Citrus Sinensis ID: 041968

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80-------
Protein Sequence
MDMNHMINAESSSSSSSSSSELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL
Secondary Structure (PSIPRED)
ccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHccccccHHHHHHHcccccccccHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHcccccccHHHHHHHccccccccHHHHHHHHHc
Coil and Loop (DISEMBL)
mdmnhminaesssssssssSELLKAQAQVWNCAFNYINSMSLKCAVElgipdvihkhgqpmtLSQIASALDIQKNKAHCIQRLMRIL
Flexible Loop (DISEMBL)
mdmnhminaessssssssSSELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL
Low Complexity Region (SEG)
MDMNHMINAEssssssssssELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL
Disordered region (IsUnstruct)
************************AQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRL****
Disordered Region (DISOPRED)
************************AQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL
Disordered Region (DISEMBL)
************************AQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL
Disordered Region (DISPRO)
*****************SSSELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL
Transmembrane Helix (TMHMM)
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Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDMNHMINAESSSSSSSSSSELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL
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	87	2.2.26 [Sep-21-2011]
Q6VMW0	366	8-hydroxyquercetin 8-O-me	N/A	no	0.816	0.193	0.690	6e-23
B6VJS4	357	Trans-resveratrol di-O-me	no	no	0.793	0.193	0.594	1e-20
Q93WU2	357	Eugenol O-methyltransfera	N/A	no	0.827	0.201	0.583	4e-20
Q93WU3	356	Chavicol O-methyltransfer	N/A	no	0.827	0.202	0.583	5e-19
Q84KK4	365	Isoflavone 4'-O-methyltra	N/A	no	0.873	0.208	0.447	1e-14
Q29U70	364	Isoflavone 4'-O-methyltra	N/A	no	0.862	0.206	0.453	1e-14
Q8GSN1	348	Myricetin O-methyltransfe	N/A	no	0.793	0.198	0.536	3e-14
B0EXJ8	355	Tabersonine 16-O-methyltr	N/A	no	0.793	0.194	0.521	4e-14
P0DH60	360	6a-hydroxymaackiain methy	N/A	no	0.862	0.208	0.453	4e-14
O24305	360	6a-hydroxymaackiain methy	N/A	no	0.862	0.208	0.426	3e-13

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

 Score =  105 bits (263), Expect = 6e-23,   Method: Composition-based stats.
 Identities = 49/71 (69%), Positives = 59/71 (83%)

Query: 17 SSSSELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNK 76
          SS  ELL+AQA VWN  ++YINSMSLKCA++LGIPD IHKHG P+TLSQ+A AL+I K K
Sbjct: 8  SSKQELLEAQAHVWNHIYSYINSMSLKCAIQLGIPDAIHKHGNPITLSQLADALNINKAK 67

Query: 77 AHCIQRLMRIL 87
          +H + RLMRIL
Sbjct: 68 SHGLFRLMRIL 78

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: 2EC: .EC: 1EC: .EC: 1EC: .EC: 8EC: 8

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

 Score = 98.6 bits (244), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 41/69 (59%), Positives = 54/69 (78%)

Query: 19 SSELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAH 78
          S+ELL AQA VWN  FN+I SMSLKCA++LGIPD+IH HG+PMTL ++ + L +   ++ 
Sbjct: 9  SAELLHAQAHVWNHIFNFIKSMSLKCAIQLGIPDIIHNHGKPMTLPELVAKLPVHPKRSQ 68

Query: 79 CIQRLMRIL 87
          C+ RLMRIL
Sbjct: 69 CVYRLMRIL 77

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: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 2

EC: 4

EC: 0

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

 Score = 96.7 bits (239), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 42/72 (58%), Positives = 55/72 (76%)

Query: 16 SSSSSELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKN 75
          S S+ +LL+AQ  VWN  + + NSMSLKCA++LGIPD++HKHG+PMTLSQ+  ++ I K 
Sbjct: 9  SLSTEQLLQAQVHVWNHMYAFANSMSLKCAIQLGIPDILHKHGRPMTLSQLLQSIPINKE 68

Query: 76 KAHCIQRLMRIL 87
          K  C QRLMR L
Sbjct: 69 KTQCFQRLMRAL 80

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 = 92.8 bits (229), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 42/72 (58%), Positives = 54/72 (75%)

Query: 16 SSSSSELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKN 75
          S S+ +LL+AQA VWN  + + NSMSLKCA++LGIPD++HKH  PMTLSQ+  A+ I K 
Sbjct: 9  SLSTEQLLQAQAHVWNHMYAFANSMSLKCAIQLGIPDILHKHDHPMTLSQLLKAIPINKE 68

Query: 76 KAHCIQRLMRIL 87
          K+   QRLMR L
Sbjct: 69 KSQSFQRLMRAL 80

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

 Score = 78.6 bits (192), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 34/76 (44%), Positives = 57/76 (75%)

Query: 12 SSSSSSSSSELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALD 71
          SSS+ S  +EL +AQ  ++   +N+++SM+LK A+ELGI DVIH HG+P+TL ++A+AL+
Sbjct: 4  SSSNGSEDTELSQAQIHLYKHVYNFVSSMALKSAMELGIADVIHSHGKPITLPELATALN 63

Query: 72 IQKNKAHCIQRLMRIL 87
          ++ +K   + R +R+L
Sbjct: 64 LRPSKIGVLHRFLRLL 79

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

Lotus japonicus (taxid: 34305)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 2

EC: 1

EC: 2

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

 Score = 78.6 bits (192), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 34/75 (45%), Positives = 54/75 (72%)

Query: 13 SSSSSSSSELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDI 72
          S++ S  SEL  AQ  ++   +N+++SM+LK A+ELGI D IH HG+PMTLS++AS+L +
Sbjct: 4  STNGSEESELYHAQIHLYKHVYNFVSSMALKSAMELGIADAIHNHGKPMTLSELASSLKL 63

Query: 73 QKNKAHCIQRLMRIL 87
            +K + + R +R+L
Sbjct: 64 HPSKVNILHRFLRLL 78

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 = 77.0 bits (188), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 37/69 (53%), Positives = 48/69 (69%)

Query: 19 SSELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAH 78
          SSE+  AQA  +   F++ +  SLKCAV+LGIPD IH HG+PM LS + ++L I  +KA 
Sbjct: 5  SSEIRNAQAHFFTQVFSFTSMSSLKCAVQLGIPDAIHSHGKPMALSDLTNSLPINPSKAP 64

Query: 79 CIQRLMRIL 87
           I RLMRIL
Sbjct: 65 YIYRLMRIL 73

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

 Score = 76.6 bits (187), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 37/71 (52%), Positives = 51/71 (71%), Gaps = 2/71 (2%)

Query: 19 SSELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASAL--DIQKNK 76
          S E   AQAQ+W+ + ++I S SLKCAV+LGIPD I  HG+P+TLS++ +AL   +  +K
Sbjct: 5  SEEFRGAQAQIWSQSCSFITSASLKCAVKLGIPDTIDNHGKPITLSELTNALVPPVHPSK 64

Query: 77 AHCIQRLMRIL 87
          A  I RLMR+L
Sbjct: 65 APFIYRLMRVL 75

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

Catharanthus roseus (taxid: 4058)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 9

EC: 4

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

 Score = 76.6 bits (187), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 34/75 (45%), Positives = 53/75 (70%)

Query: 13 SSSSSSSSELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDI 72
          S++ S  SEL  AQ  ++   +N+++SM+LK AVELGI D IH HG+PMTL ++AS+L +
Sbjct: 4  STNGSEESELYHAQIHLYKHIYNFVSSMALKSAVELGIADAIHNHGKPMTLPELASSLKL 63

Query: 73 QKNKAHCIQRLMRIL 87
            +K + + R +R+L
Sbjct: 64 HPSKVNILYRFLRLL 78

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 = 73.9 bits (180), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 32/75 (42%), Positives = 53/75 (70%)

Query: 13 SSSSSSSSELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDI 72
          S++ S  SEL  AQ  ++   +N+++SM+LK A+ELGI D IH HG+PMTL +++S+L +
Sbjct: 4  STNGSEESELYHAQIHLYKHVYNFVSSMALKSAMELGIADAIHNHGKPMTLPELSSSLKL 63

Query: 73 QKNKAHCIQRLMRIL 87
            +K + + R +R+L
Sbjct: 64 HPSKVNILYRFLRLL 78

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

Pisum sativum (taxid: 3888)

EC: 2

EC: .

EC: 1

EC: .

EC: 1

EC: .

EC: 4

EC: 6

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	87
62421312	374	3,5-dimethoxyphenol O-methyltransferase	0.770	0.179	0.746	1e-23
75129654	366	RecName: Full=8-hydroxyquercetin 8-O-met	0.816	0.193	0.690	3e-21
3077640	356	O-methyltransferase [Prunus dulcis]	0.850	0.207	0.621	3e-21
225446491	357	PREDICTED: 8-hydroxyquercetin 8-O-methyl	0.839	0.204	0.630	7e-21
147816431	357	hypothetical protein VITISV_020020 [Viti	0.839	0.204	0.630	8e-21
224121884	354	flavonoid o-methyltransferase related [P	0.839	0.206	0.643	1e-20
2282586	354	methyltransferase [Prunus armeniaca]	0.850	0.209	0.662	1e-20
225446499	358	PREDICTED: myricetin O-methyltransferase	0.850	0.206	0.594	1e-20
224135351	359	flavonoid o-methyltransferase [Populus t	0.839	0.203	0.643	2e-20
225446503	359	PREDICTED: 8-hydroxyquercetin 8-O-methyl	0.850	0.206	0.594	2e-20

>gi|62421312|gb|AAX82431.1| 3,5-dimethoxyphenol O-methyltransferase [Ruta graveolens]

 Score =  113 bits (283), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 50/67 (74%), Positives = 57/67 (85%)

Query: 21 ELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCI 80
          EL KAQ QVWNCA N +NS+SLKCAVELGIPD+IH HGQPMTLSQI SAL+IQ NK   +
Sbjct: 19 ELFKAQGQVWNCALNCVNSLSLKCAVELGIPDIIHSHGQPMTLSQICSALNIQPNKTQAM 78

Query: 81 QRLMRIL 87
          +R+MRIL
Sbjct: 79 ERVMRIL 85

Source: Ruta graveolens

Species: Ruta graveolens

Genus: Ruta

Family: Rutaceae

Order: Sapindales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|75129654|sp|Q6VMW0.1|Q8OMT_MENPI RecName: Full=8-hydroxyquercetin 8-O-methyltransferase; AltName: Full=Flavonol 8-O-methyltransferase gi|38047395|gb|AAR09600.1| flavonoid 8-O-methyltransferase [Mentha x piperita]

 Score =  105 bits (263), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 49/71 (69%), Positives = 59/71 (83%)

Query: 17 SSSSELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNK 76
          SS  ELL+AQA VWN  ++YINSMSLKCA++LGIPD IHKHG P+TLSQ+A AL+I K K
Sbjct: 8  SSKQELLEAQAHVWNHIYSYINSMSLKCAIQLGIPDAIHKHGNPITLSQLADALNINKAK 67

Query: 77 AHCIQRLMRIL 87
          +H + RLMRIL
Sbjct: 68 SHGLFRLMRIL 78

Source: Mentha x piperita

Species: Mentha x piperita

Genus: Mentha

Family: Lamiaceae

Order: Lamiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  105 bits (262), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 46/74 (62%), Positives = 59/74 (79%)

Query: 14 SSSSSSSELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQ 73
          S+  SS+ LL+AQA +WNC F++IN MSLKCAV+LGIPD+I KHG PM+LS + SAL I 
Sbjct: 4  SNEMSSANLLQAQAHIWNCIFSFINPMSLKCAVQLGIPDIIKKHGNPMSLSDLISALPIH 63

Query: 74 KNKAHCIQRLMRIL 87
            K++C+ RLMRIL
Sbjct: 64 PKKSNCVYRLMRIL 77

Source: Prunus dulcis

Species: Prunus dulcis

Genus: Prunus

Family: Rosaceae

Order: Rosales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  104 bits (259), Expect = 7e-21,   Method: Composition-based stats.
 Identities = 46/73 (63%), Positives = 56/73 (76%)

Query: 15 SSSSSSELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQK 74
          S  +SSELL AQA VWN  FN+INSMSLKCA++LGIPD+IH HG+PMTL ++ + L I  
Sbjct: 5  SVETSSELLHAQAHVWNHIFNFINSMSLKCAIQLGIPDIIHNHGKPMTLPELVAKLPIHP 64

Query: 75 NKAHCIQRLMRIL 87
           K  C+ RLMRIL
Sbjct: 65 KKVWCVYRLMRIL 77

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 =  104 bits (259), Expect = 8e-21,   Method: Composition-based stats.
 Identities = 46/73 (63%), Positives = 56/73 (76%)

Query: 15 SSSSSSELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQK 74
          S  +SSELL AQA VWN  FN+INSMSLKCA++LGIPD+IH HG+PMTL ++ + L I  
Sbjct: 5  SVETSSELLHAQAHVWNHIFNFINSMSLKCAIQLGIPDIIHNHGKPMTLPELVAKLPIHP 64

Query: 75 NKAHCIQRLMRIL 87
           K  C+ RLMRIL
Sbjct: 65 KKVWCVYRLMRIL 77

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224121884|ref|XP_002330677.1| flavonoid o-methyltransferase related [Populus trichocarpa] gi|222872281|gb|EEF09412.1| flavonoid o-methyltransferase related [Populus trichocarpa]

 Score =  103 bits (257), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 47/73 (64%), Positives = 58/73 (79%)

Query: 15 SSSSSSELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQK 74
          +  S+ ELL+AQ  VWN  FN+INSM+LKCAV+LGIPDVI KHG+PMTLS++ SAL I  
Sbjct: 5  NEESAGELLQAQTHVWNHIFNFINSMTLKCAVQLGIPDVIQKHGKPMTLSELVSALPIHP 64

Query: 75 NKAHCIQRLMRIL 87
          +KA  + RLMRIL
Sbjct: 65 SKAQYVHRLMRIL 77

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|2282586|gb|AAB71213.1| methyltransferase [Prunus armeniaca]

 Score =  103 bits (257), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 49/74 (66%), Positives = 58/74 (78%)

Query: 14 SSSSSSSELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQ 73
           S  +S ELL+AQA +WN  F++INS+SLKCAV+L IPDVI KHGQPMTLS++ SAL I 
Sbjct: 2  GSVRASHELLQAQAHIWNHIFSFINSLSLKCAVQLDIPDVIQKHGQPMTLSELVSALPIS 61

Query: 74 KNKAHCIQRLMRIL 87
            KAH I RLMRIL
Sbjct: 62 PTKAHFIPRLMRIL 75

Source: Prunus armeniaca

Species: Prunus armeniaca

Genus: Prunus

Family: Rosaceae

Order: Rosales

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 =  103 bits (257), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 44/74 (59%), Positives = 58/74 (78%)

Query: 14 SSSSSSSELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQ 73
          ++   SSELL+AQA VWN  FN+INSMSLKCA++LGIPD+IH H +PMTL ++ + L ++
Sbjct: 4  ANGERSSELLQAQAHVWNHIFNFINSMSLKCAIQLGIPDIIHNHCKPMTLHELVAKLPVR 63

Query: 74 KNKAHCIQRLMRIL 87
           NK  C+ RLMRIL
Sbjct: 64 PNKTLCVHRLMRIL 77

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224135351|ref|XP_002327196.1| flavonoid o-methyltransferase [Populus trichocarpa] gi|222835566|gb|EEE74001.1| flavonoid o-methyltransferase [Populus trichocarpa]

 Score =  103 bits (256), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 47/73 (64%), Positives = 58/73 (79%)

Query: 15 SSSSSSELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQK 74
          +  S+ ELL+AQ  VWN  FN+INSM+LKCAV+LGIPDVI KHG+PMTLS++ SAL I  
Sbjct: 5  NEESAGELLQAQTHVWNHIFNFINSMTLKCAVQLGIPDVIQKHGKPMTLSELVSALPIHP 64

Query: 75 NKAHCIQRLMRIL 87
          +KA  + RLMRIL
Sbjct: 65 SKAQYVHRLMRIL 77

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  102 bits (255), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 44/74 (59%), Positives = 57/74 (77%)

Query: 14 SSSSSSSELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQ 73
          ++   SSELL+AQ  VWN  FN+INSMSLKCA++LGIPD+IH H QPMTL ++ + L ++
Sbjct: 4  ANGGRSSELLQAQTHVWNHIFNFINSMSLKCAIQLGIPDIIHNHCQPMTLHELVAKLPVR 63

Query: 74 KNKAHCIQRLMRIL 87
           NK  C+ RLMRIL
Sbjct: 64 PNKTLCVHRLMRIL 77

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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	87
UNIPROTKB|Q6VMW0	366	OMT2 "8-hydroxyquercetin 8-O-m	0.770	0.183	0.701	3.9e-21
UNIPROTKB|B0EXJ8	355	16OMT "Tabersonine 16-O-methyl	0.770	0.188	0.521	5.7e-13
UNIPROTKB|Q8GSN1	348	Q8GSN1 "Myricetin O-methyltran	0.770	0.192	0.522	6.9e-13
UNIPROTKB|Q84KK4	365	HI4'OMT "Isoflavone 4'-O-methy	0.770	0.183	0.447	4.8e-12
UNIPROTKB|Q84KK6	367	HI4'OMT "Isoflavone 4'-O-methy	0.770	0.182	0.462	6.2e-12
UNIPROTKB|Q84KK5	357	D7OMT "Isoflavone 7-O-methyltr	0.770	0.187	0.417	2.6e-10
UNIPROTKB|A8QW53	374	OMT3 "5-pentadecatrienyl resor	0.770	0.179	0.373	5.7e-08
TAIR|locus:2132801	325	AT4G35150 [Arabidopsis thalian	0.735	0.196	0.362	6.9e-07
TAIR|locus:2132806	382	AT4G35160 [Arabidopsis thalian	0.735	0.167	0.347	2e-06

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

 Score = 248 (92.4 bits), Expect = 3.9e-21, P = 3.9e-21
 Identities = 47/67 (70%), Positives = 57/67 (85%)

Query:    21 ELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCI 80
             ELL+AQA VWN  ++YINSMSLKCA++LGIPD IHKHG P+TLSQ+A AL+I K K+H +
Sbjct:    12 ELLEAQAHVWNHIYSYINSMSLKCAIQLGIPDAIHKHGNPITLSQLADALNINKAKSHGL 71

Query:    81 QRLMRIL 87
              RLMRIL
Sbjct:    72 FRLMRIL 78

GO:0009812 "flavonoid metabolic process" evidence=IDA

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

GO:0032259 "methylation" evidence=IDA

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

 Score = 176 (67.0 bits), Expect = 5.7e-13, P = 5.7e-13
 Identities = 36/69 (52%), Positives = 50/69 (72%)

Query:    21 ELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASAL--DIQKNKAH 78
             E   AQAQ+W+ + ++I S SLKCAV+LGIPD I  HG+P+TLS++ +AL   +  +KA 
Sbjct:     7 EFRGAQAQIWSQSCSFITSASLKCAVKLGIPDTIDNHGKPITLSELTNALVPPVHPSKAP 66

Query:    79 CIQRLMRIL 87
              I RLMR+L
Sbjct:    67 FIYRLMRVL 75

GO:0005737 "cytoplasm" evidence=IDA

GO:0009821 "alkaloid biosynthetic process" evidence=IDA

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

GO:0032259 "methylation" evidence=IDA

GO:0042803 "protein homodimerization activity" evidence=IDA

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

 Score = 175 (66.7 bits), Expect = 6.9e-13, P = 6.9e-13
 Identities = 35/67 (52%), Positives = 46/67 (68%)

Query:    21 ELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCI 80
             E+  AQA  +   F++ +  SLKCAV+LGIPD IH HG+PM LS + ++L I  +KA  I
Sbjct:     7 EIRNAQAHFFTQVFSFTSMSSLKCAVQLGIPDAIHSHGKPMALSDLTNSLPINPSKAPYI 66

Query:    81 QRLMRIL 87
              RLMRIL
Sbjct:    67 YRLMRIL 73

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

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

 Score = 168 (64.2 bits), Expect = 4.8e-12, P = 4.8e-12
 Identities = 30/67 (44%), Positives = 51/67 (76%)

Query:    21 ELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCI 80
             EL +AQ  ++   +N+++SM+LK A+ELGI DVIH HG+P+TL ++A+AL+++ +K   +
Sbjct:    13 ELSQAQIHLYKHVYNFVSSMALKSAMELGIADVIHSHGKPITLPELATALNLRPSKIGVL 72

Query:    81 QRLMRIL 87
              R +R+L
Sbjct:    73 HRFLRLL 79

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

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

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

 Score = 167 (63.8 bits), Expect = 6.2e-12, P = 6.2e-12
 Identities = 31/67 (46%), Positives = 48/67 (71%)

Query:    21 ELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCI 80
             EL  AQ  ++   +N+++SM+LK A+ELGI DVIH HG+P+TL ++ASAL +  +K   +
Sbjct:    12 ELYHAQIHLYKHVYNFVSSMALKSAMELGIADVIHNHGKPITLPELASALKLHPSKVGIL 71

Query:    81 QRLMRIL 87
              R +R+L
Sbjct:    72 YRFLRLL 78

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

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

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

 Score = 152 (58.6 bits), Expect = 2.6e-10, P = 2.6e-10
 Identities = 28/67 (41%), Positives = 47/67 (70%)

Query:    21 ELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCI 80
             E+ + QA ++   + +I+SM LK  VEL IP++IH HG+P+T+S++ S L + + KA  +
Sbjct:    12 EIFQGQALLYRHIYAFIDSMCLKWIVELDIPNIIHNHGKPITVSELVSILKVPQTKAGNV 71

Query:    81 QRLMRIL 87
             QR+MR +
Sbjct:    72 QRIMRYM 78

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 = 131 (51.2 bits), Expect = 5.7e-08, P = 5.7e-08
 Identities = 25/67 (37%), Positives = 43/67 (64%)

Query:    21 ELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCI 80
             ELL+A  ++WN  ++++ S++L  A++L I D IH+ G   TLSQI   + ++  K   +
Sbjct:    10 ELLQAHVELWNQTYSFMKSVALAVALDLHIADAIHRRGGAATLSQILGEIGVRPCKLPGL 69

Query:    81 QRLMRIL 87
              R+MR+L
Sbjct:    70 HRIMRVL 76

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

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

GO:0032259 "methylation" evidence=IDA

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

 Score = 120 (47.3 bits), Expect = 6.9e-07, P = 6.9e-07
 Identities = 25/69 (36%), Positives = 42/69 (60%)

Query:    21 ELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKH--GQPMTLSQIASALDIQKNKAH 78
             E  KA   +W   F + +  + KCA++L IP+ I  H   QP+TLS+++SA  +  + +H
Sbjct:    11 EEAKASLDIWRYVFGFADIAAAKCAIDLKIPEAIENHPSSQPVTLSELSSA--VSASPSH 68

Query:    79 CIQRLMRIL 87
              ++R+MR L
Sbjct:    69 -LRRIMRFL 76

GO:0008168 "methyltransferase activity" evidence=IEA

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

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0005829 "cytosol" evidence=TAS

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

 Score = 117 (46.2 bits), Expect = 2.0e-06, P = 2.0e-06
 Identities = 24/69 (34%), Positives = 42/69 (60%)

Query:    21 ELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKH--GQPMTLSQIASALDIQKNKAH 78
             E  KA   +W   F + +  + KCA++L IP+ I  H   QP+TL++++SA  +  + +H
Sbjct:    25 EEAKASLDIWKYVFGFADIAAAKCAIDLKIPEAIENHPSSQPVTLAELSSA--VSASPSH 82

Query:    79 CIQRLMRIL 87
              ++R+MR L
Sbjct:    83 -LRRIMRFL 90


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        0.324   0.132   0.399    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       87        77   0.00091  102 3  11 22  0.45    28
                                                     29  0.50    29


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:  9
  No. of states in DFA:  546 (58 KB)
  Total size of DFA:  105 KB (2072 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:  8.46u 0.11s 8.57t   Elapsed:  00:00:00
  Total cpu time:  8.46u 0.11s 8.57t   Elapsed:  00:00:00
  Start:  Sat May 11 13:55:32 2013   End:  Sat May 11 13:55:32 2013

GO:0005634 "nucleus" evidence=ISM

GO:0008168 "methyltransferase activity" evidence=IEA

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

GO:0046983 "protein dimerization activity" evidence=IEA

GO:0005829 "cytosol" evidence=TAS

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	87
pfam08100	50	pfam08100, Dimerisation, Dimerisation domain	7e-18

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

 Score = 69.5 bits (171), Expect = 7e-18
 Identities = 24/49 (48%), Positives = 35/49 (71%), Gaps = 1/49 (2%)

Query: 40 MSLKCAVELGIPDVIHKHGQPMTLSQIASAL-DIQKNKAHCIQRLMRIL 87
          M LKCA+ELGIPD+I KHG+P++ S++AS L  +       + RL+R+L
Sbjct: 1  MVLKCAIELGIPDIIAKHGKPLSPSELASKLPTVNPEAPVMLDRLLRLL 49

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	87
PF08100	51	Dimerisation: Dimerisation domain; InterPro: IPR01	99.66
KOG3178	342	consensus Hydroxyindole-O-methyltransferase and re	98.95
TIGR02716	306	C20_methyl_CrtF C-20 methyltransferase BchU. Membe	98.87
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	97.07
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	96.57
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	96.2
PRK11569	274	transcriptional repressor IclR; Provisional	95.42
TIGR02431	248	pcaR_pcaU beta-ketoadipate pathway transcriptional	95.37
PRK10163	271	DNA-binding transcriptional repressor AllR; Provis	95.16
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	94.97
PRK09834	263	DNA-binding transcriptional activator MhpR; Provis	94.35
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	94.03
PF02082	83	Rrf2: Transcriptional regulator; InterPro: IPR0009	93.74
COG1414	246	IclR Transcriptional regulator [Transcription]	93.72
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	93.72
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	93.69
PRK15090	257	DNA-binding transcriptional regulator KdgR; Provis	93.66
COG3413	215	Predicted DNA binding protein [General function pr	93.53
PRK10857	164	DNA-binding transcriptional regulator IscR; Provis	93.51
PF02796	45	HTH_7: Helix-turn-helix domain of resolvase; Inter	93.2
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	92.91
TIGR02010	135	IscR iron-sulfur cluster assembly transcription fa	92.79
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	92.21
PF08461	66	HTH_12: Ribonuclease R winged-helix domain; InterP	92.21
cd07153	116	Fur_like Ferric uptake regulator(Fur) and related	91.9
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	91.82
PF04703	62	FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.	91.66
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	91.62
TIGR00738	132	rrf2_super rrf2 family protein (putative transcrip	91.49
TIGR02944	130	suf_reg_Xantho FeS assembly SUF system regulator,	91.32
PF09012	69	FeoC: FeoC like transcriptional regulator; InterPr	91.13
smart00418	66	HTH_ARSR helix_turn_helix, Arsenical Resistance Op	90.61
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	90.56
PRK06266	178	transcription initiation factor E subunit alpha; V	90.33
PF00165	42	HTH_AraC: Bacterial regulatory helix-turn-helix pr	90.3
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	89.98
PRK10141	117	DNA-binding transcriptional repressor ArsR; Provis	89.38
TIGR00122	69	birA_repr_reg BirA biotin operon repressor domain.	89.36
COG3355	126	Predicted transcriptional regulator [Transcription	89.16
PF12324	77	HTH_15: Helix-turn-helix domain of alkylmercury ly	89.09
smart00347	101	HTH_MARR helix_turn_helix multiple antibiotic resi	88.71
PRK06474	178	hypothetical protein; Provisional	88.67
PRK11014	141	transcriptional repressor NsrR; Provisional	88.5
smart00419	48	HTH_CRP helix_turn_helix, cAMP Regulatory protein.	88.13
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	88.02
COG1959	150	Predicted transcriptional regulator [Transcription	87.91
PRK13239	206	alkylmercury lyase; Provisional	87.37
PRK11920	153	rirA iron-responsive transcriptional regulator; Re	87.32
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	87.19
PRK13558	665	bacterio-opsin activator; Provisional	86.7
PRK11179	153	DNA-binding transcriptional regulator AsnC; Provis	86.48
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	86.42
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	86.29
PF01418	77	HTH_6: Helix-turn-helix domain, rpiR family; Inter	86.21
TIGR00373	158	conserved hypothetical protein TIGR00373. This fam	86.11
PRK11169	164	leucine-responsive transcriptional regulator; Prov	85.69
TIGR02702	203	SufR_cyano iron-sulfur cluster biosynthesis transc	85.06
COG4190	144	Predicted transcriptional regulator [Transcription	84.43
cd00090	78	HTH_ARSR Arsenical Resistance Operon Repressor and	84.17
TIGR02337	118	HpaR homoprotocatechuate degradation operon regula	84.0
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	83.56
COG1522	154	Lrp Transcriptional regulators [Transcription]	83.52
PRK11511	127	DNA-binding transcriptional activator MarA; Provis	83.49
PF13936	44	HTH_38: Helix-turn-helix domain; PDB: 2W48_A.	83.4
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	82.87
COG2345	218	Predicted transcriptional regulator [Transcription	82.78
PF10668	60	Phage_terminase: Phage terminase small subunit; In	82.7
PRK00215	205	LexA repressor; Validated	82.29
PF06163	127	DUF977: Bacterial protein of unknown function (DUF	82.0
PF03374	111	ANT: Phage antirepressor protein KilAC domain; Int	81.83
TIGR02531	88	yecD_yerC TrpR-related protein YerC/YecD. This mod	81.47
PHA00738	108	putative HTH transcription regulator	81.4
PF07381	90	DUF1495: Winged helix DNA-binding domain (DUF1495)	81.32
PF00356	46	LacI: Bacterial regulatory proteins, lacI family;	80.97
PRK11302	284	DNA-binding transcriptional regulator HexR; Provis	80.56
TIGR02844	80	spore_III_D sporulation transcriptional regulator	80.16
PRK11557	278	putative DNA-binding transcriptional regulator; Pr	80.13

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

Probab=99.66  E-value=5.8e-17  Score=93.05  Aligned_cols=48  Identities=52%  Similarity=0.924  Sum_probs=43.4

Q ss_pred             HHHHHHHHhCchHHHHhCC-CCCCHHHHHHhcC-CCCCChhhHHHHHhcC
Q 041968           40 MSLKCAVELGIPDVIHKHG-QPMTLSQIASALD-IQKNKAHCIQRLMRIL   87 (87)
Q Consensus        40 ~aL~aaveLgI~d~L~~~~-gp~S~~ELA~~~~-~~~~~~~~L~RlLR~L   87 (87)
                      |+||+|+||||||+|+++| +|+|++||+++++ .+|.++..|+|+||+|
T Consensus         1 MaLk~aveLgI~dii~~~g~~~ls~~eia~~l~~~~p~~~~~L~RimR~L   50 (51)
T PF08100_consen    1 MALKCAVELGIPDIIHNAGGGPLSLSEIAARLPTSNPSAPPMLDRIMRLL   50 (51)
T ss_dssp             HHHHHHHHTTHHHHHHHHTTS-BEHHHHHHTSTCT-TTHHHHHHHHHHHH
T ss_pred             CcHHHHHHcCcHHHHHHcCCCCCCHHHHHHHcCCCCcchHHHHHHHHHHh
Confidence            6899999999999999987 9999999999999 7888889999999986

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 ....

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

Probab=98.95  E-value=1.9e-09  Score=81.95  Aligned_cols=63  Identities=30%  Similarity=0.394  Sum_probs=54.7

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHhCchHHHHhCCCCCCHHHHHHhcC--CCCCChhhHHHHHhcC
Q 041968           22 LLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALD--IQKNKAHCIQRLMRIL   87 (87)
Q Consensus        22 ~~~~~~~l~~l~~g~~~~~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~--~~~~~~~~L~RlLR~L   87 (87)
                      +.+...+++++.+++..++++++|+||||||+|+++++   ..|+|..+.  ..|+++.+++|+||.|
T Consensus         3 e~~~~l~~~~l~~~~~~~~~lk~A~eL~v~d~l~~~~~---p~~ia~~l~~~~~~~~p~ll~r~lr~L   67 (342)
T KOG3178|consen    3 ENEASLRAMRLANGFALPMVLKAACELGVFDILANAGS---PSEIASLLPTPKNPEAPVLLDRILRLL   67 (342)
T ss_pred             hhHHHHHHHHHHhhhhhHHHHHHHHHcChHHHHHhCCC---HHHHHHhccCCCCCCChhHHHHHHHHH
Confidence            45667889999999999999999999999999998644   788888877  5667889999999976

>TIGR02716 C20_methyl_CrtF C-20 methyltransferase BchU

Probab=98.87  E-value=2.4e-09  Score=78.50  Aligned_cols=45  Identities=20%  Similarity=0.285  Sum_probs=42.0

Q ss_pred             HHHHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           38 NSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        38 ~~~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      ..++|++|++|||||.|++  +|.|++|||+++|+++   ..++|+||+|
T Consensus         3 ~~~~l~aa~~Lglfd~L~~--gp~t~~eLA~~~~~~~---~~~~~lL~~L   47 (306)
T TIGR02716         3 EFSCMKAAIELDLFSHMAE--GPKDLATLAADTGSVP---PRLEMLLETL   47 (306)
T ss_pred             hHHHHHHHHHcCcHHHHhc--CCCCHHHHHHHcCCCh---HHHHHHHHHH
Confidence            4689999999999999984  8999999999999999   9999999986

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.

>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=97.07  E-value=0.00012  Score=41.04  Aligned_cols=37  Identities=41%  Similarity=0.680  Sum_probs=31.2

Q ss_pred             hCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           48 LGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        48 LgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      +.|.+.+...++++|+.|||+.+|.+.   ..++|+|+.|
T Consensus         6 l~iL~~l~~~~~~~t~~eia~~~gl~~---stv~r~L~tL   42 (52)
T PF09339_consen    6 LRILEALAESGGPLTLSEIARALGLPK---STVHRLLQTL   42 (52)
T ss_dssp             HHHHHCHHCTBSCEEHHHHHHHHTS-H---HHHHHHHHHH
T ss_pred             HHHHHHHHcCCCCCCHHHHHHHHCcCH---HHHHHHHHHH
Confidence            457888888778899999999999999   8899998754

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.

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

Probab=96.57  E-value=0.0031  Score=36.21  Aligned_cols=41  Identities=34%  Similarity=0.477  Sum_probs=33.0

Q ss_pred             HHHHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968           38 NSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR   85 (87)
Q Consensus        38 ~~~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR   85 (87)
                      .-.+|++|.++|-|| .   +...|+.|||+.+|+++   ..+..-||
T Consensus         5 Q~e~L~~A~~~GYfd-~---PR~~tl~elA~~lgis~---st~~~~LR   45 (53)
T PF04967_consen    5 QREILKAAYELGYFD-V---PRRITLEELAEELGISK---STVSEHLR   45 (53)
T ss_pred             HHHHHHHHHHcCCCC-C---CCcCCHHHHHHHhCCCH---HHHHHHHH
Confidence            456899999999998 3   36789999999999988   65555554

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

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=96.20  E-value=0.0048  Score=37.27  Aligned_cols=37  Identities=24%  Similarity=0.421  Sum_probs=31.6

Q ss_pred             hCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           48 LGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        48 LgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      +.|.+.|.+.+++.|+.|||+.+|++.   ..++|+++.|
T Consensus         8 ~~Il~~l~~~~~~~t~~~ia~~l~i~~---~tv~r~l~~L   44 (91)
T smart00346        8 LAVLRALAEEPGGLTLAELAERLGLSK---STAHRLLNTL   44 (91)
T ss_pred             HHHHHHHHhCCCCcCHHHHHHHhCCCH---HHHHHHHHHH
Confidence            567888887657999999999999999   8899988754

>PRK11569 transcriptional repressor IclR; Provisional

Probab=95.42  E-value=0.012  Score=42.86  Aligned_cols=37  Identities=16%  Similarity=0.342  Sum_probs=31.7

Q ss_pred             hCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           48 LGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        48 LgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      |.|.+.+++.++++|+.|||+.+|.++   ..++|+|+.|
T Consensus        31 l~IL~~l~~~~~~~~lseia~~lglpk---sTv~RlL~tL   67 (274)
T PRK11569         31 LKLLEWIAESNGSVALTELAQQAGLPN---STTHRLLTTM   67 (274)
T ss_pred             HHHHHHHHhCCCCcCHHHHHHHHCcCH---HHHHHHHHHH
Confidence            456777887668999999999999999   8999999754

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

Probab=95.37  E-value=0.013  Score=41.94  Aligned_cols=37  Identities=19%  Similarity=0.366  Sum_probs=32.0

Q ss_pred             hCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           48 LGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        48 LgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      +.|.+.+.+.++|+|+.|||+.+|.++   ..++|+|.-|
T Consensus        12 l~IL~~l~~~~~~~~l~eia~~lglpk---sT~~RlL~tL   48 (248)
T TIGR02431        12 LAVIEAFGAERPRLTLTDVAEATGLTR---AAARRFLLTL   48 (248)
T ss_pred             HHHHHHHhcCCCCCCHHHHHHHHCcCH---HHHHHHHHHH
Confidence            567888887668999999999999999   8999999754

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.

