Psyllid ID: psy7778

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------
Protein Sequence
MLANGFLIGGNLLYKVKDPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGTVNAMVLPSRKKREERQDRGVLLKLF
Secondary Structure (PSIPRED)
ccccccccccEEEEEEEcHHHHHHcccccHHHHHHHHHHHHHccccEEHHHHHHHccccHHHHHHHHHHHHHcccEEEEccccccccccccccccccccccccccccccccEEcccc
Secondary Structure Prediction (SSPRO)
ccHcccccccEEEEEEccHHHHHHHccccHHHHHHHHHHHHHccccEEEHHHHHHccccHHHHHHHHHHHHHccccEEEccccccHHHHccccccEEcccHHHHHHHHHccEHHHcc
Coil and Loop (DISEMBL)
mlangfliggnllykvkdpvtneklkdsdnEEKVVYKIIEEAgnkgiwmrdirfksnlmpTQLNKILKQLETKKIIKAVKSVANIEYLtegtvnamvlpsrkkreeRQDRGVLLKLF
Flexible Loop (DISEMBL)
mlangfliggnllykvkdpvtneklkdsdneekVVYKIIeeagnkgiwmrdIRFKSNLMPTQLNKILKQLETKKIIKAVKSVanieyltegtvnamvlpsrkkreerqdrgvllklf
Low Complexity Region (SEG)
MLANGFLIGGNLLYKVKDPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGTVNAMVLPSRKKREERQDRGVLLKLF
Disordered region (IsUnstruct)
****GFLIGGNLLYKVKDPV************KVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGTVNAMV********************
Disordered Region (DISOPRED)
ML*****IGGNLLYKV****************KVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGTVNAMVLPSRKKREERQDRGVLLKLF
Disordered Region (DISEMBL)
MLANGFLIGGNLLYKVKDPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGTVNAMVLPSRKKREERQDRGVLLKLF
Disordered Region (DISPRO)
MLANGFLIGGNLLYKVKDPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGTVNAMVLPSRKKREERQDRGVLLKLF
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MLANGFLIGGNLLYKVKDPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGTVNAMVLPSRKKREERQDRGVLLKLF
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	117	2.2.26 [Sep-21-2011]
Q921X6	316	DNA-directed RNA polymera	yes	N/A	0.615	0.227	0.694	1e-21
Q9H1D9	316	DNA-directed RNA polymera	yes	N/A	0.615	0.227	0.694	1e-21
Q2T9S3	316	DNA-directed RNA polymera	yes	N/A	0.615	0.227	0.694	1e-21
Q9VD25	293	Probable DNA-directed RNA	yes	N/A	0.632	0.252	0.706	3e-21
P91529	296	Probable DNA-directed RNA	yes	N/A	0.615	0.243	0.447	2e-09
Q86JM3	293	DNA-directed RNA polymera	yes	N/A	0.606	0.242	0.366	2e-07
O94553	301	Probable DNA-directed RNA	yes	N/A	0.461	0.179	0.388	4e-07
P32910	317	DNA-directed RNA polymera	yes	N/A	0.444	0.164	0.442	7e-06

>sp|Q921X6|RPC6_MOUSE DNA-directed RNA polymerase III subunit RPC6 OS=Mus musculus GN=Polr3f PE=1 SV=1

 Score =  101 bits (252), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 50/72 (69%), Positives = 62/72 (86%)

Query: 12  LLYKVKDPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLE 71
           LLY++KD     K+K SDN+EK+VY+IIE+AGNKGIW RDIR+KSNL  T++NKILK LE
Sbjct: 72  LLYRIKDSQNAGKMKGSDNQEKLVYQIIEDAGNKGIWSRDIRYKSNLPLTEINKILKNLE 131

Query: 72  TKKIIKAVKSVA 83
           +KK+IKAVKSVA
Sbjct: 132 SKKLIKAVKSVA 143

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Specific peripheric component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs. May direct RNA Pol III binding to the TFIIIB-DNA complex. Plays a key role in sensing and limiting infection by intracellular bacteria and DNA viruses. Acts as nuclear and cytosolic DNA sensor involved in innate immune response. Can sense non-self dsDNA that serves as template for transcription into dsRNA. The non-self RNA polymerase III transcripts induce type I interferon and NF- Kappa-B through the RIG-I pathway.
Mus musculus (taxid: 10090)

>sp|Q9H1D9|RPC6_HUMAN DNA-directed RNA polymerase III subunit RPC6 OS=Homo sapiens GN=POLR3F PE=1 SV=1

 Score =  101 bits (252), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 50/72 (69%), Positives = 62/72 (86%)

Query: 12  LLYKVKDPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLE 71
           LLY++KD     K+K SDN+EK+VY+IIE+AGNKGIW RDIR+KSNL  T++NKILK LE
Sbjct: 72  LLYRIKDSQNAGKMKGSDNQEKLVYQIIEDAGNKGIWSRDIRYKSNLPLTEINKILKNLE 131

Query: 72  TKKIIKAVKSVA 83
           +KK+IKAVKSVA
Sbjct: 132 SKKLIKAVKSVA 143

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Specific peripheric component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs. May direct RNA Pol III binding to the TFIIIB-DNA complex. Plays a key role in sensing and limiting infection by intracellular bacteria and DNA viruses. Acts as nuclear and cytosolic DNA sensor involved in innate immune response. Can sense non-self dsDNA that serves as template for transcription into dsRNA. The non-self RNA polymerase III transcripts, such as Epstein-Barr virus-encoded RNAs (EBERs) induce type I interferon and NF- Kappa-B through the RIG-I pathway.

Homo sapiens (taxid: 9606)

>sp|Q2T9S3|RPC6_BOVIN DNA-directed RNA polymerase III subunit RPC6 OS=Bos taurus GN=POLR3F PE=2 SV=1

 Score =  101 bits (252), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 50/72 (69%), Positives = 62/72 (86%)

Query: 12  LLYKVKDPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLE 71
           LLY++KD     K+K SDN+EK+VY+IIE+AGNKGIW RDIR+KSNL  T++NKILK LE
Sbjct: 72  LLYRIKDSQNAGKMKGSDNQEKLVYQIIEDAGNKGIWSRDIRYKSNLPLTEINKILKNLE 131

Query: 72  TKKIIKAVKSVA 83
           +KK+IKAVKSVA
Sbjct: 132 SKKLIKAVKSVA 143

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Specific peripheric component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs. May direct RNA Pol III binding to the TFIIIB-DNA complex. Plays a key role in sensing and limiting infection by intracellular bacteria and DNA viruses. Acts as nuclear and cytosolic DNA sensor involved in innate immune response. Can sense non-self dsDNA that serves as template for transcription into dsRNA. The non-self RNA polymerase III transcripts induce type I interferon and NF- Kappa-B through the RIG-I pathway.

Bos taurus (taxid: 9913)

>sp|Q9VD25|RPC6_DROME Probable DNA-directed RNA polymerase III subunit RPC6 OS=Drosophila melanogaster GN=CG5380 PE=2 SV=1

 Score =  100 bits (248), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 53/75 (70%), Positives = 59/75 (78%), Gaps = 1/75 (1%)

Query: 9   GGNLLYKVKDPVTNEKL-KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKIL 67
           G  L+Y+ KDP     L KD+DNEEKVVY I+EE GNKGIW+RDIR KSNL   QLNKIL
Sbjct: 56  GEKLVYRAKDPEKKSALPKDADNEEKVVYGIVEEGGNKGIWIRDIRMKSNLNMIQLNKIL 115

Query: 68  KQLETKKIIKAVKSV 82
           K LETKK+IKAVKSV
Sbjct: 116 KNLETKKLIKAVKSV 130

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Specific peripheric component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs.

Drosophila melanogaster (taxid: 7227)

>sp|P91529|RPC6_CAEEL Probable DNA-directed RNA polymerase III subunit RPC6 OS=Caenorhabditis elegans GN=W09C3.4 PE=3 SV=1

 Score = 60.8 bits (146), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 34/76 (44%), Positives = 51/76 (67%), Gaps = 4/76 (5%)

Query: 9   GGNLLYKVKDPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILK 68
           GG L  KV    T+E++  ++ EE+V+Y +IEE+  +GIW++++R  S L   QL K LK
Sbjct: 66  GGVLRLKVN---TSEQIAGTE-EEQVIYSLIEESKTRGIWIKELREGSGLNQLQLRKTLK 121

Query: 69  QLETKKIIKAVKSVAN 84
            LETKK+IK +K+V  
Sbjct: 122 SLETKKLIKTIKAVGT 137

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Specific peripheric component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs.

Caenorhabditis elegans (taxid: 6239)

>sp|Q86JM3|RPC6_DICDI DNA-directed RNA polymerase III subunit rpc6 OS=Dictyostelium discoideum GN=polr3f PE=3 SV=1

 Score = 54.3 bits (129), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 26/71 (36%), Positives = 44/71 (61%)

Query: 14  YKVKDPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73
           YK  +P    K +    E+ ++Y++IE + N G W R+++  S     Q+ KILK LE++
Sbjct: 61  YKEVNPEDQAKFRGLGVEDFLIYQLIEASSNTGAWTRELKNSSGYQQVQITKILKTLESR 120

Query: 74  KIIKAVKSVAN 84
           K+IK+VKS+ +
Sbjct: 121 KLIKSVKSIQS 131

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Specific peripheric component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs. May direct RNA Pol III binding to the TFIIIB-DNA complex.

Dictyostelium discoideum (taxid: 44689)

>sp|O94553|RPC6_SCHPO Probable DNA-directed RNA polymerase III subunit rpc6 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rpc6 PE=2 SV=1

 Score = 53.5 bits (127), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 21/54 (38%), Positives = 40/54 (74%)

Query: 31  EEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVAN 84
           +E++VY  I+ +GN+GIW + +  ++NL  + +++ LK LE+K ++K++KSV N
Sbjct: 86  DEQIVYSFIKNSGNEGIWRKTLTLRTNLHVSVVDRCLKSLESKNLVKSIKSVKN 139

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Specific peripheric component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|P32910|RPC6_YEAST DNA-directed RNA polymerase III subunit RPC6 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RPC34 PE=1 SV=1

 Score = 49.3 bits (116), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 23/52 (44%), Positives = 36/52 (69%)

Query: 31  EEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV 82
           EE +VY  IE +G +GIW + I+ ++NL    + K LK LE+++ +K+VKSV
Sbjct: 89  EEALVYSYIEASGREGIWSKTIKARTNLHQHVVLKCLKSLESQRYVKSVKSV 140

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Specific peripheric component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs. Involved in recruitment of Pol III to the preinitiation complex. Involved in the configuration of an initiation-competent form of RNA polymerase.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

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	117
383863773	310	PREDICTED: DNA-directed RNA polymerase I	0.666	0.251	0.769	4e-26
380025937	311	PREDICTED: LOW QUALITY PROTEIN: DNA-dire	0.666	0.250	0.769	5e-26
66509068	311	PREDICTED: DNA-directed RNA polymerase I	0.666	0.250	0.769	5e-26
156551159	305	PREDICTED: DNA-directed RNA polymerase I	0.666	0.255	0.769	1e-25
350410921	311	PREDICTED: DNA-directed RNA polymerase I	0.666	0.250	0.756	2e-25
340714612	311	PREDICTED: DNA-directed RNA polymerase I	0.666	0.250	0.756	2e-25
307207698	331	DNA-directed RNA polymerase III subunit	0.641	0.226	0.733	2e-23
332372876	305	unknown [Dendroctonus ponderosae]	0.632	0.242	0.770	2e-23
242022647	315	DNA-directed RNA polymerase III subunit	0.666	0.247	0.679	1e-22
291222494	309	PREDICTED: Polr3f protein-like [Saccoglo	0.632	0.239	0.662	6e-22

>gi|383863773|ref|XP_003707354.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC6-like [Megachile rotundata]

 Score =  122 bits (305), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 60/78 (76%), Positives = 67/78 (85%)

Query: 6   FLIGGNLLYKVKDPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNK 65
           F  GG+LLY++KDP   +  K +DNEEK+VY IIEEAGNKGIW+RDIRFKSNLMPTQLNK
Sbjct: 71  FKQGGSLLYRLKDPSKAKVAKGADNEEKIVYTIIEEAGNKGIWIRDIRFKSNLMPTQLNK 130

Query: 66  ILKQLETKKIIKAVKSVA 83
           ILK LETKK IKAVKSVA
Sbjct: 131 ILKSLETKKFIKAVKSVA 148

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|380025937|ref|XP_003696719.1| PREDICTED: LOW QUALITY PROTEIN: DNA-directed RNA polymerase III subunit RPC6-like [Apis florea]

 Score =  121 bits (304), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 60/78 (76%), Positives = 67/78 (85%)

Query: 6   FLIGGNLLYKVKDPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNK 65
           F  GG+LLY++KDP   +  K +DNEEK+VY IIEEAGNKGIW+RDIRFKSNLMPTQLNK
Sbjct: 72  FKQGGSLLYRLKDPSKAKIAKGADNEEKIVYTIIEEAGNKGIWIRDIRFKSNLMPTQLNK 131

Query: 66  ILKQLETKKIIKAVKSVA 83
           ILK LETKK IKAVKSVA
Sbjct: 132 ILKSLETKKFIKAVKSVA 149

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|66509068|ref|XP_624984.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC6-like [Apis mellifera]

 Score =  121 bits (303), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 60/78 (76%), Positives = 67/78 (85%)

Query: 6   FLIGGNLLYKVKDPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNK 65
           F  GG+LLY++KDP   +  K +DNEEK+VY IIEEAGNKGIW+RDIRFKSNLMPTQLNK
Sbjct: 72  FKQGGSLLYRLKDPSKAKIAKGADNEEKIVYTIIEEAGNKGIWIRDIRFKSNLMPTQLNK 131

Query: 66  ILKQLETKKIIKAVKSVA 83
           ILK LETKK IKAVKSVA
Sbjct: 132 ILKSLETKKFIKAVKSVA 149

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|156551159|ref|XP_001604309.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC6-like [Nasonia vitripennis]

 Score =  120 bits (300), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 60/78 (76%), Positives = 64/78 (82%)

Query: 6   FLIGGNLLYKVKDPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNK 65
           F  G  LLYK+KDP      K +DNEE++VY IIEEAGNKGIW RDIRFKSNLMPTQLNK
Sbjct: 65  FKQGETLLYKLKDPTKARTAKGADNEERIVYTIIEEAGNKGIWTRDIRFKSNLMPTQLNK 124

Query: 66  ILKQLETKKIIKAVKSVA 83
           ILK LETKKIIKAVKSVA
Sbjct: 125 ILKSLETKKIIKAVKSVA 142

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350410921|ref|XP_003489178.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC6-like [Bombus impatiens]

 Score =  119 bits (299), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 59/78 (75%), Positives = 66/78 (84%)

Query: 6   FLIGGNLLYKVKDPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNK 65
           F  GG+LLY++KDP   +  K +DNEEK+VY IIEEAGNKGIW+RDIRFKSNLMPTQLNK
Sbjct: 72  FKQGGSLLYRLKDPSKAKIAKGADNEEKIVYTIIEEAGNKGIWIRDIRFKSNLMPTQLNK 131

Query: 66  ILKQLETKKIIKAVKSVA 83
           ILK LE KK IKAVKSVA
Sbjct: 132 ILKSLEIKKFIKAVKSVA 149

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340714612|ref|XP_003395820.1| PREDICTED: DNA-directed RNA polymerase III subunit RPC6-like [Bombus terrestris]

 Score =  119 bits (298), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 59/78 (75%), Positives = 66/78 (84%)

Query: 6   FLIGGNLLYKVKDPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNK 65
           F  GG+LLY++KDP   +  K +DNEEK+VY IIEEAGNKGIW+RDIRFKSNLMPTQLNK
Sbjct: 72  FKQGGSLLYRLKDPSKAKIAKGADNEEKIVYTIIEEAGNKGIWIRDIRFKSNLMPTQLNK 131

Query: 66  ILKQLETKKIIKAVKSVA 83
           ILK LE KK IKAVKSVA
Sbjct: 132 ILKSLEIKKFIKAVKSVA 149

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307207698|gb|EFN85335.1| DNA-directed RNA polymerase III subunit RPC6 [Harpegnathos saltator]

 Score =  113 bits (282), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 55/75 (73%), Positives = 63/75 (84%)

Query: 9   GGNLLYKVKDPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILK 68
           G +L Y++KD    + +K +DNEEK+VY IIEEAGNKGIW+RDIRFKSNL PTQLNKILK
Sbjct: 89  GESLFYRLKDLSKTKAVKGADNEEKIVYTIIEEAGNKGIWIRDIRFKSNLAPTQLNKILK 148

Query: 69  QLETKKIIKAVKSVA 83
            LETKK IKAVKSVA
Sbjct: 149 SLETKKCIKAVKSVA 163

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332372876|gb|AEE61580.1| unknown [Dendroctonus ponderosae]

 Score =  112 bits (281), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 57/74 (77%), Positives = 60/74 (81%)

Query: 10  GNLLYKVKDPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQ 69
           G L YK KDP      K SDNEEKVVYKIIEEAGNKGIW+RDIRFKSN+  TQLNK+LK 
Sbjct: 68  GELFYKFKDPTKKSANKGSDNEEKVVYKIIEEAGNKGIWIRDIRFKSNINNTQLNKVLKS 127

Query: 70  LETKKIIKAVKSVA 83
           LE KKIIKAVKSVA
Sbjct: 128 LEAKKIIKAVKSVA 141

Source: Dendroctonus ponderosae

Species: Dendroctonus ponderosae

Genus: Dendroctonus

Family: Curculionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242022647|ref|XP_002431750.1| DNA-directed RNA polymerase III subunit F, putative [Pediculus humanus corporis] gi|212517075|gb|EEB19012.1| DNA-directed RNA polymerase III subunit F, putative [Pediculus humanus corporis]

 Score =  110 bits (274), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 53/78 (67%), Positives = 64/78 (82%)

Query: 6   FLIGGNLLYKVKDPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNK 65
           F  GG L+YK KD    + +K +DNEEKVVY I+E AGNKGIW+RDIR++SNL+PTQLNK
Sbjct: 75  FNQGGKLIYKFKDVAKGDSVKGADNEEKVVYSIVEAAGNKGIWIRDIRYQSNLLPTQLNK 134

Query: 66  ILKQLETKKIIKAVKSVA 83
           ILK LE KK+IKAVKSV+
Sbjct: 135 ILKALENKKLIKAVKSVS 152

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|291222494|ref|XP_002731250.1| PREDICTED: Polr3f protein-like [Saccoglossus kowalevskii]

 Score =  107 bits (268), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 49/74 (66%), Positives = 66/74 (89%)

Query: 10  GNLLYKVKDPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQ 69
             L+YK+KDP T+ K+K SDN+EK++Y+IIEEAGNKGIW+RDIR+KSNL+ TQ++KIL+ 
Sbjct: 69  AGLVYKLKDPQTSSKMKGSDNQEKLIYQIIEEAGNKGIWIRDIRYKSNLLMTQVSKILRN 128

Query: 70  LETKKIIKAVKSVA 83
           LE+KK+IKA+KSV 
Sbjct: 129 LESKKLIKAIKSVG 142

Source: Saccoglossus kowalevskii

Species: Saccoglossus kowalevskii

Genus: Saccoglossus

Family: Harrimaniidae

Class: Enteropneusta

Phylum: Hemichordata

Superkingdom: Eukaryota

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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	117
FB|FBgn0038951	293	CG5380 [Drosophila melanogaste	0.632	0.252	0.706	3.4e-22
UNIPROTKB|F1MYX7	316	POLR3F "DNA-directed RNA polym	0.615	0.227	0.694	3.4e-22
UNIPROTKB|Q2T9S3	316	POLR3F "DNA-directed RNA polym	0.615	0.227	0.694	3.4e-22
UNIPROTKB|E2RG78	316	POLR3F "Uncharacterized protei	0.615	0.227	0.694	3.4e-22
UNIPROTKB|Q9H1D9	316	POLR3F "DNA-directed RNA polym	0.615	0.227	0.694	3.4e-22
UNIPROTKB|F1SBH4	316	POLR3F "Uncharacterized protei	0.615	0.227	0.694	3.4e-22
MGI|MGI:1924086	316	Polr3f "polymerase (RNA) III (	0.615	0.227	0.694	3.4e-22
RGD|1306428	371	Polr3f "polymerase (RNA) III (	0.615	0.194	0.694	3.4e-22
ZFIN|ZDB-GENE-040426-972	314	polr3f "polymerase (RNA) III (	0.615	0.229	0.694	3.4e-22
UNIPROTKB|E1BU41	314	POLR3F "Uncharacterized protei	0.615	0.229	0.680	5.5e-22

FB|FBgn0038951 CG5380 [Drosophila melanogaster (taxid:7227)]

 Score = 258 (95.9 bits), Expect = 3.4e-22, P = 3.4e-22
 Identities = 53/75 (70%), Positives = 59/75 (78%)

Query:     9 GGNLLYKVKDPVTNEKL-KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKIL 67
             G  L+Y+ KDP     L KD+DNEEKVVY I+EE GNKGIW+RDIR KSNL   QLNKIL
Sbjct:    56 GEKLVYRAKDPEKKSALPKDADNEEKVVYGIVEEGGNKGIWIRDIRMKSNLNMIQLNKIL 115

Query:    68 KQLETKKIIKAVKSV 82
             K LETKK+IKAVKSV
Sbjct:   116 KNLETKKLIKAVKSV 130

GO:0003899 "DNA-directed RNA polymerase activity" evidence=ISS;NAS

GO:0005666 "DNA-directed RNA polymerase III complex" evidence=ISS

GO:0006383 "transcription from RNA polymerase III promoter" evidence=NAS

GO:0005634 "nucleus" evidence=NAS

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0022008 "neurogenesis" evidence=IMP

UNIPROTKB|F1MYX7 POLR3F "DNA-directed RNA polymerase III subunit RPC6" [Bos taurus (taxid:9913)]

 Score = 258 (95.9 bits), Expect = 3.4e-22, P = 3.4e-22
 Identities = 50/72 (69%), Positives = 62/72 (86%)

Query:    12 LLYKVKDPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLE 71
             LLY++KD     K+K SDN+EK+VY+IIE+AGNKGIW RDIR+KSNL  T++NKILK LE
Sbjct:    72 LLYRIKDSQNAGKMKGSDNQEKLVYQIIEDAGNKGIWSRDIRYKSNLPLTEINKILKNLE 131

Query:    72 TKKIIKAVKSVA 83
             +KK+IKAVKSVA
Sbjct:   132 SKKLIKAVKSVA 143

GO:0045089 "positive regulation of innate immune response" evidence=IEA

GO:0032728 "positive regulation of interferon-beta production" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|Q2T9S3 POLR3F "DNA-directed RNA polymerase III subunit RPC6" [Bos taurus (taxid:9913)]

 Score = 258 (95.9 bits), Expect = 3.4e-22, P = 3.4e-22
 Identities = 50/72 (69%), Positives = 62/72 (86%)

Query:    12 LLYKVKDPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLE 71
             LLY++KD     K+K SDN+EK+VY+IIE+AGNKGIW RDIR+KSNL  T++NKILK LE
Sbjct:    72 LLYRIKDSQNAGKMKGSDNQEKLVYQIIEDAGNKGIWSRDIRYKSNLPLTEINKILKNLE 131

Query:    72 TKKIIKAVKSVA 83
             +KK+IKAVKSVA
Sbjct:   132 SKKLIKAVKSVA 143

GO:0003677 "DNA binding" evidence=IEA

GO:0045089 "positive regulation of innate immune response" evidence=ISS

GO:0032728 "positive regulation of interferon-beta production" evidence=ISS

GO:0005634 "nucleus" evidence=IEA

GO:0051607 "defense response to virus" evidence=IEA

GO:0045087 "innate immune response" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

UNIPROTKB|E2RG78 POLR3F "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 258 (95.9 bits), Expect = 3.4e-22, P = 3.4e-22
 Identities = 50/72 (69%), Positives = 62/72 (86%)

Query:    12 LLYKVKDPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLE 71
             LLY++KD     K+K SDN+EK+VY+IIE+AGNKGIW RDIR+KSNL  T++NKILK LE
Sbjct:    72 LLYRIKDSQNAGKMKGSDNQEKLVYQIIEDAGNKGIWSRDIRYKSNLPLTEINKILKNLE 131

Query:    72 TKKIIKAVKSVA 83
             +KK+IKAVKSVA
Sbjct:   132 SKKLIKAVKSVA 143

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|Q9H1D9 POLR3F "DNA-directed RNA polymerase III subunit RPC6" [Homo sapiens (taxid:9606)]

 Score = 258 (95.9 bits), Expect = 3.4e-22, P = 3.4e-22
 Identities = 50/72 (69%), Positives = 62/72 (86%)

Query:    12 LLYKVKDPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLE 71
             LLY++KD     K+K SDN+EK+VY+IIE+AGNKGIW RDIR+KSNL  T++NKILK LE
Sbjct:    72 LLYRIKDSQNAGKMKGSDNQEKLVYQIIEDAGNKGIWSRDIRYKSNLPLTEINKILKNLE 131

Query:    72 TKKIIKAVKSVA 83
             +KK+IKAVKSVA
Sbjct:   132 SKKLIKAVKSVA 143

GO:0003677 "DNA binding" evidence=IEA

GO:0045087 "innate immune response" evidence=IEA

GO:0051607 "defense response to virus" evidence=IEA

GO:0005666 "DNA-directed RNA polymerase III complex" evidence=NAS

GO:0006359 "regulation of transcription from RNA polymerase III promoter" evidence=NAS

GO:0032728 "positive regulation of interferon-beta production" evidence=IMP

GO:0045089 "positive regulation of innate immune response" evidence=IMP

GO:0003899 "DNA-directed RNA polymerase activity" evidence=NAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006383 "transcription from RNA polymerase III promoter" evidence=TAS

GO:0006385 "transcription elongation from RNA polymerase III promoter" evidence=TAS

GO:0006386 "termination of RNA polymerase III transcription" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

UNIPROTKB|F1SBH4 POLR3F "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 258 (95.9 bits), Expect = 3.4e-22, P = 3.4e-22
 Identities = 50/72 (69%), Positives = 62/72 (86%)

Query:    12 LLYKVKDPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLE 71
             LLY++KD     K+K SDN+EK+VY+IIE+AGNKGIW RDIR+KSNL  T++NKILK LE
Sbjct:    72 LLYRIKDSQNAGKMKGSDNQEKLVYQIIEDAGNKGIWSRDIRYKSNLPLTEINKILKNLE 131

Query:    72 TKKIIKAVKSVA 83
             +KK+IKAVKSVA
Sbjct:   132 SKKLIKAVKSVA 143

GO:0045089 "positive regulation of innate immune response" evidence=IEA

GO:0032728 "positive regulation of interferon-beta production" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

MGI|MGI:1924086 Polr3f "polymerase (RNA) III (DNA directed) polypeptide F" [Mus musculus (taxid:10090)]

 Score = 258 (95.9 bits), Expect = 3.4e-22, P = 3.4e-22
 Identities = 50/72 (69%), Positives = 62/72 (86%)

Query:    12 LLYKVKDPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLE 71
             LLY++KD     K+K SDN+EK+VY+IIE+AGNKGIW RDIR+KSNL  T++NKILK LE
Sbjct:    72 LLYRIKDSQNAGKMKGSDNQEKLVYQIIEDAGNKGIWSRDIRYKSNLPLTEINKILKNLE 131

Query:    72 TKKIIKAVKSVA 83
             +KK+IKAVKSVA
Sbjct:   132 SKKLIKAVKSVA 143

GO:0003677 "DNA binding" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0032728 "positive regulation of interferon-beta production" evidence=ISO

GO:0045087 "innate immune response" evidence=IEA

GO:0045089 "positive regulation of innate immune response" evidence=ISO

GO:0051607 "defense response to virus" evidence=IEA

RGD|1306428 Polr3f "polymerase (RNA) III (DNA directed) polypeptide F" [Rattus norvegicus (taxid:10116)]

 Score = 258 (95.9 bits), Expect = 3.4e-22, P = 3.4e-22
 Identities = 50/72 (69%), Positives = 62/72 (86%)

Query:    12 LLYKVKDPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLE 71
             LLY++KD     K+K SDN+EK+VY+IIE+AGNKGIW RDIR+KSNL  T++NKILK LE
Sbjct:   127 LLYRIKDSQNAGKMKGSDNQEKLVYQIIEDAGNKGIWSRDIRYKSNLPLTEINKILKNLE 186

Query:    72 TKKIIKAVKSVA 83
             +KK+IKAVKSVA
Sbjct:   187 SKKLIKAVKSVA 198

GO:0003677 "DNA binding" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0032728 "positive regulation of interferon-beta production" evidence=ISO

GO:0045089 "positive regulation of innate immune response" evidence=ISO

ZFIN|ZDB-GENE-040426-972 polr3f "polymerase (RNA) III (DNA directed) polypeptide F" [Danio rerio (taxid:7955)]

 Score = 258 (95.9 bits), Expect = 3.4e-22, P = 3.4e-22
 Identities = 50/72 (69%), Positives = 63/72 (87%)

Query:    12 LLYKVKDPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLE 71
             LLY++KD  +  K+K SDN+EK+VY+IIE+AGNKGIW RDIR+KSNL  T++NKILK LE
Sbjct:    70 LLYRLKDTQSASKVKGSDNQEKLVYQIIEDAGNKGIWSRDIRYKSNLPLTEINKILKNLE 129

Query:    72 TKKIIKAVKSVA 83
             +KK+IKAVKSVA
Sbjct:   130 SKKLIKAVKSVA 141

GO:0003677 "DNA binding" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0060041 "retina development in camera-type eye" evidence=IMP

UNIPROTKB|E1BU41 POLR3F "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 256 (95.2 bits), Expect = 5.5e-22, P = 5.5e-22
 Identities = 49/72 (68%), Positives = 62/72 (86%)

Query:    12 LLYKVKDPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLE 71
             LLY++K+     K+K SDN+EK+VY+IIE+AGNKGIW RDIR+KSNL  T++NKILK LE
Sbjct:    70 LLYRIKESQNASKMKGSDNQEKLVYQIIEDAGNKGIWSRDIRYKSNLPLTEINKILKNLE 129

Query:    72 TKKIIKAVKSVA 83
             +KK+IKAVKSVA
Sbjct:   130 SKKLIKAVKSVA 141

GO:0003677 "DNA binding" evidence=IEA

GO:0003899 "DNA-directed RNA polymerase activity" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0032728 "positive regulation of interferon-beta production" evidence=IEA

GO:0045089 "positive regulation of innate immune response" evidence=IEA

---

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)
Q2T9S3	RPC6_BOVIN	No assigned EC number	0.6944	0.6153	0.2278	yes	N/A
Q9VD25	RPC6_DROME	No assigned EC number	0.7066	0.6324	0.2525	yes	N/A
Q921X6	RPC6_MOUSE	No assigned EC number	0.6944	0.6153	0.2278	yes	N/A
Q9H1D9	RPC6_HUMAN	No assigned EC number	0.6944	0.6153	0.2278	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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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	117
pfam05158	312	pfam05158, RNA_pol_Rpc34, RNA polymerase Rpc34 sub	6e-23
COG5111	301	COG5111, RPC34, DNA-directed RNA polymerase III, s	9e-12

>gnl|CDD|218472 pfam05158, RNA_pol_Rpc34, RNA polymerase Rpc34 subunit

 Score = 90.1 bits (224), Expect = 6e-23
 Identities = 35/76 (46%), Positives = 47/76 (61%)

Query: 9   GGNLLYKVKDPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILK 68
              L+YK       +K     +EE +VY IIEE+GN+GIW R I+ ++NL  + L K LK
Sbjct: 63  NDGLVYKAVTREEAKKKATLSDEESLVYSIIEESGNEGIWTRTIKNRTNLHQSVLKKCLK 122

Query: 69  QLETKKIIKAVKSVAN 84
            LE+KK IK+VKSV  
Sbjct: 123 SLESKKYIKSVKSVKA 138

Subunit specific to RNA Pol III, the tRNA specific polymerase. The C34 subunit of yeast RNA Pol III is part of a subcomplex of three subunits which have no counterpart in the other two nuclear RNA polymerases. This subunit interacts with TFIIIB70 and is therefore participates in Pol III recruitment. Length = 312

>gnl|CDD|227442 COG5111, RPC34, DNA-directed RNA polymerase III, subunit C34 [Transcription]

 Score = 59.6 bits (144), Expect = 9e-12
 Identities = 29/76 (38%), Positives = 45/76 (59%)

Query: 9   GGNLLYKVKDPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILK 68
            G L YK         +   D+ E  VY +I ++G +GIW++ I+ ++NL    + K LK
Sbjct: 64  KGVLYYKGVLESEASPINTMDDYELTVYSLISQSGGEGIWLKTIKDRTNLHHNVVGKCLK 123

Query: 69  QLETKKIIKAVKSVAN 84
            LE+K+I+K+VKSV N
Sbjct: 124 SLESKRIVKSVKSVKN 139

Length = 301

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	117
PF05158	327	RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; Inter	100.0
KOG3233|consensus	297		100.0
COG5111	301	RPC34 DNA-directed RNA polymerase III, subunit C34	99.97
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	98.09
COG2512	258	Predicted membrane-associated trancriptional regul	98.03
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	98.0
PF13730	55	HTH_36: Helix-turn-helix domain	97.98
PF04182	75	B-block_TFIIIC: B-block binding subunit of TFIIIC;	97.95
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	97.83
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	97.75
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	97.69
TIGR01889	109	Staph_reg_Sar staphylococcal accessory regulator f	97.62
COG1846	126	MarR Transcriptional regulators [Transcription]	97.48
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	97.34
PRK10870	176	transcriptional repressor MprA; Provisional	97.29
smart00347	101	HTH_MARR helix_turn_helix multiple antibiotic resi	97.26
PF02082	83	Rrf2: Transcriptional regulator; InterPro: IPR0009	97.07
TIGR00498	199	lexA SOS regulatory protein LexA. LexA acts as a h	97.04
PRK11512	144	DNA-binding transcriptional repressor MarR; Provis	97.03
PRK13777	185	transcriptional regulator Hpr; Provisional	96.9
TIGR02337	118	HpaR homoprotocatechuate degradation operon regula	96.89
PRK03573	144	transcriptional regulator SlyA; Provisional	96.88
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	96.87
TIGR02944	130	suf_reg_Xantho FeS assembly SUF system regulator,	96.65
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	96.64
PF08784	102	RPA_C: Replication protein A C terminal; InterPro:	96.55
PRK00215	205	LexA repressor; Validated	96.52
cd00090	78	HTH_ARSR Arsenical Resistance Operon Repressor and	96.52
PRK11920	153	rirA iron-responsive transcriptional regulator; Re	96.51
TIGR02010	135	IscR iron-sulfur cluster assembly transcription fa	96.37
COG1959	150	Predicted transcriptional regulator [Transcription	96.35
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	96.22
PRK11014	141	transcriptional repressor NsrR; Provisional	96.18
TIGR01884	203	cas_HTH CRISPR locus-related DNA-binding protein.	96.15
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	96.11
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	96.1
COG3355	126	Predicted transcriptional regulator [Transcription	95.98
TIGR01610	95	phage_O_Nterm phage replication protein O, N-termi	95.97
PF02295	66	z-alpha: Adenosine deaminase z-alpha domain; Inter	95.75
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	95.68
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	95.59
cd07153	116	Fur_like Ferric uptake regulator(Fur) and related	95.56
TIGR00738	132	rrf2_super rrf2 family protein (putative transcrip	95.54
PRK10857	164	DNA-binding transcriptional regulator IscR; Provis	95.52
PF13601	80	HTH_34: Winged helix DNA-binding domain; PDB: 1UB9	95.5
COG1522	154	Lrp Transcriptional regulators [Transcription]	95.32
PF14947	77	HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_	95.3
PF10007	92	DUF2250: Uncharacterized protein conserved in arch	95.13
PRK04172	489	pheS phenylalanyl-tRNA synthetase subunit alpha; P	95.05
PF04703	62	FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.	94.81
TIGR02702	203	SufR_cyano iron-sulfur cluster biosynthesis transc	94.73
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	94.66
smart00418	66	HTH_ARSR helix_turn_helix, Arsenical Resistance Op	94.65
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	94.56
TIGR02698	130	CopY_TcrY copper transport repressor, CopY/TcrY fa	94.21
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	93.88
smart00419	48	HTH_CRP helix_turn_helix, cAMP Regulatory protein.	93.76
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	93.62
PF01475	120	FUR: Ferric uptake regulator family; InterPro: IPR	93.59
smart00421	58	HTH_LUXR helix_turn_helix, Lux Regulon. lux regulo	93.46
COG1378	247	Predicted transcriptional regulators [Transcriptio	93.44
cd07377	66	WHTH_GntR Winged helix-turn-helix (WHTH) DNA-bindi	93.37
PRK09391	230	fixK transcriptional regulator FixK; Provisional	93.1
PRK12423	202	LexA repressor; Provisional	93.06
PF03965	115	Penicillinase_R: Penicillinase repressor; InterPro	92.58
PRK03902	142	manganese transport transcriptional regulator; Pro	92.51
PF13545	76	HTH_Crp_2: Crp-like helix-turn-helix domain; PDB:	92.5
smart00529	96	HTH_DTXR Helix-turn-helix diphteria tox regulatory	92.49
PF13936	44	HTH_38: Helix-turn-helix domain; PDB: 2W48_A.	92.35
PRK09462	148	fur ferric uptake regulator; Provisional	92.09
COG1321	154	TroR Mn-dependent transcriptional regulator [Trans	92.05
PRK10141	117	DNA-binding transcriptional repressor ArsR; Provis	91.72
PRK14165	217	winged helix-turn-helix domain-containing protein/	91.65
PRK11169	164	leucine-responsive transcriptional regulator; Prov	91.48
PRK11050	152	manganese transport regulator MntR; Provisional	91.36
TIGR03697	193	NtcA_cyano global nitrogen regulator NtcA, cyanoba	91.34
PRK11753	211	DNA-binding transcriptional dual regulator Crp; Pr	91.18
COG0735	145	Fur Fe2+/Zn2+ uptake regulation proteins [Inorgani	90.86
PRK06474	178	hypothetical protein; Provisional	90.61
PRK11161	235	fumarate/nitrate reduction transcriptional regulat	90.58
PRK13918	202	CRP/FNR family transcriptional regulator; Provisio	90.39
PRK10402	226	DNA-binding transcriptional activator YeiL; Provis	89.98
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	89.9
PRK10430	239	DNA-binding transcriptional activator DcuR; Provis	89.86
PRK10163	271	DNA-binding transcriptional repressor AllR; Provis	89.39
PRK09954	362	putative kinase; Provisional	89.36
PF05732	165	RepL: Firmicute plasmid replication protein (RepL)	89.31
PRK09334	86	30S ribosomal protein S25e; Provisional	89.28
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	89.13
TIGR02431	248	pcaR_pcaU beta-ketoadipate pathway transcriptional	88.89
TIGR03879	73	near_KaiC_dom probable regulatory domain. This mod	88.66
COG1414	246	IclR Transcriptional regulator [Transcription]	88.23
PF03297	105	Ribosomal_S25: S25 ribosomal protein; InterPro: IP	88.08
PF09202	82	Rio2_N: Rio2, N-terminal; InterPro: IPR015285 This	87.99
PHA00738	108	putative HTH transcription regulator	87.9
PRK10434	256	srlR DNA-bindng transcriptional repressor SrlR; Pr	87.81
cd06170	57	LuxR_C_like C-terminal DNA-binding domain of LuxR-	87.6
smart00531	147	TFIIE Transcription initiation factor IIE.	87.22
PRK15090	257	DNA-binding transcriptional regulator KdgR; Provis	87.21
PF05158	327	RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; Inter	87.04
PF09012	69	FeoC: FeoC like transcriptional regulator; InterPr	86.72
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	86.66
PRK11569	274	transcriptional repressor IclR; Provisional	86.36
PF03444	78	HrcA_DNA-bdg: Winged helix-turn-helix transcriptio	86.26
PRK09834	263	DNA-binding transcriptional activator MhpR; Provis	86.03
PRK10046	225	dpiA two-component response regulator DpiA; Provis	85.98
cd06171	55	Sigma70_r4 Sigma70, region (SR) 4 refers to the mo	85.98
PRK11179	153	DNA-binding transcriptional regulator AsnC; Provis	85.71
PF00392	64	GntR: Bacterial regulatory proteins, gntR family;	85.49
PHA02701	183	ORF020 dsRNA-binding PKR inhibitor; Provisional	85.36
COG1725	125	Predicted transcriptional regulators [Transcriptio	84.96
PF02002	105	TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024	84.52
COG3888	321	Predicted transcriptional regulator [Transcription	84.18
PRK10906	252	DNA-binding transcriptional repressor GlpR; Provis	84.0
COG1733	120	Predicted transcriptional regulators [Transcriptio	83.8
COG3398	240	Uncharacterized protein conserved in archaea [Func	83.57
PF01638	90	HxlR: HxlR-like helix-turn-helix; InterPro: IPR002	83.54
PF06163	127	DUF977: Bacterial protein of unknown function (DUF	82.61
PRK10736	374	hypothetical protein; Provisional	82.61
TIGR02325	238	C_P_lyase_phnF phosphonates metabolism transcripti	81.87
PRK09483	217	response regulator; Provisional	81.32
PF04492	100	Phage_rep_O: Bacteriophage replication protein O ;	81.22
cd04761	49	HTH_MerR-SF Helix-Turn-Helix DNA binding domain of	81.18
PRK13509	251	transcriptional repressor UlaR; Provisional	80.78
TIGR00122	69	birA_repr_reg BirA biotin operon repressor domain.	80.46
PHA02943	165	hypothetical protein; Provisional	80.39
PRK09764	240	DNA-binding transcriptional repressor MngR; Provis	80.31
PRK06266	178	transcription initiation factor E subunit alpha; V	80.24

>PF05158 RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; InterPro: IPR007832 The family comprises a subunit specific to RNA Pol III, the tRNA specific polymerase

Probab=100.00  E-value=7.8e-38  Score=257.56  Aligned_cols=103  Identities=45%  Similarity=0.662  Sum_probs=65.6

Q ss_pred             ccceecCCeEEEEEeCccccccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778           3 ANGFLIGGNLLYKVKDPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus         3 ~~~~~~~~~l~yk~~~~e~a~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      ..+++.+++++|+++++++|+++++|+++|++||++|++|||+|||++|||.+||||+++|+||||+||+|+|||+||||
T Consensus        57 ~~~~~~~~~l~~~~~~~~~a~k~~~l~~~e~lvy~~I~~ag~~GIw~~~i~~~t~l~~~~~~k~lk~Le~k~lIK~vksv  136 (327)
T PF05158_consen   57 LKLLKKGGGLSYKAVSEEEAKKLKGLSDEERLVYQLIEEAGNKGIWTKDIKKKTNLHQTQLTKILKSLESKKLIKSVKSV  136 (327)
T ss_dssp             EEEEE-SSSEEEEE--SSS-----SSSCCHHHHHHHHHHHTTT-EEHHHHHHHCT--HHHHHHHHHHHHHTTSEEEE--S
T ss_pred             EEEEEcCCEEEEEEeCHHHHhhhcCCCHHHHHHHHHHHHhCCCCCcHHHHHHHcCCCHHHHHHHHHHHHhCCCEEEecCc
Confidence            45778889999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             c-------------------CCcccccCccccccchhhhhhh
Q psy7778          83 A-------------------NIEYLTEGTVNAMVLPSRKKRE  105 (117)
Q Consensus        83 ~-------------------gg~wYtdg~~D~~fI~~l~~~~  105 (117)
                      +                   ||+||+||+||++||+.|++.-
T Consensus       137 ~~~~rK~Yml~~l~Ps~eiTGG~wy~d~e~D~efi~~l~~~~  178 (327)
T PF05158_consen  137 KNPNRKVYMLYDLEPSEEITGGPWYTDGEFDTEFIDVLREQC  178 (327)
T ss_dssp             S-SS--EEEESSS-----------------------------
T ss_pred             CCCCeEEEEEccCCcCcccCCCCcccCCcccHHHHHHHHHHH
Confidence            7                   9999999999999999998753

The C34 subunit of Saccharomyces cerevisiae RNA Pol III is part of a subcomplex of three subunits which have no counterpart in the other two nuclear RNA polymerases. This subunit interacts with TFIIIB70 and therefore participates in Pol III recruitment [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2DK8_A 2DK5_A 2YU3_A.

>KOG3233|consensus

Probab=100.00  E-value=9.1e-35  Score=237.14  Aligned_cols=104  Identities=43%  Similarity=0.624  Sum_probs=100.3

Q ss_pred             cccceecCCeEEEEEeCccccccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778           2 LANGFLIGGNLLYKVKDPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus         2 ~~~~~~~~~~l~yk~~~~e~a~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      +.+++++++++.|+.+++..|++.++++++|++||++|++|||+|||+++||.+||||+++|+||||+||+|+|||+|||
T Consensus        56 ~l~llr~~~~l~yr~~d~~~a~~~~~~e~eEk~vy~lIe~sg~~GIW~k~ik~ksnLp~~~v~K~LkSLEsKkLIKsVKs  135 (297)
T KOG3233|consen   56 LLDLLRQNTGLVYRAKDPKSASKGKGMENEEKLVYSLIEESGNEGIWSKEIKRKSNLPQTVVNKILKSLESKKLIKSVKS  135 (297)
T ss_pred             cchhhccCCcceEeccCchhhcccccCChHHHHHHHHHHHcCCCceeeehhhhccCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence            45789999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cc-------------------CCcccccCccccccchhhhhhh
Q psy7778          82 VA-------------------NIEYLTEGTVNAMVLPSRKKRE  105 (117)
Q Consensus        82 V~-------------------gg~wYtdg~~D~~fI~~l~~~~  105 (117)
                      |+                   ||+|||||+||.+||+.|++.-
T Consensus       136 v~n~~~KvYmLy~leP~~elTGG~WytDqdlDvEfIe~L~~~c  178 (297)
T KOG3233|consen  136 VKNSRKKVYMLYDLEPDSELTGGTWYTDQDLDVEFIEVLKQIC  178 (297)
T ss_pred             hcCCCceEEEEecccccccccCCcccccccccHHHHHHHHHHH
Confidence            97                   9999999999999999999864

>COG5111 RPC34 DNA-directed RNA polymerase III, subunit C34 [Transcription]

Probab=99.97  E-value=1.5e-31  Score=216.00  Aligned_cols=106  Identities=31%  Similarity=0.473  Sum_probs=102.6

Q ss_pred             cccceecCCeEEEEEeCccccccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778           2 LANGFLIGGNLLYKVKDPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus         2 ~~~~~~~~~~l~yk~~~~e~a~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      |+.+|++++.|.|+.+-..+|++...|+++|.+||++|+++|++|||.|+|+.|||||++++-||||+||+|++||+|||
T Consensus        57 li~l~rq~~vL~y~~v~~~ea~~~~tm~~~E~~vYs~i~~SG~EGiW~Ktik~rTNlh~~vV~kcLkSlESkr~vKSvKs  136 (301)
T COG5111          57 LISLFRQKGVLYYKGVLESEASPINTMDDYELTVYSLISQSGGEGIWLKTIKDRTNLHHNVVGKCLKSLESKRIVKSVKS  136 (301)
T ss_pred             hhhHHhcCCEEEEeeeecccCCcccccchHHHHHHHHHHhcCCCceehhhhhhhccCcHHHHHHHHHHHHHHHHHHHhhh
Confidence            57889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cc-------------------CCcccccCccccccchhhhhhhhh
Q psy7778          82 VA-------------------NIEYLTEGTVNAMVLPSRKKREER  107 (117)
Q Consensus        82 V~-------------------gg~wYtdg~~D~~fI~~l~~~~~~  107 (117)
                      |+                   ||+|||||++|.+||+.|++--+|
T Consensus       137 vKnptRKiYmLYdlvPS~eiTGGpWFtD~elDvEfi~~ll~ii~r  181 (301)
T COG5111         137 VKNPTRKIYMLYDLVPSEEITGGPWFTDNELDVEFIARLLEIIER  181 (301)
T ss_pred             hcCCCceEEEEecccccccccCCCccccCcccHHHHHHHHHHHHH
Confidence            97                   999999999999999999987766

>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=98.09  E-value=1.8e-05  Score=48.99  Aligned_cols=56  Identities=11%  Similarity=0.184  Sum_probs=51.3

Q ss_pred             CCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      +||+.+..|+..|...+..++-..+|...++++.+.++++++.||.+|||....+-
T Consensus         2 glt~~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~~~~   57 (62)
T PF12802_consen    2 GLTPSQFRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKKGLVERERDP   57 (62)
T ss_dssp             TSTHHHHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE-S
T ss_pred             ccCHHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCC
Confidence            68999999999999999999999999999999999999999999999999887654

...

>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]

Probab=98.03  E-value=1.3e-05  Score=64.99  Aligned_cols=57  Identities=28%  Similarity=0.451  Sum_probs=52.3

Q ss_pred             cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778          24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      ...+|+++|+.|..+|.+.|+. |=.+||++++|+|.+++.|+|+.||++|||+..|.
T Consensus       189 ~~~~L~~~e~~il~~i~~~GGr-i~Q~eL~r~lglsktTvsR~L~~LEk~GlIe~~K~  245 (258)
T COG2512         189 NEYDLNEDEKEILDLIRERGGR-ITQAELRRALGLSKTTVSRILRRLEKRGLIEKEKK  245 (258)
T ss_pred             ccCCCCHHHHHHHHHHHHhCCE-EeHHHHHHhhCCChHHHHHHHHHHHhCCceEEEEe
Confidence            3478999999999999988864 88999999999999999999999999999999874

>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=98.00  E-value=2.7e-05  Score=46.92  Aligned_cols=48  Identities=25%  Similarity=0.410  Sum_probs=40.9

Q ss_pred             CCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCee
Q psy7778          28 SDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIK   77 (117)
Q Consensus        28 L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK   77 (117)
                      |++-++.|+.+|.+  +.++-.++|..++|++.+.+++.|+.|+.+|+|+
T Consensus         1 l~~~~~~Il~~l~~--~~~~t~~ela~~~~is~~tv~~~l~~L~~~g~I~   48 (48)
T PF13412_consen    1 LDETQRKILNYLRE--NPRITQKELAEKLGISRSTVNRYLKKLEEKGLIE   48 (48)
T ss_dssp             --HHHHHHHHHHHH--CTTS-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred             CCHHHHHHHHHHHH--cCCCCHHHHHHHhCCCHHHHHHHHHHHHHCcCcC
Confidence            56778889999998  6669999999999999999999999999999996

...

>PF13730 HTH_36: Helix-turn-helix domain

Probab=97.98  E-value=3.3e-05  Score=47.42  Aligned_cols=51  Identities=22%  Similarity=0.356  Sum_probs=45.0

Q ss_pred             cCCCHHHHHHHHHHHHhc--CCccc--HHHHHhhcCCChHHHHHHHHHHhhcCCe
Q psy7778          26 KDSDNEEKVVYKIIEEAG--NKGIW--MRDIRFKSNLMPTQLNKILKQLETKKII   76 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AG--n~GIW--tkdIk~ktnL~~~~l~K~LK~LE~k~LI   76 (117)
                      ++|++.|++||..|..--  +.|.|  .++|-..+|+..++|.|+|+.||.+|+|
T Consensus         1 ~~Ls~~~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~~~i~~L~~~G~I   55 (55)
T PF13730_consen    1 KNLSPTAKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQRAIKELEEKGLI   55 (55)
T ss_pred             CCCCHHHHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCcCC
Confidence            479999999999988764  45566  6999999999999999999999999987

>PF04182 B-block_TFIIIC: B-block binding subunit of TFIIIC; InterPro: IPR007309 Yeast transcription factor IIIC (TFIIIC) is a multisubunit protein complex that interacts with two control elements of class III promoters called the A and B blocks

Probab=97.95  E-value=2.5e-05  Score=51.95  Aligned_cols=53  Identities=21%  Similarity=0.210  Sum_probs=50.0

Q ss_pred             CHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778          29 DNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        29 ~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      |+.++.|+..|-.|+.+|||+.||-..+|+....+...+|.|+.+|||.....
T Consensus         1 t~~~~~~Le~I~rsR~~Gi~q~~L~~~~~~D~r~i~~~~k~L~~~gLI~k~~~   53 (75)
T PF04182_consen    1 TDIQYCLLERIARSRYNGITQSDLSKLLGIDPRSIFYRLKKLEKKGLIVKQSV   53 (75)
T ss_pred             CchHHHHHHHHHhcCCCCEehhHHHHHhCCCchHHHHHHHHHHHCCCEEEEEe
Confidence            46789999999999999999999999999999999999999999999988766

This family represents the subunit within TFIIIC involved in B-block binding []. Although defined as a yeast protein, it is also found in a number of other organisms.

>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=97.83  E-value=2.7e-05  Score=49.93  Aligned_cols=52  Identities=19%  Similarity=0.222  Sum_probs=47.7

Q ss_pred             CCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778          27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK   80 (117)
Q Consensus        27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK   80 (117)
                      +|++.|..||..+-  .+.+.-..+|...+|++.+++.++|+.|+.+|||....
T Consensus         5 gLs~~E~~vy~~Ll--~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~~   56 (68)
T PF01978_consen    5 GLSENEAKVYLALL--KNGPATAEEIAEELGISRSTVYRALKSLEEKGLVEREE   56 (68)
T ss_dssp             CHHHHHHHHHHHHH--HHCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CcCHHHHHHHHHHH--HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEc
Confidence            68889999998887  56678899999999999999999999999999999876

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.

>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases

Probab=97.75  E-value=0.00015  Score=47.40  Aligned_cols=58  Identities=16%  Similarity=0.189  Sum_probs=51.3

Q ss_pred             HHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCccc
Q psy7778          30 NEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYL   88 (117)
Q Consensus        30 ~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wY   88 (117)
                      +-+..|+.++..+|.+|+-..+|-.+.|++...++++|..|+.+|+|-...+ ..+.|.
T Consensus         6 ~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~~~~-~~~~W~   63 (68)
T smart00550        6 SLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCKQGG-TPPLWK   63 (68)
T ss_pred             HHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCC-CCCceE
Confidence            3567899999999999999999999999999999999999999999977554 556775

Helix-turn-helix-containing domain. Also known as Zab.

>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance

Probab=97.69  E-value=0.00021  Score=44.02  Aligned_cols=53  Identities=21%  Similarity=0.321  Sum_probs=46.9

Q ss_pred             CCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          28 SDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        28 L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      ||..|..+...|.+.|+  +-..+|...+++..+.++++++.||.+|||..-.+-
T Consensus         1 lt~~q~~iL~~l~~~~~--~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~~~~   53 (59)
T PF01047_consen    1 LTPSQFRILRILYENGG--ITQSELAEKLGISRSTVTRIIKRLEKKGLIERERDP   53 (59)
T ss_dssp             STHHHHHHHHHHHHHSS--EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEET
T ss_pred             CCHHHHHHHHHHHHcCC--CCHHHHHHHHCCChhHHHHHHHHHHHCCCEEeccCC
Confidence            57789999999998776  899999999999999999999999999999877654

This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....

>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family

Probab=97.62  E-value=0.00022  Score=49.71  Aligned_cols=57  Identities=19%  Similarity=0.232  Sum_probs=53.0

Q ss_pred             CCCHHHHHHHHHHH--HhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          27 DSDNEEKVVYKIIE--EAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        27 ~L~~eE~lVY~~Ie--~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      +|+..|..|...|.  .+.+.|+-..+|...++++.+.++++++.||.+|+|..+.+-.
T Consensus        22 ~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r~~~~~   80 (109)
T TIGR01889        22 NLSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLSKKGYLSKERSED   80 (109)
T ss_pred             CCCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEeccCCcc
Confidence            79999999999998  6677889999999999999999999999999999999998865

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.

>COG1846 MarR Transcriptional regulators [Transcription]

Probab=97.48  E-value=0.00044  Score=46.12  Aligned_cols=54  Identities=20%  Similarity=0.318  Sum_probs=51.0

Q ss_pred             CCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          28 SDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        28 L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      |+..|..|+..|...+..+.  .+|..++++..+.+++.++.||.+|||+..++-.
T Consensus        20 lt~~q~~~L~~l~~~~~~~~--~~la~~l~i~~~~vt~~l~~Le~~glv~r~~~~~   73 (126)
T COG1846          20 LTPPQYQVLLALYEAGGITV--KELAERLGLDRSTVTRLLKRLEDKGLIERLRDPE   73 (126)
T ss_pred             CCHHHHHHHHHHHHhCCCcH--HHHHHHHCCCHHHHHHHHHHHHHCCCeeecCCcc
Confidence            89999999999999998888  9999999999999999999999999999998865

>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=97.34  E-value=0.00085  Score=41.99  Aligned_cols=55  Identities=13%  Similarity=0.230  Sum_probs=43.1

Q ss_pred             CCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          28 SDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        28 L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      ||..|..|...|. ..+.++-..+|...++++.+.+++.|+.|+.+|||....+-.
T Consensus         1 lt~~q~~vL~~l~-~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~~~~~   55 (68)
T PF13463_consen    1 LTRPQWQVLRALA-HSDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVEKERDPH   55 (68)
T ss_dssp             --HHHHHHHHHHT---TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEESS
T ss_pred             CCHHHHHHHHHHH-ccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecCCCC
Confidence            5678888888888 667788889999999999999999999999999998777654

>PRK10870 transcriptional repressor MprA; Provisional

Probab=97.29  E-value=0.0008  Score=50.86  Aligned_cols=59  Identities=15%  Similarity=0.127  Sum_probs=54.1

Q ss_pred             ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      --+||..+..|...|...++.++-..+|...++++.++++++++.||++|||....+-.
T Consensus        50 ~~gLt~~q~~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~R~~~~~  108 (176)
T PRK10870         50 AQGINETLFMALITLESQENHSIQPSELSCALGSSRTNATRIADELEKRGWIERRESDN  108 (176)
T ss_pred             HCCCCHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCC
Confidence            35789999999999998889999999999999999999999999999999999988764

>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein

Probab=97.26  E-value=0.0012  Score=42.94  Aligned_cols=54  Identities=20%  Similarity=0.391  Sum_probs=48.7

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      -+|+..|..|+.+|...|  ++-.++|...++++++.+++.|+.|+++++|...++
T Consensus         6 ~~l~~~~~~il~~l~~~~--~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~~~   59 (101)
T smart00347        6 LGLTPTQFLVLRILYEEG--PLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRLPS   59 (101)
T ss_pred             cCCCHHHHHHHHHHHHcC--CcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEecCC
Confidence            468899999999999866  688889999999999999999999999999987755

>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp

Probab=97.07  E-value=0.003  Score=42.09  Aligned_cols=52  Identities=17%  Similarity=0.245  Sum_probs=43.6

Q ss_pred             HHhcCCc-ccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccC
Q psy7778          40 EEAGNKG-IWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEG   91 (117)
Q Consensus        40 e~AGn~G-IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg   91 (117)
                      ...++.+ +-.++|..++|+|.+.+.+++..|+..|+|++.++.+||-+....
T Consensus        18 a~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~~G~~GGy~L~~~   70 (83)
T PF02082_consen   18 ARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIESSRGRGGGYRLARP   70 (83)
T ss_dssp             HCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETSTTSEEEESS-
T ss_pred             HhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEecCCCCCceeecCC
Confidence            3334444 999999999999999999999999999999999999999877653

(strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.

>TIGR00498 lexA SOS regulatory protein LexA

Probab=97.04  E-value=0.0026  Score=48.04  Aligned_cols=64  Identities=20%  Similarity=0.175  Sum_probs=54.3

Q ss_pred             cCCCHHHHHHHHHHHHh---cCCcccHHHHHhhcCCC-hHHHHHHHHHHhhcCCeeeeccccCCcccc
Q psy7778          26 KDSDNEEKVVYKIIEEA---GNKGIWMRDIRFKSNLM-PTQLNKILKQLETKKIIKAVKSVANIEYLT   89 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~A---Gn~GIWtkdIk~ktnL~-~~~l~K~LK~LE~k~LIK~VKsV~gg~wYt   89 (117)
                      ++||+.|..|+..|.+.   +..+.-.++|-..+|+. .+++.+.|+.||.+|+|+...+...|.++.
T Consensus         2 ~~lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~g~i~~~~~~~~~~~~~   69 (199)
T TIGR00498         2 KPLTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALERKGYIERDPGKPRAIRIL   69 (199)
T ss_pred             CccCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHHHCCCEecCCCCCCeEEeC
Confidence            46899999999999955   45568899999999999 999999999999999999877665455444

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.

>PRK11512 DNA-binding transcriptional repressor MarR; Provisional

Probab=97.03  E-value=0.0025  Score=45.88  Aligned_cols=56  Identities=14%  Similarity=0.058  Sum_probs=50.9

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      -+||..+..|...|..  +.|+-..+|...+++..+.+++.|+.||.+|||....+-.
T Consensus        36 ~glt~~q~~vL~~l~~--~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~~~~~   91 (144)
T PRK11512         36 LDITAAQFKVLCSIRC--AACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPN   91 (144)
T ss_pred             cCCCHHHHHHHHHHHH--cCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCcc
Confidence            4799999999888864  5689999999999999999999999999999999998865

>PRK13777 transcriptional regulator Hpr; Provisional

Probab=96.90  E-value=0.0031  Score=48.88  Aligned_cols=57  Identities=18%  Similarity=0.096  Sum_probs=50.7

Q ss_pred             ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      --+|+..|..|+.+|...  .|+-.++|-..++++.++++++|+.||.+|||...++-.
T Consensus        40 ~~gLt~~q~~iL~~L~~~--~~itq~eLa~~l~l~~sTvtr~l~rLE~kGlI~R~~~~~   96 (185)
T PRK13777         40 PYDLNINEHHILWIAYHL--KGASISEIAKFGVMHVSTAFNFSKKLEERGYLTFSKKED   96 (185)
T ss_pred             HCCCCHHHHHHHHHHHhC--CCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEecCCCC
Confidence            358999999999888664  589999999999999999999999999999999887654

>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR

Probab=96.89  E-value=0.0039  Score=43.37  Aligned_cols=56  Identities=14%  Similarity=0.290  Sum_probs=49.8

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      -+|+..+..|...|..  +.|+-..+|-..+++..+.+++.|+.||.+|||....+-.
T Consensus        24 ~~lt~~q~~iL~~l~~--~~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~~~~   79 (118)
T TIGR02337        24 HGLTEQQWRILRILAE--QGSMEFTQLANQACILRPSLTGILARLERDGLVTRLKASN   79 (118)
T ss_pred             cCCCHHHHHHHHHHHH--cCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeccCCC
Confidence            5789999988888876  4478889999999999999999999999999999987764

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.

