Psyllid ID: psy1871

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------14
Protein Sequence
MGYLYAMETSSPMVLKSYKHPPKKDTKGGSSKQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTTKGDDPVA
Secondary Structure (PSIPRED)
cccEEEEHHcccccccccccccccccccccccccccHHHcccccccccccccccccHHHHHHHcccEEEcHHHHHHHHHcccccEEEcHHHHccccEEHHHHHHHHHHHHHHcccEEEEEEcccEEEEEcccccccccc
Secondary Structure Prediction (SSPRO)
ccEEEEEccccccHHHHcccccccccccccccccccccccccccccccccccccccccHHHHHccEEEEccHHHHHHHHHccccEEEcHHHHHHHHcccHHHHHHHHHHHHHcccEEEEEEcccEEEEEEccccccccc
Coil and Loop (DISEMBL)
mgylyametsspmvlksykhppkkdtkggsskqpqktqkkkeggsggkakkkkwskgkvrdklnnqvlfDKASYDKLLkevpayklitpsVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTrttkgddpva
Flexible Loop (DISEMBL)
MGYLYAMetsspmvlksykhppkkdtkggsskqpqktqkkkeggsggkakkkkwskgkvrdklnnqvlfdKASYDKLLkevpayklitpsvvserlKVRGSLARKALEELLQKGLIKQVVKHHAQViytrttkgddpva
Low Complexity Region (SEG)
MGYLYAMETSSPMVLKSYKHPPKKDTkggsskqpqktqkkkeggsggkakkkkwskgkvrdkLNNQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTTKGDDPVA
Disordered region (IsUnstruct)
***************************************************************NNQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR*********
Disordered Region (DISOPRED)
*GYLYAMETSSPMVLKSY*****************************************RDKLNNQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTT*******
Disordered Region (DISEMBL)
MGYLYAMETSSPMVLKSYK**************************************KVRDKLNNQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT********
Disordered Region (DISPRO)
*GYLYAMETSSPMVLKSYKHPPK*********************************GKVRDKLNNQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTTK******
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGYLYAMETSSPMVLKSYKHPPKKDTKGGSSKQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTTKGDDPVA
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	139	2.2.26 [Sep-21-2011]
Q962Q5	119	40S ribosomal protein S25	N/A	N/A	0.848	0.991	0.848	4e-34
P48588	117	40S ribosomal protein S25	yes	N/A	0.827	0.982	0.836	1e-32
Q8ISN9	123	40S ribosomal protein S25	N/A	N/A	0.805	0.910	0.767	1e-30
Q6PBI5	124	40S ribosomal protein S25	yes	N/A	0.582	0.653	0.802	5e-30
Q6Q311	125	40S ribosomal protein S25	N/A	N/A	0.561	0.624	0.820	5e-30
P62853	125	40S ribosomal protein S25	yes	N/A	0.561	0.624	0.820	5e-30
P62852	125	40S ribosomal protein S25	yes	N/A	0.561	0.624	0.820	5e-30
P62851	125	40S ribosomal protein S25	yes	N/A	0.561	0.624	0.820	5e-30
Q56JX5	125	40S ribosomal protein S25	yes	N/A	0.561	0.624	0.820	5e-30
Q03409	110	40S ribosomal protein S25	yes	N/A	0.776	0.981	0.576	2e-29

>sp|Q962Q5|RS25_SPOFR 40S ribosomal protein S25 OS=Spodoptera frugiperda GN=RpS25 PE=3 SV=1

 Score =  143 bits (360), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 101/119 (84%), Positives = 108/119 (90%), Gaps = 1/119 (0%)

Query: 21  PPKKDTKGGSSKQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDKASYDKLLKE 80
           PPKKDTK  S+KQPQKTQKKKEG  GGKAKKKKWSKGKVRDKLNNQVLFDK +Y+KL KE
Sbjct: 2   PPKKDTK-ASAKQPQKTQKKKEGSGGGKAKKKKWSKGKVRDKLNNQVLFDKPTYEKLYKE 60

Query: 81  VPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTTKGDDPVA 139
           VP YKLITP+VVSERLKVRGSLAR+AL EL +KGLIKQVV+HH QVIYTR TKGDDPVA
Sbjct: 61  VPQYKLITPAVVSERLKVRGSLARRALIELREKGLIKQVVQHHGQVIYTRATKGDDPVA 119

Spodoptera frugiperda (taxid: 7108)

>sp|P48588|RS25_DROME 40S ribosomal protein S25 OS=Drosophila melanogaster GN=RpS25 PE=1 SV=3

 Score =  138 bits (347), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 97/116 (83%), Positives = 107/116 (92%), Gaps = 1/116 (0%)

Query: 21  PPKKDTKGGSSKQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDKASYDKLLKE 80
           PPKKD K  S+KQPQKTQKKKEG  GGKAKKKKWSKGKVRDKLNNQVLFDKA+Y+KL KE
Sbjct: 2   PPKKDAK-SSAKQPQKTQKKKEGSGGGKAKKKKWSKGKVRDKLNNQVLFDKATYEKLYKE 60

Query: 81  VPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTTKGDD 136
           VPAYKLITPSVVSERLK+RGSLA++AL EL +KGLIKQVV+HH+QVIYTR TKGD+
Sbjct: 61  VPAYKLITPSVVSERLKIRGSLAKRALIELREKGLIKQVVQHHSQVIYTRATKGDE 116

Drosophila melanogaster (taxid: 7227)

>sp|Q8ISN9|RS25_BRABE 40S ribosomal protein S25 OS=Branchiostoma belcheri GN=RPS25 PE=2 SV=1

 Score =  131 bits (329), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 89/116 (76%), Positives = 95/116 (81%), Gaps = 4/116 (3%)

Query: 21  PPKKDTKGGSSKQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDKASYDKLLKE 80
           PPKKDTKG S    +K QK K G  GGKAKKKKWSKGKVRDKLNN VLFDKA+YDKL KE
Sbjct: 2   PPKKDTKGDS----KKGQKAKAGSGGGKAKKKKWSKGKVRDKLNNLVLFDKATYDKLYKE 57

Query: 81  VPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTTKGDD 136
           VP+YKLITPSVVSERLK+RGSLAR AL+EL  KG+IK V KH AQVIYTR TK  D
Sbjct: 58  VPSYKLITPSVVSERLKIRGSLARAALKELHSKGMIKLVSKHSAQVIYTRATKDTD 113

Branchiostoma belcheri (taxid: 7741)

>sp|Q6PBI5|RS25_DANRE 40S ribosomal protein S25 OS=Danio rerio GN=rps25 PE=2 SV=1

 Score =  129 bits (324), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 65/81 (80%), Positives = 69/81 (85%)

Query: 59  VRDKLNNQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQ 118
           VRDKLNN VLFDKA+YDKL KEVP YKLITP+VVSERLK+RGSLAR AL+ELL KGLIK 
Sbjct: 39  VRDKLNNLVLFDKATYDKLYKEVPNYKLITPAVVSERLKIRGSLARAALQELLGKGLIKL 98

Query: 119 VVKHHAQVIYTRTTKGDDPVA 139
           V KH AQVIYTR TKG D  A
Sbjct: 99  VSKHRAQVIYTRNTKGTDEAA 119

Danio rerio (taxid: 7955)

>sp|Q6Q311|RS25_SHEEP 40S ribosomal protein S25 OS=Ovis aries GN=RPS25 PE=2 SV=1

 Score =  129 bits (324), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 64/78 (82%), Positives = 68/78 (87%)

Query: 59  VRDKLNNQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQ 118
           VRDKLNN VLFDKA+YDKL KEVP YKLITP+VVSERLK+RGSLAR AL+ELL KGLIK 
Sbjct: 40  VRDKLNNLVLFDKATYDKLCKEVPNYKLITPAVVSERLKIRGSLARAALQELLSKGLIKL 99

Query: 119 VVKHHAQVIYTRTTKGDD 136
           V KH AQVIYTR TKG D
Sbjct: 100 VSKHRAQVIYTRNTKGGD 117

Ovis aries (taxid: 9940)

>sp|P62853|RS25_RAT 40S ribosomal protein S25 OS=Rattus norvegicus GN=Rps25 PE=2 SV=1

 Score =  129 bits (324), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 64/78 (82%), Positives = 68/78 (87%)

Query: 59  VRDKLNNQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQ 118
           VRDKLNN VLFDKA+YDKL KEVP YKLITP+VVSERLK+RGSLAR AL+ELL KGLIK 
Sbjct: 40  VRDKLNNLVLFDKATYDKLCKEVPNYKLITPAVVSERLKIRGSLARAALQELLSKGLIKL 99

Query: 119 VVKHHAQVIYTRTTKGDD 136
           V KH AQVIYTR TKG D
Sbjct: 100 VSKHRAQVIYTRNTKGGD 117

Rattus norvegicus (taxid: 10116)

>sp|P62852|RS25_MOUSE 40S ribosomal protein S25 OS=Mus musculus GN=Rps25 PE=2 SV=1

 Score =  129 bits (324), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 64/78 (82%), Positives = 68/78 (87%)

Query: 59  VRDKLNNQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQ 118
           VRDKLNN VLFDKA+YDKL KEVP YKLITP+VVSERLK+RGSLAR AL+ELL KGLIK 
Sbjct: 40  VRDKLNNLVLFDKATYDKLCKEVPNYKLITPAVVSERLKIRGSLARAALQELLSKGLIKL 99

Query: 119 VVKHHAQVIYTRTTKGDD 136
           V KH AQVIYTR TKG D
Sbjct: 100 VSKHRAQVIYTRNTKGGD 117

Mus musculus (taxid: 10090)

>sp|P62851|RS25_HUMAN 40S ribosomal protein S25 OS=Homo sapiens GN=RPS25 PE=1 SV=1

 Score =  129 bits (324), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 64/78 (82%), Positives = 68/78 (87%)

Query: 59  VRDKLNNQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQ 118
           VRDKLNN VLFDKA+YDKL KEVP YKLITP+VVSERLK+RGSLAR AL+ELL KGLIK 
Sbjct: 40  VRDKLNNLVLFDKATYDKLCKEVPNYKLITPAVVSERLKIRGSLARAALQELLSKGLIKL 99

Query: 119 VVKHHAQVIYTRTTKGDD 136
           V KH AQVIYTR TKG D
Sbjct: 100 VSKHRAQVIYTRNTKGGD 117

Homo sapiens (taxid: 9606)

>sp|Q56JX5|RS25_BOVIN 40S ribosomal protein S25 OS=Bos taurus GN=RPS25 PE=2 SV=1

 Score =  129 bits (324), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 64/78 (82%), Positives = 68/78 (87%)

Query: 59  VRDKLNNQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQ 118
           VRDKLNN VLFDKA+YDKL KEVP YKLITP+VVSERLK+RGSLAR AL+ELL KGLIK 
Sbjct: 40  VRDKLNNLVLFDKATYDKLCKEVPNYKLITPAVVSERLKIRGSLARAALQELLSKGLIKL 99

Query: 119 VVKHHAQVIYTRTTKGDD 136
           V KH AQVIYTR TKG D
Sbjct: 100 VSKHRAQVIYTRNTKGGD 117

Bos taurus (taxid: 9913)

>sp|Q03409|RS25_DICDI 40S ribosomal protein S25 OS=Dictyostelium discoideum GN=rps25 PE=3 SV=1

 Score =  127 bits (318), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 64/111 (57%), Positives = 83/111 (74%), Gaps = 3/111 (2%)

Query: 21  PPKKDTKGGSSKQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDKASYDKLLKE 80
           PPK    GG SKQ Q ++   +G SGG A +KKWSKG+ R+KLNN +LFDK +Y KLLKE
Sbjct: 2   PPK--AAGGKSKQIQASKAAAKGSSGG-AGRKKWSKGRSREKLNNAILFDKETYAKLLKE 58

Query: 81  VPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT 131
           +P  K+IT +VVSER+K  GSLAR+A++ELL KGLIKQ++K H   +YT+ 
Sbjct: 59  MPTAKVITTAVVSERMKCNGSLARRAIKELLSKGLIKQIIKGHGNGVYTKA 109

Dictyostelium discoideum (taxid: 44689)

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	139
110671462	120	putative ribosomal protein S25 [Diaphori	0.856	0.991	1.0	1e-59
50344516	119	S25e ribosomal protein [Platystomos albi	0.848	0.991	0.873	2e-38
342905879	118	putative ribosomal protein S25 [Rhodnius	0.841	0.991	0.854	7e-37
158292201	155	AGAP004462-PA [Anopheles gambiae str. PE	0.870	0.780	0.885	2e-36
156551257	119	PREDICTED: 40S ribosomal protein S25-lik	0.848	0.991	0.899	1e-35
187129228	116	ribosomal protein S25 homolog 2 [Acyrtho	0.827	0.991	0.922	3e-35
322795720	128	hypothetical protein SINV_07669 [Solenop	0.841	0.914	0.898	3e-35
110756725	119	PREDICTED: 40S ribosomal protein S25 iso	0.848	0.991	0.890	5e-35
328785959	127	PREDICTED: 40S ribosomal protein S25 iso	0.848	0.929	0.890	6e-35
157103243	201	ribosomal protein S25, putative [Aedes a	0.848	0.587	0.739	8e-35

>gi|110671462|gb|ABG81982.1| putative ribosomal protein S25 [Diaphorina citri]

 Score =  234 bits (596), Expect = 1e-59,   Method: Compositional matrix adjust.
 Identities = 119/119 (100%), Positives = 119/119 (100%)

Query: 21  PPKKDTKGGSSKQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDKASYDKLLKE 80
           PPKKDTKGGSSKQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDKASYDKLLKE
Sbjct: 2   PPKKDTKGGSSKQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDKASYDKLLKE 61

Query: 81  VPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTTKGDDPVA 139
           VPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTTKGDDPVA
Sbjct: 62  VPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTTKGDDPVA 120

Source: Diaphorina citri

Species: Diaphorina citri

Genus: Diaphorina

Family: Psyllidae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|50344516|emb|CAH04344.1| S25e ribosomal protein [Platystomos albinus]

 Score =  163 bits (413), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 104/119 (87%), Positives = 111/119 (93%), Gaps = 1/119 (0%)

Query: 21  PPKKDTKGGSSKQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDKASYDKLLKE 80
           PPKKD+K  SSKQPQKTQKKKEG  GGKAKKK+WSKGKVRDKLNNQVLFDKA+YDKL KE
Sbjct: 2   PPKKDSKA-SSKQPQKTQKKKEGSGGGKAKKKRWSKGKVRDKLNNQVLFDKATYDKLYKE 60

Query: 81  VPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTTKGDDPVA 139
           VP+YKLITPSVVSERLKVRGSLAR+AL EL QKGLIKQVV+H AQ+IYTRTTKGDDPVA
Sbjct: 61  VPSYKLITPSVVSERLKVRGSLARRALIELQQKGLIKQVVQHRAQLIYTRTTKGDDPVA 119

Source: Platystomos albinus

Species: Platystomos albinus

Genus: Platystomos

Family: Anthribidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|342905879|gb|AEL79223.1| putative ribosomal protein S25 [Rhodnius prolixus]

 Score =  158 bits (399), Expect = 7e-37,   Method: Compositional matrix adjust.
 Identities = 100/117 (85%), Positives = 107/117 (91%)

Query: 21  PPKKDTKGGSSKQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDKASYDKLLKE 80
           PPKKDTKGGSSKQP K  KKKEGGSGGKAKKKKWSKGKVRDKL+NQVLFD  +YDKLLK+
Sbjct: 2   PPKKDTKGGSSKQPAKNPKKKEGGSGGKAKKKKWSKGKVRDKLDNQVLFDSGTYDKLLKD 61

Query: 81  VPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTTKGDDP 137
           VP+YKLITPS+VSERLKVRGSLARKAL ELL KG IKQVVKHH+QVIYTR TK +DP
Sbjct: 62  VPSYKLITPSIVSERLKVRGSLARKALNELLNKGYIKQVVKHHSQVIYTRATKTEDP 118

Source: Rhodnius prolixus

Species: Rhodnius prolixus

Genus: Rhodnius

Family: Reduviidae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|158292201|ref|XP_313760.4| AGAP004462-PA [Anopheles gambiae str. PEST] gi|157017323|gb|EAA09243.4| AGAP004462-PA [Anopheles gambiae str. PEST]

 Score =  157 bits (396), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 108/122 (88%), Positives = 115/122 (94%), Gaps = 1/122 (0%)

Query: 18  YKHPPKKDTKGGSSKQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDKASYDKL 77
           +K PPKKDTK GS+KQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDKA+YDKL
Sbjct: 35  FKMPPKKDTK-GSAKQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDKATYDKL 93

Query: 78  LKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTTKGDDP 137
            KEVPAYKLITPSVVSERLK+RGSLA++ L EL QKGLIK VV+HHAQVIYTRTTKGDDP
Sbjct: 94  YKEVPAYKLITPSVVSERLKIRGSLAKRGLRELCQKGLIKLVVQHHAQVIYTRTTKGDDP 153

Query: 138 VA 139
           VA
Sbjct: 154 VA 155

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|156551257|ref|XP_001599263.1| PREDICTED: 40S ribosomal protein S25-like [Nasonia vitripennis]

 Score =  154 bits (389), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 107/119 (89%), Positives = 115/119 (96%), Gaps = 1/119 (0%)

Query: 21  PPKKDTKGGSSKQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDKASYDKLLKE 80
           PPKKDTK GSSKQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDK++Y+KLLKE
Sbjct: 2   PPKKDTK-GSSKQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDKSTYEKLLKE 60

Query: 81  VPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTTKGDDPVA 139
           VPAYKLITPS+VSERLK+RGSLAR+AL EL QKGLIKQVV+HHAQ+IYTRTTKGDDP A
Sbjct: 61  VPAYKLITPSIVSERLKIRGSLARRALIELQQKGLIKQVVQHHAQLIYTRTTKGDDPAA 119

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|187129228|ref|NP_001119663.1| ribosomal protein S25 homolog 2 [Acyrthosiphon pisum] gi|89473738|gb|ABD72681.1| RpS25-like [Acyrthosiphon pisum] gi|239788353|dbj|BAH70863.1| ACYPI000038 [Acyrthosiphon pisum]

 Score =  152 bits (385), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 107/116 (92%), Positives = 112/116 (96%), Gaps = 1/116 (0%)

Query: 21  PPKKDTKGGSSKQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDKASYDKLLKE 80
           PPKKDTK GSSKQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDK SYDKLLKE
Sbjct: 2   PPKKDTK-GSSKQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDKVSYDKLLKE 60

Query: 81  VPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTTKGDD 136
           VP+YKLITPSVVSERLKVRGSLARKALEEL QKGLIKQV++HHAQ+IYTR TKGD+
Sbjct: 61  VPSYKLITPSVVSERLKVRGSLARKALEELCQKGLIKQVIQHHAQLIYTRVTKGDE 116

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322795720|gb|EFZ18399.1| hypothetical protein SINV_07669 [Solenopsis invicta]

 Score =  152 bits (385), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 106/118 (89%), Positives = 113/118 (95%), Gaps = 1/118 (0%)

Query: 20  HPPKKDTKGGSSKQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDKASYDKLLK 79
            PPKKDTK GSSKQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDKA+Y+KLLK
Sbjct: 10  QPPKKDTK-GSSKQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDKATYEKLLK 68

Query: 80  EVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTTKGDDP 137
           EVP YKLITPS+VSERLK+RGSLAR+AL EL QKGLIKQVV+HHAQ+IYTRTTKGDDP
Sbjct: 69  EVPQYKLITPSIVSERLKIRGSLARRALIELQQKGLIKQVVQHHAQLIYTRTTKGDDP 126

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|110756725|ref|XP_001119888.1| PREDICTED: 40S ribosomal protein S25 isoform 1 [Apis mellifera] gi|380026017|ref|XP_003696758.1| PREDICTED: 40S ribosomal protein S25-like [Apis florea]

 Score =  152 bits (384), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 106/119 (89%), Positives = 114/119 (95%), Gaps = 1/119 (0%)

Query: 21  PPKKDTKGGSSKQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDKASYDKLLKE 80
           PPKKDTK GSSKQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDK++Y+KLLKE
Sbjct: 2   PPKKDTK-GSSKQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDKSTYEKLLKE 60

Query: 81  VPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTTKGDDPVA 139
           VP YKLITPS+VSERLK+RGSLAR+AL EL QKGLIKQVV+HHAQ+IYTRTTKGDDP A
Sbjct: 61  VPQYKLITPSIVSERLKIRGSLARRALIELQQKGLIKQVVQHHAQLIYTRTTKGDDPAA 119

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328785959|ref|XP_003250683.1| PREDICTED: 40S ribosomal protein S25 isoform 2 [Apis mellifera]

 Score =  152 bits (383), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 106/119 (89%), Positives = 114/119 (95%), Gaps = 1/119 (0%)

Query: 21  PPKKDTKGGSSKQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDKASYDKLLKE 80
           PPKKDTK GSSKQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDK++Y+KLLKE
Sbjct: 10  PPKKDTK-GSSKQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDKSTYEKLLKE 68

Query: 81  VPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTTKGDDPVA 139
           VP YKLITPS+VSERLK+RGSLAR+AL EL QKGLIKQVV+HHAQ+IYTRTTKGDDP A
Sbjct: 69  VPQYKLITPSIVSERLKIRGSLARRALIELQQKGLIKQVVQHHAQLIYTRTTKGDDPAA 127

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157103243|ref|XP_001647888.1| ribosomal protein S25, putative [Aedes aegypti] gi|157103245|ref|XP_001647889.1| ribosomal protein S25, putative [Aedes aegypti] gi|108884720|gb|EAT48945.1| AAEL000068-PB [Aedes aegypti] gi|108884721|gb|EAT48946.1| AAEL000068-PA [Aedes aegypti]

 Score =  151 bits (382), Expect = 8e-35,   Method: Compositional matrix adjust.
 Identities = 88/119 (73%), Positives = 99/119 (83%), Gaps = 1/119 (0%)

Query: 21  PPKKDTKGGSSKQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDKASYDKLLKE 80
           PPKKDTKG + +  +  +KK+  G G   KKK  SKGKVRDKLNNQVLFDKA+Y+KL KE
Sbjct: 84  PPKKDTKGAAKQPQKTQKKKEGSGGGKAKKKKW-SKGKVRDKLNNQVLFDKATYEKLYKE 142

Query: 81  VPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTTKGDDPVA 139
           VPAYKLITPSVVSERLK+RGSLA++ L EL QKGLI+ VV HHAQVIYTRTTKGDDPVA
Sbjct: 143 VPAYKLITPSVVSERLKIRGSLAKRGLRELCQKGLIRMVVHHHAQVIYTRTTKGDDPVA 201

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	139
FB|FBgn0086472	117	RpS25 "Ribosomal protein S25"	0.532	0.632	0.824	5e-28
UNIPROTKB|Q56JX5	125	RPS25 "40S ribosomal protein S	0.553	0.616	0.794	4e-26
UNIPROTKB|P62851	125	RPS25 "40S ribosomal protein S	0.553	0.616	0.794	4e-26
UNIPROTKB|F2Z5G8	125	RPS25 "Uncharacterized protein	0.553	0.616	0.794	4e-26
MGI|MGI:1922867	125	Rps25 "ribosomal protein S25"	0.553	0.616	0.794	4e-26
RGD|621043	125	Rps25 "ribosomal protein s25"	0.553	0.616	0.794	4e-26
ZFIN|ZDB-GENE-040426-1788	132	rps25 "ribosomal protein S25"	0.553	0.583	0.792	5.2e-26
UNIPROTKB|F1NU56	139	RPS25 "Uncharacterized protein	0.553	0.553	0.794	6.6e-26
WB|WBGene00004494	117	rps-25 [Caenorhabditis elegans	0.546	0.649	0.697	2.6e-22
TAIR|locus:505006559	108	AT4G34555 "AT4G34555" [Arabido	0.517	0.666	0.597	1.9e-19

FB|FBgn0086472 RpS25 "Ribosomal protein S25" [Drosophila melanogaster (taxid:7227)]

 Score = 313 (115.2 bits), Expect = 5.0e-28, P = 5.0e-28
 Identities = 61/74 (82%), Positives = 70/74 (94%)

Query:    63 LNNQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKH 122
             LNNQVLFDKA+Y+KL KEVPAYKLITPSVVSERLK+RGSLA++AL EL +KGLIKQVV+H
Sbjct:    43 LNNQVLFDKATYEKLYKEVPAYKLITPSVVSERLKIRGSLAKRALIELREKGLIKQVVQH 102

Query:   123 HAQVIYTRTTKGDD 136
             H+QVIYTR TKGD+
Sbjct:   103 HSQVIYTRATKGDE 116

GO:0022627 "cytosolic small ribosomal subunit" evidence=ISS;NAS

GO:0006412 "translation" evidence=ISS;NAS

GO:0003735 "structural constituent of ribosome" evidence=ISS;IDA;NAS

GO:0005840 "ribosome" evidence=IDA;NAS

UNIPROTKB|Q56JX5 RPS25 "40S ribosomal protein S25" [Bos taurus (taxid:9913)]

 Score = 295 (108.9 bits), Expect = 4.0e-26, P = 4.0e-26
 Identities = 62/78 (79%), Positives = 66/78 (84%)

Query:    63 LNNQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKH 122
             LNN VLFDKA+YDKL KEVP YKLITP+VVSERLK+RGSLAR AL+ELL KGLIK V KH
Sbjct:    44 LNNLVLFDKATYDKLCKEVPNYKLITPAVVSERLKIRGSLARAALQELLSKGLIKLVSKH 103

Query:   123 HAQVIYTRTTKGDD-PVA 139
              AQVIYTR TKG D P A
Sbjct:   104 RAQVIYTRNTKGGDAPAA 121

GO:0022627 "cytosolic small ribosomal subunit" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

UNIPROTKB|P62851 RPS25 "40S ribosomal protein S25" [Homo sapiens (taxid:9606)]

 Score = 295 (108.9 bits), Expect = 4.0e-26, P = 4.0e-26
 Identities = 62/78 (79%), Positives = 66/78 (84%)

Query:    63 LNNQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKH 122
             LNN VLFDKA+YDKL KEVP YKLITP+VVSERLK+RGSLAR AL+ELL KGLIK V KH
Sbjct:    44 LNNLVLFDKATYDKLCKEVPNYKLITPAVVSERLKIRGSLARAALQELLSKGLIKLVSKH 103

Query:   123 HAQVIYTRTTKGDD-PVA 139
              AQVIYTR TKG D P A
Sbjct:   104 RAQVIYTRNTKGGDAPAA 121

GO:0000028 "ribosomal small subunit assembly" evidence=IEA

GO:0003735 "structural constituent of ribosome" evidence=IEA

GO:0022627 "cytosolic small ribosomal subunit" evidence=IDA

GO:0006412 "translation" evidence=IC;NAS;TAS

GO:0015935 "small ribosomal subunit" evidence=IDA

GO:0005840 "ribosome" evidence=NAS;IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0003723 "RNA binding" evidence=NAS

GO:0005829 "cytosol" evidence=TAS

GO:0006413 "translational initiation" evidence=TAS

GO:0006414 "translational elongation" evidence=TAS

GO:0006415 "translational termination" evidence=TAS

GO:0006614 "SRP-dependent cotranslational protein targeting to membrane" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0016032 "viral reproduction" evidence=TAS

GO:0016070 "RNA metabolic process" evidence=TAS

GO:0016071 "mRNA metabolic process" evidence=TAS

GO:0019058 "viral infectious cycle" evidence=TAS

GO:0019083 "viral transcription" evidence=TAS

GO:0044267 "cellular protein metabolic process" evidence=TAS

GO:0000184 "nuclear-transcribed mRNA catabolic process, nonsense-mediated decay" evidence=TAS

GO:0005737 "cytoplasm" evidence=IDA

UNIPROTKB|F2Z5G8 RPS25 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 295 (108.9 bits), Expect = 4.0e-26, P = 4.0e-26
 Identities = 62/78 (79%), Positives = 66/78 (84%)

Query:    63 LNNQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKH 122
             LNN VLFDKA+YDKL KEVP YKLITP+VVSERLK+RGSLAR AL+ELL KGLIK V KH
Sbjct:    44 LNNLVLFDKATYDKLCKEVPNYKLITPAVVSERLKIRGSLARAALQELLSKGLIKLVSKH 103

Query:   123 HAQVIYTRTTKGDD-PVA 139
              AQVIYTR TKG D P A
Sbjct:   104 RAQVIYTRNTKGGDAPAA 121

GO:0022627 "cytosolic small ribosomal subunit" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

MGI|MGI:1922867 Rps25 "ribosomal protein S25" [Mus musculus (taxid:10090)]

 Score = 295 (108.9 bits), Expect = 4.0e-26, P = 4.0e-26
 Identities = 62/78 (79%), Positives = 66/78 (84%)

Query:    63 LNNQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKH 122
             LNN VLFDKA+YDKL KEVP YKLITP+VVSERLK+RGSLAR AL+ELL KGLIK V KH
Sbjct:    44 LNNLVLFDKATYDKLCKEVPNYKLITPAVVSERLKIRGSLARAALQELLSKGLIKLVSKH 103

Query:   123 HAQVIYTRTTKGDD-PVA 139
              AQVIYTR TKG D P A
Sbjct:   104 RAQVIYTRNTKGGDAPAA 121

GO:0000028 "ribosomal small subunit assembly" evidence=ISO

GO:0003735 "structural constituent of ribosome" evidence=ISO

GO:0005730 "nucleolus" evidence=ISO

GO:0005840 "ribosome" evidence=ISO

GO:0015935 "small ribosomal subunit" evidence=ISO

GO:0022627 "cytosolic small ribosomal subunit" evidence=ISO

GO:0030529 "ribonucleoprotein complex" evidence=IEA

RGD|621043 Rps25 "ribosomal protein s25" [Rattus norvegicus (taxid:10116)]

 Score = 295 (108.9 bits), Expect = 4.0e-26, P = 4.0e-26
 Identities = 62/78 (79%), Positives = 66/78 (84%)

Query:    63 LNNQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKH 122
             LNN VLFDKA+YDKL KEVP YKLITP+VVSERLK+RGSLAR AL+ELL KGLIK V KH
Sbjct:    44 LNNLVLFDKATYDKLCKEVPNYKLITPAVVSERLKIRGSLARAALQELLSKGLIKLVSKH 103

Query:   123 HAQVIYTRTTKGDD-PVA 139
              AQVIYTR TKG D P A
Sbjct:   104 RAQVIYTRNTKGGDAPAA 121

GO:0000028 "ribosomal small subunit assembly" evidence=IMP

GO:0003735 "structural constituent of ribosome" evidence=IMP

GO:0005730 "nucleolus" evidence=IEA;ISO

GO:0005737 "cytoplasm" evidence=ISO

GO:0005840 "ribosome" evidence=ISO

GO:0015935 "small ribosomal subunit" evidence=ISO

GO:0022627 "cytosolic small ribosomal subunit" evidence=ISO;IDA

ZFIN|ZDB-GENE-040426-1788 rps25 "ribosomal protein S25" [Danio rerio (taxid:7955)]

 Score = 294 (108.6 bits), Expect = 5.2e-26, P = 5.2e-26
 Identities = 61/77 (79%), Positives = 65/77 (84%)

Query:    63 LNNQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKH 122
             LNN VLFDKA+YDKL KEVP YKLITP+VVSERLK+RGSLAR AL+ELL KGLIK V KH
Sbjct:    51 LNNLVLFDKATYDKLYKEVPNYKLITPAVVSERLKIRGSLARAALQELLGKGLIKLVSKH 110

Query:   123 HAQVIYTRTTKGDDPVA 139
              AQVIYTR TKG D  A
Sbjct:   111 RAQVIYTRNTKGTDEAA 127

GO:0005840 "ribosome" evidence=IEA

GO:0030529 "ribonucleoprotein complex" evidence=IEA

UNIPROTKB|F1NU56 RPS25 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 293 (108.2 bits), Expect = 6.6e-26, P = 6.6e-26
 Identities = 62/78 (79%), Positives = 66/78 (84%)

Query:    63 LNNQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKH 122
             LNN VLFDKA+YDKL KEVP YKLITP+VVSERLK+RGSLAR AL+ELL KGLIK V KH
Sbjct:    58 LNNLVLFDKATYDKLCKEVPNYKLITPAVVSERLKIRGSLARAALQELLGKGLIKLVSKH 117

Query:   123 HAQVIYTRTTKGDD-PVA 139
              AQVIYTR TKG D P A
Sbjct:   118 RAQVIYTRNTKGGDAPAA 135

GO:0005730 "nucleolus" evidence=IEA

GO:0022627 "cytosolic small ribosomal subunit" evidence=IEA

WB|WBGene00004494 rps-25 [Caenorhabditis elegans (taxid:6239)]

 Score = 259 (96.2 bits), Expect = 2.6e-22, P = 2.6e-22
 Identities = 53/76 (69%), Positives = 60/76 (78%)

Query:    63 LNNQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKH 122
             LNN VLFD+A+YDKL KEV  YKLITPSVVSERLKVR SLA+  L+EL  KGL+K VV H
Sbjct:    40 LNNMVLFDQATYDKLYKEVITYKLITPSVVSERLKVRASLAKAGLKELQAKGLVKCVVHH 99

Query:   123 HAQVIYTRTTKGDDPV 138
             H QV+YTR TK  D +
Sbjct:   100 HGQVVYTRATKEADVI 115

GO:0040010 "positive regulation of growth rate" evidence=IMP

GO:0009792 "embryo development ending in birth or egg hatching" evidence=IMP

TAIR|locus:505006559 AT4G34555 "AT4G34555" [Arabidopsis thaliana (taxid:3702)]

 Score = 232 (86.7 bits), Expect = 1.9e-19, P = 1.9e-19
 Identities = 43/72 (59%), Positives = 57/72 (79%)

Query:    63 LNNQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKH 122
             +NN VLFD+A+YDKLL E P +KLITPS++S+RL++ GSLAR+A+ EL+ KG I+ V  H
Sbjct:    37 VNNMVLFDQATYDKLLSEAPKFKLITPSILSDRLRINGSLARRAIRELMAKGTIRMVSAH 96

Query:   123 HAQVIYTRTTKG 134
              +Q IYTR T G
Sbjct:    97 SSQQIYTRATHG 108

GO:0003735 "structural constituent of ribosome" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISM

GO:0005840 "ribosome" evidence=ISS

GO:0006412 "translation" evidence=ISS

GO:0022627 "cytosolic small ribosomal subunit" evidence=IDA

GO:0005794 "Golgi apparatus" evidence=RCA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P62851	RS25_HUMAN	No assigned EC number	0.8205	0.5611	0.624	yes	N/A
P62853	RS25_RAT	No assigned EC number	0.8205	0.5611	0.624	yes	N/A
P62852	RS25_MOUSE	No assigned EC number	0.8205	0.5611	0.624	yes	N/A
Q03409	RS25_DICDI	No assigned EC number	0.5765	0.7769	0.9818	yes	N/A
Q6PBI5	RS25_DANRE	No assigned EC number	0.8024	0.5827	0.6532	yes	N/A
Q9N9V4	RS25_LEIIN	No assigned EC number	0.4736	0.6834	0.7916	yes	N/A
P52821	RS25_CAEEL	No assigned EC number	0.6806	0.8273	0.9829	yes	N/A
P48588	RS25_DROME	No assigned EC number	0.8362	0.8273	0.9829	yes	N/A
Q56JX5	RS25_BOVIN	No assigned EC number	0.8205	0.5611	0.624	yes	N/A
Q8ISN9	RS25_BRABE	No assigned EC number	0.7672	0.8057	0.9105	N/A	N/A
Q962Q5	RS25_SPOFR	No assigned EC number	0.8487	0.8489	0.9915	N/A	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	139
pfam03297	105	pfam03297, Ribosomal_S25, S25 ribosomal protein	5e-47
COG4901	107	COG4901, COG4901, Ribosomal protein S25 [Translati	7e-17
PRK09334	86	PRK09334, PRK09334, 30S ribosomal protein S25e; Pr	1e-05

>gnl|CDD|217479 pfam03297, Ribosomal_S25, S25 ribosomal protein

 Score =  147 bits (372), Expect = 5e-47
 Identities = 78/112 (69%), Positives = 87/112 (77%), Gaps = 8/112 (7%)

Query: 21  PPKKDTKGGSSKQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDKASYDKLLKE 80
           PPKK  K        K  K     +GGKAKKKKWSKGKV+DKLNN VLFDKA+YDKLLKE
Sbjct: 2   PPKKQQK--------KAAKAAAASAGGKAKKKKWSKGKVKDKLNNAVLFDKATYDKLLKE 53

Query: 81  VPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTT 132
           VP YKLITPSV+S+RLK+ GSLAR+AL EL +KGLIK VVKH AQ+IYTR T
Sbjct: 54  VPTYKLITPSVLSDRLKINGSLARRALRELEEKGLIKPVVKHSAQLIYTRAT 105

Length = 105

>gnl|CDD|227238 COG4901, COG4901, Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]

 Score = 70.7 bits (173), Expect = 7e-17
 Identities = 37/101 (36%), Positives = 59/101 (58%)

Query: 33  QPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDKASYDKLLKEVPAYKLITPSVV 92
           Q  K +K ++  +G    KKKWSK K +++    V  D+   DK+ KEVP  +++TP V+
Sbjct: 6   QLSKEKKAEKAKAGTAKDKKKWSKKKKKEEARRAVTVDEELLDKIRKEVPRERVVTPYVL 65

Query: 93  SERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTTK 133
           + R  + GS+AR  L  L ++G+++ V K+  Q IYTR   
Sbjct: 66  ASRYGINGSVARIVLRHLEEEGVVQLVSKNRRQAIYTRAKA 106

Length = 107

>gnl|CDD|181784 PRK09334, PRK09334, 30S ribosomal protein S25e; Provisional

 Score = 40.8 bits (96), Expect = 1e-05
 Identities = 22/82 (26%), Positives = 43/82 (52%)

Query: 48  KAKKKKWSKGKVRDKLNNQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKAL 107
           K KKKK      ++  +  +  D+    ++ KEV   K++TP  ++ +  ++ S+A+K L
Sbjct: 3   KKKKKKEGSKTEKEIKSTIITLDEELLKRVAKEVKKEKIVTPYTLASKYGIKISVAKKVL 62

Query: 108 EELLQKGLIKQVVKHHAQVIYT 129
            EL ++G++    K+    IY 
Sbjct: 63  RELEKRGVLVLYSKNRRTPIYV 84

Length = 86

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	139
KOG1767|consensus	110		100.0
PF03297	105	Ribosomal_S25: S25 ribosomal protein; InterPro: IP	100.0
COG4901	107	Ribosomal protein S25 [Translation, ribosomal stru	100.0
PRK09334	86	30S ribosomal protein S25e; Provisional	100.0
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	97.03
PF00392	64	GntR: Bacterial regulatory proteins, gntR family;	96.97
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	96.78
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	96.72
cd07377	66	WHTH_GntR Winged helix-turn-helix (WHTH) DNA-bindi	96.64
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	96.63
PF14502	48	HTH_41: Helix-turn-helix domain	96.51
smart00418	66	HTH_ARSR helix_turn_helix, Arsenical Resistance Op	96.45
PF04703	62	FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.	96.17
PF02082	83	Rrf2: Transcriptional regulator; InterPro: IPR0009	95.96
cd00090	78	HTH_ARSR Arsenical Resistance Operon Repressor and	95.94
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	95.83
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	95.71
PF08222	61	HTH_CodY: CodY helix-turn-helix domain; InterPro:	95.69
PRK13509	251	transcriptional repressor UlaR; Provisional	95.69
smart00419	48	HTH_CRP helix_turn_helix, cAMP Regulatory protein.	95.64
TIGR02325	238	C_P_lyase_phnF phosphonates metabolism transcripti	95.61
PF09012	69	FeoC: FeoC like transcriptional regulator; InterPr	95.6
PRK09764	240	DNA-binding transcriptional repressor MngR; Provis	95.59
TIGR02404	233	trehalos_R_Bsub trehalose operon repressor, B. sub	95.59
PRK10906	252	DNA-binding transcriptional repressor GlpR; Provis	95.55
TIGR02018	230	his_ut_repres histidine utilization repressor, pro	95.54
PRK11534	224	DNA-binding transcriptional regulator CsiR; Provis	95.52
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	95.5
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	95.39
PRK03837	241	transcriptional regulator NanR; Provisional	95.35
PRK10225	257	DNA-binding transcriptional repressor UxuR; Provis	95.34
PRK14165	217	winged helix-turn-helix domain-containing protein/	95.33
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	95.29
TIGR02787	251	codY_Gpos GTP-sensing transcriptional pleiotropic	95.28
PRK10434	256	srlR DNA-bindng transcriptional repressor SrlR; Pr	95.28
PHA02943	165	hypothetical protein; Provisional	95.17
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	95.09
COG1349	253	GlpR Transcriptional regulators of sugar metabolis	95.0
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	94.96
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	94.94
PRK11402	241	DNA-binding transcriptional regulator FrlR; Provis	94.85
COG1522	154	Lrp Transcriptional regulators [Transcription]	94.8
COG3355	126	Predicted transcriptional regulator [Transcription	94.8
TIGR03338	212	phnR_burk phosphonate utilization associated trans	94.74
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	94.74
PRK10421	253	DNA-binding transcriptional repressor LldR; Provis	94.73
COG2188	236	PhnF Transcriptional regulators [Transcription]	94.72
PRK14999	241	histidine utilization repressor; Provisional	94.65
PRK04984	239	fatty acid metabolism regulator; Provisional	94.53
TIGR02702	203	SufR_cyano iron-sulfur cluster biosynthesis transc	94.5
PRK09990	251	DNA-binding transcriptional regulator GlcC; Provis	94.49
PF13730	55	HTH_36: Helix-turn-helix domain	94.47
PF09397	65	Ftsk_gamma: Ftsk gamma domain; InterPro: IPR018541	94.44
TIGR02337	118	HpaR homoprotocatechuate degradation operon regula	94.41
PRK09802	269	DNA-binding transcriptional regulator AgaR; Provis	94.4
PRK11014	141	transcriptional repressor NsrR; Provisional	94.38
TIGR03337	231	phnR transcriptional regulator protein. This famil	94.32
TIGR02812	235	fadR_gamma fatty acid metabolism transcriptional r	94.3
smart00843	63	Ftsk_gamma This domain directs oriented DNA transl	94.1
PRK11523	253	DNA-binding transcriptional repressor ExuR; Provis	94.09
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	93.83
PRK10079	241	phosphonate metabolism transcriptional regulator P	93.81
PRK09464	254	pdhR transcriptional regulator PdhR; Reviewed	93.74
PRK11512	144	DNA-binding transcriptional repressor MarR; Provis	93.67
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	93.58
TIGR01884	203	cas_HTH CRISPR locus-related DNA-binding protein.	93.37
TIGR02010	135	IscR iron-sulfur cluster assembly transcription fa	93.36
PRK10411	240	DNA-binding transcriptional activator FucR; Provis	93.16
PRK11414	221	colanic acid/biofilm transcriptional regulator; Pr	93.14
smart00347	101	HTH_MARR helix_turn_helix multiple antibiotic resi	92.98
PRK03573	144	transcriptional regulator SlyA; Provisional	92.97
TIGR00738	132	rrf2_super rrf2 family protein (putative transcrip	92.94
TIGR01610	95	phage_O_Nterm phage replication protein O, N-termi	92.8
PRK10870	176	transcriptional repressor MprA; Provisional	92.77
TIGR02944	130	suf_reg_Xantho FeS assembly SUF system regulator,	92.76
PRK04424	185	fatty acid biosynthesis transcriptional regulator;	92.73
PF04157	223	EAP30: EAP30/Vps36 family; InterPro: IPR007286 EAP	92.69
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	92.52
PF13545	76	HTH_Crp_2: Crp-like helix-turn-helix domain; PDB:	92.41
TIGR01889	109	Staph_reg_Sar staphylococcal accessory regulator f	92.08
smart00529	96	HTH_DTXR Helix-turn-helix diphteria tox regulatory	92.03
PF09756	188	DDRGK: DDRGK domain; InterPro: IPR019153 This is a	91.84
PRK03902	142	manganese transport transcriptional regulator; Pro	91.69
COG2512	258	Predicted membrane-associated trancriptional regul	91.54
COG1846	126	MarR Transcriptional regulators [Transcription]	91.52
COG4465	261	CodY Pleiotropic transcriptional repressor [Transc	91.49
COG1802	230	GntR Transcriptional regulators [Transcription]	91.24
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	91.16
cd07153	116	Fur_like Ferric uptake regulator(Fur) and related	90.72
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	90.61
COG1321	154	TroR Mn-dependent transcriptional regulator [Trans	90.53
cd04761	49	HTH_MerR-SF Helix-Turn-Helix DNA binding domain of	90.48
COG1725	125	Predicted transcriptional regulators [Transcriptio	90.48
PRK11050	152	manganese transport regulator MntR; Provisional	90.43
TIGR00122	69	birA_repr_reg BirA biotin operon repressor domain.	90.39
COG1959	150	Predicted transcriptional regulator [Transcription	90.34
PRK11920	153	rirA iron-responsive transcriptional regulator; Re	90.19
PRK04158	256	transcriptional repressor CodY; Validated	90.1
PRK09954	362	putative kinase; Provisional	90.1
PF01475	120	FUR: Ferric uptake regulator family; InterPro: IPR	89.97
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	89.92
PF14947	77	HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_	89.78
PF10007	92	DUF2250: Uncharacterized protein conserved in arch	89.68
PRK11169	164	leucine-responsive transcriptional regulator; Prov	89.54
PRK06266	178	transcription initiation factor E subunit alpha; V	89.45
PF08784	102	RPA_C: Replication protein A C terminal; InterPro:	89.44
TIGR00498	199	lexA SOS regulatory protein LexA. LexA acts as a h	89.41
PF00376	38	MerR: MerR family regulatory protein; InterPro: IP	89.33
smart00422	70	HTH_MERR helix_turn_helix, mercury resistance.	89.07
PRK15481	431	transcriptional regulatory protein PtsJ; Provision	88.97
PF05158	327	RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; Inter	88.73
cd01105	88	HTH_GlnR-like Helix-Turn-Helix DNA binding domain	88.26
PRK13777	185	transcriptional regulator Hpr; Provisional	88.14
PRK10857	164	DNA-binding transcriptional regulator IscR; Provis	87.91
TIGR02698	130	CopY_TcrY copper transport repressor, CopY/TcrY fa	87.9
PRK11179	153	DNA-binding transcriptional regulator AsnC; Provis	87.75
cd01279	98	HTH_HspR-like Helix-Turn-Helix DNA binding domain	87.71
cd04766	91	HTH_HspR Helix-Turn-Helix DNA binding domain of th	87.59
PRK11753	211	DNA-binding transcriptional dual regulator Crp; Pr	87.28
PRK15090	257	DNA-binding transcriptional regulator KdgR; Provis	87.01
PRK09834	263	DNA-binding transcriptional activator MhpR; Provis	86.33
PF12728	51	HTH_17: Helix-turn-helix domain	86.24
COG2186	241	FadR Transcriptional regulators [Transcription]	85.86
TIGR01764	49	excise DNA binding domain, excisionase family. An	85.51
PRK11886	319	bifunctional biotin--[acetyl-CoA-carboxylase] synt	85.27
PRK12423	202	LexA repressor; Provisional	85.19
cd04789	102	HTH_Cfa Helix-Turn-Helix DNA binding domain of the	85.06
cd04775	102	HTH_Cfa-like Helix-Turn-Helix DNA binding domain o	84.88
COG0789	124	SoxR Predicted transcriptional regulators [Transcr	84.45
PF03965	115	Penicillinase_R: Penicillinase repressor; InterPro	84.43
cd04762	49	HTH_MerR-trunc Helix-Turn-Helix DNA binding domain	84.27
PF13601	80	HTH_34: Winged helix DNA-binding domain; PDB: 1UB9	84.08
COG0735	145	Fur Fe2+/Zn2+ uptake regulation proteins [Inorgani	83.83
PF05732	165	RepL: Firmicute plasmid replication protein (RepL)	83.8
cd04767	120	HTH_HspR-like_MBC Helix-Turn-Helix DNA binding dom	83.75
cd04770	123	HTH_HMRTR Helix-Turn-Helix DNA binding domain of H	83.42
cd04768	96	HTH_BmrR-like Helix-Turn-Helix DNA binding domain	83.34
COG1733	120	Predicted transcriptional regulators [Transcriptio	83.3
PF13411	69	MerR_1: MerR HTH family regulatory protein; PDB: 2	83.22
PRK13918	202	CRP/FNR family transcriptional regulator; Provisio	83.12
PRK15002	154	redox-sensitivie transcriptional activator SoxR; P	82.64
PRK10681	252	DNA-binding transcriptional repressor DeoR; Provis	82.33
PRK00215	205	LexA repressor; Validated	82.05
PRK05472	213	redox-sensing transcriptional repressor Rex; Provi	81.98
PRK11569	274	transcriptional repressor IclR; Provisional	81.87
TIGR00373	158	conserved hypothetical protein TIGR00373. This fam	81.73
PF13814	191	Replic_Relax: Replication-relaxation	81.68
PRK09333	150	30S ribosomal protein S19e; Provisional	81.28
cd04769	116	HTH_MerR2 Helix-Turn-Helix DNA binding domain of M	80.8
TIGR02431	248	pcaR_pcaU beta-ketoadipate pathway transcriptional	80.27
TIGR02054	120	MerD mercuric resistence transcriptional repressor	80.23
cd04781	120	HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding dom	80.12
PRK10163	271	DNA-binding transcriptional repressor AllR; Provis	80.1
PF02002	105	TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024	80.09
COG1414	246	IclR Transcriptional regulator [Transcription]	80.01

>KOG1767|consensus

Probab=100.00  E-value=1.5e-49  Score=295.19  Aligned_cols=109  Identities=67%  Similarity=0.986  Sum_probs=102.5

Q ss_pred             CCCCCCCCCCCCCCcchhhhhhccCCCCccccccccchhhhhhhccceeeCHHHHHHHHhhCCCCeeechHHHHhhhccc
Q psy1871          20 HPPKKDTKGGSSKQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVR   99 (139)
Q Consensus        20 mppK~~~~~~~~~~~~~~~k~~~a~sggk~kKKKWSKgKvkdKlnn~Vl~Dk~tydKl~KEVpk~KlITPsvlseRlkI~   99 (139)
                      ||++++..+        +++++++.+||+++||||||||+|||+||+|+||++|||||++|||+|+|||||+|+|||+||
T Consensus         2 ~~~k~q~sK--------~~k~~~~~~ggk~~KKKWskGk~kdkvnn~Vlfdqatydkl~kevp~~k~it~svl~dRlkIn   73 (110)
T KOG1767|consen    2 MPKKQQLSK--------EKKAPAASSGGKAKKKKWSKGKVKDKVNNAVLFDQATYDKLLKEVPKYKLITPSVLSDRLKIN   73 (110)
T ss_pred             CccccccCc--------hhccccccCCCcccccccccchHHHHhhhheeecHHHHHHHHHhcccceeecHHHhhhhhhhc
Confidence            666655544        578889999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHHHHHHcCCeeEEeecCceEEEeccCCCCC
Q psy1871         100 GSLARKALEELLQKGLIKQVVKHHAQVIYTRTTKGDD  136 (139)
Q Consensus       100 ~SLARkaLreL~~kGlIk~Vskh~~q~IYtra~k~~~  136 (139)
                      |||||++||||.++|+|++|++||+|.||||+++.++
T Consensus        74 gsLAr~alr~L~~kG~Ik~Vs~h~~q~IYTrat~~~~  110 (110)
T KOG1767|consen   74 GSLARAALRELSNKGVIKQVSKHSKQVIYTRATASED  110 (110)
T ss_pred             hHHHHHHHHHHHhcchHHHHhhcchheeeccccccCC
Confidence            9999999999999999999999999999999998765

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

Probab=100.00  E-value=7e-48  Score=284.60  Aligned_cols=105  Identities=73%  Similarity=1.035  Sum_probs=79.6

Q ss_pred             CCCCCCCCCCCCCCcchhhhhhccCCCCccccccccchhhhhhhccceeeCHHHHHHHHhhCCCCeeechHHHHhhhccc
Q psy1871          20 HPPKKDTKGGSSKQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVR   99 (139)
Q Consensus        20 mppK~~~~~~~~~~~~~~~k~~~a~sggk~kKKKWSKgKvkdKlnn~Vl~Dk~tydKl~KEVpk~KlITPsvlseRlkI~   99 (139)
                      ||||+++.+        +++++++++||++++||||||+++||+||+|+||++|||+|++|||+|++||||+|||||+|+
T Consensus         1 M~pK~~~~k--------~~k~~~~~~~~k~~KKKwsKgk~kek~~~~v~~d~~~~~kl~kEV~~~K~ITp~~lserlkI~   72 (105)
T PF03297_consen    1 MPPKKQKSK--------KQKAKKAKSGGKAKKKKWSKGKVKEKLNNAVLFDKETYDKLLKEVPKMKLITPSVLSERLKIN   72 (105)
T ss_dssp             -----------------------TT------SSS--SS-SCHHHCCCSCCTCHHHHHHHHHCTTSSCECHHHHHHHHCCS
T ss_pred             CCCCcccch--------hhHHHHHhccCccccccccccchHHHHhcceEecHHHHHHHHHHhccCcEeeHHHHHHhHhhH
Confidence            999975554        467778999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHHHHHHcCCeeEEeecCceEEEeccC
Q psy1871         100 GSLARKALEELLQKGLIKQVVKHHAQVIYTRTT  132 (139)
Q Consensus       100 ~SLARkaLreL~~kGlIk~Vskh~~q~IYtra~  132 (139)
                      +||||++||||+++|+|++|++||+|.||||+|
T Consensus        73 ~SlAr~~Lr~L~~kG~Ik~V~k~~~~~IYtr~~  105 (105)
T PF03297_consen   73 GSLARKALRELESKGLIKPVSKHHRQRIYTRAT  105 (105)
T ss_dssp             CHHHHHHHHHHHHCCSSEEEECCTTCEEEEES-
T ss_pred             HHHHHHHHHHHHHCCCEEEEeccCCeEEEecCC
Confidence            999999999999999999999999999999986

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.

>COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=1.3e-35  Score=220.04  Aligned_cols=106  Identities=35%  Similarity=0.565  Sum_probs=99.7

Q ss_pred             CCCCCCCCCCCCCCcchhhhhhccCCCCccccccccchhhhhhhccceeeCHHHHHHHHhhCCCCeeechHHHHhhhccc
Q psy1871          20 HPPKKDTKGGSSKQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVR   99 (139)
Q Consensus        20 mppK~~~~~~~~~~~~~~~k~~~a~sggk~kKKKWSKgKvkdKlnn~Vl~Dk~tydKl~KEVpk~KlITPsvlseRlkI~   99 (139)
                      |||+.|-.+        +.|+.++.+|+++.+|||++++.+|...++|+||+++||++++|||++++||||+|++||+|+
T Consensus         1 m~pk~qlsK--------~~Ka~~~~a~~~k~kKK~~~k~~k~~~~~av~vdee~~~ki~KEV~~~r~VTpy~la~r~gI~   72 (107)
T COG4901           1 MAPKSQLSK--------EKKAEKAKAGTAKDKKKWSKKKKKEEARRAVTVDEELLDKIRKEVPRERVVTPYVLASRYGIN   72 (107)
T ss_pred             CcchhHHHH--------HHHHHHHHhhhhhhhhccccccccchhhhhhhccHHHHHHHHHhcccceeecHHHHHHHhccc
Confidence            788866654        577788899999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHHHHHHcCCeeEEeecCceEEEeccCC
Q psy1871         100 GSLARKALEELLQKGLIKQVVKHHAQVIYTRTTK  133 (139)
Q Consensus       100 ~SLARkaLreL~~kGlIk~Vskh~~q~IYtra~k  133 (139)
                      +||||.+||+|+++|+|++|++||||.||+|+..
T Consensus        73 ~SvAr~vLR~LeeeGvv~lvsknrR~~IY~~a~a  106 (107)
T COG4901          73 GSVARIVLRHLEEEGVVQLVSKNRRQAIYTRAKA  106 (107)
T ss_pred             hHHHHHHHHHHHhCCceeeeccCccceeeecccC
Confidence            9999999999999999999999999999999764

>PRK09334 30S ribosomal protein S25e; Provisional

Probab=100.00  E-value=7.6e-35  Score=209.23  Aligned_cols=81  Identities=25%  Similarity=0.374  Sum_probs=76.7

Q ss_pred             cccccchhhhhhhccceeeCHHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871          51 KKKWSKGKVRDKLNNQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR  130 (139)
Q Consensus        51 KKKWSKgKvkdKlnn~Vl~Dk~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr  130 (139)
                      +|+=.++..++.+||+|+||++|||||++|||+|++||||+|||||+|++||||++||||+++|+|++|++||+|.|||+
T Consensus         6 ~k~~~~~~~~~~~~n~v~~dk~t~dkl~kEV~~~K~ITps~lserlkI~~SlAr~~Lr~L~~kG~Ik~V~~~~~q~IYt~   85 (86)
T PRK09334          6 KKKEGSKTEKEIKSTIITLDEELLKRVAKEVKKEKIVTPYTLASKYGIKISVAKKVLRELEKRGVLVLYSKNRRTPIYVP   85 (86)
T ss_pred             cccccccchhhhhhceeecCHHHHHHHHHHhccCcEEcHHHHHHHhcchHHHHHHHHHHHHHCCCEEEEecCCCeEEecc
Confidence            34556777899999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             c
Q psy1871         131 T  131 (139)
Q Consensus       131 a  131 (139)
                      +
T Consensus        86 ~   86 (86)
T PRK09334         86 A   86 (86)
T ss_pred             C
Confidence            4

>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=97.03  E-value=0.00074  Score=41.78  Aligned_cols=42  Identities=31%  Similarity=0.425  Sum_probs=32.7

Q ss_pred             HHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCee
Q psy1871          76 KLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIK  117 (139)
Q Consensus        76 Kl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk  117 (139)
                      +|+..+-...-+|...||++++++.+-+.+.|++|+++|+|+
T Consensus         7 ~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~~g~I~   48 (48)
T PF13412_consen    7 KILNYLRENPRITQKELAEKLGISRSTVNRYLKKLEEKGLIE   48 (48)
T ss_dssp             HHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHCcCcC
Confidence            344444334448999999999999999999999999999985

...

>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=96.97  E-value=0.0023  Score=41.84  Aligned_cols=49  Identities=27%  Similarity=0.373  Sum_probs=36.7

Q ss_pred             HHHHHHHhhCCC-----Ceee-chHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          72 ASYDKLLKEVPA-----YKLI-TPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        72 ~tydKl~KEVpk-----~KlI-TPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      ..|+.|..+|-.     -..+ |-..||++|+|+-+.+|++|+.|++.|+|....
T Consensus         4 ~i~~~l~~~I~~g~~~~g~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~~~~   58 (64)
T PF00392_consen    4 QIYDQLRQAILSGRLPPGDRLPSERELAERYGVSRTTVREALRRLEAEGLIERRP   58 (64)
T ss_dssp             HHHHHHHHHHHTTSS-TTSBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET
T ss_pred             HHHHHHHHHHHcCCCCCCCEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEEEEC
Confidence            345555554433     2455 999999999999999999999999999997654

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 ....

>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=96.78  E-value=0.0026  Score=41.53  Aligned_cols=45  Identities=22%  Similarity=0.356  Sum_probs=38.4

Q ss_pred             HHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          75 DKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        75 dKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      ++|+.-+.....+|...||+.|+|+-+-+|+=|.+|+++|+|..+
T Consensus         3 ~~Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i~r~   47 (57)
T PF08220_consen    3 QQILELLKEKGKVSVKELAEEFGVSEMTIRRDLNKLEKQGLIKRT   47 (57)
T ss_pred             HHHHHHHHHcCCEEHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            345555555678999999999999999999999999999997654

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

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=96.72  E-value=0.0071  Score=37.25  Aligned_cols=37  Identities=27%  Similarity=0.369  Sum_probs=32.2

Q ss_pred             CCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          83 AYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        83 k~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      +..+-|...||++|+|+-+-.+++|+.|++.|+|..+
T Consensus        17 ~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~~~   53 (60)
T smart00345       17 GDKLPSERELAAQLGVSRTTVREALSRLEAEGLVQRR   53 (60)
T ss_pred             CCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            3344489999999999999999999999999998654

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

Probab=96.64  E-value=0.0081  Score=37.68  Aligned_cols=49  Identities=27%  Similarity=0.361  Sum_probs=38.6

Q ss_pred             HHHHHHHHhhCC------CCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          71 KASYDKLLKEVP------AYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        71 k~tydKl~KEVp------k~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      +++++.|...+.      .-.+.|...||+.++|+-+-++++|..|++.|+|...
T Consensus         4 ~~~~~~i~~~i~~~~~~~~~~~~~~~~la~~~~is~~~v~~~l~~L~~~G~i~~~   58 (66)
T cd07377           4 EQIADQLREAILSGELKPGDRLPSERELAEELGVSRTTVREALRELEAEGLVERR   58 (66)
T ss_pred             HHHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence            456666666632      2344569999999999999999999999999998654

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

>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=96.63  E-value=0.0076  Score=39.62  Aligned_cols=46  Identities=24%  Similarity=0.322  Sum_probs=38.5

Q ss_pred             CCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871          83 AYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR  130 (139)
Q Consensus        83 k~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr  130 (139)
                      ...=.|...||+.++|.-+-+..+|+.|+++|+|......  ..+|..
T Consensus        19 ~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~~~~--~~~Y~a   64 (68)
T PF01978_consen   19 KNGPATAEEIAEELGISRSTVYRALKSLEEKGLVEREEGR--PKVYRA   64 (68)
T ss_dssp             HHCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEEEC--CEEEEE
T ss_pred             HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcCc--eEEEEE
Confidence            3344799999999999999999999999999999888743  456653

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.

>PF14502 HTH_41: Helix-turn-helix domain

Probab=96.51  E-value=0.0058  Score=40.20  Aligned_cols=41  Identities=29%  Similarity=0.284  Sum_probs=37.4

Q ss_pred             CCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecC
Q psy1871          83 AYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHH  123 (139)
Q Consensus        83 k~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~  123 (139)
                      .-++=|.+.+|++|++....-..||+.|++.|.|.+.++.|
T Consensus         3 GdRi~tI~e~~~~~~vs~GtiQ~Alk~Le~~gaI~Le~rGh   43 (48)
T PF14502_consen    3 GDRIPTISEYSEKFGVSRGTIQNALKFLEENGAIKLESRGH   43 (48)
T ss_pred             CcccCCHHHHHHHhCcchhHHHHHHHHHHHCCcEEeeecCc
Confidence            34677999999999999999999999999999999998766

>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor

Probab=96.45  E-value=0.011  Score=35.94  Aligned_cols=45  Identities=20%  Similarity=0.263  Sum_probs=37.2

Q ss_pred             eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871          85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR  130 (139)
Q Consensus        85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr  130 (139)
                      .-+|...|++.++++-+-++++|+.|.++|+|.....++ ...|.-
T Consensus         9 ~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~~~~~-~~~~~~   53 (66)
T smart00418        9 GELCVCELAEILGLSQSTVSHHLKKLREAGLVESRREGK-RVYYSL   53 (66)
T ss_pred             CCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeeecCC-EEEEEE
Confidence            346999999999999999999999999999998765544 445543

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

Probab=96.17  E-value=0.011  Score=40.12  Aligned_cols=43  Identities=19%  Similarity=0.251  Sum_probs=33.4

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEE
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIY  128 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IY  128 (139)
                      -+|...||+.++|+.+-||..|..|++.|.|+.+-..+....|
T Consensus        15 p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~~~~~~rG~~~~   57 (62)
T PF04703_consen   15 PLKTREIADALGLSIYQARYYLEKLEKEGKVERSPVRRGKSTY   57 (62)
T ss_dssp             -EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEES-SSSSS-E
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCCCccee
Confidence            3788999999999999999999999999999986543333334

>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=95.96  E-value=0.034  Score=38.11  Aligned_cols=51  Identities=27%  Similarity=0.347  Sum_probs=38.0

Q ss_pred             hCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871          80 EVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR  130 (139)
Q Consensus        80 EVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr  130 (139)
                      ..+....+|...||++++++-+..+++|+.|.+.|+|.-....+....-.|
T Consensus        19 ~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~~G~~GGy~L~~   69 (83)
T PF02082_consen   19 RHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIESSRGRGGGYRLAR   69 (83)
T ss_dssp             CTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETSTTSEEEESS
T ss_pred             hCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEecCCCCCceeecC
Confidence            344555599999999999999999999999999999876654434333333

(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.

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

Probab=95.94  E-value=0.032  Score=34.63  Aligned_cols=44  Identities=30%  Similarity=0.412  Sum_probs=37.6

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT  131 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra  131 (139)
                      +|...|++.++|..+-++++|+.|++.|+|...... +...|.-.
T Consensus        21 ~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~~~-~~~~~~~~   64 (78)
T cd00090          21 LTVSELAERLGLSQSTVSRHLKKLEEAGLVESRREG-RRVYYSLT   64 (78)
T ss_pred             cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEEEec-cEEEEEeC
Confidence            899999999999999999999999999999887554 44555544

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.

>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=95.83  E-value=0.026  Score=35.66  Aligned_cols=34  Identities=29%  Similarity=0.450  Sum_probs=31.3

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      +|++.|++.+++.-+-.-++++.|+++|+|....
T Consensus        22 ~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~~   55 (62)
T PF12802_consen   22 LTQSELAERLGISKSTVSRIVKRLEKKGLVERER   55 (62)
T ss_dssp             EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeC
Confidence            6999999999999999999999999999998864

...

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

Probab=95.71  E-value=0.042  Score=35.20  Aligned_cols=47  Identities=23%  Similarity=0.328  Sum_probs=35.0

Q ss_pred             CCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe--ecCceEEEe
Q psy1871          83 AYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV--KHHAQVIYT  129 (139)
Q Consensus        83 k~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs--kh~~q~IYt  129 (139)
                      ...-+|+..|++.+++.-+-+.++|+.|+++|+|....  .++|..+|.
T Consensus        15 ~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~~~~~d~R~~~~~   63 (68)
T PF13463_consen   15 SDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVEKERDPHDKRSKRYR   63 (68)
T ss_dssp             -TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEESSCTTSEEEE
T ss_pred             cCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecCCCCcCCeeEEE
Confidence            34567899999999999999999999999999997774  335544443

>PF08222 HTH_CodY: CodY helix-turn-helix domain; InterPro: IPR013198 This family consists of the C-terminal helix-turn-helix domain found in several bacterial GTP-sensing transcriptional pleiotropic repressor CodY proteins

Probab=95.69  E-value=0.027  Score=38.77  Aligned_cols=34  Identities=24%  Similarity=0.378  Sum_probs=29.0

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      ++|.|.|||+++|+-|+--.+||-|++-|+|..-
T Consensus         4 ~lvas~iAd~~GiTRSvIVNALRKleSaGvIesr   37 (61)
T PF08222_consen    4 RLVASKIADRVGITRSVIVNALRKLESAGVIESR   37 (61)
T ss_dssp             EE-HHHHHHHHT--HHHHHHHHHHHHHTTSEEEE
T ss_pred             eehHHHHHHHhCccHHHHHHHHHHHHhcCceeec
Confidence            6899999999999999999999999999999843

CodY has been found to repress the dipeptide transport operon (dpp) of Bacillus subtilis in nutrient-rich conditions []. The CodY protein also has a repressor effect on many genes in Lactococcus lactis during growth in milk [].; PDB: 2B0L_C.

>PRK13509 transcriptional repressor UlaR; Provisional

Probab=95.69  E-value=0.019  Score=47.01  Aligned_cols=49  Identities=27%  Similarity=0.361  Sum_probs=44.2

Q ss_pred             HHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          71 KASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        71 k~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      .+-.++|++.+-....+|...|+++|+|+.+-+|+=|++|+++|+|..+
T Consensus         4 ~~R~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le~~g~i~r~   52 (251)
T PRK13509          4 AQRHQILLELLAQLGFVTVEKVIERLGISPATARRDINKLDESGKLKKV   52 (251)
T ss_pred             HHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence            3556778888888999999999999999999999999999999999764

>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein

Probab=95.64  E-value=0.024  Score=33.85  Aligned_cols=32  Identities=25%  Similarity=0.414  Sum_probs=30.2

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQ  118 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~  118 (139)
                      +|...||+.++++-+-+.++|+.|++.|+|..
T Consensus         9 ~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~~   40 (48)
T smart00419        9 LTRQEIAELLGLTRETVSRTLKRLEKEGLISR   40 (48)
T ss_pred             cCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence            68899999999999999999999999999964

>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF

Probab=95.61  E-value=0.035  Score=43.55  Aligned_cols=39  Identities=23%  Similarity=0.371  Sum_probs=35.7

Q ss_pred             CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          82 PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        82 pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      |+.+|=|=..|+++|+|+-...|+||.+|+.+|+|...-
T Consensus        28 ~G~~LPsE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~~   66 (238)
T TIGR02325        28 AGDYLPAEMQLAERFGVNRHTVRRAIAALVERGLLRAEQ   66 (238)
T ss_pred             CCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence            567888999999999999999999999999999987653

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.

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

Probab=95.60  E-value=0.012  Score=39.35  Aligned_cols=47  Identities=15%  Similarity=0.245  Sum_probs=36.7

Q ss_pred             HHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecC
Q psy1871          77 LLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHH  123 (139)
Q Consensus        77 l~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~  123 (139)
                      |..-+-....+|...||.+|++.-+..+..|..|+.+|.|..+..+.
T Consensus         5 i~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~~~~~   51 (69)
T PF09012_consen    5 IRDYLRERGRVSLAELAREFGISPEAVEAMLEQLIRKGYIRKVDMSS   51 (69)
T ss_dssp             HHHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEEEEEE-
T ss_pred             HHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEecCCC
Confidence            33334455788999999999999999999999999999999987554

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

>PRK09764 DNA-binding transcriptional repressor MngR; Provisional

Probab=95.59  E-value=0.036  Score=44.25  Aligned_cols=39  Identities=23%  Similarity=0.387  Sum_probs=35.2

Q ss_pred             CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          82 PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        82 pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      |+.++=|=..|+++|+|+-...|+||.+|+.+|+|..+-
T Consensus        25 ~G~~LPsE~eL~~~~~VSR~TvR~Al~~L~~eGli~r~~   63 (240)
T PRK09764         25 PGDALPTESALQTEFGVSRVTVRQALRQLVEQQILESIQ   63 (240)
T ss_pred             CCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence            456787999999999999999999999999999997654

>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B

Probab=95.59  E-value=0.036  Score=43.75  Aligned_cols=39  Identities=21%  Similarity=0.244  Sum_probs=35.4

Q ss_pred             CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          82 PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        82 pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      |..+|=|=..|+++|+|+-...|+||++|+++|+|..+.
T Consensus        20 ~G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~~   58 (233)
T TIGR02404        20 EGDYLPSEHELMDQYGASRETVRKALNLLTEAGYIQKIQ   58 (233)
T ss_pred             CCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeC
Confidence            467888999999999999999999999999999987654

subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.

>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional

Probab=95.55  E-value=0.022  Score=46.75  Aligned_cols=48  Identities=17%  Similarity=0.250  Sum_probs=42.9

Q ss_pred             HHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          72 ASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        72 ~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      +-.++|+..+.....+|...|+++|+|+-+-+|+=|.+|+++|+|..+
T Consensus         5 ~R~~~Il~~l~~~~~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l~r~   52 (252)
T PRK10906          5 QRHDAIIELVKQQGYVSTEELVEHFSVSPQTIRRDLNDLAEQNKILRH   52 (252)
T ss_pred             HHHHHHHHHHHHcCCEeHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence            456777788878889999999999999999999999999999998764

>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial

Probab=95.54  E-value=0.038  Score=43.64  Aligned_cols=39  Identities=18%  Similarity=0.295  Sum_probs=35.0

Q ss_pred             CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          82 PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        82 pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      |+.+|=|-..||++|+|+-...|+||.+|+++|+|..+-
T Consensus        21 ~g~~LPsE~eLa~~~~VSR~TVR~Al~~L~~eGli~r~~   59 (230)
T TIGR02018        21 PGHRIPSEHELVAQYGCSRMTVNRALRELTDAGLLERRQ   59 (230)
T ss_pred             CCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence            567888999999999999999999999999999986543

This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.

>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional

Probab=95.52  E-value=0.032  Score=43.71  Aligned_cols=52  Identities=23%  Similarity=0.266  Sum_probs=42.8

Q ss_pred             eCHHHHHHHHhhCCC------CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEee
Q psy1871          69 FDKASYDKLLKEVPA------YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK  121 (139)
Q Consensus        69 ~Dk~tydKl~KEVpk------~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk  121 (139)
                      +-+..|+.|...|-+      .++ +...||++|+|+-+--|-||+.|+..|+|..+-+
T Consensus         8 ~~~~vy~~i~~~I~~g~l~pG~~L-~e~eLae~lgVSRtpVREAL~~L~~eGlv~~~~~   65 (224)
T PRK11534          8 TALDGYRWLKNDIIRGNFQPDEKL-RMSLLTSRYALGVGPLREALSQLVAERLVTVVNQ   65 (224)
T ss_pred             hhHHHHHHHHHHHHhCCCCCCCcC-CHHHHHHHHCCChHHHHHHHHHHHHCCCEEEeCC
Confidence            345678888887654      444 7789999999999999999999999999987543

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor

Probab=95.50  E-value=0.063  Score=32.13  Aligned_cols=45  Identities=22%  Similarity=0.317  Sum_probs=37.1

Q ss_pred             HHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          72 ASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        72 ~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      ..++-|..+    ..+|...|++.|++.-+-+++.|..|++.|+|....
T Consensus         4 ~il~~l~~~----~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~~~   48 (53)
T smart00420        4 QILELLAQQ----GKVSVEELAELLGVSEMTIRRDLNKLEEQGLLTRVH   48 (53)
T ss_pred             HHHHHHHHc----CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEee
Confidence            455555543    347999999999999999999999999999997654

>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=95.39  E-value=0.028  Score=37.29  Aligned_cols=37  Identities=24%  Similarity=0.307  Sum_probs=32.5

Q ss_pred             CCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          83 AYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        83 k~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      .-..|++..||++|+|+-+-+-..|+.|+++|+|...
T Consensus        19 ~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~~~   55 (60)
T PF01325_consen   19 EGGPVRTKDIAERLGVSPPTVTEMLKRLAEKGLVEYE   55 (60)
T ss_dssp             CTSSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCCccHHHHHHHHCCChHHHHHHHHHHHHCCCEEec
Confidence            4567899999999999999999999999999998653

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 ....

>PRK03837 transcriptional regulator NanR; Provisional

Probab=95.35  E-value=0.035  Score=43.59  Aligned_cols=50  Identities=20%  Similarity=0.239  Sum_probs=41.1

Q ss_pred             HHHHHHHHhhCCC------CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          71 KASYDKLLKEVPA------YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        71 k~tydKl~KEVpk------~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      +..|+.|...|-.      .++-+-..||++|+|+-+..|.||+.|+.+|+|...-
T Consensus        16 ~~v~~~l~~~I~~g~l~pG~~Lp~E~~Lae~~gVSRt~VREAL~~L~~eGlv~~~~   71 (241)
T PRK03837         16 EEVEERLEQMIRSGEFGPGDQLPSERELMAFFGVGRPAVREALQALKRKGLVQISH   71 (241)
T ss_pred             HHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEec
Confidence            4567777766544      3444899999999999999999999999999998754

>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional

Probab=95.34  E-value=0.048  Score=43.66  Aligned_cols=50  Identities=22%  Similarity=0.187  Sum_probs=41.4

Q ss_pred             HHHHHHHHhhCCC------CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          71 KASYDKLLKEVPA------YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        71 k~tydKl~KEVpk------~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      ...|+.|...|-.      .++-|-..||++|+|+-+-.|.||+.|+..|+|...-
T Consensus        12 ~~v~~~l~~~I~~g~l~pG~~LpsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~   67 (257)
T PRK10225         12 QEVGAMIRDLIIKTPYNPGERLPPEREIAEMLDVTRTVVREALIMLEIKGLVEVRR   67 (257)
T ss_pred             HHHHHHHHHHHHhCCCCCCCcCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEec
Confidence            4567777776643      4555788999999999999999999999999998654

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

Probab=95.33  E-value=0.042  Score=45.22  Aligned_cols=50  Identities=20%  Similarity=0.238  Sum_probs=42.2

Q ss_pred             hCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEe
Q psy1871          80 EVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYT  129 (139)
Q Consensus        80 EVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYt  129 (139)
                      .+.+.--||.+.||++++++-+-+.+.|+.|+++|+|......+.+.|+.
T Consensus        15 ~l~~~~~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~L   64 (217)
T PRK14165         15 AVNNTVKISSSEFANHTGTSSKTAARILKQLEDEGYITRTIVPRGQLITI   64 (217)
T ss_pred             ccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEEcCCceEEEE
Confidence            34444568999999999999999999999999999999876666676665

>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=95.29  E-value=0.047  Score=34.67  Aligned_cols=36  Identities=22%  Similarity=0.305  Sum_probs=33.0

Q ss_pred             eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      --+|...||+.++++-+-+.++|+.|+++|+|....
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            447999999999999999999999999999998754

>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY

Probab=95.28  E-value=0.048  Score=46.36  Aligned_cols=59  Identities=19%  Similarity=0.326  Sum_probs=50.4

Q ss_pred             hhccceeeCHHHHHHHHhhCCCC-eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          62 KLNNQVLFDKASYDKLLKEVPAY-KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        62 Klnn~Vl~Dk~tydKl~KEVpk~-KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      .++..-+-.-+..++|+.+.... -.++-+.||++++|+-|..|.+||.|++.|+|..-.
T Consensus       173 Ai~tLSySEleAv~~IL~~L~~~egrlse~eLAerlGVSRs~ireAlrkLE~aGvIe~r~  232 (251)
T TIGR02787       173 AINTLSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRS  232 (251)
T ss_pred             HHHhccHhHHHHHHHHHHHhccccccccHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecc
Confidence            34444455678899999999994 889999999999999999999999999999997543

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

>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional

Probab=95.28  E-value=0.024  Score=46.45  Aligned_cols=48  Identities=15%  Similarity=0.169  Sum_probs=43.0

Q ss_pred             HHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          72 ASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        72 ~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      +=.++|+..+....-||...||+.|+|+.+-.|+=|++|+++|+|..+
T Consensus         5 eR~~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~g~l~r~   52 (256)
T PRK10434          5 QRQAAILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVILEHAGTVIRT   52 (256)
T ss_pred             HHHHHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEE
Confidence            345678888888888999999999999999999999999999998775

>PHA02943 hypothetical protein; Provisional

Probab=95.17  E-value=0.066  Score=43.09  Aligned_cols=55  Identities=29%  Similarity=0.303  Sum_probs=45.6

Q ss_pred             HHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871          75 DKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR  130 (139)
Q Consensus        75 dKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr  130 (139)
                      +.|+.-+ +.-.-|.+.||++|+++-|-|+-+|.-||++|.|+.|..+.....+.+
T Consensus        14 ~eILE~L-k~G~~TtseIAkaLGlS~~qa~~~LyvLErEG~VkrV~~G~~tyw~l~   68 (165)
T PHA02943         14 IKTLRLL-ADGCKTTSRIANKLGVSHSMARNALYQLAKEGMVLKVEIGRAAIWCLD   68 (165)
T ss_pred             HHHHHHH-hcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCceEEEeecceEEEEEC
Confidence            3444444 667779999999999999999999999999999999987776655554

>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=95.09  E-value=0.05  Score=34.35  Aligned_cols=32  Identities=22%  Similarity=0.416  Sum_probs=29.4

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQ  118 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~  118 (139)
                      +|.+.||+++++.-|-+.++|+.|++.|+|..
T Consensus        19 ~t~~eia~~~gl~~stv~r~L~tL~~~g~v~~   50 (52)
T PF09339_consen   19 LTLSEIARALGLPKSTVHRLLQTLVEEGYVER   50 (52)
T ss_dssp             EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHHHCcCeec
Confidence            69999999999999999999999999999864

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.

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

Probab=95.00  E-value=0.034  Score=45.66  Aligned_cols=47  Identities=23%  Similarity=0.315  Sum_probs=43.3

Q ss_pred             HHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          73 SYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        73 tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      =.++|+..+-....|+...||++|+|+-...|+=|++|+++|++..+
T Consensus         6 R~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l~R~   52 (253)
T COG1349           6 RHQKILELLKEKGKVSVEELAELFGVSEMTIRRDLNELEEQGLLLRV   52 (253)
T ss_pred             HHHHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhHHHHHHCCcEEEE
Confidence            45788888999999999999999999999999999999999998765

>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=94.96  E-value=0.045  Score=35.43  Aligned_cols=50  Identities=22%  Similarity=0.251  Sum_probs=40.6

Q ss_pred             HHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEee
Q psy1871          72 ASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK  121 (139)
Q Consensus        72 ~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk  121 (139)
                      ++--+|+..+....=.|.+.|+++++|.-+.+..=|+.|++-|+|..+-.
T Consensus        10 p~R~~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~~~~~   59 (61)
T PF12840_consen   10 PTRLRILRLLASNGPMTVSELAEELGISQSTVSYHLKKLEEAGLIEVERE   59 (61)
T ss_dssp             HHHHHHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE
T ss_pred             HHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEecc
Confidence            55556666664555679999999999999999999999999999988754

...

>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=94.94  E-value=0.051  Score=34.24  Aligned_cols=34  Identities=32%  Similarity=0.462  Sum_probs=31.1

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      +|++.||+.+++.-|-.-++++.|+++|+|..-.
T Consensus        18 ~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~~   51 (59)
T PF01047_consen   18 ITQSELAEKLGISRSTVTRIIKRLEKKGLIERER   51 (59)
T ss_dssp             EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCHHHHHHHHCCChhHHHHHHHHHHHCCCEEecc
Confidence            8999999999999999999999999999998753

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 ....

>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional

Probab=94.85  E-value=0.064  Score=42.65  Aligned_cols=38  Identities=18%  Similarity=0.302  Sum_probs=34.9

Q ss_pred             CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          82 PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        82 pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      |+.+|=|=..||++|+|+-...|+||.+|+++|+|...
T Consensus        29 ~g~kLPsE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~   66 (241)
T PRK11402         29 AGQQIPTENELCTQYNVSRITIRKAISDLVADGVLIRW   66 (241)
T ss_pred             CCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            35689999999999999999999999999999998764

>COG1522 Lrp Transcriptional regulators [Transcription]

Probab=94.80  E-value=0.076  Score=38.95  Aligned_cols=48  Identities=21%  Similarity=0.333  Sum_probs=43.1

Q ss_pred             eCHHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          69 FDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        69 ~Dk~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      +|...++-|+.+.+    ++-..||++++++.+-.+.-++.|++.|+|+-+.
T Consensus         9 ~D~~IL~~L~~d~r----~~~~eia~~lglS~~~v~~Ri~~L~~~GiI~~~~   56 (154)
T COG1522           9 IDRRILRLLQEDAR----ISNAELAERVGLSPSTVLRRIKRLEEEGVIKGYT   56 (154)
T ss_pred             HHHHHHHHHHHhCC----CCHHHHHHHHCCCHHHHHHHHHHHHHCCceeeEE
Confidence            56777888888887    8999999999999999999999999999998763

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=94.80  E-value=0.14  Score=39.45  Aligned_cols=61  Identities=25%  Similarity=0.347  Sum_probs=49.2

Q ss_pred             eeCHHHHHHHHh-hCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe----ecCceEEEeccC
Q psy1871          68 LFDKASYDKLLK-EVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV----KHHAQVIYTRTT  132 (139)
Q Consensus        68 l~Dk~tydKl~K-EVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs----kh~~q~IYtra~  132 (139)
                      -.|-+.|..|+. +-|    .|.-.|||++++.-|.+.++|+-|.+.|+|...-    +++.-.||-+..
T Consensus        27 ~~Dv~v~~~LL~~~~~----~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~~~~Ggy~yiY~~i~   92 (126)
T COG3355          27 ELDVEVYKALLEENGP----LTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNLKGGGYYYLYKPID   92 (126)
T ss_pred             HHHHHHHHHHHhhcCC----cCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeeccCCCceeEEEecCC
Confidence            357788999994 544    4999999999999999999999999999998863    345556775543

>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator

Probab=94.74  E-value=0.08  Score=40.91  Aligned_cols=49  Identities=27%  Similarity=0.415  Sum_probs=39.8

Q ss_pred             CHHHHHHHHhhC------CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          70 DKASYDKLLKEV------PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        70 Dk~tydKl~KEV------pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      ....|+.|...|      |+.++ +-..||++|+|+-+--|.||+.|+..|+|...
T Consensus        13 ~~~v~~~l~~~I~~g~l~pG~~L-~e~~La~~lgVSRtpVReAL~~L~~eGlv~~~   67 (212)
T TIGR03338        13 TTLVQDEIERAILSGELPPGAKL-NESDIAARLGVSRGPVREAFRALEEAGLVRNE   67 (212)
T ss_pred             HHHHHHHHHHHHHcCCCCCCCEe-cHHHHHHHhCCChHHHHHHHHHHHHCCCEEEe
Confidence            345666666665      34566 88999999999999999999999999998754

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

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

Probab=94.74  E-value=0.06  Score=36.21  Aligned_cols=34  Identities=18%  Similarity=0.138  Sum_probs=31.7

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      +|...||+.++|.-+-++++|..|+++|+|....
T Consensus        23 ~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~~~   56 (68)
T smart00550       23 STALQLAKNLGLPKKEVNRVLYSLEKKGKVCKQG   56 (68)
T ss_pred             cCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence            8999999999999999999999999999986643

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

>PRK10421 DNA-binding transcriptional repressor LldR; Provisional

Probab=94.73  E-value=0.089  Score=42.12  Aligned_cols=50  Identities=20%  Similarity=0.256  Sum_probs=41.3

Q ss_pred             HHHHHHHHhhCC------CCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          71 KASYDKLLKEVP------AYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        71 k~tydKl~KEVp------k~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      +..|+.|...|-      ..+|-|-..||++|+|+-+-.|.||+.|+..|+|...-
T Consensus         5 ~~v~~~L~~~I~~g~l~pG~~LpsE~eLae~~gVSRtpVREAL~~Le~~GlV~~~~   60 (253)
T PRK10421          5 DEVADRVRALIEEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRR   60 (253)
T ss_pred             HHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEeC
Confidence            466777777763      34555789999999999999999999999999997543

>COG2188 PhnF Transcriptional regulators [Transcription]

Probab=94.72  E-value=0.062  Score=43.33  Aligned_cols=40  Identities=35%  Similarity=0.471  Sum_probs=36.1

Q ss_pred             CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEee
Q psy1871          82 PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK  121 (139)
Q Consensus        82 pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk  121 (139)
                      |+.++=|=..||++|+|+=...|+||++|+++|+|....+
T Consensus        27 ~G~~LPsE~eLa~~f~VSR~TvRkAL~~L~~eGli~r~~G   66 (236)
T COG2188          27 PGDKLPSERELAEQFGVSRMTVRKALDELVEEGLIVRRQG   66 (236)
T ss_pred             CCCCCCCHHHHHHHHCCcHHHHHHHHHHHHHCCcEEEEec
Confidence            4578889999999999999999999999999999987654

>PRK14999 histidine utilization repressor; Provisional

Probab=94.65  E-value=0.079  Score=42.20  Aligned_cols=38  Identities=16%  Similarity=0.284  Sum_probs=34.3

Q ss_pred             CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          82 PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        82 pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      |+.+|=|=..||++|+|+-...|+||.+|+.+|+|...
T Consensus        32 ~G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~   69 (241)
T PRK14999         32 PHDRIPSEAELVAQYGFSRMTINRALRELTDEGWLVRL   69 (241)
T ss_pred             CCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            45678799999999999999999999999999998553

>PRK04984 fatty acid metabolism regulator; Provisional

Probab=94.53  E-value=0.073  Score=41.96  Aligned_cols=49  Identities=18%  Similarity=0.272  Sum_probs=39.5

Q ss_pred             HHHHHHHHhhC------CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          71 KASYDKLLKEV------PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        71 k~tydKl~KEV------pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      +..|+.|...|      |+.+|-|-..||++|+|+-+..|.||+.|+..|+|...
T Consensus        10 ~~~~~~l~~~I~~g~l~pG~~LPsE~eLae~~gVSRt~VReAL~~L~~eGlv~~~   64 (239)
T PRK04984         10 GFAEEYIIESIWNNRFPPGSILPAERELSELIGVTRTTLREVLQRLARDGWLTIQ   64 (239)
T ss_pred             HHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            34566665555      34456689999999999999999999999999999754

>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR

Probab=94.50  E-value=0.078  Score=41.75  Aligned_cols=47  Identities=23%  Similarity=0.343  Sum_probs=38.6

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEEe----ecCceEEEeccCC
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVV----KHHAQVIYTRTTK  133 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs----kh~~q~IYtra~k  133 (139)
                      +|...||++++|+-+-.++.|+.|+++|+|....    .+++..+|.-..+
T Consensus        16 ~t~~eLA~~lgis~~tV~~~L~~Le~~GlV~r~~~~~~~gRp~~~y~LT~~   66 (203)
T TIGR02702        16 ATAAALAEALAISPQAVRRHLKDLETEGLIEYEAVVQGMGRPQYHYQLSRQ   66 (203)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEeecccCCCCCceEEEECcc
Confidence            8999999999999999999999999999998762    3455666654333

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.

>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional

Probab=94.49  E-value=0.12  Score=41.18  Aligned_cols=52  Identities=17%  Similarity=0.233  Sum_probs=43.2

Q ss_pred             CHHHHHHHHhhC------CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEee
Q psy1871          70 DKASYDKLLKEV------PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK  121 (139)
Q Consensus        70 Dk~tydKl~KEV------pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk  121 (139)
                      ....|+.|...|      |+.+|=|-..||++|+|+=+-.|-||+.|+..|+|...-+
T Consensus         9 ~~~v~~~i~~~I~~g~l~pG~~LPsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~~   66 (251)
T PRK09990          9 ADVVAERIERLIVDGVLKVGQALPSERRLCEKLGFSRSALREGLTVLRGRGIIETAQG   66 (251)
T ss_pred             HHHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCC
Confidence            356788888777      4455658899999999999999999999999999986543

>PF13730 HTH_36: Helix-turn-helix domain

Probab=94.47  E-value=0.057  Score=33.82  Aligned_cols=30  Identities=30%  Similarity=0.460  Sum_probs=28.0

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCe
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLI  116 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlI  116 (139)
                      -+-..||++++++-+-.+++|++|++.|+|
T Consensus        26 pS~~~la~~~g~s~~Tv~~~i~~L~~~G~I   55 (55)
T PF13730_consen   26 PSQETLAKDLGVSRRTVQRAIKELEEKGLI   55 (55)
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHHHHHCcCC
Confidence            367899999999999999999999999987

>PF09397 Ftsk_gamma: Ftsk gamma domain; InterPro: IPR018541 This domain directs oriented DNA translocation and forms a winged helix structure []

Probab=94.44  E-value=0.041  Score=37.78  Aligned_cols=59  Identities=10%  Similarity=0.240  Sum_probs=44.4

Q ss_pred             CHHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEE
Q psy1871          70 DKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIY  128 (139)
Q Consensus        70 Dk~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IY  128 (139)
                      +.++|++...=|-...-++.|-|--+|+|...-|-+++.+||+.|+|-+-..+..-.|+
T Consensus         4 ~D~ly~~a~~~V~~~~~~S~S~lQR~~rIGynrAariid~LE~~GiVs~~~~~~~R~Vl   62 (65)
T PF09397_consen    4 EDPLYEEAVEFVIEEGKASISLLQRKFRIGYNRAARIIDQLEEEGIVSPANGSKPREVL   62 (65)
T ss_dssp             TSTTHHHHHHHHHHCTCECHHHHHHHHT--HHHHHHHHHHHHHCTSBE---TTSEEEB-
T ss_pred             ccHHHHHHHHHHHHcCCccHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCCCCCCCCeec
Confidence            35678887777777888999999999999999999999999999999988655433343

Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding []. ; PDB: 2VE9_B 2VE8_E 2J5O_A 2J5P_A.

>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR

Probab=94.41  E-value=0.067  Score=38.25  Aligned_cols=54  Identities=11%  Similarity=0.165  Sum_probs=40.9

Q ss_pred             HHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe--ecCceEEEec
Q psy1871          77 LLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV--KHHAQVIYTR  130 (139)
Q Consensus        77 l~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs--kh~~q~IYtr  130 (139)
                      ++-.+-...-+|++.||+++++.-+..-++|+.|+++|+|....  .++|...|.-
T Consensus        33 iL~~l~~~~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~L   88 (118)
T TIGR02337        33 ILRILAEQGSMEFTQLANQACILRPSLTGILARLERDGLVTRLKASNDQRRVYISL   88 (118)
T ss_pred             HHHHHHHcCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeccCCCCCCeeEEEE
Confidence            33333334458999999999999999999999999999999863  3445544443

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.

>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional

Probab=94.40  E-value=0.06  Score=44.63  Aligned_cols=49  Identities=12%  Similarity=0.148  Sum_probs=43.3

Q ss_pred             HHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          72 ASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        72 ~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      +=.++|+..+.....||...||+.|+|+.+-+|+=|.+|+++|++..+.
T Consensus        17 eR~~~Il~~L~~~~~vtv~eLa~~l~VS~~TIRRDL~~Le~~G~l~r~~   65 (269)
T PRK09802         17 ERREQIIQRLRQQGSVQVNDLSALYGVSTVTIRNDLAFLEKQGIAVRAY   65 (269)
T ss_pred             HHHHHHHHHHHHcCCEeHHHHHHHHCCCHHHHHHHHHHHHhCCCeEEEe
Confidence            4567777788777779999999999999999999999999999998654

>PRK11014 transcriptional repressor NsrR; Provisional

Probab=94.38  E-value=0.11  Score=38.73  Aligned_cols=45  Identities=20%  Similarity=0.264  Sum_probs=37.7

Q ss_pred             CCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCce
Q psy1871          81 VPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQ  125 (139)
Q Consensus        81 Vpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q  125 (139)
                      .+.-..++...||++++|+-.-.|++|+.|...|+|..+.+.+..
T Consensus        20 ~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~~G~~GG   64 (141)
T PRK11014         20 LPEGRMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVRGKNGG   64 (141)
T ss_pred             CCCCCccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEecCCCCC
Confidence            333357899999999999999999999999999999877654433

>TIGR03337 phnR transcriptional regulator protein

Probab=94.32  E-value=0.12  Score=40.23  Aligned_cols=39  Identities=31%  Similarity=0.377  Sum_probs=35.7

Q ss_pred             CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          82 PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        82 pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      |+.++=|...|+++|+|+-...|+||++|+.+|+|....
T Consensus        21 ~g~~lPsE~eLa~~~~Vsr~Tvr~Al~~L~~eGli~~~~   59 (231)
T TIGR03337        21 PGDKLPSERDLGERFNTTRVTIREALQQLEAEGLIYRED   59 (231)
T ss_pred             CCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCeEEEeC
Confidence            567888999999999999999999999999999997654

This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Salmonella, Vibrio Aeromonas hydrophila, Hahella chejuensis and Psychromonas ingrahamii.

>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR

Probab=94.30  E-value=0.092  Score=41.38  Aligned_cols=50  Identities=16%  Similarity=0.163  Sum_probs=40.9

Q ss_pred             HHHHHHHHhhCC------CCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          71 KASYDKLLKEVP------AYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        71 k~tydKl~KEVp------k~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      +..|+.|...|-      +.++-|-..||++|+|+-+-.|-||+.|+..|+|...-
T Consensus         9 ~~v~~~l~~~I~~g~l~pG~~LpsE~~La~~lgVSRtpVREAL~~Le~eGlV~~~~   64 (235)
T TIGR02812         9 GFAEEYIVESIWNNRFPPGSILPAERELSELIGVTRTTLREVLQRLARDGWLTIQH   64 (235)
T ss_pred             HHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeC
Confidence            456666666654      34555899999999999999999999999999998654

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

>smart00843 Ftsk_gamma This domain directs oriented DNA translocation and forms a winged helix structure

Probab=94.10  E-value=0.061  Score=36.90  Aligned_cols=54  Identities=17%  Similarity=0.313  Sum_probs=48.2

Q ss_pred             CHHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecC
Q psy1871          70 DKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHH  123 (139)
Q Consensus        70 Dk~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~  123 (139)
                      ++++|+....=|....-+++|.|=-+|+|...-|-+++.+||+.|+|-+...+.
T Consensus         3 ~D~ly~~a~~~V~~~~~~S~S~lQR~~~IGynrAariid~lE~~GiV~p~~g~~   56 (63)
T smart00843        3 EDELYDEAVELVIETQKASTSLLQRRLRIGYNRAARLIDQLEEEGIVGPANGSK   56 (63)
T ss_pred             ccHHHHHHHHHHHHhCCCChHHHHHHHhcchhHHHHHHHHHHHCcCCCCCCCCC
Confidence            467889888888888999999999999999999999999999999998865443

Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding.

>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional

Probab=94.09  E-value=0.097  Score=41.89  Aligned_cols=51  Identities=16%  Similarity=0.181  Sum_probs=41.5

Q ss_pred             CHHHHHHHHhhCCC------CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          70 DKASYDKLLKEVPA------YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        70 Dk~tydKl~KEVpk------~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      -...|+.|...|-+      .+|-|-..||++|+|+-+-.|.||+.|+..|+|...-
T Consensus        10 ~~~v~~~l~~~I~~g~l~pG~~LpsE~eLae~~gVSRtpVREAL~~L~~eGlV~~~~   66 (253)
T PRK11523         10 YQQLAAELKERIEQGVYLVGDKLPAERFIADEKNVSRTVVREAIIMLEVEGYVEVRK   66 (253)
T ss_pred             HHHHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence            35567777766544      4666789999999999999999999999999997544

>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=93.83  E-value=0.11  Score=35.18  Aligned_cols=34  Identities=26%  Similarity=0.360  Sum_probs=30.2

Q ss_pred             chHHHHhhhccc-hHHHHHHHHHHHHcCCeeEEee
Q psy1871          88 TPSVVSERLKVR-GSLARKALEELLQKGLIKQVVK  121 (139)
Q Consensus        88 TPsvlseRlkI~-~SLARkaLreL~~kGlIk~Vsk  121 (139)
                      |..+|++.|+++ -|-+..-|+.|+++|+|.....
T Consensus        27 t~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~r~~~   61 (65)
T PF01726_consen   27 TVREIAEALGLKSTSTVQRHLKALERKGYIRRDPG   61 (65)
T ss_dssp             -HHHHHHHHTSSSHHHHHHHHHHHHHTTSEEEGCC
T ss_pred             CHHHHHHHhCCCChHHHHHHHHHHHHCcCccCCCC
Confidence            778999999998 9999999999999999987654

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.

>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional

Probab=93.81  E-value=0.12  Score=41.19  Aligned_cols=48  Identities=19%  Similarity=0.263  Sum_probs=38.3

Q ss_pred             HHHHHHhhC-CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          73 SYDKLLKEV-PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        73 tydKl~KEV-pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      +.++|..+. |+.+|=|=..||++|+|+-...|+||.+|+.+|+|...-
T Consensus        21 L~~~I~~~~~~G~~LPsE~eLa~~~~VSR~TVR~Al~~L~~eGli~r~~   69 (241)
T PRK10079         21 LEQELRQHYRCGDYLPAEQQLAARYEVNRHTLRRAIDQLVEKGWVQRRQ   69 (241)
T ss_pred             HHHHHhcccCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence            344443333 356888889999999999999999999999999997543

>PRK09464 pdhR transcriptional regulator PdhR; Reviewed

Probab=93.74  E-value=0.14  Score=40.89  Aligned_cols=51  Identities=20%  Similarity=0.188  Sum_probs=42.4

Q ss_pred             CHHHHHHHHhhCCC------CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          70 DKASYDKLLKEVPA------YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        70 Dk~tydKl~KEVpk------~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      .+..|+.|...|-.      .+|-|-..||++|+|+-+..|-||+.|+..|+|...-
T Consensus        12 ~~~v~~~l~~~I~~g~l~pG~~LpsE~eLa~~lgVSRtpVREAL~~L~~eGlv~~~~   68 (254)
T PRK09464         12 SDVIEQQLEFLILEGTLRPGEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRRQ   68 (254)
T ss_pred             HHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEec
Confidence            35677777777644      4555889999999999999999999999999998654

>PRK11512 DNA-binding transcriptional repressor MarR; Provisional

Probab=93.67  E-value=0.12  Score=38.33  Aligned_cols=37  Identities=24%  Similarity=0.328  Sum_probs=34.1

Q ss_pred             CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          84 YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        84 ~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      ..-+|++.||+++++.-|-.=++|..|+++|+|....
T Consensus        52 ~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~~   88 (144)
T PRK11512         52 AACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLP   88 (144)
T ss_pred             cCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecc
Confidence            3459999999999999999999999999999999873

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=93.58  E-value=0.16  Score=34.12  Aligned_cols=34  Identities=29%  Similarity=0.347  Sum_probs=32.0

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      -+|++.||+.++|+-+-+++.|+.|++.|+|...
T Consensus        20 ~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~   53 (91)
T smart00346       20 GLTLAELAERLGLSKSTAHRLLNTLQELGYVEQD   53 (91)
T ss_pred             CcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeec
Confidence            4899999999999999999999999999999764

>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein

Probab=93.37  E-value=0.17  Score=39.87  Aligned_cols=52  Identities=25%  Similarity=0.260  Sum_probs=40.1

Q ss_pred             HHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEe
Q psy1871          76 KLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYT  129 (139)
Q Consensus        76 Kl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYt  129 (139)
                      +++.-+-...-+|...||+++++.-|.+++.|+.|++.|+|.....  +...|.
T Consensus       147 ~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~~Le~~GlI~r~~~--r~~~~~  198 (203)
T TIGR01884       147 KVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLRELEKKGLVEQKGR--KGKRYS  198 (203)
T ss_pred             HHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcC--CccEEE
Confidence            3444443334589999999999999999999999999999998763  444444

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.

>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR

Probab=93.36  E-value=0.2  Score=37.14  Aligned_cols=41  Identities=24%  Similarity=0.232  Sum_probs=35.4

Q ss_pred             CCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecC
Q psy1871          83 AYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHH  123 (139)
Q Consensus        83 k~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~  123 (139)
                      .-..+|...||++++|.....+++|+.|.+.|+|.-+...+
T Consensus        22 ~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s~~G~~   62 (135)
T TIGR02010        22 ETGPVTLADISERQGISLSYLEQLFAKLRKAGLVKSVRGPG   62 (135)
T ss_pred             CCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEeCCC
Confidence            34578999999999999999999999999999997654433

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

>PRK10411 DNA-binding transcriptional activator FucR; Provisional

Probab=93.16  E-value=0.18  Score=41.15  Aligned_cols=53  Identities=23%  Similarity=0.357  Sum_probs=43.7

Q ss_pred             HHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEe
Q psy1871          74 YDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYT  129 (139)
Q Consensus        74 ydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYt  129 (139)
                      .++|+..+.+...+|...|++.|+|+-+-+|+-|.+|+++|+|+.   .|...+|.
T Consensus         6 ~~~Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~~~~l~r---~~Gga~~~   58 (240)
T PRK10411          6 QQAIVDLLLNHTSLTTEALAEQLNVSKETIRRDLNELQTQGKILR---NHGRAKYI   58 (240)
T ss_pred             HHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE---ecCeEEEe
Confidence            456777777788999999999999999999999999999999875   34444554

>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional

Probab=93.14  E-value=0.14  Score=40.07  Aligned_cols=49  Identities=16%  Similarity=0.177  Sum_probs=40.5

Q ss_pred             HHHHHHHHhhCC------CCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          71 KASYDKLLKEVP------AYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        71 k~tydKl~KEVp------k~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      +..|+.|...|-      +.++ +...||++|+|+-+-.|-||+.|+..|+|....
T Consensus        14 e~v~~~l~~~I~~g~l~pG~~L-~e~~La~~lgVSRtpVREAL~~L~~eGLV~~~~   68 (221)
T PRK11414         14 LQVENDLKHQLSIGALKPGARL-ITKNLAEQLGMSITPVREALLRLVSVNALSVAP   68 (221)
T ss_pred             HHHHHHHHHHHHhCCCCCCCcc-CHHHHHHHHCCCchhHHHHHHHHHHCCCEEecC
Confidence            557777777764      4566 568999999999999999999999999997543

>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein

Probab=92.98  E-value=0.21  Score=33.19  Aligned_cols=35  Identities=31%  Similarity=0.469  Sum_probs=32.4

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      -+|+..|++.++++-+-..++|+.|++.|+|....
T Consensus        24 ~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~~   58 (101)
T smart00347       24 PLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRLP   58 (101)
T ss_pred             CcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEecC
Confidence            48999999999999999999999999999998763

>PRK03573 transcriptional regulator SlyA; Provisional

Probab=92.97  E-value=0.19  Score=36.94  Aligned_cols=42  Identities=14%  Similarity=0.199  Sum_probs=36.0

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe--ecCceEE
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVV--KHHAQVI  127 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs--kh~~q~I  127 (139)
                      -+|++.||+++++.-|-.-+++..|+++|+|..+.  .++|...
T Consensus        46 ~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~~~~DrR~~~   89 (144)
T PRK03573         46 EQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQTCASDRRAKR   89 (144)
T ss_pred             CCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeecCCCCcCeee
Confidence            46899999999999999999999999999999984  4455443

>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator)

Probab=92.94  E-value=0.18  Score=36.47  Aligned_cols=38  Identities=26%  Similarity=0.382  Sum_probs=34.1

Q ss_pred             CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          82 PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        82 pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      ++-..+|...||++++|+.+..+++|+.|.+.|+|...
T Consensus        21 ~~~~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~~   58 (132)
T TIGR00738        21 PDEGPVSVKEIAERQGISRSYLEKILRTLRRAGLVESV   58 (132)
T ss_pred             CCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEec
Confidence            44458899999999999999999999999999998654

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.

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

Probab=92.80  E-value=0.23  Score=35.27  Aligned_cols=37  Identities=16%  Similarity=0.244  Sum_probs=33.7

Q ss_pred             CCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          83 AYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        83 k~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      ...-+|++.||+.+++.=+-..++|.+|+++|+|...
T Consensus        44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~r~   80 (95)
T TIGR01610        44 KQDRVTATVIAELTGLSRTHVSDAIKSLARRRIIFRQ   80 (95)
T ss_pred             cCCccCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeee
Confidence            3567899999999999999999999999999999754

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

>PRK10870 transcriptional repressor MprA; Provisional

Probab=92.77  E-value=0.17  Score=39.44  Aligned_cols=36  Identities=28%  Similarity=0.310  Sum_probs=33.6

Q ss_pred             eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      .-+|++.||+++++..+-.-++|..|+++|+|....
T Consensus        70 ~~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~R~~  105 (176)
T PRK10870         70 HSIQPSELSCALGSSRTNATRIADELEKRGWIERRE  105 (176)
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence            458999999999999999999999999999999973

>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial

Probab=92.76  E-value=0.16  Score=37.10  Aligned_cols=35  Identities=14%  Similarity=0.271  Sum_probs=32.4

Q ss_pred             eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      ..+|...||++++|+-+..+++|+.|++.|+|..+
T Consensus        24 ~~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~~   58 (130)
T TIGR02944        24 QPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTSK   58 (130)
T ss_pred             CCccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEec
Confidence            46899999999999999999999999999999664

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.

>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional

Probab=92.73  E-value=0.077  Score=41.88  Aligned_cols=48  Identities=19%  Similarity=0.127  Sum_probs=42.2

Q ss_pred             HHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          72 ASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        72 ~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      +=.+.|+..+.....+|...||++|+|+.+-+|+=|++|++.|++..+
T Consensus         7 ~R~~~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~~L~~~g~~~r~   54 (185)
T PRK04424          7 ERQKALQELIEENPFITDEELAEKFGVSIQTIRLDRMELGIPELRERI   54 (185)
T ss_pred             HHHHHHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHHHHhcchHHHHH
Confidence            345667777777889999999999999999999999999999998664

>PF04157 EAP30: EAP30/Vps36 family; InterPro: IPR007286 EAP30 is a subunit of the ELL complex

Probab=92.69  E-value=0.22  Score=40.04  Aligned_cols=46  Identities=28%  Similarity=0.295  Sum_probs=40.1

Q ss_pred             HHHHHHHhhC--CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCee
Q psy1871          72 ASYDKLLKEV--PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIK  117 (139)
Q Consensus        72 ~tydKl~KEV--pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk  117 (139)
                      ....+|+.=+  .....+|+..|++.++++..+|+.+|.+|+..|++-
T Consensus       174 ~~~~~il~~~~~~~~g~vt~~~l~~~~~ws~~~a~~~L~~~~~~G~l~  221 (223)
T PF04157_consen  174 KDQSRILELAEEENGGGVTASELAEKLGWSVERAKEALEELEREGLLW  221 (223)
T ss_dssp             HHHHHHHHHH--TTTSEEEHHHHHHHHTB-HHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHHhhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCEe
Confidence            4556777777  778999999999999999999999999999999974

The ELL is an 80kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity. ; PDB: 2ZME_A 3CUQ_A 1W7P_D 1U5T_B.

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=92.52  E-value=0.33  Score=33.89  Aligned_cols=45  Identities=20%  Similarity=0.361  Sum_probs=37.2

Q ss_pred             CHHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871          70 DKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQ  118 (139)
Q Consensus        70 Dk~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~  118 (139)
                      |...+.-|..+    .-+|.+.||++++++-+-+++.|+.|+++|+|..
T Consensus         5 D~~il~~L~~~----~~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~~   49 (108)
T smart00344        5 DRKILEELQKD----ARISLAELAKKVGLSPSTVHNRVKRLEEEGVIKG   49 (108)
T ss_pred             HHHHHHHHHHh----CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeec
Confidence            45555555554    2478999999999999999999999999999983

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

>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=92.41  E-value=0.39  Score=31.34  Aligned_cols=32  Identities=22%  Similarity=0.379  Sum_probs=30.5

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCee
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIK  117 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk  117 (139)
                      -+|...||+-++++-.-.-++|++|+++|+|.
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            47899999999999999999999999999997

...

>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family

Probab=92.08  E-value=0.24  Score=35.38  Aligned_cols=36  Identities=17%  Similarity=0.238  Sum_probs=33.5

Q ss_pred             eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      .-+|++.||+.+++.-|-.-++++.|+++|+|..+.
T Consensus        42 ~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r~~   77 (109)
T TIGR01889        42 GKLTLKEIIKEILIKQSALVKIIKKLSKKGYLSKER   77 (109)
T ss_pred             CcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEeccC
Confidence            458999999999999999999999999999999874

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.