>PRK10163 DNA-binding transcriptional repressor AllR; Provisional

Probab=95.16  E-value=0.017  Score=42.07  Aligned_cols=37  Identities=27%  Similarity=0.463  Sum_probs=31.5

Q ss_pred             hCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           48 LGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        48 LgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      +.|.+.+.+.++++|+.|||+.+|.++   ..++|+|..|
T Consensus        28 l~IL~~~~~~~~~~tl~eIa~~lglpk---Stv~RlL~tL   64 (271)
T PRK10163         28 IAILQYLEKSGGSSSVSDISLNLDLPL---STTFRLLKVL   64 (271)
T ss_pred             HHHHHHHHhCCCCcCHHHHHHHHCcCH---HHHHHHHHHH
Confidence            457788877668899999999999999   8899998754

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

Probab=94.97  E-value=0.034  Score=32.88  Aligned_cols=38  Identities=24%  Similarity=0.351  Sum_probs=30.1

Q ss_pred             HHhCchHHHHhCCC-CCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           46 VELGIPDVIHKHGQ-PMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        46 veLgI~d~L~~~~g-p~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .+-.|.+.|...++ ++|+.|||..+|++.   ..+.|+|.-
T Consensus         7 ~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~---~~v~r~L~~   45 (68)
T smart00550        7 LEEKILEFLENSGDETSTALQLAKNLGLPK---KEVNRVLYS   45 (68)
T ss_pred             HHHHHHHHHHHCCCCCcCHHHHHHHHCCCH---HHHHHHHHH
Confidence            45567888887655 399999999999999   778887753

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

>PRK09834 DNA-binding transcriptional activator MhpR; Provisional

Probab=94.35  E-value=0.037  Score=40.03  Aligned_cols=37  Identities=16%  Similarity=0.313  Sum_probs=31.2

Q ss_pred             hCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           48 LGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        48 LgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      +.|.+.+..+++++|+.|||+.+|+++   ..++|+|+.|
T Consensus        14 l~iL~~l~~~~~~ls~~eia~~lgl~k---stv~RlL~tL   50 (263)
T PRK09834         14 LMVLRALNRLDGGATVGLLAELTGLHR---TTVRRLLETL   50 (263)
T ss_pred             HHHHHHHHhcCCCCCHHHHHHHHCcCH---HHHHHHHHHH
Confidence            456777876667899999999999999   8899998754

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

Probab=94.03  E-value=0.04  Score=31.51  Aligned_cols=39  Identities=23%  Similarity=0.367  Sum_probs=29.7

Q ss_pred             HHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           44 CAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        44 aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      --..+.|.+.|.. ++|.|+.|||+.+|+++   ..+++-|+.
T Consensus         9 ~p~R~~Il~~L~~-~~~~t~~ela~~l~~~~---~t~s~hL~~   47 (61)
T PF12840_consen    9 DPTRLRILRLLAS-NGPMTVSELAEELGISQ---STVSYHLKK   47 (61)
T ss_dssp             SHHHHHHHHHHHH-CSTBEHHHHHHHHTS-H---HHHHHHHHH
T ss_pred             CHHHHHHHHHHhc-CCCCCHHHHHHHHCCCH---HHHHHHHHH
Confidence            3456778888843 59999999999999988   777776654

...

>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=93.74  E-value=0.069  Score=32.32  Aligned_cols=42  Identities=24%  Similarity=0.479  Sum_probs=28.0

Q ss_pred             HHHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           39 SMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        39 ~~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      ..++++.+.|.    ....+++.|..|||+.+++++   ..+.++++-|
T Consensus         8 ~~Al~~l~~la----~~~~~~~~s~~eiA~~~~i~~---~~l~kil~~L   49 (83)
T PF02082_consen    8 DYALRILLYLA----RHPDGKPVSSKEIAERLGISP---SYLRKILQKL   49 (83)
T ss_dssp             HHHHHHHHHHH----CTTTSC-BEHHHHHHHHTS-H---HHHHHHHHHH
T ss_pred             HHHHHHHHHHH----hCCCCCCCCHHHHHHHHCcCH---HHHHHHHHHH
Confidence            34555555541    122236799999999999999   9999998753

(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.

>COG1414 IclR Transcriptional regulator [Transcription]

Probab=93.72  E-value=0.058  Score=39.02  Aligned_cols=37  Identities=27%  Similarity=0.506  Sum_probs=31.1

Q ss_pred             hCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           48 LGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        48 LgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      +.|.|.|++.++++++.|||+.+|.++   ..++|+|..|
T Consensus         7 l~iL~~l~~~~~~l~l~ela~~~glpk---sT~~RlL~tL   43 (246)
T COG1414           7 LAILDLLAEGPGGLSLAELAERLGLPK---STVHRLLQTL   43 (246)
T ss_pred             HHHHHHHHhCCCCCCHHHHHHHhCcCH---HHHHHHHHHH
Confidence            567888887556678999999999999   8899998643

>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=93.72  E-value=0.06  Score=29.82  Aligned_cols=34  Identities=21%  Similarity=0.449  Sum_probs=26.2

Q ss_pred             CchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968           49 GIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR   85 (87)
Q Consensus        49 gI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR   85 (87)
                      .|...|.++++++|..|||+.++++.   ..++|-+.
T Consensus         4 ~il~~L~~~~~~it~~eLa~~l~vS~---rTi~~~i~   37 (55)
T PF08279_consen    4 QILKLLLESKEPITAKELAEELGVSR---RTIRRDIK   37 (55)
T ss_dssp             HHHHHHHHTTTSBEHHHHHHHCTS-H---HHHHHHHH
T ss_pred             HHHHHHHHcCCCcCHHHHHHHhCCCH---HHHHHHHH
Confidence            45666755568899999999999988   77777654

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 ....

>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=93.69  E-value=0.061  Score=29.14  Aligned_cols=37  Identities=16%  Similarity=0.346  Sum_probs=28.2

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .+..|.+.|.++ +.+|..|||..+|++.   ..+.+.++-
T Consensus         4 ~~~~Il~~l~~~-~~~t~~ela~~~~is~---~tv~~~l~~   40 (48)
T PF13412_consen    4 TQRKILNYLREN-PRITQKELAEKLGISR---STVNRYLKK   40 (48)
T ss_dssp             HHHHHHHHHHHC-TTS-HHHHHHHHTS-H---HHHHHHHHH
T ss_pred             HHHHHHHHHHHc-CCCCHHHHHHHhCCCH---HHHHHHHHH
Confidence            356678888874 6799999999999988   778877764

...

>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional

Probab=93.66  E-value=0.052  Score=39.01  Aligned_cols=36  Identities=11%  Similarity=0.416  Sum_probs=29.8

Q ss_pred             hCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           48 LGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        48 LgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      +.|.+.+.+. +++|++|||+.+|.++   ..++|+|+.|
T Consensus        17 l~IL~~l~~~-~~l~l~eia~~lgl~k---stv~Rll~tL   52 (257)
T PRK15090         17 FGILQALGEE-REIGITELSQRVMMSK---STVYRFLQTM   52 (257)
T ss_pred             HHHHHHhhcC-CCCCHHHHHHHHCcCH---HHHHHHHHHH
Confidence            4566777754 6899999999999999   8899999754

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

Probab=93.53  E-value=0.089  Score=37.07  Aligned_cols=43  Identities=23%  Similarity=0.309  Sum_probs=33.7

Q ss_pred             HHHHHHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968           36 YINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR   85 (87)
Q Consensus        36 ~~~~~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR   85 (87)
                      -.+-.+|+.|.++|-|| ..   .-+++.|||+.+|+.+   ..+...||
T Consensus       158 drQ~~vL~~A~~~GYFd-~P---R~~~l~dLA~~lGISk---st~~ehLR  200 (215)
T COG3413         158 DRQLEVLRLAYKMGYFD-YP---RRVSLKDLAKELGISK---STLSEHLR  200 (215)
T ss_pred             HHHHHHHHHHHHcCCCC-CC---ccCCHHHHHHHhCCCH---HHHHHHHH
Confidence            34667999999999999 33   6789999999999987   54444444

>PRK10857 DNA-binding transcriptional regulator IscR; Provisional

Probab=93.51  E-value=0.086  Score=36.25  Aligned_cols=41  Identities=15%  Similarity=0.378  Sum_probs=31.0

Q ss_pred             HHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           40 MSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        40 ~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      .+|++.+.+.    ....++|.|+.|||+++++++   ..+.++|+.|
T Consensus         9 yAl~~l~~lA----~~~~~~~vs~~eIA~~~~ip~---~~l~kIl~~L   49 (164)
T PRK10857          9 YAVTAMLDVA----LNSEAGPVPLADISERQGISL---SYLEQLFSRL   49 (164)
T ss_pred             HHHHHHHHHH----hCCCCCcCcHHHHHHHHCcCH---HHHHHHHHHH
Confidence            4555666555    223347999999999999999   9999998764

>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=93.20  E-value=0.12  Score=28.05  Aligned_cols=22  Identities=18%  Similarity=0.520  Sum_probs=18.0

Q ss_pred             CCHHHHHHhcCCCCCChhhHHHHHh
Q 041968           61 MTLSQIASALDIQKNKAHCIQRLMR   85 (87)
Q Consensus        61 ~S~~ELA~~~~~~~~~~~~L~RlLR   85 (87)
                      .|..+||..+|+..   ..++|+++
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            99999999999999   99999986

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 ....

>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=92.91  E-value=0.053  Score=29.58  Aligned_cols=36  Identities=22%  Similarity=0.478  Sum_probs=27.9

Q ss_pred             HhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           47 ELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        47 eLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      ++.|...|.+  ||.++.||++.++.++   ..+.+-|+.|
T Consensus         4 R~~Il~~L~~--~~~~~~el~~~l~~s~---~~vs~hL~~L   39 (47)
T PF01022_consen    4 RLRILKLLSE--GPLTVSELAEELGLSQ---STVSHHLKKL   39 (47)
T ss_dssp             HHHHHHHHTT--SSEEHHHHHHHHTS-H---HHHHHHHHHH
T ss_pred             HHHHHHHHHh--CCCchhhHHHhccccc---hHHHHHHHHH
Confidence            4566777774  8999999999999998   7777776643

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 ....

>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR

Probab=92.79  E-value=0.13  Score=33.76  Aligned_cols=41  Identities=20%  Similarity=0.380  Sum_probs=30.5

Q ss_pred             HHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           40 MSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        40 ~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      .++++.+.|..-    ..+++.|+.|||+.+++++   ..+.++|+.|
T Consensus         9 YAl~~l~~La~~----~~~~~~s~~~ia~~~~ip~---~~l~kil~~L   49 (135)
T TIGR02010         9 YAVTAMLDLALN----AETGPVTLADISERQGISL---SYLEQLFAKL   49 (135)
T ss_pred             HHHHHHHHHHhC----CCCCcCcHHHHHHHHCcCH---HHHHHHHHHH
Confidence            355565555321    2246899999999999999   9999998754

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

>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=92.21  E-value=0.047  Score=31.70  Aligned_cols=36  Identities=25%  Similarity=0.339  Sum_probs=27.8

Q ss_pred             HhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           47 ELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        47 eLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      |..|...|.+ .|+.|+.|||..+|++.   ..+++.|+-
T Consensus        10 E~~vy~~Ll~-~~~~t~~eIa~~l~i~~---~~v~~~L~~   45 (68)
T PF01978_consen   10 EAKVYLALLK-NGPATAEEIAEELGISR---STVYRALKS   45 (68)
T ss_dssp             HHHHHHHHHH-HCHEEHHHHHHHHTSSH---HHHHHHHHH
T ss_pred             HHHHHHHHHH-cCCCCHHHHHHHHCcCH---HHHHHHHHH
Confidence            4455555654 38999999999999998   778887764

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.

>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=92.21  E-value=0.16  Score=30.03  Aligned_cols=38  Identities=18%  Similarity=0.444  Sum_probs=29.5

Q ss_pred             chHHHHhCCCCCCHHHHHHhcCCCCCCh--hhHHHHHhcC
Q 041968           50 IPDVIHKHGQPMTLSQIASALDIQKNKA--HCIQRLMRIL   87 (87)
Q Consensus        50 I~d~L~~~~gp~S~~ELA~~~~~~~~~~--~~L~RlLR~L   87 (87)
                      |.++|.++++|++..+|+..+.....+.  ..++|-||+|
T Consensus         3 IL~~L~~~~~P~g~~~l~~~L~~~g~~~se~avRrrLr~m   42 (66)
T PF08461_consen    3 ILRILAESDKPLGRKQLAEELKLRGEELSEEAVRRRLRAM   42 (66)
T ss_pred             HHHHHHHcCCCCCHHHHHHHHHhcChhhhHHHHHHHHHHH
Confidence            5678888889999999999997543222  7789988864

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

Probab=91.90  E-value=0.18  Score=31.73  Aligned_cols=38  Identities=24%  Similarity=0.346  Sum_probs=30.0

Q ss_pred             HhCchHHHHhCCCCCCHHHHHHhcC-----CCCCChhhHHHHHhcC
Q 041968           47 ELGIPDVIHKHGQPMTLSQIASALD-----IQKNKAHCIQRLMRIL   87 (87)
Q Consensus        47 eLgI~d~L~~~~gp~S~~ELA~~~~-----~~~~~~~~L~RlLR~L   87 (87)
                      +.-|++.|.+.+++.|+.||.+.+.     ++.   ..++|.|+.|
T Consensus         3 R~~Il~~l~~~~~~~sa~ei~~~l~~~~~~i~~---~TVYR~L~~L   45 (116)
T cd07153           3 RLAILEVLLESDGHLTAEEIYERLRKKGPSISL---ATVYRTLELL   45 (116)
T ss_pred             HHHHHHHHHhCCCCCCHHHHHHHHHhcCCCCCH---HHHHHHHHHH
Confidence            3457888887678999999999984     344   7899998764

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.

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=91.82  E-value=0.19  Score=31.29  Aligned_cols=37  Identities=11%  Similarity=0.318  Sum_probs=29.8

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .+..|...|..+ ++.|..|||+.+|+++   ..+.|.++.
T Consensus         4 ~D~~il~~L~~~-~~~~~~~la~~l~~s~---~tv~~~l~~   40 (108)
T smart00344        4 IDRKILEELQKD-ARISLAELAKKVGLSP---STVHNRVKR   40 (108)
T ss_pred             HHHHHHHHHHHh-CCCCHHHHHHHHCcCH---HHHHHHHHH
Confidence            467788888874 7899999999999998   777666653

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

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

Probab=91.66  E-value=0.098  Score=30.86  Aligned_cols=36  Identities=22%  Similarity=0.307  Sum_probs=25.9

Q ss_pred             CchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           49 GIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        49 gI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      .|.+.|.+..+|.|..|||..+|++.   ...++.|..|
T Consensus         4 ~Il~~i~~~~~p~~T~eiA~~~gls~---~~aR~yL~~L   39 (62)
T PF04703_consen    4 KILEYIKEQNGPLKTREIADALGLSI---YQARYYLEKL   39 (62)
T ss_dssp             CHHHHHHHHTS-EEHHHHHHHHTS-H---HHHHHHHHHH
T ss_pred             HHHHHHHHcCCCCCHHHHHHHhCCCH---HHHHHHHHHH
Confidence            35566665358999999999999988   7777777653

>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=91.62  E-value=0.11  Score=29.09  Aligned_cols=37  Identities=22%  Similarity=0.398  Sum_probs=26.6

Q ss_pred             HhCchHHHHhCCCC-CCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           47 ELGIPDVIHKHGQP-MTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        47 eLgI~d~L~~~~gp-~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      +..|.-.|...+++ +|..|||+.++.++   ..+.|+++-
T Consensus         7 q~~vL~~l~~~~~~~~t~~~la~~l~~~~---~~vs~~v~~   44 (62)
T PF12802_consen    7 QFRVLMALARHPGEELTQSELAERLGISK---STVSRIVKR   44 (62)
T ss_dssp             HHHHHHHHHHSTTSGEEHHHHHHHHTS-H---HHHHHHHHH
T ss_pred             HHHHHHHHHHCCCCCcCHHHHHHHHCcCH---HHHHHHHHH
Confidence            34455566665433 89999999999999   888887764

...

>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator)

Probab=91.49  E-value=0.27  Score=31.61  Aligned_cols=41  Identities=20%  Similarity=0.519  Sum_probs=29.8

Q ss_pred             HHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           40 MSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        40 ~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      .+|++.+.+..    ...++|.|..|||+.+++++   ..+.++|+.|
T Consensus         9 ~al~~l~~la~----~~~~~~~s~~eia~~~~i~~---~~v~~il~~L   49 (132)
T TIGR00738         9 YALRALLDLAL----NPDEGPVSVKEIAERQGISR---SYLEKILRTL   49 (132)
T ss_pred             HHHHHHHHHHh----CCCCCcCcHHHHHHHHCcCH---HHHHHHHHHH
Confidence            45555555432    22236999999999999999   9999998754

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.

>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial

Probab=91.32  E-value=0.18  Score=32.64  Aligned_cols=27  Identities=19%  Similarity=0.454  Sum_probs=23.9

Q ss_pred             CCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           58 GQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        58 ~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      +++.|+.|||+.+++++   ..+.++|+.|
T Consensus        23 ~~~~s~~eia~~l~is~---~~v~~~l~~L   49 (130)
T TIGR02944        23 SQPYSAAEIAEQTGLNA---PTVSKILKQL   49 (130)
T ss_pred             CCCccHHHHHHHHCcCH---HHHHHHHHHH
Confidence            47899999999999999   8899888754

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=91.13  E-value=0.14  Score=30.00  Aligned_cols=33  Identities=15%  Similarity=0.387  Sum_probs=23.4

Q ss_pred             chHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           50 IPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        50 I~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      |-+.|.+ .+.+|..|||..++++|   +.+.-+|..
T Consensus         5 i~~~l~~-~~~~S~~eLa~~~~~s~---~~ve~mL~~   37 (69)
T PF09012_consen    5 IRDYLRE-RGRVSLAELAREFGISP---EAVEAMLEQ   37 (69)
T ss_dssp             HHHHHHH-S-SEEHHHHHHHTT--H---HHHHHHHHH
T ss_pred             HHHHHHH-cCCcCHHHHHHHHCcCH---HHHHHHHHH
Confidence            4566776 48999999999999999   777666643

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

>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor

Probab=90.61  E-value=0.35  Score=26.19  Aligned_cols=32  Identities=9%  Similarity=0.288  Sum_probs=25.0

Q ss_pred             chHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           50 IPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        50 I~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      |+..|.  .++.|..+|++.+++++   ..+.+.++.
T Consensus         2 il~~l~--~~~~~~~~i~~~l~is~---~~v~~~l~~   33 (66)
T smart00418        2 ILKLLA--EGELCVCELAEILGLSQ---STVSHHLKK   33 (66)
T ss_pred             HHHHhh--cCCccHHHHHHHHCCCH---HHHHHHHHH
Confidence            455565  47899999999999988   777777764

>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=90.56  E-value=0.24  Score=26.79  Aligned_cols=36  Identities=11%  Similarity=0.280  Sum_probs=25.3

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHH
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLM   84 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlL   84 (87)
                      ++..|.+.|.++ +..|..+||+.+|+++  .....|+=
T Consensus         4 ~D~~Il~~Lq~d-~r~s~~~la~~lglS~--~~v~~Ri~   39 (42)
T PF13404_consen    4 LDRKILRLLQED-GRRSYAELAEELGLSE--STVRRRIR   39 (42)
T ss_dssp             HHHHHHHHHHH--TTS-HHHHHHHHTS-H--HHHHHHHH
T ss_pred             HHHHHHHHHHHc-CCccHHHHHHHHCcCH--HHHHHHHH
Confidence            567788888874 8999999999999977  13445543

...

>PRK06266 transcription initiation factor E subunit alpha; Validated

Probab=90.33  E-value=0.53  Score=32.82  Aligned_cols=36  Identities=17%  Similarity=0.278  Sum_probs=30.1

Q ss_pred             hCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           48 LGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        48 LgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      ..|.+.|..+ |++|..|||..+|+..   ..++|+|..|
T Consensus        25 ~~Vl~~L~~~-g~~tdeeLA~~Lgi~~---~~VRk~L~~L   60 (178)
T PRK06266         25 FEVLKALIKK-GEVTDEEIAEQTGIKL---NTVRKILYKL   60 (178)
T ss_pred             hHHHHHHHHc-CCcCHHHHHHHHCCCH---HHHHHHHHHH
Confidence            3478888865 7999999999999998   8899988654

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

Probab=90.30  E-value=0.18  Score=26.57  Aligned_cols=24  Identities=29%  Similarity=0.444  Sum_probs=19.0

Q ss_pred             CCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968           59 QPMTLSQIASALDIQKNKAHCIQRLMR   85 (87)
Q Consensus        59 gp~S~~ELA~~~~~~~~~~~~L~RlLR   85 (87)
                      .+.|+.+||..+|.++   ..+.|+.+
T Consensus         7 ~~~~l~~iA~~~g~S~---~~f~r~Fk   30 (42)
T PF00165_consen    7 QKLTLEDIAEQAGFSP---SYFSRLFK   30 (42)
T ss_dssp             SS--HHHHHHHHTS-H---HHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCH---HHHHHHHH
Confidence            6799999999999988   88998876

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor

Probab=89.98  E-value=0.41  Score=25.34  Aligned_cols=33  Identities=15%  Similarity=0.348  Sum_probs=25.5

Q ss_pred             chHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           50 IPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        50 I~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      |.+.|.+. ++.|..+|+..+++++   ..++|.|..
T Consensus         5 il~~l~~~-~~~s~~~l~~~l~~s~---~tv~~~l~~   37 (53)
T smart00420        5 ILELLAQQ-GKVSVEELAELLGVSE---MTIRRDLNK   37 (53)
T ss_pred             HHHHHHHc-CCcCHHHHHHHHCCCH---HHHHHHHHH
Confidence            45556553 6799999999999988   778877754

>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional

Probab=89.38  E-value=0.43  Score=31.26  Aligned_cols=44  Identities=23%  Similarity=0.343  Sum_probs=33.5

Q ss_pred             HHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           40 MSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        40 ~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      .+|.--..+.|++.|.+ +++.++.||++.++..+   ..+.+-|+.|
T Consensus        11 kaLadptRl~IL~~L~~-~~~~~v~ela~~l~lsq---stvS~HL~~L   54 (117)
T PRK10141         11 KILSDETRLGIVLLLRE-SGELCVCDLCTALDQSQ---PKISRHLALL   54 (117)
T ss_pred             HHhCCHHHHHHHHHHHH-cCCcCHHHHHHHHCcCH---HHHHHHHHHH
Confidence            34444577888888875 37899999999999988   7777766654

>TIGR00122 birA_repr_reg BirA biotin operon repressor domain

Probab=89.36  E-value=0.36  Score=27.98  Aligned_cols=35  Identities=11%  Similarity=0.372  Sum_probs=26.9

Q ss_pred             HhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           47 ELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        47 eLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      ++.|...+.  +++.|..|||+.+|+..   ..+.|-++.
T Consensus         2 ~~~il~~L~--~~~~~~~eLa~~l~vS~---~tv~~~l~~   36 (69)
T TIGR00122         2 PLRLLALLA--DNPFSGEKLGEALGMSR---TAVNKHIQT   36 (69)
T ss_pred             hHHHHHHHH--cCCcCHHHHHHHHCCCH---HHHHHHHHH
Confidence            456777777  46889999999999988   667666543

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.

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=89.16  E-value=0.38  Score=32.19  Aligned_cols=37  Identities=14%  Similarity=0.396  Sum_probs=27.9

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR   85 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR   85 (87)
                      .|..++-+|-+..+|.|+.|||+.++.+.   ..++|-++
T Consensus        28 ~Dv~v~~~LL~~~~~~tvdelae~lnr~r---Stv~rsl~   64 (126)
T COG3355          28 LDVEVYKALLEENGPLTVDELAEILNRSR---STVYRSLQ   64 (126)
T ss_pred             HHHHHHHHHHhhcCCcCHHHHHHHHCccH---HHHHHHHH
Confidence            46666777764359999999999999987   66666554

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

Probab=89.09  E-value=0.38  Score=29.70  Aligned_cols=32  Identities=28%  Similarity=0.463  Sum_probs=22.1

Q ss_pred             chHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968           50 IPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR   85 (87)
Q Consensus        50 I~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR   85 (87)
                      ++..|++ |+|+|..+||..+|.+.   +.+...|.
T Consensus        29 LLr~LA~-G~PVt~~~LA~a~g~~~---e~v~~~L~   60 (77)
T PF12324_consen   29 LLRLLAK-GQPVTVEQLAAALGWPV---EEVRAALA   60 (77)
T ss_dssp             HHHHHTT-TS-B-HHHHHHHHT--H---HHHHHHHH
T ss_pred             HHHHHHc-CCCcCHHHHHHHHCCCH---HHHHHHHH
Confidence            5667886 79999999999999877   66666653

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

>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein

Probab=88.71  E-value=0.56  Score=27.87  Aligned_cols=37  Identities=14%  Similarity=0.381  Sum_probs=29.1

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .++.|+..|... ++.|..+|+..++.++   ..+.|.++-
T Consensus        11 ~~~~il~~l~~~-~~~~~~~la~~~~~s~---~~i~~~l~~   47 (101)
T smart00347       11 TQFLVLRILYEE-GPLSVSELAKRLGVSP---STVTRVLDR   47 (101)
T ss_pred             HHHHHHHHHHHc-CCcCHHHHHHHHCCCc---hhHHHHHHH
Confidence            356677777754 6799999999999988   778887764

>PRK06474 hypothetical protein; Provisional

Probab=88.67  E-value=0.42  Score=33.14  Aligned_cols=44  Identities=18%  Similarity=0.319  Sum_probs=33.7

Q ss_pred             HHHHHHHhCchHHHHhCCCCCCHHHHHHhc-CCCCCChhhHHHHHhcC
Q 041968           41 SLKCAVELGIPDVIHKHGQPMTLSQIASAL-DIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        41 aL~aaveLgI~d~L~~~~gp~S~~ELA~~~-~~~~~~~~~L~RlLR~L   87 (87)
                      +|.--..+.|++.|...+++.|+.||+..+ +++.   ..++|-|+.|
T Consensus         7 ~La~p~R~~Il~~L~~~~~~~ta~el~~~l~~is~---aTvYrhL~~L   51 (178)
T PRK06474          7 ILMHPVRMKICQVLMRNKEGLTPLELVKILKDVPQ---ATLYRHLQTM   51 (178)
T ss_pred             hhCCHHHHHHHHHHHhCCCCCCHHHHHHHhcCCCH---HHHHHHHHHH
Confidence            344456788889898765569999999999 4666   7799988754

>PRK11014 transcriptional repressor NsrR; Provisional

Probab=88.50  E-value=0.61  Score=30.75  Aligned_cols=41  Identities=10%  Similarity=0.329  Sum_probs=30.9

Q ss_pred             HHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           40 MSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        40 ~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      .++++.+.++..    ..|++.|..|||+..|+++   ..++++|+.|
T Consensus         9 YAl~~~i~la~~----~~g~~~s~~~ia~~~~is~---~~vrk~l~~L   49 (141)
T PRK11014          9 YGLRALIYMASL----PEGRMTSISEVTEVYGVSR---NHMVKIINQL   49 (141)
T ss_pred             HHHHHHHHHhcC----CCCCccCHHHHHHHHCcCH---HHHHHHHHHH
Confidence            456666666532    2246889999999999999   8899988754

>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein

Probab=88.13  E-value=0.39  Score=25.22  Aligned_cols=26  Identities=27%  Similarity=0.510  Sum_probs=21.8

Q ss_pred             CCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           59 QPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        59 gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      -|.|..|||+.+++++   ..+.|.|+.|
T Consensus         7 ~~~s~~~la~~l~~s~---~tv~~~l~~L   32 (48)
T smart00419        7 LPLTRQEIAELLGLTR---ETVSRTLKRL   32 (48)
T ss_pred             eccCHHHHHHHHCCCH---HHHHHHHHHH
Confidence            4689999999999998   8888887753

>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=88.02  E-value=0.51  Score=26.78  Aligned_cols=33  Identities=12%  Similarity=0.344  Sum_probs=27.0

Q ss_pred             chHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           50 IPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        50 I~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      |.+.|.+. +.+|+.|||+.+++.+   ..++|=|..
T Consensus         5 Il~~l~~~-~~~s~~ela~~~~VS~---~TiRRDl~~   37 (57)
T PF08220_consen    5 ILELLKEK-GKVSVKELAEEFGVSE---MTIRRDLNK   37 (57)
T ss_pred             HHHHHHHc-CCEEHHHHHHHHCcCH---HHHHHHHHH
Confidence            56677664 8999999999999999   888886654

This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular

>COG1959 Predicted transcriptional regulator [Transcription]

Probab=87.91  E-value=0.53  Score=31.82  Aligned_cols=26  Identities=19%  Similarity=0.415  Sum_probs=23.3

Q ss_pred             CCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           59 QPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        59 gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      ++.|+.+||+..+++|   ..|.|+|.-|
T Consensus        24 ~~~s~~~IA~~~~is~---~~L~kil~~L   49 (150)
T COG1959          24 GPVSSAEIAERQGISP---SYLEKILSKL   49 (150)
T ss_pred             CcccHHHHHHHhCcCH---HHHHHHHHHH
Confidence            4899999999999999   9999998654

>PRK13239 alkylmercury lyase; Provisional

Probab=87.37  E-value=0.78  Score=33.00  Aligned_cols=36  Identities=17%  Similarity=0.438  Sum_probs=28.9

Q ss_pred             hCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           48 LGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        48 LgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      .-|+..|++ |+|.|..+||+.+|.+.   +.+.++|+.|
T Consensus        25 ~~llr~la~-G~pvt~~~lA~~~~~~~---~~v~~~L~~l   60 (206)
T PRK13239         25 VPLLRLLAK-GRPVSVTTLAAALGWPV---EEVEAVLEAM   60 (206)
T ss_pred             HHHHHHHHc-CCCCCHHHHHHHhCCCH---HHHHHHHHhC
Confidence            345666774 79999999999999988   7788887653

>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed

Probab=87.32  E-value=0.62  Score=31.49  Aligned_cols=41  Identities=12%  Similarity=0.268  Sum_probs=30.9

Q ss_pred             HHHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           39 SMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        39 ~~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      -.++++.+.|-..     .+++.|+.|||+..++++   ..|.++|+.|
T Consensus         8 ~YAlr~L~~LA~~-----~~~~~s~~eIA~~~~is~---~~L~kIl~~L   48 (153)
T PRK11920          8 NYAIRMLMYCAAN-----DGKLSRIPEIARAYGVSE---LFLFKILQPL   48 (153)
T ss_pred             hHHHHHHHHHHhC-----CCCcCcHHHHHHHHCcCH---HHHHHHHHHH
Confidence            3466666665421     246789999999999999   9999998754

>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=87.19  E-value=0.52  Score=26.45  Aligned_cols=27  Identities=26%  Similarity=0.466  Sum_probs=23.1

Q ss_pred             CCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           58 GQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        58 ~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      ..++|..|||+.+|+++   ..+.|+|+.|
T Consensus        23 ~~~~s~~ela~~~g~s~---~tv~r~l~~L   49 (67)
T cd00092          23 QLPLTRQEIADYLGLTR---ETVSRTLKEL   49 (67)
T ss_pred             cCCcCHHHHHHHHCCCH---HHHHHHHHHH
Confidence            37899999999999998   8888888643

>PRK13558 bacterio-opsin activator; Provisional

Probab=86.70  E-value=0.76  Score=36.69  Aligned_cols=43  Identities=14%  Similarity=0.159  Sum_probs=35.4

Q ss_pred             HHHHHHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968           36 YINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR   85 (87)
Q Consensus        36 ~~~~~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR   85 (87)
                      .-+-.+|++|.+.|-|| +.   ...|..|||..+|+.+   ..+...||
T Consensus       610 ~~q~e~l~~a~~~gyf~-~p---r~~~~~e~a~~l~is~---~t~~~~lr  652 (665)
T PRK13558        610 DRQLTALQKAYVSGYFE-WP---RRVEGEELAESMGISR---STFHQHLR  652 (665)
T ss_pred             HHHHHHHHHHHHcCCCC-CC---ccCCHHHHHHHhCCCH---HHHHHHHH
Confidence            45678999999999998 43   6789999999999988   66666555

>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional

Probab=86.48  E-value=0.8  Score=30.59  Aligned_cols=28  Identities=11%  Similarity=0.339  Sum_probs=24.9

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCC
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQK   74 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~   74 (87)
                      .+..|.+.|.++ +..|.+|||+.+|+++
T Consensus        10 ~D~~Il~~Lq~d-~R~s~~eiA~~lglS~   37 (153)
T PRK11179         10 LDRGILEALMEN-ARTPYAELAKQFGVSP   37 (153)
T ss_pred             HHHHHHHHHHHc-CCCCHHHHHHHHCcCH
Confidence            678889999874 8999999999999987

>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=86.42  E-value=0.31  Score=27.06  Aligned_cols=35  Identities=20%  Similarity=0.400  Sum_probs=25.2

Q ss_pred             hCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           48 LGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        48 LgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      ..+...|.+. +++|..|||..+++++   ..+.|+++-
T Consensus         6 ~~iL~~l~~~-~~~~~~~la~~~~~~~---~~~t~~i~~   40 (59)
T PF01047_consen    6 FRILRILYEN-GGITQSELAEKLGISR---STVTRIIKR   40 (59)
T ss_dssp             HHHHHHHHHH-SSEEHHHHHHHHTS-H---HHHHHHHHH
T ss_pred             HHHHHHHHHc-CCCCHHHHHHHHCCCh---hHHHHHHHH
Confidence            3444556654 6799999999999999   777777653

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 ....

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

Probab=86.29  E-value=0.35  Score=24.99  Aligned_cols=24  Identities=29%  Similarity=0.580  Sum_probs=18.4

Q ss_pred             CCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           60 PMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        60 p~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      |+|-.|||..+|+.+   +.+.|+|.-
T Consensus         2 ~mtr~diA~~lG~t~---ETVSR~l~~   25 (32)
T PF00325_consen    2 PMTRQDIADYLGLTR---ETVSRILKK   25 (32)
T ss_dssp             E--HHHHHHHHTS-H---HHHHHHHHH
T ss_pred             CcCHHHHHHHhCCcH---HHHHHHHHH
Confidence            578899999999999   989998853

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 ....

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

Probab=86.21  E-value=0.64  Score=27.76  Aligned_cols=37  Identities=24%  Similarity=0.316  Sum_probs=24.4

Q ss_pred             hCchHHHHhCC---CCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           48 LGIPDVIHKHG---QPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        48 LgI~d~L~~~~---gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      -.|++.|-++.   ...|..|||+.+++.+   ..+.|+.|-|
T Consensus        19 ~~Ia~yil~~~~~~~~~si~elA~~~~vS~---sti~Rf~kkL   58 (77)
T PF01418_consen   19 KKIADYILENPDEIAFMSISELAEKAGVSP---STIVRFCKKL   58 (77)
T ss_dssp             HHHHHHHHH-HHHHCT--HHHHHHHCTS-H---HHHHHHHHHC
T ss_pred             HHHHHHHHhCHHHHHHccHHHHHHHcCCCH---HHHHHHHHHh
Confidence            34555444322   5789999999999999   8899988754

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.

>TIGR00373 conserved hypothetical protein TIGR00373

Probab=86.11  E-value=0.79  Score=31.28  Aligned_cols=36  Identities=14%  Similarity=0.057  Sum_probs=29.0

Q ss_pred             hCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           48 LGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        48 LgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      ..|+|+|..+ +++|-.|||..+|++.   ..++|+|..|
T Consensus        17 v~Vl~aL~~~-~~~tdEeLa~~Lgi~~---~~VRk~L~~L   52 (158)
T TIGR00373        17 GLVLFSLGIK-GEFTDEEISLELGIKL---NEVRKALYAL   52 (158)
T ss_pred             HHHHHHHhcc-CCCCHHHHHHHHCCCH---HHHHHHHHHH
Confidence            3477888754 7999999999999988   7788887643

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.

>PRK11169 leucine-responsive transcriptional regulator; Provisional

Probab=85.69  E-value=0.76  Score=31.08  Aligned_cols=29  Identities=7%  Similarity=0.234  Sum_probs=25.4

Q ss_pred             HHHhCchHHHHhCCCCCCHHHHHHhcCCCC
Q 041968           45 AVELGIPDVIHKHGQPMTLSQIASALDIQK   74 (87)
Q Consensus        45 aveLgI~d~L~~~~gp~S~~ELA~~~~~~~   74 (87)
                      .+|..|.++|.+ ++.+|..|||+++|+++
T Consensus        14 ~~D~~IL~~Lq~-d~R~s~~eiA~~lglS~   42 (164)
T PRK11169         14 RIDRNILNELQK-DGRISNVELSKRVGLSP   42 (164)
T ss_pred             HHHHHHHHHhcc-CCCCCHHHHHHHHCcCH
Confidence            368889999987 48999999999999987

>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR

Probab=85.06  E-value=0.94  Score=31.56  Aligned_cols=36  Identities=25%  Similarity=0.315  Sum_probs=28.5

Q ss_pred             hCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           48 LGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        48 LgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      ..|...|.+. ++.|..|||+.+|+++   ..+.|.|+.|
T Consensus         4 ~~IL~~L~~~-~~~t~~eLA~~lgis~---~tV~~~L~~L   39 (203)
T TIGR02702         4 EDILSYLLKQ-GQATAAALAEALAISP---QAVRRHLKDL   39 (203)
T ss_pred             HHHHHHHHHc-CCCCHHHHHHHHCcCH---HHHHHHHHHH
Confidence            3466677654 7799999999999999   8888887653

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.

