Psyllid ID: psy6501

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170----
Protein Sequence
NAGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccHHHHHHHHHHHHHccccHHHHHHHHcccHHHHHHHccccccccHHHHHHHHHHHcccccccccccccccccccccccHHHHHHHHcccccHHHHHHHHHHHHHccccHHHHHHHHcccHHHHHHHHcccccccHHHHHHHHHHc
Secondary Structure Prediction (SSPRO)
ccccccccccccccHHccccccccccccccHHHHHHHHHHHHHccccHHHHHHHHccccHHHHHHHcccccccHHHHHHHHHHHccHcccccccccccccccccHHccccccccccccccHHHHHHHHHHHHHccccHHHHHHHHccccHHHHHHHcccccccHHHHHHHHHHc
Coil and Loop (DISEMBL)
nagtnkqpgttkntaKLDRETEELKHEKVPLDLAKLLMQGrqakgwsqkdlatkinekpqivndyeggrgipnqaIIGKMERALGIRLrvnagtnkqpgttkntaKLDRETEELKHEKVPLDLAKLLMQGrqakgwsqkdlatkinekpqivndyeggrgipnqaIIGKMERAL
Flexible Loop (DISEMBL)
nagtnkqpgttkntakldreteelkhekvpLDLAKLLMQGRQAkgwsqkdlatkinekpqivndyeggrGIPNQAIIGKMERALGIRLrvnagtnkqpgttkntakldreteelkhekvpLDLAKLLMQGRQAkgwsqkdlatkinekpqivndyeggrgipnqaiigkmeral
Low Complexity Region (SEG)
NAGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL
Disordered region (IsUnstruct)
***********************************************************QIVNDYEGGRGIPNQAIIGKMERALGIRLRV************************************************************************************
Disordered Region (DISOPRED)
********************TEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL
Disordered Region (DISEMBL)
*************TAKLDRETEELKHEKVPLDLAKLLMQG********KDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQG********KDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL
Disordered Region (DISPRO)
*********************EELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLR**********************EELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
NAGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL
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	174	2.2.26 [Sep-21-2011]
Q5ZMC0	148	Endothelial differentiati	yes	N/A	0.505	0.594	0.670	1e-29
O60869	148	Endothelial differentiati	yes	N/A	0.505	0.594	0.659	7e-29
Q3T0V7	148	Endothelial differentiati	yes	N/A	0.505	0.594	0.659	7e-29
Q6PBY3	146	Endothelial differentiati	yes	N/A	0.505	0.602	0.659	1e-28
P69736	148	Endothelial differentiati	yes	N/A	0.505	0.594	0.647	2e-28
Q9JMG1	148	Endothelial differentiati	yes	N/A	0.505	0.594	0.647	2e-28
Q6GPQ6	147	Endothelial differentiati	N/A	N/A	0.511	0.605	0.629	4e-28
Q6CIP4	150	Multiprotein-bridging fac	yes	N/A	0.431	0.5	0.653	2e-21
Q9SJI8	142	Multiprotein-bridging fac	yes	N/A	0.511	0.626	0.549	1e-20
Q9LXT3	142	Multiprotein-bridging fac	no	N/A	0.511	0.626	0.538	2e-20

>sp|Q5ZMC0|EDF1_CHICK Endothelial differentiation-related factor 1 homolog OS=Gallus gallus GN=EDF1 PE=2 SV=1

 Score =  129 bits (323), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 59/88 (67%), Positives = 75/88 (85%)

Query: 2   AGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQI 61
           AG NKQ   TKNTAKLDRETEEL H++VPL++ K++ QGRQ+KG +QKDLATKINEKPQ+
Sbjct: 46  AGQNKQHFITKNTAKLDRETEELHHDRVPLEVGKVIQQGRQSKGMTQKDLATKINEKPQV 105

Query: 62  VNDYEGGRGIPNQAIIGKMERALGIRLR 89
           + DYE GR IPN  ++GK+ERA+G++LR
Sbjct: 106 IADYESGRAIPNNQVMGKIERAIGLKLR 133

Probable transcriptional coactivator.
Gallus gallus (taxid: 9031)

>sp|O60869|EDF1_HUMAN Endothelial differentiation-related factor 1 OS=Homo sapiens GN=EDF1 PE=1 SV=1

 Score =  126 bits (316), Expect = 7e-29,   Method: Compositional matrix adjust.
 Identities = 58/88 (65%), Positives = 74/88 (84%)

Query: 2   AGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQI 61
           AG NKQ   TKNTAKLDRETEEL H++V L++ K++ QGRQ+KG +QKDLATKINEKPQ+
Sbjct: 46  AGQNKQHSITKNTAKLDRETEELHHDRVTLEVGKVIQQGRQSKGLTQKDLATKINEKPQV 105

Query: 62  VNDYEGGRGIPNQAIIGKMERALGIRLR 89
           + DYE GR IPN  ++GK+ERA+G++LR
Sbjct: 106 IADYESGRAIPNNQVLGKIERAIGLKLR 133

Transcriptional coactivator stimulating NR5A1 and ligand-dependent NR1H3/LXRA and PPARG transcriptional activities. Enhances the DNA-binding activity of ATF1, ATF2, CREB1 and NR5A1. Regulates nitric oxid synthase activity probably by sequestering calmodulin in the cytoplasm. May function in endothelial cells differentiation, hormone-induced cardiomyocytes hypertrophy and lipid metabolism.

Homo sapiens (taxid: 9606)

>sp|Q3T0V7|EDF1_BOVIN Endothelial differentiation-related factor 1 OS=Bos taurus GN=EDF1 PE=2 SV=1

 Score =  126 bits (316), Expect = 7e-29,   Method: Compositional matrix adjust.
 Identities = 58/88 (65%), Positives = 74/88 (84%)

Query: 2   AGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQI 61
           AG NKQ   TKNTAKLDRETEEL H++V L++ K++ QGRQ+KG +QKDLATKINEKPQ+
Sbjct: 46  AGQNKQHSITKNTAKLDRETEELHHDRVTLEVGKVIQQGRQSKGLTQKDLATKINEKPQV 105

Query: 62  VNDYEGGRGIPNQAIIGKMERALGIRLR 89
           + DYE GR IPN  ++GK+ERA+G++LR
Sbjct: 106 IADYESGRAIPNNQVLGKIERAIGLKLR 133

Transcriptional coactivator stimulating NR5A1 and ligand-dependent NR1H3/LXRA and PPARG transcriptional activities. Enhances the DNA-binding activity of ATF1, ATF2, CREB1 and NR5A1. Regulates nitric oxid synthase activity probably by sequestering calmodulin in the cytoplasm. Might function in endothelial cells differentiation, hormone-induced cardiomyocytes hypertrophy and lipid metabolism.

Bos taurus (taxid: 9913)

>sp|Q6PBY3|EDF1_DANRE Endothelial differentiation-related factor 1 homolog OS=Danio rerio GN=edf1 PE=2 SV=1

 Score =  125 bits (315), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 58/88 (65%), Positives = 74/88 (84%)

Query: 2   AGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQI 61
           AG NKQ   TKNTAKLDRETEEL H++VPL++ K++ QGRQ KG +QKDLATKINEKPQI
Sbjct: 45  AGQNKQHVVTKNTAKLDRETEELSHQRVPLEVGKVIQQGRQNKGLTQKDLATKINEKPQI 104

Query: 62  VNDYEGGRGIPNQAIIGKMERALGIRLR 89
           + +YE G+ IPN  ++GK+ERA+G++LR
Sbjct: 105 IAEYECGKAIPNNQVMGKIERAIGLKLR 132

Probable transcriptional coactivator.

Danio rerio (taxid: 7955)

>sp|P69736|EDF1_RAT Endothelial differentiation-related factor 1 OS=Rattus norvegicus GN=Edf1 PE=1 SV=1

 Score =  124 bits (312), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 57/88 (64%), Positives = 74/88 (84%)

Query: 2   AGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQI 61
           AG NKQ   TKNTAKLDRETEEL H++V L++ K++ +GRQ+KG +QKDLATKINEKPQ+
Sbjct: 46  AGQNKQHSITKNTAKLDRETEELHHDRVTLEVGKVIQRGRQSKGLTQKDLATKINEKPQV 105

Query: 62  VNDYEGGRGIPNQAIIGKMERALGIRLR 89
           + DYE GR IPN  ++GK+ERA+G++LR
Sbjct: 106 IADYESGRAIPNNQVLGKIERAIGLKLR 133

Transcriptional coactivator stimulating NR5A1 and ligand-dependent NR1H3/LXRA and PPARG transcriptional activities. Enhances the DNA-binding activity of ATF1, ATF2, CREB1 and NR5A1. Regulates nitric oxid synthase activity probably by sequestering calmodulin in the cytoplasm. Might function in endothelial cells differentiation, hormone-induced cardiomyocytes hypertrophy and lipid metabolism.

Rattus norvegicus (taxid: 10116)

>sp|Q9JMG1|EDF1_MOUSE Endothelial differentiation-related factor 1 OS=Mus musculus GN=Edf1 PE=1 SV=1

 Score =  124 bits (312), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 57/88 (64%), Positives = 74/88 (84%)

Query: 2   AGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQI 61
           AG NKQ   TKNTAKLDRETEEL H++V L++ K++ +GRQ+KG +QKDLATKINEKPQ+
Sbjct: 46  AGQNKQHSITKNTAKLDRETEELHHDRVTLEVGKVIQRGRQSKGLTQKDLATKINEKPQV 105

Query: 62  VNDYEGGRGIPNQAIIGKMERALGIRLR 89
           + DYE GR IPN  ++GK+ERA+G++LR
Sbjct: 106 IADYESGRAIPNNQVLGKIERAIGLKLR 133

Transcriptional coactivator stimulating NR5A1 and ligand-dependent NR1H3/LXRA and PPARG transcriptional activities. Enhances the DNA-binding activity of ATF1, ATF2, CREB1 and NR5A1. Regulates nitric oxid synthase activity probably by sequestering calmodulin in the cytoplasm. Might function in endothelial cells differentiation, hormone-induced cardiomyocytes hypertrophy and lipid metabolism.

Mus musculus (taxid: 10090)

>sp|Q6GPQ6|EDF1_XENLA Endothelial differentiation-related factor 1 homolog OS=Xenopus laevis GN=edf1 PE=2 SV=1

 Score =  124 bits (310), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 56/89 (62%), Positives = 74/89 (83%)

Query: 1   NAGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQ 60
           +AG NKQ   T+NTAKLDRETEEL H++VPL++ K++ QGRQ KG +QKDLATKINEKPQ
Sbjct: 45  SAGQNKQHTITRNTAKLDRETEELHHDRVPLEVGKVIQQGRQGKGMTQKDLATKINEKPQ 104

Query: 61  IVNDYEGGRGIPNQAIIGKMERALGIRLR 89
           ++ DYE G+ IPN  ++GK+ER +G++LR
Sbjct: 105 VIADYECGKAIPNNQVMGKIERVIGLKLR 133

Probable transcriptional coactivator.

Xenopus laevis (taxid: 8355)

>sp|Q6CIP4|MBF1_KLULA Multiprotein-bridging factor 1 OS=Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) GN=MBF1 PE=3 SV=2

 Score =  101 bits (252), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 49/75 (65%), Positives = 61/75 (81%)

Query: 15  AKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQ 74
            K+DRET+ +K +K+ + + K + +GRQ K  +QKDLATKINEKP IVNDYE GRGIPNQ
Sbjct: 63  TKVDRETDIVKPKKIDVSVGKAIQKGRQDKNLTQKDLATKINEKPTIVNDYESGRGIPNQ 122

Query: 75  AIIGKMERALGIRLR 89
            I+GKMERALGI+LR
Sbjct: 123 QILGKMERALGIKLR 137

Transcriptional coactivator that stimulates transcriptional activity by bridging regulatory proteins and TBP, thereby recruiting TBP to promoters occupied by DNA-binding regulators.

Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (taxid: 284590)

>sp|Q9SJI8|MBF1A_ARATH Multiprotein-bridging factor 1a OS=Arabidopsis thaliana GN=MBF1A PE=2 SV=1

 Score = 99.4 bits (246), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 50/91 (54%), Positives = 63/91 (69%), Gaps = 2/91 (2%)

Query: 1   NAGTNK--QPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEK 58
           NAGTNK    GT+ NT  LD +TE L HE+VP +L K +MQ R  K  +Q  LA  INEK
Sbjct: 49  NAGTNKAASSGTSLNTKMLDDDTENLTHERVPTELKKAIMQARTDKKLTQSQLAQIINEK 108

Query: 59  PQIVNDYEGGRGIPNQAIIGKMERALGIRLR 89
           PQ++ +YE G+ IPNQ I+ K+ERALG +LR
Sbjct: 109 PQVIQEYESGKAIPNQQILSKLERALGAKLR 139

Transcriptional coactivator that stimulates transcriptional activity by bridging regulatory proteins and TBP, thereby recruiting TBP to promoters occupied by DNA-binding regulators.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LXT3|MBF1B_ARATH Multiprotein-bridging factor 1b OS=Arabidopsis thaliana GN=MBF1B PE=2 SV=1

 Score = 98.6 bits (244), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 49/91 (53%), Positives = 64/91 (70%), Gaps = 2/91 (2%)

Query: 1   NAGTNK--QPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEK 58
           NAG+NK    GT+ NT KLD +TE L H++VP +L K +MQ R  K  +Q  LA  INEK
Sbjct: 49  NAGSNKAASSGTSLNTKKLDDDTENLSHDRVPTELKKAIMQARGEKKLTQSQLAHLINEK 108

Query: 59  PQIVNDYEGGRGIPNQAIIGKMERALGIRLR 89
           PQ++ +YE G+ IPNQ I+ K+ERALG +LR
Sbjct: 109 PQVIQEYESGKAIPNQQILSKLERALGAKLR 139

Transcriptional coactivator that stimulates transcriptional activity by bridging regulatory proteins and TBP, thereby recruiting TBP to promoters occupied by DNA-binding regulators.

Arabidopsis thaliana (taxid: 3702)

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	174
389610049	146	multiprotein bridging factor 1 [Papilio	0.505	0.602	0.829	1e-34
357625365	147	multiprotein bridging factor 1 [Danaus p	0.505	0.598	0.829	5e-34
112984062	146	multiprotein bridging factor 1 [Bombyx m	0.505	0.602	0.818	9e-34
355428304	145	hypothetical protein [Triatoma rubida]	0.5	0.6	0.781	5e-32
66512104	147	PREDICTED: hypothetical protein LOC55087	0.5	0.591	0.770	1e-31
307214020	147	Endothelial differentiation-related fact	0.5	0.591	0.758	2e-31
383853086	147	PREDICTED: endothelial differentiation-r	0.5	0.591	0.758	2e-31
242007348	146	conserved hypothetical protein [Pediculu	0.5	0.595	0.758	4e-31
170035623	147	multiprotein bridging factor [Culex quin	0.511	0.605	0.764	4e-31
340716633	147	PREDICTED: endothelial differentiation-r	0.5	0.591	0.758	4e-31

>gi|389610049|dbj|BAM18636.1| multiprotein bridging factor 1 [Papilio xuthus]

 Score =  151 bits (381), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 73/88 (82%), Positives = 81/88 (92%)

Query: 2   AGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQI 61
           AGTNKQ GTTKNTAKLDRETEEL+HEK+PLDL KL+MQGRQAKG SQKDLATKI EKPQI
Sbjct: 44  AGTNKQHGTTKNTAKLDRETEELRHEKIPLDLGKLIMQGRQAKGMSQKDLATKICEKPQI 103

Query: 62  VNDYEGGRGIPNQAIIGKMERALGIRLR 89
           VNDYE GRGIPN  ++GK+ERA+GI+LR
Sbjct: 104 VNDYEAGRGIPNNLVLGKIERAIGIKLR 131

Source: Papilio xuthus

Species: Papilio xuthus

Genus: Papilio

Family: Papilionidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357625365|gb|EHJ75831.1| multiprotein bridging factor 1 [Danaus plexippus]

 Score =  149 bits (375), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 73/88 (82%), Positives = 80/88 (90%)

Query: 2   AGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQI 61
           AGTNKQ  TTKNTAKLDRETEEL+HEKVPLDL KL+MQGRQAKG SQKDLATKI EKPQI
Sbjct: 44  AGTNKQHVTTKNTAKLDRETEELRHEKVPLDLGKLIMQGRQAKGMSQKDLATKICEKPQI 103

Query: 62  VNDYEGGRGIPNQAIIGKMERALGIRLR 89
           VNDYE GRGIPN  ++GK+ERA+GI+LR
Sbjct: 104 VNDYEAGRGIPNNIVLGKIERAIGIKLR 131

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|112984062|ref|NP_001036824.1| multiprotein bridging factor 1 [Bombyx mori] gi|2285788|dbj|BAA21658.1| Multiprotein bridging factor 1 [Bombyx mori]

 Score =  148 bits (373), Expect = 9e-34,   Method: Compositional matrix adjust.
 Identities = 72/88 (81%), Positives = 80/88 (90%)

Query: 2   AGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQI 61
           AGTNKQ  TTKNTAKLDRETEEL+HEK+PLDL KL+MQGRQAKG SQKDLATKI EKPQI
Sbjct: 44  AGTNKQHVTTKNTAKLDRETEELRHEKIPLDLGKLIMQGRQAKGMSQKDLATKICEKPQI 103

Query: 62  VNDYEGGRGIPNQAIIGKMERALGIRLR 89
           VNDYE GRGIPN  ++GK+ERA+GI+LR
Sbjct: 104 VNDYEAGRGIPNNIVLGKIERAIGIKLR 131

Source: Bombyx mori

Species: Bombyx mori

Genus: Bombyx

Family: Bombycidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|355428304|gb|AER92468.1| hypothetical protein [Triatoma rubida]

 Score =  142 bits (358), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 68/87 (78%), Positives = 75/87 (86%)

Query: 3   GTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIV 62
           G NKQ  +TKNTAKLDRETEELKHE +PL L KL+ QGRQAKGWSQK+ AT+ NEKPQ+V
Sbjct: 45  GQNKQHVSTKNTAKLDRETEELKHETIPLSLGKLIQQGRQAKGWSQKEFATRCNEKPQVV 104

Query: 63  NDYEGGRGIPNQAIIGKMERALGIRLR 89
           NDYE GRGI NQAIIGKMER LGI+LR
Sbjct: 105 NDYEAGRGIXNQAIIGKMERVLGIKLR 131

Source: Triatoma rubida

Species: Triatoma rubida

Genus: Triatoma

Family: Reduviidae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|66512104|ref|XP_623269.1| PREDICTED: hypothetical protein LOC550875 [Apis mellifera] gi|380018246|ref|XP_003693044.1| PREDICTED: endothelial differentiation-related factor 1 homolog [Apis florea]

 Score =  140 bits (354), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 67/87 (77%), Positives = 77/87 (88%)

Query: 3   GTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIV 62
           GTNKQ   TKNTAKLDRETEELKH+K+PLDL KL+ QGRQ+KG SQKDLATK+NEK Q++
Sbjct: 46  GTNKQHVATKNTAKLDRETEELKHDKIPLDLGKLIQQGRQSKGLSQKDLATKVNEKAQVI 105

Query: 63  NDYEGGRGIPNQAIIGKMERALGIRLR 89
           NDYE GRGIPNQ +IGK+ER LGI+LR
Sbjct: 106 NDYEAGRGIPNQMVIGKIERVLGIKLR 132

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307214020|gb|EFN89227.1| Endothelial differentiation-related factor 1-like protein [Harpegnathos saltator]

 Score =  140 bits (353), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 66/87 (75%), Positives = 77/87 (88%)

Query: 3   GTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIV 62
           G N+Q  TTKNTAKLDRETEELKH+K+PLDL KL+ QGRQ+KG SQKDLATK+NEK Q++
Sbjct: 46  GANRQHVTTKNTAKLDRETEELKHDKIPLDLGKLIQQGRQSKGLSQKDLATKVNEKAQVI 105

Query: 63  NDYEGGRGIPNQAIIGKMERALGIRLR 89
           NDYE GRGIPNQ +IGK+ER LGI+LR
Sbjct: 106 NDYEAGRGIPNQMVIGKIERVLGIKLR 132

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383853086|ref|XP_003702055.1| PREDICTED: endothelial differentiation-related factor 1 homolog [Megachile rotundata]

 Score =  140 bits (352), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 66/87 (75%), Positives = 77/87 (88%)

Query: 3   GTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIV 62
           GTN+Q   TKNTAKLDRETEELKH+K+PLDL KL+ QGRQ+KG SQKDLATK+NEK Q++
Sbjct: 46  GTNRQHVATKNTAKLDRETEELKHDKIPLDLGKLIQQGRQSKGLSQKDLATKVNEKAQVI 105

Query: 63  NDYEGGRGIPNQAIIGKMERALGIRLR 89
           NDYE GRGIPNQ +IGK+ER LGI+LR
Sbjct: 106 NDYEAGRGIPNQMVIGKIERVLGIKLR 132

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242007348|ref|XP_002424503.1| conserved hypothetical protein [Pediculus humanus corporis] gi|212507921|gb|EEB11765.1| conserved hypothetical protein [Pediculus humanus corporis]

 Score =  139 bits (350), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 66/87 (75%), Positives = 75/87 (86%)

Query: 3   GTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIV 62
           G NKQ   TKN AKLDRETEELKHEK+ LD  KL+ QGRQ KGWSQK+LATKINEKPQ++
Sbjct: 45  GQNKQHVVTKNIAKLDRETEELKHEKITLDTGKLIQQGRQGKGWSQKELATKINEKPQVI 104

Query: 63  NDYEGGRGIPNQAIIGKMERALGIRLR 89
           NDYE GR IPNQA++GKME+ALGI+LR
Sbjct: 105 NDYEAGRAIPNQAVLGKMEKALGIKLR 131

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170035623|ref|XP_001845668.1| multiprotein bridging factor [Culex quinquefasciatus] gi|167877641|gb|EDS41024.1| multiprotein bridging factor [Culex quinquefasciatus]

 Score =  139 bits (350), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 68/89 (76%), Positives = 75/89 (84%)

Query: 1   NAGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQ 60
           NAGTNKQ    KNTAKLDRET+ELKH  V  D+AKL+MQGRQ+KG SQKDLATKI EKPQ
Sbjct: 45  NAGTNKQHAAPKNTAKLDRETDELKHRTVSHDVAKLIMQGRQSKGLSQKDLATKICEKPQ 104

Query: 61  IVNDYEGGRGIPNQAIIGKMERALGIRLR 89
           IVNDYE GRGIPN  I+GKMER +GI+LR
Sbjct: 105 IVNDYEAGRGIPNNLILGKMERVIGIKLR 133

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340716633|ref|XP_003396800.1| PREDICTED: endothelial differentiation-related factor 1 homolog [Bombus terrestris] gi|350396995|ref|XP_003484733.1| PREDICTED: endothelial differentiation-related factor 1 homolog [Bombus impatiens]

 Score =  139 bits (350), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 66/87 (75%), Positives = 77/87 (88%)

Query: 3   GTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIV 62
           GTNKQ   TKNTAKLDRETEELKH+K+PLDL KL+ QGRQ+KG SQKDLATK+NEK Q++
Sbjct: 46  GTNKQHVATKNTAKLDRETEELKHDKIPLDLGKLIQQGRQSKGLSQKDLATKVNEKAQVI 105

Query: 63  NDYEGGRGIPNQAIIGKMERALGIRLR 89
           NDYE GRGIPNQ +IGK+E+ LGI+LR
Sbjct: 106 NDYEAGRGIPNQMVIGKIEKVLGIKLR 132

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	174
FB|FBgn0262732	145	mbf1 "multiprotein bridging fa	0.505	0.606	0.761	9.8e-32
UNIPROTKB|Q5ZMC0	148	EDF1 "Endothelial differentiat	0.505	0.594	0.670	3.4e-29
UNIPROTKB|Q3T0V7	148	EDF1 "Endothelial differentiat	0.505	0.594	0.659	1.2e-28
UNIPROTKB|E2R2F2	148	EDF1 "Uncharacterized protein"	0.505	0.594	0.659	1.2e-28
UNIPROTKB|O60869	148	EDF1 "Endothelial differentiat	0.505	0.594	0.659	1.2e-28
UNIPROTKB|A6N8P5	148	MBF1 "Multiprotein bridging fa	0.505	0.594	0.659	1.2e-28
MGI|MGI:1891227	148	Edf1 "endothelial differentiat	0.505	0.594	0.647	3.1e-28
RGD|1308073	148	Edf1 "endothelial differentiat	0.505	0.594	0.647	3.1e-28
ZFIN|ZDB-GENE-040426-1710	146	edf1 "endothelial differentiat	0.505	0.602	0.659	5e-28
WB|WBGene00003148	156	mbf-1 [Caenorhabditis elegans	0.586	0.653	0.547	3.2e-26

FB|FBgn0262732 mbf1 "multiprotein bridging factor 1" [Drosophila melanogaster (taxid:7227)]

 Score = 348 (127.6 bits), Expect = 9.8e-32, P = 9.8e-32
 Identities = 67/88 (76%), Positives = 76/88 (86%)

Query:     2 AGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQI 61
             AGTNKQ  TTKNTAKLDRETEEL+H+K+PLD+ KL+ QGRQ+KG SQKDLATKI EK Q+
Sbjct:    44 AGTNKQHVTTKNTAKLDRETEELRHDKIPLDVGKLIQQGRQSKGLSQKDLATKICEKQQV 103

Query:    62 VNDYEGGRGIPNQAIIGKMERALGIRLR 89
             V DYE GRGIPN  I+GKMER LGI+LR
Sbjct:   104 VTDYEAGRGIPNNLILGKMERVLGIKLR 131

GO:0003713 "transcription coactivator activity" evidence=ISS;IDA

GO:0008327 "methyl-CpG binding" evidence=ISS

GO:0007417 "central nervous system development" evidence=IGI;IMP

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IDA

GO:0030674 "protein binding, bridging" evidence=IPI

GO:0007424 "open tracheal system development" evidence=IGI;IMP

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0048813 "dendrite morphogenesis" evidence=IMP

UNIPROTKB|Q5ZMC0 EDF1 "Endothelial differentiation-related factor 1 homolog" [Gallus gallus (taxid:9031)]

 Score = 324 (119.1 bits), Expect = 3.4e-29, P = 3.4e-29
 Identities = 59/88 (67%), Positives = 75/88 (85%)

Query:     2 AGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQI 61
             AG NKQ   TKNTAKLDRETEEL H++VPL++ K++ QGRQ+KG +QKDLATKINEKPQ+
Sbjct:    46 AGQNKQHFITKNTAKLDRETEELHHDRVPLEVGKVIQQGRQSKGMTQKDLATKINEKPQV 105

Query:    62 VNDYEGGRGIPNQAIIGKMERALGIRLR 89
             + DYE GR IPN  ++GK+ERA+G++LR
Sbjct:   106 IADYESGRAIPNNQVMGKIERAIGLKLR 133

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0003713 "transcription coactivator activity" evidence=IEA

GO:0005669 "transcription factor TFIID complex" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0043388 "positive regulation of DNA binding" evidence=IEA

UNIPROTKB|Q3T0V7 EDF1 "Endothelial differentiation-related factor 1" [Bos taurus (taxid:9913)]

 Score = 319 (117.4 bits), Expect = 1.2e-28, P = 1.2e-28
 Identities = 58/88 (65%), Positives = 74/88 (84%)

Query:     2 AGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQI 61
             AG NKQ   TKNTAKLDRETEEL H++V L++ K++ QGRQ+KG +QKDLATKINEKPQ+
Sbjct:    46 AGQNKQHSITKNTAKLDRETEELHHDRVTLEVGKVIQQGRQSKGLTQKDLATKINEKPQV 105

Query:    62 VNDYEGGRGIPNQAIIGKMERALGIRLR 89
             + DYE GR IPN  ++GK+ERA+G++LR
Sbjct:   106 IADYESGRAIPNNQVLGKIERAIGLKLR 133

GO:0005737 "cytoplasm" evidence=IEA

GO:0043388 "positive regulation of DNA binding" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0005669 "transcription factor TFIID complex" evidence=IEA

GO:0003713 "transcription coactivator activity" evidence=IEA

GO:0030154 "cell differentiation" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0005516 "calmodulin binding" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

UNIPROTKB|E2R2F2 EDF1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 319 (117.4 bits), Expect = 1.2e-28, P = 1.2e-28
 Identities = 58/88 (65%), Positives = 74/88 (84%)

Query:     2 AGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQI 61
             AG NKQ   TKNTAKLDRETEEL H++V L++ K++ QGRQ+KG +QKDLATKINEKPQ+
Sbjct:    46 AGQNKQHSITKNTAKLDRETEELHHDRVTLEVGKVIQQGRQSKGLTQKDLATKINEKPQV 105

Query:    62 VNDYEGGRGIPNQAIIGKMERALGIRLR 89
             + DYE GR IPN  ++GK+ERA+G++LR
Sbjct:   106 IADYESGRAIPNNQVLGKIERAIGLKLR 133

GO:0043388 "positive regulation of DNA binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0005669 "transcription factor TFIID complex" evidence=IEA

GO:0003713 "transcription coactivator activity" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

UNIPROTKB|O60869 EDF1 "Endothelial differentiation-related factor 1" [Homo sapiens (taxid:9606)]

 Score = 319 (117.4 bits), Expect = 1.2e-28, P = 1.2e-28
 Identities = 58/88 (65%), Positives = 74/88 (84%)

Query:     2 AGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQI 61
             AG NKQ   TKNTAKLDRETEEL H++V L++ K++ QGRQ+KG +QKDLATKINEKPQ+
Sbjct:    46 AGQNKQHSITKNTAKLDRETEELHHDRVTLEVGKVIQQGRQSKGLTQKDLATKINEKPQV 105

Query:    62 VNDYEGGRGIPNQAIIGKMERALGIRLR 89
             + DYE GR IPN  ++GK+ERA+G++LR
Sbjct:   106 IADYESGRAIPNNQVLGKIERAIGLKLR 133

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0005516 "calmodulin binding" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=TAS

GO:0006355 "regulation of transcription, DNA-dependent" evidence=TAS

GO:0005634 "nucleus" evidence=IDA;IMP;NAS

GO:0043388 "positive regulation of DNA binding" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA;IMP

GO:0005515 "protein binding" evidence=IPI

GO:0045446 "endothelial cell differentiation" evidence=TAS

GO:0003713 "transcription coactivator activity" evidence=IMP

GO:0019216 "regulation of lipid metabolic process" evidence=TAS

GO:0005669 "transcription factor TFIID complex" evidence=IDA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IMP

GO:0004402 "histone acetyltransferase activity" evidence=IDA

GO:0008168 "methyltransferase activity" evidence=IDA

GO:0005622 "intracellular" evidence=TAS

GO:0005730 "nucleolus" evidence=IDA

UNIPROTKB|A6N8P5 MBF1 "Multiprotein bridging factor 1" [Sus scrofa (taxid:9823)]

 Score = 319 (117.4 bits), Expect = 1.2e-28, P = 1.2e-28
 Identities = 58/88 (65%), Positives = 74/88 (84%)

Query:     2 AGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQI 61
             AG NKQ   TKNTAKLDRETEEL H++V L++ K++ QGRQ+KG +QKDLATKINEKPQ+
Sbjct:    46 AGQNKQHSITKNTAKLDRETEELHHDRVTLEVGKVIQQGRQSKGLTQKDLATKINEKPQV 105

Query:    62 VNDYEGGRGIPNQAIIGKMERALGIRLR 89
             + DYE GR IPN  ++GK+ERA+G++LR
Sbjct:   106 IADYESGRAIPNNQVLGKIERAIGLKLR 133

GO:0043388 "positive regulation of DNA binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

GO:0005669 "transcription factor TFIID complex" evidence=IEA

GO:0003713 "transcription coactivator activity" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

MGI|MGI:1891227 Edf1 "endothelial differentiation-related factor 1" [Mus musculus (taxid:10090)]

 Score = 315 (115.9 bits), Expect = 3.1e-28, P = 3.1e-28
 Identities = 57/88 (64%), Positives = 74/88 (84%)

Query:     2 AGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQI 61
             AG NKQ   TKNTAKLDRETEEL H++V L++ K++ +GRQ+KG +QKDLATKINEKPQ+
Sbjct:    46 AGQNKQHSITKNTAKLDRETEELHHDRVTLEVGKVIQRGRQSKGLTQKDLATKINEKPQV 105

Query:    62 VNDYEGGRGIPNQAIIGKMERALGIRLR 89
             + DYE GR IPN  ++GK+ERA+G++LR
Sbjct:   106 IADYESGRAIPNNQVLGKIERAIGLKLR 133

GO:0003677 "DNA binding" evidence=IEA

GO:0003713 "transcription coactivator activity" evidence=ISO

GO:0005516 "calmodulin binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0005737 "cytoplasm" evidence=ISO

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0030154 "cell differentiation" evidence=IEA

GO:0043388 "positive regulation of DNA binding" evidence=ISO

GO:0043565 "sequence-specific DNA binding" evidence=IEA

RGD|1308073 Edf1 "endothelial differentiation-related factor 1" [Rattus norvegicus (taxid:10116)]

 Score = 315 (115.9 bits), Expect = 3.1e-28, P = 3.1e-28
 Identities = 57/88 (64%), Positives = 74/88 (84%)

Query:     2 AGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQI 61
             AG NKQ   TKNTAKLDRETEEL H++V L++ K++ +GRQ+KG +QKDLATKINEKPQ+
Sbjct:    46 AGQNKQHSITKNTAKLDRETEELHHDRVTLEVGKVIQRGRQSKGLTQKDLATKINEKPQV 105

Query:    62 VNDYEGGRGIPNQAIIGKMERALGIRLR 89
             + DYE GR IPN  ++GK+ERA+G++LR
Sbjct:   106 IADYESGRAIPNNQVLGKIERAIGLKLR 133

GO:0003713 "transcription coactivator activity" evidence=IEA;ISO

GO:0005516 "calmodulin binding" evidence=IEA

GO:0005634 "nucleus" evidence=ISO

GO:0005669 "transcription factor TFIID complex" evidence=IEA;ISO

GO:0005730 "nucleolus" evidence=IEA;ISO

GO:0005737 "cytoplasm" evidence=IEA;ISO

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0030154 "cell differentiation" evidence=IEA

GO:0043388 "positive regulation of DNA binding" evidence=IEA;ISO

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISO

GO:0004402 "histone acetyltransferase activity" evidence=ISO

GO:0008168 "methyltransferase activity" evidence=ISO

ZFIN|ZDB-GENE-040426-1710 edf1 "endothelial differentiation-related factor 1" [Danio rerio (taxid:7955)]

 Score = 313 (115.2 bits), Expect = 5.0e-28, P = 5.0e-28
 Identities = 58/88 (65%), Positives = 74/88 (84%)

Query:     2 AGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQI 61
             AG NKQ   TKNTAKLDRETEEL H++VPL++ K++ QGRQ KG +QKDLATKINEKPQI
Sbjct:    45 AGQNKQHVVTKNTAKLDRETEELSHQRVPLEVGKVIQQGRQNKGLTQKDLATKINEKPQI 104

Query:    62 VNDYEGGRGIPNQAIIGKMERALGIRLR 89
             + +YE G+ IPN  ++GK+ERA+G++LR
Sbjct:   105 IAEYECGKAIPNNQVMGKIERAIGLKLR 132

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

WB|WBGene00003148 mbf-1 [Caenorhabditis elegans (taxid:6239)]

 Score = 296 (109.3 bits), Expect = 3.2e-26, P = 3.2e-26
 Identities = 58/106 (54%), Positives = 76/106 (71%)

Query:     2 AGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQI 61
             +G N+Q    KNT +LD ETEEL H+KV L L K++ Q R  KGW+QKDL+T+INEKPQ+
Sbjct:    53 SGGNRQHSANKNTLRLDEETEELHHQKVALSLGKVMQQARATKGWTQKDLSTQINEKPQV 112

Query:    62 VNDYEGGRGIPNQAIIGKMERALGIRLRVNAGTN-KQPGTTKNTAK 106
             V +YE G+ +PNQ I+ KMERALG++LR   G +   P +TK  AK
Sbjct:   113 VGEYESGKAVPNQQIMAKMERALGVKLR---GKDIGMPFSTKPPAK 155

GO:0043565 "sequence-specific DNA binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
O94700	MBF1_SCHPO	No assigned EC number	0.5287	0.4827	0.5675	yes	N/A
Q5ZMC0	EDF1_CHICK	No assigned EC number	0.6704	0.5057	0.5945	yes	N/A
O60869	EDF1_HUMAN	No assigned EC number	0.6590	0.5057	0.5945	yes	N/A
Q9JMG1	EDF1_MOUSE	No assigned EC number	0.6477	0.5057	0.5945	yes	N/A
O14467	MBF1_YEAST	No assigned EC number	0.5394	0.4367	0.5033	yes	N/A
Q752P7	MBF1_ASHGO	No assigned EC number	0.5616	0.4195	0.4802	yes	N/A
Q3T0V7	EDF1_BOVIN	No assigned EC number	0.6590	0.5057	0.5945	yes	N/A
Q6PBY3	EDF1_DANRE	No assigned EC number	0.6590	0.5057	0.6027	yes	N/A
Q6FJN0	MBF1_CANGA	No assigned EC number	0.5810	0.4252	0.4900	yes	N/A
P69736	EDF1_RAT	No assigned EC number	0.6477	0.5057	0.5945	yes	N/A
Q9SJI8	MBF1A_ARATH	No assigned EC number	0.5494	0.5114	0.6267	yes	N/A
Q6CIP4	MBF1_KLULA	No assigned EC number	0.6533	0.4310	0.5	yes	N/A

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
4th Layer	2.7.1.22	LOW CONFIDENCE prediction!
4th Layer	2.7.7.1	LOW CONFIDENCE prediction!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	174
COG1813	165	COG1813, COG1813, Predicted transcription factor,	2e-14
COG1813	165	COG1813, COG1813, Predicted transcription factor,	1e-11
pfam01381	55	pfam01381, HTH_3, Helix-turn-helix	2e-08
smart00530	56	smart00530, HTH_XRE, Helix-turn-helix XRE-family l	2e-08
smart00530	56	smart00530, HTH_XRE, Helix-turn-helix XRE-family l	4e-07
cd00093	58	cd00093, HTH_XRE, Helix-turn-helix XRE-family like	4e-07
pfam01381	55	pfam01381, HTH_3, Helix-turn-helix	5e-07
pfam08523	70	pfam08523, MBF1, Multiprotein bridging factor 1	6e-07
pfam08523	70	pfam08523, MBF1, Multiprotein bridging factor 1	6e-07
cd00093	58	cd00093, HTH_XRE, Helix-turn-helix XRE-family like	5e-06
TIGR00270	154	TIGR00270, TIGR00270, TIGR00270 family protein	7e-06
TIGR00270	154	TIGR00270, TIGR00270, TIGR00270 family protein	3e-04
PRK06424	144	PRK06424, PRK06424, transcription factor; Provisio	0.002

>gnl|CDD|224726 COG1813, COG1813, Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]

 Score = 66.7 bits (163), Expect = 2e-14
 Identities = 21/66 (31%), Positives = 36/66 (54%)

Query: 32  DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVN 91
           D  + + + R+ +G SQ+DLA K+ EK  ++   E G   PN  +  K+E+ LGI+L   
Sbjct: 79  DYGERIREAREKRGLSQEDLAAKLKEKVSVIRRIERGEATPNIKVAKKLEKLLGIKLVEK 138

Query: 92  AGTNKQ 97
               ++
Sbjct: 139 VDEEEE 144

Length = 165

>gnl|CDD|224726 COG1813, COG1813, Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]

 Score = 59.4 bits (144), Expect = 1e-11
 Identities = 18/53 (33%), Positives = 30/53 (56%)

Query: 122 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174
           D  + + + R+ +G SQ+DLA K+ EK  ++   E G   PN  +  K+E+ L
Sbjct: 79  DYGERIREAREKRGLSQEDLAAKLKEKVSVIRRIERGEATPNIKVAKKLEKLL 131

Length = 165

>gnl|CDD|201759 pfam01381, HTH_3, Helix-turn-helix

 Score = 48.3 bits (116), Expect = 2e-08
 Identities = 16/53 (30%), Positives = 28/53 (52%)

Query: 37 LMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLR 89
          L + R+  G SQ++LA K+      ++  E G+  P+   + K+  ALG+ L 
Sbjct: 1  LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLD 53

This large family of DNA binding helix-turn helix proteins includes Cro and CI. Within the Neisseria gonorrhoeae phage associated protein NGO0477, the full protein fold incorporates a helix-turn-helix motif, but the function of this member is unlikely to be that of a DNA-binding regulator, the function of most other members, so is not necessarily characteristic of the whole family. Length = 55

>gnl|CDD|197775 smart00530, HTH_XRE, Helix-turn-helix XRE-family like proteins

 Score = 47.9 bits (115), Expect = 2e-08
 Identities = 16/53 (30%), Positives = 30/53 (56%)

Query: 37 LMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLR 89
          L + R+ KG +Q++LA K+      ++  E G+  P+   + K+ +ALG+ L 
Sbjct: 2  LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLD 54

Length = 56

>gnl|CDD|197775 smart00530, HTH_XRE, Helix-turn-helix XRE-family like proteins

 Score = 44.8 bits (107), Expect = 4e-07
 Identities = 14/48 (29%), Positives = 27/48 (56%)

Query: 127 LMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174
           L + R+ KG +Q++LA K+      ++  E G+  P+   + K+ +AL
Sbjct: 2   LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKAL 49

Length = 56

>gnl|CDD|238045 cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins

 Score = 44.5 bits (106), Expect = 4e-07
 Identities = 16/55 (29%), Positives = 31/55 (56%)

Query: 34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRL 88
           + L + R+ KG +Q++LA K+      ++  E G+  P+   + K+ +ALG+ L
Sbjct: 1  GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSL 55

Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators. Length = 58

>gnl|CDD|201759 pfam01381, HTH_3, Helix-turn-helix

 Score = 44.4 bits (106), Expect = 5e-07
 Identities = 14/48 (29%), Positives = 25/48 (52%)

Query: 127 LMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174
           L + R+  G SQ++LA K+      ++  E G+  P+   + K+  AL
Sbjct: 1   LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEAL 48

This large family of DNA binding helix-turn helix proteins includes Cro and CI. Within the Neisseria gonorrhoeae phage associated protein NGO0477, the full protein fold incorporates a helix-turn-helix motif, but the function of this member is unlikely to be that of a DNA-binding regulator, the function of most other members, so is not necessarily characteristic of the whole family. Length = 55

>gnl|CDD|117100 pfam08523, MBF1, Multiprotein bridging factor 1

 Score = 44.7 bits (106), Expect = 6e-07
 Identities = 18/29 (62%), Positives = 21/29 (72%)

Query: 1  NAGTNKQPGTTKNTAKLDRETEELKHEKV 29
           AG NKQ G  +N AKLDRETE LK ++V
Sbjct: 42 AAGNNKQAGEGQNLAKLDRETEPLKPKRV 70

This domain is found in the multiprotein bridging factor 1 (MBF1) which forms a heterodimer with MBF2. It has been shown to make direct contact with the TATA-box binding protein (TBP) and interacts with Ftz-F1, stabilising the Ftz-F1-DNA complex. It is also found in the endothelial differentiation-related factor (EDF-1). Human EDF-1 is involved in the repression of endothelial differentiation, interacts with CaM and is phosphorylated by PKC. The domain is found in a wide range of eukaryotic proteins including metazoans, fungi and plants. A helix-turn-helix motif (pfam01381) is found to its C-terminus. Length = 70

>gnl|CDD|117100 pfam08523, MBF1, Multiprotein bridging factor 1

 Score = 44.7 bits (106), Expect = 6e-07
 Identities = 18/29 (62%), Positives = 21/29 (72%)

Query: 91  NAGTNKQPGTTKNTAKLDRETEELKHEKV 119
            AG NKQ G  +N AKLDRETE LK ++V
Sbjct: 42  AAGNNKQAGEGQNLAKLDRETEPLKPKRV 70

This domain is found in the multiprotein bridging factor 1 (MBF1) which forms a heterodimer with MBF2. It has been shown to make direct contact with the TATA-box binding protein (TBP) and interacts with Ftz-F1, stabilising the Ftz-F1-DNA complex. It is also found in the endothelial differentiation-related factor (EDF-1). Human EDF-1 is involved in the repression of endothelial differentiation, interacts with CaM and is phosphorylated by PKC. The domain is found in a wide range of eukaryotic proteins including metazoans, fungi and plants. A helix-turn-helix motif (pfam01381) is found to its C-terminus. Length = 70

>gnl|CDD|238045 cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins

 Score = 41.8 bits (99), Expect = 5e-06
 Identities = 14/51 (27%), Positives = 28/51 (54%)

Query: 124 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174
            + L + R+ KG +Q++LA K+      ++  E G+  P+   + K+ +AL
Sbjct: 1   GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKAL 51

Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators. Length = 58

>gnl|CDD|129371 TIGR00270, TIGR00270, TIGR00270 family protein

 Score = 43.7 bits (103), Expect = 7e-06
 Identities = 20/58 (34%), Positives = 33/58 (56%)

Query: 32  DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLR 89
           D   ++ + R+ +GWSQ+ LA KI EK  ++   E     P   ++ K+E+ L I+LR
Sbjct: 69  DYGIIIRREREKRGWSQEQLAKKIQEKESLIKKIENAEIEPEPKVVEKLEKLLKIKLR 126

[Hypothetical proteins, Conserved]. Length = 154

>gnl|CDD|129371 TIGR00270, TIGR00270, TIGR00270 family protein

 Score = 39.1 bits (91), Expect = 3e-04
 Identities = 17/53 (32%), Positives = 29/53 (54%)

Query: 122 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174
           D   ++ + R+ +GWSQ+ LA KI EK  ++   E     P   ++ K+E+ L
Sbjct: 69  DYGIIIRREREKRGWSQEQLAKKIQEKESLIKKIENAEIEPEPKVVEKLEKLL 121

[Hypothetical proteins, Conserved]. Length = 154

>gnl|CDD|102369 PRK06424, PRK06424, transcription factor; Provisional

 Score = 36.5 bits (84), Expect = 0.002
 Identities = 21/57 (36%), Positives = 31/57 (54%)

Query: 32  DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRL 88
           D A+L+   R+    SQ DLA KI E+  ++   E G  +P+     K+E+ LGI L
Sbjct: 84  DYAELVKNARERLSMSQADLAAKIFERKNVIASIERGDLLPDIKTARKLEKILGITL 140

Length = 144

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	174
PHA01976	67	helix-turn-helix protein	99.79
PF12844	64	HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_	99.72
KOG3398|consensus	135		99.72
PRK09706	135	transcriptional repressor DicA; Reviewed	99.7
PF01381	55	HTH_3: Helix-turn-helix; InterPro: IPR001387 This	99.69
PRK08359	176	transcription factor; Validated	99.66
TIGR00270	154	conserved hypothetical protein TIGR00270.	99.65
COG1476	68	Predicted transcriptional regulators [Transcriptio	99.64
TIGR03070	58	couple_hipB transcriptional regulator, y4mF family	99.64
PRK09726	88	antitoxin HipB; Provisional	99.62
PRK06424	144	transcription factor; Provisional	99.61
PRK08154	309	anaerobic benzoate catabolism transcriptional regu	99.61
PF13560	64	HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_	99.59
PRK13890	120	conjugal transfer protein TrbA; Provisional	99.58
PRK09943	185	DNA-binding transcriptional repressor PuuR; Provis	99.57
TIGR02607	78	antidote_HigA addiction module antidote protein, H	99.54
TIGR02612	150	mob_myst_A mobile mystery protein A. Members of th	99.49
TIGR02684	89	dnstrm_HI1420 probable addiction module antidote p	99.43
KOG3398|consensus	135		99.41
PRK10072	96	putative transcriptional regulator; Provisional	99.41
PF13443	63	HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3	99.35
PRK04140	317	hypothetical protein; Provisional	99.33
smart00530	56	HTH_XRE Helix-turn-helix XRE-family like proteins.	99.31
COG1813	165	Predicted transcription factor, homolog of eukaryo	99.3
TIGR03830	127	CxxCG_CxxCG_HTH putative zinc finger/helix-turn-he	99.28
cd00093	58	HTH_XRE Helix-turn-helix XRE-family like proteins.	99.25
PRK10856	331	cytoskeletal protein RodZ; Provisional	99.21
PHA01976	67	helix-turn-helix protein	99.19
PF13744	80	HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_	99.15
PRK13355	517	bifunctional HTH-domain containing protein/aminotr	99.14
TIGR03070	58	couple_hipB transcriptional regulator, y4mF family	99.14
PF01381	55	HTH_3: Helix-turn-helix; InterPro: IPR001387 This	99.12
PRK08359	176	transcription factor; Validated	99.12
COG1813	165	Predicted transcription factor, homolog of eukaryo	99.09
PF12844	64	HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_	99.07
PRK06424	144	transcription factor; Provisional	99.06
TIGR00270	154	conserved hypothetical protein TIGR00270.	99.05
PF13560	64	HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_	99.05
PHA00542	82	putative Cro-like protein	99.05
COG1476	68	Predicted transcriptional regulators [Transcriptio	99.03
COG3620	187	Predicted transcriptional regulator with C-termina	99.02
COG2944	104	Predicted transcriptional regulator [Transcription	98.96
smart00352	75	POU Found in Pit-Oct-Unc transcription factors.	98.95
PRK09726	88	antitoxin HipB; Provisional	98.94
PF07022	66	Phage_CI_repr: Bacteriophage CI repressor helix-tu	98.91
PRK09706	135	transcriptional repressor DicA; Reviewed	98.9
PRK02866	147	cyanate hydratase; Validated	98.84
TIGR00673	150	cynS cyanate hydratase. Alternate names include cy	98.79
TIGR02607	78	antidote_HigA addiction module antidote protein, H	98.78
PRK13890	120	conjugal transfer protein TrbA; Provisional	98.77
PRK10072	96	putative transcriptional regulator; Provisional	98.75
PRK09943	185	DNA-binding transcriptional repressor PuuR; Provis	98.75
COG1396	120	HipB Predicted transcriptional regulators [Transcr	98.73
COG1709	241	Predicted transcriptional regulator [Transcription	98.7
TIGR02684	89	dnstrm_HI1420 probable addiction module antidote p	98.69
COG3655	73	Predicted transcriptional regulator [Transcription	98.67
PRK08154	309	anaerobic benzoate catabolism transcriptional regu	98.67
COG3093	104	VapI Plasmid maintenance system antidote protein [	98.62
TIGR02612	150	mob_myst_A mobile mystery protein A. Members of th	98.58
PF13413	62	HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_	98.57
PRK04140	317	hypothetical protein; Provisional	98.55
COG1395	313	Predicted transcriptional regulator [Transcription	98.52
PHA00542	82	putative Cro-like protein	98.48
smart00530	56	HTH_XRE Helix-turn-helix XRE-family like proteins.	98.41
TIGR03830	127	CxxCG_CxxCG_HTH putative zinc finger/helix-turn-he	98.39
COG1709	241	Predicted transcriptional regulator [Transcription	98.35
PF08667	147	BetR: BetR domain; InterPro: IPR013975 CheY-like p	98.34
cd00093	58	HTH_XRE Helix-turn-helix XRE-family like proteins.	98.32
COG2944	104	Predicted transcriptional regulator [Transcription	98.32
COG1426	284	Predicted transcriptional regulator contains Xre-l	98.29
COG5499	120	Predicted transcription regulator containing HTH d	98.28
PF13443	63	HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3	98.22
cd01392	52	HTH_LacI Helix-turn-helix (HTH) DNA binding domain	98.21
PRK10856	331	cytoskeletal protein RodZ; Provisional	98.19
PRK02866	147	cyanate hydratase; Validated	98.16
TIGR01321	94	TrpR trp operon repressor, proteobacterial. This m	98.07
smart00352	75	POU Found in Pit-Oct-Unc transcription factors.	98.04
PF13744	80	HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_	98.03
TIGR00673	150	cynS cyanate hydratase. Alternate names include cy	97.97
PRK08099	399	bifunctional DNA-binding transcriptional repressor	97.77
PHA01083	149	hypothetical protein	97.74
COG2522	119	Predicted transcriptional regulator [General funct	97.71
COG1396	120	HipB Predicted transcriptional regulators [Transcr	97.56
COG4800	170	Predicted transcriptional regulator with an HTH do	97.54
PF08965	118	DUF1870: Domain of unknown function (DUF1870); Int	97.53
smart00354	70	HTH_LACI helix_turn _helix lactose operon represso	97.52
COG1395	313	Predicted transcriptional regulator [Transcription	97.51
PF00356	46	LacI: Bacterial regulatory proteins, lacI family;	97.48
COG3093	104	VapI Plasmid maintenance system antidote protein [	97.48
PF13413	62	HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_	97.46
PHA00675	78	hypothetical protein	97.39
TIGR03879	73	near_KaiC_dom probable regulatory domain. This mod	97.35
PF04552	160	Sigma54_DBD: Sigma-54, DNA binding domain; InterPr	97.21
PF07022	66	Phage_CI_repr: Bacteriophage CI repressor helix-tu	97.18
PF00157	75	Pou: Pou domain - N-terminal to homeobox domain; I	97.17
COG5606	91	Uncharacterized conserved small protein [Function	97.14
PF13693	78	HTH_35: Winged helix-turn-helix DNA-binding; PDB:	97.12
PF08965	118	DUF1870: Domain of unknown function (DUF1870); Int	97.12
COG3423	82	Nlp Predicted transcriptional regulator [Transcrip	97.01
TIGR01321	94	TrpR trp operon repressor, proteobacterial. This m	96.98
TIGR02147	271	Fsuc_second hypothetical protein, TIGR02147. This	96.95
PRK03975	141	tfx putative transcriptional regulator; Provisiona	96.9
COG3655	73	Predicted transcriptional regulator [Transcription	96.89
PF13384	50	HTH_23: Homeodomain-like domain; PDB: 2X48_C.	96.88
TIGR00721	137	tfx DNA-binding protein, Tfx family. Tfx from Meth	96.86
PF13936	44	HTH_38: Helix-turn-helix domain; PDB: 2W48_A.	96.69
PHA02591	83	hypothetical protein; Provisional	96.65
COG2522	119	Predicted transcriptional regulator [General funct	96.6
cd01392	52	HTH_LacI Helix-turn-helix (HTH) DNA binding domain	96.58
TIGR02293	133	TAS_TIGR02293 putative toxin-antitoxin system anti	96.55
PF14549	60	P22_Cro: DNA-binding transcriptional regulator Cro	96.54
COG3636	100	Predicted transcriptional regulator [Transcription	96.52
PHA01083	149	hypothetical protein	96.4
PF02796	45	HTH_7: Helix-turn-helix domain of resolvase; Inter	96.38
PF00356	46	LacI: Bacterial regulatory proteins, lacI family;	96.36
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	96.33
PF08535	93	KorB: KorB domain; InterPro: IPR013741 This entry	96.33
PF01710	119	HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Tr	96.31
PRK10344	92	DNA-binding transcriptional regulator Nlp; Provisi	96.15
cd04763	68	HTH_MlrA-like Helix-Turn-Helix DNA binding domain	96.11
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	96.03
PF07037	122	DUF1323: Putative transcription regulator (DUF1323	95.99
PF04814	180	HNF-1_N: Hepatocyte nuclear factor 1 (HNF-1), N te	95.98
PRK01381	99	Trp operon repressor; Provisional	95.97
TIGR02844	80	spore_III_D sporulation transcriptional regulator	95.94
COG4197	96	Uncharacterized protein conserved in bacteria, pro	95.9
smart00354	70	HTH_LACI helix_turn _helix lactose operon represso	95.89
PF06056	58	Terminase_5: Putative ATPase subunit of terminase	95.82
cd04762	49	HTH_MerR-trunc Helix-Turn-Helix DNA binding domain	95.79
PF05269	91	Phage_CII: Bacteriophage CII protein; InterPro: IP	95.77
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	95.71
COG1356	143	tfx Transcriptional regulator [DNA replication, re	95.71
TIGR02531	88	yecD_yerC TrpR-related protein YerC/YecD. This mod	95.7
PF08523	71	MBF1: Multiprotein bridging factor 1; InterPro: IP	95.7
PRK10014	342	DNA-binding transcriptional repressor MalI; Provis	95.65
PF13551	112	HTH_29: Winged helix-turn helix	95.64
PHA00675	78	hypothetical protein	95.55
COG4800	170	Predicted transcriptional regulator with an HTH do	95.5
TIGR01610	95	phage_O_Nterm phage replication protein O, N-termi	95.49
PRK09492	315	treR trehalose repressor; Provisional	95.49
PRK11303	328	DNA-binding transcriptional regulator FruR; Provis	95.45
PF05225	45	HTH_psq: helix-turn-helix, Psq domain; InterPro: I	95.38
PRK05932	455	RNA polymerase factor sigma-54; Reviewed	95.37
TIGR02405	311	trehalos_R_Ecol trehalose operon repressor, proteo	95.37
TIGR03879	73	near_KaiC_dom probable regulatory domain. This mod	95.33
PF02001	106	DUF134: Protein of unknown function DUF134; InterP	95.32
PF02376	87	CUT: CUT domain; InterPro: IPR003350 A class, also	95.31
TIGR02395	429	rpoN_sigma RNA polymerase sigma-54 factor. A sigma	95.3
PRK09526	342	lacI lac repressor; Reviewed	95.29
PRK08558	238	adenine phosphoribosyltransferase; Provisional	95.26
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	95.24
PF01371	87	Trp_repressor: Trp repressor protein; InterPro: IP	95.22
PF10668	60	Phage_terminase: Phage terminase small subunit; In	95.2
TIGR01481	329	ccpA catabolite control protein A. Catabolite cont	95.19
PRK10703	341	DNA-binding transcriptional repressor PurR; Provis	95.19
PRK04217	110	hypothetical protein; Provisional	95.16
COG2842	297	Uncharacterized ATPase, putative transposase [Gene	95.14
PRK13698	323	plasmid-partitioning protein; Provisional	95.09
COG2390	321	DeoR Transcriptional regulator, contains sigma fac	95.06
cd01104	68	HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain	95.02
cd04764	67	HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding dom	95.01
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	94.94
cd04761	49	HTH_MerR-SF Helix-Turn-Helix DNA binding domain of	94.94
COG5499	120	Predicted transcription regulator containing HTH d	94.93
PRK10727	343	DNA-binding transcriptional regulator GalR; Provis	94.91
TIGR01764	49	excise DNA binding domain, excisionase family. An	94.88
cd00569	42	HTH_Hin_like Helix-turn-helix domain of Hin and re	94.86
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	94.85
PRK10401	346	DNA-binding transcriptional regulator GalS; Provis	94.81
cd04774	96	HTH_YfmP Helix-Turn-Helix DNA binding domain of th	94.8
cd04765	99	HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding dom	94.79
PRK14987	331	gluconate operon transcriptional regulator; Provis	94.78
PRK12469	481	RNA polymerase factor sigma-54; Provisional	94.76
PF02954	42	HTH_8: Bacterial regulatory protein, Fis family; I	94.68
TIGR00180	187	parB_part ParB-like partition proteins. This model	94.61
TIGR02417	327	fruct_sucro_rep D-fructose-responsive transcriptio	94.58
cd04778	219	HTH_MerR-like_sg2 Helix-Turn-Helix DNA binding dom	94.58
PRK09744	75	DNA-binding transcriptional regulator DicC; Provis	94.52
COG1342	99	Predicted DNA-binding proteins [General function p	94.51
COG1609	333	PurR Transcriptional regulators [Transcription]	94.49
PF12728	51	HTH_17: Helix-turn-helix domain	94.48
TIGR03764	258	ICE_PFGI_1_parB integrating conjugative element, P	94.42
COG1513	151	CynS Cyanate lyase [Inorganic ion transport and me	94.37
PF13518	52	HTH_28: Helix-turn-helix domain	94.37
KOG3802|consensus	398		94.35
PF13936	44	HTH_38: Helix-turn-helix domain; PDB: 2W48_A.	94.32
PRK15418	318	transcriptional regulator LsrR; Provisional	94.31
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	94.28
PF00376	38	MerR: MerR family regulatory protein; InterPro: IP	94.26
PF13613	53	HTH_Tnp_4: Helix-turn-helix of DDE superfamily end	94.22
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	94.2
cd00131	128	PAX Paired Box domain	94.19
cd01105	88	HTH_GlnR-like Helix-Turn-Helix DNA binding domain	94.12
KOG1168|consensus	385		94.11
PRK10339	327	DNA-binding transcriptional repressor EbgR; Provis	94.1
cd06171	55	Sigma70_r4 Sigma70, region (SR) 4 refers to the mo	93.95
PF13384	50	HTH_23: Homeodomain-like domain; PDB: 2X48_C.	93.94
PF08667	147	BetR: BetR domain; InterPro: IPR013975 CheY-like p	93.93
cd04782	97	HTH_BltR Helix-Turn-Helix DNA binding domain of th	93.89
cd04787	133	HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain	93.85
PF13411	69	MerR_1: MerR HTH family regulatory protein; PDB: 2	93.84
smart00342	84	HTH_ARAC helix_turn_helix, arabinose operon contro	93.82
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	93.8
cd04784	127	HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain	93.59
cd01109	113	HTH_YyaN Helix-Turn-Helix DNA binding domain of th	93.53
cd04788	96	HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain	93.47
cd04767	120	HTH_HspR-like_MBC Helix-Turn-Helix DNA binding dom	93.46
PRK12427	231	flagellar biosynthesis sigma factor; Provisional	93.38
cd04768	96	HTH_BmrR-like Helix-Turn-Helix DNA binding domain	93.37
PRK03975	141	tfx putative transcriptional regulator; Provisiona	93.37
PHA02591	83	hypothetical protein; Provisional	93.35
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	93.33
TIGR02147	271	Fsuc_second hypothetical protein, TIGR02147. This	93.33
PRK10423	327	transcriptional repressor RbsR; Provisional	93.33
TIGR02293	133	TAS_TIGR02293 putative toxin-antitoxin system anti	93.29
PF01527	76	HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp	93.25
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	93.24
TIGR02844	80	spore_III_D sporulation transcriptional regulator	93.22
cd06571	90	Bac_DnaA_C C-terminal domain of bacterial DnaA pro	93.17
cd01106	103	HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain	93.15
smart00422	70	HTH_MERR helix_turn_helix, mercury resistance.	93.12
PF14549	60	P22_Cro: DNA-binding transcriptional regulator Cro	93.12
PF08281	54	Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013	93.11
smart00351	125	PAX Paired Box domain.	93.07
PRK10458	467	DNA cytosine methylase; Provisional	92.97
TIGR02997	298	Sig70-cyanoRpoD RNA polymerase sigma factor, cyano	92.96
PF01418	77	HTH_6: Helix-turn-helix domain, rpiR family; Inter	92.89
PRK00118	104	putative DNA-binding protein; Validated	92.87
cd04786	131	HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding dom	92.82
PRK08558	238	adenine phosphoribosyltransferase; Provisional	92.76
cd01111	107	HTH_MerD Helix-Turn-Helix DNA binding domain of th	92.7
cd04775	102	HTH_Cfa-like Helix-Turn-Helix DNA binding domain o	92.68
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	92.65
smart00421	58	HTH_LUXR helix_turn_helix, Lux Regulon. lux regulo	92.59
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	92.58
PRK09413	121	IS2 repressor TnpA; Reviewed	92.52
PF13545	76	HTH_Crp_2: Crp-like helix-turn-helix domain; PDB:	92.45
PF05225	45	HTH_psq: helix-turn-helix, Psq domain; InterPro: I	92.45
TIGR02479	224	FliA_WhiG RNA polymerase sigma factor, FliA/WhiG f	92.42
TIGR00721	137	tfx DNA-binding protein, Tfx family. Tfx from Meth	92.3
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	92.25
cd01282	112	HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding dom	92.23
PF10078	89	DUF2316: Uncharacterized protein conserved in bact	92.21
PF06056	58	Terminase_5: Putative ATPase subunit of terminase	92.19
PRK07598	415	RNA polymerase sigma factor SigC; Validated	92.19
PF14590	166	DUF4447: Domain of unknown function (DUF4447); PDB	92.18
TIGR02044	127	CueR Cu(I)-responsive transcriptional regulator. T	92.02
PRK13752	144	putative transcriptional regulator MerR; Provision	92.01
TIGR02051	124	MerR Hg(II)-responsive transcriptional regulator.	91.98
TIGR02047	127	CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional	91.97
PRK11511	127	DNA-binding transcriptional activator MarA; Provis	91.96
PF08535	93	KorB: KorB domain; InterPro: IPR013741 This entry	91.93
PF11427	50	HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C	91.92
COG2512	258	Predicted membrane-associated trancriptional regul	91.91
COG2973	103	TrpR Trp operon repressor [Transcription]	91.87
smart00419	48	HTH_CRP helix_turn_helix, cAMP Regulatory protein.	91.86
cd04773	108	HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding	91.85
cd00592	100	HTH_MerR-like Helix-Turn-Helix DNA binding domain	91.68
cd01108	127	HTH_CueR Helix-Turn-Helix DNA binding domain of Cu	91.65
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	91.64
PF07900	220	DUF1670: Protein of unknown function (DUF1670); In	91.47
cd04770	123	HTH_HMRTR Helix-Turn-Helix DNA binding domain of H	91.4
PRK05911	257	RNA polymerase sigma factor sigma-28; Reviewed	91.39
TIGR02392	270	rpoH_proteo alternative sigma factor RpoH. A sigma	91.36
cd04785	126	HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding do	91.35
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	91.34
PRK04132	846	replication factor C small subunit; Provisional	91.33
PRK10227	135	DNA-binding transcriptional regulator CueR; Provis	91.19
TIGR02054	120	MerD mercuric resistence transcriptional repressor	91.16
PF07638	185	Sigma70_ECF: ECF sigma factor	91.15
TIGR02885	231	spore_sigF RNA polymerase sigma-F factor. Members	91.03
PF00157	75	Pou: Pou domain - N-terminal to homeobox domain; I	91.02
PF05930	51	Phage_AlpA: Prophage CP4-57 regulatory protein (Al	90.99
COG1522	154	Lrp Transcriptional regulators [Transcription]	90.95
cd01110	139	HTH_SoxR Helix-Turn-Helix DNA binding domain of th	90.93
PF13022	142	HTH_Tnp_1_2: Helix-turn-helix of insertion element	90.92
PF02796	45	HTH_7: Helix-turn-helix domain of resolvase; Inter	90.92
PRK07405	317	RNA polymerase sigma factor SigD; Validated	90.9
PRK09514	140	zntR zinc-responsive transcriptional regulator; Pr	90.84
PF13542	52	HTH_Tnp_ISL3: Helix-turn-helix domain of transposa	90.81
cd04762	49	HTH_MerR-trunc Helix-Turn-Helix DNA binding domain	90.81
TIGR02885	231	spore_sigF RNA polymerase sigma-F factor. Members	90.71
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	90.66
PRK13749	121	transcriptional regulator MerD; Provisional	90.62
TIGR02394	285	rpoS_proteo RNA polymerase sigma factor RpoS. A si	90.6
PF00165	42	HTH_AraC: Bacterial regulatory helix-turn-helix pr	90.57
cd04790	172	HTH_Cfa-like_unk Helix-Turn-Helix DNA binding doma	90.57
PRK13355	517	bifunctional HTH-domain containing protein/aminotr	90.54
TIGR02980	227	SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G	90.5
TIGR01636	134	phage_rinA phage transcriptional activator, RinA f	90.5
TIGR02043	131	ZntR Zn(II)-responsive transcriptional regulator.	90.49
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	90.44
cd04783	126	HTH_MerR1 Helix-Turn-Helix DNA binding domain of t	90.41
PRK06596	284	RNA polymerase factor sigma-32; Reviewed	90.34
TIGR02393	238	RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter	90.34
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	90.23
PRK13869	405	plasmid-partitioning protein RepA; Provisional	90.2
cd04789	102	HTH_Cfa Helix-Turn-Helix DNA binding domain of the	90.17
PRK09744	75	DNA-binding transcriptional regulator DicC; Provis	90.12
PRK11512	144	DNA-binding transcriptional repressor MarR; Provis	90.1
cd01107	108	HTH_BmrR Helix-Turn-Helix DNA binding domain of th	90.04
cd04772	99	HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding d	89.9
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	89.88
PRK10219	107	DNA-binding transcriptional regulator SoxS; Provis	89.88
cd04764	67	HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding dom	89.8
PF13011	85	LZ_Tnp_IS481: leucine-zipper of insertion element	89.67
cd04761	49	HTH_MerR-SF Helix-Turn-Helix DNA binding domain of	89.56
PF02954	42	HTH_8: Bacterial regulatory protein, Fis family; I	89.54
COG1508	444	RpoN DNA-directed RNA polymerase specialized sigma	89.36
COG0789	124	SoxR Predicted transcriptional regulators [Transcr	89.33
cd01279	98	HTH_HspR-like Helix-Turn-Helix DNA binding domain	89.22
cd04780	95	HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding dom	89.22
PRK15043	243	transcriptional regulator MirA; Provisional	89.02
cd06170	57	LuxR_C_like C-terminal DNA-binding domain of LuxR-	88.97
cd01104	68	HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain	88.96
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	88.82
PF00376	38	MerR: MerR family regulatory protein; InterPro: IP	88.78
cd04779	134	HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding dom	88.69
PF08299	70	Bac_DnaA_C: Bacterial dnaA protein helix-turn-heli	88.57
cd04766	91	HTH_HspR Helix-Turn-Helix DNA binding domain of th	88.56
PF10668	60	Phage_terminase: Phage terminase small subunit; In	88.52
cd04763	68	HTH_MlrA-like Helix-Turn-Helix DNA binding domain	88.52
COG5606	91	Uncharacterized conserved small protein [Function	88.52
PF00196	58	GerE: Bacterial regulatory proteins, luxR family;	88.49
PRK00215	205	LexA repressor; Validated	88.47
COG3415	138	Transposase and inactivated derivatives [DNA repli	88.42
PF13730	55	HTH_36: Helix-turn-helix domain	88.35
PRK11891	429	aspartate carbamoyltransferase; Provisional	88.33
COG1318	182	Predicted transcriptional regulators [Transcriptio	88.33
PRK08215	258	sporulation sigma factor SigG; Reviewed	88.33
PF12728	51	HTH_17: Helix-turn-helix domain	88.23
PRK05572	252	sporulation sigma factor SigF; Validated	88.21
cd04769	116	HTH_MerR2 Helix-Turn-Helix DNA binding domain of M	88.13
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	87.96
PRK12427	231	flagellar biosynthesis sigma factor; Provisional	87.8
PF13411	69	MerR_1: MerR HTH family regulatory protein; PDB: 2	87.76
PRK00430	95	fis global DNA-binding transcriptional dual regula	87.72
TIGR00122	69	birA_repr_reg BirA biotin operon repressor domain.	87.7
PRK07500	289	rpoH2 RNA polymerase factor sigma-32; Reviewed	87.63
TIGR03453	387	partition_RepA plasmid partitioning protein RepA.	87.61
TIGR01764	49	excise DNA binding domain, excisionase family. An	87.55
PF09048	59	Cro: Cro; InterPro: IPR000655 Bacteriophage lambda	87.49
PF05269	91	Phage_CII: Bacteriophage CII protein; InterPro: IP	87.47
TIGR02392	270	rpoH_proteo alternative sigma factor RpoH. A sigma	87.44
cd04781	120	HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding dom	87.39
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	87.36
COG3311	70	AlpA Predicted transcriptional regulator [Transcri	87.32
PRK05949	327	RNA polymerase sigma factor; Validated	87.23
TIGR03209	142	P21_Cbot clostridium toxin-associated regulator Bo	87.21
PRK15320	251	transcriptional activator SprB; Provisional	87.12
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	87.07
PRK09863	584	putative frv operon regulatory protein; Provisiona	87.06
PRK11179	153	DNA-binding transcriptional regulator AsnC; Provis	86.96
PRK09210	367	RNA polymerase sigma factor RpoD; Validated	86.96
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	86.9
PRK01381	99	Trp operon repressor; Provisional	86.87
TIGR03697	193	NtcA_cyano global nitrogen regulator NtcA, cyanoba	86.82
PF07453	37	NUMOD1: NUMOD1 domain; InterPro: IPR010896 This he	86.81
PF01527	76	HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp	86.77
COG1356	143	tfx Transcriptional regulator [DNA replication, re	86.74
PF13693	78	HTH_35: Winged helix-turn-helix DNA-binding; PDB:	86.74
PF04297	101	UPF0122: Putative helix-turn-helix protein, YlxM /	86.68
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	86.65
PF02042	52	RWP-RK: RWP-RK domain; InterPro: IPR003035 This do	86.62
TIGR02393	238	RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter	86.56
PRK07122	264	RNA polymerase sigma factor SigF; Reviewed	86.55
PRK06596	284	RNA polymerase factor sigma-32; Reviewed	86.53
TIGR02337	118	HpaR homoprotocatechuate degradation operon regula	86.5
smart00760	60	Bac_DnaA_C Bacterial dnaA protein helix-turn-helix	86.4
smart00497	53	IENR1 Intron encoded nuclease repeat motif. Repeat	86.36
PRK13832	520	plasmid partitioning protein; Provisional	86.35
PRK11161	235	fumarate/nitrate reduction transcriptional regulat	86.17
PRK10572	290	DNA-binding transcriptional regulator AraC; Provis	86.15
PRK06986	236	fliA flagellar biosynthesis sigma factor; Validate	86.14
PRK13182	175	racA polar chromosome segregation protein; Reviewe	86.09
PRK13413	200	mpi multiple promoter invertase; Provisional	86.04
PRK08215	258	sporulation sigma factor SigG; Reviewed	85.98
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	85.77
PRK11924	179	RNA polymerase sigma factor; Provisional	85.72
COG1974	201	LexA SOS-response transcriptional repressors (RecA	85.65
PRK06288	268	RNA polymerase sigma factor WhiG; Reviewed	85.61
PRK07037	163	extracytoplasmic-function sigma-70 factor; Validat	85.6
PF06322	64	Phage_NinH: Phage NinH protein; InterPro: IPR01045	85.54
PRK11169	164	leucine-responsive transcriptional regulator; Prov	85.49
PRK06759	154	RNA polymerase factor sigma-70; Validated	85.45
TIGR02980	227	SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G	85.43
PRK05901	509	RNA polymerase sigma factor; Provisional	85.41
TIGR02985	161	Sig70_bacteroi1 RNA polymerase sigma-70 factor, Ba	85.39
cd07377	66	WHTH_GntR Winged helix-turn-helix (WHTH) DNA-bindi	85.24
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	85.18
TIGR02999	183	Sig-70_X6 RNA polymerase sigma factor, TIGR02999 f	85.11
cd04776	118	HTH_GnyR Helix-Turn-Helix DNA binding domain of th	85.05
TIGR02297	287	HpaA 4-hydroxyphenylacetate catabolism regulatory	85.04
cd04777	107	HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding dom	84.86
TIGR02937	158	sigma70-ECF RNA polymerase sigma factor, sigma-70	84.85
PRK12423	202	LexA repressor; Provisional	84.81
TIGR00180	187	parB_part ParB-like partition proteins. This model	84.77
PF13518	52	HTH_28: Helix-turn-helix domain	84.71
PRK09391	230	fixK transcriptional regulator FixK; Provisional	84.7
PRK05572	252	sporulation sigma factor SigF; Validated	84.69
PRK13918	202	CRP/FNR family transcriptional regulator; Provisio	84.44
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	84.43
PRK09652	182	RNA polymerase sigma factor RpoE; Provisional	84.35
TIGR02895	218	spore_sigI RNA polymerase sigma-I factor. Members	84.33
smart00422	70	HTH_MERR helix_turn_helix, mercury resistance.	84.28
PRK11753	211	DNA-binding transcriptional dual regulator Crp; Pr	84.28
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	84.19
PRK09639	166	RNA polymerase sigma factor SigX; Provisional	84.19
TIGR02531	88	yecD_yerC TrpR-related protein YerC/YecD. This mod	84.18
PRK13503	278	transcriptional activator RhaS; Provisional	84.08
PRK13501	290	transcriptional activator RhaR; Provisional	84.07
PF12833	81	HTH_18: Helix-turn-helix domain; PDB: 2K9S_A 3LSG_	84.06
PRK13502	282	transcriptional activator RhaR; Provisional	83.94
COG5484	279	Uncharacterized conserved protein [Function unknow	83.77
PF08280	59	HTH_Mga: M protein trans-acting positive regulator	83.72
smart00347	101	HTH_MARR helix_turn_helix multiple antibiotic resi	83.66
PF09012	69	FeoC: FeoC like transcriptional regulator; InterPr	83.62
PHA01082	133	putative transcription regulator	83.62
COG1513	151	CynS Cyanate lyase [Inorganic ion transport and me	83.59
TIGR02989	159	Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodop	83.51
PRK12519	194	RNA polymerase sigma factor; Provisional	83.51
PRK03341	168	arginine repressor; Provisional	83.47
PRK09413	121	IS2 repressor TnpA; Reviewed	83.37
PF13309	64	HTH_22: HTH domain	83.32
PF00440	47	TetR_N: Bacterial regulatory proteins, tetR family	83.29
PRK15411	207	rcsA colanic acid capsular biosynthesis activation	83.28
PRK08583	257	RNA polymerase sigma factor SigB; Validated	83.27
PRK07122	264	RNA polymerase sigma factor SigF; Reviewed	83.25
TIGR01950	142	SoxR redox-sensitive transcriptional activator Sox	83.24
cd00569	42	HTH_Hin_like Helix-turn-helix domain of Hin and re	83.23
PRK13777	185	transcriptional regulator Hpr; Provisional	83.19
PRK09646	194	RNA polymerase sigma factor SigK; Reviewed	83.09
PF01710	119	HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Tr	82.94
PRK09047	161	RNA polymerase factor sigma-70; Validated	82.87
PF13613	53	HTH_Tnp_4: Helix-turn-helix of DDE superfamily end	82.71
PRK13919	186	putative RNA polymerase sigma E protein; Provision	82.51
PRK06030	124	hypothetical protein; Provisional	82.47
PRK06986	236	fliA flagellar biosynthesis sigma factor; Validate	82.46
COG4565	224	CitB Response regulator of citrate/malate metaboli	82.44
PF08281	54	Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013	82.39
PRK07500	289	rpoH2 RNA polymerase factor sigma-32; Reviewed	82.38
PRK07406	373	RNA polymerase sigma factor RpoD; Validated	82.21
PRK12529	178	RNA polymerase sigma factor; Provisional	82.13
PRK01905	77	DNA-binding protein Fis; Provisional	81.86
TIGR02941	255	Sigma_B RNA polymerase sigma-B factor. This sigma	81.75
PRK05911	257	RNA polymerase sigma factor sigma-28; Reviewed	81.67
PF02001	106	DUF134: Protein of unknown function DUF134; InterP	81.66
TIGR02997	298	Sig70-cyanoRpoD RNA polymerase sigma factor, cyano	81.61
PRK15201	198	fimbriae regulatory protein FimW; Provisional	81.52
PRK09649	185	RNA polymerase sigma factor SigC; Reviewed	81.46
PRK15002	154	redox-sensitivie transcriptional activator SoxR; P	81.44
PRK12523	172	RNA polymerase sigma factor; Reviewed	81.39
PRK09954	362	putative kinase; Provisional	81.33
PRK12537	182	RNA polymerase sigma factor; Provisional	81.31
PRK09642	160	RNA polymerase sigma factor SigW; Reviewed	81.14
PRK09645	173	RNA polymerase sigma factor SigL; Provisional	81.14
PRK14845	1049	translation initiation factor IF-2; Provisional	81.1
PRK07670	251	RNA polymerase sigma factor SigD; Validated	80.94
COG3413	215	Predicted DNA binding protein [General function pr	80.94
COG3415	138	Transposase and inactivated derivatives [DNA repli	80.9
PF08822	165	DUF1804: Protein of unknown function (DUF1804); In	80.88
cd01105	88	HTH_GlnR-like Helix-Turn-Helix DNA binding domain	80.85
PRK05657	325	RNA polymerase sigma factor RpoS; Validated	80.79
COG4367	97	Uncharacterized protein conserved in bacteria [Fun	80.71
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	80.6
PRK13509	251	transcriptional repressor UlaR; Provisional	80.58
TIGR02941	255	Sigma_B RNA polymerase sigma-B factor. This sigma	80.56
PRK11050	152	manganese transport regulator MntR; Provisional	80.53
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	80.46
PRK09210	367	RNA polymerase sigma factor RpoD; Validated	80.46
PRK10411	240	DNA-binding transcriptional activator FucR; Provis	80.37
PF01371	87	Trp_repressor: Trp repressor protein; InterPro: IP	80.35
TIGR02702	203	SufR_cyano iron-sulfur cluster biosynthesis transc	80.34
PRK05602	186	RNA polymerase sigma factor; Reviewed	80.3
PF14590	166	DUF4447: Domain of unknown function (DUF4447); PDB	80.27
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	80.24
smart00421	58	HTH_LUXR helix_turn_helix, Lux Regulon. lux regulo	80.21
PRK06930	170	positive control sigma-like factor; Validated	80.18
smart00418	66	HTH_ARSR helix_turn_helix, Arsenical Resistance Op	80.16
PRK12524	196	RNA polymerase sigma factor; Provisional	80.1
cd04773	108	HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding	80.09
PRK05657	325	RNA polymerase sigma factor RpoS; Validated	80.01

>PHA01976 helix-turn-helix protein

Probab=99.79  E-value=2.7e-19  Score=115.12  Aligned_cols=64  Identities=25%  Similarity=0.549  Sum_probs=61.5

Q ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccCC
Q psy6501          31 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGT   94 (174)
Q Consensus        31 ~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~   94 (174)
                      |.||.+|+.+|+.+||||.+||+.+|+|+++|++||+|...|+.+.+.+||++|||+++||++.
T Consensus         1 m~~~~rl~~~R~~~glt~~~lA~~~gvs~~~v~~~e~g~~~p~~~~l~~ia~~l~v~~~~l~~g   64 (67)
T PHA01976          1 MSFAIQLIKARNARAWSAPELSRRAGVRHSLIYDFEADKRLPNLKTLLRLADALGVTLDWLCGR   64 (67)
T ss_pred             CcHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHHHHhcC
Confidence            4689999999999999999999999999999999999999999999999999999999999853

>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B

Probab=99.72  E-value=1.3e-17  Score=106.36  Aligned_cols=60  Identities=30%  Similarity=0.432  Sum_probs=52.8

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccC
Q psy6501          34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAG   93 (174)
Q Consensus        34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~   93 (174)
                      |++||.+|+.+|+||.+||+.+|+++++|++||+|++.|+...+.+||++|+|+++||+.
T Consensus         1 G~~lk~~r~~~~lt~~~~a~~~~i~~~~i~~~e~g~~~~~~~~l~~i~~~~~v~~~~l~~   60 (64)
T PF12844_consen    1 GERLKELREEKGLTQKDLAEKLGISRSTISKIENGKRKPSVSTLKKIAEALGVSLDELFD   60 (64)
T ss_dssp             HHHHHHHHHHCT--HHHHHHHHTS-HHHHHHHHTTSS--BHHHHHHHHHHHTS-HHHHCC
T ss_pred             CHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCcCCCHHHHHHHHHHhCCCHHHHhc
Confidence            789999999999999999999999999999999999999999999999999999999984

>KOG3398|consensus

Probab=99.72  E-value=2.2e-17  Score=115.68  Aligned_cols=90  Identities=64%  Similarity=0.951  Sum_probs=87.4

Q ss_pred             CCCCCCCCCCCccccccccchhhcccccchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHH
Q psy6501           1 NAGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKM   80 (174)
Q Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~l   80 (174)
                      ++|.|+|--.++++++||++||++.|+.+...+|..|...|..+||||++||.+|+--++.|..||+|+..|+..+|.++
T Consensus        42 ~~g~nkq~~~~~~t~klD~etE~~~~~~v~~~Vg~aIq~aR~~KgmsqkDLA~kInekpqVv~dyEsGrAIpNqqil~km  121 (135)
T KOG3398|consen   42 PAGLNKQHPSTQSTAKLDRETEELGHDRVPLEVGKAIQQARAQKGMSQKDLAQKINEKPQVIQDYESGRAIPNQQILSKM  121 (135)
T ss_pred             cccccccCCcccchhhccccccccccccccHHHHHHHHHHHHhccccHHHHHHHHccCchhhhhHhccccCchHHHHHHH
Confidence            47999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhCccccc
Q psy6501          81 ERALGIRLRV   90 (174)
Q Consensus        81 a~~L~v~~~~   90 (174)
                      .++|||.+.+
T Consensus       122 EraLgvKlrg  131 (135)
T KOG3398|consen  122 ERALGVKLRG  131 (135)
T ss_pred             HHHhceeccc
Confidence            9999998765

>PRK09706 transcriptional repressor DicA; Reviewed

Probab=99.70  E-value=2.5e-16  Score=114.84  Aligned_cols=66  Identities=17%  Similarity=0.128  Sum_probs=62.5

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccCCC
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGTN   95 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~~   95 (174)
                      .+.+|++|+.+|+.+||||.+||+.+|||+++|++||+|.+.|+.+.+.+||++|||+++||+...
T Consensus         3 ~~~~g~rlk~~R~~~gltq~~lA~~~gvs~~~is~~E~g~~~p~~~~l~~la~~l~vs~~~l~~g~   68 (135)
T PRK09706          3 NLTLGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKALQCSPTWLLFGD   68 (135)
T ss_pred             hhhHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHHHHhcCC
Confidence            357999999999999999999999999999999999999999999999999999999999998543

>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould)

Probab=99.69  E-value=7.1e-17  Score=99.79  Aligned_cols=55  Identities=29%  Similarity=0.438  Sum_probs=51.6

Q ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccc
Q psy6501          37 LMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVN   91 (174)
Q Consensus        37 ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l   91 (174)
                      |+++|+++||||+|||+.+|+|+++|++||+|.+.|+.+.+.+||++|||+++||
T Consensus         1 ik~~r~~~gls~~~la~~~gis~~~i~~~~~g~~~~~~~~~~~ia~~l~~~~~~l   55 (55)
T PF01381_consen    1 IKELRKEKGLSQKELAEKLGISRSTISRIENGKRNPSLDTLKKIAKALGVSPEYL   55 (55)
T ss_dssp             HHHHHHHTTS-HHHHHHHHTS-HHHHHHHHTTSSTSBHHHHHHHHHHHTSEHHHH
T ss_pred             CHHHHHHcCCCHHHHHHHhCCCcchhHHHhcCCCCCCHHHHHHHHHHHCCCHHHC
Confidence            7899999999999999999999999999999999999999999999999999986

; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....

>PRK08359 transcription factor; Validated

Probab=99.66  E-value=3.3e-16  Score=118.07  Aligned_cols=68  Identities=21%  Similarity=0.220  Sum_probs=64.4

Q ss_pred             cccchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccC
Q psy6501          26 HEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAG   93 (174)
Q Consensus        26 ~~~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~   93 (174)
                      ..++...||++||++|+.+||||+|||+.+|+++++|++||+|.+.|+.+.+.+||++|+|++..++.
T Consensus        79 ~~elv~dy~~rIkeaRe~kglSQeeLA~~lgvs~stI~~iE~G~~~Ps~~~l~kLak~l~VsL~e~~~  146 (176)
T PRK08359         79 TEDIVEDYAERVYEAIQKSGLSYEELSHEVGLSVNDLRRIAHGEYEPTIKEAKKLERYFKIKLIERVE  146 (176)
T ss_pred             HHHHHHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCcCCCHHHHHHHHHHhCCccccccc
Confidence            45788899999999999999999999999999999999999999999999999999999999887664

>TIGR00270 conserved hypothetical protein TIGR00270

Probab=99.65  E-value=4.3e-16  Score=115.70  Aligned_cols=66  Identities=30%  Similarity=0.545  Sum_probs=63.8

Q ss_pred             cchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccC
Q psy6501          28 KVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAG   93 (174)
Q Consensus        28 ~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~   93 (174)
                      .++..+|++|+.+|+++||||++||+++|+++++|++||+|...|+++.+.+||++|||++++++.
T Consensus        65 ~l~~~~g~~Ir~~Re~~glSqeeLA~~lgvs~s~IsriE~G~~~Ps~~~l~kLa~~Lgvsl~el~~  130 (154)
T TIGR00270        65 ELVEDYGIIIRREREKRGWSQEQLAKKIQEKESLIKKIENAEIEPEPKVVEKLEKLLKIKLREQVP  130 (154)
T ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHhCCCHHHHcc
Confidence            667889999999999999999999999999999999999999999999999999999999999985

>COG1476 Predicted transcriptional regulators [Transcription]

Probab=99.64  E-value=5.4e-16  Score=98.88  Aligned_cols=58  Identities=22%  Similarity=0.239  Sum_probs=56.6

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccC
Q psy6501          36 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAG   93 (174)
Q Consensus        36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~   93 (174)
                      ++|.+|...|+||+|||+.+|||++||..||+|+..||+....+||.+|+++++++|-
T Consensus         5 k~k~~R~~~~ltQ~elA~~vgVsRQTi~~iEkgky~Psl~La~kia~~f~~~iedIF~   62 (68)
T COG1476           5 KLKELRAELGLTQEELAKLVGVSRQTIIAIEKGKYNPSLELALKIARVFGKTIEDIFQ   62 (68)
T ss_pred             HHHHHHHHhCcCHHHHHHHcCcCHHHHHHHHcCCCCchHHHHHHHHHHhCCCHHHHHh
Confidence            8999999999999999999999999999999999999999999999999999999883

>TIGR03070 couple_hipB transcriptional regulator, y4mF family

Probab=99.64  E-value=1.3e-15  Score=94.64  Aligned_cols=57  Identities=26%  Similarity=0.355  Sum_probs=55.0

Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccc
Q psy6501          32 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRL   88 (174)
Q Consensus        32 ~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~   88 (174)
                      .+|++|+.+|+..||||++||+.+|+|+++|++||+|+..|+.+.+.+||++|||++
T Consensus         2 ~~~~~l~~~r~~~gltq~~lA~~~gvs~~~vs~~e~g~~~~~~~~~~~i~~~lgv~l   58 (58)
T TIGR03070         2 QIGMLVRARRKALGLTQADLADLAGVGLRFIRDVENGKPTVRLDKVLRVLDALGLEL   58 (58)
T ss_pred             hHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHcCCCC
Confidence            489999999999999999999999999999999999999999999999999999874

Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.

>PRK09726 antitoxin HipB; Provisional

Probab=99.62  E-value=3e-15  Score=101.48  Aligned_cols=64  Identities=25%  Similarity=0.418  Sum_probs=60.9

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccC
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAG   93 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~   93 (174)
                      ...+|.+|+.+|+.+|+||++||+.+|||+++|++||+|...|+++.+.+||++|||+++++..
T Consensus        10 ~~~l~~~lk~~R~~~gltq~elA~~~gvs~~tis~~e~g~~~ps~~~l~~ia~~lgv~~~~~~~   73 (88)
T PRK09726         10 PTQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELSMTLCDA   73 (88)
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHcCCCcchhcc
Confidence            4589999999999999999999999999999999999999999999999999999999999653

>PRK06424 transcription factor; Provisional

Probab=99.61  E-value=2.2e-15  Score=110.58  Aligned_cols=64  Identities=33%  Similarity=0.455  Sum_probs=60.4

Q ss_pred             cchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccc
Q psy6501          28 KVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVN   91 (174)
Q Consensus        28 ~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l   91 (174)
                      .++..+|++|+.+|+++||||+|||+.+|+++++|++||+|.+.|+.+.+.+||++||+++.+.
T Consensus        80 ~~~~~~g~~Ir~lRe~~GLSQ~eLA~~iGvs~stIskiE~G~~~Ps~~~l~kLa~~Lgvsl~e~  143 (144)
T PRK06424         80 DIVEDYAELVKNARERLSMSQADLAAKIFERKNVIASIERGDLLPDIKTARKLEKILGITLIEK  143 (144)
T ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCCCC
Confidence            3467899999999999999999999999999999999999999999999999999999998653

>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed

Probab=99.61  E-value=1.3e-15  Score=125.19  Aligned_cols=71  Identities=23%  Similarity=0.262  Sum_probs=66.2

Q ss_pred             cccchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccCCCC
Q psy6501          26 HEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGTNK   96 (174)
Q Consensus        26 ~~~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~~~   96 (174)
                      ++.+...+|++|+.+|+.+||||++||+++|+|+++|++||+|+..|+.+.+.+||++|||+++||++...
T Consensus        22 ~~~~~~~~g~rl~~~R~~~gltq~~lA~~~gvs~~~i~~~E~g~~~ps~~~l~~ia~~l~v~~~~l~~~~~   92 (309)
T PRK08154         22 EAPFLAALGERVRTLRARRGMSRKVLAQASGVSERYLAQLESGQGNVSILLLRRVARALGCSLADLLGDVD   92 (309)
T ss_pred             hHHHHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHhCCCHHHHhCCCC
Confidence            34556789999999999999999999999999999999999999999999999999999999999997654

>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A

Probab=99.59  E-value=3.2e-15  Score=95.41  Aligned_cols=60  Identities=28%  Similarity=0.424  Sum_probs=52.1

Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCcccccc
Q psy6501          32 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRG-IPNQAIIGKMERALGIRLRVN   91 (174)
Q Consensus        32 ~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~-~P~~~~l~~la~~L~v~~~~l   91 (174)
                      .||..|+.+|+..||||.++|+.+|+|+++|++||+|+. .|+.+.+.+||++|+++.+.+
T Consensus         1 ~lg~~lr~~R~~~gls~~~lA~~~g~s~s~v~~iE~G~~~~p~~~~l~~l~~~l~~~~~~~   61 (64)
T PF13560_consen    1 QLGRRLRRLRERAGLSQAQLADRLGVSQSTVSRIERGRRPRPSPDTLQRLARALGVPPDER   61 (64)
T ss_dssp             HHHHHHHHHHHCHTS-HHHHHHHHTS-HHHHHHHHTTSSSS-BHHHHHHHHHHTT--HHHH
T ss_pred             CHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCCHHHHHHHHHHHCcCHHHH
Confidence            489999999999999999999999999999999999999 699999999999999998754

>PRK13890 conjugal transfer protein TrbA; Provisional

Probab=99.58  E-value=7.2e-15  Score=105.11  Aligned_cols=67  Identities=12%  Similarity=0.189  Sum_probs=63.4

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccCCCC
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGTNK   96 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~~~   96 (174)
                      .+.++.+|+.+|+++||||+|||+++|+|+++|++||+|+..|+.+.+.+||++|+|+++||+....
T Consensus         3 ~~i~~~~l~~ll~~~Glsq~eLA~~~Gis~~~is~iE~g~~~ps~~~l~kIa~aL~v~~~~L~~~~~   69 (120)
T PRK13890          3 NYIFFTNVLRLLDERHMTKKELSERSGVSISFLSDLTTGKANPSLKVMEAIADALETPLPLLLESTD   69 (120)
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHCCCHHHHhccCc
Confidence            4678999999999999999999999999999999999999999999999999999999999996543

>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional

Probab=99.57  E-value=8.1e-15  Score=112.14  Aligned_cols=67  Identities=21%  Similarity=0.192  Sum_probs=63.4

Q ss_pred             cchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccCC
Q psy6501          28 KVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGT   94 (174)
Q Consensus        28 ~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~   94 (174)
                      +..+.+|.+||.+|+++||||.+||+++|+|+++|++||+|...|+...+.+||++|+|++++|+..
T Consensus         3 ~~~~~~g~~l~~~R~~~glt~~elA~~~gis~~~is~~E~g~~~p~~~~l~~ia~~l~v~~~~l~~~   69 (185)
T PRK09943          3 DEGLAPGKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSLSEFFSE   69 (185)
T ss_pred             chhhHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHHHccC
Confidence            3456799999999999999999999999999999999999999999999999999999999999953

>TIGR02607 antidote_HigA addiction module antidote protein, HigA family

Probab=99.54  E-value=2.1e-14  Score=94.83  Aligned_cols=62  Identities=16%  Similarity=0.157  Sum_probs=59.2

Q ss_pred             HHHHHHH-HHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccC
Q psy6501          32 DLAKLLM-QGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAG   93 (174)
Q Consensus        32 ~ig~~ik-~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~   93 (174)
                      ..|++|+ .+|+++|+||.+||+.+|+|+++|++||+|.+.|+.+.+.+||++|||+++||+.
T Consensus         4 ~~g~~i~~~~~~~~~~t~~~lA~~~gis~~tis~~~~g~~~~~~~~~~~l~~~l~v~~~~l~~   66 (78)
T TIGR02607         4 HPGEILREEFLEPLGLSIRALAKALGVSRSTLSRIVNGRRGITADMALRLAKALGTSPEFWLN   66 (78)
T ss_pred             CHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHcCCCHHHHHH
Confidence            3588999 8999999999999999999999999999999999999999999999999999984

Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.

>TIGR02612 mob_myst_A mobile mystery protein A

Probab=99.49  E-value=8.6e-14  Score=102.87  Aligned_cols=62  Identities=19%  Similarity=0.128  Sum_probs=57.7

Q ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCC--CCCHHHHHHHHHHhCcccccccCCCC
Q psy6501          35 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRG--IPNQAIIGKMERALGIRLRVNAGTNK   96 (174)
Q Consensus        35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~--~P~~~~l~~la~~L~v~~~~l~~~~~   96 (174)
                      .+|+.+|+.+||||.+||+++|||+++|++||+|..  .|+++.|.+||++|||+++|||.+..
T Consensus        28 ~~Ir~~R~~lGmTq~eLAerlGVS~~tIs~iE~G~~~~~psl~~L~kIA~aLgv~~~~l~~~~~   91 (150)
T TIGR02612        28 GWVRAIRKALGMSGAQLAGRLGVTPQRVEALEKSELSGTVTLKTLRAAAEALDCTFVYAFVPKT   91 (150)
T ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCCCHHHHHHHHHHcCCCHHHHhCCcc
Confidence            589999999999999999999999999999999985  48999999999999999999996443

Members of this protein family are found in mobization-related contexts more often than not, including within a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and on plasmids in Agrobacterium tumefaciens and Coxiella burnetii, always together with mobile mystery protein B, a member of the Fic protein family (pfam02661). This protein is encoded by the upstream member of the gene pair and belongs to a family of helix-turn-helix DNA binding proteins (pfam01381).

>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein

Probab=99.43  E-value=5.2e-13  Score=90.50  Aligned_cols=58  Identities=31%  Similarity=0.387  Sum_probs=54.7

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccc
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLR   89 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~   89 (174)
                      ...++.+|+.+|+++||||  ||+++|||+++|++||+|...|+.+.+.+||++||+++.
T Consensus        30 ~~~~~~~l~~~r~~~glSq--LAe~~GIs~stLs~iE~g~~~Ps~~tL~kI~~aLgi~l~   87 (89)
T TIGR02684        30 PAYIAHALGYIARARGMTQ--LARKTGLSRESLYKALSGKGNPTFDTILKVTKALGLKLT   87 (89)
T ss_pred             HHHHHHHHHHHHHHCChHH--HHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHcCCcee
Confidence            3468999999999999995  999999999999999999999999999999999999875

gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module.

>KOG3398|consensus

Probab=99.41  E-value=6.4e-13  Score=93.35  Aligned_cols=82  Identities=66%  Similarity=0.966  Sum_probs=73.8

Q ss_pred             CCCCCCCCCcccchhhhhhhhhhcccccHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHh
Q psy6501          93 GTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMER  172 (174)
Q Consensus        93 ~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~  172 (174)
                      +.+..+....+..+++++.+...+..++.+++..|.++|..+||||+|||.+++..++.|.+||+|+.+|+..++.++.+
T Consensus        44 g~nkq~~~~~~t~klD~etE~~~~~~v~~~Vg~aIq~aR~~KgmsqkDLA~kInekpqVv~dyEsGrAIpNqqil~kmEr  123 (135)
T KOG3398|consen   44 GLNKQHPSTQSTAKLDRETEELGHDRVPLEVGKAIQQARAQKGMSQKDLAQKINEKPQVIQDYESGRAIPNQQILSKMER  123 (135)
T ss_pred             cccccCCcccchhhccccccccccccccHHHHHHHHHHHHhccccHHHHHHHHccCchhhhhHhccccCchHHHHHHHHH
Confidence            34444455566678888889999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hC
Q psy6501         173 AL  174 (174)
Q Consensus       173 ~l  174 (174)
                      +|
T Consensus       124 aL  125 (135)
T KOG3398|consen  124 AL  125 (135)
T ss_pred             Hh
Confidence            86

>PRK10072 putative transcriptional regulator; Provisional

Probab=99.41  E-value=7.2e-13  Score=90.92  Aligned_cols=56  Identities=20%  Similarity=0.227  Sum_probs=51.9

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccc
Q psy6501          33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLR   89 (174)
Q Consensus        33 ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~   89 (174)
                      -+..|+.+|+..||||.+||+.+|+|.+||++||+|++.|+...+. ++++|++++.
T Consensus        34 ~~~eik~LR~~~glTQ~elA~~lGvS~~TVs~WE~G~r~P~~~~l~-Ll~~L~~~P~   89 (96)
T PRK10072         34 SFTEFEQLRKGTGLKIDDFARVLGVSVAMVKEWESRRVKPSSAELK-LMRLIQANPA   89 (96)
T ss_pred             ChHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH-HHHHHhhCHH
Confidence            3566999999999999999999999999999999999999999965 9999999984

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

Probab=99.35  E-value=3e-12  Score=81.13  Aligned_cols=58  Identities=22%  Similarity=0.226  Sum_probs=46.3

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhCcccccccC
Q psy6501          36 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGR-GIPNQAIIGKMERALGIRLRVNAG   93 (174)
Q Consensus        36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~-~~P~~~~l~~la~~L~v~~~~l~~   93 (174)
                      +|+.+..++|+|+.+||+.+|+|+++|++|-+|. ..|+.+.+.+||.+|||++++|+.
T Consensus         1 ~L~~~m~~~~it~~~La~~~gis~~tl~~~~~~~~~~~~~~~l~~ia~~l~~~~~el~~   59 (63)
T PF13443_consen    1 KLKELMAERGITQKDLARKTGISRSTLSRILNGKPSNPSLDTLEKIAKALNCSPEELFE   59 (63)
T ss_dssp             HHHHHHHHTT--HHHHHHHHT--HHHHHHHHTTT-----HHHHHHHHHHHT--HHHCTE
T ss_pred             CHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcccccccHHHHHHHHHHcCCCHHHHhh
Confidence            6899999999999999999999999999999999 799999999999999999999984

>PRK04140 hypothetical protein; Provisional

Probab=99.33  E-value=3.9e-12  Score=104.43  Aligned_cols=62  Identities=21%  Similarity=0.259  Sum_probs=58.6

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccc
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVN   91 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l   91 (174)
                      .+..|++||.+|+++||||.+||+.+|+|+++|++||+|...|+.+.+.+||++||+++.+.
T Consensus       124 v~i~GerLk~lRe~~GlSq~eLA~~lGVSr~tIskyE~G~~~Ps~e~~~kLa~~Lgv~l~~~  185 (317)
T PRK04140        124 VKIDGDVLREAREELGLSLGELASELGVSRRTISKYENGGMNASIEVAIKLEEILDVPLTKP  185 (317)
T ss_pred             ehhhHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCChHHH
Confidence            46789999999999999999999999999999999999999999999999999999986553

>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins

Probab=99.31  E-value=8.2e-12  Score=74.95  Aligned_cols=56  Identities=29%  Similarity=0.443  Sum_probs=53.3

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccc
Q psy6501          36 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVN   91 (174)
Q Consensus        36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l   91 (174)
                      +|+.+|+..|+|+.++|+.+|+++.+|++|++|...|+...+.+|+++||++++||
T Consensus         1 ~i~~~~~~~~~s~~~la~~~~i~~~~i~~~~~~~~~~~~~~~~~i~~~~~~~~~~~   56 (56)
T smart00530        1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL   56 (56)
T ss_pred             CHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHhCCChhhC
Confidence            47889999999999999999999999999999999999999999999999999875

>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]

Probab=99.30  E-value=1.2e-11  Score=91.84  Aligned_cols=70  Identities=30%  Similarity=0.494  Sum_probs=65.1

Q ss_pred             cccchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccCCC
Q psy6501          26 HEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGTN   95 (174)
Q Consensus        26 ~~~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~~   95 (174)
                      ...+..+++++|+.+|+.+||||+|||.+++++.+.|.+||+|+..|+.....+|.++|+|...+....+
T Consensus        73 ~~elvedY~e~Ir~ARE~~G~SqedLA~ki~ek~svI~~iE~g~~~P~~~~akkLEk~LgIkL~e~~~~~  142 (165)
T COG1813          73 LPELVEDYGERIREAREKRGLSQEDLAAKLKEKVSVIRRIERGEATPNIKVAKKLEKLLGIKLVEKVDEE  142 (165)
T ss_pred             HHHHHHHHHHHHHHHHHHcCCCHHHHHHHhcccHHHHHHHHhcccCccHHHHHHHHHHhCceeeeecccc
Confidence            4456789999999999999999999999999999999999999999999999999999999998887544

>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family

Probab=99.28  E-value=1.1e-11  Score=89.10  Aligned_cols=61  Identities=23%  Similarity=0.253  Sum_probs=56.2

Q ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccccccc
Q psy6501          31 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNA   92 (174)
Q Consensus        31 ~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~   92 (174)
                      +..+.+|+.+|+..|+||.+||+.+|+|+++|++||+|...|+.. +.++++.|+++++||.
T Consensus        64 ~~~~~~i~~~r~~~gltq~~lA~~lg~~~~tis~~e~g~~~p~~~-~~~l~~~l~~~p~~l~  124 (127)
T TIGR03830        64 LLTPPEIRRIRKKLGLSQREAAELLGGGVNAFSRYERGEVRPSKA-LDKLLRLLDKHPELLE  124 (127)
T ss_pred             CcCHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHH-HHHHHHHHHHChHHHH
Confidence            457889999999999999999999999999999999999999865 7889999999999974

This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.

>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins

Probab=99.25  E-value=3.5e-11  Score=72.66  Aligned_cols=58  Identities=28%  Similarity=0.441  Sum_probs=54.7

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccc
Q psy6501          34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVN   91 (174)
Q Consensus        34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l   91 (174)
                      |+.|+..|+..|+|+.++|+.+|+++++|++|++|...|+...+.+|+++|+++++|+
T Consensus         1 ~~~l~~~~~~~~~s~~~~a~~~~~~~~~v~~~~~g~~~~~~~~~~~i~~~~~~~~~~l   58 (58)
T cd00093           1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL   58 (58)
T ss_pred             ChHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCChhhC
Confidence            3578899999999999999999999999999999999999999999999999998875

Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.

>PRK10856 cytoskeletal protein RodZ; Provisional

Probab=99.21  E-value=3.4e-11  Score=99.78  Aligned_cols=65  Identities=22%  Similarity=0.207  Sum_probs=60.1

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCH------HHHHHHHHHhCcccccccCC
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQ------AIIGKMERALGIRLRVNAGT   94 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~------~~l~~la~~L~v~~~~l~~~   94 (174)
                      .+.+|++||.+|+++||||++||+++|+++++|++||+|...|..      .++..+|++|||+.++|+..
T Consensus        12 ~~~~G~~Lr~aRe~~GlSq~~vA~~l~l~~~~I~~iE~g~~~~~~~~tf~RGyir~yA~~lgv~~~~L~~~   82 (331)
T PRK10856         12 ALTTGERLRQAREQLGLTQQAVAERLCLKVSTVRDIEEDKAPADLASTFLRGYIRSYARLVHIPEEELLPG   82 (331)
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHCCCCCCChhHHHHHHHHHHHHHHHCcCHHHHHHh
Confidence            456999999999999999999999999999999999999988887      56899999999999999853

>PHA01976 helix-turn-helix protein

Probab=99.19  E-value=7e-11  Score=75.66  Aligned_cols=52  Identities=25%  Similarity=0.561  Sum_probs=49.9

Q ss_pred             HHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         123 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       123 ~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ++.+|+.+|+.+|+||.++|+++|+++++|++||+|...|+.+.+.+||++|
T Consensus         3 ~~~rl~~~R~~~glt~~~lA~~~gvs~~~v~~~e~g~~~p~~~~l~~ia~~l   54 (67)
T PHA01976          3 FAIQLIKARNARAWSAPELSRRAGVRHSLIYDFEADKRLPNLKTLLRLADAL   54 (67)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence            5789999999999999999999999999999999999999999999999976

>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A

Probab=99.15  E-value=1.5e-10  Score=76.99  Aligned_cols=61  Identities=21%  Similarity=0.273  Sum_probs=51.1

Q ss_pred             chHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhCcccc
Q psy6501          29 VPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGR-GIPNQAIIGKMERALGIRLR   89 (174)
Q Consensus        29 ~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~-~~P~~~~l~~la~~L~v~~~   89 (174)
                      +...+...|+.+|+++||||.|+|+.+|++++.||++|+|+ ..++++.|.+++..||..++
T Consensus        15 ~k~~l~~~i~~~~~~~~ltQ~e~A~~lgisq~~vS~l~~g~~~~~sl~~L~~~l~aLG~~v~   76 (80)
T PF13744_consen   15 AKAQLMAAIRELREERGLTQAELAERLGISQPRVSRLENGKIDDFSLDTLLRYLEALGGRVE   76 (80)
T ss_dssp             HHHHHHHHHHHHHHCCT--HHHHHHHHTS-HHHHHHHHTT-GCC--HHHHHHHHHHTTEEEE
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHHCCChhHHHHHHcCcccCCCHHHHHHHHHHcCCeEE
Confidence            45678888999999999999999999999999999999987 78999999999999998875

>PRK13355 bifunctional HTH-domain containing protein/aminotransferase; Provisional

Probab=99.14  E-value=1.1e-10  Score=102.00  Aligned_cols=66  Identities=21%  Similarity=0.309  Sum_probs=61.3

Q ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHh-----CCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccCCCC
Q psy6501          31 LDLAKLLMQGRQAKGWSQKDLATKI-----NEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGTNK   96 (174)
Q Consensus        31 ~~ig~~ik~~R~~~gltq~eLA~~i-----gvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~~~   96 (174)
                      +.|++||+.+|+++|+||.+||+.+     +|++++|++||+|+..|+.+.+.+||++|+|+++||++...
T Consensus         2 ~~~~~rL~~~r~~~g~tq~~la~~~~~~g~~vs~~~is~~e~g~~~p~~~~l~~la~~l~v~~~~l~~~~~   72 (517)
T PRK13355          2 TTFAERLKQAMKARGLKQEDLVHAAEARGVKLGKSHISQYVSGKTGPRRDVLPFLAAILGVSEDWLLGGES   72 (517)
T ss_pred             chHHHHHHHHHHHCCCCHHHHHHHHHhccCCcCHHHHHHHHCCCCCCCHHHHHHHHHHhCcCHHHHccCCc
Confidence            4689999999999999999999986     69999999999999999999999999999999999985443

>TIGR03070 couple_hipB transcriptional regulator, y4mF family

Probab=99.14  E-value=2.3e-10  Score=70.64  Aligned_cols=53  Identities=25%  Similarity=0.295  Sum_probs=50.2

Q ss_pred             HHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         122 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       122 ~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      .++..|+..|+..|++|.++|+.+|+++++|++||+|+..|+...+.+|+++|
T Consensus         2 ~~~~~l~~~r~~~gltq~~lA~~~gvs~~~vs~~e~g~~~~~~~~~~~i~~~l   54 (58)
T TIGR03070         2 QIGMLVRARRKALGLTQADLADLAGVGLRFIRDVENGKPTVRLDKVLRVLDAL   54 (58)
T ss_pred             hHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHc
Confidence            35788999999999999999999999999999999999999999999999886

Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.

>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould)

Probab=99.12  E-value=1.7e-10  Score=70.96  Aligned_cols=48  Identities=31%  Similarity=0.477  Sum_probs=43.9

Q ss_pred             HHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         127 LMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       127 i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      |++.|++.|+||.++|+.+|+++++|++||+|...|+.+.+.+|+++|
T Consensus         1 ik~~r~~~gls~~~la~~~gis~~~i~~~~~g~~~~~~~~~~~ia~~l   48 (55)
T PF01381_consen    1 IKELRKEKGLSQKELAEKLGISRSTISRIENGKRNPSLDTLKKIAKAL   48 (55)
T ss_dssp             HHHHHHHTTS-HHHHHHHHTS-HHHHHHHHTTSSTSBHHHHHHHHHHH
T ss_pred             CHHHHHHcCCCHHHHHHHhCCCcchhHHHhcCCCCCCHHHHHHHHHHH
Confidence            578899999999999999999999999999999999999999999875

; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....

>PRK08359 transcription factor; Validated

Probab=99.12  E-value=1.7e-10  Score=87.22  Aligned_cols=57  Identities=19%  Similarity=0.215  Sum_probs=54.7

Q ss_pred             cccHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         118 KVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       118 ~~~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      .+..+++.+|+++|+.+||||++||+.+|++.++|+.||+|...|+.+.+.+|+++|
T Consensus        81 elv~dy~~rIkeaRe~kglSQeeLA~~lgvs~stI~~iE~G~~~Ps~~~l~kLak~l  137 (176)
T PRK08359         81 DIVEDYAERVYEAIQKSGLSYEELSHEVGLSVNDLRRIAHGEYEPTIKEAKKLERYF  137 (176)
T ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCcCCCHHHHHHHHHHh
Confidence            566789999999999999999999999999999999999999999999999999987

>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]

Probab=99.09  E-value=2.6e-10  Score=84.66  Aligned_cols=58  Identities=31%  Similarity=0.519  Sum_probs=54.9

Q ss_pred             ccccHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         117 EKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       117 ~~~~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ..+..++.++|+.+|+++||||++||+++++..+.|.+||+|+..|+...+.+|.++|
T Consensus        74 ~elvedY~e~Ir~ARE~~G~SqedLA~ki~ek~svI~~iE~g~~~P~~~~akkLEk~L  131 (165)
T COG1813          74 PELVEDYGERIREAREKRGLSQEDLAAKLKEKVSVIRRIERGEATPNIKVAKKLEKLL  131 (165)
T ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHhcccHHHHHHHHhcccCccHHHHHHHHHHh
Confidence            4556889999999999999999999999999999999999999999999999999986

>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B

Probab=99.07  E-value=3.6e-10  Score=71.67  Aligned_cols=51  Identities=31%  Similarity=0.468  Sum_probs=43.8

Q ss_pred             HHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         124 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       124 ~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      +++|++.|+.+|+||.++|+.+|+++++++.||+|...|+...+.+||++|
T Consensus         1 G~~lk~~r~~~~lt~~~~a~~~~i~~~~i~~~e~g~~~~~~~~l~~i~~~~   51 (64)
T PF12844_consen    1 GERLKELREEKGLTQKDLAEKLGISRSTISKIENGKRKPSVSTLKKIAEAL   51 (64)
T ss_dssp             HHHHHHHHHHCT--HHHHHHHHTS-HHHHHHHHTTSS--BHHHHHHHHHHH
T ss_pred             CHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCcCCCHHHHHHHHHHh
Confidence            468999999999999999999999999999999999999999999999875

>PRK06424 transcription factor; Provisional

Probab=99.06  E-value=5.3e-10  Score=82.15  Aligned_cols=56  Identities=32%  Similarity=0.452  Sum_probs=53.3

Q ss_pred             ccHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         119 VPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       119 ~~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      +..+++.+|+.+|+++||||++||+.+|++.++|+.||+|...|+.+++.+|+++|
T Consensus        81 ~~~~~g~~Ir~lRe~~GLSQ~eLA~~iGvs~stIskiE~G~~~Ps~~~l~kLa~~L  136 (144)
T PRK06424         81 IVEDYAELVKNARERLSMSQADLAAKIFERKNVIASIERGDLLPDIKTARKLEKIL  136 (144)
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHh
Confidence            35778999999999999999999999999999999999999999999999999987

>TIGR00270 conserved hypothetical protein TIGR00270

Probab=99.05  E-value=5.4e-10  Score=83.08  Aligned_cols=57  Identities=30%  Similarity=0.563  Sum_probs=54.0

Q ss_pred             cccHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         118 KVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       118 ~~~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      .+..+++.+|+.+|+++||||++||+++|++.++|++||+|...|+.+.+.+|+++|
T Consensus        65 ~l~~~~g~~Ir~~Re~~glSqeeLA~~lgvs~s~IsriE~G~~~Ps~~~l~kLa~~L  121 (154)
T TIGR00270        65 ELVEDYGIIIRREREKRGWSQEQLAKKIQEKESLIKKIENAEIEPEPKVVEKLEKLL  121 (154)
T ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHh
Confidence            455678999999999999999999999999999999999999999999999999987

>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A

Probab=99.05  E-value=7.1e-10  Score=70.48  Aligned_cols=52  Identities=31%  Similarity=0.454  Sum_probs=46.7

Q ss_pred             HHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCC-CCCHHHHHHHHhhC
Q psy6501         123 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRG-IPNQAIIGKMERAL  174 (174)
Q Consensus       123 ~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~-~P~~~~l~~i~~~l  174 (174)
                      ++..|+..|+..||||.++|+.+|+++++|++||+|.. .|+.+.+.+|+++|
T Consensus         2 lg~~lr~~R~~~gls~~~lA~~~g~s~s~v~~iE~G~~~~p~~~~l~~l~~~l   54 (64)
T PF13560_consen    2 LGRRLRRLRERAGLSQAQLADRLGVSQSTVSRIERGRRPRPSPDTLQRLARAL   54 (64)
T ss_dssp             HHHHHHHHHHCHTS-HHHHHHHHTS-HHHHHHHHTTSSSS-BHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCCHHHHHHHHHHH
Confidence            67899999999999999999999999999999999999 59999999999986

>PHA00542 putative Cro-like protein

Probab=99.05  E-value=1e-09  Score=73.34  Aligned_cols=51  Identities=20%  Similarity=0.346  Sum_probs=46.8

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHh
Q psy6501          34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGR-GIPNQAIIGKMERAL   84 (174)
Q Consensus        34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~-~~P~~~~l~~la~~L   84 (174)
                      ..++...++..|+||.+||+.+|||+++|++||+|. ..|+.+.+.+||+++
T Consensus        20 ~~~l~~~l~~~glTq~elA~~lgIs~~tIsr~e~g~~~~p~~~~l~ki~~~~   71 (82)
T PHA00542         20 PDELVCALIRAGWSQEQIADATDVSQPTICRIYSGRHKDPRYSVVEKLRHLV   71 (82)
T ss_pred             HHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHHHHHH
Confidence            446778889999999999999999999999999999 589999999999985

>COG1476 Predicted transcriptional regulators [Transcription]

Probab=99.03  E-value=8.7e-10  Score=70.40  Aligned_cols=50  Identities=24%  Similarity=0.292  Sum_probs=48.1

Q ss_pred             HHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         125 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       125 ~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ..++..|...|+||.++|+.+|+++.+|..+|+|+-.|+..++.+||++|
T Consensus         4 nk~k~~R~~~~ltQ~elA~~vgVsRQTi~~iEkgky~Psl~La~kia~~f   53 (68)
T COG1476           4 NKLKELRAELGLTQEELAKLVGVSRQTIIAIEKGKYNPSLELALKIARVF   53 (68)
T ss_pred             hHHHHHHHHhCcCHHHHHHHcCcCHHHHHHHHcCCCCchHHHHHHHHHHh
Confidence            37899999999999999999999999999999999999999999999987

>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]

Probab=99.02  E-value=7.8e-10  Score=81.67  Aligned_cols=53  Identities=25%  Similarity=0.317  Sum_probs=50.2

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCc
Q psy6501          34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGI   86 (174)
Q Consensus        34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v   86 (174)
                      .+-||+.|++.|+||++||++.|||+++|.++|.|.-.|++.++.+|-++|.-
T Consensus         7 pedlrk~Rk~LGitQ~dLA~~aGVSQ~~IArlE~G~vdPrlSt~k~Il~aL~e   59 (187)
T COG3620           7 PEDLRKRRKELGITQKDLARRAGVSQPYIARLEAGKVDPRLSTVKRILEALEE   59 (187)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHcCccHHHHHHHhcCCCCccHHHHHHHHHHHHH
Confidence            57799999999999999999999999999999999999999999999998753

>COG2944 Predicted transcriptional regulator [Transcription]

Probab=98.96  E-value=2e-09  Score=74.25  Aligned_cols=45  Identities=24%  Similarity=0.273  Sum_probs=41.9

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH
Q psy6501          34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIG   78 (174)
Q Consensus        34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~   78 (174)
                      +..|+.+|+..|+||.+||..+|+|.+||++||.|+..|+..-+.
T Consensus        46 ~~eIk~iRe~~~lSQ~vFA~~L~vs~~Tv~~WEqGr~kPsg~Alk   90 (104)
T COG2944          46 PTEIKAIREKLGLSQPVFARYLGVSVSTVRKWEQGRKKPSGAALK   90 (104)
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHcCCcCCCCHHHH
Confidence            778999999999999999999999999999999999999976554

>smart00352 POU Found in Pit-Oct-Unc transcription factors

Probab=98.95  E-value=5.4e-09  Score=67.91  Aligned_cols=42  Identities=19%  Similarity=0.181  Sum_probs=38.4

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHhC------CCHHHHHHHHcCCCC
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATKIN------EKPQIVNDYEGGRGI   71 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~ig------vs~~~is~~E~G~~~   71 (174)
                      +..||++++..|++.|+||.|||+++|      +|+++||+||+|.-.
T Consensus         9 le~~~~~lk~~R~~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es~~ls   56 (75)
T smart00352        9 LEAFAKTFKQRRIKLGFTQADVGLALGALYGPDFSQTTICRFEALQLS   56 (75)
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHhcccccCcCCHHHHHHHHhcCcc
Confidence            347999999999999999999999999      499999999998753

>PRK09726 antitoxin HipB; Provisional

Probab=98.94  E-value=4.3e-09  Score=71.20  Aligned_cols=55  Identities=29%  Similarity=0.459  Sum_probs=51.8

Q ss_pred             cHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         120 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       120 ~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ...++.+|+..|...|+||.++|+.+|+++++|+.||+|...|+...+.+|+++|
T Consensus        10 ~~~l~~~lk~~R~~~gltq~elA~~~gvs~~tis~~e~g~~~ps~~~l~~ia~~l   64 (88)
T PRK09726         10 PTQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSL   64 (88)
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHc
Confidence            3467889999999999999999999999999999999999999999999999886

>PF07022 Phage_CI_repr: Bacteriophage CI repressor helix-turn-helix domain; InterPro: IPR010744 This family consists of several phage CI repressor proteins and related bacterial sequences

Probab=98.91  E-value=7.6e-10  Score=70.97  Aligned_cols=59  Identities=17%  Similarity=0.260  Sum_probs=44.4

Q ss_pred             HHHHHHHHcCCCH-HHHHHHhCCCHHHHH-HHHcCCCCCCHHHHHHHHHHhCcccccccCCC
Q psy6501          36 LLMQGRQAKGWSQ-KDLATKINEKPQIVN-DYEGGRGIPNQAIIGKMERALGIRLRVNAGTN   95 (174)
Q Consensus        36 ~ik~~R~~~gltq-~eLA~~igvs~~~is-~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~~   95 (174)
                      +|+++++..|++. .|||+.+|||+++|+ .|......| .+.+.+||..+||+++||+...
T Consensus         2 ~i~rl~~~~g~~~~~~lA~~lgis~st~s~~~~~r~~~P-~~~l~~ia~~~gvsl~WLltG~   62 (66)
T PF07022_consen    2 VIERLKEALGVKSDKELAERLGISKSTLSNNWKKRGSIP-AEWLIKIALETGVSLDWLLTGK   62 (66)
T ss_dssp             HHHHHHHHHT-SSCHHHHCCTT--HHHHH-HHHHSSS---HHHHHHHHHHH---HHHHHC-S
T ss_pred             HHHHHHHHhCCCCHHHHHHHhCcCHHHhhHHHHhCCCCC-HHHHHHHHHHHCcCHHHHHhCC
Confidence            6788888888855 699999999999999 898877777 9999999999999999998543

The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic [].; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2FJR_B.

>PRK09706 transcriptional repressor DicA; Reviewed

Probab=98.90  E-value=4.7e-09  Score=76.40  Aligned_cols=53  Identities=19%  Similarity=0.238  Sum_probs=50.5

Q ss_pred             HHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         122 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       122 ~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      .++.+|+..|...|+||.++|+.+|+++++|+.||+|...|+...+.+||++|
T Consensus         5 ~~g~rlk~~R~~~gltq~~lA~~~gvs~~~is~~E~g~~~p~~~~l~~la~~l   57 (135)
T PRK09706          5 TLGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKAL   57 (135)
T ss_pred             hHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence            46889999999999999999999999999999999999999999999999875

>PRK02866 cyanate hydratase; Validated

Probab=98.84  E-value=2.2e-08  Score=73.46  Aligned_cols=62  Identities=19%  Similarity=0.181  Sum_probs=57.9

Q ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccccccc
Q psy6501          31 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNA   92 (174)
Q Consensus        31 ~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~   92 (174)
                      ..+.+.|..+|.++|+|++++|+++|+|+.++..++.|.+.++.+...+||++|+++.+...
T Consensus         4 ~~~~e~Ll~AK~~kGLTw~~IA~~iG~S~v~vaaa~lGQ~~ls~e~A~kla~~LgL~~~~~~   65 (147)
T PRK02866          4 EELTEKILAAKKEKGLTWADIAEAIGLSEVWVTAALLGQMTLPAEEAEKVAELLGLDEDAVA   65 (147)
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHhCCCCCCHHHHHHHHHHhCCCHHHHH
Confidence            35788999999999999999999999999999999999999999999999999999977543

>TIGR00673 cynS cyanate hydratase

Probab=98.79  E-value=3.9e-08  Score=72.31  Aligned_cols=60  Identities=17%  Similarity=0.147  Sum_probs=57.4

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccccccc
Q psy6501          33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNA   92 (174)
Q Consensus        33 ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~   92 (174)
                      +.+.|..+|+++|||++++|+.+|+|+.++..++.|.+.++.+...+||++|+++.+.++
T Consensus         9 ~t~~Ll~AK~~KGLTwe~IAe~iG~sevwvaaa~lGQ~~ls~e~A~kla~lLgL~~e~~~   68 (150)
T TIGR00673         9 LADALLESKKKKGLTFADIADGLGLAEVFVAAALYGQAAAPADEARLVGAKLDLDEDSIL   68 (150)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHhCCCCCCHHHHHHHHHHhCcCHHHHH
Confidence            788999999999999999999999999999999999999999999999999999987655

Alternate names include cyanate lyase, cyanase and cyanate hydrolase.

>TIGR02607 antidote_HigA addiction module antidote protein, HigA family

Probab=98.78  E-value=2.4e-08  Score=65.56  Aligned_cols=52  Identities=17%  Similarity=0.187  Sum_probs=48.6

Q ss_pred             HHHHHH-HHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         123 LAKLLM-QGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       123 ~~~~i~-~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      .+++|+ ..|+..|+++.++|+++|+++++|+.||+|...|+...+.+|+++|
T Consensus         5 ~g~~i~~~~~~~~~~t~~~lA~~~gis~~tis~~~~g~~~~~~~~~~~l~~~l   57 (78)
T TIGR02607         5 PGEILREEFLEPLGLSIRALAKALGVSRSTLSRIVNGRRGITADMALRLAKAL   57 (78)
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHc
Confidence            456788 7899999999999999999999999999999999999999999986

Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.

>PRK13890 conjugal transfer protein TrbA; Provisional

Probab=98.77  E-value=2.5e-08  Score=71.26  Aligned_cols=52  Identities=13%  Similarity=0.272  Sum_probs=49.2

Q ss_pred             HHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         123 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       123 ~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      +...|+..+..+|+||+++|+++|+++++|++||+|+..|+...+.+||++|
T Consensus         6 ~~~~l~~ll~~~Glsq~eLA~~~Gis~~~is~iE~g~~~ps~~~l~kIa~aL   57 (120)
T PRK13890          6 FFTNVLRLLDERHMTKKELSERSGVSISFLSDLTTGKANPSLKVMEAIADAL   57 (120)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence            5678889999999999999999999999999999999999999999999986

>PRK10072 putative transcriptional regulator; Provisional

Probab=98.75  E-value=2.3e-08  Score=68.60  Aligned_cols=49  Identities=22%  Similarity=0.319  Sum_probs=43.9

Q ss_pred             HHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         125 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       125 ~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ..|+..|+..|+||.++|+.+|++.++|++||+|++.|+...+. ++++|
T Consensus        36 ~eik~LR~~~glTQ~elA~~lGvS~~TVs~WE~G~r~P~~~~l~-Ll~~L   84 (96)
T PRK10072         36 TEFEQLRKGTGLKIDDFARVLGVSVAMVKEWESRRVKPSSAELK-LMRLI   84 (96)
T ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH-HHHHH
Confidence            45888999999999999999999999999999999999998876 55553

>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional

Probab=98.75  E-value=2.9e-08  Score=75.87  Aligned_cols=54  Identities=22%  Similarity=0.219  Sum_probs=51.4

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         121 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       121 ~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ..++.+|+..|+.+|+||.++|+.+|+++++|++||+|...|+...+.+|+++|
T Consensus         6 ~~~g~~l~~~R~~~glt~~elA~~~gis~~~is~~E~g~~~p~~~~l~~ia~~l   59 (185)
T PRK09943          6 LAPGKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVY   59 (185)
T ss_pred             hHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence            447889999999999999999999999999999999999999999999999986

>COG1396 HipB Predicted transcriptional regulators [Transcription]

Probab=98.73  E-value=6.4e-08  Score=63.96  Aligned_cols=61  Identities=26%  Similarity=0.444  Sum_probs=58.0

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCcccccccC
Q psy6501          33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRG-IPNQAIIGKMERALGIRLRVNAG   93 (174)
Q Consensus        33 ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~-~P~~~~l~~la~~L~v~~~~l~~   93 (174)
                      +|.+++.+|+..|+||+++|..+|++..+++.||+|.. .|+...+..++..|+++..+++.
T Consensus         2 ~~~~~~~~r~~~~~s~~~~a~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~   63 (120)
T COG1396           2 IGERLKELRKKKGLSQEELAERLGVSRSTISRIERGRSESPSLELLARLAAALGVSLDELLE   63 (120)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCCHHHHHHHHHHHCCCHHHhcC
Confidence            68999999999999999999999999999999999999 99999999999999999887663

>COG1709 Predicted transcriptional regulator [Transcription]

Probab=98.70  E-value=1.5e-08  Score=78.18  Aligned_cols=55  Identities=33%  Similarity=0.471  Sum_probs=50.9

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCC-CCHHHHHHHHHHh
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGI-PNQAIIGKMERAL   84 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~-P~~~~l~~la~~L   84 (174)
                      ....|+.||+-|+..+.||.|||+.+|+|++.||+||.|++. |....+.++.++|
T Consensus        25 S~~pge~lrKWR~~F~vSQ~elA~~l~vSpSVISDYE~GRRk~Pg~~~vkk~V~AL   80 (241)
T COG1709          25 SEDPGETLRKWREIFNVSQTELARELGVSPSVISDYESGRRKSPGIAFVKKFVEAL   80 (241)
T ss_pred             cCChhHHHHHHHHHhCccHHHHHHHhCCCcceeehhhccCccCccHHHHHHHHHHH
Confidence            356899999999999999999999999999999999999988 9999999888775

>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein

Probab=98.69  E-value=5.9e-08  Score=65.77  Aligned_cols=53  Identities=30%  Similarity=0.324  Sum_probs=48.7

Q ss_pred             cHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         120 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       120 ~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      +..+...|+..|+.+||||  +|+.+|++++++++||+|...|+.+.+.+||++|
T Consensus        30 ~~~~~~~l~~~r~~~glSq--LAe~~GIs~stLs~iE~g~~~Ps~~tL~kI~~aL   82 (89)
T TIGR02684        30 PAYIAHALGYIARARGMTQ--LARKTGLSRESLYKALSGKGNPTFDTILKVTKAL   82 (89)
T ss_pred             HHHHHHHHHHHHHHCChHH--HHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHc
Confidence            3446778999999999995  9999999999999999999999999999999987

gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module.

>COG3655 Predicted transcriptional regulator [Transcription]

Probab=98.67  E-value=4.5e-08  Score=63.28  Aligned_cols=62  Identities=18%  Similarity=0.078  Sum_probs=57.1

Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhCcccccccC
Q psy6501          32 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGR-GIPNQAIIGKMERALGIRLRVNAG   93 (174)
Q Consensus        32 ~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~-~~P~~~~l~~la~~L~v~~~~l~~   93 (174)
                      .+.-++..+...++++..|||+.+|+|.+++|.+.+|+ ...+.++|.+||++|+|.+.+++.
T Consensus         2 ~i~~~l~~~l~~r~~~~~eLa~~igis~~~ls~l~~gk~k~I~~~tL~~iC~~LeCqpgDile   64 (73)
T COG3655           2 PIAVRLDVMLADRKISLKELAEAIGISEANLSKLKTGKVKAIRLSTLEKICKALECQPGDILE   64 (73)
T ss_pred             cchHhHHHHHHHHhhhHHHHHHHHcccHHHHHHHHcCCcceeeHHHHHHHHHHcCCChhheeE
Confidence            35668889999999999999999999999999999998 668999999999999999999983

>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed

Probab=98.67  E-value=6.8e-08  Score=79.56  Aligned_cols=56  Identities=23%  Similarity=0.294  Sum_probs=52.9

Q ss_pred             ccHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         119 VPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       119 ~~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      +...++.+|+..|+.+|+||+++|+++|+++++|++||+|+..|+...+.+|+++|
T Consensus        25 ~~~~~g~rl~~~R~~~gltq~~lA~~~gvs~~~i~~~E~g~~~ps~~~l~~ia~~l   80 (309)
T PRK08154         25 FLAALGERVRTLRARRGMSRKVLAQASGVSERYLAQLESGQGNVSILLLRRVARAL   80 (309)
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHh
Confidence            34668999999999999999999999999999999999999999999999999986

>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]

Probab=98.62  E-value=1.1e-07  Score=65.48  Aligned_cols=59  Identities=14%  Similarity=0.219  Sum_probs=52.3

Q ss_pred             HHHHHH-HHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccccccc
Q psy6501          34 AKLLMQ-GRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNA   92 (174)
Q Consensus        34 g~~ik~-~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~   92 (174)
                      |+-|++ +-+-.|+||.+||+.+||++.+|+.+-||++..+.+...+|+++||.++++.+
T Consensus        11 GEiL~eeflep~glt~~~lA~~lgV~r~~is~ling~~~iT~dmAlrL~k~fGtspefWl   70 (104)
T COG3093          11 GEILREEFLEPLGLTQTELAEALGVTRNTISELINGRRAITADMALRLAKVFGTSPEFWL   70 (104)
T ss_pred             hHHHHHHHhccccCCHHHHHHHhCCCHHHHHHHHcCCcCCCHHHHHHHHHHhCCCHHHHH
Confidence            444443 34556999999999999999999999999999999999999999999999776

>TIGR02612 mob_myst_A mobile mystery protein A

Probab=98.58  E-value=2e-07  Score=69.05  Aligned_cols=51  Identities=24%  Similarity=0.194  Sum_probs=47.4

Q ss_pred             HHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCC--CCHHHHHHHHhhC
Q psy6501         124 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGI--PNQAIIGKMERAL  174 (174)
Q Consensus       124 ~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~--P~~~~l~~i~~~l  174 (174)
                      ...|+..|...||||.++|+++|+++++|+.||+|...  |+...+.+|+++|
T Consensus        27 ~~~Ir~~R~~lGmTq~eLAerlGVS~~tIs~iE~G~~~~~psl~~L~kIA~aL   79 (150)
T TIGR02612        27 EGWVRAIRKALGMSGAQLAGRLGVTPQRVEALEKSELSGTVTLKTLRAAAEAL   79 (150)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCCCHHHHHHHHHHc
Confidence            36899999999999999999999999999999999864  8999999999986

Members of this protein family are found in mobization-related contexts more often than not, including within a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and on plasmids in Agrobacterium tumefaciens and Coxiella burnetii, always together with mobile mystery protein B, a member of the Fic protein family (pfam02661). This protein is encoded by the upstream member of the gene pair and belongs to a family of helix-turn-helix DNA binding proteins (pfam01381).

>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A

Probab=98.57  E-value=1.4e-07  Score=59.70  Aligned_cols=55  Identities=27%  Similarity=0.404  Sum_probs=41.5

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCC--CCCCH----HHHHHHHHHhCccccc
Q psy6501          36 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGR--GIPNQ----AIIGKMERALGIRLRV   90 (174)
Q Consensus        36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~--~~P~~----~~l~~la~~L~v~~~~   90 (174)
                      +||..|+++|+|++|+|..++|+.++|..+|+|.  ..|+.    ..+...|++||++.+.
T Consensus         1 ~Lr~~R~~~glsl~~va~~t~I~~~~l~aiE~~~~~~lp~~~y~rg~lr~Ya~~Lgld~~~   61 (62)
T PF13413_consen    1 RLREAREAKGLSLEDVAEETKISVSYLEAIENGDFDSLPSPVYARGYLRKYARFLGLDPDE   61 (62)
T ss_dssp             -HHHHHHCTT--HHHHHHHCS--HHHHHHHHCT-GCCSSSHHHHHHHHHHHHHHTT--HHH
T ss_pred             ChHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCcChhhCCcHHHHHHHHHHHHHHhCcCccc
Confidence            4899999999999999999999999999999997  66765    4567899999998753

>PRK04140 hypothetical protein; Provisional

Probab=98.55  E-value=1.9e-07  Score=76.96  Aligned_cols=54  Identities=22%  Similarity=0.287  Sum_probs=51.0

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         121 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       121 ~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      .-.+..|+..|+.+||||.++|+.+|++++++++||+|...|+.+.+.+|+++|
T Consensus       125 ~i~GerLk~lRe~~GlSq~eLA~~lGVSr~tIskyE~G~~~Ps~e~~~kLa~~L  178 (317)
T PRK04140        125 KIDGDVLREAREELGLSLGELASELGVSRRTISKYENGGMNASIEVAIKLEEIL  178 (317)
T ss_pred             hhhHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence            335789999999999999999999999999999999999999999999999986

>COG1395 Predicted transcriptional regulator [Transcription]

Probab=98.52  E-value=2.4e-07  Score=75.39  Aligned_cols=56  Identities=27%  Similarity=0.308  Sum_probs=54.0

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccc
Q psy6501          33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRL   88 (174)
Q Consensus        33 ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~   88 (174)
                      =|+.||+.|+++|+|..+||..+|||+.+|++||+|...|+++...+|-+.||.+.
T Consensus       126 dge~Lre~Ree~glSlG~lA~~lgVSRktV~~YE~G~~~~sleva~kLeei~g~~i  181 (313)
T COG1395         126 DGEKLREKREEMGLSLGDLATMLGVSRKTVYKYEKGLSDASLEVALKLEEIFGEDI  181 (313)
T ss_pred             chHHHHHHHHHcCcCHHHHHHHhCccHHHHHHhccCCCCccHHHHHHHHHHhcchh
Confidence            38999999999999999999999999999999999999999999999999999874

>PHA00542 putative Cro-like protein

Probab=98.48  E-value=5.5e-07  Score=60.10  Aligned_cols=49  Identities=20%  Similarity=0.354  Sum_probs=44.0

Q ss_pred             HHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCC-CCCCHHHHHHHHhhC
Q psy6501         126 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGR-GIPNQAIIGKMERAL  174 (174)
Q Consensus       126 ~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~-~~P~~~~l~~i~~~l  174 (174)
                      .+...+...|+|+.++|+.+|+++++|++||+|. ..|+.+.+.+|++++
T Consensus        22 ~l~~~l~~~glTq~elA~~lgIs~~tIsr~e~g~~~~p~~~~l~ki~~~~   71 (82)
T PHA00542         22 ELVCALIRAGWSQEQIADATDVSQPTICRIYSGRHKDPRYSVVEKLRHLV   71 (82)
T ss_pred             HHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHHHHHH
Confidence            4456678899999999999999999999999999 589999999999874

>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins

Probab=98.41  E-value=1.3e-06  Score=51.70  Aligned_cols=48  Identities=29%  Similarity=0.474  Sum_probs=44.6

Q ss_pred             HHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         127 LMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       127 i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      |+..+...++|+.++|+.+|+++.+++.|++|...|+...+.+|+++|
T Consensus         2 i~~~~~~~~~s~~~la~~~~i~~~~i~~~~~~~~~~~~~~~~~i~~~~   49 (56)
T smart00530        2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKAL   49 (56)
T ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHh
Confidence            456788899999999999999999999999999999999999999876

>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family

Probab=98.39  E-value=1.1e-06  Score=62.95  Aligned_cols=50  Identities=24%  Similarity=0.311  Sum_probs=43.1

Q ss_pred             HHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhh
Q psy6501         123 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERA  173 (174)
Q Consensus       123 ~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~  173 (174)
                      ....|+..|...|+||.++|+.+|+++++|++||+|...|+..+ ..+.++
T Consensus        66 ~~~~i~~~r~~~gltq~~lA~~lg~~~~tis~~e~g~~~p~~~~-~~l~~~  115 (127)
T TIGR03830        66 TPPEIRRIRKKLGLSQREAAELLGGGVNAFSRYERGEVRPSKAL-DKLLRL  115 (127)
T ss_pred             CHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHH-HHHHHH
Confidence            34678999999999999999999999999999999999998764 445444

This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.

>COG1709 Predicted transcriptional regulator [Transcription]

Probab=98.35  E-value=4.5e-07  Score=70.14  Aligned_cols=56  Identities=32%  Similarity=0.474  Sum_probs=50.8

Q ss_pred             ccHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCC-CCHHHHHHHHhhC
Q psy6501         119 VPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGI-PNQAIIGKMERAL  174 (174)
Q Consensus       119 ~~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~-P~~~~l~~i~~~l  174 (174)
                      .+.+.++.|+.||+..+.||.++|..+|+++|.|++||+|++. |...++.++-.+|
T Consensus        24 lS~~pge~lrKWR~~F~vSQ~elA~~l~vSpSVISDYE~GRRk~Pg~~~vkk~V~AL   80 (241)
T COG1709          24 LSEDPGETLRKWREIFNVSQTELARELGVSPSVISDYESGRRKSPGIAFVKKFVEAL   80 (241)
T ss_pred             ecCChhHHHHHHHHHhCccHHHHHHHhCCCcceeehhhccCccCccHHHHHHHHHHH
Confidence            3466789999999999999999999999999999999999988 9999999886654

>PF08667 BetR: BetR domain; InterPro: IPR013975 CheY-like phosphoacceptor (or receiver [REC]) domain is a common module in a variety of response regulators of the bacterial signal transduction systems

Probab=98.34  E-value=2e-06  Score=63.19  Aligned_cols=64  Identities=16%  Similarity=0.118  Sum_probs=60.0

Q ss_pred             hHHHHHHHHHHHHHcCCCH----HHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccC
Q psy6501          30 PLDLAKLLMQGRQAKGWSQ----KDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAG   93 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq----~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~   93 (174)
                      .+.++++|+.+..++|+.+    .+||+-+|+|.+++++--+|....++..+.+||+.||+++++|++
T Consensus         3 ~~~~~erV~~Ll~~~Gi~kr~~~s~LA~iL~Is~ssa~RKL~G~~~ftl~EI~~Ia~~fgvS~d~l~g   70 (147)
T PF08667_consen    3 DQAIAERVRELLDRKGIPKRKHASELADILGISYSSAYRKLNGKSPFTLEEIKKIAKHFGVSPDELFG   70 (147)
T ss_pred             hHHHHHHHHHHHHHcCCcchhhHHHHHHHHCCCHHHHHHHhcCCCCCCHHHHHHHHHHhCcCHHHHHh
Confidence            3578999999999999977    559999999999999999999999999999999999999999995

BetR is one of the many response regulators and is encoded mainly in Burkholderia spp. It is a N-terminal helix-turn-helix domain (HTH) and has been shown to be related to the XRE-type HTH domain (IPR001387 from INTERPRO), it has been suggested that BetR would have dimerization, protein-protein interaction, and activation/relief-of-inhibition properties [].

>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins

Probab=98.32  E-value=2.5e-06  Score=50.82  Aligned_cols=50  Identities=28%  Similarity=0.453  Sum_probs=45.8

Q ss_pred             HHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         125 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       125 ~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ..|+..+...++++.++|+.+|+++.+++.|++|...|+...+.+|++.|
T Consensus         2 ~~l~~~~~~~~~s~~~~a~~~~~~~~~v~~~~~g~~~~~~~~~~~i~~~~   51 (58)
T cd00093           2 ERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKAL   51 (58)
T ss_pred             hHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence            35677788899999999999999999999999999999999999999875

Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.

