------GRVSIADLAESSNNLINLTP 297

Drosophila ananassae (taxid: 7217)

>sp|Q9VDD1|DDRGK_DROME DDRGK domain-containing protein 1 OS=Drosophila melanogaster GN=CG5862 PE=1 SV=1

 Score = 99.8 bits (247), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 51/91 (56%), Positives = 62/91 (68%), Gaps = 15/91 (16%)

Query: 1   MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREE 60
           +EDLA  F++KTQ VIDRI  LQ  G LTGVIDDRGKFIY+S++EL +VA FIKQR    
Sbjct: 224 LEDLAVAFKLKTQQVIDRIQNLQADGTLTGVIDDRGKFIYVSEKELLAVAKFIKQR---- 279

Query: 61  LNSVATFIKQKGRVSVSELVENSNQLVTLIP 91
                      GRVS++EL E+SN L+ L P
Sbjct: 280 -----------GRVSIAELAESSNNLINLTP 299

Drosophila melanogaster (taxid: 7227)

>sp|Q295B1|DDRGK_DROPS DDRGK domain-containing protein 1 OS=Drosophila pseudoobscura pseudoobscura GN=GA19186 PE=3 SV=1

 Score = 98.6 bits (244), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 50/91 (54%), Positives = 61/91 (67%), Gaps = 15/91 (16%)

Query: 1   MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREE 60
           +EDLA  F++KTQ  I+RI +LQ  G LTGVIDDRGKFIY+S+EEL +VA FIKQR    
Sbjct: 224 LEDLAVAFKLKTQQAIERIQDLQANGTLTGVIDDRGKFIYVSEEELAAVAKFIKQR---- 279

Query: 61  LNSVATFIKQKGRVSVSELVENSNQLVTLIP 91
                      GRVS+ EL E+SN L+ L P
Sbjct: 280 -----------GRVSIVELAESSNNLINLTP 299

Drosophila pseudoobscura pseudoobscura (taxid: 46245)

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	96
170041823	287	conserved hypothetical protein [Culex qu	0.791	0.264	0.615	8e-24
312371973	253	hypothetical protein AND_20775 [Anophele	0.791	0.300	0.615	1e-23
380024518	290	PREDICTED: DDRGK domain-containing prote	0.791	0.262	0.593	5e-22
260828191	298	hypothetical protein BRAFLDRAFT_114851 [	0.802	0.258	0.597	5e-22
242006420	279	conserved hypothetical protein [Pediculu	0.791	0.272	0.593	6e-22
66525595	290	PREDICTED: DDRGK domain-containing prote	0.791	0.262	0.593	7e-22
225703086	289	DDRGK domain-containing protein 1 precur	0.791	0.262	0.593	8e-22
383860848	290	PREDICTED: DDRGK domain-containing prote	0.791	0.262	0.604	2e-21
195498433	312	GE25716 [Drosophila yakuba] gi|290463224	0.791	0.243	0.582	2e-21
194899552	312	GG24454 [Drosophila erecta] gi|290463217	0.791	0.243	0.582	2e-21

>gi|170041823|ref|XP_001848649.1| conserved hypothetical protein [Culex quinquefasciatus] gi|290463215|sp|B0WIW5.1|DDRGK_CULQU RecName: Full=DDRGK domain-containing protein 1; Flags: Precursor gi|167865408|gb|EDS28791.1| conserved hypothetical protein [Culex quinquefasciatus]

 Score =  114 bits (285), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 56/91 (61%), Positives = 67/91 (73%), Gaps = 15/91 (16%)

Query: 1   MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREE 60
           +EDLA  F++KTQ+ IDRIVELQK G L+GVIDDRGKFIYIS+EELN+VA FIKQR    
Sbjct: 208 LEDLAVQFKLKTQAAIDRIVELQKDGRLSGVIDDRGKFIYISEEELNAVAKFIKQR---- 263

Query: 61  LNSVATFIKQKGRVSVSELVENSNQLVTLIP 91
                      GRVS++EL ENSN L+ L+P
Sbjct: 264 -----------GRVSITELAENSNNLINLVP 283

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|312371973|gb|EFR20028.1| hypothetical protein AND_20775 [Anopheles darlingi]

 Score =  114 bits (284), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 56/91 (61%), Positives = 66/91 (72%), Gaps = 15/91 (16%)

Query: 1   MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREE 60
           +EDLAA F++K Q+VIDRI ELQK   LTGVIDDRGKFIYIS+EEL SVA FI+QR    
Sbjct: 171 LEDLAAHFKLKVQAVIDRIEELQKENRLTGVIDDRGKFIYISEEELKSVAKFIRQR---- 226

Query: 61  LNSVATFIKQKGRVSVSELVENSNQLVTLIP 91
                      GRVS++EL ENSNQL+ L+P
Sbjct: 227 -----------GRVSIAELAENSNQLINLVP 246

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380024518|ref|XP_003696042.1| PREDICTED: DDRGK domain-containing protein 1-like isoform 1 [Apis florea] gi|380024520|ref|XP_003696043.1| PREDICTED: DDRGK domain-containing protein 1-like isoform 2 [Apis florea]

 Score =  108 bits (270), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 54/91 (59%), Positives = 66/91 (72%), Gaps = 15/91 (16%)

Query: 1   MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREE 60
           +EDLAA F +KT SVI+RI ELQ TG+LTGVIDDRGKFIYISQEEL +VA F++QR    
Sbjct: 206 LEDLAAYFNLKTASVIERIQELQATGSLTGVIDDRGKFIYISQEELEAVAKFVRQR---- 261

Query: 61  LNSVATFIKQKGRVSVSELVENSNQLVTLIP 91
                      GR+S++EL ENSN+L+ L P
Sbjct: 262 -----------GRISITELAENSNRLINLNP 281

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|260828191|ref|XP_002609047.1| hypothetical protein BRAFLDRAFT_114851 [Branchiostoma floridae] gi|290463213|sp|C3Y431.1|DDRGK_BRAFL RecName: Full=DDRGK domain-containing protein 1; Flags: Precursor gi|229294401|gb|EEN65057.1| hypothetical protein BRAFLDRAFT_114851 [Branchiostoma floridae]

 Score =  108 bits (269), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 55/92 (59%), Positives = 66/92 (71%), Gaps = 15/92 (16%)

Query: 1   MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREE 60
           +EDLAA F M+TQ  I R+ EL++ G LTGVIDDRGKFIYISQEEL +VA FIKQR    
Sbjct: 212 LEDLAAQFNMRTQDCIQRVQELREQGRLTGVIDDRGKFIYISQEELQAVAKFIKQR---- 267

Query: 61  LNSVATFIKQKGRVSVSELVENSNQLVTLIPD 92
                      GRVS+++LVE+SNQL+ LIPD
Sbjct: 268 -----------GRVSITDLVESSNQLIHLIPD 288

Source: Branchiostoma floridae

Species: Branchiostoma floridae

Genus: Branchiostoma

Family: Branchiostomidae

Phylum: Chordata

Superkingdom: Eukaryota

>gi|242006420|ref|XP_002424048.1| conserved hypothetical protein [Pediculus humanus corporis] gi|212507354|gb|EEB11310.1| conserved hypothetical protein [Pediculus humanus corporis]

 Score =  107 bits (268), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 54/91 (59%), Positives = 66/91 (72%), Gaps = 15/91 (16%)

Query: 1   MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREE 60
           +ED+AA F++KTQ  I+RI +LQ  G LTGVIDDRGKFIYISQEEL++VA F+KQR    
Sbjct: 200 LEDIAAQFKLKTQDAINRINDLQSEGQLTGVIDDRGKFIYISQEELDAVAKFVKQR---- 255

Query: 61  LNSVATFIKQKGRVSVSELVENSNQLVTLIP 91
                      GRVS+SELVENSN+L+ L P
Sbjct: 256 -----------GRVSISELVENSNRLINLSP 275

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|66525595|ref|XP_624506.1| PREDICTED: DDRGK domain-containing protein 1-like [Apis mellifera]

 Score =  107 bits (268), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 54/91 (59%), Positives = 66/91 (72%), Gaps = 15/91 (16%)

Query: 1   MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREE 60
           +EDLAA F +KT SVI+RI ELQ TG+LTGVIDDRGKFIYISQEEL +VA F++QR    
Sbjct: 206 LEDLAAYFSLKTASVIERIQELQATGSLTGVIDDRGKFIYISQEELEAVAKFVRQR---- 261

Query: 61  LNSVATFIKQKGRVSVSELVENSNQLVTLIP 91
                      GR+S++EL ENSN+L+ L P
Sbjct: 262 -----------GRISITELAENSNRLINLNP 281

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|225703086|ref|NP_001139535.1| DDRGK domain-containing protein 1 precursor [Bombyx mori] gi|290463212|sp|C0KYB6.1|DDRGK_BOMMO RecName: Full=DDRGK domain-containing protein 1; Flags: Precursor gi|224570310|gb|ACN56793.1| DDRGK superfamily protein [Bombyx mori]

 Score =  107 bits (268), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 54/91 (59%), Positives = 63/91 (69%), Gaps = 15/91 (16%)

Query: 1   MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREE 60
           +EDLAA F++KTQ+ IDRI ELQ +G LTGVIDDRGKFIYISQ EL S+A FIKQR    
Sbjct: 210 LEDLAAHFKLKTQAAIDRITELQASGELTGVIDDRGKFIYISQSELESIAKFIKQR---- 265

Query: 61  LNSVATFIKQKGRVSVSELVENSNQLVTLIP 91
                      GRVS++EL E SN L+ L P
Sbjct: 266 -----------GRVSIAELAECSNDLINLAP 285

Source: Bombyx mori

Species: Bombyx mori

Genus: Bombyx

Family: Bombycidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383860848|ref|XP_003705900.1| PREDICTED: DDRGK domain-containing protein 1-like [Megachile rotundata]

 Score =  106 bits (265), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 55/91 (60%), Positives = 65/91 (71%), Gaps = 15/91 (16%)

Query: 1   MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREE 60
           +EDLAA F +KT SV++RI ELQ TG LTGVIDDRGKFIYISQEEL +VA F++QR    
Sbjct: 205 LEDLAAHFGLKTISVVERIQELQTTGTLTGVIDDRGKFIYISQEELEAVAKFVRQR---- 260

Query: 61  LNSVATFIKQKGRVSVSELVENSNQLVTLIP 91
                      GRVS++ELVENSN L+ L P
Sbjct: 261 -----------GRVSITELVENSNNLINLSP 280

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195498433|ref|XP_002096521.1| GE25716 [Drosophila yakuba] gi|290463224|sp|B4PQC4.1|DDRGK_DROYA RecName: Full=DDRGK domain-containing protein 1; Flags: Precursor gi|194182622|gb|EDW96233.1| GE25716 [Drosophila yakuba]

 Score =  105 bits (263), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 53/91 (58%), Positives = 64/91 (70%), Gaps = 15/91 (16%)

Query: 1   MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREE 60
           +EDLA  F++KTQ VIDRI ELQ  G LTGVIDDRGKFIY+S+EEL++VA FIKQR    
Sbjct: 227 LEDLAVAFKLKTQQVIDRIQELQADGTLTGVIDDRGKFIYVSEEELSAVAKFIKQR---- 282

Query: 61  LNSVATFIKQKGRVSVSELVENSNQLVTLIP 91
                      GRVS++EL E+SN L+ L P
Sbjct: 283 -----------GRVSIAELAESSNNLINLTP 302

Source: Drosophila yakuba

Species: Drosophila yakuba

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194899552|ref|XP_001979323.1| GG24454 [Drosophila erecta] gi|290463217|sp|B3P045.1|DDRGK_DROER RecName: Full=DDRGK domain-containing protein 1; Flags: Precursor gi|190651026|gb|EDV48281.1| GG24454 [Drosophila erecta]

 Score =  105 bits (263), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 53/91 (58%), Positives = 64/91 (70%), Gaps = 15/91 (16%)

Query: 1   MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREE 60
           +EDLA  F++KTQ VIDRI ELQ  G LTGVIDDRGKFIY+S+EEL++VA FIKQR    
Sbjct: 227 LEDLAVAFKLKTQQVIDRIQELQADGTLTGVIDDRGKFIYVSEEELSAVAKFIKQR---- 282

Query: 61  LNSVATFIKQKGRVSVSELVENSNQLVTLIP 91
                      GRVS++EL E+SN L+ L P
Sbjct: 283 -----------GRVSITELAESSNNLINLTP 302

Source: Drosophila erecta

Species: Drosophila erecta

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

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	96
ZFIN|ZDB-GENE-040426-1050	300	ddrgk1 "DDRGK domain containin	0.802	0.256	0.521	1.8e-16
UNIPROTKB|E1BUR3	308	DDRGK1 "Uncharacterized protei	0.833	0.259	0.505	6.9e-16
UNIPROTKB|C1BL82	298	ddrgk1 "DDRGK domain-containin	0.802	0.258	0.467	2.8e-15
TAIR|locus:2136457	298	AT4G27120 "AT4G27120" [Arabido	0.791	0.255	0.472	8.5e-15
UNIPROTKB|F1S8B0	312	DDRGK1 "Uncharacterized protei	0.677	0.208	0.569	7.4e-14
UNIPROTKB|F1MK36	313	DDRGK1 "DDRGK domain-containin	0.677	0.207	0.569	7.6e-14
UNIPROTKB|Q1LZB0	313	DDRGK1 "DDRGK domain-containin	0.677	0.207	0.569	7.6e-14
MGI|MGI:1924256	315	Ddrgk1 "DDRGK domain containin	0.677	0.206	0.569	1.3e-13
UNIPROTKB|E2QZV2	390	DDRGK1 "Uncharacterized protei	0.677	0.166	0.569	1.6e-13
UNIPROTKB|Q96HY6	314	DDRGK1 "DDRGK domain-containin	0.677	0.207	0.553	2.2e-13

ZFIN|ZDB-GENE-040426-1050 ddrgk1 "DDRGK domain containing 1" [Danio rerio (taxid:7955)]

 Score = 204 (76.9 bits), Expect = 1.8e-16, P = 1.8e-16
 Identities = 48/92 (52%), Positives = 61/92 (66%)

Query:     1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREE 60
             +EDLA+ F ++TQ  I R+ +L   G+LTGVIDDRGKFI+I+ EELN+VA FIKQRGR  
Sbjct:   219 LEDLASQFGLRTQDAIARLQDLIADGSLTGVIDDRGKFIFITPEELNAVAQFIKQRGR-- 276

Query:    61 LNSVATFIKQKGRVSVSELVENSNQLVTLIPD 92
                          VS+SEL + SN L+ L PD
Sbjct:   277 -------------VSISELAQASNTLINLTPD 295

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0005783 "endoplasmic reticulum" evidence=IEA;ISS

UNIPROTKB|E1BUR3 DDRGK1 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 199 (75.1 bits), Expect = 6.9e-16, P = 6.9e-16
 Identities = 48/95 (50%), Positives = 61/95 (64%)

Query:     1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREE 60
             +EDLA+   ++TQ  I+RI +L   G LTGVIDDRGKFIYI+ EE+ +VA FIKQRGR  
Sbjct:   223 LEDLASHMGLRTQDAINRIQDLMADGTLTGVIDDRGKFIYITPEEMAAVAQFIKQRGR-- 280

Query:    61 LNSVATFIKQKGRVSVSELVENSNQLVTLIPDQIA 95
                          VS++ELV+ SN L+ L PD  A
Sbjct:   281 -------------VSIAELVQASNSLINLQPDSQA 302

GO:0005783 "endoplasmic reticulum" evidence=IEA

UNIPROTKB|C1BL82 ddrgk1 "DDRGK domain-containing protein 1" [Osmerus mordax (taxid:8014)]

 Score = 193 (73.0 bits), Expect = 2.8e-15, P = 2.8e-15
 Identities = 43/92 (46%), Positives = 61/92 (66%)

Query:     1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREE 60
             +EDLA+ F ++TQ  I R+ +L   G++TGVIDDRGKFI+I+ EE+N VA FI+QRGR  
Sbjct:   217 LEDLASHFGLRTQDAISRLQDLLSDGSITGVIDDRGKFIFITPEEMNVVAQFIRQRGR-- 274

Query:    61 LNSVATFIKQKGRVSVSELVENSNQLVTLIPD 92
                          VS+++L + SN L+ LIP+
Sbjct:   275 -------------VSITDLAQASNSLINLIPE 293

GO:0005783 "endoplasmic reticulum" evidence=ISS

TAIR|locus:2136457 AT4G27120 "AT4G27120" [Arabidopsis thaliana (taxid:3702)]

 Score = 189 (71.6 bits), Expect = 8.5e-15, P = 8.5e-15
 Identities = 43/91 (47%), Positives = 58/91 (63%)

Query:     1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREE 60
             +EDLAA F ++TQ  I+RI  L+  G L+GV+DDRGK+IYIS EE+N+VA +IK++GR  
Sbjct:   204 LEDLAAEFHLRTQECINRIASLESIGRLSGVMDDRGKYIYISMEEMNAVADYIKRQGR-- 261

Query:    61 LNSVATFIKQKGRVSVSELVENSNQLVTLIP 91
                          VS+S L   SNQ + L P
Sbjct:   262 -------------VSISHLASKSNQFIDLEP 279

GO:0030244 "cellulose biosynthetic process" evidence=RCA

GO:0048193 "Golgi vesicle transport" evidence=RCA

UNIPROTKB|F1S8B0 DDRGK1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 182 (69.1 bits), Expect = 7.4e-14, P = 7.4e-14
 Identities = 37/65 (56%), Positives = 48/65 (73%)

Query:     1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREE 60
             +EDLA+   ++TQ  I+RI +L   G LTGVIDDRGKFIYI+ EEL +VA FI+QRGR  
Sbjct:   229 LEDLASQVGLRTQDTINRIQDLLAEGTLTGVIDDRGKFIYITPEELAAVANFIRQRGRVS 288

Query:    61 LNSVA 65
             +  +A
Sbjct:   289 ITELA 293

GO:0005783 "endoplasmic reticulum" evidence=IEA

UNIPROTKB|F1MK36 DDRGK1 "DDRGK domain-containing protein 1" [Bos taurus (taxid:9913)]

 Score = 182 (69.1 bits), Expect = 7.6e-14, P = 7.6e-14
 Identities = 37/65 (56%), Positives = 48/65 (73%)

Query:     1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREE 60
             +EDLA+   ++TQ  I+RI +L   G LTGVIDDRGKFIYI+ EEL +VA FI+QRGR  
Sbjct:   230 LEDLASQVGLRTQDTINRIQDLLAEGTLTGVIDDRGKFIYITPEELAAVANFIRQRGRVS 289

Query:    61 LNSVA 65
             +  +A
Sbjct:   290 ITELA 294

GO:0005783 "endoplasmic reticulum" evidence=IEA

UNIPROTKB|Q1LZB0 DDRGK1 "DDRGK domain-containing protein 1" [Bos taurus (taxid:9913)]

 Score = 182 (69.1 bits), Expect = 7.6e-14, P = 7.6e-14
 Identities = 37/65 (56%), Positives = 48/65 (73%)

Query:     1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREE 60
             +EDLA+   ++TQ  I+RI +L   G LTGVIDDRGKFIYI+ EEL +VA FI+QRGR  
Sbjct:   230 LEDLASQVGLRTQDTINRIQDLLAEGTLTGVIDDRGKFIYITPEELAAVANFIRQRGRVS 289

Query:    61 LNSVA 65
             +  +A
Sbjct:   290 ITELA 294

GO:0005783 "endoplasmic reticulum" evidence=ISS

MGI|MGI:1924256 Ddrgk1 "DDRGK domain containing 1" [Mus musculus (taxid:10090)]

 Score = 180 (68.4 bits), Expect = 1.3e-13, P = 1.3e-13
 Identities = 37/65 (56%), Positives = 47/65 (72%)

Query:     1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREE 60
             +EDLA    ++TQ  I+RI +L   G LTGVIDDRGKFIYI+ EEL +VA FI+QRGR  
Sbjct:   232 LEDLAFQMGLRTQDAINRIQDLLTEGTLTGVIDDRGKFIYITPEELAAVANFIRQRGRVS 291

Query:    61 LNSVA 65
             +  +A
Sbjct:   292 ITELA 296

GO:0003674 "molecular_function" evidence=ND

GO:0005783 "endoplasmic reticulum" evidence=ISO

GO:0008150 "biological_process" evidence=ND

UNIPROTKB|E2QZV2 DDRGK1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 182 (69.1 bits), Expect = 1.6e-13, P = 1.6e-13
 Identities = 37/65 (56%), Positives = 48/65 (73%)

Query:     1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREE 60
             +EDLA+   ++TQ  I+RI +L   G LTGVIDDRGKFIYI+ EEL +VA FI+QRGR  
Sbjct:   307 LEDLASQVGLRTQDTINRIQDLLAEGTLTGVIDDRGKFIYITPEELAAVANFIRQRGRVS 366

Query:    61 LNSVA 65
             +  +A
Sbjct:   367 ITELA 371

GO:0005783 "endoplasmic reticulum" evidence=IEA

UNIPROTKB|Q96HY6 DDRGK1 "DDRGK domain-containing protein 1" [Homo sapiens (taxid:9606)]

 Score = 178 (67.7 bits), Expect = 2.2e-13, P = 2.2e-13
 Identities = 36/65 (55%), Positives = 48/65 (73%)

Query:     1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREE 60
             +EDLA+   ++TQ  I+RI +L   G +TGVIDDRGKFIYI+ EEL +VA FI+QRGR  
Sbjct:   231 LEDLASQVGLRTQDTINRIQDLLAEGTITGVIDDRGKFIYITPEELAAVANFIRQRGRVS 290

Query:    61 LNSVA 65
             +  +A
Sbjct:   291 IAELA 295

GO:0005515 "protein binding" evidence=IPI

GO:0005783 "endoplasmic reticulum" evidence=IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9VDD1	DDRGK_DROME	No assigned EC number	0.5604	0.7916	0.2459	yes	N/A
Q6P0E5	DDRGK_DANRE	No assigned EC number	0.5217	0.8020	0.2566	yes	N/A
Q295B1	DDRGK_DROPS	No assigned EC number	0.5494	0.7916	0.2459	yes	N/A
C3Y431	DDRGK_BRAFL	No assigned EC number	0.5978	0.8020	0.2583	yes	N/A
Q55CM7	DDRGK_DICDI	No assigned EC number	0.5230	0.6770	0.1940	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	96
pfam09756	189	pfam09756, DDRGK, DDRGK domain	6e-22

>gnl|CDD|220383 pfam09756, DDRGK, DDRGK domain

 Score = 84.4 bits (209), Expect = 6e-22
 Identities = 44/86 (51%), Positives = 60/86 (69%), Gaps = 15/86 (17%)

Query: 2   EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREEL 61
           E+L+A F +KT+ VI+RI +L+  G++TGVIDDRGK+IYIS EEL +VA+FI +R     
Sbjct: 118 EELSAEFGLKTEDVIERIQDLEAQGSITGVIDDRGKYIYISPEELEAVASFINKR----- 172

Query: 62  NSVATFIKQKGRVSVSELVENSNQLV 87
                     GRVS+SEL E SN+L+
Sbjct: 173 ----------GRVSISELAEISNKLI 188

This is a family of proteins of approximately 300 residues, found in plants and vertebrates. They contain a highly conserved DDRGK motif. Length = 189

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	96
PF09756	188	DDRGK: DDRGK domain; InterPro: IPR019153 This is a	100.0
KOG3054|consensus	299		100.0
smart00418	66	HTH_ARSR helix_turn_helix, Arsenical Resistance Op	97.37
PF09743	272	DUF2042: Uncharacterized conserved protein (DUF204	96.91
PRK14165	217	winged helix-turn-helix domain-containing protein/	96.76
smart00753	88	PAM PCI/PINT associated module.	96.73
smart00088	88	PINT motif in proteasome subunits, Int-6, Nip-1 an	96.73
PF01399	105	PCI: PCI domain; InterPro: IPR000717 A homology do	96.22
PRK11169	164	leucine-responsive transcriptional regulator; Prov	96.03
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	95.98
TIGR02337	118	HpaR homoprotocatechuate degradation operon regula	95.8
cd07377	66	WHTH_GntR Winged helix-turn-helix (WHTH) DNA-bindi	95.55
smart00347	101	HTH_MARR helix_turn_helix multiple antibiotic resi	95.47
PLN03083	803	E3 UFM1-protein ligase 1 homolog; Provisional	95.45
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	95.29
COG1522	154	Lrp Transcriptional regulators [Transcription]	95.25
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	95.19
PRK06266	178	transcription initiation factor E subunit alpha; V	95.05
cd00090	78	HTH_ARSR Arsenical Resistance Operon Repressor and	94.88
PRK03573	144	transcriptional regulator SlyA; Provisional	94.51
TIGR01889	109	Staph_reg_Sar staphylococcal accessory regulator f	94.01
PRK11179	153	DNA-binding transcriptional regulator AsnC; Provis	93.93
cd04761	49	HTH_MerR-SF Helix-Turn-Helix DNA binding domain of	93.92
PF13545	76	HTH_Crp_2: Crp-like helix-turn-helix domain; PDB:	93.88
PRK11512	144	DNA-binding transcriptional repressor MarR; Provis	93.82
TIGR01884	203	cas_HTH CRISPR locus-related DNA-binding protein.	93.72
TIGR02944	130	suf_reg_Xantho FeS assembly SUF system regulator,	93.2
smart00419	48	HTH_CRP helix_turn_helix, cAMP Regulatory protein.	93.05
PRK10870	176	transcriptional repressor MprA; Provisional	92.95
PF13551	112	HTH_29: Winged helix-turn helix	92.83
TIGR01764	49	excise DNA binding domain, excisionase family. An	92.79
PRK09391	230	fixK transcriptional regulator FixK; Provisional	92.45
PF09743	272	DUF2042: Uncharacterized conserved protein (DUF204	92.35
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	92.27
smart00529	96	HTH_DTXR Helix-turn-helix diphteria tox regulatory	92.13
PRK03902	142	manganese transport transcriptional regulator; Pro	92.02
COG1339	214	Transcriptional regulator of a riboflavin/FAD bios	91.89
PRK13918	202	CRP/FNR family transcriptional regulator; Provisio	91.75
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	91.65
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	91.49
TIGR00122	69	birA_repr_reg BirA biotin operon repressor domain.	91.39
PRK04172	489	pheS phenylalanyl-tRNA synthetase subunit alpha; P	91.11
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	90.98
PF13518	52	HTH_28: Helix-turn-helix domain	90.94
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	90.84
PF09012	69	FeoC: FeoC like transcriptional regulator; InterPr	90.65
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	90.64
TIGR03697	193	NtcA_cyano global nitrogen regulator NtcA, cyanoba	90.59
COG1846	126	MarR Transcriptional regulators [Transcription]	90.49
TIGR03338	212	phnR_burk phosphonate utilization associated trans	90.37
COG3140	60	Uncharacterized protein conserved in bacteria [Fun	90.3
PRK10402	226	DNA-binding transcriptional activator YeiL; Provis	90.04
PF09012	69	FeoC: FeoC like transcriptional regulator; InterPr	89.89
cd04764	67	HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding dom	89.61
PRK10141	117	DNA-binding transcriptional repressor ArsR; Provis	89.6
PF13730	55	HTH_36: Helix-turn-helix domain	89.6
PF12728	51	HTH_17: Helix-turn-helix domain	89.44
PRK13777	185	transcriptional regulator Hpr; Provisional	89.41
PF12419	141	DUF3670: SNF2 Helicase protein ; InterPro: IPR0221	89.36
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	89.0
smart00422	70	HTH_MERR helix_turn_helix, mercury resistance.	88.87
PRK09392	236	ftrB transcriptional activator FtrB; Provisional	88.85
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	88.51
PRK10512	614	selenocysteinyl-tRNA-specific translation factor;	88.31
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	88.25
PRK11414	221	colanic acid/biofilm transcriptional regulator; Pr	88.21
PRK00215	205	LexA repressor; Validated	87.3
TIGR00498	199	lexA SOS regulatory protein LexA. LexA acts as a h	87.18
PF13411	69	MerR_1: MerR HTH family regulatory protein; PDB: 2	86.64
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	86.63
TIGR02698	130	CopY_TcrY copper transport repressor, CopY/TcrY fa	86.61
PF00392	64	GntR: Bacterial regulatory proteins, gntR family;	86.25
TIGR02702	203	SufR_cyano iron-sulfur cluster biosynthesis transc	86.25
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	86.02
TIGR02787	251	codY_Gpos GTP-sensing transcriptional pleiotropic	85.62
cd04762	49	HTH_MerR-trunc Helix-Turn-Helix DNA binding domain	85.43
TIGR02812	235	fadR_gamma fatty acid metabolism transcriptional r	85.33
PRK09954	362	putative kinase; Provisional	84.82
TIGR02051	124	MerR Hg(II)-responsive transcriptional regulator.	84.67
PF01402	39	RHH_1: Ribbon-helix-helix protein, copG family; In	84.34
PRK11161	235	fumarate/nitrate reduction transcriptional regulat	83.96
PRK11050	152	manganese transport regulator MntR; Provisional	83.85
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	83.76
TIGR00373	158	conserved hypothetical protein TIGR00373. This fam	83.69
PF14493	91	HTH_40: Helix-turn-helix domain	83.57
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	83.42
smart00342	84	HTH_ARAC helix_turn_helix, arabinose operon contro	83.26
PRK04984	239	fatty acid metabolism regulator; Provisional	82.66
PRK10421	253	DNA-binding transcriptional repressor LldR; Provis	82.42
PRK11534	224	DNA-binding transcriptional regulator CsiR; Provis	82.21
COG1654	79	BirA Biotin operon repressor [Transcription]	82.06
COG1349	253	GlpR Transcriptional regulators of sugar metabolis	82.03
PRK00135	188	scpB segregation and condensation protein B; Revie	81.77
PF14947	77	HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_	81.77
smart00351	125	PAX Paired Box domain.	81.73
PF08784	102	RPA_C: Replication protein A C terminal; InterPro:	81.73
PF13601	80	HTH_34: Winged helix DNA-binding domain; PDB: 1UB9	81.24
cd04768	96	HTH_BmrR-like Helix-Turn-Helix DNA binding domain	80.99
cd00131	128	PAX Paired Box domain	80.86
KOG2235|consensus	776		80.72
PRK11523	253	DNA-binding transcriptional repressor ExuR; Provis	80.69
PRK09464	254	pdhR transcriptional regulator PdhR; Reviewed	80.35
PRK09990	251	DNA-binding transcriptional regulator GlcC; Provis	80.17

>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues

Probab=100.00  E-value=4.5e-38  Score=236.14  Aligned_cols=73  Identities=67%  Similarity=1.022  Sum_probs=33.4

Q ss_pred             ChhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHH
Q psy11008          1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELV   80 (96)
Q Consensus         1 ledLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~   80 (96)
                      |+|||++|||+|++||+||++|+++|+|||||||||||||||++||++||+||++|               ||||++||+
T Consensus       116 ledla~~f~l~t~~~i~ri~~L~~~g~ltGv~DdrGkfIyIs~eE~~~va~fi~~r---------------GRvsi~el~  180 (188)
T PF09756_consen  116 LEDLAAEFGLRTQDVINRIQELEAEGRLTGVIDDRGKFIYISEEEMEAVAKFIKQR---------------GRVSISELA  180 (188)
T ss_dssp             HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE----------------------------------------
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHCCCceeeEcCCCCeEEecHHHHHHHHHHHHHc---------------CCccHHHHH
Confidence            58999999999999999999999999999999999999999999999999999999               999999999


Q ss_pred             Hhccccee
Q psy11008         81 ENSNQLVT   88 (96)
Q Consensus        81 ~~sN~lI~   88 (96)
                      ++||+||+
T Consensus       181 ~~~N~~i~  188 (188)
T PF09756_consen  181 QESNRLIN  188 (188)
T ss_dssp             --------
T ss_pred             HHHHhhcC
Confidence            99999996

They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.

>KOG3054|consensus

Probab=100.00  E-value=1.3e-36  Score=242.93  Aligned_cols=80  Identities=61%  Similarity=0.893  Sum_probs=77.3

Q ss_pred             ChhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHH
Q psy11008          1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELV   80 (96)
Q Consensus         1 ledLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~   80 (96)
                      |||||++|||+||++|+|||+|+++|.|||||||||||||||++||.+||+||+||               |||||+||+
T Consensus       217 ledLas~f~Lrtqd~inriq~~l~eg~ltGVmDDRGKfIYIS~eEl~AVAkfIkqr---------------GRVSIaelA  281 (299)
T KOG3054|consen  217 LEDLASEFGLRTQDSINRIQELLAEGLLTGVMDDRGKFIYISMEELAAVAKFIKQR---------------GRVSIAELA  281 (299)
T ss_pred             HHHHHHHhCccHHHHHHHHHHHHHhhhheeeecCCCceEEecHHHHHHHHHHHHHc---------------CceeHHHHH
Confidence            68999999999999999999999999999999999999999999999999999999               999999999


Q ss_pred             HhcccceeccccccC
Q psy11008         81 ENSNQLVTLIPDQIA   95 (96)
Q Consensus        81 ~~sN~lI~L~p~~~~   95 (96)
                      +.||+||+|.|...+
T Consensus       282 e~SN~lI~l~~es~s  296 (299)
T KOG3054|consen  282 EKSNQLIDLETESPS  296 (299)
T ss_pred             HhhcchhccccCCCC
Confidence            999999999877653

>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor

Probab=97.37  E-value=0.00098  Score=37.38  Aligned_cols=50  Identities=12%  Similarity=0.319  Sum_probs=44.0

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVAT   51 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~   51 (96)
                      +|||.+++++...+-..|+.|.+.|.+.-.-+.+.++.+++++.+..+..
T Consensus        14 ~~i~~~l~is~~~v~~~l~~L~~~g~i~~~~~~~~~~~~~~~~~~~~~~~   63 (66)
T smart00418       14 CELAEILGLSQSTVSHHLKKLREAGLVESRREGKRVYYSLTDEKVADLLE   63 (66)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCeeeeecCCEEEEEEchHHHHHHHH
Confidence            68999999999999999999999999998888888899999986665544

>PF09743 DUF2042: Uncharacterized conserved protein (DUF2042); InterPro: IPR018611 The ubiquitin fold modifier 1 (Ufm1) is the most recently discovered ubiquitin-like modifier whose conjugation (ufmylation) system is conserved in multicellular organisms

Probab=96.91  E-value=0.0063  Score=47.99  Aligned_cols=61  Identities=26%  Similarity=0.430  Sum_probs=52.2

Q ss_pred             CCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHH-HHHHHHhhchhchhhhhhhhccccceeHHHHHHhcc
Q psy11008          9 RMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNS-VATFIKQRGREELNSVATFIKQKGRVSVSELVENSN   84 (96)
Q Consensus         9 ~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~-Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~~sN   84 (96)
                      +|+--.||+=|+.|.+.+.|.=|....||- |||++++.. +..-+..+|              |||++.||+..-|
T Consensus        20 rLSErnciEiv~kL~~~~~ldli~T~dGke-yiT~~~L~~EI~~el~~~g--------------GRv~~~dL~~~Ln   81 (272)
T PF09743_consen   20 RLSERNCIEIVNKLIEKKLLDLIHTTDGKE-YITPEQLEKEIKDELYVHG--------------GRVNLVDLAQALN   81 (272)
T ss_pred             hcchhhHHHHHHHHHHcCCeeEEEECCCCE-EECHHHHHHHHHHHHHHcC--------------CceEHHHHHHhcC
Confidence            677788999999999999999888889985 899999865 555777887              9999999997644

Ufm1 is known to covalently attach with cellular protein(s) via a specific E1-activating enzyme (Uba5), an E2-conjugating enzyme (Ufc1), and a E3-ligating enzyme []. This entry represents E3 UFM1-protein ligase 1.

>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional

Probab=96.76  E-value=0.0054  Score=47.21  Aligned_cols=54  Identities=19%  Similarity=0.287  Sum_probs=48.3

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQ   55 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~   55 (96)
                      .|||..++++.+.+-.+++.|++.|-++-..|.|+.+|++|+.-...+.+-...
T Consensus        25 ~eLA~~L~iS~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~LTekG~~ll~~~~~d   78 (217)
T PRK14165         25 SEFANHTGTSSKTAARILKQLEDEGYITRTIVPRGQLITITEKGLDVLYNEYAD   78 (217)
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCEEEEEcCCceEEEECHHHHHHHHHHHHH
Confidence            589999999999999999999999999999999999999999988776544433

>smart00753 PAM PCI/PINT associated module

Probab=96.73  E-value=0.004  Score=39.09  Aligned_cols=45  Identities=18%  Similarity=0.336  Sum_probs=41.4

Q ss_pred             ChhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHH
Q psy11008          1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEE   45 (96)
Q Consensus         1 ledLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eE   45 (96)
                      +++||..|+++.+++-.-|.++..+|.|.|-||...++++++...
T Consensus        27 ~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~   71 (88)
T smart00753       27 LSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVD   71 (88)
T ss_pred             HHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCc
Confidence            478999999999999999999999999999999999999998654

>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15

Probab=96.73  E-value=0.004  Score=39.09  Aligned_cols=45  Identities=18%  Similarity=0.336  Sum_probs=41.4

Q ss_pred             ChhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHH
Q psy11008          1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEE   45 (96)
Q Consensus         1 ledLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eE   45 (96)
                      +++||..|+++.+++-.-|.++..+|.|.|-||...++++++...
T Consensus        27 ~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~   71 (88)
T smart00088       27 LSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVD   71 (88)
T ss_pred             HHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCc
Confidence            478999999999999999999999999999999999999998654

Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.

>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins

Probab=96.22  E-value=0.014  Score=36.33  Aligned_cols=42  Identities=17%  Similarity=0.371  Sum_probs=37.9

Q ss_pred             ChhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEc
Q psy11008          1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYIS   42 (96)
Q Consensus         1 ledLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs   42 (96)
                      ++++|..++++.+++-.-+.++..+|.|.|.||..=+.|+++
T Consensus        63 ~~~ia~~l~~~~~~vE~~l~~~I~~~~i~~~ID~~~~~v~~~  104 (105)
T PF01399_consen   63 ISEIAKALQLSEEEVESILIDLISNGLIKAKIDQVNGVVVFS  104 (105)
T ss_dssp             HHHHHHHHTCCHHHHHHHHHHHHHTTSSEEEEETTTTEEEE-
T ss_pred             hHHHHHHhccchHHHHHHHHHHHHCCCEEEEEECCCCEEEec
Confidence            468999999999999999999999999999999887777765

This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.

>PRK11169 leucine-responsive transcriptional regulator; Provisional

Probab=96.03  E-value=0.019  Score=40.74  Aligned_cols=55  Identities=13%  Similarity=0.373  Sum_probs=44.3

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccE---EeeC--CCc----eEEE-----cHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTG---VIDD--RGK----FIYI-----SQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltG---ViDD--RGK----fIyI-----s~eEl~~Va~fI~~r   56 (96)
                      .+||...|++...|..||+.|++.|.|.|   ++|.  -|.    |+-|     .++.++.+++.+.+.
T Consensus        32 ~eiA~~lglS~~tv~~Ri~rL~~~GvI~~~~~~v~p~~lg~~~~a~v~i~~~~~~~~~~~~~~~~l~~~  100 (164)
T PRK11169         32 VELSKRVGLSPTPCLERVRRLERQGFIQGYTALLNPHYLDASLLVFVEITLNRGAPDVFEQFNAAVQKL  100 (164)
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEEEECHHHhCCCEEEEEEEEEcCCChHHHHHHHHHHhcC
Confidence            58999999999999999999999999865   4553  243    5666     466788888888776

>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A

Probab=95.98  E-value=0.018  Score=34.17  Aligned_cols=43  Identities=23%  Similarity=0.294  Sum_probs=34.3

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEE---eeCCCceEEEcHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGV---IDDRGKFIYISQE   44 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGV---iDDRGKfIyIs~e   44 (96)
                      .+||..++++.+.+..-|++|.+.|-|.=.   -|.|.+++.+|++
T Consensus        22 ~~l~~~~~~~~~~vs~~i~~L~~~glv~~~~~~~d~R~~~~~LT~~   67 (68)
T PF13463_consen   22 SDLAERLGISKSTVSRIIKKLEEKGLVEKERDPHDKRSKRYRLTPA   67 (68)
T ss_dssp             HHHHHHTT--HHHHHHHHHHHHHTTSEEEEEESSCTTSEEEEE-HH
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCEEecCCCCcCCeeEEEeCCC
Confidence            589999999999999999999999999544   4567789999986

>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR

Probab=95.80  E-value=0.034  Score=36.80  Aligned_cols=54  Identities=19%  Similarity=0.233  Sum_probs=45.7

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHHHHHHHHHh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELNSVATFIKQ   55 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~~Va~fI~~   55 (96)
                      .+||..+++....+-..|+.|++.|-|+..-|   .|-+++++|++-...+......
T Consensus        46 ~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT~~G~~~~~~~~~~  102 (118)
T TIGR02337        46 TQLANQACILRPSLTGILARLERDGLVTRLKASNDQRRVYISLTPKGQALYASLSPQ  102 (118)
T ss_pred             HHHHHHhCCCchhHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHHHHHHhhHH
Confidence            48999999999999999999999999999884   5778999999877766655443

This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.

>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators

Probab=95.55  E-value=0.039  Score=31.84  Aligned_cols=38  Identities=18%  Similarity=0.368  Sum_probs=31.2

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEc
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYIS   42 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs   42 (96)
                      .|||.+|+++.+.+-.-++.|++.|-|+   -.+|+..+++
T Consensus        29 ~~la~~~~is~~~v~~~l~~L~~~G~i~---~~~~~~~~l~   66 (66)
T cd07377          29 RELAEELGVSRTTVREALRELEAEGLVE---RRPGRGTFVA   66 (66)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCEE---ecCCCeEEeC
Confidence            5899999999999999999999999865   2456676664

This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is

>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein

Probab=95.47  E-value=0.088  Score=32.13  Aligned_cols=55  Identities=16%  Similarity=0.322  Sum_probs=45.2

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .+||..++++...+-.-|+.|++.|.++=.-|   .|.+++++|+.....+.......
T Consensus        28 ~~la~~~~~s~~~i~~~l~~L~~~g~v~~~~~~~~~r~~~~~lT~~g~~~~~~~~~~~   85 (101)
T smart00347       28 SELAKRLGVSPSTVTRVLDRLEKKGLIRRLPSPEDRRSVLVSLTEEGRELIEELLEAR   85 (101)
T ss_pred             HHHHHHHCCCchhHHHHHHHHHHCCCeEecCCCCCCCeEEEEECHhHHHHHHHHHHHH
Confidence            57999999999999999999999999975433   57789999999887776655544

>PLN03083 E3 UFM1-protein ligase 1 homolog; Provisional

Probab=95.45  E-value=0.057  Score=49.09  Aligned_cols=61  Identities=30%  Similarity=0.497  Sum_probs=50.8

Q ss_pred             hCCChHHHHHHHHHHHHcCCcc--EEeeCCCceEEEcHHHHH-HHHHHHHhhchhchhhhhhhhccccceeHHHHHHhcc
Q psy11008          8 FRMKTQSVIDRIVELQKTGALT--GVIDDRGKFIYISQEELN-SVATFIKQRGREELNSVATFIKQKGRVSVSELVENSN   84 (96)
Q Consensus         8 F~lktq~vI~RI~eL~~~g~lt--GViDDRGKfIyIs~eEl~-~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~~sN   84 (96)
                      .+|+--.||+=++.|.+.|.|-  =|.--.|| =|||+++|. .+...|. +|              |||++.||+..-|
T Consensus        22 ~rLSErNcIEiV~KLie~~~ld~dll~T~DGK-EYiT~~qL~~EI~~El~-~g--------------GRvnlvdLa~~Ln   85 (803)
T PLN03083         22 VRLSERNVVELVQKLQELGIIDFDLLHTVSGK-EYITQDQLRNEIEAEIK-KL--------------GRVSLVDLADTIG   85 (803)
T ss_pred             hhcchhhHHHHHHHHHHhcccCcceEEecCCc-eeeCHHHHHHHHHHHHH-hC--------------CCeeHHHHhhhcC
Confidence            3678889999999999999773  66778999 999999996 4777784 45              9999999987655

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=95.29  E-value=0.065  Score=34.63  Aligned_cols=55  Identities=22%  Similarity=0.469  Sum_probs=43.1

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccE---EeeCC--Cc----e--EEEc-HHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTG---VIDDR--GK----F--IYIS-QEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltG---ViDDR--GK----f--IyIs-~eEl~~Va~fI~~r   56 (96)
                      .+||..+|++...+..||+.|++.|.+.|   ++|.+  |.    +  |.++ ++..+.+++.+++.
T Consensus        21 ~~la~~l~~s~~tv~~~l~~L~~~g~i~~~~~~~~~~~~g~~~~~~v~i~~~~~~~~~~v~~~l~~~   87 (108)
T smart00344       21 AELAKKVGLSPSTVHNRVKRLEEEGVIKGYTAVINPKKLGLSVTAFVGVDLESPDKLEEFLEKLEKL   87 (108)
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCeeceEEEeCHHHcCCCEEEEEEEEECChhHHHHHHHHHhCC
Confidence            58999999999999999999999998874   34422  22    2  4455 67888999888876

AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli

>COG1522 Lrp Transcriptional regulators [Transcription]

Probab=95.25  E-value=0.022  Score=38.48  Aligned_cols=55  Identities=25%  Similarity=0.481  Sum_probs=41.0

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEE---eeCC--C----ceEEEcHHH----HHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGV---IDDR--G----KFIYISQEE----LNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGV---iDDR--G----KfIyIs~eE----l~~Va~fI~~r   56 (96)
                      .+||...|++...|.+||+.|++.|-|.|.   +|.+  |    =|+-+..+.    +..++..+.+-
T Consensus        26 ~eia~~lglS~~~v~~Ri~~L~~~GiI~~~~~~v~~~~lg~~~~a~v~v~~~~~~~~~~~~~~~~~~~   93 (154)
T COG1522          26 AELAERVGLSPSTVLRRIKRLEEEGVIKGYTAVLDPEKLGLDLTAFVEVKLERSLEDLEEFAEALAKL   93 (154)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCceeeEEEEECHHHcCCCEEEEEEEEecCChhHHHHHHHHHhCC
Confidence            589999999999999999999999988764   4531  3    466665554    66666666543

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=95.19  E-value=0.038  Score=31.33  Aligned_cols=28  Identities=21%  Similarity=0.382  Sum_probs=25.6

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCcc
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALT   29 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~lt   29 (96)
                      .+||..|+++...+-..++.|++.|.|.
T Consensus        24 ~~la~~~~vs~~tv~~~l~~L~~~g~i~   51 (60)
T smart00345       24 RELAAQLGVSRTTVREALSRLEAEGLVQ   51 (60)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            5799999999999999999999999876

>PRK06266 transcription initiation factor E subunit alpha; Validated

Probab=95.05  E-value=0.14  Score=38.01  Aligned_cols=55  Identities=18%  Similarity=0.186  Sum_probs=46.6

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCcc--EEee-CCCceEE---EcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALT--GVID-DRGKFIY---ISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~lt--GViD-DRGKfIy---Is~eEl~~Va~fI~~r   56 (96)
                      ||||...|+++.+|-.-+..|.++|-++  -+-| ++|.|.|   ++.+++..+-.+-..+
T Consensus        40 eeLA~~Lgi~~~~VRk~L~~L~e~gLv~~~r~r~~~~Gr~~y~w~l~~~~i~d~ik~~~~~  100 (178)
T PRK06266         40 EEIAEQTGIKLNTVRKILYKLYDARLADYKREKDEETNWYTYTWKPELEKLPEIIKKKKME  100 (178)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCeEEeeeeccCCCcEEEEEEeCHHHHHHHHHHHHHH
Confidence            7999999999999999999999999998  5556 7899888   9998887766655444

>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors

Probab=94.88  E-value=0.21  Score=28.24  Aligned_cols=42  Identities=14%  Similarity=0.319  Sum_probs=37.4

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQ   43 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~   43 (96)
                      .|||..++++...+-..+..|.+.|-+...-+.+.++..+++
T Consensus        24 ~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~~~~~~~~~~~~   65 (78)
T cd00090          24 SELAERLGLSQSTVSRHLKKLEEAGLVESRREGRRVYYSLTD   65 (78)
T ss_pred             HHHHHHHCcCHhHHHHHHHHHHHCCCeEEEEeccEEEEEeCC
Confidence            589999999988888999999999999988887778888885

ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.

>PRK03573 transcriptional regulator SlyA; Provisional

Probab=94.51  E-value=0.18  Score=34.25  Aligned_cols=55  Identities=15%  Similarity=0.187  Sum_probs=47.2

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .|||..++++.+.+-.-|..|++.|-|+=.-|   -|.++|++|++-...++......
T Consensus        50 ~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~~~~~~~  107 (144)
T PRK03573         50 IQLAKAIGIEQPSLVRTLDQLEEKGLISRQTCASDRRAKRIKLTEKAEPLISEVEAVI  107 (144)
T ss_pred             HHHHHHhCCChhhHHHHHHHHHHCCCEeeecCCCCcCeeeeEEChHHHHHHHHHHHHH
Confidence            48999999999999999999999999998865   58999999999887777655444

>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family

Probab=94.01  E-value=0.22  Score=33.07  Aligned_cols=55  Identities=22%  Similarity=0.356  Sum_probs=46.5

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEE---eeCCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGV---IDDRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGV---iDDRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .+||..+++....+-.-|..|++.|-|+=+   -|-|-.+|++|++-...++....+.
T Consensus        47 ~eL~~~l~~~~stvs~~i~~Le~kg~I~r~~~~~D~R~~~i~lT~~G~~~~~~~~~~~  104 (109)
T TIGR01889        47 KEIIKEILIKQSALVKIIKKLSKKGYLSKERSEDDERKVIISINKEQRSKIESLISEI  104 (109)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCEeccCCcccCCeEEEEECHHHHHHHHHHHHHH
Confidence            479999999888888889999999999854   4568999999999988888776654

This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.

