Citrus Sinensis ID: 031871

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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-
Protein Sequence
MAGIGPITQDWEPVVIKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRGKK
Secondary Structure (PSIPRED)
cccccccccccccEEEccccccccccccHHHHHHHHHcccccEEEEEcccccccccccccccccccccccHHHHHHHHHHHccccccccHHHHHHHHHHHHHccccHHHHHHHHcccHHHHHHHHcccccccHHHHHHHHHHHcccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccEEEcccccccHHcccHHHHHHHHHcccEEEEEEEEccccccccccccccccHHccccccccEEEEEcEEEccccccHHHHHHHHHHHHHccccHHHHHHHHccccHHHHHHHcccccccHHHHHHHHHHHcccEcccc
Coil and Loop (DISEMBL)
magigpitqdwepvvikkkapnaatkkdEKVVNAARRAGADIETVRkshagtnkaassstslntrkldedTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEyesgkaipnqQILTKLERALgvklrgkk
Flexible Loop (DISEMBL)
magigpitqdwepvvikkkapnaatkkdekvvNAARragadietvrkshagtnkaassstslntrkldEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYEsgkaipnqqiltkleralgvklrgkk
Low Complexity Region (SEG)
MAGIGPITQDWEPVVIKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRGKK
Disordered region (IsUnstruct)
************************************************************************NLALLLSVLYCTDDRVPSELKKAIV*************************************IL***************
Disordered Region (DISOPRED)
****GPI*QDWEPVV**********************************************************************DRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG**
Disordered Region (DISEMBL)
MAGIGPITQDWEPVVIKKKA************NAARRAGADIETVRK*****************RKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRGKK
Disordered Region (DISPRO)
********QDWEPVVIKKK*P****************AGADIETVRKSHAG****************DE*TENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR***
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAGIGPITQDWEPVVIKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAxxxxxxxxxxxxxxxxxxxxxKPQVIQEYESGKAIPNQQILTKLERALGVKLRGKK
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	151	2.2.26 [Sep-21-2011]
Q9LXT3	142	Multiprotein-bridging fac	yes	no	0.940	1.0	0.801	8e-64
Q9SJI8	142	Multiprotein-bridging fac	no	no	0.940	1.0	0.801	1e-62
Q9LV58	148	Multiprotein-bridging fac	no	no	0.907	0.925	0.486	1e-31
Q5ZMC0	148	Endothelial differentiati	yes	no	0.860	0.878	0.507	1e-28
O60869	148	Endothelial differentiati	yes	no	0.860	0.878	0.514	3e-28
Q3T0V7	148	Endothelial differentiati	yes	no	0.860	0.878	0.514	3e-28
Q6GPQ6	147	Endothelial differentiati	N/A	no	0.860	0.884	0.485	9e-28
P69736	148	Endothelial differentiati	yes	no	0.860	0.878	0.507	1e-27
Q9JMG1	148	Endothelial differentiati	yes	no	0.860	0.878	0.507	1e-27
Q6PBY3	146	Endothelial differentiati	yes	no	0.860	0.890	0.482	4e-27

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

 Score =  241 bits (616), Expect = 8e-64,   Method: Compositional matrix adjust.
 Identities = 121/151 (80%), Positives = 134/151 (88%), Gaps = 9/151 (5%)

Query: 1   MAGIGPITQDWEPVVIKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSST 60
           MAGIGPITQDWEPVVI+K+APNAA K+DEK VNAARR+GADIETVRK +AG+NKAASS T
Sbjct: 1   MAGIGPITQDWEPVVIRKRAPNAAAKRDEKTVNAARRSGADIETVRKFNAGSNKAASSGT 60

Query: 61  SLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQV 120
           SLNT+KLD+DTENL         + DRVP+ELKKAI+QAR +KKLTQSQLA LINEKPQV
Sbjct: 61  SLNTKKLDDDTENL---------SHDRVPTELKKAIMQARGEKKLTQSQLAHLINEKPQV 111

Query: 121 IQEYESGKAIPNQQILTKLERALGVKLRGKK 151
           IQEYESGKAIPNQQIL+KLERALG KLRGKK
Sbjct: 112 IQEYESGKAIPNQQILSKLERALGAKLRGKK 142

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

 Score =  238 bits (607), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 121/151 (80%), Positives = 132/151 (87%), Gaps = 9/151 (5%)

Query: 1   MAGIGPITQDWEPVVIKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSST 60
           MAGIGPITQDWEPVVI+KK  NAA K+DEK VNAARR+GADIETVRK +AGTNKAASS T
Sbjct: 1   MAGIGPITQDWEPVVIRKKPANAAAKRDEKTVNAARRSGADIETVRKFNAGTNKAASSGT 60

Query: 61  SLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQV 120
           SLNT+ LD+DTENL         T +RVP+ELKKAI+QAR DKKLTQSQLAQ+INEKPQV
Sbjct: 61  SLNTKMLDDDTENL---------THERVPTELKKAIMQARTDKKLTQSQLAQIINEKPQV 111

Query: 121 IQEYESGKAIPNQQILTKLERALGVKLRGKK 151
           IQEYESGKAIPNQQIL+KLERALG KLRGKK
Sbjct: 112 IQEYESGKAIPNQQILSKLERALGAKLRGKK 142

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|Q9LV58|MBF1C_ARATH Multiprotein-bridging factor 1c OS=Arabidopsis thaliana GN=MBF1C PE=1 SV=1

 Score =  134 bits (338), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 72/148 (48%), Positives = 102/148 (68%), Gaps = 11/148 (7%)

Query: 5   GPITQDWEPVVIKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSSTS--L 62
           G +TQDWEPVV+ K    +   +D K VNAA R G  ++TV+K  AG+NK   S+    +
Sbjct: 7   GAVTQDWEPVVLHKSKQKSQDLRDPKAVNAALRNGVAVQTVKKFDAGSNKKGKSTAVPVI 66

Query: 63  NTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQ 122
           NT+KL+E+TE  A+         DRV +E++  I +AR +KK++Q+ LA+ INE+ QV+Q
Sbjct: 67  NTKKLEEETEPAAM---------DRVKAEVRLMIQKARLEKKMSQADLAKQINERTQVVQ 117

Query: 123 EYESGKAIPNQQILTKLERALGVKLRGK 150
           EYE+GKA+PNQ +L K+E+ LGVKLRGK
Sbjct: 118 EYENGKAVPNQAVLAKMEKVLGVKLRGK 145

Transcriptional coactivator that stimulates transcriptional activity by bridging regulatory proteins and TBP, thereby recruiting TBP to promoters occupied by DNA-binding regulators. Involved in the tolerance to heat and osmotic stress by partially activating the ethylene-response signal transduction pathway.

Arabidopsis thaliana (taxid: 3702)

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

 Score =  124 bits (312), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 72/142 (50%), Positives = 92/142 (64%), Gaps = 12/142 (8%)

Query: 10  DWEPV-VIKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLD 68
           DW+ V V++KK P+AA  K ++ V AA+R G D+ET +K  AG NK      + NT KLD
Sbjct: 5   DWDTVTVLRKKGPSAAQAKSKQAVLAAQRRGEDVETSKKWAAGQNK--QHFITKNTAKLD 62

Query: 69  EDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK 128
            +TE L           DRVP E+ K I Q R  K +TQ  LA  INEKPQVI +YESG+
Sbjct: 63  RETEEL---------HHDRVPLEVGKVIQQGRQSKGMTQKDLATKINEKPQVIADYESGR 113

Query: 129 AIPNQQILTKLERALGVKLRGK 150
           AIPN Q++ K+ERA+G+KLRGK
Sbjct: 114 AIPNNQVMGKIERAIGLKLRGK 135

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 =  123 bits (309), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 73/142 (51%), Positives = 91/142 (64%), Gaps = 12/142 (8%)

Query: 10  DWEPV-VIKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLD 68
           DW+ V V++KK P AA  K ++ + AA+R G D+ET +K  AG NK    S + NT KLD
Sbjct: 5   DWDTVTVLRKKGPTAAQAKSKQAILAAQRRGEDVETSKKWAAGQNK--QHSITKNTAKLD 62

Query: 69  EDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK 128
            +TE L           DRV  E+ K I Q R  K LTQ  LA  INEKPQVI +YESG+
Sbjct: 63  RETEELH---------HDRVTLEVGKVIQQGRQSKGLTQKDLATKINEKPQVIADYESGR 113

Query: 129 AIPNQQILTKLERALGVKLRGK 150
           AIPN Q+L K+ERA+G+KLRGK
Sbjct: 114 AIPNNQVLGKIERAIGLKLRGK 135

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 =  123 bits (309), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 73/142 (51%), Positives = 91/142 (64%), Gaps = 12/142 (8%)

Query: 10  DWEPV-VIKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLD 68
           DW+ V V++KK P AA  K ++ + AA+R G D+ET +K  AG NK    S + NT KLD
Sbjct: 5   DWDTVTVLRKKGPTAAQAKSKQAILAAQRRGEDVETSKKWAAGQNK--QHSITKNTAKLD 62

Query: 69  EDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK 128
            +TE L           DRV  E+ K I Q R  K LTQ  LA  INEKPQVI +YESG+
Sbjct: 63  RETEELH---------HDRVTLEVGKVIQQGRQSKGLTQKDLATKINEKPQVIADYESGR 113

Query: 129 AIPNQQILTKLERALGVKLRGK 150
           AIPN Q+L K+ERA+G+KLRGK
Sbjct: 114 AIPNNQVLGKIERAIGLKLRGK 135

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

 Score =  122 bits (305), Expect = 9e-28,   Method: Compositional matrix adjust.
 Identities = 69/142 (48%), Positives = 90/142 (63%), Gaps = 12/142 (8%)

Query: 10  DWEPV-VIKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLD 68
           DW+ V V++KK P AA  K ++ + AA+R G ++ET +K  AG NK    + + NT KLD
Sbjct: 5   DWDTVTVLRKKGPTAAQAKSKQAITAAQRRGEEVETSKKWSAGQNK--QHTITRNTAKLD 62

Query: 69  EDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK 128
            +TE L           DRVP E+ K I Q R  K +TQ  LA  INEKPQVI +YE GK
Sbjct: 63  RETEELH---------HDRVPLEVGKVIQQGRQGKGMTQKDLATKINEKPQVIADYECGK 113

Query: 129 AIPNQQILTKLERALGVKLRGK 150
           AIPN Q++ K+ER +G+KLRGK
Sbjct: 114 AIPNNQVMGKIERVIGLKLRGK 135

Probable transcriptional coactivator.

Xenopus laevis (taxid: 8355)

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

 Score =  121 bits (304), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 72/142 (50%), Positives = 91/142 (64%), Gaps = 12/142 (8%)

Query: 10  DWEPV-VIKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLD 68
           DW+ V V++KK P AA  K ++ + AA+R G D+ET +K  AG NK    S + NT KLD
Sbjct: 5   DWDTVTVLRKKGPTAAQAKSKQAILAAQRRGEDVETSKKWAAGQNK--QHSITKNTAKLD 62

Query: 69  EDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK 128
            +TE L           DRV  E+ K I + R  K LTQ  LA  INEKPQVI +YESG+
Sbjct: 63  RETEELH---------HDRVTLEVGKVIQRGRQSKGLTQKDLATKINEKPQVIADYESGR 113

Query: 129 AIPNQQILTKLERALGVKLRGK 150
           AIPN Q+L K+ERA+G+KLRGK
Sbjct: 114 AIPNNQVLGKIERAIGLKLRGK 135

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 =  121 bits (304), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 72/142 (50%), Positives = 91/142 (64%), Gaps = 12/142 (8%)

Query: 10  DWEPV-VIKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLD 68
           DW+ V V++KK P AA  K ++ + AA+R G D+ET +K  AG NK    S + NT KLD
Sbjct: 5   DWDTVTVLRKKGPTAAQAKSKQAILAAQRRGEDVETSKKWAAGQNK--QHSITKNTAKLD 62

Query: 69  EDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK 128
            +TE L           DRV  E+ K I + R  K LTQ  LA  INEKPQVI +YESG+
Sbjct: 63  RETEELH---------HDRVTLEVGKVIQRGRQSKGLTQKDLATKINEKPQVIADYESGR 113

Query: 129 AIPNQQILTKLERALGVKLRGK 150
           AIPN Q+L K+ERA+G+KLRGK
Sbjct: 114 AIPNNQVLGKIERAIGLKLRGK 135

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

 Score =  120 bits (300), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 68/141 (48%), Positives = 88/141 (62%), Gaps = 11/141 (7%)

Query: 10  DWEPVVIKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDE 69
           DW+ V + +K  +AA  K ++ V AA+R G  +ET +K  AG NK      + NT KLD 
Sbjct: 5   DWDTVTVLRKKGSAAQSKSKQAVTAAQRKGEAVETSKKWAAGQNK--QHVVTKNTAKLDR 62

Query: 70  DTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA 129
           +TE L         +  RVP E+ K I Q R +K LTQ  LA  INEKPQ+I EYE GKA
Sbjct: 63  ETEEL---------SHQRVPLEVGKVIQQGRQNKGLTQKDLATKINEKPQIIAEYECGKA 113

Query: 130 IPNQQILTKLERALGVKLRGK 150
           IPN Q++ K+ERA+G+KLRGK
Sbjct: 114 IPNNQVMGKIERAIGLKLRGK 134

Probable transcriptional coactivator.

Danio rerio (taxid: 7955)

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	151
225446629	142	PREDICTED: multiprotein-bridging factor	0.940	1.0	0.807	8e-63
422779154	142	multiprotein bridging factor 1 [Vitis ps	0.940	1.0	0.801	1e-62
297817180	142	ATMBF1B/MBF1B [Arabidopsis lyrata subsp.	0.940	1.0	0.807	2e-62
297824233	142	ATMBF1A/MBF1A [Arabidopsis lyrata subsp.	0.940	1.0	0.794	4e-62
15231105	142	multiprotein-bridging factor 1b [Arabido	0.940	1.0	0.801	5e-62
295913448	142	transcription factor [Lycoris longituba]	0.940	1.0	0.807	9e-62
18406032	142	multiprotein bridging factor 1A [Arabido	0.940	1.0	0.801	6e-61
359493778	142	PREDICTED: multiprotein-bridging factor	0.940	1.0	0.794	2e-60
192910818	142	ethylene-responsive transcriptional coac	0.940	1.0	0.788	4e-60
388519359	143	unknown [Lotus japonicus]	0.940	0.993	0.769	1e-58

>gi|225446629|ref|XP_002280992.1| PREDICTED: multiprotein-bridging factor 1a [Vitis vinifera] gi|147865629|emb|CAN83249.1| hypothetical protein VITISV_019642 [Vitis vinifera] gi|302143433|emb|CBI21994.3| unnamed protein product [Vitis vinifera]

 Score =  244 bits (623), Expect = 8e-63,   Method: Compositional matrix adjust.
 Identities = 122/151 (80%), Positives = 135/151 (89%), Gaps = 9/151 (5%)

Query: 1   MAGIGPITQDWEPVVIKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSST 60
           MAG+GP+TQDWEPVVI+KK  NAA KKDEK VNAARR+GA+IET+RKSHAGTNKAASSST
Sbjct: 1   MAGVGPLTQDWEPVVIRKKPLNAAAKKDEKAVNAARRSGAEIETLRKSHAGTNKAASSST 60

Query: 61  SLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQV 120
           SLNTRKLDE+TENLA          DRVP+ELKK+I+QAR DKKLTQSQLAQ+INEKPQ+
Sbjct: 61  SLNTRKLDEETENLA---------HDRVPTELKKSIMQARMDKKLTQSQLAQMINEKPQI 111

Query: 121 IQEYESGKAIPNQQILTKLERALGVKLRGKK 151
           IQEYESGKAIPNQQI+ KLERALGVKLRGKK
Sbjct: 112 IQEYESGKAIPNQQIIVKLERALGVKLRGKK 142

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|422779154|gb|AFX82676.1| multiprotein bridging factor 1 [Vitis pseudoreticulata]

 Score =  243 bits (621), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 121/151 (80%), Positives = 135/151 (89%), Gaps = 9/151 (5%)

Query: 1   MAGIGPITQDWEPVVIKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSST 60
           MAG+GP+TQDWEPVVI+KK  NAA +KDEK VNAARR+GA+IET+RKSHAGTNKAASSST
Sbjct: 1   MAGVGPLTQDWEPVVIRKKPLNAAARKDEKAVNAARRSGAEIETLRKSHAGTNKAASSST 60

Query: 61  SLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQV 120
           SLNTRKLDE+TENLA          DRVP+ELKK+I+QAR DKKLTQSQLAQ+INEKPQ+
Sbjct: 61  SLNTRKLDEETENLA---------HDRVPTELKKSIMQARMDKKLTQSQLAQMINEKPQI 111

Query: 121 IQEYESGKAIPNQQILTKLERALGVKLRGKK 151
           IQEYESGKAIPNQQI+ KLERALGVKLRGKK
Sbjct: 112 IQEYESGKAIPNQQIIVKLERALGVKLRGKK 142

Source: Vitis pseudoreticulata

Species: Vitis pseudoreticulata

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297817180|ref|XP_002876473.1| ATMBF1B/MBF1B [Arabidopsis lyrata subsp. lyrata] gi|297322311|gb|EFH52732.1| ATMBF1B/MBF1B [Arabidopsis lyrata subsp. lyrata]

 Score =  243 bits (620), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 122/151 (80%), Positives = 135/151 (89%), Gaps = 9/151 (5%)

Query: 1   MAGIGPITQDWEPVVIKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSST 60
           MAGIGPITQDWEPVVI+KKAPN+A K+DEK VNAARR+GADIETVRK +AG+NKAASS T
Sbjct: 1   MAGIGPITQDWEPVVIRKKAPNSAAKRDEKTVNAARRSGADIETVRKFNAGSNKAASSGT 60

Query: 61  SLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQV 120
           SLNT+KLD+DTENL         + DRVP+ELKKAI+QAR +KKLTQSQLAQLINEKPQV
Sbjct: 61  SLNTKKLDDDTENL---------SHDRVPTELKKAIMQARGEKKLTQSQLAQLINEKPQV 111

Query: 121 IQEYESGKAIPNQQILTKLERALGVKLRGKK 151
           IQEYESGKAIPNQQIL+KLERALG KLRGKK
Sbjct: 112 IQEYESGKAIPNQQILSKLERALGAKLRGKK 142

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297824233|ref|XP_002879999.1| ATMBF1A/MBF1A [Arabidopsis lyrata subsp. lyrata] gi|297325838|gb|EFH56258.1| ATMBF1A/MBF1A [Arabidopsis lyrata subsp. lyrata]

 Score =  242 bits (617), Expect = 4e-62,   Method: Compositional matrix adjust.
 Identities = 120/151 (79%), Positives = 135/151 (89%), Gaps = 9/151 (5%)

Query: 1   MAGIGPITQDWEPVVIKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSST 60
           MAG+GP+TQDWEPVVI+KKAPN+A K+D+K VNAARRAGADIETVRK +AGTNKAASS T
Sbjct: 1   MAGVGPMTQDWEPVVIRKKAPNSAAKRDDKTVNAARRAGADIETVRKFNAGTNKAASSGT 60

Query: 61  SLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQV 120
           SLNT++LD+DTENL         T +RVP+ELKKAI+QAR DKKLTQSQLAQ+INEKPQV
Sbjct: 61  SLNTKRLDDDTENL---------THERVPTELKKAIMQARTDKKLTQSQLAQIINEKPQV 111

Query: 121 IQEYESGKAIPNQQILTKLERALGVKLRGKK 151
           IQEYESGKAIPNQQIL+KLERALG KLRGKK
Sbjct: 112 IQEYESGKAIPNQQILSKLERALGAKLRGKK 142

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15231105|ref|NP_191427.1| multiprotein-bridging factor 1b [Arabidopsis thaliana] gi|75311678|sp|Q9LXT3.1|MBF1B_ARATH RecName: Full=Multiprotein-bridging factor 1b gi|11692930|gb|AAG40068.1|AF324717_1 AT3g58680 [Arabidopsis thaliana] gi|11908124|gb|AAG41491.1|AF326909_1 putative transcriptional coactivator protein [Arabidopsis thaliana] gi|12642936|gb|AAK00410.1|AF339728_1 putative transcriptional coactivator protein [Arabidopsis thaliana] gi|7630063|emb|CAB88285.1| transcriptional coactivator-like protein [Arabidopsis thaliana] gi|14596125|gb|AAK68790.1| transcriptional coactivator-like protein [Arabidopsis thaliana] gi|20148317|gb|AAM10049.1| transcriptional coactivator-like protein [Arabidopsis thaliana] gi|21536830|gb|AAM61162.1| transcriptional coactivator-like protein [Arabidopsis thaliana] gi|332646296|gb|AEE79817.1| multiprotein-bridging factor 1b [Arabidopsis thaliana]

 Score =  241 bits (616), Expect = 5e-62,   Method: Compositional matrix adjust.
 Identities = 121/151 (80%), Positives = 134/151 (88%), Gaps = 9/151 (5%)

Query: 1   MAGIGPITQDWEPVVIKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSST 60
           MAGIGPITQDWEPVVI+K+APNAA K+DEK VNAARR+GADIETVRK +AG+NKAASS T
Sbjct: 1   MAGIGPITQDWEPVVIRKRAPNAAAKRDEKTVNAARRSGADIETVRKFNAGSNKAASSGT 60

Query: 61  SLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQV 120
           SLNT+KLD+DTENL         + DRVP+ELKKAI+QAR +KKLTQSQLA LINEKPQV
Sbjct: 61  SLNTKKLDDDTENL---------SHDRVPTELKKAIMQARGEKKLTQSQLAHLINEKPQV 111

Query: 121 IQEYESGKAIPNQQILTKLERALGVKLRGKK 151
           IQEYESGKAIPNQQIL+KLERALG KLRGKK
Sbjct: 112 IQEYESGKAIPNQQILSKLERALGAKLRGKK 142

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|295913448|gb|ADG57975.1| transcription factor [Lycoris longituba] gi|295913679|gb|ADG58081.1| transcription factor [Lycoris longituba] gi|295913683|gb|ADG58083.1| transcription factor [Lycoris longituba]

 Score =  241 bits (614), Expect = 9e-62,   Method: Compositional matrix adjust.
 Identities = 122/151 (80%), Positives = 134/151 (88%), Gaps = 9/151 (5%)

Query: 1   MAGIGPITQDWEPVVIKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSST 60
           MAGIGPI+QDWE +VI+KKAPNAATKKDEK VNAARR+GA+IETV+KS AGTNKAASSST
Sbjct: 1   MAGIGPISQDWESIVIRKKAPNAATKKDEKAVNAARRSGAEIETVKKSTAGTNKAASSST 60

Query: 61  SLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQV 120
           SLNTRKLDE+TENLA          +RVPSELKK+I+QAR DKK TQ+QLAQLINEKPQV
Sbjct: 61  SLNTRKLDEETENLA---------HERVPSELKKSIMQARMDKKYTQAQLAQLINEKPQV 111

Query: 121 IQEYESGKAIPNQQILTKLERALGVKLRGKK 151
           IQEYESGKAIPNQQI+ KLER LGVKLRGKK
Sbjct: 112 IQEYESGKAIPNQQIINKLERVLGVKLRGKK 142

Source: Lycoris longituba

Species: Lycoris longituba

Genus: Lycoris

Family: Amaryllidaceae

Order: Asparagales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18406032|ref|NP_565981.1| multiprotein bridging factor 1A [Arabidopsis thaliana] gi|75265947|sp|Q9SJI8.1|MBF1A_ARATH RecName: Full=Multiprotein-bridging factor 1a gi|13878035|gb|AAK44095.1|AF370280_1 unknown protein [Arabidopsis thaliana] gi|4512684|gb|AAD21738.1| expressed protein [Arabidopsis thaliana] gi|17104599|gb|AAL34188.1| unknown protein [Arabidopsis thaliana] gi|20198082|gb|AAM15391.1| expressed protein [Arabidopsis thaliana] gi|21593718|gb|AAM65685.1| transcriptional coactivator-like protein [Arabidopsis thaliana] gi|330255061|gb|AEC10155.1| multiprotein bridging factor 1A [Arabidopsis thaliana]

 Score =  238 bits (607), Expect = 6e-61,   Method: Compositional matrix adjust.
 Identities = 121/151 (80%), Positives = 132/151 (87%), Gaps = 9/151 (5%)

Query: 1   MAGIGPITQDWEPVVIKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSST 60
           MAGIGPITQDWEPVVI+KK  NAA K+DEK VNAARR+GADIETVRK +AGTNKAASS T
Sbjct: 1   MAGIGPITQDWEPVVIRKKPANAAAKRDEKTVNAARRSGADIETVRKFNAGTNKAASSGT 60

Query: 61  SLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQV 120
           SLNT+ LD+DTENL         T +RVP+ELKKAI+QAR DKKLTQSQLAQ+INEKPQV
Sbjct: 61  SLNTKMLDDDTENL---------THERVPTELKKAIMQARTDKKLTQSQLAQIINEKPQV 111

Query: 121 IQEYESGKAIPNQQILTKLERALGVKLRGKK 151
           IQEYESGKAIPNQQIL+KLERALG KLRGKK
Sbjct: 112 IQEYESGKAIPNQQILSKLERALGAKLRGKK 142

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|359493778|ref|XP_003634667.1| PREDICTED: multiprotein-bridging factor 1a-like [Vitis vinifera] gi|147777777|emb|CAN60297.1| hypothetical protein VITISV_017760 [Vitis vinifera] gi|302142891|emb|CBI20186.3| unnamed protein product [Vitis vinifera]

 Score =  236 bits (602), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 120/151 (79%), Positives = 133/151 (88%), Gaps = 9/151 (5%)

Query: 1   MAGIGPITQDWEPVVIKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSST 60
           MAG GP+TQDWEPVVI+KK  NAA KKDEK VNAARR GA+IETV+KS AGTN+AASSST
Sbjct: 1   MAGTGPLTQDWEPVVIRKKPLNAAAKKDEKAVNAARRMGAEIETVKKSSAGTNRAASSST 60

Query: 61  SLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQV 120
           SLNTRKLDE+TENL         T +RVP+ELKK+I+QAR DKKLTQ+QLAQ+INEKPQV
Sbjct: 61  SLNTRKLDEETENL---------THERVPTELKKSIMQARLDKKLTQAQLAQMINEKPQV 111

Query: 121 IQEYESGKAIPNQQILTKLERALGVKLRGKK 151
           IQEYESGKAIPNQQI+TKLERALGVKLRGKK
Sbjct: 112 IQEYESGKAIPNQQIITKLERALGVKLRGKK 142

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|192910818|gb|ACF06517.1| ethylene-responsive transcriptional coactivator [Elaeis guineensis] gi|374256027|gb|AEZ00875.1| putative ethylene-responsive transcriptional coactivator protein, partial [Elaeis guineensis]

 Score =  235 bits (600), Expect = 4e-60,   Method: Compositional matrix adjust.
 Identities = 119/151 (78%), Positives = 132/151 (87%), Gaps = 9/151 (5%)

Query: 1   MAGIGPITQDWEPVVIKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSST 60
           MAG+GPITQDWEPVVI+KKAPNAATKKDEK VNAARR+GA+IET+RKS AG N+AASSST
Sbjct: 1   MAGVGPITQDWEPVVIRKKAPNAATKKDEKAVNAARRSGAEIETLRKSTAGINRAASSST 60

Query: 61  SLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQV 120
           SLNTRKLDE+TE L         + +RVPSELKK I++AR DKKLTQ+QLAQLINEKPQV
Sbjct: 61  SLNTRKLDEETETL---------SHERVPSELKKNIMKARMDKKLTQAQLAQLINEKPQV 111

Query: 121 IQEYESGKAIPNQQILTKLERALGVKLRGKK 151
           IQEYESGKAIPNQQI+ KLER LG KLRGKK
Sbjct: 112 IQEYESGKAIPNQQIIIKLERVLGAKLRGKK 142

Source: Elaeis guineensis

Species: Elaeis guineensis

Genus: Elaeis

Family: Arecaceae

Order: Arecales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388519359|gb|AFK47741.1| unknown [Lotus japonicus]

 Score =  231 bits (588), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 117/152 (76%), Positives = 132/152 (86%), Gaps = 10/152 (6%)

Query: 1   MAGIG-PITQDWEPVVIKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSS 59
           M+G G P++QDWEPVV++KKAP AA +KD+K VNAARRAGADIETVRK +AGTNKAASS 
Sbjct: 1   MSGAGGPVSQDWEPVVLRKKAPTAAARKDDKAVNAARRAGADIETVRKHNAGTNKAASSG 60

Query: 60  TSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQ 119
           TSLNT++LDEDTENL         T DRVP+ELKKAI+QAR DKKLTQ+QLAQ+INEKPQ
Sbjct: 61  TSLNTKRLDEDTENL---------THDRVPTELKKAIMQARMDKKLTQAQLAQIINEKPQ 111

Query: 120 VIQEYESGKAIPNQQILTKLERALGVKLRGKK 151
           VIQEYESGKAIPNQQI+ KLERALG KLRGKK
Sbjct: 112 VIQEYESGKAIPNQQIIGKLERALGAKLRGKK 143

Source: Lotus japonicus

Species: Lotus japonicus

Genus: Lotus

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	151
TAIR|locus:2098994	142	MBF1B "multiprotein bridging f	0.940	1.0	0.801	2.2e-57
TAIR|locus:2041509	142	MBF1A "multiprotein bridging f	0.940	1.0	0.801	7.5e-57
TAIR|locus:2091747	148	MBF1C "multiprotein bridging f	0.907	0.925	0.486	1.6e-31
UNIPROTKB|Q5ZMC0	148	EDF1 "Endothelial differentiat	0.860	0.878	0.507	1.9e-28
UNIPROTKB|Q3T0V7	148	EDF1 "Endothelial differentiat	0.860	0.878	0.514	1.9e-28
UNIPROTKB|E2R2F2	148	EDF1 "Uncharacterized protein"	0.860	0.878	0.514	1.9e-28
UNIPROTKB|O60869	148	EDF1 "Endothelial differentiat	0.860	0.878	0.514	1.9e-28
UNIPROTKB|A6N8P5	148	MBF1 "Multiprotein bridging fa	0.860	0.878	0.507	3.9e-28
MGI|MGI:1891227	148	Edf1 "endothelial differentiat	0.860	0.878	0.507	5e-28
RGD|1308073	148	Edf1 "endothelial differentiat	0.860	0.878	0.507	5e-28

TAIR|locus:2098994 MBF1B "multiprotein bridging factor 1B" [Arabidopsis thaliana (taxid:3702)]

 Score = 590 (212.7 bits), Expect = 2.2e-57, P = 2.2e-57
 Identities = 121/151 (80%), Positives = 134/151 (88%)

Query:     1 MAGIGPITQDWEPVVIKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSST 60
             MAGIGPITQDWEPVVI+K+APNAA K+DEK VNAARR+GADIETVRK +AG+NKAASS T
Sbjct:     1 MAGIGPITQDWEPVVIRKRAPNAAAKRDEKTVNAARRSGADIETVRKFNAGSNKAASSGT 60

Query:    61 SLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQV 120
             SLNT+KLD+DTENL+          DRVP+ELKKAI+QAR +KKLTQSQLA LINEKPQV
Sbjct:    61 SLNTKKLDDDTENLS---------HDRVPTELKKAIMQARGEKKLTQSQLAHLINEKPQV 111

Query:   121 IQEYESGKAIPNQQILTKLERALGVKLRGKK 151
             IQEYESGKAIPNQQIL+KLERALG KLRGKK
Sbjct:   112 IQEYESGKAIPNQQILSKLERALGAKLRGKK 142

GO:0003677 "DNA binding" evidence=IEA;ISS

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

GO:0005634 "nucleus" evidence=ISM;IDA

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

GO:0009723 "response to ethylene stimulus" evidence=ISS

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

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

GO:0005737 "cytoplasm" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

TAIR|locus:2041509 MBF1A "multiprotein bridging factor 1A" [Arabidopsis thaliana (taxid:3702)]

 Score = 585 (211.0 bits), Expect = 7.5e-57, P = 7.5e-57
 Identities = 121/151 (80%), Positives = 132/151 (87%)

Query:     1 MAGIGPITQDWEPVVIKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSST 60
             MAGIGPITQDWEPVVI+KK  NAA K+DEK VNAARR+GADIETVRK +AGTNKAASS T
Sbjct:     1 MAGIGPITQDWEPVVIRKKPANAAAKRDEKTVNAARRSGADIETVRKFNAGTNKAASSGT 60

Query:    61 SLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQV 120
             SLNT+ LD+DTENL         T +RVP+ELKKAI+QAR DKKLTQSQLAQ+INEKPQV
Sbjct:    61 SLNTKMLDDDTENL---------THERVPTELKKAIMQARTDKKLTQSQLAQIINEKPQV 111

Query:   121 IQEYESGKAIPNQQILTKLERALGVKLRGKK 151
             IQEYESGKAIPNQQIL+KLERALG KLRGKK
Sbjct:   112 IQEYESGKAIPNQQILSKLERALGAKLRGKK 142

GO:0003677 "DNA binding" evidence=IEA;ISS

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

GO:0005634 "nucleus" evidence=ISM

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

GO:0009723 "response to ethylene stimulus" evidence=ISS

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

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

GO:0005730 "nucleolus" evidence=IDA

GO:0009644 "response to high light intensity" evidence=RCA

GO:0042542 "response to hydrogen peroxide" evidence=RCA

TAIR|locus:2091747 MBF1C "multiprotein bridging factor 1C" [Arabidopsis thaliana (taxid:3702)]

 Score = 346 (126.9 bits), Expect = 1.6e-31, P = 1.6e-31
 Identities = 72/148 (48%), Positives = 102/148 (68%)

Query:     5 GPITQDWEPVVIKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSSTS--L 62
             G +TQDWEPVV+ K    +   +D K VNAA R G  ++TV+K  AG+NK   S+    +
Sbjct:     7 GAVTQDWEPVVLHKSKQKSQDLRDPKAVNAALRNGVAVQTVKKFDAGSNKKGKSTAVPVI 66

Query:    63 NTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQ 122
             NT+KL+E+TE  A+         DRV +E++  I +AR +KK++Q+ LA+ INE+ QV+Q
Sbjct:    67 NTKKLEEETEPAAM---------DRVKAEVRLMIQKARLEKKMSQADLAKQINERTQVVQ 117

Query:   123 EYESGKAIPNQQILTKLERALGVKLRGK 150
             EYE+GKA+PNQ +L K+E+ LGVKLRGK
Sbjct:   118 EYENGKAVPNQAVLAKMEKVLGVKLRGK 145

GO:0003677 "DNA binding" evidence=IEA;ISS

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

GO:0005634 "nucleus" evidence=ISM

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

GO:0009723 "response to ethylene stimulus" evidence=ISS

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

GO:0009737 "response to abscisic acid stimulus" evidence=IEP

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

GO:0009408 "response to heat" evidence=IEP;RCA

GO:0009414 "response to water deprivation" evidence=IEP

GO:0005730 "nucleolus" evidence=IDA

GO:0006457 "protein folding" evidence=RCA

GO:0009644 "response to high light intensity" evidence=RCA

GO:0034976 "response to endoplasmic reticulum stress" evidence=RCA

GO:0042542 "response to hydrogen peroxide" evidence=RCA

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

GO:0009873 "ethylene mediated signaling pathway" evidence=TAS

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

 Score = 317 (116.6 bits), Expect = 1.9e-28, P = 1.9e-28
 Identities = 72/142 (50%), Positives = 92/142 (64%)

Query:    10 DWEPV-VIKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLD 68
             DW+ V V++KK P+AA  K ++ V AA+R G D+ET +K  AG NK      + NT KLD
Sbjct:     5 DWDTVTVLRKKGPSAAQAKSKQAVLAAQRRGEDVETSKKWAAGQNK--QHFITKNTAKLD 62

Query:    69 EDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK 128
              +TE L           DRVP E+ K I Q R  K +TQ  LA  INEKPQVI +YESG+
Sbjct:    63 RETEELH---------HDRVPLEVGKVIQQGRQSKGMTQKDLATKINEKPQVIADYESGR 113

Query:   129 AIPNQQILTKLERALGVKLRGK 150
             AIPN Q++ K+ERA+G+KLRGK
Sbjct:   114 AIPNNQVMGKIERAIGLKLRGK 135

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 = 317 (116.6 bits), Expect = 1.9e-28, P = 1.9e-28
 Identities = 73/142 (51%), Positives = 91/142 (64%)

Query:    10 DWEPV-VIKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLD 68
             DW+ V V++KK P AA  K ++ + AA+R G D+ET +K  AG NK    S + NT KLD
Sbjct:     5 DWDTVTVLRKKGPTAAQAKSKQAILAAQRRGEDVETSKKWAAGQNK--QHSITKNTAKLD 62

Query:    69 EDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK 128
              +TE L           DRV  E+ K I Q R  K LTQ  LA  INEKPQVI +YESG+
Sbjct:    63 RETEELH---------HDRVTLEVGKVIQQGRQSKGLTQKDLATKINEKPQVIADYESGR 113

Query:   129 AIPNQQILTKLERALGVKLRGK 150
             AIPN Q+L K+ERA+G+KLRGK
Sbjct:   114 AIPNNQVLGKIERAIGLKLRGK 135

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 = 317 (116.6 bits), Expect = 1.9e-28, P = 1.9e-28
 Identities = 73/142 (51%), Positives = 91/142 (64%)

Query:    10 DWEPV-VIKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLD 68
             DW+ V V++KK P AA  K ++ + AA+R G D+ET +K  AG NK    S + NT KLD
Sbjct:     5 DWDTVTVLRKKGPTAAQAKSKQAILAAQRRGEDVETSKKWAAGQNK--QHSITKNTAKLD 62

Query:    69 EDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK 128
              +TE L           DRV  E+ K I Q R  K LTQ  LA  INEKPQVI +YESG+
Sbjct:    63 RETEELH---------HDRVTLEVGKVIQQGRQSKGLTQKDLATKINEKPQVIADYESGR 113

Query:   129 AIPNQQILTKLERALGVKLRGK 150
             AIPN Q+L K+ERA+G+KLRGK
Sbjct:   114 AIPNNQVLGKIERAIGLKLRGK 135

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 = 317 (116.6 bits), Expect = 1.9e-28, P = 1.9e-28
 Identities = 73/142 (51%), Positives = 91/142 (64%)

Query:    10 DWEPV-VIKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLD 68
             DW+ V V++KK P AA  K ++ + AA+R G D+ET +K  AG NK    S + NT KLD
Sbjct:     5 DWDTVTVLRKKGPTAAQAKSKQAILAAQRRGEDVETSKKWAAGQNK--QHSITKNTAKLD 62

Query:    69 EDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK 128
              +TE L           DRV  E+ K I Q R  K LTQ  LA  INEKPQVI +YESG+
Sbjct:    63 RETEELH---------HDRVTLEVGKVIQQGRQSKGLTQKDLATKINEKPQVIADYESGR 113

Query:   129 AIPNQQILTKLERALGVKLRGK 150
             AIPN Q+L K+ERA+G+KLRGK
Sbjct:   114 AIPNNQVLGKIERAIGLKLRGK 135

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 = 314 (115.6 bits), Expect = 3.9e-28, P = 3.9e-28
 Identities = 72/142 (50%), Positives = 91/142 (64%)

Query:    10 DWEPV-VIKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLD 68
             DW+ V V++KK P AA  K ++ + AA+R G D+ET +K  AG NK    S + NT KLD
Sbjct:     5 DWDTVTVLRKKGPTAAQAKSKQAILAAQRRGEDVETSKKWAAGQNK--QHSITKNTAKLD 62

Query:    69 EDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK 128
              +TE L           DRV  E+ K I Q R  K LTQ  LA  INEKPQVI +YESG+
Sbjct:    63 RETEELH---------HDRVTLEVGKVIQQGRQSKGLTQKDLATKINEKPQVIADYESGR 113

Query:   129 AIPNQQILTKLERALGVKLRGK 150
             AIPN Q+L K+ERA+G+KLRG+
Sbjct:   114 AIPNNQVLGKIERAIGLKLRGR 135

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 = 313 (115.2 bits), Expect = 5.0e-28, P = 5.0e-28
 Identities = 72/142 (50%), Positives = 91/142 (64%)

Query:    10 DWEPV-VIKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLD 68
             DW+ V V++KK P AA  K ++ + AA+R G D+ET +K  AG NK    S + NT KLD
Sbjct:     5 DWDTVTVLRKKGPTAAQAKSKQAILAAQRRGEDVETSKKWAAGQNK--QHSITKNTAKLD 62

Query:    69 EDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK 128
              +TE L           DRV  E+ K I + R  K LTQ  LA  INEKPQVI +YESG+
Sbjct:    63 RETEELH---------HDRVTLEVGKVIQRGRQSKGLTQKDLATKINEKPQVIADYESGR 113

Query:   129 AIPNQQILTKLERALGVKLRGK 150
             AIPN Q+L K+ERA+G+KLRGK
Sbjct:   114 AIPNNQVLGKIERAIGLKLRGK 135

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 = 313 (115.2 bits), Expect = 5.0e-28, P = 5.0e-28
 Identities = 72/142 (50%), Positives = 91/142 (64%)

Query:    10 DWEPV-VIKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLD 68
             DW+ V V++KK P AA  K ++ + AA+R G D+ET +K  AG NK    S + NT KLD
Sbjct:     5 DWDTVTVLRKKGPTAAQAKSKQAILAAQRRGEDVETSKKWAAGQNK--QHSITKNTAKLD 62

Query:    69 EDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK 128
              +TE L           DRV  E+ K I + R  K LTQ  LA  INEKPQVI +YESG+
Sbjct:    63 RETEELH---------HDRVTLEVGKVIQRGRQSKGLTQKDLATKINEKPQVIADYESGR 113

Query:   129 AIPNQQILTKLERALGVKLRGK 150
             AIPN Q+L K+ERA+G+KLRGK
Sbjct:   114 AIPNNQVLGKIERAIGLKLRGK 135

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

---

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)
Q5ZMC0	EDF1_CHICK	No assigned EC number	0.5070	0.8609	0.8783	yes	no
O94700	MBF1_SCHPO	No assigned EC number	0.3892	0.8344	0.8513	yes	no
O60869	EDF1_HUMAN	No assigned EC number	0.5140	0.8609	0.8783	yes	no
Q9JMG1	EDF1_MOUSE	No assigned EC number	0.5070	0.8609	0.8783	yes	no
P0CO30	MBF1_CRYNJ	No assigned EC number	0.3642	0.8410	0.8466	yes	no
O14467	MBF1_YEAST	No assigned EC number	0.3877	0.8543	0.8543	yes	no
Q752P7	MBF1_ASHGO	No assigned EC number	0.3907	0.8807	0.875	yes	no
Q3T0V7	EDF1_BOVIN	No assigned EC number	0.5140	0.8609	0.8783	yes	no
Q9LXT3	MBF1B_ARATH	No assigned EC number	0.8013	0.9403	1.0	yes	no
Q6PBY3	EDF1_DANRE	No assigned EC number	0.4822	0.8609	0.8904	yes	no
Q6BXQ8	MBF1_DEBHA	No assigned EC number	0.4444	0.8278	0.8333	yes	no
Q6FJN0	MBF1_CANGA	No assigned EC number	0.3918	0.8609	0.8609	yes	no
P69736	EDF1_RAT	No assigned EC number	0.5070	0.8609	0.8783	yes	no
Q9SJI8	MBF1A_ARATH	No assigned EC number	0.8013	0.9403	1.0	no	no
Q4WX89	MBF1_ASPFU	No assigned EC number	0.3137	0.8410	0.8246	yes	no
Q8TG23	MBF1_YARLI	No assigned EC number	0.3907	0.8807	0.875	yes	no
Q6CIP4	MBF1_KLULA	No assigned EC number	0.3986	0.8609	0.8666	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

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!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: GSVIVG00018751001 SubName- Full=Putative uncharacterized protein (Chromosome chr12 scaffold_18, whole genome shotgun sequence); (142 aa) (Vitis vinifera)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	151
pfam08523	70	pfam08523, MBF1, Multiprotein bridging factor 1	9e-19
COG1813	165	COG1813, COG1813, Predicted transcription factor,	1e-12
smart00530	56	smart00530, HTH_XRE, Helix-turn-helix XRE-family l	2e-10
pfam01381	55	pfam01381, HTH_3, Helix-turn-helix	4e-10
cd00093	58	cd00093, HTH_XRE, Helix-turn-helix XRE-family like	6e-10
TIGR00270	154	TIGR00270, TIGR00270, TIGR00270 family protein	6e-05
PHA01976	67	PHA01976, PHA01976, helix-turn-helix protein	2e-04
pfam12844	64	pfam12844, HTH_19, Helix-turn-helix domain	4e-04
TIGR03830	127	TIGR03830, CxxCG_CxxCG_HTH, putative zinc finger/h	0.003

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

 Score = 74.7 bits (184), Expect = 9e-19
 Identities = 33/69 (47%), Positives = 40/69 (57%), Gaps = 3/69 (4%)

Query: 9  QDWEPV-VIKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKL 67
           DW+PV VI KK P A   K +  +NAARR+GA +ET +K  AG NK A      N  KL
Sbjct: 1  SDWDPVTVIGKKGPKAKVAKTQSAINAARRSGAVVETEKKYAAGNNKQA--GEGQNLAKL 58

Query: 68 DEDTENLAL 76
          D +TE L  
Sbjct: 59 DRETEPLKP 67

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

 Score = 61.3 bits (149), Expect = 1e-12
 Identities = 24/57 (42%), Positives = 35/57 (61%)

Query: 94  KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRGK 150
           + I +AR  + L+Q  LA  + EK  VI+  E G+A PN ++  KLE+ LG+KL  K
Sbjct: 82  ERIREAREKRGLSQEDLAAKLKEKVSVIRRIERGEATPNIKVAKKLEKLLGIKLVEK 138

Length = 165

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

 Score = 52.9 bits (128), Expect = 2e-10
 Identities = 19/53 (35%), Positives = 30/53 (56%)

Query: 96  IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 148
           + + R +K LTQ +LA+ +      +   E+GK  P+ + L KL +ALGV L 
Sbjct: 2   LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLD 54

Length = 56

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

 Score = 52.1 bits (126), Expect = 4e-10
 Identities = 18/53 (33%), Positives = 29/53 (54%)

Query: 96  IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 148
           + + R +  L+Q +LA+ +      I + E+GK  P+ + L KL  ALGV 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|238045 cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins

 Score = 51.8 bits (125), Expect = 6e-10
 Identities = 20/54 (37%), Positives = 31/54 (57%)

Query: 94  KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 147
           + + + R +K LTQ +LA+ +      I   E+GK  P+ + L KL +ALGV L
Sbjct: 2   ERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSL 55

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 = 40.7 bits (95), Expect = 6e-05
 Identities = 19/55 (34%), Positives = 34/55 (61%)

Query: 96  IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRGK 150
           I + R  +  +Q QLA+ I EK  +I++ E+ +  P  +++ KLE+ L +KLR +
Sbjct: 74  IRREREKRGWSQEQLAKKIQEKESLIKKIENAEIEPEPKVVEKLEKLLKIKLREQ 128

[Hypothetical proteins, Conserved]. Length = 154

>gnl|CDD|177330 PHA01976, PHA01976, helix-turn-helix protein

 Score = 37.6 bits (87), Expect = 2e-04
 Identities = 16/52 (30%), Positives = 32/52 (61%)

Query: 96  IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 147
           +++ARN +  +  +L++    +  +I ++E+ K +PN + L +L  ALGV L
Sbjct: 7   LIKARNARAWSAPELSRRAGVRHSLIYDFEADKRLPNLKTLLRLADALGVTL 58

Length = 67

>gnl|CDD|205103 pfam12844, HTH_19, Helix-turn-helix domain

 Score = 36.4 bits (85), Expect = 4e-04
 Identities = 16/50 (32%), Positives = 27/50 (54%)

Query: 98  QARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 147
           + R  K L+Q  LA+ +      + + E+GK+ P+   L K+  ALGV +
Sbjct: 6   ELREAKGLSQEDLAEKLGISKSYLSKIENGKSDPSADKLKKIAEALGVDV 55

Members of this family contains a DNA-binding helix-turn-helix domain. Length = 64

>gnl|CDD|163542 TIGR03830, CxxCG_CxxCG_HTH, putative zinc finger/helix-turn-helix protein, YgiT family

 Score = 35.3 bits (82), Expect = 0.003
 Identities = 12/50 (24%), Positives = 24/50 (48%), Gaps = 3/50 (6%)

Query: 95  AIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQ---QILTKLER 141
            I + R    L+Q + A+L+         YE G+  P++   ++L  L++
Sbjct: 69  EIRRIRKKLGLSQREAAELLGGGVNAFSRYERGEVRPSKALDKLLRLLDK 118

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. Length = 127

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	151
KOG3398	135	consensus Transcription factor MBF1 [Transcription	99.97
PF08523	71	MBF1: Multiprotein bridging factor 1; InterPro: IP	99.8
PRK06424	144	transcription factor; Provisional	99.62
PHA01976	67	helix-turn-helix protein	99.61
PRK08359	176	transcription factor; Validated	99.54
TIGR03070	58	couple_hipB transcriptional regulator, y4mF family	99.54
PF12844	64	HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_	99.51
PF01381	55	HTH_3: Helix-turn-helix; InterPro: IPR001387 This	99.5
COG1476	68	Predicted transcriptional regulators [Transcriptio	99.47
TIGR00270	154	conserved hypothetical protein TIGR00270.	99.46
PRK09726	88	antitoxin HipB; Provisional	99.44
PF13560	64	HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_	99.44
PRK09706	135	transcriptional repressor DicA; Reviewed	99.4
PRK09943	185	DNA-binding transcriptional repressor PuuR; Provis	99.32
PRK13890	120	conjugal transfer protein TrbA; Provisional	99.32
TIGR02607	78	antidote_HigA addiction module antidote protein, H	99.3
TIGR02684	89	dnstrm_HI1420 probable addiction module antidote p	99.26
PRK08154	309	anaerobic benzoate catabolism transcriptional regu	99.26
COG1813	165	Predicted transcription factor, homolog of eukaryo	99.25
PRK10072	96	putative transcriptional regulator; Provisional	99.18
TIGR02612	150	mob_myst_A mobile mystery protein A. Members of th	99.13
PF13443	63	HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3	99.12
PRK04140	317	hypothetical protein; Provisional	99.09
smart00530	56	HTH_XRE Helix-turn-helix XRE-family like proteins.	99.07
cd00093	58	HTH_XRE Helix-turn-helix XRE-family like proteins.	99.0
TIGR03830	127	CxxCG_CxxCG_HTH putative zinc finger/helix-turn-he	98.96
PF13744	80	HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_	98.96
COG3620	187	Predicted transcriptional regulator with C-termina	98.89
PHA00542	82	putative Cro-like protein	98.84
PRK10856	331	cytoskeletal protein RodZ; Provisional	98.83
smart00352	75	POU Found in Pit-Oct-Unc transcription factors.	98.78
COG2944	104	Predicted transcriptional regulator [Transcription	98.72
PRK02866	147	cyanate hydratase; Validated	98.69
PRK13355	517	bifunctional HTH-domain containing protein/aminotr	98.68
COG1709	241	Predicted transcriptional regulator [Transcription	98.63
COG3093	104	VapI Plasmid maintenance system antidote protein [	98.56
TIGR00673	150	cynS cyanate hydratase. Alternate names include cy	98.54
COG3655	73	Predicted transcriptional regulator [Transcription	98.37
COG1396	120	HipB Predicted transcriptional regulators [Transcr	98.37
COG1395	313	Predicted transcriptional regulator [Transcription	98.3
PF07022	66	Phage_CI_repr: Bacteriophage CI repressor helix-tu	98.26
PF13413	62	HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_	98.18
PF08667	147	BetR: BetR domain; InterPro: IPR013975 CheY-like p	97.96
cd01392	52	HTH_LacI Helix-turn-helix (HTH) DNA binding domain	97.87
COG5499	120	Predicted transcription regulator containing HTH d	97.86
TIGR01321	94	TrpR trp operon repressor, proteobacterial. This m	97.85
COG1426	284	Predicted transcriptional regulator contains Xre-l	97.83
PHA01083	149	hypothetical protein	97.78
PF08965	118	DUF1870: Domain of unknown function (DUF1870); Int	97.56
PF00356	46	LacI: Bacterial regulatory proteins, lacI family;	97.56
COG4800	170	Predicted transcriptional regulator with an HTH do	97.55
smart00354	70	HTH_LACI helix_turn _helix lactose operon represso	97.51
COG2522	119	Predicted transcriptional regulator [General funct	97.37
COG5606	91	Uncharacterized conserved small protein [Function	97.11
PF00157	75	Pou: Pou domain - N-terminal to homeobox domain; I	97.08
TIGR03879	73	near_KaiC_dom probable regulatory domain. This mod	96.81
TIGR02147	271	Fsuc_second hypothetical protein, TIGR02147. This	96.78
COG3636	100	Predicted transcriptional regulator [Transcription	96.75
PF01710	119	HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Tr	96.73
PF13693	78	HTH_35: Winged helix-turn-helix DNA-binding; PDB:	96.57
PHA00675	78	hypothetical protein	96.52
PHA02591	83	hypothetical protein; Provisional	96.38
PF13384	50	HTH_23: Homeodomain-like domain; PDB: 2X48_C.	96.34
PRK10014	342	DNA-binding transcriptional repressor MalI; Provis	96.31
PF14549	60	P22_Cro: DNA-binding transcriptional regulator Cro	96.27
COG3423	82	Nlp Predicted transcriptional regulator [Transcrip	96.13
TIGR02293	133	TAS_TIGR02293 putative toxin-antitoxin system anti	96.1
PRK09492	315	treR trehalose repressor; Provisional	96.08
PF13936	44	HTH_38: Helix-turn-helix domain; PDB: 2W48_A.	96.07
PF02796	45	HTH_7: Helix-turn-helix domain of resolvase; Inter	96.05
TIGR02844	80	spore_III_D sporulation transcriptional regulator	96.05
PRK09526	342	lacI lac repressor; Reviewed	96.0
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	95.96
TIGR00721	137	tfx DNA-binding protein, Tfx family. Tfx from Meth	95.95
PF04814	180	HNF-1_N: Hepatocyte nuclear factor 1 (HNF-1), N te	95.91
PRK03975	141	tfx putative transcriptional regulator; Provisiona	95.87
PRK14987	331	gluconate operon transcriptional regulator; Provis	95.67
KOG3802	398	consensus Transcription factor OCT-1, contains POU	95.46
PF08535	93	KorB: KorB domain; InterPro: IPR013741 This entry	95.44
PF05225	45	HTH_psq: helix-turn-helix, Psq domain; InterPro: I	95.34
COG1513	151	CynS Cyanate lyase [Inorganic ion transport and me	95.34
smart00351	125	PAX Paired Box domain.	95.23
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	95.16
PRK01381	99	Trp operon repressor; Provisional	95.14
PF02001	106	DUF134: Protein of unknown function DUF134; InterP	95.14
COG4197	96	Uncharacterized protein conserved in bacteria, pro	94.98
PRK10344	92	DNA-binding transcriptional regulator Nlp; Provisi	94.96
cd00131	128	PAX Paired Box domain	94.92
cd04762	49	HTH_MerR-trunc Helix-Turn-Helix DNA binding domain	94.84
PRK08558	238	adenine phosphoribosyltransferase; Provisional	94.57
PF07037	122	DUF1323: Putative transcription regulator (DUF1323	94.56
COG1356	143	tfx Transcriptional regulator [DNA replication, re	94.45
PF01371	87	Trp_repressor: Trp repressor protein; InterPro: IP	94.44
PF06056	58	Terminase_5: Putative ATPase subunit of terminase	94.37
PF05269	91	Phage_CII: Bacteriophage CII protein; InterPro: IP	94.3
PF02376	87	CUT: CUT domain; InterPro: IPR003350 A class, also	94.24
COG2944	104	Predicted transcriptional regulator [Transcription	93.99
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	93.83
COG1342	99	Predicted DNA-binding proteins [General function p	93.78
cd04764	67	HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding dom	93.75
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	93.72
TIGR01764	49	excise DNA binding domain, excisionase family. An	93.57
cd04761	49	HTH_MerR-SF Helix-Turn-Helix DNA binding domain of	93.57
PRK15418	318	transcriptional regulator LsrR; Provisional	93.55
PF02954	42	HTH_8: Bacterial regulatory protein, Fis family; I	93.54
cd04763	68	HTH_MlrA-like Helix-Turn-Helix DNA binding domain	93.51
PRK13698	323	plasmid-partitioning protein; Provisional	93.46
PHA01976	67	helix-turn-helix protein	93.45
cd00569	42	HTH_Hin_like Helix-turn-helix domain of Hin and re	93.4
PF12728	51	HTH_17: Helix-turn-helix domain	93.37
COG2390	321	DeoR Transcriptional regulator, contains sigma fac	93.32
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	93.31
PF13518	52	HTH_28: Helix-turn-helix domain	93.26
TIGR02531	88	yecD_yerC TrpR-related protein YerC/YecD. This mod	93.21
PF00376	38	MerR: MerR family regulatory protein; InterPro: IP	93.19
cd00131	128	PAX Paired Box domain	93.13
PF01527	76	HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp	92.79
PF10668	60	Phage_terminase: Phage terminase small subunit; In	92.72
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	92.69
cd04774	96	HTH_YfmP Helix-Turn-Helix DNA binding domain of th	92.66
cd01104	68	HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain	92.65
TIGR00180	187	parB_part ParB-like partition proteins. This model	92.6
cd01104	68	HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain	92.55
cd06171	55	Sigma70_r4 Sigma70, region (SR) 4 refers to the mo	92.49
COG2842	297	Uncharacterized ATPase, putative transposase [Gene	92.43
PRK09413	121	IS2 repressor TnpA; Reviewed	92.31
PF13613	53	HTH_Tnp_4: Helix-turn-helix of DDE superfamily end	92.27
PF13411	69	MerR_1: MerR HTH family regulatory protein; PDB: 2	92.22
cd04763	68	HTH_MlrA-like Helix-Turn-Helix DNA binding domain	91.98
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	91.96
KOG1168	385	consensus Transcription factor ACJ6/BRN-3, contain	91.92
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	91.88
TIGR03070	58	couple_hipB transcriptional regulator, y4mF family	91.8
PF13411	69	MerR_1: MerR HTH family regulatory protein; PDB: 2	91.78
cd04764	67	HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding dom	91.62
TIGR01610	95	phage_O_Nterm phage replication protein O, N-termi	91.6
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	91.51
PF01381	55	HTH_3: Helix-turn-helix; InterPro: IPR001387 This	91.39
PF08281	54	Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013	91.38
PRK09744	75	DNA-binding transcriptional regulator DicC; Provis	91.35
smart00422	70	HTH_MERR helix_turn_helix, mercury resistance.	91.32
TIGR03764	258	ICE_PFGI_1_parB integrating conjugative element, P	91.2
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	91.07
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	90.82
PRK10072	96	putative transcriptional regulator; Provisional	90.71
PF13542	52	HTH_Tnp_ISL3: Helix-turn-helix domain of transposa	90.61
PRK04217	110	hypothetical protein; Provisional	90.4
PF13545	76	HTH_Crp_2: Crp-like helix-turn-helix domain; PDB:	90.33
PF01418	77	HTH_6: Helix-turn-helix domain, rpiR family; Inter	90.29
PF04552	160	Sigma54_DBD: Sigma-54, DNA binding domain; InterPr	90.06
smart00421	58	HTH_LUXR helix_turn_helix, Lux Regulon. lux regulo	89.96
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	89.83
PF14590	166	DUF4447: Domain of unknown function (DUF4447); PDB	89.82
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	89.54
smart00419	48	HTH_CRP helix_turn_helix, cAMP Regulatory protein.	89.45
PF13551	112	HTH_29: Winged helix-turn helix	89.45
cd04780	95	HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding dom	89.37
cd01105	88	HTH_GlnR-like Helix-Turn-Helix DNA binding domain	89.25
cd04773	108	HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding	89.24
PRK00118	104	putative DNA-binding protein; Validated	89.1
COG3415	138	Transposase and inactivated derivatives [DNA repli	89.05
COG2973	103	TrpR Trp operon repressor [Transcription]	88.94
PRK04132	846	replication factor C small subunit; Provisional	88.91
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	88.8
PF13560	64	HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_	88.65
cd00592	100	HTH_MerR-like Helix-Turn-Helix DNA binding domain	88.49
PF02042	52	RWP-RK: RWP-RK domain; InterPro: IPR003035 This do	88.46
cd01105	88	HTH_GlnR-like Helix-Turn-Helix DNA binding domain	88.44
PF00165	42	HTH_AraC: Bacterial regulatory helix-turn-helix pr	88.35
COG2512	258	Predicted membrane-associated trancriptional regul	88.22
PF07638	185	Sigma70_ECF: ECF sigma factor	88.07
PF13022	142	HTH_Tnp_1_2: Helix-turn-helix of insertion element	88.06
COG1522	154	Lrp Transcriptional regulators [Transcription]	88.04
smart00422	70	HTH_MERR helix_turn_helix, mercury resistance.	87.82
cd01106	103	HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain	87.79
cd04774	96	HTH_YfmP Helix-Turn-Helix DNA binding domain of th	87.69
cd04789	102	HTH_Cfa Helix-Turn-Helix DNA binding domain of the	87.6
cd04768	96	HTH_BmrR-like Helix-Turn-Helix DNA binding domain	87.46
PRK10458	467	DNA cytosine methylase; Provisional	87.43
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	87.41
cd04768	96	HTH_BmrR-like Helix-Turn-Helix DNA binding domain	87.36
cd04788	96	HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain	87.26
cd01107	108	HTH_BmrR Helix-Turn-Helix DNA binding domain of th	87.24
TIGR01636	134	phage_rinA phage transcriptional activator, RinA f	87.19
cd04765	99	HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding dom	87.16
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	87.13
TIGR02885	231	spore_sigF RNA polymerase sigma-F factor. Members	87.1
PF05930	51	Phage_AlpA: Prophage CP4-57 regulatory protein (Al	87.08
PF13551	112	HTH_29: Winged helix-turn helix	86.76
cd04766	91	HTH_HspR Helix-Turn-Helix DNA binding domain of th	86.76
PF13011	85	LZ_Tnp_IS481: leucine-zipper of insertion element	86.69
PRK09943	185	DNA-binding transcriptional repressor PuuR; Provis	86.69
PRK09706	135	transcriptional repressor DicA; Reviewed	86.68
PRK09726	88	antitoxin HipB; Provisional	86.68
PRK08154	309	anaerobic benzoate catabolism transcriptional regu	86.64
cd04775	102	HTH_Cfa-like Helix-Turn-Helix DNA binding domain o	86.52
PF11427	50	HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C	86.5
cd04780	95	HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding dom	86.37
PF09048	59	Cro: Cro; InterPro: IPR000655 Bacteriophage lambda	86.36
cd04772	99	HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding d	86.27
cd04782	97	HTH_BltR Helix-Turn-Helix DNA binding domain of th	86.07
TIGR03697	193	NtcA_cyano global nitrogen regulator NtcA, cyanoba	86.07
PF00292	125	PAX: 'Paired box' domain; InterPro: IPR001523 The	86.03
cd04766	91	HTH_HspR Helix-Turn-Helix DNA binding domain of th	85.63
PRK11512	144	DNA-binding transcriptional repressor MarR; Provis	85.58
cd01109	113	HTH_YyaN Helix-Turn-Helix DNA binding domain of th	85.43
smart00497	53	IENR1 Intron encoded nuclease repeat motif. Repeat	85.38
TIGR02044	127	CueR Cu(I)-responsive transcriptional regulator. T	85.25
cd04769	116	HTH_MerR2 Helix-Turn-Helix DNA binding domain of M	85.1
cd01279	98	HTH_HspR-like Helix-Turn-Helix DNA binding domain	85.08
PRK08215	258	sporulation sigma factor SigG; Reviewed	85.06
COG0789	124	SoxR Predicted transcriptional regulators [Transcr	85.0
cd01282	112	HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding dom	84.94
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	84.89
cd01107	108	HTH_BmrR Helix-Turn-Helix DNA binding domain of th	84.86
cd04781	120	HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding dom	84.83
cd01111	107	HTH_MerD Helix-Turn-Helix DNA binding domain of th	84.82
PRK09391	230	fixK transcriptional regulator FixK; Provisional	84.81
PRK11891	429	aspartate carbamoyltransferase; Provisional	84.76
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	84.74
PRK05572	252	sporulation sigma factor SigF; Validated	84.63
cd04784	127	HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain	84.54
PF13730	55	HTH_36: Helix-turn-helix domain	84.53
PRK11161	235	fumarate/nitrate reduction transcriptional regulat	84.33
cd06170	57	LuxR_C_like C-terminal DNA-binding domain of LuxR-	84.27
cd04783	126	HTH_MerR1 Helix-Turn-Helix DNA binding domain of t	84.25
COG1318	182	Predicted transcriptional regulators [Transcriptio	84.13
cd04770	123	HTH_HMRTR Helix-Turn-Helix DNA binding domain of H	84.1
PRK11169	164	leucine-responsive transcriptional regulator; Prov	84.1
cd01111	107	HTH_MerD Helix-Turn-Helix DNA binding domain of th	83.94
PRK00215	205	LexA repressor; Validated	83.9
PRK12427	231	flagellar biosynthesis sigma factor; Provisional	83.87
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	83.83
TIGR00122	69	birA_repr_reg BirA biotin operon repressor domain.	83.82
TIGR03209	142	P21_Cbot clostridium toxin-associated regulator Bo	83.73
PF00440	47	TetR_N: Bacterial regulatory proteins, tetR family	83.58
cd04765	99	HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding dom	83.48
TIGR02392	270	rpoH_proteo alternative sigma factor RpoH. A sigma	83.46
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	83.41
TIGR02043	131	ZntR Zn(II)-responsive transcriptional regulator.	83.35
TIGR02047	127	CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional	83.25
PF07453	37	NUMOD1: NUMOD1 domain; InterPro: IPR010896 This he	83.24
cd04767	120	HTH_HspR-like_MBC Helix-Turn-Helix DNA binding dom	83.21
cd01108	127	HTH_CueR Helix-Turn-Helix DNA binding domain of Cu	83.17
cd04788	96	HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain	83.13
TIGR02607	78	antidote_HigA addiction module antidote protein, H	83.05
smart00351	125	PAX Paired Box domain.	83.01
cd04777	107	HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding dom	82.76
PF12844	64	HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_	82.6
TIGR02054	120	MerD mercuric resistence transcriptional repressor	82.57
PF00376	38	MerR: MerR family regulatory protein; InterPro: IP	82.55
PF01710	119	HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Tr	82.36
cd01110	139	HTH_SoxR Helix-Turn-Helix DNA binding domain of th	82.29
PRK06759	154	RNA polymerase factor sigma-70; Validated	82.29
PRK13413	200	mpi multiple promoter invertase; Provisional	82.22
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	82.14
TIGR02393	238	RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter	82.03
COG1974	201	LexA SOS-response transcriptional repressors (RecA	81.93
cd04767	120	HTH_HspR-like_MBC Helix-Turn-Helix DNA binding dom	81.91
PRK06424	144	transcription factor; Provisional	81.83
PRK09514	140	zntR zinc-responsive transcriptional regulator; Pr	81.8
cd01279	98	HTH_HspR-like Helix-Turn-Helix DNA binding domain	81.65
cd04776	118	HTH_GnyR Helix-Turn-Helix DNA binding domain of th	81.63
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	81.55
PRK11179	153	DNA-binding transcriptional regulator AsnC; Provis	81.52
TIGR02999	183	Sig-70_X6 RNA polymerase sigma factor, TIGR02999 f	81.52
PRK13918	202	CRP/FNR family transcriptional regulator; Provisio	81.3
COG3311	70	AlpA Predicted transcriptional regulator [Transcri	81.29
cd04785	126	HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding do	81.29
cd04782	97	HTH_BltR Helix-Turn-Helix DNA binding domain of th	81.25
cd04787	133	HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain	81.25
PF00196	58	GerE: Bacterial regulatory proteins, luxR family;	81.22
TIGR00270	154	conserved hypothetical protein TIGR00270.	81.21
PRK13832	520	plasmid partitioning protein; Provisional	81.14
PRK11753	211	DNA-binding transcriptional dual regulator Crp; Pr	80.91
PRK07037	163	extracytoplasmic-function sigma-70 factor; Validat	80.89
PRK12423	202	LexA repressor; Provisional	80.59
TIGR02985	161	Sig70_bacteroi1 RNA polymerase sigma-70 factor, Ba	80.59
TIGR02980	227	SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G	80.57
PRK13890	120	conjugal transfer protein TrbA; Provisional	80.52
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	80.37
PRK10227	135	DNA-binding transcriptional regulator CueR; Provis	80.36
TIGR01950	142	SoxR redox-sensitive transcriptional activator Sox	80.31
smart00347	101	HTH_MARR helix_turn_helix multiple antibiotic resi	80.17
PF06322	64	Phage_NinH: Phage NinH protein; InterPro: IPR01045	80.15
PRK09514	140	zntR zinc-responsive transcriptional regulator; Pr	80.03

>KOG3398 consensus Transcription factor MBF1 [Transcription]

Probab=99.97  E-value=4.4e-30  Score=184.78  Aligned_cols=133  Identities=65%  Similarity=0.904  Sum_probs=123.5

Q ss_pred             CCCCCceeeccCCCCCccccCHHHHHHHHHcCCChhhHHhhhcCCCccCCCCcccccccccccchhhhHHHHHhhccCCc
Q 031871            8 TQDWEPVVIKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTENLALLLSVLYCTDDR   87 (151)
Q Consensus         8 ~~~w~~~~~~~~~~~~~~~~~~~~~~~a~r~g~~v~t~~k~~~g~~~~~~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~   87 (151)
                      ++||+||++-++.++..+.++++++|+|+|+|+.|+|+++|.+|.++.+  +..+++++||++++.+.+         ..
T Consensus         1 ~~dw~~vt~~~~~~~s~~~k~~~~vnaa~r~g~~v~t~~k~~~g~nkq~--~~~~~t~klD~etE~~~~---------~~   69 (135)
T KOG3398|consen    1 TSDWDPVTVLKKKAKAATLKDEKAVNAARRAGVDVETVKKFPAGLNKQH--PSTQSTAKLDRETEELGH---------DR   69 (135)
T ss_pred             CCCcccceeeecccccccccCHHHHHHHHHhcchhhhhhhhcccccccC--Ccccchhhcccccccccc---------cc
Confidence            4899999644444588899999999999999999999999999999864  457889999999999999         99


Q ss_pred             chHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCCCC
Q 031871           88 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRGKK  151 (151)
Q Consensus        88 ~~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~e~~  151 (151)
                      +...++..|.+.|..+||||+|||.+++..++.|..||+|+..|+..+|.+|.++|||.+++++
T Consensus        70 v~~~Vg~aIq~aR~~KgmsqkDLA~kInekpqVv~dyEsGrAIpNqqil~kmEraLgvKlrgk~  133 (135)
T KOG3398|consen   70 VPLEVGKAIQQARAQKGMSQKDLAQKINEKPQVIQDYESGRAIPNQQILSKMERALGVKLRGKN  133 (135)
T ss_pred             ccHHHHHHHHHHHHhccccHHHHHHHHccCchhhhhHhccccCchHHHHHHHHHHhceeccccc
Confidence            9999999999999999999999999999999999999999999999999999999999999875

>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=99.80  E-value=6.1e-21  Score=126.48  Aligned_cols=67  Identities=51%  Similarity=0.726  Sum_probs=0.0

Q ss_pred             CCCCce-eeccCCCCCccccCHHHHHHHHHcCCChhhHHhhhcCCCccCCCCcccccccccccchhhhH
Q 031871            9 QDWEPV-VIKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTENLAL   76 (151)
Q Consensus         9 ~~w~~~-~~~~~~~~~~~~~~~~~~~~a~r~g~~v~t~~k~~~g~~~~~~~~~~~~~~kl~~~~~~~~~   76 (151)
                      |||||| ||+|+.|+++++++++++|+|||+|..|+|.+||.+|+|+ +..+.+++++|||++++.++|
T Consensus         1 qDWd~vtvi~kk~p~~~~~r~~~avNaArR~G~~v~T~KK~~~g~Nk-~~~~~~~n~~KLD~etE~~~~   68 (71)
T PF08523_consen    1 QDWDPVTVIGKKGPRAKVARSESAVNAARRSGAVVETEKKYGAGNNK-HQHGEGQNAAKLDRETEELKH   68 (71)
T ss_dssp             ---------------------------------------------------------------------
T ss_pred             CCCcccceecccCCCccccCCHHHHHHHHHcCCceEEEEeeeccccc-cCCCcccccccccccccccCC
Confidence            799999 9999999999999999999999999999999999999999 667789999999999999987

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.

>PRK06424 transcription factor; Provisional

Probab=99.62  E-value=4.8e-15  Score=110.76  Aligned_cols=63  Identities=30%  Similarity=0.452  Sum_probs=60.8

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCCCC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRGKK  151 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~e~~  151 (151)
                      ...|+.+|+.+|+++||||.+||+.+|+++++|++||+|+..|+.+.+.+|+++||+++.|+.
T Consensus        82 ~~~~g~~Ir~lRe~~GLSQ~eLA~~iGvs~stIskiE~G~~~Ps~~~l~kLa~~Lgvsl~e~~  144 (144)
T PRK06424         82 VEDYAELVKNARERLSMSQADLAAKIFERKNVIASIERGDLLPDIKTARKLEKILGITLIEKA  144 (144)
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCCCCC
Confidence            578999999999999999999999999999999999999999999999999999999999874

>PHA01976 helix-turn-helix protein

Probab=99.61  E-value=1.6e-15  Score=98.48  Aligned_cols=58  Identities=28%  Similarity=0.509  Sum_probs=56.3

Q ss_pred             HHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           91 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        91 ~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      .|+.+|+.+|..+|+||.+||+.+|+++++|++||+|...|+.+.+.+||++|||+++
T Consensus         2 ~~~~rl~~~R~~~glt~~~lA~~~gvs~~~v~~~e~g~~~p~~~~l~~ia~~l~v~~~   59 (67)
T PHA01976          2 SFAIQLIKARNARAWSAPELSRRAGVRHSLIYDFEADKRLPNLKTLLRLADALGVTLD   59 (67)
T ss_pred             cHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHH
Confidence            5899999999999999999999999999999999999999999999999999999975

>PRK08359 transcription factor; Validated

Probab=99.54  E-value=3.5e-14  Score=109.13  Aligned_cols=63  Identities=17%  Similarity=0.245  Sum_probs=60.5

Q ss_pred             cchHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 031871           87 RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG  149 (151)
Q Consensus        87 ~~~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~e  149 (151)
                      .+.++|+++|+++|+.+||||.+||+.+|+++++|++||+|+..|+.+.+.+||++|+|++.+
T Consensus        81 elv~dy~~rIkeaRe~kglSQeeLA~~lgvs~stI~~iE~G~~~Ps~~~l~kLak~l~VsL~e  143 (176)
T PRK08359         81 DIVEDYAERVYEAIQKSGLSYEELSHEVGLSVNDLRRIAHGEYEPTIKEAKKLERYFKIKLIE  143 (176)
T ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCcCCCHHHHHHHHHHhCCcccc
Confidence            557899999999999999999999999999999999999999999999999999999999875

>TIGR03070 couple_hipB transcriptional regulator, y4mF family

Probab=99.54  E-value=3.2e-14  Score=88.84  Aligned_cols=57  Identities=26%  Similarity=0.353  Sum_probs=54.9

Q ss_pred             HHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 031871           91 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL  147 (151)
Q Consensus        91 ~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l  147 (151)
                      .++.+|+.+|...||||.+||+.+|+++++|++||+|+..|+.+.+.+|+++|||++
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            478999999999999999999999999999999999999999999999999999985

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.

>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=99.51  E-value=2e-14  Score=92.46  Aligned_cols=56  Identities=34%  Similarity=0.484  Sum_probs=48.4

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      |++|+++|+.+|+||.+||+.+|+++++|++||+|+..|+...+.+||++|||+++
T Consensus         1 G~~lk~~r~~~~lt~~~~a~~~~i~~~~i~~~e~g~~~~~~~~l~~i~~~~~v~~~   56 (64)
T PF12844_consen    1 GERLKELREEKGLTQKDLAEKLGISRSTISKIENGKRKPSVSTLKKIAEALGVSLD   56 (64)
T ss_dssp             HHHHHHHHHHCT--HHHHHHHHTS-HHHHHHHHTTSS--BHHHHHHHHHHHTS-HH
T ss_pred             CHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCcCCCHHHHHHHHHHhCCCHH
Confidence            68999999999999999999999999999999999999999999999999999875

>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=99.50  E-value=2.8e-14  Score=89.07  Aligned_cols=53  Identities=34%  Similarity=0.494  Sum_probs=49.0

Q ss_pred             HHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           96 IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      |+++|+++||||.|||+.+|+++++|++||+|+..|+.+.+.+|+++|||+++
T Consensus         1 ik~~r~~~gls~~~la~~~gis~~~i~~~~~g~~~~~~~~~~~ia~~l~~~~~   53 (55)
T PF01381_consen    1 IKELRKEKGLSQKELAEKLGISRSTISRIENGKRNPSLDTLKKIAKALGVSPE   53 (55)
T ss_dssp             HHHHHHHTTS-HHHHHHHHTS-HHHHHHHHTTSSTSBHHHHHHHHHHHTSEHH
T ss_pred             CHHHHHHcCCCHHHHHHHhCCCcchhHHHhcCCCCCCHHHHHHHHHHHCCCHH
Confidence            68899999999999999999999999999999999999999999999999864

; 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 ....