>COG4190 Predicted transcriptional regulator [Transcription]

Probab=84.43  E-value=0.96  Score=30.85  Aligned_cols=48  Identities=13%  Similarity=0.302  Sum_probs=36.4

Q ss_pred             HHHHHHHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           35 NYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        35 g~~~~~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      ++-..+.+-+=-.+.+.+.|+. .+|.|..|+|+.+|=++   ..+.|=||.
T Consensus        54 Sye~la~vLsp~nleLl~~Ia~-~~P~Si~ElAe~vgRdv---~nvhr~Ls~  101 (144)
T COG4190          54 SYEDLARVLSPRNLELLELIAQ-EEPASINELAELVGRDV---KNVHRTLST  101 (144)
T ss_pred             cHHHHHHHhChhHHHHHHHHHh-cCcccHHHHHHHhCcch---HHHHHHHHH
Confidence            4444444445556778888986 39999999999999998   778887764

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

Probab=84.17  E-value=1.3  Score=24.44  Aligned_cols=33  Identities=21%  Similarity=0.442  Sum_probs=24.4

Q ss_pred             CchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           49 GIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        49 gI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .|.+.+...  +.+..||+..++++.   ..+.|.++.
T Consensus        11 ~il~~l~~~--~~~~~ei~~~~~i~~---~~i~~~l~~   43 (78)
T cd00090          11 RILRLLLEG--PLTVSELAERLGLSQ---STVSRHLKK   43 (78)
T ss_pred             HHHHHHHHC--CcCHHHHHHHHCcCH---hHHHHHHHH
Confidence            455556642  399999999999988   667777654

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.

>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR

Probab=84.00  E-value=1.4  Score=27.87  Aligned_cols=36  Identities=14%  Similarity=0.255  Sum_probs=27.3

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR   85 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR   85 (87)
                      .+..|...|.+ .+++|..|||..+++++   ..+.|+++
T Consensus        29 ~q~~iL~~l~~-~~~~t~~ela~~~~~~~---~tvs~~l~   64 (118)
T TIGR02337        29 QQWRILRILAE-QGSMEFTQLANQACILR---PSLTGILA   64 (118)
T ss_pred             HHHHHHHHHHH-cCCcCHHHHHHHhCCCc---hhHHHHHH
Confidence            33446666765 37899999999999998   66777765

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.

>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=83.56  E-value=0.87  Score=26.79  Aligned_cols=31  Identities=35%  Similarity=0.611  Sum_probs=20.7

Q ss_pred             HHhCCCCCCHHHHHHhcCCC-CCChhhHHHHHhcC
Q 041968           54 IHKHGQPMTLSQIASALDIQ-KNKAHCIQRLMRIL   87 (87)
Q Consensus        54 L~~~~gp~S~~ELA~~~~~~-~~~~~~L~RlLR~L   87 (87)
                      +.+.|-|-|+.|||+.+|+. +   ..+.+.|+.|
T Consensus        19 ~~~~G~~Pt~rEIa~~~g~~S~---~tv~~~L~~L   50 (65)
T PF01726_consen   19 IEENGYPPTVREIAEALGLKST---STVQRHLKAL   50 (65)
T ss_dssp             HHHHSS---HHHHHHHHTSSSH---HHHHHHHHHH
T ss_pred             HHHcCCCCCHHHHHHHhCCCCh---HHHHHHHHHH
Confidence            44456777999999999996 5   6677666543

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.

>COG1522 Lrp Transcriptional regulators [Transcription]

Probab=83.52  E-value=1.3  Score=28.90  Aligned_cols=28  Identities=7%  Similarity=0.278  Sum_probs=24.1

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCC
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQK   74 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~   74 (87)
                      ++..|.+.|.++ ++.|..|||+++|+++
T Consensus         9 ~D~~IL~~L~~d-~r~~~~eia~~lglS~   36 (154)
T COG1522           9 IDRRILRLLQED-ARISNAELAERVGLSP   36 (154)
T ss_pred             HHHHHHHHHHHh-CCCCHHHHHHHHCCCH
Confidence            567788888874 7899999999999987

>PRK11511 DNA-binding transcriptional activator MarA; Provisional

Probab=83.49  E-value=1.7  Score=28.19  Aligned_cols=24  Identities=21%  Similarity=0.522  Sum_probs=22.0

Q ss_pred             CCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968           59 QPMTLSQIASALDIQKNKAHCIQRLMR   85 (87)
Q Consensus        59 gp~S~~ELA~~~~~~~~~~~~L~RlLR   85 (87)
                      .+.|+.+||+.+|+++   ..+.|+++
T Consensus        24 ~~~sl~~lA~~~g~S~---~~l~r~Fk   47 (127)
T PRK11511         24 SPLSLEKVSERSGYSK---WHLQRMFK   47 (127)
T ss_pred             CCCCHHHHHHHHCcCH---HHHHHHHH
Confidence            7899999999999999   88988876

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

Probab=83.40  E-value=1.1  Score=24.16  Aligned_cols=24  Identities=25%  Similarity=0.441  Sum_probs=16.9

Q ss_pred             CCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968           59 QPMTLSQIASALDIQKNKAHCIQRLMR   85 (87)
Q Consensus        59 gp~S~~ELA~~~~~~~~~~~~L~RlLR   85 (87)
                      ...|..|||..+|.++   ..+.|.+|
T Consensus        19 ~G~s~~~IA~~lg~s~---sTV~relk   42 (44)
T PF13936_consen   19 QGMSIREIAKRLGRSR---STVSRELK   42 (44)
T ss_dssp             S---HHHHHHHTT--H---HHHHHHHH
T ss_pred             cCCCHHHHHHHHCcCc---HHHHHHHh
Confidence            4599999999999999   88988875

>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=82.87  E-value=0.85  Score=25.75  Aligned_cols=31  Identities=29%  Similarity=0.506  Sum_probs=20.4

Q ss_pred             HHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           53 VIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        53 ~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .|...+++.|..+|+..++.+.   ..+.|+++-
T Consensus        11 ~l~~~~~~~t~~~l~~~~~~~~---~~vs~~i~~   41 (68)
T PF13463_consen   11 ALAHSDGPMTQSDLAERLGISK---STVSRIIKK   41 (68)
T ss_dssp             HHT--TS-BEHHHHHHHTT--H---HHHHHHHHH
T ss_pred             HHHccCCCcCHHHHHHHHCcCH---HHHHHHHHH
Confidence            3443358999999999999998   777777653

>COG2345 Predicted transcriptional regulator [Transcription]

Probab=82.78  E-value=1.3  Score=32.19  Aligned_cols=33  Identities=21%  Similarity=0.422  Sum_probs=25.9

Q ss_pred             chHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           50 IPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        50 I~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      |...|.++ +|+|+.|||..+|+++   ...+|-|-.
T Consensus        16 il~lL~~~-g~~sa~elA~~Lgis~---~avR~HL~~   48 (218)
T COG2345          16 ILELLKKS-GPVSADELAEELGISP---MAVRRHLDD   48 (218)
T ss_pred             HHHHHhcc-CCccHHHHHHHhCCCH---HHHHHHHHH
Confidence            34445554 8999999999999999   888877654

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

Probab=82.70  E-value=2  Score=25.25  Aligned_cols=28  Identities=18%  Similarity=0.345  Sum_probs=21.7

Q ss_pred             hHHHHhCCCCCCHHHHHHhcCCCCCChhhHH
Q 041968           51 PDVIHKHGQPMTLSQIASALDIQKNKAHCIQ   81 (87)
Q Consensus        51 ~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~   81 (87)
                      |++--+++|.++..|||+.+|+++   ..+.
T Consensus        13 ~e~y~~~~g~i~lkdIA~~Lgvs~---~tIr   40 (60)
T PF10668_consen   13 FEIYKESNGKIKLKDIAEKLGVSE---STIR   40 (60)
T ss_pred             HHHHHHhCCCccHHHHHHHHCCCH---HHHH
Confidence            444455579999999999999988   5554

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

>PRK00215 LexA repressor; Validated

Probab=82.29  E-value=1.8  Score=29.98  Aligned_cols=31  Identities=26%  Similarity=0.472  Sum_probs=24.5

Q ss_pred             HHhCCCCCCHHHHHHhcCC-CCCChhhHHHHHhcC
Q 041968           54 IHKHGQPMTLSQIASALDI-QKNKAHCIQRLMRIL   87 (87)
Q Consensus        54 L~~~~gp~S~~ELA~~~~~-~~~~~~~L~RlLR~L   87 (87)
                      +.+.+.+.|..|||+.+|. ++   ..+.|+++.|
T Consensus        17 ~~~~~~~~s~~ela~~~~~~~~---~tv~~~l~~L   48 (205)
T PRK00215         17 IEETGYPPSRREIADALGLRSP---SAVHEHLKAL   48 (205)
T ss_pred             HHHhCCCCCHHHHHHHhCCCCh---HHHHHHHHHH
Confidence            3444678999999999999 88   7788887643

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

Probab=82.00  E-value=1.9  Score=28.99  Aligned_cols=42  Identities=17%  Similarity=0.377  Sum_probs=34.4

Q ss_pred             HHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           42 LKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        42 L~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      =+..+...|.+.+.++ |.+|..|++..+|++-   ..+.+.+|-|
T Consensus         9 er~eLk~rIvElVRe~-GRiTi~ql~~~TGasR---~Tvk~~lreL   50 (127)
T PF06163_consen    9 EREELKARIVELVREH-GRITIKQLVAKTGASR---NTVKRYLREL   50 (127)
T ss_pred             HHHHHHHHHHHHHHHc-CCccHHHHHHHHCCCH---HHHHHHHHHH
Confidence            3556777888888775 8999999999999988   7888888753

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

Probab=81.83  E-value=2.4  Score=26.54  Aligned_cols=35  Identities=17%  Similarity=0.198  Sum_probs=29.8

Q ss_pred             hCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968           48 LGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR   85 (87)
Q Consensus        48 LgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR   85 (87)
                      ...+|.+...++..|+.|.|..+|+.+   .-|.++||
T Consensus        12 a~~~d~~~~~~~~~ti~~~AK~L~i~~---~~l~~~Lr   46 (111)
T PF03374_consen   12 AEFYDAFVDSDGLYTIREAAKLLGIGR---NKLFQWLR   46 (111)
T ss_pred             hHHHHHHHcCCCCccHHHHHHHhCCCH---HHHHHHHH
Confidence            345788877679999999999999998   77888887

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

>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD

Probab=81.47  E-value=2.2  Score=26.64  Aligned_cols=33  Identities=24%  Similarity=0.327  Sum_probs=25.9

Q ss_pred             hCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           48 LGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        48 LgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      ..|+..+.   +..|..|||+.+|++.   ..++|+.|.
T Consensus        41 ~~I~~ll~---~G~S~~eIA~~LgISr---sTIyRi~R~   73 (88)
T TIGR02531        41 LQVAKMLK---QGKTYSDIEAETGAST---ATISRVKRC   73 (88)
T ss_pred             HHHHHHHH---CCCCHHHHHHHHCcCH---HHHHHHHHh
Confidence            34555555   3479999999999999   999998873

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

>PHA00738 putative HTH transcription regulator

Probab=81.40  E-value=1.8  Score=28.31  Aligned_cols=38  Identities=21%  Similarity=0.288  Sum_probs=30.0

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      .++.|++.|.. +++.++.||++.+++..   ..+.+-|+.|
T Consensus        13 tRr~IL~lL~~-~e~~~V~eLae~l~lSQ---ptVS~HLKvL   50 (108)
T PHA00738         13 LRRKILELIAE-NYILSASLISHTLLLSY---TTVLRHLKIL   50 (108)
T ss_pred             HHHHHHHHHHH-cCCccHHHHHHhhCCCH---HHHHHHHHHH
Confidence            46678888875 35799999999999987   7777777654

>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=81.32  E-value=3.4  Score=26.05  Aligned_cols=39  Identities=15%  Similarity=0.171  Sum_probs=30.9

Q ss_pred             HHHHhCchHHHHhC-CCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968           44 CAVELGIPDVIHKH-GQPMTLSQIASALDIQKNKAHCIQRLMR   85 (87)
Q Consensus        44 aaveLgI~d~L~~~-~gp~S~~ELA~~~~~~~~~~~~L~RlLR   85 (87)
                      .-+...|+.-|.+. +.+.++.|||..+++++   ..+.-.|+
T Consensus         8 S~~R~~vl~~L~~~yp~~~~~~eIar~v~~~~---snV~GaL~   47 (90)
T PF07381_consen    8 SKVRKKVLEYLCSIYPEPAYPSEIARSVGSDY---SNVLGALR   47 (90)
T ss_pred             HHHHHHHHHHHHHcCCCcCCHHHHHHHHCCCH---HHHHHHHh
Confidence            55677888888876 69999999999999999   55554443

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

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

Probab=80.97  E-value=1.6  Score=24.08  Aligned_cols=21  Identities=24%  Similarity=0.479  Sum_probs=17.2

Q ss_pred             CHHHHHHhcCCCCCChhhHHHHHh
Q 041968           62 TLSQIASALDIQKNKAHCIQRLMR   85 (87)
Q Consensus        62 S~~ELA~~~~~~~~~~~~L~RlLR   85 (87)
                      |..|||+.+|+++   ..+.|+|+
T Consensus         1 Ti~dIA~~agvS~---~TVSr~ln   21 (46)
T PF00356_consen    1 TIKDIAREAGVSK---STVSRVLN   21 (46)
T ss_dssp             CHHHHHHHHTSSH---HHHHHHHT
T ss_pred             CHHHHHHHHCcCH---HHHHHHHh
Confidence            6789999999988   77877774

These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....

>PRK11302 DNA-binding transcriptional regulator HexR; Provisional

Probab=80.56  E-value=1.5  Score=31.48  Aligned_cols=39  Identities=18%  Similarity=0.298  Sum_probs=30.3

Q ss_pred             HHhCchHHHHhCC---CCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           46 VELGIPDVIHKHG---QPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        46 veLgI~d~L~~~~---gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      .|-.|++.|.++.   .-.|+.|||+++++++   ..+-|+.|-|
T Consensus        17 ~e~~Ia~yil~n~~~v~~~si~~lA~~~~vS~---aTv~Rf~kkl   58 (284)
T PRK11302         17 SERKVAEVILASPQTAIHSSIATLAKMANVSE---PTVNRFCRSL   58 (284)
T ss_pred             HHHHHHHHHHhCHHHHHhcCHHHHHHHhCCCH---HHHHHHHHHc
Confidence            4556666666544   4579999999999999   8899998854

>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID

Probab=80.16  E-value=2.7  Score=25.90  Aligned_cols=32  Identities=16%  Similarity=0.241  Sum_probs=25.9

Q ss_pred             CchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968           49 GIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR   85 (87)
Q Consensus        49 gI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR   85 (87)
                      -|.+.|.+  +..|+.+||+..|+..   ..+.|.|.
T Consensus        10 ~I~e~l~~--~~~ti~dvA~~~gvS~---~TVsr~L~   41 (80)
T TIGR02844        10 EIGKYIVE--TKATVRETAKVFGVSK---STVHKDVT   41 (80)
T ss_pred             HHHHHHHH--CCCCHHHHHHHhCCCH---HHHHHHhc
Confidence            35677776  7889999999999988   77877764

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

>PRK11557 putative DNA-binding transcriptional regulator; Provisional

Probab=80.13  E-value=1.7  Score=31.19  Aligned_cols=39  Identities=10%  Similarity=0.238  Sum_probs=30.0

Q ss_pred             HHhCchHHHHhCC---CCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           46 VELGIPDVIHKHG---QPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        46 veLgI~d~L~~~~---gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      .|-.|++.|-++.   .-.|+.|||+++++++   ..+.|+.|-|
T Consensus        13 ~e~~ia~yil~n~~~v~~~si~elA~~~~vS~---aTv~Rf~kkl   54 (278)
T PRK11557         13 SDRKLADYLLLQPDTARHLSSQQLANEAGVSQ---SSVVKFAQKL   54 (278)
T ss_pred             HHHHHHHHHHhCHHHHHhcCHHHHHHHhCCCH---HHHHHHHHHc
Confidence            3455666665543   5689999999999999   8899998854

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	87
1zg3_A	358	Crystal Structure Of The Isoflavanone 4'-O-Methyltr		3e-14
1zga_A	357	Crystal Structure Of Isoflavanone 4'-o-methyltransf		3e-14
1zgj_A	354	Crystal Structure Of Isoflavanone 4'-O-Methyltransf		3e-14
2qyo_A	357	Crystal Structure Of Isoflavone O-Methyltransferase		3e-13
1fp2_A	352	Crystal Structure Analysis Of Isoflavone O-Methyltr		3e-12
1fpx_A	352	Crystal Structure Analysis Of Selenomethionine Subs		2e-10

>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 = 73.6 bits (179), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 31/67 (46%), Positives = 49/67 (73%)
Query: 21 ELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCI 80
          EL  AQ  ++   +N+++SM+LK A+ELGI D IH HG+PMTLS++AS+L +  +K + +
Sbjct: 6  ELYHAQIHLYKHVYNFVSSMALKSAMELGIADAIHNHGKPMTLSELASSLKLHPSKVNIL 65
Query: 81 QRLMRIL 87
           R +R+L
Sbjct: 66 HRFLRLL 72

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

Iteration: 1
 Score = 73.6 bits (179), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 31/67 (46%), Positives = 49/67 (73%)
Query: 21 ELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCI 80
          EL  AQ  ++   +N+++SM+LK A+ELGI D IH HG+PMTLS++AS+L +  +K + +
Sbjct: 5  ELYHAQIHLYKHVYNFVSSMALKSAMELGIADAIHNHGKPMTLSELASSLKLHPSKVNIL 64
Query: 81 QRLMRIL 87
           R +R+L
Sbjct: 65 HRFLRLL 71

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

Iteration: 1
 Score = 73.6 bits (179), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 31/67 (46%), Positives = 49/67 (73%)
Query: 21 ELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCI 80
          EL  AQ  ++   +N+++SM+LK A+ELGI D IH HG+PMTLS++AS+L +  +K + +
Sbjct: 2  ELYHAQIHLYKHVYNFVSSMALKSAMELGIADAIHNHGKPMTLSELASSLKLHPSKVNIL 61
Query: 81 QRLMRIL 87
           R +R+L
Sbjct: 62 HRFLRLL 68

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

Iteration: 1
 Score = 70.1 bits (170), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 31/67 (46%), Positives = 47/67 (70%)
Query: 21 ELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCI 80
          E+ KAQA ++   + +++SMSLK ++E+ IP++IH HG+P+TLS + S L I   K   +
Sbjct: 12 EIFKAQALLYKNMYAFVDSMSLKWSIEMNIPNIIHNHGKPITLSNLVSILQIPSTKVDNV 71
Query: 81 QRLMRIL 87
          QRLMR L
Sbjct: 72 QRLMRYL 78

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

Iteration: 1
 Score = 66.6 bits (161), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 30/67 (44%), Positives = 47/67 (70%)
Query: 21 ELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCI 80
          E+ KAQA ++   + +I+SMSLK AVE+ IP++I  HG+P++LS + S L +  +K   +
Sbjct: 12 EIFKAQALLYKHIYAFIDSMSLKWAVEMNIPNIIQNHGKPISLSNLVSILQVPSSKIGNV 71
Query: 81 QRLMRIL 87
          +RLMR L
Sbjct: 72 RRLMRYL 78

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

Iteration: 1
 Score = 60.8 bits (146), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 28/67 (41%), Positives = 44/67 (65%)
Query: 21 ELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCI 80
          E+ KAQA ++   + +I+S SLK AVE  IP++I  HG+P++LS + S L +  +K   +
Sbjct: 12 EIFKAQALLYKHIYAFIDSXSLKWAVEXNIPNIIQNHGKPISLSNLVSILQVPSSKIGNV 71
Query: 81 QRLMRIL 87
          +RL R L
Sbjct: 72 RRLXRYL 78

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	87
1zg3_A	358	Isoflavanone 4'-O-methyltransferase; rossman fold,	1e-29
1fp2_A	352	Isoflavone O-methyltransferase; protein-product co	2e-26
1fp1_D	372	Isoliquiritigenin 2'-O-methyltransferase; protein-	1e-24
3lst_A	348	CALO1 methyltransferase; calicheamicin, enediyne,	3e-24
3reo_A	368	(ISO)eugenol O-methyltransferase; directed evoluti	2e-22
1x19_A	359	CRTF-related protein; methyltransferase, bacterioc	9e-22
1qzz_A	374	RDMB, aclacinomycin-10-hydroxylase; anthracycline,	1e-21
3gwz_A	369	MMCR; methyltransferase, mitomycin, S-adenosyl met	1e-21
2ip2_A	334	Probable phenazine-specific methyltransferase; pyo	3e-21
3p9c_A	364	Caffeic acid O-methyltransferase; S-adenosylmethio	3e-21
3i53_A	332	O-methyltransferase; CO-complex, rossmann-like fol	1e-19
3dp7_A	363	SAM-dependent methyltransferase; structural genomi	5e-19
1tw3_A	360	COMT, carminomycin 4-O-methyltransferase; anthracy	1e-17
2r3s_A	335	Uncharacterized protein; methyltransferase domain,	3e-15
3mcz_A	352	O-methyltransferase; adomet_mtases, S-adenosylmeth	4e-15

>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 =  106 bits (266), Expect = 1e-29
 Identities = 33/71 (46%), Positives = 51/71 (71%)

Query: 17 SSSSELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNK 76
          S  SEL  AQ  ++   +N+++SM+LK A+ELGI D IH HG+PMTLS++AS+L +  +K
Sbjct: 2  SEESELYHAQIHLYKHVYNFVSSMALKSAMELGIADAIHNHGKPMTLSELASSLKLHPSK 61

Query: 77 AHCIQRLMRIL 87
           + + R +R+L
Sbjct: 62 VNILHRFLRLL 72

>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 = 98.3 bits (245), Expect = 2e-26
 Identities = 33/77 (42%), Positives = 52/77 (67%)

Query: 11 SSSSSSSSSSELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASAL 70
          +SS +    SE+ KAQA ++   + +I+SMSLK AVE+ IP++I  HG+P++LS + S L
Sbjct: 2  ASSINGRKPSEIFKAQALLYKHIYAFIDSMSLKWAVEMNIPNIIQNHGKPISLSNLVSIL 61

Query: 71 DIQKNKAHCIQRLMRIL 87
           +  +K   ++RLMR L
Sbjct: 62 QVPSSKIGNVRRLMRYL 78

>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 = 93.4 bits (232), Expect = 1e-24
 Identities = 22/89 (24%), Positives = 36/89 (40%), Gaps = 4/89 (4%)

Query: 3  MNHMIN-AESSSSSSSSSSELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQP- 60
          M +     E +  S++S      A         N +    L  A++L + ++I K   P 
Sbjct: 1  MGNSYITKEDNQISATSEQTEDSACLSAMVLTTNLVYPAVLNAAIDLNLFEIIAKATPPG 60

Query: 61 --MTLSQIASALDIQKNKAHCIQRLMRIL 87
            M+ S+IAS L      +    RL R+L
Sbjct: 61 AFMSPSEIASKLPASTQHSDLPNRLDRML 89

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

 Score = 92.0 bits (229), Expect = 3e-24
 Identities = 16/79 (20%), Positives = 38/79 (48%), Gaps = 5/79 (6%)

Query: 9  AESSSSSSSSSSELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIAS 68
           +   S +    + L++   ++  A  Y  + +L+ A  +G+ D +     P T +++A+
Sbjct: 6  RQRPPSRAGGDMDRLQSALALYEEAMGYTYAAALRAAAAVGVADHL--VDGPRTPAELAA 63

Query: 69 ALDIQKNKAHCIQRLMRIL 87
          A       A  ++R++R+L
Sbjct: 64 ATGT---DADALRRVLRLL 79

>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 = 87.2 bits (216), Expect = 2e-22
 Identities = 17/84 (20%), Positives = 36/84 (42%), Gaps = 4/84 (4%)

Query: 8  NAESSSSSSSSSSELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQP---MTLS 64
             +      + S   +A       A   +  M+LK A+EL + +++ K   P   ++ +
Sbjct: 4  TGNAEIQIIPTHSSDEEANLFAMQLASAAVLPMALKAAIELDVLEIMAKSVPPSGYISPA 63

Query: 65 QIASALDIQ-KNKAHCIQRLMRIL 87
          +IA+ L          + R++R+L
Sbjct: 64 EIAAQLPTTNPEAPVMLDRVLRLL 87

>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 = 85.5 bits (212), Expect = 9e-22
 Identities = 16/87 (18%), Positives = 30/87 (34%), Gaps = 6/87 (6%)

Query: 2  DMNHMINAESSSSSSSSSSELLKAQAQVWNCAFN-YINSMSLKCAVELGIPDVIHKHGQP 60
            +H        S   S+++LL    +     F   I    +K A+EL +   +     P
Sbjct: 7  HHHHSSGLVPRGSHMMSNNDLLNYYHRANELVFKGLIEFSCMKAAIELDLFSHM--AEGP 64

Query: 61 MTLSQIASALDIQKNKAHCIQRLMRIL 87
            L+ +A+       +      L+  L
Sbjct: 65 KDLATLAADTGSVPPRLE---MLLETL 88

>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 = 85.1 bits (211), Expect = 1e-21
 Identities = 18/77 (23%), Positives = 29/77 (37%), Gaps = 5/77 (6%)

Query: 11 SSSSSSSSSSELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASAL 70
          SSSS         +    +     N +  M+L+ A  L + D +       TL+ +A   
Sbjct: 2  SSSSPGEPLEPTDQDLDVLLKNLGNLVTPMALRVAATLRLVDHL--LAGADTLAGLADRT 59

Query: 71 DIQKNKAHCIQRLMRIL 87
          D        + RL+R L
Sbjct: 60 DTH---PQALSRLVRHL 73

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

 Score = 85.1 bits (211), Expect = 1e-21
 Identities = 18/85 (21%), Positives = 39/85 (45%), Gaps = 7/85 (8%)

Query: 3  MNHMINAESSSSSSSSSSELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMT 62
           +HM      +  +  ++    A+  V +       + ++  AVELG+P+++ +   P T
Sbjct: 18 GSHM--TVEQTPENPGTAARAAAEETVNDILQGAWKARAIHVAVELGVPELLQEG--PRT 73

Query: 63 LSQIASALDIQKNKAHCIQRLMRIL 87
           + +A A          ++RL+R+L
Sbjct: 74 ATALAEATGAH---EQTLRRLLRLL 95

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

 Score = 83.8 bits (208), Expect = 3e-21
 Identities = 17/69 (24%), Positives = 28/69 (40%), Gaps = 5/69 (7%)

Query: 19 SSELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAH 78
          ++  L A   +         S  +  A  LG+ D+I       +   +A+A+      A 
Sbjct: 2  NNSNLAAARNLIQVVTGEWKSRCVYVATRLGLADLIESG--IDSDETLAAAVGS---DAE 56

Query: 79 CIQRLMRIL 87
           I RLMR+L
Sbjct: 57 RIHRLMRLL 65

>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 = 84.1 bits (208), Expect = 3e-21
 Identities = 19/80 (23%), Positives = 42/80 (52%), Gaps = 3/80 (3%)

Query: 11 SSSSSSSSSSELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHK-HGQPMTLSQIASA 69
           S+++  ++S    A       A + +  M+LK A+ELG+ +++    G+ +T +++A+ 
Sbjct: 6  GSTAADMAASADEDACMFALQLASSSVLPMTLKNAIELGLLEILVAAGGKSLTPTEVAAK 65

Query: 70 LDIQKN--KAHCIQRLMRIL 87
          L    N      + R++R+L
Sbjct: 66 LPSAANPEAPDMVDRILRLL 85

>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 = 79.2 bits (196), Expect = 1e-19
 Identities = 16/64 (25%), Positives = 26/64 (40%), Gaps = 5/64 (7%)

Query: 24 KAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRL 83
          +A         +    M+++ A  L + D I       T ++IASA       A  + RL
Sbjct: 4  RAAHIGLRALADLATPMAVRVAATLRVADHIAAG--HRTAAEIASAAGAH---ADSLDRL 58

Query: 84 MRIL 87
          +R L
Sbjct: 59 LRHL 62

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

 Score = 78.2 bits (193), Expect = 5e-19
 Identities = 12/72 (16%), Positives = 26/72 (36%), Gaps = 3/72 (4%)

Query: 16 SSSSSELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKN 75
          +       +AQ      AF  +     +  ++ GI  ++    +  TL +I+    + + 
Sbjct: 6  TKEQCTAAEAQRLAQEIAFGPVVFQVSRLMLKFGIFQLLSGKREGYTLQEISGRTGLTRY 65

Query: 76 KAHCIQRLMRIL 87
           A   Q L+   
Sbjct: 66 AA---QVLLEAS 74

>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 = 74.3 bits (183), Expect = 1e-17
 Identities = 13/79 (16%), Positives = 31/79 (39%), Gaps = 6/79 (7%)

Query: 9  AESSSSSSSSSSELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIAS 68
            ++  + ++  + + A   +     +    M ++ A  L + D I       T+  +A+
Sbjct: 4  NSTAEPTVAARPQQIDALRTLIRL-GSLHTPMVVRTAATLRLVDHI--LAGARTVKALAA 60

Query: 69 ALDIQKNKAHCIQRLMRIL 87
            D    +   + RL+R L
Sbjct: 61 RTDT---RPEALLRLIRHL 76

>2r3s_A Uncharacterized protein; methyltransferase domain, structural genomics, joint center structural genomics, JCSG, protein structure initiative; HET: MSE; 2.15A {Nostoc punctiforme} Length = 335

 Score = 67.4 bits (165), Expect = 3e-15
 Identities = 13/63 (20%), Positives = 22/63 (34%), Gaps = 5/63 (7%)

Query: 25 AQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLM 84
          + A  +N    Y  S ++K AVEL +   I +     +   +A      +        L 
Sbjct: 6  SPALFFNTVNAYQRSAAIKAAVELNVFTAISQG--IESSQSLAQKCQTSERGMR---MLC 60

Query: 85 RIL 87
            L
Sbjct: 61 DYL 63

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

 Score = 67.4 bits (165), Expect = 4e-15
 Identities = 15/87 (17%), Positives = 34/87 (39%), Gaps = 10/87 (11%)

Query: 1  MDMNHMINAESSSSSSSSSSELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQP 60
          M+ + +     S+   ++    L +   +   +  Y  S  L  AV   + D+       
Sbjct: 4  MNASAVETIYESTEDKAA----LTSVVDLVKLSDQYRQSAILHYAVADKLFDLTQ---TG 56

Query: 61 MTLSQIASALDIQKNKAHCIQRLMRIL 87
           T +++A++  + + KA     L+  L
Sbjct: 57 RTPAEVAASFGMVEGKAA---ILLHAL 80

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	87
4a6d_A	353	Hydroxyindole O-methyltransferase; melatonin, circ	99.43
3p9c_A	364	Caffeic acid O-methyltransferase; S-adenosylmethio	99.41
1fp2_A	352	Isoflavone O-methyltransferase; protein-product co	99.38
3dp7_A	363	SAM-dependent methyltransferase; structural genomi	99.36
1zg3_A	358	Isoflavanone 4'-O-methyltransferase; rossman fold,	99.35
3reo_A	368	(ISO)eugenol O-methyltransferase; directed evoluti	99.35
3lst_A	348	CALO1 methyltransferase; calicheamicin, enediyne,	99.23
1fp1_D	372	Isoliquiritigenin 2'-O-methyltransferase; protein-	99.22
2ip2_A	334	Probable phenazine-specific methyltransferase; pyo	99.19
1x19_A	359	CRTF-related protein; methyltransferase, bacterioc	99.18
3gwz_A	369	MMCR; methyltransferase, mitomycin, S-adenosyl met	99.18
3i53_A	332	O-methyltransferase; CO-complex, rossmann-like fol	99.11
3mcz_A	352	O-methyltransferase; adomet_mtases, S-adenosylmeth	99.11
1qzz_A	374	RDMB, aclacinomycin-10-hydroxylase; anthracycline,	99.1
2r3s_A	335	Uncharacterized protein; methyltransferase domain,	99.07
1tw3_A	360	COMT, carminomycin 4-O-methyltransferase; anthracy	98.89
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	96.11
2fu4_A	83	Ferric uptake regulation protein; DNA binding doma	95.25
3mq0_A	275	Transcriptional repressor of the blcabc operon; he	95.12
3r0a_A	123	Putative transcriptional regulator; structural gen	94.77
1mkm_A	249	ICLR transcriptional regulator; structural genomic	94.41
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	94.33
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	94.17
2xrn_A	241	HTH-type transcriptional regulator TTGV; DNA-bindi	94.11
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	93.86
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	93.63
3r4k_A	260	Transcriptional regulator, ICLR family; DNA/RNA-bi	93.58
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	93.55
2y75_A	129	HTH-type transcriptional regulator CYMR; DNA bindi	93.34
1y0u_A	96	Arsenical resistance operon repressor, putative; s	93.08
1ub9_A	100	Hypothetical protein PH1061; helix-turn-helix moti	93.06
1u2w_A	122	CADC repressor, cadmium efflux system accessory pr	93.05
2g7u_A	257	Transcriptional regulator; ICLR family, structural	93.01
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	92.78
2o0y_A	260	Transcriptional regulator; ICLR-family, structural	92.76
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	92.68
2ia2_A	265	Putative transcriptional regulator; SAD, PSI-2, st	92.66
3f6o_A	118	Probable transcriptional regulator, ARSR family pr	92.57
1sfx_A	109	Conserved hypothetical protein AF2008; structural	92.57
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	92.39
3lwf_A	159	LIN1550 protein, putative transcriptional regulato	92.35
2lnb_A	80	Z-DNA-binding protein 1; structural genomics, nort	92.19
3boq_A	160	Transcriptional regulator, MARR family; MARR famil	92.18
3jth_A	98	Transcription activator HLYU; transcription factor	92.12
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	92.07
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	92.04
2kko_A	108	Possible transcriptional regulatory protein (possi	91.98
2o03_A	131	Probable zinc uptake regulation protein FURB; DNA-	91.72
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	91.34
1xmk_A	79	Double-stranded RNA-specific adenosine deaminase;	91.34
3t8r_A	143	Staphylococcus aureus CYMR; transcriptional regula	91.34
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	91.27
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	91.23
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	91.2
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	91.2
3e6m_A	161	MARR family transcriptional regulator; APC88769, s	91.19
2w25_A	150	Probable transcriptional regulatory protein; trans	91.04
2fe3_A	145	Peroxide operon regulator; oxidative stress regula	90.93
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	90.84
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	90.81
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	90.76
1ylf_A	149	RRF2 family protein; structural genomics, transcri	90.69
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	90.64
3kp7_A	151	Transcriptional regulator TCAR; multiple drug resi	90.5
2zkz_A	99	Transcriptional repressor PAGR; protein-DNA, HTH m	90.49
1r1t_A	122	Transcriptional repressor SMTB; zinc, transcriptio	90.47
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	90.38
1ku9_A	152	Hypothetical protein MJ223; putative transcription	90.28
3i4p_A	162	Transcriptional regulator, ASNC family; PSI, struc	90.24
1jhg_A	101	Trp operon repressor; complex (regulatory protein-	90.24
3fm5_A	150	Transcriptional regulator; MCSG, PF04017, PSI, MAR	90.19
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	90.18
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	90.05
2nnn_A	140	Probable transcriptional regulator; structural gen	89.9
2jsc_A	118	Transcriptional regulator RV1994C/MT2050; cadmium,	89.88
2hr3_A	147	Probable transcriptional regulator; MCSG, structur	89.74
3bj6_A	152	Transcriptional regulator, MARR family; helix-turn	89.69
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	89.68
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	89.62
3b73_A	111	PHIH1 repressor-like protein; winged-helix-turn-he	89.55
2pg4_A	95	Uncharacterized protein; structural genomics, join	89.38
2xig_A	150	Ferric uptake regulation protein; hpfur, transcrip	89.32
2gxg_A	146	146AA long hypothetical transcriptional regulator;	89.22
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	89.17
3bja_A	139	Transcriptional regulator, MARR family, putative;	89.17
1mzb_A	136	Ferric uptake regulation protein; ferric uptake re	89.1
2fbh_A	146	Transcriptional regulator PA3341; MARR, transcript	89.05
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	89.02
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	88.84
3f6v_A	151	Possible transcriptional regulator, ARSR family pr	88.77
3nrv_A	148	Putative transcriptional regulator (MARR/EMRR FAM;	88.61
3u2r_A	168	Regulatory protein MARR; structural genomics, PSI-	88.59
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	88.58
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	88.19
2a61_A	145	Transcriptional regulator TM0710; APC4350, MCSG, m	88.07
3k0l_A	162	Repressor protein; helix-turn-helix, structural ge	87.92
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	87.82
1j5y_A	187	Transcriptional regulator, biotin repressor famil;	87.7
3cdh_A	155	Transcriptional regulator, MARR family; helix-turn	87.59
3jw4_A	148	Transcriptional regulator, MARR/EMRR family; DNA-b	87.42
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	87.35
3k69_A	162	Putative transcription regulator; putative transcr	87.09
2rdp_A	150	Putative transcriptional regulator MARR; PFAM PF01	87.03
1uly_A	192	Hypothetical protein PH1932; helix-turn-helix, str	86.96
3g3z_A	145	NMB1585, transcriptional regulator, MARR family; t	86.89
3deu_A	166	Transcriptional regulator SLYA; MARR, WING-helix,	86.85
2o3f_A	111	Putative HTH-type transcriptional regulator YBBH;	86.51
1tbx_A	99	ORF F-93, hypothetical 11.0 kDa protein; sulfolobu	86.51
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	86.31
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	86.24
1lj9_A	144	Transcriptional regulator SLYA; HTH DNA binding pr	86.23
2qww_A	154	Transcriptional regulator, MARR family; YP_013417.	86.23
3mn2_A	108	Probable ARAC family transcriptional regulator; st	86.21
2eth_A	154	Transcriptional regulator, putative, MAR family; M	86.01
2fbi_A	142	Probable transcriptional regulator; MARR, APC5816,	86.0
3oop_A	143	LIN2960 protein; protein structure initiative, PSI	85.75
2bv6_A	142	MGRA, HTH-type transcriptional regulator MGRA; mul	85.7
1p6r_A	82	Penicillinase repressor; transcription regulation,	85.67
3oio_A	113	Transcriptional regulator (ARAC-type DNA-binding c	85.63
3cjn_A	162	Transcriptional regulator, MARR family; silicibact	85.59
1on2_A	142	Transcriptional regulator MNTR; helix-turn-helix,	85.55
2fbk_A	181	Transcriptional regulator, MARR family; winged-hel	85.5
2wte_A	244	CSA3; antiviral protein, viral resistance, winged	85.34
3mwm_A	139	ZUR, putative metal uptake regulation protein; FUR	85.26
2nyx_A	168	Probable transcriptional regulatory protein, RV14;	85.22
2pex_A	153	Transcriptional regulator OHRR; transcription regu	84.95
3iwf_A	107	Transcription regulator RPIR family; transcription	84.78
3oou_A	108	LIN2118 protein; protein structure initiative, PSI	84.6
2p5k_A	64	Arginine repressor; DNA-binding domain, winged hel	84.39
1xd7_A	145	YWNA; structural genomics, protein structure initi	84.37
3kor_A	119	Possible Trp repressor; putative DNA-binding Trp r	84.17
2w57_A	150	Ferric uptake regulation protein; gene regulation,	84.1
3mkl_A	120	HTH-type transcriptional regulator GADX; PSI2, MCS	84.09
2hzt_A	107	Putative HTH-type transcriptional regulator YTCD;	83.99
1z7u_A	112	Hypothetical protein EF0647; winged-helix-turn-hel	83.89
3f3x_A	144	Transcriptional regulator, MARR family, putative;	83.88
1s3j_A	155	YUSO protein; structural genomics, MARR transcript	83.88
2g9w_A	138	Conserved hypothetical protein; DNA-binding domain	83.58
4hbl_A	149	Transcriptional regulator, MARR family; HTH, trans	83.51
1jko_C	52	HIN recombinase, DNA-invertase HIN; water-mediated	82.85
2k9s_A	107	Arabinose operon regulatory protein; activator, ar	82.79
1z91_A	147	Organic hydroperoxide resistance transcriptional;	82.72
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	82.67
3s2w_A	159	Transcriptional regulator, MARR family; structural	82.17
3nqo_A	189	MARR-family transcriptional regulator; structural	81.9
2qvo_A	95	Uncharacterized protein AF_1382; PSI, structural g	81.84
2hoe_A	380	N-acetylglucosamine kinase; TM1224, structural gen	81.74
2p4w_A	202	Transcriptional regulatory protein ARSR family; ar	81.58
3hsr_A	140	HTH-type transcriptional regulator SARZ; helix-tur	81.5
1bl0_A	129	Protein (multiple antibiotic resistance protein),	81.32
4aik_A	151	Transcriptional regulator SLYA; transcription, tra	81.24
3lsg_A	103	Two-component response regulator YESN; structural	81.11
2dk5_A	91	DNA-directed RNA polymerase III 39 kDa polypeptide	80.82