>COG2944 Predicted transcriptional regulator [Transcription]

Probab=98.32  E-value=1.7e-06  Score=59.79  Aligned_cols=45  Identities=24%  Similarity=0.273  Sum_probs=40.8

Q ss_pred             HHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHH
Q psy6501         124 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIG  168 (174)
Q Consensus       124 ~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~  168 (174)
                      ...|+..|+..++||.+||..+|++.+++++||+|+..|+-.-+.
T Consensus        46 ~~eIk~iRe~~~lSQ~vFA~~L~vs~~Tv~~WEqGr~kPsg~Alk   90 (104)
T COG2944          46 PTEIKAIREKLGLSQPVFARYLGVSVSTVRKWEQGRKKPSGAALK   90 (104)
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHcCCcCCCCHHHH
Confidence            468889999999999999999999999999999999999865543

>COG1426 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]

Probab=98.29  E-value=1.5e-06  Score=70.81  Aligned_cols=63  Identities=24%  Similarity=0.332  Sum_probs=56.0

Q ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCC--CCCCH----HHHHHHHHHhCcccccccC
Q psy6501          31 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGR--GIPNQ----AIIGKMERALGIRLRVNAG   93 (174)
Q Consensus        31 ~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~--~~P~~----~~l~~la~~L~v~~~~l~~   93 (174)
                      ..+|++||+.|+++|||++|+|.+++|.+++|..+|+|.  ..|..    ..+...|++|+++.+.|+.
T Consensus         2 ~~~Ge~Lr~~Re~~gLsL~dva~~t~I~~~~L~aiEeg~~~~lp~~~y~rG~ir~YA~~l~ld~~~l~~   70 (284)
T COG1426           2 KTLGERLRQAREEKGLSLEDVAARTKIRKSYLRALEEGNFDKLPGPVYIRGYIRSYAKFLGLDEDELLQ   70 (284)
T ss_pred             ccHHHHHHHHHHHcCCCHHHHHHHhCccHHHHHHHhcCccccccchHHHHHHHHHHHHHhCCCHHHHHH
Confidence            478999999999999999999999999999999999998  44544    3567899999999998873

>COG5499 Predicted transcription regulator containing HTH domain [Transcription]

Probab=98.28  E-value=1.9e-06  Score=59.54  Aligned_cols=58  Identities=22%  Similarity=0.254  Sum_probs=54.6

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccccccc
Q psy6501          34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNA   92 (174)
Q Consensus        34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~   92 (174)
                      -+.|+.+.+..|+|+.+||..+| |++.+|++-+|++..+.+.+.+|.+.||++.+.|.
T Consensus        62 ve~I~t~Md~~glt~~dLa~~iG-Sks~vS~iL~~rraLTle~ikkL~q~~gIpa~~lI  119 (120)
T COG5499          62 VEVIRTLMDQYGLTLADLANEIG-SKSRVSNILSGRRALTLEHIKKLHQRFGIPADVLI  119 (120)
T ss_pred             HHHHHHHHHHhCCcHHHHHHHhC-chHHHHHHHhhhhHhhHHHHHHHHHHhCcCHHHhc
Confidence            46899999999999999999999 89999999999999999999999999999988764

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

Probab=98.22  E-value=3.3e-06  Score=53.03  Aligned_cols=48  Identities=27%  Similarity=0.362  Sum_probs=37.4

Q ss_pred             HHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCC-CCCCHHHHHHHHhhC
Q psy6501         127 LMQGRQAKGWSQKDLATKINEKPQIVNDYEGGR-GIPNQAIIGKMERAL  174 (174)
Q Consensus       127 i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~-~~P~~~~l~~i~~~l  174 (174)
                      |+.....+|+++.++|+..|++++++++|-+|. ..|+.+.+.+||++|
T Consensus         2 L~~~m~~~~it~~~La~~~gis~~tl~~~~~~~~~~~~~~~l~~ia~~l   50 (63)
T PF13443_consen    2 LKELMAERGITQKDLARKTGISRSTLSRILNGKPSNPSLDTLEKIAKAL   50 (63)
T ss_dssp             HHHHHHHTT--HHHHHHHHT--HHHHHHHHTTT-----HHHHHHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcccccccHHHHHHHHHHc
Confidence            667788999999999999999999999999998 799999999999986

>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators

Probab=98.21  E-value=2.9e-06  Score=51.21  Aligned_cols=43  Identities=19%  Similarity=0.183  Sum_probs=36.1

Q ss_pred             HHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCccccccc
Q psy6501          50 DLATKINEKPQIVNDYEGGRGIPNQAI---IGKMERALGIRLRVNA   92 (174)
Q Consensus        50 eLA~~igvs~~~is~~E~G~~~P~~~~---l~~la~~L~v~~~~l~   92 (174)
                      +||+++|||+++||+|++|...++...   +..++..||+.++|+.
T Consensus         2 ~lA~~~gvs~~tvs~~l~g~~~vs~~~~~~i~~~~~~l~~~~~~~~   47 (52)
T cd01392           2 DIARAAGVSVATVSRVLNGKPRVSEETRERVLAAAEELGYRPNAAA   47 (52)
T ss_pred             cHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHHHhCCCCCHHH
Confidence            799999999999999999997666555   4558889999888754

HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre

>PRK10856 cytoskeletal protein RodZ; Provisional

Probab=98.19  E-value=4.4e-06  Score=69.52  Aligned_cols=53  Identities=23%  Similarity=0.286  Sum_probs=48.1

Q ss_pred             HHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCH------HHHHHHHhhC
Q psy6501         122 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQ------AIIGKMERAL  174 (174)
Q Consensus       122 ~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~------~~l~~i~~~l  174 (174)
                      .++.+|+++|+++||||+++|+++++++++|+.||+|...|..      .+++.+|++|
T Consensus        14 ~~G~~Lr~aRe~~GlSq~~vA~~l~l~~~~I~~iE~g~~~~~~~~tf~RGyir~yA~~l   72 (331)
T PRK10856         14 TTGERLRQAREQLGLTQQAVAERLCLKVSTVRDIEEDKAPADLASTFLRGYIRSYARLV   72 (331)
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHCCCCCCChhHHHHHHHHHHHHHHH
Confidence            4789999999999999999999999999999999999998877      4578888875

>PRK02866 cyanate hydratase; Validated

Probab=98.16  E-value=1e-05  Score=59.48  Aligned_cols=53  Identities=19%  Similarity=0.189  Sum_probs=50.2

Q ss_pred             HHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         122 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       122 ~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ++.+.|..+|.++|+|++++|+++|+++..+..++.|...++.+.+.+|+++|
T Consensus         5 ~~~e~Ll~AK~~kGLTw~~IA~~iG~S~v~vaaa~lGQ~~ls~e~A~kla~~L   57 (147)
T PRK02866          5 ELTEKILAAKKEKGLTWADIAEAIGLSEVWVTAALLGQMTLPAEEAEKVAELL   57 (147)
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHhCCCCCCHHHHHHHHHHh
Confidence            45678999999999999999999999999999999999999999999999986

>TIGR01321 TrpR trp operon repressor, proteobacterial

Probab=98.07  E-value=1.8e-05  Score=53.84  Aligned_cols=48  Identities=13%  Similarity=0.085  Sum_probs=39.0

Q ss_pred             HHHHHHHHHHH--HcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHH
Q psy6501          32 DLAKLLMQGRQ--AKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGK   79 (174)
Q Consensus        32 ~ig~~ik~~R~--~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~   79 (174)
                      .++.|++-.+.  ..++||.|+|+++|||++||++++|+...-+++.-.-
T Consensus        40 ~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~sn~lk~~~~~~~~~   89 (94)
T TIGR01321        40 DLGDRIRIVNELLNGNMSQREIASKLGVSIATITRGSNNLKTMDPNFKQF   89 (94)
T ss_pred             HHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHHHhhcccCCHHHHHH
Confidence            67788888774  5789999999999999999999999997544444333

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

>smart00352 POU Found in Pit-Oct-Unc transcription factors

Probab=98.04  E-value=1.2e-05  Score=52.39  Aligned_cols=43  Identities=19%  Similarity=0.201  Sum_probs=38.4

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHhCC------ChhHHHHHhcCCCCCC
Q psy6501         121 LDLAKLLMQGRQAKGWSQKDLATKINE------KPQIVNDYEGGRGIPN  163 (174)
Q Consensus       121 ~~~~~~i~~~R~~~glsq~ela~~lg~------~~s~i~~~E~G~~~P~  163 (174)
                      ..++..++.+|...|+||.++|+.+|.      ++++|++||+|.-.+.
T Consensus        10 e~~~~~lk~~R~~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es~~ls~~   58 (75)
T smart00352       10 EAFAKTFKQRRIKLGFTQADVGLALGALYGPDFSQTTICRFEALQLSFK   58 (75)
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhcccccCcCCHHHHHHHHhcCccHH
Confidence            457889999999999999999999995      9999999999876544

>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A

Probab=98.03  E-value=2.4e-05  Score=51.86  Aligned_cols=55  Identities=20%  Similarity=0.217  Sum_probs=43.4

Q ss_pred             cHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcC-CCCCCHHHHHHHHhhC
Q psy6501         120 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGG-RGIPNQAIIGKMERAL  174 (174)
Q Consensus       120 ~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G-~~~P~~~~l~~i~~~l  174 (174)
                      ...+...|...++.+||||.++|+.+|++++.|+++++| ...++.+.+.++..+|
T Consensus        16 k~~l~~~i~~~~~~~~ltQ~e~A~~lgisq~~vS~l~~g~~~~~sl~~L~~~l~aL   71 (80)
T PF13744_consen   16 KAQLMAAIRELREERGLTQAELAERLGISQPRVSRLENGKIDDFSLDTLLRYLEAL   71 (80)
T ss_dssp             HHHHHHHHHHHHHCCT--HHHHHHHHTS-HHHHHHHHTT-GCC--HHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHCCChhHHHHHHcCcccCCCHHHHHHHHHHc
Confidence            455677799999999999999999999999999999998 5568999988887764

>TIGR00673 cynS cyanate hydratase

Probab=97.97  E-value=3.4e-05  Score=56.87  Aligned_cols=52  Identities=19%  Similarity=0.204  Sum_probs=49.9

Q ss_pred             HHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         123 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       123 ~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      +.+.|..+|.++|+|.+++|+++|+++..+..++.|...|+.+.+.+|+++|
T Consensus         9 ~t~~Ll~AK~~KGLTwe~IAe~iG~sevwvaaa~lGQ~~ls~e~A~kla~lL   60 (150)
T TIGR00673         9 LADALLESKKKKGLTFADIADGLGLAEVFVAAALYGQAAAPADEARLVGAKL   60 (150)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHhCCCCCCHHHHHHHHHHh
Confidence            6688999999999999999999999999999999999999999999999986

Alternate names include cyanate lyase, cyanase and cyanate hydrolase.

>PRK08099 bifunctional DNA-binding transcriptional repressor/ NMN adenylyltransferase; Provisional

Probab=97.77  E-value=4.2e-05  Score=65.26  Aligned_cols=46  Identities=13%  Similarity=0.271  Sum_probs=43.7

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhCcccc
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYEGGR-GIPNQAIIGKMERALGIRLR   89 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E~G~-~~P~~~~l~~la~~L~v~~~   89 (174)
                      .|+|.+|||+.+|+|++|++.+|||+ ..||.+.|.+|+++|||+..
T Consensus         2 ~~~~~~~~~~~~~~~~~y~~~l~~~~~~~ps~~~~~~~~~~~~~~~~   48 (399)
T PRK08099          2 QGCTLQQVADASGMTKGYLSQLLNAKIKSPSAQKLEALHRFLGLEFP   48 (399)
T ss_pred             CCCcHHHHHHHhCCcHHHHHHHhcCCCCCccHHHHHHHHHHhCCChh
Confidence            68999999999999999999999999 78999999999999999944

>PHA01083 hypothetical protein

Probab=97.74  E-value=8.6e-05  Score=54.31  Aligned_cols=58  Identities=22%  Similarity=0.256  Sum_probs=49.2

Q ss_pred             HHHHHHHHHcCC-CHHHHHHHhCCCHHHHHHHHcC-CCCCCHHHHHHHHHHhCcccc-ccc
Q psy6501          35 KLLMQGRQAKGW-SQKDLATKINEKPQIVNDYEGG-RGIPNQAIIGKMERALGIRLR-VNA   92 (174)
Q Consensus        35 ~~ik~~R~~~gl-tq~eLA~~igvs~~~is~~E~G-~~~P~~~~l~~la~~L~v~~~-~l~   92 (174)
                      +-|..+.+.+++ +-++||..+|||++.||+|.+| ++.++-+....||+.+|+++. +++
T Consensus         5 kLLda~K~a~~~~sdkqLA~~LGVs~q~IS~~R~G~r~~i~de~A~~LAe~aGiDp~eall   65 (149)
T PHA01083          5 KLLDAYKKAKNYVQYKQIAHDLGVSPQKISKMRTGVRTYISDEEAIFLAESAGIDPEIALL   65 (149)
T ss_pred             HHHHHHHHHHhhccHHHHHHHhCCCHHHHHHHHcCCCCCCCHHHHHHHHHHhCCCHHHHHH
Confidence            345556666666 5578999999999999999999 999999999999999999986 554

>COG2522 Predicted transcriptional regulator [General function prediction only]

Probab=97.71  E-value=0.00011  Score=52.13  Aligned_cols=38  Identities=24%  Similarity=0.212  Sum_probs=33.4

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCC
Q psy6501          34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIP   72 (174)
Q Consensus        34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P   72 (174)
                      +.--+.++++ |+||.++|+.+|+|+++||+|-.|.+.|
T Consensus        12 a~lA~~L~ee-G~Sq~~iA~LLGltqaAVS~Yls~krg~   49 (119)
T COG2522          12 ALLAKELIEE-GLSQYRIAKLLGLTQAAVSQYLSGKRGS   49 (119)
T ss_pred             HHHHHHHHHc-CCcHHHHHHHhCCCHHHHHHHHccCCch
Confidence            4445667777 9999999999999999999999999985

>COG1396 HipB Predicted transcriptional regulators [Transcription]

Probab=97.56  E-value=0.00043  Score=45.08  Aligned_cols=51  Identities=25%  Similarity=0.464  Sum_probs=47.1

Q ss_pred             HHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCC-CCCHHHHHHHHhh
Q psy6501         123 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRG-IPNQAIIGKMERA  173 (174)
Q Consensus       123 ~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~-~P~~~~l~~i~~~  173 (174)
                      ++..++..|...|+++++++..+|++..+++.||.|.. .|....+..++..
T Consensus         2 ~~~~~~~~r~~~~~s~~~~a~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~   53 (120)
T COG1396           2 IGERLKELRKKKGLSQEELAERLGVSRSTISRIERGRSESPSLELLARLAAA   53 (120)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCCHHHHHHHHHH
Confidence            35788999999999999999999999999999999999 9999999988864

>COG4800 Predicted transcriptional regulator with an HTH domain [Transcription]

Probab=97.54  E-value=0.00051  Score=49.79  Aligned_cols=54  Identities=13%  Similarity=0.164  Sum_probs=50.1

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHh
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL   84 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L   84 (174)
                      ...|++-++.+-.++|||..|+|++.|+..+|+.++-+| +.|+.++|.+|-..+
T Consensus        14 ~E~F~~~l~~~l~Elglt~~eFak~anIP~StLYKil~G-~dpr~~tl~~I~kti   67 (170)
T COG4800          14 GEDFGSCLQKLLDELGLTPSEFAKRANIPLSTLYKILKG-SDPRYDTLTRIFKTI   67 (170)
T ss_pred             hhHHHHHHHHHHHHcCCCHHHHHHHcCCCHHHHHHHHhC-CCccHHHHHHHHHHH
Confidence            357999999999999999999999999999999999999 889999999988765

>PF08965 DUF1870: Domain of unknown function (DUF1870); InterPro: IPR015060 This family consist of hypothetical bacterial proteins

Probab=97.53  E-value=0.00037  Score=49.25  Aligned_cols=54  Identities=19%  Similarity=0.140  Sum_probs=41.7

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhC--CCHHHHHHHHcCCCCCCHHHHHHHHHHhCcc
Q psy6501          34 AKLLMQGRQAKGWSQKDLATKIN--EKPQIVNDYEGGRGIPNQAIIGKMERALGIR   87 (174)
Q Consensus        34 g~~ik~~R~~~gltq~eLA~~ig--vs~~~is~~E~G~~~P~~~~l~~la~~L~v~   87 (174)
                      +--|+.+|+..+||+.|.|..++  ++..+-.+||+|.+..+.++...+.......
T Consensus         3 ~~ELqalR~~l~lt~~EaA~~Ia~~v~~~tWq~WE~G~~~IP~~Vie~l~~m~~~R   58 (118)
T PF08965_consen    3 NLELQALRQILGLTVEEAAYYIAQDVSSRTWQQWEKGERPIPDDVIEELLEMKSQR   58 (118)
T ss_dssp             HHHHHHHHHHTT--HHHHHHHTSSS--HHHHHHHHTTSS---HHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHccCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHH
Confidence            45689999999999999999999  9999999999999999999988888766554

; PDB: 1S4K_A.

>smart00354 HTH_LACI helix_turn _helix lactose operon repressor

Probab=97.52  E-value=0.00033  Score=45.08  Aligned_cols=45  Identities=18%  Similarity=0.091  Sum_probs=36.1

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCHH---HHHHHHHHhCccccc
Q psy6501          46 WSQKDLATKINEKPQIVNDYEGGRGIPNQA---IIGKMERALGIRLRV   90 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~G~~~P~~~---~l~~la~~L~v~~~~   90 (174)
                      +|+.|+|+.+|||.+|||++.||....+.+   .+.++++.+|..+..
T Consensus         1 ~t~~~iA~~~gvS~~TVSr~ln~~~~v~~~t~~~i~~~~~~~gy~~~~   48 (70)
T smart00354        1 ATIKDVARLAGVSKATVSRVLNGNGRVSEETREKVLAAMEELGYIPNR   48 (70)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCCCCH
Confidence            489999999999999999999999765544   455677778876543

>COG1395 Predicted transcriptional regulator [Transcription]

Probab=97.51  E-value=0.00023  Score=58.18  Aligned_cols=51  Identities=27%  Similarity=0.322  Sum_probs=48.2

Q ss_pred             HHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         124 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       124 ~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ++.+++.|++.|+|..++|..+|+|+.+|+.||.|...|+.+++.+|-..|
T Consensus       127 ge~Lre~Ree~glSlG~lA~~lgVSRktV~~YE~G~~~~sleva~kLeei~  177 (313)
T COG1395         127 GEKLREKREEMGLSLGDLATMLGVSRKTVYKYEKGLSDASLEVALKLEEIF  177 (313)
T ss_pred             hHHHHHHHHHcCcCHHHHHHHhCccHHHHHHhccCCCCccHHHHHHHHHHh
Confidence            689999999999999999999999999999999999999999999987654

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

Probab=97.48  E-value=0.00048  Score=40.79  Aligned_cols=37  Identities=16%  Similarity=0.136  Sum_probs=31.7

Q ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHH
Q psy6501          47 SQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERA   83 (174)
Q Consensus        47 tq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~   83 (174)
                      |.+|+|+.+|+|.+|||++-||....+.+.-.+|-++
T Consensus         1 Ti~dIA~~agvS~~TVSr~ln~~~~vs~~tr~rI~~~   37 (46)
T PF00356_consen    1 TIKDIAREAGVSKSTVSRVLNGPPRVSEETRERILEA   37 (46)
T ss_dssp             CHHHHHHHHTSSHHHHHHHHTTCSSSTHHHHHHHHHH
T ss_pred             CHHHHHHHHCcCHHHHHHHHhCCCCCCHHHHHHHHHH
Confidence            6789999999999999999999988888776655443

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 ....

>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]

Probab=97.48  E-value=0.00038  Score=48.13  Aligned_cols=52  Identities=13%  Similarity=0.238  Sum_probs=45.5

Q ss_pred             HHHHHHHHHHh-cCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         123 LAKLLMQGRQA-KGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       123 ~~~~i~~~R~~-~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      .++.|++.=.+ .|+|+.++|+.+|+++.+|+.+-+|++..+.+.+.+|+++|
T Consensus        10 PGEiL~eeflep~glt~~~lA~~lgV~r~~is~ling~~~iT~dmAlrL~k~f   62 (104)
T COG3093          10 PGEILREEFLEPLGLTQTELAEALGVTRNTISELINGRRAITADMALRLAKVF   62 (104)
T ss_pred             chHHHHHHHhccccCCHHHHHHHhCCCHHHHHHHHcCCcCCCHHHHHHHHHHh
Confidence            34556555445 59999999999999999999999999999999999999987

>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A

Probab=97.46  E-value=0.00048  Score=43.43  Aligned_cols=44  Identities=25%  Similarity=0.360  Sum_probs=34.0

Q ss_pred             HHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcC--CCCCCHHHHHH
Q psy6501         126 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEGG--RGIPNQAIIGK  169 (174)
Q Consensus       126 ~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G--~~~P~~~~l~~  169 (174)
                      +++++|+.+|+|.+++|..++++.+.+..+|+|  ...|++.++..
T Consensus         1 ~Lr~~R~~~glsl~~va~~t~I~~~~l~aiE~~~~~~lp~~~y~rg   46 (62)
T PF13413_consen    1 RLREAREAKGLSLEDVAEETKISVSYLEAIENGDFDSLPSPVYARG   46 (62)
T ss_dssp             -HHHHHHCTT--HHHHHHHCS--HHHHHHHHCT-GCCSSSHHHHHH
T ss_pred             ChHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCcChhhCCcHHHHHH
Confidence            478899999999999999999999999999999  56688765443

>PHA00675 hypothetical protein

Probab=97.39  E-value=0.0006  Score=44.38  Aligned_cols=48  Identities=13%  Similarity=0.059  Sum_probs=42.2

Q ss_pred             hcccccchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCC
Q psy6501          23 ELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRG   70 (174)
Q Consensus        23 ~~~~~~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~   70 (174)
                      ..+...+...--+.|+.+++.-|.|+.+||.++|||+++|++|-+|++
T Consensus        17 ~h~~AKLt~~qV~~IR~l~~r~G~s~~~IA~~fGVsrstV~~I~~gk~   64 (78)
T PHA00675         17 DHPNAKLTDAEVERIRELHEVEGMSYAVLAEKFEQSKGAIAKICRYER   64 (78)
T ss_pred             CCCCcccCHHHHHHHHHHHHhcCccHHHHHHHhCCCHHHHHHHHccch
Confidence            355566677778899999999999999999999999999999999875

>TIGR03879 near_KaiC_dom probable regulatory domain

Probab=97.35  E-value=0.001  Score=43.21  Aligned_cols=43  Identities=16%  Similarity=0.217  Sum_probs=34.9

Q ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHH
Q psy6501          37 LMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKME   81 (174)
Q Consensus        37 ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la   81 (174)
                      ....|...|+|++|+|+.+|+|.++|..+.++  .++...+.++|
T Consensus        24 f~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~--~~~~~~~~~~~   66 (73)
T TIGR03879        24 AALAREEAGKTASEIAEELGRTEQTVRNHLKG--ETKAGGLVKLA   66 (73)
T ss_pred             HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc--CcccchHHHHH
Confidence            33447889999999999999999999999974  44566666665

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

>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data

Probab=97.21  E-value=0.00012  Score=54.79  Aligned_cols=104  Identities=19%  Similarity=0.265  Sum_probs=26.2

Q ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccCCCCCCCCCcccchhhhhhhhhhcccccH
Q psy6501          42 QAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGTNKQPGTTKNTAKLDRETEELKHEKVPL  121 (174)
Q Consensus        42 ~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~  121 (174)
                      .-.-||++|+|+.+|++.+|||+.-+|+..-.+.-+.-|...|...+..-.+                  .......+..
T Consensus        46 ~l~PLt~~~iA~~lgl~~STVSRav~~Ky~~t~~Gi~plk~fF~~~~~~~~~------------------~~~S~~~ik~  107 (160)
T PF04552_consen   46 ALKPLTMKDIADELGLHESTVSRAVKNKYIQTPRGIFPLKDFFSRSVSSGSG------------------EEFSSEAIKA  107 (160)
T ss_dssp             ---------------------------------------S-----SS--SS-------------------SS---TTH-H
T ss_pred             cCcCCCHHHHHHHhCCCHhHHHHHHcCceeecCCeeeeHHHhccccccCCCC------------------cccHHHHHHH
Confidence            4556899999999999999999999998654444444444443333211100                  0011122234


Q ss_pred             HHHHHHHHHHHhcCCCHHHHHHHh-----CCChhHHHHHhcCCCCCC
Q psy6501         122 DLAKLLMQGRQAKGWSQKDLATKI-----NEKPQIVNDYEGGRGIPN  163 (174)
Q Consensus       122 ~~~~~i~~~R~~~glsq~ela~~l-----g~~~s~i~~~E~G~~~P~  163 (174)
                      .+.++|.......-+|.+++++.+     .+++-||++|=..-..|+
T Consensus       108 ~i~~lI~~Ed~~~PlSD~~i~~~L~~~gi~isRRTVaKYR~~L~Ip~  154 (160)
T PF04552_consen  108 RIKELIEEEDKKKPLSDQEIAELLKEEGIKISRRTVAKYREELGIPS  154 (160)
T ss_dssp             HHHHHHTTS-TTS---HHHHHHHHTTTTS---HHHHHHHHHHHT-S-
T ss_pred             HHHHHHHhcCCCCCCCHHHHHHHHHHcCCCccHHHHHHHHHHcCCCC
Confidence            455666555555778999999998     788889988865544444

This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.

>PF07022 Phage_CI_repr: Bacteriophage CI repressor helix-turn-helix domain; InterPro: IPR010744 This family consists of several phage CI repressor proteins and related bacterial sequences

Probab=97.18  E-value=0.00035  Score=44.52  Aligned_cols=47  Identities=19%  Similarity=0.320  Sum_probs=35.2

Q ss_pred             HHHHHHHhcCC-CHHHHHHHhCCChhHHH-HHhcCCCCCCHHHHHHHHhh
Q psy6501         126 LLMQGRQAKGW-SQKDLATKINEKPQIVN-DYEGGRGIPNQAIIGKMERA  173 (174)
Q Consensus       126 ~i~~~R~~~gl-sq~ela~~lg~~~s~i~-~~E~G~~~P~~~~l~~i~~~  173 (174)
                      +|++.++..|. ++.+||+.+|+++++++ .|......| .+.+.+|++.
T Consensus         2 ~i~rl~~~~g~~~~~~lA~~lgis~st~s~~~~~r~~~P-~~~l~~ia~~   50 (66)
T PF07022_consen    2 VIERLKEALGVKSDKELAERLGISKSTLSNNWKKRGSIP-AEWLIKIALE   50 (66)
T ss_dssp             HHHHHHHHHT-SSCHHHHCCTT--HHHHH-HHHHSSS---HHHHHHHHHH
T ss_pred             HHHHHHHHhCCCCHHHHHHHhCcCHHHhhHHHHhCCCCC-HHHHHHHHHH
Confidence            45666777775 56799999999999999 899888888 8999888864

The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic [].; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2FJR_B.

>PF00157 Pou: Pou domain - N-terminal to homeobox domain; InterPro: IPR000327 POU proteins are eukaryotic transcription factors containing a bipartite DNA binding domain referred to as the POU domain

Probab=97.17  E-value=0.0025  Score=41.58  Aligned_cols=50  Identities=18%  Similarity=0.197  Sum_probs=38.2

Q ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhC------CCHHHHHHHHcCCCCCCHHHHHHHHH
Q psy6501          31 LDLAKLLMQGRQAKGWSQKDLATKIN------EKPQIVNDYEGGRGIPNQAIIGKMER   82 (174)
Q Consensus        31 ~~ig~~ik~~R~~~gltq~eLA~~ig------vs~~~is~~E~G~~~P~~~~l~~la~   82 (174)
                      ..|+..+|..|-..|+||.+++..+|      .|+++|+++|+=  ..|...+.+|-=
T Consensus        10 e~Fa~~fk~rRi~LG~TQ~dVg~al~~~~G~~~SQttI~RFE~L--~LS~kn~~klkP   65 (75)
T PF00157_consen   10 EQFAKEFKQRRIKLGYTQADVGAALGRLYGKEFSQTTICRFEAL--QLSFKNMCKLKP   65 (75)
T ss_dssp             HHHHHHHHHHHHHTT--HHHHHHHHHHHHSSGGSHHHHHHHHTT--TSCHHHHHHHHH
T ss_pred             HHHHHHHHHhhhhcccCHHHHhHHHHHhcCccccchhhhhhHhc--ccCHHHHHHHHH
Confidence            47999999999999999999998875      489999999963  445665555543

The acronym POU (pronounced 'pow') is derived from the names of three mammalian transcription factors, the pituitary-specific Pit-1, the octamer-binding proteins Oct-1 and Oct-2, and the neural Unc-86 from Caenorhabditis elegans. POU domain genes have been identified in diverse organisms including nematodes, flies, amphibians, fish and mammals but have not been yet identified in plants and fungi. The various members of the POU family have a wide variety of functions, all of which are related to the function of the neuroendocrine system [] and the development of an organism []. Some other genes are also regulated, including those for immunoglobulin light and heavy chains (Oct-2) [, ], and trophic hormone genes, such as those for prolactin and growth hormone (Pit-1). The POU domain is a bipartite domain composed of two subunits separated by a non-conserved region of 15-55 aa. The N-terminal subunit is known as the POU-specific (POUs) domain (IPR000327 from INTERPRO), while the C-terminal subunit is a homeobox domain (IPR007103 from INTERPRO). 3D structures of complexes including both POU subdomains bound to DNA are available. Both subdomains contain the structural motif 'helix-turn-helix', which directly associates with the two components of bipartite DNA binding sites, and both are required for high affinity sequence-specific DNA-binding. The domain may also be involved in protein-protein interactions []. The subdomains are connected by a flexible linker [, , ]. In proteins a POU-specific domain is always accompanied by a homeodomain. Despite of the lack of sequence homology, 3D structure of POUs is similar to 3D structure of bacteriophage lambda repressor and other members of HTH_3 family [, ]. This entry represents the POU-specific subunit of the POU domain.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3D1N_O 1AU7_A 3L1P_A 2XSD_C 1O4X_A 1HF0_B 1GT0_C 1POU_A 1CQT_B 1E3O_C ....

>COG5606 Uncharacterized conserved small protein [Function unknown]

Probab=97.14  E-value=0.0012  Score=44.08  Aligned_cols=61  Identities=16%  Similarity=0.099  Sum_probs=52.9

Q ss_pred             chHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhCcccc
Q psy6501          29 VPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGR-GIPNQAIIGKMERALGIRLR   89 (174)
Q Consensus        29 ~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~-~~P~~~~l~~la~~L~v~~~   89 (174)
                      +...++..|+..-+.++|+|+++|+.+||+++.+|.+-+|+ ..-+++.|.....+.|..++
T Consensus        25 ir~~l~~~i~~~i~q~~l~Q~qiae~lgV~qprvS~l~~gk~~~fs~dkLvtml~~~g~ei~   86 (91)
T COG5606          25 IRSALMMAIKQWIEQAALSQAQIAELLGVTQPRVSDLARGKIQDFSIDKLVTMLARAGQEID   86 (91)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHhcchhHhhHHHHHHHHHHcCCccc
Confidence            34568889999999999999999999999999999999999 55788888888877777665

>PF13693 HTH_35: Winged helix-turn-helix DNA-binding; PDB: 1NEQ_A 1NER_A

Probab=97.12  E-value=0.0011  Score=43.69  Aligned_cols=56  Identities=13%  Similarity=-0.000  Sum_probs=43.0

Q ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccC
Q psy6501          35 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAG   93 (174)
Q Consensus        35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~   93 (174)
                      ..|+..-+.+|+|+.+||...|++++|+++--   ..|....=..||++|||++..+..
T Consensus         5 adI~AaL~krG~sL~~lsr~~Gl~~~tl~nal---~r~~pk~E~~IA~aLgv~P~eIWP   60 (78)
T PF13693_consen    5 ADIKAALRKRGTSLAALSREAGLSSSTLRNAL---RRPWPKGERIIADALGVPPEEIWP   60 (78)
T ss_dssp             HHHHHHHCTTS--HHHHHHHHSS-HHHHHHTT---TSS-HHHHHHHHHHTTS-HHHHST
T ss_pred             HHHHHHHHHcCCCHHHHHHHcCCCHHHHHHHH---cCCChHHHHHHHHHHCcCHHHhCc
Confidence            45777778999999999999999999999874   455666667899999999999985

>PF08965 DUF1870: Domain of unknown function (DUF1870); InterPro: IPR015060 This family consist of hypothetical bacterial proteins

Probab=97.12  E-value=0.0015  Score=46.20  Aligned_cols=47  Identities=19%  Similarity=0.174  Sum_probs=36.6

Q ss_pred             HHHHHHHhcCCCHHHHHHHhC--CChhHHHHHhcCCCCCCHHHHHHHHh
Q psy6501         126 LLMQGRQAKGWSQKDLATKIN--EKPQIVNDYEGGRGIPNQAIIGKMER  172 (174)
Q Consensus       126 ~i~~~R~~~glsq~ela~~lg--~~~s~i~~~E~G~~~P~~~~l~~i~~  172 (174)
                      .++.+|...+||+.+.|..++  ++..+...||+|....|++++..+..
T Consensus         5 ELqalR~~l~lt~~EaA~~Ia~~v~~~tWq~WE~G~~~IP~~Vie~l~~   53 (118)
T PF08965_consen    5 ELQALRQILGLTVEEAAYYIAQDVSSRTWQQWEKGERPIPDDVIEELLE   53 (118)
T ss_dssp             HHHHHHHHTT--HHHHHHHTSSS--HHHHHHHHTTSS---HHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHHHccCCHHHHHHHHcCCCCCCHHHHHHHHH
Confidence            567889999999999999999  88889999999999999999998865

; PDB: 1S4K_A.

>COG3423 Nlp Predicted transcriptional regulator [Transcription]

Probab=97.01  E-value=0.0031  Score=41.00  Aligned_cols=55  Identities=16%  Similarity=0.113  Sum_probs=45.3

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccC
Q psy6501          36 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAG   93 (174)
Q Consensus        36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~   93 (174)
                      -|....+.+|+|...|+.+.|+|++|+.+.-. +.-|..+.  -||++|||++.++-.
T Consensus        12 dI~A~Lkk~G~Sl~~LS~~agls~~tL~n~L~-rp~pkgEr--iIA~algv~P~eIWp   66 (82)
T COG3423          12 DIIAALKKKGTSLAALSREAGLSSSTLANALD-RPWPKGER--IIADALGVPPEEIWP   66 (82)
T ss_pred             HHHHHHHHccccHHHHHHHcCCCHHHHHHHHc-CCCchHHH--HHHHHhCCCHHHhCc
Confidence            35666788999999999999999999999864 55566665  489999999988763

>TIGR01321 TrpR trp operon repressor, proteobacterial

Probab=96.98  E-value=0.004  Score=42.43  Aligned_cols=41  Identities=10%  Similarity=0.100  Sum_probs=35.4

Q ss_pred             hcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhh
Q psy6501         133 AKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERA  173 (174)
Q Consensus       133 ~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~  173 (174)
                      ..++||.++|+++|+|.++|++++++...-++++..-|.+.
T Consensus        53 ~~~~tQrEIa~~lGiS~atIsR~sn~lk~~~~~~~~~l~~~   93 (94)
T TIGR01321        53 NGNMSQREIASKLGVSIATITRGSNNLKTMDPNFKQFLRKK   93 (94)
T ss_pred             hCCCCHHHHHHHhCCChhhhhHHHhhcccCCHHHHHHHHhh
Confidence            46899999999999999999999999997777777666554

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

>TIGR02147 Fsuc_second hypothetical protein, TIGR02147

Probab=96.95  E-value=0.0019  Score=52.40  Aligned_cols=46  Identities=24%  Similarity=0.283  Sum_probs=43.4

Q ss_pred             CCCHHHHHHHhCCCH-HHHHHHHcCCCCCCHHHHHHHHHHhCccccc
Q psy6501          45 GWSQKDLATKINEKP-QIVNDYEGGRGIPNQAIIGKMERALGIRLRV   90 (174)
Q Consensus        45 gltq~eLA~~igvs~-~~is~~E~G~~~P~~~~l~~la~~L~v~~~~   90 (174)
                      .+|..++|+.+|++. ++++.+.+|++.++...+.++|++||.+..+
T Consensus        27 ~fS~R~fa~~~G~ss~s~L~~v~~Gkr~Ls~~~~~k~a~~l~L~~~E   73 (271)
T TIGR02147        27 AFSWRFFAEKAGFSSTSYLNDIIKGKKNLTKRMIPKFAEALGLDEKE   73 (271)
T ss_pred             CcCHHHHHHHhCCCCHHHHHHHHcCCCCCCHHHHHHHHHHcCCCHHH
Confidence            699999999999888 9999999999999999999999999999664

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

>PRK03975 tfx putative transcriptional regulator; Provisional

Probab=96.90  E-value=0.0019  Score=47.33  Aligned_cols=49  Identities=16%  Similarity=0.260  Sum_probs=37.9

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHcCCCC---CCHHHHHHHHHHhCccccccc
Q psy6501          43 AKGWSQKDLATKINEKPQIVNDYEGGRGI---PNQAIIGKMERALGIRLRVNA   92 (174)
Q Consensus        43 ~~gltq~eLA~~igvs~~~is~~E~G~~~---P~~~~l~~la~~L~v~~~~l~   92 (174)
                      ..|+||+|+|+.+|+|+++|+.||++-..   =...+| +++..|+-++...+
T Consensus        19 ~~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~tl-~~~~~l~a~~~v~~   70 (141)
T PRK03975         19 ERGLTQQEIADILGTSRANVSSIEKRARENIEKARETL-AFAETLNAPVRVTI   70 (141)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH-HHHHHcCCCeEEEe
Confidence            69999999999999999999999986421   011233 77778888877666

>COG3655 Predicted transcriptional regulator [Transcription]

Probab=96.89  E-value=0.0033  Score=40.76  Aligned_cols=49  Identities=20%  Similarity=0.133  Sum_probs=42.6

Q ss_pred             HHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCC-CCHHHHHHHHhhC
Q psy6501         126 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGI-PNQAIIGKMERAL  174 (174)
Q Consensus       126 ~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~-P~~~~l~~i~~~l  174 (174)
                      .+.....+++++..++++.+|++.++++.+..|+.. ....++.+||++|
T Consensus         6 ~l~~~l~~r~~~~~eLa~~igis~~~ls~l~~gk~k~I~~~tL~~iC~~L   55 (73)
T COG3655           6 RLDVMLADRKISLKELAEAIGISEANLSKLKTGKVKAIRLSTLEKICKAL   55 (73)
T ss_pred             hHHHHHHHHhhhHHHHHHHHcccHHHHHHHHcCCcceeeHHHHHHHHHHc
Confidence            445556778899999999999999999999998665 7899999999986

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

Probab=96.88  E-value=0.0022  Score=38.10  Aligned_cols=24  Identities=21%  Similarity=0.495  Sum_probs=19.3

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcC
Q psy6501          45 GWSQKDLATKINEKPQIVNDYEGG   68 (174)
Q Consensus        45 gltq~eLA~~igvs~~~is~~E~G   68 (174)
                      |+|+.++|+.+|+|++||++|-+-
T Consensus        17 G~s~~~ia~~lgvs~~Tv~~w~kr   40 (50)
T PF13384_consen   17 GWSIREIAKRLGVSRSTVYRWIKR   40 (50)
T ss_dssp             T--HHHHHHHHTS-HHHHHHHHT-
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHH
Confidence            999999999999999999999764

>TIGR00721 tfx DNA-binding protein, Tfx family

Probab=96.86  E-value=0.0022  Score=46.80  Aligned_cols=32  Identities=28%  Similarity=0.370  Sum_probs=27.5

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcC
Q psy6501          36 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEGG   68 (174)
Q Consensus        36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G   68 (174)
                      .+-.+| ..|+||+|+|+.+|+|+++|+.+|+.
T Consensus        13 ~VL~Lr-~~GlTq~EIAe~LgiS~stV~~~e~r   44 (137)
T TIGR00721        13 KVLELR-EKGLSQKEIAKELKTTRANVSAIEKR   44 (137)
T ss_pred             HHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHh
Confidence            344455 69999999999999999999999975

Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.

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

Probab=96.69  E-value=0.0021  Score=37.56  Aligned_cols=29  Identities=14%  Similarity=0.189  Sum_probs=19.8

Q ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          37 LMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        37 ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      |..+ ...|+|+.++|+.+|+|++||+++-
T Consensus        13 I~~l-~~~G~s~~~IA~~lg~s~sTV~rel   41 (44)
T PF13936_consen   13 IEAL-LEQGMSIREIAKRLGRSRSTVSREL   41 (44)
T ss_dssp             HHHH-HCS---HHHHHHHTT--HHHHHHHH
T ss_pred             HHHH-HHcCCCHHHHHHHHCcCcHHHHHHH
Confidence            4444 3699999999999999999999874

>PHA02591 hypothetical protein; Provisional

Probab=96.65  E-value=0.0045  Score=40.43  Aligned_cols=28  Identities=18%  Similarity=0.270  Sum_probs=24.6

Q ss_pred             HHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          40 GRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        40 ~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      -..++|+||+++|+.+|+++.+|++|-.
T Consensus        54 eL~eqGlSqeqIA~~LGVsqetVrKYL~   81 (83)
T PHA02591         54 ELARKGFTVEKIASLLGVSVRKVRRYLE   81 (83)
T ss_pred             HHHHcCCCHHHHHHHhCCCHHHHHHHHh
Confidence            3456899999999999999999999854

>COG2522 Predicted transcriptional regulator [General function prediction only]

Probab=96.60  E-value=0.01  Score=42.24  Aligned_cols=42  Identities=21%  Similarity=0.240  Sum_probs=34.3

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCC
Q psy6501         121 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIP  162 (174)
Q Consensus       121 ~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P  162 (174)
                      +.++..+.......|+||.++|+.+|++++.|+.|-+|++.|
T Consensus         8 PaiRa~lA~~L~eeG~Sq~~iA~LLGltqaAVS~Yls~krg~   49 (119)
T COG2522           8 PAIRALLAKELIEEGLSQYRIAKLLGLTQAAVSQYLSGKRGS   49 (119)
T ss_pred             HHHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHccCCch
Confidence            444455544444559999999999999999999999999986

>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators

Probab=96.58  E-value=0.0038  Score=37.25  Aligned_cols=34  Identities=15%  Similarity=0.106  Sum_probs=29.5

Q ss_pred             HHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhh
Q psy6501         140 DLATKINEKPQIVNDYEGGRGIPNQAIIGKMERA  173 (174)
Q Consensus       140 ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~  173 (174)
                      ++|+.+|+++++|+.|++|...+++....+|.++
T Consensus         2 ~lA~~~gvs~~tvs~~l~g~~~vs~~~~~~i~~~   35 (52)
T cd01392           2 DIARAAGVSVATVSRVLNGKPRVSEETRERVLAA   35 (52)
T ss_pred             cHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence            6899999999999999999988888887776543

HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre

>TIGR02293 TAS_TIGR02293 putative toxin-antitoxin system antitoxin component, TIGR02293 family

Probab=96.55  E-value=0.012  Score=42.72  Aligned_cols=53  Identities=4%  Similarity=-0.048  Sum_probs=41.1

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCc
Q psy6501          34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGI   86 (174)
Q Consensus        34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v   86 (174)
                      ...+..+-+..|+|++|+|..+|+|++|++++-++...++.+.-.++.....|
T Consensus        25 ~~~~~~l~~~l~ls~~el~~~lgis~~Tl~R~~~~~~~Ls~~~serl~~l~ri   77 (133)
T TIGR02293        25 IGALDRLAHLLAIGKAEIFKATGIPKATLQRRKMAHQRLSSEESDRLARVARV   77 (133)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHhhcCCCCCHHHHHHHHHHHHH
Confidence            34567778999999999999999999999999987656666655554444333

Proteins in this family are found almost exclusively in the Proteobacteria, but also in Gloeobacter violaceus PCC 7421, a cyanobacterium. This family was proposed by Makarova, et al. (2009) to be the antitoxin component of a new class of type 2 toxin-antitoxin system, or addiction module.

>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B

Probab=96.54  E-value=0.0052  Score=38.43  Aligned_cols=36  Identities=31%  Similarity=0.487  Sum_probs=25.6

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHH
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERA   83 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~   83 (174)
                      .| ++..||+.+|||+++|++|  |...|. .....|...
T Consensus         9 ~G-~~~~lAkalGVs~~aVs~W--~~~IP~-~ra~~Ie~~   44 (60)
T PF14549_consen    9 FG-GQSKLAKALGVSPQAVSQW--GERIPA-ERAYQIEKL   44 (60)
T ss_dssp             HS-SHHHHHHHHTS-HHHHHHH--HTS--H-HHHHHHHHH
T ss_pred             HC-CHHHHHHHHCCCHHHHHHh--cCccCH-HHHHHHHHH
Confidence            44 8999999999999999999  455544 555556554

>COG3636 Predicted transcriptional regulator [Transcription]

Probab=96.52  E-value=0.016  Score=39.52  Aligned_cols=56  Identities=25%  Similarity=0.242  Sum_probs=46.9

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccccc
Q psy6501          33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRV   90 (174)
Q Consensus        33 ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~   90 (174)
                      |...+-..-..+|||  ++|++.|+|+..+.+=-+...+|++.++.+++++||+....
T Consensus        39 i~~alg~var~~GMs--qvA~~aGlsRe~LYkaLS~~GNPtf~Til~V~kAlG~rl~~   94 (100)
T COG3636          39 IAAALGVVARSRGMS--QVARKAGLSREGLYKALSPGGNPTFDTILAVLKALGLRLSA   94 (100)
T ss_pred             HHHHHHHHHHhcCHH--HHHHHhCccHHHHHHHhCCCCCCcHHHHHHHHHHcCceeec
Confidence            444444455567776  58999999999999999999999999999999999998654

>PHA01083 hypothetical protein

Probab=96.40  E-value=0.011  Score=43.35  Aligned_cols=50  Identities=22%  Similarity=0.268  Sum_probs=42.4

Q ss_pred             HHHHHHHHhcCC-CHHHHHHHhCCChhHHHHHhcC-CCCCCHHHHHHHHhhC
Q psy6501         125 KLLMQGRQAKGW-SQKDLATKINEKPQIVNDYEGG-RGIPNQAIIGKMERAL  174 (174)
Q Consensus       125 ~~i~~~R~~~gl-sq~ela~~lg~~~s~i~~~E~G-~~~P~~~~l~~i~~~l  174 (174)
                      ++|...+++..+ +-+++|+.+|++++.|++|-+| +..++.+.+..||+.+
T Consensus         5 kLLda~K~a~~~~sdkqLA~~LGVs~q~IS~~R~G~r~~i~de~A~~LAe~a   56 (149)
T PHA01083          5 KLLDAYKKAKNYVQYKQIAHDLGVSPQKISKMRTGVRTYISDEEAIFLAESA   56 (149)
T ss_pred             HHHHHHHHHHhhccHHHHHHHhCCCHHHHHHHHcCCCCCCCHHHHHHHHHHh
Confidence            466666777664 5689999999999999999999 9999999999998753

>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=96.38  E-value=0.0053  Score=35.98  Aligned_cols=33  Identities=18%  Similarity=0.189  Sum_probs=24.1

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      -+.+++++ ..|+|..++|+.+|||++||.+|-+
T Consensus        11 ~~~i~~l~-~~G~si~~IA~~~gvsr~TvyR~l~   43 (45)
T PF02796_consen   11 IEEIKELY-AEGMSIAEIAKQFGVSRSTVYRYLN   43 (45)
T ss_dssp             HHHHHHHH-HTT--HHHHHHHTTS-HHHHHHHHC
T ss_pred             HHHHHHHH-HCCCCHHHHHHHHCcCHHHHHHHHh
Confidence            45566655 4569999999999999999999865

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 ....

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

Probab=96.36  E-value=0.015  Score=34.40  Aligned_cols=37  Identities=16%  Similarity=0.136  Sum_probs=33.5

Q ss_pred             CHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhh
Q psy6501         137 SQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERA  173 (174)
Q Consensus       137 sq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~  173 (174)
                      |.+|+|+..|+|+++++++-+|....+++...+|-++
T Consensus         1 Ti~dIA~~agvS~~TVSr~ln~~~~vs~~tr~rI~~~   37 (46)
T PF00356_consen    1 TIKDIAREAGVSKSTVSRVLNGPPRVSEETRERILEA   37 (46)
T ss_dssp             CHHHHHHHHTSSHHHHHHHHTTCSSSTHHHHHHHHHH
T ss_pred             CHHHHHHHHCcCHHHHHHHHhCCCCCCHHHHHHHHHH
Confidence            5789999999999999999999999999998887654

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 ....

>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A

Probab=96.33  E-value=0.011  Score=34.73  Aligned_cols=33  Identities=33%  Similarity=0.351  Sum_probs=26.6

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      -.-|..+++.-++|+.|+|+.+|+|.++++.+-
T Consensus         6 ~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l   38 (48)
T PF13412_consen    6 RKILNYLRENPRITQKELAEKLGISRSTVNRYL   38 (48)
T ss_dssp             HHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHH
Confidence            455777888888999999999999999998864

...

>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins

Probab=96.33  E-value=0.0036  Score=42.46  Aligned_cols=29  Identities=17%  Similarity=0.391  Sum_probs=20.7

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHcCCCC
Q psy6501          43 AKGWSQKDLATKINEKPQIVNDYEGGRGI   71 (174)
Q Consensus        43 ~~gltq~eLA~~igvs~~~is~~E~G~~~   71 (174)
                      +.||||.|+|+++|.|+++|+++-.=-..
T Consensus         1 ~~G~tq~eIA~~lGks~s~Vs~~l~Ll~l   29 (93)
T PF08535_consen    1 EFGWTQEEIAKRLGKSRSWVSNHLALLDL   29 (93)
T ss_dssp             HTT--HHHHHHHTT--HHHHHHHHGGGS-
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHHHcC
Confidence            47999999999999999999999864443

The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This domain includes the DNA-binding HTH motif []. ; PDB: 1R71_C.

>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition

Probab=96.31  E-value=0.02  Score=40.62  Aligned_cols=88  Identities=17%  Similarity=0.213  Sum_probs=55.5

Q ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccCCCCCCCCCcccchhhhh
Q psy6501          31 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGTNKQPGTTKNTAKLDRE  110 (174)
Q Consensus        31 ~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~~~~~~~~~~~~~l~~~  110 (174)
                      .+|-+++-...+. |.|..+.|...+||.+||.+|-+ +..+. +          +....    ..     .  .+++  
T Consensus         5 ~DlR~rVl~~~~~-g~s~~eaa~~F~VS~~Tv~~W~k-~~~~G-~----------~~~k~----r~-----~--~Kid--   58 (119)
T PF01710_consen    5 LDLRQRVLAYIEK-GKSIREAAKRFGVSRNTVYRWLK-RKETG-D----------LEPKP----RG-----R--KKID--   58 (119)
T ss_pred             HHHHHHHHHHHHc-cchHHHHHHHhCcHHHHHHHHHH-hcccc-c----------ccccc----cc-----c--cccc--
Confidence            3455666665555 88999999999999999999987 32211 0          00000    00     0  0111  


Q ss_pred             hhhhhcccccHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHh
Q psy6501         111 TEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE  156 (174)
Q Consensus       111 ~~~~~~~~~~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E  156 (174)
                               ...+...   .......++.|+|+.+|+++++|...-
T Consensus        59 ---------~~~L~~~---v~~~pd~tl~Ela~~l~Vs~~ti~~~L   92 (119)
T PF01710_consen   59 ---------RDELKAL---VEENPDATLRELAERLGVSPSTIWRAL   92 (119)
T ss_pred             ---------HHHHHHH---HHHCCCcCHHHHHHHcCCCHHHHHHHH
Confidence                     1112223   344678999999999999999887654

This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].

>PRK10344 DNA-binding transcriptional regulator Nlp; Provisional

Probab=96.15  E-value=0.021  Score=38.37  Aligned_cols=56  Identities=18%  Similarity=0.119  Sum_probs=44.7

Q ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccC
Q psy6501          35 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAG   93 (174)
Q Consensus        35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~   93 (174)
                      .-|+..-+.+|+|..+||...|+|.+|+.+--. +..|..+  ..||++|||.+..+-.
T Consensus        11 adI~AaL~KrG~sLa~lsr~~Gls~~TL~nAL~-rp~PKgE--riIA~aLGv~P~eIWP   66 (92)
T PRK10344         11 ADIIAGLRKKGTSMAAESRRNGLSSSTLANALS-RPWPKGE--MIIAKALGTDPWVIWP   66 (92)
T ss_pred             HHHHHHHHHcCCcHHHHHHHcCCChHHHHHHHc-CCCchHH--HHHHHHHCcCHHHhCc
Confidence            345666778999999999999999999988754 3445555  4699999999998874

>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators

Probab=96.11  E-value=0.072  Score=33.65  Aligned_cols=22  Identities=18%  Similarity=0.407  Sum_probs=20.4

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q psy6501          46 WSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~   67 (174)
                      +|..|+|+.+|||+++|..||.
T Consensus         1 ~~i~e~A~~~gVs~~tlr~ye~   22 (68)
T cd04763           1 YTIGEVALLTGIKPHVLRAWER   22 (68)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5788999999999999999996

Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen

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

Probab=96.03  E-value=0.017  Score=34.30  Aligned_cols=32  Identities=13%  Similarity=0.170  Sum_probs=26.5

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          36 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      .|-.+|--.|+|++|+|+.+|+|.++|+++++
T Consensus        11 ~vi~~~y~~~~t~~eIa~~lg~s~~~V~~~~~   42 (50)
T PF04545_consen   11 EVIRLRYFEGLTLEEIAERLGISRSTVRRILK   42 (50)
T ss_dssp             HHHHHHHTST-SHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHhcCCCCHHHHHHHHCCcHHHHHHHHH
Confidence            34456668999999999999999999999874

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

>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length

Probab=95.99  E-value=0.0066  Score=42.91  Aligned_cols=24  Identities=17%  Similarity=0.195  Sum_probs=21.7

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCC
Q psy6501          46 WSQKDLATKINEKPQIVNDYEGGR   69 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~G~   69 (174)
                      ||++|||+.+|+|++||++|-+-.
T Consensus         1 MT~eELA~~tG~srQTINrWvRke   24 (122)
T PF07037_consen    1 MTPEELAELTGYSRQTINRWVRKE   24 (122)
T ss_pred             CCHHHHHHHhCccHHHHHHHHHhc
Confidence            799999999999999999997543

The function of this family is unknown.

>PF04814 HNF-1_N: Hepatocyte nuclear factor 1 (HNF-1), N terminus; InterPro: IPR006899 This domain consists of the N terminus of homeobox-containing transcription factor HNF-1

Probab=95.98  E-value=0.013  Score=44.53  Aligned_cols=38  Identities=11%  Similarity=0.059  Sum_probs=31.5

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      ...+.+-||.+...++++|.++++..|||+++||.|-+
T Consensus       116 ~~~VkeeIK~fl~~h~IsQ~~V~q~TGisQS~lSq~L~  153 (180)
T PF04814_consen  116 PWRVKEEIKAFLQQHNISQREVVQVTGISQSHLSQHLN  153 (180)
T ss_dssp             HHHHHHHHHHHHHHCT--CHHHHHHHT--HHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHcCCcHHHHHHHhhhhHHHHHHHHH
Confidence            35689999999999999999999999999999999974

This region contains a dimerisation sequence [] and an acidic region that may be involved in transcription activation. Mutations and the common Ala/Val 98 polymorphism in HNF-1 cause the type 3 form of maturity-onset diabetes of the young (MODY3) [].; GO: 0045893 positive regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2GYP_B 1IC8_B 2H8R_B 1G2Y_D 1F93_H 1G39_D 1G2Z_B 1JB6_B.

>PRK01381 Trp operon repressor; Provisional

Probab=95.97  E-value=0.021  Score=39.23  Aligned_cols=56  Identities=9%  Similarity=-0.002  Sum_probs=43.7

Q ss_pred             HHHHHHHHHHHH--HcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCc
Q psy6501          31 LDLAKLLMQGRQ--AKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGI   86 (174)
Q Consensus        31 ~~ig~~ik~~R~--~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v   86 (174)
                      ..++.|++-.+.  .-++||.|+|+.+|||.+||++--|--..-+.+...-|...|+-
T Consensus        39 ~al~~R~~I~~~L~~g~~sQREIa~~lGvSiaTITRgsn~Lk~~~~~~k~~l~~~l~~   96 (99)
T PRK01381         39 EALGTRVRIVEELLRGELSQREIKQELGVGIATITRGSNSLKTAPPEFKEWLEQQLLK   96 (99)
T ss_pred             HHHHHHHHHHHHHHcCCcCHHHHHHHhCCceeeehhhHHHhccCCHHHHHHHHHHhcc
Confidence            468889988885  34599999999999999999988776655556666666666543

>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID

Probab=95.94  E-value=0.083  Score=34.95  Aligned_cols=49  Identities=10%  Similarity=-0.004  Sum_probs=40.6

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhC
Q psy6501          36 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGR-GIPNQAIIGKMERALG   85 (174)
Q Consensus        36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~-~~P~~~~l~~la~~L~   85 (174)
                      -+..+++ ..+|.+++|+.+|||.+|||+.-++. ...+.++-.++-++..
T Consensus        11 I~e~l~~-~~~ti~dvA~~~gvS~~TVsr~L~~~~~~Vs~~Tr~rV~~aa~   60 (80)
T TIGR02844        11 IGKYIVE-TKATVRETAKVFGVSKSTVHKDVTERLPEINPELAEEVKEVLD   60 (80)
T ss_pred             HHHHHHH-CCCCHHHHHHHhCCCHHHHHHHhcCCCCCCCHHHHHHHHHHHc
Confidence            3445556 88999999999999999999999986 6778888888777766

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.

>COG4197 Uncharacterized protein conserved in bacteria, prophage-related [Function unknown]

Probab=95.90  E-value=0.0068  Score=40.89  Aligned_cols=46  Identities=26%  Similarity=0.230  Sum_probs=42.1

Q ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhC--ccccccc
Q psy6501          47 SQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALG--IRLRVNA   92 (174)
Q Consensus        47 tq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~--v~~~~l~   92 (174)
                      .|+.||..+|||+++|++|-+|.+....+....|+++-+  |+..+|-
T Consensus        14 ~q~a~a~LLgvsp~~vnQw~~g~r~~~a~r~~aIerAt~g~Vs~~elr   61 (96)
T COG4197          14 GQKALARLLGVSPPSVNQWIKGRRQVAAERALAIERATSGQVSREELR   61 (96)
T ss_pred             cHHHHHHHHccCchHHHHHhhheeecCcccchHHHHHhcCCccHHHHc
Confidence            689999999999999999999999999999999999988  8777664

>smart00354 HTH_LACI helix_turn _helix lactose operon repressor

Probab=95.89  E-value=0.021  Score=36.52  Aligned_cols=38  Identities=21%  Similarity=0.130  Sum_probs=33.0

Q ss_pred             CCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhh
Q psy6501         136 WSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERA  173 (174)
Q Consensus       136 lsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~  173 (174)
                      .++.|+|+.+|++.++|+++.+|....++....+|.++
T Consensus         1 ~t~~~iA~~~gvS~~TVSr~ln~~~~v~~~t~~~i~~~   38 (70)
T smart00354        1 ATIKDVARLAGVSKATVSRVLNGNGRVSEETREKVLAA   38 (70)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHH
Confidence            36889999999999999999999888888887777654

>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []

Probab=95.82  E-value=0.011  Score=36.61  Aligned_cols=27  Identities=22%  Similarity=0.471  Sum_probs=24.1

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHcCC
Q psy6501          43 AKGWSQKDLATKINEKPQIVNDYEGGR   69 (174)
Q Consensus        43 ~~gltq~eLA~~igvs~~~is~~E~G~   69 (174)
                      -.|++++++|+.+|++.+||.+|-.-.
T Consensus        11 ~~G~~~~eIA~~Lg~~~~TV~~W~~r~   37 (58)
T PF06056_consen   11 LQGWSIKEIAEELGVPRSTVYSWKDRY   37 (58)
T ss_pred             HcCCCHHHHHHHHCCChHHHHHHHHhh
Confidence            469999999999999999999997544

Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly

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

Probab=95.79  E-value=0.017  Score=33.39  Aligned_cols=27  Identities=11%  Similarity=0.206  Sum_probs=23.2

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCC
Q psy6501          46 WSQKDLATKINEKPQIVNDYEGGRGIP   72 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~G~~~P   72 (174)
                      +|..|+|+.+|||++||.+|++-...|
T Consensus         1 ~s~~e~a~~lgvs~~tl~~~~~~g~~~   27 (49)
T cd04762           1 LTTKEAAELLGVSPSTLRRWVKEGKLK   27 (49)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHcCCCC
Confidence            588999999999999999998655444

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

>PF05269 Phage_CII: Bacteriophage CII protein; InterPro: IPR007933 The CII protein is a transcription activator, conserved in bacteriophage lambda and related phages, that plays a key role in the decision between lytic or lysogenic phage development

Probab=95.77  E-value=0.0038  Score=42.28  Aligned_cols=45  Identities=11%  Similarity=0.130  Sum_probs=32.2

Q ss_pred             HHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccc
Q psy6501          40 GRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRL   88 (174)
Q Consensus        40 ~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~   88 (174)
                      ++.-..++|+.+|+.+|++.++||+|-++    -...+..|..+|++.+
T Consensus        18 L~rlA~~gq~~vA~~~Gv~eStISR~k~~----~~~~~a~lLa~L~~~v   62 (91)
T PF05269_consen   18 LNRLASVGQKKVAEAMGVDESTISRWKND----FIEKMAMLLAALELGV   62 (91)
T ss_dssp             HHHHHHHHHHHHHHHHTSSTTTHHHHHHH----HHHHHHHHHHHTTTTH
T ss_pred             HHHHHHHhhHHHHHHhCCCHHHHHHHHhh----HHHHHHHHHHHHHhcc
Confidence            34455679999999999999999999653    2345555555555543

CII is regulated at multiple levels including transcription, translation initiation, mRNA stability, and proteolysis []. Conditions that stabilise cII favour lysogenic development. The lambda CII protein activates three specific promoters, binding to direct repeat sequences rather than the more usual inverted repeats. Structurally, CII is a homotetramer where each monomer is composed of four alpha helices and a disordered C terminus [, ]. The alpha helical region is responsible for DNA binding and multimerisation. The homotetramer has an unusual spatial arrangement that allows recognition of the direct repeat sequences.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1ZS4_C 1ZPQ_C 1XWR_A.

>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]

Probab=95.71  E-value=0.19  Score=40.34  Aligned_cols=122  Identities=15%  Similarity=0.150  Sum_probs=72.6

Q ss_pred             hHHHHHHHHHHHHHc--CC--CHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhCccccccc------------
Q psy6501          30 PLDLAKLLMQGRQAK--GW--SQKDLATKINEKPQIVNDYEGGR-GIPNQAIIGKMERALGIRLRVNA------------   92 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~--gl--tq~eLA~~igvs~~~is~~E~G~-~~P~~~~l~~la~~L~v~~~~l~------------   92 (174)
                      ....|.-+..+|+.-  .+  +..+.+.++.   ..+..++.-. +.|+..   .||+.||++.++..            
T Consensus        83 ~~I~Gei~d~LR~~~~v~vpR~~~~~~~~i~---~~~~~l~~el~r~pt~~---EIA~~L~i~~ee~~~~~~~~~~~~~~  156 (247)
T COG1191          83 RRIRGEILDYLRKNDSVKVPRSLRELGRRIE---EAIDELEQELGREPTDE---EIAEELGIDKEEYIEALLAINGSQLL  156 (247)
T ss_pred             HHHHHHHHHHHHhCCCccCcHHHHHHHHHHH---HHHHHHHHHhCCCCcHH---HHHHHhCCCHHHHHHHHHHhcccccc
Confidence            355788888898877  44  4566777775   4444444333 667766   58999999977332            


Q ss_pred             CCCCCCC--CCcc----c----chhhhhhh--h-hhcccccHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501          93 GTNKQPG--TTKN----T----AKLDRETE--E-LKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus        93 ~~~~~~~--~~~~----~----~~l~~~~~--~-~~~~~~~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      .-.....  ....    .    ..+.....  . ........+-.+.+-..|-..++|++++|+.+|+|.+.|+++++
T Consensus       157 sld~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~ai~~L~EREk~Vl~l~y~eelt~kEI~~~LgISes~VSql~k  234 (247)
T COG1191         157 SLDEDVLKDDDDDVDDQIENPDDGVEKEELLEILKEAIEPLPEREKLVLVLRYKEELTQKEIAEVLGISESRVSRLHK  234 (247)
T ss_pred             chhhhhccccccchhhccccchhHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHhccCHHHHHHHhCccHHHHHHHHH
Confidence            0000000  0000    0    00000000  0 00011234456677788888999999999999999999999886

>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]

Probab=95.71  E-value=0.0092  Score=42.63  Aligned_cols=50  Identities=14%  Similarity=0.112  Sum_probs=37.0

Q ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHH---HHHHHHhCccccccc
Q psy6501          42 QAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAII---GKMERALGIRLRVNA   92 (174)
Q Consensus        42 ~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l---~~la~~L~v~~~~l~   92 (174)
                      .++||||+|+|+.+|.++..||-+|+--. -+++..   ..|.+.++-++....
T Consensus        20 RekG~tQ~eIA~~L~TTraNvSaIEkrA~-enIekarnTL~l~~~i~spv~i~v   72 (143)
T COG1356          20 REKGLTQSEIARILKTTRANVSAIEKRAL-ENIEKARNTLLLWEQINSPVSITV   72 (143)
T ss_pred             hhccccHHHHHHHHccchhhHHHHHHHHH-HHHHHHHHHHHHHHHhCCCeEEEe
Confidence            46899999999999999999999996321 233322   357777777776665

>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD

Probab=95.70  E-value=0.023  Score=38.29  Aligned_cols=28  Identities=7%  Similarity=0.123  Sum_probs=25.3

Q ss_pred             HHHcCCCHHHHHHHhCCCHHHHHHHHcC
Q psy6501          41 RQAKGWSQKDLATKINEKPQIVNDYEGG   68 (174)
Q Consensus        41 R~~~gltq~eLA~~igvs~~~is~~E~G   68 (174)
                      ....|+|..++|+.+|+|++||++|-+|
T Consensus        46 ll~~G~S~~eIA~~LgISrsTIyRi~R~   73 (88)
T TIGR02531        46 MLKQGKTYSDIEAETGASTATISRVKRC   73 (88)
T ss_pred             HHHCCCCHHHHHHHHCcCHHHHHHHHHh
Confidence            3567999999999999999999999875

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.

>PF08523 MBF1: Multiprotein bridging factor 1; InterPro: IPR013729 This domain is found in the multiprotein bridging factor 1 (MBF1) which forms a heterodimer with MBF2

Probab=95.70  E-value=0.0029  Score=40.91  Aligned_cols=29  Identities=76%  Similarity=0.982  Sum_probs=0.8

Q ss_pred             CCCCCC-CCCCCccccccccchhhcccccc
Q psy6501           1 NAGTNK-QPGTTKNTAKLDRETEELKHEKV   29 (174)
Q Consensus         1 ~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~   29 (174)
                      .+|+|+ +.+...++.+|||+||+++|+.+
T Consensus        42 ~~g~Nk~~~~~~~n~~KLD~etE~~~~~kV   71 (71)
T PF08523_consen   42 GAGNNKHQHGEGQNAAKLDRETEELKHEKV   71 (71)
T ss_dssp             ---------------------------S--
T ss_pred             eccccccCCCcccccccccccccccCCCCC
Confidence            378999 89999999999999999998764

It has been shown to make direct contact with the TATA-box binding protein (TBP) and interacts with Ftz-F1, stabilising the Ftz-F1-DNA complex []. It is also found in the endothelial differentiation-related factor (EDF-1). Human EDF-1 is involved in the repression of endothelial differentiation, interacts with CaM and is phosphorylated by PKC []. The domain is found in a wide range of eukaryotic proteins including metazoans, fungi and plants. A helix-turn-helix motif (IPR001387 from INTERPRO) is found to its C terminus. ; PDB: 1X57_A.

>PRK10014 DNA-binding transcriptional repressor MalI; Provisional

Probab=95.65  E-value=0.031  Score=45.74  Aligned_cols=45  Identities=18%  Similarity=0.113  Sum_probs=38.8

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHH---HHHhCcccc
Q psy6501          45 GWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKM---ERALGIRLR   89 (174)
Q Consensus        45 gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~l---a~~L~v~~~   89 (174)
                      ..|.+|+|+++|||.+|||+.-||+...+.++-.++   ++.||..+.
T Consensus         6 ~~Ti~dIA~~agVS~~TVSr~Ln~~~~vs~~tr~~V~~~a~elgY~p~   53 (342)
T PRK10014          6 KITIHDVALAAGVSVSTVSLVLSGKGRISTATGERVNQAIEELGFVRN   53 (342)
T ss_pred             CCcHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCCcC
Confidence            579999999999999999999999987888777665   777887664

>PF13551 HTH_29: Winged helix-turn helix

Probab=95.64  E-value=0.18  Score=34.51  Aligned_cols=27  Identities=15%  Similarity=0.213  Sum_probs=23.6

Q ss_pred             HHcCC-CHHHHHHHhCCCHHHHHHHHcC
Q psy6501          42 QAKGW-SQKDLATKINEKPQIVNDYEGG   68 (174)
Q Consensus        42 ~~~gl-tq~eLA~~igvs~~~is~~E~G   68 (174)
                      ...|+ |..++|+.+|+|++||.+|-+.
T Consensus         8 ~~~g~~~~~~ia~~lg~s~~Tv~r~~~~   35 (112)
T PF13551_consen    8 LAEGVSTIAEIARRLGISRRTVYRWLKR   35 (112)
T ss_pred             HHcCCCcHHHHHHHHCcCHHHHHHHHHH
Confidence            56788 5999999999999999999754

>PHA00675 hypothetical protein

Probab=95.55  E-value=0.043  Score=35.79  Aligned_cols=43  Identities=14%  Similarity=0.054  Sum_probs=36.8

Q ss_pred             cccHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCC
Q psy6501         118 KVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRG  160 (174)
Q Consensus       118 ~~~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~  160 (174)
                      .+.....+.|+..++..|.|..++|+++|+++++|+.+-+|++
T Consensus        22 KLt~~qV~~IR~l~~r~G~s~~~IA~~fGVsrstV~~I~~gk~   64 (78)
T PHA00675         22 KLTDAEVERIRELHEVEGMSYAVLAEKFEQSKGAIAKICRYER   64 (78)
T ss_pred             ccCHHHHHHHHHHHHhcCccHHHHHHHhCCCHHHHHHHHccch
Confidence            3445556788888888999999999999999999999999875

>COG4800 Predicted transcriptional regulator with an HTH domain [Transcription]

Probab=95.50  E-value=0.064  Score=39.06  Aligned_cols=51  Identities=14%  Similarity=0.184  Sum_probs=42.9

Q ss_pred             HHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhh
Q psy6501         122 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERA  173 (174)
Q Consensus       122 ~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~  173 (174)
                      .++.-+...-.+.|++..+||++.|+++|++..+-+| +-|..+.+.+|-+.
T Consensus        16 ~F~~~l~~~l~Elglt~~eFak~anIP~StLYKil~G-~dpr~~tl~~I~kt   66 (170)
T COG4800          16 DFGSCLQKLLDELGLTPSEFAKRANIPLSTLYKILKG-SDPRYDTLTRIFKT   66 (170)
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHcCCCHHHHHHHHhC-CCccHHHHHHHHHH
Confidence            3445555556679999999999999999999999999 88999999888653

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

Probab=95.49  E-value=0.023  Score=38.73  Aligned_cols=54  Identities=15%  Similarity=0.045  Sum_probs=42.6

Q ss_pred             ccccccccchhhcccccchHHHHHHHHHH-H-------HHcCCCHHHHHHHhCCCHHHHHHH
Q psy6501          12 KNTAKLDRETEELKHEKVPLDLAKLLMQG-R-------QAKGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        12 ~~~~~~~~~~~~~~~~~~~~~ig~~ik~~-R-------~~~gltq~eLA~~igvs~~~is~~   65 (174)
                      -|++-.++..+.+....+.......|-.+ |       ....+||.|||+.+|+++.+|++.
T Consensus         6 g~t~~~~~~~e~l~~~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr~   67 (95)
T TIGR01610         6 GYTRMANELQEALPGADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSDA   67 (95)
T ss_pred             chhhhhHHHHHHHHhCCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHHH
Confidence            36677777778888777777777766643 3       577899999999999999999884

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

>PRK09492 treR trehalose repressor; Provisional

Probab=95.49  E-value=0.029  Score=45.39  Aligned_cols=45  Identities=11%  Similarity=0.018  Sum_probs=37.2

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHH---HHHHhCcccc
Q psy6501          45 GWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGK---MERALGIRLR   89 (174)
Q Consensus        45 gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~---la~~L~v~~~   89 (174)
                      .+|.+|+|+++|||.+|||+.-||....+.++-.+   .++.||..+.
T Consensus         4 ~~ti~dIA~~agVS~~TVSrvLn~~~~vs~~tr~rV~~~a~elgY~pn   51 (315)
T PRK09492          4 KLTIKDIARLSGVGKSTVSRVLNNESGVSEETRERVEAVINQHGFSPS   51 (315)
T ss_pred             CCcHHHHHHHhCCCHHHHhHHhCCCCCCCHHHHHHHHHHHHHHCCCcC
Confidence            47999999999999999999999987777766554   5777886554

>PRK11303 DNA-binding transcriptional regulator FruR; Provisional

Probab=95.45  E-value=0.034  Score=45.28  Aligned_cols=44  Identities=7%  Similarity=0.031  Sum_probs=35.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCC---CCCHHHHH---HHHHHhCcccc
Q psy6501          46 WSQKDLATKINEKPQIVNDYEGGRG---IPNQAIIG---KMERALGIRLR   89 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~G~~---~P~~~~l~---~la~~L~v~~~   89 (174)
                      ||.+|+|+.+|||.+|||+.-||..   ..+.++-.   +.|+.||-.+.
T Consensus         1 ~ti~dIA~~aGVS~~TVSrvLn~~~~~~~Vs~~tr~rV~~~a~elgY~pn   50 (328)
T PRK11303          1 MKLDEIARLAGVSRTTASYVINGKAKQYRVSDKTVEKVMAVVREHNYHPN   50 (328)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCCcCHHHHHHHHHHHHHhCCCCC
Confidence            5899999999999999999999985   46665554   55777886554

>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []

Probab=95.38  E-value=0.037  Score=32.47  Aligned_cols=38  Identities=21%  Similarity=0.192  Sum_probs=29.4

Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCC
Q psy6501          32 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRG   70 (174)
Q Consensus        32 ~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~   70 (174)
                      .+-..|..++... +|+.+.|+..||+++||+++-+|..
T Consensus         4 ~l~~Ai~~v~~g~-~S~r~AA~~ygVp~sTL~~r~~g~~   41 (45)
T PF05225_consen    4 DLQKAIEAVKNGK-MSIRKAAKKYGVPRSTLRRRLRGKP   41 (45)
T ss_dssp             HHHHHHHHHHTTS-S-HHHHHHHHT--HHHHHHHHHHTT
T ss_pred             HHHHHHHHHHhCC-CCHHHHHHHHCcCHHHHHHHHcCCC
Confidence            4667788888555 9999999999999999999988764

In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.

>PRK05932 RNA polymerase factor sigma-54; Reviewed

Probab=95.37  E-value=0.011  Score=51.27  Aligned_cols=103  Identities=16%  Similarity=0.182  Sum_probs=64.0

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccCCCCCCCCCcccchhhhhhhhhhcccccHHH
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGTNKQPGTTKNTAKLDRETEELKHEKVPLDL  123 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~  123 (174)
                      +-||++++|+.+|+..||||+.-+|+..-++.-+        +++.+||........+          .......+...+
T Consensus       342 kPLtlkdvAe~lglheSTVSRav~~Kyv~tp~Gi--------~~lk~FFs~~~~~~~g----------~~~S~~~Ik~~I  403 (455)
T PRK05932        342 KPLVLKDIAEELGMHESTISRATTNKYMATPRGI--------FELKYFFSSAVSTDGG----------GEASSTAIRALI  403 (455)
T ss_pred             cCccHHHHHHHhCCCccchhhhhcCceeecCCce--------EEHHHhcccccCCCCC----------ccccHHHHHHHH
Confidence            5579999999999999999999999954333333        3444555322110000          001111222334


Q ss_pred             HHHHHHHHHhcCCCHHHHHHHh-----CCChhHHHHHhcCCCCCCH
Q psy6501         124 AKLLMQGRQAKGWSQKDLATKI-----NEKPQIVNDYEGGRGIPNQ  164 (174)
Q Consensus       124 ~~~i~~~R~~~glsq~ela~~l-----g~~~s~i~~~E~G~~~P~~  164 (174)
                      ..+|...-..+-+|-.++++.+     .+++-||++|=..-..|+-
T Consensus       404 k~lI~~Ed~~~PlSD~~I~~~L~~~Gi~IaRRTVaKYRe~L~Ip~s  449 (455)
T PRK05932        404 KKLIAAENPKKPLSDSKIAELLKEQGIDVARRTVAKYREALNIPSS  449 (455)
T ss_pred             HHHHHhcCCCCCCCHHHHHHHHHHcCCCeehHHHHHHHHHcCCCCh
Confidence            4555444444569999999888     6777799999777666664

>TIGR02405 trehalos_R_Ecol trehalose operon repressor, proteobacterial

Probab=95.37  E-value=0.039  Score=44.79  Aligned_cols=45  Identities=11%  Similarity=-0.017  Sum_probs=35.9

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH---HHHHHhCccccc
Q psy6501          46 WSQKDLATKINEKPQIVNDYEGGRGIPNQAIIG---KMERALGIRLRV   90 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~---~la~~L~v~~~~   90 (174)
                      .|.+|+|+.+|||++|||++-||....+.++-.   +.++.||..+..
T Consensus         2 ~ti~dIA~~agVS~sTVSr~Ln~~~~vs~~tr~rV~~~a~~lgY~pn~   49 (311)
T TIGR02405         2 LTIKDIARLAGVGKSTVSRVLNNEPKVSIETRERVEQVIQQSGFVPSK   49 (311)
T ss_pred             CcHHHHHHHhCCCHHHHHHHhCCCCCCCHHHHHHHHHHHHHHCCCcCH
Confidence            589999999999999999999998666665544   456777776543

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

>TIGR03879 near_KaiC_dom probable regulatory domain

Probab=95.33  E-value=0.093  Score=34.10  Aligned_cols=44  Identities=16%  Similarity=0.200  Sum_probs=32.8

Q ss_pred             HHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHH
Q psy6501         125 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKM  170 (174)
Q Consensus       125 ~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i  170 (174)
                      ....-.|...|+|++++|+.+|+++++|..+.++  .+....+.++
T Consensus        22 ~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~--~~~~~~~~~~   65 (73)
T TIGR03879        22 AAAALAREEAGKTASEIAEELGRTEQTVRNHLKG--ETKAGGLVKL   65 (73)
T ss_pred             HHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc--CcccchHHHH
Confidence            3333336679999999999999999999999994  3444444444

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

>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function

Probab=95.32  E-value=0.057  Score=37.67  Aligned_cols=38  Identities=18%  Similarity=0.144  Sum_probs=30.2

Q ss_pred             HHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHh
Q psy6501          40 GRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL   84 (174)
Q Consensus        40 ~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L   84 (174)
                      |-.-.||||+|-|+.+|||++|+.++-+       .--.+||++|
T Consensus        52 L~D~egl~QeeaA~~MgVSR~T~~ril~-------~ARkKiA~AL   89 (106)
T PF02001_consen   52 LVDYEGLSQEEAAERMGVSRPTFQRILE-------SARKKIADAL   89 (106)
T ss_pred             HHHHcCCCHHHHHHHcCCcHHHHHHHHH-------HHHHHHHHHH
Confidence            3456899999999999999999999875       2334677665

>PF02376 CUT: CUT domain; InterPro: IPR003350 A class, also called ONECUT, of homeodomain proteins

Probab=95.31  E-value=0.05  Score=36.58  Aligned_cols=38  Identities=18%  Similarity=0.223  Sum_probs=32.5

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHHc
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATKI-NEKPQIVNDYEG   67 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~i-gvs~~~is~~E~   67 (174)
                      ...|..+|+...+..++||+.||+.+ |.|+.++|.+-+
T Consensus        11 T~~I~~~ik~~L~~~~IsQ~~Fa~~vL~rsqgtlsdlL~   49 (87)
T PF02376_consen   11 TKEIARRIKEWLKRNNISQRVFAKKVLNRSQGTLSDLLR   49 (87)
T ss_dssp             HHHHHHHHHHHHHHTT--HHHHHHHTTSS-HHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHhccChhHHHHHhC
Confidence            56899999999999999999999976 999999999987

The CUT domain is a DNA-binding motif which can bind independently or in cooperation with the homeodomain (IPR001356 from INTERPRO), often found downstream of the CUT domain. Proteins display two modes of DNA binding, which hinge on the homeodomain and on the linker that separates it from the cut domain, and two modes of transcriptional stimulation, which hinge on the homeodomain [].; GO: 0003677 DNA binding; PDB: 1WH6_A 2D5V_A 2CSF_A 1X2L_A 2O49_A 2O4A_A 1YSE_A 1S7E_A 1WIZ_A 1WH8_A.

>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor

Probab=95.30  E-value=0.012  Score=50.81  Aligned_cols=103  Identities=14%  Similarity=0.206  Sum_probs=64.4

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccCCCCCCCCCcccchhhhhhhhhhcccccHHH
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGTNKQPGTTKNTAKLDRETEELKHEKVPLDL  123 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~  123 (174)
                      +-||++++|+.+|++.||||+.-+|+..-++.-+        +++.+||..........         .......+...+
T Consensus       317 kPLtlkdiA~~lglheSTVSRav~~Kyi~tp~Gi--------~~lk~FFs~~~~~~~~g---------~~~S~~~Ik~~I  379 (429)
T TIGR02395       317 KPLTLREVAEELGLHESTISRAINNKYLQTPRGV--------FELKYFFSRGVQTDSGE---------GEVSSTAIKALI  379 (429)
T ss_pred             cCCcHHHHHHHhCCCccchhhhhcCceEecCCce--------EEHHHhcCCccCCCCCC---------CccCHHHHHHHH
Confidence            4589999999999999999999999954333333        24445553221100000         001111233444


Q ss_pred             HHHHHHHHHhcCCCHHHHHHHh-----CCChhHHHHHhcCCCCCC
Q psy6501         124 AKLLMQGRQAKGWSQKDLATKI-----NEKPQIVNDYEGGRGIPN  163 (174)
Q Consensus       124 ~~~i~~~R~~~glsq~ela~~l-----g~~~s~i~~~E~G~~~P~  163 (174)
                      .++|...-..+=+|-.++++.+     .+++-||++|=..-..|+
T Consensus       380 ~~lI~~E~~~~PlSD~~I~~~L~~~Gi~IaRRTVaKYRe~L~Ip~  424 (429)
T TIGR02395       380 KELIAAEDKRKPLSDQKIAELLKEKGIKIARRTVAKYREELGIPS  424 (429)
T ss_pred             HHHHHhcCCCCCCCHHHHHHHHHhcCCCeehHHHHHHHHHcCCCc
Confidence            5556555555569999999888     777779999976666665

A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations

>PRK09526 lacI lac repressor; Reviewed

Probab=95.29  E-value=0.028  Score=45.98  Aligned_cols=47  Identities=13%  Similarity=-0.096  Sum_probs=37.2

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHH---HHHHHHhCccccc
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYEGGRGIPNQAII---GKMERALGIRLRV   90 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l---~~la~~L~v~~~~   90 (174)
                      +..|.+|+|+++|||.+|||+.-||....+.++-   .++++.||..+..
T Consensus         4 ~~~ti~dIA~~aGVS~~TVSrvLn~~~~vs~~tr~rV~~~a~elgY~pn~   53 (342)
T PRK09526          4 KPVTLYDVARYAGVSYQTVSRVLNQASHVSAKTREKVEAAMAELNYVPNR   53 (342)
T ss_pred             CCCcHHHHHHHhCCCHHHHHHHhcCCCCCCHHHHHHHHHHHHHHCCCcCH
Confidence            3469999999999999999999999876666554   4566677776543

>PRK08558 adenine phosphoribosyltransferase; Provisional

Probab=95.26  E-value=0.074  Score=42.36  Aligned_cols=53  Identities=15%  Similarity=0.296  Sum_probs=41.8

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcc
Q psy6501          33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIR   87 (174)
Q Consensus        33 ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~   87 (174)
                      .-.-||.+.+-  +|.+||++.+|++.+.+++|-||+..|+.+....|.+.|.-.
T Consensus        13 ~v~~lr~lk~~--~ty~el~~~~g~p~~~l~RYv~g~~~P~~~~a~~~~~~l~~~   65 (238)
T PRK08558         13 AVRVLRSLKKT--YTYEELSSITGLPESVLNRYVNGHVLPSVERAREIVEKLGPY   65 (238)
T ss_pred             HHHHHHHHhcc--cCHHHHHHHHCCCHHHHHHHHcCCcCCCHHHHHHHHHHHHHh
Confidence            34455555544  599999999999999999999999999999777666654433

>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere

Probab=95.24  E-value=0.018  Score=34.95  Aligned_cols=28  Identities=18%  Similarity=0.244  Sum_probs=22.1

Q ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHHcCC
Q psy6501          42 QAKGWSQKDLATKINEKPQIVNDYEGGR   69 (174)
Q Consensus        42 ~~~gltq~eLA~~igvs~~~is~~E~G~   69 (174)
                      .+.|.++.++|+..||+++||++|-+.+
T Consensus        19 ~e~g~s~~~ia~~fgv~~sTv~~I~K~k   46 (53)
T PF04218_consen   19 LEEGESKRDIAREFGVSRSTVSTILKNK   46 (53)
T ss_dssp             HHCTT-HHHHHHHHT--CCHHHHHHHCH
T ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHHHhH
Confidence            4788899999999999999999997654

Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.

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

Probab=95.22  E-value=0.062  Score=36.14  Aligned_cols=36  Identities=14%  Similarity=0.134  Sum_probs=31.0

Q ss_pred             HHHHHHHHHHH--HHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          31 LDLAKLLMQGR--QAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        31 ~~ig~~ik~~R--~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ..+++|++-++  -..|+||.|+|+.+|+|-.||++.=
T Consensus        33 ~~l~~R~~va~~lL~~g~syreIa~~tgvS~aTItRvs   70 (87)
T PF01371_consen   33 EALAQRWQVAKELLDEGKSYREIAEETGVSIATITRVS   70 (87)
T ss_dssp             HHHHHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHH
Confidence            36888888887  4589999999999999999999864

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

>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=95.20  E-value=0.024  Score=35.39  Aligned_cols=24  Identities=17%  Similarity=0.291  Sum_probs=22.0

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      -+++..++|+.+|||.+||+.|-+
T Consensus        21 g~i~lkdIA~~Lgvs~~tIr~WK~   44 (60)
T PF10668_consen   21 GKIKLKDIAEKLGVSESTIRKWKS   44 (60)
T ss_pred             CCccHHHHHHHHCCCHHHHHHHhh
Confidence            469999999999999999999964

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 [].

>TIGR01481 ccpA catabolite control protein A

Probab=95.19  E-value=0.044  Score=44.58  Aligned_cols=45  Identities=16%  Similarity=0.068  Sum_probs=37.0

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH---HHHHHhCccccc
Q psy6501          46 WSQKDLATKINEKPQIVNDYEGGRGIPNQAIIG---KMERALGIRLRV   90 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~---~la~~L~v~~~~   90 (174)
                      .|.+|+|+.+|||.+|||+.-||....+.++-.   +.|+.||-.++.
T Consensus         2 ~ti~dIA~~agvS~~TVSrvLn~~~~vs~~tr~rV~~~a~~lgY~pn~   49 (329)
T TIGR01481         2 VTIYDVAREAGVSMATVSRVVNGNPNVKPATRKKVLEVIKRLDYRPNA   49 (329)
T ss_pred             CcHHHHHHHhCCCHHHHHHHhCCCCCCCHHHHHHHHHHHHHHCCCCCH
Confidence            488999999999999999999999777776655   567778876653

Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.

>PRK10703 DNA-binding transcriptional repressor PurR; Provisional

Probab=95.19  E-value=0.045  Score=44.85  Aligned_cols=44  Identities=11%  Similarity=0.036  Sum_probs=35.7

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCcccc
Q psy6501          46 WSQKDLATKINEKPQIVNDYEGGRGIPNQAI---IGKMERALGIRLR   89 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~G~~~P~~~~---l~~la~~L~v~~~   89 (174)
                      .|.+|+|+.+|||.+|||+.-||+...+.++   +.++|+.||-.+.
T Consensus         2 ~Ti~dIA~~agVS~~TVSrvLn~~~~vs~~tr~~V~~~a~elgY~pn   48 (341)
T PRK10703          2 ATIKDVAKRAGVSTTTVSHVINKTRFVAEETRNAVWAAIKELHYSPS   48 (341)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHCCCcC
Confidence            4899999999999999999999986556555   5567777876654

>PRK04217 hypothetical protein; Provisional

Probab=95.16  E-value=0.084  Score=37.08  Aligned_cols=77  Identities=8%  Similarity=-0.056  Sum_probs=53.3

Q ss_pred             CCCCccccccccchhhcccccchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcc
Q psy6501           8 PGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIR   87 (174)
Q Consensus         8 ~~~~~~~~~~~~~~~~~~~~~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~   87 (174)
                      |.|-.|.-+.--.-..+++..+...-- .+-.++...|+|++|+|+.+|+|.+||.++-.       ....+|.+.+...
T Consensus        22 ~~~~~~~~~~~~~~~~~p~~~Lt~eer-eai~l~~~eGlS~~EIAk~LGIS~sTV~r~L~-------RArkkLre~L~~~   93 (110)
T PRK04217         22 PQVRHFYPAIPPVGPPKPPIFMTYEEF-EALRLVDYEGLTQEEAGKRMGVSRGTVWRALT-------SARKKVAQMLVEG   93 (110)
T ss_pred             CCcceEeCCCCCccCCCCcccCCHHHH-HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH-------HHHHHHHHHHHhc
Confidence            444444444444445566666665553 55577888999999999999999999999975       3555677776655


Q ss_pred             ccccc
Q psy6501          88 LRVNA   92 (174)
Q Consensus        88 ~~~l~   92 (174)
                      ....+
T Consensus        94 ~~~~~   98 (110)
T PRK04217         94 RELII   98 (110)
T ss_pred             cceeE
Confidence            55444

>COG2842 Uncharacterized ATPase, putative transposase [General function prediction only]

Probab=95.14  E-value=0.068  Score=43.76  Aligned_cols=62  Identities=21%  Similarity=0.109  Sum_probs=50.9

Q ss_pred             cchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH-HHHHHhCccccc
Q psy6501          28 KVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIG-KMERALGIRLRV   90 (174)
Q Consensus        28 ~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~-~la~~L~v~~~~   90 (174)
                      ++.+..-+.++++-+-.|++|+.+|..+|+|+.+||.|-|| ..+...... +|+..++-....
T Consensus         2 ~~n~~~~k~~k~f~e~~~~~q~~~a~gi~~~~~~vsk~L~g-~~g~~~~~~a~ia~~le~~~~q   64 (297)
T COG2842           2 QINFIEIKKLKEFAEFSGMCQKYLARGIGTSAPALSKYLNG-YKGDYATNEAKIAAFLEKKGVQ   64 (297)
T ss_pred             chhHHHHHHHHHHHHhhhhhHHHHHHHhccCchhHHHHhcC-cCchHHHHHHHHHHHHcCCCcc
Confidence            34566778899999999999999999999999999999999 555555554 888888876443

>PRK13698 plasmid-partitioning protein; Provisional

Probab=95.09  E-value=0.045  Score=45.38  Aligned_cols=43  Identities=12%  Similarity=0.034  Sum_probs=36.4

Q ss_pred             hHHHHHHH-HHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCC
Q psy6501          30 PLDLAKLL-MQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIP   72 (174)
Q Consensus        30 ~~~ig~~i-k~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P   72 (174)
                      ..+.|... +.+....|+||++||+.+|+|+++|++.-+=-..|
T Consensus       160 ~iE~A~ay~~~L~~~~~~tQeeLA~~lG~SRs~Vsn~Lrla~LP  203 (323)
T PRK13698        160 AYERGLRYASRLQNEFAGNISALADAENISRKIITRCINTAKLP  203 (323)
T ss_pred             HHHHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHHHcCC
Confidence            36778887 66888999999999999999999999998655553

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

Probab=95.06  E-value=0.15  Score=42.40  Aligned_cols=64  Identities=9%  Similarity=0.052  Sum_probs=51.2

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH-------------cCCCCCCHHHHHHHHHHhCcccccccC
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE-------------GGRGIPNQAIIGKMERALGIRLRVNAG   93 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E-------------~G~~~P~~~~l~~la~~L~v~~~~l~~   93 (174)
                      ......++..+.-..||||.|+|+++|+|+.+|+++-             +.......+.-.+|.+.||+.-.+...
T Consensus        11 ~~~l~~~~A~lYY~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~GiV~I~i~~~~~~~~~Le~~L~~~fgL~~a~VVp   87 (321)
T COG2390          11 EERLLARAAWLYYVEGLTQSEIAERLGISRATVSRLLAKAREEGIVKISINSPVEGCLELEQQLKERFGLKEAIVVP   87 (321)
T ss_pred             HHHHHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCeEEEEeCCCCcchHHHHHHHHHhcCCCeEEEEc
Confidence            4568889999999999999999999999999999985             222334444557899999998776664

>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA

Probab=95.02  E-value=0.037  Score=34.77  Aligned_cols=22  Identities=14%  Similarity=0.283  Sum_probs=20.7

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q psy6501          46 WSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~   67 (174)
                      +|..|+|+.+|||++||..|++
T Consensus         1 ~s~~eva~~~gvs~~tlr~w~~   22 (68)
T cd01104           1 YTIGAVARLTGVSPDTLRAWER   22 (68)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5789999999999999999996

Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i

>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators

Probab=95.01  E-value=0.068  Score=33.63  Aligned_cols=22  Identities=27%  Similarity=0.513  Sum_probs=20.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q psy6501          46 WSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~   67 (174)
                      +|..|+|+.+|||++||..||.
T Consensus         1 ~~i~evA~~~gvs~~tlR~~~~   22 (67)
T cd04764           1 YTIKEVSEIIGVKPHTLRYYEK   22 (67)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5789999999999999999986

Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.

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

Probab=94.94  E-value=0.034  Score=30.24  Aligned_cols=22  Identities=14%  Similarity=0.167  Sum_probs=17.0

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHH
Q psy6501          45 GWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        45 gltq~eLA~~igvs~~~is~~E   66 (174)
                      .||.+|+|+.+|+++.|||+.-
T Consensus         2 ~mtr~diA~~lG~t~ETVSR~l   23 (32)
T PF00325_consen    2 PMTRQDIADYLGLTRETVSRIL   23 (32)
T ss_dssp             E--HHHHHHHHTS-HHHHHHHH
T ss_pred             CcCHHHHHHHhCCcHHHHHHHH
Confidence            4899999999999999999863

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 ....

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

Probab=94.94  E-value=0.048  Score=31.83  Aligned_cols=27  Identities=19%  Similarity=0.223  Sum_probs=22.9

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCC
Q psy6501          46 WSQKDLATKINEKPQIVNDYEGGRGIP   72 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~G~~~P   72 (174)
                      ||..|+|+.+||++++|..|++-...|
T Consensus         1 ~~~~e~a~~~gv~~~tlr~~~~~g~l~   27 (49)
T cd04761           1 YTIGELAKLTGVSPSTLRYYERIGLLS   27 (49)
T ss_pred             CcHHHHHHHHCcCHHHHHHHHHCCCCC
Confidence            578999999999999999998655444

Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>COG5499 Predicted transcription regulator containing HTH domain [Transcription]

Probab=94.93  E-value=0.075  Score=37.04  Aligned_cols=53  Identities=21%  Similarity=0.229  Sum_probs=46.5

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         121 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       121 ~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ..-.+.|+......|+|+.+++..+| |.+.++++-+|++.-+.+.+.++.+-|
T Consensus        59 P~pve~I~t~Md~~glt~~dLa~~iG-Sks~vS~iL~~rraLTle~ikkL~q~~  111 (120)
T COG5499          59 PDPVEVIRTLMDQYGLTLADLANEIG-SKSRVSNILSGRRALTLEHIKKLHQRF  111 (120)
T ss_pred             CCHHHHHHHHHHHhCCcHHHHHHHhC-chHHHHHHHhhhhHhhHHHHHHHHHHh
Confidence            34457889999999999999999999 578999999999999999999987643

>PRK10727 DNA-binding transcriptional regulator GalR; Provisional

Probab=94.91  E-value=0.055  Score=44.47  Aligned_cols=45  Identities=13%  Similarity=-0.026  Sum_probs=36.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH---HHHHHhCccccc
Q psy6501          46 WSQKDLATKINEKPQIVNDYEGGRGIPNQAIIG---KMERALGIRLRV   90 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~---~la~~L~v~~~~   90 (174)
                      .|.+|+|+.+|||.+|||+.-||....+.++-.   +.|+.||..+..
T Consensus         2 ~ti~dIA~~aGVS~~TVSrvLn~~~~Vs~~tr~rV~~~a~elgY~pn~   49 (343)
T PRK10727          2 ATIKDVARLAGVSVATVSRVINNSPKASEASRLAVHSAMESLSYHPNA   49 (343)
T ss_pred             CCHHHHHHHhCCCHHHHHHHhCCCCCCCHHHHHHHHHHHHHHCCCCCH
Confidence            389999999999999999999999777766555   556677776554

>TIGR01764 excise DNA binding domain, excisionase family

Probab=94.88  E-value=0.046  Score=31.60  Aligned_cols=28  Identities=11%  Similarity=0.102  Sum_probs=24.7

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCC
Q psy6501          46 WSQKDLATKINEKPQIVNDYEGGRGIPN   73 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~G~~~P~   73 (174)
                      ||.+|+|+.+|+|+++|.+|.+-...|.
T Consensus         2 lt~~e~a~~lgis~~ti~~~~~~g~i~~   29 (49)
T TIGR01764         2 LTVEEAAEYLGVSKDTVYRLIHEGELPA   29 (49)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHcCCCCe
Confidence            6889999999999999999997666664

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

>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella

Probab=94.86  E-value=0.13  Score=27.01  Aligned_cols=23  Identities=22%  Similarity=0.335  Sum_probs=21.3

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHH
Q psy6501          43 AKGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        43 ~~gltq~eLA~~igvs~~~is~~   65 (174)
                      ..|+|..++|+.+|+|+++|++|
T Consensus        19 ~~~~s~~~ia~~~~is~~tv~~~   41 (42)
T cd00569          19 AAGESVAEIARRLGVSRSTLYRY   41 (42)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHh
Confidence            46889999999999999999987

The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D

>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets

Probab=94.85  E-value=0.043  Score=33.08  Aligned_cols=31  Identities=16%  Similarity=0.156  Sum_probs=24.2

Q ss_pred             HHHHHHHHcC-CCHHHHHHHhCCCHHHHHHHH
Q psy6501          36 LLMQGRQAKG-WSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        36 ~ik~~R~~~g-ltq~eLA~~igvs~~~is~~E   66 (174)
                      -|+.+.+..+ +|.++||+.+|||+.||.+.-
T Consensus         5 il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i   36 (55)
T PF08279_consen    5 ILKLLLESKEPITAKELAEELGVSRRTIRRDI   36 (55)
T ss_dssp             HHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHH
T ss_pred             HHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHH
Confidence            3555655555 999999999999999998864

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 ....

>PRK10401 DNA-binding transcriptional regulator GalS; Provisional

Probab=94.81  E-value=0.066  Score=44.03  Aligned_cols=44  Identities=16%  Similarity=0.136  Sum_probs=35.2

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH---HHHHHhCcccc
Q psy6501          46 WSQKDLATKINEKPQIVNDYEGGRGIPNQAIIG---KMERALGIRLR   89 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~---~la~~L~v~~~   89 (174)
                      .|.+|+|+++|||.+|||+.-||....+.++-.   +.++.||..+.
T Consensus         2 ~ti~dIA~~aGVS~~TVSrvLn~~~~Vs~~tr~kV~~~a~elgY~pn   48 (346)
T PRK10401          2 ITIRDVARQAGVSVATVSRVLNNSALVSADTREAVMKAVSELGYRPN   48 (346)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCC
Confidence            589999999999999999999998766665554   55666776543

>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator

Probab=94.80  E-value=0.19  Score=34.29  Aligned_cols=24  Identities=13%  Similarity=0.260  Sum_probs=21.2

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCC
Q psy6501          46 WSQKDLATKINEKPQIVNDYEGGR   69 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~G~   69 (174)
                      |+..|+|+.+|||.+||..||+-.
T Consensus         1 ~~I~e~a~~~gvs~~tLR~ye~~G   24 (96)
T cd04774           1 YKVDEVAKRLGLTKRTLKYYEEIG   24 (96)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCC
Confidence            578899999999999999998643

Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.

>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators

Probab=94.79  E-value=0.5  Score=32.37  Aligned_cols=22  Identities=18%  Similarity=0.382  Sum_probs=20.4

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q psy6501          46 WSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~   67 (174)
                      +|..|+|+.+|||.+||..||.
T Consensus         1 yti~EvA~~~gVs~~tLR~ye~   22 (99)
T cd04765           1 FSIGEVAEILGLPPHVLRYWET   22 (99)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5788999999999999999985

Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.

>PRK14987 gluconate operon transcriptional regulator; Provisional

Probab=94.78  E-value=0.049  Score=44.47  Aligned_cols=45  Identities=16%  Similarity=0.109  Sum_probs=36.6

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH---HHHHHhCcccc
Q psy6501          45 GWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIG---KMERALGIRLR   89 (174)
Q Consensus        45 gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~---~la~~L~v~~~   89 (174)
                      ..|.+|+|+.+|||.+|||+.-||....+.++-.   ++++.||-.+.
T Consensus         5 ~~ti~dIA~~agVS~~TVSrvLn~~~~vs~~tr~rV~~~a~elgY~pn   52 (331)
T PRK14987          5 RPVLQDVADRVGVTKMTVSRFLRNPEQVSVALRGKIAAALDELGYIPN   52 (331)
T ss_pred             CCcHHHHHHHhCCCHHHhhhhhCCCCCCCHHHHHHHHHHHHHhCCCcc
Confidence            4699999999999999999999998766766554   56677776554

>PRK12469 RNA polymerase factor sigma-54; Provisional

Probab=94.76  E-value=0.026  Score=49.36  Aligned_cols=104  Identities=14%  Similarity=0.164  Sum_probs=64.2

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccCCCCCCCCCcccchhhhhhhhhhcccccHH
Q psy6501          43 AKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGTNKQPGTTKNTAKLDRETEELKHEKVPLD  122 (174)
Q Consensus        43 ~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~  122 (174)
                      .+=||++++|+.+|+..||||+.-+|+..-++.-+..|-.+|.-.+..--|                  .......+...
T Consensus       367 LkPLtlkdVAe~lglHeSTVSRa~~~KY~~tp~GifeLK~FFs~~v~~~~g------------------~~~Ss~~Ik~~  428 (481)
T PRK12469        367 LKPLVLRDVAEELGLHESTISRATGNKYMATPRGTFEFKHFFPRKLEAAGG------------------GECSAAAVRAL  428 (481)
T ss_pred             CcCCcHHHHHHHhCCCcchhhHHhcCceeecCCceEeHHHhhccccCCCCC------------------ccccHHHHHHH
Confidence            356799999999999999999999999554444444444444433210000                  00011112233


Q ss_pred             HHHHHHHHHHhcCCCHHHHHHHh-----CCChhHHHHHhcCCCCCCH
Q psy6501         123 LAKLLMQGRQAKGWSQKDLATKI-----NEKPQIVNDYEGGRGIPNQ  164 (174)
Q Consensus       123 ~~~~i~~~R~~~glsq~ela~~l-----g~~~s~i~~~E~G~~~P~~  164 (174)
                      +.++|...-..+=+|-.++++.+     .+++-||++|=..-..|+-
T Consensus       429 Ik~lI~~Ed~~kPLSD~~I~~~L~~~GI~IARRTVAKYRe~L~IpsS  475 (481)
T PRK12469        429 IKEMIAAEQAGDPLSDVALAEMLAGRGVLIARRTVAKYREAMKIPPA  475 (481)
T ss_pred             HHHHHHhcCCCCCCCHHHHHHHHHhcCCCeechhHHHHHHHcCCCCh
Confidence            44455444445568999988887     4555699999777666654

>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]

Probab=94.68  E-value=0.096  Score=30.04  Aligned_cols=31  Identities=13%  Similarity=0.085  Sum_probs=26.2

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHH
Q psy6501          34 AKLLMQGRQAKGWSQKDLATKINEKPQIVND   64 (174)
Q Consensus        34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~   64 (174)
                      -..|...-+..+.++.+.|+.+|||++++.+
T Consensus         7 ~~~i~~aL~~~~gn~~~aA~~Lgisr~tL~~   37 (42)
T PF02954_consen    7 KQLIRQALERCGGNVSKAARLLGISRRTLYR   37 (42)
T ss_dssp             HHHHHHHHHHTTT-HHHHHHHHTS-HHHHHH
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHCCCHHHHHH
Confidence            4578889999999999999999999999975

It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....

>TIGR00180 parB_part ParB-like partition proteins

Probab=94.61  E-value=0.084  Score=40.31  Aligned_cols=52  Identities=17%  Similarity=0.142  Sum_probs=39.2

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHH
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMER   82 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~   82 (174)
                      ..+.+..++.+....|+|++++|+.+|+|+++|+++-.=.. .+.+.+..+..
T Consensus       105 ~~e~a~~~~~l~~~~g~s~~~iA~~lg~s~~~V~r~l~l~~-lp~~v~~~~~~  156 (187)
T TIGR00180       105 PIEEAQAYKRLLEKFSMTQEDLAKKIGKSRAHITNLLRLLK-LPSEIQSAIPE  156 (187)
T ss_pred             HHHHHHHHHHHHHHhCCCHHHHHHHHCcCHHHHHHHHHHHc-CCHHHHHHHHh
Confidence            35567777787777999999999999999999999976444 33355555554

This model represents the most well-conserved core of a set of chromosomal and plasmid partition proteins related to ParB, including Spo0J, RepB, and SopB. Spo0J has been shown to bind a specific DNA sequence that, when introduced into a plasmid, can serve as partition site. Study of RepB, which has nicking-closing activity, suggests that it forms a transient protein-DNA covalent intermediate during the strand transfer reaction.

>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor

Probab=94.58  E-value=0.076  Score=43.22  Aligned_cols=44  Identities=14%  Similarity=0.156  Sum_probs=35.6

Q ss_pred             CHHHHHHHhCCCHHHHHHHHcCCC---CCCHHHHH---HHHHHhCccccc
Q psy6501          47 SQKDLATKINEKPQIVNDYEGGRG---IPNQAIIG---KMERALGIRLRV   90 (174)
Q Consensus        47 tq~eLA~~igvs~~~is~~E~G~~---~P~~~~l~---~la~~L~v~~~~   90 (174)
                      |.+|+|+.+|||.+|||+.-||..   ..+.++-.   +.|+.||-.++.
T Consensus         1 ti~dIA~~aGVS~~TVSrvLn~~~~~~~vs~~tr~rV~~~a~~lgY~pn~   50 (327)
T TIGR02417         1 TLSDIAKLAGVSKTTASYVINGKAKEYRISQETVERVMAVVREQGYQPNI   50 (327)
T ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCCCCccCHHHHHHHHHHHHHhCCCCCH
Confidence            678999999999999999999986   46666655   567778877654

Members of this family belong the lacI helix-turn-helix family (pfam00356) of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterized members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer.

>cd04778 HTH_MerR-like_sg2 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily

Probab=94.58  E-value=0.7  Score=36.36  Aligned_cols=24  Identities=21%  Similarity=0.286  Sum_probs=21.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCC
Q psy6501          46 WSQKDLATKINEKPQIVNDYEGGR   69 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~G~   69 (174)
                      ++..|||+.+|||.++|..||+-.
T Consensus         2 y~i~elA~~~Gvs~~tIR~Ye~~G   25 (219)
T cd04778           2 YRIDDLARAAGTTVRNVRAYQDRG   25 (219)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCC
Confidence            688999999999999999999543

Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 2). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>PRK09744 DNA-binding transcriptional regulator DicC; Provisional

Probab=94.52  E-value=0.061  Score=34.83  Aligned_cols=34  Identities=21%  Similarity=0.313  Sum_probs=26.2

Q ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHH
Q psy6501          47 SQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERA   83 (174)
Q Consensus        47 tq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~   83 (174)
                      |...+|+.+|||+++||+|  |...|. ....+|...
T Consensus        12 s~~kvA~aLGIs~~AVsQW--Ge~VPe-~rA~~ie~~   45 (75)
T PRK09744         12 SKTKLANAAGVRLASVAAW--GELVPE-GRAMRLQEA   45 (75)
T ss_pred             cHHHHHHHHCCCHHHHHHH--hccCcH-HHHHHHHHH
Confidence            6788999999999999999  666665 444455544

>COG1342 Predicted DNA-binding proteins [General function prediction only]

Probab=94.51  E-value=0.11  Score=35.39  Aligned_cols=43  Identities=19%  Similarity=0.101  Sum_probs=32.4

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHh
Q psy6501          34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL   84 (174)
Q Consensus        34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L   84 (174)
                      -+.|| +..-.||||+|-|.++|||++|+.+.-+       .--.++|++|
T Consensus        39 lEAlR-LvD~~~l~QeeAA~rMgISr~Tfwr~l~-------sAR~KvA~aL   81 (99)
T COG1342          39 LEALR-LVDYEGLTQEEAALRMGISRQTFWRLLT-------SARKKVADAL   81 (99)
T ss_pred             HHHHH-HHhHhhccHHHHHHHhcccHHHHHHHHH-------HHHHHHHHHH
Confidence            34443 5567899999999999999999998875       2334666664

>COG1609 PurR Transcriptional regulators [Transcription]

Probab=94.49  E-value=0.082  Score=43.93  Aligned_cols=46  Identities=17%  Similarity=0.100  Sum_probs=36.9

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH---HHHHHhCcccccc
Q psy6501          46 WSQKDLATKINEKPQIVNDYEGGRGIPNQAIIG---KMERALGIRLRVN   91 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~---~la~~L~v~~~~l   91 (174)
                      .|.+|+|+.+|||.+|||+..||....+.++-.   +.++.||-.++..
T Consensus         1 ~TikDVA~~AGVS~sTVSrvln~~~~Vs~eTr~kV~~a~~elgY~pN~~   49 (333)
T COG1609           1 ATIKDVAKLAGVSKATVSRVLNGSPYVSEETREKVLAAIKELGYRPNAV   49 (333)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHCCCCCHH
Confidence            378999999999999999999999877776655   5566677765543

>PF12728 HTH_17: Helix-turn-helix domain

Probab=94.48  E-value=0.066  Score=31.77  Aligned_cols=29  Identities=17%  Similarity=0.124  Sum_probs=25.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCH
Q psy6501          46 WSQKDLATKINEKPQIVNDYEGGRGIPNQ   74 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~G~~~P~~   74 (174)
                      ||.+|+|+.+|||.+||.+|-+-...|..
T Consensus         2 lt~~e~a~~l~is~~tv~~~~~~g~i~~~   30 (51)
T PF12728_consen    2 LTVKEAAELLGISRSTVYRWIRQGKIPPF   30 (51)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHcCCCCeE
Confidence            68999999999999999999876666654

>TIGR03764 ICE_PFGI_1_parB integrating conjugative element, PFGI_1 class, ParB family protein

Probab=94.42  E-value=0.091  Score=42.26  Aligned_cols=51  Identities=16%  Similarity=0.162  Sum_probs=33.5

Q ss_pred             HHHHHHHHHHHH---H---cCCCHHHHHHHhCC-----CHHHHHHHHcCCCCCCHHHHHHHH
Q psy6501          31 LDLAKLLMQGRQ---A---KGWSQKDLATKINE-----KPQIVNDYEGGRGIPNQAIIGKME   81 (174)
Q Consensus        31 ~~ig~~ik~~R~---~---~gltq~eLA~~igv-----s~~~is~~E~G~~~P~~~~l~~la   81 (174)
                      .+-+..++.++.   +   .++||+|||+++|-     |+++||++..=-..........|+
T Consensus       116 IE~A~~~~~l~~l~e~~~g~~ltq~ela~~lgk~g~~isrs~Isn~lrll~~L~~~i~~~l~  177 (258)
T TIGR03764       116 IEKALGVQKARALYEKELGESLSQRELARRLSADGYPISQSHISRMGDTVEYLYPAIPNLLY  177 (258)
T ss_pred             HHHHHHHHHHHHHHHhhccCCCCHHHHHHHhcccCCCCCHHHHHHHHHHHHhChHHHHHHHH
Confidence            334555555653   4   68999999999976     999999988433333333333333

Members of this protein family carry the ParB-type nuclease domain and are found in integrating conjugative elements (ICE) in the same class as PFGI-1 of Pseudomonas fluorescens Pf-5.

>COG1513 CynS Cyanate lyase [Inorganic ion transport and metabolism]

Probab=94.37  E-value=0.21  Score=35.96  Aligned_cols=62  Identities=24%  Similarity=0.203  Sum_probs=58.0

Q ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccccccc
Q psy6501          31 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNA   92 (174)
Q Consensus        31 ~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~   92 (174)
                      ..+.+.|-...+.+|+|-++||+.+|.+.-.+...--|....+.+...++++.||++-+.+.
T Consensus         7 ~~l~~~ll~~Kk~kgLsfaDl~~~lG~~ev~vaa~~ygqa~~~~~ear~v~e~L~L~~~~v~   68 (151)
T COG1513           7 LDLADALLLAKKKKGLSFADLADGLGLAEVFVAAALYGQAALPADEARAVGEALDLDEDAIL   68 (151)
T ss_pred             HHHHHHHHHHHHhcCCcHHHHHhhcCccHHHHHHHHHhhccCCHHHHHHHHHHhCCCHHHHH
Confidence            46788899999999999999999999999999999999999999999999999999988775

>PF13518 HTH_28: Helix-turn-helix domain

Probab=94.37  E-value=0.1  Score=30.73  Aligned_cols=24  Identities=17%  Similarity=0.215  Sum_probs=21.9

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      .|.|..++|..+|||+++|.+|-+
T Consensus        11 ~g~s~~~~a~~~gis~~tv~~w~~   34 (52)
T PF13518_consen   11 EGESVREIAREFGISRSTVYRWIK   34 (52)
T ss_pred             cCCCHHHHHHHHCCCHhHHHHHHH
Confidence            477999999999999999999974

>KOG3802|consensus

Probab=94.35  E-value=0.066  Score=45.30  Aligned_cols=54  Identities=19%  Similarity=0.175  Sum_probs=44.4

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHhC------CCHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATKIN------EKPQIVNDYEGGRGIPNQAIIGKMERALG   85 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~ig------vs~~~is~~E~G~~~P~~~~l~~la~~L~   85 (174)
                      ...|++.+|..|-..|+||.|+..++|      .|+.||++||.=  ..|...+.||-=.|+
T Consensus       208 LEqFAK~FKqRRIkLGfTQaDVGlALG~lyGn~FSQTTIcRFEAL--qLSFKNMCKLKPLL~  267 (398)
T KOG3802|consen  208 LEQFAKTFKQRRIKLGFTQADVGLALGALYGNVFSQTTICRFEAL--QLSFKNMCKLKPLLE  267 (398)
T ss_pred             HHHHHHHHHhheeccccchhHHHHHHHhhhCcccchhhhhHhHhh--ccCHHHHhhhHHHHH
Confidence            356999999999999999999999887      689999999963  446677777665554

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

Probab=94.32  E-value=0.062  Score=31.24  Aligned_cols=31  Identities=13%  Similarity=0.162  Sum_probs=19.7

Q ss_pred             HHHHHHHHhcCCCHHHHHHHhCCChhHHHHHh
Q psy6501         125 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYE  156 (174)
Q Consensus       125 ~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E  156 (174)
                      ..|..+. ..|+|+.++|+.+|.+++||+++-
T Consensus        11 ~~I~~l~-~~G~s~~~IA~~lg~s~sTV~rel   41 (44)
T PF13936_consen   11 NQIEALL-EQGMSIREIAKRLGRSRSTVSREL   41 (44)
T ss_dssp             -HHHHHH-CS---HHHHHHHTT--HHHHHHHH
T ss_pred             HHHHHHH-HcCCCHHHHHHHHCcCcHHHHHHH
Confidence            3454443 689999999999999999998763

>PRK15418 transcriptional regulator LsrR; Provisional

Probab=94.31  E-value=0.066  Score=44.43  Aligned_cols=60  Identities=8%  Similarity=0.005  Sum_probs=45.1

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH-----cCC--------CCCCHHHHHHHHHHhCccccccc
Q psy6501          33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE-----GGR--------GIPNQAIIGKMERALGIRLRVNA   92 (174)
Q Consensus        33 ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E-----~G~--------~~P~~~~l~~la~~L~v~~~~l~   92 (174)
                      +--++-.+--..||||+|+|+++|+|+.+||++-     .|-        .....+.-.+|.+.||+.--...
T Consensus        17 l~~~vA~lYY~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~GiV~I~I~~~~~~~~~Le~~L~~~fgLk~~iVv   89 (318)
T PRK15418         17 LVARIAWFYYHDGLTQSEIGERLGLTRLKVSRLLEKGRQSGIIRVQINSRFEGCLELENALRQHFSLQHIRVL   89 (318)
T ss_pred             HHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHcCcEEEEEeCCCccHHHHHHHHHHHhCCCEEEEE
Confidence            4557788888999999999999999999999985     332        12233444588888888765554

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

Probab=94.28  E-value=0.068  Score=32.56  Aligned_cols=32  Identities=22%  Similarity=0.219  Sum_probs=27.5

Q ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          35 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      .-|..+.+.-++|+.+||+.+++++++++++-
T Consensus         7 ~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i   38 (59)
T PF01047_consen    7 RILRILYENGGITQSELAEKLGISRSTVTRII   38 (59)
T ss_dssp             HHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCCChhHHHHHH
Confidence            45677889999999999999999999999874

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 ....

>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities

Probab=94.26  E-value=0.064  Score=30.26  Aligned_cols=25  Identities=16%  Similarity=0.263  Sum_probs=20.5

Q ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCC
Q psy6501          47 SQKDLATKINEKPQIVNDYEGGRGI   71 (174)
Q Consensus        47 tq~eLA~~igvs~~~is~~E~G~~~   71 (174)
                      |..|+|+.+|||.+||..||.-.-.
T Consensus         1 ti~e~A~~~gvs~~tlR~ye~~Gll   25 (38)
T PF00376_consen    1 TIGEVAKLLGVSPRTLRYYEREGLL   25 (38)
T ss_dssp             EHHHHHHHHTS-HHHHHHHHHTTSS
T ss_pred             CHHHHHHHHCCCHHHHHHHHHCCCC
Confidence            4579999999999999999976544

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

>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease

Probab=94.22  E-value=0.07  Score=32.23  Aligned_cols=29  Identities=14%  Similarity=-0.032  Sum_probs=25.0

Q ss_pred             HHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          39 QGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        39 ~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      -.+-+.|.++.+||...|||++|+++|=+
T Consensus        13 L~~LR~~~~~~~La~~FgIs~stvsri~~   41 (53)
T PF13613_consen   13 LMYLRLNLTFQDLAYRFGISQSTVSRIFH   41 (53)
T ss_pred             HHHHHcCCcHhHHhhheeecHHHHHHHHH
Confidence            34566899999999999999999999853

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

Probab=94.20  E-value=0.062  Score=32.70  Aligned_cols=23  Identities=13%  Similarity=0.187  Sum_probs=20.2

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ++.|..|||+.+|||++|++..-
T Consensus        22 R~~tl~elA~~lgis~st~~~~L   44 (53)
T PF04967_consen   22 RRITLEELAEELGISKSTVSEHL   44 (53)
T ss_pred             CcCCHHHHHHHhCCCHHHHHHHH
Confidence            56799999999999999998754

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

>cd00131 PAX Paired Box domain

Probab=94.19  E-value=1.5  Score=31.52  Aligned_cols=35  Identities=9%  Similarity=0.138  Sum_probs=27.7

Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          32 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        32 ~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      +.=.+|-.+- +.|+|+.++|+.+|||+++|++|-+
T Consensus        21 d~R~rIv~~~-~~G~s~~~iA~~~~Vs~~tV~r~i~   55 (128)
T cd00131          21 SIRQRIVELA-QSGIRPCDISRQLRVSHGCVSKILN   55 (128)
T ss_pred             HHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3444555443 4899999999999999999999954

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

Probab=94.12  E-value=0.15  Score=34.18  Aligned_cols=24  Identities=8%  Similarity=0.088  Sum_probs=21.6

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcC
Q psy6501          45 GWSQKDLATKINEKPQIVNDYEGG   68 (174)
Q Consensus        45 gltq~eLA~~igvs~~~is~~E~G   68 (174)
                      ++|..|+|+.+|||.+||..||.-
T Consensus         1 ~~ti~evA~~~gvs~~tLR~ye~~   24 (88)
T cd01105           1 VIGIGEVSKLTGVSPRQLRYWEEK   24 (88)
T ss_pred             CcCHHHHHHHHCcCHHHHHHHHHC
Confidence            478999999999999999999843

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

>KOG1168|consensus

Probab=94.11  E-value=0.029  Score=45.53  Aligned_cols=39  Identities=18%  Similarity=0.201  Sum_probs=34.9

Q ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHh---------CCCHHHHHHHHcCC
Q psy6501          31 LDLAKLLMQGRQAKGWSQKDLATKI---------NEKPQIVNDYEGGR   69 (174)
Q Consensus        31 ~~ig~~ik~~R~~~gltq~eLA~~i---------gvs~~~is~~E~G~   69 (174)
                      +.|++|.|+.|-+.|.||.++++.+         .+|++||.++|.=.
T Consensus       220 EaFAErFKQRRIKLGVTQADVG~ALAnLKiPGVGsLSQSTICRFESLT  267 (385)
T KOG1168|consen  220 EAFAERFKQRRIKLGVTQADVGKALANLKIPGVGSLSQSTICRFESLT  267 (385)
T ss_pred             HHHHHHHHhhhhhhcccHHHHHHHHHhCcCCCcccccccceeeeeeec
Confidence            4899999999999999999999987         47899999999643

>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional

Probab=94.10  E-value=0.059  Score=43.97  Aligned_cols=45  Identities=13%  Similarity=0.068  Sum_probs=35.9

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCC--CCHHH---HHHHHHHhCccccc
Q psy6501          46 WSQKDLATKINEKPQIVNDYEGGRGI--PNQAI---IGKMERALGIRLRV   90 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~G~~~--P~~~~---l~~la~~L~v~~~~   90 (174)
                      .|.+|+|+++|||++|||+.-||+..  .+.++   +.+.++.||..+..
T Consensus         2 ~ti~dIA~~agVS~~TVSrvln~~~~~~vs~~tr~rV~~~a~~lgY~pn~   51 (327)
T PRK10339          2 ATLKDIAIEAGVSLATVSRVLNDDPTLNVKEETKHRILEIAEKLEYKTSS   51 (327)
T ss_pred             CCHHHHHHHhCCCHHhhhhhhcCCCCCCcCHHHHHHHHHHHHHhCCCCch
Confidence            48999999999999999999999852  45444   45668888887664

>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs)

Probab=93.95  E-value=0.15  Score=29.50  Aligned_cols=29  Identities=17%  Similarity=0.106  Sum_probs=24.9

Q ss_pred             HHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          39 QGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        39 ~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      .++-..|+|++++|+.+|+|.++|.+|.+
T Consensus        20 ~~~~~~~~~~~~ia~~~~~s~~~i~~~~~   48 (55)
T cd06171          20 LLRFGEGLSYEEIAEILGISRSTVRQRLH   48 (55)
T ss_pred             HHHHhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            34445899999999999999999999864

A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas

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

Probab=93.94  E-value=0.12  Score=30.48  Aligned_cols=24  Identities=21%  Similarity=0.495  Sum_probs=19.1

Q ss_pred             CCCHHHHHHHhCCChhHHHHHhcC
Q psy6501         135 GWSQKDLATKINEKPQIVNDYEGG  158 (174)
Q Consensus       135 glsq~ela~~lg~~~s~i~~~E~G  158 (174)
                      |+|..++|+.+|+++++|.+|-+-
T Consensus        17 G~s~~~ia~~lgvs~~Tv~~w~kr   40 (50)
T PF13384_consen   17 GWSIREIAKRLGVSRSTVYRWIKR   40 (50)
T ss_dssp             T--HHHHHHHHTS-HHHHHHHHT-
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHH
Confidence            999999999999999999999764

>PF08667 BetR: BetR domain; InterPro: IPR013975 CheY-like phosphoacceptor (or receiver [REC]) domain is a common module in a variety of response regulators of the bacterial signal transduction systems

Probab=93.93  E-value=0.3  Score=36.06  Aligned_cols=52  Identities=15%  Similarity=0.121  Sum_probs=44.7

Q ss_pred             HHHHHHHHHHhcCCCH----HHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         123 LAKLLMQGRQAKGWSQ----KDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       123 ~~~~i~~~R~~~glsq----~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      +..+++.+-..+|+.+    .++|..||++.++.++--+|+...+..-+.+|++.|
T Consensus         6 ~~erV~~Ll~~~Gi~kr~~~s~LA~iL~Is~ssa~RKL~G~~~ftl~EI~~Ia~~f   61 (147)
T PF08667_consen    6 IAERVRELLDRKGIPKRKHASELADILGISYSSAYRKLNGKSPFTLEEIKKIAKHF   61 (147)
T ss_pred             HHHHHHHHHHHcCCcchhhHHHHHHHHCCCHHHHHHHhcCCCCCCHHHHHHHHHHh
Confidence            4566777777777655    679999999999999999999999999999999876

BetR is one of the many response regulators and is encoded mainly in Burkholderia spp. It is a N-terminal helix-turn-helix domain (HTH) and has been shown to be related to the XRE-type HTH domain (IPR001387 from INTERPRO), it has been suggested that BetR would have dimerization, protein-protein interaction, and activation/relief-of-inhibition properties [].

>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator

Probab=93.89  E-value=0.21  Score=33.97  Aligned_cols=22  Identities=14%  Similarity=0.241  Sum_probs=20.1

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q psy6501          46 WSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~   67 (174)
                      +|..|+|+.+|||.+||.-||+
T Consensus         1 ~~i~eva~~~gvs~~tlR~ye~   22 (97)
T cd04782           1 FTTGEFAKLCGISKQTLFHYDK   22 (97)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5789999999999999999983

Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.

>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators

Probab=93.85  E-value=0.36  Score=34.79  Aligned_cols=46  Identities=24%  Similarity=0.292  Sum_probs=32.0

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc------------CCCCCCHHHHH-----HHHHHhCcccccc
Q psy6501          46 WSQKDLATKINEKPQIVNDYEG------------GRGIPNQAIIG-----KMERALGIRLRVN   91 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~------------G~~~P~~~~l~-----~la~~L~v~~~~l   91 (174)
                      |+..|+|+.+|||.+||.-||+            |.|.-+.+.+.     +..+.+|++++++
T Consensus         1 m~IgE~A~~~gvs~~TLRyYE~~GLl~p~r~~~~gyR~Y~~~~~~~l~~I~~lr~~G~sL~eI   63 (133)
T cd04787           1 MKVKELANAAGVTPDTVRFYTRIGLLRPTRDPVNGYRLYSEKDLSRLRFILSARQLGFSLKDI   63 (133)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCCCCCCCcCCCCCeeeCCHHHHHHHHHHHHHHHcCCCHHHH
Confidence            6789999999999999999994            33333333333     3345577777664

Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules, such as, metal ions, drugs, and organic substrates. This subgroup lacks one of the c

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

Probab=93.84  E-value=0.064  Score=33.75  Aligned_cols=25  Identities=20%  Similarity=0.320  Sum_probs=21.6

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCC
Q psy6501          46 WSQKDLATKINEKPQIVNDYEGGRG   70 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~G~~   70 (174)
                      +|..|+|+.+|||+++|..||+-.-
T Consensus         1 yti~eva~~~gvs~~tlr~y~~~gl   25 (69)
T PF13411_consen    1 YTIKEVAKLLGVSPSTLRYYEREGL   25 (69)
T ss_dssp             EEHHHHHHHTTTTHHHHHHHHHTTS
T ss_pred             CcHHHHHHHHCcCHHHHHHHHHhcC
Confidence            4788999999999999999996443

>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein

Probab=93.82  E-value=0.95  Score=28.58  Aligned_cols=22  Identities=18%  Similarity=0.243  Sum_probs=18.4

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHH
Q psy6501          45 GWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        45 gltq~eLA~~igvs~~~is~~E   66 (174)
                      .+|.++||+.+|+|.++++++=
T Consensus         1 ~~~~~~la~~~~~s~~~l~~~f   22 (84)
T smart00342        1 PLTLEDLAEALGMSPRHLQRLF   22 (84)
T ss_pred             CCCHHHHHHHhCCCHHHHHHHH
Confidence            4788999999999999887763

>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]

Probab=93.80  E-value=0.1  Score=41.86  Aligned_cols=45  Identities=22%  Similarity=0.284  Sum_probs=35.8

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q psy6501          34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALG   85 (174)
Q Consensus        34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~   85 (174)
                      =+.|-.+|-..++||+|+|+.+|||+++||++++       ..+.+|-..|+
T Consensus       201 Ek~Vl~l~y~eelt~kEI~~~LgISes~VSql~k-------kai~kLr~~l~  245 (247)
T COG1191         201 EKLVLVLRYKEELTQKEIAEVLGISESRVSRLHK-------KAIKKLRKELN  245 (247)
T ss_pred             HHHHHHHHHHhccCHHHHHHHhCccHHHHHHHHH-------HHHHHHHHHhc
Confidence            3456678889999999999999999999999985       45555555543

>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators

Probab=93.59  E-value=0.16  Score=36.27  Aligned_cols=46  Identities=17%  Similarity=0.200  Sum_probs=34.8

Q ss_pred             CCHHHHHHHhCCCHHHHHHHH------------cCCCCCCHHHHH-----HHHHHhCcccccc
Q psy6501          46 WSQKDLATKINEKPQIVNDYE------------GGRGIPNQAIIG-----KMERALGIRLRVN   91 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E------------~G~~~P~~~~l~-----~la~~L~v~~~~l   91 (174)
                      |+..|+|+.+|||..||.-||            +|.+..+.+.+.     ...+.+|+++.++
T Consensus         1 m~IgevA~~~gvs~~tLRyYe~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI   63 (127)
T cd04784           1 MKIGELAKKTGCSVETIRYYEKEGLLPAPARSANNYRLYDEEHLERLLFIRRCRSLDMSLDEI   63 (127)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHH
Confidence            578999999999999999999            455666666654     3345677776654

Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.

>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB

Probab=93.53  E-value=0.25  Score=34.50  Aligned_cols=46  Identities=20%  Similarity=0.266  Sum_probs=32.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHH------------cCCCCCCHHHHHHHH-----HHhCcccccc
Q psy6501          46 WSQKDLATKINEKPQIVNDYE------------GGRGIPNQAIIGKME-----RALGIRLRVN   91 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E------------~G~~~P~~~~l~~la-----~~L~v~~~~l   91 (174)
                      ||..|+|+.+|||.+||..||            +|.+.-+.+.+..|.     +.+|+++.++
T Consensus         1 ~~i~e~a~~~gvs~~tlr~ye~~gll~~~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI   63 (113)
T cd01109           1 YTIKEVAEKTGLSADTLRYYEKEGLLPPVKRDENGIRDFTEEDLEWLEFIKCLRNTGMSIKDI   63 (113)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCCCCCCCCcCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHH
Confidence            578999999999999999999            444555555555443     3356665543

Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR

Probab=93.47  E-value=0.21  Score=33.93  Aligned_cols=22  Identities=18%  Similarity=0.480  Sum_probs=20.4

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q psy6501          46 WSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~   67 (174)
                      |+..|+|+.+|||..||.-||+
T Consensus         1 m~i~eva~~~gvs~~tlR~ye~   22 (96)
T cd04788           1 WKIGELARRTGLSVRTLHHYDH   22 (96)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            6789999999999999999994

Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.

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

Probab=93.46  E-value=0.49  Score=33.74  Aligned_cols=71  Identities=14%  Similarity=0.116  Sum_probs=46.7

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccCCCCCCCCCcccchhhhhhhhhhcccccHHHHH
Q psy6501          46 WSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAK  125 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~  125 (174)
                      +|..++|+.+|||++||..||+-.-.+...      +  +  -.-++               +..         ....-.
T Consensus         2 ysI~eVA~~~GVs~~TLR~wE~~GLl~p~r------~--~--G~R~Y---------------s~~---------dv~rL~   47 (120)
T cd04767           2 YPIGVVAELLNIHPETLRIWERHGLIKPAR------R--N--GQRLY---------------SNN---------DLKRLR   47 (120)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCCCCCCcC------C--C--CcEEE---------------CHH---------HHHHHH
Confidence            688999999999999999998754333210      0  0  00111               111         112235


Q ss_pred             HHHHHHHhcCCCHHHHHHHhCCChh
Q psy6501         126 LLMQGRQAKGWSQKDLATKINEKPQ  150 (174)
Q Consensus       126 ~i~~~R~~~glsq~ela~~lg~~~s  150 (174)
                      .|+.++...|++.+++...+..-+.
T Consensus        48 ~I~~L~~e~G~~l~eI~~~L~l~~~   72 (120)
T cd04767          48 FIKKLINEKGLNIAGVKQILSMYPC   72 (120)
T ss_pred             HHHHHHHHcCCCHHHHHHHHHhCcc
Confidence            7788888899999999988876554

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

>PRK12427 flagellar biosynthesis sigma factor; Provisional

Probab=93.38  E-value=1.3  Score=34.91  Aligned_cols=32  Identities=13%  Similarity=0.121  Sum_probs=26.2

Q ss_pred             HHHHHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         126 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       126 ~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      .+-.++-..|+|++++|+.+|++.+.|+.++.
T Consensus       190 ~vi~l~~~~~~t~~EIA~~lgis~~~V~q~~~  221 (231)
T PRK12427        190 LILHLYYQHEMSLKEIALVLDLTEARICQLNK  221 (231)
T ss_pred             HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            33345556799999999999999999998875

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

Probab=93.37  E-value=0.24  Score=33.68  Aligned_cols=23  Identities=9%  Similarity=0.112  Sum_probs=20.8

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcC
Q psy6501          46 WSQKDLATKINEKPQIVNDYEGG   68 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~G   68 (174)
                      +|..|+|+.+|||.+||.-||+-
T Consensus         1 ~ti~eva~~~gvs~~tLRyye~~   23 (96)
T cd04768           1 LTIGEFAKLAGVSIRTLRHYDDI   23 (96)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC
Confidence            57899999999999999999954

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

>PRK03975 tfx putative transcriptional regulator; Provisional

Probab=93.37  E-value=0.16  Score=37.24  Aligned_cols=26  Identities=19%  Similarity=0.322  Sum_probs=24.9

Q ss_pred             hcCCCHHHHHHHhCCChhHHHHHhcC
Q psy6501         133 AKGWSQKDLATKINEKPQIVNDYEGG  158 (174)
Q Consensus       133 ~~glsq~ela~~lg~~~s~i~~~E~G  158 (174)
                      ..|+||+++|+.+|+++++|+.||++
T Consensus        19 ~~GlTq~EIAe~LGiS~~tVs~ie~r   44 (141)
T PRK03975         19 ERGLTQQEIADILGTSRANVSSIEKR   44 (141)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            69999999999999999999999986

>PHA02591 hypothetical protein; Provisional

Probab=93.35  E-value=0.21  Score=32.72  Aligned_cols=29  Identities=17%  Similarity=0.274  Sum_probs=24.9

Q ss_pred             HHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         129 QGRQAKGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       129 ~~R~~~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      ....+.|+||+++|..+|++..+++.|-+
T Consensus        53 ~eL~eqGlSqeqIA~~LGVsqetVrKYL~   81 (83)
T PHA02591         53 HELARKGFTVEKIASLLGVSVRKVRRYLE   81 (83)
T ss_pred             HHHHHcCCCHHHHHHHhCCCHHHHHHHHh
Confidence            33457999999999999999999998854

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

Probab=93.33  E-value=0.19  Score=28.91  Aligned_cols=30  Identities=20%  Similarity=0.167  Sum_probs=23.1

Q ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHH
Q psy6501          35 KLLMQGRQAKGWSQKDLATKINEKPQIVND   64 (174)
Q Consensus        35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~   64 (174)
                      .-|..+.+....|..++|+.+|+|+++|.+
T Consensus         7 ~Il~~Lq~d~r~s~~~la~~lglS~~~v~~   36 (42)
T PF13404_consen    7 KILRLLQEDGRRSYAELAEELGLSESTVRR   36 (42)
T ss_dssp             HHHHHHHH-TTS-HHHHHHHHTS-HHHHHH
T ss_pred             HHHHHHHHcCCccHHHHHHHHCcCHHHHHH
Confidence            456778888999999999999999998864

...

>TIGR02147 Fsuc_second hypothetical protein, TIGR02147

Probab=93.33  E-value=0.31  Score=39.63  Aligned_cols=41  Identities=24%  Similarity=0.255  Sum_probs=38.1

Q ss_pred             cCCCHHHHHHHhCCCh-hHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         134 KGWSQKDLATKINEKP-QIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       134 ~glsq~ela~~lg~~~-s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ..+|-.++|+++|++. +.++.+.+|++.++...+.+++++|
T Consensus        26 p~fS~R~fa~~~G~ss~s~L~~v~~Gkr~Ls~~~~~k~a~~l   67 (271)
T TIGR02147        26 PAFSWRFFAEKAGFSSTSYLNDIIKGKKNLTKRMIPKFAEAL   67 (271)
T ss_pred             cCcCHHHHHHHhCCCCHHHHHHHHcCCCCCCHHHHHHHHHHc
Confidence            3699999999999888 9999999999999999999999876

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

>PRK10423 transcriptional repressor RbsR; Provisional

Probab=93.33  E-value=0.16  Score=41.16  Aligned_cols=41  Identities=17%  Similarity=0.114  Sum_probs=33.2

Q ss_pred             HHHHHHhCCCHHHHHHHHcCCCCCCHHHHH---HHHHHhCcccc
Q psy6501          49 KDLATKINEKPQIVNDYEGGRGIPNQAIIG---KMERALGIRLR   89 (174)
Q Consensus        49 ~eLA~~igvs~~~is~~E~G~~~P~~~~l~---~la~~L~v~~~   89 (174)
                      +|+|+.+|||.+|||+.-||....+.++-.   +.|+.||-.+.
T Consensus         2 ~dIA~~agVS~~TVSrvLn~~~~vs~~tr~rV~~~a~~lgY~pn   45 (327)
T PRK10423          2 KDVARLAGVSTSTVSHVINKDRFVSEAITAKVEAAIKELNYAPS   45 (327)
T ss_pred             hhHHHHhCCcHHHHHHHhCCCCCCCHHHHHHHHHHHHHHCCCcc
Confidence            689999999999999999998777777655   45666776554

>TIGR02293 TAS_TIGR02293 putative toxin-antitoxin system antitoxin component, TIGR02293 family

Probab=93.29  E-value=0.43  Score=34.46  Aligned_cols=48  Identities=4%  Similarity=-0.047  Sum_probs=39.3

Q ss_pred             HHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhh
Q psy6501         126 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERA  173 (174)
Q Consensus       126 ~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~  173 (174)
                      .+.......++++++++..+|++++|++++-++...++.+.-.++.++
T Consensus        27 ~~~~l~~~l~ls~~el~~~lgis~~Tl~R~~~~~~~Ls~~~serl~~l   74 (133)
T TIGR02293        27 ALDRLAHLLAIGKAEIFKATGIPKATLQRRKMAHQRLSSEESDRLARV   74 (133)
T ss_pred             HHHHHHHHHCCCHHHHHHHHCCCHHHHHHHhhcCCCCCHHHHHHHHHH
Confidence            444446778999999999999999999999998778888777666553

Proteins in this family are found almost exclusively in the Proteobacteria, but also in Gloeobacter violaceus PCC 7421, a cyanobacterium. This family was proposed by Makarova, et al. (2009) to be the antitoxin component of a new class of type 2 toxin-antitoxin system, or addiction module.

>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition

Probab=93.25  E-value=0.15  Score=32.67  Aligned_cols=32  Identities=13%  Similarity=0.184  Sum_probs=25.0

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          36 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      .+-..-..-|.|..++|...||++++|++|.+
T Consensus        14 ~~v~~~~~~g~sv~~va~~~gi~~~~l~~W~~   45 (76)
T PF01527_consen   14 QAVREYLESGESVSEVAREYGISPSTLYNWRK   45 (76)
T ss_dssp             HHHHHHHHHHCHHHHHHHHHTS-HHHHHHHHH
T ss_pred             HHHHHHHHCCCceEeeecccccccccccHHHH
Confidence            33333356799999999999999999999974

This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.

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

Probab=93.24  E-value=0.28  Score=30.34  Aligned_cols=24  Identities=8%  Similarity=0.082  Sum_probs=20.7

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          43 AKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        43 ~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ...+|+.+||+.+|+|+++++++-
T Consensus        23 ~~~~s~~ela~~~g~s~~tv~r~l   46 (67)
T cd00092          23 QLPLTRQEIADYLGLTRETVSRTL   46 (67)
T ss_pred             cCCcCHHHHHHHHCCCHHHHHHHH
Confidence            345999999999999999998764

>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID

Probab=93.22  E-value=0.75  Score=30.40  Aligned_cols=48  Identities=8%  Similarity=-0.033  Sum_probs=37.7

Q ss_pred             HHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCC-CCCCHHHHHHHHh
Q psy6501         124 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGR-GIPNQAIIGKMER  172 (174)
Q Consensus       124 ~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~-~~P~~~~l~~i~~  172 (174)
                      ...+...+. ...+..++|+..|+|.++|++.-++. ...++.+-.++-+
T Consensus         9 ~~I~e~l~~-~~~ti~dvA~~~gvS~~TVsr~L~~~~~~Vs~~Tr~rV~~   57 (80)
T TIGR02844         9 LEIGKYIVE-TKATVRETAKVFGVSKSTVHKDVTERLPEINPELAEEVKE   57 (80)
T ss_pred             HHHHHHHHH-CCCCHHHHHHHhCCCHHHHHHHhcCCCCCCCHHHHHHHHH
Confidence            344445556 66899999999999999999999875 6677777777654

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.

>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins

Probab=93.17  E-value=0.53  Score=31.54  Aligned_cols=61  Identities=15%  Similarity=0.225  Sum_probs=43.0

Q ss_pred             HHHHHHHHHhCcccccccCCCCCCCCCcccchhhhhhhhhhcccccHHHHHHHHHHHHhcCCCHHHHHHHhC-CChhHHH
Q psy6501          75 AIIGKMERALGIRLRVNAGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKIN-EKPQIVN  153 (174)
Q Consensus        75 ~~l~~la~~L~v~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~i~~~R~~~glsq~ela~~lg-~~~s~i~  153 (174)
                      ..+..+|+.|||+.+++.++.-..                   .+...=.-.+--++...|+|..++++.+| .+.++|.
T Consensus         3 ~Ii~~Va~~~~v~~~~i~~~~R~~-------------------~~~~aR~ia~yl~~~~~~~s~~~Ig~~fg~r~hStV~   63 (90)
T cd06571           3 LIIEAVAEYFGISVEDLRSKSRKK-------------------EIALARQIAMYLARELTGLSLPEIGRAFGGRDHSTVL   63 (90)
T ss_pred             HHHHHHHHHhCCCHHHHhcCCCCc-------------------CcchHHHHHHHHHHHHhCCCHHHHHHHhCCCCHhHHH
Confidence            567899999999999998644321                   11111122344467778999999999999 8888765


Q ss_pred             H
Q psy6501         154 D  154 (174)
Q Consensus       154 ~  154 (174)
                      .
T Consensus        64 ~   64 (90)
T cd06571          64 H   64 (90)
T ss_pred             H
Confidence            4

The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple copies of DnaA, which is an ATPase, bind to 9-mers at the origin and form an initial complex in which the DNA strands are being separated in an ATP-dependent step.

