Citrus Sinensis ID: 045905

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------13
Protein Sequence
MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDITLTVRSFLQAVLDPILTTPCQHVTTWFQNDDLRCLTRHMGWHFESILGTSQRSTISCAVSNGRS
Secondary Structure (PSIPRED)
ccHHHHHHHccccccccccHHHHHHHHHHHHHHHcccEEEcccccccccEEEcccccccccccccccHHHHHHHHcccccccccccHHHHHHcccccHHHHcccccHHHHHcccHHHHHHHHHHcccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHcccccccccHHHHHHHHHHHHHHHccccEEEcccccccccEEEEccHHHHHccccccccHHHHHHHcccHHHcHHHHHHHHHHcccccHHHHHccccHHHHHcccccccEEEEEccccc
Coil and Loop (DISEMBL)
MTLNELINalpfhpikAQYVAQYVYRFMWILVHSgffaqqnfgqndqerSYVATNASKLLLKDITLTVRSFLQAVLdpilttpcqhvttwfqnddLRCLTrhmgwhfesilgtsqrSTISCAVSNGRS
Flexible Loop (DISEMBL)
MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDITLTVRSFLQAVLDPILTTPCQHVTTWFQNDDLRCLTRHMGWHFesilgtsqrstiscavsngrs
Low Complexity Region (SEG)
MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDITLTVRSFLQAVLDPILTTPCQHVTTWFQNDDLRCLTRHMGWHFESILGTSQRSTISCAVSNGRS
Disordered region (IsUnstruct)
****ELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDITLTVRSFLQAVLDPILTTPCQHVTTWFQNDDLRCLTRHMGWHFESILGTS**************
Disordered Region (DISOPRED)
MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDITLTVRSFLQAVLDPILTTPCQHVTTWFQNDDLRCLTRHMGWHFESILGTSQRSTISCAVSNG**
Disordered Region (DISEMBL)
MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDITLTVRSFLQAVLDPILTTPCQHVTTWFQNDDLRCLTRHMGWHFESILGTSQRSTISCAVSNGRS
Disordered Region (DISPRO)
MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDITLTVRSFLQAVLDPILTTPCQHVTTWFQNDDLRCLTRHMGWHFESILGTSQRSTISCAVS****
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDITLTVRSFLQAVLDPILTTPCQHVTTWFQNDDLRCLTRHMGWHFESILGTSQRSTISCAVSNGRS
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	128	2.2.26 [Sep-21-2011]
B6VJS4	357	Trans-resveratrol di-O-me	no	no	0.710	0.254	0.526	8e-22
Q93WU3	356	Chavicol O-methyltransfer	N/A	no	0.695	0.25	0.410	8e-12
Q93WU2	357	Eugenol O-methyltransfera	N/A	no	0.898	0.322	0.362	3e-11
B0EXJ8	355	Tabersonine 16-O-methyltr	N/A	no	0.703	0.253	0.340	3e-09
P0DH60	360	6a-hydroxymaackiain methy	N/A	no	0.804	0.286	0.336	6e-09
O24305	360	6a-hydroxymaackiain methy	N/A	no	0.804	0.286	0.327	4e-08
Q84KK6	367	Isoflavone 4'-O-methyltra	N/A	no	0.804	0.280	0.338	8e-08
Q8GSN1	348	Myricetin O-methyltransfe	N/A	no	0.757	0.278	0.327	8e-08
Q6VMW0	366	8-hydroxyquercetin 8-O-me	N/A	no	0.804	0.281	0.333	9e-08
Q84KK5	357	Isoflavone 7-O-methyltran	N/A	no	0.804	0.288	0.314	1e-07

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

 Score =  102 bits (254), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 50/95 (52%), Positives = 64/95 (67%), Gaps = 4/95 (4%)

Query: 1   MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL 60
           MTL EL+  LP HP ++Q V    YR M ILVHSGF A Q   Q  +E  YV T+AS+LL
Sbjct: 51  MTLPELVAKLPVHPKRSQCV----YRLMRILVHSGFLAAQRVQQGKEEEGYVLTDASRLL 106

Query: 61  LKDITLTVRSFLQAVLDPILTTPCQHVTTWFQNDD 95
           L D +L++R  + A+LDPILT P  +++ WFQNDD
Sbjct: 107 LMDDSLSIRPLVLAMLDPILTKPWHYLSAWFQNDD 141

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

 Score = 68.9 bits (167), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 39/95 (41%), Positives = 58/95 (61%), Gaps = 6/95 (6%)

Query: 1   MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL 60
           MTL++L+ A+P +  K+Q       R M  LV+S FF ++N   N+QE  Y  T AS+LL
Sbjct: 54  MTLSQLLKAIPINKEKSQSFQ----RLMRALVNSNFFIEEN--SNNQEVCYWLTPASRLL 107

Query: 61  LKDITLTVRSFLQAVLDPILTTPCQHVTTWFQNDD 95
           LK   LTV   +Q VLDP  T P  +++ WF++++
Sbjct: 108 LKGAPLTVAPLVQVVLDPTFTNPWHYMSEWFKHEN 142

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

 Score = 67.4 bits (163), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 46/127 (36%), Positives = 67/127 (52%), Gaps = 12/127 (9%)

Query: 1   MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL 60
           MTL++L+ ++P +  K Q       R M  LV+S FF ++N   N+QE  Y  T AS LL
Sbjct: 54  MTLSQLLQSIPINKEKTQCFQ----RLMRALVNSNFFIEEN-NSNNQEVCYWLTPASCLL 108

Query: 61  LKDITLTVRSFLQAVLDPILTTPCQHVTTWFQNDDLRCLTRHMGWHFESILGTSQRSTIS 120
           LK+  LTV   +Q VLDP  T P  H++ WF ++      +H    FE+  G +    ++
Sbjct: 109 LKEAPLTVTPLVQVVLDPTFTNPWHHMSEWFTHE------KH-ATQFEAANGCTFWEKLA 161

Query: 121 CAVSNGR 127
              S GR
Sbjct: 162 NEPSKGR 168

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|B0EXJ8|HTOMT_CATRO Tabersonine 16-O-methyltransferase OS=Catharanthus roseus GN=16OMT PE=1 SV=1

 Score = 60.5 bits (145), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 33/97 (34%), Positives = 55/97 (56%), Gaps = 7/97 (7%)

Query: 1   MTLNELINAL--PFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASK 58
           +TL+EL NAL  P HP KA ++    YR M +L  +GF +++     + E  Y  T +S+
Sbjct: 47  ITLSELTNALVPPVHPSKAPFI----YRLMRVLAKNGFCSEEQL-DGETEPLYSLTPSSR 101

Query: 59  LLLKDITLTVRSFLQAVLDPILTTPCQHVTTWFQNDD 95
           +LLK   L +R  +  + DP+     + ++ W+QN+D
Sbjct: 102 ILLKKEPLNLRGIVLTMADPVQLKAWESLSDWYQNED 138

16-O-methyltransferase involved in the biosynthesis of vindoline. Highly specific for 16-hydroxytabersonine. No activity with tabersonine, 3-hydroxytyramine, 4-hydroxytyramine, 5-hydroxytryptamine (5HT), 2,3-dihydro-3-hydroxytabersonine, lochnericine, hoerhammericine, 16-hydroxy-2,3-dihydro-3-hydroxytabersonine, 16-hydroxylochnericine, 16-hydroxyhoerhammericine, quercetin, kaempferol and caffeic acid as substrates.

Catharanthus roseus (taxid: 4058)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 9

EC: 4

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

 Score = 59.7 bits (143), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 38/113 (33%), Positives = 54/113 (47%), Gaps = 10/113 (8%)

Query: 1   MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQN--DQERSYVATNASK 58
           MTL EL ++L  HP K   +    YRF+ +L H+GFFA+     N  ++E +YV T +SK
Sbjct: 52  MTLPELASSLKLHPSKVNIL----YRFLRLLTHNGFFAKTTVKSNGEEEETAYVLTPSSK 107

Query: 59  LLLKDITLTVRSFLQAVLDPILTTPCQHVTTWFQNDD----LRCLTRHMGWHF 107
           LL+   +  + S ++  L PI          WF  D       C T    W F
Sbjct: 108 LLVSGKSTCLSSVVKGALHPISLDLWGVSKKWFHEDKEQTLFECATGENYWDF 160

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

 Score = 57.0 bits (136), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 37/113 (32%), Positives = 53/113 (46%), Gaps = 10/113 (8%)

Query: 1   MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQN--DQERSYVATNASK 58
           MTL EL ++L  HP K   +    YRF+ +L H+GFFA+     N  ++E +YV T +SK
Sbjct: 52  MTLPELSSSLKLHPSKVNIL----YRFLRLLTHNGFFAKTTVKSNEGEEETAYVLTPSSK 107

Query: 59  LLLKDITLTVRSFLQAVLDPILTTPCQHVTTWFQNDD----LRCLTRHMGWHF 107
           LL+   +  + S ++  L P           WF  D       C T    W F
Sbjct: 108 LLVSGKSTCLSSLVKGALHPSSLDMWGVSKKWFHEDKEQTLFECATGENYWDF 160

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

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

 Score = 55.8 bits (133), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 41/121 (33%), Positives = 58/121 (47%), Gaps = 18/121 (14%)

Query: 1   MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQ-----QNF--GQNDQERSYVA 53
           +TL EL +AL  HP K   +    YRF+ +L H+GFFA+     QN   G+ ++E +Y  
Sbjct: 52  ITLPELASALKLHPSKVGIL----YRFLRLLTHNGFFAKTTVPSQNGKDGEEEEETAYAL 107

Query: 54  TNASKLLLKDITLTVRSFLQAVLDPILTTPCQHVTTWFQNDDLRCLTRHMGWHFESILGT 113
           T  SKLL+K     + S ++  L P      +    WF+ D    L       FES  G 
Sbjct: 108 TPPSKLLVKGKPTCLASIVRGALHPSSLDMWRSSEKWFKEDKELTL-------FESATGE 160

Query: 114 S 114
           S
Sbjct: 161 S 161

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|Q8GSN1|MOMT_CATRO Myricetin O-methyltransferase OS=Catharanthus roseus PE=1 SV=1

 Score = 55.8 bits (133), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 35/107 (32%), Positives = 55/107 (51%), Gaps = 10/107 (9%)

Query: 1   MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL 60
           M L++L N+LP +P KA Y+    YR M ILV +G+F+++      ++  Y  T  ++LL
Sbjct: 47  MALSDLTNSLPINPSKAPYI----YRLMRILVAAGYFSEE------EKNVYSLTPFTRLL 96

Query: 61  LKDITLTVRSFLQAVLDPILTTPCQHVTTWFQNDDLRCLTRHMGWHF 107
           LK+  L   S +  V           ++ WFQN+DL       G +F
Sbjct: 97  LKNDPLNSISMVLGVNQIAELKAWNAMSEWFQNEDLTAFETAHGKNF 143

Methylates myricetin and dihydromyricetin at 2 sites. Inactive towards 16-hydroxytabersonine, the phenylpropanoids 5-hydroxyferulate, caffeate and their CoA-esters, flavones and flavonones possessing 2 or 3 B-ring hydroxyl groups.

Catharanthus roseus (taxid: 4058)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 1

EC: 4

EC: 9

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

 Score = 55.5 bits (132), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 38/114 (33%), Positives = 60/114 (52%), Gaps = 11/114 (9%)

Query: 1   MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFF-------AQQNFGQNDQERSYVA 53
           +TL++L +AL  +  K+  +    +R M ILVHSGFF         +   + ++E +Y  
Sbjct: 52  ITLSQLADALNINKAKSHGL----FRLMRILVHSGFFDKVKVKVKVEGEDEEEEEDAYSL 107

Query: 54  TNASKLLLKDITLTVRSFLQAVLDPILTTPCQHVTTWFQNDDLRCLTRHMGWHF 107
           T AS+LLL+   L+V  F  A+ DP+ T    H++ WF+ND +       G  F
Sbjct: 108 TPASRLLLRSEPLSVAPFALAMSDPVYTETWHHLSEWFRNDAVAAFDTKYGMTF 161

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

 Score = 55.1 bits (131), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 34/108 (31%), Positives = 55/108 (50%), Gaps = 5/108 (4%)

Query: 1   MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQE-RSYVATNASKL 59
           +T++EL++ L     KA  V Q + R+M    H+GFF +    +  +E  +Y  T AS+L
Sbjct: 52  ITVSELVSILKVPQTKAGNV-QRIMRYM---AHNGFFERVRIQEEQEENEAYALTAASEL 107

Query: 60  LLKDITLTVRSFLQAVLDPILTTPCQHVTTWFQNDDLRCLTRHMGWHF 107
           L+K   L +   ++ VLDP L+     +  W   +DL      +G HF
Sbjct: 108 LVKGSELCLAPMVECVLDPTLSGSYHQLKKWIYEEDLTLFGVSLGSHF 155

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

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	128
3077640	356	O-methyltransferase [Prunus dulcis]	0.765	0.275	0.524	6e-22
359485241	351	PREDICTED: 8-hydroxyquercetin 8-O-methyl	0.968	0.353	0.436	1e-21
359485239	357	PREDICTED: 8-hydroxyquercetin 8-O-methyl	0.968	0.347	0.436	1e-21
255568371	356	o-methyltransferase, putative [Ricinus c	0.804	0.289	0.495	2e-21
225446483	357	PREDICTED: 8-hydroxyquercetin 8-O-methyl	0.710	0.254	0.568	2e-21
147864291	357	hypothetical protein VITISV_029725 [Viti	0.710	0.254	0.568	3e-21
359485243	357	PREDICTED: 8-hydroxyquercetin 8-O-methyl	0.968	0.347	0.429	3e-21
359485414	338	PREDICTED: chavicol O-methyltransferase-	0.710	0.269	0.557	4e-21
55163136	346	orcinol O-methyltransferase 4 [Rosa hybr	0.703	0.260	0.557	4e-21
123718206	346	putative orcinol O-methyltransferase [Ro	0.703	0.260	0.557	4e-21

>gi|3077640|emb|CAA11131.1| O-methyltransferase [Prunus dulcis]

 Score =  108 bits (270), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 54/103 (52%), Positives = 69/103 (66%), Gaps = 5/103 (4%)

Query: 1   MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL 60
           M+L++LI+ALP HP K+  V    YR M ILVHSGFF +Q   + D+E  YV T+AS+LL
Sbjct: 51  MSLSDLISALPIHPKKSNCV----YRLMRILVHSGFFCRQKLSELDEEEGYVLTDASRLL 106

Query: 61  LKDITLTVRSFLQAVLDPILTTPCQHVTTWFQNDD-LRCLTRH 102
           LKD  L+ R FL   LDP +T P  + +TWFQNDD   C+T H
Sbjct: 107 LKDDPLSARPFLLGALDPFMTKPWHYFSTWFQNDDPTACVTAH 149

Source: Prunus dulcis

Species: Prunus dulcis

Genus: Prunus

Family: Rosaceae

Order: Rosales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359485241|ref|XP_003633242.1| PREDICTED: 8-hydroxyquercetin 8-O-methyltransferase isoform 2 [Vitis vinifera]

 Score =  108 bits (269), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 62/142 (43%), Positives = 79/142 (55%), Gaps = 18/142 (12%)

Query: 1   MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL 60
           MTL EL+  LP HP K QYV    YR M +LV S FFA Q   Q+++E  YV T+AS+LL
Sbjct: 51  MTLPELVAKLPVHPKKTQYV----YRLMRVLVQSDFFAAQRAQQSEEEEGYVLTHASRLL 106

Query: 61  LKDITLTVRSFLQAVLDPILTTPCQHVTTWFQNDDL--------RCLTRHMG------WH 106
           LKD +L+VR FL A+LDP LT P  +V+ WFQNDD         R L  + G      + 
Sbjct: 107 LKDDSLSVRPFLLAMLDPTLTKPWHYVSAWFQNDDPTPFDTAHERTLWDYAGHEPQLNYF 166

Query: 107 FESILGTSQRSTISCAVSNGRS 128
           F   + +  R   S  V  G+ 
Sbjct: 167 FNEAMASDARLVTSVLVKEGKG 188

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359485239|ref|XP_002274019.2| PREDICTED: 8-hydroxyquercetin 8-O-methyltransferase isoform 1 [Vitis vinifera]

 Score =  107 bits (268), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 62/142 (43%), Positives = 79/142 (55%), Gaps = 18/142 (12%)

Query: 1   MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL 60
           MTL EL+  LP HP K QYV    YR M +LV S FFA Q   Q+++E  YV T+AS+LL
Sbjct: 51  MTLPELVAKLPVHPKKTQYV----YRLMRVLVQSDFFAAQRAQQSEEEEGYVLTHASRLL 106

Query: 61  LKDITLTVRSFLQAVLDPILTTPCQHVTTWFQNDDL--------RCLTRHMG------WH 106
           LKD +L+VR FL A+LDP LT P  +V+ WFQNDD         R L  + G      + 
Sbjct: 107 LKDDSLSVRPFLLAMLDPTLTKPWHYVSAWFQNDDPTPFDTAHERTLWDYAGHEPQLNYF 166

Query: 107 FESILGTSQRSTISCAVSNGRS 128
           F   + +  R   S  V  G+ 
Sbjct: 167 FNEAMASDARLVTSVLVKEGKG 188

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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 =  107 bits (267), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 53/107 (49%), Positives = 69/107 (64%), Gaps = 4/107 (3%)

Query: 1   MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL 60
           ++L++LI ALP HP KA+ +     R M IL+HSGFFA+    + D+E  YV TNASKLL
Sbjct: 50  ISLSQLIAALPIHPAKARGIP----RLMRILIHSGFFAKAKIEEKDEEEGYVLTNASKLL 105

Query: 61  LKDITLTVRSFLQAVLDPILTTPCQHVTTWFQNDDLRCLTRHMGWHF 107
           LKD  L++  FL A+LDPIL  P  +++TWFQNDD        G  F
Sbjct: 106 LKDNPLSIAPFLLAMLDPILIKPWHYLSTWFQNDDATAFDTAHGMGF 152

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225446483|ref|XP_002278057.1| PREDICTED: 8-hydroxyquercetin 8-O-methyltransferase [Vitis vinifera]

 Score =  107 bits (266), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 54/95 (56%), Positives = 66/95 (69%), Gaps = 4/95 (4%)

Query: 1   MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL 60
           MTL EL+  LP HP K QYV    YR M +LV S FFA Q   Q+++E  YV T+AS+LL
Sbjct: 51  MTLPELVAKLPVHPKKTQYV----YRLMRVLVQSDFFAAQRAQQSEEEEGYVLTHASQLL 106

Query: 61  LKDITLTVRSFLQAVLDPILTTPCQHVTTWFQNDD 95
           LKD +L+VR FL A+LDP LT P  +V+ WFQNDD
Sbjct: 107 LKDDSLSVRPFLLAMLDPTLTKPWHYVSAWFQNDD 141

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147864291|emb|CAN83014.1| hypothetical protein VITISV_029725 [Vitis vinifera]

 Score =  106 bits (265), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 54/95 (56%), Positives = 65/95 (68%), Gaps = 4/95 (4%)

Query: 1   MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL 60
           MTL EL+  LP HP K QYV    YR M +LV S FFA Q   Q+++E  YV T+AS LL
Sbjct: 51  MTLPELVAKLPVHPKKTQYV----YRLMRVLVQSDFFAAQRAQQSEEEEGYVLTHASXLL 106

Query: 61  LKDITLTVRSFLQAVLDPILTTPCQHVTTWFQNDD 95
           LKD +L+VR FL A+LDP LT P  +V+ WFQNDD
Sbjct: 107 LKDDSLSVRPFLLAMLDPTLTKPWHYVSAWFQNDD 141

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359485243|ref|XP_002277927.2| PREDICTED: 8-hydroxyquercetin 8-O-methyltransferase isoform 2 [Vitis vinifera]

 Score =  106 bits (264), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 61/142 (42%), Positives = 79/142 (55%), Gaps = 18/142 (12%)

Query: 1   MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL 60
           MTL +L+  LP HP K QYV    YR M +LV S FFA Q   Q+++E  YV T+AS+LL
Sbjct: 51  MTLPQLVAKLPVHPKKTQYV----YRLMRVLVQSDFFAAQRAQQSEEEEGYVLTHASRLL 106

Query: 61  LKDITLTVRSFLQAVLDPILTTPCQHVTTWFQNDDL--------RCLTRHMG------WH 106
           LKD +L+VR FL A+LDP LT P  +V+ WFQNDD         R L  + G      + 
Sbjct: 107 LKDDSLSVRPFLLAMLDPTLTKPWHYVSAWFQNDDPTPFDTAHERTLWDYAGHEPQLNYF 166

Query: 107 FESILGTSQRSTISCAVSNGRS 128
           F   + +  R   S  V  G+ 
Sbjct: 167 FNEAMASDARLVTSVLVKEGKG 188

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359485414|ref|XP_003633270.1| PREDICTED: chavicol O-methyltransferase-like [Vitis vinifera]

 Score =  106 bits (264), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 53/95 (55%), Positives = 66/95 (69%), Gaps = 4/95 (4%)

Query: 1   MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL 60
           MTL +L+  LP HP K QYV    YR M +LV S FFA Q   Q+++E  YV T+AS+LL
Sbjct: 65  MTLPQLVAKLPVHPKKTQYV----YRLMRVLVQSDFFAAQRAQQSEEEEGYVLTHASRLL 120

Query: 61  LKDITLTVRSFLQAVLDPILTTPCQHVTTWFQNDD 95
           LKD +L+VR FL A+LDP LT P  +V+ WFQNDD
Sbjct: 121 LKDDSLSVRPFLLAMLDPTLTKPWHYVSAWFQNDD 155

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|55163136|emb|CAH05086.1| orcinol O-methyltransferase 4 [Rosa hybrid cultivar]

 Score =  105 bits (263), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 53/95 (55%), Positives = 68/95 (71%), Gaps = 5/95 (5%)

Query: 1   MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL 60
           MTL+EL +ALP HP K+  V    YR M ILVHSGFFA++   + D+E  Y  TNAS+LL
Sbjct: 51  MTLSELTSALPIHPTKSHSV----YRLMRILVHSGFFAKKKLSKTDEE-GYTLTNASQLL 105

Query: 61  LKDITLTVRSFLQAVLDPILTTPCQHVTTWFQNDD 95
           LKD  L++  FL A+LDP+LT P  +++TWFQNDD
Sbjct: 106 LKDHPLSLTPFLTAMLDPVLTKPWNYLSTWFQNDD 140

Source: Rosa hybrid cultivar

Species: Rosa hybrid cultivar

Genus: Rosa

Family: Rosaceae

Order: Rosales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|123718206|emb|CAJ65618.1| putative orcinol O-methyltransferase [Rosa chinensis var. spontanea]

 Score =  105 bits (263), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 53/95 (55%), Positives = 68/95 (71%), Gaps = 5/95 (5%)

Query: 1   MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL 60
           MTL+EL +ALP HP K+  V    YR M ILVHSGFFA++   + D+E  Y  TNAS+LL
Sbjct: 51  MTLSELTSALPIHPTKSHSV----YRLMRILVHSGFFAKKKLSKTDEE-GYTLTNASQLL 105

Query: 61  LKDITLTVRSFLQAVLDPILTTPCQHVTTWFQNDD 95
           LKD  L++  FL A+LDP+LT P  +++TWFQNDD
Sbjct: 106 LKDHPLSLTPFLTAMLDPVLTKPWNYLSTWFQNDD 140

Source: Rosa chinensis var. spontanea

Species: Rosa chinensis

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	128
UNIPROTKB|Q6VMW0	366	OMT2 "8-hydroxyquercetin 8-O-m	0.804	0.281	0.342	7.6e-10
UNIPROTKB|B0EXJ8	355	16OMT "Tabersonine 16-O-methyl	0.703	0.253	0.340	1.2e-09
UNIPROTKB|Q84KK5	357	D7OMT "Isoflavone 7-O-methyltr	0.835	0.299	0.312	3.1e-08
UNIPROTKB|Q84KK6	367	HI4'OMT "Isoflavone 4'-O-methy	0.906	0.316	0.325	4.3e-08
UNIPROTKB|Q8GSN1	348	Q8GSN1 "Myricetin O-methyltran	0.757	0.278	0.327	2.9e-07
UNIPROTKB|Q84KK4	365	HI4'OMT "Isoflavone 4'-O-methy	0.906	0.317	0.285	2.9e-05

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

 Score = 148 (57.2 bits), Expect = 7.6e-10, P = 7.6e-10
 Identities = 39/114 (34%), Positives = 62/114 (54%)

Query:     1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNF-----GQNDQER--SYVA 53
             +TL++L +AL  +  K+  +    +R M ILVHSGFF +        G++++E   +Y  
Sbjct:    52 ITLSQLADALNINKAKSHGL----FRLMRILVHSGFFDKVKVKVKVEGEDEEEEEDAYSL 107

Query:    54 TNASKLLLKDITLTVRSFLQAVLDPILTTPCQHVTTWFQNDDLRCLTRHMGWHF 107
             T AS+LLL+   L+V  F  A+ DP+ T    H++ WF+ND +       G  F
Sbjct:   108 TPASRLLLRSEPLSVAPFALAMSDPVYTETWHHLSEWFRNDAVAAFDTKYGMTF 161

GO:0009812 "flavonoid metabolic process" evidence=IDA

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

GO:0032259 "methylation" evidence=IDA

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

 Score = 146 (56.5 bits), Expect = 1.2e-09, P = 1.2e-09
 Identities = 33/97 (34%), Positives = 55/97 (56%)

Query:     1 MTLNELINAL--PFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASK 58
             +TL+EL NAL  P HP KA ++    YR M +L  +GF +++     + E  Y  T +S+
Sbjct:    47 ITLSELTNALVPPVHPSKAPFI----YRLMRVLAKNGFCSEEQL-DGETEPLYSLTPSSR 101

Query:    59 LLLKDITLTVRSFLQAVLDPILTTPCQHVTTWFQNDD 95
             +LLK   L +R  +  + DP+     + ++ W+QN+D
Sbjct:   102 ILLKKEPLNLRGIVLTMADPVQLKAWESLSDWYQNED 138

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

 Score = 133 (51.9 bits), Expect = 3.1e-08, P = 3.1e-08
 Identities = 35/112 (31%), Positives = 56/112 (50%)

Query:     1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQER-SYVATNASKL 59
             +T++EL++ L     KA  V Q + R+M    H+GFF +    +  +E  +Y  T AS+L
Sbjct:    52 ITVSELVSILKVPQTKAGNV-QRIMRYM---AHNGFFERVRIQEEQEENEAYALTAASEL 107

Query:    60 LLKDITLTVRSFLQAVLDPILTTPCQHVTTWFQNDDLRCLTRHMGWHFESIL 111
             L+K   L +   ++ VLDP L+     +  W   +DL      +G HF   L
Sbjct:   108 LVKGSELCLAPMVECVLDPTLSGSYHQLKKWIYEEDLTLFGVSLGSHFWEFL 159

GO:0009717 "isoflavonoid biosynthetic process" evidence=IDA

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

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

 Score = 132 (51.5 bits), Expect = 4.3e-08, P = 4.3e-08
 Identities = 42/129 (32%), Positives = 62/129 (48%)

Query:     1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQ-----QNF--GQNDQERSYVA 53
             +TL EL +AL  HP K   +    YRF+ +L H+GFFA+     QN   G+ ++E +Y  
Sbjct:    52 ITLPELASALKLHPSKVGIL----YRFLRLLTHNGFFAKTTVPSQNGKDGEEEEETAYAL 107

Query:    54 TNASKLLLKDITLTVRSFLQAVLDPILTTPCQHVTTWFQND-DLRCLTRHMGWHFESILG 112
             T  SKLL+K     + S ++  L P      +    WF+ D +L       G  F   L 
Sbjct:   108 TPPSKLLVKGKPTCLASIVRGALHPSSLDMWRSSEKWFKEDKELTLFESATGESFWDFLN 167

Query:   113 T-SQRSTIS 120
               S+  T+S
Sbjct:   168 KDSESGTLS 176

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

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

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

 Score = 124 (48.7 bits), Expect = 2.9e-07, P = 2.9e-07
 Identities = 35/107 (32%), Positives = 55/107 (51%)

Query:     1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL 60
             M L++L N+LP +P KA Y+    YR M ILV +G+F+++      ++  Y  T  ++LL
Sbjct:    47 MALSDLTNSLPINPSKAPYI----YRLMRILVAAGYFSEE------EKNVYSLTPFTRLL 96

Query:    61 LKDITLTVRSFLQAVLDPILTTPCQHVTTWFQNDDLRCLTRHMGWHF 107
             LK+  L   S +  V           ++ WFQN+DL       G +F
Sbjct:    97 LKNDPLNSISMVLGVNQIAELKAWNAMSEWFQNEDLTAFETAHGKNF 143

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

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

 Score = 106 (42.4 bits), Expect = 2.9e-05, P = 2.9e-05
 Identities = 36/126 (28%), Positives = 56/126 (44%)

Query:     1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQND---QERSYVATNAS 57
             +TL EL  AL   P K   +    +RF+ +L H+GFFA+    + +   +E +Y  T  S
Sbjct:    53 ITLPELATALNLRPSKIGVL----HRFLRLLTHNGFFAKTTVSRGEGAEEETAYGLTPPS 108

Query:    58 KLLLKDITLTVRSFLQAVLDPILTTPCQHVTTWF--QNDDLRCLTRHMGWHFESILGTSQ 115
             KLL+K  +  +   ++  L P      +    WF   N++L       G  F   L    
Sbjct:   109 KLLVKSNSTCLAPIVKGALHPSSLDMWRSSKKWFLEDNEELTLFESATGESFWEFLNKET 168

Query:   116 RS-TIS 120
              S T+S
Sbjct:   169 ESDTLS 174


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        0.325   0.134   0.422    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      128       128   0.00091  102 3  11 22  0.45    30
                                                     29  0.41    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:  6
  No. of states in DFA:  578 (61 KB)
  Total size of DFA:  141 KB (2087 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:  12.30u 0.08s 12.38t   Elapsed:  00:00:02
  Total cpu time:  12.30u 0.08s 12.38t   Elapsed:  00:00:02
  Start:  Fri May 10 10:17:44 2013   End:  Fri May 10 10:17:46 2013

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

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	128
KOG3178	342	consensus Hydroxyindole-O-methyltransferase and re	99.45
TIGR02716	306	C20_methyl_CrtF C-20 methyltransferase BchU. Membe	98.94
PF00891	241	Methyltransf_2: O-methyltransferase; InterPro: IPR	98.93
PF08100	51	Dimerisation: Dimerisation domain; InterPro: IPR01	98.13
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	97.23
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	96.7
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	96.67
COG1414	246	IclR Transcriptional regulator [Transcription]	96.57
PRK15090	257	DNA-binding transcriptional regulator KdgR; Provis	96.49
PF02082	83	Rrf2: Transcriptional regulator; InterPro: IPR0009	96.41
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	96.25
smart00347	101	HTH_MARR helix_turn_helix multiple antibiotic resi	96.2
PRK09834	263	DNA-binding transcriptional activator MhpR; Provis	96.2
smart00419	48	HTH_CRP helix_turn_helix, cAMP Regulatory protein.	96.18
PRK11569	274	transcriptional repressor IclR; Provisional	96.13
smart00529	96	HTH_DTXR Helix-turn-helix diphteria tox regulatory	96.06
PRK10163	271	DNA-binding transcriptional repressor AllR; Provis	96.02
TIGR02431	248	pcaR_pcaU beta-ketoadipate pathway transcriptional	95.98
TIGR02010	135	IscR iron-sulfur cluster assembly transcription fa	95.77
TIGR02337	118	HpaR homoprotocatechuate degradation operon regula	95.74
PRK03902	142	manganese transport transcriptional regulator; Pro	95.72
TIGR00738	132	rrf2_super rrf2 family protein (putative transcrip	95.46
PF14947	77	HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_	95.36
PRK10857	164	DNA-binding transcriptional regulator IscR; Provis	95.35
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	95.16
COG1959	150	Predicted transcriptional regulator [Transcription	95.1
PRK11920	153	rirA iron-responsive transcriptional regulator; Re	95.0
PRK11512	144	DNA-binding transcriptional repressor MarR; Provis	94.91
cd00090	78	HTH_ARSR Arsenical Resistance Operon Repressor and	94.73
TIGR02944	130	suf_reg_Xantho FeS assembly SUF system regulator,	94.66
PRK03573	144	transcriptional regulator SlyA; Provisional	94.58
PRK11050	152	manganese transport regulator MntR; Provisional	94.49
PF01638	90	HxlR: HxlR-like helix-turn-helix; InterPro: IPR002	94.31
TIGR01889	109	Staph_reg_Sar staphylococcal accessory regulator f	94.24
PRK11014	141	transcriptional repressor NsrR; Provisional	94.15
COG1321	154	TroR Mn-dependent transcriptional regulator [Trans	94.07
PRK10870	176	transcriptional repressor MprA; Provisional	93.92
smart00418	66	HTH_ARSR helix_turn_helix, Arsenical Resistance Op	93.64
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	93.56
TIGR02702	203	SufR_cyano iron-sulfur cluster biosynthesis transc	93.17
PF09012	69	FeoC: FeoC like transcriptional regulator; InterPr	93.12
COG4742	260	Predicted transcriptional regulator [Transcription	93.03
TIGR01884	203	cas_HTH CRISPR locus-related DNA-binding protein.	92.85
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	92.75
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	92.7
TIGR01610	95	phage_O_Nterm phage replication protein O, N-termi	92.65
PRK14165	217	winged helix-turn-helix domain-containing protein/	92.59
PF13601	80	HTH_34: Winged helix DNA-binding domain; PDB: 1UB9	92.52
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	91.74
COG2345	218	Predicted transcriptional regulator [Transcription	91.62
cd07377	66	WHTH_GntR Winged helix-turn-helix (WHTH) DNA-bindi	91.33
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	91.14
COG3355	126	Predicted transcriptional regulator [Transcription	90.96
PF07381	90	DUF1495: Winged helix DNA-binding domain (DUF1495)	90.57
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	90.49
COG1846	126	MarR Transcriptional regulators [Transcription]	90.4
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	90.37
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	90.07
PRK13777	185	transcriptional regulator Hpr; Provisional	88.64
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	88.22
KOG2165	765	consensus Anaphase-promoting complex (APC), subuni	88.16
cd07153	116	Fur_like Ferric uptake regulator(Fur) and related	88.1
COG1733	120	Predicted transcriptional regulators [Transcriptio	88.08
PF13545	76	HTH_Crp_2: Crp-like helix-turn-helix domain; PDB:	87.3
PRK10141	117	DNA-binding transcriptional repressor ArsR; Provis	86.94
COG1378	247	Predicted transcriptional regulators [Transcriptio	86.9
PF05732	165	RepL: Firmicute plasmid replication protein (RepL)	86.84
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	86.51
PF03444	78	HrcA_DNA-bdg: Winged helix-turn-helix transcriptio	86.31
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	86.26
PRK09334	86	30S ribosomal protein S25e; Provisional	86.19
PF13814	191	Replic_Relax: Replication-relaxation	86.04
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	85.93
PRK06474	178	hypothetical protein; Provisional	85.63
PF00392	64	GntR: Bacterial regulatory proteins, gntR family;	85.57
PRK04172	489	pheS phenylalanyl-tRNA synthetase subunit alpha; P	85.5
COG1497	260	Predicted transcriptional regulator [Transcription	85.49
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	84.83
PF02796	45	HTH_7: Helix-turn-helix domain of resolvase; Inter	84.52
TIGR00122	69	birA_repr_reg BirA biotin operon repressor domain.	84.14
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	84.1
PF03297	105	Ribosomal_S25: S25 ribosomal protein; InterPro: IP	83.79
PF04703	62	FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.	83.51
PF13730	55	HTH_36: Helix-turn-helix domain	83.16
PRK04214	412	rbn ribonuclease BN/unknown domain fusion protein;	82.2
PF14394	171	DUF4423: Domain of unknown function (DUF4423)	82.04
PF03428	177	RP-C: Replication protein C N-terminal domain; Int	81.36
COG4901	107	Ribosomal protein S25 [Translation, ribosomal stru	81.33
PRK00215	205	LexA repressor; Validated	81.3
PRK05638	442	threonine synthase; Validated	81.17
PRK06266	178	transcription initiation factor E subunit alpha; V	80.57
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	80.16
COG4190	144	Predicted transcriptional regulator [Transcription	80.04

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

Probab=99.45  E-value=1.9e-13  Score=107.62  Aligned_cols=108  Identities=19%  Similarity=0.245  Sum_probs=92.1

Q ss_pred             HHHHHHhCCC--CCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcCC-CCcHHHHHHHhcChh
Q 045905            3 LNELINALPF--HPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDI-TLTVRSFLQAVLDPI   79 (128)
Q Consensus         3 ~~eLA~~~~~--~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~~-~~s~~~~~~~~~~~~   79 (128)
                      ..|||..++.  +|.++.    .++||||.|++++||++....   .+ .|++||+++.+..+. ..|++++++..+++.
T Consensus        41 p~~ia~~l~~~~~~~~p~----ll~r~lr~L~s~~i~k~~~~~---~~-~Y~~~~~~~~~l~~~~~~S~a~~~~~~~~~v  112 (342)
T KOG3178|consen   41 PSEIASLLPTPKNPEAPV----LLDRILRLLVSYSILKCRLVG---GE-VYSATPVCKYFLKDSGGGSLAPLVLLNTSKV  112 (342)
T ss_pred             HHHHHHhccCCCCCCChh----HHHHHHHHHHHhhhceeeeec---ce-eeeccchhhhheecCCCCchhHHHHHhcccc
Confidence            4688888883  454667    999999999999999987631   13 899999999998544 479999999999999


Q ss_pred             hHHHHHhHHHhhhcCCCChhhhccCCChhHhhhcCccchh
Q 045905           80 LTTPCQHVTTWFQNDDLRCLTRHMGWHFESILGTSQRSTI  119 (128)
Q Consensus        80 ~~~~~~~l~~~~~~g~~~~f~~a~G~~~fe~~~~~p~~~~  119 (128)
                      .++.|.+++++++.+. .+|..+||+.+|+|...|+.++.
T Consensus       113 ~~~~w~~l~dai~eg~-~~~~~~~G~~l~~~~~~~~~~~~  151 (342)
T KOG3178|consen  113 IMNTWQFLKDAILEGG-DAFATAHGMMLGGYGGADERFSK  151 (342)
T ss_pred             hhhhHHHHHHHHHhcc-cCCccccchhhhhhcccccccHH
Confidence            9999999999999988 68999999999999999886443

>TIGR02716 C20_methyl_CrtF C-20 methyltransferase BchU

Probab=98.94  E-value=2.2e-09  Score=83.46  Aligned_cols=85  Identities=7%  Similarity=0.031  Sum_probs=61.7

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcCCCCc----HHHHHHHhc
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDITLT----VRSFLQAVL   76 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~~~~s----~~~~~~~~~   76 (128)
                      +|++|||+++++++   .    .++||||+|+++|+|.+..       ++|++|++|+.+..+.+.+    +.+++.+..
T Consensus        24 ~t~~eLA~~~~~~~---~----~~~~lL~~L~~lgll~~~~-------~~y~~t~~~~~~l~~~~~~~~~~~~~~~~~~~   89 (306)
T TIGR02716        24 KDLATLAADTGSVP---P----RLEMLLETLRQMRVINLED-------GKWSLTEFADYMFSPTPKEPNLHQTPVAKAMA   89 (306)
T ss_pred             CCHHHHHHHcCCCh---H----HHHHHHHHHHhCCCeEecC-------CcEecchhHHhhccCCccchhhhcCchHHHHH
Confidence            48999999999955   8    9999999999999998753       6899999999777654321    123333332


Q ss_pred             ChhhHHHHHhHHHhhhcCCCChhhhc
Q 045905           77 DPILTTPCQHVTTWFQNDDLRCLTRH  102 (128)
Q Consensus        77 ~~~~~~~~~~l~~~~~~g~~~~f~~a  102 (128)
                      . .....|..|.+++++ . ++|...
T Consensus        90 ~-~~~~~~~~l~~~~r~-~-~~~~~~  112 (306)
T TIGR02716        90 F-LADDFYMGLSQAVRG-Q-KNFKGQ  112 (306)
T ss_pred             H-HHHHHHHhHHHHhcC-C-cccccc
Confidence            1 233678999999984 3 345543

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.

>PF00891 Methyltransf_2: O-methyltransferase; InterPro: IPR001077 Methyl transfer from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals

Probab=98.93  E-value=8.8e-10  Score=82.79  Aligned_cols=71  Identities=21%  Similarity=0.254  Sum_probs=62.3

Q ss_pred             ccceechHhhhhhhcCCC-CcHHHHHHHhcChhhHHHHHhHHHhhhcCCCChhhhccCCChhHhhhcCccchh
Q 045905           48 ERSYVATNASKLLLKDIT-LTVRSFLQAVLDPILTTPCQHVTTWFQNDDLRCLTRHMGWHFESILGTSQRSTI  119 (128)
Q Consensus        48 ~~~y~~T~~s~~L~~~~~-~s~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~~f~~a~G~~~fe~~~~~p~~~~  119 (128)
                      +++|+||++|+.|+.+.. .++..++.+...+..+.+|.+|.+++++|. ++|+.++|.++|+|++++|+..+
T Consensus         3 ~~~y~~t~~s~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~v~~g~-~~~~~~~g~~~~~~~~~~~~~~~   74 (241)
T PF00891_consen    3 GDRYSLTPLSELLLSDHSSPSMRGFVLFMISPELYPAWFRLTEAVRTGK-PPFEKAFGTPFFEYLEEDPELAK   74 (241)
T ss_dssp             TEEEEE-HHHHGGSTTTTTTHHHHHHHHHTCHHHHHGGGGHHHHHHHSS--HHHHHHSS-HHHHHHCSHHHHH
T ss_pred             CCEEeChHHHHHHhCCCCcCcHHHHHHHhcCHHHHHHHHHHHhhhccCC-CHHHHhcCCcHHHhhhhChHHHH
Confidence            578999999999998765 689999989889999999999999999998 89999999999999999997765

The reaction is catalysed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented. Three classes of DNA Mtases transfer the methyl group from AdoMet to the target base to form either N-6-methyladenine, or N-4-methylcytosine, or C-5- methylcytosine. In C-5-cytosine Mtases, ten conserved motifs are arranged in the same order []. Motif I (a glycine-rich or closely related consensus sequence; FAGxGG in M.HhaI []), shared by other AdoMet-Mtases [], is part of the cofactor binding site and motif IV (PCQ) is part of the catalytic site. In contrast, sequence comparison among N-6-adenine and N-4-cytosine Mtases indicated two of the conserved segments [], although more conserved segments may be present. One of them corresponds to motif I in C-5-cytosine Mtases, and the other is named (D/N/S)PP(Y/F). Crystal structures are known for a number of Mtases [, , , ]. The cofactor binding sites are almost identical and the essential catalytic amino acids coincide. The comparable protein folding and the existence of equivalent amino acids in similar secondary and tertiary positions indicate that many (if not all) AdoMet-Mtases have a common catalytic domain structure. This permits tertiary structure prediction of other DNA, RNA, protein, and small-molecule AdoMet-Mtases from their amino acid sequences []. This domain includes a range of O-methyltransferases some of which utilise S-adenosyl methionine as substrate []. In prokaryotes, the major role of DNA methylation is to protect host DNA against degradation by restriction enzymes. In eukaryotes, DNA methylation has been implicated in the control of several cellular processes, including differentiation, gene regulation, and embryonic development. O-methyltransferases have a common catalytic domain structure, which might be universal among S-adenosyl-L-methionine (AdoMet)-dependent methyltransferases []. Comparative analysis of the predicted amino acid sequences of a number of plant O-methyltransferase cDNA clones show that they share some 32-71% sequence identity, and can be grouped according to the different compounds they utilise as substrates [].; GO: 0008171 O-methyltransferase activity; PDB: 1FPQ_A 1FP1_D 3P9K_B 3P9I_D 3P9C_A 3I53_A 3I5U_A 3I64_A 3I58_A 1ZG3_A ....

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

Probab=98.13  E-value=1.6e-06  Score=50.85  Aligned_cols=28  Identities=32%  Similarity=0.558  Sum_probs=23.9

Q ss_pred             CCHHHHHHhCC-CCCCCchhhhhhHHHHHHHHH
Q 045905            1 MTLNELINALP-FHPIKAQYVAQYVYRFMWILV   32 (128)
Q Consensus         1 ~S~~eLA~~~~-~~~~~~~~~~~~L~RlLR~L~   32 (128)
                      +|++|||++++ .+|.++.    .|+||||+|+
T Consensus        23 ls~~eia~~l~~~~p~~~~----~L~RimR~L~   51 (51)
T PF08100_consen   23 LSLSEIAARLPTSNPSAPP----MLDRIMRLLV   51 (51)
T ss_dssp             BEHHHHHHTSTCT-TTHHH----HHHHHHHHHH
T ss_pred             CCHHHHHHHcCCCCcchHH----HHHHHHHHhC
Confidence            58999999999 7776777    9999999996

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 ....

>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=97.23  E-value=0.00064  Score=41.05  Aligned_cols=50  Identities=22%  Similarity=0.292  Sum_probs=36.7

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNAS   57 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s   57 (128)
                      ++..+|+..+++   +..    .+.|+++-|...|++.......|+....|.+||.|
T Consensus        19 ~t~~~l~~~~~~---~~~----~vs~~i~~L~~~glv~~~~~~~d~R~~~~~LT~~G   68 (68)
T PF13463_consen   19 MTQSDLAERLGI---SKS----TVSRIIKKLEEKGLVEKERDPHDKRSKRYRLTPAG   68 (68)
T ss_dssp             BEHHHHHHHTT-----HH----HHHHHHHHHHHTTSEEEEEESSCTTSEEEEE-HHH
T ss_pred             cCHHHHHHHHCc---CHH----HHHHHHHHHHHCCCEEecCCCCcCCeeEEEeCCCC
Confidence            467899999999   447    89999999999999966554333323579999975

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=96.70  E-value=0.003  Score=40.19  Aligned_cols=46  Identities=22%  Similarity=0.248  Sum_probs=37.4

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASK   58 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~   58 (128)
                      +|+.|||+.++++.   .    .++|+|+.|...|++.....     .+.|.+++-..
T Consensus        21 ~t~~~ia~~l~i~~---~----tv~r~l~~L~~~g~l~~~~~-----~~~y~l~~~~~   66 (91)
T smart00346       21 LTLAELAERLGLSK---S----TAHRLLNTLQELGYVEQDGQ-----NGRYRLGPKVL   66 (91)
T ss_pred             cCHHHHHHHhCCCH---H----HHHHHHHHHHHCCCeeecCC-----CCceeecHHHH
Confidence            47899999999955   7    89999999999999976531     46798887543

>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=96.67  E-value=0.0011  Score=38.47  Aligned_cols=33  Identities=30%  Similarity=0.497  Sum_probs=28.5

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceee
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQ   40 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~   40 (128)
                      +|+.|||+++|++.   .    .++|+|+.|+..|++..+
T Consensus        19 ~t~~eia~~~gl~~---s----tv~r~L~tL~~~g~v~~d   51 (52)
T PF09339_consen   19 LTLSEIARALGLPK---S----TVHRLLQTLVEEGYVERD   51 (52)
T ss_dssp             EEHHHHHHHHTS-H---H----HHHHHHHHHHHTTSEEEC
T ss_pred             CCHHHHHHHHCcCH---H----HHHHHHHHHHHCcCeecC
Confidence            37899999999955   7    899999999999999754

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.

>COG1414 IclR Transcriptional regulator [Transcription]

Probab=96.57  E-value=0.0032  Score=47.91  Aligned_cols=49  Identities=24%  Similarity=0.246  Sum_probs=41.4

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLL   61 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~   61 (128)
                      +++.|||+++|+|.   .    .++|+|..|+..|++..++.     .++|.+++-.-.|-
T Consensus        20 l~l~ela~~~glpk---s----T~~RlL~tL~~~G~v~~d~~-----~g~Y~Lg~~~~~lg   68 (246)
T COG1414          20 LSLAELAERLGLPK---S----TVHRLLQTLVELGYVEQDPE-----DGRYRLGPRLLELG   68 (246)
T ss_pred             CCHHHHHHHhCcCH---H----HHHHHHHHHHHCCCEEEcCC-----CCcEeehHHHHHHH
Confidence            47999999999966   7    89999999999999998762     46899999765553

>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional

Probab=96.49  E-value=0.0044  Score=47.10  Aligned_cols=49  Identities=24%  Similarity=0.288  Sum_probs=40.7

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLL   61 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~   61 (128)
                      +|+.|||+++|++.   .    .++|||+.|+..|++.....     .+.|.+++-...|.
T Consensus        29 l~l~eia~~lgl~k---s----tv~Rll~tL~~~G~l~~~~~-----~~~Y~lG~~~~~lg   77 (257)
T PRK15090         29 IGITELSQRVMMSK---S----TVYRFLQTMKTLGYVAQEGE-----SEKYSLTLKLFELG   77 (257)
T ss_pred             CCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCEEEcCC-----CCcEEecHHHHHHH
Confidence            57899999999965   7    89999999999999987642     47899998765554

>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=96.41  E-value=0.0031  Score=40.04  Aligned_cols=45  Identities=16%  Similarity=0.321  Sum_probs=34.5

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNA   56 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~   56 (128)
                      +|..|||+++++++   .    .|+++|+.|...|++.....    ..+.|.++.-
T Consensus        26 ~s~~eiA~~~~i~~---~----~l~kil~~L~~~Gli~s~~G----~~GGy~L~~~   70 (83)
T PF02082_consen   26 VSSKEIAERLGISP---S----YLRKILQKLKKAGLIESSRG----RGGGYRLARP   70 (83)
T ss_dssp             BEHHHHHHHHTS-H---H----HHHHHHHHHHHTTSEEEETS----TTSEEEESS-
T ss_pred             CCHHHHHHHHCcCH---H----HHHHHHHHHhhCCeeEecCC----CCCceeecCC
Confidence            47899999999965   8    99999999999999876541    1356776643

(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.