>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional

Probab=93.93  E-value=0.08  Score=37.12  Aligned_cols=55  Identities=22%  Similarity=0.371  Sum_probs=43.6

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccE---EeeC--CCc----eEEEc---HHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTG---VIDD--RGK----FIYIS---QEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltG---ViDD--RGK----fIyIs---~eEl~~Va~fI~~r   56 (96)
                      .+||...|++.+.|-.||+.|+++|.|.|   ++|.  -|.    |+.|+   ++.+..++..+.+.
T Consensus        27 ~eiA~~lglS~~tV~~Ri~rL~~~GvI~~~~~~v~~~~lg~~~~a~v~v~v~~~~~~~~~~~~l~~~   93 (153)
T PRK11179         27 AELAKQFGVSPGTIHVRVEKMKQAGIITGTRVDVNPKQLGYDVCCFIGIILKSAKDYPSALAKLESL   93 (153)
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCeeeEEEEECHHHcCCCEEEEEEEEEcccccHHHHHHHHhCC
Confidence            48999999999999999999999999974   4563  343    45543   45688888888876

>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily

Probab=93.92  E-value=0.15  Score=28.55  Aligned_cols=44  Identities=18%  Similarity=0.276  Sum_probs=33.2

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVA   50 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va   50 (96)
                      .|+|..+|++..    .|...++.|.|...-++.|... .+++++..+.
T Consensus         4 ~e~a~~~gv~~~----tlr~~~~~g~l~~~~~~~~~~~-y~~~~v~~l~   47 (49)
T cd04761           4 GELAKLTGVSPS----TLRYYERIGLLSPARTEGGYRL-YSDADLERLR   47 (49)
T ss_pred             HHHHHHHCcCHH----HHHHHHHCCCCCCCcCCCCCEE-eCHHHHHHhh
Confidence            588999999765    4567789999997666656654 5999988753

Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A

Probab=93.88  E-value=0.22  Score=30.17  Aligned_cols=44  Identities=25%  Similarity=0.479  Sum_probs=33.7

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNS   48 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~   48 (96)
                      +|||...|++.+.+-.-+++|+++|.|.   -.+|+++-..++.|++
T Consensus        32 ~~iA~~~g~sr~tv~r~l~~l~~~g~I~---~~~~~i~I~d~~~L~~   75 (76)
T PF13545_consen   32 EEIADMLGVSRETVSRILKRLKDEGIIE---VKRGKIIILDPERLEE   75 (76)
T ss_dssp             HHHHHHHTSCHHHHHHHHHHHHHTTSEE---EETTEEEESSHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCEE---EcCCEEEECCHHHHhc
Confidence            6899999999999888899999998765   2455555445665554

...

>PRK11512 DNA-binding transcriptional repressor MarR; Provisional

Probab=93.82  E-value=0.3  Score=33.42  Aligned_cols=53  Identities=9%  Similarity=0.159  Sum_probs=45.6

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELNSVATFIK   54 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~~Va~fI~   54 (96)
                      .+||..++++...+-.-|..|++.|-|.=.-|   -|.+.||+|++-...+.....
T Consensus        58 ~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~~~~~DrR~~~l~LT~~G~~~~~~~~~  113 (144)
T PRK11512         58 VELKKVLSVDLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTSGAAICEQCHQ  113 (144)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCcccCCeeEeEEChhHHHHHHHHHH
Confidence            48999999999999999999999999987754   689999999998877666443

>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein

Probab=93.72  E-value=0.098  Score=38.13  Aligned_cols=42  Identities=17%  Similarity=0.244  Sum_probs=37.6

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQE   44 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~e   44 (96)
                      .|||..++++...+-..++.|++.|-+.-.-+ |++.+++|+.
T Consensus       161 ~eia~~l~is~stv~r~L~~Le~~GlI~r~~~-r~~~~~lT~~  202 (203)
T TIGR01884       161 KNIAKKLGKSLSTISRHLRELEKKGLVEQKGR-KGKRYSLTKL  202 (203)
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcC-CccEEEeCCC
Confidence            58999999999999999999999999987654 9999999874

Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.

>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial

Probab=93.20  E-value=0.11  Score=35.08  Aligned_cols=55  Identities=16%  Similarity=0.196  Sum_probs=43.5

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .|||..++++..-+-.+++.|.+.|-+.+.-...|.|-...+-+--.+.+++..-
T Consensus        29 ~eia~~l~is~~~v~~~l~~L~~~Gli~~~~g~~ggy~l~~~~~~it~~~v~~~l   83 (130)
T TIGR02944        29 AEIAEQTGLNAPTVSKILKQLSLAGIVTSKRGVEGGYTLARAPRDITVADIVKAV   83 (130)
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCcEEecCCCCCChhhcCCccccCHHHHHHHH
Confidence            5899999999999999999999999998876666777766655444455555554

The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.

>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein

Probab=93.05  E-value=0.26  Score=27.16  Aligned_cols=28  Identities=21%  Similarity=0.496  Sum_probs=26.0

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCcc
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALT   29 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~lt   29 (96)
                      .|||..++++.+.+-.-+..|++.|-+.
T Consensus        12 ~~la~~l~~s~~tv~~~l~~L~~~g~l~   39 (48)
T smart00419       12 QEIAELLGLTRETVSRTLKRLEKEGLIS   39 (48)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            5899999999999999999999999885

>PRK10870 transcriptional repressor MprA; Provisional

Probab=92.95  E-value=0.46  Score=34.35  Aligned_cols=55  Identities=11%  Similarity=0.137  Sum_probs=47.5

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .|||..++++.+.+-.-|..|++.|-+.=.-|   -|.++|++|++-...+.......
T Consensus        75 ~eLa~~l~l~~~tvsr~v~rLe~kGlV~R~~~~~DrR~~~v~LT~~G~~~~~~i~~~~  132 (176)
T PRK10870         75 SELSCALGSSRTNATRIADELEKRGWIERRESDNDRRCLHLQLTEKGHEFLREVLPPQ  132 (176)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHHHHHHH
Confidence            48999999999999899999999999997765   48899999999888887765544

>PF13551 HTH_29: Winged helix-turn helix

Probab=92.83  E-value=0.2  Score=31.61  Aligned_cols=54  Identities=15%  Similarity=0.376  Sum_probs=44.8

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeC--C-CceEE-EcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDD--R-GKFIY-ISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDD--R-GKfIy-Is~eEl~~Va~fI~~r   56 (96)
                      .++|..+|++.+-|-+-++...+.| +.|+.++  + |+.-- +|+++.+.|-+++.+.
T Consensus        16 ~~ia~~lg~s~~Tv~r~~~~~~~~G-~~~l~~~~~~~g~~~~~l~~~~~~~l~~~~~~~   73 (112)
T PF13551_consen   16 AEIARRLGISRRTVYRWLKRYREGG-IEGLLPRKPRGGRPRKRLSEEQRAQLIELLREN   73 (112)
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHccc-HHHHHhccccCCCCCCCCCHHHHHHHHHHHHHC
Confidence            5789999998888888888888777 8888884  3 55554 9999999999999987

>TIGR01764 excise DNA binding domain, excisionase family

Probab=92.79  E-value=0.61  Score=25.45  Aligned_cols=42  Identities=19%  Similarity=0.354  Sum_probs=32.7

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSV   49 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~V   49 (96)
                      +|+|..+|++..-    |..+.++|.|.++..  |+-..++.+|++..
T Consensus         5 ~e~a~~lgis~~t----i~~~~~~g~i~~~~~--g~~~~~~~~~l~~~   46 (49)
T TIGR01764         5 EEAAEYLGVSKDT----VYRLIHEGELPAYRV--GRHYRIPREDVDEY   46 (49)
T ss_pred             HHHHHHHCCCHHH----HHHHHHcCCCCeEEe--CCeEEEeHHHHHHH
Confidence            6889999997653    555678999999876  66778898887653

An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).

>PRK09391 fixK transcriptional regulator FixK; Provisional

Probab=92.45  E-value=0.44  Score=34.65  Aligned_cols=47  Identities=15%  Similarity=0.319  Sum_probs=33.9

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVA   50 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va   50 (96)
                      +|||...|++.+.+-.-+++|+++|.|.  ...+|++.-...+.|.+++
T Consensus       183 ~~IA~~lGisretlsR~L~~L~~~GlI~--~~~~~~i~I~D~~~L~~l~  229 (230)
T PRK09391        183 RDIADYLGLTIETVSRALSQLQDRGLIG--LSGARQIELRNRQALRNLD  229 (230)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCcEE--ecCCceEEEcCHHHHHHhh
Confidence            6899999998888777799999997652  2223455555677777665

>PF09743 DUF2042: Uncharacterized conserved protein (DUF2042); InterPro: IPR018611 The ubiquitin fold modifier 1 (Ufm1) is the most recently discovered ubiquitin-like modifier whose conjugation (ufmylation) system is conserved in multicellular organisms

Probab=92.35  E-value=0.65  Score=36.77  Aligned_cols=66  Identities=27%  Similarity=0.418  Sum_probs=56.6

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVE   81 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~   81 (96)
                      -|||...|+....|=.+++++.++..  ++.=-.|-  .||.+=++.+|.-|+.+           +++.|.||++||+.
T Consensus        74 ~dL~~~LnVd~~~ie~~~~~i~~~~~--~~~l~~ge--lit~~Yld~l~~Eine~-----------Lqe~G~vsi~eLa~  138 (272)
T PF09743_consen   74 VDLAQALNVDLDHIERRAQEIVKSDK--SLQLVQGE--LITDSYLDSLAEEINEK-----------LQESGQVSISELAK  138 (272)
T ss_pred             HHHHHhcCcCHHHHHHHHHHHHhCCC--cEEEECCE--EccHHHHHHHHHHHHHH-----------HHHcCeEeHHHHHH
Confidence            48999999988888888999998887  55555675  78999999999999998           78889999999986


Q ss_pred             h
Q psy11008         82 N   82 (96)
Q Consensus        82 ~   82 (96)
                      .
T Consensus       139 ~  139 (272)
T PF09743_consen  139 Q  139 (272)
T ss_pred             h
Confidence            5

Ufm1 is known to covalently attach with cellular protein(s) via a specific E1-activating enzyme (Uba5), an E2-conjugating enzyme (Ufc1), and a E3-ligating enzyme []. This entry represents E3 UFM1-protein ligase 1.

>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis

Probab=92.27  E-value=0.59  Score=28.43  Aligned_cols=43  Identities=14%  Similarity=0.226  Sum_probs=34.3

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQE   44 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~e   44 (96)
                      +|||...|++...|-+-++.|++.|-+.-.-...-.|-.+.+|
T Consensus        26 ~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y~a~~pe   68 (68)
T PF01978_consen   26 EEIAEELGISRSTVYRALKSLEEKGLVEREEGRPKVYRAVPPE   68 (68)
T ss_dssp             HHHHHHHTSSHHHHHHHHHHHHHTTSEEEEEECCEEEEEE-HH
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcCceEEEEEeCCC
Confidence            6899999999999999999999999998776554444445443

TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.

>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element

Probab=92.13  E-value=0.67  Score=29.18  Aligned_cols=49  Identities=12%  Similarity=0.216  Sum_probs=37.4

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFI   53 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI   53 (96)
                      .+||..++++...+-..++.|++.|-|.=   .+++.+++|+.-..-+..+.
T Consensus         3 ~ela~~l~is~stvs~~l~~L~~~glI~r---~~~~~~~lT~~g~~~~~~~~   51 (96)
T smart00529        3 SEIAERLNVSPPTVTQMLKKLEKDGLVEY---EPYRGITLTEKGRRLARRLL   51 (96)
T ss_pred             HHHHHHhCCChHHHHHHHHHHHHCCCEEE---cCCCceEechhHHHHHHHHH
Confidence            58999999999999999999999854432   34478999997655544443

iron dependent repressor

>PRK03902 manganese transport transcriptional regulator; Provisional

Probab=92.02  E-value=0.84  Score=31.43  Aligned_cols=51  Identities=16%  Similarity=0.184  Sum_probs=40.6

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .+||..++++...|-.-|+.|++.|-|.=   .+++.|++|+.-... |..+..+
T Consensus        26 ~ela~~l~vs~~svs~~l~~L~~~Gli~~---~~~~~i~LT~~G~~~-a~~~~~~   76 (142)
T PRK03902         26 SDIAEALSVHPSSVTKMVQKLDKDEYLIY---EKYRGLVLTPKGKKI-GKRLVYR   76 (142)
T ss_pred             HHHHHHhCCChhHHHHHHHHHHHCCCEEE---ecCceEEECHHHHHH-HHHHHHH
Confidence            58999999999999999999999987652   366789999997664 4445433

>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]

Probab=91.89  E-value=0.41  Score=38.09  Aligned_cols=53  Identities=23%  Similarity=0.410  Sum_probs=47.6

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIK   54 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~   54 (96)
                      .+||.+.+.+.|.+-.+|++|++.|-|+=-+-.+|.+|-||+.-++-+-+-..
T Consensus        23 ~ela~~l~~S~qta~R~l~~le~~~~I~R~~~~~Gq~i~iTekG~~~L~~~~~   75 (214)
T COG1339          23 SELAKRLGVSSQTAARKLKELEDEGYITRTISKRGQLITITEKGIDLLYKEYE   75 (214)
T ss_pred             HHHHHHhCcCcHHHHHHHHhhccCCcEEEEecCCCcEEEehHhHHHHHHHHHH
Confidence            58999999999999999999999999999999999999999988776655443

>PRK13918 CRP/FNR family transcriptional regulator; Provisional

Probab=91.75  E-value=0.7  Score=31.95  Aligned_cols=46  Identities=24%  Similarity=0.263  Sum_probs=34.5

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEE-cHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYI-SQEELNSVAT   51 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyI-s~eEl~~Va~   51 (96)
                      +|||...|++.+.|-.-+.+|+++|.|.    -.++.|.| ..+.|.++|.
T Consensus       153 ~~iA~~lG~tretvsR~l~~l~~~g~I~----~~~~~i~I~d~~~L~~~~~  199 (202)
T PRK13918        153 DELAAAVGSVRETVTKVIGELSREGYIR----SGYGKIQLLDLKGLEELAE  199 (202)
T ss_pred             HHHHHHhCccHHHHHHHHHHHHHCCCEE----cCCCEEEEECHHHHHHHHh
Confidence            6899999998888777799999988764    34344555 5777776653

>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B

Probab=91.65  E-value=0.23  Score=29.28  Aligned_cols=22  Identities=27%  Similarity=0.385  Sum_probs=19.6

Q ss_pred             hhhhhhhCCChHHHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQ   23 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~   23 (96)
                      .+||...|++...|..||+.|+
T Consensus        21 ~~la~~lglS~~~v~~Ri~rL~   42 (42)
T PF13404_consen   21 AELAEELGLSESTVRRRIRRLE   42 (42)
T ss_dssp             HHHHHHHTS-HHHHHHHHHHHH
T ss_pred             HHHHHHHCcCHHHHHHHHHHhC
Confidence            5899999999999999999986

...

>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family

Probab=91.49  E-value=0.46  Score=27.76  Aligned_cols=35  Identities=23%  Similarity=0.527  Sum_probs=28.5

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCce
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKF   38 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKf   38 (96)
                      .|||..+|++...+-.-++.|++.|.|.-.  .+|+|
T Consensus        29 ~ela~~~g~s~~tv~r~l~~L~~~g~i~~~--~~~~~   63 (67)
T cd00092          29 QEIADYLGLTRETVSRTLKELEEEGLISRR--GRGKY   63 (67)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCEEec--CCCeE
Confidence            589999999999999999999999887632  24554

>TIGR00122 birA_repr_reg BirA biotin operon repressor domain

Probab=91.39  E-value=0.51  Score=28.88  Aligned_cols=30  Identities=23%  Similarity=0.216  Sum_probs=26.3

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEE
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGV   31 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGV   31 (96)
                      .+||..|+++...+-.+|+.|++.|-..-.
T Consensus        17 ~eLa~~l~vS~~tv~~~l~~L~~~g~~i~~   46 (69)
T TIGR00122        17 EKLGEALGMSRTAVNKHIQTLREWGVDVLT   46 (69)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCeEEe
Confidence            589999999999999999999998875533

This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.

>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional

Probab=91.11  E-value=0.88  Score=37.86  Aligned_cols=74  Identities=20%  Similarity=0.278  Sum_probs=53.0

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVE   81 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~   81 (96)
                      .+||..++++.+.|..-|..|++.|-++= -|.|=+++++|++-...+..-....     .-+.. ++.+|.+++.||..
T Consensus        24 ~eLA~~l~l~~~tVt~~i~~Le~kGlV~~-~~~~~~~i~LTeeG~~~~~~g~pE~-----rl~~~-l~~~~g~~~~el~~   96 (489)
T PRK04172         24 EELAEKLGLPPEAVMRAAEWLEEKGLVKV-EERVEEVYVLTEEGKKYAEEGLPER-----RLLNA-LKDGGEVSLDELKE   96 (489)
T ss_pred             HHHHHHhCcCHHHHHHHHHHHHhCCCEEE-EeeeEEEEEECHHHHHHHHhcCHHH-----HHHHh-hHhcCCcCHHHHHH
Confidence            58999999999999999999999998874 4667799999998766555433322     22222 33345577777665


Q ss_pred             h
Q psy11008         82 N   82 (96)
Q Consensus        82 ~   82 (96)
                      .
T Consensus        97 ~   97 (489)
T PRK04172         97 A   97 (489)
T ss_pred             h
Confidence            3

>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A

Probab=90.98  E-value=0.39  Score=27.49  Aligned_cols=27  Identities=19%  Similarity=0.363  Sum_probs=24.2

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCc
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGAL   28 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~l   28 (96)
                      .|||..+|++..-+-.++++|++.|-|
T Consensus        21 ~ela~~~~is~~tv~~~l~~L~~~g~I   47 (48)
T PF13412_consen   21 KELAEKLGISRSTVNRYLKKLEEKGLI   47 (48)
T ss_dssp             HHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHHCcCc
Confidence            589999999999999999999999976

...

>PF13518 HTH_28: Helix-turn-helix domain

Probab=90.94  E-value=0.26  Score=27.87  Aligned_cols=35  Identities=17%  Similarity=0.381  Sum_probs=26.9

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCc
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGK   37 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGK   37 (96)
                      .++|.+||++...|-.=++..++.| +.|+.+.+|+
T Consensus        16 ~~~a~~~gis~~tv~~w~~~y~~~G-~~~l~~~~~r   50 (52)
T PF13518_consen   16 REIAREFGISRSTVYRWIKRYREGG-IEGLKPKKRR   50 (52)
T ss_pred             HHHHHHHCCCHhHHHHHHHHHHhcC-HHHhccCCCC
Confidence            5799999997766666677777766 7899887663

>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria

Probab=90.84  E-value=0.36  Score=30.74  Aligned_cols=28  Identities=21%  Similarity=0.438  Sum_probs=25.2

Q ss_pred             hhhhhhhCCC-hHHHHHHHHHHHHcCCcc
Q psy11008          2 EDLAALFRMK-TQSVIDRIVELQKTGALT   29 (96)
Q Consensus         2 edLAa~F~lk-tq~vI~RI~eL~~~g~lt   29 (96)
                      .|||..||++ +..|-..++.|++.|.|.
T Consensus        29 rEIa~~~g~~S~~tv~~~L~~Le~kG~I~   57 (65)
T PF01726_consen   29 REIAEALGLKSTSTVQRHLKALERKGYIR   57 (65)
T ss_dssp             HHHHHHHTSSSHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHhCCCChHHHHHHHHHHHHCcCcc
Confidence            5899999998 888889999999999875

The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.

>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif

Probab=90.65  E-value=0.22  Score=30.98  Aligned_cols=33  Identities=21%  Similarity=0.291  Sum_probs=27.1

Q ss_pred             ChhhhhhhCCChHHHHHHHHHHHHcCCccEEee
Q psy11008          1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVID   33 (96)
Q Consensus         1 ledLAa~F~lktq~vI~RI~eL~~~g~ltGViD   33 (96)
                      +.|||.+|+++.+.+-.-|..|+..|.|-=+-+
T Consensus        17 ~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~~~   49 (69)
T PF09012_consen   17 LAELAREFGISPEAVEAMLEQLIRKGYIRKVDM   49 (69)
T ss_dssp             HHHHHHHTT--HHHHHHHHHHHHCCTSCEEEEE
T ss_pred             HHHHHHHHCcCHHHHHHHHHHHHHCCcEEEecC
Confidence            368999999999999999999999999875544

FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=90.64  E-value=1.4  Score=27.30  Aligned_cols=53  Identities=13%  Similarity=0.186  Sum_probs=39.3

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .|||.+++++...+-..++.|++.|-|.-  +..++...+++.=++--..++...
T Consensus        24 ~~ia~~l~i~~~tv~r~l~~L~~~g~l~~--~~~~~~y~l~~~~~~~~~~~~~~~   76 (91)
T smart00346       24 AELAERLGLSKSTAHRLLNTLQELGYVEQ--DGQNGRYRLGPKVLELGQSYLSSL   76 (91)
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHHCCCeee--cCCCCceeecHHHHHHHHHHHhcC
Confidence            58999999999999999999999999975  333445567776555555555433

>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial

Probab=90.59  E-value=0.96  Score=30.83  Aligned_cols=44  Identities=14%  Similarity=0.132  Sum_probs=32.0

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEE-cHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYI-SQEELNSV   49 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyI-s~eEl~~V   49 (96)
                      +|||...|++.+.|-.-+++|+++|.|.-    +++.|.| ..+.|...
T Consensus       147 ~~iA~~lG~tretvsR~l~~l~~~g~I~~----~~~~i~I~d~~~L~~~  191 (193)
T TIGR03697       147 QAIAEAIGSTRVTITRLLGDLRKKKLISI----HKKKITVHDPIALGQR  191 (193)
T ss_pred             HHHHHHhCCcHHHHHHHHHHHHHCCCEEe----cCCEEEEeCHHHHHHh
Confidence            68999999977777666999999987643    3445666 46655543

Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.

>COG1846 MarR Transcriptional regulators [Transcription]

Probab=90.49  E-value=1  Score=27.92  Aligned_cols=53  Identities=13%  Similarity=0.308  Sum_probs=45.1

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELNSVATFIK   54 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~~Va~fI~   54 (96)
                      .+||...+++...+-.-|+.|++.|-+.=..|   -|.+++.+|++--..++....
T Consensus        40 ~~la~~l~i~~~~vt~~l~~Le~~glv~r~~~~~DrR~~~l~lT~~G~~~~~~~~~   95 (126)
T COG1846          40 KELAERLGLDRSTVTRLLKRLEDKGLIERLRDPEDRRAVLVRLTEKGRELLEQLLP   95 (126)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCeeecCCccccceeeEEECccHHHHHHHhcc
Confidence            48999999999999999999999999988777   478899999987766665544

>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator

Probab=90.37  E-value=1.1  Score=31.75  Aligned_cols=47  Identities=26%  Similarity=0.399  Sum_probs=35.4

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceE-EEcHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFI-YISQEELNSV   49 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfI-yIs~eEl~~V   49 (96)
                      .+||..||++..-|.+-|+.|+.+|-|. +.--+|-|| .++.+++..+
T Consensus        38 ~~La~~lgVSRtpVReAL~~L~~eGlv~-~~~~~G~~V~~~~~~~~~ei   85 (212)
T TIGR03338        38 SDIAARLGVSRGPVREAFRALEEAGLVR-NEKNRGVFVREISLAEADEI   85 (212)
T ss_pred             HHHHHHhCCChHHHHHHHHHHHHCCCEE-EecCCCeEEecCCHHHHHHH
Confidence            4799999999999999999999999876 233455554 3456665544

This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.

>COG3140 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=90.30  E-value=0.55  Score=31.10  Aligned_cols=48  Identities=29%  Similarity=0.389  Sum_probs=34.4

Q ss_pred             hhhCCC---hHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhhchhchhhhhh
Q psy11008          6 ALFRMK---TQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREELNSVAT   66 (96)
Q Consensus         6 a~F~lk---tq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~   66 (96)
                      ..++|+   .|.+++||++|.++|.-+|             |-+.-||+-|+++-..+-+.++.
T Consensus         4 ~lp~LtHeqQQ~AVE~Iq~lMaeGmSsG-------------EAIa~VA~elRe~hk~~~~~~~~   54 (60)
T COG3140           4 GLPSLTHEQQQKAVERIQELMAEGMSSG-------------EAIALVAQELRENHKGENRIVAR   54 (60)
T ss_pred             ccccccHHHHHHHHHHHHHHHHccccch-------------hHHHHHHHHHHHHhccccccccc
Confidence            344444   4789999999999998776             67888999998884333333333

>PRK10402 DNA-binding transcriptional activator YeiL; Provisional

Probab=90.04  E-value=1.3  Score=32.04  Aligned_cols=48  Identities=13%  Similarity=0.220  Sum_probs=36.8

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEE-cHHHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYI-SQEELNSVATFI   53 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyI-s~eEl~~Va~fI   53 (96)
                      +|||..+|++.+.+-.-+++|+++|.|    .-.|+-|+| ..+.|.++|.-+
T Consensus       173 ~~lA~~lG~sretvsR~L~~L~~~G~I----~~~~~~i~I~d~~~L~~~~~~~  221 (226)
T PRK10402        173 TQAAEYLGVSYRHLLYVLAQFIQDGYL----KKSKRGYLIKNRKQLSGLALEL  221 (226)
T ss_pred             HHHHHHHCCcHHHHHHHHHHHHHCCCE----EeeCCEEEEeCHHHHHHHHHHh
Confidence            689999999888887779999999765    434555666 567777776654

>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif

Probab=89.89  E-value=0.21  Score=31.05  Aligned_cols=22  Identities=27%  Similarity=0.668  Sum_probs=15.1

Q ss_pred             hhhhhhccccceeHHHHHHhcc
Q psy11008         63 SVATFIKQKGRVSVSELVENSN   84 (96)
Q Consensus        63 ~~~~~~~~~GRVsi~eL~~~sN   84 (96)
                      .+.+||+++|++|+.||+..-|
T Consensus         4 ~i~~~l~~~~~~S~~eLa~~~~   25 (69)
T PF09012_consen    4 EIRDYLRERGRVSLAELAREFG   25 (69)
T ss_dssp             HHHHHHHHS-SEEHHHHHHHTT
T ss_pred             HHHHHHHHcCCcCHHHHHHHHC
Confidence            3445555559999999998765

FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.

>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators

Probab=89.61  E-value=2.1  Score=25.77  Aligned_cols=64  Identities=17%  Similarity=0.232  Sum_probs=45.0

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVE   81 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~   81 (96)
                      .|+|..+|+++.-    |.-.++.|.+... .+.|.+=+.|++++..+.....-+             +.| +|+.++.+
T Consensus         4 ~evA~~~gvs~~t----lR~~~~~g~l~~~-~~~~g~R~y~~~~l~~l~~i~~l~-------------~~g-~~l~~i~~   64 (67)
T cd04764           4 KEVSEIIGVKPHT----LRYYEKEFNLYIP-RTENGRRYYTDEDIELLKKIKTLL-------------EKG-LSIKEIKE   64 (67)
T ss_pred             HHHHHHHCcCHHH----HHHHHHhcCCCCC-CCCCCceeeCHHHHHHHHHHHHHH-------------HCC-CCHHHHHH
Confidence            5899999998763    4466777777743 566777788999999877655444             224 78888776


Q ss_pred             hcc
Q psy11008         82 NSN   84 (96)
Q Consensus        82 ~sN   84 (96)
                      ..|
T Consensus        65 ~l~   67 (67)
T cd04764          65 ILN   67 (67)
T ss_pred             HhC
Confidence            543

Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.

>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional

Probab=89.60  E-value=1.8  Score=30.44  Aligned_cols=68  Identities=16%  Similarity=0.139  Sum_probs=47.6

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhhchhchhhhhhhhc
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREELNSVATFIK   69 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~   69 (96)
                      -|||..|+++..-+=.-++.|.+.|-++.--+-|=.|.++.++-..-++.++++.-...+..+..+++
T Consensus        34 ~ela~~l~lsqstvS~HL~~L~~AGLV~~~r~Gr~~~Y~l~~~~~~~~~~~~~~~w~~~~~~l~~~l~  101 (117)
T PRK10141         34 CDLCTALDQSQPKISRHLALLRESGLLLDRKQGKWVHYRLSPHIPAWAAKIIEQAWLCEQEDVQAIVR  101 (117)
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCceEEEEEcCEEEEEECchHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            47999999977777778999999999999888777777777654444555455443334444444443

>PF13730 HTH_36: Helix-turn-helix domain

Probab=89.60  E-value=0.56  Score=27.24  Aligned_cols=27  Identities=30%  Similarity=0.406  Sum_probs=24.5

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCc
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGAL   28 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~l   28 (96)
                      +.||...|++...|..-|++|++.|-|
T Consensus        29 ~~la~~~g~s~~Tv~~~i~~L~~~G~I   55 (55)
T PF13730_consen   29 ETLAKDLGVSRRTVQRAIKELEEKGLI   55 (55)
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCcCC
Confidence            679999999999999999999999864

>PF12728 HTH_17: Helix-turn-helix domain

Probab=89.44  E-value=1.8  Score=24.88  Aligned_cols=42  Identities=14%  Similarity=0.275  Sum_probs=34.1

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSV   49 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~V   49 (96)
                      +|+|..+|++.+.    +..+...|.|..+-  .|+-++++.+++++.
T Consensus         5 ~e~a~~l~is~~t----v~~~~~~g~i~~~~--~g~~~~~~~~~l~~~   46 (51)
T PF12728_consen    5 KEAAELLGISRST----VYRWIRQGKIPPFK--IGRKWRIPKSDLDRW   46 (51)
T ss_pred             HHHHHHHCcCHHH----HHHHHHcCCCCeEE--eCCEEEEeHHHHHHH
Confidence            6899999997765    45677899999995  788899999987753

>PRK13777 transcriptional regulator Hpr; Provisional

Probab=89.41  E-value=1.2  Score=33.35  Aligned_cols=54  Identities=17%  Similarity=0.243  Sum_probs=43.8

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEe---eCCCceEEEcHHHHHHHHHHHHh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI---DDRGKFIYISQEELNSVATFIKQ   55 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi---DDRGKfIyIs~eEl~~Va~fI~~   55 (96)
                      .|||...+++...+..-|+.|++.|-|.=..   |-|-++|++|++-...+.+....
T Consensus        63 ~eLa~~l~l~~sTvtr~l~rLE~kGlI~R~~~~~DrR~~~I~LTekG~~l~~~l~~~  119 (185)
T PRK13777         63 SEIAKFGVMHVSTAFNFSKKLEERGYLTFSKKEDDKRNTYIELTEKGEELLLETMEE  119 (185)
T ss_pred             HHHHHHHCCCHhhHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHHHHHH
Confidence            4799999998777888899999999998554   56999999999877766655443

>PF12419 DUF3670: SNF2 Helicase protein ; InterPro: IPR022138 This domain family is found in bacteria, archaea and eukaryotes, and is approximately 140 amino acids in length

Probab=89.36  E-value=0.73  Score=32.57  Aligned_cols=50  Identities=16%  Similarity=0.379  Sum_probs=38.3

Q ss_pred             HHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHHHh
Q psy11008         19 IVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVEN   82 (96)
Q Consensus        19 I~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~~   82 (96)
                      +++|.+.+  .|++==||+||++.++++.++.+|+++++            ..+++|..|+.+.
T Consensus        89 f~~L~~~~--~~LV~~rg~WV~ld~~~l~~~~~~~~~~~------------~~~~lt~~e~Lr~  138 (141)
T PF12419_consen   89 FEQLVEQK--RPLVRFRGRWVELDPEELRRALAFLEKAP------------KGEKLTLAEALRA  138 (141)
T ss_pred             HHHHHHcC--CCeEEECCEEEEECHHHHHHHHHHHHhcc------------ccCCCCHHHHHHH
Confidence            44555544  47888899999999999999999999983            1125888887654

The family is found in association with PF00271 from PFAM, PF00176 from PFAM. Most of the proteins in this family are annotated as SNF2 helicases but there is little accompanying literature to confirm this.

>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism

Probab=89.00  E-value=0.5  Score=28.75  Aligned_cols=38  Identities=18%  Similarity=0.353  Sum_probs=29.2

Q ss_pred             ChhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEE
Q psy11008          1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYI   41 (96)
Q Consensus         1 ledLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyI   41 (96)
                      ++|||.+|+++..-+-.=++.|++.|.+.   =-+|-..++
T Consensus        17 ~~ela~~~~VS~~TiRRDl~~L~~~g~i~---r~~GG~~~~   54 (57)
T PF08220_consen   17 VKELAEEFGVSEMTIRRDLNKLEKQGLIK---RTHGGAVLN   54 (57)
T ss_pred             HHHHHHHHCcCHHHHHHHHHHHHHCCCEE---EEcCEEEeC
Confidence            36899999999888888899999999843   234544444

This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular

>smart00422 HTH_MERR helix_turn_helix, mercury resistance

Probab=88.87  E-value=2.2  Score=25.33  Aligned_cols=51  Identities=18%  Similarity=0.299  Sum_probs=37.8

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .|+|..+|++.+.+    ...++.|.+.....+.|.+-+.|++++..+.....-|
T Consensus         4 ~eva~~~gvs~~tl----r~~~~~gli~~~~~~~~g~r~y~~~dl~~l~~i~~lr   54 (70)
T smart00422        4 GEVAKLAGVSVRTL----RYYERIGLLPPPIRTEGGYRLYSDEDLERLRFIKRLK   54 (70)
T ss_pred             HHHHHHHCcCHHHH----HHHHHCCCCCCCccCCCCCEecCHHHHHHHHHHHHHH
Confidence            57899999976544    4557799999874444445578999999887776665

>PRK09392 ftrB transcriptional activator FtrB; Provisional

Probab=88.85  E-value=0.9  Score=32.47  Aligned_cols=46  Identities=20%  Similarity=0.257  Sum_probs=33.0

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEE-cHHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYI-SQEELNSVATF   52 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyI-s~eEl~~Va~f   52 (96)
                      +|||...|++.+.+-.-+++|+++| +  .. .+| .|.| ..+.|...|.+
T Consensus       177 ~~iA~~lG~tretvsR~l~~L~~~g-l--~~-~~~-~i~I~d~~~L~~~~~~  223 (236)
T PRK09392        177 RVLASYLGMTPENLSRAFAALASHG-V--HV-DGS-AVTITDPAGLARFAKP  223 (236)
T ss_pred             HHHHHHhCCChhHHHHHHHHHHhCC-e--Ee-eCC-EEEEcCHHHHHHhhcc
Confidence            5899999997776555589999999 5  33 345 5666 56777766654

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor

Probab=88.51  E-value=0.82  Score=25.11  Aligned_cols=28  Identities=29%  Similarity=0.483  Sum_probs=25.4

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCcc
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALT   29 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~lt   29 (96)
                      .+||..|+++...+-..|+.|++.|.|.
T Consensus        18 ~~l~~~l~~s~~tv~~~l~~L~~~g~i~   45 (53)
T smart00420       18 EELAELLGVSEMTIRRDLNKLEEQGLLT   45 (53)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            5899999999999999999999998764

>PRK10512 selenocysteinyl-tRNA-specific translation factor; Provisional

Probab=88.31  E-value=2.4  Score=36.70  Aligned_cols=67  Identities=15%  Similarity=0.240  Sum_probs=55.2

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVE   81 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~   81 (96)
                      +||+..+++....+.+-+..|.++|.+.-|-+    .+|++.+-++.+.+.+++.           ++..|.++++++-+
T Consensus       510 ~~~~~~l~~~~~~~~~~l~~l~~~g~lv~l~~----~~~~~~~~~~~~~~~~~~~-----------~~~~~~~~~~~~r~  574 (614)
T PRK10512        510 RDLAKETGTDEQAMRLTLRQAAQQGIITAIVK----DRYYRNDRIVQFANMIREL-----------DQECGSTCAADFRD  574 (614)
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHHCCCEEEecC----CEEECHHHHHHHHHHHHHH-----------HhhCCcEeHHHHHH
Confidence            68899999999998999999999999998876    5899999888776666554           45569999988876


Q ss_pred             hc
Q psy11008         82 NS   83 (96)
Q Consensus        82 ~s   83 (96)
                      ..
T Consensus       575 ~~  576 (614)
T PRK10512        575 RL  576 (614)
T ss_pred             Hh
Confidence            54

>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets

Probab=88.25  E-value=1.2  Score=25.89  Aligned_cols=34  Identities=26%  Similarity=0.418  Sum_probs=26.6

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCc
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGK   37 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGK   37 (96)
                      ++||..|+++..-+.+-|++|.+.|  .-|.-.+|+
T Consensus        19 ~eLa~~l~vS~rTi~~~i~~L~~~~--~~I~~~~~~   52 (55)
T PF08279_consen   19 KELAEELGVSRRTIRRDIKELREWG--IPIESKRGK   52 (55)
T ss_dssp             HHHHHHCTS-HHHHHHHHHHHHHTT---EEEEETTT
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHHCC--CeEEeeCCC
Confidence            6899999999999999999999999  334445554

The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....

>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional

Probab=88.21  E-value=1.5  Score=31.60  Aligned_cols=48  Identities=21%  Similarity=0.339  Sum_probs=35.7

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEE-EcHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIY-ISQEELNSVA   50 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIy-Is~eEl~~Va   50 (96)
                      ++||.+||++...|.+-|+.|+.+|-++ +.-.+|-|+- ++.+++..+.
T Consensus        38 ~~La~~lgVSRtpVREAL~~L~~eGLV~-~~~~~g~~v~~~~~~~~~ei~   86 (221)
T PRK11414         38 KNLAEQLGMSITPVREALLRLVSVNALS-VAPAQAFTVPEVSKRQLDEIN   86 (221)
T ss_pred             HHHHHHHCCCchhHHHHHHHHHHCCCEE-ecCCCceeecCCCHHHHHHHH
Confidence            4799999999999999999999999886 3344564442 4555554443

>PRK00215 LexA repressor; Validated

Probab=87.30  E-value=0.86  Score=32.80  Aligned_cols=42  Identities=12%  Similarity=0.256  Sum_probs=34.7

Q ss_pred             hhhhhhhCC-ChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHH
Q psy11008          2 EDLAALFRM-KTQSVIDRIVELQKTGALTGVIDDRGKFIYISQE   44 (96)
Q Consensus         2 edLAa~F~l-ktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~e   44 (96)
                      .|||..+|+ +...+-.+|+.|++.|.|...-++ ++-+.++++
T Consensus        27 ~ela~~~~~~~~~tv~~~l~~L~~~g~i~~~~~~-~r~~~l~~~   69 (205)
T PRK00215         27 REIADALGLRSPSAVHEHLKALERKGFIRRDPGR-SRAIEVAAP   69 (205)
T ss_pred             HHHHHHhCCCChHHHHHHHHHHHHCCCEEeCCCC-cceEEeccc
Confidence            589999999 677777889999999999887655 677788554

>TIGR00498 lexA SOS regulatory protein LexA

Probab=87.18  E-value=1.1  Score=32.14  Aligned_cols=41  Identities=12%  Similarity=0.261  Sum_probs=32.7

Q ss_pred             hhhhhhhCCC-hHHHHHHHHHHHHcCCccEEeeCCCceEEEcH
Q psy11008          2 EDLAALFRMK-TQSVIDRIVELQKTGALTGVIDDRGKFIYISQ   43 (96)
Q Consensus         2 edLAa~F~lk-tq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~   43 (96)
                      .|||..+|++ ...|-.+|+.|++.|-|... +.+.+.+.+..
T Consensus        29 ~ela~~~~~~s~~tv~~~l~~L~~~g~i~~~-~~~~~~~~~~~   70 (199)
T TIGR00498        29 REIARAVGLRSPSAAEEHLKALERKGYIERD-PGKPRAIRILD   70 (199)
T ss_pred             HHHHHHhCCCChHHHHHHHHHHHHCCCEecC-CCCCCeEEeCC
Confidence            4899999999 89999999999999998875 33333566653

LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.

>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B

Probab=86.64  E-value=4.3  Score=24.13  Aligned_cols=50  Identities=20%  Similarity=0.365  Sum_probs=37.9

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .|+|..+|++..    .|...++.|.|.-.-+++|. -|.|++.+..+.....-+
T Consensus         4 ~eva~~~gvs~~----tlr~y~~~gll~~~~~~~g~-r~y~~~dv~~l~~i~~l~   53 (69)
T PF13411_consen    4 KEVAKLLGVSPS----TLRYYEREGLLPPPRDENGY-RYYSEEDVERLREIKELR   53 (69)
T ss_dssp             HHHHHHTTTTHH----HHHHHHHTTSSTTBESTTSS-EEE-HHHHHHHHHHHHHH
T ss_pred             HHHHHHHCcCHH----HHHHHHHhcCcccccccCce-eeccHHHHHHHHHHHHHH
Confidence            589999999764    46677889999888855555 788999999887665555

>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B

Probab=86.63  E-value=1.8  Score=26.01  Aligned_cols=32  Identities=16%  Similarity=0.254  Sum_probs=27.8

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID   33 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD   33 (96)
                      .+||..+|++.+.+-..++.|++.|-|+.+-+
T Consensus        28 ~ela~~l~~~~~t~s~hL~~L~~aGli~~~~~   59 (61)
T PF12840_consen   28 SELAEELGISQSTVSYHLKKLEEAGLIEVERE   59 (61)
T ss_dssp             HHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCeEEecc
Confidence            58999999999999999999999999887644

...

>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family

Probab=86.61  E-value=2  Score=30.08  Aligned_cols=77  Identities=25%  Similarity=0.320  Sum_probs=46.5

Q ss_pred             hhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEE---EcHHHHH-HHHHHHHhh--chhchhhhhhhhccccceeHH
Q psy11008          4 LAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIY---ISQEELN-SVATFIKQR--GREELNSVATFIKQKGRVSVS   77 (96)
Q Consensus         4 LAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIy---Is~eEl~-~Va~fI~~r--gr~~~~~~~~~~~~~GRVsi~   77 (96)
                      |+..++++...+.--|..|.+.|.|.=.-+.| .|.|   ||++|+. ..++.+-.+  |..--+-|+.|+.. ..+|-.
T Consensus        28 l~~~~~~~~tTv~T~L~rL~~KG~v~~~k~gr-~~~Y~p~vs~ee~~~~~~~~~~~~~f~gs~~~ll~~l~~~-~~ls~e  105 (130)
T TIGR02698        28 LAEKKDWSDSTIKTLLGRLVDKGCLTTEKEGR-KFIYTALVSEDEAVENAAQELFSRICSRKVGAVIADLIEE-SPLSQT  105 (130)
T ss_pred             HhhccCCcHHHHHHHHHHHHHCCceeeecCCC-cEEEEecCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHhc-CCCCHH
Confidence            55556788788888899999999986544445 4555   7889883 333333222  11112335566653 567776


Q ss_pred             HHHHh
Q psy11008         78 ELVEN   82 (96)
Q Consensus        78 eL~~~   82 (96)
                      ||.+.
T Consensus       106 ele~L  110 (130)
T TIGR02698       106 DIEKL  110 (130)
T ss_pred             HHHHH
Confidence            66543

This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.

>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities

Probab=86.25  E-value=1.5  Score=26.43  Aligned_cols=36  Identities=22%  Similarity=0.431  Sum_probs=28.4

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCce
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKF   38 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKf   38 (96)
                      .+||..|+++...+.+-+..|+++|.+.- ..-+|-|
T Consensus        28 ~~la~~~~vsr~tvr~al~~L~~~g~i~~-~~~~G~~   63 (64)
T PF00392_consen   28 RELAERYGVSRTTVREALRRLEAEGLIER-RPGRGTF   63 (64)
T ss_dssp             HHHHHHHTS-HHHHHHHHHHHHHTTSEEE-ETTTEEE
T ss_pred             HHHHHHhccCCcHHHHHHHHHHHCCcEEE-ECCceEE
Confidence            47999999999999999999999998863 3444444

The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....

>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR

Probab=86.25  E-value=1.5  Score=31.92  Aligned_cols=43  Identities=19%  Similarity=0.255  Sum_probs=33.8

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEe--e--CCC-ceEEEcHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI--D--DRG-KFIYISQE   44 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi--D--DRG-KfIyIs~e   44 (96)
                      .+||..++++...|-..++.|++.|-+.-.-  +  +|- +.+++|+.
T Consensus        19 ~eLA~~lgis~~tV~~~L~~Le~~GlV~r~~~~~~~gRp~~~y~LT~~   66 (203)
T TIGR02702        19 AALAEALAISPQAVRRHLKDLETEGLIEYEAVVQGMGRPQYHYQLSRQ   66 (203)
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCeEEeecccCCCCCceEEEECcc
Confidence            5899999999999999999999999997663  2  222 34577865

All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.

>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B

Probab=86.02  E-value=2.2  Score=24.70  Aligned_cols=33  Identities=21%  Similarity=0.284  Sum_probs=28.0

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeC
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDD   34 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDD   34 (96)
                      .|||..++++.+.+-.-|+.|++.|-+.=.-|.
T Consensus        25 ~~la~~l~~~~~~vs~~v~~L~~~Glv~r~~~~   57 (62)
T PF12802_consen   25 SELAERLGISKSTVSRIVKRLEKKGLVERERDP   57 (62)
T ss_dssp             HHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE-S
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCC
Confidence            589999999999999999999999999877663

...

>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY

Probab=85.62  E-value=1.3  Score=35.83  Aligned_cols=41  Identities=12%  Similarity=0.333  Sum_probs=33.8

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEe-eCCCceEEEc
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI-DDRGKFIYIS   42 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi-DDRGKfIyIs   42 (96)
                      .+||..+|++...|.+|++.|++.|-|.+.= --+|-||-.-
T Consensus       202 ~eLAerlGVSRs~ireAlrkLE~aGvIe~r~LG~kGt~V~~l  243 (251)
T TIGR02787       202 SKIADRVGITRSVIVNALRKLESAGVIESRSLGMKGTYIKVL  243 (251)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCCCCccEeCCC
Confidence            4799999999999999999999999888765 2257777443

This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.

>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins

Probab=85.43  E-value=2.9  Score=22.40  Aligned_cols=44  Identities=18%  Similarity=0.317  Sum_probs=31.4

Q ss_pred             ChhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHH
Q psy11008          1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSV   49 (96)
Q Consensus         1 ledLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~V   49 (96)
                      +.|+|..+|++...+-    .+.++|.+...-.+ |+..+++.+|+..+
T Consensus         3 ~~e~a~~lgvs~~tl~----~~~~~g~~~~~~~~-~~~~~~~~~ei~~~   46 (49)
T cd04762           3 TKEAAELLGVSPSTLR----RWVKEGKLKAIRTP-GGHRRFPEEDLERL   46 (49)
T ss_pred             HHHHHHHHCcCHHHHH----HHHHcCCCCceeCC-CCceecCHHHHHHH
Confidence            3689999999766544    45567888876544 46667899988765

Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.

>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR

Probab=85.33  E-value=1.8  Score=31.42  Aligned_cols=37  Identities=16%  Similarity=0.323  Sum_probs=31.1

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceE
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFI   39 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfI   39 (96)
                      .+||..||++..-|.+-++.|+.+|-|+ +.--+|-|+
T Consensus        34 ~~La~~lgVSRtpVREAL~~Le~eGlV~-~~~~~G~~V   70 (235)
T TIGR02812        34 RELSELIGVTRTTLREVLQRLARDGWLT-IQHGKPTKV   70 (235)
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCEE-EeCCCccEe
Confidence            3799999999999999999999999887 344566555

Members of this family are FadR, a transcriptional regulator of fatty acid metabolism, including both biosynthesis and beta-oxidation. It is found exclusively in a subset of Gammaproteobacteria, with strictly one copy per genome. It has an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR from this family heterologously expressed in Escherichia coli show differences in regulatory response and fatty acid binding profiles. The family is nevertheless designated equivalog, as all member proteins have at least nominally the same function.