>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA

Probab=93.15  E-value=0.27  Score=33.73  Aligned_cols=22  Identities=9%  Similarity=0.228  Sum_probs=20.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q psy6501          46 WSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~   67 (174)
                      +|..|+|+.+|||++||..||+
T Consensus         1 ~ti~eva~~~gvs~~tlR~ye~   22 (103)
T cd01106           1 YTVGEVAKLTGVSVRTLHYYDE   22 (103)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5789999999999999999984

Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip

>smart00422 HTH_MERR helix_turn_helix, mercury resistance

Probab=93.12  E-value=0.16  Score=31.86  Aligned_cols=22  Identities=14%  Similarity=0.215  Sum_probs=20.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q psy6501          46 WSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~   67 (174)
                      ||..|+|+.+|||+++|..|+.
T Consensus         1 ~s~~eva~~~gvs~~tlr~~~~   22 (70)
T smart00422        1 YTIGEVAKLAGVSVRTLRYYER   22 (70)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5789999999999999999986

>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B

Probab=93.12  E-value=0.1  Score=32.61  Aligned_cols=27  Identities=33%  Similarity=0.598  Sum_probs=20.9

Q ss_pred             CHHHHHHHhCCChhHHHHHhcCCCCCCHH
Q psy6501         137 SQKDLATKINEKPQIVNDYEGGRGIPNQA  165 (174)
Q Consensus       137 sq~ela~~lg~~~s~i~~~E~G~~~P~~~  165 (174)
                      ++..+|+++|++++.|+.|  |...|...
T Consensus        11 ~~~~lAkalGVs~~aVs~W--~~~IP~~r   37 (60)
T PF14549_consen   11 GQSKLAKALGVSPQAVSQW--GERIPAER   37 (60)
T ss_dssp             SHHHHHHHHTS-HHHHHHH--HTS--HHH
T ss_pred             CHHHHHHHHCCCHHHHHHh--cCccCHHH
Confidence            7899999999999999999  66666654

>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=93.11  E-value=0.18  Score=30.12  Aligned_cols=32  Identities=16%  Similarity=0.116  Sum_probs=23.4

Q ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          35 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ..+-.++.-.|+|.+|+|+.+|+|.++|..+-
T Consensus        16 r~i~~l~~~~g~s~~eIa~~l~~s~~~v~~~l   47 (54)
T PF08281_consen   16 REIFLLRYFQGMSYAEIAEILGISESTVKRRL   47 (54)
T ss_dssp             HHHHHHHHTS---HHHHHHHCTS-HHHHHHHH
T ss_pred             HHHHHHHHHHCcCHHHHHHHHCcCHHHHHHHH
Confidence            44556778899999999999999999998763

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.

>smart00351 PAX Paired Box domain

Probab=93.07  E-value=0.32  Score=34.77  Aligned_cols=38  Identities=16%  Similarity=0.205  Sum_probs=30.0

Q ss_pred             chHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          29 VPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        29 ~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      +.+++=.+|-.+-. .|+|+.++|+.+|||++||++|-+
T Consensus        18 ~s~~~R~riv~~~~-~G~s~~~iA~~~gvs~~tV~kwi~   55 (125)
T smart00351       18 LPDEERQRIVELAQ-NGVRPCDISRQLCVSHGCVSKILG   55 (125)
T ss_pred             CCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHH
Confidence            44555556655543 799999999999999999999964

>PRK10458 DNA cytosine methylase; Provisional

Probab=92.97  E-value=0.37  Score=42.18  Aligned_cols=49  Identities=16%  Similarity=0.250  Sum_probs=38.2

Q ss_pred             HHHHHHHHcCCCHHHHHHHhC------CCHHHHHHHHcCCCC---CCHHHHHHHHHHh
Q psy6501          36 LLMQGRQAKGWSQKDLATKIN------EKPQIVNDYEGGRGI---PNQAIIGKMERAL   84 (174)
Q Consensus        36 ~ik~~R~~~gltq~eLA~~ig------vs~~~is~~E~G~~~---P~~~~l~~la~~L   84 (174)
                      .....|...++||+++|..++      .|+.+|.+||+|...   ++...+..|-+.+
T Consensus        20 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   77 (467)
T PRK10458         20 QALLEKLLEIYDVKTLAAQLNGVGENHWSRAILKRWLAGKSAWHRLSEAEFAHLQTLL   77 (467)
T ss_pred             HHHHHHHHHhcCHHHHHHHHhhcccCccCHHHHHHHHcCCCCCCCccHHHHHHHHHhc
Confidence            345566778899999999997      788999999999974   3446666676666

>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family

Probab=92.96  E-value=0.37  Score=39.42  Aligned_cols=25  Identities=12%  Similarity=0.238  Sum_probs=22.7

Q ss_pred             hcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         133 AKGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       133 ~~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      ..++|.+++|+.+|+++++|..+++
T Consensus       267 ~~~~Tl~EIa~~lgiS~erVrq~~~  291 (298)
T TIGR02997       267 GEPLTLAEIGRRLNLSRERVRQIEA  291 (298)
T ss_pred             CCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            4689999999999999999998875

This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).

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

Probab=92.89  E-value=0.18  Score=32.87  Aligned_cols=47  Identities=15%  Similarity=0.175  Sum_probs=31.6

Q ss_pred             HHHHHHHH-HHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH
Q psy6501          32 DLAKLLMQ-GRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIG   78 (174)
Q Consensus        32 ~ig~~ik~-~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~   78 (174)
                      .+++-|-. ..+-..+|..|||+.+|||+++|.++-+--..-....+.
T Consensus        20 ~Ia~yil~~~~~~~~~si~elA~~~~vS~sti~Rf~kkLG~~gf~efk   67 (77)
T PF01418_consen   20 KIADYILENPDEIAFMSISELAEKAGVSPSTIVRFCKKLGFSGFKEFK   67 (77)
T ss_dssp             HHHHHHHH-HHHHCT--HHHHHHHCTS-HHHHHHHHHHCTTTCHHHHH
T ss_pred             HHHHHHHhCHHHHHHccHHHHHHHcCCCHHHHHHHHHHhCCCCHHHHH
Confidence            34444444 556778999999999999999999987665555554443

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.

>PRK00118 putative DNA-binding protein; Validated

Probab=92.87  E-value=0.25  Score=34.32  Aligned_cols=47  Identities=19%  Similarity=0.197  Sum_probs=34.2

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCc
Q psy6501          36 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGI   86 (174)
Q Consensus        36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v   86 (174)
                      .+-.++...|+|.+|+|+.+|+|++||.++-.-    ....+.++-..+|.
T Consensus        24 evl~L~y~eg~S~~EIAe~lGIS~~TV~r~L~R----ArkkLr~~~~~~~~   70 (104)
T PRK00118         24 NYMELYYLDDYSLGEIAEEFNVSRQAVYDNIKR----TEKLLEDYEEKLHL   70 (104)
T ss_pred             HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHH----HHHHHHHHHHHHCh
Confidence            344667788999999999999999999998642    23444555555444

>cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily

Probab=92.82  E-value=1.4  Score=31.71  Aligned_cols=46  Identities=15%  Similarity=0.094  Sum_probs=32.2

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc------------CCCCCCHHHHH-----HHHHHhCcccccc
Q psy6501          46 WSQKDLATKINEKPQIVNDYEG------------GRGIPNQAIIG-----KMERALGIRLRVN   91 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~------------G~~~P~~~~l~-----~la~~L~v~~~~l   91 (174)
                      |+..|+|+.+|||..||.-||+            |.+.-+...+.     +.++.+|++++++
T Consensus         1 m~Ige~a~~~gvs~~tLRyYE~~GLl~p~~r~~~gyR~Y~~~~v~~l~~I~~lr~~GfsL~eI   63 (131)
T cd04786           1 MKIGELAKRSGMAASRIRFYEAEGLLSSVERSANGYRDYPPETVWVLEIISSAQQAGFSLDEI   63 (131)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHH
Confidence            5789999999999999999983            44444433333     2345577776654

Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic su

>PRK08558 adenine phosphoribosyltransferase; Provisional

Probab=92.76  E-value=0.36  Score=38.46  Aligned_cols=36  Identities=14%  Similarity=0.320  Sum_probs=32.8

Q ss_pred             CCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHH
Q psy6501         136 WSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKME  171 (174)
Q Consensus       136 lsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~  171 (174)
                      +|-+||++.+|++.+.+.+|=+|...|+...+..+-
T Consensus        24 ~ty~el~~~~g~p~~~l~RYv~g~~~P~~~~a~~~~   59 (238)
T PRK08558         24 YTYEELSSITGLPESVLNRYVNGHVLPSVERAREIV   59 (238)
T ss_pred             cCHHHHHHHHCCCHHHHHHHHcCCcCCCHHHHHHHH
Confidence            699999999999999999999999999998666554

>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator

Probab=92.70  E-value=0.26  Score=34.27  Aligned_cols=22  Identities=32%  Similarity=0.323  Sum_probs=20.2

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q psy6501          46 WSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~   67 (174)
                      +|..|+|+.+|||..||..||+
T Consensus         1 y~Ige~A~~~gvs~~tlR~ye~   22 (107)
T cd01111           1 YSISQLALDAGVSVHIVRDYLL   22 (107)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5788999999999999999994

Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs,

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

Probab=92.68  E-value=0.31  Score=33.49  Aligned_cols=22  Identities=14%  Similarity=0.252  Sum_probs=20.6

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q psy6501          46 WSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~   67 (174)
                      +|..|+|+.+|||++||.-||+
T Consensus         2 ~~i~eva~~~gvs~~tLR~ye~   23 (102)
T cd04775           2 YTIGQMSRKFGVSRSTLLYYES   23 (102)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            6889999999999999999994

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

>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A

Probab=92.65  E-value=0.39  Score=28.00  Aligned_cols=33  Identities=33%  Similarity=0.351  Sum_probs=25.7

Q ss_pred             HHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHh
Q psy6501         124 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE  156 (174)
Q Consensus       124 ~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E  156 (174)
                      ...+....+..++|+.++|+.+|++.++++.+-
T Consensus         6 ~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l   38 (48)
T PF13412_consen    6 RKILNYLRENPRITQKELAEKLGISRSTVNRYL   38 (48)
T ss_dssp             HHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHH
Confidence            456667777888999999999999999987753

...

>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon

Probab=92.59  E-value=0.17  Score=29.85  Aligned_cols=25  Identities=20%  Similarity=0.348  Sum_probs=22.8

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          43 AKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        43 ~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      ..|+|.+++|+.+|+|+++|..+-+
T Consensus        16 ~~g~s~~eia~~l~is~~tv~~~~~   40 (58)
T smart00421       16 AEGLTNKEIAERLGISEKTVKTHLS   40 (58)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            5799999999999999999998864

lux regulon (activates the bioluminescence operon

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

Probab=92.58  E-value=0.27  Score=31.25  Aligned_cols=28  Identities=14%  Similarity=0.004  Sum_probs=22.4

Q ss_pred             HHHHHHcC--CCHHHHHHHhCCCHHHHHHH
Q psy6501          38 MQGRQAKG--WSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        38 k~~R~~~g--ltq~eLA~~igvs~~~is~~   65 (174)
                      ..++..-+  +|+.|||+.+|++.++|++.
T Consensus        13 ~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~   42 (68)
T smart00550       13 EFLENSGDETSTALQLAKNLGLPKKEVNRV   42 (68)
T ss_pred             HHHHHCCCCCcCHHHHHHHHCCCHHHHHHH
Confidence            33444445  99999999999999999876

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

>PRK09413 IS2 repressor TnpA; Reviewed

Probab=92.52  E-value=0.37  Score=34.15  Aligned_cols=38  Identities=8%  Similarity=-0.035  Sum_probs=29.6

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      ..+|=..+-..-...|.|..++|+.+|||+++|++|-+
T Consensus        14 s~EfK~~aV~~~~~~g~sv~evA~e~gIs~~tl~~W~r   51 (121)
T PRK09413         14 TTQEKIAIVQQSFEPGMTVSLVARQHGVAASQLFLWRK   51 (121)
T ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            34444444444566799999999999999999999964

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

Probab=92.45  E-value=0.16  Score=32.44  Aligned_cols=23  Identities=13%  Similarity=0.141  Sum_probs=20.4

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ..+||++||+.+|+|+.+|++.-
T Consensus        27 ~~lt~~~iA~~~g~sr~tv~r~l   49 (76)
T PF13545_consen   27 LPLTQEEIADMLGVSRETVSRIL   49 (76)
T ss_dssp             EESSHHHHHHHHTSCHHHHHHHH
T ss_pred             ecCCHHHHHHHHCCCHHHHHHHH
Confidence            46899999999999999998764

...

>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []

Probab=92.45  E-value=0.29  Score=28.58  Aligned_cols=38  Identities=21%  Similarity=0.192  Sum_probs=26.8

Q ss_pred             HHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCC
Q psy6501         122 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRG  160 (174)
Q Consensus       122 ~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~  160 (174)
                      .+...|...+... +|+.+.|++.|++.+|+.++-+|..
T Consensus         4 ~l~~Ai~~v~~g~-~S~r~AA~~ygVp~sTL~~r~~g~~   41 (45)
T PF05225_consen    4 DLQKAIEAVKNGK-MSIRKAAKKYGVPRSTLRRRLRGKP   41 (45)
T ss_dssp             HHHHHHHHHHTTS-S-HHHHHHHHT--HHHHHHHHHHTT
T ss_pred             HHHHHHHHHHhCC-CCHHHHHHHHCcCHHHHHHHHcCCC
Confidence            3455666666333 9999999999999999999888754

In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.

>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family

Probab=92.42  E-value=0.52  Score=36.69  Aligned_cols=29  Identities=7%  Similarity=-0.002  Sum_probs=24.3

Q ss_pred             HHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         129 QGRQAKGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       129 ~~R~~~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      ..+-..|+|.+++|+.+|++.+++.....
T Consensus       185 ~l~y~~~~s~~eIA~~lgis~~tV~~~~~  213 (224)
T TIGR02479       185 SLYYYEELNLKEIGEVLGLTESRVSQIHS  213 (224)
T ss_pred             HHHHhCCCCHHHHHHHhCCCHHHHHHHHH
Confidence            44556899999999999999999987654

Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.

>TIGR00721 tfx DNA-binding protein, Tfx family

Probab=92.30  E-value=0.33  Score=35.46  Aligned_cols=26  Identities=31%  Similarity=0.397  Sum_probs=24.4

Q ss_pred             hcCCCHHHHHHHhCCChhHHHHHhcC
Q psy6501         133 AKGWSQKDLATKINEKPQIVNDYEGG  158 (174)
Q Consensus       133 ~~glsq~ela~~lg~~~s~i~~~E~G  158 (174)
                      ..|+||+++|+.+|+++++|+.+|+.
T Consensus        19 ~~GlTq~EIAe~LgiS~stV~~~e~r   44 (137)
T TIGR00721        19 EKGLSQKEIAKELKTTRANVSAIEKR   44 (137)
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHh
Confidence            69999999999999999999999874

Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=92.25  E-value=1.1  Score=35.73  Aligned_cols=29  Identities=17%  Similarity=0.116  Sum_probs=24.6

Q ss_pred             HHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         129 QGRQAKGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       129 ~~R~~~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      .++--.|+|++++|+.+|++.++|+.+..
T Consensus       213 ~l~y~~~~s~~eIA~~lgvs~~~V~~~~~  241 (256)
T PRK07408        213 EFVFLHDLTQKEAAERLGISPVTVSRRVK  241 (256)
T ss_pred             HHHHHCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            44445799999999999999999988765

>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily

Probab=92.23  E-value=0.42  Score=33.40  Aligned_cols=46  Identities=20%  Similarity=0.244  Sum_probs=31.8

Q ss_pred             CCHHHHHHHhCCCHHHHHHHH-----------cCCCCCCHHHHHHHH-----HHhCcccccc
Q psy6501          46 WSQKDLATKINEKPQIVNDYE-----------GGRGIPNQAIIGKME-----RALGIRLRVN   91 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E-----------~G~~~P~~~~l~~la-----~~L~v~~~~l   91 (174)
                      |+..|+|+.+|||.+||.-||           +|.+.-+...+..|.     +.+|+++..+
T Consensus         1 m~i~eva~~~gvs~~tlR~Ye~~GLl~p~r~~~g~R~Y~~~~~~~l~~I~~lr~~G~sl~eI   62 (112)
T cd01282           1 MRIGELAARTGVSVRSLRYYEEQGLLVPERSANGYRDYDEAAVDRVRQIRRLLAAGLTLEEI   62 (112)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHH
Confidence            578999999999999999999           455555555444333     3355555443

Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function

Probab=92.21  E-value=0.57  Score=31.61  Aligned_cols=54  Identities=13%  Similarity=0.129  Sum_probs=43.1

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcc
Q psy6501          33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIR   87 (174)
Q Consensus        33 ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~   87 (174)
                      -.+-|+.-.+..|+|.+++|..+|+|...|.++-+=. .+.+.....+-++|+--
T Consensus        11 T~~ELq~nf~~~~ls~~~ia~dL~~s~~~le~vL~l~-~~~~~~vW~lRdyL~~~   64 (89)
T PF10078_consen   11 TRQELQANFELSGLSLEQIAADLGTSPEHLEQVLNLK-QPFPEDVWILRDYLNDK   64 (89)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCC-CCCcccchHHHHHHHHH
Confidence            3566788889999999999999999999999987644 55667777777776544

>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []

Probab=92.19  E-value=0.18  Score=31.18  Aligned_cols=27  Identities=22%  Similarity=0.471  Sum_probs=23.8

Q ss_pred             hcCCCHHHHHHHhCCChhHHHHHhcCC
Q psy6501         133 AKGWSQKDLATKINEKPQIVNDYEGGR  159 (174)
Q Consensus       133 ~~glsq~ela~~lg~~~s~i~~~E~G~  159 (174)
                      ..|++++++|+.+|+++++|..|-.-.
T Consensus        11 ~~G~~~~eIA~~Lg~~~~TV~~W~~r~   37 (58)
T PF06056_consen   11 LQGWSIKEIAEELGVPRSTVYSWKDRY   37 (58)
T ss_pred             HcCCCHHHHHHHHCCChHHHHHHHHhh
Confidence            379999999999999999999987643

Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly

>PRK07598 RNA polymerase sigma factor SigC; Validated

Probab=92.19  E-value=0.51  Score=40.64  Aligned_cols=24  Identities=13%  Similarity=0.249  Sum_probs=22.3

Q ss_pred             cCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         134 KGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       134 ~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      .++|.+++|+.+|++.++|..+++
T Consensus       369 ~~~Tl~EIA~~LGvS~erVRqie~  392 (415)
T PRK07598        369 HTYSLAEIGRALDLSRERVRQIES  392 (415)
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHH
Confidence            569999999999999999999886

>PF14590 DUF4447: Domain of unknown function (DUF4447); PDB: 2OX6_B

Probab=92.18  E-value=0.76  Score=33.03  Aligned_cols=41  Identities=17%  Similarity=0.088  Sum_probs=31.8

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCH
Q psy6501          34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQ   74 (174)
Q Consensus        34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~   74 (174)
                      +--|+.+|...|+|..++|+..+.|..-|-.||.|....+.
T Consensus         9 aie~~ylr~slgl~~aqv~~l~k~se~dv~aweage~~~~~   49 (166)
T PF14590_consen    9 AIEIKYLRLSLGLTTAQVAELTKASEADVLAWEAGEKPAPG   49 (166)
T ss_dssp             HHHHHHHHHHTT--HHHHHHHHTS-HHHHHHHHTTSS---H
T ss_pred             HHHHHHHHHHcCCCHHHHHHhhccCHHHhhhhhccCCcCch
Confidence            34688999999999999999999999999999999965443

>TIGR02044 CueR Cu(I)-responsive transcriptional regulator

Probab=92.02  E-value=0.47  Score=33.86  Aligned_cols=46  Identities=17%  Similarity=0.222  Sum_probs=32.8

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc------------CCCCCCHHHHHH-----HHHHhCcccccc
Q psy6501          46 WSQKDLATKINEKPQIVNDYEG------------GRGIPNQAIIGK-----MERALGIRLRVN   91 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~------------G~~~P~~~~l~~-----la~~L~v~~~~l   91 (174)
                      |+..|+|+.+|||..||.-||.            |.+.-+.+.+..     .++.+|+++.++
T Consensus         1 m~I~e~a~~~gvs~~tlRyYe~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI   63 (127)
T TIGR02044         1 MNIGQVAKLTGLSSKMIRYYEEKGLIPPPLRSEGGYRTYTQQHLDELRLISRARQVGFSLEEC   63 (127)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHCCCCHHHH
Confidence            6789999999999999999994            444444444443     345577776654

This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.

>PRK13752 putative transcriptional regulator MerR; Provisional

Probab=92.01  E-value=1  Score=33.01  Aligned_cols=47  Identities=15%  Similarity=0.137  Sum_probs=34.1

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHH------------cCCCCCCHHHHHH-----HHHHhCcccccc
Q psy6501          45 GWSQKDLATKINEKPQIVNDYE------------GGRGIPNQAIIGK-----MERALGIRLRVN   91 (174)
Q Consensus        45 gltq~eLA~~igvs~~~is~~E------------~G~~~P~~~~l~~-----la~~L~v~~~~l   91 (174)
                      .+|..|||+.+|||..||.-||            ||.+.-+...+..     ..+.+|++++++
T Consensus         7 ~~~IgevAk~~Gvs~~TLRyYE~~GLl~p~~r~~~gyR~Y~~~~l~rl~~I~~lr~~G~sL~eI   70 (144)
T PRK13752          7 NLTIGVFAKAAGVNVETIRFYQRKGLLPEPDKPYGSIRRYGEADVTRVRFVKSAQRLGFSLDEI   70 (144)
T ss_pred             cccHHHHHHHHCcCHHHHHHHHHCCCCCCCccCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHH
Confidence            3899999999999999999999            3445445554443     345567776654

>TIGR02051 MerR Hg(II)-responsive transcriptional regulator

Probab=91.98  E-value=0.91  Score=32.29  Aligned_cols=21  Identities=19%  Similarity=0.257  Sum_probs=19.0

Q ss_pred             CHHHHHHHhCCCHHHHHHHHc
Q psy6501          47 SQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        47 tq~eLA~~igvs~~~is~~E~   67 (174)
                      |..|+|+.+|||.+||.-||.
T Consensus         1 ~I~e~a~~~gvs~~tlR~Ye~   21 (124)
T TIGR02051         1 TIGELAKAAGVNVETIRYYER   21 (124)
T ss_pred             CHHHHHHHHCcCHHHHHHHHH
Confidence            467999999999999999984

This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.

>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator

Probab=91.97  E-value=0.54  Score=33.65  Aligned_cols=46  Identities=17%  Similarity=0.216  Sum_probs=34.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHH------------cCCCCCCHHHHHHHH-----HHhCcccccc
Q psy6501          46 WSQKDLATKINEKPQIVNDYE------------GGRGIPNQAIIGKME-----RALGIRLRVN   91 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E------------~G~~~P~~~~l~~la-----~~L~v~~~~l   91 (174)
                      |+..|+|+.+|||..||.-||            ||.+..+.+.+..|.     +.+|+++..+
T Consensus         1 m~I~e~a~~~gvs~~tlR~Ye~~GLl~~~~r~~~gyR~Y~~~~l~~l~~I~~lr~lG~sL~eI   63 (127)
T TIGR02047         1 MKIGELAQKTGVSVETIRFYEKQGLLPPPARTDNNYRVYTVGHVERLAFIRNCRTLDMSLAEI   63 (127)
T ss_pred             CcHHHHHHHHCcCHHHHHHHHHCCCCCCCCcCCCCCCcCCHHHHHHHHHHHHHHHcCCCHHHH
Confidence            578999999999999999999            455555555554443     4567777655

This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.

>PRK11511 DNA-binding transcriptional activator MarA; Provisional

Probab=91.96  E-value=3  Score=29.62  Aligned_cols=23  Identities=4%  Similarity=-0.098  Sum_probs=20.6

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          45 GWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        45 gltq~eLA~~igvs~~~is~~E~   67 (174)
                      .+|.++||+.+|+|+.+++++=+
T Consensus        25 ~~sl~~lA~~~g~S~~~l~r~Fk   47 (127)
T PRK11511         25 PLSLEKVSERSGYSKWHLQRMFK   47 (127)
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHH
Confidence            59999999999999999988744

>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins

Probab=91.93  E-value=0.13  Score=34.70  Aligned_cols=31  Identities=19%  Similarity=0.457  Sum_probs=21.6

Q ss_pred             hcCCCHHHHHHHhCCChhHHHHHhcCCCCCC
Q psy6501         133 AKGWSQKDLATKINEKPQIVNDYEGGRGIPN  163 (174)
Q Consensus       133 ~~glsq~ela~~lg~~~s~i~~~E~G~~~P~  163 (174)
                      ..||||.++|+++|-+++.|+.+-.=-..|+
T Consensus         1 ~~G~tq~eIA~~lGks~s~Vs~~l~Ll~lP~   31 (93)
T PF08535_consen    1 EFGWTQEEIAKRLGKSRSWVSNHLALLDLPE   31 (93)
T ss_dssp             HTT--HHHHHHHTT--HHHHHHHHGGGS--H
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHHHcCCH
Confidence            3699999999999999999999888655554

The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This domain includes the DNA-binding HTH motif []. ; PDB: 1R71_C.

>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C

Probab=91.92  E-value=0.35  Score=29.05  Aligned_cols=32  Identities=13%  Similarity=0.256  Sum_probs=24.4

Q ss_pred             HHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCC
Q psy6501          38 MQGRQAKGWSQKDLATKINEKPQIVNDYEGGR   69 (174)
Q Consensus        38 k~~R~~~gltq~eLA~~igvs~~~is~~E~G~   69 (174)
                      -....+.|+|..++|+.+|-|+..|.+|-++-
T Consensus        13 id~m~qlG~s~~~isr~i~RSr~~Ir~yl~dP   44 (50)
T PF11427_consen   13 IDVMHQLGMSLREISRRIGRSRTCIRRYLKDP   44 (50)
T ss_dssp             HHHHHHTT--HHHHHHHHT--HHHHHHHHHSC
T ss_pred             HHHHHHhchhHHHHHHHhCccHHHHHHHhcCh
Confidence            35678999999999999999999999998753

>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]

Probab=91.91  E-value=0.34  Score=39.10  Aligned_cols=50  Identities=16%  Similarity=0.075  Sum_probs=42.2

Q ss_pred             cccchhhcccccchHHHHHHHHHHHHHcC-CCHHHHHHHhCCCHHHHHHHH
Q psy6501          17 LDRETEELKHEKVPLDLAKLLMQGRQAKG-WSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        17 ~~~~~~~~~~~~~~~~ig~~ik~~R~~~g-ltq~eLA~~igvs~~~is~~E   66 (174)
                      .++....-....+..+--+.|+.+|..-| ++|+||.+++|.|++|+|++-
T Consensus       181 ~~~~~~~~~~~~L~~~e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L  231 (258)
T COG2512         181 GDELRVLVNEYDLNEDEKEILDLIRERGGRITQAELRRALGLSKTTVSRIL  231 (258)
T ss_pred             ccccccccccCCCCHHHHHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHH
Confidence            35555555567778888899999999999 999999999999999999864

>COG2973 TrpR Trp operon repressor [Transcription]

Probab=91.87  E-value=0.89  Score=31.10  Aligned_cols=54  Identities=13%  Similarity=0.102  Sum_probs=40.3

Q ss_pred             HHHHHHHHHHHH--HcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHh
Q psy6501          31 LDLAKLLMQGRQ--AKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL   84 (174)
Q Consensus        31 ~~ig~~ik~~R~--~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L   84 (174)
                      ..+|.|++-.++  ...+||.|++.++|+|-.+|.+=-|.-..-+++...-+.+.+
T Consensus        44 eal~~Rv~Iv~eLL~ge~sQREi~~~LgvsiAtITRGSN~LK~~~~~~k~~L~~~l   99 (103)
T COG2973          44 EALGTRVRIVEELLRGELSQREIAQKLGVSIATITRGSNSLKTADPEFKQWLEKVL   99 (103)
T ss_pred             HHHHHHHHHHHHHHhccccHHHHHHHhCcchhhhccchhhhccCCHHHHHHHHHHh
Confidence            478898887776  467999999999999999998766655554555555555544

>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein

Probab=91.86  E-value=0.22  Score=28.58  Aligned_cols=23  Identities=9%  Similarity=0.086  Sum_probs=20.0

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ..+|+.++|+.+|+|++++++.-
T Consensus         7 ~~~s~~~la~~l~~s~~tv~~~l   29 (48)
T smart00419        7 LPLTRQEIAELLGLTRETVSRTL   29 (48)
T ss_pred             eccCHHHHHHHHCCCHHHHHHHH
Confidence            35799999999999999998754

>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE

Probab=91.85  E-value=0.26  Score=34.26  Aligned_cols=24  Identities=17%  Similarity=0.271  Sum_probs=21.4

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCC
Q psy6501          46 WSQKDLATKINEKPQIVNDYEGGR   69 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~G~   69 (174)
                      ||..|+|+.+|||++||..||.-.
T Consensus         1 ~~i~eva~~~gvs~~tlR~ye~~G   24 (108)
T cd04773           1 MTIGELAHLLGVPPSTLRHWEKEG   24 (108)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCC
Confidence            688999999999999999999543

Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.

>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators

Probab=91.68  E-value=0.53  Score=31.88  Aligned_cols=22  Identities=14%  Similarity=0.273  Sum_probs=20.2

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q psy6501          46 WSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~   67 (174)
                      ||..|+|+.+||++++|..|++
T Consensus         1 ~~~~eva~~~gi~~~tlr~~~~   22 (100)
T cd00592           1 YTIGEVAKLLGVSVRTLRYYEE   22 (100)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5789999999999999999974

Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators

Probab=91.65  E-value=0.52  Score=33.66  Aligned_cols=46  Identities=24%  Similarity=0.300  Sum_probs=32.4

Q ss_pred             CCHHHHHHHhCCCHHHHHHHH------------cCCCCCCHHHHHHH-----HHHhCcccccc
Q psy6501          46 WSQKDLATKINEKPQIVNDYE------------GGRGIPNQAIIGKM-----ERALGIRLRVN   91 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E------------~G~~~P~~~~l~~l-----a~~L~v~~~~l   91 (174)
                      ||..|+|+.+|||..||.-||            +|.+.-+.+.+..|     .+.+|+++.++
T Consensus         1 m~I~e~a~~~gvs~~tlRyYe~~GLl~~~~r~~~g~R~Y~~~~~~~l~~I~~lr~~G~sL~eI   63 (127)
T cd01108           1 MNIGEAAKLTGLSAKMIRYYEEIGLIPPPSRSDNGYRVYNQRDIEELRFIRRARDLGFSLEEI   63 (127)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCCCCCCCCcCCCCceecCHHHHHHHHHHHHHHHcCCCHHHH
Confidence            678999999999999999999            44455555555443     34456665543

Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements

>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=91.64  E-value=0.23  Score=30.37  Aligned_cols=32  Identities=22%  Similarity=0.320  Sum_probs=25.0

Q ss_pred             HHHHHHHHHcC--CCHHHHHHHhCCCHHHHHHHH
Q psy6501          35 KLLMQGRQAKG--WSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        35 ~~ik~~R~~~g--ltq~eLA~~igvs~~~is~~E   66 (174)
                      .-|..+...-+  +|+.|||+.++++++++++.-
T Consensus         9 ~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v   42 (62)
T PF12802_consen    9 RVLMALARHPGEELTQSELAERLGISKSTVSRIV   42 (62)
T ss_dssp             HHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHH
T ss_pred             HHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHH
Confidence            34555666666  999999999999999999864

...

>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function

Probab=91.47  E-value=0.34  Score=37.98  Aligned_cols=105  Identities=18%  Similarity=0.301  Sum_probs=56.0

Q ss_pred             HHHHHcC-CCHHHHHHHhCCCHHHHHHHH------cCCCCCCHHHHHHHHHHhCcc---cc-cccCCCCCCCCCcccchh
Q psy6501          39 QGRQAKG-WSQKDLATKINEKPQIVNDYE------GGRGIPNQAIIGKMERALGIR---LR-VNAGTNKQPGTTKNTAKL  107 (174)
Q Consensus        39 ~~R~~~g-ltq~eLA~~igvs~~~is~~E------~G~~~P~~~~l~~la~~L~v~---~~-~l~~~~~~~~~~~~~~~l  107 (174)
                      ++.++-| |||.|||..+|+|..||++.-      +|.-.|+-.....|-..+--.   +. +|-+...        ..+
T Consensus        98 EAy~QgglLT~~Dla~LL~~S~~TI~~~i~~yq~e~g~vvPtrG~i~DiGp~~tHK~~ii~~~l~g~~~--------~ei  169 (220)
T PF07900_consen   98 EAYDQGGLLTQEDLAMLLGISPRTISKDIKEYQKEHGVVVPTRGTIHDIGPGVTHKKIIIRLYLKGKPT--------PEI  169 (220)
T ss_pred             HHHHcCCcccHHHHHHHHCCCHHHHHHHHHHHHHHcCceeccCCcccccCCcchHHHHHHHHHHcCCCH--------HHH
Confidence            3333333 699999999999999999863      355556655444332110000   00 1111000        000


Q ss_pred             hhhhhhhhcccccHHHHHHHHHH-----HHhcCCCHHHHHHHhCCChhHHHHHh
Q psy6501         108 DRETEELKHEKVPLDLAKLLMQG-----RQAKGWSQKDLATKINEKPQIVNDYE  156 (174)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~i~~~-----R~~~glsq~ela~~lg~~~s~i~~~E  156 (174)
                      ..   ..  ..-...+...|+.-     -..+|++..+++..+|+|...+..|+
T Consensus       170 ar---~t--~HS~~av~rYi~~F~rV~~l~~~~~~~~eia~~tg~S~~Lv~eY~  218 (220)
T PF07900_consen  170 AR---RT--NHSPEAVDRYIKDFKRVLMLYEKGMSPEEIAFITGMSERLVKEYL  218 (220)
T ss_pred             HH---Hh--ccCHHHHHHHHHhhHHhHHHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence            00   00  11112222222211     13588999999999999999998886

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

Probab=91.40  E-value=0.67  Score=32.73  Aligned_cols=46  Identities=24%  Similarity=0.367  Sum_probs=33.1

Q ss_pred             CCHHHHHHHhCCCHHHHHHHH------------cCCCCCCHHHHHHHH-----HHhCcccccc
Q psy6501          46 WSQKDLATKINEKPQIVNDYE------------GGRGIPNQAIIGKME-----RALGIRLRVN   91 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E------------~G~~~P~~~~l~~la-----~~L~v~~~~l   91 (174)
                      ||..|+|+.+|||.+||.-||            +|.+.-+.+.+..|.     +.+|+++.++
T Consensus         1 ~~I~eva~~~gvs~~tLRyYe~~GLl~p~~r~~~gyR~Y~~~~i~~l~~I~~lr~~G~sl~eI   63 (123)
T cd04770           1 MKIGELAKAAGVSPDTIRYYERIGLLPPPQRSENGYRLYGEADLARLRFIRRAQALGFSLAEI   63 (123)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCCCCCCCCCCCCCCccCCHHHHHHHHHHHHHHHCCCCHHHH
Confidence            578999999999999999999            455555555555433     4456665544

Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed

Probab=91.39  E-value=0.82  Score=36.62  Aligned_cols=31  Identities=10%  Similarity=0.046  Sum_probs=25.6

Q ss_pred             HHHHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         127 LMQGRQAKGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       127 i~~~R~~~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      +-..+-..++|.+++|+.+|++.++|+.++.
T Consensus       213 vi~l~y~e~~t~~EIA~~lgis~~~V~~~~~  243 (257)
T PRK05911        213 VMALYYYEELVLKEIGKILGVSESRVSQIHS  243 (257)
T ss_pred             HHHHHHhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3344556899999999999999999988865

>TIGR02392 rpoH_proteo alternative sigma factor RpoH

Probab=91.36  E-value=0.6  Score=37.61  Aligned_cols=24  Identities=13%  Similarity=0.205  Sum_probs=22.2

Q ss_pred             cCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         134 KGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       134 ~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      .++|++++|+.+|+++.+|+.++.
T Consensus       235 ~~~t~~eIA~~lgvS~~~V~q~~~  258 (270)
T TIGR02392       235 DKLTLQELAAEYGVSAERIRQIEK  258 (270)
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHH
Confidence            479999999999999999998876

A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.

>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators

Probab=91.35  E-value=0.65  Score=33.14  Aligned_cols=46  Identities=24%  Similarity=0.347  Sum_probs=32.4

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc------------CCCCCCHHHHHHH-----HHHhCcccccc
Q psy6501          46 WSQKDLATKINEKPQIVNDYEG------------GRGIPNQAIIGKM-----ERALGIRLRVN   91 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~------------G~~~P~~~~l~~l-----a~~L~v~~~~l   91 (174)
                      ||..|+|+.+|||.+||.-||+            |.+.-+.+.+..|     .+.+|+++.++
T Consensus         1 ~~I~e~a~~~gvs~~tlR~Ye~~Gll~~~~r~~~g~R~Y~~~~l~~l~~I~~lr~~G~sL~eI   63 (126)
T cd04785           1 LSIGELARRTGVNVETIRYYESIGLLPEPARTAGGYRLYGAAHVERLRFIRRARDLGFSLEEI   63 (126)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCCCCCCCCcCCCCccccCHHHHHHHHHHHHHHHCCCCHHHH
Confidence            5789999999999999999993            4444555555444     34456665544

Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor

Probab=91.34  E-value=0.55  Score=27.27  Aligned_cols=27  Identities=15%  Similarity=-0.018  Sum_probs=22.5

Q ss_pred             HHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          40 GRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        40 ~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      +....++|..++|+.+++|+++++++-
T Consensus         9 l~~~~~~s~~~l~~~l~~s~~tv~~~l   35 (53)
T smart00420        9 LAQQGKVSVEELAELLGVSEMTIRRDL   35 (53)
T ss_pred             HHHcCCcCHHHHHHHHCCCHHHHHHHH
Confidence            334568999999999999999998764

>PRK04132 replication factor C small subunit; Provisional

Probab=91.33  E-value=0.6  Score=43.73  Aligned_cols=44  Identities=27%  Similarity=0.416  Sum_probs=40.4

Q ss_pred             HHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccc
Q psy6501          48 QKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVN   91 (174)
Q Consensus        48 q~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l   91 (174)
                      .+|+|++.|+....+-.|-.|++.|+...-.+||.+||++++..
T Consensus       420 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  463 (846)
T PRK04132        420 RKEIAEKTGIRADRILEYIKGKRKPSLKNYIKIAKALGINLEKT  463 (846)
T ss_pred             HHHHHHHhCCcHHHHHHHHhcCCCccHHHHHHHHHHhcccHHHH
Confidence            47899999999999999999999999999999999999997543

>PRK10227 DNA-binding transcriptional regulator CueR; Provisional

Probab=91.19  E-value=0.67  Score=33.61  Aligned_cols=46  Identities=20%  Similarity=0.289  Sum_probs=33.7

Q ss_pred             CCHHHHHHHhCCCHHHHHHHH------------cCCCCCCHHHHHHH-----HHHhCcccccc
Q psy6501          46 WSQKDLATKINEKPQIVNDYE------------GGRGIPNQAIIGKM-----ERALGIRLRVN   91 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E------------~G~~~P~~~~l~~l-----a~~L~v~~~~l   91 (174)
                      |+..|||+.+|||..||.-||            ||.+.-+...+..|     ++.+|++++.+
T Consensus         1 m~Ige~a~~~gvs~~tlRyYE~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sl~eI   63 (135)
T PRK10227          1 MNISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEES   63 (135)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCCCCCCcccCCCCcccCCHHHHHHHHHHHHHHHCCCCHHHH
Confidence            678999999999999999999            44555555555433     34567777664

>TIGR02054 MerD mercuric resistence transcriptional repressor protein MerD

Probab=91.16  E-value=0.53  Score=33.50  Aligned_cols=47  Identities=26%  Similarity=0.303  Sum_probs=33.0

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc------------CCCCCCHHHHHH-----HHHHhCcccccc
Q psy6501          45 GWSQKDLATKINEKPQIVNDYEG------------GRGIPNQAIIGK-----MERALGIRLRVN   91 (174)
Q Consensus        45 gltq~eLA~~igvs~~~is~~E~------------G~~~P~~~~l~~-----la~~L~v~~~~l   91 (174)
                      .||..|||+.+|||..||.-||+            |.+.-+...+..     .++.+|++++.+
T Consensus         3 ~~tI~elA~~~gvs~~tlR~Ye~~GLL~p~~r~~~gyR~Y~~~~l~rL~~I~~lr~~G~~L~eI   66 (120)
T TIGR02054         3 AYTISRLAEDAGVSVHVVRDYLLRGLLHPVRRTTSGYGIFDDASLQRLRFVRAAFEAGIGLGEL   66 (120)
T ss_pred             CCcHHHHHHHHCcCHHHHHHHHHCCCCCCCccCCCCCeeCCHHHHHHHHHHHHHHHcCCCHHHH
Confidence            58999999999999999999994            334333444433     334566666554

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

>PF07638 Sigma70_ECF: ECF sigma factor

Probab=91.15  E-value=0.38  Score=36.48  Aligned_cols=32  Identities=16%  Similarity=0.213  Sum_probs=27.2

Q ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          35 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      .++-.+|.-.|+|.+|+|+.+|+|..||.+.-
T Consensus       141 ~~~v~l~~~~Gls~~EIA~~lgiS~~tV~r~l  172 (185)
T PF07638_consen  141 RRVVELRFFEGLSVEEIAERLGISERTVRRRL  172 (185)
T ss_pred             HHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHH
Confidence            34556788899999999999999999998753

>TIGR02885 spore_sigF RNA polymerase sigma-F factor

Probab=91.03  E-value=6.1  Score=30.73  Aligned_cols=29  Identities=21%  Similarity=0.105  Sum_probs=25.1

Q ss_pred             HHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         129 QGRQAKGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       129 ~~R~~~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      ..+-..|+|++++|+.+|+++.+|+.+++
T Consensus       193 ~~~~~~~~t~~eIA~~lgis~~~V~~~~~  221 (231)
T TIGR02885       193 MLRYFKDKTQTEVANMLGISQVQVSRLEK  221 (231)
T ss_pred             HHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            33445799999999999999999999886

Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.

>PF00157 Pou: Pou domain - N-terminal to homeobox domain; InterPro: IPR000327 POU proteins are eukaryotic transcription factors containing a bipartite DNA binding domain referred to as the POU domain

Probab=91.02  E-value=0.43  Score=31.13  Aligned_cols=40  Identities=20%  Similarity=0.277  Sum_probs=30.1

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHhCC------ChhHHHHHhcCCC
Q psy6501         121 LDLAKLLMQGRQAKGWSQKDLATKINE------KPQIVNDYEGGRG  160 (174)
Q Consensus       121 ~~~~~~i~~~R~~~glsq~ela~~lg~------~~s~i~~~E~G~~  160 (174)
                      ..+....+..|-..|+||.+++..+|.      +.++|+++|+=.-
T Consensus        10 e~Fa~~fk~rRi~LG~TQ~dVg~al~~~~G~~~SQttI~RFE~L~L   55 (75)
T PF00157_consen   10 EQFAKEFKQRRIKLGYTQADVGAALGRLYGKEFSQTTICRFEALQL   55 (75)
T ss_dssp             HHHHHHHHHHHHHTT--HHHHHHHHHHHHSSGGSHHHHHHHHTTTS
T ss_pred             HHHHHHHHHhhhhcccCHHHHhHHHHHhcCccccchhhhhhHhccc
Confidence            456778899999999999999887653      5679999998543

The acronym POU (pronounced 'pow') is derived from the names of three mammalian transcription factors, the pituitary-specific Pit-1, the octamer-binding proteins Oct-1 and Oct-2, and the neural Unc-86 from Caenorhabditis elegans. POU domain genes have been identified in diverse organisms including nematodes, flies, amphibians, fish and mammals but have not been yet identified in plants and fungi. The various members of the POU family have a wide variety of functions, all of which are related to the function of the neuroendocrine system [] and the development of an organism []. Some other genes are also regulated, including those for immunoglobulin light and heavy chains (Oct-2) [, ], and trophic hormone genes, such as those for prolactin and growth hormone (Pit-1). The POU domain is a bipartite domain composed of two subunits separated by a non-conserved region of 15-55 aa. The N-terminal subunit is known as the POU-specific (POUs) domain (IPR000327 from INTERPRO), while the C-terminal subunit is a homeobox domain (IPR007103 from INTERPRO). 3D structures of complexes including both POU subdomains bound to DNA are available. Both subdomains contain the structural motif 'helix-turn-helix', which directly associates with the two components of bipartite DNA binding sites, and both are required for high affinity sequence-specific DNA-binding. The domain may also be involved in protein-protein interactions []. The subdomains are connected by a flexible linker [, , ]. In proteins a POU-specific domain is always accompanied by a homeodomain. Despite of the lack of sequence homology, 3D structure of POUs is similar to 3D structure of bacteriophage lambda repressor and other members of HTH_3 family [, ]. This entry represents the POU-specific subunit of the POU domain.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3D1N_O 1AU7_A 3L1P_A 2XSD_C 1O4X_A 1HF0_B 1GT0_C 1POU_A 1CQT_B 1E3O_C ....

>PF05930 Phage_AlpA: Prophage CP4-57 regulatory protein (AlpA); InterPro: IPR010260 This entry is represents phage P4, Orf88

Probab=90.99  E-value=0.07  Score=31.95  Aligned_cols=29  Identities=10%  Similarity=0.117  Sum_probs=21.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCH
Q psy6501          46 WSQKDLATKINEKPQIVNDYEGGRGIPNQ   74 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~G~~~P~~   74 (174)
                      ++.+|+++.+|+|++||.++.+....|.+
T Consensus         4 l~~~ev~~~~g~s~~ti~~~~k~g~FP~p   32 (51)
T PF05930_consen    4 LRIKEVAELLGVSRSTIYRLIKDGKFPKP   32 (51)
T ss_dssp             E-HHHHHHHHSS-HHHHHHHHHHHH---S
T ss_pred             ccHHHHHHHHCCCHHHHHHHHhcccCCCC
Confidence            57889999999999999999986666654

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. In Escherichia coli phage P4 Orf 88 is similar to AlpA of the CP4-57 cryptic prophage []. AlpA acts as a positive transcriptional regulator of slpA, a gene linked to alpA and necessary for suppression of lon mutants [, ]. The sequence of slpA suggests that it encodes an integrase gene closely related to phage P4 int and that both alpA and slpA are part of a cryptic P4-like prophage. Increase in alpA expression increases SlpA synthesis. Increased SlpA leads, in turn, to the excision and loss of the cryptic prophage. ; PDB: 1Z4H_A.

>COG1522 Lrp Transcriptional regulators [Transcription]

Probab=90.95  E-value=0.62  Score=33.85  Aligned_cols=32  Identities=19%  Similarity=0.225  Sum_probs=27.5

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHH
Q psy6501          34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~   65 (174)
                      -.-|+.+++....|+.+||+++|+|++++++-
T Consensus        11 ~~IL~~L~~d~r~~~~eia~~lglS~~~v~~R   42 (154)
T COG1522          11 RRILRLLQEDARISNAELAERVGLSPSTVLRR   42 (154)
T ss_pred             HHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHH
Confidence            45678888888999999999999999987753

>cd01110 HTH_SoxR Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator

Probab=90.93  E-value=0.52  Score=34.33  Aligned_cols=45  Identities=18%  Similarity=0.301  Sum_probs=32.6

Q ss_pred             CCHHHHHHHhCCCHHHHHHHH-----------cCCCCCCHHHHHHHH-----HHhCccccc
Q psy6501          46 WSQKDLATKINEKPQIVNDYE-----------GGRGIPNQAIIGKME-----RALGIRLRV   90 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E-----------~G~~~P~~~~l~~la-----~~L~v~~~~   90 (174)
                      ||..|+|+.+|||.+||.-||           +|.+.-+.+.+..|.     +.+|+++..
T Consensus         2 ~~I~EvA~~~Gvs~~tLRyYE~~GLl~p~r~~~g~R~Y~~~dl~~l~~I~~lr~~G~sl~e   62 (139)
T cd01110           2 LSVGEVAKRSGVAVSALHFYEQKGLIASWRNAGNQRRYPRDVLRRIAFIKVAQRLGLSLAE   62 (139)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCCCCCCCcCCCCCeEECHHHHHHHHHHHHHHHcCCCHHH
Confidence            788999999999999999998           455555555555443     335555544

Helix-turn-helix (HTH) transcriptional regulator SoxR. The global regulator, SoxR, up-regulates gene expression of another transcription activator, SoxS, which directly stimulates the oxidative stress regulon genes in E. coli. The soxRS response renders the bacterial cell resistant to superoxide-generating agents, macrophage-generated nitric oxide, organic solvents, and antibiotics. The SoxR proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the unusually long spacer between the -35 and -10 promoter elements. They also harbor a regulatory C-terminal domain containing an iron-sulfur center.

>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I

Probab=90.92  E-value=0.23  Score=36.27  Aligned_cols=26  Identities=8%  Similarity=0.180  Sum_probs=19.5

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHcCC
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYEGGR   69 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E~G~   69 (174)
                      -..|+.++|+.+||+++|+.+|-+..
T Consensus        33 ~r~T~~eiAee~Gis~~tLYrWr~~~   58 (142)
T PF13022_consen   33 ERRTQAEIAEEVGISRSTLYRWRQQN   58 (142)
T ss_dssp             --S-HHHHHHHHTS-HHHHHHHHHH-
T ss_pred             ccchHHHHHHHhCCCHHHHHHHHhcC
Confidence            35799999999999999999997543

>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=90.92  E-value=0.61  Score=27.03  Aligned_cols=25  Identities=24%  Similarity=0.322  Sum_probs=19.5

Q ss_pred             hcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         133 AKGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       133 ~~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      ..|++..++|+.+|+++++|.+|-.
T Consensus        19 ~~G~si~~IA~~~gvsr~TvyR~l~   43 (45)
T PF02796_consen   19 AEGMSIAEIAKQFGVSRSTVYRYLN   43 (45)
T ss_dssp             HTT--HHHHHHHTTS-HHHHHHHHC
T ss_pred             HCCCCHHHHHHHHCcCHHHHHHHHh
Confidence            5679999999999999999998864

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 ....

>PRK07405 RNA polymerase sigma factor SigD; Validated

Probab=90.90  E-value=0.62  Score=38.58  Aligned_cols=24  Identities=13%  Similarity=0.196  Sum_probs=22.2

Q ss_pred             cCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         134 KGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       134 ~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      .++|.+++|+.+|+++++|..+|.
T Consensus       275 ~~~Tl~EIa~~lgiS~erVRqi~~  298 (317)
T PRK07405        275 QPLTLAKIGERLNISRERVRQIER  298 (317)
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHH
Confidence            669999999999999999999886

>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional

Probab=90.84  E-value=0.64  Score=33.89  Aligned_cols=46  Identities=20%  Similarity=0.325  Sum_probs=32.0

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc------------CCCCCCHHHHHHH-----HHHhCcccccc
Q psy6501          46 WSQKDLATKINEKPQIVNDYEG------------GRGIPNQAIIGKM-----ERALGIRLRVN   91 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~------------G~~~P~~~~l~~l-----a~~L~v~~~~l   91 (174)
                      ++..|+|+.+|||..||.-||+            |.+.-+...+..|     .+.+|+++..+
T Consensus         2 ~~I~e~a~~~gvs~~tlR~Ye~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI   64 (140)
T PRK09514          2 YRIGELAKLAEVTPDTLRFYEKQGLMDPEVRTEGGYRLYTEQDLQRLRFIRRAKQLGFTLEEI   64 (140)
T ss_pred             CcHHHHHHHHCcCHHHHHHHHHCCCCCCcccCCCCCeeeCHHHHHHHHHHHHHHHcCCCHHHH
Confidence            6889999999999999999994            3444444444433     34466666544

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

Probab=90.81  E-value=1  Score=26.48  Aligned_cols=35  Identities=17%  Similarity=0.108  Sum_probs=25.4

Q ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          31 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        31 ~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ..+-..|-.+-... .|++++|+.+|+|.+||.++=
T Consensus        14 ~~~~~~i~~~~~~~-~s~~~vA~~~~vs~~TV~ri~   48 (52)
T PF13542_consen   14 KRLEQYILKLLRES-RSFKDVARELGVSWSTVRRIF   48 (52)
T ss_pred             HHHHHHHHHHHhhc-CCHHHHHHHHCCCHHHHHHHH
Confidence            34444444444444 799999999999999999874

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

Probab=90.81  E-value=0.4  Score=27.30  Aligned_cols=28  Identities=11%  Similarity=0.195  Sum_probs=22.7

Q ss_pred             CCHHHHHHHhCCChhHHHHHhcCCCCCC
Q psy6501         136 WSQKDLATKINEKPQIVNDYEGGRGIPN  163 (174)
Q Consensus       136 lsq~ela~~lg~~~s~i~~~E~G~~~P~  163 (174)
                      ++..++|+.+|++++++..|.+-...|.
T Consensus         1 ~s~~e~a~~lgvs~~tl~~~~~~g~~~~   28 (49)
T cd04762           1 LTTKEAAELLGVSPSTLRRWVKEGKLKA   28 (49)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHcCCCCc
Confidence            5788999999999999999976444443

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

>TIGR02885 spore_sigF RNA polymerase sigma-F factor

Probab=90.71  E-value=0.48  Score=37.06  Aligned_cols=29  Identities=21%  Similarity=0.105  Sum_probs=25.6

Q ss_pred             HHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          39 QGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        39 ~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      .+|-..|+|++|+|+.+|+|+.+|+++++
T Consensus       193 ~~~~~~~~t~~eIA~~lgis~~~V~~~~~  221 (231)
T TIGR02885       193 MLRYFKDKTQTEVANMLGISQVQVSRLEK  221 (231)
T ss_pred             HHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            34556899999999999999999999986

Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.

>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=90.66  E-value=0.35  Score=29.57  Aligned_cols=30  Identities=17%  Similarity=0.112  Sum_probs=25.5

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHH
Q psy6501          36 LLMQGRQAKGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~   65 (174)
                      -+..+.+...+|-+|||+.+|||..||.+-
T Consensus         5 Il~~l~~~~~~s~~ela~~~~VS~~TiRRD   34 (57)
T PF08220_consen    5 ILELLKEKGKVSVKELAEEFGVSEMTIRRD   34 (57)
T ss_pred             HHHHHHHcCCEEHHHHHHHHCcCHHHHHHH
Confidence            455667788899999999999999999864

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

>PRK13749 transcriptional regulator MerD; Provisional

Probab=90.62  E-value=0.9  Score=32.41  Aligned_cols=47  Identities=28%  Similarity=0.424  Sum_probs=34.8

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHH------------cCCCCCCHHHHHHH-----HHHhCcccccc
Q psy6501          45 GWSQKDLATKINEKPQIVNDYE------------GGRGIPNQAIIGKM-----ERALGIRLRVN   91 (174)
Q Consensus        45 gltq~eLA~~igvs~~~is~~E------------~G~~~P~~~~l~~l-----a~~L~v~~~~l   91 (174)
                      .||..|||+++|+|..||.-||            ||.+.-+...+..|     ++.+|++++++
T Consensus         3 ~~tIgelA~~~gvS~~tiR~YE~~GLl~p~~r~~~gyR~Y~~~~l~rL~~I~~~r~~G~sL~eI   66 (121)
T PRK13749          3 AYTVSRLALDAGVSVHIVRDYLLRGLLRPVACTTGGYGLFDDAALQRLCFVRAAFEAGIGLDAL   66 (121)
T ss_pred             CCcHHHHHHHHCCCHHHHHHHHHCCCCCCCCcCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHH
Confidence            4799999999999999999998            45555555554433     35677776654

>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS

Probab=90.60  E-value=0.37  Score=39.12  Aligned_cols=46  Identities=7%  Similarity=0.019  Sum_probs=37.1

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccccccc
Q psy6501          43 AKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNA   92 (174)
Q Consensus        43 ~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~   92 (174)
                      -.|+|++|+|+.+|+|.++|+.+..-    ....|.+.-...+++++.||
T Consensus       240 ~e~~s~~EIA~~Lgis~~tVk~~l~r----AlkkLr~~l~~~~~~~~~~~  285 (285)
T TIGR02394       240 YEPATLEEVAAEVGLTRERVRQIQVE----ALKKLRRILERDGVDREALF  285 (285)
T ss_pred             CCCccHHHHHHHHCCCHHHHHHHHHH----HHHHHHHHHHHhhhhhhccC
Confidence            67899999999999999999999853    34666666667778777664

A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).

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

Probab=90.57  E-value=0.37  Score=27.31  Aligned_cols=25  Identities=12%  Similarity=0.142  Sum_probs=18.1

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          43 AKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        43 ~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      ..+||.+++|+.+|+|++++++.-+
T Consensus         6 ~~~~~l~~iA~~~g~S~~~f~r~Fk   30 (42)
T PF00165_consen    6 QQKLTLEDIAEQAGFSPSYFSRLFK   30 (42)
T ss_dssp             -SS--HHHHHHHHTS-HHHHHHHHH
T ss_pred             cCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            3579999999999999999987643

>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators

Probab=90.57  E-value=0.78  Score=34.63  Aligned_cols=46  Identities=15%  Similarity=0.186  Sum_probs=33.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHH------------cCCCCCCHHHHHHH-----HHHhCcccccc
Q psy6501          46 WSQKDLATKINEKPQIVNDYE------------GGRGIPNQAIIGKM-----ERALGIRLRVN   91 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E------------~G~~~P~~~~l~~l-----a~~L~v~~~~l   91 (174)
                      +|..|||+.+|||.+||.-||            ||.+..+.+.+..|     .+.+|+++..+
T Consensus         2 ~~I~evA~~~gvs~~tLRyYe~~GLl~p~~r~~~gyR~Y~~~dl~rL~~I~~lr~~G~sL~eI   64 (172)
T cd04790           2 LTISQLARQFGLSRSTLLYYERIGLLSPSARSESNYRLYGERDLERLEQICAYRSAGVSLEDI   64 (172)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCCCCCCCccCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHH
Confidence            688999999999999999999            45555555544433     34467776654

Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain

>PRK13355 bifunctional HTH-domain containing protein/aminotransferase; Provisional

Probab=90.54  E-value=0.3  Score=42.94  Aligned_cols=29  Identities=14%  Similarity=0.285  Sum_probs=27.5

Q ss_pred             CCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         146 NEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       146 g~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ++++++|+.||+|+..|+.+.+.+|+++|
T Consensus        32 ~vs~~~is~~e~g~~~p~~~~l~~la~~l   60 (517)
T PRK13355         32 KLGKSHISQYVSGKTGPRRDVLPFLAAIL   60 (517)
T ss_pred             CcCHHHHHHHHCCCCCCCHHHHHHHHHHh
Confidence            69999999999999999999999999876

>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily

Probab=90.50  E-value=2.7  Score=32.65  Aligned_cols=38  Identities=16%  Similarity=0.144  Sum_probs=27.9

Q ss_pred             ccHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         119 VPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       119 ~~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      ++..-...+ ..+-..|+|.+++|+.+|+++++|..+.+
T Consensus       179 L~~~~r~vl-~l~y~~~~s~~eIA~~lgis~~~v~~~~~  216 (227)
T TIGR02980       179 LPERERRIL-LLRFFEDKTQSEIAERLGISQMHVSRLLR  216 (227)
T ss_pred             CCHHHHHHH-HHHHhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            333333333 34456899999999999999999988764

This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.

>TIGR01636 phage_rinA phage transcriptional activator, RinA family

Probab=90.50  E-value=1.1  Score=32.30  Aligned_cols=34  Identities=18%  Similarity=0.217  Sum_probs=30.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCc
Q psy6501          46 WSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGI   86 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v   86 (174)
                      +|..++|..+|+|+++++++.+       ..+.+||..||.
T Consensus       101 ~t~~~Ia~~l~iS~~t~~r~r~-------~~l~kla~~lG~  134 (134)
T TIGR01636       101 LTLVGLAQQLFISKSTAYRLRN-------HIIEAVAEELGM  134 (134)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHH-------HHHHHHHHHhCc
Confidence            5999999999999999999975       788899988873

This model represents a family of phage proteins, including RinA, a transcriptional activator in staphylococcal phage phi 11. This family shows similarity to ArpU, a phage-related putative autolysin regulator, and to some sporulation-specific sigma factors.

>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator

Probab=90.49  E-value=0.73  Score=33.15  Aligned_cols=46  Identities=17%  Similarity=0.235  Sum_probs=32.8

Q ss_pred             CCHHHHHHHhCCCHHHHHHHH------------cCCCCCCHHHHHHH-----HHHhCcccccc
Q psy6501          46 WSQKDLATKINEKPQIVNDYE------------GGRGIPNQAIIGKM-----ERALGIRLRVN   91 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E------------~G~~~P~~~~l~~l-----a~~L~v~~~~l   91 (174)
                      ++..|+|+.+|||..||.-||            +|.+.-+.+.+..|     .+.+|+++..+
T Consensus         2 ~~I~e~a~~~gvs~~tlR~Ye~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sl~eI   64 (131)
T TIGR02043         2 FQIGELAKLCGVTSDTLRFYEKNGLIKPAGRTDSGYRLYTDEDQKRLRFILKAKELGFTLDEI   64 (131)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCCCCCCCCcCCCCceecCHHHHHHHHHHHHHHHcCCCHHHH
Confidence            688999999999999999999            34444444444443     44567776544

This model represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=90.44  E-value=3.5  Score=32.77  Aligned_cols=37  Identities=22%  Similarity=0.149  Sum_probs=27.8

Q ss_pred             cHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         120 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       120 ~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      +..-...+ .+|-..++|++++|+.+|+++++|+.++.
T Consensus       208 ~~rer~vi-~~~~~~~~t~~eIA~~lgis~~~V~~~~~  244 (254)
T TIGR02850       208 NEREKMIL-NMRFFEGKTQMEVAEEIGISQAQVSRLEK  244 (254)
T ss_pred             CHHHHHHH-HHHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            33333333 34445789999999999999999998875

Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.

>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator

Probab=90.41  E-value=0.8  Score=32.61  Aligned_cols=46  Identities=15%  Similarity=0.229  Sum_probs=32.6

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc------------CCCCCCHHHHHHH-----HHHhCcccccc
Q psy6501          46 WSQKDLATKINEKPQIVNDYEG------------GRGIPNQAIIGKM-----ERALGIRLRVN   91 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~------------G~~~P~~~~l~~l-----a~~L~v~~~~l   91 (174)
                      ||..|+|+.+|||.+||.-||.            |.+..+.+.+..|     .+.+|+++.++
T Consensus         1 m~I~e~a~~~gvs~~tlR~Ye~~GLl~~~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI   63 (126)
T cd04783           1 LTIGELAKAAGVNVETIRYYQRRGLLPEPPRPEGGYRRYPEETVTRLRFIKRAQELGFTLDEI   63 (126)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHH
Confidence            5789999999999999999993            4455555555443     34466666544

Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.

>PRK06596 RNA polymerase factor sigma-32; Reviewed

Probab=90.34  E-value=1.3  Score=36.11  Aligned_cols=24  Identities=17%  Similarity=0.173  Sum_probs=22.3

Q ss_pred             cCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         134 KGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       134 ~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      .++|++++|+.+|++++.|+.+++
T Consensus       247 ~~~Tl~EIA~~lgvS~~rVrqi~~  270 (284)
T PRK06596        247 DKSTLQELAAEYGVSAERVRQIEK  270 (284)
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHH
Confidence            479999999999999999999986

>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain

Probab=90.34  E-value=0.76  Score=36.21  Aligned_cols=25  Identities=8%  Similarity=0.231  Sum_probs=22.8

Q ss_pred             hcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         133 AKGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       133 ~~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      ..++|++++|+.+|++.+.|+.++.
T Consensus       194 ~~~~t~~EIA~~lgis~~~V~q~~~  218 (238)
T TIGR02393       194 GRPHTLEEVGKEFNVTRERIRQIES  218 (238)
T ss_pred             CCCccHHHHHHHHCCCHHHHHHHHH
Confidence            4779999999999999999998876

This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.

>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=90.23  E-value=0.26  Score=29.43  Aligned_cols=23  Identities=9%  Similarity=0.063  Sum_probs=19.7

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E   66 (174)
                      .++|..|+|+.+|+++++++++-
T Consensus        17 ~~~t~~eia~~~gl~~stv~r~L   39 (52)
T PF09339_consen   17 GPLTLSEIARALGLPKSTVHRLL   39 (52)
T ss_dssp             SCEEHHHHHHHHTS-HHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHH
Confidence            44899999999999999999875

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.

>PRK13869 plasmid-partitioning protein RepA; Provisional

Probab=90.20  E-value=1  Score=38.61  Aligned_cols=59  Identities=12%  Similarity=0.146  Sum_probs=47.0

Q ss_pred             cchHHHHHHHHHHHH----------HcCCCHHHHHHHhCCCHHHHHHHH------------cCCCCCCHHHHHHHHHHhC
Q psy6501          28 KVPLDLAKLLMQGRQ----------AKGWSQKDLATKINEKPQIVNDYE------------GGRGIPNQAIIGKMERALG   85 (174)
Q Consensus        28 ~~~~~ig~~ik~~R~----------~~gltq~eLA~~igvs~~~is~~E------------~G~~~P~~~~l~~la~~L~   85 (174)
                      .+...+++.+..+|+          .+.+|..|+|+.+|||.+||..|+            +|++.-+.+.+..+.+.|.
T Consensus        21 ~~~~~~~~~~~~~~~~~~~p~~~k~~r~ft~~e~A~~lgvs~~tlr~~~~~g~~~~~~~~~~grR~yt~~di~~lr~~l~  100 (405)
T PRK13869         21 EHAEQLSSQLQAMSEALFPPTSHKSLRKFTSGEAARLMKISDSTLRKMTLAGEGPQPELASNGRRFYTLGQINEIRQMLA  100 (405)
T ss_pred             HHHHHHHHHHHHHHHhcCCCCCCCCCCCCCHHHHHHHhCcCHHHHHHHHHcCCCCCCccCCCCceeecHHHHHHHHHHHH
Confidence            344556666666665          257899999999999999999994            5677788899999999987


Q ss_pred             c
Q psy6501          86 I   86 (174)
Q Consensus        86 v   86 (174)
                      -
T Consensus       101 ~  101 (405)
T PRK13869        101 G  101 (405)
T ss_pred             h
Confidence            4

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

Probab=90.17  E-value=0.48  Score=32.54  Aligned_cols=25  Identities=20%  Similarity=0.112  Sum_probs=22.1

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCC
Q psy6501          46 WSQKDLATKINEKPQIVNDYEGGRG   70 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~G~~   70 (174)
                      +|..|+|+.+|||++||.-||+-.-
T Consensus         2 ~~i~eva~~~gvs~~tlR~ye~~Gl   26 (102)
T cd04789           2 YTISELAEKAGISRSTLLYYEKLGL   26 (102)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCCC
Confidence            6889999999999999999996443

Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>PRK09744 DNA-binding transcriptional regulator DicC; Provisional

Probab=90.12  E-value=0.49  Score=30.70  Aligned_cols=29  Identities=21%  Similarity=0.324  Sum_probs=24.5

Q ss_pred             CHHHHHHHhCCChhHHHHHhcCCCCCCHHHH
Q psy6501         137 SQKDLATKINEKPQIVNDYEGGRGIPNQAII  167 (174)
Q Consensus       137 sq~ela~~lg~~~s~i~~~E~G~~~P~~~~l  167 (174)
                      +...+|+.+|++++.|+.|  |+.+|.....
T Consensus        12 s~~kvA~aLGIs~~AVsQW--Ge~VPe~rA~   40 (75)
T PRK09744         12 SKTKLANAAGVRLASVAAW--GELVPEGRAM   40 (75)
T ss_pred             cHHHHHHHHCCCHHHHHHH--hccCcHHHHH
Confidence            5678999999999999999  8888876543

>PRK11512 DNA-binding transcriptional repressor MarR; Provisional

Probab=90.10  E-value=0.81  Score=33.15  Aligned_cols=43  Identities=14%  Similarity=0.036  Sum_probs=30.4

Q ss_pred             cccccchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          24 LKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        24 ~~~~~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      +.+-.+...-...|..+...-++||.+||+.+++++++|++.-
T Consensus        33 l~~~glt~~q~~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l   75 (144)
T PRK11512         33 LSPLDITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRML   75 (144)
T ss_pred             hcccCCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHH
Confidence            3333444344445666666778999999999999999998764

>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator

Probab=90.04  E-value=0.48  Score=32.85  Aligned_cols=23  Identities=13%  Similarity=0.130  Sum_probs=20.8

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcC
Q psy6501          46 WSQKDLATKINEKPQIVNDYEGG   68 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~G   68 (174)
                      +|..|+|+.+|||++||.-||.-
T Consensus         1 ~~i~eva~~~gis~~tlR~ye~~   23 (108)
T cd01107           1 FTIGEFAKLSNLSIKALRYYDKI   23 (108)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHc
Confidence            57899999999999999999954

Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.

>cd04772 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE

Probab=89.90  E-value=0.52  Score=32.20  Aligned_cols=27  Identities=41%  Similarity=0.539  Sum_probs=22.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCC
Q psy6501          46 WSQKDLATKINEKPQIVNDYEGGRGIP   72 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~G~~~P   72 (174)
                      ++..|+|+.+|||.+||..||.-.-.|
T Consensus         1 y~i~e~A~~~gvs~~tlR~Ye~~Gll~   27 (99)
T cd04772           1 YRTVDLARAIGLSPQTVRNYESLGLIP   27 (99)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHcCCCC
Confidence            467899999999999999999644433

Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.

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

Probab=89.88  E-value=1.1  Score=26.29  Aligned_cols=33  Identities=12%  Similarity=0.192  Sum_probs=26.2

Q ss_pred             HHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         125 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       125 ~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      ..+-..+-..++|..++|+.+|++.++++.+..
T Consensus        10 r~vi~~~y~~~~t~~eIa~~lg~s~~~V~~~~~   42 (50)
T PF04545_consen   10 REVIRLRYFEGLTLEEIAERLGISRSTVRRILK   42 (50)
T ss_dssp             HHHHHHHHTST-SHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHhcCCCCHHHHHHHHCCcHHHHHHHHH
Confidence            344455668899999999999999999998764

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

>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional

Probab=89.88  E-value=4.6  Score=27.44  Aligned_cols=35  Identities=9%  Similarity=-0.071  Sum_probs=26.6

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccccccc
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNA   92 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~   92 (174)
                      ..+|.++||+.+|+|+.++++.              +.+.+|+++..++
T Consensus        20 ~~~~~~~lA~~~~~S~~~l~r~--------------f~~~~g~s~~~~i   54 (107)
T PRK10219         20 QPLNIDVVAKKSGYSKWYLQRM--------------FRTVTHQTLGDYI   54 (107)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHH--------------HHHHHCcCHHHHH
Confidence            3599999999999999998875              4455666665443

>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators

Probab=89.80  E-value=0.51  Score=29.51  Aligned_cols=22  Identities=27%  Similarity=0.513  Sum_probs=20.2

Q ss_pred             CCHHHHHHHhCCChhHHHHHhc
Q psy6501         136 WSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       136 lsq~ela~~lg~~~s~i~~~E~  157 (174)
                      ++..++|+.+|++++++..||.
T Consensus         1 ~~i~evA~~~gvs~~tlR~~~~   22 (67)
T cd04764           1 YTIKEVSEIIGVKPHTLRYYEK   22 (67)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            4678999999999999999986

Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.

>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481

Probab=89.67  E-value=0.85  Score=30.51  Aligned_cols=33  Identities=15%  Similarity=0.255  Sum_probs=26.7

Q ss_pred             HHHHHHHH--HcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          35 KLLMQGRQ--AKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        35 ~~ik~~R~--~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      .|+...+.  ..|++..++|+..|||..|.++|-.
T Consensus        13 gR~~lv~~vv~~g~~~a~aA~~~gVS~~Ta~kW~~   47 (85)
T PF13011_consen   13 GRLRLVRRVVEQGWPVAHAAAEFGVSRRTAYKWLA   47 (85)
T ss_pred             HHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHH
Confidence            34444443  4899999999999999999999964

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

Probab=89.56  E-value=0.6  Score=26.96  Aligned_cols=27  Identities=19%  Similarity=0.223  Sum_probs=22.5

Q ss_pred             CCHHHHHHHhCCChhHHHHHhcCCCCC
Q psy6501         136 WSQKDLATKINEKPQIVNDYEGGRGIP  162 (174)
Q Consensus       136 lsq~ela~~lg~~~s~i~~~E~G~~~P  162 (174)
                      ++..++|+.+|++++++..|+.-...|
T Consensus         1 ~~~~e~a~~~gv~~~tlr~~~~~g~l~   27 (49)
T cd04761           1 YTIGELAKLTGVSPSTLRYYERIGLLS   27 (49)
T ss_pred             CcHHHHHHHHCcCHHHHHHHHHCCCCC
Confidence            577899999999999999997754444

Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]

Probab=89.54  E-value=1.1  Score=25.58  Aligned_cols=31  Identities=13%  Similarity=0.085  Sum_probs=25.2

Q ss_pred             HHHHHHHHHhcCCCHHHHHHHhCCChhHHHH
Q psy6501         124 AKLLMQGRQAKGWSQKDLATKINEKPQIVND  154 (174)
Q Consensus       124 ~~~i~~~R~~~glsq~ela~~lg~~~s~i~~  154 (174)
                      ...|.++-+..++++.+.|+.+|++++++..
T Consensus         7 ~~~i~~aL~~~~gn~~~aA~~Lgisr~tL~~   37 (42)
T PF02954_consen    7 KQLIRQALERCGGNVSKAARLLGISRRTLYR   37 (42)
T ss_dssp             HHHHHHHHHHTTT-HHHHHHHHTS-HHHHHH
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHCCCHHHHHH
Confidence            4678888889999999999999999998754

It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....

>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]

Probab=89.36  E-value=0.66  Score=40.20  Aligned_cols=102  Identities=15%  Similarity=0.189  Sum_probs=61.7

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccCCCCCCCCCcccchhhhhhhhhhcccccHHHHH
Q psy6501          46 WSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAK  125 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~  125 (174)
                      |+.+++|+.+|+..+|||+.-+++..-++.-+..|-.+|-..+..-.+....                 ....+..-+.+
T Consensus       331 L~LrdvA~~i~~HESTISRai~nKy~~tprG~feLK~FFs~~i~s~~gg~~~-----------------S~~~Ik~~Ik~  393 (444)
T COG1508         331 LVLRDVADEIGMHESTISRAITNKYLATPRGLFELKYFFSSSLASSEGGEAS-----------------STEAIKALIKK  393 (444)
T ss_pred             ccHHHHHHHhCccHHHHHHHHhcccccCCcceeeHHHHHHHhccCCCCCccc-----------------cHHHHHHHHHH
Confidence            8999999999999999999999995555555555555554444332221110                 00112233444


Q ss_pred             HHHHHHHhcCCCHHHHHHHh-----CCChhHHHHHhcCCCCCCH
Q psy6501         126 LLMQGRQAKGWSQKDLATKI-----NEKPQIVNDYEGGRGIPNQ  164 (174)
Q Consensus       126 ~i~~~R~~~glsq~ela~~l-----g~~~s~i~~~E~G~~~P~~  164 (174)
                      +|......+=+|...++..+     .+++-||++|=..-+.|+-
T Consensus       394 lI~~E~~~~pLSD~kIa~lLkekGi~iARRTVAKYRe~L~I~sS  437 (444)
T COG1508         394 LIEAEDKKKPLSDSKIAELLKEKGIDVARRTVAKYREELNIPSS  437 (444)
T ss_pred             HHhhccCCCCCCHHHHHHHHHHcCCchhHHhHHHHHHHcCCCch
Confidence            55555555556776666544     3445588888776666654

>COG0789 SoxR Predicted transcriptional regulators [Transcription]

Probab=89.33  E-value=0.87  Score=31.89  Aligned_cols=46  Identities=20%  Similarity=0.229  Sum_probs=32.2

Q ss_pred             CCHHHHHHHhCCCHHHHHHHH------------cCCCCCCHHHHHHH-----HHHhCcccccc
Q psy6501          46 WSQKDLATKINEKPQIVNDYE------------GGRGIPNQAIIGKM-----ERALGIRLRVN   91 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E------------~G~~~P~~~~l~~l-----a~~L~v~~~~l   91 (174)
                      ||-.|+|+.+|||..||.-||            +|.+.-+...+..+     .+.+|+++..+
T Consensus         1 ~~I~eva~~~gvs~~tLRyYE~~GLl~p~~~~~~gyR~Ys~~dl~~l~~I~~~r~~G~~L~~I   63 (124)
T COG0789           1 YTIGEVAKLTGVSVRTLRFYERKGLLSPERRDEGGYRYYTPEDLELLQIIKTLRELGFSLAEI   63 (124)
T ss_pred             CcHHHHHHHhCCCHHHHHHHHHcCCCCCcccCCCCceecCHHHHHHHHHHHHHHHcCCCHHHH
Confidence            578899999999999999999            35555555544433     33456665543

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

Probab=89.22  E-value=0.62  Score=31.76  Aligned_cols=24  Identities=17%  Similarity=0.181  Sum_probs=21.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCC
Q psy6501          46 WSQKDLATKINEKPQIVNDYEGGR   69 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~G~   69 (174)
                      +|..|+|+.+|||.++|..||+-.
T Consensus         2 ~~i~eva~~~gVs~~tLR~ye~~G   25 (98)
T cd01279           2 YPISVAAELLGIHPQTLRVYDRLG   25 (98)
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHCC
Confidence            578999999999999999998633

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

>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily

Probab=89.22  E-value=0.64  Score=31.57  Aligned_cols=27  Identities=11%  Similarity=0.150  Sum_probs=22.9

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCC
Q psy6501          46 WSQKDLATKINEKPQIVNDYEGGRGIP   72 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~G~~~P   72 (174)
                      |+..|+|+.+|||.+||.-||+-.-.|
T Consensus         1 m~I~eva~~~gvs~~tlR~Ye~~GLl~   27 (95)
T cd04780           1 MRMSELSKRSGVSVATIKYYLREGLLP   27 (95)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCCCCC
Confidence            578999999999999999999844433

Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>PRK15043 transcriptional regulator MirA; Provisional

Probab=89.02  E-value=0.69  Score=37.00  Aligned_cols=47  Identities=17%  Similarity=0.299  Sum_probs=35.8

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHH------------cCCCCCCHHHHHHHH-----HHhCcccccc
Q psy6501          45 GWSQKDLATKINEKPQIVNDYE------------GGRGIPNQAIIGKME-----RALGIRLRVN   91 (174)
Q Consensus        45 gltq~eLA~~igvs~~~is~~E------------~G~~~P~~~~l~~la-----~~L~v~~~~l   91 (174)
                      -+|..|+|+.+|||+.||..||            +|.|..+.+.+..|.     ...|+++..+
T Consensus         3 ~ytIgeVA~~~GVs~~TLR~wErr~GLL~P~Rt~~G~R~Ys~~dv~rL~~I~~l~~~G~~i~eI   66 (243)
T PRK15043          3 LYTIGEVALLCDINPVTLRAWQRRYGLLKPQRTDGGHRLFNDADIDRIREIKRWIDNGVQVSKV   66 (243)
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHhcCCCCCccCCCCCEEECHHHHHHHHHHHHHHHcCCCHHHH
Confidence            4789999999999999999998            344566666676666     5566666543

>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins

Probab=88.97  E-value=0.6  Score=27.51  Aligned_cols=25  Identities=20%  Similarity=0.230  Sum_probs=22.5

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          43 AKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        43 ~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      ..|+|.+++|+.+|+|.++|..+-.
T Consensus        13 ~~~~s~~eia~~l~~s~~tv~~~~~   37 (57)
T cd06170          13 AEGKTNKEIADILGISEKTVKTHLR   37 (57)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            4799999999999999999998864

This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental

>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA

Probab=88.96  E-value=0.63  Score=28.99  Aligned_cols=22  Identities=14%  Similarity=0.283  Sum_probs=20.3

Q ss_pred             CCHHHHHHHhCCChhHHHHHhc
Q psy6501         136 WSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       136 lsq~ela~~lg~~~s~i~~~E~  157 (174)
                      ++..++|+.+|++++++..|+.
T Consensus         1 ~s~~eva~~~gvs~~tlr~w~~   22 (68)
T cd01104           1 YTIGAVARLTGVSPDTLRAWER   22 (68)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            4778999999999999999997

Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i

>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=88.82  E-value=0.67  Score=28.52  Aligned_cols=29  Identities=14%  Similarity=0.077  Sum_probs=23.6

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHH
Q psy6501          36 LLMQGRQAKGWSQKDLATKINEKPQIVND   64 (174)
Q Consensus        36 ~ik~~R~~~gltq~eLA~~igvs~~~is~   64 (174)
                      -|+.+....++|..|||+.+|+++++++.
T Consensus        15 Il~~L~~~~~~t~~ela~~l~~~~~t~s~   43 (61)
T PF12840_consen   15 ILRLLASNGPMTVSELAEELGISQSTVSY   43 (61)
T ss_dssp             HHHHHHHCSTBEHHHHHHHHTS-HHHHHH
T ss_pred             HHHHHhcCCCCCHHHHHHHHCCCHHHHHH
Confidence            34455678999999999999999999885

...

>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities

Probab=88.78  E-value=0.41  Score=26.91  Aligned_cols=26  Identities=19%  Similarity=0.350  Sum_probs=20.6

Q ss_pred             CHHHHHHHhCCChhHHHHHhcCCCCC
Q psy6501         137 SQKDLATKINEKPQIVNDYEGGRGIP  162 (174)
Q Consensus       137 sq~ela~~lg~~~s~i~~~E~G~~~P  162 (174)
                      |..++|+.+|+++.++..||.-.-.|
T Consensus         1 ti~e~A~~~gvs~~tlR~ye~~Gll~   26 (38)
T PF00376_consen    1 TIGEVAKLLGVSPRTLRYYEREGLLP   26 (38)
T ss_dssp             EHHHHHHHHTS-HHHHHHHHHTTSS-
T ss_pred             CHHHHHHHHCCCHHHHHHHHHCCCCC
Confidence            35789999999999999999865553

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

>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily

Probab=88.69  E-value=1  Score=32.61  Aligned_cols=46  Identities=9%  Similarity=0.176  Sum_probs=31.6

Q ss_pred             CCHHHHHHHhCCCHHHHHHHH-----------cCCCCCCHHHHHHHH-----HHhCcccccc
Q psy6501          46 WSQKDLATKINEKPQIVNDYE-----------GGRGIPNQAIIGKME-----RALGIRLRVN   91 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E-----------~G~~~P~~~~l~~la-----~~L~v~~~~l   91 (174)
                      ++..|+|+.+|||++||..||           +|.+.-+.+.+..|.     ..+|++++.+
T Consensus         1 y~I~e~a~~~gvs~~TLR~Ye~~GLl~p~r~~~g~R~Y~~~~l~~l~~I~~lr~~G~sL~eI   62 (134)
T cd04779           1 YRIGQLAHLAGVSKRTIDYYTNLGLLTPERSDSNYRYYDETALDRLQLIEHLKGQRLSLAEI   62 (134)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCCCCCCccCCCCCeeECHHHHHHHHHHHHHHHCCCCHHHH
Confidence            578899999999999999999           345544554444332     3456665543

Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>PF08299 Bac_DnaA_C: Bacterial dnaA protein helix-turn-helix; InterPro: IPR013159 This entry represents the C-terminal domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication

Probab=88.57  E-value=1.2  Score=28.50  Aligned_cols=60  Identities=13%  Similarity=0.205  Sum_probs=35.9

Q ss_pred             HHHHHHHHHhCcccccccCCCCCCCCCcccchhhhhhhhhhcccccHHHHHHHHHHHHhcCCCHHHHHHHhC-CChhHHH
Q psy6501          75 AIIGKMERALGIRLRVNAGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKIN-EKPQIVN  153 (174)
Q Consensus        75 ~~l~~la~~L~v~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~i~~~R~~~glsq~ela~~lg-~~~s~i~  153 (174)
                      ..+..+|+.|||+.+++.++...           ..        +...=.-.+--.|+..++|..+++..+| ...+++.
T Consensus         4 ~Ii~~Va~~~~v~~~~i~s~~R~-----------~~--------i~~aR~va~yL~r~~~~~sl~~Ig~~fg~rdHstV~   64 (70)
T PF08299_consen    4 DIIEAVAEYFGVSVEDIRSKSRK-----------RK--------IVEARQVAMYLARELTGLSLSEIGRYFGGRDHSTVI   64 (70)
T ss_dssp             HHHHHHHHHTT--HHHHHSS--------------HH--------HHHHHHHHHHHHHHHS---HHHHHHHCTSSTHHHHH
T ss_pred             HHHHHHHHHHCCCHHHHhCCCCC-----------hh--------hcchHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHH
Confidence            56778999999999999864421           00        0111112344467778999999999999 8888764

DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; GO: 0005524 ATP binding, 0043565 sequence-specific DNA binding, 0006270 DNA-dependent DNA replication initiation, 0006275 regulation of DNA replication; PDB: 2HCB_B 3R8F_C 1L8Q_A 3PVP_B 3PVV_A 1J1V_A.

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

Probab=88.56  E-value=0.71  Score=30.91  Aligned_cols=24  Identities=21%  Similarity=0.105  Sum_probs=21.4

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCC
Q psy6501          46 WSQKDLATKINEKPQIVNDYEGGR   69 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~G~   69 (174)
                      +|..++|+.+|||++||..||.-.
T Consensus         2 ~~i~e~A~~~gvs~~tLr~ye~~G   25 (91)
T cd04766           2 YVISVAAELSGMHPQTLRLYERLG   25 (91)
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHCC
Confidence            578999999999999999998643

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

>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=88.52  E-value=0.57  Score=29.25  Aligned_cols=24  Identities=17%  Similarity=0.292  Sum_probs=21.9

Q ss_pred             CCCHHHHHHHhCCChhHHHHHhcC
Q psy6501         135 GWSQKDLATKINEKPQIVNDYEGG  158 (174)
Q Consensus       135 glsq~ela~~lg~~~s~i~~~E~G  158 (174)
                      .++..++|+++|+++++|+.|-+-
T Consensus        22 ~i~lkdIA~~Lgvs~~tIr~WK~~   45 (60)
T PF10668_consen   22 KIKLKDIAEKLGVSESTIRKWKSR   45 (60)
T ss_pred             CccHHHHHHHHCCCHHHHHHHhhh
Confidence            489999999999999999999764

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 [].

>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators

Probab=88.52  E-value=0.69  Score=29.02  Aligned_cols=22  Identities=18%  Similarity=0.407  Sum_probs=20.0

Q ss_pred             CCHHHHHHHhCCChhHHHHHhc
Q psy6501         136 WSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       136 lsq~ela~~lg~~~s~i~~~E~  157 (174)
                      ++..++|+.+|++++++..||.
T Consensus         1 ~~i~e~A~~~gVs~~tlr~ye~   22 (68)
T cd04763           1 YTIGEVALLTGIKPHVLRAWER   22 (68)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            4678999999999999999986

Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen

>COG5606 Uncharacterized conserved small protein [Function unknown]

Probab=88.52  E-value=0.73  Score=30.86  Aligned_cols=41  Identities=20%  Similarity=0.122  Sum_probs=36.2

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCC
Q psy6501         121 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGI  161 (174)
Q Consensus       121 ~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~  161 (174)
                      ..+...|..+-+..+++|+++++.+|++.+.++.+-+|+.-
T Consensus        27 ~~l~~~i~~~i~q~~l~Q~qiae~lgV~qprvS~l~~gk~~   67 (91)
T COG5606          27 SALMMAIKQWIEQAALSQAQIAELLGVTQPRVSDLARGKIQ   67 (91)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHhcchh
Confidence            45667888888999999999999999999999999998753

>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators

Probab=88.49  E-value=0.51  Score=28.70  Aligned_cols=26  Identities=23%  Similarity=0.334  Sum_probs=22.0

Q ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          42 QAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        42 ~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      -..|+|.+|+|+.+|+|..||..+-+
T Consensus        15 l~~G~~~~eIA~~l~is~~tV~~~~~   40 (58)
T PF00196_consen   15 LAQGMSNKEIAEELGISEKTVKSHRR   40 (58)
T ss_dssp             HHTTS-HHHHHHHHTSHHHHHHHHHH
T ss_pred             HHhcCCcchhHHhcCcchhhHHHHHH
Confidence            46899999999999999999988753

The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....

>PRK00215 LexA repressor; Validated

Probab=88.47  E-value=1.1  Score=34.32  Aligned_cols=56  Identities=14%  Similarity=0.237  Sum_probs=37.8

Q ss_pred             HHHHHHHHHHHHH--cCCCHHHHHHHhCC-CHHHHHHH-----HcCC--CCCCHHHHHHHHHHhCccccccc
Q psy6501          31 LDLAKLLMQGRQA--KGWSQKDLATKINE-KPQIVNDY-----EGGR--GIPNQAIIGKMERALGIRLRVNA   92 (174)
Q Consensus        31 ~~ig~~ik~~R~~--~gltq~eLA~~igv-s~~~is~~-----E~G~--~~P~~~~l~~la~~L~v~~~~l~   92 (174)
                      ..+-..|++.+..  ..+|+.|||+.+|+ ++++++++     ++|.  +.+..      ++.+.+..+++.
T Consensus         7 ~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~~~~~~------~r~~~l~~~~~~   72 (205)
T PRK00215          7 QEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALERKGFIRRDPGR------SRAIEVAAPAQL   72 (205)
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEeCCCC------cceEEecccccc
Confidence            3456667765544  45599999999999 99999999     6676  33322      456666544443

>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]

Probab=88.42  E-value=1.2  Score=32.51  Aligned_cols=32  Identities=13%  Similarity=0.163  Sum_probs=26.6

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          36 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      ++-..-...|+|..|+|+++|||.+||.+|-+
T Consensus        12 ~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~   43 (138)
T COG3415          12 RVVDAVVGEGLSCREAAKRFGVSISTVYRWVR   43 (138)
T ss_pred             HHHHHHHHcCccHHHHHHHhCccHHHHHHHHH
Confidence            33344467899999999999999999999965

>PF13730 HTH_36: Helix-turn-helix domain

Probab=88.35  E-value=0.6  Score=27.92  Aligned_cols=21  Identities=24%  Similarity=0.197  Sum_probs=19.2

Q ss_pred             CHHHHHHHhCCCHHHHHHHHc
Q psy6501          47 SQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        47 tq~eLA~~igvs~~~is~~E~   67 (174)
                      |++.||+.+|+|++||+++-+
T Consensus        27 S~~~la~~~g~s~~Tv~~~i~   47 (55)
T PF13730_consen   27 SQETLAKDLGVSRRTVQRAIK   47 (55)
T ss_pred             CHHHHHHHHCcCHHHHHHHHH
Confidence            999999999999999998753

>PRK11891 aspartate carbamoyltransferase; Provisional

Probab=88.33  E-value=0.7  Score=40.00  Aligned_cols=34  Identities=9%  Similarity=0.149  Sum_probs=31.2

Q ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcC
Q psy6501          35 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGG   68 (174)
Q Consensus        35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G   68 (174)
                      +.|+++..+.|||.++||+++|++..++.+|--=
T Consensus         6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~wl~p   39 (429)
T PRK11891          6 AFLRDAMRRLNMTREAFANRIGVSRRALDTWLLP   39 (429)
T ss_pred             HHHHHHHHHhCCCHHHHHHHhCCcHHhHHhhcCC
Confidence            5689999999999999999999999999999743

>COG1318 Predicted transcriptional regulators [Transcription]

Probab=88.33  E-value=0.71  Score=34.87  Aligned_cols=33  Identities=18%  Similarity=0.281  Sum_probs=29.9

Q ss_pred             HHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCC
Q psy6501          39 QGRQAKGWSQKDLATKINEKPQIVNDYEGGRGI   71 (174)
Q Consensus        39 ~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~   71 (174)
                      -+|...|+|..++|+.+|.+++||.++-.|...
T Consensus        55 ~arekag~Ti~EIAeelG~TeqTir~hlkgetk   87 (182)
T COG1318          55 LAREKAGMTISEIAEELGRTEQTVRNHLKGETK   87 (182)
T ss_pred             HHHHHccCcHHHHHHHhCCCHHHHHHHHhcchh
Confidence            356999999999999999999999999988764

>PRK08215 sporulation sigma factor SigG; Reviewed

Probab=88.33  E-value=0.89  Score=36.28  Aligned_cols=30  Identities=23%  Similarity=0.227  Sum_probs=25.8

Q ss_pred             HHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          38 MQGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        38 k~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      -.+|-..|+|++|+|+.+|+|+++|+++++
T Consensus       218 i~~~~~~~~t~~eIA~~lgis~~~V~~~~~  247 (258)
T PRK08215        218 LNLRFFQGKTQMEVAEEIGISQAQVSRLEK  247 (258)
T ss_pred             HHHHHhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            344556799999999999999999999986

>PF12728 HTH_17: Helix-turn-helix domain

Probab=88.23  E-value=0.78  Score=26.98  Aligned_cols=29  Identities=17%  Similarity=0.124  Sum_probs=24.3

Q ss_pred             CCHHHHHHHhCCChhHHHHHhcCCCCCCH
Q psy6501         136 WSQKDLATKINEKPQIVNDYEGGRGIPNQ  164 (174)
Q Consensus       136 lsq~ela~~lg~~~s~i~~~E~G~~~P~~  164 (174)
                      +|.+|+|+.+|++.+++..|-+-...|..
T Consensus         2 lt~~e~a~~l~is~~tv~~~~~~g~i~~~   30 (51)
T PF12728_consen    2 LTVKEAAELLGISRSTVYRWIRQGKIPPF   30 (51)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHcCCCCeE
Confidence            68899999999999999999766566543

>PRK05572 sporulation sigma factor SigF; Validated

Probab=88.21  E-value=0.91  Score=36.09  Aligned_cols=29  Identities=21%  Similarity=0.139  Sum_probs=25.5

Q ss_pred             HHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          39 QGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        39 ~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      .+|-..|+|++|+|+.+|+|+++|+++++
T Consensus       212 ~l~~~~~~s~~eIA~~lgis~~~V~~~~~  240 (252)
T PRK05572        212 YLRYFKDKTQSEVAKRLGISQVQVSRLEK  240 (252)
T ss_pred             HHHHhCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            34556799999999999999999999986

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

Probab=88.13  E-value=0.57  Score=32.88  Aligned_cols=23  Identities=17%  Similarity=0.143  Sum_probs=21.0

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcC
Q psy6501          46 WSQKDLATKINEKPQIVNDYEGG   68 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~G   68 (174)
                      ||..|+|+.+|||..||.-||.-
T Consensus         1 ~~ige~a~~~gvs~~tLryYe~~   23 (116)
T cd04769           1 MYIGELAQQTGVTIKAIRLYEEK   23 (116)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC
Confidence            68899999999999999999953

Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=87.96  E-value=1.2  Score=26.54  Aligned_cols=21  Identities=19%  Similarity=0.321  Sum_probs=18.3

Q ss_pred             CC-CHHHHHHHhCCCHHHHHHH
Q psy6501          45 GW-SQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        45 gl-tq~eLA~~igvs~~~is~~   65 (174)
                      .+ |+.+||+.+|+|+++|++.
T Consensus        19 ~l~s~~~la~~~~vs~~tv~~~   40 (60)
T smart00345       19 KLPSERELAAQLGVSRTTVREA   40 (60)
T ss_pred             cCcCHHHHHHHHCCCHHHHHHH
Confidence            35 8999999999999998864

>PRK12427 flagellar biosynthesis sigma factor; Provisional

Probab=87.80  E-value=1.1  Score=35.42  Aligned_cols=29  Identities=10%  Similarity=0.023  Sum_probs=25.4

Q ss_pred             HHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          39 QGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        39 ~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      .+|-..|+|++|+|+.+|+|+++|+++++
T Consensus       193 ~l~~~~~~t~~EIA~~lgis~~~V~q~~~  221 (231)
T PRK12427        193 HLYYQHEMSLKEIALVLDLTEARICQLNK  221 (231)
T ss_pred             HHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            34556799999999999999999999985

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

Probab=87.76  E-value=0.54  Score=29.41  Aligned_cols=28  Identities=21%  Similarity=0.399  Sum_probs=23.0

Q ss_pred             CCHHHHHHHhCCChhHHHHHhcCCCCCC
Q psy6501         136 WSQKDLATKINEKPQIVNDYEGGRGIPN  163 (174)
Q Consensus       136 lsq~ela~~lg~~~s~i~~~E~G~~~P~  163 (174)
                      ++..|+|+.+|++++++..||.-.-.|+
T Consensus         1 yti~eva~~~gvs~~tlr~y~~~gll~~   28 (69)
T PF13411_consen    1 YTIKEVAKLLGVSPSTLRYYEREGLLPP   28 (69)
T ss_dssp             EEHHHHHHHTTTTHHHHHHHHHTTSSTT
T ss_pred             CcHHHHHHHHCcCHHHHHHHHHhcCccc
Confidence            3678999999999999999998544443

>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional

Probab=87.72  E-value=1.1  Score=30.46  Aligned_cols=32  Identities=16%  Similarity=-0.076  Sum_probs=28.2

Q ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          35 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ..|+...+..+..+.+.|+.+|+|++++.+.-
T Consensus        58 ~~i~~aL~~~~gn~s~AAr~LGIsRsTL~rKL   89 (95)
T PRK00430         58 PLLDMVMQYTRGNQTRAALMLGINRGTLRKKL   89 (95)
T ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Confidence            35888889999999999999999999987654

>TIGR00122 birA_repr_reg BirA biotin operon repressor domain

Probab=87.70  E-value=1.3  Score=27.91  Aligned_cols=27  Identities=15%  Similarity=0.064  Sum_probs=22.1

Q ss_pred             HHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          40 GRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        40 ~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      +.....+|..+||+.+|+|+++|++.-
T Consensus         8 ~L~~~~~~~~eLa~~l~vS~~tv~~~l   34 (69)
T TIGR00122         8 LLADNPFSGEKLGEALGMSRTAVNKHI   34 (69)
T ss_pred             HHHcCCcCHHHHHHHHCCCHHHHHHHH
Confidence            344556899999999999999998764

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.

>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed

Probab=87.63  E-value=0.57  Score=38.25  Aligned_cols=24  Identities=17%  Similarity=0.241  Sum_probs=22.4

Q ss_pred             cCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         134 KGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       134 ~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      .++|.+++|+.+|+++++|+.++.
T Consensus       244 ~~~t~~EIa~~lgvs~~~V~q~~~  267 (289)
T PRK07500        244 DGATLEALGEELGISKERVRQIEA  267 (289)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHH
Confidence            689999999999999999999876

>TIGR03453 partition_RepA plasmid partitioning protein RepA

Probab=87.61  E-value=2.1  Score=36.25  Aligned_cols=43  Identities=14%  Similarity=0.251  Sum_probs=36.7

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHH------------cCCCCCCHHHHHHHHHHhCc
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYE------------GGRGIPNQAIIGKMERALGI   86 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E------------~G~~~P~~~~l~~la~~L~v   86 (174)
                      +-+|..|+|+.+|||.+||..||            +|++..+.+.+..|...+..
T Consensus        32 ~~~~i~eva~~~gv~~~tlr~~e~~~~~~~~~r~~~g~r~yt~~di~~l~~~~~~   86 (387)
T TIGR03453        32 RKFTSGEVAKLLGVSDSYLRQLSLEGKGPEPETLSNGRRSYTLEQINELRRHLAQ   86 (387)
T ss_pred             ccCCHHHHHHHHCcCHHHHHHHHHcCCCCCCCcCCCCceeeCHHHHHHHHHHHHh
Confidence            56899999999999999999997            45666778888888887765

Members of this family are the RepA (or ParA) protein involved in replicon partitioning. All known examples occur in bacterial species with two or more replicons, on a plasmid or the smaller chromosome. Note that an apparent exception may be seen as a pseudomolecule from assembly of an incompletely sequenced genome. Members of this family belong to a larger family that also includes the enzyme cobyrinic acid a,c-diamide synthase, but assignment of that name to members of this family would be in error.

>TIGR01764 excise DNA binding domain, excisionase family

Probab=87.55  E-value=0.92  Score=25.87  Aligned_cols=28  Identities=11%  Similarity=0.102  Sum_probs=23.5

Q ss_pred             CCHHHHHHHhCCChhHHHHHhcCCCCCC
Q psy6501         136 WSQKDLATKINEKPQIVNDYEGGRGIPN  163 (174)
Q Consensus       136 lsq~ela~~lg~~~s~i~~~E~G~~~P~  163 (174)
                      +|.+++|+.+|++++++..|-+-...|.
T Consensus         2 lt~~e~a~~lgis~~ti~~~~~~g~i~~   29 (49)
T TIGR01764         2 LTVEEAAEYLGVSKDTVYRLIHEGELPA   29 (49)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHcCCCCe
Confidence            6789999999999999998886555554

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

>PF09048 Cro: Cro; InterPro: IPR000655 Bacteriophage lambda encodes two repressors: the Cro repressor that acts to turn off early gene transcription during the lytic cycle, and the lambda or cI repressor that is required to maintain lysogenic growth

Probab=87.49  E-value=1  Score=27.93  Aligned_cols=30  Identities=10%  Similarity=0.062  Sum_probs=22.0

Q ss_pred             HHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCC
Q psy6501          39 QGRQAKGWSQKDLATKINEKPQIVNDYEGGRG   70 (174)
Q Consensus        39 ~~R~~~gltq~eLA~~igvs~~~is~~E~G~~   70 (174)
                      +.=++.|  |.+.|+.+||++++||+--+-.|
T Consensus         8 eyv~~~G--Q~kaA~~lGV~Q~AIsKAlr~gR   37 (59)
T PF09048_consen    8 EYVKEHG--QAKAARALGVTQSAISKALRAGR   37 (59)
T ss_dssp             HHHHHHH--HHHHHHHHTS-HHHHHHHHHCT-
T ss_pred             HHHHHhC--hHHHHHHcCCcHHHHHHHHHcCC
Confidence            3444555  99999999999999998766554

Together the Cro and cI repressors form a helix-turn-helix (HTH) superfamily. The lambda Cro repressor binds to DNA as a highly flexible dimer. The crystal structure of the lambda Cro repressor [] reveals a HTH DNA-binding protein with an alpha/beta fold that differs from other Cro family members, possibly by an evolutionary fold change []. Most Cro proteins, such as Enterobacteria phage P22 Cro and Bacteriophage 434 Cro, have an all-alpha structure that is thought to be ancestral to lambda Cro, where the fourth and fifth helices are replaced by a beta-sheet, possibly as a result of secondary structure switching rather than by nonhomologous replacement []. This entry represents the lambda-type Cro repressor with an alpha/beta topology.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 5CRO_A 2ECS_A 2OVG_A 6CRO_A 1D1L_A 2ORC_A 1D1M_B 3ORC_A 1ORC_A 2A63_A ....

>PF05269 Phage_CII: Bacteriophage CII protein; InterPro: IPR007933 The CII protein is a transcription activator, conserved in bacteriophage lambda and related phages, that plays a key role in the decision between lytic or lysogenic phage development

Probab=87.47  E-value=0.52  Score=31.93  Aligned_cols=24  Identities=13%  Similarity=0.250  Sum_probs=21.7

Q ss_pred             cCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         134 KGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       134 ~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      ...+|..+|+.+|++.|+|++|..
T Consensus        22 A~~gq~~vA~~~Gv~eStISR~k~   45 (91)
T PF05269_consen   22 ASVGQKKVAEAMGVDESTISRWKN   45 (91)
T ss_dssp             HHHHHHHHHHHHTSSTTTHHHHHH
T ss_pred             HHHhhHHHHHHhCCCHHHHHHHHh
Confidence            457899999999999999999975

CII is regulated at multiple levels including transcription, translation initiation, mRNA stability, and proteolysis []. Conditions that stabilise cII favour lysogenic development. The lambda CII protein activates three specific promoters, binding to direct repeat sequences rather than the more usual inverted repeats. Structurally, CII is a homotetramer where each monomer is composed of four alpha helices and a disordered C terminus [, ]. The alpha helical region is responsible for DNA binding and multimerisation. The homotetramer has an unusual spatial arrangement that allows recognition of the direct repeat sequences.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1ZS4_C 1ZPQ_C 1XWR_A.

>TIGR02392 rpoH_proteo alternative sigma factor RpoH

Probab=87.44  E-value=0.91  Score=36.56  Aligned_cols=24  Identities=13%  Similarity=0.205  Sum_probs=22.4

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      .|+|++|+|+.+|||+.+|+++++
T Consensus       235 ~~~t~~eIA~~lgvS~~~V~q~~~  258 (270)
T TIGR02392       235 DKLTLQELAAEYGVSAERIRQIEK  258 (270)
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHH
Confidence            379999999999999999999985

A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.

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

Probab=87.39  E-value=0.93  Score=31.99  Aligned_cols=24  Identities=13%  Similarity=0.122  Sum_probs=21.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCC
Q psy6501          46 WSQKDLATKINEKPQIVNDYEGGR   69 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~G~   69 (174)
                      ||..|+|+.+|||..||.-||+-.
T Consensus         1 m~IgevA~~~gvs~~tlRyYe~~G   24 (120)
T cd04781           1 LDIAEVARQSGLPASTLRYYEEKG   24 (120)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCC
Confidence            678999999999999999999543

Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, an

>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=87.36  E-value=0.9  Score=28.48  Aligned_cols=33  Identities=12%  Similarity=0.061  Sum_probs=27.7

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      .+.+..+....++|..|+|+.+|+++++|++.-
T Consensus        11 ~~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L   43 (68)
T PF01978_consen   11 AKVYLALLKNGPATAEEIAEELGISRSTVYRAL   43 (68)
T ss_dssp             HHHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHH
Confidence            445566668899999999999999999998764

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.

>COG3311 AlpA Predicted transcriptional regulator [Transcription]

Probab=87.32  E-value=0.57  Score=30.15  Aligned_cols=32  Identities=6%  Similarity=0.035  Sum_probs=27.8

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHH
Q psy6501          46 WSQKDLATKINEKPQIVNDYEGGRGIPNQAII   77 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~G~~~P~~~~l   77 (174)
                      +...|++..+|+|+++|.++.+....|....|
T Consensus        14 lrl~ev~~~~GlSrstiYr~i~~~~FPkpvkl   45 (70)
T COG3311          14 LRLPEVAQLTGLSRSTIYRLIKDGTFPKPVKL   45 (70)
T ss_pred             hhHHHHHHHHCccHHHHHHHHccCCCCCCeec
Confidence            45679999999999999999999999987644

>PRK05949 RNA polymerase sigma factor; Validated

Probab=87.23  E-value=1.3  Score=36.81  Aligned_cols=24  Identities=21%  Similarity=0.230  Sum_probs=22.0

Q ss_pred             cCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         134 KGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       134 ~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      .++|.+++|+.+|++.++|..++.
T Consensus       285 e~~Tl~EIa~~lgiS~erVrq~~~  308 (327)
T PRK05949        285 KELSLAKVGERLNLSRERVRQLEH  308 (327)
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHH
Confidence            569999999999999999998876

>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR

Probab=87.21  E-value=0.77  Score=32.86  Aligned_cols=27  Identities=19%  Similarity=0.181  Sum_probs=23.2

Q ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHH
Q psy6501          37 LMQGRQAKGWSQKDLATKINEKPQIVN   63 (174)
Q Consensus        37 ik~~R~~~gltq~eLA~~igvs~~~is   63 (174)
                      +=.++.-.|+|.+|+|+.+|+|.+||.
T Consensus       115 v~~l~~~~~~s~~EIA~~l~is~~tV~  141 (142)
T TIGR03209       115 IIYMKFFEDMKEIDIAKKLHISRQSVY  141 (142)
T ss_pred             HHHHHHHcCCCHHHHHHHHCcCHHhhc
Confidence            344667899999999999999999985

Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.

>PRK15320 transcriptional activator SprB; Provisional

Probab=87.12  E-value=0.66  Score=36.14  Aligned_cols=39  Identities=23%  Similarity=0.249  Sum_probs=31.6

Q ss_pred             HHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccccc
Q psy6501          41 RQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRV   90 (174)
Q Consensus        41 R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~   90 (174)
                      .-..|+|++|+|+.+++|.+||+.+-+           +|-+.|++.-.-
T Consensus       175 LLAkG~SNKEIAekL~LS~KTVSTYKn-----------RLLeKLgAkN~~  213 (251)
T PRK15320        175 LLSSGHPAIELAKKFGLGTKTVSIYRK-----------KVMYRLGMDSSP  213 (251)
T ss_pred             HHHcCCCHHHHHHHhccchhhHHHHHH-----------HHHHHcCCCCCc
Confidence            457899999999999999999998854           666677776443

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=87.07  E-value=1.1  Score=35.70  Aligned_cols=28  Identities=25%  Similarity=0.209  Sum_probs=24.8

Q ss_pred             HHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          40 GRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        40 ~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      +|--.|+|++|+|+.+|+|+.+|+++++
T Consensus       217 ~~~~~~~t~~eIA~~lgis~~~V~~~~~  244 (254)
T TIGR02850       217 MRFFEGKTQMEVAEEIGISQAQVSRLEK  244 (254)
T ss_pred             HHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            4445799999999999999999999985

Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.

>PRK09863 putative frv operon regulatory protein; Provisional

Probab=87.06  E-value=13  Score=33.39  Aligned_cols=98  Identities=18%  Similarity=0.049  Sum_probs=50.4

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccCCCCCCCCCcccchhhhhhhhhhcccccHH
Q psy6501          43 AKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGTNKQPGTTKNTAKLDRETEELKHEKVPLD  122 (174)
Q Consensus        43 ~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~  122 (174)
                      ...+|-++||+.+|||..||.+.-        ..+....+..++....  +.....-....-..+...   .. ......
T Consensus        15 ~~~~t~~~LA~~l~VS~RTIr~dI--------~~in~~l~~~~~~~i~--~~~Gy~l~~~~~~~~~~~---~~-~~~~e~   80 (584)
T PRK09863         15 QQDRSGGELAQQLGVSRRTIVRDI--------AYINFTLNGKAIGSIS--GSAKYHLEILNRRSLFQL---LQ-KSDNED   80 (584)
T ss_pred             cCCCCHHHHHHHhCCCHHHHHHHH--------HHHHHHHHhcchhhee--cCCceEEEeCCHHHHHHH---Hh-cCCHHH
Confidence            468999999999999999998843        3444333332332110  000000000000000000   00 000111


Q ss_pred             HHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHH
Q psy6501         123 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDY  155 (174)
Q Consensus       123 ~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~  155 (174)
                      . ..+...-.....+..++|+.+.+|++++...
T Consensus        81 ~-~il~~Ll~~~~~~~~~La~~l~vS~sTi~~d  112 (584)
T PRK09863         81 R-LLLLRLLLNTFTPMAQLASALNLSRTWVAER  112 (584)
T ss_pred             H-HHHHHHHHcCCccHHHHHHHhCCCHHHHHHH
Confidence            1 1222223356789999999999999988754

>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional

Probab=86.96  E-value=1.7  Score=31.95  Aligned_cols=31  Identities=13%  Similarity=0.102  Sum_probs=26.4

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHH
Q psy6501          34 AKLLMQGRQAKGWSQKDLATKINEKPQIVND   64 (174)
Q Consensus        34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~   64 (174)
                      -.-|..+.+.-..|..+||+.+|+|++++.+
T Consensus        12 ~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~   42 (153)
T PRK11179         12 RGILEALMENARTPYAELAKQFGVSPGTIHV   42 (153)
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHH
Confidence            4456778888999999999999999998764

>PRK09210 RNA polymerase sigma factor RpoD; Validated

Probab=86.96  E-value=1.8  Score=36.57  Aligned_cols=24  Identities=4%  Similarity=0.144  Sum_probs=22.0

Q ss_pred             cCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         134 KGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       134 ~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      .++|.+++|+.+|++.+.|+.+|.
T Consensus       324 ~~~tl~EIa~~lgvs~erVrQi~~  347 (367)
T PRK09210        324 RTRTLEEVGKVFGVTRERIRQIEA  347 (367)
T ss_pred             CCccHHHHHHHHCCCHHHHHHHHH
Confidence            448999999999999999999986

>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities

Probab=86.90  E-value=0.74  Score=26.81  Aligned_cols=29  Identities=14%  Similarity=0.055  Sum_probs=22.5

Q ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          37 LMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        37 ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      |+.+.+ ..++..|+|+.+|+|+++||..-
T Consensus         8 l~~L~~-~~~~~~el~~~l~~s~~~vs~hL   36 (47)
T PF01022_consen    8 LKLLSE-GPLTVSELAEELGLSQSTVSHHL   36 (47)
T ss_dssp             HHHHTT-SSEEHHHHHHHHTS-HHHHHHHH
T ss_pred             HHHHHh-CCCchhhHHHhccccchHHHHHH
Confidence            344444 77899999999999999999753

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 ....

>PRK01381 Trp operon repressor; Provisional

Probab=86.87  E-value=1.9  Score=29.60  Aligned_cols=51  Identities=8%  Similarity=0.034  Sum_probs=35.9

Q ss_pred             HHHHHHHHHH--hcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhh
Q psy6501         123 LAKLLMQGRQ--AKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERA  173 (174)
Q Consensus       123 ~~~~i~~~R~--~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~  173 (174)
                      +..+++-.+.  ..++||.++++.+|+|.++|++.=+--..-++.+..-|.+.
T Consensus        41 l~~R~~I~~~L~~g~~sQREIa~~lGvSiaTITRgsn~Lk~~~~~~k~~l~~~   93 (99)
T PRK01381         41 LGTRVRIVEELLRGELSQREIKQELGVGIATITRGSNSLKTAPPEFKEWLEQQ   93 (99)
T ss_pred             HHHHHHHHHHHHcCCcCHHHHHHHhCCceeeehhhHHHhccCCHHHHHHHHHH
Confidence            3444444443  34599999999999999999988776555556666665543

>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial

Probab=86.82  E-value=1.7  Score=32.38  Aligned_cols=23  Identities=13%  Similarity=0.114  Sum_probs=19.8

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ..+||+|||..+|+|+.+||+.-
T Consensus       142 ~~~t~~~iA~~lG~tretvsR~l  164 (193)
T TIGR03697       142 LRLSHQAIAEAIGSTRVTITRLL  164 (193)
T ss_pred             CCCCHHHHHHHhCCcHHHHHHHH
Confidence            34799999999999999998853

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

>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases []

Probab=86.81  E-value=0.88  Score=25.08  Aligned_cols=19  Identities=16%  Similarity=0.282  Sum_probs=17.6

Q ss_pred             CHHHHHHHhCCCHHHHHHH
Q psy6501          47 SQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        47 tq~eLA~~igvs~~~is~~   65 (174)
                      |..|.|+.+|+++++|+++
T Consensus        18 Si~eAa~~l~i~~~~I~~~   36 (37)
T PF07453_consen   18 SIREAARYLGISHSTISKY   36 (37)
T ss_pred             CHHHHHHHhCCCHHHHHHh
Confidence            7899999999999999975

>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition

Probab=86.77  E-value=1  Score=28.65  Aligned_cols=36  Identities=11%  Similarity=0.184  Sum_probs=26.5

Q ss_pred             HHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         122 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       122 ~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      ++...+-..-...|.|..++|...|++++++..|..
T Consensus        10 e~K~~~v~~~~~~g~sv~~va~~~gi~~~~l~~W~~   45 (76)
T PF01527_consen   10 EFKLQAVREYLESGESVSEVAREYGISPSTLYNWRK   45 (76)
T ss_dssp             HHHHHHHHHHHHHHCHHHHHHHHHTS-HHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCceEeeecccccccccccHHHH
Confidence            333344333456789999999999999999999975

This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.

>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]

Probab=86.74  E-value=0.63  Score=33.41  Aligned_cols=26  Identities=23%  Similarity=0.335  Sum_probs=23.8

Q ss_pred             HhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         132 QAKGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       132 ~~~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      .++||+|+++|+.+|....-||.+|.
T Consensus        20 RekG~tQ~eIA~~L~TTraNvSaIEk   45 (143)
T COG1356          20 REKGLTQSEIARILKTTRANVSAIEK   45 (143)
T ss_pred             hhccccHHHHHHHHccchhhHHHHHH
Confidence            46899999999999999999998886

>PF13693 HTH_35: Winged helix-turn-helix DNA-binding; PDB: 1NEQ_A 1NER_A

Probab=86.74  E-value=2.9  Score=27.50  Aligned_cols=47  Identities=13%  Similarity=0.020  Sum_probs=33.5

Q ss_pred             HHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         125 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       125 ~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ..|..+-+++|+|..++|...|+++++++..-   ..|.+..-..||.+|
T Consensus         5 adI~AaL~krG~sL~~lsr~~Gl~~~tl~nal---~r~~pk~E~~IA~aL   51 (78)
T PF13693_consen    5 ADIKAALRKRGTSLAALSREAGLSSSTLRNAL---RRPWPKGERIIADAL   51 (78)
T ss_dssp             HHHHHHHCTTS--HHHHHHHHSS-HHHHHHTT---TSS-HHHHHHHHHHT
T ss_pred             HHHHHHHHHcCCCHHHHHHHcCCCHHHHHHHH---cCCChHHHHHHHHHH
Confidence            45666777899999999999999999988765   456676677777664

>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT)

Probab=86.68  E-value=0.64  Score=32.13  Aligned_cols=45  Identities=18%  Similarity=0.136  Sum_probs=29.7

Q ss_pred             HHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccc
Q psy6501          40 GRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRL   88 (174)
Q Consensus        40 ~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~   88 (174)
                      +--.-++|..|+|+.+|||+++|+++-+-    ....|..+-+.|++--
T Consensus        28 lyy~eDlSlsEIAe~~~iSRqaV~d~ikr----~~~~L~~yE~kL~l~~   72 (101)
T PF04297_consen   28 LYYEEDLSLSEIAEELGISRQAVYDSIKR----AEKKLEEYEEKLGLVE   72 (101)
T ss_dssp             HHCTS---HHHHHHHCTS-HHHHHHHHHH----HHHHHHHHHHHH-HHH
T ss_pred             HHHccCCCHHHHHHHHCCCHHHHHHHHHH----HHHHHHHHHHHHhhHH
Confidence            44456899999999999999999998753    2366667776666543

Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.

>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere

Probab=86.65  E-value=0.77  Score=27.72  Aligned_cols=27  Identities=19%  Similarity=0.219  Sum_probs=20.6

Q ss_pred             HhcCCCHHHHHHHhCCChhHHHHHhcC
Q psy6501         132 QAKGWSQKDLATKINEKPQIVNDYEGG  158 (174)
Q Consensus       132 ~~~glsq~ela~~lg~~~s~i~~~E~G  158 (174)
                      -+.|.++.++|..+|++.++|+.|-..
T Consensus        19 ~e~g~s~~~ia~~fgv~~sTv~~I~K~   45 (53)
T PF04218_consen   19 LEEGESKRDIAREFGVSRSTVSTILKN   45 (53)
T ss_dssp             HHCTT-HHHHHHHHT--CCHHHHHHHC
T ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHHHh
Confidence            368889999999999999999988653

Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.

>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain

Probab=86.62  E-value=2.4  Score=25.65  Aligned_cols=29  Identities=14%  Similarity=0.000  Sum_probs=23.6

Q ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHH
Q psy6501          37 LMQGRQAKGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        37 ik~~R~~~gltq~eLA~~igvs~~~is~~   65 (174)
                      +.+++.-..++++|.|+.+||+.+++-+.
T Consensus         7 ~~~L~~~fhlp~~eAA~~Lgv~~T~LKr~   35 (52)
T PF02042_consen    7 LEDLSQYFHLPIKEAAKELGVSVTTLKRR   35 (52)
T ss_pred             HHHHHHHhCCCHHHHHHHhCCCHHHHHHH
Confidence            45778888999999999999888766544

The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].

>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain

Probab=86.56  E-value=1.1  Score=35.27  Aligned_cols=25  Identities=8%  Similarity=0.231  Sum_probs=23.3

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          43 AKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        43 ~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      ..++|++|+|+.+|+|+++|++++.
T Consensus       194 ~~~~t~~EIA~~lgis~~~V~q~~~  218 (238)
T TIGR02393       194 GRPHTLEEVGKEFNVTRERIRQIES  218 (238)
T ss_pred             CCCccHHHHHHHHCCCHHHHHHHHH
Confidence            4789999999999999999999985

This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.

>PRK07122 RNA polymerase sigma factor SigF; Reviewed

Probab=86.55  E-value=7.4  Score=31.27  Aligned_cols=31  Identities=13%  Similarity=0.124  Sum_probs=25.4

Q ss_pred             HHHHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         127 LMQGRQAKGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       127 i~~~R~~~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      +-.++-..++|.+++|+.+|++.++|..++.
T Consensus       223 vl~l~y~~~~t~~EIA~~lgis~~~V~~~~~  253 (264)
T PRK07122        223 VLVLRFFESMTQTQIAERVGISQMHVSRLLA  253 (264)
T ss_pred             HHHHHhcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3344445799999999999999999998765

>PRK06596 RNA polymerase factor sigma-32; Reviewed

Probab=86.53  E-value=0.7  Score=37.60  Aligned_cols=24  Identities=17%  Similarity=0.173  Sum_probs=22.5

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      .++|++|+|+.+|||+.+|+++++
T Consensus       247 ~~~Tl~EIA~~lgvS~~rVrqi~~  270 (284)
T PRK06596        247 DKSTLQELAAEYGVSAERVRQIEK  270 (284)
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHH
Confidence            379999999999999999999996

>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR

Probab=86.50  E-value=1.6  Score=30.37  Aligned_cols=38  Identities=8%  Similarity=-0.060  Sum_probs=27.8

Q ss_pred             cchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHH
Q psy6501          28 KVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        28 ~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~   65 (174)
                      .+...-...|..+...-++|+.+||+.+|++++++++.
T Consensus        25 ~lt~~q~~iL~~l~~~~~~t~~ela~~~~~~~~tvs~~   62 (118)
T TIGR02337        25 GLTEQQWRILRILAEQGSMEFTQLANQACILRPSLTGI   62 (118)
T ss_pred             CCCHHHHHHHHHHHHcCCcCHHHHHHHhCCCchhHHHH
Confidence            33333334566666778899999999999999999744

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.

>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain

Probab=86.40  E-value=3  Score=25.59  Aligned_cols=53  Identities=11%  Similarity=0.188  Sum_probs=35.8

Q ss_pred             HHHHHHHHHhCcccccccCCCCCCCCCcccchhhhhhhhhhcccccHHHHHHHHHHHHhcCCCHHHHHHHhC
Q psy6501          75 AIIGKMERALGIRLRVNAGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKIN  146 (174)
Q Consensus        75 ~~l~~la~~L~v~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~i~~~R~~~glsq~ela~~lg  146 (174)
                      +.+..+|+.|||+.+++.++....                   .+...=.-.+--.+...++|..+++..+|
T Consensus         4 ~I~~~Va~~~~i~~~~i~s~~R~~-------------------~~~~aR~iamyla~~~~~~sl~~Ig~~fg   56 (60)
T smart00760        4 EIIEAVAEYFGVKPEDLKSKSRKR-------------------EIVLARQIAMYLARELTDLSLPEIGKIFG   56 (60)
T ss_pred             HHHHHHHHHhCCCHHHHhcCCCCc-------------------chhHHHHHHHHHHHHHHCCCHHHHHHHhC
Confidence            567799999999999998644311                   11111112333467778999999999887

Could be involved in DNA-binding.

>smart00497 IENR1 Intron encoded nuclease repeat motif

Probab=86.36  E-value=1.2  Score=26.30  Aligned_cols=25  Identities=12%  Similarity=0.101  Sum_probs=22.6

Q ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCC
Q psy6501          47 SQKDLATKINEKPQIVNDYEGGRGI   71 (174)
Q Consensus        47 tq~eLA~~igvs~~~is~~E~G~~~   71 (174)
                      |+.|.|+.+|++.++|++.-+|...
T Consensus        19 S~~eAa~~lg~~~~~I~~~~~~~~~   43 (53)
T smart00497       19 SIREAAKYLGISHSSISKYLNTGKK   43 (53)
T ss_pred             CHHHHHHHhCCCHHHHHHHHhCCCc
Confidence            7899999999999999999998643

Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).

>PRK13832 plasmid partitioning protein; Provisional

Probab=86.35  E-value=1.5  Score=38.66  Aligned_cols=50  Identities=16%  Similarity=0.244  Sum_probs=37.7

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHH
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKME   81 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la   81 (174)
                      ..+-...++.+. ..|+|++++|..+|+|+++|+++-. -...++..+..++
T Consensus       104 PiEea~AfkrLi-e~G~T~EeIA~~lG~S~~~V~rlll-LA~L~P~lLdal~  153 (520)
T PRK13832        104 PVDQWRAIERLV-ALGWTEEAIAVALALPVRQIRKLRL-LANVLPAMLDHMA  153 (520)
T ss_pred             HHHHHHHHHHHH-hcCCCHHHHHHHHCCCHHHHHHHHH-HcCCCHHHHHHHH
Confidence            355677778887 7999999999999999999998643 2334555555555

>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional

Probab=86.17  E-value=1.3  Score=34.34  Aligned_cols=22  Identities=5%  Similarity=0.107  Sum_probs=19.3

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHH
Q psy6501          45 GWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        45 gltq~eLA~~igvs~~~is~~E   66 (174)
                      .+||++||+.+|+|+.+||+.-
T Consensus       184 ~lt~~~iA~~lG~sr~tvsR~l  205 (235)
T PRK11161        184 TMTRGDIGNYLGLTVETISRLL  205 (235)
T ss_pred             cccHHHHHHHhCCcHHHHHHHH
Confidence            4899999999999999999854

>PRK10572 DNA-binding transcriptional regulator AraC; Provisional

Probab=86.15  E-value=5.4  Score=32.01  Aligned_cols=15  Identities=0%  Similarity=0.034  Sum_probs=11.3

Q ss_pred             cCCCHHHHHHHhCCC
Q psy6501         134 KGWSQKDLATKINEK  148 (174)
Q Consensus       134 ~glsq~ela~~lg~~  148 (174)
                      .+++..++|..+|.+
T Consensus       247 t~~sI~eIA~~~GF~  261 (290)
T PRK10572        247 TRMPIATIGRNVGYD  261 (290)
T ss_pred             CCCCHHHHHHHhCCC
Confidence            457788888888776

>PRK06986 fliA flagellar biosynthesis sigma factor; Validated

Probab=86.14  E-value=7  Score=30.59  Aligned_cols=32  Identities=9%  Similarity=0.125  Sum_probs=25.9

Q ss_pred             HHHHHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         126 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       126 ~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      .+-.++-..|+|.+++|+.+|++.++|.....
T Consensus       191 ~vl~l~~~~g~s~~EIA~~lgis~~tV~~~~~  222 (236)
T PRK06986        191 LVLSLYYQEELNLKEIGAVLGVSESRVSQIHS  222 (236)
T ss_pred             HHHHhHhccCCCHHHHHHHHCCCHHHHHHHHH
Confidence            33345557899999999999999999987654

>PRK13182 racA polar chromosome segregation protein; Reviewed

Probab=86.09  E-value=1  Score=34.28  Aligned_cols=46  Identities=15%  Similarity=0.155  Sum_probs=32.1

Q ss_pred             CCHHHHHHHhCCCHHHHHHHH-----------cCCCCCCHHHHHHH-----HHHhCcccccc
Q psy6501          46 WSQKDLATKINEKPQIVNDYE-----------GGRGIPNQAIIGKM-----ERALGIRLRVN   91 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E-----------~G~~~P~~~~l~~l-----a~~L~v~~~~l   91 (174)
                      ||..++|+.+|||..||..|+           +|.+.-+.+.+..|     ....|+++.++
T Consensus         1 mti~evA~~lGVS~~TLRrw~k~g~L~~~R~~~G~R~y~~~dl~~L~~I~~l~~~Gm~i~~i   62 (175)
T PRK13182          1 MKTPFVAKKLGVSPKTVQRWVKQLNLPCEKNEYGHYIFTEEDLQLLEYVKSQIEEGQNMQDT   62 (175)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHcCCCCCCcCCCCCEEECHHHHHHHHHHHHHHHcCCCHHHH
Confidence            578999999999999999997           55555554444433     23355665554

>PRK13413 mpi multiple promoter invertase; Provisional

Probab=86.04  E-value=1.5  Score=33.63  Aligned_cols=33  Identities=15%  Similarity=0.177  Sum_probs=27.0

Q ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcC
Q psy6501          35 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGG   68 (174)
Q Consensus        35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G   68 (174)
                      ..|..++ ..|+|..++|+.+|||++||.+|-+.
T Consensus       163 ~~i~~~~-~~g~s~~~iak~lgis~~Tv~r~~k~  195 (200)
T PRK13413        163 EKIKKLL-DKGTSKSEIARKLGVSRTTLARFLKT  195 (200)
T ss_pred             HHHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHh
Confidence            3455553 56999999999999999999999763

>PRK08215 sporulation sigma factor SigG; Reviewed

Probab=85.98  E-value=3.8  Score=32.66  Aligned_cols=29  Identities=24%  Similarity=0.203  Sum_probs=25.0

Q ss_pred             HHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         129 QGRQAKGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       129 ~~R~~~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      .+|-..|+|++++|+.+|+++++|+.+++
T Consensus       219 ~~~~~~~~t~~eIA~~lgis~~~V~~~~~  247 (258)
T PRK08215        219 NLRFFQGKTQMEVAEEIGISQAQVSRLEK  247 (258)
T ss_pred             HHHHhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            44556799999999999999999998876

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

Probab=85.77  E-value=1  Score=24.37  Aligned_cols=22  Identities=14%  Similarity=0.167  Sum_probs=16.6

Q ss_pred             CCCHHHHHHHhCCChhHHHHHh
Q psy6501         135 GWSQKDLATKINEKPQIVNDYE  156 (174)
Q Consensus       135 glsq~ela~~lg~~~s~i~~~E  156 (174)
                      .+|.+|+|..+|.++.++++.-
T Consensus         2 ~mtr~diA~~lG~t~ETVSR~l   23 (32)
T PF00325_consen    2 PMTRQDIADYLGLTRETVSRIL   23 (32)
T ss_dssp             E--HHHHHHHHTS-HHHHHHHH
T ss_pred             CcCHHHHHHHhCCcHHHHHHHH
Confidence            3789999999999999998753

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 ....

>PRK11924 RNA polymerase sigma factor; Provisional

Probab=85.72  E-value=1.5  Score=32.10  Aligned_cols=29  Identities=17%  Similarity=0.111  Sum_probs=25.1

Q ss_pred             HHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          39 QGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        39 ~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      .++...|+|++|+|+.+|+|+++|.++..
T Consensus       135 ~l~~~~~~~~~eIA~~lgis~~tv~~~~~  163 (179)
T PRK11924        135 LLRYVEGLSYREIAEILGVPVGTVKSRLR  163 (179)
T ss_pred             hHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            34556899999999999999999999864

>COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]

Probab=85.65  E-value=1.2  Score=34.55  Aligned_cols=53  Identities=11%  Similarity=0.085  Sum_probs=48.4

Q ss_pred             HHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccC
Q psy6501          40 GRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAG   93 (174)
Q Consensus        40 ~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~   93 (174)
                      .+++.+.+++++++..|+++ ++..|.++-..++...+...+++|+..--+...
T Consensus         7 rq~el~~~~~~~~~~~g~~p-s~~e~~~~~~~~s~~~~~~~l~~L~~~g~i~~~   59 (201)
T COG1974           7 RQKELLDFIRSLIKETGYPP-SIREIGDALGLASPSAIHSHLKALERKGYIRRD   59 (201)
T ss_pred             HHHHHHHHHHHHHHHhCCCc-cHHHHHHhhCCCChHHHHHHHHHHhcCCcEEec
Confidence            77888999999999999999 899999999999999999999999998766553

>PRK06288 RNA polymerase sigma factor WhiG; Reviewed

Probab=85.61  E-value=3.3  Score=33.17  Aligned_cols=30  Identities=3%  Similarity=0.055  Sum_probs=24.6

Q ss_pred             HHHHHHhcCCCHHHHHHHhCCChhHHHHHh
Q psy6501         127 LMQGRQAKGWSQKDLATKINEKPQIVNDYE  156 (174)
Q Consensus       127 i~~~R~~~glsq~ela~~lg~~~s~i~~~E  156 (174)
                      +-.++-..|+|.+++|+.+|+++++|....
T Consensus       220 vl~l~~~~~~s~~eIA~~lgis~~tV~~~~  249 (268)
T PRK06288        220 VLILYYYEDLTLKEIGKVLGVTESRISQLH  249 (268)
T ss_pred             HHHHHHHcCCCHHHHHHHHCcCHHHHHHHH
Confidence            334555689999999999999999998665

>PRK07037 extracytoplasmic-function sigma-70 factor; Validated

Probab=85.60  E-value=1.8  Score=31.53  Aligned_cols=28  Identities=29%  Similarity=0.404  Sum_probs=24.8

Q ss_pred             HHHHHHcCCCHHHHHHHhCCCHHHHHHH
Q psy6501          38 MQGRQAKGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        38 k~~R~~~gltq~eLA~~igvs~~~is~~   65 (174)
                      -.++--.|+|.+|+|+.+|+|.++|...
T Consensus       118 ~~l~~~~~~s~~EIA~~lgis~~tV~~~  145 (163)
T PRK07037        118 FEMYRLHGETQKDIARELGVSPTLVNFM  145 (163)
T ss_pred             HHHHHHcCCCHHHHHHHHCCCHHHHHHH
Confidence            3466788999999999999999999976

>PF06322 Phage_NinH: Phage NinH protein; InterPro: IPR010454 This entry is represented by Bacteriophage 933W, NinH

Probab=85.54  E-value=0.98  Score=28.18  Aligned_cols=23  Identities=17%  Similarity=0.384  Sum_probs=20.7

Q ss_pred             CHHHHHHHhCCCHHHHHHHHcCC
Q psy6501          47 SQKDLATKINEKPQIVNDYEGGR   69 (174)
Q Consensus        47 tq~eLA~~igvs~~~is~~E~G~   69 (174)
                      .|.|+|+.+++++.||.+|-...
T Consensus        18 nqtEvaR~l~c~R~TVrKY~~D~   40 (64)
T PF06322_consen   18 NQTEVARRLGCNRATVRKYSRDK   40 (64)
T ss_pred             cHHHHHHHhcccHHHHHHHhccc
Confidence            79999999999999999997543

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>PRK11169 leucine-responsive transcriptional regulator; Provisional

Probab=85.49  E-value=1.5  Score=32.68  Aligned_cols=32  Identities=13%  Similarity=0.150  Sum_probs=27.2

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHH
Q psy6501          33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVND   64 (174)
Q Consensus        33 ig~~ik~~R~~~gltq~eLA~~igvs~~~is~   64 (174)
                      =-+-|..+.+.-.+|..+||+++|+|++++.+
T Consensus        16 D~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~   47 (164)
T PRK11169         16 DRNILNELQKDGRISNVELSKRVGLSPTPCLE   47 (164)
T ss_pred             HHHHHHHhccCCCCCHHHHHHHHCcCHHHHHH
Confidence            34567788899999999999999999988754

>PRK06759 RNA polymerase factor sigma-70; Validated

Probab=85.45  E-value=1.8  Score=31.12  Aligned_cols=29  Identities=14%  Similarity=-0.063  Sum_probs=25.2

Q ss_pred             HHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          38 MQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        38 k~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      -.++--.|+|.+|+|+.+|+|.++|..+-
T Consensus       115 i~l~~~~~~s~~EIA~~l~is~~tV~~~~  143 (154)
T PRK06759        115 IFERFFVGKTMGEIALETEMTYYQVRWIY  143 (154)
T ss_pred             HHHHHhcCCCHHHHHHHHCCCHHHHHHHH
Confidence            34567789999999999999999998875

>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily

Probab=85.43  E-value=1.7  Score=33.81  Aligned_cols=29  Identities=14%  Similarity=0.046  Sum_probs=25.3

Q ss_pred             HHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          39 QGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        39 ~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      .++-..|+|++|+|+.+|+|+++|..+.+
T Consensus       188 ~l~y~~~~s~~eIA~~lgis~~~v~~~~~  216 (227)
T TIGR02980       188 LLRFFEDKTQSEIAERLGISQMHVSRLLR  216 (227)
T ss_pred             HHHHhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            44556899999999999999999999874

This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.

>PRK05901 RNA polymerase sigma factor; Provisional

Probab=85.41  E-value=3.1  Score=36.85  Aligned_cols=24  Identities=4%  Similarity=0.072  Sum_probs=22.4

Q ss_pred             cCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         134 KGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       134 ~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      .++|+.++|+.+|++++.|+.+|.
T Consensus       466 e~~TL~EIa~~lGVSrERVRQIe~  489 (509)
T PRK05901        466 QPKTLDEIGQVYGVTRERIRQIES  489 (509)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHH
Confidence            569999999999999999999987

>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1

Probab=85.39  E-value=1.9  Score=30.96  Aligned_cols=30  Identities=17%  Similarity=0.091  Sum_probs=25.5

Q ss_pred             HHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          38 MQGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        38 k~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      -.++--.|+|..|+|+.+|+|+++|.....
T Consensus       122 l~l~~~~~~~~~eIA~~lgis~~tv~~~~~  151 (161)
T TIGR02985       122 FILSRFEGKSYKEIAEELGISVKTVEYHIS  151 (161)
T ss_pred             HHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            345667899999999999999999988753

This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.

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

Probab=85.24  E-value=3.5  Score=24.90  Aligned_cols=19  Identities=21%  Similarity=0.368  Sum_probs=16.8

Q ss_pred             CHHHHHHHhCCCHHHHHHH
Q psy6501          47 SQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        47 tq~eLA~~igvs~~~is~~   65 (174)
                      |..+||+.+|+|+++|++.
T Consensus        27 ~~~~la~~~~is~~~v~~~   45 (66)
T cd07377          27 SERELAEELGVSRTTVREA   45 (66)
T ss_pred             CHHHHHHHHCCCHHHHHHH
Confidence            4999999999999998854

This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=85.18  E-value=1.6  Score=28.59  Aligned_cols=23  Identities=13%  Similarity=0.200  Sum_probs=20.8

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E   66 (174)
                      .++|..|+|+.+|+++++++++-
T Consensus        19 ~~~t~~~ia~~l~i~~~tv~r~l   41 (91)
T smart00346       19 GGLTLAELAERLGLSKSTAHRLL   41 (91)
T ss_pred             CCcCHHHHHHHhCCCHHHHHHHH
Confidence            47999999999999999998874

>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family

Probab=85.11  E-value=1.9  Score=32.07  Aligned_cols=30  Identities=13%  Similarity=0.117  Sum_probs=25.5

Q ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          37 LMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        37 ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      +-.++.-.|+|.+|+|+.+|+|.+||...-
T Consensus       142 v~~l~~~~g~s~~EIA~~lgis~~tVk~~l  171 (183)
T TIGR02999       142 VVELRFFAGLTVEEIAELLGVSVRTVERDW  171 (183)
T ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Confidence            445577899999999999999999998764

This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.

>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR

Probab=85.05  E-value=1.4  Score=31.02  Aligned_cols=24  Identities=21%  Similarity=0.429  Sum_probs=21.2

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCC
Q psy6501          46 WSQKDLATKINEKPQIVNDYEGGR   69 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~G~   69 (174)
                      ++..|+|+.+|||..||.-||+-.
T Consensus         1 ~~Igeva~~~gvs~~tlRyYe~~G   24 (118)
T cd04776           1 YTISELAREFDVTPRTLRFYEDKG   24 (118)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCC
Confidence            578899999999999999999643

Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.

>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA

Probab=85.04  E-value=4.6  Score=32.23  Aligned_cols=18  Identities=17%  Similarity=0.088  Sum_probs=14.1

Q ss_pred             hcCCCHHHHHHHhCCChh
Q psy6501         133 AKGWSQKDLATKINEKPQ  150 (174)
Q Consensus       133 ~~glsq~ela~~lg~~~s  150 (174)
                      ..+++..++|..+|.+..
T Consensus       249 ~t~~sI~eIA~~~GF~s~  266 (287)
T TIGR02297       249 FTQHSINQIAYDLGYKDP  266 (287)
T ss_pred             cCCCCHHHHHHHhCCCCH
Confidence            466889999999988753

This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway.

>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily

Probab=84.86  E-value=1.5  Score=30.20  Aligned_cols=27  Identities=19%  Similarity=0.004  Sum_probs=23.1

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCC
Q psy6501          46 WSQKDLATKINEKPQIVNDYEGGRGIP   72 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~G~~~P   72 (174)
                      |+..|+|+.+|||..||.-||+-.-.|
T Consensus         1 m~Ige~a~~~gvs~~tlRyYe~~GLl~   27 (107)
T cd04777           1 MKIGKFAKKNNITIDTVRHYIDLGLLI   27 (107)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCCCcC
Confidence            578999999999999999999755443

Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family

Probab=84.85  E-value=1.8  Score=30.34  Aligned_cols=28  Identities=21%  Similarity=0.113  Sum_probs=24.2

Q ss_pred             HHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          40 GRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        40 ~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      ++--.|+|..++|+.+|+|+++|+++-+
T Consensus       121 ~~~~~g~s~~eIA~~l~~s~~~v~~~~~  148 (158)
T TIGR02937       121 LRYLEGLSYKEIAEILGISVGTVKRRLK  148 (158)
T ss_pred             hHHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            3446799999999999999999998864

Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.

>PRK12423 LexA repressor; Provisional

Probab=84.81  E-value=3.7  Score=31.64  Aligned_cols=35  Identities=9%  Similarity=0.153  Sum_probs=30.0

Q ss_pred             hHHHHHHHHHHHHHcCC--CHHHHHHHhC-CCHHHHHH
Q psy6501          30 PLDLAKLLMQGRQAKGW--SQKDLATKIN-EKPQIVND   64 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gl--tq~eLA~~ig-vs~~~is~   64 (174)
                      ...+-++|+..-.+.|+  |..|||+.+| +|+++|+.
T Consensus         8 q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~   45 (202)
T PRK12423          8 RAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARK   45 (202)
T ss_pred             HHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHH
Confidence            45778888888888898  9999999999 59998873

>TIGR00180 parB_part ParB-like partition proteins

Probab=84.77  E-value=3.3  Score=31.45  Aligned_cols=50  Identities=18%  Similarity=0.190  Sum_probs=36.2

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHH
Q psy6501         121 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKME  171 (174)
Q Consensus       121 ~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~  171 (174)
                      .+....+.......|++++++|+.+|++.++|+++-+=-..|+ .++..+.
T Consensus       106 ~e~a~~~~~l~~~~g~s~~~iA~~lg~s~~~V~r~l~l~~lp~-~v~~~~~  155 (187)
T TIGR00180       106 IEEAQAYKRLLEKFSMTQEDLAKKIGKSRAHITNLLRLLKLPS-EIQSAIP  155 (187)
T ss_pred             HHHHHHHHHHHHHhCCCHHHHHHHHCcCHHHHHHHHHHHcCCH-HHHHHHH
Confidence            3344455555556899999999999999999999988766443 4444443

This model represents the most well-conserved core of a set of chromosomal and plasmid partition proteins related to ParB, including Spo0J, RepB, and SopB. Spo0J has been shown to bind a specific DNA sequence that, when introduced into a plasmid, can serve as partition site. Study of RepB, which has nicking-closing activity, suggests that it forms a transient protein-DNA covalent intermediate during the strand transfer reaction.