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

Probab=92.03  E-value=0.26  Score=33.57  Aligned_cols=32  Identities=28%  Similarity=0.399  Sum_probs=29.2

Q ss_pred             hHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          89 PSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        89 PsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      +..||++++|+-|-..++|+.|+++|+|....
T Consensus         2 ~~ela~~l~is~stvs~~l~~L~~~glI~r~~   33 (96)
T smart00529        2 TSEIAERLNVSPPTVTQMLKKLEKDGLVEYEP   33 (96)
T ss_pred             HHHHHHHhCCChHHHHHHHHHHHHCCCEEEcC
Confidence            57899999999999999999999999987754

iron dependent repressor

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

Probab=91.84  E-value=0.27  Score=39.88  Aligned_cols=59  Identities=14%  Similarity=0.273  Sum_probs=45.3

Q ss_pred             HHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871          73 SYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT  131 (139)
Q Consensus        73 tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra  131 (139)
                      ++..+..-|...|+|....||..|+++..-+-.-|++|+..|.|.-|.-.++..||+-.
T Consensus       100 lL~~Fi~yIK~~Kvv~ledla~~f~l~t~~~i~ri~~L~~~g~ltGv~DdrGkfIyIs~  158 (188)
T PF09756_consen  100 LLQEFINYIKEHKVVNLEDLAAEFGLRTQDVINRIQELEAEGRLTGVIDDRGKFIYISE  158 (188)
T ss_dssp             HHHHHHHHHHH-SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE---
T ss_pred             HHHHHHHHHHHcceeeHHHHHHHcCCCHHHHHHHHHHHHHCCCceeeEcCCCCeEEecH
Confidence            67778888888899999999999999999999999999999999999999999999843

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

>PRK03902 manganese transport transcriptional regulator; Provisional

Probab=91.69  E-value=0.4  Score=35.63  Aligned_cols=36  Identities=19%  Similarity=0.118  Sum_probs=32.4

Q ss_pred             CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          84 YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        84 ~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      ...+|.+.||+.|+|+-+-+..+|+.|+++|+|...
T Consensus        20 ~~~~~~~ela~~l~vs~~svs~~l~~L~~~Gli~~~   55 (142)
T PRK03902         20 KGYARVSDIAEALSVHPSSVTKMVQKLDKDEYLIYE   55 (142)
T ss_pred             CCCcCHHHHHHHhCCChhHHHHHHHHHHHCCCEEEe
Confidence            456799999999999999999999999999999754

>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]

Probab=91.54  E-value=0.79  Score=38.61  Aligned_cols=81  Identities=19%  Similarity=0.172  Sum_probs=63.5

Q ss_pred             cccccchhhhhhhccceeeCHHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871          51 KKKWSKGKVRDKLNNQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR  130 (139)
Q Consensus        51 KKKWSKgKvkdKlnn~Vl~Dk~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr  130 (139)
                      .-.|+.+=-.+-..+-.-|+++-.+=|.=..-+-=-||.++|...+++.=+-.-++|++||++|+|+..-+++++.|-.+
T Consensus       175 ~~~~~~~~~~~~~~~~~~L~~~e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LEk~GlIe~~K~G~~n~V~l~  254 (258)
T COG2512         175 EPLLSRGDELRVLVNEYDLNEDEKEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLEKRGLIEKEKKGRTNIVELR  254 (258)
T ss_pred             hhccccccccccccccCCCCHHHHHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHHhCCceEEEEeCCeeEEEEe
Confidence            44588876666666666666655554444444555789999999999999999999999999999999999998887665


Q ss_pred             c
Q psy1871         131 T  131 (139)
Q Consensus       131 a  131 (139)
                      .
T Consensus       255 ~  255 (258)
T COG2512         255 D  255 (258)
T ss_pred             c
Confidence            3

>COG1846 MarR Transcriptional regulators [Transcription]

Probab=91.52  E-value=0.44  Score=32.33  Aligned_cols=41  Identities=27%  Similarity=0.385  Sum_probs=33.7

Q ss_pred             HHHHhhhccchHHHHHHHHHHHHcCCeeEEe--ecCceEEEec
Q psy1871          90 SVVSERLKVRGSLARKALEELLQKGLIKQVV--KHHAQVIYTR  130 (139)
Q Consensus        90 svlseRlkI~~SLARkaLreL~~kGlIk~Vs--kh~~q~IYtr  130 (139)
                      +.|+++++|..|-.-++|+.|+++|+|...-  .++|..++.-
T Consensus        40 ~~la~~l~i~~~~vt~~l~~Le~~glv~r~~~~~DrR~~~l~l   82 (126)
T COG1846          40 KELAERLGLDRSTVTRLLKRLEDKGLIERLRDPEDRRAVLVRL   82 (126)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHCCCeeecCCccccceeeEEE
Confidence            8999999999999999999999999999873  2344444443

>COG4465 CodY Pleiotropic transcriptional repressor [Transcription]

Probab=91.49  E-value=0.34  Score=41.26  Aligned_cols=54  Identities=19%  Similarity=0.317  Sum_probs=45.7

Q ss_pred             eeeCHHHHHHHHhhCCC-CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          67 VLFDKASYDKLLKEVPA-YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        67 Vl~Dk~tydKl~KEVpk-~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      -.-.-+.++-|..|.-. .=+++.|.||||.+|+-|+-=.|||.||+-|+|.-=|
T Consensus       184 SYSEleAve~I~eELdG~EG~lvASkiADrvGITRSVIVNALRKlESAGvIeSRS  238 (261)
T COG4465         184 SYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRS  238 (261)
T ss_pred             cHHHHHHHHHHHHhcCCccceeeehhhhhhhCchHHHHHHHHHHhhhcCceeecc
Confidence            33456677888888876 5789999999999999999999999999999997543

>COG1802 GntR Transcriptional regulators [Transcription]

Probab=91.24  E-value=0.31  Score=38.50  Aligned_cols=56  Identities=20%  Similarity=0.281  Sum_probs=46.2

Q ss_pred             cceeeCHHHHHHHHhhCCCCe-----eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          65 NQVLFDKASYDKLLKEVPAYK-----LITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        65 n~Vl~Dk~tydKl~KEVpk~K-----lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      .........|+.|...|-.-.     -|+...||++|+|+-.--|.||..|+..|+|...-
T Consensus        13 ~~~~~~~~vy~~Lr~~Il~g~l~pG~~l~e~~La~~~gvSrtPVReAL~rL~~eGlv~~~p   73 (230)
T COG1802          13 KPDTLADQVYEELREAILSGELAPGERLSEEELAEELGVSRTPVREALRRLEAEGLVEIEP   73 (230)
T ss_pred             CcccHHHHHHHHHHHHHHhCCCCCCCCccHHHHHHHhCCCCccHHHHHHHHHHCCCeEecC
Confidence            344556677888888776654     37999999999999999999999999999998763

>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=91.16  E-value=1  Score=28.07  Aligned_cols=28  Identities=32%  Similarity=0.430  Sum_probs=26.6

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcC
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKG  114 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kG  114 (139)
                      ||...||+.|+|+-...++-|.+|.+.|
T Consensus        16 it~~eLa~~l~vS~rTi~~~i~~L~~~~   43 (55)
T PF08279_consen   16 ITAKELAEELGVSRRTIRRDIKELREWG   43 (55)
T ss_dssp             BEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred             cCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence            9999999999999999999999999999

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 ....

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

Probab=90.72  E-value=0.74  Score=32.48  Aligned_cols=45  Identities=22%  Similarity=0.337  Sum_probs=37.1

Q ss_pred             eeechHHHHhhh-----ccchHHHHHHHHHHHHcCCeeEEeecCceEEEe
Q psy1871          85 KLITPSVVSERL-----KVRGSLARKALEELLQKGLIKQVVKHHAQVIYT  129 (139)
Q Consensus        85 KlITPsvlseRl-----kI~~SLARkaLreL~~kGlIk~Vskh~~q~IYt  129 (139)
                      .-+|...|.+++     +|+.+-.-+.|+.|++.|+|..+.-..+...|-
T Consensus        15 ~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~~~~~~~~~y~   64 (116)
T cd07153          15 GHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIELGDGKARYE   64 (116)
T ss_pred             CCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEEEeCCCceEEE
Confidence            457999999998     688888999999999999999987555445564

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.

>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=90.61  E-value=0.58  Score=28.96  Aligned_cols=33  Identities=27%  Similarity=0.363  Sum_probs=29.4

Q ss_pred             eeechHHHHhhhccchHHHHHHHHHHHHcCCee
Q psy1871          85 KLITPSVVSERLKVRGSLARKALEELLQKGLIK  117 (139)
Q Consensus        85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk  117 (139)
                      .=.|+..|++.+++.-|....=|+.|++.|+|.
T Consensus        14 ~~~~~~el~~~l~~s~~~vs~hL~~L~~~glV~   46 (47)
T PF01022_consen   14 GPLTVSELAEELGLSQSTVSHHLKKLREAGLVE   46 (47)
T ss_dssp             SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred             CCCchhhHHHhccccchHHHHHHHHHHHCcCee
Confidence            336899999999999999999999999999985

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 ....

>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]

Probab=90.53  E-value=0.52  Score=36.66  Aligned_cols=50  Identities=18%  Similarity=0.236  Sum_probs=39.6

Q ss_pred             HHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          71 KASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        71 k~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      ++.+.-|+.-+-+--.++...||++|+|.-+-+...|+.|++.|+|..+-
T Consensus         9 edYL~~Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~~~~   58 (154)
T COG1321           9 EDYLETIYELLEEKGFARTKDIAERLKVSPPSVTEMLKRLERLGLVEYEP   58 (154)
T ss_pred             HHHHHHHHHHHhccCcccHHHHHHHhCCCcHHHHHHHHHHHHCCCeEEec
Confidence            33444444333356788999999999999999999999999999987654

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

Probab=90.48  E-value=0.38  Score=28.91  Aligned_cols=39  Identities=18%  Similarity=0.170  Sum_probs=30.6

Q ss_pred             chHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871          88 TPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR  130 (139)
Q Consensus        88 TPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr  130 (139)
                      |+..+|+.++|+-+    .|+..+++|+|.+....+++..|+.
T Consensus         2 ~~~e~a~~~gv~~~----tlr~~~~~g~l~~~~~~~~~~~y~~   40 (49)
T cd04761           2 TIGELAKLTGVSPS----TLRYYERIGLLSPARTEGGYRLYSD   40 (49)
T ss_pred             cHHHHHHHHCcCHH----HHHHHHHCCCCCCCcCCCCCEEeCH
Confidence            77899999988766    5788899999986544457778875

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.

>COG1725 Predicted transcriptional regulators [Transcription]

Probab=90.48  E-value=0.7  Score=35.43  Aligned_cols=48  Identities=19%  Similarity=0.346  Sum_probs=41.4

Q ss_pred             CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEeccC
Q psy1871          82 PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTT  132 (139)
Q Consensus        82 pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra~  132 (139)
                      |..+|=|.-.+|..++||--..++|.++|++.|+|..   .++...|+...
T Consensus        31 pGdkLPSvRelA~~~~VNpnTv~raY~eLE~eG~i~t---~rg~G~fV~~~   78 (125)
T COG1725          31 PGDKLPSVRELAKDLGVNPNTVQRAYQELEREGIVET---KRGKGTFVTED   78 (125)
T ss_pred             CCCCCCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE---ecCeeEEEcCC
Confidence            6689999999999999999999999999999999754   56667777644

>PRK11050 manganese transport regulator MntR; Provisional

Probab=90.43  E-value=0.57  Score=35.73  Aligned_cols=34  Identities=24%  Similarity=0.300  Sum_probs=31.2

Q ss_pred             eeechHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871          85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQ  118 (139)
Q Consensus        85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~  118 (139)
                      .-+|+..||++|+|+-|-..++|+.|++.|+|..
T Consensus        50 ~~~t~~eLA~~l~is~stVsr~l~~Le~~GlI~r   83 (152)
T PRK11050         50 GEARQVDIAARLGVSQPTVAKMLKRLARDGLVEM   83 (152)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence            3479999999999999999999999999999864

>TIGR00122 birA_repr_reg BirA biotin operon repressor domain

Probab=90.39  E-value=1.5  Score=28.78  Aligned_cols=34  Identities=18%  Similarity=0.199  Sum_probs=30.5

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      +|...||++++|+-+..++.|+.|++.|+.....
T Consensus        14 ~~~~eLa~~l~vS~~tv~~~l~~L~~~g~~i~~~   47 (69)
T TIGR00122        14 FSGEKLGEALGMSRTAVNKHIQTLREWGVDVLTV   47 (69)
T ss_pred             cCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEec
Confidence            5789999999999999999999999999965444

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.

>COG1959 Predicted transcriptional regulator [Transcription]

Probab=90.34  E-value=0.53  Score=36.16  Aligned_cols=46  Identities=24%  Similarity=0.305  Sum_probs=39.5

Q ss_pred             eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871          85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR  130 (139)
Q Consensus        85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr  130 (139)
                      ..+|...||++.+|+-+.-+++|..|.+.|+|+-+-....-..-.|
T Consensus        24 ~~~s~~~IA~~~~is~~~L~kil~~L~kaGlV~S~rG~~GGy~Lar   69 (150)
T COG1959          24 GPVSSAEIAERQGISPSYLEKILSKLRKAGLVKSVRGKGGGYRLAR   69 (150)
T ss_pred             CcccHHHHHHHhCcCHHHHHHHHHHHHHcCCEEeecCCCCCccCCC
Confidence            4889999999999999999999999999999999876665544443

>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed

Probab=90.19  E-value=0.59  Score=35.87  Aligned_cols=41  Identities=22%  Similarity=0.271  Sum_probs=36.0

Q ss_pred             eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCce
Q psy1871          85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQ  125 (139)
Q Consensus        85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q  125 (139)
                      ..+|...||++++|+-+--+++|+.|.+.|+|.-+-..+.-
T Consensus        23 ~~~s~~eIA~~~~is~~~L~kIl~~L~~aGlv~S~rG~~GG   63 (153)
T PRK11920         23 KLSRIPEIARAYGVSELFLFKILQPLVEAGLVETVRGRNGG   63 (153)
T ss_pred             CcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeecCCCCC
Confidence            46799999999999999999999999999999887654443

>PRK04158 transcriptional repressor CodY; Validated

Probab=90.10  E-value=0.26  Score=41.94  Aligned_cols=60  Identities=20%  Similarity=0.348  Sum_probs=52.7

Q ss_pred             hhhhhccceeeCHHHHHHHHhhCCCC-eeechHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871          59 VRDKLNNQVLFDKASYDKLLKEVPAY-KLITPSVVSERLKVRGSLARKALEELLQKGLIKQ  118 (139)
Q Consensus        59 vkdKlnn~Vl~Dk~tydKl~KEVpk~-KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~  118 (139)
                      +++-++..-+-.-+..+-|..|.-.. =+++.|-||||.+|+-|+-=.|||-||+-|+|.-
T Consensus       173 V~~Ai~tLSySEleAv~hIf~eL~g~EG~lvASkiADrvgITRSVIVNALRK~ESAGvIES  233 (256)
T PRK04158        173 VQMAINTLSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIES  233 (256)
T ss_pred             HHHHHHhcCHhHHHHHHHHHHhcCCCcceEEeeecccccCCchhhhhhhhhhhhcccceee
Confidence            56666666666778889999999885 7889999999999999999999999999999965

>PRK09954 putative kinase; Provisional

Probab=90.10  E-value=0.32  Score=40.72  Aligned_cols=42  Identities=24%  Similarity=0.373  Sum_probs=36.4

Q ss_pred             HHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCee
Q psy1871          76 KLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIK  117 (139)
Q Consensus        76 Kl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk  117 (139)
                      +|++.+.+...||.+.||++|+|+-+-+++.|+.|+++|+|.
T Consensus         7 ~il~~l~~~~~~s~~~la~~l~~s~~~v~~~i~~L~~~g~i~   48 (362)
T PRK09954          7 EILAILRRNPLIQQNEIADILQISRSRVAAHIMDLMRKGRIK   48 (362)
T ss_pred             HHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCcC
Confidence            455555555689999999999999999999999999999985

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

Probab=89.97  E-value=1.6  Score=31.26  Aligned_cols=54  Identities=26%  Similarity=0.415  Sum_probs=41.1

Q ss_pred             HHhhCCCCeeechHHHHhhh-----ccchHHHHHHHHHHHHcCCeeEEeecCceEEEeccC
Q psy1871          77 LLKEVPAYKLITPSVVSERL-----KVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTT  132 (139)
Q Consensus        77 l~KEVpk~KlITPsvlseRl-----kI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra~  132 (139)
                      ++.+-+.  -+|+..|-++|     +|+.|-.-+.|+.|++.|+|..+...++...|-.+.
T Consensus        16 ~l~~~~~--~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~~~~~~~~~~Y~~~~   74 (120)
T PF01475_consen   16 LLKESPE--HLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRKIEFGDGESRYELST   74 (120)
T ss_dssp             HHHHHSS--SEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEETTSEEEEEESS
T ss_pred             HHHcCCC--CCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEEEEcCCCcceEeecC
Confidence            3444444  67888888887     466667799999999999999998887888887665

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 ....

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

Probab=89.92  E-value=0.64  Score=27.99  Aligned_cols=30  Identities=23%  Similarity=0.400  Sum_probs=25.9

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCe
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLI  116 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlI  116 (139)
                      +|-..||+-++.+....-++|..|+++|+|
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            577899999999999999999999999997

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 ....

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

Probab=89.78  E-value=1.1  Score=30.57  Aligned_cols=41  Identities=29%  Similarity=0.296  Sum_probs=29.6

Q ss_pred             HHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCee
Q psy1871          76 KLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIK  117 (139)
Q Consensus        76 Kl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk  117 (139)
                      .|++.+. ..-.+++.|+...+++.+.+.+.|++|+++|+|.
T Consensus        10 ~IL~~l~-~~~~~~t~i~~~~~L~~~~~~~yL~~L~~~gLI~   50 (77)
T PF14947_consen   10 DILKILS-KGGAKKTEIMYKANLNYSTLKKYLKELEEKGLIK   50 (77)
T ss_dssp             HHHHHH--TT-B-HHHHHTTST--HHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHH-cCCCCHHHHHHHhCcCHHHHHHHHHHHHHCcCee
Confidence            3444433 3445689999999999999999999999999993

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

Probab=89.68  E-value=0.5  Score=34.43  Aligned_cols=38  Identities=29%  Similarity=0.309  Sum_probs=33.5

Q ss_pred             CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEee
Q psy1871          84 YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK  121 (139)
Q Consensus        84 ~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk  121 (139)
                      +-.=+|-.+|-++++...-.+.+|++|++.|||..|..
T Consensus        19 ~~~Dy~k~ia~~l~~~~~~v~~~l~~Le~~GLler~~g   56 (92)
T PF10007_consen   19 AGPDYAKSIARRLKIPLEEVREALEKLEEMGLLERVEG   56 (92)
T ss_pred             HCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEecC
Confidence            33346889999999999999999999999999999874

>PRK11169 leucine-responsive transcriptional regulator; Provisional

Probab=89.54  E-value=0.79  Score=35.06  Aligned_cols=43  Identities=19%  Similarity=0.291  Sum_probs=35.5

Q ss_pred             HHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871          76 KLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQ  118 (139)
Q Consensus        76 Kl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~  118 (139)
                      +|+.....--=+|.+.||++++++-+-.++=|+.|++.|+|.-
T Consensus        18 ~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~GvI~~   60 (164)
T PRK11169         18 NILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQGFIQG   60 (164)
T ss_pred             HHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEE
Confidence            4444444444567899999999999999999999999999974

>PRK06266 transcription initiation factor E subunit alpha; Validated

Probab=89.45  E-value=0.45  Score=37.85  Aligned_cols=49  Identities=18%  Similarity=0.149  Sum_probs=42.8

Q ss_pred             CHHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871          70 DKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQ  118 (139)
Q Consensus        70 Dk~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~  118 (139)
                      +.++..+|+.-++....+|-..||+.|+|+..-.|++|..|.+.|||..
T Consensus        20 ~~~~~~~Vl~~L~~~g~~tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~~   68 (178)
T PRK06266         20 GDEEGFEVLKALIKKGEVTDEEIAEQTGIKLNTVRKILYKLYDARLADY   68 (178)
T ss_pred             CCccHhHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEE
Confidence            4566677777777777899999999999999999999999999999874

>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=89.44  E-value=0.58  Score=32.96  Aligned_cols=46  Identities=17%  Similarity=0.210  Sum_probs=32.8

Q ss_pred             HHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCe
Q psy1871          71 KASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLI  116 (139)
Q Consensus        71 k~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlI  116 (139)
                      +..|+=|...-..-.=|....|+++|+++..=-|.+|++|.+.|.|
T Consensus        50 ~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~I   95 (102)
T PF08784_consen   50 DKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNEGHI   95 (102)
T ss_dssp             HHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSE
T ss_pred             HHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhCCeE
Confidence            3344433331333345889999999999999999999999999986

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.

>TIGR00498 lexA SOS regulatory protein LexA

Probab=89.41  E-value=0.51  Score=36.59  Aligned_cols=53  Identities=17%  Similarity=0.186  Sum_probs=39.5

Q ss_pred             CHHHHHHHHhhCCCC-eeechHHHHhhhccc-hHHHHHHHHHHHHcCCeeEEeec
Q psy1871          70 DKASYDKLLKEVPAY-KLITPSVVSERLKVR-GSLARKALEELLQKGLIKQVVKH  122 (139)
Q Consensus        70 Dk~tydKl~KEVpk~-KlITPsvlseRlkI~-~SLARkaLreL~~kGlIk~Vskh  122 (139)
                      +.+.++-|....-.. .-.|...||+++++. -|.....|+.|+++|+|......
T Consensus         8 q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~g~i~~~~~~   62 (199)
T TIGR00498         8 QQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALERKGYIERDPGK   62 (199)
T ss_pred             HHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHHHCCCEecCCCC
Confidence            455666666433221 125677999999999 89999999999999999886543

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.

>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 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=89.33  E-value=0.64  Score=28.39  Aligned_cols=37  Identities=22%  Similarity=0.168  Sum_probs=25.6

Q ss_pred             chHHHHhhhccchHHHHHHHHHHHHcCCe-eEEeecCceEEE
Q psy1871          88 TPSVVSERLKVRGSLARKALEELLQKGLI-KQVVKHHAQVIY  128 (139)
Q Consensus        88 TPsvlseRlkI~~SLARkaLreL~~kGlI-k~Vskh~~q~IY  128 (139)
                      |...+|+.++|+.+    .||..+++||| .+.-..+....|
T Consensus         1 ti~e~A~~~gvs~~----tlR~ye~~Gll~~~~r~~~g~R~Y   38 (38)
T PF00376_consen    1 TIGEVAKLLGVSPR----TLRYYEREGLLPPPERTEGGYRRY   38 (38)
T ss_dssp             EHHHHHHHHTS-HH----HHHHHHHTTSS-SSEETTTS-EEE
T ss_pred             CHHHHHHHHCCCHH----HHHHHHHCCCCCCCccCCCCeecC
Confidence            56789999988754    69999999999 555444444444

One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....

>smart00422 HTH_MERR helix_turn_helix, mercury resistance

Probab=89.07  E-value=0.43  Score=30.65  Aligned_cols=40  Identities=18%  Similarity=0.119  Sum_probs=30.9

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEE-eecCceEEEec
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQV-VKHHAQVIYTR  130 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~V-skh~~q~IYtr  130 (139)
                      .|+..+|+.++|+-+    .||.++++|+|.+. ...++...|+.
T Consensus         1 ~s~~eva~~~gvs~~----tlr~~~~~gli~~~~~~~~g~r~y~~   41 (70)
T smart00422        1 YTIGEVAKLAGVSVR----TLRYYERIGLLPPPIRTEGGYRLYSD   41 (70)
T ss_pred             CCHHHHHHHHCcCHH----HHHHHHHCCCCCCCccCCCCCEecCH
Confidence            378999999998765    47788899999986 44556677874

>PRK15481 transcriptional regulatory protein PtsJ; Provisional

Probab=88.97  E-value=0.68  Score=39.51  Aligned_cols=49  Identities=18%  Similarity=0.284  Sum_probs=39.0

Q ss_pred             HHHHHHHHhhC------CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          71 KASYDKLLKEV------PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        71 k~tydKl~KEV------pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      +..++.|..+|      |..++=+.-.||+.|+|+-+..++|+++|+++|+|...
T Consensus         8 ~~~~~~i~~~i~~g~l~~g~~lps~r~la~~~~vsr~tv~~a~~~L~~~g~i~~~   62 (431)
T PRK15481          8 NEIFDSIRQLIQAGRLRPGDSLPPVRELASELGVNRNTVAAAYKRLVTAGLAQSQ   62 (431)
T ss_pred             HHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            34555555555      34566678899999999999999999999999999643

>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=88.73  E-value=0.86  Score=39.41  Aligned_cols=67  Identities=24%  Similarity=0.245  Sum_probs=42.5

Q ss_pred             hccceeeCHHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE--eecCceEEEecc
Q psy1871          63 LNNQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV--VKHHAQVIYTRT  131 (139)
Q Consensus        63 lnn~Vl~Dk~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V--skh~~q~IYtra  131 (139)
                      +++.---+.-.|+-|. |- .-+=|.-..|-.+.++.-+.-.++|+.|+++++|+.|  .+|+...||.-.
T Consensus        79 ~~~l~~~e~lvy~~I~-~a-g~~GIw~~~i~~~t~l~~~~~~k~lk~Le~k~lIK~vksv~~~~rK~Yml~  147 (327)
T PF05158_consen   79 LKGLSDEERLVYQLIE-EA-GNKGIWTKDIKKKTNLHQTQLTKILKSLESKKLIKSVKSVKNPNRKVYMLY  147 (327)
T ss_dssp             --SSSCCHHHHHHHHH-HH-TTT-EEHHHHHHHCT--HHHHHHHHHHHHHTTSEEEE--SS-SS--EEEES
T ss_pred             hcCCCHHHHHHHHHHH-Hh-CCCCCcHHHHHHHcCCCHHHHHHHHHHHHhCCCEEEecCcCCCCeEEEEEc
Confidence            3333333343444443 22 2345667889999999999999999999999999999  466678899754

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.

>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators

Probab=88.26  E-value=0.51  Score=32.92  Aligned_cols=41  Identities=29%  Similarity=0.246  Sum_probs=32.8

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecC-ceEEEec
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHH-AQVIYTR  130 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~-~q~IYtr  130 (139)
                      +.|+..+|+.++|+.+.    ||..+++|+|.+..... +...|+.
T Consensus         1 ~~ti~evA~~~gvs~~t----LR~ye~~Gll~p~r~~~~g~R~Ys~   42 (88)
T cd01105           1 VIGIGEVSKLTGVSPRQ----LRYWEEKGLIKSIRSDGGGQRKYSL   42 (88)
T ss_pred             CcCHHHHHHHHCcCHHH----HHHHHHCCCCCCCccCCCCceecCH
Confidence            36899999999988765    78889999999865443 7788874

Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.

>PRK13777 transcriptional regulator Hpr; Provisional

Probab=88.14  E-value=0.85  Score=36.53  Aligned_cols=37  Identities=16%  Similarity=0.011  Sum_probs=33.3

Q ss_pred             CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          84 YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        84 ~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      ..-+|++.||+.+.+..|-.-++|..|+++|+|....
T Consensus        57 ~~~itq~eLa~~l~l~~sTvtr~l~rLE~kGlI~R~~   93 (185)
T PRK13777         57 LKGASISEIAKFGVMHVSTAFNFSKKLEERGYLTFSK   93 (185)
T ss_pred             CCCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEecC
Confidence            3458999999999999998999999999999999873

>PRK10857 DNA-binding transcriptional regulator IscR; Provisional

Probab=87.91  E-value=1  Score=35.16  Aligned_cols=47  Identities=19%  Similarity=0.160  Sum_probs=37.7

Q ss_pred             CCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871          83 AYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT  131 (139)
Q Consensus        83 k~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra  131 (139)
                      .-..+|...||++++|.....+++|+.|.+.|+|.-+...+.  =|.-+
T Consensus        22 ~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s~rG~~G--Gy~La   68 (164)
T PRK10857         22 EAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSVRGPGG--GYLLG   68 (164)
T ss_pred             CCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCCCCCC--Ceecc
Confidence            345789999999999999999999999999999986433333  35543

>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family

Probab=87.90  E-value=0.81  Score=34.30  Aligned_cols=46  Identities=22%  Similarity=0.228  Sum_probs=35.9

Q ss_pred             echHHHHhh----hccchHHHHHHHHHHHHcCCeeEEeecCceEEEeccCC
Q psy1871          87 ITPSVVSER----LKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTTK  133 (139)
Q Consensus        87 ITPsvlseR----lkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra~k  133 (139)
                      +|+..|.+.    +++.-+..+..|+.|+++|+|... +.++..+|++...
T Consensus        19 ~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~KG~v~~~-k~gr~~~Y~p~vs   68 (130)
T TIGR02698        19 TTSRDIIRILAEKKDWSDSTIKTLLGRLVDKGCLTTE-KEGRKFIYTALVS   68 (130)
T ss_pred             CCHHHHHHHHhhccCCcHHHHHHHHHHHHHCCceeee-cCCCcEEEEecCC
Confidence            488885555    478999999999999999999765 4456778987543

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.

>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional

Probab=87.75  E-value=1.3  Score=33.49  Aligned_cols=46  Identities=15%  Similarity=0.285  Sum_probs=39.0

Q ss_pred             eCHHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871          69 FDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQ  118 (139)
Q Consensus        69 ~Dk~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~  118 (139)
                      +|...++-|+.+    -=++.+.||++++++-+-.++=++.|++.|+|.-
T Consensus        10 ~D~~Il~~Lq~d----~R~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~~   55 (153)
T PRK11179         10 LDRGILEALMEN----ARTPYAELAKQFGVSPGTIHVRVEKMKQAGIITG   55 (153)
T ss_pred             HHHHHHHHHHHc----CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeee
Confidence            466677777777    3357799999999999999999999999999974

>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators

Probab=87.71  E-value=0.62  Score=33.20  Aligned_cols=42  Identities=21%  Similarity=0.221  Sum_probs=33.1

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT  131 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra  131 (139)
                      +.|.+.+|+.++|+.+.    ||..++.|+|.+.-..++...|+..
T Consensus         1 ~~~i~eva~~~gVs~~t----LR~ye~~Gli~p~r~~~g~R~Ys~~   42 (98)
T cd01279           1 LYPISVAAELLGIHPQT----LRVYDRLGLVSPARTNGGGRRYSNN   42 (98)
T ss_pred             CcCHHHHHHHHCcCHHH----HHHHHHCCCCCCCcCCCCCeeECHH
Confidence            35889999999988765    6788999999885445677888753

Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.

>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator

Probab=87.59  E-value=0.69  Score=32.15  Aligned_cols=41  Identities=17%  Similarity=0.135  Sum_probs=32.6

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR  130 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr  130 (139)
                      +.|...+|+.++|+.+.    ||..++.|+|.+.-..+....|+.
T Consensus         1 ~~~i~e~A~~~gvs~~t----Lr~ye~~Gli~p~r~~~g~R~y~~   41 (91)
T cd04766           1 VYVISVAAELSGMHPQT----LRLYERLGLLSPSRTDGGTRRYSE   41 (91)
T ss_pred             CcCHHHHHHHHCcCHHH----HHHHHHCCCcCCCcCCCCCeeECH
Confidence            35889999999998765    788899999998654456677875

Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.

>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional

Probab=87.28  E-value=1.4  Score=33.25  Aligned_cols=41  Identities=22%  Similarity=0.341  Sum_probs=33.8

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEE
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIY  128 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IY  128 (139)
                      -+|...||+.++++-.-.-++|++|+++|+|..  .++...||
T Consensus       168 ~~t~~~lA~~lG~tr~tvsR~l~~l~~~gii~~--~~~~i~i~  208 (211)
T PRK11753        168 KITRQEIGRIVGCSREMVGRVLKMLEDQGLISA--HGKTIVVY  208 (211)
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEe--cCCEEEEe
Confidence            478899999999999999999999999999863  23344444

>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional

Probab=87.01  E-value=1.5  Score=35.39  Aligned_cols=36  Identities=19%  Similarity=0.187  Sum_probs=32.7

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEee
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK  121 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk  121 (139)
                      -+|.+.||++++++-|-+.++|+.|++.|++.....
T Consensus        28 ~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~~~~~   63 (257)
T PRK15090         28 EIGITELSQRVMMSKSTVYRFLQTMKTLGYVAQEGE   63 (257)
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCC
Confidence            479999999999999999999999999999877543

>PRK09834 DNA-binding transcriptional activator MhpR; Provisional

Probab=86.33  E-value=1.5  Score=35.62  Aligned_cols=37  Identities=19%  Similarity=0.349  Sum_probs=33.2

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecC
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHH  123 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~  123 (139)
                      +|.+.||++++++-|-+.++|+.|++.|+|......+
T Consensus        27 ls~~eia~~lgl~kstv~RlL~tL~~~g~v~~~~~~~   63 (263)
T PRK09834         27 ATVGLLAELTGLHRTTVRRLLETLQEEGYVRRSASDD   63 (263)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecCCC
Confidence            7899999999999999999999999999998764333

>PF12728 HTH_17: Helix-turn-helix domain

Probab=86.24  E-value=1.2  Score=27.41  Aligned_cols=40  Identities=15%  Similarity=0.128  Sum_probs=30.6

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR  130 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr  130 (139)
                      ++|+..+|+-|+|+-+-    ++.+..+|.|..+. ..+...|.+
T Consensus         1 ~lt~~e~a~~l~is~~t----v~~~~~~g~i~~~~-~g~~~~~~~   40 (51)
T PF12728_consen    1 YLTVKEAAELLGISRST----VYRWIRQGKIPPFK-IGRKWRIPK   40 (51)
T ss_pred             CCCHHHHHHHHCcCHHH----HHHHHHcCCCCeEE-eCCEEEEeH
Confidence            57999999999986555    66777899998884 556555554

>COG2186 FadR Transcriptional regulators [Transcription]

Probab=85.86  E-value=1.5  Score=35.72  Aligned_cols=58  Identities=22%  Similarity=0.377  Sum_probs=44.5

Q ss_pred             HHHHHHHHhhC------CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871          71 KASYDKLLKEV------PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT  131 (139)
Q Consensus        71 k~tydKl~KEV------pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra  131 (139)
                      ...+++|...|      |.-+|=|-..|||+|+|+=+.-|-+|+.|+.+|+|..   .++-.+|++.
T Consensus        13 ~~v~~~i~~~I~~g~~~~G~~LP~EreLae~fgVSR~~vREAl~~L~a~Glve~---r~G~Gt~V~~   76 (241)
T COG2186          13 DEVAEQIGALIVSGELPPGDRLPSERELAERFGVSRTVVREALKRLEAKGLVEI---RQGSGTFVRP   76 (241)
T ss_pred             HHHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCcHHHHHHHHHHHHCCCeee---cCCCceEecC
Confidence            44555565554      4567878899999999999999999999999999743   3445567654

>TIGR01764 excise DNA binding domain, excisionase family

Probab=85.51  E-value=1.6  Score=25.58  Aligned_cols=40  Identities=18%  Similarity=0.203  Sum_probs=29.4

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR  130 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr  130 (139)
                      ++|+..+|+.|+|+    +.-|+.|.+.|.|..+.. .+...|.+
T Consensus         1 ~lt~~e~a~~lgis----~~ti~~~~~~g~i~~~~~-g~~~~~~~   40 (49)
T TIGR01764         1 YLTVEEAAEYLGVS----KDTVYRLIHEGELPAYRV-GRHYRIPR   40 (49)
T ss_pred             CCCHHHHHHHHCCC----HHHHHHHHHcCCCCeEEe-CCeEEEeH
Confidence            47899999999875    456777888999887654 34555654

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

>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional

Probab=85.27  E-value=1.8  Score=36.15  Aligned_cols=40  Identities=20%  Similarity=0.198  Sum_probs=33.6

Q ss_pred             HHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCe
Q psy1871          77 LLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLI  116 (139)
Q Consensus        77 l~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlI  116 (139)
                      |+..+..-..++...||++|+|+-+-.++.|+.|++.|+.
T Consensus         9 il~~L~~~~~~s~~~LA~~lgvsr~tV~~~l~~L~~~G~~   48 (319)
T PRK11886          9 LLSLLADGDFHSGEQLGEELGISRAAIWKHIQTLEEWGLD   48 (319)
T ss_pred             HHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCc
Confidence            3333444577889999999999999999999999999993

>PRK12423 LexA repressor; Provisional

Probab=85.19  E-value=1.4  Score=34.85  Aligned_cols=49  Identities=20%  Similarity=0.252  Sum_probs=37.6

Q ss_pred             HHHHHHHHhhCCCCee-echHHHHhhhcc-chHHHHHHHHHHHHcCCeeEE
Q psy1871          71 KASYDKLLKEVPAYKL-ITPSVVSERLKV-RGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        71 k~tydKl~KEVpk~Kl-ITPsvlseRlkI-~~SLARkaLreL~~kGlIk~V  119 (139)
                      .+.++.|...+-...+ =|...||+.|++ +-+..+..|+.|+++|+|...
T Consensus         9 ~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~~l~~L~~~G~l~~~   59 (202)
T PRK12423          9 AAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQALAEAGLIEVV   59 (202)
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEec
Confidence            4566777665433333 388999999995 788889999999999999764

>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator

Probab=85.06  E-value=0.86  Score=32.60  Aligned_cols=40  Identities=23%  Similarity=0.205  Sum_probs=32.6

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR  130 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr  130 (139)
                      +|...||++++|+.+.    ||.-++.|+|.+.-......+|+.
T Consensus         2 ~~i~eva~~~gvs~~t----lR~ye~~Gll~~~r~~~g~R~Y~~   41 (102)
T cd04789           2 YTISELAEKAGISRST----LLYYEKLGLITGTRNANGYRLYPD   41 (102)
T ss_pred             CCHHHHHHHHCcCHHH----HHHHHHCCCCCCCcCCCCCeeCCH
Confidence            5889999999998765    779999999998654567788874

Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of 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.

>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators

Probab=84.88  E-value=1  Score=32.20  Aligned_cols=41  Identities=22%  Similarity=0.212  Sum_probs=32.0

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT  131 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra  131 (139)
                      .|...||++++|+.+    .||..++.|+|.+.-..++...|+..
T Consensus         2 ~~i~eva~~~gvs~~----tLR~ye~~Gll~~~r~~~g~R~Y~~~   42 (102)
T cd04775           2 YTIGQMSRKFGVSRS----TLLYYESIGLIPSARSEANYRLYSEA   42 (102)
T ss_pred             CCHHHHHHHHCcCHH----HHHHHHHCCCCCCCCCCCCCeeeCHH
Confidence            588999999998865    57999999999554444567788753

Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of 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 dissimil

>COG0789 SoxR Predicted transcriptional regulators [Transcription]

Probab=84.45  E-value=0.99  Score=32.11  Aligned_cols=40  Identities=23%  Similarity=0.182  Sum_probs=33.3

Q ss_pred             chHHHHhhhccchHHHHHHHHHHHHcCCeeEEeec-CceEEEecc
Q psy1871          88 TPSVVSERLKVRGSLARKALEELLQKGLIKQVVKH-HAQVIYTRT  131 (139)
Q Consensus        88 TPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh-~~q~IYtra  131 (139)
                      |...||++++|+.    +.||.-++.|||.+.... ++.++|+..
T Consensus         2 ~I~eva~~~gvs~----~tLRyYE~~GLl~p~~~~~~gyR~Ys~~   42 (124)
T COG0789           2 TIGEVAKLTGVSV----RTLRFYERKGLLSPERRDEGGYRYYTPE   42 (124)
T ss_pred             cHHHHHHHhCCCH----HHHHHHHHcCCCCCcccCCCCceecCHH
Confidence            6788999997765    579999999999998665 588999864

>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=84.43  E-value=4.1  Score=29.25  Aligned_cols=46  Identities=20%  Similarity=0.226  Sum_probs=35.8

Q ss_pred             echHHHHhhhc----cchHHHHHHHHHHHHcCCeeEEeecCceEEEeccCC
Q psy1871          87 ITPSVVSERLK----VRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTTK  133 (139)
Q Consensus        87 ITPsvlseRlk----I~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra~k  133 (139)
                      +|...|.+.|.    +.-|..+..|+.|++||+|..-. .++..+|.+...
T Consensus        18 ~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~~~~-~gr~~~Y~p~is   67 (115)
T PF03965_consen   18 ATVREIHEALPEERSWAYSTVQTLLNRLVEKGFLTREK-IGRAYVYSPLIS   67 (115)
T ss_dssp             EEHHHHHHHHCTTSS--HHHHHHHHHHHHHTTSEEEEE-ETTCEEEEESSS
T ss_pred             CCHHHHHHHHHhccccchhHHHHHHHHHHhCCceeEee-cCCceEEEeCCc
Confidence            67777777765    56889999999999999998864 467889987653

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 ....

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

Probab=84.27  E-value=1.2  Score=25.81  Aligned_cols=40  Identities=20%  Similarity=0.285  Sum_probs=28.7

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR  130 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr  130 (139)
                      +|...+|+.|+|+-+    -|+.+.++|.+.......+...|..
T Consensus         1 ~s~~e~a~~lgvs~~----tl~~~~~~g~~~~~~~~~~~~~~~~   40 (49)
T cd04762           1 LTTKEAAELLGVSPS----TLRRWVKEGKLKAIRTPGGHRRFPE   40 (49)
T ss_pred             CCHHHHHHHHCcCHH----HHHHHHHcCCCCceeCCCCceecCH
Confidence            367889999988654    4677788899876554456667764

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

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

Probab=84.08  E-value=2.2  Score=29.55  Aligned_cols=34  Identities=24%  Similarity=0.205  Sum_probs=29.5

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      =+|.+.|.+.++++-|-..+-|+.|++.|+|..-
T Consensus        14 ~~~f~~L~~~l~lt~g~Ls~hL~~Le~~GyV~~~   47 (80)
T PF13601_consen   14 EATFSELKEELGLTDGNLSKHLKKLEEAGYVEVE   47 (80)
T ss_dssp             EEEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEE
Confidence            4789999999999999999999999999999864

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

Probab=83.83  E-value=3  Score=31.76  Aligned_cols=46  Identities=24%  Similarity=0.352  Sum_probs=33.8

Q ss_pred             HHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871          71 KASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR  130 (139)
Q Consensus        71 k~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr  130 (139)
                      +++|+.|.++.|+..+-|+              -++|+.|++.|+|..+.-..+...|--
T Consensus        40 eei~~~l~~~~p~islaTV--------------Yr~L~~l~e~Glv~~~~~~~~~~~y~~   85 (145)
T COG0735          40 EELYEELREEGPGISLATV--------------YRTLKLLEEAGLVHRLEFEGGKTRYEL   85 (145)
T ss_pred             HHHHHHHHHhCCCCCHhHH--------------HHHHHHHHHCCCEEEEEeCCCEEEEec
Confidence            5667777777776555444              578999999999999987666666643

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

Probab=83.80  E-value=2.2  Score=33.53  Aligned_cols=45  Identities=22%  Similarity=0.347  Sum_probs=36.8

Q ss_pred             CCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871          83 AYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT  131 (139)
Q Consensus        83 k~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra  131 (139)
                      +.=+.|-..||+.++++-+--.++|++|+++|+|..+    ++.+|-=+
T Consensus        72 N~v~~t~~~ia~~l~iS~~Tv~r~ik~L~e~~iI~k~----~~G~Y~iN  116 (165)
T PF05732_consen   72 NAVVATQKEIAEKLGISKPTVSRAIKELEEKNIIKKI----RNGAYMIN  116 (165)
T ss_pred             CeEEeeHHHHHHHhCCCHHHHHHHHHHHHhCCcEEEc----cCCeEEEC
Confidence            3456788999999999999999999999999999876    23356544

; GO: 0006260 DNA replication, 0006276 plasmid maintenance

>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators

Probab=83.75  E-value=1.2  Score=33.72  Aligned_cols=41  Identities=29%  Similarity=0.408  Sum_probs=33.7

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT  131 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra  131 (139)
                      +.|...||++++|+.+    .||..+++|+|.+.. .++++.|+..
T Consensus         1 lysI~eVA~~~GVs~~----TLR~wE~~GLl~p~r-~~G~R~Ys~~   41 (120)
T cd04767           1 LYPIGVVAELLNIHPE----TLRIWERHGLIKPAR-RNGQRLYSNN   41 (120)
T ss_pred             CCCHHHHHHHHCcCHH----HHHHHHHCCCCCCcC-CCCcEEECHH
Confidence            3588999999998877    477999999999864 5788999853

Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind spe

>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators

Probab=83.42  E-value=0.89  Score=32.97  Aligned_cols=40  Identities=10%  Similarity=0.167  Sum_probs=31.7

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEEee-cCceEEEec
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK-HHAQVIYTR  130 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk-h~~q~IYtr  130 (139)
                      .|...||++++|+.+    .||.-++.|||.+..+ .++.+.|+.
T Consensus         1 ~~I~eva~~~gvs~~----tLRyYe~~GLl~p~~r~~~gyR~Y~~   41 (123)
T cd04770           1 MKIGELAKAAGVSPD----TIRYYERIGLLPPPQRSENGYRLYGE   41 (123)
T ss_pred             CCHHHHHHHHCcCHH----HHHHHHHCCCCCCCCCCCCCCccCCH
Confidence            377899999998765    6899999999997644 456678875

Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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.

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

Probab=83.34  E-value=1.2  Score=31.41  Aligned_cols=41  Identities=17%  Similarity=0.120  Sum_probs=33.0

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEEee-cCceEEEecc
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK-HHAQVIYTRT  131 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk-h~~q~IYtra  131 (139)
                      .|.+.||+.++|+.+    .||.-++.|+|.++.. .++...|+..
T Consensus         1 ~ti~eva~~~gvs~~----tLRyye~~Gll~p~~~~~~gyR~Y~~~   42 (96)
T cd04768           1 LTIGEFAKLAGVSIR----TLRHYDDIGLFKPAKIAENGYRYYSYA   42 (96)
T ss_pred             CCHHHHHHHHCcCHH----HHHHHHHCCCCCCCccCCCCeeeCCHH
Confidence            378899999998876    5899999999999754 5567888753

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

>COG1733 Predicted transcriptional regulators [Transcription]

Probab=83.30  E-value=2  Score=32.07  Aligned_cols=35  Identities=34%  Similarity=0.688  Sum_probs=31.0

Q ss_pred             HHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEee
Q psy1871          73 SYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK  121 (139)
Q Consensus        73 tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk  121 (139)
                      =|..|.+.+|.   ||+-+|++||           ++|++.|+|....-
T Consensus        38 RF~eL~r~i~~---Is~k~Ls~~L-----------k~Le~~Glv~R~~~   72 (120)
T COG1733          38 RFNELRRSIGG---ISPKMLSRRL-----------KELEEDGLVERVVY   72 (120)
T ss_pred             cHHHHHHHccc---cCHHHHHHHH-----------HHHHHCCCEEeeec
Confidence            58889999998   9999999986           89999999988754

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

Probab=83.22  E-value=1.6  Score=28.04  Aligned_cols=39  Identities=23%  Similarity=0.234  Sum_probs=31.0

Q ss_pred             chHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871          88 TPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR  130 (139)
Q Consensus        88 TPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr  130 (139)
                      |...||+.++|+-+    .||..+++|+|.+.-..++...|+.
T Consensus         2 ti~eva~~~gvs~~----tlr~y~~~gll~~~~~~~g~r~y~~   40 (69)
T PF13411_consen    2 TIKEVAKLLGVSPS----TLRYYEREGLLPPPRDENGYRYYSE   40 (69)
T ss_dssp             EHHHHHHHTTTTHH----HHHHHHHTTSSTTBESTTSSEEE-H
T ss_pred             cHHHHHHHHCcCHH----HHHHHHHhcCcccccccCceeeccH
Confidence            77899999998655    5899999999888775666688874

>PRK13918 CRP/FNR family transcriptional regulator; Provisional

Probab=83.12  E-value=2.5  Score=31.80  Aligned_cols=32  Identities=19%  Similarity=0.250  Sum_probs=30.3

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCee
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIK  117 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk  117 (139)
                      -+|-..||+-++++-.-.-++|++|+++|+|.
T Consensus       149 ~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~  180 (202)
T PRK13918        149 YATHDELAAAVGSVRETVTKVIGELSREGYIR  180 (202)
T ss_pred             cCCHHHHHHHhCccHHHHHHHHHHHHHCCCEE
Confidence            36999999999999999999999999999997

>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional

Probab=82.64  E-value=1.5  Score=34.19  Aligned_cols=42  Identities=38%  Similarity=0.423  Sum_probs=35.7

Q ss_pred             eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871          85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR  130 (139)
Q Consensus        85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr  130 (139)
                      .++|...||.+++|+.+    .||.-++.|||.++-..++...|+.
T Consensus        10 ~~~~IgevAk~~gvs~~----TlRyYE~~GLi~~~r~~~g~R~Y~~   51 (154)
T PRK15002         10 ALLTPGEVAKRSGVAVS----ALHFYESKGLITSIRNSGNQRRYKR   51 (154)
T ss_pred             ccccHHHHHHHHCcCHH----HHHHHHHCCCCCCccCCCCCEEECH
Confidence            67899999999999875    5899999999999655566788875

>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional

Probab=82.33  E-value=1.6  Score=35.70  Aligned_cols=44  Identities=14%  Similarity=0.077  Sum_probs=37.9

Q ss_pred             HHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcC
Q psy1871          71 KASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKG  114 (139)
Q Consensus        71 k~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kG  114 (139)
                      .+=.++|+.-+.....||...||+.|+|+....|+=|++|+..|
T Consensus         6 ~eR~~~I~~~l~~~~~v~v~eLa~~~~VS~~TIRRDL~~Le~~~   49 (252)
T PRK10681          6 DERIGQLLQALKRSDKLHLKDAAALLGVSEMTIRRDLNAHSAPV   49 (252)
T ss_pred             HHHHHHHHHHHHHcCCCcHHHHHHHhCCCHHHHHHHHHHhhcCe
Confidence            34456777788888899999999999999999999999999644

>PRK00215 LexA repressor; Validated

Probab=82.05  E-value=2.4  Score=33.03  Aligned_cols=39  Identities=18%  Similarity=0.249  Sum_probs=33.5

Q ss_pred             echHHHHhhhcc-chHHHHHHHHHHHHcCCeeEEeecCce
Q psy1871          87 ITPSVVSERLKV-RGSLARKALEELLQKGLIKQVVKHHAQ  125 (139)
Q Consensus        87 ITPsvlseRlkI-~~SLARkaLreL~~kGlIk~Vskh~~q  125 (139)
                      +|...||+.+++ .-|-+-+.|+.|+++|+|.......|.
T Consensus        24 ~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~~~~~~~r~   63 (205)
T PRK00215         24 PSRREIADALGLRSPSAVHEHLKALERKGFIRRDPGRSRA   63 (205)
T ss_pred             CCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEeCCCCcce
Confidence            588899999999 889999999999999999887544443

>PRK05472 redox-sensing transcriptional repressor Rex; Provisional

Probab=81.98  E-value=1.4  Score=34.86  Aligned_cols=50  Identities=22%  Similarity=0.219  Sum_probs=42.9

Q ss_pred             ceeeCHHHHHHHHhhCCCCe--eechHHHHhhhccchHHHHHHHHHHHHcCC
Q psy1871          66 QVLFDKASYDKLLKEVPAYK--LITPSVVSERLKVRGSLARKALEELLQKGL  115 (139)
Q Consensus        66 ~Vl~Dk~tydKl~KEVpk~K--lITPsvlseRlkI~~SLARkaLreL~~kGl  115 (139)
                      .++---+.|.+|++.+....  .||...||+.++|+.+..|+=|..|+..|.
T Consensus        10 ~~~~r~~~~~~il~~l~~~~~~~vs~~~L~~~~~v~~~tirrDl~~l~~~G~   61 (213)
T PRK05472         10 ATIKRLPLYYRYLKELKEEGVERVSSKELAEALGVDSAQIRKDLSYFGEFGK   61 (213)
T ss_pred             HHHHHhHHHHHHHHHHHHcCCcEEeHHHHHHHhCcCHHHHHHHHHHHHhcCC
Confidence            33334567888888888887  999999999999999999999999999985

>PRK11569 transcriptional repressor IclR; Provisional

Probab=81.87  E-value=2.5  Score=34.67  Aligned_cols=35  Identities=17%  Similarity=0.325  Sum_probs=32.0

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      -+|.+.||+++++.-|-+-++|..|++.|++....
T Consensus        43 ~~~lseia~~lglpksTv~RlL~tL~~~G~l~~~~   77 (274)
T PRK11569         43 SVALTELAQQAGLPNSTTHRLLTTMQQQGFVRQVG   77 (274)
T ss_pred             CcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcC
Confidence            37999999999999999999999999999997643

>TIGR00373 conserved hypothetical protein TIGR00373

Probab=81.73  E-value=3.7  Score=31.89  Aligned_cols=42  Identities=26%  Similarity=0.215  Sum_probs=36.2

Q ss_pred             HHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCee
Q psy1871          76 KLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIK  117 (139)
Q Consensus        76 Kl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk  117 (139)
                      .+..-++....+|.-.||+.|+|+..--|++|..|.+.|||.
T Consensus        18 ~Vl~aL~~~~~~tdEeLa~~Lgi~~~~VRk~L~~L~e~~Lv~   59 (158)
T TIGR00373        18 LVLFSLGIKGEFTDEEISLELGIKLNEVRKALYALYDAGLAD   59 (158)
T ss_pred             HHHHHHhccCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCce
Confidence            344455555679999999999999999999999999999995

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

>PF13814 Replic_Relax: Replication-relaxation

Probab=81.68  E-value=2.7  Score=31.76  Aligned_cols=51  Identities=20%  Similarity=0.301  Sum_probs=42.6

Q ss_pred             CCCeeechHHHHhhhccchH---HHHHHHHHHHHcCCeeEEee------cCceEEEeccC
Q psy1871          82 PAYKLITPSVVSERLKVRGS---LARKALEELLQKGLIKQVVK------HHAQVIYTRTT  132 (139)
Q Consensus        82 pk~KlITPsvlseRlkI~~S---LARkaLreL~~kGlIk~Vsk------h~~q~IYtra~  132 (139)
                      -.++++|...|+.-+.....   -+++.|+.|.+.|+|..+..      .+...||.=..
T Consensus         5 ~~~r~lt~~Qi~~l~~~~~~~~~~~~rrL~~L~~~glv~~~~~~~~~~~g~~~~vy~Lt~   64 (191)
T PF13814_consen    5 ARHRFLTTDQIARLLFPSSKSERTARRRLKRLRELGLVDRFRRRVGARGGSQPYVYYLTP   64 (191)
T ss_pred             HHhcCcCHHHHHHHHcCCCcchHHHHHHHHHHhhCCcEEeecccccccCCCcceEEEECH
Confidence            35789999999999999997   79999999999999998865      35677887543

>PRK09333 30S ribosomal protein S19e; Provisional

Probab=81.28  E-value=2.2  Score=33.81  Aligned_cols=34  Identities=24%  Similarity=0.364  Sum_probs=28.6

Q ss_pred             echHHHHhhhcc--------------chHHHHHHHHHHHHcCCeeEEe
Q psy1871          87 ITPSVVSERLKV--------------RGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        87 ITPsvlseRlkI--------------~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      |....|+..|+.              ++|+.|.+|+.||+-|+|....
T Consensus        68 vGV~~L~~~yGg~k~~G~~P~h~~~~sg~iiR~~LqqLE~~glVek~~  115 (150)
T PRK09333         68 VGVERLRTAYGGRKNRGVRPEHFVKGSGSIIRKILQQLEKAGLVEKTK  115 (150)
T ss_pred             ccHHHHHHHHCCCcCCCCCCCccccCccHHHHHHHHHHHHCCCeeeCC
Confidence            566777777777              5899999999999999998754

>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators

Probab=80.80  E-value=1.9  Score=31.33  Aligned_cols=40  Identities=15%  Similarity=0.155  Sum_probs=32.5

Q ss_pred             chHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871          88 TPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT  131 (139)
Q Consensus        88 TPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra  131 (139)
                      |...+|++++|+.+    .||.-++.|||.++..+....+|+..
T Consensus         2 ~ige~a~~~gvs~~----tLryYe~~GLi~p~~~~~~yR~Y~~~   41 (116)
T cd04769           2 YIGELAQQTGVTIK----AIRLYEEKGLLPSPKRSGNYRVYDAQ   41 (116)
T ss_pred             CHHHHHHHHCcCHH----HHHHHHHCCCCCCCCCCCCceeeCHH
Confidence            66789999988765    68999999999998666677888753

Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. 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 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.