>PRK09954 putative kinase; Provisional

Probab=84.82  E-value=2.4  Score=32.72  Aligned_cols=38  Identities=18%  Similarity=0.468  Sum_probs=29.9

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCcc--EEeeCCCceE
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALT--GVIDDRGKFI   39 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~lt--GViDDRGKfI   39 (96)
                      .+||..++++..-|-.||+.|++.|.+.  |.+-+..+||
T Consensus        21 ~~la~~l~~s~~~v~~~i~~L~~~g~i~~~~~~l~~~~~v   60 (362)
T PRK09954         21 NEIADILQISRSRVAAHIMDLMRKGRIKGKGYILTEQEYC   60 (362)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCcCCcEEEEcCCccE
Confidence            5899999999999999999999999884  3333444444

>TIGR02051 MerR Hg(II)-responsive transcriptional regulator

Probab=84.67  E-value=4.1  Score=27.96  Aligned_cols=48  Identities=19%  Similarity=0.304  Sum_probs=38.2

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIK   54 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~   54 (96)
                      .++|..+|+++.-+    .--++.|-|.-..++.|.|-|-|++.+..+. ||+
T Consensus         3 ~e~a~~~gvs~~tl----R~Ye~~GLl~~~~r~~~g~R~Y~~~~l~~l~-~I~   50 (124)
T TIGR02051         3 GELAKAAGVNVETI----RYYERKGLLPEPDRPEGGYRRYPEETVKRLR-FIK   50 (124)
T ss_pred             HHHHHHHCcCHHHH----HHHHHCCCCCCCccCCCCCEeECHHHHHHHH-HHH
Confidence            58999999977643    5668999998666777888888999998874 554

This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.

>PF01402 RHH_1: Ribbon-helix-helix protein, copG family; InterPro: IPR002145 CopG, also known as RepA, is responsible for the regulation of plasmid copy number

Probab=84.34  E-value=2.2  Score=23.41  Aligned_cols=28  Identities=29%  Similarity=0.383  Sum_probs=24.4

Q ss_pred             EEEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHHHh
Q psy11008         39 IYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVEN   82 (96)
Q Consensus        39 IyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~~   82 (96)
                      |+++++.++.+-+..++.               | .|.+++++.
T Consensus         4 i~l~~~~~~~l~~~a~~~---------------g-~s~s~~ir~   31 (39)
T PF01402_consen    4 IRLPDELYERLDELAKEL---------------G-RSRSELIRE   31 (39)
T ss_dssp             EEEEHHHHHHHHHHHHHH---------------T-SSHHHHHHH
T ss_pred             EEeCHHHHHHHHHHHHHH---------------C-cCHHHHHHH
Confidence            789999999999999999               6 888888764

It binds to the repAB promoter and controls synthesis of the plasmid replication initiator protein RepB. Many bacterial transcription regulation proteins bind DNA through a 'helix-turn-helix' motif, nevertheless CopG displays a fully defined HTH-motif structure that is involved not in DNA-binding, but in the maintenance of the intrinsic dimeric functional structure and cooperativity [, ].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2BJ3_B 2BJ8_A 2BJ1_A 2BJ9_A 2BJ7_B 1EA4_L 2CPG_C 1B01_B 2BA3_A 2K9I_B ....

>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional

Probab=83.96  E-value=3.7  Score=29.19  Aligned_cols=45  Identities=24%  Similarity=0.476  Sum_probs=33.9

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEc-HHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYIS-QEELNSVA   50 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs-~eEl~~Va   50 (96)
                      ++||...|++.+.+-.-+++|+++|.|    .-.++.|.|. .+.|.++|
T Consensus       188 ~~iA~~lG~sr~tvsR~l~~l~~~g~I----~~~~~~i~i~d~~~L~~~~  233 (235)
T PRK11161        188 GDIGNYLGLTVETISRLLGRFQKSGML----AVKGKYITIENNDALAQLA  233 (235)
T ss_pred             HHHHHHhCCcHHHHHHHHHHHHHCCCE----EecCCEEEEcCHHHHHHHh
Confidence            689999999777776668999998754    5555667774 66676665

>PRK11050 manganese transport regulator MntR; Provisional

Probab=83.85  E-value=5.2  Score=28.35  Aligned_cols=51  Identities=18%  Similarity=0.255  Sum_probs=38.2

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .|||..|+++...+-..++.|++.|.|.   ..+++-+++|+.-.. ++..+.++
T Consensus        55 ~eLA~~l~is~stVsr~l~~Le~~GlI~---r~~~~~v~LT~~G~~-l~~~~~~~  105 (152)
T PRK11050         55 VDIAARLGVSQPTVAKMLKRLARDGLVE---MRPYRGVFLTPEGEK-LAQESRER  105 (152)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCEE---EecCCceEECchHHH-HHHHHHHH
Confidence            5899999999999999999999997553   234567899986654 34444443

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

Probab=83.76  E-value=2  Score=24.72  Aligned_cols=27  Identities=19%  Similarity=0.445  Sum_probs=22.6

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCc
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGAL   28 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~l   28 (96)
                      +|||...|+..+-|-.-+..|+++|-|
T Consensus         6 ~diA~~lG~t~ETVSR~l~~l~~~glI   32 (32)
T PF00325_consen    6 QDIADYLGLTRETVSRILKKLERQGLI   32 (32)
T ss_dssp             HHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred             HHHHHHhCCcHHHHHHHHHHHHHcCCC
Confidence            699999999888887889999999864

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

>TIGR00373 conserved hypothetical protein TIGR00373

Probab=83.69  E-value=4.3  Score=29.43  Aligned_cols=52  Identities=21%  Similarity=0.337  Sum_probs=38.7

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEe---eCCCceEE---EcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI---DDRGKFIY---ISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi---DDRGKfIy---Is~eEl~~Va~fI~~r   56 (96)
                      ||||...||+..+|-.-+..|.+.|-++-.-   ++.|.+-|   |..++   +-+.|+.+
T Consensus        32 EeLa~~Lgi~~~~VRk~L~~L~e~~Lv~~~r~r~~~~gw~~Y~w~i~~~~---i~d~Ik~~   89 (158)
T TIGR00373        32 EEISLELGIKLNEVRKALYALYDAGLADYKRRKDDETGWYEYTWRINYEK---ALDVLKRK   89 (158)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCceeeeeeecCCCcEEEEEEeCHHH---HHHHHHHH
Confidence            7999999999999999999999999985433   35576654   55554   44445444

This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.

>PF14493 HTH_40: Helix-turn-helix domain

Probab=83.57  E-value=3.6  Score=26.68  Aligned_cols=66  Identities=18%  Similarity=0.340  Sum_probs=51.4

Q ss_pred             ChhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHH
Q psy11008          1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELV   80 (96)
Q Consensus         1 ledLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~   80 (96)
                      ++++|..-+++..-+.+-+.++...|.-..+    ..|  +++++++.+.+.+++-               |..+++++-
T Consensus        16 i~eIA~~R~L~~sTI~~HL~~~~~~g~~~~~----~~~--l~~e~~~~I~~~~~~~---------------~~~~lk~i~   74 (91)
T PF14493_consen   16 IEEIAKIRGLKESTIYGHLAELIESGEPLDI----EEL--LSEEEIKQIEDAIEKL---------------GSEKLKPIK   74 (91)
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHhCCCCCH----HHh--CCHHHHHHHHHHHHHc---------------CcccHHHHH
Confidence            4799999999999999999999999883222    133  8999999999999888               555666666


Q ss_pred             Hhcccce
Q psy11008         81 ENSNQLV   87 (96)
Q Consensus        81 ~~sN~lI   87 (96)
                      +.++.-+
T Consensus        75 e~l~~~~   81 (91)
T PF14493_consen   75 EALPGDY   81 (91)
T ss_pred             HHCCCCC
Confidence            6666433

>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family

Probab=83.42  E-value=1.7  Score=26.96  Aligned_cols=28  Identities=18%  Similarity=0.364  Sum_probs=24.7

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCcc
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALT   29 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~lt   29 (96)
                      .|||..++++...|-+-++.|++.|-+.
T Consensus        26 ~~iA~~L~vs~~tvt~ml~~L~~~GlV~   53 (60)
T PF01325_consen   26 KDIAERLGVSPPTVTEMLKRLAEKGLVE   53 (60)
T ss_dssp             HHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHCCChHHHHHHHHHHHHCCCEE
Confidence            4899999999999999999999999764

The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....

>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein

Probab=83.26  E-value=2.4  Score=24.56  Aligned_cols=22  Identities=23%  Similarity=0.277  Sum_probs=16.7

Q ss_pred             ChhhhhhhCCChHHHHHHHHHH
Q psy11008          1 MEDLAALFRMKTQSVIDRIVEL   22 (96)
Q Consensus         1 ledLAa~F~lktq~vI~RI~eL   22 (96)
                      +++||.++|++...+-..+.+.
T Consensus         4 ~~~la~~~~~s~~~l~~~f~~~   25 (84)
T smart00342        4 LEDLAEALGMSPRHLQRLFKKE   25 (84)
T ss_pred             HHHHHHHhCCCHHHHHHHHHHH
Confidence            4789999999877666666654

>PRK04984 fatty acid metabolism regulator; Provisional

Probab=82.66  E-value=2.5  Score=30.68  Aligned_cols=38  Identities=21%  Similarity=0.329  Sum_probs=30.5

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEc
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYIS   42 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs   42 (96)
                      .+||.+||++..-|.+-+..|+.+|.|.-   .+|+-.||+
T Consensus        35 ~eLae~~gVSRt~VReAL~~L~~eGlv~~---~~g~G~~V~   72 (239)
T PRK04984         35 RELSELIGVTRTTLREVLQRLARDGWLTI---QHGKPTKVN   72 (239)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCEEE---eCCCeeEeC
Confidence            37999999999999999999999998873   234444554

>PRK10421 DNA-binding transcriptional repressor LldR; Provisional

Probab=82.42  E-value=2.3  Score=31.34  Aligned_cols=38  Identities=24%  Similarity=0.349  Sum_probs=31.3

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEE
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIY   40 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIy   40 (96)
                      .+||..||++-.-|.+-|+.|+.+|-+. +.--+|-||-
T Consensus        30 ~eLae~~gVSRtpVREAL~~Le~~GlV~-~~~~~G~~V~   67 (253)
T PRK10421         30 RQLAMQLGVSRNSLREALAKLVSEGVLL-SRRGGGTFIR   67 (253)
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHHCCCEE-EeCCCeEEEe
Confidence            3899999999999999999999999887 3334565553

>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional

Probab=82.21  E-value=3.6  Score=29.63  Aligned_cols=47  Identities=17%  Similarity=0.324  Sum_probs=35.0

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceE-EEcHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFI-YISQEELNSV   49 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfI-yIs~eEl~~V   49 (96)
                      ++||..||++..-|.+-++.|+.+|-+. +.--+|-|| .+|++++..+
T Consensus        34 ~eLae~lgVSRtpVREAL~~L~~eGlv~-~~~~~G~~V~~~~~~~~~ei   81 (224)
T PRK11534         34 SLLTSRYALGVGPLREALSQLVAERLVT-VVNQKGYRVASMSEQELLDI   81 (224)
T ss_pred             HHHHHHHCCChHHHHHHHHHHHHCCCEE-EeCCCceEeCCCCHHHHHHH
Confidence            5899999999999999999999999886 344556443 2355554443

>COG1654 BirA Biotin operon repressor [Transcription]

Probab=82.06  E-value=1.8  Score=29.03  Aligned_cols=26  Identities=27%  Similarity=0.417  Sum_probs=24.5

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCC
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGA   27 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~   27 (96)
                      |+||+..|++...|-..|+.|.+.|-
T Consensus        23 e~La~~LgiSRtaVwK~Iq~Lr~~G~   48 (79)
T COG1654          23 EKLAEELGISRTAVWKHIQQLREEGV   48 (79)
T ss_pred             HHHHHHHCccHHHHHHHHHHHHHhCC
Confidence            68999999999999999999999985

>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]

Probab=82.03  E-value=1.6  Score=33.38  Aligned_cols=31  Identities=32%  Similarity=0.518  Sum_probs=25.9

Q ss_pred             ChhhhhhhCCChHHHHHHHHHHHHcCCccEE
Q psy11008          1 MEDLAALFRMKTQSVIDRIVELQKTGALTGV   31 (96)
Q Consensus         1 ledLAa~F~lktq~vI~RI~eL~~~g~ltGV   31 (96)
                      ++|||..|+++.+-+..=|.+|++.|.|..+
T Consensus        22 v~eLa~~~~VS~~TIRRDL~~Le~~g~l~R~   52 (253)
T COG1349          22 VEELAELFGVSEMTIRRDLNELEEQGLLLRV   52 (253)
T ss_pred             HHHHHHHhCCCHHHHHHhHHHHHHCCcEEEE
Confidence            3799999999666555569999999999875

>PRK00135 scpB segregation and condensation protein B; Reviewed

Probab=81.77  E-value=7.7  Score=29.27  Aligned_cols=81  Identities=20%  Similarity=0.270  Sum_probs=56.4

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHc----CCccEEeeCCCceEEEcHHHHHH-HHHHHHhhchhchhhh----hhhhcccc
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKT----GALTGVIDDRGKFIYISQEELNS-VATFIKQRGREELNSV----ATFIKQKG   72 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~----g~ltGViDDRGKfIyIs~eEl~~-Va~fI~~rgr~~~~~~----~~~~~~~G   72 (96)
                      ++||.-+++...++.+-|.+|.++    ++=-=+.--.|+|-+.|..|+.. |.+|....-+..|..-    -..|..++
T Consensus        24 ~~La~~l~~~~~~v~~~l~~L~~~y~~~~~gi~i~~~~~~y~l~tk~e~~~~v~~~~~~~~~~~LS~aaLEtLaiIay~q  103 (188)
T PRK00135         24 EQLAEILELEPTEVQQLLEELQEKYEGDDRGLKLIEFNDVYKLVTKEENADYLQKLVKTPIKQSLSQAALEVLAIIAYKQ  103 (188)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHhhCCCCEEEEEECCEEEEEEcHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHcC
Confidence            689999999988888888888654    43333455678898888887764 4556554323345432    35677788


Q ss_pred             ceeHHHHHHh
Q psy11008         73 RVSVSELVEN   82 (96)
Q Consensus        73 RVsi~eL~~~   82 (96)
                      -||.+|+.+.
T Consensus       104 PiTr~eI~~i  113 (188)
T PRK00135        104 PITRIEIDEI  113 (188)
T ss_pred             CcCHHHHHHH
Confidence            9999998875

>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A

Probab=81.77  E-value=5.9  Score=25.21  Aligned_cols=47  Identities=6%  Similarity=0.152  Sum_probs=34.7

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATF   52 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~f   52 (96)
                      .+|+..-+|+...+..-|..|++.|-+.+    +++..+||+.-.+.+-.+
T Consensus        23 t~i~~~~~L~~~~~~~yL~~L~~~gLI~~----~~~~Y~lTekG~~~l~~l   69 (77)
T PF14947_consen   23 TEIMYKANLNYSTLKKYLKELEEKGLIKK----KDGKYRLTEKGKEFLEEL   69 (77)
T ss_dssp             HHHHTTST--HHHHHHHHHHHHHTTSEEE----ETTEEEE-HHHHHHHHHH
T ss_pred             HHHHHHhCcCHHHHHHHHHHHHHCcCeeC----CCCEEEECccHHHHHHHH
Confidence            36788889999999999999999999844    555669999876655544

>smart00351 PAX Paired Box domain

Probab=81.73  E-value=7.4  Score=26.86  Aligned_cols=62  Identities=13%  Similarity=0.179  Sum_probs=45.5

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCC---C-ceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDR---G-KFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVS   77 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDR---G-KfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~   77 (96)
                      .++|..||++..-|..=|+...++|.+    ..+   | +-=-+++++...+..+++++               ...+..
T Consensus        37 ~~iA~~~gvs~~tV~kwi~r~~~~G~~----~pk~~gg~rp~~~~~~~~~~I~~~~~~~---------------p~~t~~   97 (125)
T smart00351       37 CDISRQLCVSHGCVSKILGRYYETGSI----RPGAIGGSKPKVATPKVVKKIADYKQEN---------------PGIFAW   97 (125)
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHcCCc----CCcCCCCCCCCccCHHHHHHHHHHHHHC---------------CCCCHH
Confidence            478999999887777778888888763    342   3 44456777777777788888               788888


Q ss_pred             HHHHh
Q psy11008         78 ELVEN   82 (96)
Q Consensus        78 eL~~~   82 (96)
                      ||++.
T Consensus        98 el~~~  102 (125)
T smart00351       98 EIRDR  102 (125)
T ss_pred             HHHHH
Confidence            87643

>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A)

Probab=81.73  E-value=1.6  Score=28.50  Aligned_cols=33  Identities=24%  Similarity=0.378  Sum_probs=29.3

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeC
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDD   34 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDD   34 (96)
                      ++||+.++|...+|.+-|++|..+|.|-=-|||
T Consensus        69 ~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd  101 (102)
T PF08784_consen   69 DEIAQQLGMSENEVRKALDFLSNEGHIYSTIDD  101 (102)
T ss_dssp             HHHHHHSTS-HHHHHHHHHHHHHTTSEEESSST
T ss_pred             HHHHHHhCcCHHHHHHHHHHHHhCCeEecccCC
Confidence            689999999999999999999999998777776

RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.

>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A

Probab=81.24  E-value=12  Score=24.18  Aligned_cols=55  Identities=7%  Similarity=0.225  Sum_probs=42.0

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCc----eEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGK----FIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGK----fIyIs~eEl~~Va~fI~~r   56 (96)
                      .+|....|++...+-.-++.|++.|-+.---.-.|+    ++-||+.-.+++..|+..-
T Consensus        18 ~~L~~~l~lt~g~Ls~hL~~Le~~GyV~~~k~~~~~~p~t~~~lT~~Gr~~~~~~~~~L   76 (80)
T PF13601_consen   18 SELKEELGLTDGNLSKHLKKLEEAGYVEVEKEFEGRRPRTWYSLTDKGREAFERYVAAL   76 (80)
T ss_dssp             HHHHHHTT--HHHHHHHHHHHHHTTSEEEEEE-SSS--EEEEEE-HHHHHHHHHHHHHH
T ss_pred             HHHHHHhCcCHHHHHHHHHHHHHCCCEEEEEeccCCCCeEEEEECHHHHHHHHHHHHHH
Confidence            478899999999999999999999999865554444    7889999998888887643

>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators

Probab=80.99  E-value=8.5  Score=25.27  Aligned_cols=47  Identities=13%  Similarity=0.184  Sum_probs=39.3

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATF   52 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~f   52 (96)
                      .|+|..+|+++.    .|.--++.|-|..+-.+.+.|=|-|++++..+..-
T Consensus         4 ~eva~~~gvs~~----tLRyye~~Gll~p~~~~~~gyR~Y~~~~l~~l~~I   50 (96)
T cd04768           4 GEFAKLAGVSIR----TLRHYDDIGLFKPAKIAENGYRYYSYAQLYQLQFI   50 (96)
T ss_pred             HHHHHHHCcCHH----HHHHHHHCCCCCCCccCCCCeeeCCHHHHHHHHHH
Confidence            589999999764    46778899999998877788999999999987643

Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.

>cd00131 PAX Paired Box domain

Probab=80.86  E-value=8.1  Score=26.99  Aligned_cols=64  Identities=14%  Similarity=0.173  Sum_probs=44.6

Q ss_pred             hhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCC-ceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHHH
Q psy11008          3 DLAALFRMKTQSVIDRIVELQKTGALTGVIDDRG-KFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVE   81 (96)
Q Consensus         3 dLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRG-KfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~   81 (96)
                      ++|..|+++..-|..=++...++|.+.-.-- .| +-=.++++....+-.+++++               +..|..||.+
T Consensus        38 ~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~~-gg~rpr~~~~~~~~~i~~~v~~~---------------p~~Tl~El~~  101 (128)
T cd00131          38 DISRQLRVSHGCVSKILNRYYETGSIRPGAI-GGSKPRVATPEVVKKIEIYKQEN---------------PGMFAWEIRD  101 (128)
T ss_pred             HHHHHHCcCHHHHHHHHHHHHHcCCcCCCCC-CCCCCCcCCHHHHHHHHHHHHHC---------------CCCCHHHHHH
Confidence            6899999988877777888999998652111 12 12245666667777788888               6777777766


Q ss_pred             h
Q psy11008         82 N   82 (96)
Q Consensus        82 ~   82 (96)
                      .
T Consensus       102 ~  102 (128)
T cd00131         102 R  102 (128)
T ss_pred             H
Confidence            5

>KOG2235|consensus

Probab=80.72  E-value=3.4  Score=37.97  Aligned_cols=61  Identities=23%  Similarity=0.386  Sum_probs=50.2

Q ss_pred             CCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHH-HHHHHHhhchhchhhhhhhhccccceeHHHHHHhcc
Q psy11008          9 RMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNS-VATFIKQRGREELNSVATFIKQKGRVSVSELVENSN   84 (96)
Q Consensus         9 ~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~-Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~~sN   84 (96)
                      +|+--.||+-++.|++.-+|-=|..-.||= ||||+.++. +-.-+-.+|              ||+|+-||+..-|
T Consensus        23 kLSerNcvEivqkLie~~~ldvvhT~dGke-YIT~~hLe~EI~dEl~v~G--------------gRaslvDla~tln   84 (776)
T KOG2235|consen   23 KLSERNCVEIVQKLIESHRLDVVHTRDGKE-YITPNHLETEIKDELIVAG--------------GRASLVDLAVTLN   84 (776)
T ss_pred             HhhhccHHHHHHHHHHhhhcceEEecCCcc-ccCHHHHHHHHHHHHHHhC--------------CcchhHHHHHHhC
Confidence            355567899999999999999999999994 999999863 555566665              8999999998766

>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional

Probab=80.69  E-value=3  Score=30.76  Aligned_cols=36  Identities=19%  Similarity=0.207  Sum_probs=31.0

Q ss_pred             hhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceE
Q psy11008          3 DLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFI   39 (96)
Q Consensus         3 dLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfI   39 (96)
                      +||..||++..-|.+-++.|+.+|-|+ +.--+|-||
T Consensus        37 eLae~~gVSRtpVREAL~~L~~eGlV~-~~~~~G~~V   72 (253)
T PRK11523         37 FIADEKNVSRTVVREAIIMLEVEGYVE-VRKGSGIHV   72 (253)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHCCCEE-EecCCeeEE
Confidence            799999999999999999999999887 333567666

>PRK09464 pdhR transcriptional regulator PdhR; Reviewed

Probab=80.35  E-value=3.3  Score=30.38  Aligned_cols=39  Identities=23%  Similarity=0.364  Sum_probs=31.1

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQ   43 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~   43 (96)
                      .+||..||++...|.+-++.|+.+|-|+=.   .|+-.||++
T Consensus        38 ~eLa~~lgVSRtpVREAL~~L~~eGlv~~~---~~~G~~V~~   76 (254)
T PRK09464         38 RELAKQFDVSRPSLREAIQRLEAKGLLLRR---QGGGTFVQS   76 (254)
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHHCCCEEEe---cCceeEEec
Confidence            479999999999999999999999988733   344445543

>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional

Probab=80.17  E-value=3.5  Score=30.19  Aligned_cols=38  Identities=16%  Similarity=0.355  Sum_probs=31.4

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEE
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIY   40 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIy   40 (96)
                      .+||..||++...|.+-++.|+.+|-|.-. --+|-||-
T Consensus        35 ~eLa~~~gVSRtpVREAL~~L~~eGlV~~~-~~~G~~V~   72 (251)
T PRK09990         35 RRLCEKLGFSRSALREGLTVLRGRGIIETA-QGRGSFVA   72 (251)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCEEEe-CCCeeEEe
Confidence            389999999999999999999999988733 34666654

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	96
1wi9_A	72	Solution Structure Of The Pci Domain From Mouse Hyp		5e-08

>pdb|1WI9|A Chain A, Solution Structure Of The Pci Domain From Mouse Hypothetical Protein Aah51541 Length = 72

Iteration: 1
 Score = 52.8 bits (125), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 26/48 (54%), Positives = 33/48 (68%)
Query: 1  MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNS 48
          +EDLA    ++TQ  I+RI +L   G LTGVIDDRGKFIYI+    +S
Sbjct: 24 LEDLAFQMGLRTQDAINRIQDLLTEGTLTGVIDDRGKFIYITPSGPSS 71

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	96
1wi9_A	72	Protein C20ORF116 homolog; helix-turn-helix motif,	8e-17

>1wi9_A Protein C20ORF116 homolog; helix-turn-helix motif, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} SCOP: a.4.5.47 Length = 72

 Score = 67.6 bits (165), Expect = 8e-17
 Identities = 25/43 (58%), Positives = 31/43 (72%)

Query: 1  MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQ 43
          +EDLA    ++TQ  I+RI +L   G LTGVIDDRGKFIYI+ 
Sbjct: 24 LEDLAFQMGLRTQDAINRIQDLLTEGTLTGVIDDRGKFIYITP 66

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	96
1wi9_A	72	Protein C20ORF116 homolog; helix-turn-helix motif,	99.94
1ub9_A	100	Hypothetical protein PH1061; helix-turn-helix moti	97.46
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	97.44
2kko_A	108	Possible transcriptional regulatory protein (possi	97.23
3jth_A	98	Transcription activator HLYU; transcription factor	97.1
3f6v_A	151	Possible transcriptional regulator, ARSR family pr	97.03
3f6o_A	118	Probable transcriptional regulator, ARSR family pr	96.93
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	96.91
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	96.83
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	96.78
1tbx_A	99	ORF F-93, hypothetical 11.0 kDa protein; sulfolobu	96.75
1u2w_A	122	CADC repressor, cadmium efflux system accessory pr	96.67
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	96.66
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	96.6
2qvo_A	95	Uncharacterized protein AF_1382; PSI, structural g	96.6
3df8_A	111	Possible HXLR family transcriptional factor; APC89	96.47
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	96.47
2hzt_A	107	Putative HTH-type transcriptional regulator YTCD;	96.4
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	96.39
2hr3_A	147	Probable transcriptional regulator; MCSG, structur	96.38
3oop_A	143	LIN2960 protein; protein structure initiative, PSI	96.37
2jsc_A	118	Transcriptional regulator RV1994C/MT2050; cadmium,	96.36
1lj9_A	144	Transcriptional regulator SLYA; HTH DNA binding pr	96.33
1r1t_A	122	Transcriptional repressor SMTB; zinc, transcriptio	96.31
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	96.26
2pjp_A	121	Selenocysteine-specific elongation factor; SELB, p	96.2
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	96.11
3s2w_A	159	Transcriptional regulator, MARR family; structural	96.11
1sfx_A	109	Conserved hypothetical protein AF2008; structural	96.1
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	96.08
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	96.05
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	96.03
3k0l_A	162	Repressor protein; helix-turn-helix, structural ge	96.01
2nnn_A	140	Probable transcriptional regulator; structural gen	96.01
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	95.98
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	95.97
3cjn_A	162	Transcriptional regulator, MARR family; silicibact	95.96
3bja_A	139	Transcriptional regulator, MARR family, putative;	95.95
2rdp_A	150	Putative transcriptional regulator MARR; PFAM PF01	95.95
2eth_A	154	Transcriptional regulator, putative, MAR family; M	95.92
3bj6_A	152	Transcriptional regulator, MARR family; helix-turn	95.91
2bv6_A	142	MGRA, HTH-type transcriptional regulator MGRA; mul	95.89
2w25_A	150	Probable transcriptional regulatory protein; trans	95.88
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	95.88
2fbi_A	142	Probable transcriptional regulator; MARR, APC5816,	95.86
2gxg_A	146	146AA long hypothetical transcriptional regulator;	95.84
3hsr_A	140	HTH-type transcriptional regulator SARZ; helix-tur	95.81
2a61_A	145	Transcriptional regulator TM0710; APC4350, MCSG, m	95.77
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	95.74
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	95.74
1s3j_A	155	YUSO protein; structural genomics, MARR transcript	95.74
1z7u_A	112	Hypothetical protein EF0647; winged-helix-turn-hel	95.74
2pg4_A	95	Uncharacterized protein; structural genomics, join	95.73
3nrv_A	148	Putative transcriptional regulator (MARR/EMRR FAM;	95.73
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	95.68
3deu_A	166	Transcriptional regulator SLYA; MARR, WING-helix,	95.67
2fbh_A	146	Transcriptional regulator PA3341; MARR, transcript	95.66
2nyx_A	168	Probable transcriptional regulatory protein, RV14;	95.64
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	95.64
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	95.62
3e6m_A	161	MARR family transcriptional regulator; APC88769, s	95.62
2fsw_A	107	PG_0823 protein; alpha-beta structure, helix-turn-	95.61
3f3x_A	144	Transcriptional regulator, MARR family, putative;	95.59
3b73_A	111	PHIH1 repressor-like protein; winged-helix-turn-he	95.59
3g3z_A	145	NMB1585, transcriptional regulator, MARR family; t	95.56
1ufm_A	84	COP9 complex subunit 4; helix-turn-helix, structur	95.53
3kp7_A	151	Transcriptional regulator TCAR; multiple drug resi	95.5
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	95.49
3cdh_A	155	Transcriptional regulator, MARR family; helix-turn	95.46
2pex_A	153	Transcriptional regulator OHRR; transcription regu	95.43
4hbl_A	149	Transcriptional regulator, MARR family; HTH, trans	95.4
2f2e_A	146	PA1607; transcription factor, helix-TRUN-helix, AP	95.35
3fm5_A	150	Transcriptional regulator; MCSG, PF04017, PSI, MAR	95.35
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	95.33
2b0l_A	102	GTP-sensing transcriptional pleiotropic repressor;	95.33
2frh_A	127	SARA, staphylococcal accessory regulator A; winged	95.31
3nqo_A	189	MARR-family transcriptional regulator; structural	95.29
3jw4_A	148	Transcriptional regulator, MARR/EMRR family; DNA-b	95.29
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	95.28
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	95.26
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	95.26
3boq_A	160	Transcriptional regulator, MARR family; MARR famil	95.25
2zkz_A	99	Transcriptional repressor PAGR; protein-DNA, HTH m	95.23
1yyv_A	131	Putative transcriptional regulator; reductive meth	95.19
2qww_A	154	Transcriptional regulator, MARR family; YP_013417.	95.04
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	95.02
1z91_A	147	Organic hydroperoxide resistance transcriptional;	94.94
1on2_A	142	Transcriptional regulator MNTR; helix-turn-helix,	94.94
4ev0_A	216	Transcription regulator, CRP family; CAMP binding,	94.85
3u2r_A	168	Regulatory protein MARR; structural genomics, PSI-	94.83
3r0a_A	123	Putative transcriptional regulator; structural gen	94.78
3i4p_A	162	Transcriptional regulator, ASNC family; PSI, struc	94.52
1ku9_A	152	Hypothetical protein MJ223; putative transcription	94.41
2fxa_A	207	Protease production regulatory protein HPR; protea	94.3
2h09_A	155	Transcriptional regulator MNTR; transcription regu	93.97
4aik_A	151	Transcriptional regulator SLYA; transcription, tra	93.94
4b8x_A	147	SCO5413, possible MARR-transcriptional regulator;	93.88
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	93.85
3dv8_A	220	Transcriptional regulator, CRP/FNR family; cyclic	93.75
1lva_A	258	Selenocysteine-specific elongation factor; winged-	93.74
3hrs_A	214	Metalloregulator SCAR; DTXR/MNTR family member, tr	93.72
3txn_A	394	26S proteasome regulatory complex subunit P42B; PC	93.38
3tqn_A	113	Transcriptional regulator, GNTR family; regulatory	93.06
3d0s_A	227	Transcriptional regulatory protein; CAMP receptor	93.03
2zcw_A	202	TTHA1359, transcriptional regulator, FNR/CRP famil	92.9
2fbk_A	181	Transcriptional regulator, MARR family; winged-hel	92.86
3fx3_A	237	Cyclic nucleotide-binding protein; helix_TURN_heli	92.73
1j5y_A	187	Transcriptional regulator, biotin repressor famil;	92.64
1ft9_A	222	Carbon monoxide oxidation system transcription reg	92.45
2qq9_A	226	Diphtheria toxin repressor; regulator, DTXR, helix	92.29
3e6c_C	250	CPRK, cyclic nucleotide-binding protein; CPRK, hal	92.23
4b4t_R	429	RPN7, 26S proteasome regulatory subunit RPN7; hydr	92.15
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	92.0
4a5n_A	131	Uncharacterized HTH-type transcriptional regulato;	91.91
1sd4_A	126	Penicillinase repressor; BLAI, MECI, methicillin,	91.9
1okr_A	123	MECI, methicillin resistance regulatory protein ME	91.78
2bgc_A	238	PRFA; bacterial infection, human pathogen, transcr	91.72
3b02_A	195	Transcriptional regulator, CRP family; structural	91.65
3ic7_A	126	Putative transcriptional regulator; helix-turn-hel	91.58
3l7w_A	108	Putative uncharacterized protein SMU.1704; PADR, t	91.49
2gau_A	232	Transcriptional regulator, CRP/FNR family; structu	91.42
3e97_A	231	Transcriptional regulator, CRP/FNR family; YP_6044	91.3
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	91.28
1uly_A	192	Hypothetical protein PH1932; helix-turn-helix, str	91.2
2wte_A	244	CSA3; antiviral protein, viral resistance, winged	91.14
3cta_A	230	Riboflavin kinase; structural genomics, transferas	91.04
3iuo_A	122	ATP-dependent DNA helicase RECQ; C-terminal, GI PS	90.86
2v7f_A	150	RPS19, RPS19E SSU ribosomal protein S19E; diamond	90.78
4b4t_O	393	26S proteasome regulatory subunit RPN9; hydrolase,	90.68
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	90.58
2co5_A	99	Viral protein F93; viral protein-winged helix comp	90.54
1y0u_A	96	Arsenical resistance operon repressor, putative; s	90.38
2esh_A	118	Conserved hypothetical protein TM0937; APC5794, st	90.14
1fx7_A	230	Iron-dependent repressor IDER; DTXR, iron-dependen	90.07
2v79_A	135	DNA replication protein DNAD; primosome, DNA-bindi	90.03
2fmy_A	220	COOA, carbon monoxide oxidation system transcripti	90.0
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	89.91
4b4t_P	445	26S proteasome regulatory subunit RPN5; hydrolase,	89.8
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	89.72
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	89.55
4fx0_A	148	Probable transcriptional repressor protein; helix-	89.46
3neu_A	125	LIN1836 protein; structural genomics, PSI-2, prote	89.08
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	89.01
2g9w_A	138	Conserved hypothetical protein; DNA-binding domain	88.95
2ba3_A	51	NIKA; dimer, bacterial conjugation, relaxase, DNA	88.89
2dk8_A	81	DNA-directed RNA polymerase III 39 kDa polypeptide	88.7
2k9i_A	55	Plasmid PRN1, complete sequence; plasmid COPY cont	88.44
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	87.79
3ihu_A	222	Transcriptional regulator, GNTR family; YP_298823.	87.64
1hsj_A	487	Fusion protein consisting of staphylococcus access	87.39
3lmm_A	583	Uncharacterized protein; multi-domained alpha-beta	87.34
1xmk_A	79	Double-stranded RNA-specific adenosine deaminase;	87.15
2hs5_A	239	Putative transcriptional regulator GNTR; APC6050,	86.95
1bia_A	321	BIRA bifunctional protein; transcription regulatio	86.43
2fu4_A	83	Ferric uptake regulation protein; DNA binding doma	86.31
3by6_A	126	Predicted transcriptional regulator; structural ge	86.24
3la7_A	243	Global nitrogen regulator; activator, DNA-binding,	86.05
3hhh_A	116	Transcriptional regulator, PADR family; PF03551, s	85.77
4ham_A	134	LMO2241 protein; structural genomics, PSI-biology,	85.68
2vn2_A	128	DNAD, chromosome replication initiation protein; D	85.45
4esf_A	117	PADR-like transcriptional regulator; PADR family,	85.39
1xma_A	145	Predicted transcriptional regulator; southea colla	84.93
1mkm_A	249	ICLR transcriptional regulator; structural genomic	84.81
2gqq_A	163	Leucine-responsive regulatory protein; helix-turn-	84.32
1yg2_A	179	Gene activator APHA; virulence factor, winged heli	84.1
3tdu_C	77	Cullin-1, CUL-1; E2:E3, ligase-protein binding com	83.9
3ri2_A	123	Transcriptional regulator, PADR-like family; PSI-b	83.72
3f8m_A	248	GNTR-family protein transcriptional regulator; PHN	83.35
1iuy_A	92	Cullin-3 homologue; winged helix, structural genom	82.75
2xvc_A	59	ESCRT-III, SSO0910; cell cycle, cell division, cyt	82.44
3rkx_A	323	Biotin-[acetyl-COA-carboxylase] ligase; biotin pro	82.42
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	81.74
3ryp_A	210	Catabolite gene activator; CAMP receptor protein (	81.59
1hw1_A	239	FADR, fatty acid metabolism regulator protein; hel	81.5
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	81.24
3o2p_E	88	Cell division control protein 53; ligase, cell cyc	80.72
2cpg_A	45	REPA protein, transcriptional repressor COPG; DNA-	80.32
2ek5_A	129	Predicted transcriptional regulators; helix-turn-h	80.06
2p4w_A	202	Transcriptional regulatory protein ARSR family; ar	80.03

>1wi9_A Protein C20ORF116 homolog; helix-turn-helix motif, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} SCOP: a.4.5.47

Probab=99.94  E-value=4.1e-28  Score=160.89  Aligned_cols=48  Identities=54%  Similarity=0.832  Sum_probs=46.3

Q ss_pred             ChhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHH
Q psy11008          1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNS   48 (96)
Q Consensus         1 ledLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~   48 (96)
                      |||||++|||+||+||+||++|+++|+|||||||||||||||++||++
T Consensus        24 LedLA~~F~l~t~~~i~RI~~Le~~g~ltGViDDRGKfIyIs~eE~~a   71 (72)
T 1wi9_A           24 LEDLAFQMGLRTQDAINRIQDLLTEGTLTGVIDDRGKFIYITPSGPSS   71 (72)
T ss_dssp             HHHHHHHHCSCHHHHHHHHHHHHHHSSSCEEECTTCCEEECCCSSCCC
T ss_pred             HHHHHHHhCCChHHHHHHHHHHHHCCCeEEEEeCCCCEEEecHHHhhc
Confidence            589999999999999999999999999999999999999999999864

>1ub9_A Hypothetical protein PH1061; helix-turn-helix motif, winged helix motif, structural genom transcription; 2.05A {Pyrococcus horikoshii} SCOP: a.4.5.28

Probab=97.46  E-value=0.0006  Score=41.18  Aligned_cols=55  Identities=11%  Similarity=0.225  Sum_probs=48.2

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEe---eCCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI---DDRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi---DDRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .|||..++++...+-..|+.|++.|-+...-   |.|.+++++|++-...+..++...
T Consensus        34 ~ela~~l~is~~tvs~~l~~L~~~gli~~~~~~~~~r~~~~~lt~~g~~~~~~~~~~~   91 (100)
T 1ub9_A           34 SQIQKVLDLTPGNLDSHIRVLERNGLVKTYKVIADRPRTVVEITDFGMEEAKRFLSSL   91 (100)
T ss_dssp             HHHHHHTTCCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCEEEEecCCCcceEEEEECHHHHHHHHHHHHHH
Confidence            4899999999999999999999999999776   677889999999888887777665

>3cuo_A Uncharacterized HTH-type transcriptional regulato; DNA-binding transcriptional regulator, structural genomics, MCSG; 2.00A {Escherichia coli K12}

Probab=97.44  E-value=0.00062  Score=41.19  Aligned_cols=55  Identities=13%  Similarity=0.277  Sum_probs=50.0

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .|||..+|++...+-..++.|++.|-+.-.-|.|.++.+++++....+..++.+.
T Consensus        42 ~ela~~l~is~~tvs~~l~~L~~~glv~~~~~~r~~~y~l~~~~~~~l~~~l~~~   96 (99)
T 3cuo_A           42 GELTRITGLSASATSQHLARMRDEGLIDSQRDAQRILYSIKNEAVNAIIATLKNV   96 (99)
T ss_dssp             HHHHHHHCCCHHHHHHHHHHHHHTTSEEEEECSSCEEEEECCHHHHHHHHHHHHH
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCEEEEecCCEEEEEEChHHHHHHHHHHHHh
Confidence            5899999999888889999999999999988888889999999999999988764

>2kko_A Possible transcriptional regulatory protein (possibly ARSR-family); NESG, DNA-binding, transcription regulation, WHTH, homodimer; NMR {Mycobacterium bovis} PDB: 3gw2_A

Probab=97.23  E-value=0.00092  Score=42.91  Aligned_cols=60  Identities=15%  Similarity=0.258  Sum_probs=52.8

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhhchhch
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREEL   61 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~rgr~~~   61 (96)
                      .|||..+|++...+-..++.|++.|-+.-.-|.|.+|.+++++.+..+..++.+...++|
T Consensus        42 ~eLa~~lgis~stvs~~L~~L~~~GlV~~~~~gr~~~y~l~~~~~~~l~~~l~~~~~~~~  101 (108)
T 2kko_A           42 EAIATATGMNLTTASANLQALKSGGLVEARREGTRQYYRIAGEDVARLFALVQVVADEHL  101 (108)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHHTSEEEEEETTEEEEEESCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEeCCEEEEEEChHHHHHHHHHHHHHhhHHh
Confidence            589999999999888999999999999988888888889999999999999988754443

>3jth_A Transcription activator HLYU; transcription factor, RTXA, DNA-binding, transcription regulation; 2.00A {Vibrio vulnificus}

Probab=97.10  E-value=0.0023  Score=39.52  Aligned_cols=55  Identities=13%  Similarity=0.299  Sum_probs=49.8

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .|||..+|++...+-..++.|++.|-+.-.-+.|..|.+++++.+..+..++..-
T Consensus        40 ~ela~~l~is~~tvs~~L~~L~~~Glv~~~~~g~~~~y~l~~~~~~~l~~~l~~~   94 (98)
T 3jth_A           40 GELCAKLQLSQSALSQHLAWLRRDGLVTTRKEAQTVYYTLKSEEVKAMIKLLHSL   94 (98)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEECCTTCCEEEECCHHHHHHHHHHHHH
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEeCCEEEEEECHHHHHHHHHHHHHH
Confidence            5899999999999999999999999999988888889999999999998887653

>3f6v_A Possible transcriptional regulator, ARSR family protein; probable transcriptional repressor ARSR family, structural genomics, PSI-2; 1.48A {Rhodococcus SP}

Probab=97.03  E-value=0.0027  Score=43.82  Aligned_cols=68  Identities=18%  Similarity=0.252  Sum_probs=59.2

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhhchhchhhhhhhhc
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREELNSVATFIK   69 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~   69 (96)
                      .+||..+|++...|-..++.|++.|-|...-|.|.+|.+++++.+..+..++...-...+..+..++.
T Consensus        75 ~eLa~~lgls~stvs~hL~~L~~aGlV~~~~~Gr~~~y~lt~~~~~~l~~~l~~~~~~~l~~l~~~l~  142 (151)
T 3f6v_A           75 NNLAAHFPASRSAISQHLRVLTEAGLVTPRKDGRFRYYRLDPQGLAQLRALFDSFWIDELDRLVADAT  142 (151)
T ss_dssp             HHHHTTSSSCHHHHHHHHHHHHHTTSEEEEEETTEEEEEECHHHHHHHHHHHHHHSCHHHHHHHHHCC
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCEEEEecCCEEEEEEChHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            58999999999988899999999999999999999999999999999999988776666666655543

>3f6o_A Probable transcriptional regulator, ARSR family protein; transcriptional regulator,RHA00566,MCSG, structural genomics, PSI-2; 1.90A {Rhodococcus SP}

Probab=96.93  E-value=0.0028  Score=40.94  Aligned_cols=55  Identities=22%  Similarity=0.323  Sum_probs=51.2

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .|||..+|++...+-..++.|++.|-+...-+.|.+|.+++++.+..+..++...
T Consensus        35 ~eLa~~l~is~~tvs~hL~~L~~~GlV~~~~~gr~~~y~l~~~~~~~l~~~~~~~   89 (118)
T 3f6o_A           35 SELAKPFDMALPSFMKHIHFLEDSGWIRTHKQGRVRTCAIEKEPFTAVEAWLAEQ   89 (118)
T ss_dssp             HHHHTTCCSCHHHHHHHHHHHHHTTSEEEEEETTEEEEEECSHHHHHHHHHHHHH
T ss_pred             HHHHHHhCcCHHHHHHHHHHHHHCCCeEEEecCCEEEEEECHHHHHHHHHHHHHH
Confidence            5899999999999999999999999999999989999999999999999888876

>2oqg_A Possible transcriptional regulator, ARSR family P; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 1.54A {Rhodococcus SP}

Probab=96.91  E-value=0.0036  Score=38.90  Aligned_cols=55  Identities=22%  Similarity=0.211  Sum_probs=48.6

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .|||..+|++...+-..++.|++.|-+.-.-+.|.+|++++++.+..+..++...
T Consensus        38 ~ela~~l~is~~tv~~~l~~L~~~gli~~~~~gr~~~y~l~~~~~~~~~~~~~~~   92 (114)
T 2oqg_A           38 SSLATRLPVSRQAIAKHLNALQACGLVESVKVGREIRYRALGAELNKTARTLERI   92 (114)
T ss_dssp             HHHHHHSSSCHHHHHHHHHHHHHTTSEEEEEETTEEEEEECSHHHHHHHHHHHHH
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCeeEEecCCEEEEEechHHHHHHHHHHHHH
Confidence            5899999999999999999999999999888888889999999988887776653

>1r1u_A CZRA, repressor protein; zinc, DNA binding, transcriptional regulation, winged HTH protein, transcription repressor; 2.00A {Staphylococcus aureus} SCOP: a.4.5.5 PDB: 1r1v_A 2kjb_A 2kjc_A

Probab=96.83  E-value=0.0043  Score=39.25  Aligned_cols=55  Identities=4%  Similarity=0.076  Sum_probs=48.5

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .|||..+|++...+-..|+.|++.|-+...-+.|..|.+++++.+..+...+...
T Consensus        43 ~ela~~l~is~stvs~~L~~L~~~Glv~~~~~gr~~~y~l~~~~~~~~~~~l~~~   97 (106)
T 1r1u_A           43 GHISHQLNLSQSNVSHQLKLLKSVHLVKAKRQGQSMIYSLDDIHVATMLKQAIHH   97 (106)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEESSHHHHHHHHHHHHH
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEeCCEEEEEEChHHHHHHHHHHHHH
Confidence            5899999999888889999999999999888877778889999998888877654

>3pqk_A Biofilm growth-associated repressor; helix-turn-helix motif, winged-helix fold, transcriptional R DNA binding, transcription; 2.09A {Xylella fastidiosa} PDB: 3pqj_A

Probab=96.78  E-value=0.0035  Score=39.05  Aligned_cols=55  Identities=7%  Similarity=0.146  Sum_probs=50.0

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .|||..+|++...+-..++.|++.|-+.-.-+.|..|..++++.+..+..++.+-
T Consensus        40 ~ela~~l~is~~tvs~~L~~L~~~Glv~~~~~g~~~~y~l~~~~~~~~~~~l~~~   94 (102)
T 3pqk_A           40 GELEQQIGIGQPTLSQQLGVLRESGIVETRRNIKQIFYRLTEAKAAQLVNALYTI   94 (102)
T ss_dssp             HHHHHHHTCCTTHHHHHHHHHHHTTSEEEECSSSCCEEEECSSTHHHHHHHHHHH
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEeCCEEEEEECcHHHHHHHHHHHHH
Confidence            5899999999999999999999999999988888899999999999888887654

>1tbx_A ORF F-93, hypothetical 11.0 kDa protein; sulfolobus spindle virus, winged helix, fusellovirus; 2.70A {Sulfolobus virus 1} SCOP: a.4.5.48

Probab=96.75  E-value=0.0064  Score=37.39  Aligned_cols=51  Identities=18%  Similarity=0.163  Sum_probs=44.6

Q ss_pred             hhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHh
Q psy11008          5 AALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQ   55 (96)
Q Consensus         5 Aa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~   55 (96)
                      |..++++...+-..|+.|++.|-+.=..|.|.+++++|++-...+......
T Consensus        33 a~~l~is~~tvs~~l~~Le~~gli~r~~~~r~~~~~LT~~G~~~~~~~~~~   83 (99)
T 1tbx_A           33 NAEFPMSTATFYDAKKFLIQEGFVKERQERGEKRLYLTEKGKLFAISLKTA   83 (99)
T ss_dssp             HTTSCCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEECHHHHHHHHHHHHH
T ss_pred             HHHcCCCHHHHHHHHHHHHHCCCEEEEecCCceEEEECHHHHHHHHHHHHH
Confidence            899999999999999999999999999999999999999877666555443

>1u2w_A CADC repressor, cadmium efflux system accessory protein; LEAD, SOFT metal ION resistance, ARSR/SM family, DNA binding protein; 1.90A {Staphylococcus aureus} SCOP: a.4.5.5 PDB: 3f72_A

Probab=96.67  E-value=0.0051  Score=40.13  Aligned_cols=55  Identities=11%  Similarity=0.179  Sum_probs=46.2

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .|||..+|++...+-..|+.|++.|-+...-+.|..|.+++++.+..++.++.+.
T Consensus        60 ~eLa~~l~is~stvs~~L~~L~~~Glv~~~~~gr~~~y~l~~~~~~~~~~~l~~~  114 (122)
T 1u2w_A           60 CDIANILGVTIANASHHLRTLYKQGVVNFRKEGKLALYSLGDEHIRQIMMIALAH  114 (122)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEC----CCEEEESCHHHHHHHHHHHHH
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEECCEEEEEECHHHHHHHHHHHHHH
Confidence            5899999999988889999999999998877777789999999999999888765

