Citrus Sinensis ID: 041844

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------
Protein Sequence
FKVPQSYGENNSSDELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNLR
Secondary Structure (PSIPRED)
ccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHccccccHHHHHHHccccccccccHHHHHHHHHHHcccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHcccccccHHHHHHHccccccccHHHHHHHHHHHHcccEEEc
Coil and Loop (DISEMBL)
fkvpqsygennssDELLQAQLLNcanpcldntfsFINSMSLKCVKLIQVgipdiihnhtkpmTLNQLLgalqihptktrcLHFLVCSLVRSGFFNLR
Flexible Loop (DISEMBL)
fkvpqsygennsSDELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVrsgffnlr
Low Complexity Region (SEG)
FKVPQSYGENNSSDELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNLR
Disordered region (IsUnstruct)
****************LQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN**
Disordered Region (DISOPRED)
*********************LNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNLR
Disordered Region (DISEMBL)
************SDELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNLR
Disordered Region (DISPRO)
**********NSSDELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNLR
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
FKVPQSYGENNSSDELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNLR
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	97	2.2.26 [Sep-21-2011]
B6VJS4	357	Trans-resveratrol di-O-me	no	no	0.824	0.224	0.475	4e-16
Q93WU2	357	Eugenol O-methyltransfera	N/A	no	0.783	0.212	0.481	2e-14
Q93WU3	356	Chavicol O-methyltransfer	N/A	no	0.783	0.213	0.469	6e-13
Q6VMW0	366	8-hydroxyquercetin 8-O-me	N/A	no	0.804	0.213	0.482	1e-12
Q29U70	364	Isoflavone 4'-O-methyltra	N/A	no	0.845	0.225	0.377	3e-10
Q8GSN1	348	Myricetin O-methyltransfe	N/A	no	0.814	0.227	0.395	6e-10
Q84KK6	367	Isoflavone 4'-O-methyltra	N/A	no	0.845	0.223	0.366	2e-09
P0DH60	360	6a-hydroxymaackiain methy	N/A	no	0.835	0.225	0.370	2e-09
O24305	360	6a-hydroxymaackiain methy	N/A	no	0.835	0.225	0.370	3e-09
Q84KK4	365	Isoflavone 4'-O-methyltra	N/A	no	0.804	0.213	0.395	6e-09

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

 Score = 83.2 bits (204), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 39/82 (47%), Positives = 58/82 (70%), Gaps = 2/82 (2%)

Query: 13 SDELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQ 72
          ++ ++ A+LL+      ++ F+FI SMSLKC   IQ+GIPDIIHNH KPMTL +L+  L 
Sbjct: 4  ANGVISAELLHAQAHVWNHIFNFIKSMSLKCA--IQLGIPDIIHNHGKPMTLPELVAKLP 61

Query: 73 IHPTKTRCLHFLVCSLVRSGFF 94
          +HP +++C++ L+  LV SGF 
Sbjct: 62 VHPKRSQCVYRLMRILVHSGFL 83

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

 Score = 77.8 bits (190), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 40/83 (48%), Positives = 58/83 (69%), Gaps = 7/83 (8%)

Query: 12 SSDELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGAL 71
          S+++LLQAQ+        ++ ++F NSMSLKC   IQ+GIPDI+H H +PMTL+QLL ++
Sbjct: 11 STEQLLQAQV-----HVWNHMYAFANSMSLKCA--IQLGIPDILHKHGRPMTLSQLLQSI 63

Query: 72 QIHPTKTRCLHFLVCSLVRSGFF 94
           I+  KT+C   L+ +LV S FF
Sbjct: 64 PINKEKTQCFQRLMRALVNSNFF 86

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

 Score = 72.8 bits (177), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 39/83 (46%), Positives = 55/83 (66%), Gaps = 7/83 (8%)

Query: 12 SSDELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGAL 71
          S+++LLQAQ         ++ ++F NSMSLKC   IQ+GIPDI+H H  PMTL+QLL A+
Sbjct: 11 STEQLLQAQA-----HVWNHMYAFANSMSLKCA--IQLGIPDILHKHDHPMTLSQLLKAI 63

Query: 72 QIHPTKTRCLHFLVCSLVRSGFF 94
           I+  K++    L+ +LV S FF
Sbjct: 64 PINKEKSQSFQRLMRALVNSNFF 86

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

 Score = 72.0 bits (175), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 41/85 (48%), Positives = 54/85 (63%), Gaps = 7/85 (8%)

Query: 11 NSSDELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGA 70
          +S  ELL+AQ         ++ +S+INSMSLKC   IQ+GIPD IH H  P+TL+QL  A
Sbjct: 8  SSKQELLEAQA-----HVWNHIYSYINSMSLKCA--IQLGIPDAIHKHGNPITLSQLADA 60

Query: 71 LQIHPTKTRCLHFLVCSLVRSGFFN 95
          L I+  K+  L  L+  LV SGFF+
Sbjct: 61 LNINKAKSHGLFRLMRILVHSGFFD 85

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|Q29U70|I4OMT_MEDTR Isoflavone 4'-O-methyltransferase OS=Medicago truncatula GN=HI4'OMT PE=1 SV=1

 Score = 63.9 bits (154), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 34/90 (37%), Positives = 55/90 (61%), Gaps = 8/90 (8%)

Query: 6  SYGENNSSD-ELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTL 64
          ++  N S + EL  AQ+         + ++F++SM+LK    +++GI D IHNH KPMTL
Sbjct: 2  AFSTNGSEESELYHAQI-----HLYKHVYNFVSSMALKSA--MELGIADAIHNHGKPMTL 54

Query: 65 NQLLGALQIHPTKTRCLHFLVCSLVRSGFF 94
          ++L  +L++HP+K   LH  +  L  +GFF
Sbjct: 55 SELASSLKLHPSKVNILHRFLRLLTHNGFF 84

2-hydroxyisoflavanone 4'-O-methyltransferase involved in the biosynthesis of the phytoalexin medicarpin. Has also an in vitro (+)-6a-hydroxymaackiain-3-0-methyltransferase activity, converting the pterocarpan 6a-hydroxymaackiain into pisatin. No activity with di- or trihydroxylated isoflavones, including daidzein and genistein, or with (-)-medicarpin and maackiain. The dual activity for either 3- or 4'-O-methylation depends upon substrate availability.

Medicago truncatula (taxid: 3880)

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 = 62.8 bits (151), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 32/81 (39%), Positives = 49/81 (60%), Gaps = 2/81 (2%)

Query: 15 ELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIH 74
          EL  +++ N         FSF +  SLKC   +Q+GIPD IH+H KPM L+ L  +L I+
Sbjct: 2  ELQSSEIRNAQAHFFTQVFSFTSMSSLKCA--VQLGIPDAIHSHGKPMALSDLTNSLPIN 59

Query: 75 PTKTRCLHFLVCSLVRSGFFN 95
          P+K   ++ L+  LV +G+F+
Sbjct: 60 PSKAPYIYRLMRILVAAGYFS 80

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

 Score = 61.6 bits (148), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 33/90 (36%), Positives = 55/90 (61%), Gaps = 8/90 (8%)

Query: 6  SYGENNSSD-ELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTL 64
          ++  N S + EL  AQ+         + ++F++SM+LK    +++GI D+IHNH KP+TL
Sbjct: 2  AFSTNGSEEIELYHAQI-----HLYKHVYNFVSSMALKSA--MELGIADVIHNHGKPITL 54

Query: 65 NQLLGALQIHPTKTRCLHFLVCSLVRSGFF 94
           +L  AL++HP+K   L+  +  L  +GFF
Sbjct: 55 PELASALKLHPSKVGILYRFLRLLTHNGFF 84

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

 Score = 61.2 bits (147), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 33/89 (37%), Positives = 53/89 (59%), Gaps = 8/89 (8%)

Query: 7  YGENNSSD-ELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLN 65
          +  N S + EL  AQ+         + ++F++SM+LK    +++GI D IHNH KPMTL 
Sbjct: 3  FSTNGSEESELYHAQI-----HLYKHIYNFVSSMALKSA--VELGIADAIHNHGKPMTLP 55

Query: 66 QLLGALQIHPTKTRCLHFLVCSLVRSGFF 94
          +L  +L++HP+K   L+  +  L  +GFF
Sbjct: 56 ELASSLKLHPSKVNILYRFLRLLTHNGFF 84

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 = 60.5 bits (145), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 33/89 (37%), Positives = 53/89 (59%), Gaps = 8/89 (8%)

Query: 7  YGENNSSD-ELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLN 65
          +  N S + EL  AQ+         + ++F++SM+LK    +++GI D IHNH KPMTL 
Sbjct: 3  FSTNGSEESELYHAQI-----HLYKHVYNFVSSMALKSA--MELGIADAIHNHGKPMTLP 55

Query: 66 QLLGALQIHPTKTRCLHFLVCSLVRSGFF 94
          +L  +L++HP+K   L+  +  L  +GFF
Sbjct: 56 ELSSSLKLHPSKVNILYRFLRLLTHNGFF 84

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

 Score = 59.3 bits (142), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 34/86 (39%), Positives = 52/86 (60%), Gaps = 8/86 (9%)

Query: 10 NNSSD-ELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLL 68
          N S D EL QAQ+         + ++F++SM+LK    +++GI D+IH+H KP+TL +L 
Sbjct: 7  NGSEDTELSQAQI-----HLYKHVYNFVSSMALKSA--MELGIADVIHSHGKPITLPELA 59

Query: 69 GALQIHPTKTRCLHFLVCSLVRSGFF 94
           AL + P+K   LH  +  L  +GFF
Sbjct: 60 TALNLRPSKIGVLHRFLRLLTHNGFF 85

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

Lotus japonicus (taxid: 34305)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 2

EC: 1

EC: 2

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	97
225446496	359	PREDICTED: myricetin O-methyltransferase	0.804	0.217	0.541	1e-16
225446499	358	PREDICTED: myricetin O-methyltransferase	0.773	0.209	0.573	1e-16
225446503	359	PREDICTED: 8-hydroxyquercetin 8-O-methyl	0.804	0.217	0.541	2e-16
147790925	363	hypothetical protein VITISV_002330 [Viti	0.804	0.214	0.541	2e-16
359485414	338	PREDICTED: chavicol O-methyltransferase-	0.896	0.257	0.505	1e-15
225446491	357	PREDICTED: 8-hydroxyquercetin 8-O-methyl	0.783	0.212	0.554	1e-15
147816431	357	hypothetical protein VITISV_020020 [Viti	0.783	0.212	0.554	1e-15
359485263	350	PREDICTED: LOW QUALITY PROTEIN: 8-hydrox	0.845	0.234	0.511	2e-15
255553585	372	o-methyltransferase, putative [Ricinus c	0.793	0.206	0.547	3e-15
356553132	358	PREDICTED: 8-hydroxyquercetin 8-O-methyl	0.865	0.234	0.5	3e-15

>gi|225446496|ref|XP_002278316.1| PREDICTED: myricetin O-methyltransferase [Vitis vinifera]

 Score = 90.1 bits (222), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 46/85 (54%), Positives = 59/85 (69%), Gaps = 7/85 (8%)

Query: 13 SDELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQ 72
          S ELLQAQ         ++ F+FINSMSLKC   IQ+GIPDIIHNH +PMTL++L+  L 
Sbjct: 9  SSELLQAQ-----THVWNHIFNFINSMSLKCA--IQLGIPDIIHNHCQPMTLHELVAKLP 61

Query: 73 IHPTKTRCLHFLVCSLVRSGFFNLR 97
          + P KT C+H L+  LV SGFF ++
Sbjct: 62 VRPNKTLCVHRLMRILVHSGFFTMQ 86

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225446499|ref|XP_002278398.1| PREDICTED: myricetin O-methyltransferase [Vitis vinifera] gi|302143369|emb|CBI21930.3| unnamed protein product [Vitis vinifera]

 Score = 90.1 bits (222), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 47/82 (57%), Positives = 57/82 (69%), Gaps = 7/82 (8%)

Query: 13 SDELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQ 72
          S ELLQAQ         ++ F+FINSMSLKC   IQ+GIPDIIHNH KPMTL++L+  L 
Sbjct: 9  SSELLQAQA-----HVWNHIFNFINSMSLKCA--IQLGIPDIIHNHCKPMTLHELVAKLP 61

Query: 73 IHPTKTRCLHFLVCSLVRSGFF 94
          + P KT C+H L+  LV SGFF
Sbjct: 62 VRPNKTLCVHRLMRILVHSGFF 83

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225446503|ref|XP_002278517.1| PREDICTED: 8-hydroxyquercetin 8-O-methyltransferase [Vitis vinifera]

 Score = 90.1 bits (222), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 46/85 (54%), Positives = 59/85 (69%), Gaps = 7/85 (8%)

Query: 13 SDELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQ 72
          S ELLQAQ         ++ F+FINSMSLKC   IQ+GIPDIIHNH +PMTL++L+  L 
Sbjct: 9  SSELLQAQ-----THVWNHIFNFINSMSLKCA--IQLGIPDIIHNHCQPMTLHELVAKLP 61

Query: 73 IHPTKTRCLHFLVCSLVRSGFFNLR 97
          + P KT C+H L+  LV SGFF ++
Sbjct: 62 VRPNKTLCVHRLMRILVHSGFFTMQ 86

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147790925|emb|CAN70493.1| hypothetical protein VITISV_002330 [Vitis vinifera]

 Score = 89.7 bits (221), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 46/85 (54%), Positives = 59/85 (69%), Gaps = 7/85 (8%)

Query: 13 SDELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQ 72
          S ELLQAQ         ++ F+FINSMSLKC   IQ+GIPDIIHNH +PMTL++L+  L 
Sbjct: 9  SSELLQAQ-----THVWNHIFNFINSMSLKCA--IQLGIPDIIHNHCQPMTLHELVAKLP 61

Query: 73 IHPTKTRCLHFLVCSLVRSGFFNLR 97
          + P KT C+H L+  LV SGFF ++
Sbjct: 62 VRPNKTLCVHRLMRILVHSGFFTMQ 86

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 = 87.4 bits (215), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 45/89 (50%), Positives = 58/89 (65%), Gaps = 2/89 (2%)

Query: 6  SYGENNSSDELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLN 65
          S GE     E+LQ       N   ++ F+F+NSMSLKC   IQ+GIPDIIHNH KPMTL 
Sbjct: 11 SPGEREREREILQVNNSKNGNQLENHIFNFVNSMSLKCA--IQLGIPDIIHNHGKPMTLP 68

Query: 66 QLLGALQIHPTKTRCLHFLVCSLVRSGFF 94
          QL+  L +HP KT+ ++ L+  LV+S FF
Sbjct: 69 QLVAKLPVHPKKTQYVYRLMRVLVQSDFF 97

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225446491|ref|XP_002278211.1| PREDICTED: 8-hydroxyquercetin 8-O-methyltransferase [Vitis vinifera]

 Score = 87.0 bits (214), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 46/83 (55%), Positives = 57/83 (68%), Gaps = 7/83 (8%)

Query: 12 SSDELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGAL 71
          +S ELL AQ         ++ F+FINSMSLKC   IQ+GIPDIIHNH KPMTL +L+  L
Sbjct: 8  TSSELLHAQA-----HVWNHIFNFINSMSLKCA--IQLGIPDIIHNHGKPMTLPELVAKL 60

Query: 72 QIHPTKTRCLHFLVCSLVRSGFF 94
           IHP K  C++ L+  LV+SGFF
Sbjct: 61 PIHPKKVWCVYRLMRILVQSGFF 83

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147816431|emb|CAN61955.1| hypothetical protein VITISV_020020 [Vitis vinifera]

 Score = 87.0 bits (214), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 46/83 (55%), Positives = 57/83 (68%), Gaps = 7/83 (8%)

Query: 12 SSDELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGAL 71
          +S ELL AQ         ++ F+FINSMSLKC   IQ+GIPDIIHNH KPMTL +L+  L
Sbjct: 8  TSSELLHAQA-----HVWNHIFNFINSMSLKCA--IQLGIPDIIHNHGKPMTLPELVAKL 60

Query: 72 QIHPTKTRCLHFLVCSLVRSGFF 94
           IHP K  C++ L+  LV+SGFF
Sbjct: 61 PIHPKKVWCVYRLMRILVQSGFF 83

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359485263|ref|XP_003633250.1| PREDICTED: LOW QUALITY PROTEIN: 8-hydroxyquercetin 8-O-methyltransferase-like [Vitis vinifera]

 Score = 86.7 bits (213), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 45/88 (51%), Positives = 58/88 (65%), Gaps = 6/88 (6%)

Query: 7  YGENNSSDELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQ 66
          +  +  S ELL AQ         ++ F+FINSMSLKC   IQ+GIPDI+HNH KPMTL +
Sbjct: 3  WANSERSSELLHAQA-----HVWNHIFNFINSMSLKCTA-IQLGIPDIVHNHGKPMTLPE 56

Query: 67 LLGALQIHPTKTRCLHFLVCSLVRSGFF 94
           +  L +HP KTRC+  L+  LV+SGFF
Sbjct: 57 QVAELSVHPKKTRCVCRLMRILVQSGFF 84

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255553585|ref|XP_002517833.1| o-methyltransferase, putative [Ricinus communis] gi|223542815|gb|EEF44351.1| o-methyltransferase, putative [Ricinus communis]

 Score = 85.9 bits (211), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 46/84 (54%), Positives = 61/84 (72%), Gaps = 7/84 (8%)

Query: 14  DELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQI 73
           DEL++AQ         + TF FI SMSLKC   +Q+GIPDII++H +PMTL++L+ ALQ+
Sbjct: 25  DELIKAQ-----THIWNETFHFIKSMSLKCA--VQLGIPDIINSHGQPMTLSELVLALQV 77

Query: 74  HPTKTRCLHFLVCSLVRSGFFNLR 97
            PTKT  L+ L+  LVRSGFFNL+
Sbjct: 78  RPTKTHHLYRLMRVLVRSGFFNLQ 101

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356553132|ref|XP_003544912.1| PREDICTED: 8-hydroxyquercetin 8-O-methyltransferase-like isoform 1 [Glycine max]

 Score = 85.9 bits (211), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 43/86 (50%), Positives = 60/86 (69%), Gaps = 2/86 (2%)

Query: 12 SSDELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGAL 71
          S DE   A+LL       ++ FSFINSMSLKCV  + +GIPDIIHN+ +PM L+ L+ +L
Sbjct: 3  SHDEEHAAKLLRAQTHIWNHIFSFINSMSLKCV--VDLGIPDIIHNYGQPMPLSNLIASL 60

Query: 72 QIHPTKTRCLHFLVCSLVRSGFFNLR 97
           IHP+KT  +H L+  ++ SGFF+L+
Sbjct: 61 PIHPSKTCFVHRLMRIMIHSGFFSLQ 86

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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	97
UNIPROTKB|Q6VMW0	366	OMT2 "8-hydroxyquercetin 8-O-m	0.804	0.213	0.494	3.7e-12
UNIPROTKB|Q8GSN1	348	Q8GSN1 "Myricetin O-methyltran	0.814	0.227	0.395	3.2e-10
UNIPROTKB|Q84KK6	367	HI4'OMT "Isoflavone 4'-O-methy	0.814	0.215	0.369	9.8e-10
UNIPROTKB|Q84KK4	365	HI4'OMT "Isoflavone 4'-O-methy	0.804	0.213	0.395	4.4e-09
UNIPROTKB|B0EXJ8	355	16OMT "Tabersonine 16-O-methyl	0.597	0.163	0.467	2.4e-08
UNIPROTKB|Q84KK5	357	D7OMT "Isoflavone 7-O-methyltr	0.618	0.168	0.370	8.3e-07
UNIPROTKB|A8QW53	374	OMT3 "5-pentadecatrienyl resor	0.824	0.213	0.321	0.00046

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

 Score = 169 (64.5 bits), Expect = 3.7e-12, P = 3.7e-12
 Identities = 42/85 (49%), Positives = 56/85 (65%)

Query:    11 NSSDELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGA 70
             +S  ELL+AQ    A+   ++ +S+INSMSLKC   IQ+GIPD IH H  P+TL+QL  A
Sbjct:     8 SSKQELLEAQ----AH-VWNHIYSYINSMSLKCA--IQLGIPDAIHKHGNPITLSQLADA 60

Query:    71 LQIHPTKTRCLHFLVCSLVRSGFFN 95
             L I+  K+  L  L+  LV SGFF+
Sbjct:    61 LNINKAKSHGLFRLMRILVHSGFFD 85

GO:0009812 "flavonoid metabolic process" evidence=IDA

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

GO:0032259 "methylation" evidence=IDA

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

 Score = 151 (58.2 bits), Expect = 3.2e-10, P = 3.2e-10
 Identities = 32/81 (39%), Positives = 49/81 (60%)

Query:    15 ELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIH 74
             EL  +++ N         FSF +  SLKC   +Q+GIPD IH+H KPM L+ L  +L I+
Sbjct:     2 ELQSSEIRNAQAHFFTQVFSFTSMSSLKCA--VQLGIPDAIHSHGKPMALSDLTNSLPIN 59

Query:    75 PTKTRCLHFLVCSLVRSGFFN 95
             P+K   ++ L+  LV +G+F+
Sbjct:    60 PSKAPYIYRLMRILVAAGYFS 80

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

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

 Score = 147 (56.8 bits), Expect = 9.8e-10, P = 9.8e-10
 Identities = 31/84 (36%), Positives = 53/84 (63%)

Query:    11 NSSDELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGA 70
             N S+E+   +L +       + ++F++SM+LK    +++GI D+IHNH KP+TL +L  A
Sbjct:     6 NGSEEI---ELYHAQIHLYKHVYNFVSSMALKSA--MELGIADVIHNHGKPITLPELASA 60

Query:    71 LQIHPTKTRCLHFLVCSLVRSGFF 94
             L++HP+K   L+  +  L  +GFF
Sbjct:    61 LKLHPSKVGILYRFLRLLTHNGFF 84

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

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

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

 Score = 141 (54.7 bits), Expect = 4.4e-09, P = 4.4e-09
 Identities = 34/86 (39%), Positives = 52/86 (60%)

Query:    10 NNSSD-ELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLL 68
             N S D EL QAQ+         + ++F++SM+LK    +++GI D+IH+H KP+TL +L 
Sbjct:     7 NGSEDTELSQAQI-----HLYKHVYNFVSSMALKSA--MELGIADVIHSHGKPITLPELA 59

Query:    69 GALQIHPTKTRCLHFLVCSLVRSGFF 94
              AL + P+K   LH  +  L  +GFF
Sbjct:    60 TALNLRPSKIGVLHRFLRLLTHNGFF 85

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

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

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

 Score = 134 (52.2 bits), Expect = 2.4e-08, P = 2.4e-08
 Identities = 29/62 (46%), Positives = 42/62 (67%)

Query:    34 SFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGAL--QIHPTKTRCLHFLVCSLVRS 91
             SFI S SLKC   +++GIPD I NH KP+TL++L  AL   +HP+K   ++ L+  L ++
Sbjct:    21 SFITSASLKCA--VKLGIPDTIDNHGKPITLSELTNALVPPVHPSKAPFIYRLMRVLAKN 78

Query:    92 GF 93
             GF
Sbjct:    79 GF 80

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 = 120 (47.3 bits), Expect = 8.3e-07, P = 8.3e-07
 Identities = 23/62 (37%), Positives = 43/62 (69%)

Query:    33 FSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSG 92
             ++FI+SM LK +  +++ IP+IIHNH KP+T+++L+  L++  TK   +  ++  +  +G
Sbjct:    25 YAFIDSMCLKWI--VELDIPNIIHNHGKPITVSELVSILKVPQTKAGNVQRIMRYMAHNG 82

Query:    93 FF 94
             FF
Sbjct:    83 FF 84

GO:0009717 "isoflavonoid biosynthetic process" evidence=IDA

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

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

 Score = 95 (38.5 bits), Expect = 0.00046, P = 0.00046
 Identities = 28/87 (32%), Positives = 44/87 (50%)

Query:    10 NNSSDELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLG 69
             +  S ELLQA +        + T+SF+ S++L     + + I D IH      TL+Q+LG
Sbjct:     5 SEDSRELLQAHV-----ELWNQTYSFMKSVALAVA--LDLHIADAIHRRGGAATLSQILG 57

Query:    70 ALQIHPTKTRCLHFLVCSLVRSGFFNL 96
              + + P K   LH ++  L  SG F +
Sbjct:    58 EIGVRPCKLPGLHRIMRVLTVSGTFTI 84


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   0.138   0.427    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       97        97   0.00091  102 3  11 22  0.46    29
                                                     29  0.44    31


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:  7
  No. of states in DFA:  523 (56 KB)
  Total size of DFA:  111 KB (2076 KB)
  Time to generate neighborhood:  0.00u 0.00s 0.00t   Elapsed:  00:00:00
  No. of threads or processors used:  24
  Search cpu time:  11.17u 0.10s 11.27t   Elapsed:  00:00:00
  Total cpu time:  11.17u 0.10s 11.27t   Elapsed:  00:00:00
  Start:  Sat May 11 08:05:21 2013   End:  Sat May 11 08:05:21 2013

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

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

GO:0032259 "methylation" 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

Your Input: GSVIVG00018677001 SubName- Full=Chromosome chr12 scaffold_18, whole genome shotgun sequence; (359 aa) (Vitis vinifera)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	97
pfam08100	50	pfam08100, Dimerisation, Dimerisation domain	9e-10

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

 Score = 49.5 bits (119), Expect = 9e-10
 Identities = 18/45 (40%), Positives = 26/45 (57%), Gaps = 3/45 (6%)

Query: 39 MSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQ-IHPTKTRCLH 82
          M LKC   I++GIPDII  H KP++ ++L   L  ++P     L 
Sbjct: 1  MVLKCA--IELGIPDIIAKHGKPLSPSELASKLPTVNPEAPVMLD 43

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	97
PF08100	51	Dimerisation: Dimerisation domain; InterPro: IPR01	99.67
TIGR02716	306	C20_methyl_CrtF C-20 methyltransferase BchU. Membe	99.13
KOG3178	342	consensus Hydroxyindole-O-methyltransferase and re	99.1
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	98.04
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	97.42
TIGR02431	248	pcaR_pcaU beta-ketoadipate pathway transcriptional	96.99
PRK11569	274	transcriptional repressor IclR; Provisional	96.99
PRK10163	271	DNA-binding transcriptional repressor AllR; Provis	96.92
COG1414	246	IclR Transcriptional regulator [Transcription]	96.71
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	96.66
PRK09834	263	DNA-binding transcriptional activator MhpR; Provis	96.55
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	96.48
PRK15090	257	DNA-binding transcriptional regulator KdgR; Provis	96.46
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	96.43
PF02082	83	Rrf2: Transcriptional regulator; InterPro: IPR0009	96.4
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	96.38
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	96.21
cd07153	116	Fur_like Ferric uptake regulator(Fur) and related	96.03
COG4190	144	Predicted transcriptional regulator [Transcription	95.93
PRK10857	164	DNA-binding transcriptional regulator IscR; Provis	95.91
TIGR02944	130	suf_reg_Xantho FeS assembly SUF system regulator,	95.89
PF09012	69	FeoC: FeoC like transcriptional regulator; InterPr	95.83
TIGR02010	135	IscR iron-sulfur cluster assembly transcription fa	95.71
smart00419	48	HTH_CRP helix_turn_helix, cAMP Regulatory protein.	95.62
smart00347	101	HTH_MARR helix_turn_helix multiple antibiotic resi	95.61
smart00418	66	HTH_ARSR helix_turn_helix, Arsenical Resistance Op	95.6
PF08461	66	HTH_12: Ribonuclease R winged-helix domain; InterP	95.55
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	95.51
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	95.44
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	95.42
TIGR00738	132	rrf2_super rrf2 family protein (putative transcrip	95.3
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	95.19
PRK06474	178	hypothetical protein; Provisional	95.05
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	95.01
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	94.95
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	94.95
PRK11014	141	transcriptional repressor NsrR; Provisional	94.88
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	94.83
COG1959	150	Predicted transcriptional regulator [Transcription	94.79
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	94.72
COG3355	126	Predicted transcriptional regulator [Transcription	94.68
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	94.54
PF04703	62	FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.	94.4
PRK10141	117	DNA-binding transcriptional repressor ArsR; Provis	94.32
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	94.32
PRK11920	153	rirA iron-responsive transcriptional regulator; Re	94.23
PRK00215	205	LexA repressor; Validated	94.11
cd00090	78	HTH_ARSR Arsenical Resistance Operon Repressor and	94.08
TIGR02702	203	SufR_cyano iron-sulfur cluster biosynthesis transc	93.7
COG2512	258	Predicted membrane-associated trancriptional regul	93.65
TIGR00122	69	birA_repr_reg BirA biotin operon repressor domain.	93.64
PRK11639	169	zinc uptake transcriptional repressor; Provisional	93.59
PRK11169	164	leucine-responsive transcriptional regulator; Prov	93.55
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	93.49
COG1522	154	Lrp Transcriptional regulators [Transcription]	93.47
TIGR02337	118	HpaR homoprotocatechuate degradation operon regula	93.47
PRK06266	178	transcription initiation factor E subunit alpha; V	93.46
PRK11179	153	DNA-binding transcriptional regulator AsnC; Provis	93.46
TIGR01610	95	phage_O_Nterm phage replication protein O, N-termi	93.17
PRK03573	144	transcriptional regulator SlyA; Provisional	93.17
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	93.02
TIGR00498	199	lexA SOS regulatory protein LexA. LexA acts as a h	92.69
PRK09462	148	fur ferric uptake regulator; Provisional	92.64
TIGR00373	158	conserved hypothetical protein TIGR00373. This fam	92.57
PRK03902	142	manganese transport transcriptional regulator; Pro	92.52
PHA00738	108	putative HTH transcription regulator	92.4
PRK15431	78	ferrous iron transport protein FeoC; Provisional	92.38
PRK11050	152	manganese transport regulator MntR; Provisional	92.38
COG0735	145	Fur Fe2+/Zn2+ uptake regulation proteins [Inorgani	92.08
PF13545	76	HTH_Crp_2: Crp-like helix-turn-helix domain; PDB:	92.08
TIGR01889	109	Staph_reg_Sar staphylococcal accessory regulator f	92.01
COG2345	218	Predicted transcriptional regulator [Transcription	91.75
PF01475	120	FUR: Ferric uptake regulator family; InterPro: IPR	91.62
PF06163	127	DUF977: Bacterial protein of unknown function (DUF	91.57
PF03444	78	HrcA_DNA-bdg: Winged helix-turn-helix transcriptio	91.0
PRK11512	144	DNA-binding transcriptional repressor MarR; Provis	90.84
TIGR02787	251	codY_Gpos GTP-sensing transcriptional pleiotropic	90.54
TIGR01884	203	cas_HTH CRISPR locus-related DNA-binding protein.	90.46
cd07377	66	WHTH_GntR Winged helix-turn-helix (WHTH) DNA-bindi	90.07
PRK14096	528	pgi glucose-6-phosphate isomerase; Provisional	90.06
TIGR03697	193	NtcA_cyano global nitrogen regulator NtcA, cyanoba	89.99
PF04182	75	B-block_TFIIIC: B-block binding subunit of TFIIIC;	89.97
PF02796	45	HTH_7: Helix-turn-helix domain of resolvase; Inter	89.16
COG3413	215	Predicted DNA binding protein [General function pr	89.11
PF02002	105	TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024	89.05
PRK12423	202	LexA repressor; Provisional	89.03
PF13601	80	HTH_34: Winged helix DNA-binding domain; PDB: 1UB9	89.02
COG1378	247	Predicted transcriptional regulators [Transcriptio	88.24
COG1321	154	TroR Mn-dependent transcriptional regulator [Trans	88.1
PRK11161	235	fumarate/nitrate reduction transcriptional regulat	88.06
PRK11753	211	DNA-binding transcriptional dual regulator Crp; Pr	87.96
PRK13918	202	CRP/FNR family transcriptional regulator; Provisio	87.84
PF00392	64	GntR: Bacterial regulatory proteins, gntR family;	87.82
smart00529	96	HTH_DTXR Helix-turn-helix diphteria tox regulatory	87.65
PRK13509	251	transcriptional repressor UlaR; Provisional	87.55
PF13730	55	HTH_36: Helix-turn-helix domain	87.31
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	87.12
PRK10870	176	transcriptional repressor MprA; Provisional	87.12
PRK09391	230	fixK transcriptional regulator FixK; Provisional	86.97
PRK10046	225	dpiA two-component response regulator DpiA; Provis	86.85
COG1675	176	TFA1 Transcription initiation factor IIE, alpha su	85.74
COG1725	125	Predicted transcriptional regulators [Transcriptio	85.17
PRK09334	86	30S ribosomal protein S25e; Provisional	84.63
PRK09802	269	DNA-binding transcriptional regulator AgaR; Provis	84.58
COG1846	126	MarR Transcriptional regulators [Transcription]	84.53
PRK04214	412	rbn ribonuclease BN/unknown domain fusion protein;	83.99
COG1510	177	Predicted transcriptional regulators [Transcriptio	83.88
COG4565	224	CitB Response regulator of citrate/malate metaboli	83.87
PF03297	105	Ribosomal_S25: S25 ribosomal protein; InterPro: IP	83.67
PRK10906	252	DNA-binding transcriptional repressor GlpR; Provis	83.29
PF08221	62	HTH_9: RNA polymerase III subunit RPC82 helix-turn	83.29
PF14947	77	HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_	83.08
PF07381	90	DUF1495: Winged helix DNA-binding domain (DUF1495)	82.92
PF00165	42	HTH_AraC: Bacterial regulatory helix-turn-helix pr	82.85
PRK10434	256	srlR DNA-bindng transcriptional repressor SrlR; Pr	82.52
PF12793	115	SgrR_N: Sugar transport-related sRNA regulator N-t	82.44
COG4189	308	Predicted transcriptional regulator [Transcription	82.1
TIGR00331	337	hrcA heat shock gene repressor HrcA. In Bacillus s	82.05
PHA02943	165	hypothetical protein; Provisional	81.91
PF08784	102	RPA_C: Replication protein A C terminal; InterPro:	81.85
PRK14165	217	winged helix-turn-helix domain-containing protein/	81.83
PRK10402	226	DNA-binding transcriptional activator YeiL; Provis	81.7
PRK04424	185	fatty acid biosynthesis transcriptional regulator;	81.54
PRK05638	442	threonine synthase; Validated	81.48
PF01418	77	HTH_6: Helix-turn-helix domain, rpiR family; Inter	80.87
PRK00082	339	hrcA heat-inducible transcription repressor; Provi	80.2

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

Probab=99.67  E-value=3.3e-17  Score=98.09  Aligned_cols=49  Identities=39%  Similarity=0.731  Sum_probs=44.5

Q ss_pred             HHHHHHHHHhcChhHHHhhCC-CCCCHHHHHHHhC-CCCCCcccHHHHHHHHH
Q 041844           39 MSLKCVKLIQVGIPDIIHNHT-KPMTLNQLLGALQ-IHPTKTRCLHFLVCSLV   89 (97)
Q Consensus        39 ~aL~~a~~veLgI~D~La~~~-gp~s~~ELA~~~g-~~~~~~~~L~RlLR~La   89 (97)
                      |+||||  |||||||+|+++| +|+|++||+++++ .+|+++..|+|+||+|+
T Consensus         1 MaLk~a--veLgI~dii~~~g~~~ls~~eia~~l~~~~p~~~~~L~RimR~L~   51 (51)
T PF08100_consen    1 MALKCA--VELGIPDIIHNAGGGPLSLSEIAARLPTSNPSAPPMLDRIMRLLV   51 (51)
T ss_dssp             HHHHHH--HHTTHHHHHHHHTTS-BEHHHHHHTSTCT-TTHHHHHHHHHHHHH
T ss_pred             CcHHHH--HHcCcHHHHHHcCCCCCCHHHHHHHcCCCCcchHHHHHHHHHHhC
Confidence            799999  9999999999997 9999999999999 78878899999999996

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 ....

>TIGR02716 C20_methyl_CrtF C-20 methyltransferase BchU

Probab=99.13  E-value=7.6e-11  Score=89.76  Aligned_cols=53  Identities=21%  Similarity=0.262  Sum_probs=49.0

Q ss_pred             HHHHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           37 NSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        37 ~s~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      ..++|++|  ++|||||+|++  +|+|++|||+++|++|   ..++|+||+|+++|+|++
T Consensus         3 ~~~~l~aa--~~Lglfd~L~~--gp~t~~eLA~~~~~~~---~~~~~lL~~L~~lgll~~   55 (306)
T TIGR02716         3 EFSCMKAA--IELDLFSHMAE--GPKDLATLAADTGSVP---PRLEMLLETLRQMRVINL   55 (306)
T ss_pred             hHHHHHHH--HHcCcHHHHhc--CCCCHHHHHHHcCCCh---HHHHHHHHHHHhCCCeEe
Confidence            46899999  99999999976  8999999999999965   899999999999999975

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.

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

Probab=99.10  E-value=1.5e-10  Score=91.71  Aligned_cols=71  Identities=23%  Similarity=0.273  Sum_probs=60.6

Q ss_pred             HHHHHHhccCcchhhHHhHHHHHHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhC--CCCCCcccHHHHHHHHHhcCcc
Q 041844           17 LQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQ--IHPTKTRCLHFLVCSLVRSGFF   94 (97)
Q Consensus        17 ~~~~~~~~~~p~~~l~~~~~~s~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g--~~~~~~~~L~RlLR~Laa~gif   94 (97)
                      -++...+     +++.+++..+|++++|  +||||||+|+++++   .+|+|..+.  ..|.+|..++|+||.|++.+++
T Consensus         4 ~~~~l~~-----~~l~~~~~~~~~lk~A--~eL~v~d~l~~~~~---p~~ia~~l~~~~~~~~p~ll~r~lr~L~s~~i~   73 (342)
T KOG3178|consen    4 NEASLRA-----MRLANGFALPMVLKAA--CELGVFDILANAGS---PSEIASLLPTPKNPEAPVLLDRILRLLVSYSIL   73 (342)
T ss_pred             hHHHHHH-----HHHHhhhhhHHHHHHH--HHcChHHHHHhCCC---HHHHHHhccCCCCCCChhHHHHHHHHHHHhhhc
Confidence            3455666     8889999999999999  99999999998655   778887776  5666889999999999999999


Q ss_pred             ccC
Q 041844           95 NLR   97 (97)
Q Consensus        95 ~e~   97 (97)
                      +++
T Consensus        74 k~~   76 (342)
T KOG3178|consen   74 KCR   76 (342)
T ss_pred             eee
Confidence            863

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

Probab=98.04  E-value=2.3e-06  Score=50.18  Aligned_cols=45  Identities=24%  Similarity=0.437  Sum_probs=39.3

Q ss_pred             cChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           49 VGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        49 LgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      +.|.+.++.+++++|+.|||+++|.+.   ..++|+|+.|+..|++..
T Consensus         6 l~iL~~l~~~~~~~t~~eia~~~gl~~---stv~r~L~tL~~~g~v~~   50 (52)
T PF09339_consen    6 LRILEALAESGGPLTLSEIARALGLPK---STVHRLLQTLVEEGYVER   50 (52)
T ss_dssp             HHHHHCHHCTBSCEEHHHHHHHHTS-H---HHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHcCCCCCCHHHHHHHHCcCH---HHHHHHHHHHHHCcCeec
Confidence            367788988888999999999999954   899999999999999864

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

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=97.42  E-value=0.00023  Score=44.82  Aligned_cols=45  Identities=18%  Similarity=0.284  Sum_probs=38.9

Q ss_pred             cChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           49 VGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        49 LgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      +.|.+.|+++++++|+.|||+.+|++.   ..++|+|+.|...|++..
T Consensus         8 ~~Il~~l~~~~~~~t~~~ia~~l~i~~---~tv~r~l~~L~~~g~l~~   52 (91)
T smart00346        8 LAVLRALAEEPGGLTLAELAERLGLSK---STAHRLLNTLQELGYVEQ   52 (91)
T ss_pred             HHHHHHHHhCCCCcCHHHHHHHhCCCH---HHHHHHHHHHHHCCCeee
Confidence            467788887657999999999999954   899999999999998863

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

Probab=96.99  E-value=0.00085  Score=49.84  Aligned_cols=45  Identities=13%  Similarity=0.229  Sum_probs=39.2

Q ss_pred             cChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           49 VGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        49 LgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      +.|.+.++.+.+|+|+.|||+.+|.+.   ..++|+|..|+..|++..
T Consensus        12 l~IL~~l~~~~~~~~l~eia~~lglpk---sT~~RlL~tL~~~G~l~~   56 (248)
T TIGR02431        12 LAVIEAFGAERPRLTLTDVAEATGLTR---AAARRFLLTLVELGYVTS   56 (248)
T ss_pred             HHHHHHHhcCCCCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEe
Confidence            367788877678999999999999955   899999999999998863

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.

>PRK11569 transcriptional repressor IclR; Provisional

Probab=96.99  E-value=0.00085  Score=50.82  Aligned_cols=44  Identities=16%  Similarity=0.297  Sum_probs=38.8

Q ss_pred             cChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           49 VGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        49 LgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      |.|.+.++++.+++|++|||+.+|.+.   ..++|+|+.|+..|++.
T Consensus        31 l~IL~~l~~~~~~~~lseia~~lglpk---sTv~RlL~tL~~~G~l~   74 (274)
T PRK11569         31 LKLLEWIAESNGSVALTELAQQAGLPN---STTHRLLTTMQQQGFVR   74 (274)
T ss_pred             HHHHHHHHhCCCCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEE
Confidence            366788887778999999999999955   89999999999999985

>PRK10163 DNA-binding transcriptional repressor AllR; Provisional

Probab=96.92  E-value=0.0011  Score=50.31  Aligned_cols=45  Identities=11%  Similarity=0.116  Sum_probs=39.2

Q ss_pred             cChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           49 VGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        49 LgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      +.|.+.++.+++++|+.|||+.+|.+.   ..++|+|..|+..|++..
T Consensus        28 l~IL~~~~~~~~~~tl~eIa~~lglpk---Stv~RlL~tL~~~G~l~~   72 (271)
T PRK10163         28 IAILQYLEKSGGSSSVSDISLNLDLPL---STTFRLLKVLQAADFVYQ   72 (271)
T ss_pred             HHHHHHHHhCCCCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEE
Confidence            367788887778899999999999955   899999999999999853

>COG1414 IclR Transcriptional regulator [Transcription]

Probab=96.71  E-value=0.002  Score=48.54  Aligned_cols=45  Identities=22%  Similarity=0.380  Sum_probs=39.0

Q ss_pred             cChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           49 VGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        49 LgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      |.|.|.|++++.++++.|||+++|.++   ..++|+|..|+..|+++.
T Consensus         7 l~iL~~l~~~~~~l~l~ela~~~glpk---sT~~RlL~tL~~~G~v~~   51 (246)
T COG1414           7 LAILDLLAEGPGGLSLAELAERLGLPK---STVHRLLQTLVELGYVEQ   51 (246)
T ss_pred             HHHHHHHHhCCCCCCHHHHHHHhCcCH---HHHHHHHHHHHHCCCEEE
Confidence            467888988556678999999999965   899999999999999874

>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=96.66  E-value=0.0027  Score=36.06  Aligned_cols=45  Identities=18%  Similarity=0.236  Sum_probs=36.2

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .+..|.+.|.++ +.+|..|||..+|++   ...+.+.++-|...|+++
T Consensus         4 ~~~~Il~~l~~~-~~~t~~ela~~~~is---~~tv~~~l~~L~~~g~I~   48 (48)
T PF13412_consen    4 TQRKILNYLREN-PRITQKELAEKLGIS---RSTVNRYLKKLEEKGLIE   48 (48)
T ss_dssp             HHHHHHHHHHHC-TTS-HHHHHHHHTS----HHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHHc-CCCCHHHHHHHhCCC---HHHHHHHHHHHHHCcCcC
Confidence            355677888774 469999999999994   489999999999999874

...

>PRK09834 DNA-binding transcriptional activator MhpR; Provisional

Probab=96.55  E-value=0.0028  Score=47.69  Aligned_cols=44  Identities=14%  Similarity=0.187  Sum_probs=38.2

Q ss_pred             cChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           49 VGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        49 LgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      +.|.+.+..+++++|+.|||+.+|++.   ..++|+++.|+..|++.
T Consensus        14 l~iL~~l~~~~~~ls~~eia~~lgl~k---stv~RlL~tL~~~g~v~   57 (263)
T PRK09834         14 LMVLRALNRLDGGATVGLLAELTGLHR---TTVRRLLETLQEEGYVR   57 (263)
T ss_pred             HHHHHHHHhcCCCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEE
Confidence            366788877777899999999999955   89999999999999985

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

Probab=96.48  E-value=0.0062  Score=37.58  Aligned_cols=46  Identities=20%  Similarity=0.216  Sum_probs=38.1

Q ss_pred             HhcChhHHHhhCCC-CCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTK-PMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~g-p~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .+=.|.+.|..+++ ++|+.|||..+|++.   ..++|+|-.|...|++.
T Consensus         7 ~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~---~~v~r~L~~L~~~G~V~   53 (68)
T smart00550        7 LEEKILEFLENSGDETSTALQLAKNLGLPK---KEVNRVLYSLEKKGKVC   53 (68)
T ss_pred             HHHHHHHHHHHCCCCCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEE
Confidence            34456777877765 399999999999955   78999999999999875

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

>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional

Probab=96.46  E-value=0.0032  Score=47.05  Aligned_cols=43  Identities=9%  Similarity=0.233  Sum_probs=36.7

Q ss_pred             ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      .|.+.+..+ +++|++|||+.+|++.   ..++|+|+.|+..|++..
T Consensus        18 ~IL~~l~~~-~~l~l~eia~~lgl~k---stv~Rll~tL~~~G~l~~   60 (257)
T PRK15090         18 GILQALGEE-REIGITELSQRVMMSK---STVYRFLQTMKTLGYVAQ   60 (257)
T ss_pred             HHHHHhhcC-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEE
Confidence            566777654 5899999999999955   899999999999999853

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

Probab=96.43  E-value=0.0033  Score=37.58  Aligned_cols=46  Identities=20%  Similarity=0.398  Sum_probs=38.4

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      ..+.|.+.|.. ++|+|+.|||+.+|+++   ..+++=|+.|...|+++.
T Consensus        11 ~R~~Il~~L~~-~~~~t~~ela~~l~~~~---~t~s~hL~~L~~aGli~~   56 (61)
T PF12840_consen   11 TRLRILRLLAS-NGPMTVSELAEELGISQ---STVSYHLKKLEEAGLIEV   56 (61)
T ss_dssp             HHHHHHHHHHH-CSTBEHHHHHHHHTS-H---HHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHhc-CCCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCeEE
Confidence            56677888833 48999999999999954   889999999999999863

...

>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=96.40  E-value=0.006  Score=38.53  Aligned_cols=33  Identities=24%  Similarity=0.490  Sum_probs=29.1

Q ss_pred             CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      +++|..|||+.+++++   ..++++|+.|...|+++
T Consensus        24 ~~~s~~eiA~~~~i~~---~~l~kil~~L~~~Gli~   56 (83)
T PF02082_consen   24 KPVSSKEIAERLGISP---SYLRKILQKLKKAGLIE   56 (83)
T ss_dssp             C-BEHHHHHHHHTS-H---HHHHHHHHHHHHTTSEE
T ss_pred             CCCCHHHHHHHHCcCH---HHHHHHHHHHhhCCeeE
Confidence            5799999999999955   99999999999999976

(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.

>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=96.38  E-value=0.0028  Score=36.22  Aligned_cols=43  Identities=16%  Similarity=0.354  Sum_probs=36.3

Q ss_pred             hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++.|...|.+  ||.++.||++.+|+++   ..+.+-|+.|...|+++
T Consensus         4 R~~Il~~L~~--~~~~~~el~~~l~~s~---~~vs~hL~~L~~~glV~   46 (47)
T PF01022_consen    4 RLRILKLLSE--GPLTVSELAEELGLSQ---STVSHHLKKLREAGLVE   46 (47)
T ss_dssp             HHHHHHHHTT--SSEEHHHHHHHHTS-H---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHh--CCCchhhHHHhccccc---hHHHHHHHHHHHCcCee
Confidence            4556677765  8999999999999954   89999999999999875

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 ....

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

Probab=96.21  E-value=0.0046  Score=36.25  Aligned_cols=44  Identities=18%  Similarity=0.228  Sum_probs=34.7

Q ss_pred             ChhHHHhhCCCC-CCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           50 GIPDIIHNHTKP-MTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        50 gI~D~La~~~gp-~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      .|.-.|..++++ +|..|||+.+++++   ..+.|+++.|...|++..
T Consensus         9 ~vL~~l~~~~~~~~t~~~la~~l~~~~---~~vs~~v~~L~~~Glv~r   53 (62)
T PF12802_consen    9 RVLMALARHPGEELTQSELAERLGISK---STVSRIVKRLEKKGLVER   53 (62)
T ss_dssp             HHHHHHHHSTTSGEEHHHHHHHHTS-H---HHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHCCCCCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEE
Confidence            344556555543 89999999999954   899999999999998863

...

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

Probab=96.03  E-value=0.013  Score=38.51  Aligned_cols=48  Identities=10%  Similarity=0.144  Sum_probs=38.1

Q ss_pred             cChhHHHhhCCCCCCHHHHHHHhCCC--CCCcccHHHHHHHHHhcCcccc
Q 041844           49 VGIPDIIHNHTKPMTLNQLLGALQIH--PTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        49 LgI~D~La~~~gp~s~~ELA~~~g~~--~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      ..|.+.|...+++.|++||.+.+.-.  ..+...++|.|..|+..|++.+
T Consensus         4 ~~Il~~l~~~~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~   53 (116)
T cd07153           4 LAILEVLLESDGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVRE   53 (116)
T ss_pred             HHHHHHHHhCCCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEE
Confidence            45678887777899999999998531  1155889999999999998763

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.

>COG4190 Predicted transcriptional regulator [Transcription]

Probab=95.93  E-value=0.015  Score=41.42  Aligned_cols=56  Identities=14%  Similarity=0.265  Sum_probs=43.3

Q ss_pred             hHHHHHHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           34 SFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        34 ~~~~s~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      +|-..+.+-+=  -.+.+...|+. .+|.|+.|||+.+|=   |...++|=||.|...|++.
T Consensus        54 Sye~la~vLsp--~nleLl~~Ia~-~~P~Si~ElAe~vgR---dv~nvhr~Ls~l~~~GlI~  109 (144)
T COG4190          54 SYEDLARVLSP--RNLELLELIAQ-EEPASINELAELVGR---DVKNVHRTLSTLADLGLIF  109 (144)
T ss_pred             cHHHHHHHhCh--hHHHHHHHHHh-cCcccHHHHHHHhCc---chHHHHHHHHHHHhcCeEE
Confidence            44444444444  55677788865 479999999999998   4489999999999999865

>PRK10857 DNA-binding transcriptional regulator IscR; Provisional

Probab=95.91  E-value=0.012  Score=42.13  Aligned_cols=36  Identities=19%  Similarity=0.281  Sum_probs=32.0

Q ss_pred             CCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           58 HTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        58 ~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      .++|+|++|||+++++++   ..|.+||+.|...|++..
T Consensus        22 ~~~~vs~~eIA~~~~ip~---~~l~kIl~~L~~aGLv~s   57 (164)
T PRK10857         22 EAGPVPLADISERQGISL---SYLEQLFSRLRKNGLVSS   57 (164)
T ss_pred             CCCcCcHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEe
Confidence            347999999999999965   899999999999999863

>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial

Probab=95.89  E-value=0.011  Score=40.00  Aligned_cols=34  Identities=9%  Similarity=0.234  Sum_probs=31.1

Q ss_pred             CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           59 TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        59 ~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++++|+.|||+++++++   ..+.++|+.|...|++.
T Consensus        23 ~~~~s~~eia~~l~is~---~~v~~~l~~L~~~Gli~   56 (130)
T TIGR02944        23 SQPYSAAEIAEQTGLNA---PTVSKILKQLSLAGIVT   56 (130)
T ss_pred             CCCccHHHHHHHHCcCH---HHHHHHHHHHHHCCcEE
Confidence            47899999999999955   89999999999999985

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.

