Citrus Sinensis ID: 040869

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-
Protein Sequence
MDANQDQGAKELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIKDKPYCMSPTVSAFVDPLFVAPFQSL
Secondary Structure (PSIPRED)
ccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcHHHHHHHccccccHHHHHHHccccccccccHHHHHHHHHHcccccEEccccccccEEcccccccccccccccHHHHHHHHcccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHcccccccHHHHHHHccccccccHHHHHHHHHHHHcccEEEEcccccccEEEEccHHHHHccccccccHHHHHHHccccccccHHcc
Coil and Loop (DISEMBL)
MDANQDQGAKELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVsaldiqptkttGLFRLMRLLVHSScfnktkvngqeeaygLTAASTLLikdkpycmsptvsafvdplfvapfqsl
Flexible Loop (DISEMBL)
MDANQDQGAKELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIKDKPYCMSPTVSAFVDPLFVAPFQSL
Low Complexity Region (SEG)
MDANQDQGAKELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIKDKPYCMSPTVSAFVDPLFVAPFQSL
Disordered region (IsUnstruct)
**************GQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIKDKPYCMSPTVSAFVDPLFVAP****
Disordered Region (DISOPRED)
***************QAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIKDKPYCMSPTVSAFVDPLFVAPFQSL
Disordered Region (DISEMBL)
*********KELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIKDKPYCMSPTVSAFVDPLFVAPFQSL
Disordered Region (DISPRO)
*******GAKELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIKDKPYCMSPTVSAFVDPLFVAPFQS*
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDANQDQGAKELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIKDKPYCMSPTVSAFVDPLFVAPFQSL
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	131	2.2.26 [Sep-21-2011]
B6VJS4	357	Trans-resveratrol di-O-me	no	no	1.0	0.366	0.436	2e-25
Q84KK4	365	Isoflavone 4'-O-methyltra	N/A	no	0.931	0.334	0.480	3e-25
Q93WU2	357	Eugenol O-methyltransfera	N/A	no	0.931	0.341	0.447	1e-24
Q6VMW0	366	8-hydroxyquercetin 8-O-me	N/A	no	0.931	0.333	0.442	2e-24
Q84KK6	367	Isoflavone 4'-O-methyltra	N/A	no	0.854	0.305	0.479	2e-24
Q93WU3	356	Chavicol O-methyltransfer	N/A	no	0.931	0.342	0.442	4e-24
P0DH60	360	6a-hydroxymaackiain methy	N/A	no	0.862	0.313	0.478	2e-23
Q84KK5	357	Isoflavone 7-O-methyltran	N/A	no	0.923	0.338	0.411	3e-23
C6TAY1	358	Flavonoid 4'-O-methyltran	no	no	0.908	0.332	0.462	2e-22
O24305	360	6a-hydroxymaackiain methy	N/A	no	0.854	0.311	0.474	7e-22

>sp|B6VJS4|ROMT_VITVI Trans-resveratrol di-O-methyltransferase OS=Vitis vinifera GN=ROMT PE=1 SV=2

 Score =  114 bits (284), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 58/133 (43%), Positives = 82/133 (61%), Gaps = 2/133 (1%)

Query: 1   MDANQDQGAKELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSAL 60
           MD      + ELL  QA ++  +F+ + SMSLKCAI+LGI DIIH+HG+ +TL ELV+ L
Sbjct: 1   MDLANGVISAELLHAQAHVWNHIFNFIKSMSLKCAIQLGIPDIIHNHGKPMTLPELVAKL 60

Query: 61  DIQPTKTTGLFRLMRLLVHSSCFNKTKV--NGQEEAYGLTAASTLLIKDKPYCMSPTVSA 118
            + P ++  ++RLMR+LVHS      +V    +EE Y LT AS LL+ D    + P V A
Sbjct: 61  PVHPKRSQCVYRLMRILVHSGFLAAQRVQQGKEEEGYVLTDASRLLLMDDSLSIRPLVLA 120

Query: 119 FVDPLFVAPFQSL 131
            +DP+   P+  L
Sbjct: 121 MLDPILTKPWHYL 133

Catalyzes the biosynthesis of pterostilbene from resveratrol. Pterostilbene has both antifungal and pharmacological properties. Also has activity toward resveratrol monomethyl ether (RME).
Vitis vinifera (taxid: 29760)
EC: 2EC: .EC: 1EC: .EC: 1EC: .EC: 2EC: 4EC: 0

>sp|Q84KK4|I4OMT_LOTJA Isoflavone 4'-O-methyltransferase OS=Lotus japonicus GN=HI4'OMT PE=1 SV=1

 Score =  113 bits (282), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 62/129 (48%), Positives = 85/129 (65%), Gaps = 7/129 (5%)

Query: 1   MDANQDQGAK--ELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVS 58
           MD +   G++  EL Q Q  LYK +++ +SSM+LK A+ELGIAD+IHSHG+ ITL EL +
Sbjct: 1   MDFSSSNGSEDTELSQAQIHLYKHVYNFVSSMALKSAMELGIADVIHSHGKPITLPELAT 60

Query: 59  ALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN---GQEE--AYGLTAASTLLIKDKPYCMS 113
           AL+++P+K   L R +RLL H+  F KT V+   G EE  AYGLT  S LL+K    C++
Sbjct: 61  ALNLRPSKIGVLHRFLRLLTHNGFFAKTTVSRGEGAEEETAYGLTPPSKLLVKSNSTCLA 120

Query: 114 PTVSAFVDP 122
           P V   + P
Sbjct: 121 PIVKGALHP 129

2-hydroxyisoflavanone 4'-O-methyltransferase involved in the biosynthesis of formononetin. Can use 2,7,4'-trihydroxyisoflavanone as substrate, but not daidzein.

Lotus japonicus (taxid: 34305)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 2

EC: 1

EC: 2

>sp|Q93WU2|EOMT1_OCIBA Eugenol O-methyltransferase OS=Ocimum basilicum GN=EOMT1 PE=1 SV=1

 Score =  111 bits (278), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 55/123 (44%), Positives = 79/123 (64%), Gaps = 1/123 (0%)

Query: 10  KELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTG 69
           ++LLQ Q  ++  M++  +SMSLKCAI+LGI DI+H HGR +TLS+L+ ++ I   KT  
Sbjct: 13  EQLLQAQVHVWNHMYAFANSMSLKCAIQLGIPDILHKHGRPMTLSQLLQSIPINKEKTQC 72

Query: 70  LFRLMRLLVHSSCF-NKTKVNGQEEAYGLTAASTLLIKDKPYCMSPTVSAFVDPLFVAPF 128
             RLMR LV+S+ F  +   N QE  Y LT AS LL+K+ P  ++P V   +DP F  P+
Sbjct: 73  FQRLMRALVNSNFFIEENNSNNQEVCYWLTPASCLLLKEAPLTVTPLVQVVLDPTFTNPW 132

Query: 129 QSL 131
             +
Sbjct: 133 HHM 135

Phenylpropene O-methyltransferase that catalyzes the methylation of the para-4-hydroxyl of eugenol to methyleugenol. Can also convert chavicol to methylchavicol but with less affinity.

Ocimum basilicum (taxid: 39350)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 1

EC: 4

EC: 6

>sp|Q6VMW0|Q8OMT_MENPI 8-hydroxyquercetin 8-O-methyltransferase OS=Mentha piperita GN=OMT2 PE=1 SV=1

 Score =  110 bits (276), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 58/131 (44%), Positives = 83/131 (63%), Gaps = 9/131 (6%)

Query: 10  KELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTG 69
           +ELL+ QA ++  ++S+++SMSLKCAI+LGI D IH HG  ITLS+L  AL+I   K+ G
Sbjct: 11  QELLEAQAHVWNHIYSYINSMSLKCAIQLGIPDAIHKHGNPITLSQLADALNINKAKSHG 70

Query: 70  LFRLMRLLVHSSCFN---------KTKVNGQEEAYGLTAASTLLIKDKPYCMSPTVSAFV 120
           LFRLMR+LVHS  F+               +E+AY LT AS LL++ +P  ++P   A  
Sbjct: 71  LFRLMRILVHSGFFDKVKVKVKVEGEDEEEEEDAYSLTPASRLLLRSEPLSVAPFALAMS 130

Query: 121 DPLFVAPFQSL 131
           DP++   +  L
Sbjct: 131 DPVYTETWHHL 141

8-O-methyltransferase active on various hydroxylated flavonoid substrates, including 7,8,3'4'-tetrahydroxy-flavone, 7,8,4'-trihydroxy-flavone and 8-hydroxy-flavone 7-methyl ether.

Mentha piperita (taxid: 34256)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 8

EC: 8

>sp|Q84KK6|I4OMT_GLYEC Isoflavone 4'-O-methyltransferase OS=Glycyrrhiza echinata GN=HI4'OMT PE=1 SV=1

 Score =  110 bits (275), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 58/121 (47%), Positives = 78/121 (64%), Gaps = 9/121 (7%)

Query: 11  ELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGL 70
           EL   Q  LYK +++ +SSM+LK A+ELGIAD+IH+HG+ ITL EL SAL + P+K   L
Sbjct: 12  ELYHAQIHLYKHVYNFVSSMALKSAMELGIADVIHNHGKPITLPELASALKLHPSKVGIL 71

Query: 71  FRLMRLLVHSSCFNKTKV------NGQEE---AYGLTAASTLLIKDKPYCMSPTVSAFVD 121
           +R +RLL H+  F KT V      +G+EE   AY LT  S LL+K KP C++  V   + 
Sbjct: 72  YRFLRLLTHNGFFAKTTVPSQNGKDGEEEEETAYALTPPSKLLVKGKPTCLASIVRGALH 131

Query: 122 P 122
           P
Sbjct: 132 P 132

2-hydroxyisoflavanone 4'-O-methyltransferase involved in the biosynthesis of formononetin. Can use 2,7,4'-trihydroxyisoflavanone, (+)-6a-hydroxymaackiain or medicarpin as substrate, but not daidzein or (-)-6a-hydroxymaackiain.

Glycyrrhiza echinata (taxid: 46348)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 2

EC: 1

EC: 2

>sp|Q93WU3|CVMT1_OCIBA Chavicol O-methyltransferase OS=Ocimum basilicum GN=CVOMT1 PE=1 SV=1

 Score =  110 bits (274), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 54/122 (44%), Positives = 77/122 (63%)

Query: 10  KELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTG 69
           ++LLQ QA ++  M++  +SMSLKCAI+LGI DI+H H   +TLS+L+ A+ I   K+  
Sbjct: 13  EQLLQAQAHVWNHMYAFANSMSLKCAIQLGIPDILHKHDHPMTLSQLLKAIPINKEKSQS 72

Query: 70  LFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIKDKPYCMSPTVSAFVDPLFVAPFQ 129
             RLMR LV+S+ F +   N QE  Y LT AS LL+K  P  ++P V   +DP F  P+ 
Sbjct: 73  FQRLMRALVNSNFFIEENSNNQEVCYWLTPASRLLLKGAPLTVAPLVQVVLDPTFTNPWH 132

Query: 130 SL 131
            +
Sbjct: 133 YM 134

Phenylpropene O-methyltransferase that catalyzes the methylation of the para-4-hydroxyl of chavicol to methylchavicol. Can also convert eugenol to methyleugenol but with less affinity.

Ocimum basilicum (taxid: 39350)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 1

EC: 4

EC: 6

>sp|P0DH60|M3OM2_PEA 6a-hydroxymaackiain methyltransferase 2 OS=Pisum sativum GN=HMM2 PE=1 SV=1

 Score =  107 bits (268), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 56/117 (47%), Positives = 77/117 (65%), Gaps = 4/117 (3%)

Query: 11  ELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGL 70
           EL   Q  LYK +++ +SSM+LK A+ELGIAD IH+HG+ +TL EL S+L + P+K   L
Sbjct: 12  ELYHAQIHLYKHIYNFVSSMALKSAVELGIADAIHNHGKPMTLPELASSLKLHPSKVNIL 71

Query: 71  FRLMRLLVHSSCFNKTKV--NGQEE--AYGLTAASTLLIKDKPYCMSPTVSAFVDPL 123
           +R +RLL H+  F KT V  NG+EE  AY LT +S LL+  K  C+S  V   + P+
Sbjct: 72  YRFLRLLTHNGFFAKTTVKSNGEEEETAYVLTPSSKLLVSGKSTCLSSVVKGALHPI 128

3-O-methyltransferase involved in the phytoalexin pisatin biosynthesis. Can use (+)-6a-hydroxymaackiain, (+)-maackiain and with a lower activity (+)-medicarpin and 2,7,4'-trihydroxyisoflavanone as substrates, but not (-)-6a-hydroxymaackiain, daidzein, formononetin or isoliquiritigenin.

Pisum sativum (taxid: 3888)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: -

>sp|Q84KK5|D7OMT_GLYEC Isoflavone 7-O-methyltransferase OS=Glycyrrhiza echinata GN=D7OMT PE=1 SV=1

 Score =  106 bits (265), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 51/124 (41%), Positives = 77/124 (62%), Gaps = 3/124 (2%)

Query: 11  ELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGL 70
           E+ QGQA LY+ +++ + SM LK  +EL I +IIH+HG+ IT+SELVS L +  TK   +
Sbjct: 12  EIFQGQALLYRHIYAFIDSMCLKWIVELDIPNIIHNHGKPITVSELVSILKVPQTKAGNV 71

Query: 71  FRLMRLLVHSSCFNKTKVNGQE---EAYGLTAASTLLIKDKPYCMSPTVSAFVDPLFVAP 127
            R+MR + H+  F + ++  ++   EAY LTAAS LL+K    C++P V   +DP     
Sbjct: 72  QRIMRYMAHNGFFERVRIQEEQEENEAYALTAASELLVKGSELCLAPMVECVLDPTLSGS 131

Query: 128 FQSL 131
           +  L
Sbjct: 132 YHQL 135

7-O-methyltransferase involved in the biosynthesis of isoformononetin. Can use daidzein as substrate, but not medicarpin or 2,7,4'-trihydroxyisoflavanone.

Glycyrrhiza echinata (taxid: 46348)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 1

EC: 5

EC: 0

>sp|C6TAY1|SOMT2_SOYBN Flavonoid 4'-O-methyltransferase OS=Glycine max PE=1 SV=1

 Score =  104 bits (259), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 56/121 (46%), Positives = 73/121 (60%), Gaps = 2/121 (1%)

Query: 4   NQDQGAKELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSH--GRAITLSELVSALD 61
           N  + A E+ QGQA LYK +   + S  LK  +EL I DIIHSH  G+ IT SELVS L 
Sbjct: 6   NNGRKASEIFQGQALLYKHLLGFIDSKCLKWMVELDIPDIIHSHSHGQPITFSELVSILQ 65

Query: 62  IQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIKDKPYCMSPTVSAFVD 121
           + PTKT  +  LMR L H+  F   +++   EAY LTAAS LL+K     ++P V  F++
Sbjct: 66  VPPTKTRQVQSLMRYLAHNGFFEIVRIHDNIEAYALTAASELLVKSSELSLAPMVEYFLE 125

Query: 122 P 122
           P
Sbjct: 126 P 126

S-adenosyl-L-methionine-dependent methyltransferase that catalyzes the 4'-methylation of naringenin (4',5,7-trihydroxyflavanone) into ponciretin (4'-methoxy-5,7-dihydroxyflavanone). In vitro, also able to convert apigenin, daidzein, genistein and quercetin into the 4'-O-methylated compounds acacetin, formononetin, biochanine A and 4'-methylated quercetin, respectively.

Glycine max (taxid: 3847)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 2

EC: 3

EC: 1

>sp|O24305|M3OM1_PEA 6a-hydroxymaackiain methyltransferase 1 OS=Pisum sativum GN=HMM1 PE=1 SV=1

 Score =  102 bits (254), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 55/116 (47%), Positives = 75/116 (64%), Gaps = 4/116 (3%)

Query: 11  ELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGL 70
           EL   Q  LYK +++ +SSM+LK A+ELGIAD IH+HG+ +TL EL S+L + P+K   L
Sbjct: 12  ELYHAQIHLYKHVYNFVSSMALKSAMELGIADAIHNHGKPMTLPELSSSLKLHPSKVNIL 71

Query: 71  FRLMRLLVHSSCFNKTKV---NGQEE-AYGLTAASTLLIKDKPYCMSPTVSAFVDP 122
           +R +RLL H+  F KT V    G+EE AY LT +S LL+  K  C+S  V   + P
Sbjct: 72  YRFLRLLTHNGFFAKTTVKSNEGEEETAYVLTPSSKLLVSGKSTCLSSLVKGALHP 127

Methyltransferase involved in the phytoalexin pisatin biosynthesis. Has both 3- and 4'-O-methyltransferase activities. Can use (+)-6a-hydroxymaackiain, 2,7,4'-trihydroxyisoflavanone and with much less activity (+)-medicarpin as substrates, but not (-)-6a-hydroxymaackiain, daidzein, formononetin or isoliquiritigenin. May be involved in formononetin biosynthesis.

Pisum sativum (taxid: 3888)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 4

EC: 6

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	131
255562994	359	o-methyltransferase, putative [Ricinus c	0.969	0.353	0.541	7e-32
224116348	372	flavonoid o-methyltransferase related [P	0.992	0.349	0.540	8e-31
224077038	359	flavonoid o-methyltransferase related [P	0.961	0.350	0.537	3e-30
147826880	328	hypothetical protein VITISV_021918 [Viti	0.954	0.381	0.503	8e-29
255563164	355	o-methyltransferase, putative [Ricinus c	0.961	0.354	0.515	1e-28
255568371	356	o-methyltransferase, putative [Ricinus c	0.984	0.362	0.488	1e-28
225446489	357	PREDICTED: 8-hydroxyquercetin 8-O-methyl	0.938	0.344	0.504	1e-28
224146520	357	flavonoid o-methyltransferase related [P	0.908	0.333	0.504	2e-28
345461935	365	desoxyhemigossypol-6-O-methyltransferase	0.954	0.342	0.468	2e-27
55163142	346	putative orcinol O-methyltransferase [Ro	0.954	0.361	0.5	2e-27

>gi|255562994|ref|XP_002522501.1| o-methyltransferase, putative [Ricinus communis] gi|223538192|gb|EEF39801.1| o-methyltransferase, putative [Ricinus communis]

 Score =  141 bits (356), Expect = 7e-32,   Method: Compositional matrix adjust.
 Identities = 71/131 (54%), Positives = 90/131 (68%), Gaps = 4/131 (3%)

Query: 1   MDANQDQGAKELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSAL 60
           MD+   Q A ELLQ Q  +Y  +F++++SM LKCA++LGI DIIH HG+ ITL ELVSAL
Sbjct: 1   MDSTDSQKATELLQAQLHVYNHIFNYINSMCLKCAVQLGIPDIIHKHGKPITLPELVSAL 60

Query: 61  DIQPTKTTGLFRLMRLLVHSSCFNKTK-VNGQEEA---YGLTAASTLLIKDKPYCMSPTV 116
            I PTK   ++RLMR+LVHS  F+ TK  NGQEE    Y LT +S LL+KD P C+ P V
Sbjct: 61  HIHPTKINFMYRLMRMLVHSGFFSITKAANGQEEGQEVYVLTPSSKLLVKDNPNCLKPFV 120

Query: 117 SAFVDPLFVAP 127
            + + P FV P
Sbjct: 121 DSLLKPDFVTP 131

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224116348|ref|XP_002331960.1| flavonoid o-methyltransferase related [Populus trichocarpa] gi|222874737|gb|EEF11868.1| flavonoid o-methyltransferase related [Populus trichocarpa]

 Score =  138 bits (347), Expect = 8e-31,   Method: Compositional matrix adjust.
 Identities = 73/135 (54%), Positives = 91/135 (67%), Gaps = 5/135 (3%)

Query: 1   MDANQDQGAKELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSAL 60
           +D  Q+Q A EL Q Q  LY  MF++L+SMSL CA +LGI DIIH+HGR ITL ELVSAL
Sbjct: 16  IDPIQEQKATELFQAQTHLYGQMFNYLNSMSLVCAAQLGIPDIIHNHGRPITLPELVSAL 75

Query: 61  DIQPTKTTGLFRLMRLLVHSSCFNKTKV----NGQEEAYGLTAASTLLIKDKPYCMSPTV 116
            I P K++ ++RLMR+LVHS  F  TK      G  EAY LT  S LL+KD   C+SP +
Sbjct: 76  HIPPNKSSCIYRLMRMLVHSGFFATTKAVIGQGGGGEAYVLTPPSQLLVKDNTNCLSPFM 135

Query: 117 SAFVDPLFVAPFQSL 131
           S  ++P FV P+ SL
Sbjct: 136 S-LINPAFVTPWHSL 149

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224077038|ref|XP_002305103.1| flavonoid o-methyltransferase related [Populus trichocarpa] gi|222848067|gb|EEE85614.1| flavonoid o-methyltransferase related [Populus trichocarpa]

 Score =  136 bits (342), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 71/132 (53%), Positives = 89/132 (67%), Gaps = 6/132 (4%)

Query: 5   QDQGAKELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQP 64
           QDQ A EL Q    L+  MF++++SMSL CA +LGI DIIH+HGR ITL  LVSAL I P
Sbjct: 6   QDQKATELFQAHTHLHSQMFNYINSMSLMCAAQLGIPDIIHNHGRPITLPHLVSALHIAP 65

Query: 65  TKTTGLFRLMRLLVHSSCFNKTKV-----NGQEEAYGLTAASTLLIKDKPYCMSPTVSAF 119
            KT+ ++RLMR+LVHS  F  TK       G+EEAY LT  S LL+KD   C+SP +S  
Sbjct: 66  NKTSIIYRLMRMLVHSGFFATTKAANGQGEGEEEAYVLTPPSQLLVKDNTNCLSPFMS-L 124

Query: 120 VDPLFVAPFQSL 131
           ++P FV P+ SL
Sbjct: 125 INPAFVTPWLSL 136

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147826880|emb|CAN73270.1| hypothetical protein VITISV_021918 [Vitis vinifera]

 Score =  131 bits (330), Expect = 8e-29,   Method: Compositional matrix adjust.
 Identities = 64/127 (50%), Positives = 88/127 (69%), Gaps = 2/127 (1%)

Query: 7   QGAKELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTK 66
           + + ELL   A ++  +F+ ++SMSLKCAIELGI DIIH+HG+ +TLSELV+ L + P K
Sbjct: 7   ETSTELLHAHAHVWNHIFNFINSMSLKCAIELGIPDIIHNHGKPMTLSELVAELPVNPEK 66

Query: 67  TTGLFRLMRLLVHSSCFNKTKV--NGQEEAYGLTAASTLLIKDKPYCMSPTVSAFVDPLF 124
           T  ++RLMRLLV S  F + +V  +GQEE Y LT AS LL+KD P    P + A +DP+ 
Sbjct: 67  TKCVYRLMRLLVQSGFFTRKRVQESGQEEGYVLTHASRLLLKDDPLSARPFLLAMLDPVL 126

Query: 125 VAPFQSL 131
           + P+Q L
Sbjct: 127 ITPWQYL 133

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255563164|ref|XP_002522586.1| o-methyltransferase, putative [Ricinus communis] gi|223538277|gb|EEF39886.1| o-methyltransferase, putative [Ricinus communis]

 Score =  131 bits (329), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 65/126 (51%), Positives = 89/126 (70%)

Query: 1   MDANQDQGAKELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSAL 60
           MD+ Q   A +LLQ Q  +Y  +F++L+SM LKC+++LGI DII +HG+ ITL ELVSAL
Sbjct: 1   MDSVQSPKATDLLQAQTHIYNHIFNNLNSMCLKCSVQLGIPDIIQNHGKPITLPELVSAL 60

Query: 61  DIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIKDKPYCMSPTVSAFV 120
           +I P KTT L+RLMR+LV+S  F  T+    +EAY LT ++ LL+KD P C+S  V A +
Sbjct: 61  NIHPGKTTCLYRLMRMLVYSGFFVTTETPDGQEAYDLTPSTRLLVKDNPNCLSSFVIALL 120

Query: 121 DPLFVA 126
            P +VA
Sbjct: 121 WPDYVA 126

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255568371|ref|XP_002525160.1| o-methyltransferase, putative [Ricinus communis] gi|223535619|gb|EEF37287.1| o-methyltransferase, putative [Ricinus communis]

 Score =  131 bits (329), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 64/131 (48%), Positives = 89/131 (67%), Gaps = 2/131 (1%)

Query: 3   ANQDQGAKELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDI 62
           A+    A ELLQ QA ++  +FS ++SMSLK A++LGI D IHSHGR I+LS+L++AL I
Sbjct: 2   ADGKYDANELLQAQAHIWNHIFSFINSMSLKSAVQLGIPDAIHSHGRPISLSQLIAALPI 61

Query: 63  QPTKTTGLFRLMRLLVHSSCFNKTKVN--GQEEAYGLTAASTLLIKDKPYCMSPTVSAFV 120
            P K  G+ RLMR+L+HS  F K K+    +EE Y LT AS LL+KD P  ++P + A +
Sbjct: 62  HPAKARGIPRLMRILIHSGFFAKAKIEEKDEEEGYVLTNASKLLLKDNPLSIAPFLLAML 121

Query: 121 DPLFVAPFQSL 131
           DP+ + P+  L
Sbjct: 122 DPILIKPWHYL 132

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225446489|ref|XP_002278190.1| PREDICTED: 8-hydroxyquercetin 8-O-methyltransferase [Vitis vinifera]

 Score =  130 bits (328), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 63/125 (50%), Positives = 87/125 (69%), Gaps = 2/125 (1%)

Query: 7   QGAKELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTK 66
           + + ELL   A ++  +F+ ++SMSLKCAIELGI DIIH+HG+ +TLSELV+ L + P K
Sbjct: 7   ETSTELLHAHAHVWNHIFNFINSMSLKCAIELGIPDIIHNHGKPMTLSELVAELPVNPEK 66

Query: 67  TTGLFRLMRLLVHSSCFNKTKV--NGQEEAYGLTAASTLLIKDKPYCMSPTVSAFVDPLF 124
           T  ++RLMRLLV S  F + +V  +GQEE Y LT AS LL+KD P    P + A +DP+ 
Sbjct: 67  TKCVYRLMRLLVQSGFFTRKRVQESGQEEGYVLTHASRLLLKDDPLSARPFLLAMLDPVL 126

Query: 125 VAPFQ 129
           + P+Q
Sbjct: 127 ITPWQ 131

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224146520|ref|XP_002326036.1| flavonoid o-methyltransferase related [Populus trichocarpa] gi|222862911|gb|EEF00418.1| flavonoid o-methyltransferase related [Populus trichocarpa]

 Score =  130 bits (326), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 61/121 (50%), Positives = 86/121 (71%), Gaps = 2/121 (1%)

Query: 11  ELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGL 70
           ELLQ QA ++  +F+ ++SMSLKCAI+LGI D+IH+HG+ +TLSELV+ L I P+K  G+
Sbjct: 12  ELLQAQAHVWNHIFNFVNSMSLKCAIQLGIPDVIHNHGKPMTLSELVAVLPIHPSKAPGI 71

Query: 71  FRLMRLLVHSSCFNKTKVNGQEEAYG--LTAASTLLIKDKPYCMSPTVSAFVDPLFVAPF 128
           +RLMR+LVHS  F     +G+ E  G  LT AS LLIKD P+ ++P + A +DP+   P+
Sbjct: 72  YRLMRILVHSGFFATQNNSGETEGEGYVLTNASQLLIKDNPFSVTPFLLAMLDPILTQPW 131

Query: 129 Q 129
            
Sbjct: 132 H 132

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|345461935|gb|AEN94899.1| desoxyhemigossypol-6-O-methyltransferase [Gossypium barbadense]

 Score =  127 bits (318), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 60/128 (46%), Positives = 91/128 (71%), Gaps = 3/128 (2%)

Query: 7   QGAKELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDI-QPT 65
           + A E LQ QA +++  F+ +S MSLKCA++LGI DIIH HG+ +T+++LV+AL I  PT
Sbjct: 9   EDAIEALQSQAHIWRHAFNFVSFMSLKCALDLGILDIIHDHGKPMTITQLVAALQILNPT 68

Query: 66  KTTGLFRLMRLLVHSSCFNKTKVNG--QEEAYGLTAASTLLIKDKPYCMSPTVSAFVDPL 123
           K   ++RLMR+LVHS  F + K++   QEE Y LT +S +L+K+ P+C++PT+ A +DP+
Sbjct: 69  KACDIYRLMRILVHSDFFARQKLDNDAQEEGYVLTNSSRILLKNNPFCITPTLKATMDPI 128

Query: 124 FVAPFQSL 131
              P+  L
Sbjct: 129 ITKPWSFL 136

Source: Gossypium barbadense

Species: Gossypium barbadense

Genus: Gossypium

Family: Malvaceae

Order: Malvales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|55163142|emb|CAH05089.1| putative orcinol O-methyltransferase [Rosa odorata var. gigantea]

 Score =  127 bits (318), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 63/126 (50%), Positives = 87/126 (69%), Gaps = 1/126 (0%)

Query: 7   QGAKELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTK 66
           + + ELL  QA ++  +FS ++SMSLK AI+LGI DII+ HG  +TLSEL SAL I PTK
Sbjct: 7   EHSNELLHAQAHIWNHIFSFINSMSLKSAIQLGIPDIINKHGYPMTLSELTSALPIHPTK 66

Query: 67  TTGLFRLMRLLVHSSCFNKTKVNG-QEEAYGLTAASTLLIKDKPYCMSPTVSAFVDPLFV 125
           +  ++RLMR+LVHS  F K K++   EE Y LT AS LL+KD P  ++P ++A +DP+  
Sbjct: 67  SHSVYRLMRILVHSGFFAKKKLSKTDEEGYTLTNASQLLLKDHPLSLTPFLTAMLDPVLT 126

Query: 126 APFQSL 131
            P+  L
Sbjct: 127 KPWNYL 132

Source: Rosa odorata var. gigantea

Species: Rosa odorata

Genus: Rosa

Family: Rosaceae

Order: Rosales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	131
UNIPROTKB|Q6VMW0	366	OMT2 "8-hydroxyquercetin 8-O-m	0.931	0.333	0.473	1.4e-25
UNIPROTKB|Q84KK4	365	HI4'OMT "Isoflavone 4'-O-methy	0.931	0.334	0.480	2.6e-24
UNIPROTKB|Q84KK6	367	HI4'OMT "Isoflavone 4'-O-methy	0.854	0.305	0.479	2.1e-22
UNIPROTKB|Q84KK5	357	D7OMT "Isoflavone 7-O-methyltr	0.984	0.361	0.402	4.3e-22
UNIPROTKB|B0EXJ8	355	16OMT "Tabersonine 16-O-methyl	0.961	0.354	0.372	1.8e-17
UNIPROTKB|Q8GSN1	348	Q8GSN1 "Myricetin O-methyltran	0.740	0.278	0.415	6.4e-16
UNIPROTKB|A8QW53	374	OMT3 "5-pentadecatrienyl resor	0.923	0.323	0.323	3.1e-13
TAIR|locus:2132806	382	AT4G35160 [Arabidopsis thalian	0.969	0.332	0.306	9.3e-07
TAIR|locus:2132801	325	AT4G35150 [Arabidopsis thalian	0.763	0.307	0.3	8.5e-06
TAIR|locus:2153423	363	OMT1 "AT5G54160" [Arabidopsis	0.748	0.269	0.295	0.00089

UNIPROTKB|Q6VMW0 OMT2 "8-hydroxyquercetin 8-O-methyltransferase" [Mentha x piperita (taxid:34256)]

 Score = 290 (107.1 bits), Expect = 1.4e-25, P = 1.4e-25
 Identities = 62/131 (47%), Positives = 87/131 (66%)

Query:    10 KELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTG 69
             +ELL+ QA ++  ++S+++SMSLKCAI+LGI D IH HG  ITLS+L  AL+I   K+ G
Sbjct:    11 QELLEAQAHVWNHIYSYINSMSLKCAIQLGIPDAIHKHGNPITLSQLADALNINKAKSHG 70

Query:    70 LFRLMRLLVHSSCFNKTKVN----GQEE-----AYGLTAASTLLIKDKPYCMSPTVSAFV 120
             LFRLMR+LVHS  F+K KV     G++E     AY LT AS LL++ +P  ++P   A  
Sbjct:    71 LFRLMRILVHSGFFDKVKVKVKVEGEDEEEEEDAYSLTPASRLLLRSEPLSVAPFALAMS 130

Query:   121 DPLFVAPFQSL 131
             DP++   +  L
Sbjct:   131 DPVYTETWHHL 141

GO:0009812 "flavonoid metabolic process" evidence=IDA

GO:0030761 "8-hydroxyquercitin 8-O-methyltransferase activity" evidence=IDA

GO:0032259 "methylation" evidence=IDA

UNIPROTKB|Q84KK4 HI4'OMT "Isoflavone 4'-O-methyltransferase" [Lotus japonicus (taxid:34305)]

 Score = 278 (102.9 bits), Expect = 2.6e-24, P = 2.6e-24
 Identities = 62/129 (48%), Positives = 85/129 (65%)

Query:     1 MDANQDQGAK--ELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVS 58
             MD +   G++  EL Q Q  LYK +++ +SSM+LK A+ELGIAD+IHSHG+ ITL EL +
Sbjct:     1 MDFSSSNGSEDTELSQAQIHLYKHVYNFVSSMALKSAMELGIADVIHSHGKPITLPELAT 60

Query:    59 ALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN---GQEE--AYGLTAASTLLIKDKPYCMS 113
             AL+++P+K   L R +RLL H+  F KT V+   G EE  AYGLT  S LL+K    C++
Sbjct:    61 ALNLRPSKIGVLHRFLRLLTHNGFFAKTTVSRGEGAEEETAYGLTPPSKLLVKSNSTCLA 120

Query:   114 PTVSAFVDP 122
             P V   + P
Sbjct:   121 PIVKGALHP 129

GO:0009701 "isoflavonoid phytoalexin biosynthetic process" evidence=IDA

GO:0030746 "isoflavone 4'-O-methyltransferase activity" evidence=IDA

UNIPROTKB|Q84KK6 HI4'OMT "Isoflavone 4'-O-methyltransferase" [Glycyrrhiza echinata (taxid:46348)]

 Score = 260 (96.6 bits), Expect = 2.1e-22, P = 2.1e-22
 Identities = 58/121 (47%), Positives = 78/121 (64%)

Query:    11 ELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGL 70
             EL   Q  LYK +++ +SSM+LK A+ELGIAD+IH+HG+ ITL EL SAL + P+K   L
Sbjct:    12 ELYHAQIHLYKHVYNFVSSMALKSAMELGIADVIHNHGKPITLPELASALKLHPSKVGIL 71

Query:    71 FRLMRLLVHSSCFNKTKV------NGQEE---AYGLTAASTLLIKDKPYCMSPTVSAFVD 121
             +R +RLL H+  F KT V      +G+EE   AY LT  S LL+K KP C++  V   + 
Sbjct:    72 YRFLRLLTHNGFFAKTTVPSQNGKDGEEEEETAYALTPPSKLLVKGKPTCLASIVRGALH 131

Query:   122 P 122
             P
Sbjct:   132 P 132

GO:0009701 "isoflavonoid phytoalexin biosynthetic process" evidence=IDA

GO:0030746 "isoflavone 4'-O-methyltransferase activity" evidence=IDA

UNIPROTKB|Q84KK5 D7OMT "Isoflavone 7-O-methyltransferase" [Glycyrrhiza echinata (taxid:46348)]

 Score = 257 (95.5 bits), Expect = 4.3e-22, P = 4.3e-22
 Identities = 54/134 (40%), Positives = 81/134 (60%)

Query:     3 ANQDQGAK--ELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSAL 60
             A+   G K  E+ QGQA LY+ +++ + SM LK  +EL I +IIH+HG+ IT+SELVS L
Sbjct:     2 ASSINGRKPSEIFQGQALLYRHIYAFIDSMCLKWIVELDIPNIIHNHGKPITVSELVSIL 61

Query:    61 DIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEE---AYGLTAASTLLIKDKPYCMSPTVS 117
              +  TK   + R+MR + H+  F + ++  ++E   AY LTAAS LL+K    C++P V 
Sbjct:    62 KVPQTKAGNVQRIMRYMAHNGFFERVRIQEEQEENEAYALTAASELLVKGSELCLAPMVE 121

Query:   118 AFVDPLFVAPFQSL 131
               +DP     +  L
Sbjct:   122 CVLDPTLSGSYHQL 135

GO:0009717 "isoflavonoid biosynthetic process" evidence=IDA

GO:0033800 "isoflavone 7-O-methyltransferase activity" evidence=IDA

UNIPROTKB|B0EXJ8 16OMT "Tabersonine 16-O-methyltransferase" [Catharanthus roseus (taxid:4058)]

 Score = 216 (81.1 bits), Expect = 1.8e-17, P = 1.8e-17
 Identities = 48/129 (37%), Positives = 80/129 (62%)

Query:     6 DQGAKELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSAL--DIQ 63
             D  ++E    QAQ++    S ++S SLKCA++LGI D I +HG+ ITLSEL +AL   + 
Sbjct:     2 DVQSEEFRGAQAQIWSQSCSFITSASLKCAVKLGIPDTIDNHGKPITLSELTNALVPPVH 61

Query:    64 PTKTTGLFRLMRLLVHSSCFNKTKVNGQEEA-YGLTAASTLLIKDKPYCMSPTVSAFVDP 122
             P+K   ++RLMR+L  +   ++ +++G+ E  Y LT +S +L+K +P  +   V    DP
Sbjct:    62 PSKAPFIYRLMRVLAKNGFCSEEQLDGETEPLYSLTPSSRILLKKEPLNLRGIVLTMADP 121

Query:   123 LFVAPFQSL 131
             + +  ++SL
Sbjct:   122 VQLKAWESL 130

GO:0005737 "cytoplasm" evidence=IDA

GO:0009821 "alkaloid biosynthetic process" evidence=IDA

GO:0030766 "11-O-demethyl-17-O-deacetylvindoline O-methyltransferase activity" evidence=IDA

GO:0032259 "methylation" evidence=IDA

GO:0042803 "protein homodimerization activity" evidence=IDA

UNIPROTKB|Q8GSN1 Q8GSN1 "Myricetin O-methyltransferase" [Catharanthus roseus (taxid:4058)]

 Score = 202 (76.2 bits), Expect = 6.4e-16, P = 6.4e-16
 Identities = 42/101 (41%), Positives = 64/101 (63%)

Query:     9 AKELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTT 68
             + E+   QA  +  +FS  S  SLKCA++LGI D IHSHG+ + LS+L ++L I P+K  
Sbjct:     5 SSEIRNAQAHFFTQVFSFTSMSSLKCAVQLGIPDAIHSHGKPMALSDLTNSLPINPSKAP 64

Query:    69 GLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIKDKP 109
              ++RLMR+LV +  F++ + N     Y LT  + LL+K+ P
Sbjct:    65 YIYRLMRILVAAGYFSEEEKN----VYSLTPFTRLLLKNDP 101

GO:0033799 "myricetin 3'-O-methyltransferase activity" evidence=IDA

UNIPROTKB|A8QW53 OMT3 "5-pentadecatrienyl resorcinol O-methyltransferase" [Sorghum bicolor (taxid:4558)]

 Score = 179 (68.1 bits), Expect = 3.1e-13, P = 3.1e-13
 Identities = 43/133 (32%), Positives = 74/133 (55%)

Query:     7 QGAKELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTK 66
             + ++ELLQ   +L+   +S + S++L  A++L IAD IH  G A TLS+++  + ++P K
Sbjct:     6 EDSRELLQAHVELWNQTYSFMKSVALAVALDLHIADAIHRRGGAATLSQILGEIGVRPCK 65

Query:    67 TTGLFRLMRLLVHSSCFN---------KTKVNGQEEAYGLTAASTLLIKDKPYC---MSP 114
               GL R+MR+L  S  F           ++ +G+E  Y LT AS+LL+  +      +SP
Sbjct:    66 LPGLHRIMRVLTVSGTFTIVQPSAETMSSESDGREPVYKLTTASSLLVSSESSATASLSP 125

Query:   115 TVSAFVDPLFVAP 127
              ++  + P   +P
Sbjct:   126 MLNHVLSPFRDSP 138

GO:0008171 "O-methyltransferase activity" evidence=IDA

GO:0008757 "S-adenosylmethionine-dependent methyltransferase activity" evidence=IDA

GO:0032259 "methylation" evidence=IDA

TAIR|locus:2132806 AT4G35160 [Arabidopsis thaliana (taxid:3702)]

 Score = 120 (47.3 bits), Expect = 9.3e-07, P = 9.3e-07
 Identities = 42/137 (30%), Positives = 67/137 (48%)

Query:     1 MDANQDQGAKELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSH--GRAITLSELVS 58
             M+ N+ +   E  +    ++K +F      + KCAI+L I + I +H   + +TL+EL S
Sbjct:    15 MEDNKRKVLDEEAKASLDIWKYVFGFADIAAAKCAIDLKIPEAIENHPSSQPVTLAELSS 74

Query:    59 ALDIQPTKTTGLFRLMRLLVHSSCFNK--TKVNGQEEAYGLTAAST-LLIKDKP-YCMSP 114
             A+   P+    L R+MR LVH   F +  TK +G    Y  T  S  L+I  +    ++P
Sbjct:    75 AVSASPSH---LRRIMRFLVHQGIFKEIPTK-DGLATGYVNTPLSRRLMITRRDGKSLAP 130

Query:   115 TVSAFVDPLFVAPFQSL 131
              V     P  +AP+  L
Sbjct:   131 FVLFETTPEMLAPWLRL 147

GO:0005634 "nucleus" evidence=ISM

GO:0008168 "methyltransferase activity" evidence=IEA

GO:0008171 "O-methyltransferase activity" evidence=IEA

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0005829 "cytosol" evidence=TAS

TAIR|locus:2132801 AT4G35150 [Arabidopsis thaliana (taxid:3702)]

 Score = 110 (43.8 bits), Expect = 8.5e-06, P = 8.5e-06
 Identities = 33/110 (30%), Positives = 55/110 (50%)

Query:     6 DQGAKELLQGQAQ----LYKLMFSHLSSMSLKCAIELGIADIIHSH--GRAITLSELVSA 59
             ++  + LL  +A+    +++ +F      + KCAI+L I + I +H   + +TLSEL SA
Sbjct:     2 EESKRNLLDEEAKASLDIWRYVFGFADIAAAKCAIDLKIPEAIENHPSSQPVTLSELSSA 61

Query:    60 LDIQPTKTTGLFRLMRLLVHSSCFNKTKV-NGQEEAYGLTAASTLLIKDK 108
             +   P+    L R+MR LVH   F +    +G    Y  T  S  ++  K
Sbjct:    62 VSASPSH---LRRIMRFLVHQGLFKEVPTKDGLATGYTNTPLSRRMMITK 108

GO:0008168 "methyltransferase activity" evidence=IEA

GO:0008171 "O-methyltransferase activity" evidence=IEA

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0005829 "cytosol" evidence=TAS

TAIR|locus:2153423 OMT1 "AT5G54160" [Arabidopsis thaliana (taxid:3702)]

 Score = 95 (38.5 bits), Expect = 0.00089, P = 0.00089
 Identities = 31/105 (29%), Positives = 53/105 (50%)

Query:    11 ELLQGQAQLYKLMFSHLS--SMSLKCAIELGIADIIHSHGRAITLSELVSALDIQ-PTKT 67
             ++   +A L+ +  +  S   M+LK A+EL + +I+  +G  ++ +E+ S L  + P   
Sbjct:    13 QVTDDEAALFAMQLASASVLPMALKSALELDLLEIMAKNGSPMSPTEIASKLPTKNPEAP 72

Query:    68 TGLFRLMRLLVHSS---CFN-KTKVNGQEEAYGLTAASTLLIKDK 108
               L R++RLL   S   C N K   +G E  YGL      L K++
Sbjct:    73 VMLDRILRLLTSYSVLTCSNRKLSGDGVERIYGLGPVCKYLTKNE 117


Parameters:
  V=100
  filter=SEG
  E=0.001

  ctxfactor=1.00

  Query                        -----  As Used  -----    -----  Computed  ----
  Frame  MatID Matrix name     Lambda    K       H      Lambda    K       H
   +0      0   BLOSUM62        0.321   0.133   0.376    same    same    same
               Q=9,R=2         0.244   0.0300  0.180     n/a     n/a     n/a

  Query
  Frame  MatID  Length  Eff.Length     E     S W   T  X   E2     S2
   +0      0      131       131   0.00091  102 3  11 22  0.37    31
                                                     29  0.42    33


Statistics:

  Database:  /share/blast/go-seqdb.fasta
   Title:  go_20130330-seqdb.fasta
   Posted:  5:47:42 AM PDT Apr 1, 2013
   Created:  5:47:42 AM PDT Apr 1, 2013
   Format:  XDF-1
   # of letters in database:  169,044,731
   # of sequences in database:  368,745
   # of database sequences satisfying E:  10
  No. of states in DFA:  527 (56 KB)
  Total size of DFA:  111 KB (2075 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  11.29u 0.12s 11.41t   Elapsed:  00:00:00
  Total cpu time:  11.29u 0.12s 11.41t   Elapsed:  00:00:00
  Start:  Sat May 11 16:12:08 2013   End:  Sat May 11 16:12:08 2013

GO:0030744 "luteolin O-methyltransferase activity" evidence=IDA

GO:0030755 "quercetin 3-O-methyltransferase activity" evidence=IDA

GO:0033799 "myricetin 3'-O-methyltransferase activity" evidence=IDA

GO:0047763 "caffeate O-methyltransferase activity" evidence=ISS;IMP

GO:0051555 "flavonol biosynthetic process" evidence=IDA

GO:0009809 "lignin biosynthetic process" evidence=IMP

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0005886 "plasma membrane" evidence=IDA

GO:0009506 "plasmodesma" evidence=IDA

GO:0006598 "polyamine catabolic process" evidence=RCA

GO:0009611 "response to wounding" evidence=RCA

GO:0009698 "phenylpropanoid metabolic process" evidence=RCA

GO:0009805 "coumarin biosynthetic process" evidence=RCA

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

GO:0016126 "sterol biosynthetic process" evidence=RCA

GO:0042398 "cellular modified amino acid biosynthetic process" evidence=RCA

GO:0005829 "cytosol" evidence=TAS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	131
pfam08100	50	pfam08100, Dimerisation, Dimerisation domain	2e-16

>gnl|CDD|219719 pfam08100, Dimerisation, Dimerisation domain

 Score = 67.6 bits (166), Expect = 2e-16
 Identities = 27/50 (54%), Positives = 32/50 (64%), Gaps = 1/50 (2%)

Query: 30 MSLKCAIELGIADIIHSHGRAITLSELVSAL-DIQPTKTTGLFRLMRLLV 78
          M LKCAIELGI DII  HG+ ++ SEL S L  + P     L RL+RLL 
Sbjct: 1  MVLKCAIELGIPDIIAKHGKPLSPSELASKLPTVNPEAPVMLDRLLRLLA 50

This domain is found at the N-terminus of a variety of plant O-methyltransferases. It has been shown to mediate dimerisation of these proteins. Length = 50

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	131
KOG3178	342	consensus Hydroxyindole-O-methyltransferase and re	99.63
TIGR02716	306	C20_methyl_CrtF C-20 methyltransferase BchU. Membe	99.55
PF08100	51	Dimerisation: Dimerisation domain; InterPro: IPR01	99.49
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	98.43
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	98.23
TIGR02431	248	pcaR_pcaU beta-ketoadipate pathway transcriptional	98.13
COG1414	246	IclR Transcriptional regulator [Transcription]	98.12
PRK11569	274	transcriptional repressor IclR; Provisional	98.11
PRK10163	271	DNA-binding transcriptional repressor AllR; Provis	98.09
PRK09834	263	DNA-binding transcriptional activator MhpR; Provis	97.98
PRK15090	257	DNA-binding transcriptional regulator KdgR; Provis	97.96
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	97.69
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	97.68
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	97.54
cd07153	116	Fur_like Ferric uptake regulator(Fur) and related	97.51
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	97.36
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	97.34
PRK10141	117	DNA-binding transcriptional repressor ArsR; Provis	97.3
PF02082	83	Rrf2: Transcriptional regulator; InterPro: IPR0009	97.28
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	97.28
COG3355	126	Predicted transcriptional regulator [Transcription	97.22
smart00419	48	HTH_CRP helix_turn_helix, cAMP Regulatory protein.	97.22
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	97.21
PRK10857	164	DNA-binding transcriptional regulator IscR; Provis	97.18
TIGR02944	130	suf_reg_Xantho FeS assembly SUF system regulator,	97.05
PF14947	77	HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_	97.05
TIGR02010	135	IscR iron-sulfur cluster assembly transcription fa	97.03
smart00347	101	HTH_MARR helix_turn_helix multiple antibiotic resi	96.99
PF08461	66	HTH_12: Ribonuclease R winged-helix domain; InterP	96.97
TIGR00738	132	rrf2_super rrf2 family protein (putative transcrip	96.96
PF04703	62	FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.	96.94
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	96.92
PRK03902	142	manganese transport transcriptional regulator; Pro	96.9
TIGR02337	118	HpaR homoprotocatechuate degradation operon regula	96.77
TIGR00122	69	birA_repr_reg BirA biotin operon repressor domain.	96.74
TIGR02702	203	SufR_cyano iron-sulfur cluster biosynthesis transc	96.74
PRK11050	152	manganese transport regulator MntR; Provisional	96.69
PF09012	69	FeoC: FeoC like transcriptional regulator; InterPr	96.68
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	96.66
COG4190	144	Predicted transcriptional regulator [Transcription	96.66
PHA00738	108	putative HTH transcription regulator	96.66
PRK06474	178	hypothetical protein; Provisional	96.66
PF07381	90	DUF1495: Winged helix DNA-binding domain (DUF1495)	96.64
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	96.64
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	96.61
COG1959	150	Predicted transcriptional regulator [Transcription	96.55
PF13601	80	HTH_34: Winged helix DNA-binding domain; PDB: 1UB9	96.51
smart00529	96	HTH_DTXR Helix-turn-helix diphteria tox regulatory	96.45
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	96.44
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	96.42
PRK11014	141	transcriptional repressor NsrR; Provisional	96.41
TIGR01884	203	cas_HTH CRISPR locus-related DNA-binding protein.	96.4
PF01475	120	FUR: Ferric uptake regulator family; InterPro: IPR	96.37
cd00090	78	HTH_ARSR Arsenical Resistance Operon Repressor and	96.35
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	96.35
smart00418	66	HTH_ARSR helix_turn_helix, Arsenical Resistance Op	96.34
TIGR01610	95	phage_O_Nterm phage replication protein O, N-termi	96.31
COG0735	145	Fur Fe2+/Zn2+ uptake regulation proteins [Inorgani	96.27
PRK09462	148	fur ferric uptake regulator; Provisional	96.25
COG4742	260	Predicted transcriptional regulator [Transcription	96.25
PRK03573	144	transcriptional regulator SlyA; Provisional	96.24
COG2345	218	Predicted transcriptional regulator [Transcription	96.23
COG1321	154	TroR Mn-dependent transcriptional regulator [Trans	96.17
PRK11639	169	zinc uptake transcriptional repressor; Provisional	96.14
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	96.12
PRK11512	144	DNA-binding transcriptional repressor MarR; Provis	96.11
TIGR01889	109	Staph_reg_Sar staphylococcal accessory regulator f	96.05
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	96.01
PRK11920	153	rirA iron-responsive transcriptional regulator; Re	95.98
cd07377	66	WHTH_GntR Winged helix-turn-helix (WHTH) DNA-bindi	95.87
PF06163	127	DUF977: Bacterial protein of unknown function (DUF	95.85
PF03444	78	HrcA_DNA-bdg: Winged helix-turn-helix transcriptio	95.82
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	95.76
PF01638	90	HxlR: HxlR-like helix-turn-helix; InterPro: IPR002	95.62
PRK06266	178	transcription initiation factor E subunit alpha; V	95.5
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	95.44
PRK11179	153	DNA-binding transcriptional regulator AsnC; Provis	95.38
COG2512	258	Predicted membrane-associated trancriptional regul	95.35
PRK11169	164	leucine-responsive transcriptional regulator; Prov	95.24
COG1522	154	Lrp Transcriptional regulators [Transcription]	95.04
PF14394	171	DUF4423: Domain of unknown function (DUF4423)	95.04
PF04182	75	B-block_TFIIIC: B-block binding subunit of TFIIIC;	95.0
PRK10870	176	transcriptional repressor MprA; Provisional	94.94
TIGR00498	199	lexA SOS regulatory protein LexA. LexA acts as a h	94.9
COG3432	95	Predicted transcriptional regulator [Transcription	94.9
COG4189	308	Predicted transcriptional regulator [Transcription	94.77
PF02796	45	HTH_7: Helix-turn-helix domain of resolvase; Inter	94.74
PRK04214	412	rbn ribonuclease BN/unknown domain fusion protein;	94.36
COG1378	247	Predicted transcriptional regulators [Transcriptio	94.32
PRK11886	319	bifunctional biotin--[acetyl-CoA-carboxylase] synt	94.31
PRK13509	251	transcriptional repressor UlaR; Provisional	94.27
TIGR02787	251	codY_Gpos GTP-sensing transcriptional pleiotropic	94.18
PRK04172	489	pheS phenylalanyl-tRNA synthetase subunit alpha; P	94.16
PRK14165	217	winged helix-turn-helix domain-containing protein/	94.13
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	93.92
PRK05638	442	threonine synthase; Validated	93.92
TIGR00373	158	conserved hypothetical protein TIGR00373. This fam	93.9
PF13545	76	HTH_Crp_2: Crp-like helix-turn-helix domain; PDB:	93.86
COG4565	224	CitB Response regulator of citrate/malate metaboli	93.79
PRK10906	252	DNA-binding transcriptional repressor GlpR; Provis	93.76
PF09929	118	DUF2161: Uncharacterized conserved protein (DUF216	93.6
TIGR02698	130	CopY_TcrY copper transport repressor, CopY/TcrY fa	93.5
PF05732	165	RepL: Firmicute plasmid replication protein (RepL)	93.4
PF00392	64	GntR: Bacterial regulatory proteins, gntR family;	93.39
PF08784	102	RPA_C: Replication protein A C terminal; InterPro:	93.36
PRK09802	269	DNA-binding transcriptional regulator AgaR; Provis	93.24
PRK10411	240	DNA-binding transcriptional activator FucR; Provis	93.05
PRK13777	185	transcriptional regulator Hpr; Provisional	92.98
COG1349	253	GlpR Transcriptional regulators of sugar metabolis	92.97
COG1497	260	Predicted transcriptional regulator [Transcription	92.96
PLN02853	492	Probable phenylalanyl-tRNA synthetase alpha chain	92.94
COG3413	215	Predicted DNA binding protein [General function pr	92.93
COG1846	126	MarR Transcriptional regulators [Transcription]	92.74
PHA02943	165	hypothetical protein; Provisional	92.63
PRK10434	256	srlR DNA-bindng transcriptional repressor SrlR; Pr	92.62
PF13730	55	HTH_36: Helix-turn-helix domain	92.56
COG5631	199	Predicted transcription regulator, contains HTH do	92.55
PTZ00326	494	phenylalanyl-tRNA synthetase alpha chain; Provisio	92.38
PRK00215	205	LexA repressor; Validated	92.26
TIGR02147	271	Fsuc_second hypothetical protein, TIGR02147. This	92.17
PF02002	105	TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024	92.1
COG1733	120	Predicted transcriptional regulators [Transcriptio	92.02
PRK10046	225	dpiA two-component response regulator DpiA; Provis	91.93
PF12324	77	HTH_15: Helix-turn-helix domain of alkylmercury ly	91.8
PRK01381	99	Trp operon repressor; Provisional	91.75
PRK15431	78	ferrous iron transport protein FeoC; Provisional	91.43
PF13384	50	HTH_23: Homeodomain-like domain; PDB: 2X48_C.	91.25
PRK09954	362	putative kinase; Provisional	90.86
PF01371	87	Trp_repressor: Trp repressor protein; InterPro: IP	90.78
PF10007	92	DUF2250: Uncharacterized protein conserved in arch	90.77
PRK12423	202	LexA repressor; Provisional	90.64
PF13936	44	HTH_38: Helix-turn-helix domain; PDB: 2W48_A.	90.6
TIGR01321	94	TrpR trp operon repressor, proteobacterial. This m	90.4
PF08221	62	HTH_9: RNA polymerase III subunit RPC82 helix-turn	90.27
PF03965	115	Penicillinase_R: Penicillinase repressor; InterPro	90.2
PF13518	52	HTH_28: Helix-turn-helix domain	90.19
PF07789	155	DUF1627: Protein of unknown function (DUF1627); In	90.17
PRK04424	185	fatty acid biosynthesis transcriptional regulator;	90.05
PF03374	111	ANT: Phage antirepressor protein KilAC domain; Int	89.82
TIGR00635	305	ruvB Holliday junction DNA helicase, RuvB subunit.	89.66
PRK09334	86	30S ribosomal protein S25e; Provisional	89.58
PRK00082	339	hrcA heat-inducible transcription repressor; Provi	89.47
PF12793	115	SgrR_N: Sugar transport-related sRNA regulator N-t	89.38
COG1510	177	Predicted transcriptional regulators [Transcriptio	89.37
PRK13239	206	alkylmercury lyase; Provisional	89.37
TIGR03697	193	NtcA_cyano global nitrogen regulator NtcA, cyanoba	89.31
PRK11642	813	exoribonuclease R; Provisional	88.84
PRK11753	211	DNA-binding transcriptional dual regulator Crp; Pr	88.75
PRK11161	235	fumarate/nitrate reduction transcriptional regulat	88.74
PRK09775	442	putative DNA-binding transcriptional regulator; Pr	88.71
PRK11534	224	DNA-binding transcriptional regulator CsiR; Provis	88.6
PF02319	71	E2F_TDP: E2F/DP family winged-helix DNA-binding do	88.36
PRK09391	230	fixK transcriptional regulator FixK; Provisional	88.34
TIGR00331	337	hrcA heat shock gene repressor HrcA. In Bacillus s	88.11
PF05584	72	Sulfolobus_pRN: Sulfolobus plasmid regulatory prot	87.99
PF03297	105	Ribosomal_S25: S25 ribosomal protein; InterPro: IP	87.96
TIGR03433	100	padR_acidobact transcriptional regulator, Acidobac	87.81
TIGR03338	212	phnR_burk phosphonate utilization associated trans	87.71
PF03428	177	RP-C: Replication protein C N-terminal domain; Int	87.66
TIGR02531	88	yecD_yerC TrpR-related protein YerC/YecD. This mod	87.6
PF00126	60	HTH_1: Bacterial regulatory helix-turn-helix prote	87.56
PF00165	42	HTH_AraC: Bacterial regulatory helix-turn-helix pr	87.53
PF01418	77	HTH_6: Helix-turn-helix domain, rpiR family; Inter	87.46
COG3682	123	Predicted transcriptional regulator [Transcription	87.44
COG1725	125	Predicted transcriptional regulators [Transcriptio	87.21
COG4901	107	Ribosomal protein S25 [Translation, ribosomal stru	87.08
PRK13918	202	CRP/FNR family transcriptional regulator; Provisio	86.96
COG1802	230	GntR Transcriptional regulators [Transcription]	86.76
COG1675	176	TFA1 Transcription initiation factor IIE, alpha su	86.74
PF03551	75	PadR: Transcriptional regulator PadR-like family;	86.27
PF08280	59	HTH_Mga: M protein trans-acting positive regulator	86.23
COG2524	294	Predicted transcriptional regulator, contains C-te	86.03
TIGR03879	73	near_KaiC_dom probable regulatory domain. This mod	85.48
KOG2165	765	consensus Anaphase-promoting complex (APC), subuni	84.99
PRK10430	239	DNA-binding transcriptional activator DcuR; Provis	84.96
PF05331	114	DUF742: Protein of unknown function (DUF742); Inte	84.92
COG2188	236	PhnF Transcriptional regulators [Transcription]	84.8
PRK11414	221	colanic acid/biofilm transcriptional regulator; Pr	84.65
PF13542	52	HTH_Tnp_ISL3: Helix-turn-helix domain of transposa	84.49
PRK00135	188	scpB segregation and condensation protein B; Revie	84.48
PHA02701	183	ORF020 dsRNA-binding PKR inhibitor; Provisional	84.33
PRK14096	528	pgi glucose-6-phosphate isomerase; Provisional	84.28
smart00421	58	HTH_LUXR helix_turn_helix, Lux Regulon. lux regulo	84.06
PF10668	60	Phage_terminase: Phage terminase small subunit; In	84.0
PRK10736	374	hypothetical protein; Provisional	83.77
PF00356	46	LacI: Bacterial regulatory proteins, lacI family;	83.7
TIGR01764	49	excise DNA binding domain, excisionase family. An	83.52
PF14338	92	Mrr_N: Mrr N-terminal domain	83.42
TIGR02719	138	repress_PhaQ poly-beta-hydroxybutyrate-responsive	83.41
smart00342	84	HTH_ARAC helix_turn_helix, arabinose operon contro	83.32
TIGR02404	233	trehalos_R_Bsub trehalose operon repressor, B. sub	83.11
PRK10402	226	DNA-binding transcriptional activator YeiL; Provis	82.88
COG2378	311	Predicted transcriptional regulator [Transcription	82.65
PF12728	51	HTH_17: Helix-turn-helix domain	82.59
PRK00080	328	ruvB Holliday junction DNA helicase RuvB; Reviewed	82.33
COG1654	79	BirA Biotin operon repressor [Transcription]	82.27
TIGR02844	80	spore_III_D sporulation transcriptional regulator	82.1
PF05491	76	RuvB_C: Holliday junction DNA helicase ruvB C-term	82.01
COG2390	321	DeoR Transcriptional regulator, contains sigma fac	81.95
PF06971	50	Put_DNA-bind_N: Putative DNA-binding protein N-ter	81.84
PHA02591	83	hypothetical protein; Provisional	81.83
PF13443	63	HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3	81.82
TIGR02325	238	C_P_lyase_phnF phosphonates metabolism transcripti	81.69
PRK13558	665	bacterio-opsin activator; Provisional	81.56
PF09681	121	Phage_rep_org_N: N-terminal phage replisome organi	81.48
smart00531	147	TFIIE Transcription initiation factor IIE.	81.37
PF11972	54	HTH_13: HTH DNA binding domain; InterPro: IPR02106	81.36
PRK14999	241	histidine utilization repressor; Provisional	81.28
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	81.22
PRK11511	127	DNA-binding transcriptional activator MarA; Provis	81.19
TIGR02018	230	his_ut_repres histidine utilization repressor, pro	80.93
PRK10219	107	DNA-binding transcriptional regulator SoxS; Provis	80.88
PF04539	78	Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624	80.87
cd04762	49	HTH_MerR-trunc Helix-Turn-Helix DNA binding domain	80.7
PRK09990	251	DNA-binding transcriptional regulator GlcC; Provis	80.61
PF04492	100	Phage_rep_O: Bacteriophage replication protein O ;	80.58
PF13551	112	HTH_29: Winged helix-turn helix	80.42
PRK09464	254	pdhR transcriptional regulator PdhR; Reviewed	80.37
PRK10225	257	DNA-binding transcriptional repressor UxuR; Provis	80.19
PRK04984	239	fatty acid metabolism regulator; Provisional	80.14
PRK09764	240	DNA-binding transcriptional repressor MngR; Provis	80.01

>KOG3178 consensus Hydroxyindole-O-methyltransferase and related SAM-dependent methyltransferases [General function prediction only]

Probab=99.63  E-value=9.9e-16  Score=119.46  Aligned_cols=116  Identities=28%  Similarity=0.334  Sum_probs=97.7

Q ss_pred             HHhHHHHHHHHHHHhHHHHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcC--CCCCCcchHHHHHHHhhcCCceeeccc
Q 040869           11 ELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALD--IQPTKTTGLFRLMRLLVHSSCFNKTKV   88 (131)
Q Consensus        11 e~~~~~~~l~~~~~~~~~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~--~~~~~~~~l~RlLr~L~~~gl~~~~~~   88 (131)
                      ++......++++++++..++++++|++|||||+|+++++   .+|||..+.  .+|++|..+.|+||.|++++++++...
T Consensus         2 ~e~~~~l~~~~l~~~~~~~~~lk~A~eL~v~d~l~~~~~---p~~ia~~l~~~~~~~~p~ll~r~lr~L~s~~i~k~~~~   78 (342)
T KOG3178|consen    2 EENEASLRAMRLANGFALPMVLKAACELGVFDILANAGS---PSEIASLLPTPKNPEAPVLLDRILRLLVSYSILKCRLV   78 (342)
T ss_pred             chhHHHHHHHHHHhhhhhHHHHHHHHHcChHHHHHhCCC---HHHHHHhccCCCCCCChhHHHHHHHHHHHhhhceeeee
Confidence            345566889999999999999999999999999997544   788888777  467789999999999999999998752


Q ss_pred             CCCCcceecchhcccccc-CcccChHHhHHhhcCchhhccCCCC
Q 040869           89 NGQEEAYGLTAASTLLIK-DKPYCMSPTVSAFVDPLFVAPFQSL  131 (131)
Q Consensus        89 ~~~~~~y~~t~~s~~L~~-~~~~sl~~~~~~~~~~~~~~~w~~L  131 (131)
                      . +. .|++||+++++.. ++..|++++++..+++..++.|.+|
T Consensus        79 ~-~~-~Y~~~~~~~~~l~~~~~~S~a~~~~~~~~~v~~~~w~~l  120 (342)
T KOG3178|consen   79 G-GE-VYSATPVCKYFLKDSGGGSLAPLVLLNTSKVIMNTWQFL  120 (342)
T ss_pred             c-ce-eeeccchhhhheecCCCCchhHHHHHhcccchhhhHHHH
Confidence            1 12 8999999997764 3457999999999999999999764

>TIGR02716 C20_methyl_CrtF C-20 methyltransferase BchU

Probab=99.55  E-value=6.3e-15  Score=113.96  Aligned_cols=71  Identities=18%  Similarity=0.200  Sum_probs=63.9

Q ss_pred             HHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhccccccC
Q 040869           28 SSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIKD  107 (131)
Q Consensus        28 ~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~~~  107 (131)
                      ...+|++|++|||||.|++  +|.|++|||+++|+   +++.++|+||+|+++|+|++.     +++|++|+.++.+..+
T Consensus         3 ~~~~l~aa~~Lglfd~L~~--gp~t~~eLA~~~~~---~~~~~~~lL~~L~~lgll~~~-----~~~y~~t~~~~~~l~~   72 (306)
T TIGR02716         3 EFSCMKAAIELDLFSHMAE--GPKDLATLAADTGS---VPPRLEMLLETLRQMRVINLE-----DGKWSLTEFADYMFSP   72 (306)
T ss_pred             hHHHHHHHHHcCcHHHHhc--CCCCHHHHHHHcCC---ChHHHHHHHHHHHhCCCeEec-----CCcEecchhHHhhccC
Confidence            4679999999999999984  79999999999999   999999999999999999986     5899999999855544


Q ss_pred             c
Q 040869          108 K  108 (131)
Q Consensus       108 ~  108 (131)
                      +
T Consensus        73 ~   73 (306)
T TIGR02716        73 T   73 (306)
T ss_pred             C
Confidence            3

Members of this protein family are the S-adenosylmethionine-depenedent C-20 methyltransferase BchU, part of the pathway of bacteriochlorophyll c production in photosynthetic green sulfur bacteria. The position modified by this enzyme represents the difference between bacteriochlorophylls c and d; strains lacking this protein can only produced bacteriochlorophyll d.

>PF08100 Dimerisation: Dimerisation domain; InterPro: IPR012967 This domain is found at the N terminus of a variety of plant O-methyltransferases

Probab=99.49  E-value=3.2e-14  Score=82.90  Aligned_cols=49  Identities=53%  Similarity=0.852  Sum_probs=42.9

Q ss_pred             HHHHHHHHhChHHHHHhCC-CCCCHHHHHhhcC-CCCCCcchHHHHHHHhh
Q 040869           30 MSLKCAIELGIADIIHSHG-RAITLSELVSALD-IQPTKTTGLFRLMRLLV   78 (131)
Q Consensus        30 ~aL~~a~~L~ifd~l~~~~-~~~s~~eLA~~~~-~~~~~~~~l~RlLr~L~   78 (131)
                      ++|++|++|||||+|+++| +++|++||+.+++ .+|.++..|+|+||+|+
T Consensus         1 MaLk~aveLgI~dii~~~g~~~ls~~eia~~l~~~~p~~~~~L~RimR~L~   51 (51)
T PF08100_consen    1 MALKCAVELGIPDIIHNAGGGPLSLSEIAARLPTSNPSAPPMLDRIMRLLV   51 (51)
T ss_dssp             HHHHHHHHTTHHHHHHHHTTS-BEHHHHHHTSTCT-TTHHHHHHHHHHHHH
T ss_pred             CcHHHHHHcCcHHHHHHcCCCCCCHHHHHHHcCCCCcchHHHHHHHHHHhC
Confidence            5899999999999999876 8999999999999 66667889999999986

It has been shown to mediate dimerisation of these proteins [].; GO: 0008168 methyltransferase activity, 0046983 protein dimerization activity; PDB: 1ZGJ_A 1ZG3_A 1ZHF_A 1ZGA_A 2QYO_A 1KYW_A 1KYZ_A 3REO_D 1FPX_A 1FP2_A ....

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

Probab=98.43  E-value=1.3e-07  Score=54.96  Aligned_cols=46  Identities=28%  Similarity=0.491  Sum_probs=41.3

Q ss_pred             hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      +.|++.|.+.++++|+.|||+++|+   +...++|+|+.|+..|++.++
T Consensus         6 l~iL~~l~~~~~~~t~~eia~~~gl---~~stv~r~L~tL~~~g~v~~d   51 (52)
T PF09339_consen    6 LRILEALAESGGPLTLSEIARALGL---PKSTVHRLLQTLVEEGYVERD   51 (52)
T ss_dssp             HHHHHCHHCTBSCEEHHHHHHHHTS----HHHHHHHHHHHHHTTSEEEC
T ss_pred             HHHHHHHHcCCCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCcCeecC
Confidence            5688889877788999999999999   999999999999999999875

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.

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=98.23  E-value=2.9e-06  Score=54.12  Aligned_cols=58  Identities=19%  Similarity=0.283  Sum_probs=49.9

Q ss_pred             hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhc
Q 040869           38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAS  101 (131)
Q Consensus        38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s  101 (131)
                      +.|++.|.+.++++|+.|||+.+|+   +...++|+++.|...|++.....   ++.|.+++..
T Consensus         8 ~~Il~~l~~~~~~~t~~~ia~~l~i---~~~tv~r~l~~L~~~g~l~~~~~---~~~y~l~~~~   65 (91)
T smart00346        8 LAVLRALAEEPGGLTLAELAERLGL---SKSTAHRLLNTLQELGYVEQDGQ---NGRYRLGPKV   65 (91)
T ss_pred             HHHHHHHHhCCCCcCHHHHHHHhCC---CHHHHHHHHHHHHHCCCeeecCC---CCceeecHHH
Confidence            5688888865478999999999999   99999999999999999998631   5789988754

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

Probab=98.13  E-value=3.6e-06  Score=63.40  Aligned_cols=59  Identities=17%  Similarity=0.233  Sum_probs=51.6

Q ss_pred             hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcccc
Q 040869           38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLL  104 (131)
Q Consensus        38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L  104 (131)
                      +.|.+.|.+.++++|+.|||+++|+   ++..++|+|..|+..|++.++     +++|.+++....|
T Consensus        12 l~IL~~l~~~~~~~~l~eia~~lgl---pksT~~RlL~tL~~~G~l~~~-----~~~Y~lG~~~~~l   70 (248)
T TIGR02431        12 LAVIEAFGAERPRLTLTDVAEATGL---TRAAARRFLLTLVELGYVTSD-----GRLFWLTPRVLRL   70 (248)
T ss_pred             HHHHHHHhcCCCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEeC-----CCEEEecHHHHHH
Confidence            5688888866689999999999999   999999999999999999875     5789999865444

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.

>COG1414 IclR Transcriptional regulator [Transcription]

Probab=98.12  E-value=4.6e-06  Score=63.10  Aligned_cols=59  Identities=22%  Similarity=0.359  Sum_probs=51.2

Q ss_pred             hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcc
Q 040869           38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAST  102 (131)
Q Consensus        38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~  102 (131)
                      +.|++.|.+.+.++++.|||+++|+   ++..++|+|..|+..|++.+++.   .++|.+++..-
T Consensus         7 l~iL~~l~~~~~~l~l~ela~~~gl---pksT~~RlL~tL~~~G~v~~d~~---~g~Y~Lg~~~~   65 (246)
T COG1414           7 LAILDLLAEGPGGLSLAELAERLGL---PKSTVHRLLQTLVELGYVEQDPE---DGRYRLGPRLL   65 (246)
T ss_pred             HHHHHHHHhCCCCCCHHHHHHHhCc---CHHHHHHHHHHHHHCCCEEEcCC---CCcEeehHHHH
Confidence            5688889875566789999999999   99999999999999999999862   57899998654

>PRK11569 transcriptional repressor IclR; Provisional

Probab=98.11  E-value=4.2e-06  Score=64.06  Aligned_cols=61  Identities=13%  Similarity=0.247  Sum_probs=52.1

Q ss_pred             hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcccc
Q 040869           38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLL  104 (131)
Q Consensus        38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L  104 (131)
                      +.|.+.|.+.++++|+.|||+.+|+   ++..++|+|+.|+..|++.++..   .++|.+++....|
T Consensus        31 l~IL~~l~~~~~~~~lseia~~lgl---pksTv~RlL~tL~~~G~l~~~~~---~~~Y~lG~~l~~L   91 (274)
T PRK11569         31 LKLLEWIAESNGSVALTELAQQAGL---PNSTTHRLLTTMQQQGFVRQVGE---LGHWAIGAHAFIV   91 (274)
T ss_pred             HHHHHHHHhCCCCcCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEcCC---CCeEecCHHHHHH
Confidence            5688888876688999999999999   99999999999999999987642   6889998765433

>PRK10163 DNA-binding transcriptional repressor AllR; Provisional

Probab=98.09  E-value=5.8e-06  Score=63.25  Aligned_cols=61  Identities=15%  Similarity=0.258  Sum_probs=52.0

Q ss_pred             hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcccc
Q 040869           38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLL  104 (131)
Q Consensus        38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L  104 (131)
                      +.|++.|.+.++++|+.|||+++|+   ++..++|+|..|+..|++.++..   .++|.+++-...|
T Consensus        28 l~IL~~~~~~~~~~tl~eIa~~lgl---pkStv~RlL~tL~~~G~l~~~~~---~~~Y~lG~~l~~L   88 (271)
T PRK10163         28 IAILQYLEKSGGSSSVSDISLNLDL---PLSTTFRLLKVLQAADFVYQDSQ---LGWWHIGLGVFNV   88 (271)
T ss_pred             HHHHHHHHhCCCCcCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEcCC---CCeEEecHHHHHH
Confidence            5688888866678999999999999   99999999999999999988642   6889998865433

>PRK09834 DNA-binding transcriptional activator MhpR; Provisional

Probab=97.98  E-value=1.1e-05  Score=61.41  Aligned_cols=61  Identities=16%  Similarity=0.234  Sum_probs=52.1

Q ss_pred             hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcccc
Q 040869           38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLL  104 (131)
Q Consensus        38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L  104 (131)
                      +.|++.|...++++|+.|||+++|+   ++..++|+|+.|+..|++.+...   +++|.+++....|
T Consensus        14 l~iL~~l~~~~~~ls~~eia~~lgl---~kstv~RlL~tL~~~g~v~~~~~---~~~Y~Lg~~~~~l   74 (263)
T PRK09834         14 LMVLRALNRLDGGATVGLLAELTGL---HRTTVRRLLETLQEEGYVRRSAS---DDSFRLTLKVRQL   74 (263)
T ss_pred             HHHHHHHHhcCCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEecC---CCcEEEcHHHHHH
Confidence            5678888765667999999999999   99999999999999999998642   6789999866544

>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional

Probab=97.96  E-value=1.3e-05  Score=60.71  Aligned_cols=60  Identities=20%  Similarity=0.330  Sum_probs=50.6

Q ss_pred             hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcccc
Q 040869           38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLL  104 (131)
Q Consensus        38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L  104 (131)
                      +.|.+.|.+ .+++|+.|||+++|+   ++..++|+|+.|+..|++.+...   .++|.+++....|
T Consensus        17 l~IL~~l~~-~~~l~l~eia~~lgl---~kstv~Rll~tL~~~G~l~~~~~---~~~Y~lG~~~~~l   76 (257)
T PRK15090         17 FGILQALGE-EREIGITELSQRVMM---SKSTVYRFLQTMKTLGYVAQEGE---SEKYSLTLKLFEL   76 (257)
T ss_pred             HHHHHHhhc-CCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEcCC---CCcEEecHHHHHH
Confidence            567777875 468999999999999   99999999999999999988642   6889999875443

>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=97.69  E-value=6.3e-05  Score=44.87  Aligned_cols=55  Identities=20%  Similarity=0.242  Sum_probs=46.8

Q ss_pred             HHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           29 SMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        29 ~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      ..+|.--.++.|+..|.. ++|+|+.|||+.+|+   ++..+++-|+.|...|+++...
T Consensus         4 ~~aL~~p~R~~Il~~L~~-~~~~t~~ela~~l~~---~~~t~s~hL~~L~~aGli~~~~   58 (61)
T PF12840_consen    4 FKALSDPTRLRILRLLAS-NGPMTVSELAEELGI---SQSTVSYHLKKLEEAGLIEVER   58 (61)
T ss_dssp             HHHHTSHHHHHHHHHHHH-CSTBEHHHHHHHHTS----HHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHhCCHHHHHHHHHHhc-CCCCCHHHHHHHHCC---CHHHHHHHHHHHHHCCCeEEec
Confidence            345666678889999943 589999999999999   9999999999999999999765

...

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

Probab=97.68  E-value=0.00017  Score=44.14  Aligned_cols=60  Identities=18%  Similarity=0.214  Sum_probs=48.2

Q ss_pred             HHHhChHHHHHhCCC-CCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869           35 AIELGIADIIHSHGR-AITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA   99 (131)
Q Consensus        35 a~~L~ifd~l~~~~~-~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~   99 (131)
                      ..+-.|.+.|.+.++ ++|+.|||+++|+   +...++|+|..|...|++.....  .++.|..+.
T Consensus         6 ~~~~~IL~~L~~~g~~~~ta~eLa~~lgl---~~~~v~r~L~~L~~~G~V~~~~~--~~~~W~i~~   66 (68)
T smart00550        6 SLEEKILEFLENSGDETSTALQLAKNLGL---PKKEVNRVLYSLEKKGKVCKQGG--TPPLWKLTD   66 (68)
T ss_pred             HHHHHHHHHHHHCCCCCcCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEecCC--CCCceEeec
Confidence            345578888987655 3999999999999   99999999999999999987541  146776654

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

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

Probab=97.54  E-value=0.00015  Score=43.64  Aligned_cols=60  Identities=20%  Similarity=0.304  Sum_probs=42.0

Q ss_pred             ChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhc
Q 040869           39 GIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAAS  101 (131)
Q Consensus        39 ~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s  101 (131)
                      -|...|....++++..+|++.+++   +...+.|+++.|...|++++.... ++ ...|.+||.+
T Consensus         7 ~vL~~l~~~~~~~t~~~l~~~~~~---~~~~vs~~i~~L~~~glv~~~~~~~d~R~~~~~LT~~G   68 (68)
T PF13463_consen    7 QVLRALAHSDGPMTQSDLAERLGI---SKSTVSRIIKKLEEKGLVEKERDPHDKRSKRYRLTPAG   68 (68)
T ss_dssp             HHHHHHT--TS-BEHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEESSCTTSEEEEE-HHH
T ss_pred             HHHHHHHccCCCcCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEecCCCCcCCeeEEEeCCCC
Confidence            344455533689999999999999   999999999999999999876532 22 2458888753

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

Probab=97.51  E-value=0.00026  Score=47.12  Aligned_cols=62  Identities=16%  Similarity=0.308  Sum_probs=46.7

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCC--CCCCcchHHHHHHHhhcCCceeecccCCCCcceecc
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDI--QPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLT   98 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~--~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t   98 (131)
                      +..|++.|.+.++++|++||.+++.-  ...+..++||.|+.|+..|++.+....++...|..+
T Consensus         3 R~~Il~~l~~~~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~~~~~~~~~y~~~   66 (116)
T cd07153           3 RLAILEVLLESDGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIELGDGKARYELN   66 (116)
T ss_pred             HHHHHHHHHhCCCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEEEeCCCceEEEeC
Confidence            45688999876789999999999842  111889999999999999999986532223456554

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.

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

Probab=97.36  E-value=0.00014  Score=44.14  Aligned_cols=47  Identities=15%  Similarity=0.243  Sum_probs=40.1

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      +..|...|-. .++.|+.|||+.+|+   +...+++.|+.|...|++....
T Consensus        10 E~~vy~~Ll~-~~~~t~~eIa~~l~i---~~~~v~~~L~~L~~~GlV~~~~   56 (68)
T PF01978_consen   10 EAKVYLALLK-NGPATAEEIAEELGI---SRSTVYRALKSLEEKGLVEREE   56 (68)
T ss_dssp             HHHHHHHHHH-HCHEEHHHHHHHHTS---SHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHH-cCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEEc
Confidence            4455656643 478999999999999   9999999999999999999875

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.

>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=97.34  E-value=0.00041  Score=41.42  Aligned_cols=45  Identities=13%  Similarity=0.220  Sum_probs=40.0

Q ss_pred             CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869           48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA   99 (131)
Q Consensus        48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~   99 (131)
                      ..++|..|||+.+|+   +...+.|+|+.|...|++....    .+.|..+|
T Consensus        23 ~~~~s~~ela~~~g~---s~~tv~r~l~~L~~~g~i~~~~----~~~~~l~~   67 (67)
T cd00092          23 QLPLTRQEIADYLGL---TRETVSRTLKELEEEGLISRRG----RGKYRVNP   67 (67)
T ss_pred             cCCcCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEecC----CCeEEeCC
Confidence            368999999999999   9999999999999999999874    47888765

>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional

Probab=97.30  E-value=0.00059  Score=46.23  Aligned_cols=65  Identities=23%  Similarity=0.290  Sum_probs=55.0

Q ss_pred             HHHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcc---eecch
Q 040869           27 LSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEA---YGLTA   99 (131)
Q Consensus        27 ~~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~---y~~t~   99 (131)
                      -..++|.--.++.|+..|.. +++.++.||++.+++   .+..+.+-|+.|...|+++...    .|+   |.+++
T Consensus         8 ~~fkaLadptRl~IL~~L~~-~~~~~v~ela~~l~l---sqstvS~HL~~L~~AGLV~~~r----~Gr~~~Y~l~~   75 (117)
T PRK10141          8 QLFKILSDETRLGIVLLLRE-SGELCVCDLCTALDQ---SQPKISRHLALLRESGLLLDRK----QGKWVHYRLSP   75 (117)
T ss_pred             HHHHHhCCHHHHHHHHHHHH-cCCcCHHHHHHHHCc---CHHHHHHHHHHHHHCCceEEEE----EcCEEEEEECc
Confidence            34567777889999999974 468999999999999   9999999999999999998765    343   77776

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

Probab=97.28  E-value=0.00053  Score=43.33  Aligned_cols=47  Identities=15%  Similarity=0.309  Sum_probs=37.5

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchh
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAA  100 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~  100 (131)
                      +++|..|||+++++   ++..+.++++.|...|+++....  .+|.|.++.-
T Consensus        24 ~~~s~~eiA~~~~i---~~~~l~kil~~L~~~Gli~s~~G--~~GGy~L~~~   70 (83)
T PF02082_consen   24 KPVSSKEIAERLGI---SPSYLRKILQKLKKAGLIESSRG--RGGGYRLARP   70 (83)
T ss_dssp             C-BEHHHHHHHHTS----HHHHHHHHHHHHHTTSEEEETS--TTSEEEESS-
T ss_pred             CCCCHHHHHHHHCc---CHHHHHHHHHHHhhCCeeEecCC--CCCceeecCC
Confidence            56999999999999   99999999999999999987641  1477876654

(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.

>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=97.28  E-value=0.00058  Score=38.56  Aligned_cols=45  Identities=20%  Similarity=0.266  Sum_probs=37.9

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCcee
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFN   84 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~   84 (131)
                      .+..|+..|.+ .+.+|..|||+.+|+   +...+.+.++-|...|+++
T Consensus         4 ~~~~Il~~l~~-~~~~t~~ela~~~~i---s~~tv~~~l~~L~~~g~I~   48 (48)
T PF13412_consen    4 TQRKILNYLRE-NPRITQKELAEKLGI---SRSTVNRYLKKLEEKGLIE   48 (48)
T ss_dssp             HHHHHHHHHHH-CTTS-HHHHHHHHTS----HHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHH-cCCCCHHHHHHHhCC---CHHHHHHHHHHHHHCcCcC
Confidence            45678889986 456999999999999   9999999999999999874

...

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=97.22  E-value=0.00079  Score=46.13  Aligned_cols=50  Identities=18%  Similarity=0.370  Sum_probs=41.0

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN   89 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~   89 (131)
                      +..++-+|-+..+|+|++|||+.++.   +.+.++|-|+-|...|++.+....
T Consensus        29 Dv~v~~~LL~~~~~~tvdelae~lnr---~rStv~rsl~~L~~~GlV~Rek~~   78 (126)
T COG3355          29 DVEVYKALLEENGPLTVDELAEILNR---SRSTVYRSLQNLLEAGLVEREKVN   78 (126)
T ss_pred             HHHHHHHHHhhcCCcCHHHHHHHHCc---cHHHHHHHHHHHHHcCCeeeeeec
Confidence            33455555423589999999999999   999999999999999999987543

>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein

Probab=97.22  E-value=0.00065  Score=37.86  Aligned_cols=41  Identities=12%  Similarity=0.173  Sum_probs=36.1

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceec
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGL   97 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~   97 (131)
                      -++|..|||+.+|+   +...+.|.|+.|...|++...     .+.|..
T Consensus         7 ~~~s~~~la~~l~~---s~~tv~~~l~~L~~~g~l~~~-----~~~~~i   47 (48)
T smart00419        7 LPLTRQEIAELLGL---TRETVSRTLKRLEKEGLISRE-----GGRIVI   47 (48)
T ss_pred             eccCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEe-----CCEEEE
Confidence            46899999999999   999999999999999999865     466654

>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=97.21  E-value=0.00044  Score=39.11  Aligned_cols=44  Identities=18%  Similarity=0.305  Sum_probs=38.9

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCcee
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFN   84 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~   84 (131)
                      .++.|...|.+  +|.++.||++.+|+   +...+.+-|+.|...|+++
T Consensus         3 ~R~~Il~~L~~--~~~~~~el~~~l~~---s~~~vs~hL~~L~~~glV~   46 (47)
T PF01022_consen    3 TRLRILKLLSE--GPLTVSELAEELGL---SQSTVSHHLKKLREAGLVE   46 (47)
T ss_dssp             HHHHHHHHHTT--SSEEHHHHHHHHTS----HHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHh--CCCchhhHHHhccc---cchHHHHHHHHHHHCcCee
Confidence            35678888884  89999999999999   9999999999999999986

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 ....

>PRK10857 DNA-binding transcriptional regulator IscR; Provisional

Probab=97.18  E-value=0.001  Score=47.51  Aligned_cols=47  Identities=15%  Similarity=0.167  Sum_probs=39.8

Q ss_pred             CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869           48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA   99 (131)
Q Consensus        48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~   99 (131)
                      ++++|+++||+++++   ++..+.++|+.|...|++.....  .+|.|.+..
T Consensus        23 ~~~vs~~eIA~~~~i---p~~~l~kIl~~L~~aGLv~s~rG--~~GGy~Lar   69 (164)
T PRK10857         23 AGPVPLADISERQGI---SLSYLEQLFSRLRKNGLVSSVRG--PGGGYLLGK   69 (164)
T ss_pred             CCcCcHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEeCCC--CCCCeeccC
Confidence            468999999999999   99999999999999999997531  146687754

>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial

Probab=97.05  E-value=0.0026  Score=43.27  Aligned_cols=47  Identities=11%  Similarity=0.243  Sum_probs=38.8

Q ss_pred             CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869           48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA   99 (131)
Q Consensus        48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~   99 (131)
                      ++++|..|||+++++   ++..+.++|+.|...|++.....  ..|.|.+..
T Consensus        23 ~~~~s~~eia~~l~i---s~~~v~~~l~~L~~~Gli~~~~g--~~ggy~l~~   69 (130)
T TIGR02944        23 SQPYSAAEIAEQTGL---NAPTVSKILKQLSLAGIVTSKRG--VEGGYTLAR   69 (130)
T ss_pred             CCCccHHHHHHHHCc---CHHHHHHHHHHHHHCCcEEecCC--CCCChhhcC
Confidence            468999999999999   99999999999999999986431  145676654

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.

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

Probab=97.05  E-value=0.00071  Score=42.32  Aligned_cols=57  Identities=16%  Similarity=0.274  Sum_probs=43.2

Q ss_pred             hHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcccccc
Q 040869           40 IADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIK  106 (131)
Q Consensus        40 ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~~  106 (131)
                      |...+.  .++.+..+|+..+++   +...+.+.+..|...|++...     ++.|.+|+.+..+..
T Consensus        11 IL~~l~--~~~~~~t~i~~~~~L---~~~~~~~yL~~L~~~gLI~~~-----~~~Y~lTekG~~~l~   67 (77)
T PF14947_consen   11 ILKILS--KGGAKKTEIMYKANL---NYSTLKKYLKELEEKGLIKKK-----DGKYRLTEKGKEFLE   67 (77)
T ss_dssp             HHHHH---TT-B-HHHHHTTST-----HHHHHHHHHHHHHTTSEEEE-----TTEEEE-HHHHHHHH
T ss_pred             HHHHHH--cCCCCHHHHHHHhCc---CHHHHHHHHHHHHHCcCeeCC-----CCEEEECccHHHHHH
Confidence            444444  478999999999999   999999999999999999764     799999999985543

>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR

Probab=97.03  E-value=0.0017  Score=44.66  Aligned_cols=48  Identities=17%  Similarity=0.192  Sum_probs=39.7

Q ss_pred             CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchh
Q 040869           48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAA  100 (131)
Q Consensus        48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~  100 (131)
                      ++++|..|||+.+++   ++..+.++|+.|...|++.....  ..|.|.++.-
T Consensus        23 ~~~~s~~~ia~~~~i---p~~~l~kil~~L~~~glv~s~~G--~~Ggy~l~~~   70 (135)
T TIGR02010        23 TGPVTLADISERQGI---SLSYLEQLFAKLRKAGLVKSVRG--PGGGYQLGRP   70 (135)
T ss_pred             CCcCcHHHHHHHHCc---CHHHHHHHHHHHHHCCceEEEeC--CCCCEeccCC
Confidence            468999999999999   99999999999999999986431  1456777653

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

>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein

Probab=96.99  E-value=0.0015  Score=41.54  Aligned_cols=68  Identities=16%  Similarity=0.242  Sum_probs=52.4

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-C-CCcceecchhccccccC
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-G-QEEAYGLTAASTLLIKD  107 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~-~~~~y~~t~~s~~L~~~  107 (131)
                      .++.|+..|.. .++++..+||+.+++   ++..+.+.++-|...|++...... + ....|.+|+.+..+...
T Consensus        11 ~~~~il~~l~~-~~~~~~~~la~~~~~---s~~~i~~~l~~L~~~g~v~~~~~~~~~r~~~~~lT~~g~~~~~~   80 (101)
T smart00347       11 TQFLVLRILYE-EGPLSVSELAKRLGV---SPSTVTRVLDRLEKKGLIRRLPSPEDRRSVLVSLTEEGRELIEE   80 (101)
T ss_pred             HHHHHHHHHHH-cCCcCHHHHHHHHCC---CchhHHHHHHHHHHCCCeEecCCCCCCCeEEEEECHhHHHHHHH
Confidence            35667888875 357999999999999   999999999999999999876421 0 02358888888765543

>PF08461 HTH_12: Ribonuclease R winged-helix domain; InterPro: IPR013668 This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaea

Probab=96.97  E-value=0.0015  Score=39.75  Aligned_cols=59  Identities=14%  Similarity=0.197  Sum_probs=46.0

Q ss_pred             hHHHHHhCCCCCCHHHHHhhcCCCCCC--cchHHHHHHHhhcCCceeecccCCCCcceecchhcc
Q 040869           40 IADIIHSHGRAITLSELVSALDIQPTK--TTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAST  102 (131)
Q Consensus        40 ifd~l~~~~~~~s~~eLA~~~~~~~~~--~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~  102 (131)
                      |.++|.++++|++..+|++.+.....+  +..++|.||+|-..|+.....    .+.+.+|+.+.
T Consensus         3 IL~~L~~~~~P~g~~~l~~~L~~~g~~~se~avRrrLr~me~~Glt~~~g----~~G~~iT~~G~   63 (66)
T PF08461_consen    3 ILRILAESDKPLGRKQLAEELKLRGEELSEEAVRRRLRAMERDGLTRKVG----RQGRIITEKGL   63 (66)
T ss_pred             HHHHHHHcCCCCCHHHHHHHHHhcChhhhHHHHHHHHHHHHHCCCccccC----CcccccCHHHH
Confidence            678888888999999999998753334  488999999999999766544    45566777654

>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator)

Probab=96.96  E-value=0.0018  Score=43.95  Aligned_cols=49  Identities=14%  Similarity=0.247  Sum_probs=39.9

Q ss_pred             CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhc
Q 040869           48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAS  101 (131)
Q Consensus        48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s  101 (131)
                      ++++|.++||+.+++   ++..++++|+.|...|++.....  .+|.|.++.-.
T Consensus        23 ~~~~s~~eia~~~~i---~~~~v~~il~~L~~~gli~~~~g--~~ggy~l~~~~   71 (132)
T TIGR00738        23 EGPVSVKEIAERQGI---SRSYLEKILRTLRRAGLVESVRG--PGGGYRLARPP   71 (132)
T ss_pred             CCcCcHHHHHHHHCc---CHHHHHHHHHHHHHCCcEEeccC--CCCCccCCCCH
Confidence            358999999999999   99999999999999999986531  14567776443

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.

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

Probab=96.94  E-value=0.0012  Score=39.82  Aligned_cols=46  Identities=13%  Similarity=0.174  Sum_probs=38.9

Q ss_pred             ChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           39 GIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        39 ~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      .|.+.|....+|++..|||+.+|+   +....+++|..|...|.+...+
T Consensus         4 ~Il~~i~~~~~p~~T~eiA~~~gl---s~~~aR~yL~~Le~eG~V~~~~   49 (62)
T PF04703_consen    4 KILEYIKEQNGPLKTREIADALGL---SIYQARYYLEKLEKEGKVERSP   49 (62)
T ss_dssp             CHHHHHHHHTS-EEHHHHHHHHTS----HHHHHHHHHHHHHCTSEEEES
T ss_pred             HHHHHHHHcCCCCCHHHHHHHhCC---CHHHHHHHHHHHHHCCCEEEec
Confidence            567777754689999999999999   9999999999999999998764

>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=96.92  E-value=0.0015  Score=38.41  Aligned_cols=48  Identities=19%  Similarity=0.311  Sum_probs=39.6

Q ss_pred             HhChHHHHHhCCCC-CCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           37 ELGIADIIHSHGRA-ITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        37 ~L~ifd~l~~~~~~-~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      ++.|+-.|...+++ +|..|||+.+++   ++..+.|+++.|...|++.+..
T Consensus         7 q~~vL~~l~~~~~~~~t~~~la~~l~~---~~~~vs~~v~~L~~~Glv~r~~   55 (62)
T PF12802_consen    7 QFRVLMALARHPGEELTQSELAERLGI---SKSTVSRIVKRLEKKGLVERER   55 (62)
T ss_dssp             HHHHHHHHHHSTTSGEEHHHHHHHHTS----HHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHHCCCCCcCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEeC
Confidence            45566677654433 899999999999   9999999999999999999875

...

>PRK03902 manganese transport transcriptional regulator; Provisional

Probab=96.90  E-value=0.0019  Score=44.76  Aligned_cols=52  Identities=13%  Similarity=0.154  Sum_probs=45.4

Q ss_pred             CCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhccccc
Q 040869           47 HGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLI  105 (131)
Q Consensus        47 ~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~  105 (131)
                      .+++.++.+||+.+++   ++..+.+.++.|...|++....    .+.|.+|+.++.+.
T Consensus        19 ~~~~~~~~ela~~l~v---s~~svs~~l~~L~~~Gli~~~~----~~~i~LT~~G~~~a   70 (142)
T PRK03902         19 EKGYARVSDIAEALSV---HPSSVTKMVQKLDKDEYLIYEK----YRGLVLTPKGKKIG   70 (142)
T ss_pred             cCCCcCHHHHHHHhCC---ChhHHHHHHHHHHHCCCEEEec----CceEEECHHHHHHH
Confidence            3578999999999999   9999999999999999998654    57799999986543

>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR

Probab=96.77  E-value=0.0037  Score=41.77  Aligned_cols=69  Identities=14%  Similarity=0.169  Sum_probs=53.8

Q ss_pred             HHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-C-CCcceecchhccccccC
Q 040869           35 AIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-G-QEEAYGLTAASTLLIKD  107 (131)
Q Consensus        35 a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~-~~~~y~~t~~s~~L~~~  107 (131)
                      ..+..|+..|.. .+++|..|||+.+++   +...+.|+++-|...|++...... | ..-.|.+|+.++.+...
T Consensus        28 ~~q~~iL~~l~~-~~~~t~~ela~~~~~---~~~tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT~~G~~~~~~   98 (118)
T TIGR02337        28 EQQWRILRILAE-QGSMEFTQLANQACI---LRPSLTGILARLERDGLVTRLKASNDQRRVYISLTPKGQALYAS   98 (118)
T ss_pred             HHHHHHHHHHHH-cCCcCHHHHHHHhCC---CchhHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHHHHHH
Confidence            344457777765 468999999999999   999999999999999999986432 1 12359999999866543

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.