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

Probab=99.43  E-value=1.4e-13  Score=101.26  Aligned_cols=62  Identities=23%  Similarity=0.309  Sum_probs=57.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           23 LKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        23 ~~~~~~l~~l~~g~~~~~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      .++...+++++.||+.+++|++|++|||||+|++.++|+|++|||+++|+++   ..+.|+||+|
T Consensus         6 ~~~~~~L~~l~~Gf~~s~~L~aa~eLglfd~L~~~~~p~t~~eLA~~~g~~~---~~l~rlLr~L   67 (353)
T 4a6d_A            6 DQAYRLLNDYANGFMVSQVLFAACELGVFDLLAEAPGPLDVAAVAAGVRASA---HGTELLLDIC   67 (353)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHSSSCBCHHHHHHHHTCCH---HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHcCHHHHHhcCCCCCCHHHHHHhhCcCH---HHHHHHHHHH
Confidence            3677788999999999999999999999999998779999999999999999   9999999975

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

Probab=99.41  E-value=2.9e-13  Score=99.95  Aligned_cols=70  Identities=24%  Similarity=0.372  Sum_probs=63.0

Q ss_pred             CcHHhHHHHHHHHHHHHHHHHHHHHHHHHHhCchHHHHhCC-CCCCHHHHHHhcCC--CCCChhhHHHHHhcC
Q 041968           18 SSSELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHG-QPMTLSQIASALDI--QKNKAHCIQRLMRIL   87 (87)
Q Consensus        18 ~~~~~~~~~~~l~~l~~g~~~~~aL~aaveLgI~d~L~~~~-gp~S~~ELA~~~~~--~~~~~~~L~RlLR~L   87 (87)
                      ...++.+++..++++.++++.+++|++|++|||||+|++++ +|+|++|||+++|+  +|.++..|+|+||+|
T Consensus        13 ~~~~~~~~~~~~~~l~~~~~~~~~l~~a~~Lgifd~L~~~g~~~~t~~eLA~~~g~~~~~~~~~~l~rlLr~L   85 (364)
T 3p9c_A           13 AASADEDACMFALQLASSSVLPMTLKNAIELGLLEILVAAGGKSLTPTEVAAKLPSAANPEAPDMVDRILRLL   85 (364)
T ss_dssp             CHHHHHHHHHHHHHHTTTTHHHHHHHHHHHHTHHHHHHHTTTCCBCHHHHHHTTTCTTCTTHHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHHhHHHHHHHHHHHHCChHHHHhhcCCCCCCHHHHHHhcCCCCCccchhhHHHHHHHH
Confidence            56778999999999999999999999999999999999865 79999999999998  884344999999975

>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=99.38  E-value=5.4e-13  Score=97.30  Aligned_cols=69  Identities=45%  Similarity=0.781  Sum_probs=62.6

Q ss_pred             cHHhHHHHHHHHHHHHHHHHHHHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           19 SSELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        19 ~~~~~~~~~~l~~l~~g~~~~~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      ..+.+++...+++++++++.+++|+++++|||||+|++.++|+|++|||+++|++|.+...++|+||+|
T Consensus        10 ~~~~~~a~~~l~~~~~~~~~~~~l~~a~~lgif~~L~~~~~~~t~~ela~~~~~~~~~~~~l~rlLr~L   78 (352)
T 1fp2_A           10 PSEIFKAQALLYKHIYAFIDSMSLKWAVEMNIPNIIQNHGKPISLSNLVSILQVPSSKIGNVRRLMRYL   78 (352)
T ss_dssp             STHHHHHHHHHHHHHTTHHHHHHHHHHHHTTHHHHHHHHTSCEEHHHHHHHHTCCGGGHHHHHHHHHHH
T ss_pred             hHHHhhHHHHHHHHHHHHHHHHHHHHHHHCChhhhhhhcCCCccHHHHHHHhCcCCCChHHHHHHHHHH
Confidence            467889999999999999999999999999999999976579999999999999765568999999975

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

Probab=99.36  E-value=7.5e-13  Score=97.32  Aligned_cols=66  Identities=17%  Similarity=0.183  Sum_probs=60.8

Q ss_pred             cHHhHHHHHHHHHHHHHHHHHHHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           19 SSELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        19 ~~~~~~~~~~l~~l~~g~~~~~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      ..+.+++..+++++++|++.+++|+++++|||||+|+++++|+|++|||+++|+++   ..++|+||+|
T Consensus         9 ~~~~~~a~~~l~~l~~g~~~~~~l~~a~~lgifd~L~~~~~~~t~~eLA~~~g~~~---~~l~rlLr~l   74 (363)
T 3dp7_A            9 QCTAAEAQRLAQEIAFGPVVFQVSRLMLKFGIFQLLSGKREGYTLQEISGRTGLTR---YAAQVLLEAS   74 (363)
T ss_dssp             CCCSTTHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHHTCTTCBCHHHHHHHHTCCH---HHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHHhhHHHHHHHHHHHHhCHHHHHHhcCCCCCHHHHHHHhCcCH---HHHHHHHHHH
Confidence            34577888999999999999999999999999999997568999999999999999   9999999975

>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=99.35  E-value=6.1e-13  Score=97.20  Aligned_cols=68  Identities=47%  Similarity=0.855  Sum_probs=60.9

Q ss_pred             HHhHHHHHHHHHHHHHHHHHHHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           20 SELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        20 ~~~~~~~~~l~~l~~g~~~~~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      ++.+++...+++++++++.+++|+++++|||||+|+++++|+|++|||+++|++|.++..|+|+||+|
T Consensus         5 ~~~~~~~~~l~~~~~~~~~~~~l~~a~~lgif~~L~~~~~~~t~~eLA~~~g~~~~~~~~l~rlLr~L   72 (358)
T 1zg3_A            5 SELYHAQIHLYKHVYNFVSSMALKSAMELGIADAIHNHGKPMTLSELASSLKLHPSKVNILHRFLRLL   72 (358)
T ss_dssp             SCCTTHHHHHHHHHTTHHHHHHHHHHHHHTHHHHHHHHTSCEEHHHHHHHTTCCTTTHHHHHHHHHHH
T ss_pred             HHhhhHHHHHHHHHHHHHHHHHHHHHHHCChHhHHhhcCCCcCHHHHHHhcCCCCcchHHHHHHHHHH
Confidence            45677788899999999999999999999999999976579999999999999765568999999985

>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=99.35  E-value=8.2e-13  Score=97.53  Aligned_cols=69  Identities=23%  Similarity=0.304  Sum_probs=59.4

Q ss_pred             cHHhHHHHHHHHHHHHHHHHHHHHHHHHHhCchHHHHhC---CCCCCHHHHHHhcC-CCCCChhhHHHHHhcC
Q 041968           19 SSELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKH---GQPMTLSQIASALD-IQKNKAHCIQRLMRIL   87 (87)
Q Consensus        19 ~~~~~~~~~~l~~l~~g~~~~~aL~aaveLgI~d~L~~~---~gp~S~~ELA~~~~-~~~~~~~~L~RlLR~L   87 (87)
                      ..++.++...++++++|++.+++|++|++|||||+|++.   ++|+|++|||+++| .+|.++..|+|+||+|
T Consensus        15 ~~~~~~~~~~~~~l~~~~~~~~~l~~a~~Lglfd~L~~~~gp~~~~t~~eLA~~~~~~~~~~~~~l~rlLr~L   87 (368)
T 3reo_A           15 HSSDEEANLFAMQLASAAVLPMALKAAIELDVLEIMAKSVPPSGYISPAEIAAQLPTTNPEAPVMLDRVLRLL   87 (368)
T ss_dssp             --CHHHHHHHHHHHHTTTHHHHHHHHHHHTTHHHHHHHHCCTTCCBCHHHHHTTSSCCCTTHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHHHHHCCchhHHhhcCCCCCCcCHHHHHHhcCcCCCcchhhHHHHHHHH
Confidence            446788889999999999999999999999999999974   35899999999998 5775456999999975

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

Probab=99.23  E-value=1.1e-11  Score=90.39  Aligned_cols=61  Identities=23%  Similarity=0.464  Sum_probs=56.8

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           22 LLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        22 ~~~~~~~l~~l~~g~~~~~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      ..++...++++++|++.+++|+++++|||||+|.  +||+|++|||+++|+++   ..++|+||+|
T Consensus        19 ~~~~~~~l~~~~~~~~~~~~l~~a~~lglf~~l~--~g~~t~~elA~~~g~~~---~~l~rlLr~l   79 (348)
T 3lst_A           19 RLQSALALYEEAMGYTYAAALRAAAAVGVADHLV--DGPRTPAELAAATGTDA---DALRRVLRLL   79 (348)
T ss_dssp             HHHHHHHHHHHHTTHHHHHHHHHHHHHTGGGGGT--TSCBCHHHHHHHHTCCH---HHHHHHHHHH
T ss_pred             CchHHHHHHHHHHHHHHHHHHHHHHHcCchhHhh--CCCCCHHHHHHHhCcCH---HHHHHHHHHH
Confidence            4578888999999999999999999999999998  47999999999999999   9999999975

>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=99.22  E-value=1.2e-11  Score=90.77  Aligned_cols=69  Identities=28%  Similarity=0.396  Sum_probs=57.2

Q ss_pred             cHHhHHHHHHHH--HHHHHHHHHHHHHHHHHhCchHHHHhCCCC---CCHHHHHHhcCC---CCCChhhHHHHHhcC
Q 041968           19 SSELLKAQAQVW--NCAFNYINSMSLKCAVELGIPDVIHKHGQP---MTLSQIASALDI---QKNKAHCIQRLMRIL   87 (87)
Q Consensus        19 ~~~~~~~~~~l~--~l~~g~~~~~aL~aaveLgI~d~L~~~~gp---~S~~ELA~~~~~---~~~~~~~L~RlLR~L   87 (87)
                      .++..+++..++  +++++++.+++|+++++|||||+|++.++|   +|++|||+++|+   +|.++..++|+||+|
T Consensus        16 ~~~~~~~~~~l~~~~l~~~~~~~~~l~~a~~lgif~~L~~~g~pg~~~t~~eLA~~~~~~~~~~~~~~~l~rlLr~L   92 (372)
T 1fp1_D           16 TSEQTEDSACLSAMVLTTNLVYPAVLNAAIDLNLFEIIAKATPPGAFMSPSEIASKLPASTQHSDLPNRLDRMLRLL   92 (372)
T ss_dssp             ---CCHHHHHHHHHHHHHTTHHHHHHHHHHHTTHHHHHHTCSSTTCCBCHHHHHTTSCGGGCCTTHHHHHHHHHHHH
T ss_pred             hhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHCChHHHHHhcCCCCCCcCHHHHHHhcCCCCCCCcChHHHHHHHHHH
Confidence            344566777777  999999999999999999999999974326   999999999999   655558999999975

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

Probab=99.19  E-value=3.6e-11  Score=86.51  Aligned_cols=59  Identities=25%  Similarity=0.304  Sum_probs=54.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           24 KAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        24 ~~~~~l~~l~~g~~~~~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      ++...+++++++++.+++|+++++|||||+|.  ++|.|++|||+++|+++   ..++|+||+|
T Consensus         7 ~~~~~l~~~~~~~~~~~~l~~~~~lgi~~~l~--~~~~t~~ela~~~~~~~---~~l~r~Lr~L   65 (334)
T 2ip2_A            7 AAARNLIQVVTGEWKSRCVYVATRLGLADLIE--SGIDSDETLAAAVGSDA---ERIHRLMRLL   65 (334)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTHHHHHH--TTCCSHHHHHHHHTCCH---HHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHcCcHHHHh--CCCCCHHHHHHHhCcCH---HHHHHHHHHH
Confidence            55678999999999999999999999999997  47999999999999999   9999999975

>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=99.18  E-value=3.6e-11  Score=87.69  Aligned_cols=64  Identities=20%  Similarity=0.292  Sum_probs=58.0

Q ss_pred             cHHhHHHHHHHHHHHH-HHHHHHHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           19 SSELLKAQAQVWNCAF-NYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        19 ~~~~~~~~~~l~~l~~-g~~~~~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      .++..+....++++++ |++.+++|+++++|||||.|++  +|.|++|||+++|+++   ..++|+||+|
T Consensus        24 ~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~lgif~~L~~--~~~t~~eLA~~~g~~~---~~l~rlLr~L   88 (359)
T 1x19_A           24 NNDLLNYYHRANELVFKGLIEFSCMKAAIELDLFSHMAE--GPKDLATLAADTGSVP---PRLEMLLETL   88 (359)
T ss_dssp             CCHHHHHHHHHHHHHTHHHHHHHHHHHHHHHTHHHHHTT--CCBCHHHHHHHHTCCH---HHHHHHHHHH
T ss_pred             ccccCCcchHHHHHHHHHHHHHHHHHHHHHcCcHHHHcC--CCCCHHHHHHHhCcCh---HHHHHHHHHH
Confidence            4456778888899987 8999999999999999999984  8999999999999999   9999999975

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

Probab=99.18  E-value=2.1e-11  Score=89.71  Aligned_cols=61  Identities=26%  Similarity=0.442  Sum_probs=56.4

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           22 LLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        22 ~~~~~~~l~~l~~g~~~~~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      +.+....+++++++++.+++|+++++|||||+|.  ++|+|++|||+++|+++   ..++|+||+|
T Consensus        35 ~~~~~~~l~~l~~~~~~~~~l~~a~~lglf~~l~--~g~~t~~eLA~~~g~~~---~~l~rlLr~L   95 (369)
T 3gwz_A           35 RAAAEETVNDILQGAWKARAIHVAVELGVPELLQ--EGPRTATALAEATGAHE---QTLRRLLRLL   95 (369)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHTTGGGGT--TSCEEHHHHHHHHTCCH---HHHHHHHHHH
T ss_pred             CChHHHHHHHHHHHHHHHHHHHHHHHCChhhhhc--CCCCCHHHHHHHHCcCH---HHHHHHHHHH
Confidence            4566678999999999999999999999999998  47999999999999999   9999999975

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

Probab=99.11  E-value=3.3e-11  Score=86.94  Aligned_cols=55  Identities=25%  Similarity=0.312  Sum_probs=51.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           28 QVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        28 ~l~~l~~g~~~~~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      .+++++.||+.+++|+++++|||||+|.  +||+|++|||+++|+++   ..++|+||+|
T Consensus         8 ~l~~~~~g~~~~~~l~~a~~lglf~~l~--~g~~t~~elA~~~~~~~---~~l~rlLr~l   62 (332)
T 3i53_A            8 IGLRALADLATPMAVRVAATLRVADHIA--AGHRTAAEIASAAGAHA---DSLDRLLRHL   62 (332)
T ss_dssp             SCHHHHTCCHHHHHHHHHHHHTHHHHHH--TTCCBHHHHHHHHTCCH---HHHHHHHHHH
T ss_pred             HHHHHHHhhHHHHHHHHHHHcChHHHHh--cCCCCHHHHHHHHCcCH---HHHHHHHHHH
Confidence            4678899999999999999999999998  47999999999999999   9999999975

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

Probab=99.11  E-value=7.2e-11  Score=85.44  Aligned_cols=57  Identities=18%  Similarity=0.158  Sum_probs=52.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           25 AQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        25 ~~~~l~~l~~g~~~~~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      ....+++++++++.+++|+++++|||||+|.  + |+|++|||+++|+++   ..++|+||+|
T Consensus        24 ~p~~l~~~~~~~~~~~~l~~a~~lgif~~l~--~-~~t~~elA~~~~~~~---~~l~rlLr~L   80 (352)
T 3mcz_A           24 SVVDLVKLSDQYRQSAILHYAVADKLFDLTQ--T-GRTPAEVAASFGMVE---GKAAILLHAL   80 (352)
T ss_dssp             SHHHHHHHHHTHHHHHHHHHHHHTTHHHHTT--S-CBCHHHHHHHHTCCH---HHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHCChHHHhC--C-CCCHHHHHHHhCcCh---HHHHHHHHHH
Confidence            3344899999999999999999999999997  3 999999999999999   9999999975

>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=99.10  E-value=4e-11  Score=87.24  Aligned_cols=60  Identities=23%  Similarity=0.284  Sum_probs=54.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           23 LKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        23 ~~~~~~l~~l~~g~~~~~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      .+....+++++++++.+++|+++++|||||.|.  ++|+|+.|||+++|+++   ..+.|+||+|
T Consensus        14 ~~~~~~l~~~~~~~~~~~~l~~~~~l~i~~~l~--~~~~t~~eLA~~~g~~~---~~l~r~Lr~L   73 (374)
T 1qzz_A           14 DQDLDVLLKNLGNLVTPMALRVAATLRLVDHLL--AGADTLAGLADRTDTHP---QALSRLVRHL   73 (374)
T ss_dssp             HHHHHHHHHTTTCCHHHHHHHHHHHTTHHHHHH--TTCCSHHHHHHHHTCCH---HHHHHHHHHH
T ss_pred             chHHHHHHHHHHhhHHHHHHHHHHHcChHHHHh--CCCCCHHHHHHHhCcCH---HHHHHHHHHH
Confidence            344557889999999999999999999999996  48999999999999999   9999999975

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

Probab=99.07  E-value=1.1e-10  Score=83.61  Aligned_cols=56  Identities=23%  Similarity=0.268  Sum_probs=52.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           27 AQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        27 ~~l~~l~~g~~~~~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      ..+++++++++.+++|+++++|||||.|++  +|.|++|||+++|+++   ..++|+||+|
T Consensus         8 ~~l~~~~~~~~~~~~l~~~~~l~i~~~l~~--~~~t~~ela~~~~~~~---~~l~r~L~~L   63 (335)
T 2r3s_A            8 ALFFNTVNAYQRSAAIKAAVELNVFTAISQ--GIESSQSLAQKCQTSE---RGMRMLCDYL   63 (335)
T ss_dssp             HHHHHHHTTHHHHHHHHHHHHTTHHHHHTT--SEECHHHHHHHHTCCH---HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcChHHHHhc--CCCCHHHHHHHhCCCc---hHHHHHHHHH
Confidence            467889999999999999999999999984  8999999999999999   9999999975

>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=98.89  E-value=1.8e-09  Score=78.29  Aligned_cols=57  Identities=21%  Similarity=0.222  Sum_probs=52.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           26 QAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        26 ~~~l~~l~~g~~~~~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      ...+++++++++.+++|+++++|||||.|.  ++|.|+.|||+.+|+++   ..+.|+||+|
T Consensus        20 ~~~~~~~~~~~~~~~~l~~~~~l~i~~~l~--~~~~t~~ela~~~~~~~---~~l~r~L~~L   76 (360)
T 1tw3_A           20 ALRTLIRLGSLHTPMVVRTAATLRLVDHIL--AGARTVKALAARTDTRP---EALLRLIRHL   76 (360)
T ss_dssp             HHHHHHHHHCSHHHHHHHHHHHTTHHHHHH--TTCCBHHHHHHHHTCCH---HHHHHHHHHH
T ss_pred             hHHHHHHHHhHHHHHHHHHHHHhCHHHHHh--CCCCCHHHHHHHhCcCH---HHHHHHHHHH
Confidence            456789999999999999999999999996  58999999999999999   9999999975

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

Probab=96.11  E-value=0.0017  Score=37.30  Aligned_cols=38  Identities=21%  Similarity=0.406  Sum_probs=31.5

Q ss_pred             HhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           47 ELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        47 eLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      +..|.+.|.++++|+|..|||+.+|++.   ..+.|++..|
T Consensus        12 ~~~IL~~L~~~~~~~s~~eLA~~lglsr---~tv~~~l~~L   49 (67)
T 2heo_A           12 EQKILQVLSDDGGPVAIFQLVKKCQVPK---KTLNQVLYRL   49 (67)
T ss_dssp             HHHHHHHHHHHCSCEEHHHHHHHHCSCH---HHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCcCHHHHHHHHCcCH---HHHHHHHHHH
Confidence            5568888877567999999999999998   8888887643

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

Probab=95.25  E-value=0.0068  Score=35.25  Aligned_cols=39  Identities=15%  Similarity=0.293  Sum_probs=31.9

Q ss_pred             HHhCchHHHHhCC-CCCCHHHHHHhc-----CCCCCChhhHHHHHhcC
Q 041968           46 VELGIPDVIHKHG-QPMTLSQIASAL-----DIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        46 veLgI~d~L~~~~-gp~S~~ELA~~~-----~~~~~~~~~L~RlLR~L   87 (87)
                      .+..|.+.|.+.+ ++.|+.||++.+     ++++   ..++|.|+.|
T Consensus        18 ~r~~IL~~l~~~~~~~~s~~el~~~l~~~~~~is~---~TVyR~L~~L   62 (83)
T 2fu4_A           18 PRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGL---ATVYRVLNQF   62 (83)
T ss_dssp             HHHHHHHHHTSGGGSSBCHHHHHHHHHHTTCCCCH---HHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCCCH---hhHHHHHHHH
Confidence            3456888887655 799999999999     7887   8999998754

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

Probab=95.12  E-value=0.0067  Score=43.14  Aligned_cols=37  Identities=19%  Similarity=0.388  Sum_probs=30.2

Q ss_pred             hCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           48 LGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        48 LgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      +.|.+.++..++++|+.|||+.+|.+.   ..++|+|+.|
T Consensus        33 l~IL~~l~~~~~~ltl~eia~~lgl~k---sTv~RlL~tL   69 (275)
T 3mq0_A           33 VRILDLVAGSPRDLTAAELTRFLDLPK---SSAHGLLAVM   69 (275)
T ss_dssp             HHHHHHHHHCSSCEEHHHHHHHHTCC-----CHHHHHHHH
T ss_pred             HHHHHHHhhCCCCCCHHHHHHHHCcCH---HHHHHHHHHH
Confidence            457888887778899999999999999   8899999754

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

Probab=94.77  E-value=0.01  Score=37.32  Aligned_cols=39  Identities=13%  Similarity=0.284  Sum_probs=31.8

Q ss_pred             HHhCchHHHHhCCCC-CCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           46 VELGIPDVIHKHGQP-MTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        46 veLgI~d~L~~~~gp-~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      .+..|...|.+.++| +|+.|||+.+++++   ..++|.++.|
T Consensus        27 ~e~~il~~L~~~~~~~~t~~eLa~~l~~s~---sTV~r~L~~L   66 (123)
T 3r0a_A           27 ADLNVMKSFLNEPDRWIDTDALSKSLKLDV---STVQRSVKKL   66 (123)
T ss_dssp             HHHHHHHHHHHSTTCCEEHHHHHHHHTSCH---HHHHHHHHHH
T ss_pred             HHHHHHHHHHHCCCCCcCHHHHHHHHCcCH---HHHHHHHHHH
Confidence            355677778776677 99999999999998   8899888653

>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=94.41  E-value=0.019  Score=39.86  Aligned_cols=37  Identities=24%  Similarity=0.349  Sum_probs=30.9

Q ss_pred             hCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           48 LGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        48 LgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      +.|.+.|.+.++++|+.|||+.+|.++   ..++|+|+.|
T Consensus        11 l~iL~~l~~~~~~~~~~ela~~~gl~~---stv~r~l~~L   47 (249)
T 1mkm_A           11 FEILDFIVKNPGDVSVSEIAEKFNMSV---SNAYKYMVVL   47 (249)
T ss_dssp             HHHHHHHHHCSSCBCHHHHHHHTTCCH---HHHHHHHHHH
T ss_pred             HHHHHHHHhCCCCCCHHHHHHHHCcCH---HHHHHHHHHH
Confidence            456777877656899999999999999   8899998754

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

Probab=94.33  E-value=0.032  Score=33.18  Aligned_cols=34  Identities=21%  Similarity=0.376  Sum_probs=28.5

Q ss_pred             chHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           50 IPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        50 I~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      |.+.|.+. |.+|+.|||+.+++++   ..++|-|..|
T Consensus         7 Il~~L~~~-g~vsv~eLa~~l~VS~---~TIRrdL~~L   40 (78)
T 1xn7_A            7 VRDLLALR-GRMEAAQISQTLNTPQ---PMINAMLQQL   40 (78)
T ss_dssp             HHHHHHHS-CSBCHHHHHHHTTCCH---HHHHHHHHHH
T ss_pred             HHHHHHHc-CCCcHHHHHHHHCcCH---HHHHHHHHHH
Confidence            56677764 8999999999999999   9999988653

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

Probab=94.17  E-value=0.017  Score=34.34  Aligned_cols=35  Identities=20%  Similarity=0.367  Sum_probs=27.1

Q ss_pred             chHHHHhC-----CCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           50 IPDVIHKH-----GQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        50 I~d~L~~~-----~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      |.+.|.+.     |+|.|+.|||+.+|+.+   ..+.|-|..|
T Consensus         9 IL~~I~~~i~~~~g~~psv~EIa~~lgvS~---~TVrr~L~~L   48 (77)
T 2jt1_A            9 IISIVQERQNMDDGAPVKTRDIADAAGLSI---YQVRLYLEQL   48 (77)
T ss_dssp             HHHHHHHHHHHHTTSCEEHHHHHHHHTCCH---HHHHHHHHHH
T ss_pred             HHHHHHHHHhhccCCCcCHHHHHHHHCCCH---HHHHHHHHHH
Confidence            45555544     78999999999999987   7788877654

>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=94.11  E-value=0.017  Score=40.14  Aligned_cols=37  Identities=22%  Similarity=0.420  Sum_probs=30.8

Q ss_pred             hCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           48 LGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        48 LgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      +.|.+.|.+.++++|+.|||+.+|+++   ..++|+|+.|
T Consensus         9 l~iL~~l~~~~~~~s~~ela~~~gl~~---stv~r~l~~L   45 (241)
T 2xrn_A            9 ASIMRALGSHPHGLSLAAIAQLVGLPR---STVQRIINAL   45 (241)
T ss_dssp             HHHHHHHHTCTTCEEHHHHHHHTTSCH---HHHHHHHHHH
T ss_pred             HHHHHHHHhCCCCCCHHHHHHHHCcCH---HHHHHHHHHH
Confidence            456777876557899999999999999   8899998754

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

Probab=93.86  E-value=0.02  Score=33.56  Aligned_cols=39  Identities=5%  Similarity=0.058  Sum_probs=31.0

Q ss_pred             HHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           45 AVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        45 aveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      -.++.|...|.+ +++.|..|||+.+|+++   ..+.|.++.|
T Consensus        24 ~~~~~il~~l~~-~~~~s~~ela~~l~is~---~tvs~~l~~L   62 (99)
T 3cuo_A           24 PKRLLILCMLSG-SPGTSAGELTRITGLSA---SATSQHLARM   62 (99)
T ss_dssp             HHHHHHHHHHTT-CCSEEHHHHHHHHCCCH---HHHHHHHHHH
T ss_pred             hHHHHHHHHHHh-CCCcCHHHHHHHHCcCH---HHHHHHHHHH
Confidence            456677777865 47999999999999998   8888877643

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

Probab=93.63  E-value=0.048  Score=31.61  Aligned_cols=35  Identities=20%  Similarity=0.302  Sum_probs=28.2

Q ss_pred             CchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           49 GIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        49 gI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      .|.+.|.+. ++.|..|||+.+|+++   ..+.|.|+.|
T Consensus         4 ~Il~~L~~~-~~~s~~eLa~~lgvs~---~tv~r~L~~L   38 (81)
T 2htj_A            4 EILEFLNRH-NGGKTAEIAEALAVTD---YQARYYLLLL   38 (81)
T ss_dssp             HHHHHHHHS-CCCCHHHHHHHHTSCH---HHHHHHHHHH
T ss_pred             HHHHHHHHc-CCCCHHHHHHHHCcCH---HHHHHHHHHH
Confidence            466777764 7899999999999998   8888887643

>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=93.58  E-value=0.0075  Score=42.42  Aligned_cols=37  Identities=22%  Similarity=0.269  Sum_probs=30.7

Q ss_pred             hCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           48 LGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        48 LgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      +.|.+.+.+.++++|+.|||+.+|.++   ..++|+|+.|
T Consensus         9 l~IL~~l~~~~~~lsl~eia~~lgl~k---sT~~RlL~tL   45 (260)
T 3r4k_A            9 LTLLTYFNHGRLEIGLSDLTRLSGMNK---ATVYRLMSEL   45 (260)
T ss_dssp             HHHHTTCBTTBSEEEHHHHHHHHCSCH---HHHHHHHHHH
T ss_pred             HHHHHHHhhCCCCCCHHHHHHHHCcCH---HHHHHHHHHH
Confidence            346777776558999999999999999   8999999754

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

Probab=93.55  E-value=0.035  Score=33.82  Aligned_cols=34  Identities=15%  Similarity=0.311  Sum_probs=28.5

Q ss_pred             chHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           50 IPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        50 I~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      |.+.|.+. |.+|+.|||+.+++++   ..++|.|..|
T Consensus         7 Il~~L~~~-g~vsv~eLA~~l~VS~---~TIRrDL~~L   40 (87)
T 2k02_A            7 VRDMLALQ-GRMEAKQLSARLQTPQ---PLIDAMLERM   40 (87)
T ss_dssp             HHHHHHHS-CSEEHHHHHHHTTCCH---HHHHHHHHHH
T ss_pred             HHHHHHHc-CCCcHHHHHHHHCcCH---HHHHHHHHHH
Confidence            56677764 8999999999999999   9999988653

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

Probab=93.34  E-value=0.067  Score=33.42  Aligned_cols=27  Identities=26%  Similarity=0.493  Sum_probs=24.1

Q ss_pred             CCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           58 GQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        58 ~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      +++.|+.|||+.+++++   ..+.|+|+.|
T Consensus        24 ~~~~s~~ela~~~~i~~---~~v~~il~~L   50 (129)
T 2y75_A           24 EGPTSLKSIAQTNNLSE---HYLEQLVSPL   50 (129)
T ss_dssp             SCCBCHHHHHHHTTSCH---HHHHHHHHHH
T ss_pred             CCcCCHHHHHHHHCcCH---HHHHHHHHHH
Confidence            47899999999999999   9999998754

>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=93.08  E-value=0.049  Score=32.35  Aligned_cols=40  Identities=15%  Similarity=0.265  Sum_probs=31.3

Q ss_pred             HHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           42 LKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        42 L~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      +.--.++.|.+.| +  ++.|..|||+.+++++   ..+.|.++.|
T Consensus        28 l~~~~r~~Il~~L-~--~~~~~~eLa~~l~is~---~tv~~~L~~L   67 (96)
T 1y0u_A           28 VTNPVRRKILRML-D--KGRSEEEIMQTLSLSK---KQLDYHLKVL   67 (96)
T ss_dssp             HSCHHHHHHHHHH-H--TTCCHHHHHHHHTCCH---HHHHHHHHHH
T ss_pred             hCCHHHHHHHHHH-c--CCCCHHHHHHHHCcCH---HHHHHHHHHH
Confidence            3344566788888 4  6899999999999998   8888887753

>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=93.06  E-value=0.032  Score=32.67  Aligned_cols=42  Identities=26%  Similarity=0.347  Sum_probs=32.8

Q ss_pred             HHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           41 SLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        41 aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      ++.--.++.|...|... ++.|..|||+.+++++   ..+.|.++.
T Consensus        12 ~l~~~~~~~iL~~L~~~-~~~~~~ela~~l~is~---~tvs~~l~~   53 (100)
T 1ub9_A           12 ILGNPVRLGIMIFLLPR-RKAPFSQIQKVLDLTP---GNLDSHIRV   53 (100)
T ss_dssp             HHHSHHHHHHHHHHHHH-SEEEHHHHHHHTTCCH---HHHHHHHHH
T ss_pred             ccCChHHHHHHHHHHhc-CCcCHHHHHHHHCcCH---HHHHHHHHH
Confidence            44445667778877653 6899999999999999   888888764

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

Probab=93.05  E-value=0.051  Score=33.91  Aligned_cols=42  Identities=14%  Similarity=0.192  Sum_probs=32.8

Q ss_pred             HHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           42 LKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        42 L~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      |.--.++.|+..|.. .++.|+.|||+.+|+++   ..+.|.|+.|
T Consensus        39 l~~~~rl~IL~~L~~-~~~~s~~eLa~~l~is~---stvs~~L~~L   80 (122)
T 1u2w_A           39 IADENRAKITYALCQ-DEELCVCDIANILGVTI---ANASHHLRTL   80 (122)
T ss_dssp             HHSHHHHHHHHHHHH-SSCEEHHHHHHHHTCCH---HHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHHH-CCCcCHHHHHHHHCcCH---HHHHHHHHHH
Confidence            333456778888875 37899999999999998   8888877653

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

Probab=93.01  E-value=0.021  Score=39.92  Aligned_cols=37  Identities=14%  Similarity=0.301  Sum_probs=30.0

Q ss_pred             hCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           48 LGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        48 LgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      +.|.+.|.+.++++|+.|||+.+|+++   ..++|+|+.|
T Consensus        17 l~iL~~l~~~~~~~~~~eia~~~gl~~---stv~r~l~~L   53 (257)
T 2g7u_A           17 FAVLLAFDAQRPNPTLAELATEAGLSR---PAVRRILLTL   53 (257)
T ss_dssp             HHHHHTCSSSCSSCBHHHHHHHHTCCH---HHHHHHHHHH
T ss_pred             HHHHHHHHhCCCCCCHHHHHHHHCcCH---HHHHHHHHHH
Confidence            345666765557899999999999999   8899998753