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

Probab=95.83  E-value=0.008  Score=36.88  Aligned_cols=42  Identities=21%  Similarity=0.462  Sum_probs=33.4

Q ss_pred             hhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           51 IPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        51 I~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      |-+.|.++ +..|+.|||..++++|   +.+.-+|..|..+|.+..
T Consensus         5 i~~~l~~~-~~~S~~eLa~~~~~s~---~~ve~mL~~l~~kG~I~~   46 (69)
T PF09012_consen    5 IRDYLRER-GRVSLAELAREFGISP---EAVEAMLEQLIRKGYIRK   46 (69)
T ss_dssp             HHHHHHHS--SEEHHHHHHHTT--H---HHHHHHHHHHHCCTSCEE
T ss_pred             HHHHHHHc-CCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCcEEE
Confidence            45777663 7999999999999955   999999999999998763

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

>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR

Probab=95.71  E-value=0.015  Score=39.84  Aligned_cols=34  Identities=26%  Similarity=0.364  Sum_probs=31.0

Q ss_pred             CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           59 TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        59 ~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      +++.|++|||+.+++++   ..+.+||+.|+..|++.
T Consensus        23 ~~~~s~~~ia~~~~ip~---~~l~kil~~L~~~glv~   56 (135)
T TIGR02010        23 TGPVTLADISERQGISL---SYLEQLFAKLRKAGLVK   56 (135)
T ss_pred             CCcCcHHHHHHHHCcCH---HHHHHHHHHHHHCCceE
Confidence            46899999999999965   89999999999999875

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

>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein

Probab=95.62  E-value=0.015  Score=32.12  Aligned_cols=33  Identities=15%  Similarity=0.269  Sum_probs=29.5

Q ss_pred             CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      -++|..|||+.+|+++   ..+.|.|+.|...|++.
T Consensus         7 ~~~s~~~la~~l~~s~---~tv~~~l~~L~~~g~l~   39 (48)
T smart00419        7 LPLTRQEIAELLGLTR---ETVSRTLKRLEKEGLIS   39 (48)
T ss_pred             eccCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEE
Confidence            3689999999999954   88999999999999875

>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein

Probab=95.61  E-value=0.025  Score=35.14  Aligned_cols=45  Identities=18%  Similarity=0.346  Sum_probs=37.1

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .++.|+..|..+ +++|..+|+..+++++   ..+.|.++.|...|++.
T Consensus        11 ~~~~il~~l~~~-~~~~~~~la~~~~~s~---~~i~~~l~~L~~~g~v~   55 (101)
T smart00347       11 TQFLVLRILYEE-GPLSVSELAKRLGVSP---STVTRVLDRLEKKGLIR   55 (101)
T ss_pred             HHHHHHHHHHHc-CCcCHHHHHHHHCCCc---hhHHHHHHHHHHCCCeE
Confidence            355666777654 5799999999999955   88999999999999986

>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor

Probab=95.60  E-value=0.028  Score=31.84  Aligned_cols=40  Identities=13%  Similarity=0.227  Sum_probs=33.3

Q ss_pred             hhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           51 IPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        51 I~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      |...|.  .++.|..||++.+++++   ..+.+.++.|...|++.
T Consensus         2 il~~l~--~~~~~~~~i~~~l~is~---~~v~~~l~~L~~~g~i~   41 (66)
T smart00418        2 ILKLLA--EGELCVCELAEILGLSQ---STVSHHLKKLREAGLVE   41 (66)
T ss_pred             HHHHhh--cCCccHHHHHHHHCCCH---HHHHHHHHHHHHCCCee
Confidence            344554  47899999999999955   78999999999999875

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

Probab=95.55  E-value=0.024  Score=34.96  Aligned_cols=45  Identities=20%  Similarity=0.324  Sum_probs=36.9

Q ss_pred             hhHHHhhCCCCCCHHHHHHHhCCCCCC--cccHHHHHHHHHhcCccc
Q 041844           51 IPDIIHNHTKPMTLNQLLGALQIHPTK--TRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        51 I~D~La~~~gp~s~~ELA~~~g~~~~~--~~~L~RlLR~Laa~gif~   95 (97)
                      |.++|.++++|++..+|+..+.....+  ...++|-||.|-..|+..
T Consensus         3 IL~~L~~~~~P~g~~~l~~~L~~~g~~~se~avRrrLr~me~~Glt~   49 (66)
T PF08461_consen    3 ILRILAESDKPLGRKQLAEELKLRGEELSEEAVRRRLRAMERDGLTR   49 (66)
T ss_pred             HHHHHHHcCCCCCHHHHHHHHHhcChhhhHHHHHHHHHHHHHCCCcc
Confidence            567788888999999999999764334  378999999999999543

>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=95.51  E-value=0.0076  Score=36.50  Aligned_cols=43  Identities=16%  Similarity=0.145  Sum_probs=34.5

Q ss_pred             ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      .|.-.|.. .+++|+.|||..+|++.   ..+++.|+.|...|++..
T Consensus        12 ~vy~~Ll~-~~~~t~~eIa~~l~i~~---~~v~~~L~~L~~~GlV~~   54 (68)
T PF01978_consen   12 KVYLALLK-NGPATAEEIAEELGISR---STVYRALKSLEEKGLVER   54 (68)
T ss_dssp             HHHHHHHH-HCHEEHHHHHHHHTSSH---HHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHH-cCCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEE
Confidence            34444432 28999999999999954   899999999999998863

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.

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=95.44  E-value=0.023  Score=36.78  Aligned_cols=45  Identities=20%  Similarity=0.316  Sum_probs=38.4

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .+..|...|..+ +++|..|||+.+|+++   ..+.|.++.|...|++.
T Consensus         4 ~D~~il~~L~~~-~~~~~~~la~~l~~s~---~tv~~~l~~L~~~g~i~   48 (108)
T smart00344        4 IDRKILEELQKD-ARISLAELAKKVGLSP---STVHNRVKRLEEEGVIK   48 (108)
T ss_pred             HHHHHHHHHHHh-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCee
Confidence            466777888764 6899999999999955   89999999999999875

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

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

Probab=95.42  E-value=0.027  Score=33.76  Aligned_cols=42  Identities=21%  Similarity=0.267  Sum_probs=33.0

Q ss_pred             HHHHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHH
Q 041844           37 NSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCS   87 (97)
Q Consensus        37 ~s~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~   87 (97)
                      .-.+|++|  .++|-||.    +...|+.|||+.+|+.+   ..+..-||-
T Consensus         5 Q~e~L~~A--~~~GYfd~----PR~~tl~elA~~lgis~---st~~~~LRr   46 (53)
T PF04967_consen    5 QREILKAA--YELGYFDV----PRRITLEELAEELGISK---STVSEHLRR   46 (53)
T ss_pred             HHHHHHHH--HHcCCCCC----CCcCCHHHHHHHhCCCH---HHHHHHHHH
Confidence            45688999  99999984    36799999999999954   555555553

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

>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator)

Probab=95.30  E-value=0.024  Score=37.99  Aligned_cols=34  Identities=18%  Similarity=0.354  Sum_probs=30.9

Q ss_pred             CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           59 TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        59 ~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      +++.|..|||+.+++++   ..++++|+.|+..|++.
T Consensus        23 ~~~~s~~eia~~~~i~~---~~v~~il~~L~~~gli~   56 (132)
T TIGR00738        23 EGPVSVKEIAERQGISR---SYLEKILRTLRRAGLVE   56 (132)
T ss_pred             CCcCcHHHHHHHHCcCH---HHHHHHHHHHHHCCcEE
Confidence            35999999999999965   89999999999999885

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.

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor

Probab=95.19  E-value=0.042  Score=30.51  Aligned_cols=42  Identities=12%  Similarity=0.230  Sum_probs=34.2

Q ss_pred             hhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           51 IPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        51 I~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      |.+.|.++ ++.|..+|++.+++.+   ..++|.|..|...|++..
T Consensus         5 il~~l~~~-~~~s~~~l~~~l~~s~---~tv~~~l~~L~~~g~i~~   46 (53)
T smart00420        5 ILELLAQQ-GKVSVEELAELLGVSE---MTIRRDLNKLEEQGLLTR   46 (53)
T ss_pred             HHHHHHHc-CCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEE
Confidence            44555554 5799999999999954   889999999999998753

>PRK06474 hypothetical protein; Provisional

Probab=95.05  E-value=0.036  Score=40.06  Aligned_cols=47  Identities=17%  Similarity=0.306  Sum_probs=39.0

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhC-CCCCCcccHHHHHHHHHhcCcccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQ-IHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g-~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      ..+.|.+.|..+++++|+.||+..++ ++   ...++|.|+.|+..|++..
T Consensus        12 ~R~~Il~~L~~~~~~~ta~el~~~l~~is---~aTvYrhL~~L~e~GLI~~   59 (178)
T PRK06474         12 VRMKICQVLMRNKEGLTPLELVKILKDVP---QATLYRHLQTMVDSGILHV   59 (178)
T ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHhcCCC---HHHHHHHHHHHHHCCCEEE
Confidence            67778888877666799999999984 53   3789999999999999863

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

Probab=95.01  E-value=0.034  Score=32.70  Aligned_cols=33  Identities=15%  Similarity=0.249  Sum_probs=30.3

Q ss_pred             CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .++|..|||+.+|+++   ..+.|+|+.|...|++.
T Consensus        24 ~~~s~~ela~~~g~s~---~tv~r~l~~L~~~g~i~   56 (67)
T cd00092          24 LPLTRQEIADYLGLTR---ETVSRTLKELEEEGLIS   56 (67)
T ss_pred             CCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEE
Confidence            6899999999999954   89999999999999886

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

Probab=94.95  E-value=0.02  Score=33.34  Aligned_cols=41  Identities=20%  Similarity=0.284  Sum_probs=33.1

Q ss_pred             hhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           51 IPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        51 I~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      +...|.++ +++|..|||..+++++   ..+.|+++.|...|++.
T Consensus         8 iL~~l~~~-~~~~~~~la~~~~~~~---~~~t~~i~~L~~~g~I~   48 (59)
T PF01047_consen    8 ILRILYEN-GGITQSELAEKLGISR---STVTRIIKRLEKKGLIE   48 (59)
T ss_dssp             HHHHHHHH-SSEEHHHHHHHHTS-H---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHc-CCCCHHHHHHHHCCCh---hHHHHHHHHHHHCCCEE
Confidence            33445444 5799999999999954   89999999999999876

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 ....

>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=94.95  E-value=0.035  Score=32.89  Aligned_cols=38  Identities=21%  Similarity=0.334  Sum_probs=29.3

Q ss_pred             HhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           55 IHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        55 La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      |....+++|..+|++.++.+   ...+.|+++.|...|+++
T Consensus        12 l~~~~~~~t~~~l~~~~~~~---~~~vs~~i~~L~~~glv~   49 (68)
T PF13463_consen   12 LAHSDGPMTQSDLAERLGIS---KSTVSRIIKKLEEKGLVE   49 (68)
T ss_dssp             HT--TS-BEHHHHHHHTT-----HHHHHHHHHHHHHTTSEE
T ss_pred             HHccCCCcCHHHHHHHHCcC---HHHHHHHHHHHHHCCCEE
Confidence            43235899999999999994   489999999999999984

>PRK11014 transcriptional repressor NsrR; Provisional

Probab=94.88  E-value=0.037  Score=38.09  Aligned_cols=48  Identities=10%  Similarity=0.260  Sum_probs=36.9

Q ss_pred             HHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           39 MSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        39 ~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .++++.  +.++..    ..+.+.|..|||+..|+++   ..++++|+.|...|++.
T Consensus         9 YAl~~~--i~la~~----~~g~~~s~~~ia~~~~is~---~~vrk~l~~L~~~Glv~   56 (141)
T PRK11014          9 YGLRAL--IYMASL----PEGRMTSISEVTEVYGVSR---NHMVKIINQLSRAGYVT   56 (141)
T ss_pred             HHHHHH--HHHhcC----CCCCccCHHHHHHHHCcCH---HHHHHHHHHHHhCCEEE
Confidence            355666  554422    2346889999999999955   89999999999999875

>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=94.83  E-value=0.035  Score=34.25  Aligned_cols=41  Identities=22%  Similarity=0.377  Sum_probs=31.8

Q ss_pred             HHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           53 DIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        53 D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      +.+.++|-|-|+.|||+.+|+.  .+..+++.|+.|...|+++
T Consensus        17 ~~~~~~G~~Pt~rEIa~~~g~~--S~~tv~~~L~~Le~kG~I~   57 (65)
T PF01726_consen   17 EYIEENGYPPTVREIAEALGLK--STSTVQRHLKALERKGYIR   57 (65)
T ss_dssp             HHHHHHSS---HHHHHHHHTSS--SHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHcCCCCCHHHHHHHhCCC--ChHHHHHHHHHHHHCcCcc
Confidence            4455567778999999999995  2489999999999999886

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.

>COG1959 Predicted transcriptional regulator [Transcription]

Probab=94.79  E-value=0.041  Score=38.78  Aligned_cols=33  Identities=18%  Similarity=0.389  Sum_probs=30.5

Q ss_pred             CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++.|+++||+..+++|   ..|.|||..|...|+++
T Consensus        24 ~~~s~~~IA~~~~is~---~~L~kil~~L~kaGlV~   56 (150)
T COG1959          24 GPVSSAEIAERQGISP---SYLEKILSKLRKAGLVK   56 (150)
T ss_pred             CcccHHHHHHHhCcCH---HHHHHHHHHHHHcCCEE
Confidence            4899999999999965   99999999999999986

>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=94.72  E-value=0.051  Score=32.88  Aligned_cols=35  Identities=14%  Similarity=0.319  Sum_probs=31.3

Q ss_pred             CCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           58 HTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        58 ~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .+++.+..+||+.+++.|   +.+..+++-|...|++.
T Consensus        19 ~~~~v~~~~iA~~L~vs~---~tvt~ml~~L~~~GlV~   53 (60)
T PF01325_consen   19 EGGPVRTKDIAERLGVSP---PTVTEMLKRLAEKGLVE   53 (60)
T ss_dssp             CTSSBBHHHHHHHHTS-H---HHHHHHHHHHHHTTSEE
T ss_pred             CCCCccHHHHHHHHCCCh---HHHHHHHHHHHHCCCEE
Confidence            568999999999999955   89999999999999875

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 ....

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=94.68  E-value=0.047  Score=38.17  Aligned_cols=45  Identities=16%  Similarity=0.280  Sum_probs=36.3

Q ss_pred             hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      |..++-+|-+..+|.|++|||+.++.   +.+.++|-++-|...|++.
T Consensus        29 Dv~v~~~LL~~~~~~tvdelae~lnr---~rStv~rsl~~L~~~GlV~   73 (126)
T COG3355          29 DVEVYKALLEENGPLTVDELAEILNR---SRSTVYRSLQNLLEAGLVE   73 (126)
T ss_pred             HHHHHHHHHhhcCCcCHHHHHHHHCc---cHHHHHHHHHHHHHcCCee
Confidence            44455555433489999999999999   4489999999999999876

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

Probab=94.54  E-value=0.033  Score=30.27  Aligned_cols=31  Identities=23%  Similarity=0.374  Sum_probs=25.3

Q ss_pred             CCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcc
Q 041844           61 PMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFF   94 (97)
Q Consensus        61 p~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif   94 (97)
                      |+|-.|||..+|+.+   +.+.|+|..|...|++
T Consensus         2 ~mtr~diA~~lG~t~---ETVSR~l~~l~~~glI   32 (32)
T PF00325_consen    2 PMTRQDIADYLGLTR---ETVSRILKKLERQGLI   32 (32)
T ss_dssp             E--HHHHHHHHTS-H---HHHHHHHHHHHHTTSE
T ss_pred             CcCHHHHHHHhCCcH---HHHHHHHHHHHHcCCC
Confidence            578899999999955   8999999999998874

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 ....

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

Probab=94.40  E-value=0.049  Score=33.59  Aligned_cols=42  Identities=17%  Similarity=0.292  Sum_probs=33.5

Q ss_pred             hhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           51 IPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        51 I~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      |-+.|....+|.|..|||+.+|++.   ...++.|..|...|.+.
T Consensus         5 Il~~i~~~~~p~~T~eiA~~~gls~---~~aR~yL~~Le~eG~V~   46 (62)
T PF04703_consen    5 ILEYIKEQNGPLKTREIADALGLSI---YQARYYLEKLEKEGKVE   46 (62)
T ss_dssp             HHHHHHHHTS-EEHHHHHHHHTS-H---HHHHHHHHHHHHCTSEE
T ss_pred             HHHHHHHcCCCCCHHHHHHHhCCCH---HHHHHHHHHHHHCCCEE
Confidence            4566655458999999999999944   88999999999999765

>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional

Probab=94.32  E-value=0.077  Score=36.32  Aligned_cols=45  Identities=18%  Similarity=0.226  Sum_probs=39.1

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      +.+.|.+.|.+ +++.++.||++.+++.+   ..+.+-|+.|...|++.
T Consensus        17 tRl~IL~~L~~-~~~~~v~ela~~l~lsq---stvS~HL~~L~~AGLV~   61 (117)
T PRK10141         17 TRLGIVLLLRE-SGELCVCDLCTALDQSQ---PKISRHLALLRESGLLL   61 (117)
T ss_pred             HHHHHHHHHHH-cCCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCceE
Confidence            67788888864 36899999999999955   88999999999999986

>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=94.32  E-value=0.065  Score=30.89  Aligned_cols=40  Identities=20%  Similarity=0.288  Sum_probs=32.4

Q ss_pred             ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcC
Q 041844           50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSG   92 (97)
Q Consensus        50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~g   92 (97)
                      .|...|.++++++|+.|||+.++++.   ..++|-+..|...|
T Consensus         4 ~il~~L~~~~~~it~~eLa~~l~vS~---rTi~~~i~~L~~~~   43 (55)
T PF08279_consen    4 QILKLLLESKEPITAKELAEELGVSR---RTIRRDIKELREWG   43 (55)
T ss_dssp             HHHHHHHHTTTSBEHHHHHHHCTS-H---HHHHHHHHHHHHTT
T ss_pred             HHHHHHHHcCCCcCHHHHHHHhCCCH---HHHHHHHHHHHHCC
Confidence            34566755667899999999999954   89999999998877

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 ....

>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed

Probab=94.23  E-value=0.074  Score=37.49  Aligned_cols=48  Identities=15%  Similarity=0.264  Sum_probs=37.0

Q ss_pred             HHHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           38 SMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        38 s~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      -.++++.  +.|-.     ..+++.|+.|||+..++++   ..|.+||+.|+..|+++
T Consensus         8 ~YAlr~L--~~LA~-----~~~~~~s~~eIA~~~~is~---~~L~kIl~~L~~aGlv~   55 (153)
T PRK11920          8 NYAIRML--MYCAA-----NDGKLSRIPEIARAYGVSE---LFLFKILQPLVEAGLVE   55 (153)
T ss_pred             hHHHHHH--HHHHh-----CCCCcCcHHHHHHHHCcCH---HHHHHHHHHHHHCCCEE
Confidence            3466666  54321     1246789999999999965   89999999999999876

>PRK00215 LexA repressor; Validated

Probab=94.11  E-value=0.1  Score=37.64  Aligned_cols=41  Identities=27%  Similarity=0.408  Sum_probs=34.2

Q ss_pred             HHHhhCCCCCCHHHHHHHhCC-CCCCcccHHHHHHHHHhcCcccc
Q 041844           53 DIIHNHTKPMTLNQLLGALQI-HPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        53 D~La~~~gp~s~~ELA~~~g~-~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      +.+.+++.+.|..|||+.+|. ++   ..+.|+++.|...|+++.
T Consensus        15 ~~~~~~~~~~s~~ela~~~~~~~~---~tv~~~l~~L~~~g~i~~   56 (205)
T PRK00215         15 DHIEETGYPPSRREIADALGLRSP---SAVHEHLKALERKGFIRR   56 (205)
T ss_pred             HHHHHhCCCCCHHHHHHHhCCCCh---HHHHHHHHHHHHCCCEEe
Confidence            334455678999999999999 65   789999999999998853

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

Probab=94.08  E-value=0.13  Score=29.77  Aligned_cols=41  Identities=17%  Similarity=0.295  Sum_probs=32.8

Q ss_pred             ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .|.+.+..  ++.+..||+..++++.   ..+.|.++.|...|++.
T Consensus        11 ~il~~l~~--~~~~~~ei~~~~~i~~---~~i~~~l~~L~~~g~i~   51 (78)
T cd00090          11 RILRLLLE--GPLTVSELAERLGLSQ---STVSRHLKKLEEAGLVE   51 (78)
T ss_pred             HHHHHHHH--CCcCHHHHHHHHCcCH---hHHHHHHHHHHHCCCeE
Confidence            34455555  3399999999999954   88999999999999875

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.

>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR

Probab=93.70  E-value=0.097  Score=38.00  Aligned_cols=42  Identities=21%  Similarity=0.274  Sum_probs=35.3

Q ss_pred             ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .|...|..+ +++|..|||+.+|+++   ..+.|.|+.|...|++.
T Consensus         5 ~IL~~L~~~-~~~t~~eLA~~lgis~---~tV~~~L~~Le~~GlV~   46 (203)
T TIGR02702         5 DILSYLLKQ-GQATAAALAEALAISP---QAVRRHLKDLETEGLIE   46 (203)
T ss_pred             HHHHHHHHc-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCeE
Confidence            355666554 6799999999999955   89999999999999885

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.

>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]

Probab=93.65  E-value=0.066  Score=41.18  Aligned_cols=45  Identities=20%  Similarity=0.293  Sum_probs=40.0

Q ss_pred             hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      |..|-|+|.++||-++-+||.+++|.+.   ..+.|++|-|..+|+++
T Consensus       197 e~~il~~i~~~GGri~Q~eL~r~lglsk---tTvsR~L~~LEk~GlIe  241 (258)
T COG2512         197 EKEILDLIRERGGRITQAELRRALGLSK---TTVSRILRRLEKRGLIE  241 (258)
T ss_pred             HHHHHHHHHHhCCEEeHHHHHHhhCCCh---HHHHHHHHHHHhCCceE
Confidence            4567788888999999999999999954   78999999999999986

>TIGR00122 birA_repr_reg BirA biotin operon repressor domain

Probab=93.64  E-value=0.097  Score=31.69  Aligned_cols=42  Identities=14%  Similarity=0.196  Sum_probs=34.6

Q ss_pred             hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcc
Q 041844           48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFF   94 (97)
Q Consensus        48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif   94 (97)
                      ++.|...+.+  ++.|..|||+.+|+..   ..++|-++.|...|+.
T Consensus         2 ~~~il~~L~~--~~~~~~eLa~~l~vS~---~tv~~~l~~L~~~g~~   43 (69)
T TIGR00122         2 PLRLLALLAD--NPFSGEKLGEALGMSR---TAVNKHIQTLREWGVD   43 (69)
T ss_pred             hHHHHHHHHc--CCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCe
Confidence            4556777765  6899999999999954   8899999999988873

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.

>PRK11639 zinc uptake transcriptional repressor; Provisional

Probab=93.59  E-value=0.13  Score=36.68  Aligned_cols=50  Identities=16%  Similarity=0.236  Sum_probs=40.4

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCC-C-CCcccHHHHHHHHHhcCcccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIH-P-TKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~-~-~~~~~L~RlLR~Laa~gif~e   96 (97)
                      .+.-|.+.|...+++.|+.||.+.+.-. | .+...++|.|+.|+..|++.+
T Consensus        27 qR~~IL~~l~~~~~hlSa~eI~~~L~~~~~~is~aTVYRtL~~L~e~Glv~~   78 (169)
T PRK11639         27 QRLEVLRLMSLQPGAISAYDLLDLLREAEPQAKPPTVYRALDFLLEQGFVHK   78 (169)
T ss_pred             HHHHHHHHHHhcCCCCCHHHHHHHHHhhCCCCCcchHHHHHHHHHHCCCEEE
Confidence            5566788887777899999999998642 1 256789999999999999863

>PRK11169 leucine-responsive transcriptional regulator; Provisional

Probab=93.55  E-value=0.1  Score=36.85  Aligned_cols=45  Identities=20%  Similarity=0.220  Sum_probs=38.2

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      +|..|.++|.+ ++.+|..|||+++|+++   ..+.|=++-|...|+++
T Consensus        15 ~D~~IL~~Lq~-d~R~s~~eiA~~lglS~---~tv~~Ri~rL~~~GvI~   59 (164)
T PRK11169         15 IDRNILNELQK-DGRISNVELSKRVGLSP---TPCLERVRRLERQGFIQ   59 (164)
T ss_pred             HHHHHHHHhcc-CCCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCeE
Confidence            67888888876 47999999999999965   77888888899999875

>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=93.49  E-value=0.13  Score=30.53  Aligned_cols=41  Identities=10%  Similarity=0.267  Sum_probs=34.7

Q ss_pred             hhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           51 IPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        51 I~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      |.+.|..+ +.+|+.|||+.+++.+   ..++|=+..|...|++.
T Consensus         5 Il~~l~~~-~~~s~~ela~~~~VS~---~TiRRDl~~L~~~g~i~   45 (57)
T PF08220_consen    5 ILELLKEK-GKVSVKELAEEFGVSE---MTIRRDLNKLEKQGLIK   45 (57)
T ss_pred             HHHHHHHc-CCEEHHHHHHHHCcCH---HHHHHHHHHHHHCCCEE
Confidence            45667553 7999999999999955   89999999999999864

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

>COG1522 Lrp Transcriptional regulators [Transcription]

Probab=93.47  E-value=0.12  Score=35.14  Aligned_cols=45  Identities=13%  Similarity=0.224  Sum_probs=37.4

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++..|-+.|..+ +++|..|||+++|+++   ..+.+-++-|...|++.
T Consensus         9 ~D~~IL~~L~~d-~r~~~~eia~~lglS~---~~v~~Ri~~L~~~GiI~   53 (154)
T COG1522           9 IDRRILRLLQED-ARISNAELAERVGLSP---STVLRRIKRLEEEGVIK   53 (154)
T ss_pred             HHHHHHHHHHHh-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCcee
Confidence            566777888764 6799999999999965   78888889999999875

>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR

Probab=93.47  E-value=0.16  Score=33.50  Aligned_cols=45  Identities=24%  Similarity=0.259  Sum_probs=36.1

Q ss_pred             hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      +..|...|..+ +++|..|||..+++++   ..+.|+++-|...|++..
T Consensus        30 q~~iL~~l~~~-~~~t~~ela~~~~~~~---~tvs~~l~~Le~~GlI~r   74 (118)
T TIGR02337        30 QWRILRILAEQ-GSMEFTQLANQACILR---PSLTGILARLERDGLVTR   74 (118)
T ss_pred             HHHHHHHHHHc-CCcCHHHHHHHhCCCc---hhHHHHHHHHHHCCCEEe
Confidence            33455556553 6899999999999955   789999999999998863

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.

>PRK06266 transcription initiation factor E subunit alpha; Validated

Probab=93.46  E-value=0.11  Score=37.72  Aligned_cols=42  Identities=7%  Similarity=0.090  Sum_probs=36.2

Q ss_pred             ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .|.++|-.+ |++|.+|||..+|++.   ..++|+|..|...|++.
T Consensus        26 ~Vl~~L~~~-g~~tdeeLA~~Lgi~~---~~VRk~L~~L~e~gLv~   67 (178)
T PRK06266         26 EVLKALIKK-GEVTDEEIAEQTGIKL---NTVRKILYKLYDARLAD   67 (178)
T ss_pred             HHHHHHHHc-CCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCeE
Confidence            467877665 5999999999999954   89999999999999876

>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional

Probab=93.46  E-value=0.12  Score=35.93  Aligned_cols=45  Identities=16%  Similarity=0.347  Sum_probs=37.9

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .+..|.+.|..+ +..|.+|||+++|+++   ..++|=++-|...|++.
T Consensus        10 ~D~~Il~~Lq~d-~R~s~~eiA~~lglS~---~tV~~Ri~rL~~~GvI~   54 (153)
T PRK11179         10 LDRGILEALMEN-ARTPYAELAKQFGVSP---GTIHVRVEKMKQAGIIT   54 (153)
T ss_pred             HHHHHHHHHHHc-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCee
Confidence            577888888764 7999999999999965   77888888899999875

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

Probab=93.17  E-value=0.18  Score=32.77  Aligned_cols=34  Identities=12%  Similarity=0.041  Sum_probs=30.8

Q ss_pred             CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           59 TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        59 ~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ..++|..|||+.+|+++   ..+.|++..|...|++.
T Consensus        45 ~~~is~~eLa~~~g~sr---~tVsr~L~~Le~~GlI~   78 (95)
T TIGR01610        45 QDRVTATVIAELTGLSR---THVSDAIKSLARRRIIF   78 (95)
T ss_pred             CCccCHHHHHHHHCcCH---HHHHHHHHHHHHCCCee
Confidence            36899999999999955   89999999999999886

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

>PRK03573 transcriptional regulator SlyA; Provisional

Probab=93.17  E-value=0.21  Score=33.86  Aligned_cols=40  Identities=23%  Similarity=0.193  Sum_probs=33.1

Q ss_pred             HHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           53 DIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        53 D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ..|...+++.|..|||..+++++   ..+.|++.-|...|++.
T Consensus        38 ~~l~~~~~~~t~~eLa~~l~~~~---~tvt~~v~~Le~~GlV~   77 (144)
T PRK03573         38 HNIHQLPPEQSQIQLAKAIGIEQ---PSLVRTLDQLEEKGLIS   77 (144)
T ss_pred             HHHHHcCCCCCHHHHHHHhCCCh---hhHHHHHHHHHHCCCEe
Confidence            34444445789999999999955   89999999999999886

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=93.02  E-value=0.15  Score=28.86  Aligned_cols=33  Identities=12%  Similarity=0.213  Sum_probs=29.1

Q ss_pred             CCC-CHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           60 KPM-TLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        60 gp~-s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      +.+ |..|||+.++++.   ..++|.++.|...|++.
T Consensus        18 ~~l~s~~~la~~~~vs~---~tv~~~l~~L~~~g~i~   51 (60)
T smart00345       18 DKLPSERELAAQLGVSR---TTVREALSRLEAEGLVQ   51 (60)
T ss_pred             CcCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEE
Confidence            456 8999999999954   89999999999999875

>TIGR00498 lexA SOS regulatory protein LexA

Probab=92.69  E-value=0.25  Score=35.42  Aligned_cols=40  Identities=15%  Similarity=0.275  Sum_probs=32.7

Q ss_pred             HhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           55 IHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        55 La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      +.+++-|.|..|||+.+|.+  .+..+++.|+.|...|++..
T Consensus        19 ~~~~~~~~~~~ela~~~~~~--s~~tv~~~l~~L~~~g~i~~   58 (199)
T TIGR00498        19 IESTGYPPSIREIARAVGLR--SPSAAEEHLKALERKGYIER   58 (199)
T ss_pred             HHhcCCCCcHHHHHHHhCCC--ChHHHHHHHHHHHHCCCEec
Confidence            33445688999999999995  13889999999999998763

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

>PRK09462 fur ferric uptake regulator; Provisional

Probab=92.64  E-value=0.21  Score=34.60  Aligned_cols=49  Identities=8%  Similarity=0.109  Sum_probs=38.4

Q ss_pred             HhcChhHHHhhC-CCCCCHHHHHHHhCC-CC-CCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNH-TKPMTLNQLLGALQI-HP-TKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~-~gp~s~~ELA~~~g~-~~-~~~~~L~RlLR~Laa~gif~   95 (97)
                      .+.-|.+.|... +++.|+.||-+.+.- .| .+...++|.|..|+..|++.
T Consensus        18 qR~~Il~~l~~~~~~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli~   69 (148)
T PRK09462         18 PRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVT   69 (148)
T ss_pred             HHHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCEE
Confidence            455677888765 479999999998853 22 25688999999999999885

>TIGR00373 conserved hypothetical protein TIGR00373

Probab=92.57  E-value=0.2  Score=35.66  Aligned_cols=42  Identities=12%  Similarity=0.017  Sum_probs=35.5

Q ss_pred             ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .|+|+|-.+ +.+|-+|||..+|++.   ..++|++..|...|++.
T Consensus        18 ~Vl~aL~~~-~~~tdEeLa~~Lgi~~---~~VRk~L~~L~e~~Lv~   59 (158)
T TIGR00373        18 LVLFSLGIK-GEFTDEEISLELGIKL---NEVRKALYALYDAGLAD   59 (158)
T ss_pred             HHHHHHhcc-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCce
Confidence            456777644 5899999999999954   88999999999999874

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

>PRK03902 manganese transport transcriptional regulator; Provisional

Probab=92.52  E-value=0.21  Score=34.23  Aligned_cols=35  Identities=17%  Similarity=0.315  Sum_probs=31.2

Q ss_pred             CCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           58 HTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        58 ~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .+++.+++|||..+++++   +.+.+.++.|...|++.
T Consensus        19 ~~~~~~~~ela~~l~vs~---~svs~~l~~L~~~Gli~   53 (142)
T PRK03902         19 EKGYARVSDIAEALSVHP---SSVTKMVQKLDKDEYLI   53 (142)
T ss_pred             cCCCcCHHHHHHHhCCCh---hHHHHHHHHHHHCCCEE
Confidence            457889999999999955   89999999999999875

>PHA00738 putative HTH transcription regulator

Probab=92.40  E-value=0.18  Score=34.42  Aligned_cols=46  Identities=13%  Similarity=0.183  Sum_probs=38.4

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      .++.|.+.|.. ++++++.||++.+++.   .+.+.+-|+.|...|++..
T Consensus        13 tRr~IL~lL~~-~e~~~V~eLae~l~lS---QptVS~HLKvLreAGLV~s   58 (108)
T PHA00738         13 LRRKILELIAE-NYILSASLISHTLLLS---YTTVLRHLKILNEQGYIEL   58 (108)
T ss_pred             HHHHHHHHHHH-cCCccHHHHHHhhCCC---HHHHHHHHHHHHHCCceEE
Confidence            55677888865 3479999999999994   3799999999999999864

>PRK15431 ferrous iron transport protein FeoC; Provisional

Probab=92.38  E-value=0.24  Score=32.06  Aligned_cols=40  Identities=15%  Similarity=0.121  Sum_probs=34.4

Q ss_pred             hHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           52 PDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        52 ~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      =|.|+.+ |-+++.|||..+++++   +.++=+|-.|+++|-++
T Consensus         8 Rd~l~~~-gr~s~~~Ls~~~~~p~---~~VeaMLe~l~~kGkve   47 (78)
T PRK15431          8 RDLLALR-GRMEAAQISQTLNTPQ---PMINAMLQQLESMGKAV   47 (78)
T ss_pred             HHHHHHc-CcccHHHHHHHHCcCH---HHHHHHHHHHHHCCCeE
Confidence            3788775 6999999999999955   89999999999999654

>PRK11050 manganese transport regulator MntR; Provisional

Probab=92.38  E-value=0.24  Score=34.71  Aligned_cols=40  Identities=15%  Similarity=0.256  Sum_probs=33.5

Q ss_pred             hHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           52 PDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        52 ~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ...+.. +++.+..|||+.+++++   ..+.|.++.|...|++.
T Consensus        43 ~~~l~~-~~~~t~~eLA~~l~is~---stVsr~l~~Le~~GlI~   82 (152)
T PRK11050         43 ADLIAE-VGEARQVDIAARLGVSQ---PTVAKMLKRLARDGLVE   82 (152)
T ss_pred             HHHHHh-cCCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEE
Confidence            345543 47899999999999955   89999999999999885

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

Probab=92.08  E-value=0.23  Score=34.78  Aligned_cols=50  Identities=10%  Similarity=0.171  Sum_probs=40.5

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCC-CC-CCcccHHHHHHHHHhcCcccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQI-HP-TKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~-~~-~~~~~L~RlLR~Laa~gif~e   96 (97)
                      -++.|.++|.+++++.|+.||=..+.- .| ..+..++|.|..|+..|++.+
T Consensus        22 qR~~vl~~L~~~~~~~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~   73 (145)
T COG0735          22 QRLAVLELLLEADGHLSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHR   73 (145)
T ss_pred             HHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEEE
Confidence            456778999888888999999988774 22 256789999999999999863

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

Probab=92.08  E-value=0.15  Score=30.81  Aligned_cols=33  Identities=15%  Similarity=0.299  Sum_probs=29.9

Q ss_pred             CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      -++|-.+||..+|++.   ..+.|+|+.|...|+++
T Consensus        27 ~~lt~~~iA~~~g~sr---~tv~r~l~~l~~~g~I~   59 (76)
T PF13545_consen   27 LPLTQEEIADMLGVSR---ETVSRILKRLKDEGIIE   59 (76)
T ss_dssp             EESSHHHHHHHHTSCH---HHHHHHHHHHHHTTSEE
T ss_pred             ecCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEE
Confidence            4789999999999965   88999999999999875

...

>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family

Probab=92.01  E-value=0.26  Score=32.40  Aligned_cols=34  Identities=18%  Similarity=0.420  Sum_probs=31.0

Q ss_pred             CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           59 TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        59 ~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++++|..|||..++.++   ..+.|+++.|...|++.
T Consensus        41 ~~~~t~~eL~~~l~~~~---stvs~~i~~Le~kg~I~   74 (109)
T TIGR01889        41 EGKLTLKEIIKEILIKQ---SALVKIIKKLSKKGYLS   74 (109)
T ss_pred             CCcCcHHHHHHHHCCCH---HHHHHHHHHHHHCCCEe
Confidence            47899999999999955   89999999999999876

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.

>COG2345 Predicted transcriptional regulator [Transcription]

Probab=91.75  E-value=0.19  Score=37.98  Aligned_cols=34  Identities=21%  Similarity=0.361  Sum_probs=31.2

Q ss_pred             CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           59 TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        59 ~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .+|+|+.|||+.+|+++   ..++|-|-.|+..|+++
T Consensus        23 ~g~~sa~elA~~Lgis~---~avR~HL~~Le~~Glv~   56 (218)
T COG2345          23 SGPVSADELAEELGISP---MAVRRHLDDLEAEGLVE   56 (218)
T ss_pred             cCCccHHHHHHHhCCCH---HHHHHHHHHHHhCccee
Confidence            37999999999999976   89999999999999875

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

Probab=91.62  E-value=0.11  Score=34.50  Aligned_cols=50  Identities=10%  Similarity=0.174  Sum_probs=38.6

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCC--CCCcccHHHHHHHHHhcCcccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIH--PTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~--~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      .+.-|.+.|.+.+++.|+.||-..+...  ..+...++|.|..|+..|++..
T Consensus         9 ~R~~Il~~l~~~~~~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~   60 (120)
T PF01475_consen    9 QRLAILELLKESPEHLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRK   60 (120)
T ss_dssp             HHHHHHHHHHHHSSSEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEE
Confidence            4456778888877899999999998631  1145679999999999998753

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

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

Probab=91.57  E-value=0.32  Score=34.10  Aligned_cols=44  Identities=18%  Similarity=0.321  Sum_probs=37.0

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFF   94 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif   94 (97)
                      +...|.+.+.++ |.+|..|++..+|++-   ..+.+.+|.|++.|-+
T Consensus        13 Lk~rIvElVRe~-GRiTi~ql~~~TGasR---~Tvk~~lreLVa~G~l   56 (127)
T PF06163_consen   13 LKARIVELVREH-GRITIKQLVAKTGASR---NTVKRYLRELVARGDL   56 (127)
T ss_pred             HHHHHHHHHHHc-CCccHHHHHHHHCCCH---HHHHHHHHHHHHcCCe
Confidence            566778877665 7999999999999954   7899999999998854

>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=91.00  E-value=0.62  Score=30.11  Aligned_cols=47  Identities=17%  Similarity=0.247  Sum_probs=37.6

Q ss_pred             HHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           39 MSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        39 ~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .+|++.  |+    +.+. .+.|+...+||+.++.+|   ..++..|..|..+|+++
T Consensus         8 ~IL~al--V~----~Y~~-~~~PVgSk~ia~~l~~s~---aTIRN~M~~Le~lGlve   54 (78)
T PF03444_consen    8 EILKAL--VE----LYIE-TGEPVGSKTIAEELGRSP---ATIRNEMADLEELGLVE   54 (78)
T ss_pred             HHHHHH--HH----HHHh-cCCCcCHHHHHHHHCCCh---HHHHHHHHHHHHCCCcc
Confidence            455555  54    3343 468999999999999965   89999999999999985

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

>PRK11512 DNA-binding transcriptional repressor MarR; Provisional

Probab=90.84  E-value=0.43  Score=32.56  Aligned_cols=40  Identities=20%  Similarity=0.159  Sum_probs=33.5

Q ss_pred             hHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           52 PDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        52 ~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .-.|.. .+++|..|||..+++++   ..+.|++.-|...|++.
T Consensus        46 L~~l~~-~~~~t~~eLa~~l~i~~---~tvsr~l~~Le~~GlI~   85 (144)
T PRK11512         46 LCSIRC-AACITPVELKKVLSVDL---GALTRMLDRLVCKGWVE   85 (144)
T ss_pred             HHHHHH-cCCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEE
Confidence            444544 36899999999999955   89999999999999886

>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY

Probab=90.54  E-value=0.38  Score=37.19  Aligned_cols=44  Identities=9%  Similarity=0.110  Sum_probs=37.3

Q ss_pred             ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      .|++.|...++-++..+||+++|+.+   ..+++-+|.|.+.|+++-
T Consensus       187 ~IL~~L~~~egrlse~eLAerlGVSR---s~ireAlrkLE~aGvIe~  230 (251)
T TIGR02787       187 HIFEELDGNEGLLVASKIADRVGITR---SVIVNALRKLESAGVIES  230 (251)
T ss_pred             HHHHHhccccccccHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEe
Confidence            56777765458999999999999965   789999999999999863

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

>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein

Probab=90.46  E-value=0.36  Score=35.00  Aligned_cols=45  Identities=7%  Similarity=0.167  Sum_probs=36.2

Q ss_pred             hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      +..|...|.++ +++|..|||+.+++++   ..++|.++.|...|++..
T Consensus       145 ~~~IL~~l~~~-g~~s~~eia~~l~is~---stv~r~L~~Le~~GlI~r  189 (203)
T TIGR01884       145 ELKVLEVLKAE-GEKSVKNIAKKLGKSL---STISRHLRELEKKGLVEQ  189 (203)
T ss_pred             HHHHHHHHHHc-CCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEE
Confidence            34555666554 5799999999999955   889999999999998863

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.

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

Probab=90.07  E-value=0.65  Score=26.68  Aligned_cols=31  Identities=13%  Similarity=0.142  Sum_probs=27.6

Q ss_pred             CCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           62 MTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        62 ~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .|..|||..+++++   ..+.+.+..|...|++.
T Consensus        26 ~~~~~la~~~~is~---~~v~~~l~~L~~~G~i~   56 (66)
T cd07377          26 PSERELAEELGVSR---TTVREALRELEAEGLVE   56 (66)
T ss_pred             CCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEE
Confidence            45999999999954   89999999999999875

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

>PRK14096 pgi glucose-6-phosphate isomerase; Provisional

Probab=90.06  E-value=0.42  Score=40.33  Aligned_cols=41  Identities=7%  Similarity=0.250  Sum_probs=33.2

Q ss_pred             hhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcC
Q 041844           51 IPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSG   92 (97)
Q Consensus        51 I~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~g   92 (97)
                      |-..+...+++.|++||++++|... +...++.|||+|++++
T Consensus       468 ~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~i~~~~~~n~  508 (528)
T PRK14096        468 VEELLKEDGGELSIEEIAAALGAPE-QVETIYKILRHLAANN  508 (528)
T ss_pred             HHHHHhccCCCCCHHHHHHHcCCCc-cHHHHHHHHHHHhcCC
Confidence            4455545568999999999999844 6789999999999874

>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial

Probab=89.99  E-value=0.34  Score=33.53  Aligned_cols=32  Identities=9%  Similarity=0.134  Sum_probs=29.5

Q ss_pred             CCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           61 PMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        61 p~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      |+|-.|||+.+|+.+   ..+.|+|+.|...|+++
T Consensus       143 ~~t~~~iA~~lG~tr---etvsR~l~~l~~~g~I~  174 (193)
T TIGR03697       143 RLSHQAIAEAIGSTR---VTITRLLGDLRKKKLIS  174 (193)
T ss_pred             CCCHHHHHHHhCCcH---HHHHHHHHHHHHCCCEE
Confidence            689999999999955   89999999999999886

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

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

Probab=89.97  E-value=0.48  Score=29.50  Aligned_cols=46  Identities=24%  Similarity=0.351  Sum_probs=37.5

Q ss_pred             HhcChhHHHhhCC-CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHT-KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~-gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++..+.+.|+++. ...+..||+..+|.||   ..+...++.|...|++.
T Consensus         3 ~~~~~Le~I~rsR~~Gi~q~~L~~~~~~D~---r~i~~~~k~L~~~gLI~   49 (75)
T PF04182_consen    3 IQYCLLERIARSRYNGITQSDLSKLLGIDP---RSIFYRLKKLEKKGLIV   49 (75)
T ss_pred             hHHHHHHHHHhcCCCCEehhHHHHHhCCCc---hHHHHHHHHHHHCCCEE
Confidence            3445667777655 7789999999999955   99999999999999875

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

>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=89.16  E-value=0.29  Score=27.63  Aligned_cols=22  Identities=5%  Similarity=0.138  Sum_probs=16.6

Q ss_pred             CCHHHHHHHhCCCCCCcccHHHHHH
Q 041844           62 MTLNQLLGALQIHPTKTRCLHFLVC   86 (97)
Q Consensus        62 ~s~~ELA~~~g~~~~~~~~L~RlLR   86 (97)
                      +|+.|||..+|++.   ..++|+++
T Consensus        22 ~si~~IA~~~gvsr---~TvyR~l~   43 (45)
T PF02796_consen   22 MSIAEIAKQFGVSR---STVYRYLN   43 (45)
T ss_dssp             --HHHHHHHTTS-H---HHHHHHHC
T ss_pred             CCHHHHHHHHCcCH---HHHHHHHh
Confidence            99999999999954   78888875

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 ....

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

Probab=89.11  E-value=0.55  Score=34.35  Aligned_cols=36  Identities=19%  Similarity=0.211  Sum_probs=30.1

Q ss_pred             hHHHHHHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCC
Q 041844           34 SFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHP   75 (97)
Q Consensus        34 ~~~~s~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~   75 (97)
                      .-.+-.+|+.|  .++|-||.    +...++.|||+.+|+.+
T Consensus       157 TdrQ~~vL~~A--~~~GYFd~----PR~~~l~dLA~~lGISk  192 (215)
T COG3413         157 TDRQLEVLRLA--YKMGYFDY----PRRVSLKDLAKELGISK  192 (215)
T ss_pred             CHHHHHHHHHH--HHcCCCCC----CccCCHHHHHHHhCCCH
Confidence            34567799999  99999985    36789999999999954

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

Probab=89.05  E-value=0.36  Score=31.50  Aligned_cols=42  Identities=19%  Similarity=0.316  Sum_probs=30.8

Q ss_pred             ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .|+|.|..+ |.++-+|||..+|+++   .-++++|..|...|+++
T Consensus        17 ~Il~~L~~~-~~l~de~la~~~~l~~---~~vRkiL~~L~~~~lv~   58 (105)
T PF02002_consen   17 RILDALLRK-GELTDEDLAKKLGLKP---KEVRKILYKLYEDGLVS   58 (105)
T ss_dssp             HHHHHHHHH---B-HHHHHHTT-S-H---HHHHHHHHHHHHHSS-E
T ss_pred             HHHHHHHHc-CCcCHHHHHHHhCCCH---HHHHHHHHHHHHCCCeE
Confidence            356777654 6899999999999954   88999999999999875

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

>PRK12423 LexA repressor; Provisional

Probab=89.03  E-value=0.82  Score=33.27  Aligned_cols=41  Identities=17%  Similarity=0.276  Sum_probs=32.3

Q ss_pred             HHHhhCCCCCCHHHHHHHhCC-CCCCcccHHHHHHHHHhcCcccc
Q 041844           53 DIIHNHTKPMTLNQLLGALQI-HPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        53 D~La~~~gp~s~~ELA~~~g~-~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      +.+.+++-+-|..|||+++|+ .+   ..+++-|+.|+..|+++.
T Consensus        17 ~~i~~~g~~Ps~~eia~~~g~~s~---~~v~~~l~~L~~~G~l~~   58 (202)
T PRK12423         17 ERIAQAGQPPSLAEIAQAFGFASR---SVARKHVQALAEAGLIEV   58 (202)
T ss_pred             HHHHHcCCCCCHHHHHHHhCCCCh---HHHHHHHHHHHHCCCEEe
Confidence            344444556799999999995 44   789999999999998863

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

Probab=89.02  E-value=0.24  Score=31.42  Aligned_cols=45  Identities=16%  Similarity=0.269  Sum_probs=35.9

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      |+|+|...|.. .+.++..||.+.+|++.   ..|.+-|+.|...|+++
T Consensus         1 vRl~Il~~L~~-~~~~~f~~L~~~l~lt~---g~Ls~hL~~Le~~GyV~   45 (80)
T PF13601_consen    1 VRLAILALLYA-NEEATFSELKEELGLTD---GNLSKHLKKLEEAGYVE   45 (80)
T ss_dssp             HHHHHHHHHHH-HSEEEHHHHHHHTT--H---HHHHHHHHHHHHTTSEE
T ss_pred             CHHHHHHHHhh-cCCCCHHHHHHHhCcCH---HHHHHHHHHHHHCCCEE
Confidence            35666677755 36899999999999944   89999999999999886

>COG1378 Predicted transcriptional regulators [Transcription]

Probab=88.24  E-value=0.67  Score=35.25  Aligned_cols=33  Identities=15%  Similarity=0.116  Sum_probs=30.0

Q ss_pred             CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      |+.|+.||++.+|++-   ..++.+||.|...|++.
T Consensus        29 g~~tA~eis~~sgvP~---~kvY~vl~sLe~kG~v~   61 (247)
T COG1378          29 GEATAKEISEASGVPR---PKVYDVLRSLEKKGLVE   61 (247)
T ss_pred             CCccHHHHHHHcCCCc---hhHHHHHHHHHHCCCEE
Confidence            7999999999999954   68999999999999875

>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]

Probab=88.10  E-value=0.98  Score=32.09  Aligned_cols=35  Identities=14%  Similarity=0.230  Sum_probs=31.5

Q ss_pred             CCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           58 HTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        58 ~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ..++....+||+.++++|   +.+..+++-|...|++.
T Consensus        21 ~~~~~~~~diA~~L~Vsp---~sVt~ml~rL~~~GlV~   55 (154)
T COG1321          21 EKGFARTKDIAERLKVSP---PSVTEMLKRLERLGLVE   55 (154)
T ss_pred             ccCcccHHHHHHHhCCCc---HHHHHHHHHHHHCCCeE
Confidence            458999999999999966   88999999999999875

>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional

Probab=88.06  E-value=0.52  Score=33.93  Aligned_cols=32  Identities=19%  Similarity=0.257  Sum_probs=29.3

Q ss_pred             CCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           61 PMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        61 p~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      |+|-.+||+.+|+.+   ..+.|+|+.|...|+++
T Consensus       184 ~lt~~~iA~~lG~sr---~tvsR~l~~l~~~g~I~  215 (235)
T PRK11161        184 TMTRGDIGNYLGLTV---ETISRLLGRFQKSGMLA  215 (235)
T ss_pred             cccHHHHHHHhCCcH---HHHHHHHHHHHHCCCEE
Confidence            689999999999965   89999999999999886

>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional

Probab=87.96  E-value=0.58  Score=32.92  Aligned_cols=32  Identities=9%  Similarity=0.090  Sum_probs=29.5

Q ss_pred             CCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           61 PMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        61 p~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++|-.|||+.+|+.+   ..+.|+|+.|...|+++
T Consensus       168 ~~t~~~lA~~lG~tr---~tvsR~l~~l~~~gii~  199 (211)
T PRK11753        168 KITRQEIGRIVGCSR---EMVGRVLKMLEDQGLIS  199 (211)
T ss_pred             CCCHHHHHHHhCCCH---HHHHHHHHHHHHCCCEE
Confidence            788999999999965   89999999999999886

>PRK13918 CRP/FNR family transcriptional regulator; Provisional

Probab=87.84  E-value=0.63  Score=32.58  Aligned_cols=32  Identities=19%  Similarity=0.258  Sum_probs=29.4

Q ss_pred             CCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           61 PMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        61 p~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      |+|-.|||..+|+.+   +.+.|+|+-|...|+++
T Consensus       149 ~~t~~~iA~~lG~tr---etvsR~l~~l~~~g~I~  180 (202)
T PRK13918        149 YATHDELAAAVGSVR---ETVTKVIGELSREGYIR  180 (202)
T ss_pred             cCCHHHHHHHhCccH---HHHHHHHHHHHHCCCEE
Confidence            689999999999965   89999999999999886

>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=87.82  E-value=0.51  Score=28.07  Aligned_cols=34  Identities=9%  Similarity=0.126  Sum_probs=28.6

Q ss_pred             CCCC-CHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           59 TKPM-TLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        59 ~gp~-s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      |..+ |..+||+..+++.   ..+++.|+.|...|++.
T Consensus        21 g~~lps~~~la~~~~vsr---~tvr~al~~L~~~g~i~   55 (64)
T PF00392_consen   21 GDRLPSERELAERYGVSR---TTVREALRRLEAEGLIE   55 (64)
T ss_dssp             TSBE--HHHHHHHHTS-H---HHHHHHHHHHHHTTSEE
T ss_pred             CCEeCCHHHHHHHhccCC---cHHHHHHHHHHHCCcEE
Confidence            4567 9999999999954   88999999999999875

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 ....