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

Probab=80.27  E-value=2.6  Score=33.80  Aligned_cols=33  Identities=24%  Similarity=0.294  Sum_probs=30.9

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQ  118 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~  118 (139)
                      =+|.++||+++++.-|-+-++|..|++.|++..
T Consensus        24 ~~~l~eia~~lglpksT~~RlL~tL~~~G~l~~   56 (248)
T TIGR02431        24 RLTLTDVAEATGLTRAAARRFLLTLVELGYVTS   56 (248)
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe
Confidence            368999999999999999999999999999875

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.

>TIGR02054 MerD mercuric resistence transcriptional repressor protein MerD

Probab=80.23  E-value=1.6  Score=32.71  Aligned_cols=43  Identities=21%  Similarity=0.273  Sum_probs=35.2

Q ss_pred             eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEee-cCceEEEecc
Q psy1871          85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK-HHAQVIYTRT  131 (139)
Q Consensus        85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk-h~~q~IYtra  131 (139)
                      ...|...||++++|+.+    .||.-++.|||.+..+ .++..+|+..
T Consensus         2 ~~~tI~elA~~~gvs~~----tlR~Ye~~GLL~p~~r~~~gyR~Y~~~   45 (120)
T TIGR02054         2 NAYTISRLAEDAGVSVH----VVRDYLLRGLLHPVRRTTSGYGIFDDA   45 (120)
T ss_pred             CCCcHHHHHHHHCcCHH----HHHHHHHCCCCCCCccCCCCCeeCCHH
Confidence            45788999999999875    5899999999999844 4678888753

This model represents a transcriptional repressor protein of the MerR family (pfam00376) whose expression is regulated by the mercury-sensitive transcriptional activator, MerR. MerD has been shown to repress the transcription of the mer operon.

>cd04781 HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily

Probab=80.12  E-value=1.8  Score=31.59  Aligned_cols=40  Identities=20%  Similarity=0.228  Sum_probs=33.6

Q ss_pred             chHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871          88 TPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT  131 (139)
Q Consensus        88 TPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra  131 (139)
                      |...||++++|+.+    .||.-++.|+|.++-.+++...|+..
T Consensus         2 ~IgevA~~~gvs~~----tlRyYe~~GLl~p~~~~~gyR~Y~~~   41 (120)
T cd04781           2 DIAEVARQSGLPAS----TLRYYEEKGLIASIGRRGLRRQYDPQ   41 (120)
T ss_pred             CHHHHHHHHCcCHH----HHHHHHHCCCCCCCcCCCCceecCHH
Confidence            67889999998765    58999999999998666788899853

Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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, an

>PRK10163 DNA-binding transcriptional repressor AllR; Provisional

Probab=80.10  E-value=3.3  Score=33.95  Aligned_cols=34  Identities=21%  Similarity=0.068  Sum_probs=31.6

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      -+|.+.||+++++.-|-+-++|..|++.|++..-
T Consensus        40 ~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~~~   73 (271)
T PRK10163         40 SSSVSDISLNLDLPLSTTFRLLKVLQAADFVYQD   73 (271)
T ss_pred             CcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEc
Confidence            4899999999999999999999999999998664

>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=80.09  E-value=1.5  Score=31.15  Aligned_cols=36  Identities=22%  Similarity=0.296  Sum_probs=27.9

Q ss_pred             CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          84 YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        84 ~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      ...+|-..|++.++++..-.|++|..|.+.|+|...
T Consensus        25 ~~~l~de~la~~~~l~~~~vRkiL~~L~~~~lv~~~   60 (105)
T PF02002_consen   25 KGELTDEDLAKKLGLKPKEVRKILYKLYEDGLVSYR   60 (105)
T ss_dssp             H--B-HHHHHHTT-S-HHHHHHHHHHHHHHSS-EEE
T ss_pred             cCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeEEE
Confidence            357899999999999999999999999999999665

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.

>COG1414 IclR Transcriptional regulator [Transcription]

Probab=80.01  E-value=3.2  Score=33.89  Aligned_cols=36  Identities=22%  Similarity=0.369  Sum_probs=32.6

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEEeec
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKH  122 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh  122 (139)
                      +|.+.||+++++.-|-+.+.|..|++.|++..-..+
T Consensus        20 l~l~ela~~~glpksT~~RlL~tL~~~G~v~~d~~~   55 (246)
T COG1414          20 LSLAELAERLGLPKSTVHRLLQTLVELGYVEQDPED   55 (246)
T ss_pred             CCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEcCCC
Confidence            789999999999999999999999999998775433

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	139
3iz6_V	108	Localization Of The Small Subunit Ribosomal Protein		8e-21
3zey_U	113	High-resolution Cryo-electron Microscopy Structure		3e-14
3izb_V	108	Localization Of The Small Subunit Ribosomal Protein		7e-14
2xzm_8	143	Crystal Structure Of The Eukaryotic 40s Ribosomal S		5e-04

>pdb|3IZ6|V Chain V, Localization Of The Small Subunit Ribosomal Proteins Into A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s Ribosome Length = 108

Iteration: 1
 Score = 95.5 bits (236), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 44/72 (61%), Positives = 57/72 (79%)
Query: 63  LNNQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKH 122
           +NN VLFDKA+YDKLL EVP YK ITPSV+SERL++ GSLAR+A+++L  +G I+ V  H
Sbjct: 37  VNNSVLFDKATYDKLLSEVPKYKQITPSVLSERLRINGSLARQAIKDLESRGAIRVVSVH 96
Query: 123 HAQVIYTRTTKG 134
            +Q+IYTR T  
Sbjct: 97  SSQLIYTRATNA 108

>pdb|3ZEY|U Chain U, High-resolution Cryo-electron Microscopy Structure Of The Trypanosoma Brucei Ribosome Length = 113

Iteration: 1
 Score = 73.6 bits (179), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 35/68 (51%), Positives = 49/68 (72%)
Query: 63  LNNQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKH 122
           L N V+FDK + DKL+KEVP YK+ITPS++S+RLK+  +LA K L+ L ++GLI+ V   
Sbjct: 42  LQNAVMFDKETMDKLMKEVPKYKVITPSIISDRLKISVALAGKGLQHLCRQGLIRLVSCS 101
Query: 123 HAQVIYTR 130
               +YTR
Sbjct: 102 SKFRVYTR 109

>pdb|3IZB|V Chain V, Localization Of The Small Subunit Ribosomal Proteins Into A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae Translating 80s Ribosome Length = 108

Iteration: 1
 Score = 72.4 bits (176), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 34/72 (47%), Positives = 50/72 (69%)
Query: 64  NNQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHH 123
            + V+ D+  YD++LKEVP Y+ ++ SV+ +RLK+ GSLAR AL  L ++G+IK + KH 
Sbjct: 37  QHAVILDQEKYDRILKEVPTYRYVSVSVLVDRLKIGGSLARIALRHLEKEGIIKPISKHS 96
Query: 124 AQVIYTRTTKGD 135
            Q IYTR T  +
Sbjct: 97  KQAIYTRATASE 108

>pdb|2XZM|8 Chain 8, Crystal Structure Of The Eukaryotic 40s Ribosomal Subunit In Complex With Initiation Factor 1. This File Contains The 40s Subunit And Initiation Factor For Molecule 1 Length = 143

Iteration: 1
 Score = 40.0 bits (92), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 21/68 (30%), Positives = 41/68 (60%), Gaps = 1/68 (1%)
Query: 63  LNNQVLFDKASYDKLLKE-VPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK 121
           +N+ V  +K + + ++       K++T S V E+LKV GSLAR+ +  +  + L+++V K
Sbjct: 39  VNHAVFIEKKNVESIINNPSKVGKVLTVSTVVEKLKVNGSLARQLMRTMADRKLVEKVAK 98
Query: 122 HHAQVIYT 129
           +  Q +Y+
Sbjct: 99  NGNQWVYS 106

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	139
3iz6_V	108	40S ribosomal protein S25 (S25E); eukaryotic ribos	8e-37
3u5c_Z	108	RP45, S31, YS23, 40S ribosomal protein S25-A; tran	3e-36
2xzm_8	143	RPS25E,; ribosome, translation; 3.93A {Tetrahymena	1e-32

>3iz6_V 40S ribosomal protein S25 (S25E); eukaryotic ribosome,homology modeling,de novo modeling,ribos proteins,novel ribosomal proteins, ribosome; 5.50A {Triticum aestivum} Length = 108

 Score =  120 bits (303), Expect = 8e-37
 Identities = 64/114 (56%), Positives = 80/114 (70%), Gaps = 7/114 (6%)

Query: 21  PPKKDTKGGSSKQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDKASYDKLLKE 80
            PKKD     S +P K         GGK KKKKWSKGK ++K+NN VLFDKA+YDKLL E
Sbjct: 2   APKKDKAPPPSSKPAK-------SGGGKQKKKKWSKGKQKEKVNNSVLFDKATYDKLLSE 54

Query: 81  VPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTTKG 134
           VP YK ITPSV+SERL++ GSLAR+A+++L  +G I+ V  H +Q+IYTR T  
Sbjct: 55  VPKYKQITPSVLSERLRINGSLARQAIKDLESRGAIRVVSVHSSQLIYTRATNA 108

>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 Length = 108

 Score =  119 bits (299), Expect = 3e-36
 Identities = 47/104 (45%), Positives = 68/104 (65%)

Query: 32  KQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDKASYDKLLKEVPAYKLITPSV 91
           +Q  K  K     +GGK  KKKWSK  ++D+  + V+ D+  YD++LKEVP Y+ ++ SV
Sbjct: 5   QQLSKAAKAAAALAGGKKSKKKWSKKSMKDRAQHAVILDQEKYDRILKEVPTYRYVSVSV 64

Query: 92  VSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTTKGD 135
           + +RLK+ GSLAR AL  L ++G+IK + KH  Q IYTR T  +
Sbjct: 65  LVDRLKIGGSLARIALRHLEKEGIIKPISKHSKQAIYTRATASE 108

>2xzm_8 RPS25E,; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_8 Length = 143

 Score =  111 bits (278), Expect = 1e-32
 Identities = 33/111 (29%), Positives = 61/111 (54%), Gaps = 1/111 (0%)

Query: 27  KGGSSKQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDKASYDKLLKEVPAY-K 85
           K  ++ Q +  +   +     K  KKKW+KGK +DK+N+ V  +K + + ++       K
Sbjct: 3   KQPAAGQKKTKEAIAKAAQAKKGGKKKWTKGKAKDKVNHAVFIEKKNVESIINNPSKVGK 62

Query: 86  LITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTTKGDD 136
           ++T S V E+LKV GSLAR+ +  +  + L+++V K+  Q +Y+      +
Sbjct: 63  VLTVSTVVEKLKVNGSLARQLMRTMADRKLVEKVAKNGNQWVYSVIGGVKE 113

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	139
3u5c_Z	108	RP45, S31, YS23, 40S ribosomal protein S25-A; tran	100.0
3iz6_V	108	40S ribosomal protein S25 (S25E); eukaryotic ribos	100.0
2xzm_8	143	RPS25E,; ribosome, translation; 3.93A {Tetrahymena	100.0
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	97.32
2b0l_A	102	GTP-sensing transcriptional pleiotropic repressor;	97.18
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	97.12
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	97.05
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	96.65
3neu_A	125	LIN1836 protein; structural genomics, PSI-2, prote	96.56
2qvo_A	95	Uncharacterized protein AF_1382; PSI, structural g	96.49
1p6r_A	82	Penicillinase repressor; transcription regulation,	96.46
2dk5_A	91	DNA-directed RNA polymerase III 39 kDa polypeptide	96.36
1xmk_A	79	Double-stranded RNA-specific adenosine deaminase;	96.32
3tqn_A	113	Transcriptional regulator, GNTR family; regulatory	96.25
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	96.22
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	96.19
4ham_A	134	LMO2241 protein; structural genomics, PSI-biology,	96.13
1sfx_A	109	Conserved hypothetical protein AF2008; structural	96.1
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	96.09
2fu4_A	83	Ferric uptake regulation protein; DNA binding doma	96.07
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	95.93
3f8m_A	248	GNTR-family protein transcriptional regulator; PHN	95.93
2gxg_A	146	146AA long hypothetical transcriptional regulator;	95.77
1okr_A	123	MECI, methicillin resistance regulatory protein ME	95.73
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	95.72
1v4r_A	102	Transcriptional repressor; helix-turn-helix, winge	95.7
3by6_A	126	Predicted transcriptional regulator; structural ge	95.67
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	95.63
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	95.62
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	95.62
3jth_A	98	Transcription activator HLYU; transcription factor	95.6
1r7j_A	95	Conserved hypothetical protein SSO10A; winged heli	95.6
1ub9_A	100	Hypothetical protein PH1061; helix-turn-helix moti	95.59
2hs5_A	239	Putative transcriptional regulator GNTR; APC6050,	95.53
1tbx_A	99	ORF F-93, hypothetical 11.0 kDa protein; sulfolobu	95.52
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	95.48
2pg4_A	95	Uncharacterized protein; structural genomics, join	95.47
2bv6_A	142	MGRA, HTH-type transcriptional regulator MGRA; mul	95.47
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	95.47
3ic7_A	126	Putative transcriptional regulator; helix-turn-hel	95.44
3hsr_A	140	HTH-type transcriptional regulator SARZ; helix-tur	95.43
1hw1_A	239	FADR, fatty acid metabolism regulator protein; hel	95.42
3r0a_A	123	Putative transcriptional regulator; structural gen	95.41
2fbi_A	142	Probable transcriptional regulator; MARR, APC5816,	95.37
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	95.34
2xvc_A	59	ESCRT-III, SSO0910; cell cycle, cell division, cyt	95.33
3bj6_A	152	Transcriptional regulator, MARR family; helix-turn	95.33
2h09_A	155	Transcriptional regulator MNTR; transcription regu	95.29
2pex_A	153	Transcriptional regulator OHRR; transcription regu	95.29
2rdp_A	150	Putative transcriptional regulator MARR; PFAM PF01	95.28
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	95.24
3cjn_A	162	Transcriptional regulator, MARR family; silicibact	95.24
2fbh_A	146	Transcriptional regulator PA3341; MARR, transcript	95.22
2kko_A	108	Possible transcriptional regulatory protein (possi	95.2
2ek5_A	129	Predicted transcriptional regulators; helix-turn-h	95.18
2a61_A	145	Transcriptional regulator TM0710; APC4350, MCSG, m	95.17
2nnn_A	140	Probable transcriptional regulator; structural gen	95.16
1y0u_A	96	Arsenical resistance operon repressor, putative; s	95.15
1ku9_A	152	Hypothetical protein MJ223; putative transcription	95.14
3oop_A	143	LIN2960 protein; protein structure initiative, PSI	95.13
2di3_A	239	Bacterial regulatory proteins, GNTR family; helix-	95.11
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	95.11
2hr3_A	147	Probable transcriptional regulator; MCSG, structur	95.09
2vn2_A	128	DNAD, chromosome replication initiation protein; D	95.04
3eet_A	272	Putative GNTR-family transcriptional regulator; st	95.04
1wi9_A	72	Protein C20ORF116 homolog; helix-turn-helix motif,	95.04
2wv0_A	243	YVOA, HTH-type transcriptional repressor YVOA; DNA	95.01
1s3j_A	155	YUSO protein; structural genomics, MARR transcript	95.0
3k0l_A	162	Repressor protein; helix-turn-helix, structural ge	94.97
1lj9_A	144	Transcriptional regulator SLYA; HTH DNA binding pr	94.94
2eth_A	154	Transcriptional regulator, putative, MAR family; M	94.92
3s2w_A	159	Transcriptional regulator, MARR family; structural	94.89
2v79_A	135	DNA replication protein DNAD; primosome, DNA-bindi	94.89
2k4b_A	99	Transcriptional regulator; DNA binding protein, wi	94.89
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	94.87
3sxy_A	218	Transcriptional regulator, GNTR family; transcript	94.85
3deu_A	166	Transcriptional regulator SLYA; MARR, WING-helix,	94.81
2qww_A	154	Transcriptional regulator, MARR family; YP_013417.	94.79
3df8_A	111	Possible HXLR family transcriptional factor; APC89	94.76
2y75_A	129	HTH-type transcriptional regulator CYMR; DNA bindi	94.74
3c7j_A	237	Transcriptional regulator, GNTR family; structural	94.72
1z91_A	147	Organic hydroperoxide resistance transcriptional;	94.71
1z7u_A	112	Hypothetical protein EF0647; winged-helix-turn-hel	94.69
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	94.69
2hzt_A	107	Putative HTH-type transcriptional regulator YTCD;	94.67
1sd4_A	126	Penicillinase repressor; BLAI, MECI, methicillin,	94.65
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	94.62
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	94.62
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	94.61
3bja_A	139	Transcriptional regulator, MARR family, putative;	94.58
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	94.57
3b73_A	111	PHIH1 repressor-like protein; winged-helix-turn-he	94.52
3g3z_A	145	NMB1585, transcriptional regulator, MARR family; t	94.48
4hbl_A	149	Transcriptional regulator, MARR family; HTH, trans	94.42
3e6m_A	161	MARR family transcriptional regulator; APC88769, s	94.4
1on2_A	142	Transcriptional regulator MNTR; helix-turn-helix,	94.37
2nyx_A	168	Probable transcriptional regulatory protein, RV14;	94.36
3nqo_A	189	MARR-family transcriptional regulator; structural	94.32
2w25_A	150	Probable transcriptional regulatory protein; trans	94.25
3bwg_A	239	Uncharacterized HTH-type transcriptional regulato;	94.2
3cdh_A	155	Transcriptional regulator, MARR family; helix-turn	94.07
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	94.05
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	94.05
3edp_A	236	LIN2111 protein; APC88337, listeria innocua CLIP11	93.94
1u2w_A	122	CADC repressor, cadmium efflux system accessory pr	93.93
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	93.91
2fsw_A	107	PG_0823 protein; alpha-beta structure, helix-turn-	93.87
3nrv_A	148	Putative transcriptional regulator (MARR/EMRR FAM;	93.85
3f3x_A	144	Transcriptional regulator, MARR family, putative;	93.84
2qc0_A	373	Uncharacterized protein; NP_719793.1, uncharacteri	93.8
3f6o_A	118	Probable transcriptional regulator, ARSR family pr	93.78
3u2r_A	168	Regulatory protein MARR; structural genomics, PSI-	93.76
3kp7_A	151	Transcriptional regulator TCAR; multiple drug resi	93.76
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	93.76
2g9w_A	138	Conserved hypothetical protein; DNA-binding domain	93.73
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	93.71
1r1t_A	122	Transcriptional repressor SMTB; zinc, transcriptio	93.68
2yu3_A	95	DNA-directed RNA polymerase III 39 kDa polypeptide	93.48
4fx0_A	148	Probable transcriptional repressor protein; helix-	93.48
2frh_A	127	SARA, staphylococcal accessory regulator A; winged	93.46
1uly_A	192	Hypothetical protein PH1932; helix-turn-helix, str	93.46
2v7f_A	150	RPS19, RPS19E SSU ribosomal protein S19E; diamond	93.43
4b8x_A	147	SCO5413, possible MARR-transcriptional regulator;	93.39
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	93.37
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	93.37
3fm5_A	150	Transcriptional regulator; MCSG, PF04017, PSI, MAR	93.29
4aik_A	151	Transcriptional regulator SLYA; transcription, tra	93.24
1ylf_A	149	RRF2 family protein; structural genomics, transcri	93.21
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	93.12
3ihu_A	222	Transcriptional regulator, GNTR family; YP_298823.	93.09
1yyv_A	131	Putative transcriptional regulator; reductive meth	93.06
3boq_A	160	Transcriptional regulator, MARR family; MARR famil	93.05
3t8r_A	143	Staphylococcus aureus CYMR; transcriptional regula	92.99
3lwf_A	159	LIN1550 protein, putative transcriptional regulato	92.92
1sfu_A	75	34L protein; protein/Z-DNA complex, DNA binding pr	92.85
3cuq_B	218	Vacuolar protein-sorting-associated protein 36; ES	92.69
2jsc_A	118	Transcriptional regulator RV1994C/MT2050; cadmium,	92.54
2w48_A	315	Sorbitol operon regulator; SORC, activator, repres	92.53
3hrs_A	214	Metalloregulator SCAR; DTXR/MNTR family member, tr	92.44
3jw4_A	148	Transcriptional regulator, MARR/EMRR family; DNA-b	92.32
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	92.32
2f2e_A	146	PA1607; transcription factor, helix-TRUN-helix, AP	92.27
2fxa_A	207	Protease production regulatory protein HPR; protea	92.14
3i4p_A	162	Transcriptional regulator, ASNC family; PSI, struc	91.91
3f6v_A	151	Possible transcriptional regulator, ARSR family pr	91.83
3eqx_A	373	FIC domain containing transcriptional regulator; F	91.7
2pjp_A	121	Selenocysteine-specific elongation factor; SELB, p	91.69
4a5n_A	131	Uncharacterized HTH-type transcriptional regulato;	91.44
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	91.43
2p4w_A	202	Transcriptional regulatory protein ARSR family; ar	90.88
3k69_A	162	Putative transcription regulator; putative transcr	90.41
2vxz_A	165	Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Py	90.41
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	90.34
1xd7_A	145	YWNA; structural genomics, protein structure initi	90.28
2wte_A	244	CSA3; antiviral protein, viral resistance, winged	90.05
2ra5_A	247	Putative transcriptional regulator; beta structure	89.65
1u5t_B	169	Defective in vacuolar protein sorting; VPS36P; ESC	89.55
1fx7_A	230	Iron-dependent repressor IDER; DTXR, iron-dependen	89.55
2gqq_A	163	Leucine-responsive regulatory protein; helix-turn-	89.5
2o03_A	131	Probable zinc uptake regulation protein FURB; DNA-	89.4
2fbk_A	181	Transcriptional regulator, MARR family; winged-hel	88.53
2xrn_A	241	HTH-type transcriptional regulator TTGV; DNA-bindi	88.17
2fe3_A	145	Peroxide operon regulator; oxidative stress regula	87.53
1mkm_A	249	ICLR transcriptional regulator; structural genomic	87.47
1bia_A	321	BIRA bifunctional protein; transcription regulatio	87.46
2p5k_A	64	Arginine repressor; DNA-binding domain, winged hel	87.41
2ve8_A	73	FTSK, DNA translocase FTSK; nucleotide-binding, ch	87.3
2qq9_A	226	Diphtheria toxin repressor; regulator, DTXR, helix	87.3
2xig_A	150	Ferric uptake regulation protein; hpfur, transcrip	87.25
1w7p_D	566	VPS36P, YLR417W; ESCRT-II complex, endosomal prote	87.05
3r4k_A	260	Transcriptional regulator, ICLR family; DNA/RNA-bi	87.04
1hsj_A	487	Fusion protein consisting of staphylococcus access	86.85
2w57_A	150	Ferric uptake regulation protein; gene regulation,	86.75
3cuq_A	234	Vacuolar-sorting protein SNF8; ESCRT, MBV, VPS, nu	86.66
3ryp_A	210	Catabolite gene activator; CAMP receptor protein (	86.44
1mzb_A	136	Ferric uptake regulation protein; ferric uptake re	86.39
2zkz_A	99	Transcriptional repressor PAGR; protein-DNA, HTH m	86.31
2zcw_A	202	TTHA1359, transcriptional regulator, FNR/CRP famil	86.15
2qlz_A	232	Transcription factor PF0095; 2.50A {Pyrococcus fur	85.87
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	85.8
3dv8_A	220	Transcriptional regulator, CRP/FNR family; cyclic	85.61
3cta_A	230	Riboflavin kinase; structural genomics, transferas	85.57
2obp_A	96	Putative DNA-binding protein; structural genomics,	85.45
4ev0_A	216	Transcription regulator, CRP family; CAMP binding,	85.23
3dkw_A	227	DNR protein; CRP-FNR, HTH, beta barrel, dimerizati	84.87
2o0y_A	260	Transcriptional regulator; ICLR-family, structural	84.39
3d0s_A	227	Transcriptional regulatory protein; CAMP receptor	84.2
2oz6_A	207	Virulence factor regulator; winged helix, helix-tu	84.07
3hh0_A	146	Transcriptional regulator, MERR family; protein st	83.77
3gpv_A	148	Transcriptional regulator, MERR family; protein st	83.76
1stz_A	338	Heat-inducible transcription repressor HRCA homol;	83.75
2g7u_A	257	Transcriptional regulator; ICLR family, structural	83.68
3f8b_A	116	Transcriptional regulator, PADR-like family; winge	83.65
1xma_A	145	Predicted transcriptional regulator; southea colla	83.39
2o0m_A	345	Transcriptional regulator, SORC family; structural	83.39
3iwz_A	230	CAP-like, catabolite activation-like protein; XCC,	83.04
2gau_A	232	Transcriptional regulator, CRP/FNR family; structu	82.99
3mwm_A	139	ZUR, putative metal uptake regulation protein; FUR	82.97
2ia2_A	265	Putative transcriptional regulator; SAD, PSI-2, st	82.65
1j5y_A	187	Transcriptional regulator, biotin repressor famil;	82.51
2p8t_A	200	Hypothetical protein PH0730; pyrococcus horikoshii	82.26
1u5t_A	233	Appears to BE functionally related to SNF7; SNF8P;	82.04
2pjp_A	121	Selenocysteine-specific elongation factor; SELB, p	82.02
3mq0_A	275	Transcriptional repressor of the blcabc operon; he	81.85
2hoe_A	380	N-acetylglucosamine kinase; TM1224, structural gen	81.8
3la7_A	243	Global nitrogen regulator; activator, DNA-binding,	81.27
3kcc_A	260	Catabolite gene activator; helix-turn-helix, CAMP,	81.17
3eyy_A	145	Putative iron uptake regulatory protein; NUR, nick	81.16
3e97_A	231	Transcriptional regulator, CRP/FNR family; YP_6044	80.97
2fmy_A	220	COOA, carbon monoxide oxidation system transcripti	80.94
1ft9_A	222	Carbon monoxide oxidation system transcription reg	80.92
4esf_A	117	PADR-like transcriptional regulator; PADR family,	80.66
3b02_A	195	Transcriptional regulator, CRP family; structural	80.43
3i71_A	68	Ethanolamine utilization protein EUTK; helix-turn-	80.36
2esh_A	118	Conserved hypothetical protein TM0937; APC5794, st	80.05
4a0z_A	190	Transcription factor FAPR; lipid homeostasis; HET:	80.02

>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=100.00  E-value=5.9e-53  Score=312.56  Aligned_cols=107  Identities=45%  Similarity=0.766  Sum_probs=69.8

Q ss_pred             CCCCCCCCCCCCCCcchhhhhhccCCCCccccccccchhhhhhhccceeeCHHHHHHHHhhCCCCeeechHHHHhhhccc
Q psy1871          20 HPPKKDTKGGSSKQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVR   99 (139)
Q Consensus        20 mppK~~~~~~~~~~~~~~~k~~~a~sggk~kKKKWSKgKvkdKlnn~Vl~Dk~tydKl~KEVpk~KlITPsvlseRlkI~   99 (139)
                      ||||+++.+        +++++++++||+++||||||||+|||+||+|+||++|||||++|||+|+|||||+|||||+|+
T Consensus         1 M~pK~~~sk--------~~k~~~a~~ggk~~KKKWsKgk~kdK~nn~VlfDk~t~dkl~KEVpk~KlITpsvlseRlkI~   72 (108)
T 3u5c_Z            1 MPPKQQLSK--------AAKAAAALAGGKKSKKKWSKKSMKDRAQHAVILDQEKYDRILKEVPTYRYVSVSVLVDRLKIG   72 (108)
T ss_dssp             -------------------------------------------CCSCSSCTTHHHHHHHHHCSSCSSBSHHHHHHTTCCC
T ss_pred             CCCccccCH--------HHHHHHHhcCCCccccccccccHHHHhhcceeeCHHHHHHHHHHccCCeEEeHHHhhhhhhhh
Confidence            999976665        477888999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHHHHHHcCCeeEEeecCceEEEeccCCC
Q psy1871         100 GSLARKALEELLQKGLIKQVVKHHAQVIYTRTTKG  134 (139)
Q Consensus       100 ~SLARkaLreL~~kGlIk~Vskh~~q~IYtra~k~  134 (139)
                      |||||++||||+++|+|++|++||+|.||||+++.
T Consensus        73 gSLAR~aLreL~~kGlIk~V~kh~~q~IYTr~~~~  107 (108)
T 3u5c_Z           73 GSLARIALRHLEKEGIIKPISKHSKQAIYTRATAS  107 (108)
T ss_dssp             TTHHHHHHHHHSSSSSCEEEECCSSCCEEECCC--
T ss_pred             HHHHHHHHHHHHHCCCEEEEecCCCEEEEecCccC
Confidence            99999999999999999999999999999999864

>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=100.00  E-value=3e-52  Score=308.78  Aligned_cols=107  Identities=58%  Similarity=0.896  Sum_probs=94.1

Q ss_pred             CCCCCCCCCCCCCCcchhhhhhccCCCCccccccccchhhhhhhccceeeCHHHHHHHHhhCCCCeeechHHHHhhhccc
Q psy1871          20 HPPKKDTKGGSSKQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVR   99 (139)
Q Consensus        20 mppK~~~~~~~~~~~~~~~k~~~a~sggk~kKKKWSKgKvkdKlnn~Vl~Dk~tydKl~KEVpk~KlITPsvlseRlkI~   99 (139)
                      ||||.+++.+       +++++++++||+++||||||||+|||+||+|+||++|||||++|||+|+|||||+|||||+|+
T Consensus         1 m~pk~~~~~k-------~~~~~~a~~ggk~~KKKWsKgk~kdk~nn~Vl~Dk~t~dkl~KEVpk~KlITpsvlseRlkI~   73 (108)
T 3iz6_V            1 MAPKKDKAPP-------PSSKPAKSGGGKQKKKKWSKGKQKEKVNNSVLFDKATYDKLLSEVPKYKQITPSVLSERLRIN   73 (108)
T ss_dssp             --------CC-------CCCCCCTTCCCCCCCCSCCCCCCSHHHHSHHHHSSHHHHHHHHHHHHHSSEEEHHHHHHHHTC
T ss_pred             CCCcccccCH-------HHHHHHHhcCCCccccccccccHHHHhcCcEeECHHHHHHHHHHccCCeEEeHHHHHhhhccc
Confidence            9999555433       356668999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHHHHHHHHcCCeeEEeecCceEEEeccCC
Q psy1871         100 GSLARKALEELLQKGLIKQVVKHHAQVIYTRTTK  133 (139)
Q Consensus       100 ~SLARkaLreL~~kGlIk~Vskh~~q~IYtra~k  133 (139)
                      |||||++||||+++|+|++|++||+|.||||++.
T Consensus        74 gSLAR~aLreL~~kGlIk~V~kh~~q~IYTr~~~  107 (108)
T 3iz6_V           74 GSLARQAIKDLESRGAIRVVSVHSSQLIYTRATN  107 (108)
T ss_dssp             CHHHHHHHHHHHHHHTSCEECCCTTSCCEEESCC
T ss_pred             HHHHHHHHHHHHHCCCEEEEecCCCEEEEecCcC
Confidence            9999999999999999999999999999999974

>2xzm_8 RPS25E,; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_8

Probab=100.00  E-value=2.4e-48  Score=299.41  Aligned_cols=112  Identities=31%  Similarity=0.494  Sum_probs=88.8

Q ss_pred             ccCCCCCCCCCCCCCCcchhhhhhccCCCCccccccccchhhhhhhccceeeCHHHHHHHHhhCCCC-eeechHHHHhhh
Q psy1871          18 YKHPPKKDTKGGSSKQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDKASYDKLLKEVPAY-KLITPSVVSERL   96 (139)
Q Consensus        18 ~~mppK~~~~~~~~~~~~~~~k~~~a~sggk~kKKKWSKgKvkdKlnn~Vl~Dk~tydKl~KEVpk~-KlITPsvlseRl   96 (139)
                      ..||||++++.+       ++++++++ +|+++||||||||+|||+||+|+||++|||||++|||+| +|||||+|||||
T Consensus         2 ~~mppk~~~k~k-------~~~~~~a~-~gk~kKKKWSKgKvkdK~nn~VlfDk~tydKL~KEVpk~gKlITpsvlseRl   73 (143)
T 2xzm_8            2 GKQPAAGQKKTK-------EAIAKAAQ-AKKGGKKKWTKGKAKDKVNHAVFIEKKNVESIINNPSKVGKVLTVSTVVEKL   73 (143)
T ss_dssp             -----------------------------CCCCSSCCCSSCCCCCCCCBSCCCHHHHHHHHTCCTTSCSEECHHHHHHHH
T ss_pred             CCCCCcccccch-------hHHHHhhc-cCccccCCcccchHHHHHhcceeecHHHHHHHHHHhcccceeecHHHHHHHh
Confidence            359999544332       23334444 489999999999999999999999999999999999999 999999999999


Q ss_pred             ccchHHHHHHHHHHHHcCCeeEEeecCceEEEeccCCCCCC
Q psy1871          97 KVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTTKGDDP  137 (139)
Q Consensus        97 kI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra~k~~~~  137 (139)
                      +||+||||++||||+++|+|++|++||+|.||||+++++++
T Consensus        74 kI~gSLARkaLreL~~kGlIk~V~kh~~q~IYTra~~~~~~  114 (143)
T 2xzm_8           74 KVNGSLARQLMRTMADRKLVEKVAKNGNQWVYSVIGGVKED  114 (143)
T ss_dssp             CBCHHHHHHHHHHHHHTTSEEEEEEETTEEEEEETTCCCCC
T ss_pred             cchHHHHHHHHHHHHHCCCEEEEecCCCeEEEecCCccchh
Confidence            99999999999999999999999999999999999987664

>1xn7_A Hypothetical protein YHGG; alpha+beta, GFT structural genomics, protein structure initiative, PSI, NESG; NMR {Escherichia coli} SCOP: a.4.5.62

Probab=97.32  E-value=0.00016  Score=49.55  Aligned_cols=47  Identities=13%  Similarity=0.148  Sum_probs=42.7

Q ss_pred             HHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          73 SYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        73 tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      +++.|+..+.....||.+.||++|+|+-+..|+-|.+|+++|+|..+
T Consensus         3 ~L~~Il~~L~~~g~vsv~eLa~~l~VS~~TIRrdL~~Le~~G~l~R~   49 (78)
T 1xn7_A            3 SLIQVRDLLALRGRMEAAQISQTLNTPQPMINAMLQQLESMGKAVRI   49 (78)
T ss_dssp             CHHHHHHHHHHSCSBCHHHHHHHTTCCHHHHHHHHHHHHHHTSEEEE
T ss_pred             hHHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence            35677777777889999999999999999999999999999999988

>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=97.18  E-value=0.00036  Score=49.13  Aligned_cols=47  Identities=21%  Similarity=0.369  Sum_probs=40.0

Q ss_pred             HHHHHhhC-CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          74 YDKLLKEV-PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        74 ydKl~KEV-pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      .+.|..++ |+.++.|...||++|+|+-+..|.+|+.|+++|+|....
T Consensus        30 ~~~I~~~l~~g~~lps~~eLa~~lgVSr~tVr~al~~L~~~GlI~~~~   77 (102)
T 2b0l_A           30 IEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRS   77 (102)
T ss_dssp             HHHHTTSSBTTEEEECHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHhhhcCCCcCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEe
Confidence            55666555 456777999999999999999999999999999997765

>2k02_A Ferrous iron transport protein C; FEOC, iron-sulfur, metal-binding, metal binding protein; NMR {Klebsiella pneumoniae subsp}

Probab=97.12  E-value=0.00024  Score=49.95  Aligned_cols=47  Identities=15%  Similarity=0.171  Sum_probs=42.3

Q ss_pred             HHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          74 YDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        74 ydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      +++|+..+.....||++.||++|+|+-+..|+-|.+|+++|+|..+.
T Consensus         4 L~~Il~~L~~~g~vsv~eLA~~l~VS~~TIRrDL~~Le~~G~l~R~~   50 (87)
T 2k02_A            4 LMEVRDMLALQGRMEAKQLSARLQTPQPLIDAMLERMEAMGKVVRIS   50 (87)
T ss_dssp             THHHHHHHHHSCSEEHHHHHHHTTCCHHHHHHHHHHHHTTCCSEEEE
T ss_pred             HHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEe
Confidence            45677777777899999999999999999999999999999999984

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

Probab=97.05  E-value=0.00042  Score=47.33  Aligned_cols=45  Identities=13%  Similarity=0.071  Sum_probs=38.4

Q ss_pred             eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEe
Q psy1871          85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYT  129 (139)
Q Consensus        85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYt  129 (139)
                      --+|...||+.|+|+-+-+|+-|..|+++|+|..+-..++...+.
T Consensus        23 ~~psv~EIa~~lgvS~~TVrr~L~~Le~kG~I~R~~ggr~~~~~~   67 (77)
T 2jt1_A           23 APVKTRDIADAAGLSIYQVRLYLEQLHDVGVLEKVNAGKGVPGLW   67 (77)
T ss_dssp             SCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEESCSSSSCCEE
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEecCCCCCcHHHH
Confidence            458999999999999999999999999999999987555544443

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

Probab=96.65  E-value=0.0056  Score=40.17  Aligned_cols=44  Identities=18%  Similarity=0.166  Sum_probs=36.1

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEEe-ecCceEEEec
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVV-KHHAQVIYTR  130 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs-kh~~q~IYtr  130 (139)
                      +|...||+.++|+-+-+++.|+.|++.|+|.... +..+...|.-
T Consensus        15 ~s~~eLa~~lgvs~~tv~r~L~~L~~~GlI~~~~~~~gr~~~y~l   59 (81)
T 2htj_A           15 GKTAEIAEALAVTDYQARYYLLLLEKAGMVQRSPLRRGMATYWFL   59 (81)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHHHHHHTSEEEECCSSSSSCEEEE
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeccCCCCcEEEEE
Confidence            8999999999999999999999999999998653 3334444443

>3neu_A LIN1836 protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG, unknown function; 1.58A {Listeria innocua}

Probab=96.56  E-value=0.0043  Score=44.32  Aligned_cols=50  Identities=22%  Similarity=0.187  Sum_probs=41.2

Q ss_pred             HHHHHHHHhhC------CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          71 KASYDKLLKEV------PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        71 k~tydKl~KEV------pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      ...|+.|...|      |..++-|-..||++|+|+-+..|+||+.|++.|+|....
T Consensus        16 ~~i~~~i~~~I~~g~~~~g~~Lps~~~La~~~~vSr~tvr~Al~~L~~~G~i~~~~   71 (125)
T 3neu_A           16 SQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKR   71 (125)
T ss_dssp             HHHHHHHHHHHHTTSSCTTCBCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             HHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCeEEEec
Confidence            44566666655      456777899999999999999999999999999986643

>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=96.49  E-value=0.0059  Score=40.97  Aligned_cols=44  Identities=5%  Similarity=0.053  Sum_probs=36.2

Q ss_pred             eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEe
Q psy1871          85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYT  129 (139)
Q Consensus        85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYt  129 (139)
                      .-+|++.||++++|.-|-.-++|..|+++|+| ....++|...|.
T Consensus        29 ~~~t~~eLa~~l~i~~~tvs~~l~~Le~~Glv-~~~~d~R~~~v~   72 (95)
T 2qvo_A           29 NDVYIQYIASKVNSPHSYVWLIIKKFEEAKMV-ECELEGRTKIIR   72 (95)
T ss_dssp             CCEEHHHHHHHSSSCHHHHHHHHHHHHHTTSE-EEEEETTEEEEE
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHCcCc-cCCCCCCeEEEE
Confidence            34899999999999999999999999999999 444555554443

>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=96.46  E-value=0.011  Score=38.54  Aligned_cols=50  Identities=20%  Similarity=0.255  Sum_probs=41.0

Q ss_pred             eechHHHHhhhc----cchHHHHHHHHHHHHcCCeeEEeecCceEEEeccCCCCC
Q psy1871          86 LITPSVVSERLK----VRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTTKGDD  136 (139)
Q Consensus        86 lITPsvlseRlk----I~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra~k~~~  136 (139)
                      -+|...|+++++    +.-|-....|+.|+++|+|..... ++..+|......++
T Consensus        23 ~~t~~ei~~~l~~~~~~s~~Tv~~~l~rL~~kGlv~r~~~-gr~~~y~~~~~~~~   76 (82)
T 1p6r_A           23 SINTNEVIKELSKTSTWSPKTIQTMLLRLIKKGALNHHKE-GRVFVYTPNIDESD   76 (82)
T ss_dssp             SEEHHHHHHHHHHHSCCCHHHHHHHHHHHHHTTSEEEEEE-TTEEEEEESCSSST
T ss_pred             CCCHHHHHHHHhhcCCccHHHHHHHHHHHHHCCCeEEEec-CCEEEEEeecCHHH
Confidence            489999999998    578899999999999999998754 55778876655443

>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=96.36  E-value=0.006  Score=42.46  Aligned_cols=44  Identities=25%  Similarity=0.176  Sum_probs=37.7

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe--ecCceEEEe
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVV--KHHAQVIYT  129 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs--kh~~q~IYt  129 (139)
                      =||+..|++++++.-+..-++|+.|+++|+|+.|.  .+.+..+|.
T Consensus        36 gi~qkeLa~~~~l~~~tvt~iLk~LE~kglIkr~~~~~~~~rKvy~   81 (91)
T 2dk5_A           36 GIWSRDVRYKSNLPLTEINKILKNLESKKLIKAVKSVAASKKKVYM   81 (91)
T ss_dssp             CEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEECCSSCSSCCEEE
T ss_pred             CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCCCCCCcEEEE
Confidence            48999999999999999999999999999999773  334555665

>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=96.32  E-value=0.0056  Score=42.12  Aligned_cols=59  Identities=8%  Similarity=0.027  Sum_probs=46.1

Q ss_pred             HHHHHHHHhhCCCCeeechHHHHhhhccchH-HHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871          71 KASYDKLLKEVPAYKLITPSVVSERLKVRGS-LARKALEELLQKGLIKQVVKHHAQVIYTRT  131 (139)
Q Consensus        71 k~tydKl~KEVpk~KlITPsvlseRlkI~~S-LARkaLreL~~kGlIk~Vskh~~q~IYtra  131 (139)
                      .++-++|+.-+.+.-=.|..+||+.|+|+.+ -+|+.|..|+++|+|.....++  ++|.-.
T Consensus        10 ~~~~~~IL~~Lk~~g~~ta~eiA~~Lgit~~~aVr~hL~~Le~eGlV~~~~~gR--P~w~LT   69 (79)
T 1xmk_A           10 AEIKEKICDYLFNVSDSSALNLAKNIGLTKARDINAVLIDMERQGDVYRQGTTP--PIWHLT   69 (79)
T ss_dssp             HHHHHHHHHHHHHTCCEEHHHHHHHHCGGGHHHHHHHHHHHHHTTSEEEECSSS--CEEEEC
T ss_pred             hhHHHHHHHHHHHcCCcCHHHHHHHcCCCcHHHHHHHHHHHHHCCCEEecCCCC--CCeEeC
Confidence            4566666655555555899999999999999 9999999999999998654444  377644

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

Probab=96.25  E-value=0.0068  Score=42.49  Aligned_cols=49  Identities=16%  Similarity=0.250  Sum_probs=39.1

Q ss_pred             HHHHHHHHhhC------CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          71 KASYDKLLKEV------PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        71 k~tydKl~KEV------pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      ...|+.|...|      |..++-|-..||++|+|+-+..|.+|+.|+++|+|..+
T Consensus        12 ~~i~~~i~~~I~~g~~~~G~~lPs~~~La~~~~vSr~tvr~al~~L~~~Gli~~~   66 (113)
T 3tqn_A           12 QQLRDKIVEAIIDGSYVEGEMIPSIRKISTEYQINPLTVSKAYQSLLDDNVIEKR   66 (113)
T ss_dssp             HHHHHHHHHHHHHTSSCTTCEECCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence            34555555554      34566699999999999999999999999999998654

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

Probab=96.22  E-value=0.017  Score=37.69  Aligned_cols=58  Identities=12%  Similarity=0.149  Sum_probs=44.4

Q ss_pred             HHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871          73 SYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT  131 (139)
Q Consensus        73 tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra  131 (139)
                      +--+|+..+-...-+|+..||++++|+-|...+.|+.|++.|+|..... ++..+|.-.
T Consensus        25 ~~~~il~~l~~~~~~s~~ela~~l~is~~tvs~~l~~L~~~glv~~~~~-~r~~~y~l~   82 (99)
T 3cuo_A           25 KRLLILCMLSGSPGTSAGELTRITGLSASATSQHLARMRDEGLIDSQRD-AQRILYSIK   82 (99)
T ss_dssp             HHHHHHHHHTTCCSEEHHHHHHHHCCCHHHHHHHHHHHHHTTSEEEEEC-SSCEEEEEC
T ss_pred             HHHHHHHHHHhCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEec-CCEEEEEEC
Confidence            3344555554444689999999999999999999999999999988753 445556543

>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=96.19  E-value=0.011  Score=38.69  Aligned_cols=36  Identities=22%  Similarity=0.392  Sum_probs=33.4

Q ss_pred             eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      .-+|+..||++++|+-|-..++|+.|++.|+|....
T Consensus        35 ~~~t~~ela~~l~is~~tv~~~l~~L~~~g~v~~~~   70 (109)
T 2d1h_A           35 KPITSEELADIFKLSKTTVENSLKKLIELGLVVRTK   70 (109)
T ss_dssp             SCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEeec
Confidence            348999999999999999999999999999998864

>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=96.13  E-value=0.0081  Score=43.08  Aligned_cols=38  Identities=24%  Similarity=0.297  Sum_probs=34.6

Q ss_pred             CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          82 PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        82 pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      |..+|-|-..||++|+|+-+-.|.||+.|+.+|+|...
T Consensus        34 pG~~LPser~La~~~gVSr~tVReAl~~L~~eGlv~~~   71 (134)
T 4ham_A           34 EGEKILSIREFASRIGVNPNTVSKAYQELERQEVIITV   71 (134)
T ss_dssp             TTCEECCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCCCccHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEE
Confidence            66788899999999999999999999999999998653

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

Probab=96.10  E-value=0.013  Score=38.27  Aligned_cols=35  Identities=20%  Similarity=0.475  Sum_probs=32.9

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEEee
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK  121 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk  121 (139)
                      +|+..||+.++|+-+-..+.|+.|+++|+|.....
T Consensus        35 ~s~~ela~~l~is~~tv~~~l~~L~~~glv~~~~~   69 (109)
T 1sfx_A           35 MRVSEIARELDLSARFVRDRLKVLLKRGFVRREIV   69 (109)
T ss_dssp             BCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEee
Confidence            89999999999999999999999999999988643

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

Probab=96.09  E-value=0.0049  Score=42.60  Aligned_cols=44  Identities=23%  Similarity=0.390  Sum_probs=36.6

Q ss_pred             HHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          76 KLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        76 Kl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      .++..+.... +|++.||++++++-|-..++|+.|+++|+|....
T Consensus        42 ~iL~~l~~~~-~t~~eLa~~l~~s~~tvs~~l~~L~~~Glv~r~~   85 (146)
T 3tgn_A           42 HILMLLSEES-LTNSELARRLNVSQAAVTKAIKSLVKEGMLETSK   85 (146)
T ss_dssp             HHHHHHTTCC-CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC--
T ss_pred             HHHHHHHhCC-CCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEecc
Confidence            3444555556 9999999999999999999999999999998764

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

Probab=96.07  E-value=0.011  Score=38.46  Aligned_cols=44  Identities=9%  Similarity=0.232  Sum_probs=38.5

Q ss_pred             eeechHHHHhhh-----ccchHHHHHHHHHHHHcCCeeEEeecCceEEE
Q psy1871          85 KLITPSVVSERL-----KVRGSLARKALEELLQKGLIKQVVKHHAQVIY  128 (139)
Q Consensus        85 KlITPsvlseRl-----kI~~SLARkaLreL~~kGlIk~Vskh~~q~IY  128 (139)
                      .-+|...|++++     +|.-+-..+.|+.|++.|+|..+....+...|
T Consensus        32 ~~~s~~el~~~l~~~~~~is~~TVyR~L~~L~~~Glv~~~~~~~~~~~y   80 (83)
T 2fu4_A           32 HHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHNFEGGKSVF   80 (83)
T ss_dssp             SSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTSEEEEECGGGCEEE
T ss_pred             CCCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCCCeEEEeeCCCceEe
Confidence            368999999999     99999999999999999999998765555556

>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=95.93  E-value=0.0053  Score=42.04  Aligned_cols=50  Identities=20%  Similarity=0.233  Sum_probs=39.6

Q ss_pred             HHHHHHHHhhCCCC---eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          71 KASYDKLLKEVPAY---KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        71 k~tydKl~KEVpk~---KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      .++..+|+..+-..   +-+|...||++|+|.-+-.++.|..|+++|+|..+.
T Consensus         9 ~~~~~~IL~~L~~~~pg~~~t~~eLA~~Lgvsr~tV~~~L~~Le~~G~I~~~g   61 (81)
T 1qbj_A            9 QDQEQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQKEA   61 (81)
T ss_dssp             HHHHHHHHHHHHHHCTTCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEES
T ss_pred             hHHHHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecC
Confidence            34444454433333   378999999999999999999999999999998875

>3f8m_A GNTR-family protein transcriptional regulator; PHNF, HUTC, winged helix-TUR UTRA, DNA-binding, transcription regulation; 1.80A {Mycobacterium smegmatis}

Probab=95.93  E-value=0.016  Score=45.61  Aligned_cols=44  Identities=23%  Similarity=0.362  Sum_probs=36.6

Q ss_pred             CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEE
Q psy1871          82 PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVI  127 (139)
Q Consensus        82 pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~I  127 (139)
                      |..++=|-..||++|+|+-...|+||++|+++|+|..  ++++..|
T Consensus        32 ~g~~lPse~~La~~~~vSr~tvr~Al~~L~~~G~i~~--~g~Gt~V   75 (248)
T 3f8m_A           32 IGDPFPAEREIAEQFEVARETVRQALRELLIDGRVER--RGRTTVV   75 (248)
T ss_dssp             TTCBCCCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEE--ETTEEEE
T ss_pred             CCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe--CCCEEEE
Confidence            4456669999999999999999999999999999977  4444433

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

Probab=95.77  E-value=0.021  Score=39.25  Aligned_cols=37  Identities=22%  Similarity=0.200  Sum_probs=34.0

Q ss_pred             CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          84 YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        84 ~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      ..-+|++.||++++++-|-..++|+.|+++|+|....
T Consensus        48 ~~~~~~~ela~~l~~s~~tvs~~l~~Le~~glv~r~~   84 (146)
T 2gxg_A           48 DGPKTMAYLANRYFVTQSAITASVDKLEEMGLVVRVR   84 (146)
T ss_dssp             TSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             cCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeec
Confidence            4458999999999999999999999999999998874

>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=95.73  E-value=0.024  Score=38.69  Aligned_cols=47  Identities=15%  Similarity=0.234  Sum_probs=39.0

Q ss_pred             eechHHHHhhhc----cchHHHHHHHHHHHHcCCeeEEeecCceEEEeccCC
Q psy1871          86 LITPSVVSERLK----VRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTTK  133 (139)
Q Consensus        86 lITPsvlseRlk----I~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra~k  133 (139)
                      -+|++.|+++++    |+-|-..++|+.|+++|+|..... .+..+|..-|.
T Consensus        24 ~~t~~ela~~l~~~~~~s~~tv~~~l~~L~~~Glv~r~~~-~rr~~~~~lT~   74 (123)
T 1okr_A           24 YASANNIIEEIQMQKDWSPKTIRTLITRLYKKGFIDRKKD-NKIFQYYSLVE   74 (123)
T ss_dssp             SEEHHHHHHHHHHHCCCCHHHHHHHHHHHHHHTSEEEEEE-TTEEEEEESSC
T ss_pred             CcCHHHHHHHHhccCCCcHhhHHHHHHHHHHCCCeEEEec-CCeEEEEEecC
Confidence            489999999999    779999999999999999998765 55566665543

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

Probab=95.72  E-value=0.027  Score=37.65  Aligned_cols=44  Identities=23%  Similarity=0.244  Sum_probs=39.4

Q ss_pred             HHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          77 LLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        77 l~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      ++.+-+.-.-+|...||++|+|.-+-.++.|..|+++|+|..+.
T Consensus        22 ~L~~~~~~~~~t~~eLA~~Lgvs~~tV~~~L~~L~~~G~I~~~g   65 (77)
T 1qgp_A           22 FLEELGEGKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQKEA   65 (77)
T ss_dssp             HHHHHCSSSCEEHHHHHHHHCCCHHHHHHHHHHHHHHTSEEEEC
T ss_pred             HHHHcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecC
Confidence            46677766679999999999999999999999999999998875

>1v4r_A Transcriptional repressor; helix-turn-helix, winged-helix, gene regulation; NMR {Streptomyces} SCOP: a.4.5.6

Probab=95.70  E-value=0.0059  Score=41.59  Aligned_cols=49  Identities=14%  Similarity=0.164  Sum_probs=39.3

Q ss_pred             HHHHHHHHhhCCC------CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          71 KASYDKLLKEVPA------YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        71 k~tydKl~KEVpk------~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      +.+++.|...|-.      .++-|...||++|+|+-+..|++|+.|++.|+|..+
T Consensus        14 ~~l~~~i~~~I~~~~l~~g~~lps~~eLa~~~~vSr~tvr~al~~L~~~Gli~~~   68 (102)
T 1v4r_A           14 ADVATHFRTLIKSGELAPGDTLPSVADIRAQFGVAAKTVSRALAVLKSEGLVSSR   68 (102)
T ss_dssp             HHHHHHHHHHTTTTSCCTTSBCCCHHHHHHHSSSCTTHHHHHTTTTTTSSCCEEE
T ss_pred             HHHHHHHHHHHHhCCCCCcCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence            4566666665544      344499999999999999999999999999999653

>3by6_A Predicted transcriptional regulator; structural genomics, PSI-2, MCSG, structure initiative, midwest center for structural genomic binding; 2.20A {Oenococcus oeni}

Probab=95.67  E-value=0.017  Score=41.46  Aligned_cols=49  Identities=20%  Similarity=0.224  Sum_probs=39.0

Q ss_pred             HHHHHHHHhhC------CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          71 KASYDKLLKEV------PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        71 k~tydKl~KEV------pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      ...|+.|...|      |..++-|-..||++|+|+-+..|.||+.|+..|+|...
T Consensus        14 ~~i~~~l~~~I~~g~~~~G~~lPse~~La~~~~vSr~tvr~Al~~L~~~Gli~~~   68 (126)
T 3by6_A           14 LQLVDRIKNEVATDVLSANDQLPSVRETALQEKINPNTVAKAYKELEAQKVIRTI   68 (126)
T ss_dssp             HHHHHHHHHHHHTTSSCTTCEECCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHHhCCCCCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence            34555555544      33455599999999999999999999999999998654

>1oyi_A Double-stranded RNA-binding protein; (alpha+beta) helix-turn-helix, viral protein; NMR {Vaccinia virus} SCOP: a.4.5.19

Probab=95.63  E-value=0.015  Score=40.50  Aligned_cols=48  Identities=15%  Similarity=0.147  Sum_probs=39.5