>2cg4_A Regulatory protein ASNC; DNA binding, FFRP, LRP family, transcription, DNA- binding, transcription regulation; 2.4A {Escherichia coli} SCOP: a.4.5.32 d.58.4.2

Probab=96.66  E-value=0.0063  Score=40.33  Aligned_cols=55  Identities=22%  Similarity=0.398  Sum_probs=44.9

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccE---EeeCC--Cc----eEEEcH---HHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTG---VIDDR--GK----FIYISQ---EELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltG---ViDDR--GK----fIyIs~---eEl~~Va~fI~~r   56 (96)
                      .|||..+|++...|-.||+.|++.|.|.+   ++|.+  |.    ||.|+-   ..++.+++.+.+.
T Consensus        26 ~ela~~lg~s~~tv~~~l~~L~~~G~i~~~~~~~~~~~~g~~~~a~v~v~~~~~~~~~~~~~~l~~~   92 (152)
T 2cg4_A           26 AELAKQFGVSPETIHVRVEKMKQAGIITGARIDVSPKQLGYDVGCFIGIILKSAKDYPSALAKLESL   92 (152)
T ss_dssp             HHHHHHHTSCHHHHHHHHHHHHHHTSEEEEEEEECTTTTTCCEEEEEEEEESSGGGHHHHHHHHHTC
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHcCCcceEEEecCHHHcCCeEEEEEEEEECCCCCHHHHHHHHhCC
Confidence            58999999999999999999999999987   45643  43    677762   3588899988876

>2pn6_A ST1022, 150AA long hypothetical transcriptional regulator; LRP/ASNC family Gln binding, structural genomics, NPPSFA; HET: GLN; 1.44A {Sulfolobus tokodaii} PDB: 2efn_A* 2e7x_A* 2e7w_A* 2yx4_A* 2efq_A* 2pmh_A* 2yx7_A* 2efp_A* 2efo_A*

Probab=96.60  E-value=0.004  Score=40.93  Aligned_cols=55  Identities=18%  Similarity=0.295  Sum_probs=45.6

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccE---EeeCC--Cc----eEEEc----HHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTG---VIDDR--GK----FIYIS----QEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltG---ViDDR--GK----fIyIs----~eEl~~Va~fI~~r   56 (96)
                      .|||..+|++...+-.||+.|++.|-|.+   ++|.+  |.    |+.++    ++.++.+++.+.+.
T Consensus        21 ~ela~~lg~s~~tv~~~l~~L~~~G~i~~~~~~~d~~~~g~~~~a~v~v~~~~~~~~~~~~~~~l~~~   88 (150)
T 2pn6_A           21 DEIAREIRIPKATLSYRIKKLEKDGVIKGYYAYINPASLNLDYIVITSVKAKYGKNYHVELGNKLAQI   88 (150)
T ss_dssp             HHHHHHHTSCHHHHHHHHHHHHHTTSSCCCCCCCCGGGGTCCEEEEEEEEECCCTTHHHHHHHHHHTS
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCcEEEEEeecCHHHhCCceEEEEEEEecCChhHHHHHHHHHhcC
Confidence            58999999999999999999999999987   56643  33    67776    56788899888875

>2qvo_A Uncharacterized protein AF_1382; PSI, structural genomics, southeast collaboratory for structural genomics; 1.85A {Archaeoglobus fulgidus dsm 4304} PDB: 3o3k_A 3ov8_A

Probab=96.60  E-value=0.011  Score=36.73  Aligned_cols=54  Identities=11%  Similarity=0.097  Sum_probs=44.4

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQ   55 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~   55 (96)
                      .|||..++++.+.+-.-|..|++.|-+.---|.|.++|++|++-...+......
T Consensus        34 ~eLa~~l~i~~~tvs~~l~~Le~~Glv~~~~d~R~~~v~LT~~G~~~~~~~~~~   87 (95)
T 2qvo_A           34 QYIASKVNSPHSYVWLIIKKFEEAKMVECELEGRTKIIRLTDKGQKIAQQIKSI   87 (95)
T ss_dssp             HHHHHHSSSCHHHHHHHHHHHHHTTSEEEEEETTEEEEEECHHHHHHHHHHHHH
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCcCccCCCCCCeEEEEEChhHHHHHHHHHHH
Confidence            589999999999999999999999999555677889999998876655554443

>3df8_A Possible HXLR family transcriptional factor; APC89000, structural genomics, midwest center for structural genomics, MCSG; 1.65A {Thermoplasma volcanium} SCOP: a.4.5.0

Probab=96.47  E-value=0.012  Score=38.03  Aligned_cols=54  Identities=13%  Similarity=0.204  Sum_probs=46.6

Q ss_pred             hhhhhhh-CCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHH------HHHHHHHHHHhh
Q psy11008          2 EDLAALF-RMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQE------ELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F-~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~e------El~~Va~fI~~r   56 (96)
                      .|||..+ |++...+-.+++.|++.|-++-..+ |..++++|+.      .+.+++.|+..-
T Consensus        46 ~eL~~~l~gis~~~ls~~L~~Le~~GlV~r~~~-r~~~y~LT~~G~~l~~~l~~l~~w~~~~  106 (111)
T 3df8_A           46 NDIRSSIPGISSTILSRRIKDLIDSGLVERRSG-QITTYALTEKGMNVRNSLMPLLQYISVL  106 (111)
T ss_dssp             HHHHHTSTTCCHHHHHHHHHHHHHTTSEEEEES-SSEEEEECHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHccCCCHHHHHHHHHHHHHCCCEEEeec-CcEEEEECccHHHHHHHHHHHHHHHHHh
Confidence            4899999 9999999999999999999999988 9999999997      466666666543

>3tgn_A ADC operon repressor ADCR; helix-turn-helix, transcriptional regulator, transcription; 2.00A {Streptococcus pneumoniae}

Probab=96.47  E-value=0.004  Score=39.41  Aligned_cols=52  Identities=21%  Similarity=0.203  Sum_probs=41.2

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEe---eCCCceEEEcHHHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI---DDRGKFIYISQEELNSVATFI   53 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi---DDRGKfIyIs~eEl~~Va~fI   53 (96)
                      .|||..++++...+-..|..|++.|-++-.-   |-|.+++++|++....+....
T Consensus        55 ~eLa~~l~~s~~tvs~~l~~L~~~Glv~r~~~~~d~R~~~~~lT~~g~~~~~~~~  109 (146)
T 3tgn_A           55 SELARRLNVSQAAVTKAIKSLVKEGMLETSKDSKDARVIFYQLTDLARPIAEEHH  109 (146)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEC----------CCEECGGGHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCeEeccCCCCCceeEEEECHhHHHHHHHHH
Confidence            5899999999999999999999999999887   678899999999888777765

>2hzt_A Putative HTH-type transcriptional regulator YTCD; DNA-binding protein, HTH-type transcription regulators, structural genomics, PSI-2; HET: CSU MSE; 2.00A {Bacillus subtilis} SCOP: a.4.5.69

Probab=96.40  E-value=0.013  Score=37.21  Aligned_cols=43  Identities=14%  Similarity=0.254  Sum_probs=38.2

Q ss_pred             hhhhhhh-CCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHH
Q psy11008          2 EDLAALF-RMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQE   44 (96)
Q Consensus         2 edLAa~F-~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~e   44 (96)
                      .|||..+ +++...+-.+++.|++.|-|....|   .|..++++|+.
T Consensus        31 ~eLa~~l~~is~~tls~~L~~Le~~GlI~r~~~~~d~r~~~y~LT~~   77 (107)
T 2hzt_A           31 SELKRLMPNITQKMLTQQLRELEADGVINRIVYNQVPPKVEYELSEY   77 (107)
T ss_dssp             HHHHHHCTTSCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECTT
T ss_pred             HHHHHHhcCCCHHHHHHHHHHHHHCCCEEEeecCCCCCeEEEEECcc
Confidence            5899999 9999999999999999999999887   35678899984

>1q1h_A TFE, transcription factor E, TFE; TFIIE, transcription initiation, preinitiation complex, RNA polymerase II, transcription bubble; 2.90A {Sulfolobus solfataricus} SCOP: a.4.5.41

Probab=96.39  E-value=0.0047  Score=38.94  Aligned_cols=50  Identities=24%  Similarity=0.416  Sum_probs=38.2

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEe---eCCCceEE---EcHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI---DDRGKFIY---ISQEELNSVAT   51 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi---DDRGKfIy---Is~eEl~~Va~   51 (96)
                      .+||..||++...|-..++.|++.|-+...-   ..+|.|+|   ++++++..+..
T Consensus        37 ~eLa~~lgvs~~tV~~~L~~L~~~GlV~~~~~~~~~~g~~v~~~~~~~~~i~~~~~   92 (110)
T 1q1h_A           37 EEIANQLNIKVNDVRKKLNLLEEQGFVSYRKTRDKDSGWFIYYWKPNIDQINEILL   92 (110)
T ss_dssp             HHHHHTTTSCHHHHHHHHHHHHHHTSCEEEEEC---CCCCEEEEECTHHHHC----
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCEEEEecccCCCceEEEEeecCHHHHHHHHH
Confidence            5899999999999999999999999998652   46788887   78777655443

>2hr3_A Probable transcriptional regulator; MCSG, structural genomics, PSI-2, protein structure initiati midwest center for structural genomics; 2.40A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=96.38  E-value=0.017  Score=36.53  Aligned_cols=54  Identities=22%  Similarity=0.268  Sum_probs=43.4

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEe---eCCCceEEEcHHHHHHHHHHHHh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI---DDRGKFIYISQEELNSVATFIKQ   55 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi---DDRGKfIyIs~eEl~~Va~fI~~   55 (96)
                      .+||..++++...+-..|+.|++.|-+.-.-   |-|.+++++|++-...+......
T Consensus        54 ~~la~~l~i~~~~vs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~~~~~~~~~  110 (147)
T 2hr3_A           54 SELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAK  110 (147)
T ss_dssp             HHHHHHTTCCHHHHHHHHHHHHHTTSEEEEC------CCEEEECHHHHHHHHHHHHH
T ss_pred             HHHHHHhCCChhhHHHHHHHHHHCCCEeeCCCCCCCCceeeEECHHHHHHHHHHHHH
Confidence            5899999999999999999999999998774   56899999999887666555443

>3oop_A LIN2960 protein; protein structure initiative, PSI-2, structural genomics, MI center for structural genomics, MCSG, unknown function; 1.78A {Listeria innocua}

Probab=96.37  E-value=0.019  Score=36.36  Aligned_cols=55  Identities=13%  Similarity=0.139  Sum_probs=46.2

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEe---eCCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI---DDRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi---DDRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .|||..++++.+.+-..|+.|++.|-+.-.-   |-|.+++++|++-...+.......
T Consensus        55 ~eLa~~l~~~~~~vs~~l~~L~~~Glv~r~~~~~D~R~~~~~LT~~G~~~~~~~~~~~  112 (143)
T 3oop_A           55 KEIALWTKKDTPTVNRIVDVLLRKELIVREISTEDRRISLLSLTDKGRKETTELRDIV  112 (143)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEEC----CCSCEEEECHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHhhHHHHHHHHHHCCCeeccCCCccCceeeeeECHHHHHHHHHHHHHH
Confidence            5899999999999999999999999999876   568899999998877766655443

>1lj9_A Transcriptional regulator SLYA; HTH DNA binding protein, structural genomics, PSI, protein structure initiative; 1.60A {Enterococcus faecalis} SCOP: a.4.5.28

Probab=96.33  E-value=0.021  Score=35.94  Aligned_cols=53  Identities=19%  Similarity=0.316  Sum_probs=44.6

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEe---eCCCceEEEcHHHHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI---DDRGKFIYISQEELNSVATFIK   54 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi---DDRGKfIyIs~eEl~~Va~fI~   54 (96)
                      .|||..++++...+-..|+.|++.|-+.-.-   |-|.+++++|++-...+.....
T Consensus        47 ~~la~~l~~s~~~vs~~l~~Le~~gli~r~~~~~d~R~~~~~lT~~G~~~~~~~~~  102 (144)
T 1lj9_A           47 EKIAELIKVDRTTAARAIKRLEEQGFIYRQEDASNKKIKRIYATEKGKNVYPIIVR  102 (144)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECSSCTTCEEEEECHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHhHHHHHHHHHHHCCCEEeecCCCCCceeeeEEChhHHHHHHHHHH
Confidence            5899999999999999999999999999887   4578899999987666554443

>1r1t_A Transcriptional repressor SMTB; zinc, transcriptional regulation, winged HTH protein, DNA binding, transcription repressor; 1.70A {Synechococcus elongatus pcc 7942} SCOP: a.4.5.5 PDB: 1r23_A 1smt_A 1r22_A

Probab=96.31  E-value=0.014  Score=38.51  Aligned_cols=55  Identities=11%  Similarity=0.130  Sum_probs=47.5

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .+||..+|++...+-..|+.|++.|-+.-.-+.|+.|.+++++.+..++..+...
T Consensus        63 ~ela~~lgis~stvs~~L~~Le~~Glv~~~~~gr~~~y~l~~~~l~~~~~~l~~~  117 (122)
T 1r1t_A           63 GDLAQAIGVSESAVSHQLRSLRNLRLVSYRKQGRHVYYQLQDHHIVALYQNALDH  117 (122)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEESSHHHHHHHHHHHHH
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEeCCEEEEEEChHHHHHHHHHHHHH
Confidence            5899999999888889999999999999888888888899999887777766543

>2dbb_A Putative HTH-type transcriptional regulator PH006; ASNC family, helix-turn-helix (HTH) domain, structural genom NPPSFA; 2.00A {Pyrococcus horikoshii}

Probab=96.26  E-value=0.012  Score=38.87  Aligned_cols=55  Identities=22%  Similarity=0.293  Sum_probs=43.9

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEE---eeCC--Cc----eEEE--cHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGV---IDDR--GK----FIYI--SQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGV---iDDR--GK----fIyI--s~eEl~~Va~fI~~r   56 (96)
                      .|||..+|++...|-.|++.|++.|.|.++   +|.+  |.    ||.|  .+...+.+++.+.+.
T Consensus        27 ~ela~~lg~s~~tv~~~l~~L~~~G~i~~~~~~~~~~~~g~~~~a~v~v~~~~~~~~~~~~~l~~~   92 (151)
T 2dbb_A           27 RELADILNTTRQRIARRIDKLKKLGIIRKFTIIPDIDKLGYMYAIVLIKSKVPSDADKVISEISDI   92 (151)
T ss_dssp             HHHHHHTTSCHHHHHHHHHHHHHHTSEEEEEEEECTGGGTEEEEEEEEEESSHHHHHHHHHHHTTC
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCEEEEEecCChHHhCCCEEEEEEEEeCCCCHHHHHHHHHcC
Confidence            589999999999999999999999999764   5543  54    5544  567777888888765

>2pjp_A Selenocysteine-specific elongation factor; SELB, protein-RNA complex, elongation factor, winged- helix, bulge, translation/RNA complex; 2.30A {Escherichia coli}

Probab=96.20  E-value=0.026  Score=37.08  Aligned_cols=68  Identities=16%  Similarity=0.280  Sum_probs=56.5

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVE   81 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~   81 (96)
                      .|||..|++....+.+=+..|..+|.|.=+-+|    +|++.+-++..+..|.+.           ++..|.+|++|+-+
T Consensus        24 ~~la~~~~~~~~~~~~~l~~l~~~G~l~~i~~~----~~~~~~~~~~~~~~l~~~-----------~~~~~~it~ae~Rd   88 (121)
T 2pjp_A           24 RDLAKETGTDEQAMRLTLRQAAQQGIITAIVKD----RYYRNDRIVEFANMIRDL-----------DQECGSTCAADFRD   88 (121)
T ss_dssp             HHHHHHTTCCHHHHHHHHHHHHHTTSEEEEETT----EEEEHHHHHHHHHHHHHH-----------HHHHSSEEHHHHHH
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCC----ceECHHHHHHHHHHHHHH-----------HHHCCCccHHHHHH
Confidence            589999999999999999999999999998776    788888888877766553           45559999999877


Q ss_pred             hcc
Q psy11008         82 NSN   84 (96)
Q Consensus        82 ~sN   84 (96)
                      ..+
T Consensus        89 ~lg   91 (121)
T 2pjp_A           89 RLG   91 (121)
T ss_dssp             HHT
T ss_pred             HHC
Confidence            654

>3eco_A MEPR; mutlidrug efflux pump regulator winged helix-turn-helix motif, DNA-binding, transcription, transcription regulation; 2.40A {Staphylococcus aureus} SCOP: a.4.5.0

Probab=96.11  E-value=0.027  Score=35.38  Aligned_cols=55  Identities=18%  Similarity=0.255  Sum_probs=45.6

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .|||..++++.+.+-..|+.|++.|-++=.-|   -|.++|++|++-...+.......
T Consensus        51 ~ela~~l~~~~~tvs~~l~~Le~~Gli~r~~~~~D~R~~~~~LT~~G~~~~~~~~~~~  108 (139)
T 3eco_A           51 NDIAKALQRTGPTVSNLLRNLERKKLIYRYVDAQDTRRKNIGLTTSGIKLVEAFTSIF  108 (139)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECCC--CCEEEEECHHHHHHHHHHHHHH
T ss_pred             HHHHHHhCCCcccHHHHHHHHHHCCCEeecCCCCCCCeeeeEECHHHHHHHHHHHHHH
Confidence            58999999999999999999999999998754   57899999998877766554443

>3s2w_A Transcriptional regulator, MARR family; structural genomics, PSI-biology, protein structure initiati midwest center for structural genomics; 2.45A {Methanosarcina mazei}

Probab=96.11  E-value=0.028  Score=36.46  Aligned_cols=55  Identities=15%  Similarity=0.215  Sum_probs=45.5

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEe---eCCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI---DDRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi---DDRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .|||..++++.+.+-..|+.|++.|-+.-.-   |-|-++|++|++-...+.......
T Consensus        68 ~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~~~DrR~~~l~LT~~G~~~~~~~~~~~  125 (159)
T 3s2w_A           68 ESLSDYLKIDKGTTARAIQKLVDEGYVFRQRDEKDRRSYRVFLTEKGKKLEPDMKKIA  125 (159)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECC---CCEEEEECHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCCCCCCeeEEEECHHHHHHHHHHHHHH
Confidence            5899999999999999999999999999877   557889999998877766655444

>1sfx_A Conserved hypothetical protein AF2008; structural genomics, HTH MOT protein structure initiative, midwest center for structural genomics; 1.55A {Archaeoglobus fulgidus} SCOP: a.4.5.50

Probab=96.10  E-value=0.02  Score=34.22  Aligned_cols=49  Identities=20%  Similarity=0.266  Sum_probs=40.0

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee--CCCceEEEcHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID--DRGKFIYISQEELNSVA   50 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD--DRGKfIyIs~eEl~~Va   50 (96)
                      .|||..++++...+-..|+.|++.|-|...-+  .|-+|+|+|+.-...+.
T Consensus        38 ~ela~~l~is~~tv~~~l~~L~~~glv~~~~~~~~r~~~~~~t~~g~~~~~   88 (109)
T 1sfx_A           38 SEIARELDLSARFVRDRLKVLLKRGFVRREIVEKGWVGYIYSAEKPEKVLK   88 (109)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEEESSSEEEEEEECCHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCEEEEeecCCceEEEEecCcHHHHHH
Confidence            58999999999999999999999999998775  45578888865544333

>1jgs_A Multiple antibiotic resistance protein MARR; transcription regulation, DNA-binding, repressor, transcription; HET: SAL; 2.30A {Escherichia coli} SCOP: a.4.5.28

Probab=96.08  E-value=0.063  Score=33.48  Aligned_cols=54  Identities=9%  Similarity=0.140  Sum_probs=44.6

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHHHHHHHHHh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELNSVATFIKQ   55 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~~Va~fI~~   55 (96)
                      .+||..++++...+-.-|+.|++.|-+.-.-|   -|.+++++|++-...+......
T Consensus        52 ~~la~~l~~~~~tvs~~l~~L~~~gli~r~~~~~d~R~~~~~lT~~G~~~~~~~~~~  108 (138)
T 1jgs_A           52 VELKKVLSVDLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTGGAAICEQCHQL  108 (138)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECTTCSSCEEEEECHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCChHHHHHHHHHHHHCCCEEecCCcccCceeEeEEChhHHHHHHHHHHH
Confidence            47999999999999999999999999998764   4778899999877666554433

>2heo_A Z-DNA binding protein 1; protein DLM1-Z-DNA complex, immune system-DNA complex; 1.70A {Mus musculus} PDB: 1j75_A

Probab=96.05  E-value=0.007  Score=36.69  Aligned_cols=36  Identities=8%  Similarity=0.120  Sum_probs=31.1

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceE
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFI   39 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfI   39 (96)
                      .|||..+|++.+.|...|+.|++.|-|.-  +.+|+|.
T Consensus        29 ~eLA~~lglsr~tv~~~l~~L~~~G~I~~--~~~G~y~   64 (67)
T 2heo_A           29 FQLVKKCQVPKKTLNQVLYRLKKEDRVSS--PSPKYWS   64 (67)
T ss_dssp             HHHHHHHCSCHHHHHHHHHHHHHTTSEEE--EETTEEE
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCcEec--CCCceEe
Confidence            68999999999999999999999999643  6678763

>2p5v_A Transcriptional regulator, LRP/ASNC family; NMB0573, structu genomics; 1.99A {Neisseria meningitidis} PDB: 2p6s_A 2p6t_A

Probab=96.03  E-value=0.013  Score=39.32  Aligned_cols=55  Identities=15%  Similarity=0.328  Sum_probs=42.8

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccE---EeeCC--Cc----eE--EEcHHH--HHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTG---VIDDR--GK----FI--YISQEE--LNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltG---ViDDR--GK----fI--yIs~eE--l~~Va~fI~~r   56 (96)
                      .|||..+|++...|-.||+.|++.|.|.+   ++|.+  |.    ||  .+.+..  ++.+++.+.+.
T Consensus        28 ~ela~~lg~s~~tv~~~l~~L~~~G~i~~~~~~~d~~~~g~~~~a~v~v~~~~~~~~~~~~~~~l~~~   95 (162)
T 2p5v_A           28 VELSERVALSPSPCLRRLKQLEDAGIVRQYAALLSPESVNLGLQAFIRVSIRKAKDAREDFAASVRKW   95 (162)
T ss_dssp             HHHHHHHTSCHHHHHHHHHHHHHTTSEEEEEEEECTGGGTCCEEEEEEEEECSSTTHHHHHHHHHTTC
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCEeeecccCChHHhcccEEEEEEEEEcCCchHHHHHHHHHhcC
Confidence            58999999999999999999999999976   45544  43    33  345644  78888888765

>3k0l_A Repressor protein; helix-turn-helix, structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG; 2.35A {Acinetobacter SP}

Probab=96.01  E-value=0.027  Score=36.72  Aligned_cols=55  Identities=18%  Similarity=0.178  Sum_probs=46.7

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .|||..++++.+.+-..|..|++.|-|+-.-|   -|.++|++|++-...+.......
T Consensus        64 ~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~~~DrR~~~l~LT~~G~~~~~~~~~~~  121 (162)
T 3k0l_A           64 AKLAERSFIKPQSANKILQDLLANGWIEKAPDPTHGRRILVTVTPSGLDKLNQCNQVV  121 (162)
T ss_dssp             HHHHHHHTSCGGGHHHHHHHHHHTTSEEEEECCSSSCCEEEEECHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCcCeEecCCCCcCCeeEeEECHhHHHHHHHHHHHH
Confidence            48999999999999999999999999998864   57889999998877666655443

>2nnn_A Probable transcriptional regulator; structural genomics, PSI-2, protein structure initiative, M center for structural genomics, MCSG; 2.40A {Pseudomonas aeruginosa}

Probab=96.01  E-value=0.026  Score=35.09  Aligned_cols=53  Identities=17%  Similarity=0.244  Sum_probs=44.0

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEe---eCCCceEEEcHHHHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI---DDRGKFIYISQEELNSVATFIK   54 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi---DDRGKfIyIs~eEl~~Va~fI~   54 (96)
                      .|||..++++...+-..|+.|++.|-+.-.-   |-|.+++++|++-...+.....
T Consensus        56 ~ela~~l~~~~~tvs~~l~~L~~~glv~r~~~~~d~R~~~~~lT~~G~~~~~~~~~  111 (140)
T 2nnn_A           56 NQLGRLTAMDAATIKGVVERLDKRGLIQRSADPDDGRRLLVSLSPAGRAELEAGLA  111 (140)
T ss_dssp             HHHHHHTTCCHHHHHHHHHHHHHTTCEEEEEETTEEEEEEEEECHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCEEeeCCCCCCCeeeeEECHhHHHHHHHHHH
Confidence            5899999999999999999999999999875   4577899999987666555433

>3bdd_A Regulatory protein MARR; putative multiple antibiotic-resistance repressor, structura genomics, joint center for structural genomics, JCSG; 2.20A {Streptococcus suis}

Probab=95.98  E-value=0.026  Score=35.21  Aligned_cols=48  Identities=10%  Similarity=0.248  Sum_probs=42.4

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELNSV   49 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~~V   49 (96)
                      .+||..++++...+-..|+.|++.|-+.-.-|   -|.+++++|++-...+
T Consensus        49 ~ela~~l~is~~~vs~~l~~L~~~gli~~~~~~~d~r~~~~~lT~~G~~~~   99 (142)
T 3bdd_A           49 LALQERLQIDRAAVTRHLKLLEESGYIIRKRNPDNQREVLVWPTEQAREAL   99 (142)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECSSSTTCEEEEECHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHH
Confidence            58999999999999999999999999998875   6788999999876655

>2lkp_A Transcriptional regulator, ARSR family; symmetric homodimer, NI(II) binding protein, DNA binding Pro transcription regulator; NMR {Mycobacterium tuberculosis}

Probab=95.97  E-value=0.025  Score=35.77  Aligned_cols=55  Identities=16%  Similarity=0.179  Sum_probs=45.4

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .+||..++++...+-..|+.|++.|.+.-.-|.|+.|..++.+++..++..+.+.
T Consensus        49 ~ela~~l~is~stvsr~l~~Le~~Glv~~~~~~r~~~~~~~~~~~~~~~~~~~~~  103 (119)
T 2lkp_A           49 TDLAEAIGMEQSAVSHQLRVLRNLGLVVGDRAGRSIVYSLYDTHVAQLLDEAIYH  103 (119)
T ss_dssp             HHHHHHHSSCHHHHHHHHHHHHHHCSEEEEEETTEEEEEESCHHHHHHHHHHHHH
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCEEEEecCCEEEEEEchHHHHHHHHHHHHH
Confidence            5899999998888889999999999998777888888888877777666655544

>3cjn_A Transcriptional regulator, MARR family; silicibacter pomeroy structural genomics, PSI-2, protein structure initiative; 1.95A {Silicibacter pomeroyi dss-3}

Probab=95.96  E-value=0.038  Score=35.64  Aligned_cols=52  Identities=13%  Similarity=0.218  Sum_probs=43.6

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEe---eCCCceEEEcHHHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI---DDRGKFIYISQEELNSVATFI   53 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi---DDRGKfIyIs~eEl~~Va~fI   53 (96)
                      .+||..++++...+-..|+.|++.|-+.-.-   |-|.+++++|++-...+....
T Consensus        70 ~ela~~l~is~~tvs~~l~~Le~~Gli~r~~~~~d~R~~~~~lT~~G~~~~~~~~  124 (162)
T 3cjn_A           70 GTLGIFAVVEQSTLSRALDGLQADGLVRREVDSDDQRSSRVYLTPAGRAVYDRLW  124 (162)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEC--CCSSEEEEECHHHHHHHHHHH
T ss_pred             HHHHHHHCCChhHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHHHH
Confidence            5899999999999999999999999998776   567889999998765554443

>3bja_A Transcriptional regulator, MARR family, putative; NP_978771.1, putative MARR-like transcription regulator, MAR structural genomics; 2.38A {Bacillus cereus}

Probab=95.95  E-value=0.023  Score=35.34  Aligned_cols=53  Identities=11%  Similarity=0.194  Sum_probs=44.3

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEe---eCCCceEEEcHHHHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI---DDRGKFIYISQEELNSVATFIK   54 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi---DDRGKfIyIs~eEl~~Va~fI~   54 (96)
                      .|||..++++...+-..|+.|++.|-+.-.-   |-|.+++++|+.-...+.....
T Consensus        51 ~ela~~l~~~~~tvs~~l~~L~~~gli~r~~~~~d~r~~~~~lT~~G~~~~~~~~~  106 (139)
T 3bja_A           51 SKLIENMGCVPSNMTTMIQRMKRDGYVMTEKNPNDQRETLVYLTKKGEETKKQVDV  106 (139)
T ss_dssp             HHHHHHCSSCCTTHHHHHHHHHHTTSEEEEECSSCTTCEEEEECHHHHHHHHHHHH
T ss_pred             HHHHHHHCCChhHHHHHHHHHHHCCCeeeccCCCCCceeEEEECHHHHHHHHHHHH
Confidence            5899999999999999999999999998775   4578899999987766655443

>2rdp_A Putative transcriptional regulator MARR; PFAM PF01047, winged-helix binding motif, structural genomics, PSI-2; 2.30A {Geobacillus stearothermophilus}

Probab=95.95  E-value=0.036  Score=35.06  Aligned_cols=54  Identities=15%  Similarity=0.233  Sum_probs=42.9

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEe---eCCCceEEEcHHHHHHHHHHHHh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI---DDRGKFIYISQEELNSVATFIKQ   55 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi---DDRGKfIyIs~eEl~~Va~fI~~   55 (96)
                      .|||..++++...+-..|+.|++.|-+.-.-   |-|.+++++|++-...+......
T Consensus        60 ~ela~~l~~~~~tvs~~l~~Le~~Glv~r~~~~~d~R~~~~~lT~~G~~~~~~~~~~  116 (150)
T 2rdp_A           60 GELSNKMYLACSTTTDLVDRMERNGLVARVRDEHDRRVVRIRLLEKGERIIEEVIEK  116 (150)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECCC---CEEEEECHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCchhHHHHHHHHHHCCCeeecCCCCCcceeEeEECHhHHHHHHHHHHH
Confidence            5899999999999999999999999998876   45788999999877666554433

>2eth_A Transcriptional regulator, putative, MAR family; MARR family, structural genomics, joint center for structura genomics, JCSG; 2.30A {Thermotoga maritima} SCOP: a.4.5.28

Probab=95.92  E-value=0.039  Score=35.54  Aligned_cols=52  Identities=13%  Similarity=0.289  Sum_probs=43.8

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEe---eCCCceEEEcHHHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI---DDRGKFIYISQEELNSVATFI   53 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi---DDRGKfIyIs~eEl~~Va~fI   53 (96)
                      .|||..++++...+-..|+.|++.|-++-.-   |-|.+++++|++-...+....
T Consensus        62 ~ela~~l~is~~tvs~~l~~Le~~Gli~r~~~~~d~R~~~~~lT~~G~~~~~~~~  116 (154)
T 2eth_A           62 KEIAEFLSTTKSNVTNVVDSLEKRGLVVREMDPVDRRTYRVVLTEKGKEIFGEIL  116 (154)
T ss_dssp             HHHHHHTTSCHHHHHHHHHHHHHTTSEEEEECTTTSSCEEEEECHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCEEeeCCCCCcceeEEEECHHHHHHHHHHH
Confidence            5899999999999999999999999999877   457889999998766655543

>3bj6_A Transcriptional regulator, MARR family; helix-turn-helix, trasnscription regulator, STR genomics, PSI-2, protein structure initiative; 2.01A {Silicibacter pomeroyi dss-3}

Probab=95.91  E-value=0.043  Score=34.80  Aligned_cols=53  Identities=17%  Similarity=0.258  Sum_probs=44.3

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEe---eCCCceEEEcHHHHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI---DDRGKFIYISQEELNSVATFIK   54 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi---DDRGKfIyIs~eEl~~Va~fI~   54 (96)
                      .|||..++++...+-..|+.|++.|-+.-.-   |-|.+++++|+.-...+.....
T Consensus        58 ~ela~~l~~~~~~vs~~l~~Le~~Glv~r~~~~~d~R~~~~~lT~~G~~~~~~~~~  113 (152)
T 3bj6_A           58 PQLGAALQMKRQYISRILQEVQRAGLIERRTNPEHARSHRYWLTPRGEAIITAIRA  113 (152)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEECCSSSTTSCEEEECHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCeeecCCcccccceeeEEChhhHHHHHHHHH
Confidence            5899999999999999999999999998876   4678899999987665555433

>2bv6_A MGRA, HTH-type transcriptional regulator MGRA; multidrug resistance regulator, virulence determinant, transcriptional factors; 2.8A {Staphylococcus aureus} SCOP: a.4.5.28

Probab=95.89  E-value=0.024  Score=35.69  Aligned_cols=52  Identities=10%  Similarity=0.163  Sum_probs=44.4

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELNSVATFI   53 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~~Va~fI   53 (96)
                      .+||..++++...+-..|+.|++.|-++=.-|   -|.+++++|++....+....
T Consensus        55 ~ela~~l~~~~~tvs~~l~~L~~~gli~r~~~~~d~R~~~~~lT~~G~~~~~~~~  109 (142)
T 2bv6_A           55 KKVVTELALDTGTVSPLLKRMEQVDLIKRERSEVDQREVFIHLTDKSETIRPELS  109 (142)
T ss_dssp             HHHHHHTTCCTTTHHHHHHHHHHTTSEEEEECSSSTTCEEEEECHHHHHHHHHHT
T ss_pred             HHHHHHHCCChhhHHHHHHHHHHCCCEEeecCCCCcceEEEEEChHHHHHHHHHH
Confidence            58999999999999999999999999998775   67789999998876655543

>2w25_A Probable transcriptional regulatory protein; transcription regulation, mutant, RV3291C, Glu104Ala, DNA-binding; 2.15A {Mycobacterium tuberculosis} PDB: 2vbw_A* 2vbx_A* 2vby_A* 2vbz_A* 2vc0_A 2vc1_A 2w24_A 2ivm_A 2w29_A 2qz8_A

Probab=95.88  E-value=0.0062  Score=40.28  Aligned_cols=55  Identities=18%  Similarity=0.358  Sum_probs=43.2

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEe---eCC--C----ceEEEc---HHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI---DDR--G----KFIYIS---QEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi---DDR--G----KfIyIs---~eEl~~Va~fI~~r   56 (96)
                      .+||..+|++...+-.||+.|++.|.|.+.-   |.|  |    -|+.++   ++..+.+++.+.+.
T Consensus        25 ~ela~~lg~s~~tv~~~l~~L~~~G~i~~~~~~~d~~~~g~~~~a~v~~~~~~~~~~~~~~~~l~~~   91 (150)
T 2w25_A           25 SELATRAGLSVSAVQSRVRRLESRGVVQGYSARINPEAVGHLLSAFVAITPLDPSQPDDAPARLEHI   91 (150)
T ss_dssp             HHHHHHHTSCHHHHHHHHHHHHHTTSEEEEEEEECTGGGTCCEEEEEEEEESCTTSCCCHHHHHTTC
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCEEEEEeccChhHcccceEEEEEEEEcCCCCHHHHHHHHhcC
Confidence            5899999999999999999999999997654   433  3    267776   55567777777655

>3bro_A Transcriptional regulator; helix_TURN_helix, multiple antibiotic resistance protein (MA structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.04A {Oenococcus oeni} SCOP: a.4.5.28

Probab=95.88  E-value=0.028  Score=35.14  Aligned_cols=52  Identities=13%  Similarity=0.222  Sum_probs=43.0

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELNSVATFI   53 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~~Va~fI   53 (96)
                      .+||..++++...+-..|+.|++.|-+.=.-|   -|.++|++|++-...+....
T Consensus        54 ~ela~~l~~~~~tvs~~l~~Le~~Gli~r~~~~~d~R~~~i~lT~~G~~~~~~~~  108 (141)
T 3bro_A           54 RDLESEFSIKSSTATVLLQRMEIKKLLYRKVSGKDSRQKCLKLTKKANKLETIIL  108 (141)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECSSCTTSEEEEECHHHHTTHHHHH
T ss_pred             HHHHHHHCCCcchHHHHHHHHHHCCCEEeeCCCcCCCeeeeEECHHHHHHHHHHH
Confidence            58999999999999999999999999987764   57789999998755544443

>2fbi_A Probable transcriptional regulator; MARR, APC5816, structural genomic protein structure initiative; 2.10A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=95.86  E-value=0.023  Score=35.45  Aligned_cols=53  Identities=11%  Similarity=0.180  Sum_probs=44.1

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELNSVATFIK   54 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~~Va~fI~   54 (96)
                      .+||..++++...+-..|+.|++.|-++-.-|   -|.+++++|++-...+.....
T Consensus        54 ~ela~~l~~s~~~vs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~~~~~~~~  109 (142)
T 2fbi_A           54 YQLANQACILRPSMTGVLARLERDGIVRRWKAPKDQRRVYVNLTEKGQQCFVSMSG  109 (142)
T ss_dssp             HHHHHHTTCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHhHHHHHHHHHHHCCCEEeecCCCCCCeeEEEECHHHHHHHHHHHH
Confidence            58999999999999999999999999998865   478899999987666555433

>2gxg_A 146AA long hypothetical transcriptional regulator; winged helix; 1.45A {Sulfolobus tokodaii} PDB: 2eb7_A 2yr2_A 3gez_A 3gf2_A* 3gfi_A 3gfm_A 3gfj_A 3gfl_A

Probab=95.84  E-value=0.051  Score=34.08  Aligned_cols=53  Identities=21%  Similarity=0.291  Sum_probs=44.4

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELNSVATFIK   54 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~~Va~fI~   54 (96)
                      .|||..++++...+-..|+.|++.|-+.-.-|   -|.+++++|++-...+.....
T Consensus        54 ~ela~~l~~s~~tvs~~l~~Le~~glv~r~~~~~d~r~~~~~lT~~G~~~~~~~~~  109 (146)
T 2gxg_A           54 AYLANRYFVTQSAITASVDKLEEMGLVVRVRDREDRRKILIEITEKGLETFNKGIE  109 (146)
T ss_dssp             HHHHHHTTCCHHHHHHHHHHHHHTTSEEEEECSSCTTCEEEEECHHHHHHHHHHHH
T ss_pred             HHHHHHhCCCchhHHHHHHHHHHCCCEEeecCCCCCceEEEEECHHHHHHHHHHHH
Confidence            58999999999999999999999999998765   577889999987766655443

>3hsr_A HTH-type transcriptional regulator SARZ; helix-turn-helix, cysteine disulfide, MARR-family transcript regulator, DNA-binding; 1.90A {Staphylococcus aureus subsp} PDB: 3hse_A 3hrm_A 4gxo_A

Probab=95.81  E-value=0.03  Score=35.68  Aligned_cols=55  Identities=11%  Similarity=0.151  Sum_probs=44.1

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEe---eCCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI---DDRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi---DDRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .|||..++++.+.+-.-|+.|++.|-++=.-   |-|.++|++|++-...+.......
T Consensus        54 ~eLa~~l~~~~~tvs~~l~~L~~~Glv~r~~~~~D~R~~~~~LT~~G~~~~~~~~~~~  111 (140)
T 3hsr_A           54 KKLGERVFLDSGTLTPLLKKLEKKDYVVRTREEKDERNLQISLTEQGKAIKSPLAEIS  111 (140)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEEC-------CEEEECHHHHHTHHHHHHHH
T ss_pred             HHHHHHHCCChhhHHHHHHHHHHCCCeEecCCCCCcceeeeeEChHHHHHHHHHHHHH
Confidence            5899999999999999999999999999875   568899999999877776655444

>2a61_A Transcriptional regulator TM0710; APC4350, MCSG, midwest center for structural genomics, PSI, protein structure initiative, MARR; 1.80A {Thermotoga maritima} SCOP: a.4.5.28

Probab=95.77  E-value=0.032  Score=34.99  Aligned_cols=52  Identities=23%  Similarity=0.374  Sum_probs=43.4

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELNSVATFI   53 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~~Va~fI   53 (96)
                      .+||..++++...+-..|+.|++.|-++-.-|   -|.+++++|++-...+....
T Consensus        51 ~~la~~l~~s~~tvs~~l~~L~~~glv~r~~~~~d~r~~~~~lT~~G~~~~~~~~  105 (145)
T 2a61_A           51 GELSVLLGVAKSTVTGLVKRLEADGYLTRTPDPADRRAYFLVITRKGEEVIEKVI  105 (145)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHHHHHH
T ss_pred             HHHHHHHCCCchhHHHHHHHHHHCCCeeecCCCCCCceEEEEECHHHHHHHHHHH
Confidence            58999999999999999999999999998864   46778999998766555443

>2htj_A P fimbrial regulatory protein KS71A; winged helix-turn-helix, PAP PILI, transcription activator; NMR {Escherichia coli} SCOP: a.4.5.73

Probab=95.74  E-value=0.0093  Score=36.23  Aligned_cols=43  Identities=12%  Similarity=0.223  Sum_probs=34.9

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEE--eeCCCceEEEcHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGV--IDDRGKFIYISQE   44 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGV--iDDRGKfIyIs~e   44 (96)
                      .|||..||++...+-..++.|++.|.|...  -..+|.|..++++
T Consensus        18 ~eLa~~lgvs~~tv~r~L~~L~~~GlI~~~~~~~gr~~~y~l~~~   62 (81)
T 2htj_A           18 AEIAEALAVTDYQARYYLLLLEKAGMVQRSPLRRGMATYWFLKGE   62 (81)
T ss_dssp             HHHHHHHTSCHHHHHHHHHHHHHHTSEEEECCSSSSSCEEEESSC
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCEEEeccCCCCcEEEEEChh
Confidence            589999999999999999999999999843  3456667776654

>1s3j_A YUSO protein; structural genomics, MARR transcriptional regulator family, PSI, protein structure initiative; HET: MSE; 2.25A {Bacillus subtilis} SCOP: a.4.5.28

Probab=95.74  E-value=0.058  Score=34.28  Aligned_cols=53  Identities=13%  Similarity=0.119  Sum_probs=43.8

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEe---eCCCceEEEcHHHHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI---DDRGKFIYISQEELNSVATFIK   54 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi---DDRGKfIyIs~eEl~~Va~fI~   54 (96)
                      .+||..++++...+-..|+.|++.|-+.-.-   |-|.+++++|++-...+.....
T Consensus        55 ~ela~~l~~s~~tvs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~~~~~~~~  110 (155)
T 1s3j_A           55 SEIAERMEVKPSAVTLMADRLEQKNLIARTHNTKDRRVIDLSLTDEGDIKFEEVLA  110 (155)
T ss_dssp             HHHHHHHTSCHHHHHHHHHHHHHTTSEEEEECSSCTTSEEEEECHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCEeecCCCCCCceEEEEECHHHHHHHHHHHH
Confidence            5899999999999999999999999998776   4578899999987665554433

>1z7u_A Hypothetical protein EF0647; winged-helix-turn-helix, MARR, structural genomics, PSI, Pro structure initiative; 2.20A {Enterococcus faecalis} SCOP: a.4.5.69

Probab=95.74  E-value=0.041  Score=35.15  Aligned_cols=45  Identities=16%  Similarity=0.180  Sum_probs=39.7

Q ss_pred             hhhhhhh-CCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHH
Q psy11008          2 EDLAALF-RMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEEL   46 (96)
Q Consensus         2 edLAa~F-~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl   46 (96)
                      .|||..+ +++...+-.+++.|++.|-|....|   .|-+++++|+.-.
T Consensus        39 ~eLa~~l~~is~~tvs~~L~~Le~~GlI~r~~~~~d~r~~~~~LT~~G~   87 (112)
T 1z7u_A           39 GELMRALDGITQRVLTDRLREMEKDGLVHRESFNELPPRVEYTLTPEGY   87 (112)
T ss_dssp             HHHHHHSTTCCHHHHHHHHHHHHHHTSEEEEEECCSSCEEEEEECHHHH
T ss_pred             HHHHHHhccCCHHHHHHHHHHHHHCCCEEEeecCCCCCeEEEEECHhHH
Confidence            5899999 9999999999999999999999886   4677889998743

>2pg4_A Uncharacterized protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2, DNA binding protein; HET: MSE CIT; 2.21A {Aeropyrum pernix} SCOP: a.4.5.48

Probab=95.73  E-value=0.033  Score=34.19  Aligned_cols=55  Identities=11%  Similarity=0.141  Sum_probs=44.4

Q ss_pred             hhhhhhhCCChHH-HHHHHHHHHHcCCcc-EEeeCCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQS-VIDRIVELQKTGALT-GVIDDRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~-vI~RI~eL~~~g~lt-GViDDRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .|||..++++... +-..|+.|++.|-+. .--|-|.+++++|++-...+.......
T Consensus        34 ~eLa~~l~is~~t~vs~~l~~Le~~Glv~~~~~drR~~~~~LT~~G~~~~~~~~~~~   90 (95)
T 2pg4_A           34 AEIVKASGVSEKTFFMGLKDRLIRAGLVKEETLSYRVKTLKLTEKGRRLAECLEKCR   90 (95)
T ss_dssp             HHHHHHHCCCHHHHHTTHHHHHHHTTSEEEEEEETTEEEEEECHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCchHHHHHHHHHHHHCCCeecCCCCCCeEEEEECHhHHHHHHHHHHHH
Confidence            5899999999999 889999999999998 112458899999998877766655543

>3nrv_A Putative transcriptional regulator (MARR/EMRR FAM; PSI-2, protein structure initiati structural genomics; HET: MSE; 2.00A {Acinetobacter SP}

Probab=95.73  E-value=0.026  Score=35.82  Aligned_cols=55  Identities=9%  Similarity=0.084  Sum_probs=42.1

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEe---eCCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI---DDRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi---DDRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .|||..++++...+-..|+.|++.|-+.-.-   |-|.+++++|++-...+.......
T Consensus        58 ~ela~~l~~~~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~~~lT~~G~~~~~~~~~~~  115 (148)
T 3nrv_A           58 QKISDILGLDKAAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEMGQELYEVASDFA  115 (148)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEC---------CCBEECHHHHHHHHHHHHHT
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCEEeecCCCCcceeEeEECHhHHHHHHHHHHHH
Confidence            4899999999999999999999999998774   467999999998877666655443

>2cyy_A Putative HTH-type transcriptional regulator PH151; structural genomics, pyrococcus horikosii OT3, NPPSFA; HET: MSE GLN; 1.80A {Pyrococcus horikoshii} SCOP: a.4.5.32 d.58.4.2

Probab=95.68  E-value=0.015  Score=38.53  Aligned_cols=55  Identities=20%  Similarity=0.432  Sum_probs=45.0

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEE---eeCC--Cc----eE--EEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGV---IDDR--GK----FI--YISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGV---iDDR--GK----fI--yIs~eEl~~Va~fI~~r   56 (96)
                      .+||..+|++...|-.||+.|++.|.|.+.   +|.+  |.    |+  .+.++.++.+++.+.+.
T Consensus        25 ~ela~~lg~s~~tv~~~l~~L~~~G~i~~~~~~~d~~~~G~~~~a~v~v~~~~~~~~~~~~~l~~~   90 (151)
T 2cyy_A           25 REISKITGLAESTIHERIRKLRESGVIKKFTAIIDPEALGYSMLAFILVKVKAGKYSEVASNLAKY   90 (151)
T ss_dssp             HHHHHHHCSCHHHHHHHHHHHHHHTSSCCCCCCCCGGGGTCCEEEEEEEEECTTCHHHHHHHHHTC
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEEEECHHHCCccEEEEEEEEECcccHHHHHHHHhcC
Confidence            589999999999999999999999999763   5543  43    44  45578899999999876

>3deu_A Transcriptional regulator SLYA; MARR, WING-helix, transcription regulator, activator, DNA-binding, repressor; HET: SAL; 2.30A {Salmonella typhimurium} SCOP: a.4.5.28

Probab=95.67  E-value=0.032  Score=37.13  Aligned_cols=55  Identities=18%  Similarity=0.257  Sum_probs=43.3

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEe---eCCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI---DDRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi---DDRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .|||..++++...+-..|..|++.|-|+=.-   |-|.++|++|++-...+.......
T Consensus        72 ~eLa~~l~i~~~tvs~~l~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~~~~~~~  129 (166)
T 3deu_A           72 IQLAKAIGIEQPSLVRTLDQLEDKGLISRQTCASDRRAKRIKLTEKAEPLIAEMEEVI  129 (166)
T ss_dssp             HHHHHHHTSCHHHHHHHHHHHHHTTSEEEC--------CEEEECGGGHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHhhHHHHHHHHHHCCCEEeeCCCCCCCeeEEEECHHHHHHHHHHHHHH
Confidence            5899999999999999999999999999776   668899999998877766655443

>2fbh_A Transcriptional regulator PA3341; MARR, transcription regulator, APC5857, structural genomics, protein structure initiative; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.28

Probab=95.66  E-value=0.044  Score=34.26  Aligned_cols=53  Identities=15%  Similarity=0.179  Sum_probs=44.6