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

Probab=87.65  E-value=0.75  Score=28.89  Aligned_cols=30  Identities=13%  Similarity=0.346  Sum_probs=26.5

Q ss_pred             HHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           64 LNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        64 ~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      ..|||+.+++++   ..+.|+++.|...|++..
T Consensus         2 ~~ela~~l~is~---stvs~~l~~L~~~glI~r   31 (96)
T smart00529        2 TSEIAERLNVSP---PTVTQMLKKLEKDGLVEY   31 (96)
T ss_pred             HHHHHHHhCCCh---HHHHHHHHHHHHCCCEEE
Confidence            579999999955   899999999999998863

iron dependent repressor

>PRK13509 transcriptional repressor UlaR; Provisional

Probab=87.55  E-value=0.88  Score=34.23  Aligned_cols=42  Identities=17%  Similarity=0.210  Sum_probs=35.5

Q ss_pred             ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .|-+.|.+ .+.+++.|||+.+|+.+   ..++|-|+.|...|++.
T Consensus         9 ~Il~~l~~-~~~~~~~ela~~l~vS~---~TirRdL~~Le~~g~i~   50 (251)
T PRK13509          9 ILLELLAQ-LGFVTVEKVIERLGISP---ATARRDINKLDESGKLK   50 (251)
T ss_pred             HHHHHHHH-cCCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEE
Confidence            45677765 47999999999999955   88999999999999874

>PF13730 HTH_36: Helix-turn-helix domain

Probab=87.31  E-value=0.79  Score=26.19  Aligned_cols=29  Identities=17%  Similarity=0.263  Sum_probs=26.3

Q ss_pred             CHHHHHHHhCCCCCCcccHHHHHHHHHhcCcc
Q 041844           63 TLNQLLGALQIHPTKTRCLHFLVCSLVRSGFF   94 (97)
Q Consensus        63 s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif   94 (97)
                      |.+.||+.+|+..   ..+.|.++.|...|++
T Consensus        27 S~~~la~~~g~s~---~Tv~~~i~~L~~~G~I   55 (55)
T PF13730_consen   27 SQETLAKDLGVSR---RTVQRAIKELEEKGLI   55 (55)
T ss_pred             CHHHHHHHHCcCH---HHHHHHHHHHHHCcCC
Confidence            8999999999954   8999999999999974

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

Probab=87.12  E-value=0.82  Score=25.75  Aligned_cols=37  Identities=8%  Similarity=0.106  Sum_probs=25.7

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHH
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVC   86 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR   86 (97)
                      ++..|.+.|..+ +..|..|||+.+|+++  .....|+-|
T Consensus         4 ~D~~Il~~Lq~d-~r~s~~~la~~lglS~--~~v~~Ri~r   40 (42)
T PF13404_consen    4 LDRKILRLLQED-GRRSYAELAEELGLSE--STVRRRIRR   40 (42)
T ss_dssp             HHHHHHHHHHH--TTS-HHHHHHHHTS-H--HHHHHHHHH
T ss_pred             HHHHHHHHHHHc-CCccHHHHHHHHCcCH--HHHHHHHHH
Confidence            566778888764 7999999999999964  245555544

...

>PRK10870 transcriptional repressor MprA; Provisional

Probab=87.12  E-value=1.1  Score=32.02  Aligned_cols=35  Identities=14%  Similarity=0.139  Sum_probs=31.0

Q ss_pred             CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           59 TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        59 ~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      ++++|..|||..+++++   ..+.|++.-|...|++..
T Consensus        69 ~~~it~~eLa~~l~l~~---~tvsr~v~rLe~kGlV~R  103 (176)
T PRK10870         69 NHSIQPSELSCALGSSR---TNATRIADELEKRGWIER  103 (176)
T ss_pred             CCCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEe
Confidence            46899999999999955   899999999999998863

>PRK09391 fixK transcriptional regulator FixK; Provisional

Probab=86.97  E-value=0.67  Score=33.79  Aligned_cols=32  Identities=16%  Similarity=0.272  Sum_probs=29.3

Q ss_pred             CCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           61 PMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        61 p~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++|-.|||+.+|+.+   ..+.|+++.|...|+++
T Consensus       179 ~lt~~~IA~~lGisr---etlsR~L~~L~~~GlI~  210 (230)
T PRK09391        179 PMSRRDIADYLGLTI---ETVSRALSQLQDRGLIG  210 (230)
T ss_pred             cCCHHHHHHHHCCCH---HHHHHHHHHHHHCCcEE
Confidence            578899999999965   89999999999999886

>PRK10046 dpiA two-component response regulator DpiA; Provisional

Probab=86.85  E-value=0.85  Score=32.72  Aligned_cols=43  Identities=9%  Similarity=0.017  Sum_probs=34.2

Q ss_pred             hhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           51 IPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        51 I~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      |.+.+++..+..|..|||+++++.+   ..+++-+.+|+.+|++..
T Consensus       167 Vl~~~~~g~~g~s~~eIa~~l~iS~---~Tv~~~~~~~~~~~~~~~  209 (225)
T PRK10046        167 VRKLFKEPGVQHTAETVAQALTISR---TTARRYLEYCASRHLIIA  209 (225)
T ss_pred             HHHHHHcCCCCcCHHHHHHHhCccH---HHHHHHHHHHHhCCeEEE
Confidence            4455654224689999999999955   889999999999998753

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

Probab=85.74  E-value=1.1  Score=32.81  Aligned_cols=42  Identities=19%  Similarity=0.260  Sum_probs=35.1

Q ss_pred             ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      -|+|++-.. |..|-.|||..+|+   +..-++|+|+.|...|++.
T Consensus        22 ~v~~~l~~k-ge~tDeela~~l~i---~~~~vrriL~~L~e~~li~   63 (176)
T COG1675          22 LVVDALLEK-GELTDEELAELLGI---KKNEVRRILYALYEDGLIS   63 (176)
T ss_pred             HHHHHHHhc-CCcChHHHHHHhCc---cHHHHHHHHHHHHhCCceE
Confidence            345777654 48999999999999   4488999999999999886

>COG1725 Predicted transcriptional regulators [Transcription]

Probab=85.17  E-value=2.4  Score=29.53  Aligned_cols=33  Identities=21%  Similarity=0.313  Sum_probs=29.0

Q ss_pred             CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .=-|+.|||..+|++|   ..+.|.-+.|...|++.
T Consensus        34 kLPSvRelA~~~~VNp---nTv~raY~eLE~eG~i~   66 (125)
T COG1725          34 KLPSVRELAKDLGVNP---NTVQRAYQELEREGIVE   66 (125)
T ss_pred             CCCcHHHHHHHhCCCH---HHHHHHHHHHHHCCCEE
Confidence            3458999999999966   89999999999999874

>PRK09334 30S ribosomal protein S25e; Provisional

Probab=84.63  E-value=1.1  Score=29.39  Aligned_cols=33  Identities=18%  Similarity=0.158  Sum_probs=29.4

Q ss_pred             CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .-+|.+.|++++++.   .++-+++||.|...|++.
T Consensus        40 K~ITps~lserlkI~---~SlAr~~Lr~L~~kG~Ik   72 (86)
T PRK09334         40 KIVTPYTLASKYGIK---ISVAKKVLRELEKRGVLV   72 (86)
T ss_pred             cEEcHHHHHHHhcch---HHHHHHHHHHHHHCCCEE
Confidence            568999999999994   489999999999999874

>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional

Probab=84.58  E-value=1.3  Score=33.83  Aligned_cols=43  Identities=12%  Similarity=0.113  Sum_probs=36.0

Q ss_pred             cChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           49 VGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        49 LgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ..|.+.|.++ +.+|+.|||+.+++++   ..++|=++.|...|++.
T Consensus        20 ~~Il~~L~~~-~~vtv~eLa~~l~VS~---~TIRRDL~~Le~~G~l~   62 (269)
T PRK09802         20 EQIIQRLRQQ-GSVQVNDLSALYGVST---VTIRNDLAFLEKQGIAV   62 (269)
T ss_pred             HHHHHHHHHc-CCEeHHHHHHHHCCCH---HHHHHHHHHHHhCCCeE
Confidence            3567778664 5799999999999955   89999999999999874

>COG1846 MarR Transcriptional regulators [Transcription]

Probab=84.53  E-value=1.4  Score=27.71  Aligned_cols=45  Identities=16%  Similarity=0.159  Sum_probs=33.4

Q ss_pred             hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      +..+...|...+ +.+..|||..+++++   ..+.|+++-|...|++..
T Consensus        24 q~~~L~~l~~~~-~~~~~~la~~l~i~~---~~vt~~l~~Le~~glv~r   68 (126)
T COG1846          24 QYQVLLALYEAG-GITVKELAERLGLDR---STVTRLLKRLEDKGLIER   68 (126)
T ss_pred             HHHHHHHHHHhC-CCcHHHHHHHHCCCH---HHHHHHHHHHHHCCCeee
Confidence            444445555543 333399999999955   899999999999998863

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

Probab=83.99  E-value=1.4  Score=35.41  Aligned_cols=36  Identities=22%  Similarity=0.361  Sum_probs=31.8

Q ss_pred             CCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           58 HTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        58 ~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      .++|.|.+||++++++++   +.+++++..|...|++.+
T Consensus       307 ~g~~~t~~~La~~l~~~~---~~v~~iL~~L~~agLI~~  342 (412)
T PRK04214        307 HGKALDVDEIRRLEPMGY---DELGELLCELARIGLLRR  342 (412)
T ss_pred             cCCCCCHHHHHHHhCCCH---HHHHHHHHHHHhCCCeEe
Confidence            568999999999999855   899999999999998753

>COG1510 Predicted transcriptional regulators [Transcription]

Probab=83.88  E-value=1.5  Score=32.30  Aligned_cols=35  Identities=20%  Similarity=0.283  Sum_probs=29.5

Q ss_pred             CCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           58 HTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        58 ~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      +.+|+|++||++++|.+-   +.+.--||.|-..|++.
T Consensus        38 s~~Pmtl~Ei~E~lg~Sk---s~vS~~lkkL~~~~lV~   72 (177)
T COG1510          38 SRKPLTLDEIAEALGMSK---SNVSMGLKKLQDWNLVK   72 (177)
T ss_pred             cCCCccHHHHHHHHCCCc---chHHHHHHHHHhcchHH
Confidence            458999999999999954   67888999998888764

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

Probab=83.87  E-value=1.5  Score=33.46  Aligned_cols=41  Identities=20%  Similarity=0.255  Sum_probs=33.7

Q ss_pred             hHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           52 PDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        52 ~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      -+.+..-+.+.|++|+|+++|++-   ...+|-|-+|++.|++.
T Consensus       164 ~~~~~~~~~~~Taeela~~~giSR---vTaRRYLeyl~~~~~l~  204 (224)
T COG4565         164 REALKEPDQELTAEELAQALGISR---VTARRYLEYLVSNGILE  204 (224)
T ss_pred             HHHHhCcCCccCHHHHHHHhCccH---HHHHHHHHHHHhcCeee
Confidence            355653358999999999999943   78999999999999875

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

Probab=83.67  E-value=1.5  Score=29.63  Aligned_cols=33  Identities=21%  Similarity=0.189  Sum_probs=29.5

Q ss_pred             CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .-+|+..||+++++.   -++-+++||.|...|++.
T Consensus        58 K~ITp~~lserlkI~---~SlAr~~Lr~L~~kG~Ik   90 (105)
T PF03297_consen   58 KLITPSVLSERLKIN---GSLARKALRELESKGLIK   90 (105)
T ss_dssp             SCECHHHHHHHHCCS---CHHHHHHHHHHHHCCSSE
T ss_pred             cEeeHHHHHHhHhhH---HHHHHHHHHHHHHCCCEE
Confidence            568999999999994   489999999999999875

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.

>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional

Probab=83.29  E-value=1.5  Score=33.14  Aligned_cols=42  Identities=10%  Similarity=0.211  Sum_probs=35.5

Q ss_pred             ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .|-+.|.+ .+.+++.|||+.+++++   ..++|=|..|...|++.
T Consensus         9 ~Il~~l~~-~~~~~~~ela~~l~vS~---~TiRRdL~~Le~~g~l~   50 (252)
T PRK10906          9 AIIELVKQ-QGYVSTEELVEHFSVSP---QTIRRDLNDLAEQNKIL   50 (252)
T ss_pred             HHHHHHHH-cCCEeHHHHHHHhCCCH---HHHHHHHHHHHHCCCEE
Confidence            45677755 46899999999999954   89999999999999875

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

Probab=83.29  E-value=3.6  Score=24.83  Aligned_cols=40  Identities=10%  Similarity=0.313  Sum_probs=30.1

Q ss_pred             hHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           52 PDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        52 ~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++.|.++ |..|+.+|+..++.++   +.++.-|-.|...|++.
T Consensus        19 ~~~Ll~~-G~ltl~~i~~~t~l~~---~~Vk~~L~~LiQh~~v~   58 (62)
T PF08221_consen   19 GEVLLSR-GRLTLREIVRRTGLSP---KQVKKALVVLIQHNLVQ   58 (62)
T ss_dssp             HHHHHHC--SEEHHHHHHHHT--H---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHc-CCcCHHHHHHHhCCCH---HHHHHHHHHHHHcCCee
Confidence            4555443 7999999999999854   88999999999988764

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

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

Probab=83.08  E-value=1.2  Score=27.80  Aligned_cols=34  Identities=9%  Similarity=0.113  Sum_probs=27.2

Q ss_pred             CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           59 TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        59 ~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .++.+..+|+..++++.   ..+.+.+..|...|+++
T Consensus        17 ~~~~~~t~i~~~~~L~~---~~~~~yL~~L~~~gLI~   50 (77)
T PF14947_consen   17 KGGAKKTEIMYKANLNY---STLKKYLKELEEKGLIK   50 (77)
T ss_dssp             TT-B-HHHHHTTST--H---HHHHHHHHHHHHTTSEE
T ss_pred             cCCCCHHHHHHHhCcCH---HHHHHHHHHHHHCcCee
Confidence            48999999999999954   89999999999999875

>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=82.92  E-value=2.2  Score=28.11  Aligned_cols=45  Identities=9%  Similarity=0.105  Sum_probs=34.4

Q ss_pred             HhcChhHHHhhC-CCCCCHHHHHHHhCCCCCCcccHHHHHHH----------HHhcCcc
Q 041844           47 IQVGIPDIIHNH-TKPMTLNQLLGALQIHPTKTRCLHFLVCS----------LVRSGFF   94 (97)
Q Consensus        47 veLgI~D~La~~-~gp~s~~ELA~~~g~~~~~~~~L~RlLR~----------Laa~gif   94 (97)
                      +...|+.-|.+. +.+.++.|||..+++++   ..+.-.|+-          |+.+|++
T Consensus        10 ~R~~vl~~L~~~yp~~~~~~eIar~v~~~~---snV~GaL~G~g~rY~~e~SLv~lGLV   65 (90)
T PF07381_consen   10 VRKKVLEYLCSIYPEPAYPSEIARSVGSDY---SNVLGALRGDGKRYNKEDSLVGLGLV   65 (90)
T ss_pred             HHHHHHHHHHHcCCCcCCHHHHHHHHCCCH---HHHHHHHhcCCCCcCcchhHHHcCCe
Confidence            566778888776 68999999999999965   666666653          6667766

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

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

Probab=82.85  E-value=1  Score=24.58  Aligned_cols=27  Identities=15%  Similarity=0.191  Sum_probs=20.4

Q ss_pred             CCCCHHHHHHHhCCCCCCcccHHHHHHHHH
Q 041844           60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLV   89 (97)
Q Consensus        60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~La   89 (97)
                      .++|++|||..+|.++   ..+.|+.+...
T Consensus         7 ~~~~l~~iA~~~g~S~---~~f~r~Fk~~~   33 (42)
T PF00165_consen    7 QKLTLEDIAEQAGFSP---SYFSRLFKKET   33 (42)
T ss_dssp             SS--HHHHHHHHTS-H---HHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHCCCH---HHHHHHHHHHH
Confidence            5799999999999954   89999988543

>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional

Probab=82.52  E-value=1.6  Score=32.94  Aligned_cols=42  Identities=10%  Similarity=0.119  Sum_probs=35.8

Q ss_pred             ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .|.+.|.++ +.+++.|||+.+++++   ..++|=++.|...|++.
T Consensus         9 ~Il~~L~~~-~~v~v~eLa~~l~VS~---~TIRRDL~~Le~~g~l~   50 (256)
T PRK10434          9 AILEYLQKQ-GKTSVEELAQYFDTTG---TTIRKDLVILEHAGTVI   50 (256)
T ss_pred             HHHHHHHHc-CCEEHHHHHHHHCCCH---HHHHHHHHHHHHCCCEE
Confidence            566778664 6899999999999955   89999999999999764

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

Probab=82.44  E-value=1.9  Score=29.26  Aligned_cols=33  Identities=21%  Similarity=0.270  Sum_probs=29.4

Q ss_pred             CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .++|++|||+.+.+.+   ...+++|+-|...|.++
T Consensus        18 ~~vtl~elA~~l~cS~---Rn~r~lLkkm~~~gWi~   50 (115)
T PF12793_consen   18 VEVTLDELAELLFCSR---RNARTLLKKMQEEGWIT   50 (115)
T ss_pred             cceeHHHHHHHhCCCH---HHHHHHHHHHHHCCCee
Confidence            5789999999999965   89999999999998764

>COG4189 Predicted transcriptional regulator [Transcription]

Probab=82.10  E-value=3.2  Score=32.56  Aligned_cols=53  Identities=19%  Similarity=0.363  Sum_probs=41.3

Q ss_pred             HHHHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           37 NSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        37 ~s~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .-.++...  +++.|...|+.. +|+.+.|||+++|.+.   ..+.-=+..|...|+++
T Consensus        16 v~kalaS~--vRv~Il~lL~~k-~plNvneiAe~lgLpq---st~s~~ik~Le~aGlir   68 (308)
T COG4189          16 VLKALASK--VRVAILQLLHRK-GPLNVNEIAEALGLPQ---STMSANIKVLEKAGLIR   68 (308)
T ss_pred             HHHHHHHH--HHHHHHHHHHHh-CCCCHHHHHHHhCCch---hhhhhhHHHHHhcCcee
Confidence            34566677  888999999864 7999999999999943   55666677788888764

>TIGR00331 hrcA heat shock gene repressor HrcA

Probab=82.05  E-value=2.5  Score=33.43  Aligned_cols=47  Identities=21%  Similarity=0.363  Sum_probs=37.1

Q ss_pred             HHHHHHHHhcChhHHHhhCCCCCCHHHHHHH--hCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           40 SLKCVKLIQVGIPDIIHNHTKPMTLNQLLGA--LQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        40 aL~~a~~veLgI~D~La~~~gp~s~~ELA~~--~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      .|++.  |+    +.+. .++|.+..+|++.  +++++   ..++|-|..|...|++..
T Consensus         7 il~aI--V~----~~l~-~~~pv~s~~l~~~~~~~vS~---aTiR~d~~~Le~~G~l~~   55 (337)
T TIGR00331         7 ILKAI--VE----EYIK-TGQPVGSKTLLEKYNLGLSS---ATIRNDMADLEDLGFIEK   55 (337)
T ss_pred             HHHHH--HH----HHHh-cCCCcCHHHHHhhcCCCCCh---HHHHHHHHHHHHCCCccC
Confidence            45555  54    4454 4689999999999  77755   899999999999998853

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

>PHA02943 hypothetical protein; Provisional

Probab=81.91  E-value=2.2  Score=31.12  Aligned_cols=42  Identities=10%  Similarity=0.086  Sum_probs=33.8

Q ss_pred             ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      .|-+.|  ..|..|.+|||+++|++-   ...+=+|+.|...|.+.+
T Consensus        15 eILE~L--k~G~~TtseIAkaLGlS~---~qa~~~LyvLErEG~Vkr   56 (165)
T PHA02943         15 KTLRLL--ADGCKTTSRIANKLGVSH---SMARNALYQLAKEGMVLK   56 (165)
T ss_pred             HHHHHH--hcCCccHHHHHHHHCCCH---HHHHHHHHHHHHcCceEE
Confidence            445666  348999999999999943   778999999999997753

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

Probab=81.85  E-value=2  Score=27.72  Aligned_cols=44  Identities=11%  Similarity=0.168  Sum_probs=33.4

Q ss_pred             hcChhHHHhh---CCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcc
Q 041844           48 QVGIPDIIHN---HTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFF   94 (97)
Q Consensus        48 eLgI~D~La~---~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif   94 (97)
                      .-.|++.|..   ....+++++|+++++.+   ..-++-.+..|+..|.+
T Consensus        49 ~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~---~~~v~~al~~L~~eG~I   95 (102)
T PF08784_consen   49 QDKVLNFIKQQPNSEEGVHVDEIAQQLGMS---ENEVRKALDFLSNEGHI   95 (102)
T ss_dssp             HHHHHHHHHC----TTTEEHHHHHHHSTS----HHHHHHHHHHHHHTTSE
T ss_pred             HHHHHHHHHhcCCCCCcccHHHHHHHhCcC---HHHHHHHHHHHHhCCeE
Confidence            3355666655   23679999999999884   47899999999999964

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

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

Probab=81.83  E-value=1.9  Score=32.37  Aligned_cols=33  Identities=6%  Similarity=0.144  Sum_probs=29.9

Q ss_pred             CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ..+|..|||+.+++++   ..+.|+++.|...|+++
T Consensus        20 ~~IS~~eLA~~L~iS~---~Tvsr~Lk~LEe~GlI~   52 (217)
T PRK14165         20 VKISSSEFANHTGTSS---KTAARILKQLEDEGYIT   52 (217)
T ss_pred             CCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEE
Confidence            5689999999999954   89999999999999885

>PRK10402 DNA-binding transcriptional activator YeiL; Provisional

Probab=81.70  E-value=1.5  Score=31.70  Aligned_cols=33  Identities=15%  Similarity=0.305  Sum_probs=29.3

Q ss_pred             CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      -+.|-.|||+.+|+.+   ..|.|+|+-|...|+++
T Consensus       168 ~~~t~~~lA~~lG~sr---etvsR~L~~L~~~G~I~  200 (226)
T PRK10402        168 YHEKHTQAAEYLGVSY---RHLLYVLAQFIQDGYLK  200 (226)
T ss_pred             ccchHHHHHHHHCCcH---HHHHHHHHHHHHCCCEE
Confidence            3568899999999965   89999999999999875

>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional

Probab=81.54  E-value=1.2  Score=32.16  Aligned_cols=42  Identities=10%  Similarity=0.117  Sum_probs=34.9

Q ss_pred             ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .|.+.|..+ +..++.|||+.+++++   ..++|=++.|...|.+.
T Consensus        11 ~Il~~l~~~-~~~~~~~La~~~~vS~---~TiRRDl~~L~~~g~~~   52 (185)
T PRK04424         11 ALQELIEEN-PFITDEELAEKFGVSI---QTIRLDRMELGIPELRE   52 (185)
T ss_pred             HHHHHHHHC-CCEEHHHHHHHHCcCH---HHHHHHHHHHhcchHHH
Confidence            456677653 6899999999999955   89999999999988764

>PRK05638 threonine synthase; Validated

Probab=81.48  E-value=2.2  Score=34.59  Aligned_cols=42  Identities=19%  Similarity=0.168  Sum_probs=32.4

Q ss_pred             hhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           51 IPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        51 I~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      |...|.+  ++++..||++.++.+. ....+++.|+.|...|+++
T Consensus       376 IL~~L~~--~~~~~~el~~~l~~~~-s~~~v~~hL~~Le~~GLV~  417 (442)
T PRK05638        376 ILKILSE--REMYGYEIWKALGKPL-KYQAVYQHIKELEELGLIE  417 (442)
T ss_pred             HHHHHhh--CCccHHHHHHHHcccC-CcchHHHHHHHHHHCCCEE
Confidence            4445543  6899999999998211 3379999999999999885

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

Probab=80.87  E-value=0.8  Score=28.46  Aligned_cols=30  Identities=20%  Similarity=0.217  Sum_probs=21.9

Q ss_pred             CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcC
Q 041844           60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSG   92 (97)
Q Consensus        60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~g   92 (97)
                      ..+|+.|||+.+++++   ..+.|+.|.|--.|
T Consensus        33 ~~~si~elA~~~~vS~---sti~Rf~kkLG~~g   62 (77)
T PF01418_consen   33 AFMSISELAEKAGVSP---STIVRFCKKLGFSG   62 (77)
T ss_dssp             CT--HHHHHHHCTS-H---HHHHHHHHHCTTTC
T ss_pred             HHccHHHHHHHcCCCH---HHHHHHHHHhCCCC
Confidence            5789999999999955   78888888665544

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

>PRK00082 hrcA heat-inducible transcription repressor; Provisional

Probab=80.20  E-value=3.2  Score=32.87  Aligned_cols=36  Identities=14%  Similarity=0.194  Sum_probs=31.2

Q ss_pred             CCCCCCHHHHHHH--hCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           58 HTKPMTLNQLLGA--LQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        58 ~~gp~s~~ELA~~--~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      .++|.+..+||+.  +++.|   ..++|-|..|...|++..
T Consensus        22 ~~~pv~s~~l~~~~~l~~S~---aTIR~dm~~Le~~G~l~~   59 (339)
T PRK00082         22 TGEPVGSKTLSKRYGLGVSS---ATIRNDMADLEELGLLEK   59 (339)
T ss_pred             cCCCcCHHHHHHHhCCCCCh---HHHHHHHHHHHhCCCcCC
Confidence            4689999999977  77755   899999999999998863

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	97
1zg3_A	358	Crystal Structure Of The Isoflavanone 4'-O-Methyltr		3e-11
1zga_A	357	Crystal Structure Of Isoflavanone 4'-o-methyltransf		3e-11
1zgj_A	354	Crystal Structure Of Isoflavanone 4'-O-Methyltransf		3e-11
2qyo_A	357	Crystal Structure Of Isoflavone O-Methyltransferase		3e-10
1fp2_A	352	Crystal Structure Analysis Of Isoflavone O-Methyltr		1e-07
1fpx_A	352	Crystal Structure Analysis Of Selenomethionine Subs		2e-06

>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 = 63.5 bits (153), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 28/64 (43%), Positives = 45/64 (70%), Gaps = 2/64 (3%)
Query: 31 NTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVR 90
          + ++F++SM+LK    +++GI D IHNH KPMTL++L  +L++HP+K   LH  +  L  
Sbjct: 17 HVYNFVSSMALKSA--MELGIADAIHNHGKPMTLSELASSLKLHPSKVNILHRFLRLLTH 74
Query: 91 SGFF 94
          +GFF
Sbjct: 75 NGFF 78

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

Iteration: 1
 Score = 63.5 bits (153), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 28/64 (43%), Positives = 45/64 (70%), Gaps = 2/64 (3%)
Query: 31 NTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVR 90
          + ++F++SM+LK    +++GI D IHNH KPMTL++L  +L++HP+K   LH  +  L  
Sbjct: 16 HVYNFVSSMALKSA--MELGIADAIHNHGKPMTLSELASSLKLHPSKVNILHRFLRLLTH 73
Query: 91 SGFF 94
          +GFF
Sbjct: 74 NGFF 77

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

Iteration: 1
 Score = 63.5 bits (153), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 28/64 (43%), Positives = 45/64 (70%), Gaps = 2/64 (3%)
Query: 31 NTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVR 90
          + ++F++SM+LK    +++GI D IHNH KPMTL++L  +L++HP+K   LH  +  L  
Sbjct: 13 HVYNFVSSMALKSA--MELGIADAIHNHGKPMTLSELASSLKLHPSKVNILHRFLRLLTH 70
Query: 91 SGFF 94
          +GFF
Sbjct: 71 NGFF 74

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

Iteration: 1
 Score = 60.1 bits (144), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 35/87 (40%), Positives = 51/87 (58%), Gaps = 7/87 (8%)
Query: 10 NNSSDELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLG 69
          N    E+ +AQ L        N ++F++SMSLK    I++ IP+IIHNH KP+TL+ L+ 
Sbjct: 7  NRKPSEIFKAQAL-----LYKNMYAFVDSMSLKWS--IEMNIPNIIHNHGKPITLSNLVS 59
Query: 70 ALQIHPTKTRCLHFLVCSLVRSGFFNL 96
           LQI  TK   +  L+  L  +GFF +
Sbjct: 60 ILQIPSTKVDNVQRLMRYLAHNGFFEI 86

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

Iteration: 1
 Score = 51.2 bits (121), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 29/82 (35%), Positives = 49/82 (59%), Gaps = 7/82 (8%)
Query: 15 ELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIH 74
          E+ +AQ L        + ++FI+SMSLK    +++ IP+II NH KP++L+ L+  LQ+ 
Sbjct: 12 EIFKAQAL-----LYKHIYAFIDSMSLKWA--VEMNIPNIIQNHGKPISLSNLVSILQVP 64
Query: 75 PTKTRCLHFLVCSLVRSGFFNL 96
           +K   +  L+  L  +GFF +
Sbjct: 65 SSKIGNVRRLMRYLAHNGFFEI 86

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

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 28/82 (34%), Positives = 46/82 (56%), Gaps = 7/82 (8%)
Query: 15 ELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIH 74
          E+ +AQ L        + ++FI+S SLK    ++  IP+II NH KP++L+ L+  LQ+ 
Sbjct: 12 EIFKAQAL-----LYKHIYAFIDSXSLKWA--VEXNIPNIIQNHGKPISLSNLVSILQVP 64
Query: 75 PTKTRCLHFLVCSLVRSGFFNL 96
           +K   +  L   L  +GFF +
Sbjct: 65 SSKIGNVRRLXRYLAHNGFFEI 86

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	97
1zg3_A	358	Isoflavanone 4'-O-methyltransferase; rossman fold,	9e-20
1fp2_A	352	Isoflavone O-methyltransferase; protein-product co	2e-16
1fp1_D	372	Isoliquiritigenin 2'-O-methyltransferase; protein-	3e-14
3lst_A	348	CALO1 methyltransferase; calicheamicin, enediyne,	1e-13
3reo_A	368	(ISO)eugenol O-methyltransferase; directed evoluti	2e-13
2ip2_A	334	Probable phenazine-specific methyltransferase; pyo	2e-12
3gwz_A	369	MMCR; methyltransferase, mitomycin, S-adenosyl met	2e-12
3i53_A	332	O-methyltransferase; CO-complex, rossmann-like fol	3e-12
3p9c_A	364	Caffeic acid O-methyltransferase; S-adenosylmethio	4e-12
1qzz_A	374	RDMB, aclacinomycin-10-hydroxylase; anthracycline,	8e-12
1tw3_A	360	COMT, carminomycin 4-O-methyltransferase; anthracy	2e-11
3dp7_A	363	SAM-dependent methyltransferase; structural genomi	2e-10
1x19_A	359	CRTF-related protein; methyltransferase, bacterioc	4e-10
3mcz_A	352	O-methyltransferase; adomet_mtases, S-adenosylmeth	4e-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 = 80.7 bits (199), Expect = 9e-20
 Identities = 32/85 (37%), Positives = 51/85 (60%), Gaps = 7/85 (8%)

Query: 11 NSSDELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGA 70
          +   EL  AQ+         + ++F++SM+LK    +++GI D IHNH KPMTL++L  +
Sbjct: 2  SEESELYHAQIH-----LYKHVYNFVSSMALKSA--MELGIADAIHNHGKPMTLSELASS 54

Query: 71 LQIHPTKTRCLHFLVCSLVRSGFFN 95
          L++HP+K   LH  +  L  +GFF 
Sbjct: 55 LKLHPSKVNILHRFLRLLTHNGFFA 79

>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 = 71.3 bits (175), Expect = 2e-16
 Identities = 30/90 (33%), Positives = 49/90 (54%), Gaps = 7/90 (7%)

Query: 5  QSYGENNSSDELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTL 64
           S        E+ +AQ L        + ++FI+SMSLK    +++ IP+II NH KP++L
Sbjct: 2  ASSINGRKPSEIFKAQAL-----LYKHIYAFIDSMSLKWA--VEMNIPNIIQNHGKPISL 54

Query: 65 NQLLGALQIHPTKTRCLHFLVCSLVRSGFF 94
          + L+  LQ+  +K   +  L+  L  +GFF
Sbjct: 55 SNLVSILQVPSSKIGNVRRLMRYLAHNGFF 84

>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 = 65.3 bits (159), Expect = 3e-14
 Identities = 14/93 (15%), Positives = 27/93 (29%), Gaps = 13/93 (13%)

Query: 9  ENNSSDELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKP---MTLN 65
             S      A L       +  T + +    L     I + + +II   T P   M+ +
Sbjct: 14 SATSEQTEDSACLS-----AMVLTTNLVYPAVLNAA--IDLNLFEIIAKATPPGAFMSPS 66

Query: 66 QLLGALQIHPTKTRCLHFL---VCSLVRSGFFN 95
          ++   L      +   + L   +  L       
Sbjct: 67 EIASKLPASTQHSDLPNRLDRMLRLLASYSVLT 99

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

 Score = 63.8 bits (156), Expect = 1e-13
 Identities = 13/83 (15%), Positives = 26/83 (31%), Gaps = 12/83 (14%)

Query: 12 SSDELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGAL 71
             + LQ+ L        +    +  + +L+      VG+ D + +   P T  +L  A 
Sbjct: 15 GDMDRLQSAL-----ALYEEAMGYTYAAALRAA--AAVGVADHLVD--GPRTPAELAAAT 65

Query: 72 QIHPTKTRCLHFLVCSLVRSGFF 94
                   L  ++  L      
Sbjct: 66 GTDA---DALRRVLRLLAVRDVV 85

>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 = 62.9 bits (153), Expect = 2e-13
 Identities = 12/88 (13%), Positives = 30/88 (34%), Gaps = 11/88 (12%)

Query: 12 SSDELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKP---MTLNQLL 68
          +     +A L       +    + +  M+LK    I++ + +I+     P   ++  ++ 
Sbjct: 14 THSSDEEANLF-----AMQLASAAVLPMALKAA--IELDVLEIMAKSVPPSGYISPAEIA 66

Query: 69 GALQI-HPTKTRCLHFLVCSLVRSGFFN 95
            L   +P     L  ++  L       
Sbjct: 67 AQLPTTNPEAPVMLDRVLRLLASYSVVT 94

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

 Score = 60.0 bits (146), Expect = 2e-12
 Identities = 14/84 (16%), Positives = 27/84 (32%), Gaps = 14/84 (16%)

Query: 11 NSSDELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGA 70
          N+S+      L+               S  +      ++G+ D+I +     +   L  A
Sbjct: 2  NNSNLAAARNLIQVV-------TGEWKSRCVYVA--TRLGLADLIESG--IDSDETLAAA 50

Query: 71 LQIHPTKTRCLHFLVCSLVRSGFF 94
          +         +H L+  LV    F
Sbjct: 51 VGSDA---ERIHRLMRLLVAFEIF 71

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

 Score = 60.1 bits (146), Expect = 2e-12
 Identities = 16/87 (18%), Positives = 28/87 (32%), Gaps = 14/87 (16%)

Query: 9   ENNSSDELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLL 68
           EN  +     A+         D       + ++     +++G+P+++     P T   L 
Sbjct: 28  ENPGTAARAAAEE-----TVNDILQGAWKARAIHVA--VELGVPELLQEG--PRTATALA 78

Query: 69  GALQIHPTKT-RCLHFLVCSLVRSGFF 94
            A   H     R L  L       G F
Sbjct: 79  EATGAHEQTLRRLLRLLAT----VGVF 101

>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 = 59.6 bits (145), Expect = 3e-12
 Identities = 13/66 (19%), Positives = 21/66 (31%), Gaps = 7/66 (10%)

Query: 29 LDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSL 88
          L         M+++      + + D I       T  ++  A   H      L  L+  L
Sbjct: 10 LRALADLATPMAVRVA--ATLRVADHIAAG--HRTAAEIASAAGAHA---DSLDRLLRHL 62

Query: 89 VRSGFF 94
          V  G F
Sbjct: 63 VAVGLF 68

>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 = 59.4 bits (144), Expect = 4e-12
 Identities = 15/93 (16%), Positives = 33/93 (35%), Gaps = 10/93 (10%)

Query: 6  SYGENNSSDELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIH-NHTKPMTL 64
          S   + ++     A +       L    S +  M+LK    I++G+ +I+     K +T 
Sbjct: 7  STAADMAASADEDACMF-----ALQLASSSVLPMTLKNA--IELGLLEILVAAGGKSLTP 59

Query: 65 NQLLGAL--QIHPTKTRCLHFLVCSLVRSGFFN 95
           ++   L    +P     +  ++  L       
Sbjct: 60 TEVAAKLPSAANPEAPDMVDRILRLLASYNVVT 92

>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 = 58.6 bits (142), Expect = 8e-12
 Identities = 15/66 (22%), Positives = 23/66 (34%), Gaps = 7/66 (10%)

Query: 29 LDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSL 88
          L N  + +  M+L+      + + D +       TL  L      HP   + L  LV  L
Sbjct: 21 LKNLGNLVTPMALRVA--ATLRLVDHLLA--GADTLAGLADRTDTHP---QALSRLVRHL 73

Query: 89 VRSGFF 94
             G  
Sbjct: 74 TVVGVL 79

>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 = 57.3 bits (139), Expect = 2e-11
 Identities = 14/83 (16%), Positives = 23/83 (27%), Gaps = 13/83 (15%)

Query: 12 SSDELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGAL 71
          +  + + A         L    S    M ++      + + D I       T+  L    
Sbjct: 13 ARPQQIDALRT------LIRLGSLHTPMVVRTA--ATLRLVDHILAG--ARTVKALAART 62

Query: 72 QIHPTKTRCLHFLVCSLVRSGFF 94
             P     L  L+  LV  G  
Sbjct: 63 DTRP---EALLRLIRHLVAIGLL 82

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

 Score = 54.3 bits (131), Expect = 2e-10
 Identities = 8/63 (12%), Positives = 21/63 (33%), Gaps = 7/63 (11%)

Query: 33 FSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCL-HFLVCSLVRS 91
          F  +     +   +++ GI  ++    +  TL ++ G   +     + L    +      
Sbjct: 24 FGPVVFQVSRL--MLKFGIFQLLSGKREGYTLQEISGRTGLTRYAAQVLLEASLT----I 77

Query: 92 GFF 94
          G  
Sbjct: 78 GTI 80

>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 = 53.6 bits (129), Expect = 4e-10
 Identities = 13/85 (15%), Positives = 23/85 (27%), Gaps = 15/85 (17%)

Query: 12 SSDELLQAQ--LLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLG 69
          S+++LL                    I    +K    I++ +   +     P  L  L  
Sbjct: 23 SNNDLLNYYHRANELV------FKGLIEFSCMKAA--IELDLFSHMAE--GPKDLATLAA 72

Query: 70 ALQIHPTKTRCLHFLVCSLVRSGFF 94
               P +   L  L   L +    
Sbjct: 73 DTGSVPPRLEML--LET-LRQMRVI 94

>3mcz_A O-methyltransferase; adomet_mtases, S-adenosylmethionine-dependent methyltransfer structural genomics, PSI-2; HET: MSE; 1.90A {Burkholderia thailandensis} Length = 352

 Score = 42.4 bits (100), Expect = 4e-06
 Identities = 8/66 (12%), Positives = 18/66 (27%), Gaps = 8/66 (12%)

Query: 29 LDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSL 88
          +  +  +  S  L     +   + D+        T  ++  +  +   K      L   L
Sbjct: 29 VKLSDQYRQSAILHYA--VADKLFDLTQ---TGRTPAEVAASFGMVEGKAA--ILLHA-L 80

Query: 89 VRSGFF 94
             G  
Sbjct: 81 AALGLL 86

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	97
3p9c_A	364	Caffeic acid O-methyltransferase; S-adenosylmethio	99.64
1zg3_A	358	Isoflavanone 4'-O-methyltransferase; rossman fold,	99.56
1fp2_A	352	Isoflavone O-methyltransferase; protein-product co	99.55
3reo_A	368	(ISO)eugenol O-methyltransferase; directed evoluti	99.54
3dp7_A	363	SAM-dependent methyltransferase; structural genomi	99.49
4a6d_A	353	Hydroxyindole O-methyltransferase; melatonin, circ	99.49
1fp1_D	372	Isoliquiritigenin 2'-O-methyltransferase; protein-	99.45
3lst_A	348	CALO1 methyltransferase; calicheamicin, enediyne,	99.42
1x19_A	359	CRTF-related protein; methyltransferase, bacterioc	99.4
3gwz_A	369	MMCR; methyltransferase, mitomycin, S-adenosyl met	99.33
3i53_A	332	O-methyltransferase; CO-complex, rossmann-like fol	99.31
2ip2_A	334	Probable phenazine-specific methyltransferase; pyo	99.31
3mcz_A	352	O-methyltransferase; adomet_mtases, S-adenosylmeth	99.27
2r3s_A	335	Uncharacterized protein; methyltransferase domain,	99.24
1qzz_A	374	RDMB, aclacinomycin-10-hydroxylase; anthracycline,	99.19
1tw3_A	360	COMT, carminomycin 4-O-methyltransferase; anthracy	99.11
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	97.07
3mq0_A	275	Transcriptional repressor of the blcabc operon; he	97.01
2fu4_A	83	Ferric uptake regulation protein; DNA binding doma	96.96
3r0a_A	123	Putative transcriptional regulator; structural gen	96.69
1mkm_A	249	ICLR transcriptional regulator; structural genomic	96.68
2xrn_A	241	HTH-type transcriptional regulator TTGV; DNA-bindi	96.57
3r4k_A	260	Transcriptional regulator, ICLR family; DNA/RNA-bi	96.55
1y0u_A	96	Arsenical resistance operon repressor, putative; s	96.5
2y75_A	129	HTH-type transcriptional regulator CYMR; DNA bindi	96.48
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	96.42
2o0y_A	260	Transcriptional regulator; ICLR-family, structural	96.34
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	96.32
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	96.32
2kko_A	108	Possible transcriptional regulatory protein (possi	96.31
3jth_A	98	Transcription activator HLYU; transcription factor	96.29
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	96.27
2g7u_A	257	Transcriptional regulator; ICLR family, structural	96.25
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	96.25
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	96.25
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	96.23
2ia2_A	265	Putative transcriptional regulator; SAD, PSI-2, st	96.21
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	96.19
3f6o_A	118	Probable transcriptional regulator, ARSR family pr	96.05
1u2w_A	122	CADC repressor, cadmium efflux system accessory pr	96.03
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	96.01
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	95.88
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	95.82
1ku9_A	152	Hypothetical protein MJ223; putative transcription	95.81
2o03_A	131	Probable zinc uptake regulation protein FURB; DNA-	95.81
1ub9_A	100	Hypothetical protein PH1061; helix-turn-helix moti	95.79
1sfx_A	109	Conserved hypothetical protein AF2008; structural	95.78
2fe3_A	145	Peroxide operon regulator; oxidative stress regula	95.7
3fm5_A	150	Transcriptional regulator; MCSG, PF04017, PSI, MAR	95.69
3lwf_A	159	LIN1550 protein, putative transcriptional regulato	95.68
3boq_A	160	Transcriptional regulator, MARR family; MARR famil	95.67
2pg4_A	95	Uncharacterized protein; structural genomics, join	95.65
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	95.64
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	95.63
2hr3_A	147	Probable transcriptional regulator; MCSG, structur	95.62
1r1t_A	122	Transcriptional repressor SMTB; zinc, transcriptio	95.55
2nnn_A	140	Probable transcriptional regulator; structural gen	95.46
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	95.46
3nrv_A	148	Putative transcriptional regulator (MARR/EMRR FAM;	95.45
3t8r_A	143	Staphylococcus aureus CYMR; transcriptional regula	95.44
3jw4_A	148	Transcriptional regulator, MARR/EMRR family; DNA-b	95.42
2fbh_A	146	Transcriptional regulator PA3341; MARR, transcript	95.37
3f6v_A	151	Possible transcriptional regulator, ARSR family pr	95.35
2gxg_A	146	146AA long hypothetical transcriptional regulator;	95.34
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	95.34
2jsc_A	118	Transcriptional regulator RV1994C/MT2050; cadmium,	95.3
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	95.25
1mzb_A	136	Ferric uptake regulation protein; ferric uptake re	95.25
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	95.25
2xig_A	150	Ferric uptake regulation protein; hpfur, transcrip	95.21
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	95.13
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	95.13
1ylf_A	149	RRF2 family protein; structural genomics, transcri	95.11
2w25_A	150	Probable transcriptional regulatory protein; trans	95.09
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	95.07
3k0l_A	162	Repressor protein; helix-turn-helix, structural ge	95.04
3deu_A	166	Transcriptional regulator SLYA; MARR, WING-helix,	95.04
3bja_A	139	Transcriptional regulator, MARR family, putative;	95.04
2fbk_A	181	Transcriptional regulator, MARR family; winged-hel	95.01
3kp7_A	151	Transcriptional regulator TCAR; multiple drug resi	95.0
3k69_A	162	Putative transcription regulator; putative transcr	94.97
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	94.97
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	94.92
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	94.9
1xd7_A	145	YWNA; structural genomics, protein structure initi	94.83
3df8_A	111	Possible HXLR family transcriptional factor; APC89	94.79
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	94.75
3b73_A	111	PHIH1 repressor-like protein; winged-helix-turn-he	94.74
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	94.73
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	94.71
3g3z_A	145	NMB1585, transcriptional regulator, MARR family; t	94.71
3i4p_A	162	Transcriptional regulator, ASNC family; PSI, struc	94.7
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	94.68
3oop_A	143	LIN2960 protein; protein structure initiative, PSI	94.67
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	94.64
2hzt_A	107	Putative HTH-type transcriptional regulator YTCD;	94.64
1z7u_A	112	Hypothetical protein EF0647; winged-helix-turn-hel	94.62
3mwm_A	139	ZUR, putative metal uptake regulation protein; FUR	94.61
3u2r_A	168	Regulatory protein MARR; structural genomics, PSI-	94.61
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	94.6
3cdh_A	155	Transcriptional regulator, MARR family; helix-turn	94.53
3bj6_A	152	Transcriptional regulator, MARR family; helix-turn	94.51
1p6r_A	82	Penicillinase repressor; transcription regulation,	94.5
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	94.5
2eth_A	154	Transcriptional regulator, putative, MAR family; M	94.47
2a61_A	145	Transcriptional regulator TM0710; APC4350, MCSG, m	94.46
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	94.39
2rdp_A	150	Putative transcriptional regulator MARR; PFAM PF01	94.39
1lj9_A	144	Transcriptional regulator SLYA; HTH DNA binding pr	94.39
1uly_A	192	Hypothetical protein PH1932; helix-turn-helix, str	94.37
3f3x_A	144	Transcriptional regulator, MARR family, putative;	94.35
1on2_A	142	Transcriptional regulator MNTR; helix-turn-helix,	94.34
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	94.28
2w57_A	150	Ferric uptake regulation protein; gene regulation,	94.21
2qww_A	154	Transcriptional regulator, MARR family; YP_013417.	94.19
2bv6_A	142	MGRA, HTH-type transcriptional regulator MGRA; mul	94.18
4hbl_A	149	Transcriptional regulator, MARR family; HTH, trans	94.09
1xmk_A	79	Double-stranded RNA-specific adenosine deaminase;	94.01
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	94.0
1tbx_A	99	ORF F-93, hypothetical 11.0 kDa protein; sulfolobu	93.97
2g9w_A	138	Conserved hypothetical protein; DNA-binding domain	93.93
3nqo_A	189	MARR-family transcriptional regulator; structural	93.93
2fbi_A	142	Probable transcriptional regulator; MARR, APC5816,	93.89
1z91_A	147	Organic hydroperoxide resistance transcriptional;	93.85
3s2w_A	159	Transcriptional regulator, MARR family; structural	93.84
2p4w_A	202	Transcriptional regulatory protein ARSR family; ar	93.8
3cjn_A	162	Transcriptional regulator, MARR family; silicibact	93.74
2pex_A	153	Transcriptional regulator OHRR; transcription regu	93.74
2nyx_A	168	Probable transcriptional regulatory protein, RV14;	93.71
4aik_A	151	Transcriptional regulator SLYA; transcription, tra	93.69
3e6m_A	161	MARR family transcriptional regulator; APC88769, s	93.67
4fx0_A	148	Probable transcriptional repressor protein; helix-	93.43
2qvo_A	95	Uncharacterized protein AF_1382; PSI, structural g	93.33
2f2e_A	146	PA1607; transcription factor, helix-TRUN-helix, AP	93.29
2k4b_A	99	Transcriptional regulator; DNA binding protein, wi	93.23
1s3j_A	155	YUSO protein; structural genomics, MARR transcript	93.22
2hoe_A	380	N-acetylglucosamine kinase; TM1224, structural gen	93.17
3hsr_A	140	HTH-type transcriptional regulator SARZ; helix-tur	93.14
2frh_A	127	SARA, staphylococcal accessory regulator A; winged	93.05
2xvc_A	59	ESCRT-III, SSO0910; cell cycle, cell division, cyt	93.01
2qm3_A	373	Predicted methyltransferase; putative methyltransf	92.97
2wte_A	244	CSA3; antiviral protein, viral resistance, winged	92.97
2fsw_A	107	PG_0823 protein; alpha-beta structure, helix-turn-	92.84
1yyv_A	131	Putative transcriptional regulator; reductive meth	92.62
4b8x_A	147	SCO5413, possible MARR-transcriptional regulator;	92.55
2dk5_A	91	DNA-directed RNA polymerase III 39 kDa polypeptide	92.49
3eyy_A	145	Putative iron uptake regulatory protein; NUR, nick	92.47
1okr_A	123	MECI, methicillin resistance regulatory protein ME	92.46
4ets_A	162	Ferric uptake regulation protein; metal binding pr	92.3
2lnb_A	80	Z-DNA-binding protein 1; structural genomics, nort	92.3
2h09_A	155	Transcriptional regulator MNTR; transcription regu	92.29
2zkz_A	99	Transcriptional repressor PAGR; protein-DNA, HTH m	92.16
4g6q_A	182	Putative uncharacterized protein; structural genom	91.94
1j5y_A	187	Transcriptional regulator, biotin repressor famil;	91.8
4a5n_A	131	Uncharacterized HTH-type transcriptional regulato;	91.74
3hrs_A	214	Metalloregulator SCAR; DTXR/MNTR family member, tr	90.96
1bja_A	95	Transcription regulatory protein MOTA; activation	90.9
1sd4_A	126	Penicillinase repressor; BLAI, MECI, methicillin,	90.83
1z6r_A	406	MLC protein; transcriptional repressor, ROK family	90.78
2obp_A	96	Putative DNA-binding protein; structural genomics,	90.75
2fxa_A	207	Protease production regulatory protein HPR; protea	90.67
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	90.6
2oz6_A	207	Virulence factor regulator; winged helix, helix-tu	90.32
3dv8_A	220	Transcriptional regulator, CRP/FNR family; cyclic	90.25
2vn2_A	128	DNAD, chromosome replication initiation protein; D	90.01
2yu3_A	95	DNA-directed RNA polymerase III 39 kDa polypeptide	89.81
3e97_A	231	Transcriptional regulator, CRP/FNR family; YP_6044	89.78
3u1d_A	151	Uncharacterized protein; GNTR-superfamily, structu	89.57
3ryp_A	210	Catabolite gene activator; CAMP receptor protein (	89.55
1z05_A	429	Transcriptional regulator, ROK family; structural	89.45
2qlz_A	232	Transcription factor PF0095; 2.50A {Pyrococcus fur	89.42
2gau_A	232	Transcriptional regulator, CRP/FNR family; structu	89.37
2fmy_A	220	COOA, carbon monoxide oxidation system transcripti	89.36
1ft9_A	222	Carbon monoxide oxidation system transcription reg	89.26
2zcw_A	202	TTHA1359, transcriptional regulator, FNR/CRP famil	89.14
3iwz_A	230	CAP-like, catabolite activation-like protein; XCC,	89.14
3d0s_A	227	Transcriptional regulatory protein; CAMP receptor	89.08
4ev0_A	216	Transcription regulator, CRP family; CAMP binding,	88.73
1jhg_A	101	Trp operon repressor; complex (regulatory protein-	88.49
1r7j_A	95	Conserved hypothetical protein SSO10A; winged heli	88.32
3dkw_A	227	DNR protein; CRP-FNR, HTH, beta barrel, dimerizati	88.27
3b02_A	195	Transcriptional regulator, CRP family; structural	88.23
3la7_A	243	Global nitrogen regulator; activator, DNA-binding,	88.09
3e6c_C	250	CPRK, cyclic nucleotide-binding protein; CPRK, hal	87.96
1zyb_A	232	Transcription regulator, CRP family; NP_813211.1,	87.93
1v4r_A	102	Transcriptional repressor; helix-turn-helix, winge	87.16
3cta_A	230	Riboflavin kinase; structural genomics, transferas	87.08
2esh_A	118	Conserved hypothetical protein TM0937; APC5794, st	86.09
2gqq_A	163	Leucine-responsive regulatory protein; helix-turn-	85.67
2w48_A	315	Sorbitol operon regulator; SORC, activator, repres	85.62
3kcc_A	260	Catabolite gene activator; helix-turn-helix, CAMP,	85.53
2bgc_A	238	PRFA; bacterial infection, human pathogen, transcr	85.18
2v79_A	135	DNA replication protein DNAD; primosome, DNA-bindi	84.82
1hsj_A	487	Fusion protein consisting of staphylococcus access	84.12
4ham_A	134	LMO2241 protein; structural genomics, PSI-biology,	83.8
3fx3_A	237	Cyclic nucleotide-binding protein; helix_TURN_heli	83.67
4esf_A	117	PADR-like transcriptional regulator; PADR family,	83.41
2b0l_A	102	GTP-sensing transcriptional pleiotropic repressor;	83.36
1p4x_A	250	Staphylococcal accessory regulator A homologue; wi	83.33
3tqn_A	113	Transcriptional regulator, GNTR family; regulatory	83.07
1o5l_A	213	Transcriptional regulator, CRP family; TM1171, str	82.45
1stz_A	338	Heat-inducible transcription repressor HRCA homol;	81.98
3oio_A	113	Transcriptional regulator (ARAC-type DNA-binding c	81.89
3mn2_A	108	Probable ARAC family transcriptional regulator; st	81.74
3iwf_A	107	Transcription regulator RPIR family; transcription	81.63
2o3f_A	111	Putative HTH-type transcriptional regulator YBBH;	81.24
3f8b_A	116	Transcriptional regulator, PADR-like family; winge	80.95
3oou_A	108	LIN2118 protein; protein structure initiative, PSI	80.73
2ek5_A	129	Predicted transcriptional regulators; helix-turn-h	80.71
1bia_A	321	BIRA bifunctional protein; transcription regulatio	80.09
3by6_A	126	Predicted transcriptional regulator; structural ge	80.03