>PF13518 HTH_28: Helix-turn-helix domain

Probab=84.71  E-value=1.3  Score=25.89  Aligned_cols=24  Identities=17%  Similarity=0.215  Sum_probs=21.5

Q ss_pred             cCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         134 KGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       134 ~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      .|.|..++|..+|++++++..|-.
T Consensus        11 ~g~s~~~~a~~~gis~~tv~~w~~   34 (52)
T PF13518_consen   11 EGESVREIAREFGISRSTVYRWIK   34 (52)
T ss_pred             cCCCHHHHHHHHCCCHhHHHHHHH
Confidence            577999999999999999988865

>PRK09391 fixK transcriptional regulator FixK; Provisional

Probab=84.70  E-value=2  Score=33.49  Aligned_cols=36  Identities=17%  Similarity=0.154  Sum_probs=26.0

Q ss_pred             hHHHHHHHHHHHHH--------cCCCHHHHHHHhCCCHHHHHHH
Q psy6501          30 PLDLAKLLMQGRQA--------KGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        30 ~~~ig~~ik~~R~~--------~gltq~eLA~~igvs~~~is~~   65 (174)
                      ...+...|..+.+.        ..+||++||..+|+++.++|+.
T Consensus       156 ~~Rla~~Ll~l~~~~g~~~~i~i~lt~~~IA~~lGisretlsR~  199 (230)
T PRK09391        156 MERVAAFLLEMDERLGGAGMMALPMSRRDIADYLGLTIETVSRA  199 (230)
T ss_pred             HHHHHHHHHHHHHHhCCCCEEEecCCHHHHHHHHCCCHHHHHHH
Confidence            34455555555443        3479999999999999998884

>PRK05572 sporulation sigma factor SigF; Validated

Probab=84.69  E-value=18  Score=28.62  Aligned_cols=38  Identities=16%  Similarity=0.081  Sum_probs=28.6

Q ss_pred             ccHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         119 VPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       119 ~~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      ++......+ ..+-..|+|++++|+.+|+++++|+.+++
T Consensus       203 L~~~~~~v~-~l~~~~~~s~~eIA~~lgis~~~V~~~~~  240 (252)
T PRK05572        203 LDERERLIV-YLRYFKDKTQSEVAKRLGISQVQVSRLEK  240 (252)
T ss_pred             CCHHHHHHH-HHHHhCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            333333444 34556899999999999999999998876

>PRK13918 CRP/FNR family transcriptional regulator; Provisional

Probab=84.44  E-value=0.98  Score=34.12  Aligned_cols=23  Identities=13%  Similarity=0.083  Sum_probs=20.2

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ..+||++||..+|+++.+||+.-
T Consensus       148 ~~~t~~~iA~~lG~tretvsR~l  170 (202)
T PRK13918        148 IYATHDELAAAVGSVRETVTKVI  170 (202)
T ss_pred             ecCCHHHHHHHhCccHHHHHHHH
Confidence            35799999999999999999854

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=84.43  E-value=1.9  Score=29.39  Aligned_cols=29  Identities=24%  Similarity=0.282  Sum_probs=23.6

Q ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHH
Q psy6501          37 LMQGRQAKGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        37 ik~~R~~~gltq~eLA~~igvs~~~is~~   65 (174)
                      |+.+...-.+|..+||+.+|+|++++++.
T Consensus         9 l~~L~~~~~~~~~~la~~l~~s~~tv~~~   37 (108)
T smart00344        9 LEELQKDARISLAELAKKVGLSPSTVHNR   37 (108)
T ss_pred             HHHHHHhCCCCHHHHHHHHCcCHHHHHHH
Confidence            44555556799999999999999998764

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

>PRK09652 RNA polymerase sigma factor RpoE; Provisional

Probab=84.35  E-value=2.1  Score=31.49  Aligned_cols=29  Identities=17%  Similarity=0.063  Sum_probs=24.8

Q ss_pred             HHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          39 QGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        39 ~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      .++.-.|+|.+|+|+.+|+|.++|+.+-.
T Consensus       138 ~l~~~~~~s~~eIA~~lgis~~tV~~~l~  166 (182)
T PRK09652        138 TLREIEGLSYEEIAEIMGCPIGTVRSRIF  166 (182)
T ss_pred             HHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            34566899999999999999999987754

>TIGR02895 spore_sigI RNA polymerase sigma-I factor

Probab=84.33  E-value=6  Score=31.06  Aligned_cols=78  Identities=15%  Similarity=0.177  Sum_probs=48.9

Q ss_pred             CCCCHHHHH---HHHHHhCcccccccCCCCCCCCCcccchhhhhhhhhhcccccHHHHHHHHHHHHhcCCCHHHHHHHhC
Q psy6501          70 GIPNQAIIG---KMERALGIRLRVNAGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKIN  146 (174)
Q Consensus        70 ~~P~~~~l~---~la~~L~v~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~i~~~R~~~glsq~ela~~lg  146 (174)
                      +.|..+.+.   +.-..||++.++|......|..        .-...............+.....+.+.+..+++++.++
T Consensus       116 ~~~~~eEI~~~~~~L~~~gi~~~dLv~~sPkh~d--------~r~~~i~ia~~~~~~~~l~~~l~~kk~LP~k~l~~~~~  187 (218)
T TIGR02895       116 NENRRLEILEYKKLLKQFGIEFVELVKVSPKHRD--------TRKKAIKIAKVIVENEELLEYLIRKKKLPIKEIEERVR  187 (218)
T ss_pred             cccHHHHHHHHHHHHHHcCCcHHHHhhcCCCCHH--------HHHHHHHHHHHHhcCHHHHHHHHHhCCCCHHHHHHHcC
Confidence            455555544   4445689999999854443321        11111111122223345667778889999999999999


Q ss_pred             CChhHHHHH
Q psy6501         147 EKPQIVNDY  155 (174)
Q Consensus       147 ~~~s~i~~~  155 (174)
                      +++.|+.++
T Consensus       188 v~rktier~  196 (218)
T TIGR02895       188 ISRKTIERY  196 (218)
T ss_pred             CCHHHHHHh
Confidence            999998654

Members of this sigma factor protein family are strictly limited to endospore-forming species in the Firmicutes lineage of bacteria, but are not universally present among such species. Sigma-I was shown to be induced by heat shock (PubMed:11157964) in Bacillus subtilis and is suggested by its phylogenetic profile to be connected to the program of sporulation (PubMed:16311624).

>smart00422 HTH_MERR helix_turn_helix, mercury resistance

Probab=84.28  E-value=1.6  Score=27.11  Aligned_cols=22  Identities=14%  Similarity=0.215  Sum_probs=19.9

Q ss_pred             CCHHHHHHHhCCChhHHHHHhc
Q psy6501         136 WSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       136 lsq~ela~~lg~~~s~i~~~E~  157 (174)
                      ++..++|+.+|++++++..|+.
T Consensus         1 ~s~~eva~~~gvs~~tlr~~~~   22 (70)
T smart00422        1 YTIGEVAKLAGVSVRTLRYYER   22 (70)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5788999999999999999976

>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional

Probab=84.28  E-value=1  Score=34.20  Aligned_cols=22  Identities=5%  Similarity=0.135  Sum_probs=20.0

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHH
Q psy6501          45 GWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        45 gltq~eLA~~igvs~~~is~~E   66 (174)
                      .+||++||+.+|+++.+||+.-
T Consensus       168 ~~t~~~lA~~lG~tr~tvsR~l  189 (211)
T PRK11753        168 KITRQEIGRIVGCSREMVGRVL  189 (211)
T ss_pred             CCCHHHHHHHhCCCHHHHHHHH
Confidence            5899999999999999999864

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=84.19  E-value=2  Score=34.31  Aligned_cols=28  Identities=18%  Similarity=0.100  Sum_probs=24.8

Q ss_pred             HHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          40 GRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        40 ~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      +|--.|+|++|+|+.+|+|.++|+++..
T Consensus       214 l~y~~~~s~~eIA~~lgvs~~~V~~~~~  241 (256)
T PRK07408        214 FVFLHDLTQKEAAERLGISPVTVSRRVK  241 (256)
T ss_pred             HHHHCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            4555799999999999999999999974

>PRK09639 RNA polymerase sigma factor SigX; Provisional

Probab=84.19  E-value=2.1  Score=31.25  Aligned_cols=30  Identities=23%  Similarity=0.246  Sum_probs=25.7

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          36 LLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      .+-.++. .|+|.+|+|+.+|+|.++|...-
T Consensus       119 ~il~l~~-~g~s~~eIA~~lgis~~tV~~~i  148 (166)
T PRK09639        119 TVLLLRF-SGYSYKEIAEALGIKESSVGTTL  148 (166)
T ss_pred             HHHHHHH-cCCCHHHHHHHHCCCHHHHHHHH
Confidence            3445667 99999999999999999998875

>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD

Probab=84.18  E-value=1.6  Score=29.40  Aligned_cols=27  Identities=7%  Similarity=0.148  Sum_probs=24.5

Q ss_pred             HhcCCCHHHHHHHhCCChhHHHHHhcC
Q psy6501         132 QAKGWSQKDLATKINEKPQIVNDYEGG  158 (174)
Q Consensus       132 ~~~glsq~ela~~lg~~~s~i~~~E~G  158 (174)
                      ...|+|..++|+.+|++++||.++-+|
T Consensus        47 l~~G~S~~eIA~~LgISrsTIyRi~R~   73 (88)
T TIGR02531        47 LKQGKTYSDIEAETGASTATISRVKRC   73 (88)
T ss_pred             HHCCCCHHHHHHHHCcCHHHHHHHHHh
Confidence            357899999999999999999999885

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.

>PRK13503 transcriptional activator RhaS; Provisional

Probab=84.08  E-value=6.5  Score=31.15  Aligned_cols=17  Identities=18%  Similarity=0.040  Sum_probs=14.1

Q ss_pred             cCCCHHHHHHHhCCChh
Q psy6501         134 KGWSQKDLATKINEKPQ  150 (174)
Q Consensus       134 ~glsq~ela~~lg~~~s  150 (174)
                      .+++..++|..+|.+..
T Consensus       235 ~~~sI~eIA~~~GF~~~  251 (278)
T PRK13503        235 SDASVTDIAYRCGFGDS  251 (278)
T ss_pred             CCCCHHHHHHHhCCCCH
Confidence            46899999999998764

>PRK13501 transcriptional activator RhaR; Provisional

Probab=84.07  E-value=6.1  Score=31.79  Aligned_cols=16  Identities=13%  Similarity=0.119  Sum_probs=10.2

Q ss_pred             cCCCHHHHHHHhCCCh
Q psy6501         134 KGWSQKDLATKINEKP  149 (174)
Q Consensus       134 ~glsq~ela~~lg~~~  149 (174)
                      -.++..++|..+|.+-
T Consensus       240 t~~sI~eIA~~~GF~~  255 (290)
T PRK13501        240 SEHRISDIAARCGFED  255 (290)
T ss_pred             CCCCHHHHHHHhCCCC
Confidence            4466777777777643

>PF12833 HTH_18: Helix-turn-helix domain; PDB: 2K9S_A 3LSG_C 3OIO_A 1D5Y_B 3GBG_A 3OOU_A 1BL0_A 1XS9_A 3MN2_B 3MKL_B

Probab=84.06  E-value=5.2  Score=25.54  Aligned_cols=19  Identities=21%  Similarity=0.167  Sum_probs=11.9

Q ss_pred             HhcCCCHHHHHHHhCCChh
Q psy6501         132 QAKGWSQKDLATKINEKPQ  150 (174)
Q Consensus       132 ~~~glsq~ela~~lg~~~s  150 (174)
                      ...+++..++|..+|.+..
T Consensus        42 ~~~~~~i~~ia~~~Gf~~~   60 (81)
T PF12833_consen   42 QNTDLSIAEIAEECGFSSQ   60 (81)
T ss_dssp             HHTT--HHHHHHHTT-SSH
T ss_pred             HhhcccHHHHHHHcCCCCH
Confidence            3467888888888888753

...

>PRK13502 transcriptional activator RhaR; Provisional

Probab=83.94  E-value=5.1  Score=31.96  Aligned_cols=16  Identities=0%  Similarity=-0.039  Sum_probs=12.3

Q ss_pred             cCCCHHHHHHHhCCCh
Q psy6501         134 KGWSQKDLATKINEKP  149 (174)
Q Consensus       134 ~glsq~ela~~lg~~~  149 (174)
                      -.++..++|..+|.+-
T Consensus       240 t~~sI~eIA~~~GF~d  255 (282)
T PRK13502        240 SPLMISEISMQCGFED  255 (282)
T ss_pred             CCCCHHHHHHHcCCCC
Confidence            3578888888888775

>COG5484 Uncharacterized conserved protein [Function unknown]

Probab=83.77  E-value=0.98  Score=36.23  Aligned_cols=28  Identities=25%  Similarity=0.443  Sum_probs=24.5

Q ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHHcCC
Q psy6501          42 QAKGWSQKDLATKINEKPQIVNDYEGGR   69 (174)
Q Consensus        42 ~~~gltq~eLA~~igvs~~~is~~E~G~   69 (174)
                      --.||..+++|+++|||++||..|-+-.
T Consensus        16 yl~gmk~~dIAeklGvspntiksWKrr~   43 (279)
T COG5484          16 YLKGMKLKDIAEKLGVSPNTIKSWKRRD   43 (279)
T ss_pred             HHhhccHHHHHHHhCCChHHHHHHHHhc
Confidence            3467999999999999999999998644

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

Probab=83.72  E-value=2.1  Score=26.24  Aligned_cols=30  Identities=23%  Similarity=0.145  Sum_probs=23.8

Q ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          37 LMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        37 ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      |..+-+...+|..+||+.+|+|..+|.++-
T Consensus        11 l~~L~~~~~~~~~ela~~l~~S~rti~~~i   40 (59)
T PF08280_consen   11 LELLLKNKWITLKELAKKLNISERTIKNDI   40 (59)
T ss_dssp             HHHHHHHTSBBHHHHHHHCTS-HHHHHHHH
T ss_pred             HHHHHcCCCCcHHHHHHHHCCCHHHHHHHH
Confidence            344556788999999999999999998764

; PDB: 2WTE_A 3SQN_A.

>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein

Probab=83.66  E-value=3.2  Score=27.24  Aligned_cols=38  Identities=16%  Similarity=0.080  Sum_probs=28.1

Q ss_pred             chHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          29 VPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        29 ~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      +...--.-|..+....++|+.++|+.+++++++|++.-
T Consensus         8 l~~~~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l   45 (101)
T smart00347        8 LTPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVL   45 (101)
T ss_pred             CCHHHHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHH
Confidence            33344445556666668999999999999999888654

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

Probab=83.62  E-value=1.4  Score=27.81  Aligned_cols=30  Identities=20%  Similarity=0.194  Sum_probs=20.8

Q ss_pred             HHHH-HHHHcCCCHHHHHHHhCCCHHHHHHH
Q psy6501          36 LLMQ-GRQAKGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        36 ~ik~-~R~~~gltq~eLA~~igvs~~~is~~   65 (174)
                      .|+. +++...+|..|||..+++++++|..+
T Consensus         4 ~i~~~l~~~~~~S~~eLa~~~~~s~~~ve~m   34 (69)
T PF09012_consen    4 EIRDYLRERGRVSLAELAREFGISPEAVEAM   34 (69)
T ss_dssp             HHHHHHHHS-SEEHHHHHHHTT--HHHHHHH
T ss_pred             HHHHHHHHcCCcCHHHHHHHHCcCHHHHHHH
Confidence            3455 66677789999999999999877543

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

>PHA01082 putative transcription regulator

Probab=83.62  E-value=0.87  Score=32.38  Aligned_cols=41  Identities=17%  Similarity=0.198  Sum_probs=34.7

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHcCCCCCC-HHHHHHHHHH
Q psy6501          43 AKGWSQKDLATKINEKPQIVNDYEGGRGIPN-QAIIGKMERA   83 (174)
Q Consensus        43 ~~gltq~eLA~~igvs~~~is~~E~G~~~P~-~~~l~~la~~   83 (174)
                      +.|+|.+|-|+.+--|.++|.+|-.|+..|+ ...|.++-..
T Consensus        28 eCgLsveeaa~LCfKsVrtVk~WD~G~~IPPeCkRLMr~~~g   69 (133)
T PHA01082         28 ECGLSVEEAAKLCFKTVSEVKQWDAGEKIPPICKRLMRWHSR   69 (133)
T ss_pred             ccCccHHHHHHHHHHhHHHHhhccCCCcCChHHHHHHHHhcc
Confidence            7899999999999999999999999997654 5666666544

>COG1513 CynS Cyanate lyase [Inorganic ion transport and metabolism]

Probab=83.59  E-value=5.6  Score=28.78  Aligned_cols=54  Identities=28%  Similarity=0.260  Sum_probs=47.7

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         121 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       121 ~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ..+.+.+-...+.+|+|=+|++..+|.++-.+...-.|....+.+-+++++++|
T Consensus         7 ~~l~~~ll~~Kk~kgLsfaDl~~~lG~~ev~vaa~~ygqa~~~~~ear~v~e~L   60 (151)
T COG1513           7 LDLADALLLAKKKKGLSFADLADGLGLAEVFVAAALYGQAALPADEARAVGEAL   60 (151)
T ss_pred             HHHHHHHHHHHHhcCCcHHHHHhhcCccHHHHHHHHHhhccCCHHHHHHHHHHh
Confidence            445667777888999999999999999999999999999999999999888765

>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family

Probab=83.51  E-value=2.5  Score=30.56  Aligned_cols=27  Identities=26%  Similarity=0.225  Sum_probs=23.6

Q ss_pred             HHHHHcCCCHHHHHHHhCCCHHHHHHH
Q psy6501          39 QGRQAKGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        39 ~~R~~~gltq~eLA~~igvs~~~is~~   65 (174)
                      .++.-.|+|.+|+|+.+|+|.++|...
T Consensus       121 ~l~~~~g~~~~eIA~~l~is~~tv~~~  147 (159)
T TIGR02989       121 QLRYQRGVSLTALAEQLGRTVNAVYKA  147 (159)
T ss_pred             HHHHhcCCCHHHHHHHhCCCHHHHHHH
Confidence            346778999999999999999999865

This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).

>PRK12519 RNA polymerase sigma factor; Provisional

Probab=83.51  E-value=1.8  Score=32.65  Aligned_cols=28  Identities=18%  Similarity=0.133  Sum_probs=24.7

Q ss_pred             HHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          40 GRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        40 ~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      +|.-.|+|++|+|+.+|+|.++|..+-.
T Consensus       152 l~~~~g~s~~EIA~~lgis~~tV~~~l~  179 (194)
T PRK12519        152 LAYYEGLSQSEIAKRLGIPLGTVKARAR  179 (194)
T ss_pred             hhhhcCCCHHHHHHHhCCCHHHHHHHHH
Confidence            4566899999999999999999998863

>PRK03341 arginine repressor; Provisional

Probab=83.47  E-value=2.2  Score=32.19  Aligned_cols=31  Identities=13%  Similarity=0.041  Sum_probs=23.5

Q ss_pred             HHHHH-HHHcCCCHHHHHHHh-----CCCHHHHHHHH
Q psy6501          36 LLMQG-RQAKGWSQKDLATKI-----NEKPQIVNDYE   66 (174)
Q Consensus        36 ~ik~~-R~~~gltq~eLA~~i-----gvs~~~is~~E   66 (174)
                      .|+++ ++..=-||+||++.+     ++|+.|||+.-
T Consensus        19 ~I~~li~~~~i~tQ~eL~~~L~~~Gi~vTQaTiSRDl   55 (168)
T PRK03341         19 RIVAILSRQSVRSQAELAALLADEGIEVTQATLSRDL   55 (168)
T ss_pred             HHHHHHHHCCCccHHHHHHHHHHcCCcccHHHHHHHH
Confidence            34444 444455999999999     99999999854

>PRK09413 IS2 repressor TnpA; Reviewed

Probab=83.37  E-value=3.5  Score=29.09  Aligned_cols=38  Identities=8%  Similarity=-0.035  Sum_probs=29.1

Q ss_pred             cHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         120 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       120 ~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      +.++...+-..-...|.+..++|..+|++++++.+|-+
T Consensus        14 s~EfK~~aV~~~~~~g~sv~evA~e~gIs~~tl~~W~r   51 (121)
T PRK09413         14 TTQEKIAIVQQSFEPGMTVSLVARQHGVAASQLFLWRK   51 (121)
T ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            34444444444456899999999999999999999954

>PF13309 HTH_22: HTH domain

Probab=83.32  E-value=3.6  Score=25.75  Aligned_cols=28  Identities=21%  Similarity=0.186  Sum_probs=22.1

Q ss_pred             HHHHHcCC-----CHHHHHHHhCCCHHHHHHHH
Q psy6501          39 QGRQAKGW-----SQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        39 ~~R~~~gl-----tq~eLA~~igvs~~~is~~E   66 (174)
                      ....++|+     +-..+|+.+|||+.||.+|-
T Consensus        31 ~~L~~~G~F~lKgav~~vA~~L~iS~~TVY~YL   63 (64)
T PF13309_consen   31 RQLYEKGIFLLKGAVEYVAEKLGISRATVYRYL   63 (64)
T ss_pred             HHHHHCCCcccCcHHHHHHHHHCCCHHHHHHHc
Confidence            34455665     77889999999999999884

>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor

Probab=83.29  E-value=5.5  Score=22.92  Aligned_cols=29  Identities=17%  Similarity=0.223  Sum_probs=23.4

Q ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHH
Q psy6501          37 LMQGRQAKGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        37 ik~~R~~~gltq~eLA~~igvs~~~is~~   65 (174)
                      +-.-+--.++|..++|+++|+|++++.++
T Consensus         8 l~~~~G~~~~s~~~Ia~~~gvs~~~~y~~   36 (47)
T PF00440_consen    8 LFAEKGYEAVSIRDIARRAGVSKGSFYRY   36 (47)
T ss_dssp             HHHHHHTTTSSHHHHHHHHTSCHHHHHHH
T ss_pred             HHHHhCHHhCCHHHHHHHHccchhhHHHH
Confidence            33344556889999999999999999876

Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....

>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional

Probab=83.28  E-value=1.3  Score=34.15  Aligned_cols=25  Identities=16%  Similarity=0.222  Sum_probs=22.9

Q ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          42 QAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        42 ~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      -..|+|-+|+|+++++|.+||..+-
T Consensus       149 la~G~snkeIA~~L~iS~~TVk~h~  173 (207)
T PRK15411        149 WMAGQGTIQISDQMNIKAKTVSSHK  173 (207)
T ss_pred             HHcCCCHHHHHHHcCCCHHHHHHHH
Confidence            4689999999999999999999875

>PRK08583 RNA polymerase sigma factor SigB; Validated

Probab=83.27  E-value=2.3  Score=33.76  Aligned_cols=29  Identities=17%  Similarity=0.146  Sum_probs=25.6

Q ss_pred             HHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          39 QGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        39 ~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      .++--.|+|++|+|+.+|+|.++|+.+..
T Consensus       215 ~l~~~~g~s~~eIA~~l~is~~tV~~~~~  243 (257)
T PRK08583        215 QCTFIENLSQKETGERLGISQMHVSRLQR  243 (257)
T ss_pred             HHHHhCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            34567899999999999999999999974

>PRK07122 RNA polymerase sigma factor SigF; Reviewed

Probab=83.25  E-value=2  Score=34.50  Aligned_cols=31  Identities=13%  Similarity=0.124  Sum_probs=26.2

Q ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          37 LMQGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        37 ik~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      +-.+|-..|+|++|+|+.+|+|.++|++++.
T Consensus       223 vl~l~y~~~~t~~EIA~~lgis~~~V~~~~~  253 (264)
T PRK07122        223 VLVLRFFESMTQTQIAERVGISQMHVSRLLA  253 (264)
T ss_pred             HHHHHhcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3345556799999999999999999999875

>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR

Probab=83.24  E-value=1.8  Score=31.64  Aligned_cols=22  Identities=18%  Similarity=0.219  Sum_probs=20.7

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q psy6501          46 WSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~   67 (174)
                      ||..|+|+.+|||..||.-||+
T Consensus         2 ~~IgevA~~~Gvs~~tLRyYE~   23 (142)
T TIGR01950         2 LTVGELAKRSGVAVSALHFYES   23 (142)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            6889999999999999999994

SoxR is a MerR-family homodimeric transcription factor with a 2Fe-2S cluster in each monomer. The motif CIGCGCxxxxxC is conserved. Oxidation of the iron-sulfur cluster activates SoxR. The physiological role in E. coli is response to oxidative stress. It is activated by superoxide, singlet oxygen, nitric oxide (NO), and hydrogen peroxide. In E. coli, SoxR increases expression of transcription factor SoxS; different downstream targets may exist in other species.

>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella

Probab=83.23  E-value=4.5  Score=20.56  Aligned_cols=23  Identities=22%  Similarity=0.335  Sum_probs=20.6

Q ss_pred             hcCCCHHHHHHHhCCChhHHHHH
Q psy6501         133 AKGWSQKDLATKINEKPQIVNDY  155 (174)
Q Consensus       133 ~~glsq~ela~~lg~~~s~i~~~  155 (174)
                      ..+++..++++.+|++.+++..|
T Consensus        19 ~~~~s~~~ia~~~~is~~tv~~~   41 (42)
T cd00569          19 AAGESVAEIARRLGVSRSTLYRY   41 (42)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHh
Confidence            46789999999999999999876

The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D

>PRK13777 transcriptional regulator Hpr; Provisional

Probab=83.19  E-value=2.7  Score=32.20  Aligned_cols=42  Identities=14%  Similarity=0.109  Sum_probs=29.2

Q ss_pred             cccccchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHH
Q psy6501          24 LKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        24 ~~~~~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~   65 (174)
                      +++-.+...=...|..+....|+||++||+.++++++|++++
T Consensus        38 l~~~gLt~~q~~iL~~L~~~~~itq~eLa~~l~l~~sTvtr~   79 (185)
T PRK13777         38 IKPYDLNINEHHILWIAYHLKGASISEIAKFGVMHVSTAFNF   79 (185)
T ss_pred             HHHCCCCHHHHHHHHHHHhCCCcCHHHHHHHHCCCHhhHHHH
Confidence            333344434345566677777899999999999988887764

>PRK09646 RNA polymerase sigma factor SigK; Reviewed

Probab=83.09  E-value=5.1  Score=30.27  Aligned_cols=42  Identities=12%  Similarity=0.133  Sum_probs=32.2

Q ss_pred             HHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcc
Q psy6501          39 QGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIR   87 (174)
Q Consensus        39 ~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~   87 (174)
                      .++--.|+|.+|+|+.+|+|.++|...-.       .-+.+|...|+++
T Consensus       152 ~l~~~~~~s~~EIA~~Lgis~~tVk~~l~-------ra~~~Lr~~l~~~  193 (194)
T PRK09646        152 TLAYYGGLTYREVAERLAVPLGTVKTRMR-------DGLIRLRDCLGVS  193 (194)
T ss_pred             HHHHHcCCCHHHHHHHhCCChHhHHHHHH-------HHHHHHHHHhccC
Confidence            36678999999999999999999988753       4455666665543

>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition

Probab=82.94  E-value=1.4  Score=31.10  Aligned_cols=26  Identities=12%  Similarity=0.192  Sum_probs=22.4

Q ss_pred             HHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          41 RQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        41 R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      -..-++|+.|+|+.+|||.++|+..-
T Consensus        67 ~~~pd~tl~Ela~~l~Vs~~ti~~~L   92 (119)
T PF01710_consen   67 EENPDATLRELAERLGVSPSTIWRAL   92 (119)
T ss_pred             HHCCCcCHHHHHHHcCCCHHHHHHHH
Confidence            34689999999999999999988765

This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].

>PRK09047 RNA polymerase factor sigma-70; Validated

Probab=82.87  E-value=2.7  Score=30.45  Aligned_cols=30  Identities=10%  Similarity=-0.064  Sum_probs=25.4

Q ss_pred             HHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          38 MQGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        38 k~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      -.++.-.|+|.+|+|+.+|+|.++|...-.
T Consensus       115 ~~l~~~~g~s~~EIA~~lgis~~tV~~~l~  144 (161)
T PRK09047        115 FLLRYWEDMDVAETAAAMGCSEGSVKTHCS  144 (161)
T ss_pred             HHHHHHhcCCHHHHHHHHCCCHHHHHHHHH
Confidence            345677899999999999999999987753

>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease

Probab=82.71  E-value=3.5  Score=24.64  Aligned_cols=32  Identities=19%  Similarity=0.048  Sum_probs=26.1

Q ss_pred             HHHHHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         126 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       126 ~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      .+--.+-+.+.+..++|...|++.+++++|=+
T Consensus        10 ll~L~~LR~~~~~~~La~~FgIs~stvsri~~   41 (53)
T PF13613_consen   10 LLTLMYLRLNLTFQDLAYRFGISQSTVSRIFH   41 (53)
T ss_pred             HHHHHHHHcCCcHhHHhhheeecHHHHHHHHH
Confidence            44445667899999999999999999988743

>PRK13919 putative RNA polymerase sigma E protein; Provisional

Probab=82.51  E-value=2.7  Score=31.33  Aligned_cols=31  Identities=6%  Similarity=0.128  Sum_probs=26.2

Q ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          37 LMQGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        37 ik~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      +-.++.-.|+|.+|+|+.+|+|.++|...-.
T Consensus       143 vl~l~~~~~~s~~eIA~~lgis~~~V~~~l~  173 (186)
T PRK13919        143 VIEVLYYQGYTHREAAQLLGLPLGTLKTRAR  173 (186)
T ss_pred             HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3345778999999999999999999998764

>PRK06030 hypothetical protein; Provisional

Probab=82.47  E-value=6  Score=28.35  Aligned_cols=62  Identities=16%  Similarity=0.232  Sum_probs=40.8

Q ss_pred             HHHHHHHHHHhCcccccccCCCCCCCCCcccchhhhhhhhhhcccccHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHH
Q psy6501          74 QAIIGKMERALGIRLRVNAGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVN  153 (174)
Q Consensus        74 ~~~l~~la~~L~v~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~  153 (174)
                      ...+..+|++|||+++++.+.........                ..-.+...|  .|+..++|..++++.+|.+.++|.
T Consensus        26 d~Ii~~Va~~f~I~~~di~sk~R~rk~i~----------------~aRqIAMYL--~r~~~~~sl~~IG~~FGRDHSTV~   87 (124)
T PRK06030         26 EAVIDLLALAFGVSGAEIASPLRGRREVS----------------RIRQIAMYV--AHVSLGWPMNEVALAFGRDRTTVG   87 (124)
T ss_pred             HHHHHHHHHHhCCCHHHHhCCCCCCcccc----------------hHHHHHHHH--HHHHcCCCHHHHHHHHCCChhHHH
Confidence            45566899999999999986443211000                112222333  577789999999999998777653

>PRK06986 fliA flagellar biosynthesis sigma factor; Validated

Probab=82.46  E-value=2.4  Score=33.26  Aligned_cols=31  Identities=6%  Similarity=0.086  Sum_probs=26.4

Q ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          37 LMQGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        37 ik~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      +-.+|-..|+|.+|+|+.+|+|.++|..+..
T Consensus       192 vl~l~~~~g~s~~EIA~~lgis~~tV~~~~~  222 (236)
T PRK06986        192 VLSLYYQEELNLKEIGAVLGVSESRVSQIHS  222 (236)
T ss_pred             HHHhHhccCCCHHHHHHHHCCCHHHHHHHHH
Confidence            3345667899999999999999999998874

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

Probab=82.44  E-value=3  Score=32.77  Aligned_cols=36  Identities=8%  Similarity=0.052  Sum_probs=28.0

Q ss_pred             HHHHHHHHHHHH--HcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          31 LDLAKLLMQGRQ--AKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        31 ~~ig~~ik~~R~--~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ..--..|++.-+  ...+|-+|+|+.+|+|+.|+.+|-
T Consensus       157 ~~Tl~~i~~~~~~~~~~~Taeela~~~giSRvTaRRYL  194 (224)
T COG4565         157 ELTLQKVREALKEPDQELTAEELAQALGISRVTARRYL  194 (224)
T ss_pred             HHHHHHHHHHHhCcCCccCHHHHHHHhCccHHHHHHHH
Confidence            333445555555  678999999999999999999984

>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription

Probab=82.39  E-value=3.7  Score=24.22  Aligned_cols=31  Identities=16%  Similarity=0.149  Sum_probs=21.6

Q ss_pred             HHHHHHHHhcCCCHHHHHHHhCCChhHHHHH
Q psy6501         125 KLLMQGRQAKGWSQKDLATKINEKPQIVNDY  155 (174)
Q Consensus       125 ~~i~~~R~~~glsq~ela~~lg~~~s~i~~~  155 (174)
                      ..+-..+-..|+|.+++|+.+|++++++..+
T Consensus        16 r~i~~l~~~~g~s~~eIa~~l~~s~~~v~~~   46 (54)
T PF08281_consen   16 REIFLLRYFQGMSYAEIAEILGISESTVKRR   46 (54)
T ss_dssp             HHHHHHHHTS---HHHHHHHCTS-HHHHHHH
T ss_pred             HHHHHHHHHHCcCHHHHHHHHCcCHHHHHHH
Confidence            3444566779999999999999999988765

Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.

>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed

Probab=82.38  E-value=2.3  Score=34.73  Aligned_cols=36  Identities=22%  Similarity=0.271  Sum_probs=29.4

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCc
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGI   86 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v   86 (174)
                      .|+|++|+|+.+|||+.+|++++.       .-+.+|-..|..
T Consensus       244 ~~~t~~EIa~~lgvs~~~V~q~~~-------~Al~kLr~~l~~  279 (289)
T PRK07500        244 DGATLEALGEELGISKERVRQIEA-------RALEKLRRALLS  279 (289)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHH-------HHHHHHHHHHHh
Confidence            689999999999999999999985       455566665543

>PRK07406 RNA polymerase sigma factor RpoD; Validated

Probab=82.21  E-value=4.5  Score=34.44  Aligned_cols=24  Identities=8%  Similarity=0.138  Sum_probs=21.9

Q ss_pred             cCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         134 KGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       134 ~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      .++|.+++|+.+|+++..|..+|.
T Consensus       330 ~~~Tl~EIA~~lgiS~eRVRQie~  353 (373)
T PRK07406        330 RMKTLEEIGQIFNVTRERIRQIEA  353 (373)
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHH
Confidence            358999999999999999999886

>PRK12529 RNA polymerase sigma factor; Provisional

Probab=82.13  E-value=3  Score=31.11  Aligned_cols=29  Identities=24%  Similarity=0.288  Sum_probs=25.0

Q ss_pred             HHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          38 MQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        38 k~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      -.+|.-.|+|.+|+|+.+|+|.+||...-
T Consensus       136 ~~L~~~~g~s~~EIA~~lgis~~tVk~~l  164 (178)
T PRK12529        136 FLMATLDGMKQKDIAQALDIALPTVKKYI  164 (178)
T ss_pred             HHHHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence            44667789999999999999999998764

>PRK01905 DNA-binding protein Fis; Provisional

Probab=81.86  E-value=4.1  Score=26.42  Aligned_cols=33  Identities=15%  Similarity=-0.006  Sum_probs=28.8

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ...|+...+..|-++.+.|+.+|+|++++...-
T Consensus        39 ~~~i~~aL~~~~gn~s~aAr~LGIsrstL~rkl   71 (77)
T PRK01905         39 KPLLEVVMEQAGGNQSLAAEYLGINRNTLRKKL   71 (77)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence            446888999999999999999999999987654

>TIGR02941 Sigma_B RNA polymerase sigma-B factor

Probab=81.75  E-value=15  Score=29.02  Aligned_cols=32  Identities=13%  Similarity=0.158  Sum_probs=26.1

Q ss_pred             HHHHHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         126 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       126 ~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      .+-.++-..|+|.+++|+.+|+++++|..+.+
T Consensus       212 ~ii~l~~~~g~s~~eIA~~lgis~~~V~~~~~  243 (255)
T TIGR02941       212 SIIHCTFEENLSQKETGERLGISQMHVSRLQR  243 (255)
T ss_pred             HHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            34455557899999999999999999987764

This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.

>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed

Probab=81.67  E-value=2.9  Score=33.43  Aligned_cols=31  Identities=10%  Similarity=0.046  Sum_probs=26.5

Q ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          37 LMQGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        37 ik~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      |-.+|--.|+|++|+|+.+|+|.++|++++.
T Consensus       213 vi~l~y~e~~t~~EIA~~lgis~~~V~~~~~  243 (257)
T PRK05911        213 VMALYYYEELVLKEIGKILGVSESRVSQIHS  243 (257)
T ss_pred             HHHHHHhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3345556899999999999999999999985

>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function

Probab=81.66  E-value=1.6  Score=30.39  Aligned_cols=26  Identities=15%  Similarity=0.182  Sum_probs=22.1

Q ss_pred             HhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         132 QAKGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       132 ~~~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      -..|++|++.|+.+|+|.+|+.++-.
T Consensus        54 D~egl~QeeaA~~MgVSR~T~~ril~   79 (106)
T PF02001_consen   54 DYEGLSQEEAAERMGVSRPTFQRILE   79 (106)
T ss_pred             HHcCCCHHHHHHHcCCcHHHHHHHHH
Confidence            35889999999999999998877543

>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family

Probab=81.61  E-value=2.4  Score=34.70  Aligned_cols=25  Identities=12%  Similarity=0.238  Sum_probs=23.1

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          43 AKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        43 ~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      ..++|.+|+|+.+|+|+.+|.+++.
T Consensus       267 ~~~~Tl~EIa~~lgiS~erVrq~~~  291 (298)
T TIGR02997       267 GEPLTLAEIGRRLNLSRERVRQIEA  291 (298)
T ss_pred             CCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            3689999999999999999999985

This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).

>PRK15201 fimbriae regulatory protein FimW; Provisional

Probab=81.52  E-value=2  Score=32.95  Aligned_cols=26  Identities=12%  Similarity=0.167  Sum_probs=22.8

Q ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          42 QAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        42 ~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      -..|+|-+|+|+.+++|++||..+-+
T Consensus       145 LAqGkTnKEIAe~L~IS~rTVkth~s  170 (198)
T PRK15201        145 IASGYHLSETAALLSLSEEQTKSLRR  170 (198)
T ss_pred             HHCCCCHHHHHHHhCCCHHHHHHHHH
Confidence            35799999999999999999988753

>PRK09649 RNA polymerase sigma factor SigC; Reviewed

Probab=81.46  E-value=2.9  Score=31.45  Aligned_cols=30  Identities=17%  Similarity=-0.018  Sum_probs=25.9

Q ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          37 LMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        37 ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      +-.+|.-.|+|.+|+|+.+|+|.++|...-
T Consensus       138 v~~L~~~~g~s~~EIA~~lgis~~tVk~~l  167 (185)
T PRK09649        138 ALLLTQLLGLSYADAAAVCGCPVGTIRSRV  167 (185)
T ss_pred             HhhhHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence            344678899999999999999999998775

>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional

Probab=81.44  E-value=2.1  Score=31.76  Aligned_cols=29  Identities=14%  Similarity=0.098  Sum_probs=24.7

Q ss_pred             HHHHcCCCHHHHHHHhCCCHHHHHHHHcC
Q psy6501          40 GRQAKGWSQKDLATKINEKPQIVNDYEGG   68 (174)
Q Consensus        40 ~R~~~gltq~eLA~~igvs~~~is~~E~G   68 (174)
                      -|...=||..|+|+.+|||..||.-||.-
T Consensus         6 ~~~~~~~~IgevAk~~gvs~~TlRyYE~~   34 (154)
T PRK15002          6 PRIKALLTPGEVAKRSGVAVSALHFYESK   34 (154)
T ss_pred             hhhcccccHHHHHHHHCcCHHHHHHHHHC
Confidence            35555689999999999999999999943

>PRK12523 RNA polymerase sigma factor; Reviewed

Probab=81.39  E-value=3.3  Score=30.56  Aligned_cols=30  Identities=13%  Similarity=0.226  Sum_probs=25.7

Q ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          37 LMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        37 ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      +-.++.-.|+|.+|+|+.+|+|.++|...-
T Consensus       127 v~~L~~~~g~s~~EIA~~lgis~~tV~~~l  156 (172)
T PRK12523        127 AFLYNRLDGMGHAEIAERLGVSVSRVRQYL  156 (172)
T ss_pred             HHHHHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence            335567799999999999999999998775

>PRK09954 putative kinase; Provisional

Probab=81.33  E-value=3  Score=34.77  Aligned_cols=33  Identities=15%  Similarity=0.021  Sum_probs=27.8

Q ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          35 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      +-|+.+++...+|+.|||+.+|+|+++|.+.-+
T Consensus         7 ~il~~l~~~~~~s~~~la~~l~~s~~~v~~~i~   39 (362)
T PRK09954          7 EILAILRRNPLIQQNEIADILQISRSRVAAHIM   39 (362)
T ss_pred             HHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            456777788899999999999999998877654

>PRK12537 RNA polymerase sigma factor; Provisional

Probab=81.31  E-value=3.1  Score=31.05  Aligned_cols=29  Identities=14%  Similarity=0.243  Sum_probs=25.3

Q ss_pred             HHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          38 MQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        38 k~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      -.++.-.|+|.+|+|+.+|+|.++|..+-
T Consensus       142 ~~l~~~~~~s~~eIA~~lgis~~tV~~~l  170 (182)
T PRK12537        142 ILHAYVDGCSHAEIAQRLGAPLGTVKAWI  170 (182)
T ss_pred             HHHHHHcCCCHHHHHHHHCCChhhHHHHH
Confidence            44566799999999999999999998875

>PRK09642 RNA polymerase sigma factor SigW; Reviewed

Probab=81.14  E-value=3.4  Score=30.01  Aligned_cols=30  Identities=10%  Similarity=-0.007  Sum_probs=25.1

Q ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          37 LMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        37 ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      +-.++.-.|+|.+|+|+.+|+|.++|...-
T Consensus       114 v~~l~~~~g~s~~EIA~~lgis~~tV~~~l  143 (160)
T PRK09642        114 VVLAHYLEEKSYQEIALQEKIEVKTVEMKL  143 (160)
T ss_pred             HHHHHHHhCCCHHHHHHHHCCCHHHHHHHH
Confidence            344667789999999999999999997653

>PRK09645 RNA polymerase sigma factor SigL; Provisional

Probab=81.14  E-value=3.4  Score=30.43  Aligned_cols=30  Identities=17%  Similarity=0.317  Sum_probs=25.0

Q ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          37 LMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        37 ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      +-.+|.-.|+|.+|+|+.+|+|.++|...-
T Consensus       126 vl~L~~~~g~s~~EIA~~lgis~~tV~~~l  155 (173)
T PRK09645        126 VLVRSYYRGWSTAQIAADLGIPEGTVKSRL  155 (173)
T ss_pred             HHHHHHHcCCCHHHHHHHHCcCHHHHHHHH
Confidence            344567789999999999999999997654

>PRK14845 translation initiation factor IF-2; Provisional

Probab=81.10  E-value=2.3  Score=40.88  Aligned_cols=50  Identities=16%  Similarity=0.291  Sum_probs=43.0

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcc
Q psy6501          33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIR   87 (174)
Q Consensus        33 ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~   87 (174)
                      +..-|+.+|+..|+|+.|++.    .+++.+.||+ ...|+.+.+..+-..|.-.
T Consensus       323 i~~el~~lr~~~~lt~~e~~~----~~~~Y~~~e~-~~~~s~~~l~~~l~~~~~~  372 (1049)
T PRK14845        323 INEELKRLRLLFGFTRNELSS----NIPFYSKYES-EEAPSYEILMEILNSIERG  372 (1049)
T ss_pred             cHHHHHHHHHhcCcchhhccc----cchhhhhhhc-ccCCCHHHHHHHHHHHHhc
Confidence            445689999999999999987    6899999999 9999999999887776633

>PRK07670 RNA polymerase sigma factor SigD; Validated

Probab=80.94  E-value=7.2  Score=30.89  Aligned_cols=122  Identities=8%  Similarity=-0.027  Sum_probs=0.0

Q ss_pred             HHHHHHHHH------cCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccc---ccccCCCCCCCCCcccc
Q psy6501          35 KLLMQGRQA------KGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRL---RVNAGTNKQPGTTKNTA  105 (174)
Q Consensus        35 ~~ik~~R~~------~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~---~~l~~~~~~~~~~~~~~  105 (174)
                      .+++..++.      +.-+.+++|+.+|++...|...-.....+....|......-+-..   ..+..............
T Consensus       109 ~~~~~~~~~~~~~~~~~~~~~eia~~l~~~~~~v~~~~~~~~~~~~~sld~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~  188 (251)
T PRK07670        109 KKVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGFFANLLSIDEKTHDQDDGENVSVTIRDDKTPTPEEKLLK  188 (251)
T ss_pred             HHHHHHHHHHHHHHCCCCCHHHHHHHhCcCHHHHHHHHHHHhccCccccCccccCCCCcchhhhhhcCcCCCCHHHHHHH


Q ss_pred             hhhhhhhhhhcccccHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         106 KLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       106 ~l~~~~~~~~~~~~~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      .-....-......++......+ .++-..|+|.+++|+.+|+++++|.....
T Consensus       189 ~~~~~~l~~~l~~L~~~~r~vl-~l~~~~~~s~~EIA~~lgis~~tV~~~~~  239 (251)
T PRK07670        189 EELIEELAEKIKQLSEKEQLVI-SLFYKEELTLTEIGQVLNLSTSRISQIHS  239 (251)
T ss_pred             HHHHHHHHHHHhcCCHHHHHHH-HHHHhcCCCHHHHHHHHCcCHHHHHHHHH

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

Probab=80.94  E-value=1.8  Score=33.68  Aligned_cols=24  Identities=21%  Similarity=0.201  Sum_probs=20.7

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      ++.|.+|||+.+|||++|++..-+
T Consensus       177 R~~~l~dLA~~lGISkst~~ehLR  200 (215)
T COG3413         177 RRVSLKDLAKELGISKSTLSEHLR  200 (215)
T ss_pred             ccCCHHHHHHHhCCCHHHHHHHHH
Confidence            456999999999999999987653

>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]

Probab=80.90  E-value=4  Score=29.80  Aligned_cols=37  Identities=16%  Similarity=0.197  Sum_probs=29.4

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         121 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       121 ~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      .++..++-..-...|+|..++|+.+|++.+|+.+|-+
T Consensus         7 ~~~R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~   43 (138)
T COG3415           7 NDLRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVR   43 (138)
T ss_pred             HHHHHHHHHHHHHcCccHHHHHHHhCccHHHHHHHHH
Confidence            3445555556667999999999999999999888855

>PF08822 DUF1804: Protein of unknown function (DUF1804); InterPro: IPR014926 This entry is represented by Bacteriophage D3112, Orf24

Probab=80.88  E-value=4.9  Score=30.26  Aligned_cols=37  Identities=8%  Similarity=-0.002  Sum_probs=32.5

Q ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          31 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        31 ~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      .+.-..+|.+---.++|.+..|..+|||.+|+.+|-.
T Consensus         5 ~e~R~~~R~~YV~~~~sLe~aA~~~gVs~~TarrWK~   41 (165)
T PF08822_consen    5 QETRDAVRRAYVFDRLSLEQAAAKCGVSYATARRWKR   41 (165)
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHH
Confidence            4556778888888999999999999999999999975

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

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

Probab=80.85  E-value=2.6  Score=28.03  Aligned_cols=27  Identities=11%  Similarity=0.062  Sum_probs=22.7

Q ss_pred             CCCHHHHHHHhCCChhHHHHHhcCCCC
Q psy6501         135 GWSQKDLATKINEKPQIVNDYEGGRGI  161 (174)
Q Consensus       135 glsq~ela~~lg~~~s~i~~~E~G~~~  161 (174)
                      +++..++|+.+|++++++..||.-.-.
T Consensus         1 ~~ti~evA~~~gvs~~tLR~ye~~Gll   27 (88)
T cd01105           1 VIGIGEVSKLTGVSPRQLRYWEEKGLI   27 (88)
T ss_pred             CcCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence            368899999999999999999874333

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

>PRK05657 RNA polymerase sigma factor RpoS; Validated

Probab=80.79  E-value=8.7  Score=31.94  Aligned_cols=40  Identities=13%  Similarity=0.052  Sum_probs=28.2

Q ss_pred             cccHHHHHHHHH---HHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         118 KVPLDLAKLLMQ---GRQAKGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       118 ~~~~~~~~~i~~---~R~~~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      .++......|..   ++...|+|.+++|+.+|+++++|..+..
T Consensus       262 ~L~~~~R~vl~lrygL~~~e~~s~~EIA~~Lgis~~tV~~~~~  304 (325)
T PRK05657        262 ELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQV  304 (325)
T ss_pred             cCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            334444444432   2235789999999999999999988764

>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=80.71  E-value=7.2  Score=26.23  Aligned_cols=52  Identities=15%  Similarity=0.029  Sum_probs=40.9

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCc
Q psy6501          33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGI   86 (174)
Q Consensus        33 ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v   86 (174)
                      -.+-++.-++...+|-+++|.++|+|.--|-++++=...|  .....+.++|.-
T Consensus        11 Tk~elqan~el~~LS~~~iA~~Ln~t~~~lekil~~tqr~--~dvW~lRd~l~~   62 (97)
T COG4367          11 TKQELQANFELCPLSDEEIATALNWTEVKLEKILQVTQRP--ADVWRLRDFLVQ   62 (97)
T ss_pred             HHHHHHHhhhhccccHHHHHHHhCCCHHHHHHHHHHhhcc--chhHHHHHHHHH
Confidence            3556777888999999999999999999999999877666  445556555543

>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=80.60  E-value=6.5  Score=22.42  Aligned_cols=30  Identities=20%  Similarity=0.163  Sum_probs=22.2

Q ss_pred             HHHHHHHHHhcCCCHHHHHHHhCCChhHHH
Q psy6501         124 AKLLMQGRQAKGWSQKDLATKINEKPQIVN  153 (174)
Q Consensus       124 ~~~i~~~R~~~glsq~ela~~lg~~~s~i~  153 (174)
                      ..+|......-..+..++|+.+|++++++.
T Consensus         6 ~~Il~~Lq~d~r~s~~~la~~lglS~~~v~   35 (42)
T PF13404_consen    6 RKILRLLQEDGRRSYAELAEELGLSESTVR   35 (42)
T ss_dssp             HHHHHHHHH-TTS-HHHHHHHHTS-HHHHH
T ss_pred             HHHHHHHHHcCCccHHHHHHHHCcCHHHHH
Confidence            456777777778999999999999998764

...

>PRK13509 transcriptional repressor UlaR; Provisional

Probab=80.58  E-value=2.5  Score=33.76  Aligned_cols=32  Identities=13%  Similarity=-0.026  Sum_probs=26.4

Q ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          35 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      .-++.+++...++.+|||+.+|||+.||.+.-
T Consensus         9 ~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL   40 (251)
T PRK13509          9 ILLELLAQLGFVTVEKVIERLGISPATARRDI   40 (251)
T ss_pred             HHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHH
Confidence            34556667777999999999999999998764

>TIGR02941 Sigma_B RNA polymerase sigma-B factor

Probab=80.56  E-value=3.1  Score=33.01  Aligned_cols=31  Identities=13%  Similarity=0.186  Sum_probs=26.6

Q ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          37 LMQGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        37 ik~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      +-.+|...|+|.+|+|+.+|+|.++|+.+..
T Consensus       213 ii~l~~~~g~s~~eIA~~lgis~~~V~~~~~  243 (255)
T TIGR02941       213 IIHCTFEENLSQKETGERLGISQMHVSRLQR  243 (255)
T ss_pred             HHHHHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            4456667899999999999999999998864

This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.

>PRK11050 manganese transport regulator MntR; Provisional

Probab=80.53  E-value=4.3  Score=29.84  Aligned_cols=36  Identities=17%  Similarity=0.121  Sum_probs=26.9

Q ss_pred             HHHHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          31 LDLAKLLMQGRQ-AKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        31 ~~ig~~ik~~R~-~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ..+-..|..+.. .-++++.+||+.+++|+++|+.+-
T Consensus        36 e~~l~~I~~~l~~~~~~t~~eLA~~l~is~stVsr~l   72 (152)
T PRK11050         36 EDYVELIADLIAEVGEARQVDIAARLGVSQPTVAKML   72 (152)
T ss_pred             HHHHHHHHHHHHhcCCCCHHHHHHHHCCCHHHHHHHH
Confidence            344455554443 367899999999999999999875

>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets

Probab=80.46  E-value=3.6  Score=24.36  Aligned_cols=31  Identities=16%  Similarity=0.156  Sum_probs=22.5

Q ss_pred             HHHHHHHhcC-CCHHHHHHHhCCChhHHHHHh
Q psy6501         126 LLMQGRQAKG-WSQKDLATKINEKPQIVNDYE  156 (174)
Q Consensus       126 ~i~~~R~~~g-lsq~ela~~lg~~~s~i~~~E  156 (174)
                      .+....+..+ +|.+++|+.+++|..+|.++-
T Consensus         5 il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i   36 (55)
T PF08279_consen    5 ILKLLLESKEPITAKELAEELGVSRRTIRRDI   36 (55)
T ss_dssp             HHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHH
T ss_pred             HHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHH
Confidence            4444444444 999999999999999987753

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 ....

>PRK09210 RNA polymerase sigma factor RpoD; Validated

Probab=80.46  E-value=2.7  Score=35.52  Aligned_cols=24  Identities=4%  Similarity=0.144  Sum_probs=22.2

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      .++|++|+|+.+|||+..|+++|.
T Consensus       324 ~~~tl~EIa~~lgvs~erVrQi~~  347 (367)
T PRK09210        324 RTRTLEEVGKVFGVTRERIRQIEA  347 (367)
T ss_pred             CCccHHHHHHHHCCCHHHHHHHHH
Confidence            458999999999999999999985

>PRK10411 DNA-binding transcriptional activator FucR; Provisional

Probab=80.37  E-value=2.6  Score=33.47  Aligned_cols=31  Identities=10%  Similarity=0.068  Sum_probs=26.3

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          36 LLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      -+..+.+...+|++|||+.+|||..||++.-
T Consensus         9 Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL   39 (240)
T PRK10411          9 IVDLLLNHTSLTTEALAEQLNVSKETIRRDL   39 (240)
T ss_pred             HHHHHHHcCCCcHHHHHHHHCcCHHHHHHHH
Confidence            4556667789999999999999999998864

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

Probab=80.35  E-value=6.1  Score=26.50  Aligned_cols=36  Identities=14%  Similarity=0.150  Sum_probs=26.9

Q ss_pred             HHHHHHHHHH--HhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         122 DLAKLLMQGR--QAKGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       122 ~~~~~i~~~R--~~~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      ++..++.-++  -..|.||.++++.+|+|..+|++.=+
T Consensus        34 ~l~~R~~va~~lL~~g~syreIa~~tgvS~aTItRvsr   71 (87)
T PF01371_consen   34 ALAQRWQVAKELLDEGKSYREIAEETGVSIATITRVSR   71 (87)
T ss_dssp             HHHHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHH
Confidence            3444554444  34789999999999999999987643

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

>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR

Probab=80.34  E-value=2.7  Score=32.30  Aligned_cols=31  Identities=19%  Similarity=0.078  Sum_probs=25.5

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          36 LLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      -|..+...-++|+.+||+.+|+++++|++.-
T Consensus         6 IL~~L~~~~~~t~~eLA~~lgis~~tV~~~L   36 (203)
T TIGR02702         6 ILSYLLKQGQATAAALAEALAISPQAVRRHL   36 (203)
T ss_pred             HHHHHHHcCCCCHHHHHHHHCcCHHHHHHHH
Confidence            3455666778999999999999999998763

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.

>PRK05602 RNA polymerase sigma factor; Reviewed

Probab=80.30  E-value=3.3  Score=30.96  Aligned_cols=29  Identities=10%  Similarity=0.048  Sum_probs=25.7

Q ss_pred             HHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          39 QGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        39 ~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      .+|.-.|+|.+|+|+.+|+|.++|.....
T Consensus       138 ~l~~~~g~s~~EIA~~lgis~~tV~~~l~  166 (186)
T PRK05602        138 VLQYYQGLSNIEAAAVMDISVDALESLLA  166 (186)
T ss_pred             hHHHhcCCCHHHHHHHhCcCHHHHHHHHH
Confidence            36677899999999999999999998863

>PF14590 DUF4447: Domain of unknown function (DUF4447); PDB: 2OX6_B

Probab=80.27  E-value=6.7  Score=28.26  Aligned_cols=41  Identities=15%  Similarity=0.070  Sum_probs=30.7

Q ss_pred             HHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHH
Q psy6501         126 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAI  166 (174)
Q Consensus       126 ~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~  166 (174)
                      .|...|...|++..++++..+.+..-+-.||.|....+.-.
T Consensus        11 e~~ylr~slgl~~aqv~~l~k~se~dv~aweage~~~~~la   51 (166)
T PF14590_consen   11 EIKYLRLSLGLTTAQVAELTKASEADVLAWEAGEKPAPGLA   51 (166)
T ss_dssp             HHHHHHHHTT--HHHHHHHHTS-HHHHHHHHTTSS---HHH
T ss_pred             HHHHHHHHcCCCHHHHHHhhccCHHHhhhhhccCCcCchHH
Confidence            56778999999999999999999999999999988765443

>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family

Probab=80.24  E-value=2  Score=26.56  Aligned_cols=25  Identities=20%  Similarity=0.324  Sum_probs=20.5

Q ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          42 QAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        42 ~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      +....+..+||+.+|||+++++..-
T Consensus        19 ~~~~v~~~~iA~~L~vs~~tvt~ml   43 (60)
T PF01325_consen   19 EGGPVRTKDIAERLGVSPPTVTEML   43 (60)
T ss_dssp             CTSSBBHHHHHHHHTS-HHHHHHHH
T ss_pred             CCCCccHHHHHHHHCCChHHHHHHH
Confidence            5567899999999999999998753

The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....

>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon

Probab=80.21  E-value=6.9  Score=22.58  Aligned_cols=25  Identities=20%  Similarity=0.348  Sum_probs=22.3

Q ss_pred             hcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         133 AKGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       133 ~~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      ..|++..++|+.+|++++++..+-.
T Consensus        16 ~~g~s~~eia~~l~is~~tv~~~~~   40 (58)
T smart00421       16 AEGLTNKEIAERLGISEKTVKTHLS   40 (58)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            5789999999999999999987754

lux regulon (activates the bioluminescence operon

>PRK06930 positive control sigma-like factor; Validated

Probab=80.18  E-value=3.8  Score=30.83  Aligned_cols=29  Identities=21%  Similarity=0.171  Sum_probs=25.5

Q ss_pred             HHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          39 QGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        39 ~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      .++...|+|.+|+|+.+|+|.++|..+..
T Consensus       124 ~L~~~eg~s~~EIA~~lgiS~~tVk~~l~  152 (170)
T PRK06930        124 LMHRGYGLSYSEIADYLNIKKSTVQSMIE  152 (170)
T ss_pred             HHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            34567999999999999999999998864

>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor

Probab=80.16  E-value=3.3  Score=24.53  Aligned_cols=24  Identities=13%  Similarity=-0.002  Sum_probs=20.9

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          43 AKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        43 ~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ...+|..++++.+|+|++++++.-
T Consensus         8 ~~~~~~~~i~~~l~is~~~v~~~l   31 (66)
T smart00418        8 EGELCVCELAEILGLSQSTVSHHL   31 (66)
T ss_pred             cCCccHHHHHHHHCCCHHHHHHHH
Confidence            567899999999999999888764

>PRK12524 RNA polymerase sigma factor; Provisional

Probab=80.10  E-value=3.6  Score=31.12  Aligned_cols=32  Identities=16%  Similarity=0.183  Sum_probs=27.2

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          36 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      .+-.++.-.|+|.+|+|+.+|+|.++|...-.
T Consensus       143 ~i~~L~~~~g~s~~eIA~~lgis~~tV~~~l~  174 (196)
T PRK12524        143 QAVVLRHIEGLSNPEIAEVMEIGVEAVESLTA  174 (196)
T ss_pred             HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            34556778999999999999999999998763

>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE

Probab=80.09  E-value=2.6  Score=29.17  Aligned_cols=27  Identities=15%  Similarity=0.226  Sum_probs=22.8

Q ss_pred             CCHHHHHHHhCCChhHHHHHhcCCCCC
Q psy6501         136 WSQKDLATKINEKPQIVNDYEGGRGIP  162 (174)
Q Consensus       136 lsq~ela~~lg~~~s~i~~~E~G~~~P  162 (174)
                      ++..++|+.+|+++.++..||.-.-.|
T Consensus         1 ~~i~eva~~~gvs~~tlR~ye~~Gll~   27 (108)
T cd04773           1 MTIGELAHLLGVPPSTLRHWEKEGLLS   27 (108)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCCCCC
Confidence            578899999999999999999854443

Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.

>PRK05657 RNA polymerase sigma factor RpoS; Validated

Probab=80.01  E-value=2.2  Score=35.53  Aligned_cols=43  Identities=12%  Similarity=0.151  Sum_probs=30.2

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccc
Q psy6501          43 AKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLR   89 (174)
Q Consensus        43 ~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~   89 (174)
                      -.|+|++|+|+.+|+|.++|.++..-    ....|.+....-|++.+
T Consensus       280 ~e~~s~~EIA~~Lgis~~tV~~~~~r----Al~kLr~~l~~~~~~~~  322 (325)
T PRK05657        280 YEAATLEDVAREIGLTRERVRQIQVE----ALRRLREILQTQGLSIE  322 (325)
T ss_pred             CCCcCHHHHHHHHCcCHHHHHHHHHH----HHHHHHHHHHhCccchh
Confidence            56899999999999999999999852    22344444444444433

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	174
1x57_A	91	Solution Structures Of The Hth Domain Of Human Edf-		1e-18
1x57_A	91	Solution Structures Of The Hth Domain Of Human Edf-		1e-16
2jvl_A	107	Nmr Structure Of The C-Terminal Domain Of Mbf1 Of T		4e-06
2jvl_A	107	Nmr Structure Of The C-Terminal Domain Of Mbf1 Of T		1e-04

>pdb|1X57|A Chain A, Solution Structures Of The Hth Domain Of Human Edf-1 Protein Length = 91

Iteration: 1
 Score = 89.4 bits (220), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 38/63 (60%), Positives = 54/63 (85%)
Query: 27 EKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGI 86
          ++V L++ K++ QGRQ+KG +QKDLATKINEKPQ++ DYE GR IPN  ++GK+ERA+G+
Sbjct: 8  DRVTLEVGKVIQQGRQSKGLTQKDLATKINEKPQVIADYESGRAIPNNQVLGKIERAIGL 67
Query: 87 RLR 89
          +LR
Sbjct: 68 KLR 70

>pdb|1X57|A Chain A, Solution Structures Of The Hth Domain Of Human Edf-1 Protein Length = 91

Iteration: 1
 Score = 82.0 bits (201), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 35/58 (60%), Positives = 49/58 (84%)
Query: 117 EKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174
           ++V L++ K++ QGRQ+KG +QKDLATKINEKPQ++ DYE GR IPN  ++GK+ERA+
Sbjct: 8   DRVTLEVGKVIQQGRQSKGLTQKDLATKINEKPQVIADYESGRAIPNNQVLGKIERAI 65

>pdb|2JVL|A Chain A, Nmr Structure Of The C-Terminal Domain Of Mbf1 Of Trichoderm Length = 107

Iteration: 1
 Score = 47.8 bits (112), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 28/76 (36%), Positives = 42/76 (55%), Gaps = 2/76 (2%)
Query: 16 KLDRETEELKHEKVPLDLAKLLMQGRQ--AKGWSQKDLATKINEKPQIVNDYEGGRGIPN 73
          K+DR  + +K + V  ++ K + QGRQ      +Q +L  +I E    V  YE G   P+
Sbjct: 18 KVDRSDDIIKPKTVGKEVGKAIEQGRQKFEPTMTQAELGKEIGETAATVASYERGTATPD 77
Query: 74 QAIIGKMERALGIRLR 89
          Q I+ KMER L ++LR
Sbjct: 78 QNILSKMERVLNVKLR 93

>pdb|2JVL|A Chain A, Nmr Structure Of The C-Terminal Domain Of Mbf1 Of Trichoderm Length = 107

Iteration: 1
 Score = 42.4 bits (98), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 26/71 (36%), Positives = 38/71 (53%), Gaps = 2/71 (2%)
Query: 106 KLDRETEELKHEKVPLDLAKLLMQGRQ--AKGWSQKDLATKINEKPQIVNDYEGGRGIPN 163
           K+DR  + +K + V  ++ K + QGRQ      +Q +L  +I E    V  YE G   P+
Sbjct: 18  KVDRSDDIIKPKTVGKEVGKAIEQGRQKFEPTMTQAELGKEIGETAATVASYERGTATPD 77
Query: 164 QAIIGKMERAL 174
           Q I+ KMER L
Sbjct: 78  QNILSKMERVL 88

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	174
2jvl_A	107	TRMBF1; coactivator, helix-turn-helix, Pro binding	5e-24
2jvl_A	107	TRMBF1; coactivator, helix-turn-helix, Pro binding	3e-21
1x57_A	91	Endothelial differentiation-related factor 1; HMBF	9e-22
1x57_A	91	Endothelial differentiation-related factor 1; HMBF	4e-19
1adr_A	76	P22 C2 repressor; transcription regulation; NMR {E	1e-06
1adr_A	76	P22 C2 repressor; transcription regulation; NMR {E	1e-05
2wiu_B	88	HTH-type transcriptional regulator HIPB; transfera	2e-06
2wiu_B	88	HTH-type transcriptional regulator HIPB; transfera	1e-04
2r1j_L	68	Repressor protein C2; protein-DNA complex, helix-t	4e-06
2r1j_L	68	Repressor protein C2; protein-DNA complex, helix-t	3e-05
2kpj_A	94	SOS-response transcriptional repressor, LEXA; NESG	5e-06
2kpj_A	94	SOS-response transcriptional repressor, LEXA; NESG	3e-05
3omt_A	73	Uncharacterized protein; structural genomics, PSI-	9e-06
3omt_A	73	Uncharacterized protein; structural genomics, PSI-	9e-05
2p5t_A	158	Putative transcriptional regulator PEZA; postsegre	4e-05
2p5t_A	158	Putative transcriptional regulator PEZA; postsegre	3e-04
3bs3_A	76	Putative DNA-binding protein; XRE-family, structur	4e-05
3bs3_A	76	Putative DNA-binding protein; XRE-family, structur	4e-04
3f6w_A	83	XRE-family like protein; helix-turn-helix, DNA bin	5e-05
3f6w_A	83	XRE-family like protein; helix-turn-helix, DNA bin	8e-04
3ivp_A	126	Putative transposon-related DNA-binding protein; A	1e-04
2ef8_A	84	C.ECOT38IS, putative transcription factor; helix-t	1e-04
3kxa_A	141	NGO0477 protein, putative uncharacterized protein;	1e-04
3op9_A	114	PLI0006 protein; structural genomics, PSI-2, prote	2e-04
3op9_A	114	PLI0006 protein; structural genomics, PSI-2, prote	2e-04
1r69_A	69	Repressor protein CI; gene regulating protein; 2.0	2e-04
3bdn_A	236	Lambda repressor; repressor, allostery; HET: DNA;	3e-04
3lfp_A	98	CSP231I C protein; transcriptional regulator, DNA	4e-04
1zug_A	71	Phage 434 CRO protein; gene regulating protein, tr	4e-04
1y7y_A	74	C.AHDI; helix-turn-helix, DNA-binding protein, tra	8e-04

>2jvl_A TRMBF1; coactivator, helix-turn-helix, Pro binding, transcription; NMR {Trichoderma reesei} Length = 107

 Score = 89.6 bits (222), Expect = 5e-24
 Identities = 31/92 (33%), Positives = 47/92 (51%), Gaps = 4/92 (4%)

Query: 2  AGTNKQPGTT--KNTAKLDRETEELKHEKVPLDLAKLLMQGRQA--KGWSQKDLATKINE 57
          A   +  G T  +   K+DR  + +K + V  ++ K + QGRQ      +Q +L  +I E
Sbjct: 2  AMDPEFAGGTEGQRLTKVDRSDDIIKPKTVGKEVGKAIEQGRQKFEPTMTQAELGKEIGE 61

Query: 58 KPQIVNDYEGGRGIPNQAIIGKMERALGIRLR 89
              V  YE G   P+Q I+ KMER L ++LR
Sbjct: 62 TAATVASYERGTATPDQNILSKMERVLNVKLR 93

>2jvl_A TRMBF1; coactivator, helix-turn-helix, Pro binding, transcription; NMR {Trichoderma reesei} Length = 107

 Score = 82.3 bits (203), Expect = 3e-21
 Identities = 29/87 (33%), Positives = 43/87 (49%), Gaps = 4/87 (4%)

Query: 92  AGTNKQPGTT--KNTAKLDRETEELKHEKVPLDLAKLLMQGRQA--KGWSQKDLATKINE 147
           A   +  G T  +   K+DR  + +K + V  ++ K + QGRQ      +Q +L  +I E
Sbjct: 2   AMDPEFAGGTEGQRLTKVDRSDDIIKPKTVGKEVGKAIEQGRQKFEPTMTQAELGKEIGE 61

Query: 148 KPQIVNDYEGGRGIPNQAIIGKMERAL 174
               V  YE G   P+Q I+ KMER L
Sbjct: 62  TAATVASYERGTATPDQNILSKMERVL 88

>1x57_A Endothelial differentiation-related factor 1; HMBF1alpha, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.35.1.12 Length = 91

 Score = 83.3 bits (206), Expect = 9e-22
 Identities = 38/69 (55%), Positives = 55/69 (79%)

Query: 21 TEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKM 80
          +     ++V L++ K++ QGRQ+KG +QKDLATKINEKPQ++ DYE GR IPN  ++GK+
Sbjct: 2  SSGSSGDRVTLEVGKVIQQGRQSKGLTQKDLATKINEKPQVIADYESGRAIPNNQVLGKI 61

Query: 81 ERALGIRLR 89
          ERA+G++LR
Sbjct: 62 ERAIGLKLR 70

>1x57_A Endothelial differentiation-related factor 1; HMBF1alpha, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.35.1.12 Length = 91

 Score = 76.3 bits (188), Expect = 4e-19
 Identities = 35/64 (54%), Positives = 50/64 (78%)

Query: 111 TEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKM 170
           +     ++V L++ K++ QGRQ+KG +QKDLATKINEKPQ++ DYE GR IPN  ++GK+
Sbjct: 2   SSGSSGDRVTLEVGKVIQQGRQSKGLTQKDLATKINEKPQVIADYESGRAIPNNQVLGKI 61

Query: 171 ERAL 174
           ERA+
Sbjct: 62  ERAI 65

>1adr_A P22 C2 repressor; transcription regulation; NMR {Enterobacteria phage P22} SCOP: a.35.1.2 Length = 76

 Score = 43.0 bits (102), Expect = 1e-06
 Identities = 8/55 (14%), Positives = 19/55 (34%)

Query: 32 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGI 86
           + + +   R+     Q  L   +      ++ +E     PN   +  + +AL  
Sbjct: 5  LMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQC 59

>1adr_A P22 C2 repressor; transcription regulation; NMR {Enterobacteria phage P22} SCOP: a.35.1.2 Length = 76

 Score = 40.7 bits (96), Expect = 1e-05
 Identities = 8/53 (15%), Positives = 19/53 (35%)

Query: 122 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174
            + + +   R+     Q  L   +      ++ +E     PN   +  + +AL
Sbjct: 5   LMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKAL 57

>2wiu_B HTH-type transcriptional regulator HIPB; transferase transcription complex, serine kinase, DNA-bindin mercury derivative, repressor; 2.35A {Escherichia coli} PDB: 3dnv_B* 3dnw_B* 3hzi_B* Length = 88

 Score = 43.3 bits (102), Expect = 2e-06
 Identities = 19/72 (26%), Positives = 33/72 (45%)

Query: 30  PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLR 89
           P  LA  +   RQ  GW+Q +LA KI  K   ++++E            K+ ++L + + 
Sbjct: 10  PTQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELSMT 69

Query: 90  VNAGTNKQPGTT 101
           +    N  P +T
Sbjct: 70  LCDAKNASPEST 81

>2wiu_B HTH-type transcriptional regulator HIPB; transferase transcription complex, serine kinase, DNA-bindin mercury derivative, repressor; 2.35A {Escherichia coli} PDB: 3dnv_B* 3dnw_B* 3hzi_B* Length = 88

 Score = 38.3 bits (89), Expect = 1e-04
 Identities = 16/55 (29%), Positives = 26/55 (47%)

Query: 120 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174
           P  LA  +   RQ  GW+Q +LA KI  K   ++++E            K+ ++L
Sbjct: 10  PTQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSL 64

>2r1j_L Repressor protein C2; protein-DNA complex, helix-turn-helix, DNA-binding, transcription, transcription regulation; 1.53A {Enterobacteria phage P22} SCOP: a.35.1.2 PDB: 3jxb_C 3jxc_L 3jxd_L Length = 68

 Score = 41.8 bits (99), Expect = 4e-06
 Identities = 8/55 (14%), Positives = 19/55 (34%)

Query: 32 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGI 86
           + + +   R+     Q  L   +      ++ +E     PN   +  + +AL  
Sbjct: 5  LMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQC 59

>2r1j_L Repressor protein C2; protein-DNA complex, helix-turn-helix, DNA-binding, transcription, transcription regulation; 1.53A {Enterobacteria phage P22} SCOP: a.35.1.2 PDB: 3jxb_C 3jxc_L 3jxd_L Length = 68

 Score = 39.5 bits (93), Expect = 3e-05
 Identities = 8/53 (15%), Positives = 19/53 (35%)

Query: 122 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174
            + + +   R+     Q  L   +      ++ +E     PN   +  + +AL
Sbjct: 5   LMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKAL 57

>2kpj_A SOS-response transcriptional repressor, LEXA; NESG, GFT, structural genomics, PSI-2, protein structure initiative; NMR {Eubacterium rectale atcc 33656} Length = 94

 Score = 42.0 bits (99), Expect = 5e-06
 Identities = 11/54 (20%), Positives = 19/54 (35%)

Query: 33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGI 86
           ++ L         +Q ++A  I   PQ  N +  G  IP    +  +     I
Sbjct: 10 FSENLNSYIAKSEKTQLEIAKSIGVSPQTFNTWCKGIAIPRMGKVQALADYFNI 63

>2kpj_A SOS-response transcriptional repressor, LEXA; NESG, GFT, structural genomics, PSI-2, protein structure initiative; NMR {Eubacterium rectale atcc 33656} Length = 94

 Score = 40.1 bits (94), Expect = 3e-05
 Identities = 10/48 (20%), Positives = 18/48 (37%)

Query: 123 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKM 170
            ++ L         +Q ++A  I   PQ  N +  G  IP    +  +
Sbjct: 10  FSENLNSYIAKSEKTQLEIAKSIGVSPQTFNTWCKGIAIPRMGKVQAL 57

>3omt_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; 1.65A {Cytophaga hutchinsonii} Length = 73

 Score = 40.8 bits (96), Expect = 9e-06
 Identities = 8/49 (16%), Positives = 19/49 (38%)

Query: 41 RQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLR 89
             KG +   L   +++    V+ +      P+   +  +  AL + +R
Sbjct: 17 LAEKGKTNLWLTETLDKNKTTVSKWCTNDVQPSLETLFDIAEALNVDVR 65

>3omt_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; 1.65A {Cytophaga hutchinsonii} Length = 73

 Score = 38.1 bits (89), Expect = 9e-05
 Identities = 7/44 (15%), Positives = 16/44 (36%)

Query: 131 RQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174
              KG +   L   +++    V+ +      P+   +  +  AL
Sbjct: 17  LAEKGKTNLWLTETLDKNKTTVSKWCTNDVQPSLETLFDIAEAL 60

>2p5t_A Putative transcriptional regulator PEZA; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae} Length = 158

 Score = 41.1 bits (96), Expect = 4e-05
 Identities = 19/127 (14%), Positives = 44/127 (34%), Gaps = 3/127 (2%)

Query: 33  LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNA 92
           + K +   R+    +Q + A  +      ++ YE G    +  +I  + +   +      
Sbjct: 2   IGKNIKSLRKTHDLTQLEFARIVGISRNSLSRYENGTSSVSTELIDIICQKFNVSYVDIV 61

Query: 93  GTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIV 152
           G +K         +L  + E +K      +L   L + + ++G S  D +         +
Sbjct: 62  GEDKML-NPVEDYELTLKIEIVKERG--ANLLSRLYRYQDSQGISIDDESNPWILMSDDL 118

Query: 153 NDYEGGR 159
           +D     
Sbjct: 119 SDLIHTN 125

>2p5t_A Putative transcriptional regulator PEZA; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae} Length = 158

 Score = 38.4 bits (89), Expect = 3e-04
 Identities = 8/48 (16%), Positives = 19/48 (39%)

Query: 123 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKM 170
           + K +   R+    +Q + A  +      ++ YE G    +  +I  +
Sbjct: 2   IGKNIKSLRKTHDLTQLEFARIVGISRNSLSRYENGTSSVSTELIDII 49

>3bs3_A Putative DNA-binding protein; XRE-family, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.65A {Bacteroides fragilis} Length = 76

 Score = 39.2 bits (92), Expect = 4e-05
 Identities = 7/49 (14%), Positives = 21/49 (42%)

Query: 41 RQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLR 89
             K  + + LA ++ +    ++ +   +  P+  ++ K+   L +  R
Sbjct: 19 LAEKQRTNRWLAEQMGKSENTISRWCSNKSQPSLDMLVKVAELLNVDPR 67

>3bs3_A Putative DNA-binding protein; XRE-family, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.65A {Bacteroides fragilis} Length = 76

 Score = 36.5 bits (85), Expect = 4e-04
 Identities = 6/44 (13%), Positives = 19/44 (43%)

Query: 131 RQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174
              K  + + LA ++ +    ++ +   +  P+  ++ K+   L
Sbjct: 19  LAEKQRTNRWLAEQMGKSENTISRWCSNKSQPSLDMLVKVAELL 62

>3f6w_A XRE-family like protein; helix-turn-helix, DNA binding protein, xenobiotic response E family of transcriptional regulators; HET: MSE BTB; 1.85A {Pseudomonas syringae PV} Length = 83

 Score = 39.3 bits (92), Expect = 5e-05
 Identities = 14/56 (25%), Positives = 23/56 (41%)

Query: 33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRL 88
          L  LL++ R A G +QK+LA ++      V+  E      +        R +G   
Sbjct: 15 LLDLLLEARSAAGITQKELAARLGRPQSFVSKTENAERRLDVIEFMDFCRGIGTDP 70

>3f6w_A XRE-family like protein; helix-turn-helix, DNA binding protein, xenobiotic response E family of transcriptional regulators; HET: MSE BTB; 1.85A {Pseudomonas syringae PV} Length = 83

 Score = 35.8 bits (83), Expect = 8e-04
 Identities = 13/52 (25%), Positives = 22/52 (42%)

Query: 123 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174
           L  LL++ R A G +QK+LA ++      V+  E      +        R +
Sbjct: 15  LLDLLLEARSAAGITQKELAARLGRPQSFVSKTENAERRLDVIEFMDFCRGI 66

>3ivp_A Putative transposon-related DNA-binding protein; APC62618, clostridium diffic structural genomics, PSI-2, protein structure initiative; HET: PG4; 2.02A {Clostridium difficile} Length = 126

 Score = 39.0 bits (91), Expect = 1e-04
 Identities = 10/105 (9%), Positives = 40/105 (38%), Gaps = 2/105 (1%)

Query: 32  DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVN 91
            L   + + R+ +G +++ +   I   P+ + + E     P+  ++  +   L + +   
Sbjct: 12  ALGLAIKEARKKQGLTREQVGAMIEIDPRYLTNIENKGQHPSLQVLYDLVSLLNVSVDEF 71

Query: 92  AGTNKQPGTTKNTAKLDRETEELKHEKVPL--DLAKLLMQGRQAK 134
                    +    +L+ + +      + +   +A  +++ ++  
Sbjct: 72  FLPASSQVKSTKRRQLENKIDNFTDADLVIMESVADGIVKSKEVG 116

>2ef8_A C.ECOT38IS, putative transcription factor; helix-turn-helix, DNA binding protein, transcription regulator; HET: CME; 1.95A {Enterobacteria phage P2} Length = 84

 Score = 38.2 bits (89), Expect = 1e-04
 Identities = 11/58 (18%), Positives = 24/58 (41%)

Query: 33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRV 90
          L +LL + R+    SQ +LA  +      ++  E      +   + ++   +  RL +
Sbjct: 11 LVQLLTKLRKEASLSQSELAIFLGLSQSDISKIESFERRLDALELFELLEVVASRLGL 68

>3kxa_A NGO0477 protein, putative uncharacterized protein; NEW protein fold, OPPF, STRU genomics, oxford protein production facility; 2.80A {Neisseria gonorrhoeae} Length = 141

 Score = 39.1 bits (91), Expect = 1e-04
 Identities = 15/77 (19%), Positives = 30/77 (38%)

Query: 12  KNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGI 71
           +  A +DR    +  +       +  +  R  KG++Q +LAT        ++  E  +  
Sbjct: 48  RRKAAMDRAAARIADKIALKAGGETFVSLRMKKGFTQSELATAAGLPQPYLSRIENSKQS 107

Query: 72  PNQAIIGKMERALGIRL 88
                + K+  ALG+  
Sbjct: 108 LQDKTVQKLANALGVSP 124

>3op9_A PLI0006 protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG, transcription regulat; HET: MSE; 1.90A {Listeria innocua} Length = 114

 Score = 38.6 bits (90), Expect = 2e-04
 Identities = 9/54 (16%), Positives = 22/54 (40%)

Query: 33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGI 86
           A+ L + ++  G     +A  +N + + V  Y  G   P+   + ++     +
Sbjct: 10 FAENLSRLKKEHGLKNHQIAELLNVQTRTVAYYMSGETKPDIEKLIRLATYFHL 63

>3op9_A PLI0006 protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG, transcription regulat; HET: MSE; 1.90A {Listeria innocua} Length = 114

 Score = 38.2 bits (89), Expect = 2e-04
 Identities = 9/48 (18%), Positives = 21/48 (43%)

Query: 123 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKM 170
            A+ L + ++  G     +A  +N + + V  Y  G   P+   + ++
Sbjct: 10  FAENLSRLKKEHGLKNHQIAELLNVQTRTVAYYMSGETKPDIEKLIRL 57

>1r69_A Repressor protein CI; gene regulating protein; 2.00A {Phage 434} SCOP: a.35.1.2 PDB: 1pra_A 1per_L 1rpe_L* 2or1_L* 1r63_A 2r63_A 1sq8_A Length = 69

 Score = 36.8 bits (86), Expect = 2e-04
 Identities = 12/54 (22%), Positives = 24/54 (44%), Gaps = 1/54 (1%)

Query: 33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGI 86
          ++  +   R   G +Q +LA K+    Q +   E G+       + ++  ALG+
Sbjct: 2  ISSRVKSKRIQLGLNQAELAQKVGTTQQSIEQLENGK-TKRPRFLPELASALGV 54

>3bdn_A Lambda repressor; repressor, allostery; HET: DNA; 3.91A {Enterobacteria phage lambda} Length = 236

 Score = 38.8 bits (90), Expect = 3e-04
 Identities = 10/54 (18%), Positives = 19/54 (35%)

Query: 33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGI 86
          L  +  + +   G SQ+ +A K+      V     G    N      + + L +
Sbjct: 18 LKAIYEKKKNELGLSQESVADKMGMGQSGVGALFNGINALNAYNAALLAKILKV 71

>3lfp_A CSP231I C protein; transcriptional regulator, DNA binding protein, helix-turn-H restriction-modification, transcription; 2.00A {Citrobacter SP} PDB: 3lis_A Length = 98

 Score = 37.2 bits (86), Expect = 4e-04
 Identities = 14/60 (23%), Positives = 24/60 (40%), Gaps = 4/60 (6%)

Query: 33 LAKLLMQGRQAKGWSQKDLATKINEKPQ----IVNDYEGGRGIPNQAIIGKMERALGIRL 88
          L + L   R   G SQ+ L              +N YE G+  P+  +  ++ + L I +
Sbjct: 2  LIRRLKDARLRAGISQEKLGVLAGIDEASASARMNQYEKGKHAPDFEMANRLAKVLKIPV 61

>1zug_A Phage 434 CRO protein; gene regulating protein, transcription regulation; NMR {Phage 434} SCOP: a.35.1.2 PDB: 2cro_A 3cro_L* Length = 71

 Score = 36.1 bits (84), Expect = 4e-04
 Identities = 15/54 (27%), Positives = 25/54 (46%), Gaps = 1/54 (1%)

Query: 33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGI 86
          L++ L + R A   +Q +LATK   K Q +   E G     + +  ++  AL  
Sbjct: 4  LSERLKKRRIALKMTQTELATKAGVKQQSIQLIEAGVTKRPRFLF-EIAMALNC 56

>1y7y_A C.AHDI; helix-turn-helix, DNA-binding protein, transcriptional regulator, transcription regulator; 1.69A {Aeromonas hydrophila} SCOP: a.35.1.3 Length = 74

 Score = 35.7 bits (83), Expect = 8e-04
 Identities = 18/68 (26%), Positives = 25/68 (36%)

Query: 21 TEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKM 80
               H    +   + L + R AKG SQ+ LA         V   E G+   +   I K+
Sbjct: 2  QSHHDHYADLVKFGQRLRELRTAKGLSQETLAFLSGLDRSYVGGVERGQRNVSLVNILKL 61

Query: 81 ERALGIRL 88
            AL I  
Sbjct: 62 ATALDIEP 69

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	174
2kpj_A	94	SOS-response transcriptional repressor, LEXA; NESG	99.76
2jvl_A	107	TRMBF1; coactivator, helix-turn-helix, Pro binding	99.75
2ewt_A	71	BLDD, putative DNA-binding protein; the DNA-bindin	99.75
1y7y_A	74	C.AHDI; helix-turn-helix, DNA-binding protein, tra	99.75
3omt_A	73	Uncharacterized protein; structural genomics, PSI-	99.74
3s8q_A	82	R-M controller protein; protein-DNA complex, helix	99.74
3ivp_A	126	Putative transposon-related DNA-binding protein; A	99.73
2b5a_A	77	C.BCLI; helix-turn-helix motif, gene regulation; 1	99.73
1x57_A	91	Endothelial differentiation-related factor 1; HMBF	99.73
3op9_A	114	PLI0006 protein; structural genomics, PSI-2, prote	99.73
3b7h_A	78	Prophage LP1 protein 11; structural genomics, PSI2	99.73
2r1j_L	68	Repressor protein C2; protein-DNA complex, helix-t	99.72
3qq6_A	78	HTH-type transcriptional regulator SINR; helix-tur	99.72
3g5g_A	99	Regulatory protein; transcriptional regulator, hel	99.72
3kz3_A	80	Repressor protein CI; five helix bundle, DNA-bindi	99.72
2k9q_A	77	Uncharacterized protein; all helix, helix-turn-hel	99.72
3vk0_A	114	NHTF, transcriptional regulator; HTH motif, XRE tr	99.71
1adr_A	76	P22 C2 repressor; transcription regulation; NMR {E	99.71
3f6w_A	83	XRE-family like protein; helix-turn-helix, DNA bin	99.71
3lfp_A	98	CSP231I C protein; transcriptional regulator, DNA	99.71
4ghj_A	101	Probable transcriptional regulator; structural gen	99.71
3mlf_A	111	Transcriptional regulator; structural genomics, he	99.69
2wiu_B	88	HTH-type transcriptional regulator HIPB; transfera	99.69
3bs3_A	76	Putative DNA-binding protein; XRE-family, structur	99.69
4ich_A	311	Transcriptional regulator; structural genomics, PS	99.69
2a6c_A	83	Helix-turn-helix motif; putative transcriptional r	99.69
2l49_A	99	C protein; P2 bacteriophage, P2 C, direct repeats,	99.68
3t76_A	88	VANU, transcriptional regulator vanug; structural	99.68
1zug_A	71	Phage 434 CRO protein; gene regulating protein, tr	99.68
1lmb_3	92	Protein (lambda repressor); protein-DNA complex, d	99.68
2xi8_A	66	Putative transcription regulator; HTH DNA-binding	99.68
1r69_A	69	Repressor protein CI; gene regulating protein; 2.0	99.67
3f52_A	117	CLP gene regulator (CLGR); helix-turn-helix motif,	99.67
1b0n_A	111	Protein (SINR protein); transcription regulator, a	99.66
2wus_R	112	RODZ, putative uncharacterized protein; structural	99.66
2ef8_A	84	C.ECOT38IS, putative transcription factor; helix-t	99.66
2o38_A	120	Hypothetical protein; alpha-beta, helix-turn-helix	99.65
1y9q_A	192	Transcriptional regulator, HTH_3 family; transcrip	99.64
3eus_A	86	DNA-binding protein; structural genomics, PSI2,MCS	99.64
3trb_A	104	Virulence-associated protein I; mobIle and extrach	99.64
3fym_A	130	Putative uncharacterized protein; HTH DNA binding,	99.64
2ppx_A	99	AGR_C_3184P, uncharacterized protein ATU1735; HTH-	99.64
3fmy_A	73	HTH-type transcriptional regulator MQSA (YGIT/B302	99.63
2bnm_A	198	Epoxidase; oxidoreductase, cupin, HTH, cation-depe	99.61
3r1f_A	135	ESX-1 secretion-associated regulator ESPR; helix-t	99.61
3cec_A	104	Putative antidote protein of plasmid maintenance;	99.6
2ofy_A	86	Putative XRE-family transcriptional regulator; tra	99.6
3kxa_A	141	NGO0477 protein, putative uncharacterized protein;	99.6
2ict_A	94	Antitoxin HIGA; helix-turn-helix, structural genom	99.58
2eby_A	113	Putative HTH-type transcriptional regulator YBAQ;	99.57
3qwg_A	123	ESX-1 secretion-associated regulator ESPR; N-termi	99.57
3bd1_A	79	CRO protein; transcription factor, helix-turn-heli	99.52
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	99.52
2awi_A	317	PRGX; repressor, pheromone, DNA binding, regulator	99.48
3bdn_A	236	Lambda repressor; repressor, allostery; HET: DNA;	99.44
2p5t_A	158	Putative transcriptional regulator PEZA; postsegre	99.42
3o9x_A	133	Uncharacterized HTH-type transcriptional regulato;	99.41
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	99.4
3pxp_A	292	Helix-turn-helix domain protein; DNA-binding, basi	99.38
1neq_A	74	DNA-binding protein NER; NMR {Enterobacteria phage	99.38
2fjr_A	189	Repressor protein CI; genetic switch, regulation,	99.33
2l1p_A	83	DNA-binding protein SATB1; PSI-biology, NESG, stru	99.28
3eus_A	86	DNA-binding protein; structural genomics, PSI2,MCS	99.17
2jvl_A	107	TRMBF1; coactivator, helix-turn-helix, Pro binding	99.16
3s8q_A	82	R-M controller protein; protein-DNA complex, helix	99.15
3qq6_A	78	HTH-type transcriptional regulator SINR; helix-tur	99.13
2ewt_A	71	BLDD, putative DNA-binding protein; the DNA-bindin	99.12
1y7y_A	74	C.AHDI; helix-turn-helix, DNA-binding protein, tra	99.12
4ghj_A	101	Probable transcriptional regulator; structural gen	99.12
2r1j_L	68	Repressor protein C2; protein-DNA complex, helix-t	99.11
3g5g_A	99	Regulatory protein; transcriptional regulator, hel	99.11
2b5a_A	77	C.BCLI; helix-turn-helix motif, gene regulation; 1	99.1
3f6w_A	83	XRE-family like protein; helix-turn-helix, DNA bin	99.1
2k9q_A	77	Uncharacterized protein; all helix, helix-turn-hel	99.09
3kz3_A	80	Repressor protein CI; five helix bundle, DNA-bindi	99.09
1adr_A	76	P22 C2 repressor; transcription regulation; NMR {E	99.08
3fmy_A	73	HTH-type transcriptional regulator MQSA (YGIT/B302	99.06
3b7h_A	78	Prophage LP1 protein 11; structural genomics, PSI2	99.05
2auw_A	170	Hypothetical protein NE0471; alpha-beta structure,	99.04
1x57_A	91	Endothelial differentiation-related factor 1; HMBF	99.04
3vk0_A	114	NHTF, transcriptional regulator; HTH motif, XRE tr	99.04
3op9_A	114	PLI0006 protein; structural genomics, PSI-2, prote	99.04
3omt_A	73	Uncharacterized protein; structural genomics, PSI-	99.03
2wiu_B	88	HTH-type transcriptional regulator HIPB; transfera	99.03
2kpj_A	94	SOS-response transcriptional repressor, LEXA; NESG	99.03
1lmb_3	92	Protein (lambda repressor); protein-DNA complex, d	99.02
3ivp_A	126	Putative transposon-related DNA-binding protein; A	99.01
3t76_A	88	VANU, transcriptional regulator vanug; structural	99.01
3lfp_A	98	CSP231I C protein; transcriptional regulator, DNA	99.01
2xi8_A	66	Putative transcription regulator; HTH DNA-binding	99.0
1r69_A	69	Repressor protein CI; gene regulating protein; 2.0	98.99
3f52_A	117	CLP gene regulator (CLGR); helix-turn-helix motif,	98.99
2a6c_A	83	Helix-turn-helix motif; putative transcriptional r	98.97
3trb_A	104	Virulence-associated protein I; mobIle and extrach	98.96
2ef8_A	84	C.ECOT38IS, putative transcription factor; helix-t	98.96
1zug_A	71	Phage 434 CRO protein; gene regulating protein, tr	98.94
3mlf_A	111	Transcriptional regulator; structural genomics, he	98.94
2ppx_A	99	AGR_C_3184P, uncharacterized protein ATU1735; HTH-	98.92
2wus_R	112	RODZ, putative uncharacterized protein; structural	98.92
3fym_A	130	Putative uncharacterized protein; HTH DNA binding,	98.92
3bs3_A	76	Putative DNA-binding protein; XRE-family, structur	98.92
2ict_A	94	Antitoxin HIGA; helix-turn-helix, structural genom	98.92
2l49_A	99	C protein; P2 bacteriophage, P2 C, direct repeats,	98.91
2o38_A	120	Hypothetical protein; alpha-beta, helix-turn-helix	98.91
3cec_A	104	Putative antidote protein of plasmid maintenance;	98.9
1nr3_A	122	MTH0916, DNA-binding protein TFX; northeast struct	98.89
1b0n_A	111	Protein (SINR protein); transcription regulator, a	98.88
1dw9_A	156	Cyanate lyase; cyanate degradation, structural gen	98.88
1y9q_A	192	Transcriptional regulator, HTH_3 family; transcrip	98.82
2eby_A	113	Putative HTH-type transcriptional regulator YBAQ;	98.81
2bnm_A	198	Epoxidase; oxidoreductase, cupin, HTH, cation-depe	98.81
3bd1_A	79	CRO protein; transcription factor, helix-turn-heli	98.8
3kxa_A	141	NGO0477 protein, putative uncharacterized protein;	98.78
2ofy_A	86	Putative XRE-family transcriptional regulator; tra	98.78
1zx4_A	192	P1 PARB, plasmid partition PAR B protein, PARB; tr	98.75
3o9x_A	133	Uncharacterized HTH-type transcriptional regulato;	98.72
3pxp_A	292	Helix-turn-helix domain protein; DNA-binding, basi	98.62
2l1p_A	83	DNA-binding protein SATB1; PSI-biology, NESG, stru	98.62
1rzs_A	61	Antirepressor, regulatory protein CRO; helix-turn-	98.6
3g7d_A	443	PHPD; non heme Fe(II) dioxygenase, cupin, biosynth	98.59
3r1f_A	135	ESX-1 secretion-associated regulator ESPR; helix-t	98.59
3qwg_A	123	ESX-1 secretion-associated regulator ESPR; N-termi	98.58
2p5t_A	158	Putative transcriptional regulator PEZA; postsegre	98.47
4ich_A	311	Transcriptional regulator; structural genomics, PS	98.46
3bdn_A	236	Lambda repressor; repressor, allostery; HET: DNA;	98.44
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	98.44
2auw_A	170	Hypothetical protein NE0471; alpha-beta structure,	98.43
1uxc_A	65	FRUR (1-57), fructose repressor; DNA-binding prote	98.37
1neq_A	74	DNA-binding protein NER; NMR {Enterobacteria phage	98.36
2pij_A	67	Prophage PFL 6 CRO; transcription factor, helix-tu	98.34
2l8n_A	67	Transcriptional repressor CYTR; bacterial gene rep	98.3
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	98.27
2fjr_A	189	Repressor protein CI; genetic switch, regulation,	98.22
1dw9_A	156	Cyanate lyase; cyanate degradation, structural gen	98.06
1s4k_A	120	Putative cytoplasmic protein YDIL; structural geno	98.06
1jhf_A	202	LEXA repressor; LEXA SOS repressor, hydrolase; 1.8	97.94
1nr3_A	122	MTH0916, DNA-binding protein TFX; northeast struct	97.93
2hin_A	71	GP39, repressor protein; transcription factor, dim	97.81
2cw1_A	65	SN4M; lambda CRO fold, de novo protein; NMR {Synth	97.74
1rzs_A	61	Antirepressor, regulatory protein CRO; helix-turn-	97.69
2l0k_A	93	Stage III sporulation protein D; SPOIIID, solution	97.66
1s4k_A	120	Putative cytoplasmic protein YDIL; structural geno	97.64
1xwr_A	97	Regulatory protein CII; all-alpha fold, DNA bindin	97.49
1uxc_A	65	FRUR (1-57), fructose repressor; DNA-binding prote	97.45
1zs4_A	83	Regulatory protein CII; helix-turn-helix, transcri	97.37
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	97.36
1zx4_A	192	P1 PARB, plasmid partition PAR B protein, PARB; tr	97.23
2l8n_A	67	Transcriptional repressor CYTR; bacterial gene rep	97.19
2pij_A	67	Prophage PFL 6 CRO; transcription factor, helix-tu	97.18
1jhg_A	101	Trp operon repressor; complex (regulatory protein-	97.13
3g7d_A	443	PHPD; non heme Fe(II) dioxygenase, cupin, biosynth	97.09
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	97.03
1u78_A	141	TC3 transposase, transposable element TC3 transpos	97.03
2ao9_A	155	Phage protein; structural genomics, nine-fold NCS.	96.93
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	96.92
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	96.88
2x48_A	55	CAG38821; archeal virus, viral protein; 2.60A {Sul	96.88
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	96.84
1jko_C	52	HIN recombinase, DNA-invertase HIN; water-mediated	96.37
2ovg_A	66	Phage lambda CRO; transcription factor, helix-turn	96.37
1e3o_C	160	Octamer-binding transcription factor 1; transcript	96.12
2hin_A	71	GP39, repressor protein; transcription factor, dim	96.1
1jhf_A	202	LEXA repressor; LEXA SOS repressor, hydrolase; 1.8	96.02
1k78_A	149	Paired box protein PAX5; paired domain, ETS domain	95.92
2jn6_A	97	Protein CGL2762, transposase; GFT PSI-2, protein s	95.78
2w7n_A	101	TRFB transcriptional repressor protein; INCP, plas	95.63
1x2l_A	101	CUT-like 2, homeobox protein CUX-2; CUT domain, hu	95.59
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	95.55
2k27_A	159	Paired box protein PAX-8; paired domain, solution	95.54
2l0k_A	93	Stage III sporulation protein D; SPOIIID, solution	95.52
2csf_A	101	DNA-binding protein SATB2; CUT domain, special AT-	95.33
3kjx_A	344	Transcriptional regulator, LACI family; LACL famil	95.19
2hsg_A	332	Glucose-resistance amylase regulator; CCPA, transc	95.15
1xwr_A	97	Regulatory protein CII; all-alpha fold, DNA bindin	95.13
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	95.09
1r71_A	178	Transcriptional repressor protein KORB; INCP, plas	95.04
1zs4_A	83	Regulatory protein CII; helix-turn-helix, transcri	95.03
2cw1_A	65	SN4M; lambda CRO fold, de novo protein; NMR {Synth	95.0
1qpz_A	340	PURA, protein (purine nucleotide synthesis repress	94.79
3me5_A	482	Cytosine-specific methyltransferase; structural ge	94.77
1j9i_A	68	GPNU1 DBD;, terminase small subunit; DNA binding d	94.76
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	94.59
2pg4_A	95	Uncharacterized protein; structural genomics, join	94.59
2vz4_A	108	Tipal, HTH-type transcriptional activator TIPA; tr	94.58
3oou_A	108	LIN2118 protein; protein structure initiative, PSI	94.53
3lsg_A	103	Two-component response regulator YESN; structural	94.46
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	94.24
2k9s_A	107	Arabinose operon regulatory protein; activator, ar	94.21
3h5t_A	366	Transcriptional regulator, LACI family; DNA-depend	94.2
1vz0_A	230	PARB, chromosome partitioning protein PARB; nuclea	94.17
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	94.12
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	94.1
2o8x_A	70	Probable RNA polymerase sigma-C factor; promoter r	94.07
1x3u_A	79	Transcriptional regulatory protein FIXJ; helix-tur	94.06
3gp4_A	142	Transcriptional regulator, MERR family; structural	94.04
3frw_A	107	Putative Trp repressor protein; structural genomic	94.01
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	94.0
3kor_A	119	Possible Trp repressor; putative DNA-binding Trp r	93.97
2w48_A	315	Sorbitol operon regulator; SORC, activator, repres	93.84
1wh8_A	111	CUT-like 2, homeobox protein CUX-2; CUT domain, st	93.75
3gpv_A	148	Transcriptional regulator, MERR family; protein st	93.74
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	93.73
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	93.66
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	93.63
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	93.62
2x48_A	55	CAG38821; archeal virus, viral protein; 2.60A {Sul	93.5
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	93.47
1wh6_A	101	CUT-like 2, homeobox protein CUX-2; CUT domain, st	93.44
2jpc_A	61	SSRB; DNA binding protein, structural genomics, PS	93.36
2jml_A	81	DNA binding domain/transcriptional regulator; anti	93.1
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	93.0
2ox6_A	166	Hypothetical protein SO3848; structural genomics,	92.99
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	92.95
2dk5_A	91	DNA-directed RNA polymerase III 39 kDa polypeptide	92.9
1wiz_A	101	DNA-binding protein SATB2; helix bundle, KIAA1034	92.8
2o20_A	332	Catabolite control protein A; CCPA, transcriptiona	92.68
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	92.67
2ao9_A	155	Phage protein; structural genomics, nine-fold NCS.	92.58
3oio_A	113	Transcriptional regulator (ARAC-type DNA-binding c	92.4
1hlv_A	131	CENP-B, major centromere autoantigen B; helix-turn	92.31
1fse_A	74	GERE; helix-turn-helix DNA-binding protein transcr	92.24
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	92.18
1s7o_A	113	Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SP	92.14
1je8_A	82	Nitrate/nitrite response regulator protein NARL; p	92.02
3c57_A	95	Two component transcriptional regulatory protein;	91.97
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	91.87
1z4h_A	66	TORI, TOR inhibition protein; winged helix, revers	91.86
3h5o_A	339	Transcriptional regulator GNTR; transcription regu	91.85
3mky_B	189	Protein SOPB; partition, F plasmid, centromere, DN	91.85
2dg6_A	222	Putative transcriptional regulator; winged-helix m	91.63
3e7l_A	63	Transcriptional regulator (NTRC family); sigma43 a	91.6
1q06_A	135	Transcriptional regulator CUER; MERR family transc	91.53
3hh0_A	146	Transcriptional regulator, MERR family; protein st	91.49
1sfx_A	109	Conserved hypothetical protein AF2008; structural	91.38
1jhg_A	101	Trp operon repressor; complex (regulatory protein-	91.26
1jko_C	52	HIN recombinase, DNA-invertase HIN; water-mediated	91.16
2rn7_A	108	IS629 ORFA; helix, all alpha, unknown function, st	91.16
2o3f_A	111	Putative HTH-type transcriptional regulator YBBH;	90.99
3bil_A	348	Probable LACI-family transcriptional regulator; st	90.96
3ulq_B	90	Transcriptional regulatory protein COMA; tetratric	90.88
3jvd_A	333	Transcriptional regulators; structural genomics, P	90.78
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	90.74
1xsv_A	113	Hypothetical UPF0122 protein SAV1236; helix-turn-h	90.73
3dbi_A	338	Sugar-binding transcriptional regulator, LACI FAM;	90.59
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	90.54
3e3m_A	355	Transcriptional regulator, LACI family; structural	90.46
3t72_q	99	RNA polymerase sigma factor RPOD, DNA-directed RN	90.37
1r8d_A	109	Transcription activator MTAN; protein-DNA complex,	90.17
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	90.13
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	90.1
1umq_A	81	Photosynthetic apparatus regulatory protein; DNA-b	89.99
1jye_A	349	Lactose operon repressor; gene regulation, protein	89.9
3g3z_A	145	NMB1585, transcriptional regulator, MARR family; t	89.88
3ctp_A	330	Periplasmic binding protein/LACI transcriptional;	89.83
1bl0_A	129	Protein (multiple antibiotic resistance protein),	89.75
3iwf_A	107	Transcription regulator RPIR family; transcription	89.71
3pvv_A	101	Chromosomal replication initiator protein DNAA; he	89.61
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	89.61
2o4a_A	93	DNA-binding protein SATB1; protein-DNA complex, tr	89.59
3mn2_A	108	Probable ARAC family transcriptional regulator; st	89.55
3oop_A	143	LIN2960 protein; protein structure initiative, PSI	89.54
2obp_A	96	Putative DNA-binding protein; structural genomics,	89.48
3r0a_A	123	Putative transcriptional regulator; structural gen	89.39
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	89.28
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	89.16
2nnn_A	140	Probable transcriptional regulator; structural gen	89.07
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	88.93
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	88.77
1b4a_A	149	Arginine repressor; helix turn helix; 2.50A {Geoba	88.77
2hr3_A	147	Probable transcriptional regulator; MCSG, structur	88.69
2jn6_A	97	Protein CGL2762, transposase; GFT PSI-2, protein s	88.65
2w25_A	150	Probable transcriptional regulatory protein; trans	88.57
3me5_A	482	Cytosine-specific methyltransferase; structural ge	88.39
2p5k_A	64	Arginine repressor; DNA-binding domain, winged hel	88.36
2rnj_A	91	Response regulator protein VRAR; HTH LUXR-type dom	88.34
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	88.3
2qvo_A	95	Uncharacterized protein AF_1382; PSI, structural g	88.28
2rdp_A	150	Putative transcriptional regulator MARR; PFAM PF01	88.25
1p4w_A	99	RCSB; solution structure, DNA binding domain, DNA	88.25
1ub9_A	100	Hypothetical protein PH1061; helix-turn-helix moti	88.22
3nrv_A	148	Putative transcriptional regulator (MARR/EMRR FAM;	88.21
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	88.18
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	88.11
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	88.09
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	88.06
1on2_A	142	Transcriptional regulator MNTR; helix-turn-helix,	88.0
3k0l_A	162	Repressor protein; helix-turn-helix, structural ge	87.9
1ntc_A	91	Protein (nitrogen regulation protein (NTRC)); heli	87.82
1j1v_A	94	Chromosomal replication initiator protein DNAA, 5'	87.82
3kp7_A	151	Transcriptional regulator TCAR; multiple drug resi	87.55
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	87.54
4hbl_A	149	Transcriptional regulator, MARR family; HTH, trans	87.38
2fbi_A	142	Probable transcriptional regulator; MARR, APC5816,	87.27
1j9i_A	68	GPNU1 DBD;, terminase small subunit; DNA binding d	87.24
1y0u_A	96	Arsenical resistance operon repressor, putative; s	87.18
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	87.14
2a61_A	145	Transcriptional regulator TM0710; APC4350, MCSG, m	87.08
2w7n_A	101	TRFB transcriptional repressor protein; INCP, plas	87.07
1yse_A	141	DNA-binding protein SATB1; all helical, DNA-bindin	87.01
1d5y_A	292	ROB transcription factor; protein-DNA complex, DNA	87.0
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	86.99
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	86.84
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	86.77
3mzy_A	164	RNA polymerase sigma-H factor; PSI, MCSG, structur	86.68
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	86.67
1u2w_A	122	CADC repressor, cadmium efflux system accessory pr	86.59
1ku9_A	152	Hypothetical protein MJ223; putative transcription	86.46
2eth_A	154	Transcriptional regulator, putative, MAR family; M	86.43
2oz6_A	207	Virulence factor regulator; winged helix, helix-tu	86.43
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	86.41
3s2w_A	159	Transcriptional regulator, MARR family; structural	86.4
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	86.31
2jml_A	81	DNA binding domain/transcriptional regulator; anti	86.31
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	86.27
1or7_A	194	Sigma-24, RNA polymerase sigma-E factor; regulatio	86.27
1g2h_A	61	Transcriptional regulatory protein TYRR homolog; p	86.2
2zkz_A	99	Transcriptional repressor PAGR; protein-DNA, HTH m	86.1
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	86.05
2pex_A	153	Transcriptional regulator OHRR; transcription regu	86.0
2wte_A	244	CSA3; antiviral protein, viral resistance, winged	85.87
3ryp_A	210	Catabolite gene activator; CAMP receptor protein (	85.84
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	85.83
1eto_A	98	FIS, factor for inversion stimulation; transcripti	85.74
4fx0_A	148	Probable transcriptional repressor protein; helix-	85.73
2fbh_A	146	Transcriptional regulator PA3341; MARR, transcript	85.67
1z91_A	147	Organic hydroperoxide resistance transcriptional;	85.66
2fmy_A	220	COOA, carbon monoxide oxidation system transcripti	85.61
1j5y_A	187	Transcriptional regulator, biotin repressor famil;	85.6
2hoe_A	380	N-acetylglucosamine kinase; TM1224, structural gen	85.58
1lj9_A	144	Transcriptional regulator SLYA; HTH DNA binding pr	85.58
3bj6_A	152	Transcriptional regulator, MARR family; helix-turn	85.57
3dv8_A	220	Transcriptional regulator, CRP/FNR family; cyclic	85.5
3mkl_A	120	HTH-type transcriptional regulator GADX; PSI2, MCS	85.47
2zcw_A	202	TTHA1359, transcriptional regulator, FNR/CRP famil	85.44
1r71_A	178	Transcriptional repressor protein KORB; INCP, plas	85.08
1u78_A	141	TC3 transposase, transposable element TC3 transpos	85.04
2gxg_A	146	146AA long hypothetical transcriptional regulator;	84.95
4dyq_A	140	Gene 1 protein; GP1, octamer, DNA-binding, viral p	84.88
1z05_A	429	Transcriptional regulator, ROK family; structural	84.79
2nyx_A	168	Probable transcriptional regulatory protein, RV14;	84.72
3e6m_A	161	MARR family transcriptional regulator; APC88769, s	84.7
4fe7_A	412	Xylose operon regulatory protein; HTH_ARAC, helix-	84.61
4ev0_A	216	Transcription regulator, CRP family; CAMP binding,	84.61
3fm5_A	150	Transcriptional regulator; MCSG, PF04017, PSI, MAR	84.58
3iwz_A	230	CAP-like, catabolite activation-like protein; XCC,	84.54
3qao_A	249	LMO0526 protein, MERR-like transcriptional regulat	84.52
3dew_A	206	Transcriptional regulator, TETR family; S genomics	84.45
3d0s_A	227	Transcriptional regulatory protein; CAMP receptor	84.41
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	84.4
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	84.35
3bja_A	139	Transcriptional regulator, MARR family, putative;	84.34
1ft9_A	222	Carbon monoxide oxidation system transcription reg	84.34
1s3j_A	155	YUSO protein; structural genomics, MARR transcript	84.34
2qww_A	154	Transcriptional regulator, MARR family; YP_013417.	84.26
1sfu_A	75	34L protein; protein/Z-DNA complex, DNA binding pr	84.23
3b02_A	195	Transcriptional regulator, CRP family; structural	84.21
3e97_A	231	Transcriptional regulator, CRP/FNR family; YP_6044	84.21
3hsr_A	140	HTH-type transcriptional regulator SARZ; helix-tur	84.18
3jw4_A	148	Transcriptional regulator, MARR/EMRR family; DNA-b	84.13
1gdt_A	183	GD resolvase, protein (gamma delta resolvase); pro	83.86
2frh_A	127	SARA, staphylococcal accessory regulator A; winged	83.85
2zhg_A	154	Redox-sensitive transcriptional activator SOXR; ox	83.74
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	83.72
3cjn_A	162	Transcriptional regulator, MARR family; silicibact	83.68
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	83.68
1zyb_A	232	Transcription regulator, CRP family; NP_813211.1,	83.53
3cdh_A	155	Transcriptional regulator, MARR family; helix-turn	83.46
2h09_A	155	Transcriptional regulator MNTR; transcription regu	83.41
2fxa_A	207	Protease production regulatory protein HPR; protea	83.38
3i4p_A	162	Transcriptional regulator, ASNC family; PSI, struc	83.33
3dkw_A	227	DNR protein; CRP-FNR, HTH, beta barrel, dimerizati	83.29
1z6r_A	406	MLC protein; transcriptional repressor, ROK family	83.1
2ox6_A	166	Hypothetical protein SO3848; structural genomics,	83.05
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	83.01
3jth_A	98	Transcription activator HLYU; transcription factor	82.96
1iuf_A	144	Centromere ABP1 protein; riken structural genomics	82.88
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	82.82
2gau_A	232	Transcriptional regulator, CRP/FNR family; structu	82.77
1e3o_C	160	Octamer-binding transcription factor 1; transcript	82.74
3deu_A	166	Transcriptional regulator SLYA; MARR, WING-helix,	82.64
3la7_A	243	Global nitrogen regulator; activator, DNA-binding,	82.57
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	82.36
3fx3_A	237	Cyclic nucleotide-binding protein; helix_TURN_heli	82.26
2o8x_A	70	Probable RNA polymerase sigma-C factor; promoter r	82.21
3e6c_C	250	CPRK, cyclic nucleotide-binding protein; CPRK, hal	82.12
3nqo_A	189	MARR-family transcriptional regulator; structural	82.04
4aik_A	151	Transcriptional regulator SLYA; transcription, tra	81.76
2ovg_A	66	Phage lambda CRO; transcription factor, helix-turn	81.72
1tbx_A	99	ORF F-93, hypothetical 11.0 kDa protein; sulfolobu	81.62
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	81.49
2jpc_A	61	SSRB; DNA binding protein, structural genomics, PS	81.44
2kko_A	108	Possible transcriptional regulatory protein (possi	81.38
4b8x_A	147	SCO5413, possible MARR-transcriptional regulator;	81.36
3kcc_A	260	Catabolite gene activator; helix-turn-helix, CAMP,	81.24
1k78_A	149	Paired box protein PAX5; paired domain, ETS domain	81.12
3gbg_A	276	TCP pilus virulence regulatory protein; cupin, hel	81.04
1vz0_A	230	PARB, chromosome partitioning protein PARB; nuclea	80.99
1xmk_A	79	Double-stranded RNA-specific adenosine deaminase;	80.98
1fse_A	74	GERE; helix-turn-helix DNA-binding protein transcr	80.94
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	80.81
2r0q_C	209	Putative transposon TN552 DNA-invertase BIN3; site	80.53
2o0m_A	345	Transcriptional regulator, SORC family; structural	80.51
2oa4_A	101	SIR5; structure, structural genomics, PSI-2, prote	80.46
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	80.45
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	80.08
3f3x_A	144	Transcriptional regulator, MARR family, putative;	80.07
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	80.06

>2kpj_A SOS-response transcriptional repressor, LEXA; NESG, GFT, structural genomics, PSI-2, protein structure initiative; NMR {Eubacterium rectale atcc 33656}

Probab=99.76  E-value=2.6e-18  Score=116.40  Aligned_cols=73  Identities=18%  Similarity=0.146  Sum_probs=67.4

Q ss_pred             ccccchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccCCCCC
Q psy6501          25 KHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGTNKQ   97 (174)
Q Consensus        25 ~~~~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~~~~   97 (174)
                      ..+..++.+|.+|+.+|+.+||||++||+.+|||+++|++||+|.+.|+.+.+.+||++|||+++||+.....
T Consensus         2 ~~~~~~~~~~~~lk~~r~~~glsq~~lA~~~gis~~~is~~e~G~~~p~~~~l~~ia~~l~v~~~~l~~~~~~   74 (94)
T 2kpj_A            2 VKDKQKAIFSENLNSYIAKSEKTQLEIAKSIGVSPQTFNTWCKGIAIPRMGKVQALADYFNINKSDLIEDKKL   74 (94)
T ss_dssp             CCCHHHHHHHHHHHHHHTTSSSCHHHHHHHHTCCHHHHHHHHTTSCCCCHHHHHHHHHHHTCCTHHHHSCSCC
T ss_pred             CccHHHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhCCCCCCHHHHHHHHHHHCcCHHHHhcCCCc
Confidence            3455678999999999999999999999999999999999999999999999999999999999999965543

>2jvl_A TRMBF1; coactivator, helix-turn-helix, Pro binding, transcription; NMR {Trichoderma reesei}

Probab=99.75  E-value=2.2e-18  Score=119.83  Aligned_cols=83  Identities=34%  Similarity=0.534  Sum_probs=79.5

Q ss_pred             CCccccccccchhhcccccchHHHHHHHHHHHH--HcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcc
Q psy6501          10 TTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQ--AKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIR   87 (174)
Q Consensus        10 ~~~~~~~~~~~~~~~~~~~~~~~ig~~ik~~R~--~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~   87 (174)
                      +..+..+||+.++.+++..+.+.+|.+|+.+|+  .+||||++||+.+|+|+++|++||+|.+.|+.+.+.+||++|||+
T Consensus        12 ~~~~~~~~d~~~~~~~~~~~~~~~g~~lk~~R~~~~~glsq~elA~~~gis~~~is~~E~G~~~p~~~~l~~ia~~l~v~   91 (107)
T 2jvl_A           12 EGQRLTKVDRSDDIIKPKTVGKEVGKAIEQGRQKFEPTMTQAELGKEIGETAATVASYERGTATPDQNILSKMERVLNVK   91 (107)
T ss_dssp             CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHTTSSSCCCHHHHHHHHTCCHHHHHHHTTTCSCCCHHHHHHHHHTTTCB
T ss_pred             cccccccccccccccCHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHCcC
Confidence            556788999999999999999999999999999  999999999999999999999999999999999999999999999


Q ss_pred             ccccc
Q psy6501          88 LRVNA   92 (174)
Q Consensus        88 ~~~l~   92 (174)
                      ++++.
T Consensus        92 ~~e~~   96 (107)
T 2jvl_A           92 LRGAN   96 (107)
T ss_dssp             SSSSS
T ss_pred             Hhhhc
Confidence            99864

>2ewt_A BLDD, putative DNA-binding protein; the DNA-binding domain of BLDD; 1.81A {Streptomyces coelicolor}

Probab=99.75  E-value=4.1e-18  Score=109.09  Aligned_cols=64  Identities=19%  Similarity=0.210  Sum_probs=61.8

Q ss_pred             chHHHHHHHHHHHHHcCCCHHHHHHHhC--CCHHHHHHHHcCCCCCCHHHHHHHHHHhCccccccc
Q psy6501          29 VPLDLAKLLMQGRQAKGWSQKDLATKIN--EKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNA   92 (174)
Q Consensus        29 ~~~~ig~~ik~~R~~~gltq~eLA~~ig--vs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~   92 (174)
                      +...+|.+|+.+|+.+|+||++||+.+|  +|+++|++||+|...|+.+.+.+||++|||+++||+
T Consensus         5 ~~~~~g~~l~~~r~~~glsq~~lA~~~g~~is~~~i~~~e~g~~~~~~~~l~~la~~l~v~~~~l~   70 (71)
T 2ewt_A            5 YAKQLGAKLRAIRTQQGLSLHGVEEKSQGRWKAVVVGSYERGDRAVTVQRLAELADFYGVPVQELL   70 (71)
T ss_dssp             HHHHHHHHHHHHHHHTTCCHHHHHHHTTTSSCHHHHHHHHHTCSCCCHHHHHHHHHHHTSCGGGGC
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHHCCcCCHHHHHHHHCCCCCCCHHHHHHHHHHHCcCHHHHc
Confidence            4668999999999999999999999999  999999999999999999999999999999999987

>1y7y_A C.AHDI; helix-turn-helix, DNA-binding protein, transcriptional regulator, transcription regulator; 1.69A {Aeromonas hydrophila} SCOP: a.35.1.3

Probab=99.75  E-value=4e-18  Score=109.78  Aligned_cols=65  Identities=28%  Similarity=0.173  Sum_probs=62.5

Q ss_pred             cchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccccccc
Q psy6501          28 KVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNA   92 (174)
Q Consensus        28 ~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~   92 (174)
                      ...+.+|.+|+.+|+.+|+||.+||+.+|+|+++|++||+|.+.|+.+.+.+||++|||+++||+
T Consensus         9 ~~~~~~~~~l~~~r~~~g~s~~~lA~~~gis~~~i~~~e~g~~~~~~~~l~~l~~~l~~~~~~l~   73 (74)
T 1y7y_A            9 ADLVKFGQRLRELRTAKGLSQETLAFLSGLDRSYVGGVERGQRNVSLVNILKLATALDIEPRELF   73 (74)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCSCCBHHHHHHHHHHTTSCGGGGC
T ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHhCcCHHHHc
Confidence            34678999999999999999999999999999999999999999999999999999999999997

>3omt_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; 1.65A {Cytophaga hutchinsonii}

Probab=99.74  E-value=9.9e-19  Score=112.96  Aligned_cols=64  Identities=14%  Similarity=0.115  Sum_probs=61.2

Q ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccCC
Q psy6501          31 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGT   94 (174)
Q Consensus        31 ~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~   94 (174)
                      +.++++|+.+|+.+|+||++||+.+|||+++|++||+|...|+.+.+.+||++|||+++||+..
T Consensus         7 ~~~~~~l~~~r~~~glsq~~lA~~~gis~~~is~~e~g~~~~~~~~l~~ia~~l~v~~~~l~~~   70 (73)
T 3omt_A            7 RKIFNRLKSVLAEKGKTNLWLTETLDKNKTTVSKWCTNDVQPSLETLFDIAEALNVDVRELIVS   70 (73)
T ss_dssp             CCCCBCHHHHHHHHTCCHHHHHHHTTCCHHHHHHHHTTSSCCCHHHHHHHHHHHTSCGGGGBCC
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHHHHhcC
Confidence            4678999999999999999999999999999999999999999999999999999999999964

>3s8q_A R-M controller protein; protein-DNA complex, helix-turn-helix; HET: DNA; 2.10A {Enterobacter SP} SCOP: a.35.1.0 PDB: 3clc_A* 3ufd_A*

Probab=99.74  E-value=4.2e-18  Score=112.29  Aligned_cols=67  Identities=18%  Similarity=0.101  Sum_probs=63.6

Q ss_pred             ccchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccC
Q psy6501          27 EKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAG   93 (174)
Q Consensus        27 ~~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~   93 (174)
                      +.+...+|.+|+.+|+.+||||++||+.+|+|+++|++||+|.+.|+.+.+.+||++|+|+++||+.
T Consensus         6 ~~~~~~~g~~lk~~R~~~glsq~~lA~~~gis~~~i~~~e~g~~~~~~~~l~~ia~~l~v~~~~l~~   72 (82)
T 3s8q_A            6 SFLLSKVSFVIKKIRLEKGMTQEDLAYKSNLDRTYISGIERNSRNLTIKSLELIMKGLEVSDVVFFE   72 (82)
T ss_dssp             CHHHHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCCCCBHHHHHHHHHHTTCCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHCCCCCCCHHHHHHHHHHHCcCHHHHhc
Confidence            3466789999999999999999999999999999999999999999999999999999999999983

>3ivp_A Putative transposon-related DNA-binding protein; APC62618, clostridium diffic structural genomics, PSI-2, protein structure initiative; HET: PG4; 2.02A {Clostridium difficile}

Probab=99.73  E-value=1.3e-17  Score=118.71  Aligned_cols=67  Identities=12%  Similarity=0.188  Sum_probs=64.1

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccCCCC
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGTNK   96 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~~~   96 (174)
                      ++.||.+|+.+|+.+||||++||+.+|||+++|++||+|.+.|+.+.+.+||++|||+++||+....
T Consensus        10 ~~~~g~~lk~~R~~~glsq~~lA~~~gis~~~is~~E~g~~~p~~~~l~~ia~~l~v~~~~l~~~~~   76 (126)
T 3ivp_A           10 FRALGLAIKEARKKQGLTREQVGAMIEIDPRYLTNIENKGQHPSLQVLYDLVSLLNVSVDEFFLPAS   76 (126)
T ss_dssp             THHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHSCCCCCHHHHHHHHHHHTCCSHHHHSCCC
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHCCCCCCCHHHHHHHHHHHCcCHHHHhCCCc
Confidence            6789999999999999999999999999999999999999999999999999999999999997544

>2b5a_A C.BCLI; helix-turn-helix motif, gene regulation; 1.54A {Bacillus caldolyticus} SCOP: a.35.1.3

Probab=99.73  E-value=7.1e-18  Score=109.54  Aligned_cols=68  Identities=22%  Similarity=0.169  Sum_probs=64.2

Q ss_pred             cccchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccC
Q psy6501          26 HEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAG   93 (174)
Q Consensus        26 ~~~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~   93 (174)
                      ...+...+|.+|+.+|+.+||||.+||+.+|+|+++|++||+|.+.|+.+.+.+||++|||+++||+.
T Consensus         4 ~~~~~~~~~~~l~~~r~~~glsq~~lA~~~gis~~~i~~~e~g~~~~~~~~l~~la~~l~~~~~~l~~   71 (77)
T 2b5a_A            4 EIEIKRKFGRTLKKIRTQKGVSQEELADLAGLHRTYISEVERGDRNISLINIHKICAALDIPASTFFR   71 (77)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCSCCBHHHHHHHHHHTTCCHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHhCcCHHHHhc
Confidence            34567789999999999999999999999999999999999999999999999999999999999983

>1x57_A Endothelial differentiation-related factor 1; HMBF1alpha, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.35.1.12

Probab=99.73  E-value=9.8e-18  Score=112.75  Aligned_cols=70  Identities=54%  Similarity=0.921  Sum_probs=65.5

Q ss_pred             ccccchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccCC
Q psy6501          25 KHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGT   94 (174)
Q Consensus        25 ~~~~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~   94 (174)
                      .++.+.+.+|.+|+.+|+.+||||++||+.+|+|+++|++||+|...|+.+.+.+||++|+|+++||+..
T Consensus         6 ~~~~~~~~~~~~l~~~r~~~glsq~~lA~~~gis~~~is~~e~g~~~p~~~~l~~la~~l~v~~~~l~~g   75 (91)
T 1x57_A            6 SGDRVTLEVGKVIQQGRQSKGLTQKDLATKINEKPQVIADYESGRAIPNNQVLGKIERAIGLKLRGKDIG   75 (91)
T ss_dssp             CSSCCCCHHHHHHHHHHHTTTCCHHHHHHHHTSCHHHHHHHHHTCSCCCHHHHHHHHHHHTBCCSSTTTT
T ss_pred             hHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHHHHccC
Confidence            4556778899999999999999999999999999999999999999999999999999999999998743

>3op9_A PLI0006 protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG, transcription regulat; HET: MSE; 1.90A {Listeria innocua}

Probab=99.73  E-value=4.3e-18  Score=119.10  Aligned_cols=68  Identities=15%  Similarity=0.246  Sum_probs=64.2

Q ss_pred             chHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccCCCC
Q psy6501          29 VPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGTNK   96 (174)
Q Consensus        29 ~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~~~   96 (174)
                      +++.+|.+|+.+|+.+||||++||+.+|||+++|++||+|.+.|+.+.+.+||++|||+++||++...
T Consensus         6 ~~~~~~~~l~~~r~~~glsq~~lA~~~gis~~~i~~~e~g~~~p~~~~l~~la~~l~v~~~~l~~~~~   73 (114)
T 3op9_A            6 IQHQFAENLSRLKKEHGLKNHQIAELLNVQTRTVAYYMSGETKPDIEKLIRLATYFHLSIDELVGYVQ   73 (114)
T ss_dssp             CCCCHHHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHHTSSCCCHHHHHHHHHHHTCCHHHHHTCCC
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHHHhcCCC
Confidence            45679999999999999999999999999999999999999999999999999999999999996554

>3b7h_A Prophage LP1 protein 11; structural genomics, PSI2, MCSG, protein structure initiative, midwest center for structural genomics; 2.00A {Lactobacillus plantarum WCFS1}

Probab=99.73  E-value=1.8e-17  Score=107.90  Aligned_cols=66  Identities=21%  Similarity=0.136  Sum_probs=63.0

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCcccccccCCC
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRG-IPNQAIIGKMERALGIRLRVNAGTN   95 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~-~P~~~~l~~la~~L~v~~~~l~~~~   95 (174)
                      .+.+|.+|+.+|+.+|+||.+||+.+|+|+++|++||+|.. .|+.+.+.+||++|||+++||+...
T Consensus         5 ~~~~~~~l~~~r~~~g~sq~~lA~~~gis~~~i~~~e~g~~~~~~~~~l~~ia~~l~~~~~~l~~~~   71 (78)
T 3b7h_A            5 GEFVSEHLMELITQQNLTINRVATLAGLNQSTVNAMFEGRSKRPTITTIRKVCGTLGISVHDFFDFP   71 (78)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHCTTCCCCCHHHHHHHHHHHTCCHHHHTCST
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHHHHHcCCCHHHHhcCC
Confidence            57899999999999999999999999999999999999999 9999999999999999999999543

>2r1j_L Repressor protein C2; protein-DNA complex, helix-turn-helix, DNA-binding, transcription, transcription regulation; 1.53A {Enterobacteria phage P22} SCOP: a.35.1.2 PDB: 3jxb_C 3jxc_L 3jxd_L

Probab=99.72  E-value=4.2e-18  Score=107.83  Aligned_cols=62  Identities=13%  Similarity=0.096  Sum_probs=60.3

Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccC
Q psy6501          32 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAG   93 (174)
Q Consensus        32 ~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~   93 (174)
                      .+|++|+.+|+.+|+||.+||+.+|+|+++|++||+|...|+.+.+.+||++|||+++||+.
T Consensus         5 ~~~~~l~~~r~~~g~s~~~lA~~~gis~~~i~~~e~g~~~~~~~~l~~i~~~l~~~~~~l~~   66 (68)
T 2r1j_L            5 LMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCSPDYLLK   66 (68)
T ss_dssp             CHHHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHTTSSCCBHHHHHHHHHHTTSCHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHHHhc
Confidence            68999999999999999999999999999999999999999999999999999999999974

>3qq6_A HTH-type transcriptional regulator SINR; helix-turn-helix motif, biofilm, repressor, SINI; 1.90A {Bacillus subtilis}

Probab=99.72  E-value=1.2e-17  Score=109.66  Aligned_cols=66  Identities=18%  Similarity=0.235  Sum_probs=61.9

Q ss_pred             chHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcC-CCCCCHHHHHHHHHHhCcccccccCC
Q psy6501          29 VPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGG-RGIPNQAIIGKMERALGIRLRVNAGT   94 (174)
Q Consensus        29 ~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G-~~~P~~~~l~~la~~L~v~~~~l~~~   94 (174)
                      ....+|.+|+.+|+++||||++||+++|||+++|++||+| ...|+.+.+.+||++|||+++||+..
T Consensus         7 ~~~~~~~~ik~~R~~~gltq~elA~~~gis~~~is~~E~G~~~~p~~~~l~~ia~~l~v~~~~l~~~   73 (78)
T 3qq6_A            7 HHHMIGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNLQTNPSIQFLEKVSAVLDVSVHTLLDE   73 (78)
T ss_dssp             -CTTHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTSCCCCBHHHHHHHHHHHTCCHHHHHHS
T ss_pred             CCCCccHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHHHHHHCcCHHHHhCC
Confidence            3457999999999999999999999999999999999999 89999999999999999999999853

>3g5g_A Regulatory protein; transcriptional regulator, helix-turn-helix, restriction- modification, transcription regulator; 2.80A {Enterobacter SP} PDB: 3fya_A

Probab=99.72  E-value=1e-17  Score=114.93  Aligned_cols=67  Identities=18%  Similarity=0.101  Sum_probs=63.7

Q ss_pred             ccchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccC
Q psy6501          27 EKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAG   93 (174)
Q Consensus        27 ~~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~   93 (174)
                      +.+...||.+|+.+|+.+||||++||+++|||+++|++||+|.+.|+.+.+.+||++|||++++|+.
T Consensus        23 ~~~~~~ig~~lr~~R~~~gltq~elA~~~gis~~~is~iE~G~~~ps~~~l~~ia~~l~v~~~~l~~   89 (99)
T 3g5g_A           23 SFLLSKVSFVIKKIRLEKGMTQEDLAYKSNLDRTYISGIERNSRNLTIKSLELIMKGLEVSDVVFFE   89 (99)
T ss_dssp             CHHHHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCSCCBHHHHHHHHHHTTCCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHHCcCHHHHhc
Confidence            3466789999999999999999999999999999999999999999999999999999999999983

>3kz3_A Repressor protein CI; five helix bundle, DNA-binding, transcription, transcription regulation; 1.64A {Enterobacteria phage lambda}

Probab=99.72  E-value=2.5e-17  Score=108.26  Aligned_cols=64  Identities=14%  Similarity=0.107  Sum_probs=61.5

Q ss_pred             chHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccccccc
Q psy6501          29 VPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNA   92 (174)
Q Consensus        29 ~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~   92 (174)
                      +++.++.+|+.+|+++||||.+||+.+|||+++|++||+|++.|+.+.+.+||++|||++++|.
T Consensus         9 ~~~~l~~~l~~~r~~~gltq~~lA~~~gvs~~~is~~e~g~~~~~~~~~~~ia~~l~v~~~~l~   72 (80)
T 3kz3_A            9 DARRLKAIWEKKKNELGLSYESVADKMGMGQSAVAALFNGINALNAYNAALLAKILKVSVEEFS   72 (80)
T ss_dssp             HHHHHHHHHHHHHHHHTCCHHHHHHHTTSCHHHHHHHHTTSSCCCHHHHHHHHHHHTSCGGGTC
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHHHh
Confidence            3568999999999999999999999999999999999999999999999999999999999887

>2k9q_A Uncharacterized protein; all helix, helix-turn-helix, plasmid, structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides thetaiotaomicron}

Probab=99.72  E-value=5.1e-18  Score=110.73  Aligned_cols=63  Identities=17%  Similarity=0.159  Sum_probs=60.6

Q ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccC
Q psy6501          31 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAG   93 (174)
Q Consensus        31 ~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~   93 (174)
                      |.+|.+|+.+|+.+||||++||+++|||+++|++||+|...|+.+.+.+||++|||+++||+.
T Consensus         1 m~~~~~lk~~r~~~glsq~~lA~~~gis~~~i~~~e~g~~~p~~~~l~~ia~~l~v~~~~l~~   63 (77)
T 2k9q_A            1 MELSNELKVERIRLSLTAKSVAEEMGISRQQLCNIEQSETAPVVVKYIAFLRSKGVDLNALFD   63 (77)
T ss_dssp             CCHHHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHTCCSCCHHHHHHHHHHHTTCCHHHHHH
T ss_pred             CcHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcCHHHHhC
Confidence            358999999999999999999999999999999999999999999999999999999999984

>3vk0_A NHTF, transcriptional regulator; HTH motif, XRE transcription factor, DNA binding protein; 1.88A {Neisseria meningitidis}

Probab=99.71  E-value=2.5e-17  Score=115.43  Aligned_cols=70  Identities=27%  Similarity=0.195  Sum_probs=65.7

Q ss_pred             cccccchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccC
Q psy6501          24 LKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAG   93 (174)
Q Consensus        24 ~~~~~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~   93 (174)
                      .++..+...+|.+||.+|+.+||||++||+++|+|+++|++||+|++.|+.+.+.+||++|||+++||+.
T Consensus        13 ~~~~~~~~~~g~~lr~~R~~~gltq~elA~~~gis~~~is~~E~G~~~p~~~~l~~ia~~l~v~~~~l~~   82 (114)
T 3vk0_A           13 PDEQDLRAVLAYNMRLFRVNKGWSQEELARQCGLDRTYVSAVERKRWNIALSNIEKMAAALGVAAYQLLL   82 (114)
T ss_dssp             CCTTCHHHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHTTTCCCCCHHHHHHHHHHHTSCHHHHTS
T ss_pred             ccHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHHHhC
Confidence            3445667889999999999999999999999999999999999999999999999999999999999985

>1adr_A P22 C2 repressor; transcription regulation; NMR {Enterobacteria phage P22} SCOP: a.35.1.2

Probab=99.71  E-value=1.1e-17  Score=108.27  Aligned_cols=64  Identities=13%  Similarity=0.099  Sum_probs=61.5

Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccCCC
Q psy6501          32 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGTN   95 (174)
Q Consensus        32 ~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~~   95 (174)
                      .+|++|+.+|+.+|+||.+||+.+|+|+++|++||+|...|+.+.+.+||++|||+++||+...
T Consensus         5 ~~~~~l~~~r~~~gls~~~lA~~~gis~~~i~~~e~g~~~~~~~~l~~ia~~l~~~~~~l~~~~   68 (76)
T 1adr_A            5 LMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCSPDYLLKGD   68 (76)
T ss_dssp             CHHHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHTTSSCCCHHHHHHHHHHTTSCHHHHHHTC
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHHHHhcCC
Confidence            6999999999999999999999999999999999999999999999999999999999999543

>3f6w_A XRE-family like protein; helix-turn-helix, DNA binding protein, xenobiotic response E family of transcriptional regulators; HET: MSE BTB; 1.85A {Pseudomonas syringae PV}

Probab=99.71  E-value=1.9e-17  Score=109.28  Aligned_cols=63  Identities=22%  Similarity=0.257  Sum_probs=61.4

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccccccc
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNA   92 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~   92 (174)
                      .+.+|.+|+.+|+.+||||++||+.+|+|+++|++||+|++.|+.+.+.+||++|||+++||+
T Consensus        12 ~~~~~~~l~~~R~~~gltq~elA~~~gis~~~is~~e~g~~~~~~~~l~~l~~~l~~~~~~l~   74 (83)
T 3f6w_A           12 YQALLDLLLEARSAAGITQKELAARLGRPQSFVSKTENAERRLDVIEFMDFCRGIGTDPYALL   74 (83)
T ss_dssp             HHHHHHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHTTSSCCCHHHHHHHHHHHTCCHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHcCCCHHHHH
Confidence            568999999999999999999999999999999999999999999999999999999999998

>3lfp_A CSP231I C protein; transcriptional regulator, DNA binding protein, helix-turn-H restriction-modification, transcription; 2.00A {Citrobacter SP} PDB: 3lis_A

Probab=99.71  E-value=6.7e-17  Score=110.22  Aligned_cols=62  Identities=23%  Similarity=0.325  Sum_probs=60.2

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHH----HHHHHcCCCCCCHHHHHHHHHHhCcccccccCC
Q psy6501          33 LAKLLMQGRQAKGWSQKDLATKINEKPQI----VNDYEGGRGIPNQAIIGKMERALGIRLRVNAGT   94 (174)
Q Consensus        33 ig~~ik~~R~~~gltq~eLA~~igvs~~~----is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~   94 (174)
                      ||.+|+.+|+.+||||++||+.+|+|+++    |++||+|.+.|+.+.+.+||++|||+++||++.
T Consensus         2 ~g~~lk~~R~~~glsq~~lA~~~gis~~~~~~~is~~E~g~~~p~~~~l~~la~~l~v~~~~l~~~   67 (98)
T 3lfp_A            2 LIRRLKDARLRAGISQEKLGVLAGIDEASASARMNQYEKGKHAPDFEMANRLAKVLKIPVSYLYTP   67 (98)
T ss_dssp             CHHHHHHHHHHHTCCHHHHHHHTTCCHHHHHHHHHHHHHTSSCCCHHHHHHHHHHHTSCGGGGGCC
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCcchhhhHHHHHHCCCCCCCHHHHHHHHHHHCcCHHHHhCC
Confidence            79999999999999999999999999999    999999999999999999999999999999963

>4ghj_A Probable transcriptional regulator; structural genomics, niaid, national institute of allergy AN infectious diseases; HET: MSE; 1.75A {Vibrio vulnificus}

Probab=99.71  E-value=3.3e-17  Score=112.85  Aligned_cols=69  Identities=16%  Similarity=0.170  Sum_probs=60.7

Q ss_pred             hhcccccchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccc--cccc
Q psy6501          22 EELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRL--RVNA   92 (174)
Q Consensus        22 ~~~~~~~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~--~~l~   92 (174)
                      ..+....+...+|++||.+|+++||||++||+++|||+++|++||+|+  |+++.+.+||.+||++.  +.|+
T Consensus        26 ~~~~~~~l~~~lG~~ir~~R~~~glTQ~eLA~~~gvs~~~is~~E~G~--~~~~~l~~i~~aL~~~~~ld~ll   96 (101)
T 4ghj_A           26 KHVTAAALAEEIGDRLKQARLNRDLTQSEVAEIAGIARKTVLNAEKGK--VQLDIMIAILMALDLTEQIDLFI   96 (101)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHTTC--CBHHHHHHHHHHTTCCGGGGGSS
T ss_pred             hhccHHHHHHHHHHHHHHHHHHcCCCHHHHHHHcCCCHHHHHHHHCCC--CCHHHHHHHHHHcCCCccHHHcC
Confidence            455666778899999999999999999999999999999999999997  46678999999999964  4555

>3mlf_A Transcriptional regulator; structural genomics, helix-turn-helix XRE-family like protei transcription regulator, PSI-2; 2.60A {Staphylococcus aureus subsp}

Probab=99.69  E-value=1e-17  Score=117.21  Aligned_cols=66  Identities=15%  Similarity=0.149  Sum_probs=62.6

Q ss_pred             cchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccC
Q psy6501          28 KVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAG   93 (174)
Q Consensus        28 ~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~   93 (174)
                      .++..+|++|+.+|+.+||||++||+.+|||+++|++||+|.+.|+.+.+.+||++|||+++||+.
T Consensus        19 ~~~~~~g~~Lk~~R~~~gltq~elA~~~gis~~~is~~E~G~~~ps~~~l~~ia~~l~v~~~~l~~   84 (111)
T 3mlf_A           19 YFQSNAMKTLKELRTDYGLTQKELGDLFKVSSRTIQNMEKDSTNIKDSLLSKYMSAFNVKYDDIFL   84 (111)
T ss_dssp             SCCCSSCEEHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHHCCTTCCHHHHHHHHHHHTCCGGGEEC
T ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHhCcCHHHHhC
Confidence            345578999999999999999999999999999999999999999999999999999999999984

>2wiu_B HTH-type transcriptional regulator HIPB; transferase transcription complex, serine kinase, DNA-bindin mercury derivative, repressor; 2.35A {Escherichia coli} PDB: 3dnv_B* 3dnw_B* 3hzi_B*

Probab=99.69  E-value=4.3e-17  Score=108.52  Aligned_cols=66  Identities=26%  Similarity=0.425  Sum_probs=61.7

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccCCC
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGTN   95 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~~   95 (174)
                      .+.+|.+|+.+|+.+|+||++||+.+|+|+++|++||+|...|+.+.+.+||++|||+++||++..
T Consensus        10 ~~~~~~~l~~~r~~~glsq~~lA~~~gis~~~i~~~e~g~~~~~~~~l~~i~~~l~~~~~~l~~~~   75 (88)
T 2wiu_B           10 PTQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELSMTLCDAKN   75 (88)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHCGGGCBHHHHHHHHHHTTCEEEEEC---
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHHhccCC
Confidence            578999999999999999999999999999999999999999999999999999999999999544

>3bs3_A Putative DNA-binding protein; XRE-family, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.65A {Bacteroides fragilis}

Probab=99.69  E-value=2e-17  Score=107.07  Aligned_cols=63  Identities=11%  Similarity=0.141  Sum_probs=60.3

Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccCC
Q psy6501          32 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGT   94 (174)
Q Consensus        32 ~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~   94 (174)
                      .+|++|+.+|+.+|+||.+||+.+|+|+++|++||+|...|+.+.+.+||++|||+++||+..
T Consensus        10 ~~~~~l~~~r~~~g~s~~~lA~~~gis~~~i~~~e~g~~~~~~~~l~~ia~~l~~~~~~l~~~   72 (76)
T 3bs3_A           10 MMLNRIKVVLAEKQRTNRWLAEQMGKSENTISRWCSNKSQPSLDMLVKVAELLNVDPRQLING   72 (76)
T ss_dssp             CCCBCHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTSSCCCHHHHHHHHHHHTSCGGGGBC-
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHHHHhcC
Confidence            489999999999999999999999999999999999999999999999999999999999953

>4ich_A Transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, transcription RE; 1.95A {Saccharomonospora viridis}

Probab=99.69  E-value=1.3e-17  Score=134.73  Aligned_cols=125  Identities=9%  Similarity=0.071  Sum_probs=22.6

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccCCCCCCCCCcccchhhh
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGTNKQPGTTKNTAKLDR  109 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~~~~~~~~~~~~~l~~  109 (174)
                      .+.+|++||.+|+++||||++||+++|||+++||+||+|++.|+.+.|.+||++|||+++||++................
T Consensus        28 ~~~~~~~l~~~r~~~g~t~~~la~~~g~s~~~is~~e~g~~~p~~~~l~~ia~~l~~~~~~l~~~~~~~~~~~~~~~~~~  107 (311)
T 4ich_A           28 SDELRRRVRGLIHSRPGAQREFAAAIGLDESKLSKSLNGTRRFSPHELVRIAEHSGVTVNWLINGRDDARTVAAVPAPTA  107 (311)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             hHHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHCCChhhhhcCCCccccccCCCCccc
Confidence            46899999999999999999999999999999999999999999999999999999999999965443211000000000