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELNSVATFIK   54 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~~Va~fI~   54 (96)
                      .+||..++++...+-..|+.|++.|-++=.-|   -|.+++++|++-...+.....
T Consensus        56 ~~la~~l~~s~~~vs~~l~~L~~~glv~r~~~~~d~R~~~~~lT~~G~~~~~~~~~  111 (146)
T 2fbh_A           56 RELAQSVGVEGPTLARLLDGLESQGLVRRLAVAEDRRAKHIVLTPKADVLIADIEA  111 (146)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEECCBTTBCSCEEEECTTHHHHHHHHHH
T ss_pred             HHHHHHhCCChhhHHHHHHHHHHCCCeeecCCCcccCeeeeEECHhHHHHHHHHHH
Confidence            58999999999999999999999999987764   588899999987766655433

>2nyx_A Probable transcriptional regulatory protein, RV14; alpha/beta, structural genomics, PSI-2; 2.30A {Mycobacterium tuberculosis}

Probab=95.64  E-value=0.058  Score=35.56  Aligned_cols=54  Identities=11%  Similarity=0.135  Sum_probs=45.2

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHHHHHHHHHh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELNSVATFIKQ   55 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~~Va~fI~~   55 (96)
                      .|||..++++.+.+-..|+.|++.|-|.-.-|   -|.+++++|++-...+......
T Consensus        63 ~eLa~~l~is~~tvs~~l~~Le~~GlV~r~~~~~DrR~~~~~LT~~G~~~~~~~~~~  119 (168)
T 2nyx_A           63 ATLATLLGVQPSATGRMVDRLVGAELIDRLPHPTSRRELLAALTKRGRDVVRQVTEH  119 (168)
T ss_dssp             HHHHHHHTSCHHHHHHHHHHHHHTTSEEEEECSSCSSCEEEEECHHHHHHHHHHHHH
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHHHHHHHHHHHHH
Confidence            58999999999999999999999999998765   5778899999887666554433

>1i1g_A Transcriptional regulator LRPA; helix-turn-helix, LRP/ASNC family; 2.90A {Pyrococcus furiosus} SCOP: a.4.5.32 d.58.4.2

Probab=95.64  E-value=0.031  Score=36.01  Aligned_cols=55  Identities=24%  Similarity=0.379  Sum_probs=43.8

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEE---eeCC--Cc----eE--EEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGV---IDDR--GK----FI--YISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGV---iDDR--GK----fI--yIs~eEl~~Va~fI~~r   56 (96)
                      .+||..+|++...+-.|++.|++.|-+.+.   +|.+  |.    |+  .+.++.+..+++.+.+.
T Consensus        22 ~ela~~lg~s~~tv~~~l~~L~~~G~i~~~~~~~~~~~~g~~~~~~v~~~~~~~~~~~~~~~l~~~   87 (141)
T 1i1g_A           22 TEIAKKLGISETAVRKRVKALEEKGIIEGYTIKINPKKLGYSLVTITGVDTKPEKLFEVAEKLKEY   87 (141)
T ss_dssp             HHHHHHHTSCHHHHHHHHHHHHHHTSSCCCCCCCCSGGGTCCEEEEEEEEECGGGHHHHHHHHHHS
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCEeccccccChHHhCccEEEEEEEEECchhHHHHHHHHhcC
Confidence            589999999999999999999999999765   3432  43    22  23678899999999886

>2cfx_A HTH-type transcriptional regulator LRPC; transcriptional regulation, DNA binding, FFRP; 2.4A {Bacillus subtilis} SCOP: a.4.5.32 d.58.4.2

Probab=95.62  E-value=0.034  Score=36.66  Aligned_cols=55  Identities=16%  Similarity=0.431  Sum_probs=44.3

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEE---eeCC--Cc----eEE--EcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGV---IDDR--GK----FIY--ISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGV---iDDR--GK----fIy--Is~eEl~~Va~fI~~r   56 (96)
                      .|||..+|++...|-.||+.|++.|.|.+.   +|.+  |.    |+.  +.++.++.++.++.+.
T Consensus        23 ~ela~~lg~s~~tv~~~l~~L~~~G~i~~~~~~~d~~~~g~~~~a~v~v~~~~~~~~~~~~~l~~~   88 (144)
T 2cfx_A           23 RELGRKIKLSPPSVTERVRQLESFGIIKQYTLEVDQKKLGLPVSCIVEATVKNADYERFKSYIQTL   88 (144)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEEEECTGGGTCCEEEEEEEEEGGGCHHHHHHHHHTC
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCeEEEecccChhhcCceEEEEEEEEECcccHHHHHHHHhcC
Confidence            589999999999999999999999999864   5644  42    333  4677788898888775

>3e6m_A MARR family transcriptional regulator; APC88769, silicibacter pomeroyi DSS, structural genomics, PSI-2, protein structure initiative; 2.20A {Silicibacter pomeroyi}

Probab=95.62  E-value=0.055  Score=35.20  Aligned_cols=55  Identities=18%  Similarity=0.219  Sum_probs=46.4

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEe---eCCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI---DDRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi---DDRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .|||..++++.+.+-.-|..|++.|-|.=.-   |-|.++|++|++-...+.......
T Consensus        71 ~eLa~~l~~~~~~vs~~l~~Le~~Glv~r~~~~~DrR~~~~~LT~~G~~~~~~~~~~~  128 (161)
T 3e6m_A           71 GQLATLGVMEQSTTSRTVDQLVDEGLAARSISDADQRKRTVVLTRKGKKKLAEISPLI  128 (161)
T ss_dssp             HHHHHHTTCCHHHHHHHHHHHHHTTSEEECC---CCCSCEEEECHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCEEeeCCcccCCeeEeeECHHHHHHHHHHHHHH
Confidence            5899999999999999999999999998765   568899999998877766655543

>2fsw_A PG_0823 protein; alpha-beta structure, helix-turn-helix, winged-helix-turn-HE structural genomics, PSI, protein structure initiative; HET: MSE; 2.16A {Porphyromonas gingivalis} SCOP: a.4.5.69

Probab=95.61  E-value=0.06  Score=34.03  Aligned_cols=44  Identities=11%  Similarity=0.044  Sum_probs=38.1

Q ss_pred             hhhhhhh-CCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHH
Q psy11008          2 EDLAALF-RMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEE   45 (96)
Q Consensus         2 edLAa~F-~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eE   45 (96)
                      .|||..+ |++...+-.+++.|++.|-+....|   .|-.++++|+.-
T Consensus        42 ~eL~~~l~gis~~~ls~~L~~Le~~GlV~r~~~~~d~r~~~y~LT~~G   89 (107)
T 2fsw_A           42 GELKRAIPGISEKMLIDELKFLCGKGLIKKKQYPEVPPRVEYSLTPLG   89 (107)
T ss_dssp             HHHHHHSTTCCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECHHH
T ss_pred             HHHHHHcccCCHHHHHHHHHHHHHCCCEEEeecCCCCCeeEEEECccH
Confidence            5899999 5999999999999999999999886   356788999964

>3f3x_A Transcriptional regulator, MARR family, putative; DNA binding protein, DNA-binding, transcription regulation; 1.90A {Sulfolobus solfataricus}

Probab=95.59  E-value=0.041  Score=34.86  Aligned_cols=55  Identities=13%  Similarity=0.121  Sum_probs=46.3

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .|||..++++...+-..|+.|++.|-++-.-|   -|.+++++|++-...+.......
T Consensus        54 ~~la~~l~~~~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~~~LT~~G~~~~~~~~~~~  111 (144)
T 3f3x_A           54 VYLANRYFVTQSAITAAVDKLEAKGLVRRIRDSKDRRIVIVEITPKGRQVLLEANEVL  111 (144)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCChhHHHHHHHHHHHCCCEEeccCCCCCceEEEEECHHHHHHHHHHHHHH
Confidence            58999999999999999999999999998875   46779999998877766655444

>3b73_A PHIH1 repressor-like protein; winged-helix-turn-helix, structural genomics, PSI-2, protein structure initiative; 2.12A {Haloarcula marismortui atcc 43049}

Probab=95.59  E-value=0.025  Score=38.10  Aligned_cols=45  Identities=22%  Similarity=0.282  Sum_probs=39.2

Q ss_pred             hhhhhhh--CCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHH
Q psy11008          2 EDLAALF--RMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSV   49 (96)
Q Consensus         2 edLAa~F--~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~V   49 (96)
                      .+||..+  +++.+.|-.|++.|++.|-|...  .|| +..||++-..-+
T Consensus        31 ~eLA~~l~~giS~~aVs~rL~~Le~~GLV~~~--~rg-~Y~LT~~G~~~l   77 (111)
T 3b73_A           31 KELEDRDEIRISKSSVSRRLKKLADHDLLQPL--ANG-VYVITEEGEAYL   77 (111)
T ss_dssp             HHHHTSTTCCSCHHHHHHHHHHHHHTTSEEEC--STT-CEEECHHHHHHH
T ss_pred             HHHHHHHhcCCCHHHHHHHHHHHHHCCCEEec--CCc-eEEECchHHHHH
Confidence            4799999  99999999999999999999986  678 888999875443

>3g3z_A NMB1585, transcriptional regulator, MARR family; transcription factor, structur genomics, oxford protein production facility; 2.10A {Neisseria meningitidis serogroup B}

Probab=95.56  E-value=0.043  Score=34.79  Aligned_cols=55  Identities=11%  Similarity=0.164  Sum_probs=45.6

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .|||..++++...+-..|..|++.|-++-.-|   -|.++|++|++-...+.......
T Consensus        49 ~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~~~LT~~G~~~~~~~~~~~  106 (145)
T 3g3z_A           49 KHIGEKWSLPKQTVSGVCKTLAGQGLIEWQEGEQDRRKRLLSLTETGKAYAAPLTESA  106 (145)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEECCCSSCGGGSCEEECHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCEeeccCCCCCceeeeeEChhHHHHHHHHHHHH
Confidence            58999999999999999999999999997654   57889999998877665554443

>1ufm_A COP9 complex subunit 4; helix-turn-helix, structural genomics, riken structural genomics/proteomics initiative, RSGI, signaling protein; NMR {Mus musculus} SCOP: a.4.5.47

Probab=95.53  E-value=0.015  Score=37.54  Aligned_cols=42  Identities=19%  Similarity=0.360  Sum_probs=37.7

Q ss_pred             ChhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEc
Q psy11008          1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYIS   42 (96)
Q Consensus         1 ledLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs   42 (96)
                      |+.||..|+++.+++-.-|..|..+|+|.|.||.--..|...
T Consensus        33 l~~La~ll~ls~~~vE~~ls~mI~~~~l~akIDq~~g~V~f~   74 (84)
T 1ufm_A           33 FEELGALLEIPAAKAEKIASQMITEGRMNGFIDQIDGIVHFE   74 (84)
T ss_dssp             HHHHHHHTTSCHHHHHHHHHHHHHTTSSCEEEETTTTEEEEC
T ss_pred             HHHHHHHHCcCHHHHHHHHHHHHhCCcEEEEEeCCCCEEEeC
Confidence            468999999999999999999999999999999877777654

>3kp7_A Transcriptional regulator TCAR; multiple drug resistance, biofilm, transcription regulation, binding, transcription regulator; 2.30A {Staphylococcus epidermidis RP62A} PDB: 3kp3_A* 3kp4_A* 3kp5_A* 3kp2_A* 3kp6_A

Probab=95.50  E-value=0.028  Score=36.04  Aligned_cols=54  Identities=15%  Similarity=0.102  Sum_probs=41.3

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccE-----EeeCCCceEEEcHHHHHHHHHHHHh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTG-----VIDDRGKFIYISQEELNSVATFIKQ   55 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltG-----ViDDRGKfIyIs~eEl~~Va~fI~~   55 (96)
                      .|||..++++...+-..|..|++.|-+.-     --|-|.++|++|++-...+......
T Consensus        55 ~eLa~~l~~~~~~vs~~l~~Le~~Glv~r~~~~~~~D~R~~~~~lT~~G~~~~~~~~~~  113 (151)
T 3kp7_A           55 GQITEKQGVNKAAVSRRVKKLLNAELVKLEKPDSNTDQRLKIIKLSNKGKKYIKERKAI  113 (151)
T ss_dssp             HHHHHHHCSCSSHHHHHHHHHHHTTSEEC-----------CCBEECHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCEEeeCCCCCCCCCeeEEEECHhHHHHHHHHHHH
Confidence            58999999999999999999999999995     3567899999999877666655443

>2fa5_A Transcriptional regulator MARR/EMRR family; multiple antibiotics resistance repressor, XCC structural genomics, X-RAY diffraction; 1.80A {Xanthomonas campestris}

Probab=95.49  E-value=0.033  Score=35.84  Aligned_cols=54  Identities=15%  Similarity=0.166  Sum_probs=40.6

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEe---eCCCceEEEcHHHHHHHHHHHHh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI---DDRGKFIYISQEELNSVATFIKQ   55 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi---DDRGKfIyIs~eEl~~Va~fI~~   55 (96)
                      .|||..++++...+-..|+.|++.|-+.-.-   |-|.+++++|++-...+......
T Consensus        67 ~ela~~l~is~~tvs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~~~~~~~~~  123 (162)
T 2fa5_A           67 SEVSDRTAMDKVAVSRAVARLLERGFIRRETHGDDRRRSMLALSPAGRQVYETVAPL  123 (162)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEC---------CCCEECHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCEeeecCCCCCCeeEEEECHHHHHHHHHHHHH
Confidence            5899999999999999999999999998765   56889999999876665554433

>3cdh_A Transcriptional regulator, MARR family; helix-turn-hleix, structura genomics, PSI-2, protein structure initiative; 2.69A {Silicibacter pomeroyi dss-3}

Probab=95.46  E-value=0.052  Score=34.74  Aligned_cols=54  Identities=17%  Similarity=0.242  Sum_probs=42.8

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEe---eCCCceEEEcHHHHHHHHHHHHh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI---DDRGKFIYISQEELNSVATFIKQ   55 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi---DDRGKfIyIs~eEl~~Va~fI~~   55 (96)
                      .|||..++++...+-..|+.|++.|-+.-.-   |-|.+++++|+.-...+......
T Consensus        61 ~ela~~l~i~~~tvs~~l~~Le~~Glv~r~~~~~d~R~~~~~lT~~G~~~~~~~~~~  117 (155)
T 3cdh_A           61 TRLAKLSLMEQSRMTRIVDQMDARGLVTRVADAKDKRRVRVRLTDDGRALAESLVAS  117 (155)
T ss_dssp             HHHHHHTTCCHHHHHHHHHHHHHTTSEEECC------CCCEEECHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCCCcCCeeEeEECHHHHHHHHHHHHH
Confidence            5899999999999999999999999998654   56789999999877666554443

>2pex_A Transcriptional regulator OHRR; transcription regulator; 1.90A {Xanthomonas campestris} PDB: 2pfb_A

Probab=95.43  E-value=0.028  Score=35.95  Aligned_cols=48  Identities=15%  Similarity=0.238  Sum_probs=38.4

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEe---eCCCceEEEcHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI---DDRGKFIYISQEELNSV   49 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi---DDRGKfIyIs~eEl~~V   49 (96)
                      .+||..++++...+-..|+.|++.|-+.=.-   |-|.+++++|++-...+
T Consensus        65 ~ela~~l~~s~~tvs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~~~  115 (153)
T 2pex_A           65 SEIGERLYLDSATLTPLLKRLQAAGLVTRTRAASDERQVIIALTETGRALR  115 (153)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEEC-------CEEEECHHHHHGG
T ss_pred             HHHHHHhCCCcccHHHHHHHHHHCCCEeecCCcccCCeeEeeECHHHHHHH
Confidence            5899999999999999999999999998776   55888999999865443

>4hbl_A Transcriptional regulator, MARR family; HTH, transcription factor, DNA binding; 2.50A {Staphylococcus epidermidis}

Probab=95.40  E-value=0.038  Score=35.58  Aligned_cols=55  Identities=9%  Similarity=0.198  Sum_probs=43.3

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEe---eCCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI---DDRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi---DDRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .|||..++++.+.+-.-|..|++.|-|+=.-   |-|.++|++|++-...+..+....
T Consensus        59 ~eLa~~l~~~~~~vs~~l~~L~~~Glv~r~~~~~D~R~~~~~LT~~G~~~~~~~~~~~  116 (149)
T 4hbl_A           59 NSIGRHLDLSSNTLTPMLKRLEQSGWVKRERQQSDKRQLIITLTDNGQQQQEAVFEAI  116 (149)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHHTSEEC---------CEEEECSHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCEeeCCCCCCcceeeeeECHHHHHHHHHHHHHH
Confidence            5899999999999999999999999998765   568899999999888877765544

>2f2e_A PA1607; transcription factor, helix-TRUN-helix, APC5613, structural genomics, PSI, protein structure initiative; HET: GLC; 1.85A {Pseudomonas aeruginosa} SCOP: a.4.5.69

Probab=95.35  E-value=0.082  Score=35.60  Aligned_cols=55  Identities=9%  Similarity=0.175  Sum_probs=43.5

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee--CCCceEEEcHHH------HHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID--DRGKFIYISQEE------LNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD--DRGKfIyIs~eE------l~~Va~fI~~r   56 (96)
                      .|||..+|++...+-.+|+.|++.|-|....+  |+..++++|+.-      +.++.+|..+.
T Consensus        41 ~eLa~~lgis~~tls~~L~~Le~~GlI~r~~~~~d~~~~y~LT~~G~~l~~~l~~l~~w~~~~  103 (146)
T 2f2e_A           41 GEFQKSLGLAKNILAARLRNLVEHGVMVAVPAESGSHQEYRLTDKGRALFPLLVAIRQWGEDY  103 (146)
T ss_dssp             HHHHHHHCCCHHHHHHHHHHHHHTTSEEEEECSSSSCEEEEECHHHHTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHHCCCEEEEecCCCCeEEEEECchHHHHHHHHHHHHHHHHHh
Confidence            58999999999999999999999999999987  554566688853      44555555543

>3fm5_A Transcriptional regulator; MCSG, PF04017, PSI, MARR, structu genomics, protein structure initiative, midwest center for structural genomics; HET: GOL; 2.00A {Rhodococcus jostii}

Probab=95.35  E-value=0.038  Score=35.34  Aligned_cols=55  Identities=18%  Similarity=0.268  Sum_probs=40.8

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEe---eCCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI---DDRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi---DDRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .|||..++++.+.+-..|+.|++.|-+.-.-   |-|.++|++|++-...+.......
T Consensus        58 ~eLa~~l~i~~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~~~LT~~G~~~~~~~~~~~  115 (150)
T 3fm5_A           58 RGVAATMGLDPSQIVGLVDELEERGLVVRTLDPSDRRNKLIAATEEGRRLRDDAKARV  115 (150)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHTTTSEEC-----------CEECHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHhHHHHHHHHHHHCCCEEeeCCccccchheeeECHHHHHHHHHHHHHH
Confidence            5899999999999999999999999998754   468899999998887776665544

>2d1h_A ST1889, 109AA long hypothetical transcriptional regulator; helix-turn-helix, intermolecular and intramolecular S-S bond structural genomics; 2.05A {Sulfolobus tokodaii} SCOP: a.4.5.50

Probab=95.33  E-value=0.083  Score=31.52  Aligned_cols=55  Identities=20%  Similarity=0.335  Sum_probs=42.3

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeC---CC---ceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDD---RG---KFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDD---RG---KfIyIs~eEl~~Va~fI~~r   56 (96)
                      .|||..+|++...+-..++.|++.|-+.-.-+.   +|   .++.++++-+..+..++.+.
T Consensus        40 ~ela~~l~is~~tv~~~l~~L~~~g~v~~~~~~~~~~gr~~~~~~l~~~~~~~~~~~~~~~  100 (109)
T 2d1h_A           40 EELADIFKLSKTTVENSLKKLIELGLVVRTKTEGKKIGRPKYYYSISSNILEKIRNDLLNC  100 (109)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEC-------CCEEEEECTTHHHHHHHHHHHH
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCeEeeccccCCCCCCCeeeecCHHHHHHHHHHHHHH
Confidence            589999999999999999999999999987652   13   35668886666666666554

>2b0l_A GTP-sensing transcriptional pleiotropic repressor; CODY, DNA-binding, nucleotide-binding, transcript regulation, winged HTH motif.; 2.90A {Bacillus subtilis} SCOP: a.4.5.66

Probab=95.33  E-value=0.05  Score=35.45  Aligned_cols=49  Identities=12%  Similarity=0.278  Sum_probs=38.0

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee-CCCceEE-EcHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID-DRGKFIY-ISQEELNSVA   50 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD-DRGKfIy-Is~eEl~~Va   50 (96)
                      .+||..||++..-|.+.++.|+++|.|.-.-. -+|-|+. ++.+++..+.
T Consensus        47 ~eLa~~lgVSr~tVr~al~~L~~~GlI~~~~gG~~G~~V~~~~~~~~~~~~   97 (102)
T 2b0l_A           47 SKIADRVGITRSVIVNALRKLESAGVIESRSLGMKGTYIKVLNNKFLIELE   97 (102)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECSSSCEEEEECCHHHHHHHH
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCEEEEeCCCCcEEEecCCHHHHHHHH
Confidence            58999999999999999999999999876543 3676664 4555555543

>2frh_A SARA, staphylococcal accessory regulator A; winged-helix protein, divalent metal binding, transcription; 2.50A {Staphylococcus aureus} SCOP: a.4.5.28 PDB: 2fnp_A 1fzp_D

Probab=95.31  E-value=0.034  Score=35.73  Aligned_cols=55  Identities=13%  Similarity=0.285  Sum_probs=45.6

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEE---eeCCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGV---IDDRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGV---iDDRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .|||..++++...+-.-|+.|++.|-+.=.   -|.|.++|++|++-...+.......
T Consensus        57 ~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~i~LT~~G~~~~~~~~~~~  114 (127)
T 2frh_A           57 KDIINHLNYKQPQVVKAVKILSQEDYFDKKRNEHDERTVLILVNAQQRKKIESLLSRV  114 (127)
T ss_dssp             HHHHHHSSSHHHHHHHHHHHHHHTTSSCCBCCSSSSCCCEEECCSHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHHHHHHH
Confidence            589999999999998999999999999864   3568999999999877666555443

>3nqo_A MARR-family transcriptional regulator; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE PG4; 2.20A {Clostridium difficile}

Probab=95.29  E-value=0.083  Score=35.91  Aligned_cols=55  Identities=13%  Similarity=0.178  Sum_probs=46.2

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .+||..++++.+.+-..|..|++.|-|+-.-|   -|.++|++|++-...+.......
T Consensus        61 ~eLa~~l~is~~tvs~~l~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~~~~~~~  118 (189)
T 3nqo_A           61 NNIARKMGTSKQNINRLVANLEKNGYVDVIPSPHDKRAINVKVTDLGKKVMVTCSRTG  118 (189)
T ss_dssp             HHHHHHHTSCHHHHHHHHHHHHHTTSEEEEECSSCSSCEEEEECHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHHHHHHHHHHHHHH
Confidence            48999999999999999999999999998875   47789999998877666555443

>3jw4_A Transcriptional regulator, MARR/EMRR family; DNA-binding protein, structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.10A {Clostridium acetobutylicum} SCOP: a.4.5.0

Probab=95.29  E-value=0.014  Score=37.28  Aligned_cols=55  Identities=27%  Similarity=0.360  Sum_probs=36.6

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEe---eCCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI---DDRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi---DDRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .|||..++++.+.+-.-|+.|++.|-++=.-   |-|.++|++|++-...+.......
T Consensus        61 ~eLa~~l~~~~~~vs~~l~~L~~~Glv~r~~~~~DrR~~~~~LT~~G~~~~~~~~~~~  118 (148)
T 3jw4_A           61 KDLAQFFGRRGASITSMLQGLEKKGYIERRIPENNARQKNIYVLPKGAALVEEFNNIF  118 (148)
T ss_dssp             HHHHHC------CHHHHHHHHHHTTSBCCC--------CCCCBCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCChhHHHHHHHHHHHCCCEEeeCCCCCchhheeeECHHHHHHHHHHHHHH
Confidence            4899999999999999999999999998776   568899999998876666554443

>3bpv_A Transcriptional regulator; MARR, DNA binding, transcription factor, winged helix motif, DNA-binding; 1.40A {Methanobacterium thermoautotrophicum} PDB: 3bpx_A*

Probab=95.28  E-value=0.038  Score=34.38  Aligned_cols=52  Identities=13%  Similarity=0.343  Sum_probs=43.0

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELNSVATFI   53 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~~Va~fI   53 (96)
                      .|||..++++...+-..|+.|++.|-+.-.-|   -|.+++++|++-...+....
T Consensus        47 ~ela~~l~~s~~tvs~~l~~L~~~glv~~~~~~~d~R~~~~~lT~~G~~~~~~~~  101 (138)
T 3bpv_A           47 DELATFFHVDKGTIARTLRRLEESGFIEREQDPENRRRYILEVTRRGEEIIPLIL  101 (138)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHTHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCEEeecCCCCceeEEeeECHhHHHHHHHHH
Confidence            58999999999999999999999999998765   46788999998765555443

>2ia0_A Putative HTH-type transcriptional regulator PF086; ASNC, PSI, structural genomics, southeast collaboratory for structural genomics; 2.37A {Pyrococcus furiosus}

Probab=95.26  E-value=0.072  Score=36.76  Aligned_cols=55  Identities=13%  Similarity=0.290  Sum_probs=43.5

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEE---eeCC--C---ceEEE--cHH--------HHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGV---IDDR--G---KFIYI--SQE--------ELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGV---iDDR--G---KfIyI--s~e--------El~~Va~fI~~r   56 (96)
                      .|||..+|++...|..||+.|++.|.|.+.   +|.+  |   -|+.|  ++.        .++.++..+.+.
T Consensus        35 ~eLA~~lglS~~tv~~~l~~L~~~G~I~~~~~~~d~~~lG~~~a~v~v~~~~~~~~~f~~~~~~~~~~~l~~~  107 (171)
T 2ia0_A           35 SELSEQLKKPESTIHFRIKKLQERGVIERYTIILGEQLKPKHLALIVLEVGKPVIEDFLERYISYISSTLSAL  107 (171)
T ss_dssp             HHHHHHHTSCHHHHHHHHHHHHHTTSEEEEEEEECTTTSCSEEEEEEEEESCC--CHHHHHHHHHHHHHHHTS
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCEEeecccCCHHHhhcceEEEEEEECCccccccchhHHHHHHHHHHCC
Confidence            589999999999999999999999999764   4543  3   25444  444        788888888876

>3ech_A MEXR, multidrug resistance operon repressor; winged helix, helix-turn-helix, protein-peptide complex; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.28 PDB: 1lnw_A 3mex_A

Probab=95.26  E-value=0.029  Score=35.63  Aligned_cols=54  Identities=15%  Similarity=0.142  Sum_probs=37.6

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHHHHHHHHHh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELNSVATFIKQ   55 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~~Va~fI~~   55 (96)
                      .|||..++++.+.+-..|..|++.|-+.-.-|   -|.++|++|++-...+......
T Consensus        55 ~eLa~~l~~~~~tvs~~l~~L~~~Glv~r~~~~~DrR~~~~~LT~~G~~~~~~~~~~  111 (142)
T 3ech_A           55 QDLGRQMCRDKALITRKIRELEGRNLVRRERNPSDQRSFQLFLTDEGLAIHLHAELI  111 (142)
T ss_dssp             HHHHHHHC---CHHHHHHHHHHHTTSEEC----------CCEECHHHHHHHHHHHHH
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHHCCCEeeccCCCCCCeeeeEECHHHHHHHHHHHHH
Confidence            58999999999999999999999999988765   5889999999877666655443

>3boq_A Transcriptional regulator, MARR family; MARR famil structural genomics, PSI-2, protein structure initiative; 2.39A {Silicibacter pomeroyi dss-3}

Probab=95.25  E-value=0.032  Score=35.84  Aligned_cols=54  Identities=15%  Similarity=0.210  Sum_probs=42.0

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEe---eCCCceEEEcHHHHHHHHHHHHh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI---DDRGKFIYISQEELNSVATFIKQ   55 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi---DDRGKfIyIs~eEl~~Va~fI~~   55 (96)
                      .+||..++++...+-..|+.|++.|-|+-.-   |-|.+++++|++-...+......
T Consensus        66 ~ela~~l~i~~~tvs~~l~~Le~~Gli~r~~~~~d~R~~~~~lT~~G~~~~~~~~~~  122 (160)
T 3boq_A           66 GKLSGALKVTNGNVSGLVNRLIKDGMVVKAMSADDRRSFSAKLTDAGLTTFKQASEA  122 (160)
T ss_dssp             HHHHHHCSSCCSCHHHHHHHHHHHTSEEEC--------CEEEECHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCChhhHHHHHHHHHHCCCEEeecCCCCCCeEEEEEChhHHHHHHHHHHH
Confidence            5899999999999999999999999998764   56889999999887766554443

>2zkz_A Transcriptional repressor PAGR; protein-DNA, HTH motif, dimer, DN binding, transcription regulation; 2.00A {Bacillus anthracis}

Probab=95.23  E-value=0.029  Score=35.28  Aligned_cols=52  Identities=6%  Similarity=0.250  Sum_probs=45.6

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIK   54 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~   54 (96)
                      .|||..+|++...+-..++.|++. -+..--+.|..|.+++++.+..+..++.
T Consensus        45 ~ela~~l~is~stvs~hL~~L~~~-lv~~~~~gr~~~y~l~~~~~~~~~~~l~   96 (99)
T 2zkz_A           45 TQIIQILKLPQSTVSQHLCKMRGK-VLKRNRQGLEIYYSINNPKVEGIIKLLN   96 (99)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHBTT-TBEEEEETTEEEEECCCHHHHHHHHHHC
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHH-hhhheEeCcEEEEEEChHHHHHHHHHHH
Confidence            589999999998888999999999 8888888777788889999998888774

>1yyv_A Putative transcriptional regulator; reductive methylation, D lysine, structural genomics, PSI; HET: MLY; 2.35A {Salmonella typhimurium} SCOP: a.4.5.69

Probab=95.19  E-value=0.075  Score=35.50  Aligned_cols=44  Identities=14%  Similarity=0.110  Sum_probs=38.8

Q ss_pred             hhhhhhh-CCChHHHHHHHHHHHHcCCccEEeeC---CCceEEEcHHH
Q psy11008          2 EDLAALF-RMKTQSVIDRIVELQKTGALTGVIDD---RGKFIYISQEE   45 (96)
Q Consensus         2 edLAa~F-~lktq~vI~RI~eL~~~g~ltGViDD---RGKfIyIs~eE   45 (96)
                      .|||..+ |++...+-.+++.|++.|-|.-..|.   |.+++++|+.-
T Consensus        52 ~eLa~~l~gis~~tls~~L~~Le~~GlV~r~~~~~d~r~~~y~LT~~G   99 (131)
T 1yyv_A           52 SDLRRXMGGVSEXMLAQSLQALEQDGFLNRVSYPVVPPHVEYSLTPLG   99 (131)
T ss_dssp             HHHHHHSTTCCHHHHHHHHHHHHHHTCEEEEEECSSSCEEEEEECHHH
T ss_pred             HHHHHHhccCCHHHHHHHHHHHHHCCcEEEEecCCCCCeEEEEECccH
Confidence            4899999 79999999999999999999998873   67799999863

>2qww_A Transcriptional regulator, MARR family; YP_013417.1, multiple antibiotic-resistance repressor (MARR) structural genomics; HET: MSE; 2.07A {Listeria monocytogenes str}

Probab=95.04  E-value=0.08  Score=33.70  Aligned_cols=54  Identities=13%  Similarity=0.083  Sum_probs=43.7

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccE--Ee---eCCCceEEEcHHHHHHHHHHHHh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTG--VI---DDRGKFIYISQEELNSVATFIKQ   55 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltG--Vi---DDRGKfIyIs~eEl~~Va~fI~~   55 (96)
                      .+||..++++.+.+-..|..|++.|-+.=  .-   |-|.+++++|++-...+......
T Consensus        59 ~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~~~~~d~R~~~~~LT~~G~~~~~~~~~~  117 (154)
T 2qww_A           59 ADLTKRLIITGSSAAANVDGLISLGLVVKLNKTIPNDSMDLTLKLSKKGEDLSKRSTAN  117 (154)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEESCC--CTTCTTCEEEECHHHHHHHHHHHSC
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCEEecCcCCCCCCceeEeEECHHHHHHHHHHHhh
Confidence            58999999999989899999999999987  44   45677999999887666555433

>1qgp_A Protein (double stranded RNA adenosine deaminase); Z-alpha-Z-DNA binding domain, RNA-editing, Z-DNA recognition, ADAR1, helix- turn-helix; NMR {Homo sapiens} SCOP: a.4.5.19

Probab=95.02  E-value=0.026  Score=35.29  Aligned_cols=38  Identities=16%  Similarity=0.183  Sum_probs=33.2

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceE
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFI   39 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfI   39 (96)
                      .+||..+|++...|-.+|..|++.|.|.++-+..|+|.
T Consensus        35 ~eLA~~Lgvs~~tV~~~L~~L~~~G~I~~~g~~~~~W~   72 (77)
T 1qgp_A           35 HDLSGKLGTPKKEINRVLYSLAKKGKLQKEAGTPPLWK   72 (77)
T ss_dssp             HHHHHHHCCCHHHHHHHHHHHHHHTSEEEECSSSCEEE
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCEEecCCCCCceE
Confidence            58999999999988899999999999999876666653

>1z91_A Organic hydroperoxide resistance transcriptional; OHRR, MARR family, bacterial transcription factor, DNA bindi protein; 2.50A {Bacillus subtilis} SCOP: a.4.5.28 PDB: 1z9c_A*

Probab=94.94  E-value=0.039  Score=34.83  Aligned_cols=49  Identities=8%  Similarity=0.215  Sum_probs=41.2

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELNSVA   50 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~~Va   50 (96)
                      .|||..++++...+-.-|..|++.|-+.-.-|   -|.+++++|++-...+.
T Consensus        58 ~~la~~l~~~~~tvs~~l~~L~~~glv~r~~~~~d~R~~~~~LT~~G~~~~~  109 (147)
T 1z91_A           58 KKMGEQLYLDSGTLTPMLKRMEQQGLITRKRSEEDERSVLISLTEDGALLKE  109 (147)
T ss_dssp             HHHHHTTTCCHHHHHHHHHHHHHHTSEECCBCSSCTTSBEEEECHHHHSGGG
T ss_pred             HHHHHHHCCCcCcHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHHHHH
Confidence            58999999999999999999999999987654   58899999998654433

>1on2_A Transcriptional regulator MNTR; helix-turn-helix, DNA-binding protein, metalloregulatory protein; 1.61A {Bacillus subtilis} SCOP: a.4.5.24 a.76.1.1 PDB: 2ev0_A 1on1_A 2ev5_A 2ev6_A* 2f5c_A 2f5d_A 2f5e_A 2f5f_A 2hyf_A* 2hyg_D 3r60_A* 3r61_A*

Probab=94.94  E-value=0.14  Score=32.85  Aligned_cols=48  Identities=15%  Similarity=0.140  Sum_probs=39.5

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATF   52 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~f   52 (96)
                      .|||..++++...|-..|+.|++.|-|.-.   +++.+++|+.-...+...
T Consensus        26 ~ela~~l~vs~~tvs~~l~~Le~~Glv~r~---~~~~~~LT~~g~~~~~~~   73 (142)
T 1on2_A           26 SDIAEALAVHPSSVTKMVQKLDKDEYLIYE---KYRGLVLTSKGKKIGKRL   73 (142)
T ss_dssp             HHHHHHHTSCHHHHHHHHHHHHHTTSEEEE---TTTEEEECHHHHHHHHHH
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHHCCCEEEe---eCceEEEchhHHHHHHHH
Confidence            589999999999999999999999988754   568999999765554443

>4ev0_A Transcription regulator, CRP family; CAMP binding, winged helix-turn-helix motif, DNA binding, transcription activator; HET: CMP; 2.40A {Thermus thermophilus}

Probab=94.85  E-value=0.03  Score=36.86  Aligned_cols=49  Identities=20%  Similarity=0.234  Sum_probs=40.4

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFI   53 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI   53 (96)
                      +|||...|++.+.+-.-+++|+++|.|.  . ++|+++-...+.|.++|.++
T Consensus       167 ~~lA~~lg~sr~tvsR~l~~l~~~g~I~--~-~~~~i~i~d~~~L~~~a~~l  215 (216)
T 4ev0_A          167 HELAALAGTSRETVSRVLHALAEEGVVR--L-GPGTVEVREAALLEEIAFGL  215 (216)
T ss_dssp             HHHHHHHTSCHHHHHHHHHHHHHTTSEE--E-ETTEEEESCHHHHHHHHTTC
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHHCCCEE--e-cCCEEEEeCHHHHHHHhhcc
Confidence            6899999998888888899999999885  2 56777667888888888753

>3u2r_A Regulatory protein MARR; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, helix-turn-helix; 2.20A {Planctomyces limnophilus}

Probab=94.83  E-value=0.053  Score=35.51  Aligned_cols=54  Identities=11%  Similarity=0.110  Sum_probs=42.6

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHHHHHHHHHh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELNSVATFIKQ   55 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~~Va~fI~~   55 (96)
                      .|||..++++.+.+-.-|..|++.|-|+-.-|   -|-++|++|++-...+......
T Consensus        66 ~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~~~DrR~~~l~LT~~G~~~~~~~~~~  122 (168)
T 3u2r_A           66 LQIADRLISRAPDITRLIDRLDDRGLVLRTRKPENRRVVEVALTDAGLKLLKDLEEP  122 (168)
T ss_dssp             HHHHHHC---CTHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCChhhHHHHHHHHHHCCCEeecCCCCCCCeeEeEECHHHHHHHHHHHHH
Confidence            58999999999999999999999999998875   5778999999877666655543

>3r0a_A Putative transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; 2.31A {Methanosarcina mazei}

Probab=94.78  E-value=0.066  Score=35.02  Aligned_cols=54  Identities=19%  Similarity=0.340  Sum_probs=40.0

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee--CC-C-ceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID--DR-G-KFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD--DR-G-KfIyIs~eEl~~Va~fI~~r   56 (96)
                      .+||..++++...|-..|+.|++.|-+...-+  |+ | .|+|... ....+...|++.
T Consensus        46 ~eLa~~l~~s~sTV~r~L~~L~~~GlV~r~~~~~d~~~~~~~y~~~-~~~~~~~~i~~~  103 (123)
T 3r0a_A           46 DALSKSLKLDVSTVQRSVKKLHEKEILQRSQQNLDGGGYVYIYKIY-SKNQIRNIIQKI  103 (123)
T ss_dssp             HHHHHHHTSCHHHHHHHHHHHHHTTSEEEEEEECTTSCEEEEEEEC-CHHHHHHHHHHH
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCEEeeCCccCCCcceEEEecC-CHHHHHHHHHHH
Confidence            58999999999999999999999999987543  44 4 3566542 345555555555

>3i4p_A Transcriptional regulator, ASNC family; PSI, structural genom protein structure initiative, midwest center for structural genomics; 2.30A {Agrobacterium tumefaciens str}

Probab=94.52  E-value=0.027  Score=38.20  Aligned_cols=55  Identities=22%  Similarity=0.364  Sum_probs=43.8

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccE---EeeCC--Cc----eEEEc--H---HHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTG---VIDDR--GK----FIYIS--Q---EELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltG---ViDDR--GK----fIyIs--~---eEl~~Va~fI~~r   56 (96)
                      .+||..+|++...|..||+.|++.|.|.|   ++|.+  |.    ||.|+  +   +.++.+++.+.+.
T Consensus        21 ~~la~~lg~s~~tv~~rl~~L~~~g~i~~~~a~~~~~~lG~~~~a~v~v~v~~~~~~~~~~~~~~l~~~   89 (162)
T 3i4p_A           21 ADLAKKVGLSTTPCWRRIQKMEEDGVIRRRVALLDPVKVNTKVTVFVSIRTASHSIEWLKRFSEVVSEF   89 (162)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSSCCCCCCCCTTTTTCCEEEEEEEECCSCCHHHHHHHHHHHHHC
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCeeeceeeeCHHHhcCcEEEEEEEEEcCCChHHHHHHHHHHhcC
Confidence            58999999999999999999999999875   45643  32    55554  2   4588899988876

>1ku9_A Hypothetical protein MJ223; putative transcription factor, homodimeric winged-helix fold, structural genomics, PSI; 2.80A {Methanocaldococcus jannaschii} SCOP: a.4.5.36

Probab=94.41  E-value=0.12  Score=32.02  Aligned_cols=40  Identities=13%  Similarity=0.212  Sum_probs=32.9

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeC---CCceEEE
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDD---RGKFIYI   41 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDD---RGKfIyI   41 (96)
                      .|||..+|++...+-..++.|++.|-+.-.-|+   |..|+.+
T Consensus        45 ~ela~~l~~~~stvs~~l~~L~~~G~v~r~~~~~d~r~~~~~~   87 (152)
T 1ku9_A           45 SDIMEELKISKGNVSMSLKKLEELGFVRKVWIKGERKNYYEAV   87 (152)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEECCTTCSSCEEEEC
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCEEEEecCCCceEEEeec
Confidence            589999999999999999999999999998642   3334444

>2fxa_A Protease production regulatory protein HPR; protease porduction, regulation, STR genomics, PSI, protein structure initiative; HET: PGE P6G 1PE; 2.40A {Bacillus subtilis} SCOP: a.4.5.28

Probab=94.30  E-value=0.14  Score=35.76  Aligned_cols=55  Identities=13%  Similarity=0.216  Sum_probs=45.4

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .+||..++++...+-..|..|++.|-|.-.-|   -|-++|++|++-...+.......
T Consensus        66 ~eLa~~l~i~~stvs~~l~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~~~~~~~  123 (207)
T 2fxa_A           66 SEIAKFGVMHVSTAFNFSKKLEERGYLRFSKRLNDKRNTYVQLTEEGTEVFWSLLEEF  123 (207)
T ss_dssp             HHHHHHTTCCHHHHHHHHHHHHHHTSEEEECC------CEEEECHHHHHHHHHHHHHC
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCCCCCceEEEEECHHHHHHHHHHHHHH
Confidence            48999999999999999999999999998875   57889999999888777766544

>2h09_A Transcriptional regulator MNTR; transcription regulator, diphtheria toxin, manganese transport, structural genomics, NPPSFA; 2.10A {Escherichia coli}

Probab=93.97  E-value=0.3  Score=31.77  Aligned_cols=49  Identities=14%  Similarity=0.120  Sum_probs=38.8

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFI   53 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI   53 (96)
                      .+||..|+++...+-..|+.|++.|-+.-   .+|+.+++|+.-...+....
T Consensus        58 ~~la~~l~vs~~tvs~~l~~Le~~Glv~r---~~~~~~~lT~~g~~~~~~~~  106 (155)
T 2h09_A           58 VDMAARLGVSQPTVAKMLKRLATMGLIEM---IPWRGVFLTAEGEKLAQESR  106 (155)
T ss_dssp             HHHHHHHTSCHHHHHHHHHHHHHTTCEEE---ETTTEEEECHHHHHHHHHHH
T ss_pred             HHHHHHhCcCHHHHHHHHHHHHHCCCEEE---ecCCceEEChhHHHHHHHHH
Confidence            48999999999999999999999986542   35688999998765554443

>4aik_A Transcriptional regulator SLYA; transcription, transcription factor; 1.85A {Yersinia pseudotuberculosis} PDB: 4aih_A 4aij_A 3qpt_A* 3q5f_A*

Probab=93.94  E-value=0.23  Score=32.83  Aligned_cols=54  Identities=17%  Similarity=0.224  Sum_probs=45.2

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHHHHHHHHHh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELNSVATFIKQ   55 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~~Va~fI~~   55 (96)
                      .|||..++++.+.+-.-|..|++.|-+.=.-|   -|.++|++|++-...+......
T Consensus        50 ~eLa~~l~~~~~tvs~~v~~Le~~GlV~R~~~~~DrR~~~l~LT~~G~~~~~~~~~~  106 (151)
T 4aik_A           50 IQLAKAIGIEQPSLVRTLDQLEEKGLITRHTSANDRRAKRIKLTEQSSPIIEQVDGV  106 (151)
T ss_dssp             HHHHHHHTSCHHHHHHHHHHHHHTTSEEEEECSSCTTCEEEEECGGGHHHHHHHHHH
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHhCCCeEeecCCCCCcchhhhcCHHHHHHHHHHHHH
Confidence            48999999999999999999999999987776   5788999999877665554433

>4b8x_A SCO5413, possible MARR-transcriptional regulator; winged helix motif; HET: CME; 1.25A {Streptomyces coelicolor}

Probab=93.88  E-value=0.3  Score=31.94  Aligned_cols=52  Identities=15%  Similarity=0.254  Sum_probs=43.2

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELNSVATFI   53 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~~Va~fI   53 (96)
                      .|||..++++.+.+-.-|..|++.|-++=.-|   -|.++|++|++-...+....
T Consensus        55 ~eLa~~l~~~~~tvs~~v~~Le~~Glv~r~~~~~DrR~~~l~LT~~G~~~~~~~~  109 (147)
T 4b8x_A           55 SKIGERLMVHPTSVTNTVDRLVRSGLVAKRPNPNDGRGTLATITDKGREVVEAAT  109 (147)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECC----CEEEEECHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHhCCCEEEeecCCcCceeEEEECHHHHHHHHHHH
Confidence            48999999999999999999999999998776   58899999998876665543

>2x4h_A Hypothetical protein SSO2273; transcription; 2.30A {Sulfolobus solfataricus}

Probab=93.85  E-value=0.26  Score=31.29  Aligned_cols=47  Identities=15%  Similarity=0.340  Sum_probs=37.7

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATF   52 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~f   52 (96)
                      .|||..++++...|-..|+.|++.|-+.-.  .  +.+++|+.-.......
T Consensus        35 ~ela~~l~is~~tv~~~l~~Le~~Gli~r~--~--~~~~Lt~~g~~~~~~~   81 (139)
T 2x4h_A           35 NRIAKDLKIAPSSVFEEVSHLEEKGLVKKK--E--DGVWITNNGTRSINYL   81 (139)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEE--T--TEEEECHHHHHHHHHH
T ss_pred             HHHHHHhCCChHHHHHHHHHHHHCCCEEec--C--CeEEEChhHHHHHHHH
Confidence            589999999999999999999999887643  2  6799999776544433

>3dv8_A Transcriptional regulator, CRP/FNR family; cyclic nucleotide-binding domain, structural genomics, joint for structural genomics; 2.55A {Eubacterium rectale atcc 33656}

Probab=93.75  E-value=0.14  Score=33.62  Aligned_cols=47  Identities=17%  Similarity=0.280  Sum_probs=38.4

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVAT   51 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~   51 (96)
                      ++||...|++.+.+-.-+++|+++|.|.-   ++|+++-...+.|.++|.
T Consensus       173 ~~lA~~lg~sr~tvsR~l~~L~~~g~I~~---~~~~i~i~d~~~L~~~a~  219 (220)
T 3dv8_A          173 ETIANHLGSHREVITRMLRYFQVEGLVKL---SRGKITILDSKRLETLQR  219 (220)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEE---ETTEEEESCHHHHHHHHH
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHHCCCEEe---CCCEEEEeCHHHHHHHhc
Confidence            68999999988888888999999998752   477777778888888774

>1lva_A Selenocysteine-specific elongation factor; winged-helix, translation; 2.12A {Moorella thermoacetica} SCOP: a.4.5.35 a.4.5.35 a.4.5.35 a.4.5.35 PDB: 2uwm_A 2ply_A 1wsu_A

Probab=93.74  E-value=0.22  Score=36.47  Aligned_cols=67  Identities=18%  Similarity=0.336  Sum_probs=57.2

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVE   81 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~   81 (96)
                      .|||..+++...++.+-+..|...|.|+=|-+|    +|++.+-++.+++.|++.           + ..|.+|++++-.
T Consensus       161 ~dl~~~l~~~~~~~~~~l~~l~~~g~lv~l~~~----~~~~~~~~~~~~~~l~~~-----------~-~~~~it~a~~Rd  224 (258)
T 1lva_A          161 KEVAGSFNLDPSELEELLHYLVREGVLVKINDE----FYWHRQALGEAREVIKNL-----------A-STGPFGLAEARD  224 (258)
T ss_dssp             HHHHHHTTCCHHHHHHHHHHHHHTTSEEESSSS----BEEEHHHHHHHHHHHHHH-----------H-TTSCBCHHHHHH
T ss_pred             HHHHhHhCCCHHHHHHHHHHHHHCCCEEEecCC----eEEcHHHHHHHHHHHHHH-----------H-hcCCcCHHHHHH
Confidence            589999999999998999999999999998776    799999999988888765           4 559999998876


Q ss_pred             hcc
Q psy11008         82 NSN   84 (96)
Q Consensus        82 ~sN   84 (96)
                      ..+
T Consensus       225 ~lg  227 (258)
T 1lva_A          225 ALG  227 (258)
T ss_dssp             HHT
T ss_pred             HhC
Confidence            543

>3hrs_A Metalloregulator SCAR; DTXR/MNTR family member, transcription; 2.70A {Streptococcus gordonii} PDB: 3hrt_A 3hru_A

Probab=93.72  E-value=0.25  Score=35.06  Aligned_cols=73  Identities=14%  Similarity=0.227  Sum_probs=52.7