>TIGR00122 birA_repr_reg BirA biotin operon repressor domain

Probab=96.74  E-value=0.0043  Score=37.66  Aligned_cols=59  Identities=19%  Similarity=0.194  Sum_probs=45.9

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcccc
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLL  104 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L  104 (131)
                      ++.|+..|.  +++.|..+||+++|+   ....+.+-++.|...|+.....    +..|...+....|
T Consensus         2 ~~~il~~L~--~~~~~~~eLa~~l~v---S~~tv~~~l~~L~~~g~~i~~~----~~g~~l~~~~~ll   60 (69)
T TIGR00122         2 PLRLLALLA--DNPFSGEKLGEALGM---SRTAVNKHIQTLREWGVDVLTV----GKGYRLPPPIPLL   60 (69)
T ss_pred             hHHHHHHHH--cCCcCHHHHHHHHCC---CHHHHHHHHHHHHHCCCeEEec----CCceEecCccccC
Confidence            466788887  467899999999999   9999999999999999865543    3556665544443

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.

>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR

Probab=96.74  E-value=0.0038  Score=45.73  Aligned_cols=65  Identities=17%  Similarity=0.123  Sum_probs=50.0

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCc----ceecchhccccc
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEE----AYGLTAASTLLI  105 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~----~y~~t~~s~~L~  105 (131)
                      +-.|+..|.. .+++|..|||+.+|+   ++..+.|.|+.|...|++.......+.|    .|.+|+.++.+.
T Consensus         3 r~~IL~~L~~-~~~~t~~eLA~~lgi---s~~tV~~~L~~Le~~GlV~r~~~~~~~gRp~~~y~LT~~G~~~~   71 (203)
T TIGR02702         3 KEDILSYLLK-QGQATAAALAEALAI---SPQAVRRHLKDLETEGLIEYEAVVQGMGRPQYHYQLSRQGREQF   71 (203)
T ss_pred             HHHHHHHHHH-cCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCeEEeecccCCCCCceEEEECcchhhhc
Confidence            3457777765 367999999999999   9999999999999999998752100122    379998887544

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.

>PRK11050 manganese transport regulator MntR; Provisional

Probab=96.69  E-value=0.0039  Score=43.86  Aligned_cols=59  Identities=15%  Similarity=0.164  Sum_probs=49.5

Q ss_pred             ChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhccccc
Q 040869           39 GIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLI  105 (131)
Q Consensus        39 ~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~  105 (131)
                      -|...+.. +++.+..|||+.+++   ++..+.|.++.|...|++....    .+.+.+|+.++.+.
T Consensus        41 ~I~~~l~~-~~~~t~~eLA~~l~i---s~stVsr~l~~Le~~GlI~r~~----~~~v~LT~~G~~l~   99 (152)
T PRK11050         41 LIADLIAE-VGEARQVDIAARLGV---SQPTVAKMLKRLARDGLVEMRP----YRGVFLTPEGEKLA   99 (152)
T ss_pred             HHHHHHHh-cCCCCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEec----CCceEECchHHHHH
Confidence            35556653 578999999999999   9999999999999999998765    56789999888664

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

Probab=96.68  E-value=0.0026  Score=38.83  Aligned_cols=45  Identities=18%  Similarity=0.341  Sum_probs=37.3

Q ss_pred             ChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           39 GIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        39 ~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      .|-+.|.. .+.+|..|||.++++   +++.+.-+|..|...|.+.+..
T Consensus         4 ~i~~~l~~-~~~~S~~eLa~~~~~---s~~~ve~mL~~l~~kG~I~~~~   48 (69)
T PF09012_consen    4 EIRDYLRE-RGRVSLAELAREFGI---SPEAVEAMLEQLIRKGYIRKVD   48 (69)
T ss_dssp             HHHHHHHH-S-SEEHHHHHHHTT-----HHHHHHHHHHHHCCTSCEEEE
T ss_pred             HHHHHHHH-cCCcCHHHHHHHHCc---CHHHHHHHHHHHHHCCcEEEec
Confidence            35677775 578999999999999   9999999999999999999875

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

>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=96.66  E-value=0.0042  Score=35.87  Aligned_cols=42  Identities=19%  Similarity=0.190  Sum_probs=35.0

Q ss_pred             hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCc
Q 040869           38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSC   82 (131)
Q Consensus        38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl   82 (131)
                      ..|...|.+.++++|+.+||+.+++   +...++|-+..|...|+
T Consensus         3 ~~il~~L~~~~~~it~~eLa~~l~v---S~rTi~~~i~~L~~~~~   44 (55)
T PF08279_consen    3 KQILKLLLESKEPITAKELAEELGV---SRRTIRRDIKELREWGI   44 (55)
T ss_dssp             HHHHHHHHHTTTSBEHHHHHHHCTS----HHHHHHHHHHHHHTT-
T ss_pred             HHHHHHHHHcCCCcCHHHHHHHhCC---CHHHHHHHHHHHHHCCC
Confidence            3467778555678999999999999   99999999999999993

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 ....

>COG4190 Predicted transcriptional regulator [Transcription]

Probab=96.66  E-value=0.0043  Score=42.79  Aligned_cols=58  Identities=10%  Similarity=0.115  Sum_probs=49.1

Q ss_pred             HHHHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           26 HLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        26 ~~~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      |-..+.+-+--.+.+.+.|+. .+|.|..|+|+.+|-   ++..++|-||.|...|++.-..
T Consensus        55 ye~la~vLsp~nleLl~~Ia~-~~P~Si~ElAe~vgR---dv~nvhr~Ls~l~~~GlI~fe~  112 (144)
T COG4190          55 YEDLARVLSPRNLELLELIAQ-EEPASINELAELVGR---DVKNVHRTLSTLADLGLIFFEE  112 (144)
T ss_pred             HHHHHHHhChhHHHHHHHHHh-cCcccHHHHHHHhCc---chHHHHHHHHHHHhcCeEEEec
Confidence            444455666667888999985 589999999999999   9999999999999999988765

>PHA00738 putative HTH transcription regulator

Probab=96.66  E-value=0.0048  Score=41.10  Aligned_cols=62  Identities=15%  Similarity=0.169  Sum_probs=49.4

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcc
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAST  102 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~  102 (131)
                      .++.|++.|.. ++++++.||++.+++   ..+.+-+-|+.|...|++...... ..-.|++++-..
T Consensus        13 tRr~IL~lL~~-~e~~~V~eLae~l~l---SQptVS~HLKvLreAGLV~srK~G-r~vyY~Ln~~~~   74 (108)
T PHA00738         13 LRRKILELIAE-NYILSASLISHTLLL---SYTTVLRHLKILNEQGYIELYKEG-RTLYAKIRENSK   74 (108)
T ss_pred             HHHHHHHHHHH-cCCccHHHHHHhhCC---CHHHHHHHHHHHHHCCceEEEEEC-CEEEEEECCCcc
Confidence            57789999985 457999999999999   999999999999999999987610 012377776544

>PRK06474 hypothetical protein; Provisional

Probab=96.66  E-value=0.0039  Score=45.05  Aligned_cols=73  Identities=21%  Similarity=0.359  Sum_probs=55.8

Q ss_pred             HHHHHHHHHhChHHHHHhCCCCCCHHHHHhhc-CCCCCCcchHHHHHHHhhcCCceeecccC---CC-Ccceecchhccc
Q 040869           29 SMSLKCAIELGIADIIHSHGRAITLSELVSAL-DIQPTKTTGLFRLMRLLVHSSCFNKTKVN---GQ-EEAYGLTAASTL  103 (131)
Q Consensus        29 ~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~-~~~~~~~~~l~RlLr~L~~~gl~~~~~~~---~~-~~~y~~t~~s~~  103 (131)
                      ..+|.-..++.|++.|...++++|+.||++.+ ++   +...++|.|+.|...|++......   ++ ...|..++..-.
T Consensus         5 ~~~La~p~R~~Il~~L~~~~~~~ta~el~~~l~~i---s~aTvYrhL~~L~e~GLI~~~~~~~~~~~~ek~y~~~~~~~~   81 (178)
T PRK06474          5 AEILMHPVRMKICQVLMRNKEGLTPLELVKILKDV---PQATLYRHLQTMVDSGILHVVKEKKVRSVSEKYYAINEEDAK   81 (178)
T ss_pred             HHhhCCHHHHHHHHHHHhCCCCCCHHHHHHHhcCC---CHHHHHHHHHHHHHCCCEEEeecccccCceeEEEEeccceee
Confidence            34666778899999998655569999999999 67   888999999999999999975421   01 134777776544


Q ss_pred             c
Q 040869          104 L  104 (131)
Q Consensus       104 L  104 (131)
                      +
T Consensus        82 ~   82 (178)
T PRK06474         82 I   82 (178)
T ss_pred             e
Confidence            4

>PF07381 DUF1495: Winged helix DNA-binding domain (DUF1495); InterPro: IPR010863 This family consists of several hypothetical archaeal proteins of around 110 residues in length

Probab=96.64  E-value=0.0053  Score=39.70  Aligned_cols=69  Identities=14%  Similarity=0.174  Sum_probs=52.6

Q ss_pred             HHHHhChHHHHHhC-CCCCCHHHHHhhcCCCCCCcchHHHHHH----------HhhcCCceeecccCCCCcceecchhcc
Q 040869           34 CAIELGIADIIHSH-GRAITLSELVSALDIQPTKTTGLFRLMR----------LLVHSSCFNKTKVNGQEEAYGLTAAST  102 (131)
Q Consensus        34 ~a~~L~ifd~l~~~-~~~~s~~eLA~~~~~~~~~~~~l~RlLr----------~L~~~gl~~~~~~~~~~~~y~~t~~s~  102 (131)
                      .=++.+|+..|.+. +.+.++.|||+.+++   ++..+.-.|+          .|+.+|++.+.....+...|.+|+-++
T Consensus         8 S~~R~~vl~~L~~~yp~~~~~~eIar~v~~---~~snV~GaL~G~g~rY~~e~SLv~lGLV~~~~~~~g~k~Y~lT~~G~   84 (90)
T PF07381_consen    8 SKVRKKVLEYLCSIYPEPAYPSEIARSVGS---DYSNVLGALRGDGKRYNKEDSLVGLGLVEEEEEKGGFKYYRLTEKGK   84 (90)
T ss_pred             HHHHHHHHHHHHHcCCCcCCHHHHHHHHCC---CHHHHHHHHhcCCCCcCcchhHHHcCCeeEeeecCCeeEEEeChhhh
Confidence            55778899999876 689999999999999   8888877774          589999993322112345799999876


Q ss_pred             ccc
Q 040869          103 LLI  105 (131)
Q Consensus       103 ~L~  105 (131)
                      .++
T Consensus        85 ~~~   87 (90)
T PF07381_consen   85 RIA   87 (90)
T ss_pred             hHH
Confidence            543

The function of this family is unknown, although one sequence (Q8U3W1 from SWISSPROT) is described as a putative HTH transcription regulator.

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor

Probab=96.64  E-value=0.0056  Score=34.39  Aligned_cols=44  Identities=14%  Similarity=0.271  Sum_probs=38.0

Q ss_pred             hHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           40 IADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        40 ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      |.+.|.+ .+++|..+|++.+++   ++..+++.|..|...|++....
T Consensus         5 il~~l~~-~~~~s~~~l~~~l~~---s~~tv~~~l~~L~~~g~i~~~~   48 (53)
T smart00420        5 ILELLAQ-QGKVSVEELAELLGV---SEMTIRRDLNKLEEQGLLTRVH   48 (53)
T ss_pred             HHHHHHH-cCCcCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEee
Confidence            5566654 357999999999999   9999999999999999998764

>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=96.61  E-value=0.0053  Score=36.14  Aligned_cols=45  Identities=13%  Similarity=0.276  Sum_probs=40.3

Q ss_pred             ChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           39 GIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        39 ~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      .|.+.|.+ .+.+|+.|||+.+|+   ++..++|=|..|...|++.+..
T Consensus         4 ~Il~~l~~-~~~~s~~ela~~~~V---S~~TiRRDl~~L~~~g~i~r~~   48 (57)
T PF08220_consen    4 QILELLKE-KGKVSVKELAEEFGV---SEMTIRRDLNKLEKQGLIKRTH   48 (57)
T ss_pred             HHHHHHHH-cCCEEHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEEc
Confidence            36777775 478999999999999   9999999999999999999875

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

>COG1959 Predicted transcriptional regulator [Transcription]

Probab=96.55  E-value=0.0057  Score=43.05  Aligned_cols=47  Identities=13%  Similarity=0.213  Sum_probs=39.9

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchh
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAA  100 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~  100 (131)
                      ++.|+++||+..++   ++..|.|+|..|...|+++-...  -.|.|.+..-
T Consensus        24 ~~~s~~~IA~~~~i---s~~~L~kil~~L~kaGlV~S~rG--~~GGy~Lar~   70 (150)
T COG1959          24 GPVSSAEIAERQGI---SPSYLEKILSKLRKAGLVKSVRG--KGGGYRLARP   70 (150)
T ss_pred             CcccHHHHHHHhCc---CHHHHHHHHHHHHHcCCEEeecC--CCCCccCCCC
Confidence            38999999999999   99999999999999999997651  1577877644

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

Probab=96.51  E-value=0.0024  Score=40.29  Aligned_cols=64  Identities=22%  Similarity=0.296  Sum_probs=49.0

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC--Ccceecchhccc
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ--EEAYGLTAASTL  103 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~--~~~y~~t~~s~~  103 (131)
                      ++++|...|.. .+.++..+|.+.+|+   +...+.+-|+.|...|+++....- ++  .-.|++|+.++.
T Consensus         1 vRl~Il~~L~~-~~~~~f~~L~~~l~l---t~g~Ls~hL~~Le~~GyV~~~k~~~~~~p~t~~~lT~~Gr~   67 (80)
T PF13601_consen    1 VRLAILALLYA-NEEATFSELKEELGL---TDGNLSKHLKKLEEAGYVEVEKEFEGRRPRTWYSLTDKGRE   67 (80)
T ss_dssp             HHHHHHHHHHH-HSEEEHHHHHHHTT-----HHHHHHHHHHHHHTTSEEEEEE-SSS--EEEEEE-HHHHH
T ss_pred             CHHHHHHHHhh-cCCCCHHHHHHHhCc---CHHHHHHHHHHHHHCCCEEEEEeccCCCCeEEEEECHHHHH
Confidence            57888999985 467999999999999   999999999999999999976432 11  124888988873

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

Probab=96.45  E-value=0.0042  Score=39.79  Aligned_cols=46  Identities=15%  Similarity=0.196  Sum_probs=41.2

Q ss_pred             HHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhccccc
Q 040869           53 LSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLI  105 (131)
Q Consensus        53 ~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~  105 (131)
                      +.+||+.+++   ++..+.|+++.|...|++....    +..|.+|+.+..+.
T Consensus         2 ~~ela~~l~i---s~stvs~~l~~L~~~glI~r~~----~~~~~lT~~g~~~~   47 (96)
T smart00529        2 TSEIAERLNV---SPPTVTQMLKKLEKDGLVEYEP----YRGITLTEKGRRLA   47 (96)
T ss_pred             HHHHHHHhCC---ChHHHHHHHHHHHHCCCEEEcC----CCceEechhHHHHH
Confidence            5799999999   9999999999999999999986    56899999887654

iron dependent repressor

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

Probab=96.44  E-value=0.0059  Score=37.06  Aligned_cols=41  Identities=20%  Similarity=0.337  Sum_probs=32.8

Q ss_pred             HhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           45 HSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        45 ~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      .+.|-|-|+.|||+.+|++  ++..+.+.|+.|...|+++...
T Consensus        20 ~~~G~~Pt~rEIa~~~g~~--S~~tv~~~L~~Le~kG~I~r~~   60 (65)
T PF01726_consen   20 EENGYPPTVREIAEALGLK--STSTVQRHLKALERKGYIRRDP   60 (65)
T ss_dssp             HHHSS---HHHHHHHHTSS--SHHHHHHHHHHHHHTTSEEEGC
T ss_pred             HHcCCCCCHHHHHHHhCCC--ChHHHHHHHHHHHHCcCccCCC
Confidence            3456788999999999992  3889999999999999999874

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.

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=96.42  E-value=0.0061  Score=39.90  Aligned_cols=47  Identities=15%  Similarity=0.259  Sum_probs=41.7

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      .+..|...|.. ++++|..+||+.+|+   ++..+.|.++.|...|++...
T Consensus         4 ~D~~il~~L~~-~~~~~~~~la~~l~~---s~~tv~~~l~~L~~~g~i~~~   50 (108)
T smart00344        4 IDRKILEELQK-DARISLAELAKKVGL---SPSTVHNRVKRLEEEGVIKGY   50 (108)
T ss_pred             HHHHHHHHHHH-hCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCeece
Confidence            46778888886 468999999999999   999999999999999999843

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

>PRK11014 transcriptional repressor NsrR; Provisional

Probab=96.41  E-value=0.0083  Score=41.51  Aligned_cols=47  Identities=13%  Similarity=0.293  Sum_probs=39.0

Q ss_pred             CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869           48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA   99 (131)
Q Consensus        48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~   99 (131)
                      +.++|..+||+..|+   ++..++++|+.|...|++.....  .+|.|.+..
T Consensus        23 g~~~s~~~ia~~~~i---s~~~vrk~l~~L~~~Glv~s~~G--~~GG~~l~~   69 (141)
T PRK11014         23 GRMTSISEVTEVYGV---SRNHMVKIINQLSRAGYVTAVRG--KNGGIRLGK   69 (141)
T ss_pred             CCccCHHHHHHHHCc---CHHHHHHHHHHHHhCCEEEEecC--CCCCeeecC
Confidence            467999999999999   99999999999999999987651  135676653

>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein

Probab=96.40  E-value=0.0074  Score=44.23  Aligned_cols=59  Identities=15%  Similarity=0.246  Sum_probs=47.5

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchh
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAA  100 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~  100 (131)
                      .++.|...|.+ .++++..|||+.+++   ++..+.|.++.|...|++.+...  ....|.+|+.
T Consensus       144 ~~~~IL~~l~~-~g~~s~~eia~~l~i---s~stv~r~L~~Le~~GlI~r~~~--r~~~~~lT~~  202 (203)
T TIGR01884       144 EELKVLEVLKA-EGEKSVKNIAKKLGK---SLSTISRHLRELEKKGLVEQKGR--KGKRYSLTKL  202 (203)
T ss_pred             HHHHHHHHHHH-cCCcCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEEcC--CccEEEeCCC
Confidence            34567777764 357999999999999   99999999999999999998741  1456888765

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.

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

Probab=96.37  E-value=0.0042  Score=41.62  Aligned_cols=66  Identities=18%  Similarity=0.308  Sum_probs=48.3

Q ss_pred             HHHHhChHHHHHhCCCCCCHHHHHhhcCC--CCCCcchHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869           34 CAIELGIADIIHSHGRAITLSELVSALDI--QPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA   99 (131)
Q Consensus        34 ~a~~L~ifd~l~~~~~~~s~~eLA~~~~~--~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~   99 (131)
                      +..+.-|++.|.+.+++.|++||.+.+.-  ...+..++||.|+.|...|++.+....++...|....
T Consensus         7 T~~R~~Il~~l~~~~~~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~~~~~~~~~~Y~~~~   74 (120)
T PF01475_consen    7 TPQRLAILELLKESPEHLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRKIEFGDGESRYELST   74 (120)
T ss_dssp             HHHHHHHHHHHHHHSSSEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEETTSEEEEEESS
T ss_pred             CHHHHHHHHHHHcCCCCCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEEEEcCCCcceEeecC
Confidence            44567789999876789999999998853  1117778999999999999999875322234565554

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 ....

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

Probab=96.35  E-value=0.0097  Score=35.37  Aligned_cols=57  Identities=21%  Similarity=0.324  Sum_probs=43.5

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA   99 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~   99 (131)
                      +..|...+..  ++.+..||++.+++   +...+.|.++.|...|++...... ....|..|+
T Consensus         9 ~~~il~~l~~--~~~~~~ei~~~~~i---~~~~i~~~l~~L~~~g~i~~~~~~-~~~~~~~~~   65 (78)
T cd00090           9 RLRILRLLLE--GPLTVSELAERLGL---SQSTVSRHLKKLEEAGLVESRREG-RRVYYSLTD   65 (78)
T ss_pred             HHHHHHHHHH--CCcCHHHHHHHHCc---CHhHHHHHHHHHHHCCCeEEEEec-cEEEEEeCC
Confidence            4456666664  23999999999999   999999999999999999976410 124566665

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.

>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=96.35  E-value=0.0069  Score=35.35  Aligned_cols=43  Identities=37%  Similarity=0.435  Sum_probs=35.3

Q ss_pred             HHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHh
Q 040869           28 SSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLL   77 (131)
Q Consensus        28 ~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L   77 (131)
                      .-.+|.+|.++|-|| .   +...|+.|||+.+|+   ++..+...||-.
T Consensus         5 Q~e~L~~A~~~GYfd-~---PR~~tl~elA~~lgi---s~st~~~~LRra   47 (53)
T PF04967_consen    5 QREILKAAYELGYFD-V---PRRITLEELAEELGI---SKSTVSEHLRRA   47 (53)
T ss_pred             HHHHHHHHHHcCCCC-C---CCcCCHHHHHHHhCC---CHHHHHHHHHHH
Confidence            346899999999998 3   367999999999999   888877777643

This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.

>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor

Probab=96.34  E-value=0.013  Score=33.89  Aligned_cols=43  Identities=12%  Similarity=0.251  Sum_probs=37.3

Q ss_pred             hHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           40 IADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        40 ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      |+..|.  .++.|..+|++.+++   +...+.+.++.|...|++....
T Consensus         2 il~~l~--~~~~~~~~i~~~l~i---s~~~v~~~l~~L~~~g~i~~~~   44 (66)
T smart00418        2 ILKLLA--EGELCVCELAEILGL---SQSTVSHHLKKLREAGLVESRR   44 (66)
T ss_pred             HHHHhh--cCCccHHHHHHHHCC---CHHHHHHHHHHHHHCCCeeeee
Confidence            455665  478999999999999   9999999999999999998654

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

Probab=96.31  E-value=0.013  Score=38.07  Aligned_cols=45  Identities=9%  Similarity=0.099  Sum_probs=39.2

Q ss_pred             CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecc
Q 040869           48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLT   98 (131)
Q Consensus        48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t   98 (131)
                      ..++|..|||+.+|+   ++..+.|.|..|...|++....   +.+.|+.+
T Consensus        45 ~~~is~~eLa~~~g~---sr~tVsr~L~~Le~~GlI~r~~---~~~~~~~n   89 (95)
T TIGR01610        45 QDRVTATVIAELTGL---SRTHVSDAIKSLARRRIIFRQG---MMGIVGVN   89 (95)
T ss_pred             CCccCHHHHHHHHCc---CHHHHHHHHHHHHHCCCeeeec---CCceeecC
Confidence            468999999999999   9999999999999999999763   14777766

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

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

Probab=96.27  E-value=0.0091  Score=41.75  Aligned_cols=66  Identities=15%  Similarity=0.315  Sum_probs=49.6

Q ss_pred             HHHhChHHHHHhCCCCCCHHHHHhhcCC--CCCCcchHHHHHHHhhcCCceeecccCCCCcceecchh
Q 040869           35 AIELGIADIIHSHGRAITLSELVSALDI--QPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAA  100 (131)
Q Consensus        35 a~~L~ifd~l~~~~~~~s~~eLA~~~~~--~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~  100 (131)
                      --++.|+++|.+++++.|+.+|-.++.-  .+..+.++||.|..|+..|++.+....++.-+|..+.-
T Consensus        21 ~qR~~vl~~L~~~~~~~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~~~~~~~~~~y~~~~~   88 (145)
T COG0735          21 PQRLAVLELLLEADGHLSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHRLEFEGGKTRYELNSE   88 (145)
T ss_pred             HHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEEEEEeCCCEEEEecCCC
Confidence            3567799999877788999999988763  23378899999999999999998753222234655544

>PRK09462 fur ferric uptake regulator; Provisional

Probab=96.25  E-value=0.012  Score=40.97  Aligned_cols=65  Identities=12%  Similarity=0.264  Sum_probs=47.4

Q ss_pred             HHHHhChHHHHHhC-CCCCCHHHHHhhcCC--CCCCcchHHHHHHHhhcCCceeecccCCCCcceecc
Q 040869           34 CAIELGIADIIHSH-GRAITLSELVSALDI--QPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLT   98 (131)
Q Consensus        34 ~a~~L~ifd~l~~~-~~~~s~~eLA~~~~~--~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t   98 (131)
                      +.-+.-|++.|... ++++|++||-+++.-  .+.+..++||.|+.|+..|++.+....++...|..+
T Consensus        16 T~qR~~Il~~l~~~~~~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli~~~~~~~~~~~y~~~   83 (148)
T PRK09462         16 TLPRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHNFEGGKSVFELT   83 (148)
T ss_pred             CHHHHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCEEEEEcCCCcEEEEeC
Confidence            44567789999864 479999999998843  112788999999999999999886422223456543

>COG4742 Predicted transcriptional regulator [Transcription]

Probab=96.25  E-value=0.0072  Score=46.26  Aligned_cols=67  Identities=9%  Similarity=0.253  Sum_probs=57.8

Q ss_pred             HHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhccccccC
Q 040869           31 SLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIKD  107 (131)
Q Consensus        31 aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~~~  107 (131)
                      .+....+.+|+=.|.  ++|.|.+||-..+++   ++..+..=++-|...|++.+.     ++.|++|+.++.++..
T Consensus         9 if~SekRk~lLllL~--egPkti~EI~~~l~v---s~~ai~pqiKkL~~~~LV~~~-----~~~Y~LS~~G~iiv~k   75 (260)
T COG4742           9 LFLSEKRKDLLLLLK--EGPKTIEEIKNELNV---SSSAILPQIKKLKDKGLVVQE-----GDRYSLSSLGKIIVEK   75 (260)
T ss_pred             HHccHHHHHHHHHHH--hCCCCHHHHHHHhCC---CcHHHHHHHHHHhhCCCEEec-----CCEEEecchHHHHHHH
Confidence            344556778888888  489999999999999   888898899999999999988     6999999999988764

>PRK03573 transcriptional regulator SlyA; Provisional

Probab=96.24  E-value=0.011  Score=40.75  Aligned_cols=65  Identities=18%  Similarity=0.233  Sum_probs=50.3

Q ss_pred             hHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-CcceecchhccccccC
Q 040869           40 IADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIKD  107 (131)
Q Consensus        40 ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~~  107 (131)
                      ++..|...+++.|..|||+.+++   ++..+.|++..|...|++...... |. .-...+|+.++.+...
T Consensus        36 vL~~l~~~~~~~t~~eLa~~l~~---~~~tvt~~v~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~~  102 (144)
T PRK03573         36 TLHNIHQLPPEQSQIQLAKAIGI---EQPSLVRTLDQLEEKGLISRQTCASDRRAKRIKLTEKAEPLISE  102 (144)
T ss_pred             HHHHHHHcCCCCCHHHHHHHhCC---ChhhHHHHHHHHHHCCCEeeecCCCCcCeeeeEEChHHHHHHHH
Confidence            45556544456899999999999   999999999999999999987532 21 1347899998866543

>COG2345 Predicted transcriptional regulator [Transcription]

Probab=96.23  E-value=0.011  Score=44.11  Aligned_cols=61  Identities=18%  Similarity=0.265  Sum_probs=48.0

Q ss_pred             ChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCC----cceecchhccc
Q 040869           39 GIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQE----EAYGLTAASTL  103 (131)
Q Consensus        39 ~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~----~~y~~t~~s~~  103 (131)
                      .|...|.+ .+|+|+.|||+++|+   ++..++|-|..|.+.|++.......|-    ..|.+|..++.
T Consensus        15 ~il~lL~~-~g~~sa~elA~~Lgi---s~~avR~HL~~Le~~Glv~~~~~~~g~GRP~~~y~Lt~~g~~   79 (218)
T COG2345          15 RILELLKK-SGPVSADELAEELGI---SPMAVRRHLDDLEAEGLVEVERQQGGRGRPAKLYRLTEKGRE   79 (218)
T ss_pred             HHHHHHhc-cCCccHHHHHHHhCC---CHHHHHHHHHHHHhCcceeeeeccCCCCCCceeeeecccchh
Confidence            35556664 589999999999999   999999999999999998865322212    35999988764

>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]

Probab=96.17  E-value=0.01  Score=42.03  Aligned_cols=53  Identities=9%  Similarity=0.063  Sum_probs=47.6

Q ss_pred             CCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcccccc
Q 040869           47 HGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIK  106 (131)
Q Consensus        47 ~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~~  106 (131)
                      ..+++...+||+.+++   .|+.+..+++-|...|++...+    .+.+.+|+.++.++.
T Consensus        21 ~~~~~~~~diA~~L~V---sp~sVt~ml~rL~~~GlV~~~~----y~gi~LT~~G~~~a~   73 (154)
T COG1321          21 EKGFARTKDIAERLKV---SPPSVTEMLKRLERLGLVEYEP----YGGVTLTEKGREKAK   73 (154)
T ss_pred             ccCcccHHHHHHHhCC---CcHHHHHHHHHHHHCCCeEEec----CCCeEEChhhHHHHH
Confidence            3689999999999999   9999999999999999999987    789999998875544

>PRK11639 zinc uptake transcriptional repressor; Provisional

Probab=96.14  E-value=0.013  Score=41.98  Aligned_cols=54  Identities=17%  Similarity=0.294  Sum_probs=44.5

Q ss_pred             HHHHhChHHHHHhCCCCCCHHHHHhhcCC--CCCCcchHHHHHHHhhcCCceeecc
Q 040869           34 CAIELGIADIIHSHGRAITLSELVSALDI--QPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        34 ~a~~L~ifd~l~~~~~~~s~~eLA~~~~~--~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      +.-+..|++.|...++++|++||.+++.-  ...+..++||.|+.|+..|++.+..
T Consensus        25 T~qR~~IL~~l~~~~~hlSa~eI~~~L~~~~~~is~aTVYRtL~~L~e~Glv~~~~   80 (169)
T PRK11639         25 TPQRLEVLRLMSLQPGAISAYDLLDLLREAEPQAKPPTVYRALDFLLEQGFVHKVE   80 (169)
T ss_pred             CHHHHHHHHHHHhcCCCCCHHHHHHHHHhhCCCCCcchHHHHHHHHHHCCCEEEEe
Confidence            45667789999876789999999998864  1227789999999999999999875

>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=96.12  E-value=0.0054  Score=35.77  Aligned_cols=47  Identities=23%  Similarity=0.375  Sum_probs=38.8

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      ++.+...|.+. +++|..+||+.+++   ++..+.|+++-|...|++....
T Consensus         5 q~~iL~~l~~~-~~~~~~~la~~~~~---~~~~~t~~i~~L~~~g~I~r~~   51 (59)
T PF01047_consen    5 QFRILRILYEN-GGITQSELAEKLGI---SRSTVTRIIKRLEKKGLIERER   51 (59)
T ss_dssp             HHHHHHHHHHH-SSEEHHHHHHHHTS----HHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHHc-CCCCHHHHHHHHCC---ChhHHHHHHHHHHHCCCEEecc
Confidence            44555666653 57999999999999   9999999999999999999864

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 ....

>PRK11512 DNA-binding transcriptional repressor MarR; Provisional

Probab=96.11  E-value=0.013  Score=40.44  Aligned_cols=66  Identities=18%  Similarity=0.202  Sum_probs=51.1

Q ss_pred             hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-CcceecchhccccccC
Q 040869           38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIKD  107 (131)
Q Consensus        38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~~  107 (131)
                      ..|+-.|.. .+++|..|||+.+++   ++..+.|++..|...|++.+.... |+ .-...+|+.++.+...
T Consensus        43 ~~vL~~l~~-~~~~t~~eLa~~l~i---~~~tvsr~l~~Le~~GlI~R~~~~~DrR~~~l~LT~~G~~~~~~  110 (144)
T PRK11512         43 FKVLCSIRC-AACITPVELKKVLSV---DLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTSGAAICEQ  110 (144)
T ss_pred             HHHHHHHHH-cCCCCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEeccCcccCCeeEeEEChhHHHHHHH
Confidence            345666664 468999999999999   999999999999999999986532 21 1346889888866543

>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family

Probab=96.05  E-value=0.012  Score=38.85  Aligned_cols=67  Identities=18%  Similarity=0.275  Sum_probs=49.9

Q ss_pred             HHhChHHHHH--hC-CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhccccc
Q 040869           36 IELGIADIIH--SH-GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLI  105 (131)
Q Consensus        36 ~~L~ifd~l~--~~-~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~  105 (131)
                      .++.|+..|.  .. ++++|..+||..+++   ++..+.|+++.|...|++.+.... |. .-.+.+|+.++.+.
T Consensus        26 ~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~---~~stvs~~i~~Le~kg~I~r~~~~~D~R~~~i~lT~~G~~~~   97 (109)
T TIGR01889        26 EELLILYYLGKLENNEGKLTLKEIIKEILI---KQSALVKIIKKLSKKGYLSKERSEDDERKVIISINKEQRSKI   97 (109)
T ss_pred             HHHHHHHHHHhhhccCCcCcHHHHHHHHCC---CHHHHHHHHHHHHHCCCEeccCCcccCCeEEEEECHHHHHHH
Confidence            3445566665  22 478999999999999   999999999999999999986532 21 12367788776554

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.

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=96.01  E-value=0.01  Score=34.17  Aligned_cols=37  Identities=16%  Similarity=0.232  Sum_probs=33.1

Q ss_pred             CCCC-CHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           48 GRAI-TLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        48 ~~~~-s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      +..+ |..|||+.+|+   +...+.+.++.|...|++....
T Consensus        17 ~~~l~s~~~la~~~~v---s~~tv~~~l~~L~~~g~i~~~~   54 (60)
T smart00345       17 GDKLPSERELAAQLGV---SRTTVREALSRLEAEGLVQRRP   54 (60)
T ss_pred             CCcCcCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEec
Confidence            3456 99999999999   9999999999999999998764

>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed

Probab=95.98  E-value=0.017  Score=40.67  Aligned_cols=47  Identities=17%  Similarity=0.312  Sum_probs=39.7

Q ss_pred             CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869           48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA   99 (131)
Q Consensus        48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~   99 (131)
                      ++++|..+||++.++   ++..|.++|..|+..|+++-...  ..|.|.++.
T Consensus        22 ~~~~s~~eIA~~~~i---s~~~L~kIl~~L~~aGlv~S~rG--~~GGy~La~   68 (153)
T PRK11920         22 GKLSRIPEIARAYGV---SELFLFKILQPLVEAGLVETVRG--RNGGVRLGR   68 (153)
T ss_pred             CCcCcHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEeecC--CCCCeeecC
Confidence            467899999999999   99999999999999999997652  146677664

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

Probab=95.87  E-value=0.026  Score=33.04  Aligned_cols=34  Identities=18%  Similarity=0.179  Sum_probs=31.0

Q ss_pred             CCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           51 ITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        51 ~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      .|..+||..+++   +...+.+.+..|...|++....
T Consensus        26 ~~~~~la~~~~i---s~~~v~~~l~~L~~~G~i~~~~   59 (66)
T cd07377          26 PSERELAEELGV---SRTTVREALRELEAEGLVERRP   59 (66)
T ss_pred             CCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEecC
Confidence            459999999999   9999999999999999998654

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

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

Probab=95.85  E-value=0.026  Score=38.58  Aligned_cols=51  Identities=18%  Similarity=0.275  Sum_probs=44.5

Q ss_pred             HHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           33 KCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        33 ~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      +..++..|.+.+.+ .|.+|..|++..+|+   +...+.+.+|.|++.|-+...+
T Consensus        10 r~eLk~rIvElVRe-~GRiTi~ql~~~TGa---sR~Tvk~~lreLVa~G~l~~~G   60 (127)
T PF06163_consen   10 REELKARIVELVRE-HGRITIKQLVAKTGA---SRNTVKRYLRELVARGDLYRHG   60 (127)
T ss_pred             HHHHHHHHHHHHHH-cCCccHHHHHHHHCC---CHHHHHHHHHHHHHcCCeEeCC
Confidence            45567788888876 478999999999999   9999999999999999888765

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

Probab=95.82  E-value=0.028  Score=35.40  Aligned_cols=50  Identities=10%  Similarity=0.001  Sum_probs=42.4

Q ss_pred             CCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceee-cccCCCCcceecchhcc
Q 040869           47 HGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNK-TKVNGQEEAYGLTAAST  102 (131)
Q Consensus        47 ~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~-~~~~~~~~~y~~t~~s~  102 (131)
                      .+.|+...+||+.++.   ++..++-.|..|..+|++.. ...   .+.|-+|..+-
T Consensus        20 ~~~PVgSk~ia~~l~~---s~aTIRN~M~~Le~lGlve~~p~~---s~GriPT~~aY   70 (78)
T PF03444_consen   20 TGEPVGSKTIAEELGR---SPATIRNEMADLEELGLVESQPHP---SGGRIPTDKAY   70 (78)
T ss_pred             cCCCcCHHHHHHHHCC---ChHHHHHHHHHHHHCCCccCCCCC---CCCCCcCHHHH
Confidence            3789999999999999   99999999999999999974 321   47788887764

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

>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=95.76  E-value=0.023  Score=33.84  Aligned_cols=38  Identities=8%  Similarity=0.242  Sum_probs=34.4

Q ss_pred             CCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           47 HGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        47 ~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      .+++++..+||+.+|+   .+..+..+++-|...|++...+
T Consensus        19 ~~~~v~~~~iA~~L~v---s~~tvt~ml~~L~~~GlV~~~~   56 (60)
T PF01325_consen   19 EGGPVRTKDIAERLGV---SPPTVTEMLKRLAEKGLVEYEP   56 (60)
T ss_dssp             CTSSBBHHHHHHHHTS----HHHHHHHHHHHHHTTSEEEET
T ss_pred             CCCCccHHHHHHHHCC---ChHHHHHHHHHHHHCCCEEecC
Confidence            4689999999999999   9999999999999999999764

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 ....

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

Probab=95.62  E-value=0.014  Score=37.33  Aligned_cols=61  Identities=20%  Similarity=0.221  Sum_probs=46.5

Q ss_pred             hHHHHHhCCCCCCHHHHHhhc-CCCCCCcchHHHHHHHhhcCCceeecccCCC--Ccceecchhccccc
Q 040869           40 IADIIHSHGRAITLSELVSAL-DIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQ--EEAYGLTAASTLLI  105 (131)
Q Consensus        40 ifd~l~~~~~~~s~~eLA~~~-~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~--~~~y~~t~~s~~L~  105 (131)
                      |...|.  .++....||.+.+ |+   ++..|.+-|+.|...|++.+......  .-.|.+|+.++.|.
T Consensus        10 IL~~l~--~g~~rf~el~~~l~~i---s~~~L~~~L~~L~~~GLv~r~~~~~~p~~v~Y~LT~~G~~l~   73 (90)
T PF01638_consen   10 ILRALF--QGPMRFSELQRRLPGI---SPKVLSQRLKELEEAGLVERRVYPEVPPRVEYSLTEKGKELL   73 (90)
T ss_dssp             HHHHHT--TSSEEHHHHHHHSTTS----HHHHHHHHHHHHHTTSEEEEEESSSSSEEEEEE-HHHHHHH
T ss_pred             HHHHHH--hCCCcHHHHHHhcchh---HHHHHHHHHHHHHHcchhhcccccCCCCCCccCCCcCHHHHH
Confidence            455565  3799999999999 89   89999999999999999988642111  13599999998775

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

>PRK06266 transcription initiation factor E subunit alpha; Validated

Probab=95.50  E-value=0.065  Score=38.79  Aligned_cols=45  Identities=11%  Similarity=0.131  Sum_probs=39.8

Q ss_pred             hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      ..|++.|.. .+++|.+|||..+|+   ....++|+|..|...|++...
T Consensus        25 ~~Vl~~L~~-~g~~tdeeLA~~Lgi---~~~~VRk~L~~L~e~gLv~~~   69 (178)
T PRK06266         25 FEVLKALIK-KGEVTDEEIAEQTGI---KLNTVRKILYKLYDARLADYK   69 (178)
T ss_pred             hHHHHHHHH-cCCcCHHHHHHHHCC---CHHHHHHHHHHHHHCCCeEEe
Confidence            448888875 468999999999999   999999999999999999943

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

Probab=95.44  E-value=0.016  Score=30.30  Aligned_cols=31  Identities=13%  Similarity=0.276  Sum_probs=25.8

Q ss_pred             CCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCce
Q 040869           50 AITLSELVSALDIQPTKTTGLFRLMRLLVHSSCF   83 (131)
Q Consensus        50 ~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~   83 (131)
                      |+|-+|||..+|+   .++.+.|+|..|...|++
T Consensus         2 ~mtr~diA~~lG~---t~ETVSR~l~~l~~~glI   32 (32)
T PF00325_consen    2 PMTRQDIADYLGL---TRETVSRILKKLERQGLI   32 (32)
T ss_dssp             E--HHHHHHHHTS----HHHHHHHHHHHHHTTSE
T ss_pred             CcCHHHHHHHhCC---cHHHHHHHHHHHHHcCCC
Confidence            5788999999999   999999999999988874

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 ....

>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional

Probab=95.38  E-value=0.032  Score=39.11  Aligned_cols=47  Identities=11%  Similarity=0.221  Sum_probs=42.3

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      .+..|.+.|.+ ++..|..+||+++|+   ++..+.|=++-|...|++...
T Consensus        10 ~D~~Il~~Lq~-d~R~s~~eiA~~lgl---S~~tV~~Ri~rL~~~GvI~~~   56 (153)
T PRK11179         10 LDRGILEALME-NARTPYAELAKQFGV---SPGTIHVRVEKMKQAGIITGT   56 (153)
T ss_pred             HHHHHHHHHHH-cCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCeeeE
Confidence            57789999986 578999999999999   999999999999999999843

>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]

Probab=95.35  E-value=0.023  Score=43.49  Aligned_cols=48  Identities=35%  Similarity=0.453  Sum_probs=43.6

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      +..|.++|.+.||-++-+||.+++|.   +...+.|++|-|..+|++++..
T Consensus       197 e~~il~~i~~~GGri~Q~eL~r~lgl---sktTvsR~L~~LEk~GlIe~~K  244 (258)
T COG2512         197 EKEILDLIRERGGRITQAELRRALGL---SKTTVSRILRRLEKRGLIEKEK  244 (258)
T ss_pred             HHHHHHHHHHhCCEEeHHHHHHhhCC---ChHHHHHHHHHHHhCCceEEEE
Confidence            44588888877888999999999999   9999999999999999999876

>PRK11169 leucine-responsive transcriptional regulator; Provisional

Probab=95.24  E-value=0.032  Score=39.59  Aligned_cols=47  Identities=17%  Similarity=0.204  Sum_probs=42.5

Q ss_pred             HHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceee
Q 040869           35 AIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNK   85 (131)
Q Consensus        35 a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~   85 (131)
                      .++..|...|.+ ++.+|..|||+++|+   ++..+.|=++-|...|++..
T Consensus        14 ~~D~~IL~~Lq~-d~R~s~~eiA~~lgl---S~~tv~~Ri~rL~~~GvI~~   60 (164)
T PRK11169         14 RIDRNILNELQK-DGRISNVELSKRVGL---SPTPCLERVRRLERQGFIQG   60 (164)
T ss_pred             HHHHHHHHHhcc-CCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCeEE
Confidence            368889999986 578999999999999   99999999999999999985

>COG1522 Lrp Transcriptional regulators [Transcription]

Probab=95.04  E-value=0.048  Score=37.66  Aligned_cols=49  Identities=14%  Similarity=0.268  Sum_probs=43.2

Q ss_pred             HHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           35 AIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        35 a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      ..+..|...|.+ +++.|..+||+++|+   ++..+.+-++-|...|++....
T Consensus         8 ~~D~~IL~~L~~-d~r~~~~eia~~lgl---S~~~v~~Ri~~L~~~GiI~~~~   56 (154)
T COG1522           8 DIDRRILRLLQE-DARISNAELAERVGL---SPSTVLRRIKRLEEEGVIKGYT   56 (154)
T ss_pred             HHHHHHHHHHHH-hCCCCHHHHHHHHCC---CHHHHHHHHHHHHHCCceeeEE
Confidence            356788899986 567999999999999   9999999999999999998764

>PF14394 DUF4423: Domain of unknown function (DUF4423)

Probab=95.04  E-value=0.11  Score=37.39  Aligned_cols=63  Identities=16%  Similarity=0.072  Sum_probs=50.2

Q ss_pred             hHHHHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhc--CCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcc
Q 040869           25 SHLSSMSLKCAIELGIADIIHSHGRAITLSELVSAL--DIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAST  102 (131)
Q Consensus        25 ~~~~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~--~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~  102 (131)
                      ..|...+++..+.+.        ++.-.+.+||+++  ++   +...+..-|..|...|++++.+    +|.|..|..+-
T Consensus        22 ~~W~~~~ir~l~~l~--------~~~~d~~~iak~l~p~i---s~~ev~~sL~~L~~~gli~k~~----~g~y~~t~~~l   86 (171)
T PF14394_consen   22 SSWYHPAIRELLPLM--------PFAPDPEWIAKRLRPKI---SAEEVRDSLEFLEKLGLIKKDG----DGKYVQTDKSL   86 (171)
T ss_pred             hhhHHHHHHHHhhcC--------CCCCCHHHHHHHhcCCC---CHHHHHHHHHHHHHCCCeEECC----CCcEEEeccee
Confidence            456666776665543        2334899999999  89   9999999999999999999987    78999887543

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

Probab=95.00  E-value=0.04  Score=34.14  Aligned_cols=50  Identities=22%  Similarity=0.278  Sum_probs=43.8

Q ss_pred             HHHhChHHHHHhCC-CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           35 AIELGIADIIHSHG-RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        35 a~~L~ifd~l~~~~-~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      ..+..+.+.|+++. .+++..||++.+|.   |+..+...++.|...|++....
T Consensus         2 ~~~~~~Le~I~rsR~~Gi~q~~L~~~~~~---D~r~i~~~~k~L~~~gLI~k~~   52 (75)
T PF04182_consen    2 DIQYCLLERIARSRYNGITQSDLSKLLGI---DPRSIFYRLKKLEKKGLIVKQS   52 (75)
T ss_pred             chHHHHHHHHHhcCCCCEehhHHHHHhCC---CchHHHHHHHHHHHCCCEEEEE
Confidence            35667888898654 68999999999999   9999999999999999999875

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

>PRK10870 transcriptional repressor MprA; Provisional

Probab=94.94  E-value=0.051  Score=39.03  Aligned_cols=67  Identities=18%  Similarity=0.179  Sum_probs=50.8

Q ss_pred             hChHHHHHhC-CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-CcceecchhccccccC
Q 040869           38 LGIADIIHSH-GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIKD  107 (131)
Q Consensus        38 L~ifd~l~~~-~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~~  107 (131)
                      ..|.-.|... ++++|..|||+.+++   ++..+.|++.-|...|++.+.... |+ .-...+|+.++.+...
T Consensus        58 ~~iL~~L~~~~~~~it~~eLa~~l~l---~~~tvsr~v~rLe~kGlV~R~~~~~DrR~~~v~LT~~G~~~~~~  127 (176)
T PRK10870         58 FMALITLESQENHSIQPSELSCALGS---SRTNATRIADELEKRGWIERRESDNDRRCLHLQLTEKGHEFLRE  127 (176)
T ss_pred             HHHHHHHhcCCCCCcCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHH
Confidence            3355555432 367999999999999   999999999999999999986532 21 2347899998866543

>TIGR00498 lexA SOS regulatory protein LexA

Probab=94.90  E-value=0.063  Score=38.97  Aligned_cols=49  Identities=14%  Similarity=0.287  Sum_probs=39.5

Q ss_pred             HHhChHHHHH----hCCCCCCHHHHHhhcCCCCCC-cchHHHHHHHhhcCCceeecc
Q 040869           36 IELGIADIIH----SHGRAITLSELVSALDIQPTK-TTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        36 ~~L~ifd~l~----~~~~~~s~~eLA~~~~~~~~~-~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      .+..|++.|.    +.+-+.|..|||+.+|+   + +..+++.|+.|...|++....
T Consensus         7 ~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~---~s~~tv~~~l~~L~~~g~i~~~~   60 (199)
T TIGR00498         7 RQQEVLDLIRAHIESTGYPPSIREIARAVGL---RSPSAAEEHLKALERKGYIERDP   60 (199)
T ss_pred             HHHHHHHHHHHHHHhcCCCCcHHHHHHHhCC---CChHHHHHHHHHHHHCCCEecCC
Confidence            3445555554    23457899999999999   8 899999999999999999874

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.

>COG3432 Predicted transcriptional regulator [Transcription]

Probab=94.90  E-value=0.017  Score=37.74  Aligned_cols=60  Identities=17%  Similarity=0.309  Sum_probs=48.2

Q ss_pred             hHHHHH-hCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCc---ceecchhcccccc
Q 040869           40 IADIIH-SHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEE---AYGLTAASTLLIK  106 (131)
Q Consensus        40 ifd~l~-~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~---~y~~t~~s~~L~~  106 (131)
                      |||+|. ..++++...-|.-.+++   +-....+++..|+..|++....    ++   .|.+|+.+.-|.+
T Consensus        20 i~dIL~~~~~~~~~~Tri~y~aNl---ny~~~~~yi~~L~~~Gli~~~~----~~~~~~y~lT~KG~~fle   83 (95)
T COG3432          20 IFDILKAISEGGIGITRIIYGANL---NYKRAQKYIEMLVEKGLIIKQD----NGRRKVYELTEKGKRFLE   83 (95)
T ss_pred             HHHHHHHhcCCCCCceeeeeecCc---CHHHHHHHHHHHHhCCCEEecc----CCccceEEEChhHHHHHH
Confidence            466665 34678889999999999   9999999999999999666554    33   6999999986643

>COG4189 Predicted transcriptional regulator [Transcription]

Probab=94.77  E-value=0.09  Score=39.95  Aligned_cols=73  Identities=11%  Similarity=0.253  Sum_probs=56.1

Q ss_pred             HHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC--CCCcceecchhcccc
Q 040869           28 SSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN--GQEEAYGLTAASTLL  104 (131)
Q Consensus        28 ~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~--~~~~~y~~t~~s~~L  104 (131)
                      ..++|...+++.|.+.|+. .+|+.+.|||+++|+   +.+.+.-=+..|...|+++.....  -|.++.+-......+
T Consensus        16 v~kalaS~vRv~Il~lL~~-k~plNvneiAe~lgL---pqst~s~~ik~Le~aGlirT~t~karkG~QKiC~s~~~ei~   90 (308)
T COG4189          16 VLKALASKVRVAILQLLHR-KGPLNVNEIAEALGL---PQSTMSANIKVLEKAGLIRTETVKARKGSQKICISTTDEIE   90 (308)
T ss_pred             HHHHHHHHHHHHHHHHHHH-hCCCCHHHHHHHhCC---chhhhhhhHHHHHhcCceeeeeeccccCceeEeEeecceEE
Confidence            4568889999999999986 579999999999999   888898899999999999865321  223444444444433

>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms

Probab=94.74  E-value=0.035  Score=30.98  Aligned_cols=23  Identities=9%  Similarity=0.508  Sum_probs=18.3

Q ss_pred             CCCHHHHHhhcCCCCCCcchHHHHHH
Q 040869           50 AITLSELVSALDIQPTKTTGLFRLMR   75 (131)
Q Consensus        50 ~~s~~eLA~~~~~~~~~~~~l~RlLr   75 (131)
                      +.|+.+||+.+|+   +...++|+++
T Consensus        21 G~si~~IA~~~gv---sr~TvyR~l~   43 (45)
T PF02796_consen   21 GMSIAEIAKQFGV---SRSTVYRYLN   43 (45)
T ss_dssp             T--HHHHHHHTTS----HHHHHHHHC
T ss_pred             CCCHHHHHHHHCc---CHHHHHHHHh
Confidence            3999999999999   9999999985

Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....

>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed

Probab=94.36  E-value=0.089  Score=42.67  Aligned_cols=45  Identities=18%  Similarity=0.251  Sum_probs=39.2

Q ss_pred             CCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecc
Q 040869           47 HGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLT   98 (131)
Q Consensus        47 ~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t   98 (131)
                      .++|.|.+||++++++   +++.+++++..|...|++.+.+    ++.|.+.
T Consensus       307 ~g~~~t~~~La~~l~~---~~~~v~~iL~~L~~agLI~~~~----~g~~~l~  351 (412)
T PRK04214        307 HGKALDVDEIRRLEPM---GYDELGELLCELARIGLLRRGE----RGQWVLA  351 (412)
T ss_pred             cCCCCCHHHHHHHhCC---CHHHHHHHHHHHHhCCCeEecC----CCceEec
Confidence            3679999999999999   9999999999999999999765    4567655

>COG1378 Predicted transcriptional regulators [Transcription]

Probab=94.32  E-value=0.083  Score=40.16  Aligned_cols=52  Identities=13%  Similarity=0.202  Sum_probs=44.1

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhccccc
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLI  105 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~  105 (131)
                      |+.|+.|||+.+|+   +...+|.+||.|...|++.....  .+..|+.-+....+.
T Consensus        29 g~~tA~eis~~sgv---P~~kvY~vl~sLe~kG~v~~~~g--~P~~y~av~p~~~i~   80 (247)
T COG1378          29 GEATAKEISEASGV---PRPKVYDVLRSLEKKGLVEVIEG--RPKKYRAVPPEELIE   80 (247)
T ss_pred             CCccHHHHHHHcCC---CchhHHHHHHHHHHCCCEEeeCC--CCceEEeCCHHHHHH
Confidence            78999999999999   99999999999999999998641  267898887765443

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

Probab=94.31  E-value=0.096  Score=40.88  Aligned_cols=56  Identities=16%  Similarity=0.246  Sum_probs=43.8

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCc-eeecccCCCCcceecchh
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSC-FNKTKVNGQEEAYGLTAA  100 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl-~~~~~~~~~~~~y~~t~~  100 (131)
                      ...|.+.|.+ +.+.+.++||+++|+   +...+.|.++.|...|+ +....    +..|.+.+-
T Consensus         6 ~~~il~~L~~-~~~~s~~~LA~~lgv---sr~tV~~~l~~L~~~G~~i~~~~----~~Gy~L~~~   62 (319)
T PRK11886          6 MLQLLSLLAD-GDFHSGEQLGEELGI---SRAAIWKHIQTLEEWGLDIFSVK----GKGYRLAEP   62 (319)
T ss_pred             HHHHHHHHHc-CCCcCHHHHHHHHCC---CHHHHHHHHHHHHHCCCceEEec----CCeEEecCc
Confidence            4567778874 578999999999999   99999999999999999 44333    345765443

>PRK13509 transcriptional repressor UlaR; Provisional

Probab=94.27  E-value=0.088  Score=39.88  Aligned_cols=47  Identities=15%  Similarity=0.172  Sum_probs=41.6

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      +..|.+.|.+ .+.++..|||+.+|+   .+..++|-|+.|...|++.+..
T Consensus         7 ~~~Il~~l~~-~~~~~~~ela~~l~v---S~~TirRdL~~Le~~g~i~r~~   53 (251)
T PRK13509          7 HQILLELLAQ-LGFVTVEKVIERLGI---SPATARRDINKLDESGKLKKVR   53 (251)
T ss_pred             HHHHHHHHHH-cCCcCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEec
Confidence            3457888875 578999999999999   9999999999999999999875

>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY

Probab=94.18  E-value=0.39  Score=36.52  Aligned_cols=46  Identities=11%  Similarity=0.195  Sum_probs=40.5

Q ss_pred             ChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           39 GIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        39 ~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      .|++.|...++-++..+||+++|+   .+..+++-+|.|.+.|++.-.+
T Consensus       187 ~IL~~L~~~egrlse~eLAerlGV---SRs~ireAlrkLE~aGvIe~r~  232 (251)
T TIGR02787       187 HIFEELDGNEGLLVASKIADRVGI---TRSVIVNALRKLESAGVIESRS  232 (251)
T ss_pred             HHHHHhccccccccHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEecc
Confidence            578888754478999999999999   9999999999999999999763

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.

>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional

Probab=94.16  E-value=0.073  Score=44.14  Aligned_cols=68  Identities=21%  Similarity=0.238  Sum_probs=53.4

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcccccc-Ccc
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIK-DKP  109 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~~-~~~  109 (131)
                      .+..|...|.. .+++|..+||+++++   ++..+.|++.-|.+.|++.....  ....|.+|+-++.+.. ..|
T Consensus         7 ~e~~vL~~L~~-~~~~s~~eLA~~l~l---~~~tVt~~i~~Le~kGlV~~~~~--~~~~i~LTeeG~~~~~~g~p   75 (489)
T PRK04172          7 NEKKVLKALKE-LKEATLEELAEKLGL---PPEAVMRAAEWLEEKGLVKVEER--VEEVYVLTEEGKKYAEEGLP   75 (489)
T ss_pred             HHHHHHHHHHh-CCCCCHHHHHHHhCc---CHHHHHHHHHHHHhCCCEEEEee--eEEEEEECHHHHHHHHhcCH
Confidence            44556677764 468999999999999   99999999999999999997641  1356999999985544 444

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

Probab=94.13  E-value=0.081  Score=39.53  Aligned_cols=54  Identities=15%  Similarity=0.170  Sum_probs=44.7

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcccccc
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIK  106 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~~  106 (131)
                      ..+|..|||+.+++   ++..+.|+++.|...|++.+.... ....+.+|+.++.+..
T Consensus        20 ~~IS~~eLA~~L~i---S~~Tvsr~Lk~LEe~GlI~R~~~~-r~~~v~LTekG~~ll~   73 (217)
T PRK14165         20 VKISSSEFANHTGT---SSKTAARILKQLEDEGYITRTIVP-RGQLITITEKGLDVLY   73 (217)
T ss_pred             CCcCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEEEcC-CceEEEECHHHHHHHH
Confidence            56999999999999   999999999999999999876421 1456899998885543

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

Probab=93.92  E-value=0.11  Score=28.66  Aligned_cols=37  Identities=16%  Similarity=0.287  Sum_probs=26.7

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHH
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRL   76 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~   76 (131)
                      ++..|...|.+ ++..|+.+||+.+|+   ++..+.+=++.
T Consensus         4 ~D~~Il~~Lq~-d~r~s~~~la~~lgl---S~~~v~~Ri~r   40 (42)
T PF13404_consen    4 LDRKILRLLQE-DGRRSYAELAEELGL---SESTVRRRIRR   40 (42)
T ss_dssp             HHHHHHHHHHH--TTS-HHHHHHHHTS----HHHHHHHHHH
T ss_pred             HHHHHHHHHHH-cCCccHHHHHHHHCc---CHHHHHHHHHH
Confidence            56778889986 578999999999999   77766554443

...

>PRK05638 threonine synthase; Validated

Probab=93.92  E-value=0.1  Score=42.70  Aligned_cols=63  Identities=22%  Similarity=0.299  Sum_probs=46.8

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcC--CCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcccc
Q 040869           37 ELGIADIIHSHGRAITLSELVSALD--IQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLL  104 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~--~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L  104 (131)
                      ++.|+..|.+  ++++..||++.++  +   ....+++.|+.|...|+++..........|.+|+.++.+
T Consensus       373 r~~IL~~L~~--~~~~~~el~~~l~~~~---s~~~v~~hL~~Le~~GLV~~~~~~g~~~~Y~Lt~~g~~~  437 (442)
T PRK05638        373 KLEILKILSE--REMYGYEIWKALGKPL---KYQAVYQHIKELEELGLIEEAYRKGRRVYYKLTEKGRRL  437 (442)
T ss_pred             HHHHHHHHhh--CCccHHHHHHHHcccC---CcchHHHHHHHHHHCCCEEEeecCCCcEEEEECcHHHHH
Confidence            3446666763  6899999999998  7   788999999999999999753110112348999887744

>TIGR00373 conserved hypothetical protein TIGR00373

Probab=93.90  E-value=0.11  Score=36.90  Aligned_cols=45  Identities=13%  Similarity=-0.012  Sum_probs=39.0

Q ss_pred             hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      ..|+++|.. .+.+|-+|||..+|+   +...++|+|..|...|++...
T Consensus        17 v~Vl~aL~~-~~~~tdEeLa~~Lgi---~~~~VRk~L~~L~e~~Lv~~~   61 (158)
T TIGR00373        17 GLVLFSLGI-KGEFTDEEISLELGI---KLNEVRKALYALYDAGLADYK   61 (158)
T ss_pred             HHHHHHHhc-cCCCCHHHHHHHHCC---CHHHHHHHHHHHHHCCCceee
Confidence            457888874 368999999999999   999999999999999999543

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.

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

Probab=93.86  E-value=0.081  Score=32.15  Aligned_cols=36  Identities=14%  Similarity=0.272  Sum_probs=33.3

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      -++|-++||..+|+   ....+.|+|+.|...|++....
T Consensus        27 ~~lt~~~iA~~~g~---sr~tv~r~l~~l~~~g~I~~~~   62 (76)
T PF13545_consen   27 LPLTQEEIADMLGV---SRETVSRILKRLKDEGIIEVKR   62 (76)
T ss_dssp             EESSHHHHHHHHTS---CHHHHHHHHHHHHHTTSEEEET
T ss_pred             ecCCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEcC
Confidence            47999999999999   9999999999999999999763

...

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

Probab=93.79  E-value=0.12  Score=38.64  Aligned_cols=45  Identities=20%  Similarity=0.314  Sum_probs=38.3

Q ss_pred             ChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           39 GIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        39 ~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      .|.+.|...+.+.|++|+|+++|+   +....+|-|-+|++.|++..+
T Consensus       162 ~i~~~~~~~~~~~Taeela~~~gi---SRvTaRRYLeyl~~~~~l~a~  206 (224)
T COG4565         162 KVREALKEPDQELTAEELAQALGI---SRVTARRYLEYLVSNGILEAE  206 (224)
T ss_pred             HHHHHHhCcCCccCHHHHHHHhCc---cHHHHHHHHHHHHhcCeeeEE
Confidence            355566633589999999999999   999999999999999999864

>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional

Probab=93.76  E-value=0.11  Score=39.50  Aligned_cols=47  Identities=13%  Similarity=0.194  Sum_probs=41.8

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      +-.|.+.|.+ .+.+++.|||+.+++   ++..++|-|..|...|++.+..
T Consensus         7 ~~~Il~~l~~-~~~~~~~ela~~l~v---S~~TiRRdL~~Le~~g~l~r~~   53 (252)
T PRK10906          7 HDAIIELVKQ-QGYVSTEELVEHFSV---SPQTIRRDLNDLAEQNKILRHH   53 (252)
T ss_pred             HHHHHHHHHH-cCCEeHHHHHHHhCC---CHHHHHHHHHHHHHCCCEEEec
Confidence            4457888875 578999999999999   9999999999999999999875

>PF09929 DUF2161: Uncharacterized conserved protein (DUF2161); InterPro: IPR018679 This family of various hypothetical prokaryotic proteins has no known function

Probab=93.60  E-value=0.17  Score=34.28  Aligned_cols=52  Identities=19%  Similarity=0.248  Sum_probs=41.0

Q ss_pred             hHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcc
Q 040869           40 IADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAST  102 (131)
Q Consensus        40 ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~  102 (131)
                      +...|.. .+|.+..+|++.+++     ....+||+. -..|-|++.+    .|.|.+|+.++
T Consensus        64 ~A~~L~~-~Gp~~~~~l~~~~~~-----~~A~~IL~~-N~YGWFeRv~----rGvY~LT~~G~  115 (118)
T PF09929_consen   64 CAAALAE-HGPSRPADLRKATGV-----PKATSILRD-NHYGWFERVE----RGVYALTPAGR  115 (118)
T ss_pred             HHHHHHH-cCCCCHHHHHHhcCC-----ChHHHHHHh-Ccccceeeec----cceEecCcchh
Confidence            3445664 479999999999998     355666664 6789999987    89999999876

>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family

Probab=93.50  E-value=0.22  Score=34.14  Aligned_cols=48  Identities=19%  Similarity=0.334  Sum_probs=39.5

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhc----CCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           36 IELGIADIIHSHGRAITLSELVSAL----DIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~----~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      .++.|..+|.+ .++.|+.||.+.+    +.   +...+.++|+-|...|++....
T Consensus         5 ~E~~VM~vlW~-~~~~t~~eI~~~l~~~~~~---~~tTv~T~L~rL~~KG~v~~~k   56 (130)
T TIGR02698         5 AEWEVMRVVWT-LGETTSRDIIRILAEKKDW---SDSTIKTLLGRLVDKGCLTTEK   56 (130)
T ss_pred             HHHHHHHHHHc-CCCCCHHHHHHHHhhccCC---cHHHHHHHHHHHHHCCceeeec
Confidence            56778888875 4689999977765    56   7889999999999999998764

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.

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

Probab=93.40  E-value=0.11  Score=37.16  Aligned_cols=46  Identities=20%  Similarity=0.244  Sum_probs=41.4

Q ss_pred             CCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcc
Q 040869           50 AITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAST  102 (131)
Q Consensus        50 ~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~  102 (131)
                      -.|..+||+.+|+   +.+.+.|.+..|...+++.+..    .|.|..+|--.
T Consensus        75 ~~t~~~ia~~l~i---S~~Tv~r~ik~L~e~~iI~k~~----~G~Y~iNP~~~  120 (165)
T PF05732_consen   75 VATQKEIAEKLGI---SKPTVSRAIKELEEKNIIKKIR----NGAYMINPNFF  120 (165)
T ss_pred             EeeHHHHHHHhCC---CHHHHHHHHHHHHhCCcEEEcc----CCeEEECcHHh
Confidence            3789999999999   9999999999999999999876    78999999743

; GO: 0006260 DNA replication, 0006276 plasmid maintenance

>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=93.39  E-value=0.11  Score=30.92  Aligned_cols=37  Identities=16%  Similarity=0.237  Sum_probs=32.0

Q ss_pred             CCCC-CHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           48 GRAI-TLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        48 ~~~~-s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      |..+ |..+||++.|+   +...+++.++.|...|++....
T Consensus        21 g~~lps~~~la~~~~v---sr~tvr~al~~L~~~g~i~~~~   58 (64)
T PF00392_consen   21 GDRLPSERELAERYGV---SRTTVREALRRLEAEGLIERRP   58 (64)
T ss_dssp             TSBE--HHHHHHHHTS----HHHHHHHHHHHHHTTSEEEET
T ss_pred             CCEeCCHHHHHHHhcc---CCcHHHHHHHHHHHCCcEEEEC
Confidence            4567 99999999999   9999999999999999998765

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 ....

>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=93.36  E-value=0.11  Score=33.86  Aligned_cols=48  Identities=10%  Similarity=0.261  Sum_probs=39.1

Q ss_pred             HHhChHHHHHh---CCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           36 IELGIADIIHS---HGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        36 ~~L~ifd~l~~---~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      ++-.|+++|..   .+.++++++|++++++   +...++..++.|+..|.+-.+
T Consensus        48 ~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~---~~~~v~~al~~L~~eG~IYsT   98 (102)
T PF08784_consen   48 LQDKVLNFIKQQPNSEEGVHVDEIAQQLGM---SENEVRKALDFLSNEGHIYST   98 (102)
T ss_dssp             HHHHHHHHHHC----TTTEEHHHHHHHSTS----HHHHHHHHHHHHHTTSEEES
T ss_pred             HHHHHHHHHHhcCCCCCcccHHHHHHHhCc---CHHHHHHHHHHHHhCCeEecc
Confidence            45567888865   2467999999999999   999999999999999987654

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.

>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional

Probab=93.24  E-value=0.15  Score=39.10  Aligned_cols=48  Identities=8%  Similarity=0.097  Sum_probs=42.3

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      -...|.+.|.+ .+.+++.|||+.+++   ++.+++|=|+.|...|++.+..
T Consensus        18 R~~~Il~~L~~-~~~vtv~eLa~~l~V---S~~TIRRDL~~Le~~G~l~r~~   65 (269)
T PRK09802         18 RREQIIQRLRQ-QGSVQVNDLSALYGV---STVTIRNDLAFLEKQGIAVRAY   65 (269)
T ss_pred             HHHHHHHHHHH-cCCEeHHHHHHHHCC---CHHHHHHHHHHHHhCCCeEEEe
Confidence            34568888876 457999999999999   9999999999999999999876

>PRK10411 DNA-binding transcriptional activator FucR; Provisional

Probab=93.05  E-value=0.21  Score=37.59  Aligned_cols=47  Identities=15%  Similarity=0.232  Sum_probs=40.7

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      ...|.+.|.+ .+.++..|||+.+++   ++..++|-|..|...|.+....
T Consensus         6 ~~~Il~~l~~-~~~~~~~eLa~~l~V---S~~TiRRdL~~L~~~~~l~r~~   52 (240)
T PRK10411          6 QQAIVDLLLN-HTSLTTEALAEQLNV---SKETIRRDLNELQTQGKILRNH   52 (240)
T ss_pred             HHHHHHHHHH-cCCCcHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEec
Confidence            3457788875 468999999999999   9999999999999999888764

>PRK13777 transcriptional regulator Hpr; Provisional

Probab=92.98  E-value=1  Score=32.77  Aligned_cols=64  Identities=16%  Similarity=0.115  Sum_probs=49.0

Q ss_pred             ChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhcccccc
Q 040869           39 GIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIK  106 (131)
Q Consensus        39 ~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~  106 (131)
                      .|.-.|.. .+++|..+||+.+++   +...+.|++.-|...|++.+.... |. .-...+|+.++.+..
T Consensus        49 ~iL~~L~~-~~~itq~eLa~~l~l---~~sTvtr~l~rLE~kGlI~R~~~~~DrR~~~I~LTekG~~l~~  114 (185)
T PRK13777         49 HILWIAYH-LKGASISEIAKFGVM---HVSTAFNFSKKLEERGYLTFSKKEDDKRNTYIELTEKGEELLL  114 (185)
T ss_pred             HHHHHHHh-CCCcCHHHHHHHHCC---CHhhHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHH
Confidence            35556654 368999999999999   999999999999999999986432 11 123678888876654

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

Probab=92.97  E-value=0.17  Score=38.44  Aligned_cols=46  Identities=11%  Similarity=0.205  Sum_probs=41.8

Q ss_pred             hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      -.|.+.|.+ .+.++++|||+.+++   .+.+++|=|+.|...|++.+..
T Consensus         8 ~~Il~~l~~-~g~v~v~eLa~~~~V---S~~TIRRDL~~Le~~g~l~R~h   53 (253)
T COG1349           8 QKILELLKE-KGKVSVEELAELFGV---SEMTIRRDLNELEEQGLLLRVH   53 (253)
T ss_pred             HHHHHHHHH-cCcEEHHHHHHHhCC---CHHHHHHhHHHHHHCCcEEEEe
Confidence            457888886 578999999999999   9999999999999999999976

>COG1497 Predicted transcriptional regulator [Transcription]

Probab=92.96  E-value=0.12  Score=39.26  Aligned_cols=74  Identities=15%  Similarity=0.184  Sum_probs=55.1

Q ss_pred             hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcc-ccccCcccChHHhH
Q 040869           38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAST-LLIKDKPYCMSPTV  116 (131)
Q Consensus        38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~-~L~~~~~~sl~~~~  116 (131)
                      +.|.-.|.....-....|||+++|+   -+..+.--++-|+..|++.+..    .+.|..|.-+. +|.+ +-..++.|+
T Consensus        13 fqIL~ei~~~qp~v~q~eIA~~lgi---T~QaVsehiK~Lv~eG~i~~~g----R~~Y~iTkkG~e~l~~-~~~dlr~f~   84 (260)
T COG1497          13 FQILSEIAVRQPRVKQKEIAKKLGI---TLQAVSEHIKELVKEGLIEKEG----RGEYEITKKGAEWLLE-QLSDLRRFS   84 (260)
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHcCC---CHHHHHHHHHHHHhccceeecC----CeeEEEehhHHHHHHH-HHHHHHHHH
Confidence            3444444433356999999999999   8999999999999999999975    78999999886 4433 222466655


Q ss_pred             Hhh
Q 040869          117 SAF  119 (131)
Q Consensus       117 ~~~  119 (131)
                      ...
T Consensus        85 ~ev   87 (260)
T COG1497          85 EEV   87 (260)
T ss_pred             HHH
Confidence            543

>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain

Probab=92.94  E-value=0.15  Score=42.38  Aligned_cols=70  Identities=9%  Similarity=0.174  Sum_probs=55.1

Q ss_pred             HHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcc-ccccCcc
Q 040869           35 AIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAST-LLIKDKP  109 (131)
Q Consensus        35 a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~-~L~~~~~  109 (131)
                      +++..|...|...+..++..+||+.+|+   +...+.+.+..|.+.|+++-....  ...|.+|.-++ ++..+.|
T Consensus         3 ~~e~~iL~~l~~~~~~~~~~~la~~~g~---~~~~v~~~~~~L~~kg~v~~~~~~--~~~~~LT~eG~~~l~~G~P   73 (492)
T PLN02853          3 MAEEALLGALSNNEEISDSGQFAASHGL---DHNEVVGVIKSLHGFRYVDAQDIK--RETWVLTEEGKKYAAEGSP   73 (492)
T ss_pred             hHHHHHHHHHHhcCCCCCHHHHHHHcCC---CHHHHHHHHHHHHhCCCEEEEEEE--EEEEEECHHHHHHHHcCCH
Confidence            4567788888753323899999999999   999999999999999988865321  57799999988 5555555

>COG3413 Predicted DNA binding protein [General function prediction only]

Probab=92.93  E-value=0.1  Score=38.49  Aligned_cols=43  Identities=26%  Similarity=0.336  Sum_probs=35.4

Q ss_pred             HHHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHH
Q 040869           27 LSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRL   76 (131)
Q Consensus        27 ~~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~   76 (131)
                      ..-.+|+.|.++|-|| .   ++..++.|||+.+|+   .+..+...||-
T Consensus       159 rQ~~vL~~A~~~GYFd-~---PR~~~l~dLA~~lGI---Skst~~ehLRr  201 (215)
T COG3413         159 RQLEVLRLAYKMGYFD-Y---PRRVSLKDLAKELGI---SKSTLSEHLRR  201 (215)
T ss_pred             HHHHHHHHHHHcCCCC-C---CccCCHHHHHHHhCC---CHHHHHHHHHH
Confidence            4678999999999998 3   367999999999999   77776666654

>COG1846 MarR Transcriptional regulators [Transcription]

Probab=92.74  E-value=0.19  Score=32.66  Aligned_cols=70  Identities=16%  Similarity=0.201  Sum_probs=51.6

Q ss_pred             HHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-CcceecchhccccccC
Q 040869           34 CAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIKD  107 (131)
Q Consensus        34 ~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~~  107 (131)
                      ...+..+...|... ++.+..+||+.+++   ++..+.|+++-|...|++...... |. .-.+.+|+.++.+...
T Consensus        21 t~~q~~~L~~l~~~-~~~~~~~la~~l~i---~~~~vt~~l~~Le~~glv~r~~~~~DrR~~~l~lT~~G~~~~~~   92 (126)
T COG1846          21 TPPQYQVLLALYEA-GGITVKELAERLGL---DRSTVTRLLKRLEDKGLIERLRDPEDRRAVLVRLTEKGRELLEQ   92 (126)
T ss_pred             CHHHHHHHHHHHHh-CCCcHHHHHHHHCC---CHHHHHHHHHHHHHCCCeeecCCccccceeeEEECccHHHHHHH
Confidence            33455566667653 34444999999999   999999999999999999987543 21 2358899988865543

>PHA02943 hypothetical protein; Provisional

Probab=92.63  E-value=0.31  Score=34.55  Aligned_cols=45  Identities=11%  Similarity=0.107  Sum_probs=39.7

Q ss_pred             hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      ..|.+.|.  .|..|..|||+++|+   +-..++=+|..|...|.+.+..
T Consensus        14 ~eILE~Lk--~G~~TtseIAkaLGl---S~~qa~~~LyvLErEG~VkrV~   58 (165)
T PHA02943         14 IKTLRLLA--DGCKTTSRIANKLGV---SHSMARNALYQLAKEGMVLKVE   58 (165)
T ss_pred             HHHHHHHh--cCCccHHHHHHHHCC---CHHHHHHHHHHHHHcCceEEEe
Confidence            35777774  578999999999999   8899999999999999999875

>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional

Probab=92.62  E-value=0.19  Score=38.14  Aligned_cols=47  Identities=17%  Similarity=0.243  Sum_probs=41.9

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      +-.|.+.|.+ .+.+++.|||+.+++   ++.+++|=|+.|...|++.+..
T Consensus         7 ~~~Il~~L~~-~~~v~v~eLa~~l~V---S~~TIRRDL~~Le~~g~l~r~~   53 (256)
T PRK10434          7 QAAILEYLQK-QGKTSVEELAQYFDT---TGTTIRKDLVILEHAGTVIRTY   53 (256)
T ss_pred             HHHHHHHHHH-cCCEEHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEEE
Confidence            4568888886 468999999999999   9999999999999999999875

>PF13730 HTH_36: Helix-turn-helix domain

Probab=92.56  E-value=0.15  Score=29.13  Aligned_cols=30  Identities=13%  Similarity=0.165  Sum_probs=27.9

Q ss_pred             CCHHHHHhhcCCCCCCcchHHHHHHHhhcCCce
Q 040869           51 ITLSELVSALDIQPTKTTGLFRLMRLLVHSSCF   83 (131)
Q Consensus        51 ~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~   83 (131)
                      .|.+.||+.+|+   ....+.|.++.|...|++
T Consensus        26 pS~~~la~~~g~---s~~Tv~~~i~~L~~~G~I   55 (55)
T PF13730_consen   26 PSQETLAKDLGV---SRRTVQRAIKELEEKGLI   55 (55)
T ss_pred             cCHHHHHHHHCc---CHHHHHHHHHHHHHCcCC
Confidence            389999999999   999999999999999975

>COG5631 Predicted transcription regulator, contains HTH domain (MarR family) [Transcription]

Probab=92.55  E-value=1.4  Score=31.72  Aligned_cols=78  Identities=21%  Similarity=0.307  Sum_probs=57.7

Q ss_pred             HHHhHHHHHHHHHHHHhC-------hHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcc
Q 040869           22 LMFSHLSSMSLKCAIELG-------IADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEA   94 (131)
Q Consensus        22 ~~~~~~~~~aL~~a~~L~-------ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~   94 (131)
                      .+++.|...|+.++...+       |..+|...+.|+++.+|+..++..  |...+.=-||-|...|+++..... ..-+
T Consensus        63 ~Af~rW~vrCmAaag~~~ls~~e~l~lH~irhrdR~K~laDic~~ln~e--Dth~itYslrKL~k~gLit~t~~g-kevT  139 (199)
T COG5631          63 EAFGRWQVRCMAAAGEFSLSGPENLLLHIIRHRDRPKSLADICQMLNRE--DTHNITYSLRKLLKGGLITRTGSG-KEVT  139 (199)
T ss_pred             HHHHHHHHHHHHHhcCCCCcchHHHHHHHHhhcCchhhHHHHHHHhccc--cchhHHHHHHHHHhccceecCCCC-ceEE
Confidence            456778989998887766       344454457999999999999982  444667778999999999987521 1245


Q ss_pred             eecchhcc
Q 040869           95 YGLTAAST  102 (131)
Q Consensus        95 y~~t~~s~  102 (131)
                      |..|+.+.
T Consensus       140 y~vTa~G~  147 (199)
T COG5631         140 YEVTALGH  147 (199)
T ss_pred             EEEecchH
Confidence            88888763

>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional

Probab=92.38  E-value=0.22  Score=41.48  Aligned_cols=70  Identities=16%  Similarity=0.212  Sum_probs=55.4

Q ss_pred             HHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcc-ccccCcc
Q 040869           35 AIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAST-LLIKDKP  109 (131)
Q Consensus        35 a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~-~L~~~~~  109 (131)
                      ..+..|...|.+..+..+..+||+.+|+   +...+.+.+..|.+.|+++-....  ...|.+|.-++ ++..+.|
T Consensus         6 ~~e~~iL~~l~~~~~~~~~~~la~~~~~---~~~~v~~~~~~L~~kg~v~~~~~~--~~~~~LT~eG~~~~~~G~P   76 (494)
T PTZ00326          6 LEENTILSKLESENEIVNSLALAESLNI---DHQKVVGAIKSLESANYITTEMKK--SNTWTLTEEGEDYLKNGSP   76 (494)
T ss_pred             HHHHHHHHHHHhcCCCCCHHHHHHHcCC---CHHHHHHHHHHHHhCCCEEEEEEE--EEEEEECHHHHHHHHcCCH
Confidence            4556677888753457999999999999   999999999999999998865321  57799999988 5555555

>PRK00215 LexA repressor; Validated

Probab=92.26  E-value=0.39  Score=34.94  Aligned_cols=40  Identities=13%  Similarity=0.267  Sum_probs=34.3

Q ss_pred             hCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           46 SHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        46 ~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      +.+.+.|..|||+++|+.  +...+.|+++.|...|+++...
T Consensus        19 ~~~~~~s~~ela~~~~~~--~~~tv~~~l~~L~~~g~i~~~~   58 (205)
T PRK00215         19 ETGYPPSRREIADALGLR--SPSAVHEHLKALERKGFIRRDP   58 (205)
T ss_pred             HhCCCCCHHHHHHHhCCC--ChHHHHHHHHHHHHCCCEEeCC
Confidence            346789999999999972  4678999999999999998765

>TIGR02147 Fsuc_second hypothetical protein, TIGR02147

Probab=92.17  E-value=0.66  Score=35.79  Aligned_cols=46  Identities=20%  Similarity=0.112  Sum_probs=39.1

Q ss_pred             CCCCHHHHHhhcC--CCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhc
Q 040869           49 RAITLSELVSALD--IQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAS  101 (131)
Q Consensus        49 ~~~s~~eLA~~~~--~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s  101 (131)
                      +...+.+||++++  +   +...+..-|..|...|++++.+    +|.|..|..+
T Consensus       136 ~~~~~~~ia~~l~p~i---s~~ev~~sL~~L~~~glikk~~----~g~y~~t~~~  183 (271)
T TIGR02147       136 FADDPEELAKRCFPKI---SAEQVKESLDLLERLGLIKKNE----DGFYKQTDKA  183 (271)
T ss_pred             CCCCHHHHHHHhCCCC---CHHHHHHHHHHHHHCCCeeECC----CCcEEeecce
Confidence            4457889999998  6   6778999999999999999886    7899988763

This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.

>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=92.10  E-value=0.15  Score=33.33  Aligned_cols=44  Identities=16%  Similarity=0.200  Sum_probs=33.3

Q ss_pred             ChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           39 GIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        39 ~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      .|++.|.. .+.++-++||..+|+   ++..++++|..|...|++...
T Consensus        17 ~Il~~L~~-~~~l~de~la~~~~l---~~~~vRkiL~~L~~~~lv~~~   60 (105)
T PF02002_consen   17 RILDALLR-KGELTDEDLAKKLGL---KPKEVRKILYKLYEDGLVSYR   60 (105)
T ss_dssp             HHHHHHHH-H--B-HHHHHHTT-S----HHHHHHHHHHHHHHSS-EEE
T ss_pred             HHHHHHHH-cCCcCHHHHHHHhCC---CHHHHHHHHHHHHHCCCeEEE
Confidence            36788874 367999999999999   999999999999999999765

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.

>COG1733 Predicted transcriptional regulators [Transcription]

Probab=92.02  E-value=0.6  Score=31.63  Aligned_cols=78  Identities=14%  Similarity=0.143  Sum_probs=58.1

Q ss_pred             HHHHHHHHHHHhHHHHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcC-CCCCCcchHHHHHHHhhcCCceeecccC--C
Q 040869           14 QGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALD-IQPTKTTGLFRLMRLLVHSSCFNKTKVN--G   90 (131)
Q Consensus        14 ~~~~~l~~~~~~~~~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~-~~~~~~~~l~RlLr~L~~~gl~~~~~~~--~   90 (131)
                      -+.+.+++++.+-|..-+|+...+           ++.-..||-+.++ +   .+..|.+-||.|...|++.+..-.  .
T Consensus        11 c~~~~~l~~ig~kW~~lIl~~L~~-----------g~~RF~eL~r~i~~I---s~k~Ls~~Lk~Le~~Glv~R~~~~~~P   76 (120)
T COG1733          11 CPVEEALEVIGGKWTLLILRDLFD-----------GPKRFNELRRSIGGI---SPKMLSRRLKELEEDGLVERVVYPEEP   76 (120)
T ss_pred             CCHHHHHHHHcCccHHHHHHHHhc-----------CCCcHHHHHHHcccc---CHHHHHHHHHHHHHCCCEEeeecCCCC
Confidence            345667777777777666554322           6788999999988 8   889999999999999999987421  1


Q ss_pred             CCcceecchhccccc
Q 040869           91 QEEAYGLTAASTLLI  105 (131)
Q Consensus        91 ~~~~y~~t~~s~~L~  105 (131)
                      ..-.|++|+.++.|.
T Consensus        77 prveY~LT~~G~~L~   91 (120)
T COG1733          77 PRVEYRLTEKGRDLL   91 (120)
T ss_pred             ceeEEEEhhhHHHHH
Confidence            123599999988665

>PRK10046 dpiA two-component response regulator DpiA; Provisional

Probab=91.93  E-value=0.33  Score=35.49  Aligned_cols=45  Identities=16%  Similarity=0.166  Sum_probs=38.0

Q ss_pred             ChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           39 GIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        39 ~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      .|.+.+.+...+.|..|||+++++   .+.++++-+.+|+..|++...
T Consensus       166 ~Vl~~~~~g~~g~s~~eIa~~l~i---S~~Tv~~~~~~~~~~~~~~~~  210 (225)
T PRK10046        166 AVRKLFKEPGVQHTAETVAQALTI---SRTTARRYLEYCASRHLIIAE  210 (225)
T ss_pred             HHHHHHHcCCCCcCHHHHHHHhCc---cHHHHHHHHHHHHhCCeEEEE
Confidence            466667642236899999999999   999999999999999999875

>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4

Probab=91.80  E-value=0.21  Score=31.30  Aligned_cols=35  Identities=14%  Similarity=0.298  Sum_probs=24.6

Q ss_pred             hHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhh
Q 040869           40 IADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLV   78 (131)
Q Consensus        40 ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~   78 (131)
                      ++..|++ |+|+|..+||.++|.   +.+.+...|..+.
T Consensus        29 LLr~LA~-G~PVt~~~LA~a~g~---~~e~v~~~L~~~p   63 (77)
T PF12324_consen   29 LLRLLAK-GQPVTVEQLAAALGW---PVEEVRAALAAMP   63 (77)
T ss_dssp             HHHHHTT-TS-B-HHHHHHHHT-----HHHHHHHHHH-T
T ss_pred             HHHHHHc-CCCcCHHHHHHHHCC---CHHHHHHHHHhCC
Confidence            6777885 899999999999999   7777777776654

99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.

>PRK01381 Trp operon repressor; Provisional

Probab=91.75  E-value=0.29  Score=32.17  Aligned_cols=42  Identities=12%  Similarity=0.134  Sum_probs=35.8

Q ss_pred             HHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcC
Q 040869           34 CAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHS   80 (131)
Q Consensus        34 ~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~   80 (131)
                      .+.+++|+..|-+  +.+|..|||+.+|+   ....+.|.=|.|...
T Consensus        41 l~~R~~I~~~L~~--g~~sQREIa~~lGv---SiaTITRgsn~Lk~~   82 (99)
T PRK01381         41 LGTRVRIVEELLR--GELSQREIKQELGV---GIATITRGSNSLKTA   82 (99)
T ss_pred             HHHHHHHHHHHHc--CCcCHHHHHHHhCC---ceeeehhhHHHhccC
Confidence            3567899998873  78999999999999   889999988888654

>PRK15431 ferrous iron transport protein FeoC; Provisional

Probab=91.43  E-value=0.47  Score=29.82  Aligned_cols=44  Identities=7%  Similarity=0.133  Sum_probs=38.6

Q ss_pred             hHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           40 IADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        40 ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      |=|.|.. .+-.++.+||.+++.   +++.++-+|..++.+|-+.+..
T Consensus         7 lRd~l~~-~gr~s~~~Ls~~~~~---p~~~VeaMLe~l~~kGkverv~   50 (78)
T PRK15431          7 VRDLLAL-RGRMEAAQISQTLNT---PQPMINAMLQQLESMGKAVRIQ   50 (78)
T ss_pred             HHHHHHH-cCcccHHHHHHHHCc---CHHHHHHHHHHHHHCCCeEeec
Confidence            4567775 468999999999999   9999999999999999999764

>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C

Probab=91.25  E-value=0.17  Score=28.33  Aligned_cols=41  Identities=10%  Similarity=0.268  Sum_probs=23.3

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCc
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSC   82 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl   82 (131)
                      .++.+...+..   +.|..+||+.+|+   ++..++|+++.....|+
T Consensus         6 ~R~~ii~l~~~---G~s~~~ia~~lgv---s~~Tv~~w~kr~~~~G~   46 (50)
T PF13384_consen    6 RRAQIIRLLRE---GWSIREIAKRLGV---SRSTVYRWIKRYREEGL   46 (50)
T ss_dssp             ----HHHHHHH---T--HHHHHHHHTS----HHHHHHHHT-------
T ss_pred             HHHHHHHHHHC---CCCHHHHHHHHCc---CHHHHHHHHHHcccccc
Confidence            34556666653   6999999999999   99999999988766663

>PRK09954 putative kinase; Provisional

Probab=90.86  E-value=0.49  Score=37.31  Aligned_cols=44  Identities=18%  Similarity=0.211  Sum_probs=38.9

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCcee
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFN   84 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~   84 (131)
                      +.+|...|.+ .+.+|..|||+.+++   ....+.+.++.|...|++.
T Consensus         5 ~~~il~~l~~-~~~~s~~~la~~l~~---s~~~v~~~i~~L~~~g~i~   48 (362)
T PRK09954          5 EKEILAILRR-NPLIQQNEIADILQI---SRSRVAAHIMDLMRKGRIK   48 (362)
T ss_pred             HHHHHHHHHH-CCCCCHHHHHHHHCC---CHHHHHHHHHHHHHCCCcC
Confidence            4568888886 468999999999999   9999999999999999985

>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression

Probab=90.78  E-value=0.5  Score=30.33  Aligned_cols=41  Identities=15%  Similarity=0.213  Sum_probs=34.5

Q ss_pred             HHHHHhChHH-HHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhc
Q 040869           33 KCAIELGIAD-IIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVH   79 (131)
Q Consensus        33 ~~a~~L~ifd-~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~   79 (131)
                      ..+-++.|+. .|.   +.+|..|||+.+|+   +...+.|+=|.|..
T Consensus        34 ~l~~R~~va~~lL~---~g~syreIa~~tgv---S~aTItRvsr~Lk~   75 (87)
T PF01371_consen   34 ALAQRWQVAKELLD---EGKSYREIAEETGV---SIATITRVSRCLKY   75 (87)
T ss_dssp             HHHHHHHHHHHHHH---TTSSHHHHHHHHTS---THHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHH---CCCCHHHHHHHhCC---CHHHHHHHHHHHHc
Confidence            3456788998 776   57999999999999   99999999998864

The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan []. The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....

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

Probab=90.77  E-value=0.62  Score=30.20  Aligned_cols=48  Identities=10%  Similarity=0.142  Sum_probs=41.9

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      ..+.|..+|.. -+|=.+.-||..+++   +...+.++++.|..+|++++..
T Consensus         8 l~~~IL~hl~~-~~~Dy~k~ia~~l~~---~~~~v~~~l~~Le~~GLler~~   55 (92)
T PF10007_consen    8 LDLKILQHLKK-AGPDYAKSIARRLKI---PLEEVREALEKLEEMGLLERVE   55 (92)
T ss_pred             hHHHHHHHHHH-HCCCcHHHHHHHHCC---CHHHHHHHHHHHHHCCCeEEec
Confidence            35677888875 368889999999999   9999999999999999999986

>PRK12423 LexA repressor; Provisional

Probab=90.64  E-value=0.64  Score=34.00  Aligned_cols=38  Identities=13%  Similarity=0.220  Sum_probs=32.3

Q ss_pred             CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      +-+-|..|||+++|+.  .+..+++-|+.|...|+++...
T Consensus        23 g~~Ps~~eia~~~g~~--s~~~v~~~l~~L~~~G~l~~~~   60 (202)
T PRK12423         23 GQPPSLAEIAQAFGFA--SRSVARKHVQALAEAGLIEVVP   60 (202)
T ss_pred             CCCCCHHHHHHHhCCC--ChHHHHHHHHHHHHCCCEEecC
Confidence            3467999999999941  6778999999999999999864

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

Probab=90.60  E-value=0.34  Score=26.81  Aligned_cols=24  Identities=13%  Similarity=0.321  Sum_probs=17.5

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHH
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMR   75 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr   75 (131)
                      ...|..+||+.+|.   ++..+.|.++
T Consensus        19 ~G~s~~~IA~~lg~---s~sTV~relk   42 (44)
T PF13936_consen   19 QGMSIREIAKRLGR---SRSTVSRELK   42 (44)
T ss_dssp             S---HHHHHHHTT-----HHHHHHHHH
T ss_pred             cCCCHHHHHHHHCc---CcHHHHHHHh
Confidence            46999999999999   9999999886

>TIGR01321 TrpR trp operon repressor, proteobacterial

Probab=90.40  E-value=0.48  Score=30.86  Aligned_cols=41  Identities=15%  Similarity=0.140  Sum_probs=34.7

Q ss_pred             HHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhc
Q 040869           34 CAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVH   79 (131)
Q Consensus        34 ~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~   79 (131)
                      .+.+.||+..|-+  +++|-.|||+++|+   ....+.|.=|.|..
T Consensus        41 l~~R~~i~~~Ll~--~~~tQrEIa~~lGi---S~atIsR~sn~lk~   81 (94)
T TIGR01321        41 LGDRIRIVNELLN--GNMSQREIASKLGV---SIATITRGSNNLKT   81 (94)
T ss_pred             HHHHHHHHHHHHh--CCCCHHHHHHHhCC---ChhhhhHHHhhccc
Confidence            4567899997763  68999999999999   88999998887763

This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.

>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2

Probab=90.27  E-value=0.45  Score=28.37  Aligned_cols=43  Identities=14%  Similarity=0.277  Sum_probs=34.5

Q ss_pred             hHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           40 IADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        40 ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      |++.|-+ .|..|+.+|++.+++   +++.++.-|-.|...|++...
T Consensus        18 V~~~Ll~-~G~ltl~~i~~~t~l---~~~~Vk~~L~~LiQh~~v~y~   60 (62)
T PF08221_consen   18 VGEVLLS-RGRLTLREIVRRTGL---SPKQVKKALVVLIQHNLVQYF   60 (62)
T ss_dssp             HHHHHHH-C-SEEHHHHHHHHT-----HHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHH-cCCcCHHHHHHHhCC---CHHHHHHHHHHHHHcCCeeee
Confidence            5666764 468999999999999   999999999999999988753

7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.

>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=90.20  E-value=0.38  Score=31.93  Aligned_cols=51  Identities=25%  Similarity=0.364  Sum_probs=40.8

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCC-CCCcchHHHHHHHhhcCCceeecc
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQ-PTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~-~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      .++.|.++|.+.+ ++|+.||.+.++-. +-....+.-+|+-|+..|+++...
T Consensus         4 ~E~~IM~~lW~~~-~~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~~~~   55 (115)
T PF03965_consen    4 LELEIMEILWESG-EATVREIHEALPEERSWAYSTVQTLLNRLVEKGFLTREK   55 (115)
T ss_dssp             HHHHHHHHHHHHS-SEEHHHHHHHHCTTSS--HHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHHhCC-CCCHHHHHHHHHhccccchhHHHHHHHHHHhCCceeEee
Confidence            5677888887654 59999999998761 225788999999999999999875

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 ....

>PF13518 HTH_28: Helix-turn-helix domain

Probab=90.19  E-value=0.67  Score=25.81  Aligned_cols=38  Identities=11%  Similarity=0.267  Sum_probs=30.4

Q ss_pred             ChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCc
Q 040869           39 GIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSC   82 (131)
Q Consensus        39 ~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl   82 (131)
                      .|...+.+  + .|+.++|+++|+   +...+++.++.....|+
T Consensus         4 ~iv~~~~~--g-~s~~~~a~~~gi---s~~tv~~w~~~y~~~G~   41 (52)
T PF13518_consen    4 QIVELYLE--G-ESVREIAREFGI---SRSTVYRWIKRYREGGI   41 (52)
T ss_pred             HHHHHHHc--C-CCHHHHHHHHCC---CHhHHHHHHHHHHhcCH
Confidence            34444442  3 499999999999   99999999999888774

>PF07789 DUF1627: Protein of unknown function (DUF1627); InterPro: IPR012432 This is a group of sequences found in hypothetical proteins predicted to be expressed in a number of bacterial species

Probab=90.17  E-value=0.6  Score=32.88  Aligned_cols=47  Identities=13%  Similarity=0.171  Sum_probs=37.4

Q ss_pred             CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecc
Q 040869           48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLT   98 (131)
Q Consensus        48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t   98 (131)
                      .|++|++|||.+.|+   ..+.+---|-.+++.|-+.+... +|.-+|+..
T Consensus         4 ~Ga~T~eELA~~FGv---ttRkvaStLa~~ta~Grl~Rv~q-~gkfRy~iP   50 (155)
T PF07789_consen    4 EGAKTAEELAGKFGV---TTRKVASTLAMVTATGRLIRVNQ-NGKFRYCIP   50 (155)
T ss_pred             cCcccHHHHHHHhCc---chhhhHHHHHHHHhcceeEEecC-CCceEEeCC
Confidence            589999999999999   88999999999999998887642 122346553

The region in question is approximately 150 amino acid residues long.