Q ss_pred             -hh-------hhhhcccccHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHH
Q psy6501         110 -ET-------EELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDY  155 (174)
Q Consensus       110 -~~-------~~~~~~~~~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~  155 (174)
                       ..       .......+......++ ..+--.+.|..++|+..|+++.++..|
T Consensus       108 ~~~~~~~~~~~~~~r~~il~aa~~l~-~~~G~~~~T~~~IA~~AGvs~gtlY~y  160 (311)
T 4ich_A          108 RSRSAPAGEPQSEARRRILETAWRLI-ARRGYHNVRIHDIASELGTSNATIHYH  160 (311)
T ss_dssp             ---------CCHHHHHHHHHHHHHHH-HHHCGGGCCHHHHHHHHTCCHHHHHHH
T ss_pred             ccCCCCCccchhhHHHHHHHHHHHHH-HHcCCccCCHHHHHHHhCCCchhHHHh
Confidence             00       0000011111111111 122225589999999999999988766

>2a6c_A Helix-turn-helix motif; putative transcriptional regulator, structural genomics, JOI for structural genomics, JCSG; HET: CIT; 1.90A {Nitrosomonas europaea} SCOP: a.35.1.13

Probab=99.69  E-value=7e-17  Score=106.99  Aligned_cols=68  Identities=18%  Similarity=0.204  Sum_probs=63.2

Q ss_pred             ccchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCcccccccCC
Q psy6501          27 EKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRG-IPNQAIIGKMERALGIRLRVNAGT   94 (174)
Q Consensus        27 ~~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~-~P~~~~l~~la~~L~v~~~~l~~~   94 (174)
                      ......+|.+|+.+|+.+||||.+||+.+|+|+++|++||+|+. .|+.+.+.+||++|||+++|++.+
T Consensus        13 ~~~~~~~~~~l~~~r~~~glsq~elA~~~gis~~~is~~e~g~~~~~~~~~l~~la~~l~~~~~~l~~~   81 (83)
T 2a6c_A           13 MKMRSQLLIVLQEHLRNSGLTQFKAAELLGVTQPRVSDLMRGKIDLFSLESLIDMITSIGLKVEINIKD   81 (83)
T ss_dssp             HHHHHHHHHHHHHHHHTTTCCHHHHHHHHTSCHHHHHHHHTTCGGGCCHHHHHHHHHHTTCCCCCCCCC
T ss_pred             ccccHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHHHHHcCCCeEEEeCC
Confidence            34467899999999999999999999999999999999999998 599999999999999999999853

>2l49_A C protein; P2 bacteriophage, P2 C, direct repeats, DNA-binding protein, binding protein; NMR {Enterobacteria phage P2} PDB: 2xcj_A

Probab=99.68  E-value=2.3e-17  Score=112.31  Aligned_cols=67  Identities=13%  Similarity=0.126  Sum_probs=63.2

Q ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHH--hCcccccccCCCCC
Q psy6501          31 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERA--LGIRLRVNAGTNKQ   97 (174)
Q Consensus        31 ~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~--L~v~~~~l~~~~~~   97 (174)
                      |.+|.+|+.+|+.+||||.+||+.+|+|+++|++||+|.+.|+.+.+.+||++  |+|+++||+.....
T Consensus         3 m~~~~~l~~~r~~~gltq~~lA~~~gis~~~is~~e~g~~~p~~~~l~~ia~~l~~~v~~~~l~~~~~~   71 (99)
T 2l49_A            3 NTISEKIVLMRKSEYLSRQQLADLTGVPYGTLSYYESGRSTPPTDVMMNILQTPQFTKYTLWFMTNQIA   71 (99)
T ss_dssp             CCTTHHHHHHHHHTTCCHHHHHHHHCCCHHHHHHHTTTSSCCCHHHHHHHHSSSSSSSSSSTTTSSCCC
T ss_pred             hHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCHHHHHcCCCC
Confidence            46899999999999999999999999999999999999999999999999999  99999999965543

>1zug_A Phage 434 CRO protein; gene regulating protein, transcription regulation; NMR {Phage 434} SCOP: a.35.1.2 PDB: 2cro_A 3cro_L*

Probab=99.68  E-value=2.8e-17  Score=104.92  Aligned_cols=64  Identities=23%  Similarity=0.104  Sum_probs=58.8

Q ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccCCC
Q psy6501          31 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGTN   95 (174)
Q Consensus        31 ~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~~   95 (174)
                      +.+|.+|+.+|+.+|+||.+||+.+|+|+++|++||+|...|... +.+||++|||+++||+...
T Consensus         2 ~~~~~~l~~~r~~~glsq~~lA~~~gis~~~i~~~e~g~~~~~~~-l~~i~~~l~~~~~~l~~~~   65 (71)
T 1zug_A            2 QTLSERLKKRRIALKMTQTELATKAGVKQQSIQLIEAGVTKRPRF-LFEIAMALNCDPVWLQYGT   65 (71)
T ss_dssp             CSHHHHHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHTTCCSSCST-HHHHHHHTTSCHHHHHHSC
T ss_pred             hHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCChHH-HHHHHHHHCCCHHHHhCCC
Confidence            468999999999999999999999999999999999999887644 9999999999999998543

>1lmb_3 Protein (lambda repressor); protein-DNA complex, double helix, transcription/DNA complex; HET: DNA; 1.80A {Enterobacteria phage lambda} SCOP: a.35.1.2 PDB: 1lrp_A 1rio_A 1lli_A*

Probab=99.68  E-value=1.7e-16  Score=106.63  Aligned_cols=65  Identities=15%  Similarity=0.108  Sum_probs=61.8

Q ss_pred             chHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccC
Q psy6501          29 VPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAG   93 (174)
Q Consensus        29 ~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~   93 (174)
                      +.+.++..|+.+|+.+||||++||+.+|+|+++|++||+|.+.|+.+.+.+||++|||+++||+.
T Consensus        14 ~~~~l~~~l~~~R~~~glsq~~lA~~~gis~~~is~~e~g~~~~~~~~l~~ia~~l~v~~~~l~~   78 (92)
T 1lmb_3           14 DARRLKAIYEKKKNELGLSQESVADKMGMGQSGVGALFNGINALNAYNAALLAKILKVSVEEFSP   78 (92)
T ss_dssp             HHHHHHHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHTTSSCCCHHHHHHHHHHHTSCGGGTCH
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHCCCHHHHhh
Confidence            45678999999999999999999999999999999999999999999999999999999999983

>2xi8_A Putative transcription regulator; HTH DNA-binding motif; HET: GOL; 1.21A {Enterococcus faecalis} PDB: 2gzu_A 1utx_A* 2xj3_A 2xiu_A

Probab=99.68  E-value=2.1e-17  Score=104.01  Aligned_cols=61  Identities=23%  Similarity=0.153  Sum_probs=58.8

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccC
Q psy6501          33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAG   93 (174)
Q Consensus        33 ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~   93 (174)
                      +|.+|+.+|+.+|+||++||+.+|+|+++|++||+|...|+.+.+.+||++|||+++||+.
T Consensus         2 ~~~~l~~~r~~~g~s~~~lA~~~gis~~~i~~~e~g~~~~~~~~l~~i~~~l~~~~~~l~~   62 (66)
T 2xi8_A            2 IINNLKLIREKKKISQSELAALLEVSRQTINGIEKNKYNPSLQLALKIAYYLNTPLEDIFQ   62 (66)
T ss_dssp             EEECHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHTTSCCCCHHHHHHHHHHTTSCHHHHEE
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHHHHhC
Confidence            5678999999999999999999999999999999999999999999999999999999985

>1r69_A Repressor protein CI; gene regulating protein; 2.00A {Phage 434} SCOP: a.35.1.2 PDB: 1pra_A 1per_L 1rpe_L* 2or1_L* 1r63_A 2r63_A 1sq8_A

Probab=99.67  E-value=6.6e-17  Score=102.65  Aligned_cols=62  Identities=19%  Similarity=0.298  Sum_probs=58.6

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccCCC
Q psy6501          33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGTN   95 (174)
Q Consensus        33 ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~~   95 (174)
                      ||++|+.+|+.+||||.+||+.+|+|+++|++||+|...|+.. +.+||++|||+++||+...
T Consensus         2 ~~~~l~~~r~~~glsq~~lA~~~gis~~~i~~~e~g~~~~~~~-l~~la~~l~~~~~~l~~~~   63 (69)
T 1r69_A            2 ISSRVKSKRIQLGLNQAELAQKVGTTQQSIEQLENGKTKRPRF-LPELASALGVSVDWLLNGT   63 (69)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHTTSCSSCTT-HHHHHHHTTCCHHHHHHCC
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCchH-HHHHHHHHCcCHHHHhCCC
Confidence            7999999999999999999999999999999999999988877 9999999999999998533

>3f52_A CLP gene regulator (CLGR); helix-turn-helix motif, transcriptional ACTI human pathogen, transcription activator; 1.75A {Corynebacterium glutamicum} PDB: 3f51_A

Probab=99.67  E-value=1.2e-16  Score=112.17  Aligned_cols=68  Identities=21%  Similarity=0.216  Sum_probs=64.0

Q ss_pred             cccchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccC
Q psy6501          26 HEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAG   93 (174)
Q Consensus        26 ~~~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~   93 (174)
                      ...+...||.+|+.+|+.+||||++||+.+|||+++|++||+|.+.|+.+.+.+||++|||++++|+.
T Consensus        22 ~~~~~~~~g~~l~~~R~~~glsq~~lA~~~gis~~~is~~E~g~~~~~~~~l~~la~~l~v~~~~l~~   89 (117)
T 3f52_A           22 EPLLREALGAALRSFRADKGVTLRELAEASRVSPGYLSELERGRKEVSSELLASVCHALGASVADVLI   89 (117)
T ss_dssp             CCCHHHHHHHHHHHHHHHHTCCHHHHHHHTTSCHHHHHHHHTTSSCCCHHHHHHHHHHHTCCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHhCCCHHHHHh
Confidence            34567789999999999999999999999999999999999999999999999999999999999883

>1b0n_A Protein (SINR protein); transcription regulator, antagonist, sporulation; 1.90A {Bacillus subtilis} SCOP: a.34.1.1 a.35.1.3 PDB: 2yal_A

Probab=99.66  E-value=3.3e-16  Score=108.53  Aligned_cols=64  Identities=19%  Similarity=0.291  Sum_probs=61.1

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcC-CCCCCHHHHHHHHHHhCcccccccCCCC
Q psy6501          33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGG-RGIPNQAIIGKMERALGIRLRVNAGTNK   96 (174)
Q Consensus        33 ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G-~~~P~~~~l~~la~~L~v~~~~l~~~~~   96 (174)
                      ||.+|+.+|+.+||||.+||+.+|+|+++|++||+| ...|+.+.+.+||++|||+++||++...
T Consensus         2 ~~~~l~~~r~~~gltq~~lA~~~gis~~~i~~~e~g~~~~p~~~~l~~ia~~l~v~~~~l~~~~~   66 (111)
T 1b0n_A            2 IGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNLQTNPSIQFLEKVSAVLDVSVHTLLDEKH   66 (111)
T ss_dssp             CHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCCSCCCHHHHHHHHHHHTCCHHHHHCCTT
T ss_pred             hHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHHHHHHCcCHHHHhcCCC
Confidence            689999999999999999999999999999999999 8999999999999999999999996543

>2wus_R RODZ, putative uncharacterized protein; structural protein, cell WALL morphogenesis, bacterial cytos bacterial actin; 2.90A {Thermotoga maritima}

Probab=99.66  E-value=9.1e-17  Score=112.66  Aligned_cols=66  Identities=14%  Similarity=0.070  Sum_probs=60.2

Q ss_pred             cchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCC------CHHHHHHHHHHhCcccccccC
Q psy6501          28 KVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIP------NQAIIGKMERALGIRLRVNAG   93 (174)
Q Consensus        28 ~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P------~~~~l~~la~~L~v~~~~l~~   93 (174)
                      +..+.+|.+||.+|+.+||||++||+++|||+++|++||+|...|      +...+.+||++|||++++|+.
T Consensus         3 ~~~~~lG~~Lr~~R~~~glSq~eLA~~~gis~~~is~iE~G~~~~~p~~~~~~~~l~~iA~~Lgv~~~~L~~   74 (112)
T 2wus_R            3 EKWKELGETFRKKREERRITLLDASLFTNINPSKLKRIEEGDLKGLDAEVYIKSYIKRYSEFLELSPDEMLK   74 (112)
T ss_dssp             HHHHHHHHHHHHHHHTTTCCHHHHHHHSSCCHHHHHHHHHTCCTTSSCHHHHHHHHHHHHHHSSCCHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCcchhHHHHHHHHHHHHhCcCHHHHHH
Confidence            446789999999999999999999999999999999999999765      357899999999999999983

>2ef8_A C.ECOT38IS, putative transcription factor; helix-turn-helix, DNA binding protein, transcription regulator; HET: CME; 1.95A {Enterobacteria phage P2}

Probab=99.66  E-value=2.6e-16  Score=103.71  Aligned_cols=64  Identities=17%  Similarity=0.116  Sum_probs=57.6

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHH----HHHHhCcccccccC
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGK----MERALGIRLRVNAG   93 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~----la~~L~v~~~~l~~   93 (174)
                      ++.+|.+|+.+|+.+||||++||+.+|+|+++|++||+|.+.|+.+.+.+    ||.+|+|+++||+.
T Consensus         8 ~~~~~~~l~~~r~~~glsq~~lA~~~gis~~~i~~~e~g~~~~~~~~l~~~~~~l~~~~~v~~~~l~~   75 (84)
T 2ef8_A            8 YRCLVQLLTKLRKEASLSQSELAIFLGLSQSDISKIESFERRLDALELFELLEVVASRLGLPMDILLK   75 (84)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTSSCCBHHHHHHHHHHHHHHHTCCHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHccccCCCHHHHHc
Confidence            57899999999999999999999999999999999999999999766655    55555999999983

>2o38_A Hypothetical protein; alpha-beta, helix-turn-helix, structural genomics, PSI-2, PR structure initiative; 1.83A {Rhodopseudomonas palustris} SCOP: a.35.1.13

Probab=99.65  E-value=4.8e-16  Score=110.20  Aligned_cols=70  Identities=14%  Similarity=0.022  Sum_probs=64.8

Q ss_pred             cchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCcccccccCCCCC
Q psy6501          28 KVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRG-IPNQAIIGKMERALGIRLRVNAGTNKQ   97 (174)
Q Consensus        28 ~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~-~P~~~~l~~la~~L~v~~~~l~~~~~~   97 (174)
                      .+...+|.+|+.+|+.+||||+|||+++|+|+++|++||+|+. .|+.+.+.+||++|||+++|++.+...
T Consensus        36 ~~~~~lg~~L~~~R~~~glTQ~eLA~~lGis~~~Is~iE~G~~~~~s~~~l~~ia~~Lgv~~~~l~~~~~~  106 (120)
T 2o38_A           36 QTKLRLAYALNAVIDRARLSQAAAAARLGINQPKVSALRNYKLEGFSVERLMTLLNALDQDVEIVIRKKPR  106 (120)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCCTTCCHHHHHHHHHHTTEEEEEEEEECCT
T ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHHHHHhCCCcEEeecCCCc
Confidence            4567799999999999999999999999999999999999998 999999999999999999999965443

>1y9q_A Transcriptional regulator, HTH_3 family; transcriptional regulaator, strucutral genomics, protein structure initiative, PSI; 1.90A {Vibrio cholerae} SCOP: a.35.1.8 b.82.1.15

Probab=99.64  E-value=4.8e-16  Score=117.80  Aligned_cols=70  Identities=17%  Similarity=0.190  Sum_probs=65.4

Q ss_pred             cccchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccCCC
Q psy6501          26 HEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGTN   95 (174)
Q Consensus        26 ~~~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~~   95 (174)
                      ...+.+.+|.+||.+|+.+||||++||+++|+|+++|++||+|.+.|+.+.+.+||++|+|+++||+...
T Consensus         5 ~~~~~~~~~~~l~~~r~~~gltq~~lA~~~gis~~~is~~e~g~~~p~~~~l~~ia~~l~v~~~~l~~~~   74 (192)
T 1y9q_A            5 DVMFKSQIANQLKNLRKSRGLSLDATAQLTGVSKAMLGQIERGESSPTIATLWKIASGLEASFSAFFAND   74 (192)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTCCHHHHHHHHSSCHHHHHHHHTTCSCCCHHHHHHHHHHHTCCSGGGGTTS
T ss_pred             hhHHHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHHHHcCCC
Confidence            3445678999999999999999999999999999999999999999999999999999999999999643

>3eus_A DNA-binding protein; structural genomics, PSI2,MCSG, protein structure initiative, midwest center for structural genomic binding; 1.80A {Silicibacter pomeroyi}

Probab=99.64  E-value=5.3e-16  Score=103.43  Aligned_cols=59  Identities=22%  Similarity=0.149  Sum_probs=56.4

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccc
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRL   88 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~   88 (174)
                      ...||.+|+.+|+.+||||++||+.+|+|+++|++||+|.+.|+.+.+.+||++|||+.
T Consensus        12 ~~~~g~~l~~~R~~~gltq~elA~~~gis~~~is~~E~G~~~p~~~~l~~ia~~l~v~~   70 (86)
T 3eus_A           12 HVYLCQRLRQARLDAGLTQADLAERLDKPQSFVAKVETRERRLDVIEFAKWMAACEGLD   70 (86)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHTTCCHHHHHHHHTTSSCCBHHHHHHHHHHTTCGG
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHCCCCCCCHHHHHHHHHHcCCCc
Confidence            34699999999999999999999999999999999999999999999999999999974

>3trb_A Virulence-associated protein I; mobIle and extrachromosomal element functions, DNA binding P; 2.00A {Coxiella burnetii}

Probab=99.64  E-value=3.2e-16  Score=108.50  Aligned_cols=63  Identities=11%  Similarity=0.060  Sum_probs=60.1

Q ss_pred             HHHHHHHHH-HHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccC
Q psy6501          31 LDLAKLLMQ-GRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAG   93 (174)
Q Consensus        31 ~~ig~~ik~-~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~   93 (174)
                      ...|++|++ +|+.+||||.+||+.+|||+++||+||+|++.|+.+.+.+||++|||+++||++
T Consensus        12 ~~pG~~Lk~~lr~~~gltq~eLA~~lGis~~~is~ie~G~~~~s~~~~~kla~~lgvs~~~ll~   75 (104)
T 3trb_A           12 IHPGEILAEELGFLDKMSANQLAKHLAIPTNRVTAILNGARSITADTALRLAKFFGTTPEFWLN   75 (104)
T ss_dssp             CCHHHHHHHHHHHTTSCCHHHHHHHHTSCHHHHHHHHTTSSCCCHHHHHHHHHHHTCCHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHHHHhC
Confidence            457999996 899999999999999999999999999999999999999999999999999984

>3fym_A Putative uncharacterized protein; HTH DNA binding, DNA binding protein; 1.00A {Staphylococcus aureus subsp}

Probab=99.64  E-value=1.1e-16  Score=115.07  Aligned_cols=63  Identities=14%  Similarity=0.111  Sum_probs=59.4

Q ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCH------HHHHHHHHHhCcccccccC
Q psy6501          31 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQ------AIIGKMERALGIRLRVNAG   93 (174)
Q Consensus        31 ~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~------~~l~~la~~L~v~~~~l~~   93 (174)
                      +.+|++||++|+++||||+|||+++|+|+++|++||+|...|++      +.+.++|++|||++++|+.
T Consensus         2 ~~~G~~lr~~R~~~gltq~elA~~~gis~~~is~iE~g~~~~~~~~~~~~~~l~~ia~~L~v~~~~l~~   70 (130)
T 3fym_A            2 KTVGEALKGRRERLGMTLTELEQRTGIKREMLVHIENNEFDQLPNKNYSEGFIRKYASVVNIEPNQLIQ   70 (130)
T ss_dssp             CCHHHHHHHHHHHTTCCHHHHHHHHCCCHHHHHHHHTTCGGGSSSGGGHHHHHHHHHHHTTCCHHHHHH
T ss_pred             hHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCchhhhHHHHHHHHHHHhCCCHHHHHH
Confidence            36999999999999999999999999999999999999988777      7799999999999999984

>2ppx_A AGR_C_3184P, uncharacterized protein ATU1735; HTH-motif, XRE-family, structural genomics, PSI-2, protein structure initiative; 2.00A {Agrobacterium tumefaciens str} SCOP: a.35.1.3

Probab=99.64  E-value=1.5e-16  Score=108.81  Aligned_cols=62  Identities=16%  Similarity=0.196  Sum_probs=56.7

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccccccc
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNA   92 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~   92 (174)
                      .+.+|.+|+.+|+.+||||++||+.+|||+++|++||+|.+.|+.. +.+||++|+|+++||+
T Consensus        28 ~~~~~~~lk~~R~~~glsq~elA~~lgvs~~~is~~E~G~~~p~~~-~~~l~~~l~~~~~~l~   89 (99)
T 2ppx_A           28 SAPRMPRIKIIRRALKLTQEEFSARYHIPLGTLRDWEQGRSEPDQP-ARAYLKIIAVDPEGTA   89 (99)
T ss_dssp             ----CCHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTSSCCCHH-HHHHHHHHHHCHHHHH
T ss_pred             hhHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHcCCCCCCHH-HHHHHHHHCcCHHHHH
Confidence            4679999999999999999999999999999999999999999998 8899999999999987

>3fmy_A HTH-type transcriptional regulator MQSA (YGIT/B3021); helix-turn-helix, DNA-binding, transcription regulation, DNA binding protein; HET: MEQ; 1.40A {Escherichia coli k-12}

Probab=99.63  E-value=5.7e-16  Score=100.29  Aligned_cols=60  Identities=18%  Similarity=0.270  Sum_probs=56.7

Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccccccc
Q psy6501          32 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNA   92 (174)
Q Consensus        32 ~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~   92 (174)
                      ..|++|+.+|+..||||+|||+.+|||+++|++||+|.+.|+...+ +++.+|+++++||.
T Consensus        11 ~~g~~lr~~R~~~gltq~elA~~~gvs~~tis~~E~G~~~p~~~~~-~l~~~l~~~p~~l~   70 (73)
T 3fmy_A           11 VAPEFIVKVRKKLSLTQKEASEIFGGGVNAFSRYEKGNAXPHPSTI-KLLRVLDKHPELLN   70 (73)
T ss_dssp             CCHHHHHHHHHHTTCCHHHHHHHHCSCTTHHHHHHTTSSCCCHHHH-HHHHHHHHCGGGHH
T ss_pred             CCHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHcCCCCCCHHHH-HHHHHHCCCHHHHH
Confidence            4699999999999999999999999999999999999999999988 99999999998863

>2bnm_A Epoxidase; oxidoreductase, cupin, HTH, cation-dependant, zinc, fosfomycin; 1.7A {Streptomyces wedmorensis} SCOP: a.35.1.3 b.82.1.10 PDB: 1zz7_A 1zz8_A 1zz9_A 1zzb_A 1zz6_A 1zzc_A 2bnn_A 2bno_A 3scf_A 3scg_A 3sch_A

Probab=99.61  E-value=1.9e-15  Score=114.91  Aligned_cols=69  Identities=22%  Similarity=0.364  Sum_probs=64.9

Q ss_pred             cchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCcccccccCCCC
Q psy6501          28 KVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRG-IPNQAIIGKMERALGIRLRVNAGTNK   96 (174)
Q Consensus        28 ~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~-~P~~~~l~~la~~L~v~~~~l~~~~~   96 (174)
                      ...+.+|.+||.+|+.+||||++||+++|+|+++|++||+|.. .|+.+.|.+||++|+|+++||+....
T Consensus         6 ~~~~~~g~~l~~~r~~~g~s~~~la~~~gis~~~ls~~e~g~~~~p~~~~l~~ia~~l~~~~~~l~~~~~   75 (198)
T 2bnm_A            6 TASTGFAELLKDRREQVKMDHAALASLLGETPETVAAWENGEGGELTLTQLGRIAHVLGTSIGALTPPAG   75 (198)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTTCTTCBHHHHHHHHHHTTSCTGGGSCCCC
T ss_pred             hHHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHHHHHhCCCHHHEEccCC
Confidence            3467899999999999999999999999999999999999999 99999999999999999999996543

>3r1f_A ESX-1 secretion-associated regulator ESPR; helix-turn-helix, transcription factor, helix-turn-helix transcription factor; 2.50A {Mycobacterium tuberculosis}

Probab=99.61  E-value=4.5e-16  Score=112.53  Aligned_cols=63  Identities=10%  Similarity=0.118  Sum_probs=60.0

Q ss_pred             HHHHHHHHHHHH------HcCCCHHHHHHHhC-----CCHHHHHHHHcCCC-CCCHHHHHHHHHHhCcccccccC
Q psy6501          31 LDLAKLLMQGRQ------AKGWSQKDLATKIN-----EKPQIVNDYEGGRG-IPNQAIIGKMERALGIRLRVNAG   93 (174)
Q Consensus        31 ~~ig~~ik~~R~------~~gltq~eLA~~ig-----vs~~~is~~E~G~~-~P~~~~l~~la~~L~v~~~~l~~   93 (174)
                      ..|++||+.+|+      .++|||++||+.+|     +|++|||+||+|.+ .|+.+.|.+||++|||+++||++
T Consensus         6 ~~~~~RL~~L~~~~~~~~~~~~T~~elA~~~~~~G~~is~s~is~~E~G~r~~Ps~~~l~~iA~~f~V~~~yl~~   80 (135)
T 3r1f_A            6 TTFAARLNRLFDTVYPPGRGPHTSAEVIAALKAEGITMSAPYLSQLRSGNRTNPSGATMAALANFFRIKAAYFTD   80 (135)
T ss_dssp             CCHHHHHHHHHHHCCCTTSCCCCHHHHHHHHHTTTCCCCHHHHHHHHHTSSCCCCHHHHHHHHHHHTSCTHHHHC
T ss_pred             HHHHHHHHHHHHhhcccCCCCCCHHHHHHHHcccCCCcCHHHHHHHHCCCCCCCCHHHHHHHHHHhCCCHHHHcC
Confidence            469999999999      57899999999999     99999999999997 89999999999999999999995

>3cec_A Putative antidote protein of plasmid maintenance; structural genomics, joint center for structural genomics, J protein structure initiative; HET: MSE; 1.60A {Nostoc punctiforme}

Probab=99.60  E-value=1.4e-15  Score=104.62  Aligned_cols=63  Identities=14%  Similarity=0.170  Sum_probs=60.7

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccccccc
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNA   92 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~   92 (174)
                      ...+|++|+.+|+.+|+||.+||+.+|+|+++|++||+|.+.|+.+.+.+||++|||+++||+
T Consensus        16 ~~~~g~~l~~~r~~~gltq~~lA~~~gis~~~is~~e~g~~~~~~~~l~~l~~~l~v~~~~ll   78 (104)
T 3cec_A           16 PIHPGEVIADILDDLDINTANFAEILGVSNQTIQEVINGQRSITVDIAIRLGKALGNGPRLWL   78 (104)
T ss_dssp             CCCHHHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHTTSSCCCHHHHHHHHHHHTSCHHHHH
T ss_pred             CCCHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCcCCCHHHHHHHHHHHCcCHHHHH
Confidence            346899999999999999999999999999999999999999999999999999999999987

>2ofy_A Putative XRE-family transcriptional regulator; transcription regulator, structural genomics, PS protein structure initiative; 1.70A {Rhodococcus SP} SCOP: a.35.1.3

Probab=99.60  E-value=1.3e-15  Score=101.13  Aligned_cols=65  Identities=23%  Similarity=0.189  Sum_probs=61.0

Q ss_pred             chHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCcccccccCCC
Q psy6501          29 VPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRG-IPNQAIIGKMERALGIRLRVNAGTN   95 (174)
Q Consensus        29 ~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~-~P~~~~l~~la~~L~v~~~~l~~~~   95 (174)
                      ....+|.+|+.+|+.+  ||++||+++|||+++|++||+|.. .|+.+.+.+||++|||+++||+...
T Consensus        13 ~~~~~g~~l~~~R~~~--sq~~lA~~~gis~~~is~~E~g~~~~p~~~~l~~ia~~l~v~~~~l~~~~   78 (86)
T 2ofy_A           13 RGQRLGELLRSARGDM--SMVTVAFDAGISVETLRKIETGRIATPAFFTIAAVARVLDLSLDDVAAVV   78 (86)
T ss_dssp             HHHHHHHHHHHHHTTS--CHHHHHHHHTCCHHHHHHHHTTCCSSCBHHHHHHHHHHTTCCHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHC--CHHHHHHHhCCCHHHHHHHHcCCCCCCCHHHHHHHHHHhCCCHHHHhccc
Confidence            3467999999999999  999999999999999999999998 9999999999999999999999644

>3kxa_A NGO0477 protein, putative uncharacterized protein; NEW protein fold, OPPF, STRU genomics, oxford protein production facility; 2.80A {Neisseria gonorrhoeae}

Probab=99.60  E-value=3.2e-16  Score=114.08  Aligned_cols=63  Identities=19%  Similarity=0.200  Sum_probs=60.6

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccccccc
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNA   92 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~   92 (174)
                      +..+|.+|+.+|+.+||||++||+.+|+|+++|++||+|.+.|+.+.+.+||++|||+++||+
T Consensus        66 ~~~~g~~L~~~R~~~glTq~elA~~lGis~s~is~~E~G~~~ps~~~l~~la~~lgv~~~~l~  128 (141)
T 3kxa_A           66 LKAGGETFVSLRMKKGFTQSELATAAGLPQPYLSRIENSKQSLQDKTVQKLANALGVSPLEVR  128 (141)
T ss_dssp             HHHSSCCHHHHHHHTTCCHHHHHHHTTCCHHHHHHHHHTCSCCCHHHHHHHHHHHTCCHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHCCCHHHHH
Confidence            456789999999999999999999999999999999999999999999999999999999998

>2ict_A Antitoxin HIGA; helix-turn-helix, structural genomics, PSI-2, protein struct initiative, northeast structural genomics consortium, NESG; 1.63A {Escherichia coli} SCOP: a.35.1.3 PDB: 2icp_A

Probab=99.58  E-value=3e-15  Score=101.05  Aligned_cols=61  Identities=10%  Similarity=0.127  Sum_probs=58.4

Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccc-ccc
Q psy6501          32 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLR-VNA   92 (174)
Q Consensus        32 ~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~-~l~   92 (174)
                      .+|++|+.+|+.+|+||.+||+.+|||+++|++||+|.+.|+.+.+.+||++|||+++ ||.
T Consensus         8 ~~g~~l~~~r~~~gltq~~lA~~~gis~~~is~~e~g~~~~~~~~~~~i~~~l~v~~~~~l~   69 (94)
T 2ict_A            8 RPGDIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVIGSSPQMWLN   69 (94)
T ss_dssp             CHHHHHHHHHHHHTCCHHHHHHHHTCCHHHHHHHHHTSSCCCHHHHHHHHHHTCSCHHHHHH
T ss_pred             ChhHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHHHHHH
Confidence            5899999999999999999999999999999999999999999999999999999999 554

>2eby_A Putative HTH-type transcriptional regulator YBAQ; hypothetical protein, JW0472, structural genomics, NPPSFA; 2.25A {Escherichia coli}

Probab=99.57  E-value=2.1e-15  Score=105.10  Aligned_cols=62  Identities=6%  Similarity=0.041  Sum_probs=60.0

Q ss_pred             HHHHHHHH-HHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccC
Q psy6501          32 DLAKLLMQ-GRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAG   93 (174)
Q Consensus        32 ~ig~~ik~-~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~   93 (174)
                      .+|++|+. +|+.+|+||.+||+.+|+|+++|++||+|.+.|+.+.+.+||++|||+++||++
T Consensus        10 ~~g~~l~~~~r~~~glsq~~lA~~~gis~~~is~~e~g~~~~~~~~l~~la~~l~~~~~~l~~   72 (113)
T 2eby_A           10 TPGDILLYEYLEPLDLKINELAELLHVHRNSVSALINNNRKLTTEMAFRLAKVFDTTVDFWLN   72 (113)
T ss_dssp             CHHHHHHHHTTTTTTCCHHHHHHHHTSCHHHHHHHHTTSSCCCHHHHHHHHHHHTCCHHHHHH
T ss_pred             ChHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHHHHHc
Confidence            58999998 999999999999999999999999999999999999999999999999999984

>3qwg_A ESX-1 secretion-associated regulator ESPR; N-terminal helix-turn-helix motif, transcription factor, transcription; 1.99A {Mycobacterium tuberculosis} PDB: 3qf3_A 3qyx_A

Probab=99.57  E-value=2.8e-15  Score=106.66  Aligned_cols=62  Identities=10%  Similarity=0.127  Sum_probs=59.3

Q ss_pred             HHHHHHHHHHH------HcCCCHHHHHHHhC-----CCHHHHHHHHcCCC-CCCHHHHHHHHHHhCcccccccC
Q psy6501          32 DLAKLLMQGRQ------AKGWSQKDLATKIN-----EKPQIVNDYEGGRG-IPNQAIIGKMERALGIRLRVNAG   93 (174)
Q Consensus        32 ~ig~~ik~~R~------~~gltq~eLA~~ig-----vs~~~is~~E~G~~-~P~~~~l~~la~~L~v~~~~l~~   93 (174)
                      .|++||+.+|+      ..+|||++||+.+|     +|+++||+||+|.+ .|+.+.|.+||++|||+++||++
T Consensus         5 ~~a~RL~~L~~~~~~~~~~~lT~~elA~~~~~~G~~iS~s~is~iE~G~r~~Ps~~~l~~iA~~f~V~~~yl~~   78 (123)
T 3qwg_A            5 TFAARLNRLFDTVYPPGRGPHTSAEVIAALKAEGITMSAPYLSQLRSGNRTNPSGATMAALANFFRIKAAYFTD   78 (123)
T ss_dssp             CHHHHHHHHHHHSSCTTTCSCCHHHHHHHHHHTTCCCCHHHHHHHHHTSSCCCCHHHHHHHHHHTTSCTHHHHC
T ss_pred             hHHHHHHHHHHhhccCCCCCCCHHHHHHHHcccCCCcCHHHHHHHHcCCCCCCCHHHHHHHHHHhCCCHHHHcC
Confidence            58999999999      77899999999998     99999999999997 89999999999999999999995

>3bd1_A CRO protein; transcription factor, helix-turn-helix, prophage, structural evolution, transcription; 1.40A {Xylella fastidiosa}

Probab=99.52  E-value=8e-15  Score=95.98  Aligned_cols=56  Identities=14%  Similarity=0.185  Sum_probs=53.7

Q ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhC--ccccccc
Q psy6501          35 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALG--IRLRVNA   92 (174)
Q Consensus        35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~--v~~~~l~   92 (174)
                      ++|+.+|+.+| ||.+||+.+|||+++|++||+|.+.| .+.+.+||++||  |+++||+
T Consensus         2 ~~l~~~r~~~g-sq~~lA~~lgvs~~~is~~e~g~~~p-~~~l~~ia~~l~~~v~~~~l~   59 (79)
T 3bd1_A            2 NAIDIAINKLG-SVSALAASLGVRQSAISNWRARGRVP-AERCIDIERVTNGAVICRELR   59 (79)
T ss_dssp             CHHHHHHHHHS-SHHHHHHHHTCCHHHHHHHHHHTCCC-GGGHHHHHHHTTTSSCHHHHC
T ss_pred             hHHHHHHHHhC-CHHHHHHHHCCCHHHHHHHHHCCCCC-HHHHHHHHHHHCCCCcHHHhC
Confidence            37999999999 99999999999999999999999988 999999999999  9999994

>3u3w_A Transcriptional activator PLCR protein; ternary complex, PLCR-PAPR7-DNA, HTH DNA-binding domain, QUO sensing; 2.40A {Bacillus thuringiensis} PDB: 2qfc_A

Probab=99.52  E-value=1.4e-14  Score=115.09  Aligned_cols=66  Identities=21%  Similarity=0.193  Sum_probs=62.2

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccCCCC
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGTNK   96 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~~~   96 (174)
                      .+.+|.+||.+|+.+||||++||+.+ +|+++||+||+|.+.|+.+.+.+||++|||+++||+....
T Consensus         3 ~~~~g~~i~~~R~~~~~tq~~la~~~-~s~~~~s~~e~g~~~~~~~~l~~i~~~l~~~~~~~~~~~~   68 (293)
T 3u3w_A            3 AEKLGSEIKKIRVLRGLTQKQLSENI-CHQSEVSRIESGAVYPSMDILQGIAAKLQIPIIHFYEVLI   68 (293)
T ss_dssp             CHHHHHHHHHHHHHTTCCHHHHHTTT-SCHHHHHHHHTTSCCCCHHHHHHHHHHHTCCTHHHHHTTT
T ss_pred             hHHHHHHHHHHHHHCCCCHHHHHHHh-CCHHHHHHHHCCCCCCCHHHHHHHHHHhCcCHHHHhCCCC
Confidence            35799999999999999999999999 9999999999999999999999999999999999996443

>2awi_A PRGX; repressor, pheromone, DNA binding, regulatory domain, transcription; 2.25A {Enterococcus faecalis} SCOP: a.35.1.11 a.118.8.4 PDB: 2axv_A 2axu_A 2aw6_A 2axz_A 2grl_A 2grm_A

Probab=99.48  E-value=1.6e-14  Score=117.76  Aligned_cols=64  Identities=19%  Similarity=0.185  Sum_probs=61.1

Q ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccCCC
Q psy6501          31 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGTN   95 (174)
Q Consensus        31 ~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~~   95 (174)
                      |.+|++||.+|+++||||++||+.+ +|+++||+||+|.+.|+.+.+.+||++|||++++|+...
T Consensus         2 m~ig~~lk~~R~~~gltq~~la~~~-is~~~is~~E~g~~~~~~~~l~~i~~~l~v~~~~~~~~~   65 (317)
T 2awi_A            2 FKIGSVLKQIRQELNYHQIDLYSGI-MSKSVYIKVEADSRPISVEELSKFSERLGVNFFEILNRA   65 (317)
T ss_dssp             CCHHHHHHHHHHHTTCCHHHHHTTT-SCHHHHHHHHTTCSCCBHHHHHHHHHHHTSCHHHHHHHT
T ss_pred             hHHHHHHHHHHHHCCCCHHHHHHHh-cCHHHHHHHHCCCCCCCHHHHHHHHHHcCCCHHHHHhhc
Confidence            5699999999999999999999999 999999999999999999999999999999999998543

>3bdn_A Lambda repressor; repressor, allostery; HET: DNA; 3.91A {Enterobacteria phage lambda}

Probab=99.44  E-value=5.4e-14  Score=109.51  Aligned_cols=65  Identities=15%  Similarity=0.108  Sum_probs=62.4

Q ss_pred             chHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccC
Q psy6501          29 VPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAG   93 (174)
Q Consensus        29 ~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~   93 (174)
                      +++.++++|+.+|+.+|+||++||+++|+|+++|++||+|.+.|+.+.+.+||++|||+++||+.
T Consensus        14 ~~~~~~~~l~~~r~~~g~t~~~lA~~~gis~~~i~~~~~g~~~p~~~~l~~ia~~l~v~~~~l~~   78 (236)
T 3bdn_A           14 DARRLKAIYEKKKNELGLSQESVADKMGMGQSGVGALFNGINALNAYNAALLAKILKVSVEEFSP   78 (236)
T ss_dssp             HHHHHHHHHHHHTTTTTCCSHHHHHHHTSCHHHHHHHTTTTSCCCHHHHHHTTTTTTSCGGGTCH
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHhCcCHHHhhc
Confidence            35689999999999999999999999999999999999999999999999999999999999984

>2p5t_A Putative transcriptional regulator PEZA; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=99.42  E-value=1.3e-14  Score=107.03  Aligned_cols=63  Identities=14%  Similarity=0.204  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccCC
Q psy6501          32 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGT   94 (174)
Q Consensus        32 ~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~   94 (174)
                      ++|.+|+.+|+.+||||++||+++|+|+++|++||+|...|+.+.+.+||+.|||+.+||++.
T Consensus         1 mig~~lk~~R~~~gltq~elA~~lgis~~~vs~~e~G~~~~~~~~~~~la~~~~v~~~~l~~~   63 (158)
T 2p5t_A            1 MIGKNIKSLRKTHDLTQLEFARIVGISRNSLSRYENGTSSVSTELIDIICQKFNVSYVDIVGE   63 (158)
T ss_dssp             ---------------------------------------------------------------
T ss_pred             ChHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHHCcCHHHHhCC
Confidence            479999999999999999999999999999999999999999999999999999999999953

>3o9x_A Uncharacterized HTH-type transcriptional regulato; HTH-XRE DNA binding motif, transcriptional regulator, bacter antitoxin, Zn binding protein, transcription regulator-DNA; HET: DNA; 2.10A {Escherichia coli} PDB: 3gn5_A* 3gn5_B* 2kz8_A

Probab=99.41  E-value=3.1e-13  Score=96.75  Aligned_cols=58  Identities=17%  Similarity=0.245  Sum_probs=53.4

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccc
Q psy6501          33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVN   91 (174)
Q Consensus        33 ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l   91 (174)
                      .|++|+.+|+..||||++||+.+|+|+++|++||+|.+.|+... .+|++.|+++++++
T Consensus        72 ~~~~l~~~R~~~glsq~~la~~~g~s~~~i~~~E~g~~~p~~~~-~~l~~~~~~~p~~~  129 (133)
T 3o9x_A           72 APEFIVKVRKKLSLTQKEASEIFGGGVNAFSRYEKGNAQPHPST-IKLLRVLDKHPELL  129 (133)
T ss_dssp             CHHHHHHHHHHTTCCHHHHHHHHCSCTTHHHHHHHTSSCCCHHH-HHHHHHHHHCGGGH
T ss_pred             CHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHH-HHHHHHHccCHHHH
Confidence            36899999999999999999999999999999999999999776 77889999988875

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=99.40  E-value=4.7e-14  Score=111.94  Aligned_cols=63  Identities=22%  Similarity=0.229  Sum_probs=60.6

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccC
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAG   93 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~   93 (174)
                      ++.+|.+||.+|+.+||||++||+.+ +|+++||+||+|.+.|+.+.+.+||++|||++++|+.
T Consensus         3 ~~~~g~~i~~~r~~~~~tq~~la~~~-~s~~~is~~e~g~~~~~~~~l~~l~~~l~~~~~~l~~   65 (293)
T 2qfc_A            3 AEKLGSEIKKIRVLRGLTQKQLSENI-CHQSEVSRIESGAVYPSMDILQGIAAKLQIPIIHFYE   65 (293)
T ss_dssp             CHHHHHHHHHHHHHHTCCTTTTTTTT-SCHHHHHHHHTSSSCCCHHHHHHHTTTSCCCTHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHH-cCHHHHHHHHCCCCCCCHHHHHHHHHHhCcCHHHHhc
Confidence            46799999999999999999999999 9999999999999999999999999999999999873

>3pxp_A Helix-turn-helix domain protein; DNA-binding, basic helix-loop-helix motif, BHLH motif, lambd repressor-like DNA-binding fold; HET: MSE MYR; 2.30A {Chloroflexus aurantiacus}

Probab=99.38  E-value=6.6e-13  Score=107.17  Aligned_cols=61  Identities=20%  Similarity=0.295  Sum_probs=58.1

Q ss_pred             hHHHHHHHHHHHHH------cCCCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCccccc
Q psy6501          30 PLDLAKLLMQGRQA------KGWSQKDLATKINEKPQIVNDYEGGRG-IPNQAIIGKMERALGIRLRV   90 (174)
Q Consensus        30 ~~~ig~~ik~~R~~------~gltq~eLA~~igvs~~~is~~E~G~~-~P~~~~l~~la~~L~v~~~~   90 (174)
                      ...||.+||.+|++      +||||+|||+.+|||+++|++||+|+. .|+.+.+.+||++|+|+.++
T Consensus         4 ~~~lG~~Lr~lR~~~~~~~~~gLtqeelA~~~gvS~~~is~iE~G~~~~ps~~~l~~lA~aL~v~~~e   71 (292)
T 3pxp_A            4 RAAFGKLVQALRREHRDEKGRVWTQEVLAERTQLPKRTIERIENGSLAHLDADILLRLADALELTIGE   71 (292)
T ss_dssp             HHHHHHHHHHHHHTCBCTTSCBCCHHHHHHHHTCCHHHHHHHHHTCCSCCCHHHHHHHHHHTTCCHHH
T ss_pred             HHHHHHHHHHHHHccCccCcCCCCHHHHHHHHCcCHHHHHHHHCCCCCCCCHHHHHHHHHhcCCCHHH
Confidence            35799999999999      999999999999999999999999996 99999999999999999875

>1neq_A DNA-binding protein NER; NMR {Enterobacteria phage MU} SCOP: a.35.1.2 PDB: 1ner_A

Probab=99.38  E-value=9.3e-13  Score=85.50  Aligned_cols=57  Identities=14%  Similarity=0.081  Sum_probs=50.3

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccC
Q psy6501          34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAG   93 (174)
Q Consensus        34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~   93 (174)
                      ..+|+.+|.++|+||.+||+++|||+++|++|++| ..|+  ....||++|||+++||+.
T Consensus        11 ~~ri~~~l~~~glT~~~LA~~~Gvs~stls~~~~~-~~p~--~~~~IA~aLgv~~~~L~~   67 (74)
T 1neq_A           11 RADVIAGLKKRKLSLSALSRQFGYAPTTLANALER-HWPK--GEQIIANALETKPEVIWP   67 (74)
T ss_dssp             HHHHHHHHHTTSCCHHHHHHHHSSCHHHHHHTTTS-SCHH--HHHHHHHHTTSCHHHHCT
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcC-CCcc--HHHHHHHHHCcCHHHHhH
Confidence            67889899999999999999999999999999997 3344  445699999999999995

>2fjr_A Repressor protein CI; genetic switch, regulation, cooperativity, transcription regulator; 1.95A {Enterobacteria phage 186} PDB: 2fkd_A

Probab=99.33  E-value=1.6e-12  Score=97.89  Aligned_cols=62  Identities=10%  Similarity=0.058  Sum_probs=58.5

Q ss_pred             chHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccC
Q psy6501          29 VPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAG   93 (174)
Q Consensus        29 ~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~   93 (174)
                      -.+.+++||+++|+.+  ||++||+++|+|+++|++||+|...| .+.+.+||++|||+++||+.
T Consensus         6 ~~~~~~~rl~~~r~~~--tq~elA~~~Gis~~~i~~~e~g~~~p-~~~l~~ia~~~~v~~~~l~~   67 (189)
T 2fjr_A            6 SNVDVLDRICEAYGFS--QKIQLANHFDIASSSLSNRYTRGAIS-YDFAAHCALETGANLQWLLT   67 (189)
T ss_dssp             CHHHHHHHHHHHHTCS--SHHHHHHHTTCCHHHHHHHHHSSSCC-HHHHHHHHHHHCCCHHHHHH
T ss_pred             ccHHHHHHHHHHHhhc--CHHHHHHHhCcCHHHHHHHHhCCCCC-HHHHHHHHHHHCCCHHHHhc
Confidence            3578999999999887  99999999999999999999999999 99999999999999999984

>2l1p_A DNA-binding protein SATB1; PSI-biology, NESG, structural genomics, protein structure in northeast structural genomics consortium; NMR {Homo sapiens} PDB: 3nzl_A*

Probab=99.28  E-value=2.9e-12  Score=83.21  Aligned_cols=53  Identities=11%  Similarity=0.065  Sum_probs=49.3

Q ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcc
Q psy6501          31 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIR   87 (174)
Q Consensus        31 ~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~   87 (174)
                      ....-+||.+|.  ||+|.+||+.+|||++|||.+|||+..|++.  .+||++||.=
T Consensus        20 ~~~~~kLK~il~--GikQ~eLAK~iGIsqsTLSaIenG~~~PsL~--~kIAk~fg~w   72 (83)
T 2l1p_A           20 TTVRNALKDLLK--DMNQSSLAKECPLSQSMISSIVNSTYYANVS--AAKCQEFGRW   72 (83)
T ss_dssp             HHHHHHHHHHHT--TSCHHHHHHHSSSCHHHHHHHHTCSSCCCCC--SHHHHHHHHH
T ss_pred             HHHHHHHHHHHH--hcCHHHHHHHcCCCHHHHHHHHcCCCCCCch--HHHHHHHHHH
Confidence            467889999999  9999999999999999999999999999999  8999999863

>3eus_A DNA-binding protein; structural genomics, PSI2,MCSG, protein structure initiative, midwest center for structural genomic binding; 1.80A {Silicibacter pomeroyi}

Probab=99.17  E-value=9.8e-11  Score=77.60  Aligned_cols=54  Identities=24%  Similarity=0.240  Sum_probs=51.5

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         121 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       121 ~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ..++..|+..|+.+||||.++|+.+|+++++|++||+|...|+.+.+.+|+++|
T Consensus        13 ~~~g~~l~~~R~~~gltq~elA~~~gis~~~is~~E~G~~~p~~~~l~~ia~~l   66 (86)
T 3eus_A           13 VYLCQRLRQARLDAGLTQADLAERLDKPQSFVAKVETRERRLDVIEFAKWMAAC   66 (86)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHTTCCHHHHHHHHTTSSCCBHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHCCCCCCCHHHHHHHHHHc
Confidence            347899999999999999999999999999999999999999999999999986

>2jvl_A TRMBF1; coactivator, helix-turn-helix, Pro binding, transcription; NMR {Trichoderma reesei}

Probab=99.16  E-value=8e-11  Score=81.33  Aligned_cols=72  Identities=36%  Similarity=0.563  Sum_probs=62.9

Q ss_pred             ccchhhhhhhhhhcccccHHHHHHHHHHHH--hcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         103 NTAKLDRETEELKHEKVPLDLAKLLMQGRQ--AKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       103 ~~~~l~~~~~~~~~~~~~~~~~~~i~~~R~--~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      +...++...+......+...++..|+..|.  ..|+||.+||+.+|+++++|++||+|...|+.+.+.+|+++|
T Consensus        15 ~~~~~d~~~~~~~~~~~~~~~g~~lk~~R~~~~~glsq~elA~~~gis~~~is~~E~G~~~p~~~~l~~ia~~l   88 (107)
T 2jvl_A           15 RLTKVDRSDDIIKPKTVGKEVGKAIEQGRQKFEPTMTQAELGKEIGETAATVASYERGTATPDQNILSKMERVL   88 (107)
T ss_dssp             CCCCCCCCCCCCCCCCCCHHHHHHHHHHHTTSSSCCCHHHHHHHHTCCHHHHHHHTTTCSCCCHHHHHHHHHTT
T ss_pred             ccccccccccccCHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence            344555555555666777889999999999  999999999999999999999999999999999999999986

>3s8q_A R-M controller protein; protein-DNA complex, helix-turn-helix; HET: DNA; 2.10A {Enterobacter SP} SCOP: a.35.1.0 PDB: 3clc_A* 3ufd_A*

Probab=99.15  E-value=1.5e-10  Score=75.63  Aligned_cols=55  Identities=20%  Similarity=0.170  Sum_probs=52.2

Q ss_pred             cHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         120 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       120 ~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ...++..|+..|..+|+||.++|+.+|+++++|++||+|...|+...+.+||++|
T Consensus         9 ~~~~g~~lk~~R~~~glsq~~lA~~~gis~~~i~~~e~g~~~~~~~~l~~ia~~l   63 (82)
T 3s8q_A            9 LSKVSFVIKKIRLEKGMTQEDLAYKSNLDRTYISGIERNSRNLTIKSLELIMKGL   63 (82)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCCCCBHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHCCCCCCCHHHHHHHHHHH
Confidence            3567899999999999999999999999999999999999999999999999986

>3qq6_A HTH-type transcriptional regulator SINR; helix-turn-helix motif, biofilm, repressor, SINI; 1.90A {Bacillus subtilis}

Probab=99.13  E-value=1.1e-10  Score=75.94  Aligned_cols=56  Identities=21%  Similarity=0.269  Sum_probs=52.1

Q ss_pred             ccHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcC-CCCCCHHHHHHHHhhC
Q psy6501         119 VPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGG-RGIPNQAIIGKMERAL  174 (174)
Q Consensus       119 ~~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G-~~~P~~~~l~~i~~~l  174 (174)
                      .+...+..|+.+|+.+||||.++|+.+|+++++|++||+| ...|+.+.+.+||++|
T Consensus         7 ~~~~~~~~ik~~R~~~gltq~elA~~~gis~~~is~~E~G~~~~p~~~~l~~ia~~l   63 (78)
T 3qq6_A            7 HHHMIGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNLQTNPSIQFLEKVSAVL   63 (78)
T ss_dssp             -CTTHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTSCCCCBHHHHHHHHHHH
T ss_pred             CCCCccHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHHHHHH
Confidence            4566789999999999999999999999999999999999 8999999999999875

>2ewt_A BLDD, putative DNA-binding protein; the DNA-binding domain of BLDD; 1.81A {Streptomyces coelicolor}

Probab=99.12  E-value=1.6e-10  Score=73.27  Aligned_cols=54  Identities=20%  Similarity=0.216  Sum_probs=51.2

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHhC--CChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         121 LDLAKLLMQGRQAKGWSQKDLATKIN--EKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       121 ~~~~~~i~~~R~~~glsq~ela~~lg--~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ..++..|+..|..+|+||+++|+.+|  +++++|++||+|...|+...+.+||++|
T Consensus         7 ~~~g~~l~~~r~~~glsq~~lA~~~g~~is~~~i~~~e~g~~~~~~~~l~~la~~l   62 (71)
T 2ewt_A            7 KQLGAKLRAIRTQQGLSLHGVEEKSQGRWKAVVVGSYERGDRAVTVQRLAELADFY   62 (71)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHTTTSSCHHHHHHHHHTCSCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHCCcCCHHHHHHHHCCCCCCCHHHHHHHHHHH
Confidence            45789999999999999999999999  9999999999999999999999999875

>1y7y_A C.AHDI; helix-turn-helix, DNA-binding protein, transcriptional regulator, transcription regulator; 1.69A {Aeromonas hydrophila} SCOP: a.35.1.3

Probab=99.12  E-value=2.5e-10  Score=72.71  Aligned_cols=54  Identities=30%  Similarity=0.244  Sum_probs=51.6

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         121 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       121 ~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ..++..|+..|...|+||.++|+.+|+++++|++||+|...|+.+.+.+|+++|
T Consensus        12 ~~~~~~l~~~r~~~g~s~~~lA~~~gis~~~i~~~e~g~~~~~~~~l~~l~~~l   65 (74)
T 1y7y_A           12 VKFGQRLRELRTAKGLSQETLAFLSGLDRSYVGGVERGQRNVSLVNILKLATAL   65 (74)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCSCCBHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHh
Confidence            567899999999999999999999999999999999999999999999999986

>4ghj_A Probable transcriptional regulator; structural genomics, niaid, national institute of allergy AN infectious diseases; HET: MSE; 1.75A {Vibrio vulnificus}

Probab=99.12  E-value=1.7e-10  Score=79.13  Aligned_cols=54  Identities=20%  Similarity=0.218  Sum_probs=49.1

Q ss_pred             ccHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         119 VPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       119 ~~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      +...++.+|+.+|+.+||||+++|+++|+++++|++||+|+  |+++.+.+|+++|
T Consensus        33 l~~~lG~~ir~~R~~~glTQ~eLA~~~gvs~~~is~~E~G~--~~~~~l~~i~~aL   86 (101)
T 4ghj_A           33 LAEEIGDRLKQARLNRDLTQSEVAEIAGIARKTVLNAEKGK--VQLDIMIAILMAL   86 (101)
T ss_dssp             HHHHHHHHHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHTTC--CBHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHcCCCHHHHHHHHCCC--CCHHHHHHHHHHc
Confidence            45678999999999999999999999999999999999997  5667899999886

>2r1j_L Repressor protein C2; protein-DNA complex, helix-turn-helix, DNA-binding, transcription, transcription regulation; 1.53A {Enterobacteria phage P22} SCOP: a.35.1.2 PDB: 3jxb_C 3jxc_L 3jxd_L

Probab=99.11  E-value=2.4e-10  Score=71.53  Aligned_cols=53  Identities=15%  Similarity=0.183  Sum_probs=50.3

Q ss_pred             HHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         122 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       122 ~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      .++..|+..|..+|+||.++|+.+|+++++|++||+|...|+.+.+.+|+++|
T Consensus         5 ~~~~~l~~~r~~~g~s~~~lA~~~gis~~~i~~~e~g~~~~~~~~l~~i~~~l   57 (68)
T 2r1j_L            5 LMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKAL   57 (68)
T ss_dssp             CHHHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHTTSSCCBHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence            46789999999999999999999999999999999999999999999999876

>3g5g_A Regulatory protein; transcriptional regulator, helix-turn-helix, restriction- modification, transcription regulator; 2.80A {Enterobacter SP} PDB: 3fya_A

Probab=99.11  E-value=2e-10  Score=78.32  Aligned_cols=56  Identities=20%  Similarity=0.178  Sum_probs=53.0

Q ss_pred             ccHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         119 VPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       119 ~~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      +...++.+|+.+|+.+|+||+++|+++|+++++|++||+|...|+...+.+||++|
T Consensus        25 ~~~~ig~~lr~~R~~~gltq~elA~~~gis~~~is~iE~G~~~ps~~~l~~ia~~l   80 (99)
T 3g5g_A           25 LLSKVSFVIKKIRLEKGMTQEDLAYKSNLDRTYISGIERNSRNLTIKSLELIMKGL   80 (99)
T ss_dssp             HHHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCSCCBHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHH
Confidence            34568899999999999999999999999999999999999999999999999987

>2b5a_A C.BCLI; helix-turn-helix motif, gene regulation; 1.54A {Bacillus caldolyticus} SCOP: a.35.1.3

Probab=99.10  E-value=3.2e-10  Score=72.85  Aligned_cols=55  Identities=25%  Similarity=0.224  Sum_probs=51.9

Q ss_pred             cHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         120 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       120 ~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ...++..|+..|..+|+||.++|+.+|+++++|++||+|...|+...+.+||++|
T Consensus         8 ~~~~~~~l~~~r~~~glsq~~lA~~~gis~~~i~~~e~g~~~~~~~~l~~la~~l   62 (77)
T 2b5a_A            8 KRKFGRTLKKIRTQKGVSQEELADLAGLHRTYISEVERGDRNISLINIHKICAAL   62 (77)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCSCCBHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHh
Confidence            3567899999999999999999999999999999999999999999999999986

>3f6w_A XRE-family like protein; helix-turn-helix, DNA binding protein, xenobiotic response E family of transcriptional regulators; HET: MSE BTB; 1.85A {Pseudomonas syringae PV}

Probab=99.10  E-value=1.9e-10  Score=75.16  Aligned_cols=54  Identities=24%  Similarity=0.334  Sum_probs=51.3

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         121 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       121 ~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ..++..|+..|..+|+||.++|+.+|+++++|++||+|+..|+.+.+.+||++|
T Consensus        13 ~~~~~~l~~~R~~~gltq~elA~~~gis~~~is~~e~g~~~~~~~~l~~l~~~l   66 (83)
T 3f6w_A           13 QALLDLLLEARSAAGITQKELAARLGRPQSFVSKTENAERRLDVIEFMDFCRGI   66 (83)
T ss_dssp             HHHHHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHTTSSCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHc
Confidence            457899999999999999999999999999999999999999999999999875

>2k9q_A Uncharacterized protein; all helix, helix-turn-helix, plasmid, structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides thetaiotaomicron}

Probab=99.09  E-value=2.2e-10  Score=74.00  Aligned_cols=52  Identities=17%  Similarity=0.102  Sum_probs=49.7

Q ss_pred             HHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         123 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       123 ~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ++..|+..|..+|+||+++|+++|+++++|++||+|+..|+...+.+|+++|
T Consensus         3 ~~~~lk~~r~~~glsq~~lA~~~gis~~~i~~~e~g~~~p~~~~l~~ia~~l   54 (77)
T 2k9q_A            3 LSNELKVERIRLSLTAKSVAEEMGISRQQLCNIEQSETAPVVVKYIAFLRSK   54 (77)
T ss_dssp             HHHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHTCCSCCHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence            5688999999999999999999999999999999999999999999999986

>3kz3_A Repressor protein CI; five helix bundle, DNA-binding, transcription, transcription regulation; 1.64A {Enterobacteria phage lambda}

Probab=99.09  E-value=2.4e-10  Score=74.43  Aligned_cols=54  Identities=17%  Similarity=0.142  Sum_probs=51.1

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         121 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       121 ~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ..+..+++..|+.+|+||.++|+.+|+++++|++||+|...|+.+.+.+||++|
T Consensus        11 ~~l~~~l~~~r~~~gltq~~lA~~~gvs~~~is~~e~g~~~~~~~~~~~ia~~l   64 (80)
T 3kz3_A           11 RRLKAIWEKKKNELGLSYESVADKMGMGQSAVAALFNGINALNAYNAALLAKIL   64 (80)
T ss_dssp             HHHHHHHHHHHHHHTCCHHHHHHHTTSCHHHHHHHHTTSSCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence            457889999999999999999999999999999999999999999999999875

>1adr_A P22 C2 repressor; transcription regulation; NMR {Enterobacteria phage P22} SCOP: a.35.1.2

Probab=99.08  E-value=3.7e-10  Score=72.29  Aligned_cols=53  Identities=15%  Similarity=0.183  Sum_probs=50.3

Q ss_pred             HHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         122 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       122 ~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      .++..|+..|..+|+||.++|+.+|+++++|++||+|...|+.+.+.+|+++|
T Consensus         5 ~~~~~l~~~r~~~gls~~~lA~~~gis~~~i~~~e~g~~~~~~~~l~~ia~~l   57 (76)
T 1adr_A            5 LMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKAL   57 (76)
T ss_dssp             CHHHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHTTSSCCCHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence            46789999999999999999999999999999999999999999999999876

>3fmy_A HTH-type transcriptional regulator MQSA (YGIT/B3021); helix-turn-helix, DNA-binding, transcription regulation, DNA binding protein; HET: MEQ; 1.40A {Escherichia coli k-12}

Probab=99.06  E-value=3.4e-10  Score=72.78  Aligned_cols=49  Identities=20%  Similarity=0.363  Sum_probs=45.2

Q ss_pred             HHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhh
Q psy6501         124 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERA  173 (174)
Q Consensus       124 ~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~  173 (174)
                      +..|+..|+..|+||+++|+.+|+++++|++||+|...|+...+ +++++
T Consensus        13 g~~lr~~R~~~gltq~elA~~~gvs~~tis~~E~G~~~p~~~~~-~l~~~   61 (73)
T 3fmy_A           13 PEFIVKVRKKLSLTQKEASEIFGGGVNAFSRYEKGNAXPHPSTI-KLLRV   61 (73)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHCSCTTHHHHHHTTSSCCCHHHH-HHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHcCCCCCCHHHH-HHHHH
Confidence            57899999999999999999999999999999999999999988 66654

>3b7h_A Prophage LP1 protein 11; structural genomics, PSI2, MCSG, protein structure initiative, midwest center for structural genomics; 2.00A {Lactobacillus plantarum WCFS1}

Probab=99.05  E-value=5.4e-10  Score=71.92  Aligned_cols=54  Identities=22%  Similarity=0.167  Sum_probs=51.1

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCC-CCCHHHHHHHHhhC
Q psy6501         121 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRG-IPNQAIIGKMERAL  174 (174)
Q Consensus       121 ~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~-~P~~~~l~~i~~~l  174 (174)
                      ..++..|+..|..+|+||.++|+.+|+++++|++||+|.. .|+.+.+.+||++|
T Consensus         6 ~~~~~~l~~~r~~~g~sq~~lA~~~gis~~~i~~~e~g~~~~~~~~~l~~ia~~l   60 (78)
T 3b7h_A            6 EFVSEHLMELITQQNLTINRVATLAGLNQSTVNAMFEGRSKRPTITTIRKVCGTL   60 (78)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHCTTCCCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHHHHHc
Confidence            4578899999999999999999999999999999999999 99999999999875

>2auw_A Hypothetical protein NE0471; alpha-beta structure, structural genomics, PSI, protein STRU initiative; 1.85A {Nitrosomonas europaea} SCOP: a.35.1.10 d.331.1.1

Probab=99.04  E-value=4.7e-10  Score=83.47  Aligned_cols=58  Identities=12%  Similarity=0.035  Sum_probs=47.3

Q ss_pred             cccccchHHH--------HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHH
Q psy6501          24 LKHEKVPLDL--------AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKME   81 (174)
Q Consensus        24 ~~~~~~~~~i--------g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la   81 (174)
                      +.|+.+....        .++||.+|+.+||||+++|+++|||+++|++||+|.+.|+...+.+..
T Consensus        74 iaPd~LY~~~~~~~~~~s~~~lk~lR~~~glTQ~elA~~LGvsr~tis~yE~G~r~iP~~~~lac~  139 (170)
T 2auw_A           74 FGRDNVYAWAKEQAGEVSHEMFGDWMHRNNLSLTTAAEALGISRRMVSYYRTAHKIIPRTIWLACL  139 (170)
T ss_dssp             BCHHHHHHHHHHHTTCCCHHHHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHTTSSCCCHHHHHHHH
T ss_pred             CCHHHHHHhhhhhccCCCcHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHH
Confidence            5666663322        458999999999999999999999999999999999977777754433

>1x57_A Endothelial differentiation-related factor 1; HMBF1alpha, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.35.1.12

Probab=99.04  E-value=4.8e-10  Score=74.73  Aligned_cols=57  Identities=61%  Similarity=1.050  Sum_probs=52.9

Q ss_pred             cccHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         118 KVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       118 ~~~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      .....++..|+..|..+|+||.++|+.+|+++++|++||+|...|+.+.+.+|+++|
T Consensus         9 ~~~~~~~~~l~~~r~~~glsq~~lA~~~gis~~~is~~e~g~~~p~~~~l~~la~~l   65 (91)
T 1x57_A            9 RVTLEVGKVIQQGRQSKGLTQKDLATKINEKPQVIADYESGRAIPNNQVLGKIERAI   65 (91)
T ss_dssp             CCCCHHHHHHHHHHHTTTCCHHHHHHHHTSCHHHHHHHHHTCSCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence            345568899999999999999999999999999999999999999999999999875

>3vk0_A NHTF, transcriptional regulator; HTH motif, XRE transcription factor, DNA binding protein; 1.88A {Neisseria meningitidis}

Probab=99.04  E-value=4.9e-10  Score=77.96  Aligned_cols=56  Identities=32%  Similarity=0.262  Sum_probs=52.7

Q ss_pred             ccHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         119 VPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       119 ~~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ....++..|+.+|+.+||||+++|+.+|+++++|++||+|+..|+...+.+||++|
T Consensus        18 ~~~~~g~~lr~~R~~~gltq~elA~~~gis~~~is~~E~G~~~p~~~~l~~ia~~l   73 (114)
T 3vk0_A           18 LRAVLAYNMRLFRVNKGWSQEELARQCGLDRTYVSAVERKRWNIALSNIEKMAAAL   73 (114)
T ss_dssp             HHHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHTTTCCCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence            34568999999999999999999999999999999999999999999999999875

>3op9_A PLI0006 protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG, transcription regulat; HET: MSE; 1.90A {Listeria innocua}

Probab=99.04  E-value=3.7e-10  Score=78.36  Aligned_cols=54  Identities=17%  Similarity=0.273  Sum_probs=51.1

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         121 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       121 ~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ..++.+|+..|+.+|+||.++|+.+|+++++|++||+|...|+.+.+.+||++|
T Consensus         8 ~~~~~~l~~~r~~~glsq~~lA~~~gis~~~i~~~e~g~~~p~~~~l~~la~~l   61 (114)
T 3op9_A            8 HQFAENLSRLKKEHGLKNHQIAELLNVQTRTVAYYMSGETKPDIEKLIRLATYF   61 (114)
T ss_dssp             CCHHHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHHTSSCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence            347889999999999999999999999999999999999999999999999875

>3omt_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; 1.65A {Cytophaga hutchinsonii}

Probab=99.03  E-value=3.9e-10  Score=72.06  Aligned_cols=51  Identities=16%  Similarity=0.122  Sum_probs=48.0

Q ss_pred             HHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         124 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       124 ~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ...|+..|..+|+||.++|+.+|+++++|++||+|...|+.+.+.+||++|
T Consensus        10 ~~~l~~~r~~~glsq~~lA~~~gis~~~is~~e~g~~~~~~~~l~~ia~~l   60 (73)
T 3omt_A           10 FNRLKSVLAEKGKTNLWLTETLDKNKTTVSKWCTNDVQPSLETLFDIAEAL   60 (73)
T ss_dssp             CBCHHHHHHHHTCCHHHHHHHTTCCHHHHHHHHTTSSCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence            357889999999999999999999999999999999999999999999875

>2wiu_B HTH-type transcriptional regulator HIPB; transferase transcription complex, serine kinase, DNA-bindin mercury derivative, repressor; 2.35A {Escherichia coli} PDB: 3dnv_B* 3dnw_B* 3hzi_B*

Probab=99.03  E-value=5.3e-10  Score=73.69  Aligned_cols=55  Identities=29%  Similarity=0.459  Sum_probs=52.0

Q ss_pred             cHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         120 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       120 ~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ...++..|+..|..+|+||.++|+.+|+++++|++||+|...|+...+.+|+++|
T Consensus        10 ~~~~~~~l~~~r~~~glsq~~lA~~~gis~~~i~~~e~g~~~~~~~~l~~i~~~l   64 (88)
T 2wiu_B           10 PTQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSL   64 (88)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHCGGGCBHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence            3567899999999999999999999999999999999999999999999999986

>2kpj_A SOS-response transcriptional repressor, LEXA; NESG, GFT, structural genomics, PSI-2, protein structure initiative; NMR {Eubacterium rectale atcc 33656}

Probab=99.03  E-value=5.4e-10  Score=75.01  Aligned_cols=54  Identities=19%  Similarity=0.196  Sum_probs=51.1

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         121 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       121 ~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ..++.+|+..|..+|+||.++|+.+|+++++|++||+|...|+.+.+.+|+++|
T Consensus         8 ~~~~~~lk~~r~~~glsq~~lA~~~gis~~~is~~e~G~~~p~~~~l~~ia~~l   61 (94)
T 2kpj_A            8 AIFSENLNSYIAKSEKTQLEIAKSIGVSPQTFNTWCKGIAIPRMGKVQALADYF   61 (94)
T ss_dssp             HHHHHHHHHHHTTSSSCHHHHHHHHTCCHHHHHHHHTTSCCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhCCCCCCHHHHHHHHHHH
Confidence            457889999999999999999999999999999999999999999999999875

>1lmb_3 Protein (lambda repressor); protein-DNA complex, double helix, transcription/DNA complex; HET: DNA; 1.80A {Enterobacteria phage lambda} SCOP: a.35.1.2 PDB: 1lrp_A 1rio_A 1lli_A*

Probab=99.02  E-value=6.7e-10  Score=73.96  Aligned_cols=55  Identities=18%  Similarity=0.154  Sum_probs=51.4

Q ss_pred             cHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         120 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       120 ~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ...++..++..|..+|+||.++|+.+|+++++|++||+|...|+.+.+.+||++|
T Consensus        15 ~~~l~~~l~~~R~~~glsq~~lA~~~gis~~~is~~e~g~~~~~~~~l~~ia~~l   69 (92)
T 1lmb_3           15 ARRLKAIYEKKKNELGLSQESVADKMGMGQSGVGALFNGINALNAYNAALLAKIL   69 (92)
T ss_dssp             HHHHHHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHTTSSCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence            3567889999999999999999999999999999999999999999999999875

>3ivp_A Putative transposon-related DNA-binding protein; APC62618, clostridium diffic structural genomics, PSI-2, protein structure initiative; HET: PG4; 2.02A {Clostridium difficile}

Probab=99.01  E-value=6.3e-10  Score=78.57  Aligned_cols=55  Identities=15%  Similarity=0.271  Sum_probs=52.1

Q ss_pred             cHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         120 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       120 ~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ...++.+|+..|..+||||.++|+.+|+++++|++||+|...|+.+.+.+||++|
T Consensus        10 ~~~~g~~lk~~R~~~glsq~~lA~~~gis~~~is~~E~g~~~p~~~~l~~ia~~l   64 (126)
T 3ivp_A           10 FRALGLAIKEARKKQGLTREQVGAMIEIDPRYLTNIENKGQHPSLQVLYDLVSLL   64 (126)
T ss_dssp             THHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHSCCCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHCCCCCCCHHHHHHHHHHH
Confidence            3568899999999999999999999999999999999999999999999999875

>3lfp_A CSP231I C protein; transcriptional regulator, DNA binding protein, helix-turn-H restriction-modification, transcription; 2.00A {Citrobacter SP} PDB: 3lis_A

Probab=99.01  E-value=4.1e-10  Score=76.18  Aligned_cols=52  Identities=25%  Similarity=0.410  Sum_probs=49.3

Q ss_pred             HHHHHHHHHHhcCCCHHHHHHHhCCChhH----HHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         123 LAKLLMQGRQAKGWSQKDLATKINEKPQI----VNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       123 ~~~~i~~~R~~~glsq~ela~~lg~~~s~----i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ++.+|+..|..+|+||.++|+.+|+++++    |++||+|...|+.+.+.+||++|
T Consensus         2 ~g~~lk~~R~~~glsq~~lA~~~gis~~~~~~~is~~E~g~~~p~~~~l~~la~~l   57 (98)
T 3lfp_A            2 LIRRLKDARLRAGISQEKLGVLAGIDEASASARMNQYEKGKHAPDFEMANRLAKVL   57 (98)
T ss_dssp             CHHHHHHHHHHHTCCHHHHHHHTTCCHHHHHHHHHHHHHTSSCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCcchhhhHHHHHHCCCCCCCHHHHHHHHHHH
Confidence            36789999999999999999999999999    99999999999999999999875

>2xi8_A Putative transcription regulator; HTH DNA-binding motif; HET: GOL; 1.21A {Enterococcus faecalis} PDB: 2gzu_A 1utx_A* 2xj3_A 2xiu_A

Probab=99.00  E-value=1.1e-09  Score=68.11  Aligned_cols=50  Identities=26%  Similarity=0.211  Sum_probs=47.2

Q ss_pred             HHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         125 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       125 ~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ..|+..|..+|+||.++|+.+|+++++|++||+|...|+.+.+.+|+++|
T Consensus         4 ~~l~~~r~~~g~s~~~lA~~~gis~~~i~~~e~g~~~~~~~~l~~i~~~l   53 (66)
T 2xi8_A            4 NNLKLIREKKKISQSELAALLEVSRQTINGIEKNKYNPSLQLALKIAYYL   53 (66)
T ss_dssp             ECHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHTTSCCCCHHHHHHHHHHT
T ss_pred             HHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence            35788899999999999999999999999999999999999999999886

>1r69_A Repressor protein CI; gene regulating protein; 2.00A {Phage 434} SCOP: a.35.1.2 PDB: 1pra_A 1per_L 1rpe_L* 2or1_L* 1r63_A 2r63_A 1sq8_A

Probab=98.99  E-value=9.2e-10  Score=69.07  Aligned_cols=51  Identities=22%  Similarity=0.336  Sum_probs=47.6

Q ss_pred             HHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         123 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       123 ~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ++..|+..|...|+||.++|+.+|+++++|++||+|...|+.. +.+|+++|
T Consensus         2 ~~~~l~~~r~~~glsq~~lA~~~gis~~~i~~~e~g~~~~~~~-l~~la~~l   52 (69)
T 1r69_A            2 ISSRVKSKRIQLGLNQAELAQKVGTTQQSIEQLENGKTKRPRF-LPELASAL   52 (69)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHTTSCSSCTT-HHHHHHHT
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCchH-HHHHHHHH
Confidence            5678999999999999999999999999999999999998877 99999876

>3f52_A CLP gene regulator (CLGR); helix-turn-helix motif, transcriptional ACTI human pathogen, transcription activator; 1.75A {Corynebacterium glutamicum} PDB: 3f51_A

Probab=98.99  E-value=9.2e-10  Score=76.68  Aligned_cols=57  Identities=23%  Similarity=0.281  Sum_probs=53.2

Q ss_pred             cccHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         118 KVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       118 ~~~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      .....++..|+..|+.+|+||.++|+.+|+++++|++||+|...|+.+.+.+||++|
T Consensus        24 ~~~~~~g~~l~~~R~~~glsq~~lA~~~gis~~~is~~E~g~~~~~~~~l~~la~~l   80 (117)
T 3f52_A           24 LLREALGAALRSFRADKGVTLRELAEASRVSPGYLSELERGRKEVSSELLASVCHAL   80 (117)
T ss_dssp             CHHHHHHHHHHHHHHHHTCCHHHHHHHTTSCHHHHHHHHTTSSCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHh
Confidence            344678999999999999999999999999999999999999999999999999875

>2a6c_A Helix-turn-helix motif; putative transcriptional regulator, structural genomics, JOI for structural genomics, JCSG; HET: CIT; 1.90A {Nitrosomonas europaea} SCOP: a.35.1.13

Probab=98.97  E-value=1.6e-09  Score=71.10  Aligned_cols=55  Identities=16%  Similarity=0.118  Sum_probs=51.3

Q ss_pred             cHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCC-CCCHHHHHHHHhhC
Q psy6501         120 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRG-IPNQAIIGKMERAL  174 (174)
Q Consensus       120 ~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~-~P~~~~l~~i~~~l  174 (174)
                      ...++..|+..|...|+||.++|+.+|+++++|++||+|+. .|+.+.+.+|+++|
T Consensus        16 ~~~~~~~l~~~r~~~glsq~elA~~~gis~~~is~~e~g~~~~~~~~~l~~la~~l   71 (83)
T 2a6c_A           16 RSQLLIVLQEHLRNSGLTQFKAAELLGVTQPRVSDLMRGKIDLFSLESLIDMITSI   71 (83)
T ss_dssp             HHHHHHHHHHHHHTTTCCHHHHHHHHTSCHHHHHHHHTTCGGGCCHHHHHHHHHHT
T ss_pred             cHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHHHHHc
Confidence            35578899999999999999999999999999999999998 59999999999986

>3trb_A Virulence-associated protein I; mobIle and extrachromosomal element functions, DNA binding P; 2.00A {Coxiella burnetii}

Probab=98.96  E-value=1e-09  Score=75.54  Aligned_cols=55  Identities=13%  Similarity=0.116  Sum_probs=50.7

Q ss_pred             cHHHHHHHHH-HHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         120 PLDLAKLLMQ-GRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       120 ~~~~~~~i~~-~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      +...+..|++ .|+..|+||.+||+.+|+++++|+.||+|+..|+.+.+.+|+++|
T Consensus        11 ~~~pG~~Lk~~lr~~~gltq~eLA~~lGis~~~is~ie~G~~~~s~~~~~kla~~l   66 (104)
T 3trb_A           11 PIHPGEILAEELGFLDKMSANQLAKHLAIPTNRVTAILNGARSITADTALRLAKFF   66 (104)
T ss_dssp             CCCHHHHHHHHHHHTTSCCHHHHHHHHTSCHHHHHHHHTTSSCCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence            3456789986 799999999999999999999999999999999999999999976

>2ef8_A C.ECOT38IS, putative transcription factor; helix-turn-helix, DNA binding protein, transcription regulator; HET: CME; 1.95A {Enterobacteria phage P2}

Probab=98.96  E-value=1.9e-09  Score=70.34  Aligned_cols=53  Identities=17%  Similarity=0.076  Sum_probs=47.0

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhh
Q psy6501         121 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERA  173 (174)
Q Consensus       121 ~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~  173 (174)
                      ..++..|+..|...|+||.++|+.+|+++++|++||+|...|+...+.+++++
T Consensus         9 ~~~~~~l~~~r~~~glsq~~lA~~~gis~~~i~~~e~g~~~~~~~~l~~~~~~   61 (84)
T 2ef8_A            9 RCLVQLLTKLRKEASLSQSELAIFLGLSQSDISKIESFERRLDALELFELLEV   61 (84)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTSSCCBHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence            45788999999999999999999999999999999999999997766655543

>1zug_A Phage 434 CRO protein; gene regulating protein, transcription regulation; NMR {Phage 434} SCOP: a.35.1.2 PDB: 2cro_A 3cro_L*

Probab=98.94  E-value=1.7e-09  Score=68.25  Aligned_cols=52  Identities=29%  Similarity=0.238  Sum_probs=47.0

Q ss_pred             HHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         122 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       122 ~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      .++..|+..|..+|+||.++|+.+|+++++|++||+|...|+.. +.+|+++|
T Consensus         3 ~~~~~l~~~r~~~glsq~~lA~~~gis~~~i~~~e~g~~~~~~~-l~~i~~~l   54 (71)
T 1zug_A            3 TLSERLKKRRIALKMTQTELATKAGVKQQSIQLIEAGVTKRPRF-LFEIAMAL   54 (71)
T ss_dssp             SHHHHHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHTTCCSSCST-HHHHHHHT
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCChHH-HHHHHHHH
Confidence            35789999999999999999999999999999999999887654 89999876

>3mlf_A Transcriptional regulator; structural genomics, helix-turn-helix XRE-family like protei transcription regulator, PSI-2; 2.60A {Staphylococcus aureus subsp}

Probab=98.94  E-value=3.7e-10  Score=78.51  Aligned_cols=55  Identities=18%  Similarity=0.229  Sum_probs=50.9

Q ss_pred             cHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         120 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       120 ~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ...++..|+.+|..+||||.++|+.+|+++++|++||+|...|+.+.+.+||++|
T Consensus        21 ~~~~g~~Lk~~R~~~gltq~elA~~~gis~~~is~~E~G~~~ps~~~l~~ia~~l   75 (111)
T 3mlf_A           21 QSNAMKTLKELRTDYGLTQKELGDLFKVSSRTIQNMEKDSTNIKDSLLSKYMSAF   75 (111)
T ss_dssp             CCSSCEEHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHHCCTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHh
Confidence            3445678999999999999999999999999999999999999999999999875

>2ppx_A AGR_C_3184P, uncharacterized protein ATU1735; HTH-motif, XRE-family, structural genomics, PSI-2, protein structure initiative; 2.00A {Agrobacterium tumefaciens str} SCOP: a.35.1.3

Probab=98.92  E-value=1e-09  Score=74.42  Aligned_cols=52  Identities=17%  Similarity=0.232  Sum_probs=46.5

Q ss_pred             HHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         122 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       122 ~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      .++..|+..|+..|+||.+||+.+|+++++|++||+|...|+.. +.+|+++|
T Consensus        30 ~~~~~lk~~R~~~glsq~elA~~lgvs~~~is~~E~G~~~p~~~-~~~l~~~l   81 (99)
T 2ppx_A           30 PRMPRIKIIRRALKLTQEEFSARYHIPLGTLRDWEQGRSEPDQP-ARAYLKII   81 (99)
T ss_dssp             --CCHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTSSCCCHH-HHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHcCCCCCCHH-HHHHHHHH
Confidence            45678999999999999999999999999999999999999988 77888764

>2wus_R RODZ, putative uncharacterized protein; structural protein, cell WALL morphogenesis, bacterial cytos bacterial actin; 2.90A {Thermotoga maritima}

Probab=98.92  E-value=2.2e-09  Score=74.79  Aligned_cols=54  Identities=17%  Similarity=0.164  Sum_probs=48.2

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCC------CHHHHHHHHhhC
Q psy6501         121 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIP------NQAIIGKMERAL  174 (174)
Q Consensus       121 ~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P------~~~~l~~i~~~l  174 (174)
                      ..++..|+.+|+.+||||+++|+.+|+++++|+.||+|...|      ...++.+||++|
T Consensus         6 ~~lG~~Lr~~R~~~glSq~eLA~~~gis~~~is~iE~G~~~~~p~~~~~~~~l~~iA~~L   65 (112)
T 2wus_R            6 KELGETFRKKREERRITLLDASLFTNINPSKLKRIEEGDLKGLDAEVYIKSYIKRYSEFL   65 (112)
T ss_dssp             HHHHHHHHHHHHTTTCCHHHHHHHSSCCHHHHHHHHHTCCTTSSCHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCcchhHHHHHHHHHHHHh
Confidence            357899999999999999999999999999999999998754      346788999886

>3fym_A Putative uncharacterized protein; HTH DNA binding, DNA binding protein; 1.00A {Staphylococcus aureus subsp}

Probab=98.92  E-value=1.6e-09  Score=77.41  Aligned_cols=53  Identities=15%  Similarity=0.166  Sum_probs=49.1

Q ss_pred             HHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCH------HHHHHHHhhC
Q psy6501         122 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQ------AIIGKMERAL  174 (174)
Q Consensus       122 ~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~------~~l~~i~~~l  174 (174)
                      .++..|+++|+++|+||+++|+++|++++++++||+|+..|.+      .++.++|++|
T Consensus         3 ~~G~~lr~~R~~~gltq~elA~~~gis~~~is~iE~g~~~~~~~~~~~~~~l~~ia~~L   61 (130)
T 3fym_A            3 TVGEALKGRRERLGMTLTELEQRTGIKREMLVHIENNEFDQLPNKNYSEGFIRKYASVV   61 (130)
T ss_dssp             CHHHHHHHHHHHTTCCHHHHHHHHCCCHHHHHHHHTTCGGGSSSGGGHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCchhhhHHHHHHHHHHHh
Confidence            4688999999999999999999999999999999999988776      7799999986

>3bs3_A Putative DNA-binding protein; XRE-family, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.65A {Bacteroides fragilis}

Probab=98.92  E-value=2.2e-09  Score=68.67  Aligned_cols=51  Identities=12%  Similarity=0.178  Sum_probs=48.1

Q ss_pred             HHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         124 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       124 ~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      +..|+..|..+|+||.++|+.+|+++++|++||+|...|+.+.+.+|+++|
T Consensus        12 ~~~l~~~r~~~g~s~~~lA~~~gis~~~i~~~e~g~~~~~~~~l~~ia~~l   62 (76)
T 3bs3_A           12 LNRIKVVLAEKQRTNRWLAEQMGKSENTISRWCSNKSQPSLDMLVKVAELL   62 (76)
T ss_dssp             CBCHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTSSCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence            457889999999999999999999999999999999999999999999875

>2ict_A Antitoxin HIGA; helix-turn-helix, structural genomics, PSI-2, protein struct initiative, northeast structural genomics consortium, NESG; 1.63A {Escherichia coli} SCOP: a.35.1.3 PDB: 2icp_A

Probab=98.92  E-value=2.9e-09  Score=71.26  Aligned_cols=53  Identities=9%  Similarity=0.159  Sum_probs=50.3

Q ss_pred             HHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         122 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       122 ~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      .++..|+..|...|+||.++|+.+|+++++|++||+|...|+.+.+.+|+++|
T Consensus         8 ~~g~~l~~~r~~~gltq~~lA~~~gis~~~is~~e~g~~~~~~~~~~~i~~~l   60 (94)
T 2ict_A            8 RPGDIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVI   60 (94)
T ss_dssp             CHHHHHHHHHHHHTCCHHHHHHHHTCCHHHHHHHHHTSSCCCHHHHHHHHHHT
T ss_pred             ChhHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence            45789999999999999999999999999999999999999999999999986

>2l49_A C protein; P2 bacteriophage, P2 C, direct repeats, DNA-binding protein, binding protein; NMR {Enterobacteria phage P2} PDB: 2xcj_A

Probab=98.91  E-value=1.9e-09  Score=72.64  Aligned_cols=51  Identities=18%  Similarity=0.283  Sum_probs=48.7

Q ss_pred             HHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhh
Q psy6501         123 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERA  173 (174)
Q Consensus       123 ~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~  173 (174)
                      ++.+|+..|..+|+||.++|+.+|+++++|++||+|...|+...+.+|+++
T Consensus         5 ~~~~l~~~r~~~gltq~~lA~~~gis~~~is~~e~g~~~p~~~~l~~ia~~   55 (99)
T 2l49_A            5 ISEKIVLMRKSEYLSRQQLADLTGVPYGTLSYYESGRSTPPTDVMMNILQT   55 (99)
T ss_dssp             TTHHHHHHHHHTTCCHHHHHHHHCCCHHHHHHHTTTSSCCCHHHHHHHHSS
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence            457899999999999999999999999999999999999999999999987

>2o38_A Hypothetical protein; alpha-beta, helix-turn-helix, structural genomics, PSI-2, PR structure initiative; 1.83A {Rhodopseudomonas palustris} SCOP: a.35.1.13

Probab=98.91  E-value=4.2e-09  Score=74.21  Aligned_cols=55  Identities=18%  Similarity=0.013  Sum_probs=51.8

Q ss_pred             cHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCC-CCCHHHHHHHHhhC
Q psy6501         120 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRG-IPNQAIIGKMERAL  174 (174)
Q Consensus       120 ~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~-~P~~~~l~~i~~~l  174 (174)
                      ...++..|+..|+.+||||.++|+.+|+++++|++||+|+. .|+.+.+.+|+++|
T Consensus        38 ~~~lg~~L~~~R~~~glTQ~eLA~~lGis~~~Is~iE~G~~~~~s~~~l~~ia~~L   93 (120)
T 2o38_A           38 KLRLAYALNAVIDRARLSQAAAAARLGINQPKVSALRNYKLEGFSVERLMTLLNAL   93 (120)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCCTTCCHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHHHHHh
Confidence            35678999999999999999999999999999999999998 99999999999986

>3cec_A Putative antidote protein of plasmid maintenance; structural genomics, joint center for structural genomics, J protein structure initiative; HET: MSE; 1.60A {Nostoc punctiforme}

Probab=98.90  E-value=2.8e-09  Score=72.72  Aligned_cols=55  Identities=13%  Similarity=0.181  Sum_probs=51.3

Q ss_pred             cHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         120 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       120 ~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ...++..|+..|...|+||.++|+.+|+++++|++||+|+..|+.+.+.+|+++|
T Consensus        16 ~~~~g~~l~~~r~~~gltq~~lA~~~gis~~~is~~e~g~~~~~~~~l~~l~~~l   70 (104)
T 3cec_A           16 PIHPGEVIADILDDLDINTANFAEILGVSNQTIQEVINGQRSITVDIAIRLGKAL   70 (104)
T ss_dssp             CCCHHHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHTTSSCCCHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCcCCCHHHHHHHHHHH
Confidence            3456889999999999999999999999999999999999999999999999875

>1nr3_A MTH0916, DNA-binding protein TFX; northeast structural genomics consortium, reduced- dimensionality PSI; NMR {Methanothermobacterthermautotrophicus} SCOP: d.236.1.1

Probab=98.89  E-value=4.9e-12  Score=89.55  Aligned_cols=51  Identities=24%  Similarity=0.383  Sum_probs=47.3

Q ss_pred             HHHHcCCCHHHHHHHhCCCHHHHHHHHcC------CCCCCHHHHHHHHHHhCcccccc
Q psy6501          40 GRQAKGWSQKDLATKINEKPQIVNDYEGG------RGIPNQAIIGKMERALGIRLRVN   91 (174)
Q Consensus        40 ~R~~~gltq~eLA~~igvs~~~is~~E~G------~~~P~~~~l~~la~~L~v~~~~l   91 (174)
                      +|+ +||||+|||+++|+|+++||+||+|      +..|++..+.+||..|+|++++.
T Consensus         1 lR~-~glTQ~eLA~~~Gvs~~~is~~E~G~~~~~~~~~p~~~~l~~la~~l~v~~~~~   57 (122)
T 1nr3_A            1 MRE-RGWSQKKIARELKTTRQNVSAIERKAMENIEKSRNTLDFVKSLKSPVRILCRRG   57 (122)
T ss_dssp             CCC-CSCSSCSTHHHHHHCCSSSCCHHHHHHTTCSSSSCHHHHHHHHCCCEEEEECCG
T ss_pred             Ccc-cCCCHHHHHHHhCCCHHHHHHHHcCCCccchhcccCHHHHHHHHHHHccccccC
Confidence            366 9999999999999999999999999      88999999999999999998753

>1b0n_A Protein (SINR protein); transcription regulator, antagonist, sporulation; 1.90A {Bacillus subtilis} SCOP: a.34.1.1 a.35.1.3 PDB: 2yal_A

Probab=98.88  E-value=3e-09  Score=73.04  Aligned_cols=52  Identities=23%  Similarity=0.340  Sum_probs=49.0

Q ss_pred             HHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcC-CCCCCHHHHHHHHhhC
Q psy6501         123 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGG-RGIPNQAIIGKMERAL  174 (174)
Q Consensus       123 ~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G-~~~P~~~~l~~i~~~l  174 (174)
                      ++..|+..|..+|+||.++|+.+|+++++|++||+| ...|+...+.+||++|
T Consensus         2 ~~~~l~~~r~~~gltq~~lA~~~gis~~~i~~~e~g~~~~p~~~~l~~ia~~l   54 (111)
T 1b0n_A            2 IGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNLQTNPSIQFLEKVSAVL   54 (111)
T ss_dssp             CHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCCSCCCHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHHHHHH
Confidence            367899999999999999999999999999999999 9999999999999875

>1dw9_A Cyanate lyase; cyanate degradation, structural genomics, PSI, protei structure initiative, midwest center for structural genomic; HET: SO4; 1.65A {Escherichia coli} SCOP: a.35.1.4 d.72.1.1 PDB: 1dwk_A* 2ivq_A 2ivb_A 2iu7_A 2iv1_A 2iuo_A 2ivg_A

Probab=98.88  E-value=6.1e-09  Score=76.11  Aligned_cols=63  Identities=16%  Similarity=0.086  Sum_probs=59.4

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccccccc
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNA   92 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~   92 (174)
                      ...+.++|..+|+++|||++++|+.+|+|+.++..++.|...|+.+.+.+|+++|+++.+...
T Consensus        11 ~~~~~~~I~~AK~~KGLTwe~IAe~iG~S~v~vtaa~lGQ~~ls~e~A~kLa~~LgL~~e~~~   73 (156)
T 1dw9_A           11 RLDLADAILLSKAKKDLSFAEIADGTGLAEAFVTAALLGQQALPADAARLVGAKLDLDEDSIL   73 (156)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHTTSSSCHHHHHHHHTTSSCCCHHHHHHHHHHTTCCHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHcCCCCCCHHHHHHHHHHhCcCHHHHH
Confidence            357899999999999999999999999999999999999999999999999999999987653

>1y9q_A Transcriptional regulator, HTH_3 family; transcriptional regulaator, strucutral genomics, protein structure initiative, PSI; 1.90A {Vibrio cholerae} SCOP: a.35.1.8 b.82.1.15

Probab=98.82  E-value=7.8e-09  Score=77.80  Aligned_cols=54  Identities=22%  Similarity=0.279  Sum_probs=51.4

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         121 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       121 ~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ..++.+|+..|+.+|+||+++|+++|+++++|++||+|+..|+.+.+.+||++|
T Consensus        10 ~~~~~~l~~~r~~~gltq~~lA~~~gis~~~is~~e~g~~~p~~~~l~~ia~~l   63 (192)
T 1y9q_A           10 SQIANQLKNLRKSRGLSLDATAQLTGVSKAMLGQIERGESSPTIATLWKIASGL   63 (192)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHSSCHHHHHHHHTTCSCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence            457899999999999999999999999999999999999999999999999875

>2eby_A Putative HTH-type transcriptional regulator YBAQ; hypothetical protein, JW0472, structural genomics, NPPSFA; 2.25A {Escherichia coli}

Probab=98.81  E-value=5.1e-09  Score=72.39  Aligned_cols=53  Identities=8%  Similarity=0.069  Sum_probs=49.8

Q ss_pred             HHHHHHHH-HHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         122 DLAKLLMQ-GRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       122 ~~~~~i~~-~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      .++..|+. .|...|+||.++|+.+|+++++|++||+|...|+...+.+||++|
T Consensus        10 ~~g~~l~~~~r~~~glsq~~lA~~~gis~~~is~~e~g~~~~~~~~l~~la~~l   63 (113)
T 2eby_A           10 TPGDILLYEYLEPLDLKINELAELLHVHRNSVSALINNNRKLTTEMAFRLAKVF   63 (113)
T ss_dssp             CHHHHHHHHTTTTTTCCHHHHHHHHTSCHHHHHHHHTTSSCCCHHHHHHHHHHH
T ss_pred             ChHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence            46789997 899999999999999999999999999999999999999999875

>2bnm_A Epoxidase; oxidoreductase, cupin, HTH, cation-dependant, zinc, fosfomycin; 1.7A {Streptomyces wedmorensis} SCOP: a.35.1.3 b.82.1.10 PDB: 1zz7_A 1zz8_A 1zz9_A 1zzb_A 1zz6_A 1zzc_A 2bnn_A 2bno_A 3scf_A 3scg_A 3sch_A

Probab=98.81  E-value=1.1e-08  Score=77.15  Aligned_cols=55  Identities=25%  Similarity=0.441  Sum_probs=52.0

Q ss_pred             cHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCC-CCCHHHHHHHHhhC
Q psy6501         120 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRG-IPNQAIIGKMERAL  174 (174)
Q Consensus       120 ~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~-~P~~~~l~~i~~~l  174 (174)
                      ...++.+|+..|+.+||||+++|+++|+++++|++||+|+. .|+...+.+||++|
T Consensus         8 ~~~~g~~l~~~r~~~g~s~~~la~~~gis~~~ls~~e~g~~~~p~~~~l~~ia~~l   63 (198)
T 2bnm_A            8 STGFAELLKDRREQVKMDHAALASLLGETPETVAAWENGEGGELTLTQLGRIAHVL   63 (198)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTTCTTCBHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHHHHHh
Confidence            34678999999999999999999999999999999999999 99999999999986

>3bd1_A CRO protein; transcription factor, helix-turn-helix, prophage, structural evolution, transcription; 1.40A {Xylella fastidiosa}

Probab=98.80  E-value=4.1e-09  Score=68.38  Aligned_cols=47  Identities=15%  Similarity=0.223  Sum_probs=44.3

Q ss_pred             HHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         126 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       126 ~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      .|+..|+..| ||.+||+++|+++++|++||+|...| .+.+.+|+++|
T Consensus         3 ~l~~~r~~~g-sq~~lA~~lgvs~~~is~~e~g~~~p-~~~l~~ia~~l   49 (79)
T 3bd1_A            3 AIDIAINKLG-SVSALAASLGVRQSAISNWRARGRVP-AERCIDIERVT   49 (79)
T ss_dssp             HHHHHHHHHS-SHHHHHHHHTCCHHHHHHHHHHTCCC-GGGHHHHHHHT
T ss_pred             HHHHHHHHhC-CHHHHHHHHCCCHHHHHHHHHCCCCC-HHHHHHHHHHH
Confidence            6788899999 99999999999999999999999988 99999999886

>3kxa_A NGO0477 protein, putative uncharacterized protein; NEW protein fold, OPPF, STRU genomics, oxford protein production facility; 2.80A {Neisseria gonorrhoeae}

Probab=98.78  E-value=3.5e-09  Score=76.61  Aligned_cols=52  Identities=21%  Similarity=0.270  Sum_probs=48.8

Q ss_pred             HHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         123 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       123 ~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ++..|+..|..+|+||.++|+.+|+++++|++||+|...|+...+.+|+++|
T Consensus        69 ~g~~L~~~R~~~glTq~elA~~lGis~s~is~~E~G~~~ps~~~l~~la~~l  120 (141)
T 3kxa_A           69 GGETFVSLRMKKGFTQSELATAAGLPQPYLSRIENSKQSLQDKTVQKLANAL  120 (141)
T ss_dssp             SSCCHHHHHHHTTCCHHHHHHHTTCCHHHHHHHHHTCSCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence            4567889999999999999999999999999999999999999999999875

>2ofy_A Putative XRE-family transcriptional regulator; transcription regulator, structural genomics, PS protein structure initiative; 1.70A {Rhodococcus SP} SCOP: a.35.1.3

Probab=98.78  E-value=1.9e-08  Score=65.98  Aligned_cols=52  Identities=25%  Similarity=0.245  Sum_probs=48.8

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCC-CCCHHHHHHHHhhC
Q psy6501         121 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRG-IPNQAIIGKMERAL  174 (174)
Q Consensus       121 ~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~-~P~~~~l~~i~~~l  174 (174)
                      ..++..|+..|+.+  +|.++|+.+|+++++|++||+|.. .|+...+.+||++|
T Consensus        15 ~~~g~~l~~~R~~~--sq~~lA~~~gis~~~is~~E~g~~~~p~~~~l~~ia~~l   67 (86)
T 2ofy_A           15 QRLGELLRSARGDM--SMVTVAFDAGISVETLRKIETGRIATPAFFTIAAVARVL   67 (86)
T ss_dssp             HHHHHHHHHHHTTS--CHHHHHHHHTCCHHHHHHHHTTCCSSCBHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHC--CHHHHHHHhCCCHHHHHHHHcCCCCCCCHHHHHHHHHHh
Confidence            45788999999888  999999999999999999999999 99999999999986

>1zx4_A P1 PARB, plasmid partition PAR B protein, PARB; translation; HET: CIT; 2.98A {Enterobacteria phage P1} PDB: 2ntz_A

Probab=98.75  E-value=5.9e-09  Score=79.04  Aligned_cols=62  Identities=16%  Similarity=0.157  Sum_probs=58.7

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHH----------------HcCCCCCCHHHHHHHHHHh---Cccccc
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDY----------------EGGRGIPNQAIIGKMERAL---GIRLRV   90 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~----------------E~G~~~P~~~~l~~la~~L---~v~~~~   90 (174)
                      ..++|.++..+ ...|+||+|+|+.+|||+++||++                |+|...|++..|.+++..|   ++++++
T Consensus        10 l~eiG~ria~~-y~~g~tQ~eIA~~lGiSr~~VSR~L~~A~~~~~lv~lfp~~~~ls~p~~~~L~k~~~~l~~~~~~l~e   88 (192)
T 1zx4_A           10 IREIGLRLMRM-KNDGMSQKDIAAKEGLSQAKVTRALQAASAPEELVALFPVQSELTFSDYKTLCAVGDEMGNKNLEFDQ   88 (192)
T ss_dssp             HHHHHHHHHHH-HHTTCCHHHHHHHHTCCHHHHHHHHHHHTSCHHHHTTCSCGGGCCHHHHHHHHHHHHHTTTCHHHHHH
T ss_pred             HHHHHHHHHHH-HHcCCCHHHHHHHhCcCHHHHHHHHHHhccchhhHHHcCCcccCccchHHHHHHHHHHhhhcCCCHHH
Confidence            46799999999 889999999999999999999998                7999999999999999999   999999


Q ss_pred             cc
Q psy6501          91 NA   92 (174)
Q Consensus        91 l~   92 (174)
                      |+
T Consensus        89 Li   90 (192)
T 1zx4_A           89 LI   90 (192)
T ss_dssp             HH
T ss_pred             HH
Confidence            88

>3o9x_A Uncharacterized HTH-type transcriptional regulato; HTH-XRE DNA binding motif, transcriptional regulator, bacter antitoxin, Zn binding protein, transcription regulator-DNA; HET: DNA; 2.10A {Escherichia coli} PDB: 3gn5_A* 3gn5_B* 2kz8_A

Probab=98.72  E-value=1.8e-08  Score=71.63  Aligned_cols=45  Identities=18%  Similarity=0.323  Sum_probs=41.5

Q ss_pred             HHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHH
Q psy6501         124 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIG  168 (174)
Q Consensus       124 ~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~  168 (174)
                      +..|+.+|+..||||.++|+.+|+++++|++||+|...|+.....
T Consensus        73 ~~~l~~~R~~~glsq~~la~~~g~s~~~i~~~E~g~~~p~~~~~~  117 (133)
T 3o9x_A           73 PEFIVKVRKKLSLTQKEASEIFGGGVNAFSRYEKGNAQPHPSTIK  117 (133)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHCSCTTHHHHHHHTSSCCCHHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHH
Confidence            467999999999999999999999999999999999999987743

>3pxp_A Helix-turn-helix domain protein; DNA-binding, basic helix-loop-helix motif, BHLH motif, lambd repressor-like DNA-binding fold; HET: MSE MYR; 2.30A {Chloroflexus aurantiacus}

Probab=98.62  E-value=7e-08  Score=77.75  Aligned_cols=54  Identities=22%  Similarity=0.328  Sum_probs=51.2

Q ss_pred             HHHHHHHHHHHHh------cCCCHHHHHHHhCCChhHHHHHhcCCC-CCCHHHHHHHHhhC
Q psy6501         121 LDLAKLLMQGRQA------KGWSQKDLATKINEKPQIVNDYEGGRG-IPNQAIIGKMERAL  174 (174)
Q Consensus       121 ~~~~~~i~~~R~~------~glsq~ela~~lg~~~s~i~~~E~G~~-~P~~~~l~~i~~~l  174 (174)
                      ..++..|+..|++      +|+||+++|+.+|++.++|++||+|+. .|+.+++.+|+++|
T Consensus         5 ~~lG~~Lr~lR~~~~~~~~~gLtqeelA~~~gvS~~~is~iE~G~~~~ps~~~l~~lA~aL   65 (292)
T 3pxp_A            5 AAFGKLVQALRREHRDEKGRVWTQEVLAERTQLPKRTIERIENGSLAHLDADILLRLADAL   65 (292)
T ss_dssp             HHHHHHHHHHHHTCBCTTSCBCCHHHHHHHHTCCHHHHHHHHHTCCSCCCHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHccCccCcCCCCHHHHHHHHCcCHHHHHHHHCCCCCCCCHHHHHHHHHhc
Confidence            4578999999999      999999999999999999999999997 99999999999987

>2l1p_A DNA-binding protein SATB1; PSI-biology, NESG, structural genomics, protein structure in northeast structural genomics consortium; NMR {Homo sapiens} PDB: 3nzl_A*

Probab=98.62  E-value=2.6e-08  Score=64.60  Aligned_cols=50  Identities=10%  Similarity=0.052  Sum_probs=43.5

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         121 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       121 ~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ..+.-.++..+.  |++|.+||+++|+++++++.+|+|+..|+..  .+||++|
T Consensus        20 ~~~~~kLK~il~--GikQ~eLAK~iGIsqsTLSaIenG~~~PsL~--~kIAk~f   69 (83)
T 2l1p_A           20 TTVRNALKDLLK--DMNQSSLAKECPLSQSMISSIVNSTYYANVS--AAKCQEF   69 (83)
T ss_dssp             HHHHHHHHHHHT--TSCHHHHHHHSSSCHHHHHHHHTCSSCCCCC--SHHHHHH
T ss_pred             HHHHHHHHHHHH--hcCHHHHHHHcCCCHHHHHHHHcCCCCCCch--HHHHHHH
Confidence            445667777776  9999999999999999999999999999988  7888875

>1rzs_A Antirepressor, regulatory protein CRO; helix-turn-helix, DNA-binding protein, structural evolution, transcription; NMR {Enterobacteria phage P22} SCOP: a.35.1.2

Probab=98.60  E-value=6.2e-08  Score=60.05  Aligned_cols=48  Identities=15%  Similarity=0.104  Sum_probs=38.1

Q ss_pred             HHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccc
Q psy6501          38 MQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLR   89 (174)
Q Consensus        38 k~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~   89 (174)
                      +++.+.. +||.+||+.+|||+++||+||  ...|. .....|+++++..+.
T Consensus         4 ~~~i~~~-~tq~~lA~~lGvs~~~Vs~we--~~~p~-~~~~~i~~~~~g~v~   51 (61)
T 1rzs_A            4 KDVIDHF-GTQRAVAKALGISDAAVSQWK--EVIPE-KDAYRLEIVTAGALK   51 (61)
T ss_dssp             HHHHHHH-SSHHHHHHHHTCCHHHHHHCC--SBCCH-HHHHHHHHHTTSCSC
T ss_pred             HHHHHHc-CCHHHHHHHhCCCHHHHHHHH--hhCCH-HHHHHHHHHHCCCce
Confidence            4444444 599999999999999999999  34454 566699999998776

>3g7d_A PHPD; non heme Fe(II) dioxygenase, cupin, biosynthetic protein; 1.80A {Streptomyces viridochromogenes} PDB: 3gbf_A 3rzz_A

Probab=98.59  E-value=7.2e-08  Score=77.84  Aligned_cols=63  Identities=14%  Similarity=0.127  Sum_probs=59.1

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCcccccccCCC
Q psy6501          33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRG-IPNQAIIGKMERALGIRLRVNAGTN   95 (174)
Q Consensus        33 ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~-~P~~~~l~~la~~L~v~~~~l~~~~   95 (174)
                      .|-.|+.+|...|+||++||++.||++..||.+|||++ .+..+.+.+||++|+|+...|+...
T Consensus       231 agv~LR~ar~ReglTQ~~LAe~TGIPq~hISeMenGKr~~IGkdeaR~LA~ALnvDYRvLLP~~  294 (443)
T 3g7d_A          231 AGSVLDLFLARRAHTRTSAAEAAGVPPADLEAALRSPASETGLTVLRTLGRALGFDYRVLLPAD  294 (443)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHCTTSHHHHHHHHHHHHHHTCCGGGGSCCC
T ss_pred             HHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHhcCCcCCccHHHHHHHHHHhCCCchhccCcc
Confidence            47899999999999999999999999999999999999 5699999999999999999999544

>3r1f_A ESX-1 secretion-associated regulator ESPR; helix-turn-helix, transcription factor, helix-turn-helix transcription factor; 2.50A {Mycobacterium tuberculosis}

Probab=98.59  E-value=6.7e-08  Score=69.38  Aligned_cols=53  Identities=9%  Similarity=0.145  Sum_probs=48.9

Q ss_pred             HHHHHHHHHHH------hcCCCHHHHHHHhC-----CChhHHHHHhcCCC-CCCHHHHHHHHhhC
Q psy6501         122 DLAKLLMQGRQ------AKGWSQKDLATKIN-----EKPQIVNDYEGGRG-IPNQAIIGKMERAL  174 (174)
Q Consensus       122 ~~~~~i~~~R~------~~glsq~ela~~lg-----~~~s~i~~~E~G~~-~P~~~~l~~i~~~l  174 (174)
                      .++++|+..|+      ..++||+++|+.+|     +++++|+.||+|++ .|+.+++.+||++|
T Consensus         7 ~~~~RL~~L~~~~~~~~~~~~T~~elA~~~~~~G~~is~s~is~~E~G~r~~Ps~~~l~~iA~~f   71 (135)
T 3r1f_A            7 TFAARLNRLFDTVYPPGRGPHTSAEVIAALKAEGITMSAPYLSQLRSGNRTNPSGATMAALANFF   71 (135)
T ss_dssp             CHHHHHHHHHHHCCCTTSCCCCHHHHHHHHHTTTCCCCHHHHHHHHHTSSCCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhcccCCCCCCHHHHHHHHcccCCCcCHHHHHHHHCCCCCCCCHHHHHHHHHHh
Confidence            46789999999      47899999999999     99999999999997 89999999999986

>3qwg_A ESX-1 secretion-associated regulator ESPR; N-terminal helix-turn-helix motif, transcription factor, transcription; 1.99A {Mycobacterium tuberculosis} PDB: 3qf3_A 3qyx_A

Probab=98.58  E-value=1.1e-07  Score=67.22  Aligned_cols=53  Identities=9%  Similarity=0.145  Sum_probs=47.8

Q ss_pred             HHHHHHHHHHH------hcCCCHHHHHHHhC-----CChhHHHHHhcCCC-CCCHHHHHHHHhhC
Q psy6501         122 DLAKLLMQGRQ------AKGWSQKDLATKIN-----EKPQIVNDYEGGRG-IPNQAIIGKMERAL  174 (174)
Q Consensus       122 ~~~~~i~~~R~------~~glsq~ela~~lg-----~~~s~i~~~E~G~~-~P~~~~l~~i~~~l  174 (174)
                      .+.++|...++      ..+|||+++|+.+|     +++++|+.||+|++ .|+.+.+.+||++|
T Consensus         5 ~~a~RL~~L~~~~~~~~~~~lT~~elA~~~~~~G~~iS~s~is~iE~G~r~~Ps~~~l~~iA~~f   69 (123)
T 3qwg_A            5 TFAARLNRLFDTVYPPGRGPHTSAEVIAALKAEGITMSAPYLSQLRSGNRTNPSGATMAALANFF   69 (123)
T ss_dssp             CHHHHHHHHHHHSSCTTTCSCCHHHHHHHHHHTTCCCCHHHHHHHHHTSSCCCCHHHHHHHHHHT
T ss_pred             hHHHHHHHHHHhhccCCCCCCCHHHHHHHHcccCCCcCHHHHHHHHcCCCCCCCHHHHHHHHHHh
Confidence            35678888888      56799999999998     99999999999997 89999999999987

>2p5t_A Putative transcriptional regulator PEZA; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=98.47  E-value=1.9e-08  Score=73.83  Aligned_cols=52  Identities=15%  Similarity=0.252  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         123 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       123 ~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ++.+|+..|...|+||.++|+++|+++++|++||+|...|+...+.+|+++|
T Consensus         2 ig~~lk~~R~~~gltq~elA~~lgis~~~vs~~e~G~~~~~~~~~~~la~~~   53 (158)
T 2p5t_A            2 IGKNIKSLRKTHDLTQLEFARIVGISRNSLSRYENGTSSVSTELIDIICQKF   53 (158)
T ss_dssp             ----------------------------------------------------
T ss_pred             hHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHH
Confidence            4578899999999999999999999999999999999999999999999876

>4ich_A Transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, transcription RE; 1.95A {Saccharomonospora viridis}

Probab=98.46  E-value=1.9e-08  Score=80.75  Aligned_cols=54  Identities=9%  Similarity=0.035  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         121 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       121 ~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ..++.+|+..|+.+|+||.++|+.+|+++++|++||+|+..|+.+.+.+||++|
T Consensus        29 ~~~~~~l~~~r~~~g~t~~~la~~~g~s~~~is~~e~g~~~p~~~~l~~ia~~l   82 (311)
T 4ich_A           29 DELRRRVRGLIHSRPGAQREFAAAIGLDESKLSKSLNGTRRFSPHELVRIAEHS   82 (311)
T ss_dssp             ------------------------------------------------------
T ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence            457899999999999999999999999999999999999999999999999876

>3bdn_A Lambda repressor; repressor, allostery; HET: DNA; 3.91A {Enterobacteria phage lambda}

Probab=98.44  E-value=1.6e-07  Score=72.63  Aligned_cols=53  Identities=19%  Similarity=0.172  Sum_probs=50.5

Q ss_pred             HHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         122 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       122 ~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      .+..+|+..|+.+|+||.++|+++|++++++++||+|...|+.+.+.+|+++|
T Consensus        17 ~~~~~l~~~r~~~g~t~~~lA~~~gis~~~i~~~~~g~~~p~~~~l~~ia~~l   69 (236)
T 3bdn_A           17 RLKAIYEKKKNELGLSQESVADKMGMGQSGVGALFNGINALNAYNAALLAKIL   69 (236)
T ss_dssp             HHHHHHHHHTTTTTCCSHHHHHHHTSCHHHHHHHTTTTSCCCHHHHHHTTTTT
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence            57889999999999999999999999999999999999999999999999876

>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo, protein-DNA, human disease; 3.20A {Homo sapiens}

Probab=98.44  E-value=7e-07  Score=68.79  Aligned_cols=51  Identities=10%  Similarity=0.031  Sum_probs=44.5

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHH
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKM   80 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~l   80 (174)
                      ...++..|+..|..+||||.+||+.+|||+++||+||++....+...+..+
T Consensus        29 ~~~~~~~Ik~~r~~~gltQ~evA~~tGISqS~ISq~e~~g~~~t~~k~a~~   79 (221)
T 2h8r_A           29 PWRAAKMIKGYMQQHNIPQREVVDVTGLNQSHLSQHLNKGTPMKTQKRAAL   79 (221)
T ss_dssp             HHHHHHHHHHHHHHHTCCHHHHHHHHTCCHHHHHHHHTTCCCCCHHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHhCCCchhHHHHHHH
Confidence            367889999999999999999999999999999999997777776655443

>2auw_A Hypothetical protein NE0471; alpha-beta structure, structural genomics, PSI, protein STRU initiative; 1.85A {Nitrosomonas europaea} SCOP: a.35.1.10 d.331.1.1

Probab=98.43  E-value=4.7e-07  Score=67.27  Aligned_cols=47  Identities=13%  Similarity=0.079  Sum_probs=42.3

Q ss_pred             HHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHH
Q psy6501         124 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKM  170 (174)
Q Consensus       124 ~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i  170 (174)
                      ..+|+.+|++.|+||+++|+.+|+++++|+.||+|++.|+..++.++
T Consensus        92 ~~~lk~lR~~~glTQ~elA~~LGvsr~tis~yE~G~r~iP~~~~lac  138 (170)
T 2auw_A           92 HEMFGDWMHRNNLSLTTAAEALGISRRMVSYYRTAHKIIPRTIWLAC  138 (170)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHTTSSCCCHHHHHHH
T ss_pred             cHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHH
Confidence            46899999999999999999999999999999999998887775543

>1uxc_A FRUR (1-57), fructose repressor; DNA-binding protein, LACI family, transc regulation; NMR {Escherichia coli} SCOP: a.35.1.5 PDB: 1uxd_A

Probab=98.37  E-value=7.1e-07  Score=56.04  Aligned_cols=47  Identities=9%  Similarity=0.019  Sum_probs=37.8

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCC---CCCHHHHHHHHH---HhCccccccc
Q psy6501          46 WSQKDLATKINEKPQIVNDYEGGRG---IPNQAIIGKMER---ALGIRLRVNA   92 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~G~~---~P~~~~l~~la~---~L~v~~~~l~   92 (174)
                      +|++|+|+.+|||++|||++.||..   .++.++..+|.+   .||..++...
T Consensus         1 ~T~~diA~~aGVS~sTVSrvLng~~~~~~vs~et~~rI~~aa~~lgY~pn~~a   53 (65)
T 1uxc_A            1 MKLDEIARLAGVSRTTASYVINGKAKQYRVSDKTVEKVMAVVREHNYHPNAVA   53 (65)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHTCTTTTTCTTHHHHHHHHHHHHHTCCCC---
T ss_pred             CCHHHHHHHHCcCHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHhCCCccHHH
Confidence            5899999999999999999999998   888877666554   6888776553

>1neq_A DNA-binding protein NER; NMR {Enterobacteria phage MU} SCOP: a.35.1.2 PDB: 1ner_A

Probab=98.36  E-value=9.8e-07  Score=56.78  Aligned_cols=48  Identities=13%  Similarity=0.059  Sum_probs=40.4

Q ss_pred             HHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         124 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       124 ~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ...|+..+.++|+|+.+||+.+|+++++|+.|++|   |.+.....||++|
T Consensus        11 ~~ri~~~l~~~glT~~~LA~~~Gvs~stls~~~~~---~~p~~~~~IA~aL   58 (74)
T 1neq_A           11 RADVIAGLKKRKLSLSALSRQFGYAPTTLANALER---HWPKGEQIIANAL   58 (74)
T ss_dssp             HHHHHHHHHTTSCCHHHHHHHHSSCHHHHHHTTTS---SCHHHHHHHHHHT
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcC---CCccHHHHHHHHH
Confidence            45677778899999999999999999999999997   4455556699886

>2pij_A Prophage PFL 6 CRO; transcription factor, helix-turn-helix, structural evolution, transcription; 1.70A {Pseudomonas fluorescens}

Probab=98.34  E-value=3.2e-07  Score=57.23  Aligned_cols=39  Identities=13%  Similarity=0.081  Sum_probs=35.7

Q ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCH
Q psy6501          35 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQ   74 (174)
Q Consensus        35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~   74 (174)
                      .+|+.+|...| ||.++|+.+|+|+++||+||+|.+.|++
T Consensus         4 ~~l~~~~~~~g-s~~~~A~~lgis~~~vs~~~~~~~~~~l   42 (67)
T 2pij_A            4 IPLSKYLEEHG-TQSALAAALGVNQSAISQMVRAGRSIEI   42 (67)
T ss_dssp             EEHHHHHHHTC-CHHHHHHHHTSCHHHHHHHHHTTCCEEE
T ss_pred             HHHHHHHHHcC-CHHHHHHHHCcCHHHHHHHHcCCCCCCe
Confidence            36889999999 9999999999999999999999887754

>2l8n_A Transcriptional repressor CYTR; bacterial gene repressor, helix turn helix binding domain, L family, transcription regulation, binding protein; NMR {Escherichia coli} PDB: 2lcv_A

Probab=98.30  E-value=1.2e-06  Score=55.26  Aligned_cols=48  Identities=21%  Similarity=0.077  Sum_probs=38.6

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHH---HHHHHHhCccccccc
Q psy6501          45 GWSQKDLATKINEKPQIVNDYEGGRGIPNQAII---GKMERALGIRLRVNA   92 (174)
Q Consensus        45 gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l---~~la~~L~v~~~~l~   92 (174)
                      .+|+.|+|+.+|||++|||+++||...++.++.   .++++.||..++.+.
T Consensus         9 ~~t~~diA~~aGVS~sTVSr~ln~~~~vs~~t~~rV~~~a~~lgY~pn~~a   59 (67)
T 2l8n_A            9 AATMKDVALKAKVSTATVSRALMNPDKVSQATRNRVEKAAREVGYLPQPMG   59 (67)
T ss_dssp             CCCHHHHHHHTTCCHHHHHHTTTCCCCSCHHHHHHHHHHHHHHCCCC----
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHhCCCccHHH
Confidence            589999999999999999999999988888774   455788888776543

>1ic8_A Hepatocyte nuclear factor 1-alpha; transcription regulation, DNA-binding, POU domain, diabetes, disease mutation, MODY3, transcription/DNA comple; 2.60A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1

Probab=98.27  E-value=2.8e-06  Score=64.46  Aligned_cols=49  Identities=10%  Similarity=0.046  Sum_probs=43.5

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIG   78 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~   78 (174)
                      ...|+.+|+.++..+|+||.+||+.+|+|+++||+|++|...++.....
T Consensus        28 p~~l~~~Ik~~l~~~gitQ~~lA~~~GiSqs~ISr~l~~~~~~~~~kra   76 (194)
T 1ic8_A           28 PWRVAKMVKSYLQQHNIPQREVVDTTGLNQSHLSQHLNKGTPMKTQKRA   76 (194)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHCCCHHHHHHHHHSBCCCCHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHhCCChHHHHHHHhcCccccccccc
Confidence            3468899999999999999999999999999999999998777766433

>2fjr_A Repressor protein CI; genetic switch, regulation, cooperativity, transcription regulator; 1.95A {Enterobacteria phage 186} PDB: 2fkd_A

Probab=98.22  E-value=1.7e-06  Score=64.59  Aligned_cols=51  Identities=8%  Similarity=0.058  Sum_probs=45.4

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         121 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       121 ~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ..+.++|+..|...  ||.++|+++|+++++++.||+|...| .+.+.+|+++|
T Consensus         8 ~~~~~rl~~~r~~~--tq~elA~~~Gis~~~i~~~e~g~~~p-~~~l~~ia~~~   58 (189)
T 2fjr_A            8 VDVLDRICEAYGFS--QKIQLANHFDIASSSLSNRYTRGAIS-YDFAAHCALET   58 (189)
T ss_dssp             HHHHHHHHHHHTCS--SHHHHHHHTTCCHHHHHHHHHSSSCC-HHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhc--CHHHHHHHhCcCHHHHHHHHhCCCCC-HHHHHHHHHHH
Confidence            45678888888766  99999999999999999999999999 99999999875

>1dw9_A Cyanate lyase; cyanate degradation, structural genomics, PSI, protei structure initiative, midwest center for structural genomic; HET: SO4; 1.65A {Escherichia coli} SCOP: a.35.1.4 d.72.1.1 PDB: 1dwk_A* 2ivq_A 2ivb_A 2iu7_A 2iv1_A 2iuo_A 2ivg_A

Probab=98.06  E-value=9e-06  Score=59.32  Aligned_cols=54  Identities=19%  Similarity=0.140  Sum_probs=51.2

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         121 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       121 ~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ..+...|..+|.++|+|.+++|+++|+++..+..++.|...|+.+.+.+|+++|
T Consensus        12 ~~~~~~I~~AK~~KGLTwe~IAe~iG~S~v~vtaa~lGQ~~ls~e~A~kLa~~L   65 (156)
T 1dw9_A           12 LDLADAILLSKAKKDLSFAEIADGTGLAEAFVTAALLGQQALPADAARLVGAKL   65 (156)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHTTSSSCHHHHHHHHTTSSCCCHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence            456789999999999999999999999999999999999999999999999986

>1s4k_A Putative cytoplasmic protein YDIL; structural genomics, MCSG, PSI, PROT structure initiative; 1.90A {Salmonella typhimurium} SCOP: a.35.1.6

Probab=98.06  E-value=6.6e-06  Score=56.94  Aligned_cols=52  Identities=15%  Similarity=0.098  Sum_probs=46.1

Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHhC--CCHHHHHHHHcCCCCCCHHHHHHHHHH
Q psy6501          32 DLAKLLMQGRQAKGWSQKDLATKIN--EKPQIVNDYEGGRGIPNQAIIGKMERA   83 (174)
Q Consensus        32 ~ig~~ik~~R~~~gltq~eLA~~ig--vs~~~is~~E~G~~~P~~~~l~~la~~   83 (174)
                      +.+.-|+.+|...||||.|.|..+|  +|..+-.+||+|.+..+.+....+...
T Consensus         3 Mn~~ELkalR~ilgLt~~EaA~~i~~~vs~rtWQqWE~G~~~IP~~i~e~~~~m   56 (120)
T 1s4k_A            3 MNALELQALRRIFDMTIEECTIYITQDNNSATWQRWEAGDIPISPEIIARLKEM   56 (120)
T ss_dssp             CCHHHHHHHHHHTTCCHHHHHHHTSSSCCHHHHHHHHHTSSCCCHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHhCCCHHHHHHHHhccCCHHHHHHHHCCCCCCCHHHHHHHHHH
Confidence            4467799999999999999999998  899999999999999998888777643

>1jhf_A LEXA repressor; LEXA SOS repressor, hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.2 b.87.1.1 PDB: 1jhh_A 3jso_A* 3jsp_A* 3k3r_E* 1jhc_A 1jhe_A 1lea_A 1leb_A

Probab=97.94  E-value=7.4e-06  Score=61.94  Aligned_cols=38  Identities=11%  Similarity=0.257  Sum_probs=36.0

Q ss_pred             hHHHHHHHHHHHHHcCC--CHHHHHHHhCCC-HHHHHHHHc
Q psy6501          30 PLDLAKLLMQGRQAKGW--SQKDLATKINEK-PQIVNDYEG   67 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gl--tq~eLA~~igvs-~~~is~~E~   67 (174)
                      ...++++|+.+|++.|+  ||.|||+++|++ +++|++|++
T Consensus         8 q~~i~~~i~~~~~~~g~~ps~~elA~~lgiss~~tv~~~~~   48 (202)
T 1jhf_A            8 QQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLK   48 (202)
T ss_dssp             HHHHHHHHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCCccHHHHHHHhCCCChHHHHHHHH
Confidence            45799999999999999  999999999999 999999987

>1nr3_A MTH0916, DNA-binding protein TFX; northeast structural genomics consortium, reduced- dimensionality PSI; NMR {Methanothermobacterthermautotrophicus} SCOP: d.236.1.1

Probab=97.93  E-value=1.2e-07  Score=66.72  Aligned_cols=43  Identities=23%  Similarity=0.462  Sum_probs=39.5

Q ss_pred             HHhcCCCHHHHHHHhCCChhHHHHHhcC------CCCCCHHHHHHHHhhC
Q psy6501         131 RQAKGWSQKDLATKINEKPQIVNDYEGG------RGIPNQAIIGKMERAL  174 (174)
Q Consensus       131 R~~~glsq~ela~~lg~~~s~i~~~E~G------~~~P~~~~l~~i~~~l  174 (174)
                      |+ +||||+++|+++|+++++|++||+|      ...|+...+.+|+.+|
T Consensus         2 R~-~glTQ~eLA~~~Gvs~~~is~~E~G~~~~~~~~~p~~~~l~~la~~l   50 (122)
T 1nr3_A            2 RE-RGWSQKKIARELKTTRQNVSAIERKAMENIEKSRNTLDFVKSLKSPV   50 (122)
T ss_dssp             CC-CSCSSCSTHHHHHHCCSSSCCHHHHHHTTCSSSSCHHHHHHHHCCCE
T ss_pred             cc-cCCCHHHHHHHhCCCHHHHHHHHcCCCccchhcccCHHHHHHHHHHH
Confidence            44 8999999999999999999999999      8899999999998754

>2hin_A GP39, repressor protein; transcription factor, dimer interface, helix-turn-helix; 1.05A {Enterobacteria phage N15} PDB: 3qws_A

Probab=97.81  E-value=2.3e-05  Score=49.92  Aligned_cols=39  Identities=15%  Similarity=0.164  Sum_probs=31.6

Q ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCc
Q psy6501          47 SQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGI   86 (174)
Q Consensus        47 tq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v   86 (174)
                      +|.+||+.+|||+++|++|++|...| ......|..+-+-
T Consensus        12 ~~~~lA~~lGVs~~aVs~W~~g~~iP-~~~~~~Ie~~T~G   50 (71)
T 2hin_A           12 DVEKAAVGVGVTPGAVYQWLQAGEIP-PLRQSDIEVRTAY   50 (71)
T ss_dssp             SHHHHHHHHTSCHHHHHHHHHHTSCC-HHHHHHHHHHTTT
T ss_pred             CHHHHHHHHCCCHHHHHHHHhCCCCC-HHHHHHHHHHhCC
Confidence            69999999999999999999986666 4556666666553

>2cw1_A SN4M; lambda CRO fold, de novo protein; NMR {Synthetic} SCOP: k.46.1.1

Probab=97.74  E-value=2.9e-05  Score=48.57  Aligned_cols=36  Identities=11%  Similarity=-0.051  Sum_probs=30.8

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCC
Q psy6501          36 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPN   73 (174)
Q Consensus        36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~   73 (174)
                      .|+.+|...  ||.++|+.+|||+++||+|+++.+.+.
T Consensus         6 ~Lk~l~~~~--sq~~~A~~Lgvsq~aVS~~~~~~r~i~   41 (65)
T 2cw1_A            6 DLKKFVEDK--NQEYAARALGLSQKLIEEVLKRGLPVY   41 (65)
T ss_dssp             CHHHHHTTS--CHHHHHHHSSSCHHHHHHHHHTTCCCB
T ss_pred             HHHHHHHHc--CHHHHHHHhCCCHHHHHHHHHhcCCce
Confidence            577777776  999999999999999999998766544

>1rzs_A Antirepressor, regulatory protein CRO; helix-turn-helix, DNA-binding protein, structural evolution, transcription; NMR {Enterobacteria phage P22} SCOP: a.35.1.2

Probab=97.69  E-value=5e-05  Score=46.65  Aligned_cols=37  Identities=16%  Similarity=0.170  Sum_probs=29.8

Q ss_pred             CCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         135 GWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       135 glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      +.||.++|+.+|+++++|+.||  ...|.. .+..|+++|
T Consensus        10 ~~tq~~lA~~lGvs~~~Vs~we--~~~p~~-~~~~i~~~~   46 (61)
T 1rzs_A           10 FGTQRAVAKALGISDAAVSQWK--EVIPEK-DAYRLEIVT   46 (61)
T ss_dssp             HSSHHHHHHHHTCCHHHHHHCC--SBCCHH-HHHHHHHHT
T ss_pred             cCCHHHHHHHhCCCHHHHHHHH--hhCCHH-HHHHHHHHH
Confidence            3599999999999999999999  445654 444888765

>2l0k_A Stage III sporulation protein D; SPOIIID, solution structure, DNA binding, bacillus subti transcription factor, transcription; NMR {Bacillus subtilis}

Probab=97.66  E-value=7.3e-05  Score=50.07  Aligned_cols=54  Identities=9%  Similarity=-0.007  Sum_probs=46.5

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhCcc
Q psy6501          34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGR-GIPNQAIIGKMERALGIR   87 (174)
Q Consensus        34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~-~~P~~~~l~~la~~L~v~   87 (174)
                      -..|..+....++|..++|+.+|||.+|||++.+|. ..++.++..++.++||..
T Consensus         9 ~~~I~~~l~~~~~ti~dlA~~~gVS~~TVsR~L~~~~~~Vs~~tr~rV~~algY~   63 (93)
T 2l0k_A            9 TIKIGKYIVETKKTVRVIAKEFGVSKSTVHKDLTERLPEINPDLANEVKEILDYH   63 (93)
T ss_dssp             HHHHHHHHHHHCCCHHHHHHHHTSCHHHHHHHHTTHHHHHCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcCCCCCCCHHHHHHHHHHHCCC
Confidence            355666777778999999999999999999999997 778999999999986654

>1s4k_A Putative cytoplasmic protein YDIL; structural genomics, MCSG, PSI, PROT structure initiative; 1.90A {Salmonella typhimurium} SCOP: a.35.1.6

Probab=97.64  E-value=0.00013  Score=50.39  Aligned_cols=48  Identities=15%  Similarity=0.136  Sum_probs=43.5

Q ss_pred             HHHHHHHHhcCCCHHHHHHHhC--CChhHHHHHhcCCCCCCHHHHHHHHh
Q psy6501         125 KLLMQGRQAKGWSQKDLATKIN--EKPQIVNDYEGGRGIPNQAIIGKMER  172 (174)
Q Consensus       125 ~~i~~~R~~~glsq~ela~~lg--~~~s~i~~~E~G~~~P~~~~l~~i~~  172 (174)
                      ..++..|...|+|+.+.|..++  ++..+...||+|+...+++++..+..
T Consensus         6 ~ELkalR~ilgLt~~EaA~~i~~~vs~rtWQqWE~G~~~IP~~i~e~~~~   55 (120)
T 1s4k_A            6 LELQALRRIFDMTIEECTIYITQDNNSATWQRWEAGDIPISPEIIARLKE   55 (120)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHTSSSCCHHHHHHHHHTSSCCCHHHHHHHHH
T ss_pred             HHHHHHHHHhCCCHHHHHHHHhccCCHHHHHHHHCCCCCCCHHHHHHHHH
Confidence            3578889999999999999998  78999999999999999999988763

>1xwr_A Regulatory protein CII; all-alpha fold, DNA binding protein; 2.56A {Bacteriophage lambda} SCOP: a.35.1.9 PDB: 1zpq_A

Probab=97.49  E-value=1.3e-05  Score=54.09  Aligned_cols=30  Identities=3%  Similarity=0.014  Sum_probs=26.6

Q ss_pred             HHHHcCCCHHHHHHHhCCCHHHHHHHHcCC
Q psy6501          40 GRQAKGWSQKDLATKINEKPQIVNDYEGGR   69 (174)
Q Consensus        40 ~R~~~gltq~eLA~~igvs~~~is~~E~G~   69 (174)
                      ++.-.+++|..+|+.+||+.++||+|++|.
T Consensus        18 l~~la~~gq~~vA~~iGV~~StISR~k~~~   47 (97)
T 1xwr_A           18 LNKIAMLGTEKTAEAVGVDKSQISRWKRDW   47 (97)
T ss_dssp             HHHHHHHCHHHHHHHHTCCTTTHHHHHHHH
T ss_pred             HHHHHHHhHHHHHHHhCCCHHHHHHHHhhh
Confidence            555667899999999999999999999974

>1uxc_A FRUR (1-57), fructose repressor; DNA-binding protein, LACI family, transc regulation; NMR {Escherichia coli} SCOP: a.35.1.5 PDB: 1uxd_A

Probab=97.45  E-value=0.00018  Score=44.80  Aligned_cols=38  Identities=8%  Similarity=0.052  Sum_probs=34.6

Q ss_pred             CCHHHHHHHhCCChhHHHHHhcCCC---CCCHHHHHHHHhh
Q psy6501         136 WSQKDLATKINEKPQIVNDYEGGRG---IPNQAIIGKMERA  173 (174)
Q Consensus       136 lsq~ela~~lg~~~s~i~~~E~G~~---~P~~~~l~~i~~~  173 (174)
                      +|++|+|+.+|+++++|+++.+|..   .+++++..+|.++
T Consensus         1 ~T~~diA~~aGVS~sTVSrvLng~~~~~~vs~et~~rI~~a   41 (65)
T 1uxc_A            1 MKLDEIARLAGVSRTTASYVINGKAKQYRVSDKTVEKVMAV   41 (65)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHTCTTTTTCTTHHHHHHHHH
T ss_pred             CCHHHHHHHHCcCHHHHHHHHcCCCCCCCCCHHHHHHHHHH
Confidence            5899999999999999999999998   8999988887764

>1zs4_A Regulatory protein CII; helix-turn-helix, transcription activator, transcription-DNA; HET: DNA; 1.70A {Enterobacteria phage lambda} SCOP: a.35.1.9

Probab=97.37  E-value=0.00016  Score=47.20  Aligned_cols=42  Identities=5%  Similarity=0.015  Sum_probs=33.0

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccc
Q psy6501          43 AKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRL   88 (174)
Q Consensus        43 ~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~   88 (174)
                      -.-++|+.+|+.+|++.++||+|.+|.    ++.+..+..+|+..+
T Consensus        22 La~~gQ~~vAe~~GvdeStISR~k~~~----~~~~~~lLa~Lglkv   63 (83)
T 1zs4_A           22 IAMLGTEKTAEAVGVDKSQISRWKRDW----IPKFSMLLAVLEWGV   63 (83)
T ss_dssp             HHHHCHHHHHHHHTSCHHHHHHHHHHT----HHHHHHHHHHHTTCC
T ss_pred             HHHHhhHHHHHHhCCCHHHHhhhhhhH----HHHHHHHHHHhccCC
Confidence            344699999999999999999999974    556666666666554

>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo, protein-DNA, human disease; 3.20A {Homo sapiens}

Probab=97.36  E-value=0.00049  Score=52.89  Aligned_cols=50  Identities=10%  Similarity=0.013  Sum_probs=43.4

Q ss_pred             cHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHH
Q psy6501         120 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGK  169 (174)
Q Consensus       120 ~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~  169 (174)
                      +..+...|+..|..+|++|.++|+++|+++++|+.||++...++...+..
T Consensus        29 ~~~~~~~Ik~~r~~~gltQ~evA~~tGISqS~ISq~e~~g~~~t~~k~a~   78 (221)
T 2h8r_A           29 PWRAAKMIKGYMQQHNIPQREVVDVTGLNQSHLSQHLNKGTPMKTQKRAA   78 (221)
T ss_dssp             HHHHHHHHHHHHHHHTCCHHHHHHHHTCCHHHHHHHHTTCCCCCHHHHHH
T ss_pred             cHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHhCCCchhHHHHHH
Confidence            45677899999999999999999999999999999999777777665543

>1zx4_A P1 PARB, plasmid partition PAR B protein, PARB; translation; HET: CIT; 2.98A {Enterobacteria phage P1} PDB: 2ntz_A

Probab=97.23  E-value=0.00044  Score=52.21  Aligned_cols=54  Identities=19%  Similarity=0.180  Sum_probs=47.7

Q ss_pred             cHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHH----------------hcCCCCCCHHHHHHHHhhC
Q psy6501         120 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDY----------------EGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       120 ~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~----------------E~G~~~P~~~~l~~i~~~l  174 (174)
                      ..+++.++... ...|+||.++|+.+|+++++|+++                ++|...|+...+.+++..|
T Consensus        10 l~eiG~ria~~-y~~g~tQ~eIA~~lGiSr~~VSR~L~~A~~~~~lv~lfp~~~~ls~p~~~~L~k~~~~l   79 (192)
T 1zx4_A           10 IREIGLRLMRM-KNDGMSQKDIAAKEGLSQAKVTRALQAASAPEELVALFPVQSELTFSDYKTLCAVGDEM   79 (192)
T ss_dssp             HHHHHHHHHHH-HHTTCCHHHHHHHHTCCHHHHHHHHHHHTSCHHHHTTCSCGGGCCHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHH-HHcCCCHHHHHHHhCcCHHHHHHHHHHhccchhhHHHcCCcccCccchHHHHHHHHHHh
Confidence            35567777777 679999999999999999999997                7999999999999999875

>2l8n_A Transcriptional repressor CYTR; bacterial gene repressor, helix turn helix binding domain, L family, transcription regulation, binding protein; NMR {Escherichia coli} PDB: 2lcv_A

Probab=97.19  E-value=0.00072  Score=42.32  Aligned_cols=39  Identities=23%  Similarity=0.143  Sum_probs=34.9

Q ss_pred             CCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhh
Q psy6501         135 GWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERA  173 (174)
Q Consensus       135 glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~  173 (174)
                      .+++.|+|+..|+++++|+++.+|....++++..+|.++
T Consensus         9 ~~t~~diA~~aGVS~sTVSr~ln~~~~vs~~t~~rV~~~   47 (67)
T 2l8n_A            9 AATMKDVALKAKVSTATVSRALMNPDKVSQATRNRVEKA   47 (67)
T ss_dssp             CCCHHHHHHHTTCCHHHHHHTTTCCCCSCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence            579999999999999999999999988899887777553

>2pij_A Prophage PFL 6 CRO; transcription factor, helix-turn-helix, structural evolution, transcription; 1.70A {Pseudomonas fluorescens}

Probab=97.18  E-value=0.00038  Score=42.81  Aligned_cols=38  Identities=13%  Similarity=0.101  Sum_probs=33.6

Q ss_pred             HHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCH
Q psy6501         126 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQ  164 (174)
Q Consensus       126 ~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~  164 (174)
                      .|...+...| ++.++|+.+|+++++|+.|++|...|.+
T Consensus         5 ~l~~~~~~~g-s~~~~A~~lgis~~~vs~~~~~~~~~~l   42 (67)
T 2pij_A            5 PLSKYLEEHG-TQSALAAALGVNQSAISQMVRAGRSIEI   42 (67)
T ss_dssp             EHHHHHHHTC-CHHHHHHHHTSCHHHHHHHHHTTCCEEE
T ss_pred             HHHHHHHHcC-CHHHHHHHHCcCHHHHHHHHcCCCCCCe
Confidence            4566788899 9999999999999999999999887754

>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=97.13  E-value=0.00075  Score=45.73  Aligned_cols=53  Identities=13%  Similarity=0.109  Sum_probs=36.3

Q ss_pred             HHHHHHHHHH-HHcC-CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHh
Q psy6501          32 DLAKLLMQGR-QAKG-WSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL   84 (174)
Q Consensus        32 ~ig~~ik~~R-~~~g-ltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L   84 (174)
                      .++.|+.-.+ ...| +||.|+|+.+|+|++|||++-+--...+.+.-..|...|
T Consensus        43 ~l~~R~~l~~~L~~ge~TQREIA~~lGiS~stISRi~r~L~~l~~~~k~~l~~~l   97 (101)
T 1jhg_A           43 ALGTRVRIIEELLRGEMSQRELKNELGAGIATITRGSNSLKAAPVELRQWLEEVL   97 (101)
T ss_dssp             HHHHHHHHHHHHHHCCSCHHHHHHHHCCCHHHHHHHHHHHHHSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCcCHHHHHHHHCCChhhhhHHHHHHHHccHHHHHHHHHHh
Confidence            3555555544 2245 999999999999999999996544445555555555554

>3g7d_A PHPD; non heme Fe(II) dioxygenase, cupin, biosynthetic protein; 1.80A {Streptomyces viridochromogenes} PDB: 3gbf_A 3rzz_A

Probab=97.09  E-value=0.00048  Score=55.82  Aligned_cols=53  Identities=11%  Similarity=0.075  Sum_probs=49.0

Q ss_pred             HHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCC-CCCHHHHHHHHhhC
Q psy6501         122 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRG-IPNQAIIGKMERAL  174 (174)
Q Consensus       122 ~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~-~P~~~~l~~i~~~l  174 (174)
                      ..+..|+..|.+.|++|.++|++.|++...|+..|+|+. .+..+.+.+|+++|
T Consensus       230 aagv~LR~ar~ReglTQ~~LAe~TGIPq~hISeMenGKr~~IGkdeaR~LA~AL  283 (443)
T 3g7d_A          230 SAGSVLDLFLARRAHTRTSAAEAAGVPPADLEAALRSPASETGLTVLRTLGRAL  283 (443)
T ss_dssp             CHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHCTTSHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHhcCCcCCccHHHHHHHHHHh
Confidence            346789999999999999999999999999999999999 66999999999986

>1ic8_A Hepatocyte nuclear factor 1-alpha; transcription regulation, DNA-binding, POU domain, diabetes, disease mutation, MODY3, transcription/DNA comple; 2.60A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1

Probab=97.03  E-value=0.0016  Score=49.18  Aligned_cols=48  Identities=10%  Similarity=0.040  Sum_probs=42.8