>PRK03573 transcriptional regulator SlyA; Provisional

Probab=96.88  E-value=0.0041  Score=44.48  Aligned_cols=58  Identities=16%  Similarity=0.083  Sum_probs=50.3

Q ss_pred             ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      --+|+..+..|...|...+ .|+-..+|...+++..++++++++.||.+|||....+-.
T Consensus        26 ~~glt~~q~~vL~~l~~~~-~~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~~~~   83 (144)
T PRK03573         26 PLELTQTHWVTLHNIHQLP-PEQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQTCAS   83 (144)
T ss_pred             hcCCCHHHHHHHHHHHHcC-CCCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeecCCC
Confidence            3479999988888887653 467789999999999999999999999999999998754

>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=96.87  E-value=0.0046  Score=40.53  Aligned_cols=57  Identities=26%  Similarity=0.293  Sum_probs=45.1

Q ss_pred             cCCCHHHHHHHHHHHHhcC-Ccc--cHHHHHhhcCCC-hHHHHHHHHHHhhcCCeeeeccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGN-KGI--WMRDIRFKSNLM-PTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn-~GI--WtkdIk~ktnL~-~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      +.||+-|+.||..|.+--. .|.  -.++|....|+. .+.+.+.|+.||.+|+|+...+.
T Consensus         2 ~~LT~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~r~~~~   62 (65)
T PF01726_consen    2 KELTERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKALERKGYIRRDPGK   62 (65)
T ss_dssp             ----HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHHHHTTSEEEGCCS
T ss_pred             CCCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCcCccCCCCC
Confidence            5789989999999887433 455  579999999998 99999999999999999987664

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.

>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial

Probab=96.65  E-value=0.0064  Score=43.18  Aligned_cols=52  Identities=21%  Similarity=0.274  Sum_probs=43.8

Q ss_pred             HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCC
Q psy7778          34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANI   85 (117)
Q Consensus        34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg   85 (117)
                      .+...+..+++..+-..+|..+.++|.+.+.++|+.|+..|+|.+.++..||
T Consensus        13 ~~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~~~g~~gg   64 (130)
T TIGR02944        13 LVLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTSKRGVEGG   64 (130)
T ss_pred             HHHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEecCCCCCC
Confidence            4444555566678999999999999999999999999999999988776655

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.

>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=96.64  E-value=0.0092  Score=37.55  Aligned_cols=48  Identities=15%  Similarity=0.259  Sum_probs=42.4

Q ss_pred             HHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778          31 EEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK   80 (117)
Q Consensus        31 eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK   80 (117)
                      .=..|+..+  +.+.+.-..+|...+|++++++.+.|+.|+.-|||+.++
T Consensus        11 ~R~~Il~~L--~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~~~~   58 (61)
T PF12840_consen   11 TRLRILRLL--ASNGPMTVSELAEELGISQSTVSYHLKKLEEAGLIEVER   58 (61)
T ss_dssp             HHHHHHHHH--HHCSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHH--hcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEec
Confidence            344788888  788999999999999999999999999999999999875

...

>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=96.55  E-value=0.0072  Score=41.49  Aligned_cols=53  Identities=15%  Similarity=0.243  Sum_probs=44.2

Q ss_pred             cCCCHHHHHHHHHHHH--hcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778          26 KDSDNEEKVVYKIIEE--AGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKA   78 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~--AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~   78 (117)
                      .+|++-.+.||++|++  ..+.|+-..+|..+.+|+...|.++|..|...|+|=+
T Consensus        43 ~~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs   97 (102)
T PF08784_consen   43 SGLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNEGHIYS   97 (102)
T ss_dssp             --S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSEEE
T ss_pred             cCCCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhCCeEec
Confidence            3799999999999998  3469999999999999999999999999999998843

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.

>PRK00215 LexA repressor; Validated

Probab=96.52  E-value=0.0096  Score=45.13  Aligned_cols=54  Identities=20%  Similarity=0.238  Sum_probs=47.3

Q ss_pred             CCHHHHHHHHHHHH---hcCCcccHHHHHhhcCC-ChHHHHHHHHHHhhcCCeeeecc
Q psy7778          28 SDNEEKVVYKIIEE---AGNKGIWMRDIRFKSNL-MPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        28 L~~eE~lVY~~Ie~---AGn~GIWtkdIk~ktnL-~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      ||+.|..|+..|.+   .++.++-.++|-..+|+ +.+++++.|+.||.+|+|....+
T Consensus         2 lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~~~~~   59 (205)
T PRK00215          2 LTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALERKGFIRRDPG   59 (205)
T ss_pred             CCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEeCCC
Confidence            67889999999984   45677889999999999 99999999999999999976543

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

Probab=96.52  E-value=0.014  Score=35.41  Aligned_cols=50  Identities=12%  Similarity=0.246  Sum_probs=43.1

Q ss_pred             HHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          30 NEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        30 ~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      ..+..|+..|...+   +-..+|...++++.+.+++.|+.|++.++|....+-
T Consensus         7 ~~~~~il~~l~~~~---~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~~~   56 (78)
T cd00090           7 PTRLRILRLLLEGP---LTVSELAERLGLSQSTVSRHLKKLEEAGLVESRREG   56 (78)
T ss_pred             hHHHHHHHHHHHCC---cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEEEec
Confidence            45677888777654   889999999999999999999999999999987654

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.

>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed

Probab=96.51  E-value=0.0089  Score=44.51  Aligned_cols=72  Identities=15%  Similarity=0.143  Sum_probs=56.6

Q ss_pred             HHHHHHHHHHHhcCCc--ccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccCccccccchhhh
Q psy7778          31 EEKVVYKIIEEAGNKG--IWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGTVNAMVLPSRK  102 (117)
Q Consensus        31 eE~lVY~~Ie~AGn~G--IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg~~D~~fI~~l~  102 (117)
                      -++.|.-++.-|.+.+  +-+++|-.+.|+|.+.|.|++..|...|||.++++.+||-+....-=+-.+-|.+.
T Consensus         7 ~~YAlr~L~~LA~~~~~~~s~~eIA~~~~is~~~L~kIl~~L~~aGlv~S~rG~~GGy~La~~p~eItl~dIi~   80 (153)
T PRK11920          7 TNYAIRMLMYCAANDGKLSRIPEIARAYGVSELFLFKILQPLVEAGLVETVRGRNGGVRLGRPAADISLFDVVR   80 (153)
T ss_pred             HhHHHHHHHHHHhCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeecCCCCCeeecCCHHHCcHHHHHH
Confidence            4666777777665433  67899999999999999999999999999999999999988765544444444443

>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR

Probab=96.37  E-value=0.016  Score=41.82  Aligned_cols=55  Identities=15%  Similarity=0.235  Sum_probs=44.8

Q ss_pred             HHHHHHHHHHHh---cCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCC
Q psy7778          31 EEKVVYKIIEEA---GNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANI   85 (117)
Q Consensus        31 eE~lVY~~Ie~A---Gn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg   85 (117)
                      .++.+.-++.-|   +..-+-.++|..++++|.+.+.|+|..|...|||.++++..||
T Consensus         7 ~~YAl~~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s~~G~~Gg   64 (135)
T TIGR02010         7 GRYAVTAMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKAGLVKSVRGPGGG   64 (135)
T ss_pred             HHHHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEeCCCCC
Confidence            455555555555   3334788999999999999999999999999999999888766

This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.

>COG1959 Predicted transcriptional regulator [Transcription]

Probab=96.35  E-value=0.015  Score=43.28  Aligned_cols=61  Identities=21%  Similarity=0.245  Sum_probs=51.7

Q ss_pred             HHHHHHHHHHHhcCCc---ccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccC
Q psy7778          31 EEKVVYKIIEEAGNKG---IWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEG   91 (117)
Q Consensus        31 eE~lVY~~Ie~AGn~G---IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg   91 (117)
                      -++.|--++.-|.+.|   +-..+|..+.|+|.+.|.|++..|...|||+++++.+||-...--
T Consensus         7 ~~yal~~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~kaGlV~S~rG~~GGy~Lar~   70 (150)
T COG1959           7 GEYALRALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLRKAGLVKSVRGKGGGYRLARP   70 (150)
T ss_pred             HhHHHHHHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHHcCCEEeecCCCCCccCCCC
Confidence            4667777777776544   668999999999999999999999999999999999988765443

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=96.22  E-value=0.02  Score=38.97  Aligned_cols=53  Identities=21%  Similarity=0.376  Sum_probs=46.0

Q ss_pred             CCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          28 SDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        28 L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      |++.++.|+.++...+  .+-..+|-.++|++.+++.+.++.|+.+|+|+.+..+
T Consensus         1 ld~~D~~il~~L~~~~--~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~~~~~~   53 (108)
T smart00344        1 LDEIDRKILEELQKDA--RISLAELAKKVGLSPSTVHNRVKRLEEEGVIKGYTAV   53 (108)
T ss_pred             CCHHHHHHHHHHHHhC--CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeceEEE
Confidence            5677888888998865  5889999999999999999999999999999965543

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

>PRK11014 transcriptional repressor NsrR; Provisional

Probab=96.18  E-value=0.021  Score=41.41  Aligned_cols=60  Identities=17%  Similarity=0.147  Sum_probs=51.1

Q ss_pred             HHHHHHHHHHHhcC-Cc--ccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCccccc
Q psy7778          31 EEKVVYKIIEEAGN-KG--IWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTE   90 (117)
Q Consensus        31 eE~lVY~~Ie~AGn-~G--IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtd   90 (117)
                      -++.+-.+|..|.. .|  +-.++|-.+.|++.+.|.|+|..|+..|||+++++..||-....
T Consensus         7 ~~YAl~~~i~la~~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~~G~~GG~~l~~   69 (141)
T PRK11014          7 TDYGLRALIYMASLPEGRMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVRGKNGGIRLGK   69 (141)
T ss_pred             HhHHHHHHHHHhcCCCCCccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEecCCCCCeeecC
Confidence            56777778877743 33  66799999999999999999999999999999999998877764

>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein

Probab=96.15  E-value=0.022  Score=43.56  Aligned_cols=55  Identities=20%  Similarity=0.292  Sum_probs=48.9

Q ss_pred             ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778          25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      ..++++.+..|+..|...|  ++-..+|...++++.+++++.|+.|+.+|+|...+.
T Consensus       138 ~~~ls~~~~~IL~~l~~~g--~~s~~eia~~l~is~stv~r~L~~Le~~GlI~r~~~  192 (203)
T TIGR01884       138 LAGLSREELKVLEVLKAEG--EKSVKNIAKKLGKSLSTISRHLRELEKKGLVEQKGR  192 (203)
T ss_pred             hcCCCHHHHHHHHHHHHcC--CcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcC
Confidence            4578888899999997654  688999999999999999999999999999998864

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.

>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=96.11  E-value=0.023  Score=36.49  Aligned_cols=44  Identities=20%  Similarity=0.413  Sum_probs=39.3

Q ss_pred             HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeee
Q psy7778          34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAV   79 (117)
Q Consensus        34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V   79 (117)
                      .||.+-+  ++..+-+.+|....|..++.++..++.|+.+|||.-.
T Consensus        12 ~Iy~l~~--~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~~~   55 (60)
T PF01325_consen   12 AIYELSE--EGGPVRTKDIAERLGVSPPTVTEMLKRLAEKGLVEYE   55 (60)
T ss_dssp             HHHHHHH--CTSSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHc--CCCCccHHHHHHHHCCChHHHHHHHHHHHHCCCEEec
Confidence            6887776  8889999999999999999999999999999999754

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 ....

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor

Probab=96.10  E-value=0.032  Score=32.47  Aligned_cols=46  Identities=9%  Similarity=0.239  Sum_probs=39.4

Q ss_pred             HHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778          33 KVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK   80 (117)
Q Consensus        33 ~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK   80 (117)
                      ..|+..+.+.  .++-..+|....+++.+.+.+.|+.|+.+++|....
T Consensus         3 ~~il~~l~~~--~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~~~   48 (53)
T smart00420        3 QQILELLAQQ--GKVSVEELAELLGVSEMTIRRDLNKLEEQGLLTRVH   48 (53)
T ss_pred             HHHHHHHHHc--CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEee
Confidence            3577777653  579999999999999999999999999999997654

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=95.98  E-value=0.03  Score=41.59  Aligned_cols=69  Identities=14%  Similarity=0.117  Sum_probs=57.7

Q ss_pred             ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc-c-CCcccccCccc
Q psy7778          25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV-A-NIEYLTEGTVN   94 (117)
Q Consensus        25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV-~-gg~wYtdg~~D   94 (117)
                      .=+|++-|..||..+=+ -|.+.-+-+|..+.|+..++++|+|++|...|||...|-- . ||..|-=-..|
T Consensus        22 ~~GLs~~Dv~v~~~LL~-~~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~~~~Ggy~yiY~~i~   92 (126)
T COG3355          22 VYGLSELDVEVYKALLE-ENGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNLKGGGYYYLYKPID   92 (126)
T ss_pred             HhCCcHHHHHHHHHHHh-hcCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeeccCCCceeEEEecCC
Confidence            45789999999998887 6788899999999999999999999999999999988865 3 66666543333

>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain

Probab=95.97  E-value=0.033  Score=38.30  Aligned_cols=57  Identities=19%  Similarity=0.110  Sum_probs=46.8

Q ss_pred             cccCCCHHHHHHHHHHHH-h-----cCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778          24 KLKDSDNEEKVVYKIIEE-A-----GNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK   80 (117)
Q Consensus        24 k~~~L~~eE~lVY~~Ie~-A-----Gn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK   80 (117)
                      ...++++.+..++-.|-. .     ...++-..+|-..+|+..++++|+|+.||.+|+|..-.
T Consensus        19 ~~~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~r~~   81 (95)
T TIGR01610        19 PGADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSDAIKSLARRRIIFRQG   81 (95)
T ss_pred             HhCCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeec
Confidence            466777777766665542 1     47889999999999999999999999999999998544

This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.

>PF02295 z-alpha: Adenosine deaminase z-alpha domain; InterPro: IPR000607 Double-stranded RNA-specific adenosine deaminase (3

Probab=95.75  E-value=0.027  Score=37.10  Aligned_cols=58  Identities=12%  Similarity=0.162  Sum_probs=48.7

Q ss_pred             HHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCccc
Q psy7778          30 NEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYL   88 (117)
Q Consensus        30 ~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wY   88 (117)
                      +.|..|+++++++|..++....+-...+.|...||++|=.|+.+|.|..... ....|+
T Consensus         4 ~~ee~Il~~L~~~g~~~a~~ia~~~~L~~~kk~VN~~LY~L~k~g~v~k~~~-~PP~W~   61 (66)
T PF02295_consen    4 DLEEKILDFLKELGGSTATAIAKALGLSVPKKEVNRVLYRLEKQGKVCKEGG-TPPKWS   61 (66)
T ss_dssp             HHHHHHHHHHHHHTSSEEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEECS-SSTEEE
T ss_pred             hHHHHHHHHHHhcCCccHHHHHHHhCcchhHHHHHHHHHHHHHCCCEeeCCC-CCCceE
Confidence            4577999999999999999999999999999999999999999999975433 344453

5 from EC) converts multiple adenosines to inosines and creates I/U mismatched base pairs in double-helical RNA substrates without apparent sequence specificity. DRADA has been found to modify adenosines in AU-rich regions more frequently, probably due to the relative ease of melting A/U base pairs compared to G/C base pairs. The protein functions to modify viral RNA genomes, and may be responsible for hypermutation of certain negative-stranded viruses. DRADA edits the mRNAs for the glutamate receptor subunits by site-selective adenosine deamination. The DRADA repeat is also found in viral E3 proteins, which contain a double-stranded RNA-binding domain.; GO: 0003723 RNA binding, 0003726 double-stranded RNA adenosine deaminase activity; PDB: 1OYI_A 3EYI_A 2L4M_A 2HEO_D 1J75_A 1SFU_B 3IRR_B 2ACJ_C 3F22_B 2L54_A ....

>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities

Probab=95.68  E-value=0.022  Score=34.84  Aligned_cols=44  Identities=14%  Similarity=0.283  Sum_probs=35.3

Q ss_pred             HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778          34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKA   78 (117)
Q Consensus        34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~   78 (117)
                      .|..++.+++ .|+-..+|-.++|+|.+++.+.|++|+..|++..
T Consensus         7 ~iL~~l~~~~-~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~~   50 (52)
T PF09339_consen    7 RILEALAESG-GPLTLSEIARALGLPKSTVHRLLQTLVEEGYVER   50 (52)
T ss_dssp             HHHHCHHCTB-SCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHcCC-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCeec
Confidence            3455555554 4478899999999999999999999999999975

One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.

>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=95.59  E-value=0.047  Score=33.65  Aligned_cols=36  Identities=19%  Similarity=0.188  Sum_probs=32.8

Q ss_pred             CcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778          45 KGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK   80 (117)
Q Consensus        45 ~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK   80 (117)
                      ..+-..+|...+|++...++++|+.|+.+|+|....
T Consensus        24 ~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~~~   59 (67)
T cd00092          24 LPLTRQEIADYLGLTRETVSRTLKELEEEGLISRRG   59 (67)
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence            457788999999999999999999999999998765

>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators

Probab=95.56  E-value=0.046  Score=37.57  Aligned_cols=56  Identities=9%  Similarity=0.161  Sum_probs=45.0

Q ss_pred             HHHHHHHHHhcCCcccHHHHHhhc-----CCChHHHHHHHHHHhhcCCeeeeccccCCcccc
Q psy7778          33 KVVYKIIEEAGNKGIWMRDIRFKS-----NLMPTQLNKILKQLETKKIIKAVKSVANIEYLT   89 (117)
Q Consensus        33 ~lVY~~Ie~AGn~GIWtkdIk~kt-----nL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYt   89 (117)
                      ..|+.++.++ +.-+-..+|-.+.     ++..++|-|+|+.|+..|+|..+..-.+..+|.
T Consensus         4 ~~Il~~l~~~-~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~~~~~~~~~y~   64 (116)
T cd07153           4 LAILEVLLES-DGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIELGDGKARYE   64 (116)
T ss_pred             HHHHHHHHhC-CCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEEEeCCCceEEE
Confidence            4688888776 4556666666555     689999999999999999999998777767774

Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.

>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator)

Probab=95.54  E-value=0.04  Score=38.71  Aligned_cols=55  Identities=16%  Similarity=0.265  Sum_probs=42.8

Q ss_pred             HHHHHHHHHHHhc---CCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCC
Q psy7778          31 EEKVVYKIIEEAG---NKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANI   85 (117)
Q Consensus        31 eE~lVY~~Ie~AG---n~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg   85 (117)
                      .+..+.-++.-|.   ...+-..+|...+++|.+.+.++|..|+..|+|.+..+-.||
T Consensus         7 ~~~al~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~~~g~~gg   64 (132)
T TIGR00738         7 TEYALRALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRRAGLVESVRGPGGG   64 (132)
T ss_pred             HHHHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEeccCCCCC
Confidence            3444444444443   346899999999999999999999999999999987665544

This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.

>PRK10857 DNA-binding transcriptional regulator IscR; Provisional

Probab=95.52  E-value=0.037  Score=41.92  Aligned_cols=55  Identities=13%  Similarity=0.218  Sum_probs=44.6

Q ss_pred             HHHHHHHHHHHh---cCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCC
Q psy7778          31 EEKVVYKIIEEA---GNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANI   85 (117)
Q Consensus        31 eE~lVY~~Ie~A---Gn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg   85 (117)
                      .+..+.-++.-|   +...+-.++|..+.|+|.+.+.|+|..|...|||.+..+..||
T Consensus         7 ~~yAl~~l~~lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s~rG~~GG   64 (164)
T PRK10857          7 GRYAVTAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSVRGPGGG   64 (164)
T ss_pred             HHHHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCCCCCCC
Confidence            455555555444   3345788999999999999999999999999999999888765

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

Probab=95.50  E-value=0.021  Score=38.42  Aligned_cols=42  Identities=21%  Similarity=0.250  Sum_probs=35.9

Q ss_pred             CCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCC
Q psy7778          44 NKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANI   85 (117)
Q Consensus        44 n~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg   85 (117)
                      +..+.-++|+..+++++..+++.|+.||..|+|+.-|...++
T Consensus        12 ~~~~~f~~L~~~l~lt~g~Ls~hL~~Le~~GyV~~~k~~~~~   53 (80)
T PF13601_consen   12 NEEATFSELKEELGLTDGNLSKHLKKLEEAGYVEVEKEFEGR   53 (80)
T ss_dssp             HSEEEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEE-SSS
T ss_pred             cCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEEEeccCC
Confidence            678999999999999999999999999999999998877644

>COG1522 Lrp Transcriptional regulators [Transcription]

Probab=95.32  E-value=0.071  Score=38.00  Aligned_cols=57  Identities=19%  Similarity=0.376  Sum_probs=50.6

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccC
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVAN   84 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~g   84 (117)
                      ..|++-++.+++++..-+.  +-.++|..+.|++.+.+.+.++.||..|+|+-..-+-+
T Consensus         4 ~~lD~~D~~IL~~L~~d~r--~~~~eia~~lglS~~~v~~Ri~~L~~~GiI~~~~~~v~   60 (154)
T COG1522           4 MKLDDIDRRILRLLQEDAR--ISNAELAERVGLSPSTVLRRIKRLEEEGVIKGYTAVLD   60 (154)
T ss_pred             ccccHHHHHHHHHHHHhCC--CCHHHHHHHHCCCHHHHHHHHHHHHHCCceeeEEEEEC
Confidence            4588888888888888877  88999999999999999999999999999998877653

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

Probab=95.30  E-value=0.057  Score=35.79  Aligned_cols=45  Identities=33%  Similarity=0.523  Sum_probs=36.4

Q ss_pred             HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778          34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKA   78 (117)
Q Consensus        34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~   78 (117)
                      +|+++++...+.|.=..+|-..+||+...+.+.|+.|+++|||+.
T Consensus         7 Ii~~IL~~l~~~~~~~t~i~~~~~L~~~~~~~yL~~L~~~gLI~~   51 (77)
T PF14947_consen    7 IIFDILKILSKGGAKKTEIMYKANLNYSTLKKYLKELEEKGLIKK   51 (77)
T ss_dssp             HHHHHHHHH-TT-B-HHHHHTTST--HHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHhCcCHHHHHHHHHHHHHCcCeeC
Confidence            678888887788888899999999999999999999999999954

>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function

Probab=95.13  E-value=0.083  Score=37.22  Aligned_cols=53  Identities=15%  Similarity=0.186  Sum_probs=46.6

Q ss_pred             CCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          28 SDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        28 L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      +++.+..|..++..+|.+=.|+  |-..+++|...+..+++.||..|||..|.+=
T Consensus         5 ~~~l~~~IL~hl~~~~~Dy~k~--ia~~l~~~~~~v~~~l~~Le~~GLler~~g~   57 (92)
T PF10007_consen    5 LDPLDLKILQHLKKAGPDYAKS--IARRLKIPLEEVREALEKLEEMGLLERVEGK   57 (92)
T ss_pred             cChhHHHHHHHHHHHCCCcHHH--HHHHHCCCHHHHHHHHHHHHHCCCeEEecCc
Confidence            5667889999999999998875  4667899999999999999999999998753

>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional

Probab=95.05  E-value=0.059  Score=46.72  Aligned_cols=53  Identities=23%  Similarity=0.275  Sum_probs=47.1

Q ss_pred             CCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778          27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      +|++.|..|...|...|  ++-+.+|-.++++..+.++++++.|+++|||.....
T Consensus         3 ~Lt~~e~~vL~~L~~~~--~~s~~eLA~~l~l~~~tVt~~i~~Le~kGlV~~~~~   55 (489)
T PRK04172          3 ELHPNEKKVLKALKELK--EATLEELAEKLGLPPEAVMRAAEWLEEKGLVKVEER   55 (489)
T ss_pred             CCCHHHHHHHHHHHhCC--CCCHHHHHHHhCcCHHHHHHHHHHHHhCCCEEEEee
Confidence            68998888998996544  789999999999999999999999999999997654

>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A

Probab=94.81  E-value=0.11  Score=34.03  Aligned_cols=50  Identities=20%  Similarity=0.155  Sum_probs=40.9

Q ss_pred             HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccC
Q psy7778          34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVAN   84 (117)
Q Consensus        34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~g   84 (117)
                      .|++.|.+. +.++-|+||-..++|...++.+.|..||+.|.|+.++.=+|
T Consensus         4 ~Il~~i~~~-~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~~~~~~rG   53 (62)
T PF04703_consen    4 KILEYIKEQ-NGPLKTREIADALGLSIYQARYYLEKLEKEGKVERSPVRRG   53 (62)
T ss_dssp             CHHHHHHHH-TS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEES-SSS
T ss_pred             HHHHHHHHc-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCCC
Confidence            366777776 77899999999999999999999999999999998775443

>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR

Probab=94.73  E-value=0.089  Score=40.18  Aligned_cols=47  Identities=17%  Similarity=0.221  Sum_probs=40.5

Q ss_pred             HHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778          33 KVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        33 ~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      ..|+..+...|.  +-..+|...++++.+++++.|+.||.+|||.....
T Consensus         4 ~~IL~~L~~~~~--~t~~eLA~~lgis~~tV~~~L~~Le~~GlV~r~~~   50 (203)
T TIGR02702         4 EDILSYLLKQGQ--ATAAALAEALAISPQAVRRHLKDLETEGLIEYEAV   50 (203)
T ss_pred             HHHHHHHHHcCC--CCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEeec
Confidence            456777766554  99999999999999999999999999999988753

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.

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=94.66  E-value=0.073  Score=31.70  Aligned_cols=35  Identities=14%  Similarity=0.250  Sum_probs=31.4

Q ss_pred             cc-cHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778          46 GI-WMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK   80 (117)
Q Consensus        46 GI-WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK   80 (117)
                      -+ -.++|....+++.+.+.++|+.|++.|+|..+.
T Consensus        19 ~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~~~~   54 (60)
T smart00345       19 KLPSERELAAQLGVSRTTVREALSRLEAEGLVQRRP   54 (60)
T ss_pred             cCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence            45 689999999999999999999999999987654

>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor

Probab=94.65  E-value=0.12  Score=30.41  Aligned_cols=38  Identities=11%  Similarity=0.204  Sum_probs=33.9

Q ss_pred             CCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778          44 NKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        44 n~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      +..+-..+|...++++.+.++++|+.|+++++|.....
T Consensus         8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~~~   45 (66)
T smart00418        8 EGELCVCELAEILGLSQSTVSHHLKKLREAGLVESRRE   45 (66)
T ss_pred             cCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeeec
Confidence            55678889999999999999999999999999986653

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=94.56  E-value=0.11  Score=33.85  Aligned_cols=45  Identities=13%  Similarity=0.268  Sum_probs=38.5

Q ss_pred             HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeee
Q psy7778          34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAV   79 (117)
Q Consensus        34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V   79 (117)
                      .|..+|...+ .++-..+|-..++++.+++.+.|+.|+..|+|...
T Consensus         9 ~Il~~l~~~~-~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~   53 (91)
T smart00346        9 AVLRALAEEP-GGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQD   53 (91)
T ss_pred             HHHHHHHhCC-CCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeec
Confidence            4666675542 47999999999999999999999999999999874

>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family

Probab=94.21  E-value=0.17  Score=36.78  Aligned_cols=52  Identities=19%  Similarity=0.207  Sum_probs=42.9

Q ss_pred             CCCHHHHHHHHHHHHhcCCcccHHHHHhh----cCCChHHHHHHHHHHhhcCCeeeec
Q psy7778          27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFK----SNLMPTQLNKILKQLETKKIIKAVK   80 (117)
Q Consensus        27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~k----tnL~~~~l~K~LK~LE~k~LIK~VK   80 (117)
                      .||+-|..|..+|=..|  ++-.++|...    .++..+++...|+.|+.||+|..-+
T Consensus         1 ~Lt~~E~~VM~vlW~~~--~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~KG~v~~~k   56 (130)
T TIGR02698         1 SISDAEWEVMRVVWTLG--ETTSRDIIRILAEKKDWSDSTIKTLLGRLVDKGCLTTEK   56 (130)
T ss_pred             CCCHHHHHHHHHHHcCC--CCCHHHHHHHHhhccCCcHHHHHHHHHHHHHCCceeeec
Confidence            37888999999998766  4677885544    5799999999999999999998654

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.

>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities

Probab=93.88  E-value=0.25  Score=29.64  Aligned_cols=41  Identities=15%  Similarity=0.306  Sum_probs=32.6

Q ss_pred             HHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778          35 VYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKA   78 (117)
Q Consensus        35 VY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~   78 (117)
                      |...+.+   .-.-..+|...++++++++++.|+.|+..|+|++
T Consensus         7 Il~~L~~---~~~~~~el~~~l~~s~~~vs~hL~~L~~~glV~~   47 (47)
T PF01022_consen    7 ILKLLSE---GPLTVSELAEELGLSQSTVSHHLKKLREAGLVEK   47 (47)
T ss_dssp             HHHHHTT---SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHh---CCCchhhHHHhccccchHHHHHHHHHHHCcCeeC
Confidence            3444444   3466789999999999999999999999999974

One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....

>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein

Probab=93.76  E-value=0.15  Score=29.40  Aligned_cols=33  Identities=21%  Similarity=0.260  Sum_probs=29.6

Q ss_pred             ccHHHHHhhcCCChHHHHHHHHHHhhcCCeeee
Q psy7778          47 IWMRDIRFKSNLMPTQLNKILKQLETKKIIKAV   79 (117)
Q Consensus        47 IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V   79 (117)
                      +-.++|...++++.+.++++|+.|+..|+|...
T Consensus         9 ~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~~~   41 (48)
T smart00419        9 LTRQEIAELLGLTRETVSRTLKRLEKEGLISRE   41 (48)
T ss_pred             cCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            456789999999999999999999999999753

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

Probab=93.62  E-value=0.13  Score=29.91  Aligned_cols=30  Identities=30%  Similarity=0.376  Sum_probs=25.5

Q ss_pred             ccHHHHHhhcCCChHHHHHHHHHHhhcCCe
Q psy7778          47 IWMRDIRFKSNLMPTQLNKILKQLETKKII   76 (117)
Q Consensus        47 IWtkdIk~ktnL~~~~l~K~LK~LE~k~LI   76 (117)
                      +-..||-.-.|+...+++|+|+.|+.+|+|
T Consensus         3 mtr~diA~~lG~t~ETVSR~l~~l~~~glI   32 (32)
T PF00325_consen    3 MTRQDIADYLGLTRETVSRILKKLERQGLI   32 (32)
T ss_dssp             --HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred             cCHHHHHHHhCCcHHHHHHHHHHHHHcCCC
Confidence            346789999999999999999999999997

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 ....

>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins

Probab=93.59  E-value=0.18  Score=35.11  Aligned_cols=62  Identities=11%  Similarity=0.139  Sum_probs=45.7

Q ss_pred             CCHHHHHHHHHHHHhcCCcccHHHHHhh-----cCCChHHHHHHHHHHhhcCCeeeeccccCCccccc
Q psy7778          28 SDNEEKVVYKIIEEAGNKGIWMRDIRFK-----SNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTE   90 (117)
Q Consensus        28 L~~eE~lVY~~Ie~AGn~GIWtkdIk~k-----tnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtd   90 (117)
                      +|+.-..|+.+|.++.. -.--.+|-..     .++..++|=|+|+.|+..|+|..+..-.+..+|.=
T Consensus         6 ~T~~R~~Il~~l~~~~~-~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~~~~~~~~~~Y~~   72 (120)
T PF01475_consen    6 LTPQRLAILELLKESPE-HLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRKIEFGDGESRYEL   72 (120)
T ss_dssp             HHHHHHHHHHHHHHHSS-SEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEETTSEEEEEE
T ss_pred             CCHHHHHHHHHHHcCCC-CCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEEEEcCCCcceEee
Confidence            35566799999999987 4444443333     47889999999999999999999988766666653

These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....

>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon

Probab=93.46  E-value=0.36  Score=27.95  Aligned_cols=43  Identities=12%  Similarity=0.244  Sum_probs=35.8

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhh
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLET   72 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~   72 (117)
                      ..||++|+.++.++.    .|...++|-..++++.+++.+.++.+..
T Consensus         2 ~~l~~~e~~i~~~~~----~g~s~~eia~~l~is~~tv~~~~~~~~~   44 (58)
T smart00421        2 ASLTPREREVLRLLA----EGLTNKEIAERLGISEKTVKTHLSNIMR   44 (58)
T ss_pred             CCCCHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            358888888777652    6789999999999999999999887754

lux regulon (activates the bioluminescence operon

>COG1378 Predicted transcriptional regulators [Transcription]

Probab=93.44  E-value=0.26  Score=39.65  Aligned_cols=52  Identities=19%  Similarity=0.287  Sum_probs=46.5

Q ss_pred             CCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778          27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK   80 (117)
Q Consensus        27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK   80 (117)
                      |||..|-.||-.+=.-|..  --++|-..+|+|++.+-.+|++||.||+|....
T Consensus        13 Glt~yEa~vY~aLl~~g~~--tA~eis~~sgvP~~kvY~vl~sLe~kG~v~~~~   64 (247)
T COG1378          13 GLTEYEAKVYLALLCLGEA--TAKEISEASGVPRPKVYDVLRSLEKKGLVEVIE   64 (247)
T ss_pred             CCCHHHHHHHHHHHHhCCc--cHHHHHHHcCCCchhHHHHHHHHHHCCCEEeeC
Confidence            7899999999988887764  458999999999999999999999999999873

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

Probab=93.37  E-value=0.32  Score=29.38  Aligned_cols=33  Identities=15%  Similarity=0.254  Sum_probs=29.9

Q ss_pred             cHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778          48 WMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK   80 (117)
Q Consensus        48 WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK   80 (117)
                      -.++|...++++.+.+++.|+.|+..|+|....
T Consensus        27 ~~~~la~~~~is~~~v~~~l~~L~~~G~i~~~~   59 (66)
T cd07377          27 SERELAEELGVSRTTVREALRELEAEGLVERRP   59 (66)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence            388999999999999999999999999987653

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

>PRK09391 fixK transcriptional regulator FixK; Provisional

Probab=93.10  E-value=0.29  Score=37.46  Aligned_cols=53  Identities=25%  Similarity=0.270  Sum_probs=41.9

Q ss_pred             ccCCCHHHHHHHHHHHHhcCCc--------ccHHHHHhhcCCChHHHHHHHHHHhhcCCee
Q psy7778          25 LKDSDNEEKVVYKIIEEAGNKG--------IWMRDIRFKSNLMPTQLNKILKQLETKKIIK   77 (117)
Q Consensus        25 ~~~L~~eE~lVY~~Ie~AGn~G--------IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK   77 (117)
                      +...+.++|++.-+.+.+...|        +-.++|-.-.|+...+++|+|+.|+..|+|+
T Consensus       150 l~~~~~~~Rla~~Ll~l~~~~g~~~~i~i~lt~~~IA~~lGisretlsR~L~~L~~~GlI~  210 (230)
T PRK09391        150 LGRKTAMERVAAFLLEMDERLGGAGMMALPMSRRDIADYLGLTIETVSRALSQLQDRGLIG  210 (230)
T ss_pred             HcCCCHHHHHHHHHHHHHHHhCCCCEEEecCCHHHHHHHHCCCHHHHHHHHHHHHHCCcEE
Confidence            3456778988777766543322        3358999999999999999999999999996

>PRK12423 LexA repressor; Provisional

Probab=93.06  E-value=0.47  Score=36.38  Aligned_cols=55  Identities=15%  Similarity=0.163  Sum_probs=46.4

Q ss_pred             CCCHHHHHHHHHHHHhc-CCcc--cHHHHHhhcCC-ChHHHHHHHHHHhhcCCeeeecc
Q psy7778          27 DSDNEEKVVYKIIEEAG-NKGI--WMRDIRFKSNL-MPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        27 ~L~~eE~lVY~~Ie~AG-n~GI--WtkdIk~ktnL-~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      .||+-++.||+.|.+.= ..|+  -.++|-...|+ ..+.+.+.|+.|+.+|+|..-.+
T Consensus         3 ~lt~~q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~~l~~L~~~G~l~~~~~   61 (202)
T PRK12423          3 TLTPKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQALAEAGLIEVVPN   61 (202)
T ss_pred             cCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEecCC
Confidence            48899999999999862 2344  78999999995 88999999999999999987554

>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea

Probab=92.58  E-value=0.63  Score=32.50  Aligned_cols=52  Identities=19%  Similarity=0.219  Sum_probs=43.0

Q ss_pred             CCHHHHHHHHHHHHhcCCcccHHHHHhhcC----CChHHHHHHHHHHhhcCCeeeecc
Q psy7778          28 SDNEEKVVYKIIEEAGNKGIWMRDIRFKSN----LMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        28 L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktn----L~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      |++-|..|..+|=+.|.  +-.++|....+    .+.+++...|+.|+.||+|..-+.
T Consensus         1 Ls~~E~~IM~~lW~~~~--~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~~~~~   56 (115)
T PF03965_consen    1 LSDLELEIMEILWESGE--ATVREIHEALPEERSWAYSTVQTLLNRLVEKGFLTREKI   56 (115)
T ss_dssp             --HHHHHHHHHHHHHSS--EEHHHHHHHHCTTSS--HHHHHHHHHHHHHTTSEEEEEE
T ss_pred             CCHHHHHHHHHHHhCCC--CCHHHHHHHHHhccccchhHHHHHHHHHHhCCceeEeec
Confidence            57789999999999998  88888887754    779999999999999999998764

Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....

>PRK03902 manganese transport transcriptional regulator; Provisional

Probab=92.51  E-value=0.4  Score=34.56  Aligned_cols=44  Identities=23%  Similarity=0.396  Sum_probs=37.2

Q ss_pred             HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeee
Q psy7778          34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAV   79 (117)
Q Consensus        34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V   79 (117)
                      .||.+++..|  .+-..+|....++..+.+++.|+.|+.+|||...
T Consensus        12 ~I~~l~~~~~--~~~~~ela~~l~vs~~svs~~l~~L~~~Gli~~~   55 (142)
T PRK03902         12 QIYLLIEEKG--YARVSDIAEALSVHPSSVTKMVQKLDKDEYLIYE   55 (142)
T ss_pred             HHHHHHhcCC--CcCHHHHHHHhCCChhHHHHHHHHHHHCCCEEEe
Confidence            6777766443  4577999999999999999999999999999854

>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=92.50  E-value=0.32  Score=30.80  Aligned_cols=32  Identities=22%  Similarity=0.289  Sum_probs=29.5

Q ss_pred             cccHHHHHhhcCCChHHHHHHHHHHhhcCCee
Q psy7778          46 GIWMRDIRFKSNLMPTQLNKILKQLETKKIIK   77 (117)
Q Consensus        46 GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK   77 (117)
                      .+-..+|-.-+|++...++++|+.|+..|+|.
T Consensus        28 ~lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I~   59 (76)
T PF13545_consen   28 PLTQEEIADMLGVSRETVSRILKRLKDEGIIE   59 (76)
T ss_dssp             ESSHHHHHHHHTSCHHHHHHHHHHHHHTTSEE
T ss_pred             cCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            34588999999999999999999999999998

...

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

Probab=92.49  E-value=0.21  Score=33.07  Aligned_cols=32  Identities=22%  Similarity=0.388  Sum_probs=29.7

Q ss_pred             HHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778          50 RDIRFKSNLMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        50 kdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      ++|-..++++.+.++++|+.|+++|||....+
T Consensus         3 ~ela~~l~is~stvs~~l~~L~~~glI~r~~~   34 (96)
T smart00529        3 SEIAERLNVSPPTVTQMLKKLEKDGLVEYEPY   34 (96)
T ss_pred             HHHHHHhCCChHHHHHHHHHHHHCCCEEEcCC
Confidence            57889999999999999999999999999775

iron dependent repressor

>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A

Probab=92.35  E-value=0.21  Score=29.96  Aligned_cols=43  Identities=26%  Similarity=0.308  Sum_probs=22.3

Q ss_pred             cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHH
Q psy7778          24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQ   69 (117)
Q Consensus        24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~   69 (117)
                      +++-||++|+..   |+.--+.|.-.+.|-...|.+.++|.+.||.
T Consensus         1 ~~~~Lt~~eR~~---I~~l~~~G~s~~~IA~~lg~s~sTV~relkR   43 (44)
T PF13936_consen    1 KYKHLTPEERNQ---IEALLEQGMSIREIAKRLGRSRSTVSRELKR   43 (44)
T ss_dssp             -----------H---HHHHHCS---HHHHHHHTT--HHHHHHHHHH
T ss_pred             CccchhhhHHHH---HHHHHHcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence            356789988865   4444568999999999999999999999873

>PRK09462 fur ferric uptake regulator; Provisional

Probab=92.09  E-value=0.72  Score=33.57  Aligned_cols=63  Identities=10%  Similarity=0.172  Sum_probs=50.4

Q ss_pred             CCCHHHHHHHHHHHHhcCCcccHHHHHhh-----cCCChHHHHHHHHHHhhcCCeeeeccccCCcccc
Q psy7778          27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFK-----SNLMPTQLNKILKQLETKKIIKAVKSVANIEYLT   89 (117)
Q Consensus        27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~k-----tnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYt   89 (117)
                      .+|++=..|+.++.++.+.-+-..+|-.+     .++..++|-|+|+.|+..|+|..+..-.+..+|.
T Consensus        14 r~T~qR~~Il~~l~~~~~~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli~~~~~~~~~~~y~   81 (148)
T PRK09462         14 KVTLPRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHNFEGGKSVFE   81 (148)
T ss_pred             CCCHHHHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCEEEEEcCCCcEEEE
Confidence            36788889999999876667777766544     3578899999999999999999997656666774

>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]

Probab=92.05  E-value=0.45  Score=35.80  Aligned_cols=52  Identities=21%  Similarity=0.300  Sum_probs=42.7

Q ss_pred             HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccc
Q psy7778          34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLT   89 (117)
Q Consensus        34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYt   89 (117)
                      .||.+++  ...-+=++||-...|..++.+++.++.|++.|||.-++.  +|.+.|
T Consensus        14 ~Iy~l~~--~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~~~~y--~gi~LT   65 (154)
T COG1321          14 TIYELLE--EKGFARTKDIAERLKVSPPSVTEMLKRLERLGLVEYEPY--GGVTLT   65 (154)
T ss_pred             HHHHHHh--ccCcccHHHHHHHhCCCcHHHHHHHHHHHHCCCeEEecC--CCeEEC
Confidence            6777777  334489999999999999999999999999999998775  444444

>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional

Probab=91.72  E-value=0.4  Score=34.74  Aligned_cols=58  Identities=14%  Similarity=0.200  Sum_probs=47.2

Q ss_pred             cccccCCCHHHH-HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778          22 NEKLKDSDNEEK-VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        22 a~k~~~L~~eE~-lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      ++.++-|.++-| .|+.++...|  +.-..+|-..++++++++++.|+.|+.-|||..-+.
T Consensus         7 ~~~fkaLadptRl~IL~~L~~~~--~~~v~ela~~l~lsqstvS~HL~~L~~AGLV~~~r~   65 (117)
T PRK10141          7 LQLFKILSDETRLGIVLLLRESG--ELCVCDLCTALDQSQPKISRHLALLRESGLLLDRKQ   65 (117)
T ss_pred             HHHHHHhCCHHHHHHHHHHHHcC--CcCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEEE
Confidence            456777888766 6777776544  466789999999999999999999999999987654

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

Probab=91.65  E-value=0.43  Score=38.05  Aligned_cols=39  Identities=21%  Similarity=0.173  Sum_probs=35.0

Q ss_pred             cCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778          43 GNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        43 Gn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      ++.+|-..+|...+++.++++++.|+.||.+|||....+
T Consensus        18 ~~~~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~GlI~R~~~   56 (217)
T PRK14165         18 NTVKISSSEFANHTGTSSKTAARILKQLEDEGYITRTIV   56 (217)
T ss_pred             CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEEc
Confidence            345799999999999999999999999999999987654

>PRK11169 leucine-responsive transcriptional regulator; Provisional

Probab=91.48  E-value=0.42  Score=35.44  Aligned_cols=55  Identities=18%  Similarity=0.320  Sum_probs=46.1

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      ..|++-++.|..++..-|...  .++|-.+.|+..+++.+-++.|+..|.|+.+..+
T Consensus        10 ~~lD~~D~~IL~~Lq~d~R~s--~~eiA~~lglS~~tv~~Ri~rL~~~GvI~~~~~~   64 (164)
T PRK11169         10 KDLDRIDRNILNELQKDGRIS--NVELSKRVGLSPTPCLERVRRLERQGFIQGYTAL   64 (164)
T ss_pred             hhHHHHHHHHHHHhccCCCCC--HHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEEE
Confidence            457777888888887766654  4999999999999999999999999999865543

>PRK11050 manganese transport regulator MntR; Provisional

Probab=91.36  E-value=0.63  Score=34.38  Aligned_cols=53  Identities=19%  Similarity=0.234  Sum_probs=41.5

Q ss_pred             HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCccccc
Q psy7778          34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTE   90 (117)
Q Consensus        34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtd   90 (117)
                      .|+.+|..  +.++-..+|-..+++.++.+++.|+.||.+|+|..-.  ..|.+.|+
T Consensus        41 ~I~~~l~~--~~~~t~~eLA~~l~is~stVsr~l~~Le~~GlI~r~~--~~~v~LT~   93 (152)
T PRK11050         41 LIADLIAE--VGEARQVDIAARLGVSQPTVAKMLKRLARDGLVEMRP--YRGVFLTP   93 (152)
T ss_pred             HHHHHHHh--cCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec--CCceEECc
Confidence            56666654  3578889999999999999999999999999997643  23444554

>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial

Probab=91.34  E-value=0.55  Score=33.98  Aligned_cols=53  Identities=19%  Similarity=0.283  Sum_probs=41.0

Q ss_pred             cCCCHHHHHHHHHHHHh---c---CCc------ccHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778          26 KDSDNEEKVVYKIIEEA---G---NKG------IWMRDIRFKSNLMPTQLNKILKQLETKKIIKA   78 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~A---G---n~G------IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~   78 (117)
                      ...+.++|+..-+...+   |   +.|      +-..+|-.-.|+...+++|+|+.|+..|+|+.
T Consensus       111 ~~~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~  175 (193)
T TIGR03697       111 AHRDMGSRLVSFLLILCRDFGVPGQRGVTIDLRLSHQAIAEAIGSTRVTITRLLGDLRKKKLISI  175 (193)
T ss_pred             HhCCHHHHHHHHHHHHHHHhCCCCCCeEEecCCCCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEe
Confidence            44566788776655432   2   234      46889999999999999999999999999974

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.

>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional

Probab=91.18  E-value=0.66  Score=34.10  Aligned_cols=54  Identities=20%  Similarity=0.263  Sum_probs=40.1

Q ss_pred             ccCCCHHHHHHHHHHHHh---c----CCcc----cHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778          25 LKDSDNEEKVVYKIIEEA---G----NKGI----WMRDIRFKSNLMPTQLNKILKQLETKKIIKA   78 (117)
Q Consensus        25 ~~~L~~eE~lVY~~Ie~A---G----n~GI----WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~   78 (117)
                      +...+..+|+.+-+.+-+   +    ..|+    -.++|...+|++..+++|+|+.|+..|+|+.
T Consensus       136 ~~~~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~lA~~lG~tr~tvsR~l~~l~~~gii~~  200 (211)
T PRK11753        136 LAFLDVTGRIAQTLLDLAKQPDAMTHPDGMQIKITRQEIGRIVGCSREMVGRVLKMLEDQGLISA  200 (211)
T ss_pred             HHhcChhhHHHHHHHHHHHhcCCcCCCCceecCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEe
Confidence            344556788766554433   2    1233    3589999999999999999999999999974

>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]

Probab=90.86  E-value=0.8  Score=33.81  Aligned_cols=62  Identities=11%  Similarity=0.148  Sum_probs=52.4

Q ss_pred             CCCHHHHHHHHHHHHhcCCcccHHHHHhh-----cCCChHHHHHHHHHHhhcCCeeeeccccCCcccc
Q psy7778          27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFK-----SNLMPTQLNKILKQLETKKIIKAVKSVANIEYLT   89 (117)
Q Consensus        27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~k-----tnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYt   89 (117)
                      .+|++-..|++++.++++- .--.+|=.+     -++..++|-+.|+.|+..|+|..+..-.+..+|.
T Consensus        18 r~T~qR~~vl~~L~~~~~~-~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~~~~~~~~~~y~   84 (145)
T COG0735          18 RLTPQRLAVLELLLEADGH-LSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHRLEFEGGKTRYE   84 (145)
T ss_pred             CcCHHHHHHHHHHHhcCCC-CCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEEEEEeCCCEEEEe
Confidence            4688888999999999887 777766544     4488899999999999999999999988888884

>PRK06474 hypothetical protein; Provisional

Probab=90.61  E-value=0.75  Score=35.04  Aligned_cols=56  Identities=11%  Similarity=0.127  Sum_probs=45.1

Q ss_pred             ccCCCHHHH-HHHHHHHHhcCCcccHHHHHhhc-CCChHHHHHHHHHHhhcCCeeeecc
Q psy7778          25 LKDSDNEEK-VVYKIIEEAGNKGIWMRDIRFKS-NLMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        25 ~~~L~~eE~-lVY~~Ie~AGn~GIWtkdIk~kt-nL~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      +.-|....| .|++.+...+. +.-..+|-... +++++++.+.|+.|+..|||..++.
T Consensus         5 ~~~La~p~R~~Il~~L~~~~~-~~ta~el~~~l~~is~aTvYrhL~~L~e~GLI~~~~~   62 (178)
T PRK06474          5 AEILMHPVRMKICQVLMRNKE-GLTPLELVKILKDVPQATLYRHLQTMVDSGILHVVKE   62 (178)
T ss_pred             HHhhCCHHHHHHHHHHHhCCC-CCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEEeec
Confidence            334555444 78888877643 48889998888 7999999999999999999999875

>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional

Probab=90.58  E-value=0.68  Score=34.87  Aligned_cols=54  Identities=15%  Similarity=0.186  Sum_probs=42.1

Q ss_pred             ccCCCHHHHHHHHHHHHhc------CCc------ccHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778          25 LKDSDNEEKVVYKIIEEAG------NKG------IWMRDIRFKSNLMPTQLNKILKQLETKKIIKA   78 (117)
Q Consensus        25 ~~~L~~eE~lVY~~Ie~AG------n~G------IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~   78 (117)
                      +...+.++|+..-+.+.+.      ..|      +-.++|-.-.|++...++|+|+.|+++|+|+-
T Consensus       151 l~~~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~lt~~~iA~~lG~sr~tvsR~l~~l~~~g~I~~  216 (235)
T PRK11161        151 LSKKNAEERLAAFIYNLSRRFAQRGFSPREFRLTMTRGDIGNYLGLTVETISRLLGRFQKSGMLAV  216 (235)
T ss_pred             HhCCCHHHHHHHHHHHHHHHHhhcCCCCceeEccccHHHHHHHhCCcHHHHHHHHHHHHHCCCEEe
Confidence            3456778887766665442      122      56789999999999999999999999999984

>PRK13918 CRP/FNR family transcriptional regulator; Provisional

Probab=90.39  E-value=0.75  Score=33.69  Aligned_cols=53  Identities=11%  Similarity=0.223  Sum_probs=42.1

Q ss_pred             ccCCCHHHHHHHHHHHHhcCC-------c-----ccHHHHHhhcCCChHHHHHHHHHHhhcCCee
Q psy7778          25 LKDSDNEEKVVYKIIEEAGNK-------G-----IWMRDIRFKSNLMPTQLNKILKQLETKKIIK   77 (117)
Q Consensus        25 ~~~L~~eE~lVY~~Ie~AGn~-------G-----IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK   77 (117)
                      +...+.++|+.+-+++-+...       +     +-..+|-.-.|+....++|+|+.|+..|+|+
T Consensus       116 l~~~~~~~Rla~~Ll~l~~~~~~~~~~~~~~~~~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~  180 (202)
T PRK13918        116 LVGQRLKNRIAAALLELSDTPLATQEDSGETMIYATHDELAAAVGSVRETVTKVIGELSREGYIR  180 (202)
T ss_pred             HHhCchHHHHHHHHHHHHHHhCCCCCCCCeEEecCCHHHHHHHhCccHHHHHHHHHHHHHCCCEE
Confidence            345567888888777655321       1     3578899999999999999999999999997

>PRK10402 DNA-binding transcriptional activator YeiL; Provisional

Probab=89.98  E-value=1  Score=34.26  Aligned_cols=53  Identities=11%  Similarity=-0.058  Sum_probs=42.6

Q ss_pred             CCCHHHHHHHHHHHHhcCCc--ccHHHHHhhcCCChHHHHHHHHHHhhcCCeeee
Q psy7778          27 DSDNEEKVVYKIIEEAGNKG--IWMRDIRFKSNLMPTQLNKILKQLETKKIIKAV   79 (117)
Q Consensus        27 ~L~~eE~lVY~~Ie~AGn~G--IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V   79 (117)
                      .++.++|+.+-+...+....  .-..+|-...|+...+|+|+|+.|+..|+|..-
T Consensus       148 ~~~~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvsR~L~~L~~~G~I~~~  202 (226)
T PRK10402        148 SFPLENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLLYVLAQFIQDGYLKKS  202 (226)
T ss_pred             cChHHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHHHHHHHHHHCCCEEee
Confidence            44678998887776554332  346899999999999999999999999999753

>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=89.90  E-value=1.3  Score=26.37  Aligned_cols=42  Identities=19%  Similarity=0.315  Sum_probs=34.2

Q ss_pred             ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHH
Q psy7778          25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQ   69 (117)
Q Consensus        25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~   69 (117)
                      +..||++|+.|..+..   -+|.-..+|-...|++...+.++.+.
T Consensus         2 l~~L~~~er~vi~~~y---~~~~t~~eIa~~lg~s~~~V~~~~~~   43 (50)
T PF04545_consen    2 LDQLPPREREVIRLRY---FEGLTLEEIAERLGISRSTVRRILKR   43 (50)
T ss_dssp             HCTS-HHHHHHHHHHH---TST-SHHHHHHHHTSCHHHHHHHHHH
T ss_pred             hhhCCHHHHHHHHHHh---cCCCCHHHHHHHHCCcHHHHHHHHHH
Confidence            5689999998887777   78899999999999999998877654

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....

>PRK10430 DNA-binding transcriptional activator DcuR; Provisional

Probab=89.86  E-value=1.4  Score=33.30  Aligned_cols=58  Identities=12%  Similarity=0.084  Sum_probs=49.0

Q ss_pred             cCCCHHHH-HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCe-eeecccc
Q psy7778          26 KDSDNEEK-VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKII-KAVKSVA   83 (117)
Q Consensus        26 ~~L~~eE~-lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LI-K~VKsV~   83 (117)
                      ..|++.|. .+..+|++--+.|..+++|-.+.|+...++.+.+..|-+.++. ..++...
T Consensus       157 ~~Lt~re~~~l~~~i~~~~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~~~~~~~~~~~~~  216 (239)
T PRK10430        157 KGLTPQTLRTLCQWIDAHQDYEFSTDELANAVNISRVSCRKYLIWLVNCHILFTSIHYGV  216 (239)
T ss_pred             CCCCHHHHHHHHHHHHhCCCCCcCHHHHHHHhCchHHHHHHHHHHHHhCCEEEEEeeccC
Confidence            35888774 5667887777899999999999999999999999999999998 5666654

>PRK10163 DNA-binding transcriptional repressor AllR; Provisional

Probab=89.39  E-value=0.75  Score=36.59  Aligned_cols=51  Identities=18%  Similarity=0.292  Sum_probs=41.0

Q ss_pred             CCHHHH--HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeee
Q psy7778          28 SDNEEK--VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAV   79 (117)
Q Consensus        28 L~~eE~--lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V   79 (117)
                      ...-++  .|..++...+ .++-..+|-.+++||.+++.+.|++|+..|++..-
T Consensus        21 ~~sl~r~l~IL~~~~~~~-~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~~~   73 (271)
T PRK10163         21 AQALERGIAILQYLEKSG-GSSSVSDISLNLDLPLSTTFRLLKVLQAADFVYQD   73 (271)
T ss_pred             chHHHHHHHHHHHHHhCC-CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEc
Confidence            444444  6777776543 56778999999999999999999999999999653

>PRK09954 putative kinase; Provisional

Probab=89.36  E-value=1.1  Score=36.54  Aligned_cols=48  Identities=21%  Similarity=0.182  Sum_probs=42.1

Q ss_pred             CCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCee
Q psy7778          28 SDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIK   77 (117)
Q Consensus        28 L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK   77 (117)
                      |++-++.|+.++.+.+  =|-..+|..+.|+..+++.+.|+.|+++|+|+
T Consensus         1 ~~~~~~~il~~l~~~~--~~s~~~la~~l~~s~~~v~~~i~~L~~~g~i~   48 (362)
T PRK09954          1 MNNREKEILAILRRNP--LIQQNEIADILQISRSRVAAHIMDLMRKGRIK   48 (362)
T ss_pred             CChHHHHHHHHHHHCC--CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCcC
Confidence            4566777888888665  48999999999999999999999999999995

>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication

Probab=89.31  E-value=0.54  Score=35.74  Aligned_cols=49  Identities=24%  Similarity=0.386  Sum_probs=39.1

Q ss_pred             HHHHHHHHHHhcCCcc---cHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778          32 EKVVYKIIEEAGNKGI---WMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK   80 (117)
Q Consensus        32 E~lVY~~Ie~AGn~GI---WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK   80 (117)
                      -++++-+++.....+.   -.++|-..+++..+++.|++|.|+.+++|..++
T Consensus        58 ~~Vl~~il~~~d~~N~v~~t~~~ia~~l~iS~~Tv~r~ik~L~e~~iI~k~~  109 (165)
T PF05732_consen   58 FRVLMYILENMDKDNAVVATQKEIAEKLGISKPTVSRAIKELEEKNIIKKIR  109 (165)
T ss_pred             HHHHHHHHHhcCCCCeEEeeHHHHHHHhCCCHHHHHHHHHHHHhCCcEEEcc
Confidence            3455556666665553   357799999999999999999999999999875

; GO: 0006260 DNA replication, 0006276 plasmid maintenance

>PRK09334 30S ribosomal protein S25e; Provisional

Probab=89.28  E-value=0.57  Score=32.79  Aligned_cols=47  Identities=17%  Similarity=0.192  Sum_probs=37.4

Q ss_pred             HHHHHHH-HhcC-CcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778          34 VVYKIIE-EAGN-KGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK   80 (117)
Q Consensus        34 lVY~~Ie-~AGn-~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK   80 (117)
                      ..|+-|. +..+ +=|---.|-.+.++.-+.-.++|+.||.+|+||.|.
T Consensus        27 ~t~dkl~kEV~~~K~ITps~lserlkI~~SlAr~~Lr~L~~kG~Ik~V~   75 (86)
T PRK09334         27 ELLKRVAKEVKKEKIVTPYTLASKYGIKISVAKKVLRELEKRGVLVLYS   75 (86)
T ss_pred             HHHHHHHHHhccCcEEcHHHHHHHhcchHHHHHHHHHHHHHCCCEEEEe
Confidence            3444443 4443 666777889999999999999999999999999993

>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=89.13  E-value=2.5  Score=25.42  Aligned_cols=40  Identities=13%  Similarity=0.195  Sum_probs=33.1

Q ss_pred             HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcC
Q psy7778          34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKK   74 (117)
Q Consensus        34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~   74 (117)
                      .|..++.++++. +-..+|..+.|+...+|.+-|+.|+..+
T Consensus         4 ~il~~L~~~~~~-it~~eLa~~l~vS~rTi~~~i~~L~~~~   43 (55)
T PF08279_consen    4 QILKLLLESKEP-ITAKELAEELGVSRRTIRRDIKELREWG   43 (55)
T ss_dssp             HHHHHHHHTTTS-BEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHcCCC-cCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence            455566555555 9999999999999999999999999888

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 ....

>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family

Probab=88.89  E-value=0.79  Score=35.64  Aligned_cols=44  Identities=11%  Similarity=0.138  Sum_probs=37.7

Q ss_pred             HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778          34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKA   78 (117)
Q Consensus        34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~   78 (117)
                      .|..++.. .+.|+-..+|-.++|||.+++.+.|++|+..|++..
T Consensus        13 ~IL~~l~~-~~~~~~l~eia~~lglpksT~~RlL~tL~~~G~l~~   56 (248)
T TIGR02431        13 AVIEAFGA-ERPRLTLTDVAEATGLTRAAARRFLLTLVELGYVTS   56 (248)
T ss_pred             HHHHHHhc-CCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe
Confidence            45556644 357888999999999999999999999999999975

Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.

>TIGR03879 near_KaiC_dom probable regulatory domain

Probab=88.66  E-value=0.72  Score=31.31  Aligned_cols=53  Identities=13%  Similarity=0.015  Sum_probs=45.6

Q ss_pred             ccccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCC
Q psy7778          21 TNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKI   75 (117)
Q Consensus        21 ~a~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~L   75 (117)
                      -|+.+..|++..+.+|.+-  .-.+|.-.++|-..+|++.+++...++.+++.+-
T Consensus         9 ~~~~l~~l~~~~r~af~L~--R~~eGlS~kEIAe~LGIS~~TVk~~l~~~~~~~~   61 (73)
T TIGR03879         9 LAERLTWVDSLAEAAAALA--REEAGKTASEIAEELGRTEQTVRNHLKGETKAGG   61 (73)
T ss_pred             HHHHHhcCCHHHHHHHHHH--HHHcCCCHHHHHHHHCcCHHHHHHHHhcCcccch
Confidence            3567889999999999887  3458999999999999999999999999887653

This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.

>COG1414 IclR Transcriptional regulator [Transcription]

Probab=88.23  E-value=1.3  Score=35.09  Aligned_cols=46  Identities=13%  Similarity=0.313  Sum_probs=40.6

Q ss_pred             HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778          34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK   80 (117)
Q Consensus        34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK   80 (117)
                      .|.+++.. +..|+-..+|-.++|||.+++.+.|.+|+..||+..-.
T Consensus         8 ~iL~~l~~-~~~~l~l~ela~~~glpksT~~RlL~tL~~~G~v~~d~   53 (246)
T COG1414           8 AILDLLAE-GPGGLSLAELAERLGLPKSTVHRLLQTLVELGYVEQDP   53 (246)
T ss_pred             HHHHHHHh-CCCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEcC
Confidence            56777777 66777899999999999999999999999999998755

>PF03297 Ribosomal_S25: S25 ribosomal protein; InterPro: IPR004977 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms

Probab=88.08  E-value=0.84  Score=32.88  Aligned_cols=57  Identities=25%  Similarity=0.199  Sum_probs=43.3

Q ss_pred             HHHHHHHH-H-hcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccc
Q psy7778          33 KVVYKIIE-E-AGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLT   89 (117)
Q Consensus        33 ~lVY~~Ie-~-AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYt   89 (117)
                      .-.|+-|. + -.-+=|-.-.|-.+.++..+.-.++|+.|+++|+|+.|..=++-.=||
T Consensus        44 ~~~~~kl~kEV~~~K~ITp~~lserlkI~~SlAr~~Lr~L~~kG~Ik~V~k~~~~~IYt  102 (105)
T PF03297_consen   44 KETYDKLLKEVPKMKLITPSVLSERLKINGSLARKALRELESKGLIKPVSKHHRQRIYT  102 (105)
T ss_dssp             CHHHHHHHHHCTTSSCECHHHHHHHHCCSCHHHHHHHHHHHHCCSSEEEECCTTCEEEE
T ss_pred             HHHHHHHHHHhccCcEeeHHHHHHhHhhHHHHHHHHHHHHHHCCCEEEEeccCCeEEEe
Confidence            34566554 2 334668888999999999999999999999999999994434444443

The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S25 ribosomal protein is a component of the 40S ribosomal subunit.; PDB: 2XZM_8 2XZN_8 3O30_Q 3U5G_Z 3IZB_V 3U5C_Z 3O2Z_Q 3IZ6_V.