>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional

Probab=90.05  E-value=0.26  Score=35.74  Aligned_cols=45  Identities=13%  Similarity=0.052  Sum_probs=39.7

Q ss_pred             hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      -.|.+.|.. .+.++..+||+.+++   ++.+++|=|+.|...|++.+.
T Consensus        10 ~~Il~~l~~-~~~~~~~~La~~~~v---S~~TiRRDl~~L~~~g~~~r~   54 (185)
T PRK04424         10 KALQELIEE-NPFITDEELAEKFGV---SIQTIRLDRMELGIPELRERI   54 (185)
T ss_pred             HHHHHHHHH-CCCEEHHHHHHHHCc---CHHHHHHHHHHHhcchHHHHH
Confidence            457778875 578999999999999   999999999999999998875

>PF03374 ANT: Phage antirepressor protein KilAC domain; InterPro: IPR005039 This entry is represented by Bacteriophage P1, Ant1 C-terminal domain, which represents the processed Ant2 chain

Probab=89.82  E-value=0.85  Score=29.89  Aligned_cols=44  Identities=18%  Similarity=0.231  Sum_probs=35.4

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      +...+|.+..+++.+|+.++|+.+|+   .+..|.++||-   .|++...
T Consensus        11 Ka~~~d~~~~~~~~~ti~~~AK~L~i---~~~~l~~~Lr~---~g~l~~~   54 (111)
T PF03374_consen   11 KAEFYDAFVDSDGLYTIREAAKLLGI---GRNKLFQWLRE---KGWLYRR   54 (111)
T ss_pred             hhHHHHHHHcCCCCccHHHHHHHhCC---CHHHHHHHHHh---CCceEEC
Confidence            34567888776789999999999999   87777777764   8888874

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Prophages P1 and P7 exist as unit copy DNA plasmids in the bacterial cell. Maintenance of the prophage state requires the continuous expression of two repressors: (i) C1 is a protein which negatively regulates the expression of lytic genes including the C1 inactivator gene coi, and (ii) C4 is an antisense RNA which specifically inhibits the synthesis of an anti-repressor Ant.; GO: 0003677 DNA binding

>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit

Probab=89.66  E-value=0.45  Score=36.44  Aligned_cols=37  Identities=19%  Similarity=0.304  Sum_probs=33.6

Q ss_pred             CCCCCHHHHHhhcCCCCCCcchHHHHHH-HhhcCCceeecc
Q 040869           48 GRAITLSELVSALDIQPTKTTGLFRLMR-LLVHSSCFNKTK   87 (131)
Q Consensus        48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr-~L~~~gl~~~~~   87 (131)
                      +++.++++||+.+|.   ++..+.++++ .|+..|++....
T Consensus       253 ~~~~~~~~ia~~lg~---~~~~~~~~~e~~Li~~~li~~~~  290 (305)
T TIGR00635       253 GGPVGLKTLAAALGE---DADTIEDVYEPYLLQIGFLQRTP  290 (305)
T ss_pred             CCcccHHHHHHHhCC---CcchHHHhhhHHHHHcCCcccCC
Confidence            568999999999999   9999999999 799999997654

RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.

>PRK09334 30S ribosomal protein S25e; Provisional

Probab=89.58  E-value=0.45  Score=30.48  Aligned_cols=36  Identities=19%  Similarity=0.164  Sum_probs=33.1

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      .-+|+..||+++++   .-+..+++||.|...|++....
T Consensus        40 K~ITps~lserlkI---~~SlAr~~Lr~L~~kG~Ik~V~   75 (86)
T PRK09334         40 KIVTPYTLASKYGI---KISVAKKVLRELEKRGVLVLYS   75 (86)
T ss_pred             cEEcHHHHHHHhcc---hHHHHHHHHHHHHHCCCEEEEe
Confidence            56999999999999   9999999999999999997653

>PRK00082 hrcA heat-inducible transcription repressor; Provisional

Probab=89.47  E-value=0.79  Score=36.39  Aligned_cols=49  Identities=14%  Similarity=0.097  Sum_probs=40.0

Q ss_pred             CCCCCCHHHHHhh--cCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhc
Q 040869           47 HGRAITLSELVSA--LDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAS  101 (131)
Q Consensus        47 ~~~~~s~~eLA~~--~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s  101 (131)
                      .++|++..+||+.  +++   ++.+++|-|..|...|++.+...   ...+-+|..+
T Consensus        22 ~~~pv~s~~l~~~~~l~~---S~aTIR~dm~~Le~~G~l~~~h~---sagrIPT~kG   72 (339)
T PRK00082         22 TGEPVGSKTLSKRYGLGV---SSATIRNDMADLEELGLLEKPHT---SSGRIPTDKG   72 (339)
T ss_pred             cCCCcCHHHHHHHhCCCC---ChHHHHHHHHHHHhCCCcCCCcC---CCCCCcCHHH
Confidence            3689999999977  888   89999999999999999998652   3445556554

>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term

Probab=89.38  E-value=0.48  Score=31.86  Aligned_cols=37  Identities=16%  Similarity=0.121  Sum_probs=34.1

Q ss_pred             CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      ..++|++|||+.+.+   .++.+.++|+-+...|.+.=.+
T Consensus        17 ~~~vtl~elA~~l~c---S~Rn~r~lLkkm~~~gWi~W~p   53 (115)
T PF12793_consen   17 PVEVTLDELAELLFC---SRRNARTLLKKMQEEGWITWQP   53 (115)
T ss_pred             CcceeHHHHHHHhCC---CHHHHHHHHHHHHHCCCeeeeC
Confidence            357899999999999   9999999999999999999765

>COG1510 Predicted transcriptional regulators [Transcription]

Probab=89.37  E-value=0.42  Score=34.52  Aligned_cols=36  Identities=19%  Similarity=0.270  Sum_probs=33.7

Q ss_pred             CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      ++|+|++||++.+|.   +.+.+..-||-|...|++...
T Consensus        39 ~~Pmtl~Ei~E~lg~---Sks~vS~~lkkL~~~~lV~~~   74 (177)
T COG1510          39 RKPLTLDEIAEALGM---SKSNVSMGLKKLQDWNLVKKV   74 (177)
T ss_pred             CCCccHHHHHHHHCC---CcchHHHHHHHHHhcchHHhh
Confidence            689999999999999   899999999999999999875

>PRK13239 alkylmercury lyase; Provisional

Probab=89.37  E-value=0.53  Score=34.95  Aligned_cols=41  Identities=12%  Similarity=0.312  Sum_probs=33.3

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcC
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHS   80 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~   80 (131)
                      +-.-|+..|++ |+|.|.++||+.+|.   +.+.+.++|+.+...
T Consensus        23 ~~~~llr~la~-G~pvt~~~lA~~~~~---~~~~v~~~L~~l~~~   63 (206)
T PRK13239         23 LLVPLLRLLAK-GRPVSVTTLAAALGW---PVEEVEAVLEAMPDT   63 (206)
T ss_pred             HHHHHHHHHHc-CCCCCHHHHHHHhCC---CHHHHHHHHHhCCCe
Confidence            33446677874 899999999999999   999999988887643

>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial

Probab=89.31  E-value=0.54  Score=33.23  Aligned_cols=36  Identities=14%  Similarity=0.153  Sum_probs=33.2

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      -|+|-+|||..+|+   .+..+.|+|+.|...|+++...
T Consensus       142 ~~~t~~~iA~~lG~---tretvsR~l~~l~~~g~I~~~~  177 (193)
T TIGR03697       142 LRLSHQAIAEAIGS---TRVTITRLLGDLRKKKLISIHK  177 (193)
T ss_pred             CCCCHHHHHHHhCC---cHHHHHHHHHHHHHCCCEEecC
Confidence            36899999999999   9999999999999999998763

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

>PRK11642 exoribonuclease R; Provisional

Probab=88.84  E-value=0.88  Score=40.25  Aligned_cols=56  Identities=20%  Similarity=0.275  Sum_probs=42.7

Q ss_pred             ChHHHHHhCCCCCCHHHHHhhcCCCC-CCcchHHHHHHHhhcCCceeecccCCCCcceecc
Q 040869           39 GIADIIHSHGRAITLSELVSALDIQP-TKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLT   98 (131)
Q Consensus        39 ~ifd~l~~~~~~~s~~eLA~~~~~~~-~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t   98 (131)
                      .|.+.|.+.+.|++..+|+++++++. .....|.+.|+.|...|.+....    .+.|...
T Consensus        23 ~Il~~l~~~~~~~~~~~L~~~l~l~~~~~~~~l~~~L~~L~~~g~l~~~~----~~~~~~~   79 (813)
T PRK11642         23 FILEHLTKREKPASREELAVELNIEGEEQLEALRRRLRAMERDGQLVFTR----RQCYALP   79 (813)
T ss_pred             HHHHHHHhcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHHHHCCCEEEcC----CceEecC
Confidence            36777765568999999999999932 12356999999999999998765    4556544

>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional

Probab=88.75  E-value=0.72  Score=33.09  Aligned_cols=35  Identities=14%  Similarity=0.158  Sum_probs=32.7

Q ss_pred             CCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           50 AITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        50 ~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      ++|-.+||+.+|+   .+..+.|+|+.|...|+++...
T Consensus       168 ~~t~~~lA~~lG~---tr~tvsR~l~~l~~~gii~~~~  202 (211)
T PRK11753        168 KITRQEIGRIVGC---SREMVGRVLKMLEDQGLISAHG  202 (211)
T ss_pred             CCCHHHHHHHhCC---CHHHHHHHHHHHHHCCCEEecC
Confidence            7899999999999   9999999999999999998763

>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional

Probab=88.74  E-value=0.61  Score=34.21  Aligned_cols=35  Identities=14%  Similarity=0.198  Sum_probs=32.9

Q ss_pred             CCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           50 AITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        50 ~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      |+|-++||..+|+   .+..+.|+|+.|...|++....
T Consensus       184 ~lt~~~iA~~lG~---sr~tvsR~l~~l~~~g~I~~~~  218 (235)
T PRK11161        184 TMTRGDIGNYLGL---TVETISRLLGRFQKSGMLAVKG  218 (235)
T ss_pred             cccHHHHHHHhCC---cHHHHHHHHHHHHHCCCEEecC
Confidence            6899999999999   9999999999999999999773

>PRK09775 putative DNA-binding transcriptional regulator; Provisional

Probab=88.71  E-value=0.9  Score=37.42  Aligned_cols=53  Identities=17%  Similarity=0.283  Sum_probs=38.8

Q ss_pred             hHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchh
Q 040869           40 IADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAA  100 (131)
Q Consensus        40 ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~  100 (131)
                      |-..|.  .+|.|+.||++.+|+   +...+-|.|+.|  .|++...... ..-.|+++.-
T Consensus         5 ~~~~L~--~g~~~~~eL~~~l~~---sq~~~s~~L~~L--~~~V~~~~~g-r~~~Y~l~~~   57 (442)
T PRK09775          5 LTTLLL--QGPLSAAELAARLGV---SQATLSRLLAAL--GDQVVRFGKA-RATRYALLRP   57 (442)
T ss_pred             HHHHHh--cCCCCHHHHHHHhCC---CHHHHHHHHHHh--hcceeEeccC-ceEEEEeccc
Confidence            445566  479999999999999   999999999999  7777665410 0123666543

>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional

Probab=88.60  E-value=0.86  Score=33.44  Aligned_cols=37  Identities=16%  Similarity=0.137  Sum_probs=34.1

Q ss_pred             CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      |..++..+||+.+|+   +...++.-|+.|...|++...+
T Consensus        28 G~~L~e~eLae~lgV---SRtpVREAL~~L~~eGlv~~~~   64 (224)
T PRK11534         28 DEKLRMSLLTSRYAL---GVGPLREALSQLVAERLVTVVN   64 (224)
T ss_pred             CCcCCHHHHHHHHCC---ChHHHHHHHHHHHHCCCEEEeC
Confidence            567899999999999   9999999999999999998765

>PF02319 E2F_TDP: E2F/DP family winged-helix DNA-binding domain; InterPro: IPR003316 The mammalian transcription factor E2F plays an important role in regulating the expression of genes that are required for passage through the cell cycle

Probab=88.36  E-value=0.18  Score=30.90  Aligned_cols=39  Identities=18%  Similarity=0.440  Sum_probs=32.9

Q ss_pred             CCCCCHHHHHhhc---CCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           48 GRAITLSELVSAL---DIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        48 ~~~~s~~eLA~~~---~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      ++.+++.++|..+   +.+. ..+.+|-++.+|.+.|++++..
T Consensus        22 ~~~i~l~~ia~~l~~~~~k~-~~RRlYDI~NVLealgli~K~~   63 (71)
T PF02319_consen   22 DKSISLNEIADKLISENVKT-QRRRLYDIINVLEALGLIEKQS   63 (71)
T ss_dssp             CTEEEHHHHHHHCHHHCCHH-HCHHHHHHHHHHHHCTSEEEEE
T ss_pred             CCcccHHHHHHHHccccccc-ccchhhHHHHHHHHhCceeecC
Confidence            3789999999999   7521 4578999999999999999864

Multiple E2F family members have been identified that bind to DNA as heterodimers, interacting with proteins known as DP - the dimerisation partners [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005667 transcription factor complex; PDB: 1CF7_B.

>PRK09391 fixK transcriptional regulator FixK; Provisional

Probab=88.34  E-value=0.7  Score=34.13  Aligned_cols=34  Identities=9%  Similarity=0.168  Sum_probs=32.0

Q ss_pred             CCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           50 AITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        50 ~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      ++|-.+||..+|+   .+..+.|+++.|...|++...
T Consensus       179 ~lt~~~IA~~lGi---sretlsR~L~~L~~~GlI~~~  212 (230)
T PRK09391        179 PMSRRDIADYLGL---TIETVSRALSQLQDRGLIGLS  212 (230)
T ss_pred             cCCHHHHHHHHCC---CHHHHHHHHHHHHHCCcEEec
Confidence            6889999999999   999999999999999999865

>TIGR00331 hrcA heat shock gene repressor HrcA

Probab=88.11  E-value=1  Score=35.74  Aligned_cols=41  Identities=17%  Similarity=0.220  Sum_probs=36.5

Q ss_pred             HHHhCCCCCCHHHHHhh--cCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           43 IIHSHGRAITLSELVSA--LDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        43 ~l~~~~~~~s~~eLA~~--~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      .+. .++|++..+|++.  +++   ++.+++|-|..|...|++.+..
T Consensus        15 ~l~-~~~pv~s~~l~~~~~~~v---S~aTiR~d~~~Le~~G~l~~~h   57 (337)
T TIGR00331        15 YIK-TGQPVGSKTLLEKYNLGL---SSATIRNDMADLEDLGFIEKPH   57 (337)
T ss_pred             HHh-cCCCcCHHHHHhhcCCCC---ChHHHHHHHHHHHHCCCccCCC
Confidence            444 3689999999999  888   8999999999999999999865

In Bacillus subtilis, hrcA is the first gene of the dnaK operon and so is itself a heat shock gene.

>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus

Probab=87.99  E-value=1.5  Score=27.21  Aligned_cols=44  Identities=23%  Similarity=0.264  Sum_probs=38.8

Q ss_pred             hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      -.|...++.  +..|.+||-+++|+   +...|-..|-.|+..|++.+.
T Consensus         8 ~~IL~~ls~--~c~TLeeL~ekTgi---~k~~LlV~LsrL~k~GiI~Rk   51 (72)
T PF05584_consen    8 QKILIILSK--RCCTLEELEEKTGI---SKNTLLVYLSRLAKRGIIERK   51 (72)
T ss_pred             HHHHHHHHh--ccCCHHHHHHHHCC---CHHHHHHHHHHHHHCCCeeee
Confidence            356667774  48999999999999   999999999999999999986

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

Probab=87.96  E-value=0.63  Score=30.93  Aligned_cols=36  Identities=22%  Similarity=0.168  Sum_probs=33.3

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      .-+|+..||+++++   .-+..+++||.|...|++....
T Consensus        58 K~ITp~~lserlkI---~~SlAr~~Lr~L~~kG~Ik~V~   93 (105)
T PF03297_consen   58 KLITPSVLSERLKI---NGSLARKALRELESKGLIKPVS   93 (105)
T ss_dssp             SCECHHHHHHHHCC---SCHHHHHHHHHHHHCCSSEEEE
T ss_pred             cEeeHHHHHHhHhh---HHHHHHHHHHHHHHCCCEEEEe
Confidence            56999999999999   9999999999999999998763

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.

>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family

Probab=87.81  E-value=1.3  Score=28.65  Aligned_cols=69  Identities=13%  Similarity=0.112  Sum_probs=47.6

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCC-----CCCCcchHHHHHHHhhcCCceeeccc--C-CC-CcceecchhccccccC
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDI-----QPTKTTGLFRLMRLLVHSSCFNKTKV--N-GQ-EEAYGLTAASTLLIKD  107 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~-----~~~~~~~l~RlLr~L~~~gl~~~~~~--~-~~-~~~y~~t~~s~~L~~~  107 (131)
                      ++=|.-.|.  .+|.+--||.+.+.-     -+.++..++++|+.|...|++.....  . +. ...|..|+.++.+...
T Consensus         6 ~~~iL~~L~--~~~~~GYei~~~l~~~~~~~~~i~~gtlY~~L~rLe~~GlI~~~~~~~~~~~~rk~y~iT~~Gr~~l~~   83 (100)
T TIGR03433         6 DLLILKTLS--LGPLHGYGIAQRIQQISEDVLQVEEGSLYPALHRLERRGWIAAEWGESENNRRAKFYRLTAAGRKQLAA   83 (100)
T ss_pred             HHHHHHHHh--cCCCCHHHHHHHHHHHcCCccccCCCcHHHHHHHHHHCCCeEEEeeecCCCCCceEEEECHHHHHHHHH
Confidence            334555565  368999999988621     11277899999999999999997311  1 11 2459999999865543

Members of this protein family are putative transcriptional regulators of the PadR family, as found in species of the Acidobacteria. This family of proteins has expanded greatly in this lineage, and where it regularly is found in the vicinity of a putative transporter protein

>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator

Probab=87.71  E-value=0.93  Score=32.87  Aligned_cols=37  Identities=16%  Similarity=0.258  Sum_probs=34.2

Q ss_pred             CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      |..++-.+||+.+|+   +...++.-|+.|...|++...+
T Consensus        32 G~~L~e~~La~~lgV---SRtpVReAL~~L~~eGlv~~~~   68 (212)
T TIGR03338        32 GAKLNESDIAARLGV---SRGPVREAFRALEEAGLVRNEK   68 (212)
T ss_pred             CCEecHHHHHHHhCC---ChHHHHHHHHHHHHCCCEEEec
Confidence            567899999999999   9999999999999999998765

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.

>PF03428 RP-C: Replication protein C N-terminal domain; InterPro: IPR005090 Proteins in this group have homology with the RepC protein of Agrobacterium Ri and Ti plasmids []

Probab=87.66  E-value=0.9  Score=32.90  Aligned_cols=57  Identities=16%  Similarity=0.155  Sum_probs=41.0

Q ss_pred             HHHHHHHHHHhChHHHHHhCCCC---CCHHHHHhhc-CCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           28 SSMSLKCAIELGIADIIHSHGRA---ITLSELVSAL-DIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        28 ~~~aL~~a~~L~ifd~l~~~~~~---~s~~eLA~~~-~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      ...+|.+.+.+==.+-+.+.+.|   .|-.+|+..+ |+   ++..+.|.++.|+..|++...+
T Consensus        45 ~l~vL~aLls~~~~~d~~~~~~piVfpSN~~La~r~~G~---s~~tlrR~l~~LveaGLI~rrD  105 (177)
T PF03428_consen   45 ALAVLDALLSFTPPDDWEPGRRPIVFPSNAQLAERLNGM---SERTLRRHLARLVEAGLIVRRD  105 (177)
T ss_pred             HHHHHHHHHHhCCcccccCCCCceeecCHHHHHHHHcCC---CHHHHHHHHHHHHHCCCeeecc
Confidence            34444444444433334322233   6889999999 99   9999999999999999999864

They may be involved in plasmid replication and stabilisation functions.

>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD

Probab=87.60  E-value=0.91  Score=29.14  Aligned_cols=35  Identities=23%  Similarity=0.329  Sum_probs=28.4

Q ss_pred             hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhh
Q 040869           38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLV   78 (131)
Q Consensus        38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~   78 (131)
                      ..|+..+.   .+.|..+||+.+|+   +...++|+.|.+.
T Consensus        41 ~~I~~ll~---~G~S~~eIA~~LgI---SrsTIyRi~R~~n   75 (88)
T TIGR02531        41 LQVAKMLK---QGKTYSDIEAETGA---STATISRVKRCLN   75 (88)
T ss_pred             HHHHHHHH---CCCCHHHHHHHHCc---CHHHHHHHHHhcc
Confidence            55666666   45899999999999   9999999887544

This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.

>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=87.56  E-value=0.98  Score=26.37  Aligned_cols=55  Identities=18%  Similarity=0.220  Sum_probs=41.3

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhh---cCCceeecccCCCCcceecchhcc
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLV---HSSCFNKTKVNGQEEAYGLTAAST  102 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~---~~gl~~~~~~~~~~~~y~~t~~s~  102 (131)
                      ++.+|..+.+   .-|...-|+.+++   +++.+.|-++.|.   ...+|...     ++.+.+|+.++
T Consensus         3 ~l~~f~~v~~---~gs~~~AA~~l~i---s~~~vs~~i~~LE~~lg~~Lf~r~-----~~~~~lT~~G~   60 (60)
T PF00126_consen    3 QLRYFLAVAE---TGSISAAAEELGI---SQSAVSRQIKQLEEELGVPLFERS-----GRGLRLTEAGE   60 (60)
T ss_dssp             HHHHHHHHHH---HSSHHHHHHHCTS---SHHHHHHHHHHHHHHHTS-SEEEC-----SSSEEE-HHHH
T ss_pred             HHHHHHHHHH---hCCHHHHHHHhhc---cchHHHHHHHHHHHHhCCeEEEEC-----CCCeeEChhhC
Confidence            4667778874   3489999999999   9999999998885   45688876     45688888753

These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....

>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A

Probab=87.53  E-value=0.75  Score=24.81  Aligned_cols=28  Identities=14%  Similarity=0.236  Sum_probs=21.9

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHHHhhc
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMRLLVH   79 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~   79 (131)
                      .++++++||..+|.   ++..+.|+.+....
T Consensus         7 ~~~~l~~iA~~~g~---S~~~f~r~Fk~~~g   34 (42)
T PF00165_consen    7 QKLTLEDIAEQAGF---SPSYFSRLFKKETG   34 (42)
T ss_dssp             SS--HHHHHHHHTS----HHHHHHHHHHHTS
T ss_pred             CCCCHHHHHHHHCC---CHHHHHHHHHHHHC
Confidence            57999999999999   99999999886543

>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []

Probab=87.46  E-value=0.64  Score=28.72  Aligned_cols=31  Identities=19%  Similarity=0.301  Sum_probs=24.2

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCc
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSC   82 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl   82 (131)
                      ...|+.|||+.+++   ++..+.|+.+.|--.|+
T Consensus        33 ~~~si~elA~~~~v---S~sti~Rf~kkLG~~gf   63 (77)
T PF01418_consen   33 AFMSISELAEKAGV---SPSTIVRFCKKLGFSGF   63 (77)
T ss_dssp             CT--HHHHHHHCTS----HHHHHHHHHHCTTTCH
T ss_pred             HHccHHHHHHHcCC---CHHHHHHHHHHhCCCCH
Confidence            46999999999999   99999999998766664

Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.

>COG3682 Predicted transcriptional regulator [Transcription]

Probab=87.44  E-value=1.3  Score=30.32  Aligned_cols=62  Identities=19%  Similarity=0.280  Sum_probs=47.7

Q ss_pred             HHHhChHHHHHhCCCCCCHHHHHhhcCCCCC-CcchHHHHHHHhhcCCceeecccCCCCcceecchh
Q 040869           35 AIELGIADIIHSHGRAITLSELVSALDIQPT-KTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAA  100 (131)
Q Consensus        35 a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~-~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~  100 (131)
                      +.+..|.++|-. .+|.|+.||-+.++...+ ....+.-+|+-|+-.|++.....   ++.|.-.|+
T Consensus         6 ~aE~eVM~ilW~-~~~~t~~eI~~~l~~~~ews~sTV~TLl~RL~KKg~l~~~kd---gr~~~y~pL   68 (123)
T COG3682           6 AAEWEVMEILWS-RGPATVREIIEELPADREWSYSTVKTLLNRLVKKGLLTRKKD---GRAFRYSPL   68 (123)
T ss_pred             HHHHHHHHHHHH-cCCccHHHHHHHHhhcccccHHHHHHHHHHHHhccchhhhhc---CCeeeeecc
Confidence            356678888875 469999999988876211 56689999999999999998763   566777775

>COG1725 Predicted transcriptional regulators [Transcription]

Probab=87.21  E-value=1  Score=30.83  Aligned_cols=45  Identities=11%  Similarity=0.183  Sum_probs=37.9

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA   99 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~   99 (131)
                      .--|+.|+|..+|+   +|-++.|--+-|...|++....   |.|.|-...
T Consensus        34 kLPSvRelA~~~~V---NpnTv~raY~eLE~eG~i~t~r---g~G~fV~~~   78 (125)
T COG1725          34 KLPSVRELAKDLGV---NPNTVQRAYQELEREGIVETKR---GKGTFVTED   78 (125)
T ss_pred             CCCcHHHHHHHhCC---CHHHHHHHHHHHHHCCCEEEec---CeeEEEcCC
Confidence            45799999999999   9999999999999999998765   256665533

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

Probab=87.08  E-value=0.77  Score=30.33  Aligned_cols=46  Identities=20%  Similarity=0.164  Sum_probs=38.0

Q ss_pred             ChHHHHHh---CCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           39 GIADIIHS---HGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        39 ~ifd~l~~---~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      .+++.+.+   ...-+|...||.+.|+   +-+..+++||.|...|++....
T Consensus        45 e~~~ki~KEV~~~r~VTpy~la~r~gI---~~SvAr~vLR~LeeeGvv~lvs   93 (107)
T COG4901          45 ELLDKIRKEVPRERVVTPYVLASRYGI---NGSVARIVLRHLEEEGVVQLVS   93 (107)
T ss_pred             HHHHHHHHhcccceeecHHHHHHHhcc---chHHHHHHHHHHHhCCceeeec
Confidence            35555543   1367999999999999   9999999999999999998764

>PRK13918 CRP/FNR family transcriptional regulator; Provisional

Probab=86.96  E-value=0.83  Score=32.58  Aligned_cols=35  Identities=14%  Similarity=0.104  Sum_probs=32.5

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      -++|-++||..+|+   .+..+.|+|+.|...|++...
T Consensus       148 ~~~t~~~iA~~lG~---tretvsR~l~~l~~~g~I~~~  182 (202)
T PRK13918        148 IYATHDELAAAVGS---VRETVTKVIGELSREGYIRSG  182 (202)
T ss_pred             ecCCHHHHHHHhCc---cHHHHHHHHHHHHHCCCEEcC
Confidence            36899999999999   999999999999999999855

>COG1802 GntR Transcriptional regulators [Transcription]

Probab=86.76  E-value=1.3  Score=32.71  Aligned_cols=37  Identities=19%  Similarity=0.233  Sum_probs=35.1

Q ss_pred             CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      |.+++-.+||+.+|+   +...++.-|+.|++.|++...+
T Consensus        37 G~~l~e~~La~~~gv---SrtPVReAL~rL~~eGlv~~~p   73 (230)
T COG1802          37 GERLSEEELAEELGV---SRTPVREALRRLEAEGLVEIEP   73 (230)
T ss_pred             CCCccHHHHHHHhCC---CCccHHHHHHHHHHCCCeEecC
Confidence            678999999999999   9999999999999999999875

>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]

Probab=86.74  E-value=1.3  Score=32.14  Aligned_cols=45  Identities=20%  Similarity=0.231  Sum_probs=38.8

Q ss_pred             hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      ..|++++.+ .+-+|-+|||..+|+   ....++|+|+.|...|++...
T Consensus        21 ~~v~~~l~~-kge~tDeela~~l~i---~~~~vrriL~~L~e~~li~~~   65 (176)
T COG1675          21 VLVVDALLE-KGELTDEELAELLGI---KKNEVRRILYALYEDGLISYR   65 (176)
T ss_pred             hHHHHHHHh-cCCcChHHHHHHhCc---cHHHHHHHHHHHHhCCceEEE
Confidence            347788874 247999999999999   999999999999999999854

>PF03551 PadR: Transcriptional regulator PadR-like family; InterPro: IPR005149 Phenolic acids, also called substituted hydroxycinnamic acids, are abundant in the plant kingdom because they are involved in the structure of plant cell walls and are present in some vacuoles

Probab=86.27  E-value=0.79  Score=27.95  Aligned_cols=60  Identities=10%  Similarity=0.159  Sum_probs=41.1

Q ss_pred             HHHHHhCCCCCCHHHHHhhcCCC-----CCCcchHHHHHHHhhcCCceeecccC--CC--Ccceecchhcc
Q 040869           41 ADIIHSHGRAITLSELVSALDIQ-----PTKTTGLFRLMRLLVHSSCFNKTKVN--GQ--EEAYGLTAAST  102 (131)
Q Consensus        41 fd~l~~~~~~~s~~eLA~~~~~~-----~~~~~~l~RlLr~L~~~gl~~~~~~~--~~--~~~y~~t~~s~  102 (131)
                      .-+|..  +|++.-||.+.+.-.     ..++..+++.|+.|...|+++.....  .+  ...|..|+.++
T Consensus         2 L~~L~~--~~~~Gyei~~~l~~~~~~~~~i~~g~lY~~L~~Le~~gli~~~~~~~~~~~~rk~Y~iT~~G~   70 (75)
T PF03551_consen    2 LGLLSE--GPMHGYEIKQELEERTGGFWKISPGSLYPALKRLEEEGLIESRWEEEGNGRPRKYYRITEKGR   70 (75)
T ss_dssp             HHHHHH--S-EEHHHHHHHHHHCSTTTEETTHHHHHHHHHHHHHTTSEEEEEEEETTSSEEEEEEESHHHH
T ss_pred             hhhhcc--CCCcHHHHHHHHHHHhCCCcccChhHHHHHHHHHHhCCCEEEeeeccCCCCCCEEEEECHHHH
Confidence            344553  678888888766421     12678899999999999999976432  11  23499999876

In plant-soil ecosystems they are released as free acids by hemicellulases produced by several fungi and bacteria. Of these weak acids, the most abundant are p-coumaric, ferulic, and caffeic acids, considered to be natural toxins that inhibit the growth of microorganisms, especially at low pHs. In spite of this chemical stress, some bacteria can use phenolic acids as a sole source of carbon. For other microorganisms, these compounds induce a specific response by which the organism adapts to its environment. The ubiquitous lactic acid bacterium Lactobacillus plantarum exhibits an inducible phenolic acid decarboxylase (PAD) activity which converts these substrates into less-toxic vinyl phenol derivatives. PadR acts as a repressor of padA gene expression in the phenolic acid stress response [].; PDB: 1XMA_B 2ESH_A 2DQL_B 3L9F_C 3ELK_B 4EJO_B 3L7W_A 3HHH_A 1YG2_A 3F8B_A ....

>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions []

Probab=86.23  E-value=0.85  Score=26.73  Aligned_cols=40  Identities=23%  Similarity=0.284  Sum_probs=32.8

Q ss_pred             HHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhh
Q 040869           35 AIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLV   78 (131)
Q Consensus        35 a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~   78 (131)
                      .-++.|++.|-+ .+.+++.|||..+|+   ....+..-+..|.
T Consensus         5 ~rq~~Ll~~L~~-~~~~~~~ela~~l~~---S~rti~~~i~~L~   44 (59)
T PF08280_consen    5 KRQLKLLELLLK-NKWITLKELAKKLNI---SERTIKNDINELN   44 (59)
T ss_dssp             HHHHHHHHHHHH-HTSBBHHHHHHHCTS----HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHc-CCCCcHHHHHHHHCC---CHHHHHHHHHHHH
Confidence            346778888876 678999999999999   8888888887775

; PDB: 2WTE_A 3SQN_A.

>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]

Probab=86.03  E-value=1.9  Score=33.26  Aligned_cols=55  Identities=16%  Similarity=0.107  Sum_probs=45.5

Q ss_pred             hCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcc-ccc
Q 040869           46 SHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAST-LLI  105 (131)
Q Consensus        46 ~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~-~L~  105 (131)
                      +.++++--+|||..++-   +|-.++-.|..|.++|+++-.+.  ..|.|.+|-.+. .|.
T Consensus        21 ~~~r~IKgeeIA~~l~r---npGTVRNqmq~LkaLgLVegvpG--PkGGY~PT~kAYe~L~   76 (294)
T COG2524          21 RKKRPIKGEEIAEVLNR---NPGTVRNQMQSLKALGLVEGVPG--PKGGYKPTSKAYEALS   76 (294)
T ss_pred             hcCCCcchHHHHHHHcc---CcchHHHHHHHHHhcCccccccC--CCCCccccHHHHHHhc
Confidence            44679999999999999   99999999999999999997641  158899997654 443

>TIGR03879 near_KaiC_dom probable regulatory domain

Probab=85.48  E-value=0.75  Score=28.55  Aligned_cols=34  Identities=15%  Similarity=0.071  Sum_probs=29.8

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceee
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNK   85 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~   85 (131)
                      ..+|..|||+.+|+   ++..+...++.+-..|.+..
T Consensus        31 eGlS~kEIAe~LGI---S~~TVk~~l~~~~~~~~~~~   64 (73)
T TIGR03879        31 AGKTASEIAEELGR---TEQTVRNHLKGETKAGGLVK   64 (73)
T ss_pred             cCCCHHHHHHHHCc---CHHHHHHHHhcCcccchHHH
Confidence            56999999999999   99999999998888876653

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

>KOG2165 consensus Anaphase-promoting complex (APC), subunit 2 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]

Probab=84.99  E-value=1.4  Score=38.22  Aligned_cols=50  Identities=16%  Similarity=0.255  Sum_probs=41.4

Q ss_pred             CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchh
Q 040869           48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAA  100 (131)
Q Consensus        48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~  100 (131)
                      ....|.+|+|+.+|+   ++..++|.|......|++.+.+.....|+|..++.
T Consensus       614 k~twt~eelse~l~i---p~~~lrrrL~fWi~~GvL~e~~~~s~tgt~T~iEs  663 (765)
T KOG2165|consen  614 KNTWTLEELSESLGI---PVPALRRRLSFWIQKGVLREEPIISDTGTLTVIES  663 (765)
T ss_pred             cccccHHHHHHHhCC---CHHHHHHHHHHHHHcCeeecCCCCCCCceeeeccc
Confidence            357999999999999   99999999999999999998752222477777763

>PRK10430 DNA-binding transcriptional activator DcuR; Provisional

Probab=84.96  E-value=1.3  Score=32.50  Aligned_cols=35  Identities=17%  Similarity=0.238  Sum_probs=32.6

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      .++|..|||+++++   .+.+++..++.|+..|++.+.
T Consensus       177 ~g~s~~eIA~~l~i---S~~Tv~~~~~~~~~~~~~~~~  211 (239)
T PRK10430        177 YEFSTDELANAVNI---SRVSCRKYLIWLVNCHILFTS  211 (239)
T ss_pred             CCcCHHHHHHHhCc---hHHHHHHHHHHHHhCCEEEEE
Confidence            67999999999999   999999999999999999665

>PF05331 DUF742: Protein of unknown function (DUF742); InterPro: IPR007995 This family consists of several uncharacterised Streptomyces proteins as well as one from Mycobacterium tuberculosis

Probab=84.92  E-value=1.7  Score=29.24  Aligned_cols=42  Identities=14%  Similarity=0.226  Sum_probs=35.6

Q ss_pred             hHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           40 IADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        40 ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      |.+...   .|.|+.|||..+++   +...++-|+--|...|++.-..
T Consensus        48 Il~lC~---~~~SVAEiAA~L~l---PlgVvrVLvsDL~~~G~v~v~~   89 (114)
T PF05331_consen   48 ILELCR---RPLSVAEIAARLGL---PLGVVRVLVSDLADAGLVRVRA   89 (114)
T ss_pred             HHHHHC---CCccHHHHHHhhCC---CchhhhhhHHHHHhCCCEEEeC
Confidence            445444   59999999999999   8888888999999999998765

The function of these proteins is unknown.

>COG2188 PhnF Transcriptional regulators [Transcription]

Probab=84.80  E-value=1.3  Score=33.10  Aligned_cols=43  Identities=9%  Similarity=0.149  Sum_probs=38.4

Q ss_pred             CCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869           51 ITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA   99 (131)
Q Consensus        51 ~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~   99 (131)
                      -|=.|||++.|+   +..+++|-|+.|+..|++.+..   |.|+|-..+
T Consensus        32 PsE~eLa~~f~V---SR~TvRkAL~~L~~eGli~r~~---G~GtfV~~~   74 (236)
T COG2188          32 PSERELAEQFGV---SRMTVRKALDELVEEGLIVRRQ---GKGTFVASP   74 (236)
T ss_pred             CCHHHHHHHHCC---cHHHHHHHHHHHHHCCcEEEEe---cCeeEEcCc
Confidence            466799999999   9999999999999999999875   378888877

>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional

Probab=84.65  E-value=2  Score=31.50  Aligned_cols=37  Identities=16%  Similarity=0.213  Sum_probs=33.9

Q ss_pred             CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      |..++..+||+.+|+   +...++.-|+.|...|++...+
T Consensus        32 G~~L~e~~La~~lgV---SRtpVREAL~~L~~eGLV~~~~   68 (221)
T PRK11414         32 GARLITKNLAEQLGM---SITPVREALLRLVSVNALSVAP   68 (221)
T ss_pred             CCccCHHHHHHHHCC---CchhHHHHHHHHHHCCCEEecC
Confidence            567889999999999   9999999999999999998765

>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3

Probab=84.49  E-value=2.1  Score=23.93  Aligned_cols=35  Identities=11%  Similarity=0.230  Sum_probs=27.4

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHh
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLL   77 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L   77 (131)
                      +--|...+.   ...|..++|+.+|+   +...+.|+++..
T Consensus        17 ~~~i~~~~~---~~~s~~~vA~~~~v---s~~TV~ri~~~~   51 (52)
T PF13542_consen   17 EQYILKLLR---ESRSFKDVARELGV---SWSTVRRIFDRY   51 (52)
T ss_pred             HHHHHHHHh---hcCCHHHHHHHHCC---CHHHHHHHHHhh
Confidence            334566665   23799999999999   999999998754

>PRK00135 scpB segregation and condensation protein B; Reviewed

Probab=84.48  E-value=2.7  Score=30.69  Aligned_cols=57  Identities=19%  Similarity=0.216  Sum_probs=42.1

Q ss_pred             hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC---CCCcceecchhc
Q 040869           38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN---GQEEAYGLTAAS  101 (131)
Q Consensus        38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~---~~~~~y~~t~~s  101 (131)
                      |.+..+|+- .+|+|-.||++..|+   +.   ..+++.|...|++.+.+..   +.+-.|..|+..
T Consensus        93 LEtLaiIay-~qPiTr~eI~~irGv---~~---~~ii~~L~~~gLI~e~gr~~~~Grp~ly~tT~~F  152 (188)
T PRK00135         93 LEVLAIIAY-KQPITRIEIDEIRGV---NS---DGALQTLLAKGLIKEVGRKEVPGRPILYGTTDEF  152 (188)
T ss_pred             HHHHHHHHH-cCCcCHHHHHHHHCC---CH---HHHHHHHHHCCCeEEcCcCCCCCCCeeeehhHHH
Confidence            446677764 479999999999999   64   8899999999999875321   113447777653

>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional

Probab=84.33  E-value=2.2  Score=31.11  Aligned_cols=47  Identities=17%  Similarity=0.188  Sum_probs=38.1

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceee
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNK   85 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~   85 (131)
                      ++-.|.|.|.+.|..+|+-+||+++|+   +...+.|-|=-|-..|.+.-
T Consensus         5 ~~~~i~~~l~~~~~~~~a~~i~k~l~i---~k~~vNr~LY~L~~~~~v~~   51 (183)
T PHA02701          5 CASLILTLLSSSGDKLPAKRIAKELGI---SKHEANRCLYRLLESDAVSC   51 (183)
T ss_pred             HHHHHHHHHHhcCCCCcHHHHHHHhCc---cHHHHHHHHHHHhhcCcEec
Confidence            456799999876646999999999999   88888887777777776643

>PRK14096 pgi glucose-6-phosphate isomerase; Provisional

Probab=84.28  E-value=1.9  Score=36.32  Aligned_cols=42  Identities=14%  Similarity=0.468  Sum_probs=33.9

Q ss_pred             hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcC
Q 040869           38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHS   80 (131)
Q Consensus        38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~   80 (131)
                      -+|-..|...+++.|+++||+++|.. ++...++.|||.|++.
T Consensus       466 ~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~i~~~~~~n  507 (528)
T PRK14096        466 KKVEELLKEDGGELSIEEIAAALGAP-EQVETIYKILRHLAAN  507 (528)
T ss_pred             HHHHHHHhccCCCCCHHHHHHHcCCC-ccHHHHHHHHHHHhcC
Confidence            44666675556899999999999983 3677899999999986

>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon

Probab=84.06  E-value=2.2  Score=23.55  Aligned_cols=26  Identities=15%  Similarity=0.198  Sum_probs=21.5

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHHHh
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMRLL   77 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L   77 (131)
                      ...|..|||+.+|+   ++..+++.++.+
T Consensus        17 ~g~s~~eia~~l~i---s~~tv~~~~~~~   42 (58)
T smart00421       17 EGLTNKEIAERLGI---SEKTVKTHLSNI   42 (58)
T ss_pred             cCCCHHHHHHHHCC---CHHHHHHHHHHH
Confidence            35899999999999   888888776654

lux regulon (activates the bioluminescence operon

>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes

Probab=84.00  E-value=1.6  Score=26.04  Aligned_cols=29  Identities=14%  Similarity=0.310  Sum_probs=22.8

Q ss_pred             HHHHHhCCCCCCHHHHHhhcCCCCCCcchHHH
Q 040869           41 ADIIHSHGRAITLSELVSALDIQPTKTTGLFR   72 (131)
Q Consensus        41 fd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~R   72 (131)
                      |++--+++|.++..|||+++|+   ++..+++
T Consensus        13 ~e~y~~~~g~i~lkdIA~~Lgv---s~~tIr~   41 (60)
T PF10668_consen   13 FEIYKESNGKIKLKDIAEKLGV---SESTIRK   41 (60)
T ss_pred             HHHHHHhCCCccHHHHHHHHCC---CHHHHHH
Confidence            4545445689999999999999   8777764

Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].

>PRK10736 hypothetical protein; Provisional

Probab=83.77  E-value=2.1  Score=34.55  Aligned_cols=51  Identities=4%  Similarity=-0.041  Sum_probs=42.3

Q ss_pred             ChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecc
Q 040869           39 GIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLT   98 (131)
Q Consensus        39 ~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t   98 (131)
                      .|.+.|.  ..|+++++|+.++|+   +...+..+|-.|.-.|++.+..    ++.|..-
T Consensus       312 ~v~~~l~--~~~~~iD~L~~~~~l---~~~~v~~~L~~LEl~G~v~~~~----g~~~~~~  362 (374)
T PRK10736        312 ELLANVG--DEVTPVDVVAERAGQ---PVPEVVTQLLELELAGWIAAVP----GGYVRLR  362 (374)
T ss_pred             HHHHhcC--CCCCCHHHHHHHHCc---CHHHHHHHHHHHHhCCcEEEcC----CcEEEEe
Confidence            4556554  368999999999999   9999999999999999999986    5666553

>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=83.70  E-value=0.88  Score=25.56  Aligned_cols=21  Identities=10%  Similarity=0.351  Sum_probs=14.1

Q ss_pred             CHHHHHhhcCCCCCCcchHHHHHH
Q 040869           52 TLSELVSALDIQPTKTTGLFRLMR   75 (131)
Q Consensus        52 s~~eLA~~~~~~~~~~~~l~RlLr   75 (131)
                      |+.|||+.+|+   +...+.|+|+
T Consensus         1 Ti~dIA~~agv---S~~TVSr~ln   21 (46)
T PF00356_consen    1 TIKDIAREAGV---SKSTVSRVLN   21 (46)
T ss_dssp             CHHHHHHHHTS---SHHHHHHHHT
T ss_pred             CHHHHHHHHCc---CHHHHHHHHh
Confidence            56788888887   5565555553

These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. 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, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....

>TIGR01764 excise DNA binding domain, excisionase family

Probab=83.52  E-value=1.3  Score=23.98  Aligned_cols=22  Identities=23%  Similarity=0.498  Sum_probs=19.9

Q ss_pred             CCHHHHHhhcCCCCCCcchHHHHHH
Q 040869           51 ITLSELVSALDIQPTKTTGLFRLMR   75 (131)
Q Consensus        51 ~s~~eLA~~~~~~~~~~~~l~RlLr   75 (131)
                      +|..|+|+.+|+   ++..++++++
T Consensus         2 lt~~e~a~~lgi---s~~ti~~~~~   23 (49)
T TIGR01764         2 LTVEEAAEYLGV---SKDTVYRLIH   23 (49)
T ss_pred             CCHHHHHHHHCC---CHHHHHHHHH
Confidence            689999999999   9999998875

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).

>PF14338 Mrr_N: Mrr N-terminal domain

Probab=83.42  E-value=6.1  Score=25.03  Aligned_cols=56  Identities=13%  Similarity=0.128  Sum_probs=34.5

Q ss_pred             CCCHHHHHhhcCCCCCCcchHHHH---HHHhhcCCceeecccCCCCcceecchhccccccCcc
Q 040869           50 AITLSELVSALDIQPTKTTGLFRL---MRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIKDKP  109 (131)
Q Consensus        50 ~~s~~eLA~~~~~~~~~~~~l~Rl---Lr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~~~~~  109 (131)
                      .+|-+|....+.-.+..+..-.|+   +-+|...|+++...    .|.|.+|+.++.+...+|
T Consensus        34 ~ls~e~~~~~~~sg~~~~~~~~ri~Wa~~~L~~aGli~~~~----rG~~~iT~~G~~~l~~~p   92 (92)
T PF14338_consen   34 GLSDEERNERLPSGQGYSRFKNRIRWARSYLKKAGLIERPK----RGIWRITEKGRKALAEHP   92 (92)
T ss_pred             CCCHHHHHHHcccCCcchhHHHhHHHHHHHHHHCCCccCCC----CCceEECHhHHHHHhhCc
Confidence            455555555543100011223333   56788999998766    799999999996655544

>TIGR02719 repress_PhaQ poly-beta-hydroxybutyrate-responsive repressor

Probab=83.41  E-value=9.1  Score=26.59  Aligned_cols=75  Identities=13%  Similarity=0.107  Sum_probs=51.3

Q ss_pred             HHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcC---CCCCCcchHHHHHHHhhcCCceeecccC--CCC--cceecchhc
Q 040869           29 SMSLKCAIELGIADIIHSHGRAITLSELVSALD---IQPTKTTGLFRLMRLLVHSSCFNKTKVN--GQE--EAYGLTAAS  101 (131)
Q Consensus        29 ~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~---~~~~~~~~l~RlLr~L~~~gl~~~~~~~--~~~--~~y~~t~~s  101 (131)
                      .+..+-.+++=|.-.|.+  +|+.--+|.+.+.   .-..++..|+++|+-|...|++......  .++  ..|.+|+.+
T Consensus        18 ~ql~kg~l~~~IL~~L~~--~p~hGYeI~q~l~~~g~~~v~~GtLYp~L~RLE~~GlI~~~~~~~~~gp~RK~Y~LTe~G   95 (138)
T TIGR02719        18 NGAPKNFLVPFLLLCLKD--WNLHGYKLIQMLMDFGFSSVDQGNVYRTLRKLEKDNLISSQWDTSAEGPAKRIYSLTDAG   95 (138)
T ss_pred             HHHHHHHHHHHHHHHHcc--CCCCHHHHHHHHHHcCCCCCCcChHHHHHHHHHHCCCEEEEeeecCCCCCcEEEEECHHH
Confidence            445666666667777763  6778877777653   2122778899999999999999864211  112  349999999


Q ss_pred             cccc
Q 040869          102 TLLI  105 (131)
Q Consensus       102 ~~L~  105 (131)
                      +...
T Consensus        96 r~~L   99 (138)
T TIGR02719        96 EQYL   99 (138)
T ss_pred             HHHH
Confidence            8543

Members of this family are transcriptional regulatory proteins found in the vicinity of poly-beta-hydroxybutyrate (PHB) operons in several species of Bacillus. This protein appears to have repressor activity modulated by PHB itself. This protein belongs to the larger PadR family (see pfam03551).

>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein

Probab=83.32  E-value=1.6  Score=26.01  Aligned_cols=29  Identities=28%  Similarity=0.409  Sum_probs=24.6

Q ss_pred             CCCHHHHHhhcCCCCCCcchHHHHHHHhhcCC
Q 040869           50 AITLSELVSALDIQPTKTTGLFRLMRLLVHSS   81 (131)
Q Consensus        50 ~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~g   81 (131)
                      ++|+++||+.+|+   ++..+.|+++......
T Consensus         1 ~~~~~~la~~~~~---s~~~l~~~f~~~~~~s   29 (84)
T smart00342        1 PLTLEDLAEALGM---SPRHLQRLFKKETGTT   29 (84)
T ss_pred             CCCHHHHHHHhCC---CHHHHHHHHHHHhCcC
Confidence            4789999999999   9999999998775544

>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B

Probab=83.11  E-value=1.8  Score=31.96  Aligned_cols=42  Identities=14%  Similarity=0.183  Sum_probs=37.0

Q ss_pred             CCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecc
Q 040869           51 ITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLT   98 (131)
Q Consensus        51 ~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t   98 (131)
                      -|=.|||++.|+   +..+++|-|+.|+..|++....   |.|+|-..
T Consensus        25 PsE~eLa~~~gV---SR~TVR~Al~~L~~eGli~r~~---G~GTfV~~   66 (233)
T TIGR02404        25 PSEHELMDQYGA---SRETVRKALNLLTEAGYIQKIQ---GKGSIVLN   66 (233)
T ss_pred             cCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEeC---CceEEEec
Confidence            478899999999   9999999999999999999876   37888743

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.

>PRK10402 DNA-binding transcriptional activator YeiL; Provisional

Probab=82.88  E-value=1.8  Score=31.70  Aligned_cols=35  Identities=11%  Similarity=0.217  Sum_probs=32.3

Q ss_pred             CCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           50 AITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        50 ~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      +.|-.+||+.+|+   .++.+.|+|+-|...|+++...
T Consensus       169 ~~t~~~lA~~lG~---sretvsR~L~~L~~~G~I~~~~  203 (226)
T PRK10402        169 HEKHTQAAEYLGV---SYRHLLYVLAQFIQDGYLKKSK  203 (226)
T ss_pred             cchHHHHHHHHCC---cHHHHHHHHHHHHHCCCEEeeC
Confidence            5788999999999   9999999999999999999763

>COG2378 Predicted transcriptional regulator [Transcription]

Probab=82.65  E-value=2.4  Score=33.26  Aligned_cols=58  Identities=17%  Similarity=0.302  Sum_probs=42.6

Q ss_pred             hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchh
Q 040869           38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAA  100 (131)
Q Consensus        38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~  100 (131)
                      +.|..+|..... +|+.+||+.+++   +.+.++|=++.|...|+--+...+ .++.|.+-+-
T Consensus        11 ~~ii~~L~~~~~-vta~~lA~~~~V---S~RTi~RDi~~L~~~gvPI~~e~G-~~~gy~~~~~   68 (311)
T COG2378          11 LQIIQILRAKET-VTAAELADEFEV---SVRTIYRDIATLRAAGVPIEGERG-KGGGYRLRPG   68 (311)
T ss_pred             HHHHHHHHhCcc-chHHHHHHhcCC---CHHHHHHHHHHHHHCCCCeEeecC-CCccEEEccC
Confidence            445666664334 999999999999   999999999999999988665421 0244555443

>PF12728 HTH_17: Helix-turn-helix domain

Probab=82.59  E-value=1.4  Score=24.62  Aligned_cols=23  Identities=26%  Similarity=0.488  Sum_probs=20.5

Q ss_pred             CCHHHHHhhcCCCCCCcchHHHHHHH
Q 040869           51 ITLSELVSALDIQPTKTTGLFRLMRL   76 (131)
Q Consensus        51 ~s~~eLA~~~~~~~~~~~~l~RlLr~   76 (131)
                      +|++|+|+.+|+   +...++++++.
T Consensus         2 lt~~e~a~~l~i---s~~tv~~~~~~   24 (51)
T PF12728_consen    2 LTVKEAAELLGI---SRSTVYRWIRQ   24 (51)
T ss_pred             CCHHHHHHHHCc---CHHHHHHHHHc
Confidence            689999999999   99999988863

>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed

Probab=82.33  E-value=1.5  Score=34.21  Aligned_cols=47  Identities=17%  Similarity=0.231  Sum_probs=38.8

Q ss_pred             CCCCCHHHHHhhcCCCCCCcchHHHHHH-HhhcCCceeecccCCCCcceecchhcc
Q 040869           48 GRAITLSELVSALDIQPTKTTGLFRLMR-LLVHSSCFNKTKVNGQEEAYGLTAAST  102 (131)
Q Consensus        48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr-~L~~~gl~~~~~~~~~~~~y~~t~~s~  102 (131)
                      +++.+++.||..+|.   ++..+..+++ +|...|++....    .|+ ..|+.+.
T Consensus       274 ~~~~~~~~~a~~lg~---~~~~~~~~~e~~Li~~~li~~~~----~gr-~~~~~~~  321 (328)
T PRK00080        274 GGPVGLDTLAAALGE---ERDTIEDVYEPYLIQQGFIQRTP----RGR-VATPKAY  321 (328)
T ss_pred             CCceeHHHHHHHHCC---CcchHHHHhhHHHHHcCCcccCC----chH-HHHHHHH
Confidence            579999999999999   9999999999 999999998664    343 4455544

>COG1654 BirA Biotin operon repressor [Transcription]

Probab=82.27  E-value=3.7  Score=25.79  Aligned_cols=51  Identities=20%  Similarity=0.264  Sum_probs=41.5

Q ss_pred             CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcccc
Q 040869           48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLL  104 (131)
Q Consensus        48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L  104 (131)
                      +.++|-++||+++|+   ....+-.-+..|...|+=-+...   ...|.+......+
T Consensus        17 ~~~~SGe~La~~Lgi---SRtaVwK~Iq~Lr~~G~~I~s~~---~kGY~L~~~~~ll   67 (79)
T COG1654          17 GNFVSGEKLAEELGI---SRTAVWKHIQQLREEGVDIESVR---GKGYLLPQLPDLL   67 (79)
T ss_pred             CCcccHHHHHHHHCc---cHHHHHHHHHHHHHhCCceEecC---CCceeccCccccC
Confidence            579999999999999   99999999999999997665541   4468887765554

>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID

Probab=82.10  E-value=2.1  Score=26.95  Aligned_cols=32  Identities=16%  Similarity=0.239  Sum_probs=26.9

Q ss_pred             hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHH
Q 040869           38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLM   74 (131)
Q Consensus        38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlL   74 (131)
                      ..|.+.|.+  +.+|+.+||+..|+   ....+.|.|
T Consensus         9 ~~I~e~l~~--~~~ti~dvA~~~gv---S~~TVsr~L   40 (80)
T TIGR02844         9 LEIGKYIVE--TKATVRETAKVFGV---SKSTVHKDV   40 (80)
T ss_pred             HHHHHHHHH--CCCCHHHHHHHhCC---CHHHHHHHh
Confidence            456777875  78999999999999   889998865

Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.

>PF05491 RuvB_C: Holliday junction DNA helicase ruvB C-terminus; InterPro: IPR008823 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair

Probab=82.01  E-value=2.3  Score=26.63  Aligned_cols=58  Identities=14%  Similarity=0.175  Sum_probs=40.2

Q ss_pred             HhChHHHHHh--CCCCCCHHHHHhhcCCCCCCcchHHHHH-HHhhcCCceeecccCCCCcceecchhcc
Q 040869           37 ELGIADIIHS--HGRAITLSELVSALDIQPTKTTGLFRLM-RLLVHSSCFNKTKVNGQEEAYGLTAAST  102 (131)
Q Consensus        37 ~L~ifd~l~~--~~~~~s~~eLA~~~~~~~~~~~~l~RlL-r~L~~~gl~~~~~~~~~~~~y~~t~~s~  102 (131)
                      +.++...|.+  .++|+.++.||..+|-   ++..+.-+. -+|...|++.+++    .|+ ..|+.+.
T Consensus        10 D~~yL~~l~~~f~ggPvGl~tlA~~l~e---d~~Tie~v~EPyLiq~G~I~RT~----rGR-~~T~~a~   70 (76)
T PF05491_consen   10 DRRYLKTLIENFKGGPVGLDTLAAALGE---DKETIEDVIEPYLIQIGFIQRTP----RGR-VATPKAY   70 (76)
T ss_dssp             HHHHHHHHHHCSTTS-B-HHHHHHHTTS----HHHHHHTTHHHHHHTTSEEEET----TEE-EE-HHHH
T ss_pred             HHHHHHHHHHHcCCCCeeHHHHHHHHCC---CHhHHHHHhhHHHHHhhhHhhCc----cHH-HhHHHHH
Confidence            3445566654  3799999999999999   999887554 5799999999987    566 5555543

Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the C-terminal region of the proteins; it is thought to be a helicase DNA-binding domain.; GO: 0003677 DNA binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 3PFI_B 1IXR_C 1HQC_B 1IXS_B 1IN8_A 1IN4_A 1IN5_A 1J7K_A 1IN6_A 1IN7_A.

>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]

Probab=81.95  E-value=1.8  Score=34.19  Aligned_cols=35  Identities=20%  Similarity=0.242  Sum_probs=33.0

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      .++|-+|||+++|+   ....+.|+|......|+++-.
T Consensus        25 ~gltQ~eIA~~Lgi---SR~~v~rlL~~Ar~~GiV~I~   59 (321)
T COG2390          25 EGLTQSEIAERLGI---SRATVSRLLAKAREEGIVKIS   59 (321)
T ss_pred             cCCCHHHHHHHhCC---CHHHHHHHHHHHHHCCeEEEE
Confidence            57999999999999   999999999999999999865

>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins

Probab=81.84  E-value=1  Score=25.83  Aligned_cols=32  Identities=22%  Similarity=0.361  Sum_probs=22.7

Q ss_pred             hChHHHHHhCC-CCCCHHHHHhhcCCCCCCcchHHH
Q 040869           38 LGIADIIHSHG-RAITLSELVSALDIQPTKTTGLFR   72 (131)
Q Consensus        38 L~ifd~l~~~~-~~~s~~eLA~~~~~~~~~~~~l~R   72 (131)
                      +.+++.|...| .-+|..+||+.+|+   ++..+++
T Consensus        15 ~r~L~~l~~~G~~~vSS~~La~~~gi---~~~qVRK   47 (50)
T PF06971_consen   15 LRYLEQLKEEGVERVSSQELAEALGI---TPAQVRK   47 (50)
T ss_dssp             HHHHHHHHHTT-SEE-HHHHHHHHTS----HHHHHH
T ss_pred             HHHHHHHHHcCCeeECHHHHHHHHCC---CHHHhcc
Confidence            34556666545 56999999999999   8887765

These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....

>PHA02591 hypothetical protein; Provisional

Probab=81.83  E-value=2.7  Score=26.45  Aligned_cols=32  Identities=13%  Similarity=0.287  Sum_probs=26.1

Q ss_pred             hHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHH
Q 040869           40 IADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRL   76 (131)
Q Consensus        40 ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~   76 (131)
                      +...|.+  .++|.++||+.+|+   +...+.+.++-
T Consensus        51 vA~eL~e--qGlSqeqIA~~LGV---sqetVrKYL~~   82 (83)
T PHA02591         51 VTHELAR--KGFTVEKIASLLGV---SVRKVRRYLES   82 (83)
T ss_pred             HHHHHHH--cCCCHHHHHHHhCC---CHHHHHHHHhc
Confidence            4455653  67999999999999   99999988864

>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A

Probab=81.82  E-value=1.2  Score=25.82  Aligned_cols=31  Identities=23%  Similarity=0.443  Sum_probs=21.3

Q ss_pred             hHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHH
Q 040869           40 IADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMR   75 (131)
Q Consensus        40 ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr   75 (131)
                      |-+.+.+  ..+|..+||+.+|+   +...+.+++.
T Consensus         2 L~~~m~~--~~it~~~La~~~gi---s~~tl~~~~~   32 (63)
T PF13443_consen    2 LKELMAE--RGITQKDLARKTGI---SRSTLSRILN   32 (63)
T ss_dssp             HHHHHHH--TT--HHHHHHHHT-----HHHHHHHHT
T ss_pred             HHHHHHH--cCCCHHHHHHHHCc---CHHHHHHHHh
Confidence            3455664  56899999999999   8888888876

>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF

Probab=81.69  E-value=2.2  Score=31.45  Aligned_cols=43  Identities=9%  Similarity=0.126  Sum_probs=37.4

Q ss_pred             CCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869           51 ITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA   99 (131)
Q Consensus        51 ~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~   99 (131)
                      -|=.|||++.|+   +..++++-|..|+..|++....   |.|+|-..+
T Consensus        33 PsE~eLa~~~~V---SR~TvR~Al~~L~~eGli~r~~---G~GtfV~~~   75 (238)
T TIGR02325        33 PAEMQLAERFGV---NRHTVRRAIAALVERGLLRAEQ---GRGTFVAAR   75 (238)
T ss_pred             cCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEec---CCEEEECCC
Confidence            377899999999   9999999999999999999876   378887543

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.

>PRK13558 bacterio-opsin activator; Provisional

Probab=81.56  E-value=1.4  Score=37.40  Aligned_cols=44  Identities=18%  Similarity=0.198  Sum_probs=36.6

Q ss_pred             HHHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHh
Q 040869           27 LSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLL   77 (131)
Q Consensus        27 ~~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L   77 (131)
                      ..-.+|.+|.+.|-|+ .+   +..|.+|||+.+|+   .+..+...||..
T Consensus       611 ~q~e~l~~a~~~gyf~-~p---r~~~~~e~a~~l~i---s~~t~~~~lr~a  654 (665)
T PRK13558        611 RQLTALQKAYVSGYFE-WP---RRVEGEELAESMGI---SRSTFHQHLRAA  654 (665)
T ss_pred             HHHHHHHHHHHcCCCC-CC---ccCCHHHHHHHhCC---CHHHHHHHHHHH
Confidence            4567899999999998 43   67999999999999   888877777654

>PF09681 Phage_rep_org_N: N-terminal phage replisome organiser (Phage_rep_org_N); InterPro: IPR010056 This entry is represented by the N-terminal domain of Bacteriophage A500, Gp45

Probab=81.48  E-value=3  Score=28.33  Aligned_cols=49  Identities=6%  Similarity=-0.048  Sum_probs=43.2

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcccc
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLL  104 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L  104 (131)
                      .|.+.++||..++-   +...+..-|.++...|+++..+    +|.|..+...+..
T Consensus        52 ipy~~e~LA~~~~~---~~~~V~~AL~~f~k~glIe~~e----d~~i~i~~~~~~~  100 (121)
T PF09681_consen   52 IPYTAEMLALEFDR---PVDTVRLALAVFQKLGLIEIDE----DGVIYIPNWEKHQ  100 (121)
T ss_pred             CCCcHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEec----CCeEEeecHHHHh
Confidence            69999999999999   9999999999999999999876    7888877765544

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. The proteins in this entry contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The low-complexity region is adjacent to this N-terminal domain.

>smart00531 TFIIE Transcription initiation factor IIE

Probab=81.37  E-value=2.5  Score=29.41  Aligned_cols=40  Identities=23%  Similarity=0.295  Sum_probs=34.1

Q ss_pred             ChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCc
Q 040869           39 GIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSC   82 (131)
Q Consensus        39 ~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl   82 (131)
                      -|++.|-. .+.+|-++||..+|+   +...++++|..|..-++
T Consensus         5 ~v~d~L~~-~~~~~dedLa~~l~i---~~n~vRkiL~~L~ed~~   44 (147)
T smart00531        5 LVLDALMR-NGCVTEEDLAELLGI---KQKQLRKILYLLYDEKL   44 (147)
T ss_pred             eehHHHHh-cCCcCHHHHHHHhCC---CHHHHHHHHHHHHhhhc
Confidence            47787765 358999999999999   99999999999999443

>PF11972 HTH_13: HTH DNA binding domain; InterPro: IPR021068 The proteins in this entry have not been characterised

Probab=81.36  E-value=3.9  Score=23.87  Aligned_cols=46  Identities=15%  Similarity=0.221  Sum_probs=32.5

Q ss_pred             hHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCccee
Q 040869           40 IADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYG   96 (131)
Q Consensus        40 ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~   96 (131)
                      +.|.+-. -.-+|+.-+|+.+|+   .+....|+++-|.   + .|-.   |.++|.
T Consensus         4 Lidll~~-~P~Vsa~mva~~L~v---T~~~A~~li~eLg---~-rEiT---Gr~R~R   49 (54)
T PF11972_consen    4 LIDLLLS-RPLVSAPMVAKELGV---TPQAAQRLIAELG---L-REIT---GRGRYR   49 (54)
T ss_pred             HHHHHHh-CccccHHHHHHHhCC---CHHHHHHHHHHhh---c-eeec---CCcccc
Confidence            4566653 234899999999999   8999999886654   4 4432   256675

They contain a C-terminal helix-turn-helix DNA binding domain.

>PRK14999 histidine utilization repressor; Provisional

Probab=81.28  E-value=2.5  Score=31.46  Aligned_cols=45  Identities=16%  Similarity=0.197  Sum_probs=38.4

Q ss_pred             CCC-CHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869           49 RAI-TLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA   99 (131)
Q Consensus        49 ~~~-s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~   99 (131)
                      ..+ |=.|||++.|+   +..++++-|+.|+..|++....   |.|+|-..+
T Consensus        34 ~~LPsE~eLa~~~gV---SR~TVR~Al~~L~~eGli~r~~---GkGTfV~~~   79 (241)
T PRK14999         34 DRIPSEAELVAQYGF---SRMTINRALRELTDEGWLVRLQ---GVGTFVAEP   79 (241)
T ss_pred             CcCCCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEec---CcEEEECCC
Confidence            345 88999999999   9999999999999999999875   378887543

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

Probab=81.22  E-value=1.8  Score=24.11  Aligned_cols=26  Identities=23%  Similarity=0.425  Sum_probs=21.5

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHHHh
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMRLL   77 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L   77 (131)
                      .+.|..|||+.+|+   +...+.++.+..
T Consensus        19 ~~~t~~eIa~~lg~---s~~~V~~~~~~a   44 (50)
T PF04545_consen   19 EGLTLEEIAERLGI---SRSTVRRILKRA   44 (50)
T ss_dssp             ST-SHHHHHHHHTS---CHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCC---cHHHHHHHHHHH
Confidence            67999999999999   889888887643

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

>PRK11511 DNA-binding transcriptional activator MarA; Provisional

Probab=81.19  E-value=3  Score=28.10  Aligned_cols=33  Identities=12%  Similarity=0.060  Sum_probs=27.7

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCcee
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFN   84 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~   84 (131)
                      .++|+++||+.+|+   ++..+.|+.+.-+...+-+
T Consensus        24 ~~~sl~~lA~~~g~---S~~~l~r~Fk~~~G~s~~~   56 (127)
T PRK11511         24 SPLSLEKVSERSGY---SKWHLQRMFKKETGHSLGQ   56 (127)
T ss_pred             CCCCHHHHHHHHCc---CHHHHHHHHHHHHCcCHHH
Confidence            68999999999999   9999999998776655443

>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial

Probab=80.93  E-value=2.5  Score=31.12  Aligned_cols=45  Identities=16%  Similarity=0.206  Sum_probs=38.3

Q ss_pred             CCC-CHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869           49 RAI-TLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA   99 (131)
Q Consensus        49 ~~~-s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~   99 (131)
                      ..+ |=.|||++.|+   +..++++-|..|+..|++....   |.|+|-..+
T Consensus        23 ~~LPsE~eLa~~~~V---SR~TVR~Al~~L~~eGli~r~~---G~GtfV~~~   68 (230)
T TIGR02018        23 HRIPSEHELVAQYGC---SRMTVNRALRELTDAGLLERRQ---GVGTFVAEP   68 (230)
T ss_pred             CcCcCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEec---CCEEEEccC
Confidence            345 88899999999   9999999999999999999876   368887543

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.

>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional

Probab=80.88  E-value=3.4  Score=26.68  Aligned_cols=34  Identities=12%  Similarity=0.170  Sum_probs=28.1

Q ss_pred             CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCcee
Q 040869           48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFN   84 (131)
Q Consensus        48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~   84 (131)
                      ..++++++||+.+|+   ++..+.|+.+......+-+
T Consensus        19 ~~~~~~~~lA~~~~~---S~~~l~r~f~~~~g~s~~~   52 (107)
T PRK10219         19 DQPLNIDVVAKKSGY---SKWYLQRMFRTVTHQTLGD   52 (107)
T ss_pred             CCCCCHHHHHHHHCC---CHHHHHHHHHHHHCcCHHH
Confidence            368999999999999   9999999998876555443

>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=80.87  E-value=1.5  Score=26.72  Aligned_cols=36  Identities=19%  Similarity=0.240  Sum_probs=27.4

Q ss_pred             CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      |..-|..|||+.+|+   ++..+..+|........+...
T Consensus        18 gr~Pt~eEiA~~lgi---s~~~v~~~l~~~~~~~Sl~~~   53 (78)
T PF04539_consen   18 GREPTDEEIAEELGI---SVEEVRELLQASRRPVSLDLP   53 (78)
T ss_dssp             SS--BHHHHHHHHTS----HHHHHHHHHHHSCCEESSHC
T ss_pred             CCCCCHHHHHHHHcc---cHHHHHHHHHhCCCCeEEeee
Confidence            578999999999999   999999999987665555543

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....

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

Probab=80.70  E-value=1.9  Score=23.13  Aligned_cols=23  Identities=22%  Similarity=0.287  Sum_probs=19.8

Q ss_pred             CCHHHHHhhcCCCCCCcchHHHHHHH
Q 040869           51 ITLSELVSALDIQPTKTTGLFRLMRL   76 (131)
Q Consensus        51 ~s~~eLA~~~~~~~~~~~~l~RlLr~   76 (131)
                      +|..|+|+.+|+   ++..+++..+.
T Consensus         1 ~s~~e~a~~lgv---s~~tl~~~~~~   23 (49)
T cd04762           1 LTTKEAAELLGV---SPSTLRRWVKE   23 (49)
T ss_pred             CCHHHHHHHHCc---CHHHHHHHHHc
Confidence            478999999999   88988888774

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.

>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional

Probab=80.61  E-value=3.1  Score=30.98  Aligned_cols=45  Identities=13%  Similarity=0.193  Sum_probs=37.6

Q ss_pred             CCCC-CHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecc
Q 040869           48 GRAI-TLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLT   98 (131)
Q Consensus        48 ~~~~-s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t   98 (131)
                      |..+ +-.+||+.+|+   +...++--|+.|...|++...+.   .|.|-..
T Consensus        28 G~~LPsE~eLa~~~gV---SRtpVREAL~~L~~eGlV~~~~~---~G~~V~~   73 (251)
T PRK09990         28 GQALPSERRLCEKLGF---SRSALREGLTVLRGRGIIETAQG---RGSFVAR   73 (251)
T ss_pred             CCcCcCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEeCC---CeeEEec
Confidence            5678 88999999999   99999999999999999997751   4555443

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

Probab=80.58  E-value=2.9  Score=27.45  Aligned_cols=35  Identities=9%  Similarity=0.170  Sum_probs=32.7

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      .-+|.+++++.+|+   ++..+.+.+..|...|++...
T Consensus        53 d~Is~sq~~e~tg~---~~~~V~~al~~Li~~~vI~~~   87 (100)
T PF04492_consen   53 DRISNSQIAEMTGL---SRDHVSKALNELIRRGVIIRD   87 (100)
T ss_pred             ceeeHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEeC
Confidence            46999999999999   999999999999999999766

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

>PF13551 HTH_29: Winged helix-turn helix

Probab=80.42  E-value=2.6  Score=27.03  Aligned_cols=27  Identities=19%  Similarity=0.399  Sum_probs=26.0

Q ss_pred             CHHHHHhhcCCCCCCcchHHHHHHHhhcCC
Q 040869           52 TLSELVSALDIQPTKTTGLFRLMRLLVHSS   81 (131)
Q Consensus        52 s~~eLA~~~~~~~~~~~~l~RlLr~L~~~g   81 (131)
                      |..++|+.+|+   ++..++|.++....-|
T Consensus        14 ~~~~ia~~lg~---s~~Tv~r~~~~~~~~G   40 (112)
T PF13551_consen   14 TIAEIARRLGI---SRRTVYRWLKRYREGG   40 (112)
T ss_pred             cHHHHHHHHCc---CHHHHHHHHHHHHccc
Confidence            79999999999   9999999999999988

>PRK09464 pdhR transcriptional regulator PdhR; Reviewed

Probab=80.37  E-value=3.1  Score=31.10  Aligned_cols=46  Identities=13%  Similarity=0.221  Sum_probs=38.4

Q ss_pred             CCCC-CHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869           48 GRAI-TLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA   99 (131)
Q Consensus        48 ~~~~-s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~   99 (131)
                      |..+ |-.+||+.+|+   +...++--|+.|.+.|+++..+   +.|.|-...
T Consensus        31 G~~LpsE~eLa~~lgV---SRtpVREAL~~L~~eGlv~~~~---~~G~~V~~~   77 (254)
T PRK09464         31 GEKLPPERELAKQFDV---SRPSLREAIQRLEAKGLLLRRQ---GGGTFVQSS   77 (254)
T ss_pred             CCcCCCHHHHHHHhCC---CHHHHHHHHHHHHHCCCEEEec---CceeEEecC
Confidence            4567 89999999999   9999999999999999999765   256666543

>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional

Probab=80.19  E-value=3.2  Score=31.06  Aligned_cols=45  Identities=18%  Similarity=0.230  Sum_probs=37.4

Q ss_pred             CCCC-CHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecc
Q 040869           48 GRAI-TLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLT   98 (131)
Q Consensus        48 ~~~~-s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t   98 (131)
                      |..+ |-.+||+++|+   +...++.-|+.|.+.|++...+   +.|.|-..
T Consensus        30 G~~LpsE~eLa~~~gV---SRtpVREAL~~L~~eGlV~~~~---~~G~~V~~   75 (257)
T PRK10225         30 GERLPPEREIAEMLDV---TRTVVREALIMLEIKGLVEVRR---GAGIYVLD   75 (257)
T ss_pred             CCcCcCHHHHHHHhCC---CHHHHHHHHHHHHHCCCEEEec---CCEEEEeC
Confidence            5678 68999999999   9999999999999999998765   14555544

>PRK04984 fatty acid metabolism regulator; Provisional

Probab=80.14  E-value=3.2  Score=30.65  Aligned_cols=45  Identities=13%  Similarity=0.165  Sum_probs=37.9

Q ss_pred             CCCC-CHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecc
Q 040869           48 GRAI-TLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLT   98 (131)
Q Consensus        48 ~~~~-s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t   98 (131)
                      |..+ |-.+||+++|+   +...++.-|+.|...|++...+   |.|.|-.+
T Consensus        28 G~~LPsE~eLae~~gV---SRt~VReAL~~L~~eGlv~~~~---g~G~~V~~   73 (239)
T PRK04984         28 GSILPAERELSELIGV---TRTTLREVLQRLARDGWLTIQH---GKPTKVNN   73 (239)
T ss_pred             CCcCCCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEeC---CCeeEeCC
Confidence            4567 78999999999   9999999999999999999765   25666543

>PRK09764 DNA-binding transcriptional repressor MngR; Provisional

Probab=80.01  E-value=2.7  Score=31.23  Aligned_cols=45  Identities=20%  Similarity=0.287  Sum_probs=38.1

Q ss_pred             CCCC-CHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecc
Q 040869           48 GRAI-TLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLT   98 (131)
Q Consensus        48 ~~~~-s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t   98 (131)
                      |..+ |=.|||+..|+   +..++++-|..|+..|++....   |.|+|-..
T Consensus        26 G~~LPsE~eL~~~~~V---SR~TvR~Al~~L~~eGli~r~~---G~GtfV~~   71 (240)
T PRK09764         26 GDALPTESALQTEFGV---SRVTVRQALRQLVEQQILESIQ---GSGTYVKE   71 (240)
T ss_pred             CCcCCCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEec---CceeEEcc
Confidence            3455 77999999999   9999999999999999999875   36778643

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	131
2qyo_A	357	Crystal Structure Of Isoflavone O-Methyltransferase		4e-25
1zg3_A	358	Crystal Structure Of The Isoflavanone 4'-O-Methyltr		2e-22
1zga_A	357	Crystal Structure Of Isoflavanone 4'-o-methyltransf		2e-22
1zgj_A	354	Crystal Structure Of Isoflavanone 4'-O-Methyltransf		2e-22
1fp2_A	352	Crystal Structure Analysis Of Isoflavone O-Methyltr		2e-21
1fpx_A	352	Crystal Structure Analysis Of Selenomethionine Subs		1e-19

>pdb|2QYO|A Chain A, Crystal Structure Of Isoflavone O-Methyltransferase Homolog In Complex With Biochanin A And Sah Length = 357

Iteration: 1
 Score =  109 bits (272), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 56/130 (43%), Positives = 78/130 (60%), Gaps = 3/130 (2%)
Query: 5   QDQGAKELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQP 64
            ++   E+ + QA LYK M++ + SMSLK +IE+ I +IIH+HG+ ITLS LVS L I  
Sbjct: 6   NNRKPSEIFKAQALLYKNMYAFVDSMSLKWSIEMNIPNIIHNHGKPITLSNLVSILQIPS 65
Query: 65  TKTTGLFRLMRLLVHSSCFN---KTKVNGQEEAYGLTAASTLLIKDKPYCMSPTVSAFVD 121
           TK   + RLMR L H+  F      ++  +EEAY LT AS LL+K    C++P V   +D
Sbjct: 66  TKVDNVQRLMRYLAHNGFFEIITNQELENEEEAYALTVASELLVKGTELCLAPMVECVLD 125
Query: 122 PLFVAPFQSL 131
           P     F +L
Sbjct: 126 PTLSTSFHNL 135

>pdb|1ZG3|A Chain A, Crystal Structure Of The Isoflavanone 4'-O-Methyltransferase Complexed With Sah And 2,7,4'-Trihydroxyisoflavanone Length = 358

Iteration: 1
 Score =  100 bits (250), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 57/118 (48%), Positives = 74/118 (62%), Gaps = 6/118 (5%)
Query: 11  ELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGL 70
           EL   Q  LYK +++ +SSM+LK A+ELGIAD IH+HG+ +TLSEL S+L + P+K   L
Sbjct: 6   ELYHAQIHLYKHVYNFVSSMALKSAMELGIADAIHNHGKPMTLSELASSLKLHPSKVNIL 65
Query: 71  FRLMRLLVHSSCFNKTKVNGQEE------AYGLTAASTLLIKDKPYCMSPTVSAFVDP 122
            R +RLL H+  F KT V G+E       AY LT  S LLI  KP C+S  V   + P
Sbjct: 66  HRFLRLLTHNGFFAKTIVKGKEGDEEEEIAYSLTPPSKLLISGKPTCLSSIVKGALHP 123

>pdb|1ZGA|A Chain A, Crystal Structure Of Isoflavanone 4'-o-methyltransferase Complexed With (+)-6a-hydroxymaackiain Length = 357

Iteration: 1
 Score =  100 bits (250), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 57/118 (48%), Positives = 74/118 (62%), Gaps = 6/118 (5%)
Query: 11  ELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGL 70
           EL   Q  LYK +++ +SSM+LK A+ELGIAD IH+HG+ +TLSEL S+L + P+K   L
Sbjct: 5   ELYHAQIHLYKHVYNFVSSMALKSAMELGIADAIHNHGKPMTLSELASSLKLHPSKVNIL 64
Query: 71  FRLMRLLVHSSCFNKTKVNGQEE------AYGLTAASTLLIKDKPYCMSPTVSAFVDP 122
            R +RLL H+  F KT V G+E       AY LT  S LLI  KP C+S  V   + P
Sbjct: 65  HRFLRLLTHNGFFAKTIVKGKEGDEEEEIAYSLTPPSKLLISGKPTCLSSIVKGALHP 122

>pdb|1ZGJ|A Chain A, Crystal Structure Of Isoflavanone 4'-O-Methyltransferase Complexed With (+)-Pisatin Length = 354

Iteration: 1
 Score =  100 bits (250), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 57/118 (48%), Positives = 74/118 (62%), Gaps = 6/118 (5%)
Query: 11  ELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGL 70
           EL   Q  LYK +++ +SSM+LK A+ELGIAD IH+HG+ +TLSEL S+L + P+K   L
Sbjct: 2   ELYHAQIHLYKHVYNFVSSMALKSAMELGIADAIHNHGKPMTLSELASSLKLHPSKVNIL 61
Query: 71  FRLMRLLVHSSCFNKTKVNGQEE------AYGLTAASTLLIKDKPYCMSPTVSAFVDP 122
            R +RLL H+  F KT V G+E       AY LT  S LLI  KP C+S  V   + P
Sbjct: 62  HRFLRLLTHNGFFAKTIVKGKEGDEEEEIAYSLTPPSKLLISGKPTCLSSIVKGALHP 119

>pdb|1FP2|A Chain A, Crystal Structure Analysis Of Isoflavone O-Methyltransferase Length = 352

Iteration: 1
 Score = 97.4 bits (241), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 48/121 (39%), Positives = 73/121 (60%), Gaps = 2/121 (1%)
Query: 11  ELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGL 70
           E+ + QA LYK +++ + SMSLK A+E+ I +II +HG+ I+LS LVS L +  +K   +
Sbjct: 12  EIFKAQALLYKHIYAFIDSMSLKWAVEMNIPNIIQNHGKPISLSNLVSILQVPSSKIGNV 71
Query: 71  FRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIKDKPYCMSPTVSAFVDPLFVAPFQS 130
            RLMR L H+  F    +  +EE+Y LT AS LL++    C++P V   +DP     +  
Sbjct: 72  RRLMRYLAHNGFFE--IITKEEESYALTVASELLVRGSDLCLAPMVECVLDPTLSGSYHE 129
Query: 131 L 131
           L
Sbjct: 130 L 130

>pdb|1FPX|A Chain A, Crystal Structure Analysis Of Selenomethionine Substituted Isoflavone O-Methyltransferase Length = 352

Iteration: 1
 Score = 91.7 bits (226), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 46/121 (38%), Positives = 70/121 (57%), Gaps = 2/121 (1%)
Query: 11  ELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGL 70
           E+ + QA LYK +++ + S SLK A+E  I +II +HG+ I+LS LVS L +  +K   +
Sbjct: 12  EIFKAQALLYKHIYAFIDSXSLKWAVEXNIPNIIQNHGKPISLSNLVSILQVPSSKIGNV 71
Query: 71  FRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIKDKPYCMSPTVSAFVDPLFVAPFQS 130
            RL R L H+  F    +  +EE+Y LT AS LL++    C++P V   +DP     +  
Sbjct: 72  RRLXRYLAHNGFFE--IITKEEESYALTVASELLVRGSDLCLAPXVECVLDPTLSGSYHE 129
Query: 131 L 131
           L
Sbjct: 130 L 130

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	131
1zg3_A	358	Isoflavanone 4'-O-methyltransferase; rossman fold,	1e-41
1fp2_A	352	Isoflavone O-methyltransferase; protein-product co	1e-39
3lst_A	348	CALO1 methyltransferase; calicheamicin, enediyne,	7e-34
3gwz_A	369	MMCR; methyltransferase, mitomycin, S-adenosyl met	5e-33
3reo_A	368	(ISO)eugenol O-methyltransferase; directed evoluti	6e-32
1fp1_D	372	Isoliquiritigenin 2'-O-methyltransferase; protein-	6e-31
3p9c_A	364	Caffeic acid O-methyltransferase; S-adenosylmethio	9e-30
1qzz_A	374	RDMB, aclacinomycin-10-hydroxylase; anthracycline,	5e-28
2ip2_A	334	Probable phenazine-specific methyltransferase; pyo	8e-28
3i53_A	332	O-methyltransferase; CO-complex, rossmann-like fol	4e-27
1tw3_A	360	COMT, carminomycin 4-O-methyltransferase; anthracy	3e-25
3dp7_A	363	SAM-dependent methyltransferase; structural genomi	9e-25
1x19_A	359	CRTF-related protein; methyltransferase, bacterioc	2e-24
2r3s_A	335	Uncharacterized protein; methyltransferase domain,	2e-22
3mcz_A	352	O-methyltransferase; adomet_mtases, S-adenosylmeth	4e-19

>1zg3_A Isoflavanone 4'-O-methyltransferase; rossman fold, plant Pro transferase; HET: 2HI SAH; 2.35A {Medicago truncatula} PDB: 1zga_A* 1zhf_A* 1zgj_A* Length = 358

 Score =  139 bits (353), Expect = 1e-41
 Identities = 58/127 (45%), Positives = 77/127 (60%), Gaps = 6/127 (4%)

Query: 11  ELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGL 70
           EL   Q  LYK +++ +SSM+LK A+ELGIAD IH+HG+ +TLSEL S+L + P+K   L
Sbjct: 6   ELYHAQIHLYKHVYNFVSSMALKSAMELGIADAIHNHGKPMTLSELASSLKLHPSKVNIL 65

Query: 71  FRLMRLLVHSSCFNKTKVNGQ------EEAYGLTAASTLLIKDKPYCMSPTVSAFVDPLF 124
            R +RLL H+  F KT V G+      E AY LT  S LLI  KP C+S  V   + P  
Sbjct: 66  HRFLRLLTHNGFFAKTIVKGKEGDEEEEIAYSLTPPSKLLISGKPTCLSSIVKGALHPSS 125

Query: 125 VAPFQSL 131
           +  + S 
Sbjct: 126 LDMWSSS 132

>1fp2_A Isoflavone O-methyltransferase; protein-product complex; HET: SAH HMO; 1.40A {Medicago sativa} SCOP: a.4.5.29 c.66.1.12 PDB: 1fpx_A* 2qyo_A* Length = 352

 Score =  134 bits (339), Expect = 1e-39
 Identities = 49/132 (37%), Positives = 78/132 (59%), Gaps = 3/132 (2%)

Query: 1   MDANQD-QGAKELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSA 59
           M ++ + +   E+ + QA LYK +++ + SMSLK A+E+ I +II +HG+ I+LS LVS 
Sbjct: 1   MASSINGRKPSEIFKAQALLYKHIYAFIDSMSLKWAVEMNIPNIIQNHGKPISLSNLVSI 60

Query: 60  LDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIKDKPYCMSPTVSAF 119
           L +  +K   + RLMR L H+  F    +  +EE+Y LT AS LL++    C++P V   
Sbjct: 61  LQVPSSKIGNVRRLMRYLAHNGFF--EIITKEEESYALTVASELLVRGSDLCLAPMVECV 118

Query: 120 VDPLFVAPFQSL 131
           +DP     +  L
Sbjct: 119 LDPTLSGSYHEL 130

>3lst_A CALO1 methyltransferase; calicheamicin, enediyne, SAH, STRU genomics, PSI-2, protein structure initiative; HET: SAH; 2.40A {Micromonospora echinospora} Length = 348

 Score =  119 bits (301), Expect = 7e-34
 Identities = 27/124 (21%), Positives = 47/124 (37%), Gaps = 10/124 (8%)

Query: 8   GAKELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKT 67
           G  + LQ    LY+    +  + +L+ A  +G+AD +       T +EL +A        
Sbjct: 15  GDMDRLQSALALYEEAMGYTYAAALRAAAAVGVADHL--VDGPRTPAELAAATGTDADA- 71

Query: 68  TGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIKDKPYCMSPTVSAFVDPLFVAP 127
             L R++RLL       ++     +  + LT     L  D P      +  F D +F   
Sbjct: 72  --LRRVLRLLAVRDVVRES-----DGRFALTDKGAALRSDSPVPARAGILMFTDTMFWTM 124

Query: 128 FQSL 131
              +
Sbjct: 125 SHRV 128

>3gwz_A MMCR; methyltransferase, mitomycin, S-adenosyl methionine, transferase; HET: MSE SAH; 1.91A {Streptomyces lavendulae} PDB: 3gxo_A* Length = 369

 Score =  117 bits (296), Expect = 5e-33
 Identities = 22/127 (17%), Positives = 48/127 (37%), Gaps = 8/127 (6%)

Query: 5   QDQGAKELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQP 64
           ++ G       +  +  ++     + ++  A+ELG+ +++       T + L  A     
Sbjct: 28  ENPGTAARAAAEETVNDILQGAWKARAIHVAVELGVPELLQEG--PRTATALAEATGAHE 85

Query: 65  TKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIKDKPYCMSPTVSAFVDPLF 124
                L RL+RLL     F+     G ++ +   A S +L+ D    ++        P  
Sbjct: 86  QT---LRRLLRLLATVGVFDDL---GHDDLFAQNALSAVLLPDPASPVATDARFQAAPWH 139

Query: 125 VAPFQSL 131
              ++ L
Sbjct: 140 WRAWEQL 146

>3reo_A (ISO)eugenol O-methyltransferase; directed evolution, saturation mutagenesis, regioselectivity transferase; HET: SAH EUG; 1.90A {Clarkia breweri} PDB: 1kyz_A* 1kyw_A* Length = 368

 Score =  114 bits (288), Expect = 6e-32
 Identities = 30/130 (23%), Positives = 52/130 (40%), Gaps = 9/130 (6%)

Query: 11  ELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGR---AITLSELVSALDIQ-PTK 66
              +      +L  + +  M+LK AIEL + +I+         I+ +E+ + L    P  
Sbjct: 17  SDEEANLFAMQLASAAVLPMALKAAIELDVLEIMAKSVPPSGYISPAEIAAQLPTTNPEA 76

Query: 67  TTGLFRLMRLLVHSSCFNKTKV----NGQEEAYGLTAASTLLIKDKP-YCMSPTVSAFVD 121
              L R++RLL   S    T         E  YGL      L K++    ++P +    D
Sbjct: 77  PVMLDRVLRLLASYSVVTYTLRELPSGKVERLYGLAPVCKFLTKNEDGVSLAPFLLLATD 136

Query: 122 PLFVAPFQSL 131
            + + P+  L
Sbjct: 137 KVLLEPWFYL 146

>1fp1_D Isoliquiritigenin 2'-O-methyltransferase; protein-substrate, protein-product complex; HET: SAH HCC; 1.82A {Medicago sativa} SCOP: a.4.5.29 c.66.1.12 PDB: 1fpq_A* Length = 372

 Score =  112 bits (281), Expect = 6e-31
 Identities = 26/133 (19%), Positives = 47/133 (35%), Gaps = 11/133 (8%)

Query: 10  KELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGR---AITLSELVSALDIQPTK 66
           +           L  + +    L  AI+L + +II         ++ SE+ S L      
Sbjct: 19  QTEDSACLSAMVLTTNLVYPAVLNAAIDLNLFEIIAKATPPGAFMSPSEIASKLPASTQH 78

Query: 67  T---TGLFRLMRLLVHSSCFNKTKVN----GQEEAYGLTAASTLLIKDKP-YCMSPTVSA 118
           +     L R++RLL   S    T       G E  YGL+     L+ D+    ++   + 
Sbjct: 79  SDLPNRLDRMLRLLASYSVLTSTTRTIEDGGAERVYGLSMVGKYLVPDESRGYLASFTTF 138

Query: 119 FVDPLFVAPFQSL 131
              P  +  + + 
Sbjct: 139 LCYPALLQVWMNF 151

>3p9c_A Caffeic acid O-methyltransferase; S-adenosylmethionine dependent O-methyltransferase; HET: SAH; 1.80A {Lolium perenne} PDB: 3p9i_A* 3p9k_A* Length = 364

 Score =  109 bits (273), Expect = 9e-30
 Identities = 29/136 (21%), Positives = 54/136 (39%), Gaps = 8/136 (5%)

Query: 4   NQDQGAKELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIH-SHGRAITLSELVSAL-- 60
             D  A           +L  S +  M+LK AIELG+ +I+  + G+++T +E+ + L  
Sbjct: 9   AADMAASADEDACMFALQLASSSVLPMTLKNAIELGLLEILVAAGGKSLTPTEVAAKLPS 68

Query: 61  DIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQ----EEAYGLTAASTLLIKDKP-YCMSPT 115
              P     + R++RLL   +        G+      +YG       L  ++    M+  
Sbjct: 69  AANPEAPDMVDRILRLLASYNVVTCLVEEGKDGRLSRSYGAAPVCKFLTPNEDGVSMAAL 128

Query: 116 VSAFVDPLFVAPFQSL 131
                D + +  +  L
Sbjct: 129 ALMNQDKVLMESWYYL 144

>1qzz_A RDMB, aclacinomycin-10-hydroxylase; anthracycline, methyltransferase, polyketide, tailoring enzymes, structural proteomics in E spine; HET: SAM; 2.10A {Streptomyces purpurascens} SCOP: a.4.5.29 c.66.1.12 PDB: 1r00_A* 1xds_A* 1xdu_A* Length = 374

 Score =  104 bits (261), Expect = 5e-28
 Identities = 26/126 (20%), Positives = 39/126 (30%), Gaps = 8/126 (6%)

Query: 7   QGAKELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTK 66
           +  +   Q    L K + + ++ M+L+ A  L + D +     A TL+ L    D  P  
Sbjct: 8   EPLEPTDQDLDVLLKNLGNLVTPMALRVAATLRLVDHL--LAGADTLAGLADRTDTHPQA 65

Query: 67  TTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIKDKPYCMSPTVSAFVDPLF-V 125
              L RL+R L             Q      T    LL    P      +          
Sbjct: 66  ---LSRLVRHLTVVGVL--EGGEKQGRPLRPTRLGMLLADGHPAQQRAWLDLNGAVSHAD 120

Query: 126 APFQSL 131
             F  L
Sbjct: 121 LAFTGL 126

>2ip2_A Probable phenazine-specific methyltransferase; pyocyanin, phenazine-1-carboxy PHZM; 1.80A {Pseudomonas aeruginosa} Length = 334

 Score =  103 bits (259), Expect = 8e-28
 Identities = 30/121 (24%), Positives = 43/121 (35%), Gaps = 11/121 (9%)

Query: 11  ELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGL 70
             L     L +++     S  +  A  LG+AD+I S     +   L +A+         +
Sbjct: 4   SNLAAARNLIQVVTGEWKSRCVYVATRLGLADLIESG--IDSDETLAAAVGSDA---ERI 58

Query: 71  FRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIKDKPYCMSPTVSAFVDPLFVAPFQS 130
            RLMRLLV    F         + Y  T  S LL +D        V  F    F A +  
Sbjct: 59  HRLMRLLVAFEIFQGD----TRDGYANTPTSHLL-RDVEGSFRDMVL-FYGEEFHAAWTP 112

Query: 131 L 131
            
Sbjct: 113 A 113

>3i53_A O-methyltransferase; CO-complex, rossmann-like fold; HET: SAH; 2.08A {Streptomyces carzinostaticus subsp} PDB: 3i58_A* 3i5u_A* 3i64_A* Length = 332

 Score =  101 bits (254), Expect = 4e-27
 Identities = 23/115 (20%), Positives = 38/115 (33%), Gaps = 9/115 (7%)

Query: 14  QGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRL 73
           +      + +    + M+++ A  L +AD I +     T +E+ SA          L RL
Sbjct: 4   RAAHIGLRALADLATPMAVRVAATLRVADHIAAG--HRTAAEIASAAGAHADS---LDRL 58

Query: 74  MRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIKDKPYCMSPTVSAFVDPLFVAPF 128
           +R LV    F +      +  YGLT     L  D        +            
Sbjct: 59  LRHLVAVGLFTRD----GQGVYGLTEFGEQLRDDHAAGKRKWLDMNSAVGRGDLG 109

>1tw3_A COMT, carminomycin 4-O-methyltransferase; anthracycline, methylate, tailoring enzyme, polyketide, S-adenosyl-L-homocystein; HET: SAH ERT; 2.35A {Streptomyces peucetius} SCOP: a.4.5.29 c.66.1.12 PDB: 1tw2_A* Length = 360

 Score = 96.6 bits (241), Expect = 3e-25
 Identities = 26/132 (19%), Positives = 39/132 (29%), Gaps = 10/132 (7%)

Query: 1   MDANQDQGAKELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSAL 60
             A     A+       +    + S  + M ++ A  L + D I     A T+  L +  
Sbjct: 5   STAEPTVAARPQQIDALRTLIRLGSLHTPMVVRTAATLRLVDHI--LAGARTVKALAART 62

Query: 61  DIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIKDKPYCMSPTVSAF- 119
           D +P     L RL+R LV      +         +  T    LL  D P           
Sbjct: 63  DTRP---EALLRLIRHLVAIGLLEED----APGEFVPTEVGELLADDHPAAQRAWHDLTQ 115