Q ss_pred             HHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          72 ASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        72 ~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      ++-.+|+.-+...- +|...||++|+|+-+-.|+-|..|++.|+|....
T Consensus        17 ~~~~~IL~lL~~~g-~sa~eLAk~LgiSk~aVr~~L~~Le~eG~I~~~~   64 (82)
T 1oyi_A           17 EIVCEAIKTIGIEG-ATAAQLTRQLNMEKREVNKALYDLQRSAMVYSSD   64 (82)
T ss_dssp             HHHHHHHHHHSSST-EEHHHHHHHSSSCHHHHHHHHHHHHHHTSSEECS
T ss_pred             HHHHHHHHHHHHcC-CCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCC
Confidence            55666654444333 9999999999999999999999999999998764

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

Probab=95.62  E-value=0.023  Score=38.29  Aligned_cols=43  Identities=26%  Similarity=0.319  Sum_probs=36.8

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR  130 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr  130 (139)
                      +|++.|+++++|+-+...+.|+.|++.|+|..... ++...|.-
T Consensus        35 ~~~~ela~~l~is~~tv~~~l~~L~~~gli~~~~~-gr~~~y~l   77 (114)
T 2oqg_A           35 QSASSLATRLPVSRQAIAKHLNALQACGLVESVKV-GREIRYRA   77 (114)
T ss_dssp             BCHHHHHHHSSSCHHHHHHHHHHHHHTTSEEEEEE-TTEEEEEE
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeEEec-CCEEEEEe
Confidence            79999999999999999999999999999987654 44555543

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

Probab=95.62  E-value=0.028  Score=38.27  Aligned_cols=44  Identities=18%  Similarity=0.266  Sum_probs=36.5

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEee--cCceEEEe
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK--HHAQVIYT  129 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk--h~~q~IYt  129 (139)
                      -+|++.||++++++-+-..++|+.|+++|+|.....  ++|...|.
T Consensus        45 ~~~~~ela~~l~is~~~vs~~l~~L~~~gli~~~~~~~d~r~~~~~   90 (142)
T 3bdd_A           45 PLHQLALQERLQIDRAAVTRHLKLLEESGYIIRKRNPDNQREVLVW   90 (142)
T ss_dssp             SBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECSSSTTCEEEE
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEE
Confidence            389999999999999999999999999999988643  34444443

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

Probab=95.60  E-value=0.044  Score=36.41  Aligned_cols=57  Identities=18%  Similarity=0.191  Sum_probs=44.5

Q ss_pred             HHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871          72 ASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR  130 (139)
Q Consensus        72 ~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr  130 (139)
                      ++--+|+..+-. .-+|.+.|++.++|+-|...+-|+.|++.|+|.... ..+...|.-
T Consensus        23 ~~r~~Il~~L~~-~~~~~~ela~~l~is~~tvs~~L~~L~~~Glv~~~~-~g~~~~y~l   79 (98)
T 3jth_A           23 ERRLQILCMLHN-QELSVGELCAKLQLSQSALSQHLAWLRRDGLVTTRK-EAQTVYYTL   79 (98)
T ss_dssp             HHHHHHHHHTTT-SCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEC-CTTCCEEEE
T ss_pred             HHHHHHHHHHhc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEE-eCCEEEEEE
Confidence            344456666655 568999999999999999999999999999998754 445556654

>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=95.60  E-value=0.025  Score=39.05  Aligned_cols=44  Identities=11%  Similarity=0.146  Sum_probs=37.2

Q ss_pred             HHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          74 YDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        74 ydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      +-.|+.-+...  ++++.||+.++++-+.+++.|+.|+++|+|...
T Consensus        10 i~~IL~~i~~~--~~~t~La~~~~ls~~~~~~~l~~L~~~GLI~~~   53 (95)
T 1r7j_A           10 IQAILEACKSG--SPKTRIMYGANLSYALTGRYIKMLMDLEIIRQE   53 (95)
T ss_dssp             HHHHHHHHTTC--BCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHcC--CCHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEE
Confidence            33455555543  999999999999999999999999999999876

>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=95.59  E-value=0.037  Score=36.06  Aligned_cols=45  Identities=13%  Similarity=0.166  Sum_probs=36.8

Q ss_pred             eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe--ecCceEEEe
Q psy1871          85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV--KHHAQVIYT  129 (139)
Q Consensus        85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs--kh~~q~IYt  129 (139)
                      .-+|++.||++++|+-|-.-+.|+.|++.|+|....  ..++...|.
T Consensus        29 ~~~~~~ela~~l~is~~tvs~~l~~L~~~gli~~~~~~~~~r~~~~~   75 (100)
T 1ub9_A           29 RKAPFSQIQKVLDLTPGNLDSHIRVLERNGLVKTYKVIADRPRTVVE   75 (100)
T ss_dssp             SEEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEE
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEecCCCcceEEEE
Confidence            358999999999999999999999999999998643  244444454

>2hs5_A Putative transcriptional regulator GNTR; APC6050, rhodococcus SP. RH structural genomics, PSI-2, protein structure initiative; 2.20A {Rhodococcus SP} SCOP: a.4.5.6 a.78.1.1

Probab=95.53  E-value=0.026  Score=43.76  Aligned_cols=49  Identities=18%  Similarity=0.307  Sum_probs=41.3

Q ss_pred             HHHHHHHHhhC------CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          71 KASYDKLLKEV------PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        71 k~tydKl~KEV------pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      ...|+.|...|      |..+| +-..||++|+|+-+--|.||+.|+..|+|...-
T Consensus        31 ~~v~~~l~~~I~~g~l~pG~~L-~e~~La~~lgVSRtpVREAL~~L~~eGlv~~~~   85 (239)
T 2hs5_A           31 TRVAGILRDAIIDGTFRPGARL-SEPDICAALDVSRNTVREAFQILIEDRLVAHEL   85 (239)
T ss_dssp             HHHHHHHHHHHHHTSSCTTCEE-CHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             HHHHHHHHHHHHcCCCCCcCEe-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeC
Confidence            45666666554      66788 999999999999999999999999999997653

>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=95.52  E-value=0.032  Score=37.04  Aligned_cols=41  Identities=15%  Similarity=0.173  Sum_probs=35.3

Q ss_pred             eeechHHH----HhhhccchHHHHHHHHHHHHcCCeeEEeecCce
Q psy1871          85 KLITPSVV----SERLKVRGSLARKALEELLQKGLIKQVVKHHAQ  125 (139)
Q Consensus        85 KlITPsvl----seRlkI~~SLARkaLreL~~kGlIk~Vskh~~q  125 (139)
                      .-+|++.|    |++++|+-+-.-++|+.|+++|+|......+..
T Consensus        21 ~~~~~~el~~~la~~l~is~~tvs~~l~~Le~~gli~r~~~~r~~   65 (99)
T 1tbx_A           21 EGIATYDLYKKVNAEFPMSTATFYDAKKFLIQEGFVKERQERGEK   65 (99)
T ss_dssp             TTCBHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTSEEEEEETTEE
T ss_pred             CCcCHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCEEEEecCCce
Confidence            44799999    999999999999999999999999887654433

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

Probab=95.48  E-value=0.033  Score=38.01  Aligned_cols=35  Identities=17%  Similarity=0.202  Sum_probs=32.8

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      -+|++.||++++++-+-..++|+.|+++|+|....
T Consensus        50 ~~~~~ela~~l~~~~~tvs~~l~~Le~~Gli~r~~   84 (141)
T 3bro_A           50 EVLQRDLESEFSIKSSTATVLLQRMEIKKLLYRKV   84 (141)
T ss_dssp             CCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CcCHHHHHHHHCCCcchHHHHHHHHHHCCCEEeeC
Confidence            47999999999999999999999999999998874

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

Probab=95.47  E-value=0.021  Score=38.01  Aligned_cols=42  Identities=12%  Similarity=0.057  Sum_probs=35.1

Q ss_pred             echHHHHhhhccchHH-HHHHHHHHHHcCCeeEEeecCceEEE
Q psy1871          87 ITPSVVSERLKVRGSL-ARKALEELLQKGLIKQVVKHHAQVIY  128 (139)
Q Consensus        87 ITPsvlseRlkI~~SL-ARkaLreL~~kGlIk~Vskh~~q~IY  128 (139)
                      +|++.||+.++|+-+- .-++|+.|+++|+|..-..++|...+
T Consensus        31 ~t~~eLa~~l~is~~t~vs~~l~~Le~~Glv~~~~~drR~~~~   73 (95)
T 2pg4_A           31 PSLAEIVKASGVSEKTFFMGLKDRLIRAGLVKEETLSYRVKTL   73 (95)
T ss_dssp             CCHHHHHHHHCCCHHHHHTTHHHHHHHTTSEEEEEEETTEEEE
T ss_pred             CCHHHHHHHHCCCchHHHHHHHHHHHHCCCeecCCCCCCeEEE
Confidence            7999999999999999 99999999999999943344454433

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

Probab=95.47  E-value=0.024  Score=39.03  Aligned_cols=35  Identities=20%  Similarity=0.167  Sum_probs=32.9

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      -+|++.||++++++-+-..++|+.|+++|+|....
T Consensus        51 ~~~~~ela~~l~~~~~tvs~~l~~L~~~gli~r~~   85 (142)
T 2bv6_A           51 PVNVKKVVTELALDTGTVSPLLKRMEQVDLIKRER   85 (142)
T ss_dssp             EEEHHHHHHHTTCCTTTHHHHHHHHHHTTSEEEEE
T ss_pred             CcCHHHHHHHHCCChhhHHHHHHHHHHCCCEEeec
Confidence            48999999999999999999999999999998864

>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=95.47  E-value=0.024  Score=38.58  Aligned_cols=33  Identities=21%  Similarity=0.361  Sum_probs=31.6

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      +|...||+.|+|+-+-.+++|+.|++.|+|...
T Consensus        34 ~s~~eLa~~lgvs~~tV~~~L~~L~~~GlV~~~   66 (110)
T 1q1h_A           34 MTDEEIANQLNIKVNDVRKKLNLLEEQGFVSYR   66 (110)
T ss_dssp             BCHHHHHHTTTSCHHHHHHHHHHHHHHTSCEEE
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            699999999999999999999999999999876

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

Probab=95.44  E-value=0.0075  Score=43.22  Aligned_cols=50  Identities=10%  Similarity=0.106  Sum_probs=39.9

Q ss_pred             CHHHHHHHHhhC------CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          70 DKASYDKLLKEV------PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        70 Dk~tydKl~KEV------pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      -...|+.|...|      |..++-|-..||++|+|+-+..|.||+.|++.|+|...
T Consensus        13 ~~~i~~~l~~~I~~g~~~~G~~lPs~~~La~~~~vSr~tvr~Al~~L~~~G~i~~~   68 (126)
T 3ic7_A           13 YLQIADRICDDILLGQYEEEGRIPSVREYASIVEVNANTVMRSYEYLQSQEVIYNK   68 (126)
T ss_dssp             TTHHHHHHHHHHHTTSSCBTSEECCTTTTTTCC-CCSGGGHHHHHHHHTTTSEEEE
T ss_pred             HHHHHHHHHHHHHhCCCCCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEE
Confidence            345677777666      34566688899999999999999999999999998654

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

Probab=95.43  E-value=0.044  Score=38.02  Aligned_cols=53  Identities=13%  Similarity=0.149  Sum_probs=40.0

Q ss_pred             HHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe--ecCceEEE
Q psy1871          76 KLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV--KHHAQVIY  128 (139)
Q Consensus        76 Kl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs--kh~~q~IY  128 (139)
                      .++..+-...-+|++.||++++++-|-.-++|+.|+++|+|....  .++|..++
T Consensus        40 ~vL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~L~~~Glv~r~~~~~D~R~~~~   94 (140)
T 3hsr_A           40 IVLMAIENDEKLNIKKLGERVFLDSGTLTPLLKKLEKKDYVVRTREEKDERNLQI   94 (140)
T ss_dssp             HHHHHSCTTCEEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEC-------CEE
T ss_pred             HHHHHHHHcCCcCHHHHHHHHCCChhhHHHHHHHHHHCCCeEecCCCCCcceeee
Confidence            344555556679999999999999999999999999999999873  34444443

>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=95.42  E-value=0.025  Score=42.90  Aligned_cols=49  Identities=18%  Similarity=0.272  Sum_probs=40.1

Q ss_pred             HHHHHHHHhhC------CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          71 KASYDKLLKEV------PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        71 k~tydKl~KEV------pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      ...|+.|...|      |+.++=|-..||++|+|+-+-.|.||+.|+.+|+|...
T Consensus        10 ~~v~~~l~~~I~~g~l~pG~~LPsE~eLa~~~gVSR~tVReAL~~L~~eGlv~~~   64 (239)
T 1hw1_A           10 GFAEEYIIESIWNNRFPPGTILPAERELSELIGVTRTTLREVLQRLARDGWLTIQ   64 (239)
T ss_dssp             HHHHHHHHHHHHTTSSCTTSBCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEe
Confidence            34566666555      45666689999999999999999999999999998754

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

Probab=95.41  E-value=0.034  Score=39.28  Aligned_cols=34  Identities=21%  Similarity=0.373  Sum_probs=32.2

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      +|...||+++++.-|-..+.|+.|+++|+|....
T Consensus        43 ~t~~eLa~~l~~s~sTV~r~L~~L~~~GlV~r~~   76 (123)
T 3r0a_A           43 IDTDALSKSLKLDVSTVQRSVKKLHEKEILQRSQ   76 (123)
T ss_dssp             EEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeeC
Confidence            8999999999999999999999999999998753

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

Probab=95.37  E-value=0.035  Score=37.81  Aligned_cols=35  Identities=9%  Similarity=0.137  Sum_probs=32.9

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      -+|++.||++++|+-+-..++|+.|+++|+|....
T Consensus        50 ~~t~~ela~~l~~s~~~vs~~l~~Le~~glv~r~~   84 (142)
T 2fbi_A           50 EMESYQLANQACILRPSMTGVLARLERDGIVRRWK   84 (142)
T ss_dssp             SEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEeec
Confidence            38999999999999999999999999999998874

>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=95.34  E-value=0.033  Score=38.15  Aligned_cols=35  Identities=26%  Similarity=0.304  Sum_probs=32.9

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      -+|++.||++++++-+-.-++|+.|+++|+|....
T Consensus        47 ~~t~~ela~~l~~~~~tvs~~l~~Le~~Gli~r~~   81 (139)
T 3eco_A           47 GLTQNDIAKALQRTGPTVSNLLRNLERKKLIYRYV   81 (139)
T ss_dssp             CEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CcCHHHHHHHhCCCcccHHHHHHHHHHCCCEeecC
Confidence            47999999999999999999999999999999873

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

Probab=95.33  E-value=0.018  Score=38.52  Aligned_cols=42  Identities=29%  Similarity=0.251  Sum_probs=35.6

Q ss_pred             HHhhCCCC-eeechHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871          77 LLKEVPAY-KLITPSVVSERLKVRGSLARKALEELLQKGLIKQ  118 (139)
Q Consensus        77 l~KEVpk~-KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~  118 (139)
                      |+.+|.+. =+|-.+-++++|+|.=..--.+||.|++||||++
T Consensus        15 lL~yIr~sGGildI~~~a~kygV~kdeV~~~LrrLe~KGLI~l   57 (59)
T 2xvc_A           15 LLDYIVNNGGFLDIEHFSKVYGVEKQEVVKLLEALKNKGLIAV   57 (59)
T ss_dssp             HHHHHHHTTSEEEHHHHHHHHCCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHcCCEEeHHHHHHHhCCCHHHHHHHHHHHHHCCCeec
Confidence            33444433 5889999999999999999999999999999986

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

Probab=95.33  E-value=0.03  Score=38.83  Aligned_cols=35  Identities=20%  Similarity=0.324  Sum_probs=33.0

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      -+|++.||+++++.-+-..++|+.|+++|+|....
T Consensus        54 ~~t~~ela~~l~~~~~~vs~~l~~Le~~Glv~r~~   88 (152)
T 3bj6_A           54 GATAPQLGAALQMKRQYISRILQEVQRAGLIERRT   88 (152)
T ss_dssp             TEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEC
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeeecC
Confidence            38999999999999999999999999999999874

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

Probab=95.29  E-value=0.016  Score=41.35  Aligned_cols=48  Identities=19%  Similarity=0.185  Sum_probs=37.1

Q ss_pred             HHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          72 ASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        72 ~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      ..++.|+.-+-...-+|++.||++|+|+-+-.+++|+.|+++|+|...
T Consensus        40 ~~~~~i~~~l~~~~~~~~~~la~~l~vs~~tvs~~l~~Le~~Glv~r~   87 (155)
T 2h09_A           40 DYVELISDLIREVGEARQVDMAARLGVSQPTVAKMLKRLATMGLIEMI   87 (155)
T ss_dssp             HHHHHHHHHHHHHSCCCHHHHHHHHTSCHHHHHHHHHHHHHTTCEEEE
T ss_pred             HHHHHHHHHHHhCCCcCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEe
Confidence            344444444333344799999999999999999999999999997654

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

Probab=95.29  E-value=0.028  Score=39.21  Aligned_cols=35  Identities=23%  Similarity=0.265  Sum_probs=32.8

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      -+|++.||++++|+-+-..++|+.|+++|+|....
T Consensus        61 ~~t~~ela~~l~~s~~tvs~~l~~Le~~glv~r~~   95 (153)
T 2pex_A           61 ERSVSEIGERLYLDSATLTPLLKRLQAAGLVTRTR   95 (153)
T ss_dssp             SEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEC
T ss_pred             CcCHHHHHHHhCCCcccHHHHHHHHHHCCCEeecC
Confidence            48999999999999999999999999999998864

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

Probab=95.28  E-value=0.035  Score=38.36  Aligned_cols=35  Identities=17%  Similarity=0.283  Sum_probs=32.8

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      -+|++.||++++++-+-.-++|+.|+++|+|....
T Consensus        56 ~~t~~ela~~l~~~~~tvs~~l~~Le~~Glv~r~~   90 (150)
T 2rdp_A           56 DLTVGELSNKMYLACSTTTDLVDRMERNGLVARVR   90 (150)
T ss_dssp             SBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCCHHHHHHHHCCCchhHHHHHHHHHHCCCeeecC
Confidence            48999999999999999999999999999998864

>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=95.24  E-value=0.034  Score=37.93  Aligned_cols=44  Identities=23%  Similarity=0.336  Sum_probs=36.5

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe--ecCceEEEe
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVV--KHHAQVIYT  129 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs--kh~~q~IYt  129 (139)
                      -+|++.||++++++-+-.-++|+.|+++|+|....  .++|...|.
T Consensus        48 ~~~~~~la~~l~~~~~tvs~~l~~L~~~gli~r~~~~~d~R~~~~~   93 (138)
T 1jgs_A           48 CITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPNDKRGVLVK   93 (138)
T ss_dssp             SBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECTTCSSCEEEE
T ss_pred             CCCHHHHHHHHCCChHHHHHHHHHHHHCCCEEecCCcccCceeEeE
Confidence            37999999999999999999999999999999864  344544443

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

Probab=95.24  E-value=0.04  Score=38.81  Aligned_cols=43  Identities=19%  Similarity=0.175  Sum_probs=35.9

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe--ecCceEEE
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVV--KHHAQVIY  128 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs--kh~~q~IY  128 (139)
                      -+|++.||++++|.-+-..++|+.|+++|+|....  .++|...|
T Consensus        66 ~~t~~ela~~l~is~~tvs~~l~~Le~~Gli~r~~~~~d~R~~~~  110 (162)
T 3cjn_A           66 GLPIGTLGIFAVVEQSTLSRALDGLQADGLVRREVDSDDQRSSRV  110 (162)
T ss_dssp             SEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEC--CCSSEEE
T ss_pred             CCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEecCCCCCCCeeEE
Confidence            48999999999999999999999999999998863  24444443

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

Probab=95.22  E-value=0.027  Score=38.55  Aligned_cols=36  Identities=19%  Similarity=0.362  Sum_probs=33.3

Q ss_pred             eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      .-+|++.||++++++-|-..++|+.|+++|+|....
T Consensus        51 ~~~t~~~la~~l~~s~~~vs~~l~~L~~~glv~r~~   86 (146)
T 2fbh_A           51 DSPTQRELAQSVGVEGPTLARLLDGLESQGLVRRLA   86 (146)
T ss_dssp             SCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEC
T ss_pred             CCCCHHHHHHHhCCChhhHHHHHHHHHHCCCeeecC
Confidence            347999999999999999999999999999998874

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

Probab=95.20  E-value=0.038  Score=38.00  Aligned_cols=44  Identities=14%  Similarity=0.121  Sum_probs=37.1

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR  130 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr  130 (139)
                      -+|+..||++++|+-|...+.|+.|++.|+|.... .++...|.-
T Consensus        38 ~~s~~eLa~~lgis~stvs~~L~~L~~~GlV~~~~-~gr~~~y~l   81 (108)
T 2kko_A           38 ERAVEAIATATGMNLTTASANLQALKSGGLVEARR-EGTRQYYRI   81 (108)
T ss_dssp             CEEHHHHHHHHTCCHHHHHHHHHHHHHHTSEEEEE-ETTEEEEEE
T ss_pred             CcCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEE-eCCEEEEEE
Confidence            36999999999999999999999999999998765 344555653

>2ek5_A Predicted transcriptional regulators; helix-turn-helix, interwined alpha helices; 2.20A {Corynebacterium glutamicum atcc 13032} PDB: 2du9_A

Probab=95.18  E-value=0.024  Score=40.94  Aligned_cols=48  Identities=10%  Similarity=0.172  Sum_probs=38.7

Q ss_pred             HHHHHHHhhC------CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          72 ASYDKLLKEV------PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        72 ~tydKl~KEV------pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      ..|+.|...|      |..++-|-..||++|+|+-+..|.||+.|+..|+|...
T Consensus         8 ~i~~~i~~~I~~g~l~~G~~LPse~~La~~~gvSr~tVr~Al~~L~~~Gli~~~   61 (129)
T 2ek5_A            8 QIASLIEDSIVDGTLSIDQRVPSTNELAAFHRINPATARNGLTLLVEAGILYKK   61 (129)
T ss_dssp             HHHHHHHHHHHTTSSCTTSCBCCHHHHHHHTTCCHHHHHHHHHHHHTTTSEEEE
T ss_pred             HHHHHHHHHHHhCCCCCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEe
Confidence            4455555544      44566689999999999999999999999999998654

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

Probab=95.17  E-value=0.037  Score=37.95  Aligned_cols=35  Identities=20%  Similarity=0.179  Sum_probs=32.9

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      -+|++.||++++++-+-..++|+.|+++|+|....
T Consensus        47 ~~~~~~la~~l~~s~~tvs~~l~~L~~~glv~r~~   81 (145)
T 2a61_A           47 PKRPGELSVLLGVAKSTVTGLVKRLEADGYLTRTP   81 (145)
T ss_dssp             CBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCCHHHHHHHHCCCchhHHHHHHHHHHCCCeeecC
Confidence            48999999999999999999999999999999874

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

Probab=95.16  E-value=0.053  Score=36.80  Aligned_cols=35  Identities=14%  Similarity=0.228  Sum_probs=32.9

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      -+|++.||++++++-|-.-++|+.|+++|+|....
T Consensus        52 ~~t~~ela~~l~~~~~tvs~~l~~L~~~glv~r~~   86 (140)
T 2nnn_A           52 PCPQNQLGRLTAMDAATIKGVVERLDKRGLIQRSA   86 (140)
T ss_dssp             SBCHHHHHHHTTCCHHHHHHHHHHHHHTTCEEEEE
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeeC
Confidence            58999999999999999999999999999998864

>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=95.15  E-value=0.04  Score=36.80  Aligned_cols=47  Identities=17%  Similarity=0.075  Sum_probs=38.0

Q ss_pred             HHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          72 ASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        72 ~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      .+-.+|+..+ . .-+|+..|+++++|+-+..++.|+.|++.|+|....
T Consensus        31 ~~r~~Il~~L-~-~~~~~~eLa~~l~is~~tv~~~L~~L~~~Glv~~~~   77 (96)
T 1y0u_A           31 PVRRKILRML-D-KGRSEEEIMQTLSLSKKQLDYHLKVLEAGFCIERVG   77 (96)
T ss_dssp             HHHHHHHHHH-H-TTCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             HHHHHHHHHH-c-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEC
Confidence            3344555555 2 337999999999999999999999999999998654

>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=95.14  E-value=0.04  Score=37.56  Aligned_cols=34  Identities=26%  Similarity=0.370  Sum_probs=32.4

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      +|++.||++++++-|-.-++|+.|+++|+|....
T Consensus        42 ~t~~ela~~l~~~~stvs~~l~~L~~~G~v~r~~   75 (152)
T 1ku9_A           42 LTISDIMEELKISKGNVSMSLKKLEELGFVRKVW   75 (152)
T ss_dssp             EEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEC
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEe
Confidence            8999999999999999999999999999998873

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

Probab=95.13  E-value=0.044  Score=37.78  Aligned_cols=36  Identities=19%  Similarity=0.242  Sum_probs=33.3

Q ss_pred             eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      .-+|++.||+++++.-|-.-++|+.|+++|+|....
T Consensus        50 ~~~t~~eLa~~l~~~~~~vs~~l~~L~~~Glv~r~~   85 (143)
T 3oop_A           50 EPISQKEIALWTKKDTPTVNRIVDVLLRKELIVREI   85 (143)
T ss_dssp             SSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEC
T ss_pred             CCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCeeccC
Confidence            458999999999999999999999999999998763

>2di3_A Bacterial regulatory proteins, GNTR family; helix-turn-helix, transcription; 2.05A {Corynebacterium glutamicum}

Probab=95.11  E-value=0.026  Score=43.24  Aligned_cols=48  Identities=29%  Similarity=0.265  Sum_probs=40.3

Q ss_pred             HHHHHHHHhhC------CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871          71 KASYDKLLKEV------PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQ  118 (139)
Q Consensus        71 k~tydKl~KEV------pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~  118 (139)
                      +..|+.|...|      |..++-+-..||++|+|+-+-.|.||+.|+..|+|..
T Consensus         7 ~~v~~~L~~~I~~g~l~pG~~LpsE~~La~~lgVSRtpVREAL~~L~~~GlV~~   60 (239)
T 2di3_A            7 ESVMDWVTEELRSGRLKIGDHLPSERALSETLGVSRSSLREALRVLEALGTIST   60 (239)
T ss_dssp             HHHHHHHHHHHHHTSSCTTCBCCCHHHHHHHHTCCHHHHHHHHHHHHHHTSEEC
T ss_pred             HHHHHHHHHHHHhCCCCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEe
Confidence            45666666655      5667778889999999999999999999999999875

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

Probab=95.11  E-value=0.054  Score=36.80  Aligned_cols=35  Identities=17%  Similarity=0.221  Sum_probs=32.8

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      -+|++.||++++++-+-..++|+.|+++|+|....
T Consensus        43 ~~~~~ela~~l~~s~~tvs~~l~~L~~~glv~~~~   77 (138)
T 3bpv_A           43 GIKQDELATFFHVDKGTIARTLRRLEESGFIEREQ   77 (138)
T ss_dssp             TCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeec
Confidence            47999999999999999999999999999999864

>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=95.09  E-value=0.034  Score=38.31  Aligned_cols=35  Identities=31%  Similarity=0.347  Sum_probs=32.8

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      -+|++.||++++|+-+-..++|+.|+++|+|....
T Consensus        50 ~~~~~~la~~l~i~~~~vs~~l~~Le~~glv~r~~   84 (147)
T 2hr3_A           50 DVTPSELAAAERMRSSNLAALLRELERGGLIVRHA   84 (147)
T ss_dssp             CBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEC
T ss_pred             CCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeCC
Confidence            48999999999999999999999999999998863

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

Probab=95.04  E-value=0.018  Score=41.27  Aligned_cols=37  Identities=30%  Similarity=0.419  Sum_probs=33.4

Q ss_pred             eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEee
Q psy1871          85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK  121 (139)
Q Consensus        85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk  121 (139)
                      ..+||+.||++++++.+-..++|+.|+++|+|.....
T Consensus        50 ~~ps~~~LA~~l~~s~~~V~~~l~~Le~kGlI~~~~~   86 (128)
T 2vn2_A           50 LFPTPAELAERMTVSAAECMEMVRRLLQKGMIAIEEH   86 (128)
T ss_dssp             SSCCHHHHHHTSSSCHHHHHHHHHHHHHTTSSEECC-
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEeE
Confidence            4489999999999999999999999999999988643

>3eet_A Putative GNTR-family transcriptional regulator; structural genomics, PSI-2, protein structure initiative; 1.97A {Streptomyces avermitilis}

Probab=95.04  E-value=0.037  Score=44.25  Aligned_cols=38  Identities=24%  Similarity=0.373  Sum_probs=33.8

Q ss_pred             CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          82 PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        82 pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      |..++=|-..||++|+|+-...|+||+.|+++|+|...
T Consensus        49 ~g~~lPse~~La~~~~vSr~tvr~Al~~L~~~G~i~~~   86 (272)
T 3eet_A           49 PHTRLPSQARIREEYGVSDTVALEARKVLMAEGLVEGR   86 (272)
T ss_dssp             TTSBCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             CcCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            34577799999999999999999999999999998654

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

Probab=95.04  E-value=0.025  Score=39.01  Aligned_cols=61  Identities=15%  Similarity=0.289  Sum_probs=56.5

Q ss_pred             HHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871          71 KASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT  131 (139)
Q Consensus        71 k~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra  131 (139)
                      +.++..+...|...|++.-..||..|+++-..+..-|++|++.|.|.=|.-.|.-.||+-.
T Consensus         6 ~~ll~~Fi~yIk~~Kvv~LedLA~~F~l~t~~~i~RI~~Le~~g~ltGViDDRGKfIyIs~   66 (72)
T 1wi9_A            6 SGFLTEFINYIKKSKVVLLEDLAFQMGLRTQDAINRIQDLLTEGTLTGVIDDRGKFIYITP   66 (72)
T ss_dssp             CCHHHHHHHHHHHCSEECHHHHHHHHCSCHHHHHHHHHHHHHHSSSCEEECTTCCEEECCC
T ss_pred             HHHHHHHHHHHHHcCeeeHHHHHHHhCCChHHHHHHHHHHHHCCCeEEEEeCCCCEEEecH
Confidence            4677888889999999999999999999999999999999999999999989999999843

>2wv0_A YVOA, HTH-type transcriptional repressor YVOA; DNA-binding, transcription regulation, transcriptional regulator, GNTR/HUTC family; 2.40A {Bacillus subtilis}

Probab=95.01  E-value=0.038  Score=43.24  Aligned_cols=38  Identities=24%  Similarity=0.423  Sum_probs=33.6

Q ss_pred             CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          82 PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        82 pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      |+.++=|-..||++|+|+-+..|+||+.|+++|+|...
T Consensus        30 ~g~~lPse~~La~~~~vSr~tvr~Al~~L~~~G~i~~~   67 (243)
T 2wv0_A           30 PDMPLPSEREYAEQFGISRMTVRQALSNLVNEGLLYRL   67 (243)
T ss_dssp             TTCBCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             CcCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEe
Confidence            45566689999999999999999999999999998643

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

Probab=95.00  E-value=0.053  Score=37.64  Aligned_cols=36  Identities=28%  Similarity=0.314  Sum_probs=33.4

Q ss_pred             eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      .-+|++.||+.++|+-+-..++|+.|+++|+|....
T Consensus        50 ~~~t~~ela~~l~~s~~tvs~~l~~Le~~glv~r~~   85 (155)
T 1s3j_A           50 GSLKVSEIAERMEVKPSAVTLMADRLEQKNLIARTH   85 (155)
T ss_dssp             SEEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeecC
Confidence            358999999999999999999999999999998874

>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=94.97  E-value=0.039  Score=39.20  Aligned_cols=43  Identities=23%  Similarity=0.399  Sum_probs=36.4

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe--ecCceEEE
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVV--KHHAQVIY  128 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs--kh~~q~IY  128 (139)
                      =+|++.||++++|.-+-.-++|+.|+++|+|....  .++|..++
T Consensus        60 ~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~~~DrR~~~l  104 (162)
T 3k0l_A           60 NLSNAKLAERSFIKPQSANKILQDLLANGWIEKAPDPTHGRRILV  104 (162)
T ss_dssp             TCCHHHHHHHHTSCGGGHHHHHHHHHHTTSEEEEECCSSSCCEEE
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHCcCeEecCCCCcCCeeEe
Confidence            38999999999999999999999999999999874  34444433

>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=94.94  E-value=0.044  Score=37.62  Aligned_cols=35  Identities=26%  Similarity=0.340  Sum_probs=32.9

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      -+|++.||++++++-|-.-++|+.|+++|+|....
T Consensus        43 ~~t~~~la~~l~~s~~~vs~~l~~Le~~gli~r~~   77 (144)
T 1lj9_A           43 GIIQEKIAELIKVDRTTAARAIKRLEEQGFIYRQE   77 (144)
T ss_dssp             TEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CcCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEeec
Confidence            48999999999999999999999999999999864

>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=94.92  E-value=0.055  Score=37.97  Aligned_cols=35  Identities=17%  Similarity=0.213  Sum_probs=32.9

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      -+|++.||++++|+-+-.-++|+.|+++|+|....
T Consensus        58 ~~t~~ela~~l~is~~tvs~~l~~Le~~Gli~r~~   92 (154)
T 2eth_A           58 PKKMKEIAEFLSTTKSNVTNVVDSLEKRGLVVREM   92 (154)
T ss_dssp             CBCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeeC
Confidence            48999999999999999999999999999998864

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

Probab=94.89  E-value=0.054  Score=38.22  Aligned_cols=35  Identities=20%  Similarity=0.336  Sum_probs=32.8

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      =+|++.||+++++.-+-.-++|+.|+++|+|....
T Consensus        64 ~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~   98 (159)
T 3s2w_A           64 GINQESLSDYLKIDKGTTARAIQKLVDEGYVFRQR   98 (159)
T ss_dssp             SEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence            48999999999999999999999999999998863

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

Probab=94.89  E-value=0.041  Score=40.44  Aligned_cols=36  Identities=19%  Similarity=0.254  Sum_probs=34.0

Q ss_pred             CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          84 YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        84 ~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      ...+||..||++++++.+-.-++|+.|+++|+|..-
T Consensus        49 ~~~ps~~~LA~~~~~s~~~v~~~L~~L~~KGlI~i~   84 (135)
T 2v79_A           49 SYFPTPNQLQEGMSISVEECTNRLRMFIQKGFLFIE   84 (135)
T ss_dssp             CCSCCHHHHHTTSSSCHHHHHHHHHHHHHHTSCEEE
T ss_pred             CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            477899999999999999999999999999999984

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

Probab=94.89  E-value=0.053  Score=37.98  Aligned_cols=58  Identities=7%  Similarity=0.046  Sum_probs=44.9

Q ss_pred             eCHHHHHHHHhhCCCCeeechHHHHhhhcc----chHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871          69 FDKASYDKLLKEVPAYKLITPSVVSERLKV----RGSLARKALEELLQKGLIKQVVKHHAQVIYTRT  131 (139)
Q Consensus        69 ~Dk~tydKl~KEVpk~KlITPsvlseRlkI----~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra  131 (139)
                      ..-..++-|..+-    =+|...|++++.+    .-+-..++|+.|+++|+|.... .+|..+|...
T Consensus        36 ~e~~VL~~L~~~~----~~t~~eL~~~l~~~~~~s~sTVt~~L~rLe~KGlV~R~~-~gR~~~Y~p~   97 (99)
T 2k4b_A           36 AELIVMRVIWSLG----EARVDEIYAQIPQELEWSLATVKTLLGRLVKKEMLSTEK-EGRKFVYRPL   97 (99)
T ss_dssp             SCSHHHHHHHHHS----CEEHHHHHHTCCGGGCCCHHHHHHHHHHHHHTTSCEEEE-ETTEEEEECC
T ss_pred             HHHHHHHHHHhCC----CCCHHHHHHHHhcccCCCHhhHHHHHHHHHHCCCEEEEe-CCCEEEEEEe
Confidence            3445677776533    3799999999985    4678889999999999999875 4667788754

>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=94.87  E-value=0.045  Score=39.09  Aligned_cols=46  Identities=20%  Similarity=0.288  Sum_probs=37.5

Q ss_pred             CHHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          70 DKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        70 Dk~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      |...++-|..+    .-+|...||++++++-+-.++.|+.|++.|+|..+
T Consensus         7 d~~il~~L~~~----~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~   52 (144)
T 2cfx_A            7 DLNIIEELKKD----SRLSMRELGRKIKLSPPSVTERVRQLESFGIIKQY   52 (144)
T ss_dssp             HHHHHHHHHHC----SCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHc----CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEE
Confidence            34455555444    33899999999999999999999999999999864

>3sxy_A Transcriptional regulator, GNTR family; transcription factor, metal-binding, structur genomics, PSI-2, protein structure initiative; 1.65A {Thermotoga maritima} PDB: 3dbw_A 3fms_A*

Probab=94.85  E-value=0.034  Score=42.04  Aligned_cols=50  Identities=30%  Similarity=0.357  Sum_probs=42.1

Q ss_pred             eCHHHHHHHHhhC------CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          69 FDKASYDKLLKEV------PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        69 ~Dk~tydKl~KEV------pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      +-...|+.|...|      |..++ +-..||++|+|+-+--|.||+.|+..|+|...
T Consensus        13 l~~~v~~~l~~~I~~g~l~pG~~L-~e~~La~~lgVSRtpVREAL~~L~~eGlv~~~   68 (218)
T 3sxy_A           13 VRTKVYNLLKEMILNHELKLGEKL-NVRELSEKLGISFTPVRDALLQLATEGLVKVV   68 (218)
T ss_dssp             -CHHHHHHHHHHHHTTSSCTTCEE-CHHHHHHHHTCCHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHHHHHHHhCCCCCCCEe-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            4456777777765      55677 99999999999999999999999999999664

>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=94.81  E-value=0.034  Score=40.22  Aligned_cols=42  Identities=14%  Similarity=0.209  Sum_probs=33.2

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEEe--ecCceEEE
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVV--KHHAQVIY  128 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs--kh~~q~IY  128 (139)
                      +|++.||++++|.-+-.-++|+.|+++|+|....  .++|..++
T Consensus        69 ~t~~eLa~~l~i~~~tvs~~l~~Le~~GlV~r~~~~~DrR~~~l  112 (166)
T 3deu_A           69 QSQIQLAKAIGIEQPSLVRTLDQLEDKGLISRQTCASDRRAKRI  112 (166)
T ss_dssp             EEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEC--------CEE
T ss_pred             CCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEeeCCCCCCCeeEE
Confidence            8999999999999999999999999999998863  24444433

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

Probab=94.79  E-value=0.042  Score=38.27  Aligned_cols=32  Identities=28%  Similarity=0.478  Sum_probs=31.2

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQ  118 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~  118 (139)
                      +|++.||+++++.-|-.-++|+.|+++|+|..
T Consensus        56 ~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r   87 (154)
T 2qww_A           56 ISVADLTKRLIITGSSAAANVDGLISLGLVVK   87 (154)
T ss_dssp             EEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence            89999999999999999999999999999987

>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=94.76  E-value=0.053  Score=37.75  Aligned_cols=42  Identities=10%  Similarity=0.287  Sum_probs=35.9

Q ss_pred             echHHHHhhh-ccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871          87 ITPSVVSERL-KVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR  130 (139)
Q Consensus        87 ITPsvlseRl-kI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr  130 (139)
                      +|++.|++.+ +|+-+..-+.|+.|++.|+|.....  +...|.=
T Consensus        43 ~~~~eL~~~l~gis~~~ls~~L~~Le~~GlV~r~~~--r~~~y~L   85 (111)
T 3df8_A           43 QNFNDIRSSIPGISSTILSRRIKDLIDSGLVERRSG--QITTYAL   85 (111)
T ss_dssp             BCHHHHHHTSTTCCHHHHHHHHHHHHHTTSEEEEES--SSEEEEE
T ss_pred             CCHHHHHHHccCCCHHHHHHHHHHHHHCCCEEEeec--CcEEEEE
Confidence            6699999999 9999999999999999999987654  5555653

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

Probab=94.74  E-value=0.042  Score=38.54  Aligned_cols=36  Identities=11%  Similarity=0.184  Sum_probs=32.4

Q ss_pred             eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      ..+|...||++++|+-+..+++|+.|.+.|+|..+.
T Consensus        25 ~~~s~~ela~~~~i~~~~v~~il~~L~~~Glv~~~~   60 (129)
T 2y75_A           25 GPTSLKSIAQTNNLSEHYLEQLVSPLRNAGLVKSIR   60 (129)
T ss_dssp             CCBCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEEC-
T ss_pred             CcCCHHHHHHHHCcCHHHHHHHHHHHHHCCceEecC
Confidence            567999999999999999999999999999986553

>3c7j_A Transcriptional regulator, GNTR family; structural genomics, PSI-2, protein structure initiative, midwest center for STR genomics; HET: MSE; 2.10A {Pseudomonas syringae PV}

Probab=94.72  E-value=0.037  Score=43.05  Aligned_cols=47  Identities=19%  Similarity=0.222  Sum_probs=39.3

Q ss_pred             HHHHHHhhC------CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          73 SYDKLLKEV------PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        73 tydKl~KEV------pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      .|+.|...|      |+.++ +...||++|+|+-+-.|.+|+.|+..|+|..+.
T Consensus        31 v~~~L~~~I~~g~l~pG~~L-~e~~La~~lgVSr~~VReAL~~L~~~Glv~~~~   83 (237)
T 3c7j_A           31 IEEKLRNAIIDGSLPSGTAL-RQQELATLFGVSRMPVREALRQLEAQSLLRVET   83 (237)
T ss_dssp             HHHHHHHHHHTSSSCTTCBC-CHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEET
T ss_pred             HHHHHHHHHHhCCCCCcCee-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeC
Confidence            566666554      44566 999999999999999999999999999987653

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

Probab=94.71  E-value=0.034  Score=38.29  Aligned_cols=35  Identities=23%  Similarity=0.289  Sum_probs=32.8

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      -+|++.||++++|+-+-..++|+.|+++|+|....
T Consensus        54 ~~~~~~la~~l~~~~~tvs~~l~~L~~~glv~r~~   88 (147)
T 1z91_A           54 TLTVKKMGEQLYLDSGTLTPMLKRMEQQGLITRKR   88 (147)
T ss_dssp             EEEHHHHHHTTTCCHHHHHHHHHHHHHHTSEECCB
T ss_pred             CCCHHHHHHHHCCCcCcHHHHHHHHHHCCCEEecc
Confidence            68999999999999999999999999999998763

>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=94.69  E-value=0.066  Score=36.92  Aligned_cols=43  Identities=19%  Similarity=0.233  Sum_probs=36.4

Q ss_pred             echHHHHhhh-ccchHHHHHHHHHHHHcCCeeEEee--cCceEEEe
Q psy1871          87 ITPSVVSERL-KVRGSLARKALEELLQKGLIKQVVK--HHAQVIYT  129 (139)
Q Consensus        87 ITPsvlseRl-kI~~SLARkaLreL~~kGlIk~Vsk--h~~q~IYt  129 (139)
                      +|++.|++++ +|+-+..-+.|+.|++.|+|.....  +++...|.
T Consensus        36 ~~~~eLa~~l~~is~~tvs~~L~~Le~~GlI~r~~~~~d~r~~~~~   81 (112)
T 1z7u_A           36 KRNGELMRALDGITQRVLTDRLREMEKDGLVHRESFNELPPRVEYT   81 (112)
T ss_dssp             BCHHHHHHHSTTCCHHHHHHHHHHHHHHTSEEEEEECCSSCEEEEE
T ss_pred             CCHHHHHHHhccCCHHHHHHHHHHHHHCCCEEEeecCCCCCeEEEE
Confidence            6999999999 9999999999999999999988643  34555554

>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=94.69  E-value=0.073  Score=36.18  Aligned_cols=43  Identities=21%  Similarity=0.234  Sum_probs=36.7

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR  130 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr  130 (139)
                      +|+..||+.++|+-|...+.|+.|++.|+|..... ++...|.-
T Consensus        40 ~~~~ela~~l~is~stvs~~L~~L~~~Glv~~~~~-gr~~~y~l   82 (106)
T 1r1u_A           40 ASVGHISHQLNLSQSNVSHQLKLLKSVHLVKAKRQ-GQSMIYSL   82 (106)
T ss_dssp             BCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEE-TTEEEEEE
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEe-CCEEEEEE
Confidence            69999999999999999999999999999987653 45555653

>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=94.67  E-value=0.072  Score=36.46  Aligned_cols=47  Identities=19%  Similarity=0.280  Sum_probs=37.9

Q ss_pred             eechHHHHhhh-ccchHHHHHHHHHHHHcCCeeEEee--cCceEEEeccC
Q psy1871          86 LITPSVVSERL-KVRGSLARKALEELLQKGLIKQVVK--HHAQVIYTRTT  132 (139)
Q Consensus        86 lITPsvlseRl-kI~~SLARkaLreL~~kGlIk~Vsk--h~~q~IYtra~  132 (139)
                      -+|++.|++++ +|+-+..-+.|+.|++.|+|.....  .++...|.=..
T Consensus        27 ~~~~~eLa~~l~~is~~tls~~L~~Le~~GlI~r~~~~~d~r~~~y~LT~   76 (107)
T 2hzt_A           27 KKRTSELKRLMPNITQKMLTQQLRELEADGVINRIVYNQVPPKVEYELSE   76 (107)
T ss_dssp             CBCHHHHHHHCTTSCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECT
T ss_pred             CCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEEeecCCCCCeEEEEECc
Confidence            36999999999 9999999999999999999998642  24555555433

>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=94.65  E-value=0.09  Score=35.87  Aligned_cols=43  Identities=16%  Similarity=0.317  Sum_probs=36.3

Q ss_pred             echHHHHhhhc----cchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871          87 ITPSVVSERLK----VRGSLARKALEELLQKGLIKQVVKHHAQVIYTR  130 (139)
Q Consensus        87 ITPsvlseRlk----I~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr  130 (139)
                      +|+..|+++++    +.-|-...+|+-|+++|+|..... ++..+|..
T Consensus        25 ~t~~el~~~l~~~~~~~~~Tvt~~l~rLe~kGlv~R~~~-~r~~~~~~   71 (126)
T 1sd4_A           25 VSANEIVVEIQKYKEVSDKTIRTLITRLYKKEIIKRYKS-ENIYFYSS   71 (126)
T ss_dssp             EEHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTSEEEEEE-TTEEEEEE
T ss_pred             CCHHHHHHHHhhcCCCChhhHHHHHHHHHHCCceEEEeC-CCeEEEEE
Confidence            79999999998    578999999999999999998764 44556653

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

Probab=94.62  E-value=0.057  Score=39.16  Aligned_cols=46  Identities=24%  Similarity=0.297  Sum_probs=37.6

Q ss_pred             CHHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          70 DKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        70 Dk~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      |...++-|..+-+    +|...||++++++-+-.++.|+.|++.|+|..+
T Consensus        12 ~~~il~~L~~~~~----~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~   57 (162)
T 2p5v_A           12 DIKILQVLQENGR----LTNVELSERVALSPSPCLRRLKQLEDAGIVRQY   57 (162)
T ss_dssp             HHHHHHHHHHCTT----CCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHcCC----CCHHHHHHHHCcCHHHHHHHHHHHHHCCCEeee
Confidence            3455555554433    699999999999999999999999999999864

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

Probab=94.62  E-value=0.063  Score=36.74  Aligned_cols=45  Identities=16%  Similarity=0.188  Sum_probs=38.1

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT  131 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra  131 (139)
                      -+|.+.||++++|+-|-..+.|+.|++.|+|.... ..+...|+-.
T Consensus        45 ~~s~~ela~~l~is~stvsr~l~~Le~~Glv~~~~-~~r~~~~~~~   89 (119)
T 2lkp_A           45 PLPVTDLAEAIGMEQSAVSHQLRVLRNLGLVVGDR-AGRSIVYSLY   89 (119)
T ss_dssp             CCCHHHHHHHHSSCHHHHHHHHHHHHHHCSEEEEE-ETTEEEEEES
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEe-cCCEEEEEEc
Confidence            47999999999999999999999999999997654 4556667644

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

Probab=94.61  E-value=0.08  Score=34.15  Aligned_cols=34  Identities=9%  Similarity=0.067  Sum_probs=31.3

Q ss_pred             eeechHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871          85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQ  118 (139)
Q Consensus        85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~  118 (139)
                      .-+|...||++|+|.-+...++|+.|++.|+|..
T Consensus        24 ~~~s~~eLA~~lglsr~tv~~~l~~L~~~G~I~~   57 (67)
T 2heo_A           24 GPVAIFQLVKKCQVPKKTLNQVLYRLKKEDRVSS   57 (67)
T ss_dssp             SCEEHHHHHHHHCSCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEec
Confidence            4589999999999999999999999999999744

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

Probab=94.58  E-value=0.045  Score=37.13  Aligned_cols=43  Identities=9%  Similarity=0.140  Sum_probs=36.0

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe--ecCceEEE
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVV--KHHAQVIY  128 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs--kh~~q~IY  128 (139)
                      -+|++.||++++++-|-.-++|+.|+++|+|....  .++|...|
T Consensus        47 ~~~~~ela~~l~~~~~tvs~~l~~L~~~gli~r~~~~~d~r~~~~   91 (139)
T 3bja_A           47 KVSMSKLIENMGCVPSNMTTMIQRMKRDGYVMTEKNPNDQRETLV   91 (139)
T ss_dssp             SEEHHHHHHHCSSCCTTHHHHHHHHHHTTSEEEEECSSCTTCEEE
T ss_pred             CcCHHHHHHHHCCChhHHHHHHHHHHHCCCeeeccCCCCCceeEE
Confidence            48999999999999999999999999999998863  23444433

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

Probab=94.57  E-value=0.044  Score=38.07  Aligned_cols=36  Identities=22%  Similarity=0.253  Sum_probs=32.8

Q ss_pred             eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      .-+|.+.||++++|+-|-..++|+.|+++|+|....
T Consensus        30 ~~~s~~ela~~l~is~~tv~~~l~~Le~~Gli~r~~   65 (139)
T 2x4h_A           30 EGAKINRIAKDLKIAPSSVFEEVSHLEEKGLVKKKE   65 (139)
T ss_dssp             SCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             CCcCHHHHHHHhCCChHHHHHHHHHHHHCCCEEecC
Confidence            458999999999999999999999999999987643

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

Probab=94.52  E-value=0.056  Score=38.84  Aligned_cols=49  Identities=16%  Similarity=0.306  Sum_probs=40.8

Q ss_pred             eeeCHHHHHHHHhhCCCCeeechHHHHhhh--ccchHHHHHHHHHHHHcCCeeEE
Q psy1871          67 VLFDKASYDKLLKEVPAYKLITPSVVSERL--KVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        67 Vl~Dk~tydKl~KEVpk~KlITPsvlseRl--kI~~SLARkaLreL~~kGlIk~V  119 (139)
                      ...|..+++-|..+-    -+||+.||+.+  +|+-+-.++-|+.|++.|+|...
T Consensus        12 d~~d~~IL~~L~~~g----~~s~~eLA~~l~~giS~~aVs~rL~~Le~~GLV~~~   62 (111)
T 3b73_A           12 TIWDDRILEIIHEEG----NGSPKELEDRDEIRISKSSVSRRLKKLADHDLLQPL   62 (111)
T ss_dssp             CHHHHHHHHHHHHHS----CBCHHHHHTSTTCCSCHHHHHHHHHHHHHTTSEEEC
T ss_pred             CHHHHHHHHHHHHcC----CCCHHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEec
Confidence            344666777666654    47999999999  99999999999999999999875

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

Probab=94.48  E-value=0.039  Score=38.17  Aligned_cols=34  Identities=18%  Similarity=0.173  Sum_probs=32.3

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      +|++.||+.+++.-+-.-++|+.|+++|+|....
T Consensus        46 ~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~   79 (145)
T 3g3z_A           46 RTQKHIGEKWSLPKQTVSGVCKTLAGQGLIEWQE   79 (145)
T ss_dssp             BCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEECC
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeecc
Confidence            8999999999999999999999999999998753

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

Probab=94.42  E-value=0.029  Score=39.34  Aligned_cols=44  Identities=20%  Similarity=0.246  Sum_probs=33.2

Q ss_pred             eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe--ecCceEEE
Q psy1871          85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV--KHHAQVIY  128 (139)
Q Consensus        85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs--kh~~q~IY  128 (139)
                      .-+|++.||++++++-+-.-++|+.|+++|+|....  .++|...+
T Consensus        54 ~~~~~~eLa~~l~~~~~~vs~~l~~L~~~Glv~r~~~~~D~R~~~~   99 (149)
T 4hbl_A           54 NPQTLNSIGRHLDLSSNTLTPMLKRLEQSGWVKRERQQSDKRQLII   99 (149)
T ss_dssp             SSEEHHHHHHHHTCCHHHHHHHHHHHHHHTSEEC---------CEE
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeeCCCCCCcceeee
Confidence            347999999999999999999999999999998763  33444333

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

Probab=94.40  E-value=0.069  Score=37.87  Aligned_cols=36  Identities=14%  Similarity=0.240  Sum_probs=33.3

Q ss_pred             eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      .=+|++.||++++|.-+-.-++|+.|+++|+|....
T Consensus        66 ~~~t~~eLa~~l~~~~~~vs~~l~~Le~~Glv~r~~  101 (161)
T 3e6m_A           66 GELTVGQLATLGVMEQSTTSRTVDQLVDEGLAARSI  101 (161)
T ss_dssp             SEEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEECC
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeeC
Confidence            358999999999999999999999999999998763

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

Probab=94.37  E-value=0.049  Score=38.07  Aligned_cols=34  Identities=21%  Similarity=0.151  Sum_probs=31.8

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      -+|++.||++++|+-|-..++|+.|+++|+|...
T Consensus        22 ~~~~~ela~~l~vs~~tvs~~l~~Le~~Glv~r~   55 (142)
T 1on2_A           22 YARVSDIAEALAVHPSSVTKMVQKLDKDEYLIYE   55 (142)
T ss_dssp             SCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence            3899999999999999999999999999999764

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

Probab=94.36  E-value=0.1  Score=37.47  Aligned_cols=35  Identities=20%  Similarity=0.277  Sum_probs=32.7

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      -+|++.||++++|+-|-.-++|+.|+++|+|....
T Consensus        59 ~~t~~eLa~~l~is~~tvs~~l~~Le~~GlV~r~~   93 (168)
T 2nyx_A           59 PINLATLATLLGVQPSATGRMVDRLVGAELIDRLP   93 (168)
T ss_dssp             SEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEecc
Confidence            38999999999999999999999999999998863

>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=94.32  E-value=0.081  Score=39.09  Aligned_cols=35  Identities=9%  Similarity=0.170  Sum_probs=33.0

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      -+|++.||+++++.-|-.-++|+.|+++|+|....
T Consensus        57 ~~t~~eLa~~l~is~~tvs~~l~~Le~~GlV~r~~   91 (189)
T 3nqo_A           57 ETTLNNIARKMGTSKQNINRLVANLEKNGYVDVIP   91 (189)
T ss_dssp             GCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecc
Confidence            57999999999999999999999999999999874

>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=94.25  E-value=0.074  Score=37.97  Aligned_cols=46  Identities=17%  Similarity=0.212  Sum_probs=37.2

Q ss_pred             CHHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          70 DKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        70 Dk~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      |...+.-|..+    .-+|.+.||++++++-+-.++.|+.|++.|+|..+
T Consensus         9 ~~~iL~~L~~~----~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~   54 (150)
T 2w25_A            9 DRILVRELAAD----GRATLSELATRAGLSVSAVQSRVRRLESRGVVQGY   54 (150)
T ss_dssp             HHHHHHHHHHC----TTCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHc----CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            33455555443    23799999999999999999999999999999765

>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=94.20  E-value=0.11  Score=40.45  Aligned_cols=37  Identities=38%  Similarity=0.323  Sum_probs=33.0