>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=92.78  E-value=0.08  Score=31.60  Aligned_cols=36  Identities=8%  Similarity=0.224  Sum_probs=28.1

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      ..+.|...|.  .||.|+.|||+.+|+++   ..+.+-|+.
T Consensus        24 ~r~~Il~~L~--~~~~~~~ela~~l~is~---~tvs~~L~~   59 (102)
T 3pqk_A           24 VRLMLVCTLV--EGEFSVGELEQQIGIGQ---PTLSQQLGV   59 (102)
T ss_dssp             HHHHHHHHHH--TCCBCHHHHHHHHTCCT---THHHHHHHH
T ss_pred             HHHHHHHHHH--hCCCCHHHHHHHHCcCH---HHHHHHHHH
Confidence            4556677776  37899999999999998   777777664

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

Probab=92.76  E-value=0.021  Score=40.07  Aligned_cols=36  Identities=11%  Similarity=0.286  Sum_probs=29.0

Q ss_pred             CchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           49 GIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        49 gI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      .|.+.|.+.++++|+.|||+.+|+++   ..++|+|+.|
T Consensus        27 ~iL~~l~~~~~~~~~~eia~~~gl~k---stv~r~l~tL   62 (260)
T 2o0y_A           27 DLLELFDAAHPTRSLKELVEGTKLPK---TTVVRLVATM   62 (260)
T ss_dssp             HHHTTCBTTBSSBCHHHHHHHHCCCH---HHHHHHHHHH
T ss_pred             HHHHHHhhCCCCcCHHHHHHHHCcCH---HHHHHHHHHH
Confidence            45566654457999999999999999   8899998754

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

Probab=92.68  E-value=0.22  Score=30.26  Aligned_cols=37  Identities=19%  Similarity=0.466  Sum_probs=29.5

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      .++.|+..|.+  ++.|..|||+.+++++   ..+.|.++.|
T Consensus        33 ~~~~il~~L~~--~~~s~~ela~~l~is~---stvsr~l~~L   69 (119)
T 2lkp_A           33 SRLMILTQLRN--GPLPVTDLAEAIGMEQ---SAVSHQLRVL   69 (119)
T ss_dssp             HHHHHHHHHHH--CCCCHHHHHHHHSSCH---HHHHHHHHHH
T ss_pred             HHHHHHHHHHH--CCCCHHHHHHHHCcCH---HHHHHHHHHH
Confidence            45667777775  5799999999999998   8888877643

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

Probab=92.66  E-value=0.019  Score=40.40  Aligned_cols=37  Identities=27%  Similarity=0.399  Sum_probs=30.1

Q ss_pred             hCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           48 LGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        48 LgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      +.|.+.|...++++|+.|||+.+|.++   ..++|+|+.|
T Consensus        24 l~iL~~l~~~~~~~~~~eia~~~gl~~---stv~r~l~tL   60 (265)
T 2ia2_A           24 LAVIRCFDHRNQRRTLSDVARATDLTR---ATARRFLLTL   60 (265)
T ss_dssp             HHHHHTCCSSCSSEEHHHHHHHHTCCH---HHHHHHHHHH
T ss_pred             HHHHHHHHhCCCCCCHHHHHHHHCcCH---HHHHHHHHHH
Confidence            345676765458899999999999999   8899998754

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

Probab=92.57  E-value=0.045  Score=33.85  Aligned_cols=42  Identities=17%  Similarity=0.283  Sum_probs=32.5

Q ss_pred             HHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           41 SLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        41 aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      +|.--..+.|...|.  .+|.|+.|||+.+|+++   ..+.+.|+.|
T Consensus        14 al~~~~R~~Il~~L~--~~~~~~~eLa~~l~is~---~tvs~hL~~L   55 (118)
T 3f6o_A           14 ALADPTRRAVLGRLS--RGPATVSELAKPFDMAL---PSFMKHIHFL   55 (118)
T ss_dssp             HHTSHHHHHHHHHHH--TCCEEHHHHHTTCCSCH---HHHHHHHHHH
T ss_pred             HhCCHHHHHHHHHHH--hCCCCHHHHHHHhCcCH---HHHHHHHHHH
Confidence            333446777888887  48999999999999998   7787777643

>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=92.57  E-value=0.054  Score=31.76  Aligned_cols=38  Identities=21%  Similarity=0.419  Sum_probs=29.4

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      .+..|...|... ++.|..|||+.+++++   ..+.|.++.|
T Consensus        21 ~~~~il~~l~~~-~~~s~~ela~~l~is~---~tv~~~l~~L   58 (109)
T 1sfx_A           21 SDVRIYSLLLER-GGMRVSEIARELDLSA---RFVRDRLKVL   58 (109)
T ss_dssp             HHHHHHHHHHHH-CCBCHHHHHHHHTCCH---HHHHHHHHHH
T ss_pred             HHHHHHHHHHHc-CCCCHHHHHHHHCCCH---HHHHHHHHHH
Confidence            345566667653 7899999999999999   8888887643

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

Probab=92.39  E-value=0.074  Score=32.16  Aligned_cols=37  Identities=11%  Similarity=0.352  Sum_probs=28.7

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      .++.|+..|.+  ++.|+.|||+.+|+++   ..+.|.|+.|
T Consensus        27 ~r~~IL~~L~~--~~~~~~ela~~l~is~---stvs~~L~~L   63 (106)
T 1r1u_A           27 NRIRIMELLSV--SEASVGHISHQLNLSQ---SNVSHQLKLL   63 (106)
T ss_dssp             HHHHHHHHHHH--CCBCHHHHHHHHTCCH---HHHHHHHHHH
T ss_pred             HHHHHHHHHHh--CCCCHHHHHHHHCcCH---HHHHHHHHHH
Confidence            44566666763  7899999999999998   7788877643

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

Probab=92.35  E-value=0.077  Score=35.19  Aligned_cols=43  Identities=23%  Similarity=0.409  Sum_probs=32.1

Q ss_pred             HHHHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           38 NSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        38 ~~~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      .-.+|++.+.|..    ...++|.|+.|||+.+++++   ..+.++|+.|
T Consensus        26 ~~yAlr~L~~LA~----~~~~~~~s~~eIA~~~~i~~---~~l~kil~~L   68 (159)
T 3lwf_A           26 GRYGLTITLELAK----RIGDGPISLRSIAQDKNLSE---HYLEQLIGPL   68 (159)
T ss_dssp             HHHHHHHHHHHHH----TTTSCCBCHHHHHHHHTCCH---HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHh----cCCCCCcCHHHHHHHHCcCH---HHHHHHHHHH
Confidence            3456666666543    22247899999999999999   9999998754

>2lnb_A Z-DNA-binding protein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative, immune system; NMR {Homo sapiens}

Probab=92.19  E-value=0.052  Score=32.84  Aligned_cols=34  Identities=21%  Similarity=0.411  Sum_probs=26.9

Q ss_pred             CchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968           49 GIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR   85 (87)
Q Consensus        49 gI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR   85 (87)
                      .|.+.|.++|+|+++.|||+.+|+|.   --+.++|.
T Consensus        23 kVLe~LkeaG~PlkageIae~~GvdK---KeVdKaik   56 (80)
T 2lnb_A           23 RILQVLTEAGSPVKLAQLVKECQAPK---RELNQVLY   56 (80)
T ss_dssp             HHHHHHHHHTSCEEHHHHHHHHTSCH---HHHHHHHH
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHCCCH---HHHHHHHH
Confidence            45677777789999999999999987   55555553

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

Probab=92.18  E-value=0.37  Score=30.14  Aligned_cols=37  Identities=8%  Similarity=0.259  Sum_probs=27.6

Q ss_pred             HhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           47 ELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        47 eLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      ++.|...|...++++|..|||+.+++++   ..+.|+++-
T Consensus        49 ~~~iL~~L~~~~~~~~~~ela~~l~i~~---~tvs~~l~~   85 (160)
T 3boq_A           49 KFDAMAQLARNPDGLSMGKLSGALKVTN---GNVSGLVNR   85 (160)
T ss_dssp             HHHHHHHHHHCTTCEEHHHHHHHCSSCC---SCHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHCCCh---hhHHHHHHH
Confidence            4446666744457999999999999998   667776653

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

Probab=92.12  E-value=0.039  Score=32.75  Aligned_cols=39  Identities=15%  Similarity=0.347  Sum_probs=30.8

Q ss_pred             HHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           44 CAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        44 aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      --.++.|...|.+  ++.|+.|||+.+|+++   ..+.|.|+.|
T Consensus        22 ~~~r~~Il~~L~~--~~~~~~ela~~l~is~---~tvs~~L~~L   60 (98)
T 3jth_A           22 NERRLQILCMLHN--QELSVGELCAKLQLSQ---SALSQHLAWL   60 (98)
T ss_dssp             SHHHHHHHHHTTT--SCEEHHHHHHHHTCCH---HHHHHHHHHH
T ss_pred             CHHHHHHHHHHhc--CCCCHHHHHHHHCcCH---HHHHHHHHHH
Confidence            3355677777874  7999999999999998   7788877653

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

Probab=92.07  E-value=0.072  Score=32.05  Aligned_cols=37  Identities=16%  Similarity=0.253  Sum_probs=29.0

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      .++.|...|.  .++.|..|||+.+|+++   ..+.|.++.|
T Consensus        22 ~r~~IL~~L~--~~~~~~~ela~~l~is~---~tv~~~l~~L   58 (114)
T 2oqg_A           22 TRWEILTELG--RADQSASSLATRLPVSR---QAIAKHLNAL   58 (114)
T ss_dssp             HHHHHHHHHH--HSCBCHHHHHHHSSSCH---HHHHHHHHHH
T ss_pred             HHHHHHHHHH--cCCCCHHHHHHHHCcCH---HHHHHHHHHH
Confidence            4556677774  37899999999999999   8888887643

>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=92.04  E-value=0.49  Score=29.10  Aligned_cols=38  Identities=16%  Similarity=0.289  Sum_probs=27.0

Q ss_pred             HHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           45 AVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        45 aveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      ..+..|...|... ++.|..|||+.+++++   ..+.|+++-
T Consensus        37 ~~~~~vL~~l~~~-~~~t~~eLa~~l~~~~---~tvs~~l~~   74 (142)
T 3ech_A           37 PPDVHVLKLIDEQ-RGLNLQDLGRQMCRDK---ALITRKIRE   74 (142)
T ss_dssp             HHHHHHHHHHHHT-TTCCHHHHHHHHC------CHHHHHHHH
T ss_pred             HHHHHHHHHHHhC-CCcCHHHHHHHhCCCH---HHHHHHHHH
Confidence            4566677778764 6899999999999998   777777653

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

Probab=91.98  E-value=0.093  Score=31.99  Aligned_cols=36  Identities=19%  Similarity=0.229  Sum_probs=27.9

Q ss_pred             HhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           47 ELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        47 eLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      ++.|...|.  .++.|+.|||+.+|+++   ..+.|.|+.|
T Consensus        27 r~~IL~~L~--~~~~s~~eLa~~lgis~---stvs~~L~~L   62 (108)
T 2kko_A           27 RLQILDLLA--QGERAVEAIATATGMNL---TTASANLQAL   62 (108)
T ss_dssp             THHHHHHHT--TCCEEHHHHHHHHTCCH---HHHHHHHHHH
T ss_pred             HHHHHHHHH--cCCcCHHHHHHHHCcCH---HHHHHHHHHH
Confidence            345566666  37899999999999998   8788877643

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

Probab=91.72  E-value=0.092  Score=33.19  Aligned_cols=41  Identities=10%  Similarity=0.175  Sum_probs=32.9

Q ss_pred             HHHHhCchHHHHhCCCCCCHHHHHHhc-----CCCCCChhhHHHHHhcC
Q 041968           44 CAVELGIPDVIHKHGQPMTLSQIASAL-----DIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        44 aaveLgI~d~L~~~~gp~S~~ELA~~~-----~~~~~~~~~L~RlLR~L   87 (87)
                      +-.+.-|.+.|.+.+++.|+.||.+.+     +++.   ..++|.|+.|
T Consensus        10 T~qR~~Il~~l~~~~~~~sa~ei~~~l~~~~~~is~---~TVYR~L~~L   55 (131)
T 2o03_A           10 TRQRAAISTLLETLDDFRSAQELHDELRRRGENIGL---TTVYRTLQSM   55 (131)
T ss_dssp             HHHHHHHHHHHHHCCSCEEHHHHHHHHHHTTCCCCH---HHHHHHHHHH
T ss_pred             CHHHHHHHHHHHhCCCCCCHHHHHHHHHHhCCCCCH---hhHHHHHHHH
Confidence            445667888888767899999999998     5566   8899998764

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

Probab=91.34  E-value=0.074  Score=32.16  Aligned_cols=36  Identities=14%  Similarity=0.159  Sum_probs=27.5

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      ....|.+.|.++ | +|+.|||+.+|++.   ..++|.|.-
T Consensus        18 ~~~~IL~lL~~~-g-~sa~eLAk~LgiSk---~aVr~~L~~   53 (82)
T 1oyi_A           18 IVCEAIKTIGIE-G-ATAAQLTRQLNMEK---REVNKALYD   53 (82)
T ss_dssp             HHHHHHHHHSSS-T-EEHHHHHHHSSSCH---HHHHHHHHH
T ss_pred             HHHHHHHHHHHc-C-CCHHHHHHHHCcCH---HHHHHHHHH
Confidence            445566777753 4 99999999999998   777777653

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

Probab=91.34  E-value=0.08  Score=31.64  Aligned_cols=36  Identities=14%  Similarity=0.120  Sum_probs=28.1

Q ss_pred             HhCchHHHHhCCCCCCHHHHHHhcCCCCCChh-hHHHHHhc
Q 041968           47 ELGIPDVIHKHGQPMTLSQIASALDIQKNKAH-CIQRLMRI   86 (87)
Q Consensus        47 eLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~-~L~RlLR~   86 (87)
                      +-.|.+.|.+. ||.|+.+||+.+|+.+   . .+.|.|..
T Consensus        13 ~~~IL~~Lk~~-g~~ta~eiA~~Lgit~---~~aVr~hL~~   49 (79)
T 1xmk_A           13 KEKICDYLFNV-SDSSALNLAKNIGLTK---ARDINAVLID   49 (79)
T ss_dssp             HHHHHHHHHHT-CCEEHHHHHHHHCGGG---HHHHHHHHHH
T ss_pred             HHHHHHHHHHc-CCcCHHHHHHHcCCCc---HHHHHHHHHH
Confidence            34566677764 7999999999999999   7 77777653

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

Probab=91.34  E-value=0.093  Score=33.87  Aligned_cols=42  Identities=17%  Similarity=0.231  Sum_probs=30.9

Q ss_pred             HHHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           39 SMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        39 ~~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      ..+|++.+.|...    ..+++.|..|||+.+++++   ..+.++|+.|
T Consensus        11 ~yAl~~L~~La~~----~~~~~~s~~~IA~~~~i~~---~~l~kil~~L   52 (143)
T 3t8r_A           11 RYGLTLMISLAKK----EGQGCISLKSIAEENNLSD---LYLEQLVGPL   52 (143)
T ss_dssp             HHHHHHHHHHHTT----TTSCCEEHHHHHHHTTCCH---HHHHHHHHHH
T ss_pred             HHHHHHHHHHHhC----CCCCCcCHHHHHHHHCcCH---HHHHHHHHHH
Confidence            4456666655431    2236899999999999999   9999998754

>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=91.27  E-value=0.064  Score=31.48  Aligned_cols=27  Identities=19%  Similarity=0.449  Sum_probs=23.4

Q ss_pred             CCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           58 GQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        58 ~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      +++.|..|||+.+|+++   ..+.|.++.|
T Consensus        34 ~~~~t~~ela~~l~is~---~tv~~~l~~L   60 (109)
T 2d1h_A           34 EKPITSEELADIFKLSK---TTVENSLKKL   60 (109)
T ss_dssp             CSCEEHHHHHHHHTCCH---HHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHCcCH---HHHHHHHHHH
Confidence            47899999999999999   8888888653

>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=91.23  E-value=0.12  Score=32.74  Aligned_cols=37  Identities=11%  Similarity=0.363  Sum_probs=29.1

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .+..|.+.|.+ +++.|..|||+.+|+++   ..+.|.++.
T Consensus         6 ~d~~il~~L~~-~~~~s~~ela~~lg~s~---~tv~~~l~~   42 (144)
T 2cfx_A            6 IDLNIIEELKK-DSRLSMRELGRKIKLSP---PSVTERVRQ   42 (144)
T ss_dssp             HHHHHHHHHHH-CSCCCHHHHHHHHTCCH---HHHHHHHHH
T ss_pred             HHHHHHHHHHH-cCCCCHHHHHHHHCcCH---HHHHHHHHH
Confidence            35567788876 47899999999999988   777776653

>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=91.20  E-value=0.074  Score=32.18  Aligned_cols=37  Identities=19%  Similarity=0.394  Sum_probs=27.8

Q ss_pred             HhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           47 ELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        47 eLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .+.|...+.+.|++.|..|||+.+|++.   ..+.+.|+.
T Consensus        20 ~l~Il~~l~~~g~~~s~~eLa~~lgvs~---~tV~~~L~~   56 (110)
T 1q1h_A           20 VIDVLRILLDKGTEMTDEEIANQLNIKV---NDVRKKLNL   56 (110)
T ss_dssp             THHHHHHHHHHCSCBCHHHHHHTTTSCH---HHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHCcCH---HHHHHHHHH
Confidence            3456666654455899999999999988   778777764

>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=91.20  E-value=0.11  Score=32.97  Aligned_cols=37  Identities=19%  Similarity=0.358  Sum_probs=29.5

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .+..|...|.+ +++.|..|||+.+|+++   ..+.|.++-
T Consensus         4 ~~~~il~~L~~-~~~~~~~ela~~lg~s~---~tv~~~l~~   40 (150)
T 2pn6_A            4 IDLRILKILQY-NAKYSLDEIAREIRIPK---ATLSYRIKK   40 (150)
T ss_dssp             HHHHHHHHHTT-CTTSCHHHHHHHHTSCH---HHHHHHHHH
T ss_pred             HHHHHHHHHHH-cCCCCHHHHHHHHCcCH---HHHHHHHHH
Confidence            45667888876 47899999999999998   777776654

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

Probab=91.19  E-value=0.45  Score=30.03  Aligned_cols=36  Identities=14%  Similarity=0.173  Sum_probs=27.6

Q ss_pred             HhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           47 ELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        47 eLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      +..|...|... +++|..|||+.+++++   ..+.|+++-
T Consensus        55 q~~vL~~l~~~-~~~t~~eLa~~l~~~~---~~vs~~l~~   90 (161)
T 3e6m_A           55 KLRLLSSLSAY-GELTVGQLATLGVMEQ---STTSRTVDQ   90 (161)
T ss_dssp             HHHHHHHHHHH-SEEEHHHHHHHTTCCH---HHHHHHHHH
T ss_pred             HHHHHHHHHhC-CCCCHHHHHHHHCCCH---HHHHHHHHH
Confidence            33455667654 6899999999999999   778777653

>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=91.04  E-value=0.13  Score=32.72  Aligned_cols=37  Identities=16%  Similarity=0.194  Sum_probs=29.0

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .+..|...|.+ +++.|..|||+.+|+++   ..+.|.++-
T Consensus         8 ~~~~iL~~L~~-~~~~s~~ela~~lg~s~---~tv~~~l~~   44 (150)
T 2w25_A            8 IDRILVRELAA-DGRATLSELATRAGLSV---SAVQSRVRR   44 (150)
T ss_dssp             HHHHHHHHHHH-CTTCCHHHHHHHHTSCH---HHHHHHHHH
T ss_pred             HHHHHHHHHHH-cCCCCHHHHHHHHCcCH---HHHHHHHHH
Confidence            35567777876 47899999999999988   777776653

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

Probab=90.93  E-value=0.15  Score=32.74  Aligned_cols=41  Identities=15%  Similarity=0.156  Sum_probs=32.4

Q ss_pred             HHHHhCchHHHHhCCCCCCHHHHHHhc-----CCCCCChhhHHHHHhcC
Q 041968           44 CAVELGIPDVIHKHGQPMTLSQIASAL-----DIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        44 aaveLgI~d~L~~~~gp~S~~ELA~~~-----~~~~~~~~~L~RlLR~L   87 (87)
                      +-.+.-|.+.|.+.+++.|+.||.+.+     ++++   ..++|.|+.|
T Consensus        21 T~qR~~Il~~L~~~~~~~sa~ei~~~l~~~~~~is~---aTVYR~L~~L   66 (145)
T 2fe3_A           21 TPQRHAILEYLVNSMAHPTADDIYKALEGKFPNMSV---ATVYNNLRVF   66 (145)
T ss_dssp             CHHHHHHHHHHHHCSSCCCHHHHHHHHGGGCTTCCH---HHHHHHHHHH
T ss_pred             CHHHHHHHHHHHhCCCCCCHHHHHHHHHHhCCCCCh---hhHHHHHHHH
Confidence            345566888888767899999999999     4555   8899998764

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

Probab=90.84  E-value=0.15  Score=32.36  Aligned_cols=37  Identities=16%  Similarity=0.374  Sum_probs=29.1

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .+..|.+.|.+ +++.|..|||+.+|+++   ..+.|.++-
T Consensus        10 ~d~~il~~L~~-~~~~s~~ela~~lg~s~---~tv~~~l~~   46 (151)
T 2dbb_A           10 VDMQLVKILSE-NSRLTYRELADILNTTR---QRIARRIDK   46 (151)
T ss_dssp             HHHHHHHHHHH-CTTCCHHHHHHHTTSCH---HHHHHHHHH
T ss_pred             HHHHHHHHHHH-cCCCCHHHHHHHHCcCH---HHHHHHHHH
Confidence            45567788876 47899999999999988   767666653

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

Probab=90.81  E-value=0.14  Score=33.06  Aligned_cols=37  Identities=11%  Similarity=0.223  Sum_probs=28.9

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .+..|.+.|.+ ++++|..|||+.+|+++   ..+.|.++-
T Consensus        11 ~~~~il~~L~~-~~~~s~~ela~~lg~s~---~tv~~~l~~   47 (162)
T 2p5v_A           11 TDIKILQVLQE-NGRLTNVELSERVALSP---SPCLRRLKQ   47 (162)
T ss_dssp             HHHHHHHHHHH-CTTCCHHHHHHHHTSCH---HHHHHHHHH
T ss_pred             HHHHHHHHHHH-cCCCCHHHHHHHHCcCH---HHHHHHHHH
Confidence            35567777876 47899999999999988   777776653

>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=90.76  E-value=0.15  Score=32.60  Aligned_cols=37  Identities=14%  Similarity=0.280  Sum_probs=29.0

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .+..|.+.|.++ ++.|..|||+.+|+++   ..+.|.++-
T Consensus         8 ~~~~il~~L~~~-~~~s~~ela~~lg~s~---~tv~~~l~~   44 (151)
T 2cyy_A            8 IDKKIIKILQND-GKAPLREISKITGLAE---STIHERIRK   44 (151)
T ss_dssp             HHHHHHHHHHHC-TTCCHHHHHHHHCSCH---HHHHHHHHH
T ss_pred             HHHHHHHHHHHc-CCCCHHHHHHHHCcCH---HHHHHHHHH
Confidence            355677778764 7899999999999988   777776653

>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=90.69  E-value=0.13  Score=33.21  Aligned_cols=42  Identities=17%  Similarity=0.160  Sum_probs=32.5

Q ss_pred             HHHHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           38 NSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        38 ~~~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      ...+|++.+.|...     .+++.|+.|||+.+++++   ..+.++|+.|
T Consensus        13 ~~yAl~~L~~La~~-----~~~~~~~~~iA~~~~i~~---~~l~kil~~L   54 (149)
T 1ylf_A           13 FSIAVHILSILKNN-----PSSLCTSDYMAESVNTNP---VVIRKIMSYL   54 (149)
T ss_dssp             HHHHHHHHHHHHHS-----CGGGCCHHHHHHHHTSCH---HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhC-----CCCCcCHHHHHHHHCcCH---HHHHHHHHHH
Confidence            34577777766431     247899999999999999   9999998754

>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=90.64  E-value=0.085  Score=30.93  Aligned_cols=37  Identities=22%  Similarity=0.311  Sum_probs=28.4

Q ss_pred             HHhCchHHHHhCC--CCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968           46 VELGIPDVIHKHG--QPMTLSQIASALDIQKNKAHCIQRLMR   85 (87)
Q Consensus        46 veLgI~d~L~~~~--gp~S~~ELA~~~~~~~~~~~~L~RlLR   85 (87)
                      .+-.|.+.|.+.+  +++|+.|||+.+|++.   ..+.|.|.
T Consensus        15 ~~~~IL~~L~~~~~~~~~t~~eLA~~Lgvs~---~tV~~~L~   53 (77)
T 1qgp_A           15 QEQRILKFLEELGEGKATTAHDLSGKLGTPK---KEINRVLY   53 (77)
T ss_dssp             HHHHHHHHHHHHCSSSCEEHHHHHHHHCCCH---HHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCCcCHHHHHHHHCcCH---HHHHHHHH
Confidence            4566777787643  4899999999999988   66777664

>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=90.50  E-value=1.1  Score=27.65  Aligned_cols=32  Identities=16%  Similarity=0.343  Sum_probs=25.8

Q ss_pred             chHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           50 IPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        50 I~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      |...| . .++.|..|||+.+++++   ..+.|+++-
T Consensus        43 iL~~l-~-~~~~t~~eLa~~l~~~~---~~vs~~l~~   74 (151)
T 3kp7_A           43 VLNML-S-IEALTVGQITEKQGVNK---AAVSRRVKK   74 (151)
T ss_dssp             HHHHH-H-HSCBCHHHHHHHHCSCS---SHHHHHHHH
T ss_pred             HHHHH-H-cCCcCHHHHHHHHCCCH---HHHHHHHHH
Confidence            66667 4 48999999999999999   777777653

>2zkz_A Transcriptional repressor PAGR; protein-DNA, HTH motif, dimer, DN binding, transcription regulation; 2.00A {Bacillus anthracis}

Probab=90.49  E-value=0.08  Score=31.80  Aligned_cols=38  Identities=16%  Similarity=0.314  Sum_probs=28.0

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      .++.|+..+.. .|+.|+.|||+.+|+++   ..+.|-|+.|
T Consensus        28 ~Rl~IL~~l~~-~~~~~~~ela~~l~is~---stvs~hL~~L   65 (99)
T 2zkz_A           28 MRLKIVNELYK-HKALNVTQIIQILKLPQ---STVSQHLCKM   65 (99)
T ss_dssp             HHHHHHHHHHH-HSCEEHHHHHHHHTCCH---HHHHHHHHHH
T ss_pred             HHHHHHHHHHH-CCCcCHHHHHHHHCcCH---HHHHHHHHHH
Confidence            45556644443 27899999999999998   7788777643

>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=90.47  E-value=0.13  Score=32.25  Aligned_cols=37  Identities=14%  Similarity=0.373  Sum_probs=29.4

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      .++.|+..|.+  ++.|+.|||+.+|+++   ..+.|.|+.|
T Consensus        47 ~rl~IL~~L~~--~~~s~~ela~~lgis~---stvs~~L~~L   83 (122)
T 1r1t_A           47 NRLRLLSLLAR--SELCVGDLAQAIGVSE---SAVSHQLRSL   83 (122)
T ss_dssp             HHHHHHHHHTT--CCBCHHHHHHHHTCCH---HHHHHHHHHH
T ss_pred             HHHHHHHHHHc--CCCCHHHHHHHHCcCH---HHHHHHHHHH
Confidence            45667777763  7899999999999998   7788777643

>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=90.38  E-value=0.16  Score=32.32  Aligned_cols=37  Identities=11%  Similarity=0.248  Sum_probs=28.9

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .+..|.+.|.++ ++.|..|||+.+|+++   ..+.|.++-
T Consensus         9 ~d~~il~~L~~~-~~~s~~ela~~lg~s~---~tv~~~l~~   45 (152)
T 2cg4_A            9 LDRGILEALMGN-ARTAYAELAKQFGVSP---ETIHVRVEK   45 (152)
T ss_dssp             HHHHHHHHHHHC-TTSCHHHHHHHHTSCH---HHHHHHHHH
T ss_pred             HHHHHHHHHHHc-CCCCHHHHHHHHCcCH---HHHHHHHHH
Confidence            355677778764 7899999999999988   777766653

>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=90.28  E-value=0.11  Score=31.97  Aligned_cols=34  Identities=21%  Similarity=0.360  Sum_probs=26.3

Q ss_pred             chHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           50 IPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        50 I~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      +...|....+|.|..|||+.+|+++   ..+.|+++-
T Consensus        31 il~~L~~~~~~~t~~ela~~l~~~~---stvs~~l~~   64 (152)
T 1ku9_A           31 VYAILYLSDKPLTISDIMEELKISK---GNVSMSLKK   64 (152)
T ss_dssp             HHHHHHHCSSCEEHHHHHHHHTCCH---HHHHHHHHH
T ss_pred             HHHHHHHcCCCCCHHHHHHHHCcCH---HHHHHHHHH
Confidence            4555542347899999999999998   888888764

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

Probab=90.24  E-value=0.15  Score=33.16  Aligned_cols=36  Identities=8%  Similarity=0.258  Sum_probs=28.5

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR   85 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR   85 (87)
                      .+..|.+.|.+ ++++|..|||+.+|+++   ..+.|-++
T Consensus         4 ~d~~il~~L~~-~~~~s~~~la~~lg~s~---~tv~~rl~   39 (162)
T 3i4p_A            4 LDRKILRILQE-DSTLAVADLAKKVGLST---TPCWRRIQ   39 (162)
T ss_dssp             HHHHHHHHHTT-CSCSCHHHHHHHHTCCH---HHHHHHHH
T ss_pred             HHHHHHHHHHH-CCCCCHHHHHHHHCcCH---HHHHHHHH
Confidence            46678888886 48999999999999988   66655544

>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=90.24  E-value=0.15  Score=31.86  Aligned_cols=39  Identities=15%  Similarity=0.154  Sum_probs=31.7

Q ss_pred             HHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           44 CAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        44 aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      .+..+||+..|.+  |+.|-.|||+.+|++.   ..+.|+=|+|
T Consensus        44 l~~R~~l~~~L~~--ge~TQREIA~~lGiS~---stISRi~r~L   82 (101)
T 1jhg_A           44 LGTRVRIIEELLR--GEMSQRELKNELGAGI---ATITRGSNSL   82 (101)
T ss_dssp             HHHHHHHHHHHHH--CCSCHHHHHHHHCCCH---HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHc--CCcCHHHHHHHHCCCh---hhhhHHHHHH
Confidence            4456888988873  7899999999999999   8888876643

>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=90.19  E-value=0.12  Score=32.21  Aligned_cols=38  Identities=8%  Similarity=0.118  Sum_probs=29.2

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .+..|...|...++++|..|||+.+++++   ..+.|+++-
T Consensus        40 ~q~~vL~~l~~~~~~~t~~eLa~~l~i~~---~tvs~~l~~   77 (150)
T 3fm5_A           40 RSYSVLVLACEQAEGVNQRGVAATMGLDP---SQIVGLVDE   77 (150)
T ss_dssp             HHHHHHHHHHHSTTCCCSHHHHHHHTCCH---HHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCCcCHHHHHHHHCCCH---hHHHHHHHH
Confidence            44555666766567899999999999998   777777653

>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=90.18  E-value=0.18  Score=31.51  Aligned_cols=36  Identities=17%  Similarity=0.354  Sum_probs=28.0

Q ss_pred             HhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           47 ELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        47 eLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      +..|...|.+ +++.|..|||+.+|+++   ..+.|.++.
T Consensus         6 ~~~il~~L~~-~~~~~~~ela~~lg~s~---~tv~~~l~~   41 (141)
T 1i1g_A            6 DKIILEILEK-DARTPFTEIAKKLGISE---TAVRKRVKA   41 (141)
T ss_dssp             HHHHHHHHHH-CTTCCHHHHHHHHTSCH---HHHHHHHHH
T ss_pred             HHHHHHHHHH-cCCCCHHHHHHHHCcCH---HHHHHHHHH
Confidence            4556777776 47899999999999988   777776653

>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=90.05  E-value=0.16  Score=31.06  Aligned_cols=37  Identities=14%  Similarity=0.262  Sum_probs=27.8

Q ss_pred             HhCchHHHHhCCC-CCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           47 ELGIPDVIHKHGQ-PMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        47 eLgI~d~L~~~~g-p~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      +..|...|...++ +.|..|||+.+++++   ..+.|+++-
T Consensus        36 ~~~iL~~l~~~~~~~~~~~ela~~l~~~~---~tvs~~l~~   73 (141)
T 3bro_A           36 QMTIIDYLSRNKNKEVLQRDLESEFSIKS---STATVLLQR   73 (141)
T ss_dssp             HHHHHHHHHHTTTSCCBHHHHHHHHTCCH---HHHHHHHHH
T ss_pred             HHHHHHHHHHCCCCCcCHHHHHHHHCCCc---chHHHHHHH
Confidence            3445566766543 899999999999998   777777754

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

Probab=89.90  E-value=0.15  Score=31.05  Aligned_cols=37  Identities=8%  Similarity=0.106  Sum_probs=29.4

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .++.|...|... ++.|..|||+.+++++   ..+.|+++-
T Consensus        39 ~~~~iL~~l~~~-~~~t~~ela~~l~~~~---~tvs~~l~~   75 (140)
T 2nnn_A           39 TQWAALVRLGET-GPCPQNQLGRLTAMDA---ATIKGVVER   75 (140)
T ss_dssp             HHHHHHHHHHHH-SSBCHHHHHHHTTCCH---HHHHHHHHH
T ss_pred             HHHHHHHHHHHc-CCCCHHHHHHHHCCCH---HHHHHHHHH
Confidence            355677777764 6999999999999998   878887764

>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=89.74  E-value=0.27  Score=30.32  Aligned_cols=38  Identities=24%  Similarity=0.323  Sum_probs=29.7

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .++.|...|....++.|..|||+.+++++   ..+.|+++-
T Consensus        36 ~~~~iL~~l~~~~~~~~~~~la~~l~i~~---~~vs~~l~~   73 (147)
T 2hr3_A           36 SQLVVLGAIDRLGGDVTPSELAAAERMRS---SNLAALLRE   73 (147)
T ss_dssp             HHHHHHHHHHHTTSCBCHHHHHHHTTCCH---HHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHhCCCh---hhHHHHHHH
Confidence            45667777776347899999999999998   778777754

>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=89.69  E-value=0.9  Score=27.97  Aligned_cols=36  Identities=19%  Similarity=0.331  Sum_probs=27.6

Q ss_pred             HhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           47 ELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        47 eLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      +..|...|... +++|..|||+.+++++   ..+.|+++-
T Consensus        42 ~~~iL~~l~~~-~~~t~~ela~~l~~~~---~~vs~~l~~   77 (152)
T 3bj6_A           42 QRAILEGLSLT-PGATAPQLGAALQMKR---QYISRILQE   77 (152)
T ss_dssp             HHHHHHHHHHS-TTEEHHHHHHHHTCCH---HHHHHHHHH
T ss_pred             HHHHHHHHHhC-CCCCHHHHHHHHCCCH---HHHHHHHHH
Confidence            34455566654 6899999999999998   778777754

>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=89.68  E-value=0.13  Score=31.51  Aligned_cols=38  Identities=21%  Similarity=0.187  Sum_probs=29.3

Q ss_pred             HHhCchHHHHhCC-CCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           46 VELGIPDVIHKHG-QPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        46 veLgI~d~L~~~~-gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .+..|...|...+ ++.|..|||+.+++++   ..+.|+++-
T Consensus        32 ~~~~vL~~l~~~~~~~~t~~ela~~l~~~~---~tvs~~l~~   70 (139)
T 3eco_A           32 EQGHTLGYLYAHQQDGLTQNDIAKALQRTG---PTVSNLLRN   70 (139)
T ss_dssp             HHHHHHHHHHHSTTTCEEHHHHHHHHTCCH---HHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCCcCHHHHHHHhCCCc---ccHHHHHHH
Confidence            3455666677654 6999999999999998   778777653

>1qbj_A Protein (double-stranded RNA specific adenosine D (ADAR1)); protein-Z-DNA complex, hydrolase-DNA complex; HET: DNA; 2.10A {Homo sapiens} SCOP: a.4.5.19 PDB: 3f21_A* 3f22_A* 3f23_A* 3irr_A* 3irq_D* 2gxb_A 2acj_A 2l54_A

Probab=89.62  E-value=0.18  Score=29.99  Aligned_cols=38  Identities=21%  Similarity=0.300  Sum_probs=27.7

Q ss_pred             HHHhCchHHHHhCC--CCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968           45 AVELGIPDVIHKHG--QPMTLSQIASALDIQKNKAHCIQRLMR   85 (87)
Q Consensus        45 aveLgI~d~L~~~~--gp~S~~ELA~~~~~~~~~~~~L~RlLR   85 (87)
                      -++..|.+.|.+.+  .++|+.|||+.+|++.   ..+.|.|.
T Consensus        10 ~~~~~IL~~L~~~~pg~~~t~~eLA~~Lgvsr---~tV~~~L~   49 (81)
T 1qbj_A           10 DQEQRILKFLEELGEGKATTAHDLSGKLGTPK---KEINRVLY   49 (81)
T ss_dssp             HHHHHHHHHHHHHCTTCCBCHHHHHHHHTCCH---HHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCCcCHHHHHHHHCcCH---HHHHHHHH
Confidence            34566777777642  4899999999999987   55665553