Query: 120 VDPLFVAPFQSL 131
                   F  L
Sbjct: 116 AVARADISFTRL 127

>3dp7_A SAM-dependent methyltransferase; structural genomics, protein structure initiative, NEW YORK structural genomix research; 2.33A {Bacteroides vulgatus} Length = 363

 Score = 95.5 bits (238), Expect = 9e-25
 Identities = 19/131 (14%), Positives = 38/131 (29%), Gaps = 11/131 (8%)

Query: 1   MDANQDQGAKELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSAL 60
           M     +      + Q    ++ F  +     +  ++ GI  ++       TL E+    
Sbjct: 1   MSLRYTKEQCTAAEAQRLAQEIAFGPVVFQVSRLMLKFGIFQLLSGKREGYTLQEISGRT 60

Query: 61  DIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIKDKPYCMSPTVSAFV 120
            +          L+   +            +E+ Y L  A   L+ DK   M+     F 
Sbjct: 61  GLTR---YAAQVLLEASLTIGTILL-----EEDRYVLAKAGWFLLNDK---MARVNMEFN 109

Query: 121 DPLFVAPFQSL 131
             +       L
Sbjct: 110 HDVNYQGLFHL 120

>1x19_A CRTF-related protein; methyltransferase, bacteriochllochlorophyll, BCHU, SAM, SAH, adenosylmethyonine, S-adenosylhomocysteine, ADO-Met; 2.27A {Chlorobium tepidum} PDB: 1x1a_A* 1x1b_A* 1x1c_A* 1x1d_A* Length = 359

 Score = 95.2 bits (237), Expect = 2e-24
 Identities = 19/124 (15%), Positives = 39/124 (31%), Gaps = 11/124 (8%)

Query: 2   DANQDQGAKELLQGQAQLYKLMFS-HLSSMSLKCAIELGIADIIHSHGRAITLSELVSAL 60
             +      +LL    +  +L+F   +    +K AIEL +   +        L+ L +  
Sbjct: 17  RGSHMMSNNDLLNYYHRANELVFKGLIEFSCMKAAIELDLFSHM--AEGPKDLATLAADT 74

Query: 61  DIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIKDKPYCMSPTVSAFV 120
              P     L  L+  L      N      ++  + LT  +  +    P   +   +   
Sbjct: 75  GSVP---PRLEMLLETLRQMRVINL-----EDGKWSLTEFADYMFSPTPKEPNLHQTPVA 126

Query: 121 DPLF 124
             + 
Sbjct: 127 KAMA 130

>2r3s_A Uncharacterized protein; methyltransferase domain, structural genomics, joint center structural genomics, JCSG, protein structure initiative; HET: MSE; 2.15A {Nostoc punctiforme} Length = 335

 Score = 89.0 bits (221), Expect = 2e-22
 Identities = 22/117 (18%), Positives = 41/117 (35%), Gaps = 11/117 (9%)

Query: 16  QAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMR 75
            A  +  + ++  S ++K A+EL +   I       +   L            G+  L  
Sbjct: 7   PALFFNTVNAYQRSAAIKAAVELNVFTAI--SQGIESSQSLAQKCQTSE---RGMRMLCD 61

Query: 76  LLVHSSCFNKTKVNGQEEAYGLTA-ASTLLIKDKPYCMSPTVSAFVDPLFVAPFQSL 131
            LV      K     Q E Y LT+ ++  L +   + +   +   + P+    F  L
Sbjct: 62  YLVIIGFMTK-----QAEGYRLTSDSAMFLDRQSKFYVGDAIEFLLSPMITNGFNDL 113

>3mcz_A O-methyltransferase; adomet_mtases, S-adenosylmethionine-dependent methyltransfer structural genomics, PSI-2; HET: MSE; 1.90A {Burkholderia thailandensis} Length = 352

 Score = 80.1 bits (198), Expect = 4e-19
 Identities = 22/123 (17%), Positives = 37/123 (30%), Gaps = 14/123 (11%)

Query: 10  KELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTG 69
           K  L     L KL   +  S  L  A+   + D+        T +E+ ++  +       
Sbjct: 19  KAALTSVVDLVKLSDQYRQSAILHYAVADKLFDLTQ---TGRTPAEVAASFGMVE---GK 72

Query: 70  LFRLMRLLVHSSCFNKTKVNGQEEAYGLTA-ASTLLIKDKPYCMSPTVSAFVDPLFVAPF 128
              L+  L       K     + +A+  TA     L       + P V      L    +
Sbjct: 73  AAILLHALAALGLLTK-----EGDAFRNTALTERYLTTTSADYIGPIVEH--QYLQWDNW 125

Query: 129 QSL 131
             L
Sbjct: 126 PRL 128

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	131
3p9c_A	364	Caffeic acid O-methyltransferase; S-adenosylmethio	99.84
1fp2_A	352	Isoflavone O-methyltransferase; protein-product co	99.84
1zg3_A	358	Isoflavanone 4'-O-methyltransferase; rossman fold,	99.82
3lst_A	348	CALO1 methyltransferase; calicheamicin, enediyne,	99.82
4a6d_A	353	Hydroxyindole O-methyltransferase; melatonin, circ	99.81
2ip2_A	334	Probable phenazine-specific methyltransferase; pyo	99.8
1fp1_D	372	Isoliquiritigenin 2'-O-methyltransferase; protein-	99.8
3gwz_A	369	MMCR; methyltransferase, mitomycin, S-adenosyl met	99.79
3reo_A	368	(ISO)eugenol O-methyltransferase; directed evoluti	99.79
3i53_A	332	O-methyltransferase; CO-complex, rossmann-like fol	99.78
3dp7_A	363	SAM-dependent methyltransferase; structural genomi	99.77
2r3s_A	335	Uncharacterized protein; methyltransferase domain,	99.76
1x19_A	359	CRTF-related protein; methyltransferase, bacterioc	99.75
1qzz_A	374	RDMB, aclacinomycin-10-hydroxylase; anthracycline,	99.74
3mcz_A	352	O-methyltransferase; adomet_mtases, S-adenosylmeth	99.73
1tw3_A	360	COMT, carminomycin 4-O-methyltransferase; anthracy	99.73
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	98.24
3mq0_A	275	Transcriptional repressor of the blcabc operon; he	98.22
1y0u_A	96	Arsenical resistance operon repressor, putative; s	97.97
1mkm_A	249	ICLR transcriptional regulator; structural genomic	97.96
3r4k_A	260	Transcriptional regulator, ICLR family; DNA/RNA-bi	97.95
2xrn_A	241	HTH-type transcriptional regulator TTGV; DNA-bindi	97.95
2fu4_A	83	Ferric uptake regulation protein; DNA binding doma	97.9
3b73_A	111	PHIH1 repressor-like protein; winged-helix-turn-he	97.81
2o0y_A	260	Transcriptional regulator; ICLR-family, structural	97.79
2g7u_A	257	Transcriptional regulator; ICLR family, structural	97.75
2ia2_A	265	Putative transcriptional regulator; SAD, PSI-2, st	97.72
1u2w_A	122	CADC repressor, cadmium efflux system accessory pr	97.63
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	97.62
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	97.62
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	97.59
3jth_A	98	Transcription activator HLYU; transcription factor	97.53
3f6o_A	118	Probable transcriptional regulator, ARSR family pr	97.5
2o03_A	131	Probable zinc uptake regulation protein FURB; DNA-	97.5
2y75_A	129	HTH-type transcriptional regulator CYMR; DNA bindi	97.49
2fe3_A	145	Peroxide operon regulator; oxidative stress regula	97.47
2kko_A	108	Possible transcriptional regulatory protein (possi	97.43
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	97.41
1on2_A	142	Transcriptional regulator MNTR; helix-turn-helix,	97.39
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	97.38
1ub9_A	100	Hypothetical protein PH1061; helix-turn-helix moti	97.38
2jsc_A	118	Transcriptional regulator RV1994C/MT2050; cadmium,	97.38
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	97.36
2wte_A	244	CSA3; antiviral protein, viral resistance, winged	97.3
3r0a_A	123	Putative transcriptional regulator; structural gen	97.29
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	97.26
1xmk_A	79	Double-stranded RNA-specific adenosine deaminase;	97.25
1mzb_A	136	Ferric uptake regulation protein; ferric uptake re	97.23
2xig_A	150	Ferric uptake regulation protein; hpfur, transcrip	97.23
3f6v_A	151	Possible transcriptional regulator, ARSR family pr	97.22
2hzt_A	107	Putative HTH-type transcriptional regulator YTCD;	97.2
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	97.19
3mwm_A	139	ZUR, putative metal uptake regulation protein; FUR	97.18
3fm5_A	150	Transcriptional regulator; MCSG, PF04017, PSI, MAR	97.17
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	97.14
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	97.13
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	97.12
3df8_A	111	Possible HXLR family transcriptional factor; APC89	97.09
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	97.09
2pg4_A	95	Uncharacterized protein; structural genomics, join	97.07
1r1t_A	122	Transcriptional repressor SMTB; zinc, transcriptio	97.06
2gxg_A	146	146AA long hypothetical transcriptional regulator;	97.01
1tbx_A	99	ORF F-93, hypothetical 11.0 kDa protein; sulfolobu	97.01
2hr3_A	147	Probable transcriptional regulator; MCSG, structur	97.0
2lnb_A	80	Z-DNA-binding protein 1; structural genomics, nort	96.99
1r7j_A	95	Conserved hypothetical protein SSO10A; winged heli	96.98
3bja_A	139	Transcriptional regulator, MARR family, putative;	96.98
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	96.97
1s3j_A	155	YUSO protein; structural genomics, MARR transcript	96.97
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	96.97
3kp7_A	151	Transcriptional regulator TCAR; multiple drug resi	96.96
3boq_A	160	Transcriptional regulator, MARR family; MARR famil	96.96
3lwf_A	159	LIN1550 protein, putative transcriptional regulato	96.96
1z7u_A	112	Hypothetical protein EF0647; winged-helix-turn-hel	96.96
4a5n_A	131	Uncharacterized HTH-type transcriptional regulato;	96.95
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	96.95
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	96.95
2qvo_A	95	Uncharacterized protein AF_1382; PSI, structural g	96.94
2h09_A	155	Transcriptional regulator MNTR; transcription regu	96.92
1ylf_A	149	RRF2 family protein; structural genomics, transcri	96.89
2fbh_A	146	Transcriptional regulator PA3341; MARR, transcript	96.87
3deu_A	166	Transcriptional regulator SLYA; MARR, WING-helix,	96.87
2nnn_A	140	Probable transcriptional regulator; structural gen	96.86
2qww_A	154	Transcriptional regulator, MARR family; YP_013417.	96.86
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	96.86
3k0l_A	162	Repressor protein; helix-turn-helix, structural ge	96.86
3nrv_A	148	Putative transcriptional regulator (MARR/EMRR FAM;	96.85
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	96.85
1ku9_A	152	Hypothetical protein MJ223; putative transcription	96.85
3t8r_A	143	Staphylococcus aureus CYMR; transcriptional regula	96.83
3cdh_A	155	Transcriptional regulator, MARR family; helix-turn	96.83
2w57_A	150	Ferric uptake regulation protein; gene regulation,	96.83
2f2e_A	146	PA1607; transcription factor, helix-TRUN-helix, AP	96.82
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	96.82
2a61_A	145	Transcriptional regulator TM0710; APC4350, MCSG, m	96.81
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	96.81
3f3x_A	144	Transcriptional regulator, MARR family, putative;	96.81
3oop_A	143	LIN2960 protein; protein structure initiative, PSI	96.8
2fsw_A	107	PG_0823 protein; alpha-beta structure, helix-turn-	96.77
3bj6_A	152	Transcriptional regulator, MARR family; helix-turn	96.77
2zkz_A	99	Transcriptional repressor PAGR; protein-DNA, HTH m	96.76
1xd7_A	145	YWNA; structural genomics, protein structure initi	96.74
1sfx_A	109	Conserved hypothetical protein AF2008; structural	96.74
3g3z_A	145	NMB1585, transcriptional regulator, MARR family; t	96.74
2nyx_A	168	Probable transcriptional regulatory protein, RV14;	96.74
1bja_A	95	Transcription regulatory protein MOTA; activation	96.71
3jw4_A	148	Transcriptional regulator, MARR/EMRR family; DNA-b	96.7
3e6m_A	161	MARR family transcriptional regulator; APC88769, s	96.68
3cjn_A	162	Transcriptional regulator, MARR family; silicibact	96.67
2obp_A	96	Putative DNA-binding protein; structural genomics,	96.67
2pex_A	153	Transcriptional regulator OHRR; transcription regu	96.67
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	96.66
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	96.66
4aik_A	151	Transcriptional regulator SLYA; transcription, tra	96.65
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	96.65
3hsr_A	140	HTH-type transcriptional regulator SARZ; helix-tur	96.63
1yyv_A	131	Putative transcriptional regulator; reductive meth	96.61
2eth_A	154	Transcriptional regulator, putative, MAR family; M	96.61
3k69_A	162	Putative transcription regulator; putative transcr	96.6
2rdp_A	150	Putative transcriptional regulator MARR; PFAM PF01	96.59
1lj9_A	144	Transcriptional regulator SLYA; HTH DNA binding pr	96.59
2bv6_A	142	MGRA, HTH-type transcriptional regulator MGRA; mul	96.57
1p6r_A	82	Penicillinase repressor; transcription regulation,	96.56
2fbi_A	142	Probable transcriptional regulator; MARR, APC5816,	96.54
2qm3_A	373	Predicted methyltransferase; putative methyltransf	96.52
3u2r_A	168	Regulatory protein MARR; structural genomics, PSI-	96.49
1z91_A	147	Organic hydroperoxide resistance transcriptional;	96.49
4hbl_A	149	Transcriptional regulator, MARR family; HTH, trans	96.48
3s2w_A	159	Transcriptional regulator, MARR family; structural	96.47
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	96.44
3eyy_A	145	Putative iron uptake regulatory protein; NUR, nick	96.43
2w25_A	150	Probable transcriptional regulatory protein; trans	96.42
2k4b_A	99	Transcriptional regulator; DNA binding protein, wi	96.39
3u1d_A	151	Uncharacterized protein; GNTR-superfamily, structu	96.38
3hrs_A	214	Metalloregulator SCAR; DTXR/MNTR family member, tr	96.37
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	96.36
4ets_A	162	Ferric uptake regulation protein; metal binding pr	96.35
2fbk_A	181	Transcriptional regulator, MARR family; winged-hel	96.33
2frh_A	127	SARA, staphylococcal accessory regulator A; winged	96.32
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	96.32
3nqo_A	189	MARR-family transcriptional regulator; structural	96.26
1okr_A	123	MECI, methicillin resistance regulatory protein ME	96.23
2p4w_A	202	Transcriptional regulatory protein ARSR family; ar	96.22
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	96.19
1j5y_A	187	Transcriptional regulator, biotin repressor famil;	96.16
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	96.13
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	96.12
2g9w_A	138	Conserved hypothetical protein; DNA-binding domain	96.09
2dk5_A	91	DNA-directed RNA polymerase III 39 kDa polypeptide	96.09
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	96.07
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	96.06
2qlz_A	232	Transcription factor PF0095; 2.50A {Pyrococcus fur	96.06
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	96.04
4b8x_A	147	SCO5413, possible MARR-transcriptional regulator;	95.91
3i4p_A	162	Transcriptional regulator, ASNC family; PSI, struc	95.9
1uly_A	192	Hypothetical protein PH1932; helix-turn-helix, str	95.89
2xvc_A	59	ESCRT-III, SSO0910; cell cycle, cell division, cyt	95.86
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	95.85
2fxa_A	207	Protease production regulatory protein HPR; protea	95.81
4fx0_A	148	Probable transcriptional repressor protein; helix-	95.76
2esh_A	118	Conserved hypothetical protein TM0937; APC5794, st	95.75
2hoe_A	380	N-acetylglucosamine kinase; TM1224, structural gen	95.62
4esf_A	117	PADR-like transcriptional regulator; PADR family,	95.54
2vn2_A	128	DNAD, chromosome replication initiation protein; D	95.52
3cta_A	230	Riboflavin kinase; structural genomics, transferas	95.5
1fx7_A	230	Iron-dependent repressor IDER; DTXR, iron-dependen	95.27
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	95.22
1sd4_A	126	Penicillinase repressor; BLAI, MECI, methicillin,	95.13
3f8b_A	116	Transcriptional regulator, PADR-like family; winge	95.08
1z6r_A	406	MLC protein; transcriptional repressor, ROK family	94.97
4g6q_A	182	Putative uncharacterized protein; structural genom	94.94
2p5k_A	64	Arginine repressor; DNA-binding domain, winged hel	94.91
1v4r_A	102	Transcriptional repressor; helix-turn-helix, winge	94.83
1jhg_A	101	Trp operon repressor; complex (regulatory protein-	94.83
2v79_A	135	DNA replication protein DNAD; primosome, DNA-bindi	94.83
2qq9_A	226	Diphtheria toxin repressor; regulator, DTXR, helix	94.82
3elk_A	117	Putative transcriptional regulator TA0346; structu	94.76
1yg2_A	179	Gene activator APHA; virulence factor, winged heli	94.62
3l7w_A	108	Putative uncharacterized protein SMU.1704; PADR, t	94.39
3hhh_A	116	Transcriptional regulator, PADR family; PF03551, s	94.37
1bia_A	321	BIRA bifunctional protein; transcription regulatio	94.33
1xma_A	145	Predicted transcriptional regulator; southea colla	94.03
1z05_A	429	Transcriptional regulator, ROK family; structural	93.83
1hsj_A	487	Fusion protein consisting of staphylococcus access	93.62
1sfu_A	75	34L protein; protein/Z-DNA complex, DNA binding pr	93.42
3kor_A	119	Possible Trp repressor; putative DNA-binding Trp r	93.39
4esb_A	115	Transcriptional regulator, PADR family; DNA bindin	93.29
3rkx_A	323	Biotin-[acetyl-COA-carboxylase] ligase; biotin pro	93.24
2yu3_A	95	DNA-directed RNA polymerase III 39 kDa polypeptide	93.15
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	92.86
3e6c_C	250	CPRK, cyclic nucleotide-binding protein; CPRK, hal	92.73
3i71_A	68	Ethanolamine utilization protein EUTK; helix-turn-	92.64
3frw_A	107	Putative Trp repressor protein; structural genomic	92.27
2o0m_A	345	Transcriptional regulator, SORC family; structural	91.98
3tqn_A	113	Transcriptional regulator, GNTR family; regulatory	91.96
2w48_A	315	Sorbitol operon regulator; SORC, activator, repres	91.92
2ek5_A	129	Predicted transcriptional regulators; helix-turn-h	91.76
1stz_A	338	Heat-inducible transcription repressor HRCA homol;	91.66
2p8t_A	200	Hypothetical protein PH0730; pyrococcus horikoshii	91.66
3ri2_A	123	Transcriptional regulator, PADR-like family; PSI-b	91.6
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	91.43
2b0l_A	102	GTP-sensing transcriptional pleiotropic repressor;	91.27
2co5_A	99	Viral protein F93; viral protein-winged helix comp	91.09
2gqq_A	163	Leucine-responsive regulatory protein; helix-turn-	91.0
2pjp_A	121	Selenocysteine-specific elongation factor; SELB, p	90.73
1cf7_A	76	Protein (transcription factor E2F-4); E2F, winged-	90.54
3c7j_A	237	Transcriptional regulator, GNTR family; structural	90.49
3dv8_A	220	Transcriptional regulator, CRP/FNR family; cyclic	90.38
3by6_A	126	Predicted transcriptional regulator; structural ge	90.28
3lmm_A	583	Uncharacterized protein; multi-domained alpha-beta	90.16
3e97_A	231	Transcriptional regulator, CRP/FNR family; YP_6044	90.08
2oz6_A	207	Virulence factor regulator; winged helix, helix-tu	90.05
3neu_A	125	LIN1836 protein; structural genomics, PSI-2, prote	89.88
2gau_A	232	Transcriptional regulator, CRP/FNR family; structu	89.78
3ryp_A	210	Catabolite gene activator; CAMP receptor protein (	89.7
2dql_A	115	PEX protein; circadian clock associated protein, c	89.56
2zcw_A	202	TTHA1359, transcriptional regulator, FNR/CRP famil	89.48
3iwz_A	230	CAP-like, catabolite activation-like protein; XCC,	89.46
4ham_A	134	LMO2241 protein; structural genomics, PSI-biology,	89.41
4ev0_A	216	Transcription regulator, CRP family; CAMP binding,	89.21
3d0s_A	227	Transcriptional regulatory protein; CAMP receptor	89.19
3la7_A	243	Global nitrogen regulator; activator, DNA-binding,	88.88
3dkw_A	227	DNR protein; CRP-FNR, HTH, beta barrel, dimerizati	88.82
3l9f_A	204	Putative uncharacterized protein SMU.1604C; PADR,	88.72
2qc0_A	373	Uncharacterized protein; NP_719793.1, uncharacteri	88.66
3b02_A	195	Transcriptional regulator, CRP family; structural	88.66
3maj_A	382	DNA processing chain A; MCSG, PSI-2, structural ge	88.49
1zyb_A	232	Transcription regulator, CRP family; NP_813211.1,	88.3
2zfw_A	148	PEX; five alpha-helices + one beta-sheet, circadia	88.26
1ft9_A	222	Carbon monoxide oxidation system transcription reg	88.15
1lva_A	258	Selenocysteine-specific elongation factor; winged-	88.03
2o3f_A	111	Putative HTH-type transcriptional regulator YBBH;	87.87
2fmy_A	220	COOA, carbon monoxide oxidation system transcripti	87.85
2qlz_A	232	Transcription factor PF0095; 2.50A {Pyrococcus fur	87.85
3eqx_A	373	FIC domain containing transcriptional regulator; F	87.73
2bgc_A	238	PRFA; bacterial infection, human pathogen, transcr	87.65
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	87.54
2vxz_A	165	Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Py	87.38
3oio_A	113	Transcriptional regulator (ARAC-type DNA-binding c	87.14
3f8m_A	248	GNTR-family protein transcriptional regulator; PHN	87.03
3iwf_A	107	Transcription regulator RPIR family; transcription	86.92
3u5c_Z	108	RP45, S31, YS23, 40S ribosomal protein S25-A; tran	86.82
3kcc_A	260	Catabolite gene activator; helix-turn-helix, CAMP,	86.75
3qph_A	342	TRMB, A global transcription regulator; transcript	86.49
3edp_A	236	LIN2111 protein; APC88337, listeria innocua CLIP11	86.46
1hw1_A	239	FADR, fatty acid metabolism regulator protein; hel	86.26
2wv0_A	243	YVOA, HTH-type transcriptional repressor YVOA; DNA	86.19
3sxy_A	218	Transcriptional regulator, GNTR family; transcript	86.16
2xzm_8	143	RPS25E,; ribosome, translation; 3.93A {Tetrahymena	86.08
3ic7_A	126	Putative transcriptional regulator; helix-turn-hel	85.82
3bwg_A	239	Uncharacterized HTH-type transcriptional regulato;	85.67
3mn2_A	108	Probable ARAC family transcriptional regulator; st	85.27
1jko_C	52	HIN recombinase, DNA-invertase HIN; water-mediated	85.07
2hs5_A	239	Putative transcriptional regulator GNTR; APC6050,	84.81
2e1n_A	138	PEX, period extender; circadian clock, DNA binding	84.78
3oou_A	108	LIN2118 protein; protein structure initiative, PSI	84.33
2x48_A	55	CAG38821; archeal virus, viral protein; 2.60A {Sul	84.31
3ke2_A	117	Uncharacterized protein YP_928783.1; structural ge	83.84
2k9s_A	107	Arabinose operon regulatory protein; activator, ar	83.82
1bl0_A	129	Protein (multiple antibiotic resistance protein),	83.53
3ihu_A	222	Transcriptional regulator, GNTR family; YP_298823.	83.41
1uxc_A	65	FRUR (1-57), fructose repressor; DNA-binding prote	82.55
3eet_A	272	Putative GNTR-family transcriptional regulator; st	82.42
2z99_A	219	Putative uncharacterized protein; winged helix dom	82.39
3lsg_A	103	Two-component response regulator YESN; structural	82.16
2jpc_A	61	SSRB; DNA binding protein, structural genomics, PS	81.99
3fx3_A	237	Cyclic nucleotide-binding protein; helix_TURN_heli	81.9
3l4g_A	508	Phenylalanyl-tRNA synthetase alpha chain; aminoacy	81.66
2di3_A	239	Bacterial regulatory proteins, GNTR family; helix-	80.96
3mkl_A	120	HTH-type transcriptional regulator GADX; PSI2, MCS	80.76
3lmm_A	583	Uncharacterized protein; multi-domained alpha-beta	80.7
1o5l_A	213	Transcriptional regulator, CRP family; TM1171, str	80.1
1fse_A	74	GERE; helix-turn-helix DNA-binding protein transcr	80.08

>3p9c_A Caffeic acid O-methyltransferase; S-adenosylmethionine dependent O-methyltransferase; HET: SAH; 1.80A {Lolium perenne} PDB: 3p9i_A* 3p9k_A*

Probab=99.84  E-value=5.1e-21  Score=149.74  Aligned_cols=124  Identities=22%  Similarity=0.289  Sum_probs=105.4

Q ss_pred             ChHHHhHHHHHHHHHHHhHHHHHHHHHHHHhChHHHHHhCC-CCCCHHHHHhhcCC--CCCCcchHHHHHHHhhcCCcee
Q 040869            8 GAKELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHG-RAITLSELVSALDI--QPTKTTGLFRLMRLLVHSSCFN   84 (131)
Q Consensus         8 ~~~e~~~~~~~l~~~~~~~~~~~aL~~a~~L~ifd~l~~~~-~~~s~~eLA~~~~~--~~~~~~~l~RlLr~L~~~gl~~   84 (131)
                      ..+|+.+++..+++++++++.+++|++|++|||||+|++++ +|+|++|||+++|+  +|.++..|+|+||+|++.|+|+
T Consensus        13 ~~~~~~~~~~~~~~l~~~~~~~~~l~~a~~Lgifd~L~~~g~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L~~~g~l~   92 (364)
T 3p9c_A           13 AASADEDACMFALQLASSSVLPMTLKNAIELGLLEILVAAGGKSLTPTEVAAKLPSAANPEAPDMVDRILRLLASYNVVT   92 (364)
T ss_dssp             CHHHHHHHHHHHHHHTTTTHHHHHHHHHHHHTHHHHHHHTTTCCBCHHHHHHTTTCTTCTTHHHHHHHHHHHHHHTTSEE
T ss_pred             cchHHHHHHHHHHHHHHhHHHHHHHHHHHHCChHHHHhhcCCCCCCHHHHHHhcCCCCCccchhhHHHHHHHHHhCCCEE
Confidence            56678889999999999999999999999999999999754 79999999999996  4434459999999999999999


Q ss_pred             ecccC--CC--CcceecchhccccccC-cccChHHhHHhhcCchhhccCCCC
Q 040869           85 KTKVN--GQ--EEAYGLTAASTLLIKD-KPYCMSPTVSAFVDPLFVAPFQSL  131 (131)
Q Consensus        85 ~~~~~--~~--~~~y~~t~~s~~L~~~-~~~sl~~~~~~~~~~~~~~~w~~L  131 (131)
                      +....  +|  +++|++||.++.|+.+ ++.++++++.+..++.+|++|.+|
T Consensus        93 ~~~~~~~~g~~~~~y~~t~~s~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~L  144 (364)
T 3p9c_A           93 CLVEEGKDGRLSRSYGAAPVCKFLTPNEDGVSMAALALMNQDKVLMESWYYL  144 (364)
T ss_dssp             EEEEECSSSCEEEEEEECGGGGGSSCCTTSCCTHHHHHHHTSHHHHGGGGGH
T ss_pred             EeccccCCCCcCCEEecCHHHHHHcCCCCCCCHHHHHHHhcCHHHHHHHhCH
Confidence            86210  11  3689999999988765 467999999998888899999864

>1fp2_A Isoflavone O-methyltransferase; protein-product complex; HET: SAH HMO; 1.40A {Medicago sativa} SCOP: a.4.5.29 c.66.1.12 PDB: 1fpx_A* 2qyo_A*

Probab=99.84  E-value=4e-21  Score=149.07  Aligned_cols=125  Identities=38%  Similarity=0.689  Sum_probs=107.8

Q ss_pred             ccCChHHHhHHHHHHHHHHHhHHHHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCcee
Q 040869            5 QDQGAKELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFN   84 (131)
Q Consensus         5 ~~~~~~e~~~~~~~l~~~~~~~~~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~   84 (131)
                      ....++|.+++...+++++++++.+++|+++++||||+.|++.++|+|++|||+++|++|.+++.++|+||+|++.|+|+
T Consensus         6 ~~~~~~~~~~a~~~l~~~~~~~~~~~~l~~a~~lgif~~L~~~~~~~t~~ela~~~~~~~~~~~~l~rlLr~L~~~gll~   85 (352)
T 1fp2_A            6 NGRKPSEIFKAQALLYKHIYAFIDSMSLKWAVEMNIPNIIQNHGKPISLSNLVSILQVPSSKIGNVRRLMRYLAHNGFFE   85 (352)
T ss_dssp             --CCSTHHHHHHHHHHHHHTTHHHHHHHHHHHHTTHHHHHHHHTSCEEHHHHHHHHTCCGGGHHHHHHHHHHHHHTTSEE
T ss_pred             cCCChHHHhhHHHHHHHHHHHHHHHHHHHHHHHCChhhhhhhcCCCccHHHHHHHhCcCCCChHHHHHHHHHHHhCCeEE
Confidence            33445688899999999999999999999999999999998645699999999999995445779999999999999999


Q ss_pred             ecccCCCCcceecchhccccccCcccChHHhHHhhcCchhhccCCCC
Q 040869           85 KTKVNGQEEAYGLTAASTLLIKDKPYCMSPTVSAFVDPLFVAPFQSL  131 (131)
Q Consensus        85 ~~~~~~~~~~y~~t~~s~~L~~~~~~sl~~~~~~~~~~~~~~~w~~L  131 (131)
                      +..  ++++.|++|+.++.|++++|.++++++.+..++.++.+|.+|
T Consensus        86 ~~~--~~~~~y~~t~~s~~L~~~~~~~~~~~~~~~~~~~~~~~~~~L  130 (352)
T 1fp2_A           86 IIT--KEEESYALTVASELLVRGSDLCLAPMVECVLDPTLSGSYHEL  130 (352)
T ss_dssp             EEE--SSSEEEEECHHHHTTSTTSSSCCHHHHHHHTCHHHHHGGGGH
T ss_pred             Eec--CCCCeEeCCHHHHHHhCCCCccHHHHHHHhcCchHHHHHHHH
Confidence            872  015899999999999998888999999998777888888764

>1zg3_A Isoflavanone 4'-O-methyltransferase; rossman fold, plant Pro transferase; HET: 2HI SAH; 2.35A {Medicago truncatula} PDB: 1zga_A* 1zhf_A* 1zgj_A*

Probab=99.82  E-value=1e-20  Score=147.15  Aligned_cols=122  Identities=47%  Similarity=0.721  Sum_probs=105.7

Q ss_pred             HHHhHHHHHHHHHHHhHHHHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeeccc-
Q 040869           10 KELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKV-   88 (131)
Q Consensus        10 ~e~~~~~~~l~~~~~~~~~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~-   88 (131)
                      +|.+++...+++++++++.+++|+++++||||++|++.++|+|++|||+++|++|.+++.++|+||+|++.|+|.+... 
T Consensus         5 ~~~~~~~~~l~~~~~~~~~~~~l~~a~~lgif~~L~~~~~~~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~gll~~~~~~   84 (358)
T 1zg3_A            5 SELYHAQIHLYKHVYNFVSSMALKSAMELGIADAIHNHGKPMTLSELASSLKLHPSKVNILHRFLRLLTHNGFFAKTIVK   84 (358)
T ss_dssp             SCCTTHHHHHHHHHTTHHHHHHHHHHHHHTHHHHHHHHTSCEEHHHHHHHTTCCTTTHHHHHHHHHHHHHTTSEEEEEEC
T ss_pred             HHhhhHHHHHHHHHHHHHHHHHHHHHHHCChHhHHhhcCCCcCHHHHHHhcCCCCcchHHHHHHHHHHhhCCcEEEeccc
Confidence            5677888999999999999999999999999999986456999999999999965568899999999999999998710 


Q ss_pred             --C-CC--CcceecchhccccccCcccChHHhHHhhcCchhhccCCCC
Q 040869           89 --N-GQ--EEAYGLTAASTLLIKDKPYCMSPTVSAFVDPLFVAPFQSL  131 (131)
Q Consensus        89 --~-~~--~~~y~~t~~s~~L~~~~~~sl~~~~~~~~~~~~~~~w~~L  131 (131)
                        . +|  +++|++|+.++.|++++|.++++++.+..++.++.+|.+|
T Consensus        85 ~~~~~g~~~~~y~~t~~s~~l~~~~~~~~~~~~~~~~~~~~~~~~~~L  132 (358)
T 1zg3_A           85 GKEGDEEEEIAYSLTPPSKLLISGKPTCLSSIVKGALHPSSLDMWSSS  132 (358)
T ss_dssp             CSSSSCCCEEEEEECHHHHTTCTTSTTCCHHHHHHHTSHHHHGGGGGH
T ss_pred             ccccCCCCCCEEeCCHHHHHHhCCCCccHHHHHHHhcCcHHHHHHHHH
Confidence              0 01  3789999999999998888999999998888888999764

>3lst_A CALO1 methyltransferase; calicheamicin, enediyne, SAH, STRU genomics, PSI-2, protein structure initiative; HET: SAH; 2.40A {Micromonospora echinospora}

Probab=99.82  E-value=1.3e-20  Score=146.15  Aligned_cols=111  Identities=23%  Similarity=0.333  Sum_probs=101.5

Q ss_pred             HHhHHHHHHHHHHHhHHHHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCC
Q 040869           11 ELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNG   90 (131)
Q Consensus        11 e~~~~~~~l~~~~~~~~~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~   90 (131)
                      ...++...+++++++++.+++|+++++||||+.|++  +|+|++|||+++|+   ++..++|+||+|++.|+|++ .   
T Consensus        18 ~~~~~~~~l~~~~~~~~~~~~l~~a~~lglf~~l~~--g~~t~~elA~~~g~---~~~~l~rlLr~l~~~g~l~~-~---   88 (348)
T 3lst_A           18 DRLQSALALYEEAMGYTYAAALRAAAAVGVADHLVD--GPRTPAELAAATGT---DADALRRVLRLLAVRDVVRE-S---   88 (348)
T ss_dssp             CHHHHHHHHHHHHTTHHHHHHHHHHHHHTGGGGGTT--SCBCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEE-E---
T ss_pred             CCchHHHHHHHHHHHHHHHHHHHHHHHcCchhHhhC--CCCCHHHHHHHhCc---CHHHHHHHHHHHHhCCCEEe-c---
Confidence            456778889999999999999999999999999983  69999999999999   99999999999999999999 5   


Q ss_pred             CCcceecchhccccccCcccChHHhHHhhcCchhhccCCCC
Q 040869           91 QEEAYGLTAASTLLIKDKPYCMSPTVSAFVDPLFVAPFQSL  131 (131)
Q Consensus        91 ~~~~y~~t~~s~~L~~~~~~sl~~~~~~~~~~~~~~~w~~L  131 (131)
                       +++|++|+.++.|++++|.++++++.+..++.+|.+|.+|
T Consensus        89 -~~~y~~t~~s~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l  128 (348)
T 3lst_A           89 -DGRFALTDKGAALRSDSPVPARAGILMFTDTMFWTMSHRV  128 (348)
T ss_dssp             -TTEEEECTTTGGGSTTSSSCSHHHHHHHTSHHHHHHHHTH
T ss_pred             -CCEEecCHHHHHHhcCCCccHHHHHHHhcCHHHHHHHHHH
Confidence             7999999999999888888999999988777788888764

>4a6d_A Hydroxyindole O-methyltransferase; melatonin, circadian clock; HET: SAM; 2.40A {Homo sapiens} PDB: 4a6e_A*

Probab=99.81  E-value=4.8e-20  Score=143.69  Aligned_cols=113  Identities=17%  Similarity=0.162  Sum_probs=98.6

Q ss_pred             HHHHHHHHHHHhHHHHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCc
Q 040869           14 QGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEE   93 (131)
Q Consensus        14 ~~~~~l~~~~~~~~~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~   93 (131)
                      ++...+++++.||+.+++|++|++|||||+|++.++|+|++|||+++|+   ++..++|+||+|++.|+|++... ++.+
T Consensus         7 ~~~~~L~~l~~Gf~~s~~L~aa~eLglfd~L~~~~~p~t~~eLA~~~g~---~~~~l~rlLr~L~~~gll~~~~~-~~~~   82 (353)
T 4a6d_A            7 QAYRLLNDYANGFMVSQVLFAACELGVFDLLAEAPGPLDVAAVAAGVRA---SAHGTELLLDICVSLKLLKVETR-GGKA   82 (353)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHSSSCBCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEEEE-TTEE
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHcCHHHHHhcCCCCCCHHHHHHhhCc---CHHHHHHHHHHHHHCCCEEEecc-Cccc
Confidence            6667789999999999999999999999999976789999999999999   99999999999999999986531 1146


Q ss_pred             ceecchhcc-ccccCcccChHHhHHhhcCchhhccCCCC
Q 040869           94 AYGLTAAST-LLIKDKPYCMSPTVSAFVDPLFVAPFQSL  131 (131)
Q Consensus        94 ~y~~t~~s~-~L~~~~~~sl~~~~~~~~~~~~~~~w~~L  131 (131)
                      .|++|+.++ +|.+++|.++++++.+.. +..|++|.+|
T Consensus        83 ~y~~t~~s~~~l~~~~~~~~~~~~~~~~-~~~~~~~~~L  120 (353)
T 4a6d_A           83 FYRNTELSSDYLTTVSPTSQCSMLKYMG-RTSYRCWGHL  120 (353)
T ss_dssp             EEEECHHHHHHHSTTSTTCCHHHHHHHH-HTHHHHHTTH
T ss_pred             eeeCCHHHHHHhhcCCchHHHHHHHHhC-HHHHHHHHHH
Confidence            899999987 678888999999998864 5678888764

>2ip2_A Probable phenazine-specific methyltransferase; pyocyanin, phenazine-1-carboxy PHZM; 1.80A {Pseudomonas aeruginosa}

Probab=99.80  E-value=2.9e-19  Score=137.20  Aligned_cols=107  Identities=24%  Similarity=0.312  Sum_probs=97.3

Q ss_pred             HHHHHHHHHHHhHHHHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCc
Q 040869           14 QGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEE   93 (131)
Q Consensus        14 ~~~~~l~~~~~~~~~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~   93 (131)
                      .++..+++++++++.+++|+++++||||+.|.  ++|+|++|||+++|+   +++.++|+||+|++.|+|.+.+    ++
T Consensus         7 ~~~~~l~~~~~~~~~~~~l~~~~~lgi~~~l~--~~~~t~~ela~~~~~---~~~~l~r~Lr~L~~~g~l~~~~----~~   77 (334)
T 2ip2_A            7 AAARNLIQVVTGEWKSRCVYVATRLGLADLIE--SGIDSDETLAAAVGS---DAERIHRLMRLLVAFEIFQGDT----RD   77 (334)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHH--TTCCSHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEET----TT
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHcCcHHHHh--CCCCCHHHHHHHhCc---CHHHHHHHHHHHHhCCceEecC----CC
Confidence            67789999999999999999999999999997  379999999999999   9999999999999999999875    68


Q ss_pred             ceecchhccccccCcccChHHhHHhhcCchhhccCCCC
Q 040869           94 AYGLTAASTLLIKDKPYCMSPTVSAFVDPLFVAPFQSL  131 (131)
Q Consensus        94 ~y~~t~~s~~L~~~~~~sl~~~~~~~~~~~~~~~w~~L  131 (131)
                      .|.+|+.++.|+ ++|.++++++.+..++.. ..|.+|
T Consensus        78 ~y~~t~~s~~l~-~~~~~~~~~~~~~~~~~~-~~~~~l  113 (334)
T 2ip2_A           78 GYANTPTSHLLR-DVEGSFRDMVLFYGEEFH-AAWTPA  113 (334)
T ss_dssp             EEEECHHHHTTS-SSTTCSHHHHHHHTTHHH-HHTTTH
T ss_pred             eEecCHHHHHHh-CCCccHHHHHHHhcCchh-hHHHHH
Confidence            999999999998 888899999988876544 788764

>1fp1_D Isoliquiritigenin 2'-O-methyltransferase; protein-substrate, protein-product complex; HET: SAH HCC; 1.82A {Medicago sativa} SCOP: a.4.5.29 c.66.1.12 PDB: 1fpq_A*

Probab=99.80  E-value=1.4e-19  Score=141.40  Aligned_cols=123  Identities=23%  Similarity=0.314  Sum_probs=102.1

Q ss_pred             hHHHhHHHHHHH--HHHHhHHHHHHHHHHHHhChHHHHHhCCCC---CCHHHHHhhcCC---CCCCcchHHHHHHHhhcC
Q 040869            9 AKELLQGQAQLY--KLMFSHLSSMSLKCAIELGIADIIHSHGRA---ITLSELVSALDI---QPTKTTGLFRLMRLLVHS   80 (131)
Q Consensus         9 ~~e~~~~~~~l~--~~~~~~~~~~aL~~a~~L~ifd~l~~~~~~---~s~~eLA~~~~~---~~~~~~~l~RlLr~L~~~   80 (131)
                      .++..+++..++  +++.+++.+++|+++++||||++|++.++|   +|++|||+++|+   +|.+++.++|+||+|++.
T Consensus        16 ~~~~~~~~~~l~~~~l~~~~~~~~~l~~a~~lgif~~L~~~g~pg~~~t~~eLA~~~~~~~~~~~~~~~l~rlLr~L~~~   95 (372)
T 1fp1_D           16 TSEQTEDSACLSAMVLTTNLVYPAVLNAAIDLNLFEIIAKATPPGAFMSPSEIASKLPASTQHSDLPNRLDRMLRLLASY   95 (372)
T ss_dssp             ---CCHHHHHHHHHHHHHTTHHHHHHHHHHHTTHHHHHHTCSSTTCCBCHHHHHTTSCGGGCCTTHHHHHHHHHHHHHHT
T ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHCChHHHHHhcCCCCCCcCHHHHHHhcCCCCCCCcChHHHHHHHHHHhhC
Confidence            344567777888  999999999999999999999999963326   999999999998   666788999999999999


Q ss_pred             Cceeeccc--CCC--CcceecchhccccccCcc-cChHHhHHhhcCchhhccCCCC
Q 040869           81 SCFNKTKV--NGQ--EEAYGLTAASTLLIKDKP-YCMSPTVSAFVDPLFVAPFQSL  131 (131)
Q Consensus        81 gl~~~~~~--~~~--~~~y~~t~~s~~L~~~~~-~sl~~~~~~~~~~~~~~~w~~L  131 (131)
                      |+|++...  .+|  +++|++|+.++.|++++| .++++++.+..++.++.+|.+|
T Consensus        96 gll~~~~~~~~~g~~~~~y~~t~~s~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~L  151 (372)
T 1fp1_D           96 SVLTSTTRTIEDGGAERVYGLSMVGKYLVPDESRGYLASFTTFLCYPALLQVWMNF  151 (372)
T ss_dssp             TSEEEEEEECTTSCEEEEEEECTTGGGGSTTCTTCCCTHHHHHHTCHHHHHHHTTH
T ss_pred             CceEecccccCCCCcCCeEecCHHHHHHhCCCCCCCHHHHHHHhcCchHHHHHHHH
Confidence            99998710  011  258999999999998887 7999999998877888888764

>3gwz_A MMCR; methyltransferase, mitomycin, S-adenosyl methionine, transferase; HET: MSE SAH; 1.91A {Streptomyces lavendulae} PDB: 3gxo_A*

Probab=99.79  E-value=9.1e-20  Score=142.55  Aligned_cols=112  Identities=18%  Similarity=0.306  Sum_probs=101.2

Q ss_pred             HHhHHHHHHHHHHHhHHHHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCC
Q 040869           11 ELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNG   90 (131)
Q Consensus        11 e~~~~~~~l~~~~~~~~~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~   90 (131)
                      ...+....+++++.+++.+++|+++++|||||.|+  ++|+|++|||+++|+   +++.++|+||+|++.|+|.+..   
T Consensus        34 ~~~~~~~~l~~l~~~~~~~~~l~~a~~lglf~~l~--~g~~t~~eLA~~~g~---~~~~l~rlLr~L~~~g~l~~~~---  105 (369)
T 3gwz_A           34 ARAAAEETVNDILQGAWKARAIHVAVELGVPELLQ--EGPRTATALAEATGA---HEQTLRRLLRLLATVGVFDDLG---  105 (369)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTGGGGT--TSCEEHHHHHHHHTC---CHHHHHHHHHHHHHTTSSEECS---
T ss_pred             CCChHHHHHHHHHHHHHHHHHHHHHHHCChhhhhc--CCCCCHHHHHHHHCc---CHHHHHHHHHHHHhCCCEEEeC---
Confidence            34466778999999999999999999999999998  479999999999999   9999999999999999999976   


Q ss_pred             CCcc-eecchhccccccCcccChHHhHHhhcCchhhccCCCC
Q 040869           91 QEEA-YGLTAASTLLIKDKPYCMSPTVSAFVDPLFVAPFQSL  131 (131)
Q Consensus        91 ~~~~-y~~t~~s~~L~~~~~~sl~~~~~~~~~~~~~~~w~~L  131 (131)
                       +++ |.+|++++.|++++|.++++++.+..++..+..|.+|
T Consensus       106 -~~~~y~~t~~s~~L~~~~~~~~~~~~~~~~~~~~~~~~~~l  146 (369)
T 3gwz_A          106 -HDDLFAQNALSAVLLPDPASPVATDARFQAAPWHWRAWEQL  146 (369)
T ss_dssp             -STTEEECCHHHHTTSCCTTCHHHHHHHHHHSHHHHHHHHTH
T ss_pred             -CCceEecCHHHHHHhcCCchhHHHHHHHcCCHHHHHHHHhH
Confidence             688 9999999999988888999999998777778888653

>3reo_A (ISO)eugenol O-methyltransferase; directed evolution, saturation mutagenesis, regioselectivity transferase; HET: SAH EUG; 1.90A {Clarkia breweri} PDB: 3tky_A* 1kyz_A* 1kyw_A*

Probab=99.79  E-value=1.5e-19  Score=141.55  Aligned_cols=124  Identities=24%  Similarity=0.327  Sum_probs=101.5

Q ss_pred             ChHHHhHHHHHHHHHHHhHHHHHHHHHHHHhChHHHHHhC---CCCCCHHHHHhhcC-CCCCCcchHHHHHHHhhcCCce
Q 040869            8 GAKELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSH---GRAITLSELVSALD-IQPTKTTGLFRLMRLLVHSSCF   83 (131)
Q Consensus         8 ~~~e~~~~~~~l~~~~~~~~~~~aL~~a~~L~ifd~l~~~---~~~~s~~eLA~~~~-~~~~~~~~l~RlLr~L~~~gl~   83 (131)
                      .++++.+....+++++.+++.+++|++|++|||||+|++.   ++|+|++|||+++| .+|.++..|+|+||+|++.|+|
T Consensus        14 ~~~~~~~~~~~~~~l~~~~~~~~~l~~a~~Lglfd~L~~~~gp~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L~~~gll   93 (368)
T 3reo_A           14 THSSDEEANLFAMQLASAAVLPMALKAAIELDVLEIMAKSVPPSGYISPAEIAAQLPTTNPEAPVMLDRVLRLLASYSVV   93 (368)
T ss_dssp             ---CHHHHHHHHHHHHTTTHHHHHHHHHHHTTHHHHHHHHCCTTCCBCHHHHHTTSSCCCTTHHHHHHHHHHHHHHTTSE
T ss_pred             CchHHHHHHHHHHHHHHHHHHHHHHHHHHHCCchhHHhhcCCCCCCcCHHHHHHhcCcCCCcchhhHHHHHHHHHhCCCe
Confidence            4456788889999999999999999999999999999863   25799999999998 4333345999999999999999


Q ss_pred             eecccC--CC--CcceecchhccccccC-cccChHHhHHhhcCchhhccCCCC
Q 040869           84 NKTKVN--GQ--EEAYGLTAASTLLIKD-KPYCMSPTVSAFVDPLFVAPFQSL  131 (131)
Q Consensus        84 ~~~~~~--~~--~~~y~~t~~s~~L~~~-~~~sl~~~~~~~~~~~~~~~w~~L  131 (131)
                      ++....  +|  +++|++|+.++.|+.+ +|.++++++.+..++.++++|.+|
T Consensus        94 ~~~~~~~~~g~~~~~y~~t~~s~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l  146 (368)
T 3reo_A           94 TYTLRELPSGKVERLYGLAPVCKFLTKNEDGVSLAPFLLLATDKVLLEPWFYL  146 (368)
T ss_dssp             EEEEEECTTSCEEEEEEECTTHHHHSCCTTSCCSHHHHHHHTCHHHHGGGGGH
T ss_pred             EEecccCCCCcccceeCcCHHHHHHhCCCCCCCHHHHHHHhcCHHHHhhhhch
Confidence            986210  11  2689999999988754 478999999998888899999764

>3i53_A O-methyltransferase; CO-complex, rossmann-like fold; HET: SAH; 2.08A {Streptomyces carzinostaticus subsp} PDB: 3i58_A* 3i5u_A* 3i64_A*

Probab=99.78  E-value=6e-20  Score=141.19  Aligned_cols=107  Identities=23%  Similarity=0.203  Sum_probs=96.2

Q ss_pred             HHHHHHHHHhHHHHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcce
Q 040869           16 QAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAY   95 (131)
Q Consensus        16 ~~~l~~~~~~~~~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y   95 (131)
                      +..+++++.+++.+++|+++++|||||+|++  +|+|++|||+++|+   ++..++|+||+|++.|+|.+..    +++|
T Consensus         6 ~~~l~~~~~g~~~~~~l~~a~~lglf~~l~~--g~~t~~elA~~~~~---~~~~l~rlLr~l~~~gl~~~~~----~~~y   76 (332)
T 3i53_A            6 AHIGLRALADLATPMAVRVAATLRVADHIAA--GHRTAAEIASAAGA---HADSLDRLLRHLVAVGLFTRDG----QGVY   76 (332)
T ss_dssp             CSSCHHHHTCCHHHHHHHHHHHHTHHHHHHT--TCCBHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEECT----TSBE
T ss_pred             HHHHHHHHHhhHHHHHHHHHHHcChHHHHhc--CCCCHHHHHHHHCc---CHHHHHHHHHHHHhCCcEEecC----CCeE
Confidence            3567899999999999999999999999983  79999999999999   9999999999999999999976    7899


Q ss_pred             ecchhccccccCcccChHHhHHhhcCchhh-ccCCCC
Q 040869           96 GLTAASTLLIKDKPYCMSPTVSAFVDPLFV-APFQSL  131 (131)
Q Consensus        96 ~~t~~s~~L~~~~~~sl~~~~~~~~~~~~~-~~w~~L  131 (131)
                      .+|+.++.|+++++.++++++.+..++..| ..|.+|
T Consensus        77 ~~t~~s~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l  113 (332)
T 3i53_A           77 GLTEFGEQLRDDHAAGKRKWLDMNSAVGRGDLGFVEL  113 (332)
T ss_dssp             EECTTGGGGSTTCTTCCHHHHCTTSHHHHHGGGGGGH
T ss_pred             EcCHhHHHHhcCCchhHHHHHHHcCCHhHHHHHHHHh
Confidence            999999999888888999999887665566 777653

>3dp7_A SAM-dependent methyltransferase; structural genomics, protein structure initiative, NEW YORK structural genomix research; 2.33A {Bacteroides vulgatus}

Probab=99.77  E-value=2.6e-19  Score=139.72  Aligned_cols=112  Identities=14%  Similarity=0.132  Sum_probs=96.2

Q ss_pred             hHHHhHHHHHHHHHHHhHHHHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeeccc
Q 040869            9 AKELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKV   88 (131)
Q Consensus         9 ~~e~~~~~~~l~~~~~~~~~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~   88 (131)
                      +.+.+++...++++++|++.+++|+++++|||||.|++.++|+|++|||+++|+   +++.++|+||+|++.|+|++.  
T Consensus         9 ~~~~~~a~~~l~~l~~g~~~~~~l~~a~~lgifd~L~~~~~~~t~~eLA~~~g~---~~~~l~rlLr~l~~~g~l~~~--   83 (363)
T 3dp7_A            9 QCTAAEAQRLAQEIAFGPVVFQVSRLMLKFGIFQLLSGKREGYTLQEISGRTGL---TRYAAQVLLEASLTIGTILLE--   83 (363)
T ss_dssp             CCCSTTHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHTCTTCBCHHHHHHHHTC---CHHHHHHHHHHHHHHTSEEEE--
T ss_pred             chhHHHHHHHHHHHHhhHHHHHHHHHHHHhCHHHHHHhcCCCCCHHHHHHHhCc---CHHHHHHHHHHHhhCCCeEec--
Confidence            446778899999999999999999999999999999965589999999999999   999999999999999999875  


Q ss_pred             CCCCcceecchhccccccCcccChHHhHHhhcCchhhccCCCC
Q 040869           89 NGQEEAYGLTAASTLLIKDKPYCMSPTVSAFVDPLFVAPFQSL  131 (131)
Q Consensus        89 ~~~~~~y~~t~~s~~L~~~~~~sl~~~~~~~~~~~~~~~w~~L  131 (131)
                         +++|++|+.+++|+++++.+  .++.+ ..+..|++|.+|
T Consensus        84 ---~~~y~~t~~s~~L~~~~~~~--~~~~~-~~~~~~~~~~~L  120 (363)
T 3dp7_A           84 ---EDRYVLAKAGWFLLNDKMAR--VNMEF-NHDVNYQGLFHL  120 (363)
T ss_dssp             ---TTEEEECHHHHHHHHCHHHH--HHHHH-HHHTTHHHHTTH
T ss_pred             ---CCEEecccchHHhhCCCccc--chhee-ecHHhhhhHHHH
Confidence               68999999999998876533  23433 345678888764

>2r3s_A Uncharacterized protein; methyltransferase domain, structural genomics, joint center structural genomics, JCSG, protein structure initiative; HET: MSE; 2.15A {Nostoc punctiforme}

Probab=99.76  E-value=1.1e-18  Score=133.50  Aligned_cols=105  Identities=21%  Similarity=0.324  Sum_probs=96.2

Q ss_pred             HHHHHHHHhHHHHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCccee
Q 040869           17 AQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYG   96 (131)
Q Consensus        17 ~~l~~~~~~~~~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~   96 (131)
                      ..+++++.+++.+++|+++++||||+.|++  +|+|++|||+++|+   +++.++|+||+|++.|+|++.     +++|+
T Consensus         8 ~~l~~~~~~~~~~~~l~~~~~l~i~~~l~~--~~~t~~ela~~~~~---~~~~l~r~L~~L~~~g~l~~~-----~~~y~   77 (335)
T 2r3s_A            8 ALFFNTVNAYQRSAAIKAAVELNVFTAISQ--GIESSQSLAQKCQT---SERGMRMLCDYLVIIGFMTKQ-----AEGYR   77 (335)
T ss_dssp             HHHHHHHTTHHHHHHHHHHHHTTHHHHHTT--SEECHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEE-----TTEEE
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcChHHHHhc--CCCCHHHHHHHhCC---CchHHHHHHHHHHhcCCeEec-----CCEEe
Confidence            578999999999999999999999999984  79999999999999   999999999999999999874     68999


Q ss_pred             cchhc-cccccCcccChHHhHHhhcCchhhccCCCC
Q 040869           97 LTAAS-TLLIKDKPYCMSPTVSAFVDPLFVAPFQSL  131 (131)
Q Consensus        97 ~t~~s-~~L~~~~~~sl~~~~~~~~~~~~~~~w~~L  131 (131)
                      +|+.+ ++|++++|.++++++.+..++..+..|.+|
T Consensus        78 ~t~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l  113 (335)
T 2r3s_A           78 LTSDSAMFLDRQSKFYVGDAIEFLLSPMITNGFNDL  113 (335)
T ss_dssp             ECHHHHHHTCTTSTTCCGGGHHHHTCHHHHGGGTTH
T ss_pred             cCHHHHHHhccCCcHHHHHHHHHhcchhhHHHHHhH
Confidence            99999 689888888999999998766788888764

>1x19_A CRTF-related protein; methyltransferase, bacteriochllochlorophyll, BCHU, SAM, SAH, adenosylmethyonine, S-adenosylhomocysteine, ADO-Met; 2.27A {Chlorobium tepidum} PDB: 1x1a_A* 1x1b_A* 1x1c_A* 1x1d_A*

Probab=99.75  E-value=1.9e-18  Score=134.24  Aligned_cols=114  Identities=18%  Similarity=0.196  Sum_probs=99.7

Q ss_pred             CChHHHhHHHHHHHHHHH-hHHHHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceee
Q 040869            7 QGAKELLQGQAQLYKLMF-SHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNK   85 (131)
Q Consensus         7 ~~~~e~~~~~~~l~~~~~-~~~~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~   85 (131)
                      +.++|..++...++++++ +++.+++|+++++||||+.|++  +|+|++|||+++|+   +++.++|+||+|++.|+|++
T Consensus        22 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~lgif~~L~~--~~~t~~eLA~~~g~---~~~~l~rlLr~L~~~gll~~   96 (359)
T 1x19_A           22 MSNNDLLNYYHRANELVFKGLIEFSCMKAAIELDLFSHMAE--GPKDLATLAADTGS---VPPRLEMLLETLRQMRVINL   96 (359)
T ss_dssp             ECCCHHHHHHHHHHHHHTHHHHHHHHHHHHHHHTHHHHHTT--CCBCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEE
T ss_pred             CCccccCCcchHHHHHHHHHHHHHHHHHHHHHcCcHHHHcC--CCCCHHHHHHHhCc---ChHHHHHHHHHHHhCCCeEe
Confidence            345577788888999886 8999999999999999999984  79999999999999   99999999999999999998


Q ss_pred             cccCCCCcceecchh-ccccccCcc---cChHHhHHhhcCchhhccCCCC
Q 040869           86 TKVNGQEEAYGLTAA-STLLIKDKP---YCMSPTVSAFVDPLFVAPFQSL  131 (131)
Q Consensus        86 ~~~~~~~~~y~~t~~-s~~L~~~~~---~sl~~~~~~~~~~~~~~~w~~L  131 (131)
                      .     +++|++|+. +++|++++|   .++++++.+. .+..+.+|.+|
T Consensus        97 ~-----~~~y~~t~~~~~~l~~~~~~~~~~~~~~~~~~-~~~~~~~~~~L  140 (359)
T 1x19_A           97 E-----DGKWSLTEFADYMFSPTPKEPNLHQTPVAKAM-AFLADDFYMGL  140 (359)
T ss_dssp             E-----TTEEEECHHHHHHSSSSCSBTTBCCHHHHHHH-HHHHHHTGGGH
T ss_pred             e-----CCeEecCHHHHHHhcCCCCCccccHHHHHHHH-HHHHHHHHHHH
Confidence            7     469999996 568888888   7999999886 45678888753

>1qzz_A RDMB, aclacinomycin-10-hydroxylase; anthracycline, methyltransferase, polyketide, tailoring enzymes, structural proteomics in E spine; HET: SAM; 2.10A {Streptomyces purpurascens} SCOP: a.4.5.29 c.66.1.12 PDB: 1r00_A* 1xds_A* 1xdu_A*

Probab=99.74  E-value=2.3e-18  Score=133.85  Aligned_cols=109  Identities=22%  Similarity=0.203  Sum_probs=96.4

Q ss_pred             HHHHHHHHHHHhHHHHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCc
Q 040869           14 QGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEE   93 (131)
Q Consensus        14 ~~~~~l~~~~~~~~~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~   93 (131)
                      +....+++++.+++.+++|++++++|||+.|.  ++|+|++|||+++|+   ++..+.|+||+|++.|+|.+..    ++
T Consensus        15 ~~~~~l~~~~~~~~~~~~l~~~~~l~i~~~l~--~~~~t~~eLA~~~g~---~~~~l~r~Lr~L~~~Gll~~~~----~~   85 (374)
T 1qzz_A           15 QDLDVLLKNLGNLVTPMALRVAATLRLVDHLL--AGADTLAGLADRTDT---HPQALSRLVRHLTVVGVLEGGE----KQ   85 (374)
T ss_dssp             HHHHHHHHTTTCCHHHHHHHHHHHTTHHHHHH--TTCCSHHHHHHHHTC---CHHHHHHHHHHHHHTTSEECCC----C-
T ss_pred             hHHHHHHHHHHhhHHHHHHHHHHHcChHHHHh--CCCCCHHHHHHHhCc---CHHHHHHHHHHHhhCCCEEEeC----CC
Confidence            34567899999999999999999999999996  479999999999999   9999999999999999999865    56


Q ss_pred             --ceecchhccccccCcccChHHhHHhhcCchhh-ccCCCC
Q 040869           94 --AYGLTAASTLLIKDKPYCMSPTVSAFVDPLFV-APFQSL  131 (131)
Q Consensus        94 --~y~~t~~s~~L~~~~~~sl~~~~~~~~~~~~~-~~w~~L  131 (131)
                        .|.+|+.++.|++++|.++++++.+..++..| ..|.+|
T Consensus        86 ~~~y~~t~~s~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l  126 (374)
T 1qzz_A           86 GRPLRPTRLGMLLADGHPAQQRAWLDLNGAVSHADLAFTGL  126 (374)
T ss_dssp             CCCCEECTTGGGGSTTCTTCHHHHHCTTSHHHHHHGGGGGH
T ss_pred             CeEEEEChHHHhhcCCCcccHHHHHHHcCChhhHHHHHHHH
Confidence              99999999999998888999999887665667 777653

>3mcz_A O-methyltransferase; adomet_mtases, S-adenosylmethionine-dependent methyltransfer structural genomics, PSI-2; HET: MSE; 1.90A {Burkholderia thailandensis}

Probab=99.73  E-value=4e-18  Score=131.65  Aligned_cols=106  Identities=20%  Similarity=0.156  Sum_probs=92.6

Q ss_pred             HhHHHHHHHHHHHhHHHHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCC
Q 040869           12 LLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQ   91 (131)
Q Consensus        12 ~~~~~~~l~~~~~~~~~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~   91 (131)
                      +..| ..+++++.+++.+++|+++++||||++|.  + |+|++|||+++|+   +++.++|+||+|++.|+|++.     
T Consensus        22 l~~p-~~l~~~~~~~~~~~~l~~a~~lgif~~l~--~-~~t~~elA~~~~~---~~~~l~rlLr~L~~~gll~~~-----   89 (352)
T 3mcz_A           22 LTSV-VDLVKLSDQYRQSAILHYAVADKLFDLTQ--T-GRTPAEVAASFGM---VEGKAAILLHALAALGLLTKE-----   89 (352)
T ss_dssp             CCSH-HHHHHHHHTHHHHHHHHHHHHTTHHHHTT--S-CBCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEE-----
T ss_pred             CCCH-HHHHHHHHHHHHHHHHHHHHHCChHHHhC--C-CCCHHHHHHHhCc---ChHHHHHHHHHHHHCCCeEec-----
Confidence            3344 44999999999999999999999999997  3 9999999999999   999999999999999999987     


Q ss_pred             Ccceecchhcc-ccccCcccChHHhHHhhcCchhhccCCCC
Q 040869           92 EEAYGLTAAST-LLIKDKPYCMSPTVSAFVDPLFVAPFQSL  131 (131)
Q Consensus        92 ~~~y~~t~~s~-~L~~~~~~sl~~~~~~~~~~~~~~~w~~L  131 (131)
                      +++|.+|+.++ +|.+++|.++++++.+.  ...++.|.+|
T Consensus        90 ~~~y~~t~~s~~~l~~~~~~~~~~~~~~~--~~~~~~~~~l  128 (352)
T 3mcz_A           90 GDAFRNTALTERYLTTTSADYIGPIVEHQ--YLQWDNWPRL  128 (352)
T ss_dssp             TTEEEECHHHHHHHSTTCTTCCHHHHHHH--HTTTTTGGGH
T ss_pred             CCeeecCHHHHhhccCCChhhHHHHHHHh--HHHHHHHHHH
Confidence            47899999998 67778888999988764  3578888653

>1tw3_A COMT, carminomycin 4-O-methyltransferase; anthracycline, methylate, tailoring enzyme, polyketide, S-adenosyl-L-homocystein; HET: SAH ERT; 2.35A {Streptomyces peucetius} SCOP: a.4.5.29 c.66.1.12 PDB: 1tw2_A*

Probab=99.73  E-value=7.7e-18  Score=130.43  Aligned_cols=107  Identities=21%  Similarity=0.203  Sum_probs=96.5

Q ss_pred             HHHHHHHHHhHHHHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcce
Q 040869           16 QAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAY   95 (131)
Q Consensus        16 ~~~l~~~~~~~~~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y   95 (131)
                      ...+++++.+++.+++|++++++|||+.|.  ++|+|++|||+++|+   ++..+.|+||+|++.|+|.+..    +++|
T Consensus        20 ~~~~~~~~~~~~~~~~l~~~~~l~i~~~l~--~~~~t~~ela~~~~~---~~~~l~r~L~~L~~~g~~~~~~----~g~y   90 (360)
T 1tw3_A           20 ALRTLIRLGSLHTPMVVRTAATLRLVDHIL--AGARTVKALAARTDT---RPEALLRLIRHLVAIGLLEEDA----PGEF   90 (360)
T ss_dssp             HHHHHHHHHCSHHHHHHHHHHHTTHHHHHH--TTCCBHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEEE----TTEE
T ss_pred             hHHHHHHHHhHHHHHHHHHHHHhCHHHHHh--CCCCCHHHHHHHhCc---CHHHHHHHHHHHHHCCCEEecC----CCeE
Confidence            466789999999999999999999999996  479999999999999   9999999999999999999865    7899


Q ss_pred             ecchhccccccCcccChHHhHHhhcCch-hhccCCCC
Q 040869           96 GLTAASTLLIKDKPYCMSPTVSAFVDPL-FVAPFQSL  131 (131)
Q Consensus        96 ~~t~~s~~L~~~~~~sl~~~~~~~~~~~-~~~~w~~L  131 (131)
                      .+|+.++.|++++|.++++++.+..++. .+..|.+|
T Consensus        91 ~~t~~s~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~l  127 (360)
T 1tw3_A           91 VPTEVGELLADDHPAAQRAWHDLTQAVARADISFTRL  127 (360)
T ss_dssp             EECTTGGGGSTTSTTCHHHHTCTTSHHHHHGGGGGGH
T ss_pred             EeCHHHHHHhcCCchhHHHHHHHhcCchhHHHHHHHH
Confidence            9999999999998889999998876554 67888653

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

Probab=98.24  E-value=8.5e-07  Score=53.30  Aligned_cols=55  Identities=13%  Similarity=0.250  Sum_probs=47.3

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecc
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLT   98 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t   98 (131)
                      +..|.++|.+.+.++|..|||+++|+   +...+.|++..|...|++....    .|.|.++
T Consensus        12 ~~~IL~~L~~~~~~~s~~eLA~~lgl---sr~tv~~~l~~L~~~G~I~~~~----~G~y~lg   66 (67)
T 2heo_A           12 EQKILQVLSDDGGPVAIFQLVKKCQV---PKKTLNQVLYRLKKEDRVSSPS----PKYWSIG   66 (67)
T ss_dssp             HHHHHHHHHHHCSCEEHHHHHHHHCS---CHHHHHHHHHHHHHTTSEEEEE----TTEEEEC
T ss_pred             HHHHHHHHHHcCCCcCHHHHHHHHCc---CHHHHHHHHHHHHHCCcEecCC----CceEeeC
Confidence            55688888765578999999999999   9999999999999999987754    6778764

>3mq0_A Transcriptional repressor of the blcabc operon; helix-turn-helix, GAF fold, transcription repressor; 1.79A {Agrobacterium tumefaciens}

Probab=98.22  E-value=8.7e-07  Score=66.73  Aligned_cols=60  Identities=17%  Similarity=0.288  Sum_probs=51.0

Q ss_pred             hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcccc
Q 040869           38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLL  104 (131)
Q Consensus        38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L  104 (131)
                      +.|++.|...++++|+.|||+++|+   +...++|+|+.|+..|++.+++    +++|.+++....|
T Consensus        33 l~IL~~l~~~~~~ltl~eia~~lgl---~ksTv~RlL~tL~~~G~v~~~~----~~~Y~LG~~~~~l   92 (275)
T 3mq0_A           33 VRILDLVAGSPRDLTAAELTRFLDL---PKSSAHGLLAVMTELDLLARSA----DGTLRIGPHSLRW   92 (275)
T ss_dssp             HHHHHHHHHCSSCEEHHHHHHHHTC---C--CHHHHHHHHHHTTSEEECT----TSEEEECTHHHHH
T ss_pred             HHHHHHHhhCCCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEECC----CCcEEehHHHHHH
Confidence            5689999876678999999999999   9999999999999999999876    6789999865443

>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=97.97  E-value=4.3e-05  Score=48.33  Aligned_cols=63  Identities=14%  Similarity=0.295  Sum_probs=53.2

Q ss_pred             HHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhccc
Q 040869           30 MSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTL  103 (131)
Q Consensus        30 ~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~  103 (131)
                      .++..-.++.|+..| .  +++|..|||+.+|+   ++..+.|.|+.|...|++.+..     +.|.+|+.++.
T Consensus        26 ~~l~~~~r~~Il~~L-~--~~~~~~eLa~~l~i---s~~tv~~~L~~L~~~Glv~~~~-----g~y~l~~~g~~   88 (96)
T 1y0u_A           26 YAVTNPVRRKILRML-D--KGRSEEEIMQTLSL---SKKQLDYHLKVLEAGFCIERVG-----ERWVVTDAGKI   88 (96)
T ss_dssp             HHHSCHHHHHHHHHH-H--TTCCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEET-----TEEEECTTTCC
T ss_pred             HHhCCHHHHHHHHHH-c--CCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEEC-----CEEEECCCchH
Confidence            455556677889988 4  67999999999999   9999999999999999999763     58999887654

>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=97.96  E-value=9.1e-06  Score=60.07  Aligned_cols=58  Identities=16%  Similarity=0.282  Sum_probs=50.5

Q ss_pred             hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcc
Q 040869           38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAST  102 (131)
Q Consensus        38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~  102 (131)
                      +.|++.|.+.++++|+.|||+++|+   ++..++|+|+.|...|++.+..    .++|.+++...
T Consensus        11 l~iL~~l~~~~~~~~~~ela~~~gl---~~stv~r~l~~L~~~G~v~~~~----~~~Y~lg~~~~   68 (249)
T 1mkm_A           11 FEILDFIVKNPGDVSVSEIAEKFNM---SVSNAYKYMVVLEEKGFVLRKK----DKRYVPGYKLI   68 (249)
T ss_dssp             HHHHHHHHHCSSCBCHHHHHHHTTC---CHHHHHHHHHHHHHTTSEEECT----TSCEEECTHHH
T ss_pred             HHHHHHHHhCCCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCcEEECC----CCcEEECHHHH
Confidence            5678888765568999999999999   9999999999999999999874    68899998543

>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=97.95  E-value=1.7e-06  Score=64.60  Aligned_cols=61  Identities=20%  Similarity=0.265  Sum_probs=51.0

Q ss_pred             hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcccc
Q 040869           38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLL  104 (131)
Q Consensus        38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L  104 (131)
                      +.|++.|.+.++++|+.|||+++|+   ++..++|+|+.|+..|++.++..   .++|.+++....|
T Consensus         9 l~IL~~l~~~~~~lsl~eia~~lgl---~ksT~~RlL~tL~~~G~v~~~~~---~~~Y~lG~~~~~l   69 (260)
T 3r4k_A            9 LTLLTYFNHGRLEIGLSDLTRLSGM---NKATVYRLMSELQEAGFVEQVEG---ARSYRLGPQVLRL   69 (260)
T ss_dssp             HHHHTTCBTTBSEEEHHHHHHHHCS---CHHHHHHHHHHHHHTTSEEECSS---SSEEEECTTHHHH
T ss_pred             HHHHHHHhhCCCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEcCC---CCcEEcCHHHHHH
Confidence            4567777754578999999999999   99999999999999999998751   3899999865444

>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=97.95  E-value=6.4e-06  Score=60.70  Aligned_cols=61  Identities=15%  Similarity=0.208  Sum_probs=51.5

Q ss_pred             hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcccc
Q 040869           38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLL  104 (131)
Q Consensus        38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L  104 (131)
                      +.|++.|.+.++++|+.|||+++|+   ++..++|+|+.|...|++.+...   .++|.+++....|
T Consensus         9 l~iL~~l~~~~~~~s~~ela~~~gl---~~stv~r~l~~L~~~G~v~~~~~---~~~Y~lg~~~~~l   69 (241)
T 2xrn_A            9 ASIMRALGSHPHGLSLAAIAQLVGL---PRSTVQRIINALEEEFLVEALGP---AGGFRLGPALGQL   69 (241)
T ss_dssp             HHHHHHHHTCTTCEEHHHHHHHTTS---CHHHHHHHHHHHHTTTSEEECGG---GCEEEECSHHHHH
T ss_pred             HHHHHHHHhCCCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEeCC---CCeEEECHHHHHH
Confidence            5678888765568999999999999   99999999999999999998751   4789999865544

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

Probab=97.90  E-value=7e-06  Score=50.64  Aligned_cols=49  Identities=12%  Similarity=0.324  Sum_probs=42.9

Q ss_pred             HHhChHHHHHhCC-CCCCHHHHHhhc-----CCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           36 IELGIADIIHSHG-RAITLSELVSAL-----DIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        36 ~~L~ifd~l~~~~-~~~s~~eLA~~~-----~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      -+..|++.|.+.+ +++|+.||++.+     ++   +...++|.|+.|...|++.+..
T Consensus        18 ~r~~IL~~l~~~~~~~~s~~el~~~l~~~~~~i---s~~TVyR~L~~L~~~Glv~~~~   72 (83)
T 2fu4_A           18 PRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEI---GLATVYRVLNQFDDAGIVTRHN   72 (83)
T ss_dssp             HHHHHHHHHTSGGGSSBCHHHHHHHHHHTTCCC---CHHHHHHHHHHHHHHTSEEEEE
T ss_pred             HHHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCC---CHhhHHHHHHHHHHCCCeEEEe
Confidence            3556889997654 799999999999     88   9999999999999999999864

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

Probab=97.81  E-value=1.7e-05  Score=52.32  Aligned_cols=62  Identities=18%  Similarity=0.197  Sum_probs=53.5

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhc--CCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhccccc
Q 040869           36 IELGIADIIHSHGRAITLSELVSAL--DIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLI  105 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~--~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~  105 (131)
                      .+-.|++.|.+ .+++|+.+||+.+  |+   .+..+.+-|+.|...|++....    .+.|.+|+.++.+.
T Consensus        14 ~d~~IL~~L~~-~g~~s~~eLA~~l~~gi---S~~aVs~rL~~Le~~GLV~~~~----rg~Y~LT~~G~~~l   77 (111)
T 3b73_A           14 WDDRILEIIHE-EGNGSPKELEDRDEIRI---SKSSVSRRLKKLADHDLLQPLA----NGVYVITEEGEAYL   77 (111)
T ss_dssp             HHHHHHHHHHH-HSCBCHHHHHTSTTCCS---CHHHHHHHHHHHHHTTSEEECS----TTCEEECHHHHHHH
T ss_pred             HHHHHHHHHHH-cCCCCHHHHHHHHhcCC---CHHHHHHHHHHHHHCCCEEecC----CceEEECchHHHHH
Confidence            45678888875 3699999999999  99   9999999999999999999875    56999999998443

>2o0y_A Transcriptional regulator; ICLR-family, structural genomics, protein structure initiative, midwest center for structural genomics, MCSG; 2.00A {Rhodococcus SP}

Probab=97.79  E-value=8.2e-06  Score=60.78  Aligned_cols=58  Identities=17%  Similarity=0.322  Sum_probs=48.5

Q ss_pred             hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcc
Q 040869           38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAST  102 (131)
Q Consensus        38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~  102 (131)
                      +.|++.|...++++|+.|||+++|+   ++..++|+|+.|...|++.+..    .++|.+++...
T Consensus        26 l~iL~~l~~~~~~~~~~eia~~~gl---~kstv~r~l~tL~~~G~v~~~~----~~~Y~lg~~~~   83 (260)
T 2o0y_A           26 IDLLELFDAAHPTRSLKELVEGTKL---PKTTVVRLVATMCARSVLTSRA----DGSYSLGPEML   83 (260)
T ss_dssp             HHHHTTCBTTBSSBCHHHHHHHHCC---CHHHHHHHHHHHHHTTSEEECT----TSCEEECHHHH
T ss_pred             HHHHHHHhhCCCCcCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEECC----CCeEEecHHHH
Confidence            4466666544578999999999999   9999999999999999999875    44899988643

>2g7u_A Transcriptional regulator; ICLR family, structural genomics, PSI, protein structure initiative, midwest center for struc genomics; 2.30A {Rhodococcus SP}

Probab=97.75  E-value=1.2e-05  Score=59.62  Aligned_cols=60  Identities=13%  Similarity=0.149  Sum_probs=50.6

Q ss_pred             hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhccccc
Q 040869           38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLI  105 (131)
Q Consensus        38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~  105 (131)
                      +.|++.|.+.++++|+.|||+++|+   ++..++|+|+.|...|++.+.     +++|.+++....|.
T Consensus        17 l~iL~~l~~~~~~~~~~eia~~~gl---~~stv~r~l~~L~~~G~v~~~-----~~~Y~Lg~~~~~l~   76 (257)
T 2g7u_A           17 FAVLLAFDAQRPNPTLAELATEAGL---SRPAVRRILLTLQKLGYVAGS-----GGRWSLTPRVLSIG   76 (257)
T ss_dssp             HHHHHTCSSSCSSCBHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEE-----TTEEEECGGGHHHH
T ss_pred             HHHHHHHHhCCCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEeC-----CCEEEEcHHHHHHH
Confidence            4567777654578999999999999   999999999999999999986     58899998754443

>2ia2_A Putative transcriptional regulator; SAD, PSI-2, structural genomics, structure initiative, midwest center for structural genomic transcription; 2.10A {Rhodococcus SP}

Probab=97.72  E-value=1.2e-05  Score=60.04  Aligned_cols=59  Identities=22%  Similarity=0.241  Sum_probs=50.0

Q ss_pred             hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcccc
Q 040869           38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLL  104 (131)
Q Consensus        38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L  104 (131)
                      +.|++.|...++++|+.|||+++|+   +...++|+|+.|...|++.+.     +++|.+++....|
T Consensus        24 l~iL~~l~~~~~~~~~~eia~~~gl---~~stv~r~l~tL~~~G~v~~~-----~~~Y~Lg~~~~~l   82 (265)
T 2ia2_A           24 LAVIRCFDHRNQRRTLSDVARATDL---TRATARRFLLTLVELGYVATD-----GSAFWLTPRVLEL   82 (265)
T ss_dssp             HHHHHTCCSSCSSEEHHHHHHHHTC---CHHHHHHHHHHHHHHTSEEES-----SSEEEECGGGGGT
T ss_pred             HHHHHHHHhCCCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEec-----CCEEEEcHHHHHH
Confidence            4567777654578999999999999   999999999999999999986     5889999865444

>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=97.63  E-value=6.2e-05  Score=49.80  Aligned_cols=68  Identities=13%  Similarity=0.162  Sum_probs=52.1

Q ss_pred             HHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchh
Q 040869           28 SSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAA  100 (131)
Q Consensus        28 ~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~  100 (131)
                      ...+|.-..++.|+..|.. .+++|+.|||+.+|+   ++..+.|.|+.|...|++..... +....|.+++-
T Consensus        35 ~~~al~~~~rl~IL~~L~~-~~~~s~~eLa~~l~i---s~stvs~~L~~L~~~Glv~~~~~-gr~~~y~l~~~  102 (122)
T 1u2w_A           35 ILKAIADENRAKITYALCQ-DEELCVCDIANILGV---TIANASHHLRTLYKQGVVNFRKE-GKLALYSLGDE  102 (122)
T ss_dssp             HHHHHHSHHHHHHHHHHHH-SSCEEHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEC-----CCEEEESCH
T ss_pred             HHHHhCCHHHHHHHHHHHH-CCCcCHHHHHHHHCc---CHHHHHHHHHHHHHCCCeEEEEE-CCEEEEEECHH
Confidence            3455556678889999975 478999999999999   99999999999999999987641 00124776654

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

Probab=97.62  E-value=5e-05  Score=47.67  Aligned_cols=65  Identities=9%  Similarity=0.137  Sum_probs=50.4

Q ss_pred             HHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchh
Q 040869           31 SLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAA  100 (131)
Q Consensus        31 aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~  100 (131)
                      ++..-.++.|+..|.. ++++|..|||+.+|+   ++..+.|.++.|...|++..... +....|.+|+-
T Consensus        20 ~l~~~~~~~il~~l~~-~~~~s~~ela~~l~i---s~~tvs~~l~~L~~~glv~~~~~-~r~~~y~l~~~   84 (99)
T 3cuo_A           20 AMSHPKRLLILCMLSG-SPGTSAGELTRITGL---SASATSQHLARMRDEGLIDSQRD-AQRILYSIKNE   84 (99)
T ss_dssp             HHCSHHHHHHHHHHTT-CCSEEHHHHHHHHCC---CHHHHHHHHHHHHHTTSEEEEEC-SSCEEEEECCH
T ss_pred             HhCChHHHHHHHHHHh-CCCcCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEEec-CCEEEEEEChH
Confidence            4445567788888874 568999999999999   99999999999999999987651 00223666654

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

Probab=97.62  E-value=5.8e-05  Score=48.69  Aligned_cols=65  Identities=18%  Similarity=0.194  Sum_probs=50.2

Q ss_pred             HHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcc
Q 040869           32 LKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAST  102 (131)
Q Consensus        32 L~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~  102 (131)
                      +.-..++.|+..|.  .+++|..|||+.+|+   ++..+.|.++.|...|++..... +....|.+|+.+.
T Consensus        18 l~~~~r~~IL~~L~--~~~~~~~ela~~l~i---s~~tv~~~l~~L~~~gli~~~~~-gr~~~y~l~~~~~   82 (114)
T 2oqg_A           18 LSDETRWEILTELG--RADQSASSLATRLPV---SRQAIAKHLNALQACGLVESVKV-GREIRYRALGAEL   82 (114)
T ss_dssp             TTCHHHHHHHHHHH--HSCBCHHHHHHHSSS---CHHHHHHHHHHHHHTTSEEEEEE-TTEEEEEECSHHH
T ss_pred             hCChHHHHHHHHHH--cCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCeeEEec-CCEEEEEechHHH
Confidence            33345677888884  368999999999999   99999999999999999987641 0012388888664

>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=97.59  E-value=0.00011  Score=46.77  Aligned_cols=64  Identities=17%  Similarity=0.197  Sum_probs=49.6

Q ss_pred             HHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869           30 MSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA   99 (131)
Q Consensus        30 ~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~   99 (131)
                      .+|.--.++.|...|.  .++.|+.|||+.+|+   ++..+.+.|+.|...|++..... +....|.+|+
T Consensus        18 ~~l~~~~r~~Il~~L~--~~~~~~~ela~~l~i---s~~tvs~~L~~L~~~Glv~~~~~-g~~~~y~l~~   81 (102)
T 3pqk_A           18 KTLSHPVRLMLVCTLV--EGEFSVGELEQQIGI---GQPTLSQQLGVLRESGIVETRRN-IKQIFYRLTE   81 (102)
T ss_dssp             HHHCSHHHHHHHHHHH--TCCBCHHHHHHHHTC---CTTHHHHHHHHHHHTTSEEEECS-SSCCEEEECS
T ss_pred             HHcCCHHHHHHHHHHH--hCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCeEEEEe-CCEEEEEECc
Confidence            3455556777888886  378999999999999   99999999999999999987651 0023466665

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

Probab=97.53  E-value=6e-05  Score=47.64  Aligned_cols=65  Identities=18%  Similarity=0.290  Sum_probs=50.5

Q ss_pred             HHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchh
Q 040869           30 MSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAA  100 (131)
Q Consensus        30 ~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~  100 (131)
                      .++.--.++.|+..|.+  +++|+.|||+.+|+   ++..+.|.|+.|...|++..... +....|.+++-
T Consensus        18 ~~l~~~~r~~Il~~L~~--~~~~~~ela~~l~i---s~~tvs~~L~~L~~~Glv~~~~~-g~~~~y~l~~~   82 (98)
T 3jth_A           18 KAMANERRLQILCMLHN--QELSVGELCAKLQL---SQSALSQHLAWLRRDGLVTTRKE-AQTVYYTLKSE   82 (98)
T ss_dssp             HHHCSHHHHHHHHHTTT--SCEEHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEECC-TTCCEEEECCH
T ss_pred             HHcCCHHHHHHHHHHhc--CCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCeEEEEe-CCEEEEEECHH
Confidence            44555667788888874  78999999999999   99999999999999999987651 00123666553

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

Probab=97.50  E-value=8.8e-05  Score=48.69  Aligned_cols=67  Identities=15%  Similarity=0.224  Sum_probs=53.8

Q ss_pred             HHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhc
Q 040869           29 SMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAS  101 (131)
Q Consensus        29 ~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s  101 (131)
                      .++|.--.++.|+..|.  .+++|+.|||+.+|+   +...+.+.|+.|...|++..... +....|.+++-.
T Consensus        12 ~~al~~~~R~~Il~~L~--~~~~~~~eLa~~l~i---s~~tvs~hL~~L~~~GlV~~~~~-gr~~~y~l~~~~   78 (118)
T 3f6o_A           12 FQALADPTRRAVLGRLS--RGPATVSELAKPFDM---ALPSFMKHIHFLEDSGWIRTHKQ-GRVRTCAIEKEP   78 (118)
T ss_dssp             HHHHTSHHHHHHHHHHH--TCCEEHHHHHTTCCS---CHHHHHHHHHHHHHTTSEEEEEE-TTEEEEEECSHH
T ss_pred             HHHhCCHHHHHHHHHHH--hCCCCHHHHHHHhCc---CHHHHHHHHHHHHHCCCeEEEec-CCEEEEEECHHH
Confidence            45666678888999998  478999999999999   99999999999999999987641 002347777754

>2o03_A Probable zinc uptake regulation protein FURB; DNA-binding, helix-turn-helix, zinc binding, GE regulation; 2.70A {Mycobacterium tuberculosis}

Probab=97.50  E-value=0.00015  Score=48.59  Aligned_cols=61  Identities=16%  Similarity=0.247  Sum_probs=49.3

Q ss_pred             HHHHhChHHHHHhCCCCCCHHHHHhhc-----CCCCCCcchHHHHHHHhhcCCceeecccCCCCcceec
Q 040869           34 CAIELGIADIIHSHGRAITLSELVSAL-----DIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGL   97 (131)
Q Consensus        34 ~a~~L~ifd~l~~~~~~~s~~eLA~~~-----~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~   97 (131)
                      +..+..|++.|.+.++++|++||.+.+     ++   +..++||.|+.|+..|++.+....++..+|..
T Consensus        10 T~qR~~Il~~l~~~~~~~sa~ei~~~l~~~~~~i---s~~TVYR~L~~L~e~Glv~~~~~~~~~~~y~~   75 (131)
T 2o03_A           10 TRQRAAISTLLETLDDFRSAQELHDELRRRGENI---GLTTVYRTLQSMASSGLVDTLHTDTGESVYRR   75 (131)
T ss_dssp             HHHHHHHHHHHHHCCSCEEHHHHHHHHHHTTCCC---CHHHHHHHHHHHHTTTSEEEEECTTSCEEEEE
T ss_pred             CHHHHHHHHHHHhCCCCCCHHHHHHHHHHhCCCC---CHhhHHHHHHHHHHCCCEEEEEeCCCceEEEe
Confidence            456677899998767899999999998     67   89999999999999999998753223345754

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

Probab=97.49  E-value=0.00014  Score=48.38  Aligned_cols=48  Identities=13%  Similarity=0.128  Sum_probs=39.2

Q ss_pred             CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchh
Q 040869           48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAA  100 (131)
Q Consensus        48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~  100 (131)
                      ++++|..|||+++|+   ++..++++|+.|...|++.....  ..|.|.++.-
T Consensus        24 ~~~~s~~ela~~~~i---~~~~v~~il~~L~~~Glv~~~~g--~~ggy~L~~~   71 (129)
T 2y75_A           24 EGPTSLKSIAQTNNL---SEHYLEQLVSPLRNAGLVKSIRG--AYGGYVLGSE   71 (129)
T ss_dssp             SCCBCHHHHHHHTTS---CHHHHHHHHHHHHHTTSEEEC------CCEEESSC
T ss_pred             CCcCCHHHHHHHHCc---CHHHHHHHHHHHHHCCceEecCC--CCCceEeCCC
Confidence            478999999999999   99999999999999999987631  0367877653

>2fe3_A Peroxide operon regulator; oxidative stress regulator, DNA binding protein; 1.75A {Bacillus subtilis} PDB: 3f8n_A 2rgv_A*

Probab=97.47  E-value=0.00021  Score=48.69  Aligned_cols=62  Identities=10%  Similarity=0.189  Sum_probs=48.8

Q ss_pred             HHHHhChHHHHHhCCCCCCHHHHHhhc-----CCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecc
Q 040869           34 CAIELGIADIIHSHGRAITLSELVSAL-----DIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLT   98 (131)
Q Consensus        34 ~a~~L~ifd~l~~~~~~~s~~eLA~~~-----~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t   98 (131)
                      +..+..|++.|.+.++++|++||.+.+     ++   +..++||.|+.|+..|++.+....++..+|..+
T Consensus        21 T~qR~~Il~~L~~~~~~~sa~ei~~~l~~~~~~i---s~aTVYR~L~~L~e~Glv~~~~~~~~~~~Y~~~   87 (145)
T 2fe3_A           21 TPQRHAILEYLVNSMAHPTADDIYKALEGKFPNM---SVATVYNNLRVFRESGLVKELTYGDASSRFDFV   87 (145)
T ss_dssp             CHHHHHHHHHHHHCSSCCCHHHHHHHHGGGCTTC---CHHHHHHHHHHHHHTTSEEEECCTTSCCEEEEC
T ss_pred             CHHHHHHHHHHHhCCCCCCHHHHHHHHHHhCCCC---ChhhHHHHHHHHHHCCCEEEEeeCCCceEEECC
Confidence            345566899998767899999999998     56   889999999999999999986532223457653

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

Probab=97.43  E-value=0.00015  Score=46.98  Aligned_cols=52  Identities=13%  Similarity=0.155  Sum_probs=43.3

Q ss_pred             HHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           31 SLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        31 aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      +|.--.++.|+..|.  .+++|+.|||+.+|+   ++..+.|.|+.|...|++....
T Consensus        21 al~~~~r~~IL~~L~--~~~~s~~eLa~~lgi---s~stvs~~L~~L~~~GlV~~~~   72 (108)
T 2kko_A           21 ALANGRRLQILDLLA--QGERAVEAIATATGM---NLTTASANLQALKSGGLVEARR   72 (108)
T ss_dssp             HHTTSTTHHHHHHHT--TCCEEHHHHHHHHTC---CHHHHHHHHHHHHHHTSEEEEE
T ss_pred             HhCCHHHHHHHHHHH--cCCcCHHHHHHHHCc---CHHHHHHHHHHHHHCCCeEEEE
Confidence            333445566777786  378999999999999   9999999999999999998764

>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=97.41  E-value=0.00014  Score=46.77  Aligned_cols=52  Identities=10%  Similarity=0.220  Sum_probs=44.2

Q ss_pred             HHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           31 SLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        31 aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      ++.--.++.|+..|..  ++.|+.|||+.+|+   ++..+.+.|+.|...|++....
T Consensus        22 ~l~~~~r~~IL~~L~~--~~~~~~ela~~l~i---s~stvs~~L~~L~~~Glv~~~~   73 (106)
T 1r1u_A           22 ALGDYNRIRIMELLSV--SEASVGHISHQLNL---SQSNVSHQLKLLKSVHLVKAKR   73 (106)
T ss_dssp             HTCSHHHHHHHHHHHH--CCBCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HhCCHHHHHHHHHHHh--CCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCeEEEE
Confidence            4444566778888873  68999999999999   9999999999999999998764

>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=97.39  E-value=0.00016  Score=48.48  Aligned_cols=51  Identities=14%  Similarity=0.154  Sum_probs=45.6

Q ss_pred             CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhccccc
Q 040869           48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLI  105 (131)
Q Consensus        48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~  105 (131)
                      ++++|..+||+.+|+   ++..+.|+++.|...|++....    .+.|.+|+.++.+.
T Consensus        20 ~~~~~~~ela~~l~v---s~~tvs~~l~~Le~~Glv~r~~----~~~~~LT~~g~~~~   70 (142)
T 1on2_A           20 KGYARVSDIAEALAV---HPSSVTKMVQKLDKDEYLIYEK----YRGLVLTSKGKKIG   70 (142)
T ss_dssp             HSSCCHHHHHHHHTS---CHHHHHHHHHHHHHTTSEEEET----TTEEEECHHHHHHH
T ss_pred             cCCCCHHHHHHHhCC---CHHHHHHHHHHHHHCCCEEEee----CceEEEchhHHHHH
Confidence            368999999999999   9999999999999999999875    57899999887554

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

Probab=97.38  E-value=0.00016  Score=44.57  Aligned_cols=46  Identities=13%  Similarity=0.242  Sum_probs=40.2

Q ss_pred             ChHHHHHhC-----CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           39 GIADIIHSH-----GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        39 ~ifd~l~~~-----~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      .|++.|.+.     |+|.|+.|||+.+|+   .+..++|-|..|...|++....
T Consensus         8 ~IL~~I~~~i~~~~g~~psv~EIa~~lgv---S~~TVrr~L~~Le~kG~I~R~~   58 (77)
T 2jt1_A            8 KIISIVQERQNMDDGAPVKTRDIADAAGL---SIYQVRLYLEQLHDVGVLEKVN   58 (77)
T ss_dssp             HHHHHHHHHHHHHTTSCEEHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEES
T ss_pred             HHHHHHHHHHhhccCCCcCHHHHHHHHCC---CHHHHHHHHHHHHHCCcEEecC
Confidence            356666554     689999999999999   8899999999999999999875

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

Probab=97.38  E-value=8.9e-05  Score=46.50  Aligned_cols=70  Identities=20%  Similarity=0.225  Sum_probs=54.4

Q ss_pred             HHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhccc
Q 040869           30 MSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTL  103 (131)
Q Consensus        30 ~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~  103 (131)
                      .++....++.|+..|.. .+++|..|||+.+|+   ++..+.|.++.|...|++...... ++ ...|.+|+.+..
T Consensus        11 ~~l~~~~~~~iL~~L~~-~~~~~~~ela~~l~i---s~~tvs~~l~~L~~~gli~~~~~~~~~r~~~~~lt~~g~~   82 (100)
T 1ub9_A           11 HILGNPVRLGIMIFLLP-RRKAPFSQIQKVLDL---TPGNLDSHIRVLERNGLVKTYKVIADRPRTVVEITDFGME   82 (100)
T ss_dssp             HHHHSHHHHHHHHHHHH-HSEEEHHHHHHHTTC---CHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECHHHHH
T ss_pred             cccCChHHHHHHHHHHh-cCCcCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEEecCCCcceEEEEECHHHHH
Confidence            45566677888888864 368999999999999   999999999999999999854311 11 245888888753

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

Probab=97.36  E-value=0.00033  Score=42.89  Aligned_cols=45  Identities=13%  Similarity=0.158  Sum_probs=39.4

Q ss_pred             hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      ..|++.|.+ .+++|..|||+.+|+   ++..+.|.|+.|...|++...
T Consensus         3 ~~Il~~L~~-~~~~s~~eLa~~lgv---s~~tv~r~L~~L~~~GlI~~~   47 (81)
T 2htj_A            3 NEILEFLNR-HNGGKTAEIAEALAV---TDYQARYYLLLLEKAGMVQRS   47 (81)
T ss_dssp             HHHHHHHHH-SCCCCHHHHHHHHTS---CHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHH-cCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEe
Confidence            357777875 368999999999999   999999999999999999854

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

Probab=97.30  E-value=0.00016  Score=53.57  Aligned_cols=63  Identities=14%  Similarity=0.196  Sum_probs=52.9

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhccccc
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLI  105 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~  105 (131)
                      .++.|...|.+ .+++|..|||+++|+   ++..+.|+++.|...|++.+...   ...|.+|+.++.+.
T Consensus       153 ~~~~IL~~L~~-~~~~s~~eLA~~lgl---sksTv~r~L~~Le~~GlV~r~~r---~~~~~LT~~G~~l~  215 (244)
T 2wte_A          153 EEMKLLNVLYE-TKGTGITELAKMLDK---SEKTLINKIAELKKFGILTQKGK---DRKVELNELGLNVI  215 (244)
T ss_dssp             HHHHHHHHHHH-HTCBCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEETT---TTEEEECHHHHHHH
T ss_pred             HHHHHHHHHHH-cCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEeCC---ccEEEECHHHHHHH
Confidence            45567777764 368999999999999   99999999999999999998642   57899999998664

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

Probab=97.29  E-value=0.00019  Score=47.52  Aligned_cols=49  Identities=12%  Similarity=0.239  Sum_probs=42.5