>COG1476 Predicted transcriptional regulators [Transcription]

Probab=99.47  E-value=9.7e-14  Score=91.07  Aligned_cols=56  Identities=29%  Similarity=0.431  Sum_probs=53.6

Q ss_pred             HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 031871           94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG  149 (151)
Q Consensus        94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~e  149 (151)
                      .+++++|.+.|+||.+||+.+|||++||..||+|+..|+.....+||+.|++++++
T Consensus         4 nk~k~~R~~~~ltQ~elA~~vgVsRQTi~~iEkgky~Psl~La~kia~~f~~~ied   59 (68)
T COG1476           4 NKLKELRAELGLTQEELAKLVGVSRQTIIAIEKGKYNPSLELALKIARVFGKTIED   59 (68)
T ss_pred             hHHHHHHHHhCcCHHHHHHHcCcCHHHHHHHHcCCCCchHHHHHHHHHHhCCCHHH
Confidence            48999999999999999999999999999999999999999999999999998764

>TIGR00270 conserved hypothetical protein TIGR00270

Probab=99.46  E-value=1.3e-13  Score=104.13  Aligned_cols=63  Identities=30%  Similarity=0.469  Sum_probs=59.7

Q ss_pred             cchHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 031871           87 RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG  149 (151)
Q Consensus        87 ~~~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~e  149 (151)
                      .+...|+.+|+.+|+++||||.+||+++|+++++|++||+|+..|+.+.+.+|+++||+++.+
T Consensus        65 ~l~~~~g~~Ir~~Re~~glSqeeLA~~lgvs~s~IsriE~G~~~Ps~~~l~kLa~~Lgvsl~e  127 (154)
T TIGR00270        65 ELVEDYGIIIRREREKRGWSQEQLAKKIQEKESLIKKIENAEIEPEPKVVEKLEKLLKIKLRE  127 (154)
T ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHhCCCHHH
Confidence            446789999999999999999999999999999999999999999999999999999999864

>PRK09726 antitoxin HipB; Provisional

Probab=99.44  E-value=5.5e-13  Score=91.54  Aligned_cols=60  Identities=25%  Similarity=0.361  Sum_probs=57.5

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      ...++.+|+.+|..+|+||.+||+.+|+++++|++||+|...|+.+.+.+||++|||+++
T Consensus        10 ~~~l~~~lk~~R~~~gltq~elA~~~gvs~~tis~~e~g~~~ps~~~l~~ia~~lgv~~~   69 (88)
T PRK09726         10 PTQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELSMT   69 (88)
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHcCCCcc
Confidence            468999999999999999999999999999999999999999999999999999999975

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

Probab=99.44  E-value=1.7e-13  Score=88.42  Aligned_cols=58  Identities=29%  Similarity=0.461  Sum_probs=50.4

Q ss_pred             HHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCCC
Q 031871           91 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA-IPNQQILTKLERALGVKLR  148 (151)
Q Consensus        91 ~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~-~p~~~~l~kLa~~Lgv~l~  148 (151)
                      .||..|+.+|+..||||.++|+.+|+|+++|++||+|+. .|+.+.+.+|+++||++.+
T Consensus         1 ~lg~~lr~~R~~~gls~~~lA~~~g~s~s~v~~iE~G~~~~p~~~~l~~l~~~l~~~~~   59 (64)
T PF13560_consen    1 QLGRRLRRLRERAGLSQAQLADRLGVSQSTVSRIERGRRPRPSPDTLQRLARALGVPPD   59 (64)
T ss_dssp             HHHHHHHHHHHCHTS-HHHHHHHHTS-HHHHHHHHTTSSSS-BHHHHHHHHHHTT--HH
T ss_pred             CHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCCHHHHHHHHHHHCcCHH
Confidence            378999999999999999999999999999999999999 5999999999999999864

>PRK09706 transcriptional repressor DicA; Reviewed

Probab=99.40  E-value=6.4e-13  Score=97.64  Aligned_cols=59  Identities=25%  Similarity=0.294  Sum_probs=56.6

Q ss_pred             HHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           90 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        90 ~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      ..|+.+|+.+|..+||||.+||+.+||++++|++||+|...|+.+.+.+||++|||+++
T Consensus         4 ~~~g~rlk~~R~~~gltq~~lA~~~gvs~~~is~~E~g~~~p~~~~l~~la~~l~vs~~   62 (135)
T PRK09706          4 LTLGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKALQCSPT   62 (135)
T ss_pred             hhHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHH
Confidence            56899999999999999999999999999999999999999999999999999999865

>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional

Probab=99.32  E-value=3.8e-12  Score=97.90  Aligned_cols=60  Identities=25%  Similarity=0.300  Sum_probs=57.4

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      .+.++.+|+.+|+++||||.+||+.+|+|+++|++||+|+..|+...+.+||++|||+++
T Consensus         5 ~~~~g~~l~~~R~~~glt~~elA~~~gis~~~is~~E~g~~~p~~~~l~~ia~~l~v~~~   64 (185)
T PRK09943          5 GLAPGKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSLS   64 (185)
T ss_pred             hhHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHH
Confidence            456999999999999999999999999999999999999999999999999999999875

>PRK13890 conjugal transfer protein TrbA; Provisional

Probab=99.32  E-value=5.1e-12  Score=91.69  Aligned_cols=60  Identities=15%  Similarity=0.295  Sum_probs=56.6

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      ...|+.+|+++|.++||||.|||+.+|+|+++|++||+|+..|+.+++.+||++|||+++
T Consensus         3 ~~i~~~~l~~ll~~~Glsq~eLA~~~Gis~~~is~iE~g~~~ps~~~l~kIa~aL~v~~~   62 (120)
T PRK13890          3 NYIFFTNVLRLLDERHMTKKELSERSGVSISFLSDLTTGKANPSLKVMEAIADALETPLP   62 (120)
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHCCCHH
Confidence            357899999999999999999999999999999999999999999999999999999654

>TIGR02607 antidote_HigA addiction module antidote protein, HigA family

Probab=99.30  E-value=8.6e-12  Score=82.86  Aligned_cols=58  Identities=14%  Similarity=0.163  Sum_probs=54.5

Q ss_pred             HHHHHHH-HHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           91 ELKKAIV-QARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        91 ~~~~~Lk-~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      ..+++|+ .+|++.|+||.+||+.+|+++++|++||+|...|+.+.+.+|+++|||+++
T Consensus         4 ~~g~~i~~~~~~~~~~t~~~lA~~~gis~~tis~~~~g~~~~~~~~~~~l~~~l~v~~~   62 (78)
T TIGR02607         4 HPGEILREEFLEPLGLSIRALAKALGVSRSTLSRIVNGRRGITADMALRLAKALGTSPE   62 (78)
T ss_pred             CHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHcCCCHH
Confidence            4578899 899999999999999999999999999999999999999999999999864

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.

>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein

Probab=99.26  E-value=1.7e-11  Score=84.71  Aligned_cols=59  Identities=27%  Similarity=0.345  Sum_probs=55.0

Q ss_pred             chHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           88 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        88 ~~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      -...++.+|+.+|+++||||  ||+++||++++|++||+|+..|+.+.+.+||++||+++.
T Consensus        29 ~~~~~~~~l~~~r~~~glSq--LAe~~GIs~stLs~iE~g~~~Ps~~tL~kI~~aLgi~l~   87 (89)
T TIGR02684        29 DPAYIAHALGYIARARGMTQ--LARKTGLSRESLYKALSGKGNPTFDTILKVTKALGLKLT   87 (89)
T ss_pred             CHHHHHHHHHHHHHHCChHH--HHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHcCCcee
Confidence            34678999999999999995  999999999999999999999999999999999999874

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.

>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed

Probab=99.26  E-value=1.8e-11  Score=101.23  Aligned_cols=60  Identities=23%  Similarity=0.339  Sum_probs=57.7

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      ...++++|+.+|+++||||.+||+.+|+|+++|++||+|+..|+.+.+.+||++|||+++
T Consensus        26 ~~~~g~rl~~~R~~~gltq~~lA~~~gvs~~~i~~~E~g~~~ps~~~l~~ia~~l~v~~~   85 (309)
T PRK08154         26 LAALGERVRTLRARRGMSRKVLAQASGVSERYLAQLESGQGNVSILLLRRVARALGCSLA   85 (309)
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHhCCCHH
Confidence            467999999999999999999999999999999999999999999999999999999875

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

Probab=99.25  E-value=1.5e-11  Score=93.36  Aligned_cols=65  Identities=37%  Similarity=0.546  Sum_probs=61.4

Q ss_pred             CcchHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCCC
Q 031871           86 DRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRGK  150 (151)
Q Consensus        86 ~~~~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~e~  150 (151)
                      ..+..+++++|+.+|+.+||||+|||++++++.+.|.+||+|+..|+...+.+|+++||+.+.++
T Consensus        74 ~elvedY~e~Ir~ARE~~G~SqedLA~ki~ek~svI~~iE~g~~~P~~~~akkLEk~LgIkL~e~  138 (165)
T COG1813          74 PELVEDYGERIREAREKRGLSQEDLAAKLKEKVSVIRRIERGEATPNIKVAKKLEKLLGIKLVEK  138 (165)
T ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHhcccHHHHHHHHhcccCccHHHHHHHHHHhCceeeee
Confidence            35578999999999999999999999999999999999999999999999999999999998764

>PRK10072 putative transcriptional regulator; Provisional

Probab=99.18  E-value=6.6e-11  Score=82.87  Aligned_cols=54  Identities=22%  Similarity=0.316  Sum_probs=50.1

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL  147 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l  147 (151)
                      ...|+.+|...||||.+||+.+|+|.++|++||+|++.|+...+ .|+++|++++
T Consensus        35 ~~eik~LR~~~glTQ~elA~~lGvS~~TVs~WE~G~r~P~~~~l-~Ll~~L~~~P   88 (96)
T PRK10072         35 FTEFEQLRKGTGLKIDDFARVLGVSVAMVKEWESRRVKPSSAEL-KLMRLIQANP   88 (96)
T ss_pred             hHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHH-HHHHHHhhCH
Confidence            44599999999999999999999999999999999999999986 5999999886

>TIGR02612 mob_myst_A mobile mystery protein A

Probab=99.13  E-value=1.2e-10  Score=87.58  Aligned_cols=55  Identities=18%  Similarity=0.194  Sum_probs=51.5

Q ss_pred             HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCC--CCHHHHHHHHHHhCCCCC
Q 031871           94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAI--PNQQILTKLERALGVKLR  148 (151)
Q Consensus        94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~--p~~~~l~kLa~~Lgv~l~  148 (151)
                      ..|+.+|...||||.+||+++|||+++|++||+|+..  |+.+.+.+||++|||++.
T Consensus        28 ~~Ir~~R~~lGmTq~eLAerlGVS~~tIs~iE~G~~~~~psl~~L~kIA~aLgv~~~   84 (150)
T TIGR02612        28 GWVRAIRKALGMSGAQLAGRLGVTPQRVEALEKSELSGTVTLKTLRAAAEALDCTFV   84 (150)
T ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCCCHHHHHHHHHHcCCCHH
Confidence            6799999999999999999999999999999999864  899999999999999853

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).

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

Probab=99.12  E-value=7.5e-11  Score=75.42  Aligned_cols=55  Identities=20%  Similarity=0.291  Sum_probs=42.4

Q ss_pred             HHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhCCCCCC
Q 031871           95 AIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK-AIPNQQILTKLERALGVKLRG  149 (151)
Q Consensus        95 ~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~-~~p~~~~l~kLa~~Lgv~l~e  149 (151)
                      +|+.+..++|+|+.+||+.+|++++++++|-+|+ ..|+.+.+.+||++|||++++
T Consensus         1 ~L~~~m~~~~it~~~La~~~gis~~tl~~~~~~~~~~~~~~~l~~ia~~l~~~~~e   56 (63)
T PF13443_consen    1 KLKELMAERGITQKDLARKTGISRSTLSRILNGKPSNPSLDTLEKIAKALNCSPEE   56 (63)
T ss_dssp             HHHHHHHHTT--HHHHHHHHT--HHHHHHHHTTT-----HHHHHHHHHHHT--HHH
T ss_pred             CHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcccccccHHHHHHHHHHcCCCHHH
Confidence            5889999999999999999999999999999998 689999999999999998753

>PRK04140 hypothetical protein; Provisional

Probab=99.09  E-value=2.5e-10  Score=95.13  Aligned_cols=60  Identities=25%  Similarity=0.313  Sum_probs=56.8

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      ....+++|+.+|+++||||.+||+.+|+|+++|++||+|+..|+.+.+.+|+++||+++.
T Consensus       124 v~i~GerLk~lRe~~GlSq~eLA~~lGVSr~tIskyE~G~~~Ps~e~~~kLa~~Lgv~l~  183 (317)
T PRK04140        124 VKIDGDVLREAREELGLSLGELASELGVSRRTISKYENGGMNASIEVAIKLEEILDVPLT  183 (317)
T ss_pred             ehhhHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCChH
Confidence            356799999999999999999999999999999999999999999999999999999864

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

Probab=99.07  E-value=5.7e-10  Score=66.55  Aligned_cols=53  Identities=36%  Similarity=0.543  Sum_probs=50.2

Q ss_pred             HHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           96 IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      |+.+|...++|+.+||+.+|+++.+|++|++|...|+.+.+.+|+++||+++.
T Consensus         2 i~~~~~~~~~s~~~la~~~~i~~~~i~~~~~~~~~~~~~~~~~i~~~~~~~~~   54 (56)
T smart00530        2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLD   54 (56)
T ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHhCCChh
Confidence            67788999999999999999999999999999999999999999999999875

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

Probab=99.00  E-value=1.7e-09  Score=64.91  Aligned_cols=55  Identities=36%  Similarity=0.529  Sum_probs=51.5

Q ss_pred             HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      +.|+..|...|+|+.++|+.+|+++.+|++|++|...|+...+.+|++.||++++
T Consensus         2 ~~l~~~~~~~~~s~~~~a~~~~~~~~~v~~~~~g~~~~~~~~~~~i~~~~~~~~~   56 (58)
T cd00093           2 ERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLD   56 (58)
T ss_pred             hHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCChh
Confidence            4578888999999999999999999999999999999999999999999999875

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

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

Probab=98.96  E-value=1.5e-09  Score=78.24  Aligned_cols=58  Identities=26%  Similarity=0.324  Sum_probs=52.2

Q ss_pred             HHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           90 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        90 ~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      ...+..|+.+|...|+||.+||+.+|+++++|++||+|+..|+.. +.+|++.|+++++
T Consensus        64 ~~~~~~i~~~r~~~gltq~~lA~~lg~~~~tis~~e~g~~~p~~~-~~~l~~~l~~~p~  121 (127)
T TIGR03830        64 LLTPPEIRRIRKKLGLSQREAAELLGGGVNAFSRYERGEVRPSKA-LDKLLRLLDKHPE  121 (127)
T ss_pred             CcCHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHH-HHHHHHHHHHChH
Confidence            456778999999999999999999999999999999999988865 6788899998875

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.

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

Probab=98.96  E-value=1.7e-09  Score=72.94  Aligned_cols=60  Identities=27%  Similarity=0.349  Sum_probs=49.4

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhCCCCC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK-AIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~-~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      ...+...|.++|+++||||.|+|+.+|++++.|+++|+|+ ..++.+.|.+++..||..++
T Consensus        16 k~~l~~~i~~~~~~~~ltQ~e~A~~lgisq~~vS~l~~g~~~~~sl~~L~~~l~aLG~~v~   76 (80)
T PF13744_consen   16 KAQLMAAIRELREERGLTQAELAERLGISQPRVSRLENGKIDDFSLDTLLRYLEALGGRVE   76 (80)
T ss_dssp             HHHHHHHHHHHHHCCT--HHHHHHHHTS-HHHHHHHHTT-GCC--HHHHHHHHHHTTEEEE
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHCCChhHHHHHHcCcccCCCHHHHHHHHHHcCCeEE
Confidence            5677888999999999999999999999999999999987 67899999999999997653

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

Probab=98.89  E-value=4.3e-09  Score=79.88  Aligned_cols=52  Identities=23%  Similarity=0.319  Sum_probs=49.1

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALG  144 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lg  144 (151)
                      .+-|++.|++.|+||++||++.|+|+++|.++|.|+..|....+.+|.++|.
T Consensus         7 pedlrk~Rk~LGitQ~dLA~~aGVSQ~~IArlE~G~vdPrlSt~k~Il~aL~   58 (187)
T COG3620           7 PEDLRKRRKELGITQKDLARRAGVSQPYIARLEAGKVDPRLSTVKRILEALE   58 (187)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHcCccHHHHHHHhcCCCCccHHHHHHHHHHHH
Confidence            5669999999999999999999999999999999999999999999999874

>PHA00542 putative Cro-like protein

Probab=98.84  E-value=1.4e-08  Score=69.02  Aligned_cols=50  Identities=22%  Similarity=0.245  Sum_probs=45.4

Q ss_pred             HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHh
Q 031871           94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK-AIPNQQILTKLERAL  143 (151)
Q Consensus        94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~-~~p~~~~l~kLa~~L  143 (151)
                      .++..++...|+||.+||+.+||++++|++||+|. ..|+.+.+.+|++++
T Consensus        21 ~~l~~~l~~~glTq~elA~~lgIs~~tIsr~e~g~~~~p~~~~l~ki~~~~   71 (82)
T PHA00542         21 DELVCALIRAGWSQEQIADATDVSQPTICRIYSGRHKDPRYSVVEKLRHLV   71 (82)
T ss_pred             HHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHHHHHH
Confidence            35667788899999999999999999999999999 479999999999876

>PRK10856 cytoskeletal protein RodZ; Provisional

Probab=98.83  E-value=6.7e-09  Score=87.11  Aligned_cols=59  Identities=20%  Similarity=0.213  Sum_probs=54.0

Q ss_pred             HHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCH------HHHHHHHHHhCCCCC
Q 031871           90 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQ------QILTKLERALGVKLR  148 (151)
Q Consensus        90 ~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~------~~l~kLa~~Lgv~l~  148 (151)
                      +.+|.+|+++|+++||||.+||+++++++++|++||+|+..+..      ..+..+|++|||+.+
T Consensus        13 ~~~G~~Lr~aRe~~GlSq~~vA~~l~l~~~~I~~iE~g~~~~~~~~tf~RGyir~yA~~lgv~~~   77 (331)
T PRK10856         13 LTTGERLRQAREQLGLTQQAVAERLCLKVSTVRDIEEDKAPADLASTFLRGYIRSYARLVHIPEE   77 (331)
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHCCCCCCChhHHHHHHHHHHHHHHHCcCHH
Confidence            46899999999999999999999999999999999999987766      458899999999865

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

Probab=98.78  E-value=3e-08  Score=66.26  Aligned_cols=53  Identities=19%  Similarity=0.178  Sum_probs=44.7

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhC------CCHHHHHHHHcCCCCCCHHHHHHHHHHh
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLIN------EKPQVIQEYESGKAIPNQQILTKLERAL  143 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lg------is~s~Is~~E~G~~~p~~~~l~kLa~~L  143 (151)
                      .+.|+.+|+..|...|+||.|||+.+|      +|+++|++||+|.  .+...+.+|--+|
T Consensus         9 le~~~~~lk~~R~~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es~~--ls~~n~~kl~p~l   67 (75)
T smart00352        9 LEAFAKTFKQRRIKLGFTQADVGLALGALYGPDFSQTTICRFEALQ--LSFKNMCKLKPLL   67 (75)
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHhcccccCcCCHHHHHHHHhcC--ccHHHHHHHHHHH
Confidence            467999999999999999999999999      5999999999986  4666666654433

>COG2944 Predicted transcriptional regulator [Transcription]

Probab=98.72  E-value=2.9e-08  Score=70.28  Aligned_cols=45  Identities=20%  Similarity=0.338  Sum_probs=40.8

Q ss_pred             HHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHH
Q 031871           92 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQIL  136 (151)
Q Consensus        92 ~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l  136 (151)
                      -+..|+.+|+..||||.+||..+|+|.+||++||+|+..|+-.-+
T Consensus        45 s~~eIk~iRe~~~lSQ~vFA~~L~vs~~Tv~~WEqGr~kPsg~Al   89 (104)
T COG2944          45 SPTEIKAIREKLGLSQPVFARYLGVSVSTVRKWEQGRKKPSGAAL   89 (104)
T ss_pred             CHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHcCCcCCCCHHH
Confidence            366799999999999999999999999999999999999976543

>PRK02866 cyanate hydratase; Validated

Probab=98.69  E-value=8.6e-08  Score=71.80  Aligned_cols=59  Identities=22%  Similarity=0.254  Sum_probs=55.5

Q ss_pred             HHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           90 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        90 ~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      ..+.+.|..+|.++|+|++++|+.+|+|..++..++.|...++.+.+.+|+++||++.+
T Consensus         4 ~~~~e~Ll~AK~~kGLTw~~IA~~iG~S~v~vaaa~lGQ~~ls~e~A~kla~~LgL~~~   62 (147)
T PRK02866          4 EELTEKILAAKKEKGLTWADIAEAIGLSEVWVTAALLGQMTLPAEEAEKVAELLGLDED   62 (147)
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHhCCCCCCHHHHHHHHHHhCCCHH
Confidence            46788999999999999999999999999999999999999999999999999998743

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

Probab=98.68  E-value=4.3e-08  Score=85.92  Aligned_cols=59  Identities=27%  Similarity=0.361  Sum_probs=55.3

Q ss_pred             HHHHHHHHHHHhcCCcCHHHHHHHh-----CCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           90 SELKKAIVQARNDKKLTQSQLAQLI-----NEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        90 ~~~~~~Lk~~R~~~glTQ~eLA~~l-----gis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      +.|+++|+.+|+++|+||.+||+.+     |+++++|++||+|+..|+.+.+.+|+++|||+++
T Consensus         2 ~~~~~rL~~~r~~~g~tq~~la~~~~~~g~~vs~~~is~~e~g~~~p~~~~l~~la~~l~v~~~   65 (517)
T PRK13355          2 TTFAERLKQAMKARGLKQEDLVHAAEARGVKLGKSHISQYVSGKTGPRRDVLPFLAAILGVSED   65 (517)
T ss_pred             chHHHHHHHHHHHCCCCHHHHHHHHHhccCCcCHHHHHHHHCCCCCCCHHHHHHHHHHhCcCHH
Confidence            3678999999999999999999996     6999999999999999999999999999999975

>COG1709 Predicted transcriptional regulator [Transcription]

Probab=98.63  E-value=2.8e-08  Score=78.57  Aligned_cols=57  Identities=26%  Similarity=0.424  Sum_probs=52.1

Q ss_pred             cchHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCC-CCHHHHHHHHHHh
Q 031871           87 RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAI-PNQQILTKLERAL  143 (151)
Q Consensus        87 ~~~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~-p~~~~l~kLa~~L  143 (151)
                      .+.++.|+.|++||+..+.||.+||+.+|+|++.||.||.|++. |....+.++-++|
T Consensus        23 vlS~~pge~lrKWR~~F~vSQ~elA~~l~vSpSVISDYE~GRRk~Pg~~~vkk~V~AL   80 (241)
T COG1709          23 VLSEDPGETLRKWREIFNVSQTELARELGVSPSVISDYESGRRKSPGIAFVKKFVEAL   80 (241)
T ss_pred             EecCChhHHHHHHHHHhCccHHHHHHHhCCCcceeehhhccCccCccHHHHHHHHHHH
Confidence            34678899999999999999999999999999999999999988 9999888887765

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

Probab=98.56  E-value=2.2e-07  Score=65.67  Aligned_cols=56  Identities=18%  Similarity=0.275  Sum_probs=49.6

Q ss_pred             HHHHHHH-HhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           93 KKAIVQA-RNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        93 ~~~Lk~~-R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      |+.|++- .+..|+||.+||+.+||++.+|+++-+|++.++.+++.+|+++||.+++
T Consensus        11 GEiL~eeflep~glt~~~lA~~lgV~r~~is~ling~~~iT~dmAlrL~k~fGtspe   67 (104)
T COG3093          11 GEILREEFLEPLGLTQTELAEALGVTRNTISELINGRRAITADMALRLAKVFGTSPE   67 (104)
T ss_pred             hHHHHHHHhccccCCHHHHHHHhCCCHHHHHHHHcCCcCCCHHHHHHHHHHhCCCHH
Confidence            5556543 5556999999999999999999999999999999999999999998864

>TIGR00673 cynS cyanate hydratase

Probab=98.54  E-value=3.7e-07  Score=68.56  Aligned_cols=56  Identities=16%  Similarity=0.174  Sum_probs=53.9

Q ss_pred             HHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 031871           92 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL  147 (151)
Q Consensus        92 ~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l  147 (151)
                      +.+.|..+|.++|||++++|+.+|+|...+..++.|...++.+.+.+|+++||++-
T Consensus         9 ~t~~Ll~AK~~KGLTwe~IAe~iG~sevwvaaa~lGQ~~ls~e~A~kla~lLgL~~   64 (150)
T TIGR00673         9 LADALLESKKKKGLTFADIADGLGLAEVFVAAALYGQAAAPADEARLVGAKLDLDE   64 (150)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHhCCCCCCHHHHHHHHHHhCcCH
Confidence            78899999999999999999999999999999999999999999999999999864

Alternate names include cyanate lyase, cyanase and cyanate hydrolase.

>COG3655 Predicted transcriptional regulator [Transcription]

Probab=98.37  E-value=7.9e-07  Score=59.14  Aligned_cols=58  Identities=19%  Similarity=0.232  Sum_probs=51.7

Q ss_pred             HHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCC-CCHHHHHHHHHHhCCCCCC
Q 031871           92 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAI-PNQQILTKLERALGVKLRG  149 (151)
Q Consensus        92 ~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~-p~~~~l~kLa~~Lgv~l~e  149 (151)
                      +..++..++.+++++..|||+.+|+|.++++.+.+|+.. ++.++|.+||++|+|.+.+
T Consensus         3 i~~~l~~~l~~r~~~~~eLa~~igis~~~ls~l~~gk~k~I~~~tL~~iC~~LeCqpgD   61 (73)
T COG3655           3 IAVRLDVMLADRKISLKELAEAIGISEANLSKLKTGKVKAIRLSTLEKICKALECQPGD   61 (73)
T ss_pred             chHhHHHHHHHHhhhHHHHHHHHcccHHHHHHHHcCCcceeeHHHHHHHHHHcCCChhh
Confidence            345678888899999999999999999999999999854 6999999999999998753

>COG1396 HipB Predicted transcriptional regulators [Transcription]

Probab=98.37  E-value=2.6e-06  Score=55.06  Aligned_cols=56  Identities=30%  Similarity=0.520  Sum_probs=52.6

Q ss_pred             HHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCC
Q 031871           92 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA-IPNQQILTKLERALGVKL  147 (151)
Q Consensus        92 ~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~-~p~~~~l~kLa~~Lgv~l  147 (151)
                      ++.+++.+|...|+||.++|..+|++..+++.||+|.. .|....+..++..|+++.
T Consensus         2 ~~~~~~~~r~~~~~s~~~~a~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~   58 (120)
T COG1396           2 IGERLKELRKKKGLSQEELAERLGVSRSTISRIERGRSESPSLELLARLAAALGVSL   58 (120)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCCHHHHHHHHHHHCCCH
Confidence            57899999999999999999999999999999999999 899999999999988754

>COG1395 Predicted transcriptional regulator [Transcription]

Probab=98.30  E-value=1.4e-06  Score=72.20  Aligned_cols=57  Identities=19%  Similarity=0.330  Sum_probs=54.2

Q ss_pred             HHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           92 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        92 ~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      -|+.|++.|+++|+|..+||..+|+|+.+|++||+|...|+.+.+.+|.+.||.++-
T Consensus       126 dge~Lre~Ree~glSlG~lA~~lgVSRktV~~YE~G~~~~sleva~kLeei~g~~iv  182 (313)
T COG1395         126 DGEKLREKREEMGLSLGDLATMLGVSRKTVYKYEKGLSDASLEVALKLEEIFGEDIV  182 (313)
T ss_pred             chHHHHHHHHHcCcCHHHHHHHhCccHHHHHHhccCCCCccHHHHHHHHHHhcchhh
Confidence            488999999999999999999999999999999999999999999999999998764

>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=98.26  E-value=3.8e-07  Score=59.35  Aligned_cols=53  Identities=19%  Similarity=0.332  Sum_probs=37.5

Q ss_pred             HHHHHHhcCCcC-HHHHHHHhCCCHHHHH-HHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           95 AIVQARNDKKLT-QSQLAQLINEKPQVIQ-EYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        95 ~Lk~~R~~~glT-Q~eLA~~lgis~s~Is-~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      +|+++++..|.+ +.+||+.+|||+++|+ .|......| .+.+.+|+..+||+++
T Consensus         2 ~i~rl~~~~g~~~~~~lA~~lgis~st~s~~~~~r~~~P-~~~l~~ia~~~gvsl~   56 (66)
T PF07022_consen    2 VIERLKEALGVKSDKELAERLGISKSTLSNNWKKRGSIP-AEWLIKIALETGVSLD   56 (66)
T ss_dssp             HHHHHHHHHT-SSCHHHHCCTT--HHHHH-HHHHSSS---HHHHHHHHHHH---HH
T ss_pred             HHHHHHHHhCCCCHHHHHHHhCcCHHHhhHHHHhCCCCC-HHHHHHHHHHHCcCHH
Confidence            456666666665 5699999999999999 898877766 9999999999999874

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.

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

Probab=98.18  E-value=7.3e-06  Score=52.86  Aligned_cols=54  Identities=24%  Similarity=0.374  Sum_probs=40.3

Q ss_pred             HHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCC--CCCCH----HHHHHHHHHhCCCCC
Q 031871           95 AIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK--AIPNQ----QILTKLERALGVKLR  148 (151)
Q Consensus        95 ~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~--~~p~~----~~l~kLa~~Lgv~l~  148 (151)
                      +|+..|+.+|+|..|+|..++|+.++|..+|+|.  ..|..    ..+.++|++||++.+
T Consensus         1 ~Lr~~R~~~glsl~~va~~t~I~~~~l~aiE~~~~~~lp~~~y~rg~lr~Ya~~Lgld~~   60 (62)
T PF13413_consen    1 RLREAREAKGLSLEDVAEETKISVSYLEAIENGDFDSLPSPVYARGYLRKYARFLGLDPD   60 (62)
T ss_dssp             -HHHHHHCTT--HHHHHHHCS--HHHHHHHHCT-GCCSSSHHHHHHHHHHHHHHTT--HH
T ss_pred             ChHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCcChhhCCcHHHHHHHHHHHHHHhCcCcc
Confidence            4899999999999999999999999999999996  44543    468899999998754

>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=97.96  E-value=2.6e-05  Score=58.48  Aligned_cols=60  Identities=15%  Similarity=0.211  Sum_probs=54.7

Q ss_pred             hHHHHHHHHHHHhcCCcCH----HHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           89 PSELKKAIVQARNDKKLTQ----SQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ----~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      ...+.++|+.+...+|+.+    .+||+.+|+|+++.++-.+|+..++...+.+|++.||++++
T Consensus         3 ~~~~~erV~~Ll~~~Gi~kr~~~s~LA~iL~Is~ssa~RKL~G~~~ftl~EI~~Ia~~fgvS~d   66 (147)
T PF08667_consen    3 DQAIAERVRELLDRKGIPKRKHASELADILGISYSSAYRKLNGKSPFTLEEIKKIAKHFGVSPD   66 (147)
T ss_pred             hHHHHHHHHHHHHHcCCcchhhHHHHHHHHCCCHHHHHHHhcCCCCCCHHHHHHHHHHhCcCHH
Confidence            3568899999999999766    56999999999999999999999999999999999999975

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 [].

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

Probab=97.87  E-value=4.3e-05  Score=46.57  Aligned_cols=40  Identities=13%  Similarity=0.185  Sum_probs=33.1

Q ss_pred             HHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCC
Q 031871          109 QLAQLINEKPQVIQEYESGKAIPNQQI---LTKLERALGVKLR  148 (151)
Q Consensus       109 eLA~~lgis~s~Is~~E~G~~~p~~~~---l~kLa~~Lgv~l~  148 (151)
                      +||+.+|+|+++|++|++|...++...   +.++++.||+.++
T Consensus         2 ~lA~~~gvs~~tvs~~l~g~~~vs~~~~~~i~~~~~~l~~~~~   44 (52)
T cd01392           2 DIARAAGVSVATVSRVLNGKPRVSEETRERVLAAAEELGYRPN   44 (52)
T ss_pred             cHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHHHhCCCCC
Confidence            799999999999999999997766554   5558888888654

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

>COG5499 Predicted transcription regulator containing HTH domain [Transcription]

Probab=97.86  E-value=2.6e-05  Score=55.61  Aligned_cols=56  Identities=20%  Similarity=0.225  Sum_probs=51.2

Q ss_pred             HHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           92 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        92 ~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      =-+.|+.++...|+|+.+||..+| |.+.+|++.+|++..+.+++.+|.+.||++.+
T Consensus        61 pve~I~t~Md~~glt~~dLa~~iG-Sks~vS~iL~~rraLTle~ikkL~q~~gIpa~  116 (120)
T COG5499          61 PVEVIRTLMDQYGLTLADLANEIG-SKSRVSNILSGRRALTLEHIKKLHQRFGIPAD  116 (120)
T ss_pred             HHHHHHHHHHHhCCcHHHHHHHhC-chHHHHHHHhhhhHhhHHHHHHHHHHhCcCHH
Confidence            356789999999999999999998 77889999999999999999999999999864

>TIGR01321 TrpR trp operon repressor, proteobacterial

Probab=97.85  E-value=6.3e-05  Score=52.45  Aligned_cols=52  Identities=12%  Similarity=0.113  Sum_probs=40.6

Q ss_pred             HHHHHHHHHHH--hcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHH
Q 031871           90 SELKKAIVQAR--NDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLER  141 (151)
Q Consensus        90 ~~~~~~Lk~~R--~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~  141 (151)
                      ..+..|++-.+  ...++||.|+|+.+|||.+||++++++-...+++.-.-|.+
T Consensus        39 ~~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~sn~lk~~~~~~~~~l~~   92 (94)
T TIGR01321        39 EDLGDRIRIVNELLNGNMSQREIASKLGVSIATITRGSNNLKTMDPNFKQFLRK   92 (94)
T ss_pred             HHHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHHHhhcccCCHHHHHHHHh
Confidence            45666666665  35789999999999999999999999988666665555543

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.

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

Probab=97.83  E-value=3.2e-05  Score=63.77  Aligned_cols=58  Identities=21%  Similarity=0.357  Sum_probs=50.9

Q ss_pred             HHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCC--CCC----HHHHHHHHHHhCCCCC
Q 031871           91 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA--IPN----QQILTKLERALGVKLR  148 (151)
Q Consensus        91 ~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~--~p~----~~~l~kLa~~Lgv~l~  148 (151)
                      .+|++||+.|+++|||+.|+|.+++|..++|..+|.|.-  .|.    ...+...|++||++.+
T Consensus         3 ~~Ge~Lr~~Re~~gLsL~dva~~t~I~~~~L~aiEeg~~~~lp~~~y~rG~ir~YA~~l~ld~~   66 (284)
T COG1426           3 TLGERLRQAREEKGLSLEDVAARTKIRKSYLRALEEGNFDKLPGPVYIRGYIRSYAKFLGLDED   66 (284)
T ss_pred             cHHHHHHHHHHHcCCCHHHHHHHhCccHHHHHHHhcCccccccchHHHHHHHHHHHHHhCCCHH
Confidence            589999999999999999999999999999999999973  332    3467889999998865

>PHA01083 hypothetical protein

Probab=97.78  E-value=4.1e-05  Score=57.26  Aligned_cols=54  Identities=17%  Similarity=0.242  Sum_probs=45.3

Q ss_pred             HHHHHHhcCCc-CHHHHHHHhCCCHHHHHHHHcC-CCCCCHHHHHHHHHHhCCCCC
Q 031871           95 AIVQARNDKKL-TQSQLAQLINEKPQVIQEYESG-KAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        95 ~Lk~~R~~~gl-TQ~eLA~~lgis~s~Is~~E~G-~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      .|....+.+++ +-.+||+.+||+++.|++|.+| ++.++.+.+..||+.+|+++.
T Consensus         6 LLda~K~a~~~~sdkqLA~~LGVs~q~IS~~R~G~r~~i~de~A~~LAe~aGiDp~   61 (149)
T PHA01083          6 LLDAYKKAKNYVQYKQIAHDLGVSPQKISKMRTGVRTYISDEEAIFLAESAGIDPE   61 (149)
T ss_pred             HHHHHHHHHhhccHHHHHHHhCCCHHHHHHHHcCCCCCCCHHHHHHHHHHhCCCHH
Confidence            34444555554 4569999999999999999999 999999999999999999864

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

Probab=97.56  E-value=0.0002  Score=51.78  Aligned_cols=50  Identities=18%  Similarity=0.172  Sum_probs=38.3

Q ss_pred             HHHHHHHhcCCcCHHHHHHHhC--CCHHHHHHHHcCCCCCCHHHHHHHHHHh
Q 031871           94 KAIVQARNDKKLTQSQLAQLIN--EKPQVIQEYESGKAIPNQQILTKLERAL  143 (151)
Q Consensus        94 ~~Lk~~R~~~glTQ~eLA~~lg--is~s~Is~~E~G~~~p~~~~l~kLa~~L  143 (151)
                      -.|+.+|...+||+.|.|..++  ++..+..+||+|++.++.+++..|....
T Consensus         4 ~ELqalR~~l~lt~~EaA~~Ia~~v~~~tWq~WE~G~~~IP~~Vie~l~~m~   55 (118)
T PF08965_consen    4 LELQALRQILGLTVEEAAYYIAQDVSSRTWQQWEKGERPIPDDVIEELLEMK   55 (118)
T ss_dssp             HHHHHHHHHTT--HHHHHHHTSSS--HHHHHHHHTTSS---HHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCHHHHHHHHHccCCHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence            4589999999999999999999  9999999999999999999888776543

; PDB: 1S4K_A.

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

Probab=97.56  E-value=0.00031  Score=42.69  Aligned_cols=40  Identities=13%  Similarity=0.189  Sum_probs=32.7

Q ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHH---HHHhCC
Q 031871          106 TQSQLAQLINEKPQVIQEYESGKAIPNQQILTKL---ERALGV  145 (151)
Q Consensus       106 TQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kL---a~~Lgv  145 (151)
                      |.+|+|+.+|+|.+|||++.+|...++.+...+|   ++.||-
T Consensus         1 Ti~dIA~~agvS~~TVSr~ln~~~~vs~~tr~rI~~~a~~lgY   43 (46)
T PF00356_consen    1 TIKDIAREAGVSKSTVSRVLNGPPRVSEETRERILEAAEELGY   43 (46)
T ss_dssp             CHHHHHHHHTSSHHHHHHHHTTCSSSTHHHHHHHHHHHHHHTB
T ss_pred             CHHHHHHHHCcCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHCC
Confidence            6789999999999999999999988887766555   445553

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 ....

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

Probab=97.55  E-value=0.00036  Score=52.05  Aligned_cols=54  Identities=17%  Similarity=0.242  Sum_probs=49.8

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHh
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERAL  143 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~L  143 (151)
                      .+.|+..|+.+..++|||..|||++.|+..+++.++.+| +.|..+++.+|-+.+
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            468999999999999999999999999999999999999 789999999887765

>smart00354 HTH_LACI helix_turn _helix lactose operon repressor

Probab=97.51  E-value=0.00032  Score=45.86  Aligned_cols=43  Identities=14%  Similarity=0.139  Sum_probs=34.9

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESGKAIPNQQI---LTKLERALGVKL  147 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~---l~kLa~~Lgv~l  147 (151)
                      +|+.|+|+.+|+|.++|+++.+|....+.+.   +.++++.+|..+
T Consensus         1 ~t~~~iA~~~gvS~~TVSr~ln~~~~v~~~t~~~i~~~~~~~gy~~   46 (70)
T smart00354        1 ATIKDVARLAGVSKATVSRVLNGNGRVSEETREKVLAAMEELGYIP   46 (70)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCCC
Confidence            4789999999999999999999987776554   555677777654

>COG2522 Predicted transcriptional regulator [General function prediction only]

Probab=97.37  E-value=0.00057  Score=49.62  Aligned_cols=43  Identities=21%  Similarity=0.349  Sum_probs=34.4

Q ss_pred             chHHHHHHHH-HHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCC
Q 031871           88 VPSELKKAIV-QARNDKKLTQSQLAQLINEKPQVIQEYESGKAIP  131 (151)
Q Consensus        88 ~~~~~~~~Lk-~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p  131 (151)
                      +-+.+...|. .++.+ |+||.++|+.+|+|++.||+|-+|++.+
T Consensus         6 vlPaiRa~lA~~L~ee-G~Sq~~iA~LLGltqaAVS~Yls~krg~   49 (119)
T COG2522           6 VLPAIRALLAKELIEE-GLSQYRIAKLLGLTQAAVSQYLSGKRGS   49 (119)
T ss_pred             HHHHHHHHHHHHHHHc-CCcHHHHHHHhCCCHHHHHHHHccCCch
Confidence            3345555554 44555 9999999999999999999999999874

>COG5606 Uncharacterized conserved small protein [Function unknown]

Probab=97.11  E-value=0.00091  Score=45.90  Aligned_cols=60  Identities=23%  Similarity=0.237  Sum_probs=52.7

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCCC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA-IPNQQILTKLERALGVKLR  148 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~-~p~~~~l~kLa~~Lgv~l~  148 (151)
                      ...+...|..+.+..+|+|+++|+.+||+++.+|.+-+|+. ..+.+.|.-+....|..++
T Consensus        26 r~~l~~~i~~~i~q~~l~Q~qiae~lgV~qprvS~l~~gk~~~fs~dkLvtml~~~g~ei~   86 (91)
T COG5606          26 RSALMMAIKQWIEQAALSQAQIAELLGVTQPRVSDLARGKIQDFSIDKLVTMLARAGQEID   86 (91)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHhcchhHhhHHHHHHHHHHcCCccc
Confidence            56788889999999999999999999999999999999994 4688888888888887654

>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=97.08  E-value=0.0024  Score=42.72  Aligned_cols=53  Identities=19%  Similarity=0.160  Sum_probs=41.7

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhC------CCHHHHHHHHcCCCCCCHHHHHHHHHHh
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLIN------EKPQVIQEYESGKAIPNQQILTKLERAL  143 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lg------is~s~Is~~E~G~~~p~~~~l~kLa~~L  143 (151)
                      ...|+..++..|...|+||.+++..+|      .|+++|+++|+=  ..+...+.+|--.|
T Consensus         9 le~Fa~~fk~rRi~LG~TQ~dVg~al~~~~G~~~SQttI~RFE~L--~LS~kn~~klkP~L   67 (75)
T PF00157_consen    9 LEQFAKEFKQRRIKLGYTQADVGAALGRLYGKEFSQTTICRFEAL--QLSFKNMCKLKPLL   67 (75)
T ss_dssp             HHHHHHHHHHHHHHTT--HHHHHHHHHHHHSSGGSHHHHHHHHTT--TSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhhhhcccCHHHHhHHHHHhcCccccchhhhhhHhc--ccCHHHHHHHHHHH
Confidence            467999999999999999999998876      489999999984  46777777665443

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 ....

>TIGR03879 near_KaiC_dom probable regulatory domain

Probab=96.81  E-value=0.0052  Score=40.95  Aligned_cols=48  Identities=23%  Similarity=0.245  Sum_probs=36.3

Q ss_pred             HHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHH
Q 031871           91 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLE  140 (151)
Q Consensus        91 ~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa  140 (151)
                      .....+...|...|+|+.|+|+.+|+|.++|..+.+..  +....+.+++
T Consensus        19 ~~r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~~--~~~~~~~~~~   66 (73)
T TIGR03879        19 LAEAAAALAREEAGKTASEIAEELGRTEQTVRNHLKGE--TKAGGLVKLA   66 (73)
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcC--cccchHHHHH
Confidence            33444444477799999999999999999999999953  4555566665

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.

>TIGR02147 Fsuc_second hypothetical protein, TIGR02147

Probab=96.78  E-value=0.0039  Score=51.15  Aligned_cols=46  Identities=15%  Similarity=0.241  Sum_probs=42.9

Q ss_pred             CcCHHHHHHHhCCCH-HHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 031871          104 KLTQSQLAQLINEKP-QVIQEYESGKAIPNQQILTKLERALGVKLRG  149 (151)
Q Consensus       104 glTQ~eLA~~lgis~-s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~e  149 (151)
                      .+|-.+||+.+|++. ++++.+.+|++.++...+.+++++||++..|
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            699999999999877 9999999999999999999999999987654

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.

>COG3636 Predicted transcriptional regulator [Transcription]

Probab=96.75  E-value=0.0067  Score=42.48  Aligned_cols=56  Identities=16%  Similarity=0.194  Sum_probs=47.3

Q ss_pred             HHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 031871           90 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL  147 (151)
Q Consensus        90 ~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l  147 (151)
                      ..+...+...-..+|||  ++|++.|+++..+.+-.+...+|+.+++.++.++||+.+
T Consensus        37 a~i~~alg~var~~GMs--qvA~~aGlsRe~LYkaLS~~GNPtf~Til~V~kAlG~rl   92 (100)
T COG3636          37 ALIAAALGVVARSRGMS--QVARKAGLSREGLYKALSPGGNPTFDTILAVLKALGLRL   92 (100)
T ss_pred             HHHHHHHHHHHHhcCHH--HHHHHhCccHHHHHHHhCCCCCCcHHHHHHHHHHcCcee
Confidence            44555555555667876  589999999999999999999999999999999999865

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

Probab=96.73  E-value=0.0065  Score=43.67  Aligned_cols=74  Identities=19%  Similarity=0.234  Sum_probs=47.7

Q ss_pred             HHHHHHHHHcCCChhhHHhhhcCCCccCCCCcccccccccccchhhhHHHHHhhccCCcchHHHHHHHHHH-HhcCCcCH
Q 031871           29 EKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQA-RNDKKLTQ  107 (151)
Q Consensus        29 ~~~~~~a~r~g~~v~t~~k~~~g~~~~~~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~~~~~~~~~Lk~~-R~~~glTQ  107 (151)
                      .+..++|++.||+..|+.+|-.-.......+..+.-.++|.                    ..    |+.+ -....+|+
T Consensus        19 ~s~~eaa~~F~VS~~Tv~~W~k~~~~G~~~~k~r~~~Kid~--------------------~~----L~~~v~~~pd~tl   74 (119)
T PF01710_consen   19 KSIREAAKRFGVSRNTVYRWLKRKETGDLEPKPRGRKKIDR--------------------DE----LKALVEENPDATL   74 (119)
T ss_pred             chHHHHHHHhCcHHHHHHHHHHhcccccccccccccccccH--------------------HH----HHHHHHHCCCcCH
Confidence            46788999999999999999762111100010111113321                    11    2222 34678999


Q ss_pred             HHHHHHhCCCHHHHHHHHc
Q 031871          108 SQLAQLINEKPQVIQEYES  126 (151)
Q Consensus       108 ~eLA~~lgis~s~Is~~E~  126 (151)
                      .|+|+.+|||+++|.....
T Consensus        75 ~Ela~~l~Vs~~ti~~~Lk   93 (119)
T PF01710_consen   75 RELAERLGVSPSTIWRALK   93 (119)
T ss_pred             HHHHHHcCCCHHHHHHHHH
Confidence            9999999999999998864

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 [].

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

Probab=96.57  E-value=0.006  Score=41.13  Aligned_cols=52  Identities=15%  Similarity=0.095  Sum_probs=38.4

Q ss_pred             HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      ..|+.....+|+|..+||+..|++.++++....   .|....-..||++|||++.
T Consensus         5 adI~AaL~krG~sL~~lsr~~Gl~~~tl~nal~---r~~pk~E~~IA~aLgv~P~   56 (78)
T PF13693_consen    5 ADIKAALRKRGTSLAALSREAGLSSSTLRNALR---RPWPKGERIIADALGVPPE   56 (78)
T ss_dssp             HHHHHHHCTTS--HHHHHHHHSS-HHHHHHTTT---SS-HHHHHHHHHHTTS-HH
T ss_pred             HHHHHHHHHcCCCHHHHHHHcCCCHHHHHHHHc---CCChHHHHHHHHHHCcCHH
Confidence            346666778999999999999999999998754   4556667789999999875

>PHA00675 hypothetical protein

Probab=96.52  E-value=0.0075  Score=40.46  Aligned_cols=39  Identities=10%  Similarity=0.049  Sum_probs=34.0

Q ss_pred             HHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCC
Q 031871           91 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA  129 (151)
Q Consensus        91 ~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~  129 (151)
                      .--+.|+.+++..|.|+.+||..+|+|+++|+.|-+|++
T Consensus        26 ~qV~~IR~l~~r~G~s~~~IA~~fGVsrstV~~I~~gk~   64 (78)
T PHA00675         26 AEVERIRELHEVEGMSYAVLAEKFEQSKGAIAKICRYER   64 (78)
T ss_pred             HHHHHHHHHHHhcCccHHHHHHHhCCCHHHHHHHHccch
Confidence            345568888878899999999999999999999999874

>PHA02591 hypothetical protein; Provisional

Probab=96.38  E-value=0.0075  Score=40.63  Aligned_cols=26  Identities=19%  Similarity=0.325  Sum_probs=23.5

Q ss_pred             hcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871          101 NDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus       101 ~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      .+.|+||.++|+.+|+++.+|++|-.
T Consensus        56 ~eqGlSqeqIA~~LGVsqetVrKYL~   81 (83)
T PHA02591         56 ARKGFTVEKIASLLGVSVRKVRRYLE   81 (83)
T ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHHh
Confidence            45799999999999999999999864

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

Probab=96.34  E-value=0.0077  Score=36.23  Aligned_cols=24  Identities=4%  Similarity=0.097  Sum_probs=19.2

Q ss_pred             CcCHHHHHHHhCCCHHHHHHHHcC
Q 031871          104 KLTQSQLAQLINEKPQVIQEYESG  127 (151)
Q Consensus       104 glTQ~eLA~~lgis~s~Is~~E~G  127 (151)
                      |+|+.++|+.+|+|++||.+|-+-
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            999999999999999999999763

>PRK10014 DNA-binding transcriptional repressor MalI; Provisional

Probab=96.31  E-value=0.011  Score=48.11  Aligned_cols=45  Identities=20%  Similarity=0.127  Sum_probs=37.9

Q ss_pred             CCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHH---HHHhCCCC
Q 031871          103 KKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKL---ERALGVKL  147 (151)
Q Consensus       103 ~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kL---a~~Lgv~l  147 (151)
                      +..|.+|+|+++|||++|||++.||+..++.++..++   ++.||..+
T Consensus         5 ~~~Ti~dIA~~agVS~~TVSr~Ln~~~~vs~~tr~~V~~~a~elgY~p   52 (342)
T PRK10014          5 KKITIHDVALAAGVSVSTVSLVLSGKGRISTATGERVNQAIEELGFVR   52 (342)
T ss_pred             CCCcHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCCc
Confidence            3579999999999999999999999988887776655   77777654

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

Probab=96.27  E-value=0.0094  Score=38.19  Aligned_cols=40  Identities=20%  Similarity=0.242  Sum_probs=28.9

Q ss_pred             cCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCC
Q 031871          102 DKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGV  145 (151)
Q Consensus       102 ~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv  145 (151)
                      ..| ++..||+.+|||+++|+.|  +. .++......|..+-+=
T Consensus         8 ~~G-~~~~lAkalGVs~~aVs~W--~~-~IP~~ra~~Ie~~T~G   47 (60)
T PF14549_consen    8 YFG-GQSKLAKALGVSPQAVSQW--GE-RIPAERAYQIEKLTNG   47 (60)
T ss_dssp             HHS-SHHHHHHHHTS-HHHHHHH--HT-S--HHHHHHHHHHTTT
T ss_pred             HHC-CHHHHHHHHCCCHHHHHHh--cC-ccCHHHHHHHHHHhCC
Confidence            345 8999999999999999999  33 3566677777776553

>COG3423 Nlp Predicted transcriptional regulator [Transcription]

Probab=96.13  E-value=0.016  Score=38.88  Aligned_cols=51  Identities=18%  Similarity=0.199  Sum_probs=40.9

Q ss_pred             HHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 031871           96 IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG  149 (151)
Q Consensus        96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~e  149 (151)
                      |....+.+|+|...|+.+.|+|++|+.....- .-|..+  .-||++|||++.|
T Consensus        13 I~A~Lkk~G~Sl~~LS~~agls~~tL~n~L~r-p~pkgE--riIA~algv~P~e   63 (82)
T COG3423          13 IIAALKKKGTSLAALSREAGLSSSTLANALDR-PWPKGE--RIIADALGVPPEE   63 (82)
T ss_pred             HHHHHHHccccHHHHHHHcCCCHHHHHHHHcC-CCchHH--HHHHHHhCCCHHH
Confidence            45556678999999999999999999998773 335554  4589999999865

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

Probab=96.10  E-value=0.018  Score=42.26  Aligned_cols=48  Identities=8%  Similarity=0.063  Sum_probs=37.7

Q ss_pred             HHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHH
Q 031871           95 AIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERA  142 (151)
Q Consensus        95 ~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~  142 (151)
                      .+..+....|+|++++|..+|++++|++++-++...++.+.-.++.+.
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            345556778999999999999999999999987767776655555443

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.

>PRK09492 treR trehalose repressor; Provisional

Probab=96.08  E-value=0.014  Score=47.02  Aligned_cols=44  Identities=14%  Similarity=0.136  Sum_probs=36.1

Q ss_pred             CcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHH---HHHHhCCCC
Q 031871          104 KLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTK---LERALGVKL  147 (151)
Q Consensus       104 glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~k---La~~Lgv~l  147 (151)
                      .+|.+|+|+.+|||.+|||++.||...++.++..+   .++.||-.+
T Consensus         4 ~~ti~dIA~~agVS~~TVSrvLn~~~~vs~~tr~rV~~~a~elgY~p   50 (315)
T PRK09492          4 KLTIKDIARLSGVGKSTVSRVLNNESGVSEETRERVEAVINQHGFSP   50 (315)
T ss_pred             CCcHHHHHHHhCCCHHHHhHHhCCCCCCCHHHHHHHHHHHHHHCCCc
Confidence            47999999999999999999999987777766555   466777544

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

Probab=96.07  E-value=0.011  Score=35.18  Aligned_cols=30  Identities=7%  Similarity=0.124  Sum_probs=20.4

Q ss_pred             HHHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871           95 AIVQARNDKKLTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus        95 ~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E  125 (151)
                      .|..++ ..|+|+.++|+.+|++++||+++-
T Consensus        12 ~I~~l~-~~G~s~~~IA~~lg~s~sTV~rel   41 (44)
T PF13936_consen   12 QIEALL-EQGMSIREIAKRLGRSRSTVSREL   41 (44)
T ss_dssp             HHHHHH-CS---HHHHHHHTT--HHHHHHHH
T ss_pred             HHHHHH-HcCCCHHHHHHHHCcCcHHHHHHH
Confidence            355554 689999999999999999999864

>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=96.05  E-value=0.015  Score=34.74  Aligned_cols=33  Identities=9%  Similarity=0.172  Sum_probs=23.6

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      .+.+.+++. .|+|..++|+.+|||++||.+|.+
T Consensus        11 ~~~i~~l~~-~G~si~~IA~~~gvsr~TvyR~l~   43 (45)
T PF02796_consen   11 IEEIKELYA-EGMSIAEIAKQFGVSRSTVYRYLN   43 (45)
T ss_dssp             HHHHHHHHH-TT--HHHHHHHTTS-HHHHHHHHC
T ss_pred             HHHHHHHHH-CCCCHHHHHHHHCcCHHHHHHHHh
Confidence            344555554 459999999999999999999875

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 ....

>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID

Probab=96.05  E-value=0.059  Score=36.45  Aligned_cols=49  Identities=10%  Similarity=0.087  Sum_probs=39.7

Q ss_pred             HHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhC
Q 031871           95 AIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK-AIPNQQILTKLERALG  144 (151)
Q Consensus        95 ~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~-~~p~~~~l~kLa~~Lg  144 (151)
                      .+..++. ..+|..++|+.+|+|.+||++..++. ..++.++..++-++..
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            3444555 78899999999999999999999986 6788888877776654

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.

>PRK09526 lacI lac repressor; Reviewed

Probab=96.00  E-value=0.016  Score=47.29  Aligned_cols=45  Identities=11%  Similarity=-0.011  Sum_probs=35.6

Q ss_pred             CCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHH---HHHHHHhCCCC
Q 031871          103 KKLTQSQLAQLINEKPQVIQEYESGKAIPNQQIL---TKLERALGVKL  147 (151)
Q Consensus       103 ~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l---~kLa~~Lgv~l  147 (151)
                      +..|.+|+|+++|||.+|||++.||...++.++.   .++++.||-.+
T Consensus         4 ~~~ti~dIA~~aGVS~~TVSrvLn~~~~vs~~tr~rV~~~a~elgY~p   51 (342)
T PRK09526          4 KPVTLYDVARYAGVSYQTVSRVLNQASHVSAKTREKVEAAMAELNYVP   51 (342)
T ss_pred             CCCcHHHHHHHhCCCHHHHHHHhcCCCCCCHHHHHHHHHHHHHHCCCc
Confidence            3469999999999999999999999877766654   45566666544

>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=95.96  E-value=0.026  Score=33.68  Aligned_cols=34  Identities=21%  Similarity=0.371  Sum_probs=26.8

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      .+-|..+...-++|+.|+|+.+|+|.++++++-+
T Consensus         6 ~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~   39 (48)
T PF13412_consen    6 RKILNYLRENPRITQKELAEKLGISRSTVNRYLK   39 (48)
T ss_dssp             HHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHH
Confidence            4456777888889999999999999999998743

...

>TIGR00721 tfx DNA-binding protein, Tfx family

Probab=95.95  E-value=0.016  Score=43.02  Aligned_cols=34  Identities=18%  Similarity=0.329  Sum_probs=28.3

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcC
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESG  127 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G  127 (151)
                      ...+-.+| ..|+||+|+|+.+|+|+++|+.+|+.
T Consensus        11 qr~VL~Lr-~~GlTq~EIAe~LgiS~stV~~~e~r   44 (137)
T TIGR00721        11 QIKVLELR-EKGLSQKEIAKELKTTRANVSAIEKR   44 (137)
T ss_pred             HHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHh
Confidence            33444555 59999999999999999999999985

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

>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=95.91  E-value=0.023  Score=44.03  Aligned_cols=54  Identities=15%  Similarity=0.115  Sum_probs=37.7

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHH
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERA  142 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~  142 (151)
                      ...+.+.||.+...++++|.++++.+||++++||.|.+-....+...-..|-.-
T Consensus       116 ~~~VkeeIK~fl~~h~IsQ~~V~q~TGisQS~lSq~L~kGt~Mk~qKR~alY~W  169 (180)
T PF04814_consen  116 PWRVKEEIKAFLQQHNISQREVVQVTGISQSHLSQHLNKGTPMKEQKRRALYRW  169 (180)
T ss_dssp             HHHHHHHHHHHHHHCT--CHHHHHHHT--HHHHHHHHCTB----HHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCcHHHHHHHhhhhHHHHHHHHHcCCCccHHHHHHHHHH
Confidence            467899999999999999999999999999999999875555565554444443

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.

>PRK03975 tfx putative transcriptional regulator; Provisional

Probab=95.87  E-value=0.016  Score=43.21  Aligned_cols=45  Identities=16%  Similarity=0.283  Sum_probs=33.8

Q ss_pred             cCCcCHHHHHHHhCCCHHHHHHHHcCCCC-C--CHHHHHHHHHHhCCCC
Q 031871          102 DKKLTQSQLAQLINEKPQVIQEYESGKAI-P--NQQILTKLERALGVKL  147 (151)
Q Consensus       102 ~~glTQ~eLA~~lgis~s~Is~~E~G~~~-p--~~~~l~kLa~~Lgv~l  147 (151)
                      ..|+||+|+|+.+|+|+++|+.+|++-.. .  ...++ +++++|+-++
T Consensus        19 ~~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~tl-~~~~~l~a~~   66 (141)
T PRK03975         19 ERGLTQQEIADILGTSRANVSSIEKRARENIEKARETL-AFAETLNAPV   66 (141)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH-HHHHHcCCCe
Confidence            59999999999999999999999996321 1  12333 6677776554

>PRK14987 gluconate operon transcriptional regulator; Provisional

Probab=95.67  E-value=0.022  Score=46.30  Aligned_cols=44  Identities=7%  Similarity=0.045  Sum_probs=35.6

Q ss_pred             CcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHH---HHHHHHhCCCC
Q 031871          104 KLTQSQLAQLINEKPQVIQEYESGKAIPNQQIL---TKLERALGVKL  147 (151)
Q Consensus       104 glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l---~kLa~~Lgv~l  147 (151)
                      ..|.+|+|+.+|||.+|||++.||....+.++-   .++++.||-.+
T Consensus         5 ~~ti~dIA~~agVS~~TVSrvLn~~~~vs~~tr~rV~~~a~elgY~p   51 (331)
T PRK14987          5 RPVLQDVADRVGVTKMTVSRFLRNPEQVSVALRGKIAAALDELGYIP   51 (331)
T ss_pred             CCcHHHHHHHhCCCHHHhhhhhCCCCCCCHHHHHHHHHHHHHhCCCc
Confidence            469999999999999999999999877776654   45566777544

>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]

Probab=95.46  E-value=0.032  Score=47.93  Aligned_cols=53  Identities=19%  Similarity=0.187  Sum_probs=43.8

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhC------CCHHHHHHHHcCCCCCCHHHHHHHHHHh
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLIN------EKPQVIQEYESGKAIPNQQILTKLERAL  143 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lg------is~s~Is~~E~G~~~p~~~~l~kLa~~L  143 (151)
                      -+.|++.+|+.|...|+||.|+...+|      .|++||+++|.  -.++..++-||--.|
T Consensus       208 LEqFAK~FKqRRIkLGfTQaDVGlALG~lyGn~FSQTTIcRFEA--LqLSFKNMCKLKPLL  266 (398)
T KOG3802|consen  208 LEQFAKTFKQRRIKLGFTQADVGLALGALYGNVFSQTTICRFEA--LQLSFKNMCKLKPLL  266 (398)
T ss_pred             HHHHHHHHHhheeccccchhHHHHHHHhhhCcccchhhhhHhHh--hccCHHHHhhhHHHH
Confidence            478999999999999999999999998      59999999998  346666666654333

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

Probab=95.44  E-value=0.014  Score=40.06  Aligned_cols=25  Identities=12%  Similarity=0.145  Sum_probs=18.9

Q ss_pred             cCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871          102 DKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus       102 ~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      +.||||.|+|+++|.|+++|+++..
T Consensus         1 ~~G~tq~eIA~~lGks~s~Vs~~l~   25 (93)
T PF08535_consen    1 EFGWTQEEIAKRLGKSRSWVSNHLA   25 (93)
T ss_dssp             HTT--HHHHHHHTT--HHHHHHHHG
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            4799999999999999999999865

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.

>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=95.34  E-value=0.053  Score=32.57  Aligned_cols=39  Identities=23%  Similarity=0.314  Sum_probs=30.6

Q ss_pred             HHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCC
Q 031871           90 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA  129 (151)
Q Consensus        90 ~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~  129 (151)
                      +.+...|..++... +|+.+.|+..||+++||.+.-+|..
T Consensus         3 e~l~~Ai~~v~~g~-~S~r~AA~~ygVp~sTL~~r~~g~~   41 (45)
T PF05225_consen    3 EDLQKAIEAVKNGK-MSIRKAAKKYGVPRSTLRRRLRGKP   41 (45)
T ss_dssp             HHHHHHHHHHHTTS-S-HHHHHHHHT--HHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHhCC-CCHHHHHHHHCcCHHHHHHHHcCCC
Confidence            46777888888555 9999999999999999999988864

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.

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

Probab=95.34  E-value=0.1  Score=38.56  Aligned_cols=59  Identities=19%  Similarity=0.160  Sum_probs=54.7

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL  147 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l  147 (151)
                      ...+.+.|-...+.+|+|-.||++.+|.+...+...--|....+.+.+.++++.||++-
T Consensus         6 i~~l~~~ll~~Kk~kgLsfaDl~~~lG~~ev~vaa~~ygqa~~~~~ear~v~e~L~L~~   64 (151)
T COG1513           6 ILDLADALLLAKKKKGLSFADLADGLGLAEVFVAAALYGQAALPADEARAVGEALDLDE   64 (151)
T ss_pred             HHHHHHHHHHHHHhcCCcHHHHHhhcCccHHHHHHHHHhhccCCHHHHHHHHHHhCCCH
Confidence            46788889999999999999999999999999999999999999999999999999763

>smart00351 PAX Paired Box domain

Probab=95.23  E-value=0.055  Score=39.21  Aligned_cols=45  Identities=9%  Similarity=0.246  Sum_probs=36.2

Q ss_pred             hhccCCcchHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           81 LYCTDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        81 ~~~~~~~~~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      .|++...+..++..+|-.+-. .|+|+.++|+.+|||+++|.+|-+
T Consensus        11 ~~~~~~~~s~~~R~riv~~~~-~G~s~~~iA~~~gvs~~tV~kwi~   55 (125)
T smart00351       11 VFVNGRPLPDEERQRIVELAQ-NGVRPCDISRQLCVSHGCVSKILG   55 (125)
T ss_pred             eecCCCCCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHH
Confidence            455666677777777776654 799999999999999999999843

>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=95.16  E-value=0.059  Score=32.46  Aligned_cols=32  Identities=13%  Similarity=0.194  Sum_probs=26.1

Q ss_pred             HHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           95 AIVQARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        95 ~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      .+-.+|-..++|+.|+|+.+|+|.++|+++++
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            34455558899999999999999999999875

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 ....

>PRK01381 Trp operon repressor; Provisional

Probab=95.14  E-value=0.05  Score=38.29  Aligned_cols=57  Identities=14%  Similarity=0.080  Sum_probs=43.5

Q ss_pred             hHHHHHHHHHHHh--cCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCC
Q 031871           89 PSELKKAIVQARN--DKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGV  145 (151)
Q Consensus        89 ~~~~~~~Lk~~R~--~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv  145 (151)
                      ...++.|++-.+.  ..++||.|+|+.+|+|.+||++--+--...+.+....|...|.-
T Consensus        38 r~al~~R~~I~~~L~~g~~sQREIa~~lGvSiaTITRgsn~Lk~~~~~~k~~l~~~l~~   96 (99)
T PRK01381         38 REALGTRVRIVEELLRGELSQREIKQELGVGIATITRGSNSLKTAPPEFKEWLEQQLLK   96 (99)
T ss_pred             HHHHHHHHHHHHHHHcCCcCHHHHHHHhCCceeeehhhHHHhccCCHHHHHHHHHHhcc
Confidence            4667888877764  44599999999999999999997765555567777777766653

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

Probab=95.14  E-value=0.051  Score=38.68  Aligned_cols=37  Identities=19%  Similarity=0.171  Sum_probs=29.0

Q ss_pred             HhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHh
Q 031871          100 RNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERAL  143 (151)
Q Consensus       100 R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~L  143 (151)
                      -...||||.|-|+.+|||++|+.++-..       --.|||++|
T Consensus        53 ~D~egl~QeeaA~~MgVSR~T~~ril~~-------ARkKiA~AL   89 (106)
T PF02001_consen   53 VDYEGLSQEEAAERMGVSRPTFQRILES-------ARKKIADAL   89 (106)
T ss_pred             HHHcCCCHHHHHHHcCCcHHHHHHHHHH-------HHHHHHHHH
Confidence            3457999999999999999999998762       235666554

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

Probab=94.98  E-value=0.014  Score=40.49  Aligned_cols=39  Identities=23%  Similarity=0.358  Sum_probs=36.3

Q ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q 031871          106 TQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALG  144 (151)
Q Consensus       106 TQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lg  144 (151)
                      .|..||..+|+++++|++|-+|.+....+....|+++.+
T Consensus        14 ~q~a~a~LLgvsp~~vnQw~~g~r~~~a~r~~aIerAt~   52 (96)
T COG4197          14 GQKALARLLGVSPPSVNQWIKGRRQVAAERALAIERATS   52 (96)
T ss_pred             cHHHHHHHHccCchHHHHHhhheeecCcccchHHHHHhc
Confidence            588999999999999999999999999888889998887

>PRK10344 DNA-binding transcriptional regulator Nlp; Provisional

Probab=94.96  E-value=0.074  Score=36.79  Aligned_cols=51  Identities=14%  Similarity=0.118  Sum_probs=39.9

Q ss_pred             HHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 031871           96 IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG  149 (151)
Q Consensus        96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~e  149 (151)
                      |+.....+|+|..+|+...|++.+|+..-... ..|.-+  ..||++|||.+.+
T Consensus        13 I~AaL~KrG~sLa~lsr~~Gls~~TL~nAL~r-p~PKgE--riIA~aLGv~P~e   63 (92)
T PRK10344         13 IIAGLRKKGTSMAAESRRNGLSSSTLANALSR-PWPKGE--MIIAKALGTDPWV   63 (92)
T ss_pred             HHHHHHHcCCcHHHHHHHcCCChHHHHHHHcC-CCchHH--HHHHHHHCcCHHH
Confidence            45555668999999999999999999887663 234444  5699999998764

>cd00131 PAX Paired Box domain

Probab=94.92  E-value=0.076  Score=38.73  Aligned_cols=44  Identities=7%  Similarity=0.283  Sum_probs=36.5

Q ss_pred             hhccCCcchHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871           81 LYCTDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus        81 ~~~~~~~~~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E  125 (151)
                      .|.|...+..++..+|-.+-. .|+|+.++|+.+|||+++|.+|-
T Consensus        11 ~~~m~~~lS~d~R~rIv~~~~-~G~s~~~iA~~~~Vs~~tV~r~i   54 (128)
T cd00131          11 VFVNGRPLPDSIRQRIVELAQ-SGIRPCDISRQLRVSHGCVSKIL   54 (128)
T ss_pred             cccCCCcCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHH
Confidence            456667777778888876654 79999999999999999999993

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

Probab=94.84  E-value=0.051  Score=31.53  Aligned_cols=24  Identities=21%  Similarity=0.411  Sum_probs=21.2

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcCC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESGK  128 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G~  128 (151)
                      +|..|+|+.+||++++|.+|++-.
T Consensus         1 ~s~~e~a~~lgvs~~tl~~~~~~g   24 (49)
T cd04762           1 LTTKEAAELLGVSPSTLRRWVKEG   24 (49)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHcC
Confidence            578999999999999999998643

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.

>PRK08558 adenine phosphoribosyltransferase; Provisional

Probab=94.57  E-value=0.13  Score=41.39  Aligned_cols=50  Identities=16%  Similarity=0.355  Sum_probs=39.3

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALG  144 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lg  144 (151)
                      -..|+.++..  +|-+||++.+|++.+.+++|-+|+..|+.+....|.+-|.
T Consensus        14 v~~lr~lk~~--~ty~el~~~~g~p~~~l~RYv~g~~~P~~~~a~~~~~~l~   63 (238)
T PRK08558         14 VRVLRSLKKT--YTYEELSSITGLPESVLNRYVNGHVLPSVERAREIVEKLG   63 (238)
T ss_pred             HHHHHHHhcc--cCHHHHHHHHCCCHHHHHHHHcCCcCCCHHHHHHHHHHHH
Confidence            4445555443  5999999999999999999999999999886666655443

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

Probab=94.56  E-value=0.034  Score=40.32  Aligned_cols=23  Identities=26%  Similarity=0.351  Sum_probs=21.2

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESG  127 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G  127 (151)
                      ||.+|||+.+|++++||++|-+-
T Consensus         1 MT~eELA~~tG~srQTINrWvRk   23 (122)
T PF07037_consen    1 MTPEELAELTGYSRQTINRWVRK   23 (122)
T ss_pred             CCHHHHHHHhCccHHHHHHHHHh
Confidence            79999999999999999999664

The function of this family is unknown.

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

Probab=94.45  E-value=0.033  Score=40.92  Aligned_cols=27  Identities=26%  Similarity=0.412  Sum_probs=24.8

Q ss_pred             hcCCcCHHHHHHHhCCCHHHHHHHHcC
Q 031871          101 NDKKLTQSQLAQLINEKPQVIQEYESG  127 (151)
Q Consensus       101 ~~~glTQ~eLA~~lgis~s~Is~~E~G  127 (151)
                      .++|+||+++|+.+|.++..||.+|+.
T Consensus        20 RekG~tQ~eIA~~L~TTraNvSaIEkr   46 (143)
T COG1356          20 REKGLTQSEIARILKTTRANVSAIEKR   46 (143)
T ss_pred             hhccccHHHHHHHHccchhhHHHHHHH
Confidence            468999999999999999999999984

>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=94.44  E-value=0.11  Score=35.71  Aligned_cols=38  Identities=13%  Similarity=0.058  Sum_probs=31.5

Q ss_pred             hHHHHHHHHHHH--hcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           89 PSELKKAIVQAR--NDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        89 ~~~~~~~Lk~~R--~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      ...++.|++-++  ...|+||.++|+.+|+|..||++.-+
T Consensus        32 ~~~l~~R~~va~~lL~~g~syreIa~~tgvS~aTItRvsr   71 (87)
T PF01371_consen   32 LEALAQRWQVAKELLDEGKSYREIAEETGVSIATITRVSR   71 (87)
T ss_dssp             HHHHHHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHH
Confidence            367788887775  45799999999999999999998643

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 ....

>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=94.37  E-value=0.054  Score=34.35  Aligned_cols=25  Identities=4%  Similarity=0.157  Sum_probs=23.1

Q ss_pred             CCcCHHHHHHHhCCCHHHHHHHHcC
Q 031871          103 KKLTQSQLAQLINEKPQVIQEYESG  127 (151)
Q Consensus       103 ~glTQ~eLA~~lgis~s~Is~~E~G  127 (151)
                      .|+++.++|+.+|++.+||..|-.-
T Consensus        12 ~G~~~~eIA~~Lg~~~~TV~~W~~r   36 (58)
T PF06056_consen   12 QGWSIKEIAEELGVPRSTVYSWKDR   36 (58)
T ss_pred             cCCCHHHHHHHHCCChHHHHHHHHh
Confidence            6999999999999999999999763

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

>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=94.30  E-value=0.0075  Score=41.83  Aligned_cols=41  Identities=15%  Similarity=0.220  Sum_probs=31.5

Q ss_pred             CCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 031871          103 KKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL  147 (151)
Q Consensus       103 ~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l  147 (151)
                      ..++|..+|+.+|++.++||+|-.+    -...+..|..+|+..+
T Consensus        22 A~~gq~~vA~~~Gv~eStISR~k~~----~~~~~a~lLa~L~~~v   62 (91)
T PF05269_consen   22 ASVGQKKVAEAMGVDESTISRWKND----FIEKMAMLLAALELGV   62 (91)
T ss_dssp             HHHHHHHHHHHHTSSTTTHHHHHHH----HHHHHHHHHHHTTTTH
T ss_pred             HHHhhHHHHHHhCCCHHHHHHHHhh----HHHHHHHHHHHHHhcc
Confidence            3478999999999999999999654    2355666666776654

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.

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

Probab=94.24  E-value=0.56  Score=32.08  Aligned_cols=58  Identities=12%  Similarity=0.130  Sum_probs=41.2

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHH-hCCCHHHHHHHHcCCCCCCHH------HHHHHHHHhCCC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQL-INEKPQVIQEYESGKAIPNQQ------ILTKLERALGVK  146 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~-lgis~s~Is~~E~G~~~p~~~------~l~kLa~~Lgv~  146 (151)
                      ...+..+|++.....+++|+.||+. +|.|+.+++.+.+--..-+.-      ...++-..|..+
T Consensus        11 T~~I~~~ik~~L~~~~IsQ~~Fa~~vL~rsqgtlsdlL~~PKpW~~L~~~gre~y~RM~nWL~~~   75 (87)
T PF02376_consen   11 TKEIARRIKEWLKRNNISQRVFAKKVLNRSQGTLSDLLRKPKPWNKLKPKGREPYIRMYNWLSLP   75 (87)
T ss_dssp             HHHHHHHHHHHHHHTT--HHHHHHHTTSS-HHHHHHHHHSCCTTCHHHHHHHHHHHHHHHHHCST
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHhccChhHHHHHhCCCCCHHHcCccccHHHHHHHHHhcCC
Confidence            4678999999999999999999998 499999999999854333322      245555555543

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.