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

Probab=89.55  E-value=0.14  Score=32.25  Aligned_cols=37  Identities=16%  Similarity=0.224  Sum_probs=29.0

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhc--CCCCCChhhHHHHHhc
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASAL--DIQKNKAHCIQRLMRI   86 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~--~~~~~~~~~L~RlLR~   86 (87)
                      .+-.|.+.|.++ |++|+.|||+.+  ++.+   ..+.+-++.
T Consensus        14 ~d~~IL~~L~~~-g~~s~~eLA~~l~~giS~---~aVs~rL~~   52 (111)
T 3b73_A           14 WDDRILEIIHEE-GNGSPKELEDRDEIRISK---SSVSRRLKK   52 (111)
T ss_dssp             HHHHHHHHHHHH-SCBCHHHHHTSTTCCSCH---HHHHHHHHH
T ss_pred             HHHHHHHHHHHc-CCCCHHHHHHHHhcCCCH---HHHHHHHHH
Confidence            356678888764 799999999999  8887   777766654

>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=89.38  E-value=0.13  Score=30.35  Aligned_cols=33  Identities=18%  Similarity=0.176  Sum_probs=24.6

Q ss_pred             chHHHHhCCCCCCHHHHHHhcCCCCCChhh-HHHHHh
Q 041968           50 IPDVIHKHGQPMTLSQIASALDIQKNKAHC-IQRLMR   85 (87)
Q Consensus        50 I~d~L~~~~gp~S~~ELA~~~~~~~~~~~~-L~RlLR   85 (87)
                      +...+.+.+++.|..|||+.+++++   .. +.|+++
T Consensus        20 ~L~~l~~~~~~~t~~eLa~~l~is~---~t~vs~~l~   53 (95)
T 2pg4_A           20 TLLEFEKKGYEPSLAEIVKASGVSE---KTFFMGLKD   53 (95)
T ss_dssp             HHHHHHHTTCCCCHHHHHHHHCCCH---HHHHTTHHH
T ss_pred             HHHHHHhcCCCCCHHHHHHHHCCCc---hHHHHHHHH
Confidence            3445555444899999999999998   77 666654

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

Probab=89.32  E-value=0.26  Score=31.92  Aligned_cols=41  Identities=12%  Similarity=0.307  Sum_probs=33.3

Q ss_pred             HHHHhCchHHHHhCCCCCCHHHHHHhc-----CCCCCChhhHHHHHhcC
Q 041968           44 CAVELGIPDVIHKHGQPMTLSQIASAL-----DIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        44 aaveLgI~d~L~~~~gp~S~~ELA~~~-----~~~~~~~~~L~RlLR~L   87 (87)
                      +-.+.-|.+.|.+.+++.|+.||...+     ++++   ..+||.|..|
T Consensus        26 T~qR~~IL~~l~~~~~~~sa~ei~~~l~~~~~~is~---aTVYR~L~~L   71 (150)
T 2xig_A           26 SKQREEVVSVLYRSGTHLSPEEITHSIRQKDKNTSI---SSVYRILNFL   71 (150)
T ss_dssp             HHHHHHHHHHHHHCSSCBCHHHHHHHHHHHSTTCCH---HHHHHHHHHH
T ss_pred             CHHHHHHHHHHHhCCCCCCHHHHHHHHHHhCCCCCH---hhHHHHHHHH
Confidence            556677899998767899999999998     4555   8899998764

>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=89.22  E-value=0.2  Score=30.83  Aligned_cols=36  Identities=11%  Similarity=0.171  Sum_probs=28.0

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .++.|...|.  .++.|..|||+.+++++   ..+.|+++-
T Consensus        38 ~~~~iL~~l~--~~~~~~~ela~~l~~s~---~tvs~~l~~   73 (146)
T 2gxg_A           38 LDFLVLRATS--DGPKTMAYLANRYFVTQ---SAITASVDK   73 (146)
T ss_dssp             HHHHHHHHHT--TSCBCHHHHHHHTTCCH---HHHHHHHHH
T ss_pred             HHHHHHHHHh--cCCcCHHHHHHHhCCCc---hhHHHHHHH
Confidence            3445556676  58999999999999998   778877764

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

Probab=89.17  E-value=0.22  Score=32.79  Aligned_cols=37  Identities=16%  Similarity=0.301  Sum_probs=28.6

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .+..|.+.|.++ +++|..|||+.+|+++   ..+.|.++-
T Consensus        18 ~d~~IL~~L~~~-~~~s~~eLA~~lglS~---~tv~~~l~~   54 (171)
T 2ia0_A           18 LDRNILRLLKKD-ARLTISELSEQLKKPE---STIHFRIKK   54 (171)
T ss_dssp             HHHHHHHHHHHC-TTCCHHHHHHHHTSCH---HHHHHHHHH
T ss_pred             HHHHHHHHHHHc-CCCCHHHHHHHHCcCH---HHHHHHHHH
Confidence            445677778764 7899999999999988   767666553

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

Probab=89.17  E-value=0.2  Score=30.50  Aligned_cols=36  Identities=11%  Similarity=0.320  Sum_probs=27.5

Q ss_pred             HhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           47 ELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        47 eLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      ++.|...|... ++.|..|||+.+++++   ..+.|+++-
T Consensus        35 ~~~iL~~l~~~-~~~~~~ela~~l~~~~---~tvs~~l~~   70 (139)
T 3bja_A           35 QFGVIQVLAKS-GKVSMSKLIENMGCVP---SNMTTMIQR   70 (139)
T ss_dssp             HHHHHHHHHHS-CSEEHHHHHHHCSSCC---TTHHHHHHH
T ss_pred             HHHHHHHHHHc-CCcCHHHHHHHHCCCh---hHHHHHHHH
Confidence            44556667653 7899999999999998   667777653

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

Probab=89.10  E-value=0.23  Score=31.47  Aligned_cols=40  Identities=15%  Similarity=0.264  Sum_probs=30.9

Q ss_pred             HHHhCchHHHHhCC-CCCCHHHHHHhc-----CCCCCChhhHHHHHhcC
Q 041968           45 AVELGIPDVIHKHG-QPMTLSQIASAL-----DIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        45 aveLgI~d~L~~~~-gp~S~~ELA~~~-----~~~~~~~~~L~RlLR~L   87 (87)
                      -.+.-|.+.|.+.+ ++.|+.||.+.+     ++++   ..++|.|+.|
T Consensus        18 ~qR~~Il~~L~~~~~~~~sa~ei~~~l~~~~~~is~---aTVYR~L~~L   63 (136)
T 1mzb_A           18 LPRVKILQMLDSAEQRHMSAEDVYKALMEAGEDVGL---ATVYRVLTQF   63 (136)
T ss_dssp             HHHHHHHHHHHCC-CCSBCHHHHHHHHHHTTCCCCH---HHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCH---HHHHHHHHHH
Confidence            34556888888766 899999999998     4555   8899998764

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

Probab=89.05  E-value=0.21  Score=30.65  Aligned_cols=37  Identities=14%  Similarity=0.190  Sum_probs=27.5

Q ss_pred             HhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           47 ELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        47 eLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      +..|...|...+++.|..|||+.+++++   ..+.|+++-
T Consensus        39 ~~~iL~~l~~~~~~~t~~~la~~l~~s~---~~vs~~l~~   75 (146)
T 2fbh_A           39 RWLVLLHLARHRDSPTQRELAQSVGVEG---PTLARLLDG   75 (146)
T ss_dssp             HHHHHHHHHHCSSCCBHHHHHHHHTCCH---HHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHhCCCh---hhHHHHHHH
Confidence            3445556623358999999999999998   777777653

>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=88.84  E-value=0.21  Score=33.31  Aligned_cols=33  Identities=24%  Similarity=0.334  Sum_probs=25.5

Q ss_pred             HHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           52 DVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        52 d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      +.+.+.|.|.|..|||+.+|+++   ..+.|.|+.|
T Consensus        16 ~~~~~~g~~~s~~eia~~lgl~~---~tv~~~l~~L   48 (196)
T 3k2z_A           16 EFIEKNGYPPSVREIARRFRITP---RGALLHLIAL   48 (196)
T ss_dssp             HHHHHHSSCCCHHHHHHHHTSCH---HHHHHHHHHH
T ss_pred             HHHHHhCCCCCHHHHHHHcCCCc---HHHHHHHHHH
Confidence            34555567999999999999987   6688877643

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

Probab=88.77  E-value=0.12  Score=33.70  Aligned_cols=44  Identities=11%  Similarity=0.194  Sum_probs=34.3

Q ss_pred             HHHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           39 SMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        39 ~~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      ..+|.--..+.|...|.  .+|.|+.|||+.+|+++   ..+.+-|+.|
T Consensus        52 l~aL~~p~R~~IL~~L~--~~~~t~~eLa~~lgls~---stvs~hL~~L   95 (151)
T 3f6v_A           52 LEVAAEPTRRRLVQLLT--SGEQTVNNLAAHFPASR---SAISQHLRVL   95 (151)
T ss_dssp             HHHHTSHHHHHHHHHGG--GCCEEHHHHHTTSSSCH---HHHHHHHHHH
T ss_pred             HHHhCCHHHHHHHHHHH--hCCCCHHHHHHHHCcCH---HHHHHHHHHH
Confidence            34455556778888887  37899999999999998   7788777654

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

Probab=88.61  E-value=0.24  Score=30.60  Aligned_cols=37  Identities=19%  Similarity=0.336  Sum_probs=28.7

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .+..|...|... +++|..|||+.+++++   ..+.|+++-
T Consensus        41 ~~~~iL~~l~~~-~~~t~~ela~~l~~~~---~tvs~~l~~   77 (148)
T 3nrv_A           41 TEWRIISVLSSA-SDCSVQKISDILGLDK---AAVSRTVKK   77 (148)
T ss_dssp             HHHHHHHHHHHS-SSBCHHHHHHHHTCCH---HHHHHHHHH
T ss_pred             HHHHHHHHHHcC-CCCCHHHHHHHHCCCH---HHHHHHHHH
Confidence            345566667764 6999999999999999   778877754

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

Probab=88.59  E-value=1  Score=28.52  Aligned_cols=38  Identities=21%  Similarity=0.155  Sum_probs=25.8

Q ss_pred             HHhCchHHHHhC-CCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           46 VELGIPDVIHKH-GQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        46 veLgI~d~L~~~-~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .+..|...|... ++++|..|||+.+++++   ..+.|+++-
T Consensus        47 ~q~~vL~~l~~~~~~~~t~~eLa~~l~~~~---~tvs~~l~~   85 (168)
T 3u2r_A           47 QQYNTLRLLRSVHPEGMATLQIADRLISRA---PDITRLIDR   85 (168)
T ss_dssp             HHHHHHHHHHHHTTSCEEHHHHHHHC---C---THHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCCcCHHHHHHHHCCCh---hhHHHHHHH
Confidence            345556667765 37999999999999999   777777653

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

Probab=88.58  E-value=0.23  Score=30.23  Aligned_cols=36  Identities=19%  Similarity=0.312  Sum_probs=28.2

Q ss_pred             HhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           47 ELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        47 eLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      ++.|...|... ++.|..|||+.+++++   ..+.|+++-
T Consensus        31 ~~~iL~~l~~~-~~~~~~ela~~l~~s~---~tvs~~l~~   66 (138)
T 3bpv_A           31 QVACLLRIHRE-PGIKQDELATFFHVDK---GTIARTLRR   66 (138)
T ss_dssp             HHHHHHHHHHS-TTCBHHHHHHHHTCCH---HHHHHHHHH
T ss_pred             HHHHHHHHHHc-CCCCHHHHHHHHCCCH---HHHHHHHHH
Confidence            44456667764 7899999999999998   778887764

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

Probab=88.19  E-value=0.24  Score=30.20  Aligned_cols=37  Identities=16%  Similarity=0.384  Sum_probs=28.7

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .++.|+..|... ++.|..|||+.+++++   ..+.|+++-
T Consensus        32 ~~~~iL~~l~~~-~~~~~~ela~~l~is~---~~vs~~l~~   68 (142)
T 3bdd_A           32 TRYSILQTLLKD-APLHQLALQERLQIDR---AAVTRHLKL   68 (142)
T ss_dssp             HHHHHHHHHHHH-CSBCHHHHHHHHTCCH---HHHHHHHHH
T ss_pred             HHHHHHHHHHhC-CCCCHHHHHHHHCCCH---HHHHHHHHH
Confidence            344566677754 6899999999999998   778887764

>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=88.07  E-value=0.22  Score=30.53  Aligned_cols=36  Identities=17%  Similarity=0.257  Sum_probs=28.1

Q ss_pred             HhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           47 ELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        47 eLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      ++.|...|... ++.|..|||+.+++++   ..+.|+++-
T Consensus        35 ~~~iL~~l~~~-~~~~~~~la~~l~~s~---~tvs~~l~~   70 (145)
T 2a61_A           35 QFDILQKIYFE-GPKRPGELSVLLGVAK---STVTGLVKR   70 (145)
T ss_dssp             HHHHHHHHHHH-CCBCHHHHHHHHTCCH---HHHHHHHHH
T ss_pred             HHHHHHHHHHc-CCCCHHHHHHHHCCCc---hhHHHHHHH
Confidence            44556667653 7899999999999998   778887764

>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=87.92  E-value=0.36  Score=30.56  Aligned_cols=36  Identities=8%  Similarity=0.175  Sum_probs=28.0

Q ss_pred             HhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           47 ELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        47 eLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      +..|...|... +++|..|||+.+++++   ..+.|+++-
T Consensus        48 q~~iL~~l~~~-~~~t~~eLa~~l~~~~---~tvs~~l~~   83 (162)
T 3k0l_A           48 QFTALSVLAAK-PNLSNAKLAERSFIKP---QSANKILQD   83 (162)
T ss_dssp             HHHHHHHHHHC-TTCCHHHHHHHHTSCG---GGHHHHHHH
T ss_pred             HHHHHHHHHHC-CCCCHHHHHHHHCCCH---HHHHHHHHH
Confidence            44466667764 6899999999999999   777777653

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

Probab=87.82  E-value=0.27  Score=30.42  Aligned_cols=27  Identities=19%  Similarity=0.276  Sum_probs=23.0

Q ss_pred             CCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           57 HGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        57 ~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .+++.|..|||+.+++++   ..+.|+++.
T Consensus        28 ~~~~~s~~ela~~l~is~---~tv~~~l~~   54 (139)
T 2x4h_A           28 SGEGAKINRIAKDLKIAP---SSVFEEVSH   54 (139)
T ss_dssp             TTSCBCHHHHHHHHTCCH---HHHHHHHHH
T ss_pred             cCCCcCHHHHHHHhCCCh---HHHHHHHHH
Confidence            358899999999999998   888887764

>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=87.70  E-value=0.29  Score=32.56  Aligned_cols=40  Identities=15%  Similarity=0.258  Sum_probs=31.2

Q ss_pred             HHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           44 CAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        44 aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .--...|.+.|.+.++++|..|||+.+|++.   ..++|=++.
T Consensus        20 ~~R~~~Il~~L~~~~~~~s~~eLa~~l~vS~---~Ti~rdi~~   59 (187)
T 1j5y_A           20 QERLKSIVRILERSKEPVSGAQLAEELSVSR---QVIVQDIAY   59 (187)
T ss_dssp             HHHHHHHHHHHHHCSSCBCHHHHHHHHTSCH---HHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCcCHHHHHHHHCcCH---HHHHHHHHH
Confidence            3455678888886567899999999999988   777775543

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

Probab=87.59  E-value=0.25  Score=30.86  Aligned_cols=36  Identities=11%  Similarity=0.238  Sum_probs=27.6

Q ss_pred             HhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           47 ELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        47 eLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      ++.|...|.. .+++|..|||+.+++++   ..+.|+++-
T Consensus        45 ~~~iL~~l~~-~~~~t~~ela~~l~i~~---~tvs~~l~~   80 (155)
T 3cdh_A           45 EWRVLACLVD-NDAMMITRLAKLSLMEQ---SRMTRIVDQ   80 (155)
T ss_dssp             HHHHHHHHSS-CSCBCHHHHHHHTTCCH---HHHHHHHHH
T ss_pred             HHHHHHHHHH-CCCcCHHHHHHHHCCCH---HHHHHHHHH
Confidence            3445556664 37899999999999998   778887764

>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=87.42  E-value=0.22  Score=30.96  Aligned_cols=36  Identities=8%  Similarity=0.053  Sum_probs=21.4

Q ss_pred             hCchHHHHhCC-CCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           48 LGIPDVIHKHG-QPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        48 LgI~d~L~~~~-gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      ..|...|...+ +++|..|||+.+++++   ..+.|+++-
T Consensus        44 ~~vL~~l~~~~~~~~t~~eLa~~l~~~~---~~vs~~l~~   80 (148)
T 3jw4_A           44 GRMIGYIYENQESGIIQKDLAQFFGRRG---ASITSMLQG   80 (148)
T ss_dssp             HHHHHHHHHHTTTCCCHHHHHHC---------CHHHHHHH
T ss_pred             HHHHHHHHhCCCCCCCHHHHHHHHCCCh---hHHHHHHHH
Confidence            34555666543 7999999999999998   667666653

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

Probab=87.35  E-value=0.33  Score=30.42  Aligned_cols=36  Identities=11%  Similarity=0.145  Sum_probs=28.1

Q ss_pred             HhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           47 ELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        47 eLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      ++.|...|.. .++.|..|||+.+++++   ..+.|+++-
T Consensus        51 ~~~iL~~l~~-~~~~t~~ela~~l~is~---~tvs~~l~~   86 (162)
T 2fa5_A           51 EWRVITILAL-YPGSSASEVSDRTAMDK---VAVSRAVAR   86 (162)
T ss_dssp             HHHHHHHHHH-STTCCHHHHHHHHTCCH---HHHHHHHHH
T ss_pred             HHHHHHHHHh-CCCCCHHHHHHHHCCCH---HHHHHHHHH
Confidence            4445666776 47999999999999998   778777764

>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=87.09  E-value=0.44  Score=31.38  Aligned_cols=41  Identities=15%  Similarity=0.318  Sum_probs=31.2

Q ss_pred             HHHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           39 SMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        39 ~~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      ..+|++.+.|...     .++++|..|||+.+++++   ..+.++|+.|
T Consensus        12 ~yAlr~l~~La~~-----~~~~~s~~~IA~~~~is~---~~l~kil~~L   52 (162)
T 3k69_A           12 SVAVHSILYLDAH-----RDSKVASRELAQSLHLNP---VMIRNILSVL   52 (162)
T ss_dssp             HHHHHHHHHHHTT-----TTSCBCHHHHHHHHTSCG---GGTHHHHHHH
T ss_pred             HHHHHHHHHHHhC-----CCCCcCHHHHHHHHCcCH---HHHHHHHHHH
Confidence            4566666665432     247899999999999999   8899988754

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

Probab=87.03  E-value=0.28  Score=30.30  Aligned_cols=36  Identities=6%  Similarity=0.105  Sum_probs=27.8

Q ss_pred             HhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           47 ELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        47 eLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      ++.|...|... ++.|..|||+.+++++   ..+.|+++-
T Consensus        44 ~~~iL~~l~~~-~~~t~~ela~~l~~~~---~tvs~~l~~   79 (150)
T 2rdp_A           44 QFVALQWLLEE-GDLTVGELSNKMYLAC---STTTDLVDR   79 (150)
T ss_dssp             HHHHHHHHHHH-CSBCHHHHHHHHTCCH---HHHHHHHHH
T ss_pred             HHHHHHHHHHc-CCCCHHHHHHHHCCCc---hhHHHHHHH
Confidence            44455667654 6899999999999998   778777764

>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=86.96  E-value=0.43  Score=32.21  Aligned_cols=38  Identities=18%  Similarity=0.215  Sum_probs=30.3

Q ss_pred             HHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           44 CAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        44 aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      -..+..|...|.  .+++|..|||+.+|+++   ..+.|.++.
T Consensus        19 d~~~~~IL~~L~--~~~~s~~eLA~~lglS~---stv~~~l~~   56 (192)
T 1uly_A           19 EDTRRKILKLLR--NKEMTISQLSEILGKTP---QTIYHHIEK   56 (192)
T ss_dssp             SHHHHHHHHHHT--TCCBCHHHHHHHHTCCH---HHHHHHHHH
T ss_pred             CHHHHHHHHHHH--cCCCCHHHHHHHHCcCH---HHHHHHHHH
Confidence            345667888887  37999999999999988   777776654

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

Probab=86.89  E-value=0.29  Score=30.21  Aligned_cols=37  Identities=8%  Similarity=0.126  Sum_probs=28.7

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .+..|...|... ++.|..|||+.+++++   ..+.|+++-
T Consensus        32 ~q~~iL~~l~~~-~~~t~~eLa~~l~~~~---~tvs~~l~~   68 (145)
T 3g3z_A           32 NLFAVLYTLATE-GSRTQKHIGEKWSLPK---QTVSGVCKT   68 (145)
T ss_dssp             HHHHHHHHHHHH-CSBCHHHHHHHHTCCH---HHHHHHHHH
T ss_pred             HHHHHHHHHHHC-CCCCHHHHHHHHCCCH---HHHHHHHHH
Confidence            345566667654 6799999999999999   778887754

>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=86.85  E-value=0.25  Score=31.76  Aligned_cols=38  Identities=18%  Similarity=0.184  Sum_probs=29.1

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .+..|...|...++++|..|||+.+++++   ..+.|+++-
T Consensus        54 ~q~~vL~~L~~~~~~~t~~eLa~~l~i~~---~tvs~~l~~   91 (166)
T 3deu_A           54 THWVTLHNIHQLPPDQSQIQLAKAIGIEQ---PSLVRTLDQ   91 (166)
T ss_dssp             HHHHHHHHHHHSCSSEEHHHHHHHHTSCH---HHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHCCCH---hhHHHHHHH
Confidence            34555666776457899999999999998   777777653

>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=86.51  E-value=0.33  Score=30.07  Aligned_cols=38  Identities=24%  Similarity=0.280  Sum_probs=28.9

Q ss_pred             HhCchHHHHhCC---CCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           47 ELGIPDVIHKHG---QPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        47 eLgI~d~L~~~~---gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      +-.|++.|-++.   ...|..|||+.+++.+   ..+.|+.|-|
T Consensus        23 e~~ia~yil~~~~~~~~~si~elA~~~~vS~---aTv~Rf~kkl   63 (111)
T 2o3f_A           23 ERKLADYILAHPHXAIESTVNEISALANSSD---AAVIRLCXSL   63 (111)
T ss_dssp             HHHHHHHHHHCHHHHHTCCHHHHHHHTTCCH---HHHHHHHHHT
T ss_pred             HHHHHHHHHHChHHHHhcCHHHHHHHHCCCH---HHHHHHHHHc
Confidence            445666655432   4679999999999999   8899998754

>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=86.51  E-value=0.29  Score=28.75  Aligned_cols=36  Identities=3%  Similarity=0.060  Sum_probs=27.6

Q ss_pred             HhCchHHHHhCCCCCCHHHH----HHhcCCCCCChhhHHHHHhc
Q 041968           47 ELGIPDVIHKHGQPMTLSQI----ASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        47 eLgI~d~L~~~~gp~S~~EL----A~~~~~~~~~~~~L~RlLR~   86 (87)
                      +..|+..|.+ .++.|..||    |+.+++++   ..+.|+++-
T Consensus        10 q~~iL~~l~~-~~~~~~~el~~~la~~l~is~---~tvs~~l~~   49 (99)
T 1tbx_A           10 EAIVLAYLYD-NEGIATYDLYKKVNAEFPMST---ATFYDAKKF   49 (99)
T ss_dssp             HHHHHHHHTT-CTTCBHHHHHHHHHTTSCCCH---HHHHHHHHH
T ss_pred             HHHHHHHHHH-cCCcCHHHHHHHHHHHcCCCH---HHHHHHHHH
Confidence            3455666665 378999999    89999998   888887764

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

Probab=86.31  E-value=0.37  Score=29.58  Aligned_cols=36  Identities=14%  Similarity=0.295  Sum_probs=27.6

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .+..|...|... + .|..|||+.+++++   ..+.|+++-
T Consensus        39 ~~~~iL~~l~~~-~-~t~~eLa~~l~~s~---~tvs~~l~~   74 (146)
T 3tgn_A           39 TQEHILMLLSEE-S-LTNSELARRLNVSQ---AAVTKAIKS   74 (146)
T ss_dssp             HHHHHHHHHTTC-C-CCHHHHHHHHTCCH---HHHHHHHHH
T ss_pred             HHHHHHHHHHhC-C-CCHHHHHHHHCCCH---HHHHHHHHH
Confidence            455566667753 4 99999999999998   777777754

>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=86.24  E-value=0.32  Score=29.59  Aligned_cols=36  Identities=11%  Similarity=0.176  Sum_probs=27.5

Q ss_pred             HhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           47 ELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        47 eLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      ++.|...|... ++.|..|||+.+++++   ..+.|+++-
T Consensus        36 ~~~iL~~l~~~-~~~~~~~la~~l~~~~---~tvs~~l~~   71 (138)
T 1jgs_A           36 QFKVLCSIRCA-ACITPVELKKVLSVDL---GALTRMLDR   71 (138)
T ss_dssp             HHHHHHHHHHH-SSBCHHHHHHHHTCCH---HHHHHHHHH
T ss_pred             HHHHHHHHHhc-CCCCHHHHHHHHCCCh---HHHHHHHHH
Confidence            44455566653 6899999999999998   778777754

>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=86.23  E-value=0.28  Score=30.13  Aligned_cols=36  Identities=8%  Similarity=0.129  Sum_probs=27.7

Q ss_pred             HhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           47 ELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        47 eLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      +..|...|... ++.|..|||+.+++++   ..+.|+++-
T Consensus        31 ~~~iL~~l~~~-~~~t~~~la~~l~~s~---~~vs~~l~~   66 (144)
T 1lj9_A           31 QYLYLVRVCEN-PGIIQEKIAELIKVDR---TTAARAIKR   66 (144)
T ss_dssp             HHHHHHHHHHS-TTEEHHHHHHHHTCCH---HHHHHHHHH
T ss_pred             HHHHHHHHHHC-cCcCHHHHHHHHCCCH---hHHHHHHHH
Confidence            34455667664 6899999999999998   778777754

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

Probab=86.23  E-value=0.27  Score=30.57  Aligned_cols=36  Identities=14%  Similarity=0.163  Sum_probs=27.9

Q ss_pred             HhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           47 ELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        47 eLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      +..|...|... +++|..|||+.+++++   ..+.|+++-
T Consensus        43 ~~~iL~~l~~~-~~~t~~eLa~~l~~~~---~tvs~~l~~   78 (154)
T 2qww_A           43 QLAMINVIYST-PGISVADLTKRLIITG---SSAAANVDG   78 (154)
T ss_dssp             HHHHHHHHHHS-TTEEHHHHHHHHTCCH---HHHHHHHHH
T ss_pred             HHHHHHHHHHC-CCCCHHHHHHHHCCCH---HHHHHHHHH
Confidence            44455567664 7899999999999998   778777754

>3mn2_A Probable ARAC family transcriptional regulator; structural genomics, PSI-2, protein structure initiative; 1.80A {Rhodopseudomonas palustris}

Probab=86.21  E-value=0.63  Score=27.75  Aligned_cols=24  Identities=17%  Similarity=0.412  Sum_probs=21.9

Q ss_pred             CCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968           59 QPMTLSQIASALDIQKNKAHCIQRLMR   85 (87)
Q Consensus        59 gp~S~~ELA~~~~~~~~~~~~L~RlLR   85 (87)
                      .+.|+++||+.+|+++   ..|.|+++
T Consensus        17 ~~~~~~~lA~~~~~s~---~~l~r~fk   40 (108)
T 3mn2_A           17 RPITIEKLTALTGISS---RGIFKAFQ   40 (108)
T ss_dssp             SCCCHHHHHHHHTCCH---HHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCH---HHHHHHHH
Confidence            7899999999999999   88998876

>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=86.01  E-value=0.36  Score=30.21  Aligned_cols=37  Identities=19%  Similarity=0.164  Sum_probs=29.1

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .++.|...|... ++.|..|||+.+++++   ..+.|+++-
T Consensus        45 ~~~~iL~~l~~~-~~~t~~ela~~l~is~---~tvs~~l~~   81 (154)
T 2eth_A           45 TELYAFLYVALF-GPKKMKEIAEFLSTTK---SNVTNVVDS   81 (154)
T ss_dssp             HHHHHHHHHHHH-CCBCHHHHHHHTTSCH---HHHHHHHHH
T ss_pred             HHHHHHHHHHHc-CCCCHHHHHHHHCCCH---HHHHHHHHH
Confidence            455667777764 6899999999999988   778877764

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

Probab=86.00  E-value=0.26  Score=30.06  Aligned_cols=37  Identities=11%  Similarity=0.164  Sum_probs=28.3

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .+..|...|... ++.|..|||+.+++++   ..+.|+++-
T Consensus        37 ~~~~iL~~l~~~-~~~t~~ela~~l~~s~---~~vs~~l~~   73 (142)
T 2fbi_A           37 QQWRVIRILRQQ-GEMESYQLANQACILR---PSMTGVLAR   73 (142)
T ss_dssp             HHHHHHHHHHHH-CSEEHHHHHHHTTCCH---HHHHHHHHH
T ss_pred             HHHHHHHHHHHc-CCCCHHHHHHHHCCCH---hHHHHHHHH
Confidence            345566667654 6899999999999998   778777754

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

Probab=85.75  E-value=0.24  Score=30.55  Aligned_cols=37  Identities=14%  Similarity=0.284  Sum_probs=28.5

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .+..|...|... +++|..|||+.+++++   ..+.|+++-
T Consensus        38 ~~~~iL~~l~~~-~~~t~~eLa~~l~~~~---~~vs~~l~~   74 (143)
T 3oop_A           38 EQWSVLEGIEAN-EPISQKEIALWTKKDT---PTVNRIVDV   74 (143)
T ss_dssp             HHHHHHHHHHHH-SSEEHHHHHHHHTCCH---HHHHHHHHH
T ss_pred             HHHHHHHHHHHc-CCcCHHHHHHHHCCCH---hhHHHHHHH
Confidence            344556667654 8999999999999999   778777653

>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=85.70  E-value=0.34  Score=29.70  Aligned_cols=37  Identities=8%  Similarity=0.338  Sum_probs=27.9

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .+..|...|... ++.|..|||+.+++++   ..+.|+++-
T Consensus        38 ~~~~iL~~l~~~-~~~~~~ela~~l~~~~---~tvs~~l~~   74 (142)
T 2bv6_A           38 PQFLVLTILWDE-SPVNVKKVVTELALDT---GTVSPLLKR   74 (142)
T ss_dssp             HHHHHHHHHHHS-SEEEHHHHHHHTTCCT---TTHHHHHHH
T ss_pred             HHHHHHHHHHHc-CCcCHHHHHHHHCCCh---hhHHHHHHH
Confidence            344556667664 6899999999999998   667777653

>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=85.67  E-value=0.21  Score=28.64  Aligned_cols=37  Identities=22%  Similarity=0.302  Sum_probs=27.4

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCC----CCCChhhHHHHHhc
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDI----QKNKAHCIQRLMRI   86 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~----~~~~~~~L~RlLR~   86 (87)
                      .+..|.+.|.+ .++.|+.||++.++.    ++   ..+.|+|+-
T Consensus        10 ~e~~vL~~L~~-~~~~t~~ei~~~l~~~~~~s~---~Tv~~~l~r   50 (82)
T 1p6r_A           10 AELEVMKVIWK-HSSINTNEVIKELSKTSTWSP---KTIQTMLLR   50 (82)
T ss_dssp             HHHHHHHHHHT-SSSEEHHHHHHHHHHHSCCCH---HHHHHHHHH
T ss_pred             HHHHHHHHHHc-CCCCCHHHHHHHHhhcCCccH---HHHHHHHHH
Confidence            34566777776 479999999999974    44   677777754

>3oio_A Transcriptional regulator (ARAC-type DNA-binding containing proteins); PSI-2, midwest center for structural genomics; 1.65A {Chromobacterium violaceum}

Probab=85.63  E-value=0.81  Score=27.53  Aligned_cols=31  Identities=16%  Similarity=0.483  Sum_probs=25.0

Q ss_pred             HHHHhC-CCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968           52 DVIHKH-GQPMTLSQIASALDIQKNKAHCIQRLMR   85 (87)
Q Consensus        52 d~L~~~-~gp~S~~ELA~~~~~~~~~~~~L~RlLR   85 (87)
                      +.|.++ ..+.|+.+||+.+|+++   ..|.|+++
T Consensus        14 ~~i~~~~~~~~~~~~lA~~~~~S~---~~l~r~fk   45 (113)
T 3oio_A           14 SLMEANIEEPLSTDDIAYYVGVSR---RQLERLFK   45 (113)
T ss_dssp             HHHHTCSSSCCCHHHHHHHHTSCH---HHHHHHHH
T ss_pred             HHHHhhhcCCCCHHHHHHHHCcCH---HHHHHHHH
Confidence            445443 37899999999999999   88998876

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

Probab=85.59  E-value=0.31  Score=30.62  Aligned_cols=37  Identities=3%  Similarity=0.148  Sum_probs=28.8

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .++.|...|... +++|..|||+.+++++   ..+.|+++-
T Consensus        53 ~~~~iL~~l~~~-~~~t~~ela~~l~is~---~tvs~~l~~   89 (162)
T 3cjn_A           53 AKMRALAILSAK-DGLPIGTLGIFAVVEQ---STLSRALDG   89 (162)
T ss_dssp             HHHHHHHHHHHS-CSEEHHHHHHHHTCCH---HHHHHHHHH
T ss_pred             HHHHHHHHHHHC-CCCCHHHHHHHHCCCh---hHHHHHHHH
Confidence            345566667764 7899999999999998   778887764

>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=85.55  E-value=0.44  Score=29.61  Aligned_cols=26  Identities=19%  Similarity=0.318  Sum_probs=22.3

Q ss_pred             CCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           58 GQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        58 ~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      +++.|..|||+.+++++   ..+.|+++.
T Consensus        20 ~~~~~~~ela~~l~vs~---~tvs~~l~~   45 (142)
T 1on2_A           20 KGYARVSDIAEALAVHP---SSVTKMVQK   45 (142)
T ss_dssp             HSSCCHHHHHHHHTSCH---HHHHHHHHH
T ss_pred             cCCCCHHHHHHHhCCCH---HHHHHHHHH
Confidence            37899999999999999   888887764

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

Probab=85.50  E-value=0.25  Score=32.00  Aligned_cols=36  Identities=6%  Similarity=0.115  Sum_probs=25.5

Q ss_pred             HhCchHHHHhCCCC--CCHHHHHHhcCCCCCChhhHHHHHh
Q 041968           47 ELGIPDVIHKHGQP--MTLSQIASALDIQKNKAHCIQRLMR   85 (87)
Q Consensus        47 eLgI~d~L~~~~gp--~S~~ELA~~~~~~~~~~~~L~RlLR   85 (87)
                      ++.|...|...++|  +|..|||+.+++++   ..+.|+++
T Consensus        71 ~~~iL~~L~~~~~~~~~t~~eLa~~l~is~---~tvs~~l~  108 (181)
T 2fbk_A           71 GWDLLLTLYRSAPPEGLRPTELSALAAISG---PSTSNRIV  108 (181)
T ss_dssp             HHHHHHHHHHHCCSSCBCHHHHHHHCSCCS---GGGSSHHH
T ss_pred             HHHHHHHHHHcCCCCCCCHHHHHHHHCCCH---HHHHHHHH
Confidence            44566667765544  99999999999988   55555443

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

Probab=85.34  E-value=0.38  Score=33.78  Aligned_cols=38  Identities=16%  Similarity=0.267  Sum_probs=29.4

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      .++.|...|.+. +++|..|||+.++.++   ..+.|.++-|
T Consensus       153 ~~~~IL~~L~~~-~~~s~~eLA~~lglsk---sTv~r~L~~L  190 (244)
T 2wte_A          153 EEMKLLNVLYET-KGTGITELAKMLDKSE---KTLINKIAEL  190 (244)
T ss_dssp             HHHHHHHHHHHH-TCBCHHHHHHHHTCCH---HHHHHHHHHH
T ss_pred             HHHHHHHHHHHc-CCCCHHHHHHHHCcCH---HHHHHHHHHH
Confidence            345566666653 6899999999999999   8888887643

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

Probab=85.26  E-value=0.41  Score=30.57  Aligned_cols=41  Identities=7%  Similarity=0.148  Sum_probs=31.8

Q ss_pred             HHHHhCchHHHHhCCCCCCHHHHHHhcC-----CCCCChhhHHHHHhcC
Q 041968           44 CAVELGIPDVIHKHGQPMTLSQIASALD-----IQKNKAHCIQRLMRIL   87 (87)
Q Consensus        44 aaveLgI~d~L~~~~gp~S~~ELA~~~~-----~~~~~~~~L~RlLR~L   87 (87)
                      +..+.-|.+.|.+.+++.|+.||...+.     ++.   ..++|.|..|
T Consensus        13 T~qR~~Il~~L~~~~~h~sa~eI~~~l~~~~~~is~---aTVYR~L~~L   58 (139)
T 3mwm_A           13 TRQRAAVSAALQEVEEFRSAQELHDMLKHKGDAVGL---TTVYRTLQSL   58 (139)
T ss_dssp             HHHHHHHHHHHTTCSSCEEHHHHHHHHHHTTCCCCH---HHHHHHHHHH
T ss_pred             CHHHHHHHHHHHhCCCCCCHHHHHHHHHHhCCCCCH---HHHHHHHHHH
Confidence            3456678888887668999999999984     444   8899998754