>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=96.25  E-value=0.0071  Score=36.10  Aligned_cols=42  Identities=19%  Similarity=0.278  Sum_probs=34.6

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechH
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATN   55 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~   55 (128)
                      +|..|||+.+|+++   .    .+.|+|+.|...|++....      .+.|.++|
T Consensus        26 ~s~~ela~~~g~s~---~----tv~r~l~~L~~~g~i~~~~------~~~~~l~~   67 (67)
T cd00092          26 LTRQEIADYLGLTR---E----TVSRTLKELEEEGLISRRG------RGKYRVNP   67 (67)
T ss_pred             cCHHHHHHHHCCCH---H----HHHHHHHHHHHCCCEEecC------CCeEEeCC
Confidence            47899999999944   7    8999999999999998653      25687764

>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein

Probab=96.20  E-value=0.013  Score=37.32  Aligned_cols=56  Identities=18%  Similarity=0.254  Sum_probs=43.0

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..+||..+++++   .    .+.|.++-|...|++.......+.....|.+|+.+..+...
T Consensus        25 ~~~~~la~~~~~s~---~----~i~~~l~~L~~~g~v~~~~~~~~~r~~~~~lT~~g~~~~~~   80 (101)
T smart00347       25 LSVSELAKRLGVSP---S----TVTRVLDRLEKKGLIRRLPSPEDRRSVLVSLTEEGRELIEE   80 (101)
T ss_pred             cCHHHHHHHHCCCc---h----hHHHHHHHHHHCCCeEecCCCCCCCeEEEEECHhHHHHHHH
Confidence            47889999999954   7    89999999999999986543221123479999999877654

>PRK09834 DNA-binding transcriptional activator MhpR; Provisional

Probab=96.20  E-value=0.0084  Score=45.80  Aligned_cols=50  Identities=20%  Similarity=0.230  Sum_probs=41.4

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhc
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLK   62 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~   62 (128)
                      +|+.|||+++|++.   .    .++|+|+.|...|++.....     .+.|.+++....|..
T Consensus        27 ls~~eia~~lgl~k---s----tv~RlL~tL~~~g~v~~~~~-----~~~Y~Lg~~~~~l~~   76 (263)
T PRK09834         27 ATVGLLAELTGLHR---T----TVRRLLETLQEEGYVRRSAS-----DDSFRLTLKVRQLSE   76 (263)
T ss_pred             CCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCEEEecC-----CCcEEEcHHHHHHHH
Confidence            47899999999955   7    89999999999999987642     468999987766543

>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein

Probab=96.18  E-value=0.0092  Score=33.24  Aligned_cols=33  Identities=21%  Similarity=0.303  Sum_probs=28.8

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceee
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQ   40 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~   40 (128)
                      +|..|||+.+++++   .    .+.|+|+.|...|++...
T Consensus         9 ~s~~~la~~l~~s~---~----tv~~~l~~L~~~g~l~~~   41 (48)
T smart00419        9 LTRQEIAELLGLTR---E----TVSRTLKRLEKEGLISRE   41 (48)
T ss_pred             cCHHHHHHHHCCCH---H----HHHHHHHHHHHCCCEEEe
Confidence            47899999999944   7    899999999999999754

>PRK11569 transcriptional repressor IclR; Provisional

Probab=96.13  E-value=0.0087  Score=46.04  Aligned_cols=48  Identities=15%  Similarity=0.181  Sum_probs=39.8

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL   60 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L   60 (128)
                      +|+.|||+.+|++.   .    .++|||+.|+..|++..+..     .++|.+.+-...|
T Consensus        44 ~~lseia~~lglpk---s----Tv~RlL~tL~~~G~l~~~~~-----~~~Y~lG~~l~~L   91 (274)
T PRK11569         44 VALTELAQQAGLPN---S----TTHRLLTTMQQQGFVRQVGE-----LGHWAIGAHAFIV   91 (274)
T ss_pred             cCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCEEEcCC-----CCeEecCHHHHHH
Confidence            58999999999965   7    89999999999999976542     4789998776554

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

Probab=96.06  E-value=0.012  Score=37.82  Aligned_cols=47  Identities=19%  Similarity=0.262  Sum_probs=40.2

Q ss_pred             HHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhc
Q 045905            3 LNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLK   62 (128)
Q Consensus         3 ~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~   62 (128)
                      +.|||..+++++   .    .+.|+++.|...|++....      ...|.+|+.++.+..
T Consensus         2 ~~ela~~l~is~---s----tvs~~l~~L~~~glI~r~~------~~~~~lT~~g~~~~~   48 (96)
T smart00529        2 TSEIAERLNVSP---P----TVTQMLKKLEKDGLVEYEP------YRGITLTEKGRRLAR   48 (96)
T ss_pred             HHHHHHHhCCCh---H----HHHHHHHHHHHCCCEEEcC------CCceEechhHHHHHH
Confidence            579999999954   8    9999999999999998765      357999999988764

iron dependent repressor

>PRK10163 DNA-binding transcriptional repressor AllR; Provisional

Probab=96.02  E-value=0.011  Score=45.47  Aligned_cols=49  Identities=10%  Similarity=0.057  Sum_probs=40.0

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLL   61 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~   61 (128)
                      +|+.|||+.+|++.   .    .++|||..|+..|++..+..     .+.|.+++--..|.
T Consensus        41 ~tl~eIa~~lglpk---S----tv~RlL~tL~~~G~l~~~~~-----~~~Y~lG~~l~~Lg   89 (271)
T PRK10163         41 SSVSDISLNLDLPL---S----TTFRLLKVLQAADFVYQDSQ-----LGWWHIGLGVFNVG   89 (271)
T ss_pred             cCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCEEEcCC-----CCeEEecHHHHHHH
Confidence            57899999999965   7    89999999999999976542     47899887665443

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

Probab=95.98  E-value=0.011  Score=44.71  Aligned_cols=47  Identities=23%  Similarity=0.295  Sum_probs=39.1

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLL   61 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~   61 (128)
                      +|+.|||+++|++.   .    .++|||..|+..|++..+       .+.|.+++.-..|.
T Consensus        25 ~~l~eia~~lglpk---s----T~~RlL~tL~~~G~l~~~-------~~~Y~lG~~~~~lg   71 (248)
T TIGR02431        25 LTLTDVAEATGLTR---A----AARRFLLTLVELGYVTSD-------GRLFWLTPRVLRLG   71 (248)
T ss_pred             CCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCEEeC-------CCEEEecHHHHHHH
Confidence            58999999999966   7    899999999999999753       36799998765553

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.

>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR

Probab=95.77  E-value=0.014  Score=40.32  Aligned_cols=45  Identities=13%  Similarity=0.168  Sum_probs=35.4

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNA   56 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~   56 (128)
                      +|.+|||+.+++++   .    .|.+||+.|...|++.....    ..|.|.++.-
T Consensus        26 ~s~~~ia~~~~ip~---~----~l~kil~~L~~~glv~s~~G----~~Ggy~l~~~   70 (135)
T TIGR02010        26 VTLADISERQGISL---S----YLEQLFAKLRKAGLVKSVRG----PGGGYQLGRP   70 (135)
T ss_pred             CcHHHHHHHHCcCH---H----HHHHHHHHHHHCCceEEEeC----CCCCEeccCC
Confidence            47899999999966   8    99999999999999975431    1345776654

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

>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR

Probab=95.74  E-value=0.027  Score=37.75  Aligned_cols=56  Identities=13%  Similarity=0.121  Sum_probs=43.7

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||..+++++   .    .+.|+++-|...|++.......|.....|.+|+.|+.+.+.
T Consensus        43 ~t~~ela~~~~~~~---~----tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT~~G~~~~~~   98 (118)
T TIGR02337        43 MEFTQLANQACILR---P----SLTGILARLERDGLVTRLKASNDQRRVYISLTPKGQALYAS   98 (118)
T ss_pred             cCHHHHHHHhCCCc---h----hHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHHHHHH
Confidence            47889999999944   7    89999999999999976543222212479999999988754

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.

>PRK03902 manganese transport transcriptional regulator; Provisional

Probab=95.72  E-value=0.023  Score=39.52  Aligned_cols=49  Identities=22%  Similarity=0.316  Sum_probs=40.6

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhc
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLK   62 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~   62 (128)
                      +++.|||..+++++   +    .+.++++.|...|++....      .+.|.+|+.|+.+..
T Consensus        23 ~~~~ela~~l~vs~---~----svs~~l~~L~~~Gli~~~~------~~~i~LT~~G~~~a~   71 (142)
T PRK03902         23 ARVSDIAEALSVHP---S----SVTKMVQKLDKDEYLIYEK------YRGLVLTPKGKKIGK   71 (142)
T ss_pred             cCHHHHHHHhCCCh---h----HHHHHHHHHHHCCCEEEec------CceEEECHHHHHHHH
Confidence            36789999999954   7    8999999999999987543      367999999987653

>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator)

Probab=95.46  E-value=0.02  Score=38.94  Aligned_cols=47  Identities=11%  Similarity=0.227  Sum_probs=36.1

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASK   58 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~   58 (128)
                      +|..|||+.+++++   .    .++++|+.|...|++.....    ..+.|.++.-..
T Consensus        26 ~s~~eia~~~~i~~---~----~v~~il~~L~~~gli~~~~g----~~ggy~l~~~~~   72 (132)
T TIGR00738        26 VSVKEIAERQGISR---S----YLEKILRTLRRAGLVESVRG----PGGGYRLARPPE   72 (132)
T ss_pred             CcHHHHHHHHCcCH---H----HHHHHHHHHHHCCcEEeccC----CCCCccCCCCHH
Confidence            47899999999965   8    99999999999999876431    134577765443

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.

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

Probab=95.36  E-value=0.024  Score=35.59  Aligned_cols=47  Identities=15%  Similarity=0.273  Sum_probs=36.9

Q ss_pred             CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhc
Q 045905            2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLK   62 (128)
Q Consensus         2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~   62 (128)
                      +..+|+..++++.   .    .+.+.+..|...|++...       .+.|.+|+-|+-+.+
T Consensus        21 ~~t~i~~~~~L~~---~----~~~~yL~~L~~~gLI~~~-------~~~Y~lTekG~~~l~   67 (77)
T PF14947_consen   21 KKTEIMYKANLNY---S----TLKKYLKELEEKGLIKKK-------DGKYRLTEKGKEFLE   67 (77)
T ss_dssp             -HHHHHTTST--H---H----HHHHHHHHHHHTTSEEEE-------TTEEEE-HHHHHHHH
T ss_pred             CHHHHHHHhCcCH---H----HHHHHHHHHHHCcCeeCC-------CCEEEECccHHHHHH
Confidence            4678999999944   7    899999999999999553       478999999988764

>PRK10857 DNA-binding transcriptional regulator IscR; Provisional

Probab=95.35  E-value=0.024  Score=40.76  Aligned_cols=45  Identities=11%  Similarity=0.183  Sum_probs=35.5

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNA   56 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~   56 (128)
                      +|++|||+++++|+   .    .|.+||+.|...|++.....    ..|.|.|..-
T Consensus        26 vs~~eIA~~~~ip~---~----~l~kIl~~L~~aGLv~s~rG----~~GGy~Lar~   70 (164)
T PRK10857         26 VPLADISERQGISL---S----YLEQLFSRLRKNGLVSSVRG----PGGGYLLGKD   70 (164)
T ss_pred             CcHHHHHHHHCcCH---H----HHHHHHHHHHHCCCEEeCCC----CCCCeeccCC
Confidence            58899999999966   8    99999999999999986532    1345776543

>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=95.16  E-value=0.02  Score=34.72  Aligned_cols=44  Identities=23%  Similarity=0.304  Sum_probs=33.9

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechH
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATN   55 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~   55 (128)
                      +|+.|||..++++.   .    .+++.|+-|...|++.....    ....|...+
T Consensus        23 ~t~~eIa~~l~i~~---~----~v~~~L~~L~~~GlV~~~~~----~~~~Y~a~~   66 (68)
T PF01978_consen   23 ATAEEIAEELGISR---S----TVYRALKSLEEKGLVEREEG----RPKVYRAVP   66 (68)
T ss_dssp             EEHHHHHHHHTSSH---H----HHHHHHHHHHHTTSEEEEEE----CCEEEEEE-
T ss_pred             CCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCEEEEcC----ceEEEEEeC
Confidence            47899999999944   7    89999999999999986652    134566544

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.

>COG1959 Predicted transcriptional regulator [Transcription]

Probab=95.10  E-value=0.032  Score=39.51  Aligned_cols=46  Identities=13%  Similarity=0.234  Sum_probs=36.5

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNAS   57 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s   57 (128)
                      +|+++||+..+++|   .    .|.|||..|...|++.-...    ..|.|.|..-.
T Consensus        26 ~s~~~IA~~~~is~---~----~L~kil~~L~kaGlV~S~rG----~~GGy~Lar~~   71 (150)
T COG1959          26 VSSAEIAERQGISP---S----YLEKILSKLRKAGLVKSVRG----KGGGYRLARPP   71 (150)
T ss_pred             ccHHHHHHHhCcCH---H----HHHHHHHHHHHcCCEEeecC----CCCCccCCCCh
Confidence            46899999999966   8    99999999999999976542    13567776544

>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed

Probab=95.00  E-value=0.034  Score=39.42  Aligned_cols=46  Identities=11%  Similarity=0.200  Sum_probs=36.2

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNAS   57 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s   57 (128)
                      +|..|||++.++++   .    .|.+||+.|...|++.-...    ..|.|.|+.--
T Consensus        25 ~s~~eIA~~~~is~---~----~L~kIl~~L~~aGlv~S~rG----~~GGy~La~~p   70 (153)
T PRK11920         25 SRIPEIARAYGVSE---L----FLFKILQPLVEAGLVETVRG----RNGGVRLGRPA   70 (153)
T ss_pred             CcHHHHHHHHCcCH---H----HHHHHHHHHHHCCCEEeecC----CCCCeeecCCH
Confidence            47899999999966   8    99999999999999976642    23567776543

>PRK11512 DNA-binding transcriptional repressor MarR; Provisional

Probab=94.91  E-value=0.057  Score=37.41  Aligned_cols=56  Identities=16%  Similarity=0.133  Sum_probs=43.8

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||..++++   +.    .+.|++.-|...|++......+|.-...+.+|+.|+.+...
T Consensus        55 ~t~~eLa~~l~i~---~~----tvsr~l~~Le~~GlI~R~~~~~DrR~~~l~LT~~G~~~~~~  110 (144)
T PRK11512         55 ITPVELKKVLSVD---LG----ALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTSGAAICEQ  110 (144)
T ss_pred             CCHHHHHHHHCCC---HH----HHHHHHHHHHHCCCEEeccCcccCCeeEeEEChhHHHHHHH
Confidence            5789999999994   48    99999999999999976543333222468999999988654

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

Probab=94.73  E-value=0.056  Score=32.07  Aligned_cols=49  Identities=24%  Similarity=0.342  Sum_probs=37.6

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL   60 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L   60 (128)
                      ++..||+..++++.   .    .++|.|+.|...|++......   ....|.+|+ ++.+
T Consensus        21 ~~~~ei~~~~~i~~---~----~i~~~l~~L~~~g~i~~~~~~---~~~~~~~~~-g~~~   69 (78)
T cd00090          21 LTVSELAERLGLSQ---S----TVSRHLKKLEEAGLVESRREG---RRVYYSLTD-AERL   69 (78)
T ss_pred             cCHHHHHHHHCcCH---h----HHHHHHHHHHHCCCeEEEEec---cEEEEEeCC-chHH
Confidence            47889999999944   7    899999999999999865421   136788887 5544

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.

>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial

Probab=94.66  E-value=0.036  Score=37.82  Aligned_cols=60  Identities=18%  Similarity=0.217  Sum_probs=41.2

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcCCCCcHHHHHHHhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDITLTVRSFLQAVLD   77 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~~~~s~~~~~~~~~~   77 (128)
                      +|..|||+++++++   .    .+.++|+.|...|++.....    ..+.|.+...      ....++.+++..+-+
T Consensus        26 ~s~~eia~~l~is~---~----~v~~~l~~L~~~Gli~~~~g----~~ggy~l~~~------~~~it~~~v~~~l~~   85 (130)
T TIGR02944        26 YSAAEIAEQTGLNA---P----TVSKILKQLSLAGIVTSKRG----VEGGYTLARA------PRDITVADIVKAVEG   85 (130)
T ss_pred             ccHHHHHHHHCcCH---H----HHHHHHHHHHHCCcEEecCC----CCCChhhcCC------ccccCHHHHHHHHcC
Confidence            47899999999955   8    99999999999999965431    1345766442      112246666555543

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.

>PRK03573 transcriptional regulator SlyA; Provisional

Probab=94.58  E-value=0.13  Score=35.54  Aligned_cols=56  Identities=14%  Similarity=0.217  Sum_probs=43.6

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||..+++++   .    .+.|++.-|...|++......+|.-...+.+|+.|+.+...
T Consensus        47 ~t~~eLa~~l~~~~---~----tvt~~v~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~~  102 (144)
T PRK03573         47 QSQIQLAKAIGIEQ---P----SLVRTLDQLEEKGLISRQTCASDRRAKRIKLTEKAEPLISE  102 (144)
T ss_pred             CCHHHHHHHhCCCh---h----hHHHHHHHHHHCCCEeeecCCCCcCeeeeEEChHHHHHHHH
Confidence            36789999999944   7    89999999999999976653333212468999999988764

>PRK11050 manganese transport regulator MntR; Provisional

Probab=94.49  E-value=0.074  Score=37.58  Aligned_cols=49  Identities=14%  Similarity=0.142  Sum_probs=40.8

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhc
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLK   62 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~   62 (128)
                      ++..|||+.+++++   .    .+.|.++.|...|++....      .+.+.+|+.|+.+..
T Consensus        52 ~t~~eLA~~l~is~---s----tVsr~l~~Le~~GlI~r~~------~~~v~LT~~G~~l~~  100 (152)
T PRK11050         52 ARQVDIAARLGVSQ---P----TVAKMLKRLARDGLVEMRP------YRGVFLTPEGEKLAQ  100 (152)
T ss_pred             CCHHHHHHHHCCCH---H----HHHHHHHHHHHCCCEEEec------CCceEECchHHHHHH
Confidence            47889999999944   7    8999999999999987554      356899999988854

>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=94.31  E-value=0.091  Score=33.73  Aligned_cols=54  Identities=20%  Similarity=0.277  Sum_probs=38.2

Q ss_pred             CHHHHHHhC-CCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhc
Q 045905            2 TLNELINAL-PFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLK   62 (128)
Q Consensus         2 S~~eLA~~~-~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~   62 (128)
                      ...||...+ ++++   .    .|.+-|+.|...|++...........-.|.+|+.|+.|..
T Consensus        20 rf~el~~~l~~is~---~----~L~~~L~~L~~~GLv~r~~~~~~p~~v~Y~LT~~G~~l~~   74 (90)
T PF01638_consen   20 RFSELQRRLPGISP---K----VLSQRLKELEEAGLVERRVYPEVPPRVEYSLTEKGKELLP   74 (90)
T ss_dssp             EHHHHHHHSTTS-H---H----HHHHHHHHHHHTTSEEEEEESSSSSEEEEEE-HHHHHHHH
T ss_pred             cHHHHHHhcchhHH---H----HHHHHHHHHHHcchhhcccccCCCCCCccCCCcCHHHHHH
Confidence            367899998 5743   7    8999999999999997653211111236999999998863

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.

>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family

Probab=94.24  E-value=0.11  Score=34.40  Aligned_cols=56  Identities=11%  Similarity=0.285  Sum_probs=42.8

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||..++++   ..    .+.|+++.|...|++....+.+|.-.-.+.+|+.|+-+.+.
T Consensus        44 ~t~~eL~~~l~~~---~s----tvs~~i~~Le~kg~I~r~~~~~D~R~~~i~lT~~G~~~~~~   99 (109)
T TIGR01889        44 LTLKEIIKEILIK---QS----ALVKIIKKLSKKGYLSKERSEDDERKVIISINKEQRSKIES   99 (109)
T ss_pred             CcHHHHHHHHCCC---HH----HHHHHHHHHHHCCCEeccCCcccCCeEEEEECHHHHHHHHH
Confidence            4789999999994   48    99999999999999976543332112358899999887653

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.

>PRK11014 transcriptional repressor NsrR; Provisional

Probab=94.15  E-value=0.069  Score=37.09  Aligned_cols=44  Identities=7%  Similarity=0.120  Sum_probs=34.3

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechH
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATN   55 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~   55 (128)
                      +|..|||+.+++++   .    .|+++|+.|...|++.....    ..+.|.++.
T Consensus        26 ~s~~~ia~~~~is~---~----~vrk~l~~L~~~Glv~s~~G----~~GG~~l~~   69 (141)
T PRK11014         26 TSISEVTEVYGVSR---N----HMVKIINQLSRAGYVTAVRG----KNGGIRLGK   69 (141)
T ss_pred             cCHHHHHHHHCcCH---H----HHHHHHHHHHhCCEEEEecC----CCCCeeecC
Confidence            36789999999955   8    99999999999999976542    134566654

>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]

Probab=94.07  E-value=0.12  Score=36.88  Aligned_cols=50  Identities=14%  Similarity=0.145  Sum_probs=41.5

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +...+||+.+++.|   +    .+..+++-|...|++....      .+.|.||+.|+.+...
T Consensus        25 ~~~~diA~~L~Vsp---~----sVt~ml~rL~~~GlV~~~~------y~gi~LT~~G~~~a~~   74 (154)
T COG1321          25 ARTKDIAERLKVSP---P----SVTEMLKRLERLGLVEYEP------YGGVTLTEKGREKAKE   74 (154)
T ss_pred             ccHHHHHHHhCCCc---H----HHHHHHHHHHHCCCeEEec------CCCeEEChhhHHHHHH
Confidence            35689999999955   7    7888999999999998765      4789999999876644

>PRK10870 transcriptional repressor MprA; Provisional

Probab=93.92  E-value=0.13  Score=37.17  Aligned_cols=56  Identities=16%  Similarity=0.141  Sum_probs=43.8

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||..+++++   .    .+.|++.-|...|++......+|.-...+.+|+.|+.+.+.
T Consensus        72 it~~eLa~~l~l~~---~----tvsr~v~rLe~kGlV~R~~~~~DrR~~~v~LT~~G~~~~~~  127 (176)
T PRK10870         72 IQPSELSCALGSSR---T----NATRIADELEKRGWIERRESDNDRRCLHLQLTEKGHEFLRE  127 (176)
T ss_pred             cCHHHHHHHHCCCH---H----HHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHH
Confidence            36789999999944   7    89999999999999976553333222468999999988865

>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor

Probab=93.64  E-value=0.15  Score=29.23  Aligned_cols=45  Identities=18%  Similarity=0.220  Sum_probs=34.4

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechH
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATN   55 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~   55 (128)
                      +|..||++.+++++   .    .+++.|+.|...|++.....   +....|.+|.
T Consensus        11 ~~~~~i~~~l~is~---~----~v~~~l~~L~~~g~i~~~~~---~~~~~~~~~~   55 (66)
T smart00418       11 LCVCELAEILGLSQ---S----TVSHHLKKLREAGLVESRRE---GKRVYYSLTD   55 (66)
T ss_pred             ccHHHHHHHHCCCH---H----HHHHHHHHHHHCCCeeeeec---CCEEEEEEch
Confidence            47889999999944   7    89999999999999975432   1134677766

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

Probab=93.56  E-value=0.13  Score=31.40  Aligned_cols=44  Identities=20%  Similarity=0.185  Sum_probs=33.9

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechH
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATN   55 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~   55 (128)
                      +|+.|||.++|++.   .    .++|+|--|-..|++.....    .++.|.++.
T Consensus        23 ~ta~eLa~~lgl~~---~----~v~r~L~~L~~~G~V~~~~~----~~~~W~i~~   66 (68)
T smart00550       23 STALQLAKNLGLPK---K----EVNRVLYSLEKKGKVCKQGG----TPPLWKLTD   66 (68)
T ss_pred             cCHHHHHHHHCCCH---H----HHHHHHHHHHHCCCEEecCC----CCCceEeec
Confidence            57899999999955   7    89999999999999865431    135676653

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

>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR

Probab=93.17  E-value=0.18  Score=37.09  Aligned_cols=56  Identities=20%  Similarity=0.227  Sum_probs=42.1

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeecc-CCCCc-ccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNF-GQNDQ-ERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~-~~~~~-~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.+++++   .    .++|.|..|...|++..... ...|. ...|.+|+.++.+...
T Consensus        16 ~t~~eLA~~lgis~---~----tV~~~L~~Le~~GlV~r~~~~~~~gRp~~~y~LT~~G~~~~~~   73 (203)
T TIGR02702        16 ATAAALAEALAISP---Q----AVRRHLKDLETEGLIEYEAVVQGMGRPQYHYQLSRQGREQFPQ   73 (203)
T ss_pred             CCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCeEEeecccCCCCCceEEEECcchhhhccc
Confidence            57899999999944   8    99999999999999975521 11121 2358999999876644

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.

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

Probab=93.12  E-value=0.081  Score=32.33  Aligned_cols=34  Identities=21%  Similarity=0.419  Sum_probs=28.5

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN   41 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~   41 (128)
                      +|+.|||..++++|   +    .|.-+|..|+.+|.+....
T Consensus        15 ~S~~eLa~~~~~s~---~----~ve~mL~~l~~kG~I~~~~   48 (69)
T PF09012_consen   15 VSLAELAREFGISP---E----AVEAMLEQLIRKGYIRKVD   48 (69)
T ss_dssp             EEHHHHHHHTT--H---H----HHHHHHHHHHCCTSCEEEE
T ss_pred             cCHHHHHHHHCcCH---H----HHHHHHHHHHHCCcEEEec
Confidence            47899999999954   8    9999999999999998664

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

>COG4742 Predicted transcriptional regulator [Transcription]

Probab=93.03  E-value=0.42  Score=36.93  Aligned_cols=49  Identities=18%  Similarity=0.316  Sum_probs=41.4

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      .|.+||-..+++++   .    .+.+=++-|...|++.+.+       +.|.||++|+.++..
T Consensus        27 kti~EI~~~l~vs~---~----ai~pqiKkL~~~~LV~~~~-------~~Y~LS~~G~iiv~k   75 (260)
T COG4742          27 KTIEEIKNELNVSS---S----AILPQIKKLKDKGLVVQEG-------DRYSLSSLGKIIVEK   75 (260)
T ss_pred             CCHHHHHHHhCCCc---H----HHHHHHHHHhhCCCEEecC-------CEEEecchHHHHHHH
Confidence            37899999999955   6    7777788899999998764       789999999999865

>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein

Probab=92.85  E-value=0.15  Score=37.43  Aligned_cols=46  Identities=15%  Similarity=0.215  Sum_probs=37.4

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNAS   57 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s   57 (128)
                      +|..|||+.+++++   .    .+.|.+..|...|++.....    ....|.+|+.|
T Consensus       158 ~s~~eia~~l~is~---s----tv~r~L~~Le~~GlI~r~~~----r~~~~~lT~~G  203 (203)
T TIGR01884       158 KSVKNIAKKLGKSL---S----TISRHLRELEKKGLVEQKGR----KGKRYSLTKLG  203 (203)
T ss_pred             cCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCEEEEcC----CccEEEeCCCC
Confidence            47899999999954   7    89999999999999987641    14679999864

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.

>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=92.75  E-value=0.12  Score=30.21  Aligned_cols=35  Identities=23%  Similarity=0.251  Sum_probs=29.2

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeecc
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNF   42 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~   42 (128)
                      +|..|||+.++++   +.    .+.|+++.|...|++.....
T Consensus        22 ~t~~~la~~l~~~---~~----~vs~~v~~L~~~Glv~r~~~   56 (62)
T PF12802_consen   22 LTQSELAERLGIS---KS----TVSRIVKRLEKKGLVERERD   56 (62)
T ss_dssp             EEHHHHHHHHTS----HH----HHHHHHHHHHHTTSEEEEE-
T ss_pred             cCHHHHHHHHCcC---HH----HHHHHHHHHHHCCCEEEeCC
Confidence            3688999999994   48    99999999999999976653

...

>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=92.70  E-value=0.16  Score=28.57  Aligned_cols=31  Identities=26%  Similarity=0.366  Sum_probs=25.6

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcce
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFA   38 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~   38 (128)
                      +|..|||.++|+   ...    .+.+.++-|...|++.
T Consensus        18 ~t~~ela~~~~i---s~~----tv~~~l~~L~~~g~I~   48 (48)
T PF13412_consen   18 ITQKELAEKLGI---SRS----TVNRYLKKLEEKGLIE   48 (48)
T ss_dssp             S-HHHHHHHHTS----HH----HHHHHHHHHHHTTSEE
T ss_pred             CCHHHHHHHhCC---CHH----HHHHHHHHHHHCcCcC
Confidence            578999999999   447    8999999999999863

...

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

Probab=92.65  E-value=0.2  Score=32.58  Aligned_cols=42  Identities=10%  Similarity=-0.030  Sum_probs=33.4

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceech
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVAT   54 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T   54 (128)
                      +|-.|||+.+|+++   .    .+.|+|..|...|++.....     -+.|+.+
T Consensus        48 is~~eLa~~~g~sr---~----tVsr~L~~Le~~GlI~r~~~-----~~~~~~n   89 (95)
T TIGR01610        48 VTATVIAELTGLSR---T----HVSDAIKSLARRRIIFRQGM-----MGIVGVN   89 (95)
T ss_pred             cCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCeeeecC-----CceeecC
Confidence            47789999999944   7    89999999999999975531     3566665

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

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

Probab=92.59  E-value=0.25  Score=37.20  Aligned_cols=54  Identities=13%  Similarity=0.123  Sum_probs=43.2

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcCC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDI   64 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~~   64 (128)
                      +|..|||+.+++   +.+    .+.|+++.|...|++......   ....+.+|+.|+.+....
T Consensus        22 IS~~eLA~~L~i---S~~----Tvsr~Lk~LEe~GlI~R~~~~---r~~~v~LTekG~~ll~~~   75 (217)
T PRK14165         22 ISSSEFANHTGT---SSK----TAARILKQLEDEGYITRTIVP---RGQLITITEKGLDVLYNE   75 (217)
T ss_pred             cCHHHHHHHHCc---CHH----HHHHHHHHHHHCCCEEEEEcC---CceEEEECHHHHHHHHHH
Confidence            578999999999   448    999999999999999755421   136799999999777543

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

Probab=92.52  E-value=0.22  Score=31.49  Aligned_cols=55  Identities=15%  Similarity=0.195  Sum_probs=38.9

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCc-ccceechHhhhhhhc
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQ-ERSYVATNASKLLLK   62 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~-~~~y~~T~~s~~L~~   62 (128)
                      ++..||.+.++++   ..    .|.+-|+.|...|++.......+.. ...|.+|+.|+....
T Consensus        15 ~~f~~L~~~l~lt---~g----~Ls~hL~~Le~~GyV~~~k~~~~~~p~t~~~lT~~Gr~~~~   70 (80)
T PF13601_consen   15 ATFSELKEELGLT---DG----NLSKHLKKLEEAGYVEVEKEFEGRRPRTWYSLTDKGREAFE   70 (80)
T ss_dssp             EEHHHHHHHTT-----HH----HHHHHHHHHHHTTSEEEEEE-SSS--EEEEEE-HHHHHHHH
T ss_pred             CCHHHHHHHhCcC---HH----HHHHHHHHHHHCCCEEEEEeccCCCCeEEEEECHHHHHHHH
Confidence            3678999999994   47    9999999999999997654322111 236999999986543

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=91.74  E-value=0.38  Score=27.48  Aligned_cols=33  Identities=18%  Similarity=0.140  Sum_probs=28.5

Q ss_pred             CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905            2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN   41 (128)
Q Consensus         2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~   41 (128)
                      |..|||+.++++.   .    .++|.|+.|...|++....
T Consensus        22 s~~~la~~~~vs~---~----tv~~~l~~L~~~g~i~~~~   54 (60)
T smart00345       22 SERELAAQLGVSR---T----TVREALSRLEAEGLVQRRP   54 (60)
T ss_pred             CHHHHHHHHCCCH---H----HHHHHHHHHHHCCCEEEec
Confidence            6889999999944   7    8999999999999986543

>COG2345 Predicted transcriptional regulator [Transcription]

Probab=91.62  E-value=0.41  Score=36.07  Aligned_cols=57  Identities=18%  Similarity=0.200  Sum_probs=42.6

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCC-CCc-ccceechHhhhhhhcCC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQ-NDQ-ERSYVATNASKLLLKDI   64 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~-~~~-~~~y~~T~~s~~L~~~~   64 (128)
                      +|+.|||+++|+++   .    .++|-|-.|...|++....... -|- ...|.+|.-++......
T Consensus        26 ~sa~elA~~Lgis~---~----avR~HL~~Le~~Glv~~~~~~~g~GRP~~~y~Lt~~g~~~f~~~   84 (218)
T COG2345          26 VSADELAEELGISP---M----AVRRHLDDLEAEGLVEVERQQGGRGRPAKLYRLTEKGREQFPKR   84 (218)
T ss_pred             ccHHHHHHHhCCCH---H----HHHHHHHHHHhCcceeeeeccCCCCCCceeeeecccchhhcchh
Confidence            58999999999966   8    9999999999999886542211 121 24799999987755443

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

Probab=91.33  E-value=0.38  Score=28.05  Aligned_cols=32  Identities=19%  Similarity=0.185  Sum_probs=27.4

Q ss_pred             CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceee
Q 045905            2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQ   40 (128)
Q Consensus         2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~   40 (128)
                      |..+||..++++.   .    .+++.|..|...|++...
T Consensus        27 ~~~~la~~~~is~---~----~v~~~l~~L~~~G~i~~~   58 (66)
T cd07377          27 SERELAEELGVSR---T----TVREALRELEAEGLVERR   58 (66)
T ss_pred             CHHHHHHHHCCCH---H----HHHHHHHHHHHCCCEEec
Confidence            4789999999944   7    899999999999998644

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

>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=91.14  E-value=0.18  Score=29.83  Aligned_cols=34  Identities=24%  Similarity=0.286  Sum_probs=29.0

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN   41 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~   41 (128)
                      +|+.|||+.+++++   .    .+++-|+.|...|++....
T Consensus        25 ~t~~ela~~l~~~~---~----t~s~hL~~L~~aGli~~~~   58 (61)
T PF12840_consen   25 MTVSELAEELGISQ---S----TVSYHLKKLEEAGLIEVER   58 (61)
T ss_dssp             BEHHHHHHHHTS-H---H----HHHHHHHHHHHTTSEEEEE
T ss_pred             CCHHHHHHHHCCCH---H----HHHHHHHHHHHCCCeEEec
Confidence            47899999999954   7    8999999999999998664

...

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=90.96  E-value=0.46  Score=32.88  Aligned_cols=35  Identities=26%  Similarity=0.424  Sum_probs=29.8

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeecc
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNF   42 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~   42 (128)
                      +|.+|||+.++.   +..    .++|.|+-|+..|++.....
T Consensus        43 ~tvdelae~lnr---~rS----tv~rsl~~L~~~GlV~Rek~   77 (126)
T COG3355          43 LTVDELAEILNR---SRS----TVYRSLQNLLEAGLVEREKV   77 (126)
T ss_pred             cCHHHHHHHHCc---cHH----HHHHHHHHHHHcCCeeeeee
Confidence            478999999999   557    89999999999999965543

>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=90.57  E-value=0.53  Score=30.68  Aligned_cols=52  Identities=15%  Similarity=0.098  Sum_probs=37.6

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHH----------HHhcCcc-eeeccCCCCcccceechHhhhhhhc
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWI----------LVHSGFF-AQQNFGQNDQERSYVATNASKLLLK   62 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~----------L~~~gvf-~e~~~~~~~~~~~y~~T~~s~~L~~   62 (128)
                      +++.|||..+++++   .    .+.-.|+-          |+.+|++ .+...  . +...|.+|+-|+.+++
T Consensus        26 ~~~~eIar~v~~~~---s----nV~GaL~G~g~rY~~e~SLv~lGLV~~~~~~--~-g~k~Y~lT~~G~~~~~   88 (90)
T PF07381_consen   26 AYPSEIARSVGSDY---S----NVLGALRGDGKRYNKEDSLVGLGLVEEEEEK--G-GFKYYRLTEKGKRIAE   88 (90)
T ss_pred             CCHHHHHHHHCCCH---H----HHHHHHhcCCCCcCcchhHHHcCCeeEeeec--C-CeeEEEeChhhhhHHh
Confidence            46789999999944   7    77676664          8999999 33321  1 1458999999987653

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=90.49  E-value=0.44  Score=26.47  Aligned_cols=34  Identities=18%  Similarity=0.246  Sum_probs=29.0

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN   41 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~   41 (128)
                      +|..+|+..+++++   .    .++|.|..|...|++....
T Consensus        15 ~s~~~l~~~l~~s~---~----tv~~~l~~L~~~g~i~~~~   48 (53)
T smart00420       15 VSVEELAELLGVSE---M----TIRRDLNKLEEQGLLTRVH   48 (53)
T ss_pred             cCHHHHHHHHCCCH---H----HHHHHHHHHHHCCCEEEee
Confidence            47899999999944   7    8999999999999987553

>COG1846 MarR Transcriptional regulators [Transcription]

Probab=90.40  E-value=0.48  Score=30.76  Aligned_cols=54  Identities=19%  Similarity=0.214  Sum_probs=42.4

Q ss_pred             HHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcCC
Q 045905            4 NELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDI   64 (128)
Q Consensus         4 ~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~~   64 (128)
                      .|||..+++++   .    .+.|+++-|...|++......+|.-...+.+|+.|+.+....
T Consensus        40 ~~la~~l~i~~---~----~vt~~l~~Le~~glv~r~~~~~DrR~~~l~lT~~G~~~~~~~   93 (126)
T COG1846          40 KELAERLGLDR---S----TVTRLLKRLEDKGLIERLRDPEDRRAVLVRLTEKGRELLEQL   93 (126)
T ss_pred             HHHHHHHCCCH---H----HHHHHHHHHHHCCCeeecCCccccceeeEEECccHHHHHHHh
Confidence            79999999944   8    999999999999999766543332124699999999887653

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

Probab=90.37  E-value=0.29  Score=25.81  Aligned_cols=30  Identities=23%  Similarity=0.334  Sum_probs=23.7

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcc
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFF   37 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf   37 (128)
                      +|-.|||..+|+.+   .    .+.|+|..|-..|+.
T Consensus         3 mtr~diA~~lG~t~---E----TVSR~l~~l~~~glI   32 (32)
T PF00325_consen    3 MTRQDIADYLGLTR---E----TVSRILKKLERQGLI   32 (32)
T ss_dssp             --HHHHHHHHTS-H---H----HHHHHHHHHHHTTSE
T ss_pred             cCHHHHHHHhCCcH---H----HHHHHHHHHHHcCCC
Confidence            57789999999944   7    999999999888863

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 ....

>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=90.07  E-value=0.3  Score=28.32  Aligned_cols=34  Identities=24%  Similarity=0.320  Sum_probs=28.8

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN   41 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~   41 (128)
                      +|..|||..+++   +..    .+.|+++-|...|++....
T Consensus        18 ~~~~~la~~~~~---~~~----~~t~~i~~L~~~g~I~r~~   51 (59)
T PF01047_consen   18 ITQSELAEKLGI---SRS----TVTRIIKRLEKKGLIERER   51 (59)
T ss_dssp             EEHHHHHHHHTS----HH----HHHHHHHHHHHTTSEEEEE
T ss_pred             CCHHHHHHHHCC---Chh----HHHHHHHHHHHCCCEEecc
Confidence            367899999999   448    9999999999999997554

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 ....

>PRK13777 transcriptional regulator Hpr; Provisional

Probab=88.64  E-value=1.1  Score=32.84  Aligned_cols=56  Identities=14%  Similarity=0.201  Sum_probs=43.0

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||..+.+++   +    .+.|++.-|...|++......+|.-.....+|+.|+.+...
T Consensus        60 itq~eLa~~l~l~~---s----Tvtr~l~rLE~kGlI~R~~~~~DrR~~~I~LTekG~~l~~~  115 (185)
T PRK13777         60 ASISEIAKFGVMHV---S----TAFNFSKKLEERGYLTFSKKEDDKRNTYIELTEKGEELLLE  115 (185)
T ss_pred             cCHHHHHHHHCCCH---h----hHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHH
Confidence            47889999999844   7    89999999999999976543333212458999999988754

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=88.22  E-value=0.67  Score=30.20  Aligned_cols=31  Identities=23%  Similarity=0.290  Sum_probs=27.9

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcce
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFA   38 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~   38 (128)
                      +|..|||+.+|+++   .    .++|.++.|...|++.
T Consensus        18 ~~~~~la~~l~~s~---~----tv~~~l~~L~~~g~i~   48 (108)
T smart00344       18 ISLAELAKKVGLSP---S----TVHNRVKRLEEEGVIK   48 (108)
T ss_pred             CCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCee
Confidence            47899999999955   7    8999999999999987

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

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

Probab=88.16  E-value=0.68  Score=40.33  Aligned_cols=46  Identities=15%  Similarity=0.207  Sum_probs=37.2

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechH
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATN   55 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~   55 (128)
                      .|++|||+.+|+++   +    .|+|.|-+....||+++.+...+  .+.|..++
T Consensus       617 wt~eelse~l~ip~---~----~lrrrL~fWi~~GvL~e~~~~s~--tgt~T~iE  662 (765)
T KOG2165|consen  617 WTLEELSESLGIPV---P----ALRRRLSFWIQKGVLREEPIISD--TGTLTVIE  662 (765)
T ss_pred             ccHHHHHHHhCCCH---H----HHHHHHHHHHHcCeeecCCCCCC--Cceeeecc
Confidence            47899999999976   8    99999999999999998763211  35677766

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

Probab=88.10  E-value=1  Score=29.67  Aligned_cols=48  Identities=23%  Similarity=0.365  Sum_probs=33.7

Q ss_pred             CCHHHHHHhCCC--CCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceech
Q 045905            1 MTLNELINALPF--HPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVAT   54 (128)
Q Consensus         1 ~S~~eLA~~~~~--~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T   54 (128)
                      +|++||.+++.-  +..+..    .+||.|..|+..|++......+  +..+|.++
T Consensus        17 ~sa~ei~~~l~~~~~~i~~~----TVYR~L~~L~~~Gli~~~~~~~--~~~~y~~~   66 (116)
T cd07153          17 LTAEEIYERLRKKGPSISLA----TVYRTLELLEEAGLVREIELGD--GKARYELN   66 (116)
T ss_pred             CCHHHHHHHHHhcCCCCCHH----HHHHHHHHHHhCCCEEEEEeCC--CceEEEeC
Confidence            478899888842  112557    8999999999999998765311  13467664

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.

>COG1733 Predicted transcriptional regulators [Transcription]

Probab=88.08  E-value=1.3  Score=30.13  Aligned_cols=52  Identities=21%  Similarity=0.317  Sum_probs=38.3

Q ss_pred             HHHHHHhCC-CCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhh
Q 045905            3 LNELINALP-FHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLL   61 (128)
Q Consensus         3 ~~eLA~~~~-~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~   61 (128)
                      ..||-..++ +++   .    .|.+=||.|...|++......+....-.|++|+.|+-|.
T Consensus        39 F~eL~r~i~~Is~---k----~Ls~~Lk~Le~~Glv~R~~~~~~PprveY~LT~~G~~L~   91 (120)
T COG1733          39 FNELRRSIGGISP---K----MLSRRLKELEEDGLVERVVYPEEPPRVEYRLTEKGRDLL   91 (120)
T ss_pred             HHHHHHHccccCH---H----HHHHHHHHHHHCCCEEeeecCCCCceeEEEEhhhHHHHH
Confidence            568888877 644   7    899999999999999765432111124599999998775

>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=87.30  E-value=1.2  Score=26.96  Aligned_cols=34  Identities=21%  Similarity=0.284  Sum_probs=29.2

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN   41 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~   41 (128)
                      +|-.|||..+|+..   .    .+.|+|+.|...|++.-..
T Consensus        29 lt~~~iA~~~g~sr---~----tv~r~l~~l~~~g~I~~~~   62 (76)
T PF13545_consen   29 LTQEEIADMLGVSR---E----TVSRILKRLKDEGIIEVKR   62 (76)
T ss_dssp             SSHHHHHHHHTSCH---H----HHHHHHHHHHHTTSEEEET
T ss_pred             CCHHHHHHHHCCCH---H----HHHHHHHHHHHCCCEEEcC
Confidence            46789999999944   7    8999999999999998553

...

>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional

Probab=86.94  E-value=3.3  Score=28.10  Aligned_cols=46  Identities=17%  Similarity=0.224  Sum_probs=35.6

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNA   56 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~   56 (128)
                      +++.||++.+++++   +    .+.+-|+.|...|++.....   |....|.+.+.
T Consensus        31 ~~v~ela~~l~lsq---s----tvS~HL~~L~~AGLV~~~r~---Gr~~~Y~l~~~   76 (117)
T PRK10141         31 LCVCDLCTALDQSQ---P----KISRHLALLRESGLLLDRKQ---GKWVHYRLSPH   76 (117)
T ss_pred             cCHHHHHHHHCcCH---H----HHHHHHHHHHHCCceEEEEE---cCEEEEEECch
Confidence            36789999999955   7    89999999999999976542   11346888763

>COG1378 Predicted transcriptional regulators [Transcription]

Probab=86.90  E-value=1.4  Score=33.68  Aligned_cols=50  Identities=20%  Similarity=0.253  Sum_probs=40.6

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLL   61 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~   61 (128)
                      +|+.||+...|+|-   +    .+|.+||-|...|++....    |.+..|..-+...++.
T Consensus        31 ~tA~eis~~sgvP~---~----kvY~vl~sLe~kG~v~~~~----g~P~~y~av~p~~~i~   80 (247)
T COG1378          31 ATAKEISEASGVPR---P----KVYDVLRSLEKKGLVEVIE----GRPKKYRAVPPEELIE   80 (247)
T ss_pred             ccHHHHHHHcCCCc---h----hHHHHHHHHHHCCCEEeeC----CCCceEEeCCHHHHHH
Confidence            58999999999954   6    8999999999999997653    2257898888877554

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

Probab=86.84  E-value=0.97  Score=32.52  Aligned_cols=44  Identities=16%  Similarity=0.143  Sum_probs=37.2

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNAS   57 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s   57 (128)
                      +|..+||+.++++   .+    .+.|.+..|...+|+....      .+.|-.+|-=
T Consensus        76 ~t~~~ia~~l~iS---~~----Tv~r~ik~L~e~~iI~k~~------~G~Y~iNP~~  119 (165)
T PF05732_consen   76 ATQKEIAEKLGIS---KP----TVSRAIKELEEKNIIKKIR------NGAYMINPNF  119 (165)
T ss_pred             eeHHHHHHHhCCC---HH----HHHHHHHHHHhCCcEEEcc------CCeEEECcHH
Confidence            3678999999994   37    8999999999999998664      4789999974

; GO: 0006260 DNA replication, 0006276 plasmid maintenance

>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=86.51  E-value=0.64  Score=26.07  Aligned_cols=30  Identities=23%  Similarity=0.300  Sum_probs=25.9

Q ss_pred             CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcce
Q 045905            2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFA   38 (128)
Q Consensus         2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~   38 (128)
                      ++.||++.+++   +..    .+.+-|+.|...|++.
T Consensus        17 ~~~el~~~l~~---s~~----~vs~hL~~L~~~glV~   46 (47)
T PF01022_consen   17 TVSELAEELGL---SQS----TVSHHLKKLREAGLVE   46 (47)
T ss_dssp             EHHHHHHHHTS----HH----HHHHHHHHHHHTTSEE
T ss_pred             chhhHHHhccc---cch----HHHHHHHHHHHCcCee
Confidence            57899999999   447    8999999999999874

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 ....

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

Probab=86.31  E-value=2.1  Score=27.19  Aligned_cols=48  Identities=17%  Similarity=0.097  Sum_probs=36.9

Q ss_pred             CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcce-eeccCCCCcccceechHhhhhhh
Q 045905            2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFA-QQNFGQNDQERSYVATNASKLLL   61 (128)
Q Consensus         2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~-e~~~~~~~~~~~y~~T~~s~~L~   61 (128)
                      ...+||+.++.+|   .    .++-.|..|-.+|++. .+.+     .+.|-+|..+-.+.
T Consensus        25 gSk~ia~~l~~s~---a----TIRN~M~~Le~lGlve~~p~~-----s~GriPT~~aYr~~   73 (78)
T PF03444_consen   25 GSKTIAEELGRSP---A----TIRNEMADLEELGLVESQPHP-----SGGRIPTDKAYRAL   73 (78)
T ss_pred             CHHHHHHHHCCCh---H----HHHHHHHHHHHCCCccCCCCC-----CCCCCcCHHHHHHH
Confidence            4578999999854   8    9999999999999996 3322     35688888875444

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=86.26  E-value=0.98  Score=26.94  Aligned_cols=34  Identities=15%  Similarity=0.261  Sum_probs=28.2

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN   41 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~   41 (128)
                      ++..+||+.+++.|   +    .+..+++-|...|++....
T Consensus        23 v~~~~iA~~L~vs~---~----tvt~ml~~L~~~GlV~~~~   56 (60)
T PF01325_consen   23 VRTKDIAERLGVSP---P----TVTEMLKRLAEKGLVEYEP   56 (60)
T ss_dssp             BBHHHHHHHHTS-H---H----HHHHHHHHHHHTTSEEEET
T ss_pred             ccHHHHHHHHCCCh---H----HHHHHHHHHHHCCCEEecC
Confidence            36789999999944   8    8999999999999997653

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 ....

>PRK09334 30S ribosomal protein S25e; Provisional

Probab=86.19  E-value=1.1  Score=28.92  Aligned_cols=34  Identities=12%  Similarity=0.088  Sum_probs=29.0

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN   41 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~   41 (128)
                      +|...||+++++.-   .    .-+|+||.|...|++....
T Consensus        42 ITps~lserlkI~~---S----lAr~~Lr~L~~kG~Ik~V~   75 (86)
T PRK09334         42 VTPYTLASKYGIKI---S----VAKKVLRELEKRGVLVLYS   75 (86)
T ss_pred             EcHHHHHHHhcchH---H----HHHHHHHHHHHCCCEEEEe
Confidence            58899999999944   7    8899999999999987553

>PF13814 Replic_Relax: Replication-relaxation

Probab=86.04  E-value=2  Score=30.69  Aligned_cols=59  Identities=20%  Similarity=0.143  Sum_probs=43.6

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccC---CC-CcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFG---QN-DQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~---~~-~~~~~y~~T~~s~~L~~~   63 (128)
                      +|.++|+..+..+.....    .++|.|+-|...|++......   .. ..+..|.+|+.|..++.+
T Consensus        10 lt~~Qi~~l~~~~~~~~~----~~~rrL~~L~~~glv~~~~~~~~~~~g~~~~vy~Lt~~G~~~l~~   72 (191)
T PF13814_consen   10 LTTDQIARLLFPSSKSER----TARRRLKRLRELGLVDRFRRRVGARGGSQPYVYYLTPAGARLLAD   72 (191)
T ss_pred             cCHHHHHHHHcCCCcchH----HHHHHHHHHhhCCcEEeecccccccCCCcceEEEECHHHHHHHHh
Confidence            578899998887553345    699999999999998765431   11 124689999999888753

>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=85.93  E-value=1.1  Score=27.16  Aligned_cols=34  Identities=24%  Similarity=0.381  Sum_probs=28.1

Q ss_pred             CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905            2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN   41 (128)
Q Consensus         2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~   41 (128)
                      |+.|||+.+|+.  .+.    .+.+.|+.|...|++....
T Consensus        27 t~rEIa~~~g~~--S~~----tv~~~L~~Le~kG~I~r~~   60 (65)
T PF01726_consen   27 TVREIAEALGLK--STS----TVQRHLKALERKGYIRRDP   60 (65)
T ss_dssp             -HHHHHHHHTSS--SHH----HHHHHHHHHHHTTSEEEGC
T ss_pred             CHHHHHHHhCCC--ChH----HHHHHHHHHHHCcCccCCC
Confidence            789999999994  246    8999999999999997654

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.

>PRK06474 hypothetical protein; Provisional

Probab=85.63  E-value=1.5  Score=31.83  Aligned_cols=53  Identities=21%  Similarity=0.308  Sum_probs=39.0

Q ss_pred             CCHHHHHHhCC-CCCCCchhhhhhHHHHHHHHHhcCcceeeccCC--CCcccceechHhhhhh
Q 045905            1 MTLNELINALP-FHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQ--NDQERSYVATNASKLL   60 (128)
Q Consensus         1 ~S~~eLA~~~~-~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~--~~~~~~y~~T~~s~~L   60 (128)
                      +|+.||+..++ +   ...    .++|.|+.|...|++.......  ++.+..|.+++-+-.+
T Consensus        27 ~ta~el~~~l~~i---s~a----TvYrhL~~L~e~GLI~~~~~~~~~~~~ek~y~~~~~~~~~   82 (178)
T PRK06474         27 LTPLELVKILKDV---PQA----TLYRHLQTMVDSGILHVVKEKKVRSVSEKYYAINEEDAKI   82 (178)
T ss_pred             CCHHHHHHHhcCC---CHH----HHHHHHHHHHHCCCEEEeecccccCceeEEEEeccceeee
Confidence            47899999984 5   336    8999999999999998764321  1224679888877554

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

Probab=85.57  E-value=1.4  Score=26.15  Aligned_cols=33  Identities=15%  Similarity=0.136  Sum_probs=27.4

Q ss_pred             CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905            2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN   41 (128)
Q Consensus         2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~   41 (128)
                      |..+||++++++.   .    .+++.|+.|...|++.-..
T Consensus        26 s~~~la~~~~vsr---~----tvr~al~~L~~~g~i~~~~   58 (64)
T PF00392_consen   26 SERELAERYGVSR---T----TVREALRRLEAEGLIERRP   58 (64)
T ss_dssp             -HHHHHHHHTS-H---H----HHHHHHHHHHHTTSEEEET
T ss_pred             CHHHHHHHhccCC---c----HHHHHHHHHHHCCcEEEEC
Confidence            6789999999944   7    8999999999999997554

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 ....