>COG2944 Predicted transcriptional regulator [Transcription]

Probab=93.99  E-value=0.043  Score=38.95  Aligned_cols=26  Identities=35%  Similarity=0.377  Sum_probs=22.6

Q ss_pred             HHHHHHHcCCChhhHHhhhcCCCccC
Q 031871           31 VVNAARRAGADIETVRKSHAGTNKAA   56 (151)
Q Consensus        31 ~~~~a~r~g~~v~t~~k~~~g~~~~~   56 (151)
                      +-.-|++.|++++|+++||.|..+|.
T Consensus        60 Q~vFA~~L~vs~~Tv~~WEqGr~kPs   85 (104)
T COG2944          60 QPVFARYLGVSVSTVRKWEQGRKKPS   85 (104)
T ss_pred             HHHHHHHHCCCHHHHHHHHcCCcCCC
Confidence            34578999999999999999999873

>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=93.83  E-value=0.064  Score=33.25  Aligned_cols=38  Identities=11%  Similarity=0.140  Sum_probs=26.2

Q ss_pred             HHHHHHHHH-HhcCCcCHHHHHHHhCCCHHHHHHHHcCC
Q 031871           91 ELKKAIVQA-RNDKKLTQSQLAQLINEKPQVIQEYESGK  128 (151)
Q Consensus        91 ~~~~~Lk~~-R~~~glTQ~eLA~~lgis~s~Is~~E~G~  128 (151)
                      .+.+.+.-+ +.+.|.++.++|+..||+.+||+.|.+.+
T Consensus         8 Tl~eK~~iI~~~e~g~s~~~ia~~fgv~~sTv~~I~K~k   46 (53)
T PF04218_consen    8 TLEEKLEIIKRLEEGESKRDIAREFGVSRSTVSTILKNK   46 (53)
T ss_dssp             -HHHHHHHHHHHHCTT-HHHHHHHHT--CCHHHHHHHCH
T ss_pred             CHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHhH
Confidence            344445444 45778899999999999999999997753

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.

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

Probab=93.78  E-value=0.14  Score=35.84  Aligned_cols=28  Identities=18%  Similarity=0.054  Sum_probs=24.6

Q ss_pred             HHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           99 ARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        99 ~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      +....||+|.|.|.++|||++|+.+..+
T Consensus        44 LvD~~~l~QeeAA~rMgISr~Tfwr~l~   71 (99)
T COG1342          44 LVDYEGLTQEEAALRMGISRQTFWRLLT   71 (99)
T ss_pred             HHhHhhccHHHHHHHhcccHHHHHHHHH
Confidence            3456899999999999999999998765

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

Probab=93.75  E-value=0.19  Score=31.95  Aligned_cols=22  Identities=27%  Similarity=0.567  Sum_probs=20.3

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHc
Q 031871          105 LTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      +|..|+|+.+||++++|..||+
T Consensus         1 ~~i~evA~~~gvs~~tlR~~~~   22 (67)
T cd04764           1 YTIKEVSEIIGVKPHTLRYYEK   22 (67)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            4778999999999999999986

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=93.72  E-value=0.085  Score=29.60  Aligned_cols=22  Identities=9%  Similarity=0.228  Sum_probs=17.2

Q ss_pred             CcCHHHHHHHhCCCHHHHHHHH
Q 031871          104 KLTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus       104 glTQ~eLA~~lgis~s~Is~~E  125 (151)
                      .||+.|+|+.+|+++.+||+.-
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            4799999999999999999874

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 ....

>TIGR01764 excise DNA binding domain, excisionase family

Probab=93.57  E-value=0.13  Score=29.90  Aligned_cols=27  Identities=15%  Similarity=0.235  Sum_probs=23.1

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcCCCCC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESGKAIP  131 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G~~~p  131 (151)
                      ||..|+|+.+|+++++|.+|.+....|
T Consensus         2 lt~~e~a~~lgis~~ti~~~~~~g~i~   28 (49)
T TIGR01764         2 LTVEEAAEYLGVSKDTVYRLIHEGELP   28 (49)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHcCCCC
Confidence            688999999999999999998655444

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).

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

Probab=93.57  E-value=0.13  Score=30.32  Aligned_cols=24  Identities=29%  Similarity=0.385  Sum_probs=21.1

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcCC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESGK  128 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G~  128 (151)
                      +|..|+|+.+|+++++|..|++-.
T Consensus         1 ~~~~e~a~~~gv~~~tlr~~~~~g   24 (49)
T cd04761           1 YTIGELAKLTGVSPSTLRYYERIG   24 (49)
T ss_pred             CcHHHHHHHHCcCHHHHHHHHHCC
Confidence            578899999999999999997644

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.

>PRK15418 transcriptional regulator LsrR; Provisional

Probab=93.55  E-value=0.14  Score=42.80  Aligned_cols=55  Identities=15%  Similarity=0.117  Sum_probs=40.2

Q ss_pred             HHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc-----CCC--------CCCHHHHHHHHHHhCCC
Q 031871           92 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES-----GKA--------IPNQQILTKLERALGVK  146 (151)
Q Consensus        92 ~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~-----G~~--------~p~~~~l~kLa~~Lgv~  146 (151)
                      +--++..+--..||||.|+|+++|+|+++|+++..     |-.        ....+.-.+|.+.||+.
T Consensus        17 l~~~vA~lYY~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~GiV~I~I~~~~~~~~~Le~~L~~~fgLk   84 (318)
T PRK15418         17 LVARIAWFYYHDGLTQSEIGERLGLTRLKVSRLLEKGRQSGIIRVQINSRFEGCLELENALRQHFSLQ   84 (318)
T ss_pred             HHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHcCcEEEEEeCCCccHHHHHHHHHHHhCCC
Confidence            44556666777899999999999999999999843     422        11344556777788754

>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=93.54  E-value=0.16  Score=29.80  Aligned_cols=32  Identities=22%  Similarity=0.114  Sum_probs=25.7

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ...|.......+.++.+.|+.+||+++++.+-
T Consensus         7 ~~~i~~aL~~~~gn~~~aA~~Lgisr~tL~~k   38 (42)
T PF02954_consen    7 KQLIRQALERCGGNVSKAARLLGISRRTLYRK   38 (42)
T ss_dssp             HHHHHHHHHHTTT-HHHHHHHHTS-HHHHHHH
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHH
Confidence            45577888889999999999999999999864

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 ....

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

Probab=93.51  E-value=0.49  Score=30.12  Aligned_cols=62  Identities=16%  Similarity=0.145  Sum_probs=38.8

Q ss_pred             HHHHHHcCCChhhHHhhhc--CCCccCCCCcccccccccccchhhhHHHHHhhccCCcchHHHHHHHHHHHhcCCcCHHH
Q 031871           32 VNAARRAGADIETVRKSHA--GTNKAASSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQ  109 (151)
Q Consensus        32 ~~~a~r~g~~v~t~~k~~~--g~~~~~~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~~~~~~~~~Lk~~R~~~glTQ~e  109 (151)
                      -++|++.|++..|++.|+.  |-..|..+..  .-+....+                  ....-..|+.++. .|+|.++
T Consensus         4 ~e~A~~~gVs~~tlr~ye~~~gl~~~~r~~~--g~R~yt~~------------------di~~l~~i~~l~~-~g~~l~~   62 (68)
T cd04763           4 GEVALLTGIKPHVLRAWEREFGLLKPQRSDG--GHRLFNDA------------------DIDRILEIKRWID-NGVQVSK   62 (68)
T ss_pred             HHHHHHHCcCHHHHHHHHHhcCCCCCCcCCC--CCcccCHH------------------HHHHHHHHHHHHH-cCCCHHH
Confidence            4689999999999999975  4433322111  11111111                  1223445777777 9999999


Q ss_pred             HHHHh
Q 031871          110 LAQLI  114 (151)
Q Consensus       110 LA~~l  114 (151)
                      +++.+
T Consensus        63 i~~~l   67 (68)
T cd04763          63 VKKLL   67 (68)
T ss_pred             HHHHh
Confidence            98765

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

>PRK13698 plasmid-partitioning protein; Provisional

Probab=93.46  E-value=0.14  Score=43.12  Aligned_cols=40  Identities=18%  Similarity=0.036  Sum_probs=33.5

Q ss_pred             hHHHHHHH-HHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCC
Q 031871           89 PSELKKAI-VQARNDKKLTQSQLAQLINEKPQVIQEYESGK  128 (151)
Q Consensus        89 ~~~~~~~L-k~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~  128 (151)
                      ..+.+... +.+....|+||++||+.+|+|+++|++..+=-
T Consensus       160 ~iE~A~ay~~~L~~~~~~tQeeLA~~lG~SRs~Vsn~Lrla  200 (323)
T PRK13698        160 AYERGLRYASRLQNEFAGNISALADAENISRKIITRCINTA  200 (323)
T ss_pred             HHHHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            45667766 66778999999999999999999999987743

>PHA01976 helix-turn-helix protein

Probab=93.45  E-value=0.026  Score=35.85  Aligned_cols=29  Identities=17%  Similarity=0.093  Sum_probs=24.7

Q ss_pred             HHHHHHHHHcCCChhhHHhhhcCCCccCC
Q 031871           29 EKVVNAARRAGADIETVRKSHAGTNKAAS   57 (151)
Q Consensus        29 ~~~~~~a~r~g~~v~t~~k~~~g~~~~~~   57 (151)
                      -+..+.|++.|++.+++.+||+|...|..
T Consensus        16 lt~~~lA~~~gvs~~~v~~~e~g~~~p~~   44 (67)
T PHA01976         16 WSAPELSRRAGVRHSLIYDFEADKRLPNL   44 (67)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCH
Confidence            45678999999999999999999876543

>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=93.40  E-value=0.38  Score=25.09  Aligned_cols=23  Identities=9%  Similarity=0.186  Sum_probs=20.8

Q ss_pred             cCCcCHHHHHHHhCCCHHHHHHH
Q 031871          102 DKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus       102 ~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ..+++..++|+.+|+++++|.+|
T Consensus        19 ~~~~s~~~ia~~~~is~~tv~~~   41 (42)
T cd00569          19 AAGESVAEIARRLGVSRSTLYRY   41 (42)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHh
Confidence            36789999999999999999987

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

>PF12728 HTH_17: Helix-turn-helix domain

Probab=93.37  E-value=0.14  Score=30.78  Aligned_cols=28  Identities=21%  Similarity=0.297  Sum_probs=23.6

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcCCCCCC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESGKAIPN  132 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G~~~p~  132 (151)
                      ||.+|+|+.+|||.++|.+|-+....|.
T Consensus         2 lt~~e~a~~l~is~~tv~~~~~~g~i~~   29 (51)
T PF12728_consen    2 LTVKEAAELLGISRSTVYRWIRQGKIPP   29 (51)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHcCCCCe
Confidence            6889999999999999999986555443

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

Probab=93.32  E-value=0.16  Score=42.74  Aligned_cols=58  Identities=17%  Similarity=0.165  Sum_probs=44.7

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc-----CCC--------CCCHHHHHHHHHHhCCC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES-----GKA--------IPNQQILTKLERALGVK  146 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~-----G~~--------~p~~~~l~kLa~~Lgv~  146 (151)
                      ......++..+.-..||||.|+|+++|+|+.+|+++..     |-.        ....+.-.+|.+.||++
T Consensus        11 ~~~l~~~~A~lYY~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~GiV~I~i~~~~~~~~~Le~~L~~~fgL~   81 (321)
T COG2390          11 EERLLARAAWLYYVEGLTQSEIAERLGISRATVSRLLAKAREEGIVKISINSPVEGCLELEQQLKERFGLK   81 (321)
T ss_pred             HHHHHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCeEEEEeCCCCcchHHHHHHHHHhcCCC
Confidence            35667788888889999999999999999999999843     321        12344567788888875

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

Probab=93.31  E-value=0.16  Score=30.89  Aligned_cols=31  Identities=16%  Similarity=0.171  Sum_probs=23.2

Q ss_pred             HHHHHHhcCC-cCHHHHHHHhCCCHHHHHHHH
Q 031871           95 AIVQARNDKK-LTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus        95 ~Lk~~R~~~g-lTQ~eLA~~lgis~s~Is~~E  125 (151)
                      -|..+....+ +|..+||+.+|||+.||.+.-
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            3455544444 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 ....

>PF13518 HTH_28: Helix-turn-helix domain

Probab=93.26  E-value=0.21  Score=29.79  Aligned_cols=24  Identities=4%  Similarity=0.059  Sum_probs=21.7

Q ss_pred             CCcCHHHHHHHhCCCHHHHHHHHc
Q 031871          103 KKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus       103 ~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      .|.|..++|+.+|||+++|.+|.+
T Consensus        11 ~g~s~~~~a~~~gis~~tv~~w~~   34 (52)
T PF13518_consen   11 EGESVREIAREFGISRSTVYRWIK   34 (52)
T ss_pred             cCCCHHHHHHHHCCCHhHHHHHHH
Confidence            477999999999999999999964

>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD

Probab=93.21  E-value=0.22  Score=34.25  Aligned_cols=27  Identities=11%  Similarity=0.025  Sum_probs=24.7

Q ss_pred             hcCCcCHHHHHHHhCCCHHHHHHHHcC
Q 031871          101 NDKKLTQSQLAQLINEKPQVIQEYESG  127 (151)
Q Consensus       101 ~~~glTQ~eLA~~lgis~s~Is~~E~G  127 (151)
                      ...|+|+.++|+.+|+|++||.++-+|
T Consensus        47 l~~G~S~~eIA~~LgISrsTIyRi~R~   73 (88)
T TIGR02531        47 LKQGKTYSDIEAETGASTATISRVKRC   73 (88)
T ss_pred             HHCCCCHHHHHHHHCcCHHHHHHHHHh
Confidence            457899999999999999999999885

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.

>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=93.19  E-value=0.13  Score=29.74  Aligned_cols=25  Identities=24%  Similarity=0.473  Sum_probs=20.4

Q ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCC
Q 031871          106 TQSQLAQLINEKPQVIQEYESGKAI  130 (151)
Q Consensus       106 TQ~eLA~~lgis~s~Is~~E~G~~~  130 (151)
                      |..|+|+.+|||..+|..||+-.-.
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            4679999999999999999986543

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 ....

>cd00131 PAX Paired Box domain

Probab=93.13  E-value=0.75  Score=33.43  Aligned_cols=76  Identities=11%  Similarity=0.097  Sum_probs=45.5

Q ss_pred             HHHHHHHHHcCCChhhHHhhhc-----CCCccCCCCcccccccccccchhhhHHHHHhhccCCcchHHHHHH-HHHHHhc
Q 031871           29 EKVVNAARRAGADIETVRKSHA-----GTNKAASSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKA-IVQARND  102 (151)
Q Consensus        29 ~~~~~~a~r~g~~v~t~~k~~~-----g~~~~~~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~~~~~~~~~-Lk~~R~~  102 (151)
                      .+.-..|++.|++..|+.+|-.     |...|.+.+ +..-.++.                     ...... +...+..
T Consensus        34 ~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~~g-g~rpr~~~---------------------~~~~~~i~~~v~~~   91 (128)
T cd00131          34 IRPCDISRQLRVSHGCVSKILNRYYETGSIRPGAIG-GSKPRVAT---------------------PEVVKKIEIYKQEN   91 (128)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCCCCC-CCCCCcCC---------------------HHHHHHHHHHHHHC
Confidence            3556689999999999999854     444332111 11111111                     111111 2235677


Q ss_pred             CCcCHHHHHHHh---CC-------CHHHHHHHHc
Q 031871          103 KKLTQSQLAQLI---NE-------KPQVIQEYES  126 (151)
Q Consensus       103 ~glTQ~eLA~~l---gi-------s~s~Is~~E~  126 (151)
                      -.+|+.||++.+   |+       |.++|+++..
T Consensus        92 p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~  125 (128)
T cd00131          92 PGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILR  125 (128)
T ss_pred             CCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHH
Confidence            789999999886   55       8888888754

>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition

Probab=92.79  E-value=0.15  Score=32.98  Aligned_cols=39  Identities=15%  Similarity=0.196  Sum_probs=28.8

Q ss_pred             chHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           88 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        88 ~~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      ...+|-..+-......|.|..++|+..||++++|.+|.+
T Consensus         7 ys~e~K~~~v~~~~~~g~sv~~va~~~gi~~~~l~~W~~   45 (76)
T PF01527_consen    7 YSPEFKLQAVREYLESGESVSEVAREYGISPSTLYNWRK   45 (76)
T ss_dssp             --HHHHHHHHHHHHHHHCHHHHHHHHHTS-HHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHCCCceEeeecccccccccccHHHH
Confidence            345555555555566799999999999999999999965

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.

>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=92.72  E-value=0.14  Score=32.78  Aligned_cols=25  Identities=16%  Similarity=0.315  Sum_probs=22.2

Q ss_pred             CCcCHHHHHHHhCCCHHHHHHHHcC
Q 031871          103 KKLTQSQLAQLINEKPQVIQEYESG  127 (151)
Q Consensus       103 ~glTQ~eLA~~lgis~s~Is~~E~G  127 (151)
                      -+++..|+|+.+|||.++|+.|-+-
T Consensus        21 g~i~lkdIA~~Lgvs~~tIr~WK~~   45 (60)
T PF10668_consen   21 GKIKLKDIAEKLGVSESTIRKWKSR   45 (60)
T ss_pred             CCccHHHHHHHHCCCHHHHHHHhhh
Confidence            3689999999999999999999653

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 [].

>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=92.69  E-value=0.28  Score=30.10  Aligned_cols=33  Identities=15%  Similarity=0.136  Sum_probs=27.1

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E  125 (151)
                      ...|..+...-++|+.+||+.+++++++++++-
T Consensus         6 ~~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i   38 (59)
T PF01047_consen    6 FRILRILYENGGITQSELAEKLGISRSTVTRII   38 (59)
T ss_dssp             HHHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCCChhHHHHHH
Confidence            345667778889999999999999999999874

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 ....

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

Probab=92.66  E-value=0.31  Score=33.70  Aligned_cols=68  Identities=13%  Similarity=0.100  Sum_probs=41.8

Q ss_pred             HHHHHHcCCChhhHHhhhcCC-CccCCCCcccccccccccchhhhHHHHHhhccCCcchHHHHHHHHHHHhcCCcCHHHH
Q 031871           32 VNAARRAGADIETVRKSHAGT-NKAASSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQL  110 (151)
Q Consensus        32 ~~~a~r~g~~v~t~~k~~~g~-~~~~~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~~~~~~~~~Lk~~R~~~glTQ~eL  110 (151)
                      -+.|++.|++..|++.|+.-. ..|...  ...-+..+.                  ..-..-..|..++...|++.+++
T Consensus         4 ~e~a~~~gvs~~tLR~ye~~Gll~p~r~--~~g~R~Y~~------------------~dv~~l~~I~~L~~~~G~~l~ei   63 (96)
T cd04774           4 DEVAKRLGLTKRTLKYYEEIGLVSPERS--EGRYRLYSE------------------EDLKRLERILRLREVLGFSLQEV   63 (96)
T ss_pred             HHHHHHHCcCHHHHHHHHHCCCCCCCcC--CCCCEEECH------------------HHHHHHHHHHHHHHHcCCCHHHH
Confidence            468999999999999998632 221110  000001111                  11234556778888889999999


Q ss_pred             HHHhCCCHH
Q 031871          111 AQLINEKPQ  119 (151)
Q Consensus       111 A~~lgis~s  119 (151)
                      ...+.....
T Consensus        64 ~~~l~~~~~   72 (96)
T cd04774          64 THFLERPLE   72 (96)
T ss_pred             HHHHhcccc
Confidence            887766554

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.

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

Probab=92.65  E-value=0.65  Score=29.23  Aligned_cols=62  Identities=19%  Similarity=0.131  Sum_probs=36.7

Q ss_pred             HHHHHHcCCChhhHHhhhc--CCCccCCCCcccccccccccchhhhHHHHHhhccCCcchHHHHHHHHHHHhcCCcCHHH
Q 031871           32 VNAARRAGADIETVRKSHA--GTNKAASSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQ  109 (151)
Q Consensus        32 ~~~a~r~g~~v~t~~k~~~--g~~~~~~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~~~~~~~~~Lk~~R~~~glTQ~e  109 (151)
                      -+.|++.|++.+|+++|+.  |...|..++  ..-+.       +..         +  ...--..|+.++. .|+|.++
T Consensus         4 ~eva~~~gvs~~tlr~w~~~~g~~~~~r~~--~~~r~-------yt~---------~--~v~~l~~i~~l~~-~g~~l~~   62 (68)
T cd01104           4 GAVARLTGVSPDTLRAWERRYGLPAPQRTD--GGHRL-------YSE---------A--DVARLRLIRRLTS-EGVRISQ   62 (68)
T ss_pred             HHHHHHHCcCHHHHHHHHHhCCCCCCCcCC--CCCee-------cCH---------H--HHHHHHHHHHHHH-CCCCHHH
Confidence            4689999999999999996  322221110  00011       111         0  1223455667776 8999999


Q ss_pred             HHHHh
Q 031871          110 LAQLI  114 (151)
Q Consensus       110 LA~~l  114 (151)
                      +.+.+
T Consensus        63 i~~~~   67 (68)
T cd01104          63 AAALA   67 (68)
T ss_pred             HHHHh
Confidence            88754

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

>TIGR00180 parB_part ParB-like partition proteins

Probab=92.60  E-value=0.42  Score=36.68  Aligned_cols=52  Identities=19%  Similarity=0.139  Sum_probs=39.7

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHH
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLER  141 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~  141 (151)
                      ..+.+..++++....|+|+.++|+.+|+|+++|+++..=-. .+.+.+..+..
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            35567777777777899999999999999999999877433 55555555554

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.

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

Probab=92.55  E-value=0.15  Score=32.29  Aligned_cols=22  Identities=23%  Similarity=0.437  Sum_probs=20.5

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHc
Q 031871          105 LTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      +|..|+|+.+||++++|..|++
T Consensus         1 ~s~~eva~~~gvs~~tlr~w~~   22 (68)
T cd01104           1 YTIGAVARLTGVSPDTLRAWER   22 (68)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            4788999999999999999997

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

>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=92.49  E-value=0.33  Score=28.10  Aligned_cols=29  Identities=10%  Similarity=0.184  Sum_probs=24.6

Q ss_pred             HHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           98 QARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        98 ~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      .++-..|+|+.++|+.+|++.++|.++..
T Consensus        20 ~~~~~~~~~~~~ia~~~~~s~~~i~~~~~   48 (55)
T cd06171          20 LLRFGEGLSYEEIAEILGISRSTVRQRLH   48 (55)
T ss_pred             HHHHhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            34445899999999999999999998864

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

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

Probab=92.43  E-value=0.38  Score=40.10  Aligned_cols=58  Identities=17%  Similarity=0.057  Sum_probs=47.1

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCC-HHHHHHHHHHhCCCC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPN-QQILTKLERALGVKL  147 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~-~~~l~kLa~~Lgv~l  147 (151)
                      ....-+.++++-+..+|+|..+|..+|+++.+|+.+.+| ..++ ..+-.+|+..|+.+.
T Consensus         4 n~~~~k~~k~f~e~~~~~q~~~a~gi~~~~~~vsk~L~g-~~g~~~~~~a~ia~~le~~~   62 (297)
T COG2842           4 NFIEIKKLKEFAEFSGMCQKYLARGIGTSAPALSKYLNG-YKGDYATNEAKIAAFLEKKG   62 (297)
T ss_pred             hHHHHHHHHHHHHhhhhhHHHHHHHhccCchhHHHHhcC-cCchHHHHHHHHHHHHcCCC
Confidence            355678899999999999999999999999999999998 4443 445667777776543

>PRK09413 IS2 repressor TnpA; Reviewed

Probab=92.31  E-value=0.46  Score=34.00  Aligned_cols=40  Identities=23%  Similarity=0.166  Sum_probs=32.2

Q ss_pred             cchHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           87 RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        87 ~~~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      ....+|-..+-......|.|..++|+.+||++++|++|-+
T Consensus        12 ~ys~EfK~~aV~~~~~~g~sv~evA~e~gIs~~tl~~W~r   51 (121)
T PRK09413         12 RRTTQEKIAIVQQSFEPGMTVSLVARQHGVAASQLFLWRK   51 (121)
T ss_pred             CCCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3455666666666677899999999999999999999954

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

Probab=92.27  E-value=0.13  Score=31.60  Aligned_cols=27  Identities=15%  Similarity=-0.012  Sum_probs=23.4

Q ss_pred             HhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871          100 RNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus       100 R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      +-..|.++.+||...|||++++++|-+
T Consensus        15 ~LR~~~~~~~La~~FgIs~stvsri~~   41 (53)
T PF13613_consen   15 YLRLNLTFQDLAYRFGISQSTVSRIFH   41 (53)
T ss_pred             HHHcCCcHhHHhhheeecHHHHHHHHH
Confidence            344688999999999999999999854

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

Probab=92.22  E-value=0.18  Score=31.91  Aligned_cols=23  Identities=26%  Similarity=0.483  Sum_probs=20.8

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESG  127 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G  127 (151)
                      +|..|+|+.+|+|+++|..||+-
T Consensus         1 yti~eva~~~gvs~~tlr~y~~~   23 (69)
T PF13411_consen    1 YTIKEVAKLLGVSPSTLRYYERE   23 (69)
T ss_dssp             EEHHHHHHHTTTTHHHHHHHHHT
T ss_pred             CcHHHHHHHHCcCHHHHHHHHHh
Confidence            47889999999999999999874

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

Probab=91.98  E-value=0.19  Score=32.04  Aligned_cols=22  Identities=32%  Similarity=0.510  Sum_probs=20.2

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHc
Q 031871          105 LTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      ++..|+|+.+||++++|..||.
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

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

Probab=91.96  E-value=0.24  Score=30.93  Aligned_cols=24  Identities=17%  Similarity=0.254  Sum_probs=21.1

Q ss_pred             CCcCHHHHHHHhCCCHHHHHHHHc
Q 031871          103 KKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus       103 ~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      ++.|..|||+.+|||+++++...+
T Consensus        22 R~~tl~elA~~lgis~st~~~~LR   45 (53)
T PF04967_consen   22 RRITLEELAEELGISKSTVSEHLR   45 (53)
T ss_pred             CcCCHHHHHHHhCCCHHHHHHHHH
Confidence            578999999999999999997643

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

>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]

Probab=91.92  E-value=0.11  Score=43.25  Aligned_cols=39  Identities=18%  Similarity=0.188  Sum_probs=34.7

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHh---------CCCHHHHHHHHcC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLI---------NEKPQVIQEYESG  127 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~l---------gis~s~Is~~E~G  127 (151)
                      -+.|++++++.|...|.||.|+...+         .+|++||-++|+=
T Consensus       219 LEaFAErFKQRRIKLGVTQADVG~ALAnLKiPGVGsLSQSTICRFESL  266 (385)
T KOG1168|consen  219 LEAFAERFKQRRIKLGVTQADVGKALANLKIPGVGSLSQSTICRFESL  266 (385)
T ss_pred             HHHHHHHHHhhhhhhcccHHHHHHHHHhCcCCCcccccccceeeeeee
Confidence            47899999999999999999999876         2689999999974

>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=91.88  E-value=0.45  Score=29.59  Aligned_cols=26  Identities=12%  Similarity=0.161  Sum_probs=21.8

Q ss_pred             hcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871          101 NDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus       101 ~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      ....+|+.+||+.+|+++++++++-+
T Consensus        22 ~~~~~s~~ela~~~g~s~~tv~r~l~   47 (67)
T cd00092          22 VQLPLTRQEIADYLGLTRETVSRTLK   47 (67)
T ss_pred             ccCCcCHHHHHHHHCCCHHHHHHHHH
Confidence            34569999999999999999988643

>TIGR03070 couple_hipB transcriptional regulator, y4mF family

Probab=91.80  E-value=0.061  Score=32.50  Aligned_cols=27  Identities=19%  Similarity=0.254  Sum_probs=23.2

Q ss_pred             HHHHHHHHHcCCChhhHHhhhcCCCcc
Q 031871           29 EKVVNAARRAGADIETVRKSHAGTNKA   55 (151)
Q Consensus        29 ~~~~~~a~r~g~~v~t~~k~~~g~~~~   55 (151)
                      -+..+.|.+.|++.+++.+|+.|...|
T Consensus        16 ltq~~lA~~~gvs~~~vs~~e~g~~~~   42 (58)
T TIGR03070        16 LTQADLADLAGVGLRFIRDVENGKPTV   42 (58)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHCCCCCC
Confidence            356789999999999999999998654

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.

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

Probab=91.78  E-value=0.61  Score=29.44  Aligned_cols=63  Identities=16%  Similarity=0.183  Sum_probs=38.8

Q ss_pred             HHHHHHcCCChhhHHhhhcCCCccCCCCcccccccccccchhhhHHHHHhhccCCcchHHHHHHHHHHHhcCCcCHHHHH
Q 031871           32 VNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQLA  111 (151)
Q Consensus        32 ~~~a~r~g~~v~t~~k~~~g~~~~~~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~~~~~~~~~Lk~~R~~~glTQ~eLA  111 (151)
                      -+.|+..|++.+|++.|+.-..-+.... ...-...+.+                  ....-..|+.++. .|+|..++.
T Consensus         4 ~eva~~~gvs~~tlr~y~~~gll~~~~~-~~g~r~y~~~------------------dv~~l~~i~~l~~-~G~sl~~I~   63 (69)
T PF13411_consen    4 KEVAKLLGVSPSTLRYYEREGLLPPPRD-ENGYRYYSEE------------------DVERLREIKELRK-QGMSLEEIK   63 (69)
T ss_dssp             HHHHHHTTTTHHHHHHHHHTTSSTTBES-TTSSEEE-HH------------------HHHHHHHHHHHHH-TTTHHHHHH
T ss_pred             HHHHHHHCcCHHHHHHHHHhcCcccccc-cCceeeccHH------------------HHHHHHHHHHHHH-CcCCHHHHH
Confidence            4689999999999999997433211100 0000111111                  1334566788888 999999998


Q ss_pred             HHh
Q 031871          112 QLI  114 (151)
Q Consensus       112 ~~l  114 (151)
                      +.+
T Consensus        64 ~~l   66 (69)
T PF13411_consen   64 KLL   66 (69)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            765

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

Probab=91.62  E-value=0.76  Score=29.08  Aligned_cols=64  Identities=17%  Similarity=0.176  Sum_probs=38.5

Q ss_pred             HHHHHHHcCCChhhHHhhhc-CCCccCCCCcccccccccccchhhhHHHHHhhccCCcchHHHHHHHHHHHhcCCcCHHH
Q 031871           31 VVNAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQ  109 (151)
Q Consensus        31 ~~~~a~r~g~~v~t~~k~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~~~~~~~~~Lk~~R~~~glTQ~e  109 (151)
                      .-+.|+..|++..|++.|+. |.-.+..+ . ..-+..+.                .  .-..-..|+.++. .|+|.++
T Consensus         3 i~evA~~~gvs~~tlR~~~~~g~l~~~~~-~-~g~R~y~~----------------~--~l~~l~~i~~l~~-~g~~l~~   61 (67)
T cd04764           3 IKEVSEIIGVKPHTLRYYEKEFNLYIPRT-E-NGRRYYTD----------------E--DIELLKKIKTLLE-KGLSIKE   61 (67)
T ss_pred             HHHHHHHHCcCHHHHHHHHHhcCCCCCCC-C-CCceeeCH----------------H--HHHHHHHHHHHHH-CCCCHHH
Confidence            34689999999999999986 43321110 0 00011111                1  1223455777777 8999999


Q ss_pred             HHHHhC
Q 031871          110 LAQLIN  115 (151)
Q Consensus       110 LA~~lg  115 (151)
                      +.+.++
T Consensus        62 i~~~l~   67 (67)
T cd04764          62 IKEILN   67 (67)
T ss_pred             HHHHhC
Confidence            987653

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.

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

Probab=91.60  E-value=0.58  Score=32.18  Aligned_cols=24  Identities=13%  Similarity=0.250  Sum_probs=21.9

Q ss_pred             hcCCcCHHHHHHHhCCCHHHHHHH
Q 031871          101 NDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus       101 ~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ....+||.|||+.+|+++.++++.
T Consensus        44 ~~~~is~~eLa~~~g~sr~tVsr~   67 (95)
T TIGR01610        44 KQDRVTATVIAELTGLSRTHVSDA   67 (95)
T ss_pred             cCCccCHHHHHHHHCcCHHHHHHH
Confidence            577899999999999999999984

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

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

Probab=91.51  E-value=0.27  Score=39.97  Aligned_cols=34  Identities=18%  Similarity=0.333  Sum_probs=29.2

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      -+.+-.+|-..++||+|+|+.+|||++.||++++
T Consensus       201 Ek~Vl~l~y~eelt~kEI~~~LgISes~VSql~k  234 (247)
T COG1191         201 EKLVLVLRYKEELTQKEIAEVLGISESRVSRLHK  234 (247)
T ss_pred             HHHHHHHHHHhccCHHHHHHHhCccHHHHHHHHH
Confidence            3445567777899999999999999999999987

>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=91.39  E-value=0.054  Score=32.89  Aligned_cols=27  Identities=15%  Similarity=0.256  Sum_probs=21.7

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCccC
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNKAA   56 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~~~   56 (151)
                      +.-+.|++.|++..|+.+|+.|...|.
T Consensus        11 s~~~la~~~gis~~~i~~~~~g~~~~~   37 (55)
T PF01381_consen   11 SQKELAEKLGISRSTISRIENGKRNPS   37 (55)
T ss_dssp             -HHHHHHHHTS-HHHHHHHHTTSSTSB
T ss_pred             CHHHHHHHhCCCcchhHHHhcCCCCCC
Confidence            557899999999999999999976653

; 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 ....

>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=91.38  E-value=0.54  Score=28.39  Aligned_cols=33  Identities=9%  Similarity=0.209  Sum_probs=23.8

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E  125 (151)
                      ...+-.++-..|+|..|+|+.+|+|.++|..+-
T Consensus        15 ~r~i~~l~~~~g~s~~eIa~~l~~s~~~v~~~l   47 (54)
T PF08281_consen   15 QREIFLLRYFQGMSYAEIAEILGISESTVKRRL   47 (54)
T ss_dssp             HHHHHHHHHTS---HHHHHHHCTS-HHHHHHHH
T ss_pred             HHHHHHHHHHHCcCHHHHHHHHCcCHHHHHHHH
Confidence            445566777899999999999999999998764

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.

>PRK09744 DNA-binding transcriptional regulator DicC; Provisional

Probab=91.35  E-value=0.61  Score=31.11  Aligned_cols=36  Identities=19%  Similarity=0.413  Sum_probs=27.3

Q ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q 031871          106 TQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALG  144 (151)
Q Consensus       106 TQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lg  144 (151)
                      +...+|+.+|||+++|++|  |+..|. ..+.+|..+-+
T Consensus        12 s~~kvA~aLGIs~~AVsQW--Ge~VPe-~rA~~ie~~T~   47 (75)
T PRK09744         12 SKTKLANAAGVRLASVAAW--GELVPE-GRAMRLQEASG   47 (75)
T ss_pred             cHHHHHHHHCCCHHHHHHH--hccCcH-HHHHHHHHHhC
Confidence            6788999999999999999  766554 34556665544

>smart00422 HTH_MERR helix_turn_helix, mercury resistance

Probab=91.32  E-value=0.36  Score=30.51  Aligned_cols=22  Identities=23%  Similarity=0.345  Sum_probs=19.9

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHc
Q 031871          105 LTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      +|..|+|+.+||++++|..|++
T Consensus         1 ~s~~eva~~~gvs~~tlr~~~~   22 (70)
T smart00422        1 YTIGEVAKLAGVSVRTLRYYER   22 (70)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5788999999999999999965

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

Probab=91.20  E-value=0.35  Score=39.56  Aligned_cols=42  Identities=21%  Similarity=0.218  Sum_probs=30.9

Q ss_pred             CCcCHHHHHHHhCC-----CHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q 031871          103 KKLTQSQLAQLINE-----KPQVIQEYESGKAIPNQQILTKLERALG  144 (151)
Q Consensus       103 ~glTQ~eLA~~lgi-----s~s~Is~~E~G~~~p~~~~l~kLa~~Lg  144 (151)
                      .++||.+||+++|-     |+++|+++.+=-..+...+...|+.-+|
T Consensus       135 ~~ltq~ela~~lgk~g~~isrs~Isn~lrll~~L~~~i~~~l~~glG  181 (258)
T TIGR03764       135 ESLSQRELARRLSADGYPISQSHISRMGDTVEYLYPAIPNLLYSGLG  181 (258)
T ss_pred             CCCCHHHHHHHhcccCCCCCHHHHHHHHHHHHhChHHHHHHHHccCC
Confidence            68999999999976     9999999987544455555555544443

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.

>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=91.07  E-value=0.67  Score=28.48  Aligned_cols=33  Identities=18%  Similarity=0.216  Sum_probs=25.4

Q ss_pred             HHHHHHHHhcCC--cCHHHHHHHhCCCHHHHHHHH
Q 031871           93 KKAIVQARNDKK--LTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus        93 ~~~Lk~~R~~~g--lTQ~eLA~~lgis~s~Is~~E  125 (151)
                      ...|..+...-+  +|+.+||+.++++++++++.-
T Consensus         8 ~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v   42 (62)
T PF12802_consen    8 FRVLMALARHPGEELTQSELAERLGISKSTVSRIV   42 (62)
T ss_dssp             HHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHH
T ss_pred             HHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHH
Confidence            344556666666  999999999999999999864

...

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

Probab=90.82  E-value=0.59  Score=30.18  Aligned_cols=29  Identities=17%  Similarity=0.103  Sum_probs=22.9

Q ss_pred             HHHHHhcCC--cCHHHHHHHhCCCHHHHHHH
Q 031871           96 IVQARNDKK--LTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        96 Lk~~R~~~g--lTQ~eLA~~lgis~s~Is~~  124 (151)
                      |..++..-+  +|+.|||+.+|++.+++++.
T Consensus        12 L~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~   42 (68)
T smart00550       12 LEFLENSGDETSTALQLAKNLGLPKKEVNRV   42 (68)
T ss_pred             HHHHHHCCCCCcCHHHHHHHHCCCHHHHHHH
Confidence            344444444  99999999999999999886

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

>PRK10072 putative transcriptional regulator; Provisional

Probab=90.71  E-value=0.23  Score=34.62  Aligned_cols=29  Identities=24%  Similarity=0.266  Sum_probs=25.1

Q ss_pred             HHHHHHHHHcCCChhhHHhhhcCCCccCC
Q 031871           29 EKVVNAARRAGADIETVRKSHAGTNKAAS   57 (151)
Q Consensus        29 ~~~~~~a~r~g~~v~t~~k~~~g~~~~~~   57 (151)
                      -++.+.|+..|++..|+.+|+.|...|..
T Consensus        47 lTQ~elA~~lGvS~~TVs~WE~G~r~P~~   75 (96)
T PRK10072         47 LKIDDFARVLGVSVAMVKEWESRRVKPSS   75 (96)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCH
Confidence            35678999999999999999999988643

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

Probab=90.61  E-value=1  Score=26.94  Aligned_cols=36  Identities=8%  Similarity=0.096  Sum_probs=26.7

Q ss_pred             HHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           90 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        90 ~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      ..+...|-.+.... .|++++|+.+|+|.++|.++-+
T Consensus        14 ~~~~~~i~~~~~~~-~s~~~vA~~~~vs~~TV~ri~~   49 (52)
T PF13542_consen   14 KRLEQYILKLLRES-RSFKDVARELGVSWSTVRRIFD   49 (52)
T ss_pred             HHHHHHHHHHHhhc-CCHHHHHHHHCCCHHHHHHHHH
Confidence            34444454444444 7999999999999999998854

>PRK04217 hypothetical protein; Provisional

Probab=90.40  E-value=0.52  Score=33.70  Aligned_cols=32  Identities=9%  Similarity=0.055  Sum_probs=27.6

Q ss_pred             HHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           95 AIVQARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        95 ~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      .+-.++...|+|++|+|+.+|+|.+||.++..
T Consensus        49 eai~l~~~eGlS~~EIAk~LGIS~sTV~r~L~   80 (110)
T PRK04217         49 EALRLVDYEGLTQEEAGKRMGVSRGTVWRALT   80 (110)
T ss_pred             HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            44466777899999999999999999999866

>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=90.33  E-value=0.37  Score=30.96  Aligned_cols=23  Identities=17%  Similarity=0.287  Sum_probs=20.7

Q ss_pred             CCcCHHHHHHHhCCCHHHHHHHH
Q 031871          103 KKLTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus       103 ~glTQ~eLA~~lgis~s~Is~~E  125 (151)
                      ..+||.+||..+|+|+.++++.-
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            56899999999999999999874

...

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

Probab=90.29  E-value=0.37  Score=31.79  Aligned_cols=44  Identities=14%  Similarity=0.175  Sum_probs=28.3

Q ss_pred             HHHHHHH-HHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHH
Q 031871           91 ELKKAIV-QARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQ  134 (151)
Q Consensus        91 ~~~~~Lk-~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~  134 (151)
                      .+++.|- ....-..+|..+||+.+|+|+++|.++-+.-..-...
T Consensus        20 ~Ia~yil~~~~~~~~~si~elA~~~~vS~sti~Rf~kkLG~~gf~   64 (77)
T PF01418_consen   20 KIADYILENPDEIAFMSISELAEKAGVSPSTIVRFCKKLGFSGFK   64 (77)
T ss_dssp             HHHHHHHH-HHHHCT--HHHHHHHCTS-HHHHHHHHHHCTTTCHH
T ss_pred             HHHHHHHhCHHHHHHccHHHHHHHcCCCHHHHHHHHHHhCCCCHH
Confidence            3444443 3455678999999999999999999987754444433

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.

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

Probab=90.06  E-value=0.084  Score=40.13  Aligned_cols=46  Identities=15%  Similarity=0.120  Sum_probs=1.6

Q ss_pred             cCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 031871          102 DKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL  147 (151)
Q Consensus       102 ~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l  147 (151)
                      ..-||++|+|+.+|++.+|||+.-+|+..-+..-+.-|...|...+
T Consensus        47 l~PLt~~~iA~~lgl~~STVSRav~~Ky~~t~~Gi~plk~fF~~~~   92 (160)
T PF04552_consen   47 LKPLTMKDIADELGLHESTVSRAVKNKYIQTPRGIFPLKDFFSRSV   92 (160)
T ss_dssp             --------------------------------------S-----SS
T ss_pred             CcCCCHHHHHHHhCCCHhHHHHHHcCceeecCCeeeeHHHhccccc
Confidence            3458999999999999999999999997666665667776666554

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.

>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon

Probab=89.96  E-value=0.46  Score=28.08  Aligned_cols=25  Identities=16%  Similarity=0.226  Sum_probs=22.6

Q ss_pred             cCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871          102 DKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus       102 ~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      ..|+|..++|+.+|+|+++|..+-.
T Consensus        16 ~~g~s~~eia~~l~is~~tv~~~~~   40 (58)
T smart00421       16 AEGLTNKEIAERLGISEKTVKTHLS   40 (58)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            4789999999999999999998755

lux regulon (activates the bioluminescence operon

>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=89.83  E-value=1.2  Score=26.15  Aligned_cols=30  Identities=13%  Similarity=0.224  Sum_probs=22.5

Q ss_pred             HHHHHHHhcCCcCHHHHHHHhCCCHHHHHH
Q 031871           94 KAIVQARNDKKLTQSQLAQLINEKPQVIQE  123 (151)
Q Consensus        94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~  123 (151)
                      .-|..+...-..+..++|+.+|+|.+++.+
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            446677777889999999999999998865

...

>PF14590 DUF4447: Domain of unknown function (DUF4447); PDB: 2OX6_B

Probab=89.82  E-value=1.6  Score=32.36  Aligned_cols=42  Identities=21%  Similarity=0.198  Sum_probs=32.0

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHH
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQ  134 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~  134 (151)
                      +-.|+-+|...|+|..++|+..+.|..-+-.||.|+...+.-
T Consensus         9 aie~~ylr~slgl~~aqv~~l~k~se~dv~aweage~~~~~l   50 (166)
T PF14590_consen    9 AIEIKYLRLSLGLTTAQVAELTKASEADVLAWEAGEKPAPGL   50 (166)
T ss_dssp             HHHHHHHHHHTT--HHHHHHHHTS-HHHHHHHHTTSS---HH
T ss_pred             HHHHHHHHHHcCCCHHHHHHhhccCHHHhhhhhccCCcCchH
Confidence            345788999999999999999999999999999999765543

>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=89.54  E-value=0.41  Score=29.03  Aligned_cols=26  Identities=15%  Similarity=0.195  Sum_probs=21.2

Q ss_pred             hcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871          101 NDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus       101 ~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      ...++|..|+|+.+|++++++.++-+
T Consensus        15 ~~~~~t~~eia~~~gl~~stv~r~L~   40 (52)
T PF09339_consen   15 SGGPLTLSEIARALGLPKSTVHRLLQ   40 (52)
T ss_dssp             TBSCEEHHHHHHHHTS-HHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            34458999999999999999998853

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.

>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein

Probab=89.45  E-value=0.51  Score=27.34  Aligned_cols=24  Identities=17%  Similarity=0.259  Sum_probs=20.7

Q ss_pred             CCcCHHHHHHHhCCCHHHHHHHHc
Q 031871          103 KKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus       103 ~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      ..+|+.++|+.+|+++++++++-+
T Consensus         7 ~~~s~~~la~~l~~s~~tv~~~l~   30 (48)
T smart00419        7 LPLTRQEIAELLGLTRETVSRTLK   30 (48)
T ss_pred             eccCHHHHHHHHCCCHHHHHHHHH
Confidence            468999999999999999988643

>PF13551 HTH_29: Winged helix-turn helix

Probab=89.45  E-value=1.2  Score=30.26  Aligned_cols=82  Identities=16%  Similarity=0.211  Sum_probs=45.1

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCccCCCCcccccccccccchhhhHHHHHhhccCCc-chHHHHHHHHHHHhcC-----
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTENLALLLSVLYCTDDR-VPSELKKAIVQARNDK-----  103 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~~~~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~-~~~~~~~~Lk~~R~~~-----  103 (151)
                      +...+|+..|++..|+.+|-.-....-.+   .   -+++....-.+         .. +.+..-..|.++....     
T Consensus        14 ~~~~ia~~lg~s~~Tv~r~~~~~~~~G~~---~---l~~~~~~~g~~---------~~~l~~~~~~~l~~~~~~~p~~g~   78 (112)
T PF13551_consen   14 TIAEIARRLGISRRTVYRWLKRYREGGIE---G---LLPRKPRGGRP---------RKRLSEEQRAQLIELLRENPPEGR   78 (112)
T ss_pred             cHHHHHHHHCcCHHHHHHHHHHHHcccHH---H---HHhccccCCCC---------CCCCCHHHHHHHHHHHHHCCCCCC
Confidence            36789999999999998887643321000   0   00000000000         11 2333333444444332     


Q ss_pred             -CcCHHHHHHHh-------CCCHHHHHHHHc
Q 031871          104 -KLTQSQLAQLI-------NEKPQVIQEYES  126 (151)
Q Consensus       104 -glTQ~eLA~~l-------gis~s~Is~~E~  126 (151)
                       .+|..+|++.+       .+|.++|.+|..
T Consensus        79 ~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~  109 (112)
T PF13551_consen   79 SRWTLEELAEWLIEEEFGIDVSPSTIRRILK  109 (112)
T ss_pred             CcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence             48888998855       678888888754

>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily

Probab=89.37  E-value=1.8  Score=29.76  Aligned_cols=66  Identities=15%  Similarity=0.207  Sum_probs=40.9

Q ss_pred             HHHHHHcCCChhhHHhhhcCCC-ccCCCCcccccccccccchhhhHHHHHhhccCCcchHHHHHHHHHHHhcCCcCHHHH
Q 031871           32 VNAARRAGADIETVRKSHAGTN-KAASSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQL  110 (151)
Q Consensus        32 ~~~a~r~g~~v~t~~k~~~g~~-~~~~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~~~~~~~~~Lk~~R~~~glTQ~eL  110 (151)
                      -+.|++.|+++.|++-|+.-.. .|... ...+-...+.+                  .-..-..|+.++...|++..++
T Consensus         4 ~eva~~~gvs~~tlR~Ye~~GLl~p~~r-~~~g~r~Y~~~------------------dv~~l~~I~~L~~~~G~~l~~I   64 (95)
T cd04780           4 SELSKRSGVSVATIKYYLREGLLPEGRR-LAPNQAEYSEA------------------HVERLRLIRALQQEGGLPISQI   64 (95)
T ss_pred             HHHHHHHCcCHHHHHHHHHCCCCCCCcC-CCCCCeecCHH------------------HHHHHHHHHHHHHHcCCCHHHH
Confidence            4689999999999999997333 22111 00111111111                  1233555677777789999999


Q ss_pred             HHHhCC
Q 031871          111 AQLINE  116 (151)
Q Consensus       111 A~~lgi  116 (151)
                      ++.+..
T Consensus        65 ~~~l~~   70 (95)
T cd04780          65 KEVLDA   70 (95)
T ss_pred             HHHHHh
Confidence            988764

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.

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

Probab=89.25  E-value=0.66  Score=31.38  Aligned_cols=24  Identities=13%  Similarity=0.315  Sum_probs=21.5

Q ss_pred             CcCHHHHHHHhCCCHHHHHHHHcC
Q 031871          104 KLTQSQLAQLINEKPQVIQEYESG  127 (151)
Q Consensus       104 glTQ~eLA~~lgis~s~Is~~E~G  127 (151)
                      ++|..|+|+.+||+.++|..||+-
T Consensus         1 ~~ti~evA~~~gvs~~tLR~ye~~   24 (88)
T cd01105           1 VIGIGEVSKLTGVSPRQLRYWEEK   24 (88)
T ss_pred             CcCHHHHHHHHCcCHHHHHHHHHC
Confidence            468899999999999999999863

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.

>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE

Probab=89.24  E-value=0.6  Score=32.82  Aligned_cols=23  Identities=26%  Similarity=0.541  Sum_probs=21.0

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESG  127 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G  127 (151)
                      ||..|+|+.+|||+.||..||.-
T Consensus         1 ~~i~eva~~~gvs~~tlR~ye~~   23 (108)
T cd04773           1 MTIGELAHLLGVPPSTLRHWEKE   23 (108)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC
Confidence            57899999999999999999874

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.

>PRK00118 putative DNA-binding protein; Validated

Probab=89.10  E-value=0.77  Score=32.50  Aligned_cols=33  Identities=9%  Similarity=0.090  Sum_probs=27.3

Q ss_pred             HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      ..+-.++-..|+|..++|+.+|+|+++|.++-.
T Consensus        23 Revl~L~y~eg~S~~EIAe~lGIS~~TV~r~L~   55 (104)
T PRK00118         23 RNYMELYYLDDYSLGEIAEEFNVSRQAVYDNIK   55 (104)
T ss_pred             HHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            334466677899999999999999999998854

>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]

Probab=89.05  E-value=1.1  Score=33.38  Aligned_cols=37  Identities=14%  Similarity=0.207  Sum_probs=29.5

Q ss_pred             HHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           90 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        90 ~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      .++..++-..-...|+|..++|+.+|+|.+|+.+|-+
T Consensus         7 ~~~R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~   43 (138)
T COG3415           7 NDLRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVR   43 (138)
T ss_pred             HHHHHHHHHHHHHcCccHHHHHHHhCccHHHHHHHHH
Confidence            3445555555667899999999999999999998843

>COG2973 TrpR Trp operon repressor [Transcription]

Probab=88.94  E-value=1.5  Score=30.82  Aligned_cols=56  Identities=16%  Similarity=0.124  Sum_probs=38.6

Q ss_pred             hHHHHHHHHHHH--hcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q 031871           89 PSELKKAIVQAR--NDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALG  144 (151)
Q Consensus        89 ~~~~~~~Lk~~R--~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lg  144 (151)
                      .+.++.|++-.+  .+..+||.|++..+|+|-.+|.+=-|.-...+.+...-|.+.|.
T Consensus        43 Real~~Rv~Iv~eLL~ge~sQREi~~~LgvsiAtITRGSN~LK~~~~~~k~~L~~~l~  100 (103)
T COG2973          43 REALGTRVRIVEELLRGELSQREIAQKLGVSIATITRGSNSLKTADPEFKQWLEKVLL  100 (103)
T ss_pred             HHHHHHHHHHHHHHHhccccHHHHHHHhCcchhhhccchhhhccCCHHHHHHHHHHhc
Confidence            466777776654  45689999999999999999887433333345555555555543

>PRK04132 replication factor C small subunit; Provisional

Probab=88.91  E-value=0.54  Score=44.39  Aligned_cols=43  Identities=28%  Similarity=0.461  Sum_probs=40.1

Q ss_pred             HHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 031871          107 QSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG  149 (151)
Q Consensus       107 Q~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~e  149 (151)
                      .+++|++.|+....+-.|-+|++.|+.....+||++||+++++
T Consensus       420 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  462 (846)
T PRK04132        420 RKEIAEKTGIRADRILEYIKGKRKPSLKNYIKIAKALGINLEK  462 (846)
T ss_pred             HHHHHHHhCCcHHHHHHHHhcCCCccHHHHHHHHHHhcccHHH
Confidence            5689999999999999999999999999999999999998753

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor

Probab=88.80  E-value=1.2  Score=25.93  Aligned_cols=25  Identities=20%  Similarity=0.264  Sum_probs=21.5

Q ss_pred             hcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871          101 NDKKLTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus       101 ~~~glTQ~eLA~~lgis~s~Is~~E  125 (151)
                      ...++|..++|+.+++++++++++-
T Consensus        11 ~~~~~s~~~l~~~l~~s~~tv~~~l   35 (53)
T smart00420       11 QQGKVSVEELAELLGVSEMTIRRDL   35 (53)
T ss_pred             HcCCcCHHHHHHHHCCCHHHHHHHH
Confidence            3467999999999999999998764

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

Probab=88.65  E-value=0.15  Score=32.21  Aligned_cols=27  Identities=22%  Similarity=0.329  Sum_probs=21.4

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCC-ccC
Q 031871           30 KVVNAARRAGADIETVRKSHAGTN-KAA   56 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~-~~~   56 (151)
                      +.-..|.+.|++.+++.+||.|.. .|.
T Consensus        16 s~~~lA~~~g~s~s~v~~iE~G~~~~p~   43 (64)
T PF13560_consen   16 SQAQLADRLGVSQSTVSRIERGRRPRPS   43 (64)
T ss_dssp             -HHHHHHHHTS-HHHHHHHHTTSSSS-B
T ss_pred             CHHHHHHHHCcCHHHHHHHHCCCCCCCC
Confidence            567899999999999999999988 353

>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators

Probab=88.49  E-value=1.3  Score=30.12  Aligned_cols=22  Identities=23%  Similarity=0.406  Sum_probs=20.1

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHc
Q 031871          105 LTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      +|..|+|+.+|+++++|..|++
T Consensus         1 ~~~~eva~~~gi~~~tlr~~~~   22 (100)
T cd00592           1 YTIGEVAKLLGVSVRTLRYYEE   22 (100)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5788999999999999999976

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.

>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=88.46  E-value=0.93  Score=28.19  Aligned_cols=31  Identities=6%  Similarity=-0.010  Sum_probs=25.3

Q ss_pred             HHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           96 IVQARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      +.+++.-..+++.|.|+.+||+.+++-+.-+
T Consensus         7 ~~~L~~~fhlp~~eAA~~Lgv~~T~LKr~CR   37 (52)
T PF02042_consen    7 LEDLSQYFHLPIKEAAKELGVSVTTLKRRCR   37 (52)
T ss_pred             HHHHHHHhCCCHHHHHHHhCCCHHHHHHHHH
Confidence            5667778899999999999999888776543

The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].

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

Probab=88.44  E-value=2.6  Score=28.43  Aligned_cols=65  Identities=14%  Similarity=0.112  Sum_probs=39.0

Q ss_pred             HHHHHHHcCCChhhHHhhhc-CCCccCCCCcccccccccccchhhhHHHHHhhccCCcchHHHHHHHHHHHhcCCcCHHH
Q 031871           31 VVNAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQ  109 (151)
Q Consensus        31 ~~~~a~r~g~~v~t~~k~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~~~~~~~~~Lk~~R~~~glTQ~e  109 (151)
                      .-+.|++.|++..|++.|+. |-..|..... ..-+.-+.  +                .-..-..|+.+|. .|+|.++
T Consensus         4 i~evA~~~gvs~~tLR~ye~~Gll~p~r~~~-~g~R~Ys~--~----------------dv~~l~~I~~Lr~-~G~sl~~   63 (88)
T cd01105           4 IGEVSKLTGVSPRQLRYWEEKGLIKSIRSDG-GGQRKYSL--A----------------DVDRLLVIKELLD-EGFTLAA   63 (88)
T ss_pred             HHHHHHHHCcCHHHHHHHHHCCCCCCCccCC-CCceecCH--H----------------HHHHHHHHHHHHH-CCCCHHH
Confidence            34689999999999999976 3332211110 01111111  1                1223455777776 8999999


Q ss_pred             HHHHhC
Q 031871          110 LAQLIN  115 (151)
Q Consensus       110 LA~~lg  115 (151)
                      +++.+.
T Consensus        64 i~~~l~   69 (88)
T cd01105          64 AVEKLR   69 (88)
T ss_pred             HHHHHH
Confidence            888775

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.

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

Probab=88.35  E-value=0.76  Score=26.47  Aligned_cols=31  Identities=16%  Similarity=0.126  Sum_probs=21.0

Q ss_pred             cCCcCHHHHHHHhCCCHHHHHHHHcCCCCCC
Q 031871          102 DKKLTQSQLAQLINEKPQVIQEYESGKAIPN  132 (151)
Q Consensus       102 ~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~  132 (151)
                      ..++|..|+|..+|+|++++.+.-+-....+
T Consensus         6 ~~~~~l~~iA~~~g~S~~~f~r~Fk~~~g~t   36 (42)
T PF00165_consen    6 QQKLTLEDIAEQAGFSPSYFSRLFKKETGMT   36 (42)
T ss_dssp             -SS--HHHHHHHHTS-HHHHHHHHHHHTSS-
T ss_pred             cCCCCHHHHHHHHCCCHHHHHHHHHHHHCcC
Confidence            3568999999999999999999876443333

>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]

Probab=88.22  E-value=0.96  Score=36.93  Aligned_cols=40  Identities=13%  Similarity=0.141  Sum_probs=34.9

Q ss_pred             CcchHHHHHHHHHHHhcCC-cCHHHHHHHhCCCHHHHHHHH
Q 031871           86 DRVPSELKKAIVQARNDKK-LTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus        86 ~~~~~~~~~~Lk~~R~~~g-lTQ~eLA~~lgis~s~Is~~E  125 (151)
                      ..+.++-.+.|.-++..-| ++|+||.+++|.|+++++++-
T Consensus       191 ~~L~~~e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L  231 (258)
T COG2512         191 YDLNEDEKEILDLIRERGGRITQAELRRALGLSKTTVSRIL  231 (258)
T ss_pred             CCCCHHHHHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHH
Confidence            3456777888999999999 999999999999999999864

>PF07638 Sigma70_ECF: ECF sigma factor

Probab=88.07  E-value=0.82  Score=34.84  Aligned_cols=32  Identities=13%  Similarity=0.199  Sum_probs=26.8

Q ss_pred             HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871           94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus        94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E  125 (151)
                      .++-.+|.-.|+|..|+|+.+|||+.||.+..
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            44555677789999999999999999998754

>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I

Probab=88.06  E-value=0.49  Score=35.32  Aligned_cols=25  Identities=12%  Similarity=0.252  Sum_probs=19.7

Q ss_pred             CcCHHHHHHHhCCCHHHHHHHHcCC
Q 031871          104 KLTQSQLAQLINEKPQVIQEYESGK  128 (151)
Q Consensus       104 glTQ~eLA~~lgis~s~Is~~E~G~  128 (151)
                      ..|+.++|+.+||+++++.+|-+..
T Consensus        34 r~T~~eiAee~Gis~~tLYrWr~~~   58 (142)
T PF13022_consen   34 RRTQAEIAEEVGISRSTLYRWRQQN   58 (142)
T ss_dssp             -S-HHHHHHHHTS-HHHHHHHHHH-
T ss_pred             cchHHHHHHHhCCCHHHHHHHHhcC
Confidence            4799999999999999999998654

>COG1522 Lrp Transcriptional regulators [Transcription]

Probab=88.04  E-value=1.4  Score=32.06  Aligned_cols=34  Identities=12%  Similarity=0.273  Sum_probs=27.8

Q ss_pred             HHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           91 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        91 ~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      .-.+.|+.+.....+++.+||+++|+|++++.+-
T Consensus         9 ~D~~IL~~L~~d~r~~~~eia~~lglS~~~v~~R   42 (154)
T COG1522           9 IDRRILRLLQEDARISNAELAERVGLSPSTVLRR   42 (154)
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHH
Confidence            3345577788888899999999999999988764

>smart00422 HTH_MERR helix_turn_helix, mercury resistance

Probab=87.82  E-value=3.7  Score=25.69  Aligned_cols=63  Identities=16%  Similarity=0.201  Sum_probs=36.7

Q ss_pred             HHHHHHcCCChhhHHhhhc-CCCccC-CCCcccccccccccchhhhHHHHHhhccCCcchHHHHHHHHHHHhcCCcCHHH
Q 031871           32 VNAARRAGADIETVRKSHA-GTNKAA-SSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQ  109 (151)
Q Consensus        32 ~~~a~r~g~~v~t~~k~~~-g~~~~~-~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~~~~~~~~~Lk~~R~~~glTQ~e  109 (151)
                      -+.|++.|++.+|++.|+. |-..|. ....  .-..       +..         .  ....-..+..+|. .|++.++
T Consensus         4 ~eva~~~gvs~~tlr~~~~~gli~~~~~~~~--g~r~-------y~~---------~--dl~~l~~i~~lr~-~g~~~~~   62 (70)
T smart00422        4 GEVAKLAGVSVRTLRYYERIGLLPPPIRTEG--GYRL-------YSD---------E--DLERLRFIKRLKE-LGFSLEE   62 (70)
T ss_pred             HHHHHHHCcCHHHHHHHHHCCCCCCCccCCC--CCEe-------cCH---------H--HHHHHHHHHHHHH-cCCCHHH
Confidence            4689999999999999976 222221 0100  0011       111         0  1223455666665 8888888


Q ss_pred             HHHHhC
Q 031871          110 LAQLIN  115 (151)
Q Consensus       110 LA~~lg  115 (151)
                      ++..+.
T Consensus        63 i~~~l~   68 (70)
T smart00422       63 IKELLE   68 (70)
T ss_pred             HHHHHh
Confidence            887664

>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA

Probab=87.79  E-value=0.87  Score=31.51  Aligned_cols=23  Identities=17%  Similarity=0.263  Sum_probs=20.6

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESG  127 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G  127 (151)
                      +|..|+|+.+||++++|..||+-
T Consensus         1 ~ti~eva~~~gvs~~tlR~ye~~   23 (103)
T cd01106           1 YTVGEVAKLTGVSVRTLHYYDEI   23 (103)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC
Confidence            57889999999999999999763

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

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

Probab=87.69  E-value=0.9  Score=31.32  Aligned_cols=23  Identities=13%  Similarity=0.211  Sum_probs=20.7

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESG  127 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G  127 (151)
                      ++..++|+.+|+++++|..||+-
T Consensus         1 ~~I~e~a~~~gvs~~tLR~ye~~   23 (96)
T cd04774           1 YKVDEVAKRLGLTKRTLKYYEEI   23 (96)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC
Confidence            57789999999999999999874

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.

>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator

Probab=87.60  E-value=0.91  Score=31.54  Aligned_cols=23  Identities=26%  Similarity=0.182  Sum_probs=21.2

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESG  127 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G  127 (151)
                      ++..|+|+.+|||++||..||+-
T Consensus         2 ~~i~eva~~~gvs~~tlR~ye~~   24 (102)
T cd04789           2 YTISELAEKAGISRSTLLYYEKL   24 (102)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC
Confidence            68899999999999999999874

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.

>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators

Probab=87.46  E-value=3.5  Score=28.22  Aligned_cols=20  Identities=30%  Similarity=0.260  Sum_probs=17.8

Q ss_pred             HHHHHHcCCChhhHHhhhcC
Q 031871           32 VNAARRAGADIETVRKSHAG   51 (151)
Q Consensus        32 ~~~a~r~g~~v~t~~k~~~g   51 (151)
                      -+.|++.|+++.|++-|+.-
T Consensus         4 ~eva~~~gvs~~tLRyye~~   23 (96)
T cd04768           4 GEFAKLAGVSIRTLRHYDDI   23 (96)
T ss_pred             HHHHHHHCcCHHHHHHHHHC
Confidence            46899999999999999974

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.

>PRK10458 DNA cytosine methylase; Provisional

Probab=87.43  E-value=1.5  Score=38.79  Aligned_cols=45  Identities=16%  Similarity=0.181  Sum_probs=34.4

Q ss_pred             HhcCCcCHHHHHHHhC------CCHHHHHHHHcCCCCC---CHHHHHHHHHHhC
Q 031871          100 RNDKKLTQSQLAQLIN------EKPQVIQEYESGKAIP---NQQILTKLERALG  144 (151)
Q Consensus       100 R~~~glTQ~eLA~~lg------is~s~Is~~E~G~~~p---~~~~l~kLa~~Lg  144 (151)
                      |...+++|++||+.+|      .+..+|.+||+|+..+   +...+..|-..+.
T Consensus        25 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (467)
T PRK10458         25 KLLEIYDVKTLAAQLNGVGENHWSRAILKRWLAGKSAWHRLSEAEFAHLQTLLP   78 (467)
T ss_pred             HHHHhcCHHHHHHHHhhcccCccCHHHHHHHHcCCCCCCCccHHHHHHHHHhcc
Confidence            4445789999999997      7889999999999743   4455566665553

>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=87.41  E-value=1.4  Score=27.44  Aligned_cols=29  Identities=14%  Similarity=0.168  Sum_probs=24.4

Q ss_pred             HHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           96 IVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      +..+.....+|..+||+.+|||..||.+-
T Consensus         6 l~~l~~~~~~s~~ela~~~~VS~~TiRRD   34 (57)
T PF08220_consen    6 LELLKEKGKVSVKELAEEFGVSEMTIRRD   34 (57)
T ss_pred             HHHHHHcCCEEHHHHHHHHCcCHHHHHHH
Confidence            45566677899999999999999999874

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

>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators

Probab=87.36  E-value=0.95  Score=31.06  Aligned_cols=24  Identities=21%  Similarity=0.326  Sum_probs=21.4

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcCC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESGK  128 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G~  128 (151)
                      +|..|+|+.+|||+.||.-||+-.
T Consensus         1 ~ti~eva~~~gvs~~tLRyye~~G   24 (96)
T cd04768           1 LTIGEFAKLAGVSIRTLRHYDDIG   24 (96)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCC
Confidence            478899999999999999999743

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.

>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR

Probab=87.26  E-value=1  Score=30.96  Aligned_cols=23  Identities=13%  Similarity=0.180  Sum_probs=20.9

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESG  127 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G  127 (151)
                      |+..|+|+.+|+|..+|..||+-
T Consensus         1 m~i~eva~~~gvs~~tlR~ye~~   23 (96)
T cd04788           1 WKIGELARRTGLSVRTLHHYDHI   23 (96)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC
Confidence            57889999999999999999863

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.

>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator

Probab=87.24  E-value=0.95  Score=31.72  Aligned_cols=23  Identities=22%  Similarity=0.300  Sum_probs=20.9

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESG  127 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G  127 (151)
                      ++..|+|+.+|||++||.-||+-
T Consensus         1 ~~i~eva~~~gis~~tlR~ye~~   23 (108)
T cd01107           1 FTIGEFAKLSNLSIKALRYYDKI   23 (108)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHc
Confidence            57889999999999999999874

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.

>TIGR01636 phage_rinA phage transcriptional activator, RinA family

Probab=87.19  E-value=2.5  Score=30.81  Aligned_cols=35  Identities=23%  Similarity=0.264  Sum_probs=30.6

Q ss_pred             CcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCC
Q 031871          104 KLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGV  145 (151)
Q Consensus       104 glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv  145 (151)
                      .+|..++|..+|+|++++.++.+       ..+.+||..||.
T Consensus       100 ~~t~~~Ia~~l~iS~~t~~r~r~-------~~l~kla~~lG~  134 (134)
T TIGR01636       100 PLTLVGLAQQLFISKSTAYRLRN-------HIIEAVAEELGM  134 (134)
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHH-------HHHHHHHHHhCc
Confidence            36999999999999999999876       668889988873

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.

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

Probab=87.16  E-value=0.7  Score=32.10  Aligned_cols=22  Identities=18%  Similarity=0.534  Sum_probs=20.1

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHc
Q 031871          105 LTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      +|..|+|+.+|||+++|..||+
T Consensus         1 yti~EvA~~~gVs~~tLR~ye~   22 (99)
T cd04765           1 FSIGEVAEILGLPPHVLRYWET   22 (99)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            4778999999999999999975

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.

>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=87.13  E-value=1.3  Score=27.57  Aligned_cols=29  Identities=14%  Similarity=0.126  Sum_probs=23.6

Q ss_pred             HHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           96 IVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      |+.+....++|..+||+.+|+++++++.-
T Consensus        16 l~~L~~~~~~t~~ela~~l~~~~~t~s~h   44 (61)
T PF12840_consen   16 LRLLASNGPMTVSELAEELGISQSTVSYH   44 (61)
T ss_dssp             HHHHHHCSTBEHHHHHHHHTS-HHHHHHH
T ss_pred             HHHHhcCCCCCHHHHHHHHCCCHHHHHHH
Confidence            44456889999999999999999998863

...

>TIGR02885 spore_sigF RNA polymerase sigma-F factor

Probab=87.10  E-value=1  Score=35.19  Aligned_cols=28  Identities=21%  Similarity=0.242  Sum_probs=24.8

Q ss_pred             HhcCCcCHHHHHHHhCCCHHHHHHHHcC
Q 031871          100 RNDKKLTQSQLAQLINEKPQVIQEYESG  127 (151)
Q Consensus       100 R~~~glTQ~eLA~~lgis~s~Is~~E~G  127 (151)
                      |-..|+|++++|+.+|+|+.+|+++++.
T Consensus       195 ~~~~~~t~~eIA~~lgis~~~V~~~~~~  222 (231)
T TIGR02885       195 RYFKDKTQTEVANMLGISQVQVSRLEKK  222 (231)
T ss_pred             HHHcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            4457999999999999999999999873

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.

>PF05930 Phage_AlpA: Prophage CP4-57 regulatory protein (AlpA); InterPro: IPR010260 This entry is represents phage P4, Orf88

Probab=87.08  E-value=0.29  Score=29.78  Aligned_cols=28  Identities=18%  Similarity=0.268  Sum_probs=20.4

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcCCCCCC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESGKAIPN  132 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G~~~p~  132 (151)
                      ++.+|+++.+|+|++++.++.+....|.
T Consensus         4 l~~~ev~~~~g~s~~ti~~~~k~g~FP~   31 (51)
T PF05930_consen    4 LRIKEVAELLGVSRSTIYRLIKDGKFPK   31 (51)
T ss_dssp             E-HHHHHHHHSS-HHHHHHHHHHHH---
T ss_pred             ccHHHHHHHHCCCHHHHHHHHhcccCCC
Confidence            5788999999999999999988555553

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.

>PF13551 HTH_29: Winged helix-turn helix

Probab=86.76  E-value=0.93  Score=30.91  Aligned_cols=26  Identities=8%  Similarity=0.142  Sum_probs=22.1

Q ss_pred             hcCCc-CHHHHHHHhCCCHHHHHHHHc
Q 031871          101 NDKKL-TQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus       101 ~~~gl-TQ~eLA~~lgis~s~Is~~E~  126 (151)
                      ...|+ |..++|+.+|+|++||.+|-+
T Consensus         8 ~~~g~~~~~~ia~~lg~s~~Tv~r~~~   34 (112)
T PF13551_consen    8 LAEGVSTIAEIARRLGISRRTVYRWLK   34 (112)
T ss_pred             HHcCCCcHHHHHHHHCcCHHHHHHHHH
Confidence            45678 599999999999999999843

>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator

Probab=86.76  E-value=2.1  Score=28.89  Aligned_cols=64  Identities=14%  Similarity=0.105  Sum_probs=40.4

Q ss_pred             HHHHHHcCCChhhHHhhhcC-CCccCCCCcccccccccccchhhhHHHHHhhccCCcchHHHHHHHHHHHhcCCcCHHHH
Q 031871           32 VNAARRAGADIETVRKSHAG-TNKAASSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQL  110 (151)
Q Consensus        32 ~~~a~r~g~~v~t~~k~~~g-~~~~~~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~~~~~~~~~Lk~~R~~~glTQ~eL  110 (151)
                      -+.|...|+++.|++.|+.- -..|..+.  ..-..       +..           ..-.....|+.++...|++.+++
T Consensus         5 ~e~A~~~gvs~~tLr~ye~~Gli~p~r~~--~g~R~-------y~~-----------~dv~~l~~i~~L~~d~g~~l~~i   64 (91)
T cd04766           5 SVAAELSGMHPQTLRLYERLGLLSPSRTD--GGTRR-------YSE-----------RDIERLRRIQRLTQELGVNLAGV   64 (91)
T ss_pred             HHHHHHHCcCHHHHHHHHHCCCcCCCcCC--CCCee-------ECH-----------HHHHHHHHHHHHHHHcCCCHHHH
Confidence            46899999999999999863 22221110  00111       111           11234566777888899999999


Q ss_pred             HHHhC
Q 031871          111 AQLIN  115 (151)
Q Consensus       111 A~~lg  115 (151)
                      +..+.
T Consensus        65 ~~~l~   69 (91)
T cd04766          65 KRILE   69 (91)
T ss_pred             HHHHH
Confidence            88875

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.