Q ss_pred             ccHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHH
Q psy6501         119 VPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAI  166 (174)
Q Consensus       119 ~~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~  166 (174)
                      -+..+...|+..+...|++|.++|+.+|++.++|+.|++|...++...
T Consensus        27 ~p~~l~~~Ik~~l~~~gitQ~~lA~~~GiSqs~ISr~l~~~~~~~~~k   74 (194)
T 1ic8_A           27 DPWRVAKMVKSYLQQHNIPQREVVDTTGLNQSHLSQHLNKGTPMKTQK   74 (194)
T ss_dssp             CHHHHHHHHHHHHHHTTCCHHHHHHHHCCCHHHHHHHHHSBCCCCHHH
T ss_pred             CHHHHHHHHHHHHHHcCCCHHHHHHHhCCChHHHHHHHhcCccccccc
Confidence            456778999999999999999999999999999999999987777653

>1u78_A TC3 transposase, transposable element TC3 transposase; transposon DNA, bipartite DNA-binding, HTH- motif, DNA binding protein/DNA complex; 2.69A {Caenorhabditis elegans} SCOP: a.4.1.2 a.4.1.2

Probab=97.03  E-value=0.013  Score=40.73  Aligned_cols=91  Identities=9%  Similarity=0.065  Sum_probs=57.3

Q ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccCCCCCCCCCcccchhhhh
Q psy6501          31 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGTNKQPGTTKNTAKLDRE  110 (174)
Q Consensus        31 ~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~~~~~~~~~~~~~l~~~  110 (174)
                      .+.-..|..+. ..|+|..++|+.+|+|++||.+|-+.....            |...  .-+                 
T Consensus         9 ~~~r~~i~~~~-~~G~s~~~ia~~lgis~~Tv~r~~~~~~~~------------g~~~--~~g-----------------   56 (141)
T 1u78_A            9 DTERAQLDVMK-LLNVSLHEMSRKISRSRHCIRVYLKDPVSY------------GTSK--RAP-----------------   56 (141)
T ss_dssp             HHHHHHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHHSGGGT------------TCCC--CCC-----------------
T ss_pred             HHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHccccc------------CCcC--CCC-----------------
Confidence            34444555555 579999999999999999999997632110            1000  000                 


Q ss_pred             hhhhhcccccHHHHHHHHHHHHhcCCCHHHHHHHhC--CChhHHHHHhc
Q psy6501         111 TEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKIN--EKPQIVNDYEG  157 (174)
Q Consensus       111 ~~~~~~~~~~~~~~~~i~~~R~~~glsq~ela~~lg--~~~s~i~~~E~  157 (174)
                          ....+.......|........++..+++..+|  ++.++|.+|-.
T Consensus        57 ----r~~~l~~~~~~~i~~~~~~~~~s~~~i~~~lg~~~s~~tV~r~l~  101 (141)
T 1u78_A           57 ----RRKALSVRDERNVIRAASNSCKTARDIRNELQLSASKRTILNVIK  101 (141)
T ss_dssp             ----CCCSSCHHHHHHHHHHHHHCCCCHHHHHHHTTCCSCHHHHHHHHH
T ss_pred             ----CCCcCCHHHHHHHHHHHhCCCCCHHHHHHHHCCCccHHHHHHHHH
Confidence                00011122223344445567799999999999  78889998864

>2ao9_A Phage protein; structural genomics, nine-fold NCS., PSI, protein structure initiative, midwest center for structural genomics, MCSG, U function; 1.90A {Bacillus cereus} SCOP: a.4.1.17

Probab=96.93  E-value=0.0014  Score=47.71  Aligned_cols=39  Identities=8%  Similarity=0.123  Sum_probs=34.3

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCCH-HHHHHHHHHhC
Q psy6501          45 GWSQKDLATKINEKPQIVNDYEGGRGIPNQ-AIIGKMERALG   85 (174)
Q Consensus        45 gltq~eLA~~igvs~~~is~~E~G~~~P~~-~~l~~la~~L~   85 (174)
                      |+|+.++|+.+|||++||.+|.+.  .|.. +.+.++|+.+-
T Consensus        48 ~lTv~eIA~~LGIS~~TLyrW~k~--~p~~~~~l~~vad~~l   87 (155)
T 2ao9_A           48 KRTQDEMANELGINRTTLWEWRTK--NQDFIAFKSEVADSFL   87 (155)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHHH--CHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHHc--CcchHHHHHHHHHHHH
Confidence            899999999999999999999985  5775 88888888743

>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA complex, SOX; 2.05A {Mus musculus}

Probab=96.92  E-value=0.0082  Score=44.03  Aligned_cols=53  Identities=19%  Similarity=0.244  Sum_probs=43.6

Q ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhCC------CHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q psy6501          31 LDLAKLLMQGRQAKGWSQKDLATKINE------KPQIVNDYEGGRGIPNQAIIGKMERALG   85 (174)
Q Consensus        31 ~~ig~~ik~~R~~~gltq~eLA~~igv------s~~~is~~E~G~~~P~~~~l~~la~~L~   85 (174)
                      ..|+..+|..|-..|+||.+++..+|.      |+++|+++|+-.  .+...+.++--.|.
T Consensus        16 ~~fa~~fk~~ri~lg~tQ~~vg~alg~l~g~~~Sqtti~rFE~l~--ls~kn~~klkPlL~   74 (164)
T 2xsd_C           16 EQFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQ--LSFKNMCKLKPLLN   74 (164)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHHSCCCCHHHHHHHHTTC--SBHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhcCCcccccccccccccCCCcCcchhhhhhccC--CCHHHHHHcchhHH
Confidence            689999999999999999999999988      999999999644  45566666554443

>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=96.88  E-value=0.0027  Score=35.90  Aligned_cols=33  Identities=15%  Similarity=0.114  Sum_probs=26.6

Q ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcC
Q psy6501          35 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGG   68 (174)
Q Consensus        35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G   68 (174)
                      ..|..+. ..|+|+.++|+.+|||++||.+|-+.
T Consensus        12 ~~i~~~~-~~g~s~~~IA~~lgis~~Tv~~~~~~   44 (51)
T 1tc3_C           12 AQLDVMK-LLNVSLHEMSRKISRSRHCIRVYLKD   44 (51)
T ss_dssp             HHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHHC
T ss_pred             HHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHhh
Confidence            3444443 57999999999999999999999754

>2x48_A CAG38821; archeal virus, viral protein; 2.60A {Sulfolobus islandicus rod-shaped virusorganism_taxid}

Probab=96.88  E-value=0.0026  Score=37.49  Aligned_cols=35  Identities=17%  Similarity=0.285  Sum_probs=28.8

Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          32 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        32 ~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      ..-..+..+ ...|+|+.++|+.+|+|++||++|.+
T Consensus        19 ~~~~~i~~l-~~~g~s~~eIA~~lgis~~TV~~~l~   53 (55)
T 2x48_A           19 DLVSVAHEL-AKMGYTVQQIANALGVSERKVRRYLE   53 (55)
T ss_dssp             HHHHHHHHH-HHTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            344566666 46899999999999999999999864

>1au7_A Protein PIT-1, GHF-1; complex (DNA-binding protein/DNA), pituitary, CPHD, POU domain, transcription factor, transcription/DNA complex; HET: DNA; 2.30A {Rattus norvegicus} SCOP: a.4.1.1 a.35.1.1

Probab=96.84  E-value=0.014  Score=41.95  Aligned_cols=53  Identities=13%  Similarity=0.172  Sum_probs=43.7

Q ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhCC------CHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q psy6501          31 LDLAKLLMQGRQAKGWSQKDLATKINE------KPQIVNDYEGGRGIPNQAIIGKMERALG   85 (174)
Q Consensus        31 ~~ig~~ik~~R~~~gltq~eLA~~igv------s~~~is~~E~G~~~P~~~~l~~la~~L~   85 (174)
                      ..|+...+.-|-..|+||.+++..+|.      |++||+++|+-.  .+...+.+|--.|.
T Consensus         6 ~~fa~~~k~~ri~lg~tQ~~vg~al~~l~g~~~Sqtti~rfe~l~--ls~knm~kLkPlL~   64 (146)
T 1au7_A            6 EQFANEFKVRRIKLGYTQTNVGEALAAVHGSEFSQTTICRFENLQ--LSFKNACKLKAILS   64 (146)
T ss_dssp             HHHHHHHHHHHHHHTCCHHHHHHHHHHTTSSCCCHHHHHHHHTTC--SBHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccCcHHhhhhhcchhccCCCCcchHHHHhccC--CChHHHHhcchHHH
Confidence            579999999999999999999999988      999999999644  45566666665544

>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=96.37  E-value=0.004  Score=35.60  Aligned_cols=33  Identities=15%  Similarity=0.101  Sum_probs=26.5

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCC
Q psy6501          36 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGR   69 (174)
Q Consensus        36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~   69 (174)
                      .|..+. ..|+|..++|+.+|||++||.+|-+..
T Consensus        13 ~i~~l~-~~g~s~~~ia~~lgvs~~Tv~r~l~~~   45 (52)
T 1jko_C           13 QISRLL-EKGHPRQQLAIIFGIGVSTLYRYFPAS   45 (52)
T ss_dssp             HHHHHH-HTTCCHHHHHHTTSCCHHHHHHHSCTT
T ss_pred             HHHHHH-HcCCCHHHHHHHHCCCHHHHHHHHHHc
Confidence            344443 468999999999999999999997644

>2ovg_A Phage lambda CRO; transcription factor, helix-turn-helix, bacteriophage, flexi transcription; 1.35A {Enterobacteria phage lambda} PDB: 2ecs_A 1cop_D 4cro_A* 5cro_O 1orc_A 2orc_A 2a63_A 1d1l_A 6cro_A* 3orc_A* 1d1m_B

Probab=96.37  E-value=0.0034  Score=39.06  Aligned_cols=29  Identities=17%  Similarity=0.072  Sum_probs=24.5

Q ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          37 LMQGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        37 ik~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      |+.+....  ||.+.|+.+|||+++||+|.+
T Consensus         7 L~~~~~~~--s~t~aA~~L~vtQ~AVS~~ir   35 (66)
T 2ovg_A            7 LKDYAMRF--GQTKTAKDLGVYPSSINQAIH   35 (66)
T ss_dssp             HHHHHHHH--CHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHC--CHHHHHHHhCCCHHHHHHHHH
Confidence            55555555  999999999999999999975

>1e3o_C Octamer-binding transcription factor 1; transcription factor, POU domain, dimer, DNA binding; 1.9A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1 PDB: 1gt0_C 1hf0_A* 1cqt_A* 1o4x_A 1oct_C* 1pou_A 1pog_A 1hdp_A

Probab=96.12  E-value=0.013  Score=42.64  Aligned_cols=52  Identities=19%  Similarity=0.275  Sum_probs=43.1

Q ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhCC------CHHHHHHHHcCCCCCCHHHHHHHHHHh
Q psy6501          31 LDLAKLLMQGRQAKGWSQKDLATKINE------KPQIVNDYEGGRGIPNQAIIGKMERAL   84 (174)
Q Consensus        31 ~~ig~~ik~~R~~~gltq~eLA~~igv------s~~~is~~E~G~~~P~~~~l~~la~~L   84 (174)
                      ..||..+|..|...|+||.+++..+|.      |+++|+++|.=.  .+...+.++--+|
T Consensus        10 ~~~~~~~k~~r~~lg~tQ~~vg~~lg~l~g~~~sq~ti~rfE~l~--lS~knm~klkPlL   67 (160)
T 1e3o_C           10 EQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALN--LSFKNMSKLKPLL   67 (160)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHHSCCCCHHHHHHHHHTC--SCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHhhccccCCCcCccccccccccC--CChHHHHhcchhH
Confidence            589999999999999999999999999      999999999753  4555555554443

>2hin_A GP39, repressor protein; transcription factor, dimer interface, helix-turn-helix; 1.05A {Enterobacteria phage N15} PDB: 3qws_A

Probab=96.10  E-value=0.007  Score=38.24  Aligned_cols=29  Identities=17%  Similarity=0.217  Sum_probs=25.6

Q ss_pred             CHHHHHHHhCCChhHHHHHhcCCCCCCHH
Q psy6501         137 SQKDLATKINEKPQIVNDYEGGRGIPNQA  165 (174)
Q Consensus       137 sq~ela~~lg~~~s~i~~~E~G~~~P~~~  165 (174)
                      +|.++|+.+|+++++|+.|+.|..+|...
T Consensus        12 ~~~~lA~~lGVs~~aVs~W~~g~~iP~~~   40 (71)
T 2hin_A           12 DVEKAAVGVGVTPGAVYQWLQAGEIPPLR   40 (71)
T ss_dssp             SHHHHHHHHTSCHHHHHHHHHHTSCCHHH
T ss_pred             CHHHHHHHHCCCHHHHHHHHhCCCCCHHH
Confidence            59999999999999999999997777543

>1jhf_A LEXA repressor; LEXA SOS repressor, hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.2 b.87.1.1 PDB: 1jhh_A 3jso_A* 3jsp_A* 3k3r_E* 1jhc_A 1jhe_A 1lea_A 1leb_A

Probab=96.02  E-value=0.006  Score=45.67  Aligned_cols=38  Identities=11%  Similarity=0.263  Sum_probs=34.2

Q ss_pred             HHHHHHHHHHHHhcCC--CHHHHHHHhCCC-hhHHHHHhcC
Q psy6501         121 LDLAKLLMQGRQAKGW--SQKDLATKINEK-PQIVNDYEGG  158 (174)
Q Consensus       121 ~~~~~~i~~~R~~~gl--sq~ela~~lg~~-~s~i~~~E~G  158 (174)
                      ..+.++|++.|++.|+  ||.++|+++|++ +++++.|+++
T Consensus         9 ~~i~~~i~~~~~~~g~~ps~~elA~~lgiss~~tv~~~~~~   49 (202)
T 1jhf_A            9 QEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKA   49 (202)
T ss_dssp             HHHHHHHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCccHHHHHHHhCCCChHHHHHHHHH
Confidence            3467899999999999  999999999999 9999999874

>1k78_A Paired box protein PAX5; paired domain, ETS domain, transcription factor, transcription/DNA complex; 2.25A {Homo sapiens} SCOP: a.4.1.5 a.4.1.5 PDB: 1mdm_A 6pax_A

Probab=95.92  E-value=0.18  Score=35.36  Aligned_cols=39  Identities=13%  Similarity=0.181  Sum_probs=30.7

Q ss_pred             cchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          28 KVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        28 ~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      .+..++-.+|..+. ..|+|..++|+.+|+|++||++|-+
T Consensus        32 ~~s~e~r~~iv~~~-~~G~s~~~iA~~lgis~~TV~rw~~   70 (149)
T 1k78_A           32 PLPDVVRQRIVELA-HQGVRPCDISRQLRVSHGCVSKILG   70 (149)
T ss_dssp             CCCHHHHHHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            34455555565555 4799999999999999999999964

>2jn6_A Protein CGL2762, transposase; GFT PSI-2, protein structure, structural genomics, protein structure initiative; NMR {Corynebacterium glutamicum} SCOP: a.4.1.19

Probab=95.78  E-value=0.013  Score=38.66  Aligned_cols=23  Identities=13%  Similarity=0.179  Sum_probs=21.7

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          45 GWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        45 gltq~eLA~~igvs~~~is~~E~   67 (174)
                      |+|..++|+.+|||++||.+|-+
T Consensus        23 g~s~~~ia~~~gIs~~tl~rW~~   45 (97)
T 2jn6_A           23 GASLQQIANDLGINRVTLKNWII   45 (97)
T ss_dssp             GSCHHHHHHHHTSCHHHHHHHHH
T ss_pred             CChHHHHHHHHCcCHHHHHHHHH
Confidence            89999999999999999999964

>2w7n_A TRFB transcriptional repressor protein; INCP, plasmid, repressor, DNA-binding, transcription/DNA; HET: BRU; 1.85A {Escherichia coli}

Probab=95.63  E-value=0.021  Score=38.51  Aligned_cols=36  Identities=17%  Similarity=0.118  Sum_probs=30.2

Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          32 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        32 ~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      ...-++-.+--..|+||.|+|+.+|+|+++||++-+
T Consensus        21 ~~~~~~A~lyYv~g~tQ~eIA~~lGiSR~~VsrlL~   56 (101)
T 2w7n_A           21 QQTIEIARGVLVDGKPQATFATSLGLTRGAVSQAVH   56 (101)
T ss_dssp             HHHHHHHHHHHTTCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            344566667788999999999999999999999853

>1x2l_A CUT-like 2, homeobox protein CUX-2; CUT domain, human homeobox protein CUX-2, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.35.1.7

Probab=95.59  E-value=0.038  Score=37.23  Aligned_cols=40  Identities=8%  Similarity=0.008  Sum_probs=36.2

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHH-hCCCHHHHHHHHcCC
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATK-INEKPQIVNDYEGGR   69 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~-igvs~~~is~~E~G~   69 (174)
                      ...|...|++-.+..++||+-||+. +|.++.++|.+-+--
T Consensus        19 Tk~I~~~ike~L~~~~isQ~~FA~~VLgrsQgtlS~lL~~P   59 (101)
T 1x2l_A           19 TAEIAFQVKEQLLKHNIGQRVFGHYVLGLSQGSVSEILARP   59 (101)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHTTCSCHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHHccccchHHHHhcCC
Confidence            4589999999999999999999998 899999999997653

>2elh_A CG11849-PA, LD40883P; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Drosophila melanogaster}

Probab=95.55  E-value=0.028  Score=36.46  Aligned_cols=38  Identities=13%  Similarity=0.046  Sum_probs=28.3

Q ss_pred             chHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          29 VPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        29 ~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      ...++-..+..+. ..|.|..++|+.+|||+++|.+|-+
T Consensus        23 ys~e~k~~~v~~~-~~g~s~~~iA~~~gIs~sTl~rW~k   60 (87)
T 2elh_A           23 LTPRDKIHAIQRI-HDGESKASVARDIGVPESTLRGWCK   60 (87)
T ss_dssp             CCHHHHHHHHHHH-HHTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCHHHHHHHHHHH-HCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3344433444444 4689999999999999999999963

>2k27_A Paired box protein PAX-8; paired domain, solution structure, triple frequency, 3D NMR, induced FIT, alternative splicing, developmental protein; NMR {Homo sapiens}

Probab=95.54  E-value=0.12  Score=36.82  Aligned_cols=39  Identities=13%  Similarity=0.150  Sum_probs=30.2

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCC
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGR   69 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~   69 (174)
                      ..++-..|..+. ..|+|..++|+.+|+|++||++|-+-.
T Consensus        27 s~e~r~~ii~l~-~~G~s~~~IA~~lgis~~TV~rwl~r~   65 (159)
T 2k27_A           27 PEVVRQRIVDLA-HQGVRPCDISRQLRVSHGCVSKILGRY   65 (159)
T ss_dssp             CHHHHHHHHHHH-HHTCCHHHHHHHHTCCSHHHHHHHCCS
T ss_pred             CHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            344444555555 479999999999999999999998643

>2l0k_A Stage III sporulation protein D; SPOIIID, solution structure, DNA binding, bacillus subti transcription factor, transcription; NMR {Bacillus subtilis}

Probab=95.52  E-value=0.022  Score=37.85  Aligned_cols=48  Identities=8%  Similarity=-0.026  Sum_probs=39.3

Q ss_pred             HHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCC-CCCCHHHHHHHHhh
Q psy6501         126 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGR-GIPNQAIIGKMERA  173 (174)
Q Consensus       126 ~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~-~~P~~~~l~~i~~~  173 (174)
                      .|.+.....+.+..|+|+.+|+|.+||+++.+|. ...++++..++.++
T Consensus        11 ~I~~~l~~~~~ti~dlA~~~gVS~~TVsR~L~~~~~~Vs~~tr~rV~~a   59 (93)
T 2l0k_A           11 KIGKYIVETKKTVRVIAKEFGVSKSTVHKDLTERLPEINPDLANEVKEI   59 (93)
T ss_dssp             HHHHHHHHHCCCHHHHHHHHTSCHHHHHHHHTTHHHHHCHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcCCCCCCCHHHHHHHHHH
Confidence            4445555666999999999999999999999997 67788888887654

>2csf_A DNA-binding protein SATB2; CUT domain, special AT-rich sequence-binding protein 2, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.35.1.7

Probab=95.33  E-value=0.059  Score=35.87  Aligned_cols=58  Identities=14%  Similarity=0.073  Sum_probs=46.0

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHHcCCCCCCH------HHHHHHHHHhCcc
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATKI-NEKPQIVNDYEGGRGIPNQ------AIIGKMERALGIR   87 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~i-gvs~~~is~~E~G~~~P~~------~~l~~la~~L~v~   87 (174)
                      ...|..+|+.-.+..+++|.-||+.+ +-|+.++|.+-+=...|.+      +.|.++-+.|+.+
T Consensus        19 Tk~i~~~I~~ELK~~~IsQa~FAk~vlnRsQGtLSelLR~~enPkP~~~~lW~~Lk~m~nWL~Lp   83 (101)
T 2csf_A           19 TAAIYDEIQQEMKRAKVSQALFAKVAANKSQGWLCELLRWKENPSPENRTLWENLCTIRRFLNLP   83 (101)
T ss_dssp             CTHHHHHHHHHHHHHTCCHHHHHHHHTCCCHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHTSC
T ss_pred             HHHHHHHHHHHHHHcCCcHHHHHHHHHHhchhHHHHHHhcccCCCcchhhHHHHHHHHHHHHcCC
Confidence            45899999999999999999999966 9999999999875556665      4455555555554

>3kjx_A Transcriptional regulator, LACI family; LACL family, protein structure initiative II(PSI II), NYSGXRC, structural genomics; 2.33A {Silicibacter pomeroyi}

Probab=95.19  E-value=0.031  Score=44.60  Aligned_cols=49  Identities=14%  Similarity=0.100  Sum_probs=38.9

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH---HHHHHhCcccccc
Q psy6501          43 AKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIG---KMERALGIRLRVN   91 (174)
Q Consensus        43 ~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~---~la~~L~v~~~~l   91 (174)
                      .+..|.+|+|+.+|||.+|||+.-||....+.++-.   +.++.||..+...
T Consensus         8 ~~~~ti~diA~~agVS~~TVSr~Ln~~~~vs~~tr~rV~~~~~~lgY~pn~~   59 (344)
T 3kjx_A            8 KRPLTLRDVSEASGVSEMTVSRVLRNRGDVSDATRARVLAAAKELGYVPNKI   59 (344)
T ss_dssp             --CCCHHHHHHHHCCCSHHHHHHHTTCSCCCHHHHHHHHHHHHHHTCCCCCC
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHhCCCCCHH
Confidence            456899999999999999999999999777776655   5566788776544

>2hsg_A Glucose-resistance amylase regulator; CCPA, transcriptional regulator, transcription regulator; 2.50A {Bacillus megaterium} SCOP: a.35.1.5 c.93.1.1 PDB: 1rzr_G 2jcg_A 1zvv_A 3oqo_A* 3oqm_A* 3oqn_A*

Probab=95.15  E-value=0.035  Score=43.94  Aligned_cols=46  Identities=15%  Similarity=0.078  Sum_probs=37.4

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH---HHHHHhCccccc
Q psy6501          45 GWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIG---KMERALGIRLRV   90 (174)
Q Consensus        45 gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~---~la~~L~v~~~~   90 (174)
                      ..|.+|+|+++|||.+|||+.-||....+.++-.   +.++.||..+..
T Consensus         2 ~~ti~dvA~~agVS~~TVSrvln~~~~vs~~tr~rV~~aa~~lgY~pn~   50 (332)
T 2hsg_A            2 NVTIYDVAREASVSMATVSRVVNGNPNVKPSTRKKVLETIERLGYRPNA   50 (332)
T ss_dssp             CCCHHHHHHHTTSCHHHHHHHHTTCTTSCHHHHHHHHHHHHHHTCCSCH
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHCCCcCH
Confidence            3699999999999999999999998777776654   556778876543

>1xwr_A Regulatory protein CII; all-alpha fold, DNA binding protein; 2.56A {Bacteriophage lambda} SCOP: a.35.1.9 PDB: 1zpq_A

Probab=95.13  E-value=0.0072  Score=40.53  Aligned_cols=29  Identities=3%  Similarity=0.065  Sum_probs=25.4

Q ss_pred             HHhcCCCHHHHHHHhCCChhHHHHHhcCC
Q psy6501         131 RQAKGWSQKDLATKINEKPQIVNDYEGGR  159 (174)
Q Consensus       131 R~~~glsq~ela~~lg~~~s~i~~~E~G~  159 (174)
                      +.-.+.+|..+|+.+|+++++|++|++|.
T Consensus        19 ~~la~~gq~~vA~~iGV~~StISR~k~~~   47 (97)
T 1xwr_A           19 NKIAMLGTEKTAEAVGVDKSQISRWKRDW   47 (97)
T ss_dssp             HHHHHHCHHHHHHHHTCCTTTHHHHHHHH
T ss_pred             HHHHHHhHHHHHHHhCCCHHHHHHHHhhh
Confidence            33467899999999999999999999974

>3d1n_I POU domain, class 6, transcription factor 1; protein-DNA complex, helix-turn-helix (HTH), DNA-binding, homeobox, nucleus, transcription regulation; 2.51A {Homo sapiens}

Probab=95.09  E-value=0.11  Score=37.17  Aligned_cols=50  Identities=14%  Similarity=0.168  Sum_probs=41.5

Q ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhCC------CHHHHHHHHcCCCCCCHHHHHHHHH
Q psy6501          31 LDLAKLLMQGRQAKGWSQKDLATKINE------KPQIVNDYEGGRGIPNQAIIGKMER   82 (174)
Q Consensus        31 ~~ig~~ik~~R~~~gltq~eLA~~igv------s~~~is~~E~G~~~P~~~~l~~la~   82 (174)
                      ..|++..+.-|-..|+||.+++..+|.      |+++|+++|.-.-  +...+.++.-
T Consensus         7 ~~fa~~f~~~ri~lg~tQ~~vg~al~~l~g~~~Sqsti~rfe~l~l--s~kn~~klkP   62 (151)
T 3d1n_I            7 REFAKNFKIRRLSLGLTQTQVGQAMTATEGPAYSQSAISRFEKLDI--TPKSAQKLKP   62 (151)
T ss_dssp             HHHHHHHHHHHHTTTCCHHHHHHHHSCSSSCCCCHHHHHHHHTTCS--CHHHHHHHHH
T ss_pred             HHHHHHHHHHHhhcCCCcccHHHhhccccCCCCCccccccccCCCC--ChhHHHHhch
Confidence            489999999999999999999999997      9999999997654  4454444443

>1r71_A Transcriptional repressor protein KORB; INCP, plasmid partitioning, protein-DNA complex, heilx-turn- helix motif, transcription factor; HET: BRU; 2.20A {Escherichia coli} SCOP: a.4.14.1

Probab=95.04  E-value=0.036  Score=41.12  Aligned_cols=50  Identities=18%  Similarity=0.347  Sum_probs=38.0

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHH
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKME   81 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la   81 (174)
                      +.+.+..++.+... |+||+++|+++|+|+++|+++-+=...| ...+..+.
T Consensus        38 piE~A~a~~~L~~~-G~t~eeiA~~lG~s~s~V~~~LrLl~Lp-~~v~~~v~   87 (178)
T 1r71_A           38 PREIADFIGRELAK-GKKKGDIAKEIGKSPAFITQHVTLLDLP-EKIADAFN   87 (178)
T ss_dssp             HHHHHHHHHHHHHT-TCCHHHHHHHHTCCHHHHHHHHGGGSCC-HHHHHHHH
T ss_pred             HHHHHHHHHHHHHc-CCCHHHHHHHHCcCHHHHHHHHHHHcCC-HHHHHHHH
Confidence            45667777777765 9999999999999999999998655443 35555544

>1zs4_A Regulatory protein CII; helix-turn-helix, transcription activator, transcription-DNA; HET: DNA; 1.70A {Enterobacteria phage lambda} SCOP: a.35.1.9

Probab=95.03  E-value=0.015  Score=37.83  Aligned_cols=26  Identities=4%  Similarity=0.059  Sum_probs=23.6

Q ss_pred             cCCCHHHHHHHhCCChhHHHHHhcCC
Q psy6501         134 KGWSQKDLATKINEKPQIVNDYEGGR  159 (174)
Q Consensus       134 ~glsq~ela~~lg~~~s~i~~~E~G~  159 (174)
                      ..++|..+|+.+|+++|+|++|.+|.
T Consensus        23 a~~gQ~~vAe~~GvdeStISR~k~~~   48 (83)
T 1zs4_A           23 AMLGTEKTAEAVGVDKSQISRWKRDW   48 (83)
T ss_dssp             HHHCHHHHHHHHTSCHHHHHHHHHHT
T ss_pred             HHHhhHHHHHHhCCCHHHHhhhhhhH
Confidence            44789999999999999999999975

>2cw1_A SN4M; lambda CRO fold, de novo protein; NMR {Synthetic} SCOP: k.46.1.1

Probab=95.00  E-value=0.031  Score=34.55  Aligned_cols=34  Identities=12%  Similarity=-0.001  Sum_probs=26.8

Q ss_pred             HHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCC
Q psy6501         127 LMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIP  162 (174)
Q Consensus       127 i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P  162 (174)
                      |+..+...  +|.++|+.+|+++++|+.|+++....
T Consensus         7 Lk~l~~~~--sq~~~A~~Lgvsq~aVS~~~~~~r~i   40 (65)
T 2cw1_A            7 LKKFVEDK--NQEYAARALGLSQKLIEEVLKRGLPV   40 (65)
T ss_dssp             HHHHHTTS--CHHHHHHHSSSCHHHHHHHHHTTCCC
T ss_pred             HHHHHHHc--CHHHHHHHhCCCHHHHHHHHHhcCCc
Confidence            33344444  99999999999999999999876543

>1qpz_A PURA, protein (purine nucleotide synthesis repressor); transcription regulation, DNA-binding, purine biosynthesis; HET: DNA HPA; 2.50A {Escherichia coli} SCOP: a.35.1.5 c.93.1.1 PDB: 1bdi_A* 1qp0_A* 1qp4_A* 1pnr_A* 1wet_A* 1zay_A* 1vpw_A* 2pue_A* 2puf_A* 2pug_A* 1bdh_A* 1qp7_A* 1qqa_A* 1qqb_A* 2puc_A* 2pua_A* 2pub_A* 2pud_A* 1jfs_A* 1jh9_A* ...

Probab=94.79  E-value=0.047  Score=43.40  Aligned_cols=45  Identities=13%  Similarity=0.020  Sum_probs=36.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHH---HHHHHHhCccccc
Q psy6501          46 WSQKDLATKINEKPQIVNDYEGGRGIPNQAII---GKMERALGIRLRV   90 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~G~~~P~~~~l---~~la~~L~v~~~~   90 (174)
                      .|.+|+|+++|||.+|||+.-||....+.++-   .+.++.||-.+..
T Consensus         1 ~ti~diA~~agVS~~TVSrvLn~~~~vs~~tr~rV~~~a~~lgY~pn~   48 (340)
T 1qpz_A            1 ATIKDVAKRANVSTTTVSHVINKTRFVAEETRNAVWAAIKELHYSPSA   48 (340)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHTCSCCCHHHHHHHHHHHHHHTCCCCH
T ss_pred             CCHHHHHHHHCCCHHHHHHHHcCcCCCCHHHHHHHHHHHHHhCCCCCH
Confidence            48899999999999999999999977777654   4556678876543

>3me5_A Cytosine-specific methyltransferase; structural genomics, protein structure initiative, NEW YORK structural genomix research consortium; 1.75A {Shigella flexneri 2A} PDB: 3lx6_A

Probab=94.77  E-value=0.025  Score=48.29  Aligned_cols=50  Identities=12%  Similarity=0.060  Sum_probs=31.9

Q ss_pred             HHHHHHHHHcCCCHHHHHHHh------CCCHHHHHHHHcCCCCCC---HHHHHHHHHHhCc
Q psy6501          35 KLLMQGRQAKGWSQKDLATKI------NEKPQIVNDYEGGRGIPN---QAIIGKMERALGI   86 (174)
Q Consensus        35 ~~ik~~R~~~gltq~eLA~~i------gvs~~~is~~E~G~~~P~---~~~l~~la~~L~v   86 (174)
                      +.|+++++  .+||++||+.+      +.|..+|.+||+|...|+   ...+..|...+..
T Consensus        21 ~~~~~~~~--~~~~~~~a~~l~~~~~~~~~~~~~~rw~~~~~~~~~~~~~~~~~l~~~~~~   79 (482)
T 3me5_A           21 AMLEKLLQ--IYDVKMLVAQLNGVGENHWSAAILKRALANDSAWHRLSEKEFAHLQTLLPK   79 (482)
T ss_dssp             HHHHHHHT--TSCHHHHHHHHHHTCSSCCCHHHHHHHHC-------CCTHHHHHHHTTSCC
T ss_pred             HHHHHHHH--HcCHHHHHHHHHhhccCCCCHHHHHHHHcCCCCCccccHHHHHHHHhhCCC
Confidence            44455544  47999999999      899999999999987663   4445555554443

>1j9i_A GPNU1 DBD;, terminase small subunit; DNA binding domain, homodimer, viral assembly, winged helix-turn-helix, viral protein; NMR {Enterobacteria phage lambda} SCOP: a.6.1.5

Probab=94.76  E-value=0.017  Score=35.68  Aligned_cols=24  Identities=13%  Similarity=0.238  Sum_probs=21.8

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCC
Q psy6501          46 WSQKDLATKINEKPQIVNDYEGGR   69 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~G~   69 (174)
                      ||.+|+|+.+|||++||.+|....
T Consensus         3 lt~~e~a~~LgvS~~Tl~rw~~~G   26 (68)
T 1j9i_A            3 VNKKQLADIFGASIRTIQNWQEQG   26 (68)
T ss_dssp             EEHHHHHHHTTCCHHHHHHHTTTT
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHCC
Confidence            689999999999999999998643

>2glo_A Brinker CG9653-PA; protein-DNA complex, helix-turn-helix motif, transcription/DNA complex; NMR {Drosophila melanogaster}

Probab=94.59  E-value=0.077  Score=31.60  Aligned_cols=35  Identities=11%  Similarity=0.135  Sum_probs=26.7

Q ss_pred             HHHHHHHHHHHHcCCC----HHHHHHHhCCCHHHHHHHHc
Q psy6501          32 DLAKLLMQGRQAKGWS----QKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        32 ~ig~~ik~~R~~~glt----q~eLA~~igvs~~~is~~E~   67 (174)
                      +|-..+..+ ...|.|    ..++|..+||++++|.+|-+
T Consensus         9 efK~~~~~~-~~~g~s~~~~~~~vA~~~gIs~~tl~~W~~   47 (59)
T 2glo_A            9 HFKLQVLES-YRNDNDCKGNQRATARKYNIHRRQIQKWLQ   47 (59)
T ss_dssp             HHHHHHHHH-HHHCTTTTTCHHHHHHHTTSCHHHHHHHHT
T ss_pred             HHHHHHHHH-HHcCCCcchHHHHHHHHHCcCHHHHHHHHH
Confidence            444444333 346789    99999999999999999975

>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=94.59  E-value=0.028  Score=36.75  Aligned_cols=42  Identities=10%  Similarity=0.085  Sum_probs=29.5

Q ss_pred             cccccchHHHHHHHHHH------HHHc-CCCHHHHHHHhCCCHHH-HHHH
Q psy6501          24 LKHEKVPLDLAKLLMQG------RQAK-GWSQKDLATKINEKPQI-VNDY   65 (174)
Q Consensus        24 ~~~~~~~~~ig~~ik~~------R~~~-gltq~eLA~~igvs~~~-is~~   65 (174)
                      |+++.+...+|.-++.+      .... ++|+.|||+.+|+++++ +++.
T Consensus         2 m~~~~l~~~~g~~~~~l~~L~~l~~~~~~~t~~eLa~~l~is~~t~vs~~   51 (95)
T 2pg4_A            2 MDDETLRLQFGHLIRILPTLLEFEKKGYEPSLAEIVKASGVSEKTFFMGL   51 (95)
T ss_dssp             CCCGGGGSBHHHHHHHHHHHHHHHHTTCCCCHHHHHHHHCCCHHHHHTTH
T ss_pred             CcHHHHHHHhhhHHHHHHHHHHHHhcCCCCCHHHHHHHHCCCchHHHHHH
Confidence            44555555555554443      3444 79999999999999999 7765

>2vz4_A Tipal, HTH-type transcriptional activator TIPA; transcription, resistance, antibiotic; 2.90A {Streptomyces lividans}

Probab=94.58  E-value=0.04  Score=37.22  Aligned_cols=23  Identities=13%  Similarity=0.229  Sum_probs=21.3

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          45 GWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        45 gltq~eLA~~igvs~~~is~~E~   67 (174)
                      +||..|+|+.+|||..||..||.
T Consensus         1 ~~~i~e~A~~~gvs~~tLR~ye~   23 (108)
T 2vz4_A            1 SYSVGQVAGFAGVTVRTLHHYDD   23 (108)
T ss_dssp             CBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHH
Confidence            47899999999999999999984

>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=94.53  E-value=0.48  Score=31.35  Aligned_cols=35  Identities=14%  Similarity=0.261  Sum_probs=28.0

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccccccc
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNA   92 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~   92 (174)
                      ..+|.++||+.+|+|++++++.              +.+.+|+++..++
T Consensus        20 ~~~~~~~lA~~~~~S~~~l~r~--------------fk~~~G~s~~~~~   54 (108)
T 3oou_A           20 EGMSLKTLGNDFHINAVYLGQL--------------FQKEMGEHFTDYL   54 (108)
T ss_dssp             SCCCHHHHHHHHTSCHHHHHHH--------------HHHHHSSCHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHH--------------HHHHHCcCHHHHH
Confidence            4799999999999999999876              5566777765443

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

Probab=94.46  E-value=0.44  Score=31.17  Aligned_cols=34  Identities=12%  Similarity=0.222  Sum_probs=27.3

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccccccc
Q psy6501          45 GWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNA   92 (174)
Q Consensus        45 gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~   92 (174)
                      .+|..+||+.+|+|++++++.              +.+.+|+++..++
T Consensus        19 ~~~~~~lA~~~~~S~~~l~r~--------------fk~~~g~s~~~~~   52 (103)
T 3lsg_A           19 QFTLSVLSEKLDLSSGYLSIM--------------FKKNFGIPFQDYL   52 (103)
T ss_dssp             TCCHHHHHHHTTCCHHHHHHH--------------HHHHHSSCHHHHH
T ss_pred             CCCHHHHHHHHCcCHHHHHHH--------------HHHHHCcCHHHHH
Confidence            799999999999999998875              5566677765544

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

Probab=94.24  E-value=0.045  Score=34.83  Aligned_cols=30  Identities=17%  Similarity=0.171  Sum_probs=24.7

Q ss_pred             HHHHHHHHc---CCCHHHHHHHhCCCHHHHHHH
Q psy6501          36 LLMQGRQAK---GWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        36 ~ik~~R~~~---gltq~eLA~~igvs~~~is~~   65 (174)
                      -|..+++.-   ++|..|||+++|+|+++|++.
T Consensus        19 IL~~L~~~~~~~~~t~~eLA~~Lgvs~~tV~~~   51 (77)
T 1qgp_A           19 ILKFLEELGEGKATTAHDLSGKLGTPKKEINRV   51 (77)
T ss_dssp             HHHHHHHHCSSSCEEHHHHHHHHCCCHHHHHHH
T ss_pred             HHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHH
Confidence            445566666   799999999999999999876

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

Probab=94.21  E-value=0.6  Score=30.78  Aligned_cols=46  Identities=11%  Similarity=0.141  Sum_probs=32.7

Q ss_pred             HHHHHHHHHHH---cCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccccccc
Q psy6501          33 LAKLLMQGRQA---KGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNA   92 (174)
Q Consensus        33 ig~~ik~~R~~---~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~   92 (174)
                      +-..+..+...   ..+|.++||+.+|+|++++++.              +.+.+|+++..++
T Consensus         5 i~~~~~~i~~~~~~~~~~~~~lA~~~~~S~~~l~r~--------------fk~~~G~s~~~~~   53 (107)
T 2k9s_A            5 VREACQYISDHLADSNFDIASVAQHVCLSPSRLSHL--------------FRQQLGISVLSWR   53 (107)
T ss_dssp             HHHHHHHHHHTSSCSSCCHHHHHHHTTSCHHHHHHH--------------HHHHHSSCHHHHH
T ss_pred             HHHHHHHHHHHhccCCCCHHHHHHHHCCCHHHHHHH--------------HHHHHCcCHHHHH
Confidence            33444455554   4699999999999999999876              5566677765443

>3h5t_A Transcriptional regulator, LACI family; DNA-dependent, protein structure initiative II(PSI II), NYSGXRC, 11232D), structural genomics; 2.53A {Corynebacterium glutamicum}

Probab=94.20  E-value=0.037  Score=44.49  Aligned_cols=48  Identities=8%  Similarity=-0.030  Sum_probs=36.1

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHH---HHHHHHhCcc-ccc
Q psy6501          43 AKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAII---GKMERALGIR-LRV   90 (174)
Q Consensus        43 ~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l---~~la~~L~v~-~~~   90 (174)
                      .+..|.+|+|+++|||.+|||+.-||....+.++-   .+.++.||.. +..
T Consensus         7 ~~~~Ti~diA~~aGVS~~TVSrvLn~~~~Vs~~tr~rV~~~a~~lgY~~pn~   58 (366)
T 3h5t_A            7 QQYGTLASIAAKLGISRTTVSNAYNRPEQLSAELRQRILDTAEDMGYLGPDP   58 (366)
T ss_dssp             CCTTHHHHHHHHHTSCHHHHHHHHHCGGGSCHHHHHHHHHHHHHTTC-----
T ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCCCCCH
Confidence            45679999999999999999999999866666554   4567778876 543

>1vz0_A PARB, chromosome partitioning protein PARB; nuclear protein, chromosome segregation, DNA-binding, helix-turn-helix; 2.3A {Thermus thermophilus} SCOP: a.4.14.1 d.268.1.1

Probab=94.17  E-value=0.078  Score=40.79  Aligned_cols=50  Identities=14%  Similarity=0.169  Sum_probs=37.1

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHH
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKME   81 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la   81 (174)
                      ..+.+..++.+. ..|+|++++|+.+|+|+++|+++-+=... +.+.+..+.
T Consensus       120 ~~E~a~~~~~l~-~~g~t~~~iA~~lG~s~~~V~~~l~l~~l-~~~v~~~l~  169 (230)
T 1vz0_A          120 PVEEARGYQALL-EMGLTQEEVARRVGKARSTVANALRLLQL-PPEALEALE  169 (230)
T ss_dssp             HHHHHHHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHHGGGS-CHHHHHHHH
T ss_pred             HHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHcC-CHHHHHHHH
Confidence            345666677777 78999999999999999999999764433 334444444

>1pdn_C Protein (PRD paired); protein-DNA complex, double helix, PAX, paired domain, DNA-binding protein, gene regulation/DNA complex; HET: DNA; 2.50A {Drosophila melanogaster} SCOP: a.4.1.5

Probab=94.12  E-value=0.1  Score=35.08  Aligned_cols=38  Identities=11%  Similarity=0.135  Sum_probs=29.5

Q ss_pred             chHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          29 VPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        29 ~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      +..++-.+|..+. ..|+|..++|+.+|+|++||++|-+
T Consensus        18 ~s~~~r~~i~~~~-~~g~s~~~ia~~lgis~~Tv~~w~~   55 (128)
T 1pdn_C           18 LPNNIRLKIVEMA-ADGIRPCVISRQLRVSHGCVSKILN   55 (128)
T ss_dssp             CCHHHHHHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3444445555554 4799999999999999999999964

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

Probab=94.10  E-value=0.085  Score=32.47  Aligned_cols=30  Identities=13%  Similarity=-0.037  Sum_probs=23.3

Q ss_pred             HHHHHHH-cCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          37 LMQGRQA-KGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        37 ik~~R~~-~gltq~eLA~~igvs~~~is~~E   66 (174)
                      |..+.+. ..+|..|||+.+|+|+++|++.-
T Consensus        16 L~~L~~~~~~~s~~eLA~~lglsr~tv~~~l   46 (67)
T 2heo_A           16 LQVLSDDGGPVAIFQLVKKCQVPKKTLNQVL   46 (67)
T ss_dssp             HHHHHHHCSCEEHHHHHHHHCSCHHHHHHHH
T ss_pred             HHHHHHcCCCcCHHHHHHHHCcCHHHHHHHH
Confidence            3344444 46999999999999999998764

>2o8x_A Probable RNA polymerase sigma-C factor; promoter recognition, transcription regulation, helix-turn-H motif, transcription; 3.00A {Mycobacterium tuberculosis}

Probab=94.07  E-value=0.089  Score=31.87  Aligned_cols=31  Identities=16%  Similarity=-0.012  Sum_probs=26.0

Q ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          37 LMQGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        37 ik~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      +-.++-..|+|++|+|+.+|+|+++|.++-.
T Consensus        23 il~l~~~~g~s~~eIA~~lgis~~tv~~~~~   53 (70)
T 2o8x_A           23 ALLLTQLLGLSYADAAAVCGCPVGTIRSRVA   53 (70)
T ss_dssp             HHHHHHTSCCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3445567899999999999999999998753

>1x3u_A Transcriptional regulatory protein FIXJ; helix-turn-helix; NMR {Sinorhizobium meliloti}

Probab=94.06  E-value=0.088  Score=32.82  Aligned_cols=46  Identities=17%  Similarity=0.175  Sum_probs=35.1

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHc----CCCCCCHHHHHHHHHHhCccc
Q psy6501          43 AKGWSQKDLATKINEKPQIVNDYEG----GRGIPNQAIIGKMERALGIRL   88 (174)
Q Consensus        43 ~~gltq~eLA~~igvs~~~is~~E~----G~~~P~~~~l~~la~~L~v~~   88 (174)
                      ..|+|.+|+|+.+|+|.++|..+-.    --+..+...+..++..+|++.
T Consensus        29 ~~g~s~~eIA~~l~is~~tV~~~~~r~~~kl~~~~~~~l~~~~~~~g~~~   78 (79)
T 1x3u_A           29 VAGLPNKSIAYDLDISPRTVEVHRANVMAKMKAKSLPHLVRMALAGGFGP   78 (79)
T ss_dssp             TTTCCHHHHHHHTTSCHHHHHHHHHHHHHHTTCCSHHHHHHHHHHHTCCC
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhCCCC
Confidence            6899999999999999999987653    225566677777776666543

>3gp4_A Transcriptional regulator, MERR family; structural genomics, DNA-BI transcription regulator, PSI-2; 1.85A {Listeria monocytogenes str}

Probab=94.04  E-value=0.14  Score=36.41  Aligned_cols=23  Identities=17%  Similarity=0.234  Sum_probs=21.3

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          45 GWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        45 gltq~eLA~~igvs~~~is~~E~   67 (174)
                      .||..|+|+.+|||..||.-||.
T Consensus         2 ~~~I~e~A~~~gvs~~tLR~Ye~   24 (142)
T 3gp4_A            2 SLNIKEASEKSGVSADTIRYYER   24 (142)
T ss_dssp             CBCHHHHHHHHTSCHHHHHHHHH
T ss_pred             CCcHHHHHHHHCcCHHHHHHHHH
Confidence            47899999999999999999994

>3frw_A Putative Trp repressor protein; structural genomics, APC21159, PSI-2, P structure initiative; 2.05A {Ruminococcus obeum atcc 29174} PDB: 3g1c_A

Probab=94.01  E-value=0.13  Score=34.91  Aligned_cols=36  Identities=8%  Similarity=0.142  Sum_probs=28.4

Q ss_pred             HHHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          32 DLAKLLMQGRQ-AKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        32 ~ig~~ik~~R~-~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      .+++|++-++. ..|+|+.++|+.+|+|..||+++=+
T Consensus        44 alaqR~~Ia~lL~~G~SyreIa~~tG~StaTIsRv~r   80 (107)
T 3frw_A           44 SLSQRFEVAKMLTDKRTYLDISEKTGASTATISRVNR   80 (107)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHCccHHHHHHHHH
Confidence            46666655544 4789999999999999999998643

>3l1p_A POU domain, class 5, transcription factor 1; POU, transcription factor DNA complex, pore, stem cells; HET: DNA; 2.80A {Mus musculus} PDB: 1ocp_A

Probab=94.00  E-value=0.25  Score=35.57  Aligned_cols=54  Identities=22%  Similarity=0.273  Sum_probs=42.4

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHhC------CCHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATKIN------EKPQIVNDYEGGRGIPNQAIIGKMERALG   85 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~ig------vs~~~is~~E~G~~~P~~~~l~~la~~L~   85 (174)
                      .+.|+..+|.-|-..|+||.+++..+|      .|+++|+++|+-.-  +...+.+|--.|.
T Consensus        12 l~~fa~~fk~~ri~lg~tq~~vg~al~~l~G~~~Sqtti~rfE~l~l--s~~nm~kLkPlL~   71 (155)
T 3l1p_A           12 LEQFAKLLKQKRITLGYTQADVGLTLGVLFGKVFSQTTISRFEALQL--SLKNMSKLRPLLE   71 (155)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHHHHHSCCCCHHHHHHHHTTCS--CHHHHHHHHHHHH
T ss_pred             HHHHHHHHHhhhheecccHHHHHHHHHhhcCcccccccccccccccC--ChhhHhhcchHHH
Confidence            348999999999999999999888753      88999999997544  5556556555544

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

Probab=93.97  E-value=0.11  Score=36.01  Aligned_cols=38  Identities=8%  Similarity=0.202  Sum_probs=29.5

Q ss_pred             HHHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHcCC
Q psy6501          32 DLAKLLMQGRQ-AKGWSQKDLATKINEKPQIVNDYEGGR   69 (174)
Q Consensus        32 ~ig~~ik~~R~-~~gltq~eLA~~igvs~~~is~~E~G~   69 (174)
                      .+++|++-++. ..|+|+.|+|+.+|+|..||++.-+--
T Consensus        61 aLs~R~eV~klL~~G~syreIA~~~g~S~aTIsRv~r~L   99 (119)
T 3kor_A           61 SLSQRLQVAKMIKQGYTYATIEQESGASTATISRVKRSL   99 (119)
T ss_dssp             HHHHHHHHHHHHHHTCCHHHHHHHHCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            56666554443 478999999999999999999876543

>2w48_A Sorbitol operon regulator; SORC, activator, repressor, DNA-binding, transcription, transcription regulator, transcription regulation; 3.20A {Klebsiella pneumoniae}

Probab=93.84  E-value=0.086  Score=42.16  Aligned_cols=37  Identities=11%  Similarity=0.069  Sum_probs=32.7

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ...+-.++..+....++||.|||+++|||+.||++.-
T Consensus         6 ~~~~~~~ia~l~~~~~~~~~ela~~l~vS~~tIrRdL   42 (315)
T 2w48_A            6 DIRLIVKIAQLYYEQDMTQAQIARELGIYRTTISRLL   42 (315)
T ss_dssp             HHHHHHHHHHHHHTSCCCHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHH
Confidence            3456678999999999999999999999999999874

>1wh8_A CUT-like 2, homeobox protein CUX-2; CUT domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, transcription; NMR {Homo sapiens} SCOP: a.35.1.7

Probab=93.75  E-value=0.2  Score=34.20  Aligned_cols=58  Identities=9%  Similarity=0.060  Sum_probs=46.3

Q ss_pred             CccccccccchhhcccccchHHHHHHHHHHHHHcCCCHHHHHH-HhCCCHHHHHHHHcCC
Q psy6501          11 TKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLAT-KINEKPQIVNDYEGGR   69 (174)
Q Consensus        11 ~~~~~~~~~~~~~~~~~~~~~~ig~~ik~~R~~~gltq~eLA~-~igvs~~~is~~E~G~   69 (174)
                      ..++.++|+... +...--...|..+|++..+..++||+-+|+ -+|.++.+||++-+--
T Consensus        11 ~~~~~~~qe~~~-~~~~lDTk~I~~~ikewL~~~~isQ~~FA~~ILgrsQgtlSdlL~~P   69 (111)
T 1wh8_A           11 SQAPGGIQEIVA-MSPELDTYSITKRVKEVLTDNNLGQRLFGESILGLTQGSVSDLLSRP   69 (111)
T ss_dssp             CCCCCCHHHHHH-HCCCCCHHHHHHHHHHHHHHTTCCHHHHHHHTTCCCHHHHHHHHHSC
T ss_pred             CcccccHHHHHh-ccccCCHHHHHHHHHHHHHHCCCcHHHHHHHHhccCcCcHHHHHcCC
Confidence            567788887632 222333688999999999999999999999 6799999999987644

>3gpv_A Transcriptional regulator, MERR family; protein structure initiative II(PSI II), NYSGXRC, structural genomics; 1.90A {Bacillus thuringiensis serovarkonkukian}

Probab=93.74  E-value=0.096  Score=37.48  Aligned_cols=23  Identities=9%  Similarity=0.070  Sum_probs=21.7

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          45 GWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        45 gltq~eLA~~igvs~~~is~~E~   67 (174)
                      -+|..|+|+.+|||.+||.-||.
T Consensus        16 ~~~I~evA~~~gvs~~tLR~Ye~   38 (148)
T 3gpv_A           16 YYTIGQVAKMQHLTISQIRYYDK   38 (148)
T ss_dssp             CBCHHHHHHHTTCCHHHHHHHHH
T ss_pred             ceeHHHHHHHHCcCHHHHHHHHH
Confidence            58999999999999999999994

>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=93.73  E-value=0.19  Score=27.76  Aligned_cols=26  Identities=15%  Similarity=0.187  Sum_probs=23.2

Q ss_pred             hcCCCHHHHHHHhCCChhHHHHHhcC
Q psy6501         133 AKGWSQKDLATKINEKPQIVNDYEGG  158 (174)
Q Consensus       133 ~~glsq~ela~~lg~~~s~i~~~E~G  158 (174)
                      ..|++..++|+.+|+++++|.+|-..
T Consensus        19 ~~g~s~~~IA~~lgis~~Tv~~~~~~   44 (51)
T 1tc3_C           19 LLNVSLHEMSRKISRSRHCIRVYLKD   44 (51)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHHC
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHhh
Confidence            57899999999999999999988653

>2p7v_B Sigma-70, RNA polymerase sigma factor RPOD; RSD, regulator of sigma 70, sigma 70 domain 4, transcription, regulation, helix-turn-helix; 2.60A {Escherichia coli} SCOP: a.4.13.2

Probab=93.66  E-value=0.086  Score=32.16  Aligned_cols=25  Identities=4%  Similarity=0.258  Sum_probs=22.7

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          43 AKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        43 ~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      ..|+|.+|+|+.+|+|.++|..+..
T Consensus        23 ~~g~s~~eIA~~lgis~~tV~~~~~   47 (68)
T 2p7v_B           23 NTDYTLEEVGKQFDVTRERIRQIEA   47 (68)
T ss_dssp             SSCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            4699999999999999999999863

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

Probab=93.63  E-value=0.051  Score=34.80  Aligned_cols=35  Identities=9%  Similarity=0.075  Sum_probs=29.3

Q ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHH
Q psy6501          31 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        31 ~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~   65 (174)
                      |.+-+-+..+++...+|..|||+.++||..||.+-
T Consensus         2 m~L~~Il~~L~~~g~vsv~eLa~~l~VS~~TIRrd   36 (78)
T 1xn7_A            2 ASLIQVRDLLALRGRMEAAQISQTLNTPQPMINAM   36 (78)
T ss_dssp             CCHHHHHHHHHHSCSBCHHHHHHHTTCCHHHHHHH
T ss_pred             chHHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHH
Confidence            44556677788888899999999999999999864

>3hug_A RNA polymerase sigma factor; ECF sigma factor, zinc binding anti-sigma factor, oxidative transcription regulation; 2.35A {Mycobacterium tuberculosis}

Probab=93.62  E-value=0.11  Score=33.73  Aligned_cols=31  Identities=23%  Similarity=0.356  Sum_probs=26.6

Q ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          37 LMQGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        37 ik~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      +-.+|-..|+|.+|+|+.+|+|.++|..+-.
T Consensus        45 vl~l~~~~g~s~~eIA~~lgis~~tV~~~l~   75 (92)
T 3hug_A           45 VIQRSYYRGWSTAQIATDLGIAEGTVKSRLH   75 (92)
T ss_dssp             HHHHHHTSCCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            4456678899999999999999999998763

>2x48_A CAG38821; archeal virus, viral protein; 2.60A {Sulfolobus islandicus rod-shaped virusorganism_taxid}

Probab=93.50  E-value=0.19  Score=29.05  Aligned_cols=32  Identities=13%  Similarity=0.221  Sum_probs=25.8

Q ss_pred             HHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         125 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       125 ~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      ..+... ...|+|+.++|+.+|+++++|+.|..
T Consensus        22 ~~i~~l-~~~g~s~~eIA~~lgis~~TV~~~l~   53 (55)
T 2x48_A           22 SVAHEL-AKMGYTVQQIANALGVSERKVRRYLE   53 (55)
T ss_dssp             HHHHHH-HHTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            344444 36899999999999999999998864

>1ku3_A Sigma factor SIGA; helix-turn-helix, transcription; 1.80A {Thermus aquaticus} SCOP: a.4.13.2 PDB: 1ku7_A 1rio_H 3n97_A*

Probab=93.47  E-value=0.13  Score=31.79  Aligned_cols=31  Identities=6%  Similarity=0.223  Sum_probs=25.7

Q ss_pred             HHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          37 LMQGRQA----KGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        37 ik~~R~~----~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      |-.+|-.    .|+|.+|+|+.+|+|.++|..+..
T Consensus        18 il~l~~~l~~~~~~s~~eIA~~l~is~~tV~~~~~   52 (73)
T 1ku3_A           18 VLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIEN   52 (73)
T ss_dssp             HHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHhcccCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            3344554    799999999999999999999874

>1wh6_A CUT-like 2, homeobox protein CUX-2; CUT domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, transcription; NMR {Homo sapiens} SCOP: a.35.1.7

Probab=93.44  E-value=0.1  Score=35.11  Aligned_cols=61  Identities=15%  Similarity=0.096  Sum_probs=47.9

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHH-HhCCCHHHHHHHHcCCCC---CC---HHHHHHHHHHhCccccc
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLAT-KINEKPQIVNDYEGGRGI---PN---QAIIGKMERALGIRLRV   90 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~-~igvs~~~is~~E~G~~~---P~---~~~l~~la~~L~v~~~~   90 (174)
                      ...|..+|++..+..++||+-+|+ -+|.++.++|++-+.-..   -+   -+...++-..|+.+.+.
T Consensus        19 Tk~I~~~ike~L~~~~isQ~~FA~~ILgrsqgtlSdlL~~PKpW~~L~~~Gre~fiRM~nWL~l~e~q   86 (101)
T 1wh6_A           19 TLELTRQVKEKLAKNGICQRIFGEKVLGLSQGSVSDMLSRPKPWSKLTQKGREPFIRMQLWLSDQLGQ   86 (101)
T ss_dssp             HHHHHHHHHHHHHTTTCCHHHHHHHTTCCCHHHHHHHHHSCCCTTTCCHHHHHHHHHHHHHHHHTTCS
T ss_pred             HHHHHHHHHHHHHHcCCcHHHHHHHHHccCcCcHHHHhcCCCCHHHHhHHhHHHHHHHHHHhCCcHHH
Confidence            578999999999999999999999 679999999999875522   12   35556777777766543

>2jpc_A SSRB; DNA binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium}

Probab=93.36  E-value=0.1  Score=30.80  Aligned_cols=25  Identities=12%  Similarity=0.292  Sum_probs=22.5

Q ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          42 QAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        42 ~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      -..|+|.+|+|+.+|+|.+||+.+-
T Consensus        10 ~~~g~s~~eIA~~l~is~~tV~~~~   34 (61)
T 2jpc_A           10 IDEGYTNHGISEKLHISIKTVETHR   34 (61)
T ss_dssp             HHTSCCSHHHHHHTCSCHHHHHHHH
T ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHH
Confidence            4789999999999999999998764

>2jml_A DNA binding domain/transcriptional regulator; anti-repressor, MERR, carotenogenesis; HET: DNA; NMR {Myxococcus xanthus}

Probab=93.10  E-value=0.047  Score=34.83  Aligned_cols=23  Identities=9%  Similarity=0.138  Sum_probs=21.5

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          45 GWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        45 gltq~eLA~~igvs~~~is~~E~   67 (174)
                      -+|..|+|+.+|||.+||..||.
T Consensus         5 ~~~i~e~A~~~gvs~~tlR~ye~   27 (81)
T 2jml_A            5 TLRIRTIARMTGIREATLRAWER   27 (81)
T ss_dssp             CEEHHHHHHTTSTTHHHHHHHHH
T ss_pred             cccHHHHHHHHCcCHHHHHHHHH
Confidence            47899999999999999999997

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

Probab=93.00  E-value=0.15  Score=32.22  Aligned_cols=30  Identities=13%  Similarity=0.063  Sum_probs=24.0

Q ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          37 LMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        37 ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      |..+.....+|..|||+.+|+|+++|+++-
T Consensus         6 l~~L~~~~~~s~~eLa~~lgvs~~tv~r~L   35 (81)
T 2htj_A            6 LEFLNRHNGGKTAEIAEALAVTDYQARYYL   35 (81)
T ss_dssp             HHHHHHSCCCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHcCCCCHHHHHHHHCcCHHHHHHHH
Confidence            334445567999999999999999998764

>2ox6_A Hypothetical protein SO3848; structural genomics, PSI-2, MCSG, Pro structure initiative; 1.70A {Shewanella oneidensis} SCOP: a.35.1.6

Probab=92.99  E-value=0.49  Score=33.01  Aligned_cols=40  Identities=15%  Similarity=0.058  Sum_probs=36.0

Q ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCH
Q psy6501          35 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQ   74 (174)
Q Consensus        35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~   74 (174)
                      --|+.+|...|+|..++|+..+.|..-|-.||.|....+.
T Consensus        10 ie~~ylr~slgl~~aqv~~l~k~se~dv~aweage~~~~~   49 (166)
T 2ox6_A           10 IEMSYLRQSLSLSAAQVGQLTNHSEAEVLAWENAETQAPE   49 (166)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTSSCCCH
T ss_pred             HhHHHHHHHcCCCHHHHHHHhccCHHHhhhhhhcCCcCcc
Confidence            3578999999999999999999999999999999966553

>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=92.95  E-value=0.2  Score=32.13  Aligned_cols=29  Identities=17%  Similarity=0.145  Sum_probs=22.9

Q ss_pred             HHHHHHHc---CCCHHHHHHHhCCCHHHHHHH
Q psy6501          37 LMQGRQAK---GWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        37 ik~~R~~~---gltq~eLA~~igvs~~~is~~   65 (174)
                      |..+++.-   .+|..|||+.+|+|+++|.+.
T Consensus        16 L~~L~~~~pg~~~t~~eLA~~Lgvsr~tV~~~   47 (81)
T 1qbj_A           16 LKFLEELGEGKATTAHDLSGKLGTPKKEINRV   47 (81)
T ss_dssp             HHHHHHHCTTCCBCHHHHHHHHTCCHHHHHHH
T ss_pred             HHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHH
Confidence            34444444   599999999999999998865

>2dk5_A DNA-directed RNA polymerase III 39 kDa polypeptide; structural genomics, winged helix domain, NPPSFA; NMR {Homo sapiens} SCOP: a.4.5.85

Probab=92.90  E-value=0.081  Score=34.82  Aligned_cols=32  Identities=19%  Similarity=0.061  Sum_probs=26.2

Q ss_pred             HHHHHHHH--HcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          35 KLLMQGRQ--AKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        35 ~~ik~~R~--~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ..++.+.+  ..|++|+|||+++++++++|+.+-
T Consensus        24 ~Vl~~I~~~g~~gi~qkeLa~~~~l~~~tvt~iL   57 (91)
T 2dk5_A           24 LVYQIIEDAGNKGIWSRDVRYKSNLPLTEINKIL   57 (91)
T ss_dssp             HHHHHHHHHCTTCEEHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHcCCCCcCHHHHHHHHCCCHHHHHHHH
Confidence            34566666  459999999999999999998764

>1wiz_A DNA-binding protein SATB2; helix bundle, KIAA1034 protein, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: a.35.1.7

Probab=92.80  E-value=0.39  Score=32.19  Aligned_cols=41  Identities=12%  Similarity=0.094  Sum_probs=35.8

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHH-HhCCCHHHHHHHHcCCC
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLAT-KINEKPQIVNDYEGGRG   70 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~-~igvs~~~is~~E~G~~   70 (174)
                      ...|..+|++-.+..++||.-||+ -+|.++.++|.+-+.-+
T Consensus        19 Tk~I~~~Ik~~Lk~~~isQ~~FA~~VL~rsQgtLs~lLr~P~   60 (101)
T 1wiz_A           19 SPDIYQQVRDELKRASVSQAVFARVAFNRTQGLLSEILRKEE   60 (101)
T ss_dssp             CTTHHHHHHHHHHHHTCCHHHHHHHHHSCCHHHHHHHHHTCC
T ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHHHHHhhhHHHHHHcCCC
Confidence            357899999999999999999999 57999999999976543

>2o20_A Catabolite control protein A; CCPA, transcriptional regulator, helix-turn-helix, transcrip; 1.90A {Lactococcus lactis}

Probab=92.68  E-value=0.021  Score=45.35  Aligned_cols=47  Identities=13%  Similarity=0.020  Sum_probs=0.0

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCccccc
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYEGGRGIPNQAI---IGKMERALGIRLRV   90 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~---l~~la~~L~v~~~~   90 (174)
                      ...|.+|+|+++|||.+|||+.-||....+.++   +.+.++.||-.++.
T Consensus         4 ~~~ti~diA~~agVS~~TVSrvln~~~~vs~~tr~rV~~~a~~lgY~pn~   53 (332)
T 2o20_A            4 STTTIYDVARVAGVSMATVSRVVNGNANVKEKTRQKVLEAIAELDYRPNA   53 (332)
T ss_dssp             --------------------------------------------------
T ss_pred             CCCcHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHCCCcCH
Confidence            357999999999999999999999986555554   45566778866544

>1tty_A Sigma-A, RNA polymerase sigma factor RPOD; helix-turn-helix, transcription; NMR {Thermotoga maritima} SCOP: a.4.13.2

Probab=92.67  E-value=0.19  Score=32.29  Aligned_cols=31  Identities=13%  Similarity=0.147  Sum_probs=25.6

Q ss_pred             HHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          37 LMQGRQA----KGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        37 ik~~R~~----~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      |-.+|--    .|+|.+|+|+.+|+|.++|..+..
T Consensus        26 vl~l~~~l~~~~~~s~~EIA~~lgis~~tV~~~~~   60 (87)
T 1tty_A           26 VLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEV   60 (87)
T ss_dssp             HHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            3344554    799999999999999999999864

>2ao9_A Phage protein; structural genomics, nine-fold NCS., PSI, protein structure initiative, midwest center for structural genomics, MCSG, U function; 1.90A {Bacillus cereus} SCOP: a.4.1.17

Probab=92.58  E-value=0.16  Score=36.85  Aligned_cols=37  Identities=8%  Similarity=0.151  Sum_probs=30.6

Q ss_pred             CCCHHHHHHHhCCChhHHHHHhcCCCCCCH-HHHHHHHhh
Q psy6501         135 GWSQKDLATKINEKPQIVNDYEGGRGIPNQ-AIIGKMERA  173 (174)
Q Consensus       135 glsq~ela~~lg~~~s~i~~~E~G~~~P~~-~~l~~i~~~  173 (174)
                      ++|+.++|+.+|++.+++.+|...  .|.. +.+.+++..
T Consensus        48 ~lTv~eIA~~LGIS~~TLyrW~k~--~p~~~~~l~~vad~   85 (155)
T 2ao9_A           48 KRTQDEMANELGINRTTLWEWRTK--NQDFIAFKSEVADS   85 (155)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHHH--CHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHHc--CcchHHHHHHHHHH
Confidence            799999999999999999999995  5663 666666543

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

Probab=92.40  E-value=0.75  Score=30.62  Aligned_cols=45  Identities=11%  Similarity=0.065  Sum_probs=31.1

Q ss_pred             HHHHHHHHHH--cCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccccccc
Q psy6501          34 AKLLMQGRQA--KGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNA   92 (174)
Q Consensus        34 g~~ik~~R~~--~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~   92 (174)
                      ...+..++..  ..+|.++||+.+|+|++++++.              +.+.+|+++..++
T Consensus        10 ~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~--------------fk~~~G~s~~~~~   56 (113)
T 3oio_A           10 TEAVSLMEANIEEPLSTDDIAYYVGVSRRQLERL--------------FKQYLGTVPSKYY   56 (113)
T ss_dssp             HHHHHHHHTCSSSCCCHHHHHHHHTSCHHHHHHH--------------HHHHTSSCHHHHH
T ss_pred             HHHHHHHHhhhcCCCCHHHHHHHHCcCHHHHHHH--------------HHHHHCcCHHHHH
Confidence            3334444442  4699999999999999999886              4556666655443

>1hlv_A CENP-B, major centromere autoantigen B; helix-turn-helix, protein-DNA complex, riken structural genomics/proteomics initiative, RSGI; 2.50A {Homo sapiens} SCOP: a.4.1.7 a.4.1.7 PDB: 1bw6_A

Probab=92.31  E-value=0.23  Score=34.02  Aligned_cols=42  Identities=10%  Similarity=0.186  Sum_probs=28.4

Q ss_pred             chHHHHHHHHHHHHHcC-CCHHHHHHHhCCCHHHHHHHHcCCC
Q psy6501          29 VPLDLAKLLMQGRQAKG-WSQKDLATKINEKPQIVNDYEGGRG   70 (174)
Q Consensus        29 ~~~~ig~~ik~~R~~~g-ltq~eLA~~igvs~~~is~~E~G~~   70 (174)
                      +..++=..+..+-...| .++.++|+.+||++++|++|-++..
T Consensus         8 ~t~e~K~~iv~~~~~~g~~~~~~~A~~~gvs~stl~~~~~~~~   50 (131)
T 1hlv_A            8 LTFREKSRIIQEVEENPDLRKGEIARRFNIPPSTLSTILKNKR   50 (131)
T ss_dssp             CCHHHHHHHHHHHHHCTTSCHHHHHHHHTCCHHHHHHHHHTHH
T ss_pred             CCHHHHHHHHHHHHHCCCCcHHHHHHHhCCCHHHHHHHHhchh
Confidence            34444333433332445 4566999999999999999988754

>1fse_A GERE; helix-turn-helix DNA-binding protein transcriptional regulat transcription; 2.05A {Bacillus subtilis} SCOP: a.4.6.2

Probab=92.24  E-value=0.13  Score=31.43  Aligned_cols=24  Identities=13%  Similarity=0.169  Sum_probs=22.0

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          43 AKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        43 ~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ..|+|.+|+|+.+|+|+++|+.+-
T Consensus        24 ~~g~s~~eIA~~l~is~~tV~~~~   47 (74)
T 1fse_A           24 VQDKTTKEIASELFISEKTVRNHI   47 (74)
T ss_dssp             TTTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHH
Confidence            689999999999999999998764

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

Probab=92.18  E-value=0.12  Score=33.43  Aligned_cols=35  Identities=14%  Similarity=0.155  Sum_probs=27.4

Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          32 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        32 ~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ....+|-.+....|+|-.|||+.+|+|+++|.+.-
T Consensus        17 ~~~~~IL~lL~~~g~sa~eLAk~LgiSk~aVr~~L   51 (82)
T 1oyi_A           17 EIVCEAIKTIGIEGATAAQLTRQLNMEKREVNKAL   51 (82)
T ss_dssp             HHHHHHHHHHSSSTEEHHHHHHHSSSCHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHH
Confidence            44555555555788999999999999999988753

>1s7o_A Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SPS1042/SPYM18_1152; putative DNA binding protein, structural genomics; 2.31A {Streptococcus pyogenes serotype M3} SCOP: a.4.13.3

Probab=92.14  E-value=0.25  Score=33.66  Aligned_cols=31  Identities=19%  Similarity=0.161  Sum_probs=26.4

Q ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          37 LMQGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        37 ik~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      +-.++-..|+|++|+|+.+|+|++||..+-.
T Consensus        30 vl~l~y~~g~s~~EIA~~lgiS~~tV~~~l~   60 (113)
T 1s7o_A           30 YIELYYADDYSLAEIADEFGVSRQAVYDNIK   60 (113)
T ss_dssp             HHHHHHHTCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3445667899999999999999999998864

>1je8_A Nitrate/nitrite response regulator protein NARL; protein-DNA complex, two-component response regulator, helix-turn-helix, DNA bending; 2.12A {Escherichia coli} SCOP: a.4.6.2 PDB: 1zg1_A 1zg5_A

Probab=92.02  E-value=0.23  Score=31.53  Aligned_cols=24  Identities=21%  Similarity=0.245  Sum_probs=22.1

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          43 AKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        43 ~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ..|+|.+|+|+.+|+|.+||..+-
T Consensus        34 ~~g~s~~eIA~~l~is~~tV~~~l   57 (82)
T 1je8_A           34 AQGLPNKMIARRLDITESTVKVHV   57 (82)
T ss_dssp             TTTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHH
Confidence            689999999999999999998764

>3c57_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 1.70A {Mycobacterium tuberculosis} PDB: 1zlk_A 1zlj_A

Probab=91.97  E-value=0.26  Score=32.25  Aligned_cols=24  Identities=21%  Similarity=0.436  Sum_probs=22.4

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          43 AKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        43 ~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ..|+|.+|+|+.+|+|.+||..+-
T Consensus        40 ~~g~s~~eIA~~l~is~~tV~~~l   63 (95)
T 3c57_A           40 SEGLTNKQIADRMFLAEKTVKNYV   63 (95)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHH
Confidence            899999999999999999998764

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

Probab=91.87  E-value=0.066  Score=35.04  Aligned_cols=34  Identities=9%  Similarity=0.132  Sum_probs=28.1

Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHH
Q psy6501          32 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        32 ~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~   65 (174)
                      .+-+-+..+++...+|..|||+.++||..||.+.
T Consensus         3 ~L~~Il~~L~~~g~vsv~eLA~~l~VS~~TIRrD   36 (87)
T 2k02_A            3 SLMEVRDMLALQGRMEAKQLSARLQTPQPLIDAM   36 (87)
T ss_dssp             CTHHHHHHHHHSCSEEHHHHHHHTTCCHHHHHHH
T ss_pred             hHHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHH
Confidence            4455666777888899999999999999998764

>1z4h_A TORI, TOR inhibition protein; winged helix, reverse turn, protein binding, DNA binding protein; NMR {Escherichia coli}

Probab=91.86  E-value=0.06  Score=33.01  Aligned_cols=28  Identities=11%  Similarity=0.061  Sum_probs=24.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCC
Q psy6501          46 WSQKDLATKINEKPQIVNDYEGGRGIPN   73 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~G~~~P~   73 (174)
                      ++.+|+|+.+|+|++||.+|.+....|.
T Consensus        11 l~~~eva~~lgvsrstiy~~~~~g~fP~   38 (66)
T 1z4h_A           11 VDLKFIMADTGFGKTFIYDRIKSGDLPK   38 (66)
T ss_dssp             ECHHHHHHHHSSCHHHHHHHHHHHHCCC
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHCCCCCC
Confidence            6889999999999999999997655554

>3h5o_A Transcriptional regulator GNTR; transcription regulator, GNTR,chromobacterium violaceum, PSI, SGX, DNA-binding; 2.30A {Chromobacterium violaceum}

Probab=91.85  E-value=0.03  Score=44.53  Aligned_cols=47  Identities=13%  Similarity=0.032  Sum_probs=0.0

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCccccc
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYEGGRGIPNQAI---IGKMERALGIRLRV   90 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~---l~~la~~L~v~~~~   90 (174)
                      +..|.+|+|+++|||.+|||+.-||....+.++   +.+.++.||..+..
T Consensus         3 ~~~ti~diA~~agVS~~TVSr~Ln~~~~vs~~tr~rV~~~~~~lgY~pn~   52 (339)
T 3h5o_A            3 LGVTMHDVAKAAGVSAITVSRVLNQPQQVSEQLREKVMQAVDALAYVPSR   52 (339)
T ss_dssp             --------------------------------------------------
T ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHhCCCcCH
Confidence            357999999999999999999999986555544   44566667766553

>3mky_B Protein SOPB; partition, F plasmid, centromere, DNA binding protein- complex; HET: DNA; 2.86A {Escherichia coli} PDB: 3mkw_B* 3mkz_A*

Probab=91.85  E-value=0.29  Score=36.53  Aligned_cols=42  Identities=14%  Similarity=0.103  Sum_probs=33.1

Q ss_pred             HHHHHHHHHHHHHc-CCCHHHHHHHhCCCHHHHHHHHcCCCCC
Q psy6501          31 LDLAKLLMQGRQAK-GWSQKDLATKINEKPQIVNDYEGGRGIP   72 (174)
Q Consensus        31 ~~ig~~ik~~R~~~-gltq~eLA~~igvs~~~is~~E~G~~~P   72 (174)
                      .+.|.+...+.... ..+|++||+.+|+|++.||++-+--+.|
T Consensus        27 yErg~~y~r~L~~g~~~~Q~~lA~~~giS~a~VSR~L~~A~LP   69 (189)
T 3mky_B           27 YERGQRYASRLQNEFAGNISALADAENISRKIITRCINTAKLP   69 (189)
T ss_dssp             HHHHHHHHHHHHTTTTTCHHHHHHHHTSCHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHhcCcccCHHHHHHHHCCCHHHHHHHHHHhcCC
Confidence            56777776666553 7899999999999999999998644444

>2dg6_A Putative transcriptional regulator; winged-helix motif, MERR family, gene regulation; 2.20A {Streptomyces coelicolor}

Probab=91.63  E-value=0.86  Score=34.77  Aligned_cols=24  Identities=13%  Similarity=0.124  Sum_probs=21.4

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCC
Q psy6501          46 WSQKDLATKINEKPQIVNDYEGGR   69 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~G~   69 (174)
                      ||..|+|+.+|||.+||.-||+-.
T Consensus         1 ~~IgevA~~~Gvs~~TLRyYE~~G   24 (222)
T 2dg6_A            1 MRLADLSKRSGVSTATIKYYLREG   24 (222)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHHT
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCC
Confidence            678999999999999999999643

>3e7l_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+ ATPase, response regulator, transcriptional activator, ATP-binding; 2.25A {Aquifex aeolicus} PDB: 4fth_A

Probab=91.60  E-value=0.38  Score=28.97  Aligned_cols=34  Identities=9%  Similarity=-0.019  Sum_probs=29.5

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      -..|..+.+..+.++.+.|+.+|||++++.+.-+
T Consensus        21 ~~~i~~aL~~~~gn~~~aA~~LGisr~tL~rklk   54 (63)
T 3e7l_A           21 KIFIEEKLREYDYDLKRTAEEIGIDLSNLYRKIK   54 (63)
T ss_dssp             HHHHHHHHHHTTTCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHCcCHHHHHHHHH
Confidence            4568888899999999999999999999987643

>1q06_A Transcriptional regulator CUER; MERR family transcriptional regulator, copper efflux regulator; 2.07A {Escherichia coli} SCOP: a.6.1.3 PDB: 1q05_A 1q07_A

Probab=91.53  E-value=0.31  Score=34.18  Aligned_cols=23  Identities=17%  Similarity=0.170  Sum_probs=20.9

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcC
Q psy6501          46 WSQKDLATKINEKPQIVNDYEGG   68 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~G   68 (174)
                      ||..|+|+.+|||..||..||.-
T Consensus         1 ~~I~e~A~~~gvs~~tLR~ye~~   23 (135)
T 1q06_A            1 MNISDVAKITGLTSKAIRFYEEK   23 (135)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHT
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC
Confidence            68899999999999999999853

>3hh0_A Transcriptional regulator, MERR family; protein structure initiative II(PSI II), NYSGXRC, 11183J, structural genomics; 2.67A {Bacillus cereus atcc 14579}

Probab=91.49  E-value=0.27  Score=35.02  Aligned_cols=24  Identities=13%  Similarity=0.267  Sum_probs=22.1

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      ..+|..|+|+.+|||.+||.-||.
T Consensus         3 ~~~tI~evA~~~Gvs~~tLR~ye~   26 (146)
T 3hh0_A            3 LAWLISEFASVGDVTVRALRYYDK   26 (146)
T ss_dssp             CCBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCcHHHHHHHHCcCHHHHHHHHH
Confidence            358999999999999999999994

>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=91.38  E-value=0.29  Score=31.78  Aligned_cols=34  Identities=12%  Similarity=0.137  Sum_probs=27.4

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        33 ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      -..-|..+....++|+.+||+.+|+++++|++.-
T Consensus        22 ~~~il~~l~~~~~~s~~ela~~l~is~~tv~~~l   55 (109)
T 1sfx_A           22 DVRIYSLLLERGGMRVSEIARELDLSARFVRDRL   55 (109)
T ss_dssp             HHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHH
Confidence            3344556666788999999999999999998764

>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=91.26  E-value=0.15  Score=34.23  Aligned_cols=37  Identities=11%  Similarity=0.141  Sum_probs=26.8

Q ss_pred             cC-CCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHH
Q psy6501         134 KG-WSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKM  170 (174)
Q Consensus       134 ~g-lsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i  170 (174)
                      .| +||.++|+.+|+|.++|+++.+--.-.+..+-..|
T Consensus        56 ~ge~TQREIA~~lGiS~stISRi~r~L~~l~~~~k~~l   93 (101)
T 1jhg_A           56 RGEMSQRELKNELGAGIATITRGSNSLKAAPVELRQWL   93 (101)
T ss_dssp             HCCSCHHHHHHHHCCCHHHHHHHHHHHHHSCHHHHHHH
T ss_pred             cCCcCHHHHHHHHCCChhhhhHHHHHHHHccHHHHHHH
Confidence            45 99999999999999999998553333344443333

>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=91.16  E-value=0.36  Score=26.90  Aligned_cols=27  Identities=19%  Similarity=0.188  Sum_probs=23.6

Q ss_pred             hcCCCHHHHHHHhCCChhHHHHHhcCC
Q psy6501         133 AKGWSQKDLATKINEKPQIVNDYEGGR  159 (174)
Q Consensus       133 ~~glsq~ela~~lg~~~s~i~~~E~G~  159 (174)
                      ..|++..++|+.+|+++++|.+|-...
T Consensus        19 ~~g~s~~~ia~~lgvs~~Tv~r~l~~~   45 (52)
T 1jko_C           19 EKGHPRQQLAIIFGIGVSTLYRYFPAS   45 (52)
T ss_dssp             HTTCCHHHHHHTTSCCHHHHHHHSCTT
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHHHc
Confidence            467999999999999999999987643

>2rn7_A IS629 ORFA; helix, all alpha, unknown function, structural genomics, PSI-2, protein structure initiative; NMR {Shigella flexneri}

Probab=91.16  E-value=0.17  Score=33.64  Aligned_cols=23  Identities=17%  Similarity=0.130  Sum_probs=20.9

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          45 GWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        45 gltq~eLA~~igvs~~~is~~E~   67 (174)
                      |.|..++|..+|||+++|.+|-+
T Consensus        30 g~s~~~va~~~gIs~~tl~~W~~   52 (108)
T 2rn7_A           30 WATICSIAPKIGCTPETLRVWVR   52 (108)
T ss_dssp             HHHHHHHHHHHTSCHHHHHHHHH
T ss_pred             cccHHHHHHHHCcCHHHHHHHHH
Confidence            38999999999999999999964

>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=90.99  E-value=0.44  Score=32.23  Aligned_cols=54  Identities=13%  Similarity=0.141  Sum_probs=39.9

Q ss_pred             HHHHHHHHH-HHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH-HHHHHhC
Q psy6501          32 DLAKLLMQG-RQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIG-KMERALG   85 (174)
Q Consensus        32 ~ig~~ik~~-R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~-~la~~L~   85 (174)
                      .+++-|-.- ..-..+|..|||+++|||++||.++-+--..-....+. .|+..+.
T Consensus        25 ~ia~yil~~~~~~~~~si~elA~~~~vS~aTv~Rf~kklG~~gf~efk~~l~~~~~   80 (111)
T 2o3f_A           25 KLADYILAHPHXAIESTVNEISALANSSDAAVIRLCXSLGLKGFQDLXMRVAGDLA   80 (111)
T ss_dssp             HHHHHHHHCHHHHHTCCHHHHHHHTTCCHHHHHHHHHHTTCSSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHChHHHHhcCHHHHHHHHCCCHHHHHHHHHHcCCCCHHHHHHHHHHHHH
Confidence            344444433 33468999999999999999999999877777777666 4555553

>3bil_A Probable LACI-family transcriptional regulator; structural genomics, unknown function, PSI-2, protein structure initiative; 2.50A {Corynebacterium glutamicum atcc 13032}

Probab=90.96  E-value=0.042  Score=44.00  Aligned_cols=45  Identities=16%  Similarity=0.118  Sum_probs=0.0

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCccccc
Q psy6501          46 WSQKDLATKINEKPQIVNDYEGGRGIPNQAI---IGKMERALGIRLRV   90 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~G~~~P~~~~---l~~la~~L~v~~~~   90 (174)
                      .|.+|+|+++|||.+|||+.-||....+.++   +.+.++.||..+..
T Consensus         9 ~ti~dvA~~aGVS~~TVSrvLn~~~~Vs~~tr~rV~~aa~~lgY~pn~   56 (348)
T 3bil_A            9 PTLKDVARQAGVSIATASRALADNPAVAASTRERIQQLASDLGYRANA   56 (348)
T ss_dssp             ------------------------------------------------
T ss_pred             CCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCCcCH
Confidence            6999999999999999999999975555544   45566778766543

>3ulq_B Transcriptional regulatory protein COMA; tetratricopeptide repeat, response regulator helix-turn-HELX binding, 3-helix bundle; 2.30A {Bacillus subtilis} PDB: 2krf_A

Probab=90.88  E-value=0.37  Score=31.30  Aligned_cols=23  Identities=13%  Similarity=0.313  Sum_probs=21.4

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E   66 (174)
                      .|+|.+|+|+.+|+|.+||..+-
T Consensus        43 ~G~s~~eIA~~L~iS~~TV~~~~   65 (90)
T 3ulq_B           43 KGFTNQEIADALHLSKRSIEYSL   65 (90)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHH
Confidence            89999999999999999998764

>3jvd_A Transcriptional regulators; structural genomics, PSI-2, sugar binding protein, transcrip regulation, protein structure initiative; 2.30A {Corynebacterium glutamicum}

Probab=90.78  E-value=0.045  Score=43.56  Aligned_cols=47  Identities=13%  Similarity=0.057  Sum_probs=0.0

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCccccc
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYEGGRGIPNQAI---IGKMERALGIRLRV   90 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~---l~~la~~L~v~~~~   90 (174)
                      +..|.+|+|+++|||.+|||+.-||....+.++   +.+.++.||..+..
T Consensus         5 ~~~ti~diA~~agVS~~TVSr~Ln~~~~vs~~tr~rV~~~a~~lgY~pn~   54 (333)
T 3jvd_A            5 AKSSLKEVAELAGVGYATASRALSGKGYVSPQTREKVQAAAKELNYVPNQ   54 (333)
T ss_dssp             --------------------------------------------------
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHCCCcCH
Confidence            457999999999999999999999986555554   44566777776554

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

Probab=90.74  E-value=0.22  Score=32.49  Aligned_cols=31  Identities=16%  Similarity=0.171  Sum_probs=24.8

Q ss_pred             HHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          36 LLMQGRQ-AKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        36 ~ik~~R~-~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      .|..+.. ..++|+.|||+.+|+|+++|+++-
T Consensus        26 ~l~~l~~~~~~~t~~ela~~l~is~~tv~~~l   57 (109)
T 2d1h_A           26 VLLKMVEIEKPITSEELADIFKLSKTTVENSL   57 (109)
T ss_dssp             HHHHHHHHCSCEEHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHH
Confidence            3444444 678999999999999999999864

>1xsv_A Hypothetical UPF0122 protein SAV1236; helix-turn-helix, putative DNA-binding protein, signal recognition particle, unknown function; 1.70A {Staphylococcus aureus subsp} SCOP: a.4.13.3

Probab=90.73  E-value=0.35  Score=32.80  Aligned_cols=31  Identities=19%  Similarity=0.149  Sum_probs=26.1

Q ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          37 LMQGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        37 ik~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      +-.++-..|+|.+|+|+.+|+|.+||..+-.
T Consensus        33 vl~l~~~~g~s~~EIA~~lgiS~~tV~~~l~   63 (113)
T 1xsv_A           33 YLELFYLEDYSLSEIADTFNVSRQAVYDNIR   63 (113)
T ss_dssp             HHHHHHTSCCCHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3345667899999999999999999998764

>3dbi_A Sugar-binding transcriptional regulator, LACI FAM; structural genomics, sugar-binding transcriptional regulator structure initiative, PSI-2; HET: MSE; 2.45A {Escherichia coli K12}

Probab=90.59  E-value=0.048  Score=43.26  Aligned_cols=46  Identities=15%  Similarity=0.117  Sum_probs=0.0

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCH---HHHHHHHHHhCcccccc
Q psy6501          46 WSQKDLATKINEKPQIVNDYEGGRGIPNQ---AIIGKMERALGIRLRVN   91 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~G~~~P~~---~~l~~la~~L~v~~~~l   91 (174)
                      .|.+|+|+.+|||.+|||+.-||....+.   +.+.+.++.||-.++..
T Consensus         4 ~ti~diA~~agVS~~TVSrvln~~~~vs~~tr~rV~~~a~~lgY~pn~~   52 (338)
T 3dbi_A            4 TTMLEVAKRAGVSKATVSRVLSGNGYVSQETKDRVFQAVEESGYRPNLL   52 (338)
T ss_dssp             -------------------------------------------------
T ss_pred             CCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCcCHH
Confidence            58999999999999999999999855444   44556777788766543

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

Probab=90.54  E-value=0.45  Score=33.98  Aligned_cols=31  Identities=13%  Similarity=0.156  Sum_probs=26.2

Q ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHH
Q psy6501          35 KLLMQGRQAKGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~~   65 (174)
                      .-|..+.+...+|..|||+.+|+|++++++.
T Consensus        14 ~il~~L~~~~~~s~~ela~~lg~s~~tv~~~   44 (162)
T 2p5v_A           14 KILQVLQENGRLTNVELSERVALSPSPCLRR   44 (162)
T ss_dssp             HHHHHHHHCTTCCHHHHHHHHTSCHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHH
Confidence            4566667777899999999999999998875

>3e3m_A Transcriptional regulator, LACI family; structural genomics, DNA-binding, plasmid, transcription regulation, PSI-2; 1.60A {Silicibacter pomeroyi}

Probab=90.46  E-value=0.05  Score=43.58  Aligned_cols=49  Identities=10%  Similarity=-0.024  Sum_probs=0.0

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCcccccc
Q psy6501          43 AKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAI---IGKMERALGIRLRVN   91 (174)
Q Consensus        43 ~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~---l~~la~~L~v~~~~l   91 (174)
                      .+-.|.+|+|+++|||.+|||+.-||....+.++   +.+.++.||..++..
T Consensus        10 ~~~~ti~diA~~agVS~~TVSr~Ln~~~~vs~~tr~rV~~~a~~lgY~pn~~   61 (355)
T 3e3m_A           10 HRPVTMRDVAKAAGVSRMTVSRALKKDSPISSETRERILKVVKDMNYVPDQV   61 (355)
T ss_dssp             ----------------------------------------------------
T ss_pred             CCCCcHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCCcCHH
Confidence            4457999999999999999999999985555544   556667777766543

>3t72_q RNA polymerase sigma factor RPOD, DNA-directed RN polymerase subunit beta; winged-helix motif, transcription activation, DNA-binding; 4.33A {Escherichia coli} PDB: 1tlh_B

Probab=90.37  E-value=0.43  Score=31.73  Aligned_cols=24  Identities=4%  Similarity=0.273  Sum_probs=22.5

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      .|+|.+|+|+.+|+|.++|.+++.
T Consensus        38 e~~s~~EIA~~lgiS~~tVr~~~~   61 (99)
T 3t72_q           38 TDYTLEEVGKQFDVTRERIRQIEA   61 (99)
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHH
Confidence            689999999999999999999984

>1r8d_A Transcription activator MTAN; protein-DNA complex, transcription/DNA complex; 2.70A {Bacillus subtilis} SCOP: a.6.1.3 PDB: 1jbg_A

Probab=90.17  E-value=0.29  Score=32.91  Aligned_cols=24  Identities=13%  Similarity=0.178  Sum_probs=21.5

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcC
Q psy6501          45 GWSQKDLATKINEKPQIVNDYEGG   68 (174)
Q Consensus        45 gltq~eLA~~igvs~~~is~~E~G   68 (174)
                      -+|..|+|+.+|||+.||..||.-
T Consensus         2 ~~~i~e~A~~~gvs~~tLR~ye~~   25 (109)
T 1r8d_A            2 KYQVKQVAEISGVSIRTLHHYDNI   25 (109)
T ss_dssp             CBCHHHHHHHHSCCHHHHHHHHHT
T ss_pred             CccHHHHHHHHCcCHHHHHHHHHC
Confidence            378999999999999999999853

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

Probab=90.13  E-value=0.54  Score=31.91  Aligned_cols=39  Identities=15%  Similarity=0.114  Sum_probs=29.7

Q ss_pred             cchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          28 KVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        28 ~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      .+...-..-|..+...-++|+.+||+.+|+++++|+..-
T Consensus        26 ~l~~~~~~iL~~l~~~~~~~~~ela~~l~~s~~tvs~~l   64 (138)
T 3bpv_A           26 NLTDAQVACLLRIHREPGIKQDELATFFHVDKGTIARTL   64 (138)
T ss_dssp             TCCHHHHHHHHHHHHSTTCBHHHHHHHHTCCHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHH
Confidence            344444455666666788999999999999999998754

>2d5v_A Hepatocyte nuclear factor 6; transcription factor, transcription-DNA complex; 2.00A {Rattus norvegicus} PDB: 1s7e_A

Probab=90.10  E-value=0.6  Score=33.69  Aligned_cols=58  Identities=10%  Similarity=0.058  Sum_probs=43.6

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHHcCCC-----CCCHHHHHHHHHHhCcc
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATKI-NEKPQIVNDYEGGRG-----IPNQAIIGKMERALGIR   87 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~i-gvs~~~is~~E~G~~-----~P~~~~l~~la~~L~v~   87 (174)
                      ...|...|+...+..+++|..+|+.+ |+++.++|.+-+.-.     ....+...++-..|..+
T Consensus         6 t~~i~~~i~~~l~~~~i~q~~fa~~ilg~sq~~ls~~l~~pkpw~~l~~g~~~y~rm~~WL~~p   69 (164)
T 2d5v_A            6 TKEVAQRITTELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLKSGRETFRRMWKWLQEP   69 (164)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHTSCCHHHHHHHHHSCCCGGGCSTTHHHHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHHHHcCCchHHHHHHHhcCCchhHHHHcCCCCCHHHHcccchHHHHHHHHHhcc
Confidence            46799999999999999999999966 999999999986431     12234444555555544

>1jye_A Lactose operon repressor; gene regulation, protein stability, protein DNA-binding, transcription; 1.70A {Escherichia coli} SCOP: c.93.1.1 PDB: 1lbi_A 1lbg_A* 1lbh_A 1jyf_A 3edc_A 1efa_A* 1jwl_A* 2pe5_A* 1tlf_A* 2p9h_A* 2paf_A* 1cjg_A* 1l1m_A 1osl_A 2kei_A* 2kej_A* 2kek_A* 2bjc_A 1lqc_A 1lcc_A* ...

Probab=89.90  E-value=0.059  Score=43.09  Aligned_cols=45  Identities=11%  Similarity=-0.079  Sum_probs=0.0

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCHH---HHHHHHHHhCccccc
Q psy6501          46 WSQKDLATKINEKPQIVNDYEGGRGIPNQA---IIGKMERALGIRLRV   90 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~G~~~P~~~---~l~~la~~L~v~~~~   90 (174)
                      .|.+|+|+++|||.+|||+.-||....+.+   .+.+.++.||-.+..
T Consensus         4 ~ti~diA~~aGVS~~TVSrvLn~~~~vs~~tr~rV~~~a~~lgY~pn~   51 (349)
T 1jye_A            4 VTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNR   51 (349)
T ss_dssp             ------------------------------------------------
T ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHCCCcCH
Confidence            699999999999999999999998655544   455667778776554

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

Probab=89.88  E-value=0.59  Score=32.17  Aligned_cols=42  Identities=17%  Similarity=0.135  Sum_probs=31.9

Q ss_pred             ccccchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          25 KHEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        25 ~~~~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      .+-.+...=..-|..+...-++|+.+||+.+|++++++++.-
T Consensus        25 ~~~~lt~~q~~iL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l   66 (145)
T 3g3z_A           25 GQQDLNYNLFAVLYTLATEGSRTQKHIGEKWSLPKQTVSGVC   66 (145)
T ss_dssp             HTTTCCHHHHHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHcCCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHH
Confidence            333444445566777777788999999999999999998863

>3ctp_A Periplasmic binding protein/LACI transcriptional; structural genomics, protein structure initiative; HET: XLF; 1.41A {Alkaliphilus metalliredigens}

Probab=89.83  E-value=0.061  Score=42.57  Aligned_cols=45  Identities=13%  Similarity=0.112  Sum_probs=0.0

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCccccc
Q psy6501          46 WSQKDLATKINEKPQIVNDYEGGRGIPNQAI---IGKMERALGIRLRV   90 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~G~~~P~~~~---l~~la~~L~v~~~~   90 (174)
                      .|.+|+|+++|||.+|||+.-||....+.++   +.+.++.||..+..
T Consensus         3 ~ti~diA~~agVS~~TVSrvln~~~~vs~~tr~rV~~~~~~lgY~pn~   50 (330)
T 3ctp_A            3 ANIREIAKRAGISIATVSRHLNNTGYVSEDAREKIQKVVDELNYTPNA   50 (330)
T ss_dssp             ------------------------------------------------
T ss_pred             CCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHhCCCcCH
Confidence            5899999999999999999999986555544   44566777766554

>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=89.75  E-value=1.2  Score=30.34  Aligned_cols=22  Identities=5%  Similarity=-0.026  Sum_probs=19.8

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHH
Q psy6501          44 KGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~   65 (174)
                      ..+|.++||+.+|+|++++++.
T Consensus        26 ~~~sl~~lA~~~~~S~~~l~r~   47 (129)
T 1bl0_A           26 SPLSLEKVSERSGYSKWHLQRM   47 (129)
T ss_dssp             SCCCCHHHHHHSSSCHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHH
Confidence            3599999999999999999876

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

Probab=89.71  E-value=0.35  Score=32.58  Aligned_cols=51  Identities=4%  Similarity=0.148  Sum_probs=36.7

Q ss_pred             HHHHHHH-HHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH-HHHH
Q psy6501          32 DLAKLLM-QGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIG-KMER   82 (174)
Q Consensus        32 ~ig~~ik-~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~-~la~   82 (174)
                      .+++-|- ...+-..+|..|||+.+|||++||.++-+--..-....+. .|+.
T Consensus        21 ~ia~yil~~~~~~~~~si~elA~~~~vS~aTv~Rf~kkLGf~gf~efk~~l~~   73 (107)
T 3iwf_A           21 KIAQFILNYPHKVVNMTSQEIANQLETSSTSIIRLSKKVTPGGFNELKTRLSK   73 (107)
T ss_dssp             HHHHHHHHCHHHHTTCCHHHHHHHHTSCHHHHHHHHHHHSTTHHHHHHHHHHT
T ss_pred             HHHHHHHhCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHhCCCCHHHHHHHHHH
Confidence            3444433 3445678999999999999999999998766666666555 3443

>3pvv_A Chromosomal replication initiator protein DNAA; helix-turn-helix motif, interacting with DNAA-BOX, DNAA-box; HET: DNA; 2.00A {Mycobacterium tuberculosis} PDB: 3pvp_A*

Probab=89.61  E-value=0.85  Score=30.45  Aligned_cols=66  Identities=15%  Similarity=0.153  Sum_probs=41.6

Q ss_pred             CCCCCHH-HHHHHHHHhCcccccccCCCCCCCCCcccchhhhhhhhhhcccccHHHHHHHHHHHHhcCCCHHHHHHHhCC
Q psy6501          69 RGIPNQA-IIGKMERALGIRLRVNAGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKINE  147 (174)
Q Consensus        69 ~~~P~~~-~l~~la~~L~v~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~i~~~R~~~glsq~ela~~lg~  147 (174)
                      ...++++ .+..+|++|||++++|.+..-.           ....      .+-.+...|  .|+..++|..+++..+|.
T Consensus         2 ~~~it~~~I~~~Va~~f~v~~~dl~s~~R~-----------~~i~------~aRqiAmYL--~r~~t~~Sl~~IG~~fgR   62 (101)
T 3pvv_A            2 PHMISAATIMAATAEYFDTTVEELRGPGKT-----------RALA------QSRQIAMYL--CRELTDLSLPKIGQAFGR   62 (101)
T ss_dssp             ---CCHHHHHHHHHHHTTCCHHHHHSSCCC-----------HHHH------HHHHHHHHH--HHHHCCCCHHHHHHHTTC
T ss_pred             CCCCCHHHHHHHHHHHHCCCHHHHhCCCCC-----------chhh------HHHHHHHHH--HHHHhCCCHHHHHHHHCC
Confidence            3344544 4558999999999999864421           0000      011223333  567789999999999998


Q ss_pred             ChhHHH
Q psy6501         148 KPQIVN  153 (174)
Q Consensus       148 ~~s~i~  153 (174)
                      ..++|.
T Consensus        63 DHsTV~   68 (101)
T 3pvv_A           63 DHTTVM   68 (101)
T ss_dssp             CHHHHH
T ss_pred             CHHHHH
Confidence            887653

>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=89.61  E-value=0.58  Score=32.94  Aligned_cols=31  Identities=13%  Similarity=0.097  Sum_probs=26.4

Q ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHH
Q psy6501          35 KLLMQGRQAKGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~~   65 (174)
                      .-|..+++...+|..|||+.+|+|++++++.
T Consensus        12 ~il~~L~~~~~~s~~ela~~lg~s~~tv~~~   42 (152)
T 2cg4_A           12 GILEALMGNARTAYAELAKQFGVSPETIHVR   42 (152)
T ss_dssp             HHHHHHHHCTTSCHHHHHHHHTSCHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHH
Confidence            4566677778899999999999999999875

>2o4a_A DNA-binding protein SATB1; protein-DNA complex, transcription, transcription/DNA complex; HET: DNA; 1.75A {Homo sapiens} SCOP: a.35.1.7 PDB: 2o49_A*

Probab=89.59  E-value=0.65  Score=30.65  Aligned_cols=40  Identities=13%  Similarity=0.144  Sum_probs=35.4

Q ss_pred             HHHHHHHHHHHHHcCCCHHHHHH-HhCCCHHHHHHHHcCCC
Q psy6501          31 LDLAKLLMQGRQAKGWSQKDLAT-KINEKPQIVNDYEGGRG   70 (174)
Q Consensus        31 ~~ig~~ik~~R~~~gltq~eLA~-~igvs~~~is~~E~G~~   70 (174)
                      ..|...|+.-.+..++||.-||+ -+|.|+.++|.+-+.-.
T Consensus        10 ~~I~~~ik~~Lk~~~isQ~~FA~~VL~rsQgtLs~lL~~Pk   50 (93)
T 2o4a_A           10 SEIYQWVRDELKRAGISQAVFARVAFNRTQGLLSEILRKEE   50 (93)
T ss_dssp             TTHHHHHHHHHHHHTCCHHHHHHHHHSCCHHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHHHcCCcHHHHHHHHHHHhhhHHHHHHcCCC
Confidence            47899999999999999999999 66999999999876544

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

Probab=89.55  E-value=3  Score=27.19  Aligned_cols=22  Identities=5%  Similarity=-0.049  Sum_probs=20.0

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHH
Q psy6501          44 KGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~   65 (174)
                      ..+|.++||+.+|+|++++++.
T Consensus        17 ~~~~~~~lA~~~~~s~~~l~r~   38 (108)
T 3mn2_A           17 RPITIEKLTALTGISSRGIFKA   38 (108)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHH
Confidence            4699999999999999999876

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

Probab=89.54  E-value=0.52  Score=32.34  Aligned_cols=39  Identities=21%  Similarity=0.105  Sum_probs=30.1

Q ss_pred             cchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          28 KVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        28 ~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      .+...=..-|..+...-++|+.+||+.+|++++++++.-
T Consensus        34 ~lt~~~~~iL~~l~~~~~~t~~eLa~~l~~~~~~vs~~l   72 (143)
T 3oop_A           34 DVTPEQWSVLEGIEANEPISQKEIALWTKKDTPTVNRIV   72 (143)
T ss_dssp             SSCHHHHHHHHHHHHHSSEEHHHHHHHHTCCHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHcCCcCHHHHHHHHCCCHhhHHHHH
Confidence            343444455666777789999999999999999999753

>2obp_A Putative DNA-binding protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE; 1.70A {Ralstonia eutropha} SCOP: a.4.5.71

Probab=89.48  E-value=0.79  Score=30.36  Aligned_cols=38  Identities=16%  Similarity=0.281  Sum_probs=31.8

Q ss_pred             chHHHHHHHHHHHHH------cCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          29 VPLDLAKLLMQGRQA------KGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        29 ~~~~ig~~ik~~R~~------~gltq~eLA~~igvs~~~is~~E   66 (174)
                      +.......+..++..      ..+++.+||+.++++++++++.-
T Consensus        14 l~~~q~~vL~~L~~~~~~~~g~~~s~~eLa~~l~l~~stLsR~l   57 (96)
T 2obp_A           14 IDPAIVEVLLVLREAGIENGATPWSLPKIAKRAQLPMSVLRRVL   57 (96)
T ss_dssp             CCHHHHHHHHHHHHHTSSTTCCCCBHHHHHHHHTCCHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHhhCCCCCcCHHHHHHHhCCchhhHHHHH
Confidence            556677778878777      67999999999999999998753

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

Probab=89.39  E-value=0.34  Score=33.20  Aligned_cols=33  Identities=6%  Similarity=-0.007  Sum_probs=26.5

Q ss_pred             HHHHHHHHHHcC--CCHHHHHHHhCCCHHHHHHHH
Q psy6501          34 AKLLMQGRQAKG--WSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        34 g~~ik~~R~~~g--ltq~eLA~~igvs~~~is~~E   66 (174)
                      ...+..+.+.-+  +|+.|||+.+|+|++||++.-
T Consensus        29 ~~il~~L~~~~~~~~t~~eLa~~l~~s~sTV~r~L   63 (123)
T 3r0a_A           29 LNVMKSFLNEPDRWIDTDALSKSLKLDVSTVQRSV   63 (123)
T ss_dssp             HHHHHHHHHSTTCCEEHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHH
Confidence            345666666667  999999999999999998763

>2glo_A Brinker CG9653-PA; protein-DNA complex, helix-turn-helix motif, transcription/DNA complex; NMR {Drosophila melanogaster}

Probab=89.28  E-value=0.89  Score=26.73  Aligned_cols=25  Identities=16%  Similarity=0.145  Sum_probs=22.3

Q ss_pred             hcCCC----HHHHHHHhCCChhHHHHHhc
Q psy6501         133 AKGWS----QKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       133 ~~gls----q~ela~~lg~~~s~i~~~E~  157 (174)
                      ..|.+    ..++|..+|+++++|..|-.
T Consensus        19 ~~g~s~~~~~~~vA~~~gIs~~tl~~W~~   47 (59)
T 2glo_A           19 RNDNDCKGNQRATARKYNIHRRQIQKWLQ   47 (59)
T ss_dssp             HHCTTTTTCHHHHHHHTTSCHHHHHHHHT
T ss_pred             HcCCCcchHHHHHHHHHCcCHHHHHHHHH
Confidence            46778    99999999999999999965

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

Probab=89.16  E-value=0.18  Score=32.52  Aligned_cols=28  Identities=11%  Similarity=-0.039  Sum_probs=22.6

Q ss_pred             HHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          39 QGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        39 ~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      .+....++|+.|||+.+|+|+++|++.-
T Consensus        32 ~l~~~~~~s~~ela~~l~is~~tvs~~l   59 (99)
T 3cuo_A           32 MLSGSPGTSAGELTRITGLSASATSQHL   59 (99)
T ss_dssp             HHTTCCSEEHHHHHHHHCCCHHHHHHHH
T ss_pred             HHHhCCCcCHHHHHHHHCcCHHHHHHHH
Confidence            3434447999999999999999998863

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

Probab=89.07  E-value=0.77  Score=31.10  Aligned_cols=39  Identities=8%  Similarity=-0.022  Sum_probs=29.4

Q ss_pred             cchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          28 KVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        28 ~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      .+...=..-|..+...-++|+.+||+.+|+++++|++.-
T Consensus        35 ~l~~~~~~iL~~l~~~~~~t~~ela~~l~~~~~tvs~~l   73 (140)
T 2nnn_A           35 GLTPTQWAALVRLGETGPCPQNQLGRLTAMDAATIKGVV   73 (140)
T ss_dssp             CCCHHHHHHHHHHHHHSSBCHHHHHHHTTCCHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHH
Confidence            344344455666666679999999999999999998763

>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=88.93  E-value=0.48  Score=32.57  Aligned_cols=38  Identities=11%  Similarity=0.152  Sum_probs=26.0

Q ss_pred             chHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          29 VPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        29 ~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      +...=..-|..+...-++|+.+||+.+|+++++|++.-
T Consensus        35 lt~~~~~vL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l   72 (142)
T 3ech_A           35 LTPPDVHVLKLIDEQRGLNLQDLGRQMCRDKALITRKI   72 (142)
T ss_dssp             CCHHHHHHHHHHHHTTTCCHHHHHHHHC---CHHHHHH
T ss_pred             CCHHHHHHHHHHHhCCCcCHHHHHHHhCCCHHHHHHHH
Confidence            33344455666677779999999999999999888763

>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=88.77  E-value=0.47  Score=33.19  Aligned_cols=31  Identities=19%  Similarity=0.331  Sum_probs=25.7

Q ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHH
Q psy6501          35 KLLMQGRQAKGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~~   65 (174)
                      .-|..+.+...+|+.|||+.+|+|++++++.
T Consensus         9 ~il~~L~~~~~~s~~ela~~lg~s~~tv~~~   39 (144)
T 2cfx_A            9 NIIEELKKDSRLSMRELGRKIKLSPPSVTER   39 (144)
T ss_dssp             HHHHHHHHCSCCCHHHHHHHHTCCHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHH
Confidence            3455666677899999999999999998765

>1b4a_A Arginine repressor; helix turn helix; 2.50A {Geobacillus stearothermophilus} SCOP: a.4.5.3 d.74.2.1 PDB: 1f9n_A

Probab=88.77  E-value=0.51  Score=33.82  Aligned_cols=33  Identities=12%  Similarity=-0.003  Sum_probs=27.2

Q ss_pred             HHHHHH-HHHcCCCHHHHHHHh-----CCCHHHHHHHHc
Q psy6501          35 KLLMQG-RQAKGWSQKDLATKI-----NEKPQIVNDYEG   67 (174)
Q Consensus        35 ~~ik~~-R~~~gltq~eLA~~i-----gvs~~~is~~E~   67 (174)
                      +.|+++ .+..-.||+||++.+     +||++|||+.-+
T Consensus         8 ~~I~~li~~~~~~tq~eL~~~L~~~G~~VtqaTisRDL~   46 (149)
T 1b4a_A            8 IKIREIIMSNDIETQDELVDRLREAGFNVTQATVSRDIK   46 (149)
T ss_dssp             HHHHHHHHHSCCCSHHHHHHHHHHTTCCCCHHHHHHHHH
T ss_pred             HHHHHHHHHCCCccHHHHHHHHHHcCCCcCHHHHHHHHH
Confidence            455665 666677999999999     999999999874

>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=88.69  E-value=0.73  Score=31.62  Aligned_cols=38  Identities=11%  Similarity=0.021  Sum_probs=29.7

Q ss_pred             chHHHHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          29 VPLDLAKLLMQGRQ-AKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        29 ~~~~ig~~ik~~R~-~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      +...-..-|..+.. ..++|+.+||+.+|+++++|+..-
T Consensus        33 l~~~~~~iL~~l~~~~~~~~~~~la~~l~i~~~~vs~~l   71 (147)
T 2hr3_A           33 VQFSQLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALL   71 (147)
T ss_dssp             HHHHHHHHHHHHHHTTSCBCHHHHHHHTTCCHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHH
Confidence            33334456667777 789999999999999999998763

>2jn6_A Protein CGL2762, transposase; GFT PSI-2, protein structure, structural genomics, protein structure initiative; NMR {Corynebacterium glutamicum} SCOP: a.4.1.19

Probab=88.65  E-value=0.75  Score=29.78  Aligned_cols=23  Identities=13%  Similarity=0.179  Sum_probs=21.1

Q ss_pred             CCCHHHHHHHhCCChhHHHHHhc
Q psy6501         135 GWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       135 glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      |.|..++|..+|+++++|.+|-.
T Consensus        23 g~s~~~ia~~~gIs~~tl~rW~~   45 (97)
T 2jn6_A           23 GASLQQIANDLGINRVTLKNWII   45 (97)
T ss_dssp             GSCHHHHHHHHTSCHHHHHHHHH
T ss_pred             CChHHHHHHHHCcCHHHHHHHHH
Confidence            89999999999999999998853

>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=88.57  E-value=0.49  Score=33.28  Aligned_cols=31  Identities=16%  Similarity=0.047  Sum_probs=25.9

Q ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHH
Q psy6501          35 KLLMQGRQAKGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~~   65 (174)
                      .-|..+.....+|+.|||+.+|+|++++++.
T Consensus        11 ~iL~~L~~~~~~s~~ela~~lg~s~~tv~~~   41 (150)
T 2w25_A           11 ILVRELAADGRATLSELATRAGLSVSAVQSR   41 (150)
T ss_dssp             HHHHHHHHCTTCCHHHHHHHHTSCHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHH
Confidence            4456666677899999999999999998875

>3me5_A Cytosine-specific methyltransferase; structural genomics, protein structure initiative, NEW YORK structural genomix research consortium; 1.75A {Shigella flexneri 2A} PDB: 3lx6_A

Probab=88.39  E-value=0.74  Score=39.20  Aligned_cols=38  Identities=11%  Similarity=0.045  Sum_probs=25.7

Q ss_pred             HHHHHHHHhcCCCHHHHHHHh------CCChhHHHHHhcCCCCCCH
Q psy6501         125 KLLMQGRQAKGWSQKDLATKI------NEKPQIVNDYEGGRGIPNQ  164 (174)
Q Consensus       125 ~~i~~~R~~~glsq~ela~~l------g~~~s~i~~~E~G~~~P~~  164 (174)
                      ++|.+.+  ..+||+++|+.+      +.+..++.+||+|+..|+.
T Consensus        21 ~~~~~~~--~~~~~~~~a~~l~~~~~~~~~~~~~~rw~~~~~~~~~   64 (482)
T 3me5_A           21 AMLEKLL--QIYDVKMLVAQLNGVGENHWSAAILKRALANDSAWHR   64 (482)
T ss_dssp             HHHHHHH--TTSCHHHHHHHHHHTCSSCCCHHHHHHHHC-------
T ss_pred             HHHHHHH--HHcCHHHHHHHHHhhccCCCCHHHHHHHHcCCCCCcc
Confidence            5555444  459999999999      8889999999999888753

>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=88.36  E-value=0.63  Score=27.51  Aligned_cols=28  Identities=11%  Similarity=-0.046  Sum_probs=23.6

Q ss_pred             HHHHcCCCHHHHHHHh-----CCCHHHHHHHHc
Q psy6501          40 GRQAKGWSQKDLATKI-----NEKPQIVNDYEG   67 (174)
Q Consensus        40 ~R~~~gltq~eLA~~i-----gvs~~~is~~E~   67 (174)
                      +.....+|.+||++.+     +||.+||++.-+
T Consensus        14 l~~~~~~t~~el~~~l~~~~~~vs~~Tv~R~L~   46 (64)
T 2p5k_A           14 ITSNEIETQDELVDMLKQDGYKVTQATVSRDIK   46 (64)
T ss_dssp             HHHSCCCSHHHHHHHHHHTTCCCCHHHHHHHHH
T ss_pred             HHcCCCCCHHHHHHHHHHhCCCcCHHHHHHHHH
Confidence            3445679999999999     999999998764

>2rnj_A Response regulator protein VRAR; HTH LUXR-type domain, DNA binding domain, activator, antibiotic resistance, cytoplasm, DNA-binding; NMR {Staphylococcus aureus}

Probab=88.34  E-value=0.5  Score=30.39  Aligned_cols=24  Identities=25%  Similarity=0.347  Sum_probs=21.9

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          43 AKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        43 ~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ..|+|.+|+|+.+|+|.+||..+-
T Consensus        42 ~~g~s~~eIA~~l~is~~tV~~~l   65 (91)
T 2rnj_A           42 AKGYSNQEIASASHITIKTVKTHV   65 (91)
T ss_dssp             HTTCCTTHHHHHHTCCHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHH
Confidence            689999999999999999998764

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

Probab=88.30  E-value=0.59  Score=31.80  Aligned_cols=33  Identities=12%  Similarity=0.004  Sum_probs=26.9

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ..-|..+...-++|+.+||+.+|+|+++|+..-
T Consensus        34 ~~iL~~l~~~~~~~~~ela~~l~is~~~vs~~l   66 (142)
T 3bdd_A           34 YSILQTLLKDAPLHQLALQERLQIDRAAVTRHL   66 (142)
T ss_dssp             HHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHH
Confidence            345666666778999999999999999998763

>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=88.28  E-value=0.35  Score=31.33  Aligned_cols=21  Identities=19%  Similarity=-0.005  Sum_probs=19.6

Q ss_pred             CCHHHHHHHhCCCHHHHHHHH
Q psy6501          46 WSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E   66 (174)
                      +||.+||+.+|+++++|+++-
T Consensus        31 ~t~~eLa~~l~i~~~tvs~~l   51 (95)
T 2qvo_A           31 VYIQYIASKVNSPHSYVWLII   51 (95)
T ss_dssp             EEHHHHHHHSSSCHHHHHHHH
T ss_pred             cCHHHHHHHHCcCHHHHHHHH
Confidence            999999999999999999873

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

Probab=88.25  E-value=0.95  Score=31.14  Aligned_cols=37  Identities=11%  Similarity=-0.024  Sum_probs=28.0

Q ss_pred             chHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHH
Q psy6501          29 VPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        29 ~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~   65 (174)
                      +...-..-|..+...-++|+.+||+.+|+++++|+..
T Consensus        40 l~~~~~~iL~~l~~~~~~t~~ela~~l~~~~~tvs~~   76 (150)
T 2rdp_A           40 ITPPQFVALQWLLEEGDLTVGELSNKMYLACSTTTDL   76 (150)
T ss_dssp             SCHHHHHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHHCCCchhHHHH
Confidence            3333344556666677899999999999999999876

>1p4w_A RCSB; solution structure, DNA binding domain, DNA binding protein; NMR {Erwinia amylovora} SCOP: a.4.6.2

Probab=88.25  E-value=0.42  Score=31.70  Aligned_cols=24  Identities=21%  Similarity=0.430  Sum_probs=21.7

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          43 AKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        43 ~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ..|+|.+|+|+.+|+|.+||..+-
T Consensus        47 ~~G~s~~EIA~~L~iS~~TV~~~l   70 (99)
T 1p4w_A           47 AEGFLVTEIAKKLNRSIKTISSQK   70 (99)
T ss_dssp             HHTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHH
Confidence            479999999999999999998774

>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=88.22  E-value=0.36  Score=31.05  Aligned_cols=29  Identities=3%  Similarity=0.020  Sum_probs=24.0

Q ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHH
Q psy6501          37 LMQGRQAKGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        37 ik~~R~~~gltq~eLA~~igvs~~~is~~   65 (174)
                      |..+....++|+.+||+.+|+|+++|++.
T Consensus        22 L~~L~~~~~~~~~ela~~l~is~~tvs~~   50 (100)
T 1ub9_A           22 MIFLLPRRKAPFSQIQKVLDLTPGNLDSH   50 (100)
T ss_dssp             HHHHHHHSEEEHHHHHHHTTCCHHHHHHH
T ss_pred             HHHHHhcCCcCHHHHHHHHCcCHHHHHHH
Confidence            44455567899999999999999999875

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

Probab=88.21  E-value=0.49  Score=32.66  Aligned_cols=38  Identities=8%  Similarity=0.042  Sum_probs=29.4

Q ss_pred             chHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          29 VPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        29 ~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      +...=..-|..+...-++|+.+||+.+|+++++|++.-
T Consensus        38 l~~~~~~iL~~l~~~~~~t~~ela~~l~~~~~tvs~~l   75 (148)
T 3nrv_A           38 IGMTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTV   75 (148)
T ss_dssp             CCHHHHHHHHHHHHSSSBCHHHHHHHHTCCHHHHHHHH
T ss_pred             CCHHHHHHHHHHHcCCCCCHHHHHHHHCCCHHHHHHHH
Confidence            33333455666667779999999999999999999874

>2elh_A CG11849-PA, LD40883P; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Drosophila melanogaster}

Probab=88.18  E-value=1  Score=28.72  Aligned_cols=25  Identities=16%  Similarity=0.182  Sum_probs=22.2

Q ss_pred             hcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         133 AKGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       133 ~~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      ..|.+..++|+.+|+++++|.+|-.
T Consensus        36 ~~g~s~~~iA~~~gIs~sTl~rW~k   60 (87)
T 2elh_A           36 HDGESKASVARDIGVPESTLRGWCK   60 (87)
T ss_dssp             HHTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3689999999999999999998853

>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=88.11  E-value=0.63  Score=31.68  Aligned_cols=38  Identities=16%  Similarity=0.177  Sum_probs=28.5

Q ss_pred             chHHHHHHHHHHHHHc--CCCHHHHHHHhCCCHHHHHHHH
Q psy6501          29 VPLDLAKLLMQGRQAK--GWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        29 ~~~~ig~~ik~~R~~~--gltq~eLA~~igvs~~~is~~E   66 (174)
                      +...-..-|..+...-  ++|+.+||+.+|+++++|++.-
T Consensus        29 lt~~~~~vL~~l~~~~~~~~t~~ela~~l~~~~~tvs~~l   68 (139)
T 3eco_A           29 ITNEQGHTLGYLYAHQQDGLTQNDIAKALQRTGPTVSNLL   68 (139)
T ss_dssp             CCHHHHHHHHHHHHSTTTCEEHHHHHHHHTCCHHHHHHHH
T ss_pred             CCHHHHHHHHHHHhcCCCCcCHHHHHHHhCCCcccHHHHH
Confidence            3334445566666654  8999999999999999998864

>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=88.09  E-value=0.84  Score=31.02  Aligned_cols=37  Identities=14%  Similarity=0.069  Sum_probs=27.6

Q ss_pred             chHHHHHHHHHHHHHc--CCCHHHHHHHhCCCHHHHHHH
Q psy6501          29 VPLDLAKLLMQGRQAK--GWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        29 ~~~~ig~~ik~~R~~~--gltq~eLA~~igvs~~~is~~   65 (174)
                      +...-..-|..+...-  ++|+.+||+.+|+++++|+..
T Consensus        32 lt~~~~~iL~~l~~~~~~~~~~~ela~~l~~~~~tvs~~   70 (141)
T 3bro_A           32 LTGTQMTIIDYLSRNKNKEVLQRDLESEFSIKSSTATVL   70 (141)
T ss_dssp             CCHHHHHHHHHHHHTTTSCCBHHHHHHHHTCCHHHHHHH
T ss_pred             CCHHHHHHHHHHHHCCCCCcCHHHHHHHHCCCcchHHHH
Confidence            3333344566666655  799999999999999998876

>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=88.06  E-value=1  Score=30.49  Aligned_cols=38  Identities=13%  Similarity=0.034  Sum_probs=28.4

Q ss_pred             chHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          29 VPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        29 ~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      +...=..-|..+...-++|+.+||+.+|+++++|+..-
T Consensus        32 lt~~~~~iL~~l~~~~~~~~~~la~~l~~~~~tvs~~l   69 (138)
T 1jgs_A           32 ITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRML   69 (138)
T ss_dssp             SCHHHHHHHHHHHHHSSBCHHHHHHHHTCCHHHHHHHH
T ss_pred             CCHHHHHHHHHHHhcCCCCHHHHHHHHCCChHHHHHHH
Confidence            33333445566666778999999999999999998763

>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=88.00  E-value=1.1  Score=30.82  Aligned_cols=28  Identities=14%  Similarity=0.052  Sum_probs=23.6

Q ss_pred             HHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          39 QGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        39 ~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      .+....++|+.+||+.+|+|+++|++.-
T Consensus        16 l~~~~~~~~~~ela~~l~vs~~tvs~~l   43 (142)
T 1on2_A           16 LIEEKGYARVSDIAEALAVHPSSVTKMV   43 (142)
T ss_dssp             HHHHHSSCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHhhcCCCCHHHHHHHhCCCHHHHHHHH
Confidence            3445678999999999999999988764

>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=87.90  E-value=0.65  Score=32.73  Aligned_cols=35  Identities=23%  Similarity=0.059  Sum_probs=25.7

Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          32 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        32 ~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      .=..-|..+...-++|+.+||+.+|+++++|++.-
T Consensus        47 ~q~~iL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l   81 (162)
T 3k0l_A           47 PQFTALSVLAAKPNLSNAKLAERSFIKPQSANKIL   81 (162)
T ss_dssp             HHHHHHHHHHHCTTCCHHHHHHHHTSCGGGHHHHH
T ss_pred             HHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHH
Confidence            33445556666678889999999998888888753

>1ntc_A Protein (nitrogen regulation protein (NTRC)); helix-turn-helix, FIS, four-helix bundle, transcription regulation; NMR {Salmonella typhimurium} SCOP: a.4.1.12

Probab=87.82  E-value=0.57  Score=30.37  Aligned_cols=32  Identities=9%  Similarity=0.030  Sum_probs=28.2

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHH
Q psy6501          34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~   65 (174)
                      -..|....+..+.++.+.|+.+|||++|+.+.
T Consensus        53 ~~~i~~aL~~~~gn~~~aA~~LGIsr~tL~rk   84 (91)
T 1ntc_A           53 RTLLTTALRHTQGHKQEAARLLGWGAATLTAK   84 (91)
T ss_dssp             HHHHHHHHHHTTTCTTHHHHHTTCCHHHHHHH
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHCcCHHHHHHH
Confidence            56678888889999999999999999999765

>1j1v_A Chromosomal replication initiator protein DNAA, 5'-D(*CP*CP*TP*GP*TP*GP*GP*AP*TP*AP*AP*CP*A)-3'; protein-DNA complex; 2.10A {Escherichia coli} SCOP: a.4.12.2

Probab=87.82  E-value=1.1  Score=29.32  Aligned_cols=60  Identities=10%  Similarity=0.133  Sum_probs=40.7

Q ss_pred             HHHHHHHHHhCcccccccCCCCCCCCCcccchhhhhhhhhhcccccHHHHHHHHHHHHhcCCCHHHHHHHh-CCChhHHH
Q psy6501          75 AIIGKMERALGIRLRVNAGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKI-NEKPQIVN  153 (174)
Q Consensus        75 ~~l~~la~~L~v~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~i~~~R~~~glsq~ela~~l-g~~~s~i~  153 (174)
                      ..+..+|++|||++++|.+..-.           .....      +-.  -.+--.|+..++|..+++..+ |...++|.
T Consensus         5 ~I~~~Va~~f~i~~~dl~s~~R~-----------~~i~~------aRq--iamyL~r~~t~~Sl~~IG~~fggrdHsTV~   65 (94)
T 1j1v_A            5 NIQKTVAEYYKIKVADLLSKRRS-----------RSVAR------PRQ--MAMALAKELTNHSLPEIGDAFGGRDHTTVL   65 (94)
T ss_dssp             HHHHHHHHHTTCCHHHHHSCCCC-----------HHHHH------HHH--HHHHHHHHHSCCCHHHHHHHTTSCCHHHHH
T ss_pred             HHHHHHHHHhCCCHHHHhCCCCC-----------chhHH------HHH--HHHHHHHHHHCcCHHHHHHHhCCCCHHHHH
Confidence            45568999999999999864321           00000      111  233336778999999999999 78888654

>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=87.55  E-value=0.58  Score=32.46  Aligned_cols=32  Identities=9%  Similarity=0.031  Sum_probs=26.3

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ..-|..+ ...++|+.+||+.+|+++++|++.-
T Consensus        41 ~~iL~~l-~~~~~t~~eLa~~l~~~~~~vs~~l   72 (151)
T 3kp7_A           41 SHVLNML-SIEALTVGQITEKQGVNKAAVSRRV   72 (151)
T ss_dssp             HHHHHHH-HHSCBCHHHHHHHHCSCSSHHHHHH
T ss_pred             HHHHHHH-HcCCcCHHHHHHHHCCCHHHHHHHH
Confidence            3456666 7889999999999999999998753

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

Probab=87.54  E-value=0.59  Score=32.83  Aligned_cols=31  Identities=16%  Similarity=0.168  Sum_probs=25.8

Q ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHH
Q psy6501          35 KLLMQGRQAKGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~~   65 (174)
                      .-|..+.+...+|..|||+.+|+|++++++.
T Consensus        13 ~il~~L~~~~~~s~~ela~~lg~s~~tv~~~   43 (151)
T 2dbb_A           13 QLVKILSENSRLTYRELADILNTTRQRIARR   43 (151)
T ss_dssp             HHHHHHHHCTTCCHHHHHHHTTSCHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHH
Confidence            4456666778899999999999999998764

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

Probab=87.38  E-value=0.59  Score=32.45  Aligned_cols=38  Identities=0%  Similarity=0.035  Sum_probs=28.5

Q ss_pred             chHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          29 VPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        29 ~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      +...=..-|..+...-++|+.+||+.+++++++|+..-
T Consensus        39 lt~~q~~iL~~l~~~~~~~~~eLa~~l~~~~~~vs~~l   76 (149)
T 4hbl_A           39 ITYSQYLVMLTLWEENPQTLNSIGRHLDLSSNTLTPML   76 (149)
T ss_dssp             CCHHHHHHHHHHHHSSSEEHHHHHHHHTCCHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHH
Confidence            33344455666666788999999999999999988753

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

Probab=87.27  E-value=0.71  Score=31.38  Aligned_cols=38  Identities=11%  Similarity=-0.050  Sum_probs=28.7

Q ss_pred             chHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          29 VPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        29 ~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      +...=..-|..+...-++|+.+||+.+|+++++|+..-
T Consensus        34 lt~~~~~iL~~l~~~~~~t~~ela~~l~~s~~~vs~~l   71 (142)
T 2fbi_A           34 LTEQQWRVIRILRQQGEMESYQLANQACILRPSMTGVL   71 (142)
T ss_dssp             CCHHHHHHHHHHHHHCSEEHHHHHHHTTCCHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHhHHHHHH
Confidence            33333445666667778999999999999999988754

>1j9i_A GPNU1 DBD;, terminase small subunit; DNA binding domain, homodimer, viral assembly, winged helix-turn-helix, viral protein; NMR {Enterobacteria phage lambda} SCOP: a.6.1.5

Probab=87.24  E-value=0.38  Score=29.33  Aligned_cols=27  Identities=15%  Similarity=0.235  Sum_probs=22.8

Q ss_pred             CCHHHHHHHhCCChhHHHHHhcCCCCCC
Q psy6501         136 WSQKDLATKINEKPQIVNDYEGGRGIPN  163 (174)
Q Consensus       136 lsq~ela~~lg~~~s~i~~~E~G~~~P~  163 (174)
                      ++.+++|+.+|+|++|+.+|..-.. |.
T Consensus         3 lt~~e~a~~LgvS~~Tl~rw~~~G~-P~   29 (68)
T 1j9i_A            3 VNKKQLADIFGASIRTIQNWQEQGM-PV   29 (68)
T ss_dssp             EEHHHHHHHTTCCHHHHHHHTTTTC-CC
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHCCC-Ce
Confidence            6789999999999999999987533 54

>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=87.18  E-value=0.81  Score=29.55  Aligned_cols=23  Identities=13%  Similarity=0.247  Sum_probs=21.1

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHH
Q psy6501          43 AKGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        43 ~~gltq~eLA~~igvs~~~is~~   65 (174)
                      ...+|..|||+.+|+|+++|++.
T Consensus        41 ~~~~~~~eLa~~l~is~~tv~~~   63 (96)
T 1y0u_A           41 DKGRSEEEIMQTLSLSKKQLDYH   63 (96)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHH
T ss_pred             cCCCCHHHHHHHHCcCHHHHHHH
Confidence            57799999999999999999984

>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=87.14  E-value=0.63  Score=32.11  Aligned_cols=29  Identities=14%  Similarity=0.039  Sum_probs=23.9

Q ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHH
Q psy6501          37 LMQGRQAKGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        37 ik~~R~~~gltq~eLA~~igvs~~~is~~   65 (174)
                      |..+.....+|..|||+.+|+|++++++.
T Consensus        10 l~~L~~~~~~~~~ela~~lg~s~~tv~~~   38 (141)
T 1i1g_A           10 LEILEKDARTPFTEIAKKLGISETAVRKR   38 (141)
T ss_dssp             HHHHHHCTTCCHHHHHHHHTSCHHHHHHH
T ss_pred             HHHHHHcCCCCHHHHHHHHCcCHHHHHHH
Confidence            44555666799999999999999999764

>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=87.08  E-value=1  Score=30.76  Aligned_cols=34  Identities=9%  Similarity=-0.046  Sum_probs=26.9

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        33 ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      -..-|..+...-++|+.+||+.+|+++++|+..-
T Consensus        35 ~~~iL~~l~~~~~~~~~~la~~l~~s~~tvs~~l   68 (145)
T 2a61_A           35 QFDILQKIYFEGPKRPGELSVLLGVAKSTVTGLV   68 (145)
T ss_dssp             HHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHCCCchhHHHHH
Confidence            3445556666778999999999999999998764

>2w7n_A TRFB transcriptional repressor protein; INCP, plasmid, repressor, DNA-binding, transcription/DNA; HET: BRU; 1.85A {Escherichia coli}

Probab=87.07  E-value=0.49  Score=31.72  Aligned_cols=23  Identities=22%  Similarity=0.208  Sum_probs=20.9

Q ss_pred             hcCCCHHHHHHHhCCChhHHHHH
Q psy6501         133 AKGWSQKDLATKINEKPQIVNDY  155 (174)
Q Consensus       133 ~~glsq~ela~~lg~~~s~i~~~  155 (174)
                      ..|++|.++|+.+|+|..+|+++
T Consensus        32 v~g~tQ~eIA~~lGiSR~~Vsrl   54 (101)
T 2w7n_A           32 VDGKPQATFATSLGLTRGAVSQA   54 (101)
T ss_dssp             TTCCCHHHHHHHHTCCHHHHHHH
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHH
Confidence            47899999999999999999875

>1yse_A DNA-binding protein SATB1; all helical, DNA-binding domain, T-cell development; NMR {Homo sapiens} SCOP: a.35.1.7

Probab=87.01  E-value=0.74  Score=32.65  Aligned_cols=62  Identities=13%  Similarity=0.103  Sum_probs=45.8

Q ss_pred             ccchHHHHHHHHHHHHHcCCCHHHHHH-HhCCCHHHHHHHHcCCCC------CCHHHHHHHHHHhCccc
Q psy6501          27 EKVPLDLAKLLMQGRQAKGWSQKDLAT-KINEKPQIVNDYEGGRGI------PNQAIIGKMERALGIRL   88 (174)
Q Consensus        27 ~~~~~~ig~~ik~~R~~~gltq~eLA~-~igvs~~~is~~E~G~~~------P~~~~l~~la~~L~v~~   88 (174)
                      ..+..+|..+|++-.+..++||+-||+ -+|.++.++|.+-+.-.-      +--+.+.++-..|+.+.
T Consensus        20 ~~vt~~I~~~Ik~eLk~~~IsQ~~FA~~VL~rsQGtLS~LLr~PkdPW~~LksGRE~fiRM~NWL~Lpe   88 (141)
T 1yse_A           20 TEVSSEIYQWVRDELKRAGISQAVFARVAFNRTQGLLSEILRKEEDPKTASQSLLVNLRAMQNFLQLPE   88 (141)
T ss_dssp             CSCCTHHHHHHHHHHHHHTCCHHHHHHHHCCSCTTHHHHHHHHCCCGGGCCHHHHHHHHHHHHHHHSCH
T ss_pred             ccchHHHHHHHHHHHHHcCCCHHHHHHHHHHhhhhhHHHHHcCCCCcHHHHHHHHHHHHHHHHHhcCCH
Confidence            345678999999999999999999999 568999999998764432      12344455555555553

>1d5y_A ROB transcription factor; protein-DNA complex, DNA, transcription/DNA complex; HET: DNA; 2.70A {Escherichia coli} SCOP: a.4.1.8 a.4.1.8 d.60.1.2

Probab=87.00  E-value=2.1  Score=32.95  Aligned_cols=22  Identities=14%  Similarity=0.063  Sum_probs=20.7

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHH
Q psy6501          44 KGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~   65 (174)
                      ..+|..+||+.+|+|+++++++
T Consensus        18 ~~~~~~~la~~~~~s~~~l~r~   39 (292)
T 1d5y_A           18 QPLSLDNVAAKAGYSKWHLQRM   39 (292)
T ss_dssp             SSCCCHHHHTTTSSCHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHH
Confidence            4799999999999999999998

>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=86.99  E-value=0.4  Score=33.63  Aligned_cols=30  Identities=13%  Similarity=0.101  Sum_probs=24.4

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHH
Q psy6501          36 LLMQGRQAKGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~   65 (174)
                      -|..+.+...+|..|||+.+|+|++++++.
T Consensus         8 il~~L~~~~~~~~~ela~~lg~s~~tv~~~   37 (150)
T 2pn6_A            8 ILKILQYNAKYSLDEIAREIRIPKATLSYR   37 (150)
T ss_dssp             HHHHHTTCTTSCHHHHHHHHTSCHHHHHHH
T ss_pred             HHHHHHHcCCCCHHHHHHHHCcCHHHHHHH
Confidence            345555566799999999999999998875

>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=86.84  E-value=0.67  Score=32.62  Aligned_cols=31  Identities=3%  Similarity=0.048  Sum_probs=25.7

Q ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHH
Q psy6501          35 KLLMQGRQAKGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~~   65 (174)
                      .-|..+.+...+|..+||+.+|+|++++++.
T Consensus        11 ~il~~L~~~~~~s~~ela~~lg~s~~tv~~~   41 (151)
T 2cyy_A           11 KIIKILQNDGKAPLREISKITGLAESTIHER   41 (151)
T ss_dssp             HHHHHHHHCTTCCHHHHHHHHCSCHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHH
Confidence            3455666677899999999999999998874

>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=86.77  E-value=0.83  Score=30.12  Aligned_cols=24  Identities=13%  Similarity=0.033  Sum_probs=21.5

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          43 AKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        43 ~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ..++|..|||+.+|+|+++|++.-
T Consensus        37 ~~~~~~~ela~~l~is~stvs~~L   60 (106)
T 1r1u_A           37 VSEASVGHISHQLNLSQSNVSHQL   60 (106)
T ss_dssp             HCCBCHHHHHHHHTCCHHHHHHHH
T ss_pred             hCCCCHHHHHHHHCcCHHHHHHHH
Confidence            577999999999999999998864

>3mzy_A RNA polymerase sigma-H factor; PSI, MCSG, structural genomics, midwest center for structura genomics, protein structure initiative; 2.50A {Fusobacterium nucleatum subsp}

Probab=86.68  E-value=0.85  Score=31.62  Aligned_cols=27  Identities=15%  Similarity=0.319  Sum_probs=24.3

Q ss_pred             HHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          41 RQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        41 R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      +.-.|+|.+|+|+.+|+|.++|.+.-.
T Consensus       120 ~~~~g~s~~EIA~~lgis~~tV~~~~~  146 (164)
T 3mzy_A          120 YLIRGYSYREIATILSKNLKSIDNTIQ  146 (164)
T ss_dssp             HHTTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            567999999999999999999998763

>1rp3_A RNA polymerase sigma factor sigma-28 (FLIA); transcription; 2.30A {Aquifex aeolicus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1sc5_A

Probab=86.67  E-value=0.83  Score=33.89  Aligned_cols=29  Identities=14%  Similarity=0.068  Sum_probs=25.4

Q ss_pred             HHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          39 QGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        39 ~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      .+|-..|+|++|+|+.+|+|.++|+++..
T Consensus       197 ~l~~~~g~s~~EIA~~lgis~~~V~~~~~  225 (239)
T 1rp3_A          197 QLIFYEELPAKEVAKILETSVSRVSQLKA  225 (239)
T ss_dssp             HHHHTSCCCHHHHHHHTTSCHHHHHHHHH
T ss_pred             HHHHhcCCCHHHHHHHhCCCHHHHHHHHH
Confidence            35567899999999999999999998874

>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=86.59  E-value=0.52  Score=32.12  Aligned_cols=30  Identities=10%  Similarity=-0.107  Sum_probs=24.4

Q ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          37 LMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        37 ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      |..+....++|..|||+.+|+|+++||+.-
T Consensus        48 L~~L~~~~~~s~~eLa~~l~is~stvs~~L   77 (122)
T 1u2w_A           48 TYALCQDEELCVCDIANILGVTIANASHHL   77 (122)
T ss_dssp             HHHHHHSSCEEHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHCCCcCHHHHHHHHCcCHHHHHHHH
Confidence            444444568999999999999999999764

>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=86.46  E-value=0.53  Score=32.28  Aligned_cols=38  Identities=8%  Similarity=-0.034  Sum_probs=26.7

Q ss_pred             chHHHHHHHHHHH-HHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          29 VPLDLAKLLMQGR-QAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        29 ~~~~ig~~ik~~R-~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      +...-..-+..+. ...++|+.|||+.+|++++++++.-
T Consensus        24 l~~~~~~il~~L~~~~~~~t~~ela~~l~~~~stvs~~l   62 (152)
T 1ku9_A           24 LNKSVGAVYAILYLSDKPLTISDIMEELKISKGNVSMSL   62 (152)
T ss_dssp             CCHHHHHHHHHHHHCSSCEEHHHHHHHHTCCHHHHHHHH
T ss_pred             CChhHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHH
Confidence            3333344444443 2468999999999999999988753

>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=86.43  E-value=0.97  Score=31.46  Aligned_cols=34  Identities=9%  Similarity=-0.074  Sum_probs=27.4

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        33 ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      -..-|..+...-++|+.+||+.+++++++|++.-
T Consensus        46 ~~~iL~~l~~~~~~t~~ela~~l~is~~tvs~~l   79 (154)
T 2eth_A           46 ELYAFLYVALFGPKKMKEIAEFLSTTKSNVTNVV   79 (154)
T ss_dssp             HHHHHHHHHHHCCBCHHHHHHHTTSCHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHH
Confidence            3445666666779999999999999999998753

>2oz6_A Virulence factor regulator; winged helix, helix-turn-helix, transcription factor, CAMP-B proteins, CAMP receptor protein; HET: CMP; 2.80A {Pseudomonas aeruginosa} SCOP: a.4.5.4 b.82.3.2

Probab=86.43  E-value=0.51  Score=34.21  Aligned_cols=22  Identities=5%  Similarity=0.135  Sum_probs=19.9

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHH
Q psy6501          45 GWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        45 gltq~eLA~~igvs~~~is~~E   66 (174)
                      .+||++||..+|+|+.+||+.-
T Consensus       164 ~~t~~~lA~~lg~sr~tvsR~l  185 (207)
T 2oz6_A          164 KITRQEIGRIVGCSREMVGRVL  185 (207)
T ss_dssp             ECCHHHHHHHHTSCHHHHHHHH
T ss_pred             ccCHHHHHHHhCCCHHHHHHHH
Confidence            4899999999999999999864

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

Probab=86.41  E-value=1.1  Score=29.88  Aligned_cols=29  Identities=28%  Similarity=0.189  Sum_probs=23.4

Q ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          37 LMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        37 ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      |..+.+ ..+|+.++|+.+|+|+++|++.-
T Consensus        38 l~~L~~-~~~s~~ela~~l~is~stvsr~l   66 (119)
T 2lkp_A           38 LTQLRN-GPLPVTDLAEAIGMEQSAVSHQL   66 (119)
T ss_dssp             HHHHHH-CCCCHHHHHHHHSSCHHHHHHHH
T ss_pred             HHHHHH-CCCCHHHHHHHHCcCHHHHHHHH
Confidence            334444 67999999999999999999764

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

Probab=86.40  E-value=0.5  Score=33.18  Aligned_cols=31  Identities=16%  Similarity=0.157  Sum_probs=23.6

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          36 LLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      -|..+...-++|+.+||+.+++++++|+++-
T Consensus        55 vL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l   85 (159)
T 3s2w_A           55 FLMRLYREDGINQESLSDYLKIDKGTTARAI   85 (159)
T ss_dssp             HHHHHHHSCSEEHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHCCCCCHHHHHHHHCCCHHHHHHHH
Confidence            3445555677899999999999998888764

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

Probab=86.31  E-value=0.81  Score=30.21  Aligned_cols=29  Identities=21%  Similarity=0.114  Sum_probs=23.8

Q ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          37 LMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        37 ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      |..+ ...++|..|||+.+|+|+++|++.-
T Consensus        27 L~~L-~~~~~~~~ela~~l~is~~tv~~~l   55 (114)
T 2oqg_A           27 LTEL-GRADQSASSLATRLPVSRQAIAKHL   55 (114)
T ss_dssp             HHHH-HHSCBCHHHHHHHSSSCHHHHHHHH
T ss_pred             HHHH-HcCCCCHHHHHHHHCcCHHHHHHHH
Confidence            3344 5678999999999999999998763

>2jml_A DNA binding domain/transcriptional regulator; anti-repressor, MERR, carotenogenesis; HET: DNA; NMR {Myxococcus xanthus}

Probab=86.31  E-value=0.36  Score=30.57  Aligned_cols=23  Identities=9%  Similarity=0.138  Sum_probs=21.4

Q ss_pred             CCCHHHHHHHhCCChhHHHHHhc
Q psy6501         135 GWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       135 glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      .++..++|+.+|++++++..||.
T Consensus         5 ~~~i~e~A~~~gvs~~tlR~ye~   27 (81)
T 2jml_A            5 TLRIRTIARMTGIREATLRAWER   27 (81)
T ss_dssp             CEEHHHHHHTTSTTHHHHHHHHH
T ss_pred             cccHHHHHHHHCcCHHHHHHHHH
Confidence            47889999999999999999998

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

Probab=86.27  E-value=0.71  Score=33.46  Aligned_cols=31  Identities=6%  Similarity=0.130  Sum_probs=25.9

Q ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHH
Q psy6501          35 KLLMQGRQAKGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~~   65 (174)
                      .-|..+.....+|..|||+.+|+|++++++.
T Consensus        21 ~IL~~L~~~~~~s~~eLA~~lglS~~tv~~~   51 (171)
T 2ia0_A           21 NILRLLKKDARLTISELSEQLKKPESTIHFR   51 (171)
T ss_dssp             HHHHHHHHCTTCCHHHHHHHHTSCHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHH
Confidence            3466667777899999999999999998875

>1or7_A Sigma-24, RNA polymerase sigma-E factor; regulation, DNA-binding, transmembrane, transcription; 2.00A {Escherichia coli} SCOP: a.4.13.2 a.177.1.1 PDB: 2h27_A

Probab=86.27  E-value=0.92  Score=32.63  Aligned_cols=31  Identities=16%  Similarity=0.097  Sum_probs=26.2

Q ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          37 LMQGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        37 ik~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      +-.++.-.|+|.+|+|+.+|+|.++|.+.-.
T Consensus       148 vl~l~~~~g~s~~EIA~~lgis~~tV~~~l~  178 (194)
T 1or7_A          148 AITLRELDGLSYEEIAAIMDCPVGTVRSRIF  178 (194)
T ss_dssp             HHHHHHTTCCCHHHHHHHTTSCHHHHHHHHH
T ss_pred             HhHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            3345667899999999999999999998763

>1g2h_A Transcriptional regulatory protein TYRR homolog; protein structure, , DNA-binding domain, helix- turn-helix motif; NMR {Haemophilus influenzae} SCOP: a.4.1.12

Probab=86.20  E-value=1.3  Score=26.39  Aligned_cols=33  Identities=15%  Similarity=0.057  Sum_probs=26.3

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      -..|....+.. .++.+.|+.+|||++|+.+.-+
T Consensus        23 r~~I~~aL~~~-gn~~~aA~~LGIsr~tL~rklk   55 (61)
T 1g2h_A           23 AQVLKLFYAEY-PSTRKLAQRLGVSHTAIANKLK   55 (61)
T ss_dssp             HHHHHHHHHHS-CSHHHHHHHTTSCTHHHHHHHH
T ss_pred             HHHHHHHHHHh-CCHHHHHHHhCCCHHHHHHHHH
Confidence            44566666667 6999999999999999987654

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

Probab=86.10  E-value=0.8  Score=29.91  Aligned_cols=28  Identities=7%  Similarity=-0.006  Sum_probs=23.2

Q ss_pred             HHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          39 QGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        39 ~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      .+....++|..|+|+.+|+|++++|+--
T Consensus        35 ~l~~~~~~~~~ela~~l~is~stvs~hL   62 (99)
T 2zkz_A           35 ELYKHKALNVTQIIQILKLPQSTVSQHL   62 (99)
T ss_dssp             HHHHHSCEEHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHCCCcCHHHHHHHHCcCHHHHHHHH
Confidence            3345567999999999999999999753

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

Probab=86.05  E-value=0.84  Score=31.93  Aligned_cols=32  Identities=9%  Similarity=0.041  Sum_probs=23.9

Q ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          35 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      .-|..+...-++|+.+||+.+|+++++|+..-
T Consensus        53 ~iL~~l~~~~~~t~~ela~~l~is~~tvs~~l   84 (162)
T 2fa5_A           53 RVITILALYPGSSASEVSDRTAMDKVAVSRAV   84 (162)
T ss_dssp             HHHHHHHHSTTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHH
Confidence            34555555668899999999999998887753

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

Probab=86.00  E-value=0.92  Score=31.43  Aligned_cols=33  Identities=3%  Similarity=0.032  Sum_probs=24.4

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ..-|..+...-++|+.+||+.+++++++|+..-
T Consensus        50 ~~iL~~l~~~~~~t~~ela~~l~~s~~tvs~~l   82 (153)
T 2pex_A           50 YLVMLVLWETDERSVSEIGERLYLDSATLTPLL   82 (153)
T ss_dssp             HHHHHHHHHSCSEEHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHhCCCcCHHHHHHHhCCCcccHHHHH
Confidence            344555556677888999999999998888653

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

Probab=85.87  E-value=1.3  Score=34.24  Aligned_cols=36  Identities=19%  Similarity=0.154  Sum_probs=28.7

Q ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          31 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        31 ~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ..--.-|..+.+..++|+.|||+.+|++++|+++.-
T Consensus       152 ~~~~~IL~~L~~~~~~s~~eLA~~lglsksTv~r~L  187 (244)
T 2wte_A          152 REEMKLLNVLYETKGTGITELAKMLDKSEKTLINKI  187 (244)
T ss_dssp             HHHHHHHHHHHHHTCBCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHH
Confidence            334455666667789999999999999999999874

>3ryp_A Catabolite gene activator; CAMP receptor protein (CRP), allostery, DNA binding cyclic A transcription regulator; HET: CMP; 1.60A {Escherichia coli} PDB: 2cgp_A* 3hif_A 1g6n_A* 3ryr_A* 1i5z_A* 1j59_A* 1lb2_A* 1run_A* 1zrc_A* 1zrd_A* 1zre_A* 1zrf_A* 2gzw_A* 2wc2_A 3iyd_G* 3n4m_A* 3qop_A* 3rdi_A* 3rou_A* 3rpq_A* ...