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

Probab=99.64  E-value=2.3e-16  Score=121.05  Aligned_cols=83  Identities=17%  Similarity=0.204  Sum_probs=71.7

Q ss_pred             ccCCCCcHHHHHHHHHhccCcchhhHHhHHHHHHHHHHHHHhcChhHHHhhCC-CCCCHHHHHHHhCC--CCCCcccHHH
Q 041844            7 YGENNSSDELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHT-KPMTLNQLLGALQI--HPTKTRCLHF   83 (97)
Q Consensus         7 ~~~~~~~~~~~~~~~~~~~~p~~~l~~~~~~s~aL~~a~~veLgI~D~La~~~-gp~s~~ELA~~~g~--~~~~~~~L~R   83 (97)
                      +++....+|+.+++.++     ++++++++.+++|++|  ++|||||+|++++ +|+|++|||+++|+  +|.++..|+|
T Consensus         8 ~~~~~~~~~~~~~~~~~-----~~l~~~~~~~~~l~~a--~~Lgifd~L~~~g~~~~t~~eLA~~~g~~~~~~~~~~l~r   80 (364)
T 3p9c_A            8 TAADMAASADEDACMFA-----LQLASSSVLPMTLKNA--IELGLLEILVAAGGKSLTPTEVAAKLPSAANPEAPDMVDR   80 (364)
T ss_dssp             -----CHHHHHHHHHHH-----HHHTTTTHHHHHHHHH--HHHTHHHHHHHTTTCCBCHHHHHHTTTCTTCTTHHHHHHH
T ss_pred             CCCCccchHHHHHHHHH-----HHHHHhHHHHHHHHHH--HHCChHHHHhhcCCCCCCHHHHHHhcCCCCCccchhhHHH
Confidence            34444778899999999     9999999999999999  9999999999875 79999999999997  7744559999


Q ss_pred             HHHHHHhcCcccc
Q 041844           84 LVCSLVRSGFFNL   96 (97)
Q Consensus        84 lLR~Laa~gif~e   96 (97)
                      +||+|++.|+|++
T Consensus        81 lLr~L~~~g~l~~   93 (364)
T 3p9c_A           81 ILRLLASYNVVTC   93 (364)
T ss_dssp             HHHHHHHTTSEEE
T ss_pred             HHHHHHhCCCEEE
Confidence            9999999999975

>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=99.56  E-value=1.6e-15  Score=115.01  Aligned_cols=77  Identities=42%  Similarity=0.736  Sum_probs=70.5

Q ss_pred             cHHHHHHHHHhccCcchhhHHhHHHHHHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcC
Q 041844           13 SDELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSG   92 (97)
Q Consensus        13 ~~~~~~~~~~~~~~p~~~l~~~~~~s~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~g   92 (97)
                      +++.++++.++     ++++++++.+++|+++  ++|||||+|+++++|+|++|||+++|++|.+++.|+|+||+|++.|
T Consensus         4 ~~~~~~~~~~l-----~~~~~~~~~~~~l~~a--~~lgif~~L~~~~~~~t~~eLA~~~g~~~~~~~~l~rlLr~L~~~g   76 (358)
T 1zg3_A            4 ESELYHAQIHL-----YKHVYNFVSSMALKSA--MELGIADAIHNHGKPMTLSELASSLKLHPSKVNILHRFLRLLTHNG   76 (358)
T ss_dssp             TSCCTTHHHHH-----HHHHTTHHHHHHHHHH--HHHTHHHHHHHHTSCEEHHHHHHHTTCCTTTHHHHHHHHHHHHHTT
T ss_pred             hHHhhhHHHHH-----HHHHHHHHHHHHHHHH--HHCChHhHHhhcCCCcCHHHHHHhcCCCCcchHHHHHHHHHHhhCC
Confidence            35677888899     9999999999999999  9999999998866799999999999998767899999999999999


Q ss_pred             cccc
Q 041844           93 FFNL   96 (97)
Q Consensus        93 if~e   96 (97)
                      +|++
T Consensus        77 ll~~   80 (358)
T 1zg3_A           77 FFAK   80 (358)
T ss_dssp             SEEE
T ss_pred             cEEE
Confidence            9975

>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=99.55  E-value=3.8e-15  Score=112.74  Aligned_cols=81  Identities=36%  Similarity=0.651  Sum_probs=72.8

Q ss_pred             CCCCcHHHHHHHHHhccCcchhhHHhHHHHHHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHH
Q 041844            9 ENNSSDELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSL   88 (97)
Q Consensus         9 ~~~~~~~~~~~~~~~~~~p~~~l~~~~~~s~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~L   88 (97)
                      |..+.++.++++..+     ++++++++.+++|+++  ++|||||+|+.+++|+|++|||+++|++|.+++.|+|+||+|
T Consensus         6 ~~~~~~~~~~a~~~l-----~~~~~~~~~~~~l~~a--~~lgif~~L~~~~~~~t~~ela~~~~~~~~~~~~l~rlLr~L   78 (352)
T 1fp2_A            6 NGRKPSEIFKAQALL-----YKHIYAFIDSMSLKWA--VEMNIPNIIQNHGKPISLSNLVSILQVPSSKIGNVRRLMRYL   78 (352)
T ss_dssp             --CCSTHHHHHHHHH-----HHHHTTHHHHHHHHHH--HHTTHHHHHHHHTSCEEHHHHHHHHTCCGGGHHHHHHHHHHH
T ss_pred             cCCChHHHhhHHHHH-----HHHHHHHHHHHHHHHH--HHCChhhhhhhcCCCccHHHHHHHhCcCCCChHHHHHHHHHH
Confidence            445567899999999     9999999999999999  999999999886679999999999999876678999999999


Q ss_pred             HhcCcccc
Q 041844           89 VRSGFFNL   96 (97)
Q Consensus        89 aa~gif~e   96 (97)
                      ++.|+|++
T Consensus        79 ~~~gll~~   86 (352)
T 1fp2_A           79 AHNGFFEI   86 (352)
T ss_dssp             HHTTSEEE
T ss_pred             HhCCeEEE
Confidence            99999975

>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=99.54  E-value=4.8e-15  Score=113.67  Aligned_cols=78  Identities=14%  Similarity=0.210  Sum_probs=67.5

Q ss_pred             CcHHHHHHHHHhccCcchhhHHhHHHHHHHHHHHHHhcChhHHHhhC---CCCCCHHHHHHHhC-CCCCCcccHHHHHHH
Q 041844           12 SSDELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNH---TKPMTLNQLLGALQ-IHPTKTRCLHFLVCS   87 (97)
Q Consensus        12 ~~~~~~~~~~~~~~~p~~~l~~~~~~s~aL~~a~~veLgI~D~La~~---~gp~s~~ELA~~~g-~~~~~~~~L~RlLR~   87 (97)
                      +..++.+++.++     ++++++++.+++|++|  ++|||||+|+++   ++|+|++|||+++| .+|.++..|+|+||+
T Consensus        14 ~~~~~~~~~~~~-----~~l~~~~~~~~~l~~a--~~Lglfd~L~~~~gp~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~   86 (368)
T 3reo_A           14 THSSDEEANLFA-----MQLASAAVLPMALKAA--IELDVLEIMAKSVPPSGYISPAEIAAQLPTTNPEAPVMLDRVLRL   86 (368)
T ss_dssp             ---CHHHHHHHH-----HHHHTTTHHHHHHHHH--HHTTHHHHHHHHCCTTCCBCHHHHHTTSSCCCTTHHHHHHHHHHH
T ss_pred             CchHHHHHHHHH-----HHHHHHHHHHHHHHHH--HHCCchhHHhhcCCCCCCcCHHHHHHhcCcCCCcchhhHHHHHHH
Confidence            445788889999     9999999999999999  999999999884   36899999999998 466445699999999


Q ss_pred             HHhcCcccc
Q 041844           88 LVRSGFFNL   96 (97)
Q Consensus        88 Laa~gif~e   96 (97)
                      |++.|+|++
T Consensus        87 L~~~gll~~   95 (368)
T 3reo_A           87 LASYSVVTY   95 (368)
T ss_dssp             HHHTTSEEE
T ss_pred             HHhCCCeEE
Confidence            999999975

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

Probab=99.49  E-value=1.6e-14  Score=110.23  Aligned_cols=73  Identities=16%  Similarity=0.190  Sum_probs=67.7

Q ss_pred             HHHHHHHHHhccCcchhhHHhHHHHHHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCc
Q 041844           14 DELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGF   93 (97)
Q Consensus        14 ~~~~~~~~~~~~~p~~~l~~~~~~s~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gi   93 (97)
                      .+.++++.++     ++++++++.+++|+++  ++|||||+|+.+++|+|++|||+++|++|   ..|+|+||+|++.|+
T Consensus        10 ~~~~~a~~~l-----~~l~~g~~~~~~l~~a--~~lgifd~L~~~~~~~t~~eLA~~~g~~~---~~l~rlLr~l~~~g~   79 (363)
T 3dp7_A           10 CTAAEAQRLA-----QEIAFGPVVFQVSRLM--LKFGIFQLLSGKREGYTLQEISGRTGLTR---YAAQVLLEASLTIGT   79 (363)
T ss_dssp             CCSTTHHHHH-----HHHHHHHHHHHHHHHH--HHTTHHHHHHTCTTCBCHHHHHHHHTCCH---HHHHHHHHHHHHHTS
T ss_pred             hhHHHHHHHH-----HHHHhhHHHHHHHHHH--HHhCHHHHHHhcCCCCCHHHHHHHhCcCH---HHHHHHHHHHhhCCC
Confidence            4677899999     9999999999999999  99999999987678999999999999955   899999999999999


Q ss_pred             ccc
Q 041844           94 FNL   96 (97)
Q Consensus        94 f~e   96 (97)
                      |++
T Consensus        80 l~~   82 (363)
T 3dp7_A           80 ILL   82 (363)
T ss_dssp             EEE
T ss_pred             eEe
Confidence            975

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

Probab=99.49  E-value=2.8e-14  Score=109.02  Aligned_cols=68  Identities=18%  Similarity=0.226  Sum_probs=62.2

Q ss_pred             HHHHHhccCcchhhHHhHHHHHHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           18 QAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        18 ~~~~~~~~~p~~~l~~~~~~s~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++...+     ++++.||+.|++|++|  ++|||||+|+++++|+|+.|||+++|++|   ..++|+||+|++.|+|+
T Consensus         7 ~~~~~L-----~~l~~Gf~~s~~L~aa--~eLglfd~L~~~~~p~t~~eLA~~~g~~~---~~l~rlLr~L~~~gll~   74 (353)
T 4a6d_A            7 QAYRLL-----NDYANGFMVSQVLFAA--CELGVFDLLAEAPGPLDVAAVAAGVRASA---HGTELLLDICVSLKLLK   74 (353)
T ss_dssp             HHHHHH-----HHHHHHHHHHHHHHHH--HHHTHHHHHHHSSSCBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHH-----HHHHHHHHHHHHHHHH--HHcCHHHHHhcCCCCCCHHHHHHhhCcCH---HHHHHHHHHHHHCCCEE
Confidence            455566     7889999999999999  99999999998889999999999999954   99999999999999986

>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=99.45  E-value=4.8e-14  Score=107.54  Aligned_cols=78  Identities=17%  Similarity=0.189  Sum_probs=66.4

Q ss_pred             CcHHHHHHHHHhccCcch--hhHHhHHHHHHHHHHHHHhcChhHHHhhCCCC---CCHHHHHHHhCC---CCCCcccHHH
Q 041844           12 SSDELLQAQLLNCANPCL--DNTFSFINSMSLKCVKLIQVGIPDIIHNHTKP---MTLNQLLGALQI---HPTKTRCLHF   83 (97)
Q Consensus        12 ~~~~~~~~~~~~~~~p~~--~l~~~~~~s~aL~~a~~veLgI~D~La~~~gp---~s~~ELA~~~g~---~~~~~~~L~R   83 (97)
                      ..++.++++..+     |  +++++++.+++|+++  ++|||||+|+++++|   +|++|||+++|+   +|.+++.|+|
T Consensus        15 ~~~~~~~~~~~l-----~~~~l~~~~~~~~~l~~a--~~lgif~~L~~~g~pg~~~t~~eLA~~~~~~~~~~~~~~~l~r   87 (372)
T 1fp1_D           15 ATSEQTEDSACL-----SAMVLTTNLVYPAVLNAA--IDLNLFEIIAKATPPGAFMSPSEIASKLPASTQHSDLPNRLDR   87 (372)
T ss_dssp             ----CCHHHHHH-----HHHHHHHTTHHHHHHHHH--HHTTHHHHHHTCSSTTCCBCHHHHHTTSCGGGCCTTHHHHHHH
T ss_pred             chhhhhhHHHHH-----HHHHHHHHHHHHHHHHHH--HHCChHHHHHhcCCCCCCcCHHHHHHhcCCCCCCCcChHHHHH
Confidence            344567788888     8  999999999999999  999999999874336   999999999999   7666789999


Q ss_pred             HHHHHHhcCcccc
Q 041844           84 LVCSLVRSGFFNL   96 (97)
Q Consensus        84 lLR~Laa~gif~e   96 (97)
                      +||+|++.|+|++
T Consensus        88 lLr~L~~~gll~~  100 (372)
T 1fp1_D           88 MLRLLASYSVLTS  100 (372)
T ss_dssp             HHHHHHHTTSEEE
T ss_pred             HHHHHhhCCceEe
Confidence            9999999999975

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

Probab=99.42  E-value=1.3e-13  Score=104.39  Aligned_cols=73  Identities=18%  Similarity=0.241  Sum_probs=64.8

Q ss_pred             CcHHHHHHHHHhccCcchhhHHhHHHHHHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhc
Q 041844           12 SSDELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRS   91 (97)
Q Consensus        12 ~~~~~~~~~~~~~~~p~~~l~~~~~~s~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~   91 (97)
                      ++-...++...+     ++++++++.+++|++|  ++|||||+|++  +|+|++|||+++|++|   ..|+|+||+|++.
T Consensus        15 ~~~~~~~~~~~l-----~~~~~~~~~~~~l~~a--~~lglf~~l~~--g~~t~~elA~~~g~~~---~~l~rlLr~l~~~   82 (348)
T 3lst_A           15 GDMDRLQSALAL-----YEEAMGYTYAAALRAA--AAVGVADHLVD--GPRTPAELAAATGTDA---DALRRVLRLLAVR   82 (348)
T ss_dssp             -CCCHHHHHHHH-----HHHHTTHHHHHHHHHH--HHHTGGGGGTT--SCBCHHHHHHHHTCCH---HHHHHHHHHHHHT
T ss_pred             CCCCCchHHHHH-----HHHHHHHHHHHHHHHH--HHcCchhHhhC--CCCCHHHHHHHhCcCH---HHHHHHHHHHHhC
Confidence            333455788888     9999999999999999  99999999965  7999999999999955   8999999999999


Q ss_pred             Ccccc
Q 041844           92 GFFNL   96 (97)
Q Consensus        92 gif~e   96 (97)
                      |+|++
T Consensus        83 g~l~~   87 (348)
T 3lst_A           83 DVVRE   87 (348)
T ss_dssp             TSEEE
T ss_pred             CCEEe
Confidence            99975

>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=99.40  E-value=2.8e-13  Score=102.50  Aligned_cols=74  Identities=22%  Similarity=0.262  Sum_probs=66.7

Q ss_pred             CCcHHHHHHHHHhccCcchhhHH-hHHHHHHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHH
Q 041844           11 NSSDELLQAQLLNCANPCLDNTF-SFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLV   89 (97)
Q Consensus        11 ~~~~~~~~~~~~~~~~p~~~l~~-~~~~s~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~La   89 (97)
                      +++++.++++.++     +++++ +++.+++|+++  ++|||||+|++  +|+|++|||+++|+++   ..|+|+||+|+
T Consensus        22 ~~~~~~~~~~~~~-----~~~~~~~~~~~~~l~~a--~~lgif~~L~~--~~~t~~eLA~~~g~~~---~~l~rlLr~L~   89 (359)
T 1x19_A           22 MSNNDLLNYYHRA-----NELVFKGLIEFSCMKAA--IELDLFSHMAE--GPKDLATLAADTGSVP---PRLEMLLETLR   89 (359)
T ss_dssp             ECCCHHHHHHHHH-----HHHHTHHHHHHHHHHHH--HHHTHHHHHTT--CCBCHHHHHHHHTCCH---HHHHHHHHHHH
T ss_pred             CCccccCCcchHH-----HHHHHHHHHHHHHHHHH--HHcCcHHHHcC--CCCCHHHHHHHhCcCh---HHHHHHHHHHH
Confidence            3456778888888     99887 89999999999  99999999975  8999999999999954   99999999999


Q ss_pred             hcCcccc
Q 041844           90 RSGFFNL   96 (97)
Q Consensus        90 a~gif~e   96 (97)
                      +.|+|++
T Consensus        90 ~~gll~~   96 (359)
T 1x19_A           90 QMRVINL   96 (359)
T ss_dssp             HTTSEEE
T ss_pred             hCCCeEe
Confidence            9999975

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

Probab=99.33  E-value=1.9e-12  Score=98.86  Aligned_cols=69  Identities=20%  Similarity=0.275  Sum_probs=62.2

Q ss_pred             HHHHHHHhccCcchhhHHhHHHHHHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           16 LLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        16 ~~~~~~~~~~~p~~~l~~~~~~s~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .......+     ++++++++.+++|+++  ++|||||+|++  +|+|++|||+++|++|   ..|+|+||+|++.|+|+
T Consensus        35 ~~~~~~~l-----~~l~~~~~~~~~l~~a--~~lglf~~l~~--g~~t~~eLA~~~g~~~---~~l~rlLr~L~~~g~l~  102 (369)
T 3gwz_A           35 RAAAEETV-----NDILQGAWKARAIHVA--VELGVPELLQE--GPRTATALAEATGAHE---QTLRRLLRLLATVGVFD  102 (369)
T ss_dssp             HHHHHHHH-----HHHHHHHHHHHHHHHH--HHHTTGGGGTT--SCEEHHHHHHHHTCCH---HHHHHHHHHHHHTTSSE
T ss_pred             CChHHHHH-----HHHHHHHHHHHHHHHH--HHCChhhhhcC--CCCCHHHHHHHHCcCH---HHHHHHHHHHHhCCCEE
Confidence            33556667     9999999999999999  99999999974  7999999999999955   89999999999999998


Q ss_pred             c
Q 041844           96 L   96 (97)
Q Consensus        96 e   96 (97)
                      +
T Consensus       103 ~  103 (369)
T 3gwz_A          103 D  103 (369)
T ss_dssp             E
T ss_pred             E
Confidence            6

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

Probab=99.31  E-value=1.7e-12  Score=97.10  Aligned_cols=62  Identities=21%  Similarity=0.269  Sum_probs=57.8

Q ss_pred             chhhHHhHHHHHHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           28 CLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        28 ~~~l~~~~~~s~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      +++++.+++.+++|++|  ++|||||+|++  ||+|++|||+++|++|   ..|+|+||+|++.|+|.+
T Consensus         9 l~~~~~g~~~~~~l~~a--~~lglf~~l~~--g~~t~~elA~~~~~~~---~~l~rlLr~l~~~gl~~~   70 (332)
T 3i53_A            9 GLRALADLATPMAVRVA--ATLRVADHIAA--GHRTAAEIASAAGAHA---DSLDRLLRHLVAVGLFTR   70 (332)
T ss_dssp             CHHHHTCCHHHHHHHHH--HHHTHHHHHHT--TCCBHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHhhHHHHHHHHH--HHcChHHHHhc--CCCCHHHHHHHHCcCH---HHHHHHHHHHHhCCcEEe
Confidence            38889999999999999  99999999975  7999999999999955   899999999999999976

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

Probab=99.31  E-value=3.4e-12  Score=95.13  Aligned_cols=61  Identities=18%  Similarity=0.166  Sum_probs=57.4

Q ss_pred             hhhHHhHHHHHHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           29 LDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        29 ~~l~~~~~~s~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      ++++++++.+++|+++  ++|||||+|++  +|+|++|||+++|+++   +.|+|+||+|++.|+|++
T Consensus        13 ~~~~~~~~~~~~l~~~--~~lgi~~~l~~--~~~t~~ela~~~~~~~---~~l~r~Lr~L~~~g~l~~   73 (334)
T 2ip2_A           13 IQVVTGEWKSRCVYVA--TRLGLADLIES--GIDSDETLAAAVGSDA---ERIHRLMRLLVAFEIFQG   73 (334)
T ss_dssp             HHHHHHHHHHHHHHHH--HHTTHHHHHHT--TCCSHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHHHHHHH--HHcCcHHHHhC--CCCCHHHHHHHhCcCH---HHHHHHHHHHHhCCceEe
Confidence            8899999999999999  99999999965  7999999999999955   999999999999999975

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

Probab=99.27  E-value=1.6e-12  Score=97.55  Aligned_cols=60  Identities=13%  Similarity=0.141  Sum_probs=56.1

Q ss_pred             hhhHHhHHHHHHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           29 LDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        29 ~~l~~~~~~s~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      ++++++++.+++|+++  ++|||||+|+  + |+|++|||+++|++|   ..|+|+||+|++.|+|++
T Consensus        29 ~~~~~~~~~~~~l~~a--~~lgif~~l~--~-~~t~~elA~~~~~~~---~~l~rlLr~L~~~gll~~   88 (352)
T 3mcz_A           29 VKLSDQYRQSAILHYA--VADKLFDLTQ--T-GRTPAEVAASFGMVE---GKAAILLHALAALGLLTK   88 (352)
T ss_dssp             HHHHHTHHHHHHHHHH--HHTTHHHHTT--S-CBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHHHHHHH--HHCChHHHhC--C-CCCHHHHHHHhCcCh---HHHHHHHHHHHHCCCeEe
Confidence            8889999999999999  9999999994  3 999999999999955   899999999999999975

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

Probab=99.24  E-value=6.1e-12  Score=93.24  Aligned_cols=61  Identities=18%  Similarity=0.246  Sum_probs=56.9

Q ss_pred             hhhHHhHHHHHHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           29 LDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        29 ~~l~~~~~~s~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      ++++++++.+++|+++  ++|||||+|++  +|+|++|||+++|+++   +.|+|+||+|++.|+|++
T Consensus        11 ~~~~~~~~~~~~l~~~--~~l~i~~~l~~--~~~t~~ela~~~~~~~---~~l~r~L~~L~~~g~l~~   71 (335)
T 2r3s_A           11 FNTVNAYQRSAAIKAA--VELNVFTAISQ--GIESSQSLAQKCQTSE---RGMRMLCDYLVIIGFMTK   71 (335)
T ss_dssp             HHHHTTHHHHHHHHHH--HHTTHHHHHTT--SEECHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHHHHHHH--HHcChHHHHhc--CCCCHHHHHHHhCCCc---hHHHHHHHHHHhcCCeEe
Confidence            7888899999999999  99999999975  7999999999999954   999999999999999964

>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=99.19  E-value=2.4e-11  Score=91.57  Aligned_cols=61  Identities=25%  Similarity=0.303  Sum_probs=57.0

Q ss_pred             hhhHHhHHHHHHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           29 LDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        29 ~~l~~~~~~s~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      ++++++++.+++|+++  ++|||||+|+.  +|+|++|||+++|+++   ..|+|+||+|++.|+|.+
T Consensus        21 ~~~~~~~~~~~~l~~~--~~l~i~~~l~~--~~~t~~eLA~~~g~~~---~~l~r~Lr~L~~~Gll~~   81 (374)
T 1qzz_A           21 LKNLGNLVTPMALRVA--ATLRLVDHLLA--GADTLAGLADRTDTHP---QALSRLVRHLTVVGVLEG   81 (374)
T ss_dssp             HHTTTCCHHHHHHHHH--HHTTHHHHHHT--TCCSHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEC
T ss_pred             HHHHHhhHHHHHHHHH--HHcChHHHHhC--CCCCHHHHHHHhCcCH---HHHHHHHHHHhhCCCEEE
Confidence            7888999999999999  99999999954  7999999999999954   999999999999999976

>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=99.11  E-value=5.7e-11  Score=89.32  Aligned_cols=61  Identities=21%  Similarity=0.221  Sum_probs=56.9

Q ss_pred             hhhHHhHHHHHHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           29 LDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        29 ~~l~~~~~~s~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      ++++++++.+++|+++  ++|||||+|+.  +|+|++|||+++|+++   ..++|+||+|++.|+|++
T Consensus        24 ~~~~~~~~~~~~l~~~--~~l~i~~~l~~--~~~t~~ela~~~~~~~---~~l~r~L~~L~~~g~~~~   84 (360)
T 1tw3_A           24 LIRLGSLHTPMVVRTA--ATLRLVDHILA--GARTVKALAARTDTRP---EALLRLIRHLVAIGLLEE   84 (360)
T ss_dssp             HHHHHCSHHHHHHHHH--HHTTHHHHHHT--TCCBHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHhHHHHHHHHHH--HHhCHHHHHhC--CCCCHHHHHHHhCcCH---HHHHHHHHHHHHCCCEEe
Confidence            7889999999999999  99999999954  8999999999999954   999999999999999975

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

Probab=97.07  E-value=0.00027  Score=42.42  Aligned_cols=45  Identities=16%  Similarity=0.281  Sum_probs=38.3

Q ss_pred             hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      +..|.++|.++++|+|..|||+.+|++.   ..+.|++..|...|++.
T Consensus        12 ~~~IL~~L~~~~~~~s~~eLA~~lglsr---~tv~~~l~~L~~~G~I~   56 (67)
T 2heo_A           12 EQKILQVLSDDGGPVAIFQLVKKCQVPK---KTLNQVLYRLKKEDRVS   56 (67)
T ss_dssp             HHHHHHHHHHHCSCEEHHHHHHHHCSCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHcCCCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCcEe
Confidence            4457788877667999999999999954   89999999999999864

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

Probab=97.01  E-value=0.00046  Score=51.16  Aligned_cols=45  Identities=18%  Similarity=0.258  Sum_probs=38.4

Q ss_pred             cChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           49 VGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        49 LgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      +.|.+.++.+++++|+.|||+++|++.   ..++|+|+.|+..|++..
T Consensus        33 l~IL~~l~~~~~~ltl~eia~~lgl~k---sTv~RlL~tL~~~G~v~~   77 (275)
T 3mq0_A           33 VRILDLVAGSPRDLTAAELTRFLDLPK---SSAHGLLAVMTELDLLAR   77 (275)
T ss_dssp             HHHHHHHHHCSSCEEHHHHHHHHTCC-----CHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHhhCCCCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEE
Confidence            367888888778999999999999955   899999999999999864

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

Probab=96.96  E-value=0.00042  Score=42.11  Aligned_cols=46  Identities=11%  Similarity=0.213  Sum_probs=38.3

Q ss_pred             HhcChhHHHhhCC-CCCCHHHHHHHh-----CCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHT-KPMTLNQLLGAL-----QIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~-gp~s~~ELA~~~-----g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .+..|.+.|.+++ ++.|+.||++.+     ++   +...++|.|..|+..|++.
T Consensus        18 ~r~~IL~~l~~~~~~~~s~~el~~~l~~~~~~i---s~~TVyR~L~~L~~~Glv~   69 (83)
T 2fu4_A           18 PRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEI---GLATVYRVLNQFDDAGIVT   69 (83)
T ss_dssp             HHHHHHHHHTSGGGSSBCHHHHHHHHHHTTCCC---CHHHHHHHHHHHHHHTSEE
T ss_pred             HHHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCC---CHhhHHHHHHHHHHCCCeE
Confidence            3455778887665 799999999999     77   4489999999999999875

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

Probab=96.69  E-value=0.00094  Score=43.92  Aligned_cols=46  Identities=11%  Similarity=0.159  Sum_probs=38.7

Q ss_pred             HhcChhHHHhhCCCC-CCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKP-MTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp-~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .+..|...|.++++| +|+.|||+.++++   ...++|.++.|...|++.
T Consensus        27 ~e~~il~~L~~~~~~~~t~~eLa~~l~~s---~sTV~r~L~~L~~~GlV~   73 (123)
T 3r0a_A           27 ADLNVMKSFLNEPDRWIDTDALSKSLKLD---VSTVQRSVKKLHEKEILQ   73 (123)
T ss_dssp             HHHHHHHHHHHSTTCCEEHHHHHHHHTSC---HHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHHCCCCCcCHHHHHHHHCcC---HHHHHHHHHHHHHCCCEE
Confidence            345566777777778 9999999999994   489999999999999885

>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=96.68  E-value=0.0012  Score=47.76  Aligned_cols=45  Identities=13%  Similarity=0.173  Sum_probs=38.4

Q ss_pred             cChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           49 VGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        49 LgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      +.|.+.|+++++++|+.|||+.+|++.   ..++|+|+.|...|++..
T Consensus        11 l~iL~~l~~~~~~~~~~ela~~~gl~~---stv~r~l~~L~~~G~v~~   55 (249)
T 1mkm_A           11 FEILDFIVKNPGDVSVSEIAEKFNMSV---SNAYKYMVVLEEKGFVLR   55 (249)
T ss_dssp             HHHHHHHHHCSSCBCHHHHHHHTTCCH---HHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHhCCCCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCcEEE
Confidence            356677877667899999999999954   899999999999998864

>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=96.57  E-value=0.0011  Score=48.01  Aligned_cols=44  Identities=9%  Similarity=0.159  Sum_probs=37.9

Q ss_pred             ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      .|.+.+.++++++|+.|||+.+|++.   ..++|+|+.|...|++..
T Consensus        10 ~iL~~l~~~~~~~s~~ela~~~gl~~---stv~r~l~~L~~~G~v~~   53 (241)
T 2xrn_A           10 SIMRALGSHPHGLSLAAIAQLVGLPR---STVQRIINALEEEFLVEA   53 (241)
T ss_dssp             HHHHHHHTCTTCEEHHHHHHHTTSCH---HHHHHHHHHHHTTTSEEE
T ss_pred             HHHHHHHhCCCCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEE
Confidence            56677877667899999999999954   899999999999998863

>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=96.55  E-value=0.0005  Score=50.40  Aligned_cols=44  Identities=14%  Similarity=0.182  Sum_probs=37.8

Q ss_pred             ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      .|.+.++++++++|+.|||+++|++.   ..++|+|+.|+..|++..
T Consensus        10 ~IL~~l~~~~~~lsl~eia~~lgl~k---sT~~RlL~tL~~~G~v~~   53 (260)
T 3r4k_A           10 TLLTYFNHGRLEIGLSDLTRLSGMNK---ATVYRLMSELQEAGFVEQ   53 (260)
T ss_dssp             HHHTTCBTTBSEEEHHHHHHHHCSCH---HHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHhhCCCCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEE
Confidence            56677776568999999999999954   899999999999999864

>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=96.50  E-value=0.0023  Score=39.86  Aligned_cols=44  Identities=11%  Similarity=0.187  Sum_probs=38.1

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      .++.|.+.| .  +++|..|||+.+|+++   ..++|.++.|...|++..
T Consensus        32 ~r~~Il~~L-~--~~~~~~eLa~~l~is~---~tv~~~L~~L~~~Glv~~   75 (96)
T 1y0u_A           32 VRRKILRML-D--KGRSEEEIMQTLSLSK---KQLDYHLKVLEAGFCIER   75 (96)
T ss_dssp             HHHHHHHHH-H--TTCCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHH-c--CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEE
Confidence            566788888 5  7899999999999954   899999999999998863

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

Probab=96.48  E-value=0.0023  Score=41.84  Aligned_cols=35  Identities=20%  Similarity=0.324  Sum_probs=31.4

Q ss_pred             CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           59 TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        59 ~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      +++.|..|||+.+++++   ..++|+|+.|...|++..
T Consensus        24 ~~~~s~~ela~~~~i~~---~~v~~il~~L~~~Glv~~   58 (129)
T 2y75_A           24 EGPTSLKSIAQTNNLSE---HYLEQLVSPLRNAGLVKS   58 (129)
T ss_dssp             SCCBCHHHHHHHTTSCH---HHHHHHHHHHHHTTSEEE
T ss_pred             CCcCCHHHHHHHHCcCH---HHHHHHHHHHHHCCceEe
Confidence            47899999999999955   899999999999998763

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

Probab=96.42  E-value=0.0043  Score=38.82  Aligned_cols=44  Identities=14%  Similarity=0.166  Sum_probs=37.6

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ..+.|...|.+  +++|..|||+.+|+++   ..+.+-|+.|...|++.
T Consensus        24 ~r~~Il~~L~~--~~~~~~ela~~l~is~---~tvs~~L~~L~~~Glv~   67 (102)
T 3pqk_A           24 VRLMLVCTLVE--GEFSVGELEQQIGIGQ---PTLSQQLGVLRESGIVE   67 (102)
T ss_dssp             HHHHHHHHHHT--CCBCHHHHHHHHTCCT---THHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHh--CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCeE
Confidence            55666777754  7899999999999965   79999999999999885

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

Probab=96.34  E-value=0.0014  Score=47.90  Aligned_cols=44  Identities=9%  Similarity=0.206  Sum_probs=36.7

Q ss_pred             ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      .|.+.|+.+++++|+.|||+.+|++.   ..++|+|+.|...|++..
T Consensus        27 ~iL~~l~~~~~~~~~~eia~~~gl~k---stv~r~l~tL~~~G~v~~   70 (260)
T 2o0y_A           27 DLLELFDAAHPTRSLKELVEGTKLPK---TTVVRLVATMCARSVLTS   70 (260)
T ss_dssp             HHHTTCBTTBSSBCHHHHHHHHCCCH---HHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHhhCCCCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEE
Confidence            45566655557999999999999954   899999999999998863

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

Probab=96.32  E-value=0.0041  Score=38.72  Aligned_cols=41  Identities=15%  Similarity=0.143  Sum_probs=35.3

Q ss_pred             hhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           51 IPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        51 I~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      |-+.|.++ |.+|++|||+.+++++   ..++|.|..|...|++.
T Consensus         7 Il~~L~~~-g~vsv~eLa~~l~VS~---~TIRrdL~~Le~~G~l~   47 (78)
T 1xn7_A            7 VRDLLALR-GRMEAAQISQTLNTPQ---PMINAMLQQLESMGKAV   47 (78)
T ss_dssp             HHHHHHHS-CSBCHHHHHHHTTCCH---HHHHHHHHHHHHHTSEE
T ss_pred             HHHHHHHc-CCCcHHHHHHHHCcCH---HHHHHHHHHHHHCCCEE
Confidence            45677654 7999999999999955   99999999999999874

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

Probab=96.32  E-value=0.0023  Score=39.83  Aligned_cols=34  Identities=12%  Similarity=0.189  Sum_probs=31.0

Q ss_pred             CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           59 TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        59 ~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      |+|.|+.|||+.+|+.+   ..++|-|..|...|++.
T Consensus        22 g~~psv~EIa~~lgvS~---~TVrr~L~~Le~kG~I~   55 (77)
T 2jt1_A           22 GAPVKTRDIADAAGLSI---YQVRLYLEQLHDVGVLE   55 (77)
T ss_dssp             TSCEEHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             CCCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCcEE
Confidence            78999999999999944   78999999999999875

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

Probab=96.31  E-value=0.0042  Score=39.69  Aligned_cols=44  Identities=11%  Similarity=0.144  Sum_probs=37.4

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .++.|...|..  +++|..|||+.+|+++   ..+.|.++.|...|++.
T Consensus        26 ~r~~IL~~L~~--~~~s~~eLa~~lgis~---stvs~~L~~L~~~GlV~   69 (108)
T 2kko_A           26 RRLQILDLLAQ--GERAVEAIATATGMNL---TTASANLQALKSGGLVE   69 (108)
T ss_dssp             TTHHHHHHHTT--CCEEHHHHHHHHTCCH---HHHHHHHHHHHHHTSEE
T ss_pred             HHHHHHHHHHc--CCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCeE
Confidence            45666777754  7999999999999954   89999999999999885

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

Probab=96.29  E-value=0.002  Score=40.00  Aligned_cols=44  Identities=23%  Similarity=0.375  Sum_probs=38.1

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .++.|...|.+  +++|..|||+.+|+++   ..+.|-|+.|...|++.
T Consensus        24 ~r~~Il~~L~~--~~~~~~ela~~l~is~---~tvs~~L~~L~~~Glv~   67 (98)
T 3jth_A           24 RRLQILCMLHN--QELSVGELCAKLQLSQ---SALSQHLAWLRRDGLVT   67 (98)
T ss_dssp             HHHHHHHHTTT--SCEEHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHhc--CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCeE
Confidence            55667777865  7999999999999954   89999999999999985

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

Probab=96.27  E-value=0.0032  Score=38.20  Aligned_cols=42  Identities=14%  Similarity=0.266  Sum_probs=35.4

Q ss_pred             ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .|.+.|... +++|..|||+.+|+++   ..++|.|+.|...|++.
T Consensus         4 ~Il~~L~~~-~~~s~~eLa~~lgvs~---~tv~r~L~~L~~~GlI~   45 (81)
T 2htj_A            4 EILEFLNRH-NGGKTAEIAEALAVTD---YQARYYLLLLEKAGMVQ   45 (81)
T ss_dssp             HHHHHHHHS-CCCCHHHHHHHHTSCH---HHHHHHHHHHHHHTSEE
T ss_pred             HHHHHHHHc-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEE
Confidence            356667654 6899999999999954   89999999999999886

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

Probab=96.25  E-value=0.0017  Score=47.30  Aligned_cols=44  Identities=11%  Similarity=0.134  Sum_probs=37.2

Q ss_pred             ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      .|.+.|..+++++|+.|||+.+|++.   ..++|+|+.|...|++..
T Consensus        18 ~iL~~l~~~~~~~~~~eia~~~gl~~---stv~r~l~~L~~~G~v~~   61 (257)
T 2g7u_A           18 AVLLAFDAQRPNPTLAELATEAGLSR---PAVRRILLTLQKLGYVAG   61 (257)
T ss_dssp             HHHHTCSSSCSSCBHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHhCCCCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEe
Confidence            55677765567899999999999954   899999999999998853

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

Probab=96.25  E-value=0.0033  Score=38.46  Aligned_cols=45  Identities=7%  Similarity=0.093  Sum_probs=38.3

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .++.|...|.. ++++|..|||+.+|+++   ..+.|.++.|...|++.
T Consensus        25 ~~~~il~~l~~-~~~~s~~ela~~l~is~---~tvs~~l~~L~~~glv~   69 (99)
T 3cuo_A           25 KRLLILCMLSG-SPGTSAGELTRITGLSA---SATSQHLARMRDEGLID   69 (99)
T ss_dssp             HHHHHHHHHTT-CCSEEHHHHHHHHCCCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHh-CCCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEE
Confidence            56677777854 46999999999999954   89999999999999885

>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=96.25  E-value=0.02  Score=36.99  Aligned_cols=46  Identities=11%  Similarity=0.109  Sum_probs=35.8

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      .++.|...|..+ +++|..|||+.+++++   ..+.|+++.|...|++..
T Consensus        38 ~~~~vL~~l~~~-~~~t~~eLa~~l~~~~---~tvs~~l~~L~~~Glv~r   83 (142)
T 3ech_A           38 PDVHVLKLIDEQ-RGLNLQDLGRQMCRDK---ALITRKIRELEGRNLVRR   83 (142)
T ss_dssp             HHHHHHHHHHHT-TTCCHHHHHHHHC------CHHHHHHHHHHHTTSEEC
T ss_pred             HHHHHHHHHHhC-CCcCHHHHHHHhCCCH---HHHHHHHHHHHHCCCEee
Confidence            455566667664 5899999999999955   899999999999999863

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

Probab=96.23  E-value=0.0035  Score=39.75  Aligned_cols=44  Identities=7%  Similarity=0.121  Sum_probs=37.5

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .++.|...|.+  +++|..|||+.+|+++   ..+.|.++.|...|++.
T Consensus        27 ~r~~IL~~L~~--~~~~~~ela~~l~is~---stvs~~L~~L~~~Glv~   70 (106)
T 1r1u_A           27 NRIRIMELLSV--SEASVGHISHQLNLSQ---SNVSHQLKLLKSVHLVK   70 (106)
T ss_dssp             HHHHHHHHHHH--CCBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHh--CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCeE
Confidence            55667777764  7899999999999954   89999999999999875

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

Probab=96.21  E-value=0.0014  Score=48.12  Aligned_cols=44  Identities=14%  Similarity=0.218  Sum_probs=37.2

Q ss_pred             ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      .|.+.|+.+++++|+.|||+.+|++.   ..++|+|+.|...|++..
T Consensus        25 ~iL~~l~~~~~~~~~~eia~~~gl~~---stv~r~l~tL~~~G~v~~   68 (265)
T 2ia2_A           25 AVIRCFDHRNQRRTLSDVARATDLTR---ATARRFLLTLVELGYVAT   68 (265)
T ss_dssp             HHHHTCCSSCSSEEHHHHHHHHTCCH---HHHHHHHHHHHHHTSEEE
T ss_pred             HHHHHHHhCCCCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEe
Confidence            55677765567899999999999954   899999999999998863

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

Probab=96.19  E-value=0.0046  Score=38.90  Aligned_cols=44  Identities=11%  Similarity=0.123  Sum_probs=36.9

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .++.|...|..  +++|..|||+.+|+++   ..+.|.++.|...|++.
T Consensus        22 ~r~~IL~~L~~--~~~~~~ela~~l~is~---~tv~~~l~~L~~~gli~   65 (114)
T 2oqg_A           22 TRWEILTELGR--ADQSASSLATRLPVSR---QAIAKHLNALQACGLVE   65 (114)
T ss_dssp             HHHHHHHHHHH--SCBCHHHHHHHSSSCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHc--CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCee
Confidence            45566677744  7899999999999954   89999999999999885

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

Probab=96.05  E-value=0.003  Score=40.84  Aligned_cols=44  Identities=14%  Similarity=0.206  Sum_probs=38.5

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ..+.|...|.+  +|+|+.|||+.+|+++   ..+.+.|+.|...|++.
T Consensus        19 ~R~~Il~~L~~--~~~~~~eLa~~l~is~---~tvs~hL~~L~~~GlV~   62 (118)
T 3f6o_A           19 TRRAVLGRLSR--GPATVSELAKPFDMAL---PSFMKHIHFLEDSGWIR   62 (118)
T ss_dssp             HHHHHHHHHHT--CCEEHHHHHTTCCSCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHh--CCCCHHHHHHHhCcCH---HHHHHHHHHHHHCCCeE
Confidence            66777888864  8999999999999954   89999999999999985

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

Probab=96.03  E-value=0.0054  Score=39.98  Aligned_cols=45  Identities=11%  Similarity=0.153  Sum_probs=39.0

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .++.|...|.. .+++|..|||+.+|+++   ..+.|.|+.|...|++.
T Consensus        43 ~rl~IL~~L~~-~~~~s~~eLa~~l~is~---stvs~~L~~L~~~Glv~   87 (122)
T 1u2w_A           43 NRAKITYALCQ-DEELCVCDIANILGVTI---ANASHHLRTLYKQGVVN   87 (122)
T ss_dssp             HHHHHHHHHHH-SSCEEHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHH-CCCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCeE
Confidence            56788888874 37899999999999954   89999999999999875

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

Probab=96.01  E-value=0.005  Score=39.32  Aligned_cols=41  Identities=17%  Similarity=0.170  Sum_probs=35.4

Q ss_pred             hhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           51 IPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        51 I~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      |-+.|.+. |.+|++|||+.+++++   ..++|.|..|...|++.
T Consensus         7 Il~~L~~~-g~vsv~eLA~~l~VS~---~TIRrDL~~Le~~G~l~   47 (87)
T 2k02_A            7 VRDMLALQ-GRMEAKQLSARLQTPQ---PLIDAMLERMEAMGKVV   47 (87)
T ss_dssp             HHHHHHHS-CSEEHHHHHHHTTCCH---HHHHHHHHHHHTTCCSE
T ss_pred             HHHHHHHc-CCCcHHHHHHHHCcCH---HHHHHHHHHHHHCCCEE
Confidence            45677654 7999999999999955   99999999999999875

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

Probab=95.88  E-value=0.0048  Score=39.07  Aligned_cols=45  Identities=18%  Similarity=0.242  Sum_probs=36.4

Q ss_pred             hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .+.|...+...|+++|..|||+.+|++.   ..+++.|+.|...|++.
T Consensus        20 ~l~Il~~l~~~g~~~s~~eLa~~lgvs~---~tV~~~L~~L~~~GlV~   64 (110)
T 1q1h_A           20 VIDVLRILLDKGTEMTDEEIANQLNIKV---NDVRKKLNLLEEQGFVS   64 (110)
T ss_dssp             THHHHHHHHHHCSCBCHHHHHHTTTSCH---HHHHHHHHHHHHHTSCE
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEE
Confidence            3456666644455899999999999954   88999999999999875

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

Probab=95.82  E-value=0.0043  Score=38.09  Aligned_cols=35  Identities=17%  Similarity=0.277  Sum_probs=31.3

Q ss_pred             CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           59 TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        59 ~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      .+++|..|||+.+|+++   ..++|+++.|...|++..
T Consensus        34 ~~~~t~~ela~~l~is~---~tv~~~l~~L~~~g~v~~   68 (109)
T 2d1h_A           34 EKPITSEELADIFKLSK---TTVENSLKKLIELGLVVR   68 (109)
T ss_dssp             CSCEEHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEE
T ss_pred             CCCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCeEe
Confidence            47899999999999954   899999999999998863

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

Probab=95.81  E-value=0.0054  Score=39.36  Aligned_cols=42  Identities=21%  Similarity=0.375  Sum_probs=34.4

Q ss_pred             hhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           51 IPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        51 I~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      +...|....+++|..|||+.+|+++   ..+.|+++.|...|++.
T Consensus        31 il~~L~~~~~~~t~~ela~~l~~~~---stvs~~l~~L~~~G~v~   72 (152)
T 1ku9_A           31 VYAILYLSDKPLTISDIMEELKISK---GNVSMSLKKLEELGFVR   72 (152)
T ss_dssp             HHHHHHHCSSCEEHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHcCCCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEE
Confidence            3445532347899999999999954   89999999999999886

>2o03_A Probable zinc uptake regulation protein FURB; DNA-binding, helix-turn-helix, zinc binding, GE regulation; 2.70A {Mycobacterium tuberculosis}

Probab=95.81  E-value=0.0074  Score=39.92  Aligned_cols=47  Identities=15%  Similarity=0.186  Sum_probs=39.0

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHh-----CCCCCCcccHHHHHHHHHhcCcccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGAL-----QIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~-----g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      .+.-|.+.|.+.+++.|+.||.+.+     ++   +...++|.|..|+..|++.+
T Consensus        12 qR~~Il~~l~~~~~~~sa~ei~~~l~~~~~~i---s~~TVYR~L~~L~e~Glv~~   63 (131)
T 2o03_A           12 QRAAISTLLETLDDFRSAQELHDELRRRGENI---GLTTVYRTLQSMASSGLVDT   63 (131)
T ss_dssp             HHHHHHHHHHHCCSCEEHHHHHHHHHHTTCCC---CHHHHHHHHHHHHTTTSEEE
T ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHHHHhCCCC---CHhhHHHHHHHHHHCCCEEE
Confidence            4556778887777899999999998     44   55899999999999998763

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

Probab=95.79  E-value=0.0047  Score=37.69  Aligned_cols=50  Identities=20%  Similarity=0.309  Sum_probs=39.9

Q ss_pred             HHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           40 SLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        40 aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++..-  .++.|...|..+ +++|..|||+.+|+++   ..+.|.++.|...|++.
T Consensus        12 ~l~~~--~~~~iL~~L~~~-~~~~~~ela~~l~is~---~tvs~~l~~L~~~gli~   61 (100)
T 1ub9_A           12 ILGNP--VRLGIMIFLLPR-RKAPFSQIQKVLDLTP---GNLDSHIRVLERNGLVK   61 (100)
T ss_dssp             HHHSH--HHHHHHHHHHHH-SEEEHHHHHHHTTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             ccCCh--HHHHHHHHHHhc-CCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEE
Confidence            34444  566677777543 6899999999999954   89999999999999886

>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=95.78  E-value=0.0062  Score=37.23  Aligned_cols=45  Identities=18%  Similarity=0.314  Sum_probs=36.6

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .++.|...|..+ +++|..|||+.+|+++   ..+.|.++.|...|++.
T Consensus        21 ~~~~il~~l~~~-~~~s~~ela~~l~is~---~tv~~~l~~L~~~glv~   65 (109)
T 1sfx_A           21 SDVRIYSLLLER-GGMRVSEIARELDLSA---RFVRDRLKVLLKRGFVR   65 (109)
T ss_dssp             HHHHHHHHHHHH-CCBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHHc-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEE
Confidence            344556666543 6899999999999954   89999999999999886

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

Probab=95.70  E-value=0.011  Score=39.72  Aligned_cols=50  Identities=16%  Similarity=0.127  Sum_probs=39.3

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCC-CC-CCcccHHHHHHHHHhcCcccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQI-HP-TKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~-~~-~~~~~L~RlLR~Laa~gif~e   96 (97)
                      .+.-|.+.|...+++.|+.||.+.+.- .| -+...++|.|..|+..|++..
T Consensus        23 qR~~Il~~L~~~~~~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~   74 (145)
T 2fe3_A           23 QRHAILEYLVNSMAHPTADDIYKALEGKFPNMSVATVYNNLRVFRESGLVKE   74 (145)
T ss_dssp             HHHHHHHHHHHCSSCCCHHHHHHHHGGGCTTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHHHHhCCCCChhhHHHHHHHHHHCCCEEE
Confidence            455678888777789999999999832 11 155889999999999999863

>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=95.69  E-value=0.007  Score=39.54  Aligned_cols=46  Identities=11%  Similarity=0.136  Sum_probs=37.7

Q ss_pred             hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      +..|...|..+++++|..|||+.+++++   ..+.|+++.|...|++..
T Consensus        41 q~~vL~~l~~~~~~~t~~eLa~~l~i~~---~tvs~~l~~Le~~Glv~r   86 (150)
T 3fm5_A           41 SYSVLVLACEQAEGVNQRGVAATMGLDP---SQIVGLVDELEERGLVVR   86 (150)
T ss_dssp             HHHHHHHHHHSTTCCCSHHHHHHHTCCH---HHHHHHHHHHHTTTSEEC
T ss_pred             HHHHHHHHHhCCCCcCHHHHHHHHCCCH---hHHHHHHHHHHHCCCEEe
Confidence            4445556666667899999999999954   899999999999999863

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

Probab=95.68  E-value=0.0097  Score=41.24  Aligned_cols=51  Identities=14%  Similarity=0.248  Sum_probs=38.9