>PF09202 Rio2_N: Rio2, N-terminal; InterPro: IPR015285 This N-terminal domain is found in RIO2 kinases, and is structurally homologous to the winged helix (wHTH) domain

Probab=87.99  E-value=1.2  Score=30.47  Aligned_cols=54  Identities=24%  Similarity=0.216  Sum_probs=40.2

Q ss_pred             ccCCCHHHHHHHHHHHHhcCCc--ccHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778          25 LKDSDNEEKVVYKIIEEAGNKG--IWMRDIRFKSNLMPTQLNKILKQLETKKIIKA   78 (117)
Q Consensus        25 ~~~L~~eE~lVY~~Ie~AGn~G--IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~   78 (117)
                      ++.|+++|.-|...||..-.+=  +=...|...++++..-+.++|+.|...+||..
T Consensus         1 ~r~L~~~d~rvL~aiE~gmk~hE~VP~~~I~~~s~l~~~~~~~~L~~L~~~kLv~~   56 (82)
T PF09202_consen    1 LRYLSKEDFRVLRAIEMGMKNHEWVPLELIEKISGLSEGEVEKRLKRLVKLKLVSR   56 (82)
T ss_dssp             --T--HHHHHHHHHHHTTTTT-SSEEHHHHHHHHT--HHHHHHHHHHHHHTTSEEE
T ss_pred             CCcCCHHHHHHHHHHHHcccCCccCCHHHHHHHhCcCHHHHHHHHHHHHhcCCccc
Confidence            3578999999999999643322  22568999999999999999999999999998

It adopts a structure consisting of four alpha helices followed by two beta strands and a fifth alpha helix. The domain confers DNA binding properties to the protein, as per other winged helix domains []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1TQP_A 1ZAR_A 1TQI_A 1ZAO_A 1TQM_A.

>PHA00738 putative HTH transcription regulator

Probab=87.90  E-value=1.6  Score=31.89  Aligned_cols=47  Identities=23%  Similarity=0.169  Sum_probs=37.8

Q ss_pred             HHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778          33 KVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        33 ~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      +.|...+..  +.+.-.-+|-..++|.++.|++.||.|+.-|||.+-+.
T Consensus        15 r~IL~lL~~--~e~~~V~eLae~l~lSQptVS~HLKvLreAGLV~srK~   61 (108)
T PHA00738         15 RKILELIAE--NYILSASLISHTLLLSYTTVLRHLKILNEQGYIELYKE   61 (108)
T ss_pred             HHHHHHHHH--cCCccHHHHHHhhCCCHHHHHHHHHHHHHCCceEEEEE
Confidence            455666644  23477789999999999999999999999999987653

>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional

Probab=87.81  E-value=3.5  Score=32.75  Aligned_cols=46  Identities=13%  Similarity=0.142  Sum_probs=40.2

Q ss_pred             HHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778          33 KVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK   80 (117)
Q Consensus        33 ~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK   80 (117)
                      ..|.+++.+-|.  +-..||-..++....++.|=|+.||+.|+|+.+.
T Consensus         8 ~~Il~~L~~~~~--v~v~eLa~~l~VS~~TIRRDL~~Le~~g~l~r~~   53 (256)
T PRK10434          8 AAILEYLQKQGK--TSVEELAQYFDTTGTTIRKDLVILEHAGTVIRTY   53 (256)
T ss_pred             HHHHHHHHHcCC--EEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEE
Confidence            367777777554  8999999999999999999999999999998864

>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins

Probab=87.60  E-value=2.4  Score=24.60  Aligned_cols=41  Identities=12%  Similarity=0.193  Sum_probs=33.6

Q ss_pred             CCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhh
Q psy7778          28 SDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLET   72 (117)
Q Consensus        28 L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~   72 (117)
                      ||+.|+.++.++.    .|+-.++|-..+|++..++.+.++.+..
T Consensus         1 l~~~e~~i~~~~~----~~~s~~eia~~l~~s~~tv~~~~~~~~~   41 (57)
T cd06170           1 LTPREREVLRLLA----EGKTNKEIADILGISEKTVKTHLRNIMR   41 (57)
T ss_pred             CCHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            5677777777763    6789999999999999999998887644

This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental

>smart00531 TFIIE Transcription initiation factor IIE

Probab=87.22  E-value=0.63  Score=34.30  Aligned_cols=61  Identities=23%  Similarity=0.168  Sum_probs=43.9

Q ss_pred             cccHHHHHhhcCCChHHHHHHHHHHhhcCCeeee----ccccCCcccccC-ccc-cccchhhhhhhh
Q psy7778          46 GIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAV----KSVANIEYLTEG-TVN-AMVLPSRKKREE  106 (117)
Q Consensus        46 GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V----KsV~gg~wYtdg-~~D-~~fI~~l~~~~~  106 (117)
                      -+--.||...+||+.+.|.|+|-.|...++++..    +.-.+|+||+-= .+| ..+++.++-|-.
T Consensus        15 ~~~dedLa~~l~i~~n~vRkiL~~L~ed~~~~~~~~~e~~~~~~~~~~~yw~i~y~~~~~vik~r~~   81 (147)
T smart00531       15 CVTEEDLAELLGIKQKQLRKILYLLYDEKLIKIDYKREKDPETKTWYRYYWYINYDTLLDVVKYKLD   81 (147)
T ss_pred             CcCHHHHHHHhCCCHHHHHHHHHHHHhhhcchhheeeeeCCCCceEEEEEEEecHHHHHHHHHHHHH
Confidence            3667899999999999999999999997776543    444466566543 255 466676665543

>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional

Probab=87.21  E-value=1.2  Score=34.80  Aligned_cols=44  Identities=9%  Similarity=0.218  Sum_probs=37.5

Q ss_pred             HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeee
Q psy7778          34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAV   79 (117)
Q Consensus        34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V   79 (117)
                      .|..++..  ..++-..+|-.+++||.+++.+.|++|+..|++..-
T Consensus        18 ~IL~~l~~--~~~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~~~   61 (257)
T PRK15090         18 GILQALGE--EREIGITELSQRVMMSKSTVYRFLQTMKTLGYVAQE   61 (257)
T ss_pred             HHHHHhhc--CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEc
Confidence            56666654  346788999999999999999999999999999764

>PF05158 RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; InterPro: IPR007832 The family comprises a subunit specific to RNA Pol III, the tRNA specific polymerase

Probab=87.04  E-value=1.3  Score=37.11  Aligned_cols=62  Identities=19%  Similarity=0.197  Sum_probs=49.6

Q ss_pred             CCCHHHHHHHHHHHHh-cCCcccHHHHHhh-cCCChHHHHHHHHHHhhcCCeeeeccccCCcccc
Q psy7778          27 DSDNEEKVVYKIIEEA-GNKGIWMRDIRFK-SNLMPTQLNKILKQLETKKIIKAVKSVANIEYLT   89 (117)
Q Consensus        27 ~L~~eE~lVY~~Ie~A-Gn~GIWtkdIk~k-tnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYt   89 (117)
                      ++.+-|..||+++.++ +.+|+-.+||... .+++...+-.+|..|.+.++|+-++ ..++..|.
T Consensus         6 ~~~~~~~~l~~~~~~~~~~~~~~~~~L~~~~~~~~~~~~~~~in~Ll~~~~~~~~~-~~~~l~~~   69 (327)
T PF05158_consen    6 KLSELEKKLLELCRENPSPKGFSQEDLQQLIPGLDLQELVKAINELLSSGLLKLLK-KGGGLSYK   69 (327)
T ss_dssp             -HHHHHHHHHHHHHH---SS-EEHHHHHHH-TTS-HHHHHHHHHHHHHHTSEEEEE--SSSEEEE
T ss_pred             hHHHHHHHHHHHHHHhcCCCCcCHHHHHhhcCCCCHHHHHHHHHHHHhCCCEEEEE-cCCEEEEE
Confidence            4556688999999999 8999999999999 7899999999999999999999999 55555654

The C34 subunit of Saccharomyces cerevisiae RNA Pol III is part of a subcomplex of three subunits which have no counterpart in the other two nuclear RNA polymerases. This subunit interacts with TFIIIB70 and therefore participates in Pol III recruitment [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2DK8_A 2DK5_A 2YU3_A.

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

Probab=86.72  E-value=1.2  Score=28.57  Aligned_cols=47  Identities=17%  Similarity=0.289  Sum_probs=36.0

Q ss_pred             HHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          35 VYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        35 VY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      |.++|++.  .-+-..+|-.+.++++..|.-.|..|+.+|.|..+..-.
T Consensus         5 i~~~l~~~--~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~~~~~   51 (69)
T PF09012_consen    5 IRDYLRER--GRVSLAELAREFGISPEAVEAMLEQLIRKGYIRKVDMSS   51 (69)
T ss_dssp             HHHHHHHS---SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEEEEEE-
T ss_pred             HHHHHHHc--CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEecCCC
Confidence            44455543  347789999999999999999999999999999887654

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

>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=86.66  E-value=3.9  Score=25.53  Aligned_cols=45  Identities=13%  Similarity=0.306  Sum_probs=38.5

Q ss_pred             HHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeee
Q psy7778          33 KVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAV   79 (117)
Q Consensus        33 ~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V   79 (117)
                      ..|+++|.+.  .-+-+.+|-..+|....++.+=|..|+..++|+.+
T Consensus         3 ~~Il~~l~~~--~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i~r~   47 (57)
T PF08220_consen    3 QQILELLKEK--GKVSVKELAEEFGVSEMTIRRDLNKLEKQGLIKRT   47 (57)
T ss_pred             HHHHHHHHHc--CCEEHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            3567777775  46788999999999999999999999999997654

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

>PRK11569 transcriptional repressor IclR; Provisional

Probab=86.36  E-value=1.5  Score=34.89  Aligned_cols=45  Identities=13%  Similarity=0.332  Sum_probs=38.5

Q ss_pred             HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeee
Q psy7778          34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAV   79 (117)
Q Consensus        34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V   79 (117)
                      .|..++.+ .+.++-..+|-..+|||.+++.++|.+|+..|++...
T Consensus        32 ~IL~~l~~-~~~~~~lseia~~lglpksTv~RlL~tL~~~G~l~~~   76 (274)
T PRK11569         32 KLLEWIAE-SNGSVALTELAQQAGLPNSTTHRLLTTMQQQGFVRQV   76 (274)
T ss_pred             HHHHHHHh-CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEc
Confidence            56666655 4677889999999999999999999999999999753

>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress

Probab=86.26  E-value=4.4  Score=27.94  Aligned_cols=59  Identities=10%  Similarity=0.160  Sum_probs=45.1

Q ss_pred             CCHHHHHHHH-HHHH--hcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCc
Q psy7778          28 SDNEEKVVYK-IIEE--AGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIE   86 (117)
Q Consensus        28 L~~eE~lVY~-~Ie~--AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~   86 (117)
                      ||+-++.|+. +|+.  ....=|=+++|-.+.+....+|...+..||.-|||.++.+-.+|-
T Consensus         2 Lt~rq~~IL~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lGlve~~p~~s~Gr   63 (78)
T PF03444_consen    2 LTERQREILKALVELYIETGEPVGSKTIAEELGRSPATIRNEMADLEELGLVESQPHPSGGR   63 (78)
T ss_pred             CCHHHHHHHHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHHHHHHHCCCccCCCCCCCCC
Confidence            5664444433 3332  235668899999999999999999999999999999887766664

Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent

>PRK09834 DNA-binding transcriptional activator MhpR; Provisional

Probab=86.03  E-value=1.7  Score=34.35  Aligned_cols=46  Identities=13%  Similarity=0.247  Sum_probs=38.6

Q ss_pred             HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778          34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK   80 (117)
Q Consensus        34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK   80 (117)
                      .|+.++.+. +.++-..+|-.++|+|.+++.|+|++|+..|++....
T Consensus        15 ~iL~~l~~~-~~~ls~~eia~~lgl~kstv~RlL~tL~~~g~v~~~~   60 (263)
T PRK09834         15 MVLRALNRL-DGGATVGLLAELTGLHRTTVRRLLETLQEEGYVRRSA   60 (263)
T ss_pred             HHHHHHHhc-CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEec
Confidence            456666543 4468899999999999999999999999999998664

>PRK10046 dpiA two-component response regulator DpiA; Provisional

Probab=85.98  E-value=3.1  Score=31.24  Aligned_cols=47  Identities=13%  Similarity=0.087  Sum_probs=41.2

Q ss_pred             HHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeee
Q psy7778          32 EKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAV   79 (117)
Q Consensus        32 E~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V   79 (117)
                      ++.|+++|. .|..|.-+++|-.+.++...++.+.+..|++.|++.+-
T Consensus       164 ~r~Vl~~~~-~g~~g~s~~eIa~~l~iS~~Tv~~~~~~~~~~~~~~~~  210 (225)
T PRK10046        164 LNAVRKLFK-EPGVQHTAETVAQALTISRTTARRYLEYCASRHLIIAE  210 (225)
T ss_pred             HHHHHHHHH-cCCCCcCHHHHHHHhCccHHHHHHHHHHHHhCCeEEEE
Confidence            357888886 55668899999999999999999999999999998764

>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs)

Probab=85.98  E-value=2.8  Score=23.45  Aligned_cols=45  Identities=13%  Similarity=0.113  Sum_probs=36.5

Q ss_pred             cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHh
Q psy7778          24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLE   71 (117)
Q Consensus        24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE   71 (117)
                      .+..|+++++.++.....   .|.-.++|-..+|++..++.+.+....
T Consensus         7 ~~~~l~~~~~~~~~~~~~---~~~~~~~ia~~~~~s~~~i~~~~~~~~   51 (55)
T cd06171           7 ALDKLPEREREVILLRFG---EGLSYEEIAEILGISRSTVRQRLHRAL   51 (55)
T ss_pred             HHHhCCHHHHHHHHHHHh---cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            456789988887766653   677889999999999999999887653

A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas

>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional

Probab=85.71  E-value=3.7  Score=29.96  Aligned_cols=52  Identities=12%  Similarity=0.224  Sum_probs=45.5

Q ss_pred             CCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778          27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK   80 (117)
Q Consensus        27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK   80 (117)
                      .|++-++.|...+..-|.  +-..+|-.+.|++.+++.+-++.|+..|.|+...
T Consensus         6 ~lD~~D~~Il~~Lq~d~R--~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~~~~   57 (153)
T PRK11179          6 QIDNLDRGILEALMENAR--TPYAELAKQFGVSPGTIHVRVEKMKQAGIITGTR   57 (153)
T ss_pred             ccCHHHHHHHHHHHHcCC--CCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeEE
Confidence            488888889888887755  5679999999999999999999999999998554

>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=85.49  E-value=1.7  Score=27.18  Aligned_cols=34  Identities=18%  Similarity=0.274  Sum_probs=29.4

Q ss_pred             cHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778          48 WMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        48 WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      -.++|-.+.+.+.+++.++|+.|++.|+|....+
T Consensus        26 s~~~la~~~~vsr~tvr~al~~L~~~g~i~~~~~   59 (64)
T PF00392_consen   26 SERELAERYGVSRTTVREALRRLEAEGLIERRPG   59 (64)
T ss_dssp             -HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT
T ss_pred             CHHHHHHHhccCCcHHHHHHHHHHHCCcEEEECC
Confidence            5688999999999999999999999999987654

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 ....

>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional

Probab=85.36  E-value=3.5  Score=32.55  Aligned_cols=62  Identities=11%  Similarity=0.153  Sum_probs=54.3

Q ss_pred             HHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccCccc
Q psy7778          31 EEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGTVN   94 (117)
Q Consensus        31 eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg~~D   94 (117)
                      -|++|..++...|.+ +=-.+|.++.||..+.+||+|=.|...+.|..+. =+...||..-+-|
T Consensus         5 ~~~~i~~~l~~~~~~-~~a~~i~k~l~i~k~~vNr~LY~L~~~~~v~~~~-~~pP~W~~~~~~~   66 (183)
T PHA02701          5 CASLILTLLSSSGDK-LPAKRIAKELGISKHEANRCLYRLLESDAVSCED-GCPPLWSVECEPD   66 (183)
T ss_pred             HHHHHHHHHHhcCCC-CcHHHHHHHhCccHHHHHHHHHHHhhcCcEecCC-CCCCccccccCCC
Confidence            478999999998877 9999999999999999999999999999998774 3577899877766

>COG1725 Predicted transcriptional regulators [Transcription]

Probab=84.96  E-value=1.6  Score=32.26  Aligned_cols=45  Identities=18%  Similarity=0.313  Sum_probs=38.7

Q ss_pred             CcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccC
Q psy7778          45 KGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEG   91 (117)
Q Consensus        45 ~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg   91 (117)
                      +==.+|++-..+++++++++|+.+.||..|+|.+..+  -|.|-++.
T Consensus        34 kLPSvRelA~~~~VNpnTv~raY~eLE~eG~i~t~rg--~G~fV~~~   78 (125)
T COG1725          34 KLPSVRELAKDLGVNPNTVQRAYQELEREGIVETKRG--KGTFVTED   78 (125)
T ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecC--eeEEEcCC
Confidence            3345899999999999999999999999999998876  47777766

>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors

Probab=84.52  E-value=2.1  Score=29.37  Aligned_cols=49  Identities=20%  Similarity=0.281  Sum_probs=36.2

Q ss_pred             HHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778          30 NEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK   80 (117)
Q Consensus        30 ~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK   80 (117)
                      ++...|..++-..|  .+--.+|...+||+.+.+.++|-.|...+||+..+
T Consensus        13 ~~~~~Il~~L~~~~--~l~de~la~~~~l~~~~vRkiL~~L~~~~lv~~~~   61 (105)
T PF02002_consen   13 EEAVRILDALLRKG--ELTDEDLAKKLGLKPKEVRKILYKLYEDGLVSYRR   61 (105)
T ss_dssp             STTHHHHHHHHHH----B-HHHHHHTT-S-HHHHHHHHHHHHHHSS-EEEE
T ss_pred             chHHHHHHHHHHcC--CcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeEEEE
Confidence            35567777776554  58889999999999999999999999999996664

Human TFIIE consists of two subunits, TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF []. This entry represents a helix-turn-helix (HTH) domain found in eukaryotic TFIIE-alpha []. It is also found in proteins from archaebacteria that are presumed to be TFIIE-alpha subunits [], the transcriptional regulator SarR, and also DNA-directed RNA polymerase III subunit Rpc3.; PDB: 1VD4_A 1Q1H_A.

>COG3888 Predicted transcriptional regulator [Transcription]

Probab=84.18  E-value=2  Score=36.36  Aligned_cols=51  Identities=27%  Similarity=0.362  Sum_probs=44.2

Q ss_pred             CHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778          29 DNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK   80 (117)
Q Consensus        29 ~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK   80 (117)
                      +.-|+ +....+.||..||-.-.|-.=+|+..++++-+|+.||.+|.||.=|
T Consensus         4 ~~rek-lir~Lk~a~~~GI~Q~eIeel~GlSKStvSEaLs~LE~~giv~Rrk   54 (321)
T COG3888           4 SLREK-LIRELKRAGPEGIDQTEIEELMGLSKSTVSEALSELEKQGIVKRRK   54 (321)
T ss_pred             cHHHH-HHHHHHhcCCCCccHHHHHHHhCcchhHHHHHHHHHHhcCeeeeee
Confidence            33453 4467899999999999999999999999999999999999998643

>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional

Probab=84.00  E-value=6.2  Score=31.41  Aligned_cols=56  Identities=11%  Similarity=0.192  Sum_probs=45.0

Q ss_pred             HHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccCc
Q psy7778          32 EKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGT   92 (117)
Q Consensus        32 E~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg~   92 (117)
                      ...|..++.+.|  -+-..+|....++...++.|=|+.||++|+|+.   ++||--+.+..
T Consensus         7 ~~~Il~~l~~~~--~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l~r---~~GGa~~~~~~   62 (252)
T PRK10906          7 HDAIIELVKQQG--YVSTEELVEHFSVSPQTIRRDLNDLAEQNKILR---HHGGAALPSSS   62 (252)
T ss_pred             HHHHHHHHHHcC--CEeHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE---ecCCEEecCCC
Confidence            346777776644  489999999999999999999999999999865   67776555443

>COG1733 Predicted transcriptional regulators [Transcription]

Probab=83.80  E-value=1.6  Score=31.51  Aligned_cols=34  Identities=26%  Similarity=0.463  Sum_probs=28.7

Q ss_pred             ccc-HHHHHhhcC-CChHHHHHHHHHHhhcCCeeee
Q psy7778          46 GIW-MRDIRFKSN-LMPTQLNKILKQLETKKIIKAV   79 (117)
Q Consensus        46 GIW-tkdIk~ktn-L~~~~l~K~LK~LE~k~LIK~V   79 (117)
                      |-+ -.+|++..+ +.+.+|++.||.||..|+|...
T Consensus        35 g~~RF~eL~r~i~~Is~k~Ls~~Lk~Le~~Glv~R~   70 (120)
T COG1733          35 GPKRFNELRRSIGGISPKMLSRRLKELEEDGLVERV   70 (120)
T ss_pred             CCCcHHHHHHHccccCHHHHHHHHHHHHHCCCEEee
Confidence            543 367888888 9999999999999999999754

>COG3398 Uncharacterized protein conserved in archaea [Function unknown]

Probab=83.57  E-value=2.5  Score=34.66  Aligned_cols=50  Identities=22%  Similarity=0.334  Sum_probs=43.6

Q ss_pred             HHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          32 EKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        32 E~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      -.-+|+.|..  |-|....+++...+++..+++=.|+.||+.++|++.+.-.
T Consensus       103 R~~Iy~~i~~--nPG~~lsEl~~nl~i~R~TlRyhlriLe~~~li~a~~~~g  152 (240)
T COG3398         103 RDGIYNYIKP--NPGFSLSELRANLYINRSTLRYHLRILESNPLIEAGRVGG  152 (240)
T ss_pred             HHHHHHHhcc--CCCccHHHHHHhcCCChHHHHHHHHHHHhCcchhhhccCC
Confidence            3468999876  4588889999999999999999999999999999987554

>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure

Probab=83.54  E-value=2.2  Score=28.64  Aligned_cols=35  Identities=17%  Similarity=0.330  Sum_probs=29.0

Q ss_pred             ccHHHHHhhc-CCChHHHHHHHHHHhhcCCeeeecc
Q psy7778          47 IWMRDIRFKS-NLMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        47 IWtkdIk~kt-nL~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      .=-.+|+.+. ++++.+|++.|+.||..|||.....
T Consensus        19 ~rf~el~~~l~~is~~~L~~~L~~L~~~GLv~r~~~   54 (90)
T PF01638_consen   19 MRFSELQRRLPGISPKVLSQRLKELEEAGLVERRVY   54 (90)
T ss_dssp             EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEE
T ss_pred             CcHHHHHHhcchhHHHHHHHHHHHHHHcchhhcccc
Confidence            3447889998 9999999999999999999977643

The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde []. The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH []. The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. ; PDB: 2F2E_B 3DF8_A 1Z7U_B 1YYV_A 4A5M_D 4A5N_B 2FSW_A 2HZT_D.

>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function

Probab=82.61  E-value=4.5  Score=30.31  Aligned_cols=84  Identities=18%  Similarity=0.197  Sum_probs=59.9

Q ss_pred             CCCHHHH--HHHHHHHHhcCCc-ccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccCccccccchhhhh
Q psy7778          27 DSDNEEK--VVYKIIEEAGNKG-IWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGTVNAMVLPSRKK  103 (117)
Q Consensus        27 ~L~~eE~--lVY~~Ie~AGn~G-IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg~~D~~fI~~l~~  103 (117)
                      ..|++|+  +...+||-+-..| +-++++...||++-+++.+.++.|+..|-|-.  +=.-|.|=++.    .++|-.++
T Consensus         4 ~~T~eer~eLk~rIvElVRe~GRiTi~ql~~~TGasR~Tvk~~lreLVa~G~l~~--~G~~GvF~seq----A~~dw~~~   77 (127)
T PF06163_consen    4 VFTPEEREELKARIVELVREHGRITIKQLVAKTGASRNTVKRYLRELVARGDLYR--HGRSGVFPSEQ----ARKDWDKA   77 (127)
T ss_pred             cCCHHHHHHHHHHHHHHHHHcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCCeEe--CCCccccccHH----HHHHHHHh
Confidence            4566655  6667777666655 78899999999999999999999999876643  11115565553    56777788


Q ss_pred             hhhhhhccccccc
Q psy7778         104 REERQDRGVLLKL  116 (117)
Q Consensus       104 ~~~~~~~~~~~~~  116 (117)
                      |+..-|.+.+.+|
T Consensus        78 ~~~~~~~~~~~~~   90 (127)
T PF06163_consen   78 RKKLVDPDLIWKL   90 (127)
T ss_pred             HHhhccchhhhhC
Confidence            8877776655543

>PRK10736 hypothetical protein; Provisional

Probab=82.61  E-value=3.3  Score=35.55  Aligned_cols=51  Identities=12%  Similarity=-0.012  Sum_probs=43.9

Q ss_pred             CCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778          27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK   80 (117)
Q Consensus        27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK   80 (117)
                      .++.++..||+.+..   .++-..+|-.+++|+...+.-+|=.||-+|+|.+..
T Consensus       305 ~~~~~~~~v~~~l~~---~~~~iD~L~~~~~l~~~~v~~~L~~LEl~G~v~~~~  355 (374)
T PRK10736        305 EVALPFPELLANVGD---EVTPVDVVAERAGQPVPEVVTQLLELELAGWIAAVP  355 (374)
T ss_pred             cccchHHHHHHhcCC---CCCCHHHHHHHHCcCHHHHHHHHHHHHhCCcEEEcC
Confidence            466677888888853   466789999999999999999999999999999874

>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF

Probab=81.87  E-value=3.1  Score=31.61  Aligned_cols=50  Identities=10%  Similarity=0.144  Sum_probs=42.3

Q ss_pred             HHHHHHHHHhcCCcccH--------HHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          33 KVVYKIIEEAGNKGIWM--------RDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        33 ~lVY~~Ie~AGn~GIWt--------kdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      ..|++.|.+.=..|.|.        ++|-.+.|....+|.++|..|+..|+|....+.
T Consensus        11 ~~i~~~l~~~I~~g~~~~G~~LPsE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~~G~   68 (238)
T TIGR02325        11 RQIADKIEQEIAAGHLRAGDYLPAEMQLAERFGVNRHTVRRAIAALVERGLLRAEQGR   68 (238)
T ss_pred             HHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCC
Confidence            35677777776667663        689999999999999999999999999998774

All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.

>PRK09483 response regulator; Provisional

Probab=81.32  E-value=4.7  Score=28.80  Aligned_cols=45  Identities=22%  Similarity=0.277  Sum_probs=39.8

Q ss_pred             ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778          25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK   73 (117)
Q Consensus        25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k   73 (117)
                      +..||+-|+.|+.++.    +|.-.++|-.+.++..++|...++.+-.|
T Consensus       146 ~~~Lt~rE~~vl~~~~----~G~~~~~Ia~~l~is~~TV~~~~~~i~~K  190 (217)
T PRK09483        146 FASLSERELQIMLMIT----KGQKVNEISEQLNLSPKTVNSYRYRMFSK  190 (217)
T ss_pred             ccccCHHHHHHHHHHH----CCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence            5679999999998883    88999999999999999999999888765

>PF04492 Phage_rep_O: Bacteriophage replication protein O ; InterPro: IPR006497 This entry is represented by the N-terminal domain of Bacteriophage lambda, GpO

Probab=81.22  E-value=7.7  Score=27.42  Aligned_cols=53  Identities=17%  Similarity=0.117  Sum_probs=42.3

Q ss_pred             ccCCCHHHHHHHHHHHHh------cCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCee
Q psy7778          25 LKDSDNEEKVVYKIIEEA------GNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIK   77 (117)
Q Consensus        25 ~~~L~~eE~lVY~~Ie~A------Gn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK   77 (117)
                      ..+|+.-|..||-.|---      ..+-|-.-.+-..|+++.+.++++++.|+..++|.
T Consensus        27 ~~dls~rq~ki~~ai~RkTyG~nKk~d~Is~sq~~e~tg~~~~~V~~al~~Li~~~vI~   85 (100)
T PF04492_consen   27 RADLSGRQLKILLAIIRKTYGWNKKMDRISNSQIAEMTGLSRDHVSKALNELIRRGVII   85 (100)
T ss_pred             hccccHHHHHHHHHHHHHccCCCCccceeeHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            368888777666555332      34567788899999999999999999999999993

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0006260 DNA replication

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

Probab=81.18  E-value=1.3  Score=25.61  Aligned_cols=42  Identities=7%  Similarity=0.218  Sum_probs=30.1

Q ss_pred             cHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccCcc
Q psy7778          48 WMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGTV   93 (117)
Q Consensus        48 WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg~~   93 (117)
                      ++.++...+|++..+|.    ..+.+|+|.+.+...+.-+|+..++
T Consensus         2 ~~~e~a~~~gv~~~tlr----~~~~~g~l~~~~~~~~~~~y~~~~v   43 (49)
T cd04761           2 TIGELAKLTGVSPSTLR----YYERIGLLSPARTEGGYRLYSDADL   43 (49)
T ss_pred             cHHHHHHHHCcCHHHHH----HHHHCCCCCCCcCCCCCEEeCHHHH
Confidence            46677888899887654    6688999997666666666665443

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.

>PRK13509 transcriptional repressor UlaR; Provisional

Probab=80.78  E-value=6.9  Score=31.01  Aligned_cols=49  Identities=10%  Similarity=0.202  Sum_probs=40.6

Q ss_pred             HHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCc
Q psy7778          33 KVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIE   86 (117)
Q Consensus        33 ~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~   86 (117)
                      ..|..++.+  +.-+-.++|-..+|....++.|=|+.||+.|+|..   ++||-
T Consensus         8 ~~Il~~l~~--~~~~~~~ela~~l~vS~~TirRdL~~Le~~g~i~r---~~gga   56 (251)
T PRK13509          8 QILLELLAQ--LGFVTVEKVIERLGISPATARRDINKLDESGKLKK---VRNGA   56 (251)
T ss_pred             HHHHHHHHH--cCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE---ecCCc
Confidence            367777775  44578899999999999999999999999999976   45554

>TIGR00122 birA_repr_reg BirA biotin operon repressor domain

Probab=80.46  E-value=7.3  Score=24.59  Aligned_cols=44  Identities=9%  Similarity=0.039  Sum_probs=34.1

Q ss_pred             HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778          34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK   80 (117)
Q Consensus        34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK   80 (117)
                      .+..++.++   -+-..+|..+.++..+++.+.++.|+..|+.-...
T Consensus         4 ~il~~L~~~---~~~~~eLa~~l~vS~~tv~~~l~~L~~~g~~i~~~   47 (69)
T TIGR00122         4 RLLALLADN---PFSGEKLGEALGMSRTAVNKHIQTLREWGVDVLTV   47 (69)
T ss_pred             HHHHHHHcC---CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEec
Confidence            344454433   24589999999999999999999999999955444

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.

>PHA02943 hypothetical protein; Provisional

Probab=80.39  E-value=4.2  Score=31.71  Aligned_cols=71  Identities=11%  Similarity=0.045  Sum_probs=49.8

Q ss_pred             HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccCccccccchhhhhhhhh
Q psy7778          34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGTVNAMVLPSRKKREER  107 (117)
Q Consensus        34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg~~D~~fI~~l~~~~~~  107 (117)
                      .|+.+|   .+-+--+.+|-..+|+...++.-+|+.||..|.|++|+==...-|+-+-+==+..|..++..-.|
T Consensus        15 eILE~L---k~G~~TtseIAkaLGlS~~qa~~~LyvLErEG~VkrV~~G~~tyw~l~~day~~~v~~~~Relwr   85 (165)
T PHA02943         15 KTLRLL---ADGCKTTSRIANKLGVSHSMARNALYQLAKEGMVLKVEIGRAAIWCLDEDAYTNLVFEIKRELWR   85 (165)
T ss_pred             HHHHHH---hcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCceEEEeecceEEEEEChHHHHHHHHHHHHHHHH
Confidence            566777   22235688999999999999999999999999999987444556765553112225555544443

>PRK09764 DNA-binding transcriptional repressor MngR; Provisional

Probab=80.31  E-value=8.4  Score=29.74  Aligned_cols=58  Identities=17%  Similarity=0.264  Sum_probs=45.6

Q ss_pred             HHHHHHHHhcCCccc--------HHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccCcc
Q psy7778          34 VVYKIIEEAGNKGIW--------MRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGTV   93 (117)
Q Consensus        34 lVY~~Ie~AGn~GIW--------tkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg~~   93 (117)
                      .||+.|.+.=..|-|        -++|..+.|..-.+|.++|..|+..|+|..+.+.  |.|-....+
T Consensus         9 qi~~~L~~~I~~g~~~~G~~LPsE~eL~~~~~VSR~TvR~Al~~L~~eGli~r~~G~--GtfV~~~~~   74 (240)
T PRK09764          9 QIADRIREQIARGELKPGDALPTESALQTEFGVSRVTVRQALRQLVEQQILESIQGS--GTYVKEERV   74 (240)
T ss_pred             HHHHHHHHHHHcCCCCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCc--eeEEccccc
Confidence            566667666555554        3899999999999999999999999999998875  566555443

>PRK06266 transcription initiation factor E subunit alpha; Validated

Probab=80.24  E-value=6.6  Score=30.16  Aligned_cols=50  Identities=20%  Similarity=0.250  Sum_probs=40.8

Q ss_pred             CHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778          29 DNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK   80 (117)
Q Consensus        29 ~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK   80 (117)
                      ++....|..++-..|.  +-..+|...+||+.+.+.|+|-.|+..|||...+
T Consensus        21 ~~~~~~Vl~~L~~~g~--~tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~~~r   70 (178)
T PRK06266         21 DEEGFEVLKALIKKGE--VTDEEIAEQTGIKLNTVRKILYKLYDARLADYKR   70 (178)
T ss_pred             CccHhHHHHHHHHcCC--cCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEee
Confidence            3345567776666663  7889999999999999999999999999999543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	117
2yu3_A	95	Solution Structure Of The Domain Swapped Wingedheli		3e-22
2dk5_A	91	Solution Structure Of Winged-Helix Domain In Rna Po		7e-20

>pdb|2YU3|A Chain A, Solution Structure Of The Domain Swapped Wingedhelix In Dna- Directed Rna Polymerase Iii 39 Kda Polypeptide Length = 95

Iteration: 1
 Score =  100 bits (248), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 48/72 (66%), Positives = 62/72 (86%)
Query: 12 LLYKVKDPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLE 71
          LLY++KD     K+K SDN+EK+VY+IIE+AGNKGIW RD+R+KSNL  T++NKILK LE
Sbjct: 19 LLYRIKDSQNAGKMKGSDNQEKLVYQIIEDAGNKGIWSRDVRYKSNLPLTEINKILKNLE 78
Query: 72 TKKIIKAVKSVA 83
          +KK+IKAVKSV+
Sbjct: 79 SKKLIKAVKSVS 90

>pdb|2DK5|A Chain A, Solution Structure Of Winged-Helix Domain In Rna Polymerase Iii 39kda Polypeptide Length = 91

Iteration: 1
 Score = 92.0 bits (227), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 44/60 (73%), Positives = 55/60 (91%)
Query: 24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA 83
          K+K SDN+EK+VY+IIE+AGNKGIW RD+R+KSNL  T++NKILK LE+KK+IKAVKSVA
Sbjct: 14 KMKGSDNQEKLVYQIIEDAGNKGIWSRDVRYKSNLPLTEINKILKNLESKKLIKAVKSVA 73

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	117
2yu3_A	95	DNA-directed RNA polymerase III 39 kDa polypeptide	1e-28
2dk5_A	91	DNA-directed RNA polymerase III 39 kDa polypeptide	4e-26

>2yu3_A DNA-directed RNA polymerase III 39 kDa polypeptide F variant; winged helix domain, RNA polymerase III C39 subunit, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 95

 Score = 98.7 bits (246), Expect = 1e-28
 Identities = 48/76 (63%), Positives = 62/76 (81%)

Query: 9  GGNLLYKVKDPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILK 68
             LLY++KD     K+K SDN+EK+VY+IIE+AGNKGIW RD+R+KSNL  T++NKILK
Sbjct: 16 NTGLLYRIKDSQNAGKMKGSDNQEKLVYQIIEDAGNKGIWSRDVRYKSNLPLTEINKILK 75

Query: 69 QLETKKIIKAVKSVAN 84
           LE+KK+IKAVKSV+ 
Sbjct: 76 NLESKKLIKAVKSVSG 91

>2dk5_A DNA-directed RNA polymerase III 39 kDa polypeptide; structural genomics, winged helix domain, NPPSFA; NMR {Homo sapiens} SCOP: a.4.5.85 Length = 91

 Score = 92.2 bits (229), Expect = 4e-26
 Identities = 45/71 (63%), Positives = 56/71 (78%)

Query: 14 YKVKDPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK 73
              D     K+K SDN+EK+VY+IIE+AGNKGIW RD+R+KSNL  T++NKILK LE+K
Sbjct: 4  GSSGDSQNAGKMKGSDNQEKLVYQIIEDAGNKGIWSRDVRYKSNLPLTEINKILKNLESK 63

Query: 74 KIIKAVKSVAN 84
          K+IKAVKSVA 
Sbjct: 64 KLIKAVKSVAA 74

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	117
2yu3_A	95	DNA-directed RNA polymerase III 39 kDa polypeptide	99.97
2dk5_A	91	DNA-directed RNA polymerase III 39 kDa polypeptide	99.8
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	97.81
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	97.79
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	97.72
3u2r_A	168	Regulatory protein MARR; structural genomics, PSI-	97.55
1p6r_A	82	Penicillinase repressor; transcription regulation,	97.52
3jw4_A	148	Transcriptional regulator, MARR/EMRR family; DNA-b	97.51
1sfx_A	109	Conserved hypothetical protein AF2008; structural	97.48
2frh_A	127	SARA, staphylococcal accessory regulator A; winged	97.45
2nnn_A	140	Probable transcriptional regulator; structural gen	97.45
3nrv_A	148	Putative transcriptional regulator (MARR/EMRR FAM;	97.45
3r0a_A	123	Putative transcriptional regulator; structural gen	97.44
3bj6_A	152	Transcriptional regulator, MARR family; helix-turn	97.42
2vn2_A	128	DNAD, chromosome replication initiation protein; D	97.41
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	97.4
3nqo_A	189	MARR-family transcriptional regulator; structural	97.39
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	97.39
2rdp_A	150	Putative transcriptional regulator MARR; PFAM PF01	97.37
1lj9_A	144	Transcriptional regulator SLYA; HTH DNA binding pr	97.36
3e6m_A	161	MARR family transcriptional regulator; APC88769, s	97.36
1z91_A	147	Organic hydroperoxide resistance transcriptional;	97.35
3oop_A	143	LIN2960 protein; protein structure initiative, PSI	97.34
3g3z_A	145	NMB1585, transcriptional regulator, MARR family; t	97.33
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	97.31
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	97.31
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	97.31
3k0l_A	162	Repressor protein; helix-turn-helix, structural ge	97.3
2fbi_A	142	Probable transcriptional regulator; MARR, APC5816,	97.3
1ku9_A	152	Hypothetical protein MJ223; putative transcription	97.3
4b8x_A	147	SCO5413, possible MARR-transcriptional regulator;	97.29
2a61_A	145	Transcriptional regulator TM0710; APC4350, MCSG, m	97.28
2bv6_A	142	MGRA, HTH-type transcriptional regulator MGRA; mul	97.28
2fu4_A	83	Ferric uptake regulation protein; DNA binding doma	97.27
3cjn_A	162	Transcriptional regulator, MARR family; silicibact	97.25
1okr_A	123	MECI, methicillin resistance regulatory protein ME	97.24
1sd4_A	126	Penicillinase repressor; BLAI, MECI, methicillin,	97.24
2eth_A	154	Transcriptional regulator, putative, MAR family; M	97.24
2gxg_A	146	146AA long hypothetical transcriptional regulator;	97.23
3bja_A	139	Transcriptional regulator, MARR family, putative;	97.22
2g9w_A	138	Conserved hypothetical protein; DNA-binding domain	97.22
2fbh_A	146	Transcriptional regulator PA3341; MARR, transcript	97.21
3f3x_A	144	Transcriptional regulator, MARR family, putative;	97.21
3hsr_A	140	HTH-type transcriptional regulator SARZ; helix-tur	97.2
1tbx_A	99	ORF F-93, hypothetical 11.0 kDa protein; sulfolobu	97.2
1s3j_A	155	YUSO protein; structural genomics, MARR transcript	97.19
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	97.19
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	97.18
2qww_A	154	Transcriptional regulator, MARR family; YP_013417.	97.18
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	97.17
2v79_A	135	DNA replication protein DNAD; primosome, DNA-bindi	97.14
2nyx_A	168	Probable transcriptional regulatory protein, RV14;	97.13
4hbl_A	149	Transcriptional regulator, MARR family; HTH, trans	97.11
3cdh_A	155	Transcriptional regulator, MARR family; helix-turn	97.1
2pex_A	153	Transcriptional regulator OHRR; transcription regu	97.08
2k4b_A	99	Transcriptional regulator; DNA binding protein, wi	97.05
4aik_A	151	Transcriptional regulator SLYA; transcription, tra	97.05
3fm5_A	150	Transcriptional regulator; MCSG, PF04017, PSI, MAR	97.03
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	97.03
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	97.02
3kp7_A	151	Transcriptional regulator TCAR; multiple drug resi	97.0
3s2w_A	159	Transcriptional regulator, MARR family; structural	96.98
2hr3_A	147	Probable transcriptional regulator; MCSG, structur	96.96
1hsj_A	487	Fusion protein consisting of staphylococcus access	96.94
2fxa_A	207	Protease production regulatory protein HPR; protea	96.9
3boq_A	160	Transcriptional regulator, MARR family; MARR famil	96.9
3deu_A	166	Transcriptional regulator SLYA; MARR, WING-helix,	96.86
2fbk_A	181	Transcriptional regulator, MARR family; winged-hel	96.8
2qvo_A	95	Uncharacterized protein AF_1382; PSI, structural g	96.72
1ub9_A	100	Hypothetical protein PH1061; helix-turn-helix moti	96.71
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	96.71
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	96.69
2obp_A	96	Putative DNA-binding protein; structural genomics,	96.61
2xvc_A	59	ESCRT-III, SSO0910; cell cycle, cell division, cyt	96.6
4fx0_A	148	Probable transcriptional repressor protein; helix-	96.54
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	96.53
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	96.49
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	96.4
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	96.31
1fx7_A	230	Iron-dependent repressor IDER; DTXR, iron-dependen	96.27
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	96.23
2y75_A	129	HTH-type transcriptional regulator CYMR; DNA bindi	96.23
2wte_A	244	CSA3; antiviral protein, viral resistance, winged	96.21
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	96.16
2w25_A	150	Probable transcriptional regulatory protein; trans	96.12
3t8r_A	143	Staphylococcus aureus CYMR; transcriptional regula	96.1
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	96.04
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	95.97
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	95.95
1on2_A	142	Transcriptional regulator MNTR; helix-turn-helix,	95.9
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	95.85
1y0u_A	96	Arsenical resistance operon repressor, putative; s	95.68
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	95.68
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	95.65
1r7j_A	95	Conserved hypothetical protein SSO10A; winged heli	95.65
2qq9_A	226	Diphtheria toxin repressor; regulator, DTXR, helix	95.62
3lwf_A	159	LIN1550 protein, putative transcriptional regulato	95.62
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	95.42
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	95.41
1xd7_A	145	YWNA; structural genomics, protein structure initi	95.41
3b73_A	111	PHIH1 repressor-like protein; winged-helix-turn-he	95.38
1ylf_A	149	RRF2 family protein; structural genomics, transcri	95.24
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	95.21
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	95.17
3df8_A	111	Possible HXLR family transcriptional factor; APC89	95.07
2h09_A	155	Transcriptional regulator MNTR; transcription regu	95.0
3k69_A	162	Putative transcription regulator; putative transcr	94.95
1mzb_A	136	Ferric uptake regulation protein; ferric uptake re	94.94
3jth_A	98	Transcription activator HLYU; transcription factor	94.93
2fe3_A	145	Peroxide operon regulator; oxidative stress regula	94.92
2hzt_A	107	Putative HTH-type transcriptional regulator YTCD;	94.9
1sfu_A	75	34L protein; protein/Z-DNA complex, DNA binding pr	94.77
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	94.75
1u2w_A	122	CADC repressor, cadmium efflux system accessory pr	94.64
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	94.62
1z7u_A	112	Hypothetical protein EF0647; winged-helix-turn-hel	94.52
2jsc_A	118	Transcriptional regulator RV1994C/MT2050; cadmium,	94.51
1bja_A	95	Transcription regulatory protein MOTA; activation	94.34
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	94.31
2w57_A	150	Ferric uptake regulation protein; gene regulation,	94.22
3i4p_A	162	Transcriptional regulator, ASNC family; PSI, struc	94.22
3f6o_A	118	Probable transcriptional regulator, ARSR family pr	94.21
2pg4_A	95	Uncharacterized protein; structural genomics, join	94.19
1z6r_A	406	MLC protein; transcriptional repressor, ROK family	94.09
2o03_A	131	Probable zinc uptake regulation protein FURB; DNA-	94.07
2kko_A	108	Possible transcriptional regulatory protein (possi	94.04
1z05_A	429	Transcriptional regulator, ROK family; structural	94.01
1uly_A	192	Hypothetical protein PH1932; helix-turn-helix, str	93.94
3hrs_A	214	Metalloregulator SCAR; DTXR/MNTR family member, tr	93.91
2xig_A	150	Ferric uptake regulation protein; hpfur, transcrip	93.87
2zcw_A	202	TTHA1359, transcriptional regulator, FNR/CRP famil	93.85
3cta_A	230	Riboflavin kinase; structural genomics, transferas	93.85
3b02_A	195	Transcriptional regulator, CRP family; structural	93.76
2f2e_A	146	PA1607; transcription factor, helix-TRUN-helix, AP	93.74
3ryp_A	210	Catabolite gene activator; CAMP receptor protein (	93.36
1r1t_A	122	Transcriptional repressor SMTB; zinc, transcriptio	93.3
2fsw_A	107	PG_0823 protein; alpha-beta structure, helix-turn-	93.15
3iwz_A	230	CAP-like, catabolite activation-like protein; XCC,	93.12
3eyy_A	145	Putative iron uptake regulatory protein; NUR, nick	93.11
2lnb_A	80	Z-DNA-binding protein 1; structural genomics, nort	93.06
2p4w_A	202	Transcriptional regulatory protein ARSR family; ar	92.97
1mkm_A	249	ICLR transcriptional regulator; structural genomic	92.97
1v4r_A	102	Transcriptional repressor; helix-turn-helix, winge	92.69
1jhf_A	202	LEXA repressor; LEXA SOS repressor, hydrolase; 1.8	92.67
2hoe_A	380	N-acetylglucosamine kinase; TM1224, structural gen	92.56
2oz6_A	207	Virulence factor regulator; winged helix, helix-tu	92.46
2xrn_A	241	HTH-type transcriptional regulator TTGV; DNA-bindi	92.27
1zyb_A	232	Transcription regulator, CRP family; NP_813211.1,	92.25
2pjp_A	121	Selenocysteine-specific elongation factor; SELB, p	92.06
1ft9_A	222	Carbon monoxide oxidation system transcription reg	91.9
3neu_A	125	LIN1836 protein; structural genomics, PSI-2, prote	91.82
1xmk_A	79	Double-stranded RNA-specific adenosine deaminase;	91.78
3f6v_A	151	Possible transcriptional regulator, ARSR family pr	91.67
1yyv_A	131	Putative transcriptional regulator; reductive meth	91.66
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	91.57
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	91.46
3dv8_A	220	Transcriptional regulator, CRP/FNR family; cyclic	91.4
2zkz_A	99	Transcriptional repressor PAGR; protein-DNA, HTH m	91.32
3d0s_A	227	Transcriptional regulatory protein; CAMP receptor	91.25
3kcc_A	260	Catabolite gene activator; helix-turn-helix, CAMP,	91.22
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	91.15
3rkx_A	323	Biotin-[acetyl-COA-carboxylase] ligase; biotin pro	91.13
2ek5_A	129	Predicted transcriptional regulators; helix-turn-h	91.07
2gau_A	232	Transcriptional regulator, CRP/FNR family; structu	91.02
3tqn_A	113	Transcriptional regulator, GNTR family; regulatory	90.97
3l7w_A	108	Putative uncharacterized protein SMU.1704; PADR, t	90.97
3mwm_A	139	ZUR, putative metal uptake regulation protein; FUR	90.95
3by6_A	126	Predicted transcriptional regulator; structural ge	90.91
2fmy_A	220	COOA, carbon monoxide oxidation system transcripti	90.89
3e6c_C	250	CPRK, cyclic nucleotide-binding protein; CPRK, hal	90.71
3la7_A	243	Global nitrogen regulator; activator, DNA-binding,	90.48
1fse_A	74	GERE; helix-turn-helix DNA-binding protein transcr	90.4
2p8t_A	200	Hypothetical protein PH0730; pyrococcus horikoshii	90.4
2pi2_A	270	Replication protein A 32 kDa subunit; FULL-length	90.38
3lmm_A	583	Uncharacterized protein; multi-domained alpha-beta	90.02
4ev0_A	216	Transcription regulator, CRP family; CAMP binding,	89.93
3ulq_B	90	Transcriptional regulatory protein COMA; tetratric	89.4
4a5n_A	131	Uncharacterized HTH-type transcriptional regulato;	89.4
3mq0_A	275	Transcriptional repressor of the blcabc operon; he	88.99
2w48_A	315	Sorbitol operon regulator; SORC, activator, repres	88.99
3dkw_A	227	DNR protein; CRP-FNR, HTH, beta barrel, dimerizati	88.78
3e97_A	231	Transcriptional regulator, CRP/FNR family; YP_6044	88.6
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	88.01
1je8_A	82	Nitrate/nitrite response regulator protein NARL; p	88.01
3maj_A	382	DNA processing chain A; MCSG, PSI-2, structural ge	87.96
2g7u_A	257	Transcriptional regulator; ICLR family, structural	87.67
3c57_A	95	Two component transcriptional regulatory protein;	87.28
1o5l_A	213	Transcriptional regulator, CRP family; TM1171, str	87.26
2b0l_A	102	GTP-sensing transcriptional pleiotropic repressor;	86.94
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	86.79
2xzm_8	143	RPS25E,; ribosome, translation; 3.93A {Tetrahymena	86.72
3fx3_A	237	Cyclic nucleotide-binding protein; helix_TURN_heli	86.7
4ham_A	134	LMO2241 protein; structural genomics, PSI-biology,	86.27
2o0y_A	260	Transcriptional regulator; ICLR-family, structural	85.79
3u5c_Z	108	RP45, S31, YS23, 40S ribosomal protein S25-A; tran	84.95
3edp_A	236	LIN2111 protein; APC88337, listeria innocua CLIP11	84.91
2rnj_A	91	Response regulator protein VRAR; HTH LUXR-type dom	84.84
4ets_A	162	Ferric uptake regulation protein; metal binding pr	84.79
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	84.45
3r4k_A	260	Transcriptional regulator, ICLR family; DNA/RNA-bi	84.41
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	84.3
2qlz_A	232	Transcription factor PF0095; 2.50A {Pyrococcus fur	84.16
3u1d_A	151	Uncharacterized protein; GNTR-superfamily, structu	84.09
4g6q_A	182	Putative uncharacterized protein; structural genom	83.62
2o0m_A	345	Transcriptional regulator, SORC family; structural	83.41
1xma_A	145	Predicted transcriptional regulator; southea colla	83.41
2ia2_A	265	Putative transcriptional regulator; SAD, PSI-2, st	83.3
4esb_A	115	Transcriptional regulator, PADR family; DNA bindin	83.29
3iz6_V	108	40S ribosomal protein S25 (S25E); eukaryotic ribos	83.2
1p4w_A	99	RCSB; solution structure, DNA binding domain, DNA	82.76
3hhh_A	116	Transcriptional regulator, PADR family; PF03551, s	82.56
1x3u_A	79	Transcriptional regulatory protein FIXJ; helix-tur	82.15
2esh_A	118	Conserved hypothetical protein TM0937; APC5794, st	81.81
3ic7_A	126	Putative transcriptional regulator; helix-turn-hel	81.55
4esf_A	117	PADR-like transcriptional regulator; PADR family,	81.51
2o8x_A	70	Probable RNA polymerase sigma-C factor; promoter r	80.98
3qph_A	342	TRMB, A global transcription regulator; transcript	80.81
1hw1_A	239	FADR, fatty acid metabolism regulator protein; hel	80.55
3ri2_A	123	Transcriptional regulator, PADR-like family; PSI-b	80.5
3eet_A	272	Putative GNTR-family transcriptional regulator; st	80.48
1stz_A	338	Heat-inducible transcription repressor HRCA homol;	80.43
2wv0_A	243	YVOA, HTH-type transcriptional repressor YVOA; DNA	80.28
3bwg_A	239	Uncharacterized HTH-type transcriptional regulato;	80.05

>2yu3_A DNA-directed RNA polymerase III 39 kDa polypeptide F variant; winged helix domain, RNA polymerase III C39 subunit, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.97  E-value=7.6e-31  Score=183.64  Aligned_cols=83  Identities=58%  Similarity=0.861  Sum_probs=79.9

Q ss_pred             ccceecCCeEEEEEeCccccccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778           3 ANGFLIGGNLLYKVKDPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus         3 ~~~~~~~~~l~yk~~~~e~a~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      ..+|+.+++++|+++++++|.++++||++|++||++|++|||+|||++||+.++|||+++|+||||.||+++|||+|+||
T Consensus        10 ~~l~k~~~~l~~~~~~~~~a~k~~~Lt~~E~lVy~~I~~aGn~GIw~kdL~~~tnL~~~~vtkiLK~LE~k~lIK~Vksv   89 (95)
T 2yu3_A           10 LDLLRSNTGLLYRIKDSQNAGKMKGSDNQEKLVYQIIEDAGNKGIWSRDVRYKSNLPLTEINKILKNLESKKLIKAVKSV   89 (95)
T ss_dssp             CCCCCCCCCCEEEECCSSSCCCCCSCSHHHHHHHHHHHHHTTSCEEHHHHHHHHTCCHHHHHHHHHHHHHHTSEEEECCS
T ss_pred             EEEEEcCCEEEEEEeCHHHHhhhcCCCHHHHHHHHHHHHhCCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCEEEecCc
Confidence            35788899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cCC
Q psy7778          83 ANI   85 (117)
Q Consensus        83 ~gg   85 (117)
                      ++.
T Consensus        90 ~~~   92 (95)
T 2yu3_A           90 SGP   92 (95)
T ss_dssp             CSS
T ss_pred             cCC
Confidence            864

>2dk5_A DNA-directed RNA polymerase III 39 kDa polypeptide; structural genomics, winged helix domain, NPPSFA; NMR {Homo sapiens} SCOP: a.4.5.85

Probab=99.80  E-value=6.3e-20  Score=126.04  Aligned_cols=67  Identities=67%  Similarity=0.983  Sum_probs=65.3

Q ss_pred             eCccccccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          17 KDPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        17 ~~~e~a~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      +++++|.++.+||++|.+||++|++|||+|||+++|+.++||+++++++||+.||+++|||.+++++
T Consensus         7 ~~~~~~~k~~~Lt~~q~~Vl~~I~~~g~~gi~qkeLa~~~~l~~~tvt~iLk~LE~kglIkr~~~~~   73 (91)
T 2dk5_A            7 GDSQNAGKMKGSDNQEKLVYQIIEDAGNKGIWSRDVRYKSNLPLTEINKILKNLESKKLIKAVKSVA   73 (91)
T ss_dssp             CCCCCCCCCCCSCSSHHHHHHHHHHHCTTCEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEECCSS
T ss_pred             cCHHHHhhhcCCCHHHHHHHHHHHHcCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCCC
Confidence            4789999999999999999999999999999999999999999999999999999999999999998

>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=97.81  E-value=6.3e-05  Score=50.79  Aligned_cols=58  Identities=21%  Similarity=0.211  Sum_probs=54.1

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      -+||..|..|+..|...+..|+-..+|...++++.+.++++|+.||.+|||....+-.
T Consensus        27 ~~lt~~~~~vL~~l~~~~~~~~t~~ela~~l~~~~~tvs~~l~~Le~~Gli~r~~~~~   84 (139)
T 3eco_A           27 FDITNEQGHTLGYLYAHQQDGLTQNDIAKALQRTGPTVSNLLRNLERKKLIYRYVDAQ   84 (139)
T ss_dssp             GTCCHHHHHHHHHHHHSTTTCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECCC
T ss_pred             cCCCHHHHHHHHHHHhcCCCCcCHHHHHHHhCCCcccHHHHHHHHHHCCCEeecCCCC
Confidence            5799999999999999988899999999999999999999999999999999887654

>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=97.79  E-value=8.1e-05  Score=50.05  Aligned_cols=58  Identities=17%  Similarity=0.248  Sum_probs=53.4

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      -+|+..|..|+..|...++.|+-..+|...++++.+.++++|+.||.+|||....+-.
T Consensus        30 ~~lt~~~~~iL~~l~~~~~~~~~~~ela~~l~~~~~tvs~~l~~Le~~Gli~r~~~~~   87 (141)
T 3bro_A           30 YDLTGTQMTIIDYLSRNKNKEVLQRDLESEFSIKSSTATVLLQRMEIKKLLYRKVSGK   87 (141)
T ss_dssp             TTCCHHHHHHHHHHHHTTTSCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECSS
T ss_pred             cCCCHHHHHHHHHHHHCCCCCcCHHHHHHHHCCCcchHHHHHHHHHHCCCEEeeCCCc
Confidence            4799999999999999888899999999999999999999999999999999887643

>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=97.72  E-value=7.9e-05  Score=48.79  Aligned_cols=58  Identities=21%  Similarity=0.259  Sum_probs=51.7

Q ss_pred             HHHHHHHHHHHhc-CCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccc
Q psy7778          31 EEKVVYKIIEEAG-NKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLT   89 (117)
Q Consensus        31 eE~lVY~~Ie~AG-n~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYt   89 (117)
                      .|+.|+.++.+.| .+++-.++|-.+.|++.++|++.|+.||..|+|..+-+ +.|.|+-
T Consensus        15 ~~~~IL~~L~~~~~~~~~t~~eLA~~Lgvs~~tV~~~L~~L~~~G~I~~~g~-~~~~W~i   73 (77)
T 1qgp_A           15 QEQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQKEAG-TPPLWKI   73 (77)
T ss_dssp             HHHHHHHHHHHHCSSSCEEHHHHHHHHCCCHHHHHHHHHHHHHHTSEEEECS-SSCEEEE
T ss_pred             HHHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecCC-CCCceEe
Confidence            4678999999999 68899999999999999999999999999999998864 5688864

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

Probab=97.55  E-value=0.00015  Score=50.91  Aligned_cols=57  Identities=5%  Similarity=0.168  Sum_probs=50.6

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      -+|+..|..|+..|...|+.|+-..+|...+++..+.++++|+.||.+|||....+-
T Consensus        42 ~glt~~q~~vL~~l~~~~~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~~   98 (168)
T 3u2r_A           42 FELSAQQYNTLRLLRSVHPEGMATLQIADRLISRAPDITRLIDRLDDRGLVLRTRKP   98 (168)
T ss_dssp             TTCCHHHHHHHHHHHHHTTSCEEHHHHHHHC---CTHHHHHHHHHHHTTSEEEEEET
T ss_pred             cCCCHHHHHHHHHHHhcCCCCcCHHHHHHHHCCChhhHHHHHHHHHHCCCEeecCCC
Confidence            479999999999999999999999999999999999999999999999999987764

>1p6r_A Penicillinase repressor; transcription regulation, DNA-binding, winged helix protein, bacterial resistance to antibiotics; NMR {Bacillus licheniformis} SCOP: a.4.5.39 PDB: 2p7c_B

Probab=97.52  E-value=0.00024  Score=45.32  Aligned_cols=56  Identities=20%  Similarity=0.246  Sum_probs=49.8

Q ss_pred             cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcC----CChHHHHHHHHHHhhcCCeeeecc
Q psy7778          24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSN----LMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktn----L~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      +..+||+.|..|+.+|..  +.++-..+|-...+    ++.+++++.|+.||.+|+|...++
T Consensus         3 ~~~~lt~~e~~vL~~L~~--~~~~t~~ei~~~l~~~~~~s~~Tv~~~l~rL~~kGlv~r~~~   62 (82)
T 1p6r_A            3 KIPQISDAELEVMKVIWK--HSSINTNEVIKELSKTSTWSPKTIQTMLLRLIKKGALNHHKE   62 (82)
T ss_dssp             CCCCCCHHHHHHHHHHHT--SSSEEHHHHHHHHHHHSCCCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             ccCCCCHHHHHHHHHHHc--CCCCCHHHHHHHHhhcCCccHHHHHHHHHHHHHCCCeEEEec
Confidence            356899999999999987  56899999999986    789999999999999999998864

>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=97.51  E-value=0.00013  Score=50.02  Aligned_cols=58  Identities=17%  Similarity=0.149  Sum_probs=45.5

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      -+||..|..|+..|...++.|+-..+|...++++.+.++++|+.||.+|||....+-.
T Consensus        37 ~glt~~q~~vL~~l~~~~~~~~t~~eLa~~l~~~~~~vs~~l~~L~~~Glv~r~~~~~   94 (148)
T 3jw4_A           37 LGLNSQQGRMIGYIYENQESGIIQKDLAQFFGRRGASITSMLQGLEKKGYIERRIPEN   94 (148)
T ss_dssp             TTCCHHHHHHHHHHHHHTTTCCCHHHHHHC------CHHHHHHHHHHTTSBCCC----
T ss_pred             CCCCHHHHHHHHHHHhCCCCCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEeeCCCC
Confidence            4799999999999999888899999999999999999999999999999999887643

>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=97.48  E-value=0.00043  Score=44.37  Aligned_cols=55  Identities=15%  Similarity=0.192  Sum_probs=49.0

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      -+|++.+..|+.+|...  .++-..+|-..++++.++++++|+.|+.+|+|....+-
T Consensus        16 ~~l~~~~~~il~~l~~~--~~~s~~ela~~l~is~~tv~~~l~~L~~~glv~~~~~~   70 (109)
T 1sfx_A           16 LSFKPSDVRIYSLLLER--GGMRVSEIARELDLSARFVRDRLKVLLKRGFVRREIVE   70 (109)
T ss_dssp             TCCCHHHHHHHHHHHHH--CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEEE
T ss_pred             cCCCHHHHHHHHHHHHc--CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEeec
Confidence            46888899999999764  46889999999999999999999999999999988764