>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional

Probab=85.50  E-value=1.4  Score=36.85  Aligned_cols=53  Identities=26%  Similarity=0.249  Sum_probs=43.0

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcCC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDI   64 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~~   64 (128)
                      +|..|||++++++   ..    .+.|++.-|...|++.....    ....|.||+-|+.+++..
T Consensus        21 ~s~~eLA~~l~l~---~~----tVt~~i~~Le~kGlV~~~~~----~~~~i~LTeeG~~~~~~g   73 (489)
T PRK04172         21 ATLEELAEKLGLP---PE----AVMRAAEWLEEKGLVKVEER----VEEVYVLTEEGKKYAEEG   73 (489)
T ss_pred             CCHHHHHHHhCcC---HH----HHHHHHHHHHhCCCEEEEee----eEEEEEECHHHHHHHHhc
Confidence            4788999999994   48    99999999999998875431    135799999999888754

>COG1497 Predicted transcriptional regulator [Transcription]

Probab=85.49  E-value=1.7  Score=33.45  Aligned_cols=81  Identities=19%  Similarity=0.184  Sum_probs=56.3

Q ss_pred             CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcCCCCcHHHHHHHh-cChhh
Q 045905            2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDITLTVRSFLQAV-LDPIL   80 (128)
Q Consensus         2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~~~~s~~~~~~~~-~~~~~   80 (128)
                      ...|||.++|+.+   +    .+.--++-|+..|+..+..      .+.|..|.-|.-.+.++-..++.|+... ..-..
T Consensus        27 ~q~eIA~~lgiT~---Q----aVsehiK~Lv~eG~i~~~g------R~~Y~iTkkG~e~l~~~~~dlr~f~~ev~~~l~~   93 (260)
T COG1497          27 KQKEIAKKLGITL---Q----AVSEHIKELVKEGLIEKEG------RGEYEITKKGAEWLLEQLSDLRRFSEEVELVLDY   93 (260)
T ss_pred             CHHHHHHHcCCCH---H----HHHHHHHHHHhccceeecC------CeeEEEehhHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            4579999999944   7    8999999999999998764      4689999999644333222366665555 22245


Q ss_pred             HHHHHhHHHh-hhcCC
Q 045905           81 TTPCQHVTTW-FQNDD   95 (128)
Q Consensus        81 ~~~~~~l~~~-~~~g~   95 (128)
                      ...|..+..- +++|+
T Consensus        94 ~~vw~AIA~edI~~Gd  109 (260)
T COG1497          94 VMVWTAIAKEDIKEGD  109 (260)
T ss_pred             HHHHHHhhHhhhccCC
Confidence            6677776554 45554

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

Probab=84.83  E-value=1.4  Score=25.83  Aligned_cols=28  Identities=29%  Similarity=0.278  Sum_probs=19.1

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHH
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWIL   31 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L   31 (128)
                      +|+.|||+.+|+.+   .-+-+.|+|..+-+
T Consensus        24 ~tl~elA~~lgis~---st~~~~LRrae~kl   51 (53)
T PF04967_consen   24 ITLEELAEELGISK---STVSEHLRRAERKL   51 (53)
T ss_pred             CCHHHHHHHhCCCH---HHHHHHHHHHHHHH
Confidence            58999999999954   42333566665544

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

>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=84.52  E-value=0.76  Score=25.64  Aligned_cols=22  Identities=23%  Similarity=0.496  Sum_probs=16.3

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHH
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMW   29 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR   29 (128)
                      +|..|||..+|+.   ..    .|+|+++
T Consensus        22 ~si~~IA~~~gvs---r~----TvyR~l~   43 (45)
T PF02796_consen   22 MSIAEIAKQFGVS---RS----TVYRYLN   43 (45)
T ss_dssp             --HHHHHHHTTS----HH----HHHHHHC
T ss_pred             CCHHHHHHHHCcC---HH----HHHHHHh
Confidence            4789999999994   37    8888874

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 ....

>TIGR00122 birA_repr_reg BirA biotin operon repressor domain

Probab=84.14  E-value=2.2  Score=25.65  Aligned_cols=47  Identities=19%  Similarity=0.128  Sum_probs=33.6

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL   60 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L   60 (128)
                      +|..|||+++++..   .    .++|-++.|-..|+..+..      ...|.+.+...+|
T Consensus        14 ~~~~eLa~~l~vS~---~----tv~~~l~~L~~~g~~i~~~------~~g~~l~~~~~ll   60 (69)
T TIGR00122        14 FSGEKLGEALGMSR---T----AVNKHIQTLREWGVDVLTV------GKGYRLPPPIPLL   60 (69)
T ss_pred             cCHHHHHHHHCCCH---H----HHHHHHHHHHHCCCeEEec------CCceEecCccccC
Confidence            36789999999943   7    8999999999999865443      2446665544444

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.

>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=84.10  E-value=1.4  Score=25.88  Aligned_cols=34  Identities=15%  Similarity=0.234  Sum_probs=29.5

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN   41 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~   41 (128)
                      +|+.|||+.+++.+   .    -++|=|..|...|++....
T Consensus        15 ~s~~ela~~~~VS~---~----TiRRDl~~L~~~g~i~r~~   48 (57)
T PF08220_consen   15 VSVKELAEEFGVSE---M----TIRRDLNKLEKQGLIKRTH   48 (57)
T ss_pred             EEHHHHHHHHCcCH---H----HHHHHHHHHHHCCCEEEEc
Confidence            47899999999955   7    8999999999999987654

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

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

Probab=83.79  E-value=1.5  Score=29.33  Aligned_cols=34  Identities=15%  Similarity=0.159  Sum_probs=29.4

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN   41 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~   41 (128)
                      ||...||+++++.-   .    +-+++||.|...|++....
T Consensus        60 ITp~~lserlkI~~---S----lAr~~Lr~L~~kG~Ik~V~   93 (105)
T PF03297_consen   60 ITPSVLSERLKING---S----LARKALRELESKGLIKPVS   93 (105)
T ss_dssp             ECHHHHHHHHCCSC---H----HHHHHHHHHHHCCSSEEEE
T ss_pred             eeHHHHHHhHhhHH---H----HHHHHHHHHHHCCCEEEEe
Confidence            58899999999944   7    8899999999999997654

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.

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

Probab=83.51  E-value=1.2  Score=26.95  Aligned_cols=33  Identities=15%  Similarity=0.147  Sum_probs=27.6

Q ss_pred             CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905            2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN   41 (128)
Q Consensus         2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~   41 (128)
                      +..|||+.+|++   ..    ..+++|..|...|.+...+
T Consensus        17 ~T~eiA~~~gls---~~----~aR~yL~~Le~eG~V~~~~   49 (62)
T PF04703_consen   17 KTREIADALGLS---IY----QARYYLEKLEKEGKVERSP   49 (62)
T ss_dssp             EHHHHHHHHTS----HH----HHHHHHHHHHHCTSEEEES
T ss_pred             CHHHHHHHhCCC---HH----HHHHHHHHHHHCCCEEEec
Confidence            568999999994   36    8999999999999887654

>PF13730 HTH_36: Helix-turn-helix domain

Probab=83.16  E-value=1.9  Score=24.58  Aligned_cols=29  Identities=21%  Similarity=0.212  Sum_probs=25.0

Q ss_pred             CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcc
Q 045905            2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFF   37 (128)
Q Consensus         2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf   37 (128)
                      |.+.||+.+|+.   ..    .+.|.++.|...|++
T Consensus        27 S~~~la~~~g~s---~~----Tv~~~i~~L~~~G~I   55 (55)
T PF13730_consen   27 SQETLAKDLGVS---RR----TVQRAIKELEEKGLI   55 (55)
T ss_pred             CHHHHHHHHCcC---HH----HHHHHHHHHHHCcCC
Confidence            678999999994   47    899999999998864

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

Probab=82.20  E-value=2  Score=34.98  Aligned_cols=34  Identities=12%  Similarity=0.233  Sum_probs=29.6

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN   41 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~   41 (128)
                      .|.+||++++++++   .    .++++|..|...|++.+.+
T Consensus       311 ~t~~~La~~l~~~~---~----~v~~iL~~L~~agLI~~~~  344 (412)
T PRK04214        311 LDVDEIRRLEPMGY---D----ELGELLCELARIGLLRRGE  344 (412)
T ss_pred             CCHHHHHHHhCCCH---H----HHHHHHHHHHhCCCeEecC
Confidence            47899999999955   7    8999999999999998654

>PF14394 DUF4423: Domain of unknown function (DUF4423)

Probab=82.04  E-value=2  Score=30.99  Aligned_cols=43  Identities=19%  Similarity=0.234  Sum_probs=35.6

Q ss_pred             CHHHHHHhC--CCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhh
Q 045905            2 TLNELINAL--PFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNAS   57 (128)
Q Consensus         2 S~~eLA~~~--~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s   57 (128)
                      ...+||.++  +++.   .    -++.-|.+|...|++...+      ++.|..|.-+
T Consensus        41 d~~~iak~l~p~is~---~----ev~~sL~~L~~~gli~k~~------~g~y~~t~~~   85 (171)
T PF14394_consen   41 DPEWIAKRLRPKISA---E----EVRDSLEFLEKLGLIKKDG------DGKYVQTDKS   85 (171)
T ss_pred             CHHHHHHHhcCCCCH---H----HHHHHHHHHHHCCCeEECC------CCcEEEecce
Confidence            467899999  6633   5    7889999999999998776      4789999876

>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=81.36  E-value=2.5  Score=30.87  Aligned_cols=33  Identities=18%  Similarity=0.320  Sum_probs=28.3

Q ss_pred             CHHHHHHhC-CCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905            2 TLNELINAL-PFHPIKAQYVAQYVYRFMWILVHSGFFAQQN   41 (128)
Q Consensus         2 S~~eLA~~~-~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~   41 (128)
                      |-.+|+..+ |+++   .    .|+|.++.|+..|++....
T Consensus        72 SN~~La~r~~G~s~---~----tlrR~l~~LveaGLI~rrD  105 (177)
T PF03428_consen   72 SNAQLAERLNGMSE---R----TLRRHLARLVEAGLIVRRD  105 (177)
T ss_pred             CHHHHHHHHcCCCH---H----HHHHHHHHHHHCCCeeecc
Confidence            567899999 8955   7    8999999999999987654

They may be involved in plasmid replication and stabilisation functions.

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

Probab=81.33  E-value=2  Score=28.71  Aligned_cols=34  Identities=12%  Similarity=0.024  Sum_probs=28.6

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN   41 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~   41 (128)
                      +|...||++.|++-   .    .-+++||.|...|++....
T Consensus        60 VTpy~la~r~gI~~---S----vAr~vLR~LeeeGvv~lvs   93 (107)
T COG4901          60 VTPYVLASRYGING---S----VARIVLRHLEEEGVVQLVS   93 (107)
T ss_pred             ecHHHHHHHhccch---H----HHHHHHHHHHhCCceeeec
Confidence            57889999999944   7    8899999999999987543

>PRK00215 LexA repressor; Validated

Probab=81.30  E-value=2.4  Score=30.91  Aligned_cols=34  Identities=24%  Similarity=0.349  Sum_probs=29.4

Q ss_pred             CCHHHHHHhCCC-CCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905            1 MTLNELINALPF-HPIKAQYVAQYVYRFMWILVHSGFFAQQN   41 (128)
Q Consensus         1 ~S~~eLA~~~~~-~~~~~~~~~~~L~RlLR~L~~~gvf~e~~   41 (128)
                      +|+.|||+.+|+ +.   .    .+.|+|+.|...|++....
T Consensus        24 ~s~~ela~~~~~~~~---~----tv~~~l~~L~~~g~i~~~~   58 (205)
T PRK00215         24 PSRREIADALGLRSP---S----AVHEHLKALERKGFIRRDP   58 (205)
T ss_pred             CCHHHHHHHhCCCCh---H----HHHHHHHHHHHCCCEEeCC
Confidence            378899999999 65   6    8999999999999997654

>PRK05638 threonine synthase; Validated

Probab=81.17  E-value=2.8  Score=34.49  Aligned_cols=55  Identities=25%  Similarity=0.210  Sum_probs=39.7

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhc
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLK   62 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~   62 (128)
                      ++..||++.++.+. ...    .+++.|+.|...|++.....  ++....|.+|+.++.+..
T Consensus       385 ~~~~el~~~l~~~~-s~~----~v~~hL~~Le~~GLV~~~~~--~g~~~~Y~Lt~~g~~~l~  439 (442)
T PRK05638        385 MYGYEIWKALGKPL-KYQ----AVYQHIKELEELGLIEEAYR--KGRRVYYKLTEKGRRLLE  439 (442)
T ss_pred             ccHHHHHHHHcccC-Ccc----hHHHHHHHHHHCCCEEEeec--CCCcEEEEECcHHHHHHH
Confidence            35789999998211 346    89999999999999965321  121346999999987754

>PRK06266 transcription initiation factor E subunit alpha; Validated

Probab=80.57  E-value=2.3  Score=30.91  Aligned_cols=34  Identities=12%  Similarity=0.165  Sum_probs=29.4

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN   41 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~   41 (128)
                      +|.+|||..+|++   ..    .++|+|..|...|++....
T Consensus        37 ~tdeeLA~~Lgi~---~~----~VRk~L~~L~e~gLv~~~r   70 (178)
T PRK06266         37 VTDEEIAEQTGIK---LN----TVRKILYKLYDARLADYKR   70 (178)
T ss_pred             cCHHHHHHHHCCC---HH----HHHHHHHHHHHCCCeEEee
Confidence            5789999999994   48    9999999999999998443

>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=80.16  E-value=3.5  Score=23.43  Aligned_cols=33  Identities=21%  Similarity=0.161  Sum_probs=26.1

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceee
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQ   40 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~   40 (128)
                      +|..|||+.+++   ...    .++|-|..|-..|+.-+.
T Consensus        16 it~~eLa~~l~v---S~r----Ti~~~i~~L~~~~~~I~~   48 (55)
T PF08279_consen   16 ITAKELAEELGV---SRR----TIRRDIKELREWGIPIES   48 (55)
T ss_dssp             BEHHHHHHHCTS----HH----HHHHHHHHHHHTT-EEEE
T ss_pred             cCHHHHHHHhCC---CHH----HHHHHHHHHHHCCCeEEe
Confidence            478999999999   447    899999999999944443

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=80.04  E-value=2.4  Score=29.70  Aligned_cols=33  Identities=21%  Similarity=0.234  Sum_probs=28.1

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceee
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQ   40 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~   40 (128)
                      .|+.|||+.+|=   |..    .|.|=||.|...||+.-.
T Consensus        79 ~Si~ElAe~vgR---dv~----nvhr~Ls~l~~~GlI~fe  111 (144)
T COG4190          79 ASINELAELVGR---DVK----NVHRTLSTLADLGLIFFE  111 (144)
T ss_pred             ccHHHHHHHhCc---chH----HHHHHHHHHHhcCeEEEe
Confidence            478999999998   458    999999999999977543

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	128
2qyo_A	357	Crystal Structure Of Isoflavone O-Methyltransferase		5e-08
1fp2_A	352	Crystal Structure Analysis Of Isoflavone O-Methyltr		8e-06
1zg3_A	358	Crystal Structure Of The Isoflavanone 4'-O-Methyltr		1e-05
1zga_A	357	Crystal Structure Of Isoflavanone 4'-o-methyltransf		1e-05
1zgj_A	354	Crystal Structure Of Isoflavanone 4'-O-Methyltransf		1e-05
1fpx_A	352	Crystal Structure Analysis Of Selenomethionine Subs		7e-05

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 35/111 (31%), Positives = 54/111 (48%), Gaps = 8/111 (7%)
Query: 1   MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQ-QNFGQNDQERSYVATNASKL 59
           +TL+ L++ L     K   V     R M  L H+GFF    N    ++E +Y  T AS+L
Sbjct: 52  ITLSNLVSILQIPSTKVDNVQ----RLMRYLAHNGFFEIITNQELENEEEAYALTVASEL 107
Query: 60  LLKDITLTVRSFLQAVLDPILTTPCQHVTTWFQNDDLRCLTRHMG---WHF 107
           L+K   L +   ++ VLDP L+T   ++  W   +DL     ++G   W F
Sbjct: 108 LVKGTELCLAPMVECVLDPTLSTSFHNLKKWVYEEDLTLFAVNLGCDLWEF 158

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

Iteration: 1
 Score = 45.4 bits (106), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 27/84 (32%), Positives = 39/84 (46%), Gaps = 4/84 (4%)
Query: 24  VYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDITLTVRSFLQAVLDPILTTP 83
           V R M  L H+GFF         +E SY  T AS+LL++   L +   ++ VLDP L+  
Sbjct: 71  VRRLMRYLAHNGFFEIIT----KEEESYALTVASELLVRGSDLCLAPMVECVLDPTLSGS 126
Query: 84  CQHVTTWFQNDDLRCLTRHMGWHF 107
              +  W   +DL      +G  F
Sbjct: 127 YHELKKWIYEEDLTLFGVTLGSGF 150

>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 = 44.7 bits (104), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 39/128 (30%), Positives = 58/128 (45%), Gaps = 14/128 (10%)
Query: 1   MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQ----QNFGQNDQERSYVATNA 56
           MTL+EL ++L  HP K   +    +RF+ +L H+GFFA+       G  ++E +Y  T  
Sbjct: 46  MTLSELASSLKLHPSKVNIL----HRFLRLLTHNGFFAKTIVKGKEGDEEEEIAYSLTPP 101
Query: 57  SKLLLKDITLTVRSFLQAVLDPILTTPCQHVTTWFQNDD----LRCLTRHMGWHFESILG 112
           SKLL+      + S ++  L P           WF  D       C T    W F  +  
Sbjct: 102 SKLLISGKPTCLSSIVKGALHPSSLDMWSSSKKWFNEDKEQTLFECATGESFWDF--LNK 159
Query: 113 TSQRSTIS 120
            S+ ST+S
Sbjct: 160 DSESSTLS 167

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 39/128 (30%), Positives = 58/128 (45%), Gaps = 14/128 (10%)
Query: 1   MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQ----QNFGQNDQERSYVATNA 56
           MTL+EL ++L  HP K   +    +RF+ +L H+GFFA+       G  ++E +Y  T  
Sbjct: 45  MTLSELASSLKLHPSKVNIL----HRFLRLLTHNGFFAKTIVKGKEGDEEEEIAYSLTPP 100
Query: 57  SKLLLKDITLTVRSFLQAVLDPILTTPCQHVTTWFQNDD----LRCLTRHMGWHFESILG 112
           SKLL+      + S ++  L P           WF  D       C T    W F  +  
Sbjct: 101 SKLLISGKPTCLSSIVKGALHPSSLDMWSSSKKWFNEDKEQTLFECATGESFWDF--LNK 158
Query: 113 TSQRSTIS 120
            S+ ST+S
Sbjct: 159 DSESSTLS 166

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 39/128 (30%), Positives = 58/128 (45%), Gaps = 14/128 (10%)
Query: 1   MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQ----QNFGQNDQERSYVATNA 56
           MTL+EL ++L  HP K   +    +RF+ +L H+GFFA+       G  ++E +Y  T  
Sbjct: 42  MTLSELASSLKLHPSKVNIL----HRFLRLLTHNGFFAKTIVKGKEGDEEEEIAYSLTPP 97
Query: 57  SKLLLKDITLTVRSFLQAVLDPILTTPCQHVTTWFQNDD----LRCLTRHMGWHFESILG 112
           SKLL+      + S ++  L P           WF  D       C T    W F  +  
Sbjct: 98  SKLLISGKPTCLSSIVKGALHPSSLDMWSSSKKWFNEDKEQTLFECATGESFWDF--LNK 155
Query: 113 TSQRSTIS 120
            S+ ST+S
Sbjct: 156 DSESSTLS 163

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

Iteration: 1
 Score = 42.4 bits (98), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 26/84 (30%), Positives = 38/84 (45%), Gaps = 4/84 (4%)
Query: 24  VYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDITLTVRSFLQAVLDPILTTP 83
           V R    L H+GFF         +E SY  T AS+LL++   L +   ++ VLDP L+  
Sbjct: 71  VRRLXRYLAHNGFFEIIT----KEEESYALTVASELLVRGSDLCLAPXVECVLDPTLSGS 126
Query: 84  CQHVTTWFQNDDLRCLTRHMGWHF 107
              +  W   +DL      +G  F
Sbjct: 127 YHELKKWIYEEDLTLFGVTLGSGF 150

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	128
1zg3_A	358	Isoflavanone 4'-O-methyltransferase; rossman fold,	2e-16
1fp1_D	372	Isoliquiritigenin 2'-O-methyltransferase; protein-	2e-14
1fp2_A	352	Isoflavone O-methyltransferase; protein-product co	2e-14
3reo_A	368	(ISO)eugenol O-methyltransferase; directed evoluti	2e-13
3gwz_A	369	MMCR; methyltransferase, mitomycin, S-adenosyl met	6e-13
3lst_A	348	CALO1 methyltransferase; calicheamicin, enediyne,	1e-12
3p9c_A	364	Caffeic acid O-methyltransferase; S-adenosylmethio	2e-10
3i53_A	332	O-methyltransferase; CO-complex, rossmann-like fol	2e-09
1qzz_A	374	RDMB, aclacinomycin-10-hydroxylase; anthracycline,	3e-09
1tw3_A	360	COMT, carminomycin 4-O-methyltransferase; anthracy	4e-09
2ip2_A	334	Probable phenazine-specific methyltransferase; pyo	3e-08
2r3s_A	335	Uncharacterized protein; methyltransferase domain,	1e-06
1x19_A	359	CRTF-related protein; methyltransferase, bacterioc	6e-06
3dp7_A	363	SAM-dependent methyltransferase; structural genomi	7e-06

>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 = 73.0 bits (179), Expect = 2e-16
 Identities = 36/118 (30%), Positives = 53/118 (44%), Gaps = 15/118 (12%)

Query: 1   MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNF----GQNDQERSYVATNA 56
           MTL+EL ++L  HP K   +    +RF+ +L H+GFFA+       G  ++E +Y  T  
Sbjct: 46  MTLSELASSLKLHPSKVNIL----HRFLRLLTHNGFFAKTIVKGKEGDEEEEIAYSLTPP 101

Query: 57  SKLLLKDITLTVRSFLQAVLDPILTTPCQHVTTWFQNDDLRCLTRHMGWHFESILGTS 114
           SKLL+      + S ++  L P           WF  D  + L       FE   G S
Sbjct: 102 SKLLISGKPTCLSSIVKGALHPSSLDMWSSSKKWFNEDKEQTL-------FECATGES 152

>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 = 67.2 bits (164), Expect = 2e-14
 Identities = 18/98 (18%), Positives = 34/98 (34%), Gaps = 4/98 (4%)

Query: 1   MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQND--QERSYVATNASK 58
           M+ +E+ + LP     +      + R + +L              D   ER Y  +   K
Sbjct: 63  MSPSEIASKLPASTQHSDL-PNRLDRMLRLLASYSVLTSTTRTIEDGGAERVYGLSMVGK 121

Query: 59  LLLKDITL-TVRSFLQAVLDPILTTPCQHVTTWFQNDD 95
            L+ D +   + SF   +  P L     +      ++D
Sbjct: 122 YLVPDESRGYLASFTTFLCYPALLQVWMNFKEAVVDED 159

>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 = 66.7 bits (163), Expect = 2e-14
 Identities = 32/114 (28%), Positives = 49/114 (42%), Gaps = 16/114 (14%)

Query: 1   MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL 60
           ++L+ L++ L     K   V     R M  L H+GFF         +E SY  T AS+LL
Sbjct: 52  ISLSNLVSILQVPSSKIGNV----RRLMRYLAHNGFFEIIT----KEEESYALTVASELL 103

Query: 61  LKDITLTVRSFLQAVLDPILTTPCQHVTTWFQNDDLRCLTRHMGWHFESILGTS 114
           ++   L +   ++ VLDP L+     +  W   +DL          F   LG+ 
Sbjct: 104 VRGSDLCLAPMVECVLDPTLSGSYHELKKWIYEEDLT--------LFGVTLGSG 149

>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 = 64.5 bits (157), Expect = 2e-13
 Identities = 17/98 (17%), Positives = 32/98 (32%), Gaps = 6/98 (6%)

Query: 1   MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFA--QQNFGQNDQERSYVATNASK 58
           ++  E+   LP    +A      + R + +L          +       ER Y      K
Sbjct: 60  ISPAEIAAQLPTTNPEA---PVMLDRVLRLLASYSVVTYTLRELPSGKVERLYGLAPVCK 116

Query: 59  LLLKDI-TLTVRSFLQAVLDPILTTPCQHVTTWFQNDD 95
            L K+   +++  FL    D +L  P  ++        
Sbjct: 117 FLTKNEDGVSLAPFLLLATDKVLLEPWFYLKDAILEGG 154

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

 Score = 63.1 bits (154), Expect = 6e-13
 Identities = 16/95 (16%), Positives = 28/95 (29%), Gaps = 12/95 (12%)

Query: 1   MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL 60
            T   L  A   H        Q + R + +L   G F          +  +     S +L
Sbjct: 72  RTATALAEATGAHE-------QTLRRLLRLLATVGVFDD-----LGHDDLFAQNALSAVL 119

Query: 61  LKDITLTVRSFLQAVLDPILTTPCQHVTTWFQNDD 95
           L D    V +  +    P      + +T   +  +
Sbjct: 120 LPDPASPVATDARFQAAPWHWRAWEQLTHSVRTGE 154

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

 Score = 61.9 bits (151), Expect = 1e-12
 Identities = 13/95 (13%), Positives = 26/95 (27%), Gaps = 14/95 (14%)

Query: 1   MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL 60
            T  EL  A              + R + +L       +        +  +  T+    L
Sbjct: 56  RTPAELAAATGTDA-------DALRRVLRLLAVRDVVRES-------DGRFALTDKGAAL 101

Query: 61  LKDITLTVRSFLQAVLDPILTTPCQHVTTWFQNDD 95
             D  +  R+ +    D +  T    V +    + 
Sbjct: 102 RSDSPVPARAGILMFTDTMFWTMSHRVASALGPER 136

>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 = 55.6 bits (134), Expect = 2e-10
 Identities = 15/97 (15%), Positives = 29/97 (29%), Gaps = 5/97 (5%)

Query: 1   MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQ--QNFGQNDQERSYVATNASK 58
           +T  E+   LP            V R + +L          +        RSY A    K
Sbjct: 57  LTPTEVAAKLPSAANPEA--PDMVDRILRLLASYNVVTCLVEEGKDGRLSRSYGAAPVCK 114

Query: 59  LLLKDI-TLTVRSFLQAVLDPILTTPCQHVTTWFQND 94
            L  +   +++ +      D +L     ++     + 
Sbjct: 115 FLTPNEDGVSMAALALMNQDKVLMESWYYLKDAVLDG 151

>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 = 53.0 bits (128), Expect = 2e-09
 Identities = 16/96 (16%), Positives = 26/96 (27%), Gaps = 14/96 (14%)

Query: 1   MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL 60
            T  E+ +A   H          + R +  LV  G F +      D +  Y  T   + L
Sbjct: 39  RTAAEIASAAGAHA-------DSLDRLLRHLVAVGLFTR------DGQGVYGLTEFGEQL 85

Query: 61  LKDITLTVRSFLQAVLDPILTTPC-QHVTTWFQNDD 95
             D     R +L               +    +   
Sbjct: 86  RDDHAAGKRKWLDMNSAVGRGDLGFVELAHSIRTGQ 121

>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 = 52.4 bits (126), Expect = 3e-09
 Identities = 16/95 (16%), Positives = 23/95 (24%), Gaps = 12/95 (12%)

Query: 1   MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL 60
            TL  L +    HP       Q + R +  L   G           Q R    T    LL
Sbjct: 50  DTLAGLADRTDTHP-------QALSRLVRHLTVVGVLEGGE----KQGRPLRPTRLGMLL 98

Query: 61  LKDITLTVRSFLQAVLDPILTTPC-QHVTTWFQND 94
                   R++L               +    +  
Sbjct: 99  ADGHPAQQRAWLDLNGAVSHADLAFTGLLDVVRTG 133

>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 = 51.9 bits (125), Expect = 4e-09
 Identities = 14/96 (14%), Positives = 25/96 (26%), Gaps = 14/96 (14%)

Query: 1   MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL 60
            T+  L       P       + + R +  LV  G   +      D    +V T   +LL
Sbjct: 53  RTVKALAARTDTRP-------EALLRLIRHLVAIGLLEE------DAPGEFVPTEVGELL 99

Query: 61  LKDITLTVRSFLQAVLDPILTTPC-QHVTTWFQNDD 95
             D     R++                +    +   
Sbjct: 100 ADDHPAAQRAWHDLTQAVARADISFTRLPDAIRTGR 135

>2ip2_A Probable phenazine-specific methyltransferase; pyocyanin, phenazine-1-carboxy PHZM; 1.80A {Pseudomonas aeruginosa} Length = 334

 Score = 49.2 bits (118), Expect = 3e-08
 Identities = 15/95 (15%), Positives = 27/95 (28%), Gaps = 15/95 (15%)

Query: 1   MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL 60
            +   L  A+           + ++R M +LV    F        D    Y  T  S  L
Sbjct: 42  DSDETLAAAVGSDA-------ERIHRLMRLLVAFEIFQG------DTRDGYANTPTSH-L 87

Query: 61  LKDITLTVRSFLQAVLDPILTTPCQHVTTWFQNDD 95
           L+D+  + R  +    +               +  
Sbjct: 88  LRDVEGSFRDMVLFYGEE-FHAAWTPACEALLSGT 121

>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 = 45.1 bits (107), Expect = 1e-06
 Identities = 15/96 (15%), Positives = 26/96 (27%), Gaps = 15/96 (15%)

Query: 1   MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL 60
            +   L                        LV  GF  +       Q   Y  T+ S + 
Sbjct: 40  ESSQSLAQKCQTSERGM-------RMLCDYLVIIGFMTK-------QAEGYRLTSDSAMF 85

Query: 61  L-KDITLTVRSFLQAVLDPILTTPCQHVTTWFQNDD 95
           L +     V   ++ +L P++T     +T       
Sbjct: 86  LDRQSKFYVGDAIEFLLSPMITNGFNDLTAAVLKGG 121

>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 = 42.8 bits (101), Expect = 6e-06
 Identities = 6/83 (7%), Positives = 14/83 (16%), Gaps = 14/83 (16%)

Query: 1   MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL 60
             L  L       P         +   +  L               ++  +  T  +  +
Sbjct: 65  KDLATLAADTGSVP-------PRLEMLLETLRQMRVINL-------EDGKWSLTEFADYM 110

Query: 61  LKDITLTVRSFLQAVLDPILTTP 83
                         V   +    
Sbjct: 111 FSPTPKEPNLHQTPVAKAMAFLA 133

>3dp7_A SAM-dependent methyltransferase; structural genomics, protein structure initiative, NEW YORK structural genomix research; 2.33A {Bacteroides vulgatus} Length = 363

 Score = 42.8 bits (101), Expect = 7e-06
 Identities = 16/107 (14%), Positives = 23/107 (21%), Gaps = 17/107 (15%)

Query: 1   MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL 60
            TL E+          A          +   +  G           +E  YV   A   L
Sbjct: 51  YTLQEISGRTGLTRYAA-------QVLLEASLTIGTILL-------EEDRYVLAKAGWFL 96

Query: 61  LKDITLTVRSFLQAVLDPILTTPCQHVTTWFQNDDLRCLTRHMGWHF 107
           L D    +          +      H+     N     L     W  
Sbjct: 97  LND---KMARVNMEFNHDVNYQGLFHLEEALLNGRPEGLKVFGEWPT 140

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	128
3p9c_A	364	Caffeic acid O-methyltransferase; S-adenosylmethio	99.77
1zg3_A	358	Isoflavanone 4'-O-methyltransferase; rossman fold,	99.74
3lst_A	348	CALO1 methyltransferase; calicheamicin, enediyne,	99.74
3reo_A	368	(ISO)eugenol O-methyltransferase; directed evoluti	99.74
1fp2_A	352	Isoflavone O-methyltransferase; protein-product co	99.73
1fp1_D	372	Isoliquiritigenin 2'-O-methyltransferase; protein-	99.7
3gwz_A	369	MMCR; methyltransferase, mitomycin, S-adenosyl met	99.7
2ip2_A	334	Probable phenazine-specific methyltransferase; pyo	99.69
3i53_A	332	O-methyltransferase; CO-complex, rossmann-like fol	99.68
1qzz_A	374	RDMB, aclacinomycin-10-hydroxylase; anthracycline,	99.6
3dp7_A	363	SAM-dependent methyltransferase; structural genomi	99.59
1tw3_A	360	COMT, carminomycin 4-O-methyltransferase; anthracy	99.56
4a6d_A	353	Hydroxyindole O-methyltransferase; melatonin, circ	99.47
2r3s_A	335	Uncharacterized protein; methyltransferase domain,	99.43
1x19_A	359	CRTF-related protein; methyltransferase, bacterioc	99.3
3mcz_A	352	O-methyltransferase; adomet_mtases, S-adenosylmeth	99.22
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	96.72
2hzt_A	107	Putative HTH-type transcriptional regulator YTCD;	96.69
3b73_A	111	PHIH1 repressor-like protein; winged-helix-turn-he	96.57
1z7u_A	112	Hypothetical protein EF0647; winged-helix-turn-hel	96.5
3bja_A	139	Transcriptional regulator, MARR family, putative;	96.49
2gxg_A	146	146AA long hypothetical transcriptional regulator;	96.47
4a5n_A	131	Uncharacterized HTH-type transcriptional regulato;	96.38
1ub9_A	100	Hypothetical protein PH1061; helix-turn-helix moti	96.33
2nnn_A	140	Probable transcriptional regulator; structural gen	96.3
3k0l_A	162	Repressor protein; helix-turn-helix, structural ge	96.28
2fsw_A	107	PG_0823 protein; alpha-beta structure, helix-turn-	96.26
3oop_A	143	LIN2960 protein; protein structure initiative, PSI	96.26
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	96.26
2f2e_A	146	PA1607; transcription factor, helix-TRUN-helix, AP	96.25
1on2_A	142	Transcriptional regulator MNTR; helix-turn-helix,	96.23
3df8_A	111	Possible HXLR family transcriptional factor; APC89	96.21
2eth_A	154	Transcriptional regulator, putative, MAR family; M	96.18
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	96.18
2fbh_A	146	Transcriptional regulator PA3341; MARR, transcript	96.16
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	96.13
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	96.13
3jw4_A	148	Transcriptional regulator, MARR/EMRR family; DNA-b	96.1
3nrv_A	148	Putative transcriptional regulator (MARR/EMRR FAM;	96.09
3g3z_A	145	NMB1585, transcriptional regulator, MARR family; t	96.09
3mq0_A	275	Transcriptional repressor of the blcabc operon; he	96.08
2rdp_A	150	Putative transcriptional regulator MARR; PFAM PF01	96.07
2hr3_A	147	Probable transcriptional regulator; MCSG, structur	96.06
1yyv_A	131	Putative transcriptional regulator; reductive meth	96.06
2qww_A	154	Transcriptional regulator, MARR family; YP_013417.	96.04
2qvo_A	95	Uncharacterized protein AF_1382; PSI, structural g	96.03
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	96.02
3cdh_A	155	Transcriptional regulator, MARR family; helix-turn	96.02
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	96.0
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	96.0
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	95.99
2bv6_A	142	MGRA, HTH-type transcriptional regulator MGRA; mul	95.98
3r4k_A	260	Transcriptional regulator, ICLR family; DNA/RNA-bi	95.91
1r7j_A	95	Conserved hypothetical protein SSO10A; winged heli	95.9
1z91_A	147	Organic hydroperoxide resistance transcriptional;	95.9
3e6m_A	161	MARR family transcriptional regulator; APC88769, s	95.89
1y0u_A	96	Arsenical resistance operon repressor, putative; s	95.89
1lj9_A	144	Transcriptional regulator SLYA; HTH DNA binding pr	95.88
3boq_A	160	Transcriptional regulator, MARR family; MARR famil	95.85
2frh_A	127	SARA, staphylococcal accessory regulator A; winged	95.85
3bj6_A	152	Transcriptional regulator, MARR family; helix-turn	95.84
2y75_A	129	HTH-type transcriptional regulator CYMR; DNA bindi	95.82
2a61_A	145	Transcriptional regulator TM0710; APC4350, MCSG, m	95.82
1s3j_A	155	YUSO protein; structural genomics, MARR transcript	95.82
3hsr_A	140	HTH-type transcriptional regulator SARZ; helix-tur	95.79
3nqo_A	189	MARR-family transcriptional regulator; structural	95.78
3cjn_A	162	Transcriptional regulator, MARR family; silicibact	95.76
3fm5_A	150	Transcriptional regulator; MCSG, PF04017, PSI, MAR	95.75
2xrn_A	241	HTH-type transcriptional regulator TTGV; DNA-bindi	95.73
3deu_A	166	Transcriptional regulator SLYA; MARR, WING-helix,	95.72
2pex_A	153	Transcriptional regulator OHRR; transcription regu	95.62
3s2w_A	159	Transcriptional regulator, MARR family; structural	95.61
2wte_A	244	CSA3; antiviral protein, viral resistance, winged	95.6
1mkm_A	249	ICLR transcriptional regulator; structural genomic	95.57
2nyx_A	168	Probable transcriptional regulatory protein, RV14;	95.56
2fbi_A	142	Probable transcriptional regulator; MARR, APC5816,	95.51
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	95.48
3u2r_A	168	Regulatory protein MARR; structural genomics, PSI-	95.47
2g7u_A	257	Transcriptional regulator; ICLR family, structural	95.47
2o0y_A	260	Transcriptional regulator; ICLR-family, structural	95.44
3kp7_A	151	Transcriptional regulator TCAR; multiple drug resi	95.42
2obp_A	96	Putative DNA-binding protein; structural genomics,	95.35
2pg4_A	95	Uncharacterized protein; structural genomics, join	95.32
1xd7_A	145	YWNA; structural genomics, protein structure initi	95.22
3t8r_A	143	Staphylococcus aureus CYMR; transcriptional regula	95.21
4aik_A	151	Transcriptional regulator SLYA; transcription, tra	95.2
1tbx_A	99	ORF F-93, hypothetical 11.0 kDa protein; sulfolobu	95.2
4b8x_A	147	SCO5413, possible MARR-transcriptional regulator;	95.19
3lwf_A	159	LIN1550 protein, putative transcriptional regulato	95.19
4hbl_A	149	Transcriptional regulator, MARR family; HTH, trans	95.18
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	95.12
4fx0_A	148	Probable transcriptional repressor protein; helix-	95.1
2fbk_A	181	Transcriptional regulator, MARR family; winged-hel	95.08
1ylf_A	149	RRF2 family protein; structural genomics, transcri	95.07
3f3x_A	144	Transcriptional regulator, MARR family, putative;	94.92
2fu4_A	83	Ferric uptake regulation protein; DNA binding doma	94.87
3k69_A	162	Putative transcription regulator; putative transcr	94.86
1sfx_A	109	Conserved hypothetical protein AF2008; structural	94.84
2ia2_A	265	Putative transcriptional regulator; SAD, PSI-2, st	94.83
2h09_A	155	Transcriptional regulator MNTR; transcription regu	94.75
3u1d_A	151	Uncharacterized protein; GNTR-superfamily, structu	94.71
2vn2_A	128	DNAD, chromosome replication initiation protein; D	94.7
3hrs_A	214	Metalloregulator SCAR; DTXR/MNTR family member, tr	94.51
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	94.49
2fxa_A	207	Protease production regulatory protein HPR; protea	94.29
2v79_A	135	DNA replication protein DNAD; primosome, DNA-bindi	94.22
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	93.94
3cta_A	230	Riboflavin kinase; structural genomics, transferas	93.73
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	93.51
3jth_A	98	Transcription activator HLYU; transcription factor	93.51
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	93.5
2co5_A	99	Viral protein F93; viral protein-winged helix comp	93.26
1bja_A	95	Transcription regulatory protein MOTA; activation	92.95
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	92.88
1fx7_A	230	Iron-dependent repressor IDER; DTXR, iron-dependen	92.74
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	92.25
2qm3_A	373	Predicted methyltransferase; putative methyltransf	92.21
2kko_A	108	Possible transcriptional regulatory protein (possi	91.98
3f6o_A	118	Probable transcriptional regulator, ARSR family pr	91.98
1ku9_A	152	Hypothetical protein MJ223; putative transcription	91.95
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	91.81
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	91.79
2qq9_A	226	Diphtheria toxin repressor; regulator, DTXR, helix	91.72
3f6v_A	151	Possible transcriptional regulator, ARSR family pr	91.59
1u2w_A	122	CADC repressor, cadmium efflux system accessory pr	91.56
3r0a_A	123	Putative transcriptional regulator; structural gen	91.53
4esf_A	117	PADR-like transcriptional regulator; PADR family,	91.37
1xmk_A	79	Double-stranded RNA-specific adenosine deaminase;	91.29
2jsc_A	118	Transcriptional regulator RV1994C/MT2050; cadmium,	90.83
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	90.76
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	90.65
3l7w_A	108	Putative uncharacterized protein SMU.1704; PADR, t	90.63
1hsj_A	487	Fusion protein consisting of staphylococcus access	90.19
2dk5_A	91	DNA-directed RNA polymerase III 39 kDa polypeptide	89.79
2esh_A	118	Conserved hypothetical protein TM0937; APC5794, st	89.43
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	89.37
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	89.36
2k4b_A	99	Transcriptional regulator; DNA binding protein, wi	89.04
1r1t_A	122	Transcriptional repressor SMTB; zinc, transcriptio	88.97
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	88.84
2fe3_A	145	Peroxide operon regulator; oxidative stress regula	88.3
1xma_A	145	Predicted transcriptional regulator; southea colla	87.98
1yg2_A	179	Gene activator APHA; virulence factor, winged heli	87.74
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	87.34
1okr_A	123	MECI, methicillin resistance regulatory protein ME	86.58
2o03_A	131	Probable zinc uptake regulation protein FURB; DNA-	86.44
3elk_A	117	Putative transcriptional regulator TA0346; structu	86.08
2p8t_A	200	Hypothetical protein PH0730; pyrococcus horikoshii	86.04
1mzb_A	136	Ferric uptake regulation protein; ferric uptake re	86.04
3f8b_A	116	Transcriptional regulator, PADR-like family; winge	85.89
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	85.78
2w25_A	150	Probable transcriptional regulatory protein; trans	85.05
4esb_A	115	Transcriptional regulator, PADR family; DNA bindin	83.97
3hhh_A	116	Transcriptional regulator, PADR family; PF03551, s	83.87
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	83.82
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	83.58
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	83.48
2xig_A	150	Ferric uptake regulation protein; hpfur, transcrip	83.22
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	83.1
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	82.91
2zkz_A	99	Transcriptional repressor PAGR; protein-DNA, HTH m	82.51
3ri2_A	123	Transcriptional regulator, PADR-like family; PSI-b	82.21
2p4w_A	202	Transcriptional regulatory protein ARSR family; ar	81.93
2oz6_A	207	Virulence factor regulator; winged helix, helix-tu	81.58
3b02_A	195	Transcriptional regulator, CRP family; structural	81.39
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	81.21
1v4r_A	102	Transcriptional repressor; helix-turn-helix, winge	81.19
1p6r_A	82	Penicillinase repressor; transcription regulation,	81.01
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	80.9
4g6q_A	182	Putative uncharacterized protein; structural genom	80.9
2xzm_8	143	RPS25E,; ribosome, translation; 3.93A {Tetrahymena	80.68
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	80.56
2gau_A	232	Transcriptional regulator, CRP/FNR family; structu	80.44
2pjp_A	121	Selenocysteine-specific elongation factor; SELB, p	80.22
3tqn_A	113	Transcriptional regulator, GNTR family; regulatory	80.11

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

Probab=99.77  E-value=5.5e-19  Score=138.84  Aligned_cols=114  Identities=18%  Similarity=0.163  Sum_probs=97.1

Q ss_pred             CCHHHHHHhCCC--CCCCchhhhhhHHHHHHHHHhcCcceeeccCC-CC-cccceechHhhhhhhcCC-CCcHHHHHHHh
Q 045905            1 MTLNELINALPF--HPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQ-ND-QERSYVATNASKLLLKDI-TLTVRSFLQAV   75 (128)
Q Consensus         1 ~S~~eLA~~~~~--~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~-~~-~~~~y~~T~~s~~L~~~~-~~s~~~~~~~~   75 (128)
                      +|++|||+++++  +|.++.    .|+||||+|++.|+|.+..... ++ .+++|++||+|+.|+.+. +.++++++.+.
T Consensus        57 ~t~~eLA~~~g~~~~~~~~~----~l~rlLr~L~~~g~l~~~~~~~~~g~~~~~y~~t~~s~~l~~~~~~~~~~~~~~~~  132 (364)
T 3p9c_A           57 LTPTEVAAKLPSAANPEAPD----MVDRILRLLASYNVVTCLVEEGKDGRLSRSYGAAPVCKFLTPNEDGVSMAALALMN  132 (364)
T ss_dssp             BCHHHHHHTTTCTTCTTHHH----HHHHHHHHHHHTTSEEEEEEECSSSCEEEEEEECGGGGGSSCCTTSCCTHHHHHHH
T ss_pred             CCHHHHHHhcCCCCCccchh----hHHHHHHHHHhCCCEEEeccccCCCCcCCEEecCHHHHHHcCCCCCCCHHHHHHHh
Confidence            489999999997  775566    8999999999999999873111 11 136899999999998764 46899999998


Q ss_pred             cChhhHHHHHhHHHhhhcCCCChhhhccCCChhHhhhcCccchh
Q 045905           76 LDPILTTPCQHVTTWFQNDDLRCLTRHMGWHFESILGTSQRSTI  119 (128)
Q Consensus        76 ~~~~~~~~~~~l~~~~~~g~~~~f~~a~G~~~fe~~~~~p~~~~  119 (128)
                      .++.++.+|.+|.+++++|. +||+.+||.++|+|+.++|+..+
T Consensus       133 ~~~~~~~~~~~L~~~~r~g~-~~~~~~~g~~~~~~~~~~~~~~~  175 (364)
T 3p9c_A          133 QDKVLMESWYYLKDAVLDGG-IPFNKAYGMSAFEYHGTDPRFNR  175 (364)
T ss_dssp             TSHHHHGGGGGHHHHHHHCS-CHHHHHHSSCHHHHHTTCHHHHH
T ss_pred             cCHHHHHHHhCHHHHHhhCC-ChHHHhcCCCHHHHHHhCHHHHH
Confidence            89999999999999999988 89999999999999999997654

>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=99.74  E-value=2e-18  Score=134.64  Aligned_cols=115  Identities=30%  Similarity=0.488  Sum_probs=97.8

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeecc--CC-CCc-ccceechHhhhhhhcCCCCcHHHHHHHhc
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNF--GQ-NDQ-ERSYVATNASKLLLKDITLTVRSFLQAVL   76 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~--~~-~~~-~~~y~~T~~s~~L~~~~~~s~~~~~~~~~   76 (128)
                      +|++|||++++++|.++.    .|+|+||+|++.|+|.+..+  .+ +|. +++|++|++|+.|+.+.+.++++++.+..
T Consensus        46 ~t~~eLA~~~g~~~~~~~----~l~rlLr~L~~~gll~~~~~~~~~~~g~~~~~y~~t~~s~~l~~~~~~~~~~~~~~~~  121 (358)
T 1zg3_A           46 MTLSELASSLKLHPSKVN----ILHRFLRLLTHNGFFAKTIVKGKEGDEEEEIAYSLTPPSKLLISGKPTCLSSIVKGAL  121 (358)
T ss_dssp             EEHHHHHHHTTCCTTTHH----HHHHHHHHHHHTTSEEEEEECCSSSSCCCEEEEEECHHHHTTCTTSTTCCHHHHHHHT
T ss_pred             cCHHHHHHhcCCCCcchH----HHHHHHHHHhhCCcEEEecccccccCCCCCCEEeCCHHHHHHhCCCCccHHHHHHHhc
Confidence            478999999999876778    99999999999999998710  00 000 36899999999999887778999999998


Q ss_pred             ChhhHHHHHhHHHhhhcCC-CChhhhccCCChhHhhhcCccchh
Q 045905           77 DPILTTPCQHVTTWFQNDD-LRCLTRHMGWHFESILGTSQRSTI  119 (128)
Q Consensus        77 ~~~~~~~~~~l~~~~~~g~-~~~f~~a~G~~~fe~~~~~p~~~~  119 (128)
                      ++.++.+|.+|.+++++|. .++|+.++|.++|+|+.++|+..+
T Consensus       122 ~~~~~~~~~~L~~~l~~g~~~~~~~~~~g~~~~~~~~~~p~~~~  165 (358)
T 1zg3_A          122 HPSSLDMWSSSKKWFNEDKEQTLFECATGESFWDFLNKDSESST  165 (358)
T ss_dssp             SHHHHGGGGGHHHHHHCSCCCCHHHHHHSSCHHHHHTSGGGHHH
T ss_pred             CcHHHHHHHHHHHHHhCCCCCChHHHHhCCCHHHHHhcChhhhh
Confidence            8889999999999999983 389999999999999999998765

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

Probab=99.74  E-value=3.8e-18  Score=132.75  Aligned_cols=104  Identities=14%  Similarity=0.173  Sum_probs=94.2

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcCCCCcHHHHHHHhcChhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDITLTVRSFLQAVLDPIL   80 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~~~~s~~~~~~~~~~~~~   80 (128)
                      +|++|||+++|++   +.    .|+|+||+|++.|+|.+ .      +++|++|++|+.|+.+.+.++++++.+..++.+
T Consensus        56 ~t~~elA~~~g~~---~~----~l~rlLr~l~~~g~l~~-~------~~~y~~t~~s~~l~~~~~~~~~~~~~~~~~~~~  121 (348)
T 3lst_A           56 RTPAELAAATGTD---AD----ALRRVLRLLAVRDVVRE-S------DGRFALTDKGAALRSDSPVPARAGILMFTDTMF  121 (348)
T ss_dssp             BCHHHHHHHHTCC---HH----HHHHHHHHHHHTTSEEE-E------TTEEEECTTTGGGSTTSSSCSHHHHHHHTSHHH
T ss_pred             CCHHHHHHHhCcC---HH----HHHHHHHHHHhCCCEEe-c------CCEEecCHHHHHHhcCCCccHHHHHHHhcCHHH
Confidence            4899999999994   48    99999999999999998 4      478999999999988777789999999888888


Q ss_pred             HHHHHhHHHhhhcCCCChhhhccCCChhHhhhcCccchh
Q 045905           81 TTPCQHVTTWFQNDDLRCLTRHMGWHFESILGTSQRSTI  119 (128)
Q Consensus        81 ~~~~~~l~~~~~~g~~~~f~~a~G~~~fe~~~~~p~~~~  119 (128)
                      +.+|.+|.+++++|. ++|+.++|.++|+|+.++|+..+
T Consensus       122 ~~~~~~l~~~l~~g~-~~~~~~~g~~~~~~~~~~~~~~~  159 (348)
T 3lst_A          122 WTMSHRVASALGPER-PAFADIFGSSLDAYFDGDAEVEA  159 (348)
T ss_dssp             HHHHHTHHHHTCTTC-CCHHHHHSSCHHHHHTTCHHHHH
T ss_pred             HHHHHHHHHHHhcCC-ChhhHHhCCCHHHHHHhCHHHHH
Confidence            999999999999887 78999999999999999997654

>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=99.74  E-value=2.8e-18  Score=134.89  Aligned_cols=114  Identities=18%  Similarity=0.232  Sum_probs=96.1

Q ss_pred             CCHHHHHHhCC-CCCCCchhhhhhHHHHHHHHHhcCcceeeccC-CCCc-ccceechHhhhhhhcCC-CCcHHHHHHHhc
Q 045905            1 MTLNELINALP-FHPIKAQYVAQYVYRFMWILVHSGFFAQQNFG-QNDQ-ERSYVATNASKLLLKDI-TLTVRSFLQAVL   76 (128)
Q Consensus         1 ~S~~eLA~~~~-~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~-~~~~-~~~y~~T~~s~~L~~~~-~~s~~~~~~~~~   76 (128)
                      +|++|||++++ .+|.++.    .|+|+||+|++.|+|.+.... ++|. +++|++|++|+.|+.+. +.++++++.+..
T Consensus        60 ~t~~eLA~~~~~~~~~~~~----~l~rlLr~L~~~gll~~~~~~~~~g~~~~~y~~t~~s~~l~~~~~~~~~~~~~~~~~  135 (368)
T 3reo_A           60 ISPAEIAAQLPTTNPEAPV----MLDRVLRLLASYSVVTYTLRELPSGKVERLYGLAPVCKFLTKNEDGVSLAPFLLLAT  135 (368)
T ss_dssp             BCHHHHHTTSSCCCTTHHH----HHHHHHHHHHHTTSEEEEEEECTTSCEEEEEEECTTHHHHSCCTTSCCSHHHHHHHT
T ss_pred             cCHHHHHHhcCcCCCcchh----hHHHHHHHHHhCCCeEEecccCCCCcccceeCcCHHHHHHhCCCCCCCHHHHHHHhc
Confidence            48899999998 4665567    999999999999999986211 1111 36899999999998764 568999999999