Q ss_pred             HHHHHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           36 INSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        36 ~~s~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      -...+|++.  +.|..    ...++|.|+.|||+.+++++   ..|+++|+.|...|++.
T Consensus        25 ~~~yAlr~L--~~LA~----~~~~~~~s~~eIA~~~~i~~---~~l~kil~~L~~aGlv~   75 (159)
T 3lwf_A           25 KGRYGLTIT--LELAK----RIGDGPISLRSIAQDKNLSE---HYLEQLIGPLRNAGIVK   75 (159)
T ss_dssp             HHHHHHHHH--HHHHH----TTTSCCBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHH--HHHHh----cCCCCCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCeEE
Confidence            344566666  54432    12347899999999999955   99999999999999876

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

Probab=95.67  E-value=0.0098  Score=39.02  Aligned_cols=46  Identities=17%  Similarity=0.287  Sum_probs=37.7

Q ss_pred             hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      ++.|...|....+++|..|||+.+++++   ..+.|+++.|...|++..
T Consensus        49 ~~~iL~~L~~~~~~~~~~ela~~l~i~~---~tvs~~l~~Le~~Gli~r   94 (160)
T 3boq_A           49 KFDAMAQLARNPDGLSMGKLSGALKVTN---GNVSGLVNRLIKDGMVVK   94 (160)
T ss_dssp             HHHHHHHHHHCTTCEEHHHHHHHCSSCC---SCHHHHHHHHHHHTSEEE
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHCCCh---hhHHHHHHHHHHCCCEEe
Confidence            4456666744457999999999999955   899999999999999863

>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=95.65  E-value=0.0074  Score=37.30  Aligned_cols=40  Identities=15%  Similarity=0.178  Sum_probs=33.3

Q ss_pred             HHHhhCCCCCCHHHHHHHhCCCCCCccc-HHHHHHHHHhcCccc
Q 041844           53 DIIHNHTKPMTLNQLLGALQIHPTKTRC-LHFLVCSLVRSGFFN   95 (97)
Q Consensus        53 D~La~~~gp~s~~ELA~~~g~~~~~~~~-L~RlLR~Laa~gif~   95 (97)
                      ..+..+++++|..|||+.+++++   .. +.|+++.|...|++.
T Consensus        22 ~~l~~~~~~~t~~eLa~~l~is~---~t~vs~~l~~Le~~Glv~   62 (95)
T 2pg4_A           22 LEFEKKGYEPSLAEIVKASGVSE---KTFFMGLKDRLIRAGLVK   62 (95)
T ss_dssp             HHHHHTTCCCCHHHHHHHHCCCH---HHHHTTHHHHHHHTTSEE
T ss_pred             HHHHhcCCCCCHHHHHHHHCCCc---hHHHHHHHHHHHHCCCee
Confidence            34555545899999999999954   89 999999999999875

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

Probab=95.64  E-value=0.0072  Score=38.78  Aligned_cols=45  Identities=22%  Similarity=0.168  Sum_probs=37.5

Q ss_pred             hcChhHHHhhCC-CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           48 QVGIPDIIHNHT-KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        48 eLgI~D~La~~~-gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      +..|...|..++ +++|..|||+.+++++   ..+.|+++.|...|++.
T Consensus        33 ~~~vL~~l~~~~~~~~t~~ela~~l~~~~---~tvs~~l~~Le~~Gli~   78 (139)
T 3eco_A           33 QGHTLGYLYAHQQDGLTQNDIAKALQRTG---PTVSNLLRNLERKKLIY   78 (139)
T ss_dssp             HHHHHHHHHHSTTTCEEHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHhcCCCCcCHHHHHHHhCCCc---ccHHHHHHHHHHCCCEe
Confidence            445556676665 6999999999999954   89999999999999986

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

Probab=95.63  E-value=0.0098  Score=38.05  Aligned_cols=45  Identities=13%  Similarity=0.172  Sum_probs=36.4

Q ss_pred             hcChhHHHhhCCC-CCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           48 QVGIPDIIHNHTK-PMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        48 eLgI~D~La~~~g-p~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      +..|...|..+++ ++|..|||+.+++++   ..+.|+++.|...|++.
T Consensus        36 ~~~iL~~l~~~~~~~~~~~ela~~l~~~~---~tvs~~l~~Le~~Gli~   81 (141)
T 3bro_A           36 QMTIIDYLSRNKNKEVLQRDLESEFSIKS---STATVLLQRMEIKKLLY   81 (141)
T ss_dssp             HHHHHHHHHHTTTSCCBHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHCCCCCcCHHHHHHHHCCCc---chHHHHHHHHHHCCCEE
Confidence            3445556666543 899999999999954   89999999999999885

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

Probab=95.62  E-value=0.011  Score=38.19  Aligned_cols=46  Identities=22%  Similarity=0.212  Sum_probs=37.7

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .++.|...|..+.+++|..|||+.+++++   ..+.|+++.|...|++.
T Consensus        36 ~~~~iL~~l~~~~~~~~~~~la~~l~i~~---~~vs~~l~~Le~~glv~   81 (147)
T 2hr3_A           36 SQLVVLGAIDRLGGDVTPSELAAAERMRS---SNLAALLRELERGGLIV   81 (147)
T ss_dssp             HHHHHHHHHHHTTSCBCHHHHHHHTTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHhCCCh---hhHHHHHHHHHHCCCEe
Confidence            34556666765347999999999999954   89999999999999885

>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=95.55  E-value=0.01  Score=38.90  Aligned_cols=44  Identities=9%  Similarity=0.178  Sum_probs=37.9

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .++.|+..|.+  ++.|..|||+.+|+++   ..+.|.++.|...|++.
T Consensus        47 ~rl~IL~~L~~--~~~s~~ela~~lgis~---stvs~~L~~Le~~Glv~   90 (122)
T 1r1t_A           47 NRLRLLSLLAR--SELCVGDLAQAIGVSE---SAVSHQLRSLRNLRLVS   90 (122)
T ss_dssp             HHHHHHHHHTT--CCBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHc--CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCeE
Confidence            56677888864  7899999999999954   89999999999999875

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

Probab=95.46  E-value=0.0094  Score=38.00  Aligned_cols=44  Identities=18%  Similarity=0.130  Sum_probs=36.6

Q ss_pred             hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++.|...|..+ +++|..|||+.+++++   ..+.|+++.|...|++.
T Consensus        40 ~~~iL~~l~~~-~~~t~~ela~~l~~~~---~tvs~~l~~L~~~glv~   83 (140)
T 2nnn_A           40 QWAALVRLGET-GPCPQNQLGRLTAMDA---ATIKGVVERLDKRGLIQ   83 (140)
T ss_dssp             HHHHHHHHHHH-SSBCHHHHHHHTTCCH---HHHHHHHHHHHHTTCEE
T ss_pred             HHHHHHHHHHc-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEE
Confidence            45566667554 5999999999999954   89999999999999885

>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=95.46  E-value=0.013  Score=38.75  Aligned_cols=45  Identities=18%  Similarity=0.373  Sum_probs=37.9

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .++.|...|.. ++++|..|||+.+|+++   ..+.|.++.|...|++.
T Consensus         4 ~~~~il~~L~~-~~~~~~~ela~~lg~s~---~tv~~~l~~L~~~G~i~   48 (150)
T 2pn6_A            4 IDLRILKILQY-NAKYSLDEIAREIRIPK---ATLSYRIKKLEKDGVIK   48 (150)
T ss_dssp             HHHHHHHHHTT-CTTSCHHHHHHHHTSCH---HHHHHHHHHHHHTTSSC
T ss_pred             HHHHHHHHHHH-cCCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCcEE
Confidence            45567777865 46899999999999954   89999999999999886

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

Probab=95.45  E-value=0.013  Score=37.99  Aligned_cols=44  Identities=9%  Similarity=0.166  Sum_probs=36.2

Q ss_pred             hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++.|...|..+ +++|..|||+.+++++   ..+.|+++.|...|++.
T Consensus        42 ~~~iL~~l~~~-~~~t~~ela~~l~~~~---~tvs~~l~~Le~~Glv~   85 (148)
T 3nrv_A           42 EWRIISVLSSA-SDCSVQKISDILGLDK---AAVSRTVKKLEEKKYIE   85 (148)
T ss_dssp             HHHHHHHHHHS-SSBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHcC-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEE
Confidence            34455556554 5999999999999954   89999999999999986

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

Probab=95.44  E-value=0.0098  Score=40.15  Aligned_cols=34  Identities=18%  Similarity=0.231  Sum_probs=30.9

Q ss_pred             CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           59 TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        59 ~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      +++.|+.|||+.+++++   ..|.++|+.|...|++.
T Consensus        26 ~~~~s~~~IA~~~~i~~---~~l~kil~~L~~aGlv~   59 (143)
T 3t8r_A           26 QGCISLKSIAEENNLSD---LYLEQLVGPLRNAGLIR   59 (143)
T ss_dssp             SCCEEHHHHHHHTTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             CCCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCEEE
Confidence            36899999999999955   89999999999999975

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

Probab=95.42  E-value=0.013  Score=38.12  Aligned_cols=46  Identities=11%  Similarity=0.127  Sum_probs=32.2

Q ss_pred             hcChhHHHhhCC-CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           48 QVGIPDIIHNHT-KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        48 eLgI~D~La~~~-gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      +..|...|..++ +++|..|||+.+++++   ..+.|+++.|...|++..
T Consensus        43 q~~vL~~l~~~~~~~~t~~eLa~~l~~~~---~~vs~~l~~L~~~Glv~r   89 (148)
T 3jw4_A           43 QGRMIGYIYENQESGIIQKDLAQFFGRRG---ASITSMLQGLEKKGYIER   89 (148)
T ss_dssp             HHHHHHHHHHHTTTCCCHHHHHHC---------CHHHHHHHHHHTTSBCC
T ss_pred             HHHHHHHHHhCCCCCCCHHHHHHHHCCCh---hHHHHHHHHHHHCCCEEe
Confidence            344455566554 7999999999999955   899999999999999863

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

Probab=95.37  E-value=0.013  Score=37.54  Aligned_cols=45  Identities=16%  Similarity=0.127  Sum_probs=36.3

Q ss_pred             hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++.|...|....+++|..|||+.+++++   ..+.|+++.|...|++.
T Consensus        39 ~~~iL~~l~~~~~~~t~~~la~~l~~s~---~~vs~~l~~L~~~glv~   83 (146)
T 2fbh_A           39 RWLVLLHLARHRDSPTQRELAQSVGVEG---PTLARLLDGLESQGLVR   83 (146)
T ss_dssp             HHHHHHHHHHCSSCCBHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHhCCCh---hhHHHHHHHHHHCCCee
Confidence            3445556633457999999999999954   89999999999999885

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

Probab=95.35  E-value=0.0078  Score=41.12  Aligned_cols=52  Identities=10%  Similarity=0.082  Sum_probs=42.7

Q ss_pred             HHHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           38 SMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        38 s~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      ..+|.--  ..+.|...|.+  +++|+.|||+.+|+++   ..+.+-|+.|...|++..
T Consensus        52 l~aL~~p--~R~~IL~~L~~--~~~t~~eLa~~lgls~---stvs~hL~~L~~aGlV~~  103 (151)
T 3f6v_A           52 LEVAAEP--TRRRLVQLLTS--GEQTVNNLAAHFPASR---SAISQHLRVLTEAGLVTP  103 (151)
T ss_dssp             HHHHTSH--HHHHHHHHGGG--CCEEHHHHHTTSSSCH---HHHHHHHHHHHHTTSEEE
T ss_pred             HHHhCCH--HHHHHHHHHHh--CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEE
Confidence            3444455  67788888864  7999999999999954   899999999999999863

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

Probab=95.34  E-value=0.013  Score=37.65  Aligned_cols=44  Identities=14%  Similarity=0.120  Sum_probs=36.6

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .++.|...|.  .+++|..|||+.+++++   ..+.|+++.|...|++.
T Consensus        38 ~~~~iL~~l~--~~~~~~~ela~~l~~s~---~tvs~~l~~Le~~glv~   81 (146)
T 2gxg_A           38 LDFLVLRATS--DGPKTMAYLANRYFVTQ---SAITASVDKLEEMGLVV   81 (146)
T ss_dssp             HHHHHHHHHT--TSCBCHHHHHHHTTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHh--cCCcCHHHHHHHhCCCc---hhHHHHHHHHHHCCCEE
Confidence            3445556676  57999999999999954   89999999999999886

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

Probab=95.34  E-value=0.017  Score=36.76  Aligned_cols=44  Identities=16%  Similarity=0.244  Sum_probs=37.7

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .++.|+..|.+  ++.|..|||+.+++++   ..+.|.++.|...|++.
T Consensus        33 ~~~~il~~L~~--~~~s~~ela~~l~is~---stvsr~l~~Le~~Glv~   76 (119)
T 2lkp_A           33 SRLMILTQLRN--GPLPVTDLAEAIGMEQ---SAVSHQLRVLRNLGLVV   76 (119)
T ss_dssp             HHHHHHHHHHH--CCCCHHHHHHHHSSCH---HHHHHHHHHHHHHCSEE
T ss_pred             HHHHHHHHHHH--CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEE
Confidence            56677777876  6899999999999954   89999999999999874

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

Probab=95.25  E-value=0.015  Score=37.48  Aligned_cols=45  Identities=20%  Similarity=0.278  Sum_probs=36.0

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      .+..|...|..+ + +|..|||+.+++++   ..+.|+++.|...|++..
T Consensus        39 ~~~~iL~~l~~~-~-~t~~eLa~~l~~s~---~tvs~~l~~L~~~Glv~r   83 (146)
T 3tgn_A           39 TQEHILMLLSEE-S-LTNSELARRLNVSQ---AAVTKAIKSLVKEGMLET   83 (146)
T ss_dssp             HHHHHHHHHTTC-C-CCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEC
T ss_pred             HHHHHHHHHHhC-C-CCHHHHHHHHCCCH---HHHHHHHHHHHHCCCeEe
Confidence            344555666553 3 99999999999954   899999999999999863

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

Probab=95.25  E-value=0.02  Score=38.02  Aligned_cols=50  Identities=12%  Similarity=0.135  Sum_probs=37.8

Q ss_pred             HhcChhHHHhhCC-CCCCHHHHHHHhCC-C-CCCcccHHHHHHHHHhcCcccc
Q 041844           47 IQVGIPDIIHNHT-KPMTLNQLLGALQI-H-PTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        47 veLgI~D~La~~~-gp~s~~ELA~~~g~-~-~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      .+.-|.+.|.+.+ ++.|+.||.+.+.- . .-+...++|.|..|+..|++.+
T Consensus        19 qR~~Il~~L~~~~~~~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~   71 (136)
T 1mzb_A           19 PRVKILQMLDSAEQRHMSAEDVYKALMEAGEDVGLATVYRVLTQFEAAGLVVR   71 (136)
T ss_dssp             HHHHHHHHHHCC-CCSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTSEEE
T ss_pred             HHHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCcEEE
Confidence            4455778887766 89999999999831 1 1155889999999999998863

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

Probab=95.25  E-value=0.016  Score=37.58  Aligned_cols=35  Identities=20%  Similarity=0.312  Sum_probs=31.4

Q ss_pred             CCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           58 HTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        58 ~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .+++.|..|||+.+++++   ..+.|+++.|...|++.
T Consensus        28 ~~~~~s~~ela~~l~is~---~tv~~~l~~Le~~Gli~   62 (139)
T 2x4h_A           28 SGEGAKINRIAKDLKIAP---SSVFEEVSHLEEKGLVK   62 (139)
T ss_dssp             TTSCBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             cCCCcCHHHHHHHhCCCh---HHHHHHHHHHHHCCCEE
Confidence            457899999999999954   89999999999999885

>2xig_A Ferric uptake regulation protein; hpfur, transcription, homeostasis; HET: CIT; 1.85A {Helicobacter pylori}

Probab=95.21  E-value=0.02  Score=38.82  Aligned_cols=50  Identities=6%  Similarity=0.153  Sum_probs=39.2

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCC--CCCCcccHHHHHHHHHhcCcccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQI--HPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~--~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      .+.-|.+.|...+++.|+.||.+.+.-  +..+...++|.|..|+..|++.+
T Consensus        28 qR~~IL~~l~~~~~~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~   79 (150)
T 2xig_A           28 QREEVVSVLYRSGTHLSPEEITHSIRQKDKNTSISSVYRILNFLEKENFISV   79 (150)
T ss_dssp             HHHHHHHHHHHCSSCBCHHHHHHHHHHHSTTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCCcEEE
Confidence            555678888777789999999999831  11155899999999999998853

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

Probab=95.13  E-value=0.02  Score=37.99  Aligned_cols=45  Identities=16%  Similarity=0.287  Sum_probs=37.6

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .+..|.+.|.++ +++|..|||+++|+++   ..+.|.++.|...|++.
T Consensus         6 ~d~~il~~L~~~-~~~s~~ela~~lg~s~---~tv~~~l~~L~~~G~i~   50 (144)
T 2cfx_A            6 IDLNIIEELKKD-SRLSMRELGRKIKLSP---PSVTERVRQLESFGIIK   50 (144)
T ss_dssp             HHHHHHHHHHHC-SCCCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHHc-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCeE
Confidence            345667777664 6899999999999954   89999999999999875

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

Probab=95.13  E-value=0.017  Score=36.74  Aligned_cols=45  Identities=20%  Similarity=0.217  Sum_probs=36.4

Q ss_pred             hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      ++.|...|..+ +++|..|||+.+++++   ..+.|+++.|...|++..
T Consensus        31 ~~~iL~~l~~~-~~~~~~ela~~l~~s~---~tvs~~l~~L~~~glv~~   75 (138)
T 3bpv_A           31 QVACLLRIHRE-PGIKQDELATFFHVDK---GTIARTLRRLEESGFIER   75 (138)
T ss_dssp             HHHHHHHHHHS-TTCBHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHc-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEe
Confidence            34455566554 7899999999999954   899999999999998863

>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=95.11  E-value=0.016  Score=39.00  Aligned_cols=49  Identities=12%  Similarity=0.205  Sum_probs=38.2

Q ss_pred             HHHHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           37 NSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        37 ~s~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ...++++.  +.|..    + .+++.|+.|||+.+++++   ..|+++|+.|...|++.
T Consensus        13 ~~yAl~~L--~~La~----~-~~~~~~~~~iA~~~~i~~---~~l~kil~~L~~~Glv~   61 (149)
T 1ylf_A           13 FSIAVHIL--SILKN----N-PSSLCTSDYMAESVNTNP---VVIRKIMSYLKQAGFVY   61 (149)
T ss_dssp             HHHHHHHH--HHHHH----S-CGGGCCHHHHHHHHTSCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHH--HHHHh----C-CCCCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCcEE
Confidence            34566766  54432    1 246899999999999955   99999999999999876

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

Probab=95.09  E-value=0.02  Score=38.05  Aligned_cols=45  Identities=16%  Similarity=0.099  Sum_probs=37.4

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .+..|...|..+ +++|..|||+.+|+++   ..+.|.++.|...|++.
T Consensus         8 ~~~~iL~~L~~~-~~~s~~ela~~lg~s~---~tv~~~l~~L~~~G~i~   52 (150)
T 2w25_A            8 IDRILVRELAAD-GRATLSELATRAGLSV---SAVQSRVRRLESRGVVQ   52 (150)
T ss_dssp             HHHHHHHHHHHC-TTCCHHHHHHHHTSCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHHc-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEE
Confidence            455666777653 6899999999999954   89999999999999884

>3k2z_A LEXA repressor; winged helix-turn-helix, SOS system, autoca cleavage, DNA damage, DNA repair, DNA replication, DNA-BIND hydrolase; 1.37A {Thermotoga maritima}

Probab=95.07  E-value=0.02  Score=40.01  Aligned_cols=40  Identities=18%  Similarity=0.436  Sum_probs=34.0

Q ss_pred             HHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           53 DIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        53 D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      +.+.+++.|.|..|||+.+|+++   ..++|.|+.|...|++.
T Consensus        16 ~~~~~~g~~~s~~eia~~lgl~~---~tv~~~l~~Le~~G~i~   55 (196)
T 3k2z_A           16 EFIEKNGYPPSVREIARRFRITP---RGALLHLIALEKKGYIE   55 (196)
T ss_dssp             HHHHHHSSCCCHHHHHHHHTSCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHhCCCCCHHHHHHHcCCCc---HHHHHHHHHHHHCCCEE
Confidence            44556677999999999999954   57999999999999875

>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=95.04  E-value=0.028  Score=37.19  Aligned_cols=44  Identities=14%  Similarity=0.256  Sum_probs=36.3

Q ss_pred             hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      +..|...|..+ +++|..|||+.+++++   ..+.|+++.|...|++.
T Consensus        48 q~~iL~~l~~~-~~~t~~eLa~~l~~~~---~tvs~~l~~Le~~Glv~   91 (162)
T 3k0l_A           48 QFTALSVLAAK-PNLSNAKLAERSFIKP---QSANKILQDLLANGWIE   91 (162)
T ss_dssp             HHHHHHHHHHC-TTCCHHHHHHHHTSCG---GGHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHC-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCcCeE
Confidence            33455566654 5899999999999955   89999999999999986

>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=95.04  E-value=0.014  Score=39.29  Aligned_cols=46  Identities=20%  Similarity=0.092  Sum_probs=37.6

Q ss_pred             hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      ++.|...|...++++|..|||+.++++   ...+.|+++.|...|++..
T Consensus        55 q~~vL~~L~~~~~~~t~~eLa~~l~i~---~~tvs~~l~~Le~~GlV~r  100 (166)
T 3deu_A           55 HWVTLHNIHQLPPDQSQIQLAKAIGIE---QPSLVRTLDQLEDKGLISR  100 (166)
T ss_dssp             HHHHHHHHHHSCSSEEHHHHHHHHTSC---HHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHCCC---HhhHHHHHHHHHHCCCEEe
Confidence            444555666656789999999999994   4899999999999999863

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

Probab=95.04  E-value=0.021  Score=36.23  Aligned_cols=44  Identities=14%  Similarity=0.400  Sum_probs=36.1

Q ss_pred             hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++.|...|..+ +++|..|||+.+++++   ..+.|+++.|...|++.
T Consensus        35 ~~~iL~~l~~~-~~~~~~ela~~l~~~~---~tvs~~l~~L~~~gli~   78 (139)
T 3bja_A           35 QFGVIQVLAKS-GKVSMSKLIENMGCVP---SNMTTMIQRMKRDGYVM   78 (139)
T ss_dssp             HHHHHHHHHHS-CSEEHHHHHHHCSSCC---TTHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHc-CCcCHHHHHHHHCCCh---hHHHHHHHHHHHCCCee
Confidence            44455566553 6899999999999955   89999999999999885

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

Probab=95.01  E-value=0.015  Score=39.41  Aligned_cols=46  Identities=11%  Similarity=0.112  Sum_probs=37.1

Q ss_pred             hcChhHHHhhCCCC--CCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           48 QVGIPDIIHNHTKP--MTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        48 eLgI~D~La~~~gp--~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      ++.|...|..+++|  +|..|||+.+++++   ..+.|+++.|...|++..
T Consensus        71 ~~~iL~~L~~~~~~~~~t~~eLa~~l~is~---~tvs~~l~~Le~~GlV~r  118 (181)
T 2fbk_A           71 GWDLLLTLYRSAPPEGLRPTELSALAAISG---PSTSNRIVRLLEKGLIER  118 (181)
T ss_dssp             HHHHHHHHHHHCCSSCBCHHHHHHHCSCCS---GGGSSHHHHHHHHTSEEC
T ss_pred             HHHHHHHHHHcCCCCCCCHHHHHHHHCCCH---HHHHHHHHHHHHCcCEEe
Confidence            44455667665544  99999999999955   899999999999998863

>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=95.00  E-value=0.13  Score=33.38  Aligned_cols=43  Identities=12%  Similarity=0.220  Sum_probs=36.0

Q ss_pred             hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      +..|...| . .+++|..|||+.+++++   ..+.|+++.|...|++.
T Consensus        40 q~~iL~~l-~-~~~~t~~eLa~~l~~~~---~~vs~~l~~Le~~Glv~   82 (151)
T 3kp7_A           40 QSHVLNML-S-IEALTVGQITEKQGVNK---AAVSRRVKKLLNAELVK   82 (151)
T ss_dssp             HHHHHHHH-H-HSCBCHHHHHHHHCSCS---SHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHH-H-cCCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEE
Confidence            33456667 3 47999999999999955   89999999999999986

>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=94.97  E-value=0.035  Score=38.27  Aligned_cols=48  Identities=15%  Similarity=0.420  Sum_probs=37.3

Q ss_pred             HHHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           38 SMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        38 s~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ..+|++.  +.|..    + .++++|..|||+.+++++   ..|.++|+.|...|++.
T Consensus        12 ~yAlr~l--~~La~----~-~~~~~s~~~IA~~~~is~---~~l~kil~~L~~aGlv~   59 (162)
T 3k69_A           12 SVAVHSI--LYLDA----H-RDSKVASRELAQSLHLNP---VMIRNILSVLHKHGYLT   59 (162)
T ss_dssp             HHHHHHH--HHHHT----T-TTSCBCHHHHHHHHTSCG---GGTHHHHHHHHHTTSSE
T ss_pred             HHHHHHH--HHHHh----C-CCCCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEE
Confidence            3466666  44332    1 247899999999999965   99999999999999875

>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=94.97  E-value=0.023  Score=37.88  Aligned_cols=45  Identities=20%  Similarity=0.254  Sum_probs=37.7

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .+..|.+.|.++ +++|..|||+.+|+++   ..+.|.++.|...|++.
T Consensus         8 ~~~~il~~L~~~-~~~s~~ela~~lg~s~---~tv~~~l~~L~~~G~i~   52 (151)
T 2cyy_A            8 IDKKIIKILQND-GKAPLREISKITGLAE---STIHERIRKLRESGVIK   52 (151)
T ss_dssp             HHHHHHHHHHHC-TTCCHHHHHHHHCSCH---HHHHHHHHHHHHHTSSC
T ss_pred             HHHHHHHHHHHc-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCeE
Confidence            455667777664 6899999999999954   89999999999999875

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

Probab=94.92  E-value=0.023  Score=38.26  Aligned_cols=45  Identities=13%  Similarity=0.181  Sum_probs=37.5

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .+..|.+.|.++ +++|..|||+++|+++   ..+.|.++.|...|++.
T Consensus        11 ~~~~il~~L~~~-~~~s~~ela~~lg~s~---~tv~~~l~~L~~~G~i~   55 (162)
T 2p5v_A           11 TDIKILQVLQEN-GRLTNVELSERVALSP---SPCLRRLKQLEDAGIVR   55 (162)
T ss_dssp             HHHHHHHHHHHC-TTCCHHHHHHHHTSCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHHc-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEe
Confidence            455667777664 6899999999999954   89999999999999875

>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=94.90  E-value=0.025  Score=36.90  Aligned_cols=44  Identities=16%  Similarity=0.206  Sum_probs=36.5

Q ss_pred             hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      +..|...|.. ++++|..|||+.+|+++   ..+.|.++.|...|++.
T Consensus         6 ~~~il~~L~~-~~~~~~~ela~~lg~s~---~tv~~~l~~L~~~G~i~   49 (141)
T 1i1g_A            6 DKIILEILEK-DARTPFTEIAKKLGISE---TAVRKRVKALEEKGIIE   49 (141)
T ss_dssp             HHHHHHHHHH-CTTCCHHHHHHHHTSCH---HHHHHHHHHHHHHTSSC
T ss_pred             HHHHHHHHHH-cCCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEe
Confidence            4456677765 36899999999999954   89999999999999885

>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=94.83  E-value=0.029  Score=37.59  Aligned_cols=47  Identities=6%  Similarity=0.210  Sum_probs=36.0

Q ss_pred             HHHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           38 SMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        38 s~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      ..++++.  +.|      +.+.+. |+.|||+.+++++   ..|.+||+.|...|++..
T Consensus         9 ~yAl~~L--~~L------a~~~~~-s~~~IA~~~~i~~---~~l~kIl~~L~~aGlv~s   55 (145)
T 1xd7_A            9 AVAIHIL--SLI------SMDEKT-SSEIIADSVNTNP---VVVRRMISLLKKADILTS   55 (145)
T ss_dssp             HHHHHHH--HHH------HTCSCC-CHHHHHHHHTSCH---HHHHHHHHHHHHTTSEEC
T ss_pred             HHHHHHH--HHH------HhCCCC-CHHHHHHHHCcCH---HHHHHHHHHHHHCCceEe
Confidence            4466666  443      333345 9999999999955   999999999999999863

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

Probab=94.79  E-value=0.037  Score=35.55  Aligned_cols=34  Identities=18%  Similarity=0.272  Sum_probs=30.1

Q ss_pred             CCCC--HHHHHHHh-CCCCCCcccHHHHHHHHHhcCcccc
Q 041844           60 KPMT--LNQLLGAL-QIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        60 gp~s--~~ELA~~~-g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      |+.+  ..||++.+ |+.+   ..|.|.|+.|...|+++.
T Consensus        39 g~~~~~~~eL~~~l~gis~---~~ls~~L~~Le~~GlV~r   75 (111)
T 3df8_A           39 GSTRQNFNDIRSSIPGISS---TILSRRIKDLIDSGLVER   75 (111)
T ss_dssp             SSSCBCHHHHHHTSTTCCH---HHHHHHHHHHHHTTSEEE
T ss_pred             CCCCCCHHHHHHHccCCCH---HHHHHHHHHHHHCCCEEE
Confidence            6777  99999999 8954   899999999999999863

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

Probab=94.75  E-value=0.026  Score=37.39  Aligned_cols=45  Identities=13%  Similarity=0.248  Sum_probs=37.8

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .+..|.+.|.. ++++|..|||+.+|+++   ..+.|.++.|...|++.
T Consensus        10 ~d~~il~~L~~-~~~~s~~ela~~lg~s~---~tv~~~l~~L~~~G~i~   54 (151)
T 2dbb_A           10 VDMQLVKILSE-NSRLTYRELADILNTTR---QRIARRIDKLKKLGIIR   54 (151)
T ss_dssp             HHHHHHHHHHH-CTTCCHHHHHHHTTSCH---HHHHHHHHHHHHHTSEE
T ss_pred             HHHHHHHHHHH-cCCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEE
Confidence            45567777876 47899999999999954   88999999999999875

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

Probab=94.74  E-value=0.016  Score=38.15  Aligned_cols=46  Identities=15%  Similarity=0.102  Sum_probs=38.0

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHh--CCCCCCcccHHHHHHHHHhcCcccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGAL--QIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~--g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      ++-.|.+.|.++ |++|+.|||+.+  |+.+   ..+.+-++.|...|+++.
T Consensus        14 ~d~~IL~~L~~~-g~~s~~eLA~~l~~giS~---~aVs~rL~~Le~~GLV~~   61 (111)
T 3b73_A           14 WDDRILEIIHEE-GNGSPKELEDRDEIRISK---SSVSRRLKKLADHDLLQP   61 (111)
T ss_dssp             HHHHHHHHHHHH-SCBCHHHHHTSTTCCSCH---HHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHHc-CCCCHHHHHHHHhcCCCH---HHHHHHHHHHHHCCCEEe
Confidence            455667778654 699999999999  8854   899999999999999863

>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=94.73  E-value=0.027  Score=37.49  Aligned_cols=45  Identities=16%  Similarity=0.357  Sum_probs=37.4

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .+..|.+.|.++ +++|..|||+++|+++   ..+.|.++.|...|++.
T Consensus         9 ~d~~il~~L~~~-~~~s~~ela~~lg~s~---~tv~~~l~~L~~~G~i~   53 (152)
T 2cg4_A            9 LDRGILEALMGN-ARTAYAELAKQFGVSP---ETIHVRVEKMKQAGIIT   53 (152)
T ss_dssp             HHHHHHHHHHHC-TTSCHHHHHHHHTSCH---HHHHHHHHHHHHHTSEE
T ss_pred             HHHHHHHHHHHc-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHcCCcc
Confidence            345566777664 6899999999999954   89999999999999875

>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=94.71  E-value=0.02  Score=35.11  Aligned_cols=46  Identities=20%  Similarity=0.263  Sum_probs=36.8

Q ss_pred             HhcChhHHHhhCC--CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHT--KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~--gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .+-.|.+.|...+  +++|+.|||+++|++   ...+.|.|..|...|++.
T Consensus        15 ~~~~IL~~L~~~~~~~~~t~~eLA~~Lgvs---~~tV~~~L~~L~~~G~I~   62 (77)
T 1qgp_A           15 QEQRILKFLEELGEGKATTAHDLSGKLGTP---KKEINRVLYSLAKKGKLQ   62 (77)
T ss_dssp             HHHHHHHHHHHHCSSSCEEHHHHHHHHCCC---HHHHHHHHHHHHHHTSEE
T ss_pred             HHHHHHHHHHHcCCCCCcCHHHHHHHHCcC---HHHHHHHHHHHHHCCCEE
Confidence            4455666776543  489999999999994   478999999999999874

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

Probab=94.71  E-value=0.022  Score=36.82  Aligned_cols=44  Identities=7%  Similarity=0.073  Sum_probs=36.0

Q ss_pred             hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      +..|...|..+ +++|..|||+.+++++   ..+.|+++.|...|++.
T Consensus        33 q~~iL~~l~~~-~~~t~~eLa~~l~~~~---~tvs~~l~~Le~~Glv~   76 (145)
T 3g3z_A           33 LFAVLYTLATE-GSRTQKHIGEKWSLPK---QTVSGVCKTLAGQGLIE   76 (145)
T ss_dssp             HHHHHHHHHHH-CSBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHC-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEe
Confidence            44455566554 5799999999999954   89999999999999986

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

Probab=94.70  E-value=0.029  Score=38.09  Aligned_cols=45  Identities=9%  Similarity=0.160  Sum_probs=38.2

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .+..|.+.|.+ ++++|..|||+++|+++   ..+.|-++.|...|++.
T Consensus         4 ~d~~il~~L~~-~~~~s~~~la~~lg~s~---~tv~~rl~~L~~~g~i~   48 (162)
T 3i4p_A            4 LDRKILRILQE-DSTLAVADLAKKVGLST---TPCWRRIQKMEEDGVIR   48 (162)
T ss_dssp             HHHHHHHHHTT-CSCSCHHHHHHHHTCCH---HHHHHHHHHHHHTTSSC
T ss_pred             HHHHHHHHHHH-CCCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCee
Confidence            45667788865 47999999999999955   89999999999999875

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

Probab=94.68  E-value=0.029  Score=36.76  Aligned_cols=45  Identities=11%  Similarity=0.129  Sum_probs=37.0

Q ss_pred             hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      ++.|...|.. .+++|..|||+.+++++   ..+.|+++.|...|++..
T Consensus        51 ~~~iL~~l~~-~~~~t~~ela~~l~is~---~tvs~~l~~Le~~glv~r   95 (162)
T 2fa5_A           51 EWRVITILAL-YPGSSASEVSDRTAMDK---VAVSRAVARLLERGFIRR   95 (162)
T ss_dssp             HHHHHHHHHH-STTCCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEC
T ss_pred             HHHHHHHHHh-CCCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEee
Confidence            4455666765 36899999999999954   899999999999999863

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

Probab=94.67  E-value=0.014  Score=37.62  Aligned_cols=44  Identities=14%  Similarity=0.166  Sum_probs=36.0

Q ss_pred             hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      +..|...|..+ +++|..|||+.+++++   ..+.|+++.|...|++.
T Consensus        39 ~~~iL~~l~~~-~~~t~~eLa~~l~~~~---~~vs~~l~~L~~~Glv~   82 (143)
T 3oop_A           39 QWSVLEGIEAN-EPISQKEIALWTKKDT---PTVNRIVDVLLRKELIV   82 (143)
T ss_dssp             HHHHHHHHHHH-SSEEHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHc-CCcCHHHHHHHHCCCH---hhHHHHHHHHHHCCCee
Confidence            34445556544 7999999999999954   89999999999999986

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

Probab=94.64  E-value=0.016  Score=36.70  Aligned_cols=43  Identities=21%  Similarity=0.134  Sum_probs=35.3

Q ss_pred             hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ...|-+.|... | +|+.|||+++|+..   ..++|.|..|...|++.
T Consensus        19 ~~~IL~lL~~~-g-~sa~eLAk~LgiSk---~aVr~~L~~Le~eG~I~   61 (82)
T 1oyi_A           19 VCEAIKTIGIE-G-ATAAQLTRQLNMEK---REVNKALYDLQRSAMVY   61 (82)
T ss_dssp             HHHHHHHHSSS-T-EEHHHHHHHSSSCH---HHHHHHHHHHHHHTSSE
T ss_pred             HHHHHHHHHHc-C-CCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEE
Confidence            34556777653 3 99999999999954   89999999999999875

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

Probab=94.64  E-value=0.021  Score=36.25  Aligned_cols=41  Identities=17%  Similarity=0.159  Sum_probs=33.7

Q ss_pred             hhHHHhhCCCCCCHHHHHHHh-CCCCCCcccHHHHHHHHHhcCcccc
Q 041844           51 IPDIIHNHTKPMTLNQLLGAL-QIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        51 I~D~La~~~gp~s~~ELA~~~-g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      |...|.  .++++..||++.+ |+++   ..+.+.|+.|...|+++.
T Consensus        19 IL~~L~--~~~~~~~eLa~~l~~is~---~tls~~L~~Le~~GlI~r   60 (107)
T 2hzt_A           19 ILXHLT--HGKKRTSELKRLMPNITQ---KMLTQQLRELEADGVINR   60 (107)
T ss_dssp             HHHHHT--TCCBCHHHHHHHCTTSCH---HHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHH--hCCCCHHHHHHHhcCCCH---HHHHHHHHHHHHCCCEEE
Confidence            334453  3799999999999 9954   899999999999999863

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

Probab=94.62  E-value=0.026  Score=36.05  Aligned_cols=39  Identities=21%  Similarity=0.255  Sum_probs=32.9

Q ss_pred             hHHHhhCCCCCCHHHHHHHh-CCCCCCcccHHHHHHHHHhcCccc
Q 041844           52 PDIIHNHTKPMTLNQLLGAL-QIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        52 ~D~La~~~gp~s~~ELA~~~-g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ...|..  ++++..|||+.+ ++++   ..+.|.++.|...|++.
T Consensus        28 L~~L~~--~~~~~~eLa~~l~~is~---~tvs~~L~~Le~~GlI~   67 (112)
T 1z7u_A           28 MDELFQ--GTKRNGELMRALDGITQ---RVLTDRLREMEKDGLVH   67 (112)
T ss_dssp             HHHHHH--SCBCHHHHHHHSTTCCH---HHHHHHHHHHHHHTSEE
T ss_pred             HHHHHh--CCCCHHHHHHHhccCCH---HHHHHHHHHHHHCCCEE
Confidence            344544  789999999999 9944   89999999999999986

>3mwm_A ZUR, putative metal uptake regulation protein; FUR, regulatory metal, graded transcription regulation, transcription; 2.40A {Streptomyces coelicolor}

Probab=94.61  E-value=0.03  Score=37.48  Aligned_cols=50  Identities=10%  Similarity=0.081  Sum_probs=39.0

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCC-CC-CCcccHHHHHHHHHhcCcccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQI-HP-TKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~-~~-~~~~~L~RlLR~Laa~gif~e   96 (97)
                      .+.-|.+.|.+.+++.|+.||.+.+.- .| -+...++|.|..|+..|++.+
T Consensus        15 qR~~Il~~L~~~~~h~sa~eI~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~   66 (139)
T 3mwm_A           15 QRAAVSAALQEVEEFRSAQELHDMLKHKGDAVGLTTVYRTLQSLADAGEVDV   66 (139)
T ss_dssp             HHHHHHHHHTTCSSCEEHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTSSEE
T ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHHHCCCEEE
Confidence            445677888776789999999999842 11 156889999999999998753

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

Probab=94.61  E-value=0.02  Score=38.19  Aligned_cols=45  Identities=16%  Similarity=0.109  Sum_probs=34.6

Q ss_pred             hcChhHHHhhC-CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           48 QVGIPDIIHNH-TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        48 eLgI~D~La~~-~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++.|...|..+ ++++|..|||+.+++++   ..+.|+++.|...|++.
T Consensus        48 q~~vL~~l~~~~~~~~t~~eLa~~l~~~~---~tvs~~l~~Le~~Glv~   93 (168)
T 3u2r_A           48 QYNTLRLLRSVHPEGMATLQIADRLISRA---PDITRLIDRLDDRGLVL   93 (168)
T ss_dssp             HHHHHHHHHHHTTSCEEHHHHHHHC---C---THHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHhcCCCCcCHHHHHHHHCCCh---hhHHHHHHHHHHCCCEe
Confidence            44455566665 37999999999999955   89999999999999986

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

Probab=94.60  E-value=0.023  Score=36.19  Aligned_cols=45  Identities=20%  Similarity=0.211  Sum_probs=36.9

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .++.|...|..+ +++|..|||+.+++++   ..+.|+++.|...|++.
T Consensus        32 ~~~~iL~~l~~~-~~~~~~ela~~l~is~---~~vs~~l~~L~~~gli~   76 (142)
T 3bdd_A           32 TRYSILQTLLKD-APLHQLALQERLQIDR---AAVTRHLKLLEESGYII   76 (142)
T ss_dssp             HHHHHHHHHHHH-CSBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHhC-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEE
Confidence            345566667654 5899999999999954   89999999999999875

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

Probab=94.53  E-value=0.027  Score=36.72  Aligned_cols=44  Identities=9%  Similarity=0.141  Sum_probs=35.9

Q ss_pred             hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++.|...|.. .+++|..|||+.++++   ...+.|+++.|...|++.
T Consensus        45 ~~~iL~~l~~-~~~~t~~ela~~l~i~---~~tvs~~l~~Le~~Glv~   88 (155)
T 3cdh_A           45 EWRVLACLVD-NDAMMITRLAKLSLME---QSRMTRIVDQMDARGLVT   88 (155)
T ss_dssp             HHHHHHHHSS-CSCBCHHHHHHHTTCC---HHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHH-CCCcCHHHHHHHHCCC---HHHHHHHHHHHHHCCCEE
Confidence            3445555654 3689999999999994   489999999999999986

>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=94.51  E-value=0.022  Score=36.86  Aligned_cols=44  Identities=23%  Similarity=0.240  Sum_probs=36.1

Q ss_pred             hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++.|...|..+ +++|..|||+.+++++   ..+.|+++.|...|++.
T Consensus        42 ~~~iL~~l~~~-~~~t~~ela~~l~~~~---~~vs~~l~~Le~~Glv~   85 (152)
T 3bj6_A           42 QRAILEGLSLT-PGATAPQLGAALQMKR---QYISRILQEVQRAGLIE   85 (152)
T ss_dssp             HHHHHHHHHHS-TTEEHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHhC-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCee
Confidence            34455566654 5899999999999954   89999999999999886

>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=94.50  E-value=0.016  Score=34.86  Aligned_cols=47  Identities=13%  Similarity=0.340  Sum_probs=36.2

Q ss_pred             hcChhHHHhhCCCCCCHHHHHHHhCCCC-CCcccHHHHHHHHHhcCccc
Q 041844           48 QVGIPDIIHNHTKPMTLNQLLGALQIHP-TKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        48 eLgI~D~La~~~gp~s~~ELA~~~g~~~-~~~~~L~RlLR~Laa~gif~   95 (97)
                      +..|.+.|.. .++.|..||++.++.++ -++..+.|+++.|...|++.
T Consensus        11 e~~vL~~L~~-~~~~t~~ei~~~l~~~~~~s~~Tv~~~l~rL~~kGlv~   58 (82)
T 1p6r_A           11 ELEVMKVIWK-HSSINTNEVIKELSKTSTWSPKTIQTMLLRLIKKGALN   58 (82)
T ss_dssp             HHHHHHHHHT-SSSEEHHHHHHHHHHHSCCCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHc-CCCCCHHHHHHHHhhcCCccHHHHHHHHHHHHHCCCeE
Confidence            4455666665 47999999999997421 14588999999999999886

>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=94.50  E-value=0.038  Score=34.41  Aligned_cols=46  Identities=20%  Similarity=0.258  Sum_probs=36.7

Q ss_pred             HhcChhHHHhhCC--CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHT--KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~--gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++-.|.+.|.+.+  .++|+.|||+++|++.   ..+.|.|..|...|++.
T Consensus        11 ~~~~IL~~L~~~~pg~~~t~~eLA~~Lgvsr---~tV~~~L~~Le~~G~I~   58 (81)
T 1qbj_A           11 QEQRILKFLEELGEGKATTAHDLSGKLGTPK---KEINRVLYSLAKKGKLQ   58 (81)
T ss_dssp             HHHHHHHHHHHHCTTCCBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHHcCCCCCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEE
Confidence            4555667776543  4799999999999943   78999999999999875

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

Probab=94.47  E-value=0.026  Score=37.01  Aligned_cols=45  Identities=13%  Similarity=0.092  Sum_probs=37.1

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .++.|...|..+ +++|..|||+.+++++   ..+.|+++.|...|++.
T Consensus        45 ~~~~iL~~l~~~-~~~t~~ela~~l~is~---~tvs~~l~~Le~~Gli~   89 (154)
T 2eth_A           45 TELYAFLYVALF-GPKKMKEIAEFLSTTK---SNVTNVVDSLEKRGLVV   89 (154)
T ss_dssp             HHHHHHHHHHHH-CCBCHHHHHHHTTSCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHHc-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEE
Confidence            355566667654 5899999999999944   89999999999999886

>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=94.46  E-value=0.025  Score=36.23  Aligned_cols=44  Identities=23%  Similarity=0.195  Sum_probs=36.0

Q ss_pred             hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++.|...|..+ +++|..|||+.+++++   ..+.|+++.|...|++.
T Consensus        35 ~~~iL~~l~~~-~~~~~~~la~~l~~s~---~tvs~~l~~L~~~glv~   78 (145)
T 2a61_A           35 QFDILQKIYFE-GPKRPGELSVLLGVAK---STVTGLVKRLEADGYLT   78 (145)
T ss_dssp             HHHHHHHHHHH-CCBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHc-CCCCHHHHHHHHCCCc---hhHHHHHHHHHHCCCee
Confidence            44455566553 6899999999999954   89999999999999885

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

Probab=94.39  E-value=0.036  Score=38.17  Aligned_cols=45  Identities=18%  Similarity=0.354  Sum_probs=38.0

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++..|.+.|..+ +++|..|||+++|+++   ..+.|.++.|...|++.
T Consensus        18 ~d~~IL~~L~~~-~~~s~~eLA~~lglS~---~tv~~~l~~L~~~G~I~   62 (171)
T 2ia0_A           18 LDRNILRLLKKD-ARLTISELSEQLKKPE---STIHFRIKKLQERGVIE   62 (171)
T ss_dssp             HHHHHHHHHHHC-TTCCHHHHHHHHTSCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHHc-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEE
Confidence            456677778764 6899999999999954   89999999999999875

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

Probab=94.39  E-value=0.027  Score=36.36  Aligned_cols=44  Identities=16%  Similarity=0.147  Sum_probs=35.7

Q ss_pred             hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++.|...|..+ +++|..|||+.+++++   ..+.|+++.|...|++.
T Consensus        44 ~~~iL~~l~~~-~~~t~~ela~~l~~~~---~tvs~~l~~Le~~Glv~   87 (150)
T 2rdp_A           44 QFVALQWLLEE-GDLTVGELSNKMYLAC---STTTDLVDRMERNGLVA   87 (150)
T ss_dssp             HHHHHHHHHHH-CSBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHc-CCCCHHHHHHHHCCCc---hhHHHHHHHHHHCCCee
Confidence            34445556553 6899999999999954   89999999999999885

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

Probab=94.39  E-value=0.025  Score=36.30  Aligned_cols=44  Identities=9%  Similarity=0.068  Sum_probs=36.0

Q ss_pred             hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++.|...|..+ +++|..|||+.+++++   ..+.|+++.|...|++.
T Consensus        31 ~~~iL~~l~~~-~~~t~~~la~~l~~s~---~~vs~~l~~Le~~gli~   74 (144)
T 1lj9_A           31 QYLYLVRVCEN-PGIIQEKIAELIKVDR---TTAARAIKRLEEQGFIY   74 (144)
T ss_dssp             HHHHHHHHHHS-TTEEHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHC-cCcCHHHHHHHHCCCH---hHHHHHHHHHHHCCCEE
Confidence            34455566654 5899999999999954   89999999999999885

>1uly_A Hypothetical protein PH1932; helix-turn-helix, structural genomics, DNA binding protein; 2.50A {Pyrococcus horikoshii} SCOP: a.4.5.58 PDB: 2cwe_A

Probab=94.37  E-value=0.045  Score=38.62  Aligned_cols=44  Identities=25%  Similarity=0.362  Sum_probs=38.4

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .+..|...|.+  +++|..|||+.+|+++   ..+.|.++.|...|++.
T Consensus        21 ~~~~IL~~L~~--~~~s~~eLA~~lglS~---stv~~~l~~Le~~GlI~   64 (192)
T 1uly_A           21 TRRKILKLLRN--KEMTISQLSEILGKTP---QTIYHHIEKLKEAGLVE   64 (192)
T ss_dssp             HHHHHHHHHTT--CCBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHc--CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEE
Confidence            66778888863  7999999999999954   89999999999999875

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

Probab=94.35  E-value=0.023  Score=36.63  Aligned_cols=43  Identities=12%  Similarity=0.124  Sum_probs=35.3

Q ss_pred             hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++.|...|..++ + |..|||+.+++++   ..+.|+++.|...|++.
T Consensus        39 ~~~iL~~l~~~~-~-~~~~la~~l~~~~---~tvs~~l~~Le~~Glv~   81 (144)
T 3f3x_A           39 DFSILKATSEEP-R-SMVYLANRYFVTQ---SAITAAVDKLEAKGLVR   81 (144)
T ss_dssp             HHHHHHHHHHSC-E-EHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHCC-C-CHHHHHHHHCCCh---hHHHHHHHHHHHCCCEE
Confidence            445566676654 4 9999999999954   89999999999999886

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

Probab=94.34  E-value=0.033  Score=36.22  Aligned_cols=33  Identities=18%  Similarity=0.325  Sum_probs=30.3

Q ss_pred             CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      +++|..|||+.+++++   ..+.|+++.|...|++.
T Consensus        21 ~~~~~~ela~~l~vs~---~tvs~~l~~Le~~Glv~   53 (142)
T 1on2_A           21 GYARVSDIAEALAVHP---SSVTKMVQKLDKDEYLI   53 (142)
T ss_dssp             SSCCHHHHHHHHTSCH---HHHHHHHHHHHHTTSEE
T ss_pred             CCCCHHHHHHHhCCCH---HHHHHHHHHHHHCCCEE
Confidence            6899999999999954   89999999999999885

>2w57_A Ferric uptake regulation protein; gene regulation, transcription regulation, transport, iron, repressor, DNA-binding, transcription; 2.60A {Vibrio cholerae}

Probab=94.21  E-value=0.029  Score=37.98  Aligned_cols=50  Identities=8%  Similarity=0.105  Sum_probs=38.3

Q ss_pred             HhcChhHHHhhCC-CCCCHHHHHHHhCC-CC-CCcccHHHHHHHHHhcCcccc
Q 041844           47 IQVGIPDIIHNHT-KPMTLNQLLGALQI-HP-TKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        47 veLgI~D~La~~~-gp~s~~ELA~~~g~-~~-~~~~~L~RlLR~Laa~gif~e   96 (97)
                      .+.-|.+.|.+.+ ++.|+.||.+.+.- .| .+...++|.|+.|+..|++..
T Consensus        18 qR~~Il~~L~~~~~~h~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~~   70 (150)
T 2w57_A           18 PRLKILEVLQQPECQHISAEELYKKLIDLGEEIGLATVYRVLNQFDDAGIVTR   70 (150)
T ss_dssp             HHHHHHHHHTSGGGSSEEHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHHHCCcEEE
Confidence            4455778887666 79999999999832 11 155889999999999998853

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

Probab=94.19  E-value=0.029  Score=36.50  Aligned_cols=45  Identities=18%  Similarity=0.183  Sum_probs=36.8

Q ss_pred             hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      ++.|...|..+ +++|..|||+.+++++   ..+.|+++.|...|++..
T Consensus        43 ~~~iL~~l~~~-~~~t~~eLa~~l~~~~---~tvs~~l~~Le~~Glv~r   87 (154)
T 2qww_A           43 QLAMINVIYST-PGISVADLTKRLIITG---SSAAANVDGLISLGLVVK   87 (154)
T ss_dssp             HHHHHHHHHHS-TTEEHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHC-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEe
Confidence            44555566654 6899999999999954   899999999999998863

>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=94.18  E-value=0.038  Score=35.44  Aligned_cols=44  Identities=11%  Similarity=0.272  Sum_probs=36.2