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVE   81 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~   81 (96)
                      .|||..++++...+-..|+.|++.|-++=.   +.+.|++|++-.......+..+     .-+..|+...=-++..+..+
T Consensus        24 ~~lA~~l~vs~~tvs~~l~~Le~~GlV~r~---~~~~i~LT~~G~~~~~~~~~~h-----~~~e~~l~~~lg~~~~e~~~   95 (214)
T 3hrs_A           24 KEIAQLMQVSPPAVTEMMKKLLAEELLIKD---KKAGYLLTDLGLKLVSDLYRKH-----RLIEVFLVHHLGYTTEEIHE   95 (214)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEE---TTTEEEECHHHHHHHHHHHHHH-----HHHHHHHHHTTCCCHHHHHH
T ss_pred             HHHHHHHCCChhHHHHHHHHHHHCCCEEEe---cCCCeEECHHHHHHHHHHHHHH-----HHHHHHHHHHhCCCHHHHHH
Confidence            589999999999999999999999988654   3378999999887766665544     24455555433355554433


Q ss_pred             h
Q psy11008         82 N   82 (96)
Q Consensus        82 ~   82 (96)
                      .
T Consensus        96 ~   96 (214)
T 3hrs_A           96 E   96 (214)
T ss_dssp             H
T ss_pred             H
Confidence            3

>3txn_A 26S proteasome regulatory complex subunit P42B; PCI domain, alpha solenoid, regulatory PART LID, hydrolase, protein binding; 2.50A {Drosophila melanogaster} PDB: 3txm_A

Probab=93.38  E-value=0.078  Score=42.18  Aligned_cols=45  Identities=11%  Similarity=0.293  Sum_probs=41.1

Q ss_pred             ChhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHH
Q psy11008          1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEE   45 (96)
Q Consensus         1 ledLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eE   45 (96)
                      ++++|..||++.+++-.-+-.|..+|.|.|.||--.+.++++++.
T Consensus       319 l~~iA~~l~ls~~evE~~L~~lI~dg~I~a~IDq~~giv~~~~~~  363 (394)
T 3txn_A          319 VAHVAESIQLPMPQVEKKLSQMILDKKFSGILDQGEGVLIVFEET  363 (394)
T ss_dssp             HHHHHHHHTCCHHHHHHHHHHHHHTTSSCEEEETTTTEEEECCC-
T ss_pred             HHHHHHHHCcCHHHHHHHHHHHHHCCCeeEEEcCCCCEEEECCCc
Confidence            468999999999999999999999999999999999999997764

>3tqn_A Transcriptional regulator, GNTR family; regulatory functions; 2.80A {Coxiella burnetii}

Probab=93.06  E-value=0.5  Score=30.42  Aligned_cols=47  Identities=11%  Similarity=0.180  Sum_probs=37.5

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVAT   51 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~   51 (96)
                      .+||.+||++..-|.+-++.|+++|-|.-+   +|+-.||++-..+.+..
T Consensus        37 ~~La~~~~vSr~tvr~al~~L~~~Gli~~~---~~~G~~V~~~~~~~~~~   83 (113)
T 3tqn_A           37 RKISTEYQINPLTVSKAYQSLLDDNVIEKR---RGLGMLVKAGARQRLLT   83 (113)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEE---TTTEEEECTTHHHHHHH
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCEEEe---cCCeEEEeCCchHHHHH
Confidence            479999999999999999999999987543   67777787765554444

>3d0s_A Transcriptional regulatory protein; CAMP receptor protein (CRP), dimer, inactive(APO, unliganded allostery, DNA binding, cyclic AMP; 2.00A {Mycobacterium tuberculosis} PDB: 3i54_A* 3i59_A* 3mzh_A* 3h3u_A* 3r6s_A*

Probab=93.03  E-value=0.2  Score=33.31  Aligned_cols=46  Identities=17%  Similarity=0.263  Sum_probs=36.4

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVA   50 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va   50 (96)
                      +|||...|++.+.+-.-+++|+++|.|.=   ++|+++-...+.|.++|
T Consensus       181 ~~lA~~lg~sr~tvsR~l~~l~~~g~I~~---~~~~i~i~d~~~L~~~a  226 (227)
T 3d0s_A          181 EEIAQLVGASRETVNKALADFAHRGWIRL---EGKSVLISDSERLARRA  226 (227)
T ss_dssp             HHHHHHHTSCHHHHHHHHHHHHHTTSEEE---ETTEEEESCHHHHHHHH
T ss_pred             HHHHHHhCCcHHHHHHHHHHHHHCCCEEe---cCCEEEEcCHHHHHHhh
Confidence            58999999998888888999999997642   45665555777787765

>2zcw_A TTHA1359, transcriptional regulator, FNR/CRP family; stationary phase, DNA-binding, transcription regulation; 1.50A {Thermus thermophilus}

Probab=92.90  E-value=0.21  Score=32.88  Aligned_cols=47  Identities=26%  Similarity=0.339  Sum_probs=37.6

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVAT   51 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~   51 (96)
                      ++||...|++.+.+-.-+++|+++|.|.  . ++|++.-..++.|.++|.
T Consensus       150 ~~lA~~lg~sr~tvsR~l~~L~~~g~I~--~-~~~~i~i~d~~~L~~~~~  196 (202)
T 2zcw_A          150 DELAAAVGSVRETVTKVIGELAREGYIR--S-GYGKIQLLDLKGLKELAE  196 (202)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEE--E-ETTEEEESCHHHHHHHHT
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHHCCCEE--e-CCCEEEEeCHHHHHHHhc
Confidence            6899999998888888899999999886  2 456655557777877764

>2fbk_A Transcriptional regulator, MARR family; winged-helix-turn-helix; 2.30A {Deinococcus radiodurans} SCOP: a.4.5.28

Probab=92.86  E-value=0.063  Score=35.82  Aligned_cols=54  Identities=24%  Similarity=0.312  Sum_probs=42.2

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEe---eCCCceEEEcHHHHHHHHHHHHh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI---DDRGKFIYISQEELNSVATFIKQ   55 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi---DDRGKfIyIs~eEl~~Va~fI~~   55 (96)
                      .+||..++++...+-..|+.|++.|-|.-.-   |-|.++|++|+.-...+......
T Consensus        90 ~eLa~~l~is~~tvs~~l~~Le~~GlV~r~~~~~DrR~~~~~LT~~G~~~~~~~~~~  146 (181)
T 2fbk_A           90 TELSALAAISGPSTSNRIVRLLEKGLIERREDERDRRSASIRLTPQGRALVTHLLPA  146 (181)
T ss_dssp             HHHHHHCSCCSGGGSSHHHHHHHHTSEECCC-------CCBEECHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCcCEEecCCCCCCCeeEEEECHHHHHHHHHHHHH
Confidence            4899999999999999999999999998774   56788999999877766554443

>3fx3_A Cyclic nucleotide-binding protein; helix_TURN_helix, CAMP regulatory protein, structural genomi 2, protein structure initiative; 2.20A {Ruegeria pomeroyi} PDB: 3h3z_A*

Probab=92.73  E-value=0.24  Score=33.20  Aligned_cols=47  Identities=19%  Similarity=0.126  Sum_probs=37.0

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATF   52 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~f   52 (96)
                      ++||...|++.+.+-.-+++|+++| |  . -++|+++-...+.|.++|.+
T Consensus       182 ~~iA~~lg~sr~tvsR~l~~L~~~g-i--~-~~~~~i~I~d~~~L~~~~~~  228 (237)
T 3fx3_A          182 MLIAGRLGMKPESLSRAFSRLKAAG-V--T-VKRNHAEIEDIALLRDYAES  228 (237)
T ss_dssp             HHHHHHTTCCHHHHHHHHHHHGGGT-E--E-CCTTEEEESCHHHHHHHHCC
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHHCC-e--E-eeCCEEEEcCHHHHHHHhcC
Confidence            6899999998888888899999999 5  2 35666555578888887754

>1j5y_A Transcriptional regulator, biotin repressor famil; structural genomics, TM1602, BIOT repressor family, JCSG, conserved hypothetical protein; 2.30A {Thermotoga maritima} SCOP: a.4.5.1 d.94.2.1

Probab=92.64  E-value=0.28  Score=33.89  Aligned_cols=54  Identities=19%  Similarity=0.206  Sum_probs=38.3

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCC-ccE----E-eeCCC-ce--EEE-------cHHHHHHHHHHHHh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGA-LTG----V-IDDRG-KF--IYI-------SQEELNSVATFIKQ   55 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~-ltG----V-iDDRG-Kf--IyI-------s~eEl~~Va~fI~~   55 (96)
                      .|||..||++..-|..+|+.|++.|. |.+    . +.... .+  ++.       +++|+.++...+..
T Consensus        40 ~eLa~~l~vS~~Ti~rdi~~L~~~G~~I~~~~~Gy~l~~~~~~l~~~~~~~~~~~~~~~e~~~l~~~~~~  109 (187)
T 1j5y_A           40 AQLAEELSVSRQVIVQDIAYLRSLGYNIVATPRGYVLAGGKSGVSRLVAVKHAPEEIKEELLCVVRNGGR  109 (187)
T ss_dssp             HHHHHHHTSCHHHHHHHHHHHHHHTCCCEEETTEEECCTTTCSEEEEEEEECCGGGHHHHHHHHHHTTCE
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCeEEEECCEEEECCcccccceeeeecCccccCHHHHHHHHHhCCC
Confidence            58999999999999999999999998 764    2 12221 11  222       67777777655544

>1ft9_A Carbon monoxide oxidation system transcription regulator; heme sensor, catabolite gene activator protein; HET: HEM; 2.60A {Rhodospirillum rubrum} SCOP: a.4.5.4 b.82.3.1

Probab=92.45  E-value=0.18  Score=33.68  Aligned_cols=48  Identities=21%  Similarity=0.205  Sum_probs=37.4

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEE-cHHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYI-SQEELNSVATF   52 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyI-s~eEl~~Va~f   52 (96)
                      ++||...|++.+.+-.-+++|+++|.|.=   .+|+.|.| ..+.|.++|.+
T Consensus       167 ~~lA~~lG~sr~tvsR~l~~L~~~g~I~~---~~~~i~~i~d~~~L~~~~~~  215 (222)
T 1ft9_A          167 EEIANLIGSSRQTTSTALNSLIKEGYISR---QGRGHYTIPNLVRLKAAADG  215 (222)
T ss_dssp             HHHHHHHCSCHHHHHHHHHHHHHTTSSEE---CSTTCEECSSHHHHHHTC--
T ss_pred             HHHHHHhCCcHHHHHHHHHHHHHCCcEEE---cCCceEEEcCHHHHHHHHhc
Confidence            68999999998888888999999998642   56665555 88888877753

>2qq9_A Diphtheria toxin repressor; regulator, DTXR, helix-turn-helix, metal ION, ACT DNA-binding, ferrous iron, transcription; 1.71A {Corynebacterium diphtheriae} PDB: 2tdx_A 1ddn_A 1g3t_A 1g3s_A 1g3w_A 2qqa_A 2qqb_A 2dtr_A 1bi0_A 1bi2_A 1bi3_A 1dpr_A 1bi1_A 1fwz_A 1g3y_A 1c0w_A* 3glx_A 1p92_A 1xcv_A 1f5t_A ...

Probab=92.29  E-value=0.43  Score=33.88  Aligned_cols=52  Identities=6%  Similarity=0.195  Sum_probs=42.8

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .+||..++++...+-.-|+.|++.|-+.=.   +.++|++|++-........+.+
T Consensus        28 ~~la~~l~vs~~tvs~~l~~Le~~GlV~r~---~~~~v~LT~~G~~~~~~~~~~~   79 (226)
T 2qq9_A           28 ARIAERLEQSGPTVSQTVARMERDGLVVVA---SDRSLQMTPTGRTLATAVMRKH   79 (226)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEC---TTSBEEECHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCEEEe---CCCCeEECHHHHHHHHHHHHHH
Confidence            589999999999999999999999987653   3488999999877766655543

>3e6c_C CPRK, cyclic nucleotide-binding protein; CPRK, halorespiration; HET: DNA 3C4; 1.80A {Desulfitobacterium hafniense} SCOP: a.4.5.4 b.82.3.2 PDB: 3e6b_A* 3e5u_C* 3e6d_A 3e5x_A* 3e5q_A 2h6b_A* 2h6c_A

Probab=92.23  E-value=0.22  Score=33.95  Aligned_cols=48  Identities=15%  Similarity=0.254  Sum_probs=39.7

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATF   52 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~f   52 (96)
                      ++||...|++.+.+-.-+++|+++|.|.=   ++|+++-+..+.|.++|.+
T Consensus       181 ~~iA~~lG~sr~tvsR~l~~L~~~g~I~~---~~~~i~i~d~~~L~~~a~~  228 (250)
T 3e6c_C          181 KSIGEITGVHHVTVSRVLASLKRENILDK---KKNKIIVYNLGELKHLSEQ  228 (250)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEE---CSSEEEESCHHHHHHHHTS
T ss_pred             HHHHHHhCCcHHHHHHHHHHHHHCCCeEe---CCCEEEEecHHHHHHHHcc
Confidence            68999999988888888999999987742   5677777788888888776

>4b4t_R RPN7, 26S proteasome regulatory subunit RPN7; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=92.15  E-value=0.16  Score=39.30  Aligned_cols=44  Identities=14%  Similarity=0.213  Sum_probs=39.4

Q ss_pred             ChhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHH
Q psy11008          1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQE   44 (96)
Q Consensus         1 ledLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~e   44 (96)
                      |+.+|..||++.+++=+-+..|..+|+|.|.||--.+.|+..+.
T Consensus       350 l~~mA~~l~~s~~~~E~~L~~lI~~g~l~akID~~~giv~~~~~  393 (429)
T 4b4t_R          350 LKSMASAFGVSVAFLDNDLGKFIPNKQLNCVIDRVNGIVETNRP  393 (429)
T ss_dssp             HHHHHHHHTSCHHHHHHHHHHHHHHTSSCEEEETTTTEEEECC-
T ss_pred             HHHHHHHhCcCHHHHHHHHHHHHHcCCeEEEEcCCCCEEEECCC
Confidence            46799999999999999999999999999999988888988754

>1p4x_A Staphylococcal accessory regulator A homologue; winged-helix protein, transcription; 2.20A {Staphylococcus aureus} SCOP: a.4.5.28 a.4.5.28

Probab=92.00  E-value=0.46  Score=34.97  Aligned_cols=54  Identities=19%  Similarity=0.285  Sum_probs=46.3

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHHHHHHHHHh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELNSVATFIKQ   55 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~~Va~fI~~   55 (96)
                      .|||..++++...+-..|..|++.|-+.=.-|   -|.++|++|++-...+......
T Consensus       178 ~eLa~~l~i~~~tvt~~v~rLe~~GlV~R~~~~~DrR~~~i~LT~~G~~~~~~~~~~  234 (250)
T 1p4x_A          178 KDLIETIHHKYPQTVRALNNLKKQGYLIKERSTEDERKILIHMDDAQQDHAEQLLAQ  234 (250)
T ss_dssp             HHHHHHSSSCHHHHHHHHHHHHHHTSSEEEECSSSTTCEEEECCHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCChhhHHHHHHHHHHCCCEEeeCCCCCCCeEEEEECHHHHHHHHHHHHH
Confidence            48999999999999999999999999998875   5899999999987766655443

>4a5n_A Uncharacterized HTH-type transcriptional regulato; activator, DNA binding, MARR-like; 1.81A {Bacillus subtilis} PDB: 4a5m_A

Probab=91.91  E-value=0.52  Score=32.09  Aligned_cols=55  Identities=5%  Similarity=0.078  Sum_probs=46.0

Q ss_pred             hhhhhhh-CCChHHHHHHHHHHHHcCCccEEeeC---CCceEEEcHH------HHHHHHHHHHhh
Q psy11008          2 EDLAALF-RMKTQSVIDRIVELQKTGALTGVIDD---RGKFIYISQE------ELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F-~lktq~vI~RI~eL~~~g~ltGViDD---RGKfIyIs~e------El~~Va~fI~~r   56 (96)
                      .||+... |++...+-.++++|++.|-++=..++   |..++++|+.      .+.+++.|-.+.
T Consensus        43 ~eL~~~l~gIs~~~Ls~~L~~Le~~GLV~R~~~~~d~r~v~y~LT~~G~~l~~~l~~l~~W~~~~  107 (131)
T 4a5n_A           43 NEFRRICPSITQRMLTLQLRELEADGIVHREVYHQVPPKVEYSLTEFGRTLEPIVLQMKEWGESN  107 (131)
T ss_dssp             HHHHHHCTTSCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECTTGGGGHHHHHHHHHHHHHH
T ss_pred             HHHHHHhcccCHHHHHHHHHHHHHCCCEEEEecCCCCCeEEEEECHhHHHHHHHHHHHHHHHHHH
Confidence            5899999 99999999999999999999988763   4567789987      677777776665

>1sd4_A Penicillinase repressor; BLAI, MECI, methicillin, B-lactam, DNA binding PR; 2.00A {Staphylococcus aureus} SCOP: a.4.5.39 PDB: 1xsd_A

Probab=91.90  E-value=1  Score=27.99  Aligned_cols=38  Identities=11%  Similarity=0.255  Sum_probs=30.7

Q ss_pred             hhhhhhhCC----ChHHHHHHHHHHHHcCCccEEeeCCCceEE
Q psy11008          2 EDLAALFRM----KTQSVIDRIVELQKTGALTGVIDDRGKFIY   40 (96)
Q Consensus         2 edLAa~F~l----ktq~vI~RI~eL~~~g~ltGViDDRGKfIy   40 (96)
                      .|||..++.    +...+-.-|..|++.|-|.=.-|+| .|+|
T Consensus        28 ~el~~~l~~~~~~~~~Tvt~~l~rLe~kGlv~R~~~~r-~~~~   69 (126)
T 1sd4_A           28 NEIVVEIQKYKEVSDKTIRTLITRLYKKEIIKRYKSEN-IYFY   69 (126)
T ss_dssp             HHHHHHHHTTSCCCHHHHHHHHHHHHHTTSEEEEEETT-EEEE
T ss_pred             HHHHHHHhhcCCCChhhHHHHHHHHHHCCceEEEeCCC-eEEE
Confidence            478888874    6677777799999999999998877 6666

>1okr_A MECI, methicillin resistance regulatory protein MECI; bacterial antibiotic resistance, MECI protein, transcriptional regulatory element; 2.4A {Staphylococcus aureus} SCOP: a.4.5.39 PDB: 1sax_A 1sd7_A 2d45_A 1sd6_A

Probab=91.78  E-value=0.31  Score=30.31  Aligned_cols=47  Identities=13%  Similarity=0.163  Sum_probs=35.5

Q ss_pred             hhhhhhhC----CChHHHHHHHHHHHHcCCccEEeeCCCc-eEEEcHHHHHH
Q psy11008          2 EDLAALFR----MKTQSVIDRIVELQKTGALTGVIDDRGK-FIYISQEELNS   48 (96)
Q Consensus         2 edLAa~F~----lktq~vI~RI~eL~~~g~ltGViDDRGK-fIyIs~eEl~~   48 (96)
                      .|||..++    ++...+-.-|+.|++.|-+.=.-|||-. |+++|++.-..
T Consensus        28 ~ela~~l~~~~~~s~~tv~~~l~~L~~~Glv~r~~~~rr~~~~~lT~~g~~~   79 (123)
T 1okr_A           28 NNIIEEIQMQKDWSPKTIRTLITRLYKKGFIDRKKDNKIFQYYSLVEESDIK   79 (123)
T ss_dssp             HHHHHHHHHHCCCCHHHHHHHHHHHHHHTSEEEEEETTEEEEEESSCHHHHH
T ss_pred             HHHHHHHhccCCCcHhhHHHHHHHHHHCCCeEEEecCCeEEEEEecCHHHHH
Confidence            47888888    6678888889999999999988875432 35677765443

>2bgc_A PRFA; bacterial infection, human pathogen, transcriptional regulat transcription; HET: PR3; 2.3A {Listeria monocytogenes} SCOP: a.4.5.4 b.82.3.3 PDB: 2beo_A* 1omi_A

Probab=91.72  E-value=0.33  Score=32.93  Aligned_cols=48  Identities=15%  Similarity=0.188  Sum_probs=38.2

Q ss_pred             hhhhhhhCCCh-HHHHHHHHHHHHcCCccEEeeCCCceEEE-cHHHHHHHHHHH
Q psy11008          2 EDLAALFRMKT-QSVIDRIVELQKTGALTGVIDDRGKFIYI-SQEELNSVATFI   53 (96)
Q Consensus         2 edLAa~F~lkt-q~vI~RI~eL~~~g~ltGViDDRGKfIyI-s~eEl~~Va~fI   53 (96)
                      +|||...|++. +.+-.-+++|+++|.|.=   ++|+ |+| .++.|..+|.|+
T Consensus       173 ~~lA~~lG~sr~etvsR~l~~l~~~glI~~---~~~~-i~I~d~~~L~~~~~~~  222 (238)
T 2bgc_A          173 QELGYSSGIAHSSAVSRIISKLKQEKVIVY---KNSC-FYVQNLDYLKRYAPKL  222 (238)
T ss_dssp             HHHHHHTTCCCHHHHHHHHHHHHHTTSEEE---ETTE-EEESCHHHHHHHCHHH
T ss_pred             HHHHHHhCCChHHHHHHHHHHHHHCCCEEe---cCCE-EEEeCHHHHHHHhcCC
Confidence            68999999999 788888999999987642   2444 555 788999998884

>3b02_A Transcriptional regulator, CRP family; structural genomics, riken structural genomics/proteomics in RSGI; 1.92A {Thermus thermophilus} PDB: 2zdb_A

Probab=91.65  E-value=0.33  Score=31.84  Aligned_cols=46  Identities=17%  Similarity=0.254  Sum_probs=35.7

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVA   50 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va   50 (96)
                      +|||...|++.+.+-.-+++|+++|.|.=   ++|++.-..++.|.++|
T Consensus       143 ~~lA~~lg~sr~tvsR~l~~L~~~g~I~~---~~~~i~i~d~~~L~~~~  188 (195)
T 3b02_A          143 EEIADATASIRESVSKVLADLRREGLIAT---AYRRVYLLDLAALEREA  188 (195)
T ss_dssp             HHHHHTTTSCHHHHHHHHHHHHHHTSEEE---ETTEEEECCHHHHHHHH
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHHCCCEEe---cCCEEEEeCHHHHHHHh
Confidence            68999999988888888999999997641   35565455677777765

>3ic7_A Putative transcriptional regulator; helix-turn-helix, structural genomics, PSI-2, protein struct initiative; 2.82A {Bacteroides thetaiotaomicron}

Probab=91.58  E-value=0.26  Score=32.50  Aligned_cols=81  Identities=15%  Similarity=0.219  Sum_probs=54.7

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhh-chhchhhhhhhhccccceeHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQR-GREELNSVATFIKQKGRVSVSELV   80 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~r-gr~~~~~~~~~~~~~GRVsi~eL~   80 (96)
                      .+||.+||++..-|.+-++.|+++|-|.-.   +|+=.||++...+.+....+.+ -|+.+.+.+.-.... .++..++.
T Consensus        39 ~~La~~~~vSr~tvr~Al~~L~~~G~i~~~---~~~G~~V~~~~~~~~~~~~~~~~~~~~le~~~~~~~~~-~~~~~~l~  114 (126)
T 3ic7_A           39 REYASIVEVNANTVMRSYEYLQSQEVIYNK---RGIGFFVASGAKMLIHSLRKEQFLKEEVGSFFRQLYTL-GISIKEIE  114 (126)
T ss_dssp             TTTTTCC-CCSGGGHHHHHHHHTTTSEEEE---TTTEEEECTTHHHHHHHHHHTTCCCCCSHHHHHHHHHT-TCCHHHHH
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCcEEEE---cCCccEEccCcHHHHHHHHHHHHHHHHHHHHHHHHHHc-CCCHHHHH
Confidence            479999999999999999999999987644   6666777777666665555443 344555555544443 35666666


Q ss_pred             Hhcccc
Q psy11008         81 ENSNQL   86 (96)
Q Consensus        81 ~~sN~l   86 (96)
                      +...++
T Consensus       115 ~l~~~~  120 (126)
T 3ic7_A          115 KMYYEF  120 (126)
T ss_dssp             HHHHTH
T ss_pred             HHHHHH
Confidence            654443

>3l7w_A Putative uncharacterized protein SMU.1704; PADR, transcriptional factor, transcription; HET: MSE; 2.20A {Streptococcus mutans} SCOP: a.4.5.0

Probab=91.49  E-value=1.2  Score=28.29  Aligned_cols=54  Identities=15%  Similarity=0.310  Sum_probs=42.4

Q ss_pred             hhhhhhCCChHHHHHHHHHHHHcCCccEEeeC-CC---ceEEEcHHHHHHHHHHHHhh
Q psy11008          3 DLAALFRMKTQSVIDRIVELQKTGALTGVIDD-RG---KFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         3 dLAa~F~lktq~vI~RI~eL~~~g~ltGViDD-RG---KfIyIs~eEl~~Va~fI~~r   56 (96)
                      +|+..++++...+-.-+..|++.|-|+...+. .|   |+..||+.-.+.+..+...-
T Consensus        31 ~l~~~~~i~~~tly~~L~~Le~~GlI~~~~~~~~~r~r~~y~LT~~G~~~l~~~~~~~   88 (108)
T 3l7w_A           31 TIKLIASIKESTLYPILKKLEKAGYLSTYTQEHQGRRRKYYHLTDSGEKHLVYLTKEW   88 (108)
T ss_dssp             HHTTTCCCCHHHHHHHHHHHHHTTSEEEEEEEETTEEEEEEEECHHHHHHHHHHHHHH
T ss_pred             HHHHHhCCCcChHHHHHHHHHHCCCeEEEeecCCCCcceEEEECHHHHHHHHHHHHHH
Confidence            35555799999999999999999999998763 23   46669999888887776554

>2gau_A Transcriptional regulator, CRP/FNR family; structural genomics, porphyromona gingivalis, PSI, protein structure initiative; 1.90A {Porphyromonas gingivalis} SCOP: a.4.5.4 b.82.3.2

Probab=91.42  E-value=0.43  Score=31.79  Aligned_cols=47  Identities=23%  Similarity=0.290  Sum_probs=36.1

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVAT   51 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~   51 (96)
                      +|||...|++.+.+-.-+++|+++|.|.   -++|+++-+..+.|.++|.
T Consensus       184 ~~lA~~lg~sr~tvsR~l~~l~~~g~I~---~~~~~i~i~d~~~L~~~~~  230 (232)
T 2gau_A          184 EELATLSNMTVSNAIRTLSTFVSERMLA---LDGKRIKIIDCDRLQKTAR  230 (232)
T ss_dssp             HHHHHHTTSCHHHHHHHHHHHHHTTSEE---EETTEEEESCHHHHHHHHH
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHHCCCEe---eCCCEEEEeCHHHHHHHhh
Confidence            6899999999888888899999998764   1355555557777777663

>3e97_A Transcriptional regulator, CRP/FNR family; YP_604437.1, structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.86A {Deinococcus geothermalis dsm 11300}

Probab=91.30  E-value=0.26  Score=32.83  Aligned_cols=47  Identities=13%  Similarity=0.193  Sum_probs=37.0

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVAT   51 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~   51 (96)
                      ++||...|++.+.+-.-+++|+++|.|.  . ++|++.-...+.|.++|.
T Consensus       179 ~~iA~~lg~sr~tvsR~l~~L~~~g~I~--~-~~~~i~i~d~~~L~~~a~  225 (231)
T 3e97_A          179 QDIMARTSSSRETVSRVLKRLEAHNILE--V-SPRSVTLLDLAALEALSF  225 (231)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEE--E-CSSCEEESCHHHHHHCC-
T ss_pred             HHHHHHhCCcHHHHHHHHHHHHHCCcEE--e-cCCEEEEeCHHHHHHHHh
Confidence            6899999998888888899999998875  2 466666667777777665

>1qbj_A Protein (double-stranded RNA specific adenosine D (ADAR1)); protein-Z-DNA complex, hydrolase-DNA complex; HET: DNA; 2.10A {Homo sapiens} SCOP: a.4.5.19 PDB: 3f21_A* 3f22_A* 3f23_A* 3irr_A* 3irq_D* 2gxb_A 2acj_A 2l54_A

Probab=91.28  E-value=0.32  Score=30.99  Aligned_cols=43  Identities=14%  Similarity=0.143  Sum_probs=32.3

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQE   44 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~e   44 (96)
                      .+||..+|++...|-.+|..|+++|.|.=+-...|.|.-.++.
T Consensus        31 ~eLA~~Lgvsr~tV~~~L~~Le~~G~I~~~g~~~~~W~i~~~~   73 (81)
T 1qbj_A           31 HDLSGKLGTPKKEINRVLYSLAKKGKLQKEAGTPPLWKIAVST   73 (81)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEESSSSCEEEEC---
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCEEecCCCCCeeEEeCcH
Confidence            5899999999999999999999999996443445666544444

>1uly_A Hypothetical protein PH1932; helix-turn-helix, structural genomics, DNA binding protein; 2.50A {Pyrococcus horikoshii} SCOP: a.4.5.58 PDB: 2cwe_A

Probab=91.20  E-value=0.76  Score=32.53  Aligned_cols=55  Identities=16%  Similarity=0.248  Sum_probs=40.7

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEE---eeCC--------CceEE-EcHH----HHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGV---IDDR--------GKFIY-ISQE----ELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGV---iDDR--------GKfIy-Is~e----El~~Va~fI~~r   56 (96)
                      .|||..+|++...|-.+|+.|++.|-|.+.   .+-+        .-++| |+.+    .+..++..+.+.
T Consensus        37 ~eLA~~lglS~stv~~~l~~Le~~GlI~~~~~~~~~~~~~~~~g~~~~~~~v~~~~~~~~~~~~~~~~~~~  107 (192)
T 1uly_A           37 SQLSEILGKTPQTIYHHIEKLKEAGLVEVKRTEMKGNLVEKYYGRTADVFYINLYLGDEELRYIARSRLKT  107 (192)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEEEEETTEEEEEEEESSSEEEECSCSSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCEEEEeccccccchhhhcCcceEEEEEecCCchhHHHHHHHHHHHh
Confidence            589999999999999999999999999998   3433        12343 5543    456666666654

>2wte_A CSA3; antiviral protein, viral resistance, winged helix-turn-helix prnai nucleotide-binding domain; HET: MSE; 1.80A {Sulfolobus solfataricus}

Probab=91.14  E-value=0.32  Score=35.97  Aligned_cols=44  Identities=27%  Similarity=0.467  Sum_probs=39.4

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELN   47 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~   47 (96)
                      .|||..+|++...+-.+++.|++.|-+...  .|.+.+++|+.-..
T Consensus       170 ~eLA~~lglsksTv~r~L~~Le~~GlV~r~--~r~~~~~LT~~G~~  213 (244)
T 2wte_A          170 TELAKMLDKSEKTLINKIAELKKFGILTQK--GKDRKVELNELGLN  213 (244)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEE--TTTTEEEECHHHHH
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCEEEe--CCccEEEECHHHHH
Confidence            589999999999999999999999999886  77889999987655

>3cta_A Riboflavin kinase; structural genomics, transferase, PSI-2, protein structure initiative; 2.20A {Thermoplasma acidophilum dsm 1728} SCOP: a.4.5.28 b.43.5.2

Probab=91.04  E-value=0.87  Score=32.02  Aligned_cols=50  Identities=28%  Similarity=0.503  Sum_probs=42.0

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVAT   51 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~   51 (96)
                      .++|..++++...+-..|+.||+.|-+.=..|.|++.+.+|++-..-+..
T Consensus        31 s~aA~~L~isq~avSr~I~~LE~~~L~~R~~~~R~~~v~LT~~G~~l~~~   80 (230)
T 3cta_A           31 SKLADMLGISQQSASRIIIDLEKNGYITRTVTKRGQILNITEKGLDVLYT   80 (230)
T ss_dssp             HHHHHHHTSCHHHHHHHHHHHHHTTSEEEEEETTEEEEEECHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCEEEEEcCCeEEEEECHHHHHHHHH
Confidence            47899999988888899999999887777777789999999987655543

>3iuo_A ATP-dependent DNA helicase RECQ; C-terminal, GI PSI, MCSG, structural genomics, midwest center for structur genomics; 1.60A {Porphyromonas gingivalis}

Probab=90.86  E-value=0.19  Score=33.67  Aligned_cols=72  Identities=15%  Similarity=0.328  Sum_probs=50.1

Q ss_pred             ChhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceE--EEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHH
Q psy11008          1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFI--YISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSE   78 (96)
Q Consensus         1 ledLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfI--yIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~e   78 (96)
                      ++++|..=||+...+.+-|.++...|.-..+ ++   ||  .+++++...+.+++++.|...|..+-..+.  |++|-.+
T Consensus        35 leeIA~~R~L~~~TI~~Hl~~~v~~G~~l~i-~~---~i~~~l~~~~~~~I~~~~~~~~~~~Lk~i~e~l~--~~~sy~e  108 (122)
T 3iuo_A           35 LDDIAVSHGLDFPELLSEVETIVYSGTRINI-DY---FINEVMDEDHLEDIFEYFKESTTDSLEEAMQELG--KDYSEEE  108 (122)
T ss_dssp             HHHHHHHTTCCHHHHHHHHHHHHHTTCCCCC-HH---HHHHHSCHHHHHHHHHHHHHCSCCCHHHHHHHHT--TTSCHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHHHHHHcCCccCH-HH---HcccccCHHHHHHHHHHHHHcCcccHHHHHHHcc--CcCCHHH
Confidence            4799999999999999999999999963332 21   21  234999999999999985444444333332  3444433

>2v7f_A RPS19, RPS19E SSU ribosomal protein S19E; diamond blackfan anemia small ribosomal subunit; 1.15A {Pyrococcus abyssi} SCOP: a.4.5.84

Probab=90.78  E-value=0.21  Score=35.29  Aligned_cols=54  Identities=20%  Similarity=0.327  Sum_probs=42.5

Q ss_pred             hhhhhhhC--------------CChHHHHHHHHHHHHcCCccEEeeCCCceEE-EcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFR--------------MKTQSVIDRIVELQKTGALTGVIDDRGKFIY-ISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~--------------lktq~vI~RI~eL~~~g~ltGViDDRGKfIy-Is~eEl~~Va~fI~~r   56 (96)
                      .+||..||              .+..-+..-++.|+++|-|.-. -.+|.||- .++++++.+|..|.+.
T Consensus        71 ~~La~~~gg~k~~g~~p~~~~~vSr~tVR~AL~~Le~~GlV~~~-~~~G~~Vt~~~~~~l~~ia~~i~~~  139 (150)
T 2v7f_A           71 ERLRTYYGGRKNRGHAPERFYKAGGSIIRKALQQLEAAGFVEKV-PGKGRVITPKGRSFLDKIATELKKE  139 (150)
T ss_dssp             HHHHHHHCC----CCCTTSCCCHHHHHHHHHHHHHHHTTSEEEE-TTTEEEECHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCccCCcCCccccccchHHHHHHHHHHHHCCCEEEe-CCCceEECCCCHHHHHHHHHHHHHH
Confidence            47999999              9888899999999999999754 35677763 3566788888777654

>4b4t_O 26S proteasome regulatory subunit RPN9; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=90.68  E-value=0.2  Score=38.73  Aligned_cols=41  Identities=24%  Similarity=0.379  Sum_probs=37.4

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEc
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYIS   42 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs   42 (96)
                      ++||..++++..+|=+=+-++...|.|.|-||---..|+|+
T Consensus       311 ~~ia~~l~i~~~evE~lli~aI~~glI~GkIDQv~~~v~v~  351 (393)
T 4b4t_O          311 EDISKATHLPKDNVEHLVMRAISLGLLKGSIDQVNELVTIS  351 (393)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHHSCSSSCEETTTTEECC-
T ss_pred             HHHHHHhCcCHHHHHHHHHHHHHcCCEEEEEcCCCCEEEEE
Confidence            68999999999998888999999999999999988899886

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=90.58  E-value=0.28  Score=34.31  Aligned_cols=43  Identities=16%  Similarity=0.434  Sum_probs=37.2

Q ss_pred             ChhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcH
Q psy11008          1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQ   43 (96)
Q Consensus         1 ledLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~   43 (96)
                      |+++|..|+++.+++-..+..|..+|.|.|.||.--..+.+.+
T Consensus       359 l~~la~~l~~~~~~~E~~l~~lI~~~~i~a~id~~~g~v~~~~  401 (434)
T 4b4t_Q          359 ISHISKIIGLDTQQVEGKLSQMILDKIFYGVLDQGNGWLYVYE  401 (434)
T ss_dssp             HHHHHHHHTCCHHHHHHHHHHHHHHTSSCCEEETTTTEEECC-
T ss_pred             HHHHHHHhCcCHHHHHHHHHHHHhCCCcceecccccCeEeeCC
Confidence            3679999999999999999999999999999998777777644

>2co5_A Viral protein F93; viral protein-winged helix complex, winged helix, DNA-bindin WHTH, disulfide bond, STIV; 2.2A {Sulfolobus turreted icosahedral virus} SCOP: a.4.5.48

Probab=90.54  E-value=1.5  Score=28.52  Aligned_cols=55  Identities=11%  Similarity=0.182  Sum_probs=46.3

Q ss_pred             hhhhhhh--CCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALF--RMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F--~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .+|+..|  .++...+---+..|+++|-|+..-+++-||.-||++--+.+.++..+.
T Consensus        32 ~ei~~~~~~~is~GtlYp~L~rLe~~GlI~~~~~~~rk~Y~iT~~Gr~~l~~~~~~~   88 (99)
T 2co5_A           32 SEILKRFDIDISDGVLYPLIDSLIDDKILREEEAPDGKVLFLTEKGMKEFEELHEFF   88 (99)
T ss_dssp             HHHHHHHCCBCCHHHHHHHHHHHHHTTSEEEECCTTSCEEEECHHHHHHHHHHHHHH
T ss_pred             HHHHHHhCCCCCCCcHHHHHHHHHHCCCEEEeeCCCcEEEEECHHHHHHHHHHHHhH
Confidence            4666666  577778888899999999999988777789999999999988887765

>1y0u_A Arsenical resistance operon repressor, putative; structural genomics, protein structure initiative, PSI; HET: MSE; 1.60A {Archaeoglobus fulgidus} SCOP: a.4.5.5

Probab=90.38  E-value=0.42  Score=29.27  Aligned_cols=39  Identities=8%  Similarity=0.063  Sum_probs=32.7

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQE   44 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~e   44 (96)
                      .|||..++++...+-..++.|++.|-+.-.-   | +.+++++
T Consensus        47 ~eLa~~l~is~~tv~~~L~~L~~~Glv~~~~---g-~y~l~~~   85 (96)
T 1y0u_A           47 EEIMQTLSLSKKQLDYHLKVLEAGFCIERVG---E-RWVVTDA   85 (96)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEET---T-EEEECTT
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCEEEEC---C-EEEECCC
Confidence            5899999999999999999999999997543   5 6677764

>2esh_A Conserved hypothetical protein TM0937; APC5794, structural genomics, PSI, protein structure initiative; 2.30A {Thermotoga maritima} SCOP: a.4.5.61

Probab=90.14  E-value=0.48  Score=30.61  Aligned_cols=58  Identities=12%  Similarity=0.194  Sum_probs=43.3

Q ss_pred             CCh-HHHHHHHHHHHHcCCccEEeeC----CCceEEEcHHHHHHHHHHHHhhchhchhhhhhhh
Q psy11008         10 MKT-QSVIDRIVELQKTGALTGVIDD----RGKFIYISQEELNSVATFIKQRGREELNSVATFI   68 (96)
Q Consensus        10 lkt-q~vI~RI~eL~~~g~ltGViDD----RGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~   68 (96)
                      ++. ..+-.-+..|++.|-|+-..+.    +=|+.+||+.-...+..+...- .+-...+..|+
T Consensus        46 is~~~tly~~L~~Le~~GlI~~~~~~~~~~~r~~Y~LT~~G~~~l~~~~~~~-~~~~~~~~~~l  108 (118)
T 2esh_A           46 IGHMGNIYRVLADLEESGFLSTEWDTTVSPPRKIYRITPQGKLYLREILRSL-EDMKRRIETLE  108 (118)
T ss_dssp             CCCCCCHHHHHHHHHHTTSEEEEEECSSSSCEEEEEECHHHHHHHHHHHHHH-HHHHHHHHHHH
T ss_pred             CCCcchHHHHHHHHHHCCCeEEEeecCCCCCceEEEEChHHHHHHHHHHHHH-HHHHHHHHHHH
Confidence            777 7788889999999999998753    3478899999998888887665 22333444444

>1fx7_A Iron-dependent repressor IDER; DTXR, iron-dependent regulator, signaling protein; 2.00A {Mycobacterium tuberculosis} SCOP: a.4.5.24 a.76.1.1 b.34.1.2 PDB: 1u8r_A

Probab=90.07  E-value=0.78  Score=32.46  Aligned_cols=51  Identities=10%  Similarity=0.218  Sum_probs=42.0

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQ   55 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~   55 (96)
                      .+||..++++...+-.-|+.|++.|-++=.-|   +.|++|+.-...+......
T Consensus        28 ~~La~~l~vs~~tvs~~l~~Le~~GlV~r~~~---~~v~LT~~G~~~~~~~~~~   78 (230)
T 1fx7_A           28 ARIAERLDQSGPTVSQTVSRMERDGLLRVAGD---RHLELTEKGRALAIAVMRK   78 (230)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEECTT---SCEEECHHHHHHHHHHHHH
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCC---ccEEECHHHHHHHHHHHHH
Confidence            58999999999999999999999999876443   6999999877766555443

>2v79_A DNA replication protein DNAD; primosome, DNA-binding protein; HET: DNA; 2.00A {Bacillus subtilis}

Probab=90.03  E-value=1.5  Score=29.84  Aligned_cols=54  Identities=13%  Similarity=0.156  Sum_probs=43.1

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccE--EeeCCCc---eEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTG--VIDDRGK---FIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltG--ViDDRGK---fIyIs~eEl~~Va~fI~~r   56 (96)
                      ++||..+|++..+|.+.|+.|++.|-|.=  ..|..|+   +++++| =+++++.++.+.
T Consensus        55 ~~LA~~~~~s~~~v~~~L~~L~~KGlI~i~~~~d~~g~~~~~ydL~p-L~ekL~~~~~~~  113 (135)
T 2v79_A           55 NQLQEGMSISVEECTNRLRMFIQKGFLFIEECEDQNGIKFEKYSLQP-LWGKLYEYIQLA  113 (135)
T ss_dssp             HHHHTTSSSCHHHHHHHHHHHHHHTSCEEEEEECTTCCEEEEEECHH-HHHHHHHHHHHH
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCEEEEeEecCCCceEEEeeHHH-HHHHHHHHHHHH
Confidence            68999999999999999999999999885  5577675   444443 467788887665

>2fmy_A COOA, carbon monoxide oxidation system transcription RE COOA-1; DNA transcription regulator, DNA binding protein; HET: HEM; 2.20A {Carboxydothermus hydrogenoformans} PDB: 2hkx_A*

Probab=90.00  E-value=0.61  Score=30.92  Aligned_cols=45  Identities=18%  Similarity=0.348  Sum_probs=34.7

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCC-CceEEE-cHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDR-GKFIYI-SQEELNSVA   50 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDR-GKfIyI-s~eEl~~Va   50 (96)
                      +|||...|++.+.+-.-+++|+++|.|    .-+ |+.|.| .++.|.++|
T Consensus       171 ~~lA~~lg~sr~tvsR~l~~l~~~g~I----~~~~~~~i~i~d~~~L~~~~  217 (220)
T 2fmy_A          171 EEIALMLGTTRQTVSVLLNDFKKMGIL----ERVNQRTLLLKDLQKLKEFS  217 (220)
T ss_dssp             HHHHHHHTSCHHHHHHHHHHHHHTTSE----EESSSSEEEESCHHHHHHHC
T ss_pred             HHHHHHhCCcHHHHHHHHHHHHHCCCE----EEcCCCEEEEcCHHHHHHHh
Confidence            689999999988888889999999875    332 345666 777777655

>1oyi_A Double-stranded RNA-binding protein; (alpha+beta) helix-turn-helix, viral protein; NMR {Vaccinia virus} SCOP: a.4.5.19

Probab=89.91  E-value=0.24  Score=32.51  Aligned_cols=30  Identities=17%  Similarity=0.310  Sum_probs=27.2

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEE
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGV   31 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGV   31 (96)
                      .+||.++|++.+.|-.+|..|+++|.|.-.
T Consensus        34 ~eLAk~LgiSk~aVr~~L~~Le~eG~I~~~   63 (82)
T 1oyi_A           34 AQLTRQLNMEKREVNKALYDLQRSAMVYSS   63 (82)
T ss_dssp             HHHHHHSSSCHHHHHHHHHHHHHHTSSEEC
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCEEeC
Confidence            489999999999999999999999988653

>4b4t_P 26S proteasome regulatory subunit RPN5; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=89.80  E-value=0.3  Score=38.19  Aligned_cols=43  Identities=14%  Similarity=0.277  Sum_probs=36.9

Q ss_pred             ChhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcH
Q psy11008          1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQ   43 (96)
Q Consensus         1 ledLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~   43 (96)
                      ++.||..++++.+++-.-+-+|..+|+|.|.||---..|+...
T Consensus       362 l~~la~lL~l~~~evE~~ls~mI~~g~i~akIDq~~giV~F~~  404 (445)
T 4b4t_P          362 LLRLNELLDLTESQTETYISDLVNQGIIYAKVNRPAKIVNFEK  404 (445)
T ss_dssp             HHHHHHHHTSCHHHHHHHHHHHHHHTSSCCEEETTTTEEEC--
T ss_pred             HHHHHHHhCcCHHHHHHHHHHHHHCCCEEEEEcCCCCEEEECC
Confidence            4689999999999999999999999999999996555787654

>2jt1_A PEFI protein; solution structure, winged helix-turn-helix, transcripti regulatory protein, structural genomics, PSI-2; NMR {Salmonella typhimurium LT2}

Probab=89.72  E-value=0.45  Score=30.17  Aligned_cols=31  Identities=23%  Similarity=0.216  Sum_probs=26.7

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEe
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI   32 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi   32 (96)
                      .|||..||+++..|-.-+..|++.|.|.=+-
T Consensus        28 ~EIa~~lgvS~~TVrr~L~~Le~kG~I~R~~   58 (77)
T 2jt1_A           28 RDIADAAGLSIYQVRLYLEQLHDVGVLEKVN   58 (77)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEES
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCcEEecC
Confidence            6899999998877777899999999996544

>3k2z_A LEXA repressor; winged helix-turn-helix, SOS system, autoca cleavage, DNA damage, DNA repair, DNA replication, DNA-BIND hydrolase; 1.37A {Thermotoga maritima}

Probab=89.55  E-value=0.3  Score=33.83  Aligned_cols=30  Identities=20%  Similarity=0.452  Sum_probs=27.0

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEE
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGV   31 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGV   31 (96)
                      .|||..||++...+-.+++.|++.|-|..-
T Consensus        28 ~eia~~lgl~~~tv~~~l~~Le~~G~i~~~   57 (196)
T 3k2z_A           28 REIARRFRITPRGALLHLIALEKKGYIERK   57 (196)
T ss_dssp             HHHHHHHTSCHHHHHHHHHHHHHTTSEECC
T ss_pred             HHHHHHcCCCcHHHHHHHHHHHHCCCEEec
Confidence            589999999999888999999999999653

>4fx0_A Probable transcriptional repressor protein; helix-turn-helix, DNA binding, transcription regulator; 2.70A {Mycobacterium tuberculosis} PDB: 4fx4_A*

Probab=89.46  E-value=0.66  Score=30.50  Aligned_cols=52  Identities=17%  Similarity=0.303  Sum_probs=37.7

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEe---eCCCceEEEcHHHHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI---DDRGKFIYISQEELNSVATFIK   54 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi---DDRGKfIyIs~eEl~~Va~fI~   54 (96)
                      .|||..+++..+.+-.-|..|++.|-+. .-   |-|.+.|++|++-...+.+...
T Consensus        56 ~eLa~~l~~~~~tvsr~v~~Le~~glVr-~~~~~DrR~~~v~LT~~G~~~~~~~~~  110 (148)
T 4fx0_A           56 SELAARIGVERTTLTRNLEVMRRDGLVR-VMAGADARCKRIELTAKGRAALQKAVP  110 (148)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSBC------------CCBCHHHHHHHHHHHH
T ss_pred             HHHHHHHCCChhhHHHHHHHHHHCCCEE-eeCCCCCCeeEEEECHHHHHHHHHHHH
Confidence            4899999999999999999999999884 33   4588999999988777666543

>3neu_A LIN1836 protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG, unknown function; 1.58A {Listeria innocua}

Probab=89.08  E-value=1.3  Score=29.01  Aligned_cols=73  Identities=12%  Similarity=0.238  Sum_probs=44.7