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

Probab=85.22  E-value=3.1  Score=26.32  Aligned_cols=37  Identities=19%  Similarity=0.381  Sum_probs=28.7

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .+..|...|... +++|..|||+.+++++   ..+.|+++-
T Consensus        46 ~~~~iL~~L~~~-~~~t~~eLa~~l~is~---~tvs~~l~~   82 (168)
T 2nyx_A           46 PQFRTLVILSNH-GPINLATLATLLGVQP---SATGRMVDR   82 (168)
T ss_dssp             HHHHHHHHHHHH-CSEEHHHHHHHHTSCH---HHHHHHHHH
T ss_pred             HHHHHHHHHHHc-CCCCHHHHHHHhCCCH---HHHHHHHHH
Confidence            345566667654 6899999999999998   778877754

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

Probab=84.95  E-value=0.35  Score=30.09  Aligned_cols=36  Identities=14%  Similarity=0.215  Sum_probs=28.2

Q ss_pred             HhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           47 ELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        47 eLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      ++.|...|... +++|..|||+.+++++   ..+.|+++-
T Consensus        49 ~~~iL~~l~~~-~~~t~~ela~~l~~s~---~tvs~~l~~   84 (153)
T 2pex_A           49 QYLVMLVLWET-DERSVSEIGERLYLDS---ATLTPLLKR   84 (153)
T ss_dssp             HHHHHHHHHHS-CSEEHHHHHHHHTCCH---HHHHHHHHH
T ss_pred             HHHHHHHHHhC-CCcCHHHHHHHhCCCc---ccHHHHHHH
Confidence            44566667664 7899999999999998   778877764

>3iwf_A Transcription regulator RPIR family; transcriptional, N-terminal, PSI, MCSG, structural genomics, midwest center structural genomics; 1.40A {Staphylococcus epidermidis}

Probab=84.78  E-value=0.4  Score=29.66  Aligned_cols=38  Identities=29%  Similarity=0.301  Sum_probs=29.1

Q ss_pred             HhCchHHHHhCC---CCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           47 ELGIPDVIHKHG---QPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        47 eLgI~d~L~~~~---gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      +-.|++.|-++.   ...|..|||+.+++++   ..+.|+.|.|
T Consensus        19 e~~ia~yil~~~~~~~~~si~elA~~~~vS~---aTv~Rf~kkL   59 (107)
T 3iwf_A           19 EKKIAQFILNYPHKVVNMTSQEIANQLETSS---TSIIRLSKKV   59 (107)
T ss_dssp             HHHHHHHHHHCHHHHTTCCHHHHHHHHTSCH---HHHHHHHHHH
T ss_pred             HHHHHHHHHhCHHHHHHCCHHHHHHHHCCCH---HHHHHHHHHh
Confidence            445666665433   5789999999999999   8899988753

>3oou_A LIN2118 protein; protein structure initiative, PSI-2, structural genomics, MI center for structural genomics, MCSG, unknown function; HET: BTB; 1.57A {Listeria innocua}

Probab=84.60  E-value=0.81  Score=27.30  Aligned_cols=24  Identities=17%  Similarity=0.397  Sum_probs=21.9

Q ss_pred             CCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968           59 QPMTLSQIASALDIQKNKAHCIQRLMR   85 (87)
Q Consensus        59 gp~S~~ELA~~~~~~~~~~~~L~RlLR   85 (87)
                      .+.|+.+||+.+|+++   ..|.|+++
T Consensus        20 ~~~~~~~lA~~~~~S~---~~l~r~fk   43 (108)
T 3oou_A           20 EGMSLKTLGNDFHINA---VYLGQLFQ   43 (108)
T ss_dssp             SCCCHHHHHHHHTSCH---HHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCH---HHHHHHHH
Confidence            6899999999999999   88999876

>2p5k_A Arginine repressor; DNA-binding domain, winged helix-turn-helix (WHTH), DNA binding protein; 1.00A {Bacillus subtilis} SCOP: a.4.5.3 PDB: 2p5l_C*

Probab=84.39  E-value=0.98  Score=24.27  Aligned_cols=30  Identities=13%  Similarity=0.334  Sum_probs=24.0

Q ss_pred             HHHHhCCCCCCHHHHHHhc-----CCCCCChhhHHHHHh
Q 041968           52 DVIHKHGQPMTLSQIASAL-----DIQKNKAHCIQRLMR   85 (87)
Q Consensus        52 d~L~~~~gp~S~~ELA~~~-----~~~~~~~~~L~RlLR   85 (87)
                      ..+.. +++.|+.||++.+     +++.   ..++|-|.
T Consensus        12 ~ll~~-~~~~t~~el~~~l~~~~~~vs~---~Tv~R~L~   46 (64)
T 2p5k_A           12 EIITS-NEIETQDELVDMLKQDGYKVTQ---ATVSRDIK   46 (64)
T ss_dssp             HHHHH-SCCCSHHHHHHHHHHTTCCCCH---HHHHHHHH
T ss_pred             HHHHc-CCCCCHHHHHHHHHHhCCCcCH---HHHHHHHH
Confidence            34444 4799999999999     8887   88998775

>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=84.37  E-value=0.74  Score=29.37  Aligned_cols=40  Identities=10%  Similarity=0.248  Sum_probs=29.5

Q ss_pred             HHHHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           38 NSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        38 ~~~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      ...+|++.+.|.      ...+. |+.|||+.+++++   ..|.++|+.|
T Consensus         8 ~~yAl~~L~~La------~~~~~-s~~~IA~~~~i~~---~~l~kIl~~L   47 (145)
T 1xd7_A            8 LAVAIHILSLIS------MDEKT-SSEIIADSVNTNP---VVVRRMISLL   47 (145)
T ss_dssp             HHHHHHHHHHHH------TCSCC-CHHHHHHHHTSCH---HHHHHHHHHH
T ss_pred             HHHHHHHHHHHH------hCCCC-CHHHHHHHHCcCH---HHHHHHHHHH
Confidence            345666666553      22235 9999999999999   9999998754

>3kor_A Possible Trp repressor; putative DNA-binding Trp repressor, TRPR like protein, struc genomics, transcription; 1.60A {Staphylococcus aureus}

Probab=84.17  E-value=1.3  Score=28.50  Aligned_cols=39  Identities=21%  Similarity=0.277  Sum_probs=31.0

Q ss_pred             HHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           43 KCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        43 ~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      ..+-++.|+..|.+  | .|-.|||+.+|+.+   ..+.|+-|.|
T Consensus        61 aLs~R~eV~klL~~--G-~syreIA~~~g~S~---aTIsRv~r~L   99 (119)
T 3kor_A           61 SLSQRLQVAKMIKQ--G-YTYATIEQESGAST---ATISRVKRSL   99 (119)
T ss_dssp             HHHHHHHHHHHHHH--T-CCHHHHHHHHCCCH---HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHc--C-CCHHHHHHHHCCCH---HHHHHHHHHH
Confidence            34555888888885  3 99999999999999   7788876653

>2w57_A Ferric uptake regulation protein; gene regulation, transcription regulation, transport, iron, repressor, DNA-binding, transcription; 2.60A {Vibrio cholerae}

Probab=84.10  E-value=0.33  Score=31.40  Aligned_cols=40  Identities=18%  Similarity=0.299  Sum_probs=31.1

Q ss_pred             HHHhCchHHHHhCC-CCCCHHHHHHhc-----CCCCCChhhHHHHHhcC
Q 041968           45 AVELGIPDVIHKHG-QPMTLSQIASAL-----DIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        45 aveLgI~d~L~~~~-gp~S~~ELA~~~-----~~~~~~~~~L~RlLR~L   87 (87)
                      -.+.-|.+.|.+.+ ++.|+.||.+.+     ++++   ..+||.|+.|
T Consensus        17 ~qR~~Il~~L~~~~~~h~sa~ei~~~l~~~~~~is~---aTVYR~L~~L   62 (150)
T 2w57_A           17 LPRLKILEVLQQPECQHISAEELYKKLIDLGEEIGL---ATVYRVLNQF   62 (150)
T ss_dssp             HHHHHHHHHHTSGGGSSEEHHHHHHHHHHTTCCCCH---HHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCCCH---HHHHHHHHHH
Confidence            34556788887666 799999999998     3455   8899998764

>3mkl_A HTH-type transcriptional regulator GADX; PSI2, MCSG, structural genomics, protein structure initiativ midwest center for structural genomics; 2.15A {Escherichia coli}

Probab=84.09  E-value=1.2  Score=27.10  Aligned_cols=32  Identities=28%  Similarity=0.399  Sum_probs=25.2

Q ss_pred             hHHHHhC-CCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968           51 PDVIHKH-GQPMTLSQIASALDIQKNKAHCIQRLMR   85 (87)
Q Consensus        51 ~d~L~~~-~gp~S~~ELA~~~~~~~~~~~~L~RlLR   85 (87)
                      .+.|.++ ..+.|+.+||+.+|+++   ..|.|+++
T Consensus        13 ~~~i~~~~~~~~~~~~lA~~~~~S~---~~l~r~fk   45 (120)
T 3mkl_A           13 CTVINNNIAHEWTLARIASELLMSP---SLLKKKLR   45 (120)
T ss_dssp             HHHHHTSTTSCCCHHHHHHHTTCCH---HHHHHHHH
T ss_pred             HHHHHHhccCCCCHHHHHHHHCcCH---HHHHHHHH
Confidence            3444433 36899999999999999   88999875

>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=83.99  E-value=0.57  Score=28.23  Aligned_cols=31  Identities=10%  Similarity=0.167  Sum_probs=24.2

Q ss_pred             hHHHHhCCCCCCHHHHHHhc-CCCCCChhhHHHHHhc
Q 041968           51 PDVIHKHGQPMTLSQIASAL-DIQKNKAHCIQRLMRI   86 (87)
Q Consensus        51 ~d~L~~~~gp~S~~ELA~~~-~~~~~~~~~L~RlLR~   86 (87)
                      ...|.  .++.+..||++.+ ++++   ..+.|.|+-
T Consensus        20 L~~L~--~~~~~~~eLa~~l~~is~---~tls~~L~~   51 (107)
T 2hzt_A           20 LXHLT--HGKKRTSELKRLMPNITQ---KMLTQQLRE   51 (107)
T ss_dssp             HHHHT--TCCBCHHHHHHHCTTSCH---HHHHHHHHH
T ss_pred             HHHHH--hCCCCHHHHHHHhcCCCH---HHHHHHHHH
Confidence            33444  3789999999999 9998   778777764

>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=83.89  E-value=0.63  Score=28.27  Aligned_cols=31  Identities=16%  Similarity=0.225  Sum_probs=24.3

Q ss_pred             hHHHHhCCCCCCHHHHHHhc-CCCCCChhhHHHHHhc
Q 041968           51 PDVIHKHGQPMTLSQIASAL-DIQKNKAHCIQRLMRI   86 (87)
Q Consensus        51 ~d~L~~~~gp~S~~ELA~~~-~~~~~~~~~L~RlLR~   86 (87)
                      ...|.+  ++.+..|||+.+ ++++   ..+.|.++-
T Consensus        28 L~~L~~--~~~~~~eLa~~l~~is~---~tvs~~L~~   59 (112)
T 1z7u_A           28 MDELFQ--GTKRNGELMRALDGITQ---RVLTDRLRE   59 (112)
T ss_dssp             HHHHHH--SCBCHHHHHHHSTTCCH---HHHHHHHHH
T ss_pred             HHHHHh--CCCCHHHHHHHhccCCH---HHHHHHHHH
Confidence            334543  689999999999 9998   888887764

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

Probab=83.88  E-value=0.37  Score=29.66  Aligned_cols=36  Identities=8%  Similarity=0.167  Sum_probs=27.2

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .+..|...|... ++ |..|||..+++++   ..+.|+++-
T Consensus        38 ~~~~iL~~l~~~-~~-~~~~la~~l~~~~---~tvs~~l~~   73 (144)
T 3f3x_A           38 LDFSILKATSEE-PR-SMVYLANRYFVTQ---SAITAAVDK   73 (144)
T ss_dssp             HHHHHHHHHHHS-CE-EHHHHHHHHTCCH---HHHHHHHHH
T ss_pred             HHHHHHHHHHHC-CC-CHHHHHHHHCCCh---hHHHHHHHH
Confidence            344566667765 44 9999999999999   778777754

>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=83.88  E-value=3.1  Score=25.49  Aligned_cols=35  Identities=17%  Similarity=0.335  Sum_probs=27.3

Q ss_pred             hCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           48 LGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        48 LgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      +.|...|... ++.|..|||+.+++++   ..+.|+++-
T Consensus        40 ~~iL~~l~~~-~~~t~~ela~~l~~s~---~tvs~~l~~   74 (155)
T 1s3j_A           40 LFVLASLKKH-GSLKVSEIAERMEVKP---SAVTLMADR   74 (155)
T ss_dssp             HHHHHHHHHH-SEEEHHHHHHHHTSCH---HHHHHHHHH
T ss_pred             HHHHHHHHHc-CCCCHHHHHHHHCCCH---HHHHHHHHH
Confidence            3455666653 6899999999999998   778887764

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

Probab=83.58  E-value=0.42  Score=30.02  Aligned_cols=38  Identities=18%  Similarity=0.336  Sum_probs=28.2

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcC----CCCCChhhHHHHHhc
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALD----IQKNKAHCIQRLMRI   86 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~----~~~~~~~~L~RlLR~   86 (87)
                      .+..|...|.+..++.|..||++.++    +++   ..+.|++.-
T Consensus        10 ~e~~vL~~L~~~~~~~t~~el~~~l~~~~~~~~---~Tvt~~l~r   51 (138)
T 2g9w_A           10 LERAVMDHLWSRTEPQTVRQVHEALSARRDLAY---TTVMAVLQR   51 (138)
T ss_dssp             HHHHHHHHHHTCSSCEEHHHHHHHHTTTCCCCH---HHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCCCHHHHHHHHhccCCCCH---HHHHHHHHH
Confidence            35566777876347999999999998    455   777777753

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

Probab=83.51  E-value=0.43  Score=29.74  Aligned_cols=36  Identities=17%  Similarity=0.337  Sum_probs=27.6

Q ss_pred             HhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           47 ELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        47 eLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      +..|...|... +++|..|||+.+++++   ..+.|+++-
T Consensus        43 q~~iL~~l~~~-~~~~~~eLa~~l~~~~---~~vs~~l~~   78 (149)
T 4hbl_A           43 QYLVMLTLWEE-NPQTLNSIGRHLDLSS---NTLTPMLKR   78 (149)
T ss_dssp             HHHHHHHHHHS-SSEEHHHHHHHHTCCH---HHHHHHHHH
T ss_pred             HHHHHHHHHHC-CCCCHHHHHHHHCCCH---HHHHHHHHH
Confidence            44445566654 8999999999999999   777777653

>1jko_C HIN recombinase, DNA-invertase HIN; water-mediated recognition, protein-DNA complex, A10G mutant, DNA binding protein/DNA complex; 2.24A {Synthetic} SCOP: a.4.1.2 PDB: 1ijw_C* 1jj6_C* 1jj8_C* 1hcr_A 1jkp_C 1jkq_C 1jkr_C

Probab=82.85  E-value=1.1  Score=22.58  Aligned_cols=22  Identities=18%  Similarity=0.173  Sum_probs=19.7

Q ss_pred             CCHHHHHHhcCCCCCChhhHHHHHh
Q 041968           61 MTLSQIASALDIQKNKAHCIQRLMR   85 (87)
Q Consensus        61 ~S~~ELA~~~~~~~~~~~~L~RlLR   85 (87)
                      .|..|||..+|++.   ..++|.++
T Consensus        22 ~s~~~ia~~lgvs~---~Tv~r~l~   43 (52)
T 1jko_C           22 HPRQQLAIIFGIGV---STLYRYFP   43 (52)
T ss_dssp             CCHHHHHHTTSCCH---HHHHHHSC
T ss_pred             CCHHHHHHHHCCCH---HHHHHHHH
Confidence            79999999999998   88888775

>2k9s_A Arabinose operon regulatory protein; activator, arabinose catabolism, carbohydrate metabolism, cytoplasm, DNA-binding, repressor, transcription; NMR {Escherichia coli}

Probab=82.79  E-value=1.5  Score=26.05  Aligned_cols=24  Identities=13%  Similarity=0.312  Sum_probs=21.9

Q ss_pred             CCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968           59 QPMTLSQIASALDIQKNKAHCIQRLMR   85 (87)
Q Consensus        59 gp~S~~ELA~~~~~~~~~~~~L~RlLR   85 (87)
                      .+.|+++||+.+|+++   ..|.|+++
T Consensus        19 ~~~~~~~lA~~~~~S~---~~l~r~fk   42 (107)
T 2k9s_A           19 SNFDIASVAQHVCLSP---SRLSHLFR   42 (107)
T ss_dssp             SSCCHHHHHHHTTSCH---HHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCH---HHHHHHHH
Confidence            6899999999999999   88998876

>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=82.72  E-value=0.32  Score=29.92  Aligned_cols=37  Identities=8%  Similarity=0.216  Sum_probs=28.5

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .++.|...|... ++.|..|||+.+++++   ..+.|+++-
T Consensus        41 ~~~~iL~~l~~~-~~~~~~~la~~l~~~~---~tvs~~l~~   77 (147)
T 1z91_A           41 PQYLALLLLWEH-ETLTVKKMGEQLYLDS---GTLTPMLKR   77 (147)
T ss_dssp             HHHHHHHHHHHH-SEEEHHHHHHTTTCCH---HHHHHHHHH
T ss_pred             HHHHHHHHHHHC-CCCCHHHHHHHHCCCc---CcHHHHHHH
Confidence            345556667654 6899999999999998   778887764

>1tc3_C Protein (TC3 transposase); DNA binding, helix-turn-helix, TC1/mariner family, complex (transposase/DNA), DNA binding protein/DNA complex; HET: DNA; 2.45A {Caenorhabditis elegans} SCOP: a.4.1.2

Probab=82.67  E-value=1.1  Score=22.15  Aligned_cols=23  Identities=17%  Similarity=0.595  Sum_probs=20.2

Q ss_pred             CCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968           60 PMTLSQIASALDIQKNKAHCIQRLMR   85 (87)
Q Consensus        60 p~S~~ELA~~~~~~~~~~~~L~RlLR   85 (87)
                      ..|..|||+.+|+++   ..++|.++
T Consensus        21 g~s~~~IA~~lgis~---~Tv~~~~~   43 (51)
T 1tc3_C           21 NVSLHEMSRKISRSR---HCIRVYLK   43 (51)
T ss_dssp             TCCHHHHHHHHTCCH---HHHHHHHH
T ss_pred             CCCHHHHHHHHCcCH---HHHHHHHh
Confidence            379999999999998   88888875

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

Probab=82.17  E-value=0.42  Score=30.08  Aligned_cols=33  Identities=12%  Similarity=0.164  Sum_probs=25.8

Q ss_pred             chHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           50 IPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        50 I~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      |...|... +++|..|||+.+++++   ..+.|+++-
T Consensus        55 vL~~l~~~-~~~t~~eLa~~l~~~~---~tvs~~l~~   87 (159)
T 3s2w_A           55 FLMRLYRE-DGINQESLSDYLKIDK---GTTARAIQK   87 (159)
T ss_dssp             HHHHHHHS-CSEEHHHHHHHHTCCH---HHHHHHHHH
T ss_pred             HHHHHHHC-CCCCHHHHHHHHCCCH---HHHHHHHHH
Confidence            44556654 7899999999999999   777777653

>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=81.90  E-value=0.66  Score=30.38  Aligned_cols=39  Identities=23%  Similarity=0.175  Sum_probs=30.0

Q ss_pred             HHHhCchHHHHhC-CCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           45 AVELGIPDVIHKH-GQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        45 aveLgI~d~L~~~-~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      ..+..|...|... ++++|..|||+.+++++   ..+.|+++-
T Consensus        41 ~~q~~vL~~L~~~~~~~~t~~eLa~~l~is~---~tvs~~l~~   80 (189)
T 3nqo_A           41 SRQYMTILSILHLPEEETTLNNIARKMGTSK---QNINRLVAN   80 (189)
T ss_dssp             HHHHHHHHHHHHSCGGGCCHHHHHHHHTSCH---HHHHHHHHH
T ss_pred             HHHHHHHHHHHhccCCCcCHHHHHHHHCCCH---HHHHHHHHH
Confidence            3455666677753 37999999999999998   778777754

>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=81.84  E-value=0.25  Score=29.18  Aligned_cols=25  Identities=12%  Similarity=0.204  Sum_probs=21.1

Q ss_pred             CCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           59 QPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        59 gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      +++|..|||+.+++++   ..+.|++.-
T Consensus        29 ~~~t~~eLa~~l~i~~---~tvs~~l~~   53 (95)
T 2qvo_A           29 NDVYIQYIASKVNSPH---SYVWLIIKK   53 (95)
T ss_dssp             CCEEHHHHHHHSSSCH---HHHHHHHHH
T ss_pred             CCcCHHHHHHHHCcCH---HHHHHHHHH
Confidence            3499999999999999   888887754

>2hoe_A N-acetylglucosamine kinase; TM1224, structural genomics, PSI-2, protein structure initiative, joint center structural genomics, JCSG; 2.46A {Thermotoga maritima} SCOP: a.4.5.63 c.55.1.10 c.55.1.10

Probab=81.74  E-value=0.54  Score=34.19  Aligned_cols=45  Identities=18%  Similarity=0.244  Sum_probs=30.3

Q ss_pred             HHHHHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           37 INSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        37 ~~~~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      -.+.++|..-+..|.+.|. + +++|-.|||+.+|+.+   ..+.++++-
T Consensus        12 ~~~~~~~~~~~~~il~~l~-~-~~~sr~~la~~~gls~---~tv~~~v~~   56 (380)
T 2hoe_A           12 HMPKSVRAENISRILKRIM-K-SPVSRVELAEELGLTK---TTVGEIAKI   56 (380)
T ss_dssp             ----------CCCSHHHHH-H-SCBCHHHHHHHHTCCH---HHHHHHHHH
T ss_pred             cCchhHHHHHHHHHHHHHH-c-CCcCHHHHHHHHCcCH---HHHHHHHHH
Confidence            3477888888889999998 4 8999999999999998   777777653

>2p4w_A Transcriptional regulatory protein ARSR family; archaea, PHR, heat shock, transcriptional regulation, winged DNA binding; 2.60A {Pyrococcus furiosus} SCOP: a.4.5.64

Probab=81.58  E-value=0.74  Score=31.33  Aligned_cols=38  Identities=21%  Similarity=0.372  Sum_probs=29.1

Q ss_pred             HHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           45 AVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        45 aveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      -..+.|...|.+  +|.|..|||+.+|+++   ..+.+.|+.|
T Consensus        15 ~~rl~IL~~L~~--~~~s~~eLa~~l~is~---stvs~hLk~L   52 (202)
T 2p4w_A           15 ETRRRILFLLTK--RPYFVSELSRELGVGQ---KAVLEHLRIL   52 (202)
T ss_dssp             HHHHHHHHHHHH--SCEEHHHHHHHHTCCH---HHHHHHHHHH
T ss_pred             HHHHHHHHHHHh--CCCCHHHHHHHHCcCH---HHHHHHHHHH
Confidence            345556666653  7999999999999998   8888877643

>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=81.50  E-value=0.3  Score=30.15  Aligned_cols=34  Identities=6%  Similarity=0.187  Sum_probs=25.8

Q ss_pred             CchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           49 GIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        49 gI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .|...|.. .++.|..|||+.+++++   ..+.|+++-
T Consensus        40 ~vL~~l~~-~~~~t~~eLa~~l~~~~---~tvs~~l~~   73 (140)
T 3hsr_A           40 IVLMAIEN-DEKLNIKKLGERVFLDS---GTLTPLLKK   73 (140)
T ss_dssp             HHHHHSCT-TCEEEHHHHHHHHTCCH---HHHHHHHHH
T ss_pred             HHHHHHHH-cCCcCHHHHHHHHCCCh---hhHHHHHHH
Confidence            34444554 37999999999999999   778777653

>1bl0_A Protein (multiple antibiotic resistance protein), DNA (5'- D(*CP*CP*GP*AP*TP*GP*CP*CP*AP*CP*GP*TP*TP*TP*TP*GP*CP*TP*AP *AP*AP*TP* CP*C)-3')...; transcriptional activator; HET: DNA; 2.30A {Escherichia coli} SCOP: a.4.1.8 a.4.1.8 PDB: 1xs9_A

Probab=81.32  E-value=1.1  Score=27.61  Aligned_cols=32  Identities=22%  Similarity=0.445  Sum_probs=25.0

Q ss_pred             hHHHHhC-CCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968           51 PDVIHKH-GQPMTLSQIASALDIQKNKAHCIQRLMR   85 (87)
Q Consensus        51 ~d~L~~~-~gp~S~~ELA~~~~~~~~~~~~L~RlLR   85 (87)
                      .+.|.++ ..+.|+++||+.+|+++   ..|.|+++
T Consensus        17 ~~~i~~~~~~~~sl~~lA~~~~~S~---~~l~r~fk   49 (129)
T 1bl0_A           17 LDWIEDNLESPLSLEKVSERSGYSK---WHLQRMFK   49 (129)
T ss_dssp             HHHHHTTTTSCCCCHHHHHHSSSCH---HHHHHHHH
T ss_pred             HHHHHHccCCCCCHHHHHHHHCcCH---HHHHHHHH
Confidence            3444433 36799999999999999   88998876

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

Probab=81.24  E-value=0.95  Score=28.72  Aligned_cols=33  Identities=18%  Similarity=0.200  Sum_probs=25.5

Q ss_pred             chHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968           50 IPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR   85 (87)
Q Consensus        50 I~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR   85 (87)
                      +.-.|.+.+++.+..|||+.+++++   ..+.|++.
T Consensus        36 vL~~L~~~~~~~~~~eLa~~l~~~~---~tvs~~v~   68 (151)
T 4aik_A           36 TLYNINRLPPEQSQIQLAKAIGIEQ---PSLVRTLD   68 (151)
T ss_dssp             HHHHHHHSCTTSCHHHHHHHHTSCH---HHHHHHHH
T ss_pred             HHHHHHHcCCCCcHHHHHHHHCcCH---HHHHHHHH
Confidence            4445665567788899999999999   77777765

>3lsg_A Two-component response regulator YESN; structural genomics, PSI-2, protein structure initiative, MCSG; 2.05A {Fusobacterium nucleatum}

Probab=81.11  E-value=1.2  Score=26.23  Aligned_cols=24  Identities=21%  Similarity=0.419  Sum_probs=21.7

Q ss_pred             CCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968           59 QPMTLSQIASALDIQKNKAHCIQRLMR   85 (87)
Q Consensus        59 gp~S~~ELA~~~~~~~~~~~~L~RlLR   85 (87)
                      ++.|+.+||+.+|+++   ..|.|+++
T Consensus        18 ~~~~~~~lA~~~~~S~---~~l~r~fk   41 (103)
T 3lsg_A           18 SQFTLSVLSEKLDLSS---GYLSIMFK   41 (103)
T ss_dssp             TTCCHHHHHHHTTCCH---HHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCH---HHHHHHHH
Confidence            5899999999999999   88988875

>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=80.82  E-value=0.6  Score=28.16  Aligned_cols=36  Identities=11%  Similarity=0.207  Sum_probs=26.8

Q ss_pred             CchHHHHhCC-CCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           49 GIPDVIHKHG-QPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        49 gI~d~L~~~~-gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      .|...|..++ ..++..||+..++.+.   ..+.|+|+.|
T Consensus        24 ~Vl~~I~~~g~~gi~qkeLa~~~~l~~---~tvt~iLk~L   60 (91)
T 2dk5_A           24 LVYQIIEDAGNKGIWSRDVRYKSNLPL---TEINKILKNL   60 (91)
T ss_dssp             HHHHHHHHHCTTCEEHHHHHHHTTCCH---HHHHHHHHHH
T ss_pred             HHHHHHHHcCCCCcCHHHHHHHHCCCH---HHHHHHHHHH
Confidence            3455555432 4799999999999998   8888887643

---

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	87
d1fp2a1	101	a.4.5.29 (A:8-108) Isoflavone O-methyltransferase	4e-28
d1fp1d1	110	a.4.5.29 (D:19-128) Chalcone O-methyltransferase {	2e-18
d1kyza1	107	a.4.5.29 (A:13-119) Caffeic acid/5-hydroxyferulic	6e-16
d1qzza1	92	a.4.5.29 (A:10-101) Aclacinomycin-10-hydroxylase R	8e-16
d1tw3a1	85	a.4.5.29 (A:14-98) Carminomycin 4-O-methyltransfer	9e-11
d1mkma1	75	a.4.5.33 (A:1-75) Transcriptional regulator IclR,	4e-04

>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 = 95.4 bits (237), Expect = 4e-28
 Identities = 31/69 (44%), Positives = 48/69 (69%)

Query: 19 SSELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAH 78
           SE+ KAQA ++   + +I+SMSLK AVE+ IP++I  HG+P++LS + S L +  +K  
Sbjct: 3  PSEIFKAQALLYKHIYAFIDSMSLKWAVEMNIPNIIQNHGKPISLSNLVSILQVPSSKIG 62

Query: 79 CIQRLMRIL 87
           ++RLMR L
Sbjct: 63 NVRRLMRYL 71

>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 = 71.0 bits (174), Expect = 2e-18
 Identities = 17/70 (24%), Positives = 31/70 (44%), Gaps = 6/70 (8%)

Query: 24 KAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQP---MTLSQIASALDI---QKNKA 77
           A         N +    L  A++L + ++I K   P   M+ S+IAS L       +  
Sbjct: 5  SACLSAMVLTTNLVYPAVLNAAIDLNLFEIIAKATPPGAFMSPSEIASKLPASTQHSDLP 64

Query: 78 HCIQRLMRIL 87
          + + R++R+L
Sbjct: 65 NRLDRMLRLL 74

>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 = 64.5 bits (157), Expect = 6e-16
 Identities = 18/58 (31%), Positives = 30/58 (51%), Gaps = 3/58 (5%)

Query: 33 AFNYINSMSLKCAVELGIPDVIHKHGQPMTLS--QIASALDI-QKNKAHCIQRLMRIL 87
          A   +  M LK A+EL + ++I K G    +S  +IAS L     +    + R++R+L
Sbjct: 15 ASASVLPMILKSALELDLLEIIAKAGPGAQISPIEIASQLPTTNPDAPVMLDRMLRLL 72

>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 = 63.6 bits (155), Expect = 8e-16
 Identities = 14/64 (21%), Positives = 25/64 (39%), Gaps = 5/64 (7%)

Query: 24 KAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRL 83
          +    +     N +  M+L+ A  L + D +       TL+ +A   D        + RL
Sbjct: 6  QDLDVLLKNLGNLVTPMALRVAATLRLVDHL--LAGADTLAGLADRTDTH---PQALSRL 60

Query: 84 MRIL 87
          +R L
Sbjct: 61 VRHL 64

>d1tw3a1 a.4.5.29 (A:14-98) Carminomycin 4-O-methyltransferase {Streptomyces peucetius [TaxId: 1950]} Length = 85

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Plant O-methyltransferase, N-terminal domain
domain: Carminomycin 4-O-methyltransferase
species: Streptomyces peucetius [TaxId: 1950]

 Score = 51.0 bits (122), Expect = 9e-11
 Identities = 12/53 (22%), Positives = 22/53 (41%), Gaps = 5/53 (9%)

Query: 35 NYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL 87
          +    M ++ A  L + D  H      T+  +A+  D +      + RL+R L
Sbjct: 11 SLHTPMVVRTAATLRLVD--HILAGARTVKALAARTDTR---PEALLRLIRHL 58

>d1mkma1 a.4.5.33 (A:1-75) Transcriptional regulator IclR, N-terminal domain {Thermotoga maritima [TaxId: 2336]} Length = 75

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]

 Score = 33.5 bits (77), Expect = 4e-04
 Identities = 10/40 (25%), Positives = 21/40 (52%), Gaps = 3/40 (7%)

Query: 48 LGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL 87
            I D I K+   +++S+IA   ++  + A+   + M +L
Sbjct: 8  FEILDFIVKNPGDVSVSEIAEKFNMSVSNAY---KYMVVL 44

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	87
d1fp2a1	101	Isoflavone O-methyltransferase {Alfalfa (Medicago	99.82
d1fp1d1	110	Chalcone O-methyltransferase {Alfalfa (Medicago sa	99.71
d1kyza1	107	Caffeic acid/5-hydroxyferulic acid 3/5-O-methyltra	99.69
d1tw3a1	85	Carminomycin 4-O-methyltransferase {Streptomyces p	99.54
d1qzza1	92	Aclacinomycin-10-hydroxylase RdmB {Streptomyces pu	99.53
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	97.11
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	94.83
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	94.18
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	93.82
d1ulya_	190	Hypothetical protein PH1932 {Pyrococcus horikoshii	93.58
d1xd7a_	127	Hypothetical protein ywnA {Bacillus subtilis [TaxI	93.51
d2hoea1	62	N-acetylglucosamine kinase {Thermotoga maritima [T	92.78
d1r1ta_	98	SmtB repressor {Cyanobacteria (Synechococcus), pcc	92.62
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	92.58
d2hr3a1	145	Probable transcriptional regulator PA3067 {Pseudom	92.56
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	92.39
d1ub9a_	100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	92.39
d1z6ra1	70	Mlc protein N-terminal domain {Escherichia coli [T	92.39
d1r1ua_	94	Metal-sensing transcriptional repressor CzrA {Stap	92.18
d1lvaa3	64	C-terminal fragment of elongation factor SelB {Moo	92.11
d1ylfa1	138	Hypothetical protein BC1842 {Bacillus cereus [TaxI	91.61
d1bl0a1	54	MarA {Escherichia coli [TaxId: 562]}	91.49
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	91.44
d1u2wa1	108	Cadmium efflux system accessory protein CadC {Stap	91.32
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	91.1
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	90.71
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	90.67
d1d5ya1	54	Rob transcription factor, N-terminal domain {Esche	90.66
d2p4wa1	194	Transcriptional regulatory protein PF1790 {Pyrococ	89.46
d2o3fa1	83	Putative transcriptional regulator YbbH {Bacillus	89.16
d1s3ja_	143	Putative transcriptional regulator YusO {Bacillus	88.56
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	87.65
d3broa1	135	Transcriptional regulator OEOE1854 {Oenococcus oen	87.19
d2etha1	140	Putative transcriptional regulator TM0816 {Thermot	85.93
d1q1ha_	88	Transcription factor E/IIe-alpha, N-terminal domai	85.89
d1gdta1	43	gamma,delta resolvase (C-terminal domain) {Escheri	84.19
d1efaa1	59	Lac repressor (LacR), N-terminal domain {Escherich	84.05
d2a61a1	139	Transcriptional regulator TM0710 {Thermotoga marit	83.37
d2fbha1	137	Transcriptional regulator PA3341 {Pseudomonas aeru	81.54
d1j75a_	57	Dlm-1 {Mouse (Mus musculus) [TaxId: 10090]}	81.37
d1v7ba1	74	Transcriptional regulator Cgl2612 {Corynebacterium	81.04
d2a6ca1	69	HTH-motif protein NE1354 {Nitrosomonas europaea [T	80.63

>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=99.82  E-value=4.9e-21  Score=120.55  Aligned_cols=70  Identities=44%  Similarity=0.770  Sum_probs=65.8

Q ss_pred             CcHHhHHHHHHHHHHHHHHHHHHHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           18 SSSELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        18 ~~~~~~~~~~~l~~l~~g~~~~~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      .++|.++++.++|+++|||+.+++|++|++|||||+|++++||+|++|||+.+|+++.+++.|.|+||+|
T Consensus         2 ~~~e~~qaq~~l~~~~~gf~~s~aL~~aveLgi~d~l~~~~~p~t~~eLa~~~~~~~~~~~~L~RlLR~L   71 (101)
T d1fp2a1           2 KPSEIFKAQALLYKHIYAFIDSMSLKWAVEMNIPNIIQNHGKPISLSNLVSILQVPSSKIGNVRRLMRYL   71 (101)
T ss_dssp             CSTHHHHHHHHHHHHHTTHHHHHHHHHHHHTTHHHHHHHHTSCEEHHHHHHHHTCCGGGHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHHHHHhHHHHHHHHHHHHcCcHHHHHHcCCCCCHHHHHHHcCCCCccchHHHHHHHHH
Confidence            4678999999999999999999999999999999999987899999999999999887878999999986

>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=99.71  E-value=4.7e-18  Score=108.53  Aligned_cols=67  Identities=25%  Similarity=0.345  Sum_probs=58.6