>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=97.45  E-value=0.00026  Score=48.41  Aligned_cols=59  Identities=22%  Similarity=0.187  Sum_probs=53.0

Q ss_pred             ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      --+|+..|..|...|...+..|+-..+|...++++.+.++++|+.||.+|||....+-.
T Consensus        32 ~~~lt~~q~~vL~~l~~~~~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~~~   90 (127)
T 2frh_A           32 EFSISFEEFAVLTYISENKEKEYYLKDIINHLNYKQPQVVKAVKILSQEDYFDKKRNEH   90 (127)
T ss_dssp             TTCCCHHHHHHHHHHHHTCCSEEEHHHHHHHSSSHHHHHHHHHHHHHHTTSSCCBCCSS
T ss_pred             HcCCCHHHHHHHHHHHhccCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCC
Confidence            34799999999999988766899999999999999999999999999999998876654

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

Probab=97.45  E-value=0.00046  Score=46.09  Aligned_cols=54  Identities=7%  Similarity=0.116  Sum_probs=49.6

Q ss_pred             CCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      +|+..|..|+..|...|  |+-..+|...++++.+.++++|+.||.+|+|....+-
T Consensus        35 ~l~~~~~~iL~~l~~~~--~~t~~ela~~l~~~~~tvs~~l~~L~~~glv~r~~~~   88 (140)
T 2nnn_A           35 GLTPTQWAALVRLGETG--PCPQNQLGRLTAMDAATIKGVVERLDKRGLIQRSADP   88 (140)
T ss_dssp             CCCHHHHHHHHHHHHHS--SBCHHHHHHHTTCCHHHHHHHHHHHHHTTCEEEEEET
T ss_pred             CCCHHHHHHHHHHHHcC--CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeeCCC
Confidence            89999999999998766  8999999999999999999999999999999987553

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

Probab=97.45  E-value=0.00036  Score=47.49  Aligned_cols=55  Identities=18%  Similarity=0.144  Sum_probs=48.1

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      -+|+..|..|+..|...|  |+-..+|...++++++.++++|+.||.+|||....+-
T Consensus        36 ~~l~~~~~~iL~~l~~~~--~~t~~ela~~l~~~~~tvs~~l~~Le~~Glv~r~~~~   90 (148)
T 3nrv_A           36 FGIGMTEWRIISVLSSAS--DCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHS   90 (148)
T ss_dssp             GTCCHHHHHHHHHHHHSS--SBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC----
T ss_pred             cCCCHHHHHHHHHHHcCC--CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeecCC
Confidence            379999999999998876  9999999999999999999999999999999987654

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

Probab=97.44  E-value=0.00046  Score=47.72  Aligned_cols=60  Identities=13%  Similarity=0.092  Sum_probs=52.6

Q ss_pred             cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      ..-+|++.|..||.++..++...+-..+|..+++++.+++.+.|+.|+.+|+|.......
T Consensus        20 ~~~gLt~~e~~il~~L~~~~~~~~t~~eLa~~l~~s~sTV~r~L~~L~~~GlV~r~~~~~   79 (123)
T 3r0a_A           20 CALNLTKADLNVMKSFLNEPDRWIDTDALSKSLKLDVSTVQRSVKKLHEKEILQRSQQNL   79 (123)
T ss_dssp             HHHTCCHHHHHHHHHHHHSTTCCEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEEEEC
T ss_pred             HHcCCCHHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeeCCcc
Confidence            356899999999999987765449999999999999999999999999999999876543

>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=97.42  E-value=0.00046  Score=47.00  Aligned_cols=56  Identities=7%  Similarity=0.138  Sum_probs=50.8

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      .+|+..+..|+..|...|  |+-..+|...++++.+.++++|+.||.+|||....+-.
T Consensus        36 ~~lt~~~~~iL~~l~~~~--~~t~~ela~~l~~~~~~vs~~l~~Le~~Glv~r~~~~~   91 (152)
T 3bj6_A           36 EGVTVGQRAILEGLSLTP--GATAPQLGAALQMKRQYISRILQEVQRAGLIERRTNPE   91 (152)
T ss_dssp             TTCCHHHHHHHHHHHHST--TEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECCSS
T ss_pred             cCCCHHHHHHHHHHHhCC--CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeeecCCcc
Confidence            479999999999998765  89999999999999999999999999999999987643

>2vn2_A DNAD, chromosome replication initiation protein; DNA replication, primosome; 2.3A {Geobacillus kaustophilus HTA426}

Probab=97.41  E-value=0.00041  Score=48.60  Aligned_cols=61  Identities=11%  Similarity=0.073  Sum_probs=51.6

Q ss_pred             cccc--CCCHHHHHHHHHHHHh---cCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          23 EKLK--DSDNEEKVVYKIIEEA---GNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        23 ~k~~--~L~~eE~lVY~~Ie~A---Gn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      ..++  +|++.|..||-.|...   |+.++-..+|..++|+..+.++++|+.||++|||.-..+-.
T Consensus        23 ~~y~~lgLt~~e~~vll~L~~~~~~~~~~ps~~~LA~~l~~s~~~V~~~l~~Le~kGlI~~~~~~~   88 (128)
T 2vn2_A           23 GHYKQLGLGEGELVLLLHMQSFFEEGVLFPTPAELAERMTVSAAECMEMVRRLLQKGMIAIEEHTD   88 (128)
T ss_dssp             TTTTTTTCCHHHHHHHHHHHHHHTTTCSSCCHHHHHHTSSSCHHHHHHHHHHHHHTTSSEECC---
T ss_pred             HHHHHcCCCHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEeEEC
Confidence            4455  8999999999999876   56669999999999999999999999999999998876643

>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=97.40  E-value=0.00055  Score=45.87  Aligned_cols=55  Identities=16%  Similarity=0.082  Sum_probs=49.4

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      -+|+..|..|+..|...|  |+-..+|...++++++.++++|+.||.+|||....+-
T Consensus        30 ~~lt~~~~~iL~~l~~~~--~~~~~~la~~l~~~~~tvs~~l~~L~~~gli~r~~~~   84 (138)
T 1jgs_A           30 LDITAAQFKVLCSIRCAA--CITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNP   84 (138)
T ss_dssp             TTSCHHHHHHHHHHHHHS--SBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECT
T ss_pred             cCCCHHHHHHHHHHHhcC--CCCHHHHHHHHCCChHHHHHHHHHHHHCCCEEecCCc
Confidence            479999999999997644  7899999999999999999999999999999987654

>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=97.39  E-value=0.00039  Score=50.34  Aligned_cols=59  Identities=12%  Similarity=0.112  Sum_probs=54.3

Q ss_pred             cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      .+.+||..|..|...|....+.|+-..+|...++++.+.++++|+.||.+|||....+-
T Consensus        35 ~~~~lt~~q~~vL~~L~~~~~~~~t~~eLa~~l~is~~tvs~~l~~Le~~GlV~r~~~~   93 (189)
T 3nqo_A           35 YFGILTSRQYMTILSILHLPEEETTLNNIARKMGTSKQNINRLVANLEKNGYVDVIPSP   93 (189)
T ss_dssp             HHCSSCHHHHHHHHHHHHSCGGGCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEECS
T ss_pred             HHccCCHHHHHHHHHHHhccCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCC
Confidence            45579999999999999887889999999999999999999999999999999988764

>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=97.39  E-value=0.00028  Score=47.98  Aligned_cols=56  Identities=16%  Similarity=0.309  Sum_probs=45.0

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      -+||+.|..|...|...|  |+-..+|...++++.+.++++|+.||.+|||....+-.
T Consensus        33 ~~lt~~~~~vL~~l~~~~--~~t~~eLa~~l~~~~~tvs~~l~~L~~~Glv~r~~~~~   88 (142)
T 3ech_A           33 LDLTPPDVHVLKLIDEQR--GLNLQDLGRQMCRDKALITRKIRELEGRNLVRRERNPS   88 (142)
T ss_dssp             CCCCHHHHHHHHHHHHTT--TCCHHHHHHHHC---CHHHHHHHHHHHTTSEEC-----
T ss_pred             CCCCHHHHHHHHHHHhCC--CcCHHHHHHHhCCCHHHHHHHHHHHHHCCCEeeccCCC
Confidence            579999999999998866  89999999999999999999999999999999887653

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

Probab=97.37  E-value=0.0006  Score=46.31  Aligned_cols=55  Identities=13%  Similarity=0.195  Sum_probs=49.9

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      -+|+..|..|+..|...|  |+-..+|...++++.+.++++|+.||.+|||....+-
T Consensus        38 ~~l~~~~~~iL~~l~~~~--~~t~~ela~~l~~~~~tvs~~l~~Le~~Glv~r~~~~   92 (150)
T 2rdp_A           38 YPITPPQFVALQWLLEEG--DLTVGELSNKMYLACSTTTDLVDRMERNGLVARVRDE   92 (150)
T ss_dssp             SSSCHHHHHHHHHHHHHC--SBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECC
T ss_pred             CCCCHHHHHHHHHHHHcC--CCCHHHHHHHHCCCchhHHHHHHHHHHCCCeeecCCC
Confidence            479999999999998865  7999999999999999999999999999999987654

>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=97.36  E-value=0.00044  Score=46.68  Aligned_cols=55  Identities=16%  Similarity=0.109  Sum_probs=49.8

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      -+||..+..|+..|...|  |+-..+|...++++++.++++|+.||.+|+|....+-
T Consensus        25 ~~lt~~~~~iL~~l~~~~--~~t~~~la~~l~~s~~~vs~~l~~Le~~gli~r~~~~   79 (144)
T 1lj9_A           25 LSLTRGQYLYLVRVCENP--GIIQEKIAELIKVDRTTAARAIKRLEEQGFIYRQEDA   79 (144)
T ss_dssp             GTCTTTHHHHHHHHHHST--TEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECS
T ss_pred             cCCCHHHHHHHHHHHHCc--CcCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEeecCC
Confidence            479999999999998754  8999999999999999999999999999999987654

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

Probab=97.36  E-value=0.00054  Score=47.68  Aligned_cols=56  Identities=9%  Similarity=0.063  Sum_probs=49.6

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      -+|+..|..|+..|...|  |+-..+|-..++++.+.++++|+.||.+|||....+-.
T Consensus        49 ~glt~~q~~vL~~l~~~~--~~t~~eLa~~l~~~~~~vs~~l~~Le~~Glv~r~~~~~  104 (161)
T 3e6m_A           49 EKLPTPKLRLLSSLSAYG--ELTVGQLATLGVMEQSTTSRTVDQLVDEGLAARSISDA  104 (161)
T ss_dssp             HTCCHHHHHHHHHHHHHS--EEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEECC---
T ss_pred             cCCCHHHHHHHHHHHhCC--CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeeCCcc
Confidence            479999999999998876  89999999999999999999999999999999887643

>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=97.35  E-value=0.00048  Score=46.65  Aligned_cols=55  Identities=15%  Similarity=0.169  Sum_probs=50.2

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      -+|+..|..|+..|...|  ++-..+|...++++++.++++|+.||.+|||....+-
T Consensus        36 ~~l~~~~~~iL~~l~~~~--~~~~~~la~~l~~~~~tvs~~l~~L~~~glv~r~~~~   90 (147)
T 1z91_A           36 LNITYPQYLALLLLWEHE--TLTVKKMGEQLYLDSGTLTPMLKRMEQQGLITRKRSE   90 (147)
T ss_dssp             TCCCHHHHHHHHHHHHHS--EEEHHHHHHTTTCCHHHHHHHHHHHHHHTSEECCBCS
T ss_pred             cCCCHHHHHHHHHHHHCC--CCCHHHHHHHHCCCcCcHHHHHHHHHHCCCEEeccCC
Confidence            479999999999998876  8999999999999999999999999999999987663

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

Probab=97.34  E-value=0.00067  Score=45.97  Aligned_cols=56  Identities=23%  Similarity=0.205  Sum_probs=49.2

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      -+|++.|..|+..|...  .|+-..+|...++++.+.++++|+.||.+|||....+-.
T Consensus        33 ~~lt~~~~~iL~~l~~~--~~~t~~eLa~~l~~~~~~vs~~l~~L~~~Glv~r~~~~~   88 (143)
T 3oop_A           33 YDVTPEQWSVLEGIEAN--EPISQKEIALWTKKDTPTVNRIVDVLLRKELIVREISTE   88 (143)
T ss_dssp             SSSCHHHHHHHHHHHHH--SSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEC---
T ss_pred             CCCCHHHHHHHHHHHHc--CCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCeeccCCCc
Confidence            47999999999999876  689999999999999999999999999999999887654

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

Probab=97.33  E-value=0.00073  Score=45.89  Aligned_cols=57  Identities=16%  Similarity=0.106  Sum_probs=51.2

Q ss_pred             ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      -.+||..|..|...|...|  |+-..+|...++++.+.++++|+.||.+|||....+-.
T Consensus        26 ~~~lt~~q~~iL~~l~~~~--~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~~~   82 (145)
T 3g3z_A           26 QQDLNYNLFAVLYTLATEG--SRTQKHIGEKWSLPKQTVSGVCKTLAGQGLIEWQEGEQ   82 (145)
T ss_dssp             TTTCCHHHHHHHHHHHHHC--SBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEECCCSS
T ss_pred             HcCCCHHHHHHHHHHHHCC--CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeeccCCC
Confidence            4579999999999998877  59999999999999999999999999999999876643

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

Probab=97.31  E-value=0.0009  Score=44.75  Aligned_cols=55  Identities=9%  Similarity=0.073  Sum_probs=49.9

Q ss_pred             CCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      +|+..+..|+..|...|  ++-..+|...++++++.++++|+.||.+|+|....+-.
T Consensus        28 ~l~~~~~~iL~~l~~~~--~~~~~ela~~l~is~~~vs~~l~~L~~~gli~~~~~~~   82 (142)
T 3bdd_A           28 GISLTRYSILQTLLKDA--PLHQLALQERLQIDRAAVTRHLKLLEESGYIIRKRNPD   82 (142)
T ss_dssp             SSCHHHHHHHHHHHHHC--SBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECSS
T ss_pred             CCCHHHHHHHHHHHhCC--CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCC
Confidence            89999999999998765  79999999999999999999999999999999887643

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

Probab=97.31  E-value=0.0008  Score=44.92  Aligned_cols=55  Identities=13%  Similarity=0.147  Sum_probs=49.8

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      -+|++.|..|+..|...  .|+-..+|...++++.+.++++|+.||.+|+|....+-
T Consensus        25 ~~l~~~~~~iL~~l~~~--~~~~~~ela~~l~~s~~tvs~~l~~L~~~glv~~~~~~   79 (138)
T 3bpv_A           25 LNLTDAQVACLLRIHRE--PGIKQDELATFFHVDKGTIARTLRRLEESGFIEREQDP   79 (138)
T ss_dssp             GTCCHHHHHHHHHHHHS--TTCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEET
T ss_pred             cCCCHHHHHHHHHHHHc--CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeecCC
Confidence            47999999999999874  68999999999999999999999999999999987654

>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=97.31  E-value=0.00068  Score=45.08  Aligned_cols=60  Identities=20%  Similarity=0.232  Sum_probs=51.7

Q ss_pred             HHHHHHHHHHHhc-CCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccC
Q psy7778          31 EEKVVYKIIEEAG-NKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEG   91 (117)
Q Consensus        31 eE~lVY~~Ie~AG-n~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg   91 (117)
                      -++.|+.++.+.| .+++-..+|-.+.|++.+.|++.|+.|+..|+|..+-+ +.|.|+--.
T Consensus        11 ~~~~IL~~L~~~~pg~~~t~~eLA~~Lgvsr~tV~~~L~~Le~~G~I~~~g~-~~~~W~i~~   71 (81)
T 1qbj_A           11 QEQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQKEAG-TPPLWKIAV   71 (81)
T ss_dssp             HHHHHHHHHHHHCTTCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEESS-SSCEEEEC-
T ss_pred             HHHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecCC-CCCeeEEeC
Confidence            4677889999887 68899999999999999999999999999999998853 568887543

>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=97.30  E-value=0.00045  Score=48.15  Aligned_cols=56  Identities=14%  Similarity=0.149  Sum_probs=51.2

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      -+|+..|..|+..|...|  |+-..+|...++++.+.++++|+.||.+|||....+-.
T Consensus        42 ~glt~~q~~iL~~l~~~~--~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~~~   97 (162)
T 3k0l_A           42 LEISLPQFTALSVLAAKP--NLSNAKLAERSFIKPQSANKILQDLLANGWIEKAPDPT   97 (162)
T ss_dssp             TTCCHHHHHHHHHHHHCT--TCCHHHHHHHHTSCGGGHHHHHHHHHHTTSEEEEECCS
T ss_pred             cCCCHHHHHHHHHHHHCC--CCCHHHHHHHHCCCHHHHHHHHHHHHHCcCeEecCCCC
Confidence            489999999999998765  89999999999999999999999999999999887654

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

Probab=97.30  E-value=0.00082  Score=44.95  Aligned_cols=55  Identities=15%  Similarity=0.271  Sum_probs=49.6

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      .+|+..|..|+..|...|  |+-..+|...++++.+.++++|+.||.+|+|....+-
T Consensus        32 ~~lt~~~~~iL~~l~~~~--~~t~~ela~~l~~s~~~vs~~l~~Le~~glv~r~~~~   86 (142)
T 2fbi_A           32 HGLTEQQWRVIRILRQQG--EMESYQLANQACILRPSMTGVLARLERDGIVRRWKAP   86 (142)
T ss_dssp             HTCCHHHHHHHHHHHHHC--SEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEEET
T ss_pred             cCCCHHHHHHHHHHHHcC--CCCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEeecCC
Confidence            479999999999998765  6999999999999999999999999999999987654

>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=97.30  E-value=0.0011  Score=44.38  Aligned_cols=57  Identities=19%  Similarity=0.217  Sum_probs=49.6

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      -++++.+..|+.++..+ +.++-..+|..+++++.++++++|+.||.+|+|...++-.
T Consensus        22 ~gl~~~~~~il~~L~~~-~~~~t~~ela~~l~~~~stvs~~l~~L~~~G~v~r~~~~~   78 (152)
T 1ku9_A           22 HGLNKSVGAVYAILYLS-DKPLTISDIMEELKISKGNVSMSLKKLEELGFVRKVWIKG   78 (152)
T ss_dssp             TTCCHHHHHHHHHHHHC-SSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECCTT
T ss_pred             cCCChhHHHHHHHHHHc-CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEecCC
Confidence            47999888899888433 4689999999999999999999999999999999887543

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

Probab=97.29  E-value=0.00056  Score=47.78  Aligned_cols=58  Identities=9%  Similarity=0.045  Sum_probs=53.0

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      -+||..|..|..+|..+.+.++-..+|-..+++..+.++++++.||.+|||....+-.
T Consensus        31 ~gLt~~q~~vL~~L~~~~~~~~t~~eLa~~l~~~~~tvs~~v~~Le~~Glv~r~~~~~   88 (147)
T 4b8x_A           31 YGLTFARYEALVLLTFSKSGELPMSKIGERLMVHPTSVTNTVDRLVRSGLVAKRPNPN   88 (147)
T ss_dssp             GTCCHHHHHHHHHHHTSGGGEEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECC-
T ss_pred             cCCCHHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHhCCCEEEeecCC
Confidence            4799999999999988888889999999999999999999999999999999988754

>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=97.28  E-value=0.00088  Score=45.08  Aligned_cols=55  Identities=9%  Similarity=0.056  Sum_probs=49.6

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      .+|+..|..|+..|...|  |+-..+|...++++.+.++++|+.||.+|+|....+-
T Consensus        29 ~~l~~~~~~iL~~l~~~~--~~~~~~la~~l~~s~~tvs~~l~~L~~~glv~r~~~~   83 (145)
T 2a61_A           29 FGITPAQFDILQKIYFEG--PKRPGELSVLLGVAKSTVTGLVKRLEADGYLTRTPDP   83 (145)
T ss_dssp             HTCCHHHHHHHHHHHHHC--CBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEET
T ss_pred             cCCCHHHHHHHHHHHHcC--CCCHHHHHHHHCCCchhHHHHHHHHHHCCCeeecCCC
Confidence            379999999999998754  7999999999999999999999999999999987654

>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=97.28  E-value=0.00049  Score=46.48  Aligned_cols=55  Identities=16%  Similarity=0.215  Sum_probs=49.6

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      -+|++.|..|+..|...|  ++-..+|...++++.+.++++|+.||.+|||....+-
T Consensus        33 ~~l~~~~~~iL~~l~~~~--~~~~~ela~~l~~~~~tvs~~l~~L~~~gli~r~~~~   87 (142)
T 2bv6_A           33 YNLTYPQFLVLTILWDES--PVNVKKVVTELALDTGTVSPLLKRMEQVDLIKRERSE   87 (142)
T ss_dssp             HTCCHHHHHHHHHHHHSS--EEEHHHHHHHTTCCTTTHHHHHHHHHHTTSEEEEECS
T ss_pred             cCCCHHHHHHHHHHHHcC--CcCHHHHHHHHCCChhhHHHHHHHHHHCCCEEeecCC
Confidence            379999999999998755  7999999999999999999999999999999987764

>2fu4_A Ferric uptake regulation protein; DNA binding domain, helix-turn-helix, DNA binding protein; 1.80A {Escherichia coli}

Probab=97.27  E-value=0.00067  Score=43.18  Aligned_cols=62  Identities=10%  Similarity=0.163  Sum_probs=53.1

Q ss_pred             CCCHHHHHHHHHHHHhcCCcccHHHHHhhc-----CCChHHHHHHHHHHhhcCCeeeeccccCCccc
Q psy7778          27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKS-----NLMPTQLNKILKQLETKKIIKAVKSVANIEYL   88 (117)
Q Consensus        27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~kt-----nL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wY   88 (117)
                      .+|+....|+.++.+++...+-..+|-...     +++.++|.+.|+.|+..|+|..+..-.+..+|
T Consensus        14 ~~t~~r~~IL~~l~~~~~~~~s~~el~~~l~~~~~~is~~TVyR~L~~L~~~Glv~~~~~~~~~~~y   80 (83)
T 2fu4_A           14 KVTLPRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHNFEGGKSVF   80 (83)
T ss_dssp             CCCHHHHHHHHHHTSGGGSSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTSEEEEECGGGCEEE
T ss_pred             CcCHHHHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCCCeEEEeeCCCceEe
Confidence            377888899999987643578899999998     99999999999999999999998876666666

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

Probab=97.25  E-value=0.00086  Score=46.31  Aligned_cols=55  Identities=9%  Similarity=0.162  Sum_probs=49.2

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      .+|+..|..|+..|...|  |+-..+|...++++.+.++++|+.||.+|||....+-
T Consensus        48 ~~lt~~~~~iL~~l~~~~--~~t~~ela~~l~is~~tvs~~l~~Le~~Gli~r~~~~  102 (162)
T 3cjn_A           48 LGLSTAKMRALAILSAKD--GLPIGTLGIFAVVEQSTLSRALDGLQADGLVRREVDS  102 (162)
T ss_dssp             HTCCHHHHHHHHHHHHSC--SEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEC-
T ss_pred             cCCCHHHHHHHHHHHHCC--CCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEecCCC
Confidence            479999999999998754  7999999999999999999999999999999987654

>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=97.24  E-value=0.00055  Score=45.77  Aligned_cols=56  Identities=21%  Similarity=0.168  Sum_probs=50.5

Q ss_pred             cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcC----CChHHHHHHHHHHhhcCCeeeecc
Q psy7778          24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSN----LMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktn----L~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      ++.+||+.|..|+.+|..  +.++-..+|-...+    ++.++++++|+.||.+|||...++
T Consensus         4 ~~~~lt~~~~~vL~~l~~--~~~~t~~ela~~l~~~~~~s~~tv~~~l~~L~~~Glv~r~~~   63 (123)
T 1okr_A            4 KTYEISSAEWEVMNIIWM--KKYASANNIIEEIQMQKDWSPKTIRTLITRLYKKGFIDRKKD   63 (123)
T ss_dssp             CCCCCCHHHHHHHHHHHH--HSSEEHHHHHHHHHHHCCCCHHHHHHHHHHHHHHTSEEEEEE
T ss_pred             ccccCCHHHHHHHHHHHh--CCCcCHHHHHHHHhccCCCcHhhHHHHHHHHHHCCCeEEEec
Confidence            356899999999999987  45899999999998    889999999999999999999876

>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=97.24  E-value=0.00074  Score=45.32  Aligned_cols=56  Identities=25%  Similarity=0.270  Sum_probs=49.6

Q ss_pred             cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcC----CChHHHHHHHHHHhhcCCeeeecc
Q psy7778          24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSN----LMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktn----L~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      +..+||+.|..|+.+|-+.  .|+-.++|-.+++    +..++++++|+.||.+|||...++
T Consensus         4 ~~~~Lt~~q~~vL~~L~~~--~~~t~~el~~~l~~~~~~~~~Tvt~~l~rLe~kGlv~R~~~   63 (126)
T 1sd4_A            4 KQVEISMAEWDVMNIIWDK--KSVSANEIVVEIQKYKEVSDKTIRTLITRLYKKEIIKRYKS   63 (126)
T ss_dssp             -CCCCCHHHHHHHHHHHHS--SSEEHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             CCCCCCHHHHHHHHHHHhc--CCCCHHHHHHHHhhcCCCChhhHHHHHHHHHHCCceEEEeC
Confidence            3458999999999999885  4899999999997    589999999999999999999875

>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=97.24  E-value=0.00078  Score=46.44  Aligned_cols=56  Identities=13%  Similarity=0.157  Sum_probs=50.3

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      .+|+..|..|+..|...+  ++-..+|...++++.+.++++|+.||.+|||....+-.
T Consensus        40 ~~lt~~~~~iL~~l~~~~--~~t~~ela~~l~is~~tvs~~l~~Le~~Gli~r~~~~~   95 (154)
T 2eth_A           40 SDMKTTELYAFLYVALFG--PKKMKEIAEFLSTTKSNVTNVVDSLEKRGLVVREMDPV   95 (154)
T ss_dssp             HHSBHHHHHHHHHHHHHC--CBCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEEEECTT
T ss_pred             cCCCHHHHHHHHHHHHcC--CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeeCCCC
Confidence            368899999999998766  79999999999999999999999999999999887543

>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=97.23  E-value=0.0009  Score=45.09  Aligned_cols=55  Identities=9%  Similarity=0.077  Sum_probs=49.6

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      .+|+..|..|...|.   +.|+-..+|...++++.+.++++|+.||.+|||....+-.
T Consensus        33 ~~l~~~~~~iL~~l~---~~~~~~~ela~~l~~s~~tvs~~l~~Le~~glv~r~~~~~   87 (146)
T 2gxg_A           33 LNLSYLDFLVLRATS---DGPKTMAYLANRYFVTQSAITASVDKLEEMGLVVRVRDRE   87 (146)
T ss_dssp             TTCCHHHHHHHHHHT---TSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEECSS
T ss_pred             cCCCHHHHHHHHHHh---cCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeecCCC
Confidence            469999999998886   6789999999999999999999999999999999887643

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

Probab=97.22  E-value=0.00067  Score=45.22  Aligned_cols=56  Identities=9%  Similarity=0.183  Sum_probs=49.8

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      -+|+..|..|+..|...  .++-..+|...++++.+.++++|+.||.+|+|....+-.
T Consensus        29 ~~l~~~~~~iL~~l~~~--~~~~~~ela~~l~~~~~tvs~~l~~L~~~gli~r~~~~~   84 (139)
T 3bja_A           29 YDISYVQFGVIQVLAKS--GKVSMSKLIENMGCVPSNMTTMIQRMKRDGYVMTEKNPN   84 (139)
T ss_dssp             GTCCHHHHHHHHHHHHS--CSEEHHHHHHHCSSCCTTHHHHHHHHHHTTSEEEEECSS
T ss_pred             cCCCHHHHHHHHHHHHc--CCcCHHHHHHHHCCChhHHHHHHHHHHHCCCeeeccCCC
Confidence            47999999999999764  479999999999999999999999999999999876543

>2g9w_A Conserved hypothetical protein; DNA-binding domain, bacterial transcription repressor, DNA B protein; 1.80A {Mycobacterium tuberculosis} SCOP: a.4.5.39

Probab=97.22  E-value=0.00085  Score=46.70  Aligned_cols=57  Identities=18%  Similarity=0.239  Sum_probs=50.7

Q ss_pred             cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcC----CChHHHHHHHHHHhhcCCeeeecc
Q psy7778          24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSN----LMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktn----L~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      +..+||+.|..|+.+|-.. +.++-.++|-..++    +..+++++.|+.||.+|||...++
T Consensus         3 ~~~~lt~~e~~vL~~L~~~-~~~~t~~el~~~l~~~~~~~~~Tvt~~l~rLe~kGlv~r~~~   63 (138)
T 2g9w_A            3 KLTRLGDLERAVMDHLWSR-TEPQTVRQVHEALSARRDLAYTTVMAVLQRLAKKNLVLQIRD   63 (138)
T ss_dssp             CGGGCCHHHHHHHHHHHTC-SSCEEHHHHHHHHTTTCCCCHHHHHHHHHHHHHTTSEEEEC-
T ss_pred             ccccCCHHHHHHHHHHHhc-CCCCCHHHHHHHHhccCCCCHHHHHHHHHHHHHCCCEEEEec
Confidence            3568999999999999875 35899999999997    899999999999999999999875

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

Probab=97.21  E-value=0.001  Score=44.71  Aligned_cols=57  Identities=11%  Similarity=0.156  Sum_probs=49.8

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      -+|++.|..|+..|.. .+.++-..+|...++++.+.++++|+.||.+|||....+-.
T Consensus        33 ~~l~~~~~~iL~~l~~-~~~~~t~~~la~~l~~s~~~vs~~l~~L~~~glv~r~~~~~   89 (146)
T 2fbh_A           33 LGLSQARWLVLLHLAR-HRDSPTQRELAQSVGVEGPTLARLLDGLESQGLVRRLAVAE   89 (146)
T ss_dssp             GCCTTTHHHHHHHHHH-CSSCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECCBT
T ss_pred             CCCCHHHHHHHHHHHH-cCCCCCHHHHHHHhCCChhhHHHHHHHHHHCCCeeecCCCc
Confidence            4789999999988832 45689999999999999999999999999999999887653

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

Probab=97.21  E-value=0.00089  Score=45.39  Aligned_cols=53  Identities=11%  Similarity=0.172  Sum_probs=48.4

Q ss_pred             CCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      +||+.|..|+..|...+.   -..+|...++++++.+++.|+.||.+|||....+-
T Consensus        34 ~lt~~~~~iL~~l~~~~~---~~~~la~~l~~~~~tvs~~l~~Le~~Glv~r~~~~   86 (144)
T 3f3x_A           34 NLSYLDFSILKATSEEPR---SMVYLANRYFVTQSAITAAVDKLEAKGLVRRIRDS   86 (144)
T ss_dssp             SCCHHHHHHHHHHHHSCE---EHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEET
T ss_pred             CCCHHHHHHHHHHHHCCC---CHHHHHHHHCCChhHHHHHHHHHHHCCCEEeccCC
Confidence            899999999999987654   89999999999999999999999999999987664

>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=97.20  E-value=0.00048  Score=46.91  Aligned_cols=56  Identities=20%  Similarity=0.242  Sum_probs=48.7

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      -+||+.|..|...|..  +.|+-..+|...++++.+.++++++.||.+|||....+-.
T Consensus        32 ~glt~~q~~vL~~l~~--~~~~t~~eLa~~l~~~~~tvs~~l~~L~~~Glv~r~~~~~   87 (140)
T 3hsr_A           32 YDLTYTGYIVLMAIEN--DEKLNIKKLGERVFLDSGTLTPLLKKLEKKDYVVRTREEK   87 (140)
T ss_dssp             GTCCHHHHHHHHHSCT--TCEEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEC---
T ss_pred             cCCCHHHHHHHHHHHH--cCCcCHHHHHHHHCCChhhHHHHHHHHHHCCCeEecCCCC
Confidence            4799999999988865  5689999999999999999999999999999999887654

>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=97.20  E-value=0.00061  Score=44.40  Aligned_cols=54  Identities=17%  Similarity=0.147  Sum_probs=46.9

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHH----HhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDI----RFKSNLMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdI----k~ktnL~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      .+|+..|..|+..|..  +.|+-..+|    ...++++.+.++++|+.||.+|||....+
T Consensus         4 ~~lt~~q~~iL~~l~~--~~~~~~~el~~~la~~l~is~~tvs~~l~~Le~~gli~r~~~   61 (99)
T 1tbx_A            4 TPFFYPEAIVLAYLYD--NEGIATYDLYKKVNAEFPMSTATFYDAKKFLIQEGFVKERQE   61 (99)
T ss_dssp             CSSBCHHHHHHHHHTT--CTTCBHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             CCCCHHHHHHHHHHHH--cCCcCHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCEEEEec
Confidence            3688888888888865  567889999    88999999999999999999999988755

>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=97.19  E-value=0.0011  Score=45.21  Aligned_cols=55  Identities=15%  Similarity=0.297  Sum_probs=49.8

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      .+|+..|..|+..|...|  |+-..+|...++++.+.++++|+.||.+|||....+-
T Consensus        33 ~~l~~~~~~iL~~l~~~~--~~t~~ela~~l~~s~~tvs~~l~~Le~~glv~r~~~~   87 (155)
T 1s3j_A           33 QGVTPAQLFVLASLKKHG--SLKVSEIAERMEVKPSAVTLMADRLEQKNLIARTHNT   87 (155)
T ss_dssp             TTCCHHHHHHHHHHHHHS--EEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEECS
T ss_pred             cCCCHHHHHHHHHHHHcC--CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeecCCC
Confidence            489999999999998754  7999999999999999999999999999999987654

>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=97.19  E-value=0.00039  Score=53.97  Aligned_cols=57  Identities=16%  Similarity=0.128  Sum_probs=54.3

Q ss_pred             CCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      +||..|..|...|.+.++.|+-.++|..+.++..+.++++|+.||.+|||....+-+
T Consensus        31 ~lt~~q~~vL~~L~~~~~~~~~~~el~~~l~~~~~t~t~~l~rLe~~G~i~R~~~~~   87 (250)
T 1p4x_A           31 DMTIKEFILLTYLFHQQENTLPFKKIVSDLCYKQSDLVQHIKVLVKHSYISKVRSKI   87 (250)
T ss_dssp             SSCHHHHHHHHHHHSCSCSEEEHHHHHHHSSSCGGGTHHHHHHHHHTTSCEEEECSS
T ss_pred             CCCHHHHHHHHHHHhcCCCCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEecCCCC
Confidence            799999999999999888999999999999999999999999999999999988875

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

Probab=97.18  E-value=0.00068  Score=45.83  Aligned_cols=55  Identities=13%  Similarity=0.227  Sum_probs=46.3

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      -+||+.+..|...|...|   +-..+|...++++.+.++++|+.||.+|||....+-.
T Consensus        34 ~~lt~~~~~iL~~l~~~~---~t~~eLa~~l~~s~~tvs~~l~~L~~~Glv~r~~~~~   88 (146)
T 3tgn_A           34 VALTNTQEHILMLLSEES---LTNSELARRLNVSQAAVTKAIKSLVKEGMLETSKDSK   88 (146)
T ss_dssp             SCCCHHHHHHHHHHTTCC---CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC-----
T ss_pred             cCCCHHHHHHHHHHHhCC---CCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEeccCCC
Confidence            478999999999997654   9999999999999999999999999999999887643

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

Probab=97.18  E-value=0.0011  Score=45.36  Aligned_cols=55  Identities=9%  Similarity=0.062  Sum_probs=48.1

Q ss_pred             CCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeee--ecccc
Q psy7778          27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKA--VKSVA   83 (117)
Q Consensus        27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~--VKsV~   83 (117)
                      +|+..|..|+..|...  .|+-..+|...++++.+.++++|+.||.+|||..  ..+-.
T Consensus        38 ~lt~~~~~iL~~l~~~--~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~~~~~   94 (154)
T 2qww_A           38 GLTIQQLAMINVIYST--PGISVADLTKRLIITGSSAAANVDGLISLGLVVKLNKTIPN   94 (154)
T ss_dssp             TCCHHHHHHHHHHHHS--TTEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEESCC--CT
T ss_pred             CCCHHHHHHHHHHHHC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCcCCCC
Confidence            7999999999999875  4799999999999999999999999999999998  65543

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

Probab=97.17  E-value=0.0011  Score=45.59  Aligned_cols=55  Identities=11%  Similarity=0.078  Sum_probs=47.2

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      -+|+..|..|+..|..  +.|+-..+|...++++.+.++++|+.||.+|||....+-
T Consensus        45 ~~lt~~~~~iL~~l~~--~~~~t~~ela~~l~is~~tvs~~l~~Le~~glv~r~~~~   99 (162)
T 2fa5_A           45 YGMAIPEWRVITILAL--YPGSSASEVSDRTAMDKVAVSRAVARLLERGFIRRETHG   99 (162)
T ss_dssp             HCCCHHHHHHHHHHHH--STTCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC----
T ss_pred             cCCCHHHHHHHHHHHh--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeeecCC
Confidence            4799999999999987  458999999999999999999999999999999987654

>2v79_A DNA replication protein DNAD; primosome, DNA-binding protein; HET: DNA; 2.00A {Bacillus subtilis}

Probab=97.14  E-value=0.00092  Score=47.91  Aligned_cols=52  Identities=10%  Similarity=0.020  Sum_probs=47.9

Q ss_pred             CCCHHHHHHHHHHHHh---cCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778          27 DSDNEEKVVYKIIEEA---GNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKA   78 (117)
Q Consensus        27 ~L~~eE~lVY~~Ie~A---Gn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~   78 (117)
                      +||+.|.+|+-.|...   |+.++-..+|..++|+..+.+.++|..|++||+|.-
T Consensus        29 gLs~~E~~lLl~L~~~~~~g~~~ps~~~LA~~~~~s~~~v~~~L~~L~~KGlI~i   83 (135)
T 2v79_A           29 GLNETELILLLKIKMHLEKGSYFPTPNQLQEGMSISVEECTNRLRMFIQKGFLFI   83 (135)
T ss_dssp             TCCHHHHHHHHHHHHHHTTTCCSCCHHHHHTTSSSCHHHHHHHHHHHHHHTSCEE
T ss_pred             CCCHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            7999999988888775   778899999999999999999999999999999985

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

Probab=97.13  E-value=0.0013  Score=46.25  Aligned_cols=55  Identities=11%  Similarity=0.176  Sum_probs=50.0

Q ss_pred             CCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      +|+..|..|+..|...|  |+-..+|...++++.+.++++|+.||.+|||....+-.
T Consensus        42 ~lt~~~~~iL~~L~~~~--~~t~~eLa~~l~is~~tvs~~l~~Le~~GlV~r~~~~~   96 (168)
T 2nyx_A           42 NITIPQFRTLVILSNHG--PINLATLATLLGVQPSATGRMVDRLVGAELIDRLPHPT   96 (168)
T ss_dssp             SCCHHHHHHHHHHHHHC--SEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEECSS
T ss_pred             CCCHHHHHHHHHHHHcC--CCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEeccCCC
Confidence            89999999999998755  79999999999999999999999999999998876643

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

Probab=97.11  E-value=0.0011  Score=45.59  Aligned_cols=56  Identities=18%  Similarity=0.153  Sum_probs=47.4

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      -+||..|..|...|...  .|+-..+|...++++.+.++++|+.||.+|||....+-.
T Consensus        37 ~~lt~~q~~iL~~l~~~--~~~~~~eLa~~l~~~~~~vs~~l~~L~~~Glv~r~~~~~   92 (149)
T 4hbl_A           37 FGITYSQYLVMLTLWEE--NPQTLNSIGRHLDLSSNTLTPMLKRLEQSGWVKRERQQS   92 (149)
T ss_dssp             TTCCHHHHHHHHHHHHS--SSEEHHHHHHHHTCCHHHHHHHHHHHHHHTSEEC-----
T ss_pred             cCCCHHHHHHHHHHHHC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeeCCCCC
Confidence            57999999999999765  689999999999999999999999999999999887643

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

Probab=97.10  E-value=0.00098  Score=45.71  Aligned_cols=55  Identities=11%  Similarity=0.218  Sum_probs=48.1

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      .+|+..|..|+..|...  .|+-..+|...++++.+.++++|+.||.+|||....+-
T Consensus        39 ~~lt~~~~~iL~~l~~~--~~~t~~ela~~l~i~~~tvs~~l~~Le~~Glv~r~~~~   93 (155)
T 3cdh_A           39 QGLRVPEWRVLACLVDN--DAMMITRLAKLSLMEQSRMTRIVDQMDARGLVTRVADA   93 (155)
T ss_dssp             TTCCHHHHHHHHHHSSC--SCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEECC--
T ss_pred             cCCCHHHHHHHHHHHHC--CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCC
Confidence            47999999999998654  48999999999999999999999999999999987654

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

Probab=97.08  E-value=0.0019  Score=44.16  Aligned_cols=56  Identities=16%  Similarity=0.202  Sum_probs=48.8

Q ss_pred             ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      --+|+..|..|+..|...  .++-..+|...++++.+.++++|+.||.+|||....+-
T Consensus        42 ~~~l~~~~~~iL~~l~~~--~~~t~~ela~~l~~s~~tvs~~l~~Le~~glv~r~~~~   97 (153)
T 2pex_A           42 ALDLTYPQYLVMLVLWET--DERSVSEIGERLYLDSATLTPLLKRLQAAGLVTRTRAA   97 (153)
T ss_dssp             TTTCCHHHHHHHHHHHHS--CSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEC--
T ss_pred             HCCCCHHHHHHHHHHHhC--CCcCHHHHHHHhCCCcccHHHHHHHHHHCCCEeecCCc
Confidence            347999999999999764  57999999999999999999999999999999987753

>2k4b_A Transcriptional regulator; DNA binding protein, winged helix; NMR {Lactococcus lactis subsp}

Probab=97.05  E-value=0.00071  Score=46.25  Aligned_cols=56  Identities=18%  Similarity=0.218  Sum_probs=48.1

Q ss_pred             cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcC----CChHHHHHHHHHHhhcCCeeeecc
Q psy7778          24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSN----LMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktn----L~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      +..+||+.|..|+.+|-+.|  ++-.++|-.+.+    +..++|+++|+.||.||+|...++
T Consensus        29 ~~~~LT~~e~~VL~~L~~~~--~~t~~eL~~~l~~~~~~s~sTVt~~L~rLe~KGlV~R~~~   88 (99)
T 2k4b_A           29 VEFNVSNAELIVMRVIWSLG--EARVDEIYAQIPQELEWSLATVKTLLGRLVKKEMLSTEKE   88 (99)
T ss_dssp             --CCCCCSCSHHHHHHHHHS--CEEHHHHHHTCCGGGCCCHHHHHHHHHHHHHTTSCEEEEE
T ss_pred             cCCCCCHHHHHHHHHHHhCC--CCCHHHHHHHHhcccCCCHhhHHHHHHHHHHCCCEEEEeC
Confidence            45579999999999998744  899999999987    568999999999999999998764

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

Probab=97.05  E-value=0.0018  Score=45.55  Aligned_cols=57  Identities=18%  Similarity=0.077  Sum_probs=49.8

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      -+||..+..|...|..+|. |+-..+|-..+++..+.++++++.||.+|||....+-.
T Consensus        27 ~gLt~~q~~vL~~L~~~~~-~~~~~eLa~~l~~~~~tvs~~v~~Le~~GlV~R~~~~~   83 (151)
T 4aik_A           27 LELTQTHWVTLYNINRLPP-EQSQIQLAKAIGIEQPSLVRTLDQLEEKGLITRHTSAN   83 (151)
T ss_dssp             GCCCHHHHHHHHHHHHSCT-TSCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEECSS
T ss_pred             cCCCHHHHHHHHHHHHcCC-CCcHHHHHHHHCcCHHHHHHHHHHHHhCCCeEeecCCC
Confidence            4799999988888877654 67668999999999999999999999999999887754

>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=97.03  E-value=0.0015  Score=44.63  Aligned_cols=58  Identities=16%  Similarity=0.205  Sum_probs=47.3

Q ss_pred             ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      --+||..|..|...|...+ .++-..+|...++++.+.++++|+.||.+|||....+-.
T Consensus        34 ~~glt~~q~~vL~~l~~~~-~~~t~~eLa~~l~i~~~tvs~~l~~Le~~Glv~r~~~~~   91 (150)
T 3fm5_A           34 PTGLRVRSYSVLVLACEQA-EGVNQRGVAATMGLDPSQIVGLVDELEERGLVVRTLDPS   91 (150)
T ss_dssp             GGTCCHHHHHHHHHHHHST-TCCCSHHHHHHHTCCHHHHHHHHHHHHTTTSEEC-----
T ss_pred             HcCCCHHHHHHHHHHHhCC-CCcCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEeeCCcc
Confidence            3479999999998886543 469999999999999999999999999999999877653

>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=97.03  E-value=0.0012  Score=51.30  Aligned_cols=59  Identities=14%  Similarity=0.087  Sum_probs=54.2

Q ss_pred             ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      --+||..|..|...|...++.|+-..+|...+++..+.++++++.||.+|||....+-.
T Consensus       153 ~~gLt~~q~~vL~~L~~~~~~~~t~~eLa~~l~i~~~tvt~~v~rLe~~GlV~R~~~~~  211 (250)
T 1p4x_A          153 HLTLSFVEFTILAIITSQNKNIVLLKDLIETIHHKYPQTVRALNNLKKQGYLIKERSTE  211 (250)
T ss_dssp             HCSSCHHHHHHHHHHHTTTTCCEEHHHHHHHSSSCHHHHHHHHHHHHHHTSSEEEECSS
T ss_pred             hCCCCHHHHHHHHHHHhCCCCCcCHHHHHHHHCCChhhHHHHHHHHHHCCCEEeeCCCC
Confidence            34799999999999998887789999999999999999999999999999999988764

>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=97.02  E-value=0.0028  Score=40.59  Aligned_cols=57  Identities=18%  Similarity=0.110  Sum_probs=46.6

Q ss_pred             ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      ..+|++.+..+...+-.+ +.++-..+|-..+|++.++++++|+.|+.+|+|....+-
T Consensus        16 ~~~l~~~~~~~l~~l~~~-~~~~t~~ela~~l~is~~tv~~~l~~L~~~g~v~~~~~~   72 (109)
T 2d1h_A           16 CYKITDTDVAVLLKMVEI-EKPITSEELADIFKLSKTTVENSLKKLIELGLVVRTKTE   72 (109)
T ss_dssp             HHTCCHHHHHHHHHHHHH-CSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEC-
T ss_pred             hhcCCHHHHHHHHHHHHc-CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEeeccc
Confidence            468888777655444432 567999999999999999999999999999999988654

>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=97.00  E-value=0.00088  Score=45.89  Aligned_cols=52  Identities=15%  Similarity=0.218  Sum_probs=46.4

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK   80 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK   80 (117)
                      -+||+.|..|+..|   .+.|+-..+|...++++.+.++++|+.||.+|||...+
T Consensus        34 ~~lt~~q~~iL~~l---~~~~~t~~eLa~~l~~~~~~vs~~l~~Le~~Glv~r~~   85 (151)
T 3kp7_A           34 YGISAEQSHVLNML---SIEALTVGQITEKQGVNKAAVSRRVKKLLNAELVKLEK   85 (151)
T ss_dssp             HTCCHHHHHHHHHH---HHSCBCHHHHHHHHCSCSSHHHHHHHHHHHTTSEEC--
T ss_pred             CCCCHHHHHHHHHH---HcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeeC
Confidence            47999999999999   45789999999999999999999999999999999854

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

Probab=96.98  E-value=0.0014  Score=45.38  Aligned_cols=56  Identities=5%  Similarity=-0.020  Sum_probs=49.7

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      -+|+..|..|+..|...  .|+-..+|...++++.+.++++|+.||.+|||....+-.
T Consensus        46 ~~lt~~q~~vL~~l~~~--~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~~~  101 (159)
T 3s2w_A           46 YGIGSGQFPFLMRLYRE--DGINQESLSDYLKIDKGTTARAIQKLVDEGYVFRQRDEK  101 (159)
T ss_dssp             GTCCTTTHHHHHHHHHS--CSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECC-
T ss_pred             cCCCHHHHHHHHHHHHC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCCC
Confidence            47999899999898764  689999999999999999999999999999999887653

>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=96.96  E-value=0.0012  Score=44.58  Aligned_cols=57  Identities=14%  Similarity=0.179  Sum_probs=48.1

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      .+|+..+..|+..|..+ +.|+-..+|...++++.+.++++|+.||.+|||....+-.
T Consensus        31 ~~l~~~~~~iL~~l~~~-~~~~~~~~la~~l~i~~~~vs~~l~~Le~~glv~r~~~~~   87 (147)
T 2hr3_A           31 DPVQFSQLVVLGAIDRL-GGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQ   87 (147)
T ss_dssp             CHHHHHHHHHHHHHHHT-TSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEC---
T ss_pred             cCCCHHHHHHHHHHHHc-CCCCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeCCCCC
Confidence            35778888898888873 4589999999999999999999999999999999886643

>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=96.94  E-value=0.0013  Score=52.98  Aligned_cols=58  Identities=22%  Similarity=0.267  Sum_probs=53.2

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      -+||..|..|...|.+....|+-.++|..++++..+.++++|+.||.+|||....+-+
T Consensus       400 ~~lt~~q~~vl~~l~~~~~~~~~~~~l~~~~~~~~~~~t~~~~~le~~g~v~r~~~~~  457 (487)
T 1hsj_A          400 FNLNYEEIYILNHILRSESNEISSKEIAKCSEFKPYYLTKALQKLKDLKLLSKKRSLQ  457 (487)
T ss_dssp             CCCCHHHHHHHHHHHTCSCSEEEHHHHHHSSCCCHHHHHHHHHHHHTTTTSCCEECCS
T ss_pred             cCCCHHHHHHHHHHHhCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeecCCCC
Confidence            4799999999999988766899999999999999999999999999999999888765

>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=96.90  E-value=0.0024  Score=47.27  Aligned_cols=56  Identities=16%  Similarity=0.126  Sum_probs=50.4

Q ss_pred             ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      --+|+..|..|+..|...|  |+-..+|...+++..+.++++|+.||.+|||....+-
T Consensus        43 ~~gLt~~q~~iL~~L~~~~--~~t~~eLa~~l~i~~stvs~~l~~Le~~GlV~r~~~~   98 (207)
T 2fxa_A           43 PYDLNINEHHILWIAYQLN--GASISEIAKFGVMHVSTAFNFSKKLEERGYLRFSKRL   98 (207)
T ss_dssp             GGTCCHHHHHHHHHHHHHT--SEEHHHHHHHTTCCHHHHHHHHHHHHHHTSEEEECC-
T ss_pred             HcCCCHHHHHHHHHHHHCC--CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCC
Confidence            3489999999999998765  8999999999999999999999999999999988764

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

Probab=96.90  E-value=0.0011  Score=45.57  Aligned_cols=56  Identities=7%  Similarity=0.066  Sum_probs=47.7

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      -+|+..|..|+..|.. .+.|+-..+|...++++.+.+++.|+.||.+|||....+-
T Consensus        43 ~~l~~~~~~iL~~L~~-~~~~~~~~ela~~l~i~~~tvs~~l~~Le~~Gli~r~~~~   98 (160)
T 3boq_A           43 TGLSLAKFDAMAQLAR-NPDGLSMGKLSGALKVTNGNVSGLVNRLIKDGMVVKAMSA   98 (160)
T ss_dssp             HSCCHHHHHHHHHHHH-CTTCEEHHHHHHHCSSCCSCHHHHHHHHHHHTSEEEC---
T ss_pred             cCCCHHHHHHHHHHHH-cCCCCCHHHHHHHHCCChhhHHHHHHHHHHCCCEEeecCC
Confidence            4799999999999943 3458999999999999999999999999999999987654

>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=96.86  E-value=0.0032  Score=44.51  Aligned_cols=58  Identities=16%  Similarity=0.092  Sum_probs=48.7

Q ss_pred             ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      --+|+..|..|+..|..+ +.|+-..+|...+++..+.++++|+.||.+|||....+-.
T Consensus        48 ~~glt~~q~~vL~~L~~~-~~~~t~~eLa~~l~i~~~tvs~~l~~Le~~GlV~r~~~~~  105 (166)
T 3deu_A           48 PLELTQTHWVTLHNIHQL-PPDQSQIQLAKAIGIEQPSLVRTLDQLEDKGLISRQTCAS  105 (166)
T ss_dssp             TTTCCHHHHHHHHHHHHS-CSSEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEC----
T ss_pred             hcCCCHHHHHHHHHHHHc-CCCCCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEeeCCCC
Confidence            347999999999999774 3579999999999999999999999999999999887653

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

Probab=96.80  E-value=0.001  Score=47.33  Aligned_cols=57  Identities=7%  Similarity=0.063  Sum_probs=50.9

Q ss_pred             cCCCHHHHHHHHHHHHhcC-CcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGN-KGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn-~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      .+|+..|..|+..|...|. .|+-..+|...++++.+.+++.|+.||.+|||....+-
T Consensus        65 ~glt~~~~~iL~~L~~~~~~~~~t~~eLa~~l~is~~tvs~~l~~Le~~GlV~r~~~~  122 (181)
T 2fbk_A           65 SGLNAAGWDLLLTLYRSAPPEGLRPTELSALAAISGPSTSNRIVRLLEKGLIERREDE  122 (181)
T ss_dssp             TTCCHHHHHHHHHHHHHCCSSCBCHHHHHHHCSCCSGGGSSHHHHHHHHTSEECCC--
T ss_pred             cCCCHHHHHHHHHHHHcCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCcCEEecCCC
Confidence            4799999999999998876 48999999999999999999999999999999987653

>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=96.72  E-value=0.002  Score=42.10  Aligned_cols=50  Identities=18%  Similarity=0.203  Sum_probs=39.8

Q ss_pred             CCCHHHHHHHHHHHHh--cCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCe
Q psy7778          27 DSDNEEKVVYKIIEEA--GNKGIWMRDIRFKSNLMPTQLNKILKQLETKKII   76 (117)
Q Consensus        27 ~L~~eE~lVY~~Ie~A--Gn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LI   76 (117)
                      +|+.-+..|...|-..  ++..+-..+|-..++++.+.++++|+.||.+|||
T Consensus         9 ~l~~~~~~iL~~l~~~~~~~~~~t~~eLa~~l~i~~~tvs~~l~~Le~~Glv   60 (95)
T 2qvo_A            9 LFKEKALEILMTIYYESLGGNDVYIQYIASKVNSPHSYVWLIIKKFEEAKMV   60 (95)
T ss_dssp             HSCHHHHHHHHHHHHHHHTTCCEEHHHHHHHSSSCHHHHHHHHHHHHHTTSE
T ss_pred             CCchhHHHHHHHHHHccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCcCc
Confidence            4777665555555333  2334999999999999999999999999999999

>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=96.71  E-value=0.0064  Score=38.71  Aligned_cols=51  Identities=16%  Similarity=0.206  Sum_probs=42.5

Q ss_pred             HHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          30 NEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        30 ~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      +-...|+..+...  .++-..+|...+|++++++++.|+.||..|+|...++.
T Consensus        16 ~~~~~iL~~L~~~--~~~~~~ela~~l~is~~tvs~~l~~L~~~gli~~~~~~   66 (100)
T 1ub9_A           16 PVRLGIMIFLLPR--RKAPFSQIQKVLDLTPGNLDSHIRVLERNGLVKTYKVI   66 (100)
T ss_dssp             HHHHHHHHHHHHH--SEEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEEEC
T ss_pred             hHHHHHHHHHHhc--CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEecC
Confidence            3455677777654  47899999999999999999999999999999976643

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

Probab=96.71  E-value=0.0059  Score=38.41  Aligned_cols=51  Identities=18%  Similarity=0.337  Sum_probs=42.2

Q ss_pred             CCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778          27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKA   78 (117)
Q Consensus        27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~   78 (117)
                      .|++-+..|+.++.+.+ ..+-..+|-.++|++.+++.++|+.|+..|+|.+
T Consensus         7 ~m~~~~~~IL~~L~~~~-~~~s~~eLA~~lglsr~tv~~~l~~L~~~G~I~~   57 (67)
T 2heo_A            7 TGDNLEQKILQVLSDDG-GPVAIFQLVKKCQVPKKTLNQVLYRLKKEDRVSS   57 (67)
T ss_dssp             --CHHHHHHHHHHHHHC-SCEEHHHHHHHHCSCHHHHHHHHHHHHHTTSEEE
T ss_pred             cccHHHHHHHHHHHHcC-CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEec
Confidence            46665567888887643 4689999999999999999999999999999865

>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=96.69  E-value=0.004  Score=45.72  Aligned_cols=53  Identities=25%  Similarity=0.204  Sum_probs=46.6

Q ss_pred             CCCHHHHHHHHHHHHh---cCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeee
Q psy7778          27 DSDNEEKVVYKIIEEA---GNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAV   79 (117)
Q Consensus        27 ~L~~eE~lVY~~Ie~A---Gn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V   79 (117)
                      +||+-|+.|+..|.+.   .......++|-...|++.+.+.+.|+.||.+|+|..-
T Consensus         2 ~lt~~q~~il~~I~~~~~~~g~~~s~~eia~~lgl~~~tv~~~l~~Le~~G~i~~~   57 (196)
T 3k2z_A            2 DLTERQRKVLLFIEEFIEKNGYPPSVREIARRFRITPRGALLHLIALEKKGYIERK   57 (196)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEECC
T ss_pred             CcCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCcHHHHHHHHHHHHCCCEEec
Confidence            6899899999999764   2345899999999999999999999999999999864

>2obp_A Putative DNA-binding protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE; 1.70A {Ralstonia eutropha} SCOP: a.4.5.71

Probab=96.61  E-value=0.0095  Score=40.94  Aligned_cols=56  Identities=20%  Similarity=0.226  Sum_probs=48.5

Q ss_pred             cCCCHHHHHHHHHHHHh----cCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778          26 KDSDNEEKVVYKIIEEA----GNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~A----Gn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      .+|++-+..||..+.++    ....+-..+|..++.|+++.++|.|+.||.+|||....+
T Consensus        12 ~gl~~~q~~vL~~L~~~~~~~~g~~~s~~eLa~~l~l~~stLsR~l~rLe~~GLV~r~~~   71 (96)
T 2obp_A           12 DGIDPAIVEVLLVLREAGIENGATPWSLPKIAKRAQLPMSVLRRVLTQLQAAGLADVSVE   71 (96)
T ss_dssp             -CCCHHHHHHHHHHHHHTSSTTCCCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             cCCCHHHHHHHHHHHHHHhhCCCCCcCHHHHHHHhCCchhhHHHHHHHHHHCCCEEeecC
Confidence            57999999999988766    445578899999999999999999999999999996554

>2xvc_A ESCRT-III, SSO0910; cell cycle, cell division, cytokinesis, winged-helix; 2.15A {Sulfolobus solfataricus}

Probab=96.60  E-value=0.0052  Score=39.61  Aligned_cols=45  Identities=18%  Similarity=0.248  Sum_probs=40.0

Q ss_pred             HHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCee
Q psy7778          32 EKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIK   77 (117)
Q Consensus        32 E~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK   77 (117)
                      |..+|+.|.++|.= |=..+.-.+.+.+...+-.+|+.||+||||+
T Consensus        12 e~~lL~yIr~sGGi-ldI~~~a~kygV~kdeV~~~LrrLe~KGLI~   56 (59)
T 2xvc_A           12 ERELLDYIVNNGGF-LDIEHFSKVYGVEKQEVVKLLEALKNKGLIA   56 (59)
T ss_dssp             HHHHHHHHHHTTSE-EEHHHHHHHHCCCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHcCCE-EeHHHHHHHhCCCHHHHHHHHHHHHHCCCee
Confidence            66899999998742 4578889999999999999999999999997

>4fx0_A Probable transcriptional repressor protein; helix-turn-helix, DNA binding, transcription regulator; 2.70A {Mycobacterium tuberculosis} PDB: 4fx4_A*

Probab=96.54  E-value=0.0044  Score=43.38  Aligned_cols=56  Identities=13%  Similarity=0.184  Sum_probs=43.2

Q ss_pred             ccCCCHHHHHHHHHHHHhc---CCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778          25 LKDSDNEEKVVYKIIEEAG---NKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        25 ~~~L~~eE~lVY~~Ie~AG---n~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      --+||..|..|...|...+   +.++-..+|-..+++..+.++++|+.||.+|||. ..+
T Consensus        28 ~~gLt~~q~~vL~~l~~~~~~~~~~~t~~eLa~~l~~~~~tvsr~v~~Le~~glVr-~~~   86 (148)
T 4fx0_A           28 PSGLTNTQFSTLAVISLSEGSAGIDLTMSELAARIGVERTTLTRNLEVMRRDGLVR-VMA   86 (148)
T ss_dssp             GGTCCHHHHHHHHHHHC---------CHHHHHHHHTCCHHHHHHHHHHHHHTTSBC----
T ss_pred             HcCCCHHHHHHHHHHHHhcCCCCCCcCHHHHHHHHCCChhhHHHHHHHHHHCCCEE-eeC
Confidence            3579999998888887654   3569999999999999999999999999999994 444

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

Probab=96.53  E-value=0.0077  Score=38.33  Aligned_cols=46  Identities=13%  Similarity=0.101  Sum_probs=39.2

Q ss_pred             HHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778          33 KVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK   80 (117)
Q Consensus        33 ~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK   80 (117)
                      ..|+.++...|  ++-..+|-..+|++.+++.+.|+.|+..|+|....
T Consensus         3 ~~Il~~L~~~~--~~s~~eLa~~lgvs~~tv~r~L~~L~~~GlI~~~~   48 (81)
T 2htj_A            3 NEILEFLNRHN--GGKTAEIAEALAVTDYQARYYLLLLEKAGMVQRSP   48 (81)
T ss_dssp             HHHHHHHHHSC--CCCHHHHHHHHTSCHHHHHHHHHHHHHHTSEEEEC
T ss_pred             HHHHHHHHHcC--CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEec
Confidence            35677776654  58999999999999999999999999999998543

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

Probab=96.49  E-value=0.009  Score=38.04  Aligned_cols=50  Identities=8%  Similarity=0.203  Sum_probs=42.3

Q ss_pred             HHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778          30 NEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        30 ~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      +....|+..|..  +.++-..+|...+|++++++++.|+.|+..|+|...+.
T Consensus        24 ~~~~~il~~l~~--~~~~s~~ela~~l~is~~tvs~~l~~L~~~glv~~~~~   73 (99)
T 3cuo_A           24 PKRLLILCMLSG--SPGTSAGELTRITGLSASATSQHLARMRDEGLIDSQRD   73 (99)
T ss_dssp             HHHHHHHHHHTT--CCSEEHHHHHHHHCCCHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             hHHHHHHHHHHh--CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEec
Confidence            345567777743  45789999999999999999999999999999998763