Q ss_pred             CCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          83 AYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        83 k~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      +.++=|-..||++|+|+-+..|+||+.|+++|+|...
T Consensus        26 g~~lPse~~La~~~~vSr~tvr~Al~~L~~~g~i~~~   62 (239)
T 3bwg_A           26 GDKLPVLETLMAQFEVSKSTITKSLELLEQKGAIFQV   62 (239)
T ss_dssp             TCBCCCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEe
Confidence            4556599999999999999999999999999999654

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

Probab=94.07  E-value=0.061  Score=37.56  Aligned_cols=43  Identities=12%  Similarity=0.193  Sum_probs=36.0

Q ss_pred             HHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          77 LLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        77 l~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      ++..+-...-+|++.||++++|.-+-.-++|+.|+++|+|...
T Consensus        48 iL~~l~~~~~~t~~ela~~l~i~~~tvs~~l~~Le~~Glv~r~   90 (155)
T 3cdh_A           48 VLACLVDNDAMMITRLAKLSLMEQSRMTRIVDQMDARGLVTRV   90 (155)
T ss_dssp             HHHHHSSCSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             HHHHHHHCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence            3333434445899999999999999999999999999999875

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

Probab=94.05  E-value=0.086  Score=39.28  Aligned_cols=46  Identities=28%  Similarity=0.344  Sum_probs=37.6

Q ss_pred             CHHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          70 DKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        70 Dk~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      |...++-|..+-    -+|...||++++++-+-.++.|+.|++.|+|..+
T Consensus        19 d~~IL~~L~~~~----~~s~~eLA~~lglS~~tv~~~l~~L~~~G~I~~~   64 (171)
T 2ia0_A           19 DRNILRLLKKDA----RLTISELSEQLKKPESTIHFRIKKLQERGVIERY   64 (171)
T ss_dssp             HHHHHHHHHHCT----TCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHcC----CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEee
Confidence            345555555442    3799999999999999999999999999999754

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

Probab=94.05  E-value=0.079  Score=37.76  Aligned_cols=46  Identities=15%  Similarity=0.230  Sum_probs=37.4

Q ss_pred             CHHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          70 DKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        70 Dk~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      |...++-|..+    .-+|...||++++++-+-.++.|+.|++.|+|..+
T Consensus        11 d~~il~~L~~~----~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~   56 (151)
T 2dbb_A           11 DMQLVKILSEN----SRLTYRELADILNTTRQRIARRIDKLKKLGIIRKF   56 (151)
T ss_dssp             HHHHHHHHHHC----TTCCHHHHHHHTTSCHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHHHc----CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            34455545443    34799999999999999999999999999999864

>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=93.94  E-value=0.067  Score=41.74  Aligned_cols=48  Identities=15%  Similarity=0.258  Sum_probs=36.7

Q ss_pred             HHHHHHHhhC------CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          72 ASYDKLLKEV------PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        72 ~tydKl~KEV------pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      ..++.|...|      |+.++=|-..||++|+|+-...|+||++|+++|+|...
T Consensus        13 ~i~~~l~~~I~~g~~~~g~~lPse~~La~~~~vSr~tvr~Al~~L~~~G~i~~~   66 (236)
T 3edp_A           13 VIASKIKDSINRDEYKTGMLMPNETALQEIYSSSRTTIRRAVDLLVEEGLVVRK   66 (236)
T ss_dssp             HHHHHHHHHHHTTSSCCCC--CCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHhCCCCCcCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            3444554443      33556699999999999999999999999999998654

>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=93.93  E-value=0.085  Score=36.97  Aligned_cols=45  Identities=16%  Similarity=0.169  Sum_probs=35.8

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT  131 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra  131 (139)
                      -+|.+.|++.++|+-|...+.|+.|++.|+|.... .++...|+-+
T Consensus        56 ~~s~~eLa~~l~is~stvs~~L~~L~~~Glv~~~~-~gr~~~y~l~  100 (122)
T 1u2w_A           56 ELCVCDIANILGVTIANASHHLRTLYKQGVVNFRK-EGKLALYSLG  100 (122)
T ss_dssp             CEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC-----CCEEEES
T ss_pred             CcCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEE-ECCEEEEEEC
Confidence            37999999999999999999999999999998753 3455566643

>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=93.91  E-value=0.084  Score=37.77  Aligned_cols=46  Identities=15%  Similarity=0.257  Sum_probs=37.4

Q ss_pred             CHHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          70 DKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        70 Dk~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      |...++-|..+    .-+|...||++++++-+-.++.|+.|++.|+|..+
T Consensus        10 d~~il~~L~~~----~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~   55 (152)
T 2cg4_A           10 DRGILEALMGN----ARTAYAELAKQFGVSPETIHVRVEKMKQAGIITGA   55 (152)
T ss_dssp             HHHHHHHHHHC----TTSCHHHHHHHHTSCHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHHHc----CCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcceE
Confidence            34455545444    34799999999999999999999999999999864

>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=93.87  E-value=0.16  Score=34.57  Aligned_cols=45  Identities=22%  Similarity=0.256  Sum_probs=36.5

Q ss_pred             eechHHHHhhhc-cchHHHHHHHHHHHHcCCeeEEee--cCceEEEec
Q psy1871          86 LITPSVVSERLK-VRGSLARKALEELLQKGLIKQVVK--HHAQVIYTR  130 (139)
Q Consensus        86 lITPsvlseRlk-I~~SLARkaLreL~~kGlIk~Vsk--h~~q~IYtr  130 (139)
                      -+|++.|++++. |+-+..-+.|+.|++.|+|.....  .++...|.=
T Consensus        38 ~~~~~eL~~~l~gis~~~ls~~L~~Le~~GlV~r~~~~~d~r~~~y~L   85 (107)
T 2fsw_A           38 IIRYGELKRAIPGISEKMLIDELKFLCGKGLIKKKQYPEVPPRVEYSL   85 (107)
T ss_dssp             CEEHHHHHHHSTTCCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEE
T ss_pred             CcCHHHHHHHcccCCHHHHHHHHHHHHHCCCEEEeecCCCCCeeEEEE
Confidence            379999999995 999999999999999999987642  345555543

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

Probab=93.85  E-value=0.063  Score=37.10  Aligned_cols=35  Identities=14%  Similarity=0.153  Sum_probs=32.2

Q ss_pred             eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      .-+|++.||++++++-|-.-++|+.|+++|+|...
T Consensus        53 ~~~t~~ela~~l~~~~~tvs~~l~~Le~~Glv~r~   87 (148)
T 3nrv_A           53 SDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVN   87 (148)
T ss_dssp             SSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC-
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEee
Confidence            36899999999999999999999999999999876

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

Probab=93.84  E-value=0.15  Score=35.13  Aligned_cols=33  Identities=24%  Similarity=0.358  Sum_probs=31.6

Q ss_pred             chHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          88 TPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        88 TPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      |++.||+++++.-|-.-++|+.|+++|+|....
T Consensus        52 ~~~~la~~l~~~~~tvs~~l~~Le~~Glv~r~~   84 (144)
T 3f3x_A           52 SMVYLANRYFVTQSAITAAVDKLEAKGLVRRIR   84 (144)
T ss_dssp             EHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CHHHHHHHHCCChhHHHHHHHHHHHCCCEEecc
Confidence            999999999999999999999999999998874

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

Probab=93.78  E-value=0.15  Score=35.38  Aligned_cols=43  Identities=14%  Similarity=0.023  Sum_probs=36.6

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR  130 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr  130 (139)
                      +|++.||+.++|+-+...+-|+.|++.|+|..... ++..+|.-
T Consensus        32 ~~~~eLa~~l~is~~tvs~hL~~L~~~GlV~~~~~-gr~~~y~l   74 (118)
T 3f6o_A           32 ATVSELAKPFDMALPSFMKHIHFLEDSGWIRTHKQ-GRVRTCAI   74 (118)
T ss_dssp             EEHHHHHTTCCSCHHHHHHHHHHHHHTTSEEEEEE-TTEEEEEE
T ss_pred             CCHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEec-CCEEEEEE
Confidence            59999999999999999999999999999987544 45555653

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

Probab=93.76  E-value=0.11  Score=37.06  Aligned_cols=35  Identities=17%  Similarity=0.291  Sum_probs=30.0

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      -+|++.||++++|.-+-.-++|+.|+++|+|....
T Consensus        62 ~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~   96 (168)
T 3u2r_A           62 GMATLQIADRLISRAPDITRLIDRLDDRGLVLRTR   96 (168)
T ss_dssp             CEEHHHHHHHC---CTHHHHHHHHHHHTTSEEEEE
T ss_pred             CcCHHHHHHHHCCChhhHHHHHHHHHHCCCEeecC
Confidence            58999999999999999999999999999999864

>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=93.76  E-value=0.041  Score=38.43  Aligned_cols=36  Identities=19%  Similarity=0.334  Sum_probs=33.1

Q ss_pred             CCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871          83 AYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQ  118 (139)
Q Consensus        83 k~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~  118 (139)
                      ...-+|++.||+++++.-|-.-++|+.|+++|+|..
T Consensus        48 ~~~~~t~~eLa~~l~~~~~~vs~~l~~Le~~Glv~r   83 (151)
T 3kp7_A           48 SIEALTVGQITEKQGVNKAAVSRRVKKLLNAELVKL   83 (151)
T ss_dssp             HHSCBCHHHHHHHHCSCSSHHHHHHHHHHHTTSEEC
T ss_pred             HcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence            445589999999999999999999999999999986

>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=93.76  E-value=0.048  Score=37.69  Aligned_cols=35  Identities=11%  Similarity=0.178  Sum_probs=28.6

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      -+|++.||++++|+-|-.-++|+.|+++|+|....
T Consensus        51 ~~t~~eLa~~l~~~~~tvs~~l~~L~~~Glv~r~~   85 (142)
T 3ech_A           51 GLNLQDLGRQMCRDKALITRKIRELEGRNLVRRER   85 (142)
T ss_dssp             TCCHHHHHHHHC---CHHHHHHHHHHHTTSEEC--
T ss_pred             CcCHHHHHHHhCCCHHHHHHHHHHHHHCCCEeecc
Confidence            37999999999999999999999999999998763

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

Probab=93.73  E-value=0.14  Score=36.38  Aligned_cols=43  Identities=23%  Similarity=0.215  Sum_probs=35.3

Q ss_pred             eechHHHHhhhc----cchHHHHHHHHHHHHcCCeeEEeecCceEEEe
Q psy1871          86 LITPSVVSERLK----VRGSLARKALEELLQKGLIKQVVKHHAQVIYT  129 (139)
Q Consensus        86 lITPsvlseRlk----I~~SLARkaLreL~~kGlIk~Vskh~~q~IYt  129 (139)
                      -+|...|++++.    |.-|-...+|+.|+++|+|..... ++..+|.
T Consensus        24 ~~t~~el~~~l~~~~~~~~~Tvt~~l~rLe~kGlv~r~~~-~r~~~~~   70 (138)
T 2g9w_A           24 PQTVRQVHEALSARRDLAYTTVMAVLQRLAKKNLVLQIRD-DRAHRYA   70 (138)
T ss_dssp             CEEHHHHHHHHTTTCCCCHHHHHHHHHHHHHTTSEEEEC----CCEEE
T ss_pred             CCCHHHHHHHHhccCCCCHHHHHHHHHHHHHCCCEEEEec-CCeEEEE
Confidence            489999999998    899999999999999999998764 4455664

>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=93.71  E-value=0.13  Score=34.33  Aligned_cols=44  Identities=14%  Similarity=0.260  Sum_probs=37.0

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT  131 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra  131 (139)
                      .|+..|++.++|+-|...+.|+.|++.|+|.... ..+...|.-+
T Consensus        37 ~~~~ela~~l~is~~tvs~~L~~L~~~Glv~~~~-~g~~~~y~l~   80 (102)
T 3pqk_A           37 FSVGELEQQIGIGQPTLSQQLGVLRESGIVETRR-NIKQIFYRLT   80 (102)
T ss_dssp             BCHHHHHHHHTCCTTHHHHHHHHHHHTTSEEEEC-SSSCCEEEEC
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEE-eCCEEEEEEC
Confidence            7999999999999999999999999999998654 3445566543

>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=93.68  E-value=0.14  Score=36.23  Aligned_cols=54  Identities=17%  Similarity=0.179  Sum_probs=41.3

Q ss_pred             HHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871          76 KLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT  131 (139)
Q Consensus        76 Kl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra  131 (139)
                      +|+..+-. .-.|.+.||++++|+-|...+.|+.|++.|+|.... .++...|+-+
T Consensus        50 ~IL~~L~~-~~~s~~ela~~lgis~stvs~~L~~Le~~Glv~~~~-~gr~~~y~l~  103 (122)
T 1r1t_A           50 RLLSLLAR-SELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRK-QGRHVYYQLQ  103 (122)
T ss_dssp             HHHHHHTT-CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE-ETTEEEEEES
T ss_pred             HHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEE-eCCEEEEEEC
Confidence            34444432 337999999999999999999999999999998754 3455667644

>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=93.48  E-value=0.086  Score=37.42  Aligned_cols=36  Identities=31%  Similarity=0.168  Sum_probs=33.6

Q ss_pred             eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      +=|+...|..++++.-....++|+.||.+|+|+.|.
T Consensus        52 ~GIw~kdL~~~tnL~~~~vtkiLK~LE~k~lIK~Vk   87 (95)
T 2yu3_A           52 KGIWSRDVRYKSNLPLTEINKILKNLESKKLIKAVK   87 (95)
T ss_dssp             SCEEHHHHHHHHTCCHHHHHHHHHHHHHHTSEEEEC
T ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCEEEec
Confidence            457899999999999999999999999999999994

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

Probab=93.48  E-value=0.072  Score=38.17  Aligned_cols=37  Identities=22%  Similarity=0.310  Sum_probs=29.4

Q ss_pred             eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEee
Q psy1871          85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK  121 (139)
Q Consensus        85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk  121 (139)
                      .-+|++.||++++|.-+-.-++|+.|+++|+|...+.
T Consensus        51 ~~~t~~eLa~~l~~~~~tvsr~v~~Le~~glVr~~~~   87 (148)
T 4fx0_A           51 IDLTMSELAARIGVERTTLTRNLEVMRRDGLVRVMAG   87 (148)
T ss_dssp             ---CHHHHHHHHTCCHHHHHHHHHHHHHTTSBC----
T ss_pred             CCcCHHHHHHHHCCChhhHHHHHHHHHHCCCEEeeCC
Confidence            3489999999999999999999999999999966543

>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=93.46  E-value=0.05  Score=37.88  Aligned_cols=35  Identities=17%  Similarity=0.106  Sum_probs=32.6

Q ss_pred             eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      .-+|++.||+++++.-|-.-++|+.|+++|+|...
T Consensus        52 ~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~   86 (127)
T 2frh_A           52 KEYYLKDIINHLNYKQPQVVKAVKILSQEDYFDKK   86 (127)
T ss_dssp             SEEEHHHHHHHSSSHHHHHHHHHHHHHHTTSSCCB
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence            45899999999999999999999999999999875

>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=93.46  E-value=0.16  Score=38.83  Aligned_cols=43  Identities=30%  Similarity=0.294  Sum_probs=36.4

Q ss_pred             HHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          76 KLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        76 Kl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      +|+..+.+ .-+|...||++++++-+-.++-|+.|++.|+|...
T Consensus        24 ~IL~~L~~-~~~s~~eLA~~lglS~stv~~~l~~Le~~GlI~~~   66 (192)
T 1uly_A           24 KILKLLRN-KEMTISQLSEILGKTPQTIYHHIEKLKEAGLVEVK   66 (192)
T ss_dssp             HHHHHHTT-CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            44444443 34899999999999999999999999999999987

>2v7f_A RPS19, RPS19E SSU ribosomal protein S19E; diamond blackfan anemia small ribosomal subunit; 1.15A {Pyrococcus abyssi} SCOP: a.4.5.84

Probab=93.43  E-value=0.063  Score=40.55  Aligned_cols=31  Identities=29%  Similarity=0.433  Sum_probs=29.1

Q ss_pred             hHHHHhhhc--------------cchHHHHHHHHHHHHcCCeeEE
Q psy1871          89 PSVVSERLK--------------VRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        89 PsvlseRlk--------------I~~SLARkaLreL~~kGlIk~V  119 (139)
                      ...|++.|+              ++.+..|.||+.|++.|+|...
T Consensus        70 ~~~La~~~gg~k~~g~~p~~~~~vSr~tVR~AL~~Le~~GlV~~~  114 (150)
T 2v7f_A           70 IERLRTYYGGRKNRGHAPERFYKAGGSIIRKALQQLEAAGFVEKV  114 (150)
T ss_dssp             HHHHHHHHCC----CCCTTSCCCHHHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHCCCccCCcCCccccccchHHHHHHHHHHHHCCCEEEe
Confidence            489999999              9999999999999999999765

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

Probab=93.39  E-value=0.13  Score=36.51  Aligned_cols=35  Identities=23%  Similarity=0.373  Sum_probs=32.9

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      -+|++.||++++|.-|-.-++|..|+++|+|....
T Consensus        51 ~~t~~eLa~~l~~~~~tvs~~v~~Le~~Glv~r~~   85 (147)
T 4b8x_A           51 ELPMSKIGERLMVHPTSVTNTVDRLVRSGLVAKRP   85 (147)
T ss_dssp             EEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CcCHHHHHHHHCCCHHHHHHHHHHHHhCCCEEEee
Confidence            47999999999999999999999999999999874

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

Probab=93.37  E-value=0.079  Score=37.14  Aligned_cols=35  Identities=26%  Similarity=0.374  Sum_probs=31.9

Q ss_pred             eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      .-+|++.||++++|.-+-.-++|+.|+++|+|...
T Consensus        62 ~~~t~~ela~~l~is~~tvs~~l~~Le~~glv~r~   96 (162)
T 2fa5_A           62 PGSSASEVSDRTAMDKVAVSRAVARLLERGFIRRE   96 (162)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC-
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeee
Confidence            35899999999999999999999999999999875

>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=93.37  E-value=0.079  Score=37.05  Aligned_cols=33  Identities=21%  Similarity=0.382  Sum_probs=30.9

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      +|.+.||++++++-+..++.|+.|++.|+|..+
T Consensus        19 ~~~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~   51 (141)
T 1i1g_A           19 TPFTEIAKKLGISETAVRKRVKALEEKGIIEGY   51 (141)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHHHHHHTSSCCC
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHHHCCCEecc
Confidence            599999999999999999999999999999753

>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=93.29  E-value=0.066  Score=37.28  Aligned_cols=33  Identities=18%  Similarity=0.289  Sum_probs=31.2

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      +|++.||++++|.-+-.-++|+.|+++|+|...
T Consensus        55 ~t~~eLa~~l~i~~~tvs~~l~~Le~~Glv~r~   87 (150)
T 3fm5_A           55 VNQRGVAATMGLDPSQIVGLVDELEERGLVVRT   87 (150)
T ss_dssp             CCSHHHHHHHTCCHHHHHHHHHHHHTTTSEEC-
T ss_pred             cCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEee
Confidence            899999999999999999999999999999875

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

Probab=93.24  E-value=0.1  Score=37.44  Aligned_cols=35  Identities=17%  Similarity=0.269  Sum_probs=32.4

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      .+|++.||++++|.-|-.-++|..|+++|+|....
T Consensus        46 ~~~~~eLa~~l~~~~~tvs~~v~~Le~~GlV~R~~   80 (151)
T 4aik_A           46 EQSQIQLAKAIGIEQPSLVRTLDQLEEKGLITRHT   80 (151)
T ss_dssp             TSCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCcHHHHHHHHCcCHHHHHHHHHHHHhCCCeEeec
Confidence            46899999999999999999999999999998763

>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=93.21  E-value=0.11  Score=37.73  Aligned_cols=37  Identities=22%  Similarity=0.246  Sum_probs=32.7

Q ss_pred             eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEee
Q psy1871          85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK  121 (139)
Q Consensus        85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk  121 (139)
                      ..+|...||++++|+-+..+++|+.|.+.|+|.-+..
T Consensus        29 ~~~~~~~iA~~~~i~~~~l~kil~~L~~~Glv~s~rG   65 (149)
T 1ylf_A           29 SLCTSDYMAESVNTNPVVIRKIMSYLKQAGFVYVNRG   65 (149)
T ss_dssp             GGCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEC--
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEccC
Confidence            4689999999999999999999999999999876554

>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=93.12  E-value=0.096  Score=37.20  Aligned_cols=34  Identities=12%  Similarity=0.239  Sum_probs=31.8

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      -+|...||++++++-|-.++.|+.|++.|+|..+
T Consensus        17 ~~~~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~   50 (150)
T 2pn6_A           17 KYSLDEIAREIRIPKATLSYRIKKLEKDGVIKGY   50 (150)
T ss_dssp             TSCHHHHHHHHTSCHHHHHHHHHHHHHTTSSCCC
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEE
Confidence            4899999999999999999999999999999863

>3ihu_A Transcriptional regulator, GNTR family; YP_298823.1, DNA binding protein, structural genomics, joint for structural genomics, JCSG; HET: MSE; 1.92A {Ralstonia eutropha}

Probab=93.09  E-value=0.13  Score=38.83  Aligned_cols=49  Identities=16%  Similarity=0.337  Sum_probs=40.0

Q ss_pred             HHHHHHHHhhC------CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          71 KASYDKLLKEV------PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        71 k~tydKl~KEV------pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      ...|+.|...|      |..+|- -..||++|+|+-+--|.||+.|+..|+|...-
T Consensus        19 ~~v~~~l~~~I~~g~l~pG~~L~-E~~La~~lgVSRtpVREAl~~L~~eGlv~~~~   73 (222)
T 3ihu_A           19 DTVFFGIMSGLELGTFVPGQRLV-ETDLVAHFGVGRNSVREALQRLAAEGIVDLQR   73 (222)
T ss_dssp             HHHHHHHHHHHHHTSSCTTCEEC-HHHHHHHHTCCHHHHHHHHHHHHHTTSEEECS
T ss_pred             HHHHHHHHHHHHhCCCCCCCccC-HHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence            45677776654      445665 99999999999999999999999999997653

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

Probab=93.06  E-value=0.2  Score=35.91  Aligned_cols=45  Identities=20%  Similarity=0.248  Sum_probs=36.8

Q ss_pred             eeechHHHHhhh-ccchHHHHHHHHHHHHcCCeeEEee--cCceEEEe
Q psy1871          85 KLITPSVVSERL-KVRGSLARKALEELLQKGLIKQVVK--HHAQVIYT  129 (139)
Q Consensus        85 KlITPsvlseRl-kI~~SLARkaLreL~~kGlIk~Vsk--h~~q~IYt  129 (139)
                      .-+|++.|++++ +|+-+..-+.|+.|++.|+|.....  .++...|.
T Consensus        47 g~~~~~eLa~~l~gis~~tls~~L~~Le~~GlV~r~~~~~d~r~~~y~   94 (131)
T 1yyv_A           47 GTHRFSDLRRXMGGVSEXMLAQSLQALEQDGFLNRVSYPVVPPHVEYS   94 (131)
T ss_dssp             CCEEHHHHHHHSTTCCHHHHHHHHHHHHHHTCEEEEEECSSSCEEEEE
T ss_pred             CCCCHHHHHHHhccCCHHHHHHHHHHHHHCCcEEEEecCCCCCeEEEE
Confidence            347999999999 7999999999999999999987642  24555554

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

Probab=93.05  E-value=0.057  Score=37.82  Aligned_cols=34  Identities=18%  Similarity=0.285  Sum_probs=32.3

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      -+|++.||++++|.-+-.-++|+.|+++|+|...
T Consensus        62 ~~~~~ela~~l~i~~~tvs~~l~~Le~~Gli~r~   95 (160)
T 3boq_A           62 GLSMGKLSGALKVTNGNVSGLVNRLIKDGMVVKA   95 (160)
T ss_dssp             CEEHHHHHHHCSSCCSCHHHHHHHHHHHTSEEEC
T ss_pred             CCCHHHHHHHHCCChhhHHHHHHHHHHCCCEEee
Confidence            4899999999999999999999999999999875

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

Probab=92.99  E-value=0.24  Score=36.06  Aligned_cols=40  Identities=18%  Similarity=0.198  Sum_probs=35.0

Q ss_pred             CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEee
Q psy1871          82 PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK  121 (139)
Q Consensus        82 pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk  121 (139)
                      +.-..+|...||++++|+-+..+++|+.|.+.|+|.-+..
T Consensus        24 ~~~~~~s~~~IA~~~~i~~~~l~kil~~L~~aGlv~s~rG   63 (143)
T 3t8r_A           24 EGQGCISLKSIAEENNLSDLYLEQLVGPLRNAGLIRSVRG   63 (143)
T ss_dssp             TTSCCEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEECSS
T ss_pred             CCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCEEEecCC
Confidence            4445799999999999999999999999999999876543

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

Probab=92.92  E-value=0.25  Score=37.11  Aligned_cols=44  Identities=11%  Similarity=0.171  Sum_probs=36.8

Q ss_pred             CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCce
Q psy1871          82 PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQ  125 (139)
Q Consensus        82 pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q  125 (139)
                      +.-..+|...||++++|+-+..+++|..|.+.|+|.-+...+..
T Consensus        40 ~~~~~~s~~eIA~~~~i~~~~l~kil~~L~~aGlv~s~rG~~GG   83 (159)
T 3lwf_A           40 IGDGPISLRSIAQDKNLSEHYLEQLIGPLRNAGIVKSIRGAHGG   83 (159)
T ss_dssp             TTSCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECSTTCE
T ss_pred             CCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCeEEEecCCCCc
Confidence            33457899999999999999999999999999999876543333

>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=92.85  E-value=0.49  Score=32.54  Aligned_cols=53  Identities=19%  Similarity=0.255  Sum_probs=45.8

Q ss_pred             CHHHHHHH---HhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeec
Q psy1871          70 DKASYDKL---LKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKH  122 (139)
Q Consensus        70 Dk~tydKl---~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh  122 (139)
                      |-+.|+.+   ..+.|--..+|...||-+|+++=+-+.++|=.|+++|.+..+..+
T Consensus        10 ~~~~~~~v~~~i~~L~~~~~~Ta~~IAkkLg~sK~~vNr~LY~L~kkG~V~~~~~~   65 (75)
T 1sfu_A           10 DAEIFSLVKKEVLSLNTNDYTTAISLSNRLKINKKKINQQLYKLQKEDTVKMVPSN   65 (75)
T ss_dssp             SHHHHHHHHHHHHTSCTTCEECHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEECCS
T ss_pred             hHHHHHHHHHHHHhCCCCcchHHHHHHHHHCCCHHHHHHHHHHHHHCCCEecCCCC
Confidence            55778877   556677788999999999999999999999999999999887543

>3cuq_B Vacuolar protein-sorting-associated protein 36; ESCRT, MBV, VPS, nucleus, protein transport, transc transcription regulation, transport, endosome; 2.61A {Homo sapiens} PDB: 2zme_B

Probab=92.69  E-value=0.15  Score=40.49  Aligned_cols=47  Identities=11%  Similarity=0.002  Sum_probs=37.9

Q ss_pred             CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871          84 YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT  131 (139)
Q Consensus        84 ~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra  131 (139)
                      ...||++.++++|++...+|+..|.+++.+|++-.=.... ..-|.++
T Consensus       166 ~g~vt~~~la~~l~ws~~~a~e~L~~~e~~G~l~~D~~~e-g~~y~pn  212 (218)
T 3cuq_B          166 KGSLTSEEFAKLVGMSVLLAKERLLLAEKMGHLCRDDSVE-GLRFYPN  212 (218)
T ss_dssp             TSCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEESSS-CEEEEEC
T ss_pred             CCCcCHHHHHHHhCCCHHHHHHHHHHHHHcCCEEEECCCC-ceEEehh
Confidence            4689999999999999999999999999999987654333 3335444

>2w48_A Sorbitol operon regulator; SORC, activator, repressor, DNA-binding, transcription, transcription regulator, transcription regulation; 3.20A {Klebsiella pneumoniae}

Probab=92.53  E-value=0.13  Score=41.46  Aligned_cols=35  Identities=11%  Similarity=0.273  Sum_probs=32.4

Q ss_pred             eeechHHHHhhhccchHHHHHHHHHHHHcCCee-EE
Q psy1871          85 KLITPSVVSERLKVRGSLARKALEELLQKGLIK-QV  119 (139)
Q Consensus        85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk-~V  119 (139)
                      .-+|...||++|+|+-+..|+-|.+|+++|+|+ .+
T Consensus        20 ~~~~~~ela~~l~vS~~tIrRdL~~l~~~G~v~iri   55 (315)
T 2w48_A           20 QDMTQAQIARELGIYRTTISRLLKRGREQGIVTIAI   55 (315)
T ss_dssp             SCCCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEEe
Confidence            348999999999999999999999999999997 55

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

Probab=92.44  E-value=0.28  Score=37.58  Aligned_cols=37  Identities=16%  Similarity=0.232  Sum_probs=33.6

Q ss_pred             CCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          83 AYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        83 k~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      ...-+|...||++|+|+-+-..++|+.|+++|+|...
T Consensus        17 ~~~~~~~~~lA~~l~vs~~tvs~~l~~Le~~GlV~r~   53 (214)
T 3hrs_A           17 RHNKITNKEIAQLMQVSPPAVTEMMKKLLAEELLIKD   53 (214)
T ss_dssp             SCSCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             cCCCcCHHHHHHHHCCChhHHHHHHHHHHHCCCEEEe
Confidence            3457899999999999999999999999999998765

>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=92.32  E-value=0.064  Score=37.30  Aligned_cols=34  Identities=24%  Similarity=0.267  Sum_probs=26.2

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      -+|++.||+++++.-+-.-++|+.|+++|+|...
T Consensus        57 ~~t~~eLa~~l~~~~~~vs~~l~~L~~~Glv~r~   90 (148)
T 3jw4_A           57 GIIQKDLAQFFGRRGASITSMLQGLEKKGYIERR   90 (148)
T ss_dssp             CCCHHHHHHC------CHHHHHHHHHHTTSBCCC
T ss_pred             CCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEee
Confidence            4799999999999999999999999999999876

>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=92.27  E-value=0.28  Score=35.55  Aligned_cols=35  Identities=17%  Similarity=0.260  Sum_probs=32.5

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      -+|.+.|+++++|+-+..-+.|+.|++.|+|....
T Consensus        37 ~~~~~eLa~~lgis~~tls~~L~~Le~~GlI~r~~   71 (146)
T 2f2e_A           37 LTRFGEFQKSLGLAKNILAARLRNLVEHGVMVAVP   71 (146)
T ss_dssp             CCSHHHHHHHHCCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEEe
Confidence            36899999999999999999999999999999864

>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=92.14  E-value=0.16  Score=38.51  Aligned_cols=34  Identities=15%  Similarity=0.048  Sum_probs=32.5

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      +|++.||++++|.-+-.-++|+.|+++|+|....
T Consensus        63 ~t~~eLa~~l~i~~stvs~~l~~Le~~GlV~r~~   96 (207)
T 2fxa_A           63 ASISEIAKFGVMHVSTAFNFSKKLEERGYLRFSK   96 (207)
T ss_dssp             EEHHHHHHHTTCCHHHHHHHHHHHHHHTSEEEEC
T ss_pred             cCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence            8999999999999999999999999999998874

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

Probab=91.91  E-value=0.19  Score=36.75  Aligned_cols=43  Identities=7%  Similarity=0.272  Sum_probs=34.8

Q ss_pred             HHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          77 LLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        77 l~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      |+..+..---+|...||++++++-+-.++-|+.|++.|+|..+
T Consensus         8 il~~L~~~~~~s~~~la~~lg~s~~tv~~rl~~L~~~g~i~~~   50 (162)
T 3i4p_A            8 ILRILQEDSTLAVADLAKKVGLSTTPCWRRIQKMEEDGVIRRR   50 (162)
T ss_dssp             HHHHHTTCSCSCHHHHHHHHTCCHHHHHHHHHHHHHTTSSCCC
T ss_pred             HHHHHHHCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeec
Confidence            3333333334599999999999999999999999999999853

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

Probab=91.83  E-value=0.34  Score=35.70  Aligned_cols=58  Identities=14%  Similarity=0.134  Sum_probs=44.3

Q ss_pred             HHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871          72 ASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT  131 (139)
Q Consensus        72 ~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra  131 (139)
                      ++--+|+..+-. .=.|+..|++.++|.-|...+-|+.|++.|+|.... ..+..+|.-+
T Consensus        58 p~R~~IL~~L~~-~~~t~~eLa~~lgls~stvs~hL~~L~~aGlV~~~~-~Gr~~~y~lt  115 (151)
T 3f6v_A           58 PTRRRLVQLLTS-GEQTVNNLAAHFPASRSAISQHLRVLTEAGLVTPRK-DGRFRYYRLD  115 (151)
T ss_dssp             HHHHHHHHHGGG-CCEEHHHHHTTSSSCHHHHHHHHHHHHHTTSEEEEE-ETTEEEEEEC
T ss_pred             HHHHHHHHHHHh-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEe-cCCEEEEEEC
Confidence            444556555542 337999999999999999999999999999998765 4445666543

>3eqx_A FIC domain containing transcriptional regulator; FIC family protein, structural genomics, joint center for ST genomics, JCSG; HET: MSE PGE; 1.60A {Shewanella oneidensis}

Probab=91.70  E-value=0.15  Score=43.07  Aligned_cols=45  Identities=13%  Similarity=0.142  Sum_probs=38.0

Q ss_pred             CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEe
Q psy1871          84 YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYT  129 (139)
Q Consensus        84 ~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYt  129 (139)
                      ..++|...+++.++++-.-|++.|++|.+.|+|..+... |..+|.
T Consensus       309 ~p~~t~~~~~~~~~~S~~TA~r~L~~L~e~GiL~~~~~g-R~~~y~  353 (373)
T 3eqx_A          309 QPYCRIQNLVESGLAKRQTASVYLKQLCDIGVLEEVQSG-KEKLFV  353 (373)
T ss_dssp             CSEEEHHHHHHTSSSCHHHHHHHHHHHHHTTSCEEC--C-CSCEEE
T ss_pred             CCCccHHHHHHHhCcCHHHHHHHHHHHHHCCcEEEeCCC-CceEee
Confidence            458999999999999999999999999999999998654 445675

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

Probab=91.69  E-value=0.4  Score=33.76  Aligned_cols=51  Identities=18%  Similarity=0.156  Sum_probs=42.3

Q ss_pred             HHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeec
Q psy1871          71 KASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKH  122 (139)
Q Consensus        71 k~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh  122 (139)
                      ++..++|...+-. .-.++..|++++++.-+.++.+|+.|.+.|.|..+...
T Consensus         6 ~~l~~~i~~~~~~-~p~~~~~la~~~~~~~~~~~~~l~~l~~~G~l~~i~~~   56 (121)
T 2pjp_A            6 QAIWQKAEPLFGD-EPWWVRDLAKETGTDEQAMRLTLRQAAQQGIITAIVKD   56 (121)
T ss_dssp             HHHHHHHGGGCSS-SCEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEETT
T ss_pred             HHHHHHHHHHHHh-CCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCC
Confidence            3456677776644 34588999999999999999999999999999999854

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

Probab=91.44  E-value=0.35  Score=35.32  Aligned_cols=49  Identities=18%  Similarity=0.188  Sum_probs=39.1

Q ss_pred             eechHHHHhhh-ccchHHHHHHHHHHHHcCCeeEEe--ecCceEEEeccCCC
Q psy1871          86 LITPSVVSERL-KVRGSLARKALEELLQKGLIKQVV--KHHAQVIYTRTTKG  134 (139)
Q Consensus        86 lITPsvlseRl-kI~~SLARkaLreL~~kGlIk~Vs--kh~~q~IYtra~k~  134 (139)
                      -.+++.|++.+ +|+-+.--..|++|++.|+|....  ..++...|.=..++
T Consensus        39 ~~rf~eL~~~l~gIs~~~Ls~~L~~Le~~GLV~R~~~~~d~r~v~y~LT~~G   90 (131)
T 4a5n_A           39 KKRFNEFRRICPSITQRMLTLQLRELEADGIVHREVYHQVPPKVEYSLTEFG   90 (131)
T ss_dssp             CBCHHHHHHHCTTSCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECTTG
T ss_pred             CcCHHHHHHHhcccCHHHHHHHHHHHHHCCCEEEEecCCCCCeEEEEECHhH
Confidence            46899999999 999999999999999999998864  23455666654443

>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=91.43  E-value=0.1  Score=37.36  Aligned_cols=45  Identities=18%  Similarity=0.186  Sum_probs=36.5

Q ss_pred             HHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          71 KASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        71 k~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      ...++-|..+    .-+|.+.||++++++-+-.++.|+.|++.|+|..+
T Consensus        10 ~~il~~L~~~----~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~   54 (151)
T 2cyy_A           10 KKIIKILQND----GKAPLREISKITGLAESTIHERIRKLRESGVIKKF   54 (151)
T ss_dssp             HHHHHHHHHC----TTCCHHHHHHHHCSCHHHHHHHHHHHHHHTSSCCC
T ss_pred             HHHHHHHHHc----CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEE
Confidence            3445444443    24799999999999999999999999999999764

>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=90.88  E-value=0.46  Score=36.68  Aligned_cols=44  Identities=25%  Similarity=0.230  Sum_probs=36.7

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEEeec----CceEEEec
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKH----HAQVIYTR  130 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh----~~q~IYtr  130 (139)
                      .|++.|+++++|+-|.....|+.|++.|+|......    ++..+|.-
T Consensus        29 ~s~~eLa~~l~is~stvs~hLk~Le~~GLV~~~~~~~~~g~~~~~Y~L   76 (202)
T 2p4w_A           29 YFVSELSRELGVGQKAVLEHLRILEEAGLIESRVEKIPRGRPRKYYMI   76 (202)
T ss_dssp             EEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECCBTTBCCCEEEEE
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEeeccCCCCceEEEEE
Confidence            699999999999999999999999999999886542    44445543

>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=90.41  E-value=0.25  Score=36.88  Aligned_cols=38  Identities=16%  Similarity=0.292  Sum_probs=33.8

Q ss_pred             eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeec
Q psy1871          85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKH  122 (139)
Q Consensus        85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh  122 (139)
                      ..+|...||++++|+-+..+++|+.|.+.|+|.-+...
T Consensus        27 ~~~s~~~IA~~~~is~~~l~kil~~L~~aGlv~s~rG~   64 (162)
T 3k69_A           27 SKVASRELAQSLHLNPVMIRNILSVLHKHGYLTGTVGK   64 (162)
T ss_dssp             SCBCHHHHHHHHTSCGGGTHHHHHHHHHTTSSEEECST
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeecCC
Confidence            56899999999999999999999999999998665433

>2vxz_A Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Pyrobaculum spherical virus}

Probab=90.41  E-value=0.47  Score=37.11  Aligned_cols=43  Identities=19%  Similarity=0.207  Sum_probs=38.2

Q ss_pred             CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceE
Q psy1871          84 YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQV  126 (139)
Q Consensus        84 ~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~  126 (139)
                      .--.|.|.|+..++++-|-|+-+|..|+++|+|..|..+.+..
T Consensus        22 ~G~~~t~~Iak~LGlShg~aq~~Ly~LeREG~V~~Vk~GK~ay   64 (165)
T 2vxz_A           22 DGCKTTSLIQQRLGLSHGRAKALIYVLEKEGRVTRVAFGNVAL   64 (165)
T ss_dssp             TCCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSCEEEEETTEEE
T ss_pred             hCCccHHHHHHHhCCcHHHHHHHHHHHHhcCceEEEEEccEEE
Confidence            4456999999999999999999999999999999998776543

>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=90.34  E-value=0.23  Score=37.24  Aligned_cols=34  Identities=21%  Similarity=0.194  Sum_probs=31.0

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      .|...||+.|+++-+-+++.|+.|+++|+|....
T Consensus        25 ~s~~eia~~lgl~~~tv~~~l~~Le~~G~i~~~~   58 (196)
T 3k2z_A           25 PSVREIARRFRITPRGALLHLIALEKKGYIERKN   58 (196)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHHHHHTTSEECC-
T ss_pred             CCHHHHHHHcCCCcHHHHHHHHHHHHCCCEEecC
Confidence            6899999999999999999999999999997653

>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=90.28  E-value=0.28  Score=35.47  Aligned_cols=34  Identities=6%  Similarity=0.266  Sum_probs=31.6

Q ss_pred             chHHHHhhhccchHHHHHHHHHHHHcCCeeEEee
Q psy1871          88 TPSVVSERLKVRGSLARKALEELLQKGLIKQVVK  121 (139)
Q Consensus        88 TPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk  121 (139)
                      |...||++++|+-+..+++|..|.+.|+|.-+..
T Consensus        25 s~~~IA~~~~i~~~~l~kIl~~L~~aGlv~s~rG   58 (145)
T 1xd7_A           25 SSEIIADSVNTNPVVVRRMISLLKKADILTSRAG   58 (145)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHHHHHHTTSEECCSS
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHCCceEeecC
Confidence            8899999999999999999999999999976654

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

Probab=90.05  E-value=0.35  Score=38.47  Aligned_cols=33  Identities=15%  Similarity=0.153  Sum_probs=31.8

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      +|.+.||+++++.-|-..+.|+.|++.|+|...
T Consensus       167 ~s~~eLA~~lglsksTv~r~L~~Le~~GlV~r~  199 (244)
T 2wte_A          167 TGITELAKMLDKSEKTLINKIAELKKFGILTQK  199 (244)
T ss_dssp             BCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence            799999999999999999999999999999876

>2ra5_A Putative transcriptional regulator; beta structure, UTRA domain, structural genomics, PSI-2, protein structure initiative; HET: SRT; 2.40A {Streptomyces coelicolor A3} SCOP: d.190.1.2

Probab=89.65  E-value=0.081  Score=41.43  Aligned_cols=36  Identities=25%  Similarity=0.339  Sum_probs=4.5

Q ss_pred             CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          84 YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        84 ~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      .++=|-..||++|+|+-+..|+||+.|+++|+|...
T Consensus        38 ~~lPse~~La~~~~vSr~tvr~Al~~L~~~G~i~~~   73 (247)
T 2ra5_A           38 SLLGNEIELAARLGLSRPTVRQAIQSLVDKGLLVRR   73 (247)
T ss_dssp             ------------------------------CEEEEE
T ss_pred             CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            455588999999999999999999999999998654

>1u5t_B Defective in vacuolar protein sorting; VPS36P; ESCRT, endosomal, trafficking, protein complex, transport protein; 3.60A {Saccharomyces cerevisiae} SCOP: a.4.5.54 a.4.5.54

Probab=89.55  E-value=0.32  Score=37.24  Aligned_cols=44  Identities=9%  Similarity=0.110  Sum_probs=36.6

Q ss_pred             echH-H-HHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871          87 ITPS-V-VSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT  131 (139)
Q Consensus        87 ITPs-v-lseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra  131 (139)
                      ||.+ . +++++++...+|+.+|.+++++|++-.=..... .-|-.|
T Consensus       119 vt~~~~~la~~~~ws~~~a~e~L~~~e~~G~l~~D~~~~G-~~y~~N  164 (169)
T 1u5t_B          119 LTQILSSNNSKSNWTLGILMEVLQNCVDEGDLLIDKQLSG-IYYYKN  164 (169)
T ss_dssp             HHHHHHTSCTTCCCCHHHHHHHHHHHHHHTSEEEEECSSC-EEEEEC
T ss_pred             ccHHHHHHHHHhCCCHHHHHHHHHHHHHcCCEEEECCCCc-ceEEee
Confidence            8999 9 999999999999999999999999977654444 345444

>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=89.55  E-value=0.29  Score=37.55  Aligned_cols=34  Identities=24%  Similarity=0.502  Sum_probs=31.1

Q ss_pred             ech--HHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          87 ITP--SVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        87 ITP--svlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      +|+  ..||++++++-+-..++|+.|+++|+|....
T Consensus        23 ~~~~~~~La~~l~vs~~tvs~~l~~Le~~GlV~r~~   58 (230)
T 1fx7_A           23 VTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAG   58 (230)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEECT
T ss_pred             CCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeC
Confidence            577  9999999999999999999999999997753

>2gqq_A Leucine-responsive regulatory protein; helix-turn-helix, transcription; 3.20A {Escherichia coli} PDB: 2l4a_A

Probab=89.50  E-value=0.035  Score=40.58  Aligned_cols=35  Identities=14%  Similarity=0.264  Sum_probs=31.7

Q ss_pred             CCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871          83 AYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQ  118 (139)
Q Consensus        83 k~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~  118 (139)
                      +.++ |...||++|+|+-+-.|.+|+.|++.|+|..
T Consensus        25 ~~~l-s~~eLa~~lgvSr~~vr~al~~L~~~Gli~~   59 (163)
T 2gqq_A           25 DGRI-SNVELSKRVGLSPTPCLERVRRLERQGFIQG   59 (163)
T ss_dssp             CSSC-CTTGGGTSSSCCTTTSSSTHHHHHHHTSEEE
T ss_pred             CCCC-CHHHHHHHHCcCHHHHHHHHHHHHHCCcEEE
Confidence            3444 9999999999999999999999999999985

>2o03_A Probable zinc uptake regulation protein FURB; DNA-binding, helix-turn-helix, zinc binding, GE regulation; 2.70A {Mycobacterium tuberculosis}

Probab=89.40  E-value=0.72  Score=32.66  Aligned_cols=46  Identities=13%  Similarity=0.348  Sum_probs=39.0

Q ss_pred             eeechHHHHhhh-----ccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871          85 KLITPSVVSERL-----KVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR  130 (139)
Q Consensus        85 KlITPsvlseRl-----kI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr  130 (139)
                      .-+|...|.+++     +|..+-.-+.|+.|++.|+|..+.-......|-.
T Consensus        25 ~~~sa~ei~~~l~~~~~~is~~TVYR~L~~L~e~Glv~~~~~~~~~~~y~~   75 (131)
T 2o03_A           25 DFRSAQELHDELRRRGENIGLTTVYRTLQSMASSGLVDTLHTDTGESVYRR   75 (131)
T ss_dssp             SCEEHHHHHHHHHHTTCCCCHHHHHHHHHHHHTTTSEEEEECTTSCEEEEE
T ss_pred             CCCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCCCEEEEEeCCCceEEEe
Confidence            358999999999     8999999999999999999999976666566643

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

Probab=88.53  E-value=0.13  Score=37.38  Aligned_cols=34  Identities=26%  Similarity=0.428  Sum_probs=32.0

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      -+|++.||++++|+-+-.-++|+.|+++|+|...
T Consensus        86 ~~t~~eLa~~l~is~~tvs~~l~~Le~~GlV~r~  119 (181)
T 2fbk_A           86 GLRPTELSALAAISGPSTSNRIVRLLEKGLIERR  119 (181)
T ss_dssp             CBCHHHHHHHCSCCSGGGSSHHHHHHHHTSEECC
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHCcCEEec
Confidence            3799999999999999999999999999999876

>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=88.17  E-value=0.6  Score=36.15  Aligned_cols=34  Identities=9%  Similarity=0.198  Sum_probs=31.9

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      -+|.+.||+++++.-|-+.++|+.|++.|+|...
T Consensus        21 ~~s~~ela~~~gl~~stv~r~l~~L~~~G~v~~~   54 (241)
T 2xrn_A           21 GLSLAAIAQLVGLPRSTVQRIINALEEEFLVEAL   54 (241)
T ss_dssp             CEEHHHHHHHTTSCHHHHHHHHHHHHTTTSEEEC
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence            4799999999999999999999999999999774

>2fe3_A Peroxide operon regulator; oxidative stress regulator, DNA binding protein; 1.75A {Bacillus subtilis} PDB: 3f8n_A 2rgv_A*

Probab=87.53  E-value=0.87  Score=32.85  Aligned_cols=45  Identities=16%  Similarity=0.183  Sum_probs=37.8

Q ss_pred             eeechHHHHhhh-----ccchHHHHHHHHHHHHcCCeeEEeecCceEEEe
Q psy1871          85 KLITPSVVSERL-----KVRGSLARKALEELLQKGLIKQVVKHHAQVIYT  129 (139)
Q Consensus        85 KlITPsvlseRl-----kI~~SLARkaLreL~~kGlIk~Vskh~~q~IYt  129 (139)
                      .-+|...|.+++     +|+.+..-+.|+.|++.|+|..+.-..+...|-
T Consensus        36 ~~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~~~~~~~~~Y~   85 (145)
T 2fe3_A           36 AHPTADDIYKALEGKFPNMSVATVYNNLRVFRESGLVKELTYGDASSRFD   85 (145)
T ss_dssp             SCCCHHHHHHHHGGGCTTCCHHHHHHHHHHHHHTTSEEEECCTTSCCEEE
T ss_pred             CCCCHHHHHHHHHHhCCCCChhhHHHHHHHHHHCCCEEEEeeCCCceEEE
Confidence            357999999999     788999999999999999999987655555664

>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=87.47  E-value=0.74  Score=35.60  Aligned_cols=34  Identities=24%  Similarity=0.255  Sum_probs=31.9

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      -+|.+.||+++++.-|-+.+.|+.|++.|+|...
T Consensus        23 ~~~~~ela~~~gl~~stv~r~l~~L~~~G~v~~~   56 (249)
T 1mkm_A           23 DVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRK   56 (249)
T ss_dssp             CBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEC
Confidence            4799999999999999999999999999999775

>1bia_A BIRA bifunctional protein; transcription regulation; 2.30A {Escherichia coli} SCOP: a.4.5.1 b.34.1.1 d.104.1.2 PDB: 1bib_A* 1hxd_A* 2ewn_A*

Probab=87.46  E-value=0.9  Score=36.92  Aligned_cols=49  Identities=16%  Similarity=0.094  Sum_probs=40.4

Q ss_pred             HHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEee
Q psy1871          73 SYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK  121 (139)
Q Consensus        73 tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk  121 (139)
                      ...+|+.-+..-..+|...||++|+|+-+-.++-|+.|++.|++..-..
T Consensus         6 r~~~Il~~L~~~~~~s~~eLa~~l~vS~~ti~r~l~~L~~~G~~i~~~~   54 (321)
T 1bia_A            6 VPLKLIALLANGEFHSGEQLGETLGMSRAAINKHIQTLRDWGVDVFTVP   54 (321)
T ss_dssp             HHHHHHHHHTTSSCBCHHHHHHHHTSCHHHHHHHHHHHHHTTCCCEEET
T ss_pred             HHHHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHHHHhCCCcEEEec
Confidence            3445666666667899999999999999999999999999999864433

>2p5k_A Arginine repressor; DNA-binding domain, winged helix-turn-helix (WHTH), DNA binding protein; 1.00A {Bacillus subtilis} SCOP: a.4.5.3 PDB: 2p5l_C*

Probab=87.41  E-value=1.4  Score=26.61  Aligned_cols=40  Identities=18%  Similarity=0.299  Sum_probs=31.6

Q ss_pred             eeechHHHHhhh-----ccchHHHHHHHHHHHHcCCeeEEeecCceEEE
Q psy1871          85 KLITPSVVSERL-----KVRGSLARKALEELLQKGLIKQVVKHHAQVIY  128 (139)
Q Consensus        85 KlITPsvlseRl-----kI~~SLARkaLreL~~kGlIk~Vskh~~q~IY  128 (139)
                      ..+|...|++.|     +|+-+-.++-|+   +-|+| .+........|
T Consensus        18 ~~~t~~el~~~l~~~~~~vs~~Tv~R~L~---~lg~v-~~~~~~~~~~Y   62 (64)
T 2p5k_A           18 EIETQDELVDMLKQDGYKVTQATVSRDIK---ELHLV-KVPTNNGSYKY   62 (64)
T ss_dssp             CCCSHHHHHHHHHHTTCCCCHHHHHHHHH---HHTCE-EEEETTTEEEE
T ss_pred             CCCCHHHHHHHHHHhCCCcCHHHHHHHHH---HcCCE-EEecCCCceee
Confidence            468999999999     999998887777   45899 66655555556

>2ve8_A FTSK, DNA translocase FTSK; nucleotide-binding, chromosome partition, ATP-binding, DNA-binding, winged helix, bacterial cell division; HET: DNA; 1.4A {Pseudomonas aeruginosa} SCOP: a.4.5.67 PDB: 2ve9_A* 2j5o_A*

Probab=87.30  E-value=0.26  Score=33.85  Aligned_cols=59  Identities=17%  Similarity=0.274  Sum_probs=48.5

Q ss_pred             HHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEe
Q psy1871          71 KASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYT  129 (139)
Q Consensus        71 k~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYt  129 (139)
                      .++|+....=|-...-.+.|.|=-||+|-..-|-+++..||+.|+|-+-..+..-.|+.
T Consensus         9 D~Ly~~A~~~V~~~~~aS~S~lQR~lrIGYnRAArlid~lE~~GiVgp~~gsk~ReVL~   67 (73)
T 2ve8_A            9 DPLYDEAVRFVTESRRASISAVQRKLKIGYNRAARMIEAMEMAGVVTPMNTNGSREVIA   67 (73)
T ss_dssp             CTTHHHHHHHHHHHCCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSBCCCCTTSCCCBCS
T ss_pred             cHHHHHHHHHHHhcCCccHHHHHHHHccChHHHHHHHHHHHHCCcCCcccCCCCceEeC
Confidence            46777777777777888999999999999999999999999999998876544334444

>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=87.30  E-value=0.52  Score=36.22  Aligned_cols=32  Identities=19%  Similarity=0.370  Sum_probs=29.3

Q ss_pred             chHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          88 TPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        88 TPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      +.+.||++++|.-+-..++|+.|+++|+|...
T Consensus        26 ~~~~la~~l~vs~~tvs~~l~~Le~~GlV~r~   57 (226)
T 2qq9_A           26 LRARIAERLEQSGPTVSQTVARMERDGLVVVA   57 (226)
T ss_dssp             BHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             cHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            44999999999999999999999999998764

>2xig_A Ferric uptake regulation protein; hpfur, transcription, homeostasis; HET: CIT; 1.85A {Helicobacter pylori}

Probab=87.25  E-value=1.3  Score=32.16  Aligned_cols=45  Identities=13%  Similarity=0.177  Sum_probs=38.3

Q ss_pred             eechHHHHhhh-----ccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871          86 LITPSVVSERL-----KVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR  130 (139)
Q Consensus        86 lITPsvlseRl-----kI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr  130 (139)
                      -+|...|.+++     +|..+-.-+.|+.|++.|+|..+.-..+...|-.
T Consensus        42 ~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~~~~~~~~~Y~~   91 (150)
T 2xig_A           42 HLSPEEITHSIRQKDKNTSISSVYRILNFLEKENFISVLETSKSGRRYEI   91 (150)
T ss_dssp             CBCHHHHHHHHHHHSTTCCHHHHHHHHHHHHHTTSEEEEEETTTEEEEEE
T ss_pred             CCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCCcEEEEEeCCCceEEEe
Confidence            57899999988     6888889999999999999999977666666754

>1w7p_D VPS36P, YLR417W; ESCRT-II complex, endosomal protein sorting, protein transpo; 3.60A {Saccharomyces cerevisiae} SCOP: a.4.5.54 a.4.5.54

Probab=87.05  E-value=1.2  Score=40.15  Aligned_cols=60  Identities=10%  Similarity=0.068  Sum_probs=45.8

Q ss_pred             HHHHHHHHhhCCCCeeechHHHHhhhc-------cchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871          71 KASYDKLLKEVPAYKLITPSVVSERLK-------VRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT  131 (139)
Q Consensus        71 k~tydKl~KEVpk~KlITPsvlseRlk-------I~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra  131 (139)
                      .....+|+.-+.....||...|+++|+       +...+|+.+|++++.+|++-.=..... .-|.++
T Consensus       493 ~~~~~~il~l~~~~g~vT~~~la~~lg~~~~~~~Ws~~~A~e~L~~~e~eG~l~rDd~~~G-~~yypN  559 (566)
T 1w7p_D          493 DVVKEKLVDLIGDNPGSDLLRLTQILSSNNSKSNWTLGILMEVLQNCVDEGDLLIDKQLSG-IYYYKN  559 (566)
T ss_dssp             HHHHHHHHHHHTTSTTCCHHHHHHHHSCSSSCCCBCHHHHHHHHHHHHHTTSEEEEEETTE-EEEEEC
T ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCccccCcccHHHHHHHHHHHHHcCCEEEECCCCc-eEEehh
Confidence            355566655455567999999999999       999999999999999999976544443 234443