Q ss_pred             HHhChHHHHHhCCCC-CCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           36 IELGIADIIHSHGRA-ITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~-~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      .+..|+..|.+.++| +|+.|||+++++   +...++|.|+.|...|++.+..
T Consensus        27 ~e~~il~~L~~~~~~~~t~~eLa~~l~~---s~sTV~r~L~~L~~~GlV~r~~   76 (123)
T 3r0a_A           27 ADLNVMKSFLNEPDRWIDTDALSKSLKL---DVSTVQRSVKKLHEKEILQRSQ   76 (123)
T ss_dssp             HHHHHHHHHHHSTTCCEEHHHHHHHHTS---CHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHHHCCCCCcCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEeeC
Confidence            355677778766677 999999999999   9999999999999999998753

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

Probab=97.26  E-value=0.001  Score=44.09  Aligned_cols=68  Identities=15%  Similarity=0.139  Sum_probs=48.7

Q ss_pred             HHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhcccccc
Q 040869           35 AIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIK  106 (131)
Q Consensus        35 a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~  106 (131)
                      ..++.|+..|... +++|..|||+.+++   ++..+.|+++.|...|++...... |+ ...+.+|+.++.+..
T Consensus        37 ~~~~~vL~~l~~~-~~~t~~eLa~~l~~---~~~tvs~~l~~L~~~Glv~r~~~~~DrR~~~~~LT~~G~~~~~  106 (142)
T 3ech_A           37 PPDVHVLKLIDEQ-RGLNLQDLGRQMCR---DKALITRKIRELEGRNLVRRERNPSDQRSFQLFLTDEGLAIHL  106 (142)
T ss_dssp             HHHHHHHHHHHHT-TTCCHHHHHHHHC------CHHHHHHHHHHHTTSEEC----------CCEECHHHHHHHH
T ss_pred             HHHHHHHHHHHhC-CCcCHHHHHHHhCC---CHHHHHHHHHHHHHCCCEeeccCCCCCCeeeeEECHHHHHHHH
Confidence            4566688888763 58999999999999   999999999999999999986421 11 134789998886654

>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=97.25  E-value=0.00033  Score=43.35  Aligned_cols=61  Identities=10%  Similarity=0.114  Sum_probs=49.2

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcc-hHHHHHHHhhcCCceeecccCCCCcceecchhcc
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTT-GLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAST  102 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~-~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~  102 (131)
                      .+=.|.+.|.. .+|.|+.+||+.+|+   .+. .++|.|..|...|++.....  |.-.|.+|+.++
T Consensus        12 ~~~~IL~~Lk~-~g~~ta~eiA~~Lgi---t~~~aVr~hL~~Le~eGlV~~~~~--gRP~w~LT~~g~   73 (79)
T 1xmk_A           12 IKEKICDYLFN-VSDSSALNLAKNIGL---TKARDINAVLIDMERQGDVYRQGT--TPPIWHLTDKKR   73 (79)
T ss_dssp             HHHHHHHHHHH-TCCEEHHHHHHHHCG---GGHHHHHHHHHHHHHTTSEEEECS--SSCEEEECHHHH
T ss_pred             HHHHHHHHHHH-cCCcCHHHHHHHcCC---CcHHHHHHHHHHHHHCCCEEecCC--CCCCeEeCHhHH
Confidence            34467778876 469999999999999   898 99999999999999986531  133788888765

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

Probab=97.23  E-value=0.00039  Score=46.84  Aligned_cols=60  Identities=15%  Similarity=0.337  Sum_probs=47.1

Q ss_pred             HHHhChHHHHHhCC-CCCCHHHHHhhc-----CCCCCCcchHHHHHHHhhcCCceeecccCCCCcceec
Q 040869           35 AIELGIADIIHSHG-RAITLSELVSAL-----DIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGL   97 (131)
Q Consensus        35 a~~L~ifd~l~~~~-~~~s~~eLA~~~-----~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~   97 (131)
                      ..+..|++.|.+.+ +++|++||.+.+     ++   +..++||.|+.|+..|++.+....++..+|..
T Consensus        18 ~qR~~Il~~L~~~~~~~~sa~ei~~~l~~~~~~i---s~aTVYR~L~~L~e~Glv~~~~~~~~~~~Y~~   83 (136)
T 1mzb_A           18 LPRVKILQMLDSAEQRHMSAEDVYKALMEAGEDV---GLATVYRVLTQFEAAGLVVRHNFDGGHAVFEL   83 (136)
T ss_dssp             HHHHHHHHHHHCC-CCSBCHHHHHHHHHHTTCCC---CHHHHHHHHHHHHHHTSEEEECSSSSSCEEEE
T ss_pred             HHHHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCC---CHHHHHHHHHHHHHCCcEEEEEeCCCceEEEe
Confidence            34566899998666 799999999998     56   88999999999999999998653222345764

>2xig_A Ferric uptake regulation protein; hpfur, transcription, homeostasis; HET: CIT; 1.85A {Helicobacter pylori}

Probab=97.23  E-value=0.00045  Score=47.36  Aligned_cols=61  Identities=8%  Similarity=0.296  Sum_probs=48.9

Q ss_pred             HHHHhChHHHHHhCCCCCCHHHHHhhc-----CCCCCCcchHHHHHHHhhcCCceeecccCCCCcceec
Q 040869           34 CAIELGIADIIHSHGRAITLSELVSAL-----DIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGL   97 (131)
Q Consensus        34 ~a~~L~ifd~l~~~~~~~s~~eLA~~~-----~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~   97 (131)
                      +..+.-|++.|.+.++++|++||.+.+     ++   +..++||.|+.|+..|++.+....++..+|..
T Consensus        26 T~qR~~IL~~l~~~~~~~sa~ei~~~l~~~~~~i---s~aTVYR~L~~L~e~Glv~~~~~~~~~~~Y~~   91 (150)
T 2xig_A           26 SKQREEVVSVLYRSGTHLSPEEITHSIRQKDKNT---SISSVYRILNFLEKENFISVLETSKSGRRYEI   91 (150)
T ss_dssp             HHHHHHHHHHHHHCSSCBCHHHHHHHHHHHSTTC---CHHHHHHHHHHHHHTTSEEEEEETTTEEEEEE
T ss_pred             CHHHHHHHHHHHhCCCCCCHHHHHHHHHHhCCCC---CHhhHHHHHHHHHHCCcEEEEEeCCCceEEEe
Confidence            556677899998767899999999998     56   88999999999999999998653222345765

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

Probab=97.22  E-value=0.00019  Score=49.38  Aligned_cols=69  Identities=12%  Similarity=0.160  Sum_probs=56.0

Q ss_pred             HHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcc
Q 040869           28 SSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAST  102 (131)
Q Consensus        28 ~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~  102 (131)
                      ..++|.--.++.|+..|.  .+++|+.|||+.+|+   +...+.+.|+.|...|++..... +....|.+|+...
T Consensus        51 ~l~aL~~p~R~~IL~~L~--~~~~t~~eLa~~lgl---s~stvs~hL~~L~~aGlV~~~~~-Gr~~~y~lt~~~~  119 (151)
T 3f6v_A           51 QLEVAAEPTRRRLVQLLT--SGEQTVNNLAAHFPA---SRSAISQHLRVLTEAGLVTPRKD-GRFRYYRLDPQGL  119 (151)
T ss_dssp             HHHHHTSHHHHHHHHHGG--GCCEEHHHHHTTSSS---CHHHHHHHHHHHHHTTSEEEEEE-TTEEEEEECHHHH
T ss_pred             HHHHhCCHHHHHHHHHHH--hCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEEec-CCEEEEEEChHHH
Confidence            456777788899999997  378999999999999   99999999999999999987651 0012488887653

>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=97.20  E-value=0.00047  Score=44.40  Aligned_cols=62  Identities=21%  Similarity=0.154  Sum_probs=48.5

Q ss_pred             ChHHHHHhCCCCCCHHHHHhhc-CCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhccccc
Q 040869           39 GIADIIHSHGRAITLSELVSAL-DIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLI  105 (131)
Q Consensus        39 ~ifd~l~~~~~~~s~~eLA~~~-~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~  105 (131)
                      .|...|.  .++++..||++.+ |+   ++..+.+.|+.|...|++.+.... ++ .-.|.+|+.++.+.
T Consensus        18 ~IL~~L~--~~~~~~~eLa~~l~~i---s~~tls~~L~~Le~~GlI~r~~~~~d~r~~~y~LT~~G~~l~   82 (107)
T 2hzt_A           18 VILXHLT--HGKKRTSELKRLMPNI---TQKMLTQQLRELEADGVINRIVYNQVPPKVEYELSEYGRSLE   82 (107)
T ss_dssp             HHHHHHT--TCCBCHHHHHHHCTTS---CHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECTTGGGGH
T ss_pred             HHHHHHH--hCCCCHHHHHHHhcCC---CHHHHHHHHHHHHHCCCEEEeecCCCCCeEEEEECccHHHHH
Confidence            3444554  3689999999999 99   999999999999999999976422 11 13599999987654

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

Probab=97.19  E-value=0.00054  Score=42.23  Aligned_cols=44  Identities=7%  Similarity=0.114  Sum_probs=39.7

Q ss_pred             ChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           39 GIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        39 ~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      .|.+.|.+ .+.++++|||+.+++   ++..++|.|..|...|++.+.
T Consensus         6 ~Il~~L~~-~g~vsv~eLa~~l~V---S~~TIRrdL~~Le~~G~l~R~   49 (78)
T 1xn7_A            6 QVRDLLAL-RGRMEAAQISQTLNT---PQPMINAMLQQLESMGKAVRI   49 (78)
T ss_dssp             HHHHHHHH-SCSBCHHHHHHHTTC---CHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHH-cCCCcHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEe
Confidence            36677775 478999999999999   999999999999999999987

>3mwm_A ZUR, putative metal uptake regulation protein; FUR, regulatory metal, graded transcription regulation, transcription; 2.40A {Streptomyces coelicolor}

Probab=97.18  E-value=0.00047  Score=46.70  Aligned_cols=62  Identities=13%  Similarity=0.174  Sum_probs=48.9

Q ss_pred             HHHHhChHHHHHhCCCCCCHHHHHhhc-----CCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecc
Q 040869           34 CAIELGIADIIHSHGRAITLSELVSAL-----DIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLT   98 (131)
Q Consensus        34 ~a~~L~ifd~l~~~~~~~s~~eLA~~~-----~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t   98 (131)
                      +..+..|++.|.+.++++|++||.+.+     ++   +..++||.|..|+..|++.+....++..+|...
T Consensus        13 T~qR~~Il~~L~~~~~h~sa~eI~~~l~~~~~~i---s~aTVYR~L~~L~e~Glv~~~~~~~g~~~Y~~~   79 (139)
T 3mwm_A           13 TRQRAAVSAALQEVEEFRSAQELHDMLKHKGDAV---GLTTVYRTLQSLADAGEVDVLRTAEGESVYRRC   79 (139)
T ss_dssp             HHHHHHHHHHHTTCSSCEEHHHHHHHHHHTTCCC---CHHHHHHHHHHHHHTTSSEEEECTTSCEEEECC
T ss_pred             CHHHHHHHHHHHhCCCCCCHHHHHHHHHHhCCCC---CHHHHHHHHHHHHHCCCEEEEEcCCCceEEEEC
Confidence            445677899998766899999999988     45   889999999999999999986532233457654

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

Probab=97.17  E-value=0.00028  Score=47.39  Aligned_cols=70  Identities=9%  Similarity=0.114  Sum_probs=51.3

Q ss_pred             HHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-CcceecchhccccccC
Q 040869           35 AIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIKD  107 (131)
Q Consensus        35 a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~~  107 (131)
                      ..++.|...|...++++|..|||+.+++   ++..+.|+++.|...|++...... |. .-.+.+|+.++.+...
T Consensus        39 ~~q~~vL~~l~~~~~~~t~~eLa~~l~i---~~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~~~LT~~G~~~~~~  110 (150)
T 3fm5_A           39 VRSYSVLVLACEQAEGVNQRGVAATMGL---DPSQIVGLVDELEERGLVVRTLDPSDRRNKLIAATEEGRRLRDD  110 (150)
T ss_dssp             HHHHHHHHHHHHSTTCCCSHHHHHHHTC---CHHHHHHHHHHHHTTTSEEC-----------CEECHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCcCHHHHHHHHCC---CHhHHHHHHHHHHHCCCEEeeCCccccchheeeECHHHHHHHHH
Confidence            3455577777655678999999999999   999999999999999999976421 11 1238899998866543

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

Probab=97.14  E-value=0.00041  Score=46.16  Aligned_cols=51  Identities=20%  Similarity=0.290  Sum_probs=44.8

Q ss_pred             CCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhccccc
Q 040869           47 HGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLI  105 (131)
Q Consensus        47 ~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~  105 (131)
                      .++++|..+||+.+++   ++..+.|+++.|...|++...     .+.|.+|+.++.+.
T Consensus        28 ~~~~~s~~ela~~l~i---s~~tv~~~l~~Le~~Gli~r~-----~~~~~Lt~~g~~~~   78 (139)
T 2x4h_A           28 SGEGAKINRIAKDLKI---APSSVFEEVSHLEEKGLVKKK-----EDGVWITNNGTRSI   78 (139)
T ss_dssp             TTSCBCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEE-----TTEEEECHHHHHHH
T ss_pred             cCCCcCHHHHHHHhCC---ChHHHHHHHHHHHHCCCEEec-----CCeEEEChhHHHHH
Confidence            3578999999999999   999999999999999999976     36799999887554

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

Probab=97.13  E-value=0.00079  Score=41.75  Aligned_cols=62  Identities=16%  Similarity=0.225  Sum_probs=46.4

Q ss_pred             HHhChHHHHHhCC--CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcc
Q 040869           36 IELGIADIIHSHG--RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAST  102 (131)
Q Consensus        36 ~~L~ifd~l~~~~--~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~  102 (131)
                      .+-.|.+.|.+.+  .++|+.|||+++|+   +...+.|.|..|...|++...+.  .++.|...+...
T Consensus        11 ~~~~IL~~L~~~~pg~~~t~~eLA~~Lgv---sr~tV~~~L~~Le~~G~I~~~g~--~~~~W~i~~~~~   74 (81)
T 1qbj_A           11 QEQRILKFLEELGEGKATTAHDLSGKLGT---PKKEINRVLYSLAKKGKLQKEAG--TPPLWKIAVSTQ   74 (81)
T ss_dssp             HHHHHHHHHHHHCTTCCBCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEESS--SSCEEEEC----
T ss_pred             HHHHHHHHHHHcCCCCCcCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEecCC--CCCeeEEeCcHH
Confidence            4566778886533  47999999999999   99999999999999999987531  146777766554

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

Probab=97.12  E-value=0.00052  Score=42.06  Aligned_cols=59  Identities=17%  Similarity=0.222  Sum_probs=46.4

Q ss_pred             HHhChHHHHHhCC--CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869           36 IELGIADIIHSHG--RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA   99 (131)
Q Consensus        36 ~~L~ifd~l~~~~--~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~   99 (131)
                      .+-.|.+.|...+  .++|+.|||+++|+   +...+.|.|..|...|++...+.  .++.|..+|
T Consensus        15 ~~~~IL~~L~~~~~~~~~t~~eLA~~Lgv---s~~tV~~~L~~L~~~G~I~~~g~--~~~~W~i~~   75 (77)
T 1qgp_A           15 QEQRILKFLEELGEGKATTAHDLSGKLGT---PKKEINRVLYSLAKKGKLQKEAG--TPPLWKIAV   75 (77)
T ss_dssp             HHHHHHHHHHHHCSSSCEEHHHHHHHHCC---CHHHHHHHHHHHHHHTSEEEECS--SSCEEEECC
T ss_pred             HHHHHHHHHHHcCCCCCcCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEecCC--CCCceEecC
Confidence            3566778887533  38999999999999   99999999999999999987541  146666554

>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=97.09  E-value=0.00048  Score=44.83  Aligned_cols=74  Identities=18%  Similarity=0.261  Sum_probs=55.2

Q ss_pred             HHHHHHHHhHHHHHHHHHHHHhChHHHHHhCCCCCC--HHHHHhhc-CCCCCCcchHHHHHHHhhcCCceeecccCCCCc
Q 040869           17 AQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAIT--LSELVSAL-DIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEE   93 (131)
Q Consensus        17 ~~l~~~~~~~~~~~aL~~a~~L~ifd~l~~~~~~~s--~~eLA~~~-~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~   93 (131)
                      ..++++..+.|...         |...|.  .++.+  ..||++.+ |+   ++..+.+.|+.|...|++++...  ...
T Consensus        18 ~~~l~~l~~~wrl~---------IL~~L~--~g~~~~~~~eL~~~l~gi---s~~~ls~~L~~Le~~GlV~r~~~--r~~   81 (111)
T 3df8_A           18 ESVLHLLGKKYTML---------IISVLG--NGSTRQNFNDIRSSIPGI---SSTILSRRIKDLIDSGLVERRSG--QIT   81 (111)
T ss_dssp             SSTHHHHHSTTHHH---------HHHHHT--SSSSCBCHHHHHHTSTTC---CHHHHHHHHHHHHHTTSEEEEES--SSE
T ss_pred             HHHHHHHcCccHHH---------HHHHHh--cCCCCCCHHHHHHHccCC---CHHHHHHHHHHHHHCCCEEEeec--CcE
Confidence            44455555555433         444555  35777  99999999 99   99999999999999999998641  135


Q ss_pred             ceecchhcccccc
Q 040869           94 AYGLTAASTLLIK  106 (131)
Q Consensus        94 ~y~~t~~s~~L~~  106 (131)
                      .|.+|+.++.+..
T Consensus        82 ~y~LT~~G~~l~~   94 (111)
T 3df8_A           82 TYALTEKGMNVRN   94 (111)
T ss_dssp             EEEECHHHHHHHH
T ss_pred             EEEECccHHHHHH
Confidence            6999999886653

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

Probab=97.09  E-value=0.00054  Score=43.13  Aligned_cols=45  Identities=7%  Similarity=0.076  Sum_probs=40.1

Q ss_pred             ChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           39 GIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        39 ~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      .|.+.|.+ .+.+|++|||+.+++   ++..++|.|..|...|++.+..
T Consensus         6 ~Il~~L~~-~g~vsv~eLA~~l~V---S~~TIRrDL~~Le~~G~l~R~~   50 (87)
T 2k02_A            6 EVRDMLAL-QGRMEAKQLSARLQT---PQPLIDAMLERMEAMGKVVRIS   50 (87)
T ss_dssp             HHHHHHHH-SCSEEHHHHHHHTTC---CHHHHHHHHHHHHTTCCSEEEE
T ss_pred             HHHHHHHH-cCCCcHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEEe
Confidence            36777775 478999999999999   9999999999999999999873

>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=97.07  E-value=0.00031  Score=44.14  Aligned_cols=64  Identities=16%  Similarity=0.183  Sum_probs=47.8

Q ss_pred             hHHHHHhCCCCCCHHHHHhhcCCCCCCcch-HHHHHHHhhcCCceeecccCCCCcceecchhcccccc
Q 040869           40 IADIIHSHGRAITLSELVSALDIQPTKTTG-LFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIK  106 (131)
Q Consensus        40 ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~-l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~~  106 (131)
                      ++..|...+.++|..|||+.+++   ++.. +.|+++.|...|++.....+.....+.+|+.++.+..
T Consensus        20 ~L~~l~~~~~~~t~~eLa~~l~i---s~~t~vs~~l~~Le~~Glv~~~~~drR~~~~~LT~~G~~~~~   84 (95)
T 2pg4_A           20 TLLEFEKKGYEPSLAEIVKASGV---SEKTFFMGLKDRLIRAGLVKEETLSYRVKTLKLTEKGRRLAE   84 (95)
T ss_dssp             HHHHHHHTTCCCCHHHHHHHHCC---CHHHHHTTHHHHHHHTTSEEEEEEETTEEEEEECHHHHHHHH
T ss_pred             HHHHHHhcCCCCCHHHHHHHHCC---CchHHHHHHHHHHHHCCCeecCCCCCCeEEEEECHhHHHHHH
Confidence            45556554448999999999999   9999 9999999999999984321001234788888876553

>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=97.06  E-value=0.00059  Score=45.15  Aligned_cols=52  Identities=13%  Similarity=0.211  Sum_probs=44.5

Q ss_pred             HHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           31 SLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        31 aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      +|.--.++.|+..|.  .++.++.|||+.+|+   ++..+.+.|+.|...|++....
T Consensus        42 aL~~~~rl~IL~~L~--~~~~s~~ela~~lgi---s~stvs~~L~~Le~~Glv~~~~   93 (122)
T 1r1t_A           42 VLADPNRLRLLSLLA--RSELCVGDLAQAIGV---SESAVSHQLRSLRNLRLVSYRK   93 (122)
T ss_dssp             HHCCHHHHHHHHHHT--TCCBCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HhCCHHHHHHHHHHH--cCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCeEEEE
Confidence            444446778888887  368999999999999   9999999999999999998764

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

Probab=97.01  E-value=0.0046  Score=40.78  Aligned_cols=66  Identities=6%  Similarity=0.033  Sum_probs=51.6

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhcccccc
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIK  106 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~  106 (131)
                      .++.|+..|.  .+++|..|||+.+++   ++..+.|+++.|...|++...... ++ ...+.+|+.++.+..
T Consensus        38 ~~~~iL~~l~--~~~~~~~ela~~l~~---s~~tvs~~l~~Le~~glv~r~~~~~d~r~~~~~lT~~G~~~~~  105 (146)
T 2gxg_A           38 LDFLVLRATS--DGPKTMAYLANRYFV---TQSAITASVDKLEEMGLVVRVRDREDRRKILIEITEKGLETFN  105 (146)
T ss_dssp             HHHHHHHHHT--TSCBCHHHHHHHTTC---CHHHHHHHHHHHHHTTSEEEEECSSCTTCEEEEECHHHHHHHH
T ss_pred             HHHHHHHHHh--cCCcCHHHHHHHhCC---CchhHHHHHHHHHHCCCEEeecCCCCCceEEEEECHHHHHHHH
Confidence            3455777776  578999999999999   999999999999999999976421 11 124789998886554

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

Probab=97.01  E-value=0.00051  Score=43.23  Aligned_cols=66  Identities=14%  Similarity=0.215  Sum_probs=51.9

Q ss_pred             HhChHHHHHhCCCCCCHHHH----HhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhccccccC
Q 040869           37 ELGIADIIHSHGRAITLSEL----VSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIKD  107 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eL----A~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~~~  107 (131)
                      ++.|+..|.. .+++|..||    |+.+++   ++..+.|+++.|...|++.+.... ....|.+|+.++.+...
T Consensus        10 q~~iL~~l~~-~~~~~~~el~~~la~~l~i---s~~tvs~~l~~Le~~gli~r~~~~-r~~~~~LT~~G~~~~~~   79 (99)
T 1tbx_A           10 EAIVLAYLYD-NEGIATYDLYKKVNAEFPM---STATFYDAKKFLIQEGFVKERQER-GEKRLYLTEKGKLFAIS   79 (99)
T ss_dssp             HHHHHHHHTT-CTTCBHHHHHHHHHTTSCC---CHHHHHHHHHHHHHTTSEEEEEET-TEEEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHH-cCCcCHHHHHHHHHHHcCC---CHHHHHHHHHHHHHCCCEEEEecC-CceEEEECHHHHHHHHH
Confidence            4556777764 468999999    999999   999999999999999999875310 13468899998866543

>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=97.00  E-value=0.00096  Score=44.32  Aligned_cols=69  Identities=19%  Similarity=0.188  Sum_probs=53.0

Q ss_pred             HHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhcccccc
Q 040869           35 AIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIK  106 (131)
Q Consensus        35 a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~  106 (131)
                      ..++.|+..|....+++|..+||+.+|+   ++..+.|+++.|...|++...... ++ .-.+.+|+.++.+..
T Consensus        35 ~~~~~iL~~l~~~~~~~~~~~la~~l~i---~~~~vs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~~~~  105 (147)
T 2hr3_A           35 FSQLVVLGAIDRLGGDVTPSELAAAERM---RSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLY  105 (147)
T ss_dssp             HHHHHHHHHHHHTTSCBCHHHHHHHTTC---CHHHHHHHHHHHHHTTSEEEEC------CCEEEECHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHhCC---ChhhHHHHHHHHHHCCCEeeCCCCCCCCceeeEECHHHHHHHH
Confidence            3456677788753468999999999999   999999999999999999876421 11 233889999886554

>2lnb_A Z-DNA-binding protein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, immune system; NMR {Homo sapiens}

Probab=96.99  E-value=0.00073  Score=41.48  Aligned_cols=55  Identities=16%  Similarity=0.230  Sum_probs=47.6

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecc
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLT   98 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t   98 (131)
                      +=.|++.|.+++.|+++.|||+++|+   |...+.+.|..|...|.+....    .-.|+++
T Consensus        21 eekVLe~LkeaG~PlkageIae~~Gv---dKKeVdKaik~LKkEgkI~SPk----RCyw~~~   75 (80)
T 2lnb_A           21 EQRILQVLTEAGSPVKLAQLVKECQA---PKRELNQVLYRMKKELKVSLTS----PATWCLG   75 (80)
T ss_dssp             HHHHHHHHHHHTSCEEHHHHHHHHTS---CHHHHHHHHHHHHHTTSEEEEE----TTEEEES
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHCC---CHHHHHHHHHHHHHcCCccCCC----CceeeCC
Confidence            34578889888899999999999999   9999999999999999887665    5677765

>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=96.98  E-value=0.00077  Score=42.88  Aligned_cols=56  Identities=13%  Similarity=0.182  Sum_probs=47.4

Q ss_pred             hHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcccccc
Q 040869           40 IADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIK  106 (131)
Q Consensus        40 ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~~  106 (131)
                      |...|.  .+ ++..+||..+|+   +++.+.+.++.|...|++....     +.|.+|+.++.+..
T Consensus        13 IL~~i~--~~-~~~t~La~~~~l---s~~~~~~~l~~L~~~GLI~~~~-----~~~~LT~kG~~~l~   68 (95)
T 1r7j_A           13 ILEACK--SG-SPKTRIMYGANL---SYALTGRYIKMLMDLEIIRQEG-----KQYMLTKKGEELLE   68 (95)
T ss_dssp             HHHHHT--TC-BCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEET-----TEEEECHHHHHHHH
T ss_pred             HHHHHH--cC-CCHHHHHHHhCc---CHHHHHHHHHHHHHCCCeEEEC-----CeeEEChhHHHHHH
Confidence            444454  24 999999999999   9999999999999999999874     56999999986553

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

Probab=96.98  E-value=0.00067  Score=44.54  Aligned_cols=67  Identities=13%  Similarity=0.245  Sum_probs=51.8

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhcccccc
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIK  106 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~  106 (131)
                      .++.|+..|.. .+++|..+||+.+++   ++..+.|+++.|...|++...... ++ ...|.+|+.++.+..
T Consensus        34 ~~~~iL~~l~~-~~~~~~~ela~~l~~---~~~tvs~~l~~L~~~gli~r~~~~~d~r~~~~~lT~~G~~~~~  102 (139)
T 3bja_A           34 VQFGVIQVLAK-SGKVSMSKLIENMGC---VPSNMTTMIQRMKRDGYVMTEKNPNDQRETLVYLTKKGEETKK  102 (139)
T ss_dssp             HHHHHHHHHHH-SCSEEHHHHHHHCSS---CCTTHHHHHHHHHHTTSEEEEECSSCTTCEEEEECHHHHHHHH
T ss_pred             HHHHHHHHHHH-cCCcCHHHHHHHHCC---ChhHHHHHHHHHHHCCCeeeccCCCCCceeEEEECHHHHHHHH
Confidence            34557777765 468999999999999   999999999999999999875421 11 123789999886654

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

Probab=96.97  E-value=0.0006  Score=45.00  Aligned_cols=69  Identities=16%  Similarity=0.180  Sum_probs=53.3

Q ss_pred             HHhChHHHHHhCC-CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-CcceecchhccccccC
Q 040869           36 IELGIADIIHSHG-RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIKD  107 (131)
Q Consensus        36 ~~L~ifd~l~~~~-~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~~  107 (131)
                      .++.|+..|...+ +++|..|||+.+++   ++..+.|+++.|...|++...... |+ ...+.+|+.++.+...
T Consensus        32 ~~~~vL~~l~~~~~~~~t~~ela~~l~~---~~~tvs~~l~~Le~~Gli~r~~~~~D~R~~~~~LT~~G~~~~~~  103 (139)
T 3eco_A           32 EQGHTLGYLYAHQQDGLTQNDIAKALQR---TGPTVSNLLRNLERKKLIYRYVDAQDTRRKNIGLTTSGIKLVEA  103 (139)
T ss_dssp             HHHHHHHHHHHSTTTCEEHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEEECCC--CCEEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCCcCHHHHHHHhCC---CcccHHHHHHHHHHCCCEeecCCCCCCCeeeeEECHHHHHHHHH
Confidence            3455777777654 58999999999999   999999999999999999976422 11 2347899998866543

>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=96.97  E-value=0.0032  Score=42.05  Aligned_cols=66  Identities=12%  Similarity=0.207  Sum_probs=50.8

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhcccccc
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIK  106 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~  106 (131)
                      ++.|+..|.. .+++|..+||+.+++   ++..+.|+++.|...|++...... ++ .-.|.+|+.++.+..
T Consensus        39 ~~~iL~~l~~-~~~~t~~ela~~l~~---s~~tvs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~~~~  106 (155)
T 1s3j_A           39 QLFVLASLKK-HGSLKVSEIAERMEV---KPSAVTLMADRLEQKNLIARTHNTKDRRVIDLSLTDEGDIKFE  106 (155)
T ss_dssp             HHHHHHHHHH-HSEEEHHHHHHHHTS---CHHHHHHHHHHHHHTTSEEEEECSSCTTSEEEEECHHHHHHHH
T ss_pred             HHHHHHHHHH-cCCCCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEeecCCCCCCceEEEEECHHHHHHHH
Confidence            3446777764 368999999999999   999999999999999999986421 11 124788998876543

>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=96.97  E-value=0.001  Score=43.76  Aligned_cols=67  Identities=15%  Similarity=0.203  Sum_probs=51.3

Q ss_pred             HhChHHHHHhCCC-CCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhcccccc
Q 040869           37 ELGIADIIHSHGR-AITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIK  106 (131)
Q Consensus        37 ~L~ifd~l~~~~~-~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~  106 (131)
                      ++.|+..|...++ ++|..+||+.+++   ++..+.|+++.|...|++...... ++ ...+.+|+.++.+..
T Consensus        36 ~~~iL~~l~~~~~~~~~~~ela~~l~~---~~~tvs~~l~~Le~~Gli~r~~~~~d~R~~~i~lT~~G~~~~~  105 (141)
T 3bro_A           36 QMTIIDYLSRNKNKEVLQRDLESEFSI---KSSTATVLLQRMEIKKLLYRKVSGKDSRQKCLKLTKKANKLET  105 (141)
T ss_dssp             HHHHHHHHHHTTTSCCBHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEEECSSCTTSEEEEECHHHHTTHH
T ss_pred             HHHHHHHHHHCCCCCcCHHHHHHHHCC---CcchHHHHHHHHHHCCCEEeeCCCcCCCeeeeEECHHHHHHHH
Confidence            4446777765443 8999999999999   999999999999999999876421 11 124778988876654

>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=96.96  E-value=0.0053  Score=40.98  Aligned_cols=66  Identities=14%  Similarity=0.218  Sum_probs=49.2

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec---ccCCC-CcceecchhccccccC
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT---KVNGQ-EEAYGLTAASTLLIKD  107 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~---~~~~~-~~~y~~t~~s~~L~~~  107 (131)
                      ++.|+..| . .+++|..|||+.+++   ++..+.|+++.|...|++...   .+.|+ .-.+.+|+.++.+...
T Consensus        40 q~~iL~~l-~-~~~~t~~eLa~~l~~---~~~~vs~~l~~Le~~Glv~r~~~~~~~D~R~~~~~lT~~G~~~~~~  109 (151)
T 3kp7_A           40 QSHVLNML-S-IEALTVGQITEKQGV---NKAAVSRRVKKLLNAELVKLEKPDSNTDQRLKIIKLSNKGKKYIKE  109 (151)
T ss_dssp             HHHHHHHH-H-HSCBCHHHHHHHHCS---CSSHHHHHHHHHHHTTSEEC-----------CCBEECHHHHHHHHH
T ss_pred             HHHHHHHH-H-cCCcCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEeeCCCCCCCCCeeEEEECHhHHHHHHH
Confidence            33477778 4 578999999999999   999999999999999999962   11111 2347889988866543

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

Probab=96.96  E-value=0.0039  Score=41.91  Aligned_cols=67  Identities=15%  Similarity=0.184  Sum_probs=50.8

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhcccccc
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIK  106 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~  106 (131)
                      ++.|+..|....+++|..+||+.+++   ++..+.|+++.|...|++...... ++ .-.+.+|+.++.+..
T Consensus        49 ~~~iL~~L~~~~~~~~~~ela~~l~i---~~~tvs~~l~~Le~~Gli~r~~~~~d~R~~~~~lT~~G~~~~~  117 (160)
T 3boq_A           49 KFDAMAQLARNPDGLSMGKLSGALKV---TNGNVSGLVNRLIKDGMVVKAMSADDRRSFSAKLTDAGLTTFK  117 (160)
T ss_dssp             HHHHHHHHHHCTTCEEHHHHHHHCSS---CCSCHHHHHHHHHHHTSEEEC--------CEEEECHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHCC---ChhhHHHHHHHHHHCCCEEeecCCCCCCeEEEEEChhHHHHHH
Confidence            45578888433578999999999999   999999999999999999986421 11 123789998886554

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

Probab=96.96  E-value=0.0013  Score=45.76  Aligned_cols=61  Identities=11%  Similarity=0.166  Sum_probs=45.5

Q ss_pred             CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhccccccCcccChHHhHHhh
Q 040869           48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIKDKPYCMSPTVSAF  119 (131)
Q Consensus        48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~~~~~~sl~~~~~~~  119 (131)
                      ++++|..+||+.+++   ++..++++|..|...|++.....  ..|.|.++.-..      .-++.+.+...
T Consensus        42 ~~~~s~~eIA~~~~i---~~~~l~kil~~L~~aGlv~s~rG--~~GGy~Lar~p~------eItL~dVi~av  102 (159)
T 3lwf_A           42 DGPISLRSIAQDKNL---SEHYLEQLIGPLRNAGIVKSIRG--AHGGYVLNGDPE------KITAGDIIRTL  102 (159)
T ss_dssp             SCCBCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEECS--TTCEEEECSCTT------TCBHHHHHHHH
T ss_pred             CCCcCHHHHHHHHCc---CHHHHHHHHHHHHHCCeEEEecC--CCCceEecCCHH------HCCHHHHHHHH
Confidence            468999999999999   99999999999999999997641  135677654321      12555555554

>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=96.96  E-value=0.00064  Score=44.11  Aligned_cols=61  Identities=21%  Similarity=0.213  Sum_probs=47.7

Q ss_pred             hHHHHHhCCCCCCHHHHHhhc-CCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhccccc
Q 040869           40 IADIIHSHGRAITLSELVSAL-DIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLI  105 (131)
Q Consensus        40 ifd~l~~~~~~~s~~eLA~~~-~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~  105 (131)
                      |...|..  ++++..|||+.+ ++   ++..+.+.|+.|...|++...... ++ .-.|.+|+.++.+.
T Consensus        27 IL~~L~~--~~~~~~eLa~~l~~i---s~~tvs~~L~~Le~~GlI~r~~~~~d~r~~~~~LT~~G~~~~   90 (112)
T 1z7u_A           27 LMDELFQ--GTKRNGELMRALDGI---TQRVLTDRLREMEKDGLVHRESFNELPPRVEYTLTPEGYALY   90 (112)
T ss_dssp             HHHHHHH--SCBCHHHHHHHSTTC---CHHHHHHHHHHHHHHTSEEEEEECCSSCEEEEEECHHHHHHH
T ss_pred             HHHHHHh--CCCCHHHHHHHhccC---CHHHHHHHHHHHHHCCCEEEeecCCCCCeEEEEECHhHHHHH
Confidence            4444553  689999999999 99   999999999999999999976421 11 13499999987654

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

Probab=96.95  E-value=0.00099  Score=44.89  Aligned_cols=78  Identities=12%  Similarity=0.032  Sum_probs=57.9

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhc-CCCCCCcchHHHHHHHhhcCCceeecccC-CC-
Q 040869           15 GQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSAL-DIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-   91 (131)
Q Consensus        15 ~~~~l~~~~~~~~~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~-~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-   91 (131)
                      |...+++++.+-|...+|.         .|.  .++.+..||++.+ |+   ++..|.+.|+.|...|++.+.... +. 
T Consensus        15 pi~~~l~~lg~kW~l~IL~---------~L~--~g~~rf~eL~~~l~gI---s~~~Ls~~L~~Le~~GLV~R~~~~~d~r   80 (131)
T 4a5n_A           15 PVEFTLDVIGGKWKGILFY---------HMI--DGKKRFNEFRRICPSI---TQRMLTLQLRELEADGIVHREVYHQVPP   80 (131)
T ss_dssp             HHHHHHHHHCSSSHHHHHH---------HHT--TSCBCHHHHHHHCTTS---CHHHHHHHHHHHHHTTSEEEEEECSSSC
T ss_pred             cHHHHHHHHcCcCHHHHHH---------HHh--cCCcCHHHHHHHhccc---CHHHHHHHHHHHHHCCCEEEEecCCCCC
Confidence            3455566666666554443         333  3789999999999 99   999999999999999999986432 11 


Q ss_pred             Ccceecchhcccccc
Q 040869           92 EEAYGLTAASTLLIK  106 (131)
Q Consensus        92 ~~~y~~t~~s~~L~~  106 (131)
                      .-.|.+|+.++.|..
T Consensus        81 ~v~y~LT~~G~~l~~   95 (131)
T 4a5n_A           81 KVEYSLTEFGRTLEP   95 (131)
T ss_dssp             EEEEEECTTGGGGHH
T ss_pred             eEEEEECHhHHHHHH
Confidence            135999999987753

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

Probab=96.95  E-value=0.00078  Score=44.23  Aligned_cols=66  Identities=17%  Similarity=0.195  Sum_probs=50.9

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhcccccc
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIK  106 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~  106 (131)
                      ++.|+..|.. .+++|..|||+.+++   ++..+.|+++.|...|++...... ++ ...|.+|+.++.+..
T Consensus        31 ~~~iL~~l~~-~~~~~~~ela~~l~~---s~~tvs~~l~~L~~~glv~~~~~~~d~R~~~~~lT~~G~~~~~   98 (138)
T 3bpv_A           31 QVACLLRIHR-EPGIKQDELATFFHV---DKGTIARTLRRLEESGFIEREQDPENRRRYILEVTRRGEEIIP   98 (138)
T ss_dssp             HHHHHHHHHH-STTCBHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHTHH
T ss_pred             HHHHHHHHHH-cCCCCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEeecCCCCceeEEeeECHhHHHHHH
Confidence            4456777765 478999999999999   999999999999999999985421 00 123788998876554

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

Probab=96.95  E-value=0.00086  Score=41.76  Aligned_cols=59  Identities=14%  Similarity=0.086  Sum_probs=45.2

Q ss_pred             HHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchh
Q 040869           35 AIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAA  100 (131)
Q Consensus        35 a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~  100 (131)
                      .....|.+.|.+ .+ +|+.|||+++|+   +...++|.|..|...|++.....  .+-.|..+..
T Consensus        17 ~~~~~IL~lL~~-~g-~sa~eLAk~Lgi---Sk~aVr~~L~~Le~eG~I~~~~~--~PP~W~~~~~   75 (82)
T 1oyi_A           17 EIVCEAIKTIGI-EG-ATAAQLTRQLNM---EKREVNKALYDLQRSAMVYSSDD--IPPRWFMTTE   75 (82)
T ss_dssp             HHHHHHHHHHSS-ST-EEHHHHHHHSSS---CHHHHHHHHHHHHHHTSSEECSS--SSCEEESCC-
T ss_pred             HHHHHHHHHHHH-cC-CCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEeCCC--CCCcceeccC
Confidence            345667888885 33 999999999999   99999999999999999987641  1334555543

>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=96.94  E-value=0.00025  Score=44.69  Aligned_cols=53  Identities=8%  Similarity=0.147  Sum_probs=41.9

Q ss_pred             CCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcccccc
Q 040869           50 AITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIK  106 (131)
Q Consensus        50 ~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~~  106 (131)
                      ++|..+||+.+++   ++..+.|+++.|...|++..... .....|.+|+.++.+..
T Consensus        30 ~~t~~eLa~~l~i---~~~tvs~~l~~Le~~Glv~~~~d-~R~~~v~LT~~G~~~~~   82 (95)
T 2qvo_A           30 DVYIQYIASKVNS---PHSYVWLIIKKFEEAKMVECELE-GRTKIIRLTDKGQKIAQ   82 (95)
T ss_dssp             CEEHHHHHHHSSS---CHHHHHHHHHHHHHTTSEEEEEE-TTEEEEEECHHHHHHHH
T ss_pred             CcCHHHHHHHHCc---CHHHHHHHHHHHHHCcCccCCCC-CCeEEEEEChhHHHHHH
Confidence            4999999999999   99999999999999999943320 00124899998886653

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

Probab=96.92  E-value=0.0012  Score=44.75  Aligned_cols=58  Identities=14%  Similarity=0.168  Sum_probs=47.9

Q ss_pred             HHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcccccc
Q 040869           41 ADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIK  106 (131)
Q Consensus        41 fd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~~  106 (131)
                      ...|.. ++++|..+||+.+|+   +...+.|.++.|...|++....    +..+.+|+.++.+..
T Consensus        46 ~~~l~~-~~~~~~~~la~~l~v---s~~tvs~~l~~Le~~Glv~r~~----~~~~~lT~~g~~~~~  103 (155)
T 2h09_A           46 SDLIRE-VGEARQVDMAARLGV---SQPTVAKMLKRLATMGLIEMIP----WRGVFLTAEGEKLAQ  103 (155)
T ss_dssp             HHHHHH-HSCCCHHHHHHHHTS---CHHHHHHHHHHHHHTTCEEEET----TTEEEECHHHHHHHH
T ss_pred             HHHHHh-CCCcCHHHHHHHhCc---CHHHHHHHHHHHHHCCCEEEec----CCceEEChhHHHHHH
Confidence            335543 367999999999999   9999999999999999998875    567889998875543

>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=96.89  E-value=0.00087  Score=45.74  Aligned_cols=60  Identities=10%  Similarity=0.099  Sum_probs=44.9

Q ss_pred             HHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchh
Q 040869           30 MSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAA  100 (131)
Q Consensus        30 ~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~  100 (131)
                      .+|++.+.|...     .++++|..+||+.+++   ++..+.++|+.|...|++....   |.|.|.++.-
T Consensus        15 yAl~~L~~La~~-----~~~~~~~~~iA~~~~i---~~~~l~kil~~L~~~Glv~s~r---G~GGy~L~~~   74 (149)
T 1ylf_A           15 IAVHILSILKNN-----PSSLCTSDYMAESVNT---NPVVIRKIMSYLKQAGFVYVNR---GPGGAGLLKD   74 (149)
T ss_dssp             HHHHHHHHHHHS-----CGGGCCHHHHHHHHTS---CHHHHHHHHHHHHHTTSEEEC------CCEEESSC
T ss_pred             HHHHHHHHHHhC-----CCCCcCHHHHHHHHCc---CHHHHHHHHHHHHHCCcEEEcc---CCCceEeCCC
Confidence            356666655321     2468999999999999   9999999999999999998764   1466776653

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

Probab=96.87  E-value=0.0012  Score=43.63  Aligned_cols=67  Identities=19%  Similarity=0.194  Sum_probs=51.2

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhcccccc
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIK  106 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~  106 (131)
                      ++.|+..|....+++|..+||+.+++   ++..+.|+++.|...|++...... ++ .-.+.+|+.++.+..
T Consensus        39 ~~~iL~~l~~~~~~~t~~~la~~l~~---s~~~vs~~l~~L~~~glv~r~~~~~d~R~~~~~lT~~G~~~~~  107 (146)
T 2fbh_A           39 RWLVLLHLARHRDSPTQRELAQSVGV---EGPTLARLLDGLESQGLVRRLAVAEDRRAKHIVLTPKADVLIA  107 (146)
T ss_dssp             HHHHHHHHHHCSSCCBHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEECCBTTBCSCEEEECTTHHHHHH
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHhCC---ChhhHHHHHHHHHHCCCeeecCCCcccCeeeeEECHhHHHHHH
Confidence            34477777223578999999999999   999999999999999999986421 11 224788988876553

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

Probab=96.87  E-value=0.00083  Score=46.20  Aligned_cols=68  Identities=18%  Similarity=0.185  Sum_probs=51.9

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhcccccc
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIK  106 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~  106 (131)
                      .++.|+..|...++++|..|||+.+++   ++..+.|+++.|...|++.+.... |+ ...+.+|+.++.+..
T Consensus        54 ~q~~vL~~L~~~~~~~t~~eLa~~l~i---~~~tvs~~l~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~  123 (166)
T 3deu_A           54 THWVTLHNIHQLPPDQSQIQLAKAIGI---EQPSLVRTLDQLEDKGLISRQTCASDRRAKRIKLTEKAEPLIA  123 (166)
T ss_dssp             HHHHHHHHHHHSCSSEEHHHHHHHHTS---CHHHHHHHHHHHHHTTSEEEC--------CEEEECGGGHHHHH
T ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHCC---CHhhHHHHHHHHHHCCCEEeeCCCCCCCeeEEEECHHHHHHHH
Confidence            345577777754578999999999999   999999999999999999986421 11 234889998886654

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

Probab=96.86  E-value=0.00072  Score=44.44  Aligned_cols=67  Identities=6%  Similarity=0.001  Sum_probs=52.1

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhcccccc
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIK  106 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~  106 (131)
                      .++.|+..|.. .+++|..|||+.+++   ++..+.|+++.|...|++...... ++ ...|.+|+.++.+..
T Consensus        39 ~~~~iL~~l~~-~~~~t~~ela~~l~~---~~~tvs~~l~~L~~~glv~r~~~~~d~R~~~~~lT~~G~~~~~  107 (140)
T 2nnn_A           39 TQWAALVRLGE-TGPCPQNQLGRLTAM---DAATIKGVVERLDKRGLIQRSADPDDGRRLLVSLSPAGRAELE  107 (140)
T ss_dssp             HHHHHHHHHHH-HSSBCHHHHHHHTTC---CHHHHHHHHHHHHHTTCEEEEEETTEEEEEEEEECHHHHHHHH
T ss_pred             HHHHHHHHHHH-cCCCCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEeeCCCCCCCeeeeEECHhHHHHHH
Confidence            35667888865 358999999999999   999999999999999999975321 00 124889999886554

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

Probab=96.86  E-value=0.01  Score=39.58  Aligned_cols=67  Identities=18%  Similarity=0.184  Sum_probs=51.3

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceee--cccC-CC-Ccceecchhcccccc
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNK--TKVN-GQ-EEAYGLTAASTLLIK  106 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~--~~~~-~~-~~~y~~t~~s~~L~~  106 (131)
                      .++.|+..|.. .+++|..+||+.+++   ++..+.|+++.|...|++..  .... ++ .-.+.+|+.++.+..
T Consensus        42 ~~~~iL~~l~~-~~~~t~~eLa~~l~~---~~~tvs~~l~~Le~~Glv~r~~~~~~~d~R~~~~~LT~~G~~~~~  112 (154)
T 2qww_A           42 QQLAMINVIYS-TPGISVADLTKRLII---TGSSAAANVDGLISLGLVVKLNKTIPNDSMDLTLKLSKKGEDLSK  112 (154)
T ss_dssp             HHHHHHHHHHH-STTEEHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEESCC--CTTCTTCEEEECHHHHHHHH
T ss_pred             HHHHHHHHHHH-CCCCCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEecCcCCCCCCceeEeEECHHHHHHHH
Confidence            34557777775 367999999999999   99999999999999999998  4321 11 125889999886554

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

Probab=96.86  E-value=0.0011  Score=43.06  Aligned_cols=52  Identities=13%  Similarity=0.252  Sum_probs=44.3

Q ss_pred             HHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           31 SLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        31 aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      ++....++.|+..|.+  ++.|..|||+.+|+   ++..+.|.++.|...|++....
T Consensus        28 ~l~~~~~~~il~~L~~--~~~s~~ela~~l~i---s~stvsr~l~~Le~~Glv~~~~   79 (119)
T 2lkp_A           28 ALATPSRLMILTQLRN--GPLPVTDLAEAIGM---EQSAVSHQLRVLRNLGLVVGDR   79 (119)
T ss_dssp             HHCCHHHHHHHHHHHH--CCCCHHHHHHHHSS---CHHHHHHHHHHHHHHCSEEEEE
T ss_pred             HhCCHHHHHHHHHHHH--CCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEEe
Confidence            3444567788888885  58999999999999   9999999999999999998654

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

Probab=96.86  E-value=0.0016  Score=44.32  Aligned_cols=66  Identities=9%  Similarity=0.082  Sum_probs=52.2

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhcccccc
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIK  106 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~  106 (131)
                      ++.|+..|.. .+++|..|||+.+++   ++..+.|+++.|...|++...... ++ ...+.+|+.++.+..
T Consensus        48 q~~iL~~l~~-~~~~t~~eLa~~l~~---~~~tvs~~l~~Le~~Glv~r~~~~~DrR~~~l~LT~~G~~~~~  115 (162)
T 3k0l_A           48 QFTALSVLAA-KPNLSNAKLAERSFI---KPQSANKILQDLLANGWIEKAPDPTHGRRILVTVTPSGLDKLN  115 (162)
T ss_dssp             HHHHHHHHHH-CTTCCHHHHHHHHTS---CGGGHHHHHHHHHHTTSEEEEECCSSSCCEEEEECHHHHHHHH
T ss_pred             HHHHHHHHHH-CCCCCHHHHHHHHCC---CHHHHHHHHHHHHHCcCeEecCCCCcCCeeEeEECHhHHHHHH
Confidence            4457777775 368999999999999   999999999999999999986432 11 134889999886654

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

Probab=96.85  E-value=0.00091  Score=44.55  Aligned_cols=67  Identities=15%  Similarity=0.198  Sum_probs=50.8

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhcccccc
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIK  106 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~  106 (131)
                      .++.|+..|... +++|..|||+.+++   ++..+.|+++.|...|++...... |+ ...+.+|+.++.+..
T Consensus        41 ~~~~iL~~l~~~-~~~t~~ela~~l~~---~~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~~~lT~~G~~~~~  109 (148)
T 3nrv_A           41 TEWRIISVLSSA-SDCSVQKISDILGL---DKAAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEMGQELYE  109 (148)
T ss_dssp             HHHHHHHHHHHS-SSBCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEC---------CCBEECHHHHHHHH
T ss_pred             HHHHHHHHHHcC-CCCCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEeecCCCCcceeEeEECHhHHHHHH
Confidence            455577777753 58999999999999   999999999999999999976421 11 245889998886654

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

Probab=96.85  E-value=0.001  Score=45.02  Aligned_cols=66  Identities=12%  Similarity=0.159  Sum_probs=49.9

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhcccccc
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIK  106 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~  106 (131)
                      ++.|+..|.. .+++|..|||+.+++   ++..+.|+++.|...|++...... ++ ...|.+|+.++.+..
T Consensus        51 ~~~iL~~l~~-~~~~t~~ela~~l~i---s~~tvs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~~~~  118 (162)
T 2fa5_A           51 EWRVITILAL-YPGSSASEVSDRTAM---DKVAVSRAVARLLERGFIRRETHGDDRRRSMLALSPAGRQVYE  118 (162)
T ss_dssp             HHHHHHHHHH-STTCCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEC---------CCCEECHHHHHHHH
T ss_pred             HHHHHHHHHh-CCCCCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEeeecCCCCCCeeEEEECHHHHHHHH
Confidence            4457777775 468999999999999   999999999999999999875421 11 245889999886553

>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=96.85  E-value=0.0014  Score=43.39  Aligned_cols=58  Identities=16%  Similarity=0.266  Sum_probs=43.3

Q ss_pred             ChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869           39 GIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA   99 (131)
Q Consensus        39 ~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~   99 (131)
                      .++..|....+++|..|||+.+|+   ++..+.|+++.|...|++......++...|..+.
T Consensus        30 ~il~~L~~~~~~~t~~ela~~l~~---~~stvs~~l~~L~~~G~v~r~~~~~d~r~~~~~~   87 (152)
T 1ku9_A           30 AVYAILYLSDKPLTISDIMEELKI---SKGNVSMSLKKLEELGFVRKVWIKGERKNYYEAV   87 (152)
T ss_dssp             HHHHHHHHCSSCEEHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEECCTTCSSCEEEEC
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEEecCCCceEEEeec
Confidence            355566422478999999999999   9999999999999999999853211134455554

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

Probab=96.83  E-value=0.0015  Score=44.40  Aligned_cols=47  Identities=15%  Similarity=0.197  Sum_probs=39.1

Q ss_pred             CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869           48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA   99 (131)
Q Consensus        48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~   99 (131)
                      ++++|..+||+.+++   ++..+.++|..|...|++.....  ..|.|.++.
T Consensus        26 ~~~~s~~~IA~~~~i---~~~~l~kil~~L~~aGlv~s~rG--~~GGy~Lar   72 (143)
T 3t8r_A           26 QGCISLKSIAEENNL---SDLYLEQLVGPLRNAGLIRSVRG--AKGGYQLRV   72 (143)
T ss_dssp             SCCEEHHHHHHHTTC---CHHHHHHHHHHHHHTTSEEECSS--SSSEEEESS
T ss_pred             CCCcCHHHHHHHHCc---CHHHHHHHHHHHHHCCEEEecCC--CCCCeeecC
Confidence            368999999999999   99999999999999999986541  135677654

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

Probab=96.83  E-value=0.0011  Score=44.52  Aligned_cols=66  Identities=11%  Similarity=0.133  Sum_probs=50.8

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhcccccc
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIK  106 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~  106 (131)
                      ++.|+..|.. .+++|..+||+.+++   ++..+.|+++.|...|++...... ++ ...+.+|+.++.+..
T Consensus        45 ~~~iL~~l~~-~~~~t~~ela~~l~i---~~~tvs~~l~~Le~~Glv~r~~~~~d~R~~~~~lT~~G~~~~~  112 (155)
T 3cdh_A           45 EWRVLACLVD-NDAMMITRLAKLSLM---EQSRMTRIVDQMDARGLVTRVADAKDKRRVRVRLTDDGRALAE  112 (155)
T ss_dssp             HHHHHHHHSS-CSCBCHHHHHHHTTC---CHHHHHHHHHHHHHTTSEEECC------CCCEEECHHHHHHHH
T ss_pred             HHHHHHHHHH-CCCcCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEeccCCCcCCeeEeEECHHHHHHHH
Confidence            4456777764 468999999999999   999999999999999999975421 11 234889999886554

>2w57_A Ferric uptake regulation protein; gene regulation, transcription regulation, transport, iron, repressor, DNA-binding, transcription; 2.60A {Vibrio cholerae}

Probab=96.83  E-value=0.00061  Score=46.68  Aligned_cols=60  Identities=17%  Similarity=0.359  Sum_probs=46.7

Q ss_pred             HHHhChHHHHHhCC-CCCCHHHHHhhc-----CCCCCCcchHHHHHHHhhcCCceeecccCCCCcceec
Q 040869           35 AIELGIADIIHSHG-RAITLSELVSAL-----DIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGL   97 (131)
Q Consensus        35 a~~L~ifd~l~~~~-~~~s~~eLA~~~-----~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~   97 (131)
                      ..+.-|++.|.+.+ +++|++||.+.+     ++   +..++||.|+.|+..|++.+....++..+|..
T Consensus        17 ~qR~~Il~~L~~~~~~h~sa~ei~~~l~~~~~~i---s~aTVYR~L~~L~e~Glv~~~~~~~~~~~Y~~   82 (150)
T 2w57_A           17 LPRLKILEVLQQPECQHISAEELYKKLIDLGEEI---GLATVYRVLNQFDDAGIVTRHHFEGGKSVFEL   82 (150)
T ss_dssp             HHHHHHHHHHTSGGGSSEEHHHHHHHHHHTTCCC---CHHHHHHHHHHHHHTTSEEEEECGGGCEEEEE
T ss_pred             HHHHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCC---CHHHHHHHHHHHHHCCcEEEEEeCCCceEEEe
Confidence            34566899997656 799999999998     56   88999999999999999998642112345764

>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=96.82  E-value=0.0018  Score=44.05  Aligned_cols=54  Identities=20%  Similarity=0.271  Sum_probs=45.0

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CCCcceecchhccccc
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQEEAYGLTAASTLLI  105 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~~~~y~~t~~s~~L~  105 (131)
                      ++++..||++.+|+   ++..+.+.|+.|...|++++.... +..-.|.+|+.++.+.
T Consensus        36 g~~~~~eLa~~lgi---s~~tls~~L~~Le~~GlI~r~~~~~d~~~~y~LT~~G~~l~   90 (146)
T 2f2e_A           36 GLTRFGEFQKSLGL---AKNILAARLRNLVEHGVMVAVPAESGSHQEYRLTDKGRALF   90 (146)
T ss_dssp             TCCSHHHHHHHHCC---CHHHHHHHHHHHHHTTSEEEEECSSSSCEEEEECHHHHTTH
T ss_pred             CCCCHHHHHHHhCC---CHHHHHHHHHHHHHCCCEEEEecCCCCeEEEEECchHHHHH
Confidence            68999999999999   999999999999999999986521 1123699999987654

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

Probab=96.82  E-value=0.0016  Score=42.84  Aligned_cols=66  Identities=17%  Similarity=0.157  Sum_probs=52.4

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhccccc
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLI  105 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~  105 (131)
                      .++.|+..|.. .+++|..+||+.+++   ++..+.|+++.|...|++...... ++ ...|.+|+.++.+.
T Consensus        32 ~~~~iL~~l~~-~~~~~~~ela~~l~i---s~~~vs~~l~~L~~~gli~~~~~~~d~r~~~~~lT~~G~~~~   99 (142)
T 3bdd_A           32 TRYSILQTLLK-DAPLHQLALQERLQI---DRAAVTRHLKLLEESGYIIRKRNPDNQREVLVWPTEQAREAL   99 (142)
T ss_dssp             HHHHHHHHHHH-HCSBCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEEECSSSTTCEEEEECHHHHHHH
T ss_pred             HHHHHHHHHHh-CCCCCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHH
Confidence            44557777765 368999999999999   999999999999999999876421 11 23488999988666

>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=96.81  E-value=0.00078  Score=44.59  Aligned_cols=67  Identities=15%  Similarity=0.109  Sum_probs=51.7

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhcccccc
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIK  106 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~  106 (131)
                      .++.|+..|.. .+++|..+||+.+++   ++..+.|+++.|...|++...... ++ ...|.+|+.++.+..
T Consensus        34 ~~~~iL~~l~~-~~~~~~~~la~~l~~---s~~tvs~~l~~L~~~glv~r~~~~~d~r~~~~~lT~~G~~~~~  102 (145)
T 2a61_A           34 AQFDILQKIYF-EGPKRPGELSVLLGV---AKSTVTGLVKRLEADGYLTRTPDPADRRAYFLVITRKGEEVIE  102 (145)
T ss_dssp             HHHHHHHHHHH-HCCBCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHHH
T ss_pred             HHHHHHHHHHH-cCCCCHHHHHHHHCC---CchhHHHHHHHHHHCCCeeecCCCCCCceEEEEECHHHHHHHH
Confidence            34557777765 368999999999999   999999999999999999986421 10 124889999886553

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

Probab=96.81  E-value=0.0013  Score=43.53  Aligned_cols=67  Identities=18%  Similarity=0.236  Sum_probs=49.8

Q ss_pred             HHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhcccccc
Q 040869           35 AIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIK  106 (131)
Q Consensus        35 a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~  106 (131)
                      ..++.|...|.. .+ +|..|||+.+|+   ++..+.|+++.|...|++...... ++ ...|.+|+.++.+..
T Consensus        38 ~~~~~iL~~l~~-~~-~t~~eLa~~l~~---s~~tvs~~l~~L~~~Glv~r~~~~~d~R~~~~~lT~~g~~~~~  106 (146)
T 3tgn_A           38 NTQEHILMLLSE-ES-LTNSELARRLNV---SQAAVTKAIKSLVKEGMLETSKDSKDARVIFYQLTDLARPIAE  106 (146)
T ss_dssp             HHHHHHHHHHTT-CC-CCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEC----------CCEECGGGHHHHH
T ss_pred             HHHHHHHHHHHh-CC-CCHHHHHHHHCC---CHHHHHHHHHHHHHCCCeEeccCCCCCceeEEEECHhHHHHHH
Confidence            355667778875 34 999999999999   999999999999999999976421 11 245889998876553

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

Probab=96.81  E-value=0.0092  Score=39.39  Aligned_cols=66  Identities=6%  Similarity=0.086  Sum_probs=51.1

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhcccccc
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIK  106 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~  106 (131)
                      .++.|+..|... ++ |..+||+.+++   ++..+.|+++.|...|++...... ++ .-.+.+|+.++.+..
T Consensus        38 ~~~~iL~~l~~~-~~-~~~~la~~l~~---~~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~~~LT~~G~~~~~  105 (144)
T 3f3x_A           38 LDFSILKATSEE-PR-SMVYLANRYFV---TQSAITAAVDKLEAKGLVRRIRDSKDRRIVIVEITPKGRQVLL  105 (144)
T ss_dssp             HHHHHHHHHHHS-CE-EHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHHH
T ss_pred             HHHHHHHHHHHC-CC-CHHHHHHHHCC---ChhHHHHHHHHHHHCCCEEeccCCCCCceEEEEECHHHHHHHH
Confidence            345677778764 34 99999999999   999999999999999999986421 00 114899999886654

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

Probab=96.80  E-value=0.00073  Score=44.83  Aligned_cols=69  Identities=12%  Similarity=0.124  Sum_probs=52.7

Q ss_pred             HHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-CcceecchhccccccC
Q 040869           35 AIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIKD  107 (131)
Q Consensus        35 a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~~  107 (131)
                      ..++.|+..|... +++|..|||+.+++   ++..+.|+++.|...|++...... ++ ...+.+|+.++.+...
T Consensus        37 ~~~~~iL~~l~~~-~~~t~~eLa~~l~~---~~~~vs~~l~~L~~~Glv~r~~~~~D~R~~~~~LT~~G~~~~~~  107 (143)
T 3oop_A           37 PEQWSVLEGIEAN-EPISQKEIALWTKK---DTPTVNRIVDVLLRKELIVREISTEDRRISLLSLTDKGRKETTE  107 (143)
T ss_dssp             HHHHHHHHHHHHH-SSEEHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEEC----CCSCEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHHHHc-CCcCHHHHHHHHCC---CHhhHHHHHHHHHHCCCeeccCCCccCceeeeeECHHHHHHHHH
Confidence            3455577777653 78999999999999   999999999999999999976422 11 2348899998866543

>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=96.77  E-value=0.00097  Score=42.83  Aligned_cols=76  Identities=18%  Similarity=0.226  Sum_probs=54.3

Q ss_pred             HHHHHHHHHhHHHHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhc-CCCCCCcchHHHHHHHhhcCCceeecccC-CC-C
Q 040869           16 QAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSAL-DIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-E   92 (131)
Q Consensus        16 ~~~l~~~~~~~~~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~-~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~   92 (131)
                      ...++++..+.|...         |...|.  .++++..||++.+ |+   ++..+.+.|+.|...|++...... ++ .
T Consensus        15 ~~~~l~~l~~~~~~~---------IL~~L~--~~~~~~~eL~~~l~gi---s~~~ls~~L~~Le~~GlV~r~~~~~d~r~   80 (107)
T 2fsw_A           15 VRKSMQIFAGKWTLL---------IIFQIN--RRIIRYGELKRAIPGI---SEKMLIDELKFLCGKGLIKKKQYPEVPPR   80 (107)
T ss_dssp             HHHHHHHHTSSSHHH---------HHHHHT--TSCEEHHHHHHHSTTC---CHHHHHHHHHHHHHTTSEEEEEECSSSCE
T ss_pred             HHHHHHHHcCccHHH---------HHHHHH--hCCcCHHHHHHHcccC---CHHHHHHHHHHHHHCCCEEEeecCCCCCe
Confidence            344455555544433         334454  3689999999999 49   999999999999999999976421 11 1


Q ss_pred             cceecchhccccc
Q 040869           93 EAYGLTAASTLLI  105 (131)
Q Consensus        93 ~~y~~t~~s~~L~  105 (131)
                      -.|.+|+.++.+.
T Consensus        81 ~~y~LT~~G~~l~   93 (107)
T 2fsw_A           81 VEYSLTPLGEKVL   93 (107)
T ss_dssp             EEEEECHHHHTTH
T ss_pred             eEEEECccHHHHH
Confidence            3599999987655

>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=96.77  E-value=0.0082  Score=39.88  Aligned_cols=66  Identities=17%  Similarity=0.198  Sum_probs=51.4

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhcccccc
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIK  106 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~  106 (131)
                      ++.|+..|.. .+++|..+||+.+++   ++..+.|+++.|...|++...... ++ ...+.+|+.++.+..
T Consensus        42 ~~~iL~~l~~-~~~~t~~ela~~l~~---~~~~vs~~l~~Le~~Glv~r~~~~~d~R~~~~~lT~~G~~~~~  109 (152)
T 3bj6_A           42 QRAILEGLSL-TPGATAPQLGAALQM---KRQYISRILQEVQRAGLIERRTNPEHARSHRYWLTPRGEAIIT  109 (152)
T ss_dssp             HHHHHHHHHH-STTEEHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEECCSSSTTSCEEEECHHHHHHHH
T ss_pred             HHHHHHHHHh-CCCCCHHHHHHHHCC---CHHHHHHHHHHHHHCCCeeecCCcccccceeeEEChhhHHHHH
Confidence            4457777765 358999999999999   999999999999999999986421 11 124789998876543

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

Probab=96.76  E-value=0.00091  Score=42.45  Aligned_cols=53  Identities=8%  Similarity=0.261  Sum_probs=42.5

Q ss_pred             HHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           30 MSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        30 ~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      .+|.--.++.|+..+.. .++.|+.|||+.+|+   ++..+.+.|+.|... ++....
T Consensus        22 ~aL~~~~Rl~IL~~l~~-~~~~~~~ela~~l~i---s~stvs~hL~~L~~~-lv~~~~   74 (99)
T 2zkz_A           22 KTMAHPMRLKIVNELYK-HKALNVTQIIQILKL---PQSTVSQHLCKMRGK-VLKRNR   74 (99)
T ss_dssp             HHHCSHHHHHHHHHHHH-HSCEEHHHHHHHHTC---CHHHHHHHHHHHBTT-TBEEEE
T ss_pred             HHhCCHHHHHHHHHHHH-CCCcCHHHHHHHHCc---CHHHHHHHHHHHHHH-hhhheE
Confidence            34445567778855543 368999999999999   999999999999999 988654

>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=96.74  E-value=0.0019  Score=43.79  Aligned_cols=45  Identities=9%  Similarity=0.166  Sum_probs=37.6

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchh
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAA  100 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~  100 (131)
                      +. |..+||+..++   ++..|.++|+.|...|++....   |.|.|.++.-
T Consensus        23 ~~-s~~~IA~~~~i---~~~~l~kIl~~L~~aGlv~s~r---G~GGy~Lar~   67 (145)
T 1xd7_A           23 KT-SSEIIADSVNT---NPVVVRRMISLLKKADILTSRA---GVPGASLKKD   67 (145)
T ss_dssp             CC-CHHHHHHHHTS---CHHHHHHHHHHHHHTTSEECCS---SSSSCEESSC
T ss_pred             CC-CHHHHHHHHCc---CHHHHHHHHHHHHHCCceEeec---CCCCceecCC
Confidence            35 99999999999   9999999999999999998765   1455766543

>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=96.74  E-value=0.0014  Score=41.10  Aligned_cols=48  Identities=13%  Similarity=0.251  Sum_probs=41.1

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      .++.|+..|.. .+++|..|||+.+|+   ++..+.|.++.|...|++....
T Consensus        21 ~~~~il~~l~~-~~~~s~~ela~~l~i---s~~tv~~~l~~L~~~glv~~~~   68 (109)
T 1sfx_A           21 SDVRIYSLLLE-RGGMRVSEIARELDL---SARFVRDRLKVLLKRGFVRREI   68 (109)
T ss_dssp             HHHHHHHHHHH-HCCBCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHHH-cCCCCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEEe
Confidence            45567777764 368999999999999   9999999999999999999764

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

Probab=96.74  E-value=0.0011  Score=44.04  Aligned_cols=67  Identities=6%  Similarity=0.030  Sum_probs=52.4

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhcccccc
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIK  106 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~  106 (131)
                      .++.|+..|... +++|..+||+.+++   ++..+.|+++.|...|++...... |+ ...+.+|+.++.+..
T Consensus        32 ~q~~iL~~l~~~-~~~t~~eLa~~l~~---~~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~~~LT~~G~~~~~  100 (145)
T 3g3z_A           32 NLFAVLYTLATE-GSRTQKHIGEKWSL---PKQTVSGVCKTLAGQGLIEWQEGEQDRRKRLLSLTETGKAYAA  100 (145)
T ss_dssp             HHHHHHHHHHHH-CSBCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEECCCSSCGGGSCEEECHHHHHHHH
T ss_pred             HHHHHHHHHHHC-CCCCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEeeccCCCCCceeeeeEChhHHHHHH
Confidence            455577777653 57999999999999   999999999999999999975421 11 234899999886653

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

Probab=96.74  E-value=0.0086  Score=40.89  Aligned_cols=67  Identities=16%  Similarity=0.209  Sum_probs=51.9

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhcccccc
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIK  106 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~  106 (131)
                      .++.|+..|.. .+++|..|||+.+++   ++..+.|+++.|...|++.+.... ++ ...+.+|+.++.+..
T Consensus        46 ~~~~iL~~L~~-~~~~t~~eLa~~l~i---s~~tvs~~l~~Le~~GlV~r~~~~~DrR~~~~~LT~~G~~~~~  114 (168)
T 2nyx_A           46 PQFRTLVILSN-HGPINLATLATLLGV---QPSATGRMVDRLVGAELIDRLPHPTSRRELLAALTKRGRDVVR  114 (168)
T ss_dssp             HHHHHHHHHHH-HCSEEHHHHHHHHTS---CHHHHHHHHHHHHHTTSEEEEECSSCSSCEEEEECHHHHHHHH
T ss_pred             HHHHHHHHHHH-cCCCCHHHHHHHhCC---CHHHHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHHHHHHHH
Confidence            34557777765 358999999999999   999999999999999999985421 11 123789998876554

>1bja_A Transcription regulatory protein MOTA; activation domain, middle mode transcription, alpha helical structure, transcription regulation; 2.19A {Enterobacteria phage T4} SCOP: a.4.5.9 PDB: 1i1s_A

Probab=96.71  E-value=0.0018  Score=41.39  Aligned_cols=63  Identities=16%  Similarity=0.141  Sum_probs=51.2

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHh-hcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhccccccC
Q 040869           36 IELGIADIIHSHGRAITLSELVS-ALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIKD  107 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~-~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~~~  107 (131)
                      .++.|+-.|++.+ +.|+.+||+ ..++   +...+.|=++.|...|++...+    ++ +.+|+.++.+...
T Consensus        17 ~QfsiL~~L~~~~-~~t~~~Lae~~l~~---drstvsrnl~~L~r~GlVe~~~----~D-l~LT~~G~~~l~~   80 (95)
T 1bja_A           17 KTATILITIAKKD-FITAAEVREVHPDL---GNAVVNSNIGVLIKKGLVEKSG----DG-LIITGEAQDIISN   80 (95)
T ss_dssp             HHHHHHHHHHHST-TBCHHHHHHTCTTS---CHHHHHHHHHHHHTTTSEEEET----TE-EEECHHHHHHHHH
T ss_pred             HHHHHHHHHHHCC-CCCHHHHHHHHhcc---cHHHHHHHHHHHHHCCCeecCC----CC-eeeCHhHHHHHHH
Confidence            3455677777754 999999999 9999   9999999999999999999332    44 8999998865543

>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=96.70  E-value=0.001  Score=44.43  Aligned_cols=67  Identities=7%  Similarity=0.115  Sum_probs=44.6

Q ss_pred             HhChHHHHHhCC-CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhcccccc
Q 040869           37 ELGIADIIHSHG-RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIK  106 (131)
Q Consensus        37 ~L~ifd~l~~~~-~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~  106 (131)
                      ++.|+..|...+ +++|..|||+.+++   ++..+.|+++.|...|++...... |+ ...+.+|+.++.+..
T Consensus        43 q~~vL~~l~~~~~~~~t~~eLa~~l~~---~~~~vs~~l~~L~~~Glv~r~~~~~DrR~~~~~LT~~G~~~~~  112 (148)
T 3jw4_A           43 QGRMIGYIYENQESGIIQKDLAQFFGR---RGASITSMLQGLEKKGYIERRIPENNARQKNIYVLPKGAALVE  112 (148)
T ss_dssp             HHHHHHHHHHHTTTCCCHHHHHHC---------CHHHHHHHHHHTTSBCCC--------CCCCBCHHHHHHHH
T ss_pred             HHHHHHHHHhCCCCCCCHHHHHHHHCC---ChhHHHHHHHHHHHCCCEEeeCCCCCchhheeeECHHHHHHHH
Confidence            344666776543 78999999999999   999999999999999999876421 11 234789999886654

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

Probab=96.68  E-value=0.0062  Score=41.20  Aligned_cols=67  Identities=13%  Similarity=0.149  Sum_probs=51.6

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-CcceecchhccccccC
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIKD  107 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~~  107 (131)
                      ++.|+..|... +++|..|||+.+++   ++..+.|+++.|...|++...... |+ ...+.+|+.++.+...
T Consensus        55 q~~vL~~l~~~-~~~t~~eLa~~l~~---~~~~vs~~l~~Le~~Glv~r~~~~~DrR~~~~~LT~~G~~~~~~  123 (161)
T 3e6m_A           55 KLRLLSSLSAY-GELTVGQLATLGVM---EQSTTSRTVDQLVDEGLAARSISDADQRKRTVVLTRKGKKKLAE  123 (161)
T ss_dssp             HHHHHHHHHHH-SEEEHHHHHHHTTC---CHHHHHHHHHHHHHTTSEEECC---CCCSCEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHhC-CCCCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEeeCCcccCCeeEeeECHHHHHHHHH
Confidence            34477777653 58999999999999   999999999999999999986432 11 2348899998866543

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

Probab=96.67  E-value=0.0011  Score=44.78  Aligned_cols=67  Identities=13%  Similarity=0.104  Sum_probs=52.0

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhcccccc
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIK  106 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~  106 (131)
                      .++.|+..|.. .+++|..+||+.+++   ++..+.|+++.|...|++...... ++ ...|.+|+.++.+..
T Consensus        53 ~~~~iL~~l~~-~~~~t~~ela~~l~i---s~~tvs~~l~~Le~~Gli~r~~~~~d~R~~~~~lT~~G~~~~~  121 (162)
T 3cjn_A           53 AKMRALAILSA-KDGLPIGTLGIFAVV---EQSTLSRALDGLQADGLVRREVDSDDQRSSRVYLTPAGRAVYD  121 (162)
T ss_dssp             HHHHHHHHHHH-SCSEEHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEEEC--CCSSEEEEECHHHHHHHH
T ss_pred             HHHHHHHHHHH-CCCCCHHHHHHHHCC---ChhHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHH
Confidence            34557777775 468999999999999   999999999999999999976421 11 234889998876553

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

Probab=96.67  E-value=0.0017  Score=41.55  Aligned_cols=55  Identities=13%  Similarity=0.117  Sum_probs=45.8

Q ss_pred             CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhccccc
Q 040869           48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLI  105 (131)
Q Consensus        48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~  105 (131)
                      +++++..+||+.+++   +...|.|++..|...|++......++.+...+|+.++.+.
T Consensus        34 g~~~s~~eLa~~l~l---~~stLsR~l~rLe~~GLV~r~~~~D~R~~v~LT~~G~~~l   88 (96)
T 2obp_A           34 ATPWSLPKIAKRAQL---PMSVLRRVLTQLQAAGLADVSVEADGRGHASLTQEGAALA   88 (96)
T ss_dssp             CCCCBHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEEECTTSCEEEEECHHHHHHH
T ss_pred             CCCcCHHHHHHHhCC---chhhHHHHHHHHHHCCCEEeecCCCCceeEEECHHHHHHH
Confidence            478999999999999   9999999999999999999854334455678888877543

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

Probab=96.67  E-value=0.0016  Score=43.69  Aligned_cols=68  Identities=15%  Similarity=0.176  Sum_probs=52.0

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-CcceecchhccccccC
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIKD  107 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~~  107 (131)
                      .++.|+..|.. .+++|..+||+.+++   ++..+.|+++.|...|++...... ++ .-.+.+|+.++.+...
T Consensus        48 ~~~~iL~~l~~-~~~~t~~ela~~l~~---s~~tvs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~~~~~  117 (153)
T 2pex_A           48 PQYLVMLVLWE-TDERSVSEIGERLYL---DSATLTPLLKRLQAAGLVTRTRAASDERQVIIALTETGRALRSK  117 (153)
T ss_dssp             HHHHHHHHHHH-SCSEEHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEEC-------CEEEECHHHHHGGGG
T ss_pred             HHHHHHHHHHh-CCCcCHHHHHHHhCC---CcccHHHHHHHHHHCCCEeecCCcccCCeeEeeECHHHHHHHHH
Confidence            34557777775 468999999999999   999999999999999999986421 11 1248899998866544

>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=96.66  E-value=0.0013  Score=41.38  Aligned_cols=37  Identities=22%  Similarity=0.283  Sum_probs=34.7

Q ss_pred             CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      ++++|..|||+.+|+   ++..+.|+++.|...|++.+..
T Consensus        34 ~~~~t~~ela~~l~i---s~~tv~~~l~~L~~~g~v~~~~   70 (109)
T 2d1h_A           34 EKPITSEELADIFKL---SKTTVENSLKKLIELGLVVRTK   70 (109)
T ss_dssp             CSCEEHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCeEeec
Confidence            478999999999999   9999999999999999999865

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

Probab=96.66  E-value=0.0012  Score=42.33  Aligned_cols=48  Identities=19%  Similarity=0.286  Sum_probs=40.4

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      .++.|+..+...|.++|..+||+.+|+   +...+++.|+.|...|++...
T Consensus        19 ~~l~Il~~l~~~g~~~s~~eLa~~lgv---s~~tV~~~L~~L~~~GlV~~~   66 (110)
T 1q1h_A           19 DVIDVLRILLDKGTEMTDEEIANQLNI---KVNDVRKKLNLLEEQGFVSYR   66 (110)
T ss_dssp             TTHHHHHHHHHHCSCBCHHHHHHTTTS---CHHHHHHHHHHHHHHTSCEEE
T ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEE
Confidence            345677777433557999999999999   999999999999999999876

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

Probab=96.65  E-value=0.0028  Score=43.02  Aligned_cols=68  Identities=16%  Similarity=0.160  Sum_probs=52.1

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-CcceecchhccccccC
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIKD  107 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~~  107 (131)
                      ++.|.-.|...+++.+..|||+.+++   ++..+.|+++.|...|++.+.... |+ .-...+|+.++.+...
T Consensus        33 q~~vL~~L~~~~~~~~~~eLa~~l~~---~~~tvs~~v~~Le~~GlV~R~~~~~DrR~~~l~LT~~G~~~~~~  102 (151)
T 4aik_A           33 HWVTLYNINRLPPEQSQIQLAKAIGI---EQPSLVRTLDQLEEKGLITRHTSANDRRAKRIKLTEQSSPIIEQ  102 (151)
T ss_dssp             HHHHHHHHHHSCTTSCHHHHHHHHTS---CHHHHHHHHHHHHHTTSEEEEECSSCTTCEEEEECGGGHHHHHH
T ss_pred             HHHHHHHHHHcCCCCcHHHHHHHHCc---CHHHHHHHHHHHHhCCCeEeecCCCCCcchhhhcCHHHHHHHHH
Confidence            33456666655667899999999999   999999999999999999976532 21 1247889998866543

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

Probab=96.65  E-value=0.0015  Score=42.88  Aligned_cols=66  Identities=18%  Similarity=0.203  Sum_probs=51.0

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhcccccc
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIK  106 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~  106 (131)
                      ++.|+..|.. .+++|..+||+.+++   ++..+.++++.|...|++...... ++ ...+.+|+.++.+..
T Consensus        36 ~~~iL~~l~~-~~~~~~~~la~~l~~---~~~tvs~~l~~L~~~gli~r~~~~~d~R~~~~~lT~~G~~~~~  103 (138)
T 1jgs_A           36 QFKVLCSIRC-AACITPVELKKVLSV---DLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTGGAAICE  103 (138)
T ss_dssp             HHHHHHHHHH-HSSBCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEEECTTCSSCEEEEECHHHHHHHH
T ss_pred             HHHHHHHHHh-cCCCCHHHHHHHHCC---ChHHHHHHHHHHHHCCCEEecCCcccCceeEeEEChhHHHHHH
Confidence            4446666764 368999999999999   999999999999999999986421 11 123889999886654

>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=96.63  E-value=0.0046  Score=40.87  Aligned_cols=66  Identities=12%  Similarity=0.141  Sum_probs=50.0

Q ss_pred             hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-CcceecchhccccccC
Q 040869           38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIKD  107 (131)
Q Consensus        38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~~  107 (131)
                      +.|...|.. .+++|..|||+.+++   ++..+.|+++.|...|++...... |+ ...+.+|+.++.+...
T Consensus        39 ~~vL~~l~~-~~~~t~~eLa~~l~~---~~~tvs~~l~~L~~~Glv~r~~~~~D~R~~~~~LT~~G~~~~~~  106 (140)
T 3hsr_A           39 YIVLMAIEN-DEKLNIKKLGERVFL---DSGTLTPLLKKLEKKDYVVRTREEKDERNLQISLTEQGKAIKSP  106 (140)
T ss_dssp             HHHHHHSCT-TCEEEHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEEC-------CEEEECHHHHHTHHH
T ss_pred             HHHHHHHHH-cCCcCHHHHHHHHCC---ChhhHHHHHHHHHHCCCeEecCCCCCcceeeeeEChHHHHHHHH
Confidence            335555654 468999999999999   999999999999999999976422 11 2358899998866543

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

Probab=96.61  E-value=0.0012  Score=44.28  Aligned_cols=76  Identities=14%  Similarity=0.163  Sum_probs=54.9

Q ss_pred             HHHHHHHHHhHHHHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhc-CCCCCCcchHHHHHHHhhcCCceeecccC-CC-C
Q 040869           16 QAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSAL-DIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-E   92 (131)
Q Consensus        16 ~~~l~~~~~~~~~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~-~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~   92 (131)
                      ...++++..+.|...         |...|.  .++++..||++.+ |+   ++..+.+.|+.|...|++.+.... ++ .
T Consensus        25 ~~~~l~~l~~~w~l~---------IL~~L~--~g~~~~~eLa~~l~gi---s~~tls~~L~~Le~~GlV~r~~~~~d~r~   90 (131)
T 1yyv_A           25 SREVLKHVTSRWGVL---------ILVALR--DGTHRFSDLRRXMGGV---SEXMLAQSLQALEQDGFLNRVSYPVVPPH   90 (131)
T ss_dssp             HHHHHHHHHSHHHHH---------HHHHGG--GCCEEHHHHHHHSTTC---CHHHHHHHHHHHHHHTCEEEEEECSSSCE
T ss_pred             HHHHHHHHcCCcHHH---------HHHHHH--cCCCCHHHHHHHhccC---CHHHHHHHHHHHHHCCcEEEEecCCCCCe
Confidence            344555555555543         333344  3689999999999 79   999999999999999999976421 11 1


Q ss_pred             cceecchhccccc
Q 040869           93 EAYGLTAASTLLI  105 (131)
Q Consensus        93 ~~y~~t~~s~~L~  105 (131)
                      -.|.+|+.++.+.
T Consensus        91 ~~y~LT~~G~~l~  103 (131)
T 1yyv_A           91 VEYSLTPLGEQVS  103 (131)
T ss_dssp             EEEEECHHHHHHH
T ss_pred             EEEEECccHHHHH
Confidence            3599999987654

>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=96.61  E-value=0.0018  Score=43.55  Aligned_cols=68  Identities=10%  Similarity=0.024  Sum_probs=52.7

Q ss_pred             HHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhcccccc
Q 040869           35 AIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIK  106 (131)
Q Consensus        35 a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~  106 (131)
                      ..++.|+..|... +++|..+||+.+++   ++..+.|+++.|...|++...... ++ ...|.+|+.++.+..
T Consensus        44 ~~~~~iL~~l~~~-~~~t~~ela~~l~i---s~~tvs~~l~~Le~~Gli~r~~~~~d~R~~~~~lT~~G~~~~~  113 (154)
T 2eth_A           44 TTELYAFLYVALF-GPKKMKEIAEFLST---TKSNVTNVVDSLEKRGLVVREMDPVDRRTYRVVLTEKGKEIFG  113 (154)
T ss_dssp             HHHHHHHHHHHHH-CCBCHHHHHHHTTS---CHHHHHHHHHHHHHTTSEEEEECTTTSSCEEEEECHHHHHHHH
T ss_pred             HHHHHHHHHHHHc-CCCCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEeeCCCCCcceeEEEECHHHHHHHH
Confidence            3456677778653 58999999999999   999999999999999999986421 11 124788998886654

>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=96.60  E-value=0.0042  Score=43.10  Aligned_cols=48  Identities=17%  Similarity=0.258  Sum_probs=39.8

Q ss_pred             CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchh
Q 040869           48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAA  100 (131)
Q Consensus        48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~  100 (131)
                      ++++|..+||+.+++   ++..+.++|..|...|++.....  ..|.|.+..-
T Consensus        26 ~~~~s~~~IA~~~~i---s~~~l~kil~~L~~aGlv~s~rG--~~GGy~Lar~   73 (162)
T 3k69_A           26 DSKVASRELAQSLHL---NPVMIRNILSVLHKHGYLTGTVG--KNGGYQLDLA   73 (162)
T ss_dssp             TSCBCHHHHHHHHTS---CGGGTHHHHHHHHHTTSSEEECS--TTCEEECCSC
T ss_pred             CCCcCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEeecC--CCCCeEecCC
Confidence            478999999999999   99999999999999999976541  1356876643

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

Probab=96.59  E-value=0.0015  Score=43.43  Aligned_cols=66  Identities=9%  Similarity=0.109  Sum_probs=50.9

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhcccccc
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIK  106 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~  106 (131)
                      ++.|+..|.. .+++|..+||+.+++   ++..+.|+++.|...|++...... ++ ...+.+|+.++.+..
T Consensus        44 ~~~iL~~l~~-~~~~t~~ela~~l~~---~~~tvs~~l~~Le~~Glv~r~~~~~d~R~~~~~lT~~G~~~~~  111 (150)
T 2rdp_A           44 QFVALQWLLE-EGDLTVGELSNKMYL---ACSTTTDLVDRMERNGLVARVRDEHDRRVVRIRLLEKGERIIE  111 (150)
T ss_dssp             HHHHHHHHHH-HCSBCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEEECCC---CEEEEECHHHHHHHH
T ss_pred             HHHHHHHHHH-cCCCCHHHHHHHHCC---CchhHHHHHHHHHHCCCeeecCCCCCcceeEeEECHhHHHHHH
Confidence            4446777765 368999999999999   999999999999999999975421 11 124889998886654

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

Probab=96.59  E-value=0.0016  Score=43.06  Aligned_cols=66  Identities=8%  Similarity=0.027  Sum_probs=51.1

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhcccccc
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIK  106 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~  106 (131)
                      ++.|+..|.. .+++|..+||+.+++   ++..+.|+++.|...|++...... ++ ...+.+|+.++.+..
T Consensus        31 ~~~iL~~l~~-~~~~t~~~la~~l~~---s~~~vs~~l~~Le~~gli~r~~~~~d~R~~~~~lT~~G~~~~~   98 (144)
T 1lj9_A           31 QYLYLVRVCE-NPGIIQEKIAELIKV---DRTTAARAIKRLEEQGFIYRQEDASNKKIKRIYATEKGKNVYP   98 (144)
T ss_dssp             HHHHHHHHHH-STTEEHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEEECSSCTTCEEEEECHHHHHHHH
T ss_pred             HHHHHHHHHH-CcCcCHHHHHHHHCC---CHhHHHHHHHHHHHCCCEEeecCCCCCceeeeEEChhHHHHHH
Confidence            3446777765 358999999999999   999999999999999999986421 11 123789999886554

>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=96.57  E-value=0.0016  Score=43.03  Aligned_cols=67  Identities=15%  Similarity=0.221  Sum_probs=51.8

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhcccccc
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIK  106 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~  106 (131)
                      .++.|+..|.. .+++|..+||+.+++   ++..+.|+++.|...|++...... ++ .-.+.+|+.++.+..
T Consensus        38 ~~~~iL~~l~~-~~~~~~~ela~~l~~---~~~tvs~~l~~L~~~gli~r~~~~~d~R~~~~~lT~~G~~~~~  106 (142)
T 2bv6_A           38 PQFLVLTILWD-ESPVNVKKVVTELAL---DTGTVSPLLKRMEQVDLIKRERSEVDQREVFIHLTDKSETIRP  106 (142)
T ss_dssp             HHHHHHHHHHH-SSEEEHHHHHHHTTC---CTTTHHHHHHHHHHTTSEEEEECSSSTTCEEEEECHHHHHHHH
T ss_pred             HHHHHHHHHHH-cCCcCHHHHHHHHCC---ChhhHHHHHHHHHHCCCEEeecCCCCcceEEEEEChHHHHHHH
Confidence            34557777775 357999999999999   999999999999999999976421 11 124788998876554

>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=96.56  E-value=0.0013  Score=40.01  Aligned_cols=48  Identities=19%  Similarity=0.339  Sum_probs=41.0

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcC----CCCCCcchHHHHHHHhhcCCceeecc
Q 040869           36 IELGIADIIHSHGRAITLSELVSALD----IQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~----~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      .+..|...|.. .+++|+.||++.++    +   ++..+.|+|+.|...|++....
T Consensus        10 ~e~~vL~~L~~-~~~~t~~ei~~~l~~~~~~---s~~Tv~~~l~rL~~kGlv~r~~   61 (82)
T 1p6r_A           10 AELEVMKVIWK-HSSINTNEVIKELSKTSTW---SPKTIQTMLLRLIKKGALNHHK   61 (82)
T ss_dssp             HHHHHHHHHHT-SSSEEHHHHHHHHHHHSCC---CHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHHc-CCCCCHHHHHHHHhhcCCc---cHHHHHHHHHHHHHCCCeEEEe
Confidence            45567788875 57899999999997    5   7889999999999999999875

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

Probab=96.54  E-value=0.0012  Score=43.35  Aligned_cols=67  Identities=12%  Similarity=0.079  Sum_probs=51.4

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhcccccc
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIK  106 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~  106 (131)
                      .++.|+..|.. .+++|..+||+.+++   ++..+.|+++.|...|++...... ++ ...|.+|+.++.+..
T Consensus        37 ~~~~iL~~l~~-~~~~t~~ela~~l~~---s~~~vs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~~~~  105 (142)
T 2fbi_A           37 QQWRVIRILRQ-QGEMESYQLANQACI---LRPSMTGVLARLERDGIVRRWKAPKDQRRVYVNLTEKGQQCFV  105 (142)
T ss_dssp             HHHHHHHHHHH-HCSEEHHHHHHHTTC---CHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHHH
T ss_pred             HHHHHHHHHHH-cCCCCHHHHHHHHCC---CHhHHHHHHHHHHHCCCEEeecCCCCCCeeEEEECHHHHHHHH
Confidence            35557777765 357999999999999   999999999999999999876321 10 123788998886553

>2qm3_A Predicted methyltransferase; putative methyltransferase, structural genomics, pyrococcus PSI-2, protein structure initiative; HET: MSE; 2.05A {Pyrococcus furiosus dsm 3638}

Probab=96.52  E-value=0.00087  Score=52.01  Aligned_cols=56  Identities=9%  Similarity=0.071  Sum_probs=47.8

Q ss_pred             ChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcc-cccc
Q 040869           39 GIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAST-LLIK  106 (131)
Q Consensus        39 ~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~-~L~~  106 (131)
                      +||..| +  +|.|+.|||.++|.   ++..+.++|+.|++.|+++..     ++ |.+|+.+. +|.+
T Consensus        47 ~ll~~L-~--~~~t~~eLa~~~g~---~~~~v~~~L~~l~~~gll~~~-----~~-~~lt~~~~~~l~~  103 (373)
T 2qm3_A           47 NVLSAV-L--ASDDIWRIVDLSEE---PLPLVVAILESLNELGYVTFE-----DG-VKLTEKGEELVAE  103 (373)
T ss_dssp             HHHHHH-H--HCSCHHHHHHHHTS---CHHHHHHHHHHHHHTTSEECS-----SS-SEECHHHHHHHHH
T ss_pred             HHHHHh-c--CCCCHHHHHHHhCC---ChHHHHHHHHHHhhCCcEEEC-----CC-EEECHHHHHHHHh
Confidence            778888 3  58999999999999   999999999999999999864     44 99999766 4443

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

Probab=96.49  E-value=0.0014  Score=44.85  Aligned_cols=68  Identities=16%  Similarity=0.173  Sum_probs=49.3

Q ss_pred             HHhChHHHHHhC-CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhcccccc
Q 040869           36 IELGIADIIHSH-GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIK  106 (131)
Q Consensus        36 ~~L~ifd~l~~~-~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~  106 (131)
                      .++.|...|... ++++|..|||+.+++   ++..+.|+++.|...|++...... |+ .-.+.+|+.++.+..
T Consensus        47 ~q~~vL~~l~~~~~~~~t~~eLa~~l~~---~~~tvs~~l~~Le~~Glv~r~~~~~DrR~~~l~LT~~G~~~~~  117 (168)
T 3u2r_A           47 QQYNTLRLLRSVHPEGMATLQIADRLIS---RAPDITRLIDRLDDRGLVLRTRKPENRRVVEVALTDAGLKLLK  117 (168)
T ss_dssp             HHHHHHHHHHHHTTSCEEHHHHHHHC------CTHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCCcCHHHHHHHHCC---ChhhHHHHHHHHHHCCCEeecCCCCCCCeeEeEECHHHHHHHH
Confidence            345567777654 368999999999999   999999999999999999986421 10 124788998886654

>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=96.49  E-value=0.0024  Score=42.30  Aligned_cols=68  Identities=10%  Similarity=0.166  Sum_probs=52.6

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-CcceecchhccccccC
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIKD  107 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~~  107 (131)
                      .++.|+..|.. .+++|..+||+.+++   ++..+.|+++.|...|++...... ++ ...+.+|+.++.+...
T Consensus        41 ~~~~iL~~l~~-~~~~~~~~la~~l~~---~~~tvs~~l~~L~~~glv~r~~~~~d~R~~~~~LT~~G~~~~~~  110 (147)
T 1z91_A           41 PQYLALLLLWE-HETLTVKKMGEQLYL---DSGTLTPMLKRMEQQGLITRKRSEEDERSVLISLTEDGALLKEK  110 (147)
T ss_dssp             HHHHHHHHHHH-HSEEEHHHHHHTTTC---CHHHHHHHHHHHHHHTSEECCBCSSCTTSBEEEECHHHHSGGGG
T ss_pred             HHHHHHHHHHH-CCCCCHHHHHHHHCC---CcCcHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHHHHHH
Confidence            44556777765 358999999999999   999999999999999999976421 11 2237899998876654

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

Probab=96.48  E-value=0.014  Score=38.90  Aligned_cols=67  Identities=13%  Similarity=0.149  Sum_probs=50.2

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhcccccc
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIK  106 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~  106 (131)
                      .++.|...|.. .+++|..|||+.+++   ++..+.|+++.|...|++...... |+ ...+.+|+.++.+..
T Consensus        42 ~q~~iL~~l~~-~~~~~~~eLa~~l~~---~~~~vs~~l~~L~~~Glv~r~~~~~D~R~~~~~LT~~G~~~~~  110 (149)
T 4hbl_A           42 SQYLVMLTLWE-ENPQTLNSIGRHLDL---SSNTLTPMLKRLEQSGWVKRERQQSDKRQLIITLTDNGQQQQE  110 (149)
T ss_dssp             HHHHHHHHHHH-SSSEEHHHHHHHHTC---CHHHHHHHHHHHHHHTSEEC---------CEEEECSHHHHHHH
T ss_pred             HHHHHHHHHHH-CCCCCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEeeCCCCCCcceeeeeECHHHHHHHH
Confidence            34556777765 478999999999999   999999999999999999976421 11 234889998886653

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

Probab=96.47  E-value=0.0018  Score=43.85  Aligned_cols=66  Identities=17%  Similarity=0.095  Sum_probs=50.9

Q ss_pred             hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-CcceecchhccccccC
Q 040869           38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIKD  107 (131)
Q Consensus        38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~~  107 (131)
                      +.|+..|.. .+++|..|||+.+++   ++..+.|+++.|...|++...... ++ ...+.+|+.++.+...
T Consensus        53 ~~vL~~l~~-~~~~t~~eLa~~l~~---~~~tvs~~l~~Le~~Glv~r~~~~~DrR~~~l~LT~~G~~~~~~  120 (159)
T 3s2w_A           53 FPFLMRLYR-EDGINQESLSDYLKI---DKGTTARAIQKLVDEGYVFRQRDEKDRRSYRVFLTEKGKKLEPD  120 (159)
T ss_dssp             HHHHHHHHH-SCSEEHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEEECC---CCEEEEECHHHHHHHHH
T ss_pred             HHHHHHHHH-CCCCCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEecCCCCCCeeEEEECHHHHHHHHH
Confidence            336666765 468999999999999   999999999999999999976422 11 1247899998866543

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

Probab=96.44  E-value=0.0041  Score=41.85  Aligned_cols=47  Identities=15%  Similarity=0.263  Sum_probs=41.4