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

Probab=96.40  E-value=0.013  Score=39.74  Aligned_cols=56  Identities=16%  Similarity=0.243  Sum_probs=43.0

Q ss_pred             ccCCCHHHHHHHHHHHH-h-cCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778          25 LKDSDNEEKVVYKIIEE-A-GNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK   80 (117)
Q Consensus        25 ~~~L~~eE~lVY~~Ie~-A-Gn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK   80 (117)
                      +.+|++.+..+...|.. + .+.++-.++|..++|++.+.++++|+.||.+|||....
T Consensus         8 ~~~lt~~~~~~L~~l~~l~~~~~~~s~~ela~~l~is~~tv~~~l~~Le~~Gli~r~~   65 (139)
T 2x4h_A            8 MSNLSRREFSYLLTIKRYNDSGEGAKINRIAKDLKIAPSSVFEEVSHLEEKGLVKKKE   65 (139)
T ss_dssp             ---CCHHHHHHHHHHHHHHTTTSCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             HhhcCHHHHHHHHHHHHHHhcCCCcCHHHHHHHhCCChHHHHHHHHHHHHCCCEEecC
Confidence            34678755444445543 2 35689999999999999999999999999999998765

>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=96.31  E-value=0.012  Score=40.91  Aligned_cols=54  Identities=22%  Similarity=0.285  Sum_probs=46.8

Q ss_pred             CCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      .|++-++.|+.++...  ..+-.++|-.++|++.+++.+.|+.|+.+|+|+.+..+
T Consensus         2 ~ld~~d~~il~~L~~~--~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~~~~   55 (144)
T 2cfx_A            2 KLDQIDLNIIEELKKD--SRLSMRELGRKIKLSPPSVTERVRQLESFGIIKQYTLE   55 (144)
T ss_dssp             CCCHHHHHHHHHHHHC--SCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEEE
T ss_pred             CCCHHHHHHHHHHHHc--CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEecc
Confidence            3788888888888764  45889999999999999999999999999999976543

>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=96.27  E-value=0.0055  Score=46.03  Aligned_cols=56  Identities=7%  Similarity=0.178  Sum_probs=46.2

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccH--HHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWM--RDIRFKSNLMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWt--kdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      ++||+-+..++..|...+..|+-.  .+|..++++..+.++++|+.||.+|||....+
T Consensus         2 ~~lt~~~e~~L~~L~~l~~~~~~~~~~~La~~l~vs~~tvs~~l~~Le~~GlV~r~~~   59 (230)
T 1fx7_A            2 NELVDTTEMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGD   59 (230)
T ss_dssp             CTTSSHHHHHHHHHHHHHHHTSCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEECTT
T ss_pred             CCCCHHHHHHHHHHHHHhhcCCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCC
Confidence            467776656666665555468877  99999999999999999999999999998876

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

Probab=96.23  E-value=0.014  Score=38.25  Aligned_cols=54  Identities=9%  Similarity=0.107  Sum_probs=43.3

Q ss_pred             ccCCCH-HHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778          25 LKDSDN-EEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        25 ~~~L~~-eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      ++.|++ -...|+.++ ..|  ++-..+|...++++.+++++.|+.|+..|+|...+.
T Consensus        15 ~~~l~~~~r~~IL~~L-~~~--~~~~~ela~~l~is~~tv~~~l~~L~~~gli~~~~~   69 (114)
T 2oqg_A           15 FAALSDETRWEILTEL-GRA--DQSASSLATRLPVSRQAIAKHLNALQACGLVESVKV   69 (114)
T ss_dssp             HHHTTCHHHHHHHHHH-HHS--CBCHHHHHHHSSSCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             HHHhCChHHHHHHHHH-HcC--CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeEEec
Confidence            444554 345677777 333  588999999999999999999999999999988765

>2y75_A HTH-type transcriptional regulator CYMR; DNA binding protein; 2.00A {Bacillus subtilis}

Probab=96.23  E-value=0.011  Score=40.32  Aligned_cols=56  Identities=14%  Similarity=0.229  Sum_probs=40.9

Q ss_pred             HHHHHHHh-cCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCccccc
Q psy7778          35 VYKIIEEA-GNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTE   90 (117)
Q Consensus        35 VY~~Ie~A-Gn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtd   90 (117)
                      +...+... ++..+-.++|..++|+|.+.+.|+|..|+..|||.+..+..||-....
T Consensus        14 iL~~la~~~~~~~~s~~ela~~~~i~~~~v~~il~~L~~~Glv~~~~g~~ggy~L~~   70 (129)
T 2y75_A           14 IMIELAKKHGEGPTSLKSIAQTNNLSEHYLEQLVSPLRNAGLVKSIRGAYGGYVLGS   70 (129)
T ss_dssp             HHHHHHHTTTSCCBCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEEC----CCEEESS
T ss_pred             HHHHHHhCCCCCcCCHHHHHHHHCcCHHHHHHHHHHHHHCCceEecCCCCCceEeCC
Confidence            33344443 345688899999999999999999999999999999887666544443

>2wte_A CSA3; antiviral protein, viral resistance, winged helix-turn-helix prnai nucleotide-binding domain; HET: MSE; 1.80A {Sulfolobus solfataricus}

Probab=96.21  E-value=0.012  Score=45.61  Aligned_cols=52  Identities=17%  Similarity=0.221  Sum_probs=46.9

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeee
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAV   79 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V   79 (117)
                      .+|++.+..|...+.+.  .|+-..+|-.++|++.+++++.|+.|+.+|+|...
T Consensus       148 ~~L~~~~~~IL~~L~~~--~~~s~~eLA~~lglsksTv~r~L~~Le~~GlV~r~  199 (244)
T 2wte_A          148 RDYSREEMKLLNVLYET--KGTGITELAKMLDKSEKTLINKIAELKKFGILTQK  199 (244)
T ss_dssp             SCCCHHHHHHHHHHHHH--TCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCCHHHHHHHHHHHHc--CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence            38999898888888654  47899999999999999999999999999999987

>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=96.16  E-value=0.0085  Score=41.58  Aligned_cols=53  Identities=19%  Similarity=0.219  Sum_probs=44.5

Q ss_pred             CCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          28 SDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        28 L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      |++-+..|...+...  .++-..+|..+.|++.+++.+.|+.|+..|+|+.+..+
T Consensus         1 ld~~~~~il~~L~~~--~~~~~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~~~~   53 (150)
T 2pn6_A            1 MDEIDLRILKILQYN--AKYSLDEIAREIRIPKATLSYRIKKLEKDGVIKGYYAY   53 (150)
T ss_dssp             CCHHHHHHHHHHTTC--TTSCHHHHHHHHTSCHHHHHHHHHHHHHTTSSCCCCCC
T ss_pred             CChHHHHHHHHHHHc--CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEEEee
Confidence            466677777777654  36899999999999999999999999999999976544

>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=96.12  E-value=0.017  Score=40.26  Aligned_cols=54  Identities=7%  Similarity=0.260  Sum_probs=46.6

Q ss_pred             CCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      .|++-++.|..++...  ..+-..+|-.++|++.+.+.+.|+.||..|+|..+..+
T Consensus         4 ~ld~~~~~iL~~L~~~--~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~~~~   57 (150)
T 2w25_A            4 ALDDIDRILVRELAAD--GRATLSELATRAGLSVSAVQSRVRRLESRGVVQGYSAR   57 (150)
T ss_dssp             CCCHHHHHHHHHHHHC--TTCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEEEE
T ss_pred             ccCHHHHHHHHHHHHc--CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEEec
Confidence            3788888888888654  46889999999999999999999999999999876654

>3t8r_A Staphylococcus aureus CYMR; transcriptional regulator protein, dimer, sulfenic acid, UNK function; 1.70A {Staphylococcus aureus} PDB: 3t8t_A

Probab=96.10  E-value=0.019  Score=40.75  Aligned_cols=63  Identities=17%  Similarity=0.152  Sum_probs=47.4

Q ss_pred             CCH-HHHHHHHHHHHhcC---CcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCccccc
Q psy7778          28 SDN-EEKVVYKIIEEAGN---KGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTE   90 (117)
Q Consensus        28 L~~-eE~lVY~~Ie~AGn---~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtd   90 (117)
                      +|. .+..+--++.-|.+   .-+-.++|-.+.|+|.+.|.|+|..|...|||.++.+.+||-...-
T Consensus         6 ls~~~~yAl~~L~~La~~~~~~~~s~~~IA~~~~i~~~~l~kil~~L~~aGlv~s~rG~~GGy~Lar   72 (143)
T 3t8r_A            6 ISTKGRYGLTLMISLAKKEGQGCISLKSIAEENNLSDLYLEQLVGPLRNAGLIRSVRGAKGGYQLRV   72 (143)
T ss_dssp             -CHHHHHHHHHHHHHHTTTTSCCEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEECSSSSSEEEESS
T ss_pred             cChHHHHHHHHHHHHHhCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCEEEecCCCCCCeeecC
Confidence            444 34444444444432   3488999999999999999999999999999999999987755543

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

Probab=96.04  E-value=0.018  Score=40.63  Aligned_cols=54  Identities=20%  Similarity=0.344  Sum_probs=47.4

Q ss_pred             CCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      .|++-++.|+.++...|  .+-.++|-.+.|++.+++.+.|+.|+..|+|+.+..+
T Consensus         7 ~ld~~~~~il~~L~~~~--~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~~~~   60 (162)
T 2p5v_A            7 TLDKTDIKILQVLQENG--RLTNVELSERVALSPSPCLRRLKQLEDAGIVRQYAAL   60 (162)
T ss_dssp             CCCHHHHHHHHHHHHCT--TCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEEEE
T ss_pred             CCCHHHHHHHHHHHHcC--CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEeeeccc
Confidence            58888888888887755  4889999999999999999999999999999976654

>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=95.97  E-value=0.016  Score=40.55  Aligned_cols=54  Identities=20%  Similarity=0.377  Sum_probs=47.0

Q ss_pred             CCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      .|++-++.|+.++...|  .+-..+|..++|++.+++.+.|+.|+..|+|+.+..+
T Consensus         4 ~ld~~~~~il~~L~~~~--~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~~~~   57 (151)
T 2cyy_A            4 PLDEIDKKIIKILQNDG--KAPLREISKITGLAESTIHERIRKLRESGVIKKFTAI   57 (151)
T ss_dssp             CCCHHHHHHHHHHHHCT--TCCHHHHHHHHCSCHHHHHHHHHHHHHHTSSCCCCCC
T ss_pred             CcCHHHHHHHHHHHHcC--CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEEE
Confidence            48888888888887754  6889999999999999999999999999999876543

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

Probab=95.95  E-value=0.019  Score=39.91  Aligned_cols=54  Identities=17%  Similarity=0.240  Sum_probs=47.0

Q ss_pred             CCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      .|++-++.|+.++...  ..+-.++|-.++|++.+++.+.|+.|+..|+|+.+..+
T Consensus         6 ~ld~~d~~il~~L~~~--~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~~~~   59 (151)
T 2dbb_A            6 KLDRVDMQLVKILSEN--SRLTYRELADILNTTRQRIARRIDKLKKLGIIRKFTII   59 (151)
T ss_dssp             CCCHHHHHHHHHHHHC--TTCCHHHHHHHTTSCHHHHHHHHHHHHHHTSEEEEEEE
T ss_pred             hCCHHHHHHHHHHHHc--CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEEec
Confidence            4888788888888764  46899999999999999999999999999999976554

>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=95.90  E-value=0.02  Score=39.02  Aligned_cols=45  Identities=22%  Similarity=0.356  Sum_probs=37.7

Q ss_pred             HHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778          35 VYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        35 VY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      ||.++..  +.++-..+|...++++.+.++++|+.||.+|||....+
T Consensus        13 i~~l~~~--~~~~~~~ela~~l~vs~~tvs~~l~~Le~~Glv~r~~~   57 (142)
T 1on2_A           13 IYMLIEE--KGYARVSDIAEALAVHPSSVTKMVQKLDKDEYLIYEKY   57 (142)
T ss_dssp             HHHHHHH--HSSCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEETT
T ss_pred             HHHHHhh--cCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEeeC
Confidence            4444443  34789999999999999999999999999999988764

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

Probab=95.85  E-value=0.023  Score=41.15  Aligned_cols=57  Identities=7%  Similarity=0.204  Sum_probs=47.7

Q ss_pred             cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      ....|++-++.|+.++...|  .+-.++|-.++|++.+++.+.|+.|+..|+|+.+..+
T Consensus        11 ~~~~ld~~d~~IL~~L~~~~--~~s~~eLA~~lglS~~tv~~~l~~L~~~G~I~~~~~~   67 (171)
T 2ia0_A           11 SEIHLDDLDRNILRLLKKDA--RLTISELSEQLKKPESTIHFRIKKLQERGVIERYTII   67 (171)
T ss_dssp             ---CCCHHHHHHHHHHHHCT--TCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEEEE
T ss_pred             CcCCCCHHHHHHHHHHHHcC--CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeeccc
Confidence            44568888888888887654  5899999999999999999999999999999876554

>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=95.68  E-value=0.029  Score=36.40  Aligned_cols=46  Identities=26%  Similarity=0.281  Sum_probs=39.4

Q ss_pred             HHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778          31 EEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK   80 (117)
Q Consensus        31 eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK   80 (117)
                      ....|+.+|    +.++-..+|..+++++++++++.|+.|+..|+|....
T Consensus        32 ~r~~Il~~L----~~~~~~~eLa~~l~is~~tv~~~L~~L~~~Glv~~~~   77 (96)
T 1y0u_A           32 VRRKILRML----DKGRSEEEIMQTLSLSKKQLDYHLKVLEAGFCIERVG   77 (96)
T ss_dssp             HHHHHHHHH----HTTCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             HHHHHHHHH----cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEC
Confidence            345677777    2458889999999999999999999999999999876

>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=95.68  E-value=0.021  Score=37.83  Aligned_cols=54  Identities=17%  Similarity=0.231  Sum_probs=44.1

Q ss_pred             cccCCCHH-HHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778          24 KLKDSDNE-EKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK   80 (117)
Q Consensus        24 k~~~L~~e-E~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK   80 (117)
                      -++.|.++ ...|+..+.   +.++-..+|...+|++++.+++.|+.|+..|+|...+
T Consensus        19 ~~~~l~~~~r~~IL~~L~---~~~~~~~ela~~l~is~stvs~~L~~L~~~Glv~~~~   73 (106)
T 1r1u_A           19 IFKALGDYNRIRIMELLS---VSEASVGHISHQLNLSQSNVSHQLKLLKSVHLVKAKR   73 (106)
T ss_dssp             HHHHTCSHHHHHHHHHHH---HCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHhCCHHHHHHHHHHH---hCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEE
Confidence            35556654 446777775   3467889999999999999999999999999999876

>2jt1_A PEFI protein; solution structure, winged helix-turn-helix, transcripti regulatory protein, structural genomics, PSI-2; NMR {Salmonella typhimurium LT2}

Probab=95.65  E-value=0.051  Score=35.66  Aligned_cols=53  Identities=23%  Similarity=0.287  Sum_probs=45.1

Q ss_pred             HHHHHHHHHHh-----cCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCC
Q psy7778          32 EKVVYKIIEEA-----GNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANI   85 (117)
Q Consensus        32 E~lVY~~Ie~A-----Gn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg   85 (117)
                      ...|+++|.+.     |. -+-.++|-...|+..+++.+-|+.||.+|+|+.+.+-.+.
T Consensus         6 ~~~IL~~I~~~i~~~~g~-~psv~EIa~~lgvS~~TVrr~L~~Le~kG~I~R~~ggr~~   63 (77)
T 2jt1_A            6 VTKIISIVQERQNMDDGA-PVKTRDIADAAGLSIYQVRLYLEQLHDVGVLEKVNAGKGV   63 (77)
T ss_dssp             HHHHHHHHHHHHHHHTTS-CEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEESCSSSS
T ss_pred             HHHHHHHHHHHHhhccCC-CcCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEecCCCCCc
Confidence            45788888887     33 4899999999999999999999999999999998765443

>1r7j_A Conserved hypothetical protein SSO10A; winged helix-turn-helix, two-stranded antiparallel coiled CO structural genomics, PSI; 1.47A {Sulfolobus solfataricus} SCOP: a.4.5.49 PDB: 1xsx_A

Probab=95.65  E-value=0.032  Score=37.35  Aligned_cols=47  Identities=21%  Similarity=0.265  Sum_probs=42.1

Q ss_pred             HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778          34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      .||.++..-.+ |+=..+|-..+||+...+++.+..|+.+|||....+
T Consensus         9 Ii~~IL~~i~~-~~~~t~La~~~~ls~~~~~~~l~~L~~~GLI~~~~~   55 (95)
T 1r7j_A            9 IIQAILEACKS-GSPKTRIMYGANLSYALTGRYIKMLMDLEIIRQEGK   55 (95)
T ss_dssp             HHHHHHHHHTT-CBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETT
T ss_pred             HHHHHHHHHHc-CCCHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEECC
Confidence            68888888774 489999999999999999999999999999998743

>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=95.62  E-value=0.0099  Score=44.69  Aligned_cols=55  Identities=11%  Similarity=0.151  Sum_probs=43.3

Q ss_pred             CCCHHHHHHHHHHHHhcCCcccH--HHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778          27 DSDNEEKVVYKIIEEAGNKGIWM--RDIRFKSNLMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        27 ~L~~eE~lVY~~Ie~AGn~GIWt--kdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      +||+-+..++..|...+..|+..  .+|..+.++..+.++++|+.||.+|||....+
T Consensus         3 ~lt~~~e~yL~~i~~l~~~~~~~~~~~la~~l~vs~~tvs~~l~~Le~~GlV~r~~~   59 (226)
T 2qq9_A            3 DLVATTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASD   59 (226)
T ss_dssp             CHHHHHHHHHHHHHHHHHHTCCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEECTT
T ss_pred             CCCHHHHHHHHHHHHHhhcCCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCC
Confidence            46664444445555544457776  99999999999999999999999999998775

>3lwf_A LIN1550 protein, putative transcriptional regulator; structural genomics, JOI for structural genomics, JCSG; HET: SO4; 2.06A {Listeria innocua}

Probab=95.62  E-value=0.027  Score=41.15  Aligned_cols=64  Identities=20%  Similarity=0.228  Sum_probs=49.6

Q ss_pred             CCCH-HHHHHHHHHHHh---cCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCccccc
Q psy7778          27 DSDN-EEKVVYKIIEEA---GNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTE   90 (117)
Q Consensus        27 ~L~~-eE~lVY~~Ie~A---Gn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtd   90 (117)
                      .+|. .+..+--++.-|   ++.-+-.++|..+.|+|.+.+.|+|..|...|||.++.+..||-+..-
T Consensus        21 ~lS~~~~yAlr~L~~LA~~~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~aGlv~s~rG~~GGy~Lar   88 (159)
T 3lwf_A           21 KITTKGRYGLTITLELAKRIGDGPISLRSIAQDKNLSEHYLEQLIGPLRNAGIVKSIRGAHGGYVLNG   88 (159)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTTSCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECSTTCEEEECS
T ss_pred             eCchHHHHHHHHHHHHHhcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCeEEEecCCCCceEecC
Confidence            3555 344554444444   334488999999999999999999999999999999999988765543

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

Probab=95.42  E-value=0.043  Score=36.53  Aligned_cols=58  Identities=5%  Similarity=0.048  Sum_probs=45.5

Q ss_pred             HHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccC
Q psy7778          30 NEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEG   91 (117)
Q Consensus        30 ~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg   91 (117)
                      +.+..|+..+.+   .++-..+|...+|++++.+++.|+.||..|+|...+. ..+.+|+..
T Consensus        32 ~~~~~il~~L~~---~~~s~~ela~~l~is~stvsr~l~~Le~~Glv~~~~~-~r~~~~~~~   89 (119)
T 2lkp_A           32 PSRLMILTQLRN---GPLPVTDLAEAIGMEQSAVSHQLRVLRNLGLVVGDRA-GRSIVYSLY   89 (119)
T ss_dssp             HHHHHHHHHHHH---CCCCHHHHHHHHSSCHHHHHHHHHHHHHHCSEEEEEE-TTEEEEEES
T ss_pred             HHHHHHHHHHHH---CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEec-CCEEEEEEc
Confidence            356667777776   3678899999999999999999999999999987652 233456554

>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=95.41  E-value=0.041  Score=38.33  Aligned_cols=53  Identities=9%  Similarity=0.158  Sum_probs=46.2

Q ss_pred             CCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778          27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      .|++-++.|..++...|  .+-..+|-.+.|++.+++.+.|+.|+..|+|+.+..
T Consensus         5 ~ld~~d~~il~~L~~~~--~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~~~   57 (152)
T 2cg4_A            5 LIDNLDRGILEALMGNA--RTAYAELAKQFGVSPETIHVRVEKMKQAGIITGARI   57 (152)
T ss_dssp             CCCHHHHHHHHHHHHCT--TSCHHHHHHHHTSCHHHHHHHHHHHHHHTSEEEEEE
T ss_pred             ccCHHHHHHHHHHHHcC--CCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcceEEE
Confidence            47887888888887654  588999999999999999999999999999997654

>1xd7_A YWNA; structural genomics, protein structure initiative, winged HE binding, hypothetical protein, PSI; 2.30A {Bacillus subtilis subsp} SCOP: a.4.5.55

Probab=95.41  E-value=0.054  Score=38.10  Aligned_cols=57  Identities=12%  Similarity=0.032  Sum_probs=44.5

Q ss_pred             HHHHHHHHHHHhcC-CcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccc
Q psy7778          31 EEKVVYKIIEEAGN-KGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLT   89 (117)
Q Consensus        31 eE~lVY~~Ie~AGn-~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYt   89 (117)
                      .+..+--++.-|.+ .+ -+++|..+.|+|.+.|.|+|..|...|||.++.+ +||-...
T Consensus         8 ~~yAl~~L~~La~~~~~-s~~~IA~~~~i~~~~l~kIl~~L~~aGlv~s~rG-~GGy~La   65 (145)
T 1xd7_A            8 LAVAIHILSLISMDEKT-SSEIIADSVNTNPVVVRRMISLLKKADILTSRAG-VPGASLK   65 (145)
T ss_dssp             HHHHHHHHHHHHTCSCC-CHHHHHHHHTSCHHHHHHHHHHHHHTTSEECCSS-SSSCEES
T ss_pred             HHHHHHHHHHHHhCCCC-CHHHHHHHHCcCHHHHHHHHHHHHHCCceEeecC-CCCceec
Confidence            34445445544432 24 8899999999999999999999999999999999 7765443

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

Probab=95.38  E-value=0.052  Score=37.77  Aligned_cols=50  Identities=14%  Similarity=0.281  Sum_probs=45.0

Q ss_pred             CCHHHHHHHHHHHHhcCCcccHHHHHhhc--CCChHHHHHHHHHHhhcCCeeee
Q psy7778          28 SDNEEKVVYKIIEEAGNKGIWMRDIRFKS--NLMPTQLNKILKQLETKKIIKAV   79 (117)
Q Consensus        28 L~~eE~lVY~~Ie~AGn~GIWtkdIk~kt--nL~~~~l~K~LK~LE~k~LIK~V   79 (117)
                      |++-++.|+.++...|  .+-..+|-...  ++..+.+++.|+.|+..|||...
T Consensus        11 md~~d~~IL~~L~~~g--~~s~~eLA~~l~~giS~~aVs~rL~~Le~~GLV~~~   62 (111)
T 3b73_A           11 MTIWDDRILEIIHEEG--NGSPKELEDRDEIRISKSSVSRRLKKLADHDLLQPL   62 (111)
T ss_dssp             CCHHHHHHHHHHHHHS--CBCHHHHHTSTTCCSCHHHHHHHHHHHHHTTSEEEC
T ss_pred             cCHHHHHHHHHHHHcC--CCCHHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEec
Confidence            7787788888998766  68899999999  99999999999999999999986

>1ylf_A RRF2 family protein; structural genomics, transcription regulator, P protein structure initiative; 2.50A {Bacillus cereus atcc 14579} SCOP: a.4.5.55

Probab=95.24  E-value=0.063  Score=37.92  Aligned_cols=61  Identities=11%  Similarity=-0.039  Sum_probs=43.4

Q ss_pred             CCCH-HHHHHHHHHHHh--cCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCccc
Q psy7778          27 DSDN-EEKVVYKIIEEA--GNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYL   88 (117)
Q Consensus        27 ~L~~-eE~lVY~~Ie~A--Gn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wY   88 (117)
                      .+|. -+..+--++.-|  ++.-+-.++|..+.|+|.+.+.|++..|...|||.++.+ +||-..
T Consensus         8 ~ls~~~~yAl~~L~~La~~~~~~~~~~~iA~~~~i~~~~l~kil~~L~~~Glv~s~rG-~GGy~L   71 (149)
T 1ylf_A            8 KISSRFSIAVHILSILKNNPSSLCTSDYMAESVNTNPVVIRKIMSYLKQAGFVYVNRG-PGGAGL   71 (149)
T ss_dssp             CCCHHHHHHHHHHHHHHHSCGGGCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEC----CCEEE
T ss_pred             CCChHHHHHHHHHHHHHhCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEccC-CCceEe
Confidence            3444 344444444444  334578999999999999999999999999999999998 655433

>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=95.21  E-value=0.033  Score=37.92  Aligned_cols=52  Identities=27%  Similarity=0.359  Sum_probs=43.3

Q ss_pred             CCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778          28 SDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        28 L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      |++-++.|...+...|  .+-..+|..+.|++.+++.+.|+.|+..|+|+.+..
T Consensus         2 ld~~~~~il~~L~~~~--~~~~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~~~   53 (141)
T 1i1g_A            2 IDERDKIILEILEKDA--RTPFTEIAKKLGISETAVRKRVKALEEKGIIEGYTI   53 (141)
T ss_dssp             CCSHHHHHHHHHHHCT--TCCHHHHHHHHTSCHHHHHHHHHHHHHHTSSCCCCC
T ss_pred             CCHHHHHHHHHHHHcC--CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEecccc
Confidence            5666777777876543  578999999999999999999999999999976543

>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=95.17  E-value=0.043  Score=36.20  Aligned_cols=48  Identities=21%  Similarity=0.244  Sum_probs=39.0

Q ss_pred             HHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778          32 EKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK   80 (117)
Q Consensus        32 E~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK   80 (117)
                      ...|+..+-..|.. +-..+|-..+|++.+.+.++|+.|+..|+|...+
T Consensus        20 ~l~Il~~l~~~g~~-~s~~eLa~~lgvs~~tV~~~L~~L~~~GlV~~~~   67 (110)
T 1q1h_A           20 VIDVLRILLDKGTE-MTDEEIANQLNIKVNDVRKKLNLLEEQGFVSYRK   67 (110)
T ss_dssp             THHHHHHHHHHCSC-BCHHHHHHTTTSCHHHHHHHHHHHHHHTSCEEEE
T ss_pred             HHHHHHHHHHcCCC-CCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEe
Confidence            33455555455544 8899999999999999999999999999998763

>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=95.07  E-value=0.05  Score=36.72  Aligned_cols=53  Identities=17%  Similarity=0.282  Sum_probs=40.5

Q ss_pred             HHHHHHHHhcCCcccHHHHHhhc-CCChHHHHHHHHHHhhcCCeeeeccccCCcccc
Q psy7778          34 VVYKIIEEAGNKGIWMRDIRFKS-NLMPTQLNKILKQLETKKIIKAVKSVANIEYLT   89 (117)
Q Consensus        34 lVY~~Ie~AGn~GIWtkdIk~kt-nL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYt   89 (117)
                      .|...+. .|..-+--.+|.... ++.+++|++.|+.||..|||.....  ...+|.
T Consensus        31 ~IL~~L~-~g~~~~~~~eL~~~l~gis~~~ls~~L~~Le~~GlV~r~~~--r~~~y~   84 (111)
T 3df8_A           31 LIISVLG-NGSTRQNFNDIRSSIPGISSTILSRRIKDLIDSGLVERRSG--QITTYA   84 (111)
T ss_dssp             HHHHHHT-SSSSCBCHHHHHHTSTTCCHHHHHHHHHHHHHTTSEEEEES--SSEEEE
T ss_pred             HHHHHHh-cCCCCCCHHHHHHHccCCCHHHHHHHHHHHHHCCCEEEeec--CcEEEE
Confidence            4555554 343333479999999 9999999999999999999998766  445554

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

Probab=95.00  E-value=0.059  Score=37.22  Aligned_cols=53  Identities=23%  Similarity=0.330  Sum_probs=41.1

Q ss_pred             HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCccccc
Q psy7778          34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTE   90 (117)
Q Consensus        34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtd   90 (117)
                      .|+.+|...|  ++-..+|-...++.++.++++|+.||.+|||....+  .|.+.|+
T Consensus        44 ~i~~~l~~~~--~~~~~~la~~l~vs~~tvs~~l~~Le~~Glv~r~~~--~~~~lT~   96 (155)
T 2h09_A           44 LISDLIREVG--EARQVDMAARLGVSQPTVAKMLKRLATMGLIEMIPW--RGVFLTA   96 (155)
T ss_dssp             HHHHHHHHHS--CCCHHHHHHHHTSCHHHHHHHHHHHHHTTCEEEETT--TEEEECH
T ss_pred             HHHHHHHhCC--CcCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEecC--CceEECh
Confidence            3444665544  577899999999999999999999999999987754  3444443

>3k69_A Putative transcription regulator; putative transcriptional regulator, structural genomics, JOI for structural genomics, JCSG; HET: MSE; 1.95A {Lactobacillus plantarum} SCOP: a.4.5.0

Probab=94.95  E-value=0.026  Score=41.03  Aligned_cols=59  Identities=15%  Similarity=0.126  Sum_probs=47.0

Q ss_pred             HHHHHHHHHHhc--CCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCccccc
Q psy7778          32 EKVVYKIIEEAG--NKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTE   90 (117)
Q Consensus        32 E~lVY~~Ie~AG--n~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtd   90 (117)
                      +..|--++.-|.  +.-+-.++|-.+.|+|.+.|.|++..|...|||.++.+.+||-...-
T Consensus        12 ~yAlr~l~~La~~~~~~~s~~~IA~~~~is~~~l~kil~~L~~aGlv~s~rG~~GGy~Lar   72 (162)
T 3k69_A           12 SVAVHSILYLDAHRDSKVASRELAQSLHLNPVMIRNILSVLHKHGYLTGTVGKNGGYQLDL   72 (162)
T ss_dssp             HHHHHHHHHHHTTTTSCBCHHHHHHHHTSCGGGTHHHHHHHHHTTSSEEECSTTCEEECCS
T ss_pred             HHHHHHHHHHHhCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeecCCCCCeEecC
Confidence            444444444443  34488999999999999999999999999999999999987765544

>1mzb_A Ferric uptake regulation protein; ferric uptake regulator, iron, DTXR, gene regulation; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.42

Probab=94.94  E-value=0.072  Score=37.09  Aligned_cols=63  Identities=8%  Similarity=0.114  Sum_probs=50.6

Q ss_pred             CCCHHHHHHHHHHHHhcCCcccHHHHHhhc-----CCChHHHHHHHHHHhhcCCeeeeccccCCcccc
Q psy7778          27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKS-----NLMPTQLNKILKQLETKKIIKAVKSVANIEYLT   89 (117)
Q Consensus        27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~kt-----nL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYt   89 (117)
                      .+|++-+.|+.++.+++..-.-..+|-.+.     ++..++|-|.|+.|+..|+|..+..-.+...|.
T Consensus        15 r~T~qR~~Il~~L~~~~~~~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~~~~~~~~~Y~   82 (136)
T 1mzb_A           15 KVTLPRVKILQMLDSAEQRHMSAEDVYKALMEAGEDVGLATVYRVLTQFEAAGLVVRHNFDGGHAVFE   82 (136)
T ss_dssp             CCCHHHHHHHHHHHCC-CCSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTSEEEECSSSSSCEEE
T ss_pred             CCCHHHHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCcEEEEEeCCCceEEE
Confidence            478888899999987653456666776655     899999999999999999999998766666775

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

Probab=94.93  E-value=0.066  Score=34.50  Aligned_cols=54  Identities=19%  Similarity=0.250  Sum_probs=42.4

Q ss_pred             ccCCCHH-HHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778          25 LKDSDNE-EKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        25 ~~~L~~e-E~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      ++-|.++ ...|+.++.+   .+.-..+|...+|++++++++.|+.|+..|+|...+.
T Consensus        17 ~~~l~~~~r~~Il~~L~~---~~~~~~ela~~l~is~~tvs~~L~~L~~~Glv~~~~~   71 (98)
T 3jth_A           17 LKAMANERRLQILCMLHN---QELSVGELCAKLQLSQSALSQHLAWLRRDGLVTTRKE   71 (98)
T ss_dssp             HHHHCSHHHHHHHHHTTT---SCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECC
T ss_pred             HHHcCCHHHHHHHHHHhc---CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEe
Confidence            3444443 3356666654   5788999999999999999999999999999987653

>2fe3_A Peroxide operon regulator; oxidative stress regulator, DNA binding protein; 1.75A {Bacillus subtilis} PDB: 3f8n_A 2rgv_A*

Probab=94.92  E-value=0.1  Score=36.77  Aligned_cols=62  Identities=8%  Similarity=0.051  Sum_probs=51.3

Q ss_pred             CCCHHHHHHHHHHHHhcCCcccHHHHHhhc-----CCChHHHHHHHHHHhhcCCeeeeccccCCcccc
Q psy7778          27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKS-----NLMPTQLNKILKQLETKKIIKAVKSVANIEYLT   89 (117)
Q Consensus        27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~kt-----nL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYt   89 (117)
                      .+|++-..|+.++.++ +.-+--.+|-...     ++..++|-|.|+.|+..|+|..+..-.+...|.
T Consensus        19 r~T~qR~~Il~~L~~~-~~~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~~~~~~~~~Y~   85 (145)
T 2fe3_A           19 RITPQRHAILEYLVNS-MAHPTADDIYKALEGKFPNMSVATVYNNLRVFRESGLVKELTYGDASSRFD   85 (145)
T ss_dssp             CCCHHHHHHHHHHHHC-SSCCCHHHHHHHHGGGCTTCCHHHHHHHHHHHHHTTSEEEECCTTSCCEEE
T ss_pred             CCCHHHHHHHHHHHhC-CCCCCHHHHHHHHHHhCCCCChhhHHHHHHHHHHCCCEEEEeeCCCceEEE
Confidence            4788888999999875 3456667776665     899999999999999999999998877667774

>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=94.90  E-value=0.074  Score=35.33  Aligned_cols=47  Identities=15%  Similarity=0.227  Sum_probs=38.9

Q ss_pred             HHHHHHHHhcCCcccHHHHHhhc-CCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          34 VVYKIIEEAGNKGIWMRDIRFKS-NLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        34 lVY~~Ie~AGn~GIWtkdIk~kt-nL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      .|...+.   +.++-..+|.... ++.++++++.|+.||.+|||....+-.
T Consensus        18 ~IL~~L~---~~~~~~~eLa~~l~~is~~tls~~L~~Le~~GlI~r~~~~~   65 (107)
T 2hzt_A           18 VILXHLT---HGKKRTSELKRLMPNITQKMLTQQLRELEADGVINRIVYNQ   65 (107)
T ss_dssp             HHHHHHT---TCCBCHHHHHHHCTTSCHHHHHHHHHHHHHTTSEEEEEECS
T ss_pred             HHHHHHH---hCCCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEEeecCC
Confidence            3444443   4568889999999 999999999999999999999877643

>1sfu_A 34L protein; protein/Z-DNA complex, DNA binding protein/DNA complex; 2.00A {Yaba-like disease virus} SCOP: a.4.5.19

Probab=94.77  E-value=0.12  Score=34.41  Aligned_cols=56  Identities=14%  Similarity=0.193  Sum_probs=47.5

Q ss_pred             HHHHHHHHhcCCc-ccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCccccc
Q psy7778          34 VVYKIIEEAGNKG-IWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTE   90 (117)
Q Consensus        34 lVY~~Ie~AGn~G-IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtd   90 (117)
                      +|-+.|..-+..+ +-..+|-++.|++-+.++|+|=.|+.+|++..+.+ +-..|+-+
T Consensus        16 ~v~~~i~~L~~~~~~Ta~~IAkkLg~sK~~vNr~LY~L~kkG~V~~~~~-~PP~W~~~   72 (75)
T 1sfu_A           16 LVKKEVLSLNTNDYTTAISLSNRLKINKKKINQQLYKLQKEDTVKMVPS-NPPKWFKN   72 (75)
T ss_dssp             HHHHHHHTSCTTCEECHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEECC-SSCEEEEC
T ss_pred             HHHHHHHhCCCCcchHHHHHHHHHCCCHHHHHHHHHHHHHCCCEecCCC-CCCCccCC
Confidence            5556667667766 99999999999999999999999999999999977 66667643

>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=94.64  E-value=0.1  Score=35.43  Aligned_cols=46  Identities=11%  Similarity=0.112  Sum_probs=38.3

Q ss_pred             HHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778          33 KVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK   80 (117)
Q Consensus        33 ~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK   80 (117)
                      ..|+..+..  +.++-..+|...+|++++++++.|+.|+..|+|...+
T Consensus        45 l~IL~~L~~--~~~~s~~eLa~~l~is~stvs~~L~~L~~~Glv~~~~   90 (122)
T 1u2w_A           45 AKITYALCQ--DEELCVCDIANILGVTIANASHHLRTLYKQGVVNFRK   90 (122)
T ss_dssp             HHHHHHHHH--SSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC-
T ss_pred             HHHHHHHHH--CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEE
Confidence            356666654  3467889999999999999999999999999998765

>1oyi_A Double-stranded RNA-binding protein; (alpha+beta) helix-turn-helix, viral protein; NMR {Vaccinia virus} SCOP: a.4.5.19

Probab=94.62  E-value=0.11  Score=34.85  Aligned_cols=56  Identities=14%  Similarity=0.178  Sum_probs=44.0

Q ss_pred             HHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccCccc
Q psy7778          35 VYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGTVN   94 (117)
Q Consensus        35 VY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg~~D   94 (117)
                      |..++.   ..|+--.+|-.+.|++.+.+++.|+.||..|+|... +=+...||-.-.-|
T Consensus        22 IL~lL~---~~g~sa~eLAk~LgiSk~aVr~~L~~Le~eG~I~~~-~~~PP~W~~~~~~~   77 (82)
T 1oyi_A           22 AIKTIG---IEGATAAQLTRQLNMEKREVNKALYDLQRSAMVYSS-DDIPPRWFMTTEAD   77 (82)
T ss_dssp             HHHHHS---SSTEEHHHHHHHSSSCHHHHHHHHHHHHHHTSSEEC-SSSSCEEESCC---
T ss_pred             HHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeC-CCCCCcceeccCcc
Confidence            335555   455999999999999999999999999999999886 44567788766655

>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=94.52  E-value=0.053  Score=36.33  Aligned_cols=49  Identities=6%  Similarity=0.028  Sum_probs=40.9

Q ss_pred             HHHHHHHHHHhcCCcccHHHHHhhc-CCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          32 EKVVYKIIEEAGNKGIWMRDIRFKS-NLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        32 E~lVY~~Ie~AGn~GIWtkdIk~kt-nL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      ...|...+..   .++-..+|...+ ++.++++++.|+.||.+|||....+-.
T Consensus        24 ~~~IL~~L~~---~~~~~~eLa~~l~~is~~tvs~~L~~Le~~GlI~r~~~~~   73 (112)
T 1z7u_A           24 KLSLMDELFQ---GTKRNGELMRALDGITQRVLTDRLREMEKDGLVHRESFNE   73 (112)
T ss_dssp             HHHHHHHHHH---SCBCHHHHHHHSTTCCHHHHHHHHHHHHHHTSEEEEEECC
T ss_pred             HHHHHHHHHh---CCCCHHHHHHHhccCCHHHHHHHHHHHHHCCCEEEeecCC
Confidence            4456666653   468899999999 999999999999999999999887643

>1bja_A Transcription regulatory protein MOTA; activation domain, middle mode transcription, alpha helical structure, transcription regulation; 2.19A {Enterobacteria phage T4} SCOP: a.4.5.9 PDB: 1i1s_A

Probab=94.34  E-value=0.11  Score=35.61  Aligned_cols=50  Identities=14%  Similarity=0.141  Sum_probs=46.2

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHh-hcCCChHHHHHHHHHHhhcCCee
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRF-KSNLMPTQLNKILKQLETKKIIK   77 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~-ktnL~~~~l~K~LK~LE~k~LIK   77 (117)
                      -+|+.-|.-+.-.|...+  .+-..+|.. ...|..++|++.|+.|+.+|||.
T Consensus        12 ~~L~~~QfsiL~~L~~~~--~~t~~~Lae~~l~~drstvsrnl~~L~r~GlVe   62 (95)
T 1bja_A           12 DVLNEKTATILITIAKKD--FITAAEVREVHPDLGNAVVNSNIGVLIKKGLVE   62 (95)
T ss_dssp             TSSCHHHHHHHHHHHHST--TBCHHHHHHTCTTSCHHHHHHHHHHHHTTTSEE
T ss_pred             cCCCHHHHHHHHHHHHCC--CCCHHHHHHHHhcccHHHHHHHHHHHHHCCCee
Confidence            579999998888887666  999999999 99999999999999999999998

>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=94.31  E-value=0.081  Score=34.39  Aligned_cols=54  Identities=15%  Similarity=0.196  Sum_probs=42.5

Q ss_pred             cccCCCHH-HHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778          24 KLKDSDNE-EKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK   80 (117)
Q Consensus        24 k~~~L~~e-E~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK   80 (117)
                      -++-|.++ -..|...+.+ |  ..-..+|...+|++++++++.|+.|+..|+|...+
T Consensus        16 ~~~~l~~~~r~~Il~~L~~-~--~~~~~ela~~l~is~~tvs~~L~~L~~~Glv~~~~   70 (102)
T 3pqk_A           16 LLKTLSHPVRLMLVCTLVE-G--EFSVGELEQQIGIGQPTLSQQLGVLRESGIVETRR   70 (102)
T ss_dssp             HHHHHCSHHHHHHHHHHHT-C--CBCHHHHHHHHTCCTTHHHHHHHHHHHTTSEEEEC
T ss_pred             HHHHcCCHHHHHHHHHHHh-C--CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEE
Confidence            34445543 3456667743 3  48889999999999999999999999999998765

>2w57_A Ferric uptake regulation protein; gene regulation, transcription regulation, transport, iron, repressor, DNA-binding, transcription; 2.60A {Vibrio cholerae}

Probab=94.22  E-value=0.11  Score=36.91  Aligned_cols=63  Identities=8%  Similarity=0.116  Sum_probs=50.7

Q ss_pred             CCCHHHHHHHHHHHHhcCCcccHHHHHhhc-----CCChHHHHHHHHHHhhcCCeeeeccccCCcccc
Q psy7778          27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKS-----NLMPTQLNKILKQLETKKIIKAVKSVANIEYLT   89 (117)
Q Consensus        27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~kt-----nL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYt   89 (117)
                      .+|++-..|+.++.+++..-+-..+|-...     ++..++|-|.|+.|+..|+|..+..-.+...|.
T Consensus        14 r~T~qR~~Il~~L~~~~~~h~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~~~~~~~~~Y~   81 (150)
T 2w57_A           14 KVTLPRLKILEVLQQPECQHISAEELYKKLIDLGEEIGLATVYRVLNQFDDAGIVTRHHFEGGKSVFE   81 (150)
T ss_dssp             CCCHHHHHHHHHHTSGGGSSEEHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTSEEEEECGGGCEEEE
T ss_pred             CCCHHHHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHHHCCcEEEEEeCCCceEEE
Confidence            478888899999987652456666665554     899999999999999999999998766666775

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

Probab=94.22  E-value=0.087  Score=37.43  Aligned_cols=53  Identities=17%  Similarity=0.303  Sum_probs=45.2

Q ss_pred             CCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          28 SDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        28 L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      |++-++.|..++..-|  -+-.++|-.+.|+..+++.+.|+.|+..|+|+.+..+
T Consensus         1 lD~~d~~il~~L~~~~--~~s~~~la~~lg~s~~tv~~rl~~L~~~g~i~~~~a~   53 (162)
T 3i4p_A            1 MDRLDRKILRILQEDS--TLAVADLAKKVGLSTTPCWRRIQKMEEDGVIRRRVAL   53 (162)
T ss_dssp             CCHHHHHHHHHHTTCS--CSCHHHHHHHHTCCHHHHHHHHHHHHHTTSSCCCCCC
T ss_pred             CCHHHHHHHHHHHHCC--CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeceee
Confidence            5677778888887654  4689999999999999999999999999999976554

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

Probab=94.21  E-value=0.12  Score=34.69  Aligned_cols=63  Identities=10%  Similarity=0.095  Sum_probs=47.4

Q ss_pred             ccccCCCHH-HHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccc
Q psy7778          23 EKLKDSDNE-EKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLT   89 (117)
Q Consensus        23 ~k~~~L~~e-E~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYt   89 (117)
                      .-++-|+++ -..|..++.   +.++-..+|...+|++++.+++.|+.|+..|||...+. ....+|.
T Consensus        10 ~~~~al~~~~R~~Il~~L~---~~~~~~~eLa~~l~is~~tvs~hL~~L~~~GlV~~~~~-gr~~~y~   73 (118)
T 3f6o_A           10 GIFQALADPTRRAVLGRLS---RGPATVSELAKPFDMALPSFMKHIHFLEDSGWIRTHKQ-GRVRTCA   73 (118)
T ss_dssp             HHHHHHTSHHHHHHHHHHH---TCCEEHHHHHTTCCSCHHHHHHHHHHHHHTTSEEEEEE-TTEEEEE
T ss_pred             HHHHHhCCHHHHHHHHHHH---hCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEec-CCEEEEE
Confidence            345555553 346777776   35678899999999999999999999999999988765 2334453

>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=94.19  E-value=0.068  Score=34.43  Aligned_cols=42  Identities=14%  Similarity=0.116  Sum_probs=35.3

Q ss_pred             HHHHHHHhcCCcccHHHHHhhcCCChHH-HHHHHHHHhhcCCee
Q psy7778          35 VYKIIEEAGNKGIWMRDIRFKSNLMPTQ-LNKILKQLETKKIIK   77 (117)
Q Consensus        35 VY~~Ie~AGn~GIWtkdIk~ktnL~~~~-l~K~LK~LE~k~LIK   77 (117)
                      +...+...| .|+-..+|...++++.+. ++++|+.||.+|||.
T Consensus        20 ~L~~l~~~~-~~~t~~eLa~~l~is~~t~vs~~l~~Le~~Glv~   62 (95)
T 2pg4_A           20 TLLEFEKKG-YEPSLAEIVKASGVSEKTFFMGLKDRLIRAGLVK   62 (95)
T ss_dssp             HHHHHHHTT-CCCCHHHHHHHHCCCHHHHHTTHHHHHHHTTSEE
T ss_pred             HHHHHHhcC-CCCCHHHHHHHHCCCchHHHHHHHHHHHHCCCee
Confidence            333444432 379999999999999999 999999999999999

>1z6r_A MLC protein; transcriptional repressor, ROK family protein, DNA binding P helix-turn-helix, phosphotransferase system; 2.70A {Escherichia coli} SCOP: a.4.5.63 c.55.1.10 c.55.1.10 PDB: 3bp8_A

Probab=94.09  E-value=0.07  Score=42.53  Aligned_cols=48  Identities=19%  Similarity=0.453  Sum_probs=42.8

Q ss_pred             HHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778          31 EEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK   80 (117)
Q Consensus        31 eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK   80 (117)
                      .++.|+++|...|  .+-..+|-++|+|..++++++++.|+..|+|.+..
T Consensus        17 n~~~il~~l~~~~--~~sr~~la~~~~ls~~tv~~~v~~L~~~g~i~~~~   64 (406)
T 1z6r_A           17 NAGAVYRLIDQLG--PVSRIDLSRLAQLAPASITKIVHEMLEAHLVQELE   64 (406)
T ss_dssp             HHHHHHHHHHSSC--SCCHHHHHHHTTCCHHHHHHHHHHHHHHTSEEEC-
T ss_pred             HHHHHHHHHHHcC--CcCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEeec
Confidence            4568999999754  59999999999999999999999999999999964

>2o03_A Probable zinc uptake regulation protein FURB; DNA-binding, helix-turn-helix, zinc binding, GE regulation; 2.70A {Mycobacterium tuberculosis}

Probab=94.07  E-value=0.1  Score=36.11  Aligned_cols=61  Identities=8%  Similarity=0.148  Sum_probs=49.8

Q ss_pred             CCHHHHHHHHHHHHhcCCcccHHHHHhhc-----CCChHHHHHHHHHHhhcCCeeeeccccCCcccc
Q psy7778          28 SDNEEKVVYKIIEEAGNKGIWMRDIRFKS-----NLMPTQLNKILKQLETKKIIKAVKSVANIEYLT   89 (117)
Q Consensus        28 L~~eE~lVY~~Ie~AGn~GIWtkdIk~kt-----nL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYt   89 (117)
                      +|++-..|+.++.++ +.-+-..+|-.+.     +++.++|-|.|+.|+..|+|..+..-.+...|.
T Consensus         9 ~T~qR~~Il~~l~~~-~~~~sa~ei~~~l~~~~~~is~~TVYR~L~~L~e~Glv~~~~~~~~~~~y~   74 (131)
T 2o03_A            9 STRQRAAISTLLETL-DDFRSAQELHDELRRRGENIGLTTVYRTLQSMASSGLVDTLHTDTGESVYR   74 (131)
T ss_dssp             HHHHHHHHHHHHHHC-CSCEEHHHHHHHHHHTTCCCCHHHHHHHHHHHHTTTSEEEEECTTSCEEEE
T ss_pred             CCHHHHHHHHHHHhC-CCCCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCCCEEEEEeCCCceEEE
Confidence            456667899999865 3456666776665     899999999999999999999999887777774

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

Probab=94.04  E-value=0.1  Score=34.80  Aligned_cols=53  Identities=13%  Similarity=0.125  Sum_probs=41.6

Q ss_pred             ccCCCHH-HHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778          25 LKDSDNE-EKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK   80 (117)
Q Consensus        25 ~~~L~~e-E~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK   80 (117)
                      ++.|+++ ...|+..+.   +.++-..+|...+|++++++++.|+.|+..|+|...+
T Consensus        19 ~~al~~~~r~~IL~~L~---~~~~s~~eLa~~lgis~stvs~~L~~L~~~GlV~~~~   72 (108)
T 2kko_A           19 GKALANGRRLQILDLLA---QGERAVEAIATATGMNLTTASANLQALKSGGLVEARR   72 (108)
T ss_dssp             HHHHTTSTTHHHHHHHT---TCCEEHHHHHHHHTCCHHHHHHHHHHHHHHTSEEEEE
T ss_pred             HHHhCCHHHHHHHHHHH---cCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEE
Confidence            4444442 334566664   3567889999999999999999999999999998876

>1z05_A Transcriptional regulator, ROK family; structural genomics, protein structure initiative, midwest center for structural genomics; 2.00A {Vibrio cholerae o1 biovar eltor} SCOP: a.4.5.63 c.55.1.10 c.55.1.10

Probab=94.01  E-value=0.11  Score=41.97  Aligned_cols=48  Identities=29%  Similarity=0.468  Sum_probs=44.0

Q ss_pred             HHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778          31 EEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK   80 (117)
Q Consensus        31 eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK   80 (117)
                      -++.|+++|...|  .+-..+|-++|+|..++++++++.|+..|+|.+..
T Consensus        40 n~~~il~~l~~~~--~~sr~ela~~~gls~~tv~~~v~~L~~~gli~~~~   87 (429)
T 1z05_A           40 NAGRVYKLIDQKG--PISRIDLSKESELAPASITKITRELIDAHLIHETT   87 (429)
T ss_dssp             HHHHHHHHHHHHC--SBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEC
T ss_pred             HHHHHHHHHHHcC--CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecc
Confidence            4568999999865  59999999999999999999999999999999986

>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=93.94  E-value=0.088  Score=39.09  Aligned_cols=50  Identities=8%  Similarity=0.252  Sum_probs=43.5

Q ss_pred             CCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778          28 SDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK   80 (117)
Q Consensus        28 L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK   80 (117)
                      +++-+..|+.++. .  .++-..+|..++|++++++++.|+.||..|+|....
T Consensus        18 ~d~~~~~IL~~L~-~--~~~s~~eLA~~lglS~stv~~~l~~Le~~GlI~~~~   67 (192)
T 1uly_A           18 LEDTRRKILKLLR-N--KEMTISQLSEILGKTPQTIYHHIEKLKEAGLVEVKR   67 (192)
T ss_dssp             HSHHHHHHHHHHT-T--CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCHHHHHHHHHHH-c--CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEe
Confidence            4556777888886 2  469999999999999999999999999999999884

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

Probab=93.91  E-value=0.063  Score=40.08  Aligned_cols=46  Identities=15%  Similarity=0.289  Sum_probs=40.3

Q ss_pred             HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778          34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      .||.+.+  .+.++-..+|-...++..+.++++|+.||.+|||...++
T Consensus        10 ~I~~l~~--~~~~~~~~~lA~~l~vs~~tvs~~l~~Le~~GlV~r~~~   55 (214)
T 3hrs_A           10 CLYELGT--RHNKITNKEIAQLMQVSPPAVTEMMKKLLAEELLIKDKK   55 (214)
T ss_dssp             HHHHTTS--SCSCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETT
T ss_pred             HHHHHHh--cCCCcCHHHHHHHHCCChhHHHHHHHHHHHCCCEEEecC
Confidence            5666544  356899999999999999999999999999999998875

>2xig_A Ferric uptake regulation protein; hpfur, transcription, homeostasis; HET: CIT; 1.85A {Helicobacter pylori}

Probab=93.87  E-value=0.13  Score=36.50  Aligned_cols=62  Identities=15%  Similarity=0.225  Sum_probs=50.1

Q ss_pred             CCCHHHHHHHHHHHHhcCCcccHHHHHhhc-----CCChHHHHHHHHHHhhcCCeeeeccccCCcccc
Q psy7778          27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKS-----NLMPTQLNKILKQLETKKIIKAVKSVANIEYLT   89 (117)
Q Consensus        27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~kt-----nL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYt   89 (117)
                      .+|++-..|+.++.+++. -+--.+|-...     ++..++|-|.|+.|+..|+|..+..-.+...|.
T Consensus        24 r~T~qR~~IL~~l~~~~~-~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~~~~~~~~~Y~   90 (150)
T 2xig_A           24 KNSKQREEVVSVLYRSGT-HLSPEEITHSIRQKDKNTSISSVYRILNFLEKENFISVLETSKSGRRYE   90 (150)
T ss_dssp             -CHHHHHHHHHHHHHCSS-CBCHHHHHHHHHHHSTTCCHHHHHHHHHHHHHTTSEEEEEETTTEEEEE
T ss_pred             CCCHHHHHHHHHHHhCCC-CCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCCcEEEEEeCCCceEEE
Confidence            367777799999987743 56666666555     799999999999999999999998877767774

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

Probab=93.85  E-value=0.19  Score=35.21  Aligned_cols=54  Identities=9%  Similarity=0.149  Sum_probs=45.3

Q ss_pred             ccCCCHHHHHHHHHHHHhcCCc-----------ccHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778          25 LKDSDNEEKVVYKIIEEAGNKG-----------IWMRDIRFKSNLMPTQLNKILKQLETKKIIKA   78 (117)
Q Consensus        25 ~~~L~~eE~lVY~~Ie~AGn~G-----------IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~   78 (117)
                      +...+.++++.+-+++-+...|           +-..+|-.-.|+....++|+|+.|+..|+|+.
T Consensus       114 ~~~~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~lA~~lg~sr~tvsR~l~~L~~~g~I~~  178 (202)
T 2zcw_A          114 LATQRLKNRMAAALLELSETPLAHEEEGKVVLKATHDELAAAVGSVRETVTKVIGELAREGYIRS  178 (202)
T ss_dssp             HHHCCHHHHHHHHHHHHTTSTTEEEETTEEEEECCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HhcCCHHHHHHHHHHHHHHhcCCCCCCcEEccCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEe
Confidence            4456778998888888776554           45689999999999999999999999999973

>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=93.85  E-value=0.096  Score=38.96  Aligned_cols=51  Identities=18%  Similarity=0.152  Sum_probs=43.4

Q ss_pred             CHHHHHHHHHHHHhcC----CcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeee
Q psy7778          29 DNEEKVVYKIIEEAGN----KGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAV   79 (117)
Q Consensus        29 ~~eE~lVY~~Ie~AGn----~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V   79 (117)
                      ++.+..++..|...|.    .|+-..++-.++++.++.+++.|+.||..+||...
T Consensus         6 ~~~~l~~l~~l~~~~~l~~~~~~s~s~aA~~L~isq~avSr~I~~LE~~~L~~R~   60 (230)
T 3cta_A            6 DDQYYRAIKKIKEAAEASNRAYLTSSKLADMLGISQQSASRIIIDLEKNGYITRT   60 (230)
T ss_dssp             -CHHHHHHHHHHHHTTTSSEEECCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHHHhcccccCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEE
Confidence            4466777778877664    67889999999999999999999999999999876

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

Probab=93.76  E-value=0.17  Score=35.37  Aligned_cols=55  Identities=13%  Similarity=0.191  Sum_probs=45.8

Q ss_pred             cccCCCHHHHHHHHHHHHhcCCc-----------ccHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778          24 KLKDSDNEEKVVYKIIEEAGNKG-----------IWMRDIRFKSNLMPTQLNKILKQLETKKIIKA   78 (117)
Q Consensus        24 k~~~L~~eE~lVY~~Ie~AGn~G-----------IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~   78 (117)
                      .+...+.++|+.+-+.+-+...|           +-..+|-.-.|+...+++|+|+.|+..|+|+.
T Consensus       106 ~l~~~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~lA~~lg~sr~tvsR~l~~L~~~g~I~~  171 (195)
T 3b02_A          106 HLQTGELRARIARYLLFLADTPLSARDRQGIYVTVSHEEIADATASIRESVSKVLADLRREGLIAT  171 (195)
T ss_dssp             HHTSSCHHHHHHHHHHHHTTSTTEEEETTEEEEECCHHHHHHTTTSCHHHHHHHHHHHHHHTSEEE
T ss_pred             HHhcCCHHHHHHHHHHHHHHHcCCCCCCCeeeccCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEe
Confidence            35567789998888887665444           45789999999999999999999999999974

>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=93.74  E-value=0.11  Score=36.51  Aligned_cols=46  Identities=13%  Similarity=0.086  Sum_probs=38.0

Q ss_pred             HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      +|...+.   +.++-..+|...+++.++++++.|+.||..|||.....-
T Consensus        28 ~IL~~L~---~g~~~~~eLa~~lgis~~tls~~L~~Le~~GlI~r~~~~   73 (146)
T 2f2e_A           28 LIVRDAF---EGLTRFGEFQKSLGLAKNILAARLRNLVEHGVMVAVPAE   73 (146)
T ss_dssp             HHHHHHH---TTCCSHHHHHHHHCCCHHHHHHHHHHHHHTTSEEEEECS
T ss_pred             HHHHHHH---hCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEEecC
Confidence            4444443   346788999999999999999999999999999987653

>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=93.36  E-value=0.26  Score=34.33  Aligned_cols=54  Identities=22%  Similarity=0.244  Sum_probs=43.9

Q ss_pred             ccCCCHHHHHHHHHHHHhcCCc-----------ccHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778          25 LKDSDNEEKVVYKIIEEAGNKG-----------IWMRDIRFKSNLMPTQLNKILKQLETKKIIKA   78 (117)
Q Consensus        25 ~~~L~~eE~lVY~~Ie~AGn~G-----------IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~   78 (117)
                      +...+.++|+..-+++-+...|           +-..+|-.-.|+...+++|+|+.|+..|+|..
T Consensus       135 ~~~~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~iA~~lg~sr~tvsR~l~~L~~~g~I~~  199 (210)
T 3ryp_A          135 LAFLDVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVGRILKMLEDQNLISA  199 (210)
T ss_dssp             HHHSCHHHHHHHHHHHHTTSTTCEEETTEEEEECCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HhhCCHHHHHHHHHHHHHHhcCcCCCCCceEeccCHHHHHHHhCCcHHHHHHHHHHHHHCCcEEe
Confidence            3446678888887877765433           34689999999999999999999999999974

>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=93.30  E-value=0.17  Score=34.62  Aligned_cols=53  Identities=9%  Similarity=0.202  Sum_probs=40.6

Q ss_pred             HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCccccc
Q psy7778          34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTE   90 (117)
Q Consensus        34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtd   90 (117)
                      .|+..+.   +.+.-..+|...+|++++.+++.|+.||..|+|..-+. ..+.+|+-
T Consensus        50 ~IL~~L~---~~~~s~~ela~~lgis~stvs~~L~~Le~~Glv~~~~~-gr~~~y~l  102 (122)
T 1r1t_A           50 RLLSLLA---RSELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRKQ-GRHVYYQL  102 (122)
T ss_dssp             HHHHHHT---TCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEE-TTEEEEEE
T ss_pred             HHHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEe-CCEEEEEE
Confidence            4555553   34678899999999999999999999999999988653 22345543

>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=93.15  E-value=0.22  Score=32.82  Aligned_cols=46  Identities=20%  Similarity=0.133  Sum_probs=37.8

Q ss_pred             HHHHHHHHhcCCcccHHHHHhhc-CCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          34 VVYKIIEEAGNKGIWMRDIRFKS-NLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        34 lVY~~Ie~AGn~GIWtkdIk~kt-nL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      .|...+.   +.++--.+|.... ++.++++++.|+.||..|||....+-
T Consensus        29 ~IL~~L~---~~~~~~~eL~~~l~gis~~~ls~~L~~Le~~GlV~r~~~~   75 (107)
T 2fsw_A           29 LIIFQIN---RRIIRYGELKRAIPGISEKMLIDELKFLCGKGLIKKKQYP   75 (107)
T ss_dssp             HHHHHHT---TSCEEHHHHHHHSTTCCHHHHHHHHHHHHHTTSEEEEEEC
T ss_pred             HHHHHHH---hCCcCHHHHHHHcccCCHHHHHHHHHHHHHCCCEEEeecC
Confidence            3444453   4568899999999 59999999999999999999987654

>3iwz_A CAP-like, catabolite activation-like protein; XCC, pathogenicity, CRP, CLP, C-DI-GMP receptor, quorum SENS binding, transcription; 2.30A {Xanthomonas campestris PV}

Probab=93.12  E-value=0.29  Score=34.53  Aligned_cols=54  Identities=13%  Similarity=0.195  Sum_probs=44.6