Q ss_pred             ChhhHHHHHhHHHhhhcCCCChhhhccCCChhHhhhcCccchh
Q 045905           77 DPILTTPCQHVTTWFQNDDLRCLTRHMGWHFESILGTSQRSTI  119 (128)
Q Consensus        77 ~~~~~~~~~~l~~~~~~g~~~~f~~a~G~~~fe~~~~~p~~~~  119 (128)
                      ++.++.+|.+|.+++++|. ++|+.++|.++|+|+.++|++.+
T Consensus       136 ~~~~~~~~~~l~~~~r~g~-~~~~~~~g~~~~~~~~~~~~~~~  177 (368)
T 3reo_A          136 DKVLLEPWFYLKDAILEGG-IPFNKAYGMNIFDYHGTDHRINK  177 (368)
T ss_dssp             CHHHHGGGGGHHHHHHHCS-CHHHHHSSSCHHHHHTTCHHHHH
T ss_pred             CHHHHhhhhchHHHHhcCC-CHHHHHhCCCHHHHHhhCHHHHH
Confidence            9999999999999999988 89999999999999999998754

>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=99.73  E-value=2.5e-18  Score=133.85  Aligned_cols=110  Identities=28%  Similarity=0.447  Sum_probs=96.9

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcCCCCcHHHHHHHhcChhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDITLTVRSFLQAVLDPIL   80 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~~~~s~~~~~~~~~~~~~   80 (128)
                      +|++|||++++++|.++.    .|+|+||+|++.|+|.+...    +++.|++|++|+.|+.+.+.++++++.+..++.+
T Consensus        52 ~t~~ela~~~~~~~~~~~----~l~rlLr~L~~~gll~~~~~----~~~~y~~t~~s~~L~~~~~~~~~~~~~~~~~~~~  123 (352)
T 1fp2_A           52 ISLSNLVSILQVPSSKIG----NVRRLMRYLAHNGFFEIITK----EEESYALTVASELLVRGSDLCLAPMVECVLDPTL  123 (352)
T ss_dssp             EEHHHHHHHHTCCGGGHH----HHHHHHHHHHHTTSEEEEES----SSEEEEECHHHHTTSTTSSSCCHHHHHHHTCHHH
T ss_pred             ccHHHHHHHhCcCCCChH----HHHHHHHHHHhCCeEEEecC----CCCeEeCCHHHHHHhCCCCccHHHHHHHhcCchH
Confidence            378999999999776678    99999999999999998720    0478999999999998877789999999988888


Q ss_pred             HHHHHhHHHhhh-cCCCChhhhccCCChhHhhhcCccchh
Q 045905           81 TTPCQHVTTWFQ-NDDLRCLTRHMGWHFESILGTSQRSTI  119 (128)
Q Consensus        81 ~~~~~~l~~~~~-~g~~~~f~~a~G~~~fe~~~~~p~~~~  119 (128)
                      +.+|.+|.++++ +|. ++|+.++|.++|+|+.++|+..+
T Consensus       124 ~~~~~~L~~~l~~~g~-~~~~~~~g~~~~~~~~~~~~~~~  162 (352)
T 1fp2_A          124 SGSYHELKKWIYEEDL-TLFGVTLGSGFWDFLDKNPEYNT  162 (352)
T ss_dssp             HHGGGGHHHHHTCSSC-CHHHHHHSSCHHHHHHHCHHHHH
T ss_pred             HHHHHHHHHHHHhcCC-ChHHHHcCCCHHHHHHhChHHHH
Confidence            999999999999 666 89999999999999999998765

>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=99.70  E-value=9.1e-18  Score=131.64  Aligned_cols=115  Identities=17%  Similarity=0.223  Sum_probs=83.8

Q ss_pred             CCHHHHHHhCCC---CCCCchhhhhhHHHHHHHHHhcCcceeeccC-CCC-cccceechHhhhhhhcCCC-CcHHHHHHH
Q 045905            1 MTLNELINALPF---HPIKAQYVAQYVYRFMWILVHSGFFAQQNFG-QND-QERSYVATNASKLLLKDIT-LTVRSFLQA   74 (128)
Q Consensus         1 ~S~~eLA~~~~~---~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~-~~~-~~~~y~~T~~s~~L~~~~~-~s~~~~~~~   74 (128)
                      +|++|||+++++   +|.++.    .|+|+||+|++.|+|.+.... ++| .+++|++|++|+.|+.+.+ .++++++.+
T Consensus        63 ~t~~eLA~~~~~~~~~~~~~~----~l~rlLr~L~~~gll~~~~~~~~~g~~~~~y~~t~~s~~L~~~~~~~~~~~~~~~  138 (372)
T 1fp1_D           63 MSPSEIASKLPASTQHSDLPN----RLDRMLRLLASYSVLTSTTRTIEDGGAERVYGLSMVGKYLVPDESRGYLASFTTF  138 (372)
T ss_dssp             BCHHHHHTTSCGGGCCTTHHH----HHHHHHHHHHHTTSEEEEEEECTTSCEEEEEEECTTGGGGSTTCTTCCCTHHHHH
T ss_pred             cCHHHHHHhcCCCCCCCcChH----HHHHHHHHHhhCCceEecccccCCCCcCCeEecCHHHHHHhCCCCCCCHHHHHHH
Confidence            478999999999   765677    999999999999999987200 000 0258999999999998766 679999999


Q ss_pred             hcChhhHHHHHhHHHhhhcCCCChhhhccCCChhHhhhcCccchh
Q 045905           75 VLDPILTTPCQHVTTWFQNDDLRCLTRHMGWHFESILGTSQRSTI  119 (128)
Q Consensus        75 ~~~~~~~~~~~~l~~~~~~g~~~~f~~a~G~~~fe~~~~~p~~~~  119 (128)
                      ..++.++.+|.+|.+++++|..+||+.++|.++|+|+.++|+..+
T Consensus       139 ~~~~~~~~~~~~L~~~l~~g~~~~~~~~~g~~~~~~~~~~~~~~~  183 (372)
T 1fp1_D          139 LCYPALLQVWMNFKEAVVDEDIDLFKNVHGVTKYEFMGKDKKMNQ  183 (372)
T ss_dssp             HTCHHHHHHHTTHHHHHHSCC--------------CCSSCHHHHH
T ss_pred             hcCchHHHHHHHHHHHHHcCCCChhHHHhCCCHHHHHHhCHHHHH
Confidence            988889999999999999982389999999999999999998764

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

Probab=99.70  E-value=2.2e-17  Score=129.61  Aligned_cols=105  Identities=17%  Similarity=0.184  Sum_probs=94.8

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccc-eechHhhhhhhcCCCCcHHHHHHHhcChh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERS-YVATNASKLLLKDITLTVRSFLQAVLDPI   79 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~-y~~T~~s~~L~~~~~~s~~~~~~~~~~~~   79 (128)
                      +|++|||+++|++   +.    .|+|+||+|++.|+|.+..      +++ |.+|++|+.|+.+.+.++++++.++.++.
T Consensus        72 ~t~~eLA~~~g~~---~~----~l~rlLr~L~~~g~l~~~~------~~~~y~~t~~s~~L~~~~~~~~~~~~~~~~~~~  138 (369)
T 3gwz_A           72 RTATALAEATGAH---EQ----TLRRLLRLLATVGVFDDLG------HDDLFAQNALSAVLLPDPASPVATDARFQAAPW  138 (369)
T ss_dssp             EEHHHHHHHHTCC---HH----HHHHHHHHHHHTTSSEECS------STTEEECCHHHHTTSCCTTCHHHHHHHHHHSHH
T ss_pred             CCHHHHHHHHCcC---HH----HHHHHHHHHHhCCCEEEeC------CCceEecCHHHHHHhcCCchhHHHHHHHcCCHH
Confidence            4789999999994   48    9999999999999999875      467 99999999998877778999999988887


Q ss_pred             hHHHHHhHHHhhhcCCCChhhhccCCChhHhhhcCccchh
Q 045905           80 LTTPCQHVTTWFQNDDLRCLTRHMGWHFESILGTSQRSTI  119 (128)
Q Consensus        80 ~~~~~~~l~~~~~~g~~~~f~~a~G~~~fe~~~~~p~~~~  119 (128)
                      ++..|.+|.+++++|. ++|...+|.++|+|+.++|+..+
T Consensus       139 ~~~~~~~l~~~l~~g~-~~~~~~~g~~~~~~~~~~~~~~~  177 (369)
T 3gwz_A          139 HWRAWEQLTHSVRTGE-ASFDVANGTSFWQLTHEDPKARE  177 (369)
T ss_dssp             HHHHHHTHHHHHHHSS-CSHHHHHSSCHHHHHHHCHHHHH
T ss_pred             HHHHHHhHHHHHhCCC-ChhHhhcCCCHHHHHHhCHHHHH
Confidence            8899999999999988 78999999999999999998665

>2ip2_A Probable phenazine-specific methyltransferase; pyocyanin, phenazine-1-carboxy PHZM; 1.80A {Pseudomonas aeruginosa}

Probab=99.69  E-value=3.6e-17  Score=125.97  Aligned_cols=103  Identities=18%  Similarity=0.168  Sum_probs=92.2

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcCCCCcHHHHHHHhcChhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDITLTVRSFLQAVLDPIL   80 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~~~~s~~~~~~~~~~~~~   80 (128)
                      +|++|||+++|++   +.    .|+|+||+|++.|+|.+..      ++.|.+|++|+.|+ +.+.++++++.+..++.+
T Consensus        42 ~t~~ela~~~~~~---~~----~l~r~Lr~L~~~g~l~~~~------~~~y~~t~~s~~l~-~~~~~~~~~~~~~~~~~~  107 (334)
T 2ip2_A           42 DSDETLAAAVGSD---AE----RIHRLMRLLVAFEIFQGDT------RDGYANTPTSHLLR-DVEGSFRDMVLFYGEEFH  107 (334)
T ss_dssp             CSHHHHHHHHTCC---HH----HHHHHHHHHHHTTSEEEET------TTEEEECHHHHTTS-SSTTCSHHHHHHHTTHHH
T ss_pred             CCHHHHHHHhCcC---HH----HHHHHHHHHHhCCceEecC------CCeEecCHHHHHHh-CCCccHHHHHHHhcCchh
Confidence            5899999999994   48    9999999999999999875      47899999999999 666689999999888766


Q ss_pred             HHHHHhHHHhhhcCCCChhhhccCCChhHhhhcCccchh
Q 045905           81 TTPCQHVTTWFQNDDLRCLTRHMGWHFESILGTSQRSTI  119 (128)
Q Consensus        81 ~~~~~~l~~~~~~g~~~~f~~a~G~~~fe~~~~~p~~~~  119 (128)
                       ..|.+|.++++++. ++|+.++|.++|+|+.++|+..+
T Consensus       108 -~~~~~l~~~l~~~~-~~~~~~~g~~~~~~~~~~~~~~~  144 (334)
T 2ip2_A          108 -AAWTPACEALLSGT-PGFELAFGEDFYSYLKRCPDAGR  144 (334)
T ss_dssp             -HHTTTHHHHHHHCC-CHHHHHHSSCHHHHHHHCHHHHH
T ss_pred             -hHHHHHHHHHhcCC-ChhhhhcCCCHHHHHhhChHHHH
Confidence             99999999999988 79999999999999999997654

>3i53_A O-methyltransferase; CO-complex, rossmann-like fold; HET: SAH; 2.08A {Streptomyces carzinostaticus subsp} PDB: 3i58_A* 3i5u_A* 3i64_A*

Probab=99.68  E-value=2.2e-17  Score=127.32  Aligned_cols=105  Identities=19%  Similarity=0.163  Sum_probs=93.1

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcCCCCcHHHHHHHhcChhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDITLTVRSFLQAVLDPIL   80 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~~~~s~~~~~~~~~~~~~   80 (128)
                      +|++|||++++++   +.    .|+|+||+|++.|||.+..      +++|.+|++|+.|+.+.+.++++++.+..++..
T Consensus        39 ~t~~elA~~~~~~---~~----~l~rlLr~l~~~gl~~~~~------~~~y~~t~~s~~l~~~~~~~~~~~~~~~~~~~~  105 (332)
T 3i53_A           39 RTAAEIASAAGAH---AD----SLDRLLRHLVAVGLFTRDG------QGVYGLTEFGEQLRDDHAAGKRKWLDMNSAVGR  105 (332)
T ss_dssp             CBHHHHHHHHTCC---HH----HHHHHHHHHHHTTSEEECT------TSBEEECTTGGGGSTTCTTCCHHHHCTTSHHHH
T ss_pred             CCHHHHHHHHCcC---HH----HHHHHHHHHHhCCcEEecC------CCeEEcCHhHHHHhcCCchhHHHHHHHcCCHhH
Confidence            5899999999994   48    9999999999999999875      478999999999987777789999888776666


Q ss_pred             H-HHHHhHHHhhhcCCCChhhhccCCChhHhhhcCccchh
Q 045905           81 T-TPCQHVTTWFQNDDLRCLTRHMGWHFESILGTSQRSTI  119 (128)
Q Consensus        81 ~-~~~~~l~~~~~~g~~~~f~~a~G~~~fe~~~~~p~~~~  119 (128)
                      + ..|.+|.+++++|. ++|+.++|.++|+|+.++|+..+
T Consensus       106 ~~~~~~~l~~~l~~~~-~~~~~~~g~~~~~~~~~~~~~~~  144 (332)
T 3i53_A          106 GDLGFVELAHSIRTGQ-PAYPVRYGTSFWEDLGSDPVLSA  144 (332)
T ss_dssp             HGGGGGGHHHHHHHSS-CSHHHHHSSCHHHHHHHCHHHHH
T ss_pred             HHHHHHHhHHHHhcCC-CHHHHhhCCCHHHHHHhCHHHHH
Confidence            7 89999999999988 78999999999999999998654

>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=99.60  E-value=5.8e-16  Score=120.67  Aligned_cols=105  Identities=15%  Similarity=0.085  Sum_probs=91.9

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCccc--ceechHhhhhhhcCCCCcHHHHHHHhcCh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQER--SYVATNASKLLLKDITLTVRSFLQAVLDP   78 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~--~y~~T~~s~~L~~~~~~s~~~~~~~~~~~   78 (128)
                      +|++|||+++|++   +.    .|+|+||+|++.|+|.+..      ++  .|.+|++|+.|+.+.+.++++++.+..++
T Consensus        50 ~t~~eLA~~~g~~---~~----~l~r~Lr~L~~~Gll~~~~------~~~~~y~~t~~s~~l~~~~~~~~~~~~~~~~~~  116 (374)
T 1qzz_A           50 DTLAGLADRTDTH---PQ----ALSRLVRHLTVVGVLEGGE------KQGRPLRPTRLGMLLADGHPAQQRAWLDLNGAV  116 (374)
T ss_dssp             CSHHHHHHHHTCC---HH----HHHHHHHHHHHTTSEECCC------C-CCCCEECTTGGGGSTTCTTCHHHHHCTTSHH
T ss_pred             CCHHHHHHHhCcC---HH----HHHHHHHHHhhCCCEEEeC------CCCeEEEEChHHHhhcCCCcccHHHHHHHcCCh
Confidence            5899999999994   48    9999999999999999854      35  89999999999988777899998888776


Q ss_pred             hhH-HHHHhHHHhhhcCCCChhhhccCCChhHhhhcCccchh
Q 045905           79 ILT-TPCQHVTTWFQNDDLRCLTRHMGWHFESILGTSQRSTI  119 (128)
Q Consensus        79 ~~~-~~~~~l~~~~~~g~~~~f~~a~G~~~fe~~~~~p~~~~  119 (128)
                      ..+ ..|.+|.+++++|. ++|+..+|.++|+++..+|+..+
T Consensus       117 ~~~~~~~~~l~~~l~~~~-~~~~~~~g~~~~~~~~~~~~~~~  157 (374)
T 1qzz_A          117 SHADLAFTGLLDVVRTGR-PAYAGRYGRPFWEDLSADVALAD  157 (374)
T ss_dssp             HHHHGGGGGHHHHHHHSC-CSHHHHHSSCHHHHHHHCHHHHH
T ss_pred             hhHHHHHHHHHHHHhcCC-ChhhhhhCCCHHHHHhhChHHHH
Confidence            677 89999999999987 78999999999999998887654

>3dp7_A SAM-dependent methyltransferase; structural genomics, protein structure initiative, NEW YORK structural genomix research; 2.33A {Bacteroides vulgatus}

Probab=99.59  E-value=1.5e-15  Score=118.93  Aligned_cols=101  Identities=16%  Similarity=0.056  Sum_probs=84.6

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcCCCCcHHHHHHHhcChhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDITLTVRSFLQAVLDPIL   80 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~~~~s~~~~~~~~~~~~~   80 (128)
                      +|++|||+++|++   +.    .|+|+||+|++.|+|.+.       +++|++|++|+.|+.+.+  ...+ +....+.+
T Consensus        51 ~t~~eLA~~~g~~---~~----~l~rlLr~l~~~g~l~~~-------~~~y~~t~~s~~L~~~~~--~~~~-~~~~~~~~  113 (363)
T 3dp7_A           51 YTLQEISGRTGLT---RY----AAQVLLEASLTIGTILLE-------EDRYVLAKAGWFLLNDKM--ARVN-MEFNHDVN  113 (363)
T ss_dssp             BCHHHHHHHHTCC---HH----HHHHHHHHHHHHTSEEEE-------TTEEEECHHHHHHHHCHH--HHHH-HHHHHHTT
T ss_pred             CCHHHHHHHhCcC---HH----HHHHHHHHHhhCCCeEec-------CCEEecccchHHhhCCCc--ccch-heeecHHh
Confidence            4899999999994   48    999999999999999875       378999999999997653  3333 33445678


Q ss_pred             HHHHHhHHHhhhcCCCChhhhccC--CChhHhhhcCccchh
Q 045905           81 TTPCQHVTTWFQNDDLRCLTRHMG--WHFESILGTSQRSTI  119 (128)
Q Consensus        81 ~~~~~~l~~~~~~g~~~~f~~a~G--~~~fe~~~~~p~~~~  119 (128)
                      +++|.+|.+++++|. ++|..++|  .++|+|+.++|+..+
T Consensus       114 ~~~~~~L~~~lr~g~-~~~~~~~g~~~~~~~~~~~~~~~~~  153 (363)
T 3dp7_A          114 YQGLFHLEEALLNGR-PEGLKVFGEWPTIYEGLSQLPEQVQ  153 (363)
T ss_dssp             HHHHTTHHHHHHHSS-CGGGGGTCCCSSHHHHGGGSCHHHH
T ss_pred             hhhHHHHHHHHhcCC-CccccccCchHhHHHHHhhCHHHHH
Confidence            899999999999988 67999999  689999999998554

>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=99.56  E-value=1.9e-15  Score=117.36  Aligned_cols=105  Identities=14%  Similarity=0.153  Sum_probs=92.0

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcCCCCcHHHHHHHhcChh-
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDITLTVRSFLQAVLDPI-   79 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~~~~s~~~~~~~~~~~~-   79 (128)
                      +|++|||++++++   +.    .|+|+||+|++.|+|.+..      +++|.+|++|+.|+.+.+.++++++.+..++. 
T Consensus        53 ~t~~ela~~~~~~---~~----~l~r~L~~L~~~g~~~~~~------~g~y~~t~~s~~l~~~~~~~~~~~~~~~~~~~~  119 (360)
T 1tw3_A           53 RTVKALAARTDTR---PE----ALLRLIRHLVAIGLLEEDA------PGEFVPTEVGELLADDHPAAQRAWHDLTQAVAR  119 (360)
T ss_dssp             CBHHHHHHHHTCC---HH----HHHHHHHHHHHTTSEEEEE------TTEEEECTTGGGGSTTSTTCHHHHTCTTSHHHH
T ss_pred             CCHHHHHHHhCcC---HH----HHHHHHHHHHHCCCEEecC------CCeEEeCHHHHHHhcCCchhHHHHHHHhcCchh
Confidence            4789999999994   48    9999999999999999865      47899999999999887778999887777655 


Q ss_pred             hHHHHHhHHHhhhcCCCChhhhccCCChhHhhhcCccchh
Q 045905           80 LTTPCQHVTTWFQNDDLRCLTRHMGWHFESILGTSQRSTI  119 (128)
Q Consensus        80 ~~~~~~~l~~~~~~g~~~~f~~a~G~~~fe~~~~~p~~~~  119 (128)
                      .+..|.+|.+++++|. ++|+..+|.++|+++..+|+...
T Consensus       120 ~~~~~~~l~~~l~~g~-~~~~~~~g~~~~~~~~~~p~~~~  158 (360)
T 1tw3_A          120 ADISFTRLPDAIRTGR-PTYESIYGKPFYEDLAGRPDLRA  158 (360)
T ss_dssp             HGGGGGGHHHHHHHCC-CCHHHHHSSCHHHHHHTCHHHHH
T ss_pred             HHHHHHHHHHHHHcCC-CHHHHhcCCCHHHHHHhChHHHH
Confidence            6789999999999987 68999999999999998887654

>4a6d_A Hydroxyindole O-methyltransferase; melatonin, circadian clock; HET: SAM; 2.40A {Homo sapiens} PDB: 4a6e_A*

Probab=99.47  E-value=4.6e-14  Score=110.34  Aligned_cols=107  Identities=11%  Similarity=0.016  Sum_probs=87.9

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhh-hhcCCCCcHHHHHHHhcChh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKL-LLKDITLTVRSFLQAVLDPI   79 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~-L~~~~~~s~~~~~~~~~~~~   79 (128)
                      +|++|||+++++   ++.    .|+|+||+|++.|+|.+...   +..++|++|++|+. |+.+.+.++.+++.+.. +.
T Consensus        44 ~t~~eLA~~~g~---~~~----~l~rlLr~L~~~gll~~~~~---~~~~~y~~t~~s~~~l~~~~~~~~~~~~~~~~-~~  112 (353)
T 4a6d_A           44 LDVAAVAAGVRA---SAH----GTELLLDICVSLKLLKVETR---GGKAFYRNTELSSDYLTTVSPTSQCSMLKYMG-RT  112 (353)
T ss_dssp             BCHHHHHHHHTC---CHH----HHHHHHHHHHHTTSEEEEEE---TTEEEEEECHHHHHHHSTTSTTCCHHHHHHHH-HT
T ss_pred             CCHHHHHHhhCc---CHH----HHHHHHHHHHHCCCEEEecc---CccceeeCCHHHHHHhhcCCchHHHHHHHHhC-HH
Confidence            478999999999   448    99999999999999986542   11468999999985 55566678888877754 57


Q ss_pred             hHHHHHhHHHhhhcCCCChhhhccC---CChhHhhhcCccchh
Q 045905           80 LTTPCQHVTTWFQNDDLRCLTRHMG---WHFESILGTSQRSTI  119 (128)
Q Consensus        80 ~~~~~~~l~~~~~~g~~~~f~~a~G---~~~fe~~~~~p~~~~  119 (128)
                      .+..|.+|.+++++|. ++|..++|   .++|+++.++|+...
T Consensus       113 ~~~~~~~L~~~vr~g~-~~~~~~~g~~~~~~~~~~~~~~~~~~  154 (353)
T 4a6d_A          113 SYRCWGHLADAVREGR-NQYLETFGVPAEELFTAIYRSEGERL  154 (353)
T ss_dssp             HHHHHTTHHHHHHHTS-CCHHHHHSCCCSSHHHHHTSSHHHHH
T ss_pred             HHHHHHHHHHHHhcCC-ChhHHhcCCChHHHHHHHhhCHHHHH
Confidence            7899999999999988 78999998   468999999997654

>2r3s_A Uncharacterized protein; methyltransferase domain, structural genomics, joint center structural genomics, JCSG, protein structure initiative; HET: MSE; 2.15A {Nostoc punctiforme}

Probab=99.43  E-value=9.6e-14  Score=106.36  Aligned_cols=98  Identities=17%  Similarity=0.210  Sum_probs=82.6

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhh-hhhhcCCCCcHHHHHHHhcChh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNAS-KLLLKDITLTVRSFLQAVLDPI   79 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s-~~L~~~~~~s~~~~~~~~~~~~   79 (128)
                      +|++|||+++|++   +.    .|+|+||+|++.|+|.+.       +++|++|++| +.|+.+.+.++++++.+..++.
T Consensus        40 ~t~~ela~~~~~~---~~----~l~r~L~~L~~~g~l~~~-------~~~y~~t~~~~~~l~~~~~~~~~~~~~~~~~~~  105 (335)
T 2r3s_A           40 ESSQSLAQKCQTS---ER----GMRMLCDYLVIIGFMTKQ-------AEGYRLTSDSAMFLDRQSKFYVGDAIEFLLSPM  105 (335)
T ss_dssp             ECHHHHHHHHTCC---HH----HHHHHHHHHHHTTSEEEE-------TTEEEECHHHHHHTCTTSTTCCGGGHHHHTCHH
T ss_pred             CCHHHHHHHhCCC---ch----HHHHHHHHHHhcCCeEec-------CCEEecCHHHHHHhccCCcHHHHHHHHHhcchh
Confidence            4789999999994   48    999999999999999864       3789999999 7888777777889988888878


Q ss_pred             hHHHHHhHHHhhhcCCCChhhhccCCChhHhhhcCccchh
Q 045905           80 LTTPCQHVTTWFQNDDLRCLTRHMGWHFESILGTSQRSTI  119 (128)
Q Consensus        80 ~~~~~~~l~~~~~~g~~~~f~~a~G~~~fe~~~~~p~~~~  119 (128)
                      ++..|.+|.++++++. ++|+     + |+++.++|+...
T Consensus       106 ~~~~~~~l~~~l~~~~-~~~~-----~-~~~~~~~~~~~~  138 (335)
T 2r3s_A          106 ITNGFNDLTAAVLKGG-TAIS-----S-EGTLSPEHPVWV  138 (335)
T ss_dssp             HHGGGTTHHHHHHHTS-CCST-----T-TGGGSTTCTHHH
T ss_pred             hHHHHHhHHHHHhcCC-CCCC-----C-cccccCCHHHHH
Confidence            8899999999999987 5665     3 777777776554

>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=99.30  E-value=1.6e-12  Score=101.15  Aligned_cols=90  Identities=7%  Similarity=-0.078  Sum_probs=74.1

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHh-hhhhhcCCC---CcHHHHHHHhc
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNA-SKLLLKDIT---LTVRSFLQAVL   76 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~-s~~L~~~~~---~s~~~~~~~~~   76 (128)
                      +|++|||+++|++   +.    .|+|+||+|++.|+|.+.+       ++|++|+. +++|+.+.+   .++++++.+. 
T Consensus        65 ~t~~eLA~~~g~~---~~----~l~rlLr~L~~~gll~~~~-------~~y~~t~~~~~~l~~~~~~~~~~~~~~~~~~-  129 (359)
T 1x19_A           65 KDLATLAADTGSV---PP----RLEMLLETLRQMRVINLED-------GKWSLTEFADYMFSPTPKEPNLHQTPVAKAM-  129 (359)
T ss_dssp             BCHHHHHHHHTCC---HH----HHHHHHHHHHHTTSEEEET-------TEEEECHHHHHHSSSSCSBTTBCCHHHHHHH-
T ss_pred             CCHHHHHHHhCcC---hH----HHHHHHHHHHhCCCeEeeC-------CeEecCHHHHHHhcCCCCCccccHHHHHHHH-
Confidence            4889999999994   48    9999999999999999864       58999996 667777666   6788888776 


Q ss_pred             ChhhHHHHHhHHHhhhcCCCChhhhccCCChhHhhhcCcc
Q 045905           77 DPILTTPCQHVTTWFQNDDLRCLTRHMGWHFESILGTSQR  116 (128)
Q Consensus        77 ~~~~~~~~~~l~~~~~~g~~~~f~~a~G~~~fe~~~~~p~  116 (128)
                      .+.++.+|.+|.+++++|.+           |+|+.+||+
T Consensus       130 ~~~~~~~~~~L~~~l~~g~~-----------~~~~~~~p~  158 (359)
T 1x19_A          130 AFLADDFYMGLSQAVRGQKN-----------FKGQVPYPP  158 (359)
T ss_dssp             HHHHHHTGGGHHHHHTTSCC-----------CCCSSCSSC
T ss_pred             HHHHHHHHHHHHHHHhcCCC-----------CcccccCch
Confidence            45788999999999998762           666666666

>3mcz_A O-methyltransferase; adomet_mtases, S-adenosylmethionine-dependent methyltransfer structural genomics, PSI-2; HET: MSE; 1.90A {Burkholderia thailandensis}

Probab=99.22  E-value=9.9e-12  Score=96.06  Aligned_cols=86  Identities=6%  Similarity=0.063  Sum_probs=69.4

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhh-hcCCCCcHHHHHHHhcChh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL-LKDITLTVRSFLQAVLDPI   79 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L-~~~~~~s~~~~~~~~~~~~   79 (128)
                      +|++|||+++|+++   .    .|+|+||+|++.|+|.+..       +.|.+|+.|+.+ .++.+.++..++.+.  ..
T Consensus        57 ~t~~elA~~~~~~~---~----~l~rlLr~L~~~gll~~~~-------~~y~~t~~s~~~l~~~~~~~~~~~~~~~--~~  120 (352)
T 3mcz_A           57 RTPAEVAASFGMVE---G----KAAILLHALAALGLLTKEG-------DAFRNTALTERYLTTTSADYIGPIVEHQ--YL  120 (352)
T ss_dssp             BCHHHHHHHHTCCH---H----HHHHHHHHHHHTTSEEEET-------TEEEECHHHHHHHSTTCTTCCHHHHHHH--HT
T ss_pred             CCHHHHHHHhCcCh---H----HHHHHHHHHHHCCCeEecC-------CeeecCHHHHhhccCCChhhHHHHHHHh--HH
Confidence            48999999999944   8    9999999999999999864       579999999854 455566777776654  35


Q ss_pred             hHHHHHhHHHhhhcCCCChhhhc
Q 045905           80 LTTPCQHVTTWFQNDDLRCLTRH  102 (128)
Q Consensus        80 ~~~~~~~l~~~~~~g~~~~f~~a  102 (128)
                      ++..|.+|.+++++|.+.+|+..
T Consensus       121 ~~~~~~~l~~~l~~g~~~~f~~~  143 (352)
T 3mcz_A          121 QWDNWPRLGEILRSEKPLAFQQE  143 (352)
T ss_dssp             TTTTGGGHHHHHTCSSCCTTSHH
T ss_pred             HHHHHHHHHHHHhCCCCCCcccc
Confidence            67899999999999875555543

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

Probab=96.72  E-value=0.0053  Score=40.34  Aligned_cols=57  Identities=19%  Similarity=0.212  Sum_probs=44.6

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhh-cCC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLL-KDI   64 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~-~~~   64 (128)
                      +|..|||+.+++   +..    .+.|+++-|...|++.......|+....|.+|+.|+.+. ...
T Consensus        46 ~~~~ela~~l~i---s~~----~vs~~l~~L~~~gli~~~~~~~d~r~~~~~lT~~G~~~~~~~~  103 (142)
T 3bdd_A           46 LHQLALQERLQI---DRA----AVTRHLKLLEESGYIIRKRNPDNQREVLVWPTEQAREALITNP  103 (142)
T ss_dssp             BCHHHHHHHHTC---CHH----HHHHHHHHHHHTTSEEEEECSSSTTCEEEEECHHHHHHHTTSC
T ss_pred             CCHHHHHHHHCC---CHH----HHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHHHH
Confidence            478999999999   448    999999999999999765432222234699999999888 553

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

Probab=96.69  E-value=0.0025  Score=41.09  Aligned_cols=54  Identities=13%  Similarity=0.139  Sum_probs=41.9

Q ss_pred             CCHHHHHHhC-CCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhh
Q 045905            1 MTLNELINAL-PFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLL   61 (128)
Q Consensus         1 ~S~~eLA~~~-~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~   61 (128)
                      ++..||++.+ ++   ++.    .|.|.|+.|...|++......++.....|.+|+.|+.+.
T Consensus        28 ~~~~eLa~~l~~i---s~~----tls~~L~~Le~~GlI~r~~~~~d~r~~~y~LT~~G~~l~   82 (107)
T 2hzt_A           28 KRTSELKRLMPNI---TQK----MLTQQLRELEADGVINRIVYNQVPPKVEYELSEYGRSLE   82 (107)
T ss_dssp             BCHHHHHHHCTTS---CHH----HHHHHHHHHHHTTSEEEEEECSSSCEEEEEECTTGGGGH
T ss_pred             CCHHHHHHHhcCC---CHH----HHHHHHHHHHHCCCEEEeecCCCCCeEEEEECccHHHHH
Confidence            4689999999 99   448    999999999999999765432222224699999997765

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

Probab=96.57  E-value=0.0026  Score=41.96  Aligned_cols=51  Identities=18%  Similarity=0.122  Sum_probs=42.8

Q ss_pred             CCHHHHHHhC--CCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcCC
Q 045905            1 MTLNELINAL--PFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDI   64 (128)
Q Consensus         1 ~S~~eLA~~~--~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~~   64 (128)
                      +|+.|||..+  ++.   .+    .+.+-|+.|...|++....      .+.|.+|+.++.+..+.
T Consensus        28 ~s~~eLA~~l~~giS---~~----aVs~rL~~Le~~GLV~~~~------rg~Y~LT~~G~~~l~~~   80 (111)
T 3b73_A           28 GSPKELEDRDEIRIS---KS----SVSRRLKKLADHDLLQPLA------NGVYVITEEGEAYLNGE   80 (111)
T ss_dssp             BCHHHHHTSTTCCSC---HH----HHHHHHHHHHHTTSEEECS------TTCEEECHHHHHHHTTC
T ss_pred             CCHHHHHHHHhcCCC---HH----HHHHHHHHHHHCCCEEecC------CceEEECchHHHHHHHH
Confidence            4789999999  884   47    8999999999999998654      35899999998777543

>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=96.50  E-value=0.0037  Score=40.62  Aligned_cols=55  Identities=16%  Similarity=0.213  Sum_probs=42.3

Q ss_pred             CCHHHHHHhC-CCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhc
Q 045905            1 MTLNELINAL-PFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLK   62 (128)
Q Consensus         1 ~S~~eLA~~~-~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~   62 (128)
                      ++..|||+.+ ++   +..    .+.|.|+.|...|++.......+.....|.+|+.|+.+..
T Consensus        36 ~~~~eLa~~l~~i---s~~----tvs~~L~~Le~~GlI~r~~~~~d~r~~~~~LT~~G~~~~~   91 (112)
T 1z7u_A           36 KRNGELMRALDGI---TQR----VLTDRLREMEKDGLVHRESFNELPPRVEYTLTPEGYALYD   91 (112)
T ss_dssp             BCHHHHHHHSTTC---CHH----HHHHHHHHHHHHTSEEEEEECCSSCEEEEEECHHHHHHHH
T ss_pred             CCHHHHHHHhccC---CHH----HHHHHHHHHHHCCCEEEeecCCCCCeEEEEECHhHHHHHH
Confidence            4789999999 99   448    9999999999999997654322222246999999987753

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

Probab=96.49  E-value=0.0038  Score=40.92  Aligned_cols=56  Identities=13%  Similarity=0.220  Sum_probs=42.8

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.+++++   .    .+.|+++.|...|++.......+.....|.+|+.|+.+...
T Consensus        48 ~~~~ela~~l~~~~---~----tvs~~l~~L~~~gli~r~~~~~d~r~~~~~lT~~G~~~~~~  103 (139)
T 3bja_A           48 VSMSKLIENMGCVP---S----NMTTMIQRMKRDGYVMTEKNPNDQRETLVYLTKKGEETKKQ  103 (139)
T ss_dssp             EEHHHHHHHCSSCC---T----THHHHHHHHHHTTSEEEEECSSCTTCEEEEECHHHHHHHHH
T ss_pred             cCHHHHHHHHCCCh---h----HHHHHHHHHHHCCCeeeccCCCCCceeEEEECHHHHHHHHH
Confidence            36789999999955   7    89999999999999976543222222458999999988753

>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=96.47  E-value=0.0062  Score=40.28  Aligned_cols=56  Identities=11%  Similarity=-0.016  Sum_probs=43.4

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.++++   ..    .+.|+++-|...|++.......|.....+.+|+.|+.+...
T Consensus        51 ~~~~ela~~l~~s---~~----tvs~~l~~Le~~glv~r~~~~~d~r~~~~~lT~~G~~~~~~  106 (146)
T 2gxg_A           51 KTMAYLANRYFVT---QS----AITASVDKLEEMGLVVRVRDREDRRKILIEITEKGLETFNK  106 (146)
T ss_dssp             BCHHHHHHHTTCC---HH----HHHHHHHHHHHTTSEEEEECSSCTTCEEEEECHHHHHHHHH
T ss_pred             cCHHHHHHHhCCC---ch----hHHHHHHHHHHCCCEEeecCCCCCceEEEEECHHHHHHHHH
Confidence            4789999999994   48    99999999999999976543222223458999999988754

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

Probab=96.38  E-value=0.0054  Score=41.51  Aligned_cols=55  Identities=15%  Similarity=0.140  Sum_probs=42.4

Q ss_pred             CCHHHHHHhC-CCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhc
Q 045905            1 MTLNELINAL-PFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLK   62 (128)
Q Consensus         1 ~S~~eLA~~~-~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~   62 (128)
                      ++..||+..+ ++.   +.    .|.+.|+.|...|++......++.....|.+|+.|+.|..
T Consensus        40 ~rf~eL~~~l~gIs---~~----~Ls~~L~~Le~~GLV~R~~~~~d~r~v~y~LT~~G~~l~~   95 (131)
T 4a5n_A           40 KRFNEFRRICPSIT---QR----MLTLQLRELEADGIVHREVYHQVPPKVEYSLTEFGRTLEP   95 (131)
T ss_dssp             BCHHHHHHHCTTSC---HH----HHHHHHHHHHHTTSEEEEEECSSSCEEEEEECTTGGGGHH
T ss_pred             cCHHHHHHHhcccC---HH----HHHHHHHHHHHCCCEEEEecCCCCCeEEEEECHhHHHHHH
Confidence            3688999999 884   47    9999999999999997654322211246999999998864

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

Probab=96.33  E-value=0.0048  Score=38.47  Aligned_cols=54  Identities=7%  Similarity=0.061  Sum_probs=40.6

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLL   61 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~   61 (128)
                      +|..|||+.++++   ..    .+.|.|+.|...|++......+++....|.+|+.++.+.
T Consensus        31 ~~~~ela~~l~is---~~----tvs~~l~~L~~~gli~~~~~~~~~r~~~~~lt~~g~~~~   84 (100)
T 1ub9_A           31 APFSQIQKVLDLT---PG----NLDSHIRVLERNGLVKTYKVIADRPRTVVEITDFGMEEA   84 (100)
T ss_dssp             EEHHHHHHHTTCC---HH----HHHHHHHHHHHTTSEEEEEECSSSCEEEEEECHHHHHHH
T ss_pred             cCHHHHHHHHCcC---HH----HHHHHHHHHHHCCCEEEEecCCCcceEEEEECHHHHHHH
Confidence            3678999999994   48    899999999999999754321122235799999996554

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

Probab=96.30  E-value=0.0046  Score=40.57  Aligned_cols=56  Identities=13%  Similarity=0.055  Sum_probs=42.6

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.+++   +..    .+.|+++.|...|++.......+.....|.+|+.|+.+...
T Consensus        53 ~t~~ela~~l~~---~~~----tvs~~l~~L~~~glv~r~~~~~d~R~~~~~lT~~G~~~~~~  108 (140)
T 2nnn_A           53 CPQNQLGRLTAM---DAA----TIKGVVERLDKRGLIQRSADPDDGRRLLVSLSPAGRAELEA  108 (140)
T ss_dssp             BCHHHHHHHTTC---CHH----HHHHHHHHHHHTTCEEEEEETTEEEEEEEEECHHHHHHHHH
T ss_pred             CCHHHHHHHHCC---CHH----HHHHHHHHHHHCCCEEeeCCCCCCCeeeeEECHhHHHHHHH
Confidence            478999999999   448    99999999999999976532121112359999999887653

>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=96.28  E-value=0.0083  Score=40.77  Aligned_cols=56  Identities=13%  Similarity=0.110  Sum_probs=44.1

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.+++++   .    .+.|+++-|...|++......+|.-...+.+|+.|+.+...
T Consensus        61 ~t~~eLa~~l~~~~---~----tvs~~l~~Le~~Glv~r~~~~~DrR~~~l~LT~~G~~~~~~  116 (162)
T 3k0l_A           61 LSNAKLAERSFIKP---Q----SANKILQDLLANGWIEKAPDPTHGRRILVTVTPSGLDKLNQ  116 (162)
T ss_dssp             CCHHHHHHHHTSCG---G----GHHHHHHHHHHTTSEEEEECCSSSCCEEEEECHHHHHHHHH
T ss_pred             CCHHHHHHHHCCCH---H----HHHHHHHHHHHCcCeEecCCCCcCCeeEeEECHhHHHHHHH
Confidence            57899999999944   7    89999999999999976543232222469999999988754

>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=96.26  E-value=0.0046  Score=39.81  Aligned_cols=54  Identities=17%  Similarity=0.282  Sum_probs=41.2

Q ss_pred             CHHHHHHhCC-CCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhc
Q 045905            2 TLNELINALP-FHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLK   62 (128)
Q Consensus         2 S~~eLA~~~~-~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~   62 (128)
                      +..||++.++ +   ++.    .|.+.|+.|...|++......++.....|.+|+.|+.+..
T Consensus        40 ~~~eL~~~l~gi---s~~----~ls~~L~~Le~~GlV~r~~~~~d~r~~~y~LT~~G~~l~~   94 (107)
T 2fsw_A           40 RYGELKRAIPGI---SEK----MLIDELKFLCGKGLIKKKQYPEVPPRVEYSLTPLGEKVLP   94 (107)
T ss_dssp             EHHHHHHHSTTC---CHH----HHHHHHHHHHHTTSEEEEEECSSSCEEEEEECHHHHTTHH
T ss_pred             CHHHHHHHcccC---CHH----HHHHHHHHHHHCCCEEEeecCCCCCeeEEEECccHHHHHH
Confidence            6789999995 8   448    9999999999999997654322211246999999987653

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

Probab=96.26  E-value=0.0043  Score=41.17  Aligned_cols=56  Identities=9%  Similarity=0.064  Sum_probs=42.3

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.++++   +.    .+.|+++-|...|++.......|.-...+.+|+.|+.+...
T Consensus        52 ~t~~eLa~~l~~~---~~----~vs~~l~~L~~~Glv~r~~~~~D~R~~~~~LT~~G~~~~~~  107 (143)
T 3oop_A           52 ISQKEIALWTKKD---TP----TVNRIVDVLLRKELIVREISTEDRRISLLSLTDKGRKETTE  107 (143)
T ss_dssp             EEHHHHHHHHTCC---HH----HHHHHHHHHHHTTSEEEEC----CCSCEEEECHHHHHHHHH
T ss_pred             cCHHHHHHHHCCC---Hh----hHHHHHHHHHHCCCeeccCCCccCceeeeeECHHHHHHHHH
Confidence            3678999999994   48    99999999999999976543222223468999999988754

>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=96.26  E-value=0.0068  Score=39.83  Aligned_cols=56  Identities=9%  Similarity=0.106  Sum_probs=43.1

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.+++   +..    .+.|+++.|...|++......+|.....+.+|+.|+.+...
T Consensus        51 ~~~~ela~~l~~---~~~----tvs~~l~~Le~~Gli~r~~~~~d~R~~~i~lT~~G~~~~~~  106 (141)
T 3bro_A           51 VLQRDLESEFSI---KSS----TATVLLQRMEIKKLLYRKVSGKDSRQKCLKLTKKANKLETI  106 (141)
T ss_dssp             CBHHHHHHHHTC---CHH----HHHHHHHHHHHTTSEEEEECSSCTTSEEEEECHHHHTTHHH
T ss_pred             cCHHHHHHHHCC---Ccc----hHHHHHHHHHHCCCEEeeCCCcCCCeeeeEECHHHHHHHHH
Confidence            478999999999   447    89999999999999976543222212368899999887653

>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=96.25  E-value=0.0062  Score=41.57  Aligned_cols=53  Identities=15%  Similarity=0.224  Sum_probs=42.4

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLL   61 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~   61 (128)
                      ++..||++.+++   ...    .|.+.|+.|...|++......++. ...|.+|+.|+.|.
T Consensus        38 ~~~~eLa~~lgi---s~~----tls~~L~~Le~~GlI~r~~~~~d~-~~~y~LT~~G~~l~   90 (146)
T 2f2e_A           38 TRFGEFQKSLGL---AKN----ILAARLRNLVEHGVMVAVPAESGS-HQEYRLTDKGRALF   90 (146)
T ss_dssp             CSHHHHHHHHCC---CHH----HHHHHHHHHHHTTSEEEEECSSSS-CEEEEECHHHHTTH
T ss_pred             CCHHHHHHHhCC---CHH----HHHHHHHHHHHCCCEEEEecCCCC-eEEEEECchHHHHH
Confidence            478999999999   448    999999999999999765432333 45799999998765

>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=96.23  E-value=0.0056  Score=40.86  Aligned_cols=49  Identities=22%  Similarity=0.327  Sum_probs=41.8

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhc
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLK   62 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~   62 (128)
                      +|..|||+.+++++   .    .+.|+++.|...|++....      .+.|.+|+.|+.+..
T Consensus        23 ~~~~ela~~l~vs~---~----tvs~~l~~Le~~Glv~r~~------~~~~~LT~~g~~~~~   71 (142)
T 1on2_A           23 ARVSDIAEALAVHP---S----SVTKMVQKLDKDEYLIYEK------YRGLVLTSKGKKIGK   71 (142)
T ss_dssp             CCHHHHHHHHTSCH---H----HHHHHHHHHHHTTSEEEET------TTEEEECHHHHHHHH
T ss_pred             CCHHHHHHHhCCCH---H----HHHHHHHHHHHCCCEEEee------CceEEEchhHHHHHH
Confidence            47899999999944   8    8999999999999997664      367999999987764

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

Probab=96.21  E-value=0.0061  Score=39.67  Aligned_cols=51  Identities=16%  Similarity=0.223  Sum_probs=41.5

Q ss_pred             CCHHHHHHhC-CCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhc
Q 045905            1 MTLNELINAL-PFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLK   62 (128)
Q Consensus         1 ~S~~eLA~~~-~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~   62 (128)
                      +|..||++.+ ++.   +.    .|.|.|+.|...|++.....    ....|.+|+.|+.|..
T Consensus        43 ~~~~eL~~~l~gis---~~----~ls~~L~~Le~~GlV~r~~~----r~~~y~LT~~G~~l~~   94 (111)
T 3df8_A           43 QNFNDIRSSIPGIS---ST----ILSRRIKDLIDSGLVERRSG----QITTYALTEKGMNVRN   94 (111)
T ss_dssp             BCHHHHHHTSTTCC---HH----HHHHHHHHHHHTTSEEEEES----SSEEEEECHHHHHHHH
T ss_pred             CCHHHHHHHccCCC---HH----HHHHHHHHHHHCCCEEEeec----CcEEEEECccHHHHHH
Confidence            3589999999 894   48    99999999999999976531    1357999999988763

>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=96.18  E-value=0.0093  Score=40.11  Aligned_cols=56  Identities=14%  Similarity=0.127  Sum_probs=43.3

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.+++   +..    .+.|+++.|...|++.......+.....|.+|+.|+.+...
T Consensus        59 ~t~~ela~~l~i---s~~----tvs~~l~~Le~~Gli~r~~~~~d~R~~~~~lT~~G~~~~~~  114 (154)
T 2eth_A           59 KKMKEIAEFLST---TKS----NVTNVVDSLEKRGLVVREMDPVDRRTYRVVLTEKGKEIFGE  114 (154)
T ss_dssp             BCHHHHHHHTTS---CHH----HHHHHHHHHHHTTSEEEEECTTTSSCEEEEECHHHHHHHHH
T ss_pred             CCHHHHHHHHCC---CHH----HHHHHHHHHHHCCCEEeeCCCCCcceeEEEECHHHHHHHHH
Confidence            478999999999   447    89999999999999976543222222458999999988754

>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=96.18  E-value=0.0045  Score=41.08  Aligned_cols=56  Identities=9%  Similarity=0.064  Sum_probs=38.3

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.+++++   .    .+.|+++-|...|++......+|.-...+.+|+.|+.+...
T Consensus        52 ~t~~eLa~~l~~~~---~----tvs~~l~~L~~~Glv~r~~~~~DrR~~~~~LT~~G~~~~~~  107 (142)
T 3ech_A           52 LNLQDLGRQMCRDK---A----LITRKIRELEGRNLVRRERNPSDQRSFQLFLTDEGLAIHLH  107 (142)
T ss_dssp             CCHHHHHHHHC------C----HHHHHHHHHHHTTSEEC----------CCEECHHHHHHHHH
T ss_pred             cCHHHHHHHhCCCH---H----HHHHHHHHHHHCCCEeeccCCCCCCeeeeEECHHHHHHHHH
Confidence            57899999999954   7    89999999999999976543222212358999999988754

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

Probab=96.16  E-value=0.0077  Score=39.73  Aligned_cols=56  Identities=18%  Similarity=0.246  Sum_probs=43.3

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.++++   ..    .+.|+++-|...|++.......|.....+.+|+.|+.+...
T Consensus        53 ~t~~~la~~l~~s---~~----~vs~~l~~L~~~glv~r~~~~~d~R~~~~~lT~~G~~~~~~  108 (146)
T 2fbh_A           53 PTQRELAQSVGVE---GP----TLARLLDGLESQGLVRRLAVAEDRRAKHIVLTPKADVLIAD  108 (146)
T ss_dssp             CBHHHHHHHHTCC---HH----HHHHHHHHHHHTTSEEEECCBTTBCSCEEEECTTHHHHHHH
T ss_pred             CCHHHHHHHhCCC---hh----hHHHHHHHHHHCCCeeecCCCcccCeeeeEECHhHHHHHHH
Confidence            4789999999994   48    89999999999999976543222222458999999888653

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

Probab=96.13  E-value=0.0029  Score=37.77  Aligned_cols=41  Identities=5%  Similarity=0.144  Sum_probs=33.5

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceech
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVAT   54 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T   54 (128)
                      +|..|||+++|++.   .    .+.|+|..|...|++....      .++|.++
T Consensus        26 ~s~~eLA~~lglsr---~----tv~~~l~~L~~~G~I~~~~------~G~y~lg   66 (67)
T 2heo_A           26 VAIFQLVKKCQVPK---K----TLNQVLYRLKKEDRVSSPS------PKYWSIG   66 (67)
T ss_dssp             EEHHHHHHHHCSCH---H----HHHHHHHHHHHTTSEEEEE------TTEEEEC
T ss_pred             cCHHHHHHHHCcCH---H----HHHHHHHHHHHCCcEecCC------CceEeeC
Confidence            46899999999944   7    8999999999999976543      4678764

>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=96.13  E-value=0.0051  Score=40.53  Aligned_cols=56  Identities=16%  Similarity=0.148  Sum_probs=43.0

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.++++   +.    .+.|+++-|...|++.......|.-...+.+|+.|+.+...
T Consensus        48 ~t~~ela~~l~~~---~~----tvs~~l~~Le~~Gli~r~~~~~D~R~~~~~LT~~G~~~~~~  103 (139)
T 3eco_A           48 LTQNDIAKALQRT---GP----TVSNLLRNLERKKLIYRYVDAQDTRRKNIGLTTSGIKLVEA  103 (139)
T ss_dssp             EEHHHHHHHHTCC---HH----HHHHHHHHHHHTTSEEEEECCC--CCEEEEECHHHHHHHHH
T ss_pred             cCHHHHHHHhCCC---cc----cHHHHHHHHHHCCCEeecCCCCCCCeeeeEECHHHHHHHHH
Confidence            3678999999994   48    99999999999999976543232223468999999988754

>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=96.10  E-value=0.006  Score=40.71  Aligned_cols=56  Identities=9%  Similarity=0.145  Sum_probs=36.5

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.+++++   .    .+.|+++-|...|++......+|.-...+.+|+.|+.+...
T Consensus        58 ~t~~eLa~~l~~~~---~----~vs~~l~~L~~~Glv~r~~~~~DrR~~~~~LT~~G~~~~~~  113 (148)
T 3jw4_A           58 IIQKDLAQFFGRRG---A----SITSMLQGLEKKGYIERRIPENNARQKNIYVLPKGAALVEE  113 (148)
T ss_dssp             CCHHHHHHC-------------CHHHHHHHHHHTTSBCCC--------CCCCBCHHHHHHHHH
T ss_pred             CCHHHHHHHHCCCh---h----HHHHHHHHHHHCCCEEeeCCCCCchhheeeECHHHHHHHHH
Confidence            47899999999954   7    89999999999999975543222212468999999988754

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

Probab=96.09  E-value=0.005  Score=40.98  Aligned_cols=56  Identities=11%  Similarity=0.129  Sum_probs=40.8