>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=87.04  E-value=0.85  Score=35.73  Aligned_cols=44  Identities=20%  Similarity=0.177  Sum_probs=36.2

Q ss_pred             HHhhCCC-CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          77 LLKEVPA-YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        77 l~KEVpk-~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      |+.-+-. -.-+|.+.||+++++.-|-+-++|+.|++.|+|....
T Consensus        11 IL~~l~~~~~~lsl~eia~~lgl~ksT~~RlL~tL~~~G~v~~~~   55 (260)
T 3r4k_A           11 LLTYFNHGRLEIGLSDLTRLSGMNKATVYRLMSELQEAGFVEQVE   55 (260)
T ss_dssp             HHTTCBTTBSEEEHHHHHHHHCSCHHHHHHHHHHHHHTTSEEECS
T ss_pred             HHHHHhhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcC
Confidence            4444443 2568999999999999999999999999999987643

>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=86.85  E-value=0.42  Score=39.36  Aligned_cols=35  Identities=17%  Similarity=0.176  Sum_probs=32.8

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      =+|+..||+++++.-+-.-++|..|+++|+|....
T Consensus       420 ~~~~~~l~~~~~~~~~~~t~~~~~le~~g~v~r~~  454 (487)
T 1hsj_A          420 EISSKEIAKCSEFKPYYLTKALQKLKDLKLLSKKR  454 (487)
T ss_dssp             EEEHHHHHHSSCCCHHHHHHHHHHHHTTTTSCCEE
T ss_pred             CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeecC
Confidence            48999999999999999999999999999998874

>2w57_A Ferric uptake regulation protein; gene regulation, transcription regulation, transport, iron, repressor, DNA-binding, transcription; 2.60A {Vibrio cholerae}

Probab=86.75  E-value=1.4  Score=32.12  Aligned_cols=45  Identities=9%  Similarity=0.234  Sum_probs=36.7

Q ss_pred             eeechHHHHhhh-----ccchHHHHHHHHHHHHcCCeeEEeecCceEEEe
Q psy1871          85 KLITPSVVSERL-----KVRGSLARKALEELLQKGLIKQVVKHHAQVIYT  129 (139)
Q Consensus        85 KlITPsvlseRl-----kI~~SLARkaLreL~~kGlIk~Vskh~~q~IYt  129 (139)
                      .-+|...|.+++     .|..+..-+.|+.|++.|+|..+.-......|-
T Consensus        32 ~h~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~~~~~~~~~Y~   81 (150)
T 2w57_A           32 QHISAEELYKKLIDLGEEIGLATVYRVLNQFDDAGIVTRHHFEGGKSVFE   81 (150)
T ss_dssp             SSEEHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTSEEEEECGGGCEEEE
T ss_pred             CCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHHHCCcEEEEEeCCCceEEE
Confidence            357888888888     688888899999999999999987555555664

>3cuq_A Vacuolar-sorting protein SNF8; ESCRT, MBV, VPS, nucleus, protein transport, transc transcription regulation, transport, endosome; 2.61A {Homo sapiens} PDB: 2zme_A

Probab=86.66  E-value=0.52  Score=38.24  Aligned_cols=46  Identities=28%  Similarity=0.325  Sum_probs=37.4

Q ss_pred             CCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEE
Q psy1871          83 AYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIY  128 (139)
Q Consensus        83 k~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IY  128 (139)
                      ..-+||++.|++.+++....|+.+|.+|+.+|++=.=........|
T Consensus       165 ~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~GllwvD~q~~ge~~Y  210 (234)
T 3cuq_A          165 KNGYVTVSEIKASLKWETERARQVLEHLLKEGLAWLDLQAPGEAHY  210 (234)
T ss_dssp             TTSEECHHHHHHHHTCCHHHHHHHHHHHHHHTSCEEESSSSSSCEE
T ss_pred             hcCcCcHHHHHHHhCCCHHHHHHHHHHHHhCCCEEEeCCCCCccee
Confidence            4578999999999999999999999999999997543333333445

>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=86.44  E-value=1.3  Score=31.54  Aligned_cols=33  Identities=18%  Similarity=0.195  Sum_probs=30.8

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQ  118 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~  118 (139)
                      -+|...||+.++++-+-.-++|++|+++|+|..
T Consensus       167 ~~t~~~iA~~lg~sr~tvsR~l~~L~~~g~I~~  199 (210)
T 3ryp_A          167 KITRQEIGQIVGCSRETVGRILKMLEDQNLISA  199 (210)
T ss_dssp             ECCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             ccCHHHHHHHhCCcHHHHHHHHHHHHHCCcEEe
Confidence            468999999999999999999999999999974

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

Probab=86.39  E-value=0.97  Score=32.18  Aligned_cols=45  Identities=13%  Similarity=0.202  Sum_probs=36.9

Q ss_pred             eeechHHHHhhh-----ccchHHHHHHHHHHHHcCCeeEEeecCceEEEe
Q psy1871          85 KLITPSVVSERL-----KVRGSLARKALEELLQKGLIKQVVKHHAQVIYT  129 (139)
Q Consensus        85 KlITPsvlseRl-----kI~~SLARkaLreL~~kGlIk~Vskh~~q~IYt  129 (139)
                      .-+|+..|.+++     +|..+-.-+.|+.|++.|+|..+.-......|-
T Consensus        33 ~~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~~~~~~~~~Y~   82 (136)
T 1mzb_A           33 RHMSAEDVYKALMEAGEDVGLATVYRVLTQFEAAGLVVRHNFDGGHAVFE   82 (136)
T ss_dssp             CSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTSEEEECSSSSSCEEE
T ss_pred             CCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCcEEEEEeCCCceEEE
Confidence            357888998888     788888999999999999999987544445564

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

Probab=86.31  E-value=1  Score=30.24  Aligned_cols=43  Identities=16%  Similarity=0.277  Sum_probs=35.8

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT  131 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra  131 (139)
                      .|.+.|+++++++-|...+-|+.|++. +|..- +.++...|.-+
T Consensus        42 ~~~~ela~~l~is~stvs~hL~~L~~~-lv~~~-~~gr~~~y~l~   84 (99)
T 2zkz_A           42 LNVTQIIQILKLPQSTVSQHLCKMRGK-VLKRN-RQGLEIYYSIN   84 (99)
T ss_dssp             EEHHHHHHHHTCCHHHHHHHHHHHBTT-TBEEE-EETTEEEEECC
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHHHHHH-hhhhe-EeCcEEEEEEC
Confidence            799999999999999999999999999 87654 44556667643

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

Probab=86.15  E-value=1.2  Score=31.87  Aligned_cols=32  Identities=19%  Similarity=0.261  Sum_probs=30.3

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQ  118 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~  118 (139)
                      +|...||+.++++-.-.-++|++|+++|+|..
T Consensus       147 ~t~~~lA~~lg~sr~tvsR~l~~L~~~g~I~~  178 (202)
T 2zcw_A          147 ATHDELAAAVGSVRETVTKVIGELAREGYIRS  178 (202)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEe
Confidence            79999999999999999999999999999974

>2qlz_A Transcription factor PF0095; 2.50A {Pyrococcus furiosus} PDB: 2quf_A

Probab=85.87  E-value=0.58  Score=37.17  Aligned_cols=44  Identities=18%  Similarity=0.266  Sum_probs=36.6

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCc-----eEEEec
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHA-----QVIYTR  130 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~-----q~IYtr  130 (139)
                      +|.+.|++.++|+-+.....|+.|++.|+|.......+     ...|.-
T Consensus        26 ~s~~ELa~~lglS~stVs~hL~~Le~aGLV~~~~~~gr~~GRp~~~Y~L   74 (232)
T 2qlz_A           26 CYFSLLSSKVSVSSTAVAKHLKIMEREGVLQSYEKEERFIGPTKKYYKI   74 (232)
T ss_dssp             TCSSSSCTTCCCCHHHHHHHHHHHHHTTSEEEEEECC-----CEEEEEE
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeeecCCCCCCccEEEEE
Confidence            68899999999999999999999999999998544444     555653

>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=85.80  E-value=0.93  Score=35.91  Aligned_cols=35  Identities=14%  Similarity=0.203  Sum_probs=33.0

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      -+|++.||+++++.-|-.=++|..|+++|+|....
T Consensus       174 ~~t~~eLa~~l~i~~~tvt~~v~rLe~~GlV~R~~  208 (250)
T 1p4x_A          174 IVLLKDLIETIHHKYPQTVRALNNLKKQGYLIKER  208 (250)
T ss_dssp             CEEHHHHHHHSSSCHHHHHHHHHHHHHHTSSEEEE
T ss_pred             CcCHHHHHHHHCCChhhHHHHHHHHHHCCCEEeeC
Confidence            48999999999999999999999999999999874

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

Probab=85.61  E-value=1.4  Score=31.61  Aligned_cols=33  Identities=21%  Similarity=0.313  Sum_probs=30.7

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQ  118 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~  118 (139)
                      -+|...||+.++++-+-.-++|++|+++|+|..
T Consensus       169 ~~t~~~lA~~lg~sr~tvsR~l~~L~~~g~I~~  201 (220)
T 3dv8_A          169 KITHETIANHLGSHREVITRMLRYFQVEGLVKL  201 (220)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             cCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEe
Confidence            468999999999999999999999999999964

>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=85.57  E-value=1.7  Score=33.04  Aligned_cols=38  Identities=21%  Similarity=0.322  Sum_probs=33.6

Q ss_pred             CCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          83 AYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        83 k~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      ...-+|.+.+|++|+|+-|-.-+.|+.||+.|+|....
T Consensus        24 ~~~~~s~s~aA~~L~isq~avSr~I~~LE~~~L~~R~~   61 (230)
T 3cta_A           24 NRAYLTSSKLADMLGISQQSASRIIIDLEKNGYITRTV   61 (230)
T ss_dssp             SEEECCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             cCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEE
Confidence            34557899999999999999999999999999987753

>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=85.45  E-value=1.3  Score=31.10  Aligned_cols=39  Identities=23%  Similarity=0.278  Sum_probs=34.3

Q ss_pred             CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEee
Q psy1871          82 PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK  121 (139)
Q Consensus        82 pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk  121 (139)
                      |.-. ++++.|++++.+.-|--.+.|..|+..|+|.....
T Consensus        33 ~g~~-~s~~eLa~~l~l~~stLsR~l~rLe~~GLV~r~~~   71 (96)
T 2obp_A           33 GATP-WSLPKIAKRAQLPMSVLRRVLTQLQAAGLADVSVE   71 (96)
T ss_dssp             TCCC-CBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             CCCC-cCHHHHHHHhCCchhhHHHHHHHHHHCCCEEeecC
Confidence            4444 49999999999999999999999999999997543

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

Probab=85.23  E-value=1.5  Score=31.35  Aligned_cols=34  Identities=12%  Similarity=0.171  Sum_probs=31.3

Q ss_pred             eeechHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871          85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQ  118 (139)
Q Consensus        85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~  118 (139)
                      --+|...||+.++++-+-.-++|++|.++|+|..
T Consensus       162 ~~~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~~  195 (216)
T 4ev0_A          162 FQIRHHELAALAGTSRETVSRVLHALAEEGVVRL  195 (216)
T ss_dssp             EECCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEe
Confidence            4479999999999999999999999999999974

>3dkw_A DNR protein; CRP-FNR, HTH, beta barrel, dimerization helix, homodimer, transcription regulator; 3.60A {Pseudomonas aeruginosa}

Probab=84.87  E-value=1.2  Score=32.17  Aligned_cols=32  Identities=16%  Similarity=0.340  Sum_probs=30.2

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQ  118 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~  118 (139)
                      +|-..||+.++++-+-.-++|++|+++|+|..
T Consensus       179 ~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~~  210 (227)
T 3dkw_A          179 VAKQLVAGHLSIQPETFSRIMHRLGDEGIIHL  210 (227)
T ss_dssp             SCTHHHHHHTTSCHHHHHHHHHHHHHHTSEEE
T ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHHHCCcEEe
Confidence            68899999999999999999999999999965

>2o0y_A Transcriptional regulator; ICLR-family, structural genomics, protein structure initiative, midwest center for structural genomics, MCSG; 2.00A {Rhodococcus SP}

Probab=84.39  E-value=1  Score=35.16  Aligned_cols=35  Identities=6%  Similarity=0.067  Sum_probs=32.3

Q ss_pred             eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      .-+|.+.||+++++.-|-+.++|+.|++.|+|...
T Consensus        37 ~~~~~~eia~~~gl~kstv~r~l~tL~~~G~v~~~   71 (260)
T 2o0y_A           37 PTRSLKELVEGTKLPKTTVVRLVATMCARSVLTSR   71 (260)
T ss_dssp             SSBCHHHHHHHHCCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEC
Confidence            35799999999999999999999999999998764

>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=84.20  E-value=1.7  Score=31.46  Aligned_cols=32  Identities=19%  Similarity=0.356  Sum_probs=30.3

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQ  118 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~  118 (139)
                      +|...||+.++++-.-.-++|++|.++|+|..
T Consensus       178 ~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~~  209 (227)
T 3d0s_A          178 LTQEEIAQLVGASRETVNKALADFAHRGWIRL  209 (227)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEe
Confidence            79999999999999999999999999999965

>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=84.07  E-value=1.2  Score=31.61  Aligned_cols=33  Identities=18%  Similarity=0.308  Sum_probs=30.6

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQ  118 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~  118 (139)
                      -+|...||+-++++-.-.-++|++|+++|+|..
T Consensus       164 ~~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~~  196 (207)
T 2oz6_A          164 KITRQEIGRIVGCSREMVGRVLKSLEEQGLVHV  196 (207)
T ss_dssp             ECCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             ccCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEe
Confidence            479999999999999999999999999999864

>3hh0_A Transcriptional regulator, MERR family; protein structure initiative II(PSI II), NYSGXRC, 11183J, structural genomics; 2.67A {Bacillus cereus atcc 14579}

Probab=83.77  E-value=0.73  Score=33.90  Aligned_cols=42  Identities=19%  Similarity=0.056  Sum_probs=34.8

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEee-cCceEEEecc
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK-HHAQVIYTRT  131 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk-h~~q~IYtra  131 (139)
                      .+|+..||+.++|+.+    .||.-++.|+|.++.+ .++...|+..
T Consensus         4 ~~tI~evA~~~Gvs~~----tLR~ye~~GLl~p~~r~~~g~R~Y~~~   46 (146)
T 3hh0_A            4 AWLISEFASVGDVTVR----ALRYYDKINLLKPSDYTEGGHRLYTKD   46 (146)
T ss_dssp             CBCHHHHHHHHTCCHH----HHHHHHHTTSSCCSEECTTSCEEBCHH
T ss_pred             CCcHHHHHHHHCcCHH----HHHHHHHCCCCCCCeECCCCCEeeCHH
Confidence            6899999999999875    5899999999999743 4677888853

>3gpv_A Transcriptional regulator, MERR family; protein structure initiative II(PSI II), NYSGXRC, structural genomics; 1.90A {Bacillus thuringiensis serovarkonkukian}

Probab=83.76  E-value=0.7  Score=33.92  Aligned_cols=46  Identities=13%  Similarity=0.153  Sum_probs=34.2

Q ss_pred             CCCe--eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEee-cCceEEEecc
Q psy1871          82 PAYK--LITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK-HHAQVIYTRT  131 (139)
Q Consensus        82 pk~K--lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk-h~~q~IYtra  131 (139)
                      +.|+  .+|...||+.++|+.+    .||.-++.|+|.++.+ .+..+.|+..
T Consensus        10 k~M~~~~~~I~evA~~~gvs~~----tLR~Ye~~Gll~p~~r~~~g~R~Y~~~   58 (148)
T 3gpv_A           10 KRMNDMYYTIGQVAKMQHLTIS----QIRYYDKQGLFPFLQRNEKGDRIFNEE   58 (148)
T ss_dssp             -----CCBCHHHHHHHTTCCHH----HHHHHHHTTCCTTCEECTTCCEEBCHH
T ss_pred             CccccCceeHHHHHHHHCcCHH----HHHHHHHCCCCCCCcCCCCCCeecCHH
Confidence            3454  7899999999999865    5889999999986544 4677888753

>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=83.75  E-value=0.61  Score=38.78  Aligned_cols=40  Identities=20%  Similarity=0.175  Sum_probs=34.9

Q ss_pred             CCCCeeechHHHHhhh--ccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          81 VPAYKLITPSVVSERL--KVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        81 Vpk~KlITPsvlseRl--kI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      +-...-|+..+||++|  +|+-...|+-|.+||+.|+|..+.
T Consensus        31 l~~~~pV~s~~La~~~~l~VS~aTIRrDL~~LE~~GlL~r~H   72 (338)
T 1stz_A           31 IENKKPVSSQRVLEVSNIEFSSATIRNDMKKLEYLGYIYQPH   72 (338)
T ss_dssp             HHHCSCBCHHHHHHHSCCCSCHHHHHHHHHHHHHTTSEECCS
T ss_pred             HHcCCCccHHHHHHHhCCCCCHHHHHHHHHHHHHCCCEEEcc
Confidence            4555779999999999  888889999999999999998743

>2g7u_A Transcriptional regulator; ICLR family, structural genomics, PSI, protein structure initiative, midwest center for struc genomics; 2.30A {Rhodococcus SP}

Probab=83.68  E-value=1.1  Score=34.77  Aligned_cols=44  Identities=16%  Similarity=0.110  Sum_probs=36.4

Q ss_pred             HHHhhCCCC-eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          76 KLLKEVPAY-KLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        76 Kl~KEVpk~-KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      +|+..+-.. .-+|.+.||+++++.-|-+.++|+.|++.|+|...
T Consensus        18 ~iL~~l~~~~~~~~~~eia~~~gl~~stv~r~l~~L~~~G~v~~~   62 (257)
T 2g7u_A           18 AVLLAFDAQRPNPTLAELATEAGLSRPAVRRILLTLQKLGYVAGS   62 (257)
T ss_dssp             HHHHTCSSSCSSCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeC
Confidence            344455432 45799999999999999999999999999999764

>3f8b_A Transcriptional regulator, PADR-like family; winged helix turn helix, transcription regulator; 2.00A {Lactococcus lactis subsp} SCOP: a.4.5.0 PDB: 3f8c_A* 3f8f_A*

Probab=83.65  E-value=2.5  Score=29.48  Aligned_cols=42  Identities=10%  Similarity=0.138  Sum_probs=32.1

Q ss_pred             chHHHHhhh--------ccchHHHHHHHHHHHHcCCeeEEe----ecCceEEEe
Q psy1871          88 TPSVVSERL--------KVRGSLARKALEELLQKGLIKQVV----KHHAQVIYT  129 (139)
Q Consensus        88 TPsvlseRl--------kI~~SLARkaLreL~~kGlIk~Vs----kh~~q~IYt  129 (139)
                      +.|.|.+++        .|+-+.-..+|+.|+++|+|....    ..++..+|.
T Consensus        27 ~Gyei~~~l~~~~~~~~~i~~gtly~~L~rLe~~GlI~~~~~~~~~~~~rk~Y~   80 (116)
T 3f8b_A           27 YVYGIIKQVKEASNGEMELNEATLYTIFKRLEKDGIISSYWGDESQGGRRKYYR   80 (116)
T ss_dssp             CHHHHHHHHHHHTTTCCCCCHHHHHHHHHHHHHTTSEEEEEEC----CCEEEEE
T ss_pred             CHHHHHHHHHHHhCCCCCCCcchHHHHHHHHHHCCCEEEEeeccCCCCCceEEE
Confidence            567777666        799999999999999999999864    234555664

>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=83.39  E-value=2.7  Score=30.67  Aligned_cols=43  Identities=16%  Similarity=0.212  Sum_probs=33.8

Q ss_pred             echHHHHhhh--------ccchHHHHHHHHHHHHcCCeeEEee----cCceEEEe
Q psy1871          87 ITPSVVSERL--------KVRGSLARKALEELLQKGLIKQVVK----HHAQVIYT  129 (139)
Q Consensus        87 ITPsvlseRl--------kI~~SLARkaLreL~~kGlIk~Vsk----h~~q~IYt  129 (139)
                      .+.+.|++++        .|+-+.--.+|+.|+++|+|.....    .++..+|.
T Consensus        55 ~~gyeI~~~l~~~~~~~~~is~gtLy~~L~rLE~~GlI~~~~~~~~~~~~rk~Y~  109 (145)
T 1xma_A           55 SYGYEISKNIRIKTDELYVIKETTLYSAFARLEKNGYIKSYYGEETQGKRRTYYR  109 (145)
T ss_dssp             EEHHHHHHHHHHHHTTSCCCCHHHHHHHHHHHHHTTSEEEEEEEEC--CEEEEEE
T ss_pred             CCHHHHHHHHHHhhCCccCcChhHHHHHHHHHHHCCCEEEEEeccCCCCCeEEEE
Confidence            5888888887        5999999999999999999988642    34555664

>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=83.39  E-value=0.22  Score=40.65  Aligned_cols=43  Identities=21%  Similarity=0.280  Sum_probs=0.0

Q ss_pred             HHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871          76 KLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQ  118 (139)
Q Consensus        76 Kl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~  118 (139)
                      .|+..+-...-+|...||++|+|+-+..|+.|+.|+++|+|..
T Consensus        24 ~iL~~l~~~~~~t~~eLa~~l~vs~~Tv~r~l~~Le~~Glv~~   66 (345)
T 2o0m_A           24 QILRNIYWMQPIGRRSLSETMGITERVLRTETDVLKQLNLIEP   66 (345)
T ss_dssp             -------------------------------------------
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            4555555556799999999999999999999999999999973

>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=83.04  E-value=1.4  Score=31.84  Aligned_cols=32  Identities=16%  Similarity=0.342  Sum_probs=30.4

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQ  118 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~  118 (139)
                      +|-..||+.++++-+-.-++|++|+++|+|..
T Consensus       188 lt~~~lA~~lg~sr~tvsR~l~~L~~~g~I~~  219 (230)
T 3iwz_A          188 VSRQELARLVGCSREMAGRVLKKLQADGLLHA  219 (230)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEE
Confidence            68999999999999999999999999999975

>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=82.99  E-value=1.4  Score=32.10  Aligned_cols=33  Identities=9%  Similarity=0.138  Sum_probs=30.8

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQ  118 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~  118 (139)
                      -+|...||+.++++-...-++|++|.++|+|..
T Consensus       180 ~~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~~  212 (232)
T 2gau_A          180 YLSREELATLSNMTVSNAIRTLSTFVSERMLAL  212 (232)
T ss_dssp             CCCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             ccCHHHHHHHhCCCHHHHHHHHHHHHHCCCEee
Confidence            479999999999999999999999999999864

>3mwm_A ZUR, putative metal uptake regulation protein; FUR, regulatory metal, graded transcription regulation, transcription; 2.40A {Streptomyces coelicolor}

Probab=82.97  E-value=2.4  Score=30.44  Aligned_cols=47  Identities=15%  Similarity=0.268  Sum_probs=37.8

Q ss_pred             eeechHHHHhhh-----ccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871          85 KLITPSVVSERL-----KVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT  131 (139)
Q Consensus        85 KlITPsvlseRl-----kI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra  131 (139)
                      .-+|...|.+++     +|+.+---+.|+.|++.|+|..+.-.....-|-.+
T Consensus        28 ~h~sa~eI~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~~~~~~g~~~Y~~~   79 (139)
T 3mwm_A           28 EFRSAQELHDMLKHKGDAVGLTTVYRTLQSLADAGEVDVLRTAEGESVYRRC   79 (139)
T ss_dssp             SCEEHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTSSEEEECTTSCEEEECC
T ss_pred             CCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHHHCCCEEEEEcCCCceEEEEC
Confidence            367888888888     58888889999999999999998765555667543

>2ia2_A Putative transcriptional regulator; SAD, PSI-2, structural genomics, structure initiative, midwest center for structural genomic transcription; 2.10A {Rhodococcus SP}

Probab=82.65  E-value=1.2  Score=34.86  Aligned_cols=43  Identities=19%  Similarity=0.174  Sum_probs=35.5

Q ss_pred             HHhhCCC-CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          77 LLKEVPA-YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        77 l~KEVpk-~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      |+.-+-. -.-+|.+.||+++++.-|-+.++|+.|++.|+|...
T Consensus        26 iL~~l~~~~~~~~~~eia~~~gl~~stv~r~l~tL~~~G~v~~~   69 (265)
T 2ia2_A           26 VIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVATD   69 (265)
T ss_dssp             HHHTCCSSCSSEEHHHHHHHHTCCHHHHHHHHHHHHHHTSEEES
T ss_pred             HHHHHHhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEec
Confidence            3444432 245899999999999999999999999999999763

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

Probab=82.51  E-value=1.3  Score=32.96  Aligned_cols=45  Identities=13%  Similarity=0.206  Sum_probs=36.5

Q ss_pred             HHHHHhhCCC-CeeechHHHHhhhccchHHHHHHHHHHHHcCC-eeE
Q psy1871          74 YDKLLKEVPA-YKLITPSVVSERLKVRGSLARKALEELLQKGL-IKQ  118 (139)
Q Consensus        74 ydKl~KEVpk-~KlITPsvlseRlkI~~SLARkaLreL~~kGl-Ik~  118 (139)
                      ..+|+..+.. -..+|...||++|+|+-+..++=|+.|++.|+ |.-
T Consensus        23 ~~~Il~~L~~~~~~~s~~eLa~~l~vS~~Ti~rdi~~L~~~G~~I~~   69 (187)
T 1j5y_A           23 LKSIVRILERSKEPVSGAQLAEELSVSRQVIVQDIAYLRSLGYNIVA   69 (187)
T ss_dssp             HHHHHHHHHHCSSCBCHHHHHHHHTSCHHHHHHHHHHHHHHTCCCEE
T ss_pred             HHHHHHHHHHcCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEE
Confidence            4445555542 35699999999999999999999999999999 753

>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=82.26  E-value=2.5  Score=33.35  Aligned_cols=50  Identities=16%  Similarity=0.197  Sum_probs=41.3

Q ss_pred             eeeCHHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871          67 VLFDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQ  118 (139)
Q Consensus        67 Vl~Dk~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~  118 (139)
                      ..+..+-|=++.-+. + .-|+...||++|+++-+-.+.+|+.|.++|+|..
T Consensus        13 ls~s~EdYLk~I~~L-~-~~V~~~~LA~~LgvS~~SV~~~lkkL~e~GLV~~   62 (200)
T 2p8t_A           13 PEYTVEDVLAVIFLL-K-EPLGRKQISERLELGEGSVRTLLRKLSHLDIIRS   62 (200)
T ss_dssp             -CCCHHHHHHHHHHT-T-SCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCCHHHHHHHHHHH-c-CCccHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE
Confidence            455667777766666 2 4599999999999999999999999999999854

>1u5t_A Appears to BE functionally related to SNF7; SNF8P; ESCRT, endosomal, trafficking, protein complex, transport protein; 3.60A {Saccharomyces cerevisiae} SCOP: a.4.5.54 a.4.5.54 PDB: 1w7p_A

Probab=82.04  E-value=1.5  Score=35.49  Aligned_cols=46  Identities=20%  Similarity=0.282  Sum_probs=36.7

Q ss_pred             CCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEE
Q psy1871          83 AYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIY  128 (139)
Q Consensus        83 k~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IY  128 (139)
                      ..-+||++.|++.|++....|+.+|.+|+..|++=.=........|
T Consensus       178 ~~g~vt~~~L~~~lgW~~~Ra~~~L~~l~~~G~lwvD~q~~~e~~Y  223 (233)
T 1u5t_A          178 ILGYSSISLLKANLGWEAVRSKSALDEMVANGLLWIDYQGGAEALY  223 (233)
T ss_dssp             TTSCCBHHHHHHHHCCCSHHHHHHHHHHHHTTSSEEECSSSSSCEE
T ss_pred             hcCcCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEeCCCCCccce
Confidence            4578999999999999999999999999999997543333223444

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

Probab=82.02  E-value=0.97  Score=31.71  Aligned_cols=59  Identities=14%  Similarity=0.134  Sum_probs=51.6

Q ss_pred             hhccceeeCHHHHHHHHhhCCC----CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          62 KLNNQVLFDKASYDKLLKEVPA----YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        62 Klnn~Vl~Dk~tydKl~KEVpk----~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      ++.+-++|..++++++...+-.    ..-||++.+-|.++++-..|-.+|+.|-+.|+.+.+.
T Consensus        52 ~i~~~~~~~~~~~~~~~~~l~~~~~~~~~it~ae~Rd~lg~sRK~ai~lLE~~Dr~g~TrR~g  114 (121)
T 2pjp_A           52 AIVKDRYYRNDRIVEFANMIRDLDQECGSTCAADFRDRLGVGRKLAIQILEYFDRIGFTRRRG  114 (121)
T ss_dssp             EEETTEEEEHHHHHHHHHHHHHHHHHHSSEEHHHHHHHHTSCHHHHHHHHHHHHHHTSEEEET
T ss_pred             EecCCceECHHHHHHHHHHHHHHHHHCCCccHHHHHHHHCCcHHHHHHHHHHHhhcCCeEeeC
Confidence            3567789999999998887766    3779999999999999999999999999999998874

>3mq0_A Transcriptional repressor of the blcabc operon; helix-turn-helix, GAF fold, transcription repressor; 1.79A {Agrobacterium tumefaciens}

Probab=81.85  E-value=1  Score=35.71  Aligned_cols=34  Identities=18%  Similarity=0.165  Sum_probs=29.9

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      -+|.+.||+++++.-|-+-++|+.|++.|+|...
T Consensus        45 ~ltl~eia~~lgl~ksTv~RlL~tL~~~G~v~~~   78 (275)
T 3mq0_A           45 DLTAAELTRFLDLPKSSAHGLLAVMTELDLLARS   78 (275)
T ss_dssp             CEEHHHHHHHHTCC--CHHHHHHHHHHTTSEEEC
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEC
Confidence            4899999999999999999999999999998764

>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=81.80  E-value=2.1  Score=34.79  Aligned_cols=35  Identities=14%  Similarity=0.246  Sum_probs=32.9

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      -+|-+.||++++++-+-..+++++|++.|+|..+.
T Consensus        33 ~~sr~~la~~~gls~~tv~~~v~~L~~~gli~~~~   67 (380)
T 2hoe_A           33 PVSRVELAEELGLTKTTVGEIAKIFLEKGIVVEEK   67 (380)
T ss_dssp             CBCHHHHHHHHTCCHHHHHHHHHHHHHHTSEEEEE
T ss_pred             CcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeec
Confidence            47999999999999999999999999999999874

>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=81.27  E-value=1.7  Score=32.34  Aligned_cols=32  Identities=16%  Similarity=0.270  Sum_probs=30.3

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQ  118 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~  118 (139)
                      +|-..||+.++++-.-.-++|++|+++|+|..
T Consensus       194 lt~~~lA~~lG~sr~tvsR~l~~L~~~GlI~~  225 (243)
T 3la7_A          194 LSHQAIAEAIGSTRVTVTRLLGDLREKKMISI  225 (243)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHHCCcHHHHHHHHHHHHHCCCEEE
Confidence            68899999999999999999999999999974

>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=81.17  E-value=2.4  Score=31.99  Aligned_cols=33  Identities=18%  Similarity=0.195  Sum_probs=30.6

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQ  118 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~  118 (139)
                      -+|-..||+.++++-.-.-++|++|+++|+|..
T Consensus       217 ~lt~~~lA~~lG~sr~tvsR~l~~L~~~GlI~~  249 (260)
T 3kcc_A          217 KITRQEIGQIVGCSRETVGRILKMLEDQNLISA  249 (260)
T ss_dssp             ECCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             cCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE
Confidence            368899999999999999999999999999974

>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=81.16  E-value=2.7  Score=30.34  Aligned_cols=44  Identities=23%  Similarity=0.261  Sum_probs=35.0

Q ss_pred             eechHHHHhhh-----ccchHHHHHHHHHHHHcCCeeEEeecCceEEEe
Q psy1871          86 LITPSVVSERL-----KVRGSLARKALEELLQKGLIKQVVKHHAQVIYT  129 (139)
Q Consensus        86 lITPsvlseRl-----kI~~SLARkaLreL~~kGlIk~Vskh~~q~IYt  129 (139)
                      -+|...|-+++     +|+.+---+.|+.|++.|+|..+.-..+..-|-
T Consensus        33 h~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Glv~~i~~~~~~~~Y~   81 (145)
T 3eyy_A           33 HATPDDILGEVRKTASGINISTVYRTLELLEELGLVSHAHLGHGAPTYH   81 (145)
T ss_dssp             SBCHHHHHHHHHTTCTTCCHHHHHHHHHHHHHHTSEEEEECGGGCEEEE
T ss_pred             CCCHHHHHHHHHhhCCCCCHhHHHHHHHHHHHCCcEEEEEeCCCceEEE
Confidence            36777777777     577788889999999999999997655555665

>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=80.97  E-value=1.8  Score=31.43  Aligned_cols=33  Identities=9%  Similarity=0.147  Sum_probs=30.7

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQ  118 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~  118 (139)
                      -+|-..||+.++++-.-.-++|++|.++|+|..
T Consensus       175 ~~t~~~iA~~lg~sr~tvsR~l~~L~~~g~I~~  207 (231)
T 3e97_A          175 PLGTQDIMARTSSSRETVSRVLKRLEAHNILEV  207 (231)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCCHHHHHHHhCCcHHHHHHHHHHHHHCCcEEe
Confidence            369999999999999999999999999999974

>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=80.94  E-value=1.8  Score=31.33  Aligned_cols=33  Identities=9%  Similarity=0.175  Sum_probs=30.4

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQ  118 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~  118 (139)
                      -+|...||+.++++-.-.-++|++|+++|+|..
T Consensus       167 ~~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~~  199 (220)
T 2fmy_A          167 GLNTEEIALMLGTTRQTVSVLLNDFKKMGILER  199 (220)
T ss_dssp             SSCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             cCCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEE
Confidence            368899999999999999999999999999864

>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=80.92  E-value=1.6  Score=31.69  Aligned_cols=32  Identities=19%  Similarity=0.324  Sum_probs=30.2

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQ  118 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~  118 (139)
                      +|...||+.++++-.-.-++|++|+++|+|..
T Consensus       164 ~t~~~lA~~lG~sr~tvsR~l~~L~~~g~I~~  195 (222)
T 1ft9_A          164 FTVEEIANLIGSSRQTTSTALNSLIKEGYISR  195 (222)
T ss_dssp             CCHHHHHHHHCSCHHHHHHHHHHHHHTTSSEE
T ss_pred             CCHHHHHHHhCCcHHHHHHHHHHHHHCCcEEE
Confidence            79999999999999999999999999999865

>4esf_A PADR-like transcriptional regulator; PADR family, DNA binding protein, HTH fold; 2.20A {Bacillus cereus}

Probab=80.66  E-value=3.9  Score=28.73  Aligned_cols=43  Identities=19%  Similarity=0.165  Sum_probs=33.6

Q ss_pred             echHHHHhhh------ccchHHHHHHHHHHHHcCCeeEEee----cCceEEEe
Q psy1871          87 ITPSVVSERL------KVRGSLARKALEELLQKGLIKQVVK----HHAQVIYT  129 (139)
Q Consensus        87 ITPsvlseRl------kI~~SLARkaLreL~~kGlIk~Vsk----h~~q~IYt  129 (139)
                      .+.|.|.+++      .|+-+.--.+|+.|+++|+|.....    .++..+|.
T Consensus        25 ~~Gyei~~~l~~~g~~~is~gtlY~~L~rLe~~GlI~~~~~~~~~g~~rk~Y~   77 (117)
T 4esf_A           25 TYGYEITRHLNDLGFTEVVEGTVYTILVRLEKKKLVNIEKKPSDMGPPRKFYS   77 (117)
T ss_dssp             BCHHHHHHHHHHHTCTTCCHHHHHHHHHHHHHTTCEEEEEEC-----CEEEEE
T ss_pred             CCHHHHHHHHHHcCCCCCCccHHHHHHHHHHHCCCEEEEeecCCCCCCceEEE
Confidence            4678888887      7999999999999999999998742    23455664

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

Probab=80.43  E-value=1.6  Score=31.10  Aligned_cols=33  Identities=18%  Similarity=0.278  Sum_probs=30.6

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQ  118 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~  118 (139)
                      -+|...||+.++++-.-.-++|++|+++|+|..
T Consensus       139 ~~t~~~lA~~lg~sr~tvsR~l~~L~~~g~I~~  171 (195)
T 3b02_A          139 TVSHEEIADATASIRESVSKVLADLRREGLIAT  171 (195)
T ss_dssp             ECCHHHHHHTTTSCHHHHHHHHHHHHHHTSEEE
T ss_pred             cCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEe
Confidence            379999999999999999999999999999864

>3i71_A Ethanolamine utilization protein EUTK; helix-turn-helix, unknown function; HET: FLC; 2.10A {Escherichia coli}

Probab=80.36  E-value=3.8  Score=27.64  Aligned_cols=33  Identities=27%  Similarity=0.362  Sum_probs=30.5

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      .|.-+|+.+|+.....||.+|..|.+.|-+..-
T Consensus        19 MTaGEVAA~f~w~Le~ar~aLeqLf~~G~LRKR   51 (68)
T 3i71_A           19 MTAGEVAAHFGWPLEKARNALEQLFSAGTLRKR   51 (68)
T ss_dssp             BCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             ccHHHHHHHhCCcHHHHHHHHHHHHhcchhhhh
Confidence            588999999999999999999999999998753

>2esh_A Conserved hypothetical protein TM0937; APC5794, structural genomics, PSI, protein structure initiative; 2.30A {Thermotoga maritima} SCOP: a.4.5.61

Probab=80.05  E-value=2.2  Score=29.55  Aligned_cols=43  Identities=19%  Similarity=0.259  Sum_probs=33.2

Q ss_pred             echHHHHhhhc--------cch-HHHHHHHHHHHHcCCeeEEee---cCceEEEe
Q psy1871          87 ITPSVVSERLK--------VRG-SLARKALEELLQKGLIKQVVK---HHAQVIYT  129 (139)
Q Consensus        87 ITPsvlseRlk--------I~~-SLARkaLreL~~kGlIk~Vsk---h~~q~IYt  129 (139)
                      .+.+.|++.+.        |+- +.--.+|+.|++.|+|.....   .++..+|.
T Consensus        27 ~~gyel~~~l~~~g~~~~~is~~~tly~~L~~Le~~GlI~~~~~~~~~~~r~~Y~   81 (118)
T 2esh_A           27 SHGYELAERLAEFGIEIPGIGHMGNIYRVLADLEESGFLSTEWDTTVSPPRKIYR   81 (118)
T ss_dssp             BCHHHHHHHHHTTCCSSTTCCCCCCHHHHHHHHHHTTSEEEEEECSSSSCEEEEE
T ss_pred             CCHHHHHHHHHHhCCcccCCCCcchHHHHHHHHHHCCCeEEEeecCCCCCceEEE
Confidence            47888888884        777 778899999999999988653   34555664

>4a0z_A Transcription factor FAPR; lipid homeostasis; HET: MLC; 1.90A {Staphylococcus aureus} PDB: 4a0y_A 4a0x_A* 4a12_A

Probab=80.02  E-value=0.51  Score=36.32  Aligned_cols=48  Identities=17%  Similarity=0.142  Sum_probs=42.0

Q ss_pred             HHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          72 ASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        72 ~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      +=.+.|+..+.....+|...||++|+|+.+..|+=|.||...|++..+
T Consensus        12 eR~~~i~~~l~~~~~~~~~~la~~~~vs~~TiRrDl~eL~~~~l~~r~   59 (190)
T 4a0z_A           12 KRREAIRQQIDSNPFITDHELSDLFQVSIQTIRLDRTYLNIPELRKRI   59 (190)
T ss_dssp             HHHHHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHHHHTCCCHHHHH
T ss_pred             HHHHHHHHHHHHCCCEeHHHHHHHHCCCHHHHHHHHHHhcCcchhhHh
Confidence            345677888888899999999999999999999999999999987654

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	139
d2hs5a1	69	Putative transcriptional regulator RHA1_ro03477 {R	96.9
d1hw1a1	74	Fatty acid responsive transcription factor FadR, N	96.76
d3bwga1	78	Transcriptional regulator YydK {Bacillus subtilis	96.61
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	96.17
d3ctaa1	85	Ta1064 (RFK), N-terminal domain {Thermoplasma acid	96.1
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	95.81
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	95.76
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	95.68
d2b0la1	91	GTP-sensing transcriptional pleiotropic repressor	95.61
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	95.45
d3broa1	135	Transcriptional regulator OEOE1854 {Oenococcus oen	95.31
d1v4ra1	100	Transcriptional repressor TraR, N-terminal domain	95.04
d1lnwa_	141	MexR repressor {Pseudomonas aeruginosa [TaxId: 287	95.03
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	94.96
d2a61a1	139	Transcriptional regulator TM0710 {Thermotoga marit	94.88
d2etha1	140	Putative transcriptional regulator TM0816 {Thermot	94.86
d1ub9a_	100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	94.77
d2dk5a1	78	DNA-directed RNA polymerase III subunit RPC6, RPO3	94.73
d3deua1	140	Transcriptional regulator SlyA {Salmonella typhimu	94.55
d2fbha1	137	Transcriptional regulator PA3341 {Pseudomonas aeru	94.37
d1wi9a_	72	Hypothetical protein C20orf116 homolog {Mouse (Mus	94.37
d2bv6a1	136	Transcriptional regulator MgrA {Staphylococcus aur	94.23
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	94.21
d2hr3a1	145	Probable transcriptional regulator PA3067 {Pseudom	94.13
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	94.11
d2ev0a1	61	Manganese transport regulator MntR {Bacillus subti	94.0
d1okra_	120	Methicillin resistance regulatory protein MecI {St	93.77
d2fbia1	136	Probable transcriptional regulator PA4135 {Pseudom	93.6
d1hsja1	115	Staphylococcal accessory regulator A homolog, SarR	93.46
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	93.35
d1lj9a_	144	Transcriptional regulator SlyA {Enterococcus faeca	93.29
d1xd7a_	127	Hypothetical protein ywnA {Bacillus subtilis [TaxI	93.28
d1z91a1	137	Organic hydroperoxide resistance transcriptional r	93.28
d1i5za1	69	Catabolite gene activator protein (CAP), C-termina	93.08
d2ve8a1	67	DNA translocase FtsK {Pseudomonas aeruginosa [TaxI	93.07
d2hoea1	62	N-acetylglucosamine kinase {Thermotoga maritima [T	93.04
d1jgsa_	138	Multiple antibiotic resistance repressor, MarR {Es	93.02
d2isya1	63	Iron-dependent regulator IdeR {Mycobacterium tuber	93.0
d1s3ja_	143	Putative transcriptional regulator YusO {Bacillus	93.0
d2frha1	115	Pleiotropic regulator of virulence genes, SarA {St	92.94
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	92.9
d1p6ra_	82	Penicillinase repressor BlaI {Bacillus licheniform	92.67
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	92.62
d1p4xa1	125	Staphylococcal accessory regulator A homolog, SarS	92.51
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	92.39
d1z6ra1	70	Mlc protein N-terminal domain {Escherichia coli [T	92.23
d2j5pa1	69	DNA translocase FtsK {Escherichia coli [TaxId: 562	91.71
d1p4xa2	125	Staphylococcal accessory regulator A homolog, SarS	91.46
d1ylfa1	138	Hypothetical protein BC1842 {Bacillus cereus [TaxI	90.9
d2fswa1	102	Hypothetical protein PG0823 {Porphyromonas gingiva	90.87
d1lvaa3	64	C-terminal fragment of elongation factor SelB {Moo	90.85
d1u5ta2	68	Vacuolar sorting protein SNF8 {Baker's yeast (Sacc	90.61
d1r1ta_	98	SmtB repressor {Cyanobacteria (Synechococcus), pcc	90.56
d1ulya_	190	Hypothetical protein PH1932 {Pyrococcus horikoshii	90.48
d1r8ea1	118	Transcription activator BmrR {Bacillus subtilis [T	89.46
d1stza1	87	Heat-inducible transcription repressor HrcA, N-ter	89.05
d2g9wa1	122	Hypothetical protein Rv1846c {Mycobacterium tuberc	88.94
d1sd4a_	122	Penicillinase repressor BlaI {Staphylococcus aureu	88.69
d1sfua_	70	34L {Yaba-like disease virus, YLDV [TaxId: 132475]	88.38
d2hzta1	95	Putative transcriptional regulator YtcD {Bacillus	88.21
d1r8da_	109	Multidrug transporter activator MtaN {Bacillus sub	87.17
d2fxaa1	162	Protease production regulatory protein Hpr {Bacill	87.05
d2gaua1	81	Transcriptional regulator PG0396, C-terminal domai	86.8
d2p4wa1	194	Transcriptional regulatory protein PF1790 {Pyrococ	86.53
d1zyba1	73	Probable transcription regulator BT4300, C-termina	86.36
d2fbka1	172	Transcriptional regulator DR1159 {Deinococcus radi	85.71
d1dpua_	69	C-terminal domain of RPA32 {Human (Homo sapiens) [	85.69
d3e5ua1	80	Chlorophenol reduction protein CprK {Desulfitobact	83.48
d1u2wa1	108	Cadmium efflux system accessory protein CadC {Stap	83.35
d1r1ua_	94	Metal-sensing transcriptional repressor CzrA {Stap	83.04
d1tw3a1	85	Carminomycin 4-O-methyltransferase {Streptomyces p	82.28
d1q1ha_	88	Transcription factor E/IIe-alpha, N-terminal domai	81.8
d2zcwa1	82	Transcriptional regulator TTHA1359, C-terminal dom	81.7
d1ft9a1	80	CO-sensing protein CooA, C-terminal domain {Rhodos	81.63
d1ldja1	90	Anaphase promoting complex (APC) {Human (Homo sapi	81.16
d1ufma_	84	COP9 signalosome complex subunit 4, GSN4 {Mouse (M	80.83

>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=96.90  E-value=0.0012  Score=41.89  Aligned_cols=37  Identities=22%  Similarity=0.392  Sum_probs=33.6

Q ss_pred             CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          82 PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        82 pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      |..++ +...||++|+|+-+..|.||+.|+++|+|...
T Consensus        22 ~G~~l-~~~~La~~~~vSr~tvr~Al~~L~~~Gli~~~   58 (69)
T d2hs5a1          22 PGARL-SEPDICAALDVSRNTVREAFQILIEDRLVAHE   58 (69)
T ss_dssp             TTCEE-CHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CcCcc-CHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEE
Confidence            56776 78999999999999999999999999998765

>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=96.76  E-value=0.0028  Score=40.87  Aligned_cols=57  Identities=18%  Similarity=0.230  Sum_probs=43.9

Q ss_pred             HHHHHHHHhhC--CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871          71 KASYDKLLKEV--PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR  130 (139)
Q Consensus        71 k~tydKl~KEV--pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr  130 (139)
                      +.+.++|....  |+.+|=+-..||++|+|+-+.+|+||+.|+++|+|...   ++...|++
T Consensus        10 e~i~~~I~~g~~~~G~~LPs~~eLa~~~~vSr~tvr~Al~~L~~~G~i~~~---~g~G~~V~   68 (74)
T d1hw1a1          10 EYIIESIWNNRFPPGTILPAERELSELIGVTRTTLREVLQRLARDGWLTIQ---HGKPTKVN   68 (74)
T ss_dssp             HHHHHHHHTTSSCTTSBCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE---TTEEEEEC
T ss_pred             HHHHHHHHcCCCCCcCCCccHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEE---eCceEEEC
Confidence            34455555554  55677788999999999999999999999999998654   44455654

>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=96.61  E-value=0.0024  Score=41.01  Aligned_cols=48  Identities=33%  Similarity=0.329  Sum_probs=38.4

Q ss_pred             CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEeccC
Q psy1871          82 PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTT  132 (139)
Q Consensus        82 pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra~  132 (139)
                      |..+|-|-..||++|+|+-+..|+||+.|+++|+|...   ++...|++..
T Consensus        18 ~G~~LPse~~La~~~~vSr~tvr~Al~~L~~~Gli~~~---~g~G~~V~~~   65 (78)
T d3bwga1          18 QGDKLPVLETLMAQFEVSKSTITKSLELLEQKGAIFQV---RGSGIFVRKH   65 (78)
T ss_dssp             TTCBCCCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEE---TTTEEEECCC
T ss_pred             CcCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEE---cCcEEEEccC
Confidence            45677799999999999999999999999999998654   2334555443

>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=96.17  E-value=0.0047  Score=38.64  Aligned_cols=47  Identities=15%  Similarity=0.083  Sum_probs=39.9

Q ss_pred             HHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871          72 ASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQ  118 (139)
Q Consensus        72 ~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~  118 (139)
                      ++--+|+.-...-.++|...||++|+|+-+-.++-|+.|++.|++..
T Consensus         5 ~~~~~iL~~L~~~~~~s~~eLa~~l~vS~~ti~r~i~~L~~~G~~I~   51 (63)
T d1biaa1           5 TVPLKLIALLANGEFHSGEQLGETLGMSRAAINKHIQTLRDWGVDVF   51 (63)
T ss_dssp             HHHHHHHHHHTTSSCBCHHHHHHHHTSCHHHHHHHHHHHHHTTCCCE
T ss_pred             HHHHHHHHHHHHCCcCCHHHHHHHHCcCHHHHHHHHHHHHHCCCcEE
Confidence            44456666666778899999999999999999999999999998643

>d3ctaa1 a.4.5.28 (A:5-89) Ta1064 (RFK), N-terminal domain {Thermoplasma acidophilum [TaxId: 2303]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Ta1064 (RFK), N-terminal domain
species: Thermoplasma acidophilum [TaxId: 2303]

Probab=96.10  E-value=0.011  Score=38.74  Aligned_cols=48  Identities=21%  Similarity=0.292  Sum_probs=39.4

Q ss_pred             hCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEE
Q psy1871          80 EVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIY  128 (139)
Q Consensus        80 EVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IY  128 (139)
                      +..+-.-||++.||+++++.-|-.-++|..|++.|+|..-. ++|...|
T Consensus        15 ~~~~~~~lt~~eLa~~l~i~~~~vs~~l~~Le~~GlV~r~~-D~R~~~i   62 (85)
T d3ctaa1          15 EASNRAYLTSSKLADMLGISQQSASRIIIDLEKNGYITRTV-TKRGQIL   62 (85)
T ss_dssp             TTSSEEECCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEE-ETTEEEE
T ss_pred             hccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeec-ccccccc
Confidence            34455679999999999999999999999999999999854 4444443

>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=95.81  E-value=0.01  Score=39.36  Aligned_cols=34  Identities=21%  Similarity=0.406  Sum_probs=32.1

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      +|++.||++++|+-|-..++|+.|+++|+|...-
T Consensus        37 ~t~~eLa~~~~i~~~tvs~~l~~L~~~GlV~r~~   70 (109)
T d2d1ha1          37 ITSEELADIFKLSKTTVENSLKKLIELGLVVRTK   70 (109)
T ss_dssp             EEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCHHHHHHHHCccHhHHHHHHHHHHHCCCEEEee
Confidence            6999999999999999999999999999998763

>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=95.76  E-value=0.011  Score=39.46  Aligned_cols=47  Identities=21%  Similarity=0.410  Sum_probs=38.9

Q ss_pred             eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe--ecCceEEEecc
Q psy1871          85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV--KHHAQVIYTRT  131 (139)
Q Consensus        85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs--kh~~q~IYtra  131 (139)
                      .-+|++.||+.++|.-|-...+|+.|+++|+|....  .+++..+|...
T Consensus        33 g~~t~~eia~~~~i~~~~v~~~l~~L~~~GlV~r~~~~~~~r~~~~~a~   81 (109)
T d1sfxa_          33 GGMRVSEIARELDLSARFVRDRLKVLLKRGFVRREIVEKGWVGYIYSAE   81 (109)
T ss_dssp             CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEEESSSEEEEEEEC
T ss_pred             CCCCHHHHHHHhCCCcchHHHHHHHHHhCCCEEEEeccCCCccccccCC
Confidence            346999999999999999999999999999998753  34566667643

>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=95.68  E-value=0.01  Score=36.83  Aligned_cols=46  Identities=15%  Similarity=0.273  Sum_probs=38.2

Q ss_pred             CHHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          70 DKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        70 Dk~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      |...+.-|..+ +.   +|...||++++++.+..+.=|+.|++.|+|..+
T Consensus         7 D~~IL~~L~~~-~r---~s~~eiA~~l~ls~~~v~~Ri~rL~~~GiI~~~   52 (63)
T d2cg4a1           7 DRGILEALMGN-AR---TAYAELAKQFGVSPETIHVRVEKMKQAGIITGA   52 (63)
T ss_dssp             HHHHHHHHHHC-TT---SCHHHHHHHHTSCHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHHHc-CC---CCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEeE
Confidence            55666666655 33   488999999999999999999999999999854

>d2b0la1 a.4.5.66 (A:167-257) GTP-sensing transcriptional pleiotropic repressor CodY, C-terminal domain {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CodY HTH domain
domain: GTP-sensing transcriptional pleiotropic repressor CodY, C-terminal domain
species: Bacillus subtilis [TaxId: 1423]

Probab=95.61  E-value=0.0066  Score=41.74  Aligned_cols=62  Identities=18%  Similarity=0.303  Sum_probs=51.3

Q ss_pred             hhhhhccceeeCHHHHHHHHhhCCC-CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          59 VRDKLNNQVLFDKASYDKLLKEVPA-YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        59 vkdKlnn~Vl~Dk~tydKl~KEVpk-~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      ++--++..-+-+-+..+.|..|... .=++..|.||||.+|+-|+-=.+||.||+-|+|.-=|
T Consensus         6 v~~Ai~tLSySEleAv~hIf~eL~g~EGllvASkiADrvgiTRSVIVNALRK~ESAGvIEsrS   68 (91)
T d2b0la1           6 VQMAISSLSYSELEAIEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRS   68 (91)
T ss_dssp             HHHHHHTSCHHHHHHHHHHTTSSBTTEEEECHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHhcCHHHHHHHHHHHHHcCCCcceEeehhhhhhhCchHHHHHHHHHHhhhcceeeecc
Confidence            3444455555566788899999985 5799999999999999999999999999999997654

>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=95.45  E-value=0.012  Score=40.10  Aligned_cols=45  Identities=24%  Similarity=0.334  Sum_probs=37.0

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEEe-ecCceEEEecc
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVV-KHHAQVIYTRT  131 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs-kh~~q~IYtra  131 (139)
                      +|++.||++++|.-|-+-.+|+.|+++|+|..+. .+.+-..|...
T Consensus        42 lt~~ela~~l~vsk~~vs~~l~~L~~~GlV~r~~~~~drr~~~~~~   87 (151)
T d1ku9a_          42 LTISDIMEELKISKGNVSMSLKKLEELGFVRKVWIKGERKNYYEAV   87 (151)
T ss_dssp             EEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECCTTCSSCEEEEC
T ss_pred             cCHHHHHHHhCCCcchHHHHHHHHHHCCCEEEEEcCCCCceeEEeC
Confidence            8999999999999999999999999999999874 33333344433

>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=95.31  E-value=0.014  Score=39.24  Aligned_cols=43  Identities=21%  Similarity=0.210  Sum_probs=36.2