>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481

Probab=86.69  E-value=1.5  Score=30.01  Aligned_cols=31  Identities=6%  Similarity=0.064  Sum_probs=25.5

Q ss_pred             HHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           96 IVQARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      |-..-.+.|++..++|+..|||..|..+|..
T Consensus        17 lv~~vv~~g~~~a~aA~~~gVS~~Ta~kW~~   47 (85)
T PF13011_consen   17 LVRRVVEQGWPVAHAAAEFGVSRRTAYKWLA   47 (85)
T ss_pred             HHHHHHHcCCcHHHHHHHhCCCHHHHHHHHH
Confidence            3344456899999999999999999999954

>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional

Probab=86.69  E-value=0.24  Score=37.72  Aligned_cols=47  Identities=11%  Similarity=-0.000  Sum_probs=35.8

Q ss_pred             ccCHHHHHHHHHcCCChhhHHhhhcCCCccCCCCcccccccccccch
Q 031871           26 KKDEKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTE   72 (151)
Q Consensus        26 ~~~~~~~~~a~r~g~~v~t~~k~~~g~~~~~~~~~~~~~~kl~~~~~   72 (151)
                      .++-++.+.|+++|++.+|+.+||.|...|....+.+.+..|+...+
T Consensus        18 ~~glt~~elA~~~gis~~~is~~E~g~~~p~~~~l~~ia~~l~v~~~   64 (185)
T PRK09943         18 QQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSLS   64 (185)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHH
Confidence            34446678999999999999999999988766555566666665544

>PRK09706 transcriptional repressor DicA; Reviewed

Probab=86.68  E-value=0.23  Score=36.11  Aligned_cols=29  Identities=3%  Similarity=0.023  Sum_probs=24.6

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCccCCC
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNKAASS   58 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~~~~~   58 (151)
                      ++...|.+.|++.+|+.+|+.|...|..+
T Consensus        20 tq~~lA~~~gvs~~~is~~E~g~~~p~~~   48 (135)
T PRK09706         20 SQRSLAKAVKVSHVSISQWERDETEPTGK   48 (135)
T ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCCCCHH
Confidence            56789999999999999999998776443

>PRK09726 antitoxin HipB; Provisional

Probab=86.68  E-value=0.24  Score=33.48  Aligned_cols=44  Identities=9%  Similarity=0.072  Sum_probs=31.6

Q ss_pred             cCHHHHHHHHHcCCChhhHHhhhcCCCccCCCCccccccccccc
Q 031871           27 KDEKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDED   70 (151)
Q Consensus        27 ~~~~~~~~a~r~g~~v~t~~k~~~g~~~~~~~~~~~~~~kl~~~   70 (151)
                      ++-+.-++|++.|++.+|+.+|+.|...|..+.+.+.+..++..
T Consensus        24 ~gltq~elA~~~gvs~~tis~~e~g~~~ps~~~l~~ia~~lgv~   67 (88)
T PRK09726         24 NGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELS   67 (88)
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHcCCC
Confidence            34467789999999999999999998765444444444444443

>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed

Probab=86.64  E-value=0.38  Score=39.79  Aligned_cols=57  Identities=9%  Similarity=0.075  Sum_probs=39.4

Q ss_pred             eccCCCCCccccCHHHHHHHHHcCCChhhHHhhhcCCCccCCCCcccccccccccch
Q 031871           16 IKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTE   72 (151)
Q Consensus        16 ~~~~~~~~~~~~~~~~~~~a~r~g~~v~t~~k~~~g~~~~~~~~~~~~~~kl~~~~~   72 (151)
                      +|.+-...+..++-++...|.+.|++.+++.+||.|...|....+.+.+..|+.+.+
T Consensus        29 ~g~rl~~~R~~~gltq~~lA~~~gvs~~~i~~~E~g~~~ps~~~l~~ia~~l~v~~~   85 (309)
T PRK08154         29 LGERVRTLRARRGMSRKVLAQASGVSERYLAQLESGQGNVSILLLRRVARALGCSLA   85 (309)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHhCCCHH
Confidence            444433334445556788999999999999999999988765555555555555433

>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators

Probab=86.52  E-value=1.1  Score=31.03  Aligned_cols=23  Identities=22%  Similarity=0.198  Sum_probs=21.1

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESG  127 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G  127 (151)
                      +|..|+|+.+|||++||..||+-
T Consensus         2 ~~i~eva~~~gvs~~tLR~ye~~   24 (102)
T cd04775           2 YTIGQMSRKFGVSRSTLLYYESI   24 (102)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC
Confidence            67899999999999999999874

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

>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C

Probab=86.50  E-value=1.1  Score=27.56  Aligned_cols=34  Identities=12%  Similarity=0.234  Sum_probs=25.0

Q ss_pred             HHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCC
Q 031871           95 AIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK  128 (151)
Q Consensus        95 ~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~  128 (151)
                      .--..+.+.|++..++|+.+|-|+..|.+|.+.-
T Consensus        11 aqid~m~qlG~s~~~isr~i~RSr~~Ir~yl~dP   44 (50)
T PF11427_consen   11 AQIDVMHQLGMSLREISRRIGRSRTCIRRYLKDP   44 (50)
T ss_dssp             HHHHHHHHTT--HHHHHHHHT--HHHHHHHHHSC
T ss_pred             HHHHHHHHhchhHHHHHHHhCccHHHHHHHhcCh
Confidence            3345677899999999999999999999998753

>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily

Probab=86.37  E-value=1.2  Score=30.70  Aligned_cols=24  Identities=17%  Similarity=0.146  Sum_probs=21.4

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcCC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESGK  128 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G~  128 (151)
                      |+..|||+.+|++.++|..||+-.
T Consensus         1 m~I~eva~~~gvs~~tlR~Ye~~G   24 (95)
T cd04780           1 MRMSELSKRSGVSVATIKYYLREG   24 (95)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCC
Confidence            578899999999999999999744

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.

>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=86.36  E-value=0.56  Score=29.94  Aligned_cols=33  Identities=9%  Similarity=0.082  Sum_probs=23.8

Q ss_pred             HHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCC
Q 031871           96 IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAI  130 (151)
Q Consensus        96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~  130 (151)
                      |.++-.+.|  |.+.|+.+||+++.|++-.+-.+.
T Consensus         6 L~eyv~~~G--Q~kaA~~lGV~Q~AIsKAlr~gR~   38 (59)
T PF09048_consen    6 LAEYVKEHG--QAKAARALGVTQSAISKALRAGRN   38 (59)
T ss_dssp             HHHHHHHHH--HHHHHHHHTS-HHHHHHHHHCT-E
T ss_pred             HHHHHHHhC--hHHHHHHcCCcHHHHHHHHHcCCc
Confidence            334444555  999999999999999998775553

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 ....

>cd04772 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE

Probab=86.27  E-value=1.2  Score=30.81  Aligned_cols=24  Identities=33%  Similarity=0.446  Sum_probs=20.9

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcCC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESGK  128 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G~  128 (151)
                      ++..|+|+.+|||.+||..||+-.
T Consensus         1 y~i~e~A~~~gvs~~tlR~Ye~~G   24 (99)
T cd04772           1 YRTVDLARAIGLSPQTVRNYESLG   24 (99)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHcC
Confidence            367899999999999999999743

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.

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

Probab=86.07  E-value=1.2  Score=30.56  Aligned_cols=22  Identities=23%  Similarity=0.403  Sum_probs=20.2

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHc
Q 031871          105 LTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      +|..|+|+.+|||..+|..||+
T Consensus         1 ~~i~eva~~~gvs~~tlR~ye~   22 (97)
T cd04782           1 FTTGEFAKLCGISKQTLFHYDK   22 (97)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            4788999999999999999986

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.

>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial

Probab=86.07  E-value=1.7  Score=32.32  Aligned_cols=23  Identities=17%  Similarity=0.247  Sum_probs=20.5

Q ss_pred             CCcCHHHHHHHhCCCHHHHHHHH
Q 031871          103 KKLTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus       103 ~glTQ~eLA~~lgis~s~Is~~E  125 (151)
                      ..+||.|||..+|+++.+|++.-
T Consensus       142 ~~~t~~~iA~~lG~tretvsR~l  164 (193)
T TIGR03697       142 LRLSHQAIAEAIGSTRVTITRLL  164 (193)
T ss_pred             CCCCHHHHHHHhCCcHHHHHHHH
Confidence            45899999999999999999863

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.

>PF00292 PAX: 'Paired box' domain; InterPro: IPR001523 The paired box is a conserved 124 amino acid N-terminal domain of unknown function that usually, but not always, precedes a homeobox domain (see IPR001356 from INTERPRO) [, ]

Probab=86.03  E-value=2.2  Score=31.21  Aligned_cols=45  Identities=13%  Similarity=0.324  Sum_probs=33.9

Q ss_pred             hhccCCcchHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           81 LYCTDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        81 ~~~~~~~~~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      .|+++..+..++..+|-++-. .|+...++|+.+.||.+.|++|.+
T Consensus        11 ~~~nGrPLp~~~R~rIvela~-~G~rp~~Isr~l~Vs~gcVsKIl~   55 (125)
T PF00292_consen   11 VFINGRPLPNELRQRIVELAK-EGVRPCDISRQLRVSHGCVSKILS   55 (125)
T ss_dssp             EEETTSSS-HHHHHHHHHHHH-TT--HHHHHHHHT--HHHHHHHHH
T ss_pred             eeeCCccCcHHHHHHHHHHhh-hcCCHHHHHHHHccchhHHHHHHH
Confidence            477778888899888888775 599999999999999999999843

Paired box genes are expressed in alternate segments of the developing fruit fly, the observed grouping of segments into pairs depending on the position of the segment in the segmental array, and not on the identity of the segment as in the case of homeotic genes. This implies that the genes affect different processes from those altered by homeotic genes.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 6PAX_A 1K78_E 1MDM_A 2K27_A 1PDN_C.

>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator

Probab=85.63  E-value=1.3  Score=29.98  Aligned_cols=23  Identities=30%  Similarity=0.313  Sum_probs=20.8

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESG  127 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G  127 (151)
                      +|..++|+.+|||+++|..||.-
T Consensus         2 ~~i~e~A~~~gvs~~tLr~ye~~   24 (91)
T cd04766           2 YVISVAAELSGMHPQTLRLYERL   24 (91)
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHC
Confidence            57889999999999999999863

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.

>PRK11512 DNA-binding transcriptional repressor MarR; Provisional

Probab=85.58  E-value=2.5  Score=30.68  Aligned_cols=32  Identities=13%  Similarity=0.173  Sum_probs=26.1

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ...|..+...-++||.+||+.++++++++++.
T Consensus        43 ~~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~   74 (144)
T PRK11512         43 FKVLCSIRCAACITPVELKKVLSVDLGALTRM   74 (144)
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHH
Confidence            34455555667899999999999999999886

>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB

Probab=85.43  E-value=1.3  Score=31.08  Aligned_cols=24  Identities=17%  Similarity=0.220  Sum_probs=21.1

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcCC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESGK  128 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G~  128 (151)
                      +|..|+|+.+|||++||..||+-.
T Consensus         1 ~~i~e~a~~~gvs~~tlr~ye~~g   24 (113)
T cd01109           1 YTIKEVAEKTGLSADTLRYYEKEG   24 (113)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCC
Confidence            578899999999999999998743

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.

>smart00497 IENR1 Intron encoded nuclease repeat motif

Probab=85.38  E-value=1.4  Score=26.33  Aligned_cols=25  Identities=12%  Similarity=0.123  Sum_probs=22.4

Q ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCC
Q 031871          106 TQSQLAQLINEKPQVIQEYESGKAI  130 (151)
Q Consensus       106 TQ~eLA~~lgis~s~Is~~E~G~~~  130 (151)
                      |+.|.|+.+|+++++|++.-+|...
T Consensus        19 S~~eAa~~lg~~~~~I~~~~~~~~~   43 (53)
T smart00497       19 SIREAAKYLGISHSSISKYLNTGKK   43 (53)
T ss_pred             CHHHHHHHhCCCHHHHHHHHhCCCc
Confidence            7889999999999999999998643

Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).

>TIGR02044 CueR Cu(I)-responsive transcriptional regulator

Probab=85.25  E-value=1.3  Score=31.82  Aligned_cols=24  Identities=25%  Similarity=0.376  Sum_probs=21.6

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcCC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESGK  128 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G~  128 (151)
                      |+..|+|+.+|||..||.-||+-.
T Consensus         1 m~I~e~a~~~gvs~~tlRyYe~~G   24 (127)
T TIGR02044         1 MNIGQVAKLTGLSSKMIRYYEEKG   24 (127)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCC
Confidence            678999999999999999999744

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.

>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators

Probab=85.10  E-value=1  Score=31.91  Aligned_cols=23  Identities=26%  Similarity=0.274  Sum_probs=21.1

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESG  127 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G  127 (151)
                      ||..|+|+.+|||+.||.-||.-
T Consensus         1 ~~ige~a~~~gvs~~tLryYe~~   23 (116)
T cd04769           1 MYIGELAQQTGVTIKAIRLYEEK   23 (116)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC
Confidence            67899999999999999999974

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.

>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators

Probab=85.08  E-value=1.5  Score=30.31  Aligned_cols=22  Identities=27%  Similarity=0.454  Sum_probs=20.3

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHc
Q 031871          105 LTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      +|..++|+.+|||+++|..||+
T Consensus         2 ~~i~eva~~~gVs~~tLR~ye~   23 (98)
T cd01279           2 YPISVAAELLGIHPQTLRVYDR   23 (98)
T ss_pred             cCHHHHHHHHCcCHHHHHHHHH
Confidence            5788999999999999999976

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.

>PRK08215 sporulation sigma factor SigG; Reviewed

Probab=85.06  E-value=1.6  Score=34.91  Aligned_cols=31  Identities=23%  Similarity=0.181  Sum_probs=26.0

Q ss_pred             HHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           96 IVQARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      +-.+|-..|+|+.|+|+.+|+|+++|+++++
T Consensus       217 vi~~~~~~~~t~~eIA~~lgis~~~V~~~~~  247 (258)
T PRK08215        217 ILNLRFFQGKTQMEVAEEIGISQAQVSRLEK  247 (258)
T ss_pred             HHHHHHhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3334555799999999999999999999987

>COG0789 SoxR Predicted transcriptional regulators [Transcription]

Probab=85.00  E-value=1  Score=31.65  Aligned_cols=23  Identities=22%  Similarity=0.300  Sum_probs=20.8

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESG  127 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G  127 (151)
                      +|..++|+.+|||..||.-||+-
T Consensus         1 ~~I~eva~~~gvs~~tLRyYE~~   23 (124)
T COG0789           1 YTIGEVAKLTGVSVRTLRFYERK   23 (124)
T ss_pred             CcHHHHHHHhCCCHHHHHHHHHc
Confidence            57889999999999999999873

>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily

Probab=84.94  E-value=1.5  Score=30.94  Aligned_cols=23  Identities=17%  Similarity=0.229  Sum_probs=20.9

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESG  127 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G  127 (151)
                      |+..|+|+.+|+|.+||..||+-
T Consensus         1 m~i~eva~~~gvs~~tlR~Ye~~   23 (112)
T cd01282           1 MRIGELAARTGVSVRSLRYYEEQ   23 (112)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHC
Confidence            57889999999999999999873

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.

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=84.89  E-value=2.3  Score=25.38  Aligned_cols=21  Identities=24%  Similarity=0.366  Sum_probs=18.6

Q ss_pred             Cc-CHHHHHHHhCCCHHHHHHH
Q 031871          104 KL-TQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus       104 gl-TQ~eLA~~lgis~s~Is~~  124 (151)
                      .+ |+.+||+.+|+|++++.+.
T Consensus        19 ~l~s~~~la~~~~vs~~tv~~~   40 (60)
T smart00345       19 KLPSERELAAQLGVSRTTVREA   40 (60)
T ss_pred             cCcCHHHHHHHHCCCHHHHHHH
Confidence            46 8999999999999998875

>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator

Probab=84.86  E-value=5.3  Score=27.86  Aligned_cols=68  Identities=13%  Similarity=0.100  Sum_probs=38.1

Q ss_pred             HHHHHHcCCChhhHHhhhcCCC-ccCCCCcccccccccccchhhhHHHHHhhccCCcchHHHHHHHHHHHhcCCcCHHHH
Q 031871           32 VNAARRAGADIETVRKSHAGTN-KAASSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQL  110 (151)
Q Consensus        32 ~~~a~r~g~~v~t~~k~~~g~~-~~~~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~~~~~~~~~Lk~~R~~~glTQ~eL  110 (151)
                      -+.|++.|++++|++-|+.-.. .|........-+.-+..                  .-..-..|+.+|. .|++.+++
T Consensus         4 ~eva~~~gis~~tlR~ye~~GLi~p~~~~~~ngyR~Y~~~------------------~i~~l~~I~~lr~-~G~sl~~i   64 (108)
T cd01107           4 GEFAKLSNLSIKALRYYDKIGLLKPAYVDPDTGYRYYSAE------------------QLERLNRIKYLRD-LGFPLEEI   64 (108)
T ss_pred             HHHHHHHCcCHHHHHHHHHcCCCCCCcCCCCCCccccCHH------------------HHHHHHHHHHHHH-cCCCHHHH
Confidence            4689999999999999997422 22110000000111110                  1122344555554 88999998


Q ss_pred             HHHhCCCH
Q 031871          111 AQLINEKP  118 (151)
Q Consensus       111 A~~lgis~  118 (151)
                      ...+....
T Consensus        65 ~~l~~~~~   72 (108)
T cd01107          65 KEILDADN   72 (108)
T ss_pred             HHHHhcCC
Confidence            88776544

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.

>cd04781 HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily

Probab=84.83  E-value=1.5  Score=31.28  Aligned_cols=24  Identities=17%  Similarity=0.220  Sum_probs=21.6

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcCC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESGK  128 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G~  128 (151)
                      ||..|+|+.+|||..+|.-||+-.
T Consensus         1 m~IgevA~~~gvs~~tlRyYe~~G   24 (120)
T cd04781           1 LDIAEVARQSGLPASTLRYYEEKG   24 (120)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCC
Confidence            578999999999999999999743

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

>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator

Probab=84.82  E-value=1.5  Score=30.80  Aligned_cols=24  Identities=21%  Similarity=0.192  Sum_probs=21.1

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcCC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESGK  128 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G~  128 (151)
                      +|..|+|+.+|||..||..||+-.
T Consensus         1 y~Ige~A~~~gvs~~tlR~ye~~G   24 (107)
T cd01111           1 YSISQLALDAGVSVHIVRDYLLRG   24 (107)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCC
Confidence            477899999999999999998743

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,

>PRK09391 fixK transcriptional regulator FixK; Provisional

Probab=84.81  E-value=2.5  Score=33.09  Aligned_cols=22  Identities=5%  Similarity=0.169  Sum_probs=19.7

Q ss_pred             CCcCHHHHHHHhCCCHHHHHHH
Q 031871          103 KKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus       103 ~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ..+||.+||..+|+++.++++.
T Consensus       178 i~lt~~~IA~~lGisretlsR~  199 (230)
T PRK09391        178 LPMSRRDIADYLGLTIETVSRA  199 (230)
T ss_pred             ecCCHHHHHHHHCCCHHHHHHH
Confidence            3489999999999999999985

>PRK11891 aspartate carbamoyltransferase; Provisional

Probab=84.76  E-value=1.2  Score=38.88  Aligned_cols=36  Identities=11%  Similarity=0.118  Sum_probs=32.0

Q ss_pred             HHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcC
Q 031871           92 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESG  127 (151)
Q Consensus        92 ~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G  127 (151)
                      -.+-|++++.+.|||..+||+++|++..++.+|.--
T Consensus         4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~wl~p   39 (429)
T PRK11891          4 QQAFLRDAMRRLNMTREAFANRIGVSRRALDTWLLP   39 (429)
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHhCCcHHhHHhhcCC
Confidence            356689999999999999999999999999999653

>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=84.74  E-value=1.6  Score=27.68  Aligned_cols=34  Identities=9%  Similarity=0.057  Sum_probs=27.4

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      .+.+..+....++|..++|+.+|++++++++.-+
T Consensus        11 ~~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~   44 (68)
T PF01978_consen   11 AKVYLALLKNGPATAEEIAEELGISRSTVYRALK   44 (68)
T ss_dssp             HHHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            4445556677889999999999999999988643

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.

>PRK05572 sporulation sigma factor SigF; Validated

Probab=84.63  E-value=1.7  Score=34.64  Aligned_cols=29  Identities=24%  Similarity=0.180  Sum_probs=25.3

Q ss_pred             HHhcCCcCHHHHHHHhCCCHHHHHHHHcC
Q 031871           99 ARNDKKLTQSQLAQLINEKPQVIQEYESG  127 (151)
Q Consensus        99 ~R~~~glTQ~eLA~~lgis~s~Is~~E~G  127 (151)
                      ++-..|+|++++|+.+|+|+++|+++++.
T Consensus       213 l~~~~~~s~~eIA~~lgis~~~V~~~~~r  241 (252)
T PRK05572        213 LRYFKDKTQSEVAKRLGISQVQVSRLEKK  241 (252)
T ss_pred             HHHhCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            45567999999999999999999999873

>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators

Probab=84.54  E-value=1.1  Score=32.18  Aligned_cols=24  Identities=21%  Similarity=0.253  Sum_probs=21.3

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcCC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESGK  128 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G~  128 (151)
                      |+..|+|+.+|+|+.||.-||+-.
T Consensus         1 m~IgevA~~~gvs~~tLRyYe~~G   24 (127)
T cd04784           1 MKIGELAKKTGCSVETIRYYEKEG   24 (127)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCC
Confidence            578899999999999999998743

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.

>PF13730 HTH_36: Helix-turn-helix domain

Probab=84.53  E-value=1.3  Score=26.80  Aligned_cols=21  Identities=19%  Similarity=0.188  Sum_probs=19.0

Q ss_pred             CHHHHHHHhCCCHHHHHHHHc
Q 031871          106 TQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus       106 TQ~eLA~~lgis~s~Is~~E~  126 (151)
                      |++.||+.+|+|+.||.++-+
T Consensus        27 S~~~la~~~g~s~~Tv~~~i~   47 (55)
T PF13730_consen   27 SQETLAKDLGVSRRTVQRAIK   47 (55)
T ss_pred             CHHHHHHHHCcCHHHHHHHHH
Confidence            899999999999999998743

>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional

Probab=84.33  E-value=2.1  Score=33.21  Aligned_cols=22  Identities=9%  Similarity=0.220  Sum_probs=20.0

Q ss_pred             CcCHHHHHHHhCCCHHHHHHHH
Q 031871          104 KLTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus       104 glTQ~eLA~~lgis~s~Is~~E  125 (151)
                      .+||++||..+|+++.++++.-
T Consensus       184 ~lt~~~iA~~lG~sr~tvsR~l  205 (235)
T PRK11161        184 TMTRGDIGNYLGLTVETISRLL  205 (235)
T ss_pred             cccHHHHHHHhCCcHHHHHHHH
Confidence            4899999999999999999964

>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins

Probab=84.27  E-value=1.5  Score=25.89  Aligned_cols=25  Identities=8%  Similarity=0.169  Sum_probs=22.2

Q ss_pred             cCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871          102 DKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus       102 ~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      ..|+|..++|+.+|+|+++|..+-.
T Consensus        13 ~~~~s~~eia~~l~~s~~tv~~~~~   37 (57)
T cd06170          13 AEGKTNKEIADILGISEKTVKTHLR   37 (57)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            3689999999999999999998754

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

>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator

Probab=84.25  E-value=1.1  Score=32.11  Aligned_cols=24  Identities=25%  Similarity=0.304  Sum_probs=21.3

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcCC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESGK  128 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G~  128 (151)
                      |+..|+|+.+|+|+.||..||+-.
T Consensus         1 m~I~e~a~~~gvs~~tlR~Ye~~G   24 (126)
T cd04783           1 LTIGELAKAAGVNVETIRYYQRRG   24 (126)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCC
Confidence            578899999999999999998743

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.

>COG1318 Predicted transcriptional regulators [Transcription]

Probab=84.13  E-value=1.4  Score=34.14  Aligned_cols=33  Identities=21%  Similarity=0.301  Sum_probs=29.9

Q ss_pred             HHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCC
Q 031871           98 QARNDKKLTQSQLAQLINEKPQVIQEYESGKAI  130 (151)
Q Consensus        98 ~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~  130 (151)
                      -+|...|+|..++|+.+|.+.+||.++-+|...
T Consensus        55 ~arekag~Ti~EIAeelG~TeqTir~hlkgetk   87 (182)
T COG1318          55 LAREKAGMTISEIAEELGRTEQTVRNHLKGETK   87 (182)
T ss_pred             HHHHHccCcHHHHHHHhCCCHHHHHHHHhcchh
Confidence            356899999999999999999999999998754

>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators

Probab=84.10  E-value=1.2  Score=31.68  Aligned_cols=23  Identities=26%  Similarity=0.372  Sum_probs=20.9

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESG  127 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G  127 (151)
                      ||..|+|+.+|||+.+|.-||+-
T Consensus         1 ~~I~eva~~~gvs~~tLRyYe~~   23 (123)
T cd04770           1 MKIGELAKAAGVSPDTIRYYERI   23 (123)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC
Confidence            57899999999999999999873

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.

>PRK11169 leucine-responsive transcriptional regulator; Provisional

Probab=84.10  E-value=1.7  Score=32.66  Aligned_cols=31  Identities=13%  Similarity=0.324  Sum_probs=26.4

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHH
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQE  123 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~  123 (151)
                      .+-|..+...-.+|..+||+++|+|++++.+
T Consensus        17 ~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~   47 (164)
T PRK11169         17 RNILNELQKDGRISNVELSKRVGLSPTPCLE   47 (164)
T ss_pred             HHHHHHhccCCCCCHHHHHHHHCcCHHHHHH
Confidence            4556778888899999999999999988765

>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator

Probab=83.94  E-value=4  Score=28.66  Aligned_cols=19  Identities=26%  Similarity=0.256  Sum_probs=17.3

Q ss_pred             HHHHHHcCCChhhHHhhhc
Q 031871           32 VNAARRAGADIETVRKSHA   50 (151)
Q Consensus        32 ~~~a~r~g~~v~t~~k~~~   50 (151)
                      -+.|++.|+++.|++-|+.
T Consensus         4 ge~A~~~gvs~~tlR~ye~   22 (107)
T cd01111           4 SQLALDAGVSVHIVRDYLL   22 (107)
T ss_pred             HHHHHHHCcCHHHHHHHHH
Confidence            4689999999999999986

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,

>PRK00215 LexA repressor; Validated

Probab=83.90  E-value=2.3  Score=32.75  Aligned_cols=35  Identities=14%  Similarity=0.210  Sum_probs=26.6

Q ss_pred             HHHHHHHHHHHh--cCCcCHHHHHHHhCC-CHHHHHHH
Q 031871           90 SELKKAIVQARN--DKKLTQSQLAQLINE-KPQVIQEY  124 (151)
Q Consensus        90 ~~~~~~Lk~~R~--~~glTQ~eLA~~lgi-s~s~Is~~  124 (151)
                      ..+-..|.+.+.  ...+|+.|||+.+|+ ++++++++
T Consensus         7 ~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~   44 (205)
T PRK00215          7 QEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEH   44 (205)
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHH
Confidence            345555665443  445699999999999 99999998

>PRK12427 flagellar biosynthesis sigma factor; Provisional

Probab=83.87  E-value=1.8  Score=34.23  Aligned_cols=29  Identities=7%  Similarity=0.155  Sum_probs=25.2

Q ss_pred             HHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           98 QARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        98 ~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      .+|-..|+|++++|+.+|+|++.|+++++
T Consensus       193 ~l~~~~~~t~~EIA~~lgis~~~V~q~~~  221 (231)
T PRK12427        193 HLYYQHEMSLKEIALVLDLTEARICQLNK  221 (231)
T ss_pred             HHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            34456799999999999999999999876

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=83.83  E-value=2  Score=34.30  Aligned_cols=28  Identities=21%  Similarity=0.125  Sum_probs=24.8

Q ss_pred             HHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           99 ARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        99 ~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      +|-..|+|++++|+.+|+|+.+|+++++
T Consensus       217 ~~~~~~~t~~eIA~~lgis~~~V~~~~~  244 (254)
T TIGR02850       217 MRFFEGKTQMEVAEEIGISQAQVSRLEK  244 (254)
T ss_pred             HHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3445799999999999999999999986

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.

>TIGR00122 birA_repr_reg BirA biotin operon repressor domain

Probab=83.82  E-value=2.6  Score=26.78  Aligned_cols=25  Identities=8%  Similarity=0.194  Sum_probs=20.8

Q ss_pred             hcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871          101 NDKKLTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus       101 ~~~glTQ~eLA~~lgis~s~Is~~E  125 (151)
                      .+..++..+||+.+|+|+++|.+.-
T Consensus        10 ~~~~~~~~eLa~~l~vS~~tv~~~l   34 (69)
T TIGR00122        10 ADNPFSGEKLGEALGMSRTAVNKHI   34 (69)
T ss_pred             HcCCcCHHHHHHHHCCCHHHHHHHH
Confidence            3445889999999999999988763

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.

>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR

Probab=83.73  E-value=1.5  Score=31.42  Aligned_cols=30  Identities=13%  Similarity=0.199  Sum_probs=24.7

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHH
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQ  122 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is  122 (151)
                      .+.+-.++-..|+|.+|+|+.+|+|.+||.
T Consensus       112 ~r~v~~l~~~~~~s~~EIA~~l~is~~tV~  141 (142)
T TIGR03209       112 QKKIIYMKFFEDMKEIDIAKKLHISRQSVY  141 (142)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCcCHHhhc
Confidence            444555677789999999999999999985

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.

>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=83.58  E-value=5.1  Score=23.51  Aligned_cols=32  Identities=6%  Similarity=0.102  Sum_probs=25.8

Q ss_pred             HHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           95 AIVQARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        95 ~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      .+-..+--.++|..++|+++|++++++.++-.
T Consensus         7 ~l~~~~G~~~~s~~~Ia~~~gvs~~~~y~~f~   38 (47)
T PF00440_consen    7 ELFAEKGYEAVSIRDIARRAGVSKGSFYRYFP   38 (47)
T ss_dssp             HHHHHHHTTTSSHHHHHHHHTSCHHHHHHHCS
T ss_pred             HHHHHhCHHhCCHHHHHHHHccchhhHHHHcC
Confidence            34445566789999999999999999998743

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 ....

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

Probab=83.48  E-value=4.5  Score=27.98  Aligned_cols=19  Identities=16%  Similarity=0.029  Sum_probs=17.1

Q ss_pred             HHHHHHcCCChhhHHhhhc
Q 031871           32 VNAARRAGADIETVRKSHA   50 (151)
Q Consensus        32 ~~~a~r~g~~v~t~~k~~~   50 (151)
                      -+.|+..|++.+|++.|+.
T Consensus         4 ~EvA~~~gVs~~tLR~ye~   22 (99)
T cd04765           4 GEVAEILGLPPHVLRYWET   22 (99)
T ss_pred             HHHHHHHCcCHHHHHHHHH
Confidence            4689999999999999974

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.

>TIGR02392 rpoH_proteo alternative sigma factor RpoH

Probab=83.46  E-value=2.1  Score=34.63  Aligned_cols=24  Identities=29%  Similarity=0.307  Sum_probs=22.6

Q ss_pred             CCcCHHHHHHHhCCCHHHHHHHHc
Q 031871          103 KKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus       103 ~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      .++|++|+|+.+|||+.+|+++++
T Consensus       235 ~~~t~~eIA~~lgvS~~~V~q~~~  258 (270)
T TIGR02392       235 DKLTLQELAAEYGVSAERIRQIEK  258 (270)
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHH
Confidence            489999999999999999999986

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.

>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=83.41  E-value=2.5  Score=25.01  Aligned_cols=29  Identities=17%  Similarity=0.125  Sum_probs=22.3

Q ss_pred             HHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871           96 IVQARNDKKLTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus        96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E  125 (151)
                      |..+.. ..++..|||+.+|+++++|++.-
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            334444 77999999999999999999863

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 ....

>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator

Probab=83.35  E-value=4.2  Score=29.49  Aligned_cols=21  Identities=19%  Similarity=0.235  Sum_probs=18.2

Q ss_pred             HHHHHHHcCCChhhHHhhhcC
Q 031871           31 VVNAARRAGADIETVRKSHAG   51 (151)
Q Consensus        31 ~~~~a~r~g~~v~t~~k~~~g   51 (151)
                      .-+.|++.|+++.|++-|+.-
T Consensus         4 I~e~a~~~gvs~~tlR~Ye~~   24 (131)
T TIGR02043         4 IGELAKLCGVTSDTLRFYEKN   24 (131)
T ss_pred             HHHHHHHHCcCHHHHHHHHHC
Confidence            346899999999999999973

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.

>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator

Probab=83.25  E-value=1.3  Score=31.93  Aligned_cols=24  Identities=25%  Similarity=0.266  Sum_probs=21.3

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcCC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESGK  128 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G~  128 (151)
                      |+..|+|+.+|||..||..||+-.
T Consensus         1 m~I~e~a~~~gvs~~tlR~Ye~~G   24 (127)
T TIGR02047         1 MKIGELAQKTGVSVETIRFYEKQG   24 (127)
T ss_pred             CcHHHHHHHHCcCHHHHHHHHHCC
Confidence            578899999999999999998743

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.

>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases []

Probab=83.24  E-value=1.6  Score=24.57  Aligned_cols=19  Identities=16%  Similarity=0.295  Sum_probs=17.5

Q ss_pred             CHHHHHHHhCCCHHHHHHH
Q 031871          106 TQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus       106 TQ~eLA~~lgis~s~Is~~  124 (151)
                      |+.|.|+.+|+++++|+++
T Consensus        18 Si~eAa~~l~i~~~~I~~~   36 (37)
T PF07453_consen   18 SIREAARYLGISHSTISKY   36 (37)
T ss_pred             CHHHHHHHhCCCHHHHHHh
Confidence            7889999999999999875

>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators

Probab=83.21  E-value=3.1  Score=30.15  Aligned_cols=71  Identities=21%  Similarity=0.138  Sum_probs=44.6

Q ss_pred             HHHHHHHcCCChhhHHhhhc-CCCccCCCCcccccccccccchhhhHHHHHhhccCCcchHHHHHHHHHHHhcCCcCHHH
Q 031871           31 VVNAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQ  109 (151)
Q Consensus        31 ~~~~a~r~g~~v~t~~k~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~~~~~~~~~Lk~~R~~~glTQ~e  109 (151)
                      .-+.|++.|++..|++.|+. |-..|..    ..-..+      +.           .....--+.|+.++.+.|++.++
T Consensus         4 I~eVA~~~GVs~~TLR~wE~~GLl~p~r----~~G~R~------Ys-----------~~dv~rL~~I~~L~~e~G~~l~e   62 (120)
T cd04767           4 IGVVAELLNIHPETLRIWERHGLIKPAR----RNGQRL------YS-----------NNDLKRLRFIKKLINEKGLNIAG   62 (120)
T ss_pred             HHHHHHHHCcCHHHHHHHHHCCCCCCcC----CCCcEE------EC-----------HHHHHHHHHHHHHHHHcCCCHHH
Confidence            34689999999999999986 3332211    000000      11           11233456788888889999999


Q ss_pred             HHHHhCCCHHHHH
Q 031871          110 LAQLINEKPQVIQ  122 (151)
Q Consensus       110 LA~~lgis~s~Is  122 (151)
                      +...+..-+...+
T Consensus        63 I~~~L~l~~~~~~   75 (120)
T cd04767          63 VKQILSMYPCWSI   75 (120)
T ss_pred             HHHHHHhCccccc
Confidence            9988766544333

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

>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators

Probab=83.17  E-value=1.9  Score=31.10  Aligned_cols=24  Identities=21%  Similarity=0.272  Sum_probs=21.4

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcCC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESGK  128 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G~  128 (151)
                      ||..|+|+.+|||+.||.-||+-.
T Consensus         1 m~I~e~a~~~gvs~~tlRyYe~~G   24 (127)
T cd01108           1 MNIGEAAKLTGLSAKMIRYYEEIG   24 (127)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCC
Confidence            578999999999999999998743

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

>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR

Probab=83.13  E-value=9.3  Score=26.04  Aligned_cols=66  Identities=14%  Similarity=0.160  Sum_probs=38.6

Q ss_pred             HHHHHHcCCChhhHHhhhcC-CCccCCCCcccccccccccchhhhHHHHHhhccCCcchHHHHHHHHHHHhcCCcCHHHH
Q 031871           32 VNAARRAGADIETVRKSHAG-TNKAASSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQL  110 (151)
Q Consensus        32 ~~~a~r~g~~v~t~~k~~~g-~~~~~~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~~~~~~~~~Lk~~R~~~glTQ~eL  110 (151)
                      -+.|++.|+++.|++-|+.- --.|.... ...-+.-+.  +                .-..-..|+.+|. .|++.+++
T Consensus         4 ~eva~~~gvs~~tlR~ye~~Gll~p~~r~-~~gyR~Y~~--~----------------~l~~l~~I~~lr~-~G~~l~eI   63 (96)
T cd04788           4 GELARRTGLSVRTLHHYDHIGLLSPSQRT-EGGHRLYDR--A----------------DIRRLHQIIALRR-LGFSLREI   63 (96)
T ss_pred             HHHHHHHCcCHHHHHHHHHCCCCCCCccC-CCCceeeCH--H----------------HHHHHHHHHHHHH-cCCCHHHH
Confidence            46899999999999999973 22221110 000111111  1                1122444666654 69999999


Q ss_pred             HHHhCCC
Q 031871          111 AQLINEK  117 (151)
Q Consensus       111 A~~lgis  117 (151)
                      ...+...
T Consensus        64 ~~~l~~~   70 (96)
T cd04788          64 GRALDGP   70 (96)
T ss_pred             HHHHhCC
Confidence            9988654

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.

>TIGR02607 antidote_HigA addiction module antidote protein, HigA family

Probab=83.05  E-value=0.49  Score=30.59  Aligned_cols=26  Identities=15%  Similarity=0.201  Sum_probs=22.9

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCcc
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNKA   55 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~~   55 (151)
                      +..+.|++.|++..|+.+|++|...+
T Consensus        20 t~~~lA~~~gis~~tis~~~~g~~~~   45 (78)
T TIGR02607        20 SIRALAKALGVSRSTLSRIVNGRRGI   45 (78)
T ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCCC
Confidence            45689999999999999999998764

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.

>smart00351 PAX Paired Box domain

Probab=83.01  E-value=7  Score=28.07  Aligned_cols=21  Identities=14%  Similarity=0.109  Sum_probs=17.8

Q ss_pred             HHHHHHHHcCCChhhHHhhhc
Q 031871           30 KVVNAARRAGADIETVRKSHA   50 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~   50 (151)
                      +.-..|++.|++..|+.+|-.
T Consensus        35 s~~~iA~~~gvs~~tV~kwi~   55 (125)
T smart00351       35 RPCDISRQLCVSHGCVSKILG   55 (125)
T ss_pred             CHHHHHHHHCcCHHHHHHHHH
Confidence            456789999999999998854

>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily

Probab=82.76  E-value=2  Score=29.84  Aligned_cols=23  Identities=13%  Similarity=0.141  Sum_probs=20.9

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESG  127 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G  127 (151)
                      |+..|+|+.+|+|..||.-||+-
T Consensus         1 m~Ige~a~~~gvs~~tlRyYe~~   23 (107)
T cd04777           1 MKIGKFAKKNNITIDTVRHYIDL   23 (107)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC
Confidence            57889999999999999999873

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.

>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=82.60  E-value=0.34  Score=30.22  Aligned_cols=29  Identities=21%  Similarity=0.256  Sum_probs=21.3

Q ss_pred             CHHHHHHHHHcCCChhhHHhhhcCCCccC
Q 031871           28 DEKVVNAARRAGADIETVRKSHAGTNKAA   56 (151)
Q Consensus        28 ~~~~~~~a~r~g~~v~t~~k~~~g~~~~~   56 (151)
                      +-++-..|...|++.+++.+|++|...|.
T Consensus        12 ~lt~~~~a~~~~i~~~~i~~~e~g~~~~~   40 (64)
T PF12844_consen   12 GLTQKDLAEKLGISRSTISKIENGKRKPS   40 (64)
T ss_dssp             T--HHHHHHHHTS-HHHHHHHHTTSS--B
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHCCCcCCC
Confidence            34677889999999999999999987653

>TIGR02054 MerD mercuric resistence transcriptional repressor protein MerD

Probab=82.57  E-value=2.3  Score=30.70  Aligned_cols=25  Identities=24%  Similarity=0.224  Sum_probs=22.6

Q ss_pred             CcCHHHHHHHhCCCHHHHHHHHcCC
Q 031871          104 KLTQSQLAQLINEKPQVIQEYESGK  128 (151)
Q Consensus       104 glTQ~eLA~~lgis~s~Is~~E~G~  128 (151)
                      .+|..|||+.+|+|..||.-||+-.
T Consensus         3 ~~tI~elA~~~gvs~~tlR~Ye~~G   27 (120)
T TIGR02054         3 AYTISRLAEDAGVSVHVVRDYLLRG   27 (120)
T ss_pred             CCcHHHHHHHHCcCHHHHHHHHHCC
Confidence            5899999999999999999998743

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.

>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=82.55  E-value=1.1  Score=25.74  Aligned_cols=20  Identities=20%  Similarity=0.142  Sum_probs=16.7

Q ss_pred             HHHHHHcCCChhhHHhhhcC
Q 031871           32 VNAARRAGADIETVRKSHAG   51 (151)
Q Consensus        32 ~~~a~r~g~~v~t~~k~~~g   51 (151)
                      -+.|+..|+++.|++.|+.-
T Consensus         3 ~e~A~~~gvs~~tlR~ye~~   22 (38)
T PF00376_consen    3 GEVAKLLGVSPRTLRYYERE   22 (38)
T ss_dssp             HHHHHHHTS-HHHHHHHHHT
T ss_pred             HHHHHHHCCCHHHHHHHHHC
Confidence            36799999999999999974

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 ....

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

Probab=82.36  E-value=2.8  Score=29.87  Aligned_cols=37  Identities=5%  Similarity=0.102  Sum_probs=30.2

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      ..+|.+++-...+. |.|..++|...+||.+||.+|.+
T Consensus         4 S~DlR~rVl~~~~~-g~s~~eaa~~F~VS~~Tv~~W~k   40 (119)
T PF01710_consen    4 SLDLRQRVLAYIEK-GKSIREAAKRFGVSRNTVYRWLK   40 (119)
T ss_pred             CHHHHHHHHHHHHc-cchHHHHHHHhCcHHHHHHHHHH
Confidence            35667777666555 78999999999999999999955

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 [].

>cd01110 HTH_SoxR Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator

Probab=82.29  E-value=2.1  Score=31.53  Aligned_cols=23  Identities=17%  Similarity=0.219  Sum_probs=21.3

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESG  127 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G  127 (151)
                      ||..|+|+.+||+.+||.-||+-
T Consensus         2 ~~I~EvA~~~Gvs~~tLRyYE~~   24 (139)
T cd01110           2 LSVGEVAKRSGVAVSALHFYEQK   24 (139)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC
Confidence            78899999999999999999873

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.

>PRK06759 RNA polymerase factor sigma-70; Validated

Probab=82.29  E-value=2.7  Score=30.26  Aligned_cols=33  Identities=15%  Similarity=-0.089  Sum_probs=26.7

Q ss_pred             HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      ..+-.++-..|+|.+|+|+.+|+|.++|..+-.
T Consensus       112 r~ii~l~~~~~~s~~EIA~~l~is~~tV~~~~~  144 (154)
T PRK06759        112 KYIIFERFFVGKTMGEIALETEMTYYQVRWIYR  144 (154)
T ss_pred             HHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            344445667899999999999999999988754

>PRK13413 mpi multiple promoter invertase; Provisional

Probab=82.22  E-value=2.3  Score=32.73  Aligned_cols=32  Identities=16%  Similarity=0.229  Sum_probs=25.9

Q ss_pred             HHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcC
Q 031871           95 AIVQARNDKKLTQSQLAQLINEKPQVIQEYESG  127 (151)
Q Consensus        95 ~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G  127 (151)
                      .+..++ ..|+|..++|+.+|||++|+.++-+.
T Consensus       164 ~i~~~~-~~g~s~~~iak~lgis~~Tv~r~~k~  195 (200)
T PRK13413        164 KIKKLL-DKGTSKSEIARKLGVSRTTLARFLKT  195 (200)
T ss_pred             HHHHHH-HCCCCHHHHHHHHCCCHHHHHHHHHh
Confidence            344443 46899999999999999999999763

>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=82.14  E-value=4.2  Score=25.59  Aligned_cols=36  Identities=17%  Similarity=0.267  Sum_probs=25.2

Q ss_pred             HHHHHHHHHHH-hcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871           90 SELKKAIVQAR-NDKKLTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus        90 ~~~~~~Lk~~R-~~~glTQ~eLA~~lgis~s~Is~~E  125 (151)
                      +++-+.|-.+. .....+..+||+.+|+|+++++..-
T Consensus         7 e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml   43 (60)
T PF01325_consen    7 EDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTEML   43 (60)
T ss_dssp             HHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHHHH
Confidence            33444444443 4566899999999999999998763

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 ....

>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain

Probab=82.03  E-value=2.6  Score=33.28  Aligned_cols=26  Identities=19%  Similarity=0.221  Sum_probs=23.8

Q ss_pred             cCCcCHHHHHHHhCCCHHHHHHHHcC
Q 031871          102 DKKLTQSQLAQLINEKPQVIQEYESG  127 (151)
Q Consensus       102 ~~glTQ~eLA~~lgis~s~Is~~E~G  127 (151)
                      ..++|++++|+.+|+|+.+|++++..
T Consensus       194 ~~~~t~~EIA~~lgis~~~V~q~~~~  219 (238)
T TIGR02393       194 GRPHTLEEVGKEFNVTRERIRQIESK  219 (238)
T ss_pred             CCCccHHHHHHHHCCCHHHHHHHHHH
Confidence            57899999999999999999999873

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.

>COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]

Probab=81.93  E-value=1.6  Score=34.35  Aligned_cols=48  Identities=15%  Similarity=0.115  Sum_probs=42.7

Q ss_pred             HHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCC
Q 031871           98 QARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVK  146 (151)
Q Consensus        98 ~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~  146 (151)
                      +.+++.+.++.++++..|+++ ++..|.++-..++...+....++|+.+
T Consensus         6 rrq~el~~~~~~~~~~~g~~p-s~~e~~~~~~~~s~~~~~~~l~~L~~~   53 (201)
T COG1974           6 RRQKELLDFIRSLIKETGYPP-SIREIGDALGLASPSAIHSHLKALERK   53 (201)
T ss_pred             HHHHHHHHHHHHHHHHhCCCc-cHHHHHHhhCCCChHHHHHHHHHHhcC
Confidence            366777889999999999999 999999999999999999999988764

>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators

Probab=81.91  E-value=2.2  Score=30.89  Aligned_cols=23  Identities=22%  Similarity=0.414  Sum_probs=20.9

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESG  127 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G  127 (151)
                      ++..++|+.+||++++|..||+-
T Consensus         2 ysI~eVA~~~GVs~~TLR~wE~~   24 (120)
T cd04767           2 YPIGVVAELLNIHPETLRIWERH   24 (120)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC
Confidence            67899999999999999999863

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

>PRK06424 transcription factor; Provisional

Probab=81.83  E-value=0.5  Score=35.34  Aligned_cols=28  Identities=7%  Similarity=-0.033  Sum_probs=23.8

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCccCC
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNKAAS   57 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~~~~   57 (151)
                      ++.++|.+.|++.+++.+||+|...|..
T Consensus        99 SQ~eLA~~iGvs~stIskiE~G~~~Ps~  126 (144)
T PRK06424         99 SQADLAAKIFERKNVIASIERGDLLPDI  126 (144)
T ss_pred             CHHHHHHHhCCCHHHHHHHHCCCCCCCH
Confidence            4558899999999999999999987643

>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional

Probab=81.80  E-value=4.4  Score=29.75  Aligned_cols=21  Identities=19%  Similarity=0.113  Sum_probs=18.2

Q ss_pred             HHHHHHHcCCChhhHHhhhcC
Q 031871           31 VVNAARRAGADIETVRKSHAG   51 (151)
Q Consensus        31 ~~~~a~r~g~~v~t~~k~~~g   51 (151)
                      .-+.|++.|+++.|+|-|+.-
T Consensus         4 I~e~a~~~gvs~~tlR~Ye~~   24 (140)
T PRK09514          4 IGELAKLAEVTPDTLRFYEKQ   24 (140)
T ss_pred             HHHHHHHHCcCHHHHHHHHHC
Confidence            346899999999999999973

>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators

Probab=81.65  E-value=5.2  Score=27.50  Aligned_cols=66  Identities=18%  Similarity=0.207  Sum_probs=40.7

Q ss_pred             HHHHHHHcCCChhhHHhhhc-CCCccCCCCcccccccccccchhhhHHHHHhhccCCcchHHHHHHHHHHHhcCCcCHHH
Q 031871           31 VVNAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQ  109 (151)
Q Consensus        31 ~~~~a~r~g~~v~t~~k~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~~~~~~~~~Lk~~R~~~glTQ~e  109 (151)
                      .-+.|++.|++.+|++.|+. |-..|..+.  ..-..       +..           ..-..-..|+.++...|++.++
T Consensus         4 i~eva~~~gVs~~tLR~ye~~Gli~p~r~~--~g~R~-------Ys~-----------~dv~~l~~I~~L~~~~G~~l~~   63 (98)
T cd01279           4 ISVAAELLGIHPQTLRVYDRLGLVSPARTN--GGGRR-------YSN-----------NDLELLRQVQRLSQDEGFNLAG   63 (98)
T ss_pred             HHHHHHHHCcCHHHHHHHHHCCCCCCCcCC--CCCee-------ECH-----------HHHHHHHHHHHHHHHCCCCHHH
Confidence            34689999999999999976 222211000  00000       111           1223456677788889999999


Q ss_pred             HHHHhCC
Q 031871          110 LAQLINE  116 (151)
Q Consensus       110 LA~~lgi  116 (151)
                      +...+..
T Consensus        64 i~~~l~l   70 (98)
T cd01279          64 IKRIIEL   70 (98)
T ss_pred             HHHHHHh
Confidence            9988754

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.

>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR

Probab=81.63  E-value=2.4  Score=30.31  Aligned_cols=23  Identities=30%  Similarity=0.455  Sum_probs=20.7

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESG  127 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G  127 (151)
                      ++..|+|+.+|||..||.-||+-
T Consensus         1 ~~Igeva~~~gvs~~tlRyYe~~   23 (118)
T cd04776           1 YTISELAREFDVTPRTLRFYEDK   23 (118)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC
Confidence            46789999999999999999873

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.

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=81.55  E-value=3.6  Score=27.06  Aligned_cols=22  Identities=18%  Similarity=0.188  Sum_probs=20.4

Q ss_pred             CCcCHHHHHHHhCCCHHHHHHH
Q 031871          103 KKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus       103 ~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      .++|..|+|+.+|+++++++++
T Consensus        19 ~~~t~~~ia~~l~i~~~tv~r~   40 (91)
T smart00346       19 GGLTLAELAERLGLSKSTAHRL   40 (91)
T ss_pred             CCcCHHHHHHHhCCCHHHHHHH
Confidence            4799999999999999999887

>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional

Probab=81.52  E-value=4.3  Score=29.99  Aligned_cols=31  Identities=13%  Similarity=0.214  Sum_probs=25.9

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHH
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQE  123 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~  123 (151)
                      ..-|..+...-..|..+||+.+|+|++++.+
T Consensus        12 ~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~   42 (153)
T PRK11179         12 RGILEALMENARTPYAELAKQFGVSPGTIHV   42 (153)
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHH
Confidence            4446777778889999999999999988765

>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family

Probab=81.52  E-value=2.7  Score=31.23  Aligned_cols=33  Identities=18%  Similarity=0.211  Sum_probs=26.9

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E  125 (151)
                      ...+-.++...|+|.+|+|+.+|+|.++|...-
T Consensus       139 ~r~v~~l~~~~g~s~~EIA~~lgis~~tVk~~l  171 (183)
T TIGR02999       139 QAEVVELRFFAGLTVEEIAELLGVSVRTVERDW  171 (183)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Confidence            344555677789999999999999999998754

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.

>PRK13918 CRP/FNR family transcriptional regulator; Provisional

Probab=81.30  E-value=1.6  Score=32.95  Aligned_cols=23  Identities=13%  Similarity=0.130  Sum_probs=20.3

Q ss_pred             CCcCHHHHHHHhCCCHHHHHHHH
Q 031871          103 KKLTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus       103 ~glTQ~eLA~~lgis~s~Is~~E  125 (151)
                      ..+||.+||..+|+++.+|++..
T Consensus       148 ~~~t~~~iA~~lG~tretvsR~l  170 (202)
T PRK13918        148 IYATHDELAAAVGSVRETVTKVI  170 (202)
T ss_pred             ecCCHHHHHHHhCccHHHHHHHH
Confidence            35799999999999999999863

>COG3311 AlpA Predicted transcriptional regulator [Transcription]

Probab=81.29  E-value=2.6  Score=27.80  Aligned_cols=30  Identities=20%  Similarity=0.213  Sum_probs=25.6

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcCCCCCCHH
Q 031871          105 LTQSQLAQLINEKPQVIQEYESGKAIPNQQ  134 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G~~~p~~~  134 (151)
                      +...|+++.+|+|+++|.++.+....|..-
T Consensus        14 lrl~ev~~~~GlSrstiYr~i~~~~FPkpv   43 (70)
T COG3311          14 LRLPEVAQLTGLSRSTIYRLIKDGTFPKPV   43 (70)
T ss_pred             hhHHHHHHHHCccHHHHHHHHccCCCCCCe
Confidence            456799999999999999999988777653

>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators

Probab=81.29  E-value=2.4  Score=30.44  Aligned_cols=24  Identities=29%  Similarity=0.290  Sum_probs=21.3

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcCC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESGK  128 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G~  128 (151)
                      ||..|+|+.+|||..+|..||+-.
T Consensus         1 ~~I~e~a~~~gvs~~tlR~Ye~~G   24 (126)
T cd04785           1 LSIGELARRTGVNVETIRYYESIG   24 (126)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCC
Confidence            578899999999999999998743

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.

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

Probab=81.25  E-value=6.7  Score=26.84  Aligned_cols=19  Identities=16%  Similarity=0.079  Sum_probs=17.2

Q ss_pred             HHHHHHcCCChhhHHhhhc
Q 031871           32 VNAARRAGADIETVRKSHA   50 (151)
Q Consensus        32 ~~~a~r~g~~v~t~~k~~~   50 (151)
                      -+.|++.|++..|++-|+.
T Consensus         4 ~eva~~~gvs~~tlR~ye~   22 (97)
T cd04782           4 GEFAKLCGISKQTLFHYDK   22 (97)
T ss_pred             HHHHHHHCcCHHHHHHHHH
Confidence            4689999999999999986

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=81.25  E-value=2.5  Score=30.72  Aligned_cols=23  Identities=17%  Similarity=0.278  Sum_probs=20.8

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESG  127 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G  127 (151)
                      |+..|+|+.+|||..||.-||+-
T Consensus         1 m~IgE~A~~~gvs~~TLRyYE~~   23 (133)
T cd04787           1 MKVKELANAAGVTPDTVRFYTRI   23 (133)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC
Confidence            57889999999999999999863

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

>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=81.22  E-value=1.7  Score=26.77  Aligned_cols=25  Identities=4%  Similarity=0.207  Sum_probs=20.9

Q ss_pred             cCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871          102 DKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus       102 ~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      ..|++..++|+.+|+|+.+|..+-+
T Consensus        16 ~~G~~~~eIA~~l~is~~tV~~~~~   40 (58)
T PF00196_consen   16 AQGMSNKEIAEELGISEKTVKSHRR   40 (58)
T ss_dssp             HTTS-HHHHHHHHTSHHHHHHHHHH
T ss_pred             HhcCCcchhHHhcCcchhhHHHHHH
Confidence            4699999999999999999987643

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 ....

>TIGR00270 conserved hypothetical protein TIGR00270

Probab=81.21  E-value=0.58  Score=35.33  Aligned_cols=41  Identities=7%  Similarity=0.008  Sum_probs=29.0

Q ss_pred             CHHHHHHHHHcCCChhhHHhhhcCCCccCCCCccccccccc
Q 031871           28 DEKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLD   68 (151)
Q Consensus        28 ~~~~~~~a~r~g~~v~t~~k~~~g~~~~~~~~~~~~~~kl~   68 (151)
                      +-++-+.|.+.|++.+++.+||+|...|..+...+....|+
T Consensus        82 glSqeeLA~~lgvs~s~IsriE~G~~~Ps~~~l~kLa~~Lg  122 (154)
T TIGR00270        82 GWSQEQLAKKIQEKESLIKKIENAEIEPEPKVVEKLEKLLK  122 (154)
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHhC
Confidence            33556789999999999999999998765443333333333

>PRK13832 plasmid partitioning protein; Provisional

Probab=81.14  E-value=4.3  Score=36.35  Aligned_cols=50  Identities=16%  Similarity=0.114  Sum_probs=36.5

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHH
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLE  140 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa  140 (151)
                      ..+-...++++. +.|+|+.++|+.+|+|+++|+++-. -.......+..++
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            355677777777 7999999999999999999998644 2234444444443

>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional

Probab=80.91  E-value=1.7  Score=32.93  Aligned_cols=23  Identities=9%  Similarity=0.309  Sum_probs=20.6

Q ss_pred             CcCHHHHHHHhCCCHHHHHHHHc
Q 031871          104 KLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus       104 glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      .+||++||..+|+++.+++++-+
T Consensus       168 ~~t~~~lA~~lG~tr~tvsR~l~  190 (211)
T PRK11753        168 KITRQEIGRIVGCSREMVGRVLK  190 (211)
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHH
Confidence            58999999999999999999743

>PRK07037 extracytoplasmic-function sigma-70 factor; Validated

Probab=80.89  E-value=3  Score=30.34  Aligned_cols=29  Identities=14%  Similarity=0.141  Sum_probs=24.6

Q ss_pred             HHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           96 IVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      +-.++--.|+|.+|+|+.+|+|.++|...
T Consensus       117 v~~l~~~~~~s~~EIA~~lgis~~tV~~~  145 (163)
T PRK07037        117 AFEMYRLHGETQKDIARELGVSPTLVNFM  145 (163)
T ss_pred             HHHHHHHcCCCHHHHHHHHCCCHHHHHHH
Confidence            44455667999999999999999999986

>PRK12423 LexA repressor; Provisional

Probab=80.59  E-value=5.3  Score=30.99  Aligned_cols=35  Identities=11%  Similarity=0.116  Sum_probs=28.7

Q ss_pred             hHHHHHHHHHHHhcCCc--CHHHHHHHhC-CCHHHHHH
Q 031871           89 PSELKKAIVQARNDKKL--TQSQLAQLIN-EKPQVIQE  123 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~gl--TQ~eLA~~lg-is~s~Is~  123 (151)
                      ...+-..|+....+.|+  |..|||+.+| .|++++++
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            35677788888788888  9999999999 58988764

>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1

Probab=80.59  E-value=3.2  Score=29.63  Aligned_cols=29  Identities=7%  Similarity=-0.044  Sum_probs=24.5

Q ss_pred             HHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           98 QARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        98 ~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      .++-..|+|..|+|+.+|+|+++|.....
T Consensus       123 ~l~~~~~~~~~eIA~~lgis~~tv~~~~~  151 (161)
T TIGR02985       123 ILSRFEGKSYKEIAEELGISVKTVEYHIS  151 (161)
T ss_pred             HHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            34556799999999999999999988654

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.

>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily

Probab=80.57  E-value=3  Score=32.46  Aligned_cols=31  Identities=19%  Similarity=0.127  Sum_probs=25.8

Q ss_pred             HHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           96 IVQARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      +-.++-..|+|++|+|+.+|+|+++|..+..
T Consensus       186 vl~l~y~~~~s~~eIA~~lgis~~~v~~~~~  216 (227)
T TIGR02980       186 ILLLRFFEDKTQSEIAERLGISQMHVSRLLR  216 (227)
T ss_pred             HHHHHHhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3334556799999999999999999999865

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.

>PRK13890 conjugal transfer protein TrbA; Provisional

Probab=80.52  E-value=0.58  Score=33.70  Aligned_cols=28  Identities=14%  Similarity=0.236  Sum_probs=23.6

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCccCC
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNKAAS   57 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~~~~   57 (151)
                      +.-+.|+++|++.+++.+|+.|...|..
T Consensus        20 sq~eLA~~~Gis~~~is~iE~g~~~ps~   47 (120)
T PRK13890         20 TKKELSERSGVSISFLSDLTTGKANPSL   47 (120)
T ss_pred             CHHHHHHHHCcCHHHHHHHHcCCCCCCH
Confidence            4567999999999999999999876533

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=80.37  E-value=3.4  Score=28.24  Aligned_cols=29  Identities=14%  Similarity=0.392  Sum_probs=23.2

Q ss_pred             HHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           96 IVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      |..+.....+|..+||+.+|++++++.+.
T Consensus         9 l~~L~~~~~~~~~~la~~l~~s~~tv~~~   37 (108)
T smart00344        9 LEELQKDARISLAELAKKVGLSPSTVHNR   37 (108)
T ss_pred             HHHHHHhCCCCHHHHHHHHCcCHHHHHHH
Confidence            44444556799999999999999998764

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

>PRK10227 DNA-binding transcriptional regulator CueR; Provisional

Probab=80.36  E-value=2.7  Score=30.81  Aligned_cols=24  Identities=21%  Similarity=0.322  Sum_probs=21.5

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcCC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESGK  128 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G~  128 (151)
                      |+..|||+.+|+|..||.-||+-.
T Consensus         1 m~Ige~a~~~gvs~~tlRyYE~~G   24 (135)
T PRK10227          1 MNISDVAKITGLTSKAIRFYEEKG   24 (135)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCC
Confidence            678899999999999999998744

>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR

Probab=80.31  E-value=2.6  Score=31.18  Aligned_cols=23  Identities=30%  Similarity=0.294  Sum_probs=21.2

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESG  127 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G  127 (151)
                      ||..|+|+.+|+|+.||.-||+-
T Consensus         2 ~~IgevA~~~Gvs~~tLRyYE~~   24 (142)
T TIGR01950         2 LTVGELAKRSGVAVSALHFYESK   24 (142)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC
Confidence            68899999999999999999873

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.

>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein

Probab=80.17  E-value=5.8  Score=26.00  Aligned_cols=35  Identities=14%  Similarity=0.158  Sum_probs=27.1

Q ss_pred             HHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           90 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        90 ~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ..-...|..+....++++.++|+.+++++++|++.
T Consensus        10 ~~~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~   44 (101)
T smart00347       10 PTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRV   44 (101)
T ss_pred             HHHHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHH
Confidence            34444556666666899999999999999988875

>PF06322 Phage_NinH: Phage NinH protein; InterPro: IPR010454 This entry is represented by Bacteriophage 933W, NinH

Probab=80.15  E-value=2.1  Score=27.61  Aligned_cols=23  Identities=17%  Similarity=0.388  Sum_probs=20.7

Q ss_pred             CHHHHHHHhCCCHHHHHHHHcCC
Q 031871          106 TQSQLAQLINEKPQVIQEYESGK  128 (151)
Q Consensus       106 TQ~eLA~~lgis~s~Is~~E~G~  128 (151)
                      .|.|+|+.+++++.||.+|-...
T Consensus        18 nqtEvaR~l~c~R~TVrKY~~D~   40 (64)
T PF06322_consen   18 NQTEVARRLGCNRATVRKYSRDK   40 (64)
T ss_pred             cHHHHHHHhcccHHHHHHHhccc
Confidence            79999999999999999997643

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional

Probab=80.03  E-value=2.7  Score=30.90  Aligned_cols=24  Identities=25%  Similarity=0.397  Sum_probs=21.6

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcCC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESGK  128 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G~  128 (151)
                      ++..|+|+.+|||+.||..||+-.
T Consensus         2 ~~I~e~a~~~gvs~~tlR~Ye~~G   25 (140)
T PRK09514          2 YRIGELAKLAEVTPDTLRFYEKQG   25 (140)
T ss_pred             CcHHHHHHHHCcCHHHHHHHHHCC
Confidence            678999999999999999998743

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	151
1x57_A	91	Solution Structures Of The Hth Domain Of Human Edf-		9e-18
2jvl_A	107	Nmr Structure Of The C-Terminal Domain Of Mbf1 Of T		3e-08

>pdb|1X57|A Chain A, Solution Structures Of The Hth Domain Of Human Edf-1 Protein Length = 91

Iteration: 1
 Score = 85.5 bits (210), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 42/68 (61%), Positives = 50/68 (73%)
Query: 83  CTDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERA 142
            + DRV  E+ K I Q R  K LTQ  LA  INEKPQVI +YESG+AIPN Q+L K+ERA
Sbjct: 5   SSGDRVTLEVGKVIQQGRQSKGLTQKDLATKINEKPQVIADYESGRAIPNNQVLGKIERA 64
Query: 143 LGVKLRGK 150
           +G+KLRGK
Sbjct: 65  IGLKLRGK 72

>pdb|2JVL|A Chain A, Nmr Structure Of The C-Terminal Domain Of Mbf1 Of Trichoderm Length = 107

Iteration: 1
 Score = 53.9 bits (128), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 29/64 (45%), Positives = 39/64 (60%), Gaps = 2/64 (3%)
Query: 88  VPSELKKAIVQARN--DKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGV 145
           V  E+ KAI Q R   +  +TQ++L + I E    +  YE G A P+Q IL+K+ER L V
Sbjct: 31  VGKEVGKAIEQGRQKFEPTMTQAELGKEIGETAATVASYERGTATPDQNILSKMERVLNV 90
Query: 146 KLRG 149
           KLRG
Sbjct: 91  KLRG 94

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	151
2jvl_A	107	TRMBF1; coactivator, helix-turn-helix, Pro binding	7e-25
1x57_A	91	Endothelial differentiation-related factor 1; HMBF	2e-22
1adr_A	76	P22 C2 repressor; transcription regulation; NMR {E	1e-09
2r1j_L	68	Repressor protein C2; protein-DNA complex, helix-t	4e-09
2wiu_B	88	HTH-type transcriptional regulator HIPB; transfera	3e-08
1r69_A	69	Repressor protein CI; gene regulating protein; 2.0	6e-08
1zug_A	71	Phage 434 CRO protein; gene regulating protein, tr	1e-07
3omt_A	73	Uncharacterized protein; structural genomics, PSI-	1e-07
2p5t_A	158	Putative transcriptional regulator PEZA; postsegre	1e-07
2kpj_A	94	SOS-response transcriptional repressor, LEXA; NESG	1e-07
3ivp_A	126	Putative transposon-related DNA-binding protein; A	2e-07
3op9_A	114	PLI0006 protein; structural genomics, PSI-2, prote	3e-07
3bs3_A	76	Putative DNA-binding protein; XRE-family, structur	3e-07
3bdn_A	236	Lambda repressor; repressor, allostery; HET: DNA;	3e-07
4ghj_A	101	Probable transcriptional regulator; structural gen	5e-07
3kxa_A	141	NGO0477 protein, putative uncharacterized protein;	7e-07
3f6w_A	83	XRE-family like protein; helix-turn-helix, DNA bin	1e-06
3mlf_A	111	Transcriptional regulator; structural genomics, he	1e-06
2ef8_A	84	C.ECOT38IS, putative transcription factor; helix-t	2e-06
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-06
3lfp_A	98	CSP231I C protein; transcriptional regulator, DNA	7e-06
3o9x_A	133	Uncharacterized HTH-type transcriptional regulato;	1e-05
2ewt_A	71	BLDD, putative DNA-binding protein; the DNA-bindin	2e-05
2bnm_A	198	Epoxidase; oxidoreductase, cupin, HTH, cation-depe	2e-05
2l49_A	99	C protein; P2 bacteriophage, P2 C, direct repeats,	1e-04
1y7y_A	74	C.AHDI; helix-turn-helix, DNA-binding protein, tra	1e-04
3eus_A	86	DNA-binding protein; structural genomics, PSI2,MCS	1e-04
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	2e-04
3fmy_A	73	HTH-type transcriptional regulator MQSA (YGIT/B302	8e-04

>2jvl_A TRMBF1; coactivator, helix-turn-helix, Pro binding, transcription; NMR {Trichoderma reesei} Length = 107

 Score = 91.1 bits (226), Expect = 7e-25
 Identities = 33/104 (31%), Positives = 48/104 (46%), Gaps = 11/104 (10%)

Query: 50  AGTNKAASSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARN--DKKLTQ 107
           A   + A  +      K+D   + +             V  E+ KAI Q R   +  +TQ
Sbjct: 2   AMDPEFAGGTEGQRLTKVDRSDDIIK---------PKTVGKEVGKAIEQGRQKFEPTMTQ 52

Query: 108 SQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRGKK 151
           ++L + I E    +  YE G A P+Q IL+K+ER L VKLRG  
Sbjct: 53  AELGKEIGETAATVASYERGTATPDQNILSKMERVLNVKLRGAN 96

>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 = 84.1 bits (208), Expect = 2e-22
 Identities = 42/68 (61%), Positives = 50/68 (73%)

Query: 84  TDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERAL 143
           + DRV  E+ K I Q R  K LTQ  LA  INEKPQVI +YESG+AIPN Q+L K+ERA+
Sbjct: 6   SGDRVTLEVGKVIQQGRQSKGLTQKDLATKINEKPQVIADYESGRAIPNNQVLGKIERAI 65

Query: 144 GVKLRGKK 151
           G+KLRGK 
Sbjct: 66  GLKLRGKD 73

>1adr_A P22 C2 repressor; transcription regulation; NMR {Enterobacteria phage P22} SCOP: a.35.1.2 Length = 76

 Score = 50.7 bits (122), Expect = 1e-09
 Identities = 13/55 (23%), Positives = 25/55 (45%)

Query: 91  ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGV 145
            + + I   R   K+ Q+ L +++      I ++E  +  PN + L  L +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 = 49.1 bits (118), Expect = 4e-09
 Identities = 13/55 (23%), Positives = 25/55 (45%)

Query: 91  ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGV 145
            + + I   R   K+ Q+ L +++      I ++E  +  PN + L  L +AL  
Sbjct: 5   LMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQC 59

>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 = 47.5 bits (113), Expect = 3e-08
 Identities = 15/61 (24%), Positives = 27/61 (44%)

Query: 87  RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVK 146
             P++L  A+   R     TQS+LA+ I  K   I  +E+           K+ ++L + 
Sbjct: 8   YSPTQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELS 67

Query: 147 L 147
           +
Sbjct: 68  M 68

>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 = 46.1 bits (110), Expect = 6e-08
 Identities = 17/50 (34%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 96  IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGV 145
           +   R    L Q++LAQ +    Q I++ E+GK     + L +L  ALGV
Sbjct: 6   VKSKRIQLGLNQAELAQKVGTTQQSIEQLENGKT-KRPRFLPELASALGV 54

>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 = 45.4 bits (108), Expect = 1e-07
 Identities = 15/56 (26%), Positives = 26/56 (46%), Gaps = 1/56 (1%)

Query: 90  SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGV 145
             L + + + R   K+TQ++LA     K Q IQ  E+G     + +  ++  AL  
Sbjct: 2   QTLSERLKKRRIALKMTQTELATKAGVKQQSIQLIEAGVTKRPRFLF-EIAMALNC 56

>3omt_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; 1.65A {Cytophaga hutchinsonii} Length = 73

 Score = 45.4 bits (108), Expect = 1e-07
 Identities = 9/53 (16%), Positives = 23/53 (43%)

Query: 96  IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 148
           +     +K  T   L + +++    + ++ +    P+ + L  +  AL V +R
Sbjct: 13  LKSVLAEKGKTNLWLTETLDKNKTTVSKWCTNDVQPSLETLFDIAEALNVDVR 65

>2p5t_A Putative transcriptional regulator PEZA; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae} Length = 158

 Score = 47.2 bits (112), Expect = 1e-07
 Identities = 11/54 (20%), Positives = 25/54 (46%)

Query: 92  LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGV 145
           + K I   R    LTQ + A+++      +  YE+G +  + +++  + +   V
Sbjct: 2   IGKNIKSLRKTHDLTQLEFARIVGISRNSLSRYENGTSSVSTELIDIICQKFNV 55

>2kpj_A SOS-response transcriptional repressor, LEXA; NESG, GFT, structural genomics, PSI-2, protein structure initiative; NMR {Eubacterium rectale atcc 33656} Length = 94

 Score = 45.9 bits (109), Expect = 1e-07
 Identities = 11/56 (19%), Positives = 20/56 (35%)

Query: 92  LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 147
             + +       + TQ ++A+ I   PQ    +  G AIP    +  L     +  
Sbjct: 10  FSENLNSYIAKSEKTQLEIAKSIGVSPQTFNTWCKGIAIPRMGKVQALADYFNINK 65

>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 = 46.4 bits (110), Expect = 2e-07
 Identities = 17/57 (29%), Positives = 28/57 (49%)

Query: 91  ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 147
            L  AI +AR  + LT+ Q+  +I   P+ +   E+    P+ Q+L  L   L V +
Sbjct: 12  ALGLAIKEARKKQGLTREQVGAMIEIDPRYLTNIENKGQHPSLQVLYDLVSLLNVSV 68

>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 = 45.5 bits (108), Expect = 3e-07
 Identities = 11/55 (20%), Positives = 28/55 (50%)

Query: 91  ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGV 145
           +  + + + + +  L   Q+A+L+N + + +  Y SG+  P+ + L +L     +
Sbjct: 9   QFAENLSRLKKEHGLKNHQIAELLNVQTRTVAYYMSGETKPDIEKLIRLATYFHL 63

>3bs3_A Putative DNA-binding protein; XRE-family, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.65A {Bacteroides fragilis} Length = 76

 Score = 44.6 bits (106), Expect = 3e-07
 Identities = 14/53 (26%), Positives = 24/53 (45%)

Query: 96  IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 148
           I     +K+ T   LA+ + +    I  + S K+ P+  +L K+   L V  R
Sbjct: 15  IKVVLAEKQRTNRWLAEQMGKSENTISRWCSNKSQPSLDMLVKVAELLNVDPR 67

>3bdn_A Lambda repressor; repressor, allostery; HET: DNA; 3.91A {Enterobacteria phage lambda} Length = 236

 Score = 46.9 bits (111), Expect = 3e-07
 Identities = 11/59 (18%), Positives = 20/59 (33%)

Query: 87  RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGV 145
                LK    + +N+  L+Q  +A  +      +    +G    N      L + L V
Sbjct: 13  EDARRLKAIYEKKKNELGLSQESVADKMGMGQSGVGALFNGINALNAYNAALLAKILKV 71

>4ghj_A Probable transcriptional regulator; structural genomics, niaid, national institute of allergy AN infectious diseases; HET: MSE; 1.75A {Vibrio vulnificus} Length = 101

 Score = 44.6 bits (105), Expect = 5e-07
 Identities = 21/80 (26%), Positives = 39/80 (48%), Gaps = 3/80 (3%)

Query: 67  LDEDTENLALLLSVLYC-TDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE 125
           +D  TENL    + +   T   +  E+   + QAR ++ LTQS++A++     + +   E
Sbjct: 11  VDLGTENLYFQSNAMKHVTAAALAEEIGDRLKQARLNRDLTQSEVAEIAGIARKTVLNAE 70

Query: 126 SGKAIPNQQILTKLERALGV 145
            GK   +  I+  +  AL +
Sbjct: 71  KGKVQLD--IMIAILMALDL 88

>3kxa_A NGO0477 protein, putative uncharacterized protein; NEW protein fold, OPPF, STRU genomics, oxford protein production facility; 2.80A {Neisseria gonorrhoeae} Length = 141

 Score = 44.9 bits (106), Expect = 7e-07
 Identities = 24/111 (21%), Positives = 35/111 (31%), Gaps = 4/111 (3%)

Query: 37  RAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAI 96
           R    I+ V+     T  AA     +            A+  +     D        +  
Sbjct: 18  RINGQIKCVKPISPNTTPAAEHIEHVR----KNPRRKAAMDRAAARIADKIALKAGGETF 73

Query: 97  VQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 147
           V  R  K  TQS+LA         +   E+ K     + + KL  ALGV  
Sbjct: 74  VSLRMKKGFTQSELATAAGLPQPYLSRIENSKQSLQDKTVQKLANALGVSP 124

>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 = 43.1 bits (102), Expect = 1e-06
 Identities = 10/57 (17%), Positives = 23/57 (40%)

Query: 91  ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 147
            L   +++AR+   +TQ +LA  +      + + E+ +   +        R +G   
Sbjct: 14  ALLDLLLEARSAAGITQKELAARLGRPQSFVSKTENAERRLDVIEFMDFCRGIGTDP 70

>3mlf_A Transcriptional regulator; structural genomics, helix-turn-helix XRE-family like protei transcription regulator, PSI-2; 2.60A {Staphylococcus aureus subsp} Length = 111

 Score = 43.9 bits (103), Expect = 1e-06
 Identities = 17/58 (29%), Positives = 23/58 (39%)

Query: 90  SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 147
           S   K + + R D  LTQ +L  L     + IQ  E         +L+K   A  VK 
Sbjct: 22  SNAMKTLKELRTDYGLTQKELGDLFKVSSRTIQNMEKDSTNIKDSLLSKYMSAFNVKY 79

>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 = 42.5 bits (100), Expect = 2e-06
 Identities = 13/56 (23%), Positives = 26/56 (46%)

Query: 92  LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 147
           L + + + R +  L+QS+LA  +      I + ES +   +   L +L   +  +L
Sbjct: 11  LVQLLTKLRKEASLSQSELAIFLGLSQSDISKIESFERRLDALELFELLEVVASRL 66

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 44.5 bits (104), Expect = 5e-06
 Identities = 26/187 (13%), Positives = 52/187 (27%), Gaps = 63/187 (33%)

Query: 11  WEPVVIKK---KAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKL 67
                            T + ++V +        +     +H   +  + +        L
Sbjct: 254 QNAKAWNAFNLSCKILLTTRFKQVTDF-------LSAATTTHISLDHHSMT--------L 298

Query: 68  DEDTENLALLLSVLYCTDDRVPSELKK------AIVQA-------RND--KKLTQSQLAQ 112
             D E  +LLL  L C    +P E+        +I+           D  K +   +L  
Sbjct: 299 TPD-EVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTT 357

Query: 113 LI-----NEKPQVIQEY--------ESGKAIPNQ---------------QILTKLERALG 144
           +I       +P   ++          S   IP                  ++ KL +   
Sbjct: 358 IIESSLNVLEPAEYRKMFDRLSVFPPSAH-IPTILLSLIWFDVIKSDVMVVVNKLHKYSL 416

Query: 145 VKLRGKK 151
           V+ + K+
Sbjct: 417 VEKQPKE 423

>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 = 41.4 bits (97), Expect = 7e-06
 Identities = 12/52 (23%), Positives = 23/52 (44%), Gaps = 4/52 (7%)

Query: 98  QARNDKKLTQSQLAQLINEKPQV----IQEYESGKAIPNQQILTKLERALGV 145
            AR    ++Q +L  L           + +YE GK  P+ ++  +L + L +
Sbjct: 8   DARLRAGISQEKLGVLAGIDEASASARMNQYEKGKHAPDFEMANRLAKVLKI 59

>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 Length = 133

 Score = 41.3 bits (96), Expect = 1e-05
 Identities = 12/75 (16%), Positives = 28/75 (37%)