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.++++   +.    .+.|+++-|...|++.......|.....+.+|+.|+.+...
T Consensus        55 ~t~~ela~~l~~~---~~----tvs~~l~~Le~~Glv~r~~~~~D~R~~~~~lT~~G~~~~~~  110 (148)
T 3nrv_A           55 CSVQKISDILGLD---KA----AVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEMGQELYEV  110 (148)
T ss_dssp             BCHHHHHHHHTCC---HH----HHHHHHHHHHHTTSEEC---------CCBEECHHHHHHHHH
T ss_pred             CCHHHHHHHHCCC---HH----HHHHHHHHHHHCCCEEeecCCCCcceeEeEECHhHHHHHHH
Confidence            4789999999994   48    99999999999999976543222223469999999988754

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

Probab=96.09  E-value=0.0076  Score=40.01  Aligned_cols=56  Identities=18%  Similarity=0.092  Sum_probs=43.7

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||..++++   ..    .+.|+++-|...|++.......|.-...+.+|+.|+.+...
T Consensus        46 ~t~~eLa~~l~~~---~~----tvs~~l~~Le~~Glv~r~~~~~D~R~~~~~LT~~G~~~~~~  101 (145)
T 3g3z_A           46 RTQKHIGEKWSLP---KQ----TVSGVCKTLAGQGLIEWQEGEQDRRKRLLSLTETGKAYAAP  101 (145)
T ss_dssp             BCHHHHHHHHTCC---HH----HHHHHHHHHHHTTSEEECCCSSCGGGSCEEECHHHHHHHHH
T ss_pred             CCHHHHHHHHCCC---HH----HHHHHHHHHHHCCCEeeccCCCCCceeeeeEChhHHHHHHH
Confidence            4789999999994   48    99999999999999976543222222469999999988754

>3mq0_A Transcriptional repressor of the blcabc operon; helix-turn-helix, GAF fold, transcription repressor; 1.79A {Agrobacterium tumefaciens}

Probab=96.08  E-value=0.0034  Score=47.17  Aligned_cols=47  Identities=13%  Similarity=0.113  Sum_probs=38.0

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL   60 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L   60 (128)
                      +|+.|||+++|++.   .    .++|+|+.|+..|++..+.      ++.|.+++.--.|
T Consensus        46 ltl~eia~~lgl~k---s----Tv~RlL~tL~~~G~v~~~~------~~~Y~LG~~~~~l   92 (275)
T 3mq0_A           46 LTAAELTRFLDLPK---S----SAHGLLAVMTELDLLARSA------DGTLRIGPHSLRW   92 (275)
T ss_dssp             EEHHHHHHHHTCC---------CHHHHHHHHHHTTSEEECT------TSEEEECTHHHHH
T ss_pred             CCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCEEECC------CCcEEehHHHHHH
Confidence            47899999999965   7    8999999999999998764      3689999875444

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

Probab=96.07  E-value=0.0078  Score=40.04  Aligned_cols=56  Identities=11%  Similarity=0.144  Sum_probs=42.5

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.+++   +..    .+.|+++.|...|++.......+.....+.+|+.|+.+...
T Consensus        57 ~t~~ela~~l~~---~~~----tvs~~l~~Le~~Glv~r~~~~~d~R~~~~~lT~~G~~~~~~  112 (150)
T 2rdp_A           57 LTVGELSNKMYL---ACS----TTTDLVDRMERNGLVARVRDEHDRRVVRIRLLEKGERIIEE  112 (150)
T ss_dssp             BCHHHHHHHHTC---CHH----HHHHHHHHHHHTTSEEEEECCC---CEEEEECHHHHHHHHH
T ss_pred             CCHHHHHHHHCC---Cch----hHHHHHHHHHHCCCeeecCCCCCcceeEeEECHhHHHHHHH
Confidence            478999999999   448    99999999999999976543222222458999999988754

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

Probab=96.06  E-value=0.0087  Score=39.65  Aligned_cols=56  Identities=14%  Similarity=0.158  Sum_probs=41.9

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.+++   +..    .+.|+++.|...|++.......|.....+.+|+.|+.+...
T Consensus        51 ~~~~~la~~l~i---~~~----~vs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~~~~~  106 (147)
T 2hr3_A           51 VTPSELAAAERM---RSS----NLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYG  106 (147)
T ss_dssp             BCHHHHHHHTTC---CHH----HHHHHHHHHHHTTSEEEEC------CCEEEECHHHHHHHHH
T ss_pred             CCHHHHHHHhCC---Chh----hHHHHHHHHHHCCCEeeCCCCCCCCceeeEECHHHHHHHHH
Confidence            478999999999   448    99999999999999976543222222458999999988754

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

Probab=96.06  E-value=0.0063  Score=40.89  Aligned_cols=54  Identities=11%  Similarity=0.182  Sum_probs=41.5

Q ss_pred             CHHHHHHhC-CCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhc
Q 045905            2 TLNELINAL-PFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLK   62 (128)
Q Consensus         2 S~~eLA~~~-~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~   62 (128)
                      +..||++.+ ++   ++.    .|.|.|+.|...|++......++.....|.+|+.|+.|..
T Consensus        50 ~~~eLa~~l~gi---s~~----tls~~L~~Le~~GlV~r~~~~~d~r~~~y~LT~~G~~l~~  104 (131)
T 1yyv_A           50 RFSDLRRXMGGV---SEX----MLAQSLQALEQDGFLNRVSYPVVPPHVEYSLTPLGEQVSD  104 (131)
T ss_dssp             EHHHHHHHSTTC---CHH----HHHHHHHHHHHHTCEEEEEECSSSCEEEEEECHHHHHHHH
T ss_pred             CHHHHHHHhccC---CHH----HHHHHHHHHHHCCcEEEEecCCCCCeEEEEECccHHHHHH
Confidence            578999999 69   448    9999999999999997654322221246999999987753

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

Probab=96.04  E-value=0.0094  Score=39.88  Aligned_cols=56  Identities=11%  Similarity=0.128  Sum_probs=42.2

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCccee--eccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQ--QNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e--~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.++++   ..    .+.|+++-|...|++..  .....|.....+.+|+.|+.+...
T Consensus        56 ~t~~eLa~~l~~~---~~----tvs~~l~~Le~~Glv~r~~~~~~~d~R~~~~~LT~~G~~~~~~  113 (154)
T 2qww_A           56 ISVADLTKRLIIT---GS----SAAANVDGLISLGLVVKLNKTIPNDSMDLTLKLSKKGEDLSKR  113 (154)
T ss_dssp             EEHHHHHHHHTCC---HH----HHHHHHHHHHHTTSEEESCC--CTTCTTCEEEECHHHHHHHHH
T ss_pred             CCHHHHHHHHCCC---HH----HHHHHHHHHHHCCCEEecCcCCCCCCceeEeEECHHHHHHHHH
Confidence            3678999999994   47    89999999999999976  432222212369999999988754

>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=96.03  E-value=0.0062  Score=38.26  Aligned_cols=52  Identities=6%  Similarity=0.066  Sum_probs=40.0

Q ss_pred             CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      |..|||+.++++   ..    .+.|++.-|...|++....+   +....|.+|+.|+.+...
T Consensus        32 t~~eLa~~l~i~---~~----tvs~~l~~Le~~Glv~~~~d---~R~~~v~LT~~G~~~~~~   83 (95)
T 2qvo_A           32 YIQYIASKVNSP---HS----YVWLIIKKFEEAKMVECELE---GRTKIIRLTDKGQKIAQQ   83 (95)
T ss_dssp             EHHHHHHHSSSC---HH----HHHHHHHHHHHTTSEEEEEE---TTEEEEEECHHHHHHHHH
T ss_pred             CHHHHHHHHCcC---HH----HHHHHHHHHHHCcCccCCCC---CCeEEEEEChhHHHHHHH
Confidence            678999999994   48    99999999999999932221   111359999999988653

>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=96.02  E-value=0.009  Score=39.17  Aligned_cols=56  Identities=16%  Similarity=0.130  Sum_probs=43.2

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.+++   +..    .+.|+++.|...|++.......|.....+.+|+.|+.+...
T Consensus        49 ~~~~~la~~l~~---~~~----tvs~~l~~L~~~gli~r~~~~~d~R~~~~~lT~~G~~~~~~  104 (138)
T 1jgs_A           49 ITPVELKKVLSV---DLG----ALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTGGAAICEQ  104 (138)
T ss_dssp             BCHHHHHHHHTC---CHH----HHHHHHHHHHHTTSEEEEECTTCSSCEEEEECHHHHHHHHH
T ss_pred             CCHHHHHHHHCC---ChH----HHHHHHHHHHHCCCEEecCCcccCceeEeEEChhHHHHHHH
Confidence            478899999999   448    99999999999999976543222222358999999888653

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

Probab=96.02  E-value=0.0091  Score=40.06  Aligned_cols=56  Identities=11%  Similarity=0.127  Sum_probs=41.7

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.+++   +..    .+.|+++.|...|++......++.....+.+|+.|+.+...
T Consensus        58 ~t~~ela~~l~i---~~~----tvs~~l~~Le~~Glv~r~~~~~d~R~~~~~lT~~G~~~~~~  113 (155)
T 3cdh_A           58 MMITRLAKLSLM---EQS----RMTRIVDQMDARGLVTRVADAKDKRRVRVRLTDDGRALAES  113 (155)
T ss_dssp             BCHHHHHHHTTC---CHH----HHHHHHHHHHHTTSEEECC------CCCEEECHHHHHHHHH
T ss_pred             cCHHHHHHHHCC---CHH----HHHHHHHHHHHCCCEEeccCCCcCCeeEeEECHHHHHHHHH
Confidence            478999999999   448    99999999999999976542222212458999999888654

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

Probab=96.00  E-value=0.007  Score=40.86  Aligned_cols=56  Identities=14%  Similarity=0.247  Sum_probs=40.5

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.+++   +..    .+.|+++-|...|++.......+.....|.+|+.|+.+...
T Consensus        64 ~t~~ela~~l~i---s~~----tvs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~~~~~  119 (162)
T 2fa5_A           64 SSASEVSDRTAM---DKV----AVSRAVARLLERGFIRRETHGDDRRRSMLALSPAGRQVYET  119 (162)
T ss_dssp             CCHHHHHHHHTC---CHH----HHHHHHHHHHHTTSEEC---------CCCEECHHHHHHHHH
T ss_pred             CCHHHHHHHHCC---CHH----HHHHHHHHHHHCCCEeeecCCCCCCeeEEEECHHHHHHHHH
Confidence            478999999999   447    89999999999999976542222222468999999988754

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

Probab=96.00  E-value=0.0062  Score=39.91  Aligned_cols=56  Identities=16%  Similarity=0.177  Sum_probs=42.6

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.+++   +..    .+.|+++.|...|++.......|.....|.+|+.|+.+...
T Consensus        44 ~~~~ela~~l~~---s~~----tvs~~l~~L~~~glv~~~~~~~d~R~~~~~lT~~G~~~~~~   99 (138)
T 3bpv_A           44 IKQDELATFFHV---DKG----TIARTLRRLEESGFIEREQDPENRRRYILEVTRRGEEIIPL   99 (138)
T ss_dssp             CBHHHHHHHHTC---CHH----HHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHTHHH
T ss_pred             CCHHHHHHHHCC---CHH----HHHHHHHHHHHCCCEEeecCCCCceeEEeeECHhHHHHHHH
Confidence            478999999999   448    99999999999999976542222112358999999888654

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

Probab=95.99  E-value=0.0074  Score=39.96  Aligned_cols=56  Identities=18%  Similarity=0.227  Sum_probs=40.3

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.++++   ..    .+.|+++-|...|++......+|.....|.+|+.|+.+...
T Consensus        52 ~t~~eLa~~l~~s---~~----tvs~~l~~L~~~Glv~r~~~~~d~R~~~~~lT~~g~~~~~~  107 (146)
T 3tgn_A           52 LTNSELARRLNVS---QA----AVTKAIKSLVKEGMLETSKDSKDARVIFYQLTDLARPIAEE  107 (146)
T ss_dssp             CCHHHHHHHHTCC---HH----HHHHHHHHHHHTTSEEC----------CCEECGGGHHHHHH
T ss_pred             CCHHHHHHHHCCC---HH----HHHHHHHHHHHCCCeEeccCCCCCceeEEEECHhHHHHHHH
Confidence            5789999999994   48    99999999999999976543222223579999999888654

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

Probab=95.98  E-value=0.0096  Score=39.28  Aligned_cols=56  Identities=9%  Similarity=0.154  Sum_probs=43.1

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.+++++   .    .+.|+++.|...|++.......|.....+.+|+.|+.+...
T Consensus        52 ~~~~ela~~l~~~~---~----tvs~~l~~L~~~gli~r~~~~~d~R~~~~~lT~~G~~~~~~  107 (142)
T 2bv6_A           52 VNVKKVVTELALDT---G----TVSPLLKRMEQVDLIKRERSEVDQREVFIHLTDKSETIRPE  107 (142)
T ss_dssp             EEHHHHHHHTTCCT---T----THHHHHHHHHHTTSEEEEECSSSTTCEEEEECHHHHHHHHH
T ss_pred             cCHHHHHHHHCCCh---h----hHHHHHHHHHHCCCEEeecCCCCcceEEEEEChHHHHHHHH
Confidence            36789999999954   7    89999999999999976543222223468999999888754

>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=95.91  E-value=0.0035  Score=46.67  Aligned_cols=48  Identities=29%  Similarity=0.326  Sum_probs=39.6

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL   60 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L   60 (128)
                      +|+.|||+++|++.   .    .++|+|+.|...|++..+..     .+.|.+++.--.|
T Consensus        22 lsl~eia~~lgl~k---s----T~~RlL~tL~~~G~v~~~~~-----~~~Y~lG~~~~~l   69 (260)
T 3r4k_A           22 IGLSDLTRLSGMNK---A----TVYRLMSELQEAGFVEQVEG-----ARSYRLGPQVLRL   69 (260)
T ss_dssp             EEHHHHHHHHCSCH---H----HHHHHHHHHHHTTSEEECSS-----SSEEEECTTHHHH
T ss_pred             CCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCEEEcCC-----CCcEEcCHHHHHH
Confidence            47899999999955   7    89999999999999987642     3789998875544

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

Probab=95.90  E-value=0.0069  Score=38.61  Aligned_cols=49  Identities=16%  Similarity=0.285  Sum_probs=42.0

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      ++..+||..+++++   .    .+++.+..|...|++....       +.|.+|+-|+.+.+.
T Consensus        21 ~~~t~La~~~~ls~---~----~~~~~l~~L~~~GLI~~~~-------~~~~LT~kG~~~l~~   69 (95)
T 1r7j_A           21 SPKTRIMYGANLSY---A----LTGRYIKMLMDLEIIRQEG-------KQYMLTKKGEELLED   69 (95)
T ss_dssp             BCHHHHHHHHTCCH---H----HHHHHHHHHHHTTSEEEET-------TEEEECHHHHHHHHH
T ss_pred             CCHHHHHHHhCcCH---H----HHHHHHHHHHHCCCeEEEC-------CeeEEChhHHHHHHH
Confidence            36789999999955   8    9999999999999998764       459999999988754

>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=95.90  E-value=0.017  Score=38.19  Aligned_cols=57  Identities=11%  Similarity=0.181  Sum_probs=43.8

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcCC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDI   64 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~~   64 (128)
                      +|..|||+.+++   +..    .+.|+++.|...|++.......+.....+.+|+.|+.+....
T Consensus        55 ~~~~~la~~l~~---~~~----tvs~~l~~L~~~glv~r~~~~~d~R~~~~~LT~~G~~~~~~~  111 (147)
T 1z91_A           55 LTVKKMGEQLYL---DSG----TLTPMLKRMEQQGLITRKRSEEDERSVLISLTEDGALLKEKA  111 (147)
T ss_dssp             EEHHHHHHTTTC---CHH----HHHHHHHHHHHHTSEECCBCSSCTTSBEEEECHHHHSGGGGT
T ss_pred             CCHHHHHHHHCC---CcC----cHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHHHHHHH
Confidence            367899999999   448    999999999999999765432222234589999999888654

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

Probab=95.89  E-value=0.0096  Score=40.40  Aligned_cols=56  Identities=21%  Similarity=0.213  Sum_probs=42.6

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.+++   +..    .+.|+++-|...|++......+|.-...+.+|+.|+.+...
T Consensus        68 ~t~~eLa~~l~~---~~~----~vs~~l~~Le~~Glv~r~~~~~DrR~~~~~LT~~G~~~~~~  123 (161)
T 3e6m_A           68 LTVGQLATLGVM---EQS----TTSRTVDQLVDEGLAARSISDADQRKRTVVLTRKGKKKLAE  123 (161)
T ss_dssp             EEHHHHHHHTTC---CHH----HHHHHHHHHHHTTSEEECC---CCCSCEEEECHHHHHHHHH
T ss_pred             CCHHHHHHHHCC---CHH----HHHHHHHHHHHCCCEEeeCCcccCCeeEeeECHHHHHHHHH
Confidence            367899999999   448    99999999999999976543222222468999999988754

>1y0u_A Arsenical resistance operon repressor, putative; structural genomics, protein structure initiative, PSI; HET: MSE; 1.60A {Archaeoglobus fulgidus} SCOP: a.4.5.5

Probab=95.89  E-value=0.0072  Score=37.97  Aligned_cols=46  Identities=15%  Similarity=0.242  Sum_probs=38.5

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL   60 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L   60 (128)
                      +|..|||+.+++++   .    .++|.|+.|...|++....       +.|.+|+.++.+
T Consensus        44 ~~~~eLa~~l~is~---~----tv~~~L~~L~~~Glv~~~~-------g~y~l~~~g~~~   89 (96)
T 1y0u_A           44 RSEEEIMQTLSLSK---K----QLDYHLKVLEAGFCIERVG-------ERWVVTDAGKIV   89 (96)
T ss_dssp             CCHHHHHHHHTCCH---H----HHHHHHHHHHHTTSEEEET-------TEEEECTTTCCC
T ss_pred             CCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCEEEEC-------CEEEECCCchHH
Confidence            47899999999944   7    8999999999999998653       489999987543

>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=95.88  E-value=0.01  Score=39.17  Aligned_cols=56  Identities=16%  Similarity=0.150  Sum_probs=42.9

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.+++   +..    .+.|+++-|...|++.......|.....+.+|+.|+.+...
T Consensus        44 ~t~~~la~~l~~---s~~----~vs~~l~~Le~~gli~r~~~~~d~R~~~~~lT~~G~~~~~~   99 (144)
T 1lj9_A           44 IIQEKIAELIKV---DRT----TAARAIKRLEEQGFIYRQEDASNKKIKRIYATEKGKNVYPI   99 (144)
T ss_dssp             EEHHHHHHHHTC---CHH----HHHHHHHHHHHTTSEEEEECSSCTTCEEEEECHHHHHHHHH
T ss_pred             cCHHHHHHHHCC---CHh----HHHHHHHHHHHCCCEEeecCCCCCceeeeEEChhHHHHHHH
Confidence            367899999999   448    99999999999999976543222212358999999988753

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

Probab=95.85  E-value=0.0083  Score=40.40  Aligned_cols=56  Identities=18%  Similarity=0.195  Sum_probs=40.6

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.+++++   .    .+.|+++-|...|++.......|.....+.+|+.|+.+...
T Consensus        63 ~~~~ela~~l~i~~---~----tvs~~l~~Le~~Gli~r~~~~~d~R~~~~~lT~~G~~~~~~  118 (160)
T 3boq_A           63 LSMGKLSGALKVTN---G----NVSGLVNRLIKDGMVVKAMSADDRRSFSAKLTDAGLTTFKQ  118 (160)
T ss_dssp             EEHHHHHHHCSSCC---S----CHHHHHHHHHHHTSEEEC--------CEEEECHHHHHHHHH
T ss_pred             CCHHHHHHHHCCCh---h----hHHHHHHHHHHCCCEEeecCCCCCCeEEEEEChhHHHHHHH
Confidence            36789999999955   7    89999999999999976543222212358999999988754

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

Probab=95.85  E-value=0.0073  Score=39.79  Aligned_cols=56  Identities=16%  Similarity=0.316  Sum_probs=43.0

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.+++   +..    .+.|++.-|...|++.......|.-...+.+|+.|+.+...
T Consensus        54 ~t~~eLa~~l~~---~~~----tvs~~l~~Le~~Glv~r~~~~~D~R~~~i~LT~~G~~~~~~  109 (127)
T 2frh_A           54 YYLKDIINHLNY---KQP----QVVKAVKILSQEDYFDKKRNEHDERTVLILVNAQQRKKIES  109 (127)
T ss_dssp             EEHHHHHHHSSS---HHH----HHHHHHHHHHHTTSSCCBCCSSSSCCCEEECCSHHHHHHHH
T ss_pred             cCHHHHHHHHCC---CHH----HHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHH
Confidence            367899999999   447    99999999999999976543233222458899999988754

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

Probab=95.84  E-value=0.0093  Score=39.75  Aligned_cols=56  Identities=20%  Similarity=0.309  Sum_probs=43.0

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.+++   +..    .+.|+++-|...|++.......|.....+.+|+.|+.+...
T Consensus        55 ~t~~ela~~l~~---~~~----~vs~~l~~Le~~Glv~r~~~~~d~R~~~~~lT~~G~~~~~~  110 (152)
T 3bj6_A           55 ATAPQLGAALQM---KRQ----YISRILQEVQRAGLIERRTNPEHARSHRYWLTPRGEAIITA  110 (152)
T ss_dssp             EEHHHHHHHHTC---CHH----HHHHHHHHHHHTTSEEEECCSSSTTSCEEEECHHHHHHHHH
T ss_pred             CCHHHHHHHHCC---CHH----HHHHHHHHHHHCCCeeecCCcccccceeeEEChhhHHHHHH
Confidence            367899999999   448    99999999999999976543222222468999999887653

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

Probab=95.82  E-value=0.0082  Score=39.77  Aligned_cols=45  Identities=13%  Similarity=0.196  Sum_probs=34.2

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNA   56 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~   56 (128)
                      +|..|||+++++++   .    .++|+|+.|...|++.....    ..+.|.++.-
T Consensus        27 ~s~~ela~~~~i~~---~----~v~~il~~L~~~Glv~~~~g----~~ggy~L~~~   71 (129)
T 2y75_A           27 TSLKSIAQTNNLSE---H----YLEQLVSPLRNAGLVKSIRG----AYGGYVLGSE   71 (129)
T ss_dssp             BCHHHHHHHTTSCH---H----HHHHHHHHHHHTTSEEEC--------CCEEESSC
T ss_pred             CCHHHHHHHHCcCH---H----HHHHHHHHHHHCCceEecCC----CCCceEeCCC
Confidence            47899999999955   8    99999999999999875531    1256777653

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

Probab=95.82  E-value=0.0055  Score=40.49  Aligned_cols=56  Identities=14%  Similarity=0.097  Sum_probs=42.7

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.++++   ..    .+.|+++.|...|++.......+.....|.+|+.|+.+...
T Consensus        48 ~~~~~la~~l~~s---~~----tvs~~l~~L~~~glv~r~~~~~d~r~~~~~lT~~G~~~~~~  103 (145)
T 2a61_A           48 KRPGELSVLLGVA---KS----TVTGLVKRLEADGYLTRTPDPADRRAYFLVITRKGEEVIEK  103 (145)
T ss_dssp             BCHHHHHHHHTCC---HH----HHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHHHH
T ss_pred             CCHHHHHHHHCCC---ch----hHHHHHHHHHHCCCeeecCCCCCCceEEEEECHHHHHHHHH
Confidence            4789999999994   48    99999999999999976542221112358999999988753

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

Probab=95.82  E-value=0.0087  Score=40.01  Aligned_cols=56  Identities=9%  Similarity=0.146  Sum_probs=43.1

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.++++   ..    .+.|+++-|...|++.......|.....|.+|+.|+.+...
T Consensus        52 ~t~~ela~~l~~s---~~----tvs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~~~~~  107 (155)
T 1s3j_A           52 LKVSEIAERMEVK---PS----AVTLMADRLEQKNLIARTHNTKDRRVIDLSLTDEGDIKFEE  107 (155)
T ss_dssp             EEHHHHHHHHTSC---HH----HHHHHHHHHHHTTSEEEEECSSCTTSEEEEECHHHHHHHHH
T ss_pred             CCHHHHHHHHCCC---HH----HHHHHHHHHHHCCCEeecCCCCCCceEEEEECHHHHHHHHH
Confidence            3678999999994   48    99999999999999976543222222468999999888754

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

Probab=95.79  E-value=0.0067  Score=40.24  Aligned_cols=56  Identities=7%  Similarity=0.119  Sum_probs=41.6

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.+++   ++.    .+.|+++-|...|++......+|.-...+.+|+.|+.+...
T Consensus        51 ~t~~eLa~~l~~---~~~----tvs~~l~~L~~~Glv~r~~~~~D~R~~~~~LT~~G~~~~~~  106 (140)
T 3hsr_A           51 LNIKKLGERVFL---DSG----TLTPLLKKLEKKDYVVRTREEKDERNLQISLTEQGKAIKSP  106 (140)
T ss_dssp             EEHHHHHHHHTC---CHH----HHHHHHHHHHHTTSEEEEC-------CEEEECHHHHHTHHH
T ss_pred             cCHHHHHHHHCC---Chh----hHHHHHHHHHHCCCeEecCCCCCcceeeeeEChHHHHHHHH
Confidence            367899999999   448    99999999999999976543222212468999999988754

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

Probab=95.78  E-value=0.016  Score=40.66  Aligned_cols=56  Identities=16%  Similarity=0.190  Sum_probs=44.2

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.+++   +..    .+.|+++-|...|++.......|.-...+.+|+.|+.+...
T Consensus        58 ~t~~eLa~~l~i---s~~----tvs~~l~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~~  113 (189)
T 3nqo_A           58 TTLNNIARKMGT---SKQ----NINRLVANLEKNGYVDVIPSPHDKRAINVKVTDLGKKVMVT  113 (189)
T ss_dssp             CCHHHHHHHHTS---CHH----HHHHHHHHHHHTTSEEEEECSSCSSCEEEEECHHHHHHHHH
T ss_pred             cCHHHHHHHHCC---CHH----HHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHHHHHHHHH
Confidence            578999999999   448    89999999999999976543233222468999999988764

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

Probab=95.76  E-value=0.0099  Score=40.16  Aligned_cols=56  Identities=11%  Similarity=0.057  Sum_probs=42.3

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.+++   +..    .+.|+++-|...|++.......+.....|.+|+.|+.+...
T Consensus        67 ~t~~ela~~l~i---s~~----tvs~~l~~Le~~Gli~r~~~~~d~R~~~~~lT~~G~~~~~~  122 (162)
T 3cjn_A           67 LPIGTLGIFAVV---EQS----TLSRALDGLQADGLVRREVDSDDQRSSRVYLTPAGRAVYDR  122 (162)
T ss_dssp             EEHHHHHHHHTC---CHH----HHHHHHHHHHHTTSEEEEEC--CCSSEEEEECHHHHHHHHH
T ss_pred             CCHHHHHHHHCC---Chh----HHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHH
Confidence            367899999999   448    89999999999999976542222222458999999888654

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

Probab=95.75  E-value=0.0078  Score=40.24  Aligned_cols=56  Identities=11%  Similarity=0.134  Sum_probs=39.7

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.+++   +..    .+.|++.-|...|++.......|.-...+.+|+.|+.+...
T Consensus        55 ~t~~eLa~~l~i---~~~----tvs~~l~~Le~~Glv~r~~~~~D~R~~~~~LT~~G~~~~~~  110 (150)
T 3fm5_A           55 VNQRGVAATMGL---DPS----QIVGLVDELEERGLVVRTLDPSDRRNKLIAATEEGRRLRDD  110 (150)
T ss_dssp             CCSHHHHHHHTC---CHH----HHHHHHHHHHTTTSEEC-----------CEECHHHHHHHHH
T ss_pred             cCHHHHHHHHCC---CHh----HHHHHHHHHHHCCCEEeeCCccccchheeeECHHHHHHHHH
Confidence            478899999999   448    99999999999999976543222112358999999988754

>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=95.73  E-value=0.0064  Score=44.68  Aligned_cols=49  Identities=12%  Similarity=0.081  Sum_probs=40.1

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLL   61 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~   61 (128)
                      +|+.|||+++|++.   .    .++|+|+.|...|++.....     .++|.+++....|.
T Consensus        22 ~s~~ela~~~gl~~---s----tv~r~l~~L~~~G~v~~~~~-----~~~Y~lg~~~~~lg   70 (241)
T 2xrn_A           22 LSLAAIAQLVGLPR---S----TVQRIINALEEEFLVEALGP-----AGGFRLGPALGQLI   70 (241)
T ss_dssp             EEHHHHHHHTTSCH---H----HHHHHHHHHHTTTSEEECGG-----GCEEEECSHHHHHH
T ss_pred             CCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCEEEeCC-----CCeEEECHHHHHHH
Confidence            37899999999944   7    89999999999999987642     37899998765554

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

Probab=95.72  E-value=0.0072  Score=41.55  Aligned_cols=56  Identities=14%  Similarity=0.219  Sum_probs=41.1

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.+++   +..    .+.|+++-|...|++......+|.-...+.+|+.|+.+...
T Consensus        69 ~t~~eLa~~l~i---~~~----tvs~~l~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~~  124 (166)
T 3deu_A           69 QSQIQLAKAIGI---EQP----SLVRTLDQLEDKGLISRQTCASDRRAKRIKLTEKAEPLIAE  124 (166)
T ss_dssp             EEHHHHHHHHTS---CHH----HHHHHHHHHHHTTSEEEC--------CEEEECGGGHHHHHH
T ss_pred             CCHHHHHHHHCC---CHh----hHHHHHHHHHHCCCEEeeCCCCCCCeeEEEECHHHHHHHHH
Confidence            367899999999   448    99999999999999976543222212468999999988754

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

Probab=95.62  E-value=0.026  Score=37.65  Aligned_cols=57  Identities=11%  Similarity=0.162  Sum_probs=42.1

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcCC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDI   64 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~~   64 (128)
                      +|..|||+.+++   +..    .+.|+++-|...|++......++.....+.+|+.|+.+....
T Consensus        62 ~t~~ela~~l~~---s~~----tvs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~~~~~~  118 (153)
T 2pex_A           62 RSVSEIGERLYL---DSA----TLTPLLKRLQAAGLVTRTRAASDERQVIIALTETGRALRSKA  118 (153)
T ss_dssp             EEHHHHHHHHTC---CHH----HHHHHHHHHHHTTSEEEEC-------CEEEECHHHHHGGGGS
T ss_pred             cCHHHHHHHhCC---Ccc----cHHHHHHHHHHCCCEeecCCcccCCeeEeeECHHHHHHHHHH
Confidence            367899999999   447    899999999999999765422221123689999999888654

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

Probab=95.61  E-value=0.01  Score=40.16  Aligned_cols=56  Identities=20%  Similarity=0.189  Sum_probs=42.5

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.++++   +.    .+.|++.-|...|++......+|.-...+.+|+.|+.+...
T Consensus        65 ~t~~eLa~~l~~~---~~----tvs~~l~~Le~~Glv~r~~~~~DrR~~~l~LT~~G~~~~~~  120 (159)
T 3s2w_A           65 INQESLSDYLKID---KG----TTARAIQKLVDEGYVFRQRDEKDRRSYRVFLTEKGKKLEPD  120 (159)
T ss_dssp             EEHHHHHHHHTCC---HH----HHHHHHHHHHHTTSEEEEECC---CCEEEEECHHHHHHHHH
T ss_pred             CCHHHHHHHHCCC---HH----HHHHHHHHHHHCCCEEEecCCCCCCeeEEEECHHHHHHHHH
Confidence            3678999999994   48    99999999999999976543222212368999999988754

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

Probab=95.60  E-value=0.011  Score=43.81  Aligned_cols=50  Identities=16%  Similarity=0.138  Sum_probs=42.3

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhc
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLK   62 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~   62 (128)
                      +|..|||++++++   ..    .+.|+++.|...|++.....     .+.|.+|+.++.+..
T Consensus       167 ~s~~eLA~~lgls---ks----Tv~r~L~~Le~~GlV~r~~r-----~~~~~LT~~G~~l~~  216 (244)
T 2wte_A          167 TGITELAKMLDKS---EK----TLINKIAELKKFGILTQKGK-----DRKVELNELGLNVIK  216 (244)
T ss_dssp             BCHHHHHHHHTCC---HH----HHHHHHHHHHHTTSEEEETT-----TTEEEECHHHHHHHH
T ss_pred             CCHHHHHHHHCcC---HH----HHHHHHHHHHHCCCEEEeCC-----ccEEEECHHHHHHHH
Confidence            4789999999994   48    89999999999999987642     467999999988853

>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=95.57  E-value=0.012  Score=43.22  Aligned_cols=47  Identities=17%  Similarity=0.410  Sum_probs=38.8

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL   60 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L   60 (128)
                      +|+.|||++++++.   .    .++|+|+.|...|++....      .+.|.+++....|
T Consensus        24 ~~~~ela~~~gl~~---s----tv~r~l~~L~~~G~v~~~~------~~~Y~lg~~~~~l   70 (249)
T 1mkm_A           24 VSVSEIAEKFNMSV---S----NAYKYMVVLEEKGFVLRKK------DKRYVPGYKLIEY   70 (249)
T ss_dssp             BCHHHHHHHTTCCH---H----HHHHHHHHHHHTTSEEECT------TSCEEECTHHHHH
T ss_pred             CCHHHHHHHHCcCH---H----HHHHHHHHHHHCCcEEECC------CCcEEECHHHHHH
Confidence            47899999999954   7    8999999999999998663      4789998865433

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

Probab=95.56  E-value=0.012  Score=40.40  Aligned_cols=56  Identities=14%  Similarity=0.128  Sum_probs=43.3

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.+++   +..    .+.|+++.|...|++.......|.....+.+|+.|+.+...
T Consensus        60 ~t~~eLa~~l~i---s~~----tvs~~l~~Le~~GlV~r~~~~~DrR~~~~~LT~~G~~~~~~  115 (168)
T 2nyx_A           60 INLATLATLLGV---QPS----ATGRMVDRLVGAELIDRLPHPTSRRELLAALTKRGRDVVRQ  115 (168)
T ss_dssp             EEHHHHHHHHTS---CHH----HHHHHHHHHHHTTSEEEEECSSCSSCEEEEECHHHHHHHHH
T ss_pred             CCHHHHHHHhCC---CHH----HHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHHHHHHHHH
Confidence            367899999999   448    99999999999999976543222222458999999988754

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

Probab=95.51  E-value=0.0096  Score=39.07  Aligned_cols=56  Identities=11%  Similarity=0.023  Sum_probs=42.4

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.+++   +..    .+.|+++.|...|++.......|.....|.+|+.|+.+...
T Consensus        51 ~t~~ela~~l~~---s~~----~vs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~~~~~  106 (142)
T 2fbi_A           51 MESYQLANQACI---LRP----SMTGVLARLERDGIVRRWKAPKDQRRVYVNLTEKGQQCFVS  106 (142)
T ss_dssp             EEHHHHHHHTTC---CHH----HHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHHHH
T ss_pred             CCHHHHHHHHCC---CHh----HHHHHHHHHHHCCCEEeecCCCCCCeeEEEECHHHHHHHHH
Confidence            367899999999   447    99999999999999976542222112358999999988754

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

Probab=95.48  E-value=0.016  Score=38.36  Aligned_cols=48  Identities=15%  Similarity=0.199  Sum_probs=40.6

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhc
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLK   62 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~   62 (128)
                      +|..|||++++++   ..    .+.|+++.|...|++....       +.|.+|+.++.+..
T Consensus        32 ~s~~ela~~l~is---~~----tv~~~l~~Le~~Gli~r~~-------~~~~Lt~~g~~~~~   79 (139)
T 2x4h_A           32 AKINRIAKDLKIA---PS----SVFEEVSHLEEKGLVKKKE-------DGVWITNNGTRSIN   79 (139)
T ss_dssp             BCHHHHHHHHTCC---HH----HHHHHHHHHHHTTSEEEET-------TEEEECHHHHHHHH
T ss_pred             cCHHHHHHHhCCC---hH----HHHHHHHHHHHCCCEEecC-------CeEEEChhHHHHHH
Confidence            4789999999994   47    8999999999999997653       56999999987754

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

Probab=95.47  E-value=0.0091  Score=40.79  Aligned_cols=56  Identities=21%  Similarity=0.186  Sum_probs=40.6

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.+++++   .    .+.|+++-|...|++......+|.-...+.+|+.|+.+...
T Consensus        63 ~t~~eLa~~l~~~~---~----tvs~~l~~Le~~Glv~r~~~~~DrR~~~l~LT~~G~~~~~~  118 (168)
T 3u2r_A           63 MATLQIADRLISRA---P----DITRLIDRLDDRGLVLRTRKPENRRVVEVALTDAGLKLLKD  118 (168)
T ss_dssp             EEHHHHHHHC---C---T----HHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHHHH
T ss_pred             cCHHHHHHHHCCCh---h----hHHHHHHHHHHCCCEeecCCCCCCCeeEeEECHHHHHHHHH
Confidence            36889999999955   7    89999999999999976543222111358999999988754

>2g7u_A Transcriptional regulator; ICLR family, structural genomics, PSI, protein structure initiative, midwest center for struc genomics; 2.30A {Rhodococcus SP}

Probab=95.47  E-value=0.021  Score=42.23  Aligned_cols=49  Identities=20%  Similarity=0.187  Sum_probs=40.8

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|+.|||+++|++.   .    .++|+|+.|...|++....       +.|.+++....|...
T Consensus        30 ~~~~eia~~~gl~~---s----tv~r~l~~L~~~G~v~~~~-------~~Y~Lg~~~~~l~~~   78 (257)
T 2g7u_A           30 PTLAELATEAGLSR---P----AVRRILLTLQKLGYVAGSG-------GRWSLTPRVLSIGQH   78 (257)
T ss_dssp             CBHHHHHHHHTCCH---H----HHHHHHHHHHHTTSEEEET-------TEEEECGGGHHHHTT
T ss_pred             CCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCEEeCC-------CEEEEcHHHHHHHHH
Confidence            47899999999954   7    8999999999999998652       689999987666543

>2o0y_A Transcriptional regulator; ICLR-family, structural genomics, protein structure initiative, midwest center for structural genomics, MCSG; 2.00A {Rhodococcus SP}

Probab=95.44  E-value=0.012  Score=43.68  Aligned_cols=47  Identities=15%  Similarity=0.193  Sum_probs=38.8

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL   60 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L   60 (128)
                      +|+.|||+++|++.   .    .++|+|+.|...|++....      .+.|.+++..-.|
T Consensus        39 ~~~~eia~~~gl~k---s----tv~r~l~tL~~~G~v~~~~------~~~Y~lg~~~~~l   85 (260)
T 2o0y_A           39 RSLKELVEGTKLPK---T----TVVRLVATMCARSVLTSRA------DGSYSLGPEMLRW   85 (260)
T ss_dssp             BCHHHHHHHHCCCH---H----HHHHHHHHHHHTTSEEECT------TSCEEECHHHHHH
T ss_pred             cCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCEEECC------CCeEEecHHHHHH
Confidence            47899999999954   7    8999999999999998764      2489998875444

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

Probab=95.42  E-value=0.019  Score=38.34  Aligned_cols=56  Identities=13%  Similarity=0.175  Sum_probs=40.7

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceee--ccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQ--NFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~--~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.+++++   .    .+.|+++-|...|++...  ...+|.-...+.+|+.|+.+...
T Consensus        52 ~t~~eLa~~l~~~~---~----~vs~~l~~Le~~Glv~r~~~~~~~D~R~~~~~lT~~G~~~~~~  109 (151)
T 3kp7_A           52 LTVGQITEKQGVNK---A----AVSRRVKKLLNAELVKLEKPDSNTDQRLKIIKLSNKGKKYIKE  109 (151)
T ss_dssp             BCHHHHHHHHCSCS---S----HHHHHHHHHHHTTSEEC-----------CCBEECHHHHHHHHH
T ss_pred             cCHHHHHHHHCCCH---H----HHHHHHHHHHHCCCEEeeCCCCCCCCCeeEEEECHhHHHHHHH
Confidence            47899999999955   7    899999999999999852  12122112468999999988754

>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=95.35  E-value=0.023  Score=36.54  Aligned_cols=53  Identities=11%  Similarity=0.067  Sum_probs=42.6

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhc
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLK   62 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~   62 (128)
                      ++..|||+.+++   +..    .|.|++.-|...|++..... +++ .++..+|+.|+.+..
T Consensus        37 ~s~~eLa~~l~l---~~s----tLsR~l~rLe~~GLV~r~~~-~D~-R~~v~LT~~G~~~l~   89 (96)
T 2obp_A           37 WSLPKIAKRAQL---PMS----VLRRVLTQLQAAGLADVSVE-ADG-RGHASLTQEGAALAA   89 (96)
T ss_dssp             CBHHHHHHHHTC---CHH----HHHHHHHHHHHTTSEEEEEC-TTS-CEEEEECHHHHHHHH
T ss_pred             cCHHHHHHHhCC---chh----hHHHHHHHHHHCCCEEeecC-CCC-ceeEEECHHHHHHHH
Confidence            368899999999   557    99999999999999986543 332 456899999988764

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

Probab=95.32  E-value=0.0068  Score=37.96  Aligned_cols=54  Identities=13%  Similarity=0.164  Sum_probs=41.4

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhh-HHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQY-VYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~-L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.++++   ..    . +.|+++.|...|++....  .+.....+.+|+.|+.+...
T Consensus        31 ~t~~eLa~~l~is---~~----t~vs~~l~~Le~~Glv~~~~--~drR~~~~~LT~~G~~~~~~   85 (95)
T 2pg4_A           31 PSLAEIVKASGVS---EK----TFFMGLKDRLIRAGLVKEET--LSYRVKTLKLTEKGRRLAEC   85 (95)
T ss_dssp             CCHHHHHHHHCCC---HH----HHHTTHHHHHHHTTSEEEEE--EETTEEEEEECHHHHHHHHH
T ss_pred             CCHHHHHHHHCCC---ch----HHHHHHHHHHHHCCCeecCC--CCCCeEEEEECHhHHHHHHH
Confidence            4789999999994   47    8 999999999999998332  11112358999999888643

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

Probab=95.22  E-value=0.014  Score=39.70  Aligned_cols=43  Identities=9%  Similarity=0.162  Sum_probs=34.2

Q ss_pred             CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHh
Q 045905            2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNA   56 (128)
Q Consensus         2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~   56 (128)
                      |..|||+++++++   .    .|.+||+.|...|++....    | .+.|.|+.-
T Consensus        25 s~~~IA~~~~i~~---~----~l~kIl~~L~~aGlv~s~r----G-~GGy~Lar~   67 (145)
T 1xd7_A           25 SSEIIADSVNTNP---V----VVRRMISLLKKADILTSRA----G-VPGASLKKD   67 (145)
T ss_dssp             CHHHHHHHHTSCH---H----HHHHHHHHHHHTTSEECCS----S-SSSCEESSC
T ss_pred             CHHHHHHHHCcCH---H----HHHHHHHHHHHCCceEeec----C-CCCceecCC
Confidence            5789999999966   8    9999999999999997654    2 345666543

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

Probab=95.21  E-value=0.015  Score=39.61  Aligned_cols=45  Identities=11%  Similarity=0.175  Sum_probs=34.8

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNA   56 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~   56 (128)
                      +|..|||+.+++++   .    .|+++|+.|...|++.....    ..|.|.++.-
T Consensus        29 ~s~~~IA~~~~i~~---~----~l~kil~~L~~aGlv~s~rG----~~GGy~Lar~   73 (143)
T 3t8r_A           29 ISLKSIAEENNLSD---L----YLEQLVGPLRNAGLIRSVRG----AKGGYQLRVP   73 (143)
T ss_dssp             EEHHHHHHHTTCCH---H----HHHHHHHHHHHTTSEEECSS----SSSEEEESSC
T ss_pred             cCHHHHHHHHCcCH---H----HHHHHHHHHHHCCEEEecCC----CCCCeeecCC
Confidence            36889999999965   8    99999999999999875541    1345776543

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

Probab=95.20  E-value=0.036  Score=37.55  Aligned_cols=55  Identities=13%  Similarity=0.201  Sum_probs=42.9

Q ss_pred             CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +..|||..+++   +..    .+.|++.-|...|++......+|.-...+.+|+.|+.+...
T Consensus        48 ~~~eLa~~l~~---~~~----tvs~~v~~Le~~GlV~R~~~~~DrR~~~l~LT~~G~~~~~~  102 (151)
T 4aik_A           48 SQIQLAKAIGI---EQP----SLVRTLDQLEEKGLITRHTSANDRRAKRIKLTEQSSPIIEQ  102 (151)
T ss_dssp             CHHHHHHHHTS---CHH----HHHHHHHHHHHTTSEEEEECSSCTTCEEEEECGGGHHHHHH
T ss_pred             cHHHHHHHHCc---CHH----HHHHHHHHHHhCCCeEeecCCCCCcchhhhcCHHHHHHHHH
Confidence            56899999999   448    99999999999999976543333212358999999988754

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

Probab=95.20  E-value=0.025  Score=35.36  Aligned_cols=53  Identities=19%  Similarity=0.307  Sum_probs=41.6

Q ss_pred             CCHHHH----HHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNEL----INALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eL----A~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..||    |+.+++   +..    .+.|+++.|...|++......   ....|.+|+.|+.+...
T Consensus        23 ~~~~el~~~la~~l~i---s~~----tvs~~l~~Le~~gli~r~~~~---r~~~~~LT~~G~~~~~~   79 (99)
T 1tbx_A           23 IATYDLYKKVNAEFPM---STA----TFYDAKKFLIQEGFVKERQER---GEKRLYLTEKGKLFAIS   79 (99)
T ss_dssp             CBHHHHHHHHHTTSCC---CHH----HHHHHHHHHHHTTSEEEEEET---TEEEEEECHHHHHHHHH
T ss_pred             cCHHHHHHHHHHHcCC---CHH----HHHHHHHHHHHCCCEEEEecC---CceEEEECHHHHHHHHH
Confidence            367788    899999   448    999999999999999764321   13579999999988754

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

Probab=95.19  E-value=0.015  Score=39.22  Aligned_cols=56  Identities=14%  Similarity=0.162  Sum_probs=42.2

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||..+++   +..    .+.|++.-|...|++......+|.-.....+|+.|+.+.+.
T Consensus        52 ~t~~eLa~~l~~---~~~----tvs~~v~~Le~~Glv~r~~~~~DrR~~~l~LT~~G~~~~~~  107 (147)
T 4b8x_A           52 LPMSKIGERLMV---HPT----SVTNTVDRLVRSGLVAKRPNPNDGRGTLATITDKGREVVEA  107 (147)
T ss_dssp             EEHHHHHHHHTC---CHH----HHHHHHHHHHHTTSEEEEECC----CEEEEECHHHHHHHHH
T ss_pred             cCHHHHHHHHCC---CHH----HHHHHHHHHHhCCCEEEeecCCcCceeEEEECHHHHHHHHH
Confidence            367899999999   448    99999999999999976653333212358999999988753

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

Probab=95.19  E-value=0.016  Score=40.41  Aligned_cols=44  Identities=14%  Similarity=0.246  Sum_probs=34.8

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechH
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATN   55 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~   55 (128)
                      +|..|||+.+++++   .    .|+++|+.|...|++.....    ..|.|.|+.
T Consensus        45 ~s~~eIA~~~~i~~---~----~l~kil~~L~~aGlv~s~rG----~~GGy~Lar   88 (159)
T 3lwf_A           45 ISLRSIAQDKNLSE---H----YLEQLIGPLRNAGIVKSIRG----AHGGYVLNG   88 (159)
T ss_dssp             BCHHHHHHHHTCCH---H----HHHHHHHHHHHTTSEEEECS----TTCEEEECS
T ss_pred             cCHHHHHHHHCcCH---H----HHHHHHHHHHHCCeEEEecC----CCCceEecC
Confidence            47899999999965   8    99999999999999976542    134577653

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

Probab=95.18  E-value=0.0097  Score=39.86  Aligned_cols=56  Identities=14%  Similarity=0.167  Sum_probs=40.3

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.++++   +.    .+.|+++-|...|++......+|.-...+.+|+.|+.+...
T Consensus        56 ~~~~eLa~~l~~~---~~----~vs~~l~~L~~~Glv~r~~~~~D~R~~~~~LT~~G~~~~~~  111 (149)
T 4hbl_A           56 QTLNSIGRHLDLS---SN----TLTPMLKRLEQSGWVKRERQQSDKRQLIITLTDNGQQQQEA  111 (149)
T ss_dssp             EEHHHHHHHHTCC---HH----HHHHHHHHHHHHTSEEC---------CEEEECSHHHHHHHH
T ss_pred             CCHHHHHHHHCCC---HH----HHHHHHHHHHHCCCEeeCCCCCCcceeeeeECHHHHHHHHH
Confidence            3678999999994   48    99999999999999976543222212469999999988754

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

Probab=95.12  E-value=0.027  Score=35.92  Aligned_cols=50  Identities=20%  Similarity=0.214  Sum_probs=38.9

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL   60 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L   60 (128)
                      +|..|||+.+++++   .    .+.|.|+.|...|++.....   +....|.+|+-+...
T Consensus        35 ~~~~ela~~l~is~---~----tv~~~l~~L~~~gli~~~~~---gr~~~y~l~~~~~~~   84 (114)
T 2oqg_A           35 QSASSLATRLPVSR---Q----AIAKHLNALQACGLVESVKV---GREIRYRALGAELNK   84 (114)
T ss_dssp             BCHHHHHHHSSSCH---H----HHHHHHHHHHHTTSEEEEEE---TTEEEEEECSHHHHH
T ss_pred             CCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCeeEEec---CCEEEEEechHHHHH
Confidence            47899999999944   7    89999999999999976542   112459999987544

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

Probab=95.10  E-value=0.018  Score=38.91  Aligned_cols=55  Identities=13%  Similarity=0.168  Sum_probs=38.2

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.+++   ++.    .+.|++.-|...|++....+ +|.-.....+|+.|+.+...
T Consensus        53 ~t~~eLa~~l~~---~~~----tvsr~v~~Le~~glVr~~~~-~DrR~~~v~LT~~G~~~~~~  107 (148)
T 4fx0_A           53 LTMSELAARIGV---ERT----TLTRNLEVMRRDGLVRVMAG-ADARCKRIELTAKGRAALQK  107 (148)
T ss_dssp             -CHHHHHHHHTC---CHH----HHHHHHHHHHHTTSBC------------CCBCHHHHHHHHH
T ss_pred             cCHHHHHHHHCC---Chh----hHHHHHHHHHHCCCEEeeCC-CCCCeeEEEECHHHHHHHHH
Confidence            478999999999   448    99999999999999854332 22212368999999988654

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

Probab=95.08  E-value=0.013  Score=40.61  Aligned_cols=56  Identities=13%  Similarity=0.126  Sum_probs=41.3

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.+++++   .    .+.|+++-|...|++.......|.....+.+|+.|+.+...
T Consensus        87 ~t~~eLa~~l~is~---~----tvs~~l~~Le~~GlV~r~~~~~DrR~~~~~LT~~G~~~~~~  142 (181)
T 2fbk_A           87 LRPTELSALAAISG---P----STSNRIVRLLEKGLIERREDERDRRSASIRLTPQGRALVTH  142 (181)
T ss_dssp             BCHHHHHHHCSCCS---G----GGSSHHHHHHHHTSEECCC-------CCBEECHHHHHHHHH
T ss_pred             CCHHHHHHHHCCCH---H----HHHHHHHHHHHCcCEEecCCCCCCCeeEEEECHHHHHHHHH
Confidence            47899999999955   7    88999999999999976542222112368999999988754

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

Probab=95.07  E-value=0.017  Score=39.47  Aligned_cols=44  Identities=14%  Similarity=0.116  Sum_probs=34.1

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNA   56 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~   56 (128)
                      +|..|||+.+++++   .    .|+++|+.|...|++.....     .|.|.++.-
T Consensus        31 ~~~~~iA~~~~i~~---~----~l~kil~~L~~~Glv~s~rG-----~GGy~L~~~   74 (149)
T 1ylf_A           31 CTSDYMAESVNTNP---V----VIRKIMSYLKQAGFVYVNRG-----PGGAGLLKD   74 (149)
T ss_dssp             CCHHHHHHHHTSCH---H----HHHHHHHHHHHTTSEEEC--------CCEEESSC
T ss_pred             cCHHHHHHHHCcCH---H----HHHHHHHHHHHCCcEEEccC-----CCceEeCCC
Confidence            47899999999965   8    99999999999999875541     345766553

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

Probab=94.92  E-value=0.016  Score=38.37  Aligned_cols=55  Identities=11%  Similarity=0.012  Sum_probs=42.0