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      .+..|.+.|.+ ++++|..|||+++|+   ++..+.|.++.|...|++...
T Consensus         6 ~d~~il~~L~~-~~~~s~~ela~~lg~---s~~tv~~~l~~L~~~G~i~~~   52 (144)
T 2cfx_A            6 IDLNIIEELKK-DSRLSMRELGRKIKL---SPPSVTERVRQLESFGIIKQY   52 (144)
T ss_dssp             HHHHHHHHHHH-CSCCCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHH-cCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCeEEE
Confidence            35568888875 478999999999999   999999999999999999864

>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=96.43  E-value=0.002  Score=43.81  Aligned_cols=62  Identities=10%  Similarity=0.183  Sum_probs=45.2

Q ss_pred             HHHhChHHHHHhCCCCCCHHHHHhhcCC--CCCCcchHHHHHHHhhcCCceeecccCCCCcceec
Q 040869           35 AIELGIADIIHSHGRAITLSELVSALDI--QPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGL   97 (131)
Q Consensus        35 a~~L~ifd~l~~~~~~~s~~eLA~~~~~--~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~   97 (131)
                      ..+..|++.|.+.+ +.|++||.+.+.-  ...+..++||.|+.|+..|++.+....++..+|..
T Consensus        19 ~qR~~Il~~l~~~~-h~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Glv~~i~~~~~~~~Y~~   82 (145)
T 3eyy_A           19 PQRQLVLEAVDTLE-HATPDDILGEVRKTASGINISTVYRTLELLEELGLVSHAHLGHGAPTYHL   82 (145)
T ss_dssp             HHHHHHHHHHHHHS-SBCHHHHHHHHHTTCTTCCHHHHHHHHHHHHHHTSEEEEECGGGCEEEEE
T ss_pred             HHHHHHHHHHHhcC-CCCHHHHHHHHHhhCCCCCHhHHHHHHHHHHHCCcEEEEEeCCCceEEEe
Confidence            35566888887655 8999999998732  11188899999999999999998653222335764

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

Probab=96.42  E-value=0.0042  Score=41.98  Aligned_cols=47  Identities=17%  Similarity=0.162  Sum_probs=41.2

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      .+..|...|.+ ++++|..|||+++|+   ++..+.|.++.|...|++...
T Consensus         8 ~~~~iL~~L~~-~~~~s~~ela~~lg~---s~~tv~~~l~~L~~~G~i~~~   54 (150)
T 2w25_A            8 IDRILVRELAA-DGRATLSELATRAGL---SVSAVQSRVRRLESRGVVQGY   54 (150)
T ss_dssp             HHHHHHHHHHH-CTTCCHHHHHHHHTS---CHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHH-cCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEE
Confidence            45667888875 468999999999999   999999999999999999764

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

Probab=96.39  E-value=0.0015  Score=41.86  Aligned_cols=50  Identities=18%  Similarity=0.185  Sum_probs=40.4

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCCC-CCCcchHHHHHHHhhcCCceeecc
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDIQ-PTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~-~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      +..|...|.+ .+++|+.||+++++.. +-++..+.|+|+.|...|++.+..
T Consensus        37 e~~VL~~L~~-~~~~t~~eL~~~l~~~~~~s~sTVt~~L~rLe~KGlV~R~~   87 (99)
T 2k4b_A           37 ELIVMRVIWS-LGEARVDEIYAQIPQELEWSLATVKTLLGRLVKKEMLSTEK   87 (99)
T ss_dssp             CSHHHHHHHH-HSCEEHHHHHHTCCGGGCCCHHHHHHHHHHHHHTTSCEEEE
T ss_pred             HHHHHHHHHh-CCCCCHHHHHHHHhcccCCCHhhHHHHHHHHHHCCCEEEEe
Confidence            4557888875 4689999999999751 115789999999999999999875

>3u1d_A Uncharacterized protein; GNTR-superfamily, structural genomics, PSI-biology, midwest for structural genomics, MCSG; 1.80A {Halomicrobium mukohataei}

Probab=96.38  E-value=0.0053  Score=42.38  Aligned_cols=67  Identities=18%  Similarity=0.192  Sum_probs=52.1

Q ss_pred             HHhChHHHHHhCC-CCCCHHHHHhhcC-CCCCCcchHHHHHHHhhcCCceeecccCC---CC----cceecchhccccc
Q 040869           36 IELGIADIIHSHG-RAITLSELVSALD-IQPTKTTGLFRLMRLLVHSSCFNKTKVNG---QE----EAYGLTAASTLLI  105 (131)
Q Consensus        36 ~~L~ifd~l~~~~-~~~s~~eLA~~~~-~~~~~~~~l~RlLr~L~~~gl~~~~~~~~---~~----~~y~~t~~s~~L~  105 (131)
                      .++.|+..|.... +..|+.||++.++ +   +...++|-|+.|+..|++.+....+   +.    ..|.+|+.++.+.
T Consensus        30 tR~~IL~~Ll~~p~~~~ta~eL~~~l~~l---S~aTVyrhL~~L~eaGLV~~~~~~~~~~~rGrP~k~Y~LT~~Gr~~l  105 (151)
T 3u1d_A           30 TRLDVLHQILAQPDGVLSVEELLYRNPDE---TEANLRYHVDELVDRGIVEKIPVPRAKSVDDPPTTFYAVTGEGIALL  105 (151)
T ss_dssp             HHHHHHHHHHHSTTSCBCHHHHHHHCTTS---CHHHHHHHHHHHHHTTSEEEEECCCCTTSSSCCCEEEEECHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCCCCHHHHHHhcCCC---CHHHHHHHHHHHHHCCCeEEeecCcCcccCCCCceEEEECHHHHHHH
Confidence            6677788776443 5689999999999 9   9999999999999999999653210   11    2699999998443

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

Probab=96.37  E-value=0.0025  Score=45.95  Aligned_cols=52  Identities=21%  Similarity=0.301  Sum_probs=46.9

Q ss_pred             CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcccccc
Q 040869           48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIK  106 (131)
Q Consensus        48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~~  106 (131)
                      +++++..+||+.+++   ++..+.++++.|...|++....    .+.+.+|+.++.+..
T Consensus        18 ~~~~~~~~lA~~l~v---s~~tvs~~l~~Le~~GlV~r~~----~~~i~LT~~G~~~~~   69 (214)
T 3hrs_A           18 HNKITNKEIAQLMQV---SPPAVTEMMKKLLAEELLIKDK----KAGYLLTDLGLKLVS   69 (214)
T ss_dssp             CSCCCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEET----TTEEEECHHHHHHHH
T ss_pred             CCCcCHHHHHHHHCC---ChhHHHHHHHHHHHCCCEEEec----CCCeEECHHHHHHHH
Confidence            578999999999999   9999999999999999999886    678999999886653

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

Probab=96.36  E-value=0.0033  Score=42.39  Aligned_cols=47  Identities=19%  Similarity=0.273  Sum_probs=41.7

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      .+..|...|.+ ++++|..|||+++|+   ++..+.|.++.|...|++...
T Consensus         4 ~~~~il~~L~~-~~~~~~~ela~~lg~---s~~tv~~~l~~L~~~G~i~~~   50 (150)
T 2pn6_A            4 IDLRILKILQY-NAKYSLDEIAREIRI---PKATLSYRIKKLEKDGVIKGY   50 (150)
T ss_dssp             HHHHHHHHHTT-CTTSCHHHHHHHHTS---CHHHHHHHHHHHHHTTSSCCC
T ss_pred             HHHHHHHHHHH-cCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCcEEEE
Confidence            46678888875 468999999999999   999999999999999999864

>4ets_A Ferric uptake regulation protein; metal binding protein, transcription factor; 2.10A {Campylobacter jejuni subsp}

Probab=96.35  E-value=0.0049  Score=42.70  Aligned_cols=64  Identities=11%  Similarity=0.126  Sum_probs=45.7

Q ss_pred             HHHhChHHHHHhCCCCCCHHHHHhhcCC----CCCCcchHHHHHHHhhcCCceeecccCCCCcceecc
Q 040869           35 AIELGIADIIHSHGRAITLSELVSALDI----QPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLT   98 (131)
Q Consensus        35 a~~L~ifd~l~~~~~~~s~~eLA~~~~~----~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t   98 (131)
                      .-+.-|++.|.+.++++|++||.+.+.-    ...+..++||.|..|+..|++.+....++..+|...
T Consensus        33 ~qR~~IL~~L~~~~~h~sA~eI~~~l~~~~~~~~is~aTVYRtL~~L~e~Glv~~i~~~~~~~~Y~~~  100 (162)
T 4ets_A           33 KQREVLLKTLYHSDTHYTPESLYMEIKQAEPDLNVGIATVYRTLNLLEEAEMVTSISFGSAGKKYELA  100 (162)
T ss_dssp             HHHHHHHHHHHSCCSCBCHHHHHHHHHHHCGGGCCCHHHHHHHHHHHHHTTSEEECC-----CCEEEC
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHCCCEEEEEeCCCceEEEeC
Confidence            3566789999876789999999887621    011788999999999999999987422223457654

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

Probab=96.33  E-value=0.0013  Score=45.59  Aligned_cols=67  Identities=10%  Similarity=0.107  Sum_probs=50.7

Q ss_pred             HhChHHHHHhCCCC--CCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhcccccc
Q 040869           37 ELGIADIIHSHGRA--ITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIK  106 (131)
Q Consensus        37 ~L~ifd~l~~~~~~--~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~  106 (131)
                      ++.|+..|...++|  +|..|||+.+++   ++..+.|+++.|...|++...... ++ .-.+.+|+.++.+..
T Consensus        71 ~~~iL~~L~~~~~~~~~t~~eLa~~l~i---s~~tvs~~l~~Le~~GlV~r~~~~~DrR~~~~~LT~~G~~~~~  141 (181)
T 2fbk_A           71 GWDLLLTLYRSAPPEGLRPTELSALAAI---SGPSTSNRIVRLLEKGLIERREDERDRRSASIRLTPQGRALVT  141 (181)
T ss_dssp             HHHHHHHHHHHCCSSCBCHHHHHHHCSC---CSGGGSSHHHHHHHHTSEECCC-------CCBEECHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCCCCHHHHHHHHCC---CHHHHHHHHHHHHHCcCEEecCCCCCCCeeEEEECHHHHHHHH
Confidence            45577777654443  999999999999   999999999999999999976421 11 134889999886654

>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=96.32  E-value=0.0019  Score=42.45  Aligned_cols=67  Identities=15%  Similarity=0.301  Sum_probs=51.5

Q ss_pred             HhChHHHHHhC-CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhcccccc
Q 040869           37 ELGIADIIHSH-GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIK  106 (131)
Q Consensus        37 ~L~ifd~l~~~-~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~  106 (131)
                      ++.|...|... ++++|..|||+.+++   ++..+.|+++.|...|++...... |+ ...+.+|+.++.+..
T Consensus        39 q~~vL~~l~~~~~~~~t~~eLa~~l~~---~~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~i~LT~~G~~~~~  108 (127)
T 2frh_A           39 EFAVLTYISENKEKEYYLKDIINHLNY---KQPQVVKAVKILSQEDYFDKKRNEHDERTVLILVNAQQRKKIE  108 (127)
T ss_dssp             HHHHHHHHHHTCCSEEEHHHHHHHSSS---HHHHHHHHHHHHHHTTSSCCBCCSSSSCCCEEECCSHHHHHHH
T ss_pred             HHHHHHHHHhccCCCcCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHH
Confidence            44466667653 268999999999999   999999999999999999985422 11 234789998886654

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

Probab=96.32  E-value=0.0049  Score=42.18  Aligned_cols=47  Identities=13%  Similarity=0.252  Sum_probs=41.3

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      .+..|...|.+ ++++|..|||+++|+   ++..+.|.++.|...|++...
T Consensus        11 ~~~~il~~L~~-~~~~s~~ela~~lg~---s~~tv~~~l~~L~~~G~i~~~   57 (162)
T 2p5v_A           11 TDIKILQVLQE-NGRLTNVELSERVAL---SPSPCLRRLKQLEDAGIVRQY   57 (162)
T ss_dssp             HHHHHHHHHHH-CTTCCHHHHHHHHTS---CHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHH-cCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEeee
Confidence            35568888876 468999999999999   999999999999999999864

>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=96.26  E-value=0.0041  Score=43.55  Aligned_cols=70  Identities=10%  Similarity=0.047  Sum_probs=54.5

Q ss_pred             HHHHhChHHHHHhC-CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhcccccc
Q 040869           34 CAIELGIADIIHSH-GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIK  106 (131)
Q Consensus        34 ~a~~L~ifd~l~~~-~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~  106 (131)
                      ...++.|...|... ++++|..+||+.+++   ++..+.|+++.|...|++...... +. ...+.+|+.++.+..
T Consensus        40 t~~q~~vL~~L~~~~~~~~t~~eLa~~l~i---s~~tvs~~l~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~  112 (189)
T 3nqo_A           40 TSRQYMTILSILHLPEEETTLNNIARKMGT---SKQNINRLVANLEKNGYVDVIPSPHDKRAINVKVTDLGKKVMV  112 (189)
T ss_dssp             CHHHHHHHHHHHHSCGGGCCHHHHHHHHTS---CHHHHHHHHHHHHHTTSEEEEECSSCSSCEEEEECHHHHHHHH
T ss_pred             CHHHHHHHHHHHhccCCCcCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHHHHHHHH
Confidence            44566677788753 368999999999999   999999999999999999986432 11 134789998886654

>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=96.23  E-value=0.0013  Score=42.69  Aligned_cols=62  Identities=15%  Similarity=0.266  Sum_probs=47.6

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcC----CCCCCcchHHHHHHHhhcCCceeecccCCCCcc---eecchhccccc
Q 040869           37 ELGIADIIHSHGRAITLSELVSALD----IQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEA---YGLTAASTLLI  105 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~----~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~---y~~t~~s~~L~  105 (131)
                      ++.|...|.. .+++|..|||+.++    +   ++..+.|+++.|...|++.....   +.+   +.+|+.++.+.
T Consensus        12 ~~~vL~~l~~-~~~~t~~ela~~l~~~~~~---s~~tv~~~l~~L~~~Glv~r~~~---~rr~~~~~lT~~g~~~~   80 (123)
T 1okr_A           12 EWEVMNIIWM-KKYASANNIIEEIQMQKDW---SPKTIRTLITRLYKKGFIDRKKD---NKIFQYYSLVEESDIKY   80 (123)
T ss_dssp             HHHHHHHHHH-HSSEEHHHHHHHHHHHCCC---CHHHHHHHHHHHHHHTSEEEEEE---TTEEEEEESSCHHHHHH
T ss_pred             HHHHHHHHHh-CCCcCHHHHHHHHhccCCC---cHhhHHHHHHHHHHCCCeEEEec---CCeEEEEEecCHHHHHH
Confidence            3455666654 46899999999999    6   68999999999999999998652   222   36788777554

>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=96.22  E-value=0.0057  Score=43.93  Aligned_cols=68  Identities=15%  Similarity=0.176  Sum_probs=51.0

Q ss_pred             HHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC--C-C-Ccceecchhcc
Q 040869           30 MSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN--G-Q-EEAYGLTAAST  102 (131)
Q Consensus        30 ~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~--~-~-~~~y~~t~~s~  102 (131)
                      .+|.--.++.|...|..  +|+|..|||+.+|+   ++..+.+.|+.|...|++......  . + .-.|.+|+-..
T Consensus        10 kaL~~~~rl~IL~~L~~--~~~s~~eLa~~l~i---s~stvs~hLk~Le~~GLV~~~~~~~~~g~~~~~Y~Lt~~~~   81 (202)
T 2p4w_A           10 DVLGNETRRRILFLLTK--RPYFVSELSRELGV---GQKAVLEHLRILEEAGLIESRVEKIPRGRPRKYYMIKKGLR   81 (202)
T ss_dssp             HHHHSHHHHHHHHHHHH--SCEEHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEEECCBTTBCCCEEEEECTTEE
T ss_pred             HHhCCHHHHHHHHHHHh--CCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCceEEEeeccCCCCceEEEEEChHHH
Confidence            45555667777877863  78999999999999   999999999999999999975421  0 1 12366666543

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

Probab=96.19  E-value=0.0059  Score=41.20  Aligned_cols=47  Identities=17%  Similarity=0.285  Sum_probs=41.4

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      .+..|...|.+ ++++|..|||+++|+   ++..+.|.++.|...|++...
T Consensus        10 ~d~~il~~L~~-~~~~s~~ela~~lg~---s~~tv~~~l~~L~~~G~i~~~   56 (151)
T 2dbb_A           10 VDMQLVKILSE-NSRLTYRELADILNT---TRQRIARRIDKLKKLGIIRKF   56 (151)
T ss_dssp             HHHHHHHHHHH-CTTCCHHHHHHHTTS---CHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHHHH-cCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEE
Confidence            45578888876 578999999999999   999999999999999999864

>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=96.16  E-value=0.0073  Score=42.49  Aligned_cols=60  Identities=13%  Similarity=0.145  Sum_probs=48.5

Q ss_pred             HHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCc-eeecccCCCCcceecchhc
Q 040869           34 CAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSC-FNKTKVNGQEEAYGLTAAS  101 (131)
Q Consensus        34 ~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl-~~~~~~~~~~~~y~~t~~s  101 (131)
                      .--...|.+.|.+.++++|..|||+++|+   +.+.++|=++.|...|+ +...     .+.|..++..
T Consensus        20 ~~R~~~Il~~L~~~~~~~s~~eLa~~l~v---S~~Ti~rdi~~L~~~G~~I~~~-----~~Gy~l~~~~   80 (187)
T 1j5y_A           20 QERLKSIVRILERSKEPVSGAQLAEELSV---SRQVIVQDIAYLRSLGYNIVAT-----PRGYVLAGGK   80 (187)
T ss_dssp             HHHHHHHHHHHHHCSSCBCHHHHHHHHTS---CHHHHHHHHHHHHHHTCCCEEE-----TTEEECCTTT
T ss_pred             HHHHHHHHHHHHHcCCCcCHHHHHHHHCc---CHHHHHHHHHHHHHCCCeEEEE-----CCEEEECCcc
Confidence            34556788889765578999999999999   99999999999999998 7653     4557776644

>3k2z_A LEXA repressor; winged helix-turn-helix, SOS system, autoca cleavage, DNA damage, DNA repair, DNA replication, DNA-BIND hydrolase; 1.37A {Thermotoga maritima}

Probab=96.13  E-value=0.0054  Score=43.43  Aligned_cols=42  Identities=14%  Similarity=0.275  Sum_probs=35.8

Q ss_pred             HHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           43 IIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        43 ~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      .+.+.+.|.|..|||+.+|+   +...++|.|+.|...|++....
T Consensus        17 ~~~~~g~~~s~~eia~~lgl---~~~tv~~~l~~Le~~G~i~~~~   58 (196)
T 3k2z_A           17 FIEKNGYPPSVREIARRFRI---TPRGALLHLIALEKKGYIERKN   58 (196)
T ss_dssp             HHHHHSSCCCHHHHHHHHTS---CHHHHHHHHHHHHHTTSEECC-
T ss_pred             HHHHhCCCCCHHHHHHHcCC---CcHHHHHHHHHHHHCCCEEecC
Confidence            34444679999999999999   7789999999999999998764

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

Probab=96.12  E-value=0.0059  Score=41.30  Aligned_cols=47  Identities=9%  Similarity=0.220  Sum_probs=41.3

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      .+..|...|.+ ++++|..|||+++|+   ++..+.|.++.|...|++...
T Consensus         9 ~d~~il~~L~~-~~~~s~~ela~~lg~---s~~tv~~~l~~L~~~G~i~~~   55 (152)
T 2cg4_A            9 LDRGILEALMG-NARTAYAELAKQFGV---SPETIHVRVEKMKQAGIITGA   55 (152)
T ss_dssp             HHHHHHHHHHH-CTTSCHHHHHHHHTS---CHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHHHH-cCCCCHHHHHHHHCc---CHHHHHHHHHHHHHcCCcceE
Confidence            35567888876 478999999999999   999999999999999999864

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

Probab=96.09  E-value=0.005  Score=41.15  Aligned_cols=49  Identities=16%  Similarity=0.262  Sum_probs=41.9

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcC----CCCCCcchHHHHHHHhhcCCceeecc
Q 040869           36 IELGIADIIHSHGRAITLSELVSALD----IQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~----~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      .+..|..+|....+++|..||++.++    +   ++..+.|+++-|...|++....
T Consensus        10 ~e~~vL~~L~~~~~~~t~~el~~~l~~~~~~---~~~Tvt~~l~rLe~kGlv~r~~   62 (138)
T 2g9w_A           10 LERAVMDHLWSRTEPQTVRQVHEALSARRDL---AYTTVMAVLQRLAKKNLVLQIR   62 (138)
T ss_dssp             HHHHHHHHHHTCSSCEEHHHHHHHHTTTCCC---CHHHHHHHHHHHHHTTSEEEEC
T ss_pred             HHHHHHHHHHhcCCCCCHHHHHHHHhccCCC---CHHHHHHHHHHHHHCCCEEEEe
Confidence            45667788875346899999999997    7   8899999999999999999875

>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=96.09  E-value=0.0075  Score=38.02  Aligned_cols=48  Identities=17%  Similarity=0.216  Sum_probs=40.2

Q ss_pred             HhChHHHHHhCC-CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           37 ELGIADIIHSHG-RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        37 ~L~ifd~l~~~~-~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      ++.|+..|..++ ..++..|||+++++   +...+.|+|+.|...|++.+..
T Consensus        22 q~~Vl~~I~~~g~~gi~qkeLa~~~~l---~~~tvt~iLk~LE~kglIkr~~   70 (91)
T 2dk5_A           22 EKLVYQIIEDAGNKGIWSRDVRYKSNL---PLTEINKILKNLESKKLIKAVK   70 (91)
T ss_dssp             HHHHHHHHHHHCTTCEEHHHHHHHTTC---CHHHHHHHHHHHHHTTSEEEEC
T ss_pred             HHHHHHHHHHcCCCCcCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEec
Confidence            345677776533 47999999999999   9999999999999999999653

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

Probab=96.07  E-value=0.0078  Score=41.88  Aligned_cols=47  Identities=15%  Similarity=0.261  Sum_probs=41.3

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      .+..|...|.+ ++++|..|||+++|+   ++..+.|.++.|...|++...
T Consensus        18 ~d~~IL~~L~~-~~~~s~~eLA~~lgl---S~~tv~~~l~~L~~~G~I~~~   64 (171)
T 2ia0_A           18 LDRNILRLLKK-DARLTISELSEQLKK---PESTIHFRIKKLQERGVIERY   64 (171)
T ss_dssp             HHHHHHHHHHH-CTTCCHHHHHHHHTS---CHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHH-cCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEee
Confidence            45578888876 468999999999999   999999999999999999754

>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=96.06  E-value=0.0054  Score=41.48  Aligned_cols=47  Identities=19%  Similarity=0.270  Sum_probs=41.3

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      .+..|...|.+ ++++|..|||+++|+   ++..+.|.++.|...|++...
T Consensus         8 ~~~~il~~L~~-~~~~s~~ela~~lg~---s~~tv~~~l~~L~~~G~i~~~   54 (151)
T 2cyy_A            8 IDKKIIKILQN-DGKAPLREISKITGL---AESTIHERIRKLRESGVIKKF   54 (151)
T ss_dssp             HHHHHHHHHHH-CTTCCHHHHHHHHCS---CHHHHHHHHHHHHHHTSSCCC
T ss_pred             HHHHHHHHHHH-cCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCeEEE
Confidence            45668888876 468999999999999   999999999999999999864

>2qlz_A Transcription factor PF0095; 2.50A {Pyrococcus furiosus} PDB: 2quf_A

Probab=96.06  E-value=0.0022  Score=47.23  Aligned_cols=69  Identities=12%  Similarity=0.182  Sum_probs=52.2

Q ss_pred             HHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceee-cccCC--C--Ccceecchhcc
Q 040869           29 SMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNK-TKVNG--Q--EEAYGLTAAST  102 (131)
Q Consensus        29 ~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~-~~~~~--~--~~~y~~t~~s~  102 (131)
                      ..+|.--.++.|+..|.  .+|+|..|||+.+|+   ++..+.+.|+.|...|++.. .....  |  ...|.+|+.+.
T Consensus         6 lkaL~~~~R~~IL~~L~--~g~~s~~ELa~~lgl---S~stVs~hL~~Le~aGLV~~~~~~gr~~GRp~~~Y~Lt~~~~   79 (232)
T 2qlz_A            6 FYILGNKVRRDLLSHLT--CMECYFSLLSSKVSV---SSTAVAKHLKIMEREGVLQSYEKEERFIGPTKKYYKISIAKS   79 (232)
T ss_dssp             HHHHTSHHHHHHHHHHT--TTTTCSSSSCTTCCC---CHHHHHHHHHHHHHTTSEEEEEECC-----CEEEEEECCCEE
T ss_pred             HHHhCCHHHHHHHHHHH--hCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEeeecCCCCCCccEEEEEccchh
Confidence            34555567788888887  378999999999999   99999999999999999997 33100  0  11388777543

>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=96.04  E-value=0.0057  Score=40.63  Aligned_cols=46  Identities=15%  Similarity=0.227  Sum_probs=40.2

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      +..|...|.+ ++++|..|||+++|+   ++..+.|.++.|...|++...
T Consensus         6 ~~~il~~L~~-~~~~~~~ela~~lg~---s~~tv~~~l~~L~~~G~i~~~   51 (141)
T 1i1g_A            6 DKIILEILEK-DARTPFTEIAKKLGI---SETAVRKRVKALEEKGIIEGY   51 (141)
T ss_dssp             HHHHHHHHHH-CTTCCHHHHHHHHTS---CHHHHHHHHHHHHHHTSSCCC
T ss_pred             HHHHHHHHHH-cCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEecc
Confidence            5567778875 468999999999999   999999999999999999754

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

Probab=95.91  E-value=0.0036  Score=42.14  Aligned_cols=64  Identities=13%  Similarity=0.108  Sum_probs=48.8

Q ss_pred             hHHHHHhC-CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhcccccc
Q 040869           40 IADIIHSH-GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIK  106 (131)
Q Consensus        40 ifd~l~~~-~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~  106 (131)
                      |...|... ++++|..|||+.+++   ++..+.|+++.|...|++.+.... |+ .-...+|+.++.+..
T Consensus        40 vL~~L~~~~~~~~t~~eLa~~l~~---~~~tvs~~v~~Le~~Glv~r~~~~~DrR~~~l~LT~~G~~~~~  106 (147)
T 4b8x_A           40 ALVLLTFSKSGELPMSKIGERLMV---HPTSVTNTVDRLVRSGLVAKRPNPNDGRGTLATITDKGREVVE  106 (147)
T ss_dssp             HHHHHHTSGGGEEEHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEEECC----CEEEEECHHHHHHHH
T ss_pred             HHHHHHHCCCCCcCHHHHHHHHCC---CHHHHHHHHHHHHhCCCEEEeecCCcCceeEEEECHHHHHHHH
Confidence            44555432 368999999999999   999999999999999999986532 11 123788999886654

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

Probab=95.90  E-value=0.0076  Score=41.40  Aligned_cols=47  Identities=13%  Similarity=0.334  Sum_probs=42.0

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      .+..|.+.|.+ ++++|..|||+++|+   ++..+.|-++.|...|++...
T Consensus         4 ~d~~il~~L~~-~~~~s~~~la~~lg~---s~~tv~~rl~~L~~~g~i~~~   50 (162)
T 3i4p_A            4 LDRKILRILQE-DSTLAVADLAKKVGL---STTPCWRRIQKMEEDGVIRRR   50 (162)
T ss_dssp             HHHHHHHHHTT-CSCSCHHHHHHHHTC---CHHHHHHHHHHHHHTTSSCCC
T ss_pred             HHHHHHHHHHH-CCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCeeec
Confidence            46678888975 578999999999999   999999999999999999854

>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=95.89  E-value=0.011  Score=42.00  Aligned_cols=52  Identities=12%  Similarity=0.187  Sum_probs=45.0

Q ss_pred             HHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           30 MSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        30 ~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      .++....+..|...|.  .+++|..|||+.+|+   ++..+.|.++.|...|++...
T Consensus        15 k~l~d~~~~~IL~~L~--~~~~s~~eLA~~lgl---S~stv~~~l~~Le~~GlI~~~   66 (192)
T 1uly_A           15 KVMLEDTRRKILKLLR--NKEMTISQLSEILGK---TPQTIYHHIEKLKEAGLVEVK   66 (192)
T ss_dssp             HHHHSHHHHHHHHHHT--TCCBCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHhCCHHHHHHHHHHH--cCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEE
Confidence            3444566778898897  368999999999999   999999999999999999876

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

Probab=95.86  E-value=0.007  Score=34.92  Aligned_cols=46  Identities=13%  Similarity=0.268  Sum_probs=41.6

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceee
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNK   85 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~   85 (131)
                      +-.|.+.|..++|-+.++..|++.|+   +++.+..+||.|...|++.-
T Consensus        12 e~~lL~yIr~sGGildI~~~a~kygV---~kdeV~~~LrrLe~KGLI~l   57 (59)
T 2xvc_A           12 ERELLDYIVNNGGFLDIEHFSKVYGV---EKQEVVKLLEALKNKGLIAV   57 (59)
T ss_dssp             HHHHHHHHHHTTSEEEHHHHHHHHCC---CHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHcCCEEeHHHHHHHhCC---CHHHHHHHHHHHHHCCCeec
Confidence            44578888888899999999999999   99999999999999999874

>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=95.81  E-value=0.0048  Score=44.07  Aligned_cols=65  Identities=17%  Similarity=0.104  Sum_probs=49.9

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhccccc
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLI  105 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~  105 (131)
                      ++.|...|... +++|..+||+.+++   ++..+.|+++.|...|++...... |+ .-.+.+|+.++.+.
T Consensus        50 q~~iL~~L~~~-~~~t~~eLa~~l~i---~~stvs~~l~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~  116 (207)
T 2fxa_A           50 EHHILWIAYQL-NGASISEIAKFGVM---HVSTAFNFSKKLEERGYLRFSKRLNDKRNTYVQLTEEGTEVF  116 (207)
T ss_dssp             HHHHHHHHHHH-TSEEHHHHHHHTTC---CHHHHHHHHHHHHHHTSEEEECC------CEEEECHHHHHHH
T ss_pred             HHHHHHHHHHC-CCcCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEecCCCCCceEEEEECHHHHHHH
Confidence            44466777643 58999999999999   999999999999999999986421 11 12578999887554

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

Probab=95.76  E-value=0.0064  Score=41.02  Aligned_cols=66  Identities=18%  Similarity=0.233  Sum_probs=42.8

Q ss_pred             hChHHHHHhC----CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCC-Ccceecchhcccccc
Q 040869           38 LGIADIIHSH----GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQ-EEAYGLTAASTLLIK  106 (131)
Q Consensus        38 L~ifd~l~~~----~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~-~~~y~~t~~s~~L~~  106 (131)
                      +.|...|...    ++++|..|||+.+++   ++..+.|+++.|...|++....+.|+ .-...+|+.++.+..
T Consensus        36 ~~vL~~l~~~~~~~~~~~t~~eLa~~l~~---~~~tvsr~v~~Le~~glVr~~~~~DrR~~~v~LT~~G~~~~~  106 (148)
T 4fx0_A           36 FSTLAVISLSEGSAGIDLTMSELAARIGV---ERTTLTRNLEVMRRDGLVRVMAGADARCKRIELTAKGRAALQ  106 (148)
T ss_dssp             HHHHHHHHC---------CHHHHHHHHTC---CHHHHHHHHHHHHHTTSBC-----------CCBCHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCCCCcCHHHHHHHHCC---ChhhHHHHHHHHHHCCCEEeeCCCCCCeeEEEECHHHHHHHH
Confidence            3455556432    257999999999999   99999999999999999965432121 134788998886543

>2esh_A Conserved hypothetical protein TM0937; APC5794, structural genomics, PSI, protein structure initiative; 2.30A {Thermotoga maritima} SCOP: a.4.5.61

Probab=95.75  E-value=0.028  Score=36.55  Aligned_cols=70  Identities=16%  Similarity=0.179  Sum_probs=53.4

Q ss_pred             HHHHHHhChHHHHHhCCCCCCHHHHHhhcC--------CCCCCc-chHHHHHHHhhcCCceeecccC-CC--Ccceecch
Q 040869           32 LKCAIELGIADIIHSHGRAITLSELVSALD--------IQPTKT-TGLFRLMRLLVHSSCFNKTKVN-GQ--EEAYGLTA   99 (131)
Q Consensus        32 L~~a~~L~ifd~l~~~~~~~s~~eLA~~~~--------~~~~~~-~~l~RlLr~L~~~gl~~~~~~~-~~--~~~y~~t~   99 (131)
                      ++-..++-|...|..  +|.+..||++.+.        +   ++ ..++++|+.|...|++...... ++  ...|.+|+
T Consensus        10 ~~~~~~~~IL~~L~~--~~~~gyel~~~l~~~g~~~~~i---s~~~tly~~L~~Le~~GlI~~~~~~~~~~~r~~Y~LT~   84 (118)
T 2esh_A           10 RGWWLASTILLLVAE--KPSHGYELAERLAEFGIEIPGI---GHMGNIYRVLADLEESGFLSTEWDTTVSPPRKIYRITP   84 (118)
T ss_dssp             HHHHHHHHHHHHHHH--SCBCHHHHHHHHHTTCCSSTTC---CCCCCHHHHHHHHHHTTSEEEEEECSSSSCEEEEEECH
T ss_pred             ccchHHHHHHHHHHc--CCCCHHHHHHHHHHhCCcccCC---CCcchHHHHHHHHHHCCCeEEEeecCCCCCceEEEECh
Confidence            445567777888874  7899999999983        6   88 9999999999999999875321 11  23599999


Q ss_pred             hcccccc
Q 040869          100 ASTLLIK  106 (131)
Q Consensus       100 ~s~~L~~  106 (131)
                      .++.+..
T Consensus        85 ~G~~~l~   91 (118)
T 2esh_A           85 QGKLYLR   91 (118)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9985543

>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=95.62  E-value=0.0091  Score=46.26  Aligned_cols=57  Identities=16%  Similarity=0.184  Sum_probs=43.0

Q ss_pred             HHHHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           26 HLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        26 ~~~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      +..+++++...+..|++.|.  .+++|-.|||+++|+   .+..+.++++.|...|++.+..
T Consensus        11 ~~~~~~~~~~~~~~il~~l~--~~~~sr~~la~~~gl---s~~tv~~~v~~L~~~gli~~~~   67 (380)
T 2hoe_A           11 HHMPKSVRAENISRILKRIM--KSPVSRVELAEELGL---TKTTVGEIAKIFLEKGIVVEEK   67 (380)
T ss_dssp             -----------CCCSHHHHH--HSCBCHHHHHHHHTC---CHHHHHHHHHHHHHHTSEEEEE
T ss_pred             ccCchhHHHHHHHHHHHHHH--cCCcCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEeec
Confidence            34578888888889999998  479999999999999   9999999999999999999864

>4esf_A PADR-like transcriptional regulator; PADR family, DNA binding protein, HTH fold; 2.20A {Bacillus cereus}

Probab=95.54  E-value=0.032  Score=36.49  Aligned_cols=70  Identities=20%  Similarity=0.214  Sum_probs=52.3

Q ss_pred             HHHHHHHhChHHHHHhCCCCCCHHHHHhhc------CCCCCCcchHHHHHHHhhcCCceeecccC--CC--Ccceecchh
Q 040869           31 SLKCAIELGIADIIHSHGRAITLSELVSAL------DIQPTKTTGLFRLMRLLVHSSCFNKTKVN--GQ--EEAYGLTAA  100 (131)
Q Consensus        31 aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~------~~~~~~~~~l~RlLr~L~~~gl~~~~~~~--~~--~~~y~~t~~  100 (131)
                      .++-.+++-|..+|..  +|.+.-||++.+      ++   ++..|+++|+.|...|++......  ++  ...|.+|+.
T Consensus         7 l~~g~l~~~IL~lL~~--~p~~Gyei~~~l~~~g~~~i---s~gtlY~~L~rLe~~GlI~~~~~~~~~g~~rk~Y~LT~~   81 (117)
T 4esf_A            7 MLKGSLEGCVLEIISR--RETYGYEITRHLNDLGFTEV---VEGTVYTILVRLEKKKLVNIEKKPSDMGPPRKFYSLNEA   81 (117)
T ss_dssp             HHHHHHHHHHHHHHHH--SCBCHHHHHHHHHHHTCTTC---CHHHHHHHHHHHHHTTCEEEEEEC-----CEEEEEECHH
T ss_pred             HHHChHHHHHHHHHHc--CCCCHHHHHHHHHHcCCCCC---CccHHHHHHHHHHHCCCEEEEeecCCCCCCceEEEECHH
Confidence            3444556666667774  789999999998      67   889999999999999999875321  11  235999999


Q ss_pred             ccccc
Q 040869          101 STLLI  105 (131)
Q Consensus       101 s~~L~  105 (131)
                      ++...
T Consensus        82 G~~~l   86 (117)
T 4esf_A           82 GRQEL   86 (117)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            98544

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

Probab=95.52  E-value=0.019  Score=38.10  Aligned_cols=53  Identities=17%  Similarity=0.194  Sum_probs=41.2

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-C-C--Ccceecchhcccc
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-G-Q--EEAYGLTAASTLL  104 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~-~--~~~y~~t~~s~~L  104 (131)
                      ...|.++||+++|+   ++..+.|+++.|...|++...... + |  ...|.++|+-.-|
T Consensus        50 ~~ps~~~LA~~l~~---s~~~V~~~l~~Le~kGlI~~~~~~~~~g~~~~~Ydl~pl~~kL  106 (128)
T 2vn2_A           50 LFPTPAELAERMTV---SAAECMEMVRRLLQKGMIAIEEHTDEQGIRNEKYTLEPLWEKL  106 (128)
T ss_dssp             SSCCHHHHHHTSSS---CHHHHHHHHHHHHHTTSSEECC----------CEECHHHHHHH
T ss_pred             CCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEEeEECCCCcEEEEEehHHHHHHH
Confidence            34799999999999   999999999999999999986432 1 1  1469999886544

>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=95.50  E-value=0.0082  Score=43.42  Aligned_cols=54  Identities=17%  Similarity=0.185  Sum_probs=44.9

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcccccc
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIK  106 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~~  106 (131)
                      +++|..++|+++++   ++..+.|.++.|...|+|.+.... ....+.+|+.++.+..
T Consensus        26 ~~~s~s~aA~~L~i---sq~avSr~I~~LE~~~L~~R~~~~-R~~~v~LT~~G~~l~~   79 (230)
T 3cta_A           26 AYLTSSKLADMLGI---SQQSASRIIIDLEKNGYITRTVTK-RGQILNITEKGLDVLY   79 (230)
T ss_dssp             EECCHHHHHHHHTS---CHHHHHHHHHHHHHTTSEEEEEET-TEEEEEECHHHHHHHH
T ss_pred             CCcCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEEEcC-CeEEEEECHHHHHHHH
Confidence            56899999999999   999999999999999999987310 1356899999986654

>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=95.27  E-value=0.016  Score=41.95  Aligned_cols=49  Identities=10%  Similarity=0.069  Sum_probs=42.7

Q ss_pred             CCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcccccc
Q 040869           51 ITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIK  106 (131)
Q Consensus        51 ~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~~  106 (131)
                      .+..+||+.+++   ++..+.++++.|...|++....    ...+.+|+.++.+..
T Consensus        25 ~~~~~La~~l~v---s~~tvs~~l~~Le~~GlV~r~~----~~~v~LT~~G~~~~~   73 (230)
T 1fx7_A           25 PLRARIAERLDQ---SGPTVSQTVSRMERDGLLRVAG----DRHLELTEKGRALAI   73 (230)
T ss_dssp             CCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEECT----TSCEEECHHHHHHHH
T ss_pred             CcHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEeC----CccEEECHHHHHHHH
Confidence            344999999999   9999999999999999999876    567999999886543

>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=95.22  E-value=0.014  Score=43.07  Aligned_cols=68  Identities=18%  Similarity=0.225  Sum_probs=52.2

Q ss_pred             HHhChHHHHHhCC-CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhcccccc
Q 040869           36 IELGIADIIHSHG-RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIK  106 (131)
Q Consensus        36 ~~L~ifd~l~~~~-~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~  106 (131)
                      .++.|...|...+ +++|..|||+.+++   ++..+.|+++-|...|++.+.... |. .-...+|+.++.+..
T Consensus       159 ~q~~vL~~L~~~~~~~~t~~eLa~~l~i---~~~tvt~~v~rLe~~GlV~R~~~~~DrR~~~i~LT~~G~~~~~  229 (250)
T 1p4x_A          159 VEFTILAIITSQNKNIVLLKDLIETIHH---KYPQTVRALNNLKKQGYLIKERSTEDERKILIHMDDAQQDHAE  229 (250)
T ss_dssp             HHHHHHHHHHTTTTCCEEHHHHHHHSSS---CHHHHHHHHHHHHHHTSSEEEECSSSTTCEEEECCHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCCCcCHHHHHHHHCC---ChhhHHHHHHHHHHCCCEEeeCCCCCCCeEEEEECHHHHHHHH
Confidence            3445677777554 36999999999999   999999999999999999986532 21 123678888886654

>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=95.13  E-value=0.012  Score=38.11  Aligned_cols=51  Identities=16%  Similarity=0.268  Sum_probs=40.7

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCC-CCCcchHHHHHHHhhcCCceeecc
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQ-PTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~-~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      .+..|...|.. .+++|..|||+.++.. +-++..+.++++-|...|++....
T Consensus        11 ~q~~vL~~L~~-~~~~t~~el~~~l~~~~~~~~~Tvt~~l~rLe~kGlv~R~~   62 (126)
T 1sd4_A           11 AEWDVMNIIWD-KKSVSANEIVVEIQKYKEVSDKTIRTLITRLYKKEIIKRYK   62 (126)
T ss_dssp             HHHHHHHHHHH-SSSEEHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHHh-cCCCCHHHHHHHHhhcCCCChhhHHHHHHHHHHCCceEEEe
Confidence            35567777776 3689999999999730 017889999999999999999875

>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=95.08  E-value=0.06  Score=35.00  Aligned_cols=72  Identities=8%  Similarity=0.184  Sum_probs=53.0

Q ss_pred             HHHHHHHHhChHHHHHhCCCCCCHHHHHhhc--------CCCCCCcchHHHHHHHhhcCCceeecccC--CC--Ccceec
Q 040869           30 MSLKCAIELGIADIIHSHGRAITLSELVSAL--------DIQPTKTTGLFRLMRLLVHSSCFNKTKVN--GQ--EEAYGL   97 (131)
Q Consensus        30 ~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~--------~~~~~~~~~l~RlLr~L~~~gl~~~~~~~--~~--~~~y~~   97 (131)
                      ..++-.+++-|..+|.+  +|.+..||.+.+        ++   ++..++++|+.|...|++......  ++  ...|.+
T Consensus         7 ~~~~g~l~~~IL~~L~~--~~~~Gyei~~~l~~~~~~~~~i---~~gtly~~L~rLe~~GlI~~~~~~~~~~~~rk~Y~L   81 (116)
T 3f8b_A            7 EMLRAQTNVILLNVLKQ--GDNYVYGIIKQVKEASNGEMEL---NEATLYTIFKRLEKDGIISSYWGDESQGGRRKYYRL   81 (116)
T ss_dssp             HHHHHHHHHHHHHHHHH--CCBCHHHHHHHHHHHTTTCCCC---CHHHHHHHHHHHHHTTSEEEEEEC----CCEEEEEE
T ss_pred             HHHhchHHHHHHHHHHh--CCCCHHHHHHHHHHHhCCCCCC---CcchHHHHHHHHHHCCCEEEEeeccCCCCCceEEEE
Confidence            34445566667777774  789999999887        56   889999999999999999875311  11  234999


Q ss_pred             chhcccccc
Q 040869           98 TAASTLLIK  106 (131)
Q Consensus        98 t~~s~~L~~  106 (131)
                      |+.++....
T Consensus        82 T~~G~~~l~   90 (116)
T 3f8b_A           82 TEIGHENMR   90 (116)
T ss_dssp             CHHHHHHHH
T ss_pred             CHHHHHHHH
Confidence            999985443

>1z6r_A MLC protein; transcriptional repressor, ROK family protein, DNA binding P helix-turn-helix, phosphotransferase system; 2.70A {Escherichia coli} SCOP: a.4.5.63 c.55.1.10 c.55.1.10 PDB: 3bp8_A

Probab=94.97  E-value=0.037  Score=43.03  Aligned_cols=52  Identities=6%  Similarity=0.132  Sum_probs=44.6

Q ss_pred             HHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           32 LKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        32 L~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      ++..-+..|++.|.+ .+++|-.|||+++|+   .+..+.++++.|...|++.+..
T Consensus        13 ~r~~n~~~il~~l~~-~~~~sr~~la~~~~l---s~~tv~~~v~~L~~~g~i~~~~   64 (406)
T 1z6r_A           13 IKQTNAGAVYRLIDQ-LGPVSRIDLSRLAQL---APASITKIVHEMLEAHLVQELE   64 (406)
T ss_dssp             HHHHHHHHHHHHHHS-SCSCCHHHHHHHTTC---CHHHHHHHHHHHHHHTSEEEC-
T ss_pred             HHHhHHHHHHHHHHH-cCCcCHHHHHHHHCC---CHHHHHHHHHHHHHCCcEEeec
Confidence            455556668888985 579999999999999   9999999999999999999853

>4g6q_A Putative uncharacterized protein; structural genomics, PSI-biology, protein structure initiati midwest center for structural genomics, MCSG; 2.08A {Kribbella flavida}

Probab=94.94  E-value=0.009  Score=42.03  Aligned_cols=71  Identities=25%  Similarity=0.350  Sum_probs=53.6

Q ss_pred             HHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcC-CCCCCcchHHHHHHHhhcCCceeecccC--CC--Ccceecchhccc
Q 040869           29 SMSLKCAIELGIADIIHSHGRAITLSELVSALD-IQPTKTTGLFRLMRLLVHSSCFNKTKVN--GQ--EEAYGLTAASTL  103 (131)
Q Consensus        29 ~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~-~~~~~~~~l~RlLr~L~~~gl~~~~~~~--~~--~~~y~~t~~s~~  103 (131)
                      ..+|.--+++.|+..|.  +++.|+.|||+.++ +   +...+.+-|+.|...|+++.....  .|  ...|.+++-+..
T Consensus        17 ~~~La~P~Rl~il~~L~--~~~~~~~~l~~~l~~~---~~~~~s~Hl~~L~~aglv~~~~e~~~~g~~er~y~~~~~~~~   91 (182)
T 4g6q_A           17 VDLLHHPLRWRITQLLI--GRSLTTRELAELLPDV---ATTTLYRQVGILVKAGVLMVTAEHQVRGAVERTYTLNTQAGD   91 (182)
T ss_dssp             HHHTTSHHHHHHHHHTT--TSCEEHHHHHHHCTTB---CHHHHHHHHHHHHHHTSEEEEEEEEETTEEEEEEEECTTTTT
T ss_pred             HHHhCCHHHHHHHHHHH--hCCCCHHHHHHHhcCC---CHHHHHHHHHHHHHCCCeEEEEeecccCcceeEEEecccccc
Confidence            34555668889999997  47999999999996 8   888999999999999999854311  01  235777776544


Q ss_pred             c
Q 040869          104 L  104 (131)
Q Consensus       104 L  104 (131)
                      +
T Consensus        92 ~   92 (182)
T 4g6q_A           92 A   92 (182)
T ss_dssp             S
T ss_pred             C
Confidence            4

>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=94.91  E-value=0.039  Score=31.46  Aligned_cols=36  Identities=25%  Similarity=0.282  Sum_probs=29.1

Q ss_pred             HHHHHhCCCCCCHHHHHhhc-----CCCCCCcchHHHHHHHhhcCCce
Q 040869           41 ADIIHSHGRAITLSELVSAL-----DIQPTKTTGLFRLMRLLVHSSCF   83 (131)
Q Consensus        41 fd~l~~~~~~~s~~eLA~~~-----~~~~~~~~~l~RlLr~L~~~gl~   83 (131)
                      ...+.. .+++|++||++.+     ++   +..+++|-|.   ..|++
T Consensus        11 ~~ll~~-~~~~t~~el~~~l~~~~~~v---s~~Tv~R~L~---~lg~v   51 (64)
T 2p5k_A           11 REIITS-NEIETQDELVDMLKQDGYKV---TQATVSRDIK---ELHLV   51 (64)
T ss_dssp             HHHHHH-SCCCSHHHHHHHHHHTTCCC---CHHHHHHHHH---HHTCE
T ss_pred             HHHHHc-CCCCCHHHHHHHHHHhCCCc---CHHHHHHHHH---HcCCE
Confidence            344543 5789999999999     99   9999999999   45777

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

Probab=94.83  E-value=0.016  Score=36.61  Aligned_cols=52  Identities=8%  Similarity=0.185  Sum_probs=39.5

Q ss_pred             HHHHHHhChHH-HHHhCCCCC-CHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           32 LKCAIELGIAD-IIHSHGRAI-TLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        32 L~~a~~L~ifd-~l~~~~~~~-s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      +.-.++..|.+ .+. .+..+ |..+||+.+|+   +...+++-++.|...|++....
T Consensus        16 l~~~i~~~I~~~~l~-~g~~lps~~eLa~~~~v---Sr~tvr~al~~L~~~Gli~~~~   69 (102)
T 1v4r_A           16 VATHFRTLIKSGELA-PGDTLPSVADIRAQFGV---AAKTVSRALAVLKSEGLVSSRG   69 (102)
T ss_dssp             HHHHHHHHTTTTSCC-TTSBCCCHHHHHHHSSS---CTTHHHHHTTTTTTSSCCEEET
T ss_pred             HHHHHHHHHHhCCCC-CcCCCcCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEeC
Confidence            33334444444 233 24566 99999999999   9999999999999999998765

>1jhg_A Trp operon repressor; complex (regulatory protein-peptide), DNA-binding regulatory complex (regulatory protein-peptide) complex; HET: TRP; 1.30A {Escherichia coli} SCOP: a.4.12.1 PDB: 1co0_A* 1mi7_R 1p6z_R 1wrp_R* 1zt9_A* 2oz9_R* 3ssw_R 3wrp_A 1rcs_A* 1wrs_R* 1wrt_R 2xdi_A 3ssx_R* 1trr_A* 1tro_A*

Probab=94.83  E-value=0.037  Score=35.59  Aligned_cols=42  Identities=14%  Similarity=0.105  Sum_probs=35.7

Q ss_pred             HHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcC
Q 040869           34 CAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHS   80 (131)
Q Consensus        34 ~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~   80 (131)
                      .+.++||+..|.+  +.+|..|||+.+|+   +...+.|+=|+|...
T Consensus        44 l~~R~~l~~~L~~--ge~TQREIA~~lGi---S~stISRi~r~L~~l   85 (101)
T 1jhg_A           44 LGTRVRIIEELLR--GEMSQRELKNELGA---GIATITRGSNSLKAA   85 (101)
T ss_dssp             HHHHHHHHHHHHH--CCSCHHHHHHHHCC---CHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHc--CCcCHHHHHHHHCC---ChhhhhHHHHHHHHc
Confidence            4567899998874  67999999999999   999999998887543

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

Probab=94.83  E-value=0.036  Score=37.26  Aligned_cols=53  Identities=15%  Similarity=0.145  Sum_probs=42.8

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC--CC--Ccceecchhcccc
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN--GQ--EEAYGLTAASTLL  104 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~--~~--~~~y~~t~~s~~L  104 (131)
                      ...|.++||+++|+   ++..+.|+++.|...|++......  +|  ...|.++|+-.-|
T Consensus        50 ~~ps~~~LA~~~~~---s~~~v~~~L~~L~~KGlI~i~~~~d~~g~~~~~ydL~pL~ekL  106 (135)
T 2v79_A           50 YFPTPNQLQEGMSI---SVEECTNRLRMFIQKGFLFIEECEDQNGIKFEKYSLQPLWGKL  106 (135)
T ss_dssp             CSCCHHHHHTTSSS---CHHHHHHHHHHHHHHTSCEEEEEECTTCCEEEEEECHHHHHHH
T ss_pred             CCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEEeEecCCCceEEEeeHHHHHHHH
Confidence            56899999999999   999999999999999999984221  11  1479999986544

>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=94.82  E-value=0.024  Score=41.00  Aligned_cols=51  Identities=6%  Similarity=0.046  Sum_probs=43.9

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcccccc
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIK  106 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~~  106 (131)
                      .+.+..+||+++++   ++..+.++++.|...|++....    ...+.+|+.++.+..
T Consensus        23 ~~~~~~~la~~l~v---s~~tvs~~l~~Le~~GlV~r~~----~~~v~LT~~G~~~~~   73 (226)
T 2qq9_A           23 VTPLRARIAERLEQ---SGPTVSQTVARMERDGLVVVAS----DRSLQMTPTGRTLAT   73 (226)
T ss_dssp             CCCBHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEECT----TSBEEECHHHHHHHH
T ss_pred             CCccHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEeC----CCCeEECHHHHHHHH
Confidence            34456999999999   9999999999999999999876    577999999886553

>3elk_A Putative transcriptional regulator TA0346; structural genomics, PSI-2, prote structure initiative; 1.70A {Thermoplasma acidophilum}

Probab=94.76  E-value=0.039  Score=36.07  Aligned_cols=72  Identities=17%  Similarity=0.166  Sum_probs=53.9

Q ss_pred             HHHHHHHHhChHHHHHhCCCCCCHHHHHhhcC------CCCCCcchHHHHHHHhhcCCceeeccc-C-CC--Ccceecch
Q 040869           30 MSLKCAIELGIADIIHSHGRAITLSELVSALD------IQPTKTTGLFRLMRLLVHSSCFNKTKV-N-GQ--EEAYGLTA   99 (131)
Q Consensus        30 ~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~------~~~~~~~~l~RlLr~L~~~gl~~~~~~-~-~~--~~~y~~t~   99 (131)
                      ..++-.+++-|...|..  +|.+..||++.+.      +   ++..+++.|+.|...|++..... . .+  ...|.+|+
T Consensus         9 ~l~~g~l~~~IL~lL~~--~p~~gyel~~~l~~~~~~~i---~~gtly~~L~~Le~~GlI~~~~~~~~~~~~rk~Y~lT~   83 (117)
T 3elk_A            9 RILHGLITLYILKELVK--RPMHGYELQKSMFETTGQAL---PQGSIYILLKTMKERGFVISESSVNEKGQQLTVYHITD   83 (117)
T ss_dssp             HHHHHHHHHHHHHHHHH--SCEEHHHHHHHHHHHHSCCC---CTTHHHHHHHHHHHHTSEEEEEEEC-CCCEEEEEEECH
T ss_pred             HHHhhHHHHHHHHHHHc--CCCCHHHHHHHHHHHhCCCC---CcchHHHHHHHHHHCCCEEEEeeecCCCCCceEEEECH
Confidence            34455566777778874  7899999999886      6   77899999999999999986532 1 11  23599999


Q ss_pred             hcccccc
Q 040869          100 ASTLLIK  106 (131)
Q Consensus       100 ~s~~L~~  106 (131)
                      .++....
T Consensus        84 ~G~~~l~   90 (117)
T 3elk_A           84 AGKKFLC   90 (117)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9985443

>1yg2_A Gene activator APHA; virulence factor, winged helix, transcripti factor, transcription; 2.20A {Vibrio cholerae} SCOP: a.4.5.61

Probab=94.62  E-value=0.046  Score=38.05  Aligned_cols=63  Identities=11%  Similarity=0.152  Sum_probs=48.4

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhc--------CCCCCCcchHHHHHHHhhcCCceeecccC-CC---Ccceecchhccc
Q 040869           36 IELGIADIIHSHGRAITLSELVSAL--------DIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ---EEAYGLTAASTL  103 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~--------~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~---~~~y~~t~~s~~  103 (131)
                      +++-|...|..  +|.+..||++.+        ++   ++..+++.|+-|...|++...... ++   ...|.+|+.++.
T Consensus         3 l~~~iL~lL~~--~~~~gyel~~~l~~~~~~~~~~---s~~~ly~~L~~Le~~GlI~~~~~~~~~~~~r~~Y~lT~~G~~   77 (179)
T 1yg2_A            3 LPHVILTVLST--RDATGYDITKEFSASIGYFWKA---SHQQVYRELNKMGEQGLVTCVLEPQEGKPDRKVYSITQAGRS   77 (179)
T ss_dssp             HHHHHHHHHHH--CCBCHHHHHHHHTTGGGGTCCC---CHHHHHHHHHHHHHTTSEEECCC---------CEEECHHHHH
T ss_pred             hHHHHHHHHhc--CCCCHHHHHHHHHHHhCCccCC---CcCcHHHHHHHHHHCCCeEEEeecCCCCCCceEEEeChHHHH
Confidence            45567777874  799999999998        46   889999999999999999875422 11   235999999873

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

Probab=94.39  E-value=0.032  Score=35.79  Aligned_cols=67  Identities=16%  Similarity=0.227  Sum_probs=49.9

Q ss_pred             HHHHhChHHHHHhCCCCCCHHHHHhhc----CCCCCCcchHHHHHHHhhcCCceeecccC-CCC--cceecchhccccc
Q 040869           34 CAIELGIADIIHSHGRAITLSELVSAL----DIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQE--EAYGLTAASTLLI  105 (131)
Q Consensus        34 ~a~~L~ifd~l~~~~~~~s~~eLA~~~----~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~~--~~y~~t~~s~~L~  105 (131)
                      -..++-|...|..  +|.+..+|++.+    ++   ++..++++|+.|...|++...... ++.  ..|.+|+.++...
T Consensus         8 g~l~~~IL~~L~~--~~~~gyel~~~l~~~~~i---~~~tly~~L~~Le~~GlI~~~~~~~~~r~r~~y~LT~~G~~~l   81 (108)
T 3l7w_A            8 LLIEYLILAIVSK--HDSYGYDISQTIKLIASI---KESTLYPILKKLEKAGYLSTYTQEHQGRRRKYYHLTDSGEKHL   81 (108)
T ss_dssp             HHHHHHHHHHHHH--SCEEHHHHHHHHTTTCCC---CHHHHHHHHHHHHHTTSEEEEEEEETTEEEEEEEECHHHHHHH
T ss_pred             HHHHHHHHHHHHc--CCCcHHHHHHHHHHHhCC---CcChHHHHHHHHHHCCCeEEEeecCCCCcceEEEECHHHHHHH
Confidence            3456667777774  688888888775    77   899999999999999999875321 111  2499999998544

>3hhh_A Transcriptional regulator, PADR family; PF03551, structural PSI-2, protein structure initiative, midwest center for STR genomics, MCSG; 2.70A {Enterococcus faecalis} SCOP: a.4.5.0

Probab=94.37  E-value=0.062  Score=35.03  Aligned_cols=70  Identities=19%  Similarity=0.177  Sum_probs=51.9

Q ss_pred             HHHHHHHhChHHHHHhCCCCCCHHHHHhhc------CCCCCCcchHHHHHHHhhcCCceeecccC--CC--Ccceecchh
Q 040869           31 SLKCAIELGIADIIHSHGRAITLSELVSAL------DIQPTKTTGLFRLMRLLVHSSCFNKTKVN--GQ--EEAYGLTAA  100 (131)
Q Consensus        31 aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~------~~~~~~~~~l~RlLr~L~~~gl~~~~~~~--~~--~~~y~~t~~  100 (131)
                      .++-.+++-|..+|.+  +|.+.-||++.+      ++   ++..++++|+-|...|+++.....  ++  ...|.+|+.
T Consensus         9 l~~g~l~~~IL~lL~~--~p~~Gyei~~~l~~~g~~~i---s~gtlY~~L~rLe~~GlI~~~~~~~~~g~~rk~Y~lT~~   83 (116)
T 3hhh_A            9 LLKGILEGLVLAIIQR--KETYGYEITKILNDQGFTEI---VEGTVYTILLRLEKNQWVIAEKKPSEKGPMRKFYRLTSS   83 (116)
T ss_dssp             HHTTHHHHHHHHHHHH--SCBCHHHHHHHHHTTSCSSC---CHHHHHHHHHHHHHTTSEEEEEEECC--CEEEEEEECHH
T ss_pred             HHhhhHHHHHHHHHhc--CCCCHHHHHHHHHHcCCCCC---CccHHHHHHHHHHHCCCEEEEeeecCCCCCceEEEECHH
Confidence            3444455666777774  789999999998      56   889999999999999999875321  11  235999999


Q ss_pred             ccccc
Q 040869          101 STLLI  105 (131)
Q Consensus       101 s~~L~  105 (131)
                      ++...
T Consensus        84 G~~~l   88 (116)
T 3hhh_A           84 GEAEL   88 (116)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            98544

>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=94.33  E-value=0.045  Score=41.70  Aligned_cols=56  Identities=14%  Similarity=0.153  Sum_probs=44.8

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA   99 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~   99 (131)
                      +..|.+.|.+ ++++|.+|||+++++   ++..++|-++.|...|+..+...   +..|.+.+
T Consensus         7 ~~~Il~~L~~-~~~~s~~eLa~~l~v---S~~ti~r~l~~L~~~G~~i~~~~---g~GY~l~~   62 (321)
T 1bia_A            7 PLKLIALLAN-GEFHSGEQLGETLGM---SRAAINKHIQTLRDWGVDVFTVP---GKGYSLPE   62 (321)
T ss_dssp             HHHHHHHHTT-SSCBCHHHHHHHHTS---CHHHHHHHHHHHHHTTCCCEEET---TTEEECSS
T ss_pred             HHHHHHHHHc-CCCcCHHHHHHHHCC---CHHHHHHHHHHHHhCCCcEEEec---CCCcEEee
Confidence            4557788863 578999999999999   99999999999999998865431   34577654

>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=94.03  E-value=0.035  Score=37.70  Aligned_cols=71  Identities=14%  Similarity=0.113  Sum_probs=53.3

Q ss_pred             HHHHHHHhChHHHHHhCCCCCCHHHHHhhc--------CCCCCCcchHHHHHHHhhcCCceeecccC--CC--Ccceecc
Q 040869           31 SLKCAIELGIADIIHSHGRAITLSELVSAL--------DIQPTKTTGLFRLMRLLVHSSCFNKTKVN--GQ--EEAYGLT   98 (131)
Q Consensus        31 aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~--------~~~~~~~~~l~RlLr~L~~~gl~~~~~~~--~~--~~~y~~t   98 (131)
                      .++-..++-|...|..  +|++..||++.+        ++   ++..|+++|+.|...|++......  ++  ...|.+|
T Consensus        37 ~~~g~~~~~IL~~L~~--~~~~gyeI~~~l~~~~~~~~~i---s~gtLy~~L~rLE~~GlI~~~~~~~~~~~~rk~Y~LT  111 (145)
T 1xma_A           37 VIRGYVDTIILSLLIE--GDSYGYEISKNIRIKTDELYVI---KETTLYSAFARLEKNGYIKSYYGEETQGKRRTYYRIT  111 (145)
T ss_dssp             SGGGTHHHHHHHHHHH--CCEEHHHHHHHHHHHHTTSCCC---CHHHHHHHHHHHHHTTSEEEEEEEEC--CEEEEEEEC
T ss_pred             HhcCcHHHHHHHHHHh--CCCCHHHHHHHHHHhhCCccCc---ChhHHHHHHHHHHHCCCEEEEEeccCCCCCeEEEEEC
Confidence            3444567777788874  689999999888        47   889999999999999999875321  11  2359999


Q ss_pred             hhcccccc
Q 040869           99 AASTLLIK  106 (131)
Q Consensus        99 ~~s~~L~~  106 (131)
                      +.++.+..
T Consensus       112 ~~G~~~l~  119 (145)
T 1xma_A          112 PEGIKYYK  119 (145)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99986543

>1z05_A Transcriptional regulator, ROK family; structural genomics, protein structure initiative, midwest center for structural genomics; 2.00A {Vibrio cholerae o1 biovar eltor} SCOP: a.4.5.63 c.55.1.10 c.55.1.10

Probab=93.83  E-value=0.064  Score=42.10  Aligned_cols=52  Identities=13%  Similarity=0.215  Sum_probs=45.9

Q ss_pred             HHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           32 LKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        32 L~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      ++..-+..|++.|.+ .+++|..|||+.+|+   .+..+.++++.|...|++.+..
T Consensus        36 ~r~~n~~~il~~l~~-~~~~sr~ela~~~gl---s~~tv~~~v~~L~~~gli~~~~   87 (429)
T 1z05_A           36 IKQINAGRVYKLIDQ-KGPISRIDLSKESEL---APASITKITRELIDAHLIHETT   87 (429)
T ss_dssp             HHHHHHHHHHHHHHH-HCSBCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEEC
T ss_pred             HHHHHHHHHHHHHHH-cCCcCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEecc
Confidence            566667778999975 479999999999999   9999999999999999999864

>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=93.62  E-value=0.038  Score=43.62  Aligned_cols=66  Identities=17%  Similarity=0.130  Sum_probs=50.2

Q ss_pred             HhChHHHHHhC-CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhccccc
Q 040869           37 ELGIADIIHSH-GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLI  105 (131)
Q Consensus        37 ~L~ifd~l~~~-~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~  105 (131)
                      +..|...|.+. ++++|..|||+++++   ++..+.|+++.|...|++.+.... |. .-...+|+.++.+.
T Consensus       406 q~~vl~~l~~~~~~~~~~~~l~~~~~~---~~~~~t~~~~~le~~g~v~r~~~~~D~R~~~i~lT~~g~~~~  474 (487)
T 1hsj_A          406 EIYILNHILRSESNEISSKEIAKCSEF---KPYYLTKALQKLKDLKLLSKKRSLQDERTVIVYVTDTQKANI  474 (487)
T ss_dssp             HHHHHHHHHTCSCSEEEHHHHHHSSCC---CHHHHHHHHHHHHTTTTSCCEECCSSSSCCEEECCSSHHHHH
T ss_pred             HHHHHHHHHhCCCCCcCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEeecCCCCCCCeEEEEECHHHHHHH
Confidence            34467777653 268999999999999   999999999999999999986532 21 12367788777654

>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=93.42  E-value=0.039  Score=33.56  Aligned_cols=42  Identities=12%  Similarity=0.075  Sum_probs=35.6

Q ss_pred             HHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           42 DIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        42 d~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      +.|.. ++..|+.+||+++|+   +...+.|+|-.|...|.+...+
T Consensus        22 ~~L~~-~~~~Ta~~IAkkLg~---sK~~vNr~LY~L~kkG~V~~~~   63 (75)
T 1sfu_A           22 LSLNT-NDYTTAISLSNRLKI---NKKKINQQLYKLQKEDTVKMVP   63 (75)
T ss_dssp             HTSCT-TCEECHHHHHHHTTC---CHHHHHHHHHHHHHTTSEEEEC
T ss_pred             HhCCC-CcchHHHHHHHHHCC---CHHHHHHHHHHHHHCCCEecCC
Confidence            34543 455999999999999   9999999999999999998764

>3kor_A Possible Trp repressor; putative DNA-binding Trp repressor, TRPR like protein, struc genomics, transcription; 1.60A {Staphylococcus aureus}

Probab=93.39  E-value=0.15  Score=33.65  Aligned_cols=41  Identities=20%  Similarity=0.226  Sum_probs=34.9

Q ss_pred             HHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhc
Q 040869           33 KCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVH   79 (131)
Q Consensus        33 ~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~   79 (131)
                      ..+-++.|+..|.+   ..|..|||+.+|+   +...+.|+-|.|..
T Consensus        61 aLs~R~eV~klL~~---G~syreIA~~~g~---S~aTIsRv~r~L~~  101 (119)
T 3kor_A           61 SLSQRLQVAKMIKQ---GYTYATIEQESGA---STATISRVKRSLQW  101 (119)
T ss_dssp             HHHHHHHHHHHHHH---TCCHHHHHHHHCC---CHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHc---CCCHHHHHHHHCC---CHHHHHHHHHHHhc
Confidence            45566889999984   3999999999999   99999999998853

>4esb_A Transcriptional regulator, PADR family; DNA binding protein, HTH fold; 2.50A {Bacillus cereus}

Probab=93.29  E-value=0.065  Score=34.83  Aligned_cols=65  Identities=17%  Similarity=0.163  Sum_probs=49.0

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcC------CCCCCcchHHHHHHHhhcCCceeecccC--CC--Ccceecchhccccc
Q 040869           36 IELGIADIIHSHGRAITLSELVSALD------IQPTKTTGLFRLMRLLVHSSCFNKTKVN--GQ--EEAYGLTAASTLLI  105 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~------~~~~~~~~l~RlLr~L~~~gl~~~~~~~--~~--~~~y~~t~~s~~L~  105 (131)
                      +++-|..+|..  +|.+.-||++.+.      +   ++..|+++|+.|...|++......  ++  ...|.+|+.++...
T Consensus        10 l~~~IL~~L~~--~~~~Gyei~~~l~~~~~~~i---s~gtlY~~L~rLe~~GlI~~~~~~~~~g~~rk~Y~LT~~G~~~l   84 (115)
T 4esb_A           10 LEGCILYIISQ--EEVYGYELSTKLNKHGFTFV---SEGSIYPLLLRMQKEKLIEGTLKASSLGPKRKYYHITDKGLEQL   84 (115)
T ss_dssp             HHHHHHHHHHH--SCEEHHHHHHHHHHTTCTTC---CHHHHHHHHHHHHHTTSEEEEEEECTTSCEEEEEEECHHHHHHH
T ss_pred             HHHHHHHHHHc--CCCCHHHHHHHHHHcCCCCC---CcChHHHHHHHHHHCCCeEEEeeecCCCCCcEEEEECHHHHHHH
Confidence            44556667763  7899999999884      6   889999999999999999865321  11  13499999998544

>3rkx_A Biotin-[acetyl-COA-carboxylase] ligase; biotin protein ligase, 3 domains, enzyme DNA binding, biotin coupling domains; 2.10A {Staphylococcus aureus} PDB: 3rir_A* 3rkw_A 3rky_A* 3v7c_A* 3v7s_A* 3v8j_A 3v7r_A 3v8k_A* 3v8l_A* 4dq2_A*

Probab=93.24  E-value=0.091  Score=40.17  Aligned_cols=61  Identities=11%  Similarity=0.171  Sum_probs=46.9

Q ss_pred             HhChHHHHHhC-CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhccc
Q 040869           37 ELGIADIIHSH-GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTL  103 (131)
Q Consensus        37 ~L~ifd~l~~~-~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~  103 (131)
                      +-.|.+.|.++ +.++|.+|||+++|+   +...+.+-++.|...|+.-+...   +..|.+.+....
T Consensus         5 ~~~iL~~L~~~~g~~~Sg~eLa~~lgv---Sr~aV~k~i~~L~~~G~~i~~~~---~~GY~L~~~~~~   66 (323)
T 3rkx_A            5 SQDVLQLLYKNKPNYISGQSIAESLNI---SRTAVKKVIDQLKLEGCKIDSVN---HKGHLLQQLPDI   66 (323)
T ss_dssp             HHHHHHHHHHHTTSCBCHHHHHHHHTS---CHHHHHHHHHHHHHTTCEEEEET---TTEEEEEECCSS
T ss_pred             HHHHHHHHHhCCCCccCHHHHHHHHCC---CHHHHHHHHHHHHhcCCeEEEeC---CCeEEEecCccc
Confidence            34577888532 469999999999999   99999999999999999665421   456887764333

>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=93.15  E-value=0.057  Score=34.31  Aligned_cols=49  Identities=16%  Similarity=0.198  Sum_probs=41.8

Q ss_pred             HHhChHHHHHhCC-CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           36 IELGIADIIHSHG-RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        36 ~~L~ifd~l~~~~-~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      -+.-|..+|..++ .++...||..++++   +...+.|+|+.|...|++.+..
T Consensus        38 ~E~lVy~~I~~aGn~GIw~kdL~~~tnL---~~~~vtkiLK~LE~k~lIK~Vk   87 (95)
T 2yu3_A           38 QEKLVYQIIEDAGNKGIWSRDVRYKSNL---PLTEINKILKNLESKKLIKAVK   87 (95)
T ss_dssp             HHHHHHHHHHHHTTSCEEHHHHHHHHTC---CHHHHHHHHHHHHHHTSEEEEC
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHhCC---CHHHHHHHHHHHHhCCCEEEec
Confidence            3455777786544 57999999999999   9999999999999999999875

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

Probab=92.86  E-value=0.073  Score=39.22  Aligned_cols=66  Identities=17%  Similarity=0.285  Sum_probs=50.4

Q ss_pred             HhChHHHHHhCC-CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhccccc
Q 040869           37 ELGIADIIHSHG-RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLI  105 (131)
Q Consensus        37 ~L~ifd~l~~~~-~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~  105 (131)
                      +..|...|.+.+ +++|..|||+++++   ++..+.|+++-|...|++.+.... |. .-...+|+.++.+.
T Consensus        36 q~~vL~~L~~~~~~~~~~~el~~~l~~---~~~t~t~~l~rLe~~G~i~R~~~~~DrR~~~i~LT~~G~~~~  104 (250)
T 1p4x_A           36 EFILLTYLFHQQENTLPFKKIVSDLCY---KQSDLVQHIKVLVKHSYISKVRSKIDERNTYISISEEQREKI  104 (250)
T ss_dssp             HHHHHHHHHSCSCSEEEHHHHHHHSSS---CGGGTHHHHHHHHHTTSCEEEECSSSTTSEEEECCHHHHHHH
T ss_pred             HHHHHHHHHhcCCCCcCHHHHHHHHCC---CHhhHHHHHHHHHHCCCEEecCCCCCCCeEEEEECHHHHHHH
Confidence            345666776543 57999999999999   999999999999999999986532 21 12367888887654

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

Probab=92.73  E-value=0.12  Score=36.98  Aligned_cols=36  Identities=11%  Similarity=0.195  Sum_probs=33.5

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      -++|-.+||..+|+   .+..+.|+++.|...|+++...
T Consensus       176 ~~~t~~~iA~~lG~---sr~tvsR~l~~L~~~g~I~~~~  211 (250)
T 3e6c_C          176 MPLSQKSIGEITGV---HHVTVSRVLASLKRENILDKKK  211 (250)
T ss_dssp             CCCCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEECS
T ss_pred             CCCCHHHHHHHhCC---cHHHHHHHHHHHHHCCCeEeCC
Confidence            37899999999999   9999999999999999999764

>3i71_A Ethanolamine utilization protein EUTK; helix-turn-helix, unknown function; HET: FLC; 2.10A {Escherichia coli}

Probab=92.64  E-value=0.35  Score=27.95  Aligned_cols=52  Identities=13%  Similarity=0.187  Sum_probs=42.3

Q ss_pred             HHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchh
Q 040869           41 ADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAA  100 (131)
Q Consensus        41 fd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~  100 (131)
                      ...|+....++|+.|+|+..|.   +....+--|..|-+.|-+++.     +.+|.+-|-
T Consensus         9 Lall~s~~QGMTaGEVAA~f~w---~Le~ar~aLeqLf~~G~LRKR-----sSRYrlkph   60 (68)
T 3i71_A            9 LALLTSVRQGMTAGEVAAHFGW---PLEKARNALEQLFSAGTLRKR-----SSRYRLKPH   60 (68)
T ss_dssp             HHHHHHCTTCBCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEE-----CCEEEECC-
T ss_pred             HHHHHHHhccccHHHHHHHhCC---cHHHHHHHHHHHHhcchhhhh-----ccccccCcc
Confidence            3445544578999999999999   888888899999999999987     578887664

>3frw_A Putative Trp repressor protein; structural genomics, APC21159, PSI-2, P structure initiative; 2.05A {Ruminococcus obeum atcc 29174} PDB: 3g1c_A

Probab=92.27  E-value=0.19  Score=32.60  Aligned_cols=41  Identities=15%  Similarity=0.160  Sum_probs=35.0

Q ss_pred             HHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhc
Q 040869           33 KCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVH   79 (131)
Q Consensus        33 ~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~   79 (131)
                      ..+-++.|+..|.+   +.|..+|++.+|+   +...+.|+-|.|..
T Consensus        44 alaqR~~Ia~lL~~---G~SyreIa~~tG~---StaTIsRv~r~L~~   84 (107)
T 3frw_A           44 SLSQRFEVAKMLTD---KRTYLDISEKTGA---STATISRVNRSLNY   84 (107)
T ss_dssp             HHHHHHHHHHHHHT---TCCHHHHHHHHCC---CHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHc---CCCHHHHHHHHCc---cHHHHHHHHHHHHc
Confidence            34567889999983   4999999999999   99999999998864

>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=91.98  E-value=0.029  Score=43.09  Aligned_cols=59  Identities=17%  Similarity=0.085  Sum_probs=0.0

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcccc
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLL  104 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L  104 (131)
                      +..|...|.. .+++|..|||+++++   ++..++|.++.|...|+++...     ....+|+.++.+
T Consensus        22 ~~~iL~~l~~-~~~~t~~eLa~~l~v---s~~Tv~r~l~~Le~~Glv~~~~-----~gi~LT~~G~~~   80 (345)
T 2o0m_A           22 RFQILRNIYW-MQPIGRRSLSETMGI---TERVLRTETDVLKQLNLIEPSK-----SGMTLTERGLEV   80 (345)
T ss_dssp             --------------------------------------------------------------------
T ss_pred             HHHHHHHHHH-cCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEEe-----cceEEcHHHHHH
Confidence            4557777764 468999999999999   9999999999999999997442     224556555533

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

Probab=91.96  E-value=0.15  Score=32.84  Aligned_cols=46  Identities=11%  Similarity=0.202  Sum_probs=37.3

Q ss_pred             CCCC-CHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869           48 GRAI-TLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA   99 (131)
Q Consensus        48 ~~~~-s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~   99 (131)
                      |..+ |..+||+.+|+   +...+++.++.|...|++....   +.|.|-..+
T Consensus        30 G~~lPs~~~La~~~~v---Sr~tvr~al~~L~~~Gli~~~~---~~G~~V~~~   76 (113)
T 3tqn_A           30 GEMIPSIRKISTEYQI---NPLTVSKAYQSLLDDNVIEKRR---GLGMLVKAG   76 (113)
T ss_dssp             TCEECCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEET---TTEEEECTT
T ss_pred             CCcCcCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEec---CCeEEEeCC
Confidence            3455 99999999999   9999999999999999998765   145554443

>2w48_A Sorbitol operon regulator; SORC, activator, repressor, DNA-binding, transcription, transcription regulator, transcription regulation; 3.20A {Klebsiella pneumoniae}

Probab=91.92  E-value=0.17  Score=38.12  Aligned_cols=37  Identities=16%  Similarity=0.204  Sum_probs=33.9

Q ss_pred             CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCcee-ecc
Q 040869           48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFN-KTK   87 (131)
Q Consensus        48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~-~~~   87 (131)
                      .+++|..|||+++|+   +...++|.|..|...|+++ +..
T Consensus        19 ~~~~~~~ela~~l~v---S~~tIrRdL~~l~~~G~v~iri~   56 (315)
T 2w48_A           19 EQDMTQAQIARELGI---YRTTISRLLKRGREQGIVTIAIN   56 (315)
T ss_dssp             TSCCCHHHHHHHTTC---CHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             cCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCcEEEEec
Confidence            367999999999999   9999999999999999997 654

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

Probab=91.76  E-value=0.25  Score=32.65  Aligned_cols=45  Identities=16%  Similarity=0.164  Sum_probs=37.1

Q ss_pred             CCCC-CHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecc
Q 040869           48 GRAI-TLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLT   98 (131)
Q Consensus        48 ~~~~-s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t   98 (131)
                      |..+ |..+||+.+|+   +...+++-++.|...|++....   |.|.|-..
T Consensus        25 G~~LPse~~La~~~gv---Sr~tVr~Al~~L~~~Gli~~~~---g~G~~V~~   70 (129)
T 2ek5_A           25 DQRVPSTNELAAFHRI---NPATARNGLTLLVEAGILYKKR---GIGMFVSA   70 (129)
T ss_dssp             TSCBCCHHHHHHHTTC---CHHHHHHHHHHHHTTTSEEEET---TTEEEECT
T ss_pred             CCcCcCHHHHHHHHCc---CHHHHHHHHHHHHHCCcEEEec---CCEEEEec
Confidence            4456 99999999999   9999999999999999998765   14555443

>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=91.66  E-value=0.25  Score=38.01  Aligned_cols=41  Identities=7%  Similarity=0.136  Sum_probs=36.9

Q ss_pred             HHHhCCCCCCHHHHHhhc--CCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           43 IIHSHGRAITLSELVSAL--DIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        43 ~l~~~~~~~s~~eLA~~~--~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      .|.. ++|++..+||++.  ++   ++.+++|-|..|...|++.+..
T Consensus        30 yl~~-~~pV~s~~La~~~~l~V---S~aTIRrDL~~LE~~GlL~r~H   72 (338)
T 1stz_A           30 YIEN-KKPVSSQRVLEVSNIEF---SSATIRNDMKKLEYLGYIYQPH   72 (338)
T ss_dssp             HHHH-CSCBCHHHHHHHSCCCS---CHHHHHHHHHHHHHTTSEECCS
T ss_pred             HHHc-CCCccHHHHHHHhCCCC---CHHHHHHHHHHHHHCCCEEEcc
Confidence            5554 6899999999999  88   8999999999999999999875

>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=91.66  E-value=0.22  Score=35.76  Aligned_cols=49  Identities=14%  Similarity=0.171  Sum_probs=42.3

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhccccc
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLI  105 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~  105 (131)
                      +|++..+||+++|+   .++.+...++.|...|++...     .+...+|+.++.++
T Consensus        29 ~~V~~~~LA~~Lgv---S~~SV~~~lkkL~e~GLV~~~-----~~Gv~LTe~G~~~A   77 (200)
T 2p8t_A           29 EPLGRKQISERLEL---GEGSVRTLLRKLSHLDIIRSK-----QRGHFLTLKGKEIR   77 (200)
T ss_dssp             SCBCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEC-------CEEECHHHHHHH
T ss_pred             CCccHHHHHHHhCC---CHHHHHHHHHHHHHCCCEEEe-----CCCeEECHHHHHHH
Confidence            68999999999999   999999999999999999876     35678888887554

>1tc3_C Protein (TC3 transposase); DNA binding, helix-turn-helix, TC1/mariner family, complex (transposase/DNA), DNA binding protein/DNA complex; HET: DNA; 2.45A {Caenorhabditis elegans} SCOP: a.4.1.2

Probab=91.43  E-value=0.19  Score=26.26  Aligned_cols=29  Identities=10%  Similarity=0.116  Sum_probs=24.1

Q ss_pred             CCCHHHHHhhcCCCCCCcchHHHHHHHhhcCC
Q 040869           50 AITLSELVSALDIQPTKTTGLFRLMRLLVHSS   81 (131)
Q Consensus        50 ~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~g   81 (131)
                      .+|..+||+.+|+   +...++|.++.....|
T Consensus        21 g~s~~~IA~~lgi---s~~Tv~~~~~~~~~~g   49 (51)
T 1tc3_C           21 NVSLHEMSRKISR---SRHCIRVYLKDPVSYG   49 (51)
T ss_dssp             TCCHHHHHHHHTC---CHHHHHHHHHCSTTTT
T ss_pred             CCCHHHHHHHHCc---CHHHHHHHHhhHHhcC
Confidence            5899999999999   9999999987554433

>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=91.27  E-value=0.22  Score=31.60  Aligned_cols=37  Identities=11%  Similarity=0.234  Sum_probs=33.3

Q ss_pred             CCCC-CHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           48 GRAI-TLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        48 ~~~~-s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      ++.+ |..+||+.+|+   +...+++-++.|...|++....
T Consensus        40 g~~lps~~eLa~~lgV---Sr~tVr~al~~L~~~GlI~~~~   77 (102)
T 2b0l_A           40 NEGLLVASKIADRVGI---TRSVIVNALRKLESAGVIESRS   77 (102)
T ss_dssp             TEEEECHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCcCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEEe
Confidence            4455 99999999999   9999999999999999998764

>2co5_A Viral protein F93; viral protein-winged helix complex, winged helix, DNA-bindin WHTH, disulfide bond, STIV; 2.2A {Sulfolobus turreted icosahedral virus} SCOP: a.4.5.48

Probab=91.09  E-value=0.25  Score=31.30  Aligned_cols=55  Identities=16%  Similarity=0.182  Sum_probs=39.7

Q ss_pred             CCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcccccc
Q 040869           50 AITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIK  106 (131)
Q Consensus        50 ~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~~  106 (131)
                      .-...+|.+..+... ++..++.+|+-|...|+++... ......|.+|+.++....
T Consensus        28 ~~i~~ei~~~~~~~i-s~GtlYp~L~rLe~~GlI~~~~-~~~rk~Y~iT~~Gr~~l~   82 (99)
T 2co5_A           28 KRLRSEILKRFDIDI-SDGVLYPLIDSLIDDKILREEE-APDGKVLFLTEKGMKEFE   82 (99)
T ss_dssp             GGHHHHHHHHHCCBC-CHHHHHHHHHHHHHTTSEEEEC-CTTSCEEEECHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCC-CCCcHHHHHHHHHHCCCEEEee-CCCcEEEEECHHHHHHHH
Confidence            344577777765311 7889999999999999998753 111346999999985443

>2gqq_A Leucine-responsive regulatory protein; helix-turn-helix, transcription; 3.20A {Escherichia coli} PDB: 2l4a_A

Probab=91.00  E-value=0.037  Score=37.84  Aligned_cols=46  Identities=17%  Similarity=0.213  Sum_probs=38.6

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceee
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNK   85 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~   85 (131)
                      ++..|.+.|.. ++.+|..+||+++|+   +...+++-++.|...|++..
T Consensus        14 l~~~Il~~l~~-~~~ls~~eLa~~lgv---Sr~~vr~al~~L~~~Gli~~   59 (163)
T 2gqq_A           14 IDRNILNELQK-DGRISNVELSKRVGL---SPTPCLERVRRLERQGFIQG   59 (163)
T ss_dssp             HHHHHHHHHHH-CSSCCTTGGGTSSSC---CTTTSSSTHHHHHHHTSEEE
T ss_pred             HHHHHHHHHHh-CCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCcEEE
Confidence            34456776765 677899999999999   88999999999999999874

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

Probab=90.73  E-value=0.21  Score=32.54  Aligned_cols=45  Identities=7%  Similarity=0.061  Sum_probs=38.5

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchh
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAA  100 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~  100 (131)
                      .|.++.|+|+.+|+   ++..+.++++.|+..|.+..-.    .+.|-++..
T Consensus        19 ~p~~~~~la~~~~~---~~~~~~~~l~~l~~~G~l~~i~----~~~~~~~~~   63 (121)
T 2pjp_A           19 EPWWVRDLAKETGT---DEQAMRLTLRQAAQQGIITAIV----KDRYYRNDR   63 (121)
T ss_dssp             SCEEHHHHHHHTTC---CHHHHHHHHHHHHHTTSEEEEE----TTEEEEHHH
T ss_pred             CCCCHHHHHHHhCC---CHHHHHHHHHHHHHCCCEEEec----CCceECHHH
Confidence            57799999999999   9999999999999999888876    566655543

>1cf7_A Protein (transcription factor E2F-4); E2F, winged-helix, DNA-binding domain, cell cycle, transcription/DNA complex; HET: DNA; 2.60A {Homo sapiens} SCOP: a.4.5.17

Probab=90.54  E-value=0.26  Score=29.90  Aligned_cols=38  Identities=11%  Similarity=0.239  Sum_probs=33.4

Q ss_pred             CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      ++.+++.++|..+++.  ..+.+|.+..+|.+.|++++..
T Consensus        28 ~~~i~l~~aa~~L~v~--~kRRiYDI~NVLe~igli~K~~   65 (76)
T 1cf7_A           28 DGVLDLKLAADTLAVR--QKRRIYDITNVLEGIGLIEKKS   65 (76)
T ss_dssp             TTEEEHHHHHHHTTTC--CTHHHHHHHHHHHHHTSEEEEE
T ss_pred             CCcCcHHHHHHHhCCc--cceehhhHHHHHhHhcceeecC
Confidence            4779999999999982  4678999999999999999874

>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=90.49  E-value=0.27  Score=35.61  Aligned_cols=37  Identities=19%  Similarity=0.248  Sum_probs=34.5

Q ss_pred             CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      |..++..+||+.+|+   +...+++-|+.|...|++...+
T Consensus        47 G~~L~e~~La~~lgV---Sr~~VReAL~~L~~~Glv~~~~   83 (237)
T 3c7j_A           47 GTALRQQELATLFGV---SRMPVREALRQLEAQSLLRVET   83 (237)
T ss_dssp             TCBCCHHHHHHHHTS---CHHHHHHHHHHHHHTTSEEEET
T ss_pred             cCeeCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEeC
Confidence            567899999999999   9999999999999999999875

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

Probab=90.38  E-value=0.31  Score=33.68  Aligned_cols=34  Identities=15%  Similarity=0.199  Sum_probs=32.6

Q ss_pred             CCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           50 AITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        50 ~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      ++|-++||..+|+   .+..+.|+++.|...|+++..
T Consensus       169 ~~t~~~lA~~lg~---sr~tvsR~l~~L~~~g~I~~~  202 (220)
T 3dv8_A          169 KITHETIANHLGS---HREVITRMLRYFQVEGLVKLS  202 (220)
T ss_dssp             CCCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEE
T ss_pred             cCCHHHHHHHhCC---CHHHHHHHHHHHHHCCCEEeC
Confidence            8999999999999   999999999999999999876

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

Probab=90.28  E-value=0.25  Score=32.41  Aligned_cols=44  Identities=7%  Similarity=0.076  Sum_probs=36.8

Q ss_pred             CCCC-CHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceec
Q 040869           48 GRAI-TLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGL   97 (131)
Q Consensus        48 ~~~~-s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~   97 (131)
                      |..+ |..+||+.+|+   +...+++-++.|...|++....   |.|.|-.
T Consensus        32 G~~lPse~~La~~~~v---Sr~tvr~Al~~L~~~Gli~~~~---g~G~~V~   76 (126)
T 3by6_A           32 NDQLPSVRETALQEKI---NPNTVAKAYKELEAQKVIRTIP---GKGTFIT   76 (126)
T ss_dssp             TCEECCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEET---TTEEEEC
T ss_pred             CCcCcCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEec---CCeEEEc
Confidence            4556 99999999999   9999999999999999998765   1455544

>3lmm_A Uncharacterized protein; multi-domained alpha-beta protein, structural genomics, PSI- 2, protein structure initiative; 3.00A {Corynebacterium diphtheriae}

Probab=90.16  E-value=0.27  Score=40.53  Aligned_cols=57  Identities=9%  Similarity=0.023  Sum_probs=48.3

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhc-----CCceeecccCCCCcceecchhcc
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVH-----SSCFNKTKVNGQEEAYGLTAAST  102 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~-----~gl~~~~~~~~~~~~y~~t~~s~  102 (131)
                      +..|...|.+ .+.+|..+||+.+++   ++..+.|.|+.|+.     .|+++..     ++.|.+++...
T Consensus       432 ~~~iL~~l~~-~~~it~~~la~~l~~---s~~~~~~~L~~L~~~~~~~~glie~~-----g~~y~L~~~~~  493 (583)
T 3lmm_A          432 IAIVLYLLFQ-RPFITIDVVARGLQS---GKEAARNALEAARQTTVAGAPLIIAH-----DGVWLLGNACR  493 (583)
T ss_dssp             HHHHHHHHHH-SSSBCHHHHHHHHTS---CHHHHHHHHHHHHTCEETTEESEEEE-----TTEEEECHHHH
T ss_pred             HHHHHHHHHH-CCCcCHHHHHHHhCc---CHHHHHHHHHHHHhhhccccceEEEe-----CCEEEECHHHH
Confidence            4457777775 468999999999999   99999999999999     8899986     47899998644

>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=90.08  E-value=0.36  Score=33.73  Aligned_cols=36  Identities=6%  Similarity=0.134  Sum_probs=33.3

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      -++|-.+||..+|+   .+..+.|+|+.|...|++....
T Consensus       174 ~~~t~~~iA~~lg~---sr~tvsR~l~~L~~~g~I~~~~  209 (231)
T 3e97_A          174 LPLGTQDIMARTSS---SRETVSRVLKRLEAHNILEVSP  209 (231)
T ss_dssp             ECCCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEECS
T ss_pred             cCCCHHHHHHHhCC---cHHHHHHHHHHHHHCCcEEecC
Confidence            37899999999999   9999999999999999998763

>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=90.05  E-value=0.27  Score=33.65  Aligned_cols=34  Identities=15%  Similarity=0.111  Sum_probs=32.2

Q ss_pred             CCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           50 AITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        50 ~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      ++|-.+||..+|+   .+..+.|+++.|...|++...
T Consensus       164 ~~t~~~lA~~lg~---sr~tvsR~l~~l~~~g~I~~~  197 (207)
T 2oz6_A          164 KITRQEIGRIVGC---SREMVGRVLKSLEEQGLVHVK  197 (207)
T ss_dssp             ECCHHHHHHHHTS---CHHHHHHHHHHHHHTTSEEEE
T ss_pred             ccCHHHHHHHhCC---CHHHHHHHHHHHHHCCCEEec
Confidence            5899999999999   999999999999999999876

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

Probab=89.88  E-value=0.36  Score=31.54  Aligned_cols=46  Identities=9%  Similarity=0.139  Sum_probs=37.6

Q ss_pred             CCCC-CHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869           48 GRAI-TLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA   99 (131)
Q Consensus        48 ~~~~-s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~   99 (131)
                      |..+ |..+||+.+|+   +...+++-++.|...|++....   |.|.|-..+
T Consensus        34 g~~Lps~~~La~~~~v---Sr~tvr~Al~~L~~~G~i~~~~---g~G~~V~~~   80 (125)
T 3neu_A           34 EDKLPSVREMGVKLAV---NPNTVSRAYQELERAGYIYAKR---GMGSFVTSD   80 (125)
T ss_dssp             TCBCCCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEET---TTEEEECCC
T ss_pred             CCCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCeEEEec---CCEEEEecC
Confidence            3445 79999999999   9999999999999999999765   256665543

>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=89.78  E-value=0.39  Score=33.55  Aligned_cols=36  Identities=11%  Similarity=0.165  Sum_probs=33.4

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      -++|-++||..+|+   .+..+.|+++.|...|++....
T Consensus       179 ~~~t~~~lA~~lg~---sr~tvsR~l~~l~~~g~I~~~~  214 (232)
T 2gau_A          179 IYLSREELATLSNM---TVSNAIRTLSTFVSERMLALDG  214 (232)
T ss_dssp             CCCCHHHHHHHTTS---CHHHHHHHHHHHHHTTSEEEET
T ss_pred             cccCHHHHHHHhCC---CHHHHHHHHHHHHHCCCEeeCC
Confidence            47899999999999   9999999999999999998763

>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=89.70  E-value=0.29  Score=33.58  Aligned_cols=35  Identities=14%  Similarity=0.199  Sum_probs=32.8

Q ss_pred             CCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           50 AITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        50 ~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      ++|-.+||..+|+   .+..+.|+++.|...|++....
T Consensus       167 ~~t~~~iA~~lg~---sr~tvsR~l~~L~~~g~I~~~~  201 (210)
T 3ryp_A          167 KITRQEIGQIVGC---SRETVGRILKMLEDQNLISAHG  201 (210)
T ss_dssp             ECCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEET
T ss_pred             ccCHHHHHHHhCC---cHHHHHHHHHHHHHCCcEEeCC
Confidence            6899999999999   9999999999999999999763

>2dql_A PEX protein; circadian clock associated protein, circadian clock protein; 1.70A {Anabaena SP}

Probab=89.56  E-value=0.49  Score=30.55  Aligned_cols=62  Identities=13%  Similarity=0.146  Sum_probs=45.6

Q ss_pred             hHHHHHhCCCCCCHHHHHhhc-------CCCCCCcchHHHHHHHhhcCCceeecccC---CCC--cceecchhcccccc
Q 040869           40 IADIIHSHGRAITLSELVSAL-------DIQPTKTTGLFRLMRLLVHSSCFNKTKVN---GQE--EAYGLTAASTLLIK  106 (131)
Q Consensus        40 ifd~l~~~~~~~s~~eLA~~~-------~~~~~~~~~l~RlLr~L~~~gl~~~~~~~---~~~--~~y~~t~~s~~L~~  106 (131)
                      |..+|.  .+|.+--||.+.+       ++   ++..|+++|+-|...|++......   +++  ..|++|+.++....
T Consensus        27 IL~lL~--~~~~~Gyei~~~l~~~~~~~~i---s~gtLY~~L~rLe~~GlI~~~~~~~~~~~~~rk~Y~LT~~G~~~l~  100 (115)
T 2dql_A           27 ILYVLL--QGESYGTELIQQLETEHPTYRL---SDTVLYSAIKFLEDNRAITGYWKKLEGRGRPRRMYQVSPEWQHQAE  100 (115)
T ss_dssp             HHHHHT--TSCBCHHHHHHHHHHHCTTEEC---CHHHHHHHHHHHHHTTSEEEEEECCTTCSSCEEEEEECGGGHHHHH
T ss_pred             HHHHHH--hCCCCHHHHHHHHHHHcCCCCC---CcchHHHHHHHHHHCCCEEEEeeecCCCCCCcEEEEECHHHHHHHH
Confidence            555665  3788888887776       36   889999999999999999875321   111  34999999985543

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

Probab=89.48  E-value=0.33  Score=33.34  Aligned_cols=34  Identities=15%  Similarity=0.159  Sum_probs=32.3