Probab=85.84  E-value=0.56  Score=34.07  Aligned_cols=22  Identities=5%  Similarity=0.098  Sum_probs=20.1

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHH
Q psy6501          45 GWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        45 gltq~eLA~~igvs~~~is~~E   66 (174)
                      .+||++||..+|+|+.+||+.-
T Consensus       167 ~~t~~~iA~~lg~sr~tvsR~l  188 (210)
T 3ryp_A          167 KITRQEIGQIVGCSRETVGRIL  188 (210)
T ss_dssp             ECCHHHHHHHHTCCHHHHHHHH
T ss_pred             ccCHHHHHHHhCCcHHHHHHHH
Confidence            5899999999999999999864

>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=85.83  E-value=1.3  Score=32.62  Aligned_cols=36  Identities=11%  Similarity=0.051  Sum_probs=28.6

Q ss_pred             hHHHHHHHHHHHHHcC--CCHHHHHHHhCCCHHHHHHH
Q psy6501          30 PLDLAKLLMQGRQAKG--WSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~g--ltq~eLA~~igvs~~~is~~   65 (174)
                      ...+-+.|.+...+.|  .|+.|||+.+|+|+++++++
T Consensus         7 q~~il~~I~~~~~~~g~~~s~~eia~~lgl~~~tv~~~   44 (196)
T 3k2z_A            7 QRKVLLFIEEFIEKNGYPPSVREIARRFRITPRGALLH   44 (196)
T ss_dssp             HHHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCcHHHHHH
Confidence            3456677777766666  79999999999999888774

>1eto_A FIS, factor for inversion stimulation; transcriptional activation region, DNA-binding protein, transcription activator; 1.90A {Escherichia coli} SCOP: a.4.1.12 PDB: 1etq_A 1ety_A 1fia_A 3fis_A 3iv5_A* 3jr9_A* 3jra_A* 3jrb_A* 3jrc_A* 3jrd_A* 3jre_A* 3jrf_A* 3jrg_A* 3jrh_A* 3jri_A* 1f36_A 1etv_A 1etk_A 1etx_A 1fip_A ...

Probab=85.74  E-value=1.5  Score=29.02  Aligned_cols=33  Identities=15%  Similarity=-0.113  Sum_probs=28.5

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      -..|..+.+..+..+.+.|+.+|||++++.+.-
T Consensus        60 r~~I~~aL~~~~gn~~~AA~~LGIsR~TL~rkL   92 (98)
T 1eto_A           60 QPLLDMVMQYTLGNQTRAALMMGINRGTLRKKL   92 (98)
T ss_dssp             HHHHHHHHHHTTTCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHH
Confidence            456778888899999999999999999998754

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

Probab=85.73  E-value=0.91  Score=31.81  Aligned_cols=22  Identities=14%  Similarity=0.190  Sum_probs=18.3

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHH
Q psy6501          45 GWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        45 gltq~eLA~~igvs~~~is~~E   66 (174)
                      ++||.+||+.+++++++|++.-
T Consensus        52 ~~t~~eLa~~l~~~~~tvsr~v   73 (148)
T 4fx0_A           52 DLTMSELAARIGVERTTLTRNL   73 (148)
T ss_dssp             --CHHHHHHHHTCCHHHHHHHH
T ss_pred             CcCHHHHHHHHCCChhhHHHHH
Confidence            4899999999999999998764

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

Probab=85.67  E-value=0.74  Score=31.46  Aligned_cols=31  Identities=16%  Similarity=0.240  Sum_probs=24.9

Q ss_pred             HHHHHH-HHHcCCCHHHHHHHhCCCHHHHHHH
Q psy6501          35 KLLMQG-RQAKGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        35 ~~ik~~-R~~~gltq~eLA~~igvs~~~is~~   65 (174)
                      .-|..+ ...-++|+.+||+.+|+++++|+..
T Consensus        41 ~iL~~l~~~~~~~t~~~la~~l~~s~~~vs~~   72 (146)
T 2fbh_A           41 LVLLHLARHRDSPTQRELAQSVGVEGPTLARL   72 (146)
T ss_dssp             HHHHHHHHCSSCCBHHHHHHHHTCCHHHHHHH
T ss_pred             HHHHHHHHcCCCCCHHHHHHHhCCChhhHHHH
Confidence            345555 5567899999999999999999876

>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=85.66  E-value=0.8  Score=31.42  Aligned_cols=39  Identities=5%  Similarity=0.008  Sum_probs=29.5

Q ss_pred             cchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          28 KVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        28 ~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      .+...-..-|..+...-++|+.+||+.+++++++|+..-
T Consensus        37 ~l~~~~~~iL~~l~~~~~~~~~~la~~l~~~~~tvs~~l   75 (147)
T 1z91_A           37 NITYPQYLALLLLWEHETLTVKKMGEQLYLDSGTLTPML   75 (147)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEHHHHHHTTTCCHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCcCcHHHHH
Confidence            344444455666666778999999999999999998754

>2fmy_A COOA, carbon monoxide oxidation system transcription RE COOA-1; DNA transcription regulator, DNA binding protein; HET: HEM; 2.20A {Carboxydothermus hydrogenoformans} PDB: 2hkx_A*

Probab=85.61  E-value=1.3  Score=32.54  Aligned_cols=23  Identities=17%  Similarity=0.206  Sum_probs=20.3

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ..+||++||..+|+|+.+||+.-
T Consensus       166 ~~~t~~~lA~~lg~sr~tvsR~l  188 (220)
T 2fmy_A          166 LGLNTEEIALMLGTTRQTVSVLL  188 (220)
T ss_dssp             CSSCHHHHHHHHTSCHHHHHHHH
T ss_pred             ccCCHHHHHHHhCCcHHHHHHHH
Confidence            35899999999999999999764

>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=85.60  E-value=0.71  Score=33.90  Aligned_cols=30  Identities=13%  Similarity=0.070  Sum_probs=23.1

Q ss_pred             HHHHHHH-cCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          37 LMQGRQA-KGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        37 ik~~R~~-~gltq~eLA~~igvs~~~is~~E   66 (174)
                      |..+++. ..+|.+|||+.+|||++||.+.-
T Consensus        27 l~~L~~~~~~~s~~eLa~~l~vS~~Ti~rdi   57 (187)
T 1j5y_A           27 VRILERSKEPVSGAQLAEELSVSRQVIVQDI   57 (187)
T ss_dssp             HHHHHHCSSCBCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHcCCCcCHHHHHHHHCcCHHHHHHHH
Confidence            3444443 34999999999999999998753

>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=85.58  E-value=0.32  Score=39.70  Aligned_cols=31  Identities=16%  Similarity=0.176  Sum_probs=27.6

Q ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          35 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      .-|+.+| ...+|..|||+.+|+|++||+++-
T Consensus        24 ~il~~l~-~~~~sr~~la~~~gls~~tv~~~v   54 (380)
T 2hoe_A           24 RILKRIM-KSPVSRVELAEELGLTKTTVGEIA   54 (380)
T ss_dssp             CSHHHHH-HSCBCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHH-cCCcCHHHHHHHHCcCHHHHHHHH
Confidence            3478889 899999999999999999999863

>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=85.58  E-value=0.73  Score=31.50  Aligned_cols=32  Identities=16%  Similarity=0.077  Sum_probs=25.6

Q ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          35 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      .-|..+...-++|+.+||+.+|+++++|+..-
T Consensus        33 ~iL~~l~~~~~~t~~~la~~l~~s~~~vs~~l   64 (144)
T 1lj9_A           33 LYLVRVCENPGIIQEKIAELIKVDRTTAARAI   64 (144)
T ss_dssp             HHHHHHHHSTTEEHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHCcCcCHHHHHHHHCCCHhHHHHHH
Confidence            34555556678999999999999999998753

>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=85.57  E-value=0.85  Score=31.48  Aligned_cols=35  Identities=14%  Similarity=0.101  Sum_probs=25.9

Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          32 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        32 ~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      .-..-|..+...-++|+.+||+.+|+++++|++.-
T Consensus        41 ~~~~iL~~l~~~~~~t~~ela~~l~~~~~~vs~~l   75 (152)
T 3bj6_A           41 GQRAILEGLSLTPGATAPQLGAALQMKRQYISRIL   75 (152)
T ss_dssp             HHHHHHHHHHHSTTEEHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHH
Confidence            33444555556668999999999999999888753

>3dv8_A Transcriptional regulator, CRP/FNR family; cyclic nucleotide-binding domain, structural genomics, joint for structural genomics; 2.55A {Eubacterium rectale atcc 33656}

Probab=85.50  E-value=1.4  Score=32.05  Aligned_cols=22  Identities=5%  Similarity=0.237  Sum_probs=20.2

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHH
Q psy6501          45 GWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        45 gltq~eLA~~igvs~~~is~~E   66 (174)
                      .+||++||..+|+|+.+||+.-
T Consensus       169 ~~t~~~lA~~lg~sr~tvsR~l  190 (220)
T 3dv8_A          169 KITHETIANHLGSHREVITRML  190 (220)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHH
T ss_pred             cCCHHHHHHHhCCCHHHHHHHH
Confidence            7899999999999999998874

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

Probab=85.47  E-value=5.6  Score=26.46  Aligned_cols=26  Identities=12%  Similarity=0.340  Sum_probs=21.8

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHcCC
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYEGGR   69 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E~G~   69 (174)
                      ..+|..+||+.+|+|++++++.=+-.
T Consensus        22 ~~~~~~~lA~~~~~S~~~l~r~fk~~   47 (120)
T 3mkl_A           22 HEWTLARIASELLMSPSLLKKKLREE   47 (120)
T ss_dssp             SCCCHHHHHHHTTCCHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHc
Confidence            37999999999999999998875433

>2zcw_A TTHA1359, transcriptional regulator, FNR/CRP family; stationary phase, DNA-binding, transcription regulation; 1.50A {Thermus thermophilus}

Probab=85.44  E-value=0.6  Score=33.89  Aligned_cols=22  Identities=14%  Similarity=0.163  Sum_probs=19.7

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHH
Q psy6501          45 GWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        45 gltq~eLA~~igvs~~~is~~E   66 (174)
                      .+||++||..+|+|+.+||+.-
T Consensus       146 ~~t~~~lA~~lg~sr~tvsR~l  167 (202)
T 2zcw_A          146 KATHDELAAAVGSVRETVTKVI  167 (202)
T ss_dssp             ECCHHHHHHHHTCCHHHHHHHH
T ss_pred             CCCHHHHHHHhCCCHHHHHHHH
Confidence            3899999999999999998764

>1r71_A Transcriptional repressor protein KORB; INCP, plasmid partitioning, protein-DNA complex, heilx-turn- helix motif, transcription factor; HET: BRU; 2.20A {Escherichia coli} SCOP: a.4.14.1

Probab=85.08  E-value=2  Score=31.52  Aligned_cols=45  Identities=20%  Similarity=0.319  Sum_probs=32.5

Q ss_pred             HHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHH
Q psy6501         124 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKM  170 (174)
Q Consensus       124 ~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i  170 (174)
                      ...++.+.. .|+|+.++|+++|.++++|+++-+=-..|+ .++..+
T Consensus        42 A~a~~~L~~-~G~t~eeiA~~lG~s~s~V~~~LrLl~Lp~-~v~~~v   86 (178)
T 1r71_A           42 ADFIGRELA-KGKKKGDIAKEIGKSPAFITQHVTLLDLPE-KIADAF   86 (178)
T ss_dssp             HHHHHHHHH-TTCCHHHHHHHHTCCHHHHHHHHGGGSCCH-HHHHHH
T ss_pred             HHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHcCCH-HHHHHH
Confidence            334443333 499999999999999999999988666555 444444

>1u78_A TC3 transposase, transposable element TC3 transposase; transposon DNA, bipartite DNA-binding, HTH- motif, DNA binding protein/DNA complex; 2.69A {Caenorhabditis elegans} SCOP: a.4.1.2 a.4.1.2

Probab=85.04  E-value=2  Score=29.13  Aligned_cols=36  Identities=3%  Similarity=0.090  Sum_probs=28.1

Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHhC--CCHHHHHHHHc
Q psy6501          32 DLAKLLMQGRQAKGWSQKDLATKIN--EKPQIVNDYEG   67 (174)
Q Consensus        32 ~ig~~ik~~R~~~gltq~eLA~~ig--vs~~~is~~E~   67 (174)
                      ..-..|..+....++|..++|..+|  +|.+||.+|-.
T Consensus        64 ~~~~~i~~~~~~~~~s~~~i~~~lg~~~s~~tV~r~l~  101 (141)
T 1u78_A           64 RDERNVIRAASNSCKTARDIRNELQLSASKRTILNVIK  101 (141)
T ss_dssp             HHHHHHHHHHHHCCCCHHHHHHHTTCCSCHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCCCHHHHHHHHCCCccHHHHHHHHH
Confidence            3345555556677899999999998  79999999864

>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=84.95  E-value=1.1  Score=30.61  Aligned_cols=32  Identities=9%  Similarity=-0.084  Sum_probs=24.7

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ..-|..+. ..++|+.+||+.+|+++++|+..-
T Consensus        40 ~~iL~~l~-~~~~~~~ela~~l~~s~~tvs~~l   71 (146)
T 2gxg_A           40 FLVLRATS-DGPKTMAYLANRYFVTQSAITASV   71 (146)
T ss_dssp             HHHHHHHT-TSCBCHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHh-cCCcCHHHHHHHhCCCchhHHHHH
Confidence            34455555 778999999999999999888753

>4dyq_A Gene 1 protein; GP1, octamer, DNA-binding, viral protein; 1.50A {Shigella phage SF6} PDB: 4dyc_A 4dyr_A 3hef_A 4dzj_A 4dzp_A

Probab=84.88  E-value=0.71  Score=32.46  Aligned_cols=46  Identities=13%  Similarity=0.050  Sum_probs=33.9

Q ss_pred             HcCCCHHHHHHHhCC-CHHHHHHHHcCCCCCCHHHHHHHHHHhCccccccc
Q psy6501          43 AKGWSQKDLATKINE-KPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNA   92 (174)
Q Consensus        43 ~~gltq~eLA~~igv-s~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~   92 (174)
                      ..|.|..++|...|| |.+||.+|-+-.    .+....+.++-....+.++
T Consensus        26 ~~G~sl~~i~~~~~~ps~~T~~~W~~~~----~ef~e~~~~Ar~~~~~~~~   72 (140)
T 4dyq_A           26 SSGESLLKVCKRPGMPDKSTVFRWLAKH----EDFRDKYAKATEARADSIF   72 (140)
T ss_dssp             HTTCCHHHHHTSTTCCCHHHHHHHHHHC----HHHHHHHHHHHHHHHHHHH
T ss_pred             HCCCcHHHHHhcCCCCCHHHHHHHHHcC----HHHHHHHHHHHHHHHHHHH
Confidence            489999999999999 999999998643    3455555555555554443

>1z05_A Transcriptional regulator, ROK family; structural genomics, protein structure initiative, midwest center for structural genomics; 2.00A {Vibrio cholerae o1 biovar eltor} SCOP: a.4.5.63 c.55.1.10 c.55.1.10

Probab=84.79  E-value=0.9  Score=37.60  Aligned_cols=33  Identities=15%  Similarity=0.128  Sum_probs=29.4

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ..-|+.+|....+|..|||+.+|+|++||+++-
T Consensus        42 ~~il~~l~~~~~~sr~ela~~~gls~~tv~~~v   74 (429)
T 1z05_A           42 GRVYKLIDQKGPISRIDLSKESELAPASITKIT   74 (429)
T ss_dssp             HHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHH
Confidence            456888999999999999999999999999863

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

Probab=84.72  E-value=0.82  Score=32.49  Aligned_cols=33  Identities=15%  Similarity=0.074  Sum_probs=25.9

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ..-|..+...-++|+.+||+.+|+++++|++.-
T Consensus        48 ~~iL~~L~~~~~~t~~eLa~~l~is~~tvs~~l   80 (168)
T 2nyx_A           48 FRTLVILSNHGPINLATLATLLGVQPSATGRMV   80 (168)
T ss_dssp             HHHHHHHHHHCSEEHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHH
Confidence            344555666678999999999999999998763

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

Probab=84.70  E-value=0.82  Score=32.15  Aligned_cols=32  Identities=16%  Similarity=-0.047  Sum_probs=24.7

Q ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          35 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      .-|..+...-++|+.+||+.+|+++++|++.-
T Consensus        57 ~vL~~l~~~~~~t~~eLa~~l~~~~~~vs~~l   88 (161)
T 3e6m_A           57 RLLSSLSAYGELTVGQLATLGVMEQSTTSRTV   88 (161)
T ss_dssp             HHHHHHHHHSEEEHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHH
Confidence            34555666678899999999999999888753

>4fe7_A Xylose operon regulatory protein; HTH_ARAC, helix-turn-helix, PBP, periplasmic binding protein binding transcription regulator, DNA xylose; HET: XYS; 2.90A {Escherichia coli} PDB: 4fe4_A

Probab=84.61  E-value=10  Score=30.58  Aligned_cols=48  Identities=8%  Similarity=0.114  Sum_probs=34.6

Q ss_pred             HHHHHHHHHHHH--HcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccccccc
Q psy6501          31 LDLAKLLMQGRQ--AKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNA   92 (174)
Q Consensus        31 ~~ig~~ik~~R~--~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~   92 (174)
                      ..+...+..+..  ...+|.+++|+.+|+|++++++.              +.+.+|+++..+.
T Consensus       305 ~~~~~~~~~i~~~~~~~~~~~~~a~~~~~s~~~l~r~--------------f~~~~g~s~~~~~  354 (412)
T 4fe7_A          305 PAVIQAMHYIRNHACKGIKVDQVLDAVGISRSNLEKR--------------FKEEVGETIHAMI  354 (412)
T ss_dssp             HHHHHHHHHHHHHGGGTCCHHHHHHHTTCCHHHHHHH--------------HHHHHSSCHHHHH
T ss_pred             HHHHHHHHHHHhhccCCCCHHHHHHHHCcCHHHHHHH--------------HHHHHCcCHHHHH
Confidence            445555555555  36899999999999999999876              4556666655443

>4ev0_A Transcription regulator, CRP family; CAMP binding, winged helix-turn-helix motif, DNA binding, transcription activator; HET: CMP; 2.40A {Thermus thermophilus}

Probab=84.61  E-value=0.69  Score=33.70  Aligned_cols=23  Identities=13%  Similarity=0.046  Sum_probs=20.3

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ..+||+++|..+|+|+.+||+.-
T Consensus       162 ~~~t~~~lA~~lg~sr~tvsR~l  184 (216)
T 4ev0_A          162 FQIRHHELAALAGTSRETVSRVL  184 (216)
T ss_dssp             EECCHHHHHHHHTSCHHHHHHHH
T ss_pred             CCCCHHHHHHHhCCCHHHHHHHH
Confidence            34799999999999999999864

>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=84.58  E-value=1.4  Score=30.39  Aligned_cols=32  Identities=16%  Similarity=0.288  Sum_probs=23.9

Q ss_pred             HHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHH
Q psy6501          34 AKLLMQGRQA-KGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        34 g~~ik~~R~~-~gltq~eLA~~igvs~~~is~~   65 (174)
                      ..-|..+... .++|+.+||+.+++++++|++.
T Consensus        42 ~~vL~~l~~~~~~~t~~eLa~~l~i~~~tvs~~   74 (150)
T 3fm5_A           42 YSVLVLACEQAEGVNQRGVAATMGLDPSQIVGL   74 (150)
T ss_dssp             HHHHHHHHHSTTCCCSHHHHHHHTCCHHHHHHH
T ss_pred             HHHHHHHHhCCCCcCHHHHHHHHCCCHhHHHHH
Confidence            3444455433 4689999999999999999885

>3iwz_A CAP-like, catabolite activation-like protein; XCC, pathogenicity, CRP, CLP, C-DI-GMP receptor, quorum SENS binding, transcription; 2.30A {Xanthomonas campestris PV}

Probab=84.54  E-value=0.69  Score=34.08  Aligned_cols=21  Identities=14%  Similarity=0.154  Sum_probs=19.6

Q ss_pred             CCHHHHHHHhCCCHHHHHHHH
Q psy6501          46 WSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E   66 (174)
                      +||++||..+|+|+.+||+.-
T Consensus       188 lt~~~lA~~lg~sr~tvsR~l  208 (230)
T 3iwz_A          188 VSRQELARLVGCSREMAGRVL  208 (230)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHH
T ss_pred             CCHHHHHHHhCCcHHHHHHHH
Confidence            799999999999999999875

>3qao_A LMO0526 protein, MERR-like transcriptional regulator; structural genomics, the center for structural genomics of I diseases, csgid; 1.87A {Listeria monocytogenes}

Probab=84.52  E-value=1.3  Score=34.37  Aligned_cols=48  Identities=19%  Similarity=0.263  Sum_probs=34.8

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHH------------cCCCCCCHHHHHHH-----HHHhCcccccc
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYE------------GGRGIPNQAIIGKM-----ERALGIRLRVN   91 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E------------~G~~~P~~~~l~~l-----a~~L~v~~~~l   91 (174)
                      ..+|..|+|+.+|||..||.-||            +|.|.-+...+..|     .+.+|+++..+
T Consensus         2 ~~~tI~evA~~~gvs~~TLRyYe~~GLL~p~~~~~~GyR~Y~~~dl~~L~~I~~lr~~G~sL~eI   66 (249)
T 3qao_A            2 NAMQIKELAELTGVSVRTLHHYDKIGLLVPQKDDWNGYRIYSEKDVDKLQQILFFKELDFPLKKI   66 (249)
T ss_dssp             CCBCHHHHHHHHCCCHHHHHHHHHTTSSCCEECTTTCCEEBCHHHHHHHHHHHHHHHTTCCHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHCCCCCCceECCCCCeeeCHHHHHHHHHHHHHHHCCCCHHHH
Confidence            35899999999999999999999            44455555555443     34567776654

>3dew_A Transcriptional regulator, TETR family; S genomics, PSI-2, protein structure initiative, midwest CENT structural genomics, MCSG; HET: MSE; 1.75A {Geobacter sulfurreducens}

Probab=84.45  E-value=1.8  Score=30.59  Aligned_cols=43  Identities=14%  Similarity=0.101  Sum_probs=28.9

Q ss_pred             cccccchHHHHHHHHHHHHHcC---CCHHHHHHHhCCCHHHHHHHH
Q psy6501          24 LKHEKVPLDLAKLLMQGRQAKG---WSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        24 ~~~~~~~~~ig~~ik~~R~~~g---ltq~eLA~~igvs~~~is~~E   66 (174)
                      |+++.....|-+.-..+-.++|   +|..++|+++|||++++.+|=
T Consensus         4 ~~~~~~r~~Il~aa~~l~~~~G~~~~t~~~Ia~~agvs~~t~Y~~F   49 (206)
T 3dew_A            4 MTRADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHF   49 (206)
T ss_dssp             ----CHHHHHHHHHHHHHHHHCGGGCCHHHHHHHHTCCHHHHHHHS
T ss_pred             CCchHHHHHHHHHHHHHHhcCCcccCcHHHHHHHhCCCHHHHHHHc
Confidence            3444444455555555555555   799999999999999999883

>3d0s_A Transcriptional regulatory protein; CAMP receptor protein (CRP), dimer, inactive(APO, unliganded allostery, DNA binding, cyclic AMP; 2.00A {Mycobacterium tuberculosis} PDB: 3i54_A* 3i59_A* 3mzh_A* 3h3u_A* 3r6s_A*

Probab=84.41  E-value=0.71  Score=34.05  Aligned_cols=22  Identities=18%  Similarity=0.261  Sum_probs=19.8

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHH
Q psy6501          45 GWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        45 gltq~eLA~~igvs~~~is~~E   66 (174)
                      .+||++||..+|+|+.+||+.-
T Consensus       177 ~~t~~~lA~~lg~sr~tvsR~l  198 (227)
T 3d0s_A          177 DLTQEEIAQLVGASRETVNKAL  198 (227)
T ss_dssp             CCCHHHHHHHHTSCHHHHHHHH
T ss_pred             CCCHHHHHHHhCCcHHHHHHHH
Confidence            4899999999999999999864

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

Probab=84.35  E-value=1.2  Score=30.51  Aligned_cols=32  Identities=19%  Similarity=0.251  Sum_probs=24.3

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ..-|..+... ++|+.+||+.+|+++++|+..-
T Consensus        41 ~~iL~~l~~~-~~t~~eLa~~l~~s~~tvs~~l   72 (146)
T 3tgn_A           41 EHILMLLSEE-SLTNSELARRLNVSQAAVTKAI   72 (146)
T ss_dssp             HHHHHHHTTC-CCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHhC-CCCHHHHHHHHCCCHHHHHHHH
Confidence            3444445444 4999999999999999999753

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

Probab=84.34  E-value=0.69  Score=31.30  Aligned_cols=38  Identities=8%  Similarity=-0.010  Sum_probs=27.5

Q ss_pred             chHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          29 VPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        29 ~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      +...=..-|..+....++|+.+||+.+|+++++|+..-
T Consensus        31 l~~~~~~iL~~l~~~~~~~~~ela~~l~~~~~tvs~~l   68 (139)
T 3bja_A           31 ISYVQFGVIQVLAKSGKVSMSKLIENMGCVPSNMTTMI   68 (139)
T ss_dssp             CCHHHHHHHHHHHHSCSEEHHHHHHHCSSCCTTHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCcCHHHHHHHHCCChhHHHHHH
Confidence            33334445556666678999999999999998887653

>1ft9_A Carbon monoxide oxidation system transcription regulator; heme sensor, catabolite gene activator protein; HET: HEM; 2.60A {Rhodospirillum rubrum} SCOP: a.4.5.4 b.82.3.1

Probab=84.34  E-value=0.72  Score=33.98  Aligned_cols=21  Identities=14%  Similarity=0.207  Sum_probs=19.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHH
Q psy6501          46 WSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E   66 (174)
                      +||++||..+|+|+.+||+.-
T Consensus       164 ~t~~~lA~~lG~sr~tvsR~l  184 (222)
T 1ft9_A          164 FTVEEIANLIGSSRQTTSTAL  184 (222)
T ss_dssp             CCHHHHHHHHCSCHHHHHHHH
T ss_pred             CCHHHHHHHhCCcHHHHHHHH
Confidence            899999999999999998764

>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=84.34  E-value=1  Score=31.10  Aligned_cols=33  Identities=15%  Similarity=0.194  Sum_probs=25.8

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ..-|..+...-++|+.+||+.+|+++++|+..-
T Consensus        40 ~~iL~~l~~~~~~t~~ela~~l~~s~~tvs~~l   72 (155)
T 1s3j_A           40 LFVLASLKKHGSLKVSEIAERMEVKPSAVTLMA   72 (155)
T ss_dssp             HHHHHHHHHHSEEEHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHH
Confidence            344555566678999999999999999998764

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

Probab=84.26  E-value=0.94  Score=31.38  Aligned_cols=31  Identities=13%  Similarity=0.055  Sum_probs=24.3

Q ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHH
Q psy6501          35 KLLMQGRQAKGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~~   65 (174)
                      .-|..+...-++|+.+||+.+|+++++|++.
T Consensus        45 ~iL~~l~~~~~~t~~eLa~~l~~~~~tvs~~   75 (154)
T 2qww_A           45 AMINVIYSTPGISVADLTKRLIITGSSAAAN   75 (154)
T ss_dssp             HHHHHHHHSTTEEHHHHHHHHTCCHHHHHHH
T ss_pred             HHHHHHHHCCCCCHHHHHHHHCCCHHHHHHH
Confidence            4455555666789999999999999988875

>1sfu_A 34L protein; protein/Z-DNA complex, DNA binding protein/DNA complex; 2.00A {Yaba-like disease virus} SCOP: a.4.5.19

Probab=84.23  E-value=0.39  Score=30.40  Aligned_cols=36  Identities=8%  Similarity=0.011  Sum_probs=27.7

Q ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          31 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        31 ~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ..+-..|..+......|-.++|+++|++++.|+++-
T Consensus        15 ~~v~~~i~~L~~~~~~Ta~~IAkkLg~sK~~vNr~L   50 (75)
T 1sfu_A           15 SLVKKEVLSLNTNDYTTAISLSNRLKINKKKINQQL   50 (75)
T ss_dssp             HHHHHHHHTSCTTCEECHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHhCCCCcchHHHHHHHHHCCCHHHHHHHH
Confidence            344555666666666899999999999999888753

>3b02_A Transcriptional regulator, CRP family; structural genomics, riken structural genomics/proteomics in RSGI; 1.92A {Thermus thermophilus} PDB: 2zdb_A

Probab=84.21  E-value=0.57  Score=33.84  Aligned_cols=22  Identities=14%  Similarity=0.086  Sum_probs=19.7

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHH
Q psy6501          45 GWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        45 gltq~eLA~~igvs~~~is~~E   66 (174)
                      .+||++||..+|+|+.+||+.-
T Consensus       139 ~~t~~~lA~~lg~sr~tvsR~l  160 (195)
T 3b02_A          139 TVSHEEIADATASIRESVSKVL  160 (195)
T ss_dssp             ECCHHHHHHTTTSCHHHHHHHH
T ss_pred             cCCHHHHHHHhCCCHHHHHHHH
Confidence            3899999999999999998764

>3e97_A Transcriptional regulator, CRP/FNR family; YP_604437.1, structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.86A {Deinococcus geothermalis dsm 11300}

Probab=84.21  E-value=0.72  Score=34.10  Aligned_cols=23  Identities=9%  Similarity=0.125  Sum_probs=20.5

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ..+||++||..+|+|+.+||+.-
T Consensus       174 ~~~t~~~iA~~lg~sr~tvsR~l  196 (231)
T 3e97_A          174 LPLGTQDIMARTSSSRETVSRVL  196 (231)
T ss_dssp             ECCCHHHHHHHHTCCHHHHHHHH
T ss_pred             cCCCHHHHHHHhCCcHHHHHHHH
Confidence            35899999999999999999864

>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=84.18  E-value=0.48  Score=32.58  Aligned_cols=33  Identities=12%  Similarity=0.067  Sum_probs=24.8

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ..-|..+...-++|+.+||+.+++++++|++.-
T Consensus        39 ~~vL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l   71 (140)
T 3hsr_A           39 YIVLMAIENDEKLNIKKLGERVFLDSGTLTPLL   71 (140)
T ss_dssp             HHHHHHSCTTCEEEHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHcCCcCHHHHHHHHCCChhhHHHHH
Confidence            344555555668899999999999999888753

>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=84.13  E-value=0.76  Score=31.74  Aligned_cols=33  Identities=18%  Similarity=0.191  Sum_probs=18.4

Q ss_pred             HHHHHHHHHHH--cCCCHHHHHHHhCCCHHHHHHH
Q psy6501          33 LAKLLMQGRQA--KGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        33 ig~~ik~~R~~--~gltq~eLA~~igvs~~~is~~   65 (174)
                      -..-|..+...  -++|+.+||+.+++++++|++.
T Consensus        43 q~~vL~~l~~~~~~~~t~~eLa~~l~~~~~~vs~~   77 (148)
T 3jw4_A           43 QGRMIGYIYENQESGIIQKDLAQFFGRRGASITSM   77 (148)
T ss_dssp             HHHHHHHHHHHTTTCCCHHHHHHC------CHHHH
T ss_pred             HHHHHHHHHhCCCCCCCHHHHHHHHCCChhHHHHH
Confidence            34455555555  6888888888888888877765

>1gdt_A GD resolvase, protein (gamma delta resolvase); protein-DNA complex, double helix, overhanging base, DNA binding protein/DNA complex; 3.00A {Escherichia coli} SCOP: a.4.1.2 c.53.1.1 PDB: 1zr4_A 1zr2_A 2gm4_A 1res_A 1ret_A

Probab=83.86  E-value=1.8  Score=31.37  Aligned_cols=33  Identities=9%  Similarity=0.113  Sum_probs=26.5

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCC
Q psy6501          36 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGR   69 (174)
Q Consensus        36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~   69 (174)
                      .|..+. ..|+|..++|+.+|+|++||.+|-+..
T Consensus       150 ~i~~~~-~~G~s~~~Ia~~l~is~~tv~r~l~~~  182 (183)
T 1gdt_A          150 AVLNMW-QQGLGASHISKTMNIARSTVYKVINES  182 (183)
T ss_dssp             HHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHHSC
T ss_pred             HHHHHH-HCCCCHHHHHHHHCcCHHHHHHHHhhc
Confidence            444444 479999999999999999999986543

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

Probab=83.85  E-value=0.71  Score=31.43  Aligned_cols=32  Identities=22%  Similarity=0.167  Sum_probs=22.8

Q ss_pred             HHHHHHHHHH--cCCCHHHHHHHhCCCHHHHHHH
Q psy6501          34 AKLLMQGRQA--KGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        34 g~~ik~~R~~--~gltq~eLA~~igvs~~~is~~   65 (174)
                      ..-|..+...  .++|+.+||+.+++++++|++.
T Consensus        40 ~~vL~~l~~~~~~~~t~~eLa~~l~~~~~tvs~~   73 (127)
T 2frh_A           40 FAVLTYISENKEKEYYLKDIINHLNYKQPQVVKA   73 (127)
T ss_dssp             HHHHHHHHHTCCSEEEHHHHHHHSSSHHHHHHHH
T ss_pred             HHHHHHHHhccCCCcCHHHHHHHHCCCHHHHHHH
Confidence            3445555555  6788888888888888888764

>2zhg_A Redox-sensitive transcriptional activator SOXR; oxidative stress, MERR family, activator; HET: DNA; 2.80A {Escherichia coli} PDB: 2zhh_A

Probab=83.74  E-value=1  Score=32.19  Aligned_cols=24  Identities=13%  Similarity=0.122  Sum_probs=22.1

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      .-+|..|+|+.+|||..||..||.
T Consensus        10 ~~~~i~e~A~~~gvs~~TLR~ye~   33 (154)
T 2zhg_A           10 ALLTPGEVAKRSGVAVSALHFYES   33 (154)
T ss_dssp             CCBCHHHHHHHHTSCHHHHHHHHH
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHH
Confidence            458999999999999999999984

>1pdn_C Protein (PRD paired); protein-DNA complex, double helix, PAX, paired domain, DNA-binding protein, gene regulation/DNA complex; HET: DNA; 2.50A {Drosophila melanogaster} SCOP: a.4.1.5

Probab=83.72  E-value=2.4  Score=28.04  Aligned_cols=35  Identities=9%  Similarity=0.086  Sum_probs=26.3

Q ss_pred             HHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         122 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       122 ~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      +....+.... ..|++..++|+.+|+++++|.+|-.
T Consensus        21 ~~r~~i~~~~-~~g~s~~~ia~~lgis~~Tv~~w~~   55 (128)
T 1pdn_C           21 NIRLKIVEMA-ADGIRPCVISRQLRVSHGCVSKILN   55 (128)
T ss_dssp             HHHHHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3334444443 4799999999999999999988753

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

Probab=83.68  E-value=1  Score=31.53  Aligned_cols=33  Identities=9%  Similarity=-0.053  Sum_probs=25.0

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ..-|..+...-++|+.+||+.+|+++++|++.-
T Consensus        55 ~~iL~~l~~~~~~t~~ela~~l~is~~tvs~~l   87 (162)
T 3cjn_A           55 MRALAILSAKDGLPIGTLGIFAVVEQSTLSRAL   87 (162)
T ss_dssp             HHHHHHHHHSCSEEHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHCCChhHHHHHH
Confidence            344555566678899999999999999888754

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

Probab=83.68  E-value=1.4  Score=27.79  Aligned_cols=35  Identities=11%  Similarity=0.112  Sum_probs=24.8

Q ss_pred             HHHHHHHHHHHH---cCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          32 DLAKLLMQGRQA---KGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        32 ~ig~~ik~~R~~---~gltq~eLA~~igvs~~~is~~E   66 (174)
                      .|-+.|+..-++   .-.|..|||+.+|+|.+||.+.-
T Consensus         8 ~IL~~I~~~i~~~~g~~psv~EIa~~lgvS~~TVrr~L   45 (77)
T 2jt1_A            8 KIISIVQERQNMDDGAPVKTRDIADAAGLSIYQVRLYL   45 (77)
T ss_dssp             HHHHHHHHHHHHHTTSCEEHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHHhhccCCCcCHHHHHHHHCCCHHHHHHHH
Confidence            344445444333   45689999999999999987753

>1zyb_A Transcription regulator, CRP family; NP_813211.1, structural genomics, joint center for structura genomics, JCSG; 2.15A {Bacteroides thetaiotaomicron} SCOP: a.4.5.4 b.82.3.2

Probab=83.53  E-value=0.8  Score=34.08  Aligned_cols=22  Identities=14%  Similarity=0.098  Sum_probs=19.8

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHH
Q psy6501          45 GWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        45 gltq~eLA~~igvs~~~is~~E   66 (174)
                      .+||++||..+|+|+.+||+.-
T Consensus       186 ~~t~~~lA~~lG~sr~tvsR~l  207 (232)
T 1zyb_A          186 KVKMDDLARCLDDTRLNISKTL  207 (232)
T ss_dssp             ECCHHHHHHHHTSCHHHHHHHH
T ss_pred             cCCHHHHHHHhCCChhHHHHHH
Confidence            4899999999999999999764

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

Probab=83.46  E-value=0.86  Score=31.67  Aligned_cols=32  Identities=9%  Similarity=-0.084  Sum_probs=23.3

Q ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          35 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      .-|..+...-++|+.+||+.+|+++++|+..-
T Consensus        47 ~iL~~l~~~~~~t~~ela~~l~i~~~tvs~~l   78 (155)
T 3cdh_A           47 RVLACLVDNDAMMITRLAKLSLMEQSRMTRIV   78 (155)
T ss_dssp             HHHHHHSSCSCBCHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHCCCcCHHHHHHHHCCCHHHHHHHH
Confidence            34455555567888889998888888887653

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

Probab=83.41  E-value=2.2  Score=29.77  Aligned_cols=37  Identities=19%  Similarity=0.158  Sum_probs=27.4

Q ss_pred             hHHHHHHHHHH-HHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          30 PLDLAKLLMQG-RQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        30 ~~~ig~~ik~~-R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ...+-..|..+ ....++|+.+||+.+|+|+++|+..-
T Consensus        38 ~~~~~~~i~~~l~~~~~~~~~~la~~l~vs~~tvs~~l   75 (155)
T 2h09_A           38 IDDYVELISDLIREVGEARQVDMAARLGVSQPTVAKML   75 (155)
T ss_dssp             HHHHHHHHHHHHHHHSCCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCcCHHHHHHHhCcCHHHHHHHH
Confidence            33444445433 44578999999999999999998764

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

Probab=83.38  E-value=1.6  Score=32.44  Aligned_cols=41  Identities=12%  Similarity=0.058  Sum_probs=29.8

Q ss_pred             cccchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          26 HEKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        26 ~~~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      +-.+...-...|..+...-++|+.+||+.+++++++|++.-
T Consensus        43 ~~gLt~~q~~iL~~L~~~~~~t~~eLa~~l~i~~stvs~~l   83 (207)
T 2fxa_A           43 PYDLNINEHHILWIAYQLNGASISEIAKFGVMHVSTAFNFS   83 (207)
T ss_dssp             GGTCCHHHHHHHHHHHHHTSEEHHHHHHHTTCCHHHHHHHH
T ss_pred             HcCCCHHHHHHHHHHHHCCCcCHHHHHHHHCCCHHHHHHHH
Confidence            33344444455666666678999999999999999988763

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

Probab=83.33  E-value=0.75  Score=32.90  Aligned_cols=30  Identities=17%  Similarity=0.071  Sum_probs=25.1

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHH
Q psy6501          36 LLMQGRQAKGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~   65 (174)
                      -|+.+.+...+|..+||+.+|+|++++++-
T Consensus         8 il~~L~~~~~~s~~~la~~lg~s~~tv~~r   37 (162)
T 3i4p_A            8 ILRILQEDSTLAVADLAKKVGLSTTPCWRR   37 (162)
T ss_dssp             HHHHHTTCSCSCHHHHHHHHTCCHHHHHHH
T ss_pred             HHHHHHHCCCCCHHHHHHHHCcCHHHHHHH
Confidence            456677778899999999999999988753

>3dkw_A DNR protein; CRP-FNR, HTH, beta barrel, dimerization helix, homodimer, transcription regulator; 3.60A {Pseudomonas aeruginosa}

Probab=83.29  E-value=0.64  Score=34.19  Aligned_cols=23  Identities=9%  Similarity=0.099  Sum_probs=20.4

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ..+||++||..+|+|+.+||+.-
T Consensus       177 ~~~t~~~lA~~lg~sr~tvsR~l  199 (227)
T 3dkw_A          177 IPVAKQLVAGHLSIQPETFSRIM  199 (227)
T ss_dssp             CCSCTHHHHHHTTSCHHHHHHHH
T ss_pred             ecCCHHHHHHHhCCCHHHHHHHH
Confidence            35799999999999999999874

>1z6r_A MLC protein; transcriptional repressor, ROK family protein, DNA binding P helix-turn-helix, phosphotransferase system; 2.70A {Escherichia coli} SCOP: a.4.5.63 c.55.1.10 c.55.1.10 PDB: 3bp8_A

Probab=83.10  E-value=0.81  Score=37.49  Aligned_cols=32  Identities=16%  Similarity=0.052  Sum_probs=28.8

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHH
Q psy6501          34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~   65 (174)
                      ..-|+.+|+...+|..|||+.+|+|++||+++
T Consensus        19 ~~il~~l~~~~~~sr~~la~~~~ls~~tv~~~   50 (406)
T 1z6r_A           19 GAVYRLIDQLGPVSRIDLSRLAQLAPASITKI   50 (406)
T ss_dssp             HHHHHHHHSSCSCCHHHHHHHTTCCHHHHHHH
T ss_pred             HHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHH
Confidence            44678888889999999999999999999986

>2ox6_A Hypothetical protein SO3848; structural genomics, PSI-2, MCSG, Pro structure initiative; 1.70A {Shewanella oneidensis} SCOP: a.35.1.6

Probab=83.05  E-value=4.3  Score=28.25  Aligned_cols=43  Identities=14%  Similarity=0.032  Sum_probs=36.6

Q ss_pred             HHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHH
Q psy6501         126 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIG  168 (174)
Q Consensus       126 ~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~  168 (174)
                      .|...|...|++..++++..+.+..-+-.||.|....+.-.-.
T Consensus        11 e~~ylr~slgl~~aqv~~l~k~se~dv~aweage~~~~~laqk   53 (166)
T 2ox6_A           11 EMSYLRQSLSLSAAQVGQLTNHSEAEVLAWENAETQAPELAQK   53 (166)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTSSCCCHHHHH
T ss_pred             hHHHHHHHcCCCHHHHHHHhccCHHHhhhhhhcCCcCcchHHh
Confidence            4667799999999999999999999999999998876654433

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

Probab=83.01  E-value=2.1  Score=29.20  Aligned_cols=24  Identities=17%  Similarity=0.198  Sum_probs=21.2

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          43 AKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        43 ~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ..++|+.+||+.+|+++++|++.-
T Consensus        29 ~~~~s~~ela~~l~is~~tv~~~l   52 (139)
T 2x4h_A           29 GEGAKINRIAKDLKIAPSSVFEEV   52 (139)
T ss_dssp             TSCBCHHHHHHHHTCCHHHHHHHH
T ss_pred             CCCcCHHHHHHHhCCChHHHHHHH
Confidence            468999999999999999998753

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

Probab=82.96  E-value=0.52  Score=30.50  Aligned_cols=22  Identities=14%  Similarity=0.184  Sum_probs=20.1

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHH
Q psy6501          44 KGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~   65 (174)
                      ..+|..|||+.+|+|+++|++.
T Consensus        35 ~~~~~~ela~~l~is~~tvs~~   56 (98)
T 3jth_A           35 QELSVGELCAKLQLSQSALSQH   56 (98)
T ss_dssp             SCEEHHHHHHHHTCCHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHH
Confidence            6889999999999999999864

>1iuf_A Centromere ABP1 protein; riken structural genomics/proteomics initiative, RSGI, structural genomics, DNA binding protein; NMR {Schizosaccharomyces pombe} SCOP: a.4.1.7 a.4.1.7

Probab=82.88  E-value=0.36  Score=34.06  Aligned_cols=39  Identities=13%  Similarity=0.026  Sum_probs=30.2

Q ss_pred             hHHHHHHHHHHHHH----cCCCHHHHHH----Hh--CCCHHHHHHHHcC
Q psy6501          30 PLDLAKLLMQGRQA----KGWSQKDLAT----KI--NEKPQIVNDYEGG   68 (174)
Q Consensus        30 ~~~ig~~ik~~R~~----~gltq~eLA~----~i--gvs~~~is~~E~G   68 (174)
                      ...+.+++.-+...    -++||.+||+    ..  +++++|||+|-+.
T Consensus        11 ~lT~~qK~~i~~~~~~~~~~~~q~~la~wa~~~f~~~is~stis~ilk~   59 (144)
T 1iuf_A           11 AITEHEKRALRHYFFQLQNRSGQQDLIEWFREKFGKDISQPSVSQILSS   59 (144)
T ss_dssp             CCCSHHHHHHHHHHHSSSSCCCHHHHHHHHHHHHSSCCSSSSTTHHHHH
T ss_pred             cCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHCCCCcHHHHHHHHhh
Confidence            34455666666655    5799999999    88  8999999999764

>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=82.82  E-value=1.4  Score=29.02  Aligned_cols=21  Identities=19%  Similarity=0.256  Sum_probs=19.5

Q ss_pred             CCCHHHHHHHhCCCHHHHHHH
Q psy6501          45 GWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        45 gltq~eLA~~igvs~~~is~~   65 (174)
                      .+|..+||+.+|+|+++|++-
T Consensus        33 ~~s~~eLa~~lgvs~~tV~~~   53 (110)
T 1q1h_A           33 EMTDEEIANQLNIKVNDVRKK   53 (110)
T ss_dssp             CBCHHHHHHTTTSCHHHHHHH
T ss_pred             CCCHHHHHHHHCcCHHHHHHH
Confidence            699999999999999999865

>2gau_A Transcriptional regulator, CRP/FNR family; structural genomics, porphyromona gingivalis, PSI, protein structure initiative; 1.90A {Porphyromonas gingivalis} SCOP: a.4.5.4 b.82.3.2

Probab=82.77  E-value=0.86  Score=33.69  Aligned_cols=23  Identities=22%  Similarity=-0.061  Sum_probs=20.4

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ..+||++||..+|+|+.+||+.-
T Consensus       179 ~~~t~~~lA~~lg~sr~tvsR~l  201 (232)
T 2gau_A          179 IYLSREELATLSNMTVSNAIRTL  201 (232)
T ss_dssp             CCCCHHHHHHHTTSCHHHHHHHH
T ss_pred             cccCHHHHHHHhCCCHHHHHHHH
Confidence            45899999999999999999764

>1e3o_C Octamer-binding transcription factor 1; transcription factor, POU domain, dimer, DNA binding; 1.9A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1 PDB: 1gt0_C 1hf0_A* 1cqt_A* 1o4x_A 1oct_C* 1pou_A 1pog_A 1hdp_A

Probab=82.74  E-value=1.3  Score=31.95  Aligned_cols=39  Identities=21%  Similarity=0.325  Sum_probs=34.4

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHhCC------ChhHHHHHhcCC
Q psy6501         121 LDLAKLLMQGRQAKGWSQKDLATKINE------KPQIVNDYEGGR  159 (174)
Q Consensus       121 ~~~~~~i~~~R~~~glsq~ela~~lg~------~~s~i~~~E~G~  159 (174)
                      ..++..++..|...|++|.+++..+|.      +.++|.+.|.-.
T Consensus        10 ~~~~~~~k~~r~~lg~tQ~~vg~~lg~l~g~~~sq~ti~rfE~l~   54 (160)
T 1e3o_C           10 EQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALN   54 (160)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHHSCCCCHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHhhccccCCCcCccccccccccC
Confidence            567788999999999999999999998      888999998743

>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=82.64  E-value=1.5  Score=31.10  Aligned_cols=37  Identities=19%  Similarity=-0.006  Sum_probs=26.4

Q ss_pred             chHHHHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHH
Q psy6501          29 VPLDLAKLLMQGRQ-AKGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        29 ~~~~ig~~ik~~R~-~~gltq~eLA~~igvs~~~is~~   65 (174)
                      +...=...|..+.. .-++|+.+||+.+++++++|++.
T Consensus        51 lt~~q~~vL~~L~~~~~~~t~~eLa~~l~i~~~tvs~~   88 (166)
T 3deu_A           51 LTQTHWVTLHNIHQLPPDQSQIQLAKAIGIEQPSLVRT   88 (166)
T ss_dssp             CCHHHHHHHHHHHHSCSSEEHHHHHHHHTSCHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCCCCHHHHHHHHCCCHhhHHHH
Confidence            33333445555555 45789999999999999988876

>3la7_A Global nitrogen regulator; activator, DNA-binding, transcription, transcription regulation; HET: BOG; 1.90A {Anabaena} PDB: 3la2_A* 3la3_A* 2xko_A* 2xgx_A* 2xhk_A* 2xkp_A*

Probab=82.57  E-value=0.91  Score=34.09  Aligned_cols=23  Identities=17%  Similarity=0.117  Sum_probs=20.6

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ..+||++||..+|+|+.+||+.-
T Consensus       192 ~~lt~~~lA~~lG~sr~tvsR~l  214 (243)
T 3la7_A          192 LKLSHQAIAEAIGSTRVTVTRLL  214 (243)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHH
T ss_pred             ccCCHHHHHHHHCCcHHHHHHHH
Confidence            46899999999999999999864

>2p7v_B Sigma-70, RNA polymerase sigma factor RPOD; RSD, regulator of sigma 70, sigma 70 domain 4, transcription, regulation, helix-turn-helix; 2.60A {Escherichia coli} SCOP: a.4.13.2

Probab=82.36  E-value=2  Score=25.74  Aligned_cols=25  Identities=4%  Similarity=0.258  Sum_probs=22.1

Q ss_pred             hcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         133 AKGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       133 ~~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      ..|+|.+++|+.+|+++++|..+..
T Consensus        23 ~~g~s~~eIA~~lgis~~tV~~~~~   47 (68)
T 2p7v_B           23 NTDYTLEEVGKQFDVTRERIRQIEA   47 (68)
T ss_dssp             SSCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3689999999999999999988754

>3fx3_A Cyclic nucleotide-binding protein; helix_TURN_helix, CAMP regulatory protein, structural genomi 2, protein structure initiative; 2.20A {Ruegeria pomeroyi} PDB: 3h3z_A*

Probab=82.26  E-value=0.72  Score=34.23  Aligned_cols=23  Identities=13%  Similarity=0.176  Sum_probs=20.4

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ..+||++||..+|+|+.+||+.-
T Consensus       177 l~~t~~~iA~~lg~sr~tvsR~l  199 (237)
T 3fx3_A          177 LPYDKMLIAGRLGMKPESLSRAF  199 (237)
T ss_dssp             CCSCTHHHHHHTTCCHHHHHHHH
T ss_pred             ecCCHHHHHHHhCCCHHHHHHHH
Confidence            35789999999999999999875

>2o8x_A Probable RNA polymerase sigma-C factor; promoter recognition, transcription regulation, helix-turn-H motif, transcription; 3.00A {Mycobacterium tuberculosis}

Probab=82.21  E-value=2.7  Score=24.85  Aligned_cols=28  Identities=18%  Similarity=-0.039  Sum_probs=23.6

Q ss_pred             HHHHhcCCCHHHHHHHhCCChhHHHHHh
Q psy6501         129 QGRQAKGWSQKDLATKINEKPQIVNDYE  156 (174)
Q Consensus       129 ~~R~~~glsq~ela~~lg~~~s~i~~~E  156 (174)
                      ..+-..|+|.+++|+.+|++++++..+-
T Consensus        25 ~l~~~~g~s~~eIA~~lgis~~tv~~~~   52 (70)
T 2o8x_A           25 LLTQLLGLSYADAAAVCGCPVGTIRSRV   52 (70)
T ss_dssp             HHHHTSCCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHcCCCHHHHHHHHCcCHHHHHHHH
Confidence            4455789999999999999999987654

>3e6c_C CPRK, cyclic nucleotide-binding protein; CPRK, halorespiration; HET: DNA 3C4; 1.80A {Desulfitobacterium hafniense} SCOP: a.4.5.4 b.82.3.2 PDB: 3e6b_A* 3e5u_C* 3e6d_A 3e5x_A* 3e5q_A 2h6b_A* 2h6c_A

Probab=82.12  E-value=0.96  Score=34.00  Aligned_cols=23  Identities=17%  Similarity=0.023  Sum_probs=20.3

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ..+||++||..+|+|+.+||+.-
T Consensus       176 ~~~t~~~iA~~lG~sr~tvsR~l  198 (250)
T 3e6c_C          176 MPLSQKSIGEITGVHHVTVSRVL  198 (250)
T ss_dssp             CCCCHHHHHHHHTCCHHHHHHHH
T ss_pred             CCCCHHHHHHHhCCcHHHHHHHH
Confidence            35799999999999999998864

>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=82.04  E-value=1.5  Score=31.92  Aligned_cols=33  Identities=12%  Similarity=0.106  Sum_probs=26.0

Q ss_pred             HHHHHHHHH--HcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          34 AKLLMQGRQ--AKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        34 g~~ik~~R~--~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ...|..+..  ..++|+.+||+.+|+++++|+..-
T Consensus        44 ~~vL~~L~~~~~~~~t~~eLa~~l~is~~tvs~~l   78 (189)
T 3nqo_A           44 YMTILSILHLPEEETTLNNIARKMGTSKQNINRLV   78 (189)
T ss_dssp             HHHHHHHHHSCGGGCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHhccCCCcCHHHHHHHHCCCHHHHHHHH
Confidence            344555555  568999999999999999999863

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

Probab=81.76  E-value=2.1  Score=29.98  Aligned_cols=31  Identities=19%  Similarity=-0.011  Sum_probs=23.0

Q ss_pred             HHHHHH-HHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          36 LLMQGR-QAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        36 ~ik~~R-~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      .|..+- ..-+.+|.+||+.+|+++++|++.-
T Consensus        36 vL~~L~~~~~~~~~~eLa~~l~~~~~tvs~~v   67 (151)
T 4aik_A           36 TLYNINRLPPEQSQIQLAKAIGIEQPSLVRTL   67 (151)
T ss_dssp             HHHHHHHSCTTSCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHcCCCCcHHHHHHHHCcCHHHHHHHH
Confidence            344443 3467899999999999999988763

>2ovg_A Phage lambda CRO; transcription factor, helix-turn-helix, bacteriophage, flexi transcription; 1.35A {Enterobacteria phage lambda} PDB: 2ecs_A 1cop_D 4cro_A* 5cro_O 1orc_A 2orc_A 2a63_A 1d1l_A 6cro_A* 3orc_A* 1d1m_B

Probab=81.72  E-value=1.4  Score=26.85  Aligned_cols=23  Identities=17%  Similarity=0.170  Sum_probs=20.9

Q ss_pred             CHHHHHHHhCCChhHHHHHhcCC
Q psy6501         137 SQKDLATKINEKPQIVNDYEGGR  159 (174)
Q Consensus       137 sq~ela~~lg~~~s~i~~~E~G~  159 (174)
                      ++.++|+.+|++++.|+.|.++.
T Consensus        15 s~t~aA~~L~vtQ~AVS~~ir~~   37 (66)
T 2ovg_A           15 GQTKTAKDLGVYPSSINQAIHAG   37 (66)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHHHT
T ss_pred             CHHHHHHHhCCCHHHHHHHHHhC
Confidence            99999999999999999997643

>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=81.62  E-value=0.69  Score=29.91  Aligned_cols=30  Identities=17%  Similarity=0.132  Sum_probs=23.8

Q ss_pred             HHHHHHHHcCCCHHHH----HHHhCCCHHHHHHH
Q psy6501          36 LLMQGRQAKGWSQKDL----ATKINEKPQIVNDY   65 (174)
Q Consensus        36 ~ik~~R~~~gltq~eL----A~~igvs~~~is~~   65 (174)
                      -|..+...-++|+.+|    |+.+++++++|++.
T Consensus        13 iL~~l~~~~~~~~~el~~~la~~l~is~~tvs~~   46 (99)
T 1tbx_A           13 VLAYLYDNEGIATYDLYKKVNAEFPMSTATFYDA   46 (99)
T ss_dssp             HHHHHTTCTTCBHHHHHHHHHTTSCCCHHHHHHH
T ss_pred             HHHHHHHcCCcCHHHHHHHHHHHcCCCHHHHHHH
Confidence            3444445578999999    88899999999875

>3hug_A RNA polymerase sigma factor; ECF sigma factor, zinc binding anti-sigma factor, oxidative transcription regulation; 2.35A {Mycobacterium tuberculosis}

Probab=81.49  E-value=2.6  Score=26.86  Aligned_cols=31  Identities=23%  Similarity=0.356  Sum_probs=25.5

Q ss_pred             HHHHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         127 LMQGRQAKGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       127 i~~~R~~~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      +-.++-..|+|.+++|+.+|++.++|..+-+
T Consensus        45 vl~l~~~~g~s~~eIA~~lgis~~tV~~~l~   75 (92)
T 3hug_A           45 VIQRSYYRGWSTAQIATDLGIAEGTVKSRLH   75 (92)
T ss_dssp             HHHHHHTSCCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3355667899999999999999999977643

>2jpc_A SSRB; DNA binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium}

Probab=81.44  E-value=2  Score=24.88  Aligned_cols=26  Identities=12%  Similarity=0.236  Sum_probs=22.3

Q ss_pred             HhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         132 QAKGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       132 ~~~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      -..|+|.+++|+.+|+++++|..+-+
T Consensus        10 ~~~g~s~~eIA~~l~is~~tV~~~~~   35 (61)
T 2jpc_A           10 IDEGYTNHGISEKLHISIKTVETHRM   35 (61)
T ss_dssp             HHTSCCSHHHHHHTCSCHHHHHHHHH
T ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence            36899999999999999999887643

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

Probab=81.38  E-value=1.1  Score=29.71  Aligned_cols=24  Identities=8%  Similarity=-0.048  Sum_probs=21.4

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          43 AKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        43 ~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ..++|..|||+.+|+|+++|++.-
T Consensus        36 ~~~~s~~eLa~~lgis~stvs~~L   59 (108)
T 2kko_A           36 QGERAVEAIATATGMNLTTASANL   59 (108)
T ss_dssp             TCCEEHHHHHHHHTCCHHHHHHHH
T ss_pred             cCCcCHHHHHHHHCcCHHHHHHHH
Confidence            367899999999999999999864

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

Probab=81.36  E-value=1.2  Score=31.00  Aligned_cols=23  Identities=9%  Similarity=0.157  Sum_probs=19.5

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E   66 (174)
                      -++|+.+||+.+++++++|++.-
T Consensus        50 ~~~t~~eLa~~l~~~~~tvs~~v   72 (147)
T 4b8x_A           50 GELPMSKIGERLMVHPTSVTNTV   72 (147)
T ss_dssp             GEEEHHHHHHHHTCCHHHHHHHH
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHH
Confidence            35899999999999999988773

>3kcc_A Catabolite gene activator; helix-turn-helix, CAMP, CAMP-binding, DNA-binding nucleotide-binding, transcription, transcription regulation; HET: CMP; 1.66A {Escherichia coli}

Probab=81.24  E-value=1.1  Score=34.15  Aligned_cols=22  Identities=5%  Similarity=0.098  Sum_probs=20.0

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHH
Q psy6501          45 GWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        45 gltq~eLA~~igvs~~~is~~E   66 (174)
                      .+||++||..+|+|+.+||+.-
T Consensus       217 ~lt~~~lA~~lG~sr~tvsR~l  238 (260)
T 3kcc_A          217 KITRQEIGQIVGCSRETVGRIL  238 (260)
T ss_dssp             ECCHHHHHHHHTCCHHHHHHHH
T ss_pred             cCCHHHHHHHhCCCHHHHHHHH
Confidence            5799999999999999999874

>1k78_A Paired box protein PAX5; paired domain, ETS domain, transcription factor, transcription/DNA complex; 2.25A {Homo sapiens} SCOP: a.4.1.5 a.4.1.5 PDB: 1mdm_A 6pax_A

Probab=81.12  E-value=3.1  Score=28.81  Aligned_cols=37  Identities=14%  Similarity=0.179  Sum_probs=27.5

Q ss_pred             cHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         120 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       120 ~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      ..+....|.... ..|++..++|+.+|+++++|.+|-.
T Consensus        34 s~e~r~~iv~~~-~~G~s~~~iA~~lgis~~TV~rw~~   70 (149)
T 1k78_A           34 PDVVRQRIVELA-HQGVRPCDISRQLRVSHGCVSKILG   70 (149)
T ss_dssp             CHHHHHHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            344444444444 4799999999999999999988853

>3gbg_A TCP pilus virulence regulatory protein; cupin, helix-turn-helix, ARAC family, activator, DNA-binding transcription, transcription regulation; HET: PAM; 1.90A {Vibrio cholerae}

Probab=81.04  E-value=14  Score=27.99  Aligned_cols=23  Identities=13%  Similarity=0.322  Sum_probs=18.3

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          45 GWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        45 gltq~eLA~~igvs~~~is~~E~   67 (174)
                      .+|.+++|+.+|+|++++++.=+
T Consensus       185 ~~sl~~lA~~~~~S~~~l~r~fk  207 (276)
T 3gbg_A          185 NWRWADICGELRTNRMILKKELE  207 (276)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHH
Confidence            67888888888888888877643

>1vz0_A PARB, chromosome partitioning protein PARB; nuclear protein, chromosome segregation, DNA-binding, helix-turn-helix; 2.3A {Thermus thermophilus} SCOP: a.4.14.1 d.268.1.1

Probab=80.99  E-value=2.6  Score=32.09  Aligned_cols=48  Identities=13%  Similarity=0.153  Sum_probs=34.6

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHH
Q psy6501         121 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKM  170 (174)
Q Consensus       121 ~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i  170 (174)
                      .+....+..+. ..|+|++++|+.+|.++++|+++-.--..|+ ++...+
T Consensus       121 ~E~a~~~~~l~-~~g~t~~~iA~~lG~s~~~V~~~l~l~~l~~-~v~~~l  168 (230)
T 1vz0_A          121 VEEARGYQALL-EMGLTQEEVARRVGKARSTVANALRLLQLPP-EALEAL  168 (230)
T ss_dssp             HHHHHHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHHGGGSCH-HHHHHH
T ss_pred             HHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHcCCH-HHHHHH
Confidence            33344454444 7899999999999999999999887655554 444444

>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=80.98  E-value=1.5  Score=27.86  Aligned_cols=32  Identities=19%  Similarity=0.022  Sum_probs=24.4

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHH-HHHHH
Q psy6501          34 AKLLMQGRQAKGWSQKDLATKINEKPQ-IVNDY   65 (174)
Q Consensus        34 g~~ik~~R~~~gltq~eLA~~igvs~~-~is~~   65 (174)
                      -.-+..+...-+.|..+||+.+|++.. +|++-
T Consensus        14 ~~IL~~Lk~~g~~ta~eiA~~Lgit~~~aVr~h   46 (79)
T 1xmk_A           14 EKICDYLFNVSDSSALNLAKNIGLTKARDINAV   46 (79)
T ss_dssp             HHHHHHHHHTCCEEHHHHHHHHCGGGHHHHHHH
T ss_pred             HHHHHHHHHcCCcCHHHHHHHcCCCcHHHHHHH
Confidence            334455666678999999999999998 77653

>1fse_A GERE; helix-turn-helix DNA-binding protein transcriptional regulat transcription; 2.05A {Bacillus subtilis} SCOP: a.4.6.2

Probab=80.94  E-value=3.8  Score=24.50  Aligned_cols=34  Identities=9%  Similarity=0.058  Sum_probs=25.5

Q ss_pred             HHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         122 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       122 ~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      .-...+...  ..|++.+++|+.+|++++++..+-.
T Consensus        15 ~e~~il~~~--~~g~s~~eIA~~l~is~~tV~~~~~   48 (74)
T 1fse_A           15 REREVFELL--VQDKTTKEIASELFISEKTVRNHIS   48 (74)
T ss_dssp             HHHHHHHHH--TTTCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHH--HcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            333444432  7899999999999999998876543

>1l9z_H Sigma factor SIGA; helix-turn-helix, coiled-coil, transcription/DNA complex; 6.50A {Thermus aquaticus} SCOP: i.8.1.1

Probab=80.81  E-value=1.8  Score=36.33  Aligned_cols=30  Identities=7%  Similarity=0.201  Sum_probs=25.8

Q ss_pred             HHHHHH----cCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          38 MQGRQA----KGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        38 k~~R~~----~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      -.+|-.    .++|++|+|+.+|||+.+|.+++.
T Consensus       384 I~LRygL~~~e~~TleEIAe~LgIS~erVRqi~~  417 (438)
T 1l9z_H          384 LKLRKGLIDGREHTLEEVGAYFGVTRERIRQIEN  417 (438)
T ss_pred             HHHHHhccCCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            345555    789999999999999999999985

>2r0q_C Putative transposon TN552 DNA-invertase BIN3; site-specific recombinase, resolvase, DNA-binding protein, protein-DNA complex, DNA integration, DNA invertase, DNA recombination; 3.20A {Staphylococcus aureus}

Probab=80.53  E-value=3.7  Score=30.39  Aligned_cols=36  Identities=17%  Similarity=0.236  Sum_probs=27.9

Q ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCC
Q psy6501          35 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGI   71 (174)
Q Consensus        35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~   71 (174)
                      ..|..+. ..|+|..++|+.+|+|++|+.+|-+....
T Consensus       166 ~~i~~~~-~~G~s~~~Ia~~l~is~~tv~r~l~~~~~  201 (209)
T 2r0q_C          166 HRVVEML-EEGQAISKIAKEVNITRQTVYRIKHDNGL  201 (209)
T ss_dssp             HHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHTTCC-
T ss_pred             HHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHhcccc
Confidence            3444444 37999999999999999999999875543

>2o0m_A Transcriptional regulator, SORC family; structural genomics, protein structure initiative, midwest center for structural genomics, MCSG; 1.60A {Enterococcus faecalis} SCOP: c.124.1.8

Probab=80.51  E-value=0.33  Score=39.27  Aligned_cols=35  Identities=6%  Similarity=0.052  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        33 ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      -..-|..+....++||+|||+.+|+|++||++.-+
T Consensus        22 ~~~iL~~l~~~~~~t~~eLa~~l~vs~~Tv~r~l~   56 (345)
T 2o0m_A           22 RFQILRNIYWMQPIGRRSLSETMGITERVLRTETD   56 (345)
T ss_dssp             -----------------------------------
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            34556677788899999999999999999998753

>2oa4_A SIR5; structure, structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; NMR {Silicibacter pomeroyi} SCOP: a.4.12.3

Probab=80.46  E-value=2.3  Score=28.40  Aligned_cols=30  Identities=7%  Similarity=-0.005  Sum_probs=26.0

Q ss_pred             HHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          38 MQGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        38 k~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      -.....-++|+.|.|++.+||.++|.+|++
T Consensus        43 V~~v~~g~lS~~EAa~ry~Is~~ei~~W~r   72 (101)
T 2oa4_A           43 VRGVIYGLITLAEAKQTYGLSDEEFNSWVS   72 (101)
T ss_dssp             HHHHHHTTCCHHHHHHTTCSSHHHHHHHHH
T ss_pred             HHHHHhCCCCHHHHHHHhCCCHHHHHHHHH
Confidence            345566799999999999999999999984

>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=80.45  E-value=2  Score=26.89  Aligned_cols=31  Identities=16%  Similarity=0.194  Sum_probs=24.6

Q ss_pred             HHHHHHHHhc---CCCHHHHHHHhCCChhHHHHH
Q psy6501         125 KLLMQGRQAK---GWSQKDLATKINEKPQIVNDY  155 (174)
Q Consensus       125 ~~i~~~R~~~---glsq~ela~~lg~~~s~i~~~  155 (174)
                      ..+...+...   ++|..++|+++|++.++|.+.
T Consensus        18 ~IL~~L~~~~~~~~~t~~eLA~~Lgvs~~tV~~~   51 (77)
T 1qgp_A           18 RILKFLEELGEGKATTAHDLSGKLGTPKKEINRV   51 (77)
T ss_dssp             HHHHHHHHHCSSSCEEHHHHHHHHCCCHHHHHHH
T ss_pred             HHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHH
Confidence            4555556666   799999999999999988765

>1ku3_A Sigma factor SIGA; helix-turn-helix, transcription; 1.80A {Thermus aquaticus} SCOP: a.4.13.2 PDB: 1ku7_A 1rio_H 3n97_A*

Probab=80.08  E-value=3.3  Score=25.08  Aligned_cols=24  Identities=4%  Similarity=0.159  Sum_probs=21.8

Q ss_pred             cCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         134 KGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       134 ~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      .|+|.+++|+.+|+++++|..+..
T Consensus        29 ~~~s~~eIA~~l~is~~tV~~~~~   52 (73)
T 1ku3_A           29 REHTLEEVGAYFGVTRERIRQIEN   52 (73)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHH
Confidence            789999999999999999988654

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

Probab=80.07  E-value=1.6  Score=29.79  Aligned_cols=31  Identities=13%  Similarity=0.033  Sum_probs=22.4

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHH
Q psy6501          34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~   65 (174)
                      ..-|..+...-+ |+.+||+.+|+++++|+..
T Consensus        40 ~~iL~~l~~~~~-~~~~la~~l~~~~~tvs~~   70 (144)
T 3f3x_A           40 FSILKATSEEPR-SMVYLANRYFVTQSAITAA   70 (144)
T ss_dssp             HHHHHHHHHSCE-EHHHHHHHHTCCHHHHHHH
T ss_pred             HHHHHHHHHCCC-CHHHHHHHHCCChhHHHHH
Confidence            344555555555 8888888888888888875

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

Probab=80.06  E-value=2.7  Score=26.50  Aligned_cols=31  Identities=6%  Similarity=0.057  Sum_probs=24.5

Q ss_pred             HHHHHHHHhcCCCHHHHHHHhCCChhHHHHH
Q psy6501         125 KLLMQGRQAKGWSQKDLATKINEKPQIVNDY  155 (174)
Q Consensus       125 ~~i~~~R~~~glsq~ela~~lg~~~s~i~~~  155 (174)
                      .++...++....+..++|+.+++++.+|.+.
T Consensus         6 ~Il~~L~~~g~vsv~eLa~~l~VS~~TIRrd   36 (78)
T 1xn7_A            6 QVRDLLALRGRMEAAQISQTLNTPQPMINAM   36 (78)
T ss_dssp             HHHHHHHHSCSBCHHHHHHHTTCCHHHHHHH
T ss_pred             HHHHHHHHcCCCcHHHHHHHHCcCHHHHHHH
Confidence            4455556667799999999999999988753

---

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	174
d1y7ya1	69	a.35.1.3 (A:5-73) Restriction-modification control	1e-07
d1y7ya1	69	a.35.1.3 (A:5-73) Restriction-modification control	3e-06
d1x57a1	78	a.35.1.12 (A:8-85) Endothelial differentiation-rel	5e-07
d1x57a1	78	a.35.1.12 (A:8-85) Endothelial differentiation-rel	1e-04
d2b5aa1	77	a.35.1.3 (A:1-77) Regulatory protein C.BclI {Bacil	9e-07
d2b5aa1	77	a.35.1.3 (A:1-77) Regulatory protein C.BclI {Bacil	1e-05
d1b0na2	68	a.35.1.3 (A:1-68) SinR repressor, DNA-binding doma	8e-06
d1b0na2	68	a.35.1.3 (A:1-68) SinR repressor, DNA-binding doma	1e-04
d1utxa_	66	a.35.1.3 (A:) Putative transcription regulator Cyl	1e-05
d1utxa_	66	a.35.1.3 (A:) Putative transcription regulator Cyl	2e-04
d1y9qa1	79	a.35.1.8 (A:4-82) Probable transcriptional regulat	2e-05
d1y9qa1	79	a.35.1.8 (A:4-82) Probable transcriptional regulat	3e-04
d2r1jl1	66	a.35.1.2 (L:3-68) P22 C2 repressor, DNA-binding do	5e-05
d2r1jl1	66	a.35.1.2 (L:3-68) P22 C2 repressor, DNA-binding do	6e-04
d1lmb3_	87	a.35.1.2 (3:) lambda C1 repressor, DNA-binding dom	6e-04
d2croa_	65	a.35.1.2 (A:) cro 434 {Bacteriophage 434 [TaxId: 1	0.001
d2icta1	87	a.35.1.3 (A:8-94) Antitoxin HigA {Escherichia coli	0.001
d1r69a_	63	a.35.1.2 (A:) 434 C1 repressor, DNA-binding domain	0.002
d2ppxa1	62	a.35.1.3 (A:30-91) Uncharacterized protein Atu1735	0.002
d2ppxa1	62	a.35.1.3 (A:30-91) Uncharacterized protein Atu1735	0.002

>d1y7ya1 a.35.1.3 (A:5-73) Restriction-modification controller protein C.AhdI {Aeromonas hydrophila [TaxId: 644]} Length = 69

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Restriction-modification controller protein C.AhdI
species: Aeromonas hydrophila [TaxId: 644]

 Score = 44.4 bits (105), Expect = 1e-07
 Identities = 17/56 (30%), Positives = 23/56 (41%)

Query: 33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRL 88
            + L + R AKG SQ+ LA         V   E G+   +   I K+  AL I  
Sbjct: 10 FGQRLRELRTAKGLSQETLAFLSGLDRSYVGGVERGQRNVSLVNILKLATALDIEP 65

>d1y7ya1 a.35.1.3 (A:5-73) Restriction-modification controller protein C.AhdI {Aeromonas hydrophila [TaxId: 644]} Length = 69

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Restriction-modification controller protein C.AhdI
species: Aeromonas hydrophila [TaxId: 644]

 Score = 40.9 bits (96), Expect = 3e-06
 Identities = 16/52 (30%), Positives = 22/52 (42%)

Query: 123 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174
             + L + R AKG SQ+ LA         V   E G+   +   I K+  AL
Sbjct: 10  FGQRLRELRTAKGLSQETLAFLSGLDRSYVGGVERGQRNVSLVNILKLATAL 61

>d1x57a1 a.35.1.12 (A:8-85) Endothelial differentiation-related factor 1, EDF1 {Human (Homo sapiens) [TaxId: 9606]} Length = 78

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: EDF1-like
domain: Endothelial differentiation-related factor 1, EDF1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 43.5 bits (102), Expect = 5e-07
 Identities = 38/63 (60%), Positives = 54/63 (85%)

Query: 27 EKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGI 86
          ++V L++ K++ QGRQ+KG +QKDLATKINEKPQ++ DYE GR IPN  ++GK+ERA+G+
Sbjct: 1  DRVTLEVGKVIQQGRQSKGLTQKDLATKINEKPQVIADYESGRAIPNNQVLGKIERAIGL 60

Query: 87 RLR 89
          +LR
Sbjct: 61 KLR 63

>d1x57a1 a.35.1.12 (A:8-85) Endothelial differentiation-related factor 1, EDF1 {Human (Homo sapiens) [TaxId: 9606]} Length = 78

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: EDF1-like
domain: Endothelial differentiation-related factor 1, EDF1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.5 bits (84), Expect = 1e-04
 Identities = 35/58 (60%), Positives = 49/58 (84%)

Query: 117 EKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174
           ++V L++ K++ QGRQ+KG +QKDLATKINEKPQ++ DYE GR IPN  ++GK+ERA+
Sbjct: 1   DRVTLEVGKVIQQGRQSKGLTQKDLATKINEKPQVIADYESGRAIPNNQVLGKIERAI 58

>d2b5aa1 a.35.1.3 (A:1-77) Regulatory protein C.BclI {Bacillus caldolyticus [TaxId: 1394]} Length = 77

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Regulatory protein C.BclI
species: Bacillus caldolyticus [TaxId: 1394]

 Score = 42.5 bits (100), Expect = 9e-07
 Identities = 15/56 (26%), Positives = 24/56 (42%)

Query: 33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRL 88
            + L + R  KG SQ++LA         +++ E G    +   I K+  AL I  
Sbjct: 11 FGRTLKKIRTQKGVSQEELADLAGLHRTYISEVERGDRNISLINIHKICAALDIPA 66

>d2b5aa1 a.35.1.3 (A:1-77) Regulatory protein C.BclI {Bacillus caldolyticus [TaxId: 1394]} Length = 77

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Regulatory protein C.BclI
species: Bacillus caldolyticus [TaxId: 1394]

 Score = 39.4 bits (92), Expect = 1e-05
 Identities = 14/52 (26%), Positives = 23/52 (44%)

Query: 123 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174
             + L + R  KG SQ++LA         +++ E G    +   I K+  AL
Sbjct: 11  FGRTLKKIRTQKGVSQEELADLAGLHRTYISEVERGDRNISLINIHKICAAL 62

>d1b0na2 a.35.1.3 (A:1-68) SinR repressor, DNA-binding domain {Bacillus subtilis [TaxId: 1423]} Length = 68

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: SinR repressor, DNA-binding domain
species: Bacillus subtilis [TaxId: 1423]

 Score = 39.7 bits (93), Expect = 8e-06
 Identities = 12/57 (21%), Positives = 26/57 (45%), Gaps = 1/57 (1%)

Query: 33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE-GGRGIPNQAIIGKMERALGIRL 88
          + + + Q R+ KG+S  +LA K       ++  E   +  P+   + K+   L + +
Sbjct: 2  IGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNLQTNPSIQFLEKVSAVLDVSV 58

>d1b0na2 a.35.1.3 (A:1-68) SinR repressor, DNA-binding domain {Bacillus subtilis [TaxId: 1423]} Length = 68

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: SinR repressor, DNA-binding domain
species: Bacillus subtilis [TaxId: 1423]

 Score = 36.3 bits (84), Expect = 1e-04
 Identities = 12/53 (22%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 123 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE-GGRGIPNQAIIGKMERAL 174
           + + + Q R+ KG+S  +LA K       ++  E   +  P+   + K+   L
Sbjct: 2   IGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNLQTNPSIQFLEKVSAVL 54

>d1utxa_ a.35.1.3 (A:) Putative transcription regulator CylR2 {Enterococcus faecalis [TaxId: 1351]} Length = 66

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Putative transcription regulator CylR2
species: Enterococcus faecalis [TaxId: 1351]

 Score = 39.1 bits (91), Expect = 1e-05
 Identities = 14/56 (25%), Positives = 23/56 (41%)

Query: 33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRL 88
          +   L   R+ K  SQ +LA  +    Q +N  E  +  P+  +  K+   L   L
Sbjct: 2  IINNLKLIREKKKISQSELAALLEVSRQTINGIEKNKYNPSLQLALKIAYYLNTPL 57

>d1utxa_ a.35.1.3 (A:) Putative transcription regulator CylR2 {Enterococcus faecalis [TaxId: 1351]} Length = 66

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Putative transcription regulator CylR2
species: Enterococcus faecalis [TaxId: 1351]

 Score = 35.6 bits (82), Expect = 2e-04
 Identities = 13/52 (25%), Positives = 22/52 (42%)

Query: 123 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174
           +   L   R+ K  SQ +LA  +    Q +N  E  +  P+  +  K+   L
Sbjct: 2   IINNLKLIREKKKISQSELAALLEVSRQTINGIEKNKYNPSLQLALKIAYYL 53

>d1y9qa1 a.35.1.8 (A:4-82) Probable transcriptional regulator VC1968, N-terminal domain {Vibrio cholerae [TaxId: 666]} Length = 79

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Probable transcriptional regulator VC1968, N-terminal domain
domain: Probable transcriptional regulator VC1968, N-terminal domain
species: Vibrio cholerae [TaxId: 666]

 Score = 39.1 bits (91), Expect = 2e-05
 Identities = 12/56 (21%), Positives = 20/56 (35%)

Query: 33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRL 88
          +A  L   R+++G S    A        ++   E G   P  A + K+   L    
Sbjct: 9  IANQLKNLRKSRGLSLDATAQLTGVSKAMLGQIERGESSPTIATLWKIASGLEASF 64

>d1y9qa1 a.35.1.8 (A:4-82) Probable transcriptional regulator VC1968, N-terminal domain {Vibrio cholerae [TaxId: 666]} Length = 79

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Probable transcriptional regulator VC1968, N-terminal domain
domain: Probable transcriptional regulator VC1968, N-terminal domain
species: Vibrio cholerae [TaxId: 666]

 Score = 35.7 bits (82), Expect = 3e-04
 Identities = 12/52 (23%), Positives = 20/52 (38%)

Query: 123 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174
           +A  L   R+++G S    A        ++   E G   P  A + K+   L
Sbjct: 9   IANQLKNLRKSRGLSLDATAQLTGVSKAMLGQIERGESSPTIATLWKIASGL 60

>d2r1jl1 a.35.1.2 (L:3-68) P22 C2 repressor, DNA-binding domain {Salmonella bacteriophage P22 [TaxId: 10754]} Length = 66

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: P22 C2 repressor, DNA-binding domain
species: Salmonella bacteriophage P22 [TaxId: 10754]

 Score = 37.5 bits (87), Expect = 5e-05
 Identities = 8/56 (14%), Positives = 19/56 (33%)

Query: 33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRL 88
          + + +   R+     Q  L   +      ++ +E     PN   +  + +AL    
Sbjct: 4  MGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCSP 59

>d2r1jl1 a.35.1.2 (L:3-68) P22 C2 repressor, DNA-binding domain {Salmonella bacteriophage P22 [TaxId: 10754]} Length = 66

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: P22 C2 repressor, DNA-binding domain
species: Salmonella bacteriophage P22 [TaxId: 10754]

 Score = 34.4 bits (79), Expect = 6e-04
 Identities = 8/52 (15%), Positives = 19/52 (36%)

Query: 123 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL 174
           + + +   R+     Q  L   +      ++ +E     PN   +  + +AL
Sbjct: 4   MGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKAL 55

>d1lmb3_ a.35.1.2 (3:) lambda C1 repressor, DNA-binding domain {Bacteriophage lambda [TaxId: 10710]} Length = 87

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: lambda C1 repressor, DNA-binding domain
species: Bacteriophage lambda [TaxId: 10710]

 Score = 35.1 bits (80), Expect = 6e-04
 Identities = 10/56 (17%), Positives = 20/56 (35%)

Query: 33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRL 88
          L  +  + +   G SQ+ +A K+      V     G    N      + + L + +
Sbjct: 13 LKAIYEKKKNELGLSQESVADKMGMGQSGVGALFNGINALNAYNAALLAKILKVSV 68

>d2croa_ a.35.1.2 (A:) cro 434 {Bacteriophage 434 [TaxId: 10712]} Length = 65

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: cro 434
species: Bacteriophage 434 [TaxId: 10712]

 Score = 34.0 bits (78), Expect = 0.001
 Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 1/56 (1%)

Query: 33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRL 88
          L++ L + R A   +Q +LATK   K Q +   E G     + +  ++  AL    
Sbjct: 4  LSERLKKRRIALKMTQTELATKAGVKQQSIQLIEAGVTKRPRFLF-EIAMALNCDP 58

>d2icta1 a.35.1.3 (A:8-94) Antitoxin HigA {Escherichia coli [TaxId: 562]} Length = 87

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Antitoxin HigA
species: Escherichia coli [TaxId: 562]

 Score = 34.2 bits (78), Expect = 0.001
 Identities = 6/52 (11%), Positives = 17/52 (32%)

Query: 35 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGI 86
           ++ +       S ++ A  +   P   +    G+      +  K+   +G 
Sbjct: 4  DIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVIGS 55

>d1r69a_ a.35.1.2 (A:) 434 C1 repressor, DNA-binding domain {Bacteriophage 434 [TaxId: 10712]} Length = 63

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: 434 C1 repressor, DNA-binding domain
species: Bacteriophage 434 [TaxId: 10712]

 Score = 33.3 bits (76), Expect = 0.002
 Identities = 12/56 (21%), Positives = 25/56 (44%), Gaps = 1/56 (1%)

Query: 33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRL 88
          ++  +   R   G +Q +LA K+    Q +   E G+       + ++  ALG+ +
Sbjct: 2  ISSRVKSKRIQLGLNQAELAQKVGTTQQSIEQLENGK-TKRPRFLPELASALGVSV 56

>d2ppxa1 a.35.1.3 (A:30-91) Uncharacterized protein Atu1735 {Agrobacterium tumefaciens [TaxId: 358]} Length = 62

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Uncharacterized protein Atu1735
species: Agrobacterium tumefaciens [TaxId: 358]

 Score = 33.2 bits (76), Expect = 0.002
 Identities = 9/37 (24%), Positives = 19/37 (51%)

Query: 41 RQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAII 77
          R+A   +Q++ + + +     + D+E GR  P+Q   
Sbjct: 8  RRALKLTQEEFSARYHIPLGTLRDWEQGRSEPDQPAR 44

>d2ppxa1 a.35.1.3 (A:30-91) Uncharacterized protein Atu1735 {Agrobacterium tumefaciens [TaxId: 358]} Length = 62

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Uncharacterized protein Atu1735
species: Agrobacterium tumefaciens [TaxId: 358]

 Score = 33.2 bits (76), Expect = 0.002
 Identities = 9/37 (24%), Positives = 19/37 (51%)

Query: 131 RQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAII 167
           R+A   +Q++ + + +     + D+E GR  P+Q   
Sbjct: 8   RRALKLTQEEFSARYHIPLGTLRDWEQGRSEPDQPAR 44

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	174
d1y7ya1	69	Restriction-modification controller protein C.AhdI	99.82
d2r1jl1	66	P22 C2 repressor, DNA-binding domain {Salmonella b	99.79
d2croa_	65	cro 434 {Bacteriophage 434 [TaxId: 10712]}	99.79
d1y9qa1	79	Probable transcriptional regulator VC1968, N-termi	99.79
d2b5aa1	77	Regulatory protein C.BclI {Bacillus caldolyticus [	99.79
d1x57a1	78	Endothelial differentiation-related factor 1, EDF1	99.78
d1b0na2	68	SinR repressor, DNA-binding domain {Bacillus subti	99.78
d1utxa_	66	Putative transcription regulator CylR2 {Enterococc	99.77
d1r69a_	63	434 C1 repressor, DNA-binding domain {Bacteriophag	99.77
d1lmb3_	87	lambda C1 repressor, DNA-binding domain {Bacteriop	99.72
d2icta1	87	Antitoxin HigA {Escherichia coli [TaxId: 562]}	99.71
d2a6ca1	69	HTH-motif protein NE1354 {Nitrosomonas europaea [T	99.7
d2o38a1	89	Hypothetical protein RPA3824 {Rhodopseudomonas pal	99.69
d2ofya1	82	Putative transcriptional regulator RHA1_ro04071 {R	99.68
d2ppxa1	62	Uncharacterized protein Atu1735 {Agrobacterium tum	99.54
d2auwa1	67	Hypothetical protein NE0471 C-terminal domain {Nit	99.34
d1y7ya1	69	Restriction-modification controller protein C.AhdI	99.33
d1x57a1	78	Endothelial differentiation-related factor 1, EDF1	99.32
d2r1jl1	66	P22 C2 repressor, DNA-binding domain {Salmonella b	99.27
d2croa_	65	cro 434 {Bacteriophage 434 [TaxId: 10712]}	99.24
d2b5aa1	77	Regulatory protein C.BclI {Bacillus caldolyticus [	99.23
d1y9qa1	79	Probable transcriptional regulator VC1968, N-termi	99.21
d1utxa_	66	Putative transcription regulator CylR2 {Enterococc	99.21
d1r69a_	63	434 C1 repressor, DNA-binding domain {Bacteriophag	99.19
d1b0na2	68	SinR repressor, DNA-binding domain {Bacillus subti	99.17
d1lmb3_	87	lambda C1 repressor, DNA-binding domain {Bacteriop	99.15
d2ppxa1	62	Uncharacterized protein Atu1735 {Agrobacterium tum	99.13
d2icta1	87	Antitoxin HigA {Escherichia coli [TaxId: 562]}	99.13
d2a6ca1	69	HTH-motif protein NE1354 {Nitrosomonas europaea [T	99.1
d2o38a1	89	Hypothetical protein RPA3824 {Rhodopseudomonas pal	99.03
d2ofya1	82	Putative transcriptional regulator RHA1_ro04071 {R	98.96
d2auwa1	67	Hypothetical protein NE0471 C-terminal domain {Nit	98.86
d2bnma1	71	Hydroxypropylphosphonic acid epoxidase Fom4, N-ter	98.59
d1dwka1	86	Cyanase N-terminal domain {Escherichia coli [TaxId	97.8
d2bnma1	71	Hydroxypropylphosphonic acid epoxidase Fom4, N-ter	97.58
d2hsga1	57	Glucose-resistance amylase regulator CcpA, N-termi	97.51
d1efaa1	59	Lac repressor (LacR), N-terminal domain {Escherich	97.46
d1e3oc2	75	Oct-1 {Human (Homo sapiens) [TaxId: 9606]}	97.35
d2awia1	65	PrgX {Enterococcus faecalis [TaxId: 1351]}	97.35
d1uxda_	59	Fructose repressor (FruR), N-terminal domain {Esch	97.32
d1qpza1	57	Purine repressor (PurR), N-terminal domain {Escher	97.26
d1au7a2	72	Pit-1 {Rat (Rattus norvegicus) [TaxId: 10116]}	97.19
d1ic8a2	94	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Human (H	97.16
d1nera_	74	Ner {Bacteriophage mu [TaxId: 10677]}	96.99
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	96.96
d1vz0a1	93	Putative partitioning protein ParB/Spo0J {Thermus	96.64
d2jn6a1	89	Uncharacterized protein Cgl2762 {Corynebacterium g	96.42
d1dwka1	86	Cyanase N-terminal domain {Escherichia coli [TaxId	96.37
d1efaa1	59	Lac repressor (LacR), N-terminal domain {Escherich	96.37
d1hlva1	66	DNA-binding domain of centromere binding protein B	96.21
d1r71a_	114	Transcriptional repressor protein KorB DNA-binding	96.15
d2csfa1	88	DNA-binding protein SATB2 {Human (Homo sapiens) [T	96.12
d2hsga1	57	Glucose-resistance amylase regulator CcpA, N-termi	96.12
d1qpza1	57	Purine repressor (PurR), N-terminal domain {Escher	95.84
d1x2la1	87	Homeobox protein Cux-2, CUTL2 {Human (Homo sapiens	95.48
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	95.43
d2o4aa1	83	DNA-binding protein SATB1 {Human (Homo sapiens) [T	95.43
d1gdta1	43	gamma,delta resolvase (C-terminal domain) {Escheri	95.4
d1k78a1	63	Pax-5 {Human (Homo sapiens) [TaxId: 9606]}	95.35
d1wh8a_	111	Homeobox protein Cux-2, CUTL2 {Human (Homo sapiens	95.12
d1uxda_	59	Fructose repressor (FruR), N-terminal domain {Esch	95.02
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	95.01
d1z6ra1	70	Mlc protein N-terminal domain {Escherichia coli [T	94.98
d1i5za1	69	Catabolite gene activator protein (CAP), C-termina	94.82
d1rzsa_	61	cro p22 {Bacteriophage p22 [TaxId: 10754]}	94.75
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	94.62
d2hoea1	62	N-acetylglucosamine kinase {Thermotoga maritima [T	94.6
d1jhga_	101	Trp repressor, TrpR {Escherichia coli [TaxId: 562]	94.57
d1s7ea2	80	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	94.45
d1wh6a_	101	Homeobox protein Cux-2, CUTL2 {Human (Homo sapiens	94.37
d2ox6a1	162	Hypothetical protein SO3848 {Shewanella oneidensis	94.37
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	94.33
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	94.08
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	93.76
d1zyba1	73	Probable transcription regulator BT4300, C-termina	93.76
d3e5ua1	80	Chlorophenol reduction protein CprK {Desulfitobact	93.67
d1nr3a_	122	DNA-binding protein Tfx {Archaeon Methanobacterium	93.59
d2gaua1	81	Transcriptional regulator PG0396, C-terminal domai	93.55
d1ft9a1	80	CO-sensing protein CooA, C-terminal domain {Rhodos	93.45
d1r8da_	109	Multidrug transporter activator MtaN {Bacillus sub	93.32
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	93.11
d1or7a1	68	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	93.02
d1s4ka_	120	Putative cytoplasmic protein YdiL {Salmonella typh	92.96
d1pdnc_	123	Paired protein (prd) {Fruit fly (Drosophila melano	92.82
d2ao9a1	120	Phage protein BC1890 {Bacillus cereus [TaxId: 1396	92.68
d1q06a_	127	Transcriptional regulator CueR {Escherichia coli [	92.68
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	92.67
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	92.67
d1ku3a_	61	Sigma70 (SigA, RpoD) {Thermus aquaticus [TaxId: 27	92.57
d1hlva1	66	DNA-binding domain of centromere binding protein B	92.41
d1s4ka_	120	Putative cytoplasmic protein YdiL {Salmonella typh	92.4
d2zcwa1	82	Transcriptional regulator TTHA1359, C-terminal dom	92.35
d1s7oa_	106	Hypothetical protein SPy1201 {Streptococcus pyogen	92.29
d2bgca1	100	Listeriolysin regulatory protein PrfA, C-terminal	92.27
d3ctaa1	85	Ta1064 (RFK), N-terminal domain {Thermoplasma acid	92.19
d1umqa_	60	Photosynthetic apparatus regulatory protein PprA (	91.93
d1a04a1	67	Nitrate/nitrite response regulator (NarL) {Escheri	91.87
d1au7a2	72	Pit-1 {Rat (Rattus norvegicus) [TaxId: 10116]}	91.78
d2p7vb1	68	Sigma70 (SigA, RpoD) {Escherichia coli [TaxId: 562	91.71
d2o3fa1	83	Putative transcriptional regulator YbbH {Bacillus	91.51
d2gfna1	77	Probable transcriptional regulator RHA1_ro04631 {R	91.19
d1e3oc2	75	Oct-1 {Human (Homo sapiens) [TaxId: 9606]}	90.76
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	90.67
d2jn6a1	89	Uncharacterized protein Cgl2762 {Corynebacterium g	90.53
d1xsva_	106	Hypothetical protein SAV1236 {Staphylococcus aureu	90.33
d1fsea_	67	Germination protein GerE {Bacillus subtilis [TaxId	90.24
d1rzsa_	61	cro p22 {Bacteriophage p22 [TaxId: 10754]}	90.24
d1j9ia_	68	Terminase gpNU1 subunit domain {Bacteriophage lamb	90.13
d1k78a1	63	Pax-5 {Human (Homo sapiens) [TaxId: 9606]}	90.0
d1p4wa_	87	Transcriptional regulator RcsB {Erwinia amylovora	89.71
d1yioa1	70	Response regulatory protein StyR, C-terminal domai	89.35
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	89.22
d1etxa_	89	FIS protein {Escherichia coli [TaxId: 562]}	89.17
d1l3la1	65	Quorum-sensing transcription factor TraR, C-termin	89.16
d2a61a1	139	Transcriptional regulator TM0710 {Thermotoga marit	88.56
d1ic8a2	94	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Human (H	88.42
d1r71a_	114	Transcriptional repressor protein KorB DNA-binding	88.35
d1bl0a1	54	MarA {Escherichia coli [TaxId: 562]}	87.96
d1ttya_	87	Sigma70 (SigA, RpoD) {Thermotoga maritima [TaxId:	87.83
d1vz0a1	93	Putative partitioning protein ParB/Spo0J {Thermus	87.81
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	87.42
d3broa1	135	Transcriptional regulator OEOE1854 {Oenococcus oen	87.37
d1s3ja_	143	Putative transcriptional regulator YusO {Bacillus	87.05
d1zs4a1	78	Regulatory protein cII {Bacteriophage lambda [TaxI	87.0
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	86.97
d2etha1	140	Putative transcriptional regulator TM0816 {Thermot	86.61
d1d1la_	61	cro lambda repressor {Bacteriophage lambda [TaxId:	86.54
d2ox6a1	162	Hypothetical protein SO3848 {Shewanella oneidensis	86.48
d1r8ea1	118	Transcription activator BmrR {Bacillus subtilis [T	86.47
d1v7ba1	74	Transcriptional regulator Cgl2612 {Corynebacterium	86.43
d1z91a1	137	Organic hydroperoxide resistance transcriptional r	86.42
d2id6a1	75	Transcriptional regulator TM1030 {Thermotoga marit	86.42
d1jt6a1	71	Multidrug binding protein QacR {Staphylococcus aur	85.93
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	85.88
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	85.83
d1z6ra1	70	Mlc protein N-terminal domain {Escherichia coli [T	85.83
d1g2ha_	61	Transcriptional regulator TyrR, C-terminal domain	85.76
d1t56a1	73	Ethr repressor {Mycobacterium tuberculosis [TaxId:	85.67
d1jgsa_	138	Multiple antibiotic resistance repressor, MarR {Es	85.53
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	85.41
d2g7sa1	74	Putative transcriptional regulator Atu0279 {Agroba	85.36
d2ev0a1	61	Manganese transport regulator MntR {Bacillus subti	85.02
d2i10a1	69	Putative transcriptional regulator RHA1_ro09068 {R	84.88
d2fbqa1	79	Transcriptional regulator PsrA {Pseudomonas aerugi	84.85
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	84.7
d1lj9a_	144	Transcriptional regulator SlyA {Enterococcus faeca	84.64
d1ntca_	91	DNA-binding domain of NTRC {Salmonella typhimurium	84.62
d2fq4a1	69	Transcriptional regulator BC3163 {Bacillus cereus	84.6
d1lnwa_	141	MexR repressor {Pseudomonas aeruginosa [TaxId: 287	84.59
d2vkva1	62	Tetracyclin repressor (Tet-repressor, TetR) {Esche	84.52
d2o7ta1	78	Transcriptional regulator Cgl1640/Cg1846 {Coryneba	84.44
d2d6ya1	68	Putative regulator SCO4008 {Streptomyces coelicolo	83.94
d1l8qa1	110	Chromosomal replication initiation factor DnaA C-t	83.9
d1aisb1	98	Transcription factor IIB (TFIIB), core domain {Arc	83.87
d2gena1	70	Probable transcriptional regulator PA1836 {Pseudom	83.58
d2fx0a1	73	Hemolysin II regulatory protein, HlyIIR {Bacillus	83.39
d2fbia1	136	Probable transcriptional regulator PA4135 {Pseudom	83.26
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	82.96
d2fxaa1	162	Protease production regulatory protein Hpr {Bacill	82.79
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	82.77
d2id3a1	68	Putative transcriptional regulator SCO5951 {Strept	82.62
d1d5ya1	54	Rob transcription factor, N-terminal domain {Esche	82.59
d1z0xa1	68	Transcriptional regulator EF0787 {Enterococcus fae	82.55
d1ui5a1	71	A-factor receptor homolog CprB {Streptomyces coeli	82.49
d2isya1	63	Iron-dependent regulator IdeR {Mycobacterium tuber	82.34
d2np5a1	69	Transcriptional regulator RHA1_ro04179 {Rhodococcu	82.18
d1pb6a1	72	Hypothetical transcriptional regulator YcdC {Esche	82.06
d1or7a1	68	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	81.99
d3c07a1	75	Putative transcriptional regulator SCO4850 {Strept	81.96
d2hr3a1	145	Probable transcriptional regulator PA3067 {Pseudom	81.63
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	81.44
d1ub9a_	100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	81.19
d3bwga1	78	Transcriptional regulator YydK {Bacillus subtilis	81.1
d1nera_	74	Ner {Bacteriophage mu [TaxId: 10677]}	81.08
d1tc3c_	51	Transposase tc3a1-65 {Caenorhabditis elegans [TaxI	81.0
d2g7ga1	65	Putative transcriptional regulator Rha04620 {Rhodo	80.91
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	80.86
d1a04a1	67	Nitrate/nitrite response regulator (NarL) {Escheri	80.68
d1rkta1	81	Hypothetical transcriptional regulator YfiR {Bacil	80.67
d1umqa_	60	Photosynthetic apparatus regulatory protein PprA (	80.66
d2fbha1	137	Transcriptional regulator PA3341 {Pseudomonas aeru	80.15

>d1y7ya1 a.35.1.3 (A:5-73) Restriction-modification controller protein C.AhdI {Aeromonas hydrophila [TaxId: 644]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Restriction-modification controller protein C.AhdI
species: Aeromonas hydrophila [TaxId: 644]

Probab=99.82  E-value=1.8e-20  Score=119.14  Aligned_cols=63  Identities=29%  Similarity=0.196  Sum_probs=61.0

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccccccc
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNA   92 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~   92 (174)
                      .+.||++||.+|+.+||||++||+.+|+|+++|++||+|++.|+++.+.+||++|||++++||
T Consensus         7 ~~~~g~~ik~~R~~~gltq~~lA~~~gis~~~i~~~E~g~~~p~~~~l~~ia~~l~v~~~~lF   69 (69)
T d1y7ya1           7 LVKFGQRLRELRTAKGLSQETLAFLSGLDRSYVGGVERGQRNVSLVNILKLATALDIEPRELF   69 (69)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCSCCBHHHHHHHHHHTTSCGGGGC
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHhHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHhCcCHHHHC
Confidence            357999999999999999999999999999999999999999999999999999999999986

>d2r1jl1 a.35.1.2 (L:3-68) P22 C2 repressor, DNA-binding domain {Salmonella bacteriophage P22 [TaxId: 10754]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: P22 C2 repressor, DNA-binding domain
species: Salmonella bacteriophage P22 [TaxId: 10754]

Probab=99.79  E-value=5.6e-20  Score=115.75  Aligned_cols=62  Identities=13%  Similarity=0.096  Sum_probs=60.3

Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccC
Q psy6501          32 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAG   93 (174)
Q Consensus        32 ~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~   93 (174)
                      .+|++||.+|+.+||||.+||+.+|+|+++|++||+|...|+.+.+.+||++|+|+++||+.
T Consensus         3 ~ig~rik~~R~~~g~tq~~lA~~~gvs~~~i~~~e~g~~~p~~~~l~~ia~~l~v~~~~Ll~   64 (66)
T d2r1jl1           3 LMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCSPDYLLK   64 (66)
T ss_dssp             CHHHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHTTSSCCBHHHHHHHHHHTTSCHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHHHhc
Confidence            58999999999999999999999999999999999999999999999999999999999983

>d2croa_ a.35.1.2 (A:) cro 434 {Bacteriophage 434 [TaxId: 10712]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: cro 434
species: Bacteriophage 434 [TaxId: 10712]

Probab=99.79  E-value=2.8e-20  Score=116.85  Aligned_cols=61  Identities=25%  Similarity=0.141  Sum_probs=58.0

Q ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccccccc
Q psy6501          31 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNA   92 (174)
Q Consensus        31 ~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~   92 (174)
                      ..||++|+.+|+.+||||+|||+.+|||+++|++||+|.+.|+ +.+.+||++|||+++||+
T Consensus         2 ~~i~~rlr~~R~~~gltq~~lA~~~gvs~~ti~~~E~g~~~~~-~~l~~ia~~l~v~~~~Ll   62 (65)
T d2croa_           2 QTLSERLKKRRIALKMTQTELATKAGVKQQSIQLIEAGVTKRP-RFLFEIAMALNCDPVWLQ   62 (65)
T ss_dssp             CSHHHHHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHTTCCSSC-TTHHHHHHHTTSCHHHHH
T ss_pred             hHHHHHHHHHHHHcCCCHHHHHHHHCcCHhHHHHHHCCCCCCH-HHHHHHHHHhCCCHHHHh
Confidence            3699999999999999999999999999999999999998776 889999999999999997

>d1y9qa1 a.35.1.8 (A:4-82) Probable transcriptional regulator VC1968, N-terminal domain {Vibrio cholerae [TaxId: 666]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Probable transcriptional regulator VC1968, N-terminal domain
domain: Probable transcriptional regulator VC1968, N-terminal domain
species: Vibrio cholerae [TaxId: 666]

Probab=99.79  E-value=2.3e-19  Score=116.74  Aligned_cols=65  Identities=18%  Similarity=0.205  Sum_probs=62.5

Q ss_pred             chHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccC
Q psy6501          29 VPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAG   93 (174)
Q Consensus        29 ~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~   93 (174)
                      +...||.+||.+|+.+||||++||+.+|+|+++|++||+|...|+.+.+.+||++|||+++||+.
T Consensus         5 ~~~~ig~~lr~~R~~~g~sq~~lA~~~gis~~~i~~~E~g~~~p~~~~l~~ia~~l~v~~~~l~~   69 (79)
T d1y9qa1           5 FKSQIANQLKNLRKSRGLSLDATAQLTGVSKAMLGQIERGESSPTIATLWKIASGLEASFSAFFA   69 (79)
T ss_dssp             HHHHHHHHHHHHHHHTTCCHHHHHHHHSSCHHHHHHHHTTCSCCCHHHHHHHHHHHTCCSGGGGT
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHHCcchhHHHHHHcCCCCCCHHHHHHHHHHHCCCHHHHhC
Confidence            35679999999999999999999999999999999999999999999999999999999999995

>d2b5aa1 a.35.1.3 (A:1-77) Regulatory protein C.BclI {Bacillus caldolyticus [TaxId: 1394]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Regulatory protein C.BclI
species: Bacillus caldolyticus [TaxId: 1394]

Probab=99.79  E-value=9e-20  Score=118.15  Aligned_cols=65  Identities=23%  Similarity=0.194  Sum_probs=62.6

Q ss_pred             cchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccccccc
Q psy6501          28 KVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNA   92 (174)
Q Consensus        28 ~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~   92 (174)
                      ++...||++|+.+|+.+||||++||+++|+|+++|++||+|.+.|+.+.+.+||++|||++++|+
T Consensus         6 ~~~~~~g~~ik~~R~~~gltq~~lA~~~gis~~~i~~~e~g~~~p~~~~l~~ia~~l~v~~~~l~   70 (77)
T d2b5aa1           6 EIKRKFGRTLKKIRTQKGVSQEELADLAGLHRTYISEVERGDRNISLINIHKICAALDIPASTFF   70 (77)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCSCCBHHHHHHHHHHTTCCHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHHHh
Confidence            35678999999999999999999999999999999999999999999999999999999999998

>d1x57a1 a.35.1.12 (A:8-85) Endothelial differentiation-related factor 1, EDF1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: EDF1-like
domain: Endothelial differentiation-related factor 1, EDF1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.78  E-value=1.6e-19  Score=117.29  Aligned_cols=66  Identities=58%  Similarity=1.012  Sum_probs=62.1

Q ss_pred             ccchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccccccc
Q psy6501          27 EKVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNA   92 (174)
Q Consensus        27 ~~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~   92 (174)
                      +.+.|.||++|+.+|+.+||||++||+.+|+|+++|++||+|.+.|+.+.|.+||++|||++.+..
T Consensus         1 e~~~~~iG~~I~~~R~~~gltq~~lA~~~gis~~~is~~E~G~~~p~~~~l~~la~~l~v~l~~~~   66 (78)
T d1x57a1           1 DRVTLEVGKVIQQGRQSKGLTQKDLATKINEKPQVIADYESGRAIPNNQVLGKIERAIGLKLRGKD   66 (78)
T ss_dssp             SCCCCHHHHHHHHHHHTTTCCHHHHHHHHTSCHHHHHHHHHTCSCCCHHHHHHHHHHHTBCCSSTT
T ss_pred             CcccHHHHHHHHHHHHHcCCChhHHHHcCCCCHHHHHHHHccCCCCCHHHHHHHHHHhCCcccccc
Confidence            356789999999999999999999999999999999999999999999999999999999987654

>d1b0na2 a.35.1.3 (A:1-68) SinR repressor, DNA-binding domain {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: SinR repressor, DNA-binding domain
species: Bacillus subtilis [TaxId: 1423]

Probab=99.78  E-value=1.5e-19  Score=114.45  Aligned_cols=63  Identities=19%  Similarity=0.273  Sum_probs=59.6

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCcccccccCCC
Q psy6501          33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRG-IPNQAIIGKMERALGIRLRVNAGTN   95 (174)
Q Consensus        33 ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~-~P~~~~l~~la~~L~v~~~~l~~~~   95 (174)
                      ||++||.+|+++||||.+||+++|+|+++|++||+|.+ .|+.+.+.+||++|||+++||+...
T Consensus         2 ig~~ik~~R~~~gltq~~la~~~gis~~~i~~~E~g~~~~ps~~~l~~ia~~l~v~~~~l~~~~   65 (68)
T d1b0na2           2 IGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNLQTNPSIQFLEKVSAVLDVSVHTLLDEK   65 (68)
T ss_dssp             CHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCCSCCCHHHHHHHHHHHTCCHHHHHCCT
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcCCCCCCCHHHHHHHHHHHCCcHHHHcCCC
Confidence            69999999999999999999999999999999999975 6999999999999999999999543

>d1utxa_ a.35.1.3 (A:) Putative transcription regulator CylR2 {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Putative transcription regulator CylR2
species: Enterococcus faecalis [TaxId: 1351]

Probab=99.77  E-value=6.4e-20  Score=115.54  Aligned_cols=61  Identities=23%  Similarity=0.119  Sum_probs=58.5

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccCC
Q psy6501          34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAGT   94 (174)
Q Consensus        34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~~   94 (174)
                      +.+|+.+|+.+||||+|||+.+|||+++||+||+|++.|+.+.+.+||++|||++++||+.
T Consensus         3 ~~ri~~lR~~~g~tq~elA~~~gis~~~is~~e~g~~~p~~~~l~~ia~~l~v~~~~lf~~   63 (66)
T d1utxa_           3 INNLKLIREKKKISQSELAALLEVSRQTINGIEKNKYNPSLQLALKIAYYLNTPLEDIFQW   63 (66)
T ss_dssp             EECHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHTTSCCCCHHHHHHHHHHTTSCHHHHEEE
T ss_pred             HHHHHHHHHHcCCCHHHHHHhcccCHHHHHHHHcCCCCCCHHHHHHHHHHHCCCHHHHcCC
Confidence            4689999999999999999999999999999999999999999999999999999999853

>d1r69a_ a.35.1.2 (A:) 434 C1 repressor, DNA-binding domain {Bacteriophage 434 [TaxId: 10712]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: 434 C1 repressor, DNA-binding domain
species: Bacteriophage 434 [TaxId: 10712]

Probab=99.77  E-value=1.5e-19  Score=112.78  Aligned_cols=60  Identities=20%  Similarity=0.340  Sum_probs=57.4

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccC
Q psy6501          33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAG   93 (174)
Q Consensus        33 ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~   93 (174)
                      ||++|+.+|+.+||||+|||+.+|+|+++|++||+|+ .|+.+.+.+||++|||+++||+.
T Consensus         2 ig~rik~~R~~~g~sq~elA~~~gvs~~~is~~E~g~-~~~~~~l~~ia~~l~v~~~~l~~   61 (63)
T d1r69a_           2 ISSRVKSKRIQLGLNQAELAQKVGTTQQSIEQLENGK-TKRPRFLPELASALGVSVDWLLN   61 (63)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHTTS-CSSCTTHHHHHHHTTCCHHHHHH
T ss_pred             HHHHHHHHHHHcCCcHHHHHHHhCcCHHHHHHHHCCC-CcCHHHHHHHHHHHCcCHHHHhh
Confidence            7999999999999999999999999999999999997 48899999999999999999973

>d1lmb3_ a.35.1.2 (3:) lambda C1 repressor, DNA-binding domain {Bacteriophage lambda [TaxId: 10710]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: lambda C1 repressor, DNA-binding domain
species: Bacteriophage lambda [TaxId: 10710]

Probab=99.72  E-value=1.2e-17  Score=110.47  Aligned_cols=63  Identities=16%  Similarity=0.135  Sum_probs=59.9

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccccccc
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNA   92 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~   92 (174)
                      ...+|..|+.+|+.+||||++||+.+|+|+++|++||+|.+.|+...+.+||++|+|++++|+
T Consensus        10 ~~~l~~~i~~~R~~~gltq~~lA~~lgis~~~is~~E~g~~~~s~~~l~~ia~~l~v~~~~~~   72 (87)
T d1lmb3_          10 ARRLKAIYEKKKNELGLSQESVADKMGMGQSGVGALFNGINALNAYNAALLAKILKVSVEEFS   72 (87)
T ss_dssp             HHHHHHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHTTSSCCCHHHHHHHHHHHTSCGGGTC
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHhCccHHHHHHHHhccCCCcHHHHHHHHHHHCCCHHHHC
Confidence            456788888889999999999999999999999999999999999999999999999999998

>d2icta1 a.35.1.3 (A:8-94) Antitoxin HigA {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Antitoxin HigA
species: Escherichia coli [TaxId: 562]

Probab=99.71  E-value=7.5e-18  Score=111.51  Aligned_cols=60  Identities=10%  Similarity=0.160  Sum_probs=58.4

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccC
Q psy6501          34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAG   93 (174)
Q Consensus        34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~   93 (174)
                      |++|+++|+.+||||.+||+.+|||+++||+||+|++.|+.+.+.+||++|||+++++++
T Consensus         3 Ge~lke~r~~~glsq~~LA~~lGvs~~~is~ie~g~~~~s~~~~~kla~~lgvs~~~~L~   62 (87)
T d2icta1           3 GDIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVIGSSPQMWLN   62 (87)
T ss_dssp             HHHHHHHHHHHTCCHHHHHHHHTCCHHHHHHHHHTSSCCCHHHHHHHHHHTCSCHHHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHhhcHHHHHHHHHhccCCCHHHHHHHHHHHCcCHHHHHh
Confidence            889999999999999999999999999999999999999999999999999999998873

>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=99.70  E-value=2e-17  Score=104.75  Aligned_cols=64  Identities=17%  Similarity=0.240  Sum_probs=60.0

Q ss_pred             chHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhCccccccc
Q psy6501          29 VPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGR-GIPNQAIIGKMERALGIRLRVNA   92 (174)
Q Consensus        29 ~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~-~~P~~~~l~~la~~L~v~~~~l~   92 (174)
                      +..+++.+|+.+|+.+||||+|||+.+|+++++||+||+|+ ..|+.+.|.+||++||++++..+
T Consensus         3 ~~~~l~~~i~~~r~~~gltq~elA~~~gv~~~~is~ie~g~~~~~s~~~L~~ia~~Lg~~i~~~~   67 (69)
T d2a6ca1           3 MRSQLLIVLQEHLRNSGLTQFKAAELLGVTQPRVSDLMRGKIDLFSLESLIDMITSIGLKVEINI   67 (69)
T ss_dssp             HHHHHHHHHHHHHHTTTCCHHHHHHHHTSCHHHHHHHHTTCGGGCCHHHHHHHHHHTTCCCCCCC
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHHHcCHhHHHHHHcccccchhHHHHHHHHHHhCCCcEeee
Confidence            34579999999999999999999999999999999999998 78999999999999999998765

>d2o38a1 a.35.1.13 (A:28-116) Hypothetical protein RPA3824 {Rhodopseudomonas palustris [TaxId: 1076]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE1354
domain: Hypothetical protein RPA3824
species: Rhodopseudomonas palustris [TaxId: 1076]

Probab=99.69  E-value=4.9e-17  Score=107.93  Aligned_cols=68  Identities=15%  Similarity=0.036  Sum_probs=63.2

Q ss_pred             cchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhCcccccccCCC
Q psy6501          28 KVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGR-GIPNQAIIGKMERALGIRLRVNAGTN   95 (174)
Q Consensus        28 ~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~-~~P~~~~l~~la~~L~v~~~~l~~~~   95 (174)
                      .+.+.+|.+|+.+|+++||||.+||+.+|+|+++||+||||+ ..|+++.|.+||++||+++++++...
T Consensus         7 ~~k~~l~~~i~~~r~~~gltq~~lA~~~gis~~~is~ie~G~~~~~~~~~L~~ia~~Lg~~i~~~~~~~   75 (89)
T d2o38a1           7 QTKLRLAYALNAVIDRARLSQAAAAARLGINQPKVSALRNYKLEGFSVERLMTLLNALDQDVEIVIRKK   75 (89)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCCTTCCHHHHHHHHHHTTEEEEEEEEEC
T ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHhhHhHHHHHHcCCCCCCcHHHHHHHHHHcCCCHHHeecCC
Confidence            346789999999999999999999999999999999999998 78999999999999999999998543

>d2ofya1 a.35.1.3 (A:3-84) Putative transcriptional regulator RHA1_ro04071 {Rhodococcus sp. RHA1 [TaxId: 101510]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Putative transcriptional regulator RHA1 ro04071
species: Rhodococcus sp. RHA1 [TaxId: 101510]

Probab=99.68  E-value=3.2e-17  Score=107.15  Aligned_cols=64  Identities=23%  Similarity=0.233  Sum_probs=59.3

Q ss_pred             chHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhCcccccccCC
Q psy6501          29 VPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGR-GIPNQAIIGKMERALGIRLRVNAGT   94 (174)
Q Consensus        29 ~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~-~~P~~~~l~~la~~L~v~~~~l~~~   94 (174)
                      ....||.+||.+|+  ++||.|||+++|+|++|||+||+|+ ..|++..|.+||++|||++++|+..
T Consensus        11 ~~~~lG~~ir~~R~--~~t~~eLA~~~Gvs~~~ls~iE~G~~~~ps~~tl~kia~~L~v~~~~Ll~~   75 (82)
T d2ofya1          11 RGQRLGELLRSARG--DMSMVTVAFDAGISVETLRKIETGRIATPAFFTIAAVARVLDLSLDDVAAV   75 (82)
T ss_dssp             HHHHHHHHHHHHHT--TSCHHHHHHHHTCCHHHHHHHHTTCCSSCBHHHHHHHHHHTTCCHHHHHTT
T ss_pred             HHHHHHHHHHHHHH--cCCHHHHHHHHcCCHHHHHHHHcCCcCCCCHHHHHHHHHHHCCCHHHHHhh
Confidence            35789999999995  7899999999999999999999998 6899999999999999999999953

>d2ppxa1 a.35.1.3 (A:30-91) Uncharacterized protein Atu1735 {Agrobacterium tumefaciens [TaxId: 358]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Uncharacterized protein Atu1735
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=99.54  E-value=7.3e-15  Score=90.82  Aligned_cols=55  Identities=16%  Similarity=0.247  Sum_probs=47.9

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccc
Q psy6501          36 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVN   91 (174)
Q Consensus        36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l   91 (174)
                      +||.+|+..||||++||+.+|||++||++||+|+..|+...+..|+ .+...++.+
T Consensus         3 ~ik~~R~~~gltQ~elA~~lGvs~~tvs~~E~G~~~P~~~~~~ll~-~l~~~Pe~v   57 (62)
T d2ppxa1           3 RIKIIRRALKLTQEEFSARYHIPLGTLRDWEQGRSEPDQPARAYLK-IIAVDPEGT   57 (62)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTSSCCCHHHHHHHH-HHHHCHHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHH-HHhcCHHHH
Confidence            7899999999999999999999999999999999999998876664 555555544

>d2auwa1 a.35.1.10 (A:88-154) Hypothetical protein NE0471 C-terminal domain {Nitrosomonas europaea [TaxId: 915]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE0471 C-terminal domain-like
domain: Hypothetical protein NE0471 C-terminal domain
species: Nitrosomonas europaea [TaxId: 915]

Probab=99.34  E-value=3e-12  Score=79.70  Aligned_cols=42  Identities=12%  Similarity=0.116  Sum_probs=38.4

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHH
Q psy6501          34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQA   75 (174)
Q Consensus        34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~   75 (174)
                      +++|+.+|++.||||++||+.+|||+++|++||+|++.++..
T Consensus         3 ~e~~k~~R~~~gltQ~elA~~LGvs~~ti~~yE~G~r~iP~~   44 (67)
T d2auwa1           3 HEMFGDWMHRNNLSLTTAAEALGISRRMVSYYRTAHKIIPRT   44 (67)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHTTSSCCCHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHH
Confidence            589999999999999999999999999999999999765544

>d1y7ya1 a.35.1.3 (A:5-73) Restriction-modification controller protein C.AhdI {Aeromonas hydrophila [TaxId: 644]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Restriction-modification controller protein C.AhdI
species: Aeromonas hydrophila [TaxId: 644]

Probab=99.33  E-value=2.4e-12  Score=80.79  Aligned_cols=54  Identities=30%  Similarity=0.244  Sum_probs=51.7

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         121 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       121 ~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ..+++.|++.|+.+||||+++|+.+|++++++++||+|+..|+...+.+||++|
T Consensus         8 ~~~g~~ik~~R~~~gltq~~lA~~~gis~~~i~~~E~g~~~p~~~~l~~ia~~l   61 (69)
T d1y7ya1           8 VKFGQRLRELRTAKGLSQETLAFLSGLDRSYVGGVERGQRNVSLVNILKLATAL   61 (69)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCSCCBHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHhHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHh
Confidence            357899999999999999999999999999999999999999999999999987

>d1x57a1 a.35.1.12 (A:8-85) Endothelial differentiation-related factor 1, EDF1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: EDF1-like
domain: Endothelial differentiation-related factor 1, EDF1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.32  E-value=1.8e-12  Score=83.35  Aligned_cols=56  Identities=63%  Similarity=1.053  Sum_probs=53.1

Q ss_pred             ccHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         119 VPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       119 ~~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      +.-.++..|+..|+.+||||.+||+.+|++.++|++||+|...|+.+.+.+||++|
T Consensus         3 ~~~~iG~~I~~~R~~~gltq~~lA~~~gis~~~is~~E~G~~~p~~~~l~~la~~l   58 (78)
T d1x57a1           3 VTLEVGKVIQQGRQSKGLTQKDLATKINEKPQVIADYESGRAIPNNQVLGKIERAI   58 (78)
T ss_dssp             CCCHHHHHHHHHHHTTTCCHHHHHHHHTSCHHHHHHHHHTCSCCCHHHHHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHcCCChhHHHHcCCCCHHHHHHHHccCCCCCHHHHHHHHHHh
Confidence            44578999999999999999999999999999999999999999999999999986

>d2r1jl1 a.35.1.2 (L:3-68) P22 C2 repressor, DNA-binding domain {Salmonella bacteriophage P22 [TaxId: 10754]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: P22 C2 repressor, DNA-binding domain
species: Salmonella bacteriophage P22 [TaxId: 10754]

Probab=99.27  E-value=6.7e-12  Score=77.95  Aligned_cols=53  Identities=15%  Similarity=0.183  Sum_probs=50.9

Q ss_pred             HHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         122 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       122 ~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      .++.+|+..|+.+||||.++|+.+|+++++++.||+|...|+.+.+.+||++|
T Consensus         3 ~ig~rik~~R~~~g~tq~~lA~~~gvs~~~i~~~e~g~~~p~~~~l~~ia~~l   55 (66)
T d2r1jl1           3 LMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKAL   55 (66)
T ss_dssp             CHHHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHTTSSCCBHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence            46789999999999999999999999999999999999999999999999987

>d2croa_ a.35.1.2 (A:) cro 434 {Bacteriophage 434 [TaxId: 10712]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: cro 434
species: Bacteriophage 434 [TaxId: 10712]

Probab=99.24  E-value=7.4e-12  Score=77.55  Aligned_cols=52  Identities=29%  Similarity=0.246  Sum_probs=48.3

Q ss_pred             HHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         122 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       122 ~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      .++++|+..|+.+||||+++|+.+|+++++|+.||+|...|+ +.+.+||++|
T Consensus         3 ~i~~rlr~~R~~~gltq~~lA~~~gvs~~ti~~~E~g~~~~~-~~l~~ia~~l   54 (65)
T d2croa_           3 TLSERLKKRRIALKMTQTELATKAGVKQQSIQLIEAGVTKRP-RFLFEIAMAL   54 (65)
T ss_dssp             SHHHHHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHTTCCSSC-TTHHHHHHHT
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHCcCHhHHHHHHCCCCCCH-HHHHHHHHHh
Confidence            468899999999999999999999999999999999998776 7889999987

>d2b5aa1 a.35.1.3 (A:1-77) Regulatory protein C.BclI {Bacillus caldolyticus [TaxId: 1394]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Regulatory protein C.BclI
species: Bacillus caldolyticus [TaxId: 1394]

Probab=99.23  E-value=1.6e-11  Score=78.45  Aligned_cols=54  Identities=26%  Similarity=0.232  Sum_probs=51.8

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         121 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       121 ~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ..++..|+..|+.+||||+++|+++|+++++|+.||+|...|+.+.+.+||++|
T Consensus         9 ~~~g~~ik~~R~~~gltq~~lA~~~gis~~~i~~~e~g~~~p~~~~l~~ia~~l   62 (77)
T d2b5aa1           9 RKFGRTLKKIRTQKGVSQEELADLAGLHRTYISEVERGDRNISLINIHKICAAL   62 (77)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCSCCBHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence            457899999999999999999999999999999999999999999999999987

>d1y9qa1 a.35.1.8 (A:4-82) Probable transcriptional regulator VC1968, N-terminal domain {Vibrio cholerae [TaxId: 666]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Probable transcriptional regulator VC1968, N-terminal domain
domain: Probable transcriptional regulator VC1968, N-terminal domain
species: Vibrio cholerae [TaxId: 666]

Probab=99.21  E-value=1.7e-11  Score=78.73  Aligned_cols=54  Identities=22%  Similarity=0.279  Sum_probs=51.6

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         121 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       121 ~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ..++..|+..|+.+||||+++|+.+|+++++|++||+|+..|+...+.+||++|
T Consensus         7 ~~ig~~lr~~R~~~g~sq~~lA~~~gis~~~i~~~E~g~~~p~~~~l~~ia~~l   60 (79)
T d1y9qa1           7 SQIANQLKNLRKSRGLSLDATAQLTGVSKAMLGQIERGESSPTIATLWKIASGL   60 (79)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHSSCHHHHHHHHTTCSCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHCcchhHHHHHHcCCCCCCHHHHHHHHHHH
Confidence            457899999999999999999999999999999999999999999999999986

>d1utxa_ a.35.1.3 (A:) Putative transcription regulator CylR2 {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Putative transcription regulator CylR2
species: Enterococcus faecalis [TaxId: 1351]

Probab=99.21  E-value=1.8e-11  Score=76.05  Aligned_cols=49  Identities=27%  Similarity=0.210  Sum_probs=47.5

Q ss_pred             HHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         126 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       126 ~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      +|+..|..+||||+++|+++|+++++++.||+|...|+.+.+.+||++|
T Consensus         5 ri~~lR~~~g~tq~elA~~~gis~~~is~~e~g~~~p~~~~l~~ia~~l   53 (66)
T d1utxa_           5 NLKLIREKKKISQSELAALLEVSRQTINGIEKNKYNPSLQLALKIAYYL   53 (66)
T ss_dssp             CHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHTTSCCCCHHHHHHHHHHT
T ss_pred             HHHHHHHHcCCCHHHHHHhcccCHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence            6789999999999999999999999999999999999999999999987

>d1r69a_ a.35.1.2 (A:) 434 C1 repressor, DNA-binding domain {Bacteriophage 434 [TaxId: 10712]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: 434 C1 repressor, DNA-binding domain
species: Bacteriophage 434 [TaxId: 10712]

Probab=99.19  E-value=1.2e-11  Score=76.02  Aligned_cols=51  Identities=22%  Similarity=0.366  Sum_probs=47.8

Q ss_pred             HHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         123 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       123 ~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ++++|+..|+.+||||+++|+.+|+++++|++||+|+. |+.+.+.+||++|
T Consensus         2 ig~rik~~R~~~g~sq~elA~~~gvs~~~is~~E~g~~-~~~~~l~~ia~~l   52 (63)
T d1r69a_           2 ISSRVKSKRIQLGLNQAELAQKVGTTQQSIEQLENGKT-KRPRFLPELASAL   52 (63)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHTTSC-SSCTTHHHHHHHT
T ss_pred             HHHHHHHHHHHcCCcHHHHHHHhCcCHHHHHHHHCCCC-cCHHHHHHHHHHH
Confidence            57899999999999999999999999999999999975 7888999999986

>d1b0na2 a.35.1.3 (A:1-68) SinR repressor, DNA-binding domain {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: SinR repressor, DNA-binding domain
species: Bacillus subtilis [TaxId: 1423]

Probab=99.17  E-value=2.5e-11  Score=75.77  Aligned_cols=52  Identities=23%  Similarity=0.317  Sum_probs=48.6

Q ss_pred             HHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCC-CCCHHHHHHHHhhC
Q psy6501         123 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRG-IPNQAIIGKMERAL  174 (174)
Q Consensus       123 ~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~-~P~~~~l~~i~~~l  174 (174)
                      +++.|+..|.++||||.++|+.+|+++++|++||+|.. .|+.+.+.+||++|
T Consensus         2 ig~~ik~~R~~~gltq~~la~~~gis~~~i~~~E~g~~~~ps~~~l~~ia~~l   54 (68)
T d1b0na2           2 IGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNLQTNPSIQFLEKVSAVL   54 (68)
T ss_dssp             CHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCCSCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcCCCCCCCHHHHHHHHHHH
Confidence            36789999999999999999999999999999999975 69999999999986

>d1lmb3_ a.35.1.2 (3:) lambda C1 repressor, DNA-binding domain {Bacteriophage lambda [TaxId: 10710]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: lambda C1 repressor, DNA-binding domain
species: Bacteriophage lambda [TaxId: 10710]

Probab=99.15  E-value=4.1e-11  Score=78.40  Aligned_cols=55  Identities=18%  Similarity=0.154  Sum_probs=51.3

Q ss_pred             cHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         120 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       120 ~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ...++..++..|+..||||+++|+.+|++.++|++||+|...|+.+.+.+||++|
T Consensus        10 ~~~l~~~i~~~R~~~gltq~~lA~~lgis~~~is~~E~g~~~~s~~~l~~ia~~l   64 (87)
T d1lmb3_          10 ARRLKAIYEKKKNELGLSQESVADKMGMGQSGVGALFNGINALNAYNAALLAKIL   64 (87)
T ss_dssp             HHHHHHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHTTSSCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHhCccHHHHHHHHhccCCCcHHHHHHHHHHH
Confidence            3457788889999999999999999999999999999999999999999999875

>d2ppxa1 a.35.1.3 (A:30-91) Uncharacterized protein Atu1735 {Agrobacterium tumefaciens [TaxId: 358]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Uncharacterized protein Atu1735
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=99.13  E-value=7.1e-11  Score=72.43  Aligned_cols=47  Identities=19%  Similarity=0.267  Sum_probs=43.0

Q ss_pred             HHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHh
Q psy6501         126 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMER  172 (174)
Q Consensus       126 ~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~  172 (174)
                      .|+..|+..||||+++|+.+|+++++|+.||+|+..|+...+..|+.
T Consensus         3 ~ik~~R~~~gltQ~elA~~lGvs~~tvs~~E~G~~~P~~~~~~ll~~   49 (62)
T d2ppxa1           3 RIKIIRRALKLTQEEFSARYHIPLGTLRDWEQGRSEPDQPARAYLKI   49 (62)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTSSCCCHHHHHHHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHH
Confidence            57889999999999999999999999999999999999987766653

>d2icta1 a.35.1.3 (A:8-94) Antitoxin HigA {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Antitoxin HigA
species: Escherichia coli [TaxId: 562]

Probab=99.13  E-value=5.8e-11  Score=77.68  Aligned_cols=51  Identities=10%  Similarity=0.182  Sum_probs=49.2

Q ss_pred             HHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         124 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       124 ~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ++.|++.|+.+||||.+||+.+|+++++|+.||+|++.|+.+++.+|+++|
T Consensus         3 Ge~lke~r~~~glsq~~LA~~lGvs~~~is~ie~g~~~~s~~~~~kla~~l   53 (87)
T d2icta1           3 GDIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVI   53 (87)
T ss_dssp             HHHHHHHHHHHTCCHHHHHHHHTCCHHHHHHHHHTSSCCCHHHHHHHHHHT
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHhhcHHHHHHHHHhccCCCHHHHHHHHHHH
Confidence            578999999999999999999999999999999999999999999999987

>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=99.10  E-value=1.4e-10  Score=72.56  Aligned_cols=54  Identities=17%  Similarity=0.154  Sum_probs=50.7

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCC-CCCCHHHHHHHHhhC
Q psy6501         121 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGR-GIPNQAIIGKMERAL  174 (174)
Q Consensus       121 ~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~-~~P~~~~l~~i~~~l  174 (174)
                      ..+...|+..|+.+||||+++|+.+|+++++|++||+|+ ..|+.+.+.+||.+|
T Consensus         5 ~~l~~~i~~~r~~~gltq~elA~~~gv~~~~is~ie~g~~~~~s~~~L~~ia~~L   59 (69)
T d2a6ca1           5 SQLLIVLQEHLRNSGLTQFKAAELLGVTQPRVSDLMRGKIDLFSLESLIDMITSI   59 (69)
T ss_dssp             HHHHHHHHHHHHTTTCCHHHHHHHHTSCHHHHHHHHTTCGGGCCHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHHcCHhHHHHHHcccccchhHHHHHHHHHHh
Confidence            457789999999999999999999999999999999998 779999999999986

>d2o38a1 a.35.1.13 (A:28-116) Hypothetical protein RPA3824 {Rhodopseudomonas palustris [TaxId: 1076]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE1354
domain: Hypothetical protein RPA3824
species: Rhodopseudomonas palustris [TaxId: 1076]

Probab=99.03  E-value=4.2e-10  Score=73.74  Aligned_cols=54  Identities=19%  Similarity=0.039  Sum_probs=50.9

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCC-CCCCHHHHHHHHhhC
Q psy6501         121 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGR-GIPNQAIIGKMERAL  174 (174)
Q Consensus       121 ~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~-~~P~~~~l~~i~~~l  174 (174)
                      ..++..|++.|+.+||||.++|+.+|++.++|++||+|+ ..|+.+.+.+|+.+|
T Consensus        10 ~~l~~~i~~~r~~~gltq~~lA~~~gis~~~is~ie~G~~~~~~~~~L~~ia~~L   64 (89)
T d2o38a1          10 LRLAYALNAVIDRARLSQAAAAARLGINQPKVSALRNYKLEGFSVERLMTLLNAL   64 (89)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCCTTCCHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHHhhHhHHHHHHcCCCCCCcHHHHHHHHHHc
Confidence            557889999999999999999999999999999999998 679999999999986

>d2ofya1 a.35.1.3 (A:3-84) Putative transcriptional regulator RHA1_ro04071 {Rhodococcus sp. RHA1 [TaxId: 101510]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Putative transcriptional regulator RHA1 ro04071
species: Rhodococcus sp. RHA1 [TaxId: 101510]

Probab=98.96  E-value=1.1e-09  Score=70.60  Aligned_cols=53  Identities=25%  Similarity=0.267  Sum_probs=48.3

Q ss_pred             cHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCC-CCCCHHHHHHHHhhC
Q psy6501         120 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGR-GIPNQAIIGKMERAL  174 (174)
Q Consensus       120 ~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~-~~P~~~~l~~i~~~l  174 (174)
                      ...++..|+..|+  +++|.++|+++|+++++|++||+|+ ..|+...+.+||++|
T Consensus        12 ~~~lG~~ir~~R~--~~t~~eLA~~~Gvs~~~ls~iE~G~~~~ps~~tl~kia~~L   65 (82)
T d2ofya1          12 GQRLGELLRSARG--DMSMVTVAFDAGISVETLRKIETGRIATPAFFTIAAVARVL   65 (82)
T ss_dssp             HHHHHHHHHHHHT--TSCHHHHHHHHTCCHHHHHHHHTTCCSSCBHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHH--cCCHHHHHHHHcCCHHHHHHHHcCCcCCCCHHHHHHHHHHH
Confidence            3568899999884  7899999999999999999999998 579999999999987

>d2auwa1 a.35.1.10 (A:88-154) Hypothetical protein NE0471 C-terminal domain {Nitrosomonas europaea [TaxId: 915]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: NE0471 C-terminal domain-like
domain: Hypothetical protein NE0471 C-terminal domain
species: Nitrosomonas europaea [TaxId: 915]

Probab=98.86  E-value=3.6e-09  Score=65.41  Aligned_cols=42  Identities=14%  Similarity=0.154  Sum_probs=38.3

Q ss_pred             HHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHH
Q psy6501         125 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAI  166 (174)
Q Consensus       125 ~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~  166 (174)
                      +.++.+|+..||||+++|+++|++..+|+.||+|++.++..+
T Consensus         4 e~~k~~R~~~gltQ~elA~~LGvs~~ti~~yE~G~r~iP~~v   45 (67)
T d2auwa1           4 EMFGDWMHRNNLSLTTAAEALGISRRMVSYYRTAHKIIPRTI   45 (67)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHTTSSCCCHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH
Confidence            678999999999999999999999999999999998766554

>d2bnma1 a.35.1.3 (A:6-76) Hydroxypropylphosphonic acid epoxidase Fom4, N-terminal domain {Streptomyces wedmorensis [TaxId: 43759]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Hydroxypropylphosphonic acid epoxidase Fom4, N-terminal domain
species: Streptomyces wedmorensis [TaxId: 43759]

Probab=98.59  E-value=2.9e-07  Score=54.01  Aligned_cols=62  Identities=24%  Similarity=0.416  Sum_probs=58.5

Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhCcccccccC
Q psy6501          32 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGR-GIPNQAIIGKMERALGIRLRVNAG   93 (174)
Q Consensus        32 ~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~-~~P~~~~l~~la~~L~v~~~~l~~   93 (174)
                      .|++++|+.|+.-.|....||..+|-++.+|..||||. ...++..|-+||.+||.++..|..
T Consensus         5 gfae~lk~rreqvkmdhaalas~lgetpetvaawengeggeltltqlg~ia~~lgtsigaltp   67 (71)
T d2bnma1           5 GFAELLKDRREQVKMDHAALASLLGETPETVAAWENGEGGELTLTQLGRIAHVLGTSIGALTP   67 (71)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTTCTTCBHHHHHHHHHHTTSCTGGGSC
T ss_pred             hHHHHHHHHHHHHhhhHHHHHHHHcCCchHHHHhhcCCCceeeHHHHHHHHHHHcccccccCC
Confidence            58999999999999999999999999999999999999 678999999999999999988764