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHH--HHHHHHHHHhhchhchhhhhhhhccccceeHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEE--LNSVATFIKQRGREELNSVATFIKQKGRVSVSEL   79 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eE--l~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL   79 (96)
                      .+||.+||++..-|.+-++.|+++|.|.-.   +|+=.||++..  ......   ..-|..+.+.+.-+...| ++..++
T Consensus        41 ~~La~~~~vSr~tvr~Al~~L~~~G~i~~~---~g~G~~V~~~~~~~~~~~~---~~~~~~le~~~~~~~~~g-~~~~ei  113 (125)
T 3neu_A           41 REMGVKLAVNPNTVSRAYQELERAGYIYAK---RGMGSFVTSDKALFDQLKK---ELADAITERFLEEAKSIG-LDDQTA  113 (125)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEE---TTTEEEECCCHHHHHHHHH---HHHHHHHHHHHHHHHHTT-CCHHHH
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCeEEEe---cCCEEEEecCchhhHHHHH---HHHHHHHHHHHHHHHHcC-CCHHHH
Confidence            489999999999999999999999987543   44445554422  221111   111344555555555443 455555


Q ss_pred             HH
Q psy11008         80 VE   81 (96)
Q Consensus        80 ~~   81 (96)
                      .+
T Consensus       114 ~~  115 (125)
T 3neu_A          114 IE  115 (125)
T ss_dssp             HH
T ss_pred             HH
Confidence            44

>1xn7_A Hypothetical protein YHGG; alpha+beta, GFT structural genomics, protein structure initiative, PSI, NESG; NMR {Escherichia coli} SCOP: a.4.5.62

Probab=89.01  E-value=0.25  Score=31.38  Aligned_cols=30  Identities=7%  Similarity=0.184  Sum_probs=25.6

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEE
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGV   31 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGV   31 (96)
                      +|||.+|+++..-+-.=|..|++.|.|.=+
T Consensus        20 ~eLa~~l~VS~~TIRrdL~~Le~~G~l~R~   49 (78)
T 1xn7_A           20 AQISQTLNTPQPMINAMLQQLESMGKAVRI   49 (78)
T ss_dssp             HHHHHHTTCCHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence            699999999877777779999999998543

>2g9w_A Conserved hypothetical protein; DNA-binding domain, bacterial transcription repressor, DNA B protein; 1.80A {Mycobacterium tuberculosis} SCOP: a.4.5.39

Probab=88.95  E-value=1.7  Score=28.24  Aligned_cols=45  Identities=18%  Similarity=0.267  Sum_probs=32.8

Q ss_pred             hhhhhhhC----CChHHHHHHHHHHHHcCCccEEeeCCCceEE--EcHHHH
Q psy11008          2 EDLAALFR----MKTQSVIDRIVELQKTGALTGVIDDRGKFIY--ISQEEL   46 (96)
Q Consensus         2 edLAa~F~----lktq~vI~RI~eL~~~g~ltGViDDRGKfIy--Is~eEl   46 (96)
                      .|||..++    ++...|-.-|..|++.|-|.=.-|+|...++  +|+++.
T Consensus        28 ~el~~~l~~~~~~~~~Tvt~~l~rLe~kGlv~r~~~~r~~~~~~~lt~~~~   78 (138)
T 2g9w_A           28 RQVHEALSARRDLAYTTVMAVLQRLAKKNLVLQIRDDRAHRYAPVHGRDEL   78 (138)
T ss_dssp             HHHHHHHTTTCCCCHHHHHHHHHHHHHTTSEEEEC---CCEEEESSCHHHH
T ss_pred             HHHHHHHhccCCCCHHHHHHHHHHHHHCCCEEEEecCCeEEEEeCCCHHHH
Confidence            47888887    7777788889999999999998887744443  567664

>2ba3_A NIKA; dimer, bacterial conjugation, relaxase, DNA binding, ribbon- helix-helix, DNA binding protein; NMR {Plasmid R64}

Probab=88.89  E-value=0.58  Score=26.64  Aligned_cols=29  Identities=21%  Similarity=0.290  Sum_probs=23.8

Q ss_pred             eEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHHHh
Q psy11008         38 FIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVEN   82 (96)
Q Consensus        38 fIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~~   82 (96)
                      -|.+|++|.+.+..+.++.               | +|++|++..
T Consensus        19 ~vRlt~eE~~~l~~~A~~~---------------g-~s~SeyiR~   47 (51)
T 2ba3_A           19 TLRFSPVEDETIRKKAEDS---------------G-LTVSAYIRN   47 (51)
T ss_dssp             EEEECHHHHHHHHHHHHHH---------------T-CCHHHHHHH
T ss_pred             EEEECHHHHHHHHHHHHHh---------------C-CCHHHHHHH
Confidence            3678999999999999999               5 567777654

>2dk8_A DNA-directed RNA polymerase III 39 kDa polypeptide; structural genomics, RNA_POL_RPC34 domain, RNA polymerase III C39 subunit, NPPSFA; NMR {Mus musculus} SCOP: a.4.5.85

Probab=88.70  E-value=0.73  Score=30.24  Aligned_cols=38  Identities=16%  Similarity=0.231  Sum_probs=33.6

Q ss_pred             hhhhhhhCC-ChHHHHHHHHHHHHcCCccEEeeCCCceEE
Q psy11008          2 EDLAALFRM-KTQSVIDRIVELQKTGALTGVIDDRGKFIY   40 (96)
Q Consensus         2 edLAa~F~l-ktq~vI~RI~eL~~~g~ltGViDDRGKfIy   40 (96)
                      +||+.+|.- ..++..+-|+.|.++|+|. ++-..|+.||
T Consensus        33 ~~L~~~~p~~~~~~r~~aIN~LL~~gkie-l~K~~~~liY   71 (81)
T 2dk8_A           33 QVIQNEMPHIEAQQRAVAINRLLSMGQLD-LLRSNTGLLY   71 (81)
T ss_dssp             HHHHHHCTTSCHHHHHHHHHHHHHHTSEE-EEECSSSEEE
T ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHcCCeE-EEecCCeEEE
Confidence            577788764 8899999999999999999 8888899998

>2k9i_A Plasmid PRN1, complete sequence; plasmid COPY control protein, ribbon helix helix protein, DNA binding protein; NMR {Sulfolobus islandicus} PDB: 3ft7_A

Probab=88.44  E-value=0.68  Score=25.84  Aligned_cols=29  Identities=21%  Similarity=0.380  Sum_probs=25.4

Q ss_pred             EEEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHHHhc
Q psy11008         39 IYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVENS   83 (96)
Q Consensus        39 IyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~~s   83 (96)
                      |+|+++.++.+..+.++.               |+ |.+++++.+
T Consensus        14 vrl~~el~~~l~~~a~~~---------------g~-s~s~~ir~a   42 (55)
T 2k9i_A           14 VYIPQEWHDRLMEIAKEK---------------NL-TLSDVCRLA   42 (55)
T ss_dssp             EEECHHHHHHHHHHHHHH---------------TC-CHHHHHHHH
T ss_pred             EEcCHHHHHHHHHHHHHh---------------CC-CHHHHHHHH
Confidence            789999999999999999               76 888888754

>2k02_A Ferrous iron transport protein C; FEOC, iron-sulfur, metal-binding, metal binding protein; NMR {Klebsiella pneumoniae subsp}

Probab=87.79  E-value=0.62  Score=30.48  Aligned_cols=31  Identities=10%  Similarity=0.193  Sum_probs=27.1

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEe
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI   32 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi   32 (96)
                      .|||.+|+++..-+-.=|..|++.|.|.=+-
T Consensus        20 ~eLA~~l~VS~~TIRrDL~~Le~~G~l~R~~   50 (87)
T 2k02_A           20 KQLSARLQTPQPLIDAMLERMEAMGKVVRIS   50 (87)
T ss_dssp             HHHHHHTTCCHHHHHHHHHHHHTTCCSEEEE
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCEEEEe
Confidence            6999999998777667799999999998875

>3ihu_A Transcriptional regulator, GNTR family; YP_298823.1, DNA binding protein, structural genomics, joint for structural genomics, JCSG; HET: MSE; 1.92A {Ralstonia eutropha}

Probab=87.64  E-value=1.3  Score=30.69  Aligned_cols=50  Identities=28%  Similarity=0.323  Sum_probs=39.0

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEE-EcHHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIY-ISQEELNSVATF   52 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIy-Is~eEl~~Va~f   52 (96)
                      .+||.+||++..-|.+-++.|+.+|-+.- .--+|-||- +|.+++..+-..
T Consensus        43 ~~La~~lgVSRtpVREAl~~L~~eGlv~~-~~~~G~~V~~~~~~~~~e~~~~   93 (222)
T 3ihu_A           43 TDLVAHFGVGRNSVREALQRLAAEGIVDL-QRHRGAVIRRLSLQETLDVLDV   93 (222)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEE-CSTTCEEECCCCHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCEEE-ecCCCeEEecCCHHHHHHHHHH
Confidence            47999999999999999999999998863 345676664 566766665544

>1hsj_A Fusion protein consisting of staphylococcus accessary regulator protein R and maltose...; novel fold for DNA binding; HET: GLC; 2.30A {Escherichia coli} SCOP: a.4.5.28 c.94.1.1

Probab=87.39  E-value=0.87  Score=34.29  Aligned_cols=55  Identities=13%  Similarity=0.266  Sum_probs=45.8

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .+||...++....+-.-|..|++.|-|+=.-|   -|..+|++|++-.+.+.......
T Consensus       424 ~~l~~~~~~~~~~~t~~~~~le~~g~v~r~~~~~D~R~~~i~lT~~g~~~~~~~~~~~  481 (487)
T 1hsj_A          424 KEIAKCSEFKPYYLTKALQKLKDLKLLSKKRSLQDERTVIVYVTDTQKANIQKLISEL  481 (487)
T ss_dssp             HHHHHSSCCCHHHHHHHHHHHHTTTTSCCEECCSSSSCCEEECCSSHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCEeecCCCCCCCeEEEEECHHHHHHHHHHHHHH
Confidence            58999999999988889999999999988764   69999999999877665554443

>3lmm_A Uncharacterized protein; multi-domained alpha-beta protein, structural genomics, PSI- 2, protein structure initiative; 3.00A {Corynebacterium diphtheriae}

Probab=87.34  E-value=0.58  Score=38.69  Aligned_cols=83  Identities=8%  Similarity=0.116  Sum_probs=35.6

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCC-ccEEeeCCCceEEEcHHHHHHH------HHH-HHhhchhch---hhhhhhhcc
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGA-LTGVIDDRGKFIYISQEELNSV------ATF-IKQRGREEL---NSVATFIKQ   70 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~-ltGViDDRGKfIyIs~eEl~~V------a~f-I~~rgr~~~---~~~~~~~~~   70 (96)
                      .+||..++++...+-..|+.|.+.+. -.|++.-.|...+++++=...+      +.+ ++.++.+..   ..+..|++.
T Consensus       448 ~~la~~l~~s~~~~~~~L~~L~~~~~~~~glie~~g~~y~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~~~l~~  527 (583)
T 3lmm_A          448 DVVARGLQSGKEAARNALEAARQTTVAGAPLIIAHDGVWLLGNACREILRKVEPSPFSPVRYLSTDQAELTNAAMLWLSE  527 (583)
T ss_dssp             HHHHHHHTSCHHHHHHHHHHHHTCEETTEESEEEETTEEEECHHHHHHHTSCC---------------------------
T ss_pred             HHHHHHhCcCHHHHHHHHHHHHhhhccccceEEEeCCEEEECHHHHHHhcccccccccccccccCChhHHHHHHHHHHHH
Confidence            47899999999999999999999431 1355555577788998744433      222 444443321   247789999


Q ss_pred             ccceeHHHHHHhcc
Q psy11008         71 KGRVSVSELVENSN   84 (96)
Q Consensus        71 ~GRVsi~eL~~~sN   84 (96)
                      .|++|.+|+++.|.
T Consensus       528 ~g~it~~di~~l~~  541 (583)
T 3lmm_A          528 VGDLATSDLMAMCG  541 (583)
T ss_dssp             --------------
T ss_pred             cCCcCHHHHHHHHC
Confidence            99999999999775

>1xmk_A Double-stranded RNA-specific adenosine deaminase; winged helix-turn-helix, RNA editing, interferon, ADAR1, hydrolase; 0.97A {Homo sapiens} SCOP: a.4.5.19

Probab=87.15  E-value=0.94  Score=29.06  Aligned_cols=36  Identities=11%  Similarity=0.202  Sum_probs=29.5

Q ss_pred             hhhhhhhCCChH-HHHHHHHHHHHcCCccEEeeCCCceE
Q psy11008          2 EDLAALFRMKTQ-SVIDRIVELQKTGALTGVIDDRGKFI   39 (96)
Q Consensus         2 edLAa~F~lktq-~vI~RI~eL~~~g~ltGViDDRGKfI   39 (96)
                      .+||..+|++++ .|-.-+..|+++|-+.-.  ++|+-+
T Consensus        29 ~eiA~~Lgit~~~aVr~hL~~Le~eGlV~~~--~~gRP~   65 (79)
T 1xmk_A           29 LNLAKNIGLTKARDINAVLIDMERQGDVYRQ--GTTPPI   65 (79)
T ss_dssp             HHHHHHHCGGGHHHHHHHHHHHHHTTSEEEE--CSSSCE
T ss_pred             HHHHHHcCCCcHHHHHHHHHHHHHCCCEEec--CCCCCC
Confidence            489999999999 888889999999999732  455444

>2hs5_A Putative transcriptional regulator GNTR; APC6050, rhodococcus SP. RH structural genomics, PSI-2, protein structure initiative; 2.20A {Rhodococcus SP} SCOP: a.4.5.6 a.78.1.1

Probab=86.95  E-value=1.3  Score=31.51  Aligned_cols=49  Identities=16%  Similarity=0.253  Sum_probs=36.6

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEE-EcHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIY-ISQEELNSVAT   51 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIy-Is~eEl~~Va~   51 (96)
                      .+||.+||++..-|.+-++.|+.+|-|.- .--+|-||. ++.+++..+-.
T Consensus        55 ~~La~~lgVSRtpVREAL~~L~~eGlv~~-~~~~G~~V~~~~~~~~~el~e  104 (239)
T 2hs5_A           55 PDICAALDVSRNTVREAFQILIEDRLVAH-ELNRGVFVRVPTAEDITELYI  104 (239)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEE-ETTTEEEECCCCHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCEEE-eCCCeeEEeCCCHHHHHHHHH
Confidence            48999999999999999999999998863 334565553 35555554443

>1bia_A BIRA bifunctional protein; transcription regulation; 2.30A {Escherichia coli} SCOP: a.4.5.1 b.34.1.1 d.104.1.2 PDB: 1bib_A* 1hxd_A* 2ewn_A*

Probab=86.43  E-value=0.86  Score=34.25  Aligned_cols=45  Identities=18%  Similarity=0.182  Sum_probs=33.8

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceE-------EEcHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFI-------YISQEELNS   48 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfI-------yIs~eEl~~   48 (96)
                      ++||.+|+++..-+-..|+.|++.|.+.--  .+|+..       .++++++..
T Consensus        23 ~eLa~~l~vS~~ti~r~l~~L~~~G~~i~~--~~g~GY~l~~~~~~L~~~eI~~   74 (321)
T 1bia_A           23 EQLGETLGMSRAAINKHIQTLRDWGVDVFT--VPGKGYSLPEPIQLLNAKQILG   74 (321)
T ss_dssp             HHHHHHHTSCHHHHHHHHHHHHHTTCCCEE--ETTTEEECSSCCCCCCHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHhCCCcEEE--ecCCCcEEeeccccCCHHHHHH
Confidence            689999999999999999999999987522  244433       356666654

>2fu4_A Ferric uptake regulation protein; DNA binding domain, helix-turn-helix, DNA binding protein; 1.80A {Escherichia coli}

Probab=86.31  E-value=1.1  Score=26.51  Aligned_cols=39  Identities=21%  Similarity=0.298  Sum_probs=33.4

Q ss_pred             hhhhhhh-----CCChHHHHHHHHHHHHcCCccEEeeCCCceEE
Q psy11008          2 EDLAALF-----RMKTQSVIDRIVELQKTGALTGVIDDRGKFIY   40 (96)
Q Consensus         2 edLAa~F-----~lktq~vI~RI~eL~~~g~ltGViDDRGKfIy   40 (96)
                      +||+..+     +++..-|-.-++.|++.|.|.-+-.+.|+..|
T Consensus        37 ~el~~~l~~~~~~is~~TVyR~L~~L~~~Glv~~~~~~~~~~~y   80 (83)
T 2fu4_A           37 EDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHNFEGGKSVF   80 (83)
T ss_dssp             HHHHHHHHHTTCCCCHHHHHHHHHHHHHHTSEEEEECGGGCEEE
T ss_pred             HHHHHHHHHhCCCCCHhhHHHHHHHHHHCCCeEEEeeCCCceEe
Confidence            5889999     89888888889999999999988877777666

>3by6_A Predicted transcriptional regulator; structural genomics, PSI-2, MCSG, structure initiative, midwest center for structural genomic binding; 2.20A {Oenococcus oeni}

Probab=86.24  E-value=1.8  Score=28.53  Aligned_cols=77  Identities=17%  Similarity=0.202  Sum_probs=44.8

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVE   81 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~   81 (96)
                      .+||..||++..-|.+-++.|+++|.|.- .--+|-||--+.+++..+..|   .-|..+.+.+.-....| .+.+++.+
T Consensus        39 ~~La~~~~vSr~tvr~Al~~L~~~Gli~~-~~g~G~~V~~~~~~~~~~~~~---~~r~~le~~~~~~~~~~-~~~~~l~~  113 (126)
T 3by6_A           39 RETALQEKINPNTVAKAYKELEAQKVIRT-IPGKGTFITGNTASVKNSNQN---RLLADLSQVIAELIKSG-VKGERIKK  113 (126)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEE-ETTTEEEECSCHHHHHHHHHH---HHHHHHHHHHHHHHHTT-CCHHHHHH
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCEEE-ecCCeEEEccCchhhhHhHHH---HHHHHHHHHHHHHHHcC-CCHHHHHH
Confidence            47999999999999999999999998753 233454443334443332111   11223444444443333 45555544


Q ss_pred             hc
Q psy11008         82 NS   83 (96)
Q Consensus        82 ~s   83 (96)
                      ..
T Consensus       114 l~  115 (126)
T 3by6_A          114 IV  115 (126)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>3la7_A Global nitrogen regulator; activator, DNA-binding, transcription, transcription regulation; HET: BOG; 1.90A {Anabaena} PDB: 3la2_A* 3la3_A* 2xko_A* 2xgx_A* 2xhk_A* 2xkp_A*

Probab=86.05  E-value=0.87  Score=31.06  Aligned_cols=44  Identities=14%  Similarity=0.188  Sum_probs=30.8

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNS   48 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~   48 (96)
                      +|||...|++.+.+-.-+++|+++|.|.  + ++|+++-+..+.|.+
T Consensus       197 ~~lA~~lG~sr~tvsR~l~~L~~~GlI~--~-~~~~i~I~d~~~L~~  240 (243)
T 3la7_A          197 QAIAEAIGSTRVTVTRLLGDLREKKMIS--I-HKKKITVHKPVTLSR  240 (243)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEE--E-ETTEEEECC------
T ss_pred             HHHHHHHCCcHHHHHHHHHHHHHCCCEE--E-cCCEEEECCHHHHHh
Confidence            6899999999888888899999999876  2 356655556655544

>3hhh_A Transcriptional regulator, PADR family; PF03551, structural PSI-2, protein structure initiative, midwest center for STR genomics, MCSG; 2.70A {Enterococcus faecalis} SCOP: a.4.5.0

Probab=85.77  E-value=3.9  Score=26.80  Aligned_cols=63  Identities=17%  Similarity=0.248  Sum_probs=44.8

Q ss_pred             CCChHHHHHHHHHHHHcCCccEEee--CCC---ceEEEcHHHHHHHHHHHHhhchhchhhhhhhhcccc
Q psy11008          9 RMKTQSVIDRIVELQKTGALTGVID--DRG---KFIYISQEELNSVATFIKQRGREELNSVATFIKQKG   72 (96)
Q Consensus         9 ~lktq~vI~RI~eL~~~g~ltGViD--DRG---KfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~G   72 (96)
                      +++...+-.-+..|++.|-|+...+  +.|   ||..||+.-...+..+...- .+-...+..|+..+|
T Consensus        43 ~is~gtlY~~L~rLe~~GlI~~~~~~~~~g~~rk~Y~lT~~G~~~l~~~~~~~-~~~~~~i~~il~~~~  110 (116)
T 3hhh_A           43 EIVEGTVYTILLRLEKNQWVIAEKKPSEKGPMRKFYRLTSSGEAELADFWQRW-TLLSKQVNKMKKNGG  110 (116)
T ss_dssp             SCCHHHHHHHHHHHHHTTSEEEEEEECC--CEEEEEEECHHHHHHHHHHHHHH-HHHHHHHHHHHHC--
T ss_pred             CCCccHHHHHHHHHHHCCCEEEEeeecCCCCCceEEEECHHHHHHHHHHHHHH-HHHHHHHHHHHCcCC
Confidence            6888888899999999999999874  223   56669999999988888766 233344555555544

>4ham_A LMO2241 protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, winged helix-turn-helix, four helix bundle; 1.91A {Listeria monocytogenes}

Probab=85.68  E-value=2.3  Score=27.85  Aligned_cols=36  Identities=22%  Similarity=0.434  Sum_probs=29.6

Q ss_pred             hhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceE
Q psy11008          3 DLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFI   39 (96)
Q Consensus         3 dLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfI   39 (96)
                      +||.+||++..-|.+-++.|+++|-|.-. --+|-||
T Consensus        43 ~La~~~gVSr~tVReAl~~L~~eGlv~~~-~g~G~~V   78 (134)
T 4ham_A           43 EFASRIGVNPNTVSKAYQELERQEVIITV-KGKGTFI   78 (134)
T ss_dssp             HHHHHHTCCHHHHHHHHHHHHHTTSEEEE-TTTEEEE
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHCCcEEEE-cCcEEEE
Confidence            79999999999999999999999987633 3345554

>2vn2_A DNAD, chromosome replication initiation protein; DNA replication, primosome; 2.3A {Geobacillus kaustophilus HTA426}

Probab=85.45  E-value=0.74  Score=30.39  Aligned_cols=54  Identities=9%  Similarity=0.167  Sum_probs=37.4

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee--CCCce---EEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID--DRGKF---IYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD--DRGKf---IyIs~eEl~~Va~fI~~r   56 (96)
                      ++||..++++..+|...|+.|++.|-|+=..|  |.|+.   ..++ -=+++++.|..+.
T Consensus        55 ~~LA~~l~~s~~~V~~~l~~Le~kGlI~~~~~~~~~g~~~~~Ydl~-pl~~kL~~~~~~~  113 (128)
T 2vn2_A           55 AELAERMTVSAAECMEMVRRLLQKGMIAIEEHTDEQGIRNEKYTLE-PLWEKLVHHLYTQ  113 (128)
T ss_dssp             HHHHHTSSSCHHHHHHHHHHHHHTTSSEECC----------CEECH-HHHHHHHHHHHHH
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCEEEEeEECCCCcEEEEEehH-HHHHHHHHHHHHH
Confidence            58999999999999999999999999876443  44653   3333 3466777777554

>4esf_A PADR-like transcriptional regulator; PADR family, DNA binding protein, HTH fold; 2.20A {Bacillus cereus}

Probab=85.39  E-value=5.4  Score=26.07  Aligned_cols=65  Identities=14%  Similarity=0.126  Sum_probs=44.9

Q ss_pred             CCChHHHHHHHHHHHHcCCccEEeeC----CC-ceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccce
Q psy11008          9 RMKTQSVIDRIVELQKTGALTGVIDD----RG-KFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRV   74 (96)
Q Consensus         9 ~lktq~vI~RI~eL~~~g~ltGViDD----RG-KfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRV   74 (96)
                      +++...+-.-+..|++.|-|+...+.    +. ||..||+.-...+..+...- ..-...+..++....+.
T Consensus        41 ~is~gtlY~~L~rLe~~GlI~~~~~~~~~g~~rk~Y~LT~~G~~~l~~~~~~~-~~~~~~i~~il~~~~~~  110 (117)
T 4esf_A           41 EVVEGTVYTILVRLEKKKLVNIEKKPSDMGPPRKFYSLNEAGRQELELFWKKW-DFVSSKINVLKSSNSRW  110 (117)
T ss_dssp             TCCHHHHHHHHHHHHHTTCEEEEEEC-----CEEEEEECHHHHHHHHHHHHHH-HHHHHHHHHHHTTC---
T ss_pred             CCCccHHHHHHHHHHHCCCEEEEeecCCCCCCceEEEECHHHHHHHHHHHHHH-HHHHHHHHHHHcccccC
Confidence            78888888999999999999998752    22 45559999998888887665 22233445555544443

>1xma_A Predicted transcriptional regulator; southea collaboratory for structural genomics, secsg, protein struc initiative, PSI; 2.30A {Clostridium thermocellum} SCOP: a.4.5.61

Probab=84.93  E-value=2.8  Score=28.47  Aligned_cols=48  Identities=15%  Similarity=0.261  Sum_probs=40.3

Q ss_pred             CCChHHHHHHHHHHHHcCCccEEeeC-----CCceEEEcHHHHHHHHHHHHhh
Q psy11008          9 RMKTQSVIDRIVELQKTGALTGVIDD-----RGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         9 ~lktq~vI~RI~eL~~~g~ltGViDD-----RGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      +++...+-..+..|++.|-|+-..+.     +-|+..||+.-...+..+....
T Consensus        73 ~is~gtLy~~L~rLE~~GlI~~~~~~~~~~~~rk~Y~LT~~G~~~l~~~~~~~  125 (145)
T 1xma_A           73 VIKETTLYSAFARLEKNGYIKSYYGEETQGKRRTYYRITPEGIKYYKQKCEEW  125 (145)
T ss_dssp             CCCHHHHHHHHHHHHHTTSEEEEEEEEC--CEEEEEEECHHHHHHHHHHHHHH
T ss_pred             CcChhHHHHHHHHHHHCCCEEEEEeccCCCCCeEEEEECHHHHHHHHHHHHHH
Confidence            68888888999999999999988653     4578899999888888877665

>1mkm_A ICLR transcriptional regulator; structural genomics, winged helix-turn-helix, PSI, protein structure initiative; 2.20A {Thermotoga maritima} SCOP: a.4.5.33 d.110.2.2

Probab=84.81  E-value=2.3  Score=30.31  Aligned_cols=50  Identities=12%  Similarity=0.224  Sum_probs=37.5

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIK   54 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~   54 (96)
                      .|||..+|++...+-.-++.|++.|-+.-.  +.|+| ++++.=+.--..+..
T Consensus        27 ~ela~~~gl~~stv~r~l~~L~~~G~v~~~--~~~~Y-~lg~~~~~l~~~~~~   76 (249)
T 1mkm_A           27 SEIAEKFNMSVSNAYKYMVVLEEKGFVLRK--KDKRY-VPGYKLIEYGSFVLR   76 (249)
T ss_dssp             HHHHHHTTCCHHHHHHHHHHHHHTTSEEEC--TTSCE-EECTHHHHHHHHHHH
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCcEEEC--CCCcE-EECHHHHHHHHHHHh
Confidence            589999999888888889999999999874  44555 778765443334443

>2gqq_A Leucine-responsive regulatory protein; helix-turn-helix, transcription; 3.20A {Escherichia coli} PDB: 2l4a_A

Probab=84.32  E-value=0.2  Score=33.69  Aligned_cols=55  Identities=15%  Similarity=0.347  Sum_probs=40.4

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEe---eC--CCc----eEEE-----cHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI---DD--RGK----FIYI-----SQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi---DD--RGK----fIyI-----s~eEl~~Va~fI~~r   56 (96)
                      .+||..||++...|.++++.|++.|-+.+..   |.  =|.    ++.+     +++++..+...+.+.
T Consensus        31 ~eLa~~lgvSr~~vr~al~~L~~~Gli~~~v~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~l~~~l~~~   99 (163)
T 2gqq_A           31 VELSKRVGLSPTPCLERVRRLERQGFIQGYTALLNPHYLDASLLVFVEITLNRGAPDVFEQFNTAVQKL   99 (163)
T ss_dssp             TGGGTSSSCCTTTSSSTHHHHHHHTSEEEEEEEECTTTTTCCCEEEEEEECCCCSTTHHHHHHHHHSSC
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCcEEEEEEeCCHHHcCCceEEEEEEEeccCChhHHHHHHHHHHhC
Confidence            5899999999999999999999999998643   21  121    1222     466777777777654

>1yg2_A Gene activator APHA; virulence factor, winged helix, transcripti factor, transcription; 2.20A {Vibrio cholerae} SCOP: a.4.5.61

Probab=84.10  E-value=2.8  Score=28.59  Aligned_cols=48  Identities=19%  Similarity=0.306  Sum_probs=39.2

Q ss_pred             CCChHHHHHHHHHHHHcCCccEEeeC-----CCceEEEcHHHHHHHHHHHHhh
Q psy11008          9 RMKTQSVIDRIVELQKTGALTGVIDD-----RGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         9 ~lktq~vI~RI~eL~~~g~ltGViDD-----RGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      +++...+-.-++.|++.|-|+...+.     +=|+..||+.-...+..++..-
T Consensus        34 ~~s~~~ly~~L~~Le~~GlI~~~~~~~~~~~~r~~Y~lT~~G~~~l~~~~~~~   86 (179)
T 1yg2_A           34 KASHQQVYRELNKMGEQGLVTCVLEPQEGKPDRKVYSITQAGRSALGEWFDQP   86 (179)
T ss_dssp             CCCHHHHHHHHHHHHHTTSEEECCC---------CEEECHHHHHHHHHHHHSC
T ss_pred             CCCcCcHHHHHHHHHHCCCeEEEeecCCCCCCceEEEeChHHHHHHHHHHhCc
Confidence            78899999999999999999987653     2256789999999999988875

>3tdu_C Cullin-1, CUL-1; E2:E3, ligase-protein binding complex; 1.50A {Homo sapiens} PDB: 3tdz_C

Probab=83.90  E-value=0.77  Score=29.41  Aligned_cols=41  Identities=17%  Similarity=0.285  Sum_probs=36.8

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEc
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYIS   42 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs   42 (96)
                      +.|...|..+..++-.+|..|.+.+-|.-.-||+..|.|+.
T Consensus        37 ~ql~~rF~p~~~~IKk~IE~LIereYl~R~~~~~~~y~Y~A   77 (77)
T 3tdu_C           37 TQLSSRFKPRVPVIKKCIDILIEKEYLERVDGEKDTYSYLA   77 (77)
T ss_dssp             HHHTTTCCCCHHHHHHHHHHHHHTTSEEEETTEEEEEEECC
T ss_pred             HHHhCcCCCCHHHHHHHHHHHHhhhHhhcCCCCCceEEEeC
Confidence            45778899999999999999999999999888889999973

>3f8m_A GNTR-family protein transcriptional regulator; PHNF, HUTC, winged helix-TUR UTRA, DNA-binding, transcription regulation; 1.80A {Mycobacterium smegmatis}

Probab=83.35  E-value=1.3  Score=32.05  Aligned_cols=36  Identities=19%  Similarity=0.350  Sum_probs=31.7

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceE
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFI   39 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfI   39 (96)
                      .+||.+||++..-|.+-++.|+++|.|.-  --+|-|+
T Consensus        40 ~~La~~~~vSr~tvr~Al~~L~~~G~i~~--~g~Gt~V   75 (248)
T 3f8m_A           40 REIAEQFEVARETVRQALRELLIDGRVER--RGRTTVV   75 (248)
T ss_dssp             HHHHHHTTCCHHHHHHHHHHHHHTTSEEE--ETTEEEE
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCEEe--CCCEEEE
Confidence            48999999999999999999999999976  6666665

>1iuy_A Cullin-3 homologue; winged helix, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} SCOP: a.4.5.34

Probab=82.75  E-value=1.2  Score=29.39  Aligned_cols=41  Identities=24%  Similarity=0.334  Sum_probs=35.6

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEc
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYIS   42 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs   42 (96)
                      +.|...|..+...+-.||..|.+.+-|.-.-||+..|.|+.
T Consensus        52 ~ql~~rF~p~~~~IKk~IE~LIereYleR~~~d~~~y~Y~A   92 (92)
T 1iuy_A           52 QQLKARFLPSPVVIKKRIEGLIEREYLARTPEDRKVYTYVA   92 (92)
T ss_dssp             HHTCSSCCCCHHHHHHHHHHHHHTTSEEECSSCSSEEEEC-
T ss_pred             HHHcCCCCCCHHHHHHHHHHHhhhhhhhcCCCCCCeeEecC
Confidence            35667899999999999999999999998888889999974

>2xvc_A ESCRT-III, SSO0910; cell cycle, cell division, cytokinesis, winged-helix; 2.15A {Sulfolobus solfataricus}

Probab=82.44  E-value=0.99  Score=28.82  Aligned_cols=28  Identities=18%  Similarity=0.469  Sum_probs=25.4

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCcc
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALT   29 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~lt   29 (96)
                      ++.|+.||++.++|.+-++.|++.|-|.
T Consensus        29 ~~~a~kygV~kdeV~~~LrrLe~KGLI~   56 (59)
T 2xvc_A           29 EHFSKVYGVEKQEVVKLLEALKNKGLIA   56 (59)
T ss_dssp             HHHHHHHCCCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHhCCCHHHHHHHHHHHHHCCCee
Confidence            5789999999999999999999999763

>3rkx_A Biotin-[acetyl-COA-carboxylase] ligase; biotin protein ligase, 3 domains, enzyme DNA binding, biotin coupling domains; 2.10A {Staphylococcus aureus} PDB: 3rir_A* 3rkw_A 3rky_A* 3v7c_A* 3v7s_A* 3v8j_A 3v7r_A 3v8k_A* 3v8l_A* 4dq2_A*

Probab=82.42  E-value=2.4  Score=32.31  Aligned_cols=26  Identities=19%  Similarity=0.310  Sum_probs=24.8

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCC
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGA   27 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~   27 (96)
                      ++||.+||++...|-+.|+.|++.|-
T Consensus        23 ~eLa~~lgvSr~aV~k~i~~L~~~G~   48 (323)
T 3rkx_A           23 QSIAESLNISRTAVKKVIDQLKLEGC   48 (323)
T ss_dssp             HHHHHHHTSCHHHHHHHHHHHHHTTC
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHhcCC
Confidence            68999999999999999999999997

>1pdn_C Protein (PRD paired); protein-DNA complex, double helix, PAX, paired domain, DNA-binding protein, gene regulation/DNA complex; HET: DNA; 2.50A {Drosophila melanogaster} SCOP: a.4.1.5

Probab=81.74  E-value=1.6  Score=26.41  Aligned_cols=54  Identities=17%  Similarity=0.127  Sum_probs=35.7

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCC-ceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRG-KFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRG-KfIyIs~eEl~~Va~fI~~r   56 (96)
                      .++|..||++...|-.-++...+.|.+. ---.+| +--.+++++...|..++++.
T Consensus        37 ~~ia~~lgis~~Tv~~w~~~~~~~g~~~-~~~~~g~~~~~l~~~~~~~i~~~~~~~   91 (128)
T 1pdn_C           37 CVISRQLRVSHGCVSKILNRYQETGSIR-PGVIGGSKPRIATPEIENRIEEYKRSS   91 (128)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHHCCSS-CCCCSCCCCCSSCSTHHHHHHHTTTTC
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHhhCCcc-cccCCCCCCCcCCHHHHHHHHHHHHhC
Confidence            4789999998766666677777777542 111124 44467888877787777665

>3ryp_A Catabolite gene activator; CAMP receptor protein (CRP), allostery, DNA binding cyclic A transcription regulator; HET: CMP; 1.60A {Escherichia coli} PDB: 2cgp_A* 3hif_A 1g6n_A* 3ryr_A* 1i5z_A* 1j59_A* 1lb2_A* 1run_A* 1zrc_A* 1zrd_A* 1zre_A* 1zrf_A* 2gzw_A* 2wc2_A 3iyd_G* 3n4m_A* 3qop_A* 3rdi_A* 3rou_A* 3rpq_A* ...

Probab=81.59  E-value=1.5  Score=28.51  Aligned_cols=37  Identities=14%  Similarity=0.259  Sum_probs=29.3

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEc
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYIS   42 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs   42 (96)
                      ++||...|++.+.+-.-+++|+++|.|.    -.|+.|.|-
T Consensus       171 ~~iA~~lg~sr~tvsR~l~~L~~~g~I~----~~~~~i~i~  207 (210)
T 3ryp_A          171 QEIGQIVGCSRETVGRILKMLEDQNLIS----AHGKTIVVY  207 (210)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEE----EETTEEEEE
T ss_pred             HHHHHHhCCcHHHHHHHHHHHHHCCcEE----eCCCEEEEE
Confidence            6899999998888888899999998765    344556554

>1hw1_A FADR, fatty acid metabolism regulator protein; helix-turn-helix, helix bundle, transcription; 1.50A {Escherichia coli} SCOP: a.4.5.6 a.78.1.1 PDB: 1hw2_A 1e2x_A 1h9g_A* 1h9t_A

Probab=81.50  E-value=1.4  Score=30.46  Aligned_cols=37  Identities=16%  Similarity=0.255  Sum_probs=29.6

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceE
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFI   39 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfI   39 (96)
                      .+||.+||++..-|.+-|+.|+.+|-|.= .--+|-|+
T Consensus        35 ~eLa~~~gVSR~tVReAL~~L~~eGlv~~-~~g~G~~V   71 (239)
T 1hw1_A           35 RELSELIGVTRTTLREVLQRLARDGWLTI-QHGKPTKV   71 (239)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEE-ETTEEEEE
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCcEEE-ecCCCcEe
Confidence            48999999999999999999999998763 22344444

>1p4x_A Staphylococcal accessory regulator A homologue; winged-helix protein, transcription; 2.20A {Staphylococcus aureus} SCOP: a.4.5.28 a.4.5.28

Probab=81.24  E-value=3.8  Score=30.05  Aligned_cols=48  Identities=21%  Similarity=0.352  Sum_probs=41.3

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELNSV   49 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~~V   49 (96)
                      .|||..++++...+-.-|+.|++.|-|+=.-|   .|-.+||+|++-.+.+
T Consensus        54 ~el~~~l~~~~~t~t~~l~rLe~~G~i~R~~~~~DrR~~~i~LT~~G~~~~  104 (250)
T 1p4x_A           54 KKIVSDLCYKQSDLVQHIKVLVKHSYISKVRSKIDERNTYISISEEQREKI  104 (250)
T ss_dssp             HHHHHHSSSCGGGTHHHHHHHHHTTSCEEEECSSSTTSEEEECCHHHHHHH
T ss_pred             HHHHHHHCCCHhhHHHHHHHHHHCCCEEecCCCCCCCeEEEEECHHHHHHH
Confidence            48999999998888888999999999998865   5888999999866543

>3o2p_E Cell division control protein 53; ligase, cell cycle; 2.23A {Saccharomyces cerevisiae} PDB: 3o6b_B

Probab=80.72  E-value=1.7  Score=28.52  Aligned_cols=40  Identities=23%  Similarity=0.252  Sum_probs=34.8

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEc
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYIS   42 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs   42 (96)
                      +.|...|..+..++-.||..|.+.+-|.-.=|| ..|.|+.
T Consensus        49 ~ql~~rF~p~~~~IKk~IE~LIekeYleR~~~~-~~y~YlA   88 (88)
T 3o2p_E           49 AQSHQRFNAKVSMVKRAIDSLIQKGYLQRGDDG-ESYAYLA   88 (88)
T ss_dssp             HHHTTTCCCCHHHHHHHHHHHHHTTSEEECTTS-SEEEECC
T ss_pred             HHHhccCCCCHHHHHHHHHHHHhhhHHhcCCCC-CeEEeeC
Confidence            457788999999999999999999999887556 9999973

>2cpg_A REPA protein, transcriptional repressor COPG; DNA-binding protein, plasmid, gene regulation; 1.60A {Streptococcus agalactiae} SCOP: a.43.1.3 PDB: 1b01_A* 1ea4_A*

Probab=80.32  E-value=2.6  Score=22.65  Aligned_cols=29  Identities=21%  Similarity=0.351  Sum_probs=24.8

Q ss_pred             EEEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHHHhc
Q psy11008         39 IYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVENS   83 (96)
Q Consensus        39 IyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~~s   83 (96)
                      |+++++-++.+-.+.++.               |+ |.+++++.+
T Consensus         7 v~l~~~l~~~Ld~~a~~~---------------g~-srS~~ir~a   35 (45)
T 2cpg_A            7 ITLSESVLENLEKMAREM---------------GL-SKSAMISVA   35 (45)
T ss_dssp             EEEEHHHHHHHHHHHHHH---------------TC-CHHHHHHHH
T ss_pred             EecCHHHHHHHHHHHHHH---------------Cc-CHHHHHHHH
Confidence            789999999999999999               75 888887653

>2ek5_A Predicted transcriptional regulators; helix-turn-helix, interwined alpha helices; 2.20A {Corynebacterium glutamicum atcc 13032} PDB: 2du9_A

Probab=80.06  E-value=4.1  Score=27.02  Aligned_cols=43  Identities=23%  Similarity=0.389  Sum_probs=33.7

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELN   47 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~   47 (96)
                      .+||..||++..-|.+-++.|+++|-|.-   .+|+=.||++-...
T Consensus        32 ~~La~~~gvSr~tVr~Al~~L~~~Gli~~---~~g~G~~V~~~~~~   74 (129)
T 2ek5_A           32 NELAAFHRINPATARNGLTLLVEAGILYK---KRGIGMFVSAQAPA   74 (129)
T ss_dssp             HHHHHHTTCCHHHHHHHHHHHHTTTSEEE---ETTTEEEECTTHHH
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCcEEE---ecCCEEEEecCchH
Confidence            48999999999999999999999998753   35566666654333

>2p4w_A Transcriptional regulatory protein ARSR family; archaea, PHR, heat shock, transcriptional regulation, winged DNA binding; 2.60A {Pyrococcus furiosus} SCOP: a.4.5.64

Probab=80.03  E-value=2.8  Score=29.94  Aligned_cols=32  Identities=13%  Similarity=0.377  Sum_probs=29.7

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID   33 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD   33 (96)
                      .|||..+|++...+-..++.|++.|-++..-+
T Consensus        32 ~eLa~~l~is~stvs~hLk~Le~~GLV~~~~~   63 (202)
T 2p4w_A           32 SELSRELGVGQKAVLEHLRILEEAGLIESRVE   63 (202)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCceEEEee
Confidence            48999999999999999999999999999876

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	96
d1wi9a_	72	a.4.5.47 (A:) Hypothetical protein C20orf116 homol	1e-17

>d1wi9a_ a.4.5.47 (A:) Hypothetical protein C20orf116 homolog {Mouse (Mus musculus) [TaxId: 10090]} Length = 72

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PCI domain (PINT motif)
domain: Hypothetical protein C20orf116 homolog
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 68.2 bits (167), Expect = 1e-17
 Identities = 25/43 (58%), Positives = 31/43 (72%)

Query: 1  MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQ 43
          +EDLA    ++TQ  I+RI +L   G LTGVIDDRGKFIYI+ 
Sbjct: 24 LEDLAFQMGLRTQDAINRIQDLLTEGTLTGVIDDRGKFIYITP 66

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	96
d1wi9a_	72	Hypothetical protein C20orf116 homolog {Mouse (Mus	99.91
d1ufma_	84	COP9 signalosome complex subunit 4, GSN4 {Mouse (M	96.67
d3ctaa1	85	Ta1064 (RFK), N-terminal domain {Thermoplasma acid	96.64
d1ub9a_	100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	96.41
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	96.41
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	96.37
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	96.02
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	95.95
d2fbia1	136	Probable transcriptional regulator PA4135 {Pseudom	95.48
d2gaua1	81	Transcriptional regulator PG0396, C-terminal domai	95.48
d1p4xa1	125	Staphylococcal accessory regulator A homolog, SarS	95.38
d2bgca1	100	Listeriolysin regulatory protein PrfA, C-terminal	95.35
d2etha1	140	Putative transcriptional regulator TM0816 {Thermot	95.26
d1ft9a1	80	CO-sensing protein CooA, C-terminal domain {Rhodos	95.13
d1hsja1	115	Staphylococcal accessory regulator A homolog, SarR	94.87
d2frha1	115	Pleiotropic regulator of virulence genes, SarA {St	94.85
d2a61a1	139	Transcriptional regulator TM0710 {Thermotoga marit	94.82
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	94.79
d1p4xa2	125	Staphylococcal accessory regulator A homolog, SarS	94.78
d3broa1	135	Transcriptional regulator OEOE1854 {Oenococcus oen	94.77
d2hr3a1	145	Probable transcriptional regulator PA3067 {Pseudom	94.75
d3deua1	140	Transcriptional regulator SlyA {Salmonella typhimu	94.1
d1s3ja_	143	Putative transcriptional regulator YusO {Bacillus	93.95
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	93.72
d2bv6a1	136	Transcriptional regulator MgrA {Staphylococcus aur	93.45
d3e5ua1	80	Chlorophenol reduction protein CprK {Desulfitobact	93.41
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	93.35
d1z91a1	137	Organic hydroperoxide resistance transcriptional r	93.05
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	92.95
d1jgsa_	138	Multiple antibiotic resistance repressor, MarR {Es	92.94
d1lnwa_	141	MexR repressor {Pseudomonas aeruginosa [TaxId: 287	92.77
d2fbha1	137	Transcriptional regulator PA3341 {Pseudomonas aeru	92.58
d1i5za1	69	Catabolite gene activator protein (CAP), C-termina	92.48
d1r1ta_	98	SmtB repressor {Cyanobacteria (Synechococcus), pcc	92.04
d1zyba1	73	Probable transcription regulator BT4300, C-termina	91.84
d1lj9a_	144	Transcriptional regulator SlyA {Enterococcus faeca	91.54
d2zcwa1	82	Transcriptional regulator TTHA1359, C-terminal dom	90.95
d2fxaa1	162	Protease production regulatory protein Hpr {Bacill	90.22
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	90.13
d1ldja1	90	Anaphase promoting complex (APC) {Human (Homo sapi	90.03
d2hs5a1	69	Putative transcriptional regulator RHA1_ro03477 {R	89.82
d2ev0a1	61	Manganese transport regulator MntR {Bacillus subti	89.51
d2p4wa1	194	Transcriptional regulatory protein PF1790 {Pyrococ	88.07
d1r1ua_	94	Metal-sensing transcriptional repressor CzrA {Stap	88.01
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	87.89
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	87.62
d3bwga1	78	Transcriptional regulator YydK {Bacillus subtilis	87.06
d1iuya_	92	Cullin-3 homologue {Mouse (Mus musculus) [TaxId: 1	86.7
d1u2wa1	108	Cadmium efflux system accessory protein CadC {Stap	86.6
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	85.57
d2fbka1	172	Transcriptional regulator DR1159 {Deinococcus radi	85.27
d2isya1	63	Iron-dependent regulator IdeR {Mycobacterium tuber	84.22

>d1wi9a_ a.4.5.47 (A:) Hypothetical protein C20orf116 homolog {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PCI domain (PINT motif)
domain: Hypothetical protein C20orf116 homolog
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.91  E-value=4.1e-26  Score=150.30  Aligned_cols=44  Identities=57%  Similarity=0.908  Sum_probs=42.7

Q ss_pred             ChhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHH
Q psy11008          1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQE   44 (96)
Q Consensus         1 ledLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~e   44 (96)
                      |||||++|+|+||++|+||++|+++|+||||||||||||||||.
T Consensus        24 LedLAa~F~lktqd~i~RIq~Le~~g~ltGViDDRGKfIyIS~s   67 (72)
T d1wi9a_          24 LEDLAFQMGLRTQDAINRIQDLLTEGTLTGVIDDRGKFIYITPS   67 (72)
T ss_dssp             HHHHHHHHCSCHHHHHHHHHHHHHHSSSCEEECTTCCEEECCCS
T ss_pred             HHHHHHHcCCcHHHHHHHHHHHHHCCCeeeEEcCCCCEEEEcCC
Confidence            58999999999999999999999999999999999999999984

>d1ufma_ a.4.5.47 (A:) COP9 signalosome complex subunit 4, GSN4 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PCI domain (PINT motif)
domain: COP9 signalosome complex subunit 4, GSN4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.67  E-value=0.00091  Score=41.85  Aligned_cols=45  Identities=20%  Similarity=0.366  Sum_probs=40.9

Q ss_pred             ChhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHH
Q psy11008          1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEE   45 (96)
Q Consensus         1 ledLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eE   45 (96)
                      |++||..|+++.+++-.-|.+|..+|+|.|.||.--.+||...+|
T Consensus        33 l~~la~~l~l~~~evE~~l~~mI~~~~i~akIDq~~g~V~F~~~e   77 (84)
T d1ufma_          33 FEELGALLEIPAAKAEKIASQMITEGRMNGFIDQIDGIVHFETRE   77 (84)
T ss_dssp             HHHHHHHTTSCHHHHHHHHHHHHHTTSSCEEEETTTTEEEECCSS
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHhcCeEEEEEeCCCCEEEECCCC
Confidence            478999999999999999999999999999999888899987654

>d3ctaa1 a.4.5.28 (A:5-89) Ta1064 (RFK), N-terminal domain {Thermoplasma acidophilum [TaxId: 2303]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Ta1064 (RFK), N-terminal domain
species: Thermoplasma acidophilum [TaxId: 2303]

Probab=96.64  E-value=0.0043  Score=38.07  Aligned_cols=51  Identities=27%  Similarity=0.468  Sum_probs=45.3