Q ss_pred             CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      |..|||..+++   ++.    .+.|+++-|...|++.......|.-...+.+|+.|+.+...
T Consensus        52 ~~~~la~~l~~---~~~----tvs~~l~~Le~~Glv~r~~~~~D~R~~~~~LT~~G~~~~~~  106 (144)
T 3f3x_A           52 SMVYLANRYFV---TQS----AITAAVDKLEAKGLVRRIRDSKDRRIVIVEITPKGRQVLLE  106 (144)
T ss_dssp             EHHHHHHHHTC---CHH----HHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHHHH
T ss_pred             CHHHHHHHHCC---Chh----HHHHHHHHHHHCCCEEeccCCCCCceEEEEECHHHHHHHHH
Confidence            56899999999   448    99999999999999976543221111359999999988754

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

Probab=94.87  E-value=0.024  Score=34.47  Aligned_cols=34  Identities=21%  Similarity=0.372  Sum_probs=29.1

Q ss_pred             CCHHHHHHhC-----CCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905            1 MTLNELINAL-----PFHPIKAQYVAQYVYRFMWILVHSGFFAQQN   41 (128)
Q Consensus         1 ~S~~eLA~~~-----~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~   41 (128)
                      +|+.||++.+     ++   ...    .++|.|..|...|++....
T Consensus        34 ~s~~el~~~l~~~~~~i---s~~----TVyR~L~~L~~~Glv~~~~   72 (83)
T 2fu4_A           34 VSAEDLYKRLIDMGEEI---GLA----TVYRVLNQFDDAGIVTRHN   72 (83)
T ss_dssp             BCHHHHHHHHHHTTCCC---CHH----HHHHHHHHHHHHTSEEEEE
T ss_pred             CCHHHHHHHHHHhCCCC---CHh----hHHHHHHHHHHCCCeEEEe
Confidence            4789999999     66   447    8999999999999998664

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

Probab=94.86  E-value=0.023  Score=39.56  Aligned_cols=45  Identities=18%  Similarity=0.304  Sum_probs=34.8

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNA   56 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~   56 (128)
                      +|..|||+++++++   .    .|.++|+.|...|++.....    ..|.|.|+.-
T Consensus        29 ~s~~~IA~~~~is~---~----~l~kil~~L~~aGlv~s~rG----~~GGy~Lar~   73 (162)
T 3k69_A           29 VASRELAQSLHLNP---V----MIRNILSVLHKHGYLTGTVG----KNGGYQLDLA   73 (162)
T ss_dssp             BCHHHHHHHHTSCG---G----GTHHHHHHHHHTTSSEEECS----TTCEEECCSC
T ss_pred             cCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCEEeecC----CCCCeEecCC
Confidence            47899999999966   8    99999999999999865431    1245766543

>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=94.84  E-value=0.021  Score=35.67  Aligned_cols=53  Identities=17%  Similarity=0.287  Sum_probs=39.1

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLL   61 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~   61 (128)
                      +|..|||+.++++   ..    .++|+++.|...|++...... ++....+.+|+.++.+.
T Consensus        35 ~s~~ela~~l~is---~~----tv~~~l~~L~~~glv~~~~~~-~~r~~~~~~t~~g~~~~   87 (109)
T 1sfx_A           35 MRVSEIARELDLS---AR----FVRDRLKVLLKRGFVRREIVE-KGWVGYIYSAEKPEKVL   87 (109)
T ss_dssp             BCHHHHHHHHTCC---HH----HHHHHHHHHHHTTSEEEEEEE-SSSEEEEEEECCHHHHH
T ss_pred             CCHHHHHHHHCCC---HH----HHHHHHHHHHHCCCEEEEeec-CCceEEEEecCcHHHHH
Confidence            4789999999994   48    999999999999999765421 11124567777776654

>2ia2_A Putative transcriptional regulator; SAD, PSI-2, structural genomics, structure initiative, midwest center for structural genomic transcription; 2.10A {Rhodococcus SP}

Probab=94.83  E-value=0.015  Score=43.28  Aligned_cols=46  Identities=24%  Similarity=0.303  Sum_probs=37.9

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL   60 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L   60 (128)
                      +|+.|||+++|++.   .    .++|+|+.|...|++...       ++.|.+++.-..|
T Consensus        37 ~~~~eia~~~gl~~---s----tv~r~l~tL~~~G~v~~~-------~~~Y~Lg~~~~~l   82 (265)
T 2ia2_A           37 RTLSDVARATDLTR---A----TARRFLLTLVELGYVATD-------GSAFWLTPRVLEL   82 (265)
T ss_dssp             EEHHHHHHHHTCCH---H----HHHHHHHHHHHHTSEEES-------SSEEEECGGGGGT
T ss_pred             CCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCEEec-------CCEEEEcHHHHHH
Confidence            36899999999954   7    899999999999999764       2689998865444

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

Probab=94.75  E-value=0.035  Score=37.46  Aligned_cols=49  Identities=14%  Similarity=0.102  Sum_probs=41.0

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhc
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLK   62 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~   62 (128)
                      +|..+||+.+++   +..    .+.|.++.|...|++....      .+.+.+|+.|+.+..
T Consensus        55 ~~~~~la~~l~v---s~~----tvs~~l~~Le~~Glv~r~~------~~~~~lT~~g~~~~~  103 (155)
T 2h09_A           55 ARQVDMAARLGV---SQP----TVAKMLKRLATMGLIEMIP------WRGVFLTAEGEKLAQ  103 (155)
T ss_dssp             CCHHHHHHHHTS---CHH----HHHHHHHHHHHTTCEEEET------TTEEEECHHHHHHHH
T ss_pred             cCHHHHHHHhCc---CHH----HHHHHHHHHHHCCCEEEec------CCceEEChhHHHHHH
Confidence            478899999999   447    8999999999999987654      356899999987764

>3u1d_A Uncharacterized protein; GNTR-superfamily, structural genomics, PSI-biology, midwest for structural genomics, MCSG; 1.80A {Halomicrobium mukohataei}

Probab=94.71  E-value=0.065  Score=37.14  Aligned_cols=74  Identities=16%  Similarity=0.142  Sum_probs=51.7

Q ss_pred             CCHHHHHHhCC-CCCCCchhhhhhHHHHHHHHHhcCcceeeccCCC----C-cccceechHhhhhhhcCCCCcHHHHHHH
Q 045905            1 MTLNELINALP-FHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQN----D-QERSYVATNASKLLLKDITLTVRSFLQA   74 (128)
Q Consensus         1 ~S~~eLA~~~~-~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~----~-~~~~y~~T~~s~~L~~~~~~s~~~~~~~   74 (128)
                      +|+.||+..++ +   ...    .|+|-|..|+..|++......++    | -...|.+|+.|+.+...-          
T Consensus        46 ~ta~eL~~~l~~l---S~a----TVyrhL~~L~eaGLV~~~~~~~~~~~rGrP~k~Y~LT~~Gr~~l~~y----------  108 (151)
T 3u1d_A           46 LSVEELLYRNPDE---TEA----NLRYHVDELVDRGIVEKIPVPRAKSVDDPPTTFYAVTGEGIALLRAV----------  108 (151)
T ss_dssp             BCHHHHHHHCTTS---CHH----HHHHHHHHHHHTTSEEEEECCCCTTSSSCCCEEEEECHHHHHHHHHT----------
T ss_pred             CCHHHHHHhcCCC---CHH----HHHHHHHHHHHCCCeEEeecCcCcccCCCCceEEEECHHHHHHHHHh----------
Confidence            37899999988 7   447    89999999999999986543211    1 124799999998775321          


Q ss_pred             hcChhhHHHHHhHHHhhh
Q 045905           75 VLDPILTTPCQHVTTWFQ   92 (128)
Q Consensus        75 ~~~~~~~~~~~~l~~~~~   92 (128)
                       ..-....+|..|.+.+.
T Consensus       109 -~~la~~~alr~l~~~v~  125 (151)
T 3u1d_A          109 -SMYEEAAVWRSVYEQME  125 (151)
T ss_dssp             -TCSTHHHHTHHHHHHSC
T ss_pred             -HHHhHHHHHHHHHHHhh
Confidence             01122367888888873

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

Probab=94.70  E-value=0.053  Score=36.06  Aligned_cols=54  Identities=17%  Similarity=0.222  Sum_probs=38.7

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCC-C-cccceechHhhhhhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQN-D-QERSYVATNASKLLL   61 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~-~-~~~~y~~T~~s~~L~   61 (128)
                      .|..+||+++++   +..    .+.|+++.|...|++......++ | ....|.++|+-.-|.
T Consensus        52 ps~~~LA~~l~~---s~~----~V~~~l~~Le~kGlI~~~~~~~~~g~~~~~Ydl~pl~~kL~  107 (128)
T 2vn2_A           52 PTPAELAERMTV---SAA----ECMEMVRRLLQKGMIAIEEHTDEQGIRNEKYTLEPLWEKLV  107 (128)
T ss_dssp             CCHHHHHHTSSS---CHH----HHHHHHHHHHHTTSSEECC----------CEECHHHHHHHH
T ss_pred             CCHHHHHHHHCc---CHH----HHHHHHHHHHHCCCEEEEeEECCCCcEEEEEehHHHHHHHH
Confidence            478999999999   448    89999999999999976543222 2 124799998876663

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

Probab=94.51  E-value=0.04  Score=39.72  Aligned_cols=50  Identities=18%  Similarity=0.277  Sum_probs=42.6

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      ++..|||+.+++   +++    .+.|+++-|...|++....      .+.+.+|+.|+.+...
T Consensus        21 ~~~~~lA~~l~v---s~~----tvs~~l~~Le~~GlV~r~~------~~~i~LT~~G~~~~~~   70 (214)
T 3hrs_A           21 ITNKEIAQLMQV---SPP----AVTEMMKKLLAEELLIKDK------KAGYLLTDLGLKLVSD   70 (214)
T ss_dssp             CCHHHHHHHHTC---CHH----HHHHHHHHHHHTTSEEEET------TTEEEECHHHHHHHHH
T ss_pred             cCHHHHHHHHCC---Chh----HHHHHHHHHHHCCCEEEec------CCCeEECHHHHHHHHH
Confidence            478999999999   448    9999999999999998765      3679999999887654

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

Probab=94.49  E-value=0.046  Score=34.44  Aligned_cols=46  Identities=17%  Similarity=0.187  Sum_probs=36.6

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNA   56 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~   56 (128)
                      +|+.|||+.+|+++   .    .+.+.|+.|...|++.....   |....|.+|+-
T Consensus        37 ~~~~ela~~l~is~---~----tvs~~L~~L~~~Glv~~~~~---g~~~~y~l~~~   82 (102)
T 3pqk_A           37 FSVGELEQQIGIGQ---P----TLSQQLGVLRESGIVETRRN---IKQIFYRLTEA   82 (102)
T ss_dssp             BCHHHHHHHHTCCT---T----HHHHHHHHHHHTTSEEEECS---SSCCEEEECSS
T ss_pred             CCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCeEEEEe---CCEEEEEECcH
Confidence            47899999999955   7    89999999999999976542   11356888875

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

Probab=94.29  E-value=0.039  Score=39.40  Aligned_cols=56  Identities=9%  Similarity=0.100  Sum_probs=41.6

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.+++   +..    .+.|+++.|...|++.......|.-...+.+|+.|+.+...
T Consensus        63 ~t~~eLa~~l~i---~~s----tvs~~l~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~~  118 (207)
T 2fxa_A           63 ASISEIAKFGVM---HVS----TAFNFSKKLEERGYLRFSKRLNDKRNTYVQLTEEGTEVFWS  118 (207)
T ss_dssp             EEHHHHHHHTTC---CHH----HHHHHHHHHHHHTSEEEECC------CEEEECHHHHHHHHH
T ss_pred             cCHHHHHHHHCC---CHH----HHHHHHHHHHHCCCEEEecCCCCCceEEEEECHHHHHHHHH
Confidence            367899999999   448    99999999999999976543222112368999999988643

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

Probab=94.22  E-value=0.064  Score=36.26  Aligned_cols=53  Identities=15%  Similarity=0.202  Sum_probs=40.0

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCC-CC-cccceechHhhhhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQ-ND-QERSYVATNASKLL   60 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~-~~-~~~~y~~T~~s~~L   60 (128)
                      .|..+||+++++   ++.    .+.|++.-|...|++.-....+ +| ....|.+||+=.-|
T Consensus        52 ps~~~LA~~~~~---s~~----~v~~~L~~L~~KGlI~i~~~~d~~g~~~~~ydL~pL~ekL  106 (135)
T 2v79_A           52 PTPNQLQEGMSI---SVE----ECTNRLRMFIQKGFLFIEECEDQNGIKFEKYSLQPLWGKL  106 (135)
T ss_dssp             CCHHHHHTTSSS---CHH----HHHHHHHHHHHHTSCEEEEEECTTCCEEEEEECHHHHHHH
T ss_pred             CCHHHHHHHHCc---CHH----HHHHHHHHHHHCCCEEEEeEecCCCceEEEeeHHHHHHHH
Confidence            378999999999   448    8999999999999997643212 12 12579999986555

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

Probab=93.94  E-value=0.042  Score=33.94  Aligned_cols=47  Identities=17%  Similarity=0.150  Sum_probs=37.0

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNAS   57 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s   57 (128)
                      +|..|||+.++++   ..    .+.|.|+.|...|++.....   +....|.+|+-+
T Consensus        39 ~s~~ela~~l~is---~~----tvs~~l~~L~~~glv~~~~~---~r~~~y~l~~~~   85 (99)
T 3cuo_A           39 TSAGELTRITGLS---AS----ATSQHLARMRDEGLIDSQRD---AQRILYSIKNEA   85 (99)
T ss_dssp             EEHHHHHHHHCCC---HH----HHHHHHHHHHHTTSEEEEEC---SSCEEEEECCHH
T ss_pred             cCHHHHHHHHCcC---HH----HHHHHHHHHHHCCCEEEEec---CCEEEEEEChHH
Confidence            3678999999994   47    89999999999999976542   113468888876

>3cta_A Riboflavin kinase; structural genomics, transferase, PSI-2, protein structure initiative; 2.20A {Thermoplasma acidophilum dsm 1728} SCOP: a.4.5.28 b.43.5.2

Probab=93.73  E-value=0.063  Score=38.86  Aligned_cols=53  Identities=17%  Similarity=0.167  Sum_probs=42.5

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..++|+++++   .++    .+.|.++.|-..|+|......   ....+.+|+.|+.+...
T Consensus        28 ~s~s~aA~~L~i---sq~----avSr~I~~LE~~~L~~R~~~~---R~~~v~LT~~G~~l~~~   80 (230)
T 3cta_A           28 LTSSKLADMLGI---SQQ----SASRIIIDLEKNGYITRTVTK---RGQILNITEKGLDVLYT   80 (230)
T ss_dssp             CCHHHHHHHHTS---CHH----HHHHHHHHHHHTTSEEEEEET---TEEEEEECHHHHHHHHH
T ss_pred             cCHHHHHHHHCC---CHH----HHHHHHHHHHHCCCEEEEEcC---CeEEEEECHHHHHHHHH
Confidence            468999999999   448    999999999999999876310   12579999999988753

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

Probab=93.51  E-value=0.067  Score=32.91  Aligned_cols=33  Identities=12%  Similarity=0.083  Sum_probs=29.5

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceee
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQ   40 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~   40 (128)
                      +|+.|||+.+++++   .    .++|.|..|...|++...
T Consensus        17 vsv~eLa~~l~VS~---~----TIRrdL~~Le~~G~l~R~   49 (78)
T 1xn7_A           17 MEAAQISQTLNTPQ---P----MINAMLQQLESMGKAVRI   49 (78)
T ss_dssp             BCHHHHHHHTTCCH---H----HHHHHHHHHHHHTSEEEE
T ss_pred             CcHHHHHHHHCcCH---H----HHHHHHHHHHHCCCEEEe
Confidence            57899999999944   8    999999999999998765

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

Probab=93.51  E-value=0.055  Score=33.74  Aligned_cols=47  Identities=15%  Similarity=0.224  Sum_probs=36.5

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNAS   57 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s   57 (128)
                      +|..|||+.+|+++   .    .+.|.|+.|...|++.....   |....|.+|+-.
T Consensus        37 ~~~~ela~~l~is~---~----tvs~~L~~L~~~Glv~~~~~---g~~~~y~l~~~~   83 (98)
T 3jth_A           37 LSVGELCAKLQLSQ---S----ALSQHLAWLRRDGLVTTRKE---AQTVYYTLKSEE   83 (98)
T ss_dssp             EEHHHHHHHHTCCH---H----HHHHHHHHHHHTTSEEEECC---TTCCEEEECCHH
T ss_pred             CCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCeEEEEe---CCEEEEEECHHH
Confidence            36889999999944   7    89999999999999976542   113468888754

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

Probab=93.50  E-value=0.097  Score=31.68  Aligned_cols=33  Identities=15%  Similarity=0.244  Sum_probs=28.9

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceee
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQ   40 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~   40 (128)
                      +|..|||+.+|+++   .    .++|.|+.|...|++...
T Consensus        15 ~s~~eLa~~lgvs~---~----tv~r~L~~L~~~GlI~~~   47 (81)
T 2htj_A           15 GKTAEIAEALAVTD---Y----QARYYLLLLEKAGMVQRS   47 (81)
T ss_dssp             CCHHHHHHHHTSCH---H----HHHHHHHHHHHHTSEEEE
T ss_pred             CCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCEEEe
Confidence            57899999999944   7    899999999999999743

>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=93.26  E-value=0.15  Score=32.58  Aligned_cols=52  Identities=8%  Similarity=0.197  Sum_probs=38.7

Q ss_pred             HHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            4 NELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         4 ~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      .+|.+..+..+ ++.    .|+.+|+-|...|++....  ++ ...+|.+|+.|+.....
T Consensus        32 ~ei~~~~~~~i-s~G----tlYp~L~rLe~~GlI~~~~--~~-~rk~Y~iT~~Gr~~l~~   83 (99)
T 2co5_A           32 SEILKRFDIDI-SDG----VLYPLIDSLIDDKILREEE--AP-DGKVLFLTEKGMKEFEE   83 (99)
T ss_dssp             HHHHHHHCCBC-CHH----HHHHHHHHHHHTTSEEEEC--CT-TSCEEEECHHHHHHHHH
T ss_pred             HHHHHHhCCCC-CCC----cHHHHHHHHHHCCCEEEee--CC-CcEEEEECHHHHHHHHH
Confidence            56777766533 557    8999999999999997654  11 13579999999977654

>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=92.95  E-value=0.14  Score=32.74  Aligned_cols=49  Identities=12%  Similarity=0.241  Sum_probs=40.7

Q ss_pred             CCHHHHHH-hCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELIN-ALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~-~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|+.|||+ .+++   +..    .|.|-++.|...|++..++      ++ +.+|+.|+-+...
T Consensus        31 ~t~~~Lae~~l~~---drs----tvsrnl~~L~r~GlVe~~~------~D-l~LT~~G~~~l~~   80 (95)
T 1bja_A           31 ITAAEVREVHPDL---GNA----VVNSNIGVLIKKGLVEKSG------DG-LIITGEAQDIISN   80 (95)
T ss_dssp             BCHHHHHHTCTTS---CHH----HHHHHHHHHHTTTSEEEET------TE-EEECHHHHHHHHH
T ss_pred             CCHHHHHHHHhcc---cHH----HHHHHHHHHHHCCCeecCC------CC-eeeCHhHHHHHHH
Confidence            47899999 8888   568    9999999999999998222      34 9999999988754

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

Probab=92.88  E-value=0.07  Score=33.59  Aligned_cols=33  Identities=12%  Similarity=0.064  Sum_probs=29.2

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceee
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQ   40 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~   40 (128)
                      +|+.|||+.+++++   .    .++|.|..|...|++...
T Consensus        17 vsv~eLA~~l~VS~---~----TIRrDL~~Le~~G~l~R~   49 (87)
T 2k02_A           17 MEAKQLSARLQTPQ---P----LIDAMLERMEAMGKVVRI   49 (87)
T ss_dssp             EEHHHHHHHTTCCH---H----HHHHHHHHHHTTCCSEEE
T ss_pred             CcHHHHHHHHCcCH---H----HHHHHHHHHHHCCCEEEE
Confidence            47899999999944   8    999999999999998765

>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=92.74  E-value=0.1  Score=37.74  Aligned_cols=48  Identities=13%  Similarity=0.115  Sum_probs=40.9

Q ss_pred             HHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            3 LNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         3 ~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      ..|||+++++   +..    .+.|+++-|...|++....      .+.+.+|+.|+.+...
T Consensus        27 ~~~La~~l~v---s~~----tvs~~l~~Le~~GlV~r~~------~~~v~LT~~G~~~~~~   74 (230)
T 1fx7_A           27 RARIAERLDQ---SGP----TVSQTVSRMERDGLLRVAG------DRHLELTEKGRALAIA   74 (230)
T ss_dssp             HHHHHHHHTC---CHH----HHHHHHHHHHHTTSEEECT------TSCEEECHHHHHHHHH
T ss_pred             HHHHHHHHCc---CHH----HHHHHHHHHHHCCCEEEeC------CccEEECHHHHHHHHH
Confidence            3899999999   448    8999999999999998765      3679999999988653

>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=92.25  E-value=0.12  Score=32.81  Aligned_cols=47  Identities=11%  Similarity=0.124  Sum_probs=36.0

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNAS   57 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s   57 (128)
                      +|+.|||+.+++++   .    .+.|.|+.|...|++.....   |....|.+|+-.
T Consensus        40 ~~~~ela~~l~is~---s----tvs~~L~~L~~~Glv~~~~~---gr~~~y~l~~~~   86 (106)
T 1r1u_A           40 ASVGHISHQLNLSQ---S----NVSHQLKLLKSVHLVKAKRQ---GQSMIYSLDDIH   86 (106)
T ss_dssp             BCHHHHHHHHTCCH---H----HHHHHHHHHHHTTSEEEEEE---TTEEEEEESSHH
T ss_pred             CCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCeEEEEe---CCEEEEEEChHH
Confidence            47899999999944   7    89999999999999976542   112368887654

>2qm3_A Predicted methyltransferase; putative methyltransferase, structural genomics, pyrococcus PSI-2, protein structure initiative; HET: MSE; 2.05A {Pyrococcus furiosus dsm 3638}

Probab=92.21  E-value=0.1  Score=40.32  Aligned_cols=46  Identities=11%  Similarity=0.073  Sum_probs=38.1

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLL   61 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~   61 (128)
                      +|..|||.++++++   .    .++++|+.|+..|++...       ++ |.+|+.++.+.
T Consensus        56 ~t~~eLa~~~g~~~---~----~v~~~L~~l~~~gll~~~-------~~-~~lt~~~~~~l  101 (373)
T 2qm3_A           56 DDIWRIVDLSEEPL---P----LVVAILESLNELGYVTFE-------DG-VKLTEKGEELV  101 (373)
T ss_dssp             SCHHHHHHHHTSCH---H----HHHHHHHHHHHTTSEECS-------SS-SEECHHHHHHH
T ss_pred             CCHHHHHHHhCCCh---H----HHHHHHHHHhhCCcEEEC-------CC-EEECHHHHHHH
Confidence            47899999999944   7    999999999999999653       24 99999877554

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

Probab=91.98  E-value=0.081  Score=33.87  Aligned_cols=46  Identities=9%  Similarity=0.098  Sum_probs=35.6

Q ss_pred             CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhh
Q 045905            2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNAS   57 (128)
Q Consensus         2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s   57 (128)
                      |+.|||+.+|+++   .    .+.|.|+.|...|++.....   |....|.+|+-+
T Consensus        40 s~~eLa~~lgis~---s----tvs~~L~~L~~~GlV~~~~~---gr~~~y~l~~~~   85 (108)
T 2kko_A           40 AVEAIATATGMNL---T----TASANLQALKSGGLVEARRE---GTRQYYRIAGED   85 (108)
T ss_dssp             EHHHHHHHHTCCH---H----HHHHHHHHHHHHTSEEEEEE---TTEEEEEESCHH
T ss_pred             CHHHHHHHHCcCH---H----HHHHHHHHHHHCCCeEEEEe---CCEEEEEEChHH
Confidence            6789999999944   7    89999999999999975542   112468887654

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

Probab=91.98  E-value=0.11  Score=33.75  Aligned_cols=47  Identities=15%  Similarity=0.237  Sum_probs=37.3

Q ss_pred             CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhh
Q 045905            2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASK   58 (128)
Q Consensus         2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~   58 (128)
                      |+.|||+.+|+++   .    .+.+.|+.|...|++.....   |....|.+|+-+.
T Consensus        33 ~~~eLa~~l~is~---~----tvs~hL~~L~~~GlV~~~~~---gr~~~y~l~~~~~   79 (118)
T 3f6o_A           33 TVSELAKPFDMAL---P----SFMKHIHFLEDSGWIRTHKQ---GRVRTCAIEKEPF   79 (118)
T ss_dssp             EHHHHHTTCCSCH---H----HHHHHHHHHHHTTSEEEEEE---TTEEEEEECSHHH
T ss_pred             CHHHHHHHhCcCH---H----HHHHHHHHHHHCCCeEEEec---CCEEEEEECHHHH
Confidence            6789999999944   7    89999999999999976542   1135799998664

>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=91.95  E-value=0.14  Score=33.50  Aligned_cols=48  Identities=15%  Similarity=0.225  Sum_probs=35.3

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNAS   57 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s   57 (128)
                      +|..|||+.+++++   .    .+.|+++.|...|++......++  .+.|.++..+
T Consensus        42 ~t~~ela~~l~~~~---s----tvs~~l~~L~~~G~v~r~~~~~d--~r~~~~~~~~   89 (152)
T 1ku9_A           42 LTISDIMEELKISK---G----NVSMSLKKLEELGFVRKVWIKGE--RKNYYEAVDG   89 (152)
T ss_dssp             EEHHHHHHHHTCCH---H----HHHHHHHHHHHTTSEEEECCTTC--SSCEEEECCH
T ss_pred             CCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCEEEEecCCC--ceEEEeecch
Confidence            36899999999944   7    99999999999999976532111  3456665533

>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=91.81  E-value=0.12  Score=31.49  Aligned_cols=44  Identities=14%  Similarity=0.153  Sum_probs=33.3

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechH
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATN   55 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~   55 (128)
                      +|+.|||+++|++   ..    .+.|.|.-|...|++.....    .+++|..+|
T Consensus        32 ~t~~eLA~~Lgvs---~~----tV~~~L~~L~~~G~I~~~g~----~~~~W~i~~   75 (77)
T 1qgp_A           32 TTAHDLSGKLGTP---KK----EINRVLYSLAKKGKLQKEAG----TPPLWKIAV   75 (77)
T ss_dssp             EEHHHHHHHHCCC---HH----HHHHHHHHHHHHTSEEEECS----SSCEEEECC
T ss_pred             cCHHHHHHHHCcC---HH----HHHHHHHHHHHCCCEEecCC----CCCceEecC
Confidence            4789999999994   47    89999999999999865431    135666554

>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=91.79  E-value=0.18  Score=37.30  Aligned_cols=56  Identities=14%  Similarity=0.204  Sum_probs=43.2

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.+++   ++.    .+.|++.-|...|++......+|.-.....+|+.|+.+...
T Consensus       175 ~t~~eLa~~l~i---~~~----tvt~~v~rLe~~GlV~R~~~~~DrR~~~i~LT~~G~~~~~~  230 (250)
T 1p4x_A          175 VLLKDLIETIHH---KYP----QTVRALNNLKKQGYLIKERSTEDERKILIHMDDAQQDHAEQ  230 (250)
T ss_dssp             EEHHHHHHHSSS---CHH----HHHHHHHHHHHHTSSEEEECSSSTTCEEEECCHHHHHHHHH
T ss_pred             cCHHHHHHHHCC---Chh----hHHHHHHHHHHCCCEEeeCCCCCCCeEEEEECHHHHHHHHH
Confidence            367899999999   448    99999999999999976554333212358899999888653

>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=91.72  E-value=0.18  Score=36.43  Aligned_cols=48  Identities=15%  Similarity=0.141  Sum_probs=40.7

Q ss_pred             HHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            3 LNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         3 ~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      ..+||+++++   ++.    .+.|+++-|...|++....      ...+.+|+.|+.+...
T Consensus        27 ~~~la~~l~v---s~~----tvs~~l~~Le~~GlV~r~~------~~~v~LT~~G~~~~~~   74 (226)
T 2qq9_A           27 RARIAERLEQ---SGP----TVSQTVARMERDGLVVVAS------DRSLQMTPTGRTLATA   74 (226)
T ss_dssp             HHHHHHHHTC---CHH----HHHHHHHHHHHTTSEEECT------TSBEEECHHHHHHHHH
T ss_pred             HHHHHHHHCC---CHH----HHHHHHHHHHHCCCEEEeC------CCCeEECHHHHHHHHH
Confidence            4899999999   448    8999999999999998664      3679999999988654

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

Probab=91.59  E-value=0.16  Score=34.72  Aligned_cols=50  Identities=16%  Similarity=0.224  Sum_probs=39.1

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL   60 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L   60 (128)
                      +|+.|||+.++++   ..    .+.|.|+.|...|++.....   |....|.+|+.+...
T Consensus        72 ~t~~eLa~~lgls---~s----tvs~hL~~L~~aGlV~~~~~---Gr~~~y~lt~~~~~~  121 (151)
T 3f6v_A           72 QTVNNLAAHFPAS---RS----AISQHLRVLTEAGLVTPRKD---GRFRYYRLDPQGLAQ  121 (151)
T ss_dssp             EEHHHHHTTSSSC---HH----HHHHHHHHHHHTTSEEEEEE---TTEEEEEECHHHHHH
T ss_pred             CCHHHHHHHHCcC---HH----HHHHHHHHHHHCCCEEEEec---CCEEEEEEChHHHHH
Confidence            3688999999994   47    89999999999999976542   113579999977543

>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=91.56  E-value=0.1  Score=34.13  Aligned_cols=47  Identities=11%  Similarity=0.115  Sum_probs=35.4

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNAS   57 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s   57 (128)
                      +|+.|||+.+|+++   .    .+.|.|+.|...|++.....   |....|.+|+-+
T Consensus        57 ~s~~eLa~~l~is~---s----tvs~~L~~L~~~Glv~~~~~---gr~~~y~l~~~~  103 (122)
T 1u2w_A           57 LCVCDIANILGVTI---A----NASHHLRTLYKQGVVNFRKE---GKLALYSLGDEH  103 (122)
T ss_dssp             EEHHHHHHHHTCCH---H----HHHHHHHHHHHTTSEEEC-------CCEEEESCHH
T ss_pred             cCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCeEEEEE---CCEEEEEECHHH
Confidence            36789999999944   7    89999999999999975532   112468888764

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

Probab=91.53  E-value=0.1  Score=34.22  Aligned_cols=34  Identities=15%  Similarity=0.181  Sum_probs=29.4

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN   41 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~   41 (128)
                      +|..|||+++++   +..    .++|.|+.|...|++....
T Consensus        43 ~t~~eLa~~l~~---s~s----TV~r~L~~L~~~GlV~r~~   76 (123)
T 3r0a_A           43 IDTDALSKSLKL---DVS----TVQRSVKKLHEKEILQRSQ   76 (123)
T ss_dssp             EEHHHHHHHHTS---CHH----HHHHHHHHHHHTTSEEEEE
T ss_pred             cCHHHHHHHHCc---CHH----HHHHHHHHHHHCCCEEeeC
Confidence            478999999999   448    9999999999999997643

>4esf_A PADR-like transcriptional regulator; PADR family, DNA binding protein, HTH fold; 2.20A {Bacillus cereus}

Probab=91.37  E-value=0.34  Score=31.63  Aligned_cols=44  Identities=14%  Similarity=0.098  Sum_probs=31.6

Q ss_pred             CchhhhhhHHHHHHHHHhcCcceeeccC-CCC-cccceechHhhhhhhcC
Q 045905           16 KAQYVAQYVYRFMWILVHSGFFAQQNFG-QND-QERSYVATNASKLLLKD   63 (128)
Q Consensus        16 ~~~~~~~~L~RlLR~L~~~gvf~e~~~~-~~~-~~~~y~~T~~s~~L~~~   63 (128)
                      ++.    .|+++|+-|...|++...... +++ ....|.+|+.|+.....
T Consensus        43 s~g----tlY~~L~rLe~~GlI~~~~~~~~~g~~rk~Y~LT~~G~~~l~~   88 (117)
T 4esf_A           43 VEG----TVYTILVRLEKKKLVNIEKKPSDMGPPRKFYSLNEAGRQELEL   88 (117)
T ss_dssp             CHH----HHHHHHHHHHHTTCEEEEEEC-----CEEEEEECHHHHHHHHH
T ss_pred             Ccc----HHHHHHHHHHHCCCEEEEeecCCCCCCceEEEECHHHHHHHHH
Confidence            557    899999999999999765321 111 13469999999877543

>1xmk_A Double-stranded RNA-specific adenosine deaminase; winged helix-turn-helix, RNA editing, interferon, ADAR1, hydrolase; 0.97A {Homo sapiens} SCOP: a.4.5.19

Probab=91.29  E-value=0.21  Score=30.81  Aligned_cols=49  Identities=10%  Similarity=0.054  Sum_probs=37.2

Q ss_pred             CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhh
Q 045905            2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL   60 (128)
Q Consensus         2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L   60 (128)
                      |+.|||+.+|+.+  ..    .++|.|..|...|++.....   | ...|.+|+.++-.
T Consensus        27 ta~eiA~~Lgit~--~~----aVr~hL~~Le~eGlV~~~~~---g-RP~w~LT~~g~~~   75 (79)
T 1xmk_A           27 SALNLAKNIGLTK--AR----DINAVLIDMERQGDVYRQGT---T-PPIWHLTDKKRER   75 (79)
T ss_dssp             EHHHHHHHHCGGG--HH----HHHHHHHHHHHTTSEEEECS---S-SCEEEECHHHHTT
T ss_pred             CHHHHHHHcCCCc--HH----HHHHHHHHHHHCCCEEecCC---C-CCCeEeCHhHHhH
Confidence            6889999999832  12    58999999999999864321   1 3489999998644

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

Probab=90.76  E-value=0.23  Score=30.88  Aligned_cols=46  Identities=15%  Similarity=0.160  Sum_probs=33.6

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNAS   57 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s   57 (128)
                      +|+.|||.++|++.   .    .++|.|.-|...|++.....    .+.++.++..+
T Consensus        31 ~sa~eLAk~LgiSk---~----aVr~~L~~Le~eG~I~~~~~----~PP~W~~~~~~   76 (82)
T 1oyi_A           31 ATAAQLTRQLNMEK---R----EVNKALYDLQRSAMVYSSDD----IPPRWFMTTEA   76 (82)
T ss_dssp             EEHHHHHHHSSSCH---H----HHHHHHHHHHHHTSSEECSS----SSCEEESCC--
T ss_pred             CCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCEEeCCC----CCCcceeccCc
Confidence            47899999999944   7    89999999999999865431    13456665543

>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=90.65  E-value=0.15  Score=31.57  Aligned_cols=34  Identities=18%  Similarity=0.245  Sum_probs=29.5

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN   41 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~   41 (128)
                      +|..|||+.++++   ..    .++|+++.|...|++....
T Consensus        37 ~t~~ela~~l~is---~~----tv~~~l~~L~~~g~v~~~~   70 (109)
T 2d1h_A           37 ITSEELADIFKLS---KT----TVENSLKKLIELGLVVRTK   70 (109)
T ss_dssp             EEHHHHHHHHTCC---HH----HHHHHHHHHHHTTSEEEEE
T ss_pred             CCHHHHHHHHCcC---HH----HHHHHHHHHHHCCCeEeec
Confidence            3678999999994   47    8999999999999998654

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

Probab=90.63  E-value=0.21  Score=32.01  Aligned_cols=46  Identities=15%  Similarity=0.274  Sum_probs=33.0

Q ss_pred             CCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCc-ccceechHhhhhhhc
Q 045905           10 LPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQ-ERSYVATNASKLLLK   62 (128)
Q Consensus        10 ~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~-~~~y~~T~~s~~L~~   62 (128)
                      +++   ++.    .|+++|+-|...|++.......++. ...|.+|+.|+.+..
T Consensus        36 ~~i---~~~----tly~~L~~Le~~GlI~~~~~~~~~r~r~~y~LT~~G~~~l~   82 (108)
T 3l7w_A           36 ASI---KES----TLYPILKKLEKAGYLSTYTQEHQGRRRKYYHLTDSGEKHLV   82 (108)
T ss_dssp             CCC---CHH----HHHHHHHHHHHTTSEEEEEEEETTEEEEEEEECHHHHHHHH
T ss_pred             hCC---CcC----hHHHHHHHHHHCCCeEEEeecCCCCcceEEEECHHHHHHHH
Confidence            456   457    8999999999999997553211221 236999999987754

>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=90.19  E-value=0.22  Score=39.26  Aligned_cols=55  Identities=15%  Similarity=0.211  Sum_probs=42.3

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhc
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLK   62 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~   62 (128)
                      +|..|||+++++   +..    .+.|++.-|...|++......+|.-.-...+|+.|+.+.+
T Consensus       421 ~~~~~l~~~~~~---~~~----~~t~~~~~le~~g~v~r~~~~~D~R~~~i~lT~~g~~~~~  475 (487)
T 1hsj_A          421 ISSKEIAKCSEF---KPY----YLTKALQKLKDLKLLSKKRSLQDERTVIVYVTDTQKANIQ  475 (487)
T ss_dssp             EEHHHHHHSSCC---CHH----HHHHHHHHHHTTTTSCCEECCSSSSCCEEECCSSHHHHHH
T ss_pred             cCHHHHHHHHCC---CHH----HHHHHHHHHHHCCCEeecCCCCCCCeEEEEECHHHHHHHH
Confidence            467899999999   558    9999999999999997654333311235889999988764

>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=89.79  E-value=0.45  Score=29.89  Aligned_cols=34  Identities=3%  Similarity=-0.032  Sum_probs=28.8

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN   41 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~   41 (128)
                      ++..|||.++++   +..    .+.|+|+.|...|++....
T Consensus        37 i~qkeLa~~~~l---~~~----tvt~iLk~LE~kglIkr~~   70 (91)
T 2dk5_A           37 IWSRDVRYKSNL---PLT----EINKILKNLESKKLIKAVK   70 (91)
T ss_dssp             EEHHHHHHHTTC---CHH----HHHHHHHHHHHTTSEEEEC
T ss_pred             cCHHHHHHHHCC---CHH----HHHHHHHHHHHCCCEEEec
Confidence            356799999999   447    8999999999999998544

>2esh_A Conserved hypothetical protein TM0937; APC5794, structural genomics, PSI, protein structure initiative; 2.30A {Thermotoga maritima} SCOP: a.4.5.61

Probab=89.43  E-value=0.42  Score=30.98  Aligned_cols=58  Identities=26%  Similarity=0.289  Sum_probs=38.5

Q ss_pred             CHHHHHHhCC---C-C-CCCc-hhhhhhHHHHHHHHHhcCcceeeccCCCC-cccceechHhhhhhhcC
Q 045905            2 TLNELINALP---F-H-PIKA-QYVAQYVYRFMWILVHSGFFAQQNFGQND-QERSYVATNASKLLLKD   63 (128)
Q Consensus         2 S~~eLA~~~~---~-~-~~~~-~~~~~~L~RlLR~L~~~gvf~e~~~~~~~-~~~~y~~T~~s~~L~~~   63 (128)
                      +..||++.+.   . . ..++ .    .|+++|+-|...|++.......++ ....|.+|+.|+.+...
T Consensus        28 ~gyel~~~l~~~g~~~~~is~~~----tly~~L~~Le~~GlI~~~~~~~~~~~r~~Y~LT~~G~~~l~~   92 (118)
T 2esh_A           28 HGYELAERLAEFGIEIPGIGHMG----NIYRVLADLEESGFLSTEWDTTVSPPRKIYRITPQGKLYLRE   92 (118)
T ss_dssp             CHHHHHHHHHTTCCSSTTCCCCC----CHHHHHHHHHHTTSEEEEEECSSSSCEEEEEECHHHHHHHHH
T ss_pred             CHHHHHHHHHHhCCcccCCCCcc----hHHHHHHHHHHCCCeEEEeecCCCCCceEEEEChHHHHHHHH
Confidence            3456777663   1 1 0156 6    899999999999999755321111 13469999999987644

>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=89.37  E-value=0.42  Score=30.21  Aligned_cols=33  Identities=27%  Similarity=0.364  Sum_probs=28.9

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceee
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQ   40 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~   40 (128)
                      +|..|||+.+|++   ..    .+++.|+.|...|++...
T Consensus        34 ~s~~eLa~~lgvs---~~----tV~~~L~~L~~~GlV~~~   66 (110)
T 1q1h_A           34 MTDEEIANQLNIK---VN----DVRKKLNLLEEQGFVSYR   66 (110)
T ss_dssp             BCHHHHHHTTTSC---HH----HHHHHHHHHHHHTSCEEE
T ss_pred             CCHHHHHHHHCcC---HH----HHHHHHHHHHHCCCEEEE
Confidence            4789999999994   47    899999999999999755

>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=89.36  E-value=0.49  Score=29.11  Aligned_cols=47  Identities=13%  Similarity=0.173  Sum_probs=33.4

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASK   58 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~   58 (128)
                      +|+.|||+++|++   ..    .+.|.|.-|-..|++.....    ..++|..++...
T Consensus        28 ~t~~eLA~~Lgvs---r~----tV~~~L~~Le~~G~I~~~g~----~~~~W~i~~~~~   74 (81)
T 1qbj_A           28 TTAHDLSGKLGTP---KK----EINRVLYSLAKKGKLQKEAG----TPPLWKIAVSTQ   74 (81)
T ss_dssp             BCHHHHHHHHTCC---HH----HHHHHHHHHHHTTSEEEESS----SSCEEEEC----
T ss_pred             cCHHHHHHHHCcC---HH----HHHHHHHHHHHCCCEEecCC----CCCeeEEeCcHH
Confidence            4889999999994   37    89999999999999865431    135677766653

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

Probab=89.04  E-value=0.23  Score=31.66  Aligned_cols=37  Identities=14%  Similarity=0.211  Sum_probs=29.5

Q ss_pred             CCHHHHHHhCCCCC-CCchhhhhhHHHHHHHHHhcCcceeec
Q 045905            1 MTLNELINALPFHP-IKAQYVAQYVYRFMWILVHSGFFAQQN   41 (128)
Q Consensus         1 ~S~~eLA~~~~~~~-~~~~~~~~~L~RlLR~L~~~gvf~e~~   41 (128)
                      +|..||+++++.++ -+..    .+.|+|.-|...|++....
T Consensus        50 ~t~~eL~~~l~~~~~~s~s----TVt~~L~rLe~KGlV~R~~   87 (99)
T 2k4b_A           50 ARVDEIYAQIPQELEWSLA----TVKTLLGRLVKKEMLSTEK   87 (99)
T ss_dssp             EEHHHHHHTCCGGGCCCHH----HHHHHHHHHHHTTSCEEEE
T ss_pred             CCHHHHHHHHhcccCCCHh----hHHHHHHHHHHCCCEEEEe
Confidence            36889999998631 1457    8999999999999997654

>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=88.97  E-value=0.34  Score=31.69  Aligned_cols=47  Identities=11%  Similarity=0.121  Sum_probs=35.8

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNAS   57 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s   57 (128)
                      +++.|||+.+++++   .    .+.|.|+.|...|++.....   |....|.+|+-.
T Consensus        60 ~s~~ela~~lgis~---s----tvs~~L~~Le~~Glv~~~~~---gr~~~y~l~~~~  106 (122)
T 1r1t_A           60 LCVGDLAQAIGVSE---S----AVSHQLRSLRNLRLVSYRKQ---GRHVYYQLQDHH  106 (122)
T ss_dssp             BCHHHHHHHHTCCH---H----HHHHHHHHHHHTTSEEEEEE---TTEEEEEESSHH
T ss_pred             CCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCeEEEEe---CCEEEEEEChHH
Confidence            37889999999944   7    89999999999999875542   112458887654

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

Probab=88.84  E-value=0.31  Score=31.19  Aligned_cols=34  Identities=15%  Similarity=0.289  Sum_probs=29.0

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN   41 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~   41 (128)
                      +|..|||+.++++   ..    .+.|.|+.|...|++....
T Consensus        46 ~s~~ela~~l~is---~s----tvsr~l~~Le~~Glv~~~~   79 (119)
T 2lkp_A           46 LPVTDLAEAIGME---QS----AVSHQLRVLRNLGLVVGDR   79 (119)
T ss_dssp             CCHHHHHHHHSSC---HH----HHHHHHHHHHHHCSEEEEE
T ss_pred             CCHHHHHHHHCcC---HH----HHHHHHHHHHHCCCEEEEe
Confidence            4789999999994   47    9999999999999886543

>2fe3_A Peroxide operon regulator; oxidative stress regulator, DNA binding protein; 1.75A {Bacillus subtilis} PDB: 3f8n_A 2rgv_A*

Probab=88.30  E-value=0.66  Score=31.17  Aligned_cols=48  Identities=17%  Similarity=0.295  Sum_probs=33.8

Q ss_pred             CCHHHHHHhCCC--CCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceech
Q 045905            1 MTLNELINALPF--HPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVAT   54 (128)
Q Consensus         1 ~S~~eLA~~~~~--~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T   54 (128)
                      +|+.||.+.+.-  +..+..    .+||.|..|+..|++......+  +..+|.++
T Consensus        38 ~sa~ei~~~l~~~~~~is~a----TVYR~L~~L~e~Glv~~~~~~~--~~~~Y~~~   87 (145)
T 2fe3_A           38 PTADDIYKALEGKFPNMSVA----TVYNNLRVFRESGLVKELTYGD--ASSRFDFV   87 (145)
T ss_dssp             CCHHHHHHHHGGGCTTCCHH----HHHHHHHHHHHTTSEEEECCTT--SCCEEEEC
T ss_pred             CCHHHHHHHHHHhCCCCChh----hHHHHHHHHHHCCCEEEEeeCC--CceEEECC
Confidence            478899988831  111557    8999999999999998765311  13468754

>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=87.98  E-value=0.31  Score=33.08  Aligned_cols=43  Identities=16%  Similarity=0.138  Sum_probs=31.0

Q ss_pred             CchhhhhhHHHHHHHHHhcCcceeeccC-CCC-cccceechHhhhhhhc
Q 045905           16 KAQYVAQYVYRFMWILVHSGFFAQQNFG-QND-QERSYVATNASKLLLK   62 (128)
Q Consensus        16 ~~~~~~~~L~RlLR~L~~~gvf~e~~~~-~~~-~~~~y~~T~~s~~L~~   62 (128)
                      .+.    .|+++|+-|...|++...... +++ ....|.+|+.|+.+..
T Consensus        75 s~g----tLy~~L~rLE~~GlI~~~~~~~~~~~~rk~Y~LT~~G~~~l~  119 (145)
T 1xma_A           75 KET----TLYSAFARLEKNGYIKSYYGEETQGKRRTYYRITPEGIKYYK  119 (145)
T ss_dssp             CHH----HHHHHHHHHHHTTSEEEEEEEEC--CEEEEEEECHHHHHHHH
T ss_pred             Chh----HHHHHHHHHHHCCCEEEEEeccCCCCCeEEEEECHHHHHHHH
Confidence            457    899999999999999654321 111 1346999999987754

>1yg2_A Gene activator APHA; virulence factor, winged helix, transcripti factor, transcription; 2.20A {Vibrio cholerae} SCOP: a.4.5.61

Probab=87.74  E-value=0.64  Score=32.24  Aligned_cols=55  Identities=20%  Similarity=0.195  Sum_probs=36.0

Q ss_pred             CHHHHHHhCCC------CCCCchhhhhhHHHHHHHHHhcCcceeeccCCCC--cccceechHhhhhhh
Q 045905            2 TLNELINALPF------HPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQND--QERSYVATNASKLLL   61 (128)
Q Consensus         2 S~~eLA~~~~~------~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~--~~~~y~~T~~s~~L~   61 (128)
                      +..||++.+.-      +. ...    .|++.|+-|...|++......+++  ....|.+|+.|+...
T Consensus        17 ~gyel~~~l~~~~~~~~~~-s~~----~ly~~L~~Le~~GlI~~~~~~~~~~~~r~~Y~lT~~G~~~l   79 (179)
T 1yg2_A           17 TGYDITKEFSASIGYFWKA-SHQ----QVYRELNKMGEQGLVTCVLEPQEGKPDRKVYSITQAGRSAL   79 (179)
T ss_dssp             CHHHHHHHHTTGGGGTCCC-CHH----HHHHHHHHHHHTTSEEECCC---------CEEECHHHHHHH
T ss_pred             CHHHHHHHHHHHhCCccCC-CcC----cHHHHHHHHHHCCCeEEEeecCCCCCCceEEEeChHHHHHH
Confidence            45677777731      11 457    899999999999999755332221  134799999998554

>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=87.34  E-value=0.67  Score=34.18  Aligned_cols=56  Identities=7%  Similarity=0.252  Sum_probs=42.2

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+++++   ++.    .+.|++.-|...|++....+.+|.-.-...+|+.|+.+...
T Consensus        51 ~~~~el~~~l~~---~~~----t~t~~l~rLe~~G~i~R~~~~~DrR~~~i~LT~~G~~~~~~  106 (250)
T 1p4x_A           51 LPFKKIVSDLCY---KQS----DLVQHIKVLVKHSYISKVRSKIDERNTYISISEEQREKIAE  106 (250)
T ss_dssp             EEHHHHHHHSSS---CGG----GTHHHHHHHHHTTSCEEEECSSSTTSEEEECCHHHHHHHHH
T ss_pred             cCHHHHHHHHCC---CHh----hHHHHHHHHHHCCCEEecCCCCCCCeEEEEECHHHHHHHHH
Confidence            367899999999   448    89999999999999976543332111257899999987643

>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=86.58  E-value=0.3  Score=31.26  Aligned_cols=55  Identities=15%  Similarity=0.262  Sum_probs=39.3

Q ss_pred             CCHHHHHHhCCCCC-CCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccc-eechHhhhhhhc
Q 045905            1 MTLNELINALPFHP-IKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERS-YVATNASKLLLK   62 (128)
Q Consensus         1 ~S~~eLA~~~~~~~-~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~-y~~T~~s~~L~~   62 (128)
                      +|..|||..++.++ ....    .+.|++.-|...|++.....   +.... +.+|+.|+.+..
T Consensus        25 ~t~~ela~~l~~~~~~s~~----tv~~~l~~L~~~Glv~r~~~---~rr~~~~~lT~~g~~~~~   81 (123)
T 1okr_A           25 ASANNIIEEIQMQKDWSPK----TIRTLITRLYKKGFIDRKKD---NKIFQYYSLVEESDIKYK   81 (123)
T ss_dssp             EEHHHHHHHHHHHCCCCHH----HHHHHHHHHHHHTSEEEEEE---TTEEEEEESSCHHHHHHH
T ss_pred             cCHHHHHHHHhccCCCcHh----hHHHHHHHHHHCCCeEEEec---CCeEEEEEecCHHHHHHH
Confidence            36789999988320 0347    89999999999999976542   11223 579999988764

>2o03_A Probable zinc uptake regulation protein FURB; DNA-binding, helix-turn-helix, zinc binding, GE regulation; 2.70A {Mycobacterium tuberculosis}

Probab=86.44  E-value=0.58  Score=30.88  Aligned_cols=44  Identities=23%  Similarity=0.276  Sum_probs=32.5

Q ss_pred             CCHHHHHHhC-----CCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceec
Q 045905            1 MTLNELINAL-----PFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVA   53 (128)
Q Consensus         1 ~S~~eLA~~~-----~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~   53 (128)
                      +|++||.+.+     ++   +..    .+||.|..|+..|++......+  +..+|.+
T Consensus        27 ~sa~ei~~~l~~~~~~i---s~~----TVYR~L~~L~e~Glv~~~~~~~--~~~~y~~   75 (131)
T 2o03_A           27 RSAQELHDELRRRGENI---GLT----TVYRTLQSMASSGLVDTLHTDT--GESVYRR   75 (131)
T ss_dssp             EEHHHHHHHHHHTTCCC---CHH----HHHHHHHHHHTTTSEEEEECTT--SCEEEEE
T ss_pred             CCHHHHHHHHHHhCCCC---CHh----hHHHHHHHHHHCCCEEEEEeCC--CceEEEe
Confidence            3678888887     34   557    8999999999999998765321  1346765

>3elk_A Putative transcriptional regulator TA0346; structural genomics, PSI-2, prote structure initiative; 1.70A {Thermoplasma acidophilum}

Probab=86.08  E-value=0.92  Score=29.51  Aligned_cols=41  Identities=24%  Similarity=0.365  Sum_probs=30.1