Q ss_pred             hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++.|...|..+ +++|..|||+.+++++   ..+.|+++.|...|++.
T Consensus        39 ~~~iL~~l~~~-~~~~~~ela~~l~~~~---~tvs~~l~~L~~~gli~   82 (142)
T 2bv6_A           39 QFLVLTILWDE-SPVNVKKVVTELALDT---GTVSPLLKRMEQVDLIK   82 (142)
T ss_dssp             HHHHHHHHHHS-SEEEHHHHHHHTTCCT---TTHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHc-CCcCHHHHHHHHCCCh---hhHHHHHHHHHHCCCEE
Confidence            44555566654 5899999999999955   89999999999999885

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

Probab=94.09  E-value=0.029  Score=36.62  Aligned_cols=45  Identities=22%  Similarity=0.261  Sum_probs=36.6

Q ss_pred             hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      +..|...|..+ +++|..|||+.+++++   ..+.|+++.|...|++..
T Consensus        43 q~~iL~~l~~~-~~~~~~eLa~~l~~~~---~~vs~~l~~L~~~Glv~r   87 (149)
T 4hbl_A           43 QYLVMLTLWEE-NPQTLNSIGRHLDLSS---NTLTPMLKRLEQSGWVKR   87 (149)
T ss_dssp             HHHHHHHHHHS-SSEEHHHHHHHHTCCH---HHHHHHHHHHHHHTSEEC
T ss_pred             HHHHHHHHHHC-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEee
Confidence            44445556554 7899999999999954   899999999999999863

>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=94.01  E-value=0.04  Score=34.41  Aligned_cols=42  Identities=14%  Similarity=0.136  Sum_probs=35.0

Q ss_pred             ChhHHHhhCCCCCCHHHHHHHhCCCCCCcc-cHHHHHHHHHhcCccc
Q 041844           50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTR-CLHFLVCSLVRSGFFN   95 (97)
Q Consensus        50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~-~L~RlLR~Laa~gif~   95 (97)
                      .|.+.|..+ ||.|+.|||+.+|+.+   . .++|.|..|...|++.
T Consensus        15 ~IL~~Lk~~-g~~ta~eiA~~Lgit~---~~aVr~hL~~Le~eGlV~   57 (79)
T 1xmk_A           15 KICDYLFNV-SDSSALNLAKNIGLTK---ARDINAVLIDMERQGDVY   57 (79)
T ss_dssp             HHHHHHHHT-CCEEHHHHHHHHCGGG---HHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHc-CCcCHHHHHHHcCCCc---HHHHHHHHHHHHHCCCEE
Confidence            455667554 6999999999999954   7 8999999999999874

>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=94.00  E-value=0.036  Score=35.26  Aligned_cols=44  Identities=20%  Similarity=0.170  Sum_probs=35.4

Q ss_pred             hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++.|...|..+ +++|..|||+.+++++   ..+.|+++.|...|++.
T Consensus        36 ~~~iL~~l~~~-~~~~~~~la~~l~~~~---~tvs~~l~~L~~~gli~   79 (138)
T 1jgs_A           36 QFKVLCSIRCA-ACITPVELKKVLSVDL---GALTRMLDRLVCKGWVE   79 (138)
T ss_dssp             HHHHHHHHHHH-SSBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHhc-CCCCHHHHHHHHCCCh---HHHHHHHHHHHHCCCEE
Confidence            34445556543 6899999999999954   89999999999999886

>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=93.97  E-value=0.034  Score=34.25  Aligned_cols=45  Identities=11%  Similarity=0.118  Sum_probs=35.4

Q ss_pred             hcChhHHHhhCCCCCCHHHH----HHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           48 QVGIPDIIHNHTKPMTLNQL----LGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        48 eLgI~D~La~~~gp~s~~EL----A~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      ++.|...|.. .+++|..||    |+.++++   +..+.|+++.|...|++..
T Consensus        10 q~~iL~~l~~-~~~~~~~el~~~la~~l~is---~~tvs~~l~~Le~~gli~r   58 (99)
T 1tbx_A           10 EAIVLAYLYD-NEGIATYDLYKKVNAEFPMS---TATFYDAKKFLIQEGFVKE   58 (99)
T ss_dssp             HHHHHHHHTT-CTTCBHHHHHHHHHTTSCCC---HHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHH-cCCcCHHHHHHHHHHHcCCC---HHHHHHHHHHHHHCCCEEE
Confidence            3445555654 368999999    8888994   4899999999999998863

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

Probab=93.93  E-value=0.035  Score=36.55  Aligned_cols=49  Identities=16%  Similarity=0.228  Sum_probs=37.3

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCC-CCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHP-TKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~-~~~~~L~RlLR~Laa~gif~   95 (97)
                      .+..|...|..+.+++|..||++.++.++ -++..+.|++.-|...|++.
T Consensus        10 ~e~~vL~~L~~~~~~~t~~el~~~l~~~~~~~~~Tvt~~l~rLe~kGlv~   59 (138)
T 2g9w_A           10 LERAVMDHLWSRTEPQTVRQVHEALSARRDLAYTTVMAVLQRLAKKNLVL   59 (138)
T ss_dssp             HHHHHHHHHHTCSSCEEHHHHHHHHTTTCCCCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHhcCCCCCHHHHHHHHhccCCCCHHHHHHHHHHHHHCCCEE
Confidence            34455666765447999999999998321 14589999999999999886

>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=93.93  E-value=0.039  Score=37.89  Aligned_cols=46  Identities=20%  Similarity=0.210  Sum_probs=38.0

Q ss_pred             HhcChhHHHhhC-CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNH-TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~-~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .+..|...|..+ ++++|..|||+.+++++   ..+.|+++.|...|++.
T Consensus        42 ~q~~vL~~L~~~~~~~~t~~eLa~~l~is~---~tvs~~l~~Le~~GlV~   88 (189)
T 3nqo_A           42 RQYMTILSILHLPEEETTLNNIARKMGTSK---QNINRLVANLEKNGYVD   88 (189)
T ss_dssp             HHHHHHHHHHHSCGGGCCHHHHHHHHTSCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHhccCCCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEE
Confidence            455566667654 37999999999999954   89999999999999986

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

Probab=93.89  E-value=0.028  Score=35.79  Aligned_cols=45  Identities=20%  Similarity=0.186  Sum_probs=36.5

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .++.|...|..+ +++|..|||+.+++++   ..+.|+++.|...|++.
T Consensus        37 ~~~~iL~~l~~~-~~~t~~ela~~l~~s~---~~vs~~l~~Le~~glv~   81 (142)
T 2fbi_A           37 QQWRVIRILRQQ-GEMESYQLANQACILR---PSMTGVLARLERDGIVR   81 (142)
T ss_dssp             HHHHHHHHHHHH-CSEEHHHHHHHTTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHHc-CCCCHHHHHHHHCCCH---hHHHHHHHHHHHCCCEE
Confidence            345555666553 5899999999999954   89999999999999885

>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=93.85  E-value=0.021  Score=36.80  Aligned_cols=45  Identities=13%  Similarity=0.197  Sum_probs=36.1

Q ss_pred             hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      ++.|...|..+ +++|..|||+.+++++   ..+.|+++.|...|++..
T Consensus        42 ~~~iL~~l~~~-~~~~~~~la~~l~~~~---~tvs~~l~~L~~~glv~r   86 (147)
T 1z91_A           42 QYLALLLLWEH-ETLTVKKMGEQLYLDS---GTLTPMLKRMEQQGLITR   86 (147)
T ss_dssp             HHHHHHHHHHH-SEEEHHHHHHTTTCCH---HHHHHHHHHHHHHTSEEC
T ss_pred             HHHHHHHHHHC-CCCCHHHHHHHHCCCc---CcHHHHHHHHHHCCCEEe
Confidence            44455556554 5899999999999954   899999999999998863

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

Probab=93.84  E-value=0.035  Score=36.52  Aligned_cols=43  Identities=14%  Similarity=0.098  Sum_probs=35.3

Q ss_pred             cChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           49 VGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        49 LgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ..|...|..+ +++|..|||+.+++++   ..+.|+++.|...|++.
T Consensus        53 ~~vL~~l~~~-~~~t~~eLa~~l~~~~---~tvs~~l~~Le~~Glv~   95 (159)
T 3s2w_A           53 FPFLMRLYRE-DGINQESLSDYLKIDK---GTTARAIQKLVDEGYVF   95 (159)
T ss_dssp             HHHHHHHHHS-CSEEHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHC-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEE
Confidence            3344556554 7899999999999954   89999999999999986

>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=93.80  E-value=0.042  Score=39.19  Aligned_cols=45  Identities=13%  Similarity=0.194  Sum_probs=37.7

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      ..+.|...|..  +|+|..|||+.+|+++   ..+++.|+.|...|++..
T Consensus        16 ~rl~IL~~L~~--~~~s~~eLa~~l~is~---stvs~hLk~Le~~GLV~~   60 (202)
T 2p4w_A           16 TRRRILFLLTK--RPYFVSELSRELGVGQ---KAVLEHLRILEEAGLIES   60 (202)
T ss_dssp             HHHHHHHHHHH--SCEEHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHh--CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCceEE
Confidence            55566667754  7999999999999954   899999999999999863

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

Probab=93.74  E-value=0.038  Score=36.28  Aligned_cols=44  Identities=11%  Similarity=0.101  Sum_probs=36.5

Q ss_pred             hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++.|...|..+ +++|..|||+.+++++   ..+.|+++.|...|++.
T Consensus        54 ~~~iL~~l~~~-~~~t~~ela~~l~is~---~tvs~~l~~Le~~Gli~   97 (162)
T 3cjn_A           54 KMRALAILSAK-DGLPIGTLGIFAVVEQ---STLSRALDGLQADGLVR   97 (162)
T ss_dssp             HHHHHHHHHHS-CSEEHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHC-CCCCHHHHHHHHCCCh---hHHHHHHHHHHHCCCEE
Confidence            44556667654 6899999999999954   89999999999999885

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

Probab=93.74  E-value=0.039  Score=35.87  Aligned_cols=44  Identities=14%  Similarity=0.166  Sum_probs=35.9

Q ss_pred             hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++.|...|..+ +++|..|||+.++++   ...+.|+++.|...|++.
T Consensus        49 ~~~iL~~l~~~-~~~t~~ela~~l~~s---~~tvs~~l~~Le~~glv~   92 (153)
T 2pex_A           49 QYLVMLVLWET-DERSVSEIGERLYLD---SATLTPLLKRLQAAGLVT   92 (153)
T ss_dssp             HHHHHHHHHHS-CSEEHHHHHHHHTCC---HHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHhC-CCcCHHHHHHHhCCC---cccHHHHHHHHHHCCCEe
Confidence            34455556554 689999999999994   489999999999999886

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

Probab=93.71  E-value=0.029  Score=37.53  Aligned_cols=44  Identities=27%  Similarity=0.381  Sum_probs=36.3

Q ss_pred             hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++.|...|..+ +++|..|||+.+++++   ..+.|+++.|...|++.
T Consensus        47 ~~~iL~~L~~~-~~~t~~eLa~~l~is~---~tvs~~l~~Le~~GlV~   90 (168)
T 2nyx_A           47 QFRTLVILSNH-GPINLATLATLLGVQP---SATGRMVDRLVGAELID   90 (168)
T ss_dssp             HHHHHHHHHHH-CSEEHHHHHHHHTSCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHc-CCCCHHHHHHHhCCCH---HHHHHHHHHHHHCCCEE
Confidence            44555666554 5899999999999954   89999999999999986

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

Probab=93.69  E-value=0.063  Score=35.73  Aligned_cols=41  Identities=20%  Similarity=0.098  Sum_probs=34.2

Q ss_pred             hHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           52 PDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        52 ~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      --.|...+++.+..|||+.+++++   ..+.|++..|...|++.
T Consensus        37 L~~L~~~~~~~~~~eLa~~l~~~~---~tvs~~v~~Le~~GlV~   77 (151)
T 4aik_A           37 LYNINRLPPEQSQIQLAKAIGIEQ---PSLVRTLDQLEEKGLIT   77 (151)
T ss_dssp             HHHHHHSCTTSCHHHHHHHHTSCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHcCCCCcHHHHHHHHCcCH---HHHHHHHHHHHhCCCeE
Confidence            334555567789999999999954   89999999999999885

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

Probab=93.67  E-value=0.026  Score=37.34  Aligned_cols=44  Identities=16%  Similarity=0.112  Sum_probs=35.8

Q ss_pred             hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++.|...|..+ +++|..|||+.+++++   ..+.|+++.|...|++.
T Consensus        55 q~~vL~~l~~~-~~~t~~eLa~~l~~~~---~~vs~~l~~Le~~Glv~   98 (161)
T 3e6m_A           55 KLRLLSSLSAY-GELTVGQLATLGVMEQ---STTSRTVDQLVDEGLAA   98 (161)
T ss_dssp             HHHHHHHHHHH-SEEEHHHHHHHTTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHhC-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEE
Confidence            33455556554 5899999999999954   89999999999999986

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

Probab=93.43  E-value=0.054  Score=35.95  Aligned_cols=33  Identities=15%  Similarity=0.250  Sum_probs=27.7

Q ss_pred             CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      +++|..|||+.+++++   ..+.|++..|...|++.
T Consensus        51 ~~~t~~eLa~~l~~~~---~tvsr~v~~Le~~glVr   83 (148)
T 4fx0_A           51 IDLTMSELAARIGVER---TTLTRNLEVMRRDGLVR   83 (148)
T ss_dssp             ---CHHHHHHHHTCCH---HHHHHHHHHHHHTTSBC
T ss_pred             CCcCHHHHHHHHCCCh---hhHHHHHHHHHHCCCEE
Confidence            5799999999999954   89999999999999884

>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=93.33  E-value=0.02  Score=35.41  Aligned_cols=32  Identities=0%  Similarity=0.100  Sum_probs=28.9

Q ss_pred             CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcc
Q 041844           60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFF   94 (97)
Q Consensus        60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif   94 (97)
                      +++|..|||+.+++++   ..+.|++..|...|++
T Consensus        29 ~~~t~~eLa~~l~i~~---~tvs~~l~~Le~~Glv   60 (95)
T 2qvo_A           29 NDVYIQYIASKVNSPH---SYVWLIIKKFEEAKMV   60 (95)
T ss_dssp             CCEEHHHHHHHSSSCH---HHHHHHHHHHHHTTSE
T ss_pred             CCcCHHHHHHHHCcCH---HHHHHHHHHHHHCcCc
Confidence            3499999999999954   8999999999999987

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

Probab=93.29  E-value=0.07  Score=35.79  Aligned_cols=34  Identities=15%  Similarity=0.155  Sum_probs=30.8

Q ss_pred             CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      |+++..||++.+|+++   ..|.+.|+.|...|+++.
T Consensus        36 g~~~~~eLa~~lgis~---~tls~~L~~Le~~GlI~r   69 (146)
T 2f2e_A           36 GLTRFGEFQKSLGLAK---NILAARLRNLVEHGVMVA   69 (146)
T ss_dssp             TCCSHHHHHHHHCCCH---HHHHHHHHHHHHTTSEEE
T ss_pred             CCCCHHHHHHHhCCCH---HHHHHHHHHHHHCCCEEE
Confidence            7899999999999954   899999999999999863

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

Probab=93.23  E-value=0.033  Score=35.75  Aligned_cols=48  Identities=8%  Similarity=0.151  Sum_probs=37.6

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCC-CCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHP-TKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~-~~~~~L~RlLR~Laa~gif~   95 (97)
                      .+..|-+.|.+ .+++|+.||++.++.++ -++..+.|+|.-|...|++.
T Consensus        36 ~e~~VL~~L~~-~~~~t~~eL~~~l~~~~~~s~sTVt~~L~rLe~KGlV~   84 (99)
T 2k4b_A           36 AELIVMRVIWS-LGEARVDEIYAQIPQELEWSLATVKTLLGRLVKKEMLS   84 (99)
T ss_dssp             SCSHHHHHHHH-HSCEEHHHHHHTCCGGGCCCHHHHHHHHHHHHHTTSCE
T ss_pred             HHHHHHHHHHh-CCCCCHHHHHHHHhcccCCCHhhHHHHHHHHHHCCCEE
Confidence            45566677765 36999999999998631 14578999999999999886

>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=93.22  E-value=0.031  Score=36.27  Aligned_cols=44  Identities=9%  Similarity=0.311  Sum_probs=35.8

Q ss_pred             hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++.|...|..+ +++|..|||+.+++++   ..+.|+++.|...|++.
T Consensus        39 ~~~iL~~l~~~-~~~t~~ela~~l~~s~---~tvs~~l~~Le~~glv~   82 (155)
T 1s3j_A           39 QLFVLASLKKH-GSLKVSEIAERMEVKP---SAVTLMADRLEQKNLIA   82 (155)
T ss_dssp             HHHHHHHHHHH-SEEEHHHHHHHHTSCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHc-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEe
Confidence            34455566553 5899999999999954   89999999999999885

>2hoe_A N-acetylglucosamine kinase; TM1224, structural genomics, PSI-2, protein structure initiative, joint center structural genomics, JCSG; 2.46A {Thermotoga maritima} SCOP: a.4.5.63 c.55.1.10 c.55.1.10

Probab=93.17  E-value=0.054  Score=41.11  Aligned_cols=54  Identities=13%  Similarity=0.076  Sum_probs=39.8

Q ss_pred             HHHHHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           36 INSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        36 ~~s~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      ..+.+++..  .+..|.+.|.  .+++|-.|||+.+|..+   ..+.++++.|...|++.|
T Consensus        12 ~~~~~~~~~--~~~~il~~l~--~~~~sr~~la~~~gls~---~tv~~~v~~L~~~gli~~   65 (380)
T 2hoe_A           12 HMPKSVRAE--NISRILKRIM--KSPVSRVELAEELGLTK---TTVGEIAKIFLEKGIVVE   65 (380)
T ss_dssp             ------------CCCSHHHHH--HSCBCHHHHHHHHTCCH---HHHHHHHHHHHHHTSEEE
T ss_pred             cCchhHHHH--HHHHHHHHHH--cCCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEe
Confidence            346778877  8888999997  37999999999999954   899999999999999875

>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=93.14  E-value=0.032  Score=36.04  Aligned_cols=41  Identities=15%  Similarity=0.203  Sum_probs=33.7

Q ss_pred             hhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           51 IPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        51 I~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      |...|.. .+++|..|||+.+++++   ..+.|+++.|...|++.
T Consensus        41 vL~~l~~-~~~~t~~eLa~~l~~~~---~tvs~~l~~L~~~Glv~   81 (140)
T 3hsr_A           41 VLMAIEN-DEKLNIKKLGERVFLDS---GTLTPLLKKLEKKDYVV   81 (140)
T ss_dssp             HHHHSCT-TCEEEHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHH-cCCcCHHHHHHHHCCCh---hhHHHHHHHHHHCCCeE
Confidence            3344443 37899999999999954   89999999999999886

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

Probab=93.05  E-value=0.036  Score=35.77  Aligned_cols=46  Identities=15%  Similarity=0.233  Sum_probs=36.4

Q ss_pred             hcChhHHHhhC-CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           48 QVGIPDIIHNH-TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        48 eLgI~D~La~~-~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      +..|...|..+ ++++|..|||+.+++++   ..+.|++..|...|++..
T Consensus        39 q~~vL~~l~~~~~~~~t~~eLa~~l~~~~---~tvs~~l~~Le~~Glv~r   85 (127)
T 2frh_A           39 EFAVLTYISENKEKEYYLKDIINHLNYKQ---PQVVKAVKILSQEDYFDK   85 (127)
T ss_dssp             HHHHHHHHHHTCCSEEEHHHHHHHSSSHH---HHHHHHHHHHHHTTSSCC
T ss_pred             HHHHHHHHHhccCCCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEe
Confidence            33444556554 26899999999999954   899999999999999863

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

Probab=93.01  E-value=0.093  Score=31.41  Aligned_cols=44  Identities=14%  Similarity=0.175  Sum_probs=38.4

Q ss_pred             cChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           49 VGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        49 LgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      -.|-|-|.++||-+.++..++..|++   .+-+..+||-|...|+++
T Consensus        13 ~~lL~yIr~sGGildI~~~a~kygV~---kdeV~~~LrrLe~KGLI~   56 (59)
T 2xvc_A           13 RELLDYIVNNGGFLDIEHFSKVYGVE---KQEVVKLLEALKNKGLIA   56 (59)
T ss_dssp             HHHHHHHHHTTSEEEHHHHHHHHCCC---HHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHcCCEEeHHHHHHHhCCC---HHHHHHHHHHHHHCCCee
Confidence            34567788888999999999999994   489999999999999875

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

Probab=92.97  E-value=0.055  Score=41.00  Aligned_cols=40  Identities=8%  Similarity=0.061  Sum_probs=35.6

Q ss_pred             ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ||+..| +  +|.|+.|||..+|.++   ..++++|+.|++.|+++
T Consensus        47 ~ll~~L-~--~~~t~~eLa~~~g~~~---~~v~~~L~~l~~~gll~   86 (373)
T 2qm3_A           47 NVLSAV-L--ASDDIWRIVDLSEEPL---PLVVAILESLNELGYVT   86 (373)
T ss_dssp             HHHHHH-H--HCSCHHHHHHHHTSCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHh-c--CCCCHHHHHHHhCCCh---HHHHHHHHHHhhCCcEE
Confidence            778888 4  6999999999999954   89999999999999875

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

Probab=92.97  E-value=0.063  Score=39.37  Aligned_cols=45  Identities=13%  Similarity=0.228  Sum_probs=36.1

Q ss_pred             hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      ++.|...|..+ +++|..|||+.+|+++   ..+.|+++.|...|++..
T Consensus       154 ~~~IL~~L~~~-~~~s~~eLA~~lglsk---sTv~r~L~~Le~~GlV~r  198 (244)
T 2wte_A          154 EMKLLNVLYET-KGTGITELAKMLDKSE---KTLINKIAELKKFGILTQ  198 (244)
T ss_dssp             HHHHHHHHHHH-TCBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHc-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEE
Confidence            34455555543 6899999999999954   899999999999998863

>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=92.84  E-value=0.073  Score=33.56  Aligned_cols=34  Identities=18%  Similarity=0.193  Sum_probs=30.3

Q ss_pred             CCCCCHHHHHHHhC-CCCCCcccHHHHHHHHHhcCccc
Q 041844           59 TKPMTLNQLLGALQ-IHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        59 ~gp~s~~ELA~~~g-~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .++++..||++.++ +++   ..+.+.|+.|...|+++
T Consensus        36 ~~~~~~~eL~~~l~gis~---~~ls~~L~~Le~~GlV~   70 (107)
T 2fsw_A           36 RRIIRYGELKRAIPGISE---KMLIDELKFLCGKGLIK   70 (107)
T ss_dssp             TSCEEHHHHHHHSTTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             hCCcCHHHHHHHcccCCH---HHHHHHHHHHHHCCCEE
Confidence            37999999999995 844   89999999999999986

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

Probab=92.62  E-value=0.053  Score=35.96  Aligned_cols=34  Identities=18%  Similarity=0.245  Sum_probs=30.6

Q ss_pred             CCCCHHHHHHHh-CCCCCCcccHHHHHHHHHhcCcccc
Q 041844           60 KPMTLNQLLGAL-QIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        60 gp~s~~ELA~~~-g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      ++++..||++.+ |+++   ..|.+.|+.|...|+++.
T Consensus        47 g~~~~~eLa~~l~gis~---~tls~~L~~Le~~GlV~r   81 (131)
T 1yyv_A           47 GTHRFSDLRRXMGGVSE---XMLAQSLQALEQDGFLNR   81 (131)
T ss_dssp             CCEEHHHHHHHSTTCCH---HHHHHHHHHHHHHTCEEE
T ss_pred             CCCCHHHHHHHhccCCH---HHHHHHHHHHHHCCcEEE
Confidence            799999999999 6944   899999999999999863

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

Probab=92.55  E-value=0.047  Score=36.06  Aligned_cols=34  Identities=26%  Similarity=0.436  Sum_probs=30.8

Q ss_pred             CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           59 TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        59 ~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++++|..|||+.+++++   ..+.|++.-|...|++.
T Consensus        49 ~~~~t~~eLa~~l~~~~---~tvs~~v~~Le~~Glv~   82 (147)
T 4b8x_A           49 SGELPMSKIGERLMVHP---TSVTNTVDRLVRSGLVA   82 (147)
T ss_dssp             GGEEEHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             CCCcCHHHHHHHHCCCH---HHHHHHHHHHHhCCCEE
Confidence            37899999999999954   89999999999999986

>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=92.49  E-value=0.068  Score=33.85  Aligned_cols=43  Identities=9%  Similarity=0.026  Sum_probs=34.6

Q ss_pred             ChhHHHhhCC-CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           50 GIPDIIHNHT-KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        50 gI~D~La~~~-gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .|...|..++ ..++..||+.+++++.   ..+.|+|+.|...|++.
T Consensus        24 ~Vl~~I~~~g~~gi~qkeLa~~~~l~~---~tvt~iLk~LE~kglIk   67 (91)
T 2dk5_A           24 LVYQIIEDAGNKGIWSRDVRYKSNLPL---TEINKILKNLESKKLIK   67 (91)
T ss_dssp             HHHHHHHHHCTTCEEHHHHHHHTTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHcCCCCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEE
Confidence            3445555433 5799999999999954   89999999999999886

>3eyy_A Putative iron uptake regulatory protein; NUR, nickel-uptake regulator, D-domain, dimerization domain, DB-domain, DNA-binding domain; 2.40A {Streptomyces coelicolor}

Probab=92.47  E-value=0.11  Score=34.78  Aligned_cols=48  Identities=10%  Similarity=0.105  Sum_probs=37.0

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCC-CC-CCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQI-HP-TKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~-~~-~~~~~L~RlLR~Laa~gif~   95 (97)
                      .+.-|.+.|.+++ +.|+.||.+.+.- .| .+...++|.|..|+..|++.
T Consensus        20 qR~~Il~~l~~~~-h~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Glv~   69 (145)
T 3eyy_A           20 QRQLVLEAVDTLE-HATPDDILGEVRKTASGINISTVYRTLELLEELGLVS   69 (145)
T ss_dssp             HHHHHHHHHHHHS-SBCHHHHHHHHHTTCTTCCHHHHHHHHHHHHHHTSEE
T ss_pred             HHHHHHHHHHhcC-CCCHHHHHHHHHhhCCCCCHhHHHHHHHHHHHCCcEE
Confidence            4455677777666 9999999998743 12 25688999999999999875

>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=92.46  E-value=0.038  Score=35.01  Aligned_cols=45  Identities=20%  Similarity=0.400  Sum_probs=33.9

Q ss_pred             ChhHHHhhCCCCCCHHHHHHHhCCCC-CCcccHHHHHHHHHhcCccc
Q 041844           50 GIPDIIHNHTKPMTLNQLLGALQIHP-TKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        50 gI~D~La~~~gp~s~~ELA~~~g~~~-~~~~~L~RlLR~Laa~gif~   95 (97)
                      .|...|.. .+++|..|||+.++.++ -.+..+.|++..|...|++.
T Consensus        14 ~vL~~l~~-~~~~t~~ela~~l~~~~~~s~~tv~~~l~~L~~~Glv~   59 (123)
T 1okr_A           14 EVMNIIWM-KKYASANNIIEEIQMQKDWSPKTIRTLITRLYKKGFID   59 (123)
T ss_dssp             HHHHHHHH-HSSEEHHHHHHHHHHHCCCCHHHHHHHHHHHHHHTSEE
T ss_pred             HHHHHHHh-CCCcCHHHHHHHHhccCCCcHhhHHHHHHHHHHCCCeE
Confidence            34445544 37899999999998420 03489999999999999885

>4ets_A Ferric uptake regulation protein; metal binding protein, transcription factor; 2.10A {Campylobacter jejuni subsp}

Probab=92.30  E-value=0.15  Score=35.01  Aligned_cols=50  Identities=6%  Similarity=-0.068  Sum_probs=39.1

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCC---C-CCcccHHHHHHHHHhcCcccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIH---P-TKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~---~-~~~~~L~RlLR~Laa~gif~e   96 (97)
                      .+.-|.+.|.+.+++.|+.||.+.+.-.   | .+...++|.|..|+..|++.+
T Consensus        34 qR~~IL~~L~~~~~h~sA~eI~~~l~~~~~~~~is~aTVYRtL~~L~e~Glv~~   87 (162)
T 4ets_A           34 QREVLLKTLYHSDTHYTPESLYMEIKQAEPDLNVGIATVYRTLNLLEEAEMVTS   87 (162)
T ss_dssp             HHHHHHHHHHSCCSCBCHHHHHHHHHHHCGGGCCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHHHhhcCCCCCCHHHHHHHHHHHHHCCCEEE
Confidence            4556788887777899999999887321   1 256789999999999998763

>2lnb_A Z-DNA-binding protein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, immune system; NMR {Homo sapiens}

Probab=92.30  E-value=0.11  Score=32.81  Aligned_cols=42  Identities=19%  Similarity=0.237  Sum_probs=35.2

Q ss_pred             ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcc
Q 041844           50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFF   94 (97)
Q Consensus        50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif   94 (97)
                      .|.+.|.++|+|++..|||+.+|++   ..-+.++|..|-..|.+
T Consensus        23 kVLe~LkeaG~PlkageIae~~Gvd---KKeVdKaik~LKkEgkI   64 (80)
T 2lnb_A           23 RILQVLTEAGSPVKLAQLVKECQAP---KRELNQVLYRMKKELKV   64 (80)
T ss_dssp             HHHHHHHHHTSCEEHHHHHHHHTSC---HHHHHHHHHHHHHTTSE
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHCCC---HHHHHHHHHHHHHcCCc
Confidence            4567788888999999999999994   47799999998877754

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

Probab=92.29  E-value=0.11  Score=34.19  Aligned_cols=39  Identities=13%  Similarity=0.221  Sum_probs=32.6

Q ss_pred             HHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           53 DIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        53 D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ..|.. +++.|..+||+.+|+++   ..+.|.++.|...|++.
T Consensus        47 ~~l~~-~~~~~~~~la~~l~vs~---~tvs~~l~~Le~~Glv~   85 (155)
T 2h09_A           47 DLIRE-VGEARQVDMAARLGVSQ---PTVAKMLKRLATMGLIE   85 (155)
T ss_dssp             HHHHH-HSCCCHHHHHHHHTSCH---HHHHHHHHHHHHTTCEE
T ss_pred             HHHHh-CCCcCHHHHHHHhCcCH---HHHHHHHHHHHHCCCEE
Confidence            34544 36799999999999954   89999999999999875

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

Probab=92.16  E-value=0.071  Score=33.31  Aligned_cols=44  Identities=14%  Similarity=0.372  Sum_probs=34.0

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .++.|...+..+ +++|+.|||+.+|+++   ..+.|-++.|... ++.
T Consensus        28 ~Rl~IL~~l~~~-~~~~~~ela~~l~is~---stvs~hL~~L~~~-lv~   71 (99)
T 2zkz_A           28 MRLKIVNELYKH-KALNVTQIIQILKLPQ---STVSQHLCKMRGK-VLK   71 (99)
T ss_dssp             HHHHHHHHHHHH-SCEEHHHHHHHHTCCH---HHHHHHHHHHBTT-TBE
T ss_pred             HHHHHHHHHHHC-CCcCHHHHHHHHCcCH---HHHHHHHHHHHHH-hhh
Confidence            555666433322 7899999999999954   8999999999887 764

>4g6q_A Putative uncharacterized protein; structural genomics, PSI-biology, protein structure initiati midwest center for structural genomics, MCSG; 2.08A {Kribbella flavida}

Probab=91.94  E-value=0.064  Score=37.36  Aligned_cols=44  Identities=23%  Similarity=0.317  Sum_probs=36.7

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhC-CCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQ-IHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g-~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      +.+.|...|.+  +|+|+.||++.++ ++   ...+++-|+.|...|+++
T Consensus        24 ~Rl~il~~L~~--~~~~~~~l~~~l~~~~---~~~~s~Hl~~L~~aglv~   68 (182)
T 4g6q_A           24 LRWRITQLLIG--RSLTTRELAELLPDVA---TTTLYRQVGILVKAGVLM   68 (182)
T ss_dssp             HHHHHHHHTTT--SCEEHHHHHHHCTTBC---HHHHHHHHHHHHHHTSEE
T ss_pred             HHHHHHHHHHh--CCCCHHHHHHHhcCCC---HHHHHHHHHHHHHCCCeE
Confidence            56677788854  8999999999996 63   368999999999999986

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

Probab=91.80  E-value=0.17  Score=35.04  Aligned_cols=44  Identities=18%  Similarity=0.236  Sum_probs=37.3

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGF   93 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gi   93 (97)
                      -...|.+.|.+.++++|..|||+.+|++.   ..++|=++.|...|+
T Consensus        22 R~~~Il~~L~~~~~~~s~~eLa~~l~vS~---~Ti~rdi~~L~~~G~   65 (187)
T 1j5y_A           22 RLKSIVRILERSKEPVSGAQLAEELSVSR---QVIVQDIAYLRSLGY   65 (187)
T ss_dssp             HHHHHHHHHHHCSSCBCHHHHHHHHTSCH---HHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHcCCCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCC
Confidence            45567788876667899999999999954   889999999999887

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

Probab=91.74  E-value=0.1  Score=34.95  Aligned_cols=35  Identities=17%  Similarity=0.200  Sum_probs=31.2

Q ss_pred             CCCCCHHHHHHHh-CCCCCCcccHHHHHHHHHhcCcccc
Q 041844           59 TKPMTLNQLLGAL-QIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        59 ~gp~s~~ELA~~~-g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      .|+++..||++.+ |+++   ..|.+.|+.|...|+++.
T Consensus        37 ~g~~rf~eL~~~l~gIs~---~~Ls~~L~~Le~~GLV~R   72 (131)
T 4a5n_A           37 DGKKRFNEFRRICPSITQ---RMLTLQLRELEADGIVHR   72 (131)
T ss_dssp             TSCBCHHHHHHHCTTSCH---HHHHHHHHHHHHTTSEEE
T ss_pred             cCCcCHHHHHHHhcccCH---HHHHHHHHHHHHCCCEEE
Confidence            3799999999999 8854   899999999999999863

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

Probab=90.96  E-value=0.19  Score=35.63  Aligned_cols=35  Identities=11%  Similarity=0.241  Sum_probs=31.6

Q ss_pred             CCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           58 HTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        58 ~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .++++|..+||+.+++++   ..+.|+++.|...|++.
T Consensus        17 ~~~~~~~~~lA~~l~vs~---~tvs~~l~~Le~~GlV~   51 (214)
T 3hrs_A           17 RHNKITNKEIAQLMQVSP---PAVTEMMKKLLAEELLI   51 (214)
T ss_dssp             SCSCCCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             cCCCcCHHHHHHHHCCCh---hHHHHHHHHHHHCCCEE
Confidence            458999999999999954   89999999999999885

>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=90.90  E-value=0.21  Score=32.22  Aligned_cols=42  Identities=12%  Similarity=0.139  Sum_probs=34.5

Q ss_pred             ChhHHHhhCCCCCCHHHHHH-HhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           50 GIPDIIHNHTKPMTLNQLLG-ALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        50 gI~D~La~~~gp~s~~ELA~-~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .|.=.|++++ +.|+.+||+ ..+.   |...+.|=++.|...|+++
T Consensus        20 siL~~L~~~~-~~t~~~Lae~~l~~---drstvsrnl~~L~r~GlVe   62 (95)
T 1bja_A           20 TILITIAKKD-FITAAEVREVHPDL---GNAVVNSNIGVLIKKGLVE   62 (95)
T ss_dssp             HHHHHHHHST-TBCHHHHHHTCTTS---CHHHHHHHHHHHHTTTSEE
T ss_pred             HHHHHHHHCC-CCCHHHHHHHHhcc---cHHHHHHHHHHHHHCCCee
Confidence            3444566665 999999999 9888   5589999999999999874

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

Probab=90.83  E-value=0.11  Score=32.93  Aligned_cols=47  Identities=15%  Similarity=0.304  Sum_probs=35.8

Q ss_pred             hcChhHHHhhCCCCCCHHHHHHHhCCCC-CCcccHHHHHHHHHhcCccc
Q 041844           48 QVGIPDIIHNHTKPMTLNQLLGALQIHP-TKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        48 eLgI~D~La~~~gp~s~~ELA~~~g~~~-~~~~~L~RlLR~Laa~gif~   95 (97)
                      +..|...|.++ +|+|..|||+.++.+. -++..+.+++.-|...|++.
T Consensus        12 q~~vL~~L~~~-~~~t~~el~~~l~~~~~~~~~Tvt~~l~rLe~kGlv~   59 (126)
T 1sd4_A           12 EWDVMNIIWDK-KSVSANEIVVEIQKYKEVSDKTIRTLITRLYKKEIIK   59 (126)
T ss_dssp             HHHHHHHHHHS-SSEEHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHhc-CCCCHHHHHHHHhhcCCCChhhHHHHHHHHHHCCceE
Confidence            34445556554 6899999999998531 14589999999999999886

>1z6r_A MLC protein; transcriptional repressor, ROK family protein, DNA binding P helix-turn-helix, phosphotransferase system; 2.70A {Escherichia coli} SCOP: a.4.5.63 c.55.1.10 c.55.1.10 PDB: 3bp8_A

Probab=90.78  E-value=0.23  Score=37.72  Aligned_cols=46  Identities=13%  Similarity=0.181  Sum_probs=38.4

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      -+..|.+.|.++ +++|-.|||+.+|+.+   ..+.++++.|...|++.|
T Consensus        17 n~~~il~~l~~~-~~~sr~~la~~~~ls~---~tv~~~v~~L~~~g~i~~   62 (406)
T 1z6r_A           17 NAGAVYRLIDQL-GPVSRIDLSRLAQLAP---ASITKIVHEMLEAHLVQE   62 (406)
T ss_dssp             HHHHHHHHHHSS-CSCCHHHHHHHTTCCH---HHHHHHHHHHHHHTSEEE
T ss_pred             HHHHHHHHHHHc-CCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCcEEe
Confidence            344567777654 7999999999999954   899999999999999876

>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=90.75  E-value=0.24  Score=31.82  Aligned_cols=34  Identities=18%  Similarity=0.319  Sum_probs=30.7

Q ss_pred             CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           59 TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        59 ~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      +++++..|||+.+++   +...|.|.+..|...|+++
T Consensus        34 g~~~s~~eLa~~l~l---~~stLsR~l~rLe~~GLV~   67 (96)
T 2obp_A           34 ATPWSLPKIAKRAQL---PMSVLRRVLTQLQAAGLAD   67 (96)
T ss_dssp             CCCCBHHHHHHHHTC---CHHHHHHHHHHHHHTTSEE
T ss_pred             CCCcCHHHHHHHhCC---chhhHHHHHHHHHHCCCEE
Confidence            478999999999999   4489999999999999875

>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=90.67  E-value=0.11  Score=36.45  Aligned_cols=43  Identities=12%  Similarity=0.069  Sum_probs=35.0

Q ss_pred             cChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           49 VGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        49 LgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ..|...|..+ +++|..|||+.++++   +..+.|+++.|...|++.
T Consensus        51 ~~iL~~L~~~-~~~t~~eLa~~l~i~---~stvs~~l~~Le~~GlV~   93 (207)
T 2fxa_A           51 HHILWIAYQL-NGASISEIAKFGVMH---VSTAFNFSKKLEERGYLR   93 (207)
T ss_dssp             HHHHHHHHHH-TSEEHHHHHHHTTCC---HHHHHHHHHHHHHHTSEE
T ss_pred             HHHHHHHHHC-CCcCHHHHHHHHCCC---HHHHHHHHHHHHHCCCEE
Confidence            3344455544 589999999999995   489999999999999885

>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=90.60  E-value=0.14  Score=37.41  Aligned_cols=44  Identities=16%  Similarity=0.205  Sum_probs=35.9

Q ss_pred             cChhHHHhhCC-CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           49 VGIPDIIHNHT-KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        49 LgI~D~La~~~-gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ..|...|..++ +++|..|||+.+++++   ..+.|++.-|...|++.
T Consensus       161 ~~vL~~L~~~~~~~~t~~eLa~~l~i~~---~tvt~~v~rLe~~GlV~  205 (250)
T 1p4x_A          161 FTILAIITSQNKNIVLLKDLIETIHHKY---PQTVRALNNLKKQGYLI  205 (250)
T ss_dssp             HHHHHHHHTTTTCCEEHHHHHHHSSSCH---HHHHHHHHHHHHHTSSE
T ss_pred             HHHHHHHHhCCCCCcCHHHHHHHHCCCh---hhHHHHHHHHHHCCCEE
Confidence            34455566655 3699999999999954   89999999999999886

>2oz6_A Virulence factor regulator; winged helix, helix-turn-helix, transcription factor, CAMP-B proteins, CAMP receptor protein; HET: CMP; 2.80A {Pseudomonas aeruginosa} SCOP: a.4.5.4 b.82.3.2

Probab=90.32  E-value=0.16  Score=33.89  Aligned_cols=32  Identities=13%  Similarity=0.128  Sum_probs=29.3

Q ss_pred             CCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           61 PMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        61 p~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++|-.+||+.+|+.+   ..+.|+++.|...|+++
T Consensus       164 ~~t~~~lA~~lg~sr---~tvsR~l~~l~~~g~I~  195 (207)
T 2oz6_A          164 KITRQEIGRIVGCSR---EMVGRVLKSLEEQGLVH  195 (207)
T ss_dssp             ECCHHHHHHHHTSCH---HHHHHHHHHHHHTTSEE
T ss_pred             ccCHHHHHHHhCCCH---HHHHHHHHHHHHCCCEE
Confidence            589999999999955   89999999999999875

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

Probab=90.25  E-value=0.21  Score=33.62  Aligned_cols=32  Identities=13%  Similarity=0.203  Sum_probs=29.6

Q ss_pred             CCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           61 PMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        61 p~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++|-.+||+.+|+.+   ..+.|+++.|...|+++
T Consensus       169 ~~t~~~lA~~lg~sr---~tvsR~l~~L~~~g~I~  200 (220)
T 3dv8_A          169 KITHETIANHLGSHR---EVITRMLRYFQVEGLVK  200 (220)
T ss_dssp             CCCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             cCCHHHHHHHhCCCH---HHHHHHHHHHHHCCCEE
Confidence            899999999999955   89999999999999875

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

Probab=90.01  E-value=0.33  Score=31.80  Aligned_cols=33  Identities=15%  Similarity=0.157  Sum_probs=29.3

Q ss_pred             CCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           61 PMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        61 p~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      ..|.++||+.+++++   ..+.|+++.|...|++..
T Consensus        51 ~ps~~~LA~~l~~s~---~~V~~~l~~Le~kGlI~~   83 (128)
T 2vn2_A           51 FPTPAELAERMTVSA---AECMEMVRRLLQKGMIAI   83 (128)
T ss_dssp             SCCHHHHHHTSSSCH---HHHHHHHHHHHHTTSSEE
T ss_pred             CCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEE
Confidence            379999999999944   899999999999999863

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

Probab=89.81  E-value=0.16  Score=32.80  Aligned_cols=46  Identities=9%  Similarity=0.016  Sum_probs=36.9

Q ss_pred             hcChhHHHhhCC-CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           48 QVGIPDIIHNHT-KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        48 eLgI~D~La~~~-gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      |.-|..+|.++| ..++..||..+++++.   ..+.|+++.|...|++..
T Consensus        39 E~lVy~~I~~aGn~GIw~kdL~~~tnL~~---~~vtkiLK~LE~k~lIK~   85 (95)
T 2yu3_A           39 EKLVYQIIEDAGNKGIWSRDVRYKSNLPL---TEINKILKNLESKKLIKA   85 (95)
T ss_dssp             HHHHHHHHHHHTTSCEEHHHHHHHHTCCH---HHHHHHHHHHHHHTSEEE
T ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHhCCCH---HHHHHHHHHHHhCCCEEE
Confidence            444566666554 6799999999999955   889999999999998753

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

Probab=89.78  E-value=0.24  Score=33.77  Aligned_cols=33  Identities=6%  Similarity=0.138  Sum_probs=29.9

Q ss_pred             CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      -++|-.+||+.+|+.+   ..+.|+|+.|...|+++
T Consensus       174 ~~~t~~~iA~~lg~sr---~tvsR~l~~L~~~g~I~  206 (231)
T 3e97_A          174 LPLGTQDIMARTSSSR---ETVSRVLKRLEAHNILE  206 (231)
T ss_dssp             ECCCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             cCCCHHHHHHHhCCcH---HHHHHHHHHHHHCCcEE
Confidence            3789999999999955   89999999999999876

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

Probab=89.57  E-value=0.32  Score=33.71  Aligned_cols=45  Identities=18%  Similarity=0.224  Sum_probs=35.2

Q ss_pred             hcChhHHHhhCC-CCCCHHHHHHHhC-CCCCCcccHHHHHHHHHhcCccc
Q 041844           48 QVGIPDIIHNHT-KPMTLNQLLGALQ-IHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        48 eLgI~D~La~~~-gp~s~~ELA~~~g-~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .+.|...|..+. ++.|+.||++.++ +.   ...++|-|+.|+..|+++
T Consensus        31 R~~IL~~Ll~~p~~~~ta~eL~~~l~~lS---~aTVyrhL~~L~eaGLV~   77 (151)
T 3u1d_A           31 RLDVLHQILAQPDGVLSVEELLYRNPDET---EANLRYHVDELVDRGIVE   77 (151)
T ss_dssp             HHHHHHHHHHSTTSCBCHHHHHHHCTTSC---HHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHcCCCCCCCHHHHHHhcCCCC---HHHHHHHHHHHHHCCCeE
Confidence            344555554443 6789999999988 73   489999999999999986

>3ryp_A Catabolite gene activator; CAMP receptor protein (CRP), allostery, DNA binding cyclic A transcription regulator; HET: CMP; 1.60A {Escherichia coli} PDB: 2cgp_A* 3hif_A 1g6n_A* 3ryr_A* 1i5z_A* 1j59_A* 1lb2_A* 1run_A* 1zrc_A* 1zrd_A* 1zre_A* 1zrf_A* 2gzw_A* 2wc2_A 3iyd_G* 3n4m_A* 3qop_A* 3rdi_A* 3rou_A* 3rpq_A* ...