Q ss_pred             eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe--ecCceEE
Q psy1871          85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV--KHHAQVI  127 (139)
Q Consensus        85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs--kh~~q~I  127 (139)
                      .-||+..||++++++-|-+-++|+.|+++|+|....  .++|...
T Consensus        44 ~~it~~ela~~~~~~~~~vs~~l~~L~~~g~v~r~~~~~D~R~~~   88 (135)
T d3broa1          44 KEVLQRDLESEFSIKSSTATVLLQRMEIKKLLYRKVSGKDSRQKC   88 (135)
T ss_dssp             SCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECSSCTTSEE
T ss_pred             CCCCHHHHHHHHCcCHhHHHHHHHHHHHHHHHHHHhhhhhhhhhh
Confidence            457999999999999999999999999999998763  3444443

>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=95.04  E-value=0.0065  Score=40.82  Aligned_cols=48  Identities=15%  Similarity=0.170  Sum_probs=40.5

Q ss_pred             HHHHHHHhhCCC------CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          72 ASYDKLLKEVPA------YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        72 ~tydKl~KEVpk------~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      ..++.|...|-.      .+|-|-..||++|+|+-+..|+||+.|+++|+|...
T Consensus        13 qi~~~i~~~I~~g~l~~G~~LPs~r~La~~~~vSr~tvr~Al~~L~~~Gli~~~   66 (100)
T d1v4ra1          13 DVATHFRTLIKSGELAPGDTLPSVADIRAQFGVAAKTVSRALAVLKSEGLVSSR   66 (100)
T ss_dssp             HHHHHHHHHTTTTSCCTTSBCCCHHHHHHHSSSCTTHHHHHTTTTTTSSCCEEE
T ss_pred             HHHHHHHHHHHcCCCCCcCCCccHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEe
Confidence            466677766654      567799999999999999999999999999998754

>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=95.03  E-value=0.024  Score=38.75  Aligned_cols=34  Identities=12%  Similarity=0.226  Sum_probs=32.3

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      +|++.||++++++-|-.-++|+.|+++|+|....
T Consensus        51 ~t~~~la~~l~~~~~~vsr~l~~L~~~G~v~r~~   84 (141)
T d1lnwa_          51 LNLQDLGRQMCRDKALITRKIRELEGRNLVRRER   84 (141)
T ss_dssp             CBHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCHHHHHHHHCccHhHHHHHHHHHHHhhceeeec
Confidence            7999999999999999999999999999998764

>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=94.96  E-value=0.013  Score=36.67  Aligned_cols=44  Identities=18%  Similarity=0.192  Sum_probs=36.5

Q ss_pred             HHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          76 KLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        76 Kl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      +|+.-+-...-+|-+.||+.++++-+-+..+|++|++.|+|..+
T Consensus        10 ~Il~~l~~~g~~sr~eLa~~~glS~~Tv~~~l~~L~~~Glv~e~   53 (71)
T d1z05a1          10 RVYKLIDQKGPISRIDLSKESELAPASITKITRELIDAHLIHET   53 (71)
T ss_dssp             HHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            34444444445899999999999999999999999999999876

>d2a61a1 a.4.5.28 (A:5-143) Transcriptional regulator TM0710 {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator TM0710
species: Thermotoga maritima [TaxId: 2336]

Probab=94.88  E-value=0.024  Score=38.48  Aligned_cols=35  Identities=20%  Similarity=0.179  Sum_probs=32.6

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      -+|++.||++++|.-+-.-++|+.|+++|+|....
T Consensus        44 ~~t~~~la~~l~i~~~tvs~~l~~L~~~gli~r~~   78 (139)
T d2a61a1          44 PKRPGELSVLLGVAKSTVTGLVKRLEADGYLTRTP   78 (139)
T ss_dssp             CBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCCHHHHHHHhCCCcccchHHHHHHHhcCeeeeee
Confidence            36999999999999999999999999999998764

>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=94.86  E-value=0.02  Score=38.87  Aligned_cols=34  Identities=18%  Similarity=0.242  Sum_probs=32.6

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      +|++.||++++|.-|.+-++++.|+++|+|..+.
T Consensus        47 ~t~~~La~~l~i~~~~vs~~v~~L~~~gli~r~~   80 (140)
T d2etha1          47 KKMKEIAEFLSTTKSNVTNVVDSLEKRGLVVREM   80 (140)
T ss_dssp             BCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeee
Confidence            7999999999999999999999999999999874

>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=94.77  E-value=0.039  Score=35.70  Aligned_cols=54  Identities=11%  Similarity=0.110  Sum_probs=40.9

Q ss_pred             HHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe--ecCceEEEec
Q psy1871          77 LLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV--KHHAQVIYTR  130 (139)
Q Consensus        77 l~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs--kh~~q~IYtr  130 (139)
                      |+.-+-...-+|++.|++.++|+-+..-+.|+.|++.|+|....  .+++..+|.=
T Consensus        21 IL~~L~~~~~~~~~eLa~~l~is~~~vs~~l~~L~~~glV~~~~~~~d~r~~~~~L   76 (100)
T d1ub9a_          21 IMIFLLPRRKAPFSQIQKVLDLTPGNLDSHIRVLERNGLVKTYKVIADRPRTVVEI   76 (100)
T ss_dssp             HHHHHHHHSEEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEE
T ss_pred             HHHHhccCCCeeHHHHHHHHhhccccccHHHHHHhhhceeEEEEcCcCCccccccC
Confidence            44444333347999999999999999999999999999997652  3455666653

>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=94.73  E-value=0.027  Score=37.44  Aligned_cols=46  Identities=28%  Similarity=0.213  Sum_probs=39.5

Q ss_pred             eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE--eecCceEEEec
Q psy1871          85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQV--VKHHAQVIYTR  130 (139)
Q Consensus        85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V--skh~~q~IYtr  130 (139)
                      +=|.-..|-.+.++.-+.-.++|+.||++++|+.|  .+|+...+|.-
T Consensus        28 ~GIW~~dir~ktnL~~~~l~K~LK~Lesk~lIK~VksV~~~~rK~YmL   75 (78)
T d2dk5a1          28 KGIWSRDVRYKSNLPLTEINKILKNLESKKLIKAVKSVAASKKKVYML   75 (78)
T ss_dssp             TCEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEECCSSCSSCCEEEE
T ss_pred             cceeHHHHHHHcCCCHHHHHHHHHHHHhcCCceeecccCCCCeEEEEe
Confidence            34667889999999999999999999999999999  35667778864

>d3deua1 a.4.5.28 (A:2-141) Transcriptional regulator SlyA {Salmonella typhimurium [TaxId: 90371]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator SlyA
species: Salmonella typhimurium [TaxId: 90371]

Probab=94.55  E-value=0.021  Score=38.60  Aligned_cols=44  Identities=14%  Similarity=0.165  Sum_probs=33.9

Q ss_pred             eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe--ecCceEEE
Q psy1871          85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV--KHHAQVIY  128 (139)
Q Consensus        85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs--kh~~q~IY  128 (139)
                      .-+|++.|+++++|+-+-.-++|+.|+++|+|..+.  .++|...+
T Consensus        45 ~~~t~~~la~~l~i~~~~vs~~l~~L~~~glI~~~~~~~D~R~~~l   90 (140)
T d3deua1          45 PDQSQIQLAKAIGIEQPSLVRTLDQLEDKGLISRQTCASDRRAKRI   90 (140)
T ss_dssp             SSEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEC--------CEE
T ss_pred             CCccHHHHHHHHCCCHhHHHHHHHHHHhCCCEEecccCCCCCceee
Confidence            368999999999999999999999999999998763  34444433

>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=94.37  E-value=0.027  Score=37.91  Aligned_cols=35  Identities=20%  Similarity=0.367  Sum_probs=32.8

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      -+|++.||+++++.-|..-++++.|+++|+|....
T Consensus        43 ~~t~~~la~~~~~~~~~vs~~v~~L~~~gli~r~~   77 (137)
T d2fbha1          43 SPTQRELAQSVGVEGPTLARLLDGLESQGLVRRLA   77 (137)
T ss_dssp             CCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEC
T ss_pred             CCcHHHHHHHHCCCHHHHHHHHHHHHHcCCccccC
Confidence            37999999999999999999999999999999873

>d1wi9a_ a.4.5.47 (A:) Hypothetical protein C20orf116 homolog {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PCI domain (PINT motif)
domain: Hypothetical protein C20orf116 homolog
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.37  E-value=0.021  Score=37.79  Aligned_cols=62  Identities=15%  Similarity=0.293  Sum_probs=56.3

Q ss_pred             HHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEeccC
Q psy1871          71 KASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTT  132 (139)
Q Consensus        71 k~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra~  132 (139)
                      +.++..+...|...|+|.--.||..|+++-..+..=|++|++.|.|.=|.-.|.-.||.--+
T Consensus         6 q~lL~~FI~~Ik~~Kvv~LedLAa~F~lktqd~i~RIq~Le~~g~ltGViDDRGKfIyIS~s   67 (72)
T d1wi9a_           6 SGFLTEFINYIKKSKVVLLEDLAFQMGLRTQDAINRIQDLLTEGTLTGVIDDRGKFIYITPS   67 (72)
T ss_dssp             CCHHHHHHHHHHHCSEECHHHHHHHHCSCHHHHHHHHHHHHHHSSSCEEECTTCCEEECCCS
T ss_pred             HHHHHHHHHHHHHCCEeeHHHHHHHcCCcHHHHHHHHHHHHHCCCeeeEEcCCCCEEEEcCC
Confidence            34677788888889999999999999999999999999999999999999999999998654

>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=94.23  E-value=0.035  Score=37.54  Aligned_cols=37  Identities=19%  Similarity=0.135  Sum_probs=33.6

Q ss_pred             CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          84 YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        84 ~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      ..=+|++.||+++++.-|-.-++|+.|+++|+|....
T Consensus        46 ~~~~t~~~la~~l~~~~~~~s~~l~~L~~~Gli~r~~   82 (136)
T d2bv6a1          46 ESPVNVKKVVTELALDTGTVSPLLKRMEQVDLIKRER   82 (136)
T ss_dssp             SSEEEHHHHHHHTTCCTTTHHHHHHHHHHTTSEEEEE
T ss_pred             CCCCCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEEee
Confidence            3457999999999999999999999999999998764

>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=94.21  E-value=0.054  Score=33.43  Aligned_cols=47  Identities=19%  Similarity=0.281  Sum_probs=38.3

Q ss_pred             eCHHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          69 FDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        69 ~Dk~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      +|...++-|+.+-    =+|.+.||++++++-+-..+-|+.|++.|+|+-+
T Consensus         6 ~D~~IL~~L~~n~----r~s~~~iA~~lgis~~tv~~Ri~~L~~~giI~~~   52 (63)
T d2cfxa1           6 IDLNIIEELKKDS----RLSMRELGRKIKLSPPSVTERVRQLESFGIIKQY   52 (63)
T ss_dssp             HHHHHHHHHHHCS----CCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHcC----CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeE
Confidence            3555666666552    3489999999999999999999999999999754

>d2hr3a1 a.4.5.28 (A:2-146) Probable transcriptional regulator PA3067 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Probable transcriptional regulator PA3067
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=94.13  E-value=0.028  Score=38.40  Aligned_cols=35  Identities=31%  Similarity=0.347  Sum_probs=32.7

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      -+|++.||++++|..|-+-++|..|+++|+|....
T Consensus        49 ~~t~~~La~~~~~~~~~vs~~i~~L~~~glv~r~~   83 (145)
T d2hr3a1          49 DVTPSELAAAERMRSSNLAALLRELERGGLIVRHA   83 (145)
T ss_dssp             CBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEC
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHcCCeEeee
Confidence            48999999999999999999999999999998763

>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=94.11  E-value=0.029  Score=34.19  Aligned_cols=47  Identities=19%  Similarity=0.215  Sum_probs=38.5

Q ss_pred             eCHHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          69 FDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        69 ~Dk~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      +|...++-|+++ +   =+|...||++++++.+-...-|+.|++.|+|..+
T Consensus         4 ~D~~Il~~L~~n-~---r~s~~eiA~~l~ls~~~v~~Ri~~L~~~giI~~~   50 (60)
T d2cyya1           4 IDKKIIKILQND-G---KAPLREISKITGLAESTIHERIRKLRESGVIKKF   50 (60)
T ss_dssp             HHHHHHHHHHHC-T---TCCHHHHHHHHCSCHHHHHHHHHHHHHHTSSCCC
T ss_pred             HHHHHHHHHHHc-C---CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEeE
Confidence            456666666665 2   2488999999999999999999999999999743

>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=94.00  E-value=0.029  Score=35.04  Aligned_cols=33  Identities=21%  Similarity=0.175  Sum_probs=30.4

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQ  118 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~  118 (139)
                      -++.+.||++|+|+-+-+-.+|+.|+++|+|..
T Consensus        21 ~v~~~~iA~~L~vs~~SVs~mikrL~~~GlV~~   53 (61)
T d2ev0a1          21 YARVSDIAEALAVHPSSVTKMVQKLDKDEYLIY   53 (61)
T ss_dssp             SCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC
T ss_pred             CccHHHHHHHhCCCchhHHHHHHHHHHCCCEEE
Confidence            478899999999999999999999999999753

>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=93.77  E-value=0.065  Score=35.95  Aligned_cols=46  Identities=17%  Similarity=0.266  Sum_probs=38.7

Q ss_pred             echHHHHhhh----ccchHHHHHHHHHHHHcCCeeEEeecCceEEEeccCC
Q psy1871          87 ITPSVVSERL----KVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTTK  133 (139)
Q Consensus        87 ITPsvlseRl----kI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra~k  133 (139)
                      +|+..|.+++    .+..|--..+|+-|+++|+|..- ++++..+|++...
T Consensus        22 ~t~~ei~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~r~-~~gr~~~Y~~~~~   71 (120)
T d1okra_          22 ASANNIIEEIQMQKDWSPKTIRTLITRLYKKGFIDRK-KDNKIFQYYSLVE   71 (120)
T ss_dssp             EEHHHHHHHHHHHCCCCHHHHHHHHHHHHHHTSEEEE-EETTEEEEEESSC
T ss_pred             CCHHHHHHHHhcccCccHHhHHHHHHHHHHCCCeEEE-ecCCceEEeecCC
Confidence            6899988887    58899999999999999999864 4677789987653

>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=93.60  E-value=0.068  Score=35.94  Aligned_cols=34  Identities=9%  Similarity=0.169  Sum_probs=32.4

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      +|++.||++++|.-+-.-++|+.|+++|+|....
T Consensus        45 ~t~~~la~~~~i~~~~vs~~i~~L~~~gli~r~~   78 (136)
T d2fbia1          45 MESYQLANQACILRPSMTGVLARLERDGIVRRWK   78 (136)
T ss_dssp             EEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEee
Confidence            7999999999999999999999999999998874

>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=93.46  E-value=0.026  Score=38.01  Aligned_cols=35  Identities=17%  Similarity=0.176  Sum_probs=32.8

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      =+|++.||+++++.-|-.=++|..|+++|+|....
T Consensus        48 ~~t~~ela~~l~~~~~~vs~~i~~Le~~gli~r~~   82 (115)
T d1hsja1          48 EISSKEIAKCSEFKPYYLTKALQKLKDLKLLSKKR   82 (115)
T ss_dssp             EEEHHHHHHSSCCCHHHHHHHHHHHHTTTTSCCEE
T ss_pred             CcCHHHHHHHHCCChhhHHHHHHHHHHcCCeEEEe
Confidence            48999999999999999999999999999999763

>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=93.35  E-value=0.048  Score=34.46  Aligned_cols=35  Identities=23%  Similarity=0.237  Sum_probs=32.4

Q ss_pred             eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      .-+|.+.||+.+++.-|-+.++|..|++.|++...
T Consensus        19 ~~~s~~eia~~~~~~~st~~rll~tL~~~g~l~~~   53 (75)
T d1mkma1          19 GDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRK   53 (75)
T ss_dssp             SCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEC
Confidence            35899999999999999999999999999998764

>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=93.29  E-value=0.065  Score=36.67  Aligned_cols=34  Identities=26%  Similarity=0.392  Sum_probs=32.4

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      +|++.||++++|.-|-.-++|+.|+++|+|....
T Consensus        44 ~t~~~la~~l~i~~~tvs~~l~~L~~~glI~r~~   77 (144)
T d1lj9a_          44 IIQEKIAELIKVDRTTAARAIKRLEEQGFIYRQE   77 (144)
T ss_dssp             EEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCHHHHHHHHCccHhhHHHHHHHHHhhhcccccC
Confidence            7999999999999999999999999999998864

>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=93.28  E-value=0.041  Score=37.43  Aligned_cols=38  Identities=5%  Similarity=0.211  Sum_probs=33.9

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCc
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHA  124 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~  124 (139)
                      +|-.+||+.++++-+.-|++|+.|.+.|+|+-+-..+.
T Consensus        19 ~ss~~IA~~~~~~~~~v~kIl~~L~~aglV~s~rG~~G   56 (127)
T d1xd7a_          19 TSSEIIADSVNTNPVVVRRMISLLKKADILTSRAGVPG   56 (127)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHHHHHTTSEECCSSSSS
T ss_pred             CCHHHHHHHhCcCHHHHHHHHHHHHHhCcccccCCCCC
Confidence            79999999999999999999999999999987655433

>d1z91a1 a.4.5.28 (A:8-144) Organic hydroperoxide resistance transcriptional regulator OhrR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Organic hydroperoxide resistance transcriptional regulator OhrR
species: Bacillus subtilis [TaxId: 1423]

Probab=93.28  E-value=0.019  Score=39.07  Aligned_cols=36  Identities=22%  Similarity=0.292  Sum_probs=33.3

Q ss_pred             eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      .=+|++.||++++|.-+-.-+++..|+++|+|....
T Consensus        46 ~~~t~~~La~~~~i~~~~vsr~i~~L~~~glv~r~~   81 (137)
T d1z91a1          46 ETLTVKKMGEQLYLDSGTLTPMLKRMEQQGLITRKR   81 (137)
T ss_dssp             SEEEHHHHHHTTTCCHHHHHHHHHHHHHHTSEECCB
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHhhccceEEee
Confidence            457999999999999999999999999999998873

>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=93.08  E-value=0.08  Score=32.59  Aligned_cols=40  Identities=20%  Similarity=0.285  Sum_probs=35.3

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEE
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIY  128 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IY  128 (139)
                      +|-..||+-++++-.-.-++|++|+++|+|..  .+++..||
T Consensus        30 lt~~~lA~~~G~sRetvsr~L~~l~~~glI~~--~~~~I~I~   69 (69)
T d1i5za1          30 ITRQEIGQIVGCSRETVGRILKMLEDQNLISA--HGKTIVVY   69 (69)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE--ETTEEEEC
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE--cCCEEEEC
Confidence            79999999999999999999999999999974  45666665

>d2ve8a1 a.4.5.67 (A:745-811) DNA translocase FtsK {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: FtsK C-terminal domain-like
domain: DNA translocase FtsK
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=93.07  E-value=0.018  Score=37.33  Aligned_cols=62  Identities=18%  Similarity=0.284  Sum_probs=49.3

Q ss_pred             CHHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871          70 DKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT  131 (139)
Q Consensus        70 Dk~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra  131 (139)
                      +.++|++...=|-...-.+.|.|--||+|-..-|-+++..||+.|+|-+-..+..-.|.++.
T Consensus         2 ~D~ly~~a~~~V~~~~kaS~S~lQR~l~IGYnRAariid~LE~~GiVsp~~g~~~ReVL~~~   63 (67)
T d2ve8a1           2 DDPLYDEAVRFVTESRRASISAVQRKLKIGYNRAARMIEAMEMAGVVTPMNTNGSREVIAPA   63 (67)
T ss_dssp             CCTTHHHHHHHHHHHCCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSBCCCCTTSCCCBCSCC
T ss_pred             ccHHHHHHHHHHHHhCcccHHHHHHHHhcchHHHHHHHHHHHHCcCCCCCCCCCCCeEeCCC
Confidence            34567777766666777899999999999999999999999999999987654444455543

>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=93.04  E-value=0.068  Score=32.98  Aligned_cols=35  Identities=14%  Similarity=0.272  Sum_probs=32.9

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEEee
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK  121 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk  121 (139)
                      ||-+.||+.++++.+-...++++|++.|+|.....
T Consensus        13 isr~eLa~~~gls~~TVs~~v~~L~~~GlV~e~~~   47 (62)
T d2hoea1          13 VSRVELAEELGLTKTTVGEIAKIFLEKGIVVEEKD   47 (62)
T ss_dssp             BCHHHHHHHHTCCHHHHHHHHHHHHHHTSEEEEEC
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEECCC
Confidence            69999999999999999999999999999998753

>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=93.02  E-value=0.073  Score=36.08  Aligned_cols=34  Identities=26%  Similarity=0.399  Sum_probs=32.2

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      -+|++.|++.++|.-+.+-+++..|+++|+|...
T Consensus        48 ~~t~~ela~~~~i~~~~vs~~v~~L~~~glv~r~   81 (138)
T d1jgsa_          48 CITPVELKKVLSVDLGALTRMLDRLVCKGWVERL   81 (138)
T ss_dssp             SBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCHHHHHHHHCCCHhHHHHHHHHHhhCCCEEEe
Confidence            3799999999999999999999999999999875

>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=93.00  E-value=0.052  Score=34.10  Aligned_cols=33  Identities=18%  Similarity=0.355  Sum_probs=30.5

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQ  118 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~  118 (139)
                      .++.+.||++|+|+-+-+-.+++.|.++|+|..
T Consensus        23 ~v~~~~iA~~L~vs~~SVt~mvkrL~~~Glv~~   55 (63)
T d2isya1          23 TPLRARIAERLDQSGPTVSQTVSRMERDGLLRV   55 (63)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCcHHHHHHHhCCCchhHHHHHHHHHHCCCEEE
Confidence            478899999999999999999999999999853

>d1s3ja_ a.4.5.28 (A:) Putative transcriptional regulator YusO {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Putative transcriptional regulator YusO
species: Bacillus subtilis [TaxId: 1423]

Probab=93.00  E-value=0.074  Score=35.96  Aligned_cols=35  Identities=29%  Similarity=0.334  Sum_probs=32.6

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      =+|+..||++++|.-+-+-+++..|+++|+|....
T Consensus        49 ~~t~~~la~~~~i~~~~vs~~l~~L~~~glv~r~~   83 (143)
T d1s3ja_          49 SLKVSEIAERMEVKPSAVTLMADRLEQKNLIARTH   83 (143)
T ss_dssp             EEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHhhhheeee
Confidence            37999999999999999999999999999998764

>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=92.94  E-value=0.024  Score=38.08  Aligned_cols=34  Identities=15%  Similarity=0.086  Sum_probs=32.5

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      +|++.||+++++.-|-.-++|+.|+++|+|....
T Consensus        50 ~t~~~la~~l~~~~~tvs~~i~~Le~~gli~r~~   83 (115)
T d2frha1          50 YYLKDIINHLNYKQPQVVKAVKILSQEDYFDKKR   83 (115)
T ss_dssp             EEHHHHHHHSSSHHHHHHHHHHHHHHTTSSCCBC
T ss_pred             CCHHHHHHHHCCCHhHHHHHHHHHHhhhhheeee
Confidence            7999999999999999999999999999999884

>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=92.90  E-value=0.021  Score=35.13  Aligned_cols=45  Identities=24%  Similarity=0.371  Sum_probs=36.6

Q ss_pred             CHHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871          70 DKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQ  118 (139)
Q Consensus        70 Dk~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~  118 (139)
                      |...+.-|..+ +   =+|...||++++++.+....-|+.|+++|+|..
T Consensus         5 D~kIl~~L~~n-~---r~s~~~lA~~~gls~~~v~~Ri~~L~~~giI~~   49 (60)
T d1i1ga1           5 DKIILEILEKD-A---RTPFTEIAKKLGISETAVRKRVKALEEKGIIEG   49 (60)
T ss_dssp             HHHHHHHHHHC-T---TCCHHHHHHHHTSCHHHHHHHHHHHHHHTSSCC
T ss_pred             HHHHHHHHHHc-C---CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEe
Confidence            45555555554 3   348899999999999999999999999999964

>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=92.67  E-value=0.18  Score=32.54  Aligned_cols=49  Identities=20%  Similarity=0.261  Sum_probs=38.0

Q ss_pred             echHHHHhh----hccchHHHHHHHHHHHHcCCeeEEeecCceEEEeccCCCCC
Q psy1871          87 ITPSVVSER----LKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTTKGDD  136 (139)
Q Consensus        87 ITPsvlseR----lkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra~k~~~  136 (139)
                      +|...|.+.    ..+.-+..+..|+.|++||+|.. .+.++..+|++....++
T Consensus        24 ~t~~ei~~~l~~~~~~~~tTv~T~L~rL~~KG~l~~-~k~gr~~~Y~p~is~ee   76 (82)
T d1p6ra_          24 INTNEVIKELSKTSTWSPKTIQTMLLRLIKKGALNH-HKEGRVFVYTPNIDESD   76 (82)
T ss_dssp             EEHHHHHHHHHHHSCCCHHHHHHHHHHHHHTTSEEE-EEETTEEEEEESCSSST
T ss_pred             CCHHHHHHHhccccCCcHhHHHHHHHHHHHCCCeEE-EecCCeEEEEecCCHHH
Confidence            567766544    47788899999999999999985 45677889998766544

>d1j5ya1 a.4.5.1 (A:3-67) Putative transcriptional regulator TM1602, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Biotin repressor-like
domain: Putative transcriptional regulator TM1602, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=92.62  E-value=0.046  Score=33.74  Aligned_cols=43  Identities=12%  Similarity=0.199  Sum_probs=36.2

Q ss_pred             HHHHHHhhCCCC-eeechHHHHhhhccchHHHHHHHHHHHHcCC
Q psy1871          73 SYDKLLKEVPAY-KLITPSVVSERLKVRGSLARKALEELLQKGL  115 (139)
Q Consensus        73 tydKl~KEVpk~-KlITPsvlseRlkI~~SLARkaLreL~~kGl  115 (139)
                      -..+|+..+.+. ..||...||++|+|+-...|+=|.+|++.|+
T Consensus         8 R~~~Il~~L~~~~~~vs~~~La~~l~VS~~TI~rdi~~L~~~G~   51 (65)
T d1j5ya1           8 RLKSIVRILERSKEPVSGAQLAEELSVSRQVIVQDIAYLRSLGY   51 (65)
T ss_dssp             HHHHHHHHHHHCSSCBCHHHHHHHHTSCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCC
Confidence            345566665444 5799999999999999999999999999997

>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=92.51  E-value=0.058  Score=36.61  Aligned_cols=35  Identities=14%  Similarity=0.127  Sum_probs=33.3

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      =||+..||+++++.-|-.-++|+.|+++|+|..+.
T Consensus        50 ~~t~~eia~~~~~~~~~vs~~l~~L~~~g~v~r~~   84 (125)
T d1p4xa1          50 TLPFKKIVSDLCYKQSDLVQHIKVLVKHSYISKVR   84 (125)
T ss_dssp             EEEHHHHHHHSSSCGGGTHHHHHHHHHTTSCEEEE
T ss_pred             CcCHHHHHHHhCCCcchHHHHHHHHHHCCCceeec
Confidence            48999999999999999999999999999999984

>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=92.39  E-value=0.077  Score=33.55  Aligned_cols=39  Identities=26%  Similarity=0.309  Sum_probs=32.5

Q ss_pred             echHHHHhhhcc-chHHHHHHHHHHHHcCCeeEEeecCce
Q psy1871          87 ITPSVVSERLKV-RGSLARKALEELLQKGLIKQVVKHHAQ  125 (139)
Q Consensus        87 ITPsvlseRlkI-~~SLARkaLreL~~kGlIk~Vskh~~q  125 (139)
                      .|...|++.|++ +-|.++..|..|+++|+|......+|.
T Consensus        25 Ps~rei~~~~g~~S~stv~~~l~~Le~kG~I~r~~~~~R~   64 (71)
T d1jhfa1          25 PTRAEIAQRLGFRSPNAAEEHLKALARKGVIEIVSGASRG   64 (71)
T ss_dssp             CCHHHHHHHTTCSSHHHHHHHHHHHHHTTSEEECSSSSSC
T ss_pred             CCHHHHHHHcCCCCHHHHHHHHHHHHHCcCeecCCCCCce
Confidence            467889999999 477899999999999999998544443

>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=92.23  E-value=0.061  Score=33.63  Aligned_cols=46  Identities=11%  Similarity=0.177  Sum_probs=40.6

Q ss_pred             HHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          74 YDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        74 ydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      ...|+.-+....-+|-+.||+.++++-+-..+++++|.+.|+|...
T Consensus         7 ~~~Il~~i~~~g~~sr~eLa~~~gLS~~Tvs~iv~~L~~~glv~e~   52 (70)
T d1z6ra1           7 AGAVYRLIDQLGPVSRIDLSRLAQLAPASITKIVHEMLEAHLVQEL   52 (70)
T ss_dssp             HHHHHHHHHSSCSCCHHHHHHHTTCCHHHHHHHHHHHHHHTSEEEC
T ss_pred             HHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEee
Confidence            3456667777888999999999999999999999999999999865

>d2j5pa1 a.4.5.67 (A:1261-1329) DNA translocase FtsK {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: FtsK C-terminal domain-like
domain: DNA translocase FtsK
species: Escherichia coli [TaxId: 562]

Probab=91.71  E-value=0.044  Score=35.70  Aligned_cols=59  Identities=12%  Similarity=0.229  Sum_probs=49.1

Q ss_pred             HHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEe
Q psy1871          71 KASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYT  129 (139)
Q Consensus        71 k~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYt  129 (139)
                      .++|++...=|-...-.+.|-|--||+|-..-|-+++..||+.|+|-+-..+..-.|..
T Consensus         6 D~ly~~a~~~V~~~~kaS~S~lQR~l~IGYnRAariid~LE~~GiVsp~~~~~~ReVL~   64 (69)
T d2j5pa1           6 DPLFDQAVQFVTEKRKASISGVQRQFRIGYNRAARIIEQMEAQGIVSEQGHNGNREVLA   64 (69)
T ss_dssp             CTTHHHHHHHHHHTTEEEHHHHHHHHTCCHHHHHHHHHHHHHHTSBCCCCSSSEEEBCS
T ss_pred             cHHHHHHHHHHHHhCcccHHHHHHHHhccchHHHHHHHHHHHCCcCCCCCCCCCCeEcC
Confidence            46788888878888889999999999999999999999999999998865544434444

>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=91.46  E-value=0.12  Score=35.24  Aligned_cols=34  Identities=15%  Similarity=0.228  Sum_probs=32.1

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      -+|++.||+.+++.-|-.-++++.|+++|+|...
T Consensus        49 ~~~~~~ia~~l~~~~~~vs~~v~~L~~~glV~r~   82 (125)
T d1p4xa2          49 IVLLKDLIETIHHKYPQTVRALNNLKKQGYLIKE   82 (125)
T ss_dssp             CEEHHHHHHHSSSCHHHHHHHHHHHHHHTSSEEE
T ss_pred             CccHHHHHHHHCCCcchHHHHHHHHHhccCEeee
Confidence            4899999999999999999999999999999776

>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=90.90  E-value=0.13  Score=35.12  Aligned_cols=38  Identities=21%  Similarity=0.230  Sum_probs=33.0

Q ss_pred             eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeec
Q psy1871          85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKH  122 (139)
Q Consensus        85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh  122 (139)
                      +.+|...||++++|+-...+++|+.|.+.|+|.-...+
T Consensus        22 ~~vss~~IA~~~~i~~~~l~kil~~L~~aGlv~S~rG~   59 (138)
T d1ylfa1          22 SLCTSDYMAESVNTNPVVIRKIMSYLKQAGFVYVNRGP   59 (138)
T ss_dssp             GGCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEC---
T ss_pred             CcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCeEeecCC
Confidence            46899999999999999999999999999999877664

>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=90.87  E-value=0.28  Score=32.82  Aligned_cols=49  Identities=29%  Similarity=0.418  Sum_probs=36.9

Q ss_pred             CHHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeec--CceEEEeccC
Q psy1871          70 DKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKH--HAQVIYTRTT  132 (139)
Q Consensus        70 Dk~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh--~~q~IYtra~  132 (139)
                      ..--|..|.+.+|+   ||+.+||+|           |++|++.|+|.....+  .....|.-..
T Consensus        32 g~~rF~el~~~l~g---Is~~~Ls~r-----------LkeL~~~glv~r~~~~~~p~~veY~LT~   82 (102)
T d2fswa1          32 RIIRYGELKRAIPG---ISEKMLIDE-----------LKFLCGKGLIKKKQYPEVPPRVEYSLTP   82 (102)
T ss_dssp             SCEEHHHHHHHSTT---CCHHHHHHH-----------HHHHHHTTSEEEEEECSSSCEEEEEECH
T ss_pred             CCCCHHHHHhhCcc---cchhHHHHH-----------HHHHHHCCceeecccCCCCCeehhhhhH
Confidence            34568899999987   899999998           5899999999886433  2344576443

>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=90.85  E-value=0.14  Score=31.85  Aligned_cols=39  Identities=13%  Similarity=0.175  Sum_probs=34.6

Q ss_pred             eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecC
Q psy1871          85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHH  123 (139)
Q Consensus        85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~  123 (139)
                      .--|...|++.+++.-..+|..|+.|.+.|.+..|+..+
T Consensus        22 ~PP~vrdl~~~l~~~e~~~~~lL~~l~~~G~lvkI~~d~   60 (64)
T d1lvaa3          22 QPPSFKEVAGSFNLDPSELEELLHYLVREGVLVKINDEF   60 (64)
T ss_dssp             SCCBHHHHHHHTTCCHHHHHHHHHHHHHTTSEEESSSSB
T ss_pred             CCCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecccc
Confidence            445778999999999999999999999999999997654

>d1u5ta2 a.4.5.54 (A:165-232) Vacuolar sorting protein SNF8 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Vacuolar sorting protein domain
domain: Vacuolar sorting protein SNF8
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=90.61  E-value=0.095  Score=33.90  Aligned_cols=35  Identities=20%  Similarity=0.298  Sum_probs=32.1

Q ss_pred             CCeeechHHHHhhhccchHHHHHHHHHHHHcCCee
Q psy1871          83 AYKLITPSVVSERLKVRGSLARKALEELLQKGLIK  117 (139)
Q Consensus        83 k~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk  117 (139)
                      ..=+||.+.|-++|+-.-.-|+.+|++|..+|+.=
T Consensus        14 ~~G~Vt~s~l~~~lgW~~~Ra~~aLd~lv~eGl~W   48 (68)
T d1u5ta2          14 ILGYSSISLLKANLGWEAVRSKSALDEMVANGLLW   48 (68)
T ss_dssp             TTSCCBHHHHHHHHCCCSHHHHHHHHHHHHTTSSE
T ss_pred             HcCceeHHHHHHHhCCCHHHHHHHHHHHHhcCcEE
Confidence            34689999999999999999999999999999864

>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=90.56  E-value=0.34  Score=31.85  Aligned_cols=54  Identities=19%  Similarity=0.222  Sum_probs=42.1

Q ss_pred             HHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871          76 KLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT  131 (139)
Q Consensus        76 Kl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra  131 (139)
                      +|+..+-.-. .|++.|++.++|+-|..-.=|+.|.+-|+|..- +.++...|.-+
T Consensus        27 ~Il~~L~~~~-~~v~ela~~l~is~stvS~HL~~L~~aglV~~~-r~G~~~~Y~l~   80 (98)
T d1r1ta_          27 RLLSLLARSE-LCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYR-KQGRHVYYQLQ   80 (98)
T ss_dssp             HHHHHHTTCC-BCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE-EETTEEEEEES
T ss_pred             HHHHHHHcCC-cCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEE-EECCEEEEEEC
Confidence            4444444434 699999999999999999999999999999864 55566667643

>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=90.48  E-value=0.27  Score=34.73  Aligned_cols=60  Identities=27%  Similarity=0.262  Sum_probs=43.6

Q ss_pred             HHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe----ecCceEEEeccC
Q psy1871          72 ASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV----KHHAQVIYTRTT  132 (139)
Q Consensus        72 ~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs----kh~~q~IYtra~  132 (139)
                      ++--+|+.-.-. .=.|.+.||+.+++.-+....-|+.|++.|+|..+.    .++.+.+|..+.
T Consensus        19 p~R~~Il~~L~~-~~~s~~ela~~lg~s~~~v~~hl~~L~~~glv~~~~~~~~~g~~~k~y~~~~   82 (190)
T d1ulya_          19 DTRRKILKLLRN-KEMTISQLSEILGKTPQTIYHHIEKLKEAGLVEVKRTEMKGNLVEKYYGRTA   82 (190)
T ss_dssp             HHHHHHHHHHTT-CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEEEEETTEEEEEEEESS
T ss_pred             HHHHHHHHHHHh-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEeeccCCcceEEEEEcc
Confidence            333445554432 236999999999999999999999999999997652    223466776543

>d1r8ea1 a.6.1.3 (A:3-120) Transcription activator BmrR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: Putative DNA-binding domain
superfamily: Putative DNA-binding domain
family: DNA-binding N-terminal domain of transcription activators
domain: Transcription activator BmrR
species: Bacillus subtilis [TaxId: 1423]

Probab=89.46  E-value=0.2  Score=33.27  Aligned_cols=43  Identities=21%  Similarity=0.097  Sum_probs=34.8

Q ss_pred             eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE--eecCceEEEecc
Q psy1871          85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQV--VKHHAQVIYTRT  131 (139)
Q Consensus        85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V--skh~~q~IYtra  131 (139)
                      .+.|...||+.++|+.+    .||.-++.|||.|-  ...++.+.|+..
T Consensus         2 ~yytI~evA~~~gvs~~----tlR~Ye~~GLl~P~~~r~~~gyR~Y~~~   46 (118)
T d1r8ea1           2 SYYSIGEVSKLANVSIK----ALRYYDKIDLFKPAYVDPDTSYRYYTDS   46 (118)
T ss_dssp             CEEEHHHHHHHHTCCHH----HHHHHHHTTSSCCSEECTTTCCEEEETG
T ss_pred             CcccHHHHHHHHCcCHH----HHHHHHHcCCcccccccCCCCcccccHH
Confidence            47899999999998765    58999999999873  335667899864

>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=89.05  E-value=0.22  Score=32.92  Aligned_cols=42  Identities=24%  Similarity=0.230  Sum_probs=32.1

Q ss_pred             eeechHHHHhhhcc--chHHHHHHHHHHHHcCCeeEEeecCceEE
Q psy1871          85 KLITPSVVSERLKV--RGSLARKALEELLQKGLIKQVVKHHAQVI  127 (139)
Q Consensus        85 KlITPsvlseRlkI--~~SLARkaLreL~~kGlIk~Vskh~~q~I  127 (139)
                      .=|+-..|++.+++  +-+-.|..|.+|+++|+|.. .+.++..|
T Consensus        22 ~Pv~s~~i~~~~~l~~S~aTIRn~m~~LE~~G~l~~-~h~s~Gri   65 (87)
T d1stza1          22 KPVSSQRVLEVSNIEFSSATIRNDMKKLEYLGYIYQ-PHTSAGRI   65 (87)
T ss_dssp             SCBCHHHHHHHSCCCSCHHHHHHHHHHHHHTTSEEC-CSSCSCBE
T ss_pred             CccCHHHHHHHhCCCCCHHHHHHHHHHHHHCCcccC-CCCCCCCc
Confidence            34677899999666  57888999999999999976 44444433

>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=88.94  E-value=0.38  Score=32.48  Aligned_cols=46  Identities=22%  Similarity=0.237  Sum_probs=35.5

Q ss_pred             echHHHHhhh----ccchHHHHHHHHHHHHcCCeeEEeecCceEEEeccCC
Q psy1871          87 ITPSVVSERL----KVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTTK  133 (139)
Q Consensus        87 ITPsvlseRl----kI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra~k  133 (139)
                      +|+..|.+.|    .+.-|-.+..|+.|++||+|... +.++..+|++...
T Consensus        23 ~t~~eI~~~l~~~~~~~~sTV~T~L~rL~~Kg~l~~~-~~gr~~~Y~~~i~   72 (122)
T d2g9wa1          23 QTVRQVHEALSARRDLAYTTVMAVLQRLAKKNLVLQI-RDDRAHRYAPVHG   72 (122)
T ss_dssp             EEHHHHHHHHTTTCCCCHHHHHHHHHHHHHTTSEEEE-C---CCEEEESSC
T ss_pred             ccHHHHHHHHhccCCCcHHHHHHHHHHHHHCCCEEEe-ecCCeEEEEeCCC
Confidence            6888888877    47788999999999999999875 4566779987653

>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=88.69  E-value=0.53  Score=31.82  Aligned_cols=46  Identities=20%  Similarity=0.350  Sum_probs=37.6

Q ss_pred             echHHHHhhh----ccchHHHHHHHHHHHHcCCeeEEeecCceEEEeccCC
Q psy1871          87 ITPSVVSERL----KVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTTK  133 (139)
Q Consensus        87 ITPsvlseRl----kI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra~k  133 (139)
                      +|...|.+.+    .+.-+-.+..|+-|++||+|.. .+.++..+|+....
T Consensus        21 ~t~~ei~~~l~~~~~~~~tTv~T~L~rL~~Kg~l~~-~~~gr~~~Y~~~v~   70 (122)
T d1sd4a_          21 VSANEIVVEIQKYKEVSDKTIRTLITRLYKKEIIKR-YKSENIYFYSSNIK   70 (122)
T ss_dssp             EEHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTSEEE-EEETTEEEEEECSC
T ss_pred             CCHHHHHHHhhccCCCcHhHHHHHHHHHHhhhceee-eccCCeEEEeecCC
Confidence            6888766665    7788899999999999999975 56778889987654

>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=88.38  E-value=0.93  Score=29.34  Aligned_cols=53  Identities=21%  Similarity=0.263  Sum_probs=44.5

Q ss_pred             CHHHHHHHHh---hCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeec
Q psy1871          70 DKASYDKLLK---EVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKH  122 (139)
Q Consensus        70 Dk~tydKl~K---EVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh  122 (139)
                      |.++|+-+.+   +.+.-..+|.-.||-+|+|.=+=+-+.|=.|+++|.+..+..+
T Consensus         5 ~~~i~~lvk~~l~~L~~~~~~tA~~LAk~Lg~~Kk~VNr~LY~L~~~G~v~~~~~t   60 (70)
T d1sfua_           5 DAEIFSLVKKEVLSLNTNDYTTAISLSNRLKINKKKINQQLYKLQKEDTVKMVPSN   60 (70)
T ss_dssp             SHHHHHHHHHHHHTSCTTCEECHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEECCS
T ss_pred             HHHHHHHHHHHHHhcCCCCCchHHHHHHHhCCCHHHHHHHHHHHHHCCCeecCCCc
Confidence            5566665555   4566789999999999999999999999999999999887654

>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=88.21  E-value=0.49  Score=31.07  Aligned_cols=49  Identities=27%  Similarity=0.457  Sum_probs=35.8

Q ss_pred             HHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeec--CceEEEeccCCC
Q psy1871          72 ASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKH--HAQVIYTRTTKG  134 (139)
Q Consensus        72 ~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh--~~q~IYtra~k~  134 (139)
                      --|+.|.+.+|+   ||+.+||+||           ++|++.|+|.....+  .....|.-..++
T Consensus        25 ~rF~el~~~l~g---is~~~Ls~rL-----------k~Le~~glv~r~~~~~~p~~veY~LT~~G   75 (95)
T d2hzta1          25 KRTSELKRLMPN---ITQKMLTQQL-----------RELEADGVINRIVYNQVPPKVEYELSEYG   75 (95)
T ss_dssp             BCHHHHHHHCTT---SCHHHHHHHH-----------HHHHHTTSEEEEEECSSSCEEEEEECTTG
T ss_pred             CCHHHHHHHhhc---CChhHHHHHH-----------HHHHHhHHHhheeccccccchhhhhhhhH
Confidence            457888888886   8889999885           899999999876432  334457655444

>d1r8da_ a.6.1.3 (A:) Multidrug transporter activator MtaN {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: Putative DNA-binding domain
superfamily: Putative DNA-binding domain
family: DNA-binding N-terminal domain of transcription activators
domain: Multidrug transporter activator MtaN
species: Bacillus subtilis [TaxId: 1423]

Probab=87.17  E-value=0.23  Score=32.66  Aligned_cols=40  Identities=15%  Similarity=0.101  Sum_probs=33.1

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEEee-cCceEEEec
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK-HHAQVIYTR  130 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk-h~~q~IYtr  130 (139)
                      .|...||+.++|+.    ..||.-++.|||.++.+ .++.+.|+.
T Consensus         3 ytI~e~A~~~gvs~----~tlR~Ye~~GLl~p~~r~~~gyR~Y~~   43 (109)
T d1r8da_           3 YQVKQVAEISGVSI----RTLHHYDNIELLNPSALTDAGYRLYSD   43 (109)
T ss_dssp             BCHHHHHHHHSCCH----HHHHHHHHTTSSCCSEECTTCCEEBCH
T ss_pred             ccHHHHHHHHCcCH----HHHHHHHHcCCcCCcccCCcccccccH
Confidence            38899999999874    57999999999998754 467788885

>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=87.05  E-value=0.34  Score=34.29  Aligned_cols=34  Identities=15%  Similarity=0.048  Sum_probs=32.2

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      +|++.||+.+++.-+-.-++++.|+++|+|....
T Consensus        56 ~t~~~la~~~~l~~~tvs~~i~rL~~~gli~r~~   89 (162)
T d2fxaa1          56 ASISEIAKFGVMHVSTAFNFSKKLEERGYLRFSK   89 (162)
T ss_dssp             EEHHHHHHHTTCCHHHHHHHHHHHHHHTSEEEEC
T ss_pred             cCHHHHHHHHcCCchhhHHHHHHHHHCCCceeec
Confidence            7999999999999999999999999999998764

>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=86.80  E-value=0.62  Score=28.65  Aligned_cols=32  Identities=9%  Similarity=0.143  Sum_probs=30.2

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQ  118 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~  118 (139)
                      +|-..||+-++++-.-.-++|++|+++|+|..
T Consensus        30 lt~~eLA~~~G~sretvsr~L~~l~~~glI~~   61 (81)
T d2gaua1          30 LSREELATLSNMTVSNAIRTLSTFVSERMLAL   61 (81)
T ss_dssp             CCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence            78999999999999999999999999999864

>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=86.53  E-value=0.69  Score=32.95  Aligned_cols=33  Identities=27%  Similarity=0.205  Sum_probs=31.2

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      .|++.||++|+|+-+-.++=|+.|++.|+|...
T Consensus        29 ~~~~ela~~l~~s~~~v~~HL~~L~~~Glv~~~   61 (194)
T d2p4wa1          29 YFVSELSRELGVGQKAVLEHLRILEEAGLIESR   61 (194)
T ss_dssp             EEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEE
Confidence            599999999999999999999999999999865

>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=86.36  E-value=0.59  Score=29.13  Aligned_cols=31  Identities=26%  Similarity=0.281  Sum_probs=29.8

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCee
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIK  117 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk  117 (139)
                      +|-..||+-++++-.-.-++|++|+++|+|.
T Consensus        28 lt~~elA~~lg~sr~tvsr~l~~l~~~g~I~   58 (73)
T d1zyba1          28 VKMDDLARCLDDTRLNISKTLNELQDNGLIE   58 (73)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHHHHHTTSCE
T ss_pred             cCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            6999999999999999999999999999996

>d2fbka1 a.4.5.28 (A:8-179) Transcriptional regulator DR1159 {Deinococcus radiodurans [TaxId: 1299]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator DR1159
species: Deinococcus radiodurans [TaxId: 1299]

Probab=85.71  E-value=0.11  Score=36.84  Aligned_cols=34  Identities=26%  Similarity=0.452  Sum_probs=32.2

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      +|++.||++++|.-+-.-++|..|+++|+|....
T Consensus        80 lt~~eLa~~l~i~~~tvsr~l~~Le~~GlV~r~~  113 (172)
T d2fbka1          80 LRPTELSALAAISGPSTSNRIVRLLEKGLIERRE  113 (172)
T ss_dssp             BCHHHHHHHCSCCSGGGSSHHHHHHHHTSEECCC
T ss_pred             cCHHHHHHHHCcCHhHHHHHHHHHHhCCCeeeec
Confidence            7999999999999999999999999999999874

>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=85.69  E-value=0.57  Score=29.82  Aligned_cols=41  Identities=22%  Similarity=0.257  Sum_probs=34.8

Q ss_pred             HHhhCCCCeeechHHHHhhh-ccchHHHHHHHHHHHHcCCee
Q psy1871          77 LLKEVPAYKLITPSVVSERL-KVRGSLARKALEELLQKGLIK  117 (139)
Q Consensus        77 l~KEVpk~KlITPsvlseRl-kI~~SLARkaLreL~~kGlIk  117 (139)
                      +.+.-|.-.=|....|..+| ++..+-.+.++++|.+.|+|=
T Consensus        14 ~i~s~~~~eGi~~~el~~~l~~~~~~~i~~aid~L~~eG~IY   55 (69)
T d1dpua_          14 LIKACPRPEGLNFQDLKNQLKHMSVSSIKQAVDFLSNEGHIY   55 (69)
T ss_dssp             HHHHCCCTTTEEHHHHHHHSTTSCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHhCCCccCcCHHHHHHHccCCCHHHHHHHHHHHHhCCcee
Confidence            44555666668899999999 699999999999999999973

>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=83.48  E-value=0.63  Score=28.78  Aligned_cols=31  Identities=13%  Similarity=0.258  Sum_probs=29.7

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCee
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIK  117 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk  117 (139)
                      +|...||+-++++-.-.-++|.+|.++|+|.
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            6899999999999999999999999999986

>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=83.35  E-value=0.98  Score=30.07  Aligned_cols=45  Identities=18%  Similarity=0.205  Sum_probs=35.0

Q ss_pred             eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871          86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT  131 (139)
Q Consensus        86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra  131 (139)
                      =.|+..|++.++++-|..-.=|+.|.+-|+|..- +.++...|.-+
T Consensus        45 ~~~v~ela~~l~~s~s~vS~HL~~L~~aGlv~~~-r~G~~~~Y~l~   89 (108)
T d1u2wa1          45 ELCVCDIANILGVTIANASHHLRTLYKQGVVNFR-KEGKLALYSLG   89 (108)
T ss_dssp             CEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC-----CCEEEES
T ss_pred             CccHHHHHHHHccChhHHHHHHHHHHHCCeeEEE-EECCEEEEEEC
Confidence            3789999999999999999999999999998763 44555566543

>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=83.04  E-value=1.5  Score=28.51  Aligned_cols=44  Identities=20%  Similarity=0.262  Sum_probs=36.8

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT  131 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra  131 (139)
                      .|++.|++.++++-|..-.=|+.|.+-|+|.. .+..+...|.-+
T Consensus        32 ~~v~el~~~l~~s~~~vS~HL~~L~~~glv~~-~r~G~~~~Y~l~   75 (94)
T d1r1ua_          32 ASVGHISHQLNLSQSNVSHQLKLLKSVHLVKA-KRQGQSMIYSLD   75 (94)
T ss_dssp             BCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE-EEETTEEEEEES
T ss_pred             ccHHHHHHHHCCCHHHHHHHHHHHHHCCceEE-EEECCEEEEEEC
Confidence            57899999999999999999999999999975 455566666543

>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=82.28  E-value=0.98  Score=28.70  Aligned_cols=46  Identities=17%  Similarity=0.214  Sum_probs=38.0

Q ss_pred             CHHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871          70 DKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV  120 (139)
Q Consensus        70 Dk~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs  120 (139)
                      +=..+|.|. +-|    +|...||++.++.-..-+++||-|..-|++....
T Consensus        23 ~L~ifd~l~-~gp----~s~~eLA~~~g~~~~~l~rlLr~l~a~gl~~e~~   68 (85)
T d1tw3a1          23 TLRLVDHIL-AGA----RTVKALAARTDTRPEALLRLIRHLVAIGLLEEDA   68 (85)
T ss_dssp             HTTHHHHHH-TTC----CBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HcCcHHHhc-cCC----CCHHHHHHHhCcChhHHHHHHHHHHHCCCeEecC
Confidence            335677774 334    6999999999999999999999999999997644

>d1q1ha_ a.4.5.41 (A:) Transcription factor E/IIe-alpha, N-terminal domain {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcription factor E/IIe-alpha, N-terminal domain
domain: Transcription factor E/IIe-alpha, N-terminal domain
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=81.80  E-value=0.62  Score=31.25  Aligned_cols=35  Identities=20%  Similarity=0.315  Sum_probs=32.3

Q ss_pred             eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871          85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQV  119 (139)
Q Consensus        85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V  119 (139)
                      .=||--.||+.++|+...-|++|-.|.+.||+.-+
T Consensus        32 ~evtDe~iA~~tgi~in~VRk~Ly~L~~~~L~~y~   66 (88)
T d1q1ha_          32 TEMTDEEIANQLNIKVNDVRKKLNLLEEQGFVSYR   66 (88)
T ss_dssp             SCBCHHHHHHTTTSCHHHHHHHHHHHHHHTSCEEE
T ss_pred             CcCCHHHHHHHhCCcHHHHHHHHHHHHhCCceEEE
Confidence            35789999999999999999999999999999776

>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=81.63  E-value=0.74  Score=28.51  Aligned_cols=32  Identities=19%  Similarity=0.324  Sum_probs=30.2

Q ss_pred             echHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871          87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQ  118 (139)
Q Consensus        87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~  118 (139)
                      +|-..||+-++++-.-.=++|++|.++|+|..
T Consensus        31 ~t~~eiA~~lG~sretvsr~l~~l~~~g~I~~   62 (80)
T d1ft9a1          31 FTVEEIANLIGSSRQTTSTALNSLIKEGYISR   62 (80)
T ss_dssp             CCHHHHHHHHCSCHHHHHHHHHHHHHTTSSEE
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence            68889999999999999999999999999875

>d1ldja1 a.4.5.34 (A:687-776) Anaphase promoting complex (APC) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: SCF ubiquitin ligase complex WHB domain
domain: Anaphase promoting complex (APC)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.16  E-value=0.99  Score=29.67  Aligned_cols=40  Identities=23%  Similarity=0.371  Sum_probs=35.8

Q ss_pred             HHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEe
Q psy1871          90 SVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYT  129 (139)
Q Consensus        90 svlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYt  129 (139)
                      ..+..+|..+.+.-++.|..|-++|.|.....++...+|.
T Consensus        50 ~~l~~~F~p~~~~iK~~Ie~LIereYi~R~~~~~~~y~Yv   89 (90)
T d1ldja1          50 TQLSSRFKPRVPVIKKCIDILIEKEYLERVDGEKDTYSYL   89 (90)
T ss_dssp             HHHTTTCCCCHHHHHHHHHHHHHTTSEEECSSSTTEEEEC
T ss_pred             HHHhccCCCCHHHHHHHHHHHHhhHHHhcCCCCCceeeee
Confidence            4667789999999999999999999999988888888885

>d1ufma_ a.4.5.47 (A:) COP9 signalosome complex subunit 4, GSN4 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PCI domain (PINT motif)
domain: COP9 signalosome complex subunit 4, GSN4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=80.83  E-value=3.1  Score=26.57  Aligned_cols=50  Identities=16%  Similarity=0.268  Sum_probs=41.3

Q ss_pred             CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEeccCC
Q psy1871          84 YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTTK  133 (139)
Q Consensus        84 ~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra~k  133 (139)
                      |.-|+-..||+.|++...-+-..|.+|-..|.|.--.-+....||....+
T Consensus        28 Y~~Isl~~la~~l~l~~~evE~~l~~mI~~~~i~akIDq~~g~V~F~~~e   77 (84)
T d1ufma_          28 YNNITFEELGALLEIPAAKAEKIASQMITEGRMNGFIDQIDGIVHFETRE   77 (84)
T ss_dssp             CSEEEHHHHHHHTTSCHHHHHHHHHHHHHTTSSCEEEETTTTEEEECCSS
T ss_pred             hceeeHHHHHHHHCCCHHHHHHHHHHHHhcCeEEEEEeCCCCEEEECCCC
Confidence            78899999999999999999999999999999988654445556554443