Q ss_pred             hHHHHHHHHHhcCcceeecc-CCCC-cccceechHhhhhhhcC
Q 045905           23 YVYRFMWILVHSGFFAQQNF-GQND-QERSYVATNASKLLLKD   63 (128)
Q Consensus        23 ~L~RlLR~L~~~gvf~e~~~-~~~~-~~~~y~~T~~s~~L~~~   63 (128)
                      .|+++|+-|...|++..... .+++ ....|.+|+.|+.....
T Consensus        49 tly~~L~~Le~~GlI~~~~~~~~~~~~rk~Y~lT~~G~~~l~~   91 (117)
T 3elk_A           49 SIYILLKTMKERGFVISESSVNEKGQQLTVYHITDAGKKFLCD   91 (117)
T ss_dssp             HHHHHHHHHHHHTSEEEEEEEC-CCCEEEEEEECHHHHHHHHH
T ss_pred             hHHHHHHHHHHCCCEEEEeeecCCCCCceEEEECHHHHHHHHH
Confidence            89999999999999975432 1111 13479999999877654

>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=86.04  E-value=0.75  Score=33.18  Aligned_cols=46  Identities=15%  Similarity=0.127  Sum_probs=38.1

Q ss_pred             CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhh
Q 045905            2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLL   61 (128)
Q Consensus         2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~   61 (128)
                      +..+||+++++.   ++    .++.+++.|...|++....       +...+|+.|+.+.
T Consensus        32 ~~~~LA~~LgvS---~~----SV~~~lkkL~e~GLV~~~~-------~Gv~LTe~G~~~A   77 (200)
T 2p8t_A           32 GRKQISERLELG---EG----SVRTLLRKLSHLDIIRSKQ-------RGHFLTLKGKEIR   77 (200)
T ss_dssp             CHHHHHHHHTCC---HH----HHHHHHHHHHHTTSEEEC---------CEEECHHHHHHH
T ss_pred             cHHHHHHHhCCC---HH----HHHHHHHHHHHCCCEEEeC-------CCeEECHHHHHHH
Confidence            567999999994   48    8999999999999997653       5689999998765

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

Probab=86.04  E-value=0.88  Score=30.15  Aligned_cols=48  Identities=19%  Similarity=0.308  Sum_probs=33.3

Q ss_pred             CCHHHHHHhCCC--CCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceech
Q 045905            1 MTLNELINALPF--HPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVAT   54 (128)
Q Consensus         1 ~S~~eLA~~~~~--~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T   54 (128)
                      +|+.||.+.+.-  +..+..    .+||.|..|+..|++......+  +..+|.++
T Consensus        35 ~sa~ei~~~l~~~~~~is~a----TVYR~L~~L~e~Glv~~~~~~~--~~~~Y~~~   84 (136)
T 1mzb_A           35 MSAEDVYKALMEAGEDVGLA----TVYRVLTQFEAAGLVVRHNFDG--GHAVFELA   84 (136)
T ss_dssp             BCHHHHHHHHHHTTCCCCHH----HHHHHHHHHHHHTSEEEECSSS--SSCEEEES
T ss_pred             CCHHHHHHHHHhhCCCCCHH----HHHHHHHHHHHCCcEEEEEeCC--CceEEEeC
Confidence            478888888721  111557    8999999999999998765311  13568763

>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=85.89  E-value=0.89  Score=29.43  Aligned_cols=43  Identities=12%  Similarity=0.150  Sum_probs=31.0

Q ss_pred             CchhhhhhHHHHHHHHHhcCcceeeccC-CCC-cccceechHhhhhhhc
Q 045905           16 KAQYVAQYVYRFMWILVHSGFFAQQNFG-QND-QERSYVATNASKLLLK   62 (128)
Q Consensus        16 ~~~~~~~~L~RlLR~L~~~gvf~e~~~~-~~~-~~~~y~~T~~s~~L~~   62 (128)
                      ++.    .|+++|+-|...|++...... +++ ....|.+|+.|+....
T Consensus        46 ~~g----tly~~L~rLe~~GlI~~~~~~~~~~~~rk~Y~LT~~G~~~l~   90 (116)
T 3f8b_A           46 NEA----TLYTIFKRLEKDGIISSYWGDESQGGRRKYYRLTEIGHENMR   90 (116)
T ss_dssp             CHH----HHHHHHHHHHHTTSEEEEEEC----CCEEEEEECHHHHHHHH
T ss_pred             Ccc----hHHHHHHHHHHCCCEEEEeeccCCCCCceEEEECHHHHHHHH
Confidence            557    899999999999999754321 111 1346999999987754

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

Probab=85.78  E-value=0.63  Score=28.37  Aligned_cols=33  Identities=15%  Similarity=0.186  Sum_probs=29.0

Q ss_pred             CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905            2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN   41 (128)
Q Consensus         2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~   41 (128)
                      |+.|||+.+|+.   +.    .++|-|..|...|++....
T Consensus        26 sv~EIa~~lgvS---~~----TVrr~L~~Le~kG~I~R~~   58 (77)
T 2jt1_A           26 KTRDIADAAGLS---IY----QVRLYLEQLHDVGVLEKVN   58 (77)
T ss_dssp             EHHHHHHHHTCC---HH----HHHHHHHHHHHTTSEEEES
T ss_pred             CHHHHHHHHCCC---HH----HHHHHHHHHHHCCcEEecC
Confidence            689999999994   37    8999999999999997664

>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=85.05  E-value=0.62  Score=31.09  Aligned_cols=33  Identities=21%  Similarity=0.104  Sum_probs=28.7

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceee
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQ   40 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~   40 (128)
                      +|..|||+++|+++   .    .+.|.++.|...|++...
T Consensus        22 ~s~~ela~~lg~s~---~----tv~~~l~~L~~~G~i~~~   54 (150)
T 2w25_A           22 ATLSELATRAGLSV---S----AVQSRVRRLESRGVVQGY   54 (150)
T ss_dssp             CCHHHHHHHHTSCH---H----HHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCEEEE
Confidence            57899999999944   7    899999999999999643

>4esb_A Transcriptional regulator, PADR family; DNA binding protein, HTH fold; 2.50A {Bacillus cereus}

Probab=83.97  E-value=0.67  Score=30.06  Aligned_cols=43  Identities=9%  Similarity=0.114  Sum_probs=31.4

Q ss_pred             CchhhhhhHHHHHHHHHhcCcceeecc-CCCC-cccceechHhhhhhhc
Q 045905           16 KAQYVAQYVYRFMWILVHSGFFAQQNF-GQND-QERSYVATNASKLLLK   62 (128)
Q Consensus        16 ~~~~~~~~L~RlLR~L~~~gvf~e~~~-~~~~-~~~~y~~T~~s~~L~~   62 (128)
                      ++.    .|+++|+-|...|++..... .+++ ....|.+|+.|+....
T Consensus        41 s~g----tlY~~L~rLe~~GlI~~~~~~~~~g~~rk~Y~LT~~G~~~l~   85 (115)
T 4esb_A           41 SEG----SIYPLLLRMQKEKLIEGTLKASSLGPKRKYYHITDKGLEQLE   85 (115)
T ss_dssp             CHH----HHHHHHHHHHHTTSEEEEEEECTTSCEEEEEEECHHHHHHHH
T ss_pred             CcC----hHHHHHHHHHHCCCeEEEeeecCCCCCcEEEEECHHHHHHHH
Confidence            557    89999999999999975432 1112 1246999999987754

>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=83.87  E-value=1.1  Score=29.19  Aligned_cols=56  Identities=20%  Similarity=0.279  Sum_probs=36.3

Q ss_pred             HHHHHhCC---CCCCCchhhhhhHHHHHHHHHhcCcceeecc-CCCC-cccceechHhhhhhhcC
Q 045905            4 NELINALP---FHPIKAQYVAQYVYRFMWILVHSGFFAQQNF-GQND-QERSYVATNASKLLLKD   63 (128)
Q Consensus         4 ~eLA~~~~---~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~-~~~~-~~~~y~~T~~s~~L~~~   63 (128)
                      -||++.+.   .-..++.    .|+++|+-|...|++..... .+++ ....|.+|+.|+.....
T Consensus        30 yei~~~l~~~g~~~is~g----tlY~~L~rLe~~GlI~~~~~~~~~g~~rk~Y~lT~~G~~~l~~   90 (116)
T 3hhh_A           30 YEITKILNDQGFTEIVEG----TVYTILLRLEKNQWVIAEKKPSEKGPMRKFYRLTSSGEAELAD   90 (116)
T ss_dssp             HHHHHHHHTTSCSSCCHH----HHHHHHHHHHHTTSEEEEEEECC--CEEEEEEECHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCCCcc----HHHHHHHHHHHCCCEEEEeeecCCCCCceEEEECHHHHHHHHH
Confidence            35666552   1111557    89999999999999975432 1112 13469999999877543

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

Probab=83.82  E-value=0.71  Score=31.27  Aligned_cols=33  Identities=24%  Similarity=0.258  Sum_probs=28.6

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceee
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQ   40 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~   40 (128)
                      +|..|||+++|+++   .    .+.|.++.|...|++...
T Consensus        25 ~s~~ela~~lg~s~---~----tv~~~l~~L~~~G~i~~~   57 (162)
T 2p5v_A           25 LTNVELSERVALSP---S----PCLRRLKQLEDAGIVRQY   57 (162)
T ss_dssp             CCHHHHHHHHTSCH---H----HHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCEeee
Confidence            57899999999944   7    899999999999998743

>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=83.58  E-value=0.87  Score=30.26  Aligned_cols=32  Identities=13%  Similarity=0.146  Sum_probs=28.4

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCccee
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQ   39 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e   39 (128)
                      +|..|||+++|+++   .    .+.|.++.|...|++..
T Consensus        18 ~~~~ela~~lg~s~---~----tv~~~l~~L~~~G~i~~   49 (150)
T 2pn6_A           18 YSLDEIAREIRIPK---A----TLSYRIKKLEKDGVIKG   49 (150)
T ss_dssp             SCHHHHHHHHTSCH---H----HHHHHHHHHHHTTSSCC
T ss_pred             CCHHHHHHHHCcCH---H----HHHHHHHHHHHCCcEEE
Confidence            47899999999944   7    89999999999999975

>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=83.48  E-value=0.96  Score=30.00  Aligned_cols=32  Identities=22%  Similarity=0.280  Sum_probs=28.3

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCccee
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQ   39 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e   39 (128)
                      +|..|||+++|+++   .    .+.|.++.|...|++..
T Consensus        20 ~s~~ela~~lg~s~---~----tv~~~l~~L~~~G~i~~   51 (144)
T 2cfx_A           20 LSMRELGRKIKLSP---P----SVTERVRQLESFGIIKQ   51 (144)
T ss_dssp             CCHHHHHHHHTCCH---H----HHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCeEE
Confidence            57899999999944   7    89999999999999974

>2xig_A Ferric uptake regulation protein; hpfur, transcription, homeostasis; HET: CIT; 1.85A {Helicobacter pylori}

Probab=83.22  E-value=1.2  Score=30.12  Aligned_cols=48  Identities=17%  Similarity=0.304  Sum_probs=33.2

Q ss_pred             CCHHHHHHhCCC--CCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceech
Q 045905            1 MTLNELINALPF--HPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVAT   54 (128)
Q Consensus         1 ~S~~eLA~~~~~--~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T   54 (128)
                      +|+.||.+.+.-  +..+..    -+||.|..|+..|++......+  +..+|.++
T Consensus        43 ~sa~ei~~~l~~~~~~is~a----TVYR~L~~L~e~Glv~~~~~~~--~~~~Y~~~   92 (150)
T 2xig_A           43 LSPEEITHSIRQKDKNTSIS----SVYRILNFLEKENFISVLETSK--SGRRYEIA   92 (150)
T ss_dssp             BCHHHHHHHHHHHSTTCCHH----HHHHHHHHHHHTTSEEEEEETT--TEEEEEES
T ss_pred             CCHHHHHHHHHHhCCCCCHh----hHHHHHHHHHHCCcEEEEEeCC--CceEEEec
Confidence            478888888721  111557    8999999999999998765311  13468764

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

Probab=83.10  E-value=1.2  Score=29.57  Aligned_cols=32  Identities=25%  Similarity=0.234  Sum_probs=28.1

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCccee
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQ   39 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e   39 (128)
                      +|..|||+++|+++   .    .+.|.++.|...|++..
T Consensus        24 ~s~~ela~~lg~s~---~----tv~~~l~~L~~~G~i~~   55 (151)
T 2dbb_A           24 LTYRELADILNTTR---Q----RIARRIDKLKKLGIIRK   55 (151)
T ss_dssp             CCHHHHHHHTTSCH---H----HHHHHHHHHHHHTSEEE
T ss_pred             CCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCEEE
Confidence            57899999999944   7    89999999999999974

>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=82.91  E-value=0.72  Score=30.85  Aligned_cols=32  Identities=16%  Similarity=0.155  Sum_probs=28.2

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCccee
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQ   39 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e   39 (128)
                      +|..|||+++|+++   .    .+.|.++.|...|++..
T Consensus        22 ~s~~ela~~lg~s~---~----tv~~~l~~L~~~G~i~~   53 (151)
T 2cyy_A           22 APLREISKITGLAE---S----TIHERIRKLRESGVIKK   53 (151)
T ss_dssp             CCHHHHHHHHCSCH---H----HHHHHHHHHHHHTSSCC
T ss_pred             CCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCeEE
Confidence            57899999999944   7    89999999999999864

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

Probab=82.51  E-value=0.63  Score=29.07  Aligned_cols=45  Identities=13%  Similarity=0.193  Sum_probs=34.4

Q ss_pred             CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhh
Q 045905            2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNAS   57 (128)
Q Consensus         2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s   57 (128)
                      |+.|||+.+|+++   .    .+.|.|+.|... ++.....   |....|.+|+-+
T Consensus        43 ~~~ela~~l~is~---s----tvs~hL~~L~~~-lv~~~~~---gr~~~y~l~~~~   87 (99)
T 2zkz_A           43 NVTQIIQILKLPQ---S----TVSQHLCKMRGK-VLKRNRQ---GLEIYYSINNPK   87 (99)
T ss_dssp             EHHHHHHHHTCCH---H----HHHHHHHHHBTT-TBEEEEE---TTEEEEECCCHH
T ss_pred             CHHHHHHHHCcCH---H----HHHHHHHHHHHH-hhhheEe---CcEEEEEEChHH
Confidence            6789999999944   7    899999999999 8865442   113468888754

>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=81.93  E-value=1.1  Score=32.01  Aligned_cols=51  Identities=16%  Similarity=0.228  Sum_probs=36.4

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccC-CC-CcccceechHhhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFG-QN-DQERSYVATNASK   58 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~-~~-~~~~~y~~T~~s~   58 (128)
                      +|..|||+.++++   ..    .+++.|+.|...|++...... .. +...+|.+|+-+.
T Consensus        29 ~s~~eLa~~l~is---~s----tvs~hLk~Le~~GLV~~~~~~~~~g~~~~~Y~Lt~~~~   81 (202)
T 2p4w_A           29 YFVSELSRELGVG---QK----AVLEHLRILEEAGLIESRVEKIPRGRPRKYYMIKKGLR   81 (202)
T ss_dssp             EEHHHHHHHHTCC---HH----HHHHHHHHHHHTTSEEEEECCBTTBCCCEEEEECTTEE
T ss_pred             CCHHHHHHHHCcC---HH----HHHHHHHHHHHCCceEEEeeccCCCCceEEEEEChHHH
Confidence            3678999999994   48    999999999999999765421 11 1123566666553

>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=81.58  E-value=1.1  Score=30.57  Aligned_cols=34  Identities=18%  Similarity=0.173  Sum_probs=29.3

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN   41 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~   41 (128)
                      +|-.+||+.+|+.+   .    .|.|+|+.|...|++....
T Consensus       165 ~t~~~lA~~lg~sr---~----tvsR~l~~l~~~g~I~~~~  198 (207)
T 2oz6_A          165 ITRQEIGRIVGCSR---E----MVGRVLKSLEEQGLVHVKG  198 (207)
T ss_dssp             CCHHHHHHHHTSCH---H----HHHHHHHHHHHTTSEEEET
T ss_pred             cCHHHHHHHhCCCH---H----HHHHHHHHHHHCCCEEecC
Confidence            47789999999944   7    9999999999999997553

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

Probab=81.39  E-value=1.6  Score=29.76  Aligned_cols=34  Identities=18%  Similarity=0.179  Sum_probs=29.4

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN   41 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~   41 (128)
                      +|-.|||+.+|+.+   .    .+.|+|+.|...|++....
T Consensus       140 ~t~~~lA~~lg~sr---~----tvsR~l~~L~~~g~I~~~~  173 (195)
T 3b02_A          140 VSHEEIADATASIR---E----SVSKVLADLRREGLIATAY  173 (195)
T ss_dssp             CCHHHHHHTTTSCH---H----HHHHHHHHHHHHTSEEEET
T ss_pred             CCHHHHHHHhCCCH---H----HHHHHHHHHHHCCCEEecC
Confidence            47789999999944   7    9999999999999997553

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

Probab=81.19  E-value=0.9  Score=28.39  Aligned_cols=33  Identities=12%  Similarity=0.260  Sum_probs=28.8

Q ss_pred             CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905            2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN   41 (128)
Q Consensus         2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~   41 (128)
                      |..|||+.++++.   .    .+++.|+.|...|++....
T Consensus        37 s~~eLa~~~~vSr---~----tvr~al~~L~~~Gli~~~~   69 (102)
T 1v4r_A           37 SVADIRAQFGVAA---K----TVSRALAVLKSEGLVSSRG   69 (102)
T ss_dssp             CHHHHHHHSSSCT---T----HHHHHTTTTTTSSCCEEET
T ss_pred             CHHHHHHHHCcCH---H----HHHHHHHHHHHCCCEEEeC
Confidence            7889999999954   7    8999999999999997554

>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=81.01  E-value=0.67  Score=27.71  Aligned_cols=37  Identities=16%  Similarity=0.313  Sum_probs=28.6

Q ss_pred             CCHHHHHHhCCCCC-CCchhhhhhHHHHHHHHHhcCcceeec
Q 045905            1 MTLNELINALPFHP-IKAQYVAQYVYRFMWILVHSGFFAQQN   41 (128)
Q Consensus         1 ~S~~eLA~~~~~~~-~~~~~~~~~L~RlLR~L~~~gvf~e~~   41 (128)
                      +|..||++.++.++ -++.    .+.|+|+.|...|++....
T Consensus        24 ~t~~ei~~~l~~~~~~s~~----Tv~~~l~rL~~kGlv~r~~   61 (82)
T 1p6r_A           24 INTNEVIKELSKTSTWSPK----TIQTMLLRLIKKGALNHHK   61 (82)
T ss_dssp             EEHHHHHHHHHHHSCCCHH----HHHHHHHHHHHTTSEEEEE
T ss_pred             CCHHHHHHHHhhcCCccHH----HHHHHHHHHHHCCCeEEEe
Confidence            36789999987421 1457    8999999999999997654

>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=80.90  E-value=1.2  Score=29.17  Aligned_cols=33  Identities=15%  Similarity=0.158  Sum_probs=28.3

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceee
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQ   40 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~   40 (128)
                      +|..|||+++|+++   .    .+.|.++.|...|++...
T Consensus        19 ~~~~ela~~lg~s~---~----tv~~~l~~L~~~G~i~~~   51 (141)
T 1i1g_A           19 TPFTEIAKKLGISE---T----AVRKRVKALEEKGIIEGY   51 (141)
T ss_dssp             CCHHHHHHHHTSCH---H----HHHHHHHHHHHHTSSCCC
T ss_pred             CCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCEecc
Confidence            47899999999944   7    899999999999998643

>4g6q_A Putative uncharacterized protein; structural genomics, PSI-biology, protein structure initiati midwest center for structural genomics, MCSG; 2.08A {Kribbella flavida}

Probab=80.90  E-value=3.5  Score=28.64  Aligned_cols=53  Identities=26%  Similarity=0.310  Sum_probs=38.6

Q ss_pred             CHHHHHHhCC-CCCCCchhhhhhHHHHHHHHHhcCcceeeccC--CCCcccceechHhhhhhh
Q 045905            2 TLNELINALP-FHPIKAQYVAQYVYRFMWILVHSGFFAQQNFG--QNDQERSYVATNASKLLL   61 (128)
Q Consensus         2 S~~eLA~~~~-~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~--~~~~~~~y~~T~~s~~L~   61 (128)
                      |+.|||+.++ ++   ..    .+.+-|+.|...|++......  .+..++.|.+++-+..+.
T Consensus        38 ~~~~l~~~l~~~~---~~----~~s~Hl~~L~~aglv~~~~e~~~~g~~er~y~~~~~~~~~~   93 (182)
T 4g6q_A           38 TTRELAELLPDVA---TT----TLYRQVGILVKAGVLMVTAEHQVRGAVERTYTLNTQAGDAD   93 (182)
T ss_dssp             EHHHHHHHCTTBC---HH----HHHHHHHHHHHHTSEEEEEEEEETTEEEEEEEECTTTTTSS
T ss_pred             CHHHHHHHhcCCC---HH----HHHHHHHHHHHCCCeEEEEeecccCcceeEEEeccccccCC
Confidence            6789999996 63   36    799999999999999754321  111246799998876554

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

Probab=80.68  E-value=1.2  Score=30.49  Aligned_cols=34  Identities=9%  Similarity=0.257  Sum_probs=29.4

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN   41 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~   41 (128)
                      ||...|++++.+   .-.    +-+++||.|...|++....
T Consensus        64 ITpsvlseRlkI---~gS----LARkaLreL~~kGlIk~V~   97 (143)
T 2xzm_8           64 LTVSTVVEKLKV---NGS----LARQLMRTMADRKLVEKVA   97 (143)
T ss_dssp             ECHHHHHHHHCB---CHH----HHHHHHHHHHHTTSEEEEE
T ss_pred             ecHHHHHHHhcc---hHH----HHHHHHHHHHHCCCEEEEe
Confidence            588999999999   447    8999999999999987653

>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=80.56  E-value=1.2  Score=29.66  Aligned_cols=32  Identities=13%  Similarity=0.182  Sum_probs=28.3

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCccee
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQ   39 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e   39 (128)
                      +|..|||+++|+++   .    .+.|.++.|...|++..
T Consensus        23 ~s~~ela~~lg~s~---~----tv~~~l~~L~~~G~i~~   54 (152)
T 2cg4_A           23 TAYAELAKQFGVSP---E----TIHVRVEKMKQAGIITG   54 (152)
T ss_dssp             SCHHHHHHHHTSCH---H----HHHHHHHHHHHHTSEEE
T ss_pred             CCHHHHHHHHCcCH---H----HHHHHHHHHHHcCCcce
Confidence            47899999999944   7    89999999999999974

>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=80.44  E-value=2  Score=29.89  Aligned_cols=34  Identities=15%  Similarity=0.152  Sum_probs=29.4

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN   41 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~   41 (128)
                      +|-.|||+.+|+.+   .    .|.|+|+.|...|++....
T Consensus       181 ~t~~~lA~~lg~sr---~----tvsR~l~~l~~~g~I~~~~  214 (232)
T 2gau_A          181 LSREELATLSNMTV---S----NAIRTLSTFVSERMLALDG  214 (232)
T ss_dssp             CCHHHHHHHTTSCH---H----HHHHHHHHHHHTTSEEEET
T ss_pred             cCHHHHHHHhCCCH---H----HHHHHHHHHHHCCCEeeCC
Confidence            47789999999944   7    9999999999999997553

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

Probab=80.22  E-value=2.3  Score=27.49  Aligned_cols=42  Identities=10%  Similarity=0.082  Sum_probs=32.2

Q ss_pred             CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHh
Q 045905            2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNA   56 (128)
Q Consensus         2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~   56 (128)
                      ++.|||..+++   +..    .+.++|+.|+..|.+....      ++.|-++..
T Consensus        22 ~~~~la~~~~~---~~~----~~~~~l~~l~~~G~l~~i~------~~~~~~~~~   63 (121)
T 2pjp_A           22 WVRDLAKETGT---DEQ----AMRLTLRQAAQQGIITAIV------KDRYYRNDR   63 (121)
T ss_dssp             EHHHHHHHTTC---CHH----HHHHHHHHHHHTTSEEEEE------TTEEEEHHH
T ss_pred             CHHHHHHHhCC---CHH----HHHHHHHHHHHCCCEEEec------CCceECHHH
Confidence            46799999999   447    8999999999999887665      355555444

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

Probab=80.11  E-value=1.9  Score=27.51  Aligned_cols=33  Identities=6%  Similarity=0.151  Sum_probs=28.5

Q ss_pred             CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905            2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN   41 (128)
Q Consensus         2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~   41 (128)
                      |..|||+.+|++   ..    .+++.++.|...|++....
T Consensus        35 s~~~La~~~~vS---r~----tvr~al~~L~~~Gli~~~~   67 (113)
T 3tqn_A           35 SIRKISTEYQIN---PL----TVSKAYQSLLDDNVIEKRR   67 (113)
T ss_dssp             CHHHHHHHHTCC---HH----HHHHHHHHHHHTTSEEEET
T ss_pred             CHHHHHHHHCcC---HH----HHHHHHHHHHHCCCEEEec
Confidence            678999999994   47    8999999999999987554

---

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	128
d1fp1d1	110	a.4.5.29 (D:19-128) Chalcone O-methyltransferase {	1e-11
d1kyza1	107	a.4.5.29 (A:13-119) Caffeic acid/5-hydroxyferulic	1e-10
d1fp2a1	101	a.4.5.29 (A:8-108) Isoflavone O-methyltransferase	1e-08
d1tw3a1	85	a.4.5.29 (A:14-98) Carminomycin 4-O-methyltransfer	3e-04
d1qzza1	92	a.4.5.29 (A:10-101) Aclacinomycin-10-hydroxylase R	0.001

>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 = 54.8 bits (132), Expect = 1e-11
 Identities = 12/65 (18%), Positives = 24/65 (36%), Gaps = 3/65 (4%)

Query: 1   MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFA--QQNFGQNDQERSYVATNASK 58
           M+ +E+ + LP     +  +   + R + +L          +       ER Y  +   K
Sbjct: 45  MSPSEIASKLPASTQHSD-LPNRLDRMLRLLASYSVLTSTTRTIEDGGAERVYGLSMVGK 103

Query: 59  LLLKD 63
            L+ D
Sbjct: 104 YLVPD 108

>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 = 52.5 bits (126), Expect = 1e-10
 Identities = 13/65 (20%), Positives = 24/65 (36%), Gaps = 5/65 (7%)

Query: 1   MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQND--QERSYVATNASK 58
           ++  E+ + LP     A      + R + +L            Q D   +R Y     +K
Sbjct: 45  ISPIEIASQLPTTNPDA---PVMLDRMLRLLACYIILTCSVRTQQDGKVQRLYGLATVAK 101

Query: 59  LLLKD 63
            L+K+
Sbjct: 102 YLVKN 106

>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 = 46.8 bits (111), Expect = 1e-08
 Identities = 20/63 (31%), Positives = 30/63 (47%), Gaps = 8/63 (12%)

Query: 1  MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL 60
          ++L+ L++ L     K   V     R M  L H+GFF         +E SY  T AS+LL
Sbjct: 45 ISLSNLVSILQVPSSKIGNV----RRLMRYLAHNGFFEI----ITKEEESYALTVASELL 96

Query: 61 LKD 63
          ++ 
Sbjct: 97 VRG 99

>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 = 35.2 bits (81), Expect = 3e-04
 Identities = 13/63 (20%), Positives = 19/63 (30%), Gaps = 13/63 (20%)

Query: 1  MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL 60
           T+  L       P         + R +  LV  G   +      D    +V T   +LL
Sbjct: 35 RTVKALAARTDTRPEA-------LLRLIRHLVAIGLLEE------DAPGEFVPTEVGELL 81

Query: 61 LKD 63
            D
Sbjct: 82 ADD 84

>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 = 33.6 bits (77), Expect = 0.001
 Identities = 14/60 (23%), Positives = 17/60 (28%), Gaps = 11/60 (18%)

Query: 1  MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL 60
           TL  L +    HP       Q + R +  L   G           Q R    T    LL
Sbjct: 41 DTLAGLADRTDTHP-------QALSRLVRHLTVVGVLEG----GEKQGRPLRPTRLGMLL 89

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	128
d1fp1d1	110	Chalcone O-methyltransferase {Alfalfa (Medicago sa	99.48
d1kyza1	107	Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltra	99.47
d1fp2a1	101	Isoflavone O-methyltransferase {Alfalfa (Medicago	99.43
d1tw3a1	85	Carminomycin 4-O-methyltransferase {Streptomyces p	99.27
d1qzza1	92	Aclacinomycin-10-hydroxylase RdmB {Streptomyces pu	98.99
d1fp2a2	244	Isoflavone O-methyltransferase {Alfalfa (Medicago	98.87
d1kyza2	243	Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltra	98.81
d1fp1d2	244	Chalcone O-methyltransferase {Alfalfa (Medicago sa	98.73
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	97.63
d1qzza2	256	Aclacinomycin-10-hydroxylase RdmB {Streptomyces pu	97.59
d1tw3a2	253	Carminomycin 4-O-methyltransferase {Streptomyces p	97.33
d1ub9a_	100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	96.59
d3broa1	135	Transcriptional regulator OEOE1854 {Oenococcus oen	96.24
d1lnwa_	141	MexR repressor {Pseudomonas aeruginosa [TaxId: 287	96.22
d1xd7a_	127	Hypothetical protein ywnA {Bacillus subtilis [TaxI	96.21
d2etha1	140	Putative transcriptional regulator TM0816 {Thermot	96.08
d2bv6a1	136	Transcriptional regulator MgrA {Staphylococcus aur	95.88
d2hr3a1	145	Probable transcriptional regulator PA3067 {Pseudom	95.64
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	95.63
d2a61a1	139	Transcriptional regulator TM0710 {Thermotoga marit	95.61
d1ylfa1	138	Hypothetical protein BC1842 {Bacillus cereus [TaxI	95.59
d2fbha1	137	Transcriptional regulator PA3341 {Pseudomonas aeru	95.47
d3deua1	140	Transcriptional regulator SlyA {Salmonella typhimu	95.36
d1jgsa_	138	Multiple antibiotic resistance repressor, MarR {Es	95.25
d1s3ja_	143	Putative transcriptional regulator YusO {Bacillus	95.19
d3ctaa1	85	Ta1064 (RFK), N-terminal domain {Thermoplasma acid	95.17
d1lj9a_	144	Transcriptional regulator SlyA {Enterococcus faeca	95.14
d2frha1	115	Pleiotropic regulator of virulence genes, SarA {St	95.11
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	95.02
d1z91a1	137	Organic hydroperoxide resistance transcriptional r	95.01
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	94.4
d1hsja1	115	Staphylococcal accessory regulator A homolog, SarR	94.4
d1p4xa2	125	Staphylococcal accessory regulator A homolog, SarS	94.31
d2fbia1	136	Probable transcriptional regulator PA4135 {Pseudom	94.19
d1p4xa1	125	Staphylococcal accessory regulator A homolog, SarS	93.92
d1lvaa3	64	C-terminal fragment of elongation factor SelB {Moo	93.83
d2fbka1	172	Transcriptional regulator DR1159 {Deinococcus radi	93.77
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	93.01
d2fxaa1	162	Protease production regulatory protein Hpr {Bacill	92.85
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	92.54
d2hzta1	95	Putative transcriptional regulator YtcD {Bacillus	92.37
d1z6ra1	70	Mlc protein N-terminal domain {Escherichia coli [T	91.83
d2obpa1	81	Putative DNA-binding protein ReutB4095 {Ralstonia	91.7
d2hoea1	62	N-acetylglucosamine kinase {Thermotoga maritima [T	91.45
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	91.25
d2f2ea1	142	Hypothetical protein PA1607 {Pseudomonas aeruginos	90.95
d2fswa1	102	Hypothetical protein PG0823 {Porphyromonas gingiva	90.56
d1yyva1	114	Putative transcriptional regulator YtfH {Salmonell	90.36
d1r7ja_	90	Sso10a (SSO10449) {Archaeon Sulfolobus solfataricu	89.91
d1z7ua1	108	Hypothetical protein EF0647 {Enterococcus faecalis	89.68
d1zyba1	73	Probable transcription regulator BT4300, C-termina	89.25
d1ulya_	190	Hypothetical protein PH1932 {Pyrococcus horikoshii	88.42
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	87.77
d2isya1	63	Iron-dependent regulator IdeR {Mycobacterium tuber	87.35
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	87.11
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	87.1
d2p4wa1	194	Transcriptional regulatory protein PF1790 {Pyrococ	86.91
d1r1ta_	98	SmtB repressor {Cyanobacteria (Synechococcus), pcc	86.89
d2zcwa1	82	Transcriptional regulator TTHA1359, C-terminal dom	86.72
d1r1ua_	94	Metal-sensing transcriptional repressor CzrA {Stap	86.18
d2gaua1	81	Transcriptional regulator PG0396, C-terminal domai	86.03
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	85.88
d1dpua_	69	C-terminal domain of RPA32 {Human (Homo sapiens) [	85.63
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	85.61
d2hs5a1	69	Putative transcriptional regulator RHA1_ro03477 {R	84.79
d2ev0a1	61	Manganese transport regulator MntR {Bacillus subti	84.7
d3bwga1	78	Transcriptional regulator YydK {Bacillus subtilis	84.22
d1hw1a1	74	Fatty acid responsive transcription factor FadR, N	84.17
d1ft9a1	80	CO-sensing protein CooA, C-terminal domain {Rhodos	82.58
d1i5za1	69	Catabolite gene activator protein (CAP), C-termina	82.56
d1bl0a1	54	MarA {Escherichia coli [TaxId: 562]}	81.86
d1u2wa1	108	Cadmium efflux system accessory protein CadC {Stap	81.1

>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=99.48  E-value=9.8e-15  Score=96.03  Aligned_cols=63  Identities=19%  Similarity=0.302  Sum_probs=48.1

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccC-CCC-cccceechHhhhhhhcCC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFG-QND-QERSYVATNASKLLLKDI   64 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~-~~~-~~~~y~~T~~s~~L~~~~   64 (128)
                      +|++|||+++++++++++ .+..|+||||+|+++|||.+.... ++| .+++|++||+||+|+++.
T Consensus        45 ls~~ela~~lp~~~~~p~-~~~~L~RiLRlLas~~vf~~~~~~~~~g~~e~~Y~Ltpvsk~Lv~de  109 (110)
T d1fp1d1          45 MSPSEIASKLPASTQHSD-LPNRLDRMLRLLASYSVLTSTTRTIEDGGAERVYGLSMVGKYLVPDE  109 (110)
T ss_dssp             BCHHHHHTTSCGGGCCTT-HHHHHHHHHHHHHHTTSEEEEEEECTTSCEEEEEEECTTGGGGSTTC
T ss_pred             CCHHHHHHhCCCCCCCcc-HHHHHHHHHHHHHHcCccccccccCCCCCeeeEEecchhhHhhcCCC
Confidence            589999999986433322 223899999999999999876543 223 356899999999999874

>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=99.47  E-value=1.4e-14  Score=94.98  Aligned_cols=60  Identities=20%  Similarity=0.243  Sum_probs=47.9

Q ss_pred             CCHHHHHHhCCC-CCCCchhhhhhHHHHHHHHHhcCcceeeccC-CCC-cccceechHhhhhhhcCC
Q 045905            1 MTLNELINALPF-HPIKAQYVAQYVYRFMWILVHSGFFAQQNFG-QND-QERSYVATNASKLLLKDI   64 (128)
Q Consensus         1 ~S~~eLA~~~~~-~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~-~~~-~~~~y~~T~~s~~L~~~~   64 (128)
                      +|+.|||++++. +|.++.    .|+||||+|++.|||++.... ++| .+++|++||+||+|+++.
T Consensus        45 ls~~eia~~l~~~~p~~~~----~L~RilR~Las~~vf~~~~~~~~dg~~~~~Y~LTpvsk~Lv~de  107 (107)
T d1kyza1          45 ISPIEIASQLPTTNPDAPV----MLDRMLRLLACYIILTCSVRTQQDGKVQRLYGLATVAKYLVKNE  107 (107)
T ss_dssp             BCHHHHHHTSSCCCTTHHH----HHHHHHHHHHHTTSEEEEEEECTTSCEEEEEEECHHHHHHSCCT
T ss_pred             CCHHHHHHhcCCCCCcchH----HHHHHHHHHHhcCceEEeeecCCCCCeeeEEecchhHHhhcCCC
Confidence            478899999998 453456    899999999999999886542 233 246899999999999863

>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=99.43  E-value=3e-14  Score=92.47  Aligned_cols=56  Identities=36%  Similarity=0.493  Sum_probs=48.4

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcCC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDI   64 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~~   64 (128)
                      +|++|||+++++++.++.    .|+||||+|++.|||.++.+.    +++|++||+|++|+++.
T Consensus        45 ~t~~eLa~~~~~~~~~~~----~L~RlLR~L~~~gi~~~~~~~----~~~Y~lt~~s~~Lv~~~  100 (101)
T d1fp2a1          45 ISLSNLVSILQVPSSKIG----NVRRLMRYLAHNGFFEIITKE----EESYALTVASELLVRGS  100 (101)
T ss_dssp             EEHHHHHHHHTCCGGGHH----HHHHHHHHHHHTTSEEEEESS----SEEEEECHHHHTTSTTS
T ss_pred             CCHHHHHHHcCCCCccch----HHHHHHHHHHhCCceeeecCC----CCeEecCHHHHHhhcCC
Confidence            478999999999876777    899999999999999886531    47899999999999874

>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=99.27  E-value=1.5e-12  Score=81.73  Aligned_cols=51  Identities=22%  Similarity=0.323  Sum_probs=46.0

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcCC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKDI   64 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~~   64 (128)
                      +|++|||+++|++   +.    .|.||||+|++.|+|.|++      ++.|++||+|+.|++|+
T Consensus        35 ~s~~eLA~~~g~~---~~----~l~rlLr~l~a~gl~~e~~------~~~y~lt~~s~~L~~Dh   85 (85)
T d1tw3a1          35 RTVKALAARTDTR---PE----ALLRLIRHLVAIGLLEEDA------PGEFVPTEVGELLADDH   85 (85)
T ss_dssp             CBHHHHHHHHTCC---HH----HHHHHHHHHHHTTSEEEEE------TTEEEECTTGGGGSTTS
T ss_pred             CCHHHHHHHhCcC---hh----HHHHHHHHHHHCCCeEecC------CCeEecCHHHHHhhcCC
Confidence            5899999999994   48    9999999999999999886      58999999999998763

>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=98.99  E-value=1.7e-10  Score=73.22  Aligned_cols=52  Identities=25%  Similarity=0.212  Sum_probs=44.4

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|++|||+++|++   +.    .+.||||+|+++|+|.+.++    ..+.|++|++|++|+++
T Consensus        41 ~t~~eLA~~~g~~---~~----~l~rLlr~L~a~gll~~~~d----~~~~~~~t~~g~lL~dg   92 (92)
T d1qzza1          41 DTLAGLADRTDTH---PQ----ALSRLVRHLTVVGVLEGGEK----QGRPLRPTRLGMLLADG   92 (92)
T ss_dssp             CSHHHHHHHHTCC---HH----HHHHHHHHHHHTTSEECCCC-----CCCCEECTTGGGGSTT
T ss_pred             CCHHHHHHHHCcC---ch----HHHHHHHHHHHCCCeeeecC----CCceecccHHHHhccCC
Confidence            5899999999994   48    99999999999999987752    13579999999999753

>d1fp2a2 c.66.1.12 (A:109-352) Isoflavone O-methyltransferase {Alfalfa (Medicago sativa) [TaxId: 3879]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Plant O-methyltransferase, C-terminal domain
domain: Isoflavone O-methyltransferase
species: Alfalfa (Medicago sativa) [TaxId: 3879]

Probab=98.87  E-value=3.4e-10  Score=82.95  Aligned_cols=54  Identities=22%  Similarity=0.438  Sum_probs=51.1

Q ss_pred             cHHHHHHHhcChhhHHHHHhHHHhhhcCCCChhhhccCCChhHhhhcCccchhh
Q 045905           67 TVRSFLQAVLDPILTTPCQHVTTWFQNDDLRCLTRHMGWHFESILGTSQRSTIS  120 (128)
Q Consensus        67 s~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~~f~~a~G~~~fe~~~~~p~~~~~  120 (128)
                      |+++++++.++|.++.+|..|.+|++++++++|+.+||+++|||+.+||++.+.
T Consensus         2 s~ap~~~~~~~p~~~~~w~~l~~~~~~~~~~~f~~a~G~~~~e~l~~~pe~~~~   55 (244)
T d1fp2a2           2 CLAPMVECVLDPTLSGSYHELKKWIYEEDLTLFGVTLGSGFWDFLDKNPEYNTS   55 (244)
T ss_dssp             CCHHHHHHHTCHHHHHGGGGHHHHHTCSSCCHHHHHHSSCHHHHHHHCHHHHHH
T ss_pred             ChHHHHHHHhCHHHHHHHHHHHHHHhcCCCCHHHHhhCCCHHHHHHhCHHHHHH
Confidence            689999999999999999999999999987899999999999999999998874

>d1kyza2 c.66.1.12 (A:120-362) Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase {Alfalfa (Medicago sativa) [TaxId: 3879]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Plant O-methyltransferase, C-terminal domain
domain: Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltransferase
species: Alfalfa (Medicago sativa) [TaxId: 3879]

Probab=98.81  E-value=7.9e-10  Score=80.67  Aligned_cols=53  Identities=13%  Similarity=0.120  Sum_probs=50.3

Q ss_pred             CcHHHHHHHhcChhhHHHHHhHHHhhhcCCCChhhhccCCChhHhhhcCccchh
Q 045905           66 LTVRSFLQAVLDPILTTPCQHVTTWFQNDDLRCLTRHMGWHFESILGTSQRSTI  119 (128)
Q Consensus        66 ~s~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~~f~~a~G~~~fe~~~~~p~~~~  119 (128)
                      .|+++++++..++.++++|.+|.+++++|. ++|+.+||+++|||+.+||+..+
T Consensus         3 ~s~~~~~~~~~~~~~~~~W~~L~~avrtG~-~~f~~~~G~~~~~~~~~~p~~~~   55 (243)
T d1kyza2           3 VSISALNLMNQDKVLMESWYHLKDAVLDGG-IPFNKAYGMTAFEYHGTDPRFNK   55 (243)
T ss_dssp             CCTHHHHHHHTSHHHHGGGGGHHHHHHHCS-CHHHHHHSSCHHHHGGGCHHHHH
T ss_pred             CcHHHHHHHhcCHHHHHHHHHHHHHHhhCC-CHHHhhcCCCHHHHHHhCHHHHH
Confidence            579999999999999999999999999998 79999999999999999998876

>d1fp1d2 c.66.1.12 (D:129-372) Chalcone O-methyltransferase {Alfalfa (Medicago sativa) [TaxId: 3879]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Plant O-methyltransferase, C-terminal domain
domain: Chalcone O-methyltransferase
species: Alfalfa (Medicago sativa) [TaxId: 3879]

Probab=98.73  E-value=1.2e-09  Score=79.94  Aligned_cols=54  Identities=13%  Similarity=0.125  Sum_probs=36.9

Q ss_pred             CcHHHHHHHhcChhhHHHHHhHHHhhhcCCCChhhhccCCChhHhhhcCccchh
Q 045905           66 LTVRSFLQAVLDPILTTPCQHVTTWFQNDDLRCLTRHMGWHFESILGTSQRSTI  119 (128)
Q Consensus        66 ~s~~~~~~~~~~~~~~~~~~~l~~~~~~g~~~~f~~a~G~~~fe~~~~~p~~~~  119 (128)
                      +++++++.++++|.++.+|.+|.+++++|++++|+.+||.++|||+.+||+..+
T Consensus         2 g~l~~~~~~~~~p~~~~~w~~l~~~v~~g~~~~f~~~~G~~~~e~l~~~p~~~~   55 (244)
T d1fp1d2           2 GYLASFTTFLCYPALLQVWMNFKEAVVDEDIDLFKNVHGVTKYEFMGKDKKMNQ   55 (244)
T ss_dssp             CCCTHHHHHHTCHHHHHHHTTHHHHHHSCC--------------CCSSCHHHHH
T ss_pred             ccHHHHHHHHhCHHHHHHHHHHHHHHhcCCCCHhHHhcCCCHHHHHhhCHHHHH
Confidence            357889999999999999999999999988789999999999999999999876

>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=97.63  E-value=2.3e-05  Score=46.84  Aligned_cols=47  Identities=17%  Similarity=0.410  Sum_probs=39.5

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL   60 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L   60 (128)
                      +|+.|||+++++++   .    .++|+|..|...|++..++      ++.|.+++---.|
T Consensus        21 ~s~~eia~~~~~~~---s----t~~rll~tL~~~g~l~~~~------~g~y~lG~~l~~l   67 (75)
T d1mkma1          21 VSVSEIAEKFNMSV---S----NAYKYMVVLEEKGFVLRKK------DKRYVPGYKLIEY   67 (75)
T ss_dssp             BCHHHHHHHTTCCH---H----HHHHHHHHHHHTTSEEECT------TSCEEECTHHHHH
T ss_pred             CCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCEEECC------CCCEeecHHHHHH
Confidence            58899999999965   7    8999999999999998765      4679998765433

>d1qzza2 c.66.1.12 (A:102-357) Aclacinomycin-10-hydroxylase RdmB {Streptomyces purpurascens [TaxId: 1924]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Plant O-methyltransferase, C-terminal domain
domain: Aclacinomycin-10-hydroxylase RdmB
species: Streptomyces purpurascens [TaxId: 1924]

Probab=97.59  E-value=9e-06  Score=58.86  Aligned_cols=55  Identities=11%  Similarity=-0.012  Sum_probs=45.5

Q ss_pred             CCcHHHHHHHhcChhh-HHHHHhHHHhhhcCCCChhhhccCCChhHhhhcCccchhh
Q 045905           65 TLTVRSFLQAVLDPIL-TTPCQHVTTWFQNDDLRCLTRHMGWHFESILGTSQRSTIS  120 (128)
Q Consensus        65 ~~s~~~~~~~~~~~~~-~~~~~~l~~~~~~g~~~~f~~a~G~~~fe~~~~~p~~~~~  120 (128)
                      |.++++|+.+...... ..+|.+|.+++++|. ++|+.++|+++|||+.+||+..+.
T Consensus         2 p~~~~~~~~l~~~~~~~~~~~~~L~~~~rtG~-~~~~~~~G~~~~e~~~~~p~~~~~   57 (256)
T d1qzza2           2 PAQQRAWLDLNGAVSHADLAFTGLLDVVRTGR-PAYAGRYGRPFWEDLSADVALADS   57 (256)
T ss_dssp             TTCHHHHHCTTSHHHHHHGGGGGHHHHHHHSC-CSHHHHHSSCHHHHHHHCHHHHHH
T ss_pred             cHHHHHHHhhcCchhhhHhhHHHHHHHHHhCC-chhhhhhCCCHHHHHHhCHHHHHH
Confidence            4568888877765443 357999999999998 689999999999999999987653

>d1tw3a2 c.66.1.12 (A:99-351) Carminomycin 4-O-methyltransferase {Streptomyces peucetius [TaxId: 1950]}

class: Alpha and beta proteins (a/b)
fold: S-adenosyl-L-methionine-dependent methyltransferases
superfamily: S-adenosyl-L-methionine-dependent methyltransferases
family: Plant O-methyltransferase, C-terminal domain
domain: Carminomycin 4-O-methyltransferase
species: Streptomyces peucetius [TaxId: 1950]

Probab=97.33  E-value=1.8e-05  Score=56.80  Aligned_cols=40  Identities=8%  Similarity=-0.036  Sum_probs=35.7

Q ss_pred             hhHHHHHhHHHhhhcCCCChhhhccCCChhHhhhcCccchh
Q 045905           79 ILTTPCQHVTTWFQNDDLRCLTRHMGWHFESILGTSQRSTI  119 (128)
Q Consensus        79 ~~~~~~~~l~~~~~~g~~~~f~~a~G~~~fe~~~~~p~~~~  119 (128)
                      ....+|.+|.+.+++|. ++|+.++|+++|||+.++|+..+
T Consensus        16 ~~~~~~~~L~~~vr~G~-~~~~~~~G~~~~~~~~~~~~~~~   55 (253)
T d1tw3a2          16 RADISFTRLPDAIRTGR-PTYESIYGKPFYEDLAGRPDLRA   55 (253)
T ss_dssp             HHGGGGGGHHHHHHHCC-CCHHHHHSSCHHHHHHTCHHHHH
T ss_pred             hccccHHHHHHHHHhCC-chhhhccCCCHHHHHhhCHHHHH
Confidence            44567999999999998 68999999999999999998876

>d1ub9a_ a.4.5.28 (A:) Hypothetical protein PH1061 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Hypothetical protein PH1061
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=96.59  E-value=0.0011  Score=40.74  Aligned_cols=54  Identities=7%  Similarity=0.063  Sum_probs=41.3

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLL   61 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~   61 (128)
                      +|..|||+.+++   .+.    .+.|.|+.|...|++.......+.....|.+|+.|+-+.
T Consensus        31 ~~~~eLa~~l~i---s~~----~vs~~l~~L~~~glV~~~~~~~d~r~~~~~LT~~G~~~~   84 (100)
T d1ub9a_          31 APFSQIQKVLDL---TPG----NLDSHIRVLERNGLVKTYKVIADRPRTVVEITDFGMEEA   84 (100)
T ss_dssp             EEHHHHHHHTTC---CHH----HHHHHHHHHHHTTSEEEEEECSSSCEEEEEECHHHHHHH
T ss_pred             eeHHHHHHHHhh---ccc----cccHHHHHHhhhceeEEEEcCcCCccccccCCHHHHHHH
Confidence            368899999999   448    999999999999999755432222124699999997654

>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=96.24  E-value=0.0035  Score=40.13  Aligned_cols=56  Identities=9%  Similarity=0.106  Sum_probs=44.0

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.+++   +..    .+.|++..|...|++......+|.-...+.+|+.|+.+...
T Consensus        46 it~~ela~~~~~---~~~----~vs~~l~~L~~~g~v~r~~~~~D~R~~~i~lT~~G~~~~~~  101 (135)
T d3broa1          46 VLQRDLESEFSI---KSS----TATVLLQRMEIKKLLYRKVSGKDSRQKCLKLTKKANKLETI  101 (135)
T ss_dssp             CBHHHHHHHHTC---CHH----HHHHHHHHHHHTTSEEEEECSSCTTSEEEEECHHHHTTHHH
T ss_pred             CCHHHHHHHHCc---CHh----HHHHHHHHHHHHHHHHHHhhhhhhhhhhhcccHHHHHHHHH
Confidence            578999999999   448    89999999999999975543333223469999999988754

>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=96.22  E-value=0.0042  Score=40.23  Aligned_cols=56  Identities=9%  Similarity=0.087  Sum_probs=44.2

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||..+++   +..    .+.|++..|...|++......+|.-...+.+|+.|+.+...
T Consensus        51 ~t~~~la~~l~~---~~~----~vsr~l~~L~~~G~v~r~~~~~D~R~~~l~lT~~G~~~~~~  106 (141)
T d1lnwa_          51 LNLQDLGRQMCR---DKA----LITRKIRELEGRNLVRRERNPSDQRSFQLFLTDEGLAIHQH  106 (141)
T ss_dssp             CBHHHHHHHTTC---CHH----HHHHHHHHHHHTTSEEEEECSSSSSSEEEEECHHHHHHHHH
T ss_pred             CCHHHHHHHHCc---cHh----HHHHHHHHHHHhhceeeeccCCCCcchhhccCHHHHHHHHH
Confidence            578999999999   448    99999999999999976554333223468999999887654

>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=96.21  E-value=0.0017  Score=41.72  Aligned_cols=34  Identities=12%  Similarity=0.258  Sum_probs=30.0

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN   41 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~   41 (128)
                      +|.++||+.++++|   .    .|++||+.|...|++.-..
T Consensus        19 ~ss~~IA~~~~~~~---~----~v~kIl~~L~~aglV~s~r   52 (127)
T d1xd7a_          19 TSSEIIADSVNTNP---V----VVRRMISLLKKADILTSRA   52 (127)
T ss_dssp             CCHHHHHHHHTSCH---H----HHHHHHHHHHHTTSEECCS
T ss_pred             CCHHHHHHHhCcCH---H----HHHHHHHHHHHhCcccccC
Confidence            57899999999965   8    9999999999999997554

>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=96.08  E-value=0.0053  Score=39.50  Aligned_cols=56  Identities=14%  Similarity=0.127  Sum_probs=44.6