Probab=89.55  E-value=0.21  Score=33.42  Aligned_cols=32  Identities=6%  Similarity=0.040  Sum_probs=29.4

Q ss_pred             CCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           61 PMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        61 p~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++|-.+||+.+|+.+   ..+.|+++.|...|+++
T Consensus       167 ~~t~~~iA~~lg~sr---~tvsR~l~~L~~~g~I~  198 (210)
T 3ryp_A          167 KITRQEIGQIVGCSR---ETVGRILKMLEDQNLIS  198 (210)
T ss_dssp             ECCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             ccCHHHHHHHhCCcH---HHHHHHHHHHHHCCcEE
Confidence            689999999999955   89999999999999875

>1z05_A Transcriptional regulator, ROK family; structural genomics, protein structure initiative, midwest center for structural genomics; 2.00A {Vibrio cholerae o1 biovar eltor} SCOP: a.4.5.63 c.55.1.10 c.55.1.10

Probab=89.45  E-value=0.28  Score=37.70  Aligned_cols=50  Identities=12%  Similarity=0.216  Sum_probs=40.8

Q ss_pred             HHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           41 LKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        41 L~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      +|..  -+..|.+.|.++ +++|-.|||+.+|+.+   ..+.++++.|...|++.|
T Consensus        36 ~r~~--n~~~il~~l~~~-~~~sr~ela~~~gls~---~tv~~~v~~L~~~gli~~   85 (429)
T 1z05_A           36 IKQI--NAGRVYKLIDQK-GPISRIDLSKESELAP---ASITKITRELIDAHLIHE   85 (429)
T ss_dssp             HHHH--HHHHHHHHHHHH-CSBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEE
T ss_pred             HHHH--HHHHHHHHHHHc-CCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEe
Confidence            4444  455677888664 7999999999999954   899999999999999875

>2qlz_A Transcription factor PF0095; 2.50A {Pyrococcus furiosus} PDB: 2quf_A

Probab=89.42  E-value=0.062  Score=39.31  Aligned_cols=45  Identities=7%  Similarity=0.094  Sum_probs=38.3

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      ..+.|...|..  +|+|..|||+.+|+.+   ..+.+.|+.|...|++..
T Consensus        13 ~R~~IL~~L~~--g~~s~~ELa~~lglS~---stVs~hL~~Le~aGLV~~   57 (232)
T 2qlz_A           13 VRRDLLSHLTC--MECYFSLLSSKVSVSS---TAVAKHLKIMEREGVLQS   57 (232)
T ss_dssp             HHHHHHHHHTT--TTTCSSSSCTTCCCCH---HHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHh--CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEE
Confidence            55667777864  7999999999999954   899999999999999864

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

Probab=89.37  E-value=0.27  Score=33.55  Aligned_cols=33  Identities=6%  Similarity=0.004  Sum_probs=29.9

Q ss_pred             CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      -++|-.|||+.+|+.+   ..+.|+++.|...|+++
T Consensus       179 ~~~t~~~lA~~lg~sr---~tvsR~l~~l~~~g~I~  211 (232)
T 2gau_A          179 IYLSREELATLSNMTV---SNAIRTLSTFVSERMLA  211 (232)
T ss_dssp             CCCCHHHHHHHTTSCH---HHHHHHHHHHHHTTSEE
T ss_pred             cccCHHHHHHHhCCCH---HHHHHHHHHHHHCCCEe
Confidence            4789999999999955   89999999999999875

>2fmy_A COOA, carbon monoxide oxidation system transcription RE COOA-1; DNA transcription regulator, DNA binding protein; HET: HEM; 2.20A {Carboxydothermus hydrogenoformans} PDB: 2hkx_A*

Probab=89.36  E-value=0.26  Score=33.41  Aligned_cols=33  Identities=9%  Similarity=0.183  Sum_probs=29.9

Q ss_pred             CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      -++|-.+||+.+|+.+   ..+.|+++.|...|+++
T Consensus       166 ~~~t~~~lA~~lg~sr---~tvsR~l~~l~~~g~I~  198 (220)
T 2fmy_A          166 LGLNTEEIALMLGTTR---QTVSVLLNDFKKMGILE  198 (220)
T ss_dssp             CSSCHHHHHHHHTSCH---HHHHHHHHHHHHTTSEE
T ss_pred             ccCCHHHHHHHhCCcH---HHHHHHHHHHHHCCCEE
Confidence            3789999999999955   89999999999999876

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

Probab=89.26  E-value=0.28  Score=33.34  Aligned_cols=32  Identities=13%  Similarity=0.308  Sum_probs=29.2

Q ss_pred             CCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           61 PMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        61 p~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++|-.+||+.+|+.+   ..+.|+++.|...|+++
T Consensus       163 ~~t~~~lA~~lG~sr---~tvsR~l~~L~~~g~I~  194 (222)
T 1ft9_A          163 DFTVEEIANLIGSSR---QTTSTALNSLIKEGYIS  194 (222)
T ss_dssp             CCCHHHHHHHHCSCH---HHHHHHHHHHHHTTSSE
T ss_pred             cCCHHHHHHHhCCcH---HHHHHHHHHHHHCCcEE
Confidence            589999999999955   89999999999999876

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

Probab=89.14  E-value=0.23  Score=33.33  Aligned_cols=32  Identities=19%  Similarity=0.295  Sum_probs=29.2

Q ss_pred             CCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           61 PMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        61 p~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++|-.|||+.+|+.+   ..+.|+++.|...|+++
T Consensus       146 ~~t~~~lA~~lg~sr---~tvsR~l~~L~~~g~I~  177 (202)
T 2zcw_A          146 KATHDELAAAVGSVR---ETVTKVIGELAREGYIR  177 (202)
T ss_dssp             ECCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             CCCHHHHHHHhCCCH---HHHHHHHHHHHHCCCEE
Confidence            589999999999955   89999999999999875

>3iwz_A CAP-like, catabolite activation-like protein; XCC, pathogenicity, CRP, CLP, C-DI-GMP receptor, quorum SENS binding, transcription; 2.30A {Xanthomonas campestris PV}

Probab=89.14  E-value=0.23  Score=33.68  Aligned_cols=32  Identities=9%  Similarity=0.110  Sum_probs=29.2

Q ss_pred             CCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           61 PMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        61 p~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      |+|-.+||+.+|+.+   ..+.|+++.|...|+++
T Consensus       187 ~lt~~~lA~~lg~sr---~tvsR~l~~L~~~g~I~  218 (230)
T 3iwz_A          187 RVSRQELARLVGCSR---EMAGRVLKKLQADGLLH  218 (230)
T ss_dssp             ECCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             CCCHHHHHHHhCCcH---HHHHHHHHHHHHCCCEE
Confidence            479999999999955   89999999999999876

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

Probab=89.08  E-value=0.28  Score=33.30  Aligned_cols=32  Identities=6%  Similarity=0.201  Sum_probs=29.4

Q ss_pred             CCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           61 PMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        61 p~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++|-.|||+.+|+.+   ..+.|+++.|...|+++
T Consensus       177 ~~t~~~lA~~lg~sr---~tvsR~l~~l~~~g~I~  208 (227)
T 3d0s_A          177 DLTQEEIAQLVGASR---ETVNKALADFAHRGWIR  208 (227)
T ss_dssp             CCCHHHHHHHHTSCH---HHHHHHHHHHHHTTSEE
T ss_pred             CCCHHHHHHHhCCcH---HHHHHHHHHHHHCCCEE
Confidence            689999999999955   89999999999999875

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

Probab=88.73  E-value=0.25  Score=33.16  Aligned_cols=33  Identities=9%  Similarity=0.118  Sum_probs=29.7

Q ss_pred             CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      -++|-.|||+.+|+.+   ..+.|+++.|...|+++
T Consensus       162 ~~~t~~~lA~~lg~sr---~tvsR~l~~l~~~g~I~  194 (216)
T 4ev0_A          162 FQIRHHELAALAGTSR---ETVSRVLHALAEEGVVR  194 (216)
T ss_dssp             EECCHHHHHHHHTSCH---HHHHHHHHHHHHTTSEE
T ss_pred             CCCCHHHHHHHhCCCH---HHHHHHHHHHHHCCCEE
Confidence            3689999999999955   89999999999999875

>1jhg_A Trp operon repressor; complex (regulatory protein-peptide), DNA-binding regulatory complex (regulatory protein-peptide) complex; HET: TRP; 1.30A {Escherichia coli} SCOP: a.4.12.1 PDB: 1co0_A* 1mi7_R 1p6z_R 1wrp_R* 1zt9_A* 2oz9_R* 3ssw_R 3wrp_A 1rcs_A* 1wrs_R* 1wrt_R 2xdi_A 3ssx_R* 1trr_A* 1tro_A*

Probab=88.49  E-value=0.43  Score=31.01  Aligned_cols=39  Identities=18%  Similarity=0.053  Sum_probs=32.5

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHh
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVR   90 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa   90 (97)
                      ..+||+..|..  |++|-.|||+.+|++.   ..+.|+=|.|-.
T Consensus        46 ~R~~l~~~L~~--ge~TQREIA~~lGiS~---stISRi~r~L~~   84 (101)
T 1jhg_A           46 TRVRIIEELLR--GEMSQRELKNELGAGI---ATITRGSNSLKA   84 (101)
T ss_dssp             HHHHHHHHHHH--CCSCHHHHHHHHCCCH---HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHc--CCcCHHHHHHHHCCCh---hhhhHHHHHHHH
Confidence            56788888866  7899999999999954   889999887754

>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=88.32  E-value=0.4  Score=30.16  Aligned_cols=32  Identities=3%  Similarity=-0.063  Sum_probs=29.3

Q ss_pred             CCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           62 MTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        62 ~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      ++..+||..+|+++   ..+.+.+..|...|++..
T Consensus        21 ~~~t~La~~~~ls~---~~~~~~l~~L~~~GLI~~   52 (95)
T 1r7j_A           21 SPKTRIMYGANLSY---ALTGRYIKMLMDLEIIRQ   52 (95)
T ss_dssp             BCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHhCcCH---HHHHHHHHHHHHCCCeEE
Confidence            89999999999955   999999999999998863

>3dkw_A DNR protein; CRP-FNR, HTH, beta barrel, dimerization helix, homodimer, transcription regulator; 3.60A {Pseudomonas aeruginosa}

Probab=88.27  E-value=0.27  Score=33.27  Aligned_cols=33  Identities=21%  Similarity=0.404  Sum_probs=29.7

Q ss_pred             CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      -++|-.+||+.+|+.+   ..+.|+++.|...|+++
T Consensus       177 ~~~t~~~lA~~lg~sr---~tvsR~l~~l~~~g~I~  209 (227)
T 3dkw_A          177 IPVAKQLVAGHLSIQP---ETFSRIMHRLGDEGIIH  209 (227)
T ss_dssp             CCSCTHHHHHHTTSCH---HHHHHHHHHHHHHTSEE
T ss_pred             ecCCHHHHHHHhCCCH---HHHHHHHHHHHHCCcEE
Confidence            4689999999999955   89999999999999875

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

Probab=88.23  E-value=0.24  Score=33.10  Aligned_cols=32  Identities=13%  Similarity=0.223  Sum_probs=29.2

Q ss_pred             CCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           61 PMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        61 p~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++|-.|||+.+|+.+   ..+.|+|+.|...|+++
T Consensus       139 ~~t~~~lA~~lg~sr---~tvsR~l~~L~~~g~I~  170 (195)
T 3b02_A          139 TVSHEEIADATASIR---ESVSKVLADLRREGLIA  170 (195)
T ss_dssp             ECCHHHHHHTTTSCH---HHHHHHHHHHHHHTSEE
T ss_pred             cCCHHHHHHHhCCCH---HHHHHHHHHHHHCCCEE
Confidence            589999999999955   89999999999999875

>3la7_A Global nitrogen regulator; activator, DNA-binding, transcription, transcription regulation; HET: BOG; 1.90A {Anabaena} PDB: 3la2_A* 3la3_A* 2xko_A* 2xgx_A* 2xhk_A* 2xkp_A*

Probab=88.09  E-value=0.36  Score=33.52  Aligned_cols=33  Identities=9%  Similarity=0.075  Sum_probs=29.8

Q ss_pred             CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      -++|-.|||+.+|+.+   ..+.|+|+.|...|+++
T Consensus       192 ~~lt~~~lA~~lG~sr---~tvsR~l~~L~~~GlI~  224 (243)
T 3la7_A          192 LKLSHQAIAEAIGSTR---VTVTRLLGDLREKKMIS  224 (243)
T ss_dssp             SCCCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             ccCCHHHHHHHHCCcH---HHHHHHHHHHHHCCCEE
Confidence            3789999999999955   89999999999999875

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

Probab=87.96  E-value=0.37  Score=33.43  Aligned_cols=33  Identities=15%  Similarity=0.278  Sum_probs=29.9

Q ss_pred             CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      -++|-.+||+.+|+.+   ..+.|+++.|...|+++
T Consensus       176 ~~~t~~~iA~~lG~sr---~tvsR~l~~L~~~g~I~  208 (250)
T 3e6c_C          176 MPLSQKSIGEITGVHH---VTVSRVLASLKRENILD  208 (250)
T ss_dssp             CCCCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             CCCCHHHHHHHhCCcH---HHHHHHHHHHHHCCCeE
Confidence            3789999999999955   89999999999999885

>1zyb_A Transcription regulator, CRP family; NP_813211.1, structural genomics, joint center for structura genomics, JCSG; 2.15A {Bacteroides thetaiotaomicron} SCOP: a.4.5.4 b.82.3.2

Probab=87.93  E-value=0.31  Score=33.57  Aligned_cols=32  Identities=13%  Similarity=0.179  Sum_probs=29.2

Q ss_pred             CCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           61 PMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        61 p~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++|-.|||+.+|+.+   ..+.|+++.|...|+++
T Consensus       186 ~~t~~~lA~~lG~sr---~tvsR~l~~l~~~glI~  217 (232)
T 1zyb_A          186 KVKMDDLARCLDDTR---LNISKTLNELQDNGLIE  217 (232)
T ss_dssp             ECCHHHHHHHHTSCH---HHHHHHHHHHHHTTSCE
T ss_pred             cCCHHHHHHHhCCCh---hHHHHHHHHHHHCCCEE
Confidence            589999999999955   89999999999999875

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

Probab=87.16  E-value=0.26  Score=30.64  Aligned_cols=34  Identities=6%  Similarity=0.230  Sum_probs=29.7

Q ss_pred             CCCC-CHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           59 TKPM-TLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        59 ~gp~-s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      +..+ |..|||+.+|++.   ..+++.++.|...|++.
T Consensus        32 g~~lps~~eLa~~~~vSr---~tvr~al~~L~~~Gli~   66 (102)
T 1v4r_A           32 GDTLPSVADIRAQFGVAA---KTVSRALAVLKSEGLVS   66 (102)
T ss_dssp             TSBCCCHHHHHHHSSSCT---THHHHHTTTTTTSSCCE
T ss_pred             cCCCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEE
Confidence            4556 9999999999955   88999999999999875

>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=87.08  E-value=0.35  Score=34.17  Aligned_cols=34  Identities=18%  Similarity=0.295  Sum_probs=30.4

Q ss_pred             CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      +++|..++|+.+++++   +.+.|.++.|...|+|..
T Consensus        26 ~~~s~s~aA~~L~isq---~avSr~I~~LE~~~L~~R   59 (230)
T 3cta_A           26 AYLTSSKLADMLGISQ---QSASRIIIDLEKNGYITR   59 (230)
T ss_dssp             EECCHHHHHHHHTSCH---HHHHHHHHHHHHTTSEEE
T ss_pred             CCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEE
Confidence            5789999999999954   899999999999999863

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

Probab=86.09  E-value=1.7  Score=27.71  Aligned_cols=47  Identities=21%  Similarity=0.236  Sum_probs=35.6

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhC---C-C-CCCc-ccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQ---I-H-PTKT-RCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g---~-~-~~~~-~~L~RlLR~Laa~gif~   95 (97)
                      .++-|-..|..  +|++-.||+..+.   . . ..++ ..|+++|+-|...|+++
T Consensus        14 ~~~~IL~~L~~--~~~~gyel~~~l~~~g~~~~~is~~~tly~~L~~Le~~GlI~   66 (118)
T 2esh_A           14 LASTILLLVAE--KPSHGYELAERLAEFGIEIPGIGHMGNIYRVLADLEESGFLS   66 (118)
T ss_dssp             HHHHHHHHHHH--SCBCHHHHHHHHHTTCCSSTTCCCCCCHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHc--CCCCHHHHHHHHHHhCCcccCCCCcchHHHHHHHHHHCCCeE
Confidence            44555566765  7999999999984   1 1 0267 78999999999999885

>2gqq_A Leucine-responsive regulatory protein; helix-turn-helix, transcription; 3.20A {Escherichia coli} PDB: 2l4a_A

Probab=85.67  E-value=0.12  Score=34.89  Aligned_cols=45  Identities=20%  Similarity=0.220  Sum_probs=35.3

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++..|.+.|.. ++.+|..|||+.+|+++   ..+++-++.|...|++.
T Consensus        14 l~~~Il~~l~~-~~~ls~~eLa~~lgvSr---~~vr~al~~L~~~Gli~   58 (163)
T 2gqq_A           14 IDRNILNELQK-DGRISNVELSKRVGLSP---TPCLERVRRLERQGFIQ   58 (163)
T ss_dssp             HHHHHHHHHHH-CSSCCTTGGGTSSSCCT---TTSSSTHHHHHHHTSEE
T ss_pred             HHHHHHHHHHh-CCCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCcEE
Confidence            34455565655 46789999999999965   77888999999999875

>2w48_A Sorbitol operon regulator; SORC, activator, repressor, DNA-binding, transcription, transcription regulator, transcription regulation; 3.20A {Klebsiella pneumoniae}

Probab=85.62  E-value=0.59  Score=34.64  Aligned_cols=33  Identities=21%  Similarity=0.172  Sum_probs=30.3

Q ss_pred             CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      +.+|..|||+++|++.   ..++|.|..|...|+++
T Consensus        20 ~~~~~~ela~~l~vS~---~tIrRdL~~l~~~G~v~   52 (315)
T 2w48_A           20 QDMTQAQIARELGIYR---TTISRLLKRGREQGIVT   52 (315)
T ss_dssp             SCCCHHHHHHHTTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCcEE
Confidence            6799999999999954   89999999999999885

>3kcc_A Catabolite gene activator; helix-turn-helix, CAMP, CAMP-binding, DNA-binding nucleotide-binding, transcription, transcription regulation; HET: CMP; 1.66A {Escherichia coli}

Probab=85.53  E-value=0.47  Score=33.38  Aligned_cols=32  Identities=6%  Similarity=0.040  Sum_probs=29.4

Q ss_pred             CCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           61 PMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        61 p~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++|-.+||+.+|+.+   ..+.|+|+.|...|+++
T Consensus       217 ~lt~~~lA~~lG~sr---~tvsR~l~~L~~~GlI~  248 (260)
T 3kcc_A          217 KITRQEIGQIVGCSR---ETVGRILKMLEDQNLIS  248 (260)
T ss_dssp             ECCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             cCCHHHHHHHhCCCH---HHHHHHHHHHHHCCCEE
Confidence            689999999999955   89999999999999876

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

Probab=85.18  E-value=0.87  Score=31.34  Aligned_cols=32  Identities=13%  Similarity=0.138  Sum_probs=28.8

Q ss_pred             CCCHHHHHHHhCCCCCCcc-cHHHHHHHHHhcCccc
Q 041844           61 PMTLNQLLGALQIHPTKTR-CLHFLVCSLVRSGFFN   95 (97)
Q Consensus        61 p~s~~ELA~~~g~~~~~~~-~L~RlLR~Laa~gif~   95 (97)
                      ++|-.|||+.+|+   .++ .+.|+|+.|...|+++
T Consensus       169 ~~t~~~lA~~lG~---sr~etvsR~l~~l~~~glI~  201 (238)
T 2bgc_A          169 NLTMQELGYSSGI---AHSSAVSRIISKLKQEKVIV  201 (238)
T ss_dssp             CCCHHHHHHHTTC---CCHHHHHHHHHHHHHTTSEE
T ss_pred             cCCHHHHHHHhCC---ChHHHHHHHHHHHHHCCCEE
Confidence            7899999999999   444 9999999999999875

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

Probab=84.82  E-value=0.8  Score=30.63  Aligned_cols=33  Identities=21%  Similarity=0.135  Sum_probs=29.7

Q ss_pred             CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ...|.++||+++|+++   ..+.|++..|...|+++
T Consensus        50 ~~ps~~~LA~~~~~s~---~~v~~~L~~L~~KGlI~   82 (135)
T 2v79_A           50 YFPTPNQLQEGMSISV---EECTNRLRMFIQKGFLF   82 (135)
T ss_dssp             CSCCHHHHHTTSSSCH---HHHHHHHHHHHHHTSCE
T ss_pred             CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEE
Confidence            5689999999999954   89999999999999886

>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=84.12  E-value=0.44  Score=36.50  Aligned_cols=43  Identities=9%  Similarity=0.083  Sum_probs=34.8

Q ss_pred             hhHHHhhC-CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           51 IPDIIHNH-TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        51 I~D~La~~-~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      |...|.++ ++++|..|||+.++++   +..+.|++.-|...|++..
T Consensus       409 vl~~l~~~~~~~~~~~~l~~~~~~~---~~~~t~~~~~le~~g~v~r  452 (487)
T 1hsj_A          409 ILNHILRSESNEISSKEIAKCSEFK---PYYLTKALQKLKDLKLLSK  452 (487)
T ss_dssp             HHHHHHTCSCSEEEHHHHHHSSCCC---HHHHHHHHHHHHTTTTSCC
T ss_pred             HHHHHHhCCCCCcCHHHHHHHHCCC---HHHHHHHHHHHHHCCCEee
Confidence            44455554 2689999999999995   4899999999999998864

>4ham_A LMO2241 protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, winged helix-turn-helix, four helix bundle; 1.91A {Listeria monocytogenes}

Probab=83.80  E-value=1.1  Score=29.13  Aligned_cols=34  Identities=9%  Similarity=0.205  Sum_probs=29.4

Q ss_pred             CCCC-CHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           59 TKPM-TLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        59 ~gp~-s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      |..+ |..+||+.+|++.   ..+++-++.|...|++.
T Consensus        35 G~~LPser~La~~~gVSr---~tVReAl~~L~~eGlv~   69 (134)
T 4ham_A           35 GEKILSIREFASRIGVNP---NTVSKAYQELERQEVII   69 (134)
T ss_dssp             TCEECCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             CCCCccHHHHHHHHCCCH---HHHHHHHHHHHHCCcEE
Confidence            3456 8899999999954   88999999999999875

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

Probab=83.67  E-value=0.59  Score=31.86  Aligned_cols=30  Identities=23%  Similarity=0.359  Sum_probs=27.5

Q ss_pred             CCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCc
Q 041844           61 PMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGF   93 (97)
Q Consensus        61 p~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gi   93 (97)
                      |+|-.+||+.+|+.+   ..+.|+++.|...|+
T Consensus       178 ~~t~~~iA~~lg~sr---~tvsR~l~~L~~~gi  207 (237)
T 3fx3_A          178 PYDKMLIAGRLGMKP---ESLSRAFSRLKAAGV  207 (237)
T ss_dssp             CSCTHHHHHHTTCCH---HHHHHHHHHHGGGTE
T ss_pred             cCCHHHHHHHhCCCH---HHHHHHHHHHHHCCe
Confidence            678999999999955   899999999999996

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

Probab=83.41  E-value=1.9  Score=27.85  Aligned_cols=44  Identities=11%  Similarity=0.177  Sum_probs=34.0

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHh------CCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGAL------QIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~------g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      +++-|--+|..  +|++--||+..+      ++   ++..|+++|+-|...|+++
T Consensus        12 l~~~IL~lL~~--~p~~Gyei~~~l~~~g~~~i---s~gtlY~~L~rLe~~GlI~   61 (117)
T 4esf_A           12 LEGCVLEIISR--RETYGYEITRHLNDLGFTEV---VEGTVYTILVRLEKKKLVN   61 (117)
T ss_dssp             HHHHHHHHHHH--SCBCHHHHHHHHHHHTCTTC---CHHHHHHHHHHHHHTTCEE
T ss_pred             HHHHHHHHHHc--CCCCHHHHHHHHHHcCCCCC---CccHHHHHHHHHHHCCCEE
Confidence            33334445655  799999999987      44   5589999999999999886

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

Probab=83.36  E-value=0.56  Score=29.80  Aligned_cols=34  Identities=9%  Similarity=0.163  Sum_probs=29.4

Q ss_pred             CCCC-CHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           59 TKPM-TLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        59 ~gp~-s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++.+ |..|||+.+|+..   ..+++-++.|...|++.
T Consensus        40 g~~lps~~eLa~~lgVSr---~tVr~al~~L~~~GlI~   74 (102)
T 2b0l_A           40 NEGLLVASKIADRVGITR---SVIVNALRKLESAGVIE   74 (102)
T ss_dssp             TEEEECHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             CCcCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEE
Confidence            3455 9999999999954   88999999999999875

>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=83.33  E-value=0.7  Score=33.67  Aligned_cols=42  Identities=10%  Similarity=0.237  Sum_probs=34.1

Q ss_pred             hhHHHhhCC-CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           51 IPDIIHNHT-KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        51 I~D~La~~~-gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      |-..|.+++ +++|..|||+.+++++   ..+.|++.-|...|++.
T Consensus        39 vL~~L~~~~~~~~~~~el~~~l~~~~---~t~t~~l~rLe~~G~i~   81 (250)
T 1p4x_A           39 LLTYLFHQQENTLPFKKIVSDLCYKQ---SDLVQHIKVLVKHSYIS   81 (250)
T ss_dssp             HHHHHHSCSCSEEEHHHHHHHSSSCG---GGTHHHHHHHHHTTSCE
T ss_pred             HHHHHHhcCCCCcCHHHHHHHHCCCH---hhHHHHHHHHHHCCCEE
Confidence            334455443 6899999999999954   89999999999999885

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

Probab=83.07  E-value=0.74  Score=29.32  Aligned_cols=34  Identities=15%  Similarity=0.226  Sum_probs=29.4

Q ss_pred             CCCC-CHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           59 TKPM-TLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        59 ~gp~-s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      |..+ |..|||+.+|++.   ..+++.++.|...|++.
T Consensus        30 G~~lPs~~~La~~~~vSr---~tvr~al~~L~~~Gli~   64 (113)
T 3tqn_A           30 GEMIPSIRKISTEYQINP---LTVSKAYQSLLDDNVIE   64 (113)
T ss_dssp             TCEECCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             CCcCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEE
Confidence            3456 8999999999954   88999999999999875

>1o5l_A Transcriptional regulator, CRP family; TM1171, structural GE JCSG, PSI, protein structure initiative, joint center for S genomics; 2.30A {Thermotoga maritima} SCOP: b.82.3.2

Probab=82.45  E-value=0.26  Score=33.52  Aligned_cols=32  Identities=25%  Similarity=0.384  Sum_probs=0.0

Q ss_pred             CCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           61 PMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        61 p~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++|-.+||+.+|+.+   ..+.|+++.|...|+++
T Consensus       164 ~~t~~~lA~~lg~sr---~tvsR~l~~L~~~G~I~  195 (213)
T 1o5l_A          164 PVTLEELSRLFGCAR---PALSRVFQELEREGYIE  195 (213)
T ss_dssp             -----------------------------------
T ss_pred             CCCHHHHHHHhCCCH---HHHHHHHHHHHHCCeEE
Confidence            789999999999965   89999999999999875

>1stz_A Heat-inducible transcription repressor HRCA homol; circe element, structural genomics, BSGC structure FUN NIH, protein structure initiative; 2.20A {Thermotoga maritima} SCOP: a.4.5.51 d.110.2.3

Probab=81.98  E-value=1.2  Score=34.03  Aligned_cols=39  Identities=18%  Similarity=0.254  Sum_probs=32.9

Q ss_pred             HHhhCCCCCCHHHHHHHh--CCCCCCcccHHHHHHHHHhcCcccc
Q 041844           54 IIHNHTKPMTLNQLLGAL--QIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        54 ~La~~~gp~s~~ELA~~~--g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      .|.. ++|.++.+||+..  +++|   ..++|-|..|...|++..
T Consensus        30 yl~~-~~pV~s~~La~~~~l~VS~---aTIRrDL~~LE~~GlL~r   70 (338)
T 1stz_A           30 YIEN-KKPVSSQRVLEVSNIEFSS---ATIRNDMKKLEYLGYIYQ   70 (338)
T ss_dssp             HHHH-CSCBCHHHHHHHSCCCSCH---HHHHHHHHHHHHTTSEEC
T ss_pred             HHHc-CCCccHHHHHHHhCCCCCH---HHHHHHHHHHHHCCCEEE
Confidence            4544 5899999999998  7744   899999999999998763

>3oio_A Transcriptional regulator (ARAC-type DNA-binding containing proteins); PSI-2, midwest center for structural genomics; 1.65A {Chromobacterium violaceum}

Probab=81.89  E-value=1.3  Score=27.62  Aligned_cols=35  Identities=11%  Similarity=0.241  Sum_probs=26.9

Q ss_pred             hHHHhhC-CCCCCHHHHHHHhCCCCCCcccHHHHHHHHH
Q 041844           52 PDIIHNH-TKPMTLNQLLGALQIHPTKTRCLHFLVCSLV   89 (97)
Q Consensus        52 ~D~La~~-~gp~s~~ELA~~~g~~~~~~~~L~RlLR~La   89 (97)
                      .+.|.++ ..++|+++||+.+|+++   ..|.|+.+...
T Consensus        13 ~~~i~~~~~~~~~~~~lA~~~~~S~---~~l~r~fk~~~   48 (113)
T 3oio_A           13 VSLMEANIEEPLSTDDIAYYVGVSR---RQLERLFKQYL   48 (113)
T ss_dssp             HHHHHTCSSSCCCHHHHHHHHTSCH---HHHHHHHHHHT
T ss_pred             HHHHHhhhcCCCCHHHHHHHHCcCH---HHHHHHHHHHH
Confidence            3455554 36899999999999955   88999988654

>3mn2_A Probable ARAC family transcriptional regulator; structural genomics, PSI-2, protein structure initiative; 1.80A {Rhodopseudomonas palustris}

Probab=81.74  E-value=0.98  Score=27.89  Aligned_cols=34  Identities=18%  Similarity=0.251  Sum_probs=25.8

Q ss_pred             HHHhhC-CCCCCHHHHHHHhCCCCCCcccHHHHHHHHH
Q 041844           53 DIIHNH-TKPMTLNQLLGALQIHPTKTRCLHFLVCSLV   89 (97)
Q Consensus        53 D~La~~-~gp~s~~ELA~~~g~~~~~~~~L~RlLR~La   89 (97)
                      +.|.++ ..+.|+++||+.+|+++   ..|.|+.+...
T Consensus         9 ~~i~~~~~~~~~~~~lA~~~~~s~---~~l~r~fk~~~   43 (108)
T 3mn2_A            9 EYIEANWMRPITIEKLTALTGISS---RGIFKAFQRSR   43 (108)
T ss_dssp             HHHHHHTTSCCCHHHHHHHHTCCH---HHHHHHHHHHT
T ss_pred             HHHHHcccCCCCHHHHHHHHCCCH---HHHHHHHHHHh
Confidence            444333 36899999999999955   88999988654

>3iwf_A Transcription regulator RPIR family; transcriptional, N-terminal, PSI, MCSG, structural genomics, midwest center structural genomics; 1.40A {Staphylococcus epidermidis}

Probab=81.63  E-value=0.57  Score=30.18  Aligned_cols=42  Identities=19%  Similarity=0.208  Sum_probs=30.5

Q ss_pred             hcChhHHHhhCC---CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcC
Q 041844           48 QVGIPDIIHNHT---KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSG   92 (97)
Q Consensus        48 eLgI~D~La~~~---gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~g   92 (97)
                      +-.|++.|-++.   ..+|+.|||+++++++   ..+.|+-|.|--.|
T Consensus        19 e~~ia~yil~~~~~~~~~si~elA~~~~vS~---aTv~Rf~kkLGf~g   63 (107)
T 3iwf_A           19 EKKIAQFILNYPHKVVNMTSQEIANQLETSS---TSIIRLSKKVTPGG   63 (107)
T ss_dssp             HHHHHHHHHHCHHHHTTCCHHHHHHHHTSCH---HHHHHHHHHHSTTH
T ss_pred             HHHHHHHHHhCHHHHHHCCHHHHHHHHCCCH---HHHHHHHHHhCCCC
Confidence            444556555543   5799999999999955   78888888775444

>2o3f_A Putative HTH-type transcriptional regulator YBBH; APC85504, putative transcriptional regulator YBBH; HET: MLY; 1.75A {Bacillus subtilis} SCOP: a.4.1.20

Probab=81.24  E-value=0.47  Score=30.55  Aligned_cols=42  Identities=21%  Similarity=0.190  Sum_probs=30.0

Q ss_pred             hcChhHHHhhCC---CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcC
Q 041844           48 QVGIPDIIHNHT---KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSG   92 (97)
Q Consensus        48 eLgI~D~La~~~---gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~g   92 (97)
                      +-.|++.|-++.   ..+|+.|||+++++.+   ..+.|+-|.|--.|
T Consensus        23 e~~ia~yil~~~~~~~~~si~elA~~~~vS~---aTv~Rf~kklG~~g   67 (111)
T 2o3f_A           23 ERKLADYILAHPHXAIESTVNEISALANSSD---AAVIRLCXSLGLKG   67 (111)
T ss_dssp             HHHHHHHHHHCHHHHHTCCHHHHHHHTTCCH---HHHHHHHHHTTCSS
T ss_pred             HHHHHHHHHHChHHHHhcCHHHHHHHHCCCH---HHHHHHHHHcCCCC
Confidence            444556665543   4689999999999955   78888888665544

>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=80.95  E-value=2.3  Score=27.21  Aligned_cols=46  Identities=9%  Similarity=0.179  Sum_probs=34.5

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhC------CCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQ------IHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g------~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .++-|--.|..  +|++--||...+.      ... ++..|+++|+-|...|+++
T Consensus        13 l~~~IL~~L~~--~~~~Gyei~~~l~~~~~~~~~i-~~gtly~~L~rLe~~GlI~   64 (116)
T 3f8b_A           13 TNVILLNVLKQ--GDNYVYGIIKQVKEASNGEMEL-NEATLYTIFKRLEKDGIIS   64 (116)
T ss_dssp             HHHHHHHHHHH--CCBCHHHHHHHHHHHTTTCCCC-CHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHh--CCCCHHHHHHHHHHHhCCCCCC-CcchHHHHHHHHHHCCCEE
Confidence            44444555655  8999999998872      122 5689999999999999886

>3oou_A LIN2118 protein; protein structure initiative, PSI-2, structural genomics, MI center for structural genomics, MCSG, unknown function; HET: BTB; 1.57A {Listeria innocua}

Probab=80.73  E-value=1.3  Score=27.42  Aligned_cols=29  Identities=21%  Similarity=0.185  Sum_probs=24.2

Q ss_pred             CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhc
Q 041844           60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRS   91 (97)
Q Consensus        60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~   91 (97)
                      .++|+++||+.+|+++   ..|.|+.+.....
T Consensus        20 ~~~~~~~lA~~~~~S~---~~l~r~fk~~~G~   48 (108)
T 3oou_A           20 EGMSLKTLGNDFHINA---VYLGQLFQKEMGE   48 (108)
T ss_dssp             SCCCHHHHHHHHTSCH---HHHHHHHHHHHSS
T ss_pred             CCCCHHHHHHHHCcCH---HHHHHHHHHHHCc
Confidence            5899999999999955   8899999866533

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

Probab=80.71  E-value=1.3  Score=29.00  Aligned_cols=34  Identities=21%  Similarity=0.280  Sum_probs=29.5

Q ss_pred             CCCC-CHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           59 TKPM-TLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        59 ~gp~-s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      |..+ |..+||+.+|++.   ..+++.++.|...|++.
T Consensus        25 G~~LPse~~La~~~gvSr---~tVr~Al~~L~~~Gli~   59 (129)
T 2ek5_A           25 DQRVPSTNELAAFHRINP---ATARNGLTLLVEAGILY   59 (129)
T ss_dssp             TSCBCCHHHHHHHTTCCH---HHHHHHHHHHHTTTSEE
T ss_pred             CCcCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCcEE
Confidence            3566 8999999999954   78999999999999875

>1bia_A BIRA bifunctional protein; transcription regulation; 2.30A {Escherichia coli} SCOP: a.4.5.1 b.34.1.1 d.104.1.2 PDB: 1bib_A* 1hxd_A* 2ewn_A*

Probab=80.09  E-value=1.3  Score=33.04  Aligned_cols=43  Identities=14%  Similarity=0.064  Sum_probs=35.4

Q ss_pred             cChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           49 VGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        49 LgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ..|.+.|.+ ++++|..|||+.+++++   ..++|-++.|...|+..
T Consensus         8 ~~Il~~L~~-~~~~s~~eLa~~l~vS~---~ti~r~l~~L~~~G~~i   50 (321)
T 1bia_A            8 LKLIALLAN-GEFHSGEQLGETLGMSR---AAINKHIQTLRDWGVDV   50 (321)
T ss_dssp             HHHHHHHTT-SSCBCHHHHHHHHTSCH---HHHHHHHHHHHHTTCCC
T ss_pred             HHHHHHHHc-CCCcCHHHHHHHHCCCH---HHHHHHHHHHHhCCCcE
Confidence            346677753 57899999999999954   89999999999999763

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

Probab=80.03  E-value=1.1  Score=29.23  Aligned_cols=34  Identities=9%  Similarity=0.080  Sum_probs=29.6

Q ss_pred             CCCC-CHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           59 TKPM-TLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        59 ~gp~-s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      |..+ |..+||+.+|++.   ..+++.++.|...|++.
T Consensus        32 G~~lPse~~La~~~~vSr---~tvr~Al~~L~~~Gli~   66 (126)
T 3by6_A           32 NDQLPSVRETALQEKINP---NTVAKAYKELEAQKVIR   66 (126)
T ss_dssp             TCEECCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             CCcCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEE
Confidence            3566 9999999999954   88999999999999875

---

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	97
d1fp2a1	101	a.4.5.29 (A:8-108) Isoflavone O-methyltransferase	7e-17
d1fp1d1	110	a.4.5.29 (D:19-128) Chalcone O-methyltransferase {	8e-13
d1kyza1	107	a.4.5.29 (A:13-119) Caffeic acid/5-hydroxyferulic	3e-11
d1qzza1	92	a.4.5.29 (A:10-101) Aclacinomycin-10-hydroxylase R	1e-09

>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 = 67.2 bits (164), Expect = 7e-17
 Identities = 29/82 (35%), Positives = 48/82 (58%), Gaps = 7/82 (8%)

Query: 13 SDELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQ 72
            E+ +AQ L        + ++FI+SMSLK    +++ IP+II NH KP++L+ L+  LQ
Sbjct: 3  PSEIFKAQAL-----LYKHIYAFIDSMSLKWA--VEMNIPNIIQNHGKPISLSNLVSILQ 55

Query: 73 IHPTKTRCLHFLVCSLVRSGFF 94
          +  +K   +  L+  L  +GFF
Sbjct: 56 VPSSKIGNVRRLMRYLAHNGFF 77

>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 = 57.1 bits (138), Expect = 8e-13
 Identities = 12/70 (17%), Positives = 23/70 (32%), Gaps = 8/70 (11%)

Query: 32 TFSFINSMSLKCVKLIQVGIPDIIHNHTKP---MTLNQLLGALQI---HPTKTRCLHFLV 85
          T + +    L     I + + +II   T P   M+ +++   L     H      L  ++
Sbjct: 14 TTNLVYPAVLNAA--IDLNLFEIIAKATPPGAFMSPSEIASKLPASTQHSDLPNRLDRML 71

Query: 86 CSLVRSGFFN 95
            L       
Sbjct: 72 RLLASYSVLT 81

>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 = 53.3 bits (128), Expect = 3e-11
 Identities = 10/67 (14%), Positives = 24/67 (35%), Gaps = 5/67 (7%)

Query: 32 TFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQI---HPTKTRCLHFLVCSL 88
            + +  M LK    +++ + +II        ++ +  A Q+   +P     L  ++  L
Sbjct: 15 ASASVLPMILKSA--LELDLLEIIAKAGPGAQISPIEIASQLPTTNPDAPVMLDRMLRLL 72

Query: 89 VRSGFFN 95
                 
Sbjct: 73 ACYIILT 79

>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 = 48.2 bits (115), Expect = 1e-09
 Identities = 14/66 (21%), Positives = 21/66 (31%), Gaps = 7/66 (10%)

Query: 29 LDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSL 88
          L N  + +  M+L+      + + D +       TL  L      HP        LV  L
Sbjct: 12 LKNLGNLVTPMALRVA--ATLRLVDHLLAG--ADTLAGLADRTDTHPQALSR---LVRHL 64

Query: 89 VRSGFF 94
             G  
Sbjct: 65 TVVGVL 70

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	97
d1fp2a1	101	Isoflavone O-methyltransferase {Alfalfa (Medicago	99.88
d1fp1d1	110	Chalcone O-methyltransferase {Alfalfa (Medicago sa	99.79
d1kyza1	107	Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltra	99.79
d1tw3a1	85	Carminomycin 4-O-methyltransferase {Streptomyces p	99.65
d1qzza1	92	Aclacinomycin-10-hydroxylase RdmB {Streptomyces pu	99.65
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	97.92
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	96.86
d2hoea1	62	N-acetylglucosamine kinase {Thermotoga maritima [T	96.76
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	96.66
d1r1ua_	94	Metal-sensing transcriptional repressor CzrA {Stap	96.48
d1xd7a_	127	Hypothetical protein ywnA {Bacillus subtilis [TaxI	96.41
d1z6ra1	70	Mlc protein N-terminal domain {Escherichia coli [T	96.3
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	96.14
d1ulya_	190	Hypothetical protein PH1932 {Pyrococcus horikoshii	96.11
d2hr3a1	145	Probable transcriptional regulator PA3067 {Pseudom	96.06
d1ylfa1	138	Hypothetical protein BC1842 {Bacillus cereus [TaxI	96.02
d1r1ta_	98	SmtB repressor {Cyanobacteria (Synechococcus), pcc	96.01
d1ub9a_	100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	95.79
d1lvaa3	64	C-terminal fragment of elongation factor SelB {Moo	95.69
d1u2wa1	108	Cadmium efflux system accessory protein CadC {Stap	95.68
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	95.57
d1s3ja_	143	Putative transcriptional regulator YusO {Bacillus	95.57
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	95.4
d2p4wa1	194	Transcriptional regulatory protein PF1790 {Pyrococ	95.3
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	95.22
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	94.86
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	94.86
d3broa1	135	Transcriptional regulator OEOE1854 {Oenococcus oen	94.81
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	94.77
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	94.65
d2isya1	63	Iron-dependent regulator IdeR {Mycobacterium tuber	94.34
d2etha1	140	Putative transcriptional regulator TM0816 {Thermot	94.22
d2ev0a1	61	Manganese transport regulator MntR {Bacillus subti	94.13
d1lnwa_	141	MexR repressor {Pseudomonas aeruginosa [TaxId: 287	94.13
d2fbha1	137	Transcriptional regulator PA3341 {Pseudomonas aeru	94.07
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	93.94
d3ctaa1	85	Ta1064 (RFK), N-terminal domain {Thermoplasma acid	93.48
d2a61a1	139	Transcriptional regulator TM0710 {Thermotoga marit	93.14
d1p4xa1	125	Staphylococcal accessory regulator A homolog, SarS	93.03
d2bv6a1	136	Transcriptional regulator MgrA {Staphylococcus aur	92.95
d3deua1	140	Transcriptional regulator SlyA {Salmonella typhimu	92.95
d1q1ha_	88	Transcription factor E/IIe-alpha, N-terminal domai	92.52
d2gaua1	81	Transcriptional regulator PG0396, C-terminal domai	92.51
d2g9wa1	122	Hypothetical protein Rv1846c {Mycobacterium tuberc	92.47
d1ft9a1	80	CO-sensing protein CooA, C-terminal domain {Rhodos	92.47
d2fbia1	136	Probable transcriptional regulator PA4135 {Pseudom	92.09
d1i5za1	69	Catabolite gene activator protein (CAP), C-termina	92.07
d2frha1	115	Pleiotropic regulator of virulence genes, SarA {St	92.06
d1zyba1	73	Probable transcription regulator BT4300, C-termina	91.71
d2zcwa1	82	Transcriptional regulator TTHA1359, C-terminal dom	91.43
d1bl0a1	54	MarA {Escherichia coli [TaxId: 562]}	91.29
d1p4xa2	125	Staphylococcal accessory regulator A homolog, SarS	91.01
d1lj9a_	144	Transcriptional regulator SlyA {Enterococcus faeca	90.87
d3e5ua1	80	Chlorophenol reduction protein CprK {Desulfitobact	90.41
d1hsja1	115	Staphylococcal accessory regulator A homolog, SarR	90.01
d1jgsa_	138	Multiple antibiotic resistance repressor, MarR {Es	89.98
d2fbka1	172	Transcriptional regulator DR1159 {Deinococcus radi	89.5
d1stza1	87	Heat-inducible transcription repressor HrcA, N-ter	89.34
d2dk5a1	78	DNA-directed RNA polymerase III subunit RPC6, RPO3	89.05
d1mzba_	134	Ferric uptake regulation protein, FUR {Pseudomonas	88.84
d1d5ya1	54	Rob transcription factor, N-terminal domain {Esche	87.95
d1z91a1	137	Organic hydroperoxide resistance transcriptional r	87.3
d2hs5a1	69	Putative transcriptional regulator RHA1_ro03477 {R	86.85
d2fxaa1	162	Protease production regulatory protein Hpr {Bacill	86.54
d1hw1a1	74	Fatty acid responsive transcription factor FadR, N	85.87
d3bwga1	78	Transcriptional regulator YydK {Bacillus subtilis	84.89
d2o3fa1	83	Putative transcriptional regulator YbbH {Bacillus	84.81
d1okra_	120	Methicillin resistance regulatory protein MecI {St	84.46
d2obpa1	81	Putative DNA-binding protein ReutB4095 {Ralstonia	84.29
d2bgca1	100	Listeriolysin regulatory protein PrfA, C-terminal	82.1
d1v7ba1	74	Transcriptional regulator Cgl2612 {Corynebacterium	80.11

>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=99.88  E-value=1.7e-23  Score=137.35  Aligned_cols=77  Identities=38%  Similarity=0.678  Sum_probs=72.5

Q ss_pred             cHHHHHHHHHhccCcchhhHHhHHHHHHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcC
Q 041844           13 SDELLQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSG   92 (97)
Q Consensus        13 ~~~~~~~~~~~~~~p~~~l~~~~~~s~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~g   92 (97)
                      .+|.+|+|.++     |+++|||+.|++|++|  ++|||||+|+++++|+|++|||+++|++|.+++.|.||||+|++.|
T Consensus         3 ~~e~~qaq~~l-----~~~~~gf~~s~aL~~a--veLgi~d~l~~~~~p~t~~eLa~~~~~~~~~~~~L~RlLR~L~~~g   75 (101)
T d1fp2a1           3 PSEIFKAQALL-----YKHIYAFIDSMSLKWA--VEMNIPNIIQNHGKPISLSNLVSILQVPSSKIGNVRRLMRYLAHNG   75 (101)
T ss_dssp             STHHHHHHHHH-----HHHHTTHHHHHHHHHH--HHTTHHHHHHHHTSCEEHHHHHHHHTCCGGGHHHHHHHHHHHHHTT
T ss_pred             hHHHHHHHHHH-----HHHHHhHHHHHHHHHH--HHcCcHHHHHHcCCCCCHHHHHHHcCCCCccchHHHHHHHHHHhCC
Confidence            36889999999     9999999999999999  9999999999888999999999999998777889999999999999


Q ss_pred             cccc
Q 041844           93 FFNL   96 (97)
Q Consensus        93 if~e   96 (97)
                      +|++
T Consensus        76 i~~~   79 (101)
T d1fp2a1          76 FFEI   79 (101)
T ss_dssp             SEEE
T ss_pred             ceee
Confidence            9964

>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=99.79  E-value=2.6e-20  Score=124.27  Aligned_cols=73  Identities=19%  Similarity=0.215  Sum_probs=62.7

Q ss_pred             HHHHHHhccCcchhhHHhHHHHHHHHHHHHHhcChhHHHhhCCCC---CCHHHHHHHhCC---CCCCcccHHHHHHHHHh
Q 041844           17 LQAQLLNCANPCLDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKP---MTLNQLLGALQI---HPTKTRCLHFLVCSLVR   90 (97)
Q Consensus        17 ~~~~~~~~~~p~~~l~~~~~~s~aL~~a~~veLgI~D~La~~~gp---~s~~ELA~~~g~---~~~~~~~L~RlLR~Laa   90 (97)
                      .++..+.     +++.++++.+|+||||  |||||||+|+++|+|   +|++|||+++++   +|+.+..|+||||+|++
T Consensus         4 ~~~~l~a-----~~L~~~~v~pMaLk~A--ieLgI~diI~~~G~~~~~ls~~ela~~lp~~~~~p~~~~~L~RiLRlLas   76 (110)
T d1fp1d1           4 DSACLSA-----MVLTTNLVYPAVLNAA--IDLNLFEIIAKATPPGAFMSPSEIASKLPASTQHSDLPNRLDRMLRLLAS   76 (110)
T ss_dssp             HHHHHHH-----HHHHHTTHHHHHHHHH--HHTTHHHHHHTCSSTTCCBCHHHHHTTSCGGGCCTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHH-----HHHHHhhHHHHHHHHH--HHcCCHHHHHHcCCCCCCCCHHHHHHhCCCCCCCccHHHHHHHHHHHHHH
Confidence            3455666     8889999999999999  999999999998755   899999999986   34335579999999999


Q ss_pred             cCcccc
Q 041844           91 SGFFNL   96 (97)
Q Consensus        91 ~gif~e   96 (97)
                      .|+|++
T Consensus        77 ~~vf~~   82 (110)
T d1fp1d1          77 YSVLTS   82 (110)
T ss_dssp             TTSEEE
T ss_pred             cCcccc
Confidence            999974

>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=99.79  E-value=4.5e-20  Score=122.47  Aligned_cols=66  Identities=14%  Similarity=0.158  Sum_probs=59.5

Q ss_pred             hhhHHhHHHHHHHHHHHHHhcChhHHHhhCC--CCCCHHHHHHHhCCC-CCCcccHHHHHHHHHhcCcccc
Q 041844           29 LDNTFSFINSMSLKCVKLIQVGIPDIIHNHT--KPMTLNQLLGALQIH-PTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        29 ~~l~~~~~~s~aL~~a~~veLgI~D~La~~~--gp~s~~ELA~~~g~~-~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      +++.++++.+|+||||  |||||||+|+++|  +++|+.|||++++.+ |.++..|+||||+|++.|+|++
T Consensus        12 ~~L~~~~v~pmaLk~A--ieLgI~DiI~~~G~~~~ls~~eia~~l~~~~p~~~~~L~RilR~Las~~vf~~   80 (107)
T d1kyza1          12 MQLASASVLPMILKSA--LELDLLEIIAKAGPGAQISPIEIASQLPTTNPDAPVMLDRMLRLLACYIILTC   80 (107)
T ss_dssp             HHHHTTTHHHHHHHHH--HHTTHHHHHHTTCTTCCBCHHHHHHTSSCCCTTHHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHhhHHHHHHHHH--HHcCCHHHHHHcCCCCCCCHHHHHHhcCCCCCcchHHHHHHHHHHHhcCceEE
Confidence            7789999999999999  9999999999987  578999999999984 4346689999999999999975

>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=99.65  E-value=5.7e-17  Score=102.40  Aligned_cols=61  Identities=21%  Similarity=0.221  Sum_probs=55.6

Q ss_pred             hhhHHhHHHHHHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           29 LDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        29 ~~l~~~~~~s~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      +....+|+.+++|++|  ++|||||+|+.  ||+|++|||+++|++|   +.+.|+||+|++.|+|+|
T Consensus         6 l~~l~~~~~~~aL~~a--v~L~ifd~l~~--gp~s~~eLA~~~g~~~---~~l~rlLr~l~a~gl~~e   66 (85)
T d1tw3a1           6 LIRLGSLHTPMVVRTA--ATLRLVDHILA--GARTVKALAARTDTRP---EALLRLIRHLVAIGLLEE   66 (85)
T ss_dssp             HHHHHCSHHHHHHHHH--HHTTHHHHHHT--TCCBHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHchHHHHHHHHH--HHcCcHHHhcc--CCCCHHHHHHHhCcCh---hHHHHHHHHHHHCCCeEe
Confidence            4456789999999999  99999999965  8999999999999955   999999999999999976

>d1qzza1 a.4.5.29 (A:10-101) Aclacinomycin-10-hydroxylase RdmB {Streptomyces purpurascens [TaxId: 1924]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Plant O-methyltransferase, N-terminal domain
domain: Aclacinomycin-10-hydroxylase RdmB
species: Streptomyces purpurascens [TaxId: 1924]

Probab=99.65  E-value=9.1e-17  Score=103.21  Aligned_cols=61  Identities=25%  Similarity=0.303  Sum_probs=57.0

Q ss_pred             hhhHHhHHHHHHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           29 LDNTFSFINSMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        29 ~~l~~~~~~s~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      ++++.+|+.+++|++|  ++|||||+|+.  ||+|++|||+++|++|   +.+.|+||+|+++|+|++
T Consensus        12 l~~~~~~~~~~~L~~a--veL~ifd~L~~--gp~t~~eLA~~~g~~~---~~l~rLlr~L~a~gll~~   72 (92)
T d1qzza1          12 LKNLGNLVTPMALRVA--ATLRLVDHLLA--GADTLAGLADRTDTHP---QALSRLVRHLTVVGVLEG   72 (92)
T ss_dssp             HHTTTCCHHHHHHHHH--HHTTHHHHHHT--TCCSHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEC
T ss_pred             HHHHHchHHHHHHHHH--HHcCchHHHhC--CCCCHHHHHHHHCcCc---hHHHHHHHHHHHCCCeee
Confidence            6778899999999999  99999999975  8999999999999955   999999999999999976

>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=97.92  E-value=3.7e-06  Score=50.47  Aligned_cols=45  Identities=13%  Similarity=0.173  Sum_probs=40.1

Q ss_pred             cChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           49 VGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        49 LgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      +.|.|.++.+++|+|++|||+.+|+++   ..++|++..|...|++..
T Consensus         8 l~IL~~~a~~~~~~s~~eia~~~~~~~---st~~rll~tL~~~g~l~~   52 (75)
T d1mkma1           8 FEILDFIVKNPGDVSVSEIAEKFNMSV---SNAYKYMVVLEEKGFVLR   52 (75)
T ss_dssp             HHHHHHHHHCSSCBCHHHHHHHTTCCH---HHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHhCCCCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEE
Confidence            367788988889999999999999955   899999999999999864

>d1z05a1 a.4.5.63 (A:10-80) Transcriptional regulator VC2007 N-terminal domain {Vibrio cholerae [TaxId: 666]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: Transcriptional regulator VC2007 N-terminal domain
species: Vibrio cholerae [TaxId: 666]

Probab=96.86  E-value=0.0004  Score=40.47  Aligned_cols=43  Identities=12%  Similarity=0.248  Sum_probs=37.2

Q ss_pred             ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      .|+..|..+ +++|..|||+.+|+++   ..+.++++.|...|++.+
T Consensus        10 ~Il~~l~~~-g~~sr~eLa~~~glS~---~Tv~~~l~~L~~~Glv~e   52 (71)
T d1z05a1          10 RVYKLIDQK-GPISRIDLSKESELAP---ASITKITRELIDAHLIHE   52 (71)
T ss_dssp             HHHHHHHHH-CSBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHc-CCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEEE
Confidence            467777664 6999999999999955   899999999999999875

>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=96.76  E-value=0.00067  Score=39.05  Aligned_cols=42  Identities=14%  Similarity=0.148  Sum_probs=37.0

Q ss_pred             ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      .|...|.+  +|+|-.|||+.+|.++   ..+.++++.|...|++.|
T Consensus         3 ~Il~~i~~--~pisr~eLa~~~gls~---~TVs~~v~~L~~~GlV~e   44 (62)
T d2hoea1           3 RILKRIMK--SPVSRVELAEELGLTK---TTVGEIAKIFLEKGIVVE   44 (62)
T ss_dssp             CSHHHHHH--SCBCHHHHHHHHTCCH---HHHHHHHHHHHHHTSEEE
T ss_pred             HHHHHHHH--CCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEE
Confidence            46778876  6999999999999955   899999999999999875

>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=96.66  E-value=0.00041  Score=43.06  Aligned_cols=43  Identities=14%  Similarity=0.200  Sum_probs=35.4

Q ss_pred             ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .|+..|...++|+|.+|||..+++++   ..+.|+++.|...|++.
T Consensus        25 ~iL~~L~~~~~~~t~~eLa~~~~i~~---~tvs~~l~~L~~~GlV~   67 (109)
T d2d1ha1          25 AVLLKMVEIEKPITSEELADIFKLSK---TTVENSLKKLIELGLVV   67 (109)
T ss_dssp             HHHHHHHHHCSCEEHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHCccH---hHHHHHHHHHHHCCCEE
Confidence            34444444468999999999999954   89999999999999885

>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=96.48  E-value=0.0019  Score=39.82  Aligned_cols=50  Identities=8%  Similarity=0.097  Sum_probs=41.6

Q ss_pred             HHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           40 SLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        40 aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      +|.--  .++.|...|..  +++++.||++.+|+..   ..+.+=|+.|...|+++.
T Consensus        14 aL~d~--~Rl~Il~~L~~--~~~~v~el~~~l~~s~---~~vS~HL~~L~~~glv~~   63 (94)
T d1r1ua_          14 ALGDY--NRIRIMELLSV--SEASVGHISHQLNLSQ---SNVSHQLKLLKSVHLVKA   63 (94)
T ss_dssp             HTCSH--HHHHHHHHHHH--CCBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEE
T ss_pred             HhCCH--HHHHHHHHHHc--CCccHHHHHHHHCCCH---HHHHHHHHHHHHCCceEE
Confidence            44444  67777888876  8999999999999944   899999999999999864

>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=96.41  E-value=0.0025  Score=40.52  Aligned_cols=35  Identities=6%  Similarity=0.198  Sum_probs=31.4

Q ss_pred             CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           59 TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        59 ~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      ++++|.++||+.++++|   ..+++||+.|...|+++.
T Consensus        16 ~~~~ss~~IA~~~~~~~---~~v~kIl~~L~~aglV~s   50 (127)
T d1xd7a_          16 DEKTSSEIIADSVNTNP---VVVRRMISLLKKADILTS   50 (127)
T ss_dssp             CSCCCHHHHHHHHTSCH---HHHHHHHHHHHHTTSEEC
T ss_pred             CCCCCHHHHHHHhCcCH---HHHHHHHHHHHHhCcccc
Confidence            46899999999999965   899999999999998863

>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=96.30  E-value=0.0021  Score=37.37  Aligned_cols=43  Identities=14%  Similarity=0.247  Sum_probs=37.2