Query: 66  KLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE 125
            ++++  +  +     +       +   + IV+ R    LTQ + +++          YE
Sbjct: 46  IMNKEESDAFMAQVKAFRASVNAETVAPEFIVKVRKKLSLTQKEASEIFGGGVNAFSRYE 105

Query: 126 SGKAIPNQQILTKLE 140
            G A P+   +  L 
Sbjct: 106 KGNAQPHPSTIKLLR 120

>2ewt_A BLDD, putative DNA-binding protein; the DNA-binding domain of BLDD; 1.81A {Streptomyces coelicolor} Length = 71

 Score = 39.7 bits (93), Expect = 2e-05
 Identities = 12/52 (23%), Positives = 19/52 (36%), Gaps = 2/52 (3%)

Query: 98  QARNDKKLTQSQLAQLINE--KPQVIQEYESGKAIPNQQILTKLERALGVKL 147
             R  + L+   + +      K  V+  YE G      Q L +L    GV +
Sbjct: 15  AIRTQQGLSLHGVEEKSQGRWKAVVVGSYERGDRAVTVQRLAELADFYGVPV 66

>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 Length = 198

 Score = 41.4 bits (97), Expect = 2e-05
 Identities = 12/65 (18%), Positives = 26/65 (40%), Gaps = 1/65 (1%)

Query: 84  TDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIP-NQQILTKLERA 142
                 +   + +   R   K+  + LA L+ E P+ +  +E+G+        L ++   
Sbjct: 3   NTKTASTGFAELLKDRREQVKMDHAALASLLGETPETVAAWENGEGGELTLTQLGRIAHV 62

Query: 143 LGVKL 147
           LG  +
Sbjct: 63  LGTSI 67

>2l49_A C protein; P2 bacteriophage, P2 C, direct repeats, DNA-binding protein, binding protein; NMR {Enterobacteria phage P2} PDB: 2xcj_A Length = 99

 Score = 38.4 bits (89), Expect = 1e-04
 Identities = 13/50 (26%), Positives = 25/50 (50%)

Query: 90  SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKL 139
           + + + IV  R  + L++ QLA L       +  YESG++ P   ++  +
Sbjct: 3   NTISEKIVLMRKSEYLSRQQLADLTGVPYGTLSYYESGRSTPPTDVMMNI 52

>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 = 37.6 bits (88), Expect = 1e-04
 Identities = 13/54 (24%), Positives = 23/54 (42%)

Query: 94  KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 147
           + + + R  K L+Q  LA L       +   E G+   +   + KL  AL ++ 
Sbjct: 16  QRLRELRTAKGLSQETLAFLSGLDRSYVGGVERGQRNVSLVNILKLATALDIEP 69

>3eus_A DNA-binding protein; structural genomics, PSI2,MCSG, protein structure initiative, midwest center for structural genomic binding; 1.80A {Silicibacter pomeroyi} Length = 86

 Score = 37.5 bits (87), Expect = 1e-04
 Identities = 13/53 (24%), Positives = 25/53 (47%)

Query: 92  LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALG 144
           L + + QAR D  LTQ+ LA+ +++    + + E+ +   +     K   A  
Sbjct: 15  LCQRLRQARLDAGLTQADLAERLDKPQSFVAKVETRERRLDVIEFAKWMAACE 67

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646} Length = 293

 Score = 39.4 bits (91), Expect = 2e-04
 Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 1/55 (1%)

Query: 94  KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 148
             I + R  + LTQ QL++ I  + +V +  ESG   P+  IL  +   L + + 
Sbjct: 8   SEIKKIRVLRGLTQKQLSENICHQSEVSR-IESGAVYPSMDILQGIAAKLQIPII 61

>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} Length = 73

 Score = 35.3 bits (81), Expect = 8e-04
 Identities = 12/45 (26%), Positives = 19/45 (42%)

Query: 96  IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLE 140
           IV+ R    LTQ + +++          YE G A P+   +  L 
Sbjct: 16  IVKVRKKLSLTQKEASEIFGGGVNAFSRYEKGNAXPHPSTIKLLR 60

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	151
2jvl_A	107	TRMBF1; coactivator, helix-turn-helix, Pro binding	99.67
2ewt_A	71	BLDD, putative DNA-binding protein; the DNA-bindin	99.6
3s8q_A	82	R-M controller protein; protein-DNA complex, helix	99.58
1x57_A	91	Endothelial differentiation-related factor 1; HMBF	99.56
3g5g_A	99	Regulatory protein; transcriptional regulator, hel	99.56
2kpj_A	94	SOS-response transcriptional repressor, LEXA; NESG	99.55
1y7y_A	74	C.AHDI; helix-turn-helix, DNA-binding protein, tra	99.55
3kz3_A	80	Repressor protein CI; five helix bundle, DNA-bindi	99.54
3qq6_A	78	HTH-type transcriptional regulator SINR; helix-tur	99.54
3eus_A	86	DNA-binding protein; structural genomics, PSI2,MCS	99.53
3f6w_A	83	XRE-family like protein; helix-turn-helix, DNA bin	99.53
2b5a_A	77	C.BCLI; helix-turn-helix motif, gene regulation; 1	99.53
2k9q_A	77	Uncharacterized protein; all helix, helix-turn-hel	99.53
3b7h_A	78	Prophage LP1 protein 11; structural genomics, PSI2	99.53
3omt_A	73	Uncharacterized protein; structural genomics, PSI-	99.52
3op9_A	114	PLI0006 protein; structural genomics, PSI-2, prote	99.51
2r1j_L	68	Repressor protein C2; protein-DNA complex, helix-t	99.51
3vk0_A	114	NHTF, transcriptional regulator; HTH motif, XRE tr	99.5
3ivp_A	126	Putative transposon-related DNA-binding protein; A	99.5
1adr_A	76	P22 C2 repressor; transcription regulation; NMR {E	99.5
2a6c_A	83	Helix-turn-helix motif; putative transcriptional r	99.5
3t76_A	88	VANU, transcriptional regulator vanug; structural	99.49
2wiu_B	88	HTH-type transcriptional regulator HIPB; transfera	99.49
3lfp_A	98	CSP231I C protein; transcriptional regulator, DNA	99.49
3mlf_A	111	Transcriptional regulator; structural genomics, he	99.48
1lmb_3	92	Protein (lambda repressor); protein-DNA complex, d	99.48
4ghj_A	101	Probable transcriptional regulator; structural gen	99.48
3f52_A	117	CLP gene regulator (CLGR); helix-turn-helix motif,	99.47
2xi8_A	66	Putative transcription regulator; HTH DNA-binding	99.47
3bs3_A	76	Putative DNA-binding protein; XRE-family, structur	99.46
1r69_A	69	Repressor protein CI; gene regulating protein; 2.0	99.46
3trb_A	104	Virulence-associated protein I; mobIle and extrach	99.45
1zug_A	71	Phage 434 CRO protein; gene regulating protein, tr	99.43
2wus_R	112	RODZ, putative uncharacterized protein; structural	99.43
2ef8_A	84	C.ECOT38IS, putative transcription factor; helix-t	99.43
2l49_A	99	C protein; P2 bacteriophage, P2 C, direct repeats,	99.42
1y9q_A	192	Transcriptional regulator, HTH_3 family; transcrip	99.42
2ict_A	94	Antitoxin HIGA; helix-turn-helix, structural genom	99.41
2o38_A	120	Hypothetical protein; alpha-beta, helix-turn-helix	99.41
3fmy_A	73	HTH-type transcriptional regulator MQSA (YGIT/B302	99.4
1b0n_A	111	Protein (SINR protein); transcription regulator, a	99.4
3fym_A	130	Putative uncharacterized protein; HTH DNA binding,	99.4
3cec_A	104	Putative antidote protein of plasmid maintenance;	99.4
2eby_A	113	Putative HTH-type transcriptional regulator YBAQ;	99.39
2bnm_A	198	Epoxidase; oxidoreductase, cupin, HTH, cation-depe	99.39
2ppx_A	99	AGR_C_3184P, uncharacterized protein ATU1735; HTH-	99.39
2ofy_A	86	Putative XRE-family transcriptional regulator; tra	99.36
3r1f_A	135	ESX-1 secretion-associated regulator ESPR; helix-t	99.34
3kxa_A	141	NGO0477 protein, putative uncharacterized protein;	99.33
3qwg_A	123	ESX-1 secretion-associated regulator ESPR; N-termi	99.28
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	99.27
3bd1_A	79	CRO protein; transcription factor, helix-turn-heli	99.27
4ich_A	311	Transcriptional regulator; structural genomics, PS	99.24
3pxp_A	292	Helix-turn-helix domain protein; DNA-binding, basi	99.23
2awi_A	317	PRGX; repressor, pheromone, DNA binding, regulator	99.17
3bdn_A	236	Lambda repressor; repressor, allostery; HET: DNA;	99.15
3o9x_A	133	Uncharacterized HTH-type transcriptional regulato;	99.13
2p5t_A	158	Putative transcriptional regulator PEZA; postsegre	99.13
2l1p_A	83	DNA-binding protein SATB1; PSI-biology, NESG, stru	99.12
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	99.11
1neq_A	74	DNA-binding protein NER; NMR {Enterobacteria phage	99.04
2fjr_A	189	Repressor protein CI; genetic switch, regulation,	99.02
2auw_A	170	Hypothetical protein NE0471; alpha-beta structure,	98.78
1dw9_A	156	Cyanate lyase; cyanate degradation, structural gen	98.65
1nr3_A	122	MTH0916, DNA-binding protein TFX; northeast struct	98.62
1rzs_A	61	Antirepressor, regulatory protein CRO; helix-turn-	98.42
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	98.27
1uxc_A	65	FRUR (1-57), fructose repressor; DNA-binding prote	98.26
3g7d_A	443	PHPD; non heme Fe(II) dioxygenase, cupin, biosynth	98.23
1zx4_A	192	P1 PARB, plasmid partition PAR B protein, PARB; tr	98.16
2l8n_A	67	Transcriptional repressor CYTR; bacterial gene rep	98.06
2pij_A	67	Prophage PFL 6 CRO; transcription factor, helix-tu	98.0
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	98.0
1s4k_A	120	Putative cytoplasmic protein YDIL; structural geno	97.96
2hin_A	71	GP39, repressor protein; transcription factor, dim	97.53
1jhf_A	202	LEXA repressor; LEXA SOS repressor, hydrolase; 1.8	97.46
2cw1_A	65	SN4M; lambda CRO fold, de novo protein; NMR {Synth	97.41
2l0k_A	93	Stage III sporulation protein D; SPOIIID, solution	97.37
4ich_A	311	Transcriptional regulator; structural genomics, PS	97.29
1zs4_A	83	Regulatory protein CII; helix-turn-helix, transcri	97.12
1xwr_A	97	Regulatory protein CII; all-alpha fold, DNA bindin	96.79
2ao9_A	155	Phage protein; structural genomics, nine-fold NCS.	96.56
2x48_A	55	CAG38821; archeal virus, viral protein; 2.60A {Sul	96.44
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	96.43
1jhg_A	101	Trp operon repressor; complex (regulatory protein-	96.37
3kjx_A	344	Transcriptional regulator, LACI family; LACL famil	95.64
1jko_C	52	HIN recombinase, DNA-invertase HIN; water-mediated	95.63
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	95.5
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	95.41
3h5t_A	366	Transcriptional regulator, LACI family; DNA-depend	95.26
1e3o_C	160	Octamer-binding transcription factor 1; transcript	95.24
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	95.24
2w7n_A	101	TRFB transcriptional repressor protein; INCP, plas	95.13
2ovg_A	66	Phage lambda CRO; transcription factor, helix-turn	95.08
1u78_A	141	TC3 transposase, transposable element TC3 transpos	94.88
2jn6_A	97	Protein CGL2762, transposase; GFT PSI-2, protein s	94.68
1k78_A	149	Paired box protein PAX5; paired domain, ETS domain	94.63
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	94.45
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	94.42
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	94.16
2o20_A	332	Catabolite control protein A; CCPA, transcriptiona	94.14
1j9i_A	68	GPNU1 DBD;, terminase small subunit; DNA binding d	94.0
2csf_A	101	DNA-binding protein SATB2; CUT domain, special AT-	94.0
1x2l_A	101	CUT-like 2, homeobox protein CUX-2; CUT domain, hu	93.84
2jml_A	81	DNA binding domain/transcriptional regulator; anti	93.75
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	93.66
2k27_A	159	Paired box protein PAX-8; paired domain, solution	93.49
3h5o_A	339	Transcriptional regulator GNTR; transcription regu	93.41
1wh6_A	101	CUT-like 2, homeobox protein CUX-2; CUT domain, st	93.33
1u78_A	141	TC3 transposase, transposable element TC3 transpos	93.27
3me5_A	482	Cytosine-specific methyltransferase; structural ge	93.27
3frw_A	107	Putative Trp repressor protein; structural genomic	93.15
3kor_A	119	Possible Trp repressor; putative DNA-binding Trp r	92.78
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	92.76
1r71_A	178	Transcriptional repressor protein KORB; INCP, plas	92.67
3jvd_A	333	Transcriptional regulators; structural genomics, P	92.61
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	92.6
2o8x_A	70	Probable RNA polymerase sigma-C factor; promoter r	92.55
3fmy_A	73	HTH-type transcriptional regulator MQSA (YGIT/B302	92.53
3bil_A	348	Probable LACI-family transcriptional regulator; st	92.52
3e3m_A	355	Transcriptional regulator, LACI family; structural	92.49
2w48_A	315	Sorbitol operon regulator; SORC, activator, repres	92.33
3omt_A	73	Uncharacterized protein; structural genomics, PSI-	92.28
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	92.06
2xi8_A	66	Putative transcription regulator; HTH DNA-binding	91.87
1y7y_A	74	C.AHDI; helix-turn-helix, DNA-binding protein, tra	91.86
3kz3_A	80	Repressor protein CI; five helix bundle, DNA-bindi	91.85
2dk5_A	91	DNA-directed RNA polymerase III 39 kDa polypeptide	91.78
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	91.69
1r69_A	69	Repressor protein CI; gene regulating protein; 2.0	91.59
2r1j_L	68	Repressor protein C2; protein-DNA complex, helix-t	91.59
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	91.59
3s8q_A	82	R-M controller protein; protein-DNA complex, helix	91.56
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	91.52
1vz0_A	230	PARB, chromosome partitioning protein PARB; nuclea	91.51
1hlv_A	131	CENP-B, major centromere autoantigen B; helix-turn	91.44
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	91.22
2ewt_A	71	BLDD, putative DNA-binding protein; the DNA-bindin	91.08
2ox6_A	166	Hypothetical protein SO3848; structural genomics,	91.02
1adr_A	76	P22 C2 repressor; transcription regulation; NMR {E	90.99
2jml_A	81	DNA binding domain/transcriptional regulator; anti	90.95
2b5a_A	77	C.BCLI; helix-turn-helix motif, gene regulation; 1	90.95
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	90.85
1wiz_A	101	DNA-binding protein SATB2; helix bundle, KIAA1034	90.84
3bs3_A	76	Putative DNA-binding protein; XRE-family, structur	90.81
3f6w_A	83	XRE-family like protein; helix-turn-helix, DNA bin	90.7
1x3u_A	79	Transcriptional regulatory protein FIXJ; helix-tur	90.57
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	90.56
1wh8_A	111	CUT-like 2, homeobox protein CUX-2; CUT domain, st	90.51
1fse_A	74	GERE; helix-turn-helix DNA-binding protein transcr	90.5
2jpc_A	61	SSRB; DNA binding protein, structural genomics, PS	90.38
3eus_A	86	DNA-binding protein; structural genomics, PSI2,MCS	90.28
2kpj_A	94	SOS-response transcriptional repressor, LEXA; NESG	90.12
2ofy_A	86	Putative XRE-family transcriptional regulator; tra	90.12
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	90.11
2k9q_A	77	Uncharacterized protein; all helix, helix-turn-hel	90.06
2w25_A	150	Probable transcriptional regulatory protein; trans	90.01
1zug_A	71	Phage 434 CRO protein; gene regulating protein, tr	89.85
3e7l_A	63	Transcriptional regulator (NTRC family); sigma43 a	89.84
2rn7_A	108	IS629 ORFA; helix, all alpha, unknown function, st	89.81
2vz4_A	108	Tipal, HTH-type transcriptional activator TIPA; tr	89.81
3ivp_A	126	Putative transposon-related DNA-binding protein; A	89.76
2o4a_A	93	DNA-binding protein SATB1; protein-DNA complex, tr	89.69
1z4h_A	66	TORI, TOR inhibition protein; winged helix, revers	89.63
3qwg_A	123	ESX-1 secretion-associated regulator ESPR; N-termi	89.6
1lmb_3	92	Protein (lambda repressor); protein-DNA complex, d	89.59
1je8_A	82	Nitrate/nitrite response regulator protein NARL; p	89.51
2ef8_A	84	C.ECOT38IS, putative transcription factor; helix-t	89.38
3g5g_A	99	Regulatory protein; transcriptional regulator, hel	89.31
3b7h_A	78	Prophage LP1 protein 11; structural genomics, PSI2	89.09
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	89.08
3bd1_A	79	CRO protein; transcription factor, helix-turn-heli	89.0
1yse_A	141	DNA-binding protein SATB1; all helical, DNA-bindin	88.82
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	88.75
2k27_A	159	Paired box protein PAX-8; paired domain, solution	88.73
2l49_A	99	C protein; P2 bacteriophage, P2 C, direct repeats,	88.69
3op9_A	114	PLI0006 protein; structural genomics, PSI-2, prote	88.63
3ulq_B	90	Transcriptional regulatory protein COMA; tetratric	88.59
3r0a_A	123	Putative transcriptional regulator; structural gen	88.52
3c57_A	95	Two component transcriptional regulatory protein;	88.46
1b0n_A	111	Protein (SINR protein); transcription regulator, a	88.44
3lfp_A	98	CSP231I C protein; transcriptional regulator, DNA	88.17
3vk0_A	114	NHTF, transcriptional regulator; HTH motif, XRE tr	88.15
1umq_A	81	Photosynthetic apparatus regulatory protein; DNA-b	88.13
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	88.11
1s7o_A	113	Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SP	88.06
1sfx_A	109	Conserved hypothetical protein AF2008; structural	87.71
3r1f_A	135	ESX-1 secretion-associated regulator ESPR; helix-t	87.7
2wiu_B	88	HTH-type transcriptional regulator HIPB; transfera	87.61
1r8d_A	109	Transcription activator MTAN; protein-DNA complex,	87.61
3qq6_A	78	HTH-type transcriptional regulator SINR; helix-tur	87.6
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	87.59
2pg4_A	95	Uncharacterized protein; structural genomics, join	87.57
2o3f_A	111	Putative HTH-type transcriptional regulator YBBH;	87.52
3mky_B	189	Protein SOPB; partition, F plasmid, centromere, DN	87.51
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	87.49
1xsv_A	113	Hypothetical UPF0122 protein SAV1236; helix-turn-h	87.48
1k78_A	149	Paired box protein PAX5; paired domain, ETS domain	87.31
3t76_A	88	VANU, transcriptional regulator vanug; structural	87.05
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	87.02
3nrv_A	148	Putative transcriptional regulator (MARR/EMRR FAM;	86.91
3f52_A	117	CLP gene regulator (CLGR); helix-turn-helix motif,	86.89
1x57_A	91	Endothelial differentiation-related factor 1; HMBF	86.81
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	86.56
3mlf_A	111	Transcriptional regulator; structural genomics, he	86.53
4ghj_A	101	Probable transcriptional regulator; structural gen	86.53
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	86.49
3o9x_A	133	Uncharacterized HTH-type transcriptional regulato;	86.39
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	86.35
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	86.32
2zcw_A	202	TTHA1359, transcriptional regulator, FNR/CRP famil	86.07
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	85.79
1ntc_A	91	Protein (nitrogen regulation protein (NTRC)); heli	85.77
3mzy_A	164	RNA polymerase sigma-H factor; PSI, MCSG, structur	85.66
3lsg_A	103	Two-component response regulator YESN; structural	85.43
3iwf_A	107	Transcription regulator RPIR family; transcription	85.4
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	85.39
2fbh_A	146	Transcriptional regulator PA3341; MARR, transcript	85.38
2p5k_A	64	Arginine repressor; DNA-binding domain, winged hel	85.35
1ub9_A	100	Hypothetical protein PH1061; helix-turn-helix moti	85.35
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	85.35
1sfu_A	75	34L protein; protein/Z-DNA complex, DNA binding pr	85.34
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	85.29
2hr3_A	147	Probable transcriptional regulator; MCSG, structur	85.2
3b02_A	195	Transcriptional regulator, CRP family; structural	85.17
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	85.17
2ppx_A	99	AGR_C_3184P, uncharacterized protein ATU1735; HTH-	85.14
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	85.09
4hbl_A	149	Transcriptional regulator, MARR family; HTH, trans	85.05
1ku9_A	152	Hypothetical protein MJ223; putative transcription	85.04
3oop_A	143	LIN2960 protein; protein structure initiative, PSI	85.01
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	84.92
3s2w_A	159	Transcriptional regulator, MARR family; structural	84.9
3g3z_A	145	NMB1585, transcriptional regulator, MARR family; t	84.89
1on2_A	142	Transcriptional regulator MNTR; helix-turn-helix,	84.84
2wte_A	244	CSA3; antiviral protein, viral resistance, winged	84.65
3t72_q	99	RNA polymerase sigma factor RPOD, DNA-directed RN	84.63
3fym_A	130	Putative uncharacterized protein; HTH DNA binding,	84.57
2ict_A	94	Antitoxin HIGA; helix-turn-helix, structural genom	84.56
1q06_A	135	Transcriptional regulator CUER; MERR family transc	84.53
3iwz_A	230	CAP-like, catabolite activation-like protein; XCC,	84.46
2nnn_A	140	Probable transcriptional regulator; structural gen	84.39
1u2w_A	122	CADC repressor, cadmium efflux system accessory pr	84.35
3hh0_A	146	Transcriptional regulator, MERR family; protein st	84.22
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	84.14
2vz4_A	108	Tipal, HTH-type transcriptional activator TIPA; tr	84.14
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	84.13
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	84.12
2qvo_A	95	Uncharacterized protein AF_1382; PSI, structural g	84.09
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	84.01
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	84.0
3hh0_A	146	Transcriptional regulator, MERR family; protein st	83.78
1lj9_A	144	Transcriptional regulator SLYA; HTH DNA binding pr	83.61
2oz6_A	207	Virulence factor regulator; winged helix, helix-tu	83.53
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	83.45
2rdp_A	150	Putative transcriptional regulator MARR; PFAM PF01	83.44
2qww_A	154	Transcriptional regulator, MARR family; YP_013417.	83.33
2pex_A	153	Transcriptional regulator OHRR; transcription regu	83.31
1r8d_A	109	Transcription activator MTAN; protein-DNA complex,	83.28
3gp4_A	142	Transcriptional regulator, MERR family; structural	83.18
2a61_A	145	Transcriptional regulator TM0710; APC4350, MCSG, m	83.05
3bj6_A	152	Transcriptional regulator, MARR family; helix-turn	83.01
3ryp_A	210	Catabolite gene activator; CAMP receptor protein (	82.94
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	82.93
2gxg_A	146	146AA long hypothetical transcriptional regulator;	82.86
1or7_A	194	Sigma-24, RNA polymerase sigma-E factor; regulatio	82.81
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	82.78
2rnj_A	91	Response regulator protein VRAR; HTH LUXR-type dom	82.7
1j5y_A	187	Transcriptional regulator, biotin repressor famil;	82.7
1y0u_A	96	Arsenical resistance operon repressor, putative; s	82.68
2fbi_A	142	Probable transcriptional regulator; MARR, APC5816,	82.67
2jvl_A	107	TRMBF1; coactivator, helix-turn-helix, Pro binding	82.63
1ft9_A	222	Carbon monoxide oxidation system transcription reg	82.57
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	82.51
1eto_A	98	FIS, factor for inversion stimulation; transcripti	82.5
3dv8_A	220	Transcriptional regulator, CRP/FNR family; cyclic	82.41
1z6r_A	406	MLC protein; transcriptional repressor, ROK family	82.4
3k0l_A	162	Repressor protein; helix-turn-helix, structural ge	82.39
3cdh_A	155	Transcriptional regulator, MARR family; helix-turn	82.39
3kxa_A	141	NGO0477 protein, putative uncharacterized protein;	82.28
3i4p_A	162	Transcriptional regulator, ASNC family; PSI, struc	82.27
2k9s_A	107	Arabinose operon regulatory protein; activator, ar	82.23
2zkz_A	99	Transcriptional repressor PAGR; protein-DNA, HTH m	82.15
3hsr_A	140	HTH-type transcriptional regulator SARZ; helix-tur	82.14
3cec_A	104	Putative antidote protein of plasmid maintenance;	82.12
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	82.07
3kp7_A	151	Transcriptional regulator TCAR; multiple drug resi	81.99
1p4w_A	99	RCSB; solution structure, DNA binding domain, DNA	81.98
2a6c_A	83	Helix-turn-helix motif; putative transcriptional r	81.97
3cjn_A	162	Transcriptional regulator, MARR family; silicibact	81.96
1y9q_A	192	Transcriptional regulator, HTH_3 family; transcrip	81.95
2p5t_A	158	Putative transcriptional regulator PEZA; postsegre	81.87
3oou_A	108	LIN2118 protein; protein structure initiative, PSI	81.73
2eby_A	113	Putative HTH-type transcriptional regulator YBAQ;	81.67
1g2h_A	61	Transcriptional regulatory protein TYRR homolog; p	81.63
2eth_A	154	Transcriptional regulator, putative, MAR family; M	81.57
2bnm_A	198	Epoxidase; oxidoreductase, cupin, HTH, cation-depe	81.55
2dg6_A	222	Putative transcriptional regulator; winged-helix m	81.48
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	81.28
2fmy_A	220	COOA, carbon monoxide oxidation system transcripti	81.25
1b4a_A	149	Arginine repressor; helix turn helix; 2.50A {Geoba	81.2
3e97_A	231	Transcriptional regulator, CRP/FNR family; YP_6044	81.15
3d0s_A	227	Transcriptional regulatory protein; CAMP receptor	80.92
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	80.84
4ev0_A	216	Transcription regulator, CRP family; CAMP binding,	80.84
3la7_A	243	Global nitrogen regulator; activator, DNA-binding,	80.81
1z05_A	429	Transcriptional regulator, ROK family; structural	80.81
1gdt_A	183	GD resolvase, protein (gamma delta resolvase); pro	80.75
2nyx_A	168	Probable transcriptional regulatory protein, RV14;	80.67
3jth_A	98	Transcription activator HLYU; transcription factor	80.62
2r0q_C	209	Putative transposon TN552 DNA-invertase BIN3; site	80.62
2kko_A	108	Possible transcriptional regulatory protein (possi	80.61
2hoe_A	380	N-acetylglucosamine kinase; TM1224, structural gen	80.6
3trb_A	104	Virulence-associated protein I; mobIle and extrach	80.56
1tbx_A	99	ORF F-93, hypothetical 11.0 kDa protein; sulfolobu	80.55
3e6c_C	250	CPRK, cyclic nucleotide-binding protein; CPRK, hal	80.51
2frh_A	127	SARA, staphylococcal accessory regulator A; winged	80.28
2h09_A	155	Transcriptional regulator MNTR; transcription regu	80.27
2l8n_A	67	Transcriptional repressor CYTR; bacterial gene rep	80.21
1s3j_A	155	YUSO protein; structural genomics, MARR transcript	80.17

>2jvl_A TRMBF1; coactivator, helix-turn-helix, Pro binding, transcription; NMR {Trichoderma reesei}

Probab=99.67  E-value=2e-16  Score=110.78  Aligned_cols=83  Identities=37%  Similarity=0.573  Sum_probs=77.7

Q ss_pred             CcccccccccccchhhhHHHHHhhccCCcchHHHHHHHHHHHh--cCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHH
Q 031871           59 STSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARN--DKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQIL  136 (151)
Q Consensus        59 ~~~~~~~kl~~~~~~~~~~~s~~~~~~~~~~~~~~~~Lk~~R~--~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l  136 (151)
                      +...+..++|.+++.+.+         ..+.+.++.+|+.+|.  .+||||.+||+.+|+++++|++||+|+..|+.+.+
T Consensus        11 ~~~~~~~~~d~~~~~~~~---------~~~~~~~g~~lk~~R~~~~~glsq~elA~~~gis~~~is~~E~G~~~p~~~~l   81 (107)
T 2jvl_A           11 TEGQRLTKVDRSDDIIKP---------KTVGKEVGKAIEQGRQKFEPTMTQAELGKEIGETAATVASYERGTATPDQNIL   81 (107)
T ss_dssp             CCCCCCCCCCCCCCCCCC---------CCCCHHHHHHHHHHHTTSSSCCCHHHHHHHHTCCHHHHHHHTTTCSCCCHHHH
T ss_pred             CcccccccccccccccCH---------HHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHH
Confidence            456788999999888887         7888999999999999  99999999999999999999999999999999999


Q ss_pred             HHHHHHhCCCCCCC
Q 031871          137 TKLERALGVKLRGK  150 (151)
Q Consensus       137 ~kLa~~Lgv~l~e~  150 (151)
                      .+||++|||++++.
T Consensus        82 ~~ia~~l~v~~~e~   95 (107)
T 2jvl_A           82 SKMERVLNVKLRGA   95 (107)
T ss_dssp             HHHHHTTTCBSSSS
T ss_pred             HHHHHHHCcCHhhh
Confidence            99999999999874

>2ewt_A BLDD, putative DNA-binding protein; the DNA-binding domain of BLDD; 1.81A {Streptomyces coelicolor}

Probab=99.60  E-value=1.6e-15  Score=97.20  Aligned_cols=62  Identities=21%  Similarity=0.267  Sum_probs=58.6

Q ss_pred             chHHHHHHHHHHHhcCCcCHHHHHHHhC--CCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 031871           88 VPSELKKAIVQARNDKKLTQSQLAQLIN--EKPQVIQEYESGKAIPNQQILTKLERALGVKLRG  149 (151)
Q Consensus        88 ~~~~~~~~Lk~~R~~~glTQ~eLA~~lg--is~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~e  149 (151)
                      ....++.+|+.+|..+|+||.+||+.+|  +++++|++||+|+..|+.+.+.+||++|||++++
T Consensus         5 ~~~~~g~~l~~~r~~~glsq~~lA~~~g~~is~~~i~~~e~g~~~~~~~~l~~la~~l~v~~~~   68 (71)
T 2ewt_A            5 YAKQLGAKLRAIRTQQGLSLHGVEEKSQGRWKAVVVGSYERGDRAVTVQRLAELADFYGVPVQE   68 (71)
T ss_dssp             HHHHHHHHHHHHHHHTTCCHHHHHHHTTTSSCHHHHHHHHHTCSCCCHHHHHHHHHHHTSCGGG
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHHCCcCCHHHHHHHHCCCCCCCHHHHHHHHHHHCcCHHH
Confidence            3567999999999999999999999999  9999999999999999999999999999999863

>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=99.58  E-value=3.5e-15  Score=98.53  Aligned_cols=63  Identities=22%  Similarity=0.126  Sum_probs=59.0

Q ss_pred             CcchHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           86 DRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        86 ~~~~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      ..+...++.+|+.+|..+||||.+||+.+|+++++|++||+|+..|+.+.+.+||++|||+++
T Consensus         6 ~~~~~~~g~~lk~~R~~~glsq~~lA~~~gis~~~i~~~e~g~~~~~~~~l~~ia~~l~v~~~   68 (82)
T 3s8q_A            6 SFLLSKVSFVIKKIRLEKGMTQEDLAYKSNLDRTYISGIERNSRNLTIKSLELIMKGLEVSDV   68 (82)
T ss_dssp             CHHHHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCCCCBHHHHHHHHHHTTCCHH
T ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHCCCCCCCHHHHHHHHHHHCcCHH
Confidence            344578999999999999999999999999999999999999999999999999999999874

>1x57_A Endothelial differentiation-related factor 1; HMBF1alpha, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.35.1.12

Probab=99.56  E-value=1.4e-14  Score=97.69  Aligned_cols=64  Identities=64%  Similarity=0.926  Sum_probs=60.7

Q ss_pred             CcchHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 031871           86 DRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG  149 (151)
Q Consensus        86 ~~~~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~e  149 (151)
                      +.+.+.++.+|+.+|..+||||.+||+.+|+++++|++||+|+..|+.+.+.+||++|||++++
T Consensus         8 ~~~~~~~~~~l~~~r~~~glsq~~lA~~~gis~~~is~~e~g~~~p~~~~l~~la~~l~v~~~~   71 (91)
T 1x57_A            8 DRVTLEVGKVIQQGRQSKGLTQKDLATKINEKPQVIADYESGRAIPNNQVLGKIERAIGLKLRG   71 (91)
T ss_dssp             SCCCCHHHHHHHHHHHTTTCCHHHHHHHHTSCHHHHHHHHHTCSCCCHHHHHHHHHHHTBCCSS
T ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHHH
Confidence            4556789999999999999999999999999999999999999999999999999999999876

>3g5g_A Regulatory protein; transcriptional regulator, helix-turn-helix, restriction- modification, transcription regulator; 2.80A {Enterobacter SP} PDB: 3fya_A

Probab=99.56  E-value=4.4e-15  Score=102.70  Aligned_cols=62  Identities=23%  Similarity=0.126  Sum_probs=58.7

Q ss_pred             cchHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           87 RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        87 ~~~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      .+...|+.+|+.+|.++||||.+||+.+|+++++|++||+|+..|+.+.+.+||++|||+++
T Consensus        24 ~~~~~ig~~lr~~R~~~gltq~elA~~~gis~~~is~iE~G~~~ps~~~l~~ia~~l~v~~~   85 (99)
T 3g5g_A           24 FLLSKVSFVIKKIRLEKGMTQEDLAYKSNLDRTYISGIERNSRNLTIKSLELIMKGLEVSDV   85 (99)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCSCCBHHHHHHHHHHTTCCHH
T ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHHCcCHH
Confidence            34568999999999999999999999999999999999999999999999999999999875

>2kpj_A SOS-response transcriptional repressor, LEXA; NESG, GFT, structural genomics, PSI-2, protein structure initiative; NMR {Eubacterium rectale atcc 33656}

Probab=99.55  E-value=1.6e-14  Score=98.13  Aligned_cols=62  Identities=18%  Similarity=0.240  Sum_probs=58.6

Q ss_pred             cchHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           87 RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        87 ~~~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      ...+.++.+|+.+|..+|+||.+||+.+|+|+++|++||+|+..|+.+.+.+||++|||+++
T Consensus         5 ~~~~~~~~~lk~~r~~~glsq~~lA~~~gis~~~is~~e~G~~~p~~~~l~~ia~~l~v~~~   66 (94)
T 2kpj_A            5 KQKAIFSENLNSYIAKSEKTQLEIAKSIGVSPQTFNTWCKGIAIPRMGKVQALADYFNINKS   66 (94)
T ss_dssp             HHHHHHHHHHHHHHTTSSSCHHHHHHHHTCCHHHHHHHHTTSCCCCHHHHHHHHHHHTCCTH
T ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhCCCCCCHHHHHHHHHHHCcCHH
Confidence            34578999999999999999999999999999999999999999999999999999999975

>1y7y_A C.AHDI; helix-turn-helix, DNA-binding protein, transcriptional regulator, transcription regulator; 1.69A {Aeromonas hydrophila} SCOP: a.35.1.3

Probab=99.55  E-value=1.4e-14  Score=93.17  Aligned_cols=61  Identities=23%  Similarity=0.226  Sum_probs=58.2

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG  149 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~e  149 (151)
                      ...++.+|+.+|..+|+||.+||+.+|+++++|++||+|+..|+.+.+.+||++|||++++
T Consensus        11 ~~~~~~~l~~~r~~~g~s~~~lA~~~gis~~~i~~~e~g~~~~~~~~l~~l~~~l~~~~~~   71 (74)
T 1y7y_A           11 LVKFGQRLRELRTAKGLSQETLAFLSGLDRSYVGGVERGQRNVSLVNILKLATALDIEPRE   71 (74)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCSCCBHHHHHHHHHHTTSCGGG
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHhCcCHHH
Confidence            4679999999999999999999999999999999999999999999999999999999863

>3kz3_A Repressor protein CI; five helix bundle, DNA-binding, transcription, transcription regulation; 1.64A {Enterobacteria phage lambda}

Probab=99.54  E-value=1.2e-14  Score=95.96  Aligned_cols=61  Identities=16%  Similarity=0.156  Sum_probs=58.2

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG  149 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~e  149 (151)
                      .+.++.+|+.+|.++|+||.+||+.+|+|+++|++||+|+..|+.+.+.+||++|||++++
T Consensus        10 ~~~l~~~l~~~r~~~gltq~~lA~~~gvs~~~is~~e~g~~~~~~~~~~~ia~~l~v~~~~   70 (80)
T 3kz3_A           10 ARRLKAIWEKKKNELGLSYESVADKMGMGQSAVAALFNGINALNAYNAALLAKILKVSVEE   70 (80)
T ss_dssp             HHHHHHHHHHHHHHHTCCHHHHHHHTTSCHHHHHHHHTTSSCCCHHHHHHHHHHHTSCGGG
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHH
Confidence            4679999999999999999999999999999999999999999999999999999999864

>3qq6_A HTH-type transcriptional regulator SINR; helix-turn-helix motif, biofilm, repressor, SINI; 1.90A {Bacillus subtilis}

Probab=99.54  E-value=8e-15  Score=96.82  Aligned_cols=62  Identities=23%  Similarity=0.276  Sum_probs=57.4

Q ss_pred             cchHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcC-CCCCCHHHHHHHHHHhCCCCC
Q 031871           87 RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESG-KAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        87 ~~~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G-~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      .....|+.+|+.+|+++||||.+||+.+|+|+++|++||+| +..|+.+.+.+||++|||+++
T Consensus         6 ~~~~~~~~~ik~~R~~~gltq~elA~~~gis~~~is~~E~G~~~~p~~~~l~~ia~~l~v~~~   68 (78)
T 3qq6_A            6 HHHHMIGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNLQTNPSIQFLEKVSAVLDVSVH   68 (78)
T ss_dssp             --CTTHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTSCCCCBHHHHHHHHHHHTCCHH
T ss_pred             cCCCCccHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHHHHHHCcCHH
Confidence            34568999999999999999999999999999999999999 899999999999999999864

>3eus_A DNA-binding protein; structural genomics, PSI2,MCSG, protein structure initiative, midwest center for structural genomic binding; 1.80A {Silicibacter pomeroyi}

Probab=99.53  E-value=2.3e-14  Score=96.16  Aligned_cols=58  Identities=22%  Similarity=0.158  Sum_probs=55.7

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVK  146 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~  146 (151)
                      ...|+.+|+.+|..+||||.+||+.+|+|+++|++||+|+..|+.+.+.+|+++|||+
T Consensus        12 ~~~~g~~l~~~R~~~gltq~elA~~~gis~~~is~~E~G~~~p~~~~l~~ia~~l~v~   69 (86)
T 3eus_A           12 HVYLCQRLRQARLDAGLTQADLAERLDKPQSFVAKVETRERRLDVIEFAKWMAACEGL   69 (86)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHTTCCHHHHHHHHTTSSCCBHHHHHHHHHHTTCG
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHCCCCCCCHHHHHHHHHHcCCC
Confidence            4569999999999999999999999999999999999999999999999999999986

>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=99.53  E-value=1.3e-14  Score=95.90  Aligned_cols=60  Identities=17%  Similarity=0.220  Sum_probs=57.5

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      .+.++.+|+.+|.++||||.+||+.+|+++++|++||+|+..|+.+.+.+||++|||+++
T Consensus        12 ~~~~~~~l~~~R~~~gltq~elA~~~gis~~~is~~e~g~~~~~~~~l~~l~~~l~~~~~   71 (83)
T 3f6w_A           12 YQALLDLLLEARSAAGITQKELAARLGRPQSFVSKTENAERRLDVIEFMDFCRGIGTDPY   71 (83)
T ss_dssp             HHHHHHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHTTSSCCCHHHHHHHHHHHTCCHH
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHcCCCHH
Confidence            467999999999999999999999999999999999999999999999999999999864

>2b5a_A C.BCLI; helix-turn-helix motif, gene regulation; 1.54A {Bacillus caldolyticus} SCOP: a.35.1.3

Probab=99.53  E-value=9.1e-15  Score=94.90  Aligned_cols=61  Identities=21%  Similarity=0.278  Sum_probs=57.9

Q ss_pred             chHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           88 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        88 ~~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      ....++.+|+.+|..+|+||.+||+.+|+|+++|++||+|+..|+.+.+.+||++|||+++
T Consensus         7 ~~~~~~~~l~~~r~~~glsq~~lA~~~gis~~~i~~~e~g~~~~~~~~l~~la~~l~~~~~   67 (77)
T 2b5a_A            7 IKRKFGRTLKKIRTQKGVSQEELADLAGLHRTYISEVERGDRNISLINIHKICAALDIPAS   67 (77)
T ss_dssp             HHHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCSCCBHHHHHHHHHHTTCCHH
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHhCcCHH
Confidence            3577999999999999999999999999999999999999999999999999999999864

>2k9q_A Uncharacterized protein; all helix, helix-turn-helix, plasmid, structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides thetaiotaomicron}

Probab=99.53  E-value=5.9e-15  Score=96.60  Aligned_cols=58  Identities=22%  Similarity=0.236  Sum_probs=55.5

Q ss_pred             HHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           91 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        91 ~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      .++.+|+.+|..+||||.+||+++|+++++|++||+|+..|+.+.+.+||++|||+++
T Consensus         2 ~~~~~lk~~r~~~glsq~~lA~~~gis~~~i~~~e~g~~~p~~~~l~~ia~~l~v~~~   59 (77)
T 2k9q_A            2 ELSNELKVERIRLSLTAKSVAEEMGISRQQLCNIEQSETAPVVVKYIAFLRSKGVDLN   59 (77)
T ss_dssp             CHHHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHTCCSCCHHHHHHHHHHHTTCCHH
T ss_pred             cHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCcCHH
Confidence            4789999999999999999999999999999999999999999999999999999864

>3b7h_A Prophage LP1 protein 11; structural genomics, PSI2, MCSG, protein structure initiative, midwest center for structural genomics; 2.00A {Lactobacillus plantarum WCFS1}

Probab=99.53  E-value=2.2e-14  Score=93.27  Aligned_cols=60  Identities=15%  Similarity=0.279  Sum_probs=57.3

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCCC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA-IPNQQILTKLERALGVKLR  148 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~-~p~~~~l~kLa~~Lgv~l~  148 (151)
                      ...++.+|+.+|..+|+||.+||+.+|+|+++|++||+|+. .|+.+.+.+||++|||+++
T Consensus         5 ~~~~~~~l~~~r~~~g~sq~~lA~~~gis~~~i~~~e~g~~~~~~~~~l~~ia~~l~~~~~   65 (78)
T 3b7h_A            5 GEFVSEHLMELITQQNLTINRVATLAGLNQSTVNAMFEGRSKRPTITTIRKVCGTLGISVH   65 (78)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHCTTCCCCCHHHHHHHHHHHTCCHH
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHHHHHcCCCHH
Confidence            46799999999999999999999999999999999999999 9999999999999999874

>3omt_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; 1.65A {Cytophaga hutchinsonii}

Probab=99.52  E-value=4.9e-15  Score=95.95  Aligned_cols=59  Identities=15%  Similarity=0.275  Sum_probs=55.8

Q ss_pred             HHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 031871           91 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG  149 (151)
Q Consensus        91 ~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~e  149 (151)
                      .++.+|+.+|.++|+||.+||+.+|+++++|++||+|+..|+.+.+.+||++|||++++
T Consensus         8 ~~~~~l~~~r~~~glsq~~lA~~~gis~~~is~~e~g~~~~~~~~l~~ia~~l~v~~~~   66 (73)
T 3omt_A            8 KIFNRLKSVLAEKGKTNLWLTETLDKNKTTVSKWCTNDVQPSLETLFDIAEALNVDVRE   66 (73)
T ss_dssp             CCCBCHHHHHHHHTCCHHHHHHHTTCCHHHHHHHHTTSSCCCHHHHHHHHHHHTSCGGG
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHHH
Confidence            46778999999999999999999999999999999999999999999999999999863

>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=99.51  E-value=1.1e-14  Score=102.02  Aligned_cols=61  Identities=18%  Similarity=0.413  Sum_probs=57.8

Q ss_pred             chHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           88 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        88 ~~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      +.+.++.+|+.+|..+||||.+||+.+|+|+++|++||+|+..|+.+.+.+||++|||+++
T Consensus         6 ~~~~~~~~l~~~r~~~glsq~~lA~~~gis~~~i~~~e~g~~~p~~~~l~~la~~l~v~~~   66 (114)
T 3op9_A            6 IQHQFAENLSRLKKEHGLKNHQIAELLNVQTRTVAYYMSGETKPDIEKLIRLATYFHLSID   66 (114)
T ss_dssp             CCCCHHHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHHTSSCCCHHHHHHHHHHHTCCHH
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHH
Confidence            3456999999999999999999999999999999999999999999999999999999874

>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=99.51  E-value=2e-14  Score=90.87  Aligned_cols=58  Identities=22%  Similarity=0.326  Sum_probs=55.8

Q ss_pred             HHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           91 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        91 ~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      .++.+|+.+|..+|+||.+||+.+|+|+++|++||+|+..|+.+.+.+||++||++++
T Consensus         5 ~~~~~l~~~r~~~g~s~~~lA~~~gis~~~i~~~e~g~~~~~~~~l~~i~~~l~~~~~   62 (68)
T 2r1j_L            5 LMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCSPD   62 (68)
T ss_dssp             CHHHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHTTSSCCBHHHHHHHHHHTTSCHH
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHH
Confidence            5899999999999999999999999999999999999999999999999999999864

>3vk0_A NHTF, transcriptional regulator; HTH motif, XRE transcription factor, DNA binding protein; 1.88A {Neisseria meningitidis}

Probab=99.50  E-value=2.6e-14  Score=100.50  Aligned_cols=62  Identities=19%  Similarity=0.141  Sum_probs=58.5

Q ss_pred             cchHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           87 RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        87 ~~~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      .+...++.+|+.+|..+||||.+||+.+|+++++|++||+|+..|+.+.+.+||++|||+++
T Consensus        17 ~~~~~~g~~lr~~R~~~gltq~elA~~~gis~~~is~~E~G~~~p~~~~l~~ia~~l~v~~~   78 (114)
T 3vk0_A           17 DLRAVLAYNMRLFRVNKGWSQEELARQCGLDRTYVSAVERKRWNIALSNIEKMAAALGVAAY   78 (114)
T ss_dssp             CHHHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHTTTCCCCCHHHHHHHHHHHTSCHH
T ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHH
Confidence            34568999999999999999999999999999999999999999999999999999999864

>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=99.50  E-value=6e-14  Score=99.89  Aligned_cols=60  Identities=28%  Similarity=0.372  Sum_probs=57.9

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      .+.||.+|+.+|..+||||.+||+.+|+|+++|++||+|+..|+.+.+.+||++|||+++
T Consensus        10 ~~~~g~~lk~~R~~~glsq~~lA~~~gis~~~is~~E~g~~~p~~~~l~~ia~~l~v~~~   69 (126)
T 3ivp_A           10 FRALGLAIKEARKKQGLTREQVGAMIEIDPRYLTNIENKGQHPSLQVLYDLVSLLNVSVD   69 (126)
T ss_dssp             THHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHSCCCCCHHHHHHHHHHHTCCSH
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHCCCCCCCHHHHHHHHHHHCcCHH
Confidence            468999999999999999999999999999999999999999999999999999999975

>1adr_A P22 C2 repressor; transcription regulation; NMR {Enterobacteria phage P22} SCOP: a.35.1.2

Probab=99.50  E-value=3.2e-14  Score=91.90  Aligned_cols=58  Identities=22%  Similarity=0.326  Sum_probs=55.8

Q ss_pred             HHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           91 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        91 ~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      .++.+|+.+|..+|+||.+||+.+|+|+++|++||+|+..|+.+.+.+||++|||+++
T Consensus         5 ~~~~~l~~~r~~~gls~~~lA~~~gis~~~i~~~e~g~~~~~~~~l~~ia~~l~~~~~   62 (76)
T 1adr_A            5 LMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCSPD   62 (76)
T ss_dssp             CHHHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHTTSSCCCHHHHHHHHHHTTSCHH
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHH
Confidence            5899999999999999999999999999999999999999999999999999999864

>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=99.50  E-value=8.5e-14  Score=92.66  Aligned_cols=60  Identities=20%  Similarity=0.283  Sum_probs=57.4

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCCC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA-IPNQQILTKLERALGVKLR  148 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~-~p~~~~l~kLa~~Lgv~l~  148 (151)
                      ...++.+|+.+|.++||||.+||+.+|+++++|++||+|+. .|+.+.+.+||++|||+++
T Consensus        16 ~~~~~~~l~~~r~~~glsq~elA~~~gis~~~is~~e~g~~~~~~~~~l~~la~~l~~~~~   76 (83)
T 2a6c_A           16 RSQLLIVLQEHLRNSGLTQFKAAELLGVTQPRVSDLMRGKIDLFSLESLIDMITSIGLKVE   76 (83)
T ss_dssp             HHHHHHHHHHHHHTTTCCHHHHHHHHTSCHHHHHHHHTTCGGGCCHHHHHHHHHHTTCCCC
T ss_pred             cHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHHHHHcCCCeE
Confidence            46789999999999999999999999999999999999998 5999999999999999986

>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=99.49  E-value=3.9e-14  Score=94.22  Aligned_cols=60  Identities=25%  Similarity=0.361  Sum_probs=57.6

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      ...++.+|+.+|..+|+||.+||+.+|+++++|++||+|+..|+.+.+.+||++|||+++
T Consensus        10 ~~~~~~~l~~~r~~~glsq~~lA~~~gis~~~i~~~e~g~~~~~~~~l~~i~~~l~~~~~   69 (88)
T 2wiu_B           10 PTQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELSMT   69 (88)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHCGGGCBHHHHHHHHHHTTCEEE
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHH
Confidence            568999999999999999999999999999999999999999999999999999999875

>3lfp_A CSP231I C protein; transcriptional regulator, DNA binding protein, helix-turn-H restriction-modification, transcription; 2.00A {Citrobacter SP} PDB: 3lis_A

Probab=99.49  E-value=3.3e-14  Score=97.23  Aligned_cols=57  Identities=23%  Similarity=0.419  Sum_probs=55.3

Q ss_pred             HHHHHHHHHhcCCcCHHHHHHHhCCCHHH----HHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           92 LKKAIVQARNDKKLTQSQLAQLINEKPQV----IQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        92 ~~~~Lk~~R~~~glTQ~eLA~~lgis~s~----Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      |+.+|+.+|..+||||.+||+.+|+++++    |++||+|+..|+.+.+.+||++|||+++
T Consensus         2 ~g~~lk~~R~~~glsq~~lA~~~gis~~~~~~~is~~E~g~~~p~~~~l~~la~~l~v~~~   62 (98)
T 3lfp_A            2 LIRRLKDARLRAGISQEKLGVLAGIDEASASARMNQYEKGKHAPDFEMANRLAKVLKIPVS   62 (98)
T ss_dssp             CHHHHHHHHHHHTCCHHHHHHHTTCCHHHHHHHHHHHHHTSSCCCHHHHHHHHHHHTSCGG
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCcchhhhHHHHHHCCCCCCCHHHHHHHHHHHCcCHH
Confidence            58999999999999999999999999999    9999999999999999999999999986

>3mlf_A Transcriptional regulator; structural genomics, helix-turn-helix XRE-family like protei transcription regulator, PSI-2; 2.60A {Staphylococcus aureus subsp}

Probab=99.48  E-value=1.3e-14  Score=102.19  Aligned_cols=64  Identities=27%  Similarity=0.303  Sum_probs=59.2

Q ss_pred             CcchHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 031871           86 DRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG  149 (151)
Q Consensus        86 ~~~~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~e  149 (151)
                      ..+...++.+|+.+|..+||||.+||+.+|+|+++|++||+|+..|+.+.+.+||++|||++++
T Consensus        18 ~~~~~~~g~~Lk~~R~~~gltq~elA~~~gis~~~is~~E~G~~~ps~~~l~~ia~~l~v~~~~   81 (111)
T 3mlf_A           18 LYFQSNAMKTLKELRTDYGLTQKELGDLFKVSSRTIQNMEKDSTNIKDSLLSKYMSAFNVKYDD   81 (111)
T ss_dssp             TSCCCSSCEEHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHHCCTTCCHHHHHHHHHHHTCCGGG
T ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHhCcCHHH
Confidence            3445678999999999999999999999999999999999999999999999999999999863

>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=99.48  E-value=7e-14  Score=93.95  Aligned_cols=61  Identities=18%  Similarity=0.163  Sum_probs=57.4

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG  149 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~e  149 (151)
                      ...++..|+.+|.++|+||.+||+.+|+++++|++||+|+..|+.+.+.+||++|||++++
T Consensus        15 ~~~l~~~l~~~R~~~glsq~~lA~~~gis~~~is~~e~g~~~~~~~~l~~ia~~l~v~~~~   75 (92)
T 1lmb_3           15 ARRLKAIYEKKKNELGLSQESVADKMGMGQSGVGALFNGINALNAYNAALLAKILKVSVEE   75 (92)
T ss_dssp             HHHHHHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHTTSSCCCHHHHHHHHHHHTSCGGG
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHCCCHHH
Confidence            4678899999999999999999999999999999999999999999999999999998763

>4ghj_A Probable transcriptional regulator; structural genomics, niaid, national institute of allergy AN infectious diseases; HET: MSE; 1.75A {Vibrio vulnificus}

Probab=99.48  E-value=8.7e-14  Score=97.04  Aligned_cols=58  Identities=26%  Similarity=0.354  Sum_probs=53.4

Q ss_pred             chHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 031871           88 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL  147 (151)
Q Consensus        88 ~~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l  147 (151)
                      +...+|.+|+.+|+++||||++||+++|+|+++|++||+|+  ++++.+.+|+.+||+..
T Consensus        33 l~~~lG~~ir~~R~~~glTQ~eLA~~~gvs~~~is~~E~G~--~~~~~l~~i~~aL~~~~   90 (101)
T 4ghj_A           33 LAEEIGDRLKQARLNRDLTQSEVAEIAGIARKTVLNAEKGK--VQLDIMIAILMALDLTE   90 (101)
T ss_dssp             HHHHHHHHHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHTTC--CBHHHHHHHHHHTTCCG
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHcCCCHHHHHHHHCCC--CCHHHHHHHHHHcCCCc
Confidence            35789999999999999999999999999999999999997  56678999999999964

>3f52_A CLP gene regulator (CLGR); helix-turn-helix motif, transcriptional ACTI human pathogen, transcription activator; 1.75A {Corynebacterium glutamicum} PDB: 3f51_A

Probab=99.47  E-value=5.4e-14  Score=98.83  Aligned_cols=62  Identities=26%  Similarity=0.353  Sum_probs=58.5

Q ss_pred             cchHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           87 RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        87 ~~~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      .....|+.+|+.+|..+||||.+||+.+|+|+++|++||+|+..|+.+.+.+||++|||+++
T Consensus        24 ~~~~~~g~~l~~~R~~~glsq~~lA~~~gis~~~is~~E~g~~~~~~~~l~~la~~l~v~~~   85 (117)
T 3f52_A           24 LLREALGAALRSFRADKGVTLRELAEASRVSPGYLSELERGRKEVSSELLASVCHALGASVA   85 (117)
T ss_dssp             CHHHHHHHHHHHHHHHHTCCHHHHHHHTTSCHHHHHHHHTTSSCCCHHHHHHHHHHHTCCHH
T ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHhCCCHH
Confidence            34568999999999999999999999999999999999999999999999999999999874

>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=99.47  E-value=2e-14  Score=90.35  Aligned_cols=57  Identities=30%  Similarity=0.369  Sum_probs=53.6

Q ss_pred             HHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           92 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        92 ~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      ++.+|+.+|.++|+||.+||+.+|+|+++|++||+|+..|+.+.+.+|+++||++++
T Consensus         2 ~~~~l~~~r~~~g~s~~~lA~~~gis~~~i~~~e~g~~~~~~~~l~~i~~~l~~~~~   58 (66)
T 2xi8_A            2 IINNLKLIREKKKISQSELAALLEVSRQTINGIEKNKYNPSLQLALKIAYYLNTPLE   58 (66)
T ss_dssp             EEECHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHTTSCCCCHHHHHHHHHHTTSCHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHH
Confidence            355789999999999999999999999999999999999999999999999999864

>3bs3_A Putative DNA-binding protein; XRE-family, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.65A {Bacteroides fragilis}

Probab=99.46  E-value=3.7e-14  Score=91.75  Aligned_cols=58  Identities=24%  Similarity=0.315  Sum_probs=55.5

Q ss_pred             HHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 031871           92 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG  149 (151)
Q Consensus        92 ~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~e  149 (151)
                      ++.+|+.+|..+|+||.+||+.+|+++++|++||+|+..|+.+.+.+||++|||++++
T Consensus        11 ~~~~l~~~r~~~g~s~~~lA~~~gis~~~i~~~e~g~~~~~~~~l~~ia~~l~~~~~~   68 (76)
T 3bs3_A           11 MLNRIKVVLAEKQRTNRWLAEQMGKSENTISRWCSNKSQPSLDMLVKVAELLNVDPRQ   68 (76)
T ss_dssp             CCBCHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTSSCCCHHHHHHHHHHHTSCGGG
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHHH
Confidence            6889999999999999999999999999999999999999999999999999999763

>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=99.46  E-value=7.9e-14  Score=88.45  Aligned_cols=56  Identities=30%  Similarity=0.415  Sum_probs=52.9

Q ss_pred             HHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           92 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        92 ~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      |+.+|+.+|..+|+||.+||+.+|+|+++|++||+|+..|+.. +.+||++|||+++
T Consensus         2 ~~~~l~~~r~~~glsq~~lA~~~gis~~~i~~~e~g~~~~~~~-l~~la~~l~~~~~   57 (69)
T 1r69_A            2 ISSRVKSKRIQLGLNQAELAQKVGTTQQSIEQLENGKTKRPRF-LPELASALGVSVD   57 (69)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHTTSCSSCTT-HHHHHHHTTCCHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCchH-HHHHHHHHCcCHH
Confidence            7899999999999999999999999999999999999888877 9999999999864

>3trb_A Virulence-associated protein I; mobIle and extrachromosomal element functions, DNA binding P; 2.00A {Coxiella burnetii}

Probab=99.45  E-value=1.6e-13  Score=96.00  Aligned_cols=59  Identities=12%  Similarity=0.115  Sum_probs=55.6

Q ss_pred             HHHHHHHHH-HHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           90 SELKKAIVQ-ARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        90 ~~~~~~Lk~-~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      ...|++|++ +|+++||||.+||+.+|||+++|++||+|++.|+.+.+.+|+++|||+++
T Consensus        12 ~~pG~~Lk~~lr~~~gltq~eLA~~lGis~~~is~ie~G~~~~s~~~~~kla~~lgvs~~   71 (104)
T 3trb_A           12 IHPGEILAEELGFLDKMSANQLAKHLAIPTNRVTAILNGARSITADTALRLAKFFGTTPE   71 (104)
T ss_dssp             CCHHHHHHHHHHHTTSCCHHHHHHHHTSCHHHHHHHHTTSSCCCHHHHHHHHHHHTCCHH
T ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHH
Confidence            456999996 89999999999999999999999999999999999999999999999864

>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=99.43  E-value=9.4e-14  Score=88.56  Aligned_cols=57  Identities=28%  Similarity=0.251  Sum_probs=52.4

Q ss_pred             HHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           91 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        91 ~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      .++.+|+.+|..+|+||.+||+.+|+|+++|++||+|+..|... +.+|+++|||+++
T Consensus         3 ~~~~~l~~~r~~~glsq~~lA~~~gis~~~i~~~e~g~~~~~~~-l~~i~~~l~~~~~   59 (71)
T 1zug_A            3 TLSERLKKRRIALKMTQTELATKAGVKQQSIQLIEAGVTKRPRF-LFEIAMALNCDPV   59 (71)
T ss_dssp             SHHHHHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHTTCCSSCST-HHHHHHHTTSCHH
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCChHH-HHHHHHHHCCCHH
Confidence            58999999999999999999999999999999999999876544 9999999999864

>2wus_R RODZ, putative uncharacterized protein; structural protein, cell WALL morphogenesis, bacterial cytos bacterial actin; 2.90A {Thermotoga maritima}

Probab=99.43  E-value=1.5e-13  Score=97.39  Aligned_cols=60  Identities=15%  Similarity=0.235  Sum_probs=54.5

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCC------CHHHHHHHHHHhCCCCC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIP------NQQILTKLERALGVKLR  148 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p------~~~~l~kLa~~Lgv~l~  148 (151)
                      .+.+|.+|+.+|+.+||||.+||+.+||++++|++||+|+..|      ....+.+||++|||+++
T Consensus         5 ~~~lG~~Lr~~R~~~glSq~eLA~~~gis~~~is~iE~G~~~~~p~~~~~~~~l~~iA~~Lgv~~~   70 (112)
T 2wus_R            5 WKELGETFRKKREERRITLLDASLFTNINPSKLKRIEEGDLKGLDAEVYIKSYIKRYSEFLELSPD   70 (112)
T ss_dssp             HHHHHHHHHHHHHTTTCCHHHHHHHSSCCHHHHHHHHHTCCTTSSCHHHHHHHHHHHHHHSSCCHH
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCcchhHHHHHHHHHHHHhCcCHH
Confidence            4679999999999999999999999999999999999999764      35688999999999864

>2ef8_A C.ECOT38IS, putative transcription factor; helix-turn-helix, DNA binding protein, transcription regulator; HET: CME; 1.95A {Enterobacteria phage P2}

Probab=99.43  E-value=3e-13  Score=89.02  Aligned_cols=60  Identities=22%  Similarity=0.228  Sum_probs=52.8

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHH----HHHHhCCCCC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTK----LERALGVKLR  148 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~k----La~~Lgv~l~  148 (151)
                      .+.++.+|+.+|..+||||.+||+.+|+++++|++||+|+..|+.+.+.+    |+.+|||+++
T Consensus         8 ~~~~~~~l~~~r~~~glsq~~lA~~~gis~~~i~~~e~g~~~~~~~~l~~~~~~l~~~~~v~~~   71 (84)
T 2ef8_A            8 YRCLVQLLTKLRKEASLSQSELAIFLGLSQSDISKIESFERRLDALELFELLEVVASRLGLPMD   71 (84)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTSSCCBHHHHHHHHHHHHHHHTCCHH
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHccccCCCHH
Confidence            57899999999999999999999999999999999999999999765555    5555599864

>2l49_A C protein; P2 bacteriophage, P2 C, direct repeats, DNA-binding protein, binding protein; NMR {Enterobacteria phage P2} PDB: 2xcj_A

Probab=99.42  E-value=1.1e-13  Score=94.24  Aligned_cols=59  Identities=22%  Similarity=0.353  Sum_probs=55.4

Q ss_pred             HHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHH--hCCCCC
Q 031871           90 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERA--LGVKLR  148 (151)
Q Consensus        90 ~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~--Lgv~l~  148 (151)
                      +.++.+|+.+|..+|+||.+||+.+|+++++|++||+|+..|+.+.+.+||++  |+|+++
T Consensus         3 m~~~~~l~~~r~~~gltq~~lA~~~gis~~~is~~e~g~~~p~~~~l~~ia~~l~~~v~~~   63 (99)
T 2l49_A            3 NTISEKIVLMRKSEYLSRQQLADLTGVPYGTLSYYESGRSTPPTDVMMNILQTPQFTKYTL   63 (99)
T ss_dssp             CCTTHHHHHHHHHTTCCHHHHHHHHCCCHHHHHHHTTTSSCCCHHHHHHHHSSSSSSSSSS
T ss_pred             hHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCHH
Confidence            35789999999999999999999999999999999999999999999999999  887765

>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=99.42  E-value=2.6e-13  Score=102.63  Aligned_cols=61  Identities=20%  Similarity=0.308  Sum_probs=58.3

Q ss_pred             chHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           88 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        88 ~~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      +...++.+|+.+|+++||||++||+++|+|+++|++||+|+..|+.+.+.+||++|||+++
T Consensus         8 ~~~~~~~~l~~~r~~~gltq~~lA~~~gis~~~is~~e~g~~~p~~~~l~~ia~~l~v~~~   68 (192)
T 1y9q_A            8 FKSQIANQLKNLRKSRGLSLDATAQLTGVSKAMLGQIERGESSPTIATLWKIASGLEASFS   68 (192)
T ss_dssp             HHHHHHHHHHHHHHHTTCCHHHHHHHHSSCHHHHHHHHTTCSCCCHHHHHHHHHHHTCCSG
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHH
Confidence            3567999999999999999999999999999999999999999999999999999999986

>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=99.41  E-value=2e-13  Score=92.40  Aligned_cols=59  Identities=15%  Similarity=0.246  Sum_probs=56.1

Q ss_pred             HHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           90 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        90 ~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      ..++++|+.+|..+|+||.+||+.+|+++++|++||+|+..|+.+.+.+||++|||+++
T Consensus         7 ~~~g~~l~~~r~~~gltq~~lA~~~gis~~~is~~e~g~~~~~~~~~~~i~~~l~v~~~   65 (94)
T 2ict_A            7 PRPGDIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVIGSSPQ   65 (94)
T ss_dssp             CCHHHHHHHHHHHHTCCHHHHHHHHTCCHHHHHHHHHTSSCCCHHHHHHHHHHTCSCHH
T ss_pred             CChhHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHH
Confidence            45799999999999999999999999999999999999999999999999999999864

>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=99.41  E-value=3.4e-13  Score=96.51  Aligned_cols=60  Identities=17%  Similarity=0.095  Sum_probs=57.1

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCCC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA-IPNQQILTKLERALGVKLR  148 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~-~p~~~~l~kLa~~Lgv~l~  148 (151)
                      ...++.+|+.+|.++||||.+||+.+|+++++|++||+|+. .|+.+.+.+|+++|||+++
T Consensus        38 ~~~lg~~L~~~R~~~glTQ~eLA~~lGis~~~Is~iE~G~~~~~s~~~l~~ia~~Lgv~~~   98 (120)
T 2o38_A           38 KLRLAYALNAVIDRARLSQAAAAARLGINQPKVSALRNYKLEGFSVERLMTLLNALDQDVE   98 (120)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCCTTCCHHHHHHHHHHTTEEEE
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHHHHHhCCCcE
Confidence            56799999999999999999999999999999999999998 9999999999999999864

>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=99.40  E-value=2e-13  Score=89.03  Aligned_cols=57  Identities=26%  Similarity=0.382  Sum_probs=53.1

Q ss_pred             HHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           91 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        91 ~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      ..+.+|+.+|+..||||.+||+.+|+|+++|++||+|+..|+...+ +|+++|+++++
T Consensus        11 ~~g~~lr~~R~~~gltq~elA~~~gvs~~tis~~E~G~~~p~~~~~-~l~~~l~~~p~   67 (73)
T 3fmy_A           11 VAPEFIVKVRKKLSLTQKEASEIFGGGVNAFSRYEKGNAXPHPSTI-KLLRVLDKHPE   67 (73)
T ss_dssp             CCHHHHHHHHHHTTCCHHHHHHHHCSCTTHHHHHHTTSSCCCHHHH-HHHHHHHHCGG
T ss_pred             CCHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHcCCCCCCHHHH-HHHHHHCCCHH
Confidence            3588999999999999999999999999999999999999999988 99999998764

>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=99.40  E-value=3.7e-13  Score=93.06  Aligned_cols=57  Identities=25%  Similarity=0.328  Sum_probs=54.6

Q ss_pred             HHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcC-CCCCCHHHHHHHHHHhCCCCC
Q 031871           92 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESG-KAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        92 ~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G-~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      |+.+|+.+|..+||||.+||+.+|+|+++|++||+| ...|+.+.+.+||++|||+++
T Consensus         2 ~~~~l~~~r~~~gltq~~lA~~~gis~~~i~~~e~g~~~~p~~~~l~~ia~~l~v~~~   59 (111)
T 1b0n_A            2 IGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNLQTNPSIQFLEKVSAVLDVSVH   59 (111)
T ss_dssp             CHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCCSCCCHHHHHHHHHHHTCCHH
T ss_pred             hHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHHHHHHCcCHH
Confidence            588999999999999999999999999999999999 899999999999999999864

>3fym_A Putative uncharacterized protein; HTH DNA binding, DNA binding protein; 1.00A {Staphylococcus aureus subsp}

Probab=99.40  E-value=1.7e-13  Score=99.03  Aligned_cols=58  Identities=14%  Similarity=0.161  Sum_probs=54.1

Q ss_pred             HHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCH------HHHHHHHHHhCCCCC
Q 031871           91 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQ------QILTKLERALGVKLR  148 (151)
Q Consensus        91 ~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~------~~l~kLa~~Lgv~l~  148 (151)
                      .+|++|+++|+++||||+|||+++|+|+++|++||+|+..|+.      ..+.+||++|||+++
T Consensus         3 ~~G~~lr~~R~~~gltq~elA~~~gis~~~is~iE~g~~~~~~~~~~~~~~l~~ia~~L~v~~~   66 (130)
T 3fym_A            3 TVGEALKGRRERLGMTLTELEQRTGIKREMLVHIENNEFDQLPNKNYSEGFIRKYASVVNIEPN   66 (130)
T ss_dssp             CHHHHHHHHHHHTTCCHHHHHHHHCCCHHHHHHHHTTCGGGSSSGGGHHHHHHHHHHHTTCCHH
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCchhhhHHHHHHHHHHHhCCCHH
Confidence            5899999999999999999999999999999999999987765      779999999999875

>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=99.40  E-value=3.9e-13  Score=92.65  Aligned_cols=59  Identities=24%  Similarity=0.308  Sum_probs=56.3

Q ss_pred             HHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           90 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        90 ~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      ..++.+|+.+|..+|+||.+||+.+|+|+++|++||+|+..|+.+.+.+||++|||+++
T Consensus        17 ~~~g~~l~~~r~~~gltq~~lA~~~gis~~~is~~e~g~~~~~~~~l~~l~~~l~v~~~   75 (104)
T 3cec_A           17 IHPGEVIADILDDLDINTANFAEILGVSNQTIQEVINGQRSITVDIAIRLGKALGNGPR   75 (104)
T ss_dssp             CCHHHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHTTSSCCCHHHHHHHHHHHTSCHH
T ss_pred             CCHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCcCCCHHHHHHHHHHHCcCHH
Confidence            56899999999999999999999999999999999999999999999999999999864

>2eby_A Putative HTH-type transcriptional regulator YBAQ; hypothetical protein, JW0472, structural genomics, NPPSFA; 2.25A {Escherichia coli}

Probab=99.39  E-value=3.1e-13  Score=94.33  Aligned_cols=59  Identities=8%  Similarity=0.146  Sum_probs=56.0

Q ss_pred             HHHHHHHHH-HHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           90 SELKKAIVQ-ARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        90 ~~~~~~Lk~-~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      ..+|.+|+. +|..+|+||.+||+.+|+|+++|++||+|+..|+.+.+.+||++|||+++
T Consensus         9 ~~~g~~l~~~~r~~~glsq~~lA~~~gis~~~is~~e~g~~~~~~~~l~~la~~l~~~~~   68 (113)
T 2eby_A            9 TTPGDILLYEYLEPLDLKINELAELLHVHRNSVSALINNNRKLTTEMAFRLAKVFDTTVD   68 (113)
T ss_dssp             CCHHHHHHHHTTTTTTCCHHHHHHHHTSCHHHHHHHHTTSSCCCHHHHHHHHHHHTCCHH
T ss_pred             CChHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHH
Confidence            468999998 99999999999999999999999999999999999999999999999864

>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=99.39  E-value=6.4e-13  Score=100.65  Aligned_cols=62  Identities=19%  Similarity=0.416  Sum_probs=58.7

Q ss_pred             cchHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCCC
Q 031871           87 RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA-IPNQQILTKLERALGVKLR  148 (151)
Q Consensus        87 ~~~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~-~p~~~~l~kLa~~Lgv~l~  148 (151)
                      ...+.++.+|+++|+++||||.+||+++|+|+++|++||+|+. .|+.+.+.+||++|||+++
T Consensus         6 ~~~~~~g~~l~~~r~~~g~s~~~la~~~gis~~~ls~~e~g~~~~p~~~~l~~ia~~l~~~~~   68 (198)
T 2bnm_A            6 TASTGFAELLKDRREQVKMDHAALASLLGETPETVAAWENGEGGELTLTQLGRIAHVLGTSIG   68 (198)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTTCTTCBHHHHHHHHHHTTSCTG
T ss_pred             hHHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHHHHHhCCCHH
Confidence            3457899999999999999999999999999999999999999 9999999999999999975

>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=99.39  E-value=1.4e-13  Score=94.46  Aligned_cols=58  Identities=19%  Similarity=0.257  Sum_probs=52.5

Q ss_pred             HHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           90 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        90 ~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      +.++.+|+.+|..+||||.+||+.+||++++|++||+|+..|+.. +.+|+++|||+++
T Consensus        29 ~~~~~~lk~~R~~~glsq~elA~~lgvs~~~is~~E~G~~~p~~~-~~~l~~~l~~~~~   86 (99)
T 2ppx_A           29 APRMPRIKIIRRALKLTQEEFSARYHIPLGTLRDWEQGRSEPDQP-ARAYLKIIAVDPE   86 (99)
T ss_dssp             ---CCHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTSSCCCHH-HHHHHHHHHHCHH
T ss_pred             hHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHcCCCCCCHH-HHHHHHHHCcCHH
Confidence            568999999999999999999999999999999999999999988 7899999998764

>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=99.36  E-value=1.7e-12  Score=86.20  Aligned_cols=58  Identities=19%  Similarity=0.268  Sum_probs=54.7

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCCC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA-IPNQQILTKLERALGVKLR  148 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~-~p~~~~l~kLa~~Lgv~l~  148 (151)
                      ...++.+|+.+|..+  ||.+||+.+|+++++|++||+|+. .|+.+.+.+||++|||+++
T Consensus        14 ~~~~g~~l~~~R~~~--sq~~lA~~~gis~~~is~~E~g~~~~p~~~~l~~ia~~l~v~~~   72 (86)
T 2ofy_A           14 GQRLGELLRSARGDM--SMVTVAFDAGISVETLRKIETGRIATPAFFTIAAVARVLDLSLD   72 (86)
T ss_dssp             HHHHHHHHHHHHTTS--CHHHHHHHHTCCHHHHHHHHTTCCSSCBHHHHHHHHHHTTCCHH
T ss_pred             HHHHHHHHHHHHHHC--CHHHHHHHhCCCHHHHHHHHcCCCCCCCHHHHHHHHHHhCCCHH
Confidence            456999999999999  999999999999999999999998 8999999999999999864

>3r1f_A ESX-1 secretion-associated regulator ESPR; helix-turn-helix, transcription factor, helix-turn-helix transcription factor; 2.50A {Mycobacterium tuberculosis}

Probab=99.34  E-value=1.3e-12  Score=95.26  Aligned_cols=60  Identities=10%  Similarity=0.184  Sum_probs=55.7

Q ss_pred             hHHHHHHHHHHHh------cCCcCHHHHHHHhC-----CCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCCC
Q 031871           89 PSELKKAIVQARN------DKKLTQSQLAQLIN-----EKPQVIQEYESGKA-IPNQQILTKLERALGVKLR  148 (151)
Q Consensus        89 ~~~~~~~Lk~~R~------~~glTQ~eLA~~lg-----is~s~Is~~E~G~~-~p~~~~l~kLa~~Lgv~l~  148 (151)
                      ...|+++|+.+|+      .+++||.+||+.+|     +|+++|++||+|++ .|+.+.+.+||++|||+++
T Consensus         5 ~~~~~~RL~~L~~~~~~~~~~~~T~~elA~~~~~~G~~is~s~is~~E~G~r~~Ps~~~l~~iA~~f~V~~~   76 (135)
T 3r1f_A            5 STTFAARLNRLFDTVYPPGRGPHTSAEVIAALKAEGITMSAPYLSQLRSGNRTNPSGATMAALANFFRIKAA   76 (135)
T ss_dssp             -CCHHHHHHHHHHHCCCTTSCCCCHHHHHHHHHTTTCCCCHHHHHHHHHTSSCCCCHHHHHHHHHHHTSCTH
T ss_pred             HHHHHHHHHHHHHhhcccCCCCCCHHHHHHHHcccCCCcCHHHHHHHHCCCCCCCCHHHHHHHHHHhCCCHH
Confidence            3469999999999      58899999999999     99999999999997 8999999999999999975

>3kxa_A NGO0477 protein, putative uncharacterized protein; NEW protein fold, OPPF, STRU genomics, oxford protein production facility; 2.80A {Neisseria gonorrhoeae}

Probab=99.33  E-value=5.8e-13  Score=97.65  Aligned_cols=59  Identities=27%  Similarity=0.263  Sum_probs=55.8