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.+++   +..    .+.|+++-|...|++.......|.-.....+|+.|+.+...
T Consensus        47 ~t~~~La~~l~i---~~~----~vs~~v~~L~~~gli~r~~~~~D~R~~~l~lT~~G~~~~~~  102 (140)
T d2etha1          47 KKMKEIAEFLST---TKS----NVTNVVDSLEKRGLVVREMDPVDRRTYRVVLTEKGKEIFGE  102 (140)
T ss_dssp             BCHHHHHHHTTS---CHH----HHHHHHHHHHHTTSEEEEECTTTSSCEEEEECHHHHHHHHH
T ss_pred             cCHHHHHHHHCc---CHH----HHHHHHHHHHHCCCeeeeecccccchhhhhcCHHHHHHHHH
Confidence            478999999999   448    99999999999999986554333223479999999988754

>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=95.88  E-value=0.0052  Score=39.45  Aligned_cols=56  Identities=9%  Similarity=0.154  Sum_probs=43.5

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||..+++++   .    .+.|++.-|...|++......+|.-...+.+|+.|+.+...
T Consensus        49 ~t~~~la~~l~~~~---~----~~s~~l~~L~~~Gli~r~~~~~D~R~~~l~lT~~G~~~~~~  104 (136)
T d2bv6a1          49 VNVKKVVTELALDT---G----TVSPLLKRMEQVDLIKRERSEVDQREVFIHLTDKSETIRPE  104 (136)
T ss_dssp             EEHHHHHHHTTCCT---T----THHHHHHHHHHTTSEEEEECSSSTTCEEEEECHHHHHHHHH
T ss_pred             CCHHHHHHHHCCCH---h----HHHHHHHHHHHCCCEEEeecCCcccchhhccCHHHHHHHHH
Confidence            36789999999955   7    89999999999999976554333222467999999887653

>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=95.64  E-value=0.0078  Score=38.96  Aligned_cols=56  Identities=14%  Similarity=0.158  Sum_probs=42.3

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.+++   +..    .+.|++.-|...|++......+|.-...+.+|+.|+-+...
T Consensus        50 ~t~~~La~~~~~---~~~----~vs~~i~~L~~~glv~r~~~~~DrR~~~i~LT~~G~~~~~~  105 (145)
T d2hr3a1          50 VTPSELAAAERM---RSS----NLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYG  105 (145)
T ss_dssp             BCHHHHHHHTTC---CHH----HHHHHHHHHHHTTSEEEEC------CCEEEECHHHHHHHHH
T ss_pred             CCHHHHHHHHCC---CHH----HHHHHHHHHHHcCCeEeeeCccchhHHHhccCHHHHHHHHH
Confidence            588999999999   448    99999999999999975543233223469999999988654

>d1sfxa_ a.4.5.50 (A:) Hypothetical protein AF2008 {Archaeoglobus fulgidus [TaxId: 2234]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: TrmB-like
domain: Hypothetical protein AF2008
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=95.63  E-value=0.0044  Score=38.70  Aligned_cols=53  Identities=21%  Similarity=0.344  Sum_probs=38.9

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLL   60 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L   60 (128)
                      +|..|||..++++.   .    .++++|.-|...|++......+++....|.+++..+.|
T Consensus        35 ~t~~eia~~~~i~~---~----~v~~~l~~L~~~GlV~r~~~~~~~r~~~~~a~~~~e~l   87 (109)
T d1sfxa_          35 MRVSEIARELDLSA---R----FVRDRLKVLLKRGFVRREIVEKGWVGYIYSAEKPEKVL   87 (109)
T ss_dssp             BCHHHHHHHHTCCH---H----HHHHHHHHHHHTTSEEEEEEESSSEEEEEEECCHHHHH
T ss_pred             CCHHHHHHHhCCCc---c----hHHHHHHHHHhCCCEEEEeccCCCccccccCCCHHHHH
Confidence            48899999999944   8    99999999999999975432121112357777776554

>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=95.61  E-value=0.004  Score=40.12  Aligned_cols=56  Identities=14%  Similarity=0.097  Sum_probs=43.8

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||..++++   ..    .+.|++.-|...|++......+|.-...+.+|+.|+.++..
T Consensus        45 ~t~~~la~~l~i~---~~----tvs~~l~~L~~~gli~r~~~~~D~R~~~i~LT~~G~~~~~~  100 (139)
T d2a61a1          45 KRPGELSVLLGVA---KS----TVTGLVKRLEADGYLTRTPDPADRRAYFLVITRKGEEVIEK  100 (139)
T ss_dssp             BCHHHHHHHHTCC---HH----HHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHHHH
T ss_pred             CCHHHHHHHhCCC---cc----cchHHHHHHHhcCeeeeeeccCCCCeEEEEECHHHHHHHHH
Confidence            4789999999994   48    99999999999999975543232222469999999988754

>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=95.59  E-value=0.0043  Score=40.27  Aligned_cols=34  Identities=18%  Similarity=0.284  Sum_probs=29.7

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN   41 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~   41 (128)
                      +|..|||+.+++++   .    .|+|||+.|...|++.-..
T Consensus        24 vss~~IA~~~~i~~---~----~l~kil~~L~~aGlv~S~r   57 (138)
T d1ylfa1          24 CTSDYMAESVNTNP---V----VIRKIMSYLKQAGFVYVNR   57 (138)
T ss_dssp             CCHHHHHHHHTSCH---H----HHHHHHHHHHHTTSEEEC-
T ss_pred             CcHHHHHHHHCcCH---H----HHHHHHHHHHHCCCeEeec
Confidence            57899999999966   8    9999999999999997654

>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=95.47  E-value=0.01  Score=37.85  Aligned_cols=56  Identities=18%  Similarity=0.251  Sum_probs=44.3

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||..+++   +..    .+.|++.-|...|++......+|+-...+.+|+.|+.+.+.
T Consensus        44 ~t~~~la~~~~~---~~~----~vs~~v~~L~~~gli~r~~~~~D~R~~~i~lT~~G~~~~~~   99 (137)
T d2fbha1          44 PTQRELAQSVGV---EGP----TLARLLDGLESQGLVRRLAVAEDRRAKHIVLTPKADVLIAD   99 (137)
T ss_dssp             CBHHHHHHHHTC---CHH----HHHHHHHHHHHTTSEEEECCBTTBCSCEEEECTTHHHHHHH
T ss_pred             CcHHHHHHHHCC---CHH----HHHHHHHHHHHcCCccccCCCCCCCchhhhcCHHHHHHHHH
Confidence            478899999999   448    99999999999999986654333223468999999988754

>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=95.36  E-value=0.0052  Score=39.48  Aligned_cols=56  Identities=14%  Similarity=0.219  Sum_probs=41.2

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||..+++   +.+    .+.|+++-|...|++......+|.-...+.+|+.|+-+...
T Consensus        47 ~t~~~la~~l~i---~~~----~vs~~l~~L~~~glI~~~~~~~D~R~~~l~lT~~G~~~~~~  102 (140)
T d3deua1          47 QSQIQLAKAIGI---EQP----SLVRTLDQLEDKGLISRQTCASDRRAKRIKLTEKAEPLIAE  102 (140)
T ss_dssp             EEHHHHHHHHTS---CHH----HHHHHHHHHHHTTSEEEC--------CEEEECGGGHHHHHH
T ss_pred             ccHHHHHHHHCC---CHh----HHHHHHHHHHhCCCEEecccCCCCCceeeEECHHHHHHHHH
Confidence            367899999999   458    89999999999999976554333223469999999988754

>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=95.25  E-value=0.012  Score=37.78  Aligned_cols=56  Identities=16%  Similarity=0.130  Sum_probs=44.2

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||..+++   +..    .+.|++.-|...|++......+|+-...+.+|+.|+.+...
T Consensus        49 ~t~~ela~~~~i---~~~----~vs~~v~~L~~~glv~r~~~~~D~R~~~i~lT~~G~~~~~~  104 (138)
T d1jgsa_          49 ITPVELKKVLSV---DLG----ALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTGGAAICEQ  104 (138)
T ss_dssp             BCHHHHHHHHTC---CHH----HHHHHHHHHHHTTSEEEEECTTCSSCEEEEECHHHHHHHHH
T ss_pred             CCHHHHHHHHCC---CHh----HHHHHHHHHhhCCCEEEeeccCCCCeeEEEECHHHHHHHHH
Confidence            478999999999   448    99999999999999976543333323479999999988643

>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=95.19  E-value=0.0093  Score=38.43  Aligned_cols=56  Identities=11%  Similarity=0.162  Sum_probs=43.8

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.+++   +..    .+.|++.-|...|++......+|.-.-.+.+|+.|+.+...
T Consensus        50 ~t~~~la~~~~i---~~~----~vs~~l~~L~~~glv~r~~~~~D~R~~~v~lT~~G~~~~~~  105 (143)
T d1s3ja_          50 LKVSEIAERMEV---KPS----AVTLMADRLEQKNLIARTHNTKDRRVIDLSLTDEGDIKFEE  105 (143)
T ss_dssp             EEHHHHHHHHTS---CHH----HHHHHHHHHHHTTSEEEEECSSCTTSEEEEECHHHHHHHHH
T ss_pred             CCHHHHHHHHCc---CHH----HHHHHHHHHHHhhhheeeeecCCCCceEEEECHHHHHHHHH
Confidence            368899999999   448    99999999999999975544333222359999999988754

>d3ctaa1 a.4.5.28 (A:5-89) Ta1064 (RFK), N-terminal domain {Thermoplasma acidophilum [TaxId: 2303]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Ta1064 (RFK), N-terminal domain
species: Thermoplasma acidophilum [TaxId: 2303]

Probab=95.17  E-value=0.011  Score=35.34  Aligned_cols=53  Identities=17%  Similarity=0.175  Sum_probs=42.0

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||++++++   +.    .+.|++.-|...|++....+   +....|.+|+.|+.+...
T Consensus        22 lt~~eLa~~l~i~---~~----~vs~~l~~Le~~GlV~r~~D---~R~~~i~LT~~G~~~l~~   74 (85)
T d3ctaa1          22 LTSSKLADMLGIS---QQ----SASRIIIDLEKNGYITRTVT---KRGQILNITEKGLDVLYT   74 (85)
T ss_dssp             CCHHHHHHHHTSC---HH----HHHHHHHHHHHTTSEEEEEE---TTEEEEEECHHHHHHHHH
T ss_pred             CCHHHHHHHHCCC---HH----HHHHHHHHHHHCCCeeeecc---cccccceECHHHHHHHHH
Confidence            5789999999994   48    99999999999999976432   112469999999877643

>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=95.14  E-value=0.011  Score=38.22  Aligned_cols=56  Identities=16%  Similarity=0.150  Sum_probs=44.0

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||..+++   +..    .+.|+++-|...|++......+|.-.....+|+.|+-++..
T Consensus        44 ~t~~~la~~l~i---~~~----tvs~~l~~L~~~glI~r~~~~~D~R~~~l~LT~~G~~~~~~   99 (144)
T d1lj9a_          44 IIQEKIAELIKV---DRT----TAARAIKRLEEQGFIYRQEDASNKKIKRIYATEKGKNVYPI   99 (144)
T ss_dssp             EEHHHHHHHHTC---CHH----HHHHHHHHHHHTTSEEEEECSSCTTCEEEEECHHHHHHHHH
T ss_pred             CCHHHHHHHHCc---cHh----hHHHHHHHHHhhhcccccCCCCCCCccccccCHHHHHHHHH
Confidence            367899999999   448    99999999999999976654333222468899999988754

>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=95.11  E-value=0.009  Score=37.52  Aligned_cols=55  Identities=16%  Similarity=0.318  Sum_probs=43.1

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhc
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLK   62 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~   62 (128)
                      +|..|||..+++   +..    .+.|+++.|...|++......+|.-...+.+|+.|+-+.+
T Consensus        50 ~t~~~la~~l~~---~~~----tvs~~i~~Le~~gli~r~~~~~D~R~~~i~LT~~G~~~~~  104 (115)
T d2frha1          50 YYLKDIINHLNY---KQP----QVVKAVKILSQEDYFDKKRNEHDERTVLILVNAQQRKKIE  104 (115)
T ss_dssp             EEHHHHHHHSSS---HHH----HHHHHHHHHHHTTSSCCBCCSSSSCCCEEECCSHHHHHHH
T ss_pred             CCHHHHHHHHCC---CHh----HHHHHHHHHHhhhhheeeecccCCceEEEEECHHHHHHHH
Confidence            367899999999   447    9999999999999997665433322346899999987754

>d1ku9a_ a.4.5.36 (A:) DNA-binding protein Mj223 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: DNA-binding protein Mj223
domain: DNA-binding protein Mj223
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=95.02  E-value=0.012  Score=37.97  Aligned_cols=52  Identities=13%  Similarity=0.144  Sum_probs=38.9

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKL   59 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~   59 (128)
                      +|+.|||+++|+++   .    .+.|.++.|...|++......++.....+.+|+.+.+
T Consensus        42 lt~~ela~~l~vsk---~----~vs~~l~~L~~~GlV~r~~~~~drr~~~~~~t~~g~~   93 (151)
T d1ku9a_          42 LTISDIMEELKISK---G----NVSMSLKKLEELGFVRKVWIKGERKNYYEAVDGFSSI   93 (151)
T ss_dssp             EEHHHHHHHHTCCH---H----HHHHHHHHHHHTTSEEEECCTTCSSCEEEECCHHHHH
T ss_pred             cCHHHHHHHhCCCc---c----hHHHHHHHHHHCCCEEEEEcCCCCceeEEeCCHHHHH
Confidence            47899999999944   8    9999999999999997554322211245778887753

>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=95.01  E-value=0.015  Score=37.23  Aligned_cols=56  Identities=11%  Similarity=0.189  Sum_probs=44.1

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||..+++   +..    .+.|++..|...|++......+|.-.....+|+.|+.+...
T Consensus        48 ~t~~~La~~~~i---~~~----~vsr~i~~L~~~glv~r~~~~~D~R~~~i~lT~~G~~~~~~  103 (137)
T d1z91a1          48 LTVKKMGEQLYL---DSG----TLTPMLKRMEQQGLITRKRSEEDERSVLISLTEDGALLKEK  103 (137)
T ss_dssp             EEHHHHHHTTTC---CHH----HHHHHHHHHHHHTSEECCBCSSCTTSBEEEECHHHHSGGGG
T ss_pred             CCHHHHHHHHCc---CHH----HHHHHHHHHhhccceEEeecCCCCCeEEEEECHHHHHHHHH
Confidence            367899999999   448    99999999999999976654333222458999999988764

>d1z05a1 a.4.5.63 (A:10-80) Transcriptional regulator VC2007 N-terminal domain {Vibrio cholerae [TaxId: 666]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: Transcriptional regulator VC2007 N-terminal domain
species: Vibrio cholerae [TaxId: 666]

Probab=94.40  E-value=0.014  Score=33.53  Aligned_cols=34  Identities=9%  Similarity=0.202  Sum_probs=30.1

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN   41 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~   41 (128)
                      +|..|||+.+|+++   .    .+.++++.|...|++.+..
T Consensus        21 ~sr~eLa~~~glS~---~----Tv~~~l~~L~~~Glv~e~~   54 (71)
T d1z05a1          21 ISRIDLSKESELAP---A----SITKITRELIDAHLIHETT   54 (71)
T ss_dssp             BCHHHHHHHHTCCH---H----HHHHHHHHHHHTTSEEEEC
T ss_pred             cCHHHHHHHHCCCH---H----HHHHHHHHHHHCCCEEEec
Confidence            57899999999954   8    9999999999999998764

>d1hsja1 a.4.5.28 (A:373-487) Staphylococcal accessory regulator A homolog, SarR {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Staphylococcal accessory regulator A homolog, SarR
species: Staphylococcus aureus [TaxId: 1280]

Probab=94.40  E-value=0.018  Score=36.10  Aligned_cols=55  Identities=15%  Similarity=0.211  Sum_probs=42.4

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhc
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLK   62 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~   62 (128)
                      +|..|||..+++   +..    .+.|++.-|...|++......+|.-.-...+|+.|+-+.+
T Consensus        49 ~t~~ela~~l~~---~~~----~vs~~i~~Le~~gli~r~~~~~D~R~~~i~LT~~G~~~~~  103 (115)
T d1hsja1          49 ISSKEIAKCSEF---KPY----YLTKALQKLKDLKLLSKKRSLQDERTVIVYVTDTQKANIQ  103 (115)
T ss_dssp             EEHHHHHHSSCC---CHH----HHHHHHHHHHTTTTSCCEECCSSSSCCEEECCSSHHHHHH
T ss_pred             cCHHHHHHHHCC---Chh----hHHHHHHHHHHcCCeEEEeecCCCceEEEEECHHHHHHHH
Confidence            367899999999   448    9999999999999997554333322235899999987764

>d1p4xa2 a.4.5.28 (A:126-250) Staphylococcal accessory regulator A homolog, SarS {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Staphylococcal accessory regulator A homolog, SarS
species: Staphylococcus aureus [TaxId: 1280]

Probab=94.31  E-value=0.025  Score=36.03  Aligned_cols=56  Identities=14%  Similarity=0.204  Sum_probs=43.1

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||+.+++   +.+    .+.|++.-|...|++......+|.-.-...+|+-|+-+.+.
T Consensus        50 ~~~~~ia~~l~~---~~~----~vs~~v~~L~~~glV~r~~~~~D~R~v~i~LT~~G~~~~~~  105 (125)
T d1p4xa2          50 VLLKDLIETIHH---KYP----QTVRALNNLKKQGYLIKERSTEDERKILIHMDDAQQDHAEQ  105 (125)
T ss_dssp             EEHHHHHHHSSS---CHH----HHHHHHHHHHHHTSSEEEECSSSTTCEEEECCHHHHHHHHH
T ss_pred             ccHHHHHHHHCC---Ccc----hHHHHHHHHHhccCEeeeecCCCCCeEEEEECHHHHHHHHH
Confidence            367899999999   448    89999999999999976544333222368999999877643

>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=94.19  E-value=0.016  Score=36.92  Aligned_cols=56  Identities=11%  Similarity=0.023  Sum_probs=43.7

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||..+++   +..    .+.|+++-|...|++......+|.-...+.+|+.|+-+.+.
T Consensus        45 ~t~~~la~~~~i---~~~----~vs~~i~~L~~~gli~r~~~~~D~R~~~l~lT~~G~~~~~~  100 (136)
T d2fbia1          45 MESYQLANQACI---LRP----SMTGVLARLERDGIVRRWKAPKDQRRVYVNLTEKGQQCFVS  100 (136)
T ss_dssp             EEHHHHHHHTTC---CHH----HHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHHHH
T ss_pred             CCHHHHHHHHCC---CHH----HHHHHHHHHHHCCCEEEeecCccCchhhhccCHHHHHHHHH
Confidence            367899999999   448    99999999999999976553332212459999999988754

>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=93.92  E-value=0.034  Score=35.20  Aligned_cols=55  Identities=5%  Similarity=0.225  Sum_probs=42.7

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhc
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLK   62 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~   62 (128)
                      +|..|||..+++.+   .    .+.|+++-|...|++......+|.-.-...+|+.|+-+.+
T Consensus        51 ~t~~eia~~~~~~~---~----~vs~~l~~L~~~g~v~r~~~~~D~R~~~i~lT~~G~~~~~  105 (125)
T d1p4xa1          51 LPFKKIVSDLCYKQ---S----DLVQHIKVLVKHSYISKVRSKIDERNTYISISEEQREKIA  105 (125)
T ss_dssp             EEHHHHHHHSSSCG---G----GTHHHHHHHHHTTSCEEEECSSSTTSEEEECCHHHHHHHH
T ss_pred             cCHHHHHHHhCCCc---c----hHHHHHHHHHHCCCceeecccCCCCeEEEEECHHHHHHHH
Confidence            36789999999944   7    8999999999999997665433321236899999987764

>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=93.83  E-value=0.045  Score=30.91  Aligned_cols=33  Identities=15%  Similarity=0.355  Sum_probs=28.6

Q ss_pred             CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905            2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN   41 (128)
Q Consensus         2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~   41 (128)
                      ++.|||..+|+   +..    .++.+|+.|+..|.+....
T Consensus        25 ~vrdl~~~l~~---~e~----~~~~lL~~l~~~G~lvkI~   57 (64)
T d1lvaa3          25 SFKEVAGSFNL---DPS----ELEELLHYLVREGVLVKIN   57 (64)
T ss_dssp             BHHHHHHHTTC---CHH----HHHHHHHHHHHTTSEEESS
T ss_pred             cHHHHHHHhCC---CHH----HHHHHHHHHHHCCCEEEec
Confidence            57899999999   448    8999999999999887665

>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=93.77  E-value=0.017  Score=38.56  Aligned_cols=56  Identities=13%  Similarity=0.126  Sum_probs=41.5

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||..+++++   .    .+.|++.-|...|++......+|.-.....+|+.|+.+...
T Consensus        80 lt~~eLa~~l~i~~---~----tvsr~l~~Le~~GlV~r~~~~~DrR~~~i~LT~~G~~l~~~  135 (172)
T d2fbka1          80 LRPTELSALAAISG---P----STSNRIVRLLEKGLIERREDERDRRSASIRLTPQGRALVTH  135 (172)
T ss_dssp             BCHHHHHHHCSCCS---G----GGSSHHHHHHHHTSEECCC-------CCBEECHHHHHHHHH
T ss_pred             cCHHHHHHHHCcCH---h----HHHHHHHHHHhCCCeeeeccccchhhHHhhcCHHHHHHHHH
Confidence            47899999999954   7    88899999999999986653333222458999999988754

>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=93.01  E-value=0.021  Score=35.18  Aligned_cols=34  Identities=18%  Similarity=0.245  Sum_probs=29.5

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN   41 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~   41 (128)
                      +|..|||..++++   ..    .+.|+++-|...|++....
T Consensus        37 ~t~~eLa~~~~i~---~~----tvs~~l~~L~~~GlV~r~~   70 (109)
T d2d1ha1          37 ITSEELADIFKLS---KT----TVENSLKKLIELGLVVRTK   70 (109)
T ss_dssp             EEHHHHHHHHTCC---HH----HHHHHHHHHHHTTSEEEEE
T ss_pred             CCHHHHHHHHCcc---Hh----HHHHHHHHHHHCCCEEEee
Confidence            4789999999994   48    9999999999999997554

>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=92.85  E-value=0.048  Score=36.15  Aligned_cols=56  Identities=9%  Similarity=0.100  Sum_probs=41.7

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      +|..|||..+++   +..    .+.|++.-|...|++......+|.-.....+|+.|+-+...
T Consensus        56 ~t~~~la~~~~l---~~~----tvs~~i~rL~~~gli~r~~~~~D~R~~~l~lT~~G~~~~~~  111 (162)
T d2fxaa1          56 ASISEIAKFGVM---HVS----TAFNFSKKLEERGYLRFSKRLNDKRNTYVQLTEEGTEVFWS  111 (162)
T ss_dssp             EEHHHHHHHTTC---CHH----HHHHHHHHHHHHTSEEEECC------CEEEECHHHHHHHHH
T ss_pred             cCHHHHHHHHcC---Cch----hhHHHHHHHHHCCCceeecccccCeeeeeccCHhHHHHHHH
Confidence            368899999999   448    99999999999999986543333222469999999987643

>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=92.54  E-value=0.068  Score=29.96  Aligned_cols=42  Identities=12%  Similarity=0.038  Sum_probs=32.4

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceech
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVAT   54 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T   54 (128)
                      +|..|||+.+|+.   ..    .++|=+..|-..|+-.+...     +..|.++
T Consensus        20 ~s~~eLa~~l~vS---~~----ti~r~i~~L~~~G~~I~~~~-----g~GY~L~   61 (63)
T d1biaa1          20 HSGEQLGETLGMS---RA----AINKHIQTLRDWGVDVFTVP-----GKGYSLP   61 (63)
T ss_dssp             BCHHHHHHHHTSC---HH----HHHHHHHHHHHTTCCCEEET-----TTEEECS
T ss_pred             CCHHHHHHHHCcC---HH----HHHHHHHHHHHCCCcEEEeC-----CCeEEeC
Confidence            4789999999994   47    89999999999998554432     2357764

>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=92.37  E-value=0.11  Score=31.53  Aligned_cols=53  Identities=13%  Similarity=0.148  Sum_probs=38.6

Q ss_pred             CHHHHHHhC-CCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhh
Q 045905            2 TLNELINAL-PFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLL   61 (128)
Q Consensus         2 S~~eLA~~~-~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~   61 (128)
                      ...||...+ |+++   .    .|.+=||.|...|++......+....-.|.+|+.|+-|.
T Consensus        26 rF~el~~~l~gis~---~----~Ls~rLk~Le~~glv~r~~~~~~p~~veY~LT~~G~~L~   79 (95)
T d2hzta1          26 RTSELKRLMPNITQ---K----MLTQQLRELEADGVINRIVYNQVPPKVEYELSEYGRSLE   79 (95)
T ss_dssp             CHHHHHHHCTTSCH---H----HHHHHHHHHHHTTSEEEEEECSSSCEEEEEECTTGGGGH
T ss_pred             CHHHHHHHhhcCCh---h----HHHHHHHHHHHhHHHhheeccccccchhhhhhhhHHHHH
Confidence            467888887 6743   7    899999999999999754321111123499999998886

>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=91.83  E-value=0.1  Score=29.67  Aligned_cols=35  Identities=6%  Similarity=0.183  Sum_probs=29.6

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeecc
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNF   42 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~   42 (128)
                      +|-.|||..+|+.+   +    .+.+++.-|...|++.|...
T Consensus        20 ~sr~eLa~~~gLS~---~----Tvs~iv~~L~~~glv~e~g~   54 (70)
T d1z6ra1          20 VSRIDLSRLAQLAP---A----SITKIVHEMLEAHLVQELEI   54 (70)
T ss_dssp             CCHHHHHHHTTCCH---H----HHHHHHHHHHHHTSEEEC--
T ss_pred             cCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCEEeeCC
Confidence            57899999999944   8    89999999999999987653

>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=91.70  E-value=0.11  Score=30.44  Aligned_cols=52  Identities=12%  Similarity=0.054  Sum_probs=40.7

Q ss_pred             CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhc
Q 045905            2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLK   62 (128)
Q Consensus         2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~   62 (128)
                      |+.-|+++.++|=   .    .|+|.|-.|..-|+..-.-. +| +.+.-++|+.++.|..
T Consensus        26 SLaklsKra~~PM---S----~LRR~LTqL~~aGl~~t~~~-ed-G~G~A~Lt~~G~~lca   77 (81)
T d2obpa1          26 SLPKIAKRAQLPM---S----VLRRVLTQLQAAGLADVSVE-AD-GRGHASLTQEGAALAA   77 (81)
T ss_dssp             BHHHHHHHHTCCH---H----HHHHHHHHHHHTTSEEEEEC-TT-SCEEEEECHHHHHHHH
T ss_pred             cHHHHHhhcCCcH---H----HHHHHHHHHhhcCceeeeec-cC-CcceeeccHHHHHHHH
Confidence            7888999988854   6    89999999999999864432 22 2578999999988763

>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=91.45  E-value=0.078  Score=29.61  Aligned_cols=35  Identities=17%  Similarity=0.196  Sum_probs=30.8

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeecc
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNF   42 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~   42 (128)
                      +|-.|||+.+|+.+   .    .+.++++-|...|++.|...
T Consensus        13 isr~eLa~~~gls~---~----TVs~~v~~L~~~GlV~e~~~   47 (62)
T d2hoea1          13 VSRVELAEELGLTK---T----TVGEIAKIFLEKGIVVEEKD   47 (62)
T ss_dssp             BCHHHHHHHHTCCH---H----HHHHHHHHHHHHTSEEEEEC
T ss_pred             cCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCEEECCC
Confidence            47789999999944   7    99999999999999998764

>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=91.25  E-value=0.093  Score=29.42  Aligned_cols=41  Identities=20%  Similarity=0.229  Sum_probs=31.6

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceech
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVAT   54 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T   54 (128)
                      +|..|||+.++++.   .    .++|=+..|-..|+--+..      .+.|.+.
T Consensus        23 vs~~~La~~l~VS~---~----TI~rdi~~L~~~G~~I~~~------~gGY~L~   63 (65)
T d1j5ya1          23 VSGAQLAEELSVSR---Q----VIVQDIAYLRSLGYNIVAT------PRGYVLA   63 (65)
T ss_dssp             BCHHHHHHHHTSCH---H----HHHHHHHHHHHHTCCCEEE------TTEEECC
T ss_pred             CcHHHHHHHHCCCH---H----HHHHHHHHHHHCCCeEEEe------CCCEEeC
Confidence            48899999999944   7    8999999999999743333      2457764

>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=90.95  E-value=0.14  Score=33.28  Aligned_cols=52  Identities=15%  Similarity=0.224  Sum_probs=39.2

Q ss_pred             CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhh
Q 045905            2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLL   61 (128)
Q Consensus         2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~   61 (128)
                      .+.||...+|+++   .    .|.+=|+.|...|++....... .....|.+|+.|+-|.
T Consensus        35 rf~el~~~lgis~---~----vLs~rL~~L~~~gLv~r~~~~~-p~r~~Y~LT~~G~~L~   86 (142)
T d2f2ea1          35 RFGEFQKSLGLAK---N----ILAARLRNLVEHGVMVAVPAES-GSHQEYRLTDKGRALF   86 (142)
T ss_dssp             SHHHHHHHHCCCH---H----HHHHHHHHHHHTTSEEEEECSS-SSCEEEEECHHHHTTH
T ss_pred             CHHHHHHHhhccH---H----HHHHHHHHHHHhcceeeecCCC-CCeeEEecCcCcchHH
Confidence            5789999999844   7    8889999999999997533211 1124599999998775

>d2fswa1 a.4.5.69 (A:3-104) Hypothetical protein PG0823 {Porphyromonas gingivalis [TaxId: 837]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: HxlR-like
domain: Hypothetical protein PG0823
species: Porphyromonas gingivalis [TaxId: 837]

Probab=90.56  E-value=0.19  Score=30.76  Aligned_cols=52  Identities=15%  Similarity=0.237  Sum_probs=37.6

Q ss_pred             HHHHHHhC-CCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhh
Q 045905            3 LNELINAL-PFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLL   61 (128)
Q Consensus         3 ~~eLA~~~-~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~   61 (128)
                      ..||...+ |++   +.    .|.+=|+.|...|++......+....-.|.+|+.|+-|.
T Consensus        36 F~el~~~l~gIs---~~----~Ls~rLkeL~~~glv~r~~~~~~p~~veY~LT~~G~~L~   88 (102)
T d2fswa1          36 YGELKRAIPGIS---EK----MLIDELKFLCGKGLIKKKQYPEVPPRVEYSLTPLGEKVL   88 (102)
T ss_dssp             HHHHHHHSTTCC---HH----HHHHHHHHHHHTTSEEEEEECSSSCEEEEEECHHHHTTH
T ss_pred             HHHHHhhCcccc---hh----HHHHHHHHHHHCCceeecccCCCCCeehhhhhHhHHHHH
Confidence            57888887 573   37    899999999999999754321110123499999998875

>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=90.36  E-value=0.18  Score=31.50  Aligned_cols=53  Identities=11%  Similarity=0.197  Sum_probs=38.2

Q ss_pred             HHHHHHhC-CCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhc
Q 045905            3 LNELINAL-PFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLK   62 (128)
Q Consensus         3 ~~eLA~~~-~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~   62 (128)
                      ..||...+ |+   ...    .|.+=||.|...|++...........-.|.+|+.|+-|..
T Consensus        40 F~el~~~l~gi---s~~----~Ls~rL~~Le~~glv~R~~~~~~p~~veY~LT~~G~~L~~   93 (114)
T d1yyva1          40 FSDLRRKMGGV---SEK----MLAQSLQALEQDGFLNRVSYPVVPPHVEYSLTPLGEQVSD   93 (114)
T ss_dssp             HHHHHHHSTTC---CHH----HHHHHHHHHHHHTCEEEEEECSSSCEEEEEECHHHHHHHH
T ss_pred             HHHHHHHcccc---chh----HHHHHHHHHHHHHHHhhcccCCCCchhHhHhhHhHHHHHH
Confidence            57888888 46   336    8999999999999997543211111235999999998863

>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=89.91  E-value=0.19  Score=30.22  Aligned_cols=47  Identities=17%  Similarity=0.304  Sum_probs=38.3

Q ss_pred             HHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhcC
Q 045905            3 LNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLKD   63 (128)
Q Consensus         3 ~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~~   63 (128)
                      ...|..+++++   ..    .+.+.+..|+..|+....       .+.|.+|+-|+-+.+.
T Consensus        21 kT~i~~~aNLs---~~----~~~kyl~~L~~~GLI~~~-------~~~Y~iT~kG~~~L~~   67 (90)
T d1r7ja_          21 KTRIMYGANLS---YA----LTGRYIKMLMDLEIIRQE-------GKQYMLTKKGEELLED   67 (90)
T ss_dssp             HHHHHHHHTCC---HH----HHHHHHHHHHHTTSEEEE-------TTEEEECHHHHHHHHH
T ss_pred             ccHHHHHcCCC---HH----HHHHHHHHHHHCCCeeec-------CCEEEECccHHHHHHH
Confidence            35677777884   47    899999999999999755       3789999999988754

>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=89.68  E-value=0.25  Score=30.52  Aligned_cols=54  Identities=17%  Similarity=0.223  Sum_probs=38.5

Q ss_pred             CHHHHHHhC-CCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHhhhhhhc
Q 045905            2 TLNELINAL-PFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNASKLLLK   62 (128)
Q Consensus         2 S~~eLA~~~-~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~s~~L~~   62 (128)
                      ...||...+ |+++   .    .|.+=||.|...|++......+....-.|.+|+.|+-|..
T Consensus        34 RF~el~~~l~gIS~---~----~Ls~rLk~L~~~glv~R~~~~~~p~~veY~LT~~G~~L~p   88 (108)
T d1z7ua1          34 RNGELMRALDGITQ---R----VLTDRLREMEKDGLVHRESFNELPPRVEYTLTPEGYALYD   88 (108)
T ss_dssp             CHHHHHHHSTTCCH---H----HHHHHHHHHHHHTSEEEEEECCSSCEEEEEECHHHHHHHH
T ss_pred             CHHHHHHHCcCCCh---h----HHHHHHHHHHHCCcceeeccCCCcceehhhhchhHHHHHH
Confidence            367888887 4743   7    8999999999999996543211111124999999998863

>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=89.25  E-value=0.26  Score=28.13  Aligned_cols=34  Identities=12%  Similarity=0.193  Sum_probs=29.2

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN   41 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~   41 (128)
                      +|-.|||+.+|+.+   .    .+.|.|+.|...|++....
T Consensus        28 lt~~elA~~lg~sr---~----tvsr~l~~l~~~g~I~~~~   61 (73)
T d1zyba1          28 VKMDDLARCLDDTR---L----NISKTLNELQDNGLIELHR   61 (73)
T ss_dssp             CCHHHHHHHHTSCH---H----HHHHHHHHHHHTTSCEEET
T ss_pred             cCHHHHHHHHCCCH---H----HHHHHHHHHHHCCCEEecC
Confidence            46789999999944   7    9999999999999997543

>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=88.42  E-value=0.13  Score=34.25  Aligned_cols=50  Identities=24%  Similarity=0.323  Sum_probs=37.0

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCC-CC-cccceechHhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQ-ND-QERSYVATNAS   57 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~-~~-~~~~y~~T~~s   57 (128)
                      +|+.|||+.+|+++   .    .+++-|+.|...|++....... .| ....|.+|+-+
T Consensus        33 ~s~~ela~~lg~s~---~----~v~~hl~~L~~~glv~~~~~~~~~g~~~k~y~~~~~~   84 (190)
T d1ulya_          33 MTISQLSEILGKTP---Q----TIYHHIEKLKEAGLVEVKRTEMKGNLVEKYYGRTADV   84 (190)
T ss_dssp             BCHHHHHHHHTCCH---H----HHHHHHHHHHHTTSEEEEEEEEETTEEEEEEEESSSE
T ss_pred             CCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCeEEEEeeccCCcceEEEEEcccc
Confidence            48899999999954   7    8999999999999996443211 11 12468888754

>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=87.77  E-value=0.17  Score=28.10  Aligned_cols=32  Identities=13%  Similarity=0.182  Sum_probs=26.8

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCccee
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQ   39 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e   39 (128)
                      +|..|||+++|+++   .    .+.+=++.|...||+..
T Consensus        20 ~s~~eiA~~l~ls~---~----~v~~Ri~rL~~~GiI~~   51 (63)
T d2cg4a1          20 TAYAELAKQFGVSP---E----TIHVRVEKMKQAGIITG   51 (63)
T ss_dssp             SCHHHHHHHHTSCH---H----HHHHHHHHHHHHTSEEE
T ss_pred             CCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCeEe
Confidence            58899999999954   6    77888888999999874

>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=87.35  E-value=0.4  Score=26.71  Aligned_cols=33  Identities=9%  Similarity=0.034  Sum_probs=28.4

Q ss_pred             CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905            2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN   41 (128)
Q Consensus         2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~   41 (128)
                      +..+||+.+++.|   +    .+.++++-|...|++....
T Consensus        25 ~~~~iA~~L~vs~---~----SVt~mvkrL~~~Glv~~~~   57 (63)
T d2isya1          25 LRARIAERLDQSG---P----TVSQTVSRMERDGLLRVAG   57 (63)
T ss_dssp             CHHHHHHHHTCCH---H----HHHHHHHHHHHTTSEEECT
T ss_pred             cHHHHHHHhCCCc---h----hHHHHHHHHHHCCCEEEcC
Confidence            5689999999944   8    8999999999999998654

>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=87.11  E-value=0.19  Score=27.62  Aligned_cols=31  Identities=16%  Similarity=0.196  Sum_probs=26.2

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcce
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFA   38 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~   38 (128)
                      +|+.|||+++|+++   .    .+.+=++.|...||+.
T Consensus        18 ~s~~~lA~~~gls~---~----~v~~Ri~~L~~~giI~   48 (60)
T d1i1ga1          18 TPFTEIAKKLGISE---T----AVRKRVKALEEKGIIE   48 (60)
T ss_dssp             CCHHHHHHHHTSCH---H----HHHHHHHHHHHHTSSC
T ss_pred             CCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCeE
Confidence            58899999999954   7    7788888888899886

>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=87.10  E-value=0.23  Score=27.55  Aligned_cols=32  Identities=22%  Similarity=0.280  Sum_probs=27.1

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCccee
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQ   39 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e   39 (128)
                      +|..|||+.+|+++   .    .+.+=++-|...|++..
T Consensus        20 ~s~~~iA~~lgis~---~----tv~~Ri~~L~~~giI~~   51 (63)
T d2cfxa1          20 LSMRELGRKIKLSP---P----SVTERVRQLESFGIIKQ   51 (63)
T ss_dssp             CCHHHHHHHHTCCH---H----HHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCeee
Confidence            57899999999955   7    78888888999999864

>d2p4wa1 a.4.5.64 (A:1-194) Transcriptional regulatory protein PF1790 {Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PF1790-like
domain: Transcriptional regulatory protein PF1790
species: Pyrococcus furiosus [TaxId: 2261]

Probab=86.91  E-value=0.14  Score=34.41  Aligned_cols=52  Identities=17%  Similarity=0.262  Sum_probs=38.4

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccC-CCCc-ccceechHhhhh
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFG-QNDQ-ERSYVATNASKL   59 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~-~~~~-~~~y~~T~~s~~   59 (128)
                      +|+.|||+.+|+++   .    .++|-|+.|...|++...... ..|. ..+|.+|..+..
T Consensus        29 ~~~~ela~~l~~s~---~----~v~~HL~~L~~~Glv~~~~~~~~~G~~~~~y~l~~~~~~   82 (194)
T d2p4wa1          29 YFVSELSRELGVGQ---K----AVLEHLRILEEAGLIESRVEKIPRGRPRKYYMIKKGLRL   82 (194)
T ss_dssp             EEHHHHHHHHTCCH---H----HHHHHHHHHHHTTSEEEEECCBTTBCCCEEEEECTTEEE
T ss_pred             CCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCeEEEEeecCCCCceEEEEeccccee
Confidence            36889999999954   8    999999999999999754321 1121 247888887643

>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=86.89  E-value=0.27  Score=29.66  Aligned_cols=45  Identities=11%  Similarity=0.137  Sum_probs=34.9

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechH
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATN   55 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~   55 (128)
                      +++.|||+.+|++   .+    .+.+-|+.|...|++.....   |...+|.+++
T Consensus        37 ~~v~ela~~l~is---~s----tvS~HL~~L~~aglV~~~r~---G~~~~Y~l~~   81 (98)
T d1r1ta_          37 LCVGDLAQAIGVS---ES----AVSHQLRSLRNLRLVSYRKQ---GRHVYYQLQD   81 (98)
T ss_dssp             BCHHHHHHHHTCC---HH----HHHHHHHHHHHTTSEEEEEE---TTEEEEEESS
T ss_pred             cCHHHHHHHHCcC---HH----HHHHHHHHHHHCCceEEEEE---CCEEEEEECh
Confidence            4788999999994   47    89999999999999986652   1134687764

>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=86.18  E-value=0.35  Score=28.94  Aligned_cols=45  Identities=11%  Similarity=0.137  Sum_probs=35.1

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechH
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATN   55 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~   55 (128)
                      +++.||++.+|++   .+    .+.+-|+.|...|++.....   |...+|.++.
T Consensus        32 ~~v~el~~~l~~s---~~----~vS~HL~~L~~~glv~~~r~---G~~~~Y~l~~   76 (94)
T d1r1ua_          32 ASVGHISHQLNLS---QS----NVSHQLKLLKSVHLVKAKRQ---GQSMIYSLDD   76 (94)
T ss_dssp             BCHHHHHHHHTCC---HH----HHHHHHHHHHHTTSEEEEEE---TTEEEEEESS
T ss_pred             ccHHHHHHHHCCC---HH----HHHHHHHHHHHCCceEEEEE---CCEEEEEECc
Confidence            3788999999994   47    89999999999999987652   1124588763

>d2gaua1 a.4.5.4 (A:152-232) Transcriptional regulator PG0396, C-terminal domain {Porphyromonas gingivalis [TaxId: 837]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Transcriptional regulator PG0396, C-terminal domain
species: Porphyromonas gingivalis [TaxId: 837]

Probab=86.03  E-value=0.53  Score=26.81  Aligned_cols=34  Identities=15%  Similarity=0.152  Sum_probs=29.2

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN   41 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~   41 (128)
                      +|-.|||..+|+.+   .    .+.|+|+.|...|++....
T Consensus        30 lt~~eLA~~~G~sr---e----tvsr~L~~l~~~glI~~~~   63 (81)
T d2gaua1          30 LSREELATLSNMTV---S----NAIRTLSTFVSERMLALDG   63 (81)
T ss_dssp             CCHHHHHHHTTSCH---H----HHHHHHHHHHHTTSEEEET
T ss_pred             CCHHHHHHHHCCCH---H----HHHHHHHHHHHCCCEEecC
Confidence            46789999999944   7    9999999999999997654

>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=85.88  E-value=0.41  Score=27.15  Aligned_cols=34  Identities=18%  Similarity=0.206  Sum_probs=28.7

Q ss_pred             CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905            2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN   41 (128)
Q Consensus         2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~   41 (128)
                      |+.|||+.+|+.  .+.    .+++.|..|...|++....
T Consensus        26 s~rei~~~~g~~--S~s----tv~~~l~~Le~kG~I~r~~   59 (71)
T d1jhfa1          26 TRAEIAQRLGFR--SPN----AAEEHLKALARKGVIEIVS   59 (71)
T ss_dssp             CHHHHHHHTTCS--SHH----HHHHHHHHHHHTTSEEECS
T ss_pred             CHHHHHHHcCCC--CHH----HHHHHHHHHHHCcCeecCC
Confidence            789999999983  236    7999999999999998653

>d1dpua_ a.4.5.16 (A:) C-terminal domain of RPA32 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: C-terminal domain of RPA32
domain: C-terminal domain of RPA32
species: Human (Homo sapiens) [TaxId: 9606]

Probab=85.63  E-value=0.36  Score=27.54  Aligned_cols=43  Identities=14%  Similarity=0.213  Sum_probs=32.2

Q ss_pred             CCHHHHHHhC-CCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechH
Q 045905            1 MTLNELINAL-PFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATN   55 (128)
Q Consensus         1 ~S~~eLA~~~-~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~   55 (128)
                      ++..||++++ ++++   .    .+...+.+|+..|..-.+-+     +..|.-|.
T Consensus        24 i~~~el~~~l~~~~~---~----~i~~aid~L~~eG~IYsTiD-----ddHfkstd   67 (69)
T d1dpua_          24 LNFQDLKNQLKHMSV---S----SIKQAVDFLSNEGHIYSTVD-----DDHFKSTD   67 (69)
T ss_dssp             EEHHHHHHHSTTSCH---H----HHHHHHHHHHHTTSEEECSS-----TTEEEESS
T ss_pred             cCHHHHHHHccCCCH---H----HHHHHHHHHHhCCceecccc-----cchhcccC
Confidence            4678999999 5744   6    89999999999997754432     46777663

>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=85.61  E-value=0.26  Score=26.95  Aligned_cols=31  Identities=16%  Similarity=0.144  Sum_probs=26.0

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcce
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFA   38 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~   38 (128)
                      +|..|||.++++++   .    .+.+=++.|...||+.
T Consensus        18 ~s~~eiA~~l~ls~---~----~v~~Ri~~L~~~giI~   48 (60)
T d2cyya1          18 APLREISKITGLAE---S----TIHERIRKLRESGVIK   48 (60)
T ss_dssp             CCHHHHHHHHCSCH---H----HHHHHHHHHHHHTSSC
T ss_pred             CCHHHHHHHHCcCH---H----HHHHHHHHHHHCCCeE
Confidence            58899999999944   7    7778888888889886

>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=84.79  E-value=0.43  Score=26.74  Aligned_cols=33  Identities=18%  Similarity=0.198  Sum_probs=28.3

Q ss_pred             CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905            2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN   41 (128)
Q Consensus         2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~   41 (128)
                      +..|||+.++++.   .    .+++-|+.|...|++....
T Consensus        27 ~~~~La~~~~vSr---~----tvr~Al~~L~~~Gli~~~~   59 (69)
T d2hs5a1          27 SEPDICAALDVSR---N----TVREAFQILIEDRLVAHEL   59 (69)
T ss_dssp             CHHHHHHHHTCCH---H----HHHHHHHHHHHTTSEEEET
T ss_pred             CHHHHHHHHCCCH---H----HHHHHHHHHHHCCcEEEEc
Confidence            4579999999944   7    8999999999999997664

>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=84.70  E-value=0.47  Score=26.18  Aligned_cols=34  Identities=18%  Similarity=0.366  Sum_probs=27.6

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN   41 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~   41 (128)
                      ++..+||+.+|+.+   +    .+..+++-|...|++....
T Consensus        22 v~~~~iA~~L~vs~---~----SVs~mikrL~~~GlV~~~~   55 (61)
T d2ev0a1          22 ARVSDIAEALAVHP---S----SVTKMVQKLDKDEYLIYEK   55 (61)
T ss_dssp             CCHHHHHHHHTCCH---H----HHHHHHHHHHHTTSEEC--
T ss_pred             ccHHHHHHHhCCCc---h----hHHHHHHHHHHCCCEEEcc
Confidence            36789999999944   7    8999999999999987543

>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=84.22  E-value=0.82  Score=26.04  Aligned_cols=33  Identities=15%  Similarity=0.208  Sum_probs=28.8

Q ss_pred             CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905            2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN   41 (128)
Q Consensus         2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~   41 (128)
                      |..|||+.++++   ..    .+++-|+.|...|++....
T Consensus        24 se~~La~~~~vS---r~----tvr~Al~~L~~~Gli~~~~   56 (78)
T d3bwga1          24 VLETLMAQFEVS---KS----TITKSLELLEQKGAIFQVR   56 (78)
T ss_dssp             CHHHHHHHTTCC---HH----HHHHHHHHHHHTTSEEEET
T ss_pred             CHHHHHHHHCCC---HH----HHHHHHHHHHHCCcEEEEc
Confidence            678999999994   47    8999999999999997664

>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=84.17  E-value=0.56  Score=26.75  Aligned_cols=33  Identities=15%  Similarity=0.204  Sum_probs=28.8

Q ss_pred             CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905            2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN   41 (128)
Q Consensus         2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~   41 (128)
                      |..|||+.++++.   .    .+++-++.|+..|++....
T Consensus        29 s~~eLa~~~~vSr---~----tvr~Al~~L~~~G~i~~~~   61 (74)
T d1hw1a1          29 AERELSELIGVTR---T----TLREVLQRLARDGWLTIQH   61 (74)
T ss_dssp             CHHHHHHHHTCCH---H----HHHHHHHHHHHTTSEEEET
T ss_pred             cHHHHHHHHCCCH---H----HHHHHHHHHHHCCcEEEEe
Confidence            6789999999944   7    8999999999999997665

>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=82.58  E-value=0.71  Score=26.30  Aligned_cols=33  Identities=21%  Similarity=0.325  Sum_probs=28.7

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceee
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQ   40 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~   40 (128)
                      +|-.|||..+|+.+   .    .+.|+|+.|-..|++.-.
T Consensus        31 ~t~~eiA~~lG~sr---e----tvsr~l~~l~~~g~I~~~   63 (80)
T d1ft9a1          31 FTVEEIANLIGSSR---Q----TTSTALNSLIKEGYISRQ   63 (80)
T ss_dssp             CCHHHHHHHHCSCH---H----HHHHHHHHHHHTTSSEEC
T ss_pred             CCHHHHHHHHCCCH---H----HHHHHHHHHHHCCCEEEC
Confidence            46789999999944   7    999999999999999754

>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=82.56  E-value=0.72  Score=25.56  Aligned_cols=34  Identities=15%  Similarity=0.187  Sum_probs=29.1

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeec
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQN   41 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~   41 (128)
                      +|-.|||..+|+..   +    .+.|+|+.|...|++....
T Consensus        30 lt~~~lA~~~G~sR---e----tvsr~L~~l~~~glI~~~~   63 (69)
T d1i5za1          30 ITRQEIGQIVGCSR---E----TVGRILKMLEDQNLISAHG   63 (69)
T ss_dssp             CCHHHHHHHHTCCH---H----HHHHHHHHHHHTTSEEEET
T ss_pred             CCHHHHHHHHCCCH---H----HHHHHHHHHHHCCCEEEcC
Confidence            46789999999944   7    9999999999999997653

>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=81.86  E-value=0.41  Score=25.29  Aligned_cols=29  Identities=7%  Similarity=0.080  Sum_probs=23.4

Q ss_pred             CCHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCc
Q 045905            1 MTLNELINALPFHPIKAQYVAQYVYRFMWILVHSGF   36 (128)
Q Consensus         1 ~S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gv   36 (128)
                      +|+++||+.+|+++   .    .|.|+.+..+.+.+
T Consensus        20 ~tl~~lA~~~~~s~---~----~l~r~Fk~~~g~tp   48 (54)
T d1bl0a1          20 LSLEKVSERSGYSK---W----HLQRMFKKETGHSL   48 (54)
T ss_dssp             CCCHHHHHHSSSCH---H----HHHHHHHHHHSSCH
T ss_pred             CCHHHHHHHHCcCH---H----HHHHHHHHHHCcCH
Confidence            58899999999955   7    89999988775543

>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=81.10  E-value=0.48  Score=29.03  Aligned_cols=45  Identities=11%  Similarity=0.114  Sum_probs=33.7

Q ss_pred             CHHHHHHhCCCCCCCchhhhhhHHHHHHHHHhcCcceeeccCCCCcccceechHh
Q 045905            2 TLNELINALPFHPIKAQYVAQYVYRFMWILVHSGFFAQQNFGQNDQERSYVATNA   56 (128)
Q Consensus         2 S~~eLA~~~~~~~~~~~~~~~~L~RlLR~L~~~gvf~e~~~~~~~~~~~y~~T~~   56 (128)
                      ++.|||+.+|++   .+    .+.+-|+.|...|++.....   |....|.+++-
T Consensus        47 ~v~ela~~l~~s---~s----~vS~HL~~L~~aGlv~~~r~---G~~~~Y~l~~~   91 (108)
T d1u2wa1          47 CVCDIANILGVT---IA----NASHHLRTLYKQGVVNFRKE---GKLALYSLGDE   91 (108)
T ss_dssp             EHHHHHHHHTCC---HH----HHHHHHHHHHHTTSEEEC-------CCEEEESCH
T ss_pred             cHHHHHHHHccC---hh----HHHHHHHHHHHCCeeEEEEE---CCEEEEEECHH
Confidence            678999999994   47    89999999999999986652   21346887643