Q ss_pred             ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      .|+..|.. .+|+|-.|||..+|..+   ..+.+++..|...|++.|
T Consensus         9 ~Il~~i~~-~g~~sr~eLa~~~gLS~---~Tvs~iv~~L~~~glv~e   51 (70)
T d1z6ra1           9 AVYRLIDQ-LGPVSRIDLSRLAQLAP---ASITKIVHEMLEAHLVQE   51 (70)
T ss_dssp             HHHHHHHS-SCSCCHHHHHHHTTCCH---HHHHHHHHHHHHHTSEEE
T ss_pred             HHHHHHHH-cCCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCEEe
Confidence            46777765 47999999999999954   899999999999999875

>d1ku9a_ a.4.5.36 (A:) DNA-binding protein Mj223 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: DNA-binding protein Mj223
domain: DNA-binding protein Mj223
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=96.14  E-value=0.0018  Score=41.31  Aligned_cols=43  Identities=21%  Similarity=0.370  Sum_probs=35.8

Q ss_pred             ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .|.-.|..+++|+|+.|||+.+|+++   ..+.|.++.|...|++.
T Consensus        30 ~i~~~L~~~~~plt~~ela~~l~vsk---~~vs~~l~~L~~~GlV~   72 (151)
T d1ku9a_          30 AVYAILYLSDKPLTISDIMEELKISK---GNVSMSLKKLEELGFVR   72 (151)
T ss_dssp             HHHHHHHHCSSCEEHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHhCCCCcCHHHHHHHhCCCc---chHHHHHHHHHHCCCEE
Confidence            33445555668999999999999955   89999999999999885

>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=96.11  E-value=0.0028  Score=42.37  Aligned_cols=44  Identities=25%  Similarity=0.362  Sum_probs=38.5

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ..+.|.+.|..  +|+|+.|||+.+|.++   ..+++-|+.|...|++.
T Consensus        20 ~R~~Il~~L~~--~~~s~~ela~~lg~s~---~~v~~hl~~L~~~glv~   63 (190)
T d1ulya_          20 TRRKILKLLRN--KEMTISQLSEILGKTP---QTIYHHIEKLKEAGLVE   63 (190)
T ss_dssp             HHHHHHHHHTT--CCBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHh--CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCeE
Confidence            56677888854  8999999999999955   89999999999999985

>d2hr3a1 a.4.5.28 (A:2-146) Probable transcriptional regulator PA3067 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Probable transcriptional regulator PA3067
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=96.06  E-value=0.003  Score=40.36  Aligned_cols=45  Identities=22%  Similarity=0.230  Sum_probs=37.5

Q ss_pred             hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++.+...|...+|++|..|||+.+++++   ..+.|++..|...|++.
T Consensus        36 q~~vL~~L~~~~g~~t~~~La~~~~~~~---~~vs~~i~~L~~~glv~   80 (145)
T d2hr3a1          36 QLVVLGAIDRLGGDVTPSELAAAERMRS---SNLAALLRELERGGLIV   80 (145)
T ss_dssp             HHHHHHHHHHTTSCBCHHHHHHHTTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHCCCH---HHHHHHHHHHHHcCCeE
Confidence            4445556666668999999999999954   89999999999999985

>d1ylfa1 a.4.5.55 (A:5-142) Hypothetical protein BC1842 {Bacillus cereus [TaxId: 1396]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcriptional regulator Rrf2
domain: Hypothetical protein BC1842
species: Bacillus cereus [TaxId: 1396]

Probab=96.02  E-value=0.0026  Score=40.90  Aligned_cols=38  Identities=16%  Similarity=0.336  Sum_probs=32.5

Q ss_pred             HhhC-CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           55 IHNH-TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        55 La~~-~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      |+.+ +.++|..|||+.+++++   ..|+++|+.|+..|++.
T Consensus        16 la~~~~~~vss~~IA~~~~i~~---~~l~kil~~L~~aGlv~   54 (138)
T d1ylfa1          16 LKNNPSSLCTSDYMAESVNTNP---VVIRKIMSYLKQAGFVY   54 (138)
T ss_dssp             HHHSCGGGCCHHHHHHHHTSCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHhCCCCcCcHHHHHHHHCcCH---HHHHHHHHHHHHCCCeE
Confidence            4433 36899999999999955   89999999999999886

>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=96.01  E-value=0.0049  Score=37.99  Aligned_cols=50  Identities=10%  Similarity=0.141  Sum_probs=41.2

Q ss_pred             HHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           40 SLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        40 aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      +|.--  .++.|...|..  +++++.|||+.+|+..   +.+.+-|+.|...|+++.
T Consensus        19 aL~~p--~Rl~Il~~L~~--~~~~v~ela~~l~is~---stvS~HL~~L~~aglV~~   68 (98)
T d1r1ta_          19 VLADP--NRLRLLSLLAR--SELCVGDLAQAIGVSE---SAVSHQLRSLRNLRLVSY   68 (98)
T ss_dssp             HHCCH--HHHHHHHHHTT--CCBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEE
T ss_pred             HhCCH--HHHHHHHHHHc--CCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCceEE
Confidence            44444  67777888854  8999999999999944   899999999999999863

>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=95.79  E-value=0.0018  Score=39.30  Aligned_cols=45  Identities=20%  Similarity=0.362  Sum_probs=37.9

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .++.|...|..+ +++|..|||+.+++.+   ..+.|.++.|...|+++
T Consensus        17 ~r~~IL~~L~~~-~~~~~~eLa~~l~is~---~~vs~~l~~L~~~glV~   61 (100)
T d1ub9a_          17 VRLGIMIFLLPR-RKAPFSQIQKVLDLTP---GNLDSHIRVLERNGLVK   61 (100)
T ss_dssp             HHHHHHHHHHHH-SEEEHHHHHHHTTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHhccC-CCeeHHHHHHHHhhcc---ccccHHHHHHhhhceeE
Confidence            456667777543 6899999999999954   89999999999999986

>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=95.69  E-value=0.0058  Score=35.18  Aligned_cols=42  Identities=21%  Similarity=0.381  Sum_probs=34.7

Q ss_pred             hhHHHhhCC-CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           51 IPDIIHNHT-KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        51 I~D~La~~~-gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      |-+++.++| .|-++.|||+.+|++   +..+..+||.|+..|.+.
T Consensus        12 I~~~~~~~g~~PP~vrdl~~~l~~~---e~~~~~lL~~l~~~G~lv   54 (64)
T d1lvaa3          12 LEDKYRVSRWQPPSFKEVAGSFNLD---PSELEELLHYLVREGVLV   54 (64)
T ss_dssp             HHHHHHHHTTSCCBHHHHHHHTTCC---HHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHcCCCCCcHHHHHHHhCCC---HHHHHHHHHHHHHCCCEE
Confidence            345565555 899999999999994   489999999999999753

>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=95.68  E-value=0.0049  Score=38.67  Aligned_cols=53  Identities=9%  Similarity=0.111  Sum_probs=44.1

Q ss_pred             HHHHHHHHHHhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           38 SMSLKCVKLIQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        38 s~aL~~a~~veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      ..+|.--  ..+.|+..|.. .+++|+.||++.+|+.+   ..+.+-|+.|...|+++.
T Consensus        25 ~kaLadp--~Rl~Il~~L~~-~~~~~v~ela~~l~~s~---s~vS~HL~~L~~aGlv~~   77 (108)
T d1u2wa1          25 LKAIADE--NRAKITYALCQ-DEELCVCDIANILGVTI---ANASHHLRTLYKQGVVNF   77 (108)
T ss_dssp             HHHHHSH--HHHHHHHHHHH-SSCEEHHHHHHHHTCCH---HHHHHHHHHHHHTTSEEE
T ss_pred             HHHhCCH--HHHHHHHHHHh-CCCccHHHHHHHHccCh---hHHHHHHHHHHHCCeeEE
Confidence            3455566  78899998864 37899999999999954   899999999999999874

>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=95.57  E-value=0.0094  Score=33.97  Aligned_cols=43  Identities=19%  Similarity=0.260  Sum_probs=36.7

Q ss_pred             hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCc
Q 041844           48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGF   93 (97)
Q Consensus        48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gi   93 (97)
                      ...|.+.|.++.+++|..|||+.++++.   ..++|=+..|...|+
T Consensus         9 ~~~Il~~L~~~~~~vs~~~La~~l~VS~---~TI~rdi~~L~~~G~   51 (65)
T d1j5ya1           9 LKSIVRILERSKEPVSGAQLAEELSVSR---QVIVQDIAYLRSLGY   51 (65)
T ss_dssp             HHHHHHHHHHCSSCBCHHHHHHHHTSCH---HHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHcCCCCcHHHHHHHHCCCH---HHHHHHHHHHHHCCC
Confidence            4467778877778999999999999954   899999999999885

>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=95.57  E-value=0.017  Score=36.48  Aligned_cols=41  Identities=7%  Similarity=0.340  Sum_probs=34.0

Q ss_pred             hhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           51 IPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        51 I~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      +...|..+ +++|+.|||..+++++   ..+.|++.-|...|++.
T Consensus        40 iL~~l~~~-~~~t~~~la~~~~i~~---~~vs~~l~~L~~~glv~   80 (143)
T d1s3ja_          40 VLASLKKH-GSLKVSEIAERMEVKP---SAVTLMADRLEQKNLIA   80 (143)
T ss_dssp             HHHHHHHH-SEEEHHHHHHHHTSCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHC-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHhhhhe
Confidence            34455554 5899999999999954   89999999999999885

>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=95.40  E-value=0.0049  Score=38.14  Aligned_cols=33  Identities=18%  Similarity=0.346  Sum_probs=30.6

Q ss_pred             CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      |++|+.|||..+|+++   ..+++++.-|...|++.
T Consensus        33 g~~t~~eia~~~~i~~---~~v~~~l~~L~~~GlV~   65 (109)
T d1sfxa_          33 GGMRVSEIARELDLSA---RFVRDRLKVLLKRGFVR   65 (109)
T ss_dssp             CCBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             CCCCHHHHHHHhCCCc---chHHHHHHHHHhCCCEE
Confidence            7999999999999954   89999999999999985

>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=95.30  E-value=0.0056  Score=41.26  Aligned_cols=44  Identities=14%  Similarity=0.215  Sum_probs=38.0

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ..+.|.+.|.+  +|+|+.|||+.+|+++   ..++|-|+.|...|+++
T Consensus        16 ~R~~Il~~L~~--~~~~~~ela~~l~~s~---~~v~~HL~~L~~~Glv~   59 (194)
T d2p4wa1          16 TRRRILFLLTK--RPYFVSELSRELGVGQ---KAVLEHLRILEEAGLIE   59 (194)
T ss_dssp             HHHHHHHHHHH--SCEEHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHh--CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCeE
Confidence            44566777866  8999999999999955   89999999999999986

>d2cfxa1 a.4.5.32 (A:1-63) Transcriptional regulator LrpC {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Transcriptional regulator LrpC
species: Bacillus subtilis [TaxId: 1423]

Probab=95.22  E-value=0.01  Score=33.80  Aligned_cols=45  Identities=16%  Similarity=0.287  Sum_probs=37.7

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++..|-+.|.++ +.+|..|||+.+|+.+   ..+.+=++.|...|++.
T Consensus         6 ~D~~IL~~L~~n-~r~s~~~iA~~lgis~---~tv~~Ri~~L~~~giI~   50 (63)
T d2cfxa1           6 IDLNIIEELKKD-SRLSMRELGRKIKLSP---PSVTERVRQLESFGIIK   50 (63)
T ss_dssp             HHHHHHHHHHHC-SCCCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHHc-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCee
Confidence            466777888764 7999999999999955   78888889999999875

>d1i1ga1 a.4.5.32 (A:2-61) LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: LprA
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=94.86  E-value=0.014  Score=32.78  Aligned_cols=45  Identities=16%  Similarity=0.186  Sum_probs=36.9

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++..|...|.++ +.+|..|||+++|+++   ..+.+=++.|...|++.
T Consensus         4 ~D~kIl~~L~~n-~r~s~~~lA~~~gls~---~~v~~Ri~~L~~~giI~   48 (60)
T d1i1ga1           4 RDKIILEILEKD-ARTPFTEIAKKLGISE---TAVRKRVKALEEKGIIE   48 (60)
T ss_dssp             HHHHHHHHHHHC-TTCCHHHHHHHHTSCH---HHHHHHHHHHHHHTSSC
T ss_pred             HHHHHHHHHHHc-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCeE
Confidence            456677778764 6899999999999954   78888888899999875

>d2cyya1 a.4.5.32 (A:5-64) Putative transcriptional regulator PH1519 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Putative transcriptional regulator PH1519
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=94.86  E-value=0.015  Score=32.59  Aligned_cols=45  Identities=20%  Similarity=0.254  Sum_probs=37.7

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++..|...|.++ +.+|..|||.++|+++   ..+.+=++.|...|++.
T Consensus         4 ~D~~Il~~L~~n-~r~s~~eiA~~l~ls~---~~v~~Ri~~L~~~giI~   48 (60)
T d2cyya1           4 IDKKIIKILQND-GKAPLREISKITGLAE---STIHERIRKLRESGVIK   48 (60)
T ss_dssp             HHHHHHHHHHHC-TTCCHHHHHHHHCSCH---HHHHHHHHHHHHHTSSC
T ss_pred             HHHHHHHHHHHc-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCeE
Confidence            566778888774 6899999999999954   78888889999999875

>d3broa1 a.4.5.28 (A:3-137) Transcriptional regulator OEOE1854 {Oenococcus oeni [TaxId: 1247]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator OEOE1854
species: Oenococcus oeni [TaxId: 1247]

Probab=94.81  E-value=0.014  Score=36.50  Aligned_cols=45  Identities=16%  Similarity=0.198  Sum_probs=36.5

Q ss_pred             hcChhHHHhhCC-CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           48 QVGIPDIIHNHT-KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        48 eLgI~D~La~~~-gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++.|...|..++ +++|..|||+.++++   ...+.|++..|...|++.
T Consensus        31 q~~vL~~l~~~~~~~it~~ela~~~~~~---~~~vs~~l~~L~~~g~v~   76 (135)
T d3broa1          31 QMTIIDYLSRNKNKEVLQRDLESEFSIK---SSTATVLLQRMEIKKLLY   76 (135)
T ss_dssp             HHHHHHHHHHTTTSCCBHHHHHHHHTCC---HHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHHCcC---HhHHHHHHHHHHHHHHHH
Confidence            444455566654 689999999999994   489999999999999875

>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=94.77  E-value=0.013  Score=33.30  Aligned_cols=43  Identities=14%  Similarity=0.138  Sum_probs=36.4

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGF   93 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gi   93 (97)
                      .++.|..+|.+ ++.+|..|||+.+|+..   ..++|=+..|...|+
T Consensus         6 ~~~~iL~~L~~-~~~~s~~eLa~~l~vS~---~ti~r~i~~L~~~G~   48 (63)
T d1biaa1           6 VPLKLIALLAN-GEFHSGEQLGETLGMSR---AAINKHIQTLRDWGV   48 (63)
T ss_dssp             HHHHHHHHHTT-SSCBCHHHHHHHHTSCH---HHHHHHHHHHHHTTC
T ss_pred             HHHHHHHHHHH-CCcCCHHHHHHHHCcCH---HHHHHHHHHHHHCCC
Confidence            45567788854 57899999999999954   899999999999996

>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=94.65  E-value=0.016  Score=32.75  Aligned_cols=45  Identities=16%  Similarity=0.357  Sum_probs=37.2

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++..|...|.++ +.+|..|||+++|+++   ..+.+=++.|...|++.
T Consensus         6 ~D~~IL~~L~~~-~r~s~~eiA~~l~ls~---~~v~~Ri~rL~~~GiI~   50 (63)
T d2cg4a1           6 LDRGILEALMGN-ARTAYAELAKQFGVSP---ETIHVRVEKMKQAGIIT   50 (63)
T ss_dssp             HHHHHHHHHHHC-TTSCHHHHHHHHTSCH---HHHHHHHHHHHHHTSEE
T ss_pred             HHHHHHHHHHHc-CCCCHHHHHHHHCcCH---HHHHHHHHHHHHCCCeE
Confidence            456677788764 6899999999999954   78888889999999875

>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=94.34  E-value=0.025  Score=32.41  Aligned_cols=37  Identities=11%  Similarity=0.113  Sum_probs=32.5

Q ss_pred             hhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           56 HNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        56 a~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ...+++.+..+||+.+|+.|   +.+.++++-|...|++.
T Consensus        18 ~~~~~~v~~~~iA~~L~vs~---~SVt~mvkrL~~~Glv~   54 (63)
T d2isya1          18 EEEGVTPLRARIAERLDQSG---PTVSQTVSRMERDGLLR   54 (63)
T ss_dssp             HHTTCCCCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             HhcCCCCcHHHHHHHhCCCc---hhHHHHHHHHHHCCCEE
Confidence            34567899999999999955   89999999999999986

>d2etha1 a.4.5.28 (A:1-140) Putative transcriptional regulator TM0816 {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Putative transcriptional regulator TM0816
species: Thermotoga maritima [TaxId: 2336]

Probab=94.22  E-value=0.015  Score=36.66  Aligned_cols=44  Identities=14%  Similarity=0.099  Sum_probs=36.1

Q ss_pred             hcChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           48 QVGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        48 eLgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      +.-|...|..+ +++|..|||+.+++++   ..+.|+++.|...|++.
T Consensus        34 q~~iL~~l~~~-~~~t~~~La~~l~i~~---~~vs~~v~~L~~~gli~   77 (140)
T d2etha1          34 ELYAFLYVALF-GPKKMKEIAEFLSTTK---SNVTNVVDSLEKRGLVV   77 (140)
T ss_dssp             HHHHHHHHHHH-CCBCHHHHHHHTTSCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHc-CCcCHHHHHHHHCcCH---HHHHHHHHHHHHCCCee
Confidence            34445556554 6899999999999954   89999999999999886

>d2ev0a1 a.4.5.24 (A:2-62) Manganese transport regulator MntR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Iron-dependent repressor protein
domain: Manganese transport regulator MntR
species: Bacillus subtilis [TaxId: 1423]

Probab=94.13  E-value=0.022  Score=32.41  Aligned_cols=34  Identities=18%  Similarity=0.316  Sum_probs=30.8

Q ss_pred             CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           59 TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        59 ~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      +++.+..+||+.+|+.+   +.+..+++-|...|++.
T Consensus        19 ~~~v~~~~iA~~L~vs~---~SVs~mikrL~~~GlV~   52 (61)
T d2ev0a1          19 KGYARVSDIAEALAVHP---SSVTKMVQKLDKDEYLI   52 (61)
T ss_dssp             HSSCCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             CCCccHHHHHHHhCCCc---hhHHHHHHHHHHCCCEE
Confidence            47999999999999955   89999999999999876

>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=94.13  E-value=0.085  Score=33.13  Aligned_cols=41  Identities=10%  Similarity=0.143  Sum_probs=33.6

Q ss_pred             hhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           51 IPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        51 I~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      |-..|..+ +++|..|||..++.+   ...+.|+++.|+..|++.
T Consensus        41 vL~~l~~~-~~~t~~~la~~l~~~---~~~vsr~l~~L~~~G~v~   81 (141)
T d1lnwa_          41 VLKLIDEQ-RGLNLQDLGRQMCRD---KALITRKIRELEGRNLVR   81 (141)
T ss_dssp             HHHHHHSS-TTCBHHHHHHHTTCC---HHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHC-CCCCHHHHHHHHCcc---HhHHHHHHHHHHHhhcee
Confidence            33445544 568999999999994   489999999999999885

>d2fbha1 a.4.5.28 (A:8-144) Transcriptional regulator PA3341 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator PA3341
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=94.07  E-value=0.025  Score=35.31  Aligned_cols=39  Identities=18%  Similarity=0.225  Sum_probs=33.2

Q ss_pred             HHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           54 IIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        54 ~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .|..+++++|.+|||..++++   ...+.|+++-|...|++.
T Consensus        36 ~l~~~~~~~t~~~la~~~~~~---~~~vs~~v~~L~~~gli~   74 (137)
T d2fbha1          36 HLARHRDSPTQRELAQSVGVE---GPTLARLLDGLESQGLVR   74 (137)
T ss_dssp             HHHHCSSCCBHHHHHHHHTCC---HHHHHHHHHHHHHTTSEE
T ss_pred             HHHHcCCCCcHHHHHHHHCCC---HHHHHHHHHHHHHcCCcc
Confidence            355555678999999999994   489999999999999886

>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=93.94  E-value=0.027  Score=32.67  Aligned_cols=42  Identities=19%  Similarity=0.244  Sum_probs=34.4

Q ss_pred             HHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           53 DIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        53 D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      +.+.++|-|-|..|||+.+|..  .+..+++.|..|...|+++.
T Consensus        16 ~~~~~~G~~Ps~rei~~~~g~~--S~stv~~~l~~Le~kG~I~r   57 (71)
T d1jhfa1          16 DHISQTGMPPTRAEIAQRLGFR--SPNAAEEHLKALARKGVIEI   57 (71)
T ss_dssp             HHHHHHSSCCCHHHHHHHTTCS--SHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHhCCCCCHHHHHHHcCCC--CHHHHHHHHHHHHHCcCeec
Confidence            3455567899999999999983  23789999999999998863

>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=93.48  E-value=0.018  Score=34.44  Aligned_cols=33  Identities=18%  Similarity=0.326  Sum_probs=30.4

Q ss_pred             CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      +++|..|||+.+++++   ..+.|++.-|...|++.
T Consensus        20 ~~lt~~eLa~~l~i~~---~~vs~~l~~Le~~GlV~   52 (85)
T d3ctaa1          20 AYLTSSKLADMLGISQ---QSASRIIIDLEKNGYIT   52 (85)
T ss_dssp             EECCHHHHHHHHTSCH---HHHHHHHHHHHHTTSEE
T ss_pred             CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCee
Confidence            7899999999999954   89999999999999875

>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=93.14  E-value=0.033  Score=34.97  Aligned_cols=39  Identities=21%  Similarity=0.180  Sum_probs=32.7

Q ss_pred             HHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           53 DIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        53 D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      -.|..+ ++.|.+|||..+++++   ..+.|++.-|...|++.
T Consensus        37 ~~i~~~-~~~t~~~la~~l~i~~---~tvs~~l~~L~~~gli~   75 (139)
T d2a61a1          37 QKIYFE-GPKRPGELSVLLGVAK---STVTGLVKRLEADGYLT   75 (139)
T ss_dssp             HHHHHH-CCBCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHc-CCCCHHHHHHHhCCCc---ccchHHHHHHHhcCeee
Confidence            344443 6899999999999954   89999999999999875

>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=93.03  E-value=0.028  Score=35.27  Aligned_cols=42  Identities=10%  Similarity=0.237  Sum_probs=34.1

Q ss_pred             hhHHHhhC-CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           51 IPDIIHNH-TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        51 I~D~La~~-~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      |...|..+ ++++|..|||..+++++   ..+.|+++.|...|++.
T Consensus        39 iL~~l~~~~~~~~t~~eia~~~~~~~---~~vs~~l~~L~~~g~v~   81 (125)
T d1p4xa1          39 LLTYLFHQQENTLPFKKIVSDLCYKQ---SDLVQHIKVLVKHSYIS   81 (125)
T ss_dssp             HHHHHHSCSCSEEEHHHHHHHSSSCG---GGTHHHHHHHHHTTSCE
T ss_pred             HHHHHHHhccCCcCHHHHHHHhCCCc---chHHHHHHHHHHCCCce
Confidence            33445444 36899999999999955   89999999999999885

>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=92.95  E-value=0.037  Score=34.63  Aligned_cols=43  Identities=9%  Similarity=0.257  Sum_probs=35.1

Q ss_pred             cChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           49 VGIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        49 LgI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ..+...|..+ +++|..|||..+++++   ..+.|++.-|+..|++.
T Consensus        37 ~~vL~~i~~~-~~~t~~~la~~l~~~~---~~~s~~l~~L~~~Gli~   79 (136)
T d2bv6a1          37 FLVLTILWDE-SPVNVKKVVTELALDT---GTVSPLLKRMEQVDLIK   79 (136)
T ss_dssp             HHHHHHHHHS-SEEEHHHHHHHTTCCT---TTHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHcC-CCCCHHHHHHHHCCCH---hHHHHHHHHHHHCCCEE
Confidence            3344556554 6899999999999955   88999999999999986

>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=92.95  E-value=0.043  Score=34.26  Aligned_cols=39  Identities=23%  Similarity=0.188  Sum_probs=32.9

Q ss_pred             HHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           54 IIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        54 ~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .|...++++|..|||+.++++   ...+.|+++.|...|++.
T Consensus        39 ~l~~~~~~~t~~~la~~l~i~---~~~vs~~l~~L~~~glI~   77 (140)
T d3deua1          39 NIHQLPPDQSQIQLAKAIGIE---QPSLVRTLDQLEDKGLIS   77 (140)
T ss_dssp             HHHHSCSSEEHHHHHHHHTSC---HHHHHHHHHHHHHTTSEE
T ss_pred             HHHHcCCCccHHHHHHHHCCC---HhHHHHHHHHHHhCCCEE
Confidence            354445679999999999994   489999999999999885

>d1q1ha_ a.4.5.41 (A:) Transcription factor E/IIe-alpha, N-terminal domain {Archaeon Sulfolobus solfataricus [TaxId: 2287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcription factor E/IIe-alpha, N-terminal domain
domain: Transcription factor E/IIe-alpha, N-terminal domain
species: Archaeon Sulfolobus solfataricus [TaxId: 2287]

Probab=92.52  E-value=0.046  Score=33.57  Aligned_cols=43  Identities=21%  Similarity=0.274  Sum_probs=36.1

Q ss_pred             ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .|++.|-+.++.+|=.|||+.+|+   +...++|+|-.|...|+.+
T Consensus        22 ~v~~~L~~~~~evtDe~iA~~tgi---~in~VRk~Ly~L~~~~L~~   64 (88)
T d1q1ha_          22 DVLRILLDKGTEMTDEEIANQLNI---KVNDVRKKLNLLEEQGFVS   64 (88)
T ss_dssp             HHHHHHHHHCSCBCHHHHHHTTTS---CHHHHHHHHHHHHHHTSCE
T ss_pred             HHHHHHHhccCcCCHHHHHHHhCC---cHHHHHHHHHHHHhCCceE
Confidence            466766555578999999999999   5589999999999999875

>d2gaua1 a.4.5.4 (A:152-232) Transcriptional regulator PG0396, C-terminal domain {Porphyromonas gingivalis [TaxId: 837]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Transcriptional regulator PG0396, C-terminal domain
species: Porphyromonas gingivalis [TaxId: 837]

Probab=92.51  E-value=0.048  Score=31.44  Aligned_cols=33  Identities=6%  Similarity=0.004  Sum_probs=29.9

Q ss_pred             CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      -|+|-.|||..+|+.+   ..+.|+|+.|...|+++
T Consensus        28 ~~lt~~eLA~~~G~sr---etvsr~L~~l~~~glI~   60 (81)
T d2gaua1          28 IYLSREELATLSNMTV---SNAIRTLSTFVSERMLA   60 (81)
T ss_dssp             CCCCHHHHHHHTTSCH---HHHHHHHHHHHHTTSEE
T ss_pred             ecCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEE
Confidence            3789999999999955   89999999999999876

>d2g9wa1 a.4.5.39 (A:3-124) Hypothetical protein Rv1846c {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Penicillinase repressor
domain: Hypothetical protein Rv1846c
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=92.47  E-value=0.06  Score=33.74  Aligned_cols=49  Identities=16%  Similarity=0.229  Sum_probs=40.4

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCCC-CCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQIH-PTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~~-~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .|+.|-++|.+.|+|+|+.||.+.++-+ +-....+..+|+-|+..|+++
T Consensus         8 ~E~~IM~~lW~~g~~~t~~eI~~~l~~~~~~~~sTV~T~L~rL~~Kg~l~   57 (122)
T d2g9wa1           8 LERAVMDHLWSRTEPQTVRQVHEALSARRDLAYTTVMAVLQRLAKKNLVL   57 (122)
T ss_dssp             HHHHHHHHHHTCSSCEEHHHHHHHHTTTCCCCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHcCCCCccHHHHHHHHhccCCCcHHHHHHHHHHHHHCCCEE
Confidence            5667788888877899999999999752 224578999999999999886

>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=92.47  E-value=0.051  Score=31.51  Aligned_cols=32  Identities=13%  Similarity=0.308  Sum_probs=29.6

Q ss_pred             CCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           61 PMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        61 p~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      |+|-.|||..+|+++   +.+.|+|+.|...|+++
T Consensus        30 ~~t~~eiA~~lG~sr---etvsr~l~~l~~~g~I~   61 (80)
T d1ft9a1          30 DFTVEEIANLIGSSR---QTTSTALNSLIKEGYIS   61 (80)
T ss_dssp             CCCHHHHHHHHCSCH---HHHHHHHHHHHHTTSSE
T ss_pred             CCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEE
Confidence            789999999999965   89999999999999886

>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=92.09  E-value=0.034  Score=34.77  Aligned_cols=42  Identities=19%  Similarity=0.213  Sum_probs=34.7

Q ss_pred             ChhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           50 GIPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        50 gI~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .|...|..+ +++|..|||..+++++   ..+.|+++-|...|++.
T Consensus        34 ~vL~~l~~~-~~~t~~~la~~~~i~~---~~vs~~i~~L~~~gli~   75 (136)
T d2fbia1          34 RVIRILRQQ-GEMESYQLANQACILR---PSMTGVLARLERDGIVR   75 (136)
T ss_dssp             HHHHHHHHH-CSEEHHHHHHHTTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHc-CCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEE
Confidence            344556553 6899999999999954   89999999999999986

>d1i5za1 a.4.5.4 (A:138-206) Catabolite gene activator protein (CAP), C-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Catabolite gene activator protein (CAP), C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=92.07  E-value=0.047  Score=30.93  Aligned_cols=32  Identities=6%  Similarity=0.040  Sum_probs=29.3

Q ss_pred             CCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           61 PMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        61 p~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      |+|-.|||..+|+..   +.+.|+|+.|...|+++
T Consensus        29 ~lt~~~lA~~~G~sR---etvsr~L~~l~~~glI~   60 (69)
T d1i5za1          29 KITRQEIGQIVGCSR---ETVGRILKMLEDQNLIS   60 (69)
T ss_dssp             ECCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             CCCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEE
Confidence            689999999999955   89999999999999876

>d2frha1 a.4.5.28 (A:102-216) Pleiotropic regulator of virulence genes, SarA {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Pleiotropic regulator of virulence genes, SarA
species: Staphylococcus aureus [TaxId: 1280]

Probab=92.06  E-value=0.027  Score=34.88  Aligned_cols=41  Identities=17%  Similarity=0.237  Sum_probs=33.6

Q ss_pred             HHHhhCC-CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           53 DIIHNHT-KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        53 D~La~~~-gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      ..|..++ +++|..|||..+++++   ..+.|+++.|...|++..
T Consensus        40 ~~l~~~~~~~~t~~~la~~l~~~~---~tvs~~i~~Le~~gli~r   81 (115)
T d2frha1          40 TYISENKEKEYYLKDIINHLNYKQ---PQVVKAVKILSQEDYFDK   81 (115)
T ss_dssp             HHHHHTCCSEEEHHHHHHHSSSHH---HHHHHHHHHHHHTTSSCC
T ss_pred             HHHHcCCCCCCCHHHHHHHHCCCH---hHHHHHHHHHHhhhhhee
Confidence            3454443 6799999999999944   899999999999998863

>d1zyba1 a.4.5.4 (A:148-220) Probable transcription regulator BT4300, C-terminal domain {Bacteroides thetaiotaomicron [TaxId: 818]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Probable transcription regulator BT4300, C-terminal domain
species: Bacteroides thetaiotaomicron [TaxId: 818]

Probab=91.71  E-value=0.054  Score=31.33  Aligned_cols=32  Identities=13%  Similarity=0.179  Sum_probs=29.2

Q ss_pred             CCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           61 PMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        61 p~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++|-.|||+.+|+.+   +.+.|.|+.|...|+++
T Consensus        27 ~lt~~elA~~lg~sr---~tvsr~l~~l~~~g~I~   58 (73)
T d1zyba1          27 KVKMDDLARCLDDTR---LNISKTLNELQDNGLIE   58 (73)
T ss_dssp             ECCHHHHHHHHTSCH---HHHHHHHHHHHHTTSCE
T ss_pred             ecCHHHHHHHHCCCH---HHHHHHHHHHHHCCCEE
Confidence            579999999999955   89999999999999875

>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=91.29  E-value=0.058  Score=29.00  Aligned_cols=39  Identities=15%  Similarity=0.164  Sum_probs=30.9

Q ss_pred             hhHHHhhCC-CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcC
Q 041844           51 IPDIIHNHT-KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSG   92 (97)
Q Consensus        51 I~D~La~~~-gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~g   92 (97)
                      +.+.|.++- .++|++|||+.+|+++   ..+.|+.+..+.+.
T Consensus         8 v~~yI~~~~~~~~tl~~lA~~~~~s~---~~l~r~Fk~~~g~t   47 (54)
T d1bl0a1           8 ILDWIEDNLESPLSLEKVSERSGYSK---WHLQRMFKKETGHS   47 (54)
T ss_dssp             HHHHHHTTTTSCCCCHHHHHHSSSCH---HHHHHHHHHHHSSC
T ss_pred             HHHHHHhccCCCCCHHHHHHHHCcCH---HHHHHHHHHHHCcC
Confidence            346666653 7999999999999955   89999999777554

>d1p4xa2 a.4.5.28 (A:126-250) Staphylococcal accessory regulator A homolog, SarS {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Staphylococcal accessory regulator A homolog, SarS
species: Staphylococcus aureus [TaxId: 1280]

Probab=91.01  E-value=0.066  Score=33.69  Aligned_cols=43  Identities=16%  Similarity=0.209  Sum_probs=34.7

Q ss_pred             ChhHHHhhCC-CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           50 GIPDIIHNHT-KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        50 gI~D~La~~~-gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .|...|...+ +++|..|||+.++.++   ..+.|++.-|...|++.
T Consensus        37 ~vL~~l~~~~~~~~~~~~ia~~l~~~~---~~vs~~v~~L~~~glV~   80 (125)
T d1p4xa2          37 TILAIITSQNKNIVLLKDLIETIHHKY---PQTVRALNNLKKQGYLI   80 (125)
T ss_dssp             HHHHHHHTTTTCCEEHHHHHHHSSSCH---HHHHHHHHHHHHHTSSE
T ss_pred             HHHHHHHHccCCCccHHHHHHHHCCCc---chHHHHHHHHHhccCEe
Confidence            3444565433 6799999999999954   89999999999999885

>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=90.87  E-value=0.069  Score=33.75  Aligned_cols=38  Identities=8%  Similarity=0.155  Sum_probs=32.4

Q ss_pred             HHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           54 IIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        54 ~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .|..+ +++|..|||..+++++   ..+.|+++-|...|++.
T Consensus        37 ~i~~~-~~~t~~~la~~l~i~~---~tvs~~l~~L~~~glI~   74 (144)
T d1lj9a_          37 RVCEN-PGIIQEKIAELIKVDR---TTAARAIKRLEEQGFIY   74 (144)
T ss_dssp             HHHHS-TTEEHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             HHHhC-CCCCHHHHHHHHCccH---hhHHHHHHHHHhhhccc
Confidence            35554 4799999999999954   99999999999999885

>d3e5ua1 a.4.5.4 (A:148-227) Chlorophenol reduction protein CprK {Desulfitobacterium hafniense [TaxId: 49338]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Chlorophenol reduction protein CprK
species: Desulfitobacterium hafniense [TaxId: 49338]

Probab=90.41  E-value=0.11  Score=29.93  Aligned_cols=33  Identities=15%  Similarity=0.278  Sum_probs=29.9

Q ss_pred             CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      -|+|-.|||..+|+.+   +.+.|+|..|...|+++
T Consensus        29 ~~lt~~elA~~~g~sr---etvsr~l~~l~~~glI~   61 (80)
T d3e5ua1          29 MPLSQKSIGEITGVHH---VTVSRVLASLKRENILD   61 (80)
T ss_dssp             SCCCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             eCCCHHHHHHHHCCCH---HHHHHHHHHHHHCCcEE
Confidence            4789999999999955   89999999999999876

>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=90.01  E-value=0.062  Score=33.18  Aligned_cols=34  Identities=9%  Similarity=0.160  Sum_probs=30.7

Q ss_pred             CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           59 TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        59 ~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++++|..|||..+++++   ..+.|++..|...|++.
T Consensus        46 ~~~~t~~ela~~l~~~~---~~vs~~i~~Le~~gli~   79 (115)
T d1hsja1          46 SNEISSKEIAKCSEFKP---YYLTKALQKLKDLKLLS   79 (115)
T ss_dssp             CSEEEHHHHHHSSCCCH---HHHHHHHHHHHTTTTSC
T ss_pred             CCCcCHHHHHHHHCCCh---hhHHHHHHHHHHcCCeE
Confidence            36899999999999954   89999999999999886

>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=89.98  E-value=0.11  Score=32.46  Aligned_cols=38  Identities=21%  Similarity=0.211  Sum_probs=32.2

Q ss_pred             HHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           54 IIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        54 ~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .|..+ +++|.+|||..++++   +..+.|++..|...|++.
T Consensus        42 ~l~~~-~~~t~~ela~~~~i~---~~~vs~~v~~L~~~glv~   79 (138)
T d1jgsa_          42 SIRCA-ACITPVELKKVLSVD---LGALTRMLDRLVCKGWVE   79 (138)
T ss_dssp             HHHHH-SSBCHHHHHHHHTCC---HHHHHHHHHHHHHTTSEE
T ss_pred             hHHhC-cCCCHHHHHHHHCCC---HhHHHHHHHHHhhCCCEE
Confidence            34443 589999999999994   489999999999999885

>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=89.50  E-value=0.12  Score=33.69  Aligned_cols=34  Identities=12%  Similarity=0.139  Sum_probs=30.1

Q ss_pred             CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           60 KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        60 gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      +.+|..|||+.+++++   ..+.|++.-|...|++..
T Consensus        78 ~~lt~~eLa~~l~i~~---~tvsr~l~~Le~~GlV~r  111 (172)
T d2fbka1          78 EGLRPTELSALAAISG---PSTSNRIVRLLEKGLIER  111 (172)
T ss_dssp             SCBCHHHHHHHCSCCS---GGGSSHHHHHHHHTSEEC
T ss_pred             CCcCHHHHHHHHCcCH---hHHHHHHHHHHhCCCeee
Confidence            3589999999999955   899999999999998864

>d1stza1 a.4.5.51 (A:14-100) Heat-inducible transcription repressor HrcA, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Heat-inducible transcription repressor HrcA, N-terminal domain
domain: Heat-inducible transcription repressor HrcA, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=89.34  E-value=0.26  Score=29.62  Aligned_cols=38  Identities=16%  Similarity=0.227  Sum_probs=32.1

Q ss_pred             hCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           57 NHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        57 ~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      +.|.|.+..+|++..+.+- .+..++-.|..|...|++.
T Consensus        19 ~~g~Pv~s~~i~~~~~l~~-S~aTIRn~m~~LE~~G~l~   56 (87)
T d1stza1          19 ENKKPVSSQRVLEVSNIEF-SSATIRNDMKKLEYLGYIY   56 (87)
T ss_dssp             HHCSCBCHHHHHHHSCCCS-CHHHHHHHHHHHHHTTSEE
T ss_pred             HcCCccCHHHHHHHhCCCC-CHHHHHHHHHHHHHCCccc
Confidence            3578999999999988742 3488999999999999985

>d2dk5a1 a.4.5.85 (A:8-85) DNA-directed RNA polymerase III subunit RPC6, RPO3F {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: RPO3F domain-like
domain: DNA-directed RNA polymerase III subunit RPC6, RPO3F
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.05  E-value=0.13  Score=30.68  Aligned_cols=43  Identities=9%  Similarity=0.050  Sum_probs=35.6

Q ss_pred             hhHHHhhCC-CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCcccc
Q 041844           51 IPDIIHNHT-KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        51 I~D~La~~~-gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~e   96 (97)
                      |.++|..+| ..+...+|-.+++.+.   ..|.|+++.|.+.+++.+
T Consensus        18 VY~~I~~ag~~GIW~~dir~ktnL~~---~~l~K~LK~Lesk~lIK~   61 (78)
T d2dk5a1          18 VYQIIEDAGNKGIWSRDVRYKSNLPL---TEINKILKNLESKKLIKA   61 (78)
T ss_dssp             HHHHHHHHCTTCEEHHHHHHHTTCCH---HHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHccccceeHHHHHHHcCCCH---HHHHHHHHHHHhcCCcee
Confidence            556666655 7788999999999965   889999999999998764

>d1mzba_ a.4.5.42 (A:) Ferric uptake regulation protein, FUR {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: FUR-like
domain: Ferric uptake regulation protein, FUR
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=88.84  E-value=0.15  Score=31.96  Aligned_cols=50  Identities=12%  Similarity=0.140  Sum_probs=37.0

Q ss_pred             HhcChhHHHhhCC-CCCCHHHHHHHhCCC-C-CCcccHHHHHHHHHhcCcccc
Q 041844           47 IQVGIPDIIHNHT-KPMTLNQLLGALQIH-P-TKTRCLHFLVCSLVRSGFFNL   96 (97)
Q Consensus        47 veLgI~D~La~~~-gp~s~~ELA~~~g~~-~-~~~~~L~RlLR~Laa~gif~e   96 (97)
                      .+.-|.+.|.++. .|.|+.||-+.+.-. | .+...++|.|..|+..|++.+
T Consensus        17 qR~~Il~~L~~~~~~h~sa~ei~~~l~~~~~~i~~aTVYR~L~~l~e~gli~~   69 (134)
T d1mzba_          17 PRVKILQMLDSAEQRHMSAEDVYKALMEAGEDVGLATVYRVLTQFEAAGLVVR   69 (134)
T ss_dssp             HHHHHHHHHHCC-CCSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTSEEE
T ss_pred             HHHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCccHHHHHHHHHHHHhccEEEE
Confidence            3445678886654 589999999987531 1 155789999999999999863

>d1d5ya1 a.4.1.8 (A:3-56) Rob transcription factor, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: AraC type transcriptional activator
domain: Rob transcription factor, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=87.95  E-value=0.15  Score=27.32  Aligned_cols=39  Identities=10%  Similarity=0.192  Sum_probs=30.6

Q ss_pred             ChhHHHhhC-CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhc
Q 041844           50 GIPDIIHNH-TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRS   91 (97)
Q Consensus        50 gI~D~La~~-~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~   91 (97)
                      .+.+.|.++ .+|+|+++||+.+|+++   ..+.|+.+.-...
T Consensus         7 ~i~~yi~~~~~~~itl~~lA~~~~~S~---~~l~r~Fk~~~g~   46 (54)
T d1d5ya1           7 DLLIWLEGHLDQPLSLDNVAAKAGYSK---WHLQRMFKDVTGH   46 (54)
T ss_dssp             HHHHHHHTTSSSSCCCHHHHTTTSSCH---HHHHHHHHHHHSS
T ss_pred             HHHHHHHHccCCCCCHHHHHHHHCcCH---HHHHHHHHHHHCc
Confidence            345667665 38999999999999965   8999999866543

>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=87.30  E-value=0.14  Score=31.85  Aligned_cols=38  Identities=13%  Similarity=0.348  Sum_probs=32.3

Q ss_pred             HHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           54 IIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        54 ~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .|..+ +++|..|||..++++   +..+.|++..|...|++.
T Consensus        41 ~l~~~-~~~t~~~La~~~~i~---~~~vsr~i~~L~~~glv~   78 (137)
T d1z91a1          41 LLWEH-ETLTVKKMGEQLYLD---SGTLTPMLKRMEQQGLIT   78 (137)
T ss_dssp             HHHHH-SEEEHHHHHHTTTCC---HHHHHHHHHHHHHHTSEE
T ss_pred             HHHcC-CCCCHHHHHHHHCcC---HHHHHHHHHHHhhccceE
Confidence            34433 689999999999994   489999999999999986

>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=86.85  E-value=0.2  Score=28.34  Aligned_cols=34  Identities=9%  Similarity=0.120  Sum_probs=29.9

Q ss_pred             CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           59 TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        59 ~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      |..++..|||+..|++.   ..+++.|+.|+..|++.
T Consensus        23 G~~l~~~~La~~~~vSr---~tvr~Al~~L~~~Gli~   56 (69)
T d2hs5a1          23 GARLSEPDICAALDVSR---NTVREAFQILIEDRLVA   56 (69)
T ss_dssp             TCEECHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             cCccCHHHHHHHHCCCH---HHHHHHHHHHHHCCcEE
Confidence            45678999999999954   88999999999999876

>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=86.54  E-value=0.14  Score=33.37  Aligned_cols=41  Identities=12%  Similarity=0.085  Sum_probs=33.9

Q ss_pred             hhHHHhhCCCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           51 IPDIIHNHTKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        51 I~D~La~~~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      |-.+|..+ +++|..|||+.+++++   ..+.|++.-|...|++.
T Consensus        46 vL~~l~~~-~~~t~~~la~~~~l~~---~tvs~~i~rL~~~gli~   86 (162)
T d2fxaa1          46 ILWIAYQL-NGASISEIAKFGVMHV---STAFNFSKKLEERGYLR   86 (162)
T ss_dssp             HHHHHHHH-TSEEHHHHHHHTTCCH---HHHHHHHHHHHHHTSEE
T ss_pred             HHhhhccC-CCcCHHHHHHHHcCCc---hhhHHHHHHHHHCCCce
Confidence            44455543 5899999999999944   89999999999999886

>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=85.87  E-value=0.31  Score=28.00  Aligned_cols=34  Identities=15%  Similarity=0.253  Sum_probs=29.8

Q ss_pred             CCCC-CHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           59 TKPM-TLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        59 ~gp~-s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      |..+ |..|||+.++++.   ..+++-++.|+..|++.
T Consensus        24 G~~LPs~~eLa~~~~vSr---~tvr~Al~~L~~~G~i~   58 (74)
T d1hw1a1          24 GTILPAERELSELIGVTR---TTLREVLQRLARDGWLT   58 (74)
T ss_dssp             TSBCCCHHHHHHHHTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             cCCCccHHHHHHHHCCCH---HHHHHHHHHHHHCCcEE
Confidence            3567 8999999999954   88999999999999875

>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=84.89  E-value=0.39  Score=27.51  Aligned_cols=34  Identities=12%  Similarity=0.184  Sum_probs=29.7

Q ss_pred             CCCC-CHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           59 TKPM-TLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        59 ~gp~-s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      |..+ |..|||+..+++.   ..+++.++.|+..|++.
T Consensus        19 G~~LPse~~La~~~~vSr---~tvr~Al~~L~~~Gli~   53 (78)
T d3bwga1          19 GDKLPVLETLMAQFEVSK---STITKSLELLEQKGAIF   53 (78)
T ss_dssp             TCBCCCHHHHHHHTTCCH---HHHHHHHHHHHHTTSEE
T ss_pred             cCCCcCHHHHHHHHCCCH---HHHHHHHHHHHHCCcEE
Confidence            3567 8999999999954   88999999999999875

>d2o3fa1 a.4.1.20 (A:1-83) Putative transcriptional regulator YbbH {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: RpiR-like
domain: Putative transcriptional regulator YbbH
species: Bacillus subtilis [TaxId: 1423]

Probab=84.81  E-value=0.13  Score=30.41  Aligned_cols=40  Identities=23%  Similarity=0.180  Sum_probs=29.0

Q ss_pred             ChhHHHhhCC---CCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcC
Q 041844           50 GIPDIIHNHT---KPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSG   92 (97)
Q Consensus        50 gI~D~La~~~---gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~g   92 (97)
                      .|++.|-++.   .-+|+.|||+++++++   ..+.|+.|.|--.|
T Consensus        22 ~ia~yil~~~~~~~~~si~~lA~~~~vS~---sTi~Rf~kklG~~g   64 (83)
T d2o3fa1          22 KLADYILAHPHKAIESTVNEISALANSSD---AAVIRLCKSLGLKG   64 (83)
T ss_dssp             HHHHHHHHCHHHHHTCCHHHHHHHTTCCH---HHHHHHHHHTTCSS
T ss_pred             HHHHHHHcCHHHHHHccHHHHHHHHCCCH---HHHHHHHHHhCCCC
Confidence            4456554443   5689999999999965   78888888765544

>d1okra_ a.4.5.39 (A:) Methicillin resistance regulatory protein MecI {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Penicillinase repressor
domain: Methicillin resistance regulatory protein MecI
species: Staphylococcus aureus [TaxId: 1280]

Probab=84.46  E-value=0.23  Score=30.47  Aligned_cols=48  Identities=19%  Similarity=0.362  Sum_probs=35.9

Q ss_pred             HhcChhHHHhhCCCCCCHHHHHHHhCC-CCCCcccHHHHHHHHHhcCccc
Q 041844           47 IQVGIPDIIHNHTKPMTLNQLLGALQI-HPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        47 veLgI~D~La~~~gp~s~~ELA~~~g~-~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      .|+.|-.+|.+. +|+|+.||.+.+.- .+-+...+.++|+-|...|+++
T Consensus         8 ~E~~VM~~lW~~-~~~t~~ei~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~   56 (120)
T d1okra_           8 AEWEVMNIIWMK-KYASANNIIEEIQMQKDWSPKTIRTLITRLYKKGFID   56 (120)
T ss_dssp             HHHHHHHHHHHH-SSEEHHHHHHHHHHHCCCCHHHHHHHHHHHHHHTSEE
T ss_pred             HHHHHHHHHHcC-CCCCHHHHHHHHhcccCccHHhHHHHHHHHHHCCCeE
Confidence            455666666654 69999999998742 1114578999999999999985

>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=84.29  E-value=0.52  Score=28.19  Aligned_cols=34  Identities=18%  Similarity=0.314  Sum_probs=29.5

Q ss_pred             CCCCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           59 TKPMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        59 ~gp~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      |+|.|+..|+++.+++   -+.|+|.|-.|.+-|+..
T Consensus        22 g~~WSLaklsKra~~P---MS~LRR~LTqL~~aGl~~   55 (81)
T d2obpa1          22 ATPWSLPKIAKRAQLP---MSVLRRVLTQLQAAGLAD   55 (81)
T ss_dssp             CCCCBHHHHHHHHTCC---HHHHHHHHHHHHHTTSEE
T ss_pred             CCCccHHHHHhhcCCc---HHHHHHHHHHHhhcCcee
Confidence            4799999999999983   378999999999999753

>d2bgca1 a.4.5.4 (A:138-237) Listeriolysin regulatory protein PrfA, C-terminal domain {Bacteria (Listeria monocytogenes) [TaxId: 1639]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Listeriolysin regulatory protein PrfA, C-terminal domain
species: Bacteria (Listeria monocytogenes) [TaxId: 1639]

Probab=82.10  E-value=0.67  Score=28.09  Aligned_cols=33  Identities=12%  Similarity=0.137  Sum_probs=28.3

Q ss_pred             CCCHHHHHHHhCCCCCCcccHHHHHHHHHhcCccc
Q 041844           61 PMTLNQLLGALQIHPTKTRCLHFLVCSLVRSGFFN   95 (97)
Q Consensus        61 p~s~~ELA~~~g~~~~~~~~L~RlLR~Laa~gif~   95 (97)
                      ++|-.|||..+|+.+  -..+.|+|+.|...|+++
T Consensus        31 ~lTqeeLA~~lG~s~--ReTVsR~L~~L~~~GlI~   63 (100)
T d2bgca1          31 NLTMQELGYSSGIAH--SSAVSRIISKLKQEKVIV   63 (100)
T ss_dssp             CCCHHHHHHHTTCCC--HHHHHHHHHHHHHTTSEE
T ss_pred             ccCHHHHHHHhCCch--HHHHHHHHHHHHHCCCEE
Confidence            689999999999832  257999999999999886

>d1v7ba1 a.4.1.9 (A:1-74) Transcriptional regulator Cgl2612 {Corynebacterium glutamicum [TaxId: 1718]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator Cgl2612
species: Corynebacterium glutamicum [TaxId: 1718]

Probab=80.11  E-value=1.1  Score=24.88  Aligned_cols=23  Identities=17%  Similarity=0.247  Sum_probs=18.5

Q ss_pred             hHHHhhCC-CCCCHHHHHHHhCCC
Q 041844           52 PDIIHNHT-KPMTLNQLLGALQIH   74 (97)
Q Consensus        52 ~D~La~~~-gp~s~~ELA~~~g~~   74 (97)
                      .+.+.+.| ...|+.+||+++|+.
T Consensus        14 ~~l~~~~G~~~~s~~~Ia~~agvs   37 (74)
T d1v7ba1          14 IDYIGEYSLETLSYDSLAEATGLS   37 (74)
T ss_dssp             HHHHHHSCSTTCCHHHHHHHHCSC
T ss_pred             HHHHHHhCccccCHHHHHHHhCcC
Confidence            35566666 889999999999984