Q ss_pred             CCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           50 AITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        50 ~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      ++|-++||..+|+   .+..+.|+|+.|...|++...
T Consensus       146 ~~t~~~lA~~lg~---sr~tvsR~l~~L~~~g~I~~~  179 (202)
T 2zcw_A          146 KATHDELAAAVGS---VRETVTKVIGELAREGYIRSG  179 (202)
T ss_dssp             ECCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCHHHHHHHhCC---CHHHHHHHHHHHHHCCCEEeC
Confidence            5899999999999   999999999999999999976

>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=89.46  E-value=0.32  Score=33.84  Aligned_cols=35  Identities=11%  Similarity=0.112  Sum_probs=32.6

Q ss_pred             CCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           50 AITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        50 ~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      ++|-++||..+|+   .+..+.|+|+.|...|+++...
T Consensus       187 ~lt~~~lA~~lg~---sr~tvsR~l~~L~~~g~I~~~~  221 (230)
T 3iwz_A          187 RVSRQELARLVGC---SREMAGRVLKKLQADGLLHARG  221 (230)
T ss_dssp             ECCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEET
T ss_pred             CCCHHHHHHHhCC---cHHHHHHHHHHHHHCCCEEECC
Confidence            4899999999999   9999999999999999999763

>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=89.41  E-value=0.29  Score=32.26  Aligned_cols=44  Identities=14%  Similarity=0.239  Sum_probs=37.1

Q ss_pred             CCCC-CHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceec
Q 040869           48 GRAI-TLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGL   97 (131)
Q Consensus        48 ~~~~-s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~   97 (131)
                      |..+ |..+||+.+|+   +...+++-++.|...|++....   |.|.|-.
T Consensus        35 G~~LPser~La~~~gV---Sr~tVReAl~~L~~eGlv~~~~---g~G~~V~   79 (134)
T 4ham_A           35 GEKILSIREFASRIGV---NPNTVSKAYQELERQEVIITVK---GKGTFIA   79 (134)
T ss_dssp             TCEECCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEET---TTEEEEC
T ss_pred             CCCCccHHHHHHHHCC---CHHHHHHHHHHHHHCCcEEEEc---CcEEEEe
Confidence            4456 89999999999   9999999999999999998765   2566653

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

Probab=89.21  E-value=0.32  Score=33.49  Aligned_cols=35  Identities=14%  Similarity=0.125  Sum_probs=32.8

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      -++|-.+||..+|+   .+..+.|+++.|...|+++..
T Consensus       162 ~~~t~~~lA~~lg~---sr~tvsR~l~~l~~~g~I~~~  196 (216)
T 4ev0_A          162 FQIRHHELAALAGT---SRETVSRVLHALAEEGVVRLG  196 (216)
T ss_dssp             EECCHHHHHHHHTS---CHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCCHHHHHHHhCC---CHHHHHHHHHHHHHCCCEEec
Confidence            36899999999999   999999999999999999876

>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=89.19  E-value=0.42  Score=33.27  Aligned_cols=35  Identities=9%  Similarity=0.138  Sum_probs=32.8

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      -++|-.+||..+|+   .+..+.|+++.|...|++...
T Consensus       176 ~~~t~~~lA~~lg~---sr~tvsR~l~~l~~~g~I~~~  210 (227)
T 3d0s_A          176 HDLTQEEIAQLVGA---SRETVNKALADFAHRGWIRLE  210 (227)
T ss_dssp             CCCCHHHHHHHHTS---CHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCCHHHHHHHhCC---cHHHHHHHHHHHHHCCCEEec
Confidence            36899999999999   999999999999999999876

>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=88.88  E-value=0.44  Score=33.82  Aligned_cols=36  Identities=14%  Similarity=0.149  Sum_probs=33.3

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      -++|-.+||..+|+   .+..+.|+|+.|...|++....
T Consensus       192 ~~lt~~~lA~~lG~---sr~tvsR~l~~L~~~GlI~~~~  227 (243)
T 3la7_A          192 LKLSHQAIAEAIGS---TRVTVTRLLGDLREKKMISIHK  227 (243)
T ss_dssp             SCCCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEET
T ss_pred             ccCCHHHHHHHHCC---cHHHHHHHHHHHHHCCCEEEcC
Confidence            37899999999999   9999999999999999999763

>3dkw_A DNR protein; CRP-FNR, HTH, beta barrel, dimerization helix, homodimer, transcription regulator; 3.60A {Pseudomonas aeruginosa}

Probab=88.82  E-value=0.35  Score=33.55  Aligned_cols=36  Identities=14%  Similarity=0.153  Sum_probs=33.1

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      -++|-++||..+|+   .+..+.|+++.|...|++....
T Consensus       177 ~~~t~~~lA~~lg~---sr~tvsR~l~~l~~~g~I~~~~  212 (227)
T 3dkw_A          177 IPVAKQLVAGHLSI---QPETFSRIMHRLGDEGIIHLDG  212 (227)
T ss_dssp             CCSCTHHHHHHTTS---CHHHHHHHHHHHHHHTSEEESS
T ss_pred             ecCCHHHHHHHhCC---CHHHHHHHHHHHHHCCcEEecC
Confidence            46899999999999   9999999999999999998763

>3l9f_A Putative uncharacterized protein SMU.1604C; PADR, transcription regulator; 1.80A {Streptococcus mutans}

Probab=88.72  E-value=0.3  Score=34.93  Aligned_cols=59  Identities=20%  Similarity=0.224  Sum_probs=45.7

Q ss_pred             ChHHHHHhCCCCCCHHHHHhhc--------CCCCCCcchHHHHHHHhhcCCceeecccC--CCC--cceecchhcc
Q 040869           39 GIADIIHSHGRAITLSELVSAL--------DIQPTKTTGLFRLMRLLVHSSCFNKTKVN--GQE--EAYGLTAAST  102 (131)
Q Consensus        39 ~ifd~l~~~~~~~s~~eLA~~~--------~~~~~~~~~l~RlLr~L~~~gl~~~~~~~--~~~--~~y~~t~~s~  102 (131)
                      -|...|.  .+|.+.-||++.+        ++   ++..+|+.|+-|...|+++.....  +++  ..|..|+.++
T Consensus        40 ~IL~lL~--~~p~~GYeL~~~l~~~~~~~~~~---s~g~lY~~L~rLe~~GlI~~~~~~~~~~p~rk~Y~iT~~Gr  110 (204)
T 3l9f_A           40 IILGILS--KKERSGYEINDILQNQLSYFYDG---TYGMIYPTLRKLEKDGKITKEVVIQDGRPNKNIYAITESGK  110 (204)
T ss_dssp             HHHHHTS--SCCEEHHHHHHHHHHTSTTTEEC---CTTCHHHHHHHHHHTTSEEEEEECCTTSCCEEEEEECHHHH
T ss_pred             HHHHHHH--cCCCCHHHHHHHHHHHhCCccCC---CcchHHHHHHHHHHCCCeEEEeeccCCCCCceEEEEChHHH
Confidence            4566665  4899999999987        35   788999999999999999865321  112  3599999987

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

Probab=88.66  E-value=0.34  Score=33.14  Aligned_cols=35  Identities=9%  Similarity=0.099  Sum_probs=32.7

Q ss_pred             CCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           50 AITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        50 ~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      ++|-++||..+|+   .+..+.|+|+.|...|+++...
T Consensus       139 ~~t~~~lA~~lg~---sr~tvsR~l~~L~~~g~I~~~~  173 (195)
T 3b02_A          139 TVSHEEIADATAS---IRESVSKVLADLRREGLIATAY  173 (195)
T ss_dssp             ECCHHHHHHTTTS---CHHHHHHHHHHHHHHTSEEEET
T ss_pred             cCCHHHHHHHhCC---CHHHHHHHHHHHHHCCCEEecC
Confidence            5899999999999   9999999999999999998763

>3maj_A DNA processing chain A; MCSG, PSI-2, structural genomics, protein structure initiati midwest center for structural genomics; HET: DNA; 2.05A {Rhodopseudomonas palustris}

Probab=88.49  E-value=0.3  Score=38.35  Aligned_cols=51  Identities=10%  Similarity=0.135  Sum_probs=44.1

Q ss_pred             hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceec
Q 040869           38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGL   97 (131)
Q Consensus        38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~   97 (131)
                      -.|++.|.  .+|+++++|+.++|+   +...+...|-.|.-.|++....    ++.|++
T Consensus       331 ~~vl~~l~--~~~~~~D~l~~~~gl---~~~~v~~~L~~LEl~G~v~~~~----Gg~~~~  381 (382)
T 3maj_A          331 TRILALLG--PSPVGIDDLIRLSGI---SPAVVRTILLELELAGRLERHG----GSLVSL  381 (382)
T ss_dssp             HHHHHHCC--SSCEEHHHHHHHHCC---CHHHHHHHHHHHHHTTCCEECT----TSEEEC
T ss_pred             HHHHHhhC--CCCCCHHHHHHHHCc---CHHHHHHHHHHHHhCCcEEeCC----CceEec
Confidence            34777775  379999999999999   9999999999999999999886    677765

>1zyb_A Transcription regulator, CRP family; NP_813211.1, structural genomics, joint center for structura genomics, JCSG; 2.15A {Bacteroides thetaiotaomicron} SCOP: a.4.5.4 b.82.3.2

Probab=88.30  E-value=0.46  Score=33.40  Aligned_cols=34  Identities=12%  Similarity=0.208  Sum_probs=32.2

Q ss_pred             CCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           50 AITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        50 ~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      ++|-.+||..+|+   .+..+.|+++.|...|+++..
T Consensus       186 ~~t~~~lA~~lG~---sr~tvsR~l~~l~~~glI~~~  219 (232)
T 1zyb_A          186 KVKMDDLARCLDD---TRLNISKTLNELQDNGLIELH  219 (232)
T ss_dssp             ECCHHHHHHHHTS---CHHHHHHHHHHHHHTTSCEEE
T ss_pred             cCCHHHHHHHhCC---ChhHHHHHHHHHHHCCCEEec
Confidence            5899999999999   999999999999999999876

>2zfw_A PEX; five alpha-helices + one beta-sheet, circadian clock protein; 2.90A {Synechococcus SP}

Probab=88.26  E-value=0.49  Score=32.15  Aligned_cols=63  Identities=16%  Similarity=0.199  Sum_probs=46.3

Q ss_pred             hHHHHHhCCCCCCHHHHHhhc-------CCCCCCcchHHHHHHHhhcCCceeecccCC---C--CcceecchhccccccC
Q 040869           40 IADIIHSHGRAITLSELVSAL-------DIQPTKTTGLFRLMRLLVHSSCFNKTKVNG---Q--EEAYGLTAASTLLIKD  107 (131)
Q Consensus        40 ifd~l~~~~~~~s~~eLA~~~-------~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~---~--~~~y~~t~~s~~L~~~  107 (131)
                      |..+|.  .+|.+--||.+.+       ++   ++..|+++|+.|...|++.......   +  ...|.+|+.++.....
T Consensus        49 IL~lL~--~~p~~GYeI~k~l~~~~~~~~i---s~gtLYp~L~rLE~~GlI~~~~~~~~~~g~~rk~Y~LT~~Gr~~l~~  123 (148)
T 2zfw_A           49 VLAVLR--HEDSYGTELIQHLETHWPNYRL---SDTVLYTALKFLEDEQIISGYWKKVEGRGRPRRMYQLAQANDDRSRD  123 (148)
T ss_dssp             HHHHHT--TCCEEHHHHHHHHHHHCTTEEC---CSHHHHHHHHHHHHTSSEEEECCCCTTSSCCCCEEEESSSSCSTTHH
T ss_pred             HHHHHH--hCCCcHHHHHHHHHHHcCCCCC---ChhHHHHHHHHHHHCCCEEEEeeccCCCCCCcEEEEECHHHHHHHHH
Confidence            555665  3788888888876       36   8889999999999999998753210   1  2349999999855433

>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=88.15  E-value=0.44  Score=33.20  Aligned_cols=35  Identities=9%  Similarity=0.174  Sum_probs=32.7

Q ss_pred             CCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           50 AITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        50 ~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      ++|-.+||..+|+   .+..+.|+++.|...|++....
T Consensus       163 ~~t~~~lA~~lG~---sr~tvsR~l~~L~~~g~I~~~~  197 (222)
T 1ft9_A          163 DFTVEEIANLIGS---SRQTTSTALNSLIKEGYISRQG  197 (222)
T ss_dssp             CCCHHHHHHHHCS---CHHHHHHHHHHHHHTTSSEECS
T ss_pred             cCCHHHHHHHhCC---cHHHHHHHHHHHHHCCcEEEcC
Confidence            4899999999999   9999999999999999998764

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

Probab=88.03  E-value=0.75  Score=33.75  Aligned_cols=55  Identities=18%  Similarity=0.298  Sum_probs=43.4

Q ss_pred             ChHHHHHhCC-CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchh
Q 040869           39 GIADIIHSHG-RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAA  100 (131)
Q Consensus        39 ~ifd~l~~~~-~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~  100 (131)
                      .|...+.+.+ .|-.+.||++.+++   ++..+..+|+.|+..|.+.+-.    ++.|-+...
T Consensus       145 ~i~~~~~~~g~~pp~~~dl~~~l~~---~~~~~~~~l~~l~~~g~lv~l~----~~~~~~~~~  200 (258)
T 1lva_A          145 DLEDKYRVSRWQPPSFKEVAGSFNL---DPSELEELLHYLVREGVLVKIN----DEFYWHRQA  200 (258)
T ss_dssp             HHHHHHHHHTTSCCBHHHHHHHTTC---CHHHHHHHHHHHHHTTSEEESS----SSBEEEHHH
T ss_pred             HHHHHHHHCCCCCCCHHHHHhHhCC---CHHHHHHHHHHHHHCCCEEEec----CCeEEcHHH
Confidence            4555554433 47799999999999   9999999999999999888876    677665543

>2o3f_A Putative HTH-type transcriptional regulator YBBH; APC85504, putative transcriptional regulator YBBH; HET: MLY; 1.75A {Bacillus subtilis} SCOP: a.4.1.20

Probab=87.87  E-value=0.36  Score=31.06  Aligned_cols=45  Identities=22%  Similarity=0.225  Sum_probs=33.8

Q ss_pred             HhChHHHHHhCC---CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCcee
Q 040869           37 ELGIADIIHSHG---RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFN   84 (131)
Q Consensus        37 ~L~ifd~l~~~~---~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~   84 (131)
                      +-.|.+.|-++.   ..+|+.|||+++|+   ++..+.|+.|.|--.|+-.
T Consensus        23 e~~ia~yil~~~~~~~~~si~elA~~~~v---S~aTv~Rf~kklG~~gf~e   70 (111)
T 2o3f_A           23 ERKLADYILAHPHXAIESTVNEISALANS---SDAAVIRLCXSLGLKGFQD   70 (111)
T ss_dssp             HHHHHHHHHHCHHHHHTCCHHHHHHHTTC---CHHHHHHHHHHTTCSSHHH
T ss_pred             HHHHHHHHHHChHHHHhcCHHHHHHHHCC---CHHHHHHHHHHcCCCCHHH
Confidence            344556554321   35999999999999   9999999999887777533

>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=87.85  E-value=0.46  Score=32.95  Aligned_cols=35  Identities=9%  Similarity=0.107  Sum_probs=32.9

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      -++|-.+||..+|+   .+..+.|+++.|...|++...
T Consensus       166 ~~~t~~~lA~~lg~---sr~tvsR~l~~l~~~g~I~~~  200 (220)
T 2fmy_A          166 LGLNTEEIALMLGT---TRQTVSVLLNDFKKMGILERV  200 (220)
T ss_dssp             CSSCHHHHHHHHTS---CHHHHHHHHHHHHHTTSEEES
T ss_pred             ccCCHHHHHHHhCC---cHHHHHHHHHHHHHCCCEEEc
Confidence            37999999999999   999999999999999999875

>2qlz_A Transcription factor PF0095; 2.50A {Pyrococcus furiosus} PDB: 2quf_A

Probab=87.85  E-value=1.8  Score=31.40  Aligned_cols=44  Identities=11%  Similarity=0.082  Sum_probs=37.9

Q ss_pred             ChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           39 GIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        39 ~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      -|.-.|.  .++.|..+||..+|+   +++.+.-.|+-|+..|++....
T Consensus       169 ~l~~~l~--~~~~t~~~la~~~~l---~~~~V~~~l~~L~~~~~v~~~~  212 (232)
T 2qlz_A          169 ILHYLLL--NGRATVEELSDRLNL---KEREVREKISEMARFVPVKIIN  212 (232)
T ss_dssp             HHHHHHH--SSEEEHHHHHHHHTC---CHHHHHHHHHHHTTTSCEEEET
T ss_pred             HHHHHHh--cCCCCHHHHHHHhCc---CHHHHHHHHHHHHhcCCeEEec
Confidence            3444555  479999999999999   9999999999999999998665

>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=87.73  E-value=0.41  Score=37.26  Aligned_cols=64  Identities=17%  Similarity=0.216  Sum_probs=47.9

Q ss_pred             hHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhccccccCc
Q 040869           40 IADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIKDK  108 (131)
Q Consensus        40 ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~~~~  108 (131)
                      +.+.|.+ ....|.+++++.+|+   ...+..|.|+.|+..|++++.+. +....|....+-..|.++.
T Consensus       302 ll~~l~~-~p~~t~~~~~~~~~~---S~~TA~r~L~~L~e~GiL~~~~~-gR~~~y~~~~~l~il~~~~  365 (373)
T 3eqx_A          302 LVQVIFE-QPYCRIQNLVESGLA---KRQTASVYLKQLCDIGVLEEVQS-GKEKLFVHPKFVTLMTKDS  365 (373)
T ss_dssp             HHHHHHH-CSEEEHHHHHHTSSS---CHHHHHHHHHHHHHTTSCEEC---CCSCEEECHHHHHHHHSSC
T ss_pred             HHHHHHH-CCCccHHHHHHHhCc---CHHHHHHHHHHHHHCCcEEEeCC-CCceEeehHHHHHHHhccC
Confidence            4555553 245899999999999   99999999999999999998752 1134588887777776554

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

Probab=87.65  E-value=0.7  Score=32.57  Aligned_cols=35  Identities=17%  Similarity=0.220  Sum_probs=32.6

Q ss_pred             CCCHHHHHhhcCCCCCCc-chHHHHHHHhhcCCceeecc
Q 040869           50 AITLSELVSALDIQPTKT-TGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        50 ~~s~~eLA~~~~~~~~~~-~~l~RlLr~L~~~gl~~~~~   87 (131)
                      ++|-.+||..+|+   .+ ..+.|+|+.|...|++....
T Consensus       169 ~~t~~~lA~~lG~---sr~etvsR~l~~l~~~glI~~~~  204 (238)
T 2bgc_A          169 NLTMQELGYSSGI---AHSSAVSRIISKLKQEKVIVYKN  204 (238)
T ss_dssp             CCCHHHHHHHTTC---CCHHHHHHHHHHHHHTTSEEEET
T ss_pred             cCCHHHHHHHhCC---ChHHHHHHHHHHHHHCCCEEecC
Confidence            7999999999999   99 69999999999999998763

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=87.54  E-value=0.44  Score=35.50  Aligned_cols=55  Identities=15%  Similarity=0.234  Sum_probs=42.9

Q ss_pred             hHHHHHhC-CCCCCHHHHHhhcCCCCCCcchHHHHHH-HhhcCCceeecccCCCCcceecchhcc
Q 040869           40 IADIIHSH-GRAITLSELVSALDIQPTKTTGLFRLMR-LLVHSSCFNKTKVNGQEEAYGLTAAST  102 (131)
Q Consensus        40 ifd~l~~~-~~~~s~~eLA~~~~~~~~~~~~l~RlLr-~L~~~gl~~~~~~~~~~~~y~~t~~s~  102 (131)
                      ++..+... +.+.+..++|+.+|+   +...+++.++ +|...|++....     .....|+.+.
T Consensus       268 ~l~~l~~~~~~~~~~~~~a~~lg~---~~~tl~~~l~~~l~~~gli~~~~-----~g~~~t~~~~  324 (338)
T 3pfi_A          268 YLELLTAAKQKPIGLASIAAALSE---DENTIEDVIEPYLLANGYIERTA-----KGRIASAKSY  324 (338)
T ss_dssp             HHHHHHHSCSCCBCHHHHHHHTTC---CHHHHHHTTHHHHHHTTSEEEET-----TEEEECHHHH
T ss_pred             HHHHHHHhcCCCchHHHHHHHhCC---CHHHHHHHHhHHHHHcCceecCC-----CcccccHHHH
Confidence            44444432 467889999999999   9999999999 999999998874     3456777665

>2vxz_A Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Pyrobaculum spherical virus}

Probab=87.38  E-value=0.53  Score=32.36  Aligned_cols=45  Identities=13%  Similarity=0.107  Sum_probs=40.5

Q ss_pred             hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      -.|.+.|.  .|+.|..+||+++|+   +-...+=.|..|.-.|++.+..
T Consensus        14 ~~ILE~Lk--~G~~~t~~Iak~LGl---Shg~aq~~Ly~LeREG~V~~Vk   58 (165)
T 2vxz_A           14 RDILALLA--DGCKTTSLIQQRLGL---SHGRAKALIYVLEKEGRVTRVA   58 (165)
T ss_dssp             HHHHHHHT--TCCEEHHHHHHHHTC---CHHHHHHHHHHHHHTTSCEEEE
T ss_pred             HHHHHHHH--hCCccHHHHHHHhCC---cHHHHHHHHHHHHhcCceEEEE
Confidence            35778887  589999999999999   8899999999999999999876

>3oio_A Transcriptional regulator (ARAC-type DNA-binding containing proteins); PSI-2, midwest center for structural genomics; 1.65A {Chromobacterium violaceum}

Probab=87.14  E-value=0.87  Score=28.68  Aligned_cols=42  Identities=7%  Similarity=0.190  Sum_probs=32.1

Q ss_pred             hHHHHHhC-CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCcee
Q 040869           40 IADIIHSH-GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFN   84 (131)
Q Consensus        40 ifd~l~~~-~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~   84 (131)
                      +.+.|... ..++|+++||+.+|+   ++..|.|+++......+-.
T Consensus        12 ~~~~i~~~~~~~~~~~~lA~~~~~---S~~~l~r~fk~~~G~s~~~   54 (113)
T 3oio_A           12 AVSLMEANIEEPLSTDDIAYYVGV---SRRQLERLFKQYLGTVPSK   54 (113)
T ss_dssp             HHHHHHTCSSSCCCHHHHHHHHTS---CHHHHHHHHHHHTSSCHHH
T ss_pred             HHHHHHhhhcCCCCHHHHHHHHCc---CHHHHHHHHHHHHCcCHHH
Confidence            34455533 367999999999999   9999999998876665443

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

Probab=87.03  E-value=0.78  Score=33.38  Aligned_cols=46  Identities=9%  Similarity=0.176  Sum_probs=39.3

Q ss_pred             CCCC-CHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchh
Q 040869           48 GRAI-TLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAA  100 (131)
Q Consensus        48 ~~~~-s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~  100 (131)
                      |..+ |-.+||++.|+   +...+++-|+.|+..|++.. .   |.|.|-..+.
T Consensus        33 g~~lPse~~La~~~~v---Sr~tvr~Al~~L~~~G~i~~-~---g~Gt~V~~~~   79 (248)
T 3f8m_A           33 GDPFPAEREIAEQFEV---ARETVRQALRELLIDGRVER-R---GRTTVVARPK   79 (248)
T ss_dssp             TCBCCCHHHHHHHTTC---CHHHHHHHHHHHHHTTSEEE-E---TTEEEECCCC
T ss_pred             CCcCcCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEe-C---CCEEEEccCc
Confidence            5567 99999999999   99999999999999999999 6   2677766543

>3iwf_A Transcription regulator RPIR family; transcriptional, N-terminal, PSI, MCSG, structural genomics, midwest center structural genomics; 1.40A {Staphylococcus epidermidis}

Probab=86.92  E-value=0.44  Score=30.55  Aligned_cols=44  Identities=23%  Similarity=0.273  Sum_probs=33.5

Q ss_pred             HhChHHHHHhCC---CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCce
Q 040869           37 ELGIADIIHSHG---RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCF   83 (131)
Q Consensus        37 ~L~ifd~l~~~~---~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~   83 (131)
                      +-.|.+.|-++.   ..+|+.|||+++++   ++..+.|+.|.|--.|+-
T Consensus        19 e~~ia~yil~~~~~~~~~si~elA~~~~v---S~aTv~Rf~kkLGf~gf~   65 (107)
T 3iwf_A           19 EKKIAQFILNYPHKVVNMTSQEIANQLET---SSTSIIRLSKKVTPGGFN   65 (107)
T ss_dssp             HHHHHHHHHHCHHHHTTCCHHHHHHHHTS---CHHHHHHHHHHHSTTHHH
T ss_pred             HHHHHHHHHhCHHHHHHCCHHHHHHHHCC---CHHHHHHHHHHhCCCCHH
Confidence            344555554322   46999999999999   999999999998766643

>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=86.82  E-value=0.65  Score=30.06  Aligned_cols=36  Identities=22%  Similarity=0.191  Sum_probs=33.3

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      .-+|+..|++++++   .-+..+++||.|...|++....
T Consensus        58 KlITpsvlseRlkI---~gSLAR~aLreL~~kGlIk~V~   93 (108)
T 3u5c_Z           58 RYVSVSVLVDRLKI---GGSLARIALRHLEKEGIIKPIS   93 (108)
T ss_dssp             SSBSHHHHHHTTCC---CTTHHHHHHHHHSSSSSCEEEE
T ss_pred             eEEeHHHhhhhhhh---hHHHHHHHHHHHHHCCCEEEEe
Confidence            56999999999999   9999999999999999998764

>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=86.75  E-value=0.57  Score=33.70  Aligned_cols=34  Identities=15%  Similarity=0.215  Sum_probs=32.4

Q ss_pred             CCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           50 AITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        50 ~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      ++|-.+||..+|+   .+..+.|+|+.|...|+++..
T Consensus       217 ~lt~~~lA~~lG~---sr~tvsR~l~~L~~~GlI~~~  250 (260)
T 3kcc_A          217 KITRQEIGQIVGC---SRETVGRILKMLEDQNLISAH  250 (260)
T ss_dssp             ECCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEC
T ss_pred             cCCHHHHHHHhCC---CHHHHHHHHHHHHHCCCEEEc
Confidence            6899999999999   999999999999999999976

>3qph_A TRMB, A global transcription regulator; transcriptional regulator; HET: SUC; 2.99A {Pyrococcus furiosus}

Probab=86.49  E-value=0.028  Score=43.33  Aligned_cols=60  Identities=10%  Similarity=0.029  Sum_probs=45.8

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcc
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAST  102 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~  102 (131)
                      +..+.-.|-+ .++.|+.|||+.+|+   +...+++.|+.|...|++.....  .+..|...|...
T Consensus        20 ea~vY~~Ll~-~g~~t~~eia~~~gv---~~~~Vy~~L~~L~~~GlV~~~~g--~p~~y~av~p~~   79 (342)
T 3qph_A           20 EILTYWTLLV-YGPSTAKEISTKSGI---PYNRVYDTISSLKLRGFVTEIEG--TPKVYAAYSPRI   79 (342)
T ss_dssp             TTSCSHHHHH-HHHHHHSCCSSSTTS---SSCSCCHHHHHHHHHTSEEEECC--TTCEEEECCHHH
T ss_pred             HHHHHHHHHH-cCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEEcC--ceeEEEEcCHHH
Confidence            3344445543 368999999999999   99999999999999999987641  256777766543

>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=86.46  E-value=0.88  Score=32.87  Aligned_cols=46  Identities=17%  Similarity=0.160  Sum_probs=37.3

Q ss_pred             CCCC-CHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869           48 GRAI-TLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA   99 (131)
Q Consensus        48 ~~~~-s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~   99 (131)
                      |..+ |-.+||++.|+   +...+++-++.|...|++....   |.|.|-..+
T Consensus        30 g~~lPse~~La~~~~v---Sr~tvr~Al~~L~~~G~i~~~~---g~G~~V~~~   76 (236)
T 3edp_A           30 GMLMPNETALQEIYSS---SRTTIRRAVDLLVEEGLVVRKN---GVGLYVQPK   76 (236)
T ss_dssp             CC--CCHHHHHHHTTC---CHHHHHHHHHHHHHTTSEEEET---TTEEEECCC
T ss_pred             cCCCcCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEEEC---CceEEEccC
Confidence            4567 89999999999   9999999999999999999875   256665543

>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=86.26  E-value=0.66  Score=33.06  Aligned_cols=45  Identities=13%  Similarity=0.165  Sum_probs=38.3

Q ss_pred             CCCC-CHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecc
Q 040869           48 GRAI-TLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLT   98 (131)
Q Consensus        48 ~~~~-s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t   98 (131)
                      |..+ |-.+||+++|+   +...++.-|+.|...|++....   |.|.|-..
T Consensus        28 G~~LPsE~eLa~~~gV---SR~tVReAL~~L~~eGlv~~~~---g~G~~V~~   73 (239)
T 1hw1_A           28 GTILPAERELSELIGV---TRTTLREVLQRLARDGWLTIQH---GKPTKVNN   73 (239)
T ss_dssp             TSBCCCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEET---TEEEEECC
T ss_pred             CCCCCCHHHHHHHHCC---CHHHHHHHHHHHHHCCcEEEec---CCCcEeeC
Confidence            4567 89999999999   9999999999999999999875   25666654

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

Probab=86.19  E-value=0.94  Score=32.81  Aligned_cols=45  Identities=11%  Similarity=0.138  Sum_probs=37.9

Q ss_pred             CCCC-CHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecc
Q 040869           48 GRAI-TLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLT   98 (131)
Q Consensus        48 ~~~~-s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t   98 (131)
                      |..+ |-.+||++.|+   +...+++-++.|...|++....   |.|.|-..
T Consensus        31 g~~lPse~~La~~~~v---Sr~tvr~Al~~L~~~G~i~~~~---g~G~~V~~   76 (243)
T 2wv0_A           31 DMPLPSEREYAEQFGI---SRMTVRQALSNLVNEGLLYRLK---GRGTFVSK   76 (243)
T ss_dssp             TCBCCCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEECT---TSCEEECC
T ss_pred             cCCCcCHHHHHHHHCc---CHHHHHHHHHHHHHCCcEEEeC---CCeEEEeC
Confidence            4566 89999999999   9999999999999999999765   25666544

>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=86.16  E-value=0.49  Score=33.45  Aligned_cols=37  Identities=19%  Similarity=0.204  Sum_probs=34.3

Q ss_pred             CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      |..++-.+||+.+|+   +...++.-|+.|...|++...+
T Consensus        33 G~~L~e~~La~~lgV---SRtpVREAL~~L~~eGlv~~~~   69 (218)
T 3sxy_A           33 GEKLNVRELSEKLGI---SFTPVRDALLQLATEGLVKVVP   69 (218)
T ss_dssp             TCEECHHHHHHHHTC---CHHHHHHHHHHHHHHTSEEEET
T ss_pred             CCEeCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEeC
Confidence            567899999999999   9999999999999999999765

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

Probab=86.08  E-value=0.52  Score=31.91  Aligned_cols=36  Identities=22%  Similarity=0.332  Sum_probs=33.1

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      .-+|+..|++++++   .-+..+++||.|...|++....
T Consensus        62 KlITpsvlseRlkI---~gSLARkaLreL~~kGlIk~V~   97 (143)
T 2xzm_8           62 KVLTVSTVVEKLKV---NGSLARQLMRTMADRKLVEKVA   97 (143)
T ss_dssp             SEECHHHHHHHHCB---CHHHHHHHHHHHHHTTSEEEEE
T ss_pred             eeecHHHHHHHhcc---hHHHHHHHHHHHHHCCCEEEEe
Confidence            46899999999999   9999999999999999998763

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

Probab=85.82  E-value=0.23  Score=32.60  Aligned_cols=46  Identities=11%  Similarity=0.191  Sum_probs=36.7

Q ss_pred             CCCC-CHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869           48 GRAI-TLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA   99 (131)
Q Consensus        48 ~~~~-s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~   99 (131)
                      |..+ |..+||+.+|+   +...+++-++.|...|++....   +.|.|-..+
T Consensus        32 G~~lPs~~~La~~~~v---Sr~tvr~Al~~L~~~G~i~~~~---~~G~~V~~~   78 (126)
T 3ic7_A           32 EGRIPSVREYASIVEV---NANTVMRSYEYLQSQEVIYNKR---GIGFFVASG   78 (126)
T ss_dssp             TSEECCTTTTTTCC-C---CSGGGHHHHHHHHTTTSEEEET---TTEEEECTT
T ss_pred             CCcCcCHHHHHHHHCc---CHHHHHHHHHHHHHCCcEEEEc---CCccEEccC
Confidence            3456 89999999999   9999999999999999998765   256565444

>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=85.67  E-value=1  Score=32.50  Aligned_cols=45  Identities=11%  Similarity=0.296  Sum_probs=37.7

Q ss_pred             CCCC-CHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecc
Q 040869           48 GRAI-TLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLT   98 (131)
Q Consensus        48 ~~~~-s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t   98 (131)
                      |..+ |-.+||++.|+   +...+++-|+.|...|++....   |.|.|-..
T Consensus        26 g~~lPse~~La~~~~v---Sr~tvr~Al~~L~~~g~i~~~~---g~G~~V~~   71 (239)
T 3bwg_A           26 GDKLPVLETLMAQFEV---SKSTITKSLELLEQKGAIFQVR---GSGIFVRK   71 (239)
T ss_dssp             TCBCCCHHHHHHHTTC---CHHHHHHHHHHHHHTTSEEEET---TTEEEECC
T ss_pred             CCCCcCHHHHHHHHCC---CHHHHHHHHHHHHHCCcEEEeC---CceEEEec
Confidence            4567 89999999999   9999999999999999999865   25666543

>3mn2_A Probable ARAC family transcriptional regulator; structural genomics, PSI-2, protein structure initiative; 1.80A {Rhodopseudomonas palustris}

Probab=85.27  E-value=1  Score=28.09  Aligned_cols=34  Identities=24%  Similarity=0.316  Sum_probs=28.3

Q ss_pred             CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCcee
Q 040869           48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFN   84 (131)
Q Consensus        48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~   84 (131)
                      ..++|+++||+.+|+   ++..|.|+.+......+-.
T Consensus        16 ~~~~~~~~lA~~~~~---s~~~l~r~fk~~~G~s~~~   49 (108)
T 3mn2_A           16 MRPITIEKLTALTGI---SSRGIFKAFQRSRGYSPMA   49 (108)
T ss_dssp             TSCCCHHHHHHHHTC---CHHHHHHHHHHHTSSCHHH
T ss_pred             cCCCCHHHHHHHHCC---CHHHHHHHHHHHhCcCHHH
Confidence            367999999999999   9999999998776655443

>1jko_C HIN recombinase, DNA-invertase HIN; water-mediated recognition, protein-DNA complex, A10G mutant, DNA binding protein/DNA complex; 2.24A {Synthetic} SCOP: a.4.1.2 PDB: 1ijw_C* 1jj6_C* 1jj8_C* 1hcr_A 1jkp_C 1jkq_C 1jkr_C

Probab=85.07  E-value=0.56  Score=24.71  Aligned_cols=22  Identities=18%  Similarity=0.289  Sum_probs=20.1

Q ss_pred             CCHHHHHhhcCCCCCCcchHHHHHH
Q 040869           51 ITLSELVSALDIQPTKTTGLFRLMR   75 (131)
Q Consensus        51 ~s~~eLA~~~~~~~~~~~~l~RlLr   75 (131)
                      .|..+||+.+|+   +...++|.++
T Consensus        22 ~s~~~ia~~lgv---s~~Tv~r~l~   43 (52)
T 1jko_C           22 HPRQQLAIIFGI---GVSTLYRYFP   43 (52)
T ss_dssp             CCHHHHHHTTSC---CHHHHHHHSC
T ss_pred             CCHHHHHHHHCC---CHHHHHHHHH
Confidence            899999999999   9999998765

>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=84.81  E-value=0.74  Score=33.18  Aligned_cols=37  Identities=14%  Similarity=0.322  Sum_probs=34.3

Q ss_pred             CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      |..++-.+||+.+|+   +...++.-|+.|...|++...+
T Consensus        49 G~~L~e~~La~~lgV---SRtpVREAL~~L~~eGlv~~~~   85 (239)
T 2hs5_A           49 GARLSEPDICAALDV---SRNTVREAFQILIEDRLVAHEL   85 (239)
T ss_dssp             TCEECHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEET
T ss_pred             cCEeCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEeC
Confidence            567899999999999   9999999999999999999775

>2e1n_A PEX, period extender; circadian clock, DNA binding protein, circadian clock protei; 1.80A {Synechococcus elongatus pcc 7942}

Probab=84.78  E-value=0.8  Score=30.63  Aligned_cols=62  Identities=15%  Similarity=0.190  Sum_probs=45.3

Q ss_pred             hHHHHHhCCCCCCHHHHHhhc-------CCCCCCcchHHHHHHHhhcCCceeecccC---CCC--cceecchhcccccc
Q 040869           40 IADIIHSHGRAITLSELVSAL-------DIQPTKTTGLFRLMRLLVHSSCFNKTKVN---GQE--EAYGLTAASTLLIK  106 (131)
Q Consensus        40 ifd~l~~~~~~~s~~eLA~~~-------~~~~~~~~~l~RlLr~L~~~gl~~~~~~~---~~~--~~y~~t~~s~~L~~  106 (131)
                      |..+|.  .+|.+--+|++.+       ++   ++..|+++|+-|...|++......   .++  ..|++|+.++....
T Consensus        39 IL~lL~--~~~~~Gyei~k~l~~~~~~~~i---s~gtLYp~L~rLe~~GlI~~~~~~~~~~g~~rk~Y~LT~~Gr~~l~  112 (138)
T 2e1n_A           39 VLAVLR--HEDSYGTELIQHLETHWPNYRL---SDTVLYTALKFLEDEQIISGYWKKVEGRGRPRRMYQLAQANDDRSR  112 (138)
T ss_dssp             HHHHHT--TSCEEHHHHHHHHHHHSTTEEC---CHHHHHHHHHHHHHTTSEEEEEECCTTCSSCEEEEEESCSCCHHHH
T ss_pred             HHHHHH--hCCCcHHHHHHHHHHHcCCCCC---CccHHHHHHHHHHHCCCEEEEeecccCCCCCcEEEEECHHHHHHHH
Confidence            556665  3688888887766       36   888999999999999999875321   111  34999999985543

>3oou_A LIN2118 protein; protein structure initiative, PSI-2, structural genomics, MI center for structural genomics, MCSG, unknown function; HET: BTB; 1.57A {Listeria innocua}

Probab=84.33  E-value=1.2  Score=27.79  Aligned_cols=33  Identities=15%  Similarity=0.163  Sum_probs=28.5

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCcee
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFN   84 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~   84 (131)
                      .++|+++||+.+|+   ++..|.|+.+......+-.
T Consensus        20 ~~~~~~~lA~~~~~---S~~~l~r~fk~~~G~s~~~   52 (108)
T 3oou_A           20 EGMSLKTLGNDFHI---NAVYLGQLFQKEMGEHFTD   52 (108)
T ss_dssp             SCCCHHHHHHHHTS---CHHHHHHHHHHHHSSCHHH
T ss_pred             CCCCHHHHHHHHCc---CHHHHHHHHHHHHCcCHHH
Confidence            58999999999999   9999999999877665544

>2x48_A CAG38821; archeal virus, viral protein; 2.60A {Sulfolobus islandicus rod-shaped virusorganism_taxid}

Probab=84.31  E-value=0.99  Score=24.54  Aligned_cols=24  Identities=17%  Similarity=0.319  Sum_probs=21.0

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHH
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMR   75 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr   75 (131)
                      ...|..|||+.+|+   ++..+++.++
T Consensus        30 ~g~s~~eIA~~lgi---s~~TV~~~l~   53 (55)
T 2x48_A           30 MGYTVQQIANALGV---SERKVRRYLE   53 (55)
T ss_dssp             TTCCHHHHHHHHTS---CHHHHHHHHT
T ss_pred             cCCCHHHHHHHHCc---CHHHHHHHHH
Confidence            35799999999999   9999998874

>3ke2_A Uncharacterized protein YP_928783.1; structural genomics, joint center for structural genomics, J protein structure initiative; HET: MSE; 2.50A {Shewanella amazonensis SB2B}

Probab=83.84  E-value=2.2  Score=27.86  Aligned_cols=60  Identities=12%  Similarity=0.077  Sum_probs=44.4

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC---CCCcceecchhc
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN---GQEEAYGLTAAS  101 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~---~~~~~y~~t~~s  101 (131)
                      +|=|.-+|.. +.| |+..|.+.+|.   +.+.+.+.+.+|...|+--+-..+   ...|.|..+.-+
T Consensus        22 RLyla~lId~-~~~-nvp~L~~~TGm---PRRTiQd~I~aL~elgI~~~FvQ~G~R~n~GyY~I~dWG   84 (117)
T 3ke2_A           22 KLYLAHLMDD-ARH-NLLSLGKLTGM---PRRTLQDAIASFADIGIEVEFVQDGERHNAGYYRIRTWG   84 (117)
T ss_dssp             HHHHHHHHHH-SCC-CHHHHHHHHCC---CHHHHHHHHHTGGGGTCEEEEECCTTCCSCCEEEEEECT
T ss_pred             HHHHHHHHhc-CCC-CHHHHHHHHCC---CHhHHHHHHHHhhhCCeEEEEEeccccCCCccEEEeecC
Confidence            4555666765 555 99999999999   999999999999999976653211   113778887554

>2k9s_A Arabinose operon regulatory protein; activator, arabinose catabolism, carbohydrate metabolism, cytoplasm, DNA-binding, repressor, transcription; NMR {Escherichia coli}

Probab=83.82  E-value=1.8  Score=26.83  Aligned_cols=42  Identities=14%  Similarity=0.250  Sum_probs=31.5

Q ss_pred             hHHHHHhC-C-CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCcee
Q 040869           40 IADIIHSH-G-RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFN   84 (131)
Q Consensus        40 ifd~l~~~-~-~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~   84 (131)
                      +.+.|.+. . .++|+++||+.+|+   ++..+.|+.+......+-.
T Consensus         8 ~~~~i~~~~~~~~~~~~~lA~~~~~---S~~~l~r~fk~~~G~s~~~   51 (107)
T 2k9s_A            8 ACQYISDHLADSNFDIASVAQHVCL---SPSRLSHLFRQQLGISVLS   51 (107)
T ss_dssp             HHHHHHHTSSCSSCCHHHHHHHTTS---CHHHHHHHHHHHHSSCHHH
T ss_pred             HHHHHHHHhccCCCCHHHHHHHHCC---CHHHHHHHHHHHHCcCHHH
Confidence            34445432 2 68999999999999   9999999998776655443

>1bl0_A Protein (multiple antibiotic resistance protein), DNA (5'- D(*CP*CP*GP*AP*TP*GP*CP*CP*AP*CP*GP*TP*TP*TP*TP*GP*CP*TP*AP *AP*AP*TP* CP*C)-3')...; transcriptional activator; HET: DNA; 2.30A {Escherichia coli} SCOP: a.4.1.8 a.4.1.8 PDB: 1xs9_A

Probab=83.53  E-value=1.3  Score=28.67  Aligned_cols=42  Identities=17%  Similarity=0.135  Sum_probs=31.1

Q ss_pred             hHHHHHhC-CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCcee
Q 040869           40 IADIIHSH-GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFN   84 (131)
Q Consensus        40 ifd~l~~~-~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~   84 (131)
                      +.+.|... ..++|+++||+.+|+   ++..|.|+++......+-+
T Consensus        16 ~~~~i~~~~~~~~sl~~lA~~~~~---S~~~l~r~fk~~~G~s~~~   58 (129)
T 1bl0_A           16 ILDWIEDNLESPLSLEKVSERSGY---SKWHLQRMFKKETGHSLGQ   58 (129)
T ss_dssp             HHHHHHTTTTSCCCCHHHHHHSSS---CHHHHHHHHHHHHSSCHHH
T ss_pred             HHHHHHHccCCCCCHHHHHHHHCc---CHHHHHHHHHHHHCcCHHH
Confidence            34445432 367999999999999   9999999998776554433

>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=83.41  E-value=0.99  Score=31.92  Aligned_cols=37  Identities=11%  Similarity=0.270  Sum_probs=34.2

Q ss_pred             CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      |..++-.+||+.+|+   +...++.-|+.|.+.|+++..+
T Consensus        37 G~~L~E~~La~~lgV---SRtpVREAl~~L~~eGlv~~~~   73 (222)
T 3ihu_A           37 GQRLVETDLVAHFGV---GRNSVREALQRLAAEGIVDLQR   73 (222)
T ss_dssp             TCEECHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEECS
T ss_pred             CCccCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEec
Confidence            567889999999999   9999999999999999999765

>1uxc_A FRUR (1-57), fructose repressor; DNA-binding protein, LACI family, transc regulation; NMR {Escherichia coli} SCOP: a.35.1.5 PDB: 1uxd_A

Probab=82.55  E-value=0.9  Score=26.38  Aligned_cols=22  Identities=14%  Similarity=0.218  Sum_probs=18.6

Q ss_pred             CCHHHHHhhcCCCCCCcchHHHHHH
Q 040869           51 ITLSELVSALDIQPTKTTGLFRLMR   75 (131)
Q Consensus        51 ~s~~eLA~~~~~~~~~~~~l~RlLr   75 (131)
                      +|..|||+++|+   ++..+.|+|+
T Consensus         1 ~T~~diA~~aGV---S~sTVSrvLn   22 (65)
T 1uxc_A            1 MKLDEIARLAGV---SRTTASYVIN   22 (65)
T ss_dssp             CCHHHHHHHHTS---CHHHHHHHHH
T ss_pred             CCHHHHHHHHCc---CHHHHHHHHc
Confidence            478899999999   8888888876

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

Probab=82.42  E-value=1.4  Score=32.54  Aligned_cols=47  Identities=6%  Similarity=0.094  Sum_probs=37.8

Q ss_pred             CCCC-CHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchh
Q 040869           48 GRAI-TLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAA  100 (131)
Q Consensus        48 ~~~~-s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~  100 (131)
                      |..+ |-.+||++.|+   +...+++-|+.|+..|++....   |.|.|-..+.
T Consensus        50 g~~lPse~~La~~~~v---Sr~tvr~Al~~L~~~G~i~~~~---g~G~~V~~~~   97 (272)
T 3eet_A           50 HTRLPSQARIREEYGV---SDTVALEARKVLMAEGLVEGRS---GSGTYVRERP   97 (272)
T ss_dssp             TSBCCCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEECC---C--EEECCCC
T ss_pred             cCCCcCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEec---CceEEEecCC
Confidence            4556 99999999999   9999999999999999998775   2566665543

>2z99_A Putative uncharacterized protein; winged helix domain, cell cycle, cell division, chromosome partition, cytoplasm; 2.30A {Mycobacterium tuberculosis}

Probab=82.39  E-value=0.99  Score=32.76  Aligned_cols=57  Identities=11%  Similarity=0.151  Sum_probs=43.2

Q ss_pred             hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC--CCCcceecchhc
Q 040869           38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN--GQEEAYGLTAAS  101 (131)
Q Consensus        38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~--~~~~~y~~t~~s  101 (131)
                      |.+..+|+- .+|+|-.||++..|+   +.   ..++|.|...|++.+.+..  .|+-.|..|+..
T Consensus       103 LEtLaiIAy-~QPITR~eI~~irGv---~~---~~~v~~Lle~gLI~e~Gr~~~~Gp~ly~tT~~F  161 (219)
T 2z99_A          103 LETLAVVAY-RQPVTRARVSAVRGV---NV---DAVMRTLLARGLITEVGTDADTGAVTFATTELF  161 (219)
T ss_dssp             HHHHHHHHH-HCSEEHHHHHHHHTS---CC---HHHHHHHHHTTSEEEEEECTTTCCEEEEECHHH
T ss_pred             HHHHHHHHH-cCCcCHHHHHHHHCC---CH---HHHHHHHHHCCCEEEccccCCCCCeEEEECHHH
Confidence            346667764 489999999999999   65   6899999999999987432  224457777754

>3lsg_A Two-component response regulator YESN; structural genomics, PSI-2, protein structure initiative, MCSG; 2.05A {Fusobacterium nucleatum}

Probab=82.16  E-value=1.4  Score=27.12  Aligned_cols=33  Identities=21%  Similarity=0.155  Sum_probs=28.0

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCcee
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFN   84 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~   84 (131)
                      +++++++||+.+|+   ++..|.|+++......+-.
T Consensus        18 ~~~~~~~lA~~~~~---S~~~l~r~fk~~~g~s~~~   50 (103)
T 3lsg_A           18 SQFTLSVLSEKLDL---SSGYLSIMFKKNFGIPFQD   50 (103)
T ss_dssp             TTCCHHHHHHHTTC---CHHHHHHHHHHHHSSCHHH
T ss_pred             CCCCHHHHHHHHCc---CHHHHHHHHHHHHCcCHHH
Confidence            48999999999999   9999999998877665443

>2jpc_A SSRB; DNA binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium}

Probab=81.99  E-value=1.4  Score=24.37  Aligned_cols=32  Identities=13%  Similarity=0.065  Sum_probs=23.3

Q ss_pred             hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHH
Q 040869           38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMR   75 (131)
Q Consensus        38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr   75 (131)
                      ..|+..+.   .+.|..|||+.+|+   ++..+...++
T Consensus         4 ~~vl~l~~---~g~s~~eIA~~l~i---s~~tV~~~~~   35 (61)
T 2jpc_A            4 RQVLKLID---EGYTNHGISEKLHI---SIKTVETHRM   35 (61)
T ss_dssp             HHHHHHHH---TSCCSHHHHHHTCS---CHHHHHHHHH
T ss_pred             HHHHHHHH---cCCCHHHHHHHhCC---CHHHHHHHHH
Confidence            34565554   46899999999999   8887665443

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

Probab=81.90  E-value=0.99  Score=31.54  Aligned_cols=31  Identities=16%  Similarity=0.119  Sum_probs=29.1

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCc
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSC   82 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl   82 (131)
                      -|+|-.+||..+|+   .+..+.|+++.|...|+
T Consensus       177 l~~t~~~iA~~lg~---sr~tvsR~l~~L~~~gi  207 (237)
T 3fx3_A          177 LPYDKMLIAGRLGM---KPESLSRAFSRLKAAGV  207 (237)
T ss_dssp             CCSCTHHHHHHTTC---CHHHHHHHHHHHGGGTE
T ss_pred             ecCCHHHHHHHhCC---CHHHHHHHHHHHHHCCe
Confidence            36889999999999   99999999999999996

>3l4g_A Phenylalanyl-tRNA synthetase alpha chain; aminoacylation, tRNA-binding, DNA-binding domain, four-helix acetylation, aminoacyl-tRNA synthetase; HET: PHE; 3.30A {Homo sapiens}

Probab=81.66  E-value=0.29  Score=39.85  Aligned_cols=69  Identities=10%  Similarity=0.145  Sum_probs=0.0

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCC-ceeecccCCCCcceecchhcc-ccccCcc
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSS-CFNKTKVNGQEEAYGLTAAST-LLIKDKP  109 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~g-l~~~~~~~~~~~~y~~t~~s~-~L~~~~~  109 (131)
                      ++..|...|.+.+.+++..+||+.+|+   +...+.+.+..|.+.| +++-....  ...|.+|.-++ ++..+.|
T Consensus         6 ~~~~iL~~l~~~~~~~~~~~~a~~~~~---~~~~v~~~~~~L~~~~~~v~~~~~~--~~~~~Lt~eg~~~~~~G~p   76 (508)
T 3l4g_A            6 VAELLLRRLEASDGGLDSAELAAELGM---EHQAVVGAVKSLQALGEVIEAELRS--TKHWELTAEGEEIAREGSH   76 (508)
T ss_dssp             ----------------------------------------------------------------------------
T ss_pred             HHHHHHHHHHhcCCCcCHHHHHHHcCC---CHHHHHHHHHHHHhCCCeEEEEEEE--EEEEEECHHHHHHHHcCCH
Confidence            445666777643327899999999999   9999999999999998 87754321  57799999987 4555555

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

Probab=80.96  E-value=1.4  Score=31.52  Aligned_cols=37  Identities=16%  Similarity=0.263  Sum_probs=33.1

Q ss_pred             CCCC-CHHHHHhhcCCCCCCcchHHHHHHHhhcCCceee--cc
Q 040869           48 GRAI-TLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNK--TK   87 (131)
Q Consensus        48 ~~~~-s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~--~~   87 (131)
                      |..+ +-.+||+++|+   +...++.-|+.|...|+++.  .+
T Consensus        25 G~~LpsE~~La~~lgV---SRtpVREAL~~L~~~GlV~~~~~~   64 (239)
T 2di3_A           25 GDHLPSERALSETLGV---SRSSLREALRVLEALGTISTATGS   64 (239)
T ss_dssp             TCBCCCHHHHHHHHTC---CHHHHHHHHHHHHHHTSEECCSTT
T ss_pred             CCcCCCHHHHHHHHCC---CHHHHHHHHHHHHHCCCeEeeccc
Confidence            4567 57799999999   99999999999999999997  64

>3mkl_A HTH-type transcriptional regulator GADX; PSI2, MCSG, structural genomics, protein structure initiativ midwest center for structural genomics; 2.15A {Escherichia coli}

Probab=80.76  E-value=2.2  Score=27.02  Aligned_cols=34  Identities=21%  Similarity=0.317  Sum_probs=27.0

Q ss_pred             hHHHHHhC-CCCCCHHHHHhhcCCCCCCcchHHHHHHH
Q 040869           40 IADIIHSH-GRAITLSELVSALDIQPTKTTGLFRLMRL   76 (131)
Q Consensus        40 ifd~l~~~-~~~~s~~eLA~~~~~~~~~~~~l~RlLr~   76 (131)
                      |.+.|... ..++++++||+.+|+   ++..|.|+++.
T Consensus        12 ~~~~i~~~~~~~~~~~~lA~~~~~---S~~~l~r~fk~   46 (120)
T 3mkl_A           12 VCTVINNNIAHEWTLARIASELLM---SPSLLKKKLRE   46 (120)
T ss_dssp             HHHHHHTSTTSCCCHHHHHHHTTC---CHHHHHHHHHH
T ss_pred             HHHHHHHhccCCCCHHHHHHHHCc---CHHHHHHHHHH
Confidence            44455433 368999999999999   99999999876

>3lmm_A Uncharacterized protein; multi-domained alpha-beta protein, structural genomics, PSI- 2, protein structure initiative; 3.00A {Corynebacterium diphtheriae}

Probab=80.70  E-value=0.32  Score=40.06  Aligned_cols=57  Identities=12%  Similarity=0.066  Sum_probs=0.0

Q ss_pred             ChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchh
Q 040869           39 GIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAA  100 (131)
Q Consensus        39 ~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~  100 (131)
                      .|.+.|.+ .+.+|.+||++.+|+   ++..++|+|+-|+..|++...+. +...+|..|.+
T Consensus       520 ~I~~~l~~-~g~it~~di~~l~~l---s~~qa~~~L~~Lv~~G~l~~~G~-gr~t~Y~~~~~  576 (583)
T 3lmm_A          520 AAMLWLSE-VGDLATSDLMAMCGV---SRGTAKACVDGLVDEERVVAVGG-GRSRRYRLVEL  576 (583)
T ss_dssp             --------------------------------------------------------------
T ss_pred             HHHHHHHH-cCCcCHHHHHHHHCC---CHHHHHHHHHHHHHCCcEEEeCC-CCceEEEEeec
Confidence            46677764 468999999999999   89999999999999999987641 01234655543

>1o5l_A Transcriptional regulator, CRP family; TM1171, structural GE JCSG, PSI, protein structure initiative, joint center for S genomics; 2.30A {Thermotoga maritima} SCOP: b.82.3.2

Probab=80.10  E-value=0.35  Score=33.60  Aligned_cols=34  Identities=24%  Similarity=0.314  Sum_probs=0.0

Q ss_pred             CCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           50 AITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        50 ~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      ++|-++||..+|+   .+..+.|+++.|...|+++..
T Consensus       164 ~~t~~~lA~~lg~---sr~tvsR~l~~L~~~G~I~~~  197 (213)
T 1o5l_A          164 PVTLEELSRLFGC---ARPALSRVFQELEREGYIEKH  197 (213)
T ss_dssp             -------------------------------------
T ss_pred             CCCHHHHHHHhCC---CHHHHHHHHHHHHHCCeEEEc
Confidence            7899999999999   999999999999999999865

>1fse_A GERE; helix-turn-helix DNA-binding protein transcriptional regulat transcription; 2.05A {Bacillus subtilis} SCOP: a.4.6.2

Probab=80.08  E-value=1.9  Score=24.59  Aligned_cols=34  Identities=18%  Similarity=0.155  Sum_probs=24.2

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHH
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRL   76 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~   76 (131)
                      +..|+..+.   .+.|..|||+.+|+   ++..+++.++.
T Consensus        16 e~~il~~~~---~g~s~~eIA~~l~i---s~~tV~~~~~~   49 (74)
T 1fse_A           16 EREVFELLV---QDKTTKEIASELFI---SEKTVRNHISN   49 (74)
T ss_dssp             HHHHHHHHT---TTCCHHHHHHHHTS---CHHHHHHHHHH
T ss_pred             HHHHHHHHH---cCCCHHHHHHHHCC---CHHHHHHHHHH
Confidence            334555553   45799999999999   88877665544

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	131
d1fp2a1	101	a.4.5.29 (A:8-108) Isoflavone O-methyltransferase	4e-31
d1fp1d1	110	a.4.5.29 (D:19-128) Chalcone O-methyltransferase {	1e-25
d1kyza1	107	a.4.5.29 (A:13-119) Caffeic acid/5-hydroxyferulic	6e-25
d1qzza1	92	a.4.5.29 (A:10-101) Aclacinomycin-10-hydroxylase R	8e-16
d1tw3a1	85	a.4.5.29 (A:14-98) Carminomycin 4-O-methyltransfer	4e-13

>d1fp2a1 a.4.5.29 (A:8-108) Isoflavone O-methyltransferase {Alfalfa (Medicago sativa) [TaxId: 3879]} Length = 101

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: Isoflavone O-methyltransferase
species: Alfalfa (Medicago sativa) [TaxId: 3879]

 Score =  104 bits (262), Expect = 4e-31
 Identities = 42/101 (41%), Positives = 64/101 (63%), Gaps = 2/101 (1%)

Query: 7   QGAKELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTK 66
           +   E+ + QA LYK +++ + SMSLK A+E+ I +II +HG+ I+LS LVS L +  +K
Sbjct: 1   RKPSEIFKAQALLYKHIYAFIDSMSLKWAVEMNIPNIIQNHGKPISLSNLVSILQVPSSK 60

Query: 67  TTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIKD 107
              + RLMR L H+  F    +  +EE+Y LT AS LL++ 
Sbjct: 61  IGNVRRLMRYLAHNGFF--EIITKEEESYALTVASELLVRG 99

>d1fp1d1 a.4.5.29 (D:19-128) Chalcone O-methyltransferase {Alfalfa (Medicago sativa) [TaxId: 3879]} Length = 110

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: Chalcone O-methyltransferase
species: Alfalfa (Medicago sativa) [TaxId: 3879]

 Score = 91.0 bits (226), Expect = 1e-25
 Identities = 27/105 (25%), Positives = 40/105 (38%), Gaps = 12/105 (11%)

Query: 16  QAQLY--KLMFSHLSSMSLKCAIELGIADIIHSHGR---AITLSELVSALDI---QPTKT 67
            A L    L  + +    L  AI+L + +II         ++ SE+ S L          
Sbjct: 5   SACLSAMVLTTNLVYPAVLNAAIDLNLFEIIAKATPPGAFMSPSEIASKLPASTQHSDLP 64

Query: 68  TGLFRLMRLLVHSSCFNKTKV----NGQEEAYGLTAASTLLIKDK 108
             L R++RLL   S    T       G E  YGL+     L+ D+
Sbjct: 65  NRLDRMLRLLASYSVLTSTTRTIEDGGAERVYGLSMVGKYLVPDE 109

>d1kyza1 a.4.5.29 (A:13-119) Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase {Alfalfa (Medicago sativa) [TaxId: 3879]} Length = 107

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: Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase
species: Alfalfa (Medicago sativa) [TaxId: 3879]

 Score = 89.1 bits (221), Expect = 6e-25
 Identities = 27/102 (26%), Positives = 45/102 (44%), Gaps = 9/102 (8%)

Query: 16  QAQLY--KLMFSHLSSMSLKCAIELGIADIIHSHGRAITLS--ELVSALDI-QPTKTTGL 70
           +A L+  +L  + +  M LK A+EL + +II   G    +S  E+ S L    P     L
Sbjct: 6   EANLFAMQLASASVLPMILKSALELDLLEIIAKAGPGAQISPIEIASQLPTTNPDAPVML 65

Query: 71  FRLMRLLVHSSCFNKTKV----NGQEEAYGLTAASTLLIKDK 108
            R++RLL        +         +  YGL   +  L+K++
Sbjct: 66  DRMLRLLACYIILTCSVRTQQDGKVQRLYGLATVAKYLVKNE 107

>d1qzza1 a.4.5.29 (A:10-101) Aclacinomycin-10-hydroxylase RdmB {Streptomyces purpurascens [TaxId: 1924]} Length = 92

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: Aclacinomycin-10-hydroxylase RdmB
species: Streptomyces purpurascens [TaxId: 1924]

 Score = 65.5 bits (160), Expect = 8e-16
 Identities = 23/91 (25%), Positives = 34/91 (37%), Gaps = 7/91 (7%)

Query: 14  QGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRL 73
           Q    L K + + ++ M+L+ A  L + D +     A TL+ L    D  P     L RL
Sbjct: 6   QDLDVLLKNLGNLVTPMALRVAATLRLVDHL--LAGADTLAGLADRTDTHP---QALSRL 60

Query: 74  MRLLVHSSCFNKTKVNGQEEAYGLTAASTLL 104
           +R L         +   Q      T    LL
Sbjct: 61  VRHLTVVGVLEGGE--KQGRPLRPTRLGMLL 89

>d1tw3a1 a.4.5.29 (A:14-98) Carminomycin 4-O-methyltransferase {Streptomyces peucetius [TaxId: 1950]} Length = 85

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]

 Score = 58.3 bits (141), Expect = 4e-13
 Identities = 19/86 (22%), Positives = 31/86 (36%), Gaps = 9/86 (10%)

Query: 22  LMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSS 81
            + S  + M ++ A  L + D I +     T+  L +  D +P       RL+R LV   
Sbjct: 8   RLGSLHTPMVVRTAATLRLVDHILAGA--RTVKALAARTDTRPEALL---RLIRHLVAIG 62

Query: 82  CFNKTKVNGQEEAYGLTAASTLLIKD 107
              +         +  T    LL  D
Sbjct: 63  LLEEDA----PGEFVPTEVGELLADD 84

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	131
d1fp2a1	101	Isoflavone O-methyltransferase {Alfalfa (Medicago	99.92
d1fp1d1	110	Chalcone O-methyltransferase {Alfalfa (Medicago sa	99.87
d1kyza1	107	Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltra	99.87
d1tw3a1	85	Carminomycin 4-O-methyltransferase {Streptomyces p	99.86
d1qzza1	92	Aclacinomycin-10-hydroxylase RdmB {Streptomyces pu	99.82
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	98.84
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	97.62
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	97.54
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	97.48
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	97.37
d1u2wa1	108	Cadmium efflux system accessory protein CadC {Stap	97.32
d1ub9a_	100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	97.3
d1r1ta_	98	SmtB repressor {Cyanobacteria (Synechococcus), pcc	97.3
d2hoea1	62	N-acetylglucosamine kinase {Thermotoga maritima [T	97.28
d1r1ua_	94	Metal-sensing transcriptional repressor CzrA {Stap	97.17
d2hr3a1	145	Probable transcriptional regulator PA3067 {Pseudom	97.15
d1ulya_	190	Hypothetical protein PH1932 {Pyrococcus horikoshii	97.14
d1z6ra1	70	Mlc protein N-terminal domain {Escherichia coli [T	97.13
d1ylfa1	138	Hypothetical protein BC1842 {Bacillus cereus [TaxI	97.12
d1xd7a_	127	Hypothetical protein ywnA {Bacillus subtilis [TaxI	97.09
d1lvaa3	64	C-terminal fragment of elongation factor SelB {Moo	97.07
d1s3ja_	143	Putative transcriptional regulator YusO {Bacillus	96.99
d1lnwa_	141	MexR repressor {Pseudomonas aeruginosa [TaxId: 287	96.98
d2p4wa1	194	Transcriptional regulatory protein PF1790 {Pyrococ	96.97
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	96.93
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	96.9
d3broa1	135	Transcriptional regulator OEOE1854 {Oenococcus oen	96.73
d2a61a1	139	Transcriptional regulator TM0710 {Thermotoga marit	96.71
d3ctaa1	85	Ta1064 (RFK), N-terminal domain {Thermoplasma acid	96.65
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	96.61
d2etha1	140	Putative transcriptional regulator TM0816 {Thermot	96.55
d2bv6a1	136	Transcriptional regulator MgrA {Staphylococcus aur	96.54
d2fbha1	137	Transcriptional regulator PA3341 {Pseudomonas aeru	96.51
d1r7ja_	90	Sso10a (SSO10449) {Archaeon Sulfolobus solfataricu	96.47
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	96.45
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	96.43
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	96.37
d3deua1	140	Transcriptional regulator SlyA {Salmonella typhimu	96.28
d2isya1	63	Iron-dependent regulator IdeR {Mycobacterium tuber	96.25
d2obpa1	81	Putative DNA-binding protein ReutB4095 {Ralstonia	96.13
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	96.04
d2frha1	115	Pleiotropic regulator of virulence genes, SarA {St	95.98
d2ev0a1	61	Manganese transport regulator MntR {Bacillus subti	95.97
d1z91a1	137	Organic hydroperoxide resistance transcriptional r	95.79
d1p4xa2	125	Staphylococcal accessory regulator A homolog, SarS	95.65
d2fbia1	136	Probable transcriptional regulator PA4135 {Pseudom	95.63
d2hzta1	95	Putative transcriptional regulator YtcD {Bacillus	95.61
d1jgsa_	138	Multiple antibiotic resistance repressor, MarR {Es	95.6
d1j75a_	57	Dlm-1 {Mouse (Mus musculus) [TaxId: 10090]}	95.6
d1p4xa1	125	Staphylococcal accessory regulator A homolog, SarS	95.58
d1mzba_	134	Ferric uptake regulation protein, FUR {Pseudomonas	95.56
d1lj9a_	144	Transcriptional regulator SlyA {Enterococcus faeca	95.49
d1hsja1	115	Staphylococcal accessory regulator A homolog, SarR	95.42
d1dpua_	69	C-terminal domain of RPA32 {Human (Homo sapiens) [	95.38
d1yyva1	114	Putative transcriptional regulator YtfH {Salmonell	95.04
d2g9wa1	122	Hypothetical protein Rv1846c {Mycobacterium tuberc	94.98
d2fxaa1	162	Protease production regulatory protein Hpr {Bacill	94.69
d2f2ea1	142	Hypothetical protein PA1607 {Pseudomonas aeruginos	94.62
d1zyba1	73	Probable transcription regulator BT4300, C-termina	94.57
d2fbka1	172	Transcriptional regulator DR1159 {Deinococcus radi	94.56
d1stza1	87	Heat-inducible transcription repressor HrcA, N-ter	94.49
d2hs5a1	69	Putative transcriptional regulator RHA1_ro03477 {R	94.33
d2fswa1	102	Hypothetical protein PG0823 {Porphyromonas gingiva	94.26
d1z7ua1	108	Hypothetical protein EF0647 {Enterococcus faecalis	94.22
d1q1ha_	88	Transcription factor E/IIe-alpha, N-terminal domai	94.02
d2gaua1	81	Transcriptional regulator PG0396, C-terminal domai	93.97
d1ft9a1	80	CO-sensing protein CooA, C-terminal domain {Rhodos	93.85
d1okra_	120	Methicillin resistance regulatory protein MecI {St	93.75
d1i5za1	69	Catabolite gene activator protein (CAP), C-termina	93.55
d3bwga1	78	Transcriptional regulator YydK {Bacillus subtilis	93.42
d1hw1a1	74	Fatty acid responsive transcription factor FadR, N	93.3
d2zcwa1	82	Transcriptional regulator TTHA1359, C-terminal dom	93.28
d1bl0a1	54	MarA {Escherichia coli [TaxId: 562]}	93.23
d2dk5a1	78	DNA-directed RNA polymerase III subunit RPC6, RPO3	92.77
d3e5ua1	80	Chlorophenol reduction protein CprK {Desulfitobact	92.52
d1gdta1	43	gamma,delta resolvase (C-terminal domain) {Escheri	92.51
d2gxba1	59	Z-alpha domain of dsRNA-specific adenosine deamina	92.22
d1sd4a_	122	Penicillinase repressor BlaI {Staphylococcus aureu	91.28
d1d5ya1	54	Rob transcription factor, N-terminal domain {Esche	90.9
d1p6ra_	82	Penicillinase repressor BlaI {Bacillus licheniform	90.41
d1cf7a_	67	Cell cycle transcription factor E2F-4 {Human (Homo	90.29
d2bgca1	100	Listeriolysin regulatory protein PrfA, C-terminal	90.12
d2o3fa1	83	Putative transcriptional regulator YbbH {Bacillus	90.07
d1jhga_	101	Trp repressor, TrpR {Escherichia coli [TaxId: 562]	89.84
d1xmaa_	103	Predicted transcriptional regulator {Clostridium t	89.21
d1sfua_	70	34L {Yaba-like disease virus, YLDV [TaxId: 132475]	89.18
d1v4ra1	100	Transcriptional repressor TraR, N-terminal domain	88.26
d1s6la1	60	Alkylmercury lyase MerB {Escherichia coli [TaxId:	87.96
d1xmka1	73	Z-alpha domain of dsRNA-specific adenosine deamina	87.42
d2esha1	114	Hypothetical protein TM0937 {Thermotoga maritima [	87.21
d1yg2a_	178	Hypothetical protein AphA {Vibrio cholerae [TaxId:	85.44
d1efaa1	59	Lac repressor (LacR), N-terminal domain {Escherich	85.28
d1uxda_	59	Fructose repressor (FruR), N-terminal domain {Esch	85.26
d1a04a1	67	Nitrate/nitrite response regulator (NarL) {Escheri	84.94
d1ixca1	89	LysR-type regulatory protein CbnR {Ralstonia eutro	83.36
d1hlva1	66	DNA-binding domain of centromere binding protein B	83.2
d1l0oc_	57	SigmaF {Bacillus stearothermophilus [TaxId: 1422]}	83.0
d2p8ta1	69	Hypothetical protein PH0730 {Pyrococcus horikoshii	82.88
d1l3la1	65	Quorum-sensing transcription factor TraR, C-termin	82.69
d2hsga1	57	Glucose-resistance amylase regulator CcpA, N-termi	82.64
d1fsea_	67	Germination protein GerE {Bacillus subtilis [TaxId	82.59
d1in4a1	75	Holliday junction helicase RuvB {Thermotoga mariti	80.98
d1v7ba1	74	Transcriptional regulator Cgl2612 {Corynebacterium	80.59

>d1fp2a1 a.4.5.29 (A:8-108) Isoflavone O-methyltransferase {Alfalfa (Medicago sativa) [TaxId: 3879]}

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: Isoflavone O-methyltransferase
species: Alfalfa (Medicago sativa) [TaxId: 3879]

Probab=99.92  E-value=3.4e-26  Score=148.96  Aligned_cols=98  Identities=43%  Similarity=0.699  Sum_probs=87.0

Q ss_pred             hHHHhHHHHHHHHHHHhHHHHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeeccc
Q 040869            9 AKELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKV   88 (131)
Q Consensus         9 ~~e~~~~~~~l~~~~~~~~~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~   88 (131)
                      .+|..+++..+|++++||+.+++|++|++|||||+|+++++|+|++|||+++|+++.+++.|.||||+|++.|+|.++..
T Consensus         3 ~~e~~qaq~~l~~~~~gf~~s~aL~~aveLgi~d~l~~~~~p~t~~eLa~~~~~~~~~~~~L~RlLR~L~~~gi~~~~~~   82 (101)
T d1fp2a1           3 PSEIFKAQALLYKHIYAFIDSMSLKWAVEMNIPNIIQNHGKPISLSNLVSILQVPSSKIGNVRRLMRYLAHNGFFEIITK   82 (101)
T ss_dssp             STHHHHHHHHHHHHHTTHHHHHHHHHHHHTTHHHHHHHHTSCEEHHHHHHHHTCCGGGHHHHHHHHHHHHHTTSEEEEES
T ss_pred             hHHHHHHHHHHHHHHHhHHHHHHHHHHHHcCcHHHHHHcCCCCCHHHHHHHcCCCCccchHHHHHHHHHHhCCceeeecC
Confidence            45778899999999999999999999999999999987788999999999999954456779999999999999987542


Q ss_pred             CCCCcceecchhccccccCc
Q 040869           89 NGQEEAYGLTAASTLLIKDK  108 (131)
Q Consensus        89 ~~~~~~y~~t~~s~~L~~~~  108 (131)
                        ++++|++||+|++|++++
T Consensus        83 --~~~~Y~lt~~s~~Lv~~~  100 (101)
T d1fp2a1          83 --EEESYALTVASELLVRGS  100 (101)
T ss_dssp             --SSEEEEECHHHHTTSTTS
T ss_pred             --CCCeEecCHHHHHhhcCC
Confidence              157899999999999875

>d1fp1d1 a.4.5.29 (D:19-128) Chalcone O-methyltransferase {Alfalfa (Medicago sativa) [TaxId: 3879]}

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: Chalcone O-methyltransferase
species: Alfalfa (Medicago sativa) [TaxId: 3879]

Probab=99.87  E-value=1.4e-22  Score=133.01  Aligned_cols=98  Identities=24%  Similarity=0.294  Sum_probs=81.1

Q ss_pred             HHhHHHHHHHHHHHhHHHHHHHHHHHHhChHHHHHhCCC---CCCHHHHHhhcCC---CCCCcchHHHHHHHhhcCCcee
Q 040869           11 ELLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGR---AITLSELVSALDI---QPTKTTGLFRLMRLLVHSSCFN   84 (131)
Q Consensus        11 e~~~~~~~l~~~~~~~~~~~aL~~a~~L~ifd~l~~~~~---~~s~~eLA~~~~~---~~~~~~~l~RlLr~L~~~gl~~   84 (131)
                      ++++...+.++++++++.+++|++|++|||||+|+++|+   ++|++|||.++++   +|+.+..|+||||.|++.|+|+
T Consensus         2 ~~~~~~l~a~~L~~~~v~pMaLk~AieLgI~diI~~~G~~~~~ls~~ela~~lp~~~~~p~~~~~L~RiLRlLas~~vf~   81 (110)
T d1fp1d1           2 TEDSACLSAMVLTTNLVYPAVLNAAIDLNLFEIIAKATPPGAFMSPSEIASKLPASTQHSDLPNRLDRMLRLLASYSVLT   81 (110)
T ss_dssp             CHHHHHHHHHHHHHTTHHHHHHHHHHHTTHHHHHHTCSSTTCCBCHHHHHTTSCGGGCCTTHHHHHHHHHHHHHHTTSEE
T ss_pred             chHHHHHHHHHHHHhhHHHHHHHHHHHcCCHHHHHHcCCCCCCCCHHHHHHhCCCCCCCccHHHHHHHHHHHHHHcCccc
Confidence            456778889999999999999999999999999997664   4899999999986   3323456999999999999998


Q ss_pred             ecccC--CC--CcceecchhccccccCc
Q 040869           85 KTKVN--GQ--EEAYGLTAASTLLIKDK  108 (131)
Q Consensus        85 ~~~~~--~~--~~~y~~t~~s~~L~~~~  108 (131)
                      +....  +|  ...|++||+|++|++|.
T Consensus        82 ~~~~~~~~g~~e~~Y~Ltpvsk~Lv~de  109 (110)
T d1fp1d1          82 STTRTIEDGGAERVYGLSMVGKYLVPDE  109 (110)
T ss_dssp             EEEEECTTSCEEEEEEECTTGGGGSTTC
T ss_pred             cccccCCCCCeeeEEecchhhHhhcCCC
Confidence            65332  11  23699999999999874

>d1kyza1 a.4.5.29 (A:13-119) Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase {Alfalfa (Medicago sativa) [TaxId: 3879]}

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: Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase
species: Alfalfa (Medicago sativa) [TaxId: 3879]

Probab=99.87  E-value=1.2e-22  Score=132.86  Aligned_cols=96  Identities=26%  Similarity=0.342  Sum_probs=80.0

Q ss_pred             HhHHHHHHHHHHHhHHHHHHHHHHHHhChHHHHHhCC--CCCCHHHHHhhcCC-CCCCcchHHHHHHHhhcCCceeeccc
Q 040869           12 LLQGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHG--RAITLSELVSALDI-QPTKTTGLFRLMRLLVHSSCFNKTKV   88 (131)
Q Consensus        12 ~~~~~~~l~~~~~~~~~~~aL~~a~~L~ifd~l~~~~--~~~s~~eLA~~~~~-~~~~~~~l~RlLr~L~~~gl~~~~~~   88 (131)
                      +++.....++++++++.+++|++|++|||||+|+++|  .++|+.|||.+++. +|..+..|+||||+|++.|+|++...
T Consensus         4 dee~~l~a~~L~~~~v~pmaLk~AieLgI~DiI~~~G~~~~ls~~eia~~l~~~~p~~~~~L~RilR~Las~~vf~~~~~   83 (107)
T d1kyza1           4 DEEANLFAMQLASASVLPMILKSALELDLLEIIAKAGPGAQISPIEIASQLPTTNPDAPVMLDRMLRLLACYIILTCSVR   83 (107)
T ss_dssp             HHHHHHHHHHHHTTTHHHHHHHHHHHTTHHHHHHTTCTTCCBCHHHHHHTSSCCCTTHHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             cHHHHHHHHHHHHhhHHHHHHHHHHHcCCHHHHHHcCCCCCCCHHHHHHhcCCCCCcchHHHHHHHHHHHhcCceEEeee
Confidence            4556667889999999999999999999999999765  47899999999998 34345679999999999999987532


Q ss_pred             C--CC--CcceecchhccccccC
Q 040869           89 N--GQ--EEAYGLTAASTLLIKD  107 (131)
Q Consensus        89 ~--~~--~~~y~~t~~s~~L~~~  107 (131)
                      .  +|  ..+|++||+|++|++|
T Consensus        84 ~~~dg~~~~~Y~LTpvsk~Lv~d  106 (107)
T d1kyza1          84 TQQDGKVQRLYGLATVAKYLVKN  106 (107)
T ss_dssp             ECTTSCEEEEEEECHHHHHHSCC
T ss_pred             cCCCCCeeeEEecchhHHhhcCC
Confidence            2  22  2469999999999986

>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=99.86  E-value=8.7e-22  Score=124.16  Aligned_cols=80  Identities=25%  Similarity=0.289  Sum_probs=74.3

Q ss_pred             HHHHHhHHHHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869           20 YKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA   99 (131)
Q Consensus        20 ~~~~~~~~~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~   99 (131)
                      +....+++.+++|++|+++||||+|+  ++|+|++|||+++|+   ++..+.|+||+|++.|+|++++    ++.|++||
T Consensus         6 l~~l~~~~~~~aL~~av~L~ifd~l~--~gp~s~~eLA~~~g~---~~~~l~rlLr~l~a~gl~~e~~----~~~y~lt~   76 (85)
T d1tw3a1           6 LIRLGSLHTPMVVRTAATLRLVDHIL--AGARTVKALAARTDT---RPEALLRLIRHLVAIGLLEEDA----PGEFVPTE   76 (85)
T ss_dssp             HHHHHCSHHHHHHHHHHHTTHHHHHH--TTCCBHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEEE----TTEEEECT
T ss_pred             HHHHHchHHHHHHHHHHHcCcHHHhc--cCCCCHHHHHHHhCc---ChhHHHHHHHHHHHCCCeEecC----CCeEecCH
Confidence            44557899999999999999999997  589999999999999   9999999999999999999987    79999999


Q ss_pred             hccccccCc
Q 040869          100 ASTLLIKDK  108 (131)
Q Consensus       100 ~s~~L~~~~  108 (131)
                      .|+.|++|+
T Consensus        77 ~s~~L~~Dh   85 (85)
T d1tw3a1          77 VGELLADDH   85 (85)
T ss_dssp             TGGGGSTTS
T ss_pred             HHHHhhcCC
Confidence            999999874

>d1qzza1 a.4.5.29 (A:10-101) Aclacinomycin-10-hydroxylase RdmB {Streptomyces purpurascens [TaxId: 1924]}

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: Aclacinomycin-10-hydroxylase RdmB
species: Streptomyces purpurascens [TaxId: 1924]

Probab=99.82  E-value=1.3e-20  Score=120.29  Aligned_cols=87  Identities=25%  Similarity=0.244  Sum_probs=77.7

Q ss_pred             HHHHHHHHHHHhHHHHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCc
Q 040869           14 QGQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEE   93 (131)
Q Consensus        14 ~~~~~l~~~~~~~~~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~   93 (131)
                      ...+.+++++.+++.+++|++|++|||||+|+  ++|+|++|||+++|+   +++.+.|+||+|++.|+|++.+.  +.+
T Consensus         6 ~~~d~ll~~~~~~~~~~~L~~aveL~ifd~L~--~gp~t~~eLA~~~g~---~~~~l~rLlr~L~a~gll~~~~d--~~~   78 (92)
T d1qzza1           6 QDLDVLLKNLGNLVTPMALRVAATLRLVDHLL--AGADTLAGLADRTDT---HPQALSRLVRHLTVVGVLEGGEK--QGR   78 (92)
T ss_dssp             HHHHHHHHTTTCCHHHHHHHHHHHTTHHHHHH--TTCCSHHHHHHHHTC---CHHHHHHHHHHHHHTTSEECCCC---CC
T ss_pred             hhHHHHHHHHHchHHHHHHHHHHHcCchHHHh--CCCCCHHHHHHHHCc---CchHHHHHHHHHHHCCCeeeecC--CCc
Confidence            34577889999999999999999999999998  589999999999999   99999999999999999998751  256


Q ss_pred             ceecchhccccccC
Q 040869           94 AYGLTAASTLLIKD  107 (131)
Q Consensus        94 ~y~~t~~s~~L~~~  107 (131)
                      .|++|++++.|+++
T Consensus        79 ~~~~t~~g~lL~dg   92 (92)
T d1qzza1          79 PLRPTRLGMLLADG   92 (92)
T ss_dssp             CCEECTTGGGGSTT
T ss_pred             eecccHHHHhccCC
Confidence            79999999998753

>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=98.84  E-value=1.9e-09  Score=65.15  Aligned_cols=58  Identities=16%  Similarity=0.282  Sum_probs=52.3

Q ss_pred             hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcc
Q 040869           38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAST  102 (131)
Q Consensus        38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~  102 (131)
                      +.|.+.++..++|+|+.|||+++|+   ++..++|+|..|...|++.+++    +++|.+++-.-
T Consensus         8 l~IL~~~a~~~~~~s~~eia~~~~~---~~st~~rll~tL~~~g~l~~~~----~g~y~lG~~l~   65 (75)
T d1mkma1           8 FEILDFIVKNPGDVSVSEIAEKFNM---SVSNAYKYMVVLEEKGFVLRKK----DKRYVPGYKLI   65 (75)
T ss_dssp             HHHHHHHHHCSSCBCHHHHHHHTTC---CHHHHHHHHHHHHHTTSEEECT----TSCEEECTHHH
T ss_pred             HHHHHHHHhCCCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEECC----CCCEeecHHHH
Confidence            5688899887789999999999999   9999999999999999999986    78899998643

>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=97.62  E-value=6e-05  Score=43.37  Aligned_cols=60  Identities=13%  Similarity=0.167  Sum_probs=47.9

Q ss_pred             HHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCc-eeecccCCCCcceecch
Q 040869           32 LKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSC-FNKTKVNGQEEAYGLTA   99 (131)
Q Consensus        32 L~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl-~~~~~~~~~~~~y~~t~   99 (131)
                      ++.--...|...|.+..+++|+.|||+.+++   +..+++|=+..|...|+ +...     .+.|.+.+
T Consensus         4 ~k~eR~~~Il~~L~~~~~~vs~~~La~~l~V---S~~TI~rdi~~L~~~G~~I~~~-----~gGY~L~~   64 (65)
T d1j5ya1           4 VRQERLKSIVRILERSKEPVSGAQLAEELSV---SRQVIVQDIAYLRSLGYNIVAT-----PRGYVLAG   64 (65)
T ss_dssp             HHHHHHHHHHHHHHHCSSCBCHHHHHHHHTS---CHHHHHHHHHHHHHHTCCCEEE-----TTEEECCT
T ss_pred             hHHHHHHHHHHHHHHcCCCCcHHHHHHHHCC---CHHHHHHHHHHHHHCCCeEEEe-----CCCEEeCC
Confidence            3444556788888765678999999999999   99999999999999997 4433     45787653

>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=97.54  E-value=5.9e-05  Score=43.23  Aligned_cols=56  Identities=14%  Similarity=0.171  Sum_probs=45.0

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecc
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLT   98 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t   98 (131)
                      .++.|..+|.+ ++.+|.+|||+++|+   +...++|-+..|...|+.-+...   +..|.++
T Consensus         6 ~~~~iL~~L~~-~~~~s~~eLa~~l~v---S~~ti~r~i~~L~~~G~~I~~~~---g~GY~L~   61 (63)
T d1biaa1           6 VPLKLIALLAN-GEFHSGEQLGETLGM---SRAAINKHIQTLRDWGVDVFTVP---GKGYSLP   61 (63)
T ss_dssp             HHHHHHHHHTT-SSCBCHHHHHHHHTS---CHHHHHHHHHHHHHTTCCCEEET---TTEEECS
T ss_pred             HHHHHHHHHHH-CCcCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCcEEEeC---CCeEEeC
Confidence            45678888874 678999999999999   99999999999999998544431   3458764

>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=97.48  E-value=7.1e-05  Score=43.66  Aligned_cols=50  Identities=12%  Similarity=0.184  Sum_probs=43.1

Q ss_pred             HHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           34 CAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        34 ~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      ..-+-.|+..|.. .+++|..|||+.+|+   ++..+.++++.|...|++.+.+
T Consensus         5 ~~N~~~Il~~l~~-~g~~sr~eLa~~~gl---S~~Tv~~~l~~L~~~Glv~e~~   54 (71)
T d1z05a1           5 QINAGRVYKLIDQ-KGPISRIDLSKESEL---APASITKITRELIDAHLIHETT   54 (71)
T ss_dssp             HHHHHHHHHHHHH-HCSBCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEEC
T ss_pred             HHHHHHHHHHHHH-cCCcCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEec
Confidence            3444568888875 479999999999999   9999999999999999998763

>d2d1ha1 a.4.5.50 (A:1-109) Hypothetical transcriptional regulator ST1889 {Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: TrmB-like
domain: Hypothetical transcriptional regulator ST1889
species: Sulfolobus tokodaii [TaxId: 111955]

Probab=97.37  E-value=5.8e-05  Score=47.40  Aligned_cols=47  Identities=17%  Similarity=0.199  Sum_probs=39.7

Q ss_pred             hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      ..|+..|...++|+|..|||+.+|+   ++..+.|+++.|...|++.+..
T Consensus        24 ~~iL~~L~~~~~~~t~~eLa~~~~i---~~~tvs~~l~~L~~~GlV~r~~   70 (109)
T d2d1ha1          24 VAVLLKMVEIEKPITSEELADIFKL---SKTTVENSLKKLIELGLVVRTK   70 (109)
T ss_dssp             HHHHHHHHHHCSCEEHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHCc---cHhHHHHHHHHHHHCCCEEEee
Confidence            3455555434679999999999999   9999999999999999998764

>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=97.32  E-value=0.00012  Score=46.28  Aligned_cols=56  Identities=11%  Similarity=0.119  Sum_probs=49.8

Q ss_pred             HHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           28 SSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        28 ~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      ..++|.--.++.|+..|.. ++++++.|||+.+|+   ....+.+-|+.|...|++....
T Consensus        24 ~~kaLadp~Rl~Il~~L~~-~~~~~v~ela~~l~~---s~s~vS~HL~~L~~aGlv~~~r   79 (108)
T d1u2wa1          24 ILKAIADENRAKITYALCQ-DEELCVCDIANILGV---TIANASHHLRTLYKQGVVNFRK   79 (108)
T ss_dssp             HHHHHHSHHHHHHHHHHHH-SSCEEHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEC-
T ss_pred             HHHHhCCHHHHHHHHHHHh-CCCccHHHHHHHHcc---ChhHHHHHHHHHHHCCeeEEEE
Confidence            4667888899999999864 478999999999999   9999999999999999999876

>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=97.30  E-value=6.9e-05  Score=46.27  Aligned_cols=70  Identities=20%  Similarity=0.222  Sum_probs=54.6

Q ss_pred             HHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhccccc
Q 040869           32 LKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLI  105 (131)
Q Consensus        32 L~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~  105 (131)
                      +..-.++.|...|.. .+++|..|||+.+++   .+..+.|.++.|...|+++..... ++ .-.|.+|+.++.+.
T Consensus        13 l~~p~r~~IL~~L~~-~~~~~~~eLa~~l~i---s~~~vs~~l~~L~~~glV~~~~~~~d~r~~~~~LT~~G~~~~   84 (100)
T d1ub9a_          13 LGNPVRLGIMIFLLP-RRKAPFSQIQKVLDL---TPGNLDSHIRVLERNGLVKTYKVIADRPRTVVEITDFGMEEA   84 (100)
T ss_dssp             HHSHHHHHHHHHHHH-HSEEEHHHHHHHTTC---CHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECHHHHHHH
T ss_pred             cCCHHHHHHHHHhcc-CCCeeHHHHHHHHhh---ccccccHHHHHHhhhceeEEEEcCcCCccccccCCHHHHHHH
Confidence            334567888899965 368999999999999   999999999999999999865321 11 12499999887443

>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=97.30  E-value=0.00013  Score=45.29  Aligned_cols=54  Identities=13%  Similarity=0.182  Sum_probs=48.1

Q ss_pred             HHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           29 SMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        29 ~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      .++|.--.++.|...|.  .++.++.|||+.+|+   +...+.+-|+.|...|++....
T Consensus        17 ~kaL~~p~Rl~Il~~L~--~~~~~v~ela~~l~i---s~stvS~HL~~L~~aglV~~~r   70 (98)
T d1r1ta_          17 FAVLADPNRLRLLSLLA--RSELCVGDLAQAIGV---SESAVSHQLRSLRNLRLVSYRK   70 (98)
T ss_dssp             HHHHCCHHHHHHHHHHT--TCCBCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHhCCHHHHHHHHHHH--cCCcCHHHHHHHHCc---CHHHHHHHHHHHHHCCceEEEE
Confidence            35677778889999997  478999999999999   9999999999999999999865

>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=97.28  E-value=0.00016  Score=41.21  Aligned_cols=44  Identities=16%  Similarity=0.237  Sum_probs=40.0

Q ss_pred             ChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           39 GIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        39 ~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      +|+..|.+  +|+|-.|||+.+|+   .+..+.++++.|...|++.+.+
T Consensus         3 ~Il~~i~~--~pisr~eLa~~~gl---s~~TVs~~v~~L~~~GlV~e~~   46 (62)
T d2hoea1           3 RILKRIMK--SPVSRVELAEELGL---TKTTVGEIAKIFLEKGIVVEEK   46 (62)
T ss_dssp             CSHHHHHH--SCBCHHHHHHHHTC---CHHHHHHHHHHHHHHTSEEEEE
T ss_pred             HHHHHHHH--CCcCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEECC
Confidence            57788875  68999999999999   9999999999999999999875

>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=97.17  E-value=0.00018  Score=44.32  Aligned_cols=54  Identities=9%  Similarity=0.186  Sum_probs=47.9

Q ss_pred             HHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           29 SMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        29 ~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      .++|.--.++.|+..|..  ++.++.||++.+|+   +...+.+-|+.|...|++....
T Consensus        12 fkaL~d~~Rl~Il~~L~~--~~~~v~el~~~l~~---s~~~vS~HL~~L~~~glv~~~r   65 (94)
T d1r1ua_          12 FKALGDYNRIRIMELLSV--SEASVGHISHQLNL---SQSNVSHQLKLLKSVHLVKAKR   65 (94)
T ss_dssp             HHHTCSHHHHHHHHHHHH--CCBCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHhCCHHHHHHHHHHHc--CCccHHHHHHHHCC---CHHHHHHHHHHHHHCCceEEEE
Confidence            446666788889999984  78999999999999   9999999999999999999876

>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=97.15  E-value=0.00029  Score=46.00  Aligned_cols=69  Identities=19%  Similarity=0.199  Sum_probs=53.9

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-CcceecchhccccccC
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIKD  107 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~~  107 (131)
                      .++.|...|...++++|..+||+.+++   ++..+.|++..|...|++...... |. .-.+.+|+.++.+...
T Consensus        35 ~q~~vL~~L~~~~g~~t~~~La~~~~~---~~~~vs~~i~~L~~~glv~r~~~~~DrR~~~i~LT~~G~~~~~~  105 (145)
T d2hr3a1          35 SQLVVLGAIDRLGGDVTPSELAAAERM---RSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYG  105 (145)
T ss_dssp             HHHHHHHHHHHTTSCBCHHHHHHHTTC---CHHHHHHHHHHHHHTTSEEEEC------CCEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHCC---CHHHHHHHHHHHHHcCCeEeeeCccchhHHHhccCHHHHHHHHH
Confidence            455677777665678999999999999   999999999999999999876532 11 2358999999866543

>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=97.14  E-value=0.00025  Score=48.44  Aligned_cols=68  Identities=18%  Similarity=0.278  Sum_probs=53.3

Q ss_pred             HHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC--CC--Ccceecchhc
Q 040869           29 SMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN--GQ--EEAYGLTAAS  101 (131)
Q Consensus        29 ~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~--~~--~~~y~~t~~s  101 (131)
                      ..+|.--.++.|+..|.  .+|+|+.|||+.+|+   ++..+++.|+.|...|++......  .|  ...|..|+-+
T Consensus        13 ~~~l~~p~R~~Il~~L~--~~~~s~~ela~~lg~---s~~~v~~hl~~L~~~glv~~~~~~~~~g~~~k~y~~~~~~   84 (190)
T d1ulya_          13 IKVMLEDTRRKILKLLR--NKEMTISQLSEILGK---TPQTIYHHIEKLKEAGLVEVKRTEMKGNLVEKYYGRTADV   84 (190)
T ss_dssp             HHHHHSHHHHHHHHHHT--TCCBCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEEEEEEETTEEEEEEEESSSE
T ss_pred             HHHhCCHHHHHHHHHHH--hCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCeEEEEeeccCCcceEEEEEcccc
Confidence            45677778889999996  479999999999999   999999999999999999754311  00  1237777654

>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=97.13  E-value=0.00041  Score=40.25  Aligned_cols=49  Identities=4%  Similarity=0.116  Sum_probs=42.5

Q ss_pred             HHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           35 AIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        35 a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      .-+-.|+..|.. .+++|-.|||+.+|+   .+..+.++++.|...|++.+.+
T Consensus         5 ~N~~~Il~~i~~-~g~~sr~eLa~~~gL---S~~Tvs~iv~~L~~~glv~e~g   53 (70)
T d1z6ra1           5 TNAGAVYRLIDQ-LGPVSRIDLSRLAQL---APASITKIVHEMLEAHLVQELE   53 (70)
T ss_dssp             HHHHHHHHHHHS-SCSCCHHHHHHHTTC---CHHHHHHHHHHHHHHTSEEEC-
T ss_pred             HHHHHHHHHHHH-cCCcCHHHHHHHHCc---CHHHHHHHHHHHHHCCCEEeeC
Confidence            344568888885 589999999999999   9999999999999999999764

>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=97.12  E-value=0.00034  Score=45.58  Aligned_cols=45  Identities=11%  Similarity=0.152  Sum_probs=37.5

Q ss_pred             CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecc
Q 040869           48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLT   98 (131)
Q Consensus        48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t   98 (131)
                      +.++|..+||+.+++   ++..++++|+.|...|++.-..   |.|.|.+.
T Consensus        21 ~~~vss~~IA~~~~i---~~~~l~kil~~L~~aGlv~S~r---G~GG~~L~   65 (138)
T d1ylfa1          21 SSLCTSDYMAESVNT---NPVVIRKIMSYLKQAGFVYVNR---GPGGAGLL   65 (138)
T ss_dssp             GGGCCHHHHHHHHTS---CHHHHHHHHHHHHHTTSEEEC------CCEEES
T ss_pred             CCcCcHHHHHHHHCc---CHHHHHHHHHHHHHCCCeEeec---CCCCceec
Confidence            468999999999999   9999999999999999998765   24666654

>d1xd7a_ a.4.5.55 (A:) Hypothetical protein ywnA {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcriptional regulator Rrf2
domain: Hypothetical protein ywnA
species: Bacillus subtilis [TaxId: 1423]

Probab=97.09  E-value=0.00052  Score=44.08  Aligned_cols=43  Identities=9%  Similarity=0.190  Sum_probs=37.2

Q ss_pred             HHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           41 ADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        41 fd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      .-.|+. ++++|.++||+.+++   ++..++++|+.|...|+++-..
T Consensus        10 L~~la~-~~~~ss~~IA~~~~~---~~~~v~kIl~~L~~aglV~s~r   52 (127)
T d1xd7a_          10 LSLISM-DEKTSSEIIADSVNT---NPVVVRRMISLLKKADILTSRA   52 (127)
T ss_dssp             HHHHHT-CSCCCHHHHHHHHTS---CHHHHHHHHHHHHHTTSEECCS
T ss_pred             HHHHhc-CCCCCHHHHHHHhCc---CHHHHHHHHHHHHHhCcccccC
Confidence            444554 468999999999999   9999999999999999998654