Q ss_pred             ccCCCHHHHHHHHHHHHhcCCc-----------ccHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778          25 LKDSDNEEKVVYKIIEEAGNKG-----------IWMRDIRFKSNLMPTQLNKILKQLETKKIIKA   78 (117)
Q Consensus        25 ~~~L~~eE~lVY~~Ie~AGn~G-----------IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~   78 (117)
                      +...+.++|+..-+.+-+...|           +-..+|-.-.|+...+++|+|+.|+..|+|+.
T Consensus       155 l~~~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~lt~~~lA~~lg~sr~tvsR~l~~L~~~g~I~~  219 (230)
T 3iwz_A          155 LAFLDVTDRIVRTLHDLSKEPEAMSHPQGTQLRVSRQELARLVGCSREMAGRVLKKLQADGLLHA  219 (230)
T ss_dssp             HHHCCHHHHHHHHHHHHTTSTTCEEETTEEEEECCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HhcCCHHHHHHHHHHHHHHhhCCCCCCCceecCCCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEE
Confidence            4456778888888887765443           45789999999999999999999999999974

>3eyy_A Putative iron uptake regulatory protein; NUR, nickel-uptake regulator, D-domain, dimerization domain, DB-domain, DNA-binding domain; 2.40A {Streptomyces coelicolor}

Probab=93.11  E-value=0.3  Score=34.44  Aligned_cols=61  Identities=10%  Similarity=0.055  Sum_probs=49.2

Q ss_pred             CCCHHHHHHHHHHHHhcCCcccHHHHHhhc-----CCChHHHHHHHHHHhhcCCeeeeccccCCcccc
Q psy7778          27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKS-----NLMPTQLNKILKQLETKKIIKAVKSVANIEYLT   89 (117)
Q Consensus        27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~kt-----nL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYt   89 (117)
                      .+|++-..|+.++.+++  -.-..+|-.+.     ++..++|-|.|+.|+..|+|..+..-.+...|.
T Consensus        16 r~T~qR~~Il~~l~~~~--h~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Glv~~i~~~~~~~~Y~   81 (145)
T 3eyy_A           16 RLTPQRQLVLEAVDTLE--HATPDDILGEVRKTASGINISTVYRTLELLEELGLVSHAHLGHGAPTYH   81 (145)
T ss_dssp             CCCHHHHHHHHHHHHHS--SBCHHHHHHHHHTTCTTCCHHHHHHHHHHHHHHTSEEEEECGGGCEEEE
T ss_pred             CcCHHHHHHHHHHHhcC--CCCHHHHHHHHHhhCCCCCHhHHHHHHHHHHHCCcEEEEEeCCCceEEE
Confidence            46788889999999886  56666654433     799999999999999999999998766666665

>2lnb_A Z-DNA-binding protein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, immune system; NMR {Homo sapiens}

Probab=93.06  E-value=0.2  Score=33.93  Aligned_cols=51  Identities=14%  Similarity=0.279  Sum_probs=44.9

Q ss_pred             CHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778          29 DNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK   80 (117)
Q Consensus        29 ~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK   80 (117)
                      ++-+..|++...+||. =+-..+|-.++|++-..|+|+|+.|-..+.|-+-+
T Consensus        18 ~d~eekVLe~LkeaG~-PlkageIae~~GvdKKeVdKaik~LKkEgkI~SPk   68 (80)
T 2lnb_A           18 GHLEQRILQVLTEAGS-PVKLAQLVKECQAPKRELNQVLYRMKKELKVSLTS   68 (80)
T ss_dssp             HHHHHHHHHHHHHHTS-CEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             chHHHHHHHHHHHcCC-CCCHHHHHHHHCCCHHHHHHHHHHHHHcCCccCCC
Confidence            3457899999999987 78899999999999999999999999988876543

>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=92.97  E-value=0.22  Score=37.28  Aligned_cols=53  Identities=9%  Similarity=0.164  Sum_probs=43.4

Q ss_pred             cCCCH-HHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778          26 KDSDN-EEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        26 ~~L~~-eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      +-|++ ....|+.++.   +.++-..+|...+|+++++++++|+.|+..|||...+.
T Consensus        10 kaL~~~~rl~IL~~L~---~~~~s~~eLa~~l~is~stvs~hLk~Le~~GLV~~~~~   63 (202)
T 2p4w_A           10 DVLGNETRRRILFLLT---KRPYFVSELSRELGVGQKAVLEHLRILEEAGLIESRVE   63 (202)
T ss_dssp             HHHHSHHHHHHHHHHH---HSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             HHhCCHHHHHHHHHHH---hCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEee
Confidence            33443 4556777774   34688999999999999999999999999999998775

>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=92.97  E-value=0.21  Score=37.67  Aligned_cols=45  Identities=18%  Similarity=0.165  Sum_probs=38.6

Q ss_pred             HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeee
Q psy7778          34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAV   79 (117)
Q Consensus        34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V   79 (117)
                      .|..++... ..++-..+|-.++||+.+++.++|++|+..|+|...
T Consensus        12 ~iL~~l~~~-~~~~~~~ela~~~gl~~stv~r~l~~L~~~G~v~~~   56 (249)
T 1mkm_A           12 EILDFIVKN-PGDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRK   56 (249)
T ss_dssp             HHHHHHHHC-SSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             HHHHHHHhC-CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEC
Confidence            466666554 347889999999999999999999999999999875

>1v4r_A Transcriptional repressor; helix-turn-helix, winged-helix, gene regulation; NMR {Streptomyces} SCOP: a.4.5.6

Probab=92.69  E-value=0.18  Score=32.99  Aligned_cols=61  Identities=11%  Similarity=0.106  Sum_probs=45.4

Q ss_pred             HHHHHHHHHhcCCcc--------cHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccCcccc
Q psy7778          33 KVVYKIIEEAGNKGI--------WMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGTVNA   95 (117)
Q Consensus        33 ~lVY~~Ie~AGn~GI--------WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg~~D~   95 (117)
                      ..||+.|...=-.|.        -.++|-.+.|+..+++.++|+.|+..|+|....+  .|.|......+.
T Consensus        14 ~~l~~~i~~~I~~~~l~~g~~lps~~eLa~~~~vSr~tvr~al~~L~~~Gli~~~~g--~G~~v~~~~~~~   82 (102)
T 1v4r_A           14 ADVATHFRTLIKSGELAPGDTLPSVADIRAQFGVAAKTVSRALAVLKSEGLVSSRGA--LGTVVEKNPIVI   82 (102)
T ss_dssp             HHHHHHHHHHTTTTSCCTTSBCCCHHHHHHHSSSCTTHHHHHTTTTTTSSCCEEETT--TEEESCSCCCCC
T ss_pred             HHHHHHHHHHHHhCCCCCcCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCC--CeEEEccCCccc
Confidence            356666666544443        4789999999999999999999999999987654  366655544333

>1jhf_A LEXA repressor; LEXA SOS repressor, hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.2 b.87.1.1 PDB: 1jhh_A 3jso_A* 3jsp_A* 3k3r_E* 1jhc_A 1jhe_A 1lea_A 1leb_A

Probab=92.67  E-value=0.23  Score=35.87  Aligned_cols=53  Identities=21%  Similarity=0.357  Sum_probs=46.2

Q ss_pred             cCCCHHHHHHHHHHHHh-cCCcc--cHHHHHhhcCCC-hHHHHHHHHHHhhcCCeee
Q psy7778          26 KDSDNEEKVVYKIIEEA-GNKGI--WMRDIRFKSNLM-PTQLNKILKQLETKKIIKA   78 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~A-Gn~GI--WtkdIk~ktnL~-~~~l~K~LK~LE~k~LIK~   78 (117)
                      +.||+.+..++..|.++ ...|+  ..++|-.++|+. ++.+++.++.|+.+++|..
T Consensus         2 ~~lt~~q~~i~~~i~~~~~~~g~~ps~~elA~~lgiss~~tv~~~~~~l~~~~~l~~   58 (202)
T 1jhf_A            2 KALTARQQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKALARKGVIEI   58 (202)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHHHHHHHHTTSEEE
T ss_pred             CccCHHHHHHHHHHHHHHHHhCCCccHHHHHHHhCCCChHHHHHHHHHHHHCCCcee
Confidence            46899999999999887 45688  899999999999 9999999999999887763

>2hoe_A N-acetylglucosamine kinase; TM1224, structural genomics, PSI-2, protein structure initiative, joint center structural genomics, JCSG; 2.46A {Thermotoga maritima} SCOP: a.4.5.63 c.55.1.10 c.55.1.10

Probab=92.56  E-value=0.11  Score=41.27  Aligned_cols=47  Identities=19%  Similarity=0.133  Sum_probs=42.2

Q ss_pred             HHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778          32 EKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        32 E~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      ++.|+++|.   +..+-..+|-++|||..++++++++.|+..|+|.+...
T Consensus        22 ~~~il~~l~---~~~~sr~~la~~~gls~~tv~~~v~~L~~~gli~~~~~   68 (380)
T 2hoe_A           22 ISRILKRIM---KSPVSRVELAEELGLTKTTVGEIAKIFLEKGIVVEEKD   68 (380)
T ss_dssp             CCCSHHHHH---HSCBCHHHHHHHHTCCHHHHHHHHHHHHHHTSEEEEEC
T ss_pred             HHHHHHHHH---cCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeecC
Confidence            456899998   45699999999999999999999999999999999753

>2oz6_A Virulence factor regulator; winged helix, helix-turn-helix, transcription factor, CAMP-B proteins, CAMP receptor protein; HET: CMP; 2.80A {Pseudomonas aeruginosa} SCOP: a.4.5.4 b.82.3.2

Probab=92.46  E-value=0.41  Score=33.16  Aligned_cols=54  Identities=19%  Similarity=0.248  Sum_probs=42.2

Q ss_pred             ccCCCHHHHHHHHHHHHhcCC-------c----ccHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778          25 LKDSDNEEKVVYKIIEEAGNK-------G----IWMRDIRFKSNLMPTQLNKILKQLETKKIIKA   78 (117)
Q Consensus        25 ~~~L~~eE~lVY~~Ie~AGn~-------G----IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~   78 (117)
                      +...+.++|+..-+.+-+...       |    +-..+|-.-.|+....++|+|+.|+.+|+|+.
T Consensus       132 l~~~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~~  196 (207)
T 2oz6_A          132 LAFLDVTGRVARTLLDLCQQPDAMTHPDGMQIKITRQEIGRIVGCSREMVGRVLKSLEEQGLVHV  196 (207)
T ss_dssp             HHHCCHHHHHHHHHHHHTTSTTCEEETTEEEEECCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             HhcCCHHHHHHHHHHHHHHhcCCCCCCCceecccCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEe
Confidence            345677888876666554422       2    45689999999999999999999999999974

>2xrn_A HTH-type transcriptional regulator TTGV; DNA-binding protein, tetramer gene regulator, cooperative DN binding, multidrug binding protein; 2.90A {Pseudomonas putida} PDB: 2xro_A

Probab=92.27  E-value=0.21  Score=37.65  Aligned_cols=46  Identities=15%  Similarity=0.301  Sum_probs=38.4

Q ss_pred             HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778          34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK   80 (117)
Q Consensus        34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK   80 (117)
                      .|..++... ..++-..+|-.++|||.+++.++|++|+..|+|....
T Consensus        10 ~iL~~l~~~-~~~~s~~ela~~~gl~~stv~r~l~~L~~~G~v~~~~   55 (241)
T 2xrn_A           10 SIMRALGSH-PHGLSLAAIAQLVGLPRSTVQRIINALEEEFLVEALG   55 (241)
T ss_dssp             HHHHHHHTC-TTCEEHHHHHHHTTSCHHHHHHHHHHHHTTTSEEECG
T ss_pred             HHHHHHHhC-CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeC
Confidence            355566543 3479999999999999999999999999999998753

>1zyb_A Transcription regulator, CRP family; NP_813211.1, structural genomics, joint center for structura genomics, JCSG; 2.15A {Bacteroides thetaiotaomicron} SCOP: a.4.5.4 b.82.3.2

Probab=92.25  E-value=0.3  Score=35.08  Aligned_cols=55  Identities=15%  Similarity=0.179  Sum_probs=45.6

Q ss_pred             cccCCCHHHHHHHHHHHHhcCCc------ccHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778          24 KLKDSDNEEKVVYKIIEEAGNKG------IWMRDIRFKSNLMPTQLNKILKQLETKKIIKA   78 (117)
Q Consensus        24 k~~~L~~eE~lVY~~Ie~AGn~G------IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~   78 (117)
                      .+...+.++|+..-+.+.+...|      +-..+|-.-.|+....++|+|+.|+..|+|..
T Consensus       158 ~l~~~~~~~Rl~~~L~~l~~~~~~~~~~~~t~~~lA~~lG~sr~tvsR~l~~l~~~glI~~  218 (232)
T 1zyb_A          158 DEPTLDLKSKIIRFFLSHCEKPQGEKTFKVKMDDLARCLDDTRLNISKTLNELQDNGLIEL  218 (232)
T ss_dssp             SCCCCSHHHHHHHHHHTTCSSSSSCEEEECCHHHHHHHHTSCHHHHHHHHHHHHHTTSCEE
T ss_pred             HHhhcCHHHHHHHHHHHHHhhcCCeEEecCCHHHHHHHhCCChhHHHHHHHHHHHCCCEEe
Confidence            34556778998887777665543      67889999999999999999999999999973

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

Probab=92.06  E-value=0.54  Score=32.05  Aligned_cols=61  Identities=18%  Similarity=0.314  Sum_probs=46.8

Q ss_pred             CCHHHHHHHHHHHHhc-CCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccC
Q psy7778          28 SDNEEKVVYKIIEEAG-NKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEG   91 (117)
Q Consensus        28 L~~eE~lVY~~Ie~AG-n~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg   91 (117)
                      +++++.-+.+.|..+= ..|.|.+++-...+++.+.+...|+.|...|.|-++.   .+-||+-+
T Consensus         1 ~~~~~~~l~~~i~~~~~~~p~~~~~la~~~~~~~~~~~~~l~~l~~~G~l~~i~---~~~~~~~~   62 (121)
T 2pjp_A            1 FSEEQQAIWQKAEPLFGDEPWWVRDLAKETGTDEQAMRLTLRQAAQQGIITAIV---KDRYYRND   62 (121)
T ss_dssp             CCHHHHHHHHHHGGGCSSSCEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEE---TTEEEEHH
T ss_pred             CCHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEec---CCceECHH
Confidence            3555555566665554 4899999999999999999999999999999888765   34444433

>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=91.90  E-value=0.27  Score=34.95  Aligned_cols=54  Identities=17%  Similarity=0.139  Sum_probs=44.4

Q ss_pred             ccCCCHHHHHHHHHHHHhcCCc------------ccHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778          25 LKDSDNEEKVVYKIIEEAGNKG------------IWMRDIRFKSNLMPTQLNKILKQLETKKIIKA   78 (117)
Q Consensus        25 ~~~L~~eE~lVY~~Ie~AGn~G------------IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~   78 (117)
                      +...+.++|+..-+.+.+...|            +-..+|-.-.|+...+++|+|+.|+..|+|+.
T Consensus       130 l~~~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~~t~~~lA~~lG~sr~tvsR~l~~L~~~g~I~~  195 (222)
T 1ft9_A          130 LMFHDIKQRIAGFFIDHANTTGRQTQGGVIVSVDFTVEEIANLIGSSRQTTSTALNSLIKEGYISR  195 (222)
T ss_dssp             HHTHHHHHHHHHHHHHTCBCCCSCC--CCCCEECCCHHHHHHHHCSCHHHHHHHHHHHHHTTSSEE
T ss_pred             HhcCCHHHHHHHHHHHHHHHhCCCCCCcEEEeccCCHHHHHHHhCCcHHHHHHHHHHHHHCCcEEE
Confidence            3445668888887777775444            57799999999999999999999999999974

>3neu_A LIN1836 protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG, unknown function; 1.58A {Listeria innocua}

Probab=91.82  E-value=0.29  Score=33.57  Aligned_cols=56  Identities=18%  Similarity=0.335  Sum_probs=45.3

Q ss_pred             HHHHHHHHHhcCCccc--------HHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCccccc
Q psy7778          33 KVVYKIIEEAGNKGIW--------MRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTE   90 (117)
Q Consensus        33 ~lVY~~Ie~AGn~GIW--------tkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtd   90 (117)
                      ..||..|...=..|-|        .++|-.+.|+..++|.++|+.|+..|+|....+  .|.|-.+
T Consensus        16 ~~i~~~i~~~I~~g~~~~g~~Lps~~~La~~~~vSr~tvr~Al~~L~~~G~i~~~~g--~G~~V~~   79 (125)
T 3neu_A           16 SQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRG--MGSFVTS   79 (125)
T ss_dssp             HHHHHHHHHHHHTTSSCTTCBCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETT--TEEEECC
T ss_pred             HHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCeEEEecC--CEEEEec
Confidence            3577777776555554        789999999999999999999999999988776  4666655

>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=91.78  E-value=0.22  Score=32.84  Aligned_cols=48  Identities=8%  Similarity=0.088  Sum_probs=41.7

Q ss_pred             HHHHHHHHHHHHhcCCcccHHHHHhhcCCChH-HHHHHHHHHhhcCCeeee
Q psy7778          30 NEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPT-QLNKILKQLETKKIIKAV   79 (117)
Q Consensus        30 ~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~-~l~K~LK~LE~k~LIK~V   79 (117)
                      +-...|+.++...|  +.-.++|....++... .+++.|..||..|||...
T Consensus        11 ~~~~~IL~~Lk~~g--~~ta~eiA~~Lgit~~~aVr~hL~~Le~eGlV~~~   59 (79)
T 1xmk_A           11 EIKEKICDYLFNVS--DSSALNLAKNIGLTKARDINAVLIDMERQGDVYRQ   59 (79)
T ss_dssp             HHHHHHHHHHHHTC--CEEHHHHHHHHCGGGHHHHHHHHHHHHHTTSEEEE
T ss_pred             hHHHHHHHHHHHcC--CcCHHHHHHHcCCCcHHHHHHHHHHHHHCCCEEec
Confidence            33457778999888  5779999999999999 999999999999999743

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

Probab=91.67  E-value=0.31  Score=34.75  Aligned_cols=53  Identities=8%  Similarity=0.144  Sum_probs=42.3

Q ss_pred             ccCCCHH-HHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778          25 LKDSDNE-EKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK   80 (117)
Q Consensus        25 ~~~L~~e-E~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK   80 (117)
                      ++-|.++ -..|..++.   +.++-..+|...++++++++++.|+.|+..|||...+
T Consensus        52 l~aL~~p~R~~IL~~L~---~~~~t~~eLa~~lgls~stvs~hL~~L~~aGlV~~~~  105 (151)
T 3f6v_A           52 LEVAAEPTRRRLVQLLT---SGEQTVNNLAAHFPASRSAISQHLRVLTEAGLVTPRK  105 (151)
T ss_dssp             HHHHTSHHHHHHHHHGG---GCCEEHHHHHTTSSSCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHhCCHHHHHHHHHHH---hCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEe
Confidence            4444443 345666664   4568999999999999999999999999999999875

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

Probab=91.66  E-value=0.32  Score=33.77  Aligned_cols=39  Identities=18%  Similarity=0.170  Sum_probs=34.9

Q ss_pred             CCcccHHHHHhhc-CCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          44 NKGIWMRDIRFKS-NLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        44 n~GIWtkdIk~kt-nL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      +.++--.+|.... |+.++.|++.|+.||..|||....+-
T Consensus        46 ~g~~~~~eLa~~l~gis~~tls~~L~~Le~~GlV~r~~~~   85 (131)
T 1yyv_A           46 DGTHRFSDLRRXMGGVSEXMLAQSLQALEQDGFLNRVSYP   85 (131)
T ss_dssp             GCCEEHHHHHHHSTTCCHHHHHHHHHHHHHHTCEEEEEEC
T ss_pred             cCCCCHHHHHHHhccCCHHHHHHHHHHHHHCCcEEEEecC
Confidence            4568889999999 79999999999999999999987654

>1tc3_C Protein (TC3 transposase); DNA binding, helix-turn-helix, TC1/mariner family, complex (transposase/DNA), DNA binding protein/DNA complex; HET: DNA; 2.45A {Caenorhabditis elegans} SCOP: a.4.1.2

Probab=91.57  E-value=0.37  Score=26.04  Aligned_cols=45  Identities=9%  Similarity=0.011  Sum_probs=34.5

Q ss_pred             cCCCHHHH-HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcC
Q psy7778          26 KDSDNEEK-VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKK   74 (117)
Q Consensus        26 ~~L~~eE~-lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~   74 (117)
                      ..|+++++ .|..+.    ..|.-.++|-..+|++.++|.+.++..+..|
T Consensus         4 ~~l~~~~~~~i~~~~----~~g~s~~~IA~~lgis~~Tv~~~~~~~~~~g   49 (51)
T 1tc3_C            4 SALSDTERAQLDVMK----LLNVSLHEMSRKISRSRHCIRVYLKDPVSYG   49 (51)
T ss_dssp             CCCCHHHHHHHHHHH----HTTCCHHHHHHHHTCCHHHHHHHHHCSTTTT
T ss_pred             CCCCHHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHhhHHhcC
Confidence            35777776 444443    3578899999999999999999998776543

>1xn7_A Hypothetical protein YHGG; alpha+beta, GFT structural genomics, protein structure initiative, PSI, NESG; NMR {Escherichia coli} SCOP: a.4.5.62

Probab=91.46  E-value=0.52  Score=30.71  Aligned_cols=44  Identities=20%  Similarity=0.197  Sum_probs=37.9

Q ss_pred             HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeee
Q psy7778          34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAV   79 (117)
Q Consensus        34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V   79 (117)
                      .|.++|.+.|  -+-..+|-..++....+|.+-|..||.+|+|+.+
T Consensus         6 ~Il~~L~~~g--~vsv~eLa~~l~VS~~TIRrdL~~Le~~G~l~R~   49 (78)
T 1xn7_A            6 QVRDLLALRG--RMEAAQISQTLNTPQPMINAMLQQLESMGKAVRI   49 (78)
T ss_dssp             HHHHHHHHSC--SBCHHHHHHHTTCCHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHcC--CCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence            3556665544  5888999999999999999999999999999988

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

Probab=91.40  E-value=0.36  Score=33.80  Aligned_cols=54  Identities=13%  Similarity=0.174  Sum_probs=43.4

Q ss_pred             ccCCCHHHHHHHHHHHHhcCC-----cccHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778          25 LKDSDNEEKVVYKIIEEAGNK-----GIWMRDIRFKSNLMPTQLNKILKQLETKKIIKA   78 (117)
Q Consensus        25 ~~~L~~eE~lVY~~Ie~AGn~-----GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~   78 (117)
                      +...+.++++..-+.+.+...     -+-..+|-.-.|+...+++|+|+.|+..|+|+.
T Consensus       143 ~~~~~~~~Rl~~~L~~~~~~~~~~~~~~t~~~lA~~lg~sr~tvsR~l~~L~~~g~I~~  201 (220)
T 3dv8_A          143 IMWKSLDKRVASFLLEETSIEGTNELKITHETIANHLGSHREVITRMLRYFQVEGLVKL  201 (220)
T ss_dssp             HHHSCHHHHHHHHHHHHHHHHTSSEECCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HhcCCHHHHHHHHHHHhhhhcCCceecCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEe
Confidence            344667888777777665433     467789999999999999999999999999963

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

Probab=91.32  E-value=0.59  Score=30.46  Aligned_cols=56  Identities=16%  Similarity=0.153  Sum_probs=42.0

Q ss_pred             ccccCCCHHH-HHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778          23 EKLKDSDNEE-KVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        23 ~k~~~L~~eE-~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      .-++.|.++- ..|+..+-..  .+.-..+|...+|++++.+++.|+.|+.. +|..-+.
T Consensus        19 ~~~~aL~~~~Rl~IL~~l~~~--~~~~~~ela~~l~is~stvs~hL~~L~~~-lv~~~~~   75 (99)
T 2zkz_A           19 ELLKTMAHPMRLKIVNELYKH--KALNVTQIIQILKLPQSTVSQHLCKMRGK-VLKRNRQ   75 (99)
T ss_dssp             HHHHHHCSHHHHHHHHHHHHH--SCEEHHHHHHHHTCCHHHHHHHHHHHBTT-TBEEEEE
T ss_pred             HHHHHhCCHHHHHHHHHHHHC--CCcCHHHHHHHHCcCHHHHHHHHHHHHHH-hhhheEe
Confidence            3455566543 3566444333  35888999999999999999999999999 9987653

>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=91.25  E-value=0.34  Score=34.27  Aligned_cols=54  Identities=17%  Similarity=0.167  Sum_probs=41.9

Q ss_pred             ccCCCHHHHHHHHHHHHhcC------Cc------ccHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778          25 LKDSDNEEKVVYKIIEEAGN------KG------IWMRDIRFKSNLMPTQLNKILKQLETKKIIKA   78 (117)
Q Consensus        25 ~~~L~~eE~lVY~~Ie~AGn------~G------IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~   78 (117)
                      +...+.++|+.+-+.+-+..      .|      +-..+|-.-.|+...+++|+|+.|+..|+|..
T Consensus       144 l~~~~~~~Rl~~~L~~l~~~~~~~~~~~~~i~~~~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~~  209 (227)
T 3d0s_A          144 LIFTDVPGRVAKQLLQLAQRFGTQEGGALRVTHDLTQEEIAQLVGASRETVNKALADFAHRGWIRL  209 (227)
T ss_dssp             HHHSCHHHHHHHHHHHHHHHHEEEETTEEEEECCCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             HhcCCHHHHHHHHHHHHHHHhCCcCCCceEEcCCCCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEe
Confidence            34466788877666655422      12      46789999999999999999999999999975

>3kcc_A Catabolite gene activator; helix-turn-helix, CAMP, CAMP-binding, DNA-binding nucleotide-binding, transcription, transcription regulation; HET: CMP; 1.66A {Escherichia coli}

Probab=91.22  E-value=0.62  Score=34.29  Aligned_cols=54  Identities=20%  Similarity=0.190  Sum_probs=43.6

Q ss_pred             ccCCCHHHHHHHHHHHHhcCCc-----------ccHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778          25 LKDSDNEEKVVYKIIEEAGNKG-----------IWMRDIRFKSNLMPTQLNKILKQLETKKIIKA   78 (117)
Q Consensus        25 ~~~L~~eE~lVY~~Ie~AGn~G-----------IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~   78 (117)
                      +...+.++|+.+-+++-+...|           +-..+|-.-.|+...+++|+|+.|+..|+|+.
T Consensus       185 l~~~~~~~Rla~~Ll~l~~~~~~~~~~~~~~l~lt~~~lA~~lG~sr~tvsR~l~~L~~~GlI~~  249 (260)
T 3kcc_A          185 LAFLLVTGRIAQTLLNLAKQPDAMTHPDGMQIKITRQEIGQIVGCSRETVGRILKMLEDQNLISA  249 (260)
T ss_dssp             HHHCCHHHHHHHHHHHHHTSTTCEEETTEEEEECCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HhcCCHHHHHHHHHHHHHHhcCCCCCCCceeecCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE
Confidence            3446778888887777665433           34689999999999999999999999999974

>2k02_A Ferrous iron transport protein C; FEOC, iron-sulfur, metal-binding, metal binding protein; NMR {Klebsiella pneumoniae subsp}

Probab=91.15  E-value=0.57  Score=31.42  Aligned_cols=45  Identities=9%  Similarity=0.192  Sum_probs=38.9

Q ss_pred             HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778          34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK   80 (117)
Q Consensus        34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK   80 (117)
                      .|.++|.+.|  -+-..+|-..+++...+|++-|..||.+|+|+.+.
T Consensus         6 ~Il~~L~~~g--~vsv~eLA~~l~VS~~TIRrDL~~Le~~G~l~R~~   50 (87)
T 2k02_A            6 EVRDMLALQG--RMEAKQLSARLQTPQPLIDAMLERMEAMGKVVRIS   50 (87)
T ss_dssp             HHHHHHHHSC--SEEHHHHHHHTTCCHHHHHHHHHHHHTTCCSEEEE
T ss_pred             HHHHHHHHcC--CCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEe
Confidence            3556666544  58889999999999999999999999999999995

>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=91.13  E-value=0.49  Score=37.76  Aligned_cols=54  Identities=19%  Similarity=0.188  Sum_probs=44.7

Q ss_pred             CCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCC-eeeecc
Q psy7778          28 SDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKI-IKAVKS   81 (117)
Q Consensus        28 L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~L-IK~VKs   81 (117)
                      |++-.+.|+.++.++.+.-+--.+|-.+.|+..+.|.|.++.|+..|+ |.++++
T Consensus         1 M~~~~~~iL~~L~~~~g~~~Sg~eLa~~lgvSr~aV~k~i~~L~~~G~~i~~~~~   55 (323)
T 3rkx_A            1 MSKYSQDVLQLLYKNKPNYISGQSIAESLNISRTAVKKVIDQLKLEGCKIDSVNH   55 (323)
T ss_dssp             --CHHHHHHHHHHHHTTSCBCHHHHHHHHTSCHHHHHHHHHHHHHTTCEEEEETT
T ss_pred             CchHHHHHHHHHHhCCCCccCHHHHHHHHCCCHHHHHHHHHHHHhcCCeEEEeCC
Confidence            344556788899888777899999999999999999999999999999 555544

>2ek5_A Predicted transcriptional regulators; helix-turn-helix, interwined alpha helices; 2.20A {Corynebacterium glutamicum atcc 13032} PDB: 2du9_A

Probab=91.07  E-value=0.4  Score=33.31  Aligned_cols=55  Identities=13%  Similarity=0.167  Sum_probs=42.9

Q ss_pred             HHHHHHHHhcCCcc--------cHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCccccc
Q psy7778          34 VVYKIIEEAGNKGI--------WMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTE   90 (117)
Q Consensus        34 lVY~~Ie~AGn~GI--------WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtd   90 (117)
                      .||..|...=..|-        -.++|-.+.|+..+.|.++|+.|+..|+|....+.  |.|-..
T Consensus         8 ~i~~~i~~~I~~g~l~~G~~LPse~~La~~~gvSr~tVr~Al~~L~~~Gli~~~~g~--G~~V~~   70 (129)
T 2ek5_A            8 QIASLIEDSIVDGTLSIDQRVPSTNELAAFHRINPATARNGLTLLVEAGILYKKRGI--GMFVSA   70 (129)
T ss_dssp             HHHHHHHHHHHTTSSCTTSCBCCHHHHHHHTTCCHHHHHHHHHHHHTTTSEEEETTT--EEEECT
T ss_pred             HHHHHHHHHHHhCCCCCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEecCC--EEEEec
Confidence            56777766555554        46799999999999999999999999999877653  555444

>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=91.02  E-value=0.42  Score=33.92  Aligned_cols=54  Identities=9%  Similarity=0.142  Sum_probs=42.3

Q ss_pred             ccCCCHHHHHHHHHHH---HhcC--------CcccHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778          25 LKDSDNEEKVVYKIIE---EAGN--------KGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKA   78 (117)
Q Consensus        25 ~~~L~~eE~lVY~~Ie---~AGn--------~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~   78 (117)
                      +...+.++|+.+-+++   ..|.        --+-..+|-.-.|+...+++|+|+.|+..|+|+.
T Consensus       148 l~~~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~~  212 (232)
T 2gau_A          148 LTQKHVRGRLAETLLILKENFGFENDGATLSIYLSREELATLSNMTVSNAIRTLSTFVSERMLAL  212 (232)
T ss_dssp             HHHSCHHHHHHHHHHHHHHHHCBCTTSSBBSCCCCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             HhcCCHHHHHHHHHHHHHHHcCCCCCCcEEEcccCHHHHHHHhCCCHHHHHHHHHHHHHCCCEee
Confidence            4456778887776655   3331        2356789999999999999999999999999974

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

Probab=90.97  E-value=0.4  Score=32.25  Aligned_cols=56  Identities=20%  Similarity=0.243  Sum_probs=42.6

Q ss_pred             HHHHHHHHhcCCccc--------HHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccC
Q psy7778          34 VVYKIIEEAGNKGIW--------MRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEG   91 (117)
Q Consensus        34 lVY~~Ie~AGn~GIW--------tkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg   91 (117)
                      .||+.|...=..|-|        .++|-.+.|+..+++.++|+.|+..|+|..+.+  .|.|-.+.
T Consensus        13 ~i~~~i~~~I~~g~~~~G~~lPs~~~La~~~~vSr~tvr~al~~L~~~Gli~~~~~--~G~~V~~~   76 (113)
T 3tqn_A           13 QLRDKIVEAIIDGSYVEGEMIPSIRKISTEYQINPLTVSKAYQSLLDDNVIEKRRG--LGMLVKAG   76 (113)
T ss_dssp             HHHHHHHHHHHHTSSCTTCEECCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETT--TEEEECTT
T ss_pred             HHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecC--CeEEEeCC
Confidence            567777665444444        679999999999999999999999999977654  34444443

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

Probab=90.97  E-value=0.4  Score=31.99  Aligned_cols=54  Identities=19%  Similarity=0.254  Sum_probs=38.4

Q ss_pred             HHHHHHHHHHhcCCccc-HHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCC
Q psy7778          32 EKVVYKIIEEAGNKGIW-MRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANI   85 (117)
Q Consensus        32 E~lVY~~Ie~AGn~GIW-tkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg   85 (117)
                      +..|..++.....-|-- .+.|....++...+|..+|+.||.+|||........|
T Consensus        11 ~~~IL~~L~~~~~~gyel~~~l~~~~~i~~~tly~~L~~Le~~GlI~~~~~~~~~   65 (108)
T 3l7w_A           11 EYLILAIVSKHDSYGYDISQTIKLIASIKESTLYPILKKLEKAGYLSTYTQEHQG   65 (108)
T ss_dssp             HHHHHHHHHHSCEEHHHHHHHHTTTCCCCHHHHHHHHHHHHHTTSEEEEEEEETT
T ss_pred             HHHHHHHHHcCCCcHHHHHHHHHHHhCCCcChHHHHHHHHHHCCCeEEEeecCCC
Confidence            56777777753323322 2344445799999999999999999999988654333

>3mwm_A ZUR, putative metal uptake regulation protein; FUR, regulatory metal, graded transcription regulation, transcription; 2.40A {Streptomyces coelicolor}

Probab=90.95  E-value=0.3  Score=34.18  Aligned_cols=62  Identities=8%  Similarity=0.067  Sum_probs=48.4

Q ss_pred             CCCHHHHHHHHHHHHhcCCcccHHHHHhhc-----CCChHHHHHHHHHHhhcCCeeeeccccCCcccc
Q psy7778          27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKS-----NLMPTQLNKILKQLETKKIIKAVKSVANIEYLT   89 (117)
Q Consensus        27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~kt-----nL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYt   89 (117)
                      .+|++-+.|+.++.+++. -+-..+|-.+.     ++..++|-|.|+.|+..|+|..+..-.+...|.
T Consensus        11 r~T~qR~~Il~~L~~~~~-h~sa~eI~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~~~~~g~~~Y~   77 (139)
T 3mwm_A           11 RATRQRAAVSAALQEVEE-FRSAQELHDMLKHKGDAVGLTTVYRTLQSLADAGEVDVLRTAEGESVYR   77 (139)
T ss_dssp             HHHHHHHHHHHHHTTCSS-CEEHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTSSEEEECTTSCEEEE
T ss_pred             ccCHHHHHHHHHHHhCCC-CCCHHHHHHHHHHhCCCCCHHHHHHHHHHHHHCCCEEEEEcCCCceEEE
Confidence            356677789999987653 56666665543     799999999999999999999998766666664

>3by6_A Predicted transcriptional regulator; structural genomics, PSI-2, MCSG, structure initiative, midwest center for structural genomic binding; 2.20A {Oenococcus oeni}

Probab=90.91  E-value=0.48  Score=32.67  Aligned_cols=56  Identities=18%  Similarity=0.355  Sum_probs=44.5

Q ss_pred             HHHHHHHHHhcCCcc--------cHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCccccc
Q psy7778          33 KVVYKIIEEAGNKGI--------WMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTE   90 (117)
Q Consensus        33 ~lVY~~Ie~AGn~GI--------WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtd   90 (117)
                      ..||..|...=..|.        -.++|-.+.|+..++|.++|+.|+..|+|....+  .|.|-..
T Consensus        14 ~~i~~~l~~~I~~g~~~~G~~lPse~~La~~~~vSr~tvr~Al~~L~~~Gli~~~~g--~G~~V~~   77 (126)
T 3by6_A           14 LQLVDRIKNEVATDVLSANDQLPSVRETALQEKINPNTVAKAYKELEAQKVIRTIPG--KGTFITG   77 (126)
T ss_dssp             HHHHHHHHHHHHTTSSCTTCEECCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETT--TEEEECS
T ss_pred             HHHHHHHHHHHHhCCCCCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecC--CeEEEcc
Confidence            357887777655555        4789999999999999999999999999987664  3555544

>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=90.89  E-value=0.29  Score=34.61  Aligned_cols=54  Identities=13%  Similarity=0.204  Sum_probs=42.6

Q ss_pred             ccCCCHHHHHHHHHHHHhcCC------------cccHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778          25 LKDSDNEEKVVYKIIEEAGNK------------GIWMRDIRFKSNLMPTQLNKILKQLETKKIIKA   78 (117)
Q Consensus        25 ~~~L~~eE~lVY~~Ie~AGn~------------GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~   78 (117)
                      +...+.++|+.+-+.+.+...            -+-..+|-.-.|+...+++|+|+.|+..|+|+.
T Consensus       134 l~~~~~~~Rl~~~L~~l~~~~g~~~~~~~~~~~~~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~~  199 (220)
T 2fmy_A          134 LVFKDARLRLAEFLVQAAMDTGLKVPQGIKLELGLNTEEIALMLGTTRQTVSVLLNDFKKMGILER  199 (220)
T ss_dssp             HHTHHHHHHHHHHHHHHHHHHCEEETTEEEEECSSCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHcCCHHHHHHHHHHHHHHHhCCCCCCcEEEeccCCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEE
Confidence            334566888777666655422            356789999999999999999999999999974

>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=90.71  E-value=0.44  Score=34.51  Aligned_cols=56  Identities=9%  Similarity=0.195  Sum_probs=44.3

Q ss_pred             cccCCCHHHHHHHHHHHHhcCC------------cccHHHHHhhcCCChHHHHHHHHHHhhcCCeeee
Q psy7778          24 KLKDSDNEEKVVYKIIEEAGNK------------GIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAV   79 (117)
Q Consensus        24 k~~~L~~eE~lVY~~Ie~AGn~------------GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V   79 (117)
                      .+...+.++|+..-+.+-+...            -+-..+|-.-.|+...+++|+|+.|+..|+|+.-
T Consensus       143 ~~~~~~~~~Rl~~~L~~l~~~~~~~~~~~~~i~~~~t~~~iA~~lG~sr~tvsR~l~~L~~~g~I~~~  210 (250)
T 3e6c_C          143 EMNTYNPTIRILRLFYELCSSQGKRVGDTYEITMPLSQKSIGEITGVHHVTVSRVLASLKRENILDKK  210 (250)
T ss_dssp             HHTTSCHHHHHHHHHHHHHHHHCEEETTEEEEECCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             HHhcCCHHHHHHHHHHHHHHHhCCCCCCCcEecCCCCHHHHHHHhCCcHHHHHHHHHHHHHCCCeEeC
Confidence            3556777888877666654322            3467899999999999999999999999999753

>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=90.48  E-value=0.38  Score=34.91  Aligned_cols=54  Identities=19%  Similarity=0.242  Sum_probs=42.9

Q ss_pred             ccCCCHHHHHHHHHHHHhcC------Cc------ccHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778          25 LKDSDNEEKVVYKIIEEAGN------KG------IWMRDIRFKSNLMPTQLNKILKQLETKKIIKA   78 (117)
Q Consensus        25 ~~~L~~eE~lVY~~Ie~AGn------~G------IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~   78 (117)
                      +...+.++|+..-+++-+..      .|      +-..+|-.-+|+...+++|+|+.|+.+|+|.-
T Consensus       160 l~~~~~~~Rla~~L~~l~~~~g~~~~~~~~i~~~lt~~~lA~~lG~sr~tvsR~l~~L~~~GlI~~  225 (243)
T 3la7_A          160 LAHRDMGSRLVSFLLILCRDFGVPCADGITIDLKLSHQAIAEAIGSTRVTVTRLLGDLREKKMISI  225 (243)
T ss_dssp             HHCSSHHHHHHHHHHHHHHHHEEECSSSEEECSCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HhcCCHHHHHHHHHHHHHHHhCCCCCCCeEEeccCCHHHHHHHHCCcHHHHHHHHHHHHHCCCEEE
Confidence            44567788887767665432      22      45689999999999999999999999999974

>1fse_A GERE; helix-turn-helix DNA-binding protein transcriptional regulat transcription; 2.05A {Bacillus subtilis} SCOP: a.4.6.2

Probab=90.40  E-value=0.79  Score=27.42  Aligned_cols=46  Identities=7%  Similarity=0.084  Sum_probs=38.5

Q ss_pred             ccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhh
Q psy7778          23 EKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLET   72 (117)
Q Consensus        23 ~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~   72 (117)
                      .....||+.|+.|+.++    -.|.-.++|-...|++.+++.+.++.+..
T Consensus         7 ~~~~~L~~~e~~il~~~----~~g~s~~eIA~~l~is~~tV~~~~~~~~~   52 (74)
T 1fse_A            7 QSKPLLTKREREVFELL----VQDKTTKEIASELFISEKTVRNHISNAMQ   52 (74)
T ss_dssp             -CCCCCCHHHHHHHHHH----TTTCCHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHH----HcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            34678999999998886    36779999999999999999998888654

>2p8t_A Hypothetical protein PH0730; pyrococcus horikoshii OT3, STR genomics, PSI, protein structure initiative; 1.80A {Pyrococcus horikoshii} SCOP: a.4.5.72 d.74.4.2

Probab=90.40  E-value=0.47  Score=36.33  Aligned_cols=45  Identities=18%  Similarity=0.243  Sum_probs=38.1

Q ss_pred             CCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccC
Q psy7778          44 NKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEG   91 (117)
Q Consensus        44 n~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg   91 (117)
                      +..+=+++|..+.|+..+.++..++.|+.+|||..-+   +|...|+-
T Consensus        28 ~~~V~~~~LA~~LgvS~~SV~~~lkkL~e~GLV~~~~---~Gv~LTe~   72 (200)
T 2p8t_A           28 KEPLGRKQISERLELGEGSVRTLLRKLSHLDIIRSKQ---RGHFLTLK   72 (200)
T ss_dssp             TSCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC-----CEEECHH
T ss_pred             cCCccHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEeC---CCeEECHH
Confidence            4679999999999999999999999999999997766   67666654

>2pi2_A Replication protein A 32 kDa subunit; FULL-length RPA14/32, ssDNA binding protein, OB-fold, dioxan replication, DNA binding protein; 2.00A {Homo sapiens} SCOP: b.40.4.3 PDB: 2z6k_A 1dpu_A 1z1d_A

Probab=90.38  E-value=0.051  Score=42.39  Aligned_cols=51  Identities=12%  Similarity=0.232  Sum_probs=0.0

Q ss_pred             CCCHHHHHHHHHHHHh-cCCcccHHHHHhhc-CCChHHHHHHHHHHhhcCCee
Q psy7778          27 DSDNEEKVVYKIIEEA-GNKGIWMRDIRFKS-NLMPTQLNKILKQLETKKIIK   77 (117)
Q Consensus        27 ~L~~eE~lVY~~Ie~A-Gn~GIWtkdIk~kt-nL~~~~l~K~LK~LE~k~LIK   77 (117)
                      +|++-...||++|++. .++||-..+|..+. +++...|.++|..|...|+|=
T Consensus       204 ~~~~~~~~Vl~~i~~~~~~~Gi~~~~I~~~l~~~~~~~v~~al~~L~~eG~IY  256 (270)
T 2pi2_A          204 GLTVAQNQVLNLIKACPRPEGLNFQDLKNQLKHMSVSSIKQAVDFLSNEGHIY  256 (270)
T ss_dssp             -----------------------------------------------------
T ss_pred             CCCHHHHHHHHHHHhCCCccCCCHHHHHHHhcCCCHHHHHHHHHHHHhCCEEe
Confidence            5777788999999986 56899999999999 699999999999999999984

>3lmm_A Uncharacterized protein; multi-domained alpha-beta protein, structural genomics, PSI- 2, protein structure initiative; 3.00A {Corynebacterium diphtheriae}

Probab=90.02  E-value=0.59  Score=40.27  Aligned_cols=57  Identities=12%  Similarity=0.030  Sum_probs=48.6

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhh-----cCCeeeeccccCCccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLET-----KKIIKAVKSVANIEYL   88 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~-----k~LIK~VKsV~gg~wY   88 (117)
                      ..++..+.+|+.+|.+.+  -|-.++|+..++++...+.+.|+.|..     ++||....    +.|+
T Consensus       426 ~~~~~~~~~iL~~l~~~~--~it~~~la~~l~~s~~~~~~~L~~L~~~~~~~~glie~~g----~~y~  487 (583)
T 3lmm_A          426 RQDDYRIAIVLYLLFQRP--FITIDVVARGLQSGKEAARNALEAARQTTVAGAPLIIAHD----GVWL  487 (583)
T ss_dssp             GTTCHHHHHHHHHHHHSS--SBCHHHHHHHHTSCHHHHHHHHHHHHTCEETTEESEEEET----TEEE
T ss_pred             cccchhHHHHHHHHHHCC--CcCHHHHHHHhCcCHHHHHHHHHHHHhhhccccceEEEeC----CEEE
Confidence            456667889999888754  599999999999999999999999988     88999974    6666

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

Probab=89.93  E-value=0.55  Score=32.73  Aligned_cols=51  Identities=10%  Similarity=0.265  Sum_probs=40.6

Q ss_pred             CCHHHHHHHHHHHHhcC-----CcccHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778          28 SDNEEKVVYKIIEEAGN-----KGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKA   78 (117)
Q Consensus        28 L~~eE~lVY~~Ie~AGn-----~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~   78 (117)
                      .+.++|+.+-+.+-+.+     --+-..+|-.-.|+...+++|+|+.|+..|+|+.
T Consensus       140 ~~~~~Rl~~~L~~~~~~~~~~~~~~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~~  195 (216)
T 4ev0_A          140 EEARNRVAYALLKLLRQGLGPLFQIRHHELAALAGTSRETVSRVLHALAEEGVVRL  195 (216)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCSEEECCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHHHHHHhhcCCccCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEe
Confidence            44577777767665421     2356899999999999999999999999999973

>3ulq_B Transcriptional regulatory protein COMA; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis} PDB: 2krf_A

Probab=89.40  E-value=0.85  Score=29.79  Aligned_cols=47  Identities=17%  Similarity=0.162  Sum_probs=38.5

Q ss_pred             ccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778          23 EKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK   73 (117)
Q Consensus        23 ~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k   73 (117)
                      .....||+.|+.|+.++.    +|.-.++|-...|+...+|...++.+-.|
T Consensus        25 ~~~~~Lt~rE~~Vl~l~~----~G~s~~eIA~~L~iS~~TV~~~~~~i~~K   71 (90)
T 3ulq_B           25 KEQDVLTPRECLILQEVE----KGFTNQEIADALHLSKRSIEYSLTSIFNK   71 (90)
T ss_dssp             ----CCCHHHHHHHHHHH----TTCCHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             ccccCCCHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            457789999999999975    78999999999999999999888887554

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

Probab=89.40  E-value=0.73  Score=32.49  Aligned_cols=38  Identities=16%  Similarity=0.188  Sum_probs=33.5

Q ss_pred             CCcccHHHHHhhc-CCChHHHHHHHHHHhhcCCeeeecc
Q psy7778          44 NKGIWMRDIRFKS-NLMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        44 n~GIWtkdIk~kt-nL~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      ....=-.+|.... ++.+++|++.|+.||..|||.....
T Consensus        37 ~g~~rf~eL~~~l~gIs~~~Ls~~L~~Le~~GLV~R~~~   75 (131)
T 4a5n_A           37 DGKKRFNEFRRICPSITQRMLTLQLRELEADGIVHREVY   75 (131)
T ss_dssp             TSCBCHHHHHHHCTTSCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             cCCcCHHHHHHHhcccCHHHHHHHHHHHHHCCCEEEEec
Confidence            4456778999999 9999999999999999999987654

>3mq0_A Transcriptional repressor of the blcabc operon; helix-turn-helix, GAF fold, transcription repressor; 1.79A {Agrobacterium tumefaciens}

Probab=88.99  E-value=0.39  Score=37.03  Aligned_cols=46  Identities=4%  Similarity=0.122  Sum_probs=38.3

Q ss_pred             HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778          34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK   80 (117)
Q Consensus        34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK   80 (117)
                      .|..++..++ .++-..+|-.++|||.+++.++|++|+..|++....
T Consensus        34 ~IL~~l~~~~-~~ltl~eia~~lgl~ksTv~RlL~tL~~~G~v~~~~   79 (275)
T 3mq0_A           34 RILDLVAGSP-RDLTAAELTRFLDLPKSSAHGLLAVMTELDLLARSA   79 (275)
T ss_dssp             HHHHHHHHCS-SCEEHHHHHHHHTCC--CHHHHHHHHHHTTSEEECT
T ss_pred             HHHHHHhhCC-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEECC
Confidence            5677776654 689999999999999999999999999999998764

>2w48_A Sorbitol operon regulator; SORC, activator, repressor, DNA-binding, transcription, transcription regulator, transcription regulation; 3.20A {Klebsiella pneumoniae}

Probab=88.99  E-value=0.95  Score=35.19  Aligned_cols=49  Identities=16%  Similarity=0.255  Sum_probs=44.1

Q ss_pred             HHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCee-ee
Q psy7778          31 EEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIK-AV   79 (117)
Q Consensus        31 eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK-~V   79 (117)
                      +++++..+-.---..|+-.++|-.+.|+...+|+|-|+.|+..|+|+ .+
T Consensus         6 ~~~~~~~ia~l~~~~~~~~~ela~~l~vS~~tIrRdL~~l~~~G~v~iri   55 (315)
T 2w48_A            6 DIRLIVKIAQLYYEQDMTQAQIARELGIYRTTISRLLKRGREQGIVTIAI   55 (315)
T ss_dssp             HHHHHHHHHHHHHTSCCCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEEe
Confidence            56677777777788999999999999999999999999999999998 66

>3dkw_A DNR protein; CRP-FNR, HTH, beta barrel, dimerization helix, homodimer, transcription regulator; 3.60A {Pseudomonas aeruginosa}

Probab=88.78  E-value=0.8  Score=32.14  Aligned_cols=51  Identities=16%  Similarity=0.249  Sum_probs=40.7

Q ss_pred             CCHHHHHHHHHHHHhcC---------CcccHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778          28 SDNEEKVVYKIIEEAGN---------KGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKA   78 (117)
Q Consensus        28 L~~eE~lVY~~Ie~AGn---------~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~   78 (117)
                      .+.++|+..-+++.+..         --+-..+|-.-.|+...+++|+|+.|+..|+|..
T Consensus       151 ~~~~~Rl~~~L~~~~~~~~~~~~~~~~~~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~~  210 (227)
T 3dkw_A          151 KNATHRVVRYLLTLAAHAPGENCRVEIPVAKQLVAGHLSIQPETFSRIMHRLGDEGIIHL  210 (227)
T ss_dssp             HHHHHHHHHHHHHHHCSSSSSCCCCCCCSCTHHHHHHTTSCHHHHHHHHHHHHHHTSEEE
T ss_pred             CCHHHHHHHHHHHhhhhcCCCCeEEEecCCHHHHHHHhCCCHHHHHHHHHHHHHCCcEEe
Confidence            34577877766666643         2345689999999999999999999999999964

>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=88.60  E-value=0.61  Score=33.03  Aligned_cols=47  Identities=15%  Similarity=0.225  Sum_probs=37.6

Q ss_pred             HHHHHHHHHHhcCCc-----------ccHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778          32 EKVVYKIIEEAGNKG-----------IWMRDIRFKSNLMPTQLNKILKQLETKKIIKA   78 (117)
Q Consensus        32 E~lVY~~Ie~AGn~G-----------IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~   78 (117)
                      +|+..-+.+.+...|           +-..+|-.-.|+...+++|+|+.|+..|+|+.
T Consensus       150 ~Rl~~~L~~~~~~~~~~~~~~~~~~~~t~~~iA~~lg~sr~tvsR~l~~L~~~g~I~~  207 (231)
T 3e97_A          150 AALTHVFANLYRQRLAAGVPQPEVLPLGTQDIMARTSSSRETVSRVLKRLEAHNILEV  207 (231)
T ss_dssp             HHHHHHHHHHHHHHHHHTCSSTTEECCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHHHhcCCCCCCceEecCCCHHHHHHHhCCcHHHHHHHHHHHHHCCcEEe
Confidence            776666665553222           46799999999999999999999999999973

>1ku3_A Sigma factor SIGA; helix-turn-helix, transcription; 1.80A {Thermus aquaticus} SCOP: a.4.13.2 PDB: 1ku7_A 1rio_H 3n97_A*

Probab=88.01  E-value=1.5  Score=26.73  Aligned_cols=49  Identities=12%  Similarity=0.213  Sum_probs=39.8

Q ss_pred             ccccCCCHHHHHHHHHHH-HhcCCcccHHHHHhhcCCChHHHHH----HHHHHh
Q psy7778          23 EKLKDSDNEEKVVYKIIE-EAGNKGIWMRDIRFKSNLMPTQLNK----ILKQLE   71 (117)
Q Consensus        23 ~k~~~L~~eE~lVY~~Ie-~AGn~GIWtkdIk~ktnL~~~~l~K----~LK~LE   71 (117)
                      ..+..||+.|+.|+.+.. -.|..|.-.++|-...|++..++.+    +++.|.
T Consensus         6 ~~l~~L~~~er~il~l~~~l~~~~~~s~~eIA~~l~is~~tV~~~~~ra~~kLr   59 (73)
T 1ku3_A            6 KALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLK   59 (73)
T ss_dssp             SSTTTSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHHHHH
T ss_pred             HHHHhCCHHHHHHHHHHHhcccCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence            357789999999988877 4666899999999999999998665    555565

>1je8_A Nitrate/nitrite response regulator protein NARL; protein-DNA complex, two-component response regulator, helix-turn-helix, DNA bending; 2.12A {Escherichia coli} SCOP: a.4.6.2 PDB: 1zg1_A 1zg5_A

Probab=88.01  E-value=1.1  Score=28.38  Aligned_cols=47  Identities=13%  Similarity=0.239  Sum_probs=39.1

Q ss_pred             cccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhh
Q psy7778          22 NEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLET   72 (117)
Q Consensus        22 a~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~   72 (117)
                      ...+..||+.|+.|+.++    -.|.-.++|-...|+..++|.+.++....
T Consensus        16 ~~~~~~Lt~~e~~vl~l~----~~g~s~~eIA~~l~is~~tV~~~l~r~~~   62 (82)
T 1je8_A           16 ERDVNQLTPRERDILKLI----AQGLPNKMIARRLDITESTVKVHVKHMLK   62 (82)
T ss_dssp             -CCGGGSCHHHHHHHHHH----TTTCCHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             HHHHccCCHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            346778999999999885    37899999999999999998888776644

>3maj_A DNA processing chain A; MCSG, PSI-2, structural genomics, protein structure initiati midwest center for structural genomics; HET: DNA; 2.05A {Rhodopseudomonas palustris}

Probab=87.96  E-value=0.81  Score=38.08  Aligned_cols=52  Identities=13%  Similarity=0.207  Sum_probs=46.1

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK   80 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK   80 (117)
                      ..|+++|..||+.+.   ...+-..+|-.++|++...+..+|=.||-+|+|.++.
T Consensus       324 ~~l~~~~~~vl~~l~---~~~~~~D~l~~~~gl~~~~v~~~L~~LEl~G~v~~~~  375 (382)
T 3maj_A          324 EPDTGDRTRILALLG---PSPVGIDDLIRLSGISPAVVRTILLELELAGRLERHG  375 (382)
T ss_dssp             CCCTTHHHHHHHHCC---SSCEEHHHHHHHHCCCHHHHHHHHHHHHHTTCCEECT
T ss_pred             CCCChHHHHHHHhhC---CCCCCHHHHHHHHCcCHHHHHHHHHHHHhCCcEEeCC
Confidence            358889999999884   4678899999999999999999999999999998764

>2g7u_A Transcriptional regulator; ICLR family, structural genomics, PSI, protein structure initiative, midwest center for struc genomics; 2.30A {Rhodococcus SP}

Probab=87.67  E-value=0.37  Score=36.50  Aligned_cols=36  Identities=11%  Similarity=0.169  Sum_probs=33.5

Q ss_pred             CCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeee
Q psy7778          44 NKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAV   79 (117)
Q Consensus        44 n~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V   79 (117)
                      +.++-..+|-.++|++.+++.++|++|+..|+|..-
T Consensus        27 ~~~~~~~eia~~~gl~~stv~r~l~~L~~~G~v~~~   62 (257)
T 2g7u_A           27 RPNPTLAELATEAGLSRPAVRRILLTLQKLGYVAGS   62 (257)
T ss_dssp             CSSCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeC
Confidence            468899999999999999999999999999999874

>3c57_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 1.70A {Mycobacterium tuberculosis} PDB: 1zlk_A 1zlj_A

Probab=87.28  E-value=1.1  Score=29.11  Aligned_cols=45  Identities=13%  Similarity=0.279  Sum_probs=35.0

Q ss_pred             ccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHh
Q psy7778          23 EKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLE   71 (117)
Q Consensus        23 ~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE   71 (117)
                      ..+..||+.|+.|+.++    -.|.-.++|-...|+...+|...++...
T Consensus        23 ~~l~~Lt~~e~~vl~l~----~~g~s~~eIA~~l~is~~tV~~~l~r~~   67 (95)
T 3c57_A           23 DPLSGLTDQERTLLGLL----SEGLTNKQIADRMFLAEKTVKNYVSRLL   67 (95)
T ss_dssp             ----CCCHHHHHHHHHH----HTTCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             HHHhcCCHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            45778999999999886    4688999999999999998777666553

>1o5l_A Transcriptional regulator, CRP family; TM1171, structural GE JCSG, PSI, protein structure initiative, joint center for S genomics; 2.30A {Thermotoga maritima} SCOP: b.82.3.2

Probab=87.26  E-value=0.11  Score=37.03  Aligned_cols=54  Identities=15%  Similarity=0.257  Sum_probs=2.1

Q ss_pred             ccCCCHHHHHHHHHHHHhcCCc-----ccHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778          25 LKDSDNEEKVVYKIIEEAGNKG-----IWMRDIRFKSNLMPTQLNKILKQLETKKIIKA   78 (117)
Q Consensus        25 ~~~L~~eE~lVY~~Ie~AGn~G-----IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~   78 (117)
                      +...+.++|+.+-+.+.+...|     +-..+|-.-.|+....++|+|+.|+..|+|+.
T Consensus       138 l~~~~~~~Rl~~~L~~~~~~~g~~~~~~t~~~lA~~lg~sr~tvsR~l~~L~~~G~I~~  196 (213)
T 1o5l_A          138 LTTKTLREKLMNFLVRHMNEKRELTLPVTLEELSRLFGCARPALSRVFQELEREGYIEK  196 (213)
T ss_dssp             HHCC-------------------------------------------------------
T ss_pred             HhhCCHHHHHHHHHHHHhccCCcccCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCeEEE
Confidence            4456678888877777776555     56778888899999999999999999999964

>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=86.94  E-value=0.77  Score=30.80  Aligned_cols=42  Identities=14%  Similarity=0.192  Sum_probs=34.6

Q ss_pred             cHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccc
Q psy7778          48 WMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLT   89 (117)
Q Consensus        48 WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYt   89 (117)
                      -.++|-.+.|+..++|.++|+.|+..|+|....+=..|.|-+
T Consensus        45 s~~eLa~~lgVSr~tVr~al~~L~~~GlI~~~~gG~~G~~V~   86 (102)
T 2b0l_A           45 VASKIADRVGITRSVIVNALRKLESAGVIESRSLGMKGTYIK   86 (102)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECSSSCEEEE
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEeCCCCcEEEe
Confidence            789999999999999999999999999998765222354444

>2p7v_B Sigma-70, RNA polymerase sigma factor RPOD; RSD, regulator of sigma 70, sigma 70 domain 4, transcription, regulation, helix-turn-helix; 2.60A {Escherichia coli} SCOP: a.4.13.2

Probab=86.79  E-value=2  Score=25.85  Aligned_cols=46  Identities=11%  Similarity=0.088  Sum_probs=37.0

Q ss_pred             ccCCCHHHHHHHHHHH-HhcCCcccHHHHHhhcCCChHHHHHHHHHH
Q psy7778          25 LKDSDNEEKVVYKIIE-EAGNKGIWMRDIRFKSNLMPTQLNKILKQL   70 (117)
Q Consensus        25 ~~~L~~eE~lVY~~Ie-~AGn~GIWtkdIk~ktnL~~~~l~K~LK~L   70 (117)
                      +..||+.|+.|+.+.. -.|-.|.-.++|-..+|++..++...+...
T Consensus         3 l~~L~~~er~il~l~~~l~~~~g~s~~eIA~~lgis~~tV~~~~~ra   49 (68)
T 2p7v_B            3 LAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKA   49 (68)
T ss_dssp             SCCCCHHHHHHHHHHTTTTSSSCCCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             HHcCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            5679999999988776 344589999999999999999877665543

>2xzm_8 RPS25E,; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_8

Probab=86.72  E-value=0.67  Score=34.26  Aligned_cols=57  Identities=12%  Similarity=0.150  Sum_probs=42.9

Q ss_pred             ccCCCHHHHHHHHHHH-HhcC--CcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778          25 LKDSDNEEKVVYKIIE-EAGN--KGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        25 ~~~L~~eE~lVY~~Ie-~AGn--~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      +..+---+.-.|+-|. +-.+  +=|---.|-.+.++.-+.-.++|+.||++|+|+.|-.
T Consensus        39 ~nn~VlfDk~tydKL~KEVpk~gKlITpsvlseRlkI~gSLARkaLreL~~kGlIk~V~k   98 (143)
T 2xzm_8           39 VNHAVFIEKKNVESIINNPSKVGKVLTVSTVVEKLKVNGSLARQLMRTMADRKLVEKVAK   98 (143)
T ss_dssp             CCCBSCCCHHHHHHHHTCCTTSCSEECHHHHHHHHCBCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             HhcceeecHHHHHHHHHHhcccceeecHHHHHHHhcchHHHHHHHHHHHHHCCCEEEEec
Confidence            3333333345566555 4444  4688889999999999999999999999999999943

>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=86.70  E-value=2.2  Score=30.21  Aligned_cols=52  Identities=15%  Similarity=0.185  Sum_probs=41.9