Q ss_pred             HHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           90 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        90 ~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      ..++.+|+.+|..+||||.+||+.+|+|+++|++||+|+..|+.+.+.+|+++||++++
T Consensus        67 ~~~g~~L~~~R~~~glTq~elA~~lGis~s~is~~E~G~~~ps~~~l~~la~~lgv~~~  125 (141)
T 3kxa_A           67 KAGGETFVSLRMKKGFTQSELATAAGLPQPYLSRIENSKQSLQDKTVQKLANALGVSPL  125 (141)
T ss_dssp             HHSSCCHHHHHHHTTCCHHHHHHHTTCCHHHHHHHHHTCSCCCHHHHHHHHHHHTCCHH
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHCCCHH
Confidence            45678899999999999999999999999999999999999999999999999999864

>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=99.28  E-value=6.1e-12  Score=90.50  Aligned_cols=59  Identities=10%  Similarity=0.184  Sum_probs=55.0

Q ss_pred             HHHHHHHHHHHh------cCCcCHHHHHHHhC-----CCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCCC
Q 031871           90 SELKKAIVQARN------DKKLTQSQLAQLIN-----EKPQVIQEYESGKA-IPNQQILTKLERALGVKLR  148 (151)
Q Consensus        90 ~~~~~~Lk~~R~------~~glTQ~eLA~~lg-----is~s~Is~~E~G~~-~p~~~~l~kLa~~Lgv~l~  148 (151)
                      ..|+++|..++.      ..++||.+||+.+|     +|+++|++||+|++ .|+.+.+.+||++|||+++
T Consensus         4 ~~~a~RL~~L~~~~~~~~~~~lT~~elA~~~~~~G~~iS~s~is~iE~G~r~~Ps~~~l~~iA~~f~V~~~   74 (123)
T 3qwg_A            4 TTFAARLNRLFDTVYPPGRGPHTSAEVIAALKAEGITMSAPYLSQLRSGNRTNPSGATMAALANFFRIKAA   74 (123)
T ss_dssp             CCHHHHHHHHHHHSSCTTTCSCCHHHHHHHHHHTTCCCCHHHHHHHHHTSSCCCCHHHHHHHHHHTTSCTH
T ss_pred             hhHHHHHHHHHHhhccCCCCCCCHHHHHHHHcccCCCcCHHHHHHHHcCCCCCCCHHHHHHHHHHhCCCHH
Confidence            358999999998      67899999999998     99999999999997 8999999999999999985

>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=99.27  E-value=4.6e-12  Score=99.59  Aligned_cols=58  Identities=28%  Similarity=0.348  Sum_probs=56.2

Q ss_pred             HHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           90 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        90 ~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      ..+|.+|+.+|..+||||.+||+.+ +|+++|++||+|++.|+.+.+.+||+.|||+++
T Consensus         4 ~~~g~~i~~~R~~~~~tq~~la~~~-~s~~~~s~~e~g~~~~~~~~l~~i~~~l~~~~~   61 (293)
T 3u3w_A            4 EKLGSEIKKIRVLRGLTQKQLSENI-CHQSEVSRIESGAVYPSMDILQGIAAKLQIPII   61 (293)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHTTT-SCHHHHHHHHTTSCCCCHHHHHHHHHHHTCCTH
T ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHh-CCHHHHHHHHCCCCCCCHHHHHHHHHHhCcCHH
Confidence            5799999999999999999999999 999999999999999999999999999999985

>3bd1_A CRO protein; transcription factor, helix-turn-helix, prophage, structural evolution, transcription; 1.40A {Xylella fastidiosa}

Probab=99.27  E-value=2e-12  Score=85.02  Aligned_cols=52  Identities=23%  Similarity=0.258  Sum_probs=48.8

Q ss_pred             HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhC--CCC
Q 031871           94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALG--VKL  147 (151)
Q Consensus        94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lg--v~l  147 (151)
                      ++|+.+|+.+| ||.+||+.+||++++|++||+|+..| .+.+.+|+++||  |++
T Consensus         2 ~~l~~~r~~~g-sq~~lA~~lgvs~~~is~~e~g~~~p-~~~l~~ia~~l~~~v~~   55 (79)
T 3bd1_A            2 NAIDIAINKLG-SVSALAASLGVRQSAISNWRARGRVP-AERCIDIERVTNGAVIC   55 (79)
T ss_dssp             CHHHHHHHHHS-SHHHHHHHHTCCHHHHHHHHHHTCCC-GGGHHHHHHHTTTSSCH
T ss_pred             hHHHHHHHHhC-CHHHHHHHHCCCHHHHHHHHHCCCCC-HHHHHHHHHHHCCCCcH
Confidence            36899999999 99999999999999999999999988 999999999999  874

>4ich_A Transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, transcription RE; 1.95A {Saccharomonospora viridis}

Probab=99.24  E-value=6.6e-13  Score=106.60  Aligned_cols=60  Identities=15%  Similarity=0.201  Sum_probs=0.0

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      .+.++.+|+.+|+++||||.+||+++|||+++|++||+|+..|+.+.+.+||++|||+++
T Consensus        28 ~~~~~~~l~~~r~~~g~t~~~la~~~g~s~~~is~~e~g~~~p~~~~l~~ia~~l~~~~~   87 (311)
T 4ich_A           28 SDELRRRVRGLIHSRPGAQREFAAAIGLDESKLSKSLNGTRRFSPHELVRIAEHSGVTVN   87 (311)
T ss_dssp             ------------------------------------------------------------
T ss_pred             hHHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHCCChh
Confidence            367999999999999999999999999999999999999999999999999999999985

>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=99.23  E-value=1.1e-11  Score=101.05  Aligned_cols=60  Identities=23%  Similarity=0.307  Sum_probs=57.4

Q ss_pred             HHHHHHHHHHHhc------CCcCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCCCC
Q 031871           90 SELKKAIVQARND------KKLTQSQLAQLINEKPQVIQEYESGKA-IPNQQILTKLERALGVKLRG  149 (151)
Q Consensus        90 ~~~~~~Lk~~R~~------~glTQ~eLA~~lgis~s~Is~~E~G~~-~p~~~~l~kLa~~Lgv~l~e  149 (151)
                      ..||.+|+.+|++      +||||.|||+.+|||+++|++||+|+. .|+.+.+.+||++|+|+++|
T Consensus         5 ~~lG~~Lr~lR~~~~~~~~~gLtqeelA~~~gvS~~~is~iE~G~~~~ps~~~l~~lA~aL~v~~~e   71 (292)
T 3pxp_A            5 AAFGKLVQALRREHRDEKGRVWTQEVLAERTQLPKRTIERIENGSLAHLDADILLRLADALELTIGE   71 (292)
T ss_dssp             HHHHHHHHHHHHTCBCTTSCBCCHHHHHHHHTCCHHHHHHHHHTCCSCCCHHHHHHHHHHTTCCHHH
T ss_pred             HHHHHHHHHHHHccCccCcCCCCHHHHHHHHCcCHHHHHHHHCCCCCCCCHHHHHHHHHhcCCCHHH
Confidence            5799999999999      999999999999999999999999996 99999999999999999865

>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=99.17  E-value=1.2e-11  Score=100.95  Aligned_cols=58  Identities=21%  Similarity=0.195  Sum_probs=55.5

Q ss_pred             HHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           90 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        90 ~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      +.+|.+|+.+|.++|+||++||+.+ +|+++|++||+|++.|+.+.+.+||+.|||+++
T Consensus         2 m~ig~~lk~~R~~~gltq~~la~~~-is~~~is~~E~g~~~~~~~~l~~i~~~l~v~~~   59 (317)
T 2awi_A            2 FKIGSVLKQIRQELNYHQIDLYSGI-MSKSVYIKVEADSRPISVEELSKFSERLGVNFF   59 (317)
T ss_dssp             CCHHHHHHHHHHHTTCCHHHHHTTT-SCHHHHHHHHTTCSCCBHHHHHHHHHHHTSCHH
T ss_pred             hHHHHHHHHHHHHCCCCHHHHHHHh-cCHHHHHHHHCCCCCCCHHHHHHHHHHcCCCHH
Confidence            3589999999999999999999999 999999999999999999999999999999875

>3bdn_A Lambda repressor; repressor, allostery; HET: DNA; 3.91A {Enterobacteria phage lambda}

Probab=99.15  E-value=2.5e-11  Score=94.10  Aligned_cols=60  Identities=18%  Similarity=0.170  Sum_probs=57.3

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      .+.++++|+++|.++|+||.+||+.+|+|+++|++||+|+..|+.+.+.+||++|||+++
T Consensus        15 ~~~~~~~l~~~r~~~g~t~~~lA~~~gis~~~i~~~~~g~~~p~~~~l~~ia~~l~v~~~   74 (236)
T 3bdn_A           15 ARRLKAIYEKKKNELGLSQESVADKMGMGQSGVGALFNGINALNAYNAALLAKILKVSVE   74 (236)
T ss_dssp             HHHHHHHHHHHTTTTTCCSHHHHHHHTSCHHHHHHHTTTTSCCCHHHHHHTTTTTTSCGG
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHhCcCHH
Confidence            357999999999999999999999999999999999999999999999999999999875

>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=99.13  E-value=3.5e-11  Score=86.30  Aligned_cols=55  Identities=27%  Similarity=0.390  Sum_probs=49.6

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      +.+|+.+|+.+||||.+||+.+|+|+++|++||+|+..|+... .+|+++|+++++
T Consensus        73 ~~~l~~~R~~~glsq~~la~~~g~s~~~i~~~E~g~~~p~~~~-~~l~~~~~~~p~  127 (133)
T 3o9x_A           73 PEFIVKVRKKLSLTQKEASEIFGGGVNAFSRYEKGNAQPHPST-IKLLRVLDKHPE  127 (133)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHCSCTTHHHHHHHTSSCCCHHH-HHHHHHHHHCGG
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHH-HHHHHHHccCHH
Confidence            5789999999999999999999999999999999999998876 678888886653

>2p5t_A Putative transcriptional regulator PEZA; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=99.13  E-value=4.8e-12  Score=93.63  Aligned_cols=57  Identities=19%  Similarity=0.355  Sum_probs=0.0

Q ss_pred             HHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           92 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        92 ~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      ++.+|+.+|...|+||.+||+++|+|+++|++||+|...|+.+.+.+||+.||+++.
T Consensus         2 ig~~lk~~R~~~gltq~elA~~lgis~~~vs~~e~G~~~~~~~~~~~la~~~~v~~~   58 (158)
T 2p5t_A            2 IGKNIKSLRKTHDLTQLEFARIVGISRNSLSRYENGTSSVSTELIDIICQKFNVSYV   58 (158)
T ss_dssp             ---------------------------------------------------------
T ss_pred             hHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHHCcCHH
Confidence            688999999999999999999999999999999999999999999999999999875

>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=99.12  E-value=4.8e-11  Score=79.78  Aligned_cols=53  Identities=15%  Similarity=0.157  Sum_probs=49.1

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGV  145 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv  145 (151)
                      ...+..+|+.+|.  ||+|.+||+.+||+++||+.+|+|+..|+++  .+||++||.
T Consensus        19 ~~~~~~kLK~il~--GikQ~eLAK~iGIsqsTLSaIenG~~~PsL~--~kIAk~fg~   71 (83)
T 2l1p_A           19 HTTVRNALKDLLK--DMNQSSLAKECPLSQSMISSIVNSTYYANVS--AAKCQEFGR   71 (83)
T ss_dssp             HHHHHHHHHHHHT--TSCHHHHHHHSSSCHHHHHHHHTCSSCCCCC--SHHHHHHHH
T ss_pred             HHHHHHHHHHHHH--hcCHHHHHHHcCCCHHHHHHHHcCCCCCCch--HHHHHHHHH
Confidence            4678899999999  9999999999999999999999999999988  799999973

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=99.11  E-value=1.5e-11  Score=96.65  Aligned_cols=58  Identities=28%  Similarity=0.348  Sum_probs=56.0

Q ss_pred             HHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           90 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        90 ~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      +.+|.+|+.+|..+||||.+||+.+ +|+++|++||+|+..|+.+.+.+|++.|||+++
T Consensus         4 ~~~g~~i~~~r~~~~~tq~~la~~~-~s~~~is~~e~g~~~~~~~~l~~l~~~l~~~~~   61 (293)
T 2qfc_A            4 EKLGSEIKKIRVLRGLTQKQLSENI-CHQSEVSRIESGAVYPSMDILQGIAAKLQIPII   61 (293)
T ss_dssp             HHHHHHHHHHHHHHTCCTTTTTTTT-SCHHHHHHHHTSSSCCCHHHHHHHTTTSCCCTH
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHH-cCHHHHHHHHCCCCCCCHHHHHHHHHHhCcCHH
Confidence            5799999999999999999999999 999999999999999999999999999999875

>1neq_A DNA-binding protein NER; NMR {Enterobacteria phage MU} SCOP: a.35.1.2 PDB: 1ner_A

Probab=99.04  E-value=2e-10  Score=75.62  Aligned_cols=53  Identities=15%  Similarity=0.161  Sum_probs=45.2

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      ..+|+.++.++|+||.+||+.+|+|+++|++|+++   |.+.....||++|||+++
T Consensus        11 ~~ri~~~l~~~glT~~~LA~~~Gvs~stls~~~~~---~~p~~~~~IA~aLgv~~~   63 (74)
T 1neq_A           11 RADVIAGLKKRKLSLSALSRQFGYAPTTLANALER---HWPKGEQIIANALETKPE   63 (74)
T ss_dssp             HHHHHHHHHTTSCCHHHHHHHHSSCHHHHHHTTTS---SCHHHHHHHHHHTTSCHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcC---CCccHHHHHHHHHCcCHH
Confidence            56788888899999999999999999999999997   334444569999999975

>2fjr_A Repressor protein CI; genetic switch, regulation, cooperativity, transcription regulator; 1.95A {Enterobacteria phage 186} PDB: 2fkd_A

Probab=99.02  E-value=4.9e-10  Score=84.18  Aligned_cols=56  Identities=16%  Similarity=0.135  Sum_probs=52.9

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL  147 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l  147 (151)
                      .+.++++|+++|..+  ||.+||+++|+|+++|++||+|...| .+.+.+||++|||++
T Consensus         7 ~~~~~~rl~~~r~~~--tq~elA~~~Gis~~~i~~~e~g~~~p-~~~l~~ia~~~~v~~   62 (189)
T 2fjr_A            7 NVDVLDRICEAYGFS--QKIQLANHFDIASSSLSNRYTRGAIS-YDFAAHCALETGANL   62 (189)
T ss_dssp             HHHHHHHHHHHHTCS--SHHHHHHHTTCCHHHHHHHHHSSSCC-HHHHHHHHHHHCCCH
T ss_pred             cHHHHHHHHHHHhhc--CHHHHHHHhCcCHHHHHHHHhCCCCC-HHHHHHHHHHHCCCH
Confidence            467999999999888  99999999999999999999999999 999999999999986

>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=98.78  E-value=1e-08  Score=77.60  Aligned_cols=46  Identities=11%  Similarity=0.157  Sum_probs=41.6

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHH
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTK  138 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~k  138 (151)
                      .++|+.+|+++|+||+++|+.+|||+++|++||+|++.|+...+.+
T Consensus        92 ~~~lk~lR~~~glTQ~elA~~LGvsr~tis~yE~G~r~iP~~~~la  137 (170)
T 2auw_A           92 HEMFGDWMHRNNLSLTTAAEALGISRRMVSYYRTAHKIIPRTIWLA  137 (170)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHTTSSCCCHHHHHH
T ss_pred             cHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHH
Confidence            5689999999999999999999999999999999999887776433

>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=98.65  E-value=6.1e-08  Score=72.24  Aligned_cols=60  Identities=13%  Similarity=0.119  Sum_probs=56.8

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      ...+.++|..+|.++|||++++|+.+|+|...+..++.|...|+.+.+.+|+++||++.+
T Consensus        11 ~~~~~~~I~~AK~~KGLTwe~IAe~iG~S~v~vtaa~lGQ~~ls~e~A~kLa~~LgL~~e   70 (156)
T 1dw9_A           11 RLDLADAILLSKAKKDLSFAEIADGTGLAEAFVTAALLGQQALPADAARLVGAKLDLDED   70 (156)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHTTSSSCHHHHHHHHTTSSCCCHHHHHHHHHHTTCCHH
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHcCCCCCCHHHHHHHHHHhCcCHH
Confidence            367899999999999999999999999999999999999999999999999999998754

>1nr3_A MTH0916, DNA-binding protein TFX; northeast structural genomics consortium, reduced- dimensionality PSI; NMR {Methanothermobacterthermautotrophicus} SCOP: d.236.1.1

Probab=98.62  E-value=9.9e-11  Score=83.42  Aligned_cols=48  Identities=17%  Similarity=0.268  Sum_probs=45.2

Q ss_pred             HhcCCcCHHHHHHHhCCCHHHHHHHHcC------CCCCCHHHHHHHHHHhCCCCC
Q 031871          100 RNDKKLTQSQLAQLINEKPQVIQEYESG------KAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus       100 R~~~glTQ~eLA~~lgis~s~Is~~E~G------~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      |+ +||||.+||+++|+|+++|++||+|      +..|+.+.+.+|+..|+++++
T Consensus         2 R~-~glTQ~eLA~~~Gvs~~~is~~E~G~~~~~~~~~p~~~~l~~la~~l~v~~~   55 (122)
T 1nr3_A            2 RE-RGWSQKKIARELKTTRQNVSAIERKAMENIEKSRNTLDFVKSLKSPVRILCR   55 (122)
T ss_dssp             CC-CSCSSCSTHHHHHHCCSSSCCHHHHHHTTCSSSSCHHHHHHHHCCCEEEEEC
T ss_pred             cc-cCCCHHHHHHHhCCCHHHHHHHHcCCCccchhcccCHHHHHHHHHHHccccc
Confidence            56 8999999999999999999999999      888999999999999998875

>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=98.42  E-value=3e-07  Score=57.78  Aligned_cols=41  Identities=15%  Similarity=0.110  Sum_probs=34.0

Q ss_pred             CcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 031871          104 KLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL  147 (151)
Q Consensus       104 glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l  147 (151)
                      ++||.+||+.+|||+++|++||  .. ++...+.+|+++||..+
T Consensus        10 ~~tq~~lA~~lGvs~~~Vs~we--~~-~p~~~~~~i~~~~~g~v   50 (61)
T 1rzs_A           10 FGTQRAVAKALGISDAAVSQWK--EV-IPEKDAYRLEIVTAGAL   50 (61)
T ss_dssp             HSSHHHHHHHHTCCHHHHHHCC--SB-CCHHHHHHHHHHTTSCS
T ss_pred             cCCHHHHHHHhCCCHHHHHHHH--hh-CCHHHHHHHHHHHCCCc
Confidence            4599999999999999999999  33 34456669999999655

>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo, protein-DNA, human disease; 3.20A {Homo sapiens}

Probab=98.27  E-value=2.4e-06  Score=66.95  Aligned_cols=52  Identities=12%  Similarity=0.054  Sum_probs=45.2

Q ss_pred             chHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHH
Q 031871           88 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKL  139 (151)
Q Consensus        88 ~~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kL  139 (151)
                      -...|+..|+.+|..+||||.+||+.+|||+++|++||++....+...+..+
T Consensus        28 ~~~~~~~~Ik~~r~~~gltQ~evA~~tGISqS~ISq~e~~g~~~t~~k~a~~   79 (221)
T 2h8r_A           28 DPWRAAKMIKGYMQQHNIPQREVVDVTGLNQSHLSQHLNKGTPMKTQKRAAL   79 (221)
T ss_dssp             CHHHHHHHHHHHHHHHTCCHHHHHHHHTCCHHHHHHHHTTCCCCCHHHHHHH
T ss_pred             CcHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHhCCCchhHHHHHHH
Confidence            3478899999999999999999999999999999999997777777655444

>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=98.26  E-value=2e-06  Score=54.97  Aligned_cols=44  Identities=14%  Similarity=0.121  Sum_probs=37.4

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcCCC---CCCHHHHHHHHH---HhCCCCC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESGKA---IPNQQILTKLER---ALGVKLR  148 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G~~---~p~~~~l~kLa~---~Lgv~l~  148 (151)
                      +|+.|||+.+|+|++||+++++|+.   .++.++..+|.+   .||..++
T Consensus         1 ~T~~diA~~aGVS~sTVSrvLng~~~~~~vs~et~~rI~~aa~~lgY~pn   50 (65)
T 1uxc_A            1 MKLDEIARLAGVSRTTASYVINGKAKQYRVSDKTVEKVMAVVREHNYHPN   50 (65)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHTCTTTTTCTTHHHHHHHHHHHHHTCCCC
T ss_pred             CCHHHHHHHHCcCHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHhCCCcc
Confidence            5899999999999999999999998   788877666554   6887765

>3g7d_A PHPD; non heme Fe(II) dioxygenase, cupin, biosynthetic protein; 1.80A {Streptomyces viridochromogenes} PDB: 3gbf_A 3rzz_A

Probab=98.23  E-value=1.2e-06  Score=72.47  Aligned_cols=57  Identities=19%  Similarity=0.186  Sum_probs=53.2

Q ss_pred             HHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCCC
Q 031871           92 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA-IPNQQILTKLERALGVKLR  148 (151)
Q Consensus        92 ~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~-~p~~~~l~kLa~~Lgv~l~  148 (151)
                      .+-.|+.+|...|+||.+||++.||++..|+.+|+|+. .+..+.+.+|+++|+++.+
T Consensus       231 agv~LR~ar~ReglTQ~~LAe~TGIPq~hISeMenGKr~~IGkdeaR~LA~ALnvDYR  288 (443)
T 3g7d_A          231 AGSVLDLFLARRAHTRTSAAEAAGVPPADLEAALRSPASETGLTVLRTLGRALGFDYR  288 (443)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHCTTSHHHHHHHHHHHHHHTCCGG
T ss_pred             HHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHhcCCcCCccHHHHHHHHHHhCCCch
Confidence            47789999999999999999999999999999999998 5699999999999999864

>1zx4_A P1 PARB, plasmid partition PAR B protein, PARB; translation; HET: CIT; 2.98A {Enterobacteria phage P1} PDB: 2ntz_A

Probab=98.16  E-value=5.3e-07  Score=69.33  Aligned_cols=54  Identities=9%  Similarity=0.147  Sum_probs=50.1

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH----------------HcCCCCCCHHHHHHHHHHh
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEY----------------ESGKAIPNQQILTKLERAL  143 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~----------------E~G~~~p~~~~l~kLa~~L  143 (151)
                      -.++|.++..+ ...|+||.++|+.+|||+++|+++                ++|...|+...|.+++..|
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            46789999998 789999999999999999999997                7999999999999999999

>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=98.06  E-value=7.6e-06  Score=52.52  Aligned_cols=45  Identities=13%  Similarity=0.032  Sum_probs=37.9

Q ss_pred             CcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHH---HHHHHHhCCCCC
Q 031871          104 KLTQSQLAQLINEKPQVIQEYESGKAIPNQQIL---TKLERALGVKLR  148 (151)
Q Consensus       104 glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l---~kLa~~Lgv~l~  148 (151)
                      .+|+.|+|+.+|+|++||+++++|...++.++.   .++++.||..++
T Consensus         9 ~~t~~diA~~aGVS~sTVSr~ln~~~~vs~~t~~rV~~~a~~lgY~pn   56 (67)
T 2l8n_A            9 AATMKDVALKAKVSTATVSRALMNPDKVSQATRNRVEKAAREVGYLPQ   56 (67)
T ss_dssp             CCCHHHHHHHTTCCHHHHHHTTTCCCCSCHHHHHHHHHHHHHHCCCC-
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHhCCCcc
Confidence            479999999999999999999999988888774   455778887654

>2pij_A Prophage PFL 6 CRO; transcription factor, helix-turn-helix, structural evolution, transcription; 1.70A {Pseudomonas fluorescens}

Probab=98.00  E-value=4.8e-06  Score=52.13  Aligned_cols=38  Identities=16%  Similarity=0.122  Sum_probs=34.5

Q ss_pred             HHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCH
Q 031871           95 AIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQ  133 (151)
Q Consensus        95 ~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~  133 (151)
                      +|+.+|.+.| ||.++|+.+|+|+++|++||+|.+.|++
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            5788999999 9999999999999999999999877653

>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=98.00  E-value=1.7e-05  Score=60.90  Aligned_cols=48  Identities=8%  Similarity=0.047  Sum_probs=43.1

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHH
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQIL  136 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l  136 (151)
                      ...|+.+|+.++..+|+||.+||+.+|+|+++|++|++|...++....
T Consensus        28 p~~l~~~Ik~~l~~~gitQ~~lA~~~GiSqs~ISr~l~~~~~~~~~kr   75 (194)
T 1ic8_A           28 PWRVAKMVKSYLQQHNIPQREVVDTTGLNQSHLSQHLNKGTPMKTQKR   75 (194)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHCCCHHHHHHHHHSBCCCCHHHH
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHhCCChHHHHHHHhcCcccccccc
Confidence            467899999999999999999999999999999999998877766543

>1s4k_A Putative cytoplasmic protein YDIL; structural genomics, MCSG, PSI, PROT structure initiative; 1.90A {Salmonella typhimurium} SCOP: a.35.1.6

Probab=97.96  E-value=2.3e-05  Score=55.60  Aligned_cols=49  Identities=16%  Similarity=0.233  Sum_probs=43.7

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhC--CCHHHHHHHHcCCCCCCHHHHHHHHH
Q 031871           93 KKAIVQARNDKKLTQSQLAQLIN--EKPQVIQEYESGKAIPNQQILTKLER  141 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lg--is~s~Is~~E~G~~~p~~~~l~kLa~  141 (151)
                      ...|+.+|..+||||.|.|..+|  ++..+..+||+|++.++.++...+..
T Consensus         5 ~~ELkalR~ilgLt~~EaA~~i~~~vs~rtWQqWE~G~~~IP~~i~e~~~~   55 (120)
T 1s4k_A            5 ALELQALRRIFDMTIEECTIYITQDNNSATWQRWEAGDIPISPEIIARLKE   55 (120)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHTSSSCCHHHHHHHHHTSSCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHhccCCHHHHHHHHCCCCCCCHHHHHHHHH
Confidence            45689999999999999999998  89999999999999999887776653

>2hin_A GP39, repressor protein; transcription factor, dimer interface, helix-turn-helix; 1.05A {Enterobacteria phage N15} PDB: 3qws_A

Probab=97.53  E-value=0.00016  Score=46.89  Aligned_cols=41  Identities=12%  Similarity=0.081  Sum_probs=33.7

Q ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 031871          106 TQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL  147 (151)
Q Consensus       106 TQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l  147 (151)
                      +|.+||+.||||+++|++|++|.. ++......|..+-+-.+
T Consensus        12 ~~~~lA~~lGVs~~aVs~W~~g~~-iP~~~~~~Ie~~T~G~v   52 (71)
T 2hin_A           12 DVEKAAVGVGVTPGAVYQWLQAGE-IPPLRQSDIEVRTAYKL   52 (71)
T ss_dssp             SHHHHHHHHTSCHHHHHHHHHHTS-CCHHHHHHHHHHTTTSS
T ss_pred             CHHHHHHHHCCCHHHHHHHHhCCC-CCHHHHHHHHHHhCCcc
Confidence            699999999999999999999855 45666778888776544

>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=97.46  E-value=0.0001  Score=55.69  Aligned_cols=38  Identities=18%  Similarity=0.240  Sum_probs=35.6

Q ss_pred             hHHHHHHHHHHHhcCCc--CHHHHHHHhCCC-HHHHHHHHc
Q 031871           89 PSELKKAIVQARNDKKL--TQSQLAQLINEK-PQVIQEYES  126 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~gl--TQ~eLA~~lgis-~s~Is~~E~  126 (151)
                      ...+.++|+++|+++|+  ||.|||+.+|++ +++|++|++
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            35789999999999999  999999999999 999999987

>2cw1_A SN4M; lambda CRO fold, de novo protein; NMR {Synthetic} SCOP: k.46.1.1

Probab=97.41  E-value=0.0002  Score=45.67  Aligned_cols=36  Identities=17%  Similarity=0.095  Sum_probs=30.3

Q ss_pred             HHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCC
Q 031871           95 AIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPN  132 (151)
Q Consensus        95 ~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~  132 (151)
                      .|+.++.+.  ||.++|+.+|+++++||+|+++.+.+.
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            477777776  999999999999999999998765443

>2l0k_A Stage III sporulation protein D; SPOIIID, solution structure, DNA binding, bacillus subti transcription factor, transcription; NMR {Bacillus subtilis}

Probab=97.37  E-value=0.00016  Score=49.23  Aligned_cols=52  Identities=12%  Similarity=0.072  Sum_probs=43.5

Q ss_pred             HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhCC
Q 031871           94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK-AIPNQQILTKLERALGV  145 (151)
Q Consensus        94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~-~~p~~~~l~kLa~~Lgv  145 (151)
                      ..|.++....++|..|+|+.+|+|.+||+++.++. ..++.++..++.++||.
T Consensus        10 ~~I~~~l~~~~~ti~dlA~~~gVS~~TVsR~L~~~~~~Vs~~tr~rV~~algY   62 (93)
T 2l0k_A           10 IKIGKYIVETKKTVRVIAKEFGVSKSTVHKDLTERLPEINPDLANEVKEILDY   62 (93)
T ss_dssp             HHHHHHHHHHCCCHHHHHHHHTSCHHHHHHHHTTHHHHHCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcCCCCCCCHHHHHHHHHHHCC
Confidence            34555555567999999999999999999999997 77899999999888764

>4ich_A Transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, transcription RE; 1.95A {Saccharomonospora viridis}

Probab=97.29  E-value=0.00014  Score=57.82  Aligned_cols=114  Identities=10%  Similarity=0.019  Sum_probs=27.5

Q ss_pred             eccCCCCCccccCHHHHHHHHHcCCChhhHHhhhcCCCccCCCCcccccccccccchhhhHHHHHhh-------------
Q 031871           16 IKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTENLALLLSVLY-------------   82 (151)
Q Consensus        16 ~~~~~~~~~~~~~~~~~~~a~r~g~~v~t~~k~~~g~~~~~~~~~~~~~~kl~~~~~~~~~~~s~~~-------------   82 (151)
                      ||.+-..-...++=++.+.|++.|++.+|+.+||+|...|....+.+.+..++.+.+.+-....-..             
T Consensus        31 ~~~~l~~~r~~~g~t~~~la~~~g~s~~~is~~e~g~~~p~~~~l~~ia~~l~~~~~~l~~~~~~~~~~~~~~~~~~~~~  110 (311)
T 4ich_A           31 LRRRVRGLIHSRPGAQREFAAAIGLDESKLSKSLNGTRRFSPHELVRIAEHSGVTVNWLINGRDDARTVAAVPAPTARSR  110 (311)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHCCChhhhhcCCCccccccCCCCcccccC
Confidence            4444333444455677889999999999999999999888776666666666655433321000000             


Q ss_pred             -----ccCCcchHHHHHHHHHHHhc---CCcCHHHHHHHhCCCHHHHHHHHcCCC
Q 031871           83 -----CTDDRVPSELKKAIVQARND---KKLTQSQLAQLINEKPQVIQEYESGKA  129 (151)
Q Consensus        83 -----~~~~~~~~~~~~~Lk~~R~~---~glTQ~eLA~~lgis~s~Is~~E~G~~  129 (151)
                           .........+-....++-.+   .++|..++|+.+|||+.++..+-.++.
T Consensus       111 ~~~~~~~~~~~r~~il~aa~~l~~~~G~~~~T~~~IA~~AGvs~gtlY~yF~sKe  165 (311)
T 4ich_A          111 SAPAGEPQSEARRRILETAWRLIARRGYHNVRIHDIASELGTSNATIHYHFPSKK  165 (311)
T ss_dssp             ------CCHHHHHHHHHHHHHHHHHHCGGGCCHHHHHHHHTCCHHHHHHHCSSHH
T ss_pred             CCCCccchhhHHHHHHHHHHHHHHHcCCccCCHHHHHHHhCCCchhHHHhCCCHH
Confidence                 00000011222222333333   457999999999999999999876654

>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=97.12  E-value=0.0006  Score=45.54  Aligned_cols=41  Identities=12%  Similarity=0.077  Sum_probs=34.7

Q ss_pred             CcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871          104 KLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus       104 glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      -++|..+|+.+|++.++||+|.+|.    .+.+..|..+||..+.
T Consensus        24 ~~gQ~~vAe~~GvdeStISR~k~~~----~~~~~~lLa~Lglkvv   64 (83)
T 1zs4_A           24 MLGTEKTAEAVGVDKSQISRWKRDW----IPKFSMLLAVLEWGVV   64 (83)
T ss_dssp             HHCHHHHHHHHTSCHHHHHHHHHHT----HHHHHHHHHHHTTCCC
T ss_pred             HHhhHHHHHHhCCCHHHHhhhhhhH----HHHHHHHHHHhccCCC
Confidence            3689999999999999999999974    5677788888887763

>1xwr_A Regulatory protein CII; all-alpha fold, DNA binding protein; 2.56A {Bacteriophage lambda} SCOP: a.35.1.9 PDB: 1zpq_A

Probab=96.79  E-value=7.4e-05  Score=51.42  Aligned_cols=28  Identities=11%  Similarity=0.096  Sum_probs=24.8

Q ss_pred             hcCCcCHHHHHHHhCCCHHHHHHHHcCC
Q 031871          101 NDKKLTQSQLAQLINEKPQVIQEYESGK  128 (151)
Q Consensus       101 ~~~glTQ~eLA~~lgis~s~Is~~E~G~  128 (151)
                      ...+++|..+|+.+||+.++||+|++|.
T Consensus        20 ~la~~gq~~vA~~iGV~~StISR~k~~~   47 (97)
T 1xwr_A           20 KIAMLGTEKTAEAVGVDKSQISRWKRDW   47 (97)
T ss_dssp             HHHHHCHHHHHHHHTCCTTTHHHHHHHH
T ss_pred             HHHHHhHHHHHHHhCCCHHHHHHHHhhh
Confidence            3346899999999999999999999975

>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=96.56  E-value=0.0019  Score=47.88  Aligned_cols=38  Identities=13%  Similarity=0.205  Sum_probs=32.3

Q ss_pred             CcCHHHHHHHhCCCHHHHHHHHcCCCCCCH-HHHHHHHHHh
Q 031871          104 KLTQSQLAQLINEKPQVIQEYESGKAIPNQ-QILTKLERAL  143 (151)
Q Consensus       104 glTQ~eLA~~lgis~s~Is~~E~G~~~p~~-~~l~kLa~~L  143 (151)
                      |+|+.++|+.+|||++||.+|.+.  .|.. +.+.++++.|
T Consensus        48 ~lTv~eIA~~LGIS~~TLyrW~k~--~p~~~~~l~~vad~~   86 (155)
T 2ao9_A           48 KRTQDEMANELGINRTTLWEWRTK--NQDFIAFKSEVADSF   86 (155)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHHH--CHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHHc--CcchHHHHHHHHHHH
Confidence            899999999999999999999995  4664 6777777764

>2x48_A CAG38821; archeal virus, viral protein; 2.60A {Sulfolobus islandicus rod-shaped virusorganism_taxid}

Probab=96.44  E-value=0.0059  Score=36.29  Aligned_cols=34  Identities=15%  Similarity=0.173  Sum_probs=27.6

Q ss_pred             HHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           92 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        92 ~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      ....+..+ ...|+|+.++|+.+|+|++||++|.+
T Consensus        20 ~~~~i~~l-~~~g~s~~eIA~~lgis~~TV~~~l~   53 (55)
T 2x48_A           20 LVSVAHEL-AKMGYTVQQIANALGVSERKVRRYLE   53 (55)
T ss_dssp             HHHHHHHH-HHTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            34455555 35799999999999999999999865

>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=96.43  E-value=0.0074  Score=34.14  Aligned_cols=36  Identities=8%  Similarity=0.144  Sum_probs=27.5

Q ss_pred             HHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcC
Q 031871           91 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESG  127 (151)
Q Consensus        91 ~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G  127 (151)
                      .....+..+. ..|+|+.++|+.+|+|++||.+|.+.
T Consensus         9 ~~~~~i~~~~-~~g~s~~~IA~~lgis~~Tv~~~~~~   44 (51)
T 1tc3_C            9 TERAQLDVMK-LLNVSLHEMSRKISRSRHCIRVYLKD   44 (51)
T ss_dssp             HHHHHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHHC
T ss_pred             HHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHhh
Confidence            3333444443 46899999999999999999999753

>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=96.37  E-value=0.0032  Score=43.45  Aligned_cols=55  Identities=13%  Similarity=0.066  Sum_probs=39.3

Q ss_pred             HHHHHHHHHHH--hcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q 031871           90 SELKKAIVQAR--NDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALG  144 (151)
Q Consensus        90 ~~~~~~Lk~~R--~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lg  144 (151)
                      ..+..|+.-.+  ....+||.|+|+.+|+|++||+++-+--...+.+.-..|.+.|.
T Consensus        42 ~~l~~R~~l~~~L~~ge~TQREIA~~lGiS~stISRi~r~L~~l~~~~k~~l~~~l~   98 (101)
T 1jhg_A           42 EALGTRVRIIEELLRGEMSQRELKNELGAGIATITRGSNSLKAAPVELRQWLEEVLL   98 (101)
T ss_dssp             HHHHHHHHHHHHHHHCCSCHHHHHHHHCCCHHHHHHHHHHHHHSCHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHcCCcCHHHHHHHHCCChhhhhHHHHHHHHccHHHHHHHHHHhc
Confidence            44555555443  23339999999999999999999955445567777777777664

>3kjx_A Transcriptional regulator, LACI family; LACL family, protein structure initiative II(PSI II), NYSGXRC, structural genomics; 2.33A {Silicibacter pomeroyi}

Probab=95.64  E-value=0.015  Score=46.09  Aligned_cols=47  Identities=9%  Similarity=0.101  Sum_probs=36.9

Q ss_pred             cCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHH---HHHHhCCCCC
Q 031871          102 DKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTK---LERALGVKLR  148 (151)
Q Consensus       102 ~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~k---La~~Lgv~l~  148 (151)
                      .+..|.+|+|+.+|||.+|||+..||...++.++..+   .++.||..+.
T Consensus         8 ~~~~ti~diA~~agVS~~TVSr~Ln~~~~vs~~tr~rV~~~~~~lgY~pn   57 (344)
T 3kjx_A            8 KRPLTLRDVSEASGVSEMTVSRVLRNRGDVSDATRARVLAAAKELGYVPN   57 (344)
T ss_dssp             --CCCHHHHHHHHCCCSHHHHHHHTTCSCCCHHHHHHHHHHHHHHTCCCC
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHhCCCCC
Confidence            3458999999999999999999999998887766555   4666776543

>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=95.63  E-value=0.013  Score=33.63  Aligned_cols=33  Identities=18%  Similarity=0.184  Sum_probs=26.0

Q ss_pred             HHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCC
Q 031871           95 AIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK  128 (151)
Q Consensus        95 ~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~  128 (151)
                      .+..+. ..|+|..++|+.+|+|++||.+|.+..
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 357999999999999999999997643

>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=95.50  E-value=0.029  Score=37.90  Aligned_cols=40  Identities=8%  Similarity=0.217  Sum_probs=31.0

Q ss_pred             CcchHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           86 DRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        86 ~~~~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      .....++-..+..+.. .|+|..++|+.+|+|++||.+|.+
T Consensus        16 ~~~s~~~r~~i~~~~~-~g~s~~~ia~~lgis~~Tv~~w~~   55 (128)
T 1pdn_C           16 RPLPNNIRLKIVEMAA-DGIRPCVISRQLRVSHGCVSKILN   55 (128)
T ss_dssp             SCCCHHHHHHHHHHHH-TTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CcCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3445556666665553 799999999999999999999854

>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA complex, SOX; 2.05A {Mus musculus}

Probab=95.41  E-value=0.033  Score=41.16  Aligned_cols=50  Identities=18%  Similarity=0.207  Sum_probs=41.6

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCC------CHHHHHHHHcCCCCCCHHHHHHHH
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINE------KPQVIQEYESGKAIPNQQILTKLE  140 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgi------s~s~Is~~E~G~~~p~~~~l~kLa  140 (151)
                      .+.|++.++..|...|+||.+++..+|.      |+++|+++|.-.  .+...+.+|-
T Consensus        15 l~~fa~~fk~~ri~lg~tQ~~vg~alg~l~g~~~Sqtti~rFE~l~--ls~kn~~klk   70 (164)
T 2xsd_C           15 LEQFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQ--LSFKNMCKLK   70 (164)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHHHHHSCCCCHHHHHHHHTTC--SBHHHHHHHH
T ss_pred             HHHHHHHHHHHHhhcCCcccccccccccccCCCcCcchhhhhhccC--CCHHHHHHcc
Confidence            3789999999999999999999999987      999999999743  4555555543

>3h5t_A Transcriptional regulator, LACI family; DNA-dependent, protein structure initiative II(PSI II), NYSGXRC, 11232D), structural genomics; 2.53A {Corynebacterium glutamicum}

Probab=95.26  E-value=0.017  Score=46.21  Aligned_cols=45  Identities=7%  Similarity=0.029  Sum_probs=35.8

Q ss_pred             cCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH---HHHHHhCCC
Q 031871          102 DKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILT---KLERALGVK  146 (151)
Q Consensus       102 ~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~---kLa~~Lgv~  146 (151)
                      .+..|.+|+|+++|||.+|||+..||...++.++..   +.++.||-.
T Consensus         7 ~~~~Ti~diA~~aGVS~~TVSrvLn~~~~Vs~~tr~rV~~~a~~lgY~   54 (366)
T 3h5t_A            7 QQYGTLASIAAKLGISRTTVSNAYNRPEQLSAELRQRILDTAEDMGYL   54 (366)
T ss_dssp             CCTTHHHHHHHHHTSCHHHHHHHHHCGGGSCHHHHHHHHHHHHHTTC-
T ss_pred             CCCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCC
Confidence            456799999999999999999999998777766544   456677764

>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=95.24  E-value=0.038  Score=40.55  Aligned_cols=49  Identities=18%  Similarity=0.237  Sum_probs=41.1

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCC------CHHHHHHHHcCCCCCCHHHHHHH
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINE------KPQVIQEYESGKAIPNQQILTKL  139 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgi------s~s~Is~~E~G~~~p~~~~l~kL  139 (151)
                      ...|+..++..|...|+||.+++..+|.      ++++|+++|.=.  ++...+.++
T Consensus         9 ~~~~~~~~k~~r~~lg~tQ~~vg~~lg~l~g~~~sq~ti~rfE~l~--lS~knm~kl   63 (160)
T 1e3o_C            9 LEQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEALN--LSFKNMSKL   63 (160)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHHHHHSCCCCHHHHHHHHHTC--SCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHhhccccCCCcCccccccccccC--CChHHHHhc
Confidence            3679999999999999999999999998      999999999853  455544444

>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=95.24  E-value=0.029  Score=40.63  Aligned_cols=50  Identities=14%  Similarity=0.154  Sum_probs=41.4

Q ss_pred             HHHHHHHHHHHhcCCcCHHHHHHHhCC------CHHHHHHHHcCCCCCCHHHHHHHHH
Q 031871           90 SELKKAIVQARNDKKLTQSQLAQLINE------KPQVIQEYESGKAIPNQQILTKLER  141 (151)
Q Consensus        90 ~~~~~~Lk~~R~~~glTQ~eLA~~lgi------s~s~Is~~E~G~~~p~~~~l~kLa~  141 (151)
                      +.|++.++.-|...|+||.+++..+|.      |+++|+++|.=.  ++...+.+|--
T Consensus         6 ~~fa~~~k~~ri~lg~tQ~~vg~al~~l~g~~~Sqtti~rfe~l~--ls~knm~kLkP   61 (146)
T 1au7_A            6 EQFANEFKVRRIKLGYTQTNVGEALAAVHGSEFSQTTICRFENLQ--LSFKNACKLKA   61 (146)
T ss_dssp             HHHHHHHHHHHHHHTCCHHHHHHHHHHTTSSCCCHHHHHHHHTTC--SBHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccCcHHhhhhhcchhccCCCCcchHHHHhccC--CChHHHHhcch
Confidence            678999999999999999999999987      999999999843  55555555443

>2w7n_A TRFB transcriptional repressor protein; INCP, plasmid, repressor, DNA-binding, transcription/DNA; HET: BRU; 1.85A {Escherichia coli}

Probab=95.13  E-value=0.04  Score=37.87  Aligned_cols=35  Identities=9%  Similarity=-0.021  Sum_probs=28.7

Q ss_pred             HHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           92 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        92 ~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      ...++..+--..|+||.|+|+.+|+|+++|+++.+
T Consensus        22 ~~~~~A~lyYv~g~tQ~eIA~~lGiSR~~VsrlL~   56 (101)
T 2w7n_A           22 QTIEIARGVLVDGKPQATFATSLGLTRGAVSQAVH   56 (101)
T ss_dssp             HHHHHHHHHHTTCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            44555566677899999999999999999998743

>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=95.08  E-value=0.015  Score=36.76  Aligned_cols=32  Identities=13%  Similarity=0.031  Sum_probs=25.3

Q ss_pred             HHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCC
Q 031871           96 IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA  129 (151)
Q Consensus        96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~  129 (151)
                      |+.+....  ||.++|+.|||++++||+|.++.+
T Consensus         7 L~~~~~~~--s~t~aA~~L~vtQ~AVS~~ir~~r   38 (66)
T 2ovg_A            7 LKDYAMRF--GQTKTAKDLGVYPSSINQAIHAGR   38 (66)
T ss_dssp             HHHHHHHH--CHHHHHHHHTSCHHHHHHHHHHTC
T ss_pred             HHHHHHHC--CHHHHHHHhCCCHHHHHHHHHhCC
Confidence            44444444  899999999999999999987543

>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=94.88  E-value=0.096  Score=36.13  Aligned_cols=76  Identities=8%  Similarity=0.101  Sum_probs=48.4

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCccCCCCcccccccccccchhhhHHHHHhhccCCcchHHHHHHHHHHHhcCCcCHHH
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQ  109 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~~~~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~~~~~~~~~Lk~~R~~~glTQ~e  109 (151)
                      +.-..|+..|++..|+.+|-.-.............                     ..+....-..|..+.....+|..+
T Consensus        24 s~~~ia~~lgis~~Tv~r~~~~~~~~g~~~~~gr~---------------------~~l~~~~~~~i~~~~~~~~~s~~~   82 (141)
T 1u78_A           24 SLHEMSRKISRSRHCIRVYLKDPVSYGTSKRAPRR---------------------KALSVRDERNVIRAASNSCKTARD   82 (141)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHSGGGTTCCCCCCCC---------------------CSSCHHHHHHHHHHHHHCCCCHHH
T ss_pred             CHHHHHHHHCcCHHHHHHHHHcccccCCcCCCCCC---------------------CcCCHHHHHHHHHHHhCCCCCHHH
Confidence            44668999999999999987543221000000001                     112223334444445566799999


Q ss_pred             HHHHhC--CCHHHHHHHHc
Q 031871          110 LAQLIN--EKPQVIQEYES  126 (151)
Q Consensus       110 LA~~lg--is~s~Is~~E~  126 (151)
                      +|..+|  +|.++|.+|..
T Consensus        83 i~~~lg~~~s~~tV~r~l~  101 (141)
T 1u78_A           83 IRNELQLSASKRTILNVIK  101 (141)
T ss_dssp             HHHHTTCCSCHHHHHHHHH
T ss_pred             HHHHHCCCccHHHHHHHHH
Confidence            999999  89999999975

>2jn6_A Protein CGL2762, transposase; GFT PSI-2, protein structure, structural genomics, protein structure initiative; NMR {Corynebacterium glutamicum} SCOP: a.4.1.19

Probab=94.68  E-value=0.064  Score=35.40  Aligned_cols=39  Identities=13%  Similarity=0.168  Sum_probs=29.0

Q ss_pred             chHHHHHHHHHHHhcC-CcCHHHHHHHhCCCHHHHHHHHc
Q 031871           88 VPSELKKAIVQARNDK-KLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        88 ~~~~~~~~Lk~~R~~~-glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      ....+-..+-.+.... |+|..++|+.+|||+++|.+|-+
T Consensus         6 ys~e~k~~~v~~~~~~~g~s~~~ia~~~gIs~~tl~rW~~   45 (97)
T 2jn6_A            6 YSEEFKRDAVALYENSDGASLQQIANDLGINRVTLKNWII   45 (97)
T ss_dssp             CCHHHHHHHHHHHTTGGGSCHHHHHHHHTSCHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHcCCChHHHHHHHHCcCHHHHHHHHH
Confidence            3445544444444445 89999999999999999999963

>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=94.63  E-value=0.06  Score=38.05  Aligned_cols=40  Identities=8%  Similarity=0.234  Sum_probs=31.2

Q ss_pred             CcchHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           86 DRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        86 ~~~~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      .....++-..+..+.. .|+|..++|+.+|+|++||.+|-+
T Consensus        31 ~~~s~e~r~~iv~~~~-~G~s~~~iA~~lgis~~TV~rw~~   70 (149)
T 1k78_A           31 RPLPDVVRQRIVELAH-QGVRPCDISRQLRVSHGCVSKILG   70 (149)
T ss_dssp             SCCCHHHHHHHHHHHH-TTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3445566666666653 699999999999999999999953

>2elh_A CG11849-PA, LD40883P; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Drosophila melanogaster}

Probab=94.45  E-value=0.065  Score=35.02  Aligned_cols=37  Identities=11%  Similarity=0.079  Sum_probs=27.5

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      ..++-..+..+. ..|.|..++|+.+||++++|.+|.+
T Consensus        24 s~e~k~~~v~~~-~~g~s~~~iA~~~gIs~sTl~rW~k   60 (87)
T 2elh_A           24 TPRDKIHAIQRI-HDGESKASVARDIGVPESTLRGWCK   60 (87)
T ss_dssp             CHHHHHHHHHHH-HHTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CHHHHHHHHHHH-HCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            344443444444 3689999999999999999999964

>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=94.42  E-value=0.2  Score=36.25  Aligned_cols=49  Identities=24%  Similarity=0.248  Sum_probs=40.9

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCC------CHHHHHHHHcCCCCCCHHHHHHH
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINE------KPQVIQEYESGKAIPNQQILTKL  139 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgi------s~s~Is~~E~G~~~p~~~~l~kL  139 (151)
                      .+.|++.++.-|...|+||.+++..+|.      |+++|+++|.-..  +...+.++
T Consensus         6 ~~~fa~~f~~~ri~lg~tQ~~vg~al~~l~g~~~Sqsti~rfe~l~l--s~kn~~kl   60 (151)
T 3d1n_I            6 IREFAKNFKIRRLSLGLTQTQVGQAMTATEGPAYSQSAISRFEKLDI--TPKSAQKL   60 (151)
T ss_dssp             HHHHHHHHHHHHHTTTCCHHHHHHHHSCSSSCCCCHHHHHHHHTTCS--CHHHHHHH
T ss_pred             HHHHHHHHHHHHhhcCCCcccHHHhhccccCCCCCccccccccCCCC--ChhHHHHh
Confidence            3679999999999999999999999997      9999999998653  44444444

>2glo_A Brinker CG9653-PA; protein-DNA complex, helix-turn-helix motif, transcription/DNA complex; NMR {Drosophila melanogaster}

Probab=94.16  E-value=0.09  Score=31.72  Aligned_cols=37  Identities=16%  Similarity=0.186  Sum_probs=28.2

Q ss_pred             hHHHHHHHHHHHhcCCcC----HHHHHHHhCCCHHHHHHHHc
Q 031871           89 PSELKKAIVQARNDKKLT----QSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glT----Q~eLA~~lgis~s~Is~~E~  126 (151)
                      ..+|-..+... ...|.|    ..++|+.+||++++|.+|.+
T Consensus         7 s~efK~~~~~~-~~~g~s~~~~~~~vA~~~gIs~~tl~~W~~   47 (59)
T 2glo_A            7 TPHFKLQVLES-YRNDNDCKGNQRATARKYNIHRRQIQKWLQ   47 (59)
T ss_dssp             CHHHHHHHHHH-HHHCTTTTTCHHHHHHHTTSCHHHHHHHHT
T ss_pred             CHHHHHHHHHH-HHcCCCcchHHHHHHHHHCcCHHHHHHHHH
Confidence            45555555333 345788    99999999999999999975

>2o20_A Catabolite control protein A; CCPA, transcriptional regulator, helix-turn-helix, transcrip; 1.90A {Lactococcus lactis}

Probab=94.14  E-value=0.0087  Score=47.34  Aligned_cols=45  Identities=11%  Similarity=0.071  Sum_probs=0.0

Q ss_pred             CCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH---HHHHHhCCCC
Q 031871          103 KKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILT---KLERALGVKL  147 (151)
Q Consensus       103 ~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~---kLa~~Lgv~l  147 (151)
                      +..|.+|+|+++|||.+|||+..||...++.++..   +.++.||-.+
T Consensus         4 ~~~ti~diA~~agVS~~TVSrvln~~~~vs~~tr~rV~~~a~~lgY~p   51 (332)
T 2o20_A            4 STTTIYDVARVAGVSMATVSRVVNGNANVKEKTRQKVLEAIAELDYRP   51 (332)
T ss_dssp             ------------------------------------------------
T ss_pred             CCCcHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHCCCc
Confidence            35799999999999999999999998666655544   4556666543

>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=94.00  E-value=0.038  Score=34.51  Aligned_cols=24  Identities=21%  Similarity=0.399  Sum_probs=21.8

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcCC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESGK  128 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G~  128 (151)
                      ||..|+|+.+|||++||.+|....
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            789999999999999999998743

>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=94.00  E-value=0.16  Score=34.70  Aligned_cols=59  Identities=20%  Similarity=0.232  Sum_probs=47.6

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHh-CCCHHHHHHHHcCCCCCCH------HHHHHHHHHhCCCC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLI-NEKPQVIQEYESGKAIPNQ------QILTKLERALGVKL  147 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~l-gis~s~Is~~E~G~~~p~~------~~l~kLa~~Lgv~l  147 (151)
                      ...+...|+...+.++++|.-||+.+ +-|+.+++.+.+-+..|.+      +.|.+|-..|..+.
T Consensus        19 Tk~i~~~I~~ELK~~~IsQa~FAk~vlnRsQGtLSelLR~~enPkP~~~~lW~~Lk~m~nWL~Lpe   84 (101)
T 2csf_A           19 TAAIYDEIQQEMKRAKVSQALFAKVAANKSQGWLCELLRWKENPSPENRTLWENLCTIRRFLNLPQ   84 (101)
T ss_dssp             CTHHHHHHHHHHHHHTCCHHHHHHHHTCCCHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHTSCH
T ss_pred             HHHHHHHHHHHHHHcCCcHHHHHHHHHHhchhHHHHHHhcccCCCcchhhHHHHHHHHHHHHcCCH
Confidence            46788999999999999999999975 9999999999985555544      56667777776654

>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=93.84  E-value=0.1  Score=35.87  Aligned_cols=56  Identities=9%  Similarity=0.099  Sum_probs=44.0

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHH-hCCCHHHHHHHHcCCCCC---C---HHHHHHHHHHhC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQL-INEKPQVIQEYESGKAIP---N---QQILTKLERALG  144 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~-lgis~s~Is~~E~G~~~p---~---~~~l~kLa~~Lg  144 (151)
                      ...+...|+++....++||+-||+. +|.++.+++.+.+--..-   +   .+...++-.-|.
T Consensus        19 Tk~I~~~ike~L~~~~isQ~~FA~~VLgrsQgtlS~lL~~PkpW~~L~~~Gre~yiRM~nWL~   81 (101)
T 1x2l_A           19 TAEIAFQVKEQLLKHNIGQRVFGHYVLGLSQGSVSEILARPKPWRKLTVKGKEPFIKMKQFLS   81 (101)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHTTCSCHHHHHHHHHCCCCGGGCCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHHccccchHHHHhcCCCCHHHHhHhhhHHHHHHHHHcc
Confidence            3678999999999999999999998 899999999998864321   2   345555555554

>2jml_A DNA binding domain/transcriptional regulator; anti-repressor, MERR, carotenogenesis; HET: DNA; NMR {Myxococcus xanthus}

Probab=93.75  E-value=0.092  Score=33.83  Aligned_cols=65  Identities=20%  Similarity=0.210  Sum_probs=39.5

Q ss_pred             HHHHHHHcCCChhhHHhhhc--CCCccCCCCcccccccccccchhhhHHHHHhhccCCcchHHHHHHHHHHHhcCCcCHH
Q 031871           31 VVNAARRAGADIETVRKSHA--GTNKAASSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQS  108 (151)
Q Consensus        31 ~~~~a~r~g~~v~t~~k~~~--g~~~~~~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~~~~~~~~~Lk~~R~~~glTQ~  108 (151)
                      .-+.|+..|+++.|++.|+.  |-..|..+.. ..-+..+.  +                ....-..|+.+|...|++.+
T Consensus         8 i~e~A~~~gvs~~tlR~ye~~~gl~~p~r~~~-~g~R~Y~~--~----------------dl~~l~~I~~l~~~~G~sl~   68 (81)
T 2jml_A            8 IRTIARMTGIREATLRAWERRYGFPRPLRSEG-NNYRVYSR--E----------------EVEAVRRVARLIQEEGLSVS   68 (81)
T ss_dssp             HHHHHHTTSTTHHHHHHHHHHTCCSCCBSSSC-SSSCEECH--H----------------HHHHHHHHHHHHHHTSTHHH
T ss_pred             HHHHHHHHCcCHHHHHHHHHhCCCCCCcCCCC-CCeeecCH--H----------------HHHHHHHHHHHHHHCCCCHH
Confidence            34689999999999999987  3333322110 00011111  1                12234557777777899999


Q ss_pred             HHHHHh
Q 031871          109 QLAQLI  114 (151)
Q Consensus       109 eLA~~l  114 (151)
                      ++.+.+
T Consensus        69 ei~~~l   74 (81)
T 2jml_A           69 EAIAQV   74 (81)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            988765

>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=93.66  E-value=0.21  Score=36.30  Aligned_cols=51  Identities=18%  Similarity=0.193  Sum_probs=40.7

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhC------CCHHHHHHHHcCCCCCCHHHHHHHHH
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLIN------EKPQVIQEYESGKAIPNQQILTKLER  141 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lg------is~s~Is~~E~G~~~p~~~~l~kLa~  141 (151)
                      .+.|+..++.-|...|+||.++...+|      .|+++|.++|.-.  .+...+.+|--
T Consensus        12 l~~fa~~fk~~ri~lg~tq~~vg~al~~l~G~~~Sqtti~rfE~l~--ls~~nm~kLkP   68 (155)
T 3l1p_A           12 LEQFAKLLKQKRITLGYTQADVGLTLGVLFGKVFSQTTISRFEALQ--LSLKNMSKLRP   68 (155)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHHHHHSCCCCHHHHHHHHTTC--SCHHHHHHHHH
T ss_pred             HHHHHHHHHhhhheecccHHHHHHHHHhhcCccccccccccccccc--CChhhHhhcch
Confidence            467999999999999999999888754      7999999999854  45555555433

>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=93.49  E-value=0.087  Score=37.73  Aligned_cols=38  Identities=8%  Similarity=0.240  Sum_probs=29.6

Q ss_pred             chHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           88 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        88 ~~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      ....+...|..+. ..|+|..++|+.+|+|++||.+|-+
T Consensus        26 ~s~e~r~~ii~l~-~~G~s~~~IA~~lgis~~TV~rwl~   63 (159)
T 2k27_A           26 LPEVVRQRIVDLA-HQGVRPCDISRQLRVSHGCVSKILG   63 (159)
T ss_dssp             SCHHHHHHHHHHH-HHTCCHHHHHHHHTCCSHHHHHHHC
T ss_pred             CCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3445555555555 3689999999999999999999965

>3h5o_A Transcriptional regulator GNTR; transcription regulator, GNTR,chromobacterium violaceum, PSI, SGX, DNA-binding; 2.30A {Chromobacterium violaceum}

Probab=93.41  E-value=0.014  Score=46.24  Aligned_cols=45  Identities=11%  Similarity=0.017  Sum_probs=0.0

Q ss_pred             CCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHH---HHHHHHhCCCC
Q 031871          103 KKLTQSQLAQLINEKPQVIQEYESGKAIPNQQIL---TKLERALGVKL  147 (151)
Q Consensus       103 ~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l---~kLa~~Lgv~l  147 (151)
                      +..|.+|+|+.+|||.+|||+..||...++.++.   .+.++.||-.+
T Consensus         3 ~~~ti~diA~~agVS~~TVSr~Ln~~~~vs~~tr~rV~~~~~~lgY~p   50 (339)
T 3h5o_A            3 LGVTMHDVAKAAGVSAITVSRVLNQPQQVSEQLREKVMQAVDALAYVP   50 (339)
T ss_dssp             ------------------------------------------------
T ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHhCCCc
Confidence            3578999999999999999999999866655544   44555566543

>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=93.33  E-value=0.37  Score=33.00  Aligned_cols=62  Identities=10%  Similarity=0.103  Sum_probs=49.8

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHH-hCCCHHHHHHHHcCCCC---CC---HHHHHHHHHHhCCCCCCC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQL-INEKPQVIQEYESGKAI---PN---QQILTKLERALGVKLRGK  150 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~-lgis~s~Is~~E~G~~~---p~---~~~l~kLa~~Lgv~l~e~  150 (151)
                      ...+..+|+++....+++|+.||+. +|.++.+++.+.+--..   .+   .+...++-..|..+.+++
T Consensus        19 Tk~I~~~ike~L~~~~isQ~~FA~~ILgrsqgtlSdlL~~PKpW~~L~~~Gre~fiRM~nWL~l~e~qr   87 (101)
T 1wh6_A           19 TLELTRQVKEKLAKNGICQRIFGEKVLGLSQGSVSDMLSRPKPWSKLTQKGREPFIRMQLWLSDQLGQA   87 (101)
T ss_dssp             HHHHHHHHHHHHHTTTCCHHHHHHHTTCCCHHHHHHHHHSCCCTTTCCHHHHHHHHHHHHHHHHTTCSC
T ss_pred             HHHHHHHHHHHHHHcCCcHHHHHHHHHccCcCcHHHHhcCCCCHHHHhHHhHHHHHHHHHHhCCcHHHH
Confidence            4789999999999999999999995 79999999999885432   23   566778877777666543

>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=93.27  E-value=0.16  Score=35.01  Aligned_cols=37  Identities=8%  Similarity=0.147  Sum_probs=29.0

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      .......|..+. ..|+|..++|+.+|+|++||.+|-+
T Consensus         8 s~~~r~~i~~~~-~~G~s~~~ia~~lgis~~Tv~r~~~   44 (141)
T 1u78_A            8 SDTERAQLDVMK-LLNVSLHEMSRKISRSRHCIRVYLK   44 (141)
T ss_dssp             CHHHHHHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            344455555555 4799999999999999999999863

>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=93.27  E-value=0.13  Score=44.23  Aligned_cols=51  Identities=6%  Similarity=0.040  Sum_probs=34.5

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHh------CCCHHHHHHHHcCCCCC---CHHHHHHHHHHhCC
Q 031871           93 KKAIVQARNDKKLTQSQLAQLI------NEKPQVIQEYESGKAIP---NQQILTKLERALGV  145 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~l------gis~s~Is~~E~G~~~p---~~~~l~kLa~~Lgv  145 (151)
                      ...|++++..  +||++||+.|      +.+..+|.+||+|+..|   +...+..|-..+-.
T Consensus        20 ~~~~~~~~~~--~~~~~~a~~l~~~~~~~~~~~~~~rw~~~~~~~~~~~~~~~~~l~~~~~~   79 (482)
T 3me5_A           20 QAMLEKLLQI--YDVKMLVAQLNGVGENHWSAAILKRALANDSAWHRLSEKEFAHLQTLLPK   79 (482)
T ss_dssp             HHHHHHHHTT--SCHHHHHHHHHHTCSSCCCHHHHHHHHC-------CCTHHHHHHHTTSCC
T ss_pred             HHHHHHHHHH--cCHHHHHHHHHhhccCCCCHHHHHHHHcCCCCCccccHHHHHHHHhhCCC
Confidence            3556666654  7999999999      89999999999998765   44555666555544

>3frw_A Putative Trp repressor protein; structural genomics, APC21159, PSI-2, P structure initiative; 2.05A {Ruminococcus obeum atcc 29174} PDB: 3g1c_A

Probab=93.15  E-value=0.16  Score=35.21  Aligned_cols=37  Identities=14%  Similarity=0.105  Sum_probs=29.8

Q ss_pred             HHHHHHHHHHH-hcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           90 SELKKAIVQAR-NDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        90 ~~~~~~Lk~~R-~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      ..++.|++-++ ...|+|+.++|+.+|+|.+||+++-+
T Consensus        43 ~alaqR~~Ia~lL~~G~SyreIa~~tG~StaTIsRv~r   80 (107)
T 3frw_A           43 LSLSQRFEVAKMLTDKRTYLDISEKTGASTATISRVNR   80 (107)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHCccHHHHHHHHH
Confidence            56676666554 44789999999999999999998754

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

Probab=92.78  E-value=0.14  Score=36.09  Aligned_cols=38  Identities=13%  Similarity=0.147  Sum_probs=29.7

Q ss_pred             HHHHHHHHHHH-hcCCcCHHHHHHHhCCCHHHHHHHHcC
Q 031871           90 SELKKAIVQAR-NDKKLTQSQLAQLINEKPQVIQEYESG  127 (151)
Q Consensus        90 ~~~~~~Lk~~R-~~~glTQ~eLA~~lgis~s~Is~~E~G  127 (151)
                      ..+..|++-++ ...|+|+.|+|+.+|+|..||+++-+-
T Consensus        60 ~aLs~R~eV~klL~~G~syreIA~~~g~S~aTIsRv~r~   98 (119)
T 3kor_A           60 QSLSQRLQVAKMIKQGYTYATIEQESGASTATISRVKRS   98 (119)
T ss_dssp             HHHHHHHHHHHHHHHTCCHHHHHHHHCCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            35666665554 346899999999999999999987553

>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=92.76  E-value=0.21  Score=30.72  Aligned_cols=25  Identities=12%  Similarity=0.258  Sum_probs=22.7

Q ss_pred             cCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871          102 DKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus       102 ~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      ..|+|.+|+|+.+|+|.++|..+..
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            4799999999999999999998764

>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=92.67  E-value=0.21  Score=37.37  Aligned_cols=37  Identities=19%  Similarity=0.287  Sum_probs=30.8

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      ..+.+..++.+... |+||.++|+++|+|+++|+++.+
T Consensus        38 piE~A~a~~~L~~~-G~t~eeiA~~lG~s~s~V~~~Lr   74 (178)
T 1r71_A           38 PREIADFIGRELAK-GKKKGDIAKEIGKSPAFITQHVT   74 (178)
T ss_dssp             HHHHHHHHHHHHHT-TCCHHHHHHHHTCCHHHHHHHHG
T ss_pred             HHHHHHHHHHHHHc-CCCHHHHHHHHCcCHHHHHHHHH
Confidence            35566777777664 99999999999999999999865

>3jvd_A Transcriptional regulators; structural genomics, PSI-2, sugar binding protein, transcrip regulation, protein structure initiative; 2.30A {Corynebacterium glutamicum}

Probab=92.61  E-value=0.022  Score=45.27  Aligned_cols=45  Identities=18%  Similarity=0.116  Sum_probs=0.0

Q ss_pred             CCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCC
Q 031871          103 KKLTQSQLAQLINEKPQVIQEYESGKAIPNQQI---LTKLERALGVKL  147 (151)
Q Consensus       103 ~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~---l~kLa~~Lgv~l  147 (151)
                      +..|.+|+|+++|||.+|||+..||...++.++   +.+.++.||..+
T Consensus         5 ~~~ti~diA~~agVS~~TVSr~Ln~~~~vs~~tr~rV~~~a~~lgY~p   52 (333)
T 3jvd_A            5 AKSSLKEVAELAGVGYATASRALSGKGYVSPQTREKVQAAAKELNYVP   52 (333)
T ss_dssp             ------------------------------------------------
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHCCCc
Confidence            347899999999999999999999987666555   444556666543

>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=92.60  E-value=0.13  Score=33.13  Aligned_cols=30  Identities=10%  Similarity=0.019  Sum_probs=24.2

Q ss_pred             HHHHHHhcC---CcCHHHHHHHhCCCHHHHHHH
Q 031871           95 AIVQARNDK---KLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        95 ~Lk~~R~~~---glTQ~eLA~~lgis~s~Is~~  124 (151)
                      .|..++..-   ++|..|||+.+|+++++|++.
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            344455555   799999999999999999876

>2o8x_A Probable RNA polymerase sigma-C factor; promoter recognition, transcription regulation, helix-turn-H motif, transcription; 3.00A {Mycobacterium tuberculosis}

Probab=92.55  E-value=0.22  Score=30.23  Aligned_cols=32  Identities=9%  Similarity=-0.038  Sum_probs=26.1

Q ss_pred             HHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           95 AIVQARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        95 ~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      .+-.++-..|+|+.++|+.+|+|.++|..+-.
T Consensus        22 ~il~l~~~~g~s~~eIA~~lgis~~tv~~~~~   53 (70)
T 2o8x_A           22 EALLLTQLLGLSYADAAAVCGCPVGTIRSRVA   53 (70)
T ss_dssp             HHHHHHHTSCCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            34445557899999999999999999998654

>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=92.53  E-value=0.019  Score=36.23  Aligned_cols=27  Identities=11%  Similarity=0.188  Sum_probs=23.4

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCccC
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNKAA   56 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~~~   56 (151)
                      ++.+.|.+.|++..|+.+||+|...|.
T Consensus        26 tq~elA~~~gvs~~tis~~E~G~~~p~   52 (73)
T 3fmy_A           26 TQKEASEIFGGGVNAFSRYEKGNAXPH   52 (73)
T ss_dssp             CHHHHHHHHCSCTTHHHHHHTTSSCCC
T ss_pred             CHHHHHHHhCcCHHHHHHHHcCCCCCC
Confidence            456789999999999999999987653

>3bil_A Probable LACI-family transcriptional regulator; structural genomics, unknown function, PSI-2, protein structure initiative; 2.50A {Corynebacterium glutamicum atcc 13032}

Probab=92.52  E-value=0.023  Score=45.44  Aligned_cols=43  Identities=12%  Similarity=0.050  Sum_probs=0.0

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHH---HHHHHHhCCCC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESGKAIPNQQIL---TKLERALGVKL  147 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l---~kLa~~Lgv~l  147 (151)
                      .|.+|+|+++|||.+|||+..||...++.++.   .+.++.||-.+
T Consensus         9 ~ti~dvA~~aGVS~~TVSrvLn~~~~Vs~~tr~rV~~aa~~lgY~p   54 (348)
T 3bil_A            9 PTLKDVARQAGVSIATASRALADNPAVAASTRERIQQLASDLGYRA   54 (348)
T ss_dssp             ----------------------------------------------
T ss_pred             CCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCCc
Confidence            58999999999999999999999766665554   44455666543

>3e3m_A Transcriptional regulator, LACI family; structural genomics, DNA-binding, plasmid, transcription regulation, PSI-2; 1.60A {Silicibacter pomeroyi}

Probab=92.49  E-value=0.023  Score=45.37  Aligned_cols=45  Identities=7%  Similarity=0.061  Sum_probs=0.0

Q ss_pred             CCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCC
Q 031871          103 KKLTQSQLAQLINEKPQVIQEYESGKAIPNQQI---LTKLERALGVKL  147 (151)
Q Consensus       103 ~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~---l~kLa~~Lgv~l  147 (151)
                      +-.|.+|+|+++|||.+|||+..||...++.++   +.+.++.||..+
T Consensus        11 ~~~ti~diA~~agVS~~TVSr~Ln~~~~vs~~tr~rV~~~a~~lgY~p   58 (355)
T 3e3m_A           11 RPVTMRDVAKAAGVSRMTVSRALKKDSPISSETRERILKVVKDMNYVP   58 (355)
T ss_dssp             ------------------------------------------------
T ss_pred             CCCcHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCCc
Confidence            457899999999999999999999986666555   444555566543

>2w48_A Sorbitol operon regulator; SORC, activator, repressor, DNA-binding, transcription, transcription regulator, transcription regulation; 3.20A {Klebsiella pneumoniae}

Probab=92.33  E-value=0.21  Score=39.90  Aligned_cols=36  Identities=22%  Similarity=0.192  Sum_probs=31.6

Q ss_pred             HHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871           90 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus        90 ~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E  125 (151)
                      ..+..++..+....++||.|||+.+|+|+.||++..
T Consensus         7 ~~~~~~ia~l~~~~~~~~~ela~~l~vS~~tIrRdL   42 (315)
T 2w48_A            7 IRLIVKIAQLYYEQDMTQAQIARELGIYRTTISRLL   42 (315)
T ss_dssp             HHHHHHHHHHHHTSCCCHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHH
Confidence            456677888888999999999999999999999873

>3omt_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; 1.65A {Cytophaga hutchinsonii}

Probab=92.28  E-value=0.026  Score=35.08  Aligned_cols=28  Identities=11%  Similarity=-0.020  Sum_probs=23.7

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCccCC
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNKAAS   57 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~~~~   57 (151)
                      ++.+.|++.|++.+|+.+|+.|...|..
T Consensus        23 sq~~lA~~~gis~~~is~~e~g~~~~~~   50 (73)
T 3omt_A           23 TNLWLTETLDKNKTTVSKWCTNDVQPSL   50 (73)
T ss_dssp             CHHHHHHHTTCCHHHHHHHHTTSSCCCH
T ss_pred             CHHHHHHHHCcCHHHHHHHHcCCCCCCH
Confidence            4567999999999999999999876533

>3hug_A RNA polymerase sigma factor; ECF sigma factor, zinc binding anti-sigma factor, oxidative transcription regulation; 2.35A {Mycobacterium tuberculosis}

Probab=92.06  E-value=0.25  Score=32.20  Aligned_cols=33  Identities=12%  Similarity=0.154  Sum_probs=27.3

Q ss_pred             HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      ..+-.++-..|+|.+|+|+.+|+|.++|..+..
T Consensus        43 r~vl~l~~~~g~s~~eIA~~lgis~~tV~~~l~   75 (92)
T 3hug_A           43 RAVIQRSYYRGWSTAQIATDLGIAEGTVKSRLH   75 (92)
T ss_dssp             HHHHHHHHTSCCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            334456678899999999999999999998764

>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=91.87  E-value=0.028  Score=33.68  Aligned_cols=26  Identities=8%  Similarity=-0.023  Sum_probs=22.6

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCcc
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNKA   55 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~~   55 (151)
                      +..+.|++.|++.+|+.+|+.|...|
T Consensus        16 s~~~lA~~~gis~~~i~~~e~g~~~~   41 (66)
T 2xi8_A           16 SQSELAALLEVSRQTINGIEKNKYNP   41 (66)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHTTSCCC
T ss_pred             CHHHHHHHHCcCHHHHHHHHcCCCCC
Confidence            45679999999999999999998764

>1y7y_A C.AHDI; helix-turn-helix, DNA-binding protein, transcriptional regulator, transcription regulator; 1.69A {Aeromonas hydrophila} SCOP: a.35.1.3

Probab=91.86  E-value=0.034  Score=34.18  Aligned_cols=26  Identities=19%  Similarity=0.105  Sum_probs=22.7

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCcc
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNKA   55 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~~   55 (151)
                      +..+.|++.|++.+++.+|+.|...|
T Consensus        28 s~~~lA~~~gis~~~i~~~e~g~~~~   53 (74)
T 1y7y_A           28 SQETLAFLSGLDRSYVGGVERGQRNV   53 (74)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHTTCSCC
T ss_pred             CHHHHHHHHCcCHHHHHHHHCCCCCC
Confidence            45678999999999999999998654

>3kz3_A Repressor protein CI; five helix bundle, DNA-binding, transcription, transcription regulation; 1.64A {Enterobacteria phage lambda}

Probab=91.85  E-value=0.028  Score=35.70  Aligned_cols=28  Identities=18%  Similarity=0.192  Sum_probs=23.7

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCccCC
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNKAAS   57 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~~~~   57 (151)
                      ++.+.|.+.|++.+++.+|++|...|..
T Consensus        27 tq~~lA~~~gvs~~~is~~e~g~~~~~~   54 (80)
T 3kz3_A           27 SYESVADKMGMGQSAVAALFNGINALNA   54 (80)
T ss_dssp             CHHHHHHHTTSCHHHHHHHHTTSSCCCH
T ss_pred             CHHHHHHHhCcCHHHHHHHHcCCCCCCH
Confidence            4567999999999999999999876533

>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=91.78  E-value=0.17  Score=33.76  Aligned_cols=30  Identities=10%  Similarity=-0.037  Sum_probs=24.9