>d1dwka1 a.35.1.4 (A:1-86) Cyanase 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: Cyanase N-terminal domain
domain: Cyanase N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=97.80  E-value=4.2e-05  Score=48.73  Aligned_cols=61  Identities=16%  Similarity=0.101  Sum_probs=57.2

Q ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccc
Q psy6501          31 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVN   91 (174)
Q Consensus        31 ~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l   91 (174)
                      .++-+.|-..+.++|||.+++|+.+|+|+-++...-.|....+.+...++++.|+++.+..
T Consensus        12 ~~lte~Il~AK~~kgltw~~IA~~iG~s~vwvtaa~lGQ~~l~~~~A~~l~~~L~L~~e~~   72 (86)
T d1dwka1          12 LDLADAILLSKAKKDLSFAEIADGTGLAEAFVTAALLGQQALPADAARLVGAKLDLDEDSI   72 (86)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHTTSSSCHHHHHHHHTTSSCCCHHHHHHHHHHHTCCHHHH
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHhcCCCCCHHHHHHHHHHcCCCHHHH
Confidence            4678899999999999999999999999999999999999999999999999999987644

>d2bnma1 a.35.1.3 (A:6-76) Hydroxypropylphosphonic acid epoxidase Fom4, N-terminal domain {Streptomyces wedmorensis [TaxId: 43759]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: SinR domain-like
domain: Hydroxypropylphosphonic acid epoxidase Fom4, N-terminal domain
species: Streptomyces wedmorensis [TaxId: 43759]

Probab=97.58  E-value=0.00026  Score=41.12  Aligned_cols=54  Identities=26%  Similarity=0.446  Sum_probs=47.9

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCC-CCCHHHHHHHHhhC
Q psy6501         121 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRG-IPNQAIIGKMERAL  174 (174)
Q Consensus       121 ~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~-~P~~~~l~~i~~~l  174 (174)
                      ..+.+++++.|+.-.|.-..+|..+|..|.++..||+|+. .-....+.+|+.+|
T Consensus         4 tgfae~lk~rreqvkmdhaalas~lgetpetvaawengeggeltltqlg~ia~~l   58 (71)
T d2bnma1           4 TGFAELLKDRREQVKMDHAALASLLGETPETVAAWENGEGGELTLTQLGRIAHVL   58 (71)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTTCTTCBHHHHHHHHHHT
T ss_pred             hhHHHHHHHHHHHHhhhHHHHHHHHcCCchHHHHhhcCCCceeeHHHHHHHHHHH
Confidence            4567899999999999999999999999999999999965 47788888888765

>d2hsga1 a.35.1.5 (A:2-58) Glucose-resistance amylase regulator CcpA, N-terminal domain {Bacillus megaterium [TaxId: 1404]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: GalR/LacI-like bacterial regulator
domain: Glucose-resistance amylase regulator CcpA, N-terminal domain
species: Bacillus megaterium [TaxId: 1404]

Probab=97.51  E-value=0.00014  Score=42.79  Aligned_cols=45  Identities=18%  Similarity=0.110  Sum_probs=36.3

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHH---HHHhCcccc
Q psy6501          45 GWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKM---ERALGIRLR   89 (174)
Q Consensus        45 gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~l---a~~L~v~~~   89 (174)
                      ++|.+|+|+.+|||.+|||+.-||....+.++-.+|   ++.||-.++
T Consensus         1 NvTi~dvA~~agvS~~TVSr~Ln~~~~Vs~~tr~rV~~aa~~lgY~pn   48 (57)
T d2hsga1           1 NVTIYDVAREASVSMATVSRVVNGNPNVKPSTRKKVLETIERLGYRPN   48 (57)
T ss_dssp             CCCHHHHHHHTTSCHHHHHHHHTTCTTSCHHHHHHHHHHHHHHTCCSC
T ss_pred             CcCHHHHHHHHCcCHHHHHHHhCCCCcCCHHHHHHHHHHHHHHCcCCC
Confidence            579999999999999999999999988888776655   444555443

>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=97.46  E-value=0.0001  Score=43.61  Aligned_cols=45  Identities=16%  Similarity=-0.040  Sum_probs=36.0

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHH---HHHhCccc
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKM---ERALGIRL   88 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~l---a~~L~v~~   88 (174)
                      +..|.+|+|+.+|+|.+|||++-||....+.++-.+|   ++.||..+
T Consensus         1 k~~Ti~diA~~agvS~sTVSr~l~~~~~vs~~tr~rI~~~a~~lgY~p   48 (59)
T d1efaa1           1 KPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIP   48 (59)
T ss_dssp             CCCCHHHHHHTTTSCHHHHHHHHTTCSSCCTHHHHHHHHHHHHHTCCC
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHCCCCcCCHHHHHHHHHHHHHHCCCc
Confidence            3579999999999999999999999987777766554   44555544

>d1e3oc2 a.35.1.1 (C:1-75) Oct-1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: POU-specific domain
domain: Oct-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.35  E-value=0.00016  Score=44.19  Aligned_cols=50  Identities=18%  Similarity=0.224  Sum_probs=40.2

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHhC------CCHHHHHHHHcCCCCCCHHHHHHHH
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATKIN------EKPQIVNDYEGGRGIPNQAIIGKME   81 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~ig------vs~~~is~~E~G~~~P~~~~l~~la   81 (174)
                      ...|+..+|..|-..|+||.+++..+|      .|+++|+++|+=.  .|...+.+|-
T Consensus         9 le~Fa~~fk~rRi~LG~TQ~dVG~al~~l~g~~~SQttIcRFE~l~--LS~kn~~kLk   64 (75)
T d1e3oc2           9 LEQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALN--LSFKNMSKLK   64 (75)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHHHHHSCCCCHHHHHHHHHTC--SCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccccHHHHHHHHHHHcCcchhHHHHHHHHHhc--cCHHHHHHHH
Confidence            457999999999999999999999874      6899999999643  3555555543

>d2awia1 a.35.1.11 (A:2-66) PrgX {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: PrgX N-terminal domain-like
domain: PrgX
species: Enterococcus faecalis [TaxId: 1351]

Probab=97.35  E-value=0.00032  Score=40.02  Aligned_cols=59  Identities=20%  Similarity=0.187  Sum_probs=53.4

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccccccc
Q psy6501          33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNA   92 (174)
Q Consensus        33 ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~   92 (174)
                      +|..++++|++.++-|-+|-..+ +|.+..-+.|...+..+.+.|.++++.|||+.-.++
T Consensus         3 ig~~lkqir~elnyhqidlysgi-msksiyikveadsrpisveel~kfserlginffeil   61 (65)
T d2awia1           3 IGSVLKQIRQELNYHQIDLYSGI-MSKSVYIKVEADSRPISVEELSKFSERLGVNFFEIL   61 (65)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHTTT-SCHHHHHHHHTTCSCCBHHHHHHHHHHHTSCHHHHH
T ss_pred             cchHHHHHHHHhhhhHhHHHhhh-cccceEEEEecCCCcccHHHHHHHHHHhCchHHHHH
Confidence            78999999999999999998766 689999999999999999999999999999865443

>d1uxda_ a.35.1.5 (A:) Fructose repressor (FruR), N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: GalR/LacI-like bacterial regulator
domain: Fructose repressor (FruR), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=97.32  E-value=0.00027  Score=41.74  Aligned_cols=46  Identities=7%  Similarity=-0.022  Sum_probs=38.0

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCC------CCHHHHHHHHHHhCcccccc
Q psy6501          46 WSQKDLATKINEKPQIVNDYEGGRGI------PNQAIIGKMERALGIRLRVN   91 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~G~~~------P~~~~l~~la~~L~v~~~~l   91 (174)
                      +|.+|+|+.+|||.+|||++-||...      -+-+.+.+.++.||-.++..
T Consensus         1 vTl~diA~~agvS~sTVSrvLn~~~~~~~vs~~tr~rV~~~a~~lgY~pn~~   52 (59)
T d1uxda_           1 MKLDEIARLAGVSRTTASYVINGKAKQYRVSDKTVEKVMAVVREHNYHPNAV   52 (59)
T ss_dssp             CCHHHHHHHHTSCTTHHHHHHHTCGGGTTCTTTTHHHHHHHHHHHTCCCCSC
T ss_pred             CCHHHHHHHHCcCHHHHHHHHcCCCCcCcCCHHHHHHHHHHHHHHCCCcCHH
Confidence            68999999999999999999998632      35667778888888876654

>d1qpza1 a.35.1.5 (A:2-58) Purine repressor (PurR), 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: Purine repressor (PurR), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=97.26  E-value=0.00035  Score=40.92  Aligned_cols=43  Identities=14%  Similarity=0.082  Sum_probs=34.8

Q ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHH---HHHHhCcccc
Q psy6501          47 SQKDLATKINEKPQIVNDYEGGRGIPNQAIIGK---MERALGIRLR   89 (174)
Q Consensus        47 tq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~---la~~L~v~~~   89 (174)
                      |.+|+|+.+|||.+|||++-||....+.++-.+   +++.||..++
T Consensus         2 Ti~dvA~~agVS~sTVSr~ln~~~~vs~~tr~rV~~~a~~lgY~pn   47 (57)
T d1qpza1           2 TIKDVAKRANVSTTTVSHVINKTRFVAEETRNAVWAAIKELHYSPS   47 (57)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHHTCSCCCHHHHHHHHHHHHHHTCCCC
T ss_pred             CHHHHHHHHCcCHHHHHHHHCCCCccCHHHHHHHHHHHHHHCCCCC
Confidence            789999999999999999999998888776654   4555665543

>d1au7a2 a.35.1.1 (A:5-76) Pit-1 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: POU-specific domain
domain: Pit-1
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=97.19  E-value=0.00088  Score=40.47  Aligned_cols=49  Identities=12%  Similarity=0.116  Sum_probs=40.0

Q ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhC------CCHHHHHHHHcCCCCCCHHHHHHHH
Q psy6501          31 LDLAKLLMQGRQAKGWSQKDLATKIN------EKPQIVNDYEGGRGIPNQAIIGKME   81 (174)
Q Consensus        31 ~~ig~~ik~~R~~~gltq~eLA~~ig------vs~~~is~~E~G~~~P~~~~l~~la   81 (174)
                      ..|+..+|..|-..|+||.+++..+|      .|+++|+++|+=  ..|...+.+|-
T Consensus         6 e~Fa~~fk~rRi~LG~TQ~dVG~al~~l~g~~~SQttIcRFE~l--~LS~kn~~klk   60 (72)
T d1au7a2           6 EQFANEFKVRRIKLGYTQTNVGEALAAVHGSEFSQTTICRFENL--QLSFKNACKLK   60 (72)
T ss_dssp             HHHHHHHHHHHHHHTCCHHHHHHHHHHTTSSCCCHHHHHHHHTT--CSBHHHHHHHH
T ss_pred             HHHHHHHHHHHhccCccHHHHHHHHHHhcCcccchhHHHHHHhc--ccCHHHHHHHH
Confidence            47999999999999999999999864      799999999963  34555555554

>d1ic8a2 a.35.1.1 (A:87-180) Hepatocyte nuclear factor 1a (LFB1/HNF1) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: POU-specific domain
domain: Hepatocyte nuclear factor 1a (LFB1/HNF1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.16  E-value=0.001  Score=42.41  Aligned_cols=49  Identities=10%  Similarity=0.046  Sum_probs=42.0

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIG   78 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~   78 (174)
                      ...+.+-||.....++++|.++|+..|+|+++||.|-++...-+...=.
T Consensus        26 ~~~v~~~IK~Fl~~h~I~Q~~Va~~TGlsQS~iSq~L~~g~~M~~~KR~   74 (94)
T d1ic8a2          26 PWRVAKMVKSYLQQHNIPQREVVDTTGLNQSHLSQHLNKGTPMKTQKRA   74 (94)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHCCCHHHHHHHHHSBCCCCHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCcHHHHHHHHcccHHHHHHHHhCCCCccHHHHH
Confidence            4678899999999999999999999999999999999987655544433

>d1nera_ a.35.1.2 (A:) Ner {Bacteriophage mu [TaxId: 10677]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: Ner
species: Bacteriophage mu [TaxId: 10677]

Probab=96.99  E-value=0.0011  Score=40.55  Aligned_cols=55  Identities=13%  Similarity=0.021  Sum_probs=46.6

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcccccccC
Q psy6501          36 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNAG   93 (174)
Q Consensus        36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~~   93 (174)
                      -|+..-+.+|+|..+|++..|++.+|+.+.   -..|.+.-=..||++|||.+..+..
T Consensus        13 dI~AaL~krG~sLa~lsr~~gls~stl~na---L~rp~pKgEriIA~aLg~~P~eIWP   67 (74)
T d1nera_          13 DVIAGLKKRKLSLSALSRQFGYAPTTLANA---LERHWPKGEQIIANALETKPEVIWP   67 (74)
T ss_dssp             HHHHHHTTSSCCHHHHHHHHSCCHHHHHHT---TTSSCHHHHHHHHHHTTSCHHHHST
T ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHH---HcCCChHHHHHHHHHHCcCHHHhCc
Confidence            356667789999999999999999999876   4566777777899999999998874

>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: HIN recombinase (DNA-binding domain)
species: Synthetic

Probab=96.96  E-value=0.0011  Score=37.16  Aligned_cols=31  Identities=16%  Similarity=0.134  Sum_probs=26.3

Q ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          35 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      +.++.++ ..|.|..++|+.+|||++||.+|-
T Consensus        12 ~~a~~l~-~~G~s~~~iA~~~gVSr~TiYry~   42 (47)
T d1ijwc_          12 EQISRLL-EKGHPRQQLAIIFGIGVSTLYRYF   42 (47)
T ss_dssp             HHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHS
T ss_pred             HHHHHHH-HCCCCHHHHHHHHCcCHHHHHhhC
Confidence            4556666 469999999999999999999985

>d1vz0a1 a.4.14.1 (A:116-208) Putative partitioning protein ParB/Spo0J {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: KorB DNA-binding domain-like
family: KorB DNA-binding domain-like
domain: Putative partitioning protein ParB/Spo0J
species: Thermus thermophilus [TaxId: 274]

Probab=96.64  E-value=0.002  Score=41.36  Aligned_cols=40  Identities=15%  Similarity=0.137  Sum_probs=33.2

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCC
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRG   70 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~   70 (174)
                      +.+-+..++.+. ..|+||+++|+++|.|+++|++.-+=-.
T Consensus         5 piEeA~a~~~L~-e~g~t~~~iA~~~Gks~~~V~~~LrLl~   44 (93)
T d1vz0a1           5 PVEEARGYQALL-EMGLTQEEVARRVGKARSTVANALRLLQ   44 (93)
T ss_dssp             HHHHHHHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHHGGG
T ss_pred             HHHHHHHHHHHH-HcCCCHHHHHHHHccchHHHHHHHHHHH
Confidence            455677788887 6899999999999999999999875333

>d2jn6a1 a.4.1.19 (A:1-89) Uncharacterized protein Cgl2762 {Corynebacterium glutamicum [TaxId: 1718]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Cgl2762-like
domain: Uncharacterized protein Cgl2762
species: Corynebacterium glutamicum [TaxId: 1718]

Probab=96.42  E-value=0.002  Score=40.82  Aligned_cols=44  Identities=7%  Similarity=0.101  Sum_probs=31.3

Q ss_pred             cccccchHHHHHH-HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          24 LKHEKVPLDLAKL-LMQGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        24 ~~~~~~~~~ig~~-ik~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      |+......+|=.. ++......|.|..++|+.+|||+++|++|-+
T Consensus         1 M~rk~Ys~EfK~~aV~l~~~~~g~s~~~vA~~lGIs~~tl~~W~k   45 (89)
T d2jn6a1           1 MPTKTYSEEFKRDAVALYENSDGASLQQIANDLGINRVTLKNWII   45 (89)
T ss_dssp             CCCCCCCHHHHHHHHHHHTTGGGSCHHHHHHHHTSCHHHHHHHHH
T ss_pred             CcCCCCCHHHHHHHHHHHHHcCCCcHHHHHHHHCCCHHHHHHHHH
Confidence            3334444555444 3344445699999999999999999999953

>d1dwka1 a.35.1.4 (A:1-86) Cyanase 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: Cyanase N-terminal domain
domain: Cyanase N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=96.37  E-value=0.0044  Score=39.02  Aligned_cols=54  Identities=19%  Similarity=0.140  Sum_probs=50.1

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         121 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       121 ~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      .++.+.|..++.++|+|-.++|+.+|.++..+...=.|-...+.+.+.+++++|
T Consensus        12 ~~lte~Il~AK~~kgltw~~IA~~iG~s~vwvtaa~lGQ~~l~~~~A~~l~~~L   65 (86)
T d1dwka1          12 LDLADAILLSKAKKDLSFAEIADGTGLAEAFVTAALLGQQALPADAARLVGAKL   65 (86)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHTTSSSCHHHHHHHHTTSSCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHhcCCCCCHHHHHHHHHHc
Confidence            356678899999999999999999999999999999999999999999999875

>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=96.37  E-value=0.0027  Score=37.22  Aligned_cols=39  Identities=18%  Similarity=0.003  Sum_probs=35.3

Q ss_pred             CCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhh
Q psy6501         135 GWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERA  173 (174)
Q Consensus       135 glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~  173 (174)
                      ..|..|+|++.|+|+++++++-+|....+++...+|.++
T Consensus         2 ~~Ti~diA~~agvS~sTVSr~l~~~~~vs~~tr~rI~~~   40 (59)
T d1efaa1           2 PVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAA   40 (59)
T ss_dssp             CCCHHHHHHTTTSCHHHHHHHHTTCSSCCTHHHHHHHHH
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHCCCCcCCHHHHHHHHHH
Confidence            478999999999999999999999999999988888654

>d1hlva1 a.4.1.7 (A:1-66) DNA-binding domain of centromere binding protein B (CENP-B) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Centromere-binding
domain: DNA-binding domain of centromere binding protein B (CENP-B)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.21  E-value=0.0098  Score=35.50  Aligned_cols=46  Identities=15%  Similarity=0.269  Sum_probs=32.7

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCc
Q psy6501          36 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGI   86 (174)
Q Consensus        36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v   86 (174)
                      .|+.+...-.++|.|+|+.+||+++|||.|-+.     -+.+..-.+.+|.
T Consensus        16 ii~~~e~g~k~sq~eIA~~fGv~~STvs~IlKn-----K~kil~~~~~~g~   61 (66)
T d1hlva1          16 IIQEVEENPDLRKGEIARRFNIPPSTLSTILKN-----KRAILASERKYGV   61 (66)
T ss_dssp             HHHHHHHCTTSCHHHHHHHHTCCHHHHHHHHHT-----HHHHHHHHHHHGG
T ss_pred             HHHHHHcCCcchHHHHHHHhCCChhHHHHHHHH-----HHHHHHHHHHcCc
Confidence            344444445589999999999999999999875     3444444444444

>d1r71a_ a.4.14.1 (A:) Transcriptional repressor protein KorB DNA-binding domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: KorB DNA-binding domain-like
family: KorB DNA-binding domain-like
domain: Transcriptional repressor protein KorB DNA-binding domain
species: Escherichia coli [TaxId: 562]

Probab=96.15  E-value=0.0043  Score=40.95  Aligned_cols=43  Identities=21%  Similarity=0.386  Sum_probs=35.6

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCC
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPN   73 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~   73 (174)
                      +.+.+..++.+.. .|+|++++|+++|+|+++|+++-.=-..|.
T Consensus        16 p~e~A~a~~~l~~-~g~s~~eiA~~~G~s~~~V~~~l~L~~lp~   58 (114)
T d1r71a_          16 PREIADFIGRELA-KGKKKGDIAKEIGKSPAFITQHVTLLDLPE   58 (114)
T ss_dssp             HHHHHHHHHHHHH-TTCCHHHHHHHHTCCHHHHHHHHGGGSCCH
T ss_pred             HHHHHHHHHHHHH-hCCCHHHHHHHHCCcHHHHHHHHHHhCCCH
Confidence            5678888888864 699999999999999999999986444443

>d2csfa1 a.35.1.7 (A:8-95) DNA-binding protein SATB2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: CUT domain
domain: DNA-binding protein SATB2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.12  E-value=0.0079  Score=37.89  Aligned_cols=59  Identities=14%  Similarity=0.070  Sum_probs=47.2

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHH-HhCCCHHHHHHHHcCCCCCCH------HHHHHHHHHhCccc
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLAT-KINEKPQIVNDYEGGRGIPNQ------AIIGKMERALGIRL   88 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~-~igvs~~~is~~E~G~~~P~~------~~l~~la~~L~v~~   88 (174)
                      ...|..+|++..+..+++|+-||+ -+|.|+.++|.+-+..-.|+.      +.+.++-+.|+.+.
T Consensus        12 T~~Ia~~i~~eL~~~~IsQ~~Fak~vL~rSQGtlSdLLrkpkp~~~~~~sg~e~~~rm~~wL~lPe   77 (88)
T d2csfa1          12 TAAIYDEIQQEMKRAKVSQALFAKVAANKSQGWLCELLRWKENPSPENRTLWENLCTIRRFLNLPQ   77 (88)
T ss_dssp             CTHHHHHHHHHHHHHTCCHHHHHHHHTCCCHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHTSCH
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHHccCcHHHHHHHcCCCCcchhhHHHHHHHHHHHHHHhChH
Confidence            358999999999999999999999 679999999999987555533      45556666666553

>d2hsga1 a.35.1.5 (A:2-58) Glucose-resistance amylase regulator CcpA, N-terminal domain {Bacillus megaterium [TaxId: 1404]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: GalR/LacI-like bacterial regulator
domain: Glucose-resistance amylase regulator CcpA, N-terminal domain
species: Bacillus megaterium [TaxId: 1404]

Probab=96.12  E-value=0.0073  Score=35.02  Aligned_cols=39  Identities=13%  Similarity=0.028  Sum_probs=34.9

Q ss_pred             CCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhh
Q psy6501         135 GWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERA  173 (174)
Q Consensus       135 glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~  173 (174)
                      +.|.+|+|+..|+|.+|++++-+|....++++..+|.++
T Consensus         1 NvTi~dvA~~agvS~~TVSr~Ln~~~~Vs~~tr~rV~~a   39 (57)
T d2hsga1           1 NVTIYDVAREASVSMATVSRVVNGNPNVKPSTRKKVLET   39 (57)
T ss_dssp             CCCHHHHHHHTTSCHHHHHHHHTTCTTSCHHHHHHHHHH
T ss_pred             CcCHHHHHHHHCcCHHHHHHHhCCCCcCCHHHHHHHHHH
Confidence            368899999999999999999999988999988887654

>d1qpza1 a.35.1.5 (A:2-58) Purine repressor (PurR), 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: Purine repressor (PurR), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=95.84  E-value=0.009  Score=34.61  Aligned_cols=37  Identities=16%  Similarity=0.101  Sum_probs=33.4

Q ss_pred             CHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhh
Q psy6501         137 SQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERA  173 (174)
Q Consensus       137 sq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~  173 (174)
                      |.+|+|+..|+|+++++++-+|....++++..+|-++
T Consensus         2 Ti~dvA~~agVS~sTVSr~ln~~~~vs~~tr~rV~~~   38 (57)
T d1qpza1           2 TIKDVAKRANVSTTTVSHVINKTRFVAEETRNAVWAA   38 (57)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHHTCSCCCHHHHHHHHHH
T ss_pred             CHHHHHHHHCcCHHHHHHHHCCCCccCHHHHHHHHHH
Confidence            6899999999999999999999988999988887653

>d1x2la1 a.35.1.7 (A:9-95) Homeobox protein Cux-2, CUTL2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: CUT domain
domain: Homeobox protein Cux-2, CUTL2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.48  E-value=0.013  Score=36.84  Aligned_cols=40  Identities=8%  Similarity=0.008  Sum_probs=36.1

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHH-hCCCHHHHHHHHcCC
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATK-INEKPQIVNDYEGGR   69 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~-igvs~~~is~~E~G~   69 (174)
                      ..+|..+|++..+..+++|.-||+. +|.|+.++|.+-+.-
T Consensus        11 T~~i~~~v~~~L~~~~I~Q~~Fa~~VL~rsQGtlSdLL~~P   51 (87)
T d1x2la1          11 TAEIAFQVKEQLLKHNIGQRVFGHYVLGLSQGSVSEILARP   51 (87)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHTTCSCHHHHHHHHHCC
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHHhhChHHHHHHHhCC
Confidence            5689999999999999999999995 689999999998744

>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=95.43  E-value=0.012  Score=35.21  Aligned_cols=34  Identities=15%  Similarity=0.113  Sum_probs=30.3

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        33 ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      .+.-++.+|..-.+|..|||+.+|+|++||+.+-
T Consensus         8 ~~~Il~~l~~~g~~sr~eLa~~~glS~~Tv~~~l   41 (71)
T d1z05a1           8 AGRVYKLIDQKGPISRIDLSKESELAPASITKIT   41 (71)
T ss_dssp             HHHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHH
Confidence            4567888999999999999999999999999874

>d2o4aa1 a.35.1.7 (A:370-452) DNA-binding protein SATB1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: CUT domain
domain: DNA-binding protein SATB1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.43  E-value=0.013  Score=36.53  Aligned_cols=58  Identities=14%  Similarity=0.172  Sum_probs=45.0

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHH-HhCCCHHHHHHHHcCCCCCCH------HHHHHHHHHhCcc
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLAT-KINEKPQIVNDYEGGRGIPNQ------AIIGKMERALGIR   87 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~-~igvs~~~is~~E~G~~~P~~------~~l~~la~~L~v~   87 (174)
                      ..+|..+|++..+..+++|+-||+ -+|.|+.++|++-+.-..|+.      +.+.++-..|+.+
T Consensus         3 T~eI~~~i~~eL~~~~IsQ~~Fak~vL~rSQgtlSdLL~~pkpw~~ls~sgre~f~Rm~~wL~lP   67 (83)
T d2o4aa1           3 SSEIYQWVRDELKRAGISQAVFARVAFNRTQGLLSEILRKEEDPKTASQSLLVNLRAMQNFLQLP   67 (83)
T ss_dssp             CTTHHHHHHHHHHHHTCCHHHHHHHHHSCCHHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHTSC
T ss_pred             cHHHHHHHHHHHHHcCCCHHHHHHHHHccCcHHHHHHHcCCCCchhhhHHHHHHHHHHHHHHcCh
Confidence            457899999999999999999999 679999999999986555432      2444555555544

>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=95.40  E-value=0.022  Score=30.82  Aligned_cols=33  Identities=9%  Similarity=0.120  Sum_probs=28.6

Q ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcC
Q psy6501          35 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGG   68 (174)
Q Consensus        35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G   68 (174)
                      +.|+.++ ..|++..++|+.+||++++|.++-+.
T Consensus         9 ~~V~~L~-~~G~gat~IAk~lgI~R~SVYR~L~~   41 (43)
T d1gdta1           9 DAVLNMW-QQGLGASHISKTMNIARSTVYKVINE   41 (43)
T ss_dssp             HHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHHS
T ss_pred             HHHHHHH-HcCCCHHHHHHHHCCCHHHHHHHHhh
Confidence            4677777 59999999999999999999987653

>d1k78a1 a.4.1.5 (A:19-81) Pax-5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Pax-5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.35  E-value=0.02  Score=33.76  Aligned_cols=37  Identities=11%  Similarity=0.136  Sum_probs=31.9

Q ss_pred             chHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          29 VPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        29 ~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      +.+++-++|-++= ..|+|..++|+.++||.+++++|-
T Consensus        15 ls~DLR~Riv~~~-~~G~s~r~aA~rf~VS~s~v~k~l   51 (63)
T d1k78a1          15 LPDVVRQRIVELA-HQGVRPCDISRQLRVSHGCVSKIL   51 (63)
T ss_dssp             CCHHHHHHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             CCHHHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHH
Confidence            3567788888875 489999999999999999999995

>d1wh8a_ a.35.1.7 (A:) Homeobox protein Cux-2, CUTL2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: CUT domain
domain: Homeobox protein Cux-2, CUTL2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.12  E-value=0.038  Score=36.06  Aligned_cols=40  Identities=10%  Similarity=0.072  Sum_probs=36.7

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHH-hCCCHHHHHHHHcCC
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATK-INEKPQIVNDYEGGR   69 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~-igvs~~~is~~E~G~   69 (174)
                      ..+|..+|++..+..+++|.-||+. +|.|+.++|.+-+.-
T Consensus        29 T~~Ia~~v~~~L~~~~I~Q~~Fa~~VL~rSQGtlSdLL~~P   69 (111)
T d1wh8a_          29 TYSITKRVKEVLTDNNLGQRLFGESILGLTQGSVSDLLSRP   69 (111)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHTTCCCHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHHHHcCchHHHHHHHHHccChHHHHHHHhCC
Confidence            6789999999999999999999995 689999999998754

>d1uxda_ a.35.1.5 (A:) Fructose repressor (FruR), N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: GalR/LacI-like bacterial regulator
domain: Fructose repressor (FruR), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=95.02  E-value=0.0078  Score=35.13  Aligned_cols=36  Identities=8%  Similarity=0.063  Sum_probs=28.3

Q ss_pred             CCHHHHHHHhCCChhHHHHHhcCCCC---CCHHHHHHHH
Q psy6501         136 WSQKDLATKINEKPQIVNDYEGGRGI---PNQAIIGKME  171 (174)
Q Consensus       136 lsq~ela~~lg~~~s~i~~~E~G~~~---P~~~~l~~i~  171 (174)
                      +|.+|+|+..|+|+++++++-+|...   .++++..+|.
T Consensus         1 vTl~diA~~agvS~sTVSrvLn~~~~~~~vs~~tr~rV~   39 (59)
T d1uxda_           1 MKLDEIARLAGVSRTTASYVINGKAKQYRVSDKTVEKVM   39 (59)
T ss_dssp             CCHHHHHHHHTSCTTHHHHHHHTCGGGTTCTTTTHHHHH
T ss_pred             CCHHHHHHHHCcCHHHHHHHHcCCCCcCcCCHHHHHHHH
Confidence            47899999999999999999998754   4555554443

>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: HIN recombinase (DNA-binding domain)
species: Synthetic

Probab=95.01  E-value=0.033  Score=30.78  Aligned_cols=33  Identities=15%  Similarity=0.108  Sum_probs=26.6

Q ss_pred             HHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         124 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       124 ~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      .+.++.+. +.|.+..++|..+|++++||.+|--
T Consensus        11 ~~~a~~l~-~~G~s~~~iA~~~gVSr~TiYry~p   43 (47)
T d1ijwc_          11 QEQISRLL-EKGHPRQQLAIIFGIGVSTLYRYFP   43 (47)
T ss_dssp             HHHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHSC
T ss_pred             HHHHHHHH-HCCCCHHHHHHHHCcCHHHHHhhCC
Confidence            34555555 5799999999999999999999853

>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=94.98  E-value=0.013  Score=35.20  Aligned_cols=34  Identities=15%  Similarity=0.019  Sum_probs=30.8

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        33 ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ...-++.+|+...+|..|||+.+|+|++||+++-
T Consensus         7 ~~~Il~~i~~~g~~sr~eLa~~~gLS~~Tvs~iv   40 (70)
T d1z6ra1           7 AGAVYRLIDQLGPVSRIDLSRLAQLAPASITKIV   40 (70)
T ss_dssp             HHHHHHHHHSSCSCCHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHH
Confidence            4567889999999999999999999999999875

>d1i5za1 a.4.5.4 (A:138-206) Catabolite gene activator protein (CAP), C-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Catabolite gene activator protein (CAP), C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=94.82  E-value=0.016  Score=34.49  Aligned_cols=22  Identities=5%  Similarity=0.098  Sum_probs=19.8

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHH
Q psy6501          45 GWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        45 gltq~eLA~~igvs~~~is~~E   66 (174)
                      .+||+|||..+|+|+.+|++.-
T Consensus        29 ~lt~~~lA~~~G~sRetvsr~L   50 (69)
T d1i5za1          29 KITRQEIGQIVGCSRETVGRIL   50 (69)
T ss_dssp             ECCHHHHHHHHTCCHHHHHHHH
T ss_pred             CCCHHHHHHHHCCCHHHHHHHH
Confidence            3899999999999999998864

>d1rzsa_ a.35.1.2 (A:) cro p22 {Bacteriophage p22 [TaxId: 10754]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: cro p22
species: Bacteriophage p22 [TaxId: 10754]

Probab=94.75  E-value=0.0096  Score=34.77  Aligned_cols=34  Identities=18%  Similarity=0.265  Sum_probs=26.5

Q ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHH
Q psy6501          47 SQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERA   83 (174)
Q Consensus        47 tq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~   83 (174)
                      +...+|+.+|||+++||+|  |...|.. ...+|...
T Consensus        12 ~~~k~A~algis~~AVsqW--Ge~VPe~-RA~~ie~~   45 (61)
T d1rzsa_          12 TQRAVAKALGISDAAVSQW--KEVIPEK-DAYRLEIV   45 (61)
T ss_dssp             SHHHHHHHHTCCHHHHHHC--CSBCCHH-HHHHHHHH
T ss_pred             CHHHHHHHhCCCHHHHHHH--hccCcHH-HHHHHHHH
Confidence            6788999999999999999  7777754 44455443

>d1rp3a2 a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=94.62  E-value=0.025  Score=33.47  Aligned_cols=31  Identities=16%  Similarity=0.147  Sum_probs=26.8

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          36 LLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      .+-.+|--.|+|++|+|+.+|+|+++|+..-
T Consensus        28 ~v~~l~~~~~~s~~eIA~~lgis~~tv~~~~   58 (71)
T d1rp3a2          28 LVIQLIFYEELPAKEVAKILETSVSRVSQLK   58 (71)
T ss_dssp             HHHHHHHTSCCCHHHHHHHTTSCHHHHHHHH
T ss_pred             HHHHHHHhHhCCHHHHHHHHCCCHHHHHHHH
Confidence            3445677899999999999999999999875

>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=94.60  E-value=0.019  Score=33.65  Aligned_cols=30  Identities=17%  Similarity=0.173  Sum_probs=25.7

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          36 LLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      -|+.+|+ ..+|..|||+.+|+|++||+++-
T Consensus         4 Il~~i~~-~pisr~eLa~~~gls~~TVs~~v   33 (62)
T d2hoea1           4 ILKRIMK-SPVSRVELAEELGLTKTTVGEIA   33 (62)
T ss_dssp             SHHHHHH-SCBCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHH-CCcCHHHHHHHHCcCHHHHHHHH
Confidence            3667775 57999999999999999999874

>d1jhga_ a.4.12.1 (A:) Trp repressor, TrpR {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: TrpR-like
family: Trp repressor, TrpR
domain: Trp repressor, TrpR
species: Escherichia coli [TaxId: 562]

Probab=94.57  E-value=0.034  Score=35.80  Aligned_cols=37  Identities=14%  Similarity=0.150  Sum_probs=32.1

Q ss_pred             HHHHHHHHHHHHH-cC-CCHHHHHHHhCCCHHHHHHHHc
Q psy6501          31 LDLAKLLMQGRQA-KG-WSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        31 ~~ig~~ik~~R~~-~g-ltq~eLA~~igvs~~~is~~E~   67 (174)
                      .+++.|++-++.- .| +||.++|+.+|+|..||++.-+
T Consensus        42 ~~la~R~~ia~~L~~G~~s~reI~~~~gvs~aTItR~s~   80 (101)
T d1jhga_          42 EALGTRVRIIEELLRGEMSQRELKNELGAGIATITRGSN   80 (101)
T ss_dssp             HHHHHHHHHHHHHHHCCSCHHHHHHHHCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCcCHHHHHHHhCCChHHHHHHHH
Confidence            4689999999754 77 9999999999999999998754

>d1s7ea2 a.35.1.7 (A:6-85) Hepatocyte nuclear factor 6 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: CUT domain
domain: Hepatocyte nuclear factor 6
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.45  E-value=0.017  Score=35.65  Aligned_cols=58  Identities=10%  Similarity=0.037  Sum_probs=44.5

Q ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHH-hCCCHHHHHHHHcCC-----CCCCHHHHHHHHHHhCcc
Q psy6501          30 PLDLAKLLMQGRQAKGWSQKDLATK-INEKPQIVNDYEGGR-----GIPNQAIIGKMERALGIR   87 (174)
Q Consensus        30 ~~~ig~~ik~~R~~~gltq~eLA~~-igvs~~~is~~E~G~-----~~P~~~~l~~la~~L~v~   87 (174)
                      ..+|..+|++..+..+++|.-||+. +|.|+.++|.+-+.-     -.+--+.+.++-..|+.+
T Consensus         4 T~~I~~~i~~eL~~~~IsQ~~Fa~~vL~rsQGtlSdLL~kPKPW~~l~~gre~y~RM~~wL~~p   67 (80)
T d1s7ea2           4 TKEVAQRITTELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLKSGRETFRRMWKWLQEP   67 (80)
T ss_dssp             SHHHHHHHHHHHTSSCCCHHHHHHHTSSSCSSHHHHHTTSCCTTCCCSSCHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHHccChHHHHHHHcCCCChhhhcchhHHHHHHHHHHcCH
Confidence            4579999999999999999999995 589999999987622     113445666666666644

>d1wh6a_ a.35.1.7 (A:) Homeobox protein Cux-2, CUTL2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: CUT domain
domain: Homeobox protein Cux-2, CUTL2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.37  E-value=0.041  Score=35.31  Aligned_cols=62  Identities=18%  Similarity=0.116  Sum_probs=46.1

Q ss_pred             ccchHHHHHHHHHHHHHcCCCHHHHHHH-hCCCHHHHHHHHcCCCCCC------HHHHHHHHHHhCccc
Q psy6501          27 EKVPLDLAKLLMQGRQAKGWSQKDLATK-INEKPQIVNDYEGGRGIPN------QAIIGKMERALGIRL   88 (174)
Q Consensus        27 ~~~~~~ig~~ik~~R~~~gltq~eLA~~-igvs~~~is~~E~G~~~P~------~~~l~~la~~L~v~~   88 (174)
                      +--..+|..+|++..+..+++|.-||+. +|.|+.++|.+-+.-...+      -+...++-..|+-+.
T Consensus        16 ~ldT~~I~~~v~~eL~~~~IsQ~~Fa~~VL~rSQGtlSdLL~~PKPW~kl~~~gr~~y~RM~~wL~~p~   84 (101)
T d1wh6a_          16 EVDTLELTRQVKEKLAKNGICQRIFGEKVLGLSQGSVSDMLSRPKPWSKLTQKGREPFIRMQLWLSDQL   84 (101)
T ss_dssp             CCCHHHHHHHHHHHHHTTTCCHHHHHHHTTCCCHHHHHHHHHSCCCTTTCCHHHHHHHHHHHHHHHHTT
T ss_pred             ccCHHHHHHHHHHHHHHcCCcHHHHHHHHHccChHHHHHHHhCCCCHHHHhHhhhHHHHHHHHHhcCHh
Confidence            3336789999999999999999999995 6899999999998442221      134445555555554

>d2ox6a1 a.35.1.6 (A:5-166) Hypothetical protein SO3848 {Shewanella oneidensis [TaxId: 70863]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: YdiL-like
domain: Hypothetical protein SO3848
species: Shewanella oneidensis [TaxId: 70863]

Probab=94.37  E-value=0.095  Score=34.81  Aligned_cols=40  Identities=15%  Similarity=0.058  Sum_probs=36.0

Q ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCH
Q psy6501          35 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQ   74 (174)
Q Consensus        35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~   74 (174)
                      --|+.+|...|+|..++++..+.|..-|-.||.|....+.
T Consensus         6 ie~~ylr~slglt~aqv~~l~k~se~dv~aweage~~~~~   45 (162)
T d2ox6a1           6 IEMSYLRQSLSLSAAQVGQLTNHSEAEVLAWENAETQAPE   45 (162)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTSSCCCH
T ss_pred             HHHHHHHHHcCCCHHHHHHHhccCHHHhhhhhhcCCcCch
Confidence            3578999999999999999999999999999999966554

>d1biaa1 a.4.5.1 (A:1-63) Biotin repressor, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Biotin repressor-like
domain: Biotin repressor, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=94.33  E-value=0.018  Score=33.86  Aligned_cols=31  Identities=13%  Similarity=0.063  Sum_probs=25.5

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          36 LLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      -|..+....-+|.+|||+.+|||++||.+.-
T Consensus        10 iL~~L~~~~~~s~~eLa~~l~vS~~ti~r~i   40 (63)
T d1biaa1          10 LIALLANGEFHSGEQLGETLGMSRAAINKHI   40 (63)
T ss_dssp             HHHHHTTSSCBCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHCCcCCHHHHHHHHCcCHHHHHHHH
Confidence            4455566677899999999999999999873

>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=94.08  E-value=0.03  Score=32.89  Aligned_cols=33  Identities=15%  Similarity=0.117  Sum_probs=26.6

Q ss_pred             HHHHHHHHHHcC-CCHHHHHHHhCCCHHHHHHHH
Q psy6501          34 AKLLMQGRQAKG-WSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        34 g~~ik~~R~~~g-ltq~eLA~~igvs~~~is~~E   66 (174)
                      -.-|..+++..+ +|-.+||+.+|||+.||.+.-
T Consensus        10 ~~Il~~L~~~~~~vs~~~La~~l~VS~~TI~rdi   43 (65)
T d1j5ya1          10 KSIVRILERSKEPVSGAQLAEELSVSRQVIVQDI   43 (65)
T ss_dssp             HHHHHHHHHCSSCBCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHH
Confidence            344566666665 799999999999999998865

>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=93.76  E-value=0.037  Score=32.33  Aligned_cols=30  Identities=20%  Similarity=0.361  Sum_probs=25.5

Q ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHH
Q psy6501          35 KLLMQGRQAKGWSQKDLATKINEKPQIVND   64 (174)
Q Consensus        35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~   64 (174)
                      .-|..+.+...+|+.++|+.+|+|+++|+.
T Consensus         9 ~IL~~L~~n~r~s~~~iA~~lgis~~tv~~   38 (63)
T d2cfxa1           9 NIIEELKKDSRLSMRELGRKIKLSPPSVTE   38 (63)
T ss_dssp             HHHHHHHHCSCCCHHHHHHHHTCCHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHH
Confidence            346677778899999999999999998864

>d1zyba1 a.4.5.4 (A:148-220) Probable transcription regulator BT4300, C-terminal domain {Bacteroides thetaiotaomicron [TaxId: 818]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Probable transcription regulator BT4300, C-terminal domain
species: Bacteroides thetaiotaomicron [TaxId: 818]

Probab=93.76  E-value=0.025  Score=34.14  Aligned_cols=22  Identities=14%  Similarity=0.098  Sum_probs=19.8

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHH
Q psy6501          45 GWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        45 gltq~eLA~~igvs~~~is~~E   66 (174)
                      .+||+|||+.+|+|+.+||+.-
T Consensus        27 ~lt~~elA~~lg~sr~tvsr~l   48 (73)
T d1zyba1          27 KVKMDDLARCLDDTRLNISKTL   48 (73)
T ss_dssp             ECCHHHHHHHHTSCHHHHHHHH
T ss_pred             ecCHHHHHHHHCCCHHHHHHHH
Confidence            5899999999999999998764

>d3e5ua1 a.4.5.4 (A:148-227) Chlorophenol reduction protein CprK {Desulfitobacterium hafniense [TaxId: 49338]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Chlorophenol reduction protein CprK
species: Desulfitobacterium hafniense [TaxId: 49338]

Probab=93.67  E-value=0.029  Score=34.21  Aligned_cols=23  Identities=17%  Similarity=0.023  Sum_probs=20.3

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ..+||+|||..+|+|+.+|++.-
T Consensus        29 ~~lt~~elA~~~g~sretvsr~l   51 (80)
T d3e5ua1          29 MPLSQKSIGEITGVHHVTVSRVL   51 (80)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHH
T ss_pred             eCCCHHHHHHHHCCCHHHHHHHH
Confidence            45899999999999999998764

>d1nr3a_ d.236.1.1 (A:) DNA-binding protein Tfx {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]}

class: Alpha and beta proteins (a+b)
fold: DNA-binding protein Tfx
superfamily: DNA-binding protein Tfx
family: DNA-binding protein Tfx
domain: DNA-binding protein Tfx
species: Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]

Probab=93.59  E-value=0.00066  Score=45.60  Aligned_cols=50  Identities=24%  Similarity=0.354  Sum_probs=33.3

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHcCC--CCCCHHHHHHHHHHhCccccccc
Q psy6501          43 AKGWSQKDLATKINEKPQIVNDYEGGR--GIPNQAIIGKMERALGIRLRVNA   92 (174)
Q Consensus        43 ~~gltq~eLA~~igvs~~~is~~E~G~--~~P~~~~l~~la~~L~v~~~~l~   92 (174)
                      ++||||+|+|+.+|.|++.||.+|+--  ..=....-.++...++-+..-.+
T Consensus         3 ~kGltQ~eIA~~LgTSraNIs~IEk~A~eNIekAr~Tl~~~~~l~Ap~~i~i   54 (122)
T d1nr3a_           3 ERGWSQKKIARELKTTRQNVSAIERKAMENIEKSRNTLDFVKSLKSPVRILC   54 (122)
T ss_dssp             CCSCSSCSTHHHHHHCCSSSCCHHHHHHTTCSSSSCHHHHHHHHCCCEEEEE
T ss_pred             cccCCHHHHHHHHCccHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCEEEEE
Confidence            589999999999999999999998532  11111222345566665554443

>d2gaua1 a.4.5.4 (A:152-232) Transcriptional regulator PG0396, C-terminal domain {Porphyromonas gingivalis [TaxId: 837]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Transcriptional regulator PG0396, C-terminal domain
species: Porphyromonas gingivalis [TaxId: 837]

Probab=93.55  E-value=0.026  Score=34.39  Aligned_cols=23  Identities=22%  Similarity=-0.061  Sum_probs=20.2

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ..+||+|||..+|+|+.+|++.-
T Consensus        28 ~~lt~~eLA~~~G~sretvsr~L   50 (81)
T d2gaua1          28 IYLSREELATLSNMTVSNAIRTL   50 (81)
T ss_dssp             CCCCHHHHHHHTTSCHHHHHHHH
T ss_pred             ecCCHHHHHHHHCCCHHHHHHHH
Confidence            35899999999999999998764

>d1ft9a1 a.4.5.4 (A:134-213) CO-sensing protein CooA, C-terminal domain {Rhodospirillum rubrum [TaxId: 1085]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: CO-sensing protein CooA, C-terminal domain
species: Rhodospirillum rubrum [TaxId: 1085]

Probab=93.45  E-value=0.03  Score=34.17  Aligned_cols=22  Identities=14%  Similarity=0.199  Sum_probs=19.9

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHH
Q psy6501          45 GWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        45 gltq~eLA~~igvs~~~is~~E   66 (174)
                      .+||+|||..+|+|+.||++.-
T Consensus        30 ~~t~~eiA~~lG~sretvsr~l   51 (80)
T d1ft9a1          30 DFTVEEIANLIGSSRQTTSTAL   51 (80)
T ss_dssp             CCCHHHHHHHHCSCHHHHHHHH
T ss_pred             CCCHHHHHHHHCCCHHHHHHHH
Confidence            5899999999999999999864

>d1r8da_ a.6.1.3 (A:) Multidrug transporter activator MtaN {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: Putative DNA-binding domain
superfamily: Putative DNA-binding domain
family: DNA-binding N-terminal domain of transcription activators
domain: Multidrug transporter activator MtaN
species: Bacillus subtilis [TaxId: 1423]

Probab=93.32  E-value=0.057  Score=34.78  Aligned_cols=47  Identities=17%  Similarity=0.336  Sum_probs=34.6

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHH------------cCCCCCCHHHHHHHH-----HHhCcccccc
Q psy6501          45 GWSQKDLATKINEKPQIVNDYE------------GGRGIPNQAIIGKME-----RALGIRLRVN   91 (174)
Q Consensus        45 gltq~eLA~~igvs~~~is~~E------------~G~~~P~~~~l~~la-----~~L~v~~~~l   91 (174)
                      .+|..|+|+.+|||.+||.-||            ||.+..+.+.+..|.     +.+|++++.+
T Consensus         2 ~ytI~e~A~~~gvs~~tlR~Ye~~GLl~p~~r~~~gyR~Y~~~~~~~l~~I~~lr~~G~sl~eI   65 (109)
T d1r8da_           2 KYQVKQVAEISGVSIRTLHHYDNIELLNPSALTDAGYRLYSDADLERLQQILFFKEIGFRLDEI   65 (109)
T ss_dssp             CBCHHHHHHHHSCCHHHHHHHHHTTSSCCSEECTTCCEEBCHHHHHHHHHHHHHHHTTCCHHHH
T ss_pred             cccHHHHHHHHCcCHHHHHHHHHcCCcCCcccCCcccccccHHHHHHHHHHHHHHHcCCCHHHH
Confidence            5789999999999999999999            555666666655443     3356665543

>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=93.11  E-value=0.053  Score=31.58  Aligned_cols=30  Identities=13%  Similarity=0.120  Sum_probs=26.0

Q ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHH
Q psy6501          35 KLLMQGRQAKGWSQKDLATKINEKPQIVND   64 (174)
Q Consensus        35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~   64 (174)
                      +-|+.+.+...+|..+||+++|+|.++|..
T Consensus         9 ~IL~~L~~~~r~s~~eiA~~l~ls~~~v~~   38 (63)
T d2cg4a1           9 GILEALMGNARTAYAELAKQFGVSPETIHV   38 (63)
T ss_dssp             HHHHHHHHCTTSCHHHHHHHHTSCHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHH
Confidence            457778888999999999999999998764

>d1or7a1 a.4.13.2 (A:120-187) SigmaE factor (RpoE) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: SigmaE factor (RpoE)
species: Escherichia coli [TaxId: 562]

Probab=93.02  E-value=0.075  Score=31.14  Aligned_cols=31  Identities=16%  Similarity=0.183  Sum_probs=26.9

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          36 LLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      .+-.+|.-.|+|++|+|+.+|+|.++|...-
T Consensus        25 ~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l   55 (68)
T d1or7a1          25 MAITLRELDGLSYEEIAAIMDCPVGTVRSRI   55 (68)
T ss_dssp             HHHHHHHTTCCCHHHHHHHTTSCHHHHHHHH
T ss_pred             HHHHHHHHhCCCHHHHHHHHCcCHHHHHHHH
Confidence            4556788899999999999999999998764

>d1s4ka_ a.35.1.6 (A:) Putative cytoplasmic protein YdiL {Salmonella typhimurium [TaxId: 90371]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: YdiL-like
domain: Putative cytoplasmic protein YdiL
species: Salmonella typhimurium [TaxId: 90371]

Probab=92.96  E-value=0.12  Score=33.56  Aligned_cols=46  Identities=15%  Similarity=0.160  Sum_probs=39.1

Q ss_pred             HHHHHHHhcCCCHHHHHHHhCC--ChhHHHHHhcCCCCCCHHHHHHHH
Q psy6501         126 LLMQGRQAKGWSQKDLATKINE--KPQIVNDYEGGRGIPNQAIIGKME  171 (174)
Q Consensus       126 ~i~~~R~~~glsq~ela~~lg~--~~s~i~~~E~G~~~P~~~~l~~i~  171 (174)
                      .+...|...-|+..+.|.-++-  +.++...||+|....|.+++..|.
T Consensus         7 ELQalR~if~mti~EaA~~I~~~~~s~tWQqWE~Gd~~IP~~Vi~~l~   54 (120)
T d1s4ka_           7 ELQALRRIFDMTIEECTIYITQDNNSATWQRWEAGDIPISPEIIARLK   54 (120)
T ss_dssp             HHHHHHHHTTCCHHHHHHHTSSSCCHHHHHHHHHTSSCCCHHHHHHHH
T ss_pred             HHHHHHHHHHHhHHHHHHHHhcCccHHHHHHHHcCCCCCCHHHHHHHH
Confidence            4677899999999999997765  556999999999999999977664

>d1pdnc_ a.4.1.5 (C:) Paired protein (prd) {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Paired protein (prd)
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=92.82  E-value=0.098  Score=34.62  Aligned_cols=37  Identities=11%  Similarity=0.135  Sum_probs=31.9

Q ss_pred             chHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          29 VPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        29 ~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      +.+++=.+|-.+- ..|+++.++|+.++||+++|++|-
T Consensus        17 Ls~dlR~rIv~~~-~~G~s~r~iA~~~~VS~~tV~k~l   53 (123)
T d1pdnc_          17 LPNNIRLKIVEMA-ADGIRPCVISRQLRVSHGCVSKIL   53 (123)
T ss_dssp             CCHHHHHHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             CCHHHHHHHHHHH-HhcCCHHHHHHHHCcCHHHHHHHH
Confidence            4567778888875 579999999999999999999995

>d2ao9a1 a.4.1.17 (A:13-132) Phage protein BC1890 {Bacillus cereus [TaxId: 1396]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Nanomeric phage protein-like
domain: Phage protein BC1890
species: Bacillus cereus [TaxId: 1396]

Probab=92.68  E-value=0.041  Score=35.63  Aligned_cols=37  Identities=8%  Similarity=0.201  Sum_probs=26.6

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHH-cCCCCCCHHHHHHHHHH
Q psy6501          45 GWSQKDLATKINEKPQIVNDYE-GGRGIPNQAIIGKMERA   83 (174)
Q Consensus        45 gltq~eLA~~igvs~~~is~~E-~G~~~P~~~~l~~la~~   83 (174)
                      .-||+|+|+.+|||+.++.+|- +....  +..-..+|+-
T Consensus        36 kktqeqiAeelGisr~tLyrWrt~dk~F--I~y~nevAd~   73 (120)
T d2ao9a1          36 KRTQDEMANELGINRTTLWEWRTKNQDF--IAFKSEVADS   73 (120)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHHHCHHH--HHHHHHHHHH
T ss_pred             hhhHHHHHHHhChhHHHHHHHhhcchhH--HHHHHHHHHH
Confidence            4599999999999999999998 44433  2333444443

>d1q06a_ a.6.1.3 (A:) Transcriptional regulator CueR {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: Putative DNA-binding domain
superfamily: Putative DNA-binding domain
family: DNA-binding N-terminal domain of transcription activators
domain: Transcriptional regulator CueR
species: Escherichia coli [TaxId: 562]

Probab=92.68  E-value=0.089  Score=34.75  Aligned_cols=46  Identities=20%  Similarity=0.288  Sum_probs=34.1

Q ss_pred             CCHHHHHHHhCCCHHHHHHHH------------cCCCCCCHHHHHHHH-----HHhCcccccc
Q psy6501          46 WSQKDLATKINEKPQIVNDYE------------GGRGIPNQAIIGKME-----RALGIRLRVN   91 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E------------~G~~~P~~~~l~~la-----~~L~v~~~~l   91 (174)
                      |+..|||+.+|||.+||.-||            ||.+.-+...+..|.     +.+|+++..+
T Consensus         1 m~Ige~A~~~gvs~~TlR~Ye~~GLl~p~~r~~~gyR~Y~~~~i~~l~~I~~lr~~G~sl~eI   63 (127)
T d1q06a_           1 MNISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEES   63 (127)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHTTCSCCCEECTTSCEECCHHHHHHHHHHHHHHHTTCCHHHH
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHcCCCCCCccCCcCcccchHHHHHHHHHHHHHHHcCCCHHHH
Confidence            678999999999999999999            555555666655544     4566666543

>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=92.67  E-value=0.07  Score=30.66  Aligned_cols=30  Identities=3%  Similarity=0.069  Sum_probs=25.5

Q ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHH
Q psy6501          35 KLLMQGRQAKGWSQKDLATKINEKPQIVND   64 (174)
Q Consensus        35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~   64 (174)
                      .-|..+.+...+|..++|+++|+|+++|+.
T Consensus         7 ~Il~~L~~n~r~s~~eiA~~l~ls~~~v~~   36 (60)
T d2cyya1           7 KIIKILQNDGKAPLREISKITGLAESTIHE   36 (60)
T ss_dssp             HHHHHHHHCTTCCHHHHHHHHCSCHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHH
Confidence            456777788899999999999999998763

>d1i1ga1 a.4.5.32 (A:2-61) LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: LprA
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=92.67  E-value=0.083  Score=30.40  Aligned_cols=29  Identities=14%  Similarity=0.092  Sum_probs=24.6

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHH
Q psy6501          36 LLMQGRQAKGWSQKDLATKINEKPQIVND   64 (174)
Q Consensus        36 ~ik~~R~~~gltq~eLA~~igvs~~~is~   64 (174)
                      -|..+.+.-.+|..+||+++|+|+++|..
T Consensus         8 Il~~L~~n~r~s~~~lA~~~gls~~~v~~   36 (60)
T d1i1ga1           8 ILEILEKDARTPFTEIAKKLGISETAVRK   36 (60)
T ss_dssp             HHHHHHHCTTCCHHHHHHHHTSCHHHHHH
T ss_pred             HHHHHHHcCCCCHHHHHHHHCcCHHHHHH
Confidence            45667777889999999999999998864

>d1ku3a_ a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermus aquaticus [TaxId: 271]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Thermus aquaticus [TaxId: 271]

Probab=92.57  E-value=0.1  Score=30.27  Aligned_cols=25  Identities=4%  Similarity=0.159  Sum_probs=23.1

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          43 AKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        43 ~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      ...+|++|+|+.+|||+..|+++|+
T Consensus        26 ~~~~tl~eIa~~lgiS~erVrqi~~   50 (61)
T d1ku3a_          26 GREHTLEEVGAYFGVTRERIRQIEN   50 (61)
T ss_dssp             SSCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            5679999999999999999999985

>d1hlva1 a.4.1.7 (A:1-66) DNA-binding domain of centromere binding protein B (CENP-B) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Centromere-binding
domain: DNA-binding domain of centromere binding protein B (CENP-B)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.41  E-value=0.096  Score=30.95  Aligned_cols=34  Identities=9%  Similarity=0.238  Sum_probs=26.9

Q ss_pred             HHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcC
Q psy6501         125 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGG  158 (174)
Q Consensus       125 ~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G  158 (174)
                      +.|+....-..++|.++|..+|++.++|+.|-..
T Consensus        15 ~ii~~~e~g~k~sq~eIA~~fGv~~STvs~IlKn   48 (66)
T d1hlva1          15 RIIQEVEENPDLRKGEIARRFNIPPSTLSTILKN   48 (66)
T ss_dssp             HHHHHHHHCTTSCHHHHHHHHTCCHHHHHHHHHT
T ss_pred             HHHHHHHcCCcchHHHHHHHhCCChhHHHHHHHH
Confidence            4555554445689999999999999999998664

>d1s4ka_ a.35.1.6 (A:) Putative cytoplasmic protein YdiL {Salmonella typhimurium [TaxId: 90371]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: YdiL-like
domain: Putative cytoplasmic protein YdiL
species: Salmonella typhimurium [TaxId: 90371]

Probab=92.40  E-value=0.3  Score=31.65  Aligned_cols=48  Identities=17%  Similarity=0.150  Sum_probs=40.8

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhC--CCHHHHHHHHcCCCCCCHHHHHHHH
Q psy6501          34 AKLLMQGRQAKGWSQKDLATKIN--EKPQIVNDYEGGRGIPNQAIIGKME   81 (174)
Q Consensus        34 g~~ik~~R~~~gltq~eLA~~ig--vs~~~is~~E~G~~~P~~~~l~~la   81 (174)
                      +--|+.+|+-.-||.+|-|.-++  ++..+=.+||+|.+..+.+.+..+.
T Consensus         5 ~~ELQalR~if~mti~EaA~~I~~~~~s~tWQqWE~Gd~~IP~~Vi~~l~   54 (120)
T d1s4ka_           5 ALELQALRRIFDMTIEECTIYITQDNNSATWQRWEAGDIPISPEIIARLK   54 (120)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHTSSSCCHHHHHHHHHTSSCCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhHHHHHHHHhcCccHHHHHHHHcCCCCCCHHHHHHHH
Confidence            45688999999999999999775  6778999999999998888855544

>d1s7oa_ a.4.13.3 (A:) Hypothetical protein SPy1201 {Streptococcus pyogenes [TaxId: 1314]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: YlxM/p13-like
domain: Hypothetical protein SPy1201
species: Streptococcus pyogenes [TaxId: 1314]

Probab=92.29  E-value=0.1  Score=33.69  Aligned_cols=50  Identities=18%  Similarity=0.134  Sum_probs=36.9

Q ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccc
Q psy6501          35 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRL   88 (174)
Q Consensus        35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~   88 (174)
                      ..+-.+|--.|||++|+|+.+|+|+++|+..-.-    ....|..+-.-|++.-
T Consensus        22 R~v~~L~y~~~ls~~EIA~~lgiS~~aV~~~l~R----A~~~L~~~e~kL~l~~   71 (106)
T d1s7oa_          22 MNYIELYYADDYSLAEIADEFGVSRQAVYDNIKR----TEKILETYEMKLHMYS   71 (106)
T ss_dssp             HHHHHHHHHTCCCHHHHHHHHTCCHHHHHHHHHH----HHHHHHHHHHHHCHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHH----HHHHHHHHHHHHChHH
Confidence            3455688899999999999999999999987642    2345555555565543

>d2bgca1 a.4.5.4 (A:138-237) Listeriolysin regulatory protein PrfA, C-terminal domain {Bacteria (Listeria monocytogenes) [TaxId: 1639]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Listeriolysin regulatory protein PrfA, C-terminal domain
species: Bacteria (Listeria monocytogenes) [TaxId: 1639]

Probab=92.27  E-value=0.052  Score=34.79  Aligned_cols=39  Identities=8%  Similarity=0.042  Sum_probs=30.0

Q ss_pred             CCCHHHHHHHhCCC-HHHHHHHH------------cCC-CCCCHHHHHHHHHH
Q psy6501          45 GWSQKDLATKINEK-PQIVNDYE------------GGR-GIPNQAIIGKMERA   83 (174)
Q Consensus        45 gltq~eLA~~igvs-~~~is~~E------------~G~-~~P~~~~l~~la~~   83 (174)
                      .+||+|||..+|+| +.||++.-            +++ ..++.+.|.++|..
T Consensus        31 ~lTqeeLA~~lG~s~ReTVsR~L~~L~~~GlI~~~~~~i~I~D~~~L~~~A~~   83 (100)
T d2bgca1          31 NLTMQELGYSSGIAHSSAVSRIISKLKQEKVIVYKNSCFYVQNLDYLKRYAPK   83 (100)
T ss_dssp             CCCHHHHHHHTTCCCHHHHHHHHHHHHHTTSEEEETTEEEESCHHHHHHHCHH
T ss_pred             ccCHHHHHHHhCCchHHHHHHHHHHHHHCCCEEEcCCEEEEeCHHHHHHHhcc
Confidence            58999999999997 88887754            222 45788888888764

>d3ctaa1 a.4.5.28 (A:5-89) Ta1064 (RFK), N-terminal domain {Thermoplasma acidophilum [TaxId: 2303]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Ta1064 (RFK), N-terminal domain
species: Thermoplasma acidophilum [TaxId: 2303]

Probab=92.19  E-value=0.16  Score=31.21  Aligned_cols=33  Identities=12%  Similarity=0.056  Sum_probs=25.8

Q ss_pred             HHHHHHHHHH------cCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          34 AKLLMQGRQA------KGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        34 g~~ik~~R~~------~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ...|+.++..      -++|+.|||+.+|+++++++++-
T Consensus         4 ~~~l~~l~~~~~~~~~~~lt~~eLa~~l~i~~~~vs~~l   42 (85)
T d3ctaa1           4 YRAIKKIKEAAEASNRAYLTSSKLADMLGISQQSASRII   42 (85)
T ss_dssp             HHHHHHHHHHTTTSSEEECCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHhhhccCCCCCCHHHHHHHHCCCHHHHHHHH
Confidence            3455666653      36899999999999999998864

>d1umqa_ a.4.1.12 (A:) Photosynthetic apparatus regulatory protein PprA (RegA), DNA-binding domain {Rhodobacter sphaeroides [TaxId: 1063]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: FIS-like
domain: Photosynthetic apparatus regulatory protein PprA (RegA), DNA-binding domain
species: Rhodobacter sphaeroides [TaxId: 1063]

Probab=91.93  E-value=0.15  Score=29.34  Aligned_cols=33  Identities=6%  Similarity=-0.006  Sum_probs=29.2

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      -+.|...-...|..+.+.|+.+|||++|+.+--
T Consensus        22 r~~I~~aL~~~~gn~~~aA~~LGIsR~TL~rkm   54 (60)
T d1umqa_          22 WEHIQRIYEMCDRNVSETARRLNMHRRTLQRIL   54 (60)
T ss_dssp             HHHHHHHHHHTTSCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHHhcCcHHHHHHHHCCCHHHHHHHH
Confidence            467889999999999999999999999987643

>d1a04a1 a.4.6.2 (A:150-216) Nitrate/nitrite response regulator (NarL) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Nitrate/nitrite response regulator (NarL)
species: Escherichia coli [TaxId: 562]

Probab=91.87  E-value=0.08  Score=31.10  Aligned_cols=26  Identities=19%  Similarity=0.188  Sum_probs=22.7

Q ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          42 QAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        42 ~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      -..|+|.+|+|+.+|+|+.||..+-.
T Consensus        18 l~~G~s~~eIA~~l~iS~~TV~~~~~   43 (67)
T d1a04a1          18 IAQGLPNKMIARRLDITESTVKVHVK   43 (67)
T ss_dssp             HHTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHhCCCHHHHHHHHCCCHHHHHHHHH
Confidence            35799999999999999999988753

>d1au7a2 a.35.1.1 (A:5-76) Pit-1 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: POU-specific domain
domain: Pit-1
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=91.78  E-value=0.14  Score=30.52  Aligned_cols=39  Identities=13%  Similarity=0.198  Sum_probs=32.0

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHhC------CChhHHHHHhcCC
Q psy6501         121 LDLAKLLMQGRQAKGWSQKDLATKIN------EKPQIVNDYEGGR  159 (174)
Q Consensus       121 ~~~~~~i~~~R~~~glsq~ela~~lg------~~~s~i~~~E~G~  159 (174)
                      ..+....++.|-..|+||.|++..+|      .|.++|.+.|+=.
T Consensus         6 e~Fa~~fk~rRi~LG~TQ~dVG~al~~l~g~~~SQttIcRFE~l~   50 (72)
T d1au7a2           6 EQFANEFKVRRIKLGYTQTNVGEALAAVHGSEFSQTTICRFENLQ   50 (72)
T ss_dssp             HHHHHHHHHHHHHHTCCHHHHHHHHHHTTSSCCCHHHHHHHHTTC
T ss_pred             HHHHHHHHHHHhccCccHHHHHHHHHHhcCcccchhHHHHHHhcc
Confidence            44567888999999999999998864      6778999999843

>d2p7vb1 a.4.13.2 (B:546-613) Sigma70 (SigA, RpoD) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Escherichia coli [TaxId: 562]

Probab=91.71  E-value=0.073  Score=31.64  Aligned_cols=24  Identities=4%  Similarity=0.273  Sum_probs=22.1

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      ..+|++|+|+.+|||+..|+++|.
T Consensus        24 ~~~tl~eI~~~lgiSrerVrqie~   47 (68)
T d2p7vb1          24 TDYTLEEVGKQFDVTRERIRQIEA   47 (68)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CcCCHHHHHHHHCCCHHHHHHHHH
Confidence            348999999999999999999995

>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=91.51  E-value=0.19  Score=30.78  Aligned_cols=51  Identities=12%  Similarity=0.121  Sum_probs=37.9

Q ss_pred             HHHHHHH-HHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH-HHHHH
Q psy6501          33 LAKLLMQ-GRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIG-KMERA   83 (174)
Q Consensus        33 ig~~ik~-~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~-~la~~   83 (174)
                      +++-|.. ..+-..+|.++||+.+|||++||.++-+--..-....+. .|++.
T Consensus        23 ia~yil~~~~~~~~~si~~lA~~~~vS~sTi~Rf~kklG~~gf~e~k~~l~~e   75 (83)
T d2o3fa1          23 LADYILAHPHKAIESTVNEISALANSSDAAVIRLCKSLGLKGFQDLKMRVAGD   75 (83)
T ss_dssp             HHHHHHHCHHHHHTCCHHHHHHHTTCCHHHHHHHHHHTTCSSHHHHHHHHHHH
T ss_pred             HHHHHHcCHHHHHHccHHHHHHHHCCCHHHHHHHHHHhCCCCHHHHHHHHHHH
Confidence            4444433 445578899999999999999999998877777777666 44443

>d2gfna1 a.4.1.9 (A:4-80) Probable transcriptional regulator RHA1_ro04631 {Rhodococcus sp. rha1 [TaxId: 101510]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Probable transcriptional regulator RHA1 ro04631
species: Rhodococcus sp. rha1 [TaxId: 101510]

Probab=91.19  E-value=0.19  Score=29.92  Aligned_cols=50  Identities=12%  Similarity=0.167  Sum_probs=33.0

Q ss_pred             cccccchHHHHHHHHHHHHHc---CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH
Q psy6501          24 LKHEKVPLDLAKLLMQGRQAK---GWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIG   78 (174)
Q Consensus        24 ~~~~~~~~~ig~~ik~~R~~~---gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~   78 (174)
                      ++++.....|-+....+-.+.   ++|..++|+.+|||++++..|     .|+.+.|.
T Consensus         2 vd~~~~r~~Il~aa~~l~~~~G~~~~s~~~Ia~~agvs~~~lY~~-----F~~K~~L~   54 (77)
T d2gfna1           2 VDHDERRRALADAVLALIAREGISAVTTRAVAEESGWSTGVLNHY-----FGSRHELL   54 (77)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHHCGGGCCHHHHHHHHSSCHHHHHHH-----TSSHHHHH
T ss_pred             CCHHHHHHHHHHHHHHHHHHhCccccCHHHHHHHHCCCHHHHHHH-----CcCHHHHH
Confidence            344444445444444444444   459999999999999999988     44555443

>d1e3oc2 a.35.1.1 (C:1-75) Oct-1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: POU-specific domain
domain: Oct-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.76  E-value=0.19  Score=30.09  Aligned_cols=39  Identities=21%  Similarity=0.281  Sum_probs=31.6

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHhC------CChhHHHHHhcCC
Q psy6501         121 LDLAKLLMQGRQAKGWSQKDLATKIN------EKPQIVNDYEGGR  159 (174)
Q Consensus       121 ~~~~~~i~~~R~~~glsq~ela~~lg------~~~s~i~~~E~G~  159 (174)
                      ..+....+..|-..|+||.|++..+|      .|.++|.+.|+-.
T Consensus        10 e~Fa~~fk~rRi~LG~TQ~dVG~al~~l~g~~~SQttIcRFE~l~   54 (75)
T d1e3oc2          10 EQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALN   54 (75)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHHSCCCCHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHhccccHHHHHHHHHHHcCcchhHHHHHHHHHhc
Confidence            45677888999999999999998875      4667888888743

>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=90.67  E-value=0.14  Score=32.74  Aligned_cols=33  Identities=12%  Similarity=0.134  Sum_probs=25.7

Q ss_pred             HHHHHHHHHHcC-CCHHHHHHHhCCCHHHHHHHH
Q psy6501          34 AKLLMQGRQAKG-WSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        34 g~~ik~~R~~~g-ltq~eLA~~igvs~~~is~~E   66 (174)
                      ...|..+.+..| +|+.+||+.+|+++++|+..-
T Consensus        24 ~~iL~~L~~~~~~~t~~eLa~~~~i~~~tvs~~l   57 (109)
T d2d1ha1          24 VAVLLKMVEIEKPITSEELADIFKLSKTTVENSL   57 (109)
T ss_dssp             HHHHHHHHHHCSCEEHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHCccHhHHHHHH
Confidence            345555555555 999999999999999999764

>d2jn6a1 a.4.1.19 (A:1-89) Uncharacterized protein Cgl2762 {Corynebacterium glutamicum [TaxId: 1718]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Cgl2762-like
domain: Uncharacterized protein Cgl2762
species: Corynebacterium glutamicum [TaxId: 1718]

Probab=90.53  E-value=0.12  Score=31.94  Aligned_cols=38  Identities=8%  Similarity=0.093  Sum_probs=27.3

Q ss_pred             cHHHHHHHH-HHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         120 PLDLAKLLM-QGRQAKGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       120 ~~~~~~~i~-~~R~~~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      +.++...+- ......|.|..++|..+|+++++|.+|-.
T Consensus         7 s~EfK~~aV~l~~~~~g~s~~~vA~~lGIs~~tl~~W~k   45 (89)
T d2jn6a1           7 SEEFKRDAVALYENSDGASLQQIANDLGINRVTLKNWII   45 (89)
T ss_dssp             CHHHHHHHHHHHTTGGGSCHHHHHHHHTSCHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHcCCCcHHHHHHHHCCCHHHHHHHHH
Confidence            334333333 33334589999999999999999999953

>d1xsva_ a.4.13.3 (A:) Hypothetical protein SAV1236 {Staphylococcus aureus, strain Mu50 / ATCC 700699 [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: YlxM/p13-like
domain: Hypothetical protein SAV1236
species: Staphylococcus aureus, strain Mu50 / ATCC 700699 [TaxId: 1280]

Probab=90.33  E-value=0.18  Score=32.51  Aligned_cols=48  Identities=17%  Similarity=0.171  Sum_probs=36.3

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcc
Q psy6501          36 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIR   87 (174)
Q Consensus        36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~   87 (174)
                      .+-.+|--.|||..|+|+.+|+|+++|.+--.-    ....|.....-|++-
T Consensus        25 ~vl~L~~~e~ls~~EIA~~lgiS~~aV~~~l~R----a~~~L~~ye~kL~l~   72 (106)
T d1xsva_          25 NYLELFYLEDYSLSEIADTFNVSRQAVYDNIRR----TGDLVEDYEKKLELY   72 (106)
T ss_dssp             HHHHHHHTSCCCHHHHHHHTTCCHHHHHHHHHH----HHHHHHHHHHHHCHH
T ss_pred             HHHHHHHHhCCcHHHHHHHHCcCHHHHHHHHHH----HHHHHHHHHHHHChH
Confidence            455688899999999999999999999987642    235555655556653

>d1fsea_ a.4.6.2 (A:) Germination protein GerE {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Germination protein GerE
species: Bacillus subtilis [TaxId: 1423]

Probab=90.24  E-value=0.13  Score=30.00  Aligned_cols=25  Identities=12%  Similarity=0.141  Sum_probs=22.5

Q ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          42 QAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        42 ~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      -..|+|-+|+|+.+|+|.+||..+-
T Consensus        16 ~~~G~s~~eIA~~L~is~~TV~~~~   40 (67)
T d1fsea_          16 LVQDKTTKEIASELFISEKTVRNHI   40 (67)
T ss_dssp             HTTTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHccCCHHHHHHHHCCCHHHHHHHH
Confidence            4589999999999999999998765

>d1rzsa_ a.35.1.2 (A:) cro p22 {Bacteriophage p22 [TaxId: 10754]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: cro p22
species: Bacteriophage p22 [TaxId: 10754]

Probab=90.24  E-value=0.13  Score=29.77  Aligned_cols=28  Identities=18%  Similarity=0.330  Sum_probs=24.6

Q ss_pred             CHHHHHHHhCCChhHHHHHhcCCCCCCHHH
Q psy6501         137 SQKDLATKINEKPQIVNDYEGGRGIPNQAI  166 (174)
Q Consensus       137 sq~ela~~lg~~~s~i~~~E~G~~~P~~~~  166 (174)
                      +...+|+.+|++++.|+.|  |+.+|....
T Consensus        12 ~~~k~A~algis~~AVsqW--Ge~VPe~RA   39 (61)
T d1rzsa_          12 TQRAVAKALGISDAAVSQW--KEVIPEKDA   39 (61)
T ss_dssp             SHHHHHHHHTCCHHHHHHC--CSBCCHHHH
T ss_pred             CHHHHHHHhCCCHHHHHHH--hccCcHHHH
Confidence            5778999999999999999  998887654

>d1j9ia_ a.6.1.5 (A:) Terminase gpNU1 subunit domain {Bacteriophage lambda [TaxId: 10710]}

class: All alpha proteins
fold: Putative DNA-binding domain
superfamily: Putative DNA-binding domain
family: Terminase gpNU1 subunit domain
domain: Terminase gpNU1 subunit domain
species: Bacteriophage lambda [TaxId: 10710]

Probab=90.13  E-value=0.072  Score=31.64  Aligned_cols=21  Identities=14%  Similarity=0.316  Sum_probs=19.4

Q ss_pred             CCHHHHHHHhCCCHHHHHHHH
Q psy6501          46 WSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E   66 (174)
                      +++++||+.+|||..||..|-
T Consensus         3 Vnk~~lA~iFGVS~~TI~~W~   23 (68)
T d1j9ia_           3 VNKKQLADIFGASIRTIQNWQ   23 (68)
T ss_dssp             EEHHHHHHHTTCCHHHHHHHT
T ss_pred             cCHHHHHHHhCCCHHHHHHHH
Confidence            578999999999999999995

>d1k78a1 a.4.1.5 (A:19-81) Pax-5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Pax-5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.00  E-value=0.42  Score=27.72  Aligned_cols=39  Identities=13%  Similarity=0.181  Sum_probs=32.2

Q ss_pred             cccHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         118 KVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       118 ~~~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      ..+.++.++|-++- +.|++.-++|+.++++.+++++|-+
T Consensus        14 Pls~DLR~Riv~~~-~~G~s~r~aA~rf~VS~s~v~k~l~   52 (63)
T d1k78a1          14 PLPDVVRQRIVELA-HQGVRPCDISRQLRVSHGCVSKILG   52 (63)
T ss_dssp             CCCHHHHHHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHH
Confidence            45677778877764 4899999999999999999998843

>d1p4wa_ a.4.6.2 (A:) Transcriptional regulator RcsB {Erwinia amylovora [TaxId: 552]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Transcriptional regulator RcsB
species: Erwinia amylovora [TaxId: 552]

Probab=89.71  E-value=0.26  Score=30.35  Aligned_cols=45  Identities=16%  Similarity=0.305  Sum_probs=33.8

Q ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHHcCC----CCCCHHHHHHHHHHhCc
Q psy6501          42 QAKGWSQKDLATKINEKPQIVNDYEGGR----GIPNQAIIGKMERALGI   86 (174)
Q Consensus        42 ~~~gltq~eLA~~igvs~~~is~~E~G~----~~P~~~~l~~la~~L~v   86 (174)
                      -..|+|.+|+|+.+++|.+||..+-+.-    ...+...+...|..+|+
T Consensus        34 l~~G~s~~eIA~~l~iS~~TV~~~~~~i~~Kl~~~~~~~lv~~a~~~gl   82 (87)
T d1p4wa_          34 FAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVDNDIALLNYLSSVSM   82 (87)
T ss_dssp             HHHTCCHHHHHHHHTSCHHHHHHHHHHHHHHHTCSSHHHHHHHHHHHTC
T ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCCCCHHHHHHHHHHcCC
Confidence            4579999999999999999998876432    45566666666666664

>d1yioa1 a.4.6.2 (A:131-200) Response regulatory protein StyR, C-terminal domain {Pseudomonas fluorescens [TaxId: 294]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Response regulatory protein StyR, C-terminal domain
species: Pseudomonas fluorescens [TaxId: 294]

Probab=89.35  E-value=0.17  Score=29.90  Aligned_cols=25  Identities=16%  Similarity=0.182  Sum_probs=22.3

Q ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          42 QAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        42 ~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      -..|+|-+|+|..+|+|.+||..+-
T Consensus        24 l~~G~s~~eIA~~l~iS~~TV~~~~   48 (70)
T d1yioa1          24 TIRGLMNKQIAGELGIAEVTVKVHR   48 (70)
T ss_dssp             HTTTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHcCCCHHHHHHHHCCCHHHHHHHH
Confidence            4579999999999999999998764

>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=89.22  E-value=0.11  Score=31.14  Aligned_cols=26  Identities=19%  Similarity=0.199  Sum_probs=22.7

Q ss_pred             HHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          41 RQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        41 R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      +...++|..|+|+.+|+++++++++-
T Consensus        16 ~~~~~~s~~eia~~~~~~~st~~rll   41 (75)
T d1mkma1          16 KNPGDVSVSEIAEKFNMSVSNAYKYM   41 (75)
T ss_dssp             HCSSCBCHHHHHHHTTCCHHHHHHHH
T ss_pred             hCCCCCCHHHHHHHHCcCHHHHHHHH
Confidence            34568999999999999999999874

>d1etxa_ a.4.1.12 (A:) FIS protein {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: FIS-like
domain: FIS protein
species: Escherichia coli [TaxId: 562]

Probab=89.17  E-value=0.32  Score=30.18  Aligned_cols=33  Identities=12%  Similarity=-0.108  Sum_probs=29.5

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHH
Q psy6501          33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        33 ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~   65 (174)
                      =-..|+.+.+..+..+.+.|+.+|||++|+.+.
T Consensus        50 E~~~i~~aL~~~~gn~~~aA~~LGisR~tL~~k   82 (89)
T d1etxa_          50 EQPLLDMVMQYTRGNATRAALMMGINRGTLRKK   82 (89)
T ss_dssp             HHHHHHHHHHHTTTCHHHHHHHHTSCHHHHHHH
T ss_pred             HHHHHHHHHHHcCCcHHHHHHHHCCCHHHHHHH
Confidence            356788899999999999999999999999864

>d1l3la1 a.4.6.2 (A:170-234) Quorum-sensing transcription factor TraR, C-terminal domain {Agrobacterium tumefaciens [TaxId: 358]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Quorum-sensing transcription factor TraR, C-terminal domain
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=89.16  E-value=0.18  Score=29.24  Aligned_cols=25  Identities=20%  Similarity=0.009  Sum_probs=22.3

Q ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          42 QAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        42 ~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      -..|+|-+|+|+.+|+|.+||..+-
T Consensus        16 ~~~G~s~~eIA~~l~iS~~TV~~~~   40 (65)
T d1l3la1          16 IAVGKTMEEIADVEGVKYNSVRVKL   40 (65)
T ss_dssp             HTTTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHhcCCHHHHHHHHCCCHHHHHHHH
Confidence            3579999999999999999998775

>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=88.56  E-value=0.29  Score=32.34  Aligned_cols=38  Identities=8%  Similarity=-0.036  Sum_probs=30.7

Q ss_pred             chHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          29 VPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        29 ~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      +...-...|..+...-++|+.+||+.+|+++++|+++-
T Consensus        28 lt~~q~~iL~~i~~~~~~t~~~la~~l~i~~~tvs~~l   65 (139)
T d2a61a1          28 ITPAQFDILQKIYFEGPKRPGELSVLLGVAKSTVTGLV   65 (139)
T ss_dssp             CCHHHHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHhCCCcccchHHH
Confidence            44445666777777789999999999999999998864

>d1ic8a2 a.35.1.1 (A:87-180) Hepatocyte nuclear factor 1a (LFB1/HNF1) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: POU-specific domain
domain: Hepatocyte nuclear factor 1a (LFB1/HNF1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.42  E-value=1.2  Score=27.67  Aligned_cols=48  Identities=10%  Similarity=0.063  Sum_probs=41.3

Q ss_pred             cccHHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHH
Q psy6501         118 KVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQA  165 (174)
Q Consensus       118 ~~~~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~  165 (174)
                      ..+..+.+.|+......+++|..+|+..|++.|.||.+-++....+..
T Consensus        24 ~d~~~v~~~IK~Fl~~h~I~Q~~Va~~TGlsQS~iSq~L~~g~~M~~~   71 (94)
T d1ic8a2          24 EDPWRVAKMVKSYLQQHNIPQREVVDTTGLNQSHLSQHLNKGTPMKTQ   71 (94)
T ss_dssp             SCHHHHHHHHHHHHHHTTCCHHHHHHHHCCCHHHHHHHHHSBCCCCHH
T ss_pred             cCHHHHHHHHHHHHHHcCCcHHHHHHHHcccHHHHHHHHhCCCCccHH
Confidence            345778899999999999999999999999999999999987655543

>d1r71a_ a.4.14.1 (A:) Transcriptional repressor protein KorB DNA-binding domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: KorB DNA-binding domain-like
family: KorB DNA-binding domain-like
domain: Transcriptional repressor protein KorB DNA-binding domain
species: Escherichia coli [TaxId: 562]

Probab=88.35  E-value=0.38  Score=30.95  Aligned_cols=43  Identities=21%  Similarity=0.359  Sum_probs=33.2

Q ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCH
Q psy6501         121 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQ  164 (174)
Q Consensus       121 ~~~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~  164 (174)
                      .+....++... ..|+|++++|+++|.++++|+.+-+=-..|+.
T Consensus        17 ~e~A~a~~~l~-~~g~s~~eiA~~~G~s~~~V~~~l~L~~lp~~   59 (114)
T d1r71a_          17 REIADFIGREL-AKGKKKGDIAKEIGKSPAFITQHVTLLDLPEK   59 (114)
T ss_dssp             HHHHHHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHGGGSCCHH
T ss_pred             HHHHHHHHHHH-HhCCCHHHHHHHHCCcHHHHHHHHHHhCCCHH
Confidence            44455555554 56999999999999999999999886666654

>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=87.96  E-value=0.16  Score=28.20  Aligned_cols=23  Identities=4%  Similarity=-0.025  Sum_probs=20.7

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHH
Q psy6501          43 AKGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        43 ~~gltq~eLA~~igvs~~~is~~   65 (174)
                      ...+|.++||+.+|+|+++++++
T Consensus        17 ~~~~tl~~lA~~~~~s~~~l~r~   39 (54)
T d1bl0a1          17 ESPLSLEKVSERSGYSKWHLQRM   39 (54)
T ss_dssp             TSCCCCHHHHHHSSSCHHHHHHH
T ss_pred             CCCCCHHHHHHHHCcCHHHHHHH
Confidence            46799999999999999999876

>d1ttya_ a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Thermotoga maritima [TaxId: 2336]

Probab=87.83  E-value=0.22  Score=30.95  Aligned_cols=25  Identities=12%  Similarity=0.108  Sum_probs=22.7

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          43 AKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        43 ~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      ...+|+.|+|+.+|||+..|+++|+
T Consensus        36 ~~~~tl~eI~~~lgiSrERVRQie~   60 (87)
T d1ttya_          36 GKPKTLEEVGQYFNVTRERIRQIEV   60 (87)
T ss_dssp             SSCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCcCCHHHHHHHhCCCHHHHHHHHH
Confidence            3568999999999999999999995

>d1vz0a1 a.4.14.1 (A:116-208) Putative partitioning protein ParB/Spo0J {Thermus thermophilus [TaxId: 274]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: KorB DNA-binding domain-like
family: KorB DNA-binding domain-like
domain: Putative partitioning protein ParB/Spo0J
species: Thermus thermophilus [TaxId: 274]

Probab=87.81  E-value=0.35  Score=30.26  Aligned_cols=37  Identities=14%  Similarity=0.104  Sum_probs=28.8

Q ss_pred             HHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCC
Q psy6501         126 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPN  163 (174)
Q Consensus       126 ~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~  163 (174)
                      ..+... ..|+|+.++|+++|.++++|+..-+=-..|+
T Consensus        11 a~~~L~-e~g~t~~~iA~~~Gks~~~V~~~LrLl~L~~   47 (93)
T d1vz0a1          11 GYQALL-EMGLTQEEVARRVGKARSTVANALRLLQLPP   47 (93)
T ss_dssp             HHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHHGGGSCH
T ss_pred             HHHHHH-HcCCCHHHHHHHHccchHHHHHHHHHHHHHH
Confidence            344444 5899999999999999999998776555444

>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=87.42  E-value=0.46  Score=30.16  Aligned_cols=33  Identities=12%  Similarity=0.182  Sum_probs=26.6

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      +..+..+.+.-++|+.|+|+.+|+++++|+..-
T Consensus        23 ~~v~~~L~~~g~~t~~eia~~~~i~~~~v~~~l   55 (109)
T d1sfxa_          23 VRIYSLLLERGGMRVSEIARELDLSARFVRDRL   55 (109)
T ss_dssp             HHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHhcCCCCHHHHHHHhCCCcchHHHHH
Confidence            455666777788999999999999999988763

>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=87.37  E-value=0.39  Score=31.40  Aligned_cols=37  Identities=14%  Similarity=0.080  Sum_probs=26.8

Q ss_pred             chHHHHHHHHHHHHHcC--CCHHHHHHHhCCCHHHHHHH
Q psy6501          29 VPLDLAKLLMQGRQAKG--WSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        29 ~~~~ig~~ik~~R~~~g--ltq~eLA~~igvs~~~is~~   65 (174)
                      +...-...|..+....|  +|+.|||+.+++++++++++
T Consensus        27 lt~~q~~vL~~l~~~~~~~it~~ela~~~~~~~~~vs~~   65 (135)
T d3broa1          27 LTGTQMTIIDYLSRNKNKEVLQRDLESEFSIKSSTATVL   65 (135)
T ss_dssp             CCHHHHHHHHHHHHTTTSCCBHHHHHHHHTCCHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCCCCCHHHHHHHHCcCHhHHHHH
Confidence            33344445555555544  99999999999999999974

>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=87.05  E-value=0.29  Score=32.47  Aligned_cols=39  Identities=15%  Similarity=0.149  Sum_probs=29.2

Q ss_pred             cchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          28 KVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        28 ~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      .+...-...|..+...-|+|+.+||+.+++++++|++.-
T Consensus        32 glt~~q~~iL~~l~~~~~~t~~~la~~~~i~~~~vs~~l   70 (143)
T d1s3ja_          32 GVTPAQLFVLASLKKHGSLKVSEIAERMEVKPSAVTLMA   70 (143)
T ss_dssp             TCCHHHHHHHHHHHHHSEEEHHHHHHHHTSCHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHCCCCCHHHHHHHHCcCHHHHHHHH
Confidence            344444456666777778999999999999999888764

>d1zs4a1 a.35.1.9 (A:4-81) Regulatory protein cII {Bacteriophage lambda [TaxId: 10710]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Bacteriophage CII protein
domain: Regulatory protein cII
species: Bacteriophage lambda [TaxId: 10710]

Probab=87.00  E-value=0.15  Score=30.44  Aligned_cols=24  Identities=4%  Similarity=0.118  Sum_probs=21.7

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCC
Q psy6501          46 WSQKDLATKINEKPQIVNDYEGGR   69 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~G~   69 (174)
                      +.|+.+|+.+||..+.||+|-+|-
T Consensus        21 ~Gq~k~A~amGv~esqiSRwK~~f   44 (78)
T d1zs4a1          21 LGTEKTAEAVGVDKSQISRWKRDW   44 (78)
T ss_dssp             HCHHHHHHHHTSCHHHHHHHHHHT
T ss_pred             HcchhHHHHhCCCHHHHHHHHHhh
Confidence            579999999999999999998754

>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=86.97  E-value=0.62  Score=27.15  Aligned_cols=32  Identities=16%  Similarity=0.133  Sum_probs=27.2

Q ss_pred             HHHHHHHHHhcCCCHHHHHHHhCCChhHHHHH
Q psy6501         124 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDY  155 (174)
Q Consensus       124 ~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~  155 (174)
                      ...+...+....+|..|+|+.+|+++++++.+
T Consensus         9 ~~Il~~l~~~g~~sr~eLa~~~glS~~Tv~~~   40 (71)
T d1z05a1           9 GRVYKLIDQKGPISRIDLSKESELAPASITKI   40 (71)
T ss_dssp             HHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHH
T ss_pred             HHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHH
Confidence            45666777778899999999999999998765

>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=86.61  E-value=0.39  Score=31.64  Aligned_cols=35  Identities=9%  Similarity=-0.071  Sum_probs=28.5

Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          32 DLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        32 ~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      .=-.-|..+-+.-++|+.+||+.++++++++++.-
T Consensus        33 ~q~~iL~~l~~~~~~t~~~La~~l~i~~~~vs~~v   67 (140)
T d2etha1          33 TELYAFLYVALFGPKKMKEIAEFLSTTKSNVTNVV   67 (140)
T ss_dssp             HHHHHHHHHHHHCCBCHHHHHHHTTSCHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHH
Confidence            33445666677789999999999999999999864

>d1d1la_ a.35.1.2 (A:) cro lambda repressor {Bacteriophage lambda [TaxId: 10710]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: cro lambda repressor
species: Bacteriophage lambda [TaxId: 10710]

Probab=86.54  E-value=0.59  Score=26.71  Aligned_cols=33  Identities=15%  Similarity=0.018  Sum_probs=25.8

Q ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCC
Q psy6501          37 LMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGI   71 (174)
Q Consensus        37 ik~~R~~~gltq~eLA~~igvs~~~is~~E~G~~~   71 (174)
                      |.+.-.+.|  |...|+.+||.+++||+--.-.|.
T Consensus         7 L~dyv~~~G--QaKaA~~LGv~Q~AIsKAira~R~   39 (61)
T d1d1la_           7 LKDYAMRFG--QTKTAKDLGVYQSAINKAIHAGRK   39 (61)
T ss_dssp             HHHHHHHHC--HHHHHHHHTCCTHHHHHHHHTTCC
T ss_pred             HHHHHHHHC--hHHHHHHcCccHHHHHHHHhcCCe
Confidence            344556667  999999999999999997765554

>d2ox6a1 a.35.1.6 (A:5-166) Hypothetical protein SO3848 {Shewanella oneidensis [TaxId: 70863]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: YdiL-like
domain: Hypothetical protein SO3848
species: Shewanella oneidensis [TaxId: 70863]

Probab=86.48  E-value=1.3  Score=29.03  Aligned_cols=45  Identities=16%  Similarity=0.075  Sum_probs=37.6

Q ss_pred             HHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHH
Q psy6501         126 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKM  170 (174)
Q Consensus       126 ~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i  170 (174)
                      .|...|...|++..++++..+.+..-+-.||.|....+.-...++
T Consensus         7 e~~ylr~slglt~aqv~~l~k~se~dv~aweage~~~~~laqkkl   51 (162)
T d2ox6a1           7 EMSYLRQSLSLSAAQVGQLTNHSEAEVLAWENAETQAPELAQKKL   51 (162)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTSSCCCHHHHHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHhccCHHHhhhhhhcCCcCchHHHhhh
Confidence            466779999999999999999999999999999988665444443

>d1r8ea1 a.6.1.3 (A:3-120) Transcription activator BmrR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: Putative DNA-binding domain
superfamily: Putative DNA-binding domain
family: DNA-binding N-terminal domain of transcription activators
domain: Transcription activator BmrR
species: Bacillus subtilis [TaxId: 1423]

Probab=86.47  E-value=0.17  Score=32.87  Aligned_cols=24  Identities=13%  Similarity=0.142  Sum_probs=21.2

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCC
Q psy6501          46 WSQKDLATKINEKPQIVNDYEGGR   69 (174)
Q Consensus        46 ltq~eLA~~igvs~~~is~~E~G~   69 (174)
                      +|..|+|+.+|||..||.-||+-.
T Consensus         4 ytI~evA~~~gvs~~tlR~Ye~~G   27 (118)
T d1r8ea1           4 YSIGEVSKLANVSIKALRYYDKID   27 (118)
T ss_dssp             EEHHHHHHHHTCCHHHHHHHHHTT
T ss_pred             ccHHHHHHHHCcCHHHHHHHHHcC
Confidence            578899999999999999999643

>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=86.43  E-value=0.33  Score=28.53  Aligned_cols=29  Identities=14%  Similarity=0.062  Sum_probs=23.5

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHH
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYEGGRGIPNQAII   77 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l   77 (174)
                      .++|..++|+.+|||+++|..+     .|+.+.|
T Consensus        23 ~~~s~~~Ia~~agvs~~t~Y~~-----F~~K~~L   51 (74)
T d1v7ba1          23 ETLSYDSLAEATGLSKSGLIYH-----FPSRHAL   51 (74)
T ss_dssp             TTCCHHHHHHHHCSCHHHHHHH-----CSSHHHH
T ss_pred             cccCHHHHHHHhCcCcchHhhh-----CCCHHHH
Confidence            4569999999999999999988     4455544

>d1z91a1 a.4.5.28 (A:8-144) Organic hydroperoxide resistance transcriptional regulator OhrR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Organic hydroperoxide resistance transcriptional regulator OhrR
species: Bacillus subtilis [TaxId: 1423]

Probab=86.42  E-value=0.33  Score=31.98  Aligned_cols=39  Identities=5%  Similarity=0.008  Sum_probs=30.7

Q ss_pred             cchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          28 KVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        28 ~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      .+...=..-|..+...-|+|+.+||+.++++++++++.-
T Consensus        30 gLt~~q~~vL~~l~~~~~~t~~~La~~~~i~~~~vsr~i   68 (137)
T d1z91a1          30 NITYPQYLALLLLWEHETLTVKKMGEQLYLDSGTLTPML   68 (137)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEHHHHHHTTTCCHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHH
Confidence            344444456667777889999999999999999998764

>d2id6a1 a.4.1.9 (A:1-75) Transcriptional regulator TM1030 {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator TM1030
species: Thermotoga maritima [TaxId: 2336]

Probab=86.42  E-value=0.41  Score=28.20  Aligned_cols=33  Identities=12%  Similarity=0.107  Sum_probs=25.3

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      +..+-.-.--.++|..++|+.+|||+++|..+=
T Consensus        12 a~~l~~~~G~~~~ti~~Ia~~agvs~~~iY~~F   44 (75)
T d2id6a1          12 AVEVFGKKGYDRATTDEIAEKAGVAKGLIFHYF   44 (75)
T ss_dssp             HHHHHHHHHHHHCCHHHHHHHHTCCTHHHHHHH
T ss_pred             HHHHHHHhCccccCHHHHHHHhCCCHHHHHHHC
Confidence            333444444567899999999999999999873

>d1jt6a1 a.4.1.9 (A:2-72) Multidrug binding protein QacR {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Multidrug binding protein QacR
species: Staphylococcus aureus [TaxId: 1280]

Probab=85.93  E-value=0.32  Score=28.35  Aligned_cols=24  Identities=0%  Similarity=-0.190  Sum_probs=21.2

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          43 AKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        43 ~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      -.++|..++|+.+|||++++..+=
T Consensus        19 ~~~~s~~~Ia~~agvs~~~~y~~F   42 (71)
T d1jt6a1          19 YNATTTGEIVKLSESSKGNLYYHF   42 (71)
T ss_dssp             TTTCCHHHHHHHTTCCHHHHHHHH
T ss_pred             ccccCHHHHHHHHCcCHhHHHHHC
Confidence            456799999999999999999884

>d1rp3a2 a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=85.88  E-value=0.63  Score=26.84  Aligned_cols=32  Identities=19%  Similarity=0.176  Sum_probs=26.2

Q ss_pred             HHHHHHHHhcCCCHHHHHHHhCCChhHHHHHh
Q psy6501         125 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYE  156 (174)
Q Consensus       125 ~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E  156 (174)
                      ..+-..+--.|+|.+++|+.+|++++++...-
T Consensus        27 r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~~   58 (71)
T d1rp3a2          27 KLVIQLIFYEELPAKEVAKILETSVSRVSQLK   58 (71)
T ss_dssp             HHHHHHHHTSCCCHHHHHHHTTSCHHHHHHHH
T ss_pred             HHHHHHHHhHhCCHHHHHHHHCCCHHHHHHHH
Confidence            34445677899999999999999999987654

>d1jhfa1 a.4.5.2 (A:2-72) LexA repressor, N-terminal DNA-binding domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: LexA repressor, N-terminal DNA-binding domain
domain: LexA repressor, N-terminal DNA-binding domain
species: Escherichia coli [TaxId: 562]

Probab=85.83  E-value=0.81  Score=26.87  Aligned_cols=35  Identities=11%  Similarity=0.293  Sum_probs=29.6

Q ss_pred             HHHHHHHHHHHHHcCC--CHHHHHHHhCC-CHHHHHHH
Q psy6501          31 LDLAKLLMQGRQAKGW--SQKDLATKINE-KPQIVNDY   65 (174)
Q Consensus        31 ~~ig~~ik~~R~~~gl--tq~eLA~~igv-s~~~is~~   65 (174)
                      ..+-+.|+..-...|.  |..|+|+.+|+ |+++|.++
T Consensus         8 ~~vL~~I~~~~~~~G~~Ps~rei~~~~g~~S~stv~~~   45 (71)
T d1jhfa1           8 QEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEH   45 (71)
T ss_dssp             HHHHHHHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHcCCCCHHHHHHH
Confidence            4677788888888885  89999999998 78888876

>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=85.83  E-value=0.63  Score=27.16  Aligned_cols=33  Identities=15%  Similarity=0.039  Sum_probs=28.3

Q ss_pred             HHHHHHHHHHhcCCCHHHHHHHhCCChhHHHHH
Q psy6501         123 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDY  155 (174)
Q Consensus       123 ~~~~i~~~R~~~glsq~ela~~lg~~~s~i~~~  155 (174)
                      ....++..++...+|..++|+.+|+++++++.+
T Consensus         7 ~~~Il~~i~~~g~~sr~eLa~~~gLS~~Tvs~i   39 (70)
T d1z6ra1           7 AGAVYRLIDQLGPVSRIDLSRLAQLAPASITKI   39 (70)
T ss_dssp             HHHHHHHHHSSCSCCHHHHHHHTTCCHHHHHHH
T ss_pred             HHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHH
Confidence            355777778888899999999999999999875

>d1g2ha_ a.4.1.12 (A:) Transcriptional regulator TyrR, C-terminal domain {Haemophilus influenzae [TaxId: 727]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: FIS-like
domain: Transcriptional regulator TyrR, C-terminal domain
species: Haemophilus influenzae [TaxId: 727]

Probab=85.76  E-value=1.1  Score=25.44  Aligned_cols=32  Identities=16%  Similarity=0.105  Sum_probs=25.9

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      -+-|..+.+..| +..+.|+.+|||++|+.+--
T Consensus        23 r~~I~~aL~~~g-n~~~aA~~Lgisr~tL~rKl   54 (61)
T d1g2ha_          23 AQVLKLFYAEYP-STRKLAQRLGVSHTAIANKL   54 (61)
T ss_dssp             HHHHHHHHHHSC-SHHHHHHHTTSCTHHHHHHH
T ss_pred             HHHHHHHHHHCC-CHHHHHHHHCCCHHHHHHHH
Confidence            566777777787 78899999999999987643

>d1t56a1 a.4.1.9 (A:22-94) Ethr repressor {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Ethr repressor
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=85.67  E-value=0.31  Score=28.53  Aligned_cols=22  Identities=23%  Similarity=0.101  Sum_probs=20.0

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHH
Q psy6501          44 KGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~   65 (174)
                      .++|..++|+++|||++++.++
T Consensus        22 ~~~t~~~Ia~~agvs~~t~Y~~   43 (73)
T d1t56a1          22 ADISVDDLAKGAGISRPTFYFY   43 (73)
T ss_dssp             GGCCHHHHHHHHTCCHHHHHHH
T ss_pred             ccCCHHHHHHHhCCCHHHHHHH
Confidence            3569999999999999999987

>d1jgsa_ a.4.5.28 (A:) Multiple antibiotic resistance repressor, MarR {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Multiple antibiotic resistance repressor, MarR
species: Escherichia coli [TaxId: 562]

Probab=85.53  E-value=0.78  Score=30.06  Aligned_cols=36  Identities=14%  Similarity=0.006  Sum_probs=27.6

Q ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          31 LDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        31 ~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ..=..-|..+...-++|+.+||+.++++++++++.-
T Consensus        34 ~~q~~vL~~l~~~~~~t~~ela~~~~i~~~~vs~~v   69 (138)
T d1jgsa_          34 AAQFKVLCSIRCAACITPVELKKVLSVDLGALTRML   69 (138)
T ss_dssp             HHHHHHHHHHHHHSSBCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHhHHhCcCCCHHHHHHHHCCCHhHHHHHH
Confidence            333455566666779999999999999999998753

>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=85.41  E-value=0.96  Score=25.80  Aligned_cols=31  Identities=19%  Similarity=0.337  Sum_probs=25.7

Q ss_pred             HHHHHHHHHhcCCCHHHHHHHhCCChhHHHH
Q psy6501         124 AKLLMQGRQAKGWSQKDLATKINEKPQIVND  154 (174)
Q Consensus       124 ~~~i~~~R~~~glsq~ela~~lg~~~s~i~~  154 (174)
                      ...|........++..++|+.+|++++++..
T Consensus         8 ~~IL~~L~~n~r~s~~~iA~~lgis~~tv~~   38 (63)
T d2cfxa1           8 LNIIEELKKDSRLSMRELGRKIKLSPPSVTE   38 (63)
T ss_dssp             HHHHHHHHHCSCCCHHHHHHHHTCCHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHH
Confidence            4567777777889999999999999997753

>d2g7sa1 a.4.1.9 (A:3-76) Putative transcriptional regulator Atu0279 {Agrobacterium tumefaciens [TaxId: 358]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator Atu0279
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=85.36  E-value=0.33  Score=28.59  Aligned_cols=31  Identities=10%  Similarity=0.222  Sum_probs=25.0

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH
Q psy6501          43 AKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIG   78 (174)
Q Consensus        43 ~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~   78 (174)
                      -.++|..++|+++|+|+++|..+     .|+.+.|.
T Consensus        22 ~~~~s~~~Ia~~agvs~~~iY~~-----F~sK~~L~   52 (74)
T d2g7sa1          22 YNSFSYADISQVVGIRNASIHHH-----FPSKSDLV   52 (74)
T ss_dssp             GGGCCHHHHHHHHCCCHHHHHHH-----CSSHHHHH
T ss_pred             ccccCHHHHHHHHCcCcchHHHH-----CcCHHHHH
Confidence            35689999999999999999988     55555443

>d2ev0a1 a.4.5.24 (A:2-62) Manganese transport regulator MntR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Iron-dependent repressor protein
domain: Manganese transport regulator MntR
species: Bacillus subtilis [TaxId: 1423]

Probab=85.02  E-value=0.81  Score=26.11  Aligned_cols=25  Identities=16%  Similarity=0.134  Sum_probs=21.5

Q ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          42 QAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        42 ~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      +.-..+..++|+.+|||+++++..-
T Consensus        18 ~~~~v~~~~iA~~L~vs~~SVs~mi   42 (61)
T d2ev0a1          18 EKGYARVSDIAEALAVHPSSVTKMV   42 (61)
T ss_dssp             HHSSCCHHHHHHHHTCCHHHHHHHH
T ss_pred             cCCCccHHHHHHHhCCCchhHHHHH
Confidence            4567899999999999999998753

>d2i10a1 a.4.1.9 (A:10-78) Putative transcriptional regulator RHA1_ro09068 {Rhodococcus sp. [TaxId: 1831]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator RHA1 ro09068
species: Rhodococcus sp. [TaxId: 1831]

Probab=84.88  E-value=0.42  Score=27.74  Aligned_cols=32  Identities=22%  Similarity=0.196  Sum_probs=25.0

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Q psy6501          36 LLMQGRQAKGWSQKDLATKINEKPQIVNDYEG   67 (174)
Q Consensus        36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~E~   67 (174)
                      .+-.-+--.++|..++|+++|||++++..+=.
T Consensus        11 ~lf~~~G~~~~ti~~Ia~~agvs~~~~Y~~F~   42 (69)
T d2i10a1          11 ELFWRQGYEGTSITDLTKALGINPPSLYAAFG   42 (69)
T ss_dssp             HHHHHHTTTTCCHHHHHHHHTCCHHHHHHHHC
T ss_pred             HHHHHHCcccCCHHHHHHHhCCChhHHHHHCc
Confidence            33334455678999999999999999998853

>d2fbqa1 a.4.1.9 (A:2-80) Transcriptional regulator PsrA {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator PsrA
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=84.85  E-value=0.41  Score=28.45  Aligned_cols=23  Identities=17%  Similarity=-0.052  Sum_probs=20.8

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E   66 (174)
                      .++|..++|+.+|||+++|.++=
T Consensus        23 ~~~ti~~Ia~~agvs~~s~y~~F   45 (79)
T d2fbqa1          23 AETSLRLITSKAGVNLAAVNYHF   45 (79)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHT
T ss_pred             ccccHHHHHHHHCcChhHHHHHC
Confidence            56899999999999999999883

>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=84.70  E-value=0.86  Score=26.13  Aligned_cols=32  Identities=16%  Similarity=0.149  Sum_probs=25.3

Q ss_pred             HHHHHHHHHhcC-CCHHHHHHHhCCChhHHHHH
Q psy6501         124 AKLLMQGRQAKG-WSQKDLATKINEKPQIVNDY  155 (174)
Q Consensus       124 ~~~i~~~R~~~g-lsq~ela~~lg~~~s~i~~~  155 (174)
                      ...+....+..+ +|..++|+.+++|..||.+.
T Consensus        10 ~~Il~~L~~~~~~vs~~~La~~l~VS~~TI~rd   42 (65)
T d1j5ya1          10 KSIVRILERSKEPVSGAQLAEELSVSRQVIVQD   42 (65)
T ss_dssp             HHHHHHHHHCSSCBCHHHHHHHHTSCHHHHHHH
T ss_pred             HHHHHHHHHcCCCCcHHHHHHHHCCCHHHHHHH
Confidence            345666666655 79999999999999988765

>d1lj9a_ a.4.5.28 (A:) Transcriptional regulator SlyA {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator SlyA
species: Enterococcus faecalis [TaxId: 1351]

Probab=84.64  E-value=0.4  Score=31.90  Aligned_cols=33  Identities=15%  Similarity=0.053  Sum_probs=26.8

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          34 AKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        34 g~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      ..-|..+.+.-|+|+.+||+.+++++++|+..-
T Consensus        32 ~~iL~~i~~~~~~t~~~la~~l~i~~~tvs~~l   64 (144)
T d1lj9a_          32 YLYLVRVCENPGIIQEKIAELIKVDRTTAARAI   64 (144)
T ss_dssp             HHHHHHHHHSTTEEHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHhCCCCCHHHHHHHHCccHhhHHHHH
Confidence            344556666779999999999999999999764

>d1ntca_ a.4.1.12 (A:) DNA-binding domain of NTRC {Salmonella typhimurium [TaxId: 90371]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: FIS-like
domain: DNA-binding domain of NTRC
species: Salmonella typhimurium [TaxId: 90371]

Probab=84.62  E-value=0.39  Score=29.60  Aligned_cols=30  Identities=10%  Similarity=0.061  Sum_probs=27.5

Q ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHH
Q psy6501          35 KLLMQGRQAKGWSQKDLATKINEKPQIVND   64 (174)
Q Consensus        35 ~~ik~~R~~~gltq~eLA~~igvs~~~is~   64 (174)
                      .-|+...+..+..+.+.|+.+||+++|+.+
T Consensus        54 ~lI~~aL~~~~Gn~~~AA~~LGI~R~TL~~   83 (91)
T d1ntca_          54 TLLTTALRHTQGHKQEAARLLGWGAATLTA   83 (91)
T ss_dssp             HHHHHHHHHTTTCTTHHHHHTTCCHHHHHH
T ss_pred             HHHHHHHHHhCCcHHHHHHHHCCCHHHHHH
Confidence            358999999999999999999999999875

>d2fq4a1 a.4.1.9 (A:9-77) Transcriptional regulator BC3163 {Bacillus cereus [TaxId: 1396]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator BC3163
species: Bacillus cereus [TaxId: 1396]

Probab=84.60  E-value=0.44  Score=27.71  Aligned_cols=30  Identities=17%  Similarity=0.296  Sum_probs=25.1

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHH
Q psy6501          43 AKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAII   77 (174)
Q Consensus        43 ~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l   77 (174)
                      -.++|..++|+++|||++++.++     .|+.+.|
T Consensus        22 ~~~~t~~~Ia~~agvs~~~~y~~-----F~~k~~L   51 (69)
T d2fq4a1          22 FKAVTVDKIAERAKVSKATIYKW-----WPNKAAV   51 (69)
T ss_dssp             TTTCCHHHHHHHHTCCHHHHHHH-----CSSHHHH
T ss_pred             cccCCHHHHHHHHCcCHHHHHHH-----CCCHHHH
Confidence            45669999999999999999987     6666665

>d1lnwa_ a.4.5.28 (A:) MexR repressor {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: MexR repressor
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=84.59  E-value=0.33  Score=32.20  Aligned_cols=34  Identities=12%  Similarity=0.180  Sum_probs=26.9

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          33 LAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        33 ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      -..-|..+-...|+|+.+||+.+++++++||++-
T Consensus        38 q~~vL~~l~~~~~~t~~~la~~l~~~~~~vsr~l   71 (141)
T d1lnwa_          38 DVHVLKLIDEQRGLNLQDLGRQMCRDKALITRKI   71 (141)
T ss_dssp             HHHHHHHHHSSTTCBHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHCccHhHHHHHH
Confidence            3445556666778999999999999999998864

>d2vkva1 a.4.1.9 (A:6-67) Tetracyclin repressor (Tet-repressor, TetR) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Tetracyclin repressor (Tet-repressor, TetR)
species: Escherichia coli [TaxId: 562]

Probab=84.52  E-value=0.32  Score=27.66  Aligned_cols=26  Identities=15%  Similarity=0.133  Sum_probs=22.4

Q ss_pred             HHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          41 RQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        41 R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      .--.++|..++|+.+|||+++|..+=
T Consensus        15 ~G~~~~s~~~Ia~~agvs~~tiy~~F   40 (62)
T d2vkva1          15 VGIEGLTTRKLAQKLGVEQPTLYWHV   40 (62)
T ss_dssp             HHHHHCCHHHHHHHHTSCHHHHHHHS
T ss_pred             hCcccCCHHHHHHHhCCCHHHHHHHC
Confidence            34467899999999999999999884

>d2o7ta1 a.4.1.9 (A:1-78) Transcriptional regulator Cgl1640/Cg1846 {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 Cgl1640/Cg1846
species: Corynebacterium glutamicum [TaxId: 1718]

Probab=84.44  E-value=0.37  Score=28.70  Aligned_cols=30  Identities=7%  Similarity=0.176  Sum_probs=24.8

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIG   78 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~   78 (174)
                      .++|..++|+++|||++++..+     .|+-+.|.
T Consensus        26 ~~~t~~~Ia~~agvs~~t~y~~-----F~sKe~L~   55 (78)
T d2o7ta1          26 DSLTMENIAEQAGVGVATLYRN-----FPDRFTLD   55 (78)
T ss_dssp             GGCCHHHHHHHHTCCHHHHHHH-----CSSHHHHH
T ss_pred             cccCHHHHHHHhCCCHHHHHHH-----CcCHHHHH
Confidence            6789999999999999999988     55555544

>d2d6ya1 a.4.1.9 (A:7-74) Putative regulator SCO4008 {Streptomyces coelicolor [TaxId: 1902]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative regulator SCO4008
species: Streptomyces coelicolor [TaxId: 1902]

Probab=83.94  E-value=0.48  Score=27.43  Aligned_cols=30  Identities=17%  Similarity=0.300  Sum_probs=24.0

Q ss_pred             HHHHcCCCHHHHHHHhCCCHHHHHHHHcCC
Q psy6501          40 GRQAKGWSQKDLATKINEKPQIVNDYEGGR   69 (174)
Q Consensus        40 ~R~~~gltq~eLA~~igvs~~~is~~E~G~   69 (174)
                      -+--.++|..++|+++|+|++++.++=.++
T Consensus        17 ~~G~~~~ti~~Ia~~agvs~~~~Y~~F~~K   46 (68)
T d2d6ya1          17 RHGIAGARIDRIAAEARANKQLIYAYYGNK   46 (68)
T ss_dssp             HHTTTSCCHHHHHHHHTCCHHHHHHHHSSH
T ss_pred             HhCccccCHHHHHHHHCcchhHHHHHCcCH
Confidence            334456799999999999999999885443

>d1l8qa1 a.4.12.2 (A:290-399) Chromosomal replication initiation factor DnaA C-terminal domain IV {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: TrpR-like
family: Chromosomal replication initiation factor DnaA C-terminal domain IV
domain: Chromosomal replication initiation factor DnaA C-terminal domain IV
species: Aquifex aeolicus [TaxId: 63363]

Probab=83.90  E-value=1.5  Score=27.97  Aligned_cols=59  Identities=8%  Similarity=0.073  Sum_probs=39.8

Q ss_pred             HHHHHHHHHhCcccccccCCCCCCCCCcccchhhhhhhhhhcccccHHHHHHHHHHHHhcCCCHHHHHHHhC-CChhHH
Q psy6501          75 AIIGKMERALGIRLRVNAGTNKQPGTTKNTAKLDRETEELKHEKVPLDLAKLLMQGRQAKGWSQKDLATKIN-EKPQIV  152 (174)
Q Consensus        75 ~~l~~la~~L~v~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~i~~~R~~~glsq~ela~~lg-~~~s~i  152 (174)
                      +.+..+|++|||+.+++.+..-..                   .+...=.-.+--+|+..++|..+++..+| -..++|
T Consensus        18 ~Ii~~Va~~f~i~~~di~sk~R~~-------------------~vv~aR~ia~yL~r~~t~~sl~~IG~~fg~rdHsTV   77 (110)
T d1l8qa1          18 QIVEFVANYYAVKVEDILSDKRNK-------------------RTSEARKIAMYLCRKVCSASLIEIARAFKRKDHTTV   77 (110)
T ss_dssp             HHHHHHHHHHSCCHHHHSSCCCCS-------------------SSHHHHHHHHHHHHHHHCCCHHHHHHHSSCCCSTHH
T ss_pred             HHHHHHHHHhCCCHHHHhCCCCcH-------------------HHHHHHHHHHHHHHHHcCCCHHHHHHHhCCCCccHH
Confidence            556789999999999999644321                   11111112334467778999999999997 566644

>d1aisb1 a.74.1.2 (B:1108-1205) Transcription factor IIB (TFIIB), core domain {Archaeon Pyrococcus woesei [TaxId: 2262]}

class: All alpha proteins
fold: Cyclin-like
superfamily: Cyclin-like
family: Transcription factor IIB (TFIIB), core domain
domain: Transcription factor IIB (TFIIB), core domain
species: Archaeon Pyrococcus woesei [TaxId: 2262]

Probab=83.87  E-value=0.9  Score=28.09  Aligned_cols=39  Identities=8%  Similarity=-0.008  Sum_probs=31.7

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCccccccc
Q psy6501          43 AKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERALGIRLRVNA   92 (174)
Q Consensus        43 ~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~~la~~L~v~~~~l~   92 (174)
                      ....|++|+|+.+|+|..+|.+..           ..|.+.|++++.++|
T Consensus        60 ~~~~t~~eIa~~~~is~~ti~k~y-----------k~i~~~L~l~~~~~~   98 (98)
T d1aisb1          60 KVPRTLDEIADIARVDKKEIGRSY-----------RFIARNLNLTPKKLF   98 (98)
T ss_dssp             TCCCCHHHHHHHTTSCHHHHHHHH-----------HHHHHHTTCCTTTTC
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHH-----------HHHHHHcCCCccccC
Confidence            456799999999999999998874           367778888877654

>d2gena1 a.4.1.9 (A:6-75) Probable transcriptional regulator PA1836 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Probable transcriptional regulator PA1836
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=83.58  E-value=0.51  Score=27.25  Aligned_cols=23  Identities=0%  Similarity=-0.168  Sum_probs=20.9

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E   66 (174)
                      .++|..++|+.+|||++++.++=
T Consensus        19 ~~~si~~Ia~~agvs~~t~Y~~F   41 (70)
T d2gena1          19 DATTIEMIRDRSGASIGSLYHHF   41 (70)
T ss_dssp             TTCCHHHHHHHHCCCHHHHHHHT
T ss_pred             ccCCHHHHHHHHCcCHHHHHHHC
Confidence            57799999999999999999883

>d2fx0a1 a.4.1.9 (A:4-76) Hemolysin II regulatory protein, HlyIIR {Bacillus cereus [TaxId: 1396]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Hemolysin II regulatory protein, HlyIIR
species: Bacillus cereus [TaxId: 1396]

Probab=83.39  E-value=0.52  Score=27.69  Aligned_cols=25  Identities=20%  Similarity=0.319  Sum_probs=22.0

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHcC
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYEGG   68 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E~G   68 (174)
                      .++|..++|+.+|||++++.++=.+
T Consensus        23 ~~~si~~Ia~~agvs~~~~Y~~F~~   47 (73)
T d2fx0a1          23 EGTSIQEIAKEAKVNVAMASYYFNG   47 (73)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHHTS
T ss_pred             ccCcHHHHHHHHCcChhHHHHHCcC
Confidence            6679999999999999999998543

>d2fbia1 a.4.5.28 (A:5-140) Probable transcriptional regulator PA4135 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Probable transcriptional regulator PA4135
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=83.26  E-value=0.63  Score=30.39  Aligned_cols=38  Identities=11%  Similarity=-0.050  Sum_probs=29.2

Q ss_pred             chHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          29 VPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        29 ~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      +...=...|..+...-++|+.+||+.++++++++++.-
T Consensus        28 lt~~q~~vL~~l~~~~~~t~~~la~~~~i~~~~vs~~i   65 (136)
T d2fbia1          28 LTEQQWRVIRILRQQGEMESYQLANQACILRPSMTGVL   65 (136)
T ss_dssp             CCHHHHHHHHHHHHHCSEEHHHHHHHTTCCHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHH
Confidence            43333455666777889999999999999999998764

>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=82.96  E-value=1.3  Score=25.13  Aligned_cols=30  Identities=13%  Similarity=0.145  Sum_probs=25.5

Q ss_pred             HHHHHHHHHhcCCCHHHHHHHhCCChhHHH
Q psy6501         124 AKLLMQGRQAKGWSQKDLATKINEKPQIVN  153 (174)
Q Consensus       124 ~~~i~~~R~~~glsq~ela~~lg~~~s~i~  153 (174)
                      .+.|........++..++|+++|++++++.
T Consensus         8 ~~IL~~L~~~~r~s~~eiA~~l~ls~~~v~   37 (63)
T d2cg4a1           8 RGILEALMGNARTAYAELAKQFGVSPETIH   37 (63)
T ss_dssp             HHHHHHHHHCTTSCHHHHHHHHTSCHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCcCHHHHH
Confidence            457777788888999999999999998764

>d2fxaa1 a.4.5.28 (A:6-167) Protease production regulatory protein Hpr {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Protease production regulatory protein Hpr
species: Bacillus subtilis [TaxId: 1423]

Probab=82.79  E-value=0.87  Score=31.05  Aligned_cols=39  Identities=13%  Similarity=0.093  Sum_probs=30.9

Q ss_pred             cchHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          28 KVPLDLAKLLMQGRQAKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        28 ~~~~~ig~~ik~~R~~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      .+...=..-|..+...-++|+.+||+.+++++++++..-
T Consensus        38 ~Lt~~q~~vL~~l~~~~~~t~~~la~~~~l~~~tvs~~i   76 (162)
T d2fxaa1          38 DLNINEHHILWIAYQLNGASISEIAKFGVMHVSTAFNFS   76 (162)
T ss_dssp             TCCHHHHHHHHHHHHHTSEEHHHHHHHTTCCHHHHHHHH
T ss_pred             CCCHHHHHHHhhhccCCCcCHHHHHHHHcCCchhhHHHH
Confidence            444444556777778889999999999999999999864

>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=82.77  E-value=0.93  Score=25.89  Aligned_cols=31  Identities=16%  Similarity=0.126  Sum_probs=24.1

Q ss_pred             HHHHHHHHhcCCCHHHHHHHhCCChhHHHHH
Q psy6501         125 KLLMQGRQAKGWSQKDLATKINEKPQIVNDY  155 (174)
Q Consensus       125 ~~i~~~R~~~glsq~ela~~lg~~~s~i~~~  155 (174)
                      +.|.-.....-+|.+++|+.+|+|..+|.+.
T Consensus         9 ~iL~~L~~~~~~s~~eLa~~l~vS~~ti~r~   39 (63)
T d1biaa1           9 KLIALLANGEFHSGEQLGETLGMSRAAINKH   39 (63)
T ss_dssp             HHHHHHTTSSCBCHHHHHHHHTSCHHHHHHH
T ss_pred             HHHHHHHHCCcCCHHHHHHHHCcCHHHHHHH
Confidence            4555555556689999999999999988765

>d2id3a1 a.4.1.9 (A:13-80) Putative transcriptional regulator SCO5951 {Streptomyces coelicolor [TaxId: 1902]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator SCO5951
species: Streptomyces coelicolor [TaxId: 1902]

Probab=82.62  E-value=0.51  Score=27.25  Aligned_cols=23  Identities=9%  Similarity=-0.004  Sum_probs=20.2

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E   66 (174)
                      .++|..++|+.+|+|+++|..+=
T Consensus        25 ~~~t~~~Ia~~agvs~~~iY~~F   47 (68)
T d2id3a1          25 DALDLGEIARRAGVGKTTVYRRW   47 (68)
T ss_dssp             GGCCHHHHHHHHTCCHHHHHHHH
T ss_pred             ccCCHHHHHHHHCcCHHHHHHHC
Confidence            45699999999999999998873

>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=82.59  E-value=0.22  Score=27.56  Aligned_cols=22  Identities=14%  Similarity=0.063  Sum_probs=19.9

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHH
Q psy6501          44 KGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~   65 (174)
                      ..+|.++||+.+|+|++++++.
T Consensus        18 ~~itl~~lA~~~~~S~~~l~r~   39 (54)
T d1d5ya1          18 QPLSLDNVAAKAGYSKWHLQRM   39 (54)
T ss_dssp             SSCCCHHHHTTTSSCHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHH
Confidence            4699999999999999999875

>d1z0xa1 a.4.1.9 (A:4-71) Transcriptional regulator EF0787 {Enterococcus faecalis [TaxId: 1351]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator EF0787
species: Enterococcus faecalis [TaxId: 1351]

Probab=82.55  E-value=0.23  Score=28.92  Aligned_cols=39  Identities=13%  Similarity=0.190  Sum_probs=27.4

Q ss_pred             HHHHHHHHHH---cCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHH
Q psy6501          34 AKLLMQGRQA---KGWSQKDLATKINEKPQIVNDYEGGRGIPNQAII   77 (174)
Q Consensus        34 g~~ik~~R~~---~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l   77 (174)
                      -..+.-+-+.   .++|..++|+++|||+++|..+     .++.+.|
T Consensus         9 ~aa~~l~~e~~G~~~~t~~~Ia~~agvs~~~iy~h-----F~~K~~L   50 (68)
T d1z0xa1           9 AAAFSLLEKSPTLEQLSMRKVAKQLGVQAPAIYWY-----FKNKQAL   50 (68)
T ss_dssp             HHHHHHHHHSCCGGGCCHHHHHHHHTSCHHHHHTT-----CSSHHHH
T ss_pred             HHHHHHHHHcCCccccCHHHHHHHHCcchhHHHHh-----cCCHHHH
Confidence            3344444333   4789999999999999999866     4455544

>d1ui5a1 a.4.1.9 (A:5-75) A-factor receptor homolog CprB {Streptomyces coelicolor [TaxId: 1902]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: A-factor receptor homolog CprB
species: Streptomyces coelicolor [TaxId: 1902]

Probab=82.49  E-value=0.59  Score=27.18  Aligned_cols=31  Identities=0%  Similarity=-0.064  Sum_probs=24.9

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH
Q psy6501          43 AKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIG   78 (174)
Q Consensus        43 ~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~   78 (174)
                      -.++|..++|+.+|+|++++..|     .|+.+.|.
T Consensus        23 ~~~~si~~Ia~~agvs~~~~y~~-----F~sK~~L~   53 (71)
T d1ui5a1          23 YESTTLSEIVAHAGVTKGALYFH-----FAAKEDLA   53 (71)
T ss_dssp             TTTCCHHHHHHHHTCCHHHHHHH-----CSSHHHHH
T ss_pred             ccccCHHHHHHHHCcCHhHHHHH-----CcCHHHHH
Confidence            34569999999999999999988     55655543

>d2isya1 a.4.5.24 (A:2-64) Iron-dependent regulator IdeR {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Iron-dependent repressor protein
domain: Iron-dependent regulator IdeR
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=82.34  E-value=1.6  Score=24.99  Aligned_cols=35  Identities=6%  Similarity=0.035  Sum_probs=25.1

Q ss_pred             HHHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          32 DLAKLLMQGRQ-AKGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        32 ~ig~~ik~~R~-~~gltq~eLA~~igvs~~~is~~E   66 (174)
                      +.-+.|-.+-+ ....+..++|+.+|||+++++..-
T Consensus         9 dYL~~I~~L~~~~~~v~~~~iA~~L~vs~~SVt~mv   44 (63)
T d2isya1           9 MYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTV   44 (63)
T ss_dssp             HHHHHHHHHHHTTCCCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCCcHHHHHHHhCCCchhHHHHH
Confidence            33444444433 445799999999999999998763

>d2np5a1 a.4.1.9 (A:9-77) Transcriptional regulator RHA1_ro04179 {Rhodococcus sp. [TaxId: 1831]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator RHA1 ro04179
species: Rhodococcus sp. [TaxId: 1831]

Probab=82.18  E-value=0.54  Score=27.08  Aligned_cols=31  Identities=13%  Similarity=0.104  Sum_probs=24.5

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH
Q psy6501          43 AKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIG   78 (174)
Q Consensus        43 ~~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~   78 (174)
                      -.++|..++|+.+|||+++|..+     .|+.+.|.
T Consensus        19 ~~~~ti~~Ia~~agvs~~~iy~~-----F~sK~~L~   49 (69)
T d2np5a1          19 LEGASVREVAKRAGVSIGAVQHH-----FSTKDEMF   49 (69)
T ss_dssp             GGGCCHHHHHHHHTCCHHHHHHH-----CSSHHHHH
T ss_pred             ccccCHHHHHHHhCCCHHHHHHH-----CcCHHHHH
Confidence            34569999999999999999988     45555444

>d1pb6a1 a.4.1.9 (A:14-85) Hypothetical transcriptional regulator YcdC {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Hypothetical transcriptional regulator YcdC
species: Escherichia coli [TaxId: 562]

Probab=82.06  E-value=0.6  Score=27.23  Aligned_cols=22  Identities=14%  Similarity=0.081  Sum_probs=20.6

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHH
Q psy6501          44 KGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~   65 (174)
                      .++|..++|+.+|||++++.++
T Consensus        23 ~~~ti~~Ia~~agvs~~t~y~~   44 (72)
T d1pb6a1          23 HGTRLEQIAELAGVSKTNLLYY   44 (72)
T ss_dssp             TTCCHHHHHHHTTSCHHHHHHH
T ss_pred             cccCHHHHHHHhCCChHHHHHH
Confidence            6789999999999999999988

>d1or7a1 a.4.13.2 (A:120-187) SigmaE factor (RpoE) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: SigmaE factor (RpoE)
species: Escherichia coli [TaxId: 562]

Probab=81.99  E-value=1.2  Score=25.54  Aligned_cols=31  Identities=16%  Similarity=0.240  Sum_probs=25.8

Q ss_pred             HHHHHHHHhcCCCHHHHHHHhCCChhHHHHH
Q psy6501         125 KLLMQGRQAKGWSQKDLATKINEKPQIVNDY  155 (174)
Q Consensus       125 ~~i~~~R~~~glsq~ela~~lg~~~s~i~~~  155 (174)
                      ..+-..+-..|+|.+++|+.+|++.+++...
T Consensus        24 r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~   54 (68)
T d1or7a1          24 RMAITLRELDGLSYEEIAAIMDCPVGTVRSR   54 (68)
T ss_dssp             HHHHHHHHTTCCCHHHHHHHTTSCHHHHHHH
T ss_pred             HHHHHHHHHhCCCHHHHHHHHCcCHHHHHHH
Confidence            3444677789999999999999999988764

>d3c07a1 a.4.1.9 (A:15-89) Putative transcriptional regulator SCO4850 {Streptomyces coelicolor [TaxId: 1902]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator SCO4850
species: Streptomyces coelicolor [TaxId: 1902]

Probab=81.96  E-value=0.63  Score=27.14  Aligned_cols=30  Identities=7%  Similarity=0.008  Sum_probs=24.4

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIG   78 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~   78 (174)
                      .++|..++|+.+|||++++..+     .|+.+.|.
T Consensus        24 ~~~t~~~Ia~~agvs~~~~y~~-----F~~k~~L~   53 (75)
T d3c07a1          24 DRTTMRAIAQEAGVSVGNAYYY-----FAGKEHLI   53 (75)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHH-----CSSHHHHH
T ss_pred             ccCCHHHHHHHHCcCHHHHHHH-----CcCHHHHH
Confidence            5679999999999999999988     55555553

>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=81.63  E-value=1.1  Score=29.51  Aligned_cols=39  Identities=10%  Similarity=0.001  Sum_probs=27.8

Q ss_pred             cchHHHHHHHHHHHHHc-CCCHHHHHHHhCCCHHHHHHHH
Q psy6501          28 KVPLDLAKLLMQGRQAK-GWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        28 ~~~~~ig~~ik~~R~~~-gltq~eLA~~igvs~~~is~~E   66 (174)
                      .+...-...|..+-... ++|+.+||+.+|++++++++.-
T Consensus        31 glt~~q~~vL~~L~~~~g~~t~~~La~~~~~~~~~vs~~i   70 (145)
T d2hr3a1          31 PVQFSQLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALL   70 (145)
T ss_dssp             HHHHHHHHHHHHHHHTTSCBCHHHHHHHTTCCHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHcCCCCCHHHHHHHHCCCHHHHHHHH
Confidence            34344444555554444 4999999999999999998864

>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=81.44  E-value=0.55  Score=31.09  Aligned_cols=39  Identities=8%  Similarity=-0.046  Sum_probs=26.6

Q ss_pred             cchHHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHH
Q psy6501          28 KVPLDLAKLLMQGRQA-KGWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        28 ~~~~~ig~~ik~~R~~-~gltq~eLA~~igvs~~~is~~E   66 (174)
                      .+...-|.-+-.+-.. ..+|+.|||+.+|+|++++|..-
T Consensus        23 Gl~~~~~~i~~~L~~~~~plt~~ela~~l~vsk~~vs~~l   62 (151)
T d1ku9a_          23 GLNKSVGAVYAILYLSDKPLTISDIMEELKISKGNVSMSL   62 (151)
T ss_dssp             TCCHHHHHHHHHHHHCSSCEEHHHHHHHHTCCHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHhCCCCcCHHHHHHHhCCCcchHHHHH
Confidence            3344445555455333 45899999999999999988763

>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=81.19  E-value=0.55  Score=29.09  Aligned_cols=30  Identities=3%  Similarity=0.050  Sum_probs=25.0

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHH
Q psy6501          36 LLMQGRQAKGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        36 ~ik~~R~~~gltq~eLA~~igvs~~~is~~   65 (174)
                      -|..+-..-.+|+.|||+.+|++++++|+.
T Consensus        21 IL~~L~~~~~~~~~eLa~~l~is~~~vs~~   50 (100)
T d1ub9a_          21 IMIFLLPRRKAPFSQIQKVLDLTPGNLDSH   50 (100)
T ss_dssp             HHHHHHHHSEEEHHHHHHHTTCCHHHHHHH
T ss_pred             HHHHhccCCCeeHHHHHHHHhhccccccHH
Confidence            355555667899999999999999999976

>d3bwga1 a.4.5.6 (A:5-82) Transcriptional regulator YydK {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: GntR-like transcriptional regulators
domain: Transcriptional regulator YydK
species: Bacillus subtilis [TaxId: 1423]

Probab=81.10  E-value=0.51  Score=28.17  Aligned_cols=34  Identities=6%  Similarity=0.130  Sum_probs=22.9

Q ss_pred             HHHHHHHHH--HHHHcCC-CHHHHHHHhCCCHHHHHH
Q psy6501          31 LDLAKLLMQ--GRQAKGW-SQKDLATKINEKPQIVND   64 (174)
Q Consensus        31 ~~ig~~ik~--~R~~~gl-tq~eLA~~igvs~~~is~   64 (174)
                      ..+-..|..  +.....| |..+||+.+|||+++|..
T Consensus         5 ~~i~~~I~~g~l~~G~~LPse~~La~~~~vSr~tvr~   41 (78)
T d3bwga1           5 TEIETYIEEHQLQQGDKLPVLETLMAQFEVSKSTITK   41 (78)
T ss_dssp             HHHHHHHHHTTCCTTCBCCCHHHHHHHTTCCHHHHHH
T ss_pred             HHHHHHHHcCCCCCcCCCcCHHHHHHHHCCCHHHHHH
Confidence            344444444  2333456 889999999999998875

>d1nera_ a.35.1.2 (A:) Ner {Bacteriophage mu [TaxId: 10677]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: Ner
species: Bacteriophage mu [TaxId: 10677]

Probab=81.08  E-value=3.1  Score=24.61  Aligned_cols=47  Identities=13%  Similarity=0.054  Sum_probs=37.2

Q ss_pred             HHHHHHHHhcCCCHHHHHHHhCCChhHHHHHhcCCCCCCHHHHHHHHhhC
Q psy6501         125 KLLMQGRQAKGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIGKMERAL  174 (174)
Q Consensus       125 ~~i~~~R~~~glsq~ela~~lg~~~s~i~~~E~G~~~P~~~~l~~i~~~l  174 (174)
                      ..|..+-.++|+|..+++...|++++++...-   ..|.+.--..|+.+|
T Consensus        12 adI~AaL~krG~sLa~lsr~~gls~stl~naL---~rp~pKgEriIA~aL   58 (74)
T d1nera_          12 ADVIAGLKKRKLSLSALSRQFGYAPTTLANAL---ERHWPKGEQIIANAL   58 (74)
T ss_dssp             HHHHHHHTTSSCCHHHHHHHHSCCHHHHHHTT---TSSCHHHHHHHHHHT
T ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH---cCCChHHHHHHHHHH
Confidence            45666777899999999999999999887644   567777777777664

>d1tc3c_ a.4.1.2 (C:) Transposase tc3a1-65 {Caenorhabditis elegans [TaxId: 6239]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: Transposase tc3a1-65
species: Caenorhabditis elegans [TaxId: 6239]

Probab=81.00  E-value=1.7  Score=23.51  Aligned_cols=30  Identities=13%  Similarity=0.133  Sum_probs=26.6

Q ss_pred             HHHHHcCCCHHHHHHHhCCCHHHHHHHHcC
Q psy6501          39 QGRQAKGWSQKDLATKINEKPQIVNDYEGG   68 (174)
Q Consensus        39 ~~R~~~gltq~eLA~~igvs~~~is~~E~G   68 (174)
                      ...+..|+|..|+|+.+.-|+..|.+|-|.
T Consensus        15 DVm~~L~~slhemaR~i~rSR~~ir~Yl~~   44 (51)
T d1tc3c_          15 DVMKLLNVSLHEMSRKISRSRHCIRVYLKD   44 (51)
T ss_dssp             HHHHHTTCCHHHHHHHHTCCHHHHHHHHHC
T ss_pred             HHHHHhCCcHHHHHHHHHHhHHHHHHHhcC
Confidence            356788999999999999999999999875

>d2g7ga1 a.4.1.9 (A:9-73) Putative transcriptional regulator Rha04620 {Rhodococcus sp. rha1 [TaxId: 101510]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator Rha04620
species: Rhodococcus sp. rha1 [TaxId: 101510]

Probab=80.91  E-value=1.4  Score=25.18  Aligned_cols=23  Identities=17%  Similarity=0.215  Sum_probs=20.6

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHH
Q psy6501          43 AKGWSQKDLATKINEKPQIVNDY   65 (174)
Q Consensus        43 ~~gltq~eLA~~igvs~~~is~~   65 (174)
                      .-++|..++|+.+|||+++|..+
T Consensus        17 ~G~~ti~~Ia~~agvs~~~iY~~   39 (65)
T d2g7ga1          17 DGDFRMPDLARHLNVQVSSIYHH   39 (65)
T ss_dssp             HSSCCHHHHHHHTTSCHHHHHTT
T ss_pred             cCCCCHHHHHHHhCccccchhhc
Confidence            34899999999999999999866

>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=80.86  E-value=1.4  Score=24.84  Aligned_cols=31  Identities=13%  Similarity=0.059  Sum_probs=24.7

Q ss_pred             HHHHHHHHHhcCCCHHHHHHHhCCChhHHHH
Q psy6501         124 AKLLMQGRQAKGWSQKDLATKINEKPQIVND  154 (174)
Q Consensus       124 ~~~i~~~R~~~glsq~ela~~lg~~~s~i~~  154 (174)
                      .+.|....+...++..++|+.+|++++++..
T Consensus         6 ~kIl~~L~~n~r~s~~~lA~~~gls~~~v~~   36 (60)
T d1i1ga1           6 KIILEILEKDARTPFTEIAKKLGISETAVRK   36 (60)
T ss_dssp             HHHHHHHHHCTTCCHHHHHHHHTSCHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHH
Confidence            3566666777779999999999999987643

>d1a04a1 a.4.6.2 (A:150-216) Nitrate/nitrite response regulator (NarL) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: C-terminal effector domain of the bipartite response regulators
family: GerE-like (LuxR/UhpA family of transcriptional regulators)
domain: Nitrate/nitrite response regulator (NarL)
species: Escherichia coli [TaxId: 562]

Probab=80.68  E-value=0.73  Score=26.59  Aligned_cols=25  Identities=20%  Similarity=0.220  Sum_probs=22.4

Q ss_pred             hcCCCHHHHHHHhCCChhHHHHHhc
Q psy6501         133 AKGWSQKDLATKINEKPQIVNDYEG  157 (174)
Q Consensus       133 ~~glsq~ela~~lg~~~s~i~~~E~  157 (174)
                      ..|++.+++|+.+++++.+|..+-+
T Consensus        19 ~~G~s~~eIA~~l~iS~~TV~~~~~   43 (67)
T d1a04a1          19 AQGLPNKMIARRLDITESTVKVHVK   43 (67)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HhCCCHHHHHHHHCCCHHHHHHHHH
Confidence            5899999999999999999987654

>d1rkta1 a.4.1.9 (A:2-82) Hypothetical transcriptional regulator YfiR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Hypothetical transcriptional regulator YfiR
species: Bacillus subtilis [TaxId: 1423]

Probab=80.67  E-value=0.45  Score=28.42  Aligned_cols=30  Identities=13%  Similarity=-0.044  Sum_probs=24.1

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH
Q psy6501          44 KGWSQKDLATKINEKPQIVNDYEGGRGIPNQAIIG   78 (174)
Q Consensus        44 ~gltq~eLA~~igvs~~~is~~E~G~~~P~~~~l~   78 (174)
                      .++|..++|+.+|||++++.+|     .|+.+.|.
T Consensus        30 ~~~ti~~Ia~~agvs~~t~Y~~-----F~~K~~L~   59 (81)
T d1rkta1          30 ELTTMKDVVEESGFSRGGVYLY-----FSSTEEMF   59 (81)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHTT-----CSCHHHHH
T ss_pred             ccCCHHHHHHHhCcCHHHHHHH-----CcCHHHHH
Confidence            5679999999999999999976     55555444

>d1umqa_ a.4.1.12 (A:) Photosynthetic apparatus regulatory protein PprA (RegA), DNA-binding domain {Rhodobacter sphaeroides [TaxId: 1063]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: FIS-like
domain: Photosynthetic apparatus regulatory protein PprA (RegA), DNA-binding domain
species: Rhodobacter sphaeroides [TaxId: 1063]

Probab=80.66  E-value=1.5  Score=24.71  Aligned_cols=31  Identities=6%  Similarity=0.031  Sum_probs=27.0

Q ss_pred             HHHHHHHHHhcCCCHHHHHHHhCCChhHHHH
Q psy6501         124 AKLLMQGRQAKGWSQKDLATKINEKPQIVND  154 (174)
Q Consensus       124 ~~~i~~~R~~~glsq~ela~~lg~~~s~i~~  154 (174)
                      ...|..+-...++.+.+.|+.+|+++.++.+
T Consensus        22 r~~I~~aL~~~~gn~~~aA~~LGIsR~TL~r   52 (60)
T d1umqa_          22 WEHIQRIYEMCDRNVSETARRLNMHRRTLQR   52 (60)
T ss_dssp             HHHHHHHHHHTTSCHHHHHHHHTSCHHHHHH
T ss_pred             HHHHHHHHHHhcCcHHHHHHHHCCCHHHHHH
Confidence            4678888889999999999999999997654

>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=80.15  E-value=1.1  Score=29.11  Aligned_cols=32  Identities=13%  Similarity=0.173  Sum_probs=24.8

Q ss_pred             HHHHHHHHHc-CCCHHHHHHHhCCCHHHHHHHH
Q psy6501          35 KLLMQGRQAK-GWSQKDLATKINEKPQIVNDYE   66 (174)
Q Consensus        35 ~~ik~~R~~~-gltq~eLA~~igvs~~~is~~E   66 (174)
                      .-|..+.... ++|+.+||+.+++++++++++-
T Consensus        32 ~iL~~l~~~~~~~t~~~la~~~~~~~~~vs~~v   64 (137)
T d2fbha1          32 LVLLHLARHRDSPTQRELAQSVGVEGPTLARLL   64 (137)
T ss_dssp             HHHHHHHHCSSCCBHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHH
Confidence            3455554444 7999999999999999998864