Q ss_pred             cccCCCHHHHHHHHHHHHhcCCc--------ccHHHHHhhcCCChHHHHHHHHHHhhcCC
Q psy7778          24 KLKDSDNEEKVVYKIIEEAGNKG--------IWMRDIRFKSNLMPTQLNKILKQLETKKI   75 (117)
Q Consensus        24 k~~~L~~eE~lVY~~Ie~AGn~G--------IWtkdIk~ktnL~~~~l~K~LK~LE~k~L   75 (117)
                      .+...+.++|+.+-+.+.+...|        +-..+|-.-.|+...+++|+|+.|+..|+
T Consensus       148 ~l~~~~~~~Rl~~~L~~~~~~~~~~~~~~l~~t~~~iA~~lg~sr~tvsR~l~~L~~~gi  207 (237)
T 3fx3_A          148 QLKAQTGAQRVAEFLLELCDCDTGACEVTLPYDKMLIAGRLGMKPESLSRAFSRLKAAGV  207 (237)
T ss_dssp             HCCCCCHHHHHHHHHHHHCCC-----EEECCSCTHHHHHHTTCCHHHHHHHHHHHGGGTE
T ss_pred             HHhcCCHHHHHHHHHHHHhhhcCCCeEEEecCCHHHHHHHhCCCHHHHHHHHHHHHHCCe
Confidence            45567789998888888765433        33679999999999999999999999994

>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=86.27  E-value=0.86  Score=31.31  Aligned_cols=61  Identities=21%  Similarity=0.326  Sum_probs=45.6

Q ss_pred             CCCHHHHHHHHHHHHhcCCcc--------cHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCccccc
Q psy7778          27 DSDNEEKVVYKIIEEAGNKGI--------WMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTE   90 (117)
Q Consensus        27 ~L~~eE~lVY~~Ie~AGn~GI--------WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtd   90 (117)
                      ++|-.+ .||+.|..+=-.|-        -.++|-.+.|+..++|.++|+.|+..|||....+.  |.|-.+
T Consensus        12 ~~PlY~-QI~~~i~~~I~~G~l~pG~~LPser~La~~~gVSr~tVReAl~~L~~eGlv~~~~g~--G~~V~~   80 (134)
T 4ham_A           12 QLPIYE-QIVQKIKEQVVKGVLQEGEKILSIREFASRIGVNPNTVSKAYQELERQEVIITVKGK--GTFIAN   80 (134)
T ss_dssp             SSCHHH-HHHHHHHHHHHHTSSCTTCEECCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETTT--EEEECC
T ss_pred             CCCHHH-HHHHHHHHHHHcCCCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEEcCc--EEEEeC
Confidence            344444 46777777544443        45789999999999999999999999999887763  555543

>2o0y_A Transcriptional regulator; ICLR-family, structural genomics, protein structure initiative, midwest center for structural genomics, MCSG; 2.00A {Rhodococcus SP}

Probab=85.79  E-value=0.96  Score=34.30  Aligned_cols=37  Identities=5%  Similarity=0.164  Sum_probs=34.1

Q ss_pred             CCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778          44 NKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK   80 (117)
Q Consensus        44 n~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK   80 (117)
                      +.++-..+|-.++||+.+++.++|++|+..|+|....
T Consensus        36 ~~~~~~~eia~~~gl~kstv~r~l~tL~~~G~v~~~~   72 (260)
T 2o0y_A           36 HPTRSLKELVEGTKLPKTTVVRLVATMCARSVLTSRA   72 (260)
T ss_dssp             BSSBCHHHHHHHHCCCHHHHHHHHHHHHHTTSEEECT
T ss_pred             CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEECC
Confidence            4689999999999999999999999999999998753

>3u5c_Z RP45, S31, YS23, 40S ribosomal protein S25-A; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3izb_V 3o30_Q 3o2z_Q 3u5g_Z

Probab=84.95  E-value=0.89  Score=32.08  Aligned_cols=66  Identities=15%  Similarity=0.119  Sum_probs=45.7

Q ss_pred             cccCCCHHHHHHHHHHH-Hhc-CCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccc
Q psy7778          24 KLKDSDNEEKVVYKIIE-EAG-NKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLT   89 (117)
Q Consensus        24 k~~~L~~eE~lVY~~Ie-~AG-n~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYt   89 (117)
                      ++..+---+...|+-|. +-. .+=|---.|-.+.++.-+.-.++|+.|+++|+|+.|..=+.-.=||
T Consensus        35 K~nn~VlfDk~t~dkl~KEVpk~KlITpsvlseRlkI~gSLAR~aLreL~~kGlIk~V~kh~~q~IYT  102 (108)
T 3u5c_Z           35 RAQHAVILDQEKYDRILKEVPTYRYVSVSVLVDRLKIGGSLARIALRHLEKEGIIKPISKHSKQAIYT  102 (108)
T ss_dssp             -CCSCSSCTTHHHHHHHHHCSSCSSBSHHHHHHTTCCCTTHHHHHHHHHSSSSSCEEEECCSSCCEEE
T ss_pred             HhhcceeeCHHHHHHHHHHccCCeEEeHHHhhhhhhhhHHHHHHHHHHHHHCCCEEEEecCCCEEEEe
Confidence            34444332344555553 333 3667888899999999999999999999999999995333334454

>3edp_A LIN2111 protein; APC88337, listeria innocua CLIP11262, structural GE PSI-2, protein structure initiative, midwest center for STR genomics, MCSG; 2.09A {Listeria innocua}

Probab=84.91  E-value=1.7  Score=32.57  Aligned_cols=57  Identities=12%  Similarity=0.142  Sum_probs=44.0

Q ss_pred             HHHHHHHHHhcCCccc--------HHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccC
Q psy7778          33 KVVYKIIEEAGNKGIW--------MRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEG   91 (117)
Q Consensus        33 ~lVY~~Ie~AGn~GIW--------tkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg   91 (117)
                      ..||+.|.+.=..|.|        -++|..+.|+..+++.++|..|+..|+|....+.  |.|-.+.
T Consensus        12 ~~i~~~l~~~I~~g~~~~g~~lPse~~La~~~~vSr~tvr~Al~~L~~~G~i~~~~g~--G~~V~~~   76 (236)
T 3edp_A           12 EVIASKIKDSINRDEYKTGMLMPNETALQEIYSSSRTTIRRAVDLLVEEGLVVRKNGV--GLYVQPK   76 (236)
T ss_dssp             HHHHHHHHHHHHTTSSCCCC--CCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEETTT--EEEECCC
T ss_pred             HHHHHHHHHHHHhCCCCCcCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEECCc--eEEEccC
Confidence            3566777665555544        6799999999999999999999999999888764  4444443

>2rnj_A Response regulator protein VRAR; HTH LUXR-type domain, DNA binding domain, activator, antibiotic resistance, cytoplasm, DNA-binding; NMR {Staphylococcus aureus}

Probab=84.84  E-value=1.1  Score=28.65  Aligned_cols=46  Identities=15%  Similarity=0.164  Sum_probs=38.7

Q ss_pred             ccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhh
Q psy7778          23 EKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLET   72 (117)
Q Consensus        23 ~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~   72 (117)
                      ..+..||+.|+.|+.++    -.|.-.++|-...|++.++|...++....
T Consensus        25 ~~l~~Lt~~e~~vl~l~----~~g~s~~eIA~~l~is~~tV~~~l~r~~~   70 (91)
T 2rnj_A           25 ELYEMLTEREMEILLLI----AKGYSNQEIASASHITIKTVKTHVSNILS   70 (91)
T ss_dssp             CTGGGCCSHHHHHHHHH----HTTCCTTHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             HHHhcCCHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            46788999999999885    36899999999999999998877766644

>4ets_A Ferric uptake regulation protein; metal binding protein, transcription factor; 2.10A {Campylobacter jejuni subsp}

Probab=84.79  E-value=3  Score=29.89  Aligned_cols=63  Identities=10%  Similarity=0.091  Sum_probs=45.2

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHH----Hhh---cCCChHHHHHHHHHHhhcCCeeeeccccCCcccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDI----RFK---SNLMPTQLNKILKQLETKKIIKAVKSVANIEYLT   89 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdI----k~k---tnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYt   89 (117)
                      -.+|++-+.|+.++.+++ .-+--.+|    +.+   .++..++|-|.|+.|+..|+|..+..-.+...|.
T Consensus        29 ~r~T~qR~~IL~~L~~~~-~h~sA~eI~~~l~~~~~~~~is~aTVYRtL~~L~e~Glv~~i~~~~~~~~Y~   98 (162)
T 4ets_A           29 LKYTKQREVLLKTLYHSD-THYTPESLYMEIKQAEPDLNVGIATVYRTLNLLEEAEMVTSISFGSAGKKYE   98 (162)
T ss_dssp             CCCCHHHHHHHHHHHSCC-SCBCHHHHHHHHHHHCGGGCCCHHHHHHHHHHHHHTTSEEECC-----CCEE
T ss_pred             CCCCHHHHHHHHHHHhCC-CCCCHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHCCCEEEEEeCCCceEEE
Confidence            346888889999998875 44555544    333   5799999999999999999999997655545563

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=84.45  E-value=1.6  Score=32.75  Aligned_cols=57  Identities=16%  Similarity=0.096  Sum_probs=40.1

Q ss_pred             cccCCCHHHHHHHHHHHH---hcCCcccH-------HHHHhhcCCCh---HHHHHHHHHHhhcCCeeeec
Q psy7778          24 KLKDSDNEEKVVYKIIEE---AGNKGIWM-------RDIRFKSNLMP---TQLNKILKQLETKKIIKAVK   80 (117)
Q Consensus        24 k~~~L~~eE~lVY~~Ie~---AGn~GIWt-------kdIk~ktnL~~---~~l~K~LK~LE~k~LIK~VK   80 (117)
                      .+.+|++.++.++..|-.   .|+..+-.       ..+....|.++   +.+..+|+.|+..|+|....
T Consensus       280 ~~~~l~~~~~~il~ai~~~~~~g~~~~~~~~l~~~~~~~~~~~g~~~~~~~~~~~~l~~L~~~gli~~~~  349 (386)
T 2qby_A          280 IILTLPFHSKLVLMAVVSISSEENVVSTTGAVYETYLNICKKLGVEAVTQRRVSDIINELDMVGILTAKV  349 (386)
T ss_dssp             HHHTSCHHHHHHHHHHHHHC-----CEEHHHHHHHHHHHHHHHTCCCCCHHHHHHHHHHHHHHTSEEEEE
T ss_pred             HHHcCCHHHHHHHHHHHHHHhcCCCceeHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHhCCCEEEEe
Confidence            456899999988888875   35443335       45566666554   89999999999999998753

>3r4k_A Transcriptional regulator, ICLR family; DNA/RNA-binding 3-helical bundle, profilin-like, structural joint center for structural genomics, JCSG; 2.46A {Ruegeria SP}

Probab=84.41  E-value=1.1  Score=34.10  Aligned_cols=37  Identities=14%  Similarity=0.267  Sum_probs=34.0

Q ss_pred             CCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778          44 NKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK   80 (117)
Q Consensus        44 n~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK   80 (117)
                      +.|+-..+|-.++|||.+++.+.|++|+..|+|....
T Consensus        19 ~~~lsl~eia~~lgl~ksT~~RlL~tL~~~G~v~~~~   55 (260)
T 3r4k_A           19 RLEIGLSDLTRLSGMNKATVYRLMSELQEAGFVEQVE   55 (260)
T ss_dssp             BSEEEHHHHHHHHCSCHHHHHHHHHHHHHTTSEEECS
T ss_pred             CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcC
Confidence            4789999999999999999999999999999997643

>1tty_A Sigma-A, RNA polymerase sigma factor RPOD; helix-turn-helix, transcription; NMR {Thermotoga maritima} SCOP: a.4.13.2

Probab=84.30  E-value=2.5  Score=26.78  Aligned_cols=46  Identities=15%  Similarity=0.115  Sum_probs=38.2

Q ss_pred             ccccCCCHHHHHHHHHHH-HhcCCcccHHHHHhhcCCChHHHHHHHH
Q psy7778          23 EKLKDSDNEEKVVYKIIE-EAGNKGIWMRDIRFKSNLMPTQLNKILK   68 (117)
Q Consensus        23 ~k~~~L~~eE~lVY~~Ie-~AGn~GIWtkdIk~ktnL~~~~l~K~LK   68 (117)
                      ..+..||+.|+.|+.+.. -.++.|.-.++|-..+|++..+|...+.
T Consensus        14 ~~l~~L~~~er~vl~l~~~l~~~~~~s~~EIA~~lgis~~tV~~~~~   60 (87)
T 1tty_A           14 KVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEV   60 (87)
T ss_dssp             HHHTTSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHhCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            457889999999988877 3677999999999999999988665443

>2qlz_A Transcription factor PF0095; 2.50A {Pyrococcus furiosus} PDB: 2quf_A

Probab=84.16  E-value=0.7  Score=35.53  Aligned_cols=51  Identities=14%  Similarity=0.128  Sum_probs=41.0

Q ss_pred             cCCCH-HHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeee
Q psy7778          26 KDSDN-EEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAV   79 (117)
Q Consensus        26 ~~L~~-eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V   79 (117)
                      +-|.+ -...|+.++..   ..+-..+|...+++++++++++|+.|+..|||...
T Consensus         7 kaL~~~~R~~IL~~L~~---g~~s~~ELa~~lglS~stVs~hL~~Le~aGLV~~~   58 (232)
T 2qlz_A            7 YILGNKVRRDLLSHLTC---MECYFSLLSSKVSVSSTAVAKHLKIMEREGVLQSY   58 (232)
T ss_dssp             HHHTSHHHHHHHHHHTT---TTTCSSSSCTTCCCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHhCCHHHHHHHHHHHh---CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence            33443 34568888863   35777899999999999999999999999999984

>3u1d_A Uncharacterized protein; GNTR-superfamily, structural genomics, PSI-biology, midwest for structural genomics, MCSG; 1.80A {Halomicrobium mukohataei}

Probab=84.09  E-value=3.9  Score=29.86  Aligned_cols=51  Identities=10%  Similarity=0.144  Sum_probs=40.9

Q ss_pred             HHHHHHHHHHHhcCCcccHHHHHhhcC-CChHHHHHHHHHHhhcCCeeeecc
Q psy7778          31 EEKVVYKIIEEAGNKGIWMRDIRFKSN-LMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        31 eE~lVY~~Ie~AGn~GIWtkdIk~ktn-L~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      .-..|++.+-.....-.-..+|....+ |.+++|.+.|+.|+..|+|+.+.-
T Consensus        30 tR~~IL~~Ll~~p~~~~ta~eL~~~l~~lS~aTVyrhL~~L~eaGLV~~~~~   81 (151)
T 3u1d_A           30 TRLDVLHQILAQPDGVLSVEELLYRNPDETEANLRYHVDELVDRGIVEKIPV   81 (151)
T ss_dssp             HHHHHHHHHHHSTTSCBCHHHHHHHCTTSCHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             HHHHHHHHHHcCCCCCCCHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEEeec
Confidence            344777777766433466778888888 999999999999999999998853

>4g6q_A Putative uncharacterized protein; structural genomics, PSI-biology, protein structure initiati midwest center for structural genomics, MCSG; 2.08A {Kribbella flavida}

Probab=83.62  E-value=1.8  Score=31.37  Aligned_cols=57  Identities=7%  Similarity=0.071  Sum_probs=44.2

Q ss_pred             cccccCCCHHHH-HHHHHHHHhcCCcccHHHHHhhcC-CChHHHHHHHHHHhhcCCeeeecc
Q psy7778          22 NEKLKDSDNEEK-VVYKIIEEAGNKGIWMRDIRFKSN-LMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        22 a~k~~~L~~eE~-lVY~~Ie~AGn~GIWtkdIk~ktn-L~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      +.-++-|.+.-| .|.+++   .+.+.-..+|-...+ ++++++++.|+.|+.-|||+.++-
T Consensus        14 ~~~~~~La~P~Rl~il~~L---~~~~~~~~~l~~~l~~~~~~~~s~Hl~~L~~aglv~~~~e   72 (182)
T 4g6q_A           14 SSLVDLLHHPLRWRITQLL---IGRSLTTRELAELLPDVATTTLYRQVGILVKAGVLMVTAE   72 (182)
T ss_dssp             HHHHHHTTSHHHHHHHHHT---TTSCEEHHHHHHHCTTBCHHHHHHHHHHHHHHTSEEEEEE
T ss_pred             HHHHHHhCCHHHHHHHHHH---HhCCCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCeEEEEe
Confidence            345566666555 455555   345788999999986 999999999999999999998764

>2o0m_A Transcriptional regulator, SORC family; structural genomics, protein structure initiative, midwest center for structural genomics, MCSG; 1.60A {Enterococcus faecalis} SCOP: c.124.1.8

Probab=83.41  E-value=0.22  Score=39.45  Aligned_cols=51  Identities=14%  Similarity=0.033  Sum_probs=0.0

Q ss_pred             CCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCee-eec
Q psy7778          28 SDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIK-AVK   80 (117)
Q Consensus        28 L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK-~VK   80 (117)
                      ++..+..|...|..  +.|+-.++|-.++++...+++|.|+.||.+|+|+ .+.
T Consensus        18 ~~~r~~~iL~~l~~--~~~~t~~eLa~~l~vs~~Tv~r~l~~Le~~Glv~~~~~   69 (345)
T 2o0m_A           18 VLQERFQILRNIYW--MQPIGRRSLSETMGITERVLRTETDVLKQLNLIEPSKS   69 (345)
T ss_dssp             ------------------------------------------------------
T ss_pred             hhHHHHHHHHHHHH--cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEec
Confidence            44445566666655  4589999999999999999999999999999997 543

>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=83.41  E-value=3  Score=29.48  Aligned_cols=49  Identities=18%  Similarity=0.247  Sum_probs=36.7

Q ss_pred             HHHHHHHHHHHhcCCcccHHHHHhhc--------CCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          31 EEKVVYKIIEEAGNKGIWMRDIRFKS--------NLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        31 eE~lVY~~Ie~AGn~GIWtkdIk~kt--------nL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      -+..|..++.+ +  ..---+|....        ++...+|..+|+.||.+|||.....-
T Consensus        42 ~~~~IL~~L~~-~--~~~gyeI~~~l~~~~~~~~~is~gtLy~~L~rLE~~GlI~~~~~~   98 (145)
T 1xma_A           42 VDTIILSLLIE-G--DSYGYEISKNIRIKTDELYVIKETTLYSAFARLEKNGYIKSYYGE   98 (145)
T ss_dssp             HHHHHHHHHHH-C--CEEHHHHHHHHHHHHTTSCCCCHHHHHHHHHHHHHTTSEEEEEEE
T ss_pred             HHHHHHHHHHh-C--CCCHHHHHHHHHHhhCCccCcChhHHHHHHHHHHHCCCEEEEEec
Confidence            46788888865 3  24444554444        69999999999999999999987654

>2ia2_A Putative transcriptional regulator; SAD, PSI-2, structural genomics, structure initiative, midwest center for structural genomic transcription; 2.10A {Rhodococcus SP}

Probab=83.30  E-value=1.2  Score=33.89  Aligned_cols=36  Identities=14%  Similarity=0.137  Sum_probs=33.6

Q ss_pred             CCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeee
Q psy7778          44 NKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAV   79 (117)
Q Consensus        44 n~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V   79 (117)
                      ..++-..+|-.++|||.+++.++|++|+..|++..-
T Consensus        34 ~~~~~~~eia~~~gl~~stv~r~l~tL~~~G~v~~~   69 (265)
T 2ia2_A           34 NQRRTLSDVARATDLTRATARRFLLTLVELGYVATD   69 (265)
T ss_dssp             CSSEEHHHHHHHHTCCHHHHHHHHHHHHHHTSEEES
T ss_pred             CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEec
Confidence            478999999999999999999999999999999874

>4esb_A Transcriptional regulator, PADR family; DNA binding protein, HTH fold; 2.50A {Bacillus cereus}

Probab=83.29  E-value=1.3  Score=30.16  Aligned_cols=47  Identities=17%  Similarity=0.255  Sum_probs=33.0

Q ss_pred             HHHHHHHHHHhcCCcccHHHHHhhc------CCChHHHHHHHHHHhhcCCeeeecc
Q psy7778          32 EKVVYKIIEEAGNKGIWMRDIRFKS------NLMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        32 E~lVY~~Ie~AGn~GIWtkdIk~kt------nL~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      +.+|..++.....-|   -+|....      ++.+.+|..+|+.||.+|||.+...
T Consensus        11 ~~~IL~~L~~~~~~G---yei~~~l~~~~~~~is~gtlY~~L~rLe~~GlI~~~~~   63 (115)
T 4esb_A           11 EGCILYIISQEEVYG---YELSTKLNKHGFTFVSEGSIYPLLLRMQKEKLIEGTLK   63 (115)
T ss_dssp             HHHHHHHHHHSCEEH---HHHHHHHHHTTCTTCCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             HHHHHHHHHcCCCCH---HHHHHHHHHcCCCCCCcChHHHHHHHHHHCCCeEEEee
Confidence            556666776433233   3333333      5899999999999999999998754

>3iz6_V 40S ribosomal protein S25 (S25E); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum}

Probab=83.20  E-value=0.58  Score=33.05  Aligned_cols=45  Identities=18%  Similarity=0.141  Sum_probs=36.0

Q ss_pred             CcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccc
Q psy7778          45 KGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLT   89 (117)
Q Consensus        45 ~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYt   89 (117)
                      +=|---.|-.+.++.-+.-.++|+.|+++|+|+.|..=+.-.=||
T Consensus        59 KlITpsvlseRlkI~gSLAR~aLreL~~kGlIk~V~kh~~q~IYT  103 (108)
T 3iz6_V           59 KQITPSVLSERLRINGSLARQAIKDLESRGAIRVVSVHSSQLIYT  103 (108)
T ss_dssp             SSEEEHHHHHHHHTCCHHHHHHHHHHHHHHTSCEECCCTTSCCEE
T ss_pred             eEEeHHHHHhhhcccHHHHHHHHHHHHHCCCEEEEecCCCEEEEe
Confidence            567777888999999999999999999999999994322333444

>1p4w_A RCSB; solution structure, DNA binding domain, DNA binding protein; NMR {Erwinia amylovora} SCOP: a.4.6.2

Probab=82.76  E-value=2.4  Score=28.23  Aligned_cols=44  Identities=18%  Similarity=0.152  Sum_probs=37.3

Q ss_pred             ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhh
Q psy7778          25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLET   72 (117)
Q Consensus        25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~   72 (117)
                      ...||+.|+.|+.++.    .|.-.++|-...|+...+|...++.+..
T Consensus        32 ~~~Lt~re~~Vl~l~~----~G~s~~EIA~~L~iS~~TV~~~l~ri~~   75 (99)
T 1p4w_A           32 DKRLSPKESEVLRLFA----EGFLVTEIAKKLNRSIKTISSQKKSAMM   75 (99)
T ss_dssp             SSSCCHHHHHHHHHHH----HTCCHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             cCCCCHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            5679999999998863    6899999999999999998877776644

>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=82.56  E-value=1.7  Score=29.71  Aligned_cols=47  Identities=26%  Similarity=0.314  Sum_probs=34.6

Q ss_pred             HHHHHHHHHHhcCCcccHHHHHhhc------CCChHHHHHHHHHHhhcCCeeeecc
Q psy7778          32 EKVVYKIIEEAGNKGIWMRDIRFKS------NLMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        32 E~lVY~~Ie~AGn~GIWtkdIk~kt------nL~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      +.+|..++.+.-.-|-   +|..+.      ++.+.+|..+|+.||.+|||.+...
T Consensus        15 ~~~IL~lL~~~p~~Gy---ei~~~l~~~g~~~is~gtlY~~L~rLe~~GlI~~~~~   67 (116)
T 3hhh_A           15 EGLVLAIIQRKETYGY---EITKILNDQGFTEIVEGTVYTILLRLEKNQWVIAEKK   67 (116)
T ss_dssp             HHHHHHHHHHSCBCHH---HHHHHHHTTSCSSCCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             HHHHHHHHhcCCCCHH---HHHHHHHHcCCCCCCccHHHHHHHHHHHCCCEEEEee
Confidence            5677777765433443   444443      6899999999999999999998753

>1x3u_A Transcriptional regulatory protein FIXJ; helix-turn-helix; NMR {Sinorhizobium meliloti}

Probab=82.15  E-value=1.5  Score=26.59  Aligned_cols=46  Identities=13%  Similarity=0.266  Sum_probs=38.0

Q ss_pred             ccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhh
Q psy7778          23 EKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLET   72 (117)
Q Consensus        23 ~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~   72 (117)
                      ..+..||+.|+.|+.++    -.|.-.++|-...|++..++...++....
T Consensus        12 ~~l~~L~~~e~~vl~l~----~~g~s~~eIA~~l~is~~tV~~~~~r~~~   57 (79)
T 1x3u_A           12 ARLQTLSERERQVLSAV----VAGLPNKSIAYDLDISPRTVEVHRANVMA   57 (79)
T ss_dssp             HHHHHHCHHHHHHHHHH----TTTCCHHHHHHHTTSCHHHHHHHHHHHHH
T ss_pred             HHHHhCCHHHHHHHHHH----HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            34667999999998885    37899999999999999998887776644

>2esh_A Conserved hypothetical protein TM0937; APC5794, structural genomics, PSI, protein structure initiative; 2.30A {Thermotoga maritima} SCOP: a.4.5.61

Probab=81.81  E-value=0.96  Score=30.49  Aligned_cols=48  Identities=8%  Similarity=0.107  Sum_probs=33.2

Q ss_pred             HHHHHHHHHHhcCCcccHHHHHhhc------C--CCh-HHHHHHHHHHhhcCCeeeeccc
Q psy7778          32 EKVVYKIIEEAGNKGIWMRDIRFKS------N--LMP-TQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        32 E~lVY~~Ie~AGn~GIWtkdIk~kt------n--L~~-~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      +..|..++...   ..---+|....      +  +.+ .+|..+|+.||..|||.....-
T Consensus        15 ~~~IL~~L~~~---~~~gyel~~~l~~~g~~~~~is~~~tly~~L~~Le~~GlI~~~~~~   71 (118)
T 2esh_A           15 ASTILLLVAEK---PSHGYELAERLAEFGIEIPGIGHMGNIYRVLADLEESGFLSTEWDT   71 (118)
T ss_dssp             HHHHHHHHHHS---CBCHHHHHHHHHTTCCSSTTCCCCCCHHHHHHHHHHTTSEEEEEEC
T ss_pred             HHHHHHHHHcC---CCCHHHHHHHHHHhCCcccCCCCcchHHHHHHHHHHCCCeEEEeec
Confidence            55666666542   23333444443      2  888 9999999999999999987643

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

Probab=81.55  E-value=0.67  Score=31.85  Aligned_cols=55  Identities=9%  Similarity=0.097  Sum_probs=40.7

Q ss_pred             HHHHHHHHhcCCccc--------HHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCccccc
Q psy7778          34 VVYKIIEEAGNKGIW--------MRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTE   90 (117)
Q Consensus        34 lVY~~Ie~AGn~GIW--------tkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtd   90 (117)
                      .||..|...=..|-|        .++|-.+.|+..++|.++|+.|+..|+|....+  .|.|-.+
T Consensus        15 ~i~~~l~~~I~~g~~~~G~~lPs~~~La~~~~vSr~tvr~Al~~L~~~G~i~~~~~--~G~~V~~   77 (126)
T 3ic7_A           15 QIADRICDDILLGQYEEEGRIPSVREYASIVEVNANTVMRSYEYLQSQEVIYNKRG--IGFFVAS   77 (126)
T ss_dssp             HHHHHHHHHHHTTSSCBTSEECCTTTTTTCC-CCSGGGHHHHHHHHTTTSEEEETT--TEEEECT
T ss_pred             HHHHHHHHHHHhCCCCCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEEcC--CccEEcc
Confidence            466666655444443        578999999999999999999999999988765  3444443

>4esf_A PADR-like transcriptional regulator; PADR family, DNA binding protein, HTH fold; 2.20A {Bacillus cereus}

Probab=81.51  E-value=1.3  Score=30.25  Aligned_cols=47  Identities=28%  Similarity=0.368  Sum_probs=33.3

Q ss_pred             HHHHHHHHHHhcCCcccHHHHHhhc------CCChHHHHHHHHHHhhcCCeeeecc
Q psy7778          32 EKVVYKIIEEAGNKGIWMRDIRFKS------NLMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        32 E~lVY~~Ie~AGn~GIWtkdIk~kt------nL~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      +.+|..++...-.-|   -+|....      ++.+.+|..+|+.||.+|||.+...
T Consensus        13 ~~~IL~lL~~~p~~G---yei~~~l~~~g~~~is~gtlY~~L~rLe~~GlI~~~~~   65 (117)
T 4esf_A           13 EGCVLEIISRRETYG---YEITRHLNDLGFTEVVEGTVYTILVRLEKKKLVNIEKK   65 (117)
T ss_dssp             HHHHHHHHHHSCBCH---HHHHHHHHHHTCTTCCHHHHHHHHHHHHHTTCEEEEEE
T ss_pred             HHHHHHHHHcCCCCH---HHHHHHHHHcCCCCCCccHHHHHHHHHHHCCCEEEEee
Confidence            456666666433233   2344433      7899999999999999999998754

>2o8x_A Probable RNA polymerase sigma-C factor; promoter recognition, transcription regulation, helix-turn-H motif, transcription; 3.00A {Mycobacterium tuberculosis}

Probab=80.98  E-value=5.1  Score=23.40  Aligned_cols=45  Identities=7%  Similarity=0.053  Sum_probs=36.1

Q ss_pred             ccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHH
Q psy7778          23 EKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQL   70 (117)
Q Consensus        23 ~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~L   70 (117)
                      ..+..||+.++.|+.+..   -.|.-.++|-...|++.+++.+.+...
T Consensus        11 ~~l~~L~~~~r~il~l~~---~~g~s~~eIA~~lgis~~tv~~~~~ra   55 (70)
T 2o8x_A           11 TMIADLTTDQREALLLTQ---LLGLSYADAAAVCGCPVGTIRSRVARA   55 (70)
T ss_dssp             TTTTSSCHHHHHHHHHHH---TSCCCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHhCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            457889999998887755   357889999999999999877666543

>3qph_A TRMB, A global transcription regulator; transcriptional regulator; HET: SUC; 2.99A {Pyrococcus furiosus}

Probab=80.81  E-value=0.032  Score=44.95  Aligned_cols=53  Identities=13%  Similarity=0.177  Sum_probs=44.8

Q ss_pred             CCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778          27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      +||..|-.||-.+-..|.  .-..+|-..+++|++.+..+|+.|+.+|||....+
T Consensus        15 Gls~~ea~vY~~Ll~~g~--~t~~eia~~~gv~~~~Vy~~L~~L~~~GlV~~~~g   67 (342)
T 3qph_A           15 GFTKYEILTYWTLLVYGP--STAKEISTKSGIPYNRVYDTISSLKLRGFVTEIEG   67 (342)
T ss_dssp             HHHHHTTSCSHHHHHHHH--HHHSCCSSSTTSSSCSCCHHHHHHHHHTSEEEECC
T ss_pred             CCCHHHHHHHHHHHHcCC--CCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcC
Confidence            467777788888876653  45589999999999999999999999999998754

>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=80.55  E-value=3  Score=30.37  Aligned_cols=49  Identities=14%  Similarity=0.129  Sum_probs=41.0

Q ss_pred             HHHHHHHHhcCCccc--------HHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          34 VVYKIIEEAGNKGIW--------MRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        34 lVY~~Ie~AGn~GIW--------tkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      .||+.|.+.=-.|-|        -++|-.+.|+.-+.|..+|+.|+..|||....+.
T Consensus        11 ~v~~~l~~~I~~g~l~pG~~LPsE~eLa~~~gVSR~tVReAL~~L~~eGlv~~~~g~   67 (239)
T 1hw1_A           11 FAEEYIIESIWNNRFPPGTILPAERELSELIGVTRTTLREVLQRLARDGWLTIQHGK   67 (239)
T ss_dssp             HHHHHHHHHHHTTSSCTTSBCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETTE
T ss_pred             HHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEecCC
Confidence            577777766555544        5899999999999999999999999999988763

>3eet_A Putative GNTR-family transcriptional regulator; structural genomics, PSI-2, protein structure initiative; 1.97A {Streptomyces avermitilis}

Probab=80.48  E-value=2.3  Score=32.68  Aligned_cols=56  Identities=16%  Similarity=0.064  Sum_probs=42.8

Q ss_pred             HHHHHHHHhcCCccc--------HHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccC
Q psy7778          34 VVYKIIEEAGNKGIW--------MRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEG   91 (117)
Q Consensus        34 lVY~~Ie~AGn~GIW--------tkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg   91 (117)
                      .||+.|.+.=..|.|        -++|..+.|+..+++.++|..|+..|+|....+.  |.|-...
T Consensus        33 ~i~~~l~~~I~~g~~~~g~~lPse~~La~~~~vSr~tvr~Al~~L~~~G~i~~~~g~--G~~V~~~   96 (272)
T 3eet_A           33 RVAGDLRKKIVDGSLPPHTRLPSQARIREEYGVSDTVALEARKVLMAEGLVEGRSGS--GTYVRER   96 (272)
T ss_dssp             HHHHHHHHHHHHTSSCTTSBCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEECCC----EEECCC
T ss_pred             HHHHHHHHHHHcCCCCCcCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCc--eEEEecC
Confidence            567777665555554        6899999999999999999999999999888764  4444433

>1stz_A Heat-inducible transcription repressor HRCA homol; circe element, structural genomics, BSGC structure FUN NIH, protein structure initiative; 2.20A {Thermotoga maritima} SCOP: a.4.5.51 d.110.2.3

Probab=80.43  E-value=3.9  Score=32.78  Aligned_cols=52  Identities=15%  Similarity=0.150  Sum_probs=42.4

Q ss_pred             CCHHHHHHHH-----HHHHhcCCcccHHHHHhhc--CCChHHHHHHHHHHhhcCCeeeecc
Q psy7778          28 SDNEEKVVYK-----IIEEAGNKGIWMRDIRFKS--NLMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        28 L~~eE~lVY~-----~Ie~AGn~GIWtkdIk~kt--nL~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      +++-++.|++     +|+..+.  +=+++|..+.  +....+|.+-|..||..|+|+.+-+
T Consensus        15 l~eR~~~IL~~i~~~yl~~~~p--V~s~~La~~~~l~VS~aTIRrDL~~LE~~GlL~r~Hg   73 (338)
T 1stz_A           15 LNDRQRKVLYCIVREYIENKKP--VSSQRVLEVSNIEFSSATIRNDMKKLEYLGYIYQPHT   73 (338)
T ss_dssp             CCHHHHHHHHHHHHHHHHHCSC--BCHHHHHHHSCCCSCHHHHHHHHHHHHHTTSEECCSS
T ss_pred             HHHHHHHHHHHHHHHHHHcCCC--ccHHHHHHHhCCCCCHHHHHHHHHHHHHCCCEEEccC
Confidence            5666667888     6666565  5679999999  8899999999999999999987443

>2wv0_A YVOA, HTH-type transcriptional repressor YVOA; DNA-binding, transcription regulation, transcriptional regulator, GNTR/HUTC family; 2.40A {Bacillus subtilis}

Probab=80.28  E-value=2.1  Score=32.22  Aligned_cols=57  Identities=9%  Similarity=0.127  Sum_probs=42.8

Q ss_pred             HHHHHHHHhcCCcc--------cHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccCc
Q psy7778          34 VVYKIIEEAGNKGI--------WMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGT   92 (117)
Q Consensus        34 lVY~~Ie~AGn~GI--------WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg~   92 (117)
                      .||+.|.+.=..|.        -.++|-.+.|+..+++.++|+.|+..|+|....+.  |.|-....
T Consensus        14 ~i~~~l~~~I~~g~~~~g~~lPse~~La~~~~vSr~tvr~Al~~L~~~G~i~~~~g~--G~~V~~~~   78 (243)
T 2wv0_A           14 QIMEQLKTQIKNGELQPDMPLPSEREYAEQFGISRMTVRQALSNLVNEGLLYRLKGR--GTFVSKPK   78 (243)
T ss_dssp             HHHHHHHHHHHHTSSCTTCBCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEECTTS--CEEECCCC
T ss_pred             HHHHHHHHHHHhCCCCCcCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEeCCC--eEEEeCCc
Confidence            56666655433333        35899999999999999999999999999877654  55555443

>3bwg_A Uncharacterized HTH-type transcriptional regulato; APC85486, YYDK, transcriptional regulator, structural genomi 2; 2.09A {Bacillus subtilis subsp} SCOP: a.4.5.6 d.190.1.2

Probab=80.05  E-value=2.5  Score=31.59  Aligned_cols=49  Identities=18%  Similarity=0.137  Sum_probs=38.1

Q ss_pred             HHHHHHHHhcCCcc--------cHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          34 VVYKIIEEAGNKGI--------WMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        34 lVY~~Ie~AGn~GI--------WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      .||+.|.+.=..|.        --++|-.+.|+..+++.++|+.|+..|+|....+.
T Consensus         9 ~i~~~l~~~I~~g~~~~g~~lPse~~La~~~~vSr~tvr~Al~~L~~~g~i~~~~g~   65 (239)
T 3bwg_A            9 QIATEIETYIEEHQLQQGDKLPVLETLMAQFEVSKSTITKSLELLEQKGAIFQVRGS   65 (239)
T ss_dssp             HHHHHHHHHHHHTTCCTTCBCCCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEETTT
T ss_pred             HHHHHHHHHHHhCCCCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEeCCc
Confidence            35555554333333        46799999999999999999999999999887654

---

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	117
d2dk5a1	78	a.4.5.85 (A:8-85) DNA-directed RNA polymerase III	2e-24

>d2dk5a1 a.4.5.85 (A:8-85) DNA-directed RNA polymerase III subunit RPC6, RPO3F {Human (Homo sapiens) [TaxId: 9606]} Length = 78

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: RPO3F domain-like
domain: DNA-directed RNA polymerase III subunit RPC6, RPO3F
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 86.7 bits (215), Expect = 2e-24
 Identities = 45/67 (67%), Positives = 56/67 (83%)

Query: 18 DPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIK 77
          D     K+K SDN+EK+VY+IIE+AGNKGIW RD+R+KSNL  T++NKILK LE+KK+IK
Sbjct: 1  DSQNAGKMKGSDNQEKLVYQIIEDAGNKGIWSRDVRYKSNLPLTEINKILKNLESKKLIK 60

Query: 78 AVKSVAN 84
          AVKSVA 
Sbjct: 61 AVKSVAA 67

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	117
d2dk5a1	78	DNA-directed RNA polymerase III subunit RPC6, RPO3	99.96
d3broa1	135	Transcriptional regulator OEOE1854 {Oenococcus oen	97.75
d1dpua_	69	C-terminal domain of RPA32 {Human (Homo sapiens) [	97.66
d1hsja1	115	Staphylococcal accessory regulator A homolog, SarR	97.66
d1p4xa2	125	Staphylococcal accessory regulator A homolog, SarS	97.63
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	97.62
d1p4xa1	125	Staphylococcal accessory regulator A homolog, SarS	97.57
d2frha1	115	Pleiotropic regulator of virulence genes, SarA {St	97.54
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	97.52
d2a61a1	139	Transcriptional regulator TM0710 {Thermotoga marit	97.41
d1z91a1	137	Organic hydroperoxide resistance transcriptional r	97.33
d2fbha1	137	Transcriptional regulator PA3341 {Pseudomonas aeru	97.31
d2fbia1	136	Probable transcriptional regulator PA4135 {Pseudom	97.3
d1lnwa_	141	MexR repressor {Pseudomonas aeruginosa [TaxId: 287	97.26
d2bv6a1	136	Transcriptional regulator MgrA {Staphylococcus aur	97.24
d1s3ja_	143	Putative transcriptional regulator YusO {Bacillus	97.24
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	97.23
d1lj9a_	144	Transcriptional regulator SlyA {Enterococcus faeca	97.15
d2etha1	140	Putative transcriptional regulator TM0816 {Thermot	97.14
d3deua1	140	Transcriptional regulator SlyA {Salmonella typhimu	97.12
d1jgsa_	138	Multiple antibiotic resistance repressor, MarR {Es	97.1
d1xd7a_	127	Hypothetical protein ywnA {Bacillus subtilis [TaxI	97.09
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	97.03
d2fbka1	172	Transcriptional regulator DR1159 {Deinococcus radi	96.99
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	96.93
d2fxaa1	162	Protease production regulatory protein Hpr {Bacill	96.89
d2hr3a1	145	Probable transcriptional regulator PA3067 {Pseudom	96.82
d1ub9a_	100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	96.72
d1ylfa1	138	Hypothetical protein BC1842 {Bacillus cereus [TaxI	96.56
d1okra_	120	Methicillin resistance regulatory protein MecI {St	96.32
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	95.8
d1z6ra1	70	Mlc protein N-terminal domain {Escherichia coli [T	95.77
d2ev0a1	61	Manganese transport regulator MntR {Bacillus subti	95.75
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	95.71
d2hoea1	62	N-acetylglucosamine kinase {Thermotoga maritima [T	95.64
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	95.6
d2isya1	63	Iron-dependent regulator IdeR {Mycobacterium tuber	95.59
d3ctaa1	85	Ta1064 (RFK), N-terminal domain {Thermoplasma acid	95.44
d1r7ja_	90	Sso10a (SSO10449) {Archaeon Sulfolobus solfataricu	95.04
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	94.83
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	94.82
d1stza1	87	Heat-inducible transcription repressor HrcA, N-ter	94.66
d1sfua_	70	34L {Yaba-like disease virus, YLDV [TaxId: 132475]	94.57
d2g9wa1	122	Hypothetical protein Rv1846c {Mycobacterium tuberc	94.43
d1lvaa3	64	C-terminal fragment of elongation factor SelB {Moo	94.01
d1i5za1	69	Catabolite gene activator protein (CAP), C-termina	93.13
d1xmka1	73	Z-alpha domain of dsRNA-specific adenosine deamina	93.03
d1zyba1	73	Probable transcription regulator BT4300, C-termina	92.73
d2gaua1	81	Transcriptional regulator PG0396, C-terminal domai	92.39
d1sd4a_	122	Penicillinase repressor BlaI {Staphylococcus aureu	92.22
d1w5sa1	110	CDC6-like protein APE0152, C-terminal domain {Aero	91.79
d1p6ra_	82	Penicillinase repressor BlaI {Bacillus licheniform	91.57
d3e5ua1	80	Chlorophenol reduction protein CprK {Desulfitobact	91.36
d1r1ua_	94	Metal-sensing transcriptional repressor CzrA {Stap	91.2
d2gxba1	59	Z-alpha domain of dsRNA-specific adenosine deamina	91.13
d3bwga1	78	Transcriptional regulator YydK {Bacillus subtilis	90.67
d1ft9a1	80	CO-sensing protein CooA, C-terminal domain {Rhodos	90.58
d1u2wa1	108	Cadmium efflux system accessory protein CadC {Stap	90.44
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	90.41
d1zara1	89	Rio2 serine protein kinase N-terminal domain {Arch	90.11
d1r1ta_	98	SmtB repressor {Cyanobacteria (Synechococcus), pcc	90.07
d2hs5a1	69	Putative transcriptional regulator RHA1_ro03477 {R	89.45
d1hw1a1	74	Fatty acid responsive transcription factor FadR, N	89.41
d2f2ea1	142	Hypothetical protein PA1607 {Pseudomonas aeruginos	88.89
d1a04a1	67	Nitrate/nitrite response regulator (NarL) {Escheri	88.35
d1fnna1	112	CDC6, C-terminal domain {Archaeon Pyrobaculum aero	88.29
d1v4ra1	100	Transcriptional repressor TraR, N-terminal domain	88.18
d1ulya_	190	Hypothetical protein PH1932 {Pyrococcus horikoshii	87.26
d2p4wa1	194	Transcriptional regulatory protein PF1790 {Pyrococ	86.59
d1mzba_	134	Ferric uptake regulation protein, FUR {Pseudomonas	85.51
d2hzta1	95	Putative transcriptional regulator YtcD {Bacillus	85.42
d2fswa1	102	Hypothetical protein PG0823 {Porphyromonas gingiva	84.62
d1yyva1	114	Putative transcriptional regulator YtfH {Salmonell	83.33
d1tw3a1	85	Carminomycin 4-O-methyltransferase {Streptomyces p	80.71
d1yioa1	70	Response regulatory protein StyR, C-terminal domai	80.08

>d2dk5a1 a.4.5.85 (A:8-85) DNA-directed RNA polymerase III subunit RPC6, RPO3F {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: RPO3F domain-like
domain: DNA-directed RNA polymerase III subunit RPC6, RPO3F
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.96  E-value=9.8e-31  Score=176.54  Aligned_cols=68  Identities=66%  Similarity=0.964  Sum_probs=65.6

Q ss_pred             CccccccccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCC
Q psy7778          18 DPVTNEKLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANI   85 (117)
Q Consensus        18 ~~e~a~k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg   85 (117)
                      ++++|+++++|+++|++||++|++|||+|||++|||.+||||+++|+||||+||+++|||+|+||++.
T Consensus         1 d~~~a~k~~~l~~~E~lVY~~I~~ag~~GIW~~dir~ktnL~~~~l~K~LK~Lesk~lIK~VksV~~~   68 (78)
T d2dk5a1           1 DSQNAGKMKGSDNQEKLVYQIIEDAGNKGIWSRDVRYKSNLPLTEINKILKNLESKKLIKAVKSVAAS   68 (78)
T ss_dssp             CCCCCCCCCCSCSSHHHHHHHHHHHCTTCEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEECCSSCS
T ss_pred             CHHHHHHHhCCCHHHHHHHHHHHHccccceeHHHHHHHcCCCHHHHHHHHHHHHhcCCceeecccCCC
Confidence            56889999999999999999999999999999999999999999999999999999999999999854

>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=97.75  E-value=4.5e-05  Score=50.92  Aligned_cols=57  Identities=18%  Similarity=0.265  Sum_probs=53.9

Q ss_pred             CCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      +||..|..|+..|...++.+|-..+|...+++..+.++++|+.||.+|||....+-.
T Consensus        26 glt~~q~~vL~~l~~~~~~~it~~ela~~~~~~~~~vs~~l~~L~~~g~v~r~~~~~   82 (135)
T d3broa1          26 DLTGTQMTIIDYLSRNKNKEVLQRDLESEFSIKSSTATVLLQRMEIKKLLYRKVSGK   82 (135)
T ss_dssp             TCCHHHHHHHHHHHHTTTSCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECSS
T ss_pred             CCCHHHHHHHHHHHHcCCCCCCHHHHHHHHCcCHhHHHHHHHHHHHHHHHHHHhhhh
Confidence            799999999999999888999999999999999999999999999999999888765

>d1dpua_ a.4.5.16 (A:) C-terminal domain of RPA32 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: C-terminal domain of RPA32
domain: C-terminal domain of RPA32
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.66  E-value=6.6e-05  Score=47.80  Aligned_cols=53  Identities=11%  Similarity=0.231  Sum_probs=48.4

Q ss_pred             cCCCHHHHHHHHHHHHhc-CCcccHHHHHhhc-CCChHHHHHHHHHHhhcCCeee
Q psy7778          26 KDSDNEEKVVYKIIEEAG-NKGIWMRDIRFKS-NLMPTQLNKILKQLETKKIIKA   78 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AG-n~GIWtkdIk~kt-nL~~~~l~K~LK~LE~k~LIK~   78 (117)
                      .+|++-++.||++|.... ++||-..+|+.+. |||.+.|.+++..|.+.|+|=+
T Consensus         2 nGLs~~q~~V~~~i~s~~~~eGi~~~el~~~l~~~~~~~i~~aid~L~~eG~IYs   56 (69)
T d1dpua_           2 NGLTVAQNQVLNLIKACPRPEGLNFQDLKNQLKHMSVSSIKQAVDFLSNEGHIYS   56 (69)
T ss_dssp             CCSCHHHHHHHHHHHHCCCTTTEEHHHHHHHSTTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCCHHHHHHHHHHHhCCCccCcCHHHHHHHccCCCHHHHHHHHHHHHhCCceec
Confidence            589999999999998764 5999999999998 7999999999999999999853

>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=97.66  E-value=4.4e-05  Score=51.03  Aligned_cols=60  Identities=23%  Similarity=0.264  Sum_probs=55.2

Q ss_pred             cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      +--+||..|..|..+|..+.+.|+-..+|...++++.+.++++++.||.+|||....+-.
T Consensus        26 ~~~~Lt~~q~~vL~~l~~~~~~~~t~~ela~~l~~~~~~vs~~i~~Le~~gli~r~~~~~   85 (115)
T d1hsja1          26 KKFNLNYEEIYILNHILRSESNEISSKEIAKCSEFKPYYLTKALQKLKDLKLLSKKRSLQ   85 (115)
T ss_dssp             SSCCCCHHHHHHHHHHHTCSCSEEEHHHHHHSSCCCHHHHHHHHHHHHTTTTSCCEECCS
T ss_pred             hhcCCCHHHHHHHHHHHccCCCCcCHHHHHHHHCCChhhHHHHHHHHHHcCCeEEEeecC
Confidence            345899999999999998888999999999999999999999999999999999888765

>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=97.63  E-value=5.3e-05  Score=51.56  Aligned_cols=59  Identities=14%  Similarity=0.087  Sum_probs=55.1

Q ss_pred             ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      --+||..|..|..+|..+++.|+-..+|....+++.+.++++++.||.+|||....+-.
T Consensus        28 ~~~Ls~~q~~vL~~l~~~~~~~~~~~~ia~~l~~~~~~vs~~v~~L~~~glV~r~~~~~   86 (125)
T d1p4xa2          28 HLTLSFVEFTILAIITSQNKNIVLLKDLIETIHHKYPQTVRALNNLKKQGYLIKERSTE   86 (125)
T ss_dssp             HCSSCHHHHHHHHHHHTTTTCCEEHHHHHHHSSSCHHHHHHHHHHHHHHTSSEEEECSS
T ss_pred             HcCCCHHHHHHHHHHHHccCCCccHHHHHHHHCCCcchHHHHHHHHHhccCEeeeecCC
Confidence            34899999999999999999999999999999999999999999999999998887765

>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=97.62  E-value=9.1e-05  Score=48.90  Aligned_cols=76  Identities=16%  Similarity=0.163  Sum_probs=58.5

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCccc--ccCccccccchhhhh
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYL--TEGTVNAMVLPSRKK  103 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wY--tdg~~D~~fI~~l~~  103 (117)
                      -+|++.|..||..+...|  ++-..+|-..+|++.+.++++|+.||.+|||....+=.++..|  .--..+ ++++.+++
T Consensus        16 lGlt~~e~~v~~~L~~~g--~~t~~eia~~~~i~~~~v~~~l~~L~~~GlV~r~~~~~~~r~~~~~a~~~~-e~l~~~~~   92 (109)
T d1sfxa_          16 LSFKPSDVRIYSLLLERG--GMRVSEIARELDLSARFVRDRLKVLLKRGFVRREIVEKGWVGYIYSAEKPE-KVLKEFKS   92 (109)
T ss_dssp             TCCCHHHHHHHHHHHHHC--CBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEEESSSEEEEEEECCHH-HHHHHHHH
T ss_pred             cCCCHHHHHHHHHHHhcC--CCCHHHHHHHhCCCcchHHHHHHHHHhCCCEEEEeccCCCccccccCCCHH-HHHHHHHH
Confidence            479999999999998765  6778999999999999999999999999999887665555433  222222 44555554


Q ss_pred             h
Q psy7778         104 R  104 (117)
Q Consensus       104 ~  104 (117)
                      +
T Consensus        93 ~   93 (109)
T d1sfxa_          93 S   93 (109)
T ss_dssp             H
T ss_pred             H
Confidence            4

>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=97.57  E-value=4.2e-05  Score=51.73  Aligned_cols=60  Identities=15%  Similarity=0.093  Sum_probs=55.3

Q ss_pred             cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      +--+||..|..|...|...++.++-.++|....++..+.++++++.||.+|||..+.|-.
T Consensus        28 ~~~~Lt~~q~~iL~~l~~~~~~~~t~~eia~~~~~~~~~vs~~l~~L~~~g~v~r~~~~~   87 (125)
T d1p4xa1          28 PEVDMTIKEFILLTYLFHQQENTLPFKKIVSDLCYKQSDLVQHIKVLVKHSYISKVRSKI   87 (125)
T ss_dssp             TTCSSCHHHHHHHHHHHSCSCSEEEHHHHHHHSSSCGGGTHHHHHHHHHTTSCEEEECSS
T ss_pred             HHcCCCHHHHHHHHHHHHhccCCcCHHHHHHHhCCCcchHHHHHHHHHHCCCceeecccC
Confidence            345799999999999988888889999999999999999999999999999999998865

>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=97.54  E-value=9.4e-05  Score=49.24  Aligned_cols=58  Identities=22%  Similarity=0.206  Sum_probs=54.4

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      -+||..|..|...|....+.++-..+|...+++..+.++++++.||.+|||....+-.
T Consensus        29 ~~Ls~~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~tvs~~i~~Le~~gli~r~~~~~   86 (115)
T d2frha1          29 FSISFEEFAVLTYISENKEKEYYLKDIINHLNYKQPQVVKAVKILSQEDYFDKKRNEH   86 (115)
T ss_dssp             TCCCHHHHHHHHHHHHTCCSEEEHHHHHHHSSSHHHHHHHHHHHHHHTTSSCCBCCSS
T ss_pred             cCCCHHHHHHHHHHHcCCCCCCCHHHHHHHHCCCHhHHHHHHHHHHhhhhheeeeccc
Confidence            3799999999999999988889999999999999999999999999999999988876

>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=97.52  E-value=0.00016  Score=47.30  Aligned_cols=59  Identities=15%  Similarity=0.071  Sum_probs=49.9

Q ss_pred             cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      +.-+|++.+..|+..+-.+++ ++-..+|...++++.+.++++|+.||.+|||....+-.
T Consensus        15 ~~~gLs~~~~~iL~~L~~~~~-~~t~~eLa~~~~i~~~tvs~~l~~L~~~GlV~r~~~~~   73 (109)
T d2d1ha1          15 CCYKITDTDVAVLLKMVEIEK-PITSEELADIFKLSKTTVENSLKKLIELGLVVRTKTEG   73 (109)
T ss_dssp             HHHTCCHHHHHHHHHHHHHCS-CEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEC--
T ss_pred             HhcCcCHHHHHHHHHHHHcCC-CCCHHHHHHHHCccHhHHHHHHHHHHHCCCEEEeecCC
Confidence            445899999999988865533 68999999999999999999999999999999877654

>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=97.41  E-value=0.00022  Score=47.86  Aligned_cols=55  Identities=11%  Similarity=0.090  Sum_probs=50.4

Q ss_pred             CCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      +|+..+..|...|...|  |+-..+|..+++++.+.++++++.||.+|||...++-+
T Consensus        27 glt~~q~~iL~~i~~~~--~~t~~~la~~l~i~~~tvs~~l~~L~~~gli~r~~~~~   81 (139)
T d2a61a1          27 GITPAQFDILQKIYFEG--PKRPGELSVLLGVAKSTVTGLVKRLEADGYLTRTPDPA   81 (139)
T ss_dssp             TCCHHHHHHHHHHHHHC--CBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEETT
T ss_pred             CCCHHHHHHHHHHHHcC--CCCHHHHHHHhCCCcccchHHHHHHHhcCeeeeeeccC
Confidence            79999999999998776  77889999999999999999999999999999887754

>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=97.33  E-value=0.00024  Score=47.70  Aligned_cols=56  Identities=14%  Similarity=0.178  Sum_probs=51.7

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      -+||+.+..|...|...  .|+-..+|-..+++..+.++++++.||.+|||...++-.
T Consensus        29 ~gLt~~q~~vL~~l~~~--~~~t~~~La~~~~i~~~~vsr~i~~L~~~glv~r~~~~~   84 (137)
T d1z91a1          29 LNITYPQYLALLLLWEH--ETLTVKKMGEQLYLDSGTLTPMLKRMEQQGLITRKRSEE   84 (137)
T ss_dssp             TCCCHHHHHHHHHHHHH--SEEEHHHHHHTTTCCHHHHHHHHHHHHHHTSEECCBCSS
T ss_pred             cCcCHHHHHHHHHHHcC--CCCCHHHHHHHHCcCHHHHHHHHHHHhhccceEEeecCC
Confidence            48999999999999774  589999999999999999999999999999999998875

>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=97.31  E-value=0.0003  Score=46.86  Aligned_cols=57  Identities=11%  Similarity=0.162  Sum_probs=50.8

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      -+||..|..|...|...++ |+-..+|...+++..+.++++++.||.+|||....+-.
T Consensus        24 ~glt~~q~~iL~~l~~~~~-~~t~~~la~~~~~~~~~vs~~v~~L~~~gli~r~~~~~   80 (137)
T d2fbha1          24 LGLSQARWLVLLHLARHRD-SPTQRELAQSVGVEGPTLARLLDGLESQGLVRRLAVAE   80 (137)
T ss_dssp             GCCTTTHHHHHHHHHHCSS-CCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECCBT
T ss_pred             cCCCHHHHHHHHHHHHcCC-CCcHHHHHHHHCCCHHHHHHHHHHHHHcCCccccCCCC
Confidence            4799999998888876554 89899999999999999999999999999999888754

>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=97.30  E-value=0.00036  Score=46.61  Aligned_cols=56  Identities=14%  Similarity=0.264  Sum_probs=51.1

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      -+||..|..|+..|...|  |+-..+|...++++.+.++++++.||.+|||....+-+
T Consensus        26 ~glt~~q~~vL~~l~~~~--~~t~~~la~~~~i~~~~vs~~i~~L~~~gli~r~~~~~   81 (136)
T d2fbia1          26 HGLTEQQWRVIRILRQQG--EMESYQLANQACILRPSMTGVLARLERDGIVRRWKAPK   81 (136)
T ss_dssp             HTCCHHHHHHHHHHHHHC--SEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEEETT
T ss_pred             cCCCHHHHHHHHHHHHcC--CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeecCc
Confidence            379999999999998765  68899999999999999999999999999999887765

>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=97.26  E-value=0.00051  Score=46.33  Aligned_cols=59  Identities=14%  Similarity=0.284  Sum_probs=52.5

Q ss_pred             ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCC
Q psy7778          25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANI   85 (117)
Q Consensus        25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg   85 (117)
                      --+||..|..|...|.  .+.|+-..+|...+++..+.++++++.||.+|||...++-..+
T Consensus        31 ~~~lt~~q~~vL~~l~--~~~~~t~~~la~~l~~~~~~vsr~l~~L~~~G~v~r~~~~~D~   89 (141)
T d1lnwa_          31 RLDLTPPDVHVLKLID--EQRGLNLQDLGRQMCRDKALITRKIRELEGRNLVRRERNPSDQ   89 (141)
T ss_dssp             TCCCCHHHHHHHHHHH--SSTTCBHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEECSSSS
T ss_pred             cCCCCHHHHHHHHHHH--HCCCCCHHHHHHHHCccHhHHHHHHHHHHHhhceeeeccCCCC
Confidence            3479999999999995  4678999999999999999999999999999999999887633

>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=97.24  E-value=0.00025  Score=47.55  Aligned_cols=56  Identities=16%  Similarity=0.210  Sum_probs=51.2

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      -+||..|..|...|...  .|+-..+|...++++.+.++++++.||.+|||...++-.
T Consensus        30 ~glt~~q~~vL~~i~~~--~~~t~~~la~~l~~~~~~~s~~l~~L~~~Gli~r~~~~~   85 (136)
T d2bv6a1          30 YNLTYPQFLVLTILWDE--SPVNVKKVVTELALDTGTVSPLLKRMEQVDLIKRERSEV   85 (136)
T ss_dssp             HTCCHHHHHHHHHHHHS--SEEEHHHHHHHTTCCTTTHHHHHHHHHHTTSEEEEECSS
T ss_pred             cCCCHHHHHHHHHHHcC--CCCCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEEeecCC
Confidence            38999999999999885  489999999999999999999999999999999887765

>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=97.24  E-value=0.0004  Score=46.61  Aligned_cols=56  Identities=14%  Similarity=0.290  Sum_probs=51.1

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      .+||+.|..|+..|...|  |+-..+|...++++.+.++++++.||.+|||...++-+
T Consensus        31 ~glt~~q~~iL~~l~~~~--~~t~~~la~~~~i~~~~vs~~l~~L~~~glv~r~~~~~   86 (143)
T d1s3ja_          31 QGVTPAQLFVLASLKKHG--SLKVSEIAERMEVKPSAVTLMADRLEQKNLIARTHNTK   86 (143)
T ss_dssp             TTCCHHHHHHHHHHHHHS--EEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEECSS
T ss_pred             cCCCHHHHHHHHHHHHCC--CCCHHHHHHHHCcCHHHHHHHHHHHHHhhhheeeeecC
Confidence            479999999999998765  89999999999999999999999999999998887754

>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=97.23  E-value=0.00059  Score=45.69  Aligned_cols=60  Identities=18%  Similarity=0.201  Sum_probs=53.6

Q ss_pred             ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCC
Q psy7778          25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANI   85 (117)
Q Consensus        25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg   85 (117)
                      --||+.-+-.||.++-.++ +++-..+|-.++|++.+.+++.|+.|+.+|||..+.+-...
T Consensus        21 ~~Gl~~~~~~i~~~L~~~~-~plt~~ela~~l~vsk~~vs~~l~~L~~~GlV~r~~~~~dr   80 (151)
T d1ku9a_          21 IHGLNKSVGAVYAILYLSD-KPLTISDIMEELKISKGNVSMSLKKLEELGFVRKVWIKGER   80 (151)
T ss_dssp             HTTCCHHHHHHHHHHHHCS-SCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECCTTCS
T ss_pred             HcCCCHHHHHHHHHHHhCC-CCcCHHHHHHHhCCCcchHHHHHHHHHHCCCEEEEEcCCCC
Confidence            4589999999999999876 46999999999999999999999999999999988776533

>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=97.15  E-value=0.00048  Score=46.69  Aligned_cols=55  Identities=18%  Similarity=0.160  Sum_probs=50.1

Q ss_pred             CCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      +||..|..|...|.+  +.|+-..+|...+++..+.++++++.|+.+|||....+=+
T Consensus        26 ~lt~~q~~iL~~i~~--~~~~t~~~la~~l~i~~~tvs~~l~~L~~~glI~r~~~~~   80 (144)
T d1lj9a_          26 SLTRGQYLYLVRVCE--NPGIIQEKIAELIKVDRTTAARAIKRLEEQGFIYRQEDAS   80 (144)
T ss_dssp             TCTTTHHHHHHHHHH--STTEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECSS
T ss_pred             CCCHHHHHHHHHHHh--CCCCCHHHHHHHHCccHhhHHHHHHHHHhhhcccccCCCC
Confidence            799999999999976  5689999999999999999999999999999998887754

>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=97.14  E-value=0.00045  Score=46.22  Aligned_cols=57  Identities=12%  Similarity=0.170  Sum_probs=51.3

Q ss_pred             ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      ..+||..|..|...|...|  |+-..+|..+++++.+.++++++.|+++|||...++=.
T Consensus        27 ~~~lt~~q~~iL~~l~~~~--~~t~~~La~~l~i~~~~vs~~v~~L~~~gli~r~~~~~   83 (140)
T d2etha1          27 ISDMKTTELYAFLYVALFG--PKKMKEIAEFLSTTKSNVTNVVDSLEKRGLVVREMDPV   83 (140)
T ss_dssp             HHHSBHHHHHHHHHHHHHC--CBCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEEEECTT
T ss_pred             hcCCCHHHHHHHHHHHHcC--CcCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeeeccc
Confidence            4579999999999997775  68889999999999999999999999999999988764