Q ss_pred             HHHHHh--cCCcCHHHHHHHhCCCHHHHHHHH
Q 031871           96 IVQARN--DKKLTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus        96 Lk~~R~--~~glTQ~eLA~~lgis~s~Is~~E  125 (151)
                      ++.+..  ..|++|+|||+.+++++++|+++.
T Consensus        26 l~~I~~~g~~gi~qkeLa~~~~l~~~tvt~iL   57 (91)
T 2dk5_A           26 YQIIEDAGNKGIWSRDVRYKSNLPLTEINKIL   57 (91)
T ss_dssp             HHHHHHHCTTCEEHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHcCCCCcCHHHHHHHHCCCHHHHHHHH
Confidence            555555  569999999999999999998763

>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=91.69  E-value=0.32  Score=30.21  Aligned_cols=24  Identities=13%  Similarity=0.228  Sum_probs=22.3

Q ss_pred             CCcCHHHHHHHhCCCHHHHHHHHc
Q 031871          103 KKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus       103 ~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      .|+|..|+|+.+|+|.++|..+..
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            799999999999999999998765

>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=91.59  E-value=0.075  Score=32.07  Aligned_cols=27  Identities=15%  Similarity=0.340  Sum_probs=23.1

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCccC
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNKAA   56 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~~~   56 (151)
                      +..+.|++.|++.+++.+|+.|...|.
T Consensus        16 sq~~lA~~~gis~~~i~~~e~g~~~~~   42 (69)
T 1r69_A           16 NQAELAQKVGTTQQSIEQLENGKTKRP   42 (69)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHTTSCSSC
T ss_pred             CHHHHHHHHCcCHHHHHHHHcCCCCCc
Confidence            456789999999999999999987653

>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=91.59  E-value=0.031  Score=33.69  Aligned_cols=26  Identities=4%  Similarity=0.101  Sum_probs=22.6

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCcc
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNKA   55 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~~   55 (151)
                      +..+.|++.|++.+++.+|+.|...|
T Consensus        20 s~~~lA~~~gis~~~i~~~e~g~~~~   45 (68)
T 2r1j_L           20 RQAALGKMVGVSNVAISQWERSETEP   45 (68)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHTTSSCC
T ss_pred             CHHHHHHHHCCCHHHHHHHHcCCCCC
Confidence            45678999999999999999997764

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

Probab=91.59  E-value=0.31  Score=30.97  Aligned_cols=29  Identities=7%  Similarity=-0.009  Sum_probs=23.4

Q ss_pred             HHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871           97 VQARNDKKLTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus        97 k~~R~~~glTQ~eLA~~lgis~s~Is~~E  125 (151)
                      ..+.....+|..|||+.+|+|+++++++.
T Consensus         7 ~~L~~~~~~s~~eLa~~lgvs~~tv~r~L   35 (81)
T 2htj_A            7 EFLNRHNGGKTAEIAEALAVTDYQARYYL   35 (81)
T ss_dssp             HHHHHSCCCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHcCCCCHHHHHHHHCcCHHHHHHHH
Confidence            33444567999999999999999998863

>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=91.56  E-value=0.032  Score=35.38  Aligned_cols=41  Identities=12%  Similarity=0.089  Sum_probs=28.6

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCccCCCCccccccccccc
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDED   70 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~~~~~~~~~~~~kl~~~   70 (151)
                      ++-+.|.+.|++.+|+.+||.|...|......+.+..++.+
T Consensus        26 sq~~lA~~~gis~~~i~~~e~g~~~~~~~~l~~ia~~l~v~   66 (82)
T 3s8q_A           26 TQEDLAYKSNLDRTYISGIERNSRNLTIKSLELIMKGLEVS   66 (82)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHTTCCCCBHHHHHHHHHHTTCC
T ss_pred             CHHHHHHHhCcCHHHHHHHHCCCCCCCHHHHHHHHHHHCcC
Confidence            55678999999999999999998765433333333344433

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

Probab=91.52  E-value=0.27  Score=32.41  Aligned_cols=34  Identities=15%  Similarity=0.175  Sum_probs=26.0

Q ss_pred             HHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           91 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        91 ~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ....+|-.+....|+|-.+||+.+|+|+++|.+.
T Consensus        17 ~~~~~IL~lL~~~g~sa~eLAk~LgiSk~aVr~~   50 (82)
T 1oyi_A           17 EIVCEAIKTIGIEGATAAQLTRQLNMEKREVNKA   50 (82)
T ss_dssp             HHHHHHHHHHSSSTEEHHHHHHHSSSCHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHH
Confidence            3444444444478899999999999999988775

>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=91.51  E-value=0.26  Score=38.09  Aligned_cols=49  Identities=16%  Similarity=0.125  Sum_probs=35.6

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHH
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKL  139 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kL  139 (151)
                      ..+.+..++++. +.|+|+.++|+.+|+|+++|+++.+=- ..+.+....+
T Consensus       120 ~~E~a~~~~~l~-~~g~t~~~iA~~lG~s~~~V~~~l~l~-~l~~~v~~~l  168 (230)
T 1vz0_A          120 PVEEARGYQALL-EMGLTQEEVARRVGKARSTVANALRLL-QLPPEALEAL  168 (230)
T ss_dssp             HHHHHHHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHHGG-GSCHHHHHHH
T ss_pred             HHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHH-cCCHHHHHHH
Confidence            345566677777 789999999999999999999986532 2334444333

>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=91.44  E-value=0.27  Score=33.75  Aligned_cols=42  Identities=19%  Similarity=0.287  Sum_probs=29.6

Q ss_pred             cchHHHHHHHHHHH-hcCCcCHHHHHHHhCCCHHHHHHHHcCC
Q 031871           87 RVPSELKKAIVQAR-NDKKLTQSQLAQLINEKPQVIQEYESGK  128 (151)
Q Consensus        87 ~~~~~~~~~Lk~~R-~~~glTQ~eLA~~lgis~s~Is~~E~G~  128 (151)
                      .+..++-..+..+- ..-..++.++|+.+||++++|++|-++.
T Consensus         7 ~~t~e~K~~iv~~~~~~g~~~~~~~A~~~gvs~stl~~~~~~~   49 (131)
T 1hlv_A            7 QLTFREKSRIIQEVEENPDLRKGEIARRFNIPPSTLSTILKNK   49 (131)
T ss_dssp             CCCHHHHHHHHHHHHHCTTSCHHHHHHHHTCCHHHHHHHHHTH
T ss_pred             eCCHHHHHHHHHHHHHCCCCcHHHHHHHhCCCHHHHHHHHhch
Confidence            34455555554443 4444556699999999999999998764

>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=91.22  E-value=0.31  Score=31.81  Aligned_cols=29  Identities=10%  Similarity=0.029  Sum_probs=23.0

Q ss_pred             HHHHHhcC---CcCHHHHHHHhCCCHHHHHHH
Q 031871           96 IVQARNDK---KLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        96 Lk~~R~~~---glTQ~eLA~~lgis~s~Is~~  124 (151)
                      |..++...   .+|..+||+.+|+++++|.+.
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            34445555   699999999999999988875

>2ewt_A BLDD, putative DNA-binding protein; the DNA-binding domain of BLDD; 1.81A {Streptomyces coelicolor}

Probab=91.08  E-value=0.036  Score=33.92  Aligned_cols=26  Identities=8%  Similarity=0.064  Sum_probs=22.5

Q ss_pred             HHHHHHHHcC--CChhhHHhhhcCCCcc
Q 031871           30 KVVNAARRAG--ADIETVRKSHAGTNKA   55 (151)
Q Consensus        30 ~~~~~a~r~g--~~v~t~~k~~~g~~~~   55 (151)
                      ++.+.|.+.|  ++.+++.+||.|...|
T Consensus        23 sq~~lA~~~g~~is~~~i~~~e~g~~~~   50 (71)
T 2ewt_A           23 SLHGVEEKSQGRWKAVVVGSYERGDRAV   50 (71)
T ss_dssp             CHHHHHHHTTTSSCHHHHHHHHHTCSCC
T ss_pred             CHHHHHHHHCCcCCHHHHHHHHCCCCCC
Confidence            4567899999  9999999999998764

>2ox6_A Hypothetical protein SO3848; structural genomics, PSI-2, MCSG, Pro structure initiative; 1.70A {Shewanella oneidensis} SCOP: a.35.1.6

Probab=91.02  E-value=1  Score=32.35  Aligned_cols=45  Identities=18%  Similarity=0.228  Sum_probs=37.9

Q ss_pred             HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHH
Q 031871           94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTK  138 (151)
Q Consensus        94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~k  138 (151)
                      -.|+-+|...|+|..++|+..+.|..-+-.||.|+...+.-.-.+
T Consensus        10 ie~~ylr~slgl~~aqv~~l~k~se~dv~aweage~~~~~laqkk   54 (166)
T 2ox6_A           10 IEMSYLRQSLSLSAAQVGQLTNHSEAEVLAWENAETQAPELAQKK   54 (166)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTSSCCCHHHHHH
T ss_pred             HhHHHHHHHcCCCHHHHHHHhccCHHHhhhhhhcCCcCcchHHhh
Confidence            347889999999999999999999999999999997665443333

>1adr_A P22 C2 repressor; transcription regulation; NMR {Enterobacteria phage P22} SCOP: a.35.1.2

Probab=90.99  E-value=0.04  Score=34.03  Aligned_cols=26  Identities=4%  Similarity=0.101  Sum_probs=22.6

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCcc
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNKA   55 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~~   55 (151)
                      +..+.|++.|++.+++.+|+.|...|
T Consensus        20 s~~~lA~~~gis~~~i~~~e~g~~~~   45 (76)
T 1adr_A           20 RQAALGKMVGVSNVAISQWERSETEP   45 (76)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHTTSSCC
T ss_pred             CHHHHHHHHCcCHHHHHHHHcCCCCC
Confidence            45678999999999999999997765

>2jml_A DNA binding domain/transcriptional regulator; anti-repressor, MERR, carotenogenesis; HET: DNA; NMR {Myxococcus xanthus}

Probab=90.95  E-value=0.15  Score=32.77  Aligned_cols=24  Identities=13%  Similarity=0.290  Sum_probs=22.0

Q ss_pred             CCcCHHHHHHHhCCCHHHHHHHHc
Q 031871          103 KKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus       103 ~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      .-+|..|+|+.+|||+.||..||+
T Consensus         4 m~~~i~e~A~~~gvs~~tlR~ye~   27 (81)
T 2jml_A            4 MTLRIRTIARMTGIREATLRAWER   27 (81)
T ss_dssp             CCEEHHHHHHTTSTTHHHHHHHHH
T ss_pred             CcccHHHHHHHHCcCHHHHHHHHH
Confidence            347899999999999999999997

>2b5a_A C.BCLI; helix-turn-helix motif, gene regulation; 1.54A {Bacillus caldolyticus} SCOP: a.35.1.3

Probab=90.95  E-value=0.04  Score=34.18  Aligned_cols=26  Identities=15%  Similarity=0.129  Sum_probs=22.7

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCcc
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNKA   55 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~~   55 (151)
                      +....|++.|++.+++.+|+.|...|
T Consensus        25 sq~~lA~~~gis~~~i~~~e~g~~~~   50 (77)
T 2b5a_A           25 SQEELADLAGLHRTYISEVERGDRNI   50 (77)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHTTCSCC
T ss_pred             CHHHHHHHHCCCHHHHHHHHCCCCCC
Confidence            45678999999999999999998764

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

Probab=90.85  E-value=0.26  Score=31.99  Aligned_cols=33  Identities=15%  Similarity=0.167  Sum_probs=27.3

Q ss_pred             HHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           92 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        92 ~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      +...+..++....++..|||+.+++|..||.+-
T Consensus         4 L~~Il~~L~~~g~vsv~eLa~~l~VS~~TIRrd   36 (78)
T 1xn7_A            4 LIQVRDLLALRGRMEAAQISQTLNTPQPMINAM   36 (78)
T ss_dssp             HHHHHHHHHHSCSBCHHHHHHHTTCCHHHHHHH
T ss_pred             HHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHH
Confidence            445566677788899999999999999998764

>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=90.84  E-value=0.39  Score=32.89  Aligned_cols=59  Identities=12%  Similarity=0.179  Sum_probs=47.1

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHH-hCCCHHHHHHHHcCCCCC------CHHHHHHHHHHhCCCC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQL-INEKPQVIQEYESGKAIP------NQQILTKLERALGVKL  147 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~-lgis~s~Is~~E~G~~~p------~~~~l~kLa~~Lgv~l  147 (151)
                      ...+...|++..+..+++|.-||+. +|.++.+++.+.+-...|      -.+.+.++-..|..+-
T Consensus        19 Tk~I~~~Ik~~Lk~~~isQ~~FA~~VL~rsQgtLs~lLr~P~kPW~~L~~Gre~f~RM~nWL~l~e   84 (101)
T 1wiz_A           19 SPDIYQQVRDELKRASVSQAVFARVAFNRTQGLLSEILRKEEDPRTASQSLLVNLRAMQNFLNLPE   84 (101)
T ss_dssp             CTTHHHHHHHHHHHHTCCHHHHHHHHHSCCHHHHHHHHHTCCCTTTCCHHHHHHHHHHHHHTTSCH
T ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHHHHHhhhHHHHHHcCCCCCHHHHHHHHHHHHHHHHHhcCCH
Confidence            4678889999999999999999996 799999999999866422      2456777777776654

>3bs3_A Putative DNA-binding protein; XRE-family, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.65A {Bacteroides fragilis}

Probab=90.81  E-value=0.043  Score=33.92  Aligned_cols=26  Identities=12%  Similarity=0.097  Sum_probs=22.9

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCcc
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNKA   55 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~~   55 (151)
                      +..+.|++.|++.+|+.+|+.|...|
T Consensus        25 s~~~lA~~~gis~~~i~~~e~g~~~~   50 (76)
T 3bs3_A           25 TNRWLAEQMGKSENTISRWCSNKSQP   50 (76)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHTTSSCC
T ss_pred             CHHHHHHHHCcCHHHHHHHHcCCCCC
Confidence            45679999999999999999998765

>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=90.70  E-value=0.037  Score=35.08  Aligned_cols=26  Identities=19%  Similarity=0.175  Sum_probs=22.7

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCcc
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNKA   55 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~~   55 (151)
                      ++.+.|++.|++.+++.+||.|...|
T Consensus        29 tq~elA~~~gis~~~is~~e~g~~~~   54 (83)
T 3f6w_A           29 TQKELAARLGRPQSFVSKTENAERRL   54 (83)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHTTSSCC
T ss_pred             CHHHHHHHHCcCHHHHHHHHCCCCCC
Confidence            45678999999999999999998754

>1x3u_A Transcriptional regulatory protein FIXJ; helix-turn-helix; NMR {Sinorhizobium meliloti}

Probab=90.57  E-value=0.94  Score=28.06  Aligned_cols=46  Identities=13%  Similarity=0.122  Sum_probs=35.6

Q ss_pred             cCCcCHHHHHHHhCCCHHHHHHHHcC----CCCCCHHHHHHHHHHhCCCC
Q 031871          102 DKKLTQSQLAQLINEKPQVIQEYESG----KAIPNQQILTKLERALGVKL  147 (151)
Q Consensus       102 ~~glTQ~eLA~~lgis~s~Is~~E~G----~~~p~~~~l~kLa~~Lgv~l  147 (151)
                      ..|+|.+|+|+.+|+|..+|..+..-    -...+...+..++..+|+..
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            68999999999999999999876531    24456677777877777653

>1tty_A Sigma-A, RNA polymerase sigma factor RPOD; helix-turn-helix, transcription; NMR {Thermotoga maritima} SCOP: a.4.13.2

Probab=90.56  E-value=0.45  Score=30.73  Aligned_cols=24  Identities=25%  Similarity=0.268  Sum_probs=22.3

Q ss_pred             CCcCHHHHHHHhCCCHHHHHHHHc
Q 031871          103 KKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus       103 ~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      .|+|..++|+.+|+|.++|..+..
T Consensus        37 ~~~s~~EIA~~lgis~~tV~~~~~   60 (87)
T 1tty_A           37 KPKTLEEVGQYFNVTRERIRQIEV   60 (87)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHH
Confidence            799999999999999999998764

>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=90.51  E-value=0.36  Score=33.60  Aligned_cols=57  Identities=11%  Similarity=0.137  Sum_probs=43.9

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHH-HhCCCHHHHHHHHcCCCCC---C---HHHHHHHHHHhCC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQ-LINEKPQVIQEYESGKAIP---N---QQILTKLERALGV  145 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~-~lgis~s~Is~~E~G~~~p---~---~~~l~kLa~~Lgv  145 (151)
                      ...+..+|+++....+++|+-||+ .+|.++.+|+.+.+--...   +   .+...++-..|..
T Consensus        29 Tk~I~~~ikewL~~~~isQ~~FA~~ILgrsQgtlSdlL~~PkpW~~L~~~GRe~yiRM~nWL~l   92 (111)
T 1wh8_A           29 TYSITKRVKEVLTDNNLGQRLFGESILGLTQGSVSDLLSRPKPWHKLSLKGREPFVRMQLWLND   92 (111)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHTTCCCHHHHHHHHHSCCCTTTSCHHHHHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHCCCcHHHHHHHHhccCcCcHHHHHcCCCCHHHHhHhhhHHHHHHHHHhcC
Confidence            478999999999999999999999 5899999999998854322   2   3445555555543

>1fse_A GERE; helix-turn-helix DNA-binding protein transcriptional regulat transcription; 2.05A {Bacillus subtilis} SCOP: a.4.6.2

Probab=90.50  E-value=0.73  Score=28.08  Aligned_cols=43  Identities=9%  Similarity=0.037  Sum_probs=29.5

Q ss_pred             cCCcCHHHHHHHhCCCHHHHHHHHcC----CCCCCHHHHHHHHHHhC
Q 031871          102 DKKLTQSQLAQLINEKPQVIQEYESG----KAIPNQQILTKLERALG  144 (151)
Q Consensus       102 ~~glTQ~eLA~~lgis~s~Is~~E~G----~~~p~~~~l~kLa~~Lg  144 (151)
                      ..|+|..|+|+.+|+|+++|..+-..    -...+...+...+...|
T Consensus        24 ~~g~s~~eIA~~l~is~~tV~~~~~~~~~kl~~~~~~~~~~~~~~~g   70 (74)
T 1fse_A           24 VQDKTTKEIASELFISEKTVRNHISNAMQKLGVKGRSQAVVELLRMG   70 (74)
T ss_dssp             TTTCCHHHHHHHHTSCHHHHHHHHHHHHHHHTCSSHHHHHHHHHHTT
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHhC
Confidence            67999999999999999999886542    12334444444444444

>2jpc_A SSRB; DNA binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium}

Probab=90.38  E-value=0.27  Score=29.18  Aligned_cols=44  Identities=9%  Similarity=0.108  Sum_probs=30.0

Q ss_pred             hcCCcCHHHHHHHhCCCHHHHHHHHcC----CCCCCHHHHHHHHHHhC
Q 031871          101 NDKKLTQSQLAQLINEKPQVIQEYESG----KAIPNQQILTKLERALG  144 (151)
Q Consensus       101 ~~~glTQ~eLA~~lgis~s~Is~~E~G----~~~p~~~~l~kLa~~Lg  144 (151)
                      ...|+|.+|+|+.+|+|.++|..+-..    -...+...+..++...|
T Consensus        10 ~~~g~s~~eIA~~l~is~~tV~~~~~~~~~kl~~~~~~~l~~~~~~~g   57 (61)
T 2jpc_A           10 IDEGYTNHGISEKLHISIKTVETHRMNMMRKLQVHKVTELLNCARRMR   57 (61)
T ss_dssp             HHTSCCSHHHHHHTCSCHHHHHHHHHHHHHHHTCSSHHHHHHHHHCSC
T ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHcC
Confidence            356999999999999999999876442    12334444555554444

>3eus_A DNA-binding protein; structural genomics, PSI2,MCSG, protein structure initiative, midwest center for structural genomic binding; 1.80A {Silicibacter pomeroyi}

Probab=90.28  E-value=0.056  Score=34.92  Aligned_cols=39  Identities=10%  Similarity=-0.017  Sum_probs=27.9

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCccCCCCccccccccc
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLD   68 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~~~~~~~~~~~~kl~   68 (151)
                      ++-+.|.+.|++.+++.+||+|...|....+.+....|+
T Consensus        29 tq~elA~~~gis~~~is~~E~G~~~p~~~~l~~ia~~l~   67 (86)
T 3eus_A           29 TQADLAERLDKPQSFVAKVETRERRLDVIEFAKWMAACE   67 (86)
T ss_dssp             CHHHHHHHTTCCHHHHHHHHTTSSCCBHHHHHHHHHHTT
T ss_pred             CHHHHHHHhCcCHHHHHHHHCCCCCCCHHHHHHHHHHcC
Confidence            556789999999999999999987654333333333333

>2kpj_A SOS-response transcriptional repressor, LEXA; NESG, GFT, structural genomics, PSI-2, protein structure initiative; NMR {Eubacterium rectale atcc 33656}

Probab=90.12  E-value=0.048  Score=35.71  Aligned_cols=26  Identities=15%  Similarity=0.166  Sum_probs=22.9

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCcc
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNKA   55 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~~   55 (151)
                      ++.+.|++.|++.+|+.+|+.|...|
T Consensus        24 sq~~lA~~~gis~~~is~~e~G~~~p   49 (94)
T 2kpj_A           24 TQLEIAKSIGVSPQTFNTWCKGIAIP   49 (94)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHTTSCCC
T ss_pred             CHHHHHHHHCcCHHHHHHHHhCCCCC
Confidence            45678999999999999999998765

>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=90.12  E-value=0.052  Score=34.65  Aligned_cols=26  Identities=35%  Similarity=0.455  Sum_probs=22.6

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCC-cc
Q 031871           30 KVVNAARRAGADIETVRKSHAGTN-KA   55 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~-~~   55 (151)
                      ++-+.|++.|++.+++.+||.|.. .|
T Consensus        29 sq~~lA~~~gis~~~is~~E~g~~~~p   55 (86)
T 2ofy_A           29 SMVTVAFDAGISVETLRKIETGRIATP   55 (86)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHTTCCSSC
T ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCCCC
Confidence            456899999999999999999986 54

>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=90.11  E-value=0.54  Score=30.49  Aligned_cols=31  Identities=13%  Similarity=0.314  Sum_probs=24.7

Q ss_pred             HHHHHHHh-cCCcCHHHHHHHhCCCHHHHHHH
Q 031871           94 KAIVQARN-DKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        94 ~~Lk~~R~-~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ..|..+.. ..++|+.|||+.+|+++++++++
T Consensus        25 ~~l~~l~~~~~~~t~~ela~~l~is~~tv~~~   56 (109)
T 2d1h_A           25 AVLLKMVEIEKPITSEELADIFKLSKTTVENS   56 (109)
T ss_dssp             HHHHHHHHHCSCEEHHHHHHHHTCCHHHHHHH
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHH
Confidence            33444433 77899999999999999999986

>2k9q_A Uncharacterized protein; all helix, helix-turn-helix, plasmid, structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides thetaiotaomicron}

Probab=90.06  E-value=0.043  Score=34.46  Aligned_cols=26  Identities=8%  Similarity=0.093  Sum_probs=22.5

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCcc
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNKA   55 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~~   55 (151)
                      ++.+.|.+.|++.+|+.+|+.|...|
T Consensus        17 sq~~lA~~~gis~~~i~~~e~g~~~p   42 (77)
T 2k9q_A           17 TAKSVAEEMGISRQQLCNIEQSETAP   42 (77)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHTCCSCC
T ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCCC
Confidence            45678999999999999999997654

>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=90.01  E-value=0.6  Score=32.90  Aligned_cols=32  Identities=19%  Similarity=0.146  Sum_probs=26.4

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ...|..+.....+|..+||+.+|+|++++++.
T Consensus        10 ~~iL~~L~~~~~~s~~ela~~lg~s~~tv~~~   41 (150)
T 2w25_A           10 RILVRELAADGRATLSELATRAGLSVSAVQSR   41 (150)
T ss_dssp             HHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHH
Confidence            34566666677899999999999999998875

>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=89.85  E-value=0.13  Score=31.07  Aligned_cols=26  Identities=23%  Similarity=0.351  Sum_probs=22.6

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCcc
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNKA   55 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~~   55 (151)
                      +..+.|++.|++.+++.+|+.|...|
T Consensus        18 sq~~lA~~~gis~~~i~~~e~g~~~~   43 (71)
T 1zug_A           18 TQTELATKAGVKQQSIQLIEAGVTKR   43 (71)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHTTCCSS
T ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCCC
Confidence            45678999999999999999998764

>3e7l_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+ ATPase, response regulator, transcriptional activator, ATP-binding; 2.25A {Aquifex aeolicus} PDB: 4fth_A

Probab=89.84  E-value=0.51  Score=28.83  Aligned_cols=34  Identities=12%  Similarity=-0.036  Sum_probs=28.4

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      ...|..+....+.++.+.|+.+||+++++.+..+
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            4556777778888999999999999999988653

>2rn7_A IS629 ORFA; helix, all alpha, unknown function, structural genomics, PSI-2, protein structure initiative; NMR {Shigella flexneri}

Probab=89.81  E-value=0.25  Score=32.99  Aligned_cols=23  Identities=17%  Similarity=0.209  Sum_probs=20.7

Q ss_pred             CcCHHHHHHHhCCCHHHHHHHHc
Q 031871          104 KLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus       104 glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      |.|..++|..+||++++|.+|-+
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            37999999999999999999954

>2vz4_A Tipal, HTH-type transcriptional activator TIPA; transcription, resistance, antibiotic; 2.90A {Streptomyces lividans}

Probab=89.81  E-value=0.27  Score=33.35  Aligned_cols=24  Identities=13%  Similarity=0.235  Sum_probs=21.7

Q ss_pred             CcCHHHHHHHhCCCHHHHHHHHcC
Q 031871          104 KLTQSQLAQLINEKPQVIQEYESG  127 (151)
Q Consensus       104 glTQ~eLA~~lgis~s~Is~~E~G  127 (151)
                      ++|..|+|+.+|||+.||..||+-
T Consensus         1 ~~~i~e~A~~~gvs~~tLR~ye~~   24 (108)
T 2vz4_A            1 SYSVGQVAGFAGVTVRTLHHYDDI   24 (108)
T ss_dssp             CBCHHHHHHHHTCCHHHHHHHHHH
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHC
Confidence            478999999999999999999863

>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=89.76  E-value=0.05  Score=37.47  Aligned_cols=44  Identities=5%  Similarity=-0.119  Sum_probs=31.7

Q ss_pred             HHHHHHHHHcCCChhhHHhhhcCCCccCCCCcccccccccccch
Q 031871           29 EKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTE   72 (151)
Q Consensus        29 ~~~~~~a~r~g~~v~t~~k~~~g~~~~~~~~~~~~~~kl~~~~~   72 (151)
                      =+.-+.|.+.|++.+++.+||+|...|..+...+.+..++.+.+
T Consensus        26 lsq~~lA~~~gis~~~is~~E~g~~~p~~~~l~~ia~~l~v~~~   69 (126)
T 3ivp_A           26 LTREQVGAMIEIDPRYLTNIENKGQHPSLQVLYDLVSLLNVSVD   69 (126)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHSCCCCCHHHHHHHHHHHTCCSH
T ss_pred             CCHHHHHHHhCcCHHHHHHHHCCCCCCCHHHHHHHHHHHCcCHH
Confidence            35677999999999999999999876654444444455554433

>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=89.69  E-value=0.45  Score=32.12  Aligned_cols=60  Identities=15%  Similarity=0.160  Sum_probs=47.3

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHH-hCCCHHHHHHHHcCCCCC------CHHHHHHHHHHhCCCCC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQL-INEKPQVIQEYESGKAIP------NQQILTKLERALGVKLR  148 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~-lgis~s~Is~~E~G~~~p------~~~~l~kLa~~Lgv~l~  148 (151)
                      ...+...|++.....++||.-||+. +|.++.+++.+.+-...|      -.+.+.++-..|..+-+
T Consensus         9 T~~I~~~ik~~Lk~~~isQ~~FA~~VL~rsQgtLs~lL~~Pkdpw~~l~~Gre~f~rM~nWL~l~e~   75 (93)
T 2o4a_A            9 SSEIYQWVRDELKRAGISQAVFARVAFNRTQGLLSEILRKEEDPKTASQSLLVNLRAMQNFLQLPEA   75 (93)
T ss_dssp             CTTHHHHHHHHHHHHTCCHHHHHHHHHSCCHHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHTSCHH
T ss_pred             HHHHHHHHHHHHHHcCCcHHHHHHHHHHHhhhHHHHHHcCCCCcHHHHHHHHHHHHHHHHHhCCCHH
Confidence            4568889999999999999999996 799999999999865523      14557777777776543

>1z4h_A TORI, TOR inhibition protein; winged helix, reverse turn, protein binding, DNA binding protein; NMR {Escherichia coli}

Probab=89.63  E-value=0.14  Score=31.76  Aligned_cols=29  Identities=7%  Similarity=-0.013  Sum_probs=24.2

Q ss_pred             CcCHHHHHHHhCCCHHHHHHHHcCCCCCC
Q 031871          104 KLTQSQLAQLINEKPQVIQEYESGKAIPN  132 (151)
Q Consensus       104 glTQ~eLA~~lgis~s~Is~~E~G~~~p~  132 (151)
                      =++..|+|+.+|+|++||.+|.+....|.
T Consensus        10 ~l~~~eva~~lgvsrstiy~~~~~g~fP~   38 (66)
T 1z4h_A           10 LVDLKFIMADTGFGKTFIYDRIKSGDLPK   38 (66)
T ss_dssp             EECHHHHHHHHSSCHHHHHHHHHHHHCCC
T ss_pred             ccCHHHHHHHHCcCHHHHHHHHHCCCCCC
Confidence            37899999999999999999987554453

>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=89.60  E-value=0.064  Score=37.71  Aligned_cols=81  Identities=7%  Similarity=0.004  Sum_probs=37.1

Q ss_pred             HHHHHHHHcC-----CChhhHHhhhcCCC-ccCCCCcccccccccccchhhhHHHHHhhccCCcchHHHHHHHHHHHhcC
Q 031871           30 KVVNAARRAG-----ADIETVRKSHAGTN-KAASSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDK  103 (151)
Q Consensus        30 ~~~~~a~r~g-----~~v~t~~k~~~g~~-~~~~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~~~~~~~~~Lk~~R~~~  103 (151)
                      ++.+.|...|     ++.+++..||+|.. .|....+.+.+.-++.+.+.|-.         ......+...|..++..+
T Consensus        26 T~~elA~~~~~~G~~iS~s~is~iE~G~r~~Ps~~~l~~iA~~f~V~~~yl~~---------~~~~~~~~~~l~ll~~lr   96 (123)
T 3qwg_A           26 TSAEVIAALKAEGITMSAPYLSQLRSGNRTNPSGATMAALANFFRIKAAYFTD---------DEYYEKLDKELQWLCTMR   96 (123)
T ss_dssp             CHHHHHHHHHHTTCCCCHHHHHHHHHTSSCCCCHHHHHHHHHHTTSCTHHHHC---------HHHHHHHHHHHHHHHHHC
T ss_pred             CHHHHHHHHcccCCCcCHHHHHHHHcCCCCCCCHHHHHHHHHHhCCCHHHHcC---------CccHhHHHHHHHHHHHHH
Confidence            3455566665     99999999999986 55444444555555555443332         333334444444444444


Q ss_pred             CcCHHHHHHH-hCCCHH
Q 031871          104 KLTQSQLAQL-INEKPQ  119 (151)
Q Consensus       104 glTQ~eLA~~-lgis~s  119 (151)
                      .-....||.+ .|+|+.
T Consensus        97 ~~~v~~la~r~~~Ls~e  113 (123)
T 3qwg_A           97 DDGVRRIAQRAHGLPSA  113 (123)
T ss_dssp             -----------------
T ss_pred             hhhHHHHHHHhcCCCHH
Confidence            3333444443 344443

>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=89.59  E-value=0.058  Score=34.80  Aligned_cols=27  Identities=19%  Similarity=0.155  Sum_probs=23.1

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCccC
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNKAA   56 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~~~   56 (151)
                      ++.+.|.+.|++.+|+.+|+.|...|.
T Consensus        32 sq~~lA~~~gis~~~is~~e~g~~~~~   58 (92)
T 1lmb_3           32 SQESVADKMGMGQSGVGALFNGINALN   58 (92)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHTTSSCCC
T ss_pred             CHHHHHHHHCcCHHHHHHHHcCCCCCC
Confidence            456789999999999999999987653

>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=89.51  E-value=0.76  Score=29.36  Aligned_cols=43  Identities=5%  Similarity=-0.011  Sum_probs=29.9

Q ss_pred             cCCcCHHHHHHHhCCCHHHHHHHHcC----CCCCCHHHHHHHHHHhC
Q 031871          102 DKKLTQSQLAQLINEKPQVIQEYESG----KAIPNQQILTKLERALG  144 (151)
Q Consensus       102 ~~glTQ~eLA~~lgis~s~Is~~E~G----~~~p~~~~l~kLa~~Lg  144 (151)
                      ..|+|.+|+|+.+|+|.++|..+...    -...+...+..++...|
T Consensus        34 ~~g~s~~eIA~~l~is~~tV~~~l~r~~~kL~~~~~~~l~~~a~~~g   80 (82)
T 1je8_A           34 AQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVEAAVWVHQER   80 (82)
T ss_dssp             TTTCCHHHHHHHHTSCHHHHHHHHHHHHHHTTCSSHHHHHHHHHHTT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHcCCCHHHHHHHHHHcC
Confidence            68999999999999999999876431    12334444555554444

>2ef8_A C.ECOT38IS, putative transcription factor; helix-turn-helix, DNA binding protein, transcription regulator; HET: CME; 1.95A {Enterobacteria phage P2}

Probab=89.38  E-value=0.055  Score=34.10  Aligned_cols=26  Identities=12%  Similarity=-0.005  Sum_probs=22.8

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCcc
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNKA   55 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~~   55 (151)
                      ++.+.|++.|++.+++.+|+.|...|
T Consensus        25 sq~~lA~~~gis~~~i~~~e~g~~~~   50 (84)
T 2ef8_A           25 SQSELAIFLGLSQSDISKIESFERRL   50 (84)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHTTSSCC
T ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCCC
Confidence            45679999999999999999998764

>3g5g_A Regulatory protein; transcriptional regulator, helix-turn-helix, restriction- modification, transcription regulator; 2.80A {Enterobacter SP} PDB: 3fya_A

Probab=89.31  E-value=0.066  Score=35.82  Aligned_cols=42  Identities=12%  Similarity=0.071  Sum_probs=29.1

Q ss_pred             HHHHHHHHHcCCChhhHHhhhcCCCccCCCCccccccccccc
Q 031871           29 EKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDED   70 (151)
Q Consensus        29 ~~~~~~a~r~g~~v~t~~k~~~g~~~~~~~~~~~~~~kl~~~   70 (151)
                      =++-+.|.+.|++.+++.+||.|...|......+.+..|+.+
T Consensus        42 ltq~elA~~~gis~~~is~iE~G~~~ps~~~l~~ia~~l~v~   83 (99)
T 3g5g_A           42 MTQEDLAYKSNLDRTYISGIERNSRNLTIKSLELIMKGLEVS   83 (99)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHTTCSCCBHHHHHHHHHHTTCC
T ss_pred             CCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHHCcC
Confidence            355678999999999999999998765433333333444433

>3b7h_A Prophage LP1 protein 11; structural genomics, PSI2, MCSG, protein structure initiative, midwest center for structural genomics; 2.00A {Lactobacillus plantarum WCFS1}

Probab=89.09  E-value=0.059  Score=33.45  Aligned_cols=26  Identities=23%  Similarity=0.313  Sum_probs=22.5

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCC-cc
Q 031871           30 KVVNAARRAGADIETVRKSHAGTN-KA   55 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~-~~   55 (151)
                      +....|++.|++.+|+.+|+.|.. .|
T Consensus        22 sq~~lA~~~gis~~~i~~~e~g~~~~~   48 (78)
T 3b7h_A           22 TINRVATLAGLNQSTVNAMFEGRSKRP   48 (78)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHCTTCCCC
T ss_pred             CHHHHHHHHCcCHHHHHHHHcCCCCCC
Confidence            456789999999999999999987 54

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

Probab=89.08  E-value=0.46  Score=29.46  Aligned_cols=23  Identities=9%  Similarity=0.024  Sum_probs=20.5

Q ss_pred             CCcCHHHHHHHhCCCHHHHHHHH
Q 031871          103 KKLTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus       103 ~glTQ~eLA~~lgis~s~Is~~E  125 (151)
                      ..+|..|||+.+|+++++|.+.-
T Consensus        24 ~~~s~~eLA~~lglsr~tv~~~l   46 (67)
T 2heo_A           24 GPVAIFQLVKKCQVPKKTLNQVL   46 (67)
T ss_dssp             SCEEHHHHHHHHCSCHHHHHHHH
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHH
Confidence            46999999999999999998763

>3bd1_A CRO protein; transcription factor, helix-turn-helix, prophage, structural evolution, transcription; 1.40A {Xylella fastidiosa}

Probab=89.00  E-value=0.082  Score=33.39  Aligned_cols=26  Identities=15%  Similarity=0.091  Sum_probs=23.3

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCcc
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNKA   55 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~~   55 (151)
                      +..+.|++.|++.+|+.+|+.|...|
T Consensus        13 sq~~lA~~lgvs~~~is~~e~g~~~p   38 (79)
T 3bd1_A           13 SVSALAASLGVRQSAISNWRARGRVP   38 (79)
T ss_dssp             SHHHHHHHHTCCHHHHHHHHHHTCCC
T ss_pred             CHHHHHHHHCCCHHHHHHHHHCCCCC
Confidence            56789999999999999999997765

>1yse_A DNA-binding protein SATB1; all helical, DNA-binding domain, T-cell development; NMR {Homo sapiens} SCOP: a.35.1.7

Probab=88.82  E-value=0.3  Score=35.39  Aligned_cols=61  Identities=16%  Similarity=0.196  Sum_probs=47.2

Q ss_pred             CcchHHHHHHHHHHHhcCCcCHHHHHHH-hCCCHHHHHHHHcCCCCC------CHHHHHHHHHHhCCC
Q 031871           86 DRVPSELKKAIVQARNDKKLTQSQLAQL-INEKPQVIQEYESGKAIP------NQQILTKLERALGVK  146 (151)
Q Consensus        86 ~~~~~~~~~~Lk~~R~~~glTQ~eLA~~-lgis~s~Is~~E~G~~~p------~~~~l~kLa~~Lgv~  146 (151)
                      ..+..++.+.|++..+..+++|+-||+. +|.++.+++.+.+-...|      -.+.+.++-..|..+
T Consensus        20 ~~vt~~I~~~Ik~eLk~~~IsQ~~FA~~VL~rsQGtLS~LLr~PkdPW~~LksGRE~fiRM~NWL~Lp   87 (141)
T 1yse_A           20 TEVSSEIYQWVRDELKRAGISQAVFARVAFNRTQGLLSEILRKEEDPKTASQSLLVNLRAMQNFLQLP   87 (141)
T ss_dssp             CSCCTHHHHHHHHHHHHHTCCHHHHHHHHCCSCTTHHHHHHHHCCCGGGCCHHHHHHHHHHHHHHHSC
T ss_pred             ccchHHHHHHHHHHHHHcCCCHHHHHHHHHHhhhhhHHHHHcCCCCcHHHHHHHHHHHHHHHHHhcCC
Confidence            5667899999999999999999999996 699999999998855421      234555555555544

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

Probab=88.75  E-value=0.49  Score=30.44  Aligned_cols=29  Identities=3%  Similarity=0.087  Sum_probs=23.5

Q ss_pred             HHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           96 IVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      |..+....++|+.|||+.+|++++++++.
T Consensus        30 l~~l~~~~~~s~~ela~~l~is~~tvs~~   58 (99)
T 3cuo_A           30 LCMLSGSPGTSAGELTRITGLSASATSQH   58 (99)
T ss_dssp             HHHHTTCCSEEHHHHHHHHCCCHHHHHHH
T ss_pred             HHHHHhCCCcCHHHHHHHHCcCHHHHHHH
Confidence            44444445799999999999999999886

>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=88.73  E-value=2.4  Score=29.94  Aligned_cols=80  Identities=9%  Similarity=0.005  Sum_probs=45.2

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCccCCCCcccccccccccchhhhHHHHHhhccCCcchHHHHHHHHHH-HhcCCcCHH
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQA-RNDKKLTQS  108 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~~~~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~~~~~~~~~Lk~~-R~~~glTQ~  108 (151)
                      +.-..|+..|++..|+.+|-.-....  ..+... ..-..     .+         ..+...+-..|.++ +....+|..
T Consensus        43 s~~~IA~~lgis~~TV~rwl~r~~~~--G~~~~~-~r~gr-----~~---------~~~~~~~~~~I~~~~~~~~~~s~~  105 (159)
T 2k27_A           43 RPCDISRQLRVSHGCVSKILGRYYET--GSIRPG-VIGGS-----KP---------KVATPKVVEKIGDYKRQNPTMFAW  105 (159)
T ss_dssp             CHHHHHHHHTCCSHHHHHHHCCSSTT--SCCCCC-CCCCC-----CC---------CCCCTTHHHHHHHHHHHCSSSCHH
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHhc--CCccCC-CCCCC-----CC---------CCCCHHHHHHHHHHHHHCccchHH
Confidence            34567899999999999997643321  000000 00000     00         11112233344444 345679999


Q ss_pred             HHHHHh----------CCCHHHHHHHHc
Q 031871          109 QLAQLI----------NEKPQVIQEYES  126 (151)
Q Consensus       109 eLA~~l----------gis~s~Is~~E~  126 (151)
                      +++..+          .+|.++|.+|..
T Consensus       106 ~i~~~l~~~~~~~~~~~~S~sTV~r~L~  133 (159)
T 2k27_A          106 EIRDRLLAEGVCDNDTVPSVSSINRIIR  133 (159)
T ss_dssp             HHHHHHHHHTCSCTTTSCCHHHHHHHHH
T ss_pred             HHHHHHHHhcccccCCccCHHHHHHHHH
Confidence            999887          478899888864

>2l49_A C protein; P2 bacteriophage, P2 C, direct repeats, DNA-binding protein, binding protein; NMR {Enterobacteria phage P2} PDB: 2xcj_A

Probab=88.69  E-value=0.1  Score=34.04  Aligned_cols=37  Identities=11%  Similarity=0.040  Sum_probs=27.3

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCccCCCCccccccc
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRK   66 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~~~~~~~~~~~~k   66 (151)
                      +..+.|.+.|++.+|+.+|+.|...|......+.+..
T Consensus        19 tq~~lA~~~gis~~~is~~e~g~~~p~~~~l~~ia~~   55 (99)
T 2l49_A           19 SRQQLADLTGVPYGTLSYYESGRSTPPTDVMMNILQT   55 (99)
T ss_dssp             CHHHHHHHHCCCHHHHHHHTTTSSCCCHHHHHHHHSS
T ss_pred             CHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence            4567899999999999999999876544333344444

>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=88.63  E-value=0.061  Score=36.32  Aligned_cols=42  Identities=14%  Similarity=-0.007  Sum_probs=30.2

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCccCCCCcccccccccccc
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDT   71 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~~~~~~~~~~~~kl~~~~   71 (151)
                      ++-..|.+.|++.+|+.+|+.|...|..+...+.+..++.+.
T Consensus        24 sq~~lA~~~gis~~~i~~~e~g~~~p~~~~l~~la~~l~v~~   65 (114)
T 3op9_A           24 KNHQIAELLNVQTRTVAYYMSGETKPDIEKLIRLATYFHLSI   65 (114)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHHTSSCCCHHHHHHHHHHHTCCH
T ss_pred             CHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCH
Confidence            456789999999999999999987764443344444444443

>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=88.59  E-value=0.99  Score=29.57  Aligned_cols=35  Identities=11%  Similarity=0.106  Sum_probs=26.3

Q ss_pred             HHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           90 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        90 ~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      ..-.+.|..+.  .|+|.+|+|+.+|+|..||..+-.
T Consensus        32 ~rE~~Vl~l~~--~G~s~~eIA~~L~iS~~TV~~~~~   66 (90)
T 3ulq_B           32 PRECLILQEVE--KGFTNQEIADALHLSKRSIEYSLT   66 (90)
T ss_dssp             HHHHHHHHHHH--TTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHH--cCCCHHHHHHHHCcCHHHHHHHHH
Confidence            33344444443  899999999999999999987644

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

Probab=88.52  E-value=0.56  Score=32.34  Aligned_cols=32  Identities=9%  Similarity=0.141  Sum_probs=26.1

Q ss_pred             HHHHHHHHhcCC--cCHHHHHHHhCCCHHHHHHH
Q 031871           93 KKAIVQARNDKK--LTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        93 ~~~Lk~~R~~~g--lTQ~eLA~~lgis~s~Is~~  124 (151)
                      ...|..+....+  +|+.+||+.+|+++++|++.
T Consensus        29 ~~il~~L~~~~~~~~t~~eLa~~l~~s~sTV~r~   62 (123)
T 3r0a_A           29 LNVMKSFLNEPDRWIDTDALSKSLKLDVSTVQRS   62 (123)
T ss_dssp             HHHHHHHHHSTTCCEEHHHHHHHHTSCHHHHHHH
T ss_pred             HHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHH
Confidence            445566666666  99999999999999999886

>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=88.46  E-value=0.62  Score=30.66  Aligned_cols=25  Identities=24%  Similarity=0.339  Sum_probs=22.4

Q ss_pred             cCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871          102 DKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus       102 ~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      ..|+|.+|+|+.+|+|..+|..+..
T Consensus        40 ~~g~s~~eIA~~l~is~~tV~~~l~   64 (95)
T 3c57_A           40 SEGLTNKQIADRMFLAEKTVKNYVS   64 (95)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            7899999999999999999987643

>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=88.44  E-value=0.4  Score=31.66  Aligned_cols=40  Identities=13%  Similarity=0.086  Sum_probs=27.7

Q ss_pred             HHHHHHHHcCCChhhHHhhhcC-CCccCCCCcccccccccc
Q 031871           30 KVVNAARRAGADIETVRKSHAG-TNKAASSSTSLNTRKLDE   69 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g-~~~~~~~~~~~~~~kl~~   69 (151)
                      +....|++.|++.+|+.+|+.| ...|......+.+..++.
T Consensus        16 tq~~lA~~~gis~~~i~~~e~g~~~~p~~~~l~~ia~~l~v   56 (111)
T 1b0n_A           16 SLSELAEKAGVAKSYLSSIERNLQTNPSIQFLEKVSAVLDV   56 (111)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHTTCCSCCCHHHHHHHHHHHTC
T ss_pred             CHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHHHHHHCc
Confidence            4567999999999999999999 666543333333333333

>3lfp_A CSP231I C protein; transcriptional regulator, DNA binding protein, helix-turn-H restriction-modification, transcription; 2.00A {Citrobacter SP} PDB: 3lis_A

Probab=88.17  E-value=0.086  Score=34.69  Aligned_cols=42  Identities=12%  Similarity=0.068  Sum_probs=29.7

Q ss_pred             HHHHHHHHcCCChhh----HHhhhcCCCccCCCCcccccccccccc
Q 031871           30 KVVNAARRAGADIET----VRKSHAGTNKAASSSTSLNTRKLDEDT   71 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t----~~k~~~g~~~~~~~~~~~~~~kl~~~~   71 (151)
                      ++-+.|.+.|++.++    +.+||+|...|..+...+.+..++.+.
T Consensus        16 sq~~lA~~~gis~~~~~~~is~~E~g~~~p~~~~l~~la~~l~v~~   61 (98)
T 3lfp_A           16 SQEKLGVLAGIDEASASARMNQYEKGKHAPDFEMANRLAKVLKIPV   61 (98)
T ss_dssp             CHHHHHHHTTCCHHHHHHHHHHHHHTSSCCCHHHHHHHHHHHTSCG
T ss_pred             CHHHHHHHhCCCcchhhhHHHHHHCCCCCCCHHHHHHHHHHHCcCH
Confidence            456789999999999    999999987764433334444444443

>3vk0_A NHTF, transcriptional regulator; HTH motif, XRE transcription factor, DNA binding protein; 1.88A {Neisseria meningitidis}

Probab=88.15  E-value=0.076  Score=36.07  Aligned_cols=41  Identities=20%  Similarity=0.036  Sum_probs=28.8

Q ss_pred             HHHHHHHHHcCCChhhHHhhhcCCCccCCCCcccccccccc
Q 031871           29 EKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDE   69 (151)
Q Consensus        29 ~~~~~~a~r~g~~v~t~~k~~~g~~~~~~~~~~~~~~kl~~   69 (151)
                      =++.+.|.+.|++.+++.+||.|...|....+.+.+..|+.
T Consensus        35 ltq~elA~~~gis~~~is~~E~G~~~p~~~~l~~ia~~l~v   75 (114)
T 3vk0_A           35 WSQEELARQCGLDRTYVSAVERKRWNIALSNIEKMAAALGV   75 (114)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHTTTCCCCCHHHHHHHHHHHTS
T ss_pred             CCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHhCC
Confidence            35678999999999999999999876543333333333333

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

Probab=88.11  E-value=0.32  Score=32.31  Aligned_cols=32  Identities=9%  Similarity=0.088  Sum_probs=26.3

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ...+..++....+|..|||+.+|+|..||.+.
T Consensus         5 ~~Il~~L~~~g~vsv~eLA~~l~VS~~TIRrD   36 (87)
T 2k02_A            5 MEVRDMLALQGRMEAKQLSARLQTPQPLIDAM   36 (87)
T ss_dssp             HHHHHHHHHSCSEEHHHHHHHTTCCHHHHHHH
T ss_pred             HHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHH
Confidence            44556667778899999999999999998764

>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=88.06  E-value=0.67  Score=31.82  Aligned_cols=31  Identities=6%  Similarity=0.088  Sum_probs=25.4

Q ss_pred             HHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           96 IVQARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      +-.++-..|+|+.|+|+.+|+|.++|..+-.
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            3344556899999999999999999998754

>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=87.71  E-value=1  Score=28.97  Aligned_cols=32  Identities=6%  Similarity=0.100  Sum_probs=25.5

Q ss_pred             HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871           94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus        94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E  125 (151)
                      ..|..+....++|+.+||+.+|+++++|++.-
T Consensus        24 ~il~~l~~~~~~s~~ela~~l~is~~tv~~~l   55 (109)
T 1sfx_A           24 RIYSLLLERGGMRVSEIARELDLSARFVRDRL   55 (109)
T ss_dssp             HHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHH
Confidence            34445555678999999999999999998863

>3r1f_A ESX-1 secretion-associated regulator ESPR; helix-turn-helix, transcription factor, helix-turn-helix transcription factor; 2.50A {Mycobacterium tuberculosis}

Probab=87.70  E-value=0.4  Score=34.01  Aligned_cols=43  Identities=2%  Similarity=0.016  Sum_probs=28.1

Q ss_pred             HHHHHHHHcC-----CChhhHHhhhcCCC-ccCCCCcccccccccccch
Q 031871           30 KVVNAARRAG-----ADIETVRKSHAGTN-KAASSSTSLNTRKLDEDTE   72 (151)
Q Consensus        30 ~~~~~a~r~g-----~~v~t~~k~~~g~~-~~~~~~~~~~~~kl~~~~~   72 (151)
                      +.-+.|...|     ++.+++..||+|.. .|..+.+.+.+.-++.+.+
T Consensus        28 T~~elA~~~~~~G~~is~s~is~~E~G~r~~Ps~~~l~~iA~~f~V~~~   76 (135)
T 3r1f_A           28 TSAEVIAALKAEGITMSAPYLSQLRSGNRTNPSGATMAALANFFRIKAA   76 (135)
T ss_dssp             CHHHHHHHHHTTTCCCCHHHHHHHHHTSSCCCCHHHHHHHHHHHTSCTH
T ss_pred             CHHHHHHHHcccCCCcCHHHHHHHHCCCCCCCCHHHHHHHHHHhCCCHH
Confidence            4555666666     99999999999986 5544444444444444443

>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=87.61  E-value=0.055  Score=34.50  Aligned_cols=40  Identities=10%  Similarity=0.103  Sum_probs=28.1

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCccCCCCcccccccccc
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDE   69 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~~~~~~~~~~~~kl~~   69 (151)
                      +..+.|++.|++.+++.+|+.|...|......+.+..++.
T Consensus        27 sq~~lA~~~gis~~~i~~~e~g~~~~~~~~l~~i~~~l~~   66 (88)
T 2wiu_B           27 TQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLEL   66 (88)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHCGGGCBHHHHHHHHHHTTC
T ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCC
Confidence            4567899999999999999999776543333333334443

>1r8d_A Transcription activator MTAN; protein-DNA complex, transcription/DNA complex; 2.70A {Bacillus subtilis} SCOP: a.6.1.3 PDB: 1jbg_A

Probab=87.61  E-value=0.6  Score=31.57  Aligned_cols=23  Identities=13%  Similarity=0.248  Sum_probs=21.3

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESG  127 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G  127 (151)
                      +|..|+|+.+|||+.||..||+-
T Consensus         3 ~~i~e~A~~~gvs~~tLR~ye~~   25 (109)
T 1r8d_A            3 YQVKQVAEISGVSIRTLHHYDNI   25 (109)
T ss_dssp             BCHHHHHHHHSCCHHHHHHHHHT
T ss_pred             ccHHHHHHHHCcCHHHHHHHHHC
Confidence            78999999999999999999873

>3qq6_A HTH-type transcriptional regulator SINR; helix-turn-helix motif, biofilm, repressor, SINI; 1.90A {Bacillus subtilis}

Probab=87.60  E-value=0.083  Score=33.49  Aligned_cols=26  Identities=12%  Similarity=0.166  Sum_probs=22.2

Q ss_pred             HHHHHHHHcCCChhhHHhhhcC-CCcc
Q 031871           30 KVVNAARRAGADIETVRKSHAG-TNKA   55 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g-~~~~   55 (151)
                      ++.+.|.+.|++.+++.+||.| ...|
T Consensus        25 tq~elA~~~gis~~~is~~E~G~~~~p   51 (78)
T 3qq6_A           25 SLSELAEKAGVAKSYLSSIERNLQTNP   51 (78)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHTTSCCCC
T ss_pred             CHHHHHHHHCcCHHHHHHHHcCCCCCC
Confidence            4567899999999999999999 5554

>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=87.59  E-value=0.53  Score=31.40  Aligned_cols=75  Identities=11%  Similarity=0.120  Sum_probs=45.0

Q ss_pred             HHHHHHHHcCCChhhHHhhhc-----CCCccCCCCcccccccccccchhhhHHHHHhhccCCcchHHHHHHHHHHH-hcC
Q 031871           30 KVVNAARRAGADIETVRKSHA-----GTNKAASSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQAR-NDK  103 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~-----g~~~~~~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~~~~~~~~~Lk~~R-~~~  103 (151)
                      +..+.|++.|++..|+.+|-.     |...+.... +....+++                     ..+...|..+. +..
T Consensus        35 s~~~ia~~lgis~~Tv~~w~~~~~~~g~~~~~~~~-g~~~~~l~---------------------~~~~~~i~~~~~~~~   92 (128)
T 1pdn_C           35 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG-GSKPRIAT---------------------PEIENRIEEYKRSSP   92 (128)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHHHHHHCCSSCCCCS-CCCCCSSC---------------------STHHHHHHHTTTTCT
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHhhCCcccccCC-CCCCCcCC---------------------HHHHHHHHHHHHhCc
Confidence            445689999999999998865     322111100 00111221                     22233444443 345


Q ss_pred             CcCHHHHHHHh---C-------CCHHHHHHHHc
Q 031871          104 KLTQSQLAQLI---N-------EKPQVIQEYES  126 (151)
Q Consensus       104 glTQ~eLA~~l---g-------is~s~Is~~E~  126 (151)
                      .+|..+++..+   |       +|.++|.+|..
T Consensus        93 ~~s~~~i~~~l~~~g~~~~~~~~s~~tv~r~l~  125 (128)
T 1pdn_C           93 GMFSWEIREKLIREGVCDRSTAPSVSAISRLVR  125 (128)
T ss_dssp             TCCHHHHHHHHHHTSSSCSTTCCCHHHHHHHC-
T ss_pred             chHHHHHHHHHHHcCCccccCCcCHHHHHHHHH
Confidence            79999999998   7       59999998864

>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=87.57  E-value=0.7  Score=29.99  Aligned_cols=30  Identities=0%  Similarity=0.080  Sum_probs=22.9

Q ss_pred             HHHHHHhcC-CcCHHHHHHHhCCCHHH-HHHH
Q 031871           95 AIVQARNDK-KLTQSQLAQLINEKPQV-IQEY  124 (151)
Q Consensus        95 ~Lk~~R~~~-glTQ~eLA~~lgis~s~-Is~~  124 (151)
                      .|..+.... ++|+.+||+.+|+++++ +++.
T Consensus        20 ~L~~l~~~~~~~t~~eLa~~l~is~~t~vs~~   51 (95)
T 2pg4_A           20 TLLEFEKKGYEPSLAEIVKASGVSEKTFFMGL   51 (95)
T ss_dssp             HHHHHHHTTCCCCHHHHHHHHCCCHHHHHTTH
T ss_pred             HHHHHHhcCCCCCHHHHHHHHCCCchHHHHHH
Confidence            344444554 79999999999999999 6554

>2o3f_A Putative HTH-type transcriptional regulator YBBH; APC85504, putative transcriptional regulator YBBH; HET: MLY; 1.75A {Bacillus subtilis} SCOP: a.4.1.20

Probab=87.52  E-value=0.44  Score=32.62  Aligned_cols=33  Identities=12%  Similarity=0.080  Sum_probs=26.9

Q ss_pred             CCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH
Q 031871          103 KKLTQSQLAQLINEKPQVIQEYESGKAIPNQQI  135 (151)
Q Consensus       103 ~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~  135 (151)
                      ..+|..+||+.+|+|++||.++-+--..-....
T Consensus        38 ~~~si~elA~~~~vS~aTv~Rf~kklG~~gf~e   70 (111)
T 2o3f_A           38 IESTVNEISALANSSDAAVIRLCXSLGLKGFQD   70 (111)
T ss_dssp             HTCCHHHHHHHTTCCHHHHHHHHHHTTCSSHHH
T ss_pred             HhcCHHHHHHHHCCCHHHHHHHHHHcCCCCHHH
Confidence            579999999999999999999987555444433

>3mky_B Protein SOPB; partition, F plasmid, centromere, DNA binding protein- complex; HET: DNA; 2.86A {Escherichia coli} PDB: 3mkw_B* 3mkz_A*

Probab=87.51  E-value=0.94  Score=34.33  Aligned_cols=38  Identities=16%  Similarity=0.014  Sum_probs=29.0

Q ss_pred             HHHHHHHHHHHh-cCCcCHHHHHHHhCCCHHHHHHHHcC
Q 031871           90 SELKKAIVQARN-DKKLTQSQLAQLINEKPQVIQEYESG  127 (151)
Q Consensus        90 ~~~~~~Lk~~R~-~~glTQ~eLA~~lgis~s~Is~~E~G  127 (151)
                      -+.|.....+.. ....+|++||+.+|+|++.|+++.+-
T Consensus        27 yErg~~y~r~L~~g~~~~Q~~lA~~~giS~a~VSR~L~~   65 (189)
T 3mky_B           27 YERGQRYASRLQNEFAGNISALADAENISRKIITRCINT   65 (189)
T ss_dssp             HHHHHHHHHHHHTTTTTCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCcccCHHHHHHHHCCCHHHHHHHHHH
Confidence            345555555543 34789999999999999999998763

>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=87.49  E-value=1.2  Score=31.33  Aligned_cols=31  Identities=23%  Similarity=0.260  Sum_probs=25.7

Q ss_pred             HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      .-|..+.....+|..+||+.+|+|++++++.
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            4456666677899999999999999998874

>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=87.48  E-value=0.86  Score=31.13  Aligned_cols=32  Identities=13%  Similarity=0.083  Sum_probs=26.1

Q ss_pred             HHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           95 AIVQARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        95 ~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      .+-.++-..|+|.+|+|+.+|+|.++|...-.
T Consensus        32 ~vl~l~~~~g~s~~EIA~~lgiS~~tV~~~l~   63 (113)
T 1xsv_A           32 NYLELFYLEDYSLSEIADTFNVSRQAVYDNIR   63 (113)
T ss_dssp             HHHHHHHTSCCCHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            34445667899999999999999999987643

>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=87.31  E-value=1.4  Score=30.67  Aligned_cols=77  Identities=12%  Similarity=0.139  Sum_probs=47.4

Q ss_pred             HHHHHHHHcCCChhhHHhhhc-----CCCccCCCCcccccccccccchhhhHHHHHhhccCCcchHHHHHHHHHH-HhcC
Q 031871           30 KVVNAARRAGADIETVRKSHA-----GTNKAASSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQA-RNDK  103 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~-----g~~~~~~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~~~~~~~~~Lk~~-R~~~  103 (151)
                      +....|+..|++..|+.+|-.     |...+... .+..-.                     .+...+...|..+ +...
T Consensus        50 s~~~iA~~lgis~~TV~rw~~~~~~~G~~~~~~r-~gr~~~---------------------~~~~~~~~~I~~~~~~~~  107 (149)
T 1k78_A           50 RPCDISRQLRVSHGCVSKILGRYYETGSIKPGVI-GGSKPK---------------------VATPKVVEKIAEYKRQNP  107 (149)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHHHHHHSCCCCCCC-CCCCCS---------------------SSCHHHHHHHHHHHHHCT
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHcCCCCccCC-CCCCCC---------------------CCCHHHHHHHHHHHHhCc
Confidence            455679999999999998864     32211000 000011                     1122333444444 3446


Q ss_pred             CcCHHHHHHHh--------C--CCHHHHHHHHcCC
Q 031871          104 KLTQSQLAQLI--------N--EKPQVIQEYESGK  128 (151)
Q Consensus       104 glTQ~eLA~~l--------g--is~s~Is~~E~G~  128 (151)
                      .+|..+++..+        |  +|.++|.+|....
T Consensus       108 ~~s~~~i~~~l~~~~~~~~g~~~S~sTV~r~L~~~  142 (149)
T 1k78_A          108 TMFAWEIRDRLLAERVCDNDTVPSVSSINRIIRTK  142 (149)
T ss_dssp             TCCHHHHHHHHHHTTSSCTTTSCCHHHHHHHHHCC
T ss_pred             chhHHHHHHHHHHhcccccCCCcCHHHHHHHHHHH
Confidence            79999999988        7  8999999998654

>2d5v_A Hepatocyte nuclear factor 6; transcription factor, transcription-DNA complex; 2.00A {Rattus norvegicus} PDB: 1s7e_A

Probab=87.02  E-value=1.2  Score=32.21  Aligned_cols=40  Identities=13%  Similarity=0.162  Sum_probs=35.5

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHh-CCCHHHHHHHHcCC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLI-NEKPQVIQEYESGK  128 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~l-gis~s~Is~~E~G~  128 (151)
                      ...+...|+.+....+++|..||+.+ |+++.+++.+.+.-
T Consensus         6 t~~i~~~i~~~l~~~~i~q~~fa~~ilg~sq~~ls~~l~~p   46 (164)
T 2d5v_A            6 TKEVAQRITTELKRYSIPQAIFAQRVLCRSQGTLSDLLRNP   46 (164)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHTSCCHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHHHHcCCchHHHHHHHhcCCchhHHHHcCCC
Confidence            46789999999999999999999965 99999999998743

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

Probab=86.91  E-value=1.3  Score=30.31  Aligned_cols=34  Identities=3%  Similarity=0.067  Sum_probs=27.7

Q ss_pred             HHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           91 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        91 ~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      .-...|..+...-++|+.+||+.+|++++++++.
T Consensus        41 ~~~~iL~~l~~~~~~t~~ela~~l~~~~~tvs~~   74 (148)
T 3nrv_A           41 TEWRIISVLSSASDCSVQKISDILGLDKAAVSRT   74 (148)
T ss_dssp             HHHHHHHHHHHSSSBCHHHHHHHHTCCHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHHCCCHHHHHHH
Confidence            3345566666677999999999999999999886

>3f52_A CLP gene regulator (CLGR); helix-turn-helix motif, transcriptional ACTI human pathogen, transcription activator; 1.75A {Corynebacterium glutamicum} PDB: 3f51_A

Probab=86.89  E-value=0.1  Score=35.29  Aligned_cols=40  Identities=10%  Similarity=0.060  Sum_probs=28.1

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCccCCCCcccccccccc
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDE   69 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~~~~~~~~~~~~kl~~   69 (151)
                      ++.+.|.+.|++.+++.+||+|...|..+...+.+..|+.
T Consensus        43 sq~~lA~~~gis~~~is~~E~g~~~~~~~~l~~la~~l~v   82 (117)
T 3f52_A           43 TLRELAEASRVSPGYLSELERGRKEVSSELLASVCHALGA   82 (117)
T ss_dssp             CHHHHHHHTTSCHHHHHHHHTTSSCCCHHHHHHHHHHHTC
T ss_pred             CHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHhCC
Confidence            5567899999999999999999876543333333333333

>1x57_A Endothelial differentiation-related factor 1; HMBF1alpha, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.35.1.12

Probab=86.81  E-value=0.083  Score=34.17  Aligned_cols=28  Identities=7%  Similarity=0.115  Sum_probs=23.7

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCccCC
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNKAAS   57 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~~~~   57 (151)
                      ++.+.|.+.|++.+++.+||.|...|..
T Consensus        28 sq~~lA~~~gis~~~is~~e~g~~~p~~   55 (91)
T 1x57_A           28 TQKDLATKINEKPQVIADYESGRAIPNN   55 (91)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHHTCSCCCH
T ss_pred             CHHHHHHHHCcCHHHHHHHHcCCCCCCH
Confidence            4567899999999999999999876533

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

Probab=86.56  E-value=1.4  Score=29.61  Aligned_cols=33  Identities=12%  Similarity=0.221  Sum_probs=26.7

Q ss_pred             HHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           92 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        92 ~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      -...|..+....++|+.+||+.+|++++++++.
T Consensus        31 ~~~iL~~l~~~~~~~~~ela~~l~~s~~tvs~~   63 (138)
T 3bpv_A           31 QVACLLRIHREPGIKQDELATFFHVDKGTIART   63 (138)
T ss_dssp             HHHHHHHHHHSTTCBHHHHHHHHTCCHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHH
Confidence            344456666667899999999999999999876

>3mlf_A Transcriptional regulator; structural genomics, helix-turn-helix XRE-family like protei transcription regulator, PSI-2; 2.60A {Staphylococcus aureus subsp}

Probab=86.53  E-value=0.095  Score=35.72  Aligned_cols=42  Identities=7%  Similarity=-0.034  Sum_probs=29.7

Q ss_pred             HHHHHHHHHcCCChhhHHhhhcCCCccCCCCccccccccccc
Q 031871           29 EKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDED   70 (151)
Q Consensus        29 ~~~~~~a~r~g~~v~t~~k~~~g~~~~~~~~~~~~~~kl~~~   70 (151)
                      =++.+.|.+.|++.+++.+||.|...|..+...+.+..++.+
T Consensus        37 ltq~elA~~~gis~~~is~~E~G~~~ps~~~l~~ia~~l~v~   78 (111)
T 3mlf_A           37 LTQKELGDLFKVSSRTIQNMEKDSTNIKDSLLSKYMSAFNVK   78 (111)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHCCTTCCHHHHHHHHHHHTCC
T ss_pred             CCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHhCcC
Confidence            356779999999999999999998765443333444444443

>4ghj_A Probable transcriptional regulator; structural genomics, niaid, national institute of allergy AN infectious diseases; HET: MSE; 1.75A {Vibrio vulnificus}

Probab=86.53  E-value=0.32  Score=32.85  Aligned_cols=30  Identities=23%  Similarity=0.241  Sum_probs=24.7

Q ss_pred             ccCHHHHHHHHHcCCChhhHHhhhcCCCcc
Q 031871           26 KKDEKVVNAARRAGADIETVRKSHAGTNKA   55 (151)
Q Consensus        26 ~~~~~~~~~a~r~g~~v~t~~k~~~g~~~~   55 (151)
                      .++=++.+.|.+.|++.+|+.+||.|+..|
T Consensus        47 ~~glTQ~eLA~~~gvs~~~is~~E~G~~~~   76 (101)
T 4ghj_A           47 NRDLTQSEVAEIAGIARKTVLNAEKGKVQL   76 (101)
T ss_dssp             HTTCCHHHHHHHHTSCHHHHHHHHTTCCBH
T ss_pred             HcCCCHHHHHHHcCCCHHHHHHHHCCCCCH
Confidence            344567789999999999999999997543

>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=86.49  E-value=1.5  Score=30.71  Aligned_cols=31  Identities=23%  Similarity=0.398  Sum_probs=25.7

Q ss_pred             HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      .-|..+.....+|..+||+.+|+|++++++.
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            4456666677899999999999999998875

>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=86.39  E-value=0.34  Score=33.51  Aligned_cols=26  Identities=12%  Similarity=0.234  Sum_probs=23.1

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCcc
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNKA   55 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~~   55 (151)
                      ++.++|.+.|++..|+.+||.|...|
T Consensus        86 sq~~la~~~g~s~~~i~~~E~g~~~p  111 (133)
T 3o9x_A           86 TQKEASEIFGGGVNAFSRYEKGNAQP  111 (133)
T ss_dssp             CHHHHHHHHCSCTTHHHHHHHTSSCC
T ss_pred             CHHHHHHHHCCCHHHHHHHHCCCCCC
Confidence            55678999999999999999998765

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

Probab=86.35  E-value=1.4  Score=30.96  Aligned_cols=31  Identities=23%  Similarity=0.319  Sum_probs=25.9

Q ss_pred             HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ..|..+.....+|..+||+.+|+|++++.+.
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            4456666777899999999999999998875

>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=86.32  E-value=0.99  Score=30.89  Aligned_cols=35  Identities=9%  Similarity=0.098  Sum_probs=24.9

Q ss_pred             HHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           90 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        90 ~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ..-...|..+...-++|+.+||+.+|++++++++.
T Consensus        37 ~~~~~vL~~l~~~~~~t~~eLa~~l~~~~~tvs~~   71 (142)
T 3ech_A           37 PPDVHVLKLIDEQRGLNLQDLGRQMCRDKALITRK   71 (142)
T ss_dssp             HHHHHHHHHHHHTTTCCHHHHHHHHC---CHHHHH
T ss_pred             HHHHHHHHHHHhCCCcCHHHHHHHhCCCHHHHHHH
Confidence            33345566666677999999999999999988876

>2zcw_A TTHA1359, transcriptional regulator, FNR/CRP family; stationary phase, DNA-binding, transcription regulation; 1.50A {Thermus thermophilus}

Probab=86.07  E-value=1.3  Score=31.87  Aligned_cols=22  Identities=18%  Similarity=0.247  Sum_probs=19.7

Q ss_pred             CcCHHHHHHHhCCCHHHHHHHH
Q 031871          104 KLTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus       104 glTQ~eLA~~lgis~s~Is~~E  125 (151)
                      .+||.+||..+|+++.+|++.-
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            3899999999999999999863

>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=85.79  E-value=1.7  Score=30.59  Aligned_cols=31  Identities=13%  Similarity=0.194  Sum_probs=26.3

Q ss_pred             HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ..|..+.....+|..+||+.+|+|++++.+.
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            4566677777899999999999999998875

>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=85.77  E-value=0.67  Score=30.40  Aligned_cols=33  Identities=9%  Similarity=0.084  Sum_probs=27.1

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E  125 (151)
                      ...|..+....+.++.+.|+.+|||++++.+..
T Consensus        53 ~~~i~~aL~~~~gn~~~aA~~LGIsr~tL~rkl   85 (91)
T 1ntc_A           53 RTLLTTALRHTQGHKQEAARLLGWGAATLTAKL   85 (91)
T ss_dssp             HHHHHHHHHHTTTCTTHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHCcCHHHHHHHH
Confidence            455667777788899999999999999998754

>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=85.66  E-value=1.4  Score=30.34  Aligned_cols=35  Identities=9%  Similarity=0.081  Sum_probs=27.2

Q ss_pred             HHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           90 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        90 ~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      +.-...|.  +-..|+|..|+|+.+|+|.++|.....
T Consensus       112 ~~~r~v~~--~~~~g~s~~EIA~~lgis~~tV~~~~~  146 (164)
T 3mzy_A          112 KFEKEVLT--YLIRGYSYREIATILSKNLKSIDNTIQ  146 (164)
T ss_dssp             HHHHHHHH--HHTTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHH--HHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            33334444  467899999999999999999988754

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

Probab=85.43  E-value=1.7  Score=28.42  Aligned_cols=36  Identities=14%  Similarity=0.153  Sum_probs=27.0

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCC
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK  128 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~  128 (151)
                      -..|.+--....++..+||+.+|+|+.++++.-+..
T Consensus         8 ~~~i~~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~~   43 (103)
T 3lsg_A            8 QNIIEESYTDSQFTLSVLSEKLDLSSGYLSIMFKKN   43 (103)
T ss_dssp             HHHHHHHTTCTTCCHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             HHHHHHHccCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            334444433447999999999999999999986644

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

Probab=85.40  E-value=0.68  Score=31.58  Aligned_cols=33  Identities=9%  Similarity=0.095  Sum_probs=26.4

Q ss_pred             HhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCC
Q 031871          100 RNDKKLTQSQLAQLINEKPQVIQEYESGKAIPN  132 (151)
Q Consensus       100 R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~  132 (151)
                      ..-..+|..+||+.+|+|+++|.++-+--..-.
T Consensus        31 ~~~~~~si~elA~~~~vS~aTv~Rf~kkLGf~g   63 (107)
T 3iwf_A           31 HKVVNMTSQEIANQLETSSTSIIRLSKKVTPGG   63 (107)
T ss_dssp             HHHTTCCHHHHHHHHTSCHHHHHHHHHHHSTTH
T ss_pred             HHHHHCCHHHHHHHHCCCHHHHHHHHHHhCCCC
Confidence            344689999999999999999999976444333

>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=85.39  E-value=1.5  Score=30.66  Aligned_cols=30  Identities=10%  Similarity=0.080  Sum_probs=24.9

Q ss_pred             HHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           95 AIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        95 ~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      .|..+.....+|..+||+.+|+|++++++.
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            355566666799999999999999998875

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

Probab=85.38  E-value=1.3  Score=30.11  Aligned_cols=31  Identities=19%  Similarity=0.262  Sum_probs=25.5

Q ss_pred             HHHHHH-HhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           94 KAIVQA-RNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        94 ~~Lk~~-R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ..|..+ ....++|+.+||+.+|++++++++.
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 5667899999999999999999876

>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=85.35  E-value=1.4  Score=26.20  Aligned_cols=28  Identities=11%  Similarity=0.160  Sum_probs=23.7

Q ss_pred             HHhcCCcCHHHHHHHh-----CCCHHHHHHHHc
Q 031871           99 ARNDKKLTQSQLAQLI-----NEKPQVIQEYES  126 (151)
Q Consensus        99 ~R~~~glTQ~eLA~~l-----gis~s~Is~~E~  126 (151)
                      +.....+|..||++.+     ++|.+||.+..+
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     999999998755

>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=85.35  E-value=0.72  Score=29.61  Aligned_cols=29  Identities=14%  Similarity=0.229  Sum_probs=23.3

Q ss_pred             HHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           96 IVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      |..+....++|+.+||+.+|++++++++.
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            34444456799999999999999999875

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

Probab=85.35  E-value=1.8  Score=30.75  Aligned_cols=31  Identities=16%  Similarity=0.235  Sum_probs=25.8

Q ss_pred             HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ..|..+.....+|..+||+.+|+|++++++.
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            4456666677899999999999999998875

>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=85.34  E-value=0.49  Score=30.72  Aligned_cols=35  Identities=17%  Similarity=0.207  Sum_probs=26.7

Q ss_pred             HHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           90 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        90 ~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      +.+-..|..+......|-.++|+++|++.+.|+++
T Consensus        15 ~~v~~~i~~L~~~~~~Ta~~IAkkLg~sK~~vNr~   49 (75)
T 1sfu_A           15 SLVKKEVLSLNTNDYTTAISLSNRLKINKKKINQQ   49 (75)
T ss_dssp             HHHHHHHHTSCTTCEECHHHHHHHTTCCHHHHHHH
T ss_pred             HHHHHHHHhCCCCcchHHHHHHHHHCCCHHHHHHH
Confidence            33444555556666689999999999999998876

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

Probab=85.29  E-value=1.6  Score=29.53  Aligned_cols=32  Identities=13%  Similarity=0.092  Sum_probs=25.8

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ...|..+....++|+.+||+.+|++++++++.
T Consensus        34 ~~iL~~l~~~~~~~~~ela~~l~is~~~vs~~   65 (142)
T 3bdd_A           34 YSILQTLLKDAPLHQLALQERLQIDRAAVTRH   65 (142)
T ss_dssp             HHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHH
T ss_pred             HHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHH
Confidence            34455555566899999999999999999876