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATF   52 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~f   52 (96)
                      -|||...+++.+.+-.-|+.|++.|-+.=-.|-|++||++|++-.+.+-+.
T Consensus        25 ~eLa~~l~i~~~~vs~~l~~Le~~GlV~r~~D~R~~~i~LT~~G~~~l~~~   75 (85)
T d3ctaa1          25 SKLADMLGISQQSASRIIIDLEKNGYITRTVTKRGQILNITEKGLDVLYTE   75 (85)
T ss_dssp             HHHHHHHTSCHHHHHHHHHHHHHTTSEEEEEETTEEEEEECHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCeeeecccccccceECHHHHHHHHHH
Confidence            489999999999999999999999999999999999999999876655443

>d1ub9a_ a.4.5.28 (A:) Hypothetical protein PH1061 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Hypothetical protein PH1061
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=96.41  E-value=0.0051  Score=37.23  Aligned_cols=55  Identities=9%  Similarity=0.180  Sum_probs=44.9

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .|||..++++...+-..+..|++.|-++---|   -|-+|+.+|++-.+.+..++...
T Consensus        34 ~eLa~~l~is~~~vs~~l~~L~~~glV~~~~~~~d~r~~~~~LT~~G~~~~~~~~~~~   91 (100)
T d1ub9a_          34 SQIQKVLDLTPGNLDSHIRVLERNGLVKTYKVIADRPRTVVEITDFGMEEAKRFLSSL   91 (100)
T ss_dssp             HHHHHHTTCCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECHHHHHHHHHHHHHH
T ss_pred             HHHHHHHhhccccccHHHHHHhhhceeEEEEcCcCCccccccCCHHHHHHHHHHHHHH
Confidence            58999999999999999999999999997664   45668889997766666665443

>d2cfxa1 a.4.5.32 (A:1-63) Transcriptional regulator LrpC {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Transcriptional regulator LrpC
species: Bacillus subtilis [TaxId: 1423]

Probab=96.41  E-value=0.0018  Score=38.08  Aligned_cols=29  Identities=21%  Similarity=0.437  Sum_probs=27.5

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccE
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTG   30 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltG   30 (96)
                      .+||...|++.+.|-.||+.|+++|.|.|
T Consensus        23 ~~iA~~lgis~~tv~~Ri~~L~~~giI~~   51 (63)
T d2cfxa1          23 RELGRKIKLSPPSVTERVRQLESFGIIKQ   51 (63)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCeee
Confidence            58999999999999999999999999977

>d2cg4a1 a.4.5.32 (A:4-66) Regulatory protein AsnC {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Regulatory protein AsnC
species: Escherichia coli [TaxId: 562]

Probab=96.37  E-value=0.0015  Score=38.16  Aligned_cols=30  Identities=23%  Similarity=0.527  Sum_probs=28.0

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEE
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGV   31 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGV   31 (96)
                      .+||...|++...|-.||+.|+++|-|.|.
T Consensus        23 ~eiA~~l~ls~~~v~~Ri~rL~~~GiI~~~   52 (63)
T d2cg4a1          23 AELAKQFGVSPETIHVRVEKMKQAGIITGA   52 (63)
T ss_dssp             HHHHHHHTSCHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCeEeE
Confidence            589999999999999999999999999864

>d2cyya1 a.4.5.32 (A:5-64) Putative transcriptional regulator PH1519 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Putative transcriptional regulator PH1519
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=96.02  E-value=0.0023  Score=36.96  Aligned_cols=30  Identities=13%  Similarity=0.429  Sum_probs=27.5

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEE
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGV   31 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGV   31 (96)
                      .+||...|++...|..||+.|+++|.|.|.
T Consensus        21 ~eiA~~l~ls~~~v~~Ri~~L~~~giI~~~   50 (60)
T d2cyya1          21 REISKITGLAESTIHERIRKLRESGVIKKF   50 (60)
T ss_dssp             HHHHHHHCSCHHHHHHHHHHHHHHTSSCCC
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCeEeE
Confidence            589999999999999999999999988753

>d1i1ga1 a.4.5.32 (A:2-61) LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: LprA
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=95.95  E-value=0.0026  Score=37.04  Aligned_cols=29  Identities=21%  Similarity=0.456  Sum_probs=27.1

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccE
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTG   30 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltG   30 (96)
                      .+||...|++.+.|.+||+.|+++|-|.|
T Consensus        21 ~~lA~~~gls~~~v~~Ri~~L~~~giI~~   49 (60)
T d1i1ga1          21 TEIAKKLGISETAVRKRVKALEEKGIIEG   49 (60)
T ss_dssp             HHHHHHHTSCHHHHHHHHHHHHHHTSSCC
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCeEe
Confidence            58999999999999999999999998865

>d2fbia1 a.4.5.28 (A:5-140) Probable transcriptional regulator PA4135 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Probable transcriptional regulator PA4135
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=95.48  E-value=0.017  Score=36.08  Aligned_cols=55  Identities=11%  Similarity=0.169  Sum_probs=46.8

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .|||..+++..+.+-.-|+.|++.|-|+=.-|   -|.++|++|++-...+.+.....
T Consensus        48 ~~la~~~~i~~~~vs~~i~~L~~~gli~r~~~~~D~R~~~l~lT~~G~~~~~~~~~~~  105 (136)
T d2fbia1          48 YQLANQACILRPSMTGVLARLERDGIVRRWKAPKDQRRVYVNLTEKGQQCFVSMSGDM  105 (136)
T ss_dssp             HHHHHHTTCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCEEEeecCccCchhhhccCHHHHHHHHHHHHHH
Confidence            47999999999999999999999999998876   36799999999887766655443

>d2gaua1 a.4.5.4 (A:152-232) Transcriptional regulator PG0396, C-terminal domain {Porphyromonas gingivalis [TaxId: 837]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Transcriptional regulator PG0396, C-terminal domain
species: Porphyromonas gingivalis [TaxId: 837]

Probab=95.48  E-value=0.017  Score=33.72  Aligned_cols=47  Identities=23%  Similarity=0.287  Sum_probs=39.1

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVAT   51 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~   51 (96)
                      +|||...|++.+.|-.-+++|+++|.|.-   ++|+++-..++-|..+|+
T Consensus        33 ~eLA~~~G~sretvsr~L~~l~~~glI~~---~~~~i~I~d~~~L~~~a~   79 (81)
T d2gaua1          33 EELATLSNMTVSNAIRTLSTFVSERMLAL---DGKRIKIIDCDRLQKTAR   79 (81)
T ss_dssp             HHHHHHTTSCHHHHHHHHHHHHHTTSEEE---ETTEEEESCHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCEEe---cCCEEEEcCHHHHHHHHh
Confidence            68999999999888888999999998762   667777777888887775

>d1p4xa1 a.4.5.28 (A:1-125) Staphylococcal accessory regulator A homolog, SarS {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Staphylococcal accessory regulator A homolog, SarS
species: Staphylococcus aureus [TaxId: 1280]

Probab=95.38  E-value=0.02  Score=36.26  Aligned_cols=53  Identities=23%  Similarity=0.360  Sum_probs=45.2

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEe---eCCCceEEEcHHHHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI---DDRGKFIYISQEELNSVATFIK   54 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi---DDRGKfIyIs~eEl~~Va~fI~   54 (96)
                      .|||...+++...+-.-|+.|++.|-|+=+-   |.|.++|++|++--+.++..+.
T Consensus        54 ~eia~~~~~~~~~vs~~l~~L~~~g~v~r~~~~~D~R~~~i~lT~~G~~~~~~~~~  109 (125)
T d1p4xa1          54 KKIVSDLCYKQSDLVQHIKVLVKHSYISKVRSKIDERNTYISISEEQREKIAERVT  109 (125)
T ss_dssp             HHHHHHSSSCGGGTHHHHHHHHHTTSCEEEECSSSTTSEEEECCHHHHHHHHHHHH
T ss_pred             HHHHHHhCCCcchHHHHHHHHHHCCCceeecccCCCCeEEEEECHHHHHHHHHHHH
Confidence            4899999999999999999999999998776   5689999999988666655443

>d2bgca1 a.4.5.4 (A:138-237) Listeriolysin regulatory protein PrfA, C-terminal domain {Bacteria (Listeria monocytogenes) [TaxId: 1639]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Listeriolysin regulatory protein PrfA, C-terminal domain
species: Bacteria (Listeria monocytogenes) [TaxId: 1639]

Probab=95.35  E-value=0.013  Score=37.34  Aligned_cols=50  Identities=14%  Similarity=0.145  Sum_probs=38.8

Q ss_pred             hhhhhhhCCChHHHH-HHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVI-DRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIK   54 (96)
Q Consensus         2 edLAa~F~lktq~vI-~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~   54 (96)
                      +|||...|+++-+.| .-+.+|+++|.|+-   .+|+++-...+.|.+.|..+-
T Consensus        35 eeLA~~lG~s~ReTVsR~L~~L~~~GlI~~---~~~~i~I~D~~~L~~~A~~~d   85 (100)
T d2bgca1          35 QELGYSSGIAHSSAVSRIISKLKQEKVIVY---KNSCFYVQNLDYLKRYAPKLD   85 (100)
T ss_dssp             HHHHHHTTCCCHHHHHHHHHHHHHTTSEEE---ETTEEEESCHHHHHHHCHHHH
T ss_pred             HHHHHHhCCchHHHHHHHHHHHHHCCCEEE---cCCEEEEeCHHHHHHHhcccc
Confidence            799999999875555 55899999997772   567777678888888886543

>d2etha1 a.4.5.28 (A:1-140) Putative transcriptional regulator TM0816 {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Putative transcriptional regulator TM0816
species: Thermotoga maritima [TaxId: 2336]

Probab=95.26  E-value=0.042  Score=34.23  Aligned_cols=55  Identities=13%  Similarity=0.257  Sum_probs=47.3

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeC---CCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDD---RGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDD---RGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .|||..++++.+.+-.-|..|++.|-++=.-|.   |-++|++|+.-...+.+.....
T Consensus        50 ~~La~~l~i~~~~vs~~v~~L~~~gli~r~~~~~D~R~~~l~lT~~G~~~~~~~~~~~  107 (140)
T d2etha1          50 KEIAEFLSTTKSNVTNVVDSLEKRGLVVREMDPVDRRTYRVVLTEKGKEIFGEILSNF  107 (140)
T ss_dssp             HHHHHHTTSCHHHHHHHHHHHHHTTSEEEEECTTTSSCEEEEECHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCeeeeecccccchhhhhcCHHHHHHHHHHHHHH
Confidence            489999999999999999999999999998874   6689999999887777665544

>d1ft9a1 a.4.5.4 (A:134-213) CO-sensing protein CooA, C-terminal domain {Rhodospirillum rubrum [TaxId: 1085]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: CO-sensing protein CooA, C-terminal domain
species: Rhodospirillum rubrum [TaxId: 1085]

Probab=95.13  E-value=0.014  Score=34.55  Aligned_cols=47  Identities=23%  Similarity=0.343  Sum_probs=40.2

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVA   50 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va   50 (96)
                      +|||...|++.+.|-.-+.+|+++|.|.  +..||+++....+-|.+.|
T Consensus        34 ~eiA~~lG~sretvsr~l~~l~~~g~I~--~~~~~~i~I~d~~~L~~~A   80 (80)
T d1ft9a1          34 EEIANLIGSSRQTTSTALNSLIKEGYIS--RQGRGHYTIPNLVRLKAAA   80 (80)
T ss_dssp             HHHHHHHCSCHHHHHHHHHHHHHTTSSE--ECSTTCEECSSHHHHHHTC
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCEE--ECCCCeEEECCHHHHHhhC
Confidence            6899999999999999999999998764  4568899999988887754

>d1hsja1 a.4.5.28 (A:373-487) Staphylococcal accessory regulator A homolog, SarR {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Staphylococcal accessory regulator A homolog, SarR
species: Staphylococcus aureus [TaxId: 1280]

Probab=94.87  E-value=0.028  Score=35.15  Aligned_cols=54  Identities=15%  Similarity=0.310  Sum_probs=46.3

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEe---eCCCceEEEcHHHHHHHHHHHHh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI---DDRGKFIYISQEELNSVATFIKQ   55 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi---DDRGKfIyIs~eEl~~Va~fI~~   55 (96)
                      .+||..++++...+-..|..|++.|-+.=.-   |-|.++|++|++-.+.+.+.+..
T Consensus        52 ~ela~~l~~~~~~vs~~i~~Le~~gli~r~~~~~D~R~~~i~LT~~G~~~~~~~~~~  108 (115)
T d1hsja1          52 KEIAKCSEFKPYYLTKALQKLKDLKLLSKKRSLQDERTVIVYVTDTQKANIQKLISE  108 (115)
T ss_dssp             HHHHHSSCCCHHHHHHHHHHHHTTTTSCCEECCSSSSCCEEECCSSHHHHHHHHHHH
T ss_pred             HHHHHHHCCChhhHHHHHHHHHHcCCeEEEeecCCCceEEEEECHHHHHHHHHHHHH
Confidence            4899999999999999999999999998666   56999999999887776665544

>d2frha1 a.4.5.28 (A:102-216) Pleiotropic regulator of virulence genes, SarA {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Pleiotropic regulator of virulence genes, SarA
species: Staphylococcus aureus [TaxId: 1280]

Probab=94.85  E-value=0.028  Score=35.06  Aligned_cols=55  Identities=13%  Similarity=0.284  Sum_probs=46.7

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEe---eCCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI---DDRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi---DDRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .+||..++++.+.+-.-|+.|++.|-++=.-   |.|.++|++|+.--+.+++.+.+.
T Consensus        53 ~~la~~l~~~~~tvs~~i~~Le~~gli~r~~~~~D~R~~~i~LT~~G~~~~~~~~~~~  110 (115)
T d2frha1          53 KDIINHLNYKQPQVVKAVKILSQEDYFDKKRNEHDERTVLILVNAQQRKKIESLLSRV  110 (115)
T ss_dssp             HHHHHHSSSHHHHHHHHHHHHHHTTSSCCBCCSSSSCCCEEECCSHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHhHHHHHHHHHHhhhhheeeecccCCceEEEEECHHHHHHHHHHHHHH
Confidence            4799999999999999999999999998774   568999999999887777765543

>d2a61a1 a.4.5.28 (A:5-143) Transcriptional regulator TM0710 {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator TM0710
species: Thermotoga maritima [TaxId: 2336]

Probab=94.82  E-value=0.016  Score=36.37  Aligned_cols=55  Identities=24%  Similarity=0.399  Sum_probs=46.0

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEe---eCCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI---DDRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi---DDRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .|||..+++..+.+-..|+.|++.|-++=.-   |-|.++|++|+.-...+.......
T Consensus        48 ~~la~~l~i~~~tvs~~l~~L~~~gli~r~~~~~D~R~~~i~LT~~G~~~~~~~~~~~  105 (139)
T d2a61a1          48 GELSVLLGVAKSTVTGLVKRLEADGYLTRTPDPADRRAYFLVITRKGEEVIEKVIERR  105 (139)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHHHHHHHHH
T ss_pred             HHHHHHhCCCcccchHHHHHHHhcCeeeeeeccCCCCeEEEEECHHHHHHHHHHHHHH
Confidence            5899999999999999999999999886654   568999999999887766654443

>d2d1ha1 a.4.5.50 (A:1-109) Hypothetical transcriptional regulator ST1889 {Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: TrmB-like
domain: Hypothetical transcriptional regulator ST1889
species: Sulfolobus tokodaii [TaxId: 111955]

Probab=94.79  E-value=0.016  Score=35.46  Aligned_cols=43  Identities=21%  Similarity=0.352  Sum_probs=33.1

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEe---eCCCceEEEcHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI---DDRGKFIYISQE   44 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi---DDRGKfIyIs~e   44 (96)
                      .|||..++++...+-.-|+.|++.|-|.=.-   |-||+++|++..
T Consensus        40 ~eLa~~~~i~~~tvs~~l~~L~~~GlV~r~~~~~d~rg~~~~~~~~   85 (109)
T d2d1ha1          40 EELADIFKLSKTTVENSLKKLIELGLVVRTKTEGKKIGRPKYYYSI   85 (109)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEC-------CCEEEEE
T ss_pred             HHHHHHHCccHhHHHHHHHHHHHCCCEEEeecCCCCCceeEEEeeC
Confidence            5899999999999999999999999987665   457888888743

>d1p4xa2 a.4.5.28 (A:126-250) Staphylococcal accessory regulator A homolog, SarS {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Staphylococcal accessory regulator A homolog, SarS
species: Staphylococcus aureus [TaxId: 1280]

Probab=94.78  E-value=0.055  Score=34.49  Aligned_cols=55  Identities=20%  Similarity=0.293  Sum_probs=45.8

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEe---eCCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI---DDRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi---DDRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .|||...+++...+-.-|..|++.|-++=.-   |.|-.+|++|++--+.+.+.++.-
T Consensus        53 ~~ia~~l~~~~~~vs~~v~~L~~~glV~r~~~~~D~R~v~i~LT~~G~~~~~~l~~~~  110 (125)
T d1p4xa2          53 KDLIETIHHKYPQTVRALNNLKKQGYLIKERSTEDERKILIHMDDAQQDHAEQLLAQV  110 (125)
T ss_dssp             HHHHHHSSSCHHHHHHHHHHHHHHTSSEEEECSSSTTCEEEECCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCcchHHHHHHHHHhccCEeeeecCCCCCeEEEEECHHHHHHHHHHHHHH
Confidence            4899999999999999999999999998665   468999999998876665555443

>d3broa1 a.4.5.28 (A:3-137) Transcriptional regulator OEOE1854 {Oenococcus oeni [TaxId: 1247]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator OEOE1854
species: Oenococcus oeni [TaxId: 1247]

Probab=94.77  E-value=0.05  Score=33.58  Aligned_cols=54  Identities=13%  Similarity=0.204  Sum_probs=45.5

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHHHHHHHHHh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELNSVATFIKQ   55 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~~Va~fI~~   55 (96)
                      .|||...++..+.+-.-++.|++.|-+.-.-|   -|.++|++|++-...+......
T Consensus        49 ~ela~~~~~~~~~vs~~l~~L~~~g~v~r~~~~~D~R~~~i~lT~~G~~~~~~~~~~  105 (135)
T d3broa1          49 RDLESEFSIKSSTATVLLQRMEIKKLLYRKVSGKDSRQKCLKLTKKANKLETIILSY  105 (135)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECSSCTTSEEEEECHHHHTTHHHHHHH
T ss_pred             HHHHHHHCcCHhHHHHHHHHHHHHHHHHHHhhhhhhhhhhhcccHHHHHHHHHHHHH
Confidence            58999999999999999999999999998876   5789999999876655554443

>d2hr3a1 a.4.5.28 (A:2-146) Probable transcriptional regulator PA3067 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Probable transcriptional regulator PA3067
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=94.75  E-value=0.034  Score=35.02  Aligned_cols=55  Identities=24%  Similarity=0.285  Sum_probs=45.0

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEE---eeCCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGV---IDDRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGV---iDDRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .+||..++++...+-.-|+.|++.|-+.=.   -|-|.++|++|+.-.+.+..+....
T Consensus        53 ~~La~~~~~~~~~vs~~i~~L~~~glv~r~~~~~DrR~~~i~LT~~G~~~~~~~~~~~  110 (145)
T d2hr3a1          53 SELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKR  110 (145)
T ss_dssp             HHHHHHTTCCHHHHHHHHHHHHHTTSEEEEC------CCEEEECHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHcCCeEeeeCccchhHHHhccCHHHHHHHHHHHHHH
Confidence            589999999999999999999999999644   4679999999999998887776655

>d3deua1 a.4.5.28 (A:2-141) Transcriptional regulator SlyA {Salmonella typhimurium [TaxId: 90371]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator SlyA
species: Salmonella typhimurium [TaxId: 90371]

Probab=94.10  E-value=0.073  Score=32.98  Aligned_cols=55  Identities=16%  Similarity=0.209  Sum_probs=43.3

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .|||..+++..+.+-.-|+.|++.|-++=+-|   -|-++|++|++-.+.+++.....
T Consensus        50 ~~la~~l~i~~~~vs~~l~~L~~~glI~~~~~~~D~R~~~l~lT~~G~~~~~~~~~~~  107 (140)
T d3deua1          50 IQLAKAIGIEQPSLVRTLDQLEDKGLISRQTCASDRRAKRIKLTEKAEPLIAEMEEVI  107 (140)
T ss_dssp             HHHHHHHTSCHHHHHHHHHHHHHTTSEEEC--------CEEEECGGGHHHHHHHHHHH
T ss_pred             HHHHHHHCCCHhHHHHHHHHHHhCCCEEecccCCCCCceeeEECHHHHHHHHHHHHHH
Confidence            48999999999999999999999999987766   57789999999887776655544

>d1s3ja_ a.4.5.28 (A:) Putative transcriptional regulator YusO {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Putative transcriptional regulator YusO
species: Bacillus subtilis [TaxId: 1423]

Probab=93.95  E-value=0.081  Score=32.97  Aligned_cols=55  Identities=13%  Similarity=0.122  Sum_probs=46.5

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .|||..++++.+.+-.-++.|++.|-+.=.-|   -|-++|++|++-...+.......
T Consensus        53 ~~la~~~~i~~~~vs~~l~~L~~~glv~r~~~~~D~R~~~v~lT~~G~~~~~~~~~~~  110 (143)
T d1s3ja_          53 SEIAERMEVKPSAVTLMADRLEQKNLIARTHNTKDRRVIDLSLTDEGDIKFEEVLAGR  110 (143)
T ss_dssp             HHHHHHHTSCHHHHHHHHHHHHHTTSEEEEECSSCTTSEEEEECHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHhhhheeeeecCCCCceEEEECHHHHHHHHHHHHHH
Confidence            58999999999999999999999999975554   68899999999887776665544

>d1biaa1 a.4.5.1 (A:1-63) Biotin repressor, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Biotin repressor-like
domain: Biotin repressor, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=93.72  E-value=0.028  Score=32.74  Aligned_cols=27  Identities=22%  Similarity=0.283  Sum_probs=25.1

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCc
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGAL   28 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~l   28 (96)
                      +|||.+||++..-|-.+|+.|++.|..
T Consensus        23 ~eLa~~l~vS~~ti~r~i~~L~~~G~~   49 (63)
T d1biaa1          23 EQLGETLGMSRAAINKHIQTLRDWGVD   49 (63)
T ss_dssp             HHHHHHHTSCHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCc
Confidence            689999999999999999999999863

>d2bv6a1 a.4.5.28 (A:5-140) Transcriptional regulator MgrA {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator MgrA
species: Staphylococcus aureus [TaxId: 1280]

Probab=93.45  E-value=0.11  Score=32.33  Aligned_cols=53  Identities=9%  Similarity=0.165  Sum_probs=45.2

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELNSVATFIK   54 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~~Va~fI~   54 (96)
                      .+||..++++.+.+-.-|..|++.|-++-.-|   -|.++|++|++-...+++...
T Consensus        52 ~~la~~l~~~~~~~s~~l~~L~~~Gli~r~~~~~D~R~~~l~lT~~G~~~~~~~~~  107 (136)
T d2bv6a1          52 KKVVTELALDTGTVSPLLKRMEQVDLIKRERSEVDQREVFIHLTDKSETIRPELSN  107 (136)
T ss_dssp             HHHHHHTTCCTTTHHHHHHHHHHTTSEEEEECSSSTTCEEEEECHHHHHHHHHHTT
T ss_pred             HHHHHHHCCCHhHHHHHHHHHHHCCCEEEeecCCcccchhhccCHHHHHHHHHHHH
Confidence            48999999999998899999999999998877   467799999998776665543

>d3e5ua1 a.4.5.4 (A:148-227) Chlorophenol reduction protein CprK {Desulfitobacterium hafniense [TaxId: 49338]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Chlorophenol reduction protein CprK
species: Desulfitobacterium hafniense [TaxId: 49338]

Probab=93.41  E-value=0.044  Score=32.10  Aligned_cols=46  Identities=15%  Similarity=0.296  Sum_probs=33.7

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVA   50 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va   50 (96)
                      +|||...|++.+.|-.-+++|.++|.|.   -++|+++-...+.|..+|
T Consensus        34 ~elA~~~g~sretvsr~l~~l~~~glI~---~~~~~i~I~d~~~L~~~~   79 (80)
T d3e5ua1          34 KSIGEITGVHHVTVSRVLASLKRENILD---KKKNKIIVYNLGELKHLS   79 (80)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEE---C----CEESCHHHHHHHT
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCcEE---ecCCEEEEcCHHHHHHHh
Confidence            6899999999999999999999999764   255665555777666654

>d1sfxa_ a.4.5.50 (A:) Hypothetical protein AF2008 {Archaeoglobus fulgidus [TaxId: 2234]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: TrmB-like
domain: Hypothetical protein AF2008
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=93.35  E-value=0.12  Score=31.72  Aligned_cols=55  Identities=22%  Similarity=0.173  Sum_probs=41.2

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCC-CceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDR-GKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDR-GKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .|||...|++...|-.-++.|++.|-+.-..+.. |++.+.++.....+-.-++++
T Consensus        38 ~eia~~~~i~~~~v~~~l~~L~~~GlV~r~~~~~~~r~~~~~a~~~~e~l~~~~~~   93 (109)
T d1sfxa_          38 SEIARELDLSARFVRDRLKVLLKRGFVRREIVEKGWVGYIYSAEKPEKVLKEFKSS   93 (109)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEEESSSEEEEEEECCHHHHHHHHHHH
T ss_pred             HHHHHHhCCCcchHHHHHHHHHhCCCEEEEeccCCCccccccCCCHHHHHHHHHHH
Confidence            5899999999999999999999999999887754 454445555555554444444

>d1z91a1 a.4.5.28 (A:8-144) Organic hydroperoxide resistance transcriptional regulator OhrR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Organic hydroperoxide resistance transcriptional regulator OhrR
species: Bacillus subtilis [TaxId: 1423]

Probab=93.05  E-value=0.066  Score=33.39  Aligned_cols=46  Identities=9%  Similarity=0.257  Sum_probs=41.1

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELN   47 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~   47 (96)
                      .+||...+++.+.+-.-|+.|++.|-+.-.-|   -|-++|++|++-..
T Consensus        51 ~~La~~~~i~~~~vsr~i~~L~~~glv~r~~~~~D~R~~~i~lT~~G~~   99 (137)
T d1z91a1          51 KKMGEQLYLDSGTLTPMLKRMEQQGLITRKRSEEDERSVLISLTEDGAL   99 (137)
T ss_dssp             HHHHHTTTCCHHHHHHHHHHHHHHTSEECCBCSSCTTSBEEEECHHHHS
T ss_pred             HHHHHHHCcCHHHHHHHHHHHhhccceEEeecCCCCCeEEEEECHHHHH
Confidence            48999999999999999999999999998866   48899999998754

>d1ku9a_ a.4.5.36 (A:) DNA-binding protein Mj223 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: DNA-binding protein Mj223
domain: DNA-binding protein Mj223
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=92.95  E-value=0.26  Score=30.39  Aligned_cols=44  Identities=11%  Similarity=0.204  Sum_probs=37.9

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEe---eCCCceEEEcHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI---DDRGKFIYISQEE   45 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi---DDRGKfIyIs~eE   45 (96)
                      .|||...|++.+.+-.-++.|++.|.+.=+-   |.|..|+++|+.+
T Consensus        45 ~ela~~l~vsk~~vs~~l~~L~~~GlV~r~~~~~drr~~~~~~t~~g   91 (151)
T d1ku9a_          45 SDIMEELKISKGNVSMSLKKLEELGFVRKVWIKGERKNYYEAVDGFS   91 (151)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEECCTTCSSCEEEECCHHH
T ss_pred             HHHHHHhCCCcchHHHHHHHHHHCCCEEEEEcCCCCceeEEeCCHHH
Confidence            5899999999999999999999999997554   5667888888765

>d1jgsa_ a.4.5.28 (A:) Multiple antibiotic resistance repressor, MarR {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Multiple antibiotic resistance repressor, MarR
species: Escherichia coli [TaxId: 562]

Probab=92.94  E-value=0.26  Score=30.65  Aligned_cols=51  Identities=10%  Similarity=0.163  Sum_probs=43.4

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELNSVATF   52 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~~Va~f   52 (96)
                      .|||..++++.+.+-.-|+.|++.|-++-.-|   -|.++|++|++-..-+...
T Consensus        52 ~ela~~~~i~~~~vs~~v~~L~~~glv~r~~~~~D~R~~~i~lT~~G~~~~~~~  105 (138)
T d1jgsa_          52 VELKKVLSVDLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTGGAAICEQC  105 (138)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECTTCSSCEEEEECHHHHHHHHHH
T ss_pred             HHHHHHHCCCHhHHHHHHHHHhhCCCEEEeeccCCCCeeEEEECHHHHHHHHHH
Confidence            58999999999999999999999999997766   4778999999877655443

>d1lnwa_ a.4.5.28 (A:) MexR repressor {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: MexR repressor
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=92.77  E-value=0.27  Score=30.64  Aligned_cols=51  Identities=16%  Similarity=0.201  Sum_probs=43.0

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELNSVATF   52 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~~Va~f   52 (96)
                      .|||..++++.+.+-.-|+.|++.|-|+=.-|   -|-++|++|+.-...++..
T Consensus        54 ~~la~~l~~~~~~vsr~l~~L~~~G~v~r~~~~~D~R~~~l~lT~~G~~~~~~~  107 (141)
T d1lnwa_          54 QDLGRQMCRDKALITRKIRELEGRNLVRRERNPSDQRSFQLFLTDEGLAIHQHA  107 (141)
T ss_dssp             HHHHHHTTCCHHHHHHHHHHHHHTTSEEEEECSSSSSSEEEEECHHHHHHHHHH
T ss_pred             HHHHHHHCccHhHHHHHHHHHHHhhceeeeccCCCCcchhhccCHHHHHHHHHH
Confidence            58999999999999999999999998887766   6789999999876554443

>d2fbha1 a.4.5.28 (A:8-144) Transcriptional regulator PA3341 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator PA3341
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=92.58  E-value=0.22  Score=30.53  Aligned_cols=53  Identities=15%  Similarity=0.179  Sum_probs=44.7

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELNSVATFIK   54 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~~Va~fI~   54 (96)
                      .|||..++++...+-.-|..|++.|-|+=..|   -|.+.|++|++-...+.+...
T Consensus        47 ~~la~~~~~~~~~vs~~v~~L~~~gli~r~~~~~D~R~~~i~lT~~G~~~~~~~~~  102 (137)
T d2fbha1          47 RELAQSVGVEGPTLARLLDGLESQGLVRRLAVAEDRRAKHIVLTPKADVLIADIEA  102 (137)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEECCBTTBCSCEEEECTTHHHHHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHcCCccccCCCCCCCchhhhcCHHHHHHHHHHHH
Confidence            58999999988888888999999999998877   588999999988666555443

>d1i5za1 a.4.5.4 (A:138-206) Catabolite gene activator protein (CAP), C-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Catabolite gene activator protein (CAP), C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=92.48  E-value=0.073  Score=30.57  Aligned_cols=36  Identities=14%  Similarity=0.284  Sum_probs=29.9

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEE
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYI   41 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyI   41 (96)
                      +|||...|++.+.|-.-+++|+++|.|.    -+|+-|+|
T Consensus        33 ~~lA~~~G~sRetvsr~L~~l~~~glI~----~~~~~I~I   68 (69)
T d1i5za1          33 QEIGQIVGCSRETVGRILKMLEDQNLIS----AHGKTIVV   68 (69)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEE----EETTEEEE
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCEE----EcCCEEEE
Confidence            6899999999999999999999998654    45666655

>d1r1ta_ a.4.5.5 (A:) SmtB repressor {Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: SmtB repressor
species: Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]

Probab=92.04  E-value=0.3  Score=30.06  Aligned_cols=48  Identities=13%  Similarity=0.195  Sum_probs=39.2

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSV   49 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~V   49 (96)
                      .|||..+|++...+-.-++.|++.|-++.--+.|-.|.+++++.+..+
T Consensus        40 ~ela~~l~is~stvS~HL~~L~~aglV~~~r~G~~~~Y~l~~~~i~~l   87 (98)
T d1r1ta_          40 GDLAQAIGVSESAVSHQLRSLRNLRLVSYRKQGRHVYYQLQDHHIVAL   87 (98)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEESSHHHHHH
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCceEEEEECCEEEEEEChHHHHHH
Confidence            489999999888888899999999999987766666666777765544

>d1zyba1 a.4.5.4 (A:148-220) Probable transcription regulator BT4300, C-terminal domain {Bacteroides thetaiotaomicron [TaxId: 818]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Probable transcription regulator BT4300, C-terminal domain
species: Bacteroides thetaiotaomicron [TaxId: 818]

Probab=91.84  E-value=0.09  Score=31.07  Aligned_cols=36  Identities=22%  Similarity=0.326  Sum_probs=29.6

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEE
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIY   40 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIy   40 (96)
                      +|||...|++.+.+-.-+++|+++|.|..   .+|++.-
T Consensus        31 ~elA~~lg~sr~tvsr~l~~l~~~g~I~~---~~~~i~I   66 (73)
T d1zyba1          31 DDLARCLDDTRLNISKTLNELQDNGLIEL---HRKEILI   66 (73)
T ss_dssp             HHHHHHHTSCHHHHHHHHHHHHHTTSCEE---ETTEEEE
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCEEe---cCCEEEE
Confidence            68999999999998888999999999873   4555433

>d1lj9a_ a.4.5.28 (A:) Transcriptional regulator SlyA {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator SlyA
species: Enterococcus faecalis [TaxId: 1351]

Probab=91.54  E-value=0.53  Score=29.42  Aligned_cols=55  Identities=20%  Similarity=0.332  Sum_probs=46.6

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .|||..+++..+.+-.-|+.|++.|-|+=.-|   -|-++|++|++-...+.......
T Consensus        47 ~~la~~l~i~~~tvs~~l~~L~~~glI~r~~~~~D~R~~~l~LT~~G~~~~~~~~~~~  104 (144)
T d1lj9a_          47 EKIAELIKVDRTTAARAIKRLEEQGFIYRQEDASNKKIKRIYATEKGKNVYPIIVREN  104 (144)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECSSCTTCEEEEECHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCccHhhHHHHHHHHHhhhcccccCCCCCCCccccccCHHHHHHHHHHHHHH
Confidence            48999999999999899999999999998887   46789999999887666655544

>d2fxaa1 a.4.5.28 (A:6-167) Protease production regulatory protein Hpr {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Protease production regulatory protein Hpr
species: Bacillus subtilis [TaxId: 1423]

Probab=90.22  E-value=0.48  Score=31.05  Aligned_cols=55  Identities=15%  Similarity=0.246  Sum_probs=45.4

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEe---eCCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI---DDRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi---DDRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .|||...++..+.+-.-|+.|++.|-++=.-   |.|-++|++|++-.+.+.+.....
T Consensus        59 ~~la~~~~l~~~tvs~~i~rL~~~gli~r~~~~~D~R~~~l~lT~~G~~~~~~~~~~~  116 (162)
T d2fxaa1          59 SEIAKFGVMHVSTAFNFSKKLEERGYLRFSKRLNDKRNTYVQLTEEGTEVFWSLLEEF  116 (162)
T ss_dssp             HHHHHHTTCCHHHHHHHHHHHHHHTSEEEECC------CEEEECHHHHHHHHHHHHHC
T ss_pred             HHHHHHHcCCchhhHHHHHHHHHCCCceeecccccCeeeeeccCHhHHHHHHHHHHHH
Confidence            4899999999999999999999999998665   569999999999998888877765

>d1jhfa1 a.4.5.2 (A:2-72) LexA repressor, N-terminal DNA-binding domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: LexA repressor, N-terminal DNA-binding domain
domain: LexA repressor, N-terminal DNA-binding domain
species: Escherichia coli [TaxId: 562]

Probab=90.13  E-value=0.1  Score=30.89  Aligned_cols=30  Identities=13%  Similarity=0.328  Sum_probs=25.1

Q ss_pred             hhhhhhhCCC-hHHHHHHHHHHHHcCCccEE
Q psy11008          2 EDLAALFRMK-TQSVIDRIVELQKTGALTGV   31 (96)
Q Consensus         2 edLAa~F~lk-tq~vI~RI~eL~~~g~ltGV   31 (96)
                      .|||..||++ +..|-+.|+.|++.|.|+=.
T Consensus        28 rei~~~~g~~S~stv~~~l~~Le~kG~I~r~   58 (71)
T d1jhfa1          28 AEIAQRLGFRSPNAAEEHLKALARKGVIEIV   58 (71)
T ss_dssp             HHHHHHTTCSSHHHHHHHHHHHHHTTSEEEC
T ss_pred             HHHHHHcCCCCHHHHHHHHHHHHHCcCeecC
Confidence            6899999996 55567889999999998753

>d1ldja1 a.4.5.34 (A:687-776) Anaphase promoting complex (APC) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: SCF ubiquitin ligase complex WHB domain
domain: Anaphase promoting complex (APC)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.03  E-value=0.17  Score=31.67  Aligned_cols=41  Identities=17%  Similarity=0.285  Sum_probs=36.9

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEc
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYIS   42 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs   42 (96)
                      +.|...|..+..++-.+|..|.+.|-|.=--+|++.|+|++
T Consensus        50 ~~l~~~F~p~~~~iK~~Ie~LIereYi~R~~~~~~~y~YvA   90 (90)
T d1ldja1          50 TQLSSRFKPRVPVIKKCIDILIEKEYLERVDGEKDTYSYLA   90 (90)
T ss_dssp             HHHTTTCCCCHHHHHHHHHHHHHTTSEEECSSSTTEEEECC
T ss_pred             HHHhccCCCCHHHHHHHHHHHHhhHHHhcCCCCCceeeeeC
Confidence            45677899999999999999999999988888999999985

>d2hs5a1 a.4.5.6 (A:25-93) Putative transcriptional regulator RHA1_ro03477 {Rhodococcus sp. RHA1 [TaxId: 101510]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: GntR-like transcriptional regulators
domain: Putative transcriptional regulator RHA1 ro03477
species: Rhodococcus sp. RHA1 [TaxId: 101510]

Probab=89.82  E-value=0.2  Score=29.01  Aligned_cols=37  Identities=19%  Similarity=0.291  Sum_probs=30.6

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceE
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFI   39 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfI   39 (96)
                      .+||.+||++..-|.+-++.|+++|-|.-. --+|-||
T Consensus        29 ~~La~~~~vSr~tvr~Al~~L~~~Gli~~~-~~~G~~V   65 (69)
T d2hs5a1          29 PDICAALDVSRNTVREAFQILIEDRLVAHE-LNRGVFV   65 (69)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEE-TTTEEEE
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCcEEEE-cCCEEEe
Confidence            479999999999999999999999998755 3345444

>d2ev0a1 a.4.5.24 (A:2-62) Manganese transport regulator MntR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Iron-dependent repressor protein
domain: Manganese transport regulator MntR
species: Bacillus subtilis [TaxId: 1423]

Probab=89.51  E-value=0.16  Score=29.60  Aligned_cols=28  Identities=25%  Similarity=0.334  Sum_probs=25.7

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCcc
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALT   29 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~lt   29 (96)
                      -|||..+|++...|-+-|+.|++.|-+.
T Consensus        25 ~~iA~~L~vs~~SVs~mikrL~~~GlV~   52 (61)
T d2ev0a1          25 SDIAEALAVHPSSVTKMVQKLDKDEYLI   52 (61)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHhCCCchhHHHHHHHHHHCCCEE
Confidence            4899999999999999999999999763

>d2p4wa1 a.4.5.64 (A:1-194) Transcriptional regulatory protein PF1790 {Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PF1790-like
domain: Transcriptional regulatory protein PF1790
species: Pyrococcus furiosus [TaxId: 2261]

Probab=88.07  E-value=0.4  Score=31.70  Aligned_cols=42  Identities=12%  Similarity=0.359  Sum_probs=34.5

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCc-----eEEEcH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGK-----FIYISQ   43 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGK-----fIyIs~   43 (96)
                      .+||..+|++.+-|-.-++.|++.|-++..-+..|+     |-++++
T Consensus        32 ~ela~~l~~s~~~v~~HL~~L~~~Glv~~~~~~~~~G~~~~~y~l~~   78 (194)
T d2p4wa1          32 SELSRELGVGQKAVLEHLRILEEAGLIESRVEKIPRGRPRKYYMIKK   78 (194)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECCBTTBCCCEEEEECT
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEeecCCCCceEEEEecc
Confidence            489999999999999999999999999987765543     555544

>d1r1ua_ a.4.5.5 (A:) Metal-sensing transcriptional repressor CzrA {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: Metal-sensing transcriptional repressor CzrA
species: Staphylococcus aureus [TaxId: 1280]

Probab=88.01  E-value=0.88  Score=27.74  Aligned_cols=48  Identities=4%  Similarity=0.119  Sum_probs=37.7

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSV   49 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~V   49 (96)
                      .|||..+|++...+-.-++.|.+.|-++---+-+=.|-+++.+++..+
T Consensus        35 ~el~~~l~~s~~~vS~HL~~L~~~glv~~~r~G~~~~Y~l~~~~v~~l   82 (94)
T d1r1ua_          35 GHISHQLNLSQSNVSHQLKLLKSVHLVKAKRQGQSMIYSLDDIHVATM   82 (94)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEESSHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCceEEEEECCEEEEEECcHHHHHH
Confidence            589999999888888889999999999887654444555677766554

>d1z05a1 a.4.5.63 (A:10-80) Transcriptional regulator VC2007 N-terminal domain {Vibrio cholerae [TaxId: 666]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: Transcriptional regulator VC2007 N-terminal domain
species: Vibrio cholerae [TaxId: 666]

Probab=87.89  E-value=0.24  Score=28.38  Aligned_cols=28  Identities=18%  Similarity=0.129  Sum_probs=25.9

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCcc
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALT   29 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~lt   29 (96)
                      .|||..+||+...|-..+.+|++.|-+.
T Consensus        24 ~eLa~~~glS~~Tv~~~l~~L~~~Glv~   51 (71)
T d1z05a1          24 IDLSKESELAPASITKITRELIDAHLIH   51 (71)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            4899999999999999999999999875

>d1j5ya1 a.4.5.1 (A:3-67) Putative transcriptional regulator TM1602, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Biotin repressor-like
domain: Putative transcriptional regulator TM1602, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=87.62  E-value=0.31  Score=27.87  Aligned_cols=35  Identities=17%  Similarity=0.326  Sum_probs=28.4

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCC-ccEEeeCCCceE
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGA-LTGVIDDRGKFI   39 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~-ltGViDDRGKfI   39 (96)
                      ++||.+|+++..-+..-|++|++.|. |.   -.+|-|+
T Consensus        26 ~~La~~l~VS~~TI~rdi~~L~~~G~~I~---~~~gGY~   61 (65)
T d1j5ya1          26 AQLAEELSVSRQVIVQDIAYLRSLGYNIV---ATPRGYV   61 (65)
T ss_dssp             HHHHHHHTSCHHHHHHHHHHHHHHTCCCE---EETTEEE
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCeEE---EeCCCEE
Confidence            68999999999999999999999986 33   2455564

>d3bwga1 a.4.5.6 (A:5-82) Transcriptional regulator YydK {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: GntR-like transcriptional regulators
domain: Transcriptional regulator YydK
species: Bacillus subtilis [TaxId: 1423]

Probab=87.06  E-value=0.38  Score=28.10  Aligned_cols=30  Identities=27%  Similarity=0.432  Sum_probs=27.1

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEE
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGV   31 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGV   31 (96)
                      .+||..|+++..-|.+-++.|+++|.|.-.
T Consensus        26 ~~La~~~~vSr~tvr~Al~~L~~~Gli~~~   55 (78)
T d3bwga1          26 ETLMAQFEVSKSTITKSLELLEQKGAIFQV   55 (78)
T ss_dssp             HHHHHHTTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCcEEEE
Confidence            479999999999999999999999998743

>d1iuya_ a.4.5.34 (A:) Cullin-3 homologue {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: SCF ubiquitin ligase complex WHB domain
domain: Cullin-3 homologue
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=86.70  E-value=0.22  Score=31.00  Aligned_cols=41  Identities=24%  Similarity=0.334  Sum_probs=36.1

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEc
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYIS   42 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs   42 (96)
                      +.|...|..+..++-.+|..|.+.+-|.=--||+..|+|++
T Consensus        52 ~~l~~~F~p~~~~iK~~Ie~LIekeYi~R~~~d~~~y~Y~A   92 (92)
T d1iuya_          52 QQLKARFLPSPVVIKKRIEGLIEREYLARTPEDRKVYTYVA   92 (92)
T ss_dssp             HHTCSSCCCCHHHHHHHHHHHHHTTSEEECSSCSSEEEEC-
T ss_pred             HHHhCcCCCCHHHHHHHHHHHHhhhhhhcCCCCCCeeeeeC
Confidence            35667899999999999999999999988888999999984

>d1u2wa1 a.4.5.5 (A:12-119) Cadmium efflux system accessory protein CadC {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: Cadmium efflux system accessory protein CadC
species: Staphylococcus aureus [TaxId: 1280]

Probab=86.60  E-value=0.95  Score=28.17  Aligned_cols=50  Identities=12%  Similarity=0.206  Sum_probs=37.9

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHH
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVAT   51 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~   51 (96)
                      .|||..+|++...+-.-++.|...|-++.--+.|-.|-++.++.+..+-+
T Consensus        49 ~ela~~l~~s~s~vS~HL~~L~~aGlv~~~r~G~~~~Y~l~~~~i~~ll~   98 (108)
T d1u2wa1          49 CDIANILGVTIANASHHLRTLYKQGVVNFRKEGKLALYSLGDEHIRQIMM   98 (108)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEEEC----CCEEEESCHHHHHHHH
T ss_pred             HHHHHHHccChhHHHHHHHHHHHCCeeEEEEECCEEEEEECHHHHHHHHH
Confidence            58999999988888888999999999988776666666777887766544

>d1mkma1 a.4.5.33 (A:1-75) Transcriptional regulator IclR, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcriptional regulator IclR, N-terminal domain
domain: Transcriptional regulator IclR, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=85.57  E-value=1  Score=26.12  Aligned_cols=50  Identities=16%  Similarity=0.315  Sum_probs=38.3

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQ   55 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~   55 (96)
                      .|||...|+....+-.-+..|++.|-+.=  |++|+| .+++. +-.+|..+-+
T Consensus        24 ~eia~~~~~~~st~~rll~tL~~~g~l~~--~~~g~y-~lG~~-l~~lg~~~l~   73 (75)
T d1mkma1          24 SEIAEKFNMSVSNAYKYMVVLEEKGFVLR--KKDKRY-VPGYK-LIEYGSFVLR   73 (75)
T ss_dssp             HHHHHHTTCCHHHHHHHHHHHHHTTSEEE--CTTSCE-EECTH-HHHHHHHHHH
T ss_pred             HHHHHHHCcCHHHHHHHHHHHHHCCCEEE--CCCCCE-eecHH-HHHHHHHHHh
Confidence            58999999999999999999999999984  667874 55543 4455544443

>d2fbka1 a.4.5.28 (A:8-179) Transcriptional regulator DR1159 {Deinococcus radiodurans [TaxId: 1299]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator DR1159
species: Deinococcus radiodurans [TaxId: 1299]

Probab=85.27  E-value=0.24  Score=32.24  Aligned_cols=55  Identities=24%  Similarity=0.310  Sum_probs=43.7

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHHHHHHHHHhh
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELNSVATFIKQR   56 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~~Va~fI~~r   56 (96)
                      .+||..+++....+-.-|+.|++.|-+.=.-|   -|.++|++|+.-.+.+.......
T Consensus        83 ~eLa~~l~i~~~tvsr~l~~Le~~GlV~r~~~~~DrR~~~i~LT~~G~~l~~~~~~~~  140 (172)
T d2fbka1          83 TELSALAAISGPSTSNRIVRLLEKGLIERREDERDRRSASIRLTPQGRALVTHLLPAH  140 (172)
T ss_dssp             HHHHHHCSCCSGGGSSHHHHHHHHTSEECCC-------CCBEECHHHHHHHHHHHHHH
T ss_pred             HHHHHHHCcCHhHHHHHHHHHHhCCCeeeeccccchhhHHhhcCHHHHHHHHHHHHHH
Confidence            47899999999988889999999999987765   58999999999888777765544

>d2isya1 a.4.5.24 (A:2-64) Iron-dependent regulator IdeR {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Iron-dependent repressor protein
domain: Iron-dependent regulator IdeR
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=84.22  E-value=0.47  Score=27.75  Aligned_cols=28  Identities=14%  Similarity=0.298  Sum_probs=25.8

Q ss_pred             hhhhhhhCCChHHHHHHHHHHHHcCCcc
Q psy11008          2 EDLAALFRMKTQSVIDRIVELQKTGALT   29 (96)
Q Consensus         2 edLAa~F~lktq~vI~RI~eL~~~g~lt   29 (96)
                      -|||..+|++...|-+-|+.|.+.|-++
T Consensus        27 ~~iA~~L~vs~~SVt~mvkrL~~~Glv~   54 (63)
T d2isya1          27 ARIAERLDQSGPTVSQTVSRMERDGLLR   54 (63)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHhCCCchhHHHHHHHHHHCCCEE
Confidence            4899999999999999999999999764