>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=97.12  E-value=0.00063  Score=45.36  Aligned_cols=57  Identities=16%  Similarity=0.107  Sum_probs=48.5

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      -+||..+..+...|.+. +.|+-..+|-...++..+.++++|+.||.+|||....+-.
T Consensus        27 ~glt~~~~~~L~~l~~~-~~~~t~~~la~~l~i~~~~vs~~l~~L~~~glI~~~~~~~   83 (140)
T d3deua1          27 LELTQTHWVTLHNIHQL-PPDQSQIQLAKAIGIEQPSLVRTLDQLEDKGLISRQTCAS   83 (140)
T ss_dssp             TTCCHHHHHHHHHHHHS-CSSEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEC----
T ss_pred             cCCCHHHHHHHHHHHHc-CCCccHHHHHHHHCCCHhHHHHHHHHHHhCCCEEecccCC
Confidence            47999999999899765 4589999999999999999999999999999999888754

>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=97.10  E-value=0.00077  Score=45.22  Aligned_cols=56  Identities=16%  Similarity=0.079  Sum_probs=50.7

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      -+||..|..|...|...|  |+-..+|...+++..+.++++++.||.+|||....+-.
T Consensus        30 ~~Lt~~q~~vL~~l~~~~--~~t~~ela~~~~i~~~~vs~~v~~L~~~glv~r~~~~~   85 (138)
T d1jgsa_          30 LDITAAQFKVLCSIRCAA--CITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPN   85 (138)
T ss_dssp             TTSCHHHHHHHHHHHHHS--SBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECTT
T ss_pred             cCCCHHHHHHHHhHHhCc--CCCHHHHHHHHCCCHhHHHHHHHHHhhCCCEEEeeccC
Confidence            479999999999998866  78999999999999999999999999999998776654

>d1xd7a_ a.4.5.55 (A:) Hypothetical protein ywnA {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcriptional regulator Rrf2
domain: Hypothetical protein ywnA
species: Bacillus subtilis [TaxId: 1423]

Probab=97.09  E-value=0.00081  Score=45.11  Aligned_cols=52  Identities=12%  Similarity=0.088  Sum_probs=46.6

Q ss_pred             HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCC
Q psy7778          34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANI   85 (117)
Q Consensus        34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg   85 (117)
                      .|.-+..-|.+..+-+++|-...|+|++.|.|+|+.|...|||+++++..||
T Consensus         6 Av~~L~~la~~~~~ss~~IA~~~~~~~~~v~kIl~~L~~aglV~s~rG~~GG   57 (127)
T d1xd7a_           6 AIHILSLISMDEKTSSEIIADSVNTNPVVVRRMISLLKKADILTSRAGVPGA   57 (127)
T ss_dssp             HHHHHHHHHTCSCCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEECCSSSSSC
T ss_pred             HHHHHHHHhcCCCCCHHHHHHHhCcCHHHHHHHHHHHHHhCcccccCCCCCc
Confidence            4555556677889999999999999999999999999999999999998877

>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=97.03  E-value=0.001  Score=41.51  Aligned_cols=61  Identities=20%  Similarity=0.257  Sum_probs=52.0

Q ss_pred             cCCCHHHHHHHHHHHHhcCC-c--ccHHHHHhhcCC-ChHHHHHHHHHHhhcCCeeeeccccCCc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNK-G--IWMRDIRFKSNL-MPTQLNKILKQLETKKIIKAVKSVANIE   86 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~-G--IWtkdIk~ktnL-~~~~l~K~LK~LE~k~LIK~VKsV~gg~   86 (117)
                      +.||+-|+.||+.|.+--.+ |  --.++|....|+ ..+.+...|+.||.+|+|....+..-|.
T Consensus         1 ~~LT~rQ~~vL~~I~~~~~~~G~~Ps~rei~~~~g~~S~stv~~~l~~Le~kG~I~r~~~~~R~i   65 (71)
T d1jhfa1           1 KALTARQQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKALARKGVIEIVSGASRGI   65 (71)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHHHHHHHHTTSEEECSSSSSCE
T ss_pred             CCCCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHCcCeecCCCCCcee
Confidence            46999999999999876552 4  789999999999 6889999999999999999987765443

>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=96.99  E-value=0.00027  Score=49.67  Aligned_cols=59  Identities=7%  Similarity=0.050  Sum_probs=51.2

Q ss_pred             ccCCCHHHHHHHHHHHHhc-CCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          25 LKDSDNEEKVVYKIIEEAG-NKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        25 ~~~L~~eE~lVY~~Ie~AG-n~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      -.+||..+..|...+..+| +.|+-..+|-..+++..+.++++|+.||.+|||....+-.
T Consensus        57 ~~gLt~~q~~vL~~L~~~~~~~~lt~~eLa~~l~i~~~tvsr~l~~Le~~GlV~r~~~~~  116 (172)
T d2fbka1          57 ASGLNAAGWDLLLTLYRSAPPEGLRPTELSALAAISGPSTSNRIVRLLEKGLIERREDER  116 (172)
T ss_dssp             TTTCCHHHHHHHHHHHHHCCSSCBCHHHHHHHCSCCSGGGSSHHHHHHHHTSEECCC---
T ss_pred             HcCCCHHHHHHHHHHHhhCCCCCcCHHHHHHHHCcCHhHHHHHHHHHHhCCCeeeecccc
Confidence            3589999998888888776 5789999999999999999999999999999999988754

>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=96.93  E-value=0.0013  Score=40.28  Aligned_cols=48  Identities=29%  Similarity=0.454  Sum_probs=43.4

Q ss_pred             HHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778          32 EKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        32 E~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      ...|+.+|...|  ++-..+|-..+||..++++++++.|+..|+|.+.-.
T Consensus         8 ~~~Il~~l~~~g--~~sr~eLa~~~glS~~Tv~~~l~~L~~~Glv~e~~~   55 (71)
T d1z05a1           8 AGRVYKLIDQKG--PISRIDLSKESELAPASITKITRELIDAHLIHETTV   55 (71)
T ss_dssp             HHHHHHHHHHHC--SBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECH
T ss_pred             HHHHHHHHHHcC--CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence            458999999866  699999999999999999999999999999987644

>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=96.89  E-value=0.0012  Score=46.30  Aligned_cols=56  Identities=16%  Similarity=0.138  Sum_probs=49.7

Q ss_pred             cCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          26 KDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        26 ~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      -+|+..|..|..+|...+  |+-..+|-..++++.+.++++++.||.+|||....+-.
T Consensus        37 ~~Lt~~q~~vL~~l~~~~--~~t~~~la~~~~l~~~tvs~~i~rL~~~gli~r~~~~~   92 (162)
T d2fxaa1          37 YDLNINEHHILWIAYQLN--GASISEIAKFGVMHVSTAFNFSKKLEERGYLRFSKRLN   92 (162)
T ss_dssp             GTCCHHHHHHHHHHHHHT--SEEHHHHHHHTTCCHHHHHHHHHHHHHHTSEEEECC--
T ss_pred             cCCCHHHHHHHhhhccCC--CcCHHHHHHHHcCCchhhHHHHHHHHHCCCceeecccc
Confidence            379999999999998765  78999999999999999999999999999999877643

>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=96.82  E-value=0.00082  Score=45.24  Aligned_cols=57  Identities=16%  Similarity=0.218  Sum_probs=49.2

Q ss_pred             ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      ..+||..+..|+..|..++. ++-..+|-.+.++..+.++++++.||.+|||....+=
T Consensus        29 ~~glt~~q~~vL~~L~~~~g-~~t~~~La~~~~~~~~~vs~~i~~L~~~glv~r~~~~   85 (145)
T d2hr3a1          29 ADPVQFSQLVVLGAIDRLGG-DVTPSELAAAERMRSSNLAALLRELERGGLIVRHADP   85 (145)
T ss_dssp             CCHHHHHHHHHHHHHHHTTS-CBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEC--
T ss_pred             hcCCCHHHHHHHHHHHHcCC-CCCHHHHHHHHCCCHHHHHHHHHHHHHcCCeEeeeCc
Confidence            45788899999999987643 6999999999999999999999999999999877764

>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=96.72  E-value=0.0025  Score=40.60  Aligned_cols=53  Identities=17%  Similarity=0.216  Sum_probs=46.0

Q ss_pred             CHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          29 DNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        29 ~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      ++-+..|+.++...|.  +-..+|...+++.++.++++|+.||.+|||..-++-.
T Consensus        15 ~p~r~~IL~~L~~~~~--~~~~eLa~~l~is~~~vs~~l~~L~~~glV~~~~~~~   67 (100)
T d1ub9a_          15 NPVRLGIMIFLLPRRK--APFSQIQKVLDLTPGNLDSHIRVLERNGLVKTYKVIA   67 (100)
T ss_dssp             SHHHHHHHHHHHHHSE--EEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEEECS
T ss_pred             CHHHHHHHHHhccCCC--eeHHHHHHHHhhccccccHHHHHHhhhceeEEEEcCc
Confidence            4557889999977764  7789999999999999999999999999999877644

>d1ylfa1 a.4.5.55 (A:5-142) Hypothetical protein BC1842 {Bacillus cereus [TaxId: 1396]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcriptional regulator Rrf2
domain: Hypothetical protein BC1842
species: Bacillus cereus [TaxId: 1396]

Probab=96.56  E-value=0.003  Score=42.64  Aligned_cols=58  Identities=14%  Similarity=-0.021  Sum_probs=46.3

Q ss_pred             HHHHHHHHHHHhcC--CcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccc
Q psy7778          31 EEKVVYKIIEEAGN--KGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLT   89 (117)
Q Consensus        31 eE~lVY~~Ie~AGn--~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYt   89 (117)
                      -+..|+-++.-|.+  +-+-+++|-.++++|++.+.|+|+.|...|||++..+ +||-+..
T Consensus         6 ~~~Av~~L~~la~~~~~~vss~~IA~~~~i~~~~l~kil~~L~~aGlv~S~rG-~GG~~L~   65 (138)
T d1ylfa1           6 FSIAVHILSILKNNPSSLCTSDYMAESVNTNPVVIRKIMSYLKQAGFVYVNRG-PGGAGLL   65 (138)
T ss_dssp             HHHHHHHHHHHHHSCGGGCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEC----CCEEES
T ss_pred             HHHHHHHHHHHHhCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCeEeecC-CCCceec
Confidence            35567777777744  3488999999999999999999999999999999999 5886654

>d1okra_ a.4.5.39 (A:) Methicillin resistance regulatory protein MecI {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Penicillinase repressor
domain: Methicillin resistance regulatory protein MecI
species: Staphylococcus aureus [TaxId: 1280]

Probab=96.32  E-value=0.0057  Score=40.26  Aligned_cols=56  Identities=20%  Similarity=0.144  Sum_probs=48.6

Q ss_pred             cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhc----CCChHHHHHHHHHHhhcCCeeeecc
Q psy7778          24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKS----NLMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~kt----nL~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      |.-+||+-|..|..+|=+.|  ++-.++|....    ++..+++...|+.||.||+|+.-++
T Consensus         1 K~~~lt~~E~~VM~~lW~~~--~~t~~ei~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~r~~~   60 (120)
T d1okra_           1 KTYEISSAEWEVMNIIWMKK--YASANNIIEEIQMQKDWSPKTIRTLITRLYKKGFIDRKKD   60 (120)
T ss_dssp             CCCCCCHHHHHHHHHHHHHS--SEEHHHHHHHHHHHCCCCHHHHHHHHHHHHHHTSEEEEEE
T ss_pred             CCCCCCHHHHHHHHHHHcCC--CCCHHHHHHHHhcccCccHHhHHHHHHHHHHCCCeEEEec
Confidence            34579999999999999876  78889876664    7999999999999999999998765

>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=95.80  E-value=0.015  Score=34.85  Aligned_cols=53  Identities=9%  Similarity=0.173  Sum_probs=45.4

Q ss_pred             CCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          28 SDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        28 L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      |++-++.|.+.+..-+.  +-..+|-.++|++.+++.+.++.|++.|.|+.+.-+
T Consensus         3 lD~~D~~IL~~L~~~~r--~s~~eiA~~l~ls~~~v~~Ri~rL~~~GiI~~~~~~   55 (63)
T d2cg4a1           3 IDNLDRGILEALMGNAR--TAYAELAKQFGVSPETIHVRVEKMKQAGIITGARID   55 (63)
T ss_dssp             CCHHHHHHHHHHHHCTT--SCHHHHHHHHTSCHHHHHHHHHHHHHHTSEEEEEEE
T ss_pred             CCHHHHHHHHHHHHcCC--CCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEeEEEE
Confidence            66777888888887654  588999999999999999999999999999976543

>d1z6ra1 a.4.5.63 (A:12-81) Mlc protein 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: ROK associated domain
domain: Mlc protein N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=95.77  E-value=0.012  Score=35.91  Aligned_cols=47  Identities=17%  Similarity=0.389  Sum_probs=42.2

Q ss_pred             HHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778          32 EKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK   80 (117)
Q Consensus        32 E~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK   80 (117)
                      ...|+++|..  +..+-..+|-..+||..+++++++..|+..|+|.+.-
T Consensus         7 ~~~Il~~i~~--~g~~sr~eLa~~~gLS~~Tvs~iv~~L~~~glv~e~g   53 (70)
T d1z6ra1           7 AGAVYRLIDQ--LGPVSRIDLSRLAQLAPASITKIVHEMLEAHLVQELE   53 (70)
T ss_dssp             HHHHHHHHHS--SCSCCHHHHHHHTTCCHHHHHHHHHHHHHHTSEEEC-
T ss_pred             HHHHHHHHHH--cCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeeC
Confidence            5679999985  6689999999999999999999999999999998763

>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=95.75  E-value=0.012  Score=35.61  Aligned_cols=43  Identities=23%  Similarity=0.416  Sum_probs=38.8

Q ss_pred             HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778          34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKA   78 (117)
Q Consensus        34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~   78 (117)
                      .||.+.++.|  .+-+.||-...|+..+.++..+|.|+.+|||.-
T Consensus        11 ~I~~l~~~~~--~v~~~~iA~~L~vs~~SVs~mikrL~~~GlV~~   53 (61)
T d2ev0a1          11 QIYMLIEEKG--YARVSDIAEALAVHPSSVTKMVQKLDKDEYLIY   53 (61)
T ss_dssp             HHHHHHHHHS--SCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC
T ss_pred             HHHHHHhcCC--CccHHHHHHHhCCCchhHHHHHHHHHHCCCEEE
Confidence            7898887665  688999999999999999999999999999874

>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=95.71  E-value=0.022  Score=34.18  Aligned_cols=54  Identities=22%  Similarity=0.265  Sum_probs=46.5

Q ss_pred             CCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      .|++-++.|.+.+.+.+..  -.++|-.++|++.+++.+-++.|+..|+|+.+..+
T Consensus         2 klD~~D~~IL~~L~~n~r~--s~~~iA~~lgis~~tv~~Ri~~L~~~giI~~~~~~   55 (63)
T d2cfxa1           2 KLDQIDLNIIEELKKDSRL--SMRELGRKIKLSPPSVTERVRQLESFGIIKQYTLE   55 (63)
T ss_dssp             CCCHHHHHHHHHHHHCSCC--CHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEEE
T ss_pred             CCCHHHHHHHHHHHHcCCC--CHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeEEEE
Confidence            4788788888888876654  68999999999999999999999999999876543

>d2hoea1 a.4.5.63 (A:10-71) N-acetylglucosamine kinase {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: N-acetylglucosamine kinase
species: Thermotoga maritima [TaxId: 2336]

Probab=95.64  E-value=0.0081  Score=36.24  Aligned_cols=46  Identities=20%  Similarity=0.169  Sum_probs=40.4

Q ss_pred             HHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc
Q psy7778          35 VYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA   83 (117)
Q Consensus        35 VY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~   83 (117)
                      |+.+|.. |  .|-..+|-..+||+.++++++++.|+..|+|.+.....
T Consensus         4 Il~~i~~-~--pisr~eLa~~~gls~~TVs~~v~~L~~~GlV~e~~~~~   49 (62)
T d2hoea1           4 ILKRIMK-S--PVSRVELAEELGLTKTTVGEIAKIFLEKGIVVEEKDSP   49 (62)
T ss_dssp             SHHHHHH-S--CBCHHHHHHHHTCCHHHHHHHHHHHHHHTSEEEEECCC
T ss_pred             HHHHHHH-C--CcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEECCCCC
Confidence            5677864 3  49999999999999999999999999999999987654

>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=95.60  E-value=0.017  Score=34.18  Aligned_cols=53  Identities=21%  Similarity=0.389  Sum_probs=44.3

Q ss_pred             CCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          28 SDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        28 L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      |++-++.+...+..-+  -+-..+|-.++|++.+++...++.|+..|.|+.+.-+
T Consensus         1 lD~~D~~Il~~L~~n~--r~s~~eiA~~l~ls~~~v~~Ri~~L~~~giI~~~~~~   53 (60)
T d2cyya1           1 LDEIDKKIIKILQNDG--KAPLREISKITGLAESTIHERIRKLRESGVIKKFTAI   53 (60)
T ss_dssp             CCHHHHHHHHHHHHCT--TCCHHHHHHHHCSCHHHHHHHHHHHHHHTSSCCCCCC
T ss_pred             CCHHHHHHHHHHHHcC--CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEeEEEE
Confidence            5666777777887754  4578999999999999999999999999999976543

>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=95.59  E-value=0.013  Score=35.84  Aligned_cols=43  Identities=12%  Similarity=0.217  Sum_probs=37.8

Q ss_pred             HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778          34 VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKA   78 (117)
Q Consensus        34 lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~   78 (117)
                      .||.+.++.|  .+=+.||-...|..++.+++.+|.|+.+|||.-
T Consensus        13 ~I~~L~~~~~--~v~~~~iA~~L~vs~~SVt~mvkrL~~~Glv~~   55 (63)
T d2isya1          13 TIYDLEEEGV--TPLRARIAERLDQSGPTVSQTVSRMERDGLLRV   55 (63)
T ss_dssp             HHHHHHHTTC--CCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHhcCC--CCcHHHHHHHhCCCchhHHHHHHHHHHCCCEEE
Confidence            7888766644  488899999999999999999999999999974

>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=95.44  E-value=0.0062  Score=38.65  Aligned_cols=36  Identities=11%  Similarity=0.083  Sum_probs=33.7

Q ss_pred             cCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeee
Q psy7778          43 GNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKA   78 (117)
Q Consensus        43 Gn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~   78 (117)
                      .+.+|-..+|-.++++.++.++++|+.||.+|||..
T Consensus        18 ~~~~lt~~eLa~~l~i~~~~vs~~l~~Le~~GlV~r   53 (85)
T d3ctaa1          18 NRAYLTSSKLADMLGISQQSASRIIIDLEKNGYITR   53 (85)
T ss_dssp             SEEECCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeee
Confidence            345899999999999999999999999999999997

>d1r7ja_ a.4.5.49 (A:) Sso10a (SSO10449) {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Archaeal DNA-binding protein
domain: Sso10a (SSO10449)
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=95.04  E-value=0.033  Score=36.20  Aligned_cols=47  Identities=21%  Similarity=0.281  Sum_probs=40.7

Q ss_pred             HHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778          33 KVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK   80 (117)
Q Consensus        33 ~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK   80 (117)
                      .+|+++.+.+ ..|+=...|-.++||+...+.+.|..|+.+|||+...
T Consensus         6 eIi~DIL~~~-~~g~~kT~i~~~aNLs~~~~~kyl~~L~~~GLI~~~~   52 (90)
T d1r7ja_           6 EIIQAILEAC-KSGSPKTRIMYGANLSYALTGRYIKMLMDLEIIRQEG   52 (90)
T ss_dssp             HHHHHHHHHH-TTCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             HHHHHHHHHH-hCCCCccHHHHHcCCCHHHHHHHHHHHHHCCCeeecC
Confidence            3778888877 4677788999999999999999999999999998644

>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=94.83  E-value=0.033  Score=33.04  Aligned_cols=53  Identities=26%  Similarity=0.342  Sum_probs=43.3

Q ss_pred             CCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          28 SDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        28 L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      |++-++.|..++.+-+  =+-..+|..++|++.+++...++.|+..|+|+....+
T Consensus         1 lD~~D~kIl~~L~~n~--r~s~~~lA~~~gls~~~v~~Ri~~L~~~giI~~~~~~   53 (60)
T d1i1ga1           1 IDERDKIILEILEKDA--RTPFTEIAKKLGISETAVRKRVKALEEKGIIEGYTIK   53 (60)
T ss_dssp             CCSHHHHHHHHHHHCT--TCCHHHHHHHHTSCHHHHHHHHHHHHHHTSSCCCCCC
T ss_pred             CCHHHHHHHHHHHHcC--CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEeEEEE
Confidence            4566677777777644  4588999999999999999999999999999865443

>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=94.82  E-value=0.034  Score=34.10  Aligned_cols=44  Identities=18%  Similarity=0.183  Sum_probs=37.8

Q ss_pred             HHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeee
Q psy7778          35 VYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAV   79 (117)
Q Consensus        35 VY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V   79 (117)
                      |.++|..+ +.++-..+|-.++++|.+++.|+|++|+..|++..-
T Consensus        10 IL~~~a~~-~~~~s~~eia~~~~~~~st~~rll~tL~~~g~l~~~   53 (75)
T d1mkma1          10 ILDFIVKN-PGDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRK   53 (75)
T ss_dssp             HHHHHHHC-SSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             HHHHHHhC-CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEC
Confidence            44555544 468999999999999999999999999999999875

>d1stza1 a.4.5.51 (A:14-100) Heat-inducible transcription repressor HrcA, 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: Heat-inducible transcription repressor HrcA, N-terminal domain
domain: Heat-inducible transcription repressor HrcA, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=94.66  E-value=0.072  Score=34.23  Aligned_cols=59  Identities=15%  Similarity=0.115  Sum_probs=45.4

Q ss_pred             CCHHHHHHHHHHHH---hcCCcccHHHHHhhcCCC--hHHHHHHHHHHhhcCCeeeeccccCCcc
Q psy7778          28 SDNEEKVVYKIIEE---AGNKGIWMRDIRFKSNLM--PTQLNKILKQLETKKIIKAVKSVANIEY   87 (117)
Q Consensus        28 L~~eE~lVY~~Ie~---AGn~GIWtkdIk~ktnL~--~~~l~K~LK~LE~k~LIK~VKsV~gg~w   87 (117)
                      ||+-++.|+..|-+   .-..-+-+++|....|+.  .++|...|+.||.+|||+. ....+|.=
T Consensus         2 Lt~Rq~~IL~~Ive~y~~~g~Pv~s~~i~~~~~l~~S~aTIRn~m~~LE~~G~l~~-~h~s~Gri   65 (87)
T d1stza1           2 LNDRQRKVLYCIVREYIENKKPVSSQRVLEVSNIEFSSATIRNDMKKLEYLGYIYQ-PHTSAGRI   65 (87)
T ss_dssp             CCHHHHHHHHHHHHHHHHHCSCBCHHHHHHHSCCCSCHHHHHHHHHHHHHTTSEEC-CSSCSCBE
T ss_pred             cCHHHHHHHHHHHHHHHHcCCccCHHHHHHHhCCCCCHHHHHHHHHHHHHCCcccC-CCCCCCCc
Confidence            77766666665433   235678999999998874  8999999999999999998 55555543

>d1sfua_ a.4.5.19 (A:) 34L {Yaba-like disease virus, YLDV [TaxId: 132475]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Z-DNA binding domain
domain: 34L
species: Yaba-like disease virus, YLDV [TaxId: 132475]

Probab=94.57  E-value=0.066  Score=33.84  Aligned_cols=56  Identities=16%  Similarity=0.186  Sum_probs=48.8

Q ss_pred             HHHHHHHHhc-CCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCccccc
Q psy7778          34 VVYKIIEEAG-NKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTE   90 (117)
Q Consensus        34 lVY~~Ie~AG-n~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtd   90 (117)
                      +|-+.+..-| ++++-.++|-++.|++...||++|=+|+.+|.+..+.+ +...||.+
T Consensus        11 lvk~~l~~L~~~~~~tA~~LAk~Lg~~Kk~VNr~LY~L~~~G~v~~~~~-tPP~W~~~   67 (70)
T d1sfua_          11 LVKKEVLSLNTNDYTTAISLSNRLKINKKKINQQLYKLQKEDTVKMVPS-NPPKWFKN   67 (70)
T ss_dssp             HHHHHHHTSCTTCEECHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEECC-SSCEEEEC
T ss_pred             HHHHHHHhcCCCCCchHHHHHHHhCCCHHHHHHHHHHHHHCCCeecCCC-cCCccccc
Confidence            5556666655 58999999999999999999999999999999999888 67889975

>d2g9wa1 a.4.5.39 (A:3-124) Hypothetical protein Rv1846c {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Penicillinase repressor
domain: Hypothetical protein Rv1846c
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=94.43  E-value=0.056  Score=35.74  Aligned_cols=58  Identities=17%  Similarity=0.216  Sum_probs=48.2

Q ss_pred             cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhc----CCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKS----NLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~kt----nL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      |+..|++-|..|..+|=+.| .++-.++|....    +++.+++...|+.|+.||+|+..+.-
T Consensus         1 k~~~L~~~E~~IM~~lW~~g-~~~t~~eI~~~l~~~~~~~~sTV~T~L~rL~~Kg~l~~~~~g   62 (122)
T d2g9wa1           1 KLTRLGDLERAVMDHLWSRT-EPQTVRQVHEALSARRDLAYTTVMAVLQRLAKKNLVLQIRDD   62 (122)
T ss_dssp             CGGGCCHHHHHHHHHHHTCS-SCEEHHHHHHHHTTTCCCCHHHHHHHHHHHHHTTSEEEEC--
T ss_pred             CCCCCCHHHHHHHHHHHcCC-CCccHHHHHHHHhccCCCcHHHHHHHHHHHHHCCCEEEeecC
Confidence            45679999999999999775 557788888775    57899999999999999999987753

>d1lvaa3 a.4.5.35 (A:511-574) C-terminal fragment of elongation factor SelB {Moorella thermoacetica [TaxId: 1525]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: C-terminal fragment of elongation factor SelB
domain: C-terminal fragment of elongation factor SelB
species: Moorella thermoacetica [TaxId: 1525]

Probab=94.01  E-value=0.14  Score=30.71  Aligned_cols=53  Identities=15%  Similarity=0.201  Sum_probs=43.3

Q ss_pred             CCHHHHHHHH----HHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778          28 SDNEEKVVYK----IIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK   80 (117)
Q Consensus        28 L~~eE~lVY~----~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK   80 (117)
                      ||++|..+.+    +..+||-.=-|.+||-..+|++...+...|+.|...|.+=.|+
T Consensus         1 ls~~q~~l~~~I~~~~~~~g~~PP~vrdl~~~l~~~e~~~~~lL~~l~~~G~lvkI~   57 (64)
T d1lvaa3           1 FSETQKKLLKDLEDKYRVSRWQPPSFKEVAGSFNLDPSELEELLHYLVREGVLVKIN   57 (64)
T ss_dssp             CCHHHHHHHHHHHHHHHHHTTSCCBHHHHHHHTTCCHHHHHHHHHHHHHTTSEEESS
T ss_pred             CCHHHHHHHHHHHHHHHHcCCCCCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEec
Confidence            4566655544    5567788999999999999999999999999999988776654

>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=93.13  E-value=0.17  Score=30.02  Aligned_cols=31  Identities=26%  Similarity=0.310  Sum_probs=29.4

Q ss_pred             ccHHHHHhhcCCChHHHHHHHHHHhhcCCee
Q psy7778          47 IWMRDIRFKSNLMPTQLNKILKQLETKKIIK   77 (117)
Q Consensus        47 IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK   77 (117)
                      +-..+|-.-.|+...+++|+|+.|+..|+|+
T Consensus        30 lt~~~lA~~~G~sRetvsr~L~~l~~~glI~   60 (69)
T d1i5za1          30 ITRQEIGQIVGCSRETVGRILKMLEDQNLIS   60 (69)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            7788999999999999999999999999996

>d1xmka1 a.4.5.19 (A:294-366) Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Z-DNA binding domain
domain: Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.03  E-value=0.062  Score=34.11  Aligned_cols=58  Identities=7%  Similarity=0.058  Sum_probs=47.7

Q ss_pred             CCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChH-HHHHHHHHHhhcCCeeeeccccCCccc
Q psy7778          28 SDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPT-QLNKILKQLETKKIIKAVKSVANIEYL   88 (117)
Q Consensus        28 L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~-~l~K~LK~LE~k~LIK~VKsV~gg~wY   88 (117)
                      |++.|..||+.+++.|.  .-..+|.+..||+.+ .||++|=+|+.+|.+-.. +-+...|+
T Consensus         3 ~~d~eekI~~~L~~~g~--~~Al~iak~lGl~kakeVN~~LY~L~k~g~v~k~-~~tPP~W~   61 (73)
T d1xmka1           3 MAEIKEKICDYLFNVSD--SSALNLAKNIGLTKARDINAVLIDMERQGDVYRQ-GTTPPIWH   61 (73)
T ss_dssp             HHHHHHHHHHHHHHTCC--EEHHHHHHHHCGGGHHHHHHHHHHHHHTTSEEEE-CSSSCEEE
T ss_pred             hHHHHHHHHHHHHHcCC--chHHHHHHHhCCCcHHHHhHHHHHHHHCCCeecC-CCCCCcee
Confidence            45678899999999995  558899999999995 699999999999998764 22444575

>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=92.73  E-value=0.14  Score=31.19  Aligned_cols=50  Identities=16%  Similarity=0.235  Sum_probs=40.5

Q ss_pred             CCHHHHHHHHHHHHhcC---Cc---ccHHHHHhhcCCChHHHHHHHHHHhhcCCee
Q psy7778          28 SDNEEKVVYKIIEEAGN---KG---IWMRDIRFKSNLMPTQLNKILKQLETKKIIK   77 (117)
Q Consensus        28 L~~eE~lVY~~Ie~AGn---~G---IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK   77 (117)
                      ++-++|++.-+...+..   .+   +-..+|-.-.|+....++|+|+.|+..|+|.
T Consensus         3 ~dv~~Rla~~Ll~~~~~~~~~~~i~lt~~elA~~lg~sr~tvsr~l~~l~~~g~I~   58 (73)
T d1zyba1           3 LDLKSKIIRFFLSHCEKPQGEKTFKVKMDDLARCLDDTRLNISKTLNELQDNGLIE   58 (73)
T ss_dssp             CSHHHHHHHHHHTTCSSSSSCEEEECCHHHHHHHHTSCHHHHHHHHHHHHHTTSCE
T ss_pred             CCHHHHHHHHHHHhhhhhCCCeEeecCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            45577877777665442   22   6789999999999999999999999999996

>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=92.39  E-value=0.19  Score=30.25  Aligned_cols=43  Identities=14%  Similarity=0.264  Sum_probs=34.6

Q ss_pred             HHHHHHHhcCC--c------ccHHHHHhhcCCChHHHHHHHHHHhhcCCee
Q psy7778          35 VYKIIEEAGNK--G------IWMRDIRFKSNLMPTQLNKILKQLETKKIIK   77 (117)
Q Consensus        35 VY~~Ie~AGn~--G------IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK   77 (117)
                      ++.+.+..|..  |      +-..||-.-.|+...+++|+|+.|+..|+|.
T Consensus        10 Ll~l~~~~g~~~~~~~i~~~lt~~eLA~~~G~sretvsr~L~~l~~~glI~   60 (81)
T d2gaua1          10 LLILKENFGFENDGATLSIYLSREELATLSNMTVSNAIRTLSTFVSERMLA   60 (81)
T ss_dssp             HHHHHHHHCBCTTSSBBSCCCCHHHHHHHTTSCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHhCCCCCCCEEeecCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            34455555543  3      4578999999999999999999999999997

>d1sd4a_ a.4.5.39 (A:) Penicillinase repressor BlaI {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Penicillinase repressor
domain: Penicillinase repressor BlaI
species: Staphylococcus aureus [TaxId: 1280]

Probab=92.22  E-value=0.2  Score=33.06  Aligned_cols=53  Identities=23%  Similarity=0.272  Sum_probs=45.5

Q ss_pred             CCCHHHHHHHHHHHHhcCCcccHHHHHhh----cCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778          27 DSDNEEKVVYKIIEEAGNKGIWMRDIRFK----SNLMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~k----tnL~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      .||+-|..|..+|=+.|  ++-.++|...    .+++.+++...|+.|+.||+|+.-+.
T Consensus         3 ~ls~~E~~VM~~lW~~~--~~t~~ei~~~l~~~~~~~~tTv~T~L~rL~~Kg~l~~~~~   59 (122)
T d1sd4a_           3 EISMAEWDVMNIIWDKK--SVSANEIVVEIQKYKEVSDKTIRTLITRLYKKEIIKRYKS   59 (122)
T ss_dssp             CCCHHHHHHHHHHHHSS--SEEHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             CCCHHHHHHHHHHHcCC--CCCHHHHHHHhhccCCCcHhHHHHHHHHHHhhhceeeecc
Confidence            58899999999999876  5888887766    57999999999999999999986553

>d1w5sa1 a.4.5.11 (A:300-409) CDC6-like protein APE0152, C-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Helicase DNA-binding domain
domain: CDC6-like protein APE0152, C-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=91.79  E-value=0.29  Score=32.58  Aligned_cols=59  Identities=25%  Similarity=0.243  Sum_probs=48.7

Q ss_pred             ccccCCCHHHHHHHHHHHHh---cCCcccHHHHHhhcC-----------CChHHHHHHHHHHhhcCCeeeecc
Q psy7778          23 EKLKDSDNEEKVVYKIIEEA---GNKGIWMRDIRFKSN-----------LMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        23 ~k~~~L~~eE~lVY~~Ie~A---Gn~GIWtkdIk~ktn-----------L~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      .++++||..|++|.-.|-.+   |.+-|-+.+|.....           +..+.+.+.|+.|+..|+|..-..
T Consensus         2 ~~l~~L~~H~~lvL~~I~~~~~~~~~~~~tGei~~~Y~ev~c~~~~~~P~~~t~~~~~l~~Le~lGiI~~r~~   74 (110)
T d1w5sa1           2 HELEALSIHELIILRLIAEATLGGMEWINAGLLRQRYEDASLTMYNVKPRGYTQYHIYLKHLTSLGLVDAKPS   74 (110)
T ss_dssp             CSSSSSCHHHHHHHHHHHHHHHTTCSSBCHHHHHHHHHHHHHHHSCCCCCCHHHHHHHHHHHHHTTSEEEECC
T ss_pred             chhhccCHhHHHHHHHHHHHHhcCCCCCchHHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHcCCeEEEec
Confidence            46889999999988877654   778888998887653           467899999999999999986654

>d1p6ra_ a.4.5.39 (A:) Penicillinase repressor BlaI {Bacillus licheniformis [TaxId: 1402]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Penicillinase repressor
domain: Penicillinase repressor BlaI
species: Bacillus licheniformis [TaxId: 1402]

Probab=91.57  E-value=0.34  Score=30.13  Aligned_cols=56  Identities=21%  Similarity=0.259  Sum_probs=46.3

Q ss_pred             cccCCCHHHHHHHHHHHHhcCCcccHHHHHhh----cCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778          24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFK----SNLMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~k----tnL~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      ++..||+-|..|..+|=+.|  .+-.++|...    .+.+.+++...|..|+.||++..-++
T Consensus         3 k~~~Ls~~E~~IM~~lW~~~--~~t~~ei~~~l~~~~~~~~tTv~T~L~rL~~KG~l~~~k~   62 (82)
T d1p6ra_           3 KIPQISDAELEVMKVIWKHS--SINTNEVIKELSKTSTWSPKTIQTMLLRLIKKGALNHHKE   62 (82)
T ss_dssp             CCCCCCHHHHHHHHHHHTSS--SEEHHHHHHHHHHHSCCCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             CCCCCCHHHHHHHHHHHhCC--CCCHHHHHHHhccccCCcHhHHHHHHHHHHHCCCeEEEec
Confidence            56679999999999998654  5788887544    57899999999999999999986544

>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=91.36  E-value=0.2  Score=30.26  Aligned_cols=31  Identities=13%  Similarity=0.287  Sum_probs=28.6

Q ss_pred             ccHHHHHhhcCCChHHHHHHHHHHhhcCCee
Q psy7778          47 IWMRDIRFKSNLMPTQLNKILKQLETKKIIK   77 (117)
Q Consensus        47 IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK   77 (117)
                      +-..+|-.-+|+...+++|+|+.|+..|+|+
T Consensus        31 lt~~elA~~~g~sretvsr~l~~l~~~glI~   61 (80)
T d3e5ua1          31 LSQKSIGEITGVHHVTVSRVLASLKRENILD   61 (80)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCcEE
Confidence            3468999999999999999999999999996

>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=91.20  E-value=0.14  Score=32.61  Aligned_cols=56  Identities=18%  Similarity=0.292  Sum_probs=44.9

Q ss_pred             cccccCCCHHHH-HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778          22 NEKLKDSDNEEK-VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK   80 (117)
Q Consensus        22 a~k~~~L~~eE~-lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK   80 (117)
                      |+-++.|+++-| .|+.++.+ |.  .-..+|-..+|++++.+++.|+.|+.-|||++-+
T Consensus         9 a~~fkaL~d~~Rl~Il~~L~~-~~--~~v~el~~~l~~s~~~vS~HL~~L~~~glv~~~r   65 (94)
T d1r1ua_           9 TEIFKALGDYNRIRIMELLSV-SE--ASVGHISHQLNLSQSNVSHQLKLLKSVHLVKAKR   65 (94)
T ss_dssp             HHHHHHTCSHHHHHHHHHHHH-CC--BCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHhCCHHHHHHHHHHHc-CC--ccHHHHHHHHCCCHHHHHHHHHHHHHCCceEEEE
Confidence            345677887666 56667754 44  4568999999999999999999999999998764

>d2gxba1 a.4.5.19 (A:140-198) Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Z-DNA binding domain
domain: Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.13  E-value=0.4  Score=29.19  Aligned_cols=46  Identities=26%  Similarity=0.361  Sum_probs=40.5

Q ss_pred             HHHHHHHHHHhc-CCcccHHHHHhhcCCChHHHHHHHHHHhhcCCee
Q psy7778          32 EKVVYKIIEEAG-NKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIK   77 (117)
Q Consensus        32 E~lVY~~Ie~AG-n~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK   77 (117)
                      |..|....++-| .+-+--+||-.+.++|...||++|=+|+++|...
T Consensus         1 Eq~vl~~l~~lg~~~~~tA~~LA~kl~vpKk~iNr~LYsL~~kgkl~   47 (59)
T d2gxba1           1 EQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQ   47 (59)
T ss_dssp             HHHHHHHHHHHCTTCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             ChHHHHHHHhcCCccchhHHHHHHHhCCcHHHHHHHHHHHHHccchh
Confidence            456778888877 6889999999999999999999999999998764

>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=90.67  E-value=0.17  Score=30.84  Aligned_cols=35  Identities=20%  Similarity=0.226  Sum_probs=32.1

Q ss_pred             cHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          48 WMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        48 WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      -.++|..+.+...+++.++|+.|+..|+|......
T Consensus        24 se~~La~~~~vSr~tvr~Al~~L~~~Gli~~~~g~   58 (78)
T d3bwga1          24 VLETLMAQFEVSKSTITKSLELLEQKGAIFQVRGS   58 (78)
T ss_dssp             CHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEETTT
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEEcCc
Confidence            56899999999999999999999999999988664

>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=90.58  E-value=0.31  Score=29.42  Aligned_cols=49  Identities=14%  Similarity=0.138  Sum_probs=37.0

Q ss_pred             HHHHHHHHHHHhc------CCc------ccHHHHHhhcCCChHHHHHHHHHHhhcCCeeee
Q psy7778          31 EEKVVYKIIEEAG------NKG------IWMRDIRFKSNLMPTQLNKILKQLETKKIIKAV   79 (117)
Q Consensus        31 eE~lVY~~Ie~AG------n~G------IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~V   79 (117)
                      ++|+..-+++-+.      +.|      +-..+|-.-+|++..+++|+|+.|+..|+|+--
T Consensus         3 ~~Rla~~Ll~l~~~~g~~~~~~~~i~~~~t~~eiA~~lG~sretvsr~l~~l~~~g~I~~~   63 (80)
T d1ft9a1           3 KQRIAGFFIDHANTTGRQTQGGVIVSVDFTVEEIANLIGSSRQTTSTALNSLIKEGYISRQ   63 (80)
T ss_dssp             HHHHHHHHHHTCBCCCSCC--CCCCEECCCHHHHHHHHCSCHHHHHHHHHHHHHTTSSEEC
T ss_pred             HHHHHHHHHHHHHHhCCCCCCCeEEecCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEC
Confidence            4666665665433      333      346799999999999999999999999999743

>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=90.44  E-value=0.1  Score=34.05  Aligned_cols=63  Identities=13%  Similarity=0.179  Sum_probs=44.9

Q ss_pred             cccCCCHHHH-HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccc
Q psy7778          24 KLKDSDNEEK-VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLT   89 (117)
Q Consensus        24 k~~~L~~eE~-lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYt   89 (117)
                      -++.|+++-| .|+..+..  +.+.-..+|-..+|++++++++.|+.|+.-|||++=+. ..-.||+
T Consensus        24 ~~kaLadp~Rl~Il~~L~~--~~~~~v~ela~~l~~s~s~vS~HL~~L~~aGlv~~~r~-G~~~~Y~   87 (108)
T d1u2wa1          24 ILKAIADENRAKITYALCQ--DEELCVCDIANILGVTIANASHHLRTLYKQGVVNFRKE-GKLALYS   87 (108)
T ss_dssp             HHHHHHSHHHHHHHHHHHH--SSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC-----CCEEE
T ss_pred             HHHHhCCHHHHHHHHHHHh--CCCccHHHHHHHHccChhHHHHHHHHHHHCCeeEEEEE-CCEEEEE
Confidence            4566666655 55555533  34577889999999999999999999999999988663 2233454

>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=90.41  E-value=0.66  Score=27.28  Aligned_cols=49  Identities=8%  Similarity=0.035  Sum_probs=38.4

Q ss_pred             HHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCC-eeeecc
Q psy7778          31 EEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKI-IKAVKS   81 (117)
Q Consensus        31 eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~L-IK~VKs   81 (117)
                      -...|..++.  .+.-+-..+|-.+.|+..++|.+.|+.|+..|+ |.++.+
T Consensus         6 ~~~~iL~~L~--~~~~~s~~eLa~~l~vS~~ti~r~i~~L~~~G~~I~~~~g   55 (63)
T d1biaa1           6 VPLKLIALLA--NGEFHSGEQLGETLGMSRAAINKHIQTLRDWGVDVFTVPG   55 (63)
T ss_dssp             HHHHHHHHHT--TSSCBCHHHHHHHHTSCHHHHHHHHHHHHHTTCCCEEETT
T ss_pred             HHHHHHHHHH--HCCcCCHHHHHHHHCcCHHHHHHHHHHHHHCCCcEEEeCC
Confidence            3445666663  355688899999999999999999999999998 555443

>d1zara1 a.4.5.56 (A:2-90) Rio2 serine protein kinase N-terminal domain {Archaeoglobus fulgidus [TaxId: 2234]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Rio2 serine protein kinase N-terminal domain
domain: Rio2 serine protein kinase N-terminal domain
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=90.11  E-value=0.22  Score=32.35  Aligned_cols=82  Identities=11%  Similarity=0.027  Sum_probs=60.7

Q ss_pred             cccccCCCHHHHHHHHHHHHhcCCccc--HHHHHhhcCCChHHHHHHHHHHhhcCCeeeecccc-CCcccccCccccccc
Q psy7778          22 NEKLKDSDNEEKVVYKIIEEAGNKGIW--MRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVA-NIEYLTEGTVNAMVL   98 (117)
Q Consensus        22 a~k~~~L~~eE~lVY~~Ie~AGn~GIW--tkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~-gg~wYtdg~~D~~fI   98 (117)
                      |+-+..|+++|.-|...||..-..==|  ...|...++|+..-+.++|+.|...+||.. +++. .|-=.|-+.+|.--+
T Consensus         3 ae~~~~L~~~dfRvL~aiE~gmrnhE~VP~~lI~~~a~l~~~~~~~~L~~L~k~kLv~~-~~~~Y~GYrLT~~GYD~LAL   81 (89)
T d1zara1           3 AELYGKMGKHSWRIMDAIFKNLWDYEYVPLQLISSHARIGEEKARNILKYLSDLRVVQN-RQKDYEGSTFTFIGLSLYSL   81 (89)
T ss_dssp             HHHHHTCCHHHHHHHHHHHTTTTTCSSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE-ECSSSCEEEECHHHHHHHHH
T ss_pred             HHHHHHcCHHHHHHHHHHHhccccCccccHHHHHHHHCCCHHHHHHHHHHHHHcCCeec-cCCCcceEEeeccChHHHHH
Confidence            566889999999999999965443333  578999999999999999999999999966 4443 333344455666555


Q ss_pred             hhhhhh
Q psy7778          99 PSRKKR  104 (117)
Q Consensus        99 ~~l~~~  104 (117)
                      .++-+|
T Consensus        82 ~~L~kr   87 (89)
T d1zara1          82 HRLVRS   87 (89)
T ss_dssp             HHHHHT
T ss_pred             HHHHHc
Confidence            555443

>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=90.07  E-value=0.33  Score=30.89  Aligned_cols=55  Identities=9%  Similarity=0.195  Sum_probs=43.0

Q ss_pred             ccccCCCHHHH-HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeec
Q psy7778          23 EKLKDSDNEEK-VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVK   80 (117)
Q Consensus        23 ~k~~~L~~eE~-lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VK   80 (117)
                      .-++-|.++-| .|+..+.   +...-..+|-..+|++++++++.|+.|+.-|+|++-+
T Consensus        15 ~~~kaL~~p~Rl~Il~~L~---~~~~~v~ela~~l~is~stvS~HL~~L~~aglV~~~r   70 (98)
T d1r1ta_          15 EFFAVLADPNRLRLLSLLA---RSELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRK   70 (98)
T ss_dssp             HHHHHHCCHHHHHHHHHHT---TCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHhCCHHHHHHHHHHH---cCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEE
Confidence            34666666555 4455553   3457789999999999999999999999999998754

>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=89.45  E-value=0.39  Score=28.63  Aligned_cols=48  Identities=15%  Similarity=0.146  Sum_probs=38.6

Q ss_pred             HHHHHHHHhcCCc-------ccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778          34 VVYKIIEEAGNKG-------IWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        34 lVY~~Ie~AGn~G-------IWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      .||+.|++.=-.|       +-.++|-.+.|+..+.+.++++.|+..|+|....+
T Consensus         6 qi~~~l~~~I~~g~~~~G~~l~~~~La~~~~vSr~tvr~Al~~L~~~Gli~~~~~   60 (69)
T d2hs5a1           6 RVAGILRDAIIDGTFRPGARLSEPDICAALDVSRNTVREAFQILIEDRLVAHELN   60 (69)
T ss_dssp             HHHHHHHHHHHHTSSCTTCEECHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETT
T ss_pred             HHHHHHHHHHHcCCCCCcCccCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEEcC
Confidence            4666666543333       44689999999999999999999999999998765

>d1hw1a1 a.4.5.6 (A:5-78) Fatty acid responsive transcription factor FadR, 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: GntR-like transcriptional regulators
domain: Fatty acid responsive transcription factor FadR, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=89.41  E-value=0.24  Score=30.23  Aligned_cols=35  Identities=14%  Similarity=0.161  Sum_probs=32.0

Q ss_pred             cHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccc
Q psy7778          48 WMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSV   82 (117)
Q Consensus        48 WtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV   82 (117)
                      -.++|..+.++..+++.++++.|+..|+|......
T Consensus        29 s~~eLa~~~~vSr~tvr~Al~~L~~~G~i~~~~g~   63 (74)
T d1hw1a1          29 AERELSELIGVTRTTLREVLQRLARDGWLTIQHGK   63 (74)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETTE
T ss_pred             cHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEEeCc
Confidence            56899999999999999999999999999988654

>d2f2ea1 a.4.5.69 (A:5-146) Hypothetical protein PA1607 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: HxlR-like
domain: Hypothetical protein PA1607
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=88.89  E-value=0.19  Score=34.46  Aligned_cols=33  Identities=18%  Similarity=0.226  Sum_probs=29.7

Q ss_pred             HHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778          49 MRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        49 tkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      -.+|+...++++++|++.|+.||..|||..+.+
T Consensus        36 f~el~~~lgis~~vLs~rL~~L~~~gLv~r~~~   68 (142)
T d2f2ea1          36 FGEFQKSLGLAKNILAARLRNLVEHGVMVAVPA   68 (142)
T ss_dssp             HHHHHHHHCCCHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             HHHHHHHhhccHHHHHHHHHHHHHhcceeeecC
Confidence            578899999999999999999999999987643

>d1a04a1 a.4.6.2 (A:150-216) Nitrate/nitrite response regulator (NarL) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Nitrate/nitrite response regulator (NarL)
species: Escherichia coli [TaxId: 562]

Probab=88.35  E-value=0.45  Score=28.10  Aligned_cols=45  Identities=16%  Similarity=0.264  Sum_probs=39.8

Q ss_pred             ccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778          25 LKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK   73 (117)
Q Consensus        25 ~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k   73 (117)
                      +..||+-|..|..++-+    |.-.++|-.+.++...+|...++.+-.|
T Consensus         4 l~~LT~rE~~vl~ll~~----G~s~~eIA~~l~iS~~TV~~~~~~i~~K   48 (67)
T d1a04a1           4 VNQLTPRERDILKLIAQ----GLPNKMIARRLDITESTVKVHVKHMLKK   48 (67)
T ss_dssp             GGGSCHHHHHHHHHHHT----TCCHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             cccCCHHHHHHHHHHHh----CCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            55799999999999874    8999999999999999999999888654

>d1fnna1 a.4.5.11 (A:277-388) CDC6, C-terminal domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Helicase DNA-binding domain
domain: CDC6, C-terminal domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=88.29  E-value=0.51  Score=30.82  Aligned_cols=57  Identities=21%  Similarity=0.121  Sum_probs=44.9

Q ss_pred             cccCCCHHHHHHHHHH----HHhcCCcccHHHHHhhc----------CCChHHHHHHHHHHhhcCCeeeec
Q psy7778          24 KLKDSDNEEKVVYKII----EEAGNKGIWMRDIRFKS----------NLMPTQLNKILKQLETKKIIKAVK   80 (117)
Q Consensus        24 k~~~L~~eE~lVY~~I----e~AGn~GIWtkdIk~kt----------nL~~~~l~K~LK~LE~k~LIK~VK   80 (117)
                      .+++||.++++|...|    +..++.-|-+.++-...          .+.++.+...|+.|+..|+|.+-.
T Consensus         5 ~i~~Lp~h~klvL~ai~~~~~~~~~~~ittgevy~~Y~~lc~~~~~~pls~rr~~~~l~~Le~lGiI~~r~   75 (112)
T d1fnna1           5 VLIGLPLHEKLFLLAIVRSLKISHTPYITFGDAEESYKIVCEEYGERPRVHSQLWSYLNDLREKGIVETRQ   75 (112)
T ss_dssp             HHHHSCHHHHHHHHHHHHHHHHHCSSCEEHHHHHHHHHHHHHHTTCCCCCHHHHHHHHHHHHHTTSSEEEE
T ss_pred             HHhcCCHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHHHHcCcchhhHHHHHHHHHHHHhCCCeeeee
Confidence            4788999999887665    34566777888875443          467899999999999999998754

>d1v4ra1 a.4.5.6 (A:1-100) Transcriptional repressor TraR, N-terminal domain {Streptomyces sp. [TaxId: 1931]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: GntR-like transcriptional regulators
domain: Transcriptional repressor TraR, N-terminal domain
species: Streptomyces sp. [TaxId: 1931]

Probab=88.18  E-value=0.26  Score=31.52  Aligned_cols=56  Identities=13%  Similarity=0.160  Sum_probs=45.6

Q ss_pred             HHHHHHHHhcCCccc--------HHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccC
Q psy7778          34 VVYKIIEEAGNKGIW--------MRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEG   91 (117)
Q Consensus        34 lVY~~Ie~AGn~GIW--------tkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg   91 (117)
                      .||+.|.+.=..|-|        .++|..+.++..++|.++++.|++.|||......  |.|-++.
T Consensus        13 qi~~~i~~~I~~g~l~~G~~LPs~r~La~~~~vSr~tvr~Al~~L~~~Gli~~~~g~--G~~V~~~   76 (100)
T d1v4ra1          13 DVATHFRTLIKSGELAPGDTLPSVADIRAQFGVAAKTVSRALAVLKSEGLVSSRGAL--GTVVEKN   76 (100)
T ss_dssp             HHHHHHHHHTTTTSCCTTSBCCCHHHHHHHSSSCTTHHHHHTTTTTTSSCCEEETTT--EEESCSC
T ss_pred             HHHHHHHHHHHcCCCCCcCCCccHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEecCC--EEEECCC
Confidence            478888877666655        6899999999999999999999999999987653  5555543

>d1ulya_ a.4.5.58 (A:) Hypothetical protein PH1932 {Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Hypothetical protein PH1932
domain: Hypothetical protein PH1932
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=87.26  E-value=0.56  Score=31.98  Aligned_cols=54  Identities=11%  Similarity=0.257  Sum_probs=41.9

Q ss_pred             ccCCCHHHH-HHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778          25 LKDSDNEEK-VVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        25 ~~~L~~eE~-lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      ++-|.++-+ .|+.++.   ....-..+|-..+|++++.+.++|+.|+.-|||.+.+.
T Consensus        13 ~~~l~~p~R~~Il~~L~---~~~~s~~ela~~lg~s~~~v~~hl~~L~~~glv~~~~~   67 (190)
T d1ulya_          13 IKVMLEDTRRKILKLLR---NKEMTISQLSEILGKTPQTIYHHIEKLKEAGLVEVKRT   67 (190)
T ss_dssp             HHHHHSHHHHHHHHHHT---TCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             HHHhCCHHHHHHHHHHH---hCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEe
Confidence            344444433 5777773   23577899999999999999999999999999987653

>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=86.59  E-value=0.45  Score=32.95  Aligned_cols=54  Identities=13%  Similarity=0.207  Sum_probs=41.5

Q ss_pred             ccCCCHHH-HHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeecc
Q psy7778          25 LKDSDNEE-KVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKS   81 (117)
Q Consensus        25 ~~~L~~eE-~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKs   81 (117)
                      ++-|+++- +.|++++..   .-.-..+|-.+++++++.++++|+.||.-|||.+.+-
T Consensus         9 ~~~l~~~~R~~Il~~L~~---~~~~~~ela~~l~~s~~~v~~HL~~L~~~Glv~~~~~   63 (194)
T d2p4wa1           9 LDVLGNETRRRILFLLTK---RPYFVSELSRELGVGQKAVLEHLRILEEAGLIESRVE   63 (194)
T ss_dssp             HHHHHSHHHHHHHHHHHH---SCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             HHHhCCHHHHHHHHHHHh---CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEe
Confidence            33344432 356667753   4578899999999999999999999999999987543

>d1mzba_ a.4.5.42 (A:) Ferric uptake regulation protein, FUR {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: FUR-like
domain: Ferric uptake regulation protein, FUR
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=85.51  E-value=1.4  Score=28.61  Aligned_cols=66  Identities=8%  Similarity=0.109  Sum_probs=50.5

Q ss_pred             CCCHHHHHHHHHHHHhcCCcccHHHHHh----h-cCCChHHHHHHHHHHhhcCCeeeeccccCCcccccCc
Q psy7778          27 DSDNEEKVVYKIIEEAGNKGIWMRDIRF----K-SNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGT   92 (117)
Q Consensus        27 ~L~~eE~lVY~~Ie~AGn~GIWtkdIk~----k-tnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg~   92 (117)
                      .+|++=+.|++.+.+++++=.-..+|-.    + -++..++|=|.|..|+..|+|.++..-.+...|....
T Consensus        13 R~T~qR~~Il~~L~~~~~~h~sa~ei~~~l~~~~~~i~~aTVYR~L~~l~e~gli~~~~~~~~~~~y~~~~   83 (134)
T d1mzba_          13 KVTLPRVKILQMLDSAEQRHMSAEDVYKALMEAGEDVGLATVYRVLTQFEAAGLVVRHNFDGGHAVFELAD   83 (134)
T ss_dssp             CCCHHHHHHHHHHHCC-CCSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTSEEEECSSSSSCEEEESS
T ss_pred             CCCHHHHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCccHHHHHHHHHHHHhccEEEEEeecCCceEEEecC
Confidence            3677777999999988776565566643    3 2588899999999999999999998877766765443

>d2hzta1 a.4.5.69 (A:4-98) Putative transcriptional regulator YtcD {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: HxlR-like
domain: Putative transcriptional regulator YtcD
species: Bacillus subtilis [TaxId: 1423]

Probab=85.42  E-value=0.46  Score=30.21  Aligned_cols=31  Identities=19%  Similarity=0.389  Sum_probs=27.5

Q ss_pred             HHHHHhhc-CCChHHHHHHHHHHhhcCCeeee
Q psy7778          49 MRDIRFKS-NLMPTQLNKILKQLETKKIIKAV   79 (117)
Q Consensus        49 tkdIk~kt-nL~~~~l~K~LK~LE~k~LIK~V   79 (117)
                      -.+|++.. |+++++|++.||.||..|||...
T Consensus        27 F~el~~~l~gis~~~Ls~rLk~Le~~glv~r~   58 (95)
T d2hzta1          27 TSELKRLMPNITQKMLTQQLRELEADGVINRI   58 (95)
T ss_dssp             HHHHHHHCTTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHhhcCChhHHHHHHHHHHHhHHHhhe
Confidence            57888885 99999999999999999999754

>d2fswa1 a.4.5.69 (A:3-104) Hypothetical protein PG0823 {Porphyromonas gingivalis [TaxId: 837]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: HxlR-like
domain: Hypothetical protein PG0823
species: Porphyromonas gingivalis [TaxId: 837]

Probab=84.62  E-value=0.53  Score=30.34  Aligned_cols=32  Identities=22%  Similarity=0.147  Sum_probs=27.8

Q ss_pred             cHHHHHhhc-CCChHHHHHHHHHHhhcCCeeee
Q psy7778          48 WMRDIRFKS-NLMPTQLNKILKQLETKKIIKAV   79 (117)
Q Consensus        48 WtkdIk~kt-nL~~~~l~K~LK~LE~k~LIK~V   79 (117)
                      ==.+|++.. |+++++|++.||.||..|+|...
T Consensus        35 rF~el~~~l~gIs~~~Ls~rLkeL~~~glv~r~   67 (102)
T d2fswa1          35 RYGELKRAIPGISEKMLIDELKFLCGKGLIKKK   67 (102)
T ss_dssp             EHHHHHHHSTTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CHHHHHhhCcccchhHHHHHHHHHHHCCceeec
Confidence            346888885 99999999999999999999753

>d1yyva1 a.4.5.69 (A:9-122) Putative transcriptional regulator YtfH {Salmonella typhimurium [TaxId: 90371]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: HxlR-like
domain: Putative transcriptional regulator YtfH
species: Salmonella typhimurium [TaxId: 90371]

Probab=83.33  E-value=0.52  Score=30.98  Aligned_cols=31  Identities=26%  Similarity=0.374  Sum_probs=27.6

Q ss_pred             HHHHHhhc-CCChHHHHHHHHHHhhcCCeeee
Q psy7778          49 MRDIRFKS-NLMPTQLNKILKQLETKKIIKAV   79 (117)
Q Consensus        49 tkdIk~kt-nL~~~~l~K~LK~LE~k~LIK~V   79 (117)
                      =.+|++.. |+.+++|++.||.||..|||...
T Consensus        40 F~el~~~l~gis~~~Ls~rL~~Le~~glv~R~   71 (114)
T d1yyva1          40 FSDLRRKMGGVSEKMLAQSLQALEQDGFLNRV   71 (114)
T ss_dssp             HHHHHHHSTTCCHHHHHHHHHHHHHHTCEEEE
T ss_pred             HHHHHHHccccchhHHHHHHHHHHHHHHHhhc
Confidence            46788887 89999999999999999999754

>d1tw3a1 a.4.5.29 (A:14-98) Carminomycin 4-O-methyltransferase {Streptomyces peucetius [TaxId: 1950]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Plant O-methyltransferase, N-terminal domain
domain: Carminomycin 4-O-methyltransferase
species: Streptomyces peucetius [TaxId: 1950]

Probab=80.71  E-value=1.7  Score=26.64  Aligned_cols=57  Identities=11%  Similarity=0.123  Sum_probs=43.9

Q ss_pred             HHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhcCCeeeeccccCCcccccCccc
Q psy7778          31 EEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETKKIIKAVKSVANIEYLTEGTVN   94 (117)
Q Consensus        31 eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k~LIK~VKsV~gg~wYtdg~~D   94 (117)
                      -|.-|+++|. .  ..+-..+|-.++|++...+.+.++.|.+.|++.+..    .-+|....+-
T Consensus        22 v~L~ifd~l~-~--gp~s~~eLA~~~g~~~~~l~rlLr~l~a~gl~~e~~----~~~y~lt~~s   78 (85)
T d1tw3a1          22 ATLRLVDHIL-A--GARTVKALAARTDTRPEALLRLIRHLVAIGLLEEDA----PGEFVPTEVG   78 (85)
T ss_dssp             HHTTHHHHHH-T--TCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE----TTEEEECTTG
T ss_pred             HHcCcHHHhc-c--CCCCHHHHHHHhCcChhHHHHHHHHHHHCCCeEecC----CCeEecCHHH
Confidence            3556788884 2  368889999999999999999999999999998753    2345544443

>d1yioa1 a.4.6.2 (A:131-200) Response regulatory protein StyR, C-terminal domain {Pseudomonas fluorescens [TaxId: 294]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Response regulatory protein StyR, C-terminal domain
species: Pseudomonas fluorescens [TaxId: 294]

Probab=80.08  E-value=1.4  Score=26.17  Aligned_cols=46  Identities=11%  Similarity=0.153  Sum_probs=39.8

Q ss_pred             cccCCCHHHHHHHHHHHHhcCCcccHHHHHhhcCCChHHHHHHHHHHhhc
Q psy7778          24 KLKDSDNEEKVVYKIIEEAGNKGIWMRDIRFKSNLMPTQLNKILKQLETK   73 (117)
Q Consensus        24 k~~~L~~eE~lVY~~Ie~AGn~GIWtkdIk~ktnL~~~~l~K~LK~LE~k   73 (117)
                      .+..||+-|..|..++-    .|...++|-.+.|+...+|...++.+-.|
T Consensus         9 ~~~~LT~rE~~vl~~l~----~G~s~~eIA~~l~iS~~TV~~~~~~i~~K   54 (70)
T d1yioa1           9 LFSSLTGREQQVLQLTI----RGLMNKQIAGELGIAEVTVKVHRHNIMQK   54 (70)
T ss_dssp             HHHTSCHHHHHHHHHHT----TTCCHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             HHccCCHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            45689999999998875    58999999999999999999998887554