Q ss_pred             HhHHHHHHHHHHHHHHHHHHHHHHHHHhCchHHHHhCCCC---CCHHHHHHhcCC---CCCChhhHHHHHhcC
Q 041968           21 ELLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQP---MTLSQIASALDI---QKNKAHCIQRLMRIL   87 (87)
Q Consensus        21 ~~~~~~~~l~~l~~g~~~~~aL~aaveLgI~d~L~~~~gp---~S~~ELA~~~~~---~~~~~~~L~RlLR~L   87 (87)
                      ++.++..+.+++.++++.+|+||+||||||||+|+++|+|   +|++|||+.+++   +|+++..|+|+||+|
T Consensus         2 ~~~~~~l~a~~L~~~~v~pMaLk~AieLgI~diI~~~G~~~~~ls~~ela~~lp~~~~~p~~~~~L~RiLRlL   74 (110)
T d1fp1d1           2 TEDSACLSAMVLTTNLVYPAVLNAAIDLNLFEIIAKATPPGAFMSPSEIASKLPASTQHSDLPNRLDRMLRLL   74 (110)
T ss_dssp             CHHHHHHHHHHHHHTTHHHHHHHHHHHTTHHHHHHTCSSTTCCBCHHHHHTTSCGGGCCTTHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHHHHhhHHHHHHHHHHHcCCHHHHHHcCCCCCCCCHHHHHHhCCCCCCCccHHHHHHHHHHHH
Confidence            3567788899999999999999999999999999987655   899999999986   555567899999986

>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=99.69  E-value=1.8e-17  Score=105.23  Aligned_cols=66  Identities=27%  Similarity=0.341  Sum_probs=57.7

Q ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHHHhCchHHHHhCC--CCCCHHHHHHhcCC-CCCChhhHHHHHhcC
Q 041968           22 LLKAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHG--QPMTLSQIASALDI-QKNKAHCIQRLMRIL   87 (87)
Q Consensus        22 ~~~~~~~l~~l~~g~~~~~aL~aaveLgI~d~L~~~~--gp~S~~ELA~~~~~-~~~~~~~L~RlLR~L   87 (87)
                      +.++....+++.++++.||+||+|+||||||+|+++|  +++|+.|||+++++ +|.++..|+|+||+|
T Consensus         4 dee~~l~a~~L~~~~v~pmaLk~AieLgI~DiI~~~G~~~~ls~~eia~~l~~~~p~~~~~L~RilR~L   72 (107)
T d1kyza1           4 DEEANLFAMQLASASVLPMILKSALELDLLEIIAKAGPGAQISPIEIASQLPTTNPDAPVMLDRMLRLL   72 (107)
T ss_dssp             HHHHHHHHHHHHTTTHHHHHHHHHHHTTHHHHHHTTCTTCCBCHHHHHHTSSCCCTTHHHHHHHHHHHH
T ss_pred             cHHHHHHHHHHHHhhHHHHHHHHHHHcCCHHHHHHcCCCCCCCHHHHHHhcCCCCCcchHHHHHHHHHH
Confidence            4556677889999999999999999999999999876  57899999999998 455567899999986

>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=99.54  E-value=3.6e-15  Score=90.33  Aligned_cols=53  Identities=23%  Similarity=0.238  Sum_probs=48.7

Q ss_pred             HHHHHHHHHHHHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           30 WNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        30 ~~l~~g~~~~~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      +....+|+.+++|++|++|||||+|+  +||+|++|||+++|++|   ..+.|+||+|
T Consensus         6 l~~l~~~~~~~aL~~av~L~ifd~l~--~gp~s~~eLA~~~g~~~---~~l~rlLr~l   58 (85)
T d1tw3a1           6 LIRLGSLHTPMVVRTAATLRLVDHIL--AGARTVKALAARTDTRP---EALLRLIRHL   58 (85)
T ss_dssp             HHHHHCSHHHHHHHHHHHTTHHHHHH--TTCCBHHHHHHHHTCCH---HHHHHHHHHH
T ss_pred             HHHHHchHHHHHHHHHHHcCcHHHhc--cCCCCHHHHHHHhCcCh---hHHHHHHHHH
Confidence            44557999999999999999999997  58999999999999999   9999999975

>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=99.53  E-value=2.6e-15  Score=92.47  Aligned_cols=59  Identities=24%  Similarity=0.311  Sum_probs=54.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           24 KAQAQVWNCAFNYINSMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        24 ~~~~~l~~l~~g~~~~~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      +....+++++.+|+.+++|++|++|||||+|+  +||+|++|||+++|+++   ..+.|+||+|
T Consensus         6 ~~~d~ll~~~~~~~~~~~L~~aveL~ifd~L~--~gp~t~~eLA~~~g~~~---~~l~rLlr~L   64 (92)
T d1qzza1           6 QDLDVLLKNLGNLVTPMALRVAATLRLVDHLL--AGADTLAGLADRTDTHP---QALSRLVRHL   64 (92)
T ss_dssp             HHHHHHHHTTTCCHHHHHHHHHHHTTHHHHHH--TTCCSHHHHHHHHTCCH---HHHHHHHHHH
T ss_pred             hhHHHHHHHHHchHHHHHHHHHHHcCchHHHh--CCCCCHHHHHHHHCcCc---hHHHHHHHHH
Confidence            45567888899999999999999999999998  58999999999999999   9999999975

>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=97.11  E-value=0.00011  Score=42.00  Aligned_cols=37  Identities=24%  Similarity=0.349  Sum_probs=32.3

Q ss_pred             hCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           48 LGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        48 LgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      +.|.|.++.+++|+|+.|||+.+|.++   ..++|++..|
T Consensus         8 l~IL~~~a~~~~~~s~~eia~~~~~~~---st~~rll~tL   44 (75)
T d1mkma1           8 FEILDFIVKNPGDVSVSEIAEKFNMSV---SNAYKYMVVL   44 (75)
T ss_dssp             HHHHHHHHHCSSCBCHHHHHHHTTCCH---HHHHHHHHHH
T ss_pred             HHHHHHHHhCCCCCCHHHHHHHHCcCH---HHHHHHHHHH
Confidence            457888888789999999999999999   8999998753

>d1z05a1 a.4.5.63 (A:10-80) Transcriptional regulator VC2007 N-terminal domain {Vibrio cholerae [TaxId: 666]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: Transcriptional regulator VC2007 N-terminal domain
species: Vibrio cholerae [TaxId: 666]

Probab=94.83  E-value=0.0091  Score=32.99  Aligned_cols=36  Identities=11%  Similarity=0.258  Sum_probs=29.8

Q ss_pred             HhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           47 ELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        47 eLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .-.|+..|..+ +|+|..|||+.+|+++   ..+.++++-
T Consensus         8 ~~~Il~~l~~~-g~~sr~eLa~~~glS~---~Tv~~~l~~   43 (71)
T d1z05a1           8 AGRVYKLIDQK-GPISRIDLSKESELAP---ASITKITRE   43 (71)
T ss_dssp             HHHHHHHHHHH-CSBCHHHHHHHHTCCH---HHHHHHHHH
T ss_pred             HHHHHHHHHHc-CCcCHHHHHHHHCCCH---HHHHHHHHH
Confidence            34578888764 8999999999999999   888887764

>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=94.18  E-value=0.0072  Score=35.69  Aligned_cols=35  Identities=11%  Similarity=0.263  Sum_probs=27.3

Q ss_pred             CchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           49 GIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        49 gI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .|+..|.+.+||+|+.|||..+++++   ..+.|+++-
T Consensus        25 ~iL~~L~~~~~~~t~~eLa~~~~i~~---~tvs~~l~~   59 (109)
T d2d1ha1          25 AVLLKMVEIEKPITSEELADIFKLSK---TTVENSLKK   59 (109)
T ss_dssp             HHHHHHHHHCSCEEHHHHHHHHTCCH---HHHHHHHHH
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHCccH---hHHHHHHHH
Confidence            34444544468999999999999999   888888764

>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=93.82  E-value=0.031  Score=30.37  Aligned_cols=41  Identities=15%  Similarity=0.274  Sum_probs=32.0

Q ss_pred             HHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           43 KCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        43 ~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      +.--...|.+.|.++.+++|+.|||+.++++.   ..++|=+..
T Consensus         5 k~eR~~~Il~~L~~~~~~vs~~~La~~l~VS~---~TI~rdi~~   45 (65)
T d1j5ya1           5 RQERLKSIVRILERSKEPVSGAQLAEELSVSR---QVIVQDIAY   45 (65)
T ss_dssp             HHHHHHHHHHHHHHCSSCBCHHHHHHHHTSCH---HHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCCCcHHHHHHHHCCCH---HHHHHHHHH
Confidence            33444567888877668999999999999999   888886543

>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=93.58  E-value=0.021  Score=36.39  Aligned_cols=42  Identities=19%  Similarity=0.224  Sum_probs=33.0

Q ss_pred             HHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           41 SLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        41 aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      +|.--..+.|.+.|.  .+|.|+.|||+.+|.++   ..+.+-|+.|
T Consensus        15 ~l~~p~R~~Il~~L~--~~~~s~~ela~~lg~s~---~~v~~hl~~L   56 (190)
T d1ulya_          15 VMLEDTRRKILKLLR--NKEMTISQLSEILGKTP---QTIYHHIEKL   56 (190)
T ss_dssp             HHHSHHHHHHHHHHT--TCCBCHHHHHHHHTCCH---HHHHHHHHHH
T ss_pred             HhCCHHHHHHHHHHH--hCCCCHHHHHHHHCcCH---HHHHHHHHHH
Confidence            344446677888886  48999999999999999   8788877653

>d1xd7a_ a.4.5.55 (A:) Hypothetical protein ywnA {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcriptional regulator Rrf2
domain: Hypothetical protein ywnA
species: Bacillus subtilis [TaxId: 1423]

Probab=93.51  E-value=0.025  Score=34.25  Aligned_cols=30  Identities=17%  Similarity=0.350  Sum_probs=25.7

Q ss_pred             HHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           54 IHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        54 L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      |+. ++++|..+||+.++++|   ..++++|+.|
T Consensus        13 la~-~~~~ss~~IA~~~~~~~---~~v~kIl~~L   42 (127)
T d1xd7a_          13 ISM-DEKTSSEIIADSVNTNP---VVVRRMISLL   42 (127)
T ss_dssp             HHT-CSCCCHHHHHHHHTSCH---HHHHHHHHHH
T ss_pred             Hhc-CCCCCHHHHHHHhCcCH---HHHHHHHHHH
Confidence            344 47899999999999999   9999999864

>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=92.78  E-value=0.038  Score=29.93  Aligned_cols=33  Identities=24%  Similarity=0.410  Sum_probs=27.3

Q ss_pred             CchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           49 GIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        49 gI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .|...|.+  +|+|-.|||+.+|..+   ..+.++++-
T Consensus         3 ~Il~~i~~--~pisr~eLa~~~gls~---~TVs~~v~~   35 (62)
T d2hoea1           3 RILKRIMK--SPVSRVELAEELGLTK---TTVGEIAKI   35 (62)
T ss_dssp             CSHHHHHH--SCBCHHHHHHHHTCCH---HHHHHHHHH
T ss_pred             HHHHHHHH--CCcCHHHHHHHHCcCH---HHHHHHHHH
Confidence            46788875  6899999999999998   777777653

>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=92.62  E-value=0.073  Score=31.09  Aligned_cols=38  Identities=11%  Similarity=0.271  Sum_probs=29.7

Q ss_pred             HHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           44 CAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        44 aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      --.++.|...|.  .+|.++.|||+.+|++.   ..+.+-|+.
T Consensus        22 ~p~Rl~Il~~L~--~~~~~v~ela~~l~is~---stvS~HL~~   59 (98)
T d1r1ta_          22 DPNRLRLLSLLA--RSELCVGDLAQAIGVSE---SAVSHQLRS   59 (98)
T ss_dssp             CHHHHHHHHHHT--TCCBCHHHHHHHHTCCH---HHHHHHHHH
T ss_pred             CHHHHHHHHHHH--cCCcCHHHHHHHHCcCH---HHHHHHHHH
Confidence            335667788886  48899999999999988   777666654

>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=92.58  E-value=0.024  Score=34.43  Aligned_cols=35  Identities=20%  Similarity=0.355  Sum_probs=27.2

Q ss_pred             CchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           49 GIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        49 gI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .|+-.|..+++|+|+.|||+.+|+++   ..+.|.++.
T Consensus        30 ~i~~~L~~~~~plt~~ela~~l~vsk---~~vs~~l~~   64 (151)
T d1ku9a_          30 AVYAILYLSDKPLTISDIMEELKISK---GNVSMSLKK   64 (151)
T ss_dssp             HHHHHHHHCSSCEEHHHHHHHHTCCH---HHHHHHHHH
T ss_pred             HHHHHHHhCCCCcCHHHHHHHhCCCc---chHHHHHHH
Confidence            34445655568999999999999999   777777764

>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=92.56  E-value=0.043  Score=33.34  Aligned_cols=37  Identities=24%  Similarity=0.356  Sum_probs=29.3

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR   85 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR   85 (87)
                      .+..+...|.+.+|++|..|||+.+++++   ..+.|++.
T Consensus        35 ~q~~vL~~L~~~~g~~t~~~La~~~~~~~---~~vs~~i~   71 (145)
T d2hr3a1          35 SQLVVLGAIDRLGGDVTPSELAAAERMRS---SNLAALLR   71 (145)
T ss_dssp             HHHHHHHHHHHTTSCBCHHHHHHHTTCCH---HHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCCHHHHHHHHCCCH---HHHHHHHH
Confidence            45556666766668999999999999999   77777765

>d1biaa1 a.4.5.1 (A:1-63) Biotin repressor, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Biotin repressor-like
domain: Biotin repressor, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=92.39  E-value=0.032  Score=30.30  Aligned_cols=37  Identities=16%  Similarity=0.323  Sum_probs=29.3

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .++.|..+|.+ ++..|..|||+.+|++.   ..+.|=+..
T Consensus         6 ~~~~iL~~L~~-~~~~s~~eLa~~l~vS~---~ti~r~i~~   42 (63)
T d1biaa1           6 VPLKLIALLAN-GEFHSGEQLGETLGMSR---AAINKHIQT   42 (63)
T ss_dssp             HHHHHHHHHTT-SSCBCHHHHHHHHTSCH---HHHHHHHHH
T ss_pred             HHHHHHHHHHH-CCcCCHHHHHHHHCcCH---HHHHHHHHH
Confidence            45667888865 58899999999999988   777776543

>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=92.39  E-value=0.017  Score=33.33  Aligned_cols=37  Identities=27%  Similarity=0.398  Sum_probs=30.8

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .++.|...|... ++.|..|||+.+++++   ..+.|.++.
T Consensus        17 ~r~~IL~~L~~~-~~~~~~eLa~~l~is~---~~vs~~l~~   53 (100)
T d1ub9a_          17 VRLGIMIFLLPR-RKAPFSQIQKVLDLTP---GNLDSHIRV   53 (100)
T ss_dssp             HHHHHHHHHHHH-SEEEHHHHHHHTTCCH---HHHHHHHHH
T ss_pred             HHHHHHHHhccC-CCeeHHHHHHHHhhcc---ccccHHHHH
Confidence            467778888764 7899999999999999   888887764

>d1z6ra1 a.4.5.63 (A:12-81) Mlc protein N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: Mlc protein N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=92.39  E-value=0.061  Score=29.54  Aligned_cols=36  Identities=8%  Similarity=0.194  Sum_probs=29.4

Q ss_pred             HhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           47 ELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        47 eLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .-.|+..|.++ +|+|-.|||+.+|..+   ..+.++++-
T Consensus         7 ~~~Il~~i~~~-g~~sr~eLa~~~gLS~---~Tvs~iv~~   42 (70)
T d1z6ra1           7 AGAVYRLIDQL-GPVSRIDLSRLAQLAP---ASITKIVHE   42 (70)
T ss_dssp             HHHHHHHHHSS-CSCCHHHHHHHTTCCH---HHHHHHHHH
T ss_pred             HHHHHHHHHHc-CCcCHHHHHHHHCcCH---HHHHHHHHH
Confidence            34578888864 8999999999999998   878877653

>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=92.18  E-value=0.077  Score=30.83  Aligned_cols=38  Identities=8%  Similarity=0.260  Sum_probs=29.8

Q ss_pred             HHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           44 CAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        44 aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      --.++.|...|..  ++.++.||++.+|...   ..+.+-|+.
T Consensus        17 d~~Rl~Il~~L~~--~~~~v~el~~~l~~s~---~~vS~HL~~   54 (94)
T d1r1ua_          17 DYNRIRIMELLSV--SEASVGHISHQLNLSQ---SNVSHQLKL   54 (94)
T ss_dssp             SHHHHHHHHHHHH--CCBCHHHHHHHHTCCH---HHHHHHHHH
T ss_pred             CHHHHHHHHHHHc--CCccHHHHHHHHCCCH---HHHHHHHHH
Confidence            3356677888874  7899999999999988   777766654

>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=92.11  E-value=0.041  Score=30.07  Aligned_cols=36  Identities=17%  Similarity=0.393  Sum_probs=28.2

Q ss_pred             CchHHHHhCC-CCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           49 GIPDVIHKHG-QPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        49 gI~d~L~~~~-gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      .|.+++.++| .|-++.|||..+|+++   ..+..+||.|
T Consensus        11 ~I~~~~~~~g~~PP~vrdl~~~l~~~e---~~~~~lL~~l   47 (64)
T d1lvaa3          11 DLEDKYRVSRWQPPSFKEVAGSFNLDP---SELEELLHYL   47 (64)
T ss_dssp             HHHHHHHHHTTSCCBHHHHHHHTTCCH---HHHHHHHHHH
T ss_pred             HHHHHHHHcCCCCCcHHHHHHHhCCCH---HHHHHHHHHH
Confidence            3455666656 8999999999999999   7777777753

>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=91.61  E-value=0.054  Score=33.03  Aligned_cols=27  Identities=19%  Similarity=0.282  Sum_probs=24.3

Q ss_pred             CCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           58 GQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        58 ~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      +.+.|+.+||+.+++++   ..|.++|+.|
T Consensus        21 ~~~vss~~IA~~~~i~~---~~l~kil~~L   47 (138)
T d1ylfa1          21 SSLCTSDYMAESVNTNP---VVIRKIMSYL   47 (138)
T ss_dssp             GGGCCHHHHHHHHTSCH---HHHHHHHHHH
T ss_pred             CCcCcHHHHHHHHCcCH---HHHHHHHHHH
Confidence            47899999999999999   9999999854

>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=91.49  E-value=0.074  Score=27.43  Aligned_cols=33  Identities=24%  Similarity=0.472  Sum_probs=26.6

Q ss_pred             chHHHHhC-CCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968           50 IPDVIHKH-GQPMTLSQIASALDIQKNKAHCIQRLMR   85 (87)
Q Consensus        50 I~d~L~~~-~gp~S~~ELA~~~~~~~~~~~~L~RlLR   85 (87)
                      +.+.|.++ ..|+|+++||+.+|.++   ..+.|+.+
T Consensus         8 v~~yI~~~~~~~~tl~~lA~~~~~s~---~~l~r~Fk   41 (54)
T d1bl0a1           8 ILDWIEDNLESPLSLEKVSERSGYSK---WHLQRMFK   41 (54)
T ss_dssp             HHHHHHTTTTSCCCCHHHHHHSSSCH---HHHHHHHH
T ss_pred             HHHHHHhccCCCCCHHHHHHHHCcCH---HHHHHHHH
Confidence            44556543 38999999999999999   88998876

>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=91.44  E-value=0.039  Score=32.47  Aligned_cols=34  Identities=21%  Similarity=0.394  Sum_probs=26.6

Q ss_pred             CchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           49 GIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        49 gI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .|.-.|.+. |+.|+.|||+.+|+++   ..+++++.-
T Consensus        24 ~v~~~L~~~-g~~t~~eia~~~~i~~---~~v~~~l~~   57 (109)
T d1sfxa_          24 RIYSLLLER-GGMRVSEIARELDLSA---RFVRDRLKV   57 (109)
T ss_dssp             HHHHHHHHH-CCBCHHHHHHHHTCCH---HHHHHHHHH
T ss_pred             HHHHHHHhc-CCCCHHHHHHHhCCCc---chHHHHHHH
Confidence            345556553 8999999999999999   778887753

>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=91.32  E-value=0.051  Score=32.38  Aligned_cols=44  Identities=11%  Similarity=0.135  Sum_probs=34.1

Q ss_pred             HHHHHHHHHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           39 SMSLKCAVELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        39 ~~aL~aaveLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      ..+|.--..+.|+..|.+ +++.|+.||++.+|+.+   ..+.+-|+.
T Consensus        25 ~kaLadp~Rl~Il~~L~~-~~~~~v~ela~~l~~s~---s~vS~HL~~   68 (108)
T d1u2wa1          25 LKAIADENRAKITYALCQ-DEELCVCDIANILGVTI---ANASHHLRT   68 (108)
T ss_dssp             HHHHHSHHHHHHHHHHHH-SSCEEHHHHHHHHTCCH---HHHHHHHHH
T ss_pred             HHHhCCHHHHHHHHHHHh-CCCccHHHHHHHHccCh---hHHHHHHHH
Confidence            345555678889988875 48999999999999988   667666654

>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=91.10  E-value=0.078  Score=28.21  Aligned_cols=28  Identities=11%  Similarity=0.277  Sum_probs=24.3

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCC
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQK   74 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~   74 (87)
                      ++..|.+.|.++ +..|..|||+.+|+++
T Consensus         4 ~D~~Il~~L~~n-~r~s~~eiA~~l~ls~   31 (60)
T d2cyya1           4 IDKKIIKILQND-GKAPLREISKITGLAE   31 (60)
T ss_dssp             HHHHHHHHHHHC-TTCCHHHHHHHHCSCH
T ss_pred             HHHHHHHHHHHc-CCCCHHHHHHHHCcCH
Confidence            567788889874 8899999999999987

>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=90.71  E-value=0.08  Score=28.28  Aligned_cols=28  Identities=21%  Similarity=0.330  Sum_probs=23.6

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCC
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQK   74 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~   74 (87)
                      ++..|...|.++ +.+|..|||+.+|+++
T Consensus         4 ~D~kIl~~L~~n-~r~s~~~lA~~~gls~   31 (60)
T d1i1ga1           4 RDKIILEILEKD-ARTPFTEIAKKLGISE   31 (60)
T ss_dssp             HHHHHHHHHHHC-TTCCHHHHHHHHTSCH
T ss_pred             HHHHHHHHHHHc-CCCCHHHHHHHHCcCH
Confidence            456777888874 8999999999999987

>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=90.67  E-value=0.079  Score=28.57  Aligned_cols=28  Identities=11%  Similarity=0.426  Sum_probs=24.0

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCC
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQK   74 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~   74 (87)
                      .+..|.+.|.++ +..|..|||+.+|+++
T Consensus         6 ~D~~IL~~L~~n-~r~s~~~iA~~lgis~   33 (63)
T d2cfxa1           6 IDLNIIEELKKD-SRLSMRELGRKIKLSP   33 (63)
T ss_dssp             HHHHHHHHHHHC-SCCCHHHHHHHHTCCH
T ss_pred             HHHHHHHHHHHc-CCCCHHHHHHHHCcCH
Confidence            466788888874 8999999999999987

>d1d5ya1 a.4.1.8 (A:3-56) Rob transcription factor, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: AraC type transcriptional activator
domain: Rob transcription factor, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=90.66  E-value=0.087  Score=27.17  Aligned_cols=34  Identities=24%  Similarity=0.444  Sum_probs=28.0

Q ss_pred             CchHHHHhC-CCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968           49 GIPDVIHKH-GQPMTLSQIASALDIQKNKAHCIQRLMR   85 (87)
Q Consensus        49 gI~d~L~~~-~gp~S~~ELA~~~~~~~~~~~~L~RlLR   85 (87)
                      .+.+.|.++ .+|+|+++||+.++.++   ..+.|+.+
T Consensus         7 ~i~~yi~~~~~~~itl~~lA~~~~~S~---~~l~r~Fk   41 (54)
T d1d5ya1           7 DLLIWLEGHLDQPLSLDNVAAKAGYSK---WHLQRMFK   41 (54)
T ss_dssp             HHHHHHHTTSSSSCCCHHHHTTTSSCH---HHHHHHHH
T ss_pred             HHHHHHHHccCCCCCHHHHHHHHCcCH---HHHHHHHH
Confidence            455666654 38999999999999999   99999876

>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=89.46  E-value=0.082  Score=33.87  Aligned_cols=37  Identities=22%  Similarity=0.382  Sum_probs=30.0

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      ..+.|...|.+  ||.|+.|||..+|+++   ..+.+-|+.|
T Consensus        16 ~R~~Il~~L~~--~~~~~~ela~~l~~s~---~~v~~HL~~L   52 (194)
T d2p4wa1          16 TRRRILFLLTK--RPYFVSELSRELGVGQ---KAVLEHLRIL   52 (194)
T ss_dssp             HHHHHHHHHHH--SCEEHHHHHHHHTCCH---HHHHHHHHHH
T ss_pred             HHHHHHHHHHh--CCCCHHHHHHHHCcCH---HHHHHHHHHH
Confidence            44566777764  7999999999999999   8888887754

>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=89.16  E-value=0.089  Score=29.98  Aligned_cols=37  Identities=22%  Similarity=0.282  Sum_probs=28.1

Q ss_pred             hCchHHHHhCC---CCCCHHHHHHhcCCCCCChhhHHHHHhcC
Q 041968           48 LGIPDVIHKHG---QPMTLSQIASALDIQKNKAHCIQRLMRIL   87 (87)
Q Consensus        48 LgI~d~L~~~~---gp~S~~ELA~~~~~~~~~~~~L~RlLR~L   87 (87)
                      ..|++.|-++.   .-.|+.|||+.+++++   ..+.|+.|.|
T Consensus        21 ~~ia~yil~~~~~~~~~si~~lA~~~~vS~---sTi~Rf~kkl   60 (83)
T d2o3fa1          21 RKLADYILAHPHKAIESTVNEISALANSSD---AAVIRLCKSL   60 (83)
T ss_dssp             HHHHHHHHHCHHHHHTCCHHHHHHHTTCCH---HHHHHHHHHT
T ss_pred             HHHHHHHHcCHHHHHHccHHHHHHHHCCCH---HHHHHHHHHh
Confidence            34555554432   5679999999999999   8899998754

>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=88.56  E-value=0.59  Score=27.77  Aligned_cols=47  Identities=17%  Similarity=0.340  Sum_probs=31.9

Q ss_pred             HHHHHHHHHHHHHhC-------chHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968           35 NYINSMSLKCAVELG-------IPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR   85 (87)
Q Consensus        35 g~~~~~aL~aaveLg-------I~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR   85 (87)
                      .-+.........+.|       +...|... ++.|..|||..+++++   ..+.|++.
T Consensus        18 ~~~~~~~~~~l~~~glt~~q~~iL~~l~~~-~~~t~~~la~~~~i~~---~~vs~~l~   71 (143)
T d1s3ja_          18 QKIQPEMLESMEKQGVTPAQLFVLASLKKH-GSLKVSEIAERMEVKP---SAVTLMAD   71 (143)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHHH-SEEEHHHHHHHHTSCH---HHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHHHHHC-CCCCHHHHHHHHCcCH---HHHHHHHH
Confidence            333444444444554       44556654 6899999999999998   77777765

>d2cg4a1 a.4.5.32 (A:4-66) Regulatory protein AsnC {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Regulatory protein AsnC
species: Escherichia coli [TaxId: 562]

Probab=87.65  E-value=0.18  Score=26.93  Aligned_cols=28  Identities=11%  Similarity=0.318  Sum_probs=23.7

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCC
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQK   74 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~   74 (87)
                      ++..|...|.++ +..|..|||+.+|+++
T Consensus         6 ~D~~IL~~L~~~-~r~s~~eiA~~l~ls~   33 (63)
T d2cg4a1           6 LDRGILEALMGN-ARTAYAELAKQFGVSP   33 (63)
T ss_dssp             HHHHHHHHHHHC-TTSCHHHHHHHHTSCH
T ss_pred             HHHHHHHHHHHc-CCCCHHHHHHHHCcCH
Confidence            466778888874 8899999999999977

>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=87.19  E-value=0.15  Score=30.26  Aligned_cols=38  Identities=13%  Similarity=0.262  Sum_probs=28.6

Q ss_pred             HHhCchHHHHhCC-CCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           46 VELGIPDVIHKHG-QPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        46 veLgI~d~L~~~~-gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .+..|...|..++ +++|..|||+.+++++   ..+.|++.-
T Consensus        30 ~q~~vL~~l~~~~~~~it~~ela~~~~~~~---~~vs~~l~~   68 (135)
T d3broa1          30 TQMTIIDYLSRNKNKEVLQRDLESEFSIKS---STATVLLQR   68 (135)
T ss_dssp             HHHHHHHHHHHTTTSCCBHHHHHHHHTCCH---HHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCCCHHHHHHHHCcCH---hHHHHHHHH
Confidence            3444555666543 7899999999999999   778887754

>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=85.93  E-value=0.17  Score=30.21  Aligned_cols=37  Identities=19%  Similarity=0.164  Sum_probs=28.1

Q ss_pred             HHhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           46 VELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        46 veLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .+.-+...|.+. ++.|..|||..+++++   ..+.|+++-
T Consensus        33 ~q~~iL~~l~~~-~~~t~~~La~~l~i~~---~~vs~~v~~   69 (140)
T d2etha1          33 TELYAFLYVALF-GPKKMKEIAEFLSTTK---SNVTNVVDS   69 (140)
T ss_dssp             HHHHHHHHHHHH-CCBCHHHHHHHTTSCH---HHHHHHHHH
T ss_pred             HHHHHHHHHHHc-CCcCHHHHHHHHCcCH---HHHHHHHHH
Confidence            344455667665 7899999999999999   777777653

>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=85.89  E-value=0.16  Score=29.67  Aligned_cols=35  Identities=20%  Similarity=0.408  Sum_probs=28.5

Q ss_pred             CchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           49 GIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        49 gI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      .|++.|.+.++.+|=.+||+.+|+..   ..++|+|..
T Consensus        22 ~v~~~L~~~~~evtDe~iA~~tgi~i---n~VRk~Ly~   56 (88)
T d1q1ha_          22 DVLRILLDKGTEMTDEEIANQLNIKV---NDVRKKLNL   56 (88)
T ss_dssp             HHHHHHHHHCSCBCHHHHHHTTTSCH---HHHHHHHHH
T ss_pred             HHHHHHHhccCcCCHHHHHHHhCCcH---HHHHHHHHH
Confidence            47777765457899999999999998   778888754

>d1gdta1 a.4.1.2 (A:141-183) gamma,delta resolvase (C-terminal domain) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: gamma,delta resolvase (C-terminal domain)
species: Escherichia coli [TaxId: 562]

Probab=84.19  E-value=0.38  Score=24.47  Aligned_cols=24  Identities=17%  Similarity=0.422  Sum_probs=21.7

Q ss_pred             CCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968           59 QPMTLSQIASALDIQKNKAHCIQRLMR   85 (87)
Q Consensus        59 gp~S~~ELA~~~~~~~~~~~~L~RlLR   85 (87)
                      ..+++.+||.++|++.   ..++|+|.
T Consensus        17 ~G~gat~IAk~lgI~R---~SVYR~L~   40 (43)
T d1gdta1          17 QGLGASHISKTMNIAR---STVYKVIN   40 (43)
T ss_dssp             TTCCHHHHHHHHTCCH---HHHHHHHH
T ss_pred             cCCCHHHHHHHHCCCH---HHHHHHHh
Confidence            6689999999999999   88999984

>d1efaa1 a.35.1.5 (A:2-60) Lac repressor (LacR), N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: GalR/LacI-like bacterial regulator
domain: Lac repressor (LacR), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=84.05  E-value=0.37  Score=25.86  Aligned_cols=23  Identities=22%  Similarity=0.446  Sum_probs=19.9

Q ss_pred             CCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968           60 PMTLSQIASALDIQKNKAHCIQRLMR   85 (87)
Q Consensus        60 p~S~~ELA~~~~~~~~~~~~L~RlLR   85 (87)
                      +.|..|||+.+|+++   ..+.|.|+
T Consensus         2 ~~Ti~diA~~agvS~---sTVSr~l~   24 (59)
T d1efaa1           2 PVTLYDVAEYAGVSY---QTVSRVVN   24 (59)
T ss_dssp             CCCHHHHHHTTTSCH---HHHHHHHT
T ss_pred             CCCHHHHHHHHCCCH---HHHHHHHC
Confidence            679999999999998   88888775

>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=83.37  E-value=0.29  Score=29.15  Aligned_cols=33  Identities=18%  Similarity=0.242  Sum_probs=25.2

Q ss_pred             chHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHhc
Q 041968           50 IPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLMRI   86 (87)
Q Consensus        50 I~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR~   86 (87)
                      +...|... ++.|.+|||..+++++   ..+.|++.-
T Consensus        35 iL~~i~~~-~~~t~~~la~~l~i~~---~tvs~~l~~   67 (139)
T d2a61a1          35 ILQKIYFE-GPKRPGELSVLLGVAK---STVTGLVKR   67 (139)
T ss_dssp             HHHHHHHH-CCBCHHHHHHHHTCCH---HHHHHHHHH
T ss_pred             HHHHHHHc-CCCCHHHHHHHhCCCc---ccchHHHHH
Confidence            34445554 6899999999999999   777777653

>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=81.54  E-value=0.37  Score=28.45  Aligned_cols=30  Identities=17%  Similarity=0.371  Sum_probs=23.4

Q ss_pred             HHHhCCCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968           53 VIHKHGQPMTLSQIASALDIQKNKAHCIQRLMR   85 (87)
Q Consensus        53 ~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlLR   85 (87)
                      .|..++++.|..+||..+++++   ..+.|+++
T Consensus        36 ~l~~~~~~~t~~~la~~~~~~~---~~vs~~v~   65 (137)
T d2fbha1          36 HLARHRDSPTQRELAQSVGVEG---PTLARLLD   65 (137)
T ss_dssp             HHHHCSSCCBHHHHHHHHTCCH---HHHHHHHH
T ss_pred             HHHHcCCCCcHHHHHHHHCCCH---HHHHHHHH
Confidence            4555556789999999999999   77777665

>d1j75a_ a.4.5.19 (A:) Dlm-1 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Z-DNA binding domain
domain: Dlm-1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=81.37  E-value=0.39  Score=25.65  Aligned_cols=35  Identities=20%  Similarity=0.468  Sum_probs=27.8

Q ss_pred             HhCchHHHHhCCCCCCHHHHHHhcCCCCCChhhHHHHH
Q 041968           47 ELGIPDVIHKHGQPMTLSQIASALDIQKNKAHCIQRLM   84 (87)
Q Consensus        47 eLgI~d~L~~~~gp~S~~ELA~~~~~~~~~~~~L~RlL   84 (87)
                      |-+|...|..+|+|.-+.+|+.+++++.   .-|.|+|
T Consensus         3 EQkILQVL~dagspvk~~ql~k~cqVpk---k~lNqVL   37 (57)
T d1j75a_           3 EQKILQVLSDDGGPVKIGQLVKKCQVPK---KTLNQVL   37 (57)
T ss_dssp             HHHHHHHHHHHCSCEEHHHHHHHHCSCH---HHHHHHH
T ss_pred             HHHHHHHHHhcCCchHHHHHHHHHCCCH---HHHHHHH
Confidence            4467778888889999999999999977   5555554

>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=81.04  E-value=0.79  Score=24.46  Aligned_cols=27  Identities=15%  Similarity=0.217  Sum_probs=21.3

Q ss_pred             HHHhCC-CCCCHHHHHHhcCCCCCChhhHHH
Q 041968           53 VIHKHG-QPMTLSQIASALDIQKNKAHCIQR   82 (87)
Q Consensus        53 ~L~~~~-gp~S~~ELA~~~~~~~~~~~~L~R   82 (87)
                      .+...| ...|+.+||+.+|+.+   ..+++
T Consensus        16 l~~~~G~~~~s~~~Ia~~agvs~---~t~Y~   43 (74)
T d1v7ba1          16 YIGEYSLETLSYDSLAEATGLSK---SGLIY   43 (74)
T ss_dssp             HHHHSCSTTCCHHHHHHHHCSCH---HHHHH
T ss_pred             HHHHhCccccCHHHHHHHhCcCc---chHhh
Confidence            355555 8899999999999988   66655

>d2a6ca1 a.35.1.13 (A:1-69) HTH-motif protein NE1354 {Nitrosomonas europaea [TaxId: 915]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE1354
domain: HTH-motif protein NE1354
species: Nitrosomonas europaea [TaxId: 915]

Probab=80.63  E-value=1.3  Score=23.43  Aligned_cols=25  Identities=24%  Similarity=0.313  Sum_probs=21.0

Q ss_pred             CCCCCHHHHHHhcCCCCCChhhHHHHHh
Q 041968           58 GQPMTLSQIASALDIQKNKAHCIQRLMR   85 (87)
Q Consensus        58 ~gp~S~~ELA~~~~~~~~~~~~L~RlLR   85 (87)
                      ...+|-.|+|+.+|+++   ..+.++.+
T Consensus        17 ~~gltq~elA~~~gv~~---~~is~ie~   41 (69)
T d2a6ca1          17 NSGLTQFKAAELLGVTQ---PRVSDLMR   41 (69)
T ss_dssp             TTTCCHHHHHHHHTSCH---HHHHHHHT
T ss_pred             HcCCCHHHHHHHHHcCH---hHHHHHHc
Confidence            37899999999999998   77777764