>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=97.07  E-value=0.00052  Score=39.25  Aligned_cols=51  Identities=18%  Similarity=0.320  Sum_probs=43.0

Q ss_pred             ChHHHHHhCC-CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCccee
Q 040869           39 GIADIIHSHG-RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYG   96 (131)
Q Consensus        39 ~ifd~l~~~~-~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~   96 (131)
                      +|.+++.+++ .|-++.|||+.+|+   ++..+..+|+.|+..|.+.+..    ++.|-
T Consensus        11 ~I~~~~~~~g~~PP~vrdl~~~l~~---~e~~~~~lL~~l~~~G~lvkI~----~d~yf   62 (64)
T d1lvaa3          11 DLEDKYRVSRWQPPSFKEVAGSFNL---DPSELEELLHYLVREGVLVKIN----DEFYW   62 (64)
T ss_dssp             HHHHHHHHHTTSCCBHHHHHHHTTC---CHHHHHHHHHHHHHTTSEEESS----SSBEE
T ss_pred             HHHHHHHHcCCCCCcHHHHHHHhCC---CHHHHHHHHHHHHHCCCEEEec----ccccc
Confidence            4556665545 79999999999999   9999999999999999999876    56663

>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=96.99  E-value=0.0015  Score=42.25  Aligned_cols=65  Identities=12%  Similarity=0.233  Sum_probs=50.8

Q ss_pred             ChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-CcceecchhccccccC
Q 040869           39 GIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIKD  107 (131)
Q Consensus        39 ~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~~  107 (131)
                      .|...|... +++|..+||+.+++   ++..+.|++..|...|++...... |+ .-.+.+|+.++.+...
T Consensus        39 ~iL~~l~~~-~~~t~~~la~~~~i---~~~~vs~~l~~L~~~glv~r~~~~~D~R~~~v~lT~~G~~~~~~  105 (143)
T d1s3ja_          39 FVLASLKKH-GSLKVSEIAERMEV---KPSAVTLMADRLEQKNLIARTHNTKDRRVIDLSLTDEGDIKFEE  105 (143)
T ss_dssp             HHHHHHHHH-SEEEHHHHHHHHTS---CHHHHHHHHHHHHHTTSEEEEECSSCTTSEEEEECHHHHHHHHH
T ss_pred             HHHHHHHHC-CCCCHHHHHHHHCc---CHHHHHHHHHHHHHhhhheeeeecCCCCceEEEECHHHHHHHHH
Confidence            366667653 57999999999999   999999999999999999976532 11 1248999999866544

>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=96.98  E-value=0.0018  Score=41.87  Aligned_cols=68  Identities=15%  Similarity=0.146  Sum_probs=52.2

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-CcceecchhccccccC
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIKD  107 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~~  107 (131)
                      .++.|...|.. .+++|..+||+.+++   ++..+.|+++.|...|++.+.... |+ .-.+.+|+.++.+...
T Consensus        37 ~q~~vL~~l~~-~~~~t~~~la~~l~~---~~~~vsr~l~~L~~~G~v~r~~~~~D~R~~~l~lT~~G~~~~~~  106 (141)
T d1lnwa_          37 PDVHVLKLIDE-QRGLNLQDLGRQMCR---DKALITRKIRELEGRNLVRRERNPSDQRSFQLFLTDEGLAIHQH  106 (141)
T ss_dssp             HHHHHHHHHHS-STTCBHHHHHHHTTC---CHHHHHHHHHHHHHTTSEEEEECSSSSSSEEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHHH-CCCCCHHHHHHHHCc---cHhHHHHHHHHHHHhhceeeeccCCCCcchhhccCHHHHHHHHH
Confidence            34446666764 456999999999999   999999999999999999876532 22 2347899988866543

>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=96.97  E-value=0.00031  Score=48.32  Aligned_cols=68  Identities=15%  Similarity=0.164  Sum_probs=52.4

Q ss_pred             HHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC--CC--Ccceecchhcc
Q 040869           30 MSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN--GQ--EEAYGLTAAST  102 (131)
Q Consensus        30 ~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~--~~--~~~y~~t~~s~  102 (131)
                      ++|.--.++.|...|.+  +|.|+.|||+.+|+   ++..+++-|+.|...|++......  .|  ...|.+|..+.
T Consensus        10 ~~l~~~~R~~Il~~L~~--~~~~~~ela~~l~~---s~~~v~~HL~~L~~~Glv~~~~~~~~~G~~~~~y~l~~~~~   81 (194)
T d2p4wa1          10 DVLGNETRRRILFLLTK--RPYFVSELSRELGV---GQKAVLEHLRILEEAGLIESRVEKIPRGRPRKYYMIKKGLR   81 (194)
T ss_dssp             HHHHSHHHHHHHHHHHH--SCEEHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEEECCBTTBCCCEEEEECTTEE
T ss_pred             HHhCCHHHHHHHHHHHh--CCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCeEEEEeecCCCCceEEEEecccce
Confidence            34555567788888874  79999999999999   999999999999999999864321  11  12578777654

>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=96.93  E-value=0.00052  Score=44.71  Aligned_cols=47  Identities=15%  Similarity=0.189  Sum_probs=40.5

Q ss_pred             hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      ..|+..|..+++|+|+.|||+.+|+   ++..+.+.++.|...|++....
T Consensus        29 ~~i~~~L~~~~~plt~~ela~~l~v---sk~~vs~~l~~L~~~GlV~r~~   75 (151)
T d1ku9a_          29 GAVYAILYLSDKPLTISDIMEELKI---SKGNVSMSLKKLEELGFVRKVW   75 (151)
T ss_dssp             HHHHHHHHHCSSCEEHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEEC
T ss_pred             HHHHHHHHhCCCCcCHHHHHHHhCC---CcchHHHHHHHHHHCCCEEEEE
Confidence            3466666545689999999999999   9999999999999999998764

>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=96.90  E-value=0.00036  Score=43.75  Aligned_cols=62  Identities=15%  Similarity=0.238  Sum_probs=45.0

Q ss_pred             ChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCC--Ccceecchhcccc
Q 040869           39 GIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQ--EEAYGLTAASTLL  104 (131)
Q Consensus        39 ~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~--~~~y~~t~~s~~L  104 (131)
                      .|+..|.+ .++.|+.|||+.+|+   +...++++|..|...|++.+.....+  .-.|..++....+
T Consensus        24 ~v~~~L~~-~g~~t~~eia~~~~i---~~~~v~~~l~~L~~~GlV~r~~~~~~~r~~~~~a~~~~e~l   87 (109)
T d1sfxa_          24 RIYSLLLE-RGGMRVSEIARELDL---SARFVRDRLKVLLKRGFVRREIVEKGWVGYIYSAEKPEKVL   87 (109)
T ss_dssp             HHHHHHHH-HCCBCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEEEEESSSEEEEEEECCHHHHH
T ss_pred             HHHHHHHh-cCCCCHHHHHHHhCC---CcchHHHHHHHHHhCCCEEEEeccCCCccccccCCCHHHHH
Confidence            35555553 368999999999999   99999999999999999986532110  1236666655443

>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=96.73  E-value=0.00097  Score=42.70  Aligned_cols=69  Identities=14%  Similarity=0.195  Sum_probs=53.3

Q ss_pred             HHhChHHHHHhC-CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-CcceecchhccccccC
Q 040869           36 IELGIADIIHSH-GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIKD  107 (131)
Q Consensus        36 ~~L~ifd~l~~~-~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~~  107 (131)
                      .++.|+..|... ++++|..|||+.+++   +...+.|+++.|...|++...... |. .-.+.+|+.++.+...
T Consensus        30 ~q~~vL~~l~~~~~~~it~~ela~~~~~---~~~~vs~~l~~L~~~g~v~r~~~~~D~R~~~i~lT~~G~~~~~~  101 (135)
T d3broa1          30 TQMTIIDYLSRNKNKEVLQRDLESEFSI---KSSTATVLLQRMEIKKLLYRKVSGKDSRQKCLKLTKKANKLETI  101 (135)
T ss_dssp             HHHHHHHHHHHTTTSCCBHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEEECSSCTTSEEEEECHHHHTTHHH
T ss_pred             HHHHHHHHHHHcCCCCCCHHHHHHHHCc---CHhHHHHHHHHHHHHHHHHHHhhhhhhhhhhhcccHHHHHHHHH
Confidence            344466667654 367999999999999   999999999999999999876432 11 2358999998876654

>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=96.71  E-value=0.0017  Score=41.82  Aligned_cols=65  Identities=15%  Similarity=0.100  Sum_probs=50.5

Q ss_pred             ChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-CcceecchhccccccC
Q 040869           39 GIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIKD  107 (131)
Q Consensus        39 ~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~~  107 (131)
                      -|...|.. .+++|.++||+.+++   ++..+.|++..|...|++...... |+ .-.+.+|+.++.+...
T Consensus        34 ~iL~~i~~-~~~~t~~~la~~l~i---~~~tvs~~l~~L~~~gli~r~~~~~D~R~~~i~LT~~G~~~~~~  100 (139)
T d2a61a1          34 DILQKIYF-EGPKRPGELSVLLGV---AKSTVTGLVKRLEADGYLTRTPDPADRRAYFLVITRKGEEVIEK  100 (139)
T ss_dssp             HHHHHHHH-HCCBCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHHHH
T ss_pred             HHHHHHHH-cCCCCHHHHHHHhCC---CcccchHHHHHHHhcCeeeeeeccCCCCeEEEEECHHHHHHHHH
Confidence            35555654 368999999999999   999999999999999999876432 11 2358999999876643

>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=96.65  E-value=0.00043  Score=41.69  Aligned_cols=53  Identities=17%  Similarity=0.190  Sum_probs=43.6

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhccccc
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLI  105 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~  105 (131)
                      +++|..|||+.+++   ++..+.|++..|...|++..... ...-.|.+|+.++.+.
T Consensus        20 ~~lt~~eLa~~l~i---~~~~vs~~l~~Le~~GlV~r~~D-~R~~~i~LT~~G~~~l   72 (85)
T d3ctaa1          20 AYLTSSKLADMLGI---SQQSASRIIIDLEKNGYITRTVT-KRGQILNITEKGLDVL   72 (85)
T ss_dssp             EECCHHHHHHHHTS---CHHHHHHHHHHHHHTTSEEEEEE-TTEEEEEECHHHHHHH
T ss_pred             CCCCHHHHHHHHCC---CHHHHHHHHHHHHHCCCeeeecc-cccccceECHHHHHHH
Confidence            68999999999999   99999999999999999998651 0112378898887554

>d2cfxa1 a.4.5.32 (A:1-63) Transcriptional regulator LrpC {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Transcriptional regulator LrpC
species: Bacillus subtilis [TaxId: 1423]

Probab=96.61  E-value=0.0017  Score=36.72  Aligned_cols=47  Identities=15%  Similarity=0.263  Sum_probs=41.9

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      ++.+|.+.|.+ ++.+|..|||+.+|+   ++..+.+=++.|...|++...
T Consensus         6 ~D~~IL~~L~~-n~r~s~~~iA~~lgi---s~~tv~~Ri~~L~~~giI~~~   52 (63)
T d2cfxa1           6 IDLNIIEELKK-DSRLSMRELGRKIKL---SPPSVTERVRQLESFGIIKQY   52 (63)
T ss_dssp             HHHHHHHHHHH-CSCCCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHH-cCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCeeeE
Confidence            46678889986 578999999999999   999999999999999999854

>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=96.55  E-value=0.00098  Score=42.99  Aligned_cols=68  Identities=10%  Similarity=0.034  Sum_probs=53.4

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-CcceecchhccccccC
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIKD  107 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~~  107 (131)
                      .++-|+..|.+. +++|..+||+.+++   ++..+.|+++.|...|++.+.... |. .-...+|+.++.+...
T Consensus        33 ~q~~iL~~l~~~-~~~t~~~La~~l~i---~~~~vs~~v~~L~~~gli~r~~~~~D~R~~~l~lT~~G~~~~~~  102 (140)
T d2etha1          33 TELYAFLYVALF-GPKKMKEIAEFLST---TKSNVTNVVDSLEKRGLVVREMDPVDRRTYRVVLTEKGKEIFGE  102 (140)
T ss_dssp             HHHHHHHHHHHH-CCBCHHHHHHHTTS---CHHHHHHHHHHHHHTTSEEEEECTTTSSCEEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHHHc-CCcCHHHHHHHHCc---CHHHHHHHHHHHHHCCCeeeeecccccchhhhhcCHHHHHHHHH
Confidence            445577777753 67999999999999   999999999999999999976532 21 2358899999866543

>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=96.54  E-value=0.00099  Score=42.87  Aligned_cols=66  Identities=15%  Similarity=0.238  Sum_probs=51.3

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhcccccc
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIK  106 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~  106 (131)
                      +..|...|.. .+++|..+||..+++   ++..+.|+++-|...|++.+.... |+ .-...+|+.++.+..
T Consensus        36 q~~vL~~i~~-~~~~t~~~la~~l~~---~~~~~s~~l~~L~~~Gli~r~~~~~D~R~~~l~lT~~G~~~~~  103 (136)
T d2bv6a1          36 QFLVLTILWD-ESPVNVKKVVTELAL---DTGTVSPLLKRMEQVDLIKRERSEVDQREVFIHLTDKSETIRP  103 (136)
T ss_dssp             HHHHHHHHHH-SSEEEHHHHHHHTTC---CTTTHHHHHHHHHHTTSEEEEECSSSTTCEEEEECHHHHHHHH
T ss_pred             HHHHHHHHHc-CCCCCHHHHHHHHCC---CHhHHHHHHHHHHHCCCEEEeecCCcccchhhccCHHHHHHHH
Confidence            3446666765 368999999999999   999999999999999999876532 21 124688999986654

>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=96.51  E-value=0.0015  Score=41.93  Aligned_cols=65  Identities=22%  Similarity=0.248  Sum_probs=50.1

Q ss_pred             hHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-CcceecchhccccccC
Q 040869           40 IADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIKD  107 (131)
Q Consensus        40 ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~~  107 (131)
                      +.-.|...++++|..+||+.+++   ++..+.|+++.|...|++...... |+ .-...+|+.++.+...
T Consensus        33 iL~~l~~~~~~~t~~~la~~~~~---~~~~vs~~v~~L~~~gli~r~~~~~D~R~~~i~lT~~G~~~~~~   99 (137)
T d2fbha1          33 VLLHLARHRDSPTQRELAQSVGV---EGPTLARLLDGLESQGLVRRLAVAEDRRAKHIVLTPKADVLIAD   99 (137)
T ss_dssp             HHHHHHHCSSCCBHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEECCBTTBCSCEEEECTTHHHHHHH
T ss_pred             HHHHHHHcCCCCcHHHHHHHHCC---CHHHHHHHHHHHHHcCCccccCCCCCCCchhhhcCHHHHHHHHH
Confidence            44455544567999999999999   999999999999999999976532 21 1247899998866543

>d1r7ja_ a.4.5.49 (A:) Sso10a (SSO10449) {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Archaeal DNA-binding protein
domain: Sso10a (SSO10449)
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=96.47  E-value=0.0015  Score=39.83  Aligned_cols=58  Identities=12%  Similarity=0.189  Sum_probs=47.0

Q ss_pred             HHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcccccc
Q 040869           41 ADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLIK  106 (131)
Q Consensus        41 fd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~~  106 (131)
                      +|+|....++.+...|..++++   +...+.+.+..|...|++.+.     ++.|..|+-+.-|..
T Consensus         9 ~DIL~~~~~g~~kT~i~~~aNL---s~~~~~kyl~~L~~~GLI~~~-----~~~Y~iT~kG~~~L~   66 (90)
T d1r7ja_           9 QAILEACKSGSPKTRIMYGANL---SYALTGRYIKMLMDLEIIRQE-----GKQYMLTKKGEELLE   66 (90)
T ss_dssp             HHHHHHHTTCBCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEE-----TTEEEECHHHHHHHH
T ss_pred             HHHHHHHhCCCCccHHHHHcCC---CHHHHHHHHHHHHHCCCeeec-----CCEEEECccHHHHHH
Confidence            4444322234678999999999   999999999999999999876     689999999986554

>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=96.45  E-value=0.0015  Score=36.58  Aligned_cols=47  Identities=15%  Similarity=0.205  Sum_probs=41.4

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      ++.+|...|.+ ++.+|..+||+++|+   ++..+.+=++.|...|++...
T Consensus         4 ~D~kIl~~L~~-n~r~s~~~lA~~~gl---s~~~v~~Ri~~L~~~giI~~~   50 (60)
T d1i1ga1           4 RDKIILEILEK-DARTPFTEIAKKLGI---SETAVRKRVKALEEKGIIEGY   50 (60)
T ss_dssp             HHHHHHHHHHH-CTTCCHHHHHHHHTS---CHHHHHHHHHHHHHHTSSCCC
T ss_pred             HHHHHHHHHHH-cCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCeEeE
Confidence            46678888986 568999999999999   999999999999999999754

>d2cg4a1 a.4.5.32 (A:4-66) Regulatory protein AsnC {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Regulatory protein AsnC
species: Escherichia coli [TaxId: 562]

Probab=96.43  E-value=0.002  Score=36.42  Aligned_cols=47  Identities=9%  Similarity=0.220  Sum_probs=41.7

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      ++..|...|.+ ++.+|..|||+++|+   ++..+.+=++.|...|++...
T Consensus         6 ~D~~IL~~L~~-~~r~s~~eiA~~l~l---s~~~v~~Ri~rL~~~GiI~~~   52 (63)
T d2cg4a1           6 LDRGILEALMG-NARTAYAELAKQFGV---SPETIHVRVEKMKQAGIITGA   52 (63)
T ss_dssp             HHHHHHHHHHH-CTTSCHHHHHHHHTS---CHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHHHH-cCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCeEeE
Confidence            46678888986 478999999999999   999999999999999999854

>d2cyya1 a.4.5.32 (A:5-64) Putative transcriptional regulator PH1519 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Putative transcriptional regulator PH1519
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=96.37  E-value=0.002  Score=35.98  Aligned_cols=47  Identities=19%  Similarity=0.270  Sum_probs=41.9

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      ++..|...|.+ ++.+|..|||+++|+   ++..+.+=++.|...|++...
T Consensus         4 ~D~~Il~~L~~-n~r~s~~eiA~~l~l---s~~~v~~Ri~~L~~~giI~~~   50 (60)
T d2cyya1           4 IDKKIIKILQN-DGKAPLREISKITGL---AESTIHERIRKLRESGVIKKF   50 (60)
T ss_dssp             HHHHHHHHHHH-CTTCCHHHHHHHHCS---CHHHHHHHHHHHHHHTSSCCC
T ss_pred             HHHHHHHHHHH-cCCCCHHHHHHHHCc---CHHHHHHHHHHHHHCCCeEeE
Confidence            56788999986 478999999999999   999999999999999998854

>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=96.28  E-value=0.002  Score=41.42  Aligned_cols=67  Identities=18%  Similarity=0.202  Sum_probs=50.0

Q ss_pred             hChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-CcceecchhccccccC
Q 040869           38 LGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIKD  107 (131)
Q Consensus        38 L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~~  107 (131)
                      ..+.-.|...++++|..+||+.+++   +...+.|+++.|...|++...... |+ .-.+.+|+.++.+...
T Consensus        34 ~~~L~~l~~~~~~~t~~~la~~l~i---~~~~vs~~l~~L~~~glI~~~~~~~D~R~~~l~lT~~G~~~~~~  102 (140)
T d3deua1          34 WVTLHNIHQLPPDQSQIQLAKAIGI---EQPSLVRTLDQLEDKGLISRQTCASDRRAKRIKLTEKAEPLIAE  102 (140)
T ss_dssp             HHHHHHHHHSCSSEEHHHHHHHHTS---CHHHHHHHHHHHHHTTSEEEC--------CEEEECGGGHHHHHH
T ss_pred             HHHHHHHHHcCCCccHHHHHHHHCC---CHhHHHHHHHHHHhCCCEEecccCCCCCceeeEECHHHHHHHHH
Confidence            3455556544567999999999999   999999999999999999876422 11 1358999999866543

>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=96.25  E-value=0.0057  Score=34.63  Aligned_cols=39  Identities=8%  Similarity=0.070  Sum_probs=35.6

Q ss_pred             hCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           46 SHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        46 ~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      +.+++.+..+||+.+|+   .+..+.++++-|...|++...+
T Consensus        19 ~~~~~v~~~~iA~~L~v---s~~SVt~mvkrL~~~Glv~~~~   57 (63)
T d2isya1          19 EEGVTPLRARIAERLDQ---SGPTVSQTVSRMERDGLLRVAG   57 (63)
T ss_dssp             HTTCCCCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEECT
T ss_pred             hcCCCCcHHHHHHHhCC---CchhHHHHHHHHHHCCCEEEcC
Confidence            34678999999999999   9999999999999999999775

>d2obpa1 a.4.5.71 (A:12-92) Putative DNA-binding protein ReutB4095 {Ralstonia eutropha [TaxId: 106590]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ReutB4095-like
domain: Putative DNA-binding protein ReutB4095
species: Ralstonia eutropha [TaxId: 106590]

Probab=96.13  E-value=0.0034  Score=36.86  Aligned_cols=55  Identities=13%  Similarity=0.117  Sum_probs=46.0

Q ss_pred             CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhccccc
Q 040869           48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLLI  105 (131)
Q Consensus        48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L~  105 (131)
                      +++.|+..|+++.++   +-+.|+|.|-.|.+.|+..-.-.++|.|.=++|+.++.|.
T Consensus        22 g~~WSLaklsKra~~---PMS~LRR~LTqL~~aGl~~t~~~edG~G~A~Lt~~G~~lc   76 (81)
T d2obpa1          22 ATPWSLPKIAKRAQL---PMSVLRRVLTQLQAAGLADVSVEADGRGHASLTQEGAALA   76 (81)
T ss_dssp             CCCCBHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEEECTTSCEEEEECHHHHHHH
T ss_pred             CCCccHHHHHhhcCC---cHHHHHHHHHHHhhcCceeeeeccCCcceeeccHHHHHHH
Confidence            479999999999999   9999999999999999987653335577888888877554

>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=96.04  E-value=0.0054  Score=35.44  Aligned_cols=41  Identities=12%  Similarity=0.168  Sum_probs=35.5

Q ss_pred             HhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           45 HSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        45 ~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      .+.|-|-|+.|||+.+|++  ++..+++.|..|...|+++...
T Consensus        19 ~~~G~~Ps~rei~~~~g~~--S~stv~~~l~~Le~kG~I~r~~   59 (71)
T d1jhfa1          19 SQTGMPPTRAEIAQRLGFR--SPNAAEEHLKALARKGVIEIVS   59 (71)
T ss_dssp             HHHSSCCCHHHHHHHTTCS--SHHHHHHHHHHHHHTTSEEECS
T ss_pred             HHhCCCCCHHHHHHHcCCC--CHHHHHHHHHHHHHCcCeecCC
Confidence            3457899999999999983  5778999999999999999864

>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=95.98  E-value=0.0023  Score=40.17  Aligned_cols=63  Identities=14%  Similarity=0.281  Sum_probs=48.7

Q ss_pred             hHHHHHhC-CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhccccc
Q 040869           40 IADIIHSH-GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLI  105 (131)
Q Consensus        40 ifd~l~~~-~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~  105 (131)
                      |...|... ++++|..+||+.+++   ++..+.|+++.|...|++.+.... |+ .-.+.+|+.++.+.
T Consensus        38 vL~~l~~~~~~~~t~~~la~~l~~---~~~tvs~~i~~Le~~gli~r~~~~~D~R~~~i~LT~~G~~~~  103 (115)
T d2frha1          38 VLTYISENKEKEYYLKDIINHLNY---KQPQVVKAVKILSQEDYFDKKRNEHDERTVLILVNAQQRKKI  103 (115)
T ss_dssp             HHHHHHHTCCSEEEHHHHHHHSSS---HHHHHHHHHHHHHHTTSSCCBCCSSSSCCCEEECCSHHHHHH
T ss_pred             HHHHHHcCCCCCCCHHHHHHHHCC---CHhHHHHHHHHHHhhhhheeeecccCCceEEEEECHHHHHHH
Confidence            44555443 357999999999999   999999999999999999987543 22 23478999887544

>d2ev0a1 a.4.5.24 (A:2-62) Manganese transport regulator MntR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Iron-dependent repressor protein
domain: Manganese transport regulator MntR
species: Bacillus subtilis [TaxId: 1423]

Probab=95.97  E-value=0.0045  Score=34.79  Aligned_cols=44  Identities=16%  Similarity=0.234  Sum_probs=35.9

Q ss_pred             hHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           40 IADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        40 ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      |+....+ +++.+..+||+.+|+   .+..+...++-|...|++...+
T Consensus        12 I~~l~~~-~~~v~~~~iA~~L~v---s~~SVs~mikrL~~~GlV~~~~   55 (61)
T d2ev0a1          12 IYMLIEE-KGYARVSDIAEALAV---HPSSVTKMVQKLDKDEYLIYEK   55 (61)
T ss_dssp             HHHHHHH-HSSCCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEC--
T ss_pred             HHHHHhc-CCCccHHHHHHHhCC---CchhHHHHHHHHHHCCCEEEcc
Confidence            3443333 478999999999999   9999999999999999999764

>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=95.79  E-value=0.0029  Score=40.55  Aligned_cols=65  Identities=11%  Similarity=0.178  Sum_probs=50.7

Q ss_pred             ChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-CcceecchhccccccC
Q 040869           39 GIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIKD  107 (131)
Q Consensus        39 ~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~~  107 (131)
                      .|...|.. .+++|..+||+.+++   ++..+.|++..|...|++...... |+ .-...+|+.++.+...
T Consensus        37 ~vL~~l~~-~~~~t~~~La~~~~i---~~~~vsr~i~~L~~~glv~r~~~~~D~R~~~i~lT~~G~~~~~~  103 (137)
T d1z91a1          37 LALLLLWE-HETLTVKKMGEQLYL---DSGTLTPMLKRMEQQGLITRKRSEEDERSVLISLTEDGALLKEK  103 (137)
T ss_dssp             HHHHHHHH-HSEEEHHHHHHTTTC---CHHHHHHHHHHHHHHTSEECCBCSSCTTSBEEEECHHHHSGGGG
T ss_pred             HHHHHHHc-CCCCCHHHHHHHHCc---CHHHHHHHHHHHhhccceEEeecCCCCCeEEEEECHHHHHHHHH
Confidence            35556654 368999999999999   999999999999999999976532 21 1337899999876553

>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=95.65  E-value=0.0043  Score=39.58  Aligned_cols=67  Identities=18%  Similarity=0.213  Sum_probs=50.7

Q ss_pred             HhChHHHHHhCC-CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhcccccc
Q 040869           37 ELGIADIIHSHG-RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIK  106 (131)
Q Consensus        37 ~L~ifd~l~~~~-~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~  106 (131)
                      ++.|...|...+ ++++..+||+.+++   +...+.|+++-|...|++.+.... |. .-...+|+.++.+..
T Consensus        35 q~~vL~~l~~~~~~~~~~~~ia~~l~~---~~~~vs~~v~~L~~~glV~r~~~~~D~R~v~i~LT~~G~~~~~  104 (125)
T d1p4xa2          35 EFTILAIITSQNKNIVLLKDLIETIHH---KYPQTVRALNNLKKQGYLIKERSTEDERKILIHMDDAQQDHAE  104 (125)
T ss_dssp             HHHHHHHHHTTTTCCEEHHHHHHHSSS---CHHHHHHHHHHHHHHTSSEEEECSSSTTCEEEECCHHHHHHHH
T ss_pred             HHHHHHHHHHccCCCccHHHHHHHHCC---CcchHHHHHHHHHhccCEeeeecCCCCCeEEEEECHHHHHHHH
Confidence            334566675433 57999999999999   999999999999999999876533 21 224788888876553

>d2fbia1 a.4.5.28 (A:5-140) Probable transcriptional regulator PA4135 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Probable transcriptional regulator PA4135
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=95.63  E-value=0.002  Score=41.30  Aligned_cols=67  Identities=12%  Similarity=0.091  Sum_probs=51.4

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-CcceecchhccccccC
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIKD  107 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~~  107 (131)
                      ++.|...|.. .+++|..+||+.+++   ++..+.++++.|...|++...... |+ .-...+|+.++.+...
T Consensus        32 q~~vL~~l~~-~~~~t~~~la~~~~i---~~~~vs~~i~~L~~~gli~r~~~~~D~R~~~l~lT~~G~~~~~~  100 (136)
T d2fbia1          32 QWRVIRILRQ-QGEMESYQLANQACI---LRPSMTGVLARLERDGIVRRWKAPKDQRRVYVNLTEKGQQCFVS  100 (136)
T ss_dssp             HHHHHHHHHH-HCSEEHHHHHHHTTC---CHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHH-cCCCCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEeecCccCchhhhccCHHHHHHHHH
Confidence            3445666665 368999999999999   999999999999999999976432 11 1348899988866543

>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=95.61  E-value=0.012  Score=35.81  Aligned_cols=55  Identities=22%  Similarity=0.167  Sum_probs=44.5

Q ss_pred             CCCCCHHHHHhhc-CCCCCCcchHHHHHHHhhcCCceeecccCCCC--cceecchhccccc
Q 040869           48 GRAITLSELVSAL-DIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQE--EAYGLTAASTLLI  105 (131)
Q Consensus        48 ~~~~s~~eLA~~~-~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~--~~y~~t~~s~~L~  105 (131)
                      .++....||.+.+ |+   ++..|.+=|+.|...|++.+......+  -.|.+|+.++.|.
T Consensus        22 ~g~~rF~el~~~l~gi---s~~~Ls~rLk~Le~~glv~r~~~~~~p~~veY~LT~~G~~L~   79 (95)
T d2hzta1          22 HGKKRTSELKRLMPNI---TQKMLTQQLRELEADGVINRIVYNQVPPKVEYELSEYGRSLE   79 (95)
T ss_dssp             TCCBCHHHHHHHCTTS---CHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECTTGGGGH
T ss_pred             cCCCCHHHHHHHhhcC---ChhHHHHHHHHHHHhHHHhheeccccccchhhhhhhhHHHHH
Confidence            3789999999998 89   999999999999999999976421101  2399999998775

>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=95.60  E-value=0.0056  Score=39.25  Aligned_cols=67  Identities=18%  Similarity=0.198  Sum_probs=51.6

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-CcceecchhccccccC
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIKD  107 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~~  107 (131)
                      +..+...|... +++|..|||+.+++   ++..+.|++..|...|++.+.... |+ .-.+.+|+.++.+...
T Consensus        36 q~~vL~~l~~~-~~~t~~ela~~~~i---~~~~vs~~v~~L~~~glv~r~~~~~D~R~~~i~lT~~G~~~~~~  104 (138)
T d1jgsa_          36 QFKVLCSIRCA-ACITPVELKKVLSV---DLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTGGAAICEQ  104 (138)
T ss_dssp             HHHHHHHHHHH-SSBCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEEECTTCSSCEEEEECHHHHHHHHH
T ss_pred             HHHHHHhHHhC-cCCCHHHHHHHHCC---CHhHHHHHHHHHhhCCCEEEeeccCCCCeeEEEECHHHHHHHHH
Confidence            34455566543 58999999999999   999999999999999999876432 21 1358999999876543

>d1j75a_ a.4.5.19 (A:) Dlm-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Z-DNA binding domain
domain: Dlm-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.60  E-value=0.007  Score=32.97  Aligned_cols=54  Identities=13%  Similarity=0.295  Sum_probs=45.5

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceec
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGL   97 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~   97 (131)
                      +-+|...|..+++|+-+.+|++++++   +...|.|+|-.|...+=+...+    +..|++
T Consensus         3 EQkILQVL~dagspvk~~ql~k~cqV---pkk~lNqVL~rlkke~kVsl~~----patW~l   56 (57)
T d1j75a_           3 EQKILQVLSDDGGPVKIGQLVKKCQV---PKKTLNQVLYRLKKEDRVSSPE----PATWSI   56 (57)
T ss_dssp             HHHHHHHHHHHCSCEEHHHHHHHHCS---CHHHHHHHHHHHHHTTSEEEEE----TTEEEE
T ss_pred             HHHHHHHHHhcCCchHHHHHHHHHCC---CHHHHHHHHHHHHhccccccCC----CccccC
Confidence            44688889888899999999999999   9999999999998888777665    566654

>d1p4xa1 a.4.5.28 (A:1-125) Staphylococcal accessory regulator A homolog, SarS {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Staphylococcal accessory regulator A homolog, SarS
species: Staphylococcus aureus [TaxId: 1280]

Probab=95.58  E-value=0.0054  Score=38.95  Aligned_cols=66  Identities=17%  Similarity=0.286  Sum_probs=50.1

Q ss_pred             HhChHHHHHhC-CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhccccc
Q 040869           37 ELGIADIIHSH-GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLI  105 (131)
Q Consensus        37 ~L~ifd~l~~~-~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~  105 (131)
                      ++.|...|... ++++|..|||+.+++   ++..+.|+++.|...|++.+.... |. .-...+|+.++-..
T Consensus        36 q~~iL~~l~~~~~~~~t~~eia~~~~~---~~~~vs~~l~~L~~~g~v~r~~~~~D~R~~~i~lT~~G~~~~  104 (125)
T d1p4xa1          36 EFILLTYLFHQQENTLPFKKIVSDLCY---KQSDLVQHIKVLVKHSYISKVRSKIDERNTYISISEEQREKI  104 (125)
T ss_dssp             HHHHHHHHHSCSCSEEEHHHHHHHSSS---CGGGTHHHHHHHHHTTSCEEEECSSSTTSEEEECCHHHHHHH
T ss_pred             HHHHHHHHHHhccCCcCHHHHHHHhCC---CcchHHHHHHHHHHCCCceeecccCCCCeEEEEECHHHHHHH
Confidence            44456666543 368999999999999   999999999999999999987543 21 12378888887543

>d1mzba_ a.4.5.42 (A:) Ferric uptake regulation protein, FUR {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: FUR-like
domain: Ferric uptake regulation protein, FUR
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=95.56  E-value=0.0086  Score=38.34  Aligned_cols=63  Identities=13%  Similarity=0.246  Sum_probs=44.4

Q ss_pred             HHHhChHHHHHhCC-CCCCHHHHHhhcCCC--CCCcchHHHHHHHhhcCCceeecccCCCCcceec
Q 040869           35 AIELGIADIIHSHG-RAITLSELVSALDIQ--PTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGL   97 (131)
Q Consensus        35 a~~L~ifd~l~~~~-~~~s~~eLA~~~~~~--~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~   97 (131)
                      .-+..|++.|.+.. .+.|++||-+.+.-.  ..+..++||.|+.|+..|++.+....++...|..
T Consensus        16 ~qR~~Il~~L~~~~~~h~sa~ei~~~l~~~~~~i~~aTVYR~L~~l~e~gli~~~~~~~~~~~y~~   81 (134)
T d1mzba_          16 LPRVKILQMLDSAEQRHMSAEDVYKALMEAGEDVGLATVYRVLTQFEAAGLVVRHNFDGGHAVFEL   81 (134)
T ss_dssp             HHHHHHHHHHHCC-CCSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTSEEEECSSSSSCEEEE
T ss_pred             HHHHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCccHHHHHHHHHHHHhccEEEEEeecCCceEEEe
Confidence            34567889997543 589999999877421  1177899999999999999998653222334443

>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=95.49  E-value=0.0054  Score=39.63  Aligned_cols=64  Identities=8%  Similarity=0.026  Sum_probs=49.3

Q ss_pred             hHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-CcceecchhccccccC
Q 040869           40 IADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIKD  107 (131)
Q Consensus        40 ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~~  107 (131)
                      +...|... +++|..+||+.+++   ++..+.|+++.|...|++...... |+ .-...+|+.++.+...
T Consensus        34 iL~~i~~~-~~~t~~~la~~l~i---~~~tvs~~l~~L~~~glI~r~~~~~D~R~~~l~LT~~G~~~~~~   99 (144)
T d1lj9a_          34 YLVRVCEN-PGIIQEKIAELIKV---DRTTAARAIKRLEEQGFIYRQEDASNKKIKRIYATEKGKNVYPI   99 (144)
T ss_dssp             HHHHHHHS-TTEEHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEEECSSCTTCEEEEECHHHHHHHHH
T ss_pred             HHHHHHhC-CCCCHHHHHHHHCc---cHhhHHHHHHHHHhhhcccccCCCCCCCccccccCHHHHHHHHH
Confidence            44456653 57999999999999   999999999999999999976532 11 1257889988766543

>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=95.42  E-value=0.0047  Score=38.69  Aligned_cols=64  Identities=16%  Similarity=0.101  Sum_probs=48.5

Q ss_pred             ChHHHHHhC-CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhccccc
Q 040869           39 GIADIIHSH-GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLI  105 (131)
Q Consensus        39 ~ifd~l~~~-~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~  105 (131)
                      .+...|... ++++|..|||+.+++   ++..+.|++..|...|++.+.... |+ .-...+|+.++.+.
T Consensus        36 ~vL~~l~~~~~~~~t~~ela~~l~~---~~~~vs~~i~~Le~~gli~r~~~~~D~R~~~i~LT~~G~~~~  102 (115)
T d1hsja1          36 YILNHILRSESNEISSKEIAKCSEF---KPYYLTKALQKLKDLKLLSKKRSLQDERTVIVYVTDTQKANI  102 (115)
T ss_dssp             HHHHHHHTCSCSEEEHHHHHHSSCC---CHHHHHHHHHHHHTTTTSCCEECCSSSSCCEEECCSSHHHHH
T ss_pred             HHHHHHHccCCCCcCHHHHHHHHCC---ChhhHHHHHHHHHHcCCeEEEeecCCCceEEEEECHHHHHHH
Confidence            355556532 467999999999999   999999999999999999976532 21 12377888876554

>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=95.38  E-value=0.015  Score=33.46  Aligned_cols=58  Identities=10%  Similarity=0.235  Sum_probs=45.2

Q ss_pred             HHhChHHHHHhC--CCCCCHHHHHhhc-CCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869           36 IELGIADIIHSH--GRAITLSELVSAL-DIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA   99 (131)
Q Consensus        36 ~~L~ifd~l~~~--~~~~s~~eLA~~~-~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~   99 (131)
                      .+..||.+|...  +.+++..||++++ ++   +...+...++.|...|.+-.+-.   +..|..|.
T Consensus         7 ~q~~V~~~i~s~~~~eGi~~~el~~~l~~~---~~~~i~~aid~L~~eG~IYsTiD---ddHfkstd   67 (69)
T d1dpua_           7 AQNQVLNLIKACPRPEGLNFQDLKNQLKHM---SVSSIKQAVDFLSNEGHIYSTVD---DDHFKSTD   67 (69)
T ss_dssp             HHHHHHHHHHHCCCTTTEEHHHHHHHSTTS---CHHHHHHHHHHHHHTTSEEECSS---TTEEEESS
T ss_pred             HHHHHHHHHHhCCCccCcCHHHHHHHccCC---CHHHHHHHHHHHHhCCceecccc---cchhcccC
Confidence            344567777532  3679999999998 79   99999999999999998776532   67887763

>d1yyva1 a.4.5.69 (A:9-122) Putative transcriptional regulator YtfH {Salmonella typhimurium [TaxId: 90371]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: HxlR-like
domain: Putative transcriptional regulator YtfH
species: Salmonella typhimurium [TaxId: 90371]

Probab=95.04  E-value=0.015  Score=36.53  Aligned_cols=77  Identities=14%  Similarity=0.182  Sum_probs=58.8

Q ss_pred             HHHHHHHHHhHHHHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhc-CCCCCCcchHHHHHHHhhcCCceeecccCCC--C
Q 040869           16 QAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSAL-DIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQ--E   92 (131)
Q Consensus        16 ~~~l~~~~~~~~~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~-~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~--~   92 (131)
                      ....++++.+-|....|..         |.  .++....||.+.+ |+   ++..|.+=||.|...|++.+......  .
T Consensus        14 v~~~l~~ig~kW~l~Il~~---------L~--~g~~RF~el~~~l~gi---s~~~Ls~rL~~Le~~glv~R~~~~~~p~~   79 (114)
T d1yyva1          14 SREVLKHVTSRWGVLILVA---------LR--DGTHRFSDLRRKMGGV---SEKMLAQSLQALEQDGFLNRVSYPVVPPH   79 (114)
T ss_dssp             HHHHHHHHHSHHHHHHHHH---------GG--GCCEEHHHHHHHSTTC---CHHHHHHHHHHHHHHTCEEEEEECSSSCE
T ss_pred             HHHHHHHHcCCCHHHHHHH---------Hh--cCCCCHHHHHHHcccc---chhHHHHHHHHHHHHHHHhhcccCCCCch
Confidence            4667788888888766543         22  2688899999999 79   88999999999999999997642111  1


Q ss_pred             cceecchhcccccc
Q 040869           93 EAYGLTAASTLLIK  106 (131)
Q Consensus        93 ~~y~~t~~s~~L~~  106 (131)
                      -.|.+|+.++.|..
T Consensus        80 veY~LT~~G~~L~~   93 (114)
T d1yyva1          80 VEYSLTPLGEQVSD   93 (114)
T ss_dssp             EEEEECHHHHHHHH
T ss_pred             hHhHhhHhHHHHHH
Confidence            23999999997763

>d2g9wa1 a.4.5.39 (A:3-124) Hypothetical protein Rv1846c {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Penicillinase repressor
domain: Hypothetical protein Rv1846c
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=94.98  E-value=0.014  Score=36.91  Aligned_cols=52  Identities=15%  Similarity=0.221  Sum_probs=43.4

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCC-CCCCcchHHHHHHHhhcCCceeecc
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDI-QPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~-~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      .++.|.++|.+.++|+|+.||.+.++- .+-....+..+|+-|...|+++...
T Consensus         8 ~E~~IM~~lW~~g~~~t~~eI~~~l~~~~~~~~sTV~T~L~rL~~Kg~l~~~~   60 (122)
T d2g9wa1           8 LERAVMDHLWSRTEPQTVRQVHEALSARRDLAYTTVMAVLQRLAKKNLVLQIR   60 (122)
T ss_dssp             HHHHHHHHHHTCSSCEEHHHHHHHHTTTCCCCHHHHHHHHHHHHHTTSEEEEC
T ss_pred             HHHHHHHHHHcCCCCccHHHHHHHHhccCCCcHHHHHHHHHHHHHCCCEEEee
Confidence            567788999876789999999999864 2226679999999999999999875

>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=94.69  E-value=0.0086  Score=39.78  Aligned_cols=62  Identities=16%  Similarity=0.094  Sum_probs=48.3

Q ss_pred             hHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-Ccceecchhccccc
Q 040869           40 IADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLI  105 (131)
Q Consensus        40 ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~  105 (131)
                      |...|.. .+++|..+||+.+++   +...+.++++.|...|++...... |. .-...+|+.++.+.
T Consensus        46 vL~~l~~-~~~~t~~~la~~~~l---~~~tvs~~i~rL~~~gli~r~~~~~D~R~~~l~lT~~G~~~~  109 (162)
T d2fxaa1          46 ILWIAYQ-LNGASISEIAKFGVM---HVSTAFNFSKKLEERGYLRFSKRLNDKRNTYVQLTEEGTEVF  109 (162)
T ss_dssp             HHHHHHH-HTSEEHHHHHHHTTC---CHHHHHHHHHHHHHHTSEEEECC------CEEEECHHHHHHH
T ss_pred             HHhhhcc-CCCcCHHHHHHHHcC---CchhhHHHHHHHHHCCCceeecccccCeeeeeccCHhHHHHH
Confidence            6666664 357999999999999   999999999999999999976532 21 23488899888554

>d2f2ea1 a.4.5.69 (A:5-146) Hypothetical protein PA1607 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: HxlR-like
domain: Hypothetical protein PA1607
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=94.62  E-value=0.032  Score=36.29  Aligned_cols=73  Identities=16%  Similarity=0.188  Sum_probs=53.4

Q ss_pred             HHHHHHhHHHHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CCCcceec
Q 040869           19 LYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQEEAYGL   97 (131)
Q Consensus        19 l~~~~~~~~~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~~~~y~~   97 (131)
                      .++++..-|....|+.         |.  .++....||.+.+|+   .+..|.+=|+.|...|++.+.... .....|.+
T Consensus        13 ~l~ilg~kW~l~Il~~---------l~--~G~~rf~el~~~lgi---s~~vLs~rL~~L~~~gLv~r~~~~~p~r~~Y~L   78 (142)
T d2f2ea1          13 PLDVIGDGWSMLIVRD---------AF--EGLTRFGEFQKSLGL---AKNILAARLRNLVEHGVMVAVPAESGSHQEYRL   78 (142)
T ss_dssp             THHHHCSSSHHHHHHH---------HH--TTCCSHHHHHHHHCC---CHHHHHHHHHHHHHTTSEEEEECSSSSCEEEEE
T ss_pred             HHHHHcCCCHHHHHHH---------HH--cCCCCHHHHHHHhhc---cHHHHHHHHHHHHHhcceeeecCCCCCeeEEec
Confidence            4455555566555443         22  378999999999999   889999999999999999874321 11234999


Q ss_pred             chhccccc
Q 040869           98 TAASTLLI  105 (131)
Q Consensus        98 t~~s~~L~  105 (131)
                      |+.++.|.
T Consensus        79 T~~G~~L~   86 (142)
T d2f2ea1          79 TDKGRALF   86 (142)
T ss_dssp             CHHHHTTH
T ss_pred             CcCcchHH
Confidence            99998775

>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=94.57  E-value=0.02  Score=32.94  Aligned_cols=41  Identities=10%  Similarity=0.168  Sum_probs=35.7

Q ss_pred             CCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecc
Q 040869           50 AITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLT   98 (131)
Q Consensus        50 ~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t   98 (131)
                      ++|-+|||..+|+   ....+.|.|..|...|+++..     .+++...
T Consensus        27 ~lt~~elA~~lg~---sr~tvsr~l~~l~~~g~I~~~-----~~~i~I~   67 (73)
T d1zyba1          27 KVKMDDLARCLDD---TRLNISKTLNELQDNGLIELH-----RKEILIP   67 (73)
T ss_dssp             ECCHHHHHHHHTS---CHHHHHHHHHHHHHTTSCEEE-----TTEEEES
T ss_pred             ecCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEec-----CCEEEEc
Confidence            5899999999999   999999999999999999865     4555543

>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=94.56  E-value=0.0064  Score=40.56  Aligned_cols=65  Identities=11%  Similarity=0.127  Sum_probs=47.7

Q ss_pred             hHHHHHhCC--CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-CC-CcceecchhccccccC
Q 040869           40 IADIIHSHG--RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ-EEAYGLTAASTLLIKD  107 (131)
Q Consensus        40 ifd~l~~~~--~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~-~~~y~~t~~s~~L~~~  107 (131)
                      |.-.|...+  .++|..|||+.+++   ++..+.|++..|...|++.+.... |+ .-...+|+.++.+...
T Consensus        67 vL~~L~~~~~~~~lt~~eLa~~l~i---~~~tvsr~l~~Le~~GlV~r~~~~~DrR~~~i~LT~~G~~l~~~  135 (172)
T d2fbka1          67 LLLTLYRSAPPEGLRPTELSALAAI---SGPSTSNRIVRLLEKGLIERREDERDRRSASIRLTPQGRALVTH  135 (172)
T ss_dssp             HHHHHHHHCCSSCBCHHHHHHHCSC---CSGGGSSHHHHHHHHTSEECCC-------CCBEECHHHHHHHHH
T ss_pred             HHHHHHhhCCCCCcCHHHHHHHHCc---CHhHHHHHHHHHHhCCCeeeeccccchhhHHhhcCHHHHHHHHH
Confidence            444454323  35999999999999   999999999999999999987532 21 1347899998866543

>d1stza1 a.4.5.51 (A:14-100) Heat-inducible transcription repressor HrcA, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Heat-inducible transcription repressor HrcA, N-terminal domain
domain: Heat-inducible transcription repressor HrcA, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=94.49  E-value=0.034  Score=33.22  Aligned_cols=51  Identities=8%  Similarity=0.053  Sum_probs=39.0

Q ss_pred             CCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhc
Q 040869           47 HGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAAS  101 (131)
Q Consensus        47 ~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s  101 (131)
                      .+.|++..+|++..|++- ++..++-.|..|...|++.....   .+.+-+|..+
T Consensus        20 ~g~Pv~s~~i~~~~~l~~-S~aTIRn~m~~LE~~G~l~~~h~---s~GriPT~~g   70 (87)
T d1stza1          20 NKKPVSSQRVLEVSNIEF-SSATIRNDMKKLEYLGYIYQPHT---SAGRIPTDKG   70 (87)
T ss_dssp             HCSCBCHHHHHHHSCCCS-CHHHHHHHHHHHHHTTSEECCSS---CSCBEECHHH
T ss_pred             cCCccCHHHHHHHhCCCC-CHHHHHHHHHHHHHCCcccCCCC---CCCCcccHHH
Confidence            378999999999977611 57899999999999999987542   3334555554

>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=94.33  E-value=0.02  Score=32.54  Aligned_cols=46  Identities=11%  Similarity=0.241  Sum_probs=38.4

Q ss_pred             CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869           48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA   99 (131)
Q Consensus        48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~   99 (131)
                      |..++..+||+..|+   +...+++-++.|...|++.....   .|.|-.+|
T Consensus        23 G~~l~~~~La~~~~v---Sr~tvr~Al~~L~~~Gli~~~~~---~G~~V~~p   68 (69)
T d2hs5a1          23 GARLSEPDICAALDV---SRNTVREAFQILIEDRLVAHELN---RGVFVRVP   68 (69)
T ss_dssp             TCEECHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEETT---TEEEECCC
T ss_pred             cCccCHHHHHHHHCC---CHHHHHHHHHHHHHCCcEEEEcC---CEEEecCC
Confidence            456789999999999   99999999999999999998752   56665443

>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=94.26  E-value=0.023  Score=34.88  Aligned_cols=77  Identities=17%  Similarity=0.211  Sum_probs=57.5

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhc-CCCCCCcchHHHHHHHhhcCCceeecccCCCC-
Q 040869           15 GQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSAL-DIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQE-   92 (131)
Q Consensus        15 ~~~~l~~~~~~~~~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~-~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~-   92 (131)
                      |....++++.+-|....|+.         |.  .++....||.+.+ |+   .+..|.+=|+.|...|++.+....+.+ 
T Consensus         9 pv~~~l~ilg~kW~l~Il~~---------L~--~g~~rF~el~~~l~gI---s~~~Ls~rLkeL~~~glv~r~~~~~~p~   74 (102)
T d2fswa1           9 PVRKSMQIFAGKWTLLIIFQ---------IN--RRIIRYGELKRAIPGI---SEKMLIDELKFLCGKGLIKKKQYPEVPP   74 (102)
T ss_dssp             HHHHHHHHHTSSSHHHHHHH---------HT--TSCEEHHHHHHHSTTC---CHHHHHHHHHHHHHTTSEEEEEECSSSC
T ss_pred             CHHHHHHHHcCCCHHHHHHH---------Hc--cCCCCHHHHHhhCccc---chhHHHHHHHHHHHCCceeecccCCCCC
Confidence            45667777777777655433         33  3689999999998 89   899999999999999999876421111 


Q ss_pred             -cceecchhccccc
Q 040869           93 -EAYGLTAASTLLI  105 (131)
Q Consensus        93 -~~y~~t~~s~~L~  105 (131)
                       -.|.+|+.++.|.
T Consensus        75 ~veY~LT~~G~~L~   88 (102)
T d2fswa1          75 RVEYSLTPLGEKVL   88 (102)
T ss_dssp             EEEEEECHHHHTTH
T ss_pred             eehhhhhHhHHHHH
Confidence             2399999998775

>d1z7ua1 a.4.5.69 (A:1-108) Hypothetical protein EF0647 {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: HxlR-like
domain: Hypothetical protein EF0647
species: Enterococcus faecalis [TaxId: 1351]

Probab=94.22  E-value=0.024  Score=35.23  Aligned_cols=78  Identities=15%  Similarity=0.110  Sum_probs=56.0

Q ss_pred             HHHHHHHHHHhHHHHHHHHHHHHhChHHHHHhCCCCCCHHHHHhhc-CCCCCCcchHHHHHHHhhcCCceeecccCCCC-
Q 040869           15 GQAQLYKLMFSHLSSMSLKCAIELGIADIIHSHGRAITLSELVSAL-DIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQE-   92 (131)
Q Consensus        15 ~~~~l~~~~~~~~~~~aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~-~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~-   92 (131)
                      +-...++++.+-|....|.         .|..  ++....||.+.+ |+   .+..|.+=|+.|...|++.+....+.+ 
T Consensus         8 ~i~~al~iig~kW~~~Il~---------~L~~--g~~RF~el~~~l~gI---S~~~Ls~rLk~L~~~glv~R~~~~~~p~   73 (108)
T d1z7ua1           8 SINLALSTINGKWKLSLMD---------ELFQ--GTKRNGELMRALDGI---TQRVLTDRLREMEKDGLVHRESFNELPP   73 (108)
T ss_dssp             HHHHHHHTTCSTTHHHHHH---------HHHH--SCBCHHHHHHHSTTC---CHHHHHHHHHHHHHHTSEEEEEECCSSC
T ss_pred             cHHHHHHHHcCCCHHHHHH---------HHHc--CCCCHHHHHHHCcCC---ChhHHHHHHHHHHHCCcceeeccCCCcc
Confidence            3445566666666655443         3432  688999999998 79   999999999999999999875421111 


Q ss_pred             -cceecchhcccccc
Q 040869           93 -EAYGLTAASTLLIK  106 (131)
Q Consensus        93 -~~y~~t~~s~~L~~  106 (131)
                       -.|.+|+.++.|..
T Consensus        74 ~veY~LT~~G~~L~p   88 (108)
T d1z7ua1          74 RVEYTLTPEGYALYD   88 (108)
T ss_dssp             EEEEEECHHHHHHHH
T ss_pred             eehhhhchhHHHHHH
Confidence             23999999987753

>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=94.02  E-value=0.019  Score=34.52  Aligned_cols=45  Identities=20%  Similarity=0.326  Sum_probs=38.7

Q ss_pred             ChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           39 GIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        39 ~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      .|++.|.+.++-+|=.+||+++|+   ....++|+|-.|-..|++...
T Consensus        22 ~v~~~L~~~~~evtDe~iA~~tgi---~in~VRk~Ly~L~~~~L~~y~   66 (88)
T d1q1ha_          22 DVLRILLDKGTEMTDEEIANQLNI---KVNDVRKKLNLLEEQGFVSYR   66 (88)
T ss_dssp             HHHHHHHHHCSCBCHHHHHHTTTS---CHHHHHHHHHHHHHHTSCEEE
T ss_pred             HHHHHHHhccCcCCHHHHHHHhCC---cHHHHHHHHHHHHhCCceEEE
Confidence            478777643567999999999999   999999999999999998654

>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=93.97  E-value=0.037  Score=31.99  Aligned_cols=36  Identities=11%  Similarity=0.165  Sum_probs=33.4

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      -|+|-+|||..+|+   .+..+.|+|+.|...|+++...
T Consensus        28 ~~lt~~eLA~~~G~---sretvsr~L~~l~~~glI~~~~   63 (81)
T d2gaua1          28 IYLSREELATLSNM---TVSNAIRTLSTFVSERMLALDG   63 (81)
T ss_dssp             CCCCHHHHHHHTTS---CHHHHHHHHHHHHHTTSEEEET
T ss_pred             ecCCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEecC
Confidence            47999999999999   9999999999999999999763

>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=93.85  E-value=0.036  Score=32.11  Aligned_cols=35  Identities=9%  Similarity=0.174  Sum_probs=32.9

Q ss_pred             CCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           50 AITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        50 ~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      |+|-+|||..+|+   ....+.|+|+.|...|+++...
T Consensus        30 ~~t~~eiA~~lG~---sretvsr~l~~l~~~g~I~~~~   64 (80)
T d1ft9a1          30 DFTVEEIANLIGS---SRQTTSTALNSLIKEGYISRQG   64 (80)
T ss_dssp             CCCHHHHHHHHCS---CHHHHHHHHHHHHHTTSSEECS
T ss_pred             CCCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEECC
Confidence            7899999999999   9999999999999999999763

>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=93.75  E-value=0.018  Score=36.04  Aligned_cols=48  Identities=15%  Similarity=0.286  Sum_probs=40.8

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhc----CCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           36 IELGIADIIHSHGRAITLSELVSAL----DIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~----~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      .++.|..+|... +|+|+.||.+.+    ++   +...+..+|+-|...|++....
T Consensus         8 ~E~~VM~~lW~~-~~~t~~ei~~~l~~~~~~---~~sTv~t~L~rL~~Kg~l~r~~   59 (120)
T d1okra_           8 AEWEVMNIIWMK-KYASANNIIEEIQMQKDW---SPKTIRTLITRLYKKGFIDRKK   59 (120)
T ss_dssp             HHHHHHHHHHHH-SSEEHHHHHHHHHHHCCC---CHHHHHHHHHHHHHHTSEEEEE
T ss_pred             HHHHHHHHHHcC-CCCCHHHHHHHHhcccCc---cHHhHHHHHHHHHHCCCeEEEe
Confidence            567788888863 689999998887    56   8889999999999999998765

>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=93.55  E-value=0.031  Score=31.51  Aligned_cols=34  Identities=15%  Similarity=0.215  Sum_probs=32.4

Q ss_pred             CCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           50 AITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        50 ~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      |+|-+|||..+|+   ....+.|+|+.|...|+++..
T Consensus        29 ~lt~~~lA~~~G~---sRetvsr~L~~l~~~glI~~~   62 (69)
T d1i5za1          29 KITRQEIGQIVGC---SRETVGRILKMLEDQNLISAH   62 (69)
T ss_dssp             ECCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCHHHHHHHHCC---CHHHHHHHHHHHHHCCCEEEc
Confidence            6999999999999   999999999999999999876

>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=93.42  E-value=0.053  Score=31.32  Aligned_cols=45  Identities=11%  Similarity=0.296  Sum_probs=38.0

Q ss_pred             CCCC-CHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecc
Q 040869           48 GRAI-TLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLT   98 (131)
Q Consensus        48 ~~~~-s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t   98 (131)
                      |..+ |..+||+..++   +...+++-++.|...|++....   +.|.|-..
T Consensus        19 G~~LPse~~La~~~~v---Sr~tvr~Al~~L~~~Gli~~~~---g~G~~V~~   64 (78)
T d3bwga1          19 GDKLPVLETLMAQFEV---SKSTITKSLELLEQKGAIFQVR---GSGIFVRK   64 (78)
T ss_dssp             TCBCCCHHHHHHHTTC---CHHHHHHHHHHHHHTTSEEEET---TTEEEECC
T ss_pred             cCCCcCHHHHHHHHCC---CHHHHHHHHHHHHHCCcEEEEc---CcEEEEcc
Confidence            4567 89999999999   9999999999999999999875   25666543

>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=93.30  E-value=0.044  Score=31.56  Aligned_cols=43  Identities=14%  Similarity=0.192  Sum_probs=36.6

Q ss_pred             CCCC-CHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCccee
Q 040869           48 GRAI-TLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYG   96 (131)
Q Consensus        48 ~~~~-s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~   96 (131)
                      |..+ |..+||+.+++   +...+++-++.|+..|++....   +.|.|-
T Consensus        24 G~~LPs~~eLa~~~~v---Sr~tvr~Al~~L~~~G~i~~~~---g~G~~V   67 (74)
T d1hw1a1          24 GTILPAERELSELIGV---TRTTLREVLQRLARDGWLTIQH---GKPTKV   67 (74)
T ss_dssp             TSBCCCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEET---TEEEEE
T ss_pred             cCCCccHHHHHHHHCC---CHHHHHHHHHHHHHCCcEEEEe---CceEEE
Confidence            4567 89999999999   9999999999999999999875   245554

>d1bl0a1 a.4.1.8 (A:9-62) MarA {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: AraC type transcriptional activator
domain: MarA
species: Escherichia coli [TaxId: 562]

Probab=93.23  E-value=0.043  Score=29.31  Aligned_cols=40  Identities=18%  Similarity=0.179  Sum_probs=32.8

Q ss_pred             hHHHHHhC-CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCc
Q 040869           40 IADIIHSH-GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSC   82 (131)
Q Consensus        40 ifd~l~~~-~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl   82 (131)
                      +.+.|.++ ..++|+++||+.+|+   ++..+.|+.+..+...+
T Consensus         8 v~~yI~~~~~~~~tl~~lA~~~~~---s~~~l~r~Fk~~~g~tp   48 (54)
T d1bl0a1           8 ILDWIEDNLESPLSLEKVSERSGY---SKWHLQRMFKKETGHSL   48 (54)
T ss_dssp             HHHHHHTTTTSCCCCHHHHHHSSS---CHHHHHHHHHHHHSSCH
T ss_pred             HHHHHHhccCCCCCHHHHHHHHCc---CHHHHHHHHHHHHCcCH
Confidence            55666643 379999999999999   99999999998876654

>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=92.77  E-value=0.059  Score=31.54  Aligned_cols=45  Identities=16%  Similarity=0.251  Sum_probs=40.1

Q ss_pred             hHHHHHhCC-CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           40 IADIIHSHG-RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        40 ifd~l~~~~-~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      |+++|..+| .++...+|-.++++   +...+.|+|+.|.+.+++.+..
T Consensus        18 VY~~I~~ag~~GIW~~dir~ktnL---~~~~l~K~LK~Lesk~lIK~Vk   63 (78)
T d2dk5a1          18 VYQIIEDAGNKGIWSRDVRYKSNL---PLTEINKILKNLESKKLIKAVK   63 (78)
T ss_dssp             HHHHHHHHCTTCEEHHHHHHHTTC---CHHHHHHHHHHHHHTTSEEEEC
T ss_pred             HHHHHHHccccceeHHHHHHHcCC---CHHHHHHHHHHHHhcCCceeec
Confidence            677776555 68999999999999   9999999999999999999875

>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=92.52  E-value=0.061  Score=31.02  Aligned_cols=35  Identities=9%  Similarity=0.170  Sum_probs=32.2

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeec
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKT   86 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~   86 (131)
                      -|+|-+|||..+|+   ....+.|+|..|...|+++..
T Consensus        29 ~~lt~~elA~~~g~---sretvsr~l~~l~~~glI~~~   63 (80)
T d3e5ua1          29 MPLSQKSIGEITGV---HHVTVSRVLASLKRENILDKK   63 (80)
T ss_dssp             SCCCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEC-
T ss_pred             eCCCHHHHHHHHCC---CHHHHHHHHHHHHHCCcEEec
Confidence            47999999999999   999999999999999999865

>d1gdta1 a.4.1.2 (A:141-183) gamma,delta resolvase (C-terminal domain) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: gamma,delta resolvase (C-terminal domain)
species: Escherichia coli [TaxId: 562]

Probab=92.51  E-value=0.047  Score=28.32  Aligned_cols=24  Identities=8%  Similarity=0.426  Sum_probs=22.2

Q ss_pred             CCCCHHHHHhhcCCCCCCcchHHHHHH
Q 040869           49 RAITLSELVSALDIQPTKTTGLFRLMR   75 (131)
Q Consensus        49 ~~~s~~eLA~~~~~~~~~~~~l~RlLr   75 (131)
                      ..+++.+||+++|+   ....+||+|.
T Consensus        17 ~G~gat~IAk~lgI---~R~SVYR~L~   40 (43)
T d1gdta1          17 QGLGASHISKTMNI---ARSTVYKVIN   40 (43)
T ss_dssp             TTCCHHHHHHHHTC---CHHHHHHHHH
T ss_pred             cCCCHHHHHHHHCC---CHHHHHHHHh
Confidence            57999999999999   9999999985

>d2gxba1 a.4.5.19 (A:140-198) Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Z-DNA binding domain
domain: Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.22  E-value=0.11  Score=28.59  Aligned_cols=45  Identities=18%  Similarity=0.249  Sum_probs=37.5

Q ss_pred             ChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           39 GIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        39 ~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      +.+..|.. +...++.+||.++++   +...+.|+|=.|...|.+.+..
T Consensus         6 ~~l~~lg~-~~~~tA~~LA~kl~v---pKk~iNr~LYsL~~kgkl~k~~   50 (59)
T d2gxba1           6 KFLEELGE-GKATTAHDLSGKLGT---PKKEINRVLYSLAKKGKLQKEA   50 (59)
T ss_dssp             HHHHHHCT-TCCBCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEEC
T ss_pred             HHHHhcCC-ccchhHHHHHHHhCC---cHHHHHHHHHHHHHccchhhcC
Confidence            34555543 578999999999999   9999999999999999888764

>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=91.28  E-value=0.11  Score=32.51  Aligned_cols=52  Identities=15%  Similarity=0.290  Sum_probs=41.7

Q ss_pred             HHHhChHHHHHhCCCCCCHHHHHhhcCC-CCCCcchHHHHHHHhhcCCceeecc
Q 040869           35 AIELGIADIIHSHGRAITLSELVSALDI-QPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        35 a~~L~ifd~l~~~~~~~s~~eLA~~~~~-~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      ..++.|.++|.+. +|+|+.||.+.++- .+-...++.-+|+-|...|++....
T Consensus         6 ~~E~~VM~~lW~~-~~~t~~ei~~~l~~~~~~~~tTv~T~L~rL~~Kg~l~~~~   58 (122)
T d1sd4a_           6 MAEWDVMNIIWDK-KSVSANEIVVEIQKYKEVSDKTIRTLITRLYKKEIIKRYK   58 (122)
T ss_dssp             HHHHHHHHHHHHS-SSEEHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHHHcC-CCCCHHHHHHHhhccCCCcHhHHHHHHHHHHhhhceeeec
Confidence            3567788889874 59999999998753 1226779999999999999998765

>d1d5ya1 a.4.1.8 (A:3-56) Rob transcription factor, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: AraC type transcriptional activator
domain: Rob transcription factor, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=90.90  E-value=0.12  Score=27.37  Aligned_cols=40  Identities=10%  Similarity=0.201  Sum_probs=32.3

Q ss_pred             ChHHHHHhC-CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCC
Q 040869           39 GIADIIHSH-GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSS   81 (131)
Q Consensus        39 ~ifd~l~~~-~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~g   81 (131)
                      ++.+.|.++ .+++|+++||+.+|+   ++..+.|+.+.-+...
T Consensus         7 ~i~~yi~~~~~~~itl~~lA~~~~~---S~~~l~r~Fk~~~g~t   47 (54)
T d1d5ya1           7 DLLIWLEGHLDQPLSLDNVAAKAGY---SKWHLQRMFKDVTGHA   47 (54)
T ss_dssp             HHHHHHHTTSSSSCCCHHHHTTTSS---CHHHHHHHHHHHHSSC
T ss_pred             HHHHHHHHccCCCCCHHHHHHHHCc---CHHHHHHHHHHHHCcC
Confidence            456667643 479999999999999   9999999998766543

>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=90.41  E-value=0.15  Score=29.76  Aligned_cols=51  Identities=18%  Similarity=0.296  Sum_probs=40.2

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCC-CCCCcchHHHHHHHhhcCCceeecc
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDI-QPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~-~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      .++.|.++|-+ .+|+|+.||.+.++- .+-....+..+|+-|...|++....
T Consensus        10 ~E~~IM~~lW~-~~~~t~~ei~~~l~~~~~~~~tTv~T~L~rL~~KG~l~~~k   61 (82)
T d1p6ra_          10 AELEVMKVIWK-HSSINTNEVIKELSKTSTWSPKTIQTMLLRLIKKGALNHHK   61 (82)
T ss_dssp             HHHHHHHHHHT-SSSEEHHHHHHHHHHHSCCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHHHh-CCCCCHHHHHHHhccccCCcHhHHHHHHHHHHHCCCeEEEe
Confidence            56778888986 468999998777642 1116778999999999999999765

>d1cf7a_ a.4.5.17 (A:) Cell cycle transcription factor E2F-4 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Cell cycle transcription factor e2f-dp
domain: Cell cycle transcription factor E2F-4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.29  E-value=0.13  Score=29.15  Aligned_cols=44  Identities=9%  Similarity=0.255  Sum_probs=35.9

Q ss_pred             HHHHHhC-CCCCCHHHHHhhcCCCCCC-cchHHHHHHHhhcCCceeecc
Q 040869           41 ADIIHSH-GRAITLSELVSALDIQPTK-TTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        41 fd~l~~~-~~~~s~~eLA~~~~~~~~~-~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      ...+..+ ++.+++.+.|.++++   . .+.+|.|..+|.+.|++++..
T Consensus        15 l~l~~~~~~~~~~L~~aa~~L~v---~~kRRiYDI~NVLe~igli~K~~   60 (67)
T d1cf7a_          15 VSLLQEAKDGVLDLKLAADTLAV---RQKRRIYDITNVLEGIGLIEKKS   60 (67)
T ss_dssp             HHHHHHSSTTEEEHHHHHHHTTT---CCTHHHHHHHHHHHHHTSEEEEE
T ss_pred             HHHHhhCCCCeeeHHHHHHHhcC---cchhhHHHHHHHHhhhhhhhccc
Confidence            3444433 366899999999998   5 589999999999999999875

>d2bgca1 a.4.5.4 (A:138-237) Listeriolysin regulatory protein PrfA, C-terminal domain {Bacteria (Listeria monocytogenes) [TaxId: 1639]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Listeriolysin regulatory protein PrfA, C-terminal domain
species: Bacteria (Listeria monocytogenes) [TaxId: 1639]

Probab=90.12  E-value=0.2  Score=30.34  Aligned_cols=42  Identities=14%  Similarity=0.225  Sum_probs=34.9

Q ss_pred             CCCHHHHHhhcCCCCCC-cchHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869           50 AITLSELVSALDIQPTK-TTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA   99 (131)
Q Consensus        50 ~~s~~eLA~~~~~~~~~-~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~   99 (131)
                      ++|-+|||..+|+   . ...+.|+|+.|...|+++..     .+.+....
T Consensus        31 ~lTqeeLA~~lG~---s~ReTVsR~L~~L~~~GlI~~~-----~~~i~I~D   73 (100)
T d2bgca1          31 NLTMQELGYSSGI---AHSSAVSRIISKLKQEKVIVYK-----NSCFYVQN   73 (100)
T ss_dssp             CCCHHHHHHHTTC---CCHHHHHHHHHHHHHTTSEEEE-----TTEEEESC
T ss_pred             ccCHHHHHHHhCC---chHHHHHHHHHHHHHCCCEEEc-----CCEEEEeC
Confidence            5999999999998   6 46899999999999999976     45554443

>d2o3fa1 a.4.1.20 (A:1-83) Putative transcriptional regulator YbbH {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: RpiR-like
domain: Putative transcriptional regulator YbbH
species: Bacillus subtilis [TaxId: 1423]

Probab=90.07  E-value=0.1  Score=30.62  Aligned_cols=41  Identities=22%  Similarity=0.263  Sum_probs=31.8

Q ss_pred             ChHHHHHhCC---CCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCc
Q 040869           39 GIADIIHSHG---RAITLSELVSALDIQPTKTTGLFRLMRLLVHSSC   82 (131)
Q Consensus        39 ~ifd~l~~~~---~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl   82 (131)
                      .|.+.|-++.   .-+|+.|||+++++   ++..+.|+.+.|--.|+
T Consensus        22 ~ia~yil~~~~~~~~~si~~lA~~~~v---S~sTi~Rf~kklG~~gf   65 (83)
T d2o3fa1          22 KLADYILAHPHKAIESTVNEISALANS---SDAAVIRLCKSLGLKGF   65 (83)
T ss_dssp             HHHHHHHHCHHHHHTCCHHHHHHHTTC---CHHHHHHHHHHTTCSSH
T ss_pred             HHHHHHHcCHHHHHHccHHHHHHHHCC---CHHHHHHHHHHhCCCCH
Confidence            4555554322   46999999999999   99999999998877665

>d1jhga_ a.4.12.1 (A:) Trp repressor, TrpR {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: TrpR-like
family: Trp repressor, TrpR
domain: Trp repressor, TrpR
species: Escherichia coli [TaxId: 562]

Probab=89.84  E-value=0.22  Score=30.39  Aligned_cols=44  Identities=14%  Similarity=0.066  Sum_probs=37.1

Q ss_pred             HHHHHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhc
Q 040869           31 SLKCAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVH   79 (131)
Q Consensus        31 aL~~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~   79 (131)
                      .-..+.++.|+..|.+  |.+|..+|++.+|+   ....+.|.=|.|..
T Consensus        41 ~~~la~R~~ia~~L~~--G~~s~reI~~~~gv---s~aTItR~s~~Lk~   84 (101)
T d1jhga_          41 REALGTRVRIIEELLR--GEMSQRELKNELGA---GIATITRGSNSLKA   84 (101)
T ss_dssp             HHHHHHHHHHHHHHHH--CCSCHHHHHHHHCC---CHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHc--CCcCHHHHHHHhCC---ChHHHHHHHHHHHh
Confidence            3456778999998874  56999999999999   99999999998864

>d1xmaa_ a.4.5.61 (A:) Predicted transcriptional regulator {Clostridium thermocellum [TaxId: 1515]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PadR-like
domain: Predicted transcriptional regulator
species: Clostridium thermocellum [TaxId: 1515]

Probab=89.21  E-value=0.11  Score=31.59  Aligned_cols=67  Identities=13%  Similarity=0.103  Sum_probs=45.5

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCC-----CCCCcchHHHHHHHhhcCCceeecccC--CCC--cceecchhcccc
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDI-----QPTKTTGLFRLMRLLVHSSCFNKTKVN--GQE--EAYGLTAASTLL  104 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~-----~~~~~~~l~RlLr~L~~~gl~~~~~~~--~~~--~~y~~t~~s~~L  104 (131)
                      +++=|.-+|.+  +|++.-||.+.+.-     -..++..++..|+-|...|+++.....  +++  ..|..|+.++..
T Consensus         8 l~~~IL~lL~~--~~~~GYei~~~l~~~~~~~~~is~gslY~~L~rLe~~GlI~~~~~~~~~g~~rk~Y~iT~~G~~~   83 (103)
T d1xmaa_           8 VDTIILSLLIE--GDSYGYEISKNIRIKTDELYVIKETTLYSAFARLEKNGYIKSYYGEETQGKRRTYYRITPEGIKY   83 (103)
T ss_dssp             HHHHHHHHHHH--CCEEHHHHHHHHHHHHTTSCCCCHHHHHHHHHHHHHTTSEEEEEEEEC--CEEEEEEECHHHHHH
T ss_pred             HHHHHHHHHhh--CCccHHHHHHHHHHHcCCeecCCCCchHHHHHHHHHCCCeEEEeeccCCCCCceEEEECHHHHHH
Confidence            34445666664  68899998887531     111778999999999999999843211  111  249999999843

>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=89.18  E-value=0.094  Score=29.95  Aligned_cols=42  Identities=12%  Similarity=0.075  Sum_probs=35.5

Q ss_pred             HHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecc
Q 040869           42 DIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTK   87 (131)
Q Consensus        42 d~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~   87 (131)
                      +.|.. ++.+|+.+||+++|+   ....+-|.|=.|...|.+...+
T Consensus        17 ~~L~~-~~~~tA~~LAk~Lg~---~Kk~VNr~LY~L~~~G~v~~~~   58 (70)
T d1sfua_          17 LSLNT-NDYTTAISLSNRLKI---NKKKINQQLYKLQKEDTVKMVP   58 (70)
T ss_dssp             HTSCT-TCEECHHHHHHHTTC---CHHHHHHHHHHHHHTTSEEEEC
T ss_pred             HhcCC-CCCchHHHHHHHhCC---CHHHHHHHHHHHHHCCCeecCC
Confidence            33443 578999999999999   8999999999999999988764

>d1v4ra1 a.4.5.6 (A:1-100) Transcriptional repressor TraR, N-terminal domain {Streptomyces sp. [TaxId: 1931]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: GntR-like transcriptional regulators
domain: Transcriptional repressor TraR, N-terminal domain
species: Streptomyces sp. [TaxId: 1931]

Probab=88.26  E-value=0.15  Score=30.78  Aligned_cols=44  Identities=7%  Similarity=0.154  Sum_probs=37.1

Q ss_pred             CCCC-CHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceec
Q 040869           48 GRAI-TLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGL   97 (131)
Q Consensus        48 ~~~~-s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~   97 (131)
                      |..+ |..+||+.+|+   +...+++-++.|...|++....   +.|.|-.
T Consensus        30 G~~LPs~r~La~~~~v---Sr~tvr~Al~~L~~~Gli~~~~---g~G~~V~   74 (100)
T d1v4ra1          30 GDTLPSVADIRAQFGV---AAKTVSRALAVLKSEGLVSSRG---ALGTVVE   74 (100)
T ss_dssp             TSBCCCHHHHHHHSSS---CTTHHHHHTTTTTTSSCCEEET---TTEEESC
T ss_pred             cCCCccHHHHHHHHCC---CHHHHHHHHHHHHHCCcEEEec---CCEEEEC
Confidence            3456 99999999999   9999999999999999999775   2566643

>d1s6la1 a.4.5.79 (A:21-80) Alkylmercury lyase MerB {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MerB N-terminal domain-like
domain: Alkylmercury lyase MerB
species: Escherichia coli [TaxId: 562]

Probab=87.96  E-value=0.29  Score=26.83  Aligned_cols=35  Identities=14%  Similarity=0.256  Sum_probs=25.6

Q ss_pred             hHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhh
Q 040869           40 IADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLV   78 (131)
Q Consensus        40 ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~   78 (131)
                      +...|++ |.|+|.+.||..+|.   +.+.+...|-.+.
T Consensus         7 LLr~LA~-G~PVs~~~LA~alg~---~~~eV~~aL~~~p   41 (60)
T d1s6la1           7 LLRELAK-GRPVSRTTLAGILDW---PAERVAAVLEQAT   41 (60)
T ss_dssp             HHHHHHT-TCCBCHHHHHHHHTC---CHHHHHHHHTTCC
T ss_pred             HHHHHhC-CCCcCHHHHHHHhCC---CHHHHHHHHHhCC
Confidence            3456775 799999999999999   7665555554433

>d1xmka1 a.4.5.19 (A:294-366) Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Z-DNA binding domain
domain: Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.42  E-value=0.42  Score=27.34  Aligned_cols=58  Identities=10%  Similarity=0.126  Sum_probs=44.1

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcc-hHHHHHHHhhcCCceeecccCCCCcceecch
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTT-GLFRLMRLLVHSSCFNKTKVNGQEEAYGLTA   99 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~-~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~   99 (131)
                      .+-.|.+.|.. .++.++-.||+.+|+   +.. -+.|+|=.|...|-+...+..  +-.|.++.
T Consensus         6 ~eekI~~~L~~-~g~~~Al~iak~lGl---~kakeVN~~LY~L~k~g~v~k~~~t--PP~W~L~~   64 (73)
T d1xmka1           6 IKEKICDYLFN-VSDSSALNLAKNIGL---TKARDINAVLIDMERQGDVYRQGTT--PPIWHLTD   64 (73)
T ss_dssp             HHHHHHHHHHH-TCCEEHHHHHHHHCG---GGHHHHHHHHHHHHHTTSEEEECSS--SCEEEECH
T ss_pred             HHHHHHHHHHH-cCCchHHHHHHHhCC---CcHHHHhHHHHHHHHCCCeecCCCC--CCceeeec
Confidence            45678889976 468999999999999   774 599999999999988865311  33455554

>d2esha1 a.4.5.61 (A:4-117) Hypothetical protein TM0937 {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PadR-like
domain: Hypothetical protein TM0937
species: Thermotoga maritima [TaxId: 2336]

Probab=87.21  E-value=0.64  Score=28.40  Aligned_cols=66  Identities=17%  Similarity=0.166  Sum_probs=46.1

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcC---C---CCCCcchHHHHHHHhhcCCceeecccC-CCC--cceecchhcccc
Q 040869           37 ELGIADIIHSHGRAITLSELVSALD---I---QPTKTTGLFRLMRLLVHSSCFNKTKVN-GQE--EAYGLTAASTLL  104 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~---~---~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~~--~~y~~t~~s~~L  104 (131)
                      ++=|...|.+  +|.+--||.+.+.   .   ...++..++.+|+-|...|+++..... +++  ..|..|+.++..
T Consensus        12 ~~~iL~lL~~--~~~~GYei~~~i~~~~~~~~~~~~~gtiY~~L~rLe~~G~I~~~~~~~~g~~rk~Y~IT~~G~~~   86 (114)
T d2esha1          12 ASTILLLVAE--KPSHGYELAERLAEFGIEIPGIGHMGNIYRVLADLEESGFLSTEWDTTVSPPRKIYRITPQGKLY   86 (114)
T ss_dssp             HHHHHHHHHH--SCBCHHHHHHHHHTTCCSSTTCCCCCCHHHHHHHHHHTTSEEEEEECSSSSCEEEEEECHHHHHH
T ss_pred             HHHHHHHHhc--CCccHHHHHHHHHHhcCCCcccCCCCcHHHHHHHHHHCCCeEEEeecCCCCCcEEEEECHHHHHH
Confidence            3335566764  7899999988762   1   122567899999999999999864322 221  359999999843

>d1yg2a_ a.4.5.61 (A:) Hypothetical protein AphA {Vibrio cholerae [TaxId: 666]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PadR-like
domain: Hypothetical protein AphA
species: Vibrio cholerae [TaxId: 666]

Probab=85.44  E-value=0.61  Score=30.41  Aligned_cols=64  Identities=11%  Similarity=0.132  Sum_probs=46.2

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCC-----CCCCcchHHHHHHHhhcCCceeecccC-CC---Ccceecchhcc
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDI-----QPTKTTGLFRLMRLLVHSSCFNKTKVN-GQ---EEAYGLTAAST  102 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~-----~~~~~~~l~RlLr~L~~~gl~~~~~~~-~~---~~~y~~t~~s~  102 (131)
                      +..|.-.|..  +|.|--||.+.+.-     =+.+...+|+.|+-|...|+++..... +|   ...|..|+.++
T Consensus         3 ~~~iLg~L~~--~~~~GYei~~~~~~~~~~~w~~s~g~iY~~L~kLe~~Gli~~~~~~~~~~~~rk~Y~iT~~Gr   75 (178)
T d1yg2a_           3 PHVILTVLST--RDATGYDITKEFSASIGYFWKASHQQVYRELNKMGEQGLVTCVLEPQEGKPDRKVYSITQAGR   75 (178)
T ss_dssp             HHHHHHHHHH--CCBCHHHHHHHHTTGGGGTCCCCHHHHHHHHHHHHHTTSEEECCC---------CEEECHHHH
T ss_pred             HHHHHHHHhh--CCCCHHHHHHHHHHHhCCccCCCCCcHHHHHHHHHHCCCeEEEeeecCCCCCceEEEECHHHH
Confidence            3446666774  79999999998853     122788899999999999999864322 11   24699999987

>d1efaa1 a.35.1.5 (A:2-60) Lac repressor (LacR), N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: GalR/LacI-like bacterial regulator
domain: Lac repressor (LacR), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=85.28  E-value=0.26  Score=27.01  Aligned_cols=51  Identities=14%  Similarity=0.111  Sum_probs=31.2

Q ss_pred             CCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccC-----CCCcceecchhcccccc
Q 040869           50 AITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVN-----GQEEAYGLTAASTLLIK  106 (131)
Q Consensus        50 ~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~-----~~~~~y~~t~~s~~L~~  106 (131)
                      ++|..|||+.+|+   ++..+.|.|+-   .+-+.+....     -..-.|..++..+.|..
T Consensus         2 ~~Ti~diA~~agv---S~sTVSr~l~~---~~~vs~~tr~rI~~~a~~lgY~pn~~Ar~L~~   57 (59)
T d1efaa1           2 PVTLYDVAEYAGV---SYQTVSRVVNQ---ASHVSAKTREKVEAAMAELNYIPNRVAQQLAG   57 (59)
T ss_dssp             CCCHHHHHHTTTS---CHHHHHHHHTT---CSSCCTHHHHHHHHHHHHHTCCCCHHHHHHTT
T ss_pred             CCCHHHHHHHHCC---CHHHHHHHHCC---CCcCCHHHHHHHHHHHHHHCCCcCHHHHHHhc
Confidence            6899999999999   88888877753   2223322100     00234777776666653

>d1uxda_ a.35.1.5 (A:) Fructose repressor (FruR), N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: GalR/LacI-like bacterial regulator
domain: Fructose repressor (FruR), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=85.26  E-value=0.33  Score=26.50  Aligned_cols=22  Identities=14%  Similarity=0.218  Sum_probs=19.2

Q ss_pred             CCHHHHHhhcCCCCCCcchHHHHHH
Q 040869           51 ITLSELVSALDIQPTKTTGLFRLMR   75 (131)
Q Consensus        51 ~s~~eLA~~~~~~~~~~~~l~RlLr   75 (131)
                      +|+.|||+.+|+   +...+.|+|+
T Consensus         1 vTl~diA~~agv---S~sTVSrvLn   22 (59)
T d1uxda_           1 MKLDEIARLAGV---SRTTASYVIN   22 (59)
T ss_dssp             CCHHHHHHHHTS---CTTHHHHHHH
T ss_pred             CCHHHHHHHHCc---CHHHHHHHHc
Confidence            588999999999   8888888886

>d1a04a1 a.4.6.2 (A:150-216) Nitrate/nitrite response regulator (NarL) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Nitrate/nitrite response regulator (NarL)
species: Escherichia coli [TaxId: 562]

Probab=84.94  E-value=0.52  Score=25.98  Aligned_cols=35  Identities=17%  Similarity=0.198  Sum_probs=27.1

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHH
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRL   76 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~   76 (131)
                      -+..|+..+.   .+.|..|||+++++   .+..+..-++.
T Consensus        10 rE~~vl~ll~---~G~s~~eIA~~l~i---S~~TV~~~~~~   44 (67)
T d1a04a1          10 RERDILKLIA---QGLPNKMIARRLDI---TESTVKVHVKH   44 (67)
T ss_dssp             HHHHHHHHHH---TTCCHHHHHHHHTC---CHHHHHHHHHH
T ss_pred             HHHHHHHHHH---hCCCHHHHHHHHCC---CHHHHHHHHHH
Confidence            4567788887   46999999999999   88876654443

>d1ixca1 a.4.5.37 (A:1-89) LysR-type regulatory protein CbnR {Ralstonia eutropha [TaxId: 106590]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: LysR-like transcriptional regulators
domain: LysR-type regulatory protein CbnR
species: Ralstonia eutropha [TaxId: 106590]

Probab=83.36  E-value=0.35  Score=28.30  Aligned_cols=59  Identities=17%  Similarity=0.199  Sum_probs=43.6

Q ss_pred             HhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHHhh---cCCceeecccCCCCcceecchhcccccc
Q 040869           37 ELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRLLV---HSSCFNKTKVNGQEEAYGLTAASTLLIK  106 (131)
Q Consensus        37 ~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~---~~gl~~~~~~~~~~~~y~~t~~s~~L~~  106 (131)
                      +|.+|-.+.+   .-|...-|+++++   .++.+.+-++.|.   ..-+|.+.     ++.+.+||.++.|..
T Consensus         5 ~L~~f~~v~e---~gs~~~AA~~L~i---sq~avs~~i~~LE~~lg~~Lf~R~-----~~~~~lT~~G~~l~~   66 (89)
T d1ixca1           5 QLKYFIAVAE---AGNMAAAAKRLHV---SQPPITRQMQALEADLGVVLLERS-----HRGIELTAAGHAFLE   66 (89)
T ss_dssp             HHHHHHHHHH---HSSHHHHHHHHTC---CHHHHHHHHHHHHHHHTSCCBC----------CCBCHHHHHHHH
T ss_pred             HHHHHHHHHH---hCCHHHHHHHhCC---ChHHHHHHHHHHHhcCCceeeEec-----CCccCccHhHHHHHH
Confidence            5667778874   3489999999999   8899998888875   45688876     577899999987654

>d1hlva1 a.4.1.7 (A:1-66) DNA-binding domain of centromere binding protein B (CENP-B) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Centromere-binding
domain: DNA-binding domain of centromere binding protein B (CENP-B)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.20  E-value=0.66  Score=25.91  Aligned_cols=39  Identities=10%  Similarity=0.167  Sum_probs=30.7

Q ss_pred             HHHHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHH
Q 040869           34 CAIELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRL   76 (131)
Q Consensus        34 ~a~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~   76 (131)
                      ..-++.|...+.. +..++-.|||+..|+   +...|..+++-
T Consensus        10 ~~eK~~ii~~~e~-g~k~sq~eIA~~fGv---~~STvs~IlKn   48 (66)
T d1hlva1          10 FREKSRIIQEVEE-NPDLRKGEIARRFNI---PPSTLSTILKN   48 (66)
T ss_dssp             HHHHHHHHHHHHH-CTTSCHHHHHHHHTC---CHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHc-CCcchHHHHHHHhCC---ChhHHHHHHHH
Confidence            3456777777774 344799999999999   99999999863

>d1l0oc_ a.4.13.2 (C:) SigmaF {Bacillus stearothermophilus [TaxId: 1422]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: SigmaF
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=83.00  E-value=0.54  Score=25.25  Aligned_cols=26  Identities=27%  Similarity=0.362  Sum_probs=22.7

Q ss_pred             CCCCCHHHHHhhcCCCCCCcchHHHHHHH
Q 040869           48 GRAITLSELVSALDIQPTKTTGLFRLMRL   76 (131)
Q Consensus        48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~   76 (131)
                      |..-|.+|||+.+|+   +++.+...|.+
T Consensus        29 gRePT~~EiA~~l~~---~~e~V~~~l~a   54 (57)
T d1l0oc_          29 GRAPTVTEIADHLGI---SPEDVVLAQEA   54 (57)
T ss_dssp             TSCCBHHHHHHHHTS---CHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHCc---CHHHHHHHHHH
Confidence            578999999999999   88888877765

>d2p8ta1 a.4.5.72 (A:14-82) Hypothetical protein PH0730 {Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PH0730 N-terminal domain-like
domain: Hypothetical protein PH0730
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=82.88  E-value=1.5  Score=24.59  Aligned_cols=49  Identities=14%  Similarity=0.169  Sum_probs=40.4

Q ss_pred             CCCCCHHHHHhhcCCCCCCcchHHHHHHHhhcCCceeecccCCCCcceecchhcccc
Q 040869           48 GRAITLSELVSALDIQPTKTTGLFRLMRLLVHSSCFNKTKVNGQEEAYGLTAASTLL  104 (131)
Q Consensus        48 ~~~~s~~eLA~~~~~~~~~~~~l~RlLr~L~~~gl~~~~~~~~~~~~y~~t~~s~~L  104 (131)
                      ..|+.-.-||+.+++   .+..++-.++.|...|+++-..    .| -.+|..++.+
T Consensus        15 ~qPiGRr~La~~L~l---~Er~vRte~~~Lk~~gLI~~~~----~G-m~lTe~G~~~   63 (69)
T d2p8ta1          15 KEPLGRKQISERLEL---GEGSVRTLLRKLSHLDIIRSKQ----RG-HFLTLKGKEI   63 (69)
T ss_dssp             TSCBCHHHHHHHHTC---CHHHHHHHHHHHHHTTSEEEC------C-EEECHHHHHH
T ss_pred             cCCccHHHHHHHcCC---cHHHHHHHHHHHHHCCCeeeeC----CC-CEECHhHHHH
Confidence            379999999999999   9999999999999999999875    34 4567666544

>d1l3la1 a.4.6.2 (A:170-234) Quorum-sensing transcription factor TraR, C-terminal domain {Agrobacterium tumefaciens [TaxId: 358]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Quorum-sensing transcription factor TraR, C-terminal domain
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=82.69  E-value=0.67  Score=25.35  Aligned_cols=34  Identities=18%  Similarity=0.120  Sum_probs=26.4

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHH
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMR   75 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr   75 (131)
                      -+..|+..+.   .+.|..|||+++++   .+..+...++
T Consensus         8 rE~~vl~l~~---~G~s~~eIA~~l~i---S~~TV~~~~~   41 (65)
T d1l3la1           8 KEATYLRWIA---VGKTMEEIADVEGV---KYNSVRVKLR   41 (65)
T ss_dssp             HHHHHHHHHT---TTCCHHHHHHHHTC---CHHHHHHHHH
T ss_pred             HHHHHHHHHH---hcCCHHHHHHHHCC---CHHHHHHHHH
Confidence            4566777776   57999999999999   8887665444

>d2hsga1 a.35.1.5 (A:2-58) Glucose-resistance amylase regulator CcpA, N-terminal domain {Bacillus megaterium [TaxId: 1404]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: GalR/LacI-like bacterial regulator
domain: Glucose-resistance amylase regulator CcpA, N-terminal domain
species: Bacillus megaterium [TaxId: 1404]

Probab=82.64  E-value=0.37  Score=26.15  Aligned_cols=22  Identities=9%  Similarity=0.300  Sum_probs=18.9

Q ss_pred             CCHHHHHhhcCCCCCCcchHHHHHH
Q 040869           51 ITLSELVSALDIQPTKTTGLFRLMR   75 (131)
Q Consensus        51 ~s~~eLA~~~~~~~~~~~~l~RlLr   75 (131)
                      +|+.|||+++|+   +...+.|.|+
T Consensus         2 vTi~dvA~~agv---S~~TVSr~Ln   23 (57)
T d2hsga1           2 VTIYDVAREASV---SMATVSRVVN   23 (57)
T ss_dssp             CCHHHHHHHTTS---CHHHHHHHHT
T ss_pred             cCHHHHHHHHCc---CHHHHHHHhC
Confidence            688999999999   8888888776

>d1fsea_ a.4.6.2 (A:) Germination protein GerE {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Germination protein GerE
species: Bacillus subtilis [TaxId: 1423]

Probab=82.59  E-value=0.65  Score=25.49  Aligned_cols=35  Identities=17%  Similarity=0.128  Sum_probs=26.8

Q ss_pred             HHhChHHHHHhCCCCCCHHHHHhhcCCCCCCcchHHHHHHH
Q 040869           36 IELGIADIIHSHGRAITLSELVSALDIQPTKTTGLFRLMRL   76 (131)
Q Consensus        36 ~~L~ifd~l~~~~~~~s~~eLA~~~~~~~~~~~~l~RlLr~   76 (131)
                      -+..|+..+.   .+.|..|||..+|+   .+..+...++.
T Consensus         8 rE~~vl~l~~---~G~s~~eIA~~L~i---s~~TV~~~~~~   42 (67)
T d1fsea_           8 REREVFELLV---QDKTTKEIASELFI---SEKTVRNHISN   42 (67)
T ss_dssp             HHHHHHHHHT---TTCCHHHHHHHHTS---CHHHHHHHHHH
T ss_pred             HHHHHHHHHH---ccCCHHHHHHHHCC---CHHHHHHHHHH
Confidence            4566777776   57999999999999   88876655543

>d1in4a1 a.4.5.11 (A:255-329) Holliday junction helicase RuvB {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Helicase DNA-binding domain
domain: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

Probab=80.98  E-value=1.5  Score=25.05  Aligned_cols=57  Identities=18%  Similarity=0.287  Sum_probs=42.6

Q ss_pred             HhChHHHHHh--CCCCCCHHHHHhhcCCCCCCcchHHHHHH-HhhcCCceeecccCCCCcceecchhc
Q 040869           37 ELGIADIIHS--HGRAITLSELVSALDIQPTKTTGLFRLMR-LLVHSSCFNKTKVNGQEEAYGLTAAS  101 (131)
Q Consensus        37 ~L~ifd~l~~--~~~~~s~~eLA~~~~~~~~~~~~l~RlLr-~L~~~gl~~~~~~~~~~~~y~~t~~s  101 (131)
                      +.++...|.+  .++|+.++.||..++-   +.+.+.-+.- +|...|++.++.    .|+ ..|+.+
T Consensus         7 Dr~yL~~l~~~f~ggPvGl~tlAa~l~e---~~~TiEdviEPyLiq~G~i~RTp----RGR-~~T~~~   66 (75)
T d1in4a1           7 DRKILKTIIEIYRGGPVGLNALAASLGV---EADTLSEVYEPYLLQAGFLARTP----RGR-IVTEKA   66 (75)
T ss_dssp             HHHHHHHHHHHSTTCCBCHHHHHHHHTS---CHHHHHHHTHHHHHHTTSEEEET----TEE-EECHHH
T ss_pred             HHHHHHHHHHHhCCCCCcHHHHHHHHcC---ChhHHHHHhhHHHHHhhHHhhCC----chH-HhHHHH
Confidence            3445555543  3799999999999999   9998887775 689999999987    555 344443

>d1v7ba1 a.4.1.9 (A:1-74) Transcriptional regulator Cgl2612 {Corynebacterium glutamicum [TaxId: 1718]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator Cgl2612
species: Corynebacterium glutamicum [TaxId: 1718]

Probab=80.59  E-value=0.84  Score=25.27  Aligned_cols=27  Identities=19%  Similarity=0.324  Sum_probs=21.1

Q ss_pred             HHHhCC-CCCCHHHHHhhcCCCCCCcchHHH
Q 040869           43 IIHSHG-RAITLSELVSALDIQPTKTTGLFR   72 (131)
Q Consensus        43 ~l~~~~-~~~s~~eLA~~~~~~~~~~~~l~R   72 (131)
                      .+.+.| ..+|..+||+++|+   .+..+++
T Consensus        16 l~~~~G~~~~s~~~Ia~~agv---s~~t~Y~   43 (74)
T d1v7ba1          16 YIGEYSLETLSYDSLAEATGL---SKSGLIY   43 (74)
T ss_dssp             HHHHSCSTTCCHHHHHHHHCS---CHHHHHH
T ss_pred             HHHHhCccccCHHHHHHHhCc---CcchHhh
Confidence            344445 68999999999999   7777765