>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=85.20  E-value=1.6  Score=29.75  Aligned_cols=32  Identities=13%  Similarity=0.071  Sum_probs=26.3

Q ss_pred             HHHHHHHHh-cCCcCHHHHHHHhCCCHHHHHHH
Q 031871           93 KKAIVQARN-DKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        93 ~~~Lk~~R~-~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ...|..+.. ..++|+.+||+.+|++++++++.
T Consensus        38 ~~iL~~l~~~~~~~~~~~la~~l~i~~~~vs~~   70 (147)
T 2hr3_A           38 LVVLGAIDRLGGDVTPSELAAAERMRSSNLAAL   70 (147)
T ss_dssp             HHHHHHHHHTTSCBCHHHHHHHTTCCHHHHHHH
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHH
Confidence            345566666 67899999999999999998876

>3b02_A Transcriptional regulator, CRP family; structural genomics, riken structural genomics/proteomics in RSGI; 1.92A {Thermus thermophilus} PDB: 2zdb_A

Probab=85.17  E-value=1.4  Score=31.56  Aligned_cols=22  Identities=5%  Similarity=0.139  Sum_probs=19.7

Q ss_pred             CcCHHHHHHHhCCCHHHHHHHH
Q 031871          104 KLTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus       104 glTQ~eLA~~lgis~s~Is~~E  125 (151)
                      .+||.+||..+|+++.+|++.-
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            3799999999999999999873

>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=85.17  E-value=1.8  Score=29.16  Aligned_cols=34  Identities=15%  Similarity=0.068  Sum_probs=26.4

Q ss_pred             HHHHHHHHHHhcC--CcCHHHHHHHhCCCHHHHHHH
Q 031871           91 ELKKAIVQARNDK--KLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        91 ~~~~~Lk~~R~~~--glTQ~eLA~~lgis~s~Is~~  124 (151)
                      .-...|..+....  ++|+.+||+.+|++++++++.
T Consensus        35 ~~~~iL~~l~~~~~~~~~~~ela~~l~~~~~tvs~~   70 (141)
T 3bro_A           35 TQMTIIDYLSRNKNKEVLQRDLESEFSIKSSTATVL   70 (141)
T ss_dssp             HHHHHHHHHHHTTTSCCBHHHHHHHHTCCHHHHHHH
T ss_pred             HHHHHHHHHHHCCCCCcCHHHHHHHHCCCcchHHHH
Confidence            3344555665555  799999999999999998876

>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=85.14  E-value=0.56  Score=30.78  Aligned_cols=26  Identities=15%  Similarity=0.164  Sum_probs=22.9

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCcc
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNKA   55 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~~   55 (151)
                      ++-+.|.+.|++.+|+.+||.|...|
T Consensus        45 sq~elA~~lgvs~~~is~~E~G~~~p   70 (99)
T 2ppx_A           45 TQEEFSARYHIPLGTLRDWEQGRSEP   70 (99)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHTTSSCC
T ss_pred             CHHHHHHHhCcCHHHHHHHHcCCCCC
Confidence            55779999999999999999998764

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

Probab=85.05  E-value=1.4  Score=30.41  Aligned_cols=35  Identities=3%  Similarity=0.066  Sum_probs=28.5

Q ss_pred             HHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           90 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        90 ~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ..-...|..+....++|+.+||+.+|+++++++++
T Consensus        41 ~~q~~iL~~l~~~~~~~~~eLa~~l~~~~~~vs~~   75 (149)
T 4hbl_A           41 YSQYLVMLTLWEENPQTLNSIGRHLDLSSNTLTPM   75 (149)
T ss_dssp             HHHHHHHHHHHHSSSEEHHHHHHHHTCCHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHH
Confidence            33445566666678999999999999999999986

>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=85.04  E-value=1.4  Score=30.00  Aligned_cols=35  Identities=14%  Similarity=0.085  Sum_probs=26.1

Q ss_pred             HHHHHHHHHHH-hcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           90 SELKKAIVQAR-NDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        90 ~~~~~~Lk~~R-~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ......|..+. ...++|+.+||+.+|++++++++.
T Consensus        26 ~~~~~il~~L~~~~~~~t~~ela~~l~~~~stvs~~   61 (152)
T 1ku9_A           26 KSVGAVYAILYLSDKPLTISDIMEELKISKGNVSMS   61 (152)
T ss_dssp             HHHHHHHHHHHHCSSCEEHHHHHHHHTCCHHHHHHH
T ss_pred             hhHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHH
Confidence            33344444443 356899999999999999999886

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

Probab=85.01  E-value=1.5  Score=29.86  Aligned_cols=33  Identities=6%  Similarity=0.145  Sum_probs=26.8

Q ss_pred             HHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           92 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        92 ~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      -...|..+....++|+.+||+.+|+++++++++
T Consensus        39 ~~~iL~~l~~~~~~t~~eLa~~l~~~~~~vs~~   71 (143)
T 3oop_A           39 QWSVLEGIEANEPISQKEIALWTKKDTPTVNRI   71 (143)
T ss_dssp             HHHHHHHHHHHSSEEHHHHHHHHTCCHHHHHHH
T ss_pred             HHHHHHHHHHcCCcCHHHHHHHHCCCHhhHHHH
Confidence            344455666668899999999999999999886

>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=84.92  E-value=1.5  Score=29.63  Aligned_cols=34  Identities=15%  Similarity=0.201  Sum_probs=26.7

Q ss_pred             HHHHHHHHHHhcC--CcCHHHHHHHhCCCHHHHHHH
Q 031871           91 ELKKAIVQARNDK--KLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        91 ~~~~~Lk~~R~~~--glTQ~eLA~~lgis~s~Is~~  124 (151)
                      .-...|..+....  ++|+.+||+.+|++++++++.
T Consensus        32 ~~~~vL~~l~~~~~~~~t~~ela~~l~~~~~tvs~~   67 (139)
T 3eco_A           32 EQGHTLGYLYAHQQDGLTQNDIAKALQRTGPTVSNL   67 (139)
T ss_dssp             HHHHHHHHHHHSTTTCEEHHHHHHHHTCCHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCCcCHHHHHHHhCCCcccHHHH
Confidence            3344555565554  899999999999999999986

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

Probab=84.90  E-value=1.1  Score=31.31  Aligned_cols=31  Identities=6%  Similarity=0.131  Sum_probs=25.7

Q ss_pred             HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ..|..+....++|+.+||+.+|+++++++++
T Consensus        54 ~vL~~l~~~~~~t~~eLa~~l~~~~~tvs~~   84 (159)
T 3s2w_A           54 PFLMRLYREDGINQESLSDYLKIDKGTTARA   84 (159)
T ss_dssp             HHHHHHHHSCSEEHHHHHHHHTCCHHHHHHH
T ss_pred             HHHHHHHHCCCCCHHHHHHHHCCCHHHHHHH
Confidence            3455555667899999999999999999986

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

Probab=84.89  E-value=1.6  Score=29.81  Aligned_cols=35  Identities=11%  Similarity=0.078  Sum_probs=27.9

Q ss_pred             HHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           90 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        90 ~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ..-...|..+...-++|+.+||+.+|+++++++++
T Consensus        31 ~~q~~iL~~l~~~~~~t~~eLa~~l~~~~~tvs~~   65 (145)
T 3g3z_A           31 YNLFAVLYTLATEGSRTQKHIGEKWSLPKQTVSGV   65 (145)
T ss_dssp             HHHHHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHH
Confidence            33445566666667899999999999999999886

>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=84.84  E-value=1.5  Score=30.11  Aligned_cols=25  Identities=12%  Similarity=0.223  Sum_probs=21.7

Q ss_pred             HhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871          100 RNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus       100 R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ....++|+.+||+.+|+++++|++.
T Consensus        18 ~~~~~~~~~ela~~l~vs~~tvs~~   42 (142)
T 1on2_A           18 EEKGYARVSDIAEALAVHPSSVTKM   42 (142)
T ss_dssp             HHHSSCCHHHHHHHHTSCHHHHHHH
T ss_pred             hhcCCCCHHHHHHHhCCCHHHHHHH
Confidence            3456899999999999999998875

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

Probab=84.65  E-value=1.4  Score=34.27  Aligned_cols=35  Identities=14%  Similarity=0.163  Sum_probs=27.9

Q ss_pred             HHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           90 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        90 ~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ..-...|..+....++|+.+||+.+|++++++++.
T Consensus       152 ~~~~~IL~~L~~~~~~s~~eLA~~lglsksTv~r~  186 (244)
T 2wte_A          152 REEMKLLNVLYETKGTGITELAKMLDKSEKTLINK  186 (244)
T ss_dssp             HHHHHHHHHHHHHTCBCHHHHHHHHTCCHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHH
Confidence            33444556656667899999999999999999987

>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=84.63  E-value=1.4  Score=29.60  Aligned_cols=24  Identities=13%  Similarity=0.238  Sum_probs=22.3

Q ss_pred             CCcCHHHHHHHhCCCHHHHHHHHc
Q 031871          103 KKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus       103 ~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      .++|..|+|+.+|+|..+|..++.
T Consensus        38 e~~s~~EIA~~lgiS~~tVr~~~~   61 (99)
T 3t72_q           38 TDYTLEEVGKQFDVTRERIRQIEA   61 (99)
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHH
Confidence            689999999999999999999876

>3fym_A Putative uncharacterized protein; HTH DNA binding, DNA binding protein; 1.00A {Staphylococcus aureus subsp}

Probab=84.57  E-value=0.34  Score=33.89  Aligned_cols=45  Identities=7%  Similarity=0.071  Sum_probs=31.5

Q ss_pred             CHHHHHHHHHcCCChhhHHhhhcCCCccCCCC------cccccccccccch
Q 031871           28 DEKVVNAARRAGADIETVRKSHAGTNKAASSS------TSLNTRKLDEDTE   72 (151)
Q Consensus        28 ~~~~~~~a~r~g~~v~t~~k~~~g~~~~~~~~------~~~~~~kl~~~~~   72 (151)
                      +=++-+.|.+.|++.+++.+||+|...|..+.      ..+.+..|+.+.+
T Consensus        16 gltq~elA~~~gis~~~is~iE~g~~~~~~~~~~~~~~l~~ia~~L~v~~~   66 (130)
T 3fym_A           16 GMTLTELEQRTGIKREMLVHIENNEFDQLPNKNYSEGFIRKYASVVNIEPN   66 (130)
T ss_dssp             TCCHHHHHHHHCCCHHHHHHHHTTCGGGSSSGGGHHHHHHHHHHHTTCCHH
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHCCCCCCCchhhhHHHHHHHHHHHhCCCHH
Confidence            34567899999999999999999987654432      3344455554443

>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=84.56  E-value=0.58  Score=30.15  Aligned_cols=26  Identities=15%  Similarity=0.086  Sum_probs=22.8

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCcc
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNKA   55 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~~   55 (151)
                      +..+.|++.|++.+|+.+|+.|...|
T Consensus        23 tq~~lA~~~gis~~~is~~e~g~~~~   48 (94)
T 2ict_A           23 SLREFARAMEIAPSTASRLLTGKAAL   48 (94)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHTSSCC
T ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCCC
Confidence            45679999999999999999998764

>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=84.53  E-value=1.1  Score=31.66  Aligned_cols=24  Identities=21%  Similarity=0.322  Sum_probs=21.4

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcCC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESGK  128 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G~  128 (151)
                      ||..|+|+.+|||+.||..||+-.
T Consensus         1 ~~I~e~A~~~gvs~~tLR~ye~~G   24 (135)
T 1q06_A            1 MNISDVAKITGLTSKAIRFYEEKG   24 (135)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHTT
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHCC
Confidence            578999999999999999998743

>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=84.46  E-value=1.7  Score=31.67  Aligned_cols=22  Identities=14%  Similarity=0.250  Sum_probs=20.1

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHc
Q 031871          105 LTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      +||++||..+|+++.+|++.-+
T Consensus       188 lt~~~lA~~lg~sr~tvsR~l~  209 (230)
T 3iwz_A          188 VSRQELARLVGCSREMAGRVLK  209 (230)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCHHHHHHHhCCcHHHHHHHHH
Confidence            7999999999999999998754

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

Probab=84.39  E-value=1.7  Score=29.19  Aligned_cols=32  Identities=22%  Similarity=0.204  Sum_probs=25.9

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ...|..+....++|+.+||+.+|++++++++.
T Consensus        41 ~~iL~~l~~~~~~t~~ela~~l~~~~~tvs~~   72 (140)
T 2nnn_A           41 WAALVRLGETGPCPQNQLGRLTAMDAATIKGV   72 (140)
T ss_dssp             HHHHHHHHHHSSBCHHHHHHHTTCCHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHH
Confidence            44455555556899999999999999999886

>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=84.35  E-value=1.2  Score=30.37  Aligned_cols=29  Identities=10%  Similarity=0.096  Sum_probs=23.8

Q ss_pred             HHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           96 IVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      |..+.....+|..+||+.+|++++++++.
T Consensus        48 L~~L~~~~~~s~~eLa~~l~is~stvs~~   76 (122)
T 1u2w_A           48 TYALCQDEELCVCDIANILGVTIANASHH   76 (122)
T ss_dssp             HHHHHHSSCEEHHHHHHHHTCCHHHHHHH
T ss_pred             HHHHHHCCCcCHHHHHHHHCcCHHHHHHH
Confidence            34444467799999999999999999986

>3hh0_A Transcriptional regulator, MERR family; protein structure initiative II(PSI II), NYSGXRC, 11183J, structural genomics; 2.67A {Bacillus cereus atcc 14579}

Probab=84.22  E-value=1.2  Score=31.94  Aligned_cols=26  Identities=12%  Similarity=0.106  Sum_probs=23.1

Q ss_pred             CCcCHHHHHHHhCCCHHHHHHHHcCC
Q 031871          103 KKLTQSQLAQLINEKPQVIQEYESGK  128 (151)
Q Consensus       103 ~glTQ~eLA~~lgis~s~Is~~E~G~  128 (151)
                      ..+|..|+|+.+|||.+||..||+-.
T Consensus         3 ~~~tI~evA~~~Gvs~~tLR~ye~~G   28 (146)
T 3hh0_A            3 LAWLISEFASVGDVTVRALRYYDKIN   28 (146)
T ss_dssp             CCBCHHHHHHHHTCCHHHHHHHHHTT
T ss_pred             CCCcHHHHHHHHCcCHHHHHHHHHCC
Confidence            35899999999999999999999743

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

Probab=84.14  E-value=2  Score=27.64  Aligned_cols=35  Identities=9%  Similarity=0.144  Sum_probs=24.9

Q ss_pred             HHHHHHHHHHHhc---CCcCHHHHHHHhCCCHHHHHHH
Q 031871           90 SELKKAIVQARND---KKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        90 ~~~~~~Lk~~R~~---~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ..+-+.|+....+   .-.|..|||+.+|+|.++|.+.
T Consensus         7 ~~IL~~I~~~i~~~~g~~psv~EIa~~lgvS~~TVrr~   44 (77)
T 2jt1_A            7 TKIISIVQERQNMDDGAPVKTRDIADAAGLSIYQVRLY   44 (77)
T ss_dssp             HHHHHHHHHHHHHHTTSCEEHHHHHHHHTCCHHHHHHH
T ss_pred             HHHHHHHHHHHhhccCCCcCHHHHHHHHCCCHHHHHHH
Confidence            3444455544333   4578999999999999988765

>2vz4_A Tipal, HTH-type transcriptional activator TIPA; transcription, resistance, antibiotic; 2.90A {Streptomyces lividans}

Probab=84.14  E-value=2  Score=28.88  Aligned_cols=65  Identities=17%  Similarity=0.245  Sum_probs=37.9

Q ss_pred             HHHHHHcCCChhhHHhhhc-CCCccCC-CCcccccccccccchhhhHHHHHhhccCCcchHHHHHHHHHHHhcCCcCHHH
Q 031871           32 VNAARRAGADIETVRKSHA-GTNKAAS-SSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQ  109 (151)
Q Consensus        32 ~~~a~r~g~~v~t~~k~~~-g~~~~~~-~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~~~~~~~~~Lk~~R~~~glTQ~e  109 (151)
                      -+.|+..|+++.|++.|+. |--.|.. +..+  -+.-+.  +                ....-..|+.+| ..|+|..+
T Consensus         5 ~e~A~~~gvs~~tLR~ye~~Gll~p~~r~~~g--~R~Y~~--~----------------dl~~l~~I~~lr-~~G~sl~~   63 (108)
T 2vz4_A            5 GQVAGFAGVTVRTLHHYDDIGLLVPSERSHAG--HRRYSD--A----------------DLDRLQQILFYR-ELGFPLDE   63 (108)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHTSSCCSEECSSC--CEEBCH--H----------------HHHHHHHHHHHH-HTTCCHHH
T ss_pred             HHHHHHHCcCHHHHHHHHHCCCCCCCccCCCC--CeecCH--H----------------HHHHHHHHHHHH-HCCCCHHH
Confidence            4689999999999999976 4333321 1000  011111  1                112234455564 46999999


Q ss_pred             HHHHhCCC
Q 031871          110 LAQLINEK  117 (151)
Q Consensus       110 LA~~lgis  117 (151)
                      ++..+..+
T Consensus        64 I~~~l~~~   71 (108)
T 2vz4_A           64 VAALLDDP   71 (108)
T ss_dssp             HHHHHTC-
T ss_pred             HHHHHhCC
Confidence            99988653

>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=84.13  E-value=1.3  Score=32.52  Aligned_cols=32  Identities=9%  Similarity=0.233  Sum_probs=26.5

Q ss_pred             HHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           95 AIVQARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        95 ~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      .+-.++-..|+|.+|+|+.+|+|.++|..+..
T Consensus       194 ~vl~l~~~~g~s~~EIA~~lgis~~~V~~~~~  225 (239)
T 1rp3_A          194 LVIQLIFYEELPAKEVAKILETSVSRVSQLKA  225 (239)
T ss_dssp             HHHHHHHTSCCCHHHHHHHTTSCHHHHHHHHH
T ss_pred             HHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHH
Confidence            34445557899999999999999999998764

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

Probab=84.12  E-value=2.2  Score=29.68  Aligned_cols=32  Identities=6%  Similarity=-0.061  Sum_probs=26.0

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ...|..+....++|+.+||+.+|+++++|++.
T Consensus        52 ~~iL~~l~~~~~~t~~ela~~l~is~~tvs~~   83 (162)
T 2fa5_A           52 WRVITILALYPGSSASEVSDRTAMDKVAVSRA   83 (162)
T ss_dssp             HHHHHHHHHSTTCCHHHHHHHHTCCHHHHHHH
T ss_pred             HHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHH
Confidence            34455565667899999999999999998876

>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=84.09  E-value=0.97  Score=29.38  Aligned_cols=20  Identities=10%  Similarity=0.022  Sum_probs=19.0

Q ss_pred             cCHHHHHHHhCCCHHHHHHH
Q 031871          105 LTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~  124 (151)
                      +|+.+||+.+|+++++++++
T Consensus        31 ~t~~eLa~~l~i~~~tvs~~   50 (95)
T 2qvo_A           31 VYIQYIASKVNSPHSYVWLI   50 (95)
T ss_dssp             EEHHHHHHHSSSCHHHHHHH
T ss_pred             cCHHHHHHHHCcCHHHHHHH
Confidence            99999999999999998886

>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=84.01  E-value=1.5  Score=30.28  Aligned_cols=29  Identities=7%  Similarity=0.165  Sum_probs=23.8

Q ss_pred             HHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           96 IVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      |..+.....+|..+||+.+|+|++++++.
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            44555566799999999999999998874

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

Probab=84.00  E-value=1.5  Score=30.00  Aligned_cols=24  Identities=13%  Similarity=0.167  Sum_probs=21.1

Q ss_pred             hcCCcCHHHHHHHhCCCHHHHHHH
Q 031871          101 NDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus       101 ~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ...++|+.+||+.+|+++++|++.
T Consensus        28 ~~~~~s~~ela~~l~is~~tv~~~   51 (139)
T 2x4h_A           28 SGEGAKINRIAKDLKIAPSSVFEE   51 (139)
T ss_dssp             TTSCBCHHHHHHHHTCCHHHHHHH
T ss_pred             cCCCcCHHHHHHHhCCChHHHHHH
Confidence            356799999999999999998875

>3hh0_A Transcriptional regulator, MERR family; protein structure initiative II(PSI II), NYSGXRC, 11183J, structural genomics; 2.67A {Bacillus cereus atcc 14579}

Probab=83.78  E-value=1.6  Score=31.19  Aligned_cols=21  Identities=10%  Similarity=0.061  Sum_probs=18.5

Q ss_pred             HHHHHHHcCCChhhHHhhhcC
Q 031871           31 VVNAARRAGADIETVRKSHAG   51 (151)
Q Consensus        31 ~~~~a~r~g~~v~t~~k~~~g   51 (151)
                      .-+.|++.|+++.|++-|+.-
T Consensus         7 I~evA~~~Gvs~~tLR~ye~~   27 (146)
T 3hh0_A            7 ISEFASVGDVTVRALRYYDKI   27 (146)
T ss_dssp             HHHHHHHHTCCHHHHHHHHHT
T ss_pred             HHHHHHHHCcCHHHHHHHHHC
Confidence            456899999999999999974

>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=83.61  E-value=1.3  Score=30.10  Aligned_cols=31  Identities=16%  Similarity=0.216  Sum_probs=25.2

Q ss_pred             HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ..|..+...-++|+.+||+.+|++++++++.
T Consensus        33 ~iL~~l~~~~~~t~~~la~~l~~s~~~vs~~   63 (144)
T 1lj9_A           33 LYLVRVCENPGIIQEKIAELIKVDRTTAARA   63 (144)
T ss_dssp             HHHHHHHHSTTEEHHHHHHHHTCCHHHHHHH
T ss_pred             HHHHHHHHCcCcCHHHHHHHHCCCHhHHHHH
Confidence            3355555566899999999999999999886

>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=83.53  E-value=0.82  Score=32.89  Aligned_cols=23  Identities=9%  Similarity=0.309  Sum_probs=20.4

Q ss_pred             CcCHHHHHHHhCCCHHHHHHHHc
Q 031871          104 KLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus       104 glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      .+||.+||..+|+++.+|++.-+
T Consensus       164 ~~t~~~lA~~lg~sr~tvsR~l~  186 (207)
T 2oz6_A          164 KITRQEIGRIVGCSREMVGRVLK  186 (207)
T ss_dssp             ECCHHHHHHHHTSCHHHHHHHHH
T ss_pred             ccCHHHHHHHhCCCHHHHHHHHH
Confidence            48999999999999999998743

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

Probab=83.45  E-value=2.2  Score=30.95  Aligned_cols=31  Identities=19%  Similarity=0.277  Sum_probs=25.8

Q ss_pred             HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ..|..+.....+|..+||+.+|+|++++.+.
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            4456666677899999999999999998875

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

Probab=83.44  E-value=2.3  Score=29.03  Aligned_cols=32  Identities=13%  Similarity=0.039  Sum_probs=25.8

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ...|..+....++|+.+||+.+|++++++++.
T Consensus        45 ~~iL~~l~~~~~~t~~ela~~l~~~~~tvs~~   76 (150)
T 2rdp_A           45 FVALQWLLEEGDLTVGELSNKMYLACSTTTDL   76 (150)
T ss_dssp             HHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCCCchhHHHH
Confidence            34455555556899999999999999999886

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

Probab=83.33  E-value=1.8  Score=29.79  Aligned_cols=32  Identities=6%  Similarity=-0.049  Sum_probs=26.0

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ...|..+....++|+.+||+.+|+++++++++
T Consensus        44 ~~iL~~l~~~~~~t~~eLa~~l~~~~~tvs~~   75 (154)
T 2qww_A           44 LAMINVIYSTPGISVADLTKRLIITGSSAAAN   75 (154)
T ss_dssp             HHHHHHHHHSTTEEHHHHHHHHTCCHHHHHHH
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHH
Confidence            34455565667899999999999999998876

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

Probab=83.31  E-value=2.3  Score=29.33  Aligned_cols=34  Identities=3%  Similarity=0.027  Sum_probs=27.2

Q ss_pred             HHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           91 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        91 ~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      .-...|..+....++|+.+||+.+|+++++++++
T Consensus        48 ~~~~iL~~l~~~~~~t~~ela~~l~~s~~tvs~~   81 (153)
T 2pex_A           48 PQYLVMLVLWETDERSVSEIGERLYLDSATLTPL   81 (153)
T ss_dssp             HHHHHHHHHHHSCSEEHHHHHHHHTCCHHHHHHH
T ss_pred             HHHHHHHHHHhCCCcCHHHHHHHhCCCcccHHHH
Confidence            3344556666667899999999999999998876

>1r8d_A Transcription activator MTAN; protein-DNA complex, transcription/DNA complex; 2.70A {Bacillus subtilis} SCOP: a.6.1.3 PDB: 1jbg_A

Probab=83.28  E-value=2.1  Score=28.79  Aligned_cols=19  Identities=21%  Similarity=0.281  Sum_probs=17.2

Q ss_pred             HHHHHHcCCChhhHHhhhc
Q 031871           32 VNAARRAGADIETVRKSHA   50 (151)
Q Consensus        32 ~~~a~r~g~~v~t~~k~~~   50 (151)
                      -+.|+..|+++.|++.|+.
T Consensus         6 ~e~A~~~gvs~~tLR~ye~   24 (109)
T 1r8d_A            6 KQVAEISGVSIRTLHHYDN   24 (109)
T ss_dssp             HHHHHHHSCCHHHHHHHHH
T ss_pred             HHHHHHHCcCHHHHHHHHH
Confidence            4689999999999999976

>3gp4_A Transcriptional regulator, MERR family; structural genomics, DNA-BI transcription regulator, PSI-2; 1.85A {Listeria monocytogenes str}

Probab=83.18  E-value=0.88  Score=32.47  Aligned_cols=23  Identities=17%  Similarity=0.234  Sum_probs=21.5

Q ss_pred             CcCHHHHHHHhCCCHHHHHHHHc
Q 031871          104 KLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus       104 glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      .+|..|+|+.+|||+.||..||.
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            47899999999999999999987

>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=83.05  E-value=2.2  Score=28.88  Aligned_cols=32  Identities=6%  Similarity=0.049  Sum_probs=25.4

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ...|..+....++|+.+||+.+|++++++++.
T Consensus        36 ~~iL~~l~~~~~~~~~~la~~l~~s~~tvs~~   67 (145)
T 2a61_A           36 FDILQKIYFEGPKRPGELSVLLGVAKSTVTGL   67 (145)
T ss_dssp             HHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCCCchhHHHH
Confidence            33445555566899999999999999999876

>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=83.01  E-value=2  Score=29.44  Aligned_cols=33  Identities=18%  Similarity=0.106  Sum_probs=26.4

Q ss_pred             HHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           92 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        92 ~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      -...|..+...-++|+.+||+.+|++++++++.
T Consensus        42 ~~~iL~~l~~~~~~t~~ela~~l~~~~~~vs~~   74 (152)
T 3bj6_A           42 QRAILEGLSLTPGATAPQLGAALQMKRQYISRI   74 (152)
T ss_dssp             HHHHHHHHHHSTTEEHHHHHHHHTCCHHHHHHH
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHH
Confidence            344455565666899999999999999998876

>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=82.94  E-value=0.91  Score=32.71  Aligned_cols=23  Identities=13%  Similarity=0.309  Sum_probs=20.5

Q ss_pred             CcCHHHHHHHhCCCHHHHHHHHc
Q 031871          104 KLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus       104 glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      .+||.+||..+|+++.+|++.-+
T Consensus       167 ~~t~~~iA~~lg~sr~tvsR~l~  189 (210)
T 3ryp_A          167 KITRQEIGQIVGCSRETVGRILK  189 (210)
T ss_dssp             ECCHHHHHHHHTCCHHHHHHHHH
T ss_pred             ccCHHHHHHHhCCcHHHHHHHHH
Confidence            47999999999999999998753

>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=82.93  E-value=1.7  Score=28.76  Aligned_cols=23  Identities=4%  Similarity=0.089  Sum_probs=20.7

Q ss_pred             cCCcCHHHHHHHhCCCHHHHHHH
Q 031871          102 DKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus       102 ~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ..++|..+||+.+|+++++|++.
T Consensus        37 ~~~~~~~ela~~l~is~stvs~~   59 (106)
T 1r1u_A           37 VSEASVGHISHQLNLSQSNVSHQ   59 (106)
T ss_dssp             HCCBCHHHHHHHHTCCHHHHHHH
T ss_pred             hCCCCHHHHHHHHCcCHHHHHHH
Confidence            46789999999999999999885

>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=82.86  E-value=2.3  Score=28.87  Aligned_cols=31  Identities=16%  Similarity=-0.008  Sum_probs=25.4

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ...|..+. ..++|+.+||+.+|++++++++.
T Consensus        40 ~~iL~~l~-~~~~~~~ela~~l~~s~~tvs~~   70 (146)
T 2gxg_A           40 FLVLRATS-DGPKTMAYLANRYFVTQSAITAS   70 (146)
T ss_dssp             HHHHHHHT-TSCBCHHHHHHHTTCCHHHHHHH
T ss_pred             HHHHHHHh-cCCcCHHHHHHHhCCCchhHHHH
Confidence            44455566 77899999999999999998876

>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=82.81  E-value=1.7  Score=31.09  Aligned_cols=32  Identities=9%  Similarity=0.114  Sum_probs=26.6

Q ss_pred             HHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           95 AIVQARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        95 ~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      .+-.++-..|+|.+|+|+.+|+|.++|.....
T Consensus       147 ~vl~l~~~~g~s~~EIA~~lgis~~tV~~~l~  178 (194)
T 1or7_A          147 MAITLRELDGLSYEEIAAIMDCPVGTVRSRIF  178 (194)
T ss_dssp             HHHHHHHTTCCCHHHHHHHTTSCHHHHHHHHH
T ss_pred             HHhHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            34445667899999999999999999988754

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

Probab=82.78  E-value=2.7  Score=28.56  Aligned_cols=31  Identities=19%  Similarity=0.319  Sum_probs=24.2

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ...|..+...- +|+.+||+.+|++++++++.
T Consensus        41 ~~iL~~l~~~~-~t~~eLa~~l~~s~~tvs~~   71 (146)
T 3tgn_A           41 EHILMLLSEES-LTNSELARRLNVSQAAVTKA   71 (146)
T ss_dssp             HHHHHHHTTCC-CCHHHHHHHHTCCHHHHHHH
T ss_pred             HHHHHHHHhCC-CCHHHHHHHHCCCHHHHHHH
Confidence            33455555444 99999999999999999876

>2rnj_A Response regulator protein VRAR; HTH LUXR-type domain, DNA binding domain, activator, antibiotic resistance, cytoplasm, DNA-binding; NMR {Staphylococcus aureus}

Probab=82.70  E-value=0.74  Score=29.83  Aligned_cols=43  Identities=7%  Similarity=0.027  Sum_probs=29.5

Q ss_pred             cCCcCHHHHHHHhCCCHHHHHHHHcC----CCCCCHHHHHHHHHHhC
Q 031871          102 DKKLTQSQLAQLINEKPQVIQEYESG----KAIPNQQILTKLERALG  144 (151)
Q Consensus       102 ~~glTQ~eLA~~lgis~s~Is~~E~G----~~~p~~~~l~kLa~~Lg  144 (151)
                      ..|+|.+|+|+.+|+|.++|..+-..    -...+...+..++...|
T Consensus        42 ~~g~s~~eIA~~l~is~~tV~~~l~r~~~kL~~~~~~~l~~~a~~~g   88 (91)
T 2rnj_A           42 AKGYSNQEIASASHITIKTVKTHVSNILSKLEVQDRTQAVIYAFQHN   88 (91)
T ss_dssp             HTTCCTTHHHHHHTCCHHHHHHHHHHHHHHTTCCSSHHHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHcC
Confidence            57999999999999999999876431    12233444555555444

>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=82.70  E-value=2.1  Score=31.43  Aligned_cols=31  Identities=19%  Similarity=0.206  Sum_probs=23.8

Q ss_pred             HHHHHHHhc-CCcCHHHHHHHhCCCHHHHHHH
Q 031871           94 KAIVQARND-KKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        94 ~~Lk~~R~~-~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      .-|..++.. ..+|..+||+.+|+|++||.+.
T Consensus        25 ~Il~~L~~~~~~~s~~eLa~~l~vS~~Ti~rd   56 (187)
T 1j5y_A           25 SIVRILERSKEPVSGAQLAEELSVSRQVIVQD   56 (187)
T ss_dssp             HHHHHHHHCSSCBCHHHHHHHHTSCHHHHHHH
T ss_pred             HHHHHHHHcCCCcCHHHHHHHHCcCHHHHHHH
Confidence            334445544 3499999999999999999874

>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=82.68  E-value=1.7  Score=28.16  Aligned_cols=23  Identities=13%  Similarity=0.182  Sum_probs=20.8

Q ss_pred             cCCcCHHHHHHHhCCCHHHHHHH
Q 031871          102 DKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus       102 ~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ...+|..|||+.+|+|+++|++.
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            46799999999999999999985

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

Probab=82.67  E-value=1.7  Score=29.30  Aligned_cols=32  Identities=16%  Similarity=0.054  Sum_probs=25.7

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ...|..+....++|+.+||+.+|++++++++.
T Consensus        39 ~~iL~~l~~~~~~t~~ela~~l~~s~~~vs~~   70 (142)
T 2fbi_A           39 WRVIRILRQQGEMESYQLANQACILRPSMTGV   70 (142)
T ss_dssp             HHHHHHHHHHCSEEHHHHHHHTTCCHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCCCHhHHHHH
Confidence            34455555566899999999999999998876

>2jvl_A TRMBF1; coactivator, helix-turn-helix, Pro binding, transcription; NMR {Trichoderma reesei}

Probab=82.63  E-value=0.25  Score=33.25  Aligned_cols=28  Identities=18%  Similarity=0.207  Sum_probs=23.9

Q ss_pred             HHHHHHHHHcCCChhhHHhhhcCCCccC
Q 031871           29 EKVVNAARRAGADIETVRKSHAGTNKAA   56 (151)
Q Consensus        29 ~~~~~~a~r~g~~v~t~~k~~~g~~~~~   56 (151)
                      -++.+.|++.|++.+++.+||.|...|.
T Consensus        50 lsq~elA~~~gis~~~is~~E~G~~~p~   77 (107)
T 2jvl_A           50 MTQAELGKEIGETAATVASYERGTATPD   77 (107)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHTTTCSCCC
T ss_pred             CCHHHHHHHHCcCHHHHHHHHcCCCCCC
Confidence            3567799999999999999999987653

>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=82.57  E-value=1.5  Score=32.11  Aligned_cols=21  Identities=24%  Similarity=0.305  Sum_probs=19.3

Q ss_pred             CcCHHHHHHHhCCCHHHHHHH
Q 031871          104 KLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus       104 glTQ~eLA~~lgis~s~Is~~  124 (151)
                      .+||.+||..+|+++.+|++.
T Consensus       163 ~~t~~~lA~~lG~sr~tvsR~  183 (222)
T 1ft9_A          163 DFTVEEIANLIGSSRQTTSTA  183 (222)
T ss_dssp             CCCHHHHHHHHCSCHHHHHHH
T ss_pred             cCCHHHHHHHhCCcHHHHHHH
Confidence            389999999999999999976

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

Probab=82.51  E-value=2  Score=28.77  Aligned_cols=28  Identities=25%  Similarity=0.343  Sum_probs=22.5

Q ss_pred             HHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           96 IVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      |..+.. ..+|+.++|+.+|+++++|++.
T Consensus        38 l~~L~~-~~~s~~ela~~l~is~stvsr~   65 (119)
T 2lkp_A           38 LTQLRN-GPLPVTDLAEAIGMEQSAVSHQ   65 (119)
T ss_dssp             HHHHHH-CCCCHHHHHHHHSSCHHHHHHH
T ss_pred             HHHHHH-CCCCHHHHHHHHCcCHHHHHHH
Confidence            333433 5789999999999999999885

>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=82.50  E-value=1.8  Score=29.02  Aligned_cols=34  Identities=6%  Similarity=-0.028  Sum_probs=27.7

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      ...|..+....+..+.+.|+.+||+++++.+..+
T Consensus        60 r~~I~~aL~~~~gn~~~AA~~LGIsR~TL~rkLk   93 (98)
T 1eto_A           60 QPLLDMVMQYTLGNQTRAALMMGINRGTLRKKLK   93 (98)
T ss_dssp             HHHHHHHHHHTTTCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHH
Confidence            4456677777888999999999999999987643

>3dv8_A Transcriptional regulator, CRP/FNR family; cyclic nucleotide-binding domain, structural genomics, joint for structural genomics; 2.55A {Eubacterium rectale atcc 33656}

Probab=82.41  E-value=1.8  Score=31.35  Aligned_cols=22  Identities=23%  Similarity=0.357  Sum_probs=20.4

Q ss_pred             CcCHHHHHHHhCCCHHHHHHHH
Q 031871          104 KLTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus       104 glTQ~eLA~~lgis~s~Is~~E  125 (151)
                      .+||.+||..+|+++.+++++-
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            6899999999999999999874

>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=82.40  E-value=1.8  Score=35.27  Aligned_cols=32  Identities=13%  Similarity=0.109  Sum_probs=28.6

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ...|+.+|....+|..|||+.+|+|++||+++
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            44577888888999999999999999999986

>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=82.39  E-value=1.6  Score=30.68  Aligned_cols=35  Identities=20%  Similarity=0.134  Sum_probs=28.1

Q ss_pred             HHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           90 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        90 ~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ..-...|..+...-++|+.+||+.+|+++++++++
T Consensus        46 ~~q~~iL~~l~~~~~~t~~eLa~~l~~~~~tvs~~   80 (162)
T 3k0l_A           46 LPQFTALSVLAAKPNLSNAKLAERSFIKPQSANKI   80 (162)
T ss_dssp             HHHHHHHHHHHHCTTCCHHHHHHHHTSCGGGHHHH
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHH
Confidence            33445566666677999999999999999998876

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

Probab=82.39  E-value=2.2  Score=29.49  Aligned_cols=33  Identities=9%  Similarity=0.084  Sum_probs=26.7

Q ss_pred             HHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           92 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        92 ~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      -...|..+....++|+.+||+.+|++++++++.
T Consensus        45 ~~~iL~~l~~~~~~t~~ela~~l~i~~~tvs~~   77 (155)
T 3cdh_A           45 EWRVLACLVDNDAMMITRLAKLSLMEQSRMTRI   77 (155)
T ss_dssp             HHHHHHHHSSCSCBCHHHHHHHTTCCHHHHHHH
T ss_pred             HHHHHHHHHHCCCcCHHHHHHHHCCCHHHHHHH
Confidence            344556666667899999999999999998876

>3kxa_A NGO0477 protein, putative uncharacterized protein; NEW protein fold, OPPF, STRU genomics, oxford protein production facility; 2.80A {Neisseria gonorrhoeae}

Probab=82.28  E-value=0.21  Score=35.62  Aligned_cols=28  Identities=11%  Similarity=0.058  Sum_probs=23.7

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCccCC
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNKAAS   57 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~~~~   57 (151)
                      ++-+.|.+.|++.+++.+||.|...|..
T Consensus        83 Tq~elA~~lGis~s~is~~E~G~~~ps~  110 (141)
T 3kxa_A           83 TQSELATAAGLPQPYLSRIENSKQSLQD  110 (141)
T ss_dssp             CHHHHHHHTTCCHHHHHHHHHTCSCCCH
T ss_pred             CHHHHHHHHCcCHHHHHHHHcCCCCCCH
Confidence            5567999999999999999999876533

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

Probab=82.27  E-value=2.2  Score=30.49  Aligned_cols=31  Identities=16%  Similarity=0.133  Sum_probs=25.8

Q ss_pred             HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      .-|..+.....+|..+||+.+|+|++++.+-
T Consensus         7 ~il~~L~~~~~~s~~~la~~lg~s~~tv~~r   37 (162)
T 3i4p_A            7 KILRILQEDSTLAVADLAKKVGLSTTPCWRR   37 (162)
T ss_dssp             HHHHHHTTCSCSCHHHHHHHHTCCHHHHHHH
T ss_pred             HHHHHHHHCCCCCHHHHHHHHCcCHHHHHHH
Confidence            3466777778899999999999999988764

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

Probab=82.23  E-value=3.3  Score=27.16  Aligned_cols=26  Identities=12%  Similarity=0.149  Sum_probs=22.7

Q ss_pred             CCcCHHHHHHHhCCCHHHHHHHHcCC
Q 031871          103 KKLTQSQLAQLINEKPQVIQEYESGK  128 (151)
Q Consensus       103 ~glTQ~eLA~~lgis~s~Is~~E~G~  128 (151)
                      ..+|..+||+.+|+|++++++.-+..
T Consensus        19 ~~~~~~~lA~~~~~S~~~l~r~fk~~   44 (107)
T 2k9s_A           19 SNFDIASVAQHVCLSPSRLSHLFRQQ   44 (107)
T ss_dssp             SSCCHHHHHHHTTSCHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            56999999999999999999987643

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

Probab=82.15  E-value=1.4  Score=28.96  Aligned_cols=28  Identities=14%  Similarity=0.211  Sum_probs=22.9

Q ss_pred             HHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871           98 QARNDKKLTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus        98 ~~R~~~glTQ~eLA~~lgis~s~Is~~E  125 (151)
                      .+....+++..++|+.+|++++++++.-
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            3444567999999999999999998753

>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=82.14  E-value=1.1  Score=30.65  Aligned_cols=32  Identities=16%  Similarity=0.212  Sum_probs=26.1

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ...|..+....++|+.+||+.+++++++++++
T Consensus        39 ~~vL~~l~~~~~~t~~eLa~~l~~~~~tvs~~   70 (140)
T 3hsr_A           39 YIVLMAIENDEKLNIKKLGERVFLDSGTLTPL   70 (140)
T ss_dssp             HHHHHHSCTTCEEEHHHHHHHHTCCHHHHHHH
T ss_pred             HHHHHHHHHcCCcCHHHHHHHHCCChhhHHHH
Confidence            44455555567899999999999999999886

>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=82.12  E-value=0.22  Score=32.98  Aligned_cols=26  Identities=19%  Similarity=0.242  Sum_probs=22.7

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCcc
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNKA   55 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~~   55 (151)
                      +..+.|++.|++.+|+.+|++|...|
T Consensus        33 tq~~lA~~~gis~~~is~~e~g~~~~   58 (104)
T 3cec_A           33 NTANFAEILGVSNQTIQEVINGQRSI   58 (104)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHTTSSCC
T ss_pred             CHHHHHHHHCcCHHHHHHHHcCCcCC
Confidence            45678999999999999999998764

>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=82.07  E-value=2.9  Score=28.10  Aligned_cols=32  Identities=13%  Similarity=0.173  Sum_probs=25.7

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ...|..+....++|+.+||+.+|+++++++++
T Consensus        37 ~~iL~~l~~~~~~~~~~la~~l~~~~~tvs~~   68 (138)
T 1jgs_A           37 FKVLCSIRCAACITPVELKKVLSVDLGALTRM   68 (138)
T ss_dssp             HHHHHHHHHHSSBCHHHHHHHHTCCHHHHHHH
T ss_pred             HHHHHHHHhcCCCCHHHHHHHHCCChHHHHHH
Confidence            34455555567899999999999999999876

>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=81.99  E-value=1.3  Score=30.61  Aligned_cols=31  Identities=10%  Similarity=0.075  Sum_probs=25.9

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ...|..+ ...++|+.+||+.+|++++++++.
T Consensus        41 ~~iL~~l-~~~~~t~~eLa~~l~~~~~~vs~~   71 (151)
T 3kp7_A           41 SHVLNML-SIEALTVGQITEKQGVNKAAVSRR   71 (151)
T ss_dssp             HHHHHHH-HHSCBCHHHHHHHHCSCSSHHHHH
T ss_pred             HHHHHHH-HcCCcCHHHHHHHHCCCHHHHHHH
Confidence            4455666 778999999999999999998876

>1p4w_A RCSB; solution structure, DNA binding domain, DNA binding protein; NMR {Erwinia amylovora} SCOP: a.4.6.2

Probab=81.98  E-value=2.6  Score=28.05  Aligned_cols=43  Identities=12%  Similarity=0.201  Sum_probs=31.7

Q ss_pred             CCcCHHHHHHHhCCCHHHHHHHHcC----CCCCCHHHHHHHHHHhCC
Q 031871          103 KKLTQSQLAQLINEKPQVIQEYESG----KAIPNQQILTKLERALGV  145 (151)
Q Consensus       103 ~glTQ~eLA~~lgis~s~Is~~E~G----~~~p~~~~l~kLa~~Lgv  145 (151)
                      .|+|.+|+|+.+|+|..+|..+-..    -...+...+..++...|+
T Consensus        48 ~G~s~~EIA~~L~iS~~TV~~~l~ri~~KLgv~~r~elv~~a~~~gl   94 (99)
T 1p4w_A           48 EGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVDNDIALLNYLSSVSM   94 (99)
T ss_dssp             HTCCHHHHHHHHTSCHHHHHHHHHHHHHHHTCSSHHHHHHHHHHHTC
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHcCC
Confidence            6999999999999999998876542    133455566666666665

>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=81.97  E-value=0.19  Score=32.00  Aligned_cols=24  Identities=21%  Similarity=0.127  Sum_probs=21.9

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCC
Q 031871           30 KVVNAARRAGADIETVRKSHAGTN   53 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~   53 (151)
                      ++.+.|++.|++.+++.+|+.|..
T Consensus        33 sq~elA~~~gis~~~is~~e~g~~   56 (83)
T 2a6c_A           33 TQFKAAELLGVTQPRVSDLMRGKI   56 (83)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHTTCG
T ss_pred             CHHHHHHHHCcCHHHHHHHHcCCC
Confidence            567899999999999999999986

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

Probab=81.96  E-value=2.2  Score=29.66  Aligned_cols=32  Identities=9%  Similarity=0.081  Sum_probs=26.3

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ...|..+....++|+.+||+.+|+++++++++
T Consensus        55 ~~iL~~l~~~~~~t~~ela~~l~is~~tvs~~   86 (162)
T 3cjn_A           55 MRALAILSAKDGLPIGTLGIFAVVEQSTLSRA   86 (162)
T ss_dssp             HHHHHHHHHSCSEEHHHHHHHHTCCHHHHHHH
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHCCChhHHHHH
Confidence            44555666667899999999999999999886

>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=81.95  E-value=0.25  Score=36.22  Aligned_cols=43  Identities=9%  Similarity=0.061  Sum_probs=30.3

Q ss_pred             HHHHHHHHHcCCChhhHHhhhcCCCccCCCCcccccccccccc
Q 031871           29 EKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDT   71 (151)
Q Consensus        29 ~~~~~~a~r~g~~v~t~~k~~~g~~~~~~~~~~~~~~kl~~~~   71 (151)
                      -++.+.|++.|++.+++.+||+|...|..+.+.+.+..|+.+.
T Consensus        25 ltq~~lA~~~gis~~~is~~e~g~~~p~~~~l~~ia~~l~v~~   67 (192)
T 1y9q_A           25 LSLDATAQLTGVSKAMLGQIERGESSPTIATLWKIASGLEASF   67 (192)
T ss_dssp             CCHHHHHHHHSSCHHHHHHHHTTCSCCCHHHHHHHHHHHTCCS
T ss_pred             CCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCH
Confidence            3567899999999999999999987654433334444444443

>2p5t_A Putative transcriptional regulator PEZA; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=81.87  E-value=0.28  Score=35.17  Aligned_cols=47  Identities=15%  Similarity=0.209  Sum_probs=0.0

Q ss_pred             ccCHHHHHHHHHcCCChhhHHhhhcCCCccCCCCcccccccccccch
Q 031871           26 KKDEKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTE   72 (151)
Q Consensus        26 ~~~~~~~~~a~r~g~~v~t~~k~~~g~~~~~~~~~~~~~~kl~~~~~   72 (151)
                      .++-++.+.|++.|++.+|+.+|+.|...|......+....++.+..
T Consensus        12 ~~gltq~elA~~lgis~~~vs~~e~G~~~~~~~~~~~la~~~~v~~~   58 (158)
T 2p5t_A           12 THDLTQLEFARIVGISRNSLSRYENGTSSVSTELIDIICQKFNVSYV   58 (158)
T ss_dssp             -----------------------------------------------
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHHCcCHH
Confidence            34456678999999999999999999887655555555555555433

>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=81.73  E-value=3.4  Score=27.18  Aligned_cols=26  Identities=4%  Similarity=0.028  Sum_probs=22.9

Q ss_pred             CCcCHHHHHHHhCCCHHHHHHHHcCC
Q 031871          103 KKLTQSQLAQLINEKPQVIQEYESGK  128 (151)
Q Consensus       103 ~glTQ~eLA~~lgis~s~Is~~E~G~  128 (151)
                      ..+|..+||+.+|+|+.+++++-+..
T Consensus        20 ~~~~~~~lA~~~~~S~~~l~r~fk~~   45 (108)
T 3oou_A           20 EGMSLKTLGNDFHINAVYLGQLFQKE   45 (108)
T ss_dssp             SCCCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            37999999999999999999986644

>2eby_A Putative HTH-type transcriptional regulator YBAQ; hypothetical protein, JW0472, structural genomics, NPPSFA; 2.25A {Escherichia coli}

Probab=81.67  E-value=0.23  Score=33.29  Aligned_cols=27  Identities=15%  Similarity=0.055  Sum_probs=23.4

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCccC
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNKAA   56 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~~~   56 (151)
                      +....|++.|++.+|+.+|+.|...|.
T Consensus        26 sq~~lA~~~gis~~~is~~e~g~~~~~   52 (113)
T 2eby_A           26 KINELAELLHVHRNSVSALINNNRKLT   52 (113)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHTTSSCCC
T ss_pred             CHHHHHHHHCcCHHHHHHHHcCCCCCC
Confidence            567899999999999999999987653

>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=81.63  E-value=2.9  Score=25.17  Aligned_cols=32  Identities=13%  Similarity=0.054  Sum_probs=24.4

Q ss_pred             HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      ..|..+.... .++.+.|+.+|||++++.+..+
T Consensus        24 ~~I~~aL~~~-gn~~~aA~~LGIsr~tL~rklk   55 (61)
T 1g2h_A           24 QVLKLFYAEY-PSTRKLAQRLGVSHTAIANKLK   55 (61)
T ss_dssp             HHHHHHHHHS-CSHHHHHHHTTSCTHHHHHHHH
T ss_pred             HHHHHHHHHh-CCHHHHHHHhCCCHHHHHHHHH
Confidence            3455555555 5899999999999999987654

>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=81.57  E-value=2.4  Score=29.36  Aligned_cols=31  Identities=6%  Similarity=0.039  Sum_probs=25.1

Q ss_pred             HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ..|..+....++|+.+||+.+|++++++++.
T Consensus        48 ~iL~~l~~~~~~t~~ela~~l~is~~tvs~~   78 (154)
T 2eth_A           48 YAFLYVALFGPKKMKEIAEFLSTTKSNVTNV   78 (154)
T ss_dssp             HHHHHHHHHCCBCHHHHHHHTTSCHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCCCHHHHHHH
Confidence            3455555556899999999999999999886

>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=81.55  E-value=0.3  Score=35.76  Aligned_cols=42  Identities=17%  Similarity=0.069  Sum_probs=30.3

Q ss_pred             HHHHHHHHHcCCChhhHHhhhcCCC-ccCCCCccccccccccc
Q 031871           29 EKVVNAARRAGADIETVRKSHAGTN-KAASSSTSLNTRKLDED   70 (151)
Q Consensus        29 ~~~~~~a~r~g~~v~t~~k~~~g~~-~~~~~~~~~~~~kl~~~   70 (151)
                      -++.+.|++.|++.+++.+||+|.. .|....+.+.+..|+.+
T Consensus        24 ~s~~~la~~~gis~~~ls~~e~g~~~~p~~~~l~~ia~~l~~~   66 (198)
T 2bnm_A           24 MDHAALASLLGETPETVAAWENGEGGELTLTQLGRIAHVLGTS   66 (198)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHTTTCTTCBHHHHHHHHHHTTSC
T ss_pred             CCHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHHHHHhCCC
Confidence            3567899999999999999999988 66444344444444443

>2dg6_A Putative transcriptional regulator; winged-helix motif, MERR family, gene regulation; 2.20A {Streptomyces coelicolor}

Probab=81.48  E-value=2.6  Score=32.39  Aligned_cols=64  Identities=13%  Similarity=0.171  Sum_probs=37.4

Q ss_pred             HHHHHHcCCChhhHHhhhc-CCCccCCCCcccccccccccchhhhHHHHHhhccCCcchHHHHHHHHHHHhcCCcCHHHH
Q 031871           32 VNAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQL  110 (151)
Q Consensus        32 ~~~a~r~g~~v~t~~k~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~~~~~~~~~Lk~~R~~~glTQ~eL  110 (151)
                      -+.|++.|+++.|+|.|+. |-..|.... ...-+.-+.  +                ....-..|+.+|...|+|.+++
T Consensus         4 gevA~~~Gvs~~TLRyYE~~GLl~p~~R~-~~gyR~Y~~--~----------------dl~~L~~I~~lr~~~G~sL~eI   64 (222)
T 2dg6_A            4 ADLSKRSGVSTATIKYYLREGLLPPGRQV-NATTAEYDE--D----------------HLRRLRLVRALIQVGKVPVATA   64 (222)
T ss_dssp             HHHHHHHTCCHHHHHHHHHHTSSCCC----------CCH--H----------------HHHHHHHHHHHHHTTCCCHHHH
T ss_pred             HHHHHHHCcCHHHHHHHHHCCCCCCCeeC-CCCceeeCH--H----------------HHHHHHHHHHHHHcCCCCHHHH
Confidence            4689999999999999987 333321100 000011111  1                1233455777777779999988


Q ss_pred             HHHh
Q 031871          111 AQLI  114 (151)
Q Consensus       111 A~~l  114 (151)
                      .+.+
T Consensus        65 k~~l   68 (222)
T 2dg6_A           65 REVL   68 (222)
T ss_dssp             HHHH
T ss_pred             HHHH
Confidence            8766

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

Probab=81.28  E-value=1.8  Score=28.53  Aligned_cols=24  Identities=21%  Similarity=0.159  Sum_probs=21.3

Q ss_pred             hcCCcCHHHHHHHhCCCHHHHHHH
Q 031871          101 NDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus       101 ~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ....+|..+||+.+|+++++|++.
T Consensus        31 ~~~~~~~~ela~~l~is~~tv~~~   54 (114)
T 2oqg_A           31 GRADQSASSLATRLPVSRQAIAKH   54 (114)
T ss_dssp             HHSCBCHHHHHHHSSSCHHHHHHH
T ss_pred             HcCCCCHHHHHHHHCcCHHHHHHH
Confidence            456799999999999999999885

>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=81.25  E-value=1.1  Score=32.70  Aligned_cols=22  Identities=14%  Similarity=0.244  Sum_probs=20.2

Q ss_pred             CCcCHHHHHHHhCCCHHHHHHH
Q 031871          103 KKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus       103 ~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ..+||.+||..+|+++.++++.
T Consensus       166 ~~~t~~~lA~~lg~sr~tvsR~  187 (220)
T 2fmy_A          166 LGLNTEEIALMLGTTRQTVSVL  187 (220)
T ss_dssp             CSSCHHHHHHHHTSCHHHHHHH
T ss_pred             ccCCHHHHHHHhCCcHHHHHHH
Confidence            4689999999999999999986

>1b4a_A Arginine repressor; helix turn helix; 2.50A {Geobacillus stearothermophilus} SCOP: a.4.5.3 d.74.2.1 PDB: 1f9n_A

Probab=81.20  E-value=2.2  Score=30.88  Aligned_cols=33  Identities=15%  Similarity=0.106  Sum_probs=26.9

Q ss_pred             HHHHHH-HhcCCcCHHHHHHHh-----CCCHHHHHHHHc
Q 031871           94 KAIVQA-RNDKKLTQSQLAQLI-----NEKPQVIQEYES  126 (151)
Q Consensus        94 ~~Lk~~-R~~~glTQ~eLA~~l-----gis~s~Is~~E~  126 (151)
                      ..|+++ ....-.||.||++.+     ++|++||++.-+
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            445555 566778999999999     999999999865

>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=81.15  E-value=1.1  Score=32.83  Aligned_cols=23  Identities=4%  Similarity=0.034  Sum_probs=20.6

Q ss_pred             CCcCHHHHHHHhCCCHHHHHHHH
Q 031871          103 KKLTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus       103 ~glTQ~eLA~~lgis~s~Is~~E  125 (151)
                      ..+||.+||..+|+++.+|++.-
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            45899999999999999999973

>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=80.92  E-value=1.1  Score=32.72  Aligned_cols=22  Identities=27%  Similarity=0.475  Sum_probs=19.9

Q ss_pred             CCcCHHHHHHHhCCCHHHHHHH
Q 031871          103 KKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus       103 ~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ..+||.+||..+|+++.+|++.
T Consensus       176 ~~~t~~~lA~~lg~sr~tvsR~  197 (227)
T 3d0s_A          176 HDLTQEEIAQLVGASRETVNKA  197 (227)
T ss_dssp             CCCCHHHHHHHHTSCHHHHHHH
T ss_pred             CCCCHHHHHHHhCCcHHHHHHH
Confidence            3589999999999999999986

>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=80.84  E-value=1.9  Score=31.76  Aligned_cols=35  Identities=9%  Similarity=-0.023  Sum_probs=26.3

Q ss_pred             HHHHHHHHHHHhcCC--cCHHHHHHHhCCCHHHHHHH
Q 031871           90 SELKKAIVQARNDKK--LTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        90 ~~~~~~Lk~~R~~~g--lTQ~eLA~~lgis~s~Is~~  124 (151)
                      ..+-+.|.+...+.|  .|+.|||+.+|++.+++.+.
T Consensus         8 ~~il~~I~~~~~~~g~~~s~~eia~~lgl~~~tv~~~   44 (196)
T 3k2z_A            8 RKVLLFIEEFIEKNGYPPSVREIARRFRITPRGALLH   44 (196)
T ss_dssp             HHHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCCCHHHHHHHcCCCcHHHHHH
Confidence            345556666555554  89999999999999888774

>4ev0_A Transcription regulator, CRP family; CAMP binding, winged helix-turn-helix motif, DNA binding, transcription activator; HET: CMP; 2.40A {Thermus thermophilus}

Probab=80.84  E-value=1.2  Score=32.25  Aligned_cols=41  Identities=15%  Similarity=0.287  Sum_probs=29.8

Q ss_pred             CCcCHHHHHHHhCCCHHHHHHHHc-----C-------C-CCCCHHHHHHHHHHh
Q 031871          103 KKLTQSQLAQLINEKPQVIQEYES-----G-------K-AIPNQQILTKLERAL  143 (151)
Q Consensus       103 ~glTQ~eLA~~lgis~s~Is~~E~-----G-------~-~~p~~~~l~kLa~~L  143 (151)
                      ..+||.++|..+|+++.+|++.-+     |       + ..++.+.|.+++..|
T Consensus       162 ~~~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~~~~~~i~i~d~~~L~~~a~~l  215 (216)
T 4ev0_A          162 FQIRHHELAALAGTSRETVSRVLHALAEEGVVRLGPGTVEVREAALLEEIAFGL  215 (216)
T ss_dssp             EECCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEETTEEEESCHHHHHHHHTTC
T ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEecCCEEEEeCHHHHHHHhhcc
Confidence            357999999999999999998732     2       1 234667777776543

>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=80.81  E-value=3.2  Score=30.88  Aligned_cols=24  Identities=17%  Similarity=0.237  Sum_probs=21.2

Q ss_pred             CCcCHHHHHHHhCCCHHHHHHHHc
Q 031871          103 KKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus       103 ~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      ..+||.+||..+|+++.+|+++-+
T Consensus       192 ~~lt~~~lA~~lG~sr~tvsR~l~  215 (243)
T 3la7_A          192 LKLSHQAIAEAIGSTRVTVTRLLG  215 (243)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             ccCCHHHHHHHHCCcHHHHHHHHH
Confidence            468999999999999999998743

>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=80.81  E-value=2.1  Score=35.35  Aligned_cols=33  Identities=9%  Similarity=0.107  Sum_probs=28.8

Q ss_pred             HHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           92 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        92 ~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ....|+.+|....+|..|||+.+|+|++||+++
T Consensus        41 ~~~il~~l~~~~~~sr~ela~~~gls~~tv~~~   73 (429)
T 1z05_A           41 AGRVYKLIDQKGPISRIDLSKESELAPASITKI   73 (429)
T ss_dssp             HHHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHH
T ss_pred             HHHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHH
Confidence            344577788888999999999999999999986

>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=80.75  E-value=2.6  Score=30.56  Aligned_cols=32  Identities=13%  Similarity=0.196  Sum_probs=25.8

Q ss_pred             HHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcC
Q 031871           95 AIVQARNDKKLTQSQLAQLINEKPQVIQEYESG  127 (151)
Q Consensus        95 ~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G  127 (151)
                      .|.++. ..|+|..++|+.+|++++||.++.+.
T Consensus       150 ~i~~~~-~~G~s~~~Ia~~l~is~~tv~r~l~~  181 (183)
T 1gdt_A          150 AVLNMW-QQGLGASHISKTMNIARSTVYKVINE  181 (183)
T ss_dssp             HHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHHS
T ss_pred             HHHHHH-HCCCCHHHHHHHHCcCHHHHHHHHhh
Confidence            344444 36899999999999999999998764

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

Probab=80.67  E-value=2.4  Score=29.97  Aligned_cols=32  Identities=19%  Similarity=0.292  Sum_probs=25.5

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ...|..+...-++|+.+||+.+|++++++++.
T Consensus        48 ~~iL~~L~~~~~~t~~eLa~~l~is~~tvs~~   79 (168)
T 2nyx_A           48 FRTLVILSNHGPINLATLATLLGVQPSATGRM   79 (168)
T ss_dssp             HHHHHHHHHHCSEEHHHHHHHHTSCHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHH
Confidence            34455555556899999999999999999886

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

Probab=80.62  E-value=1.4  Score=28.56  Aligned_cols=22  Identities=9%  Similarity=0.220  Sum_probs=20.3

Q ss_pred             CCcCHHHHHHHhCCCHHHHHHH
Q 031871          103 KKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus       103 ~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ..+|..|||+.+|+|++++++.
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            6799999999999999999875

>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=80.62  E-value=3.4  Score=30.65  Aligned_cols=36  Identities=14%  Similarity=0.218  Sum_probs=27.9

Q ss_pred             HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCC
Q 031871           94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAI  130 (151)
Q Consensus        94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~  130 (151)
                      ..|.++.. .|+|..++|+.+|++++|+.++.+....
T Consensus       166 ~~i~~~~~-~G~s~~~Ia~~l~is~~tv~r~l~~~~~  201 (209)
T 2r0q_C          166 HRVVEMLE-EGQAISKIAKEVNITRQTVYRIKHDNGL  201 (209)
T ss_dssp             HHHHHHHH-TTCCHHHHHHHHTCCHHHHHHHHTTCC-
T ss_pred             HHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHhcccc
Confidence            34444443 6999999999999999999999876543

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

Probab=80.61  E-value=2  Score=28.69  Aligned_cols=23  Identities=4%  Similarity=-0.052  Sum_probs=20.8

Q ss_pred             cCCcCHHHHHHHhCCCHHHHHHH
Q 031871          102 DKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus       102 ~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ...+|..|||+.+|+++++|++.
T Consensus        36 ~~~~s~~eLa~~lgis~stvs~~   58 (108)
T 2kko_A           36 QGERAVEAIATATGMNLTTASAN   58 (108)
T ss_dssp             TCCEEHHHHHHHHTCCHHHHHHH
T ss_pred             cCCcCHHHHHHHHCcCHHHHHHH
Confidence            36789999999999999999886

>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=80.60  E-value=1.5  Score=35.64  Aligned_cols=28  Identities=11%  Similarity=0.190  Sum_probs=25.5

Q ss_pred             HHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           96 IVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      |+.+| ...+|..|||+.+|+|++||+++
T Consensus        26 l~~l~-~~~~sr~~la~~~gls~~tv~~~   53 (380)
T 2hoe_A           26 LKRIM-KSPVSRVELAEELGLTKTTVGEI   53 (380)
T ss_dssp             HHHHH-HSCBCHHHHHHHHTCCHHHHHHH
T ss_pred             HHHHH-cCCcCHHHHHHHHCcCHHHHHHH
Confidence            66778 78899999999999999999986

>3trb_A Virulence-associated protein I; mobIle and extrachromosomal element functions, DNA binding P; 2.00A {Coxiella burnetii}

Probab=80.56  E-value=0.27  Score=33.28  Aligned_cols=27  Identities=11%  Similarity=0.092  Sum_probs=23.4

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCccC
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNKAA   56 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~~~   56 (151)
                      ++.+.|.+.|++.+|+.+|++|+..+.
T Consensus        29 tq~eLA~~lGis~~~is~ie~G~~~~s   55 (104)
T 3trb_A           29 SANQLAKHLAIPTNRVTAILNGARSIT   55 (104)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHTTSSCCC
T ss_pred             CHHHHHHHHCcCHHHHHHHHcCCCCCC
Confidence            467789999999999999999987653

>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=80.55  E-value=1.5  Score=28.32  Aligned_cols=31  Identities=3%  Similarity=0.021  Sum_probs=24.9

Q ss_pred             HHHHHHHhcCCcCHHHH----HHHhCCCHHHHHHH
Q 031871           94 KAIVQARNDKKLTQSQL----AQLINEKPQVIQEY  124 (151)
Q Consensus        94 ~~Lk~~R~~~glTQ~eL----A~~lgis~s~Is~~  124 (151)
                      ..|..+....++|+.+|    |+.+|++++++++.
T Consensus        12 ~iL~~l~~~~~~~~~el~~~la~~l~is~~tvs~~   46 (99)
T 1tbx_A           12 IVLAYLYDNEGIATYDLYKKVNAEFPMSTATFYDA   46 (99)
T ss_dssp             HHHHHHTTCTTCBHHHHHHHHHTTSCCCHHHHHHH
T ss_pred             HHHHHHHHcCCcCHHHHHHHHHHHcCCCHHHHHHH
Confidence            34555555678999999    89999999998875

>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=80.51  E-value=2.6  Score=31.43  Aligned_cols=23  Identities=9%  Similarity=0.147  Sum_probs=20.6

Q ss_pred             CCcCHHHHHHHhCCCHHHHHHHH
Q 031871          103 KKLTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus       103 ~glTQ~eLA~~lgis~s~Is~~E  125 (151)
                      ..+||.+||..+|+++.+|++.-
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            46899999999999999999873

>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=80.28  E-value=1.5  Score=29.83  Aligned_cols=32  Identities=9%  Similarity=0.087  Sum_probs=25.6

Q ss_pred             HHHHHHHHhc--CCcCHHHHHHHhCCCHHHHHHH
Q 031871           93 KKAIVQARND--KKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        93 ~~~Lk~~R~~--~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ...|..+...  .++|+.+||+.++++++++++.
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  7899999999999999998876

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

Probab=80.27  E-value=2.9  Score=29.15  Aligned_cols=35  Identities=11%  Similarity=0.154  Sum_probs=25.5

Q ss_pred             HHHHHHHHHH-HhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           90 SELKKAIVQA-RNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        90 ~~~~~~Lk~~-R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ..+...|..+ ....++|+.+||+.+|+|+++|++.
T Consensus        39 ~~~~~~i~~~l~~~~~~~~~~la~~l~vs~~tvs~~   74 (155)
T 2h09_A           39 DDYVELISDLIREVGEARQVDMAARLGVSQPTVAKM   74 (155)
T ss_dssp             HHHHHHHHHHHHHHSCCCHHHHHHHHTSCHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCcCHHHHHHHhCcCHHHHHHH
Confidence            3344444433 3446799999999999999998876

>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=80.21  E-value=1.7  Score=27.05  Aligned_cols=23  Identities=17%  Similarity=0.203  Sum_probs=20.3

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCC
Q 031871           30 KVVNAARRAGADIETVRKSHAGT   52 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~   52 (151)
                      ++-+.|+++|++..|+.++.+|.
T Consensus        11 t~~diA~~aGVS~sTVSr~ln~~   33 (67)
T 2l8n_A           11 TMKDVALKAKVSTATVSRALMNP   33 (67)
T ss_dssp             CHHHHHHHTTCCHHHHHHTTTCC
T ss_pred             CHHHHHHHHCCCHHHHHHHHcCC
Confidence            46789999999999999998774

>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=80.17  E-value=2  Score=29.60  Aligned_cols=32  Identities=16%  Similarity=0.245  Sum_probs=25.3

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ...|..+....++|+.+||+.+|+++++|++.
T Consensus        40 ~~iL~~l~~~~~~t~~ela~~l~~s~~tvs~~   71 (155)
T 1s3j_A           40 LFVLASLKKHGSLKVSEIAERMEVKPSAVTLM   71 (155)
T ss_dssp             HHHHHHHHHHSEEEHHHHHHHHTSCHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHH
Confidence            33445555556899999999999999999876

---

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	151
d1y7ya1	69	a.35.1.3 (A:5-73) Restriction-modification control	2e-10
d1x57a1	78	a.35.1.12 (A:8-85) Endothelial differentiation-rel	8e-10
d2b5aa1	77	a.35.1.3 (A:1-77) Regulatory protein C.BclI {Bacil	3e-09
d1y9qa1	79	a.35.1.8 (A:4-82) Probable transcriptional regulat	2e-08
d1utxa_	66	a.35.1.3 (A:) Putative transcription regulator Cyl	4e-08
d2r1jl1	66	a.35.1.2 (L:3-68) P22 C2 repressor, DNA-binding do	2e-07
d1b0na2	68	a.35.1.3 (A:1-68) SinR repressor, DNA-binding doma	1e-06
d2croa_	65	a.35.1.2 (A:) cro 434 {Bacteriophage 434 [TaxId: 1	7e-06
d1lmb3_	87	a.35.1.2 (3:) lambda C1 repressor, DNA-binding dom	3e-05
d1r69a_	63	a.35.1.2 (A:) 434 C1 repressor, DNA-binding domain	5e-05
d2ppxa1	62	a.35.1.3 (A:30-91) Uncharacterized protein Atu1735	9e-05
d2icta1	87	a.35.1.3 (A:8-94) Antitoxin HigA {Escherichia coli	3e-04
d2auwa1	67	a.35.1.10 (A:88-154) Hypothetical protein NE0471 C	0.004

>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 = 51.3 bits (123), Expect = 2e-10
 Identities = 13/57 (22%), Positives = 24/57 (42%)

Query: 91  ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 147
           +  + + + R  K L+Q  LA L       +   E G+   +   + KL  AL ++ 
Sbjct: 9   KFGQRLRELRTAKGLSQETLAFLSGLDRSYVGGVERGQRNVSLVNILKLATALDIEP 65

>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 = 50.0 bits (119), Expect = 8e-10
 Identities = 42/65 (64%), Positives = 49/65 (75%)

Query: 86  DRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGV 145
           DRV  E+ K I Q R  K LTQ  LA  INEKPQVI +YESG+AIPN Q+L K+ERA+G+
Sbjct: 1   DRVTLEVGKVIQQGRQSKGLTQKDLATKINEKPQVIADYESGRAIPNNQVLGKIERAIGL 60

Query: 146 KLRGK 150
           KLRGK
Sbjct: 61  KLRGK 65

>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 = 48.7 bits (116), Expect = 3e-09
 Identities = 13/57 (22%), Positives = 24/57 (42%)

Query: 91  ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 147
           +  + + + R  K ++Q +LA L       I E E G    +   + K+  AL +  
Sbjct: 10  KFGRTLKKIRTQKGVSQEELADLAGLHRTYISEVERGDRNISLINIHKICAALDIPA 66

>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 = 46.5 bits (110), Expect = 2e-08
 Identities = 14/64 (21%), Positives = 25/64 (39%)

Query: 84  TDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERAL 143
           TD    S++   +   R  + L+    AQL      ++ + E G++ P    L K+   L
Sbjct: 1   TDVMFKSQIANQLKNLRKSRGLSLDATAQLTGVSKAMLGQIERGESSPTIATLWKIASGL 60

Query: 144 GVKL 147
               
Sbjct: 61  EASF 64

>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 = 45.6 bits (108), Expect = 4e-08
 Identities = 17/56 (30%), Positives = 26/56 (46%)

Query: 92  LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 147
           +   +   R  KK++QS+LA L+    Q I   E  K  P+ Q+  K+   L   L
Sbjct: 2   IINNLKLIREKKKISQSELAALLEVSRQTINGIEKNKYNPSLQLALKIAYYLNTPL 57

>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 = 43.3 bits (102), Expect = 2e-07
 Identities = 13/56 (23%), Positives = 25/56 (44%)

Query: 92  LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 147
           + + I   R   K+ Q+ L +++      I ++E  +  PN + L  L +AL    
Sbjct: 4   MGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCSP 59

>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 = 41.6 bits (98), Expect = 1e-06
 Identities = 14/57 (24%), Positives = 25/57 (43%), Gaps = 1/57 (1%)

Query: 92  LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESG-KAIPNQQILTKLERALGVKL 147
           + + I Q R +K  + S+LA+        +   E   +  P+ Q L K+   L V +
Sbjct: 2   IGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNLQTNPSIQFLEKVSAVLDVSV 58

>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 = 39.4 bits (92), Expect = 7e-06
 Identities = 15/58 (25%), Positives = 26/58 (44%), Gaps = 1/58 (1%)

Query: 90  SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 147
             L + + + R   K+TQ++LA     K Q IQ  E+G     + +  ++  AL    
Sbjct: 2   QTLSERLKKRRIALKMTQTELATKAGVKQQSIQLIEAGVTKRPRFLF-EIAMALNCDP 58

>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 = 38.5 bits (89), Expect = 3e-05
 Identities = 11/56 (19%), Positives = 21/56 (37%)

Query: 92  LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 147
           LK    + +N+  L+Q  +A  +      +    +G    N      L + L V +
Sbjct: 13  LKAIYEKKKNELGLSQESVADKMGMGQSGVGALFNGINALNAYNAALLAKILKVSV 68

>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 = 37.2 bits (86), Expect = 5e-05
 Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 1/56 (1%)

Query: 92  LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 147
           +   +   R    L Q++LAQ +    Q I++ E+GK     + L +L  ALGV +
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 = 36.3 bits (84), Expect = 9e-05
 Identities = 11/44 (25%), Positives = 21/44 (47%)

Query: 96  IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKL 139
           I   R   KLTQ + +   +     ++++E G++ P+Q     L
Sbjct: 4   IKIIRRALKLTQEEFSARYHIPLGTLRDWEQGRSEPDQPARAYL 47

>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 = 35.3 bits (81), Expect = 3e-04
 Identities = 9/50 (18%), Positives = 22/50 (44%)

Query: 96  IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGV 145
           I ++ ++  ++  + A+ +   P       +GKA    ++  KL   +G 
Sbjct: 6   IQESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVIGS 55

>d2auwa1 a.35.1.10 (A:88-154) Hypothetical protein NE0471 C-terminal domain {Nitrosomonas europaea [TaxId: 915]} Length = 67

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]

 Score = 32.0 bits (73), Expect = 0.004
 Identities = 6/37 (16%), Positives = 15/37 (40%), Gaps = 1/37 (2%)

Query: 96  IVQARNDKKLTQSQLAQLINEKPQVIQEYESG-KAIP 131
                +   L+ +  A+ +    +++  Y +  K IP
Sbjct: 6   FGDWMHRNNLSLTTAAEALGISRRMVSYYRTAHKIIP 42

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	151
d1x57a1	78	Endothelial differentiation-related factor 1, EDF1	99.7
d1y7ya1	69	Restriction-modification controller protein C.AhdI	99.68
d2b5aa1	77	Regulatory protein C.BclI {Bacillus caldolyticus [	99.62
d1y9qa1	79	Probable transcriptional regulator VC1968, N-termi	99.61
d2r1jl1	66	P22 C2 repressor, DNA-binding domain {Salmonella b	99.61
d2croa_	65	cro 434 {Bacteriophage 434 [TaxId: 10712]}	99.6
d1b0na2	68	SinR repressor, DNA-binding domain {Bacillus subti	99.6
d1utxa_	66	Putative transcription regulator CylR2 {Enterococc	99.58
d1r69a_	63	434 C1 repressor, DNA-binding domain {Bacteriophag	99.58
d2a6ca1	69	HTH-motif protein NE1354 {Nitrosomonas europaea [T	99.58
d2icta1	87	Antitoxin HigA {Escherichia coli [TaxId: 562]}	99.54
d1lmb3_	87	lambda C1 repressor, DNA-binding domain {Bacteriop	99.54
d2o38a1	89	Hypothetical protein RPA3824 {Rhodopseudomonas pal	99.49
d2ofya1	82	Putative transcriptional regulator RHA1_ro04071 {R	99.48
d2ppxa1	62	Uncharacterized protein Atu1735 {Agrobacterium tum	99.35
d2auwa1	67	Hypothetical protein NE0471 C-terminal domain {Nit	99.18
d2bnma1	71	Hydroxypropylphosphonic acid epoxidase Fom4, N-ter	98.41
d1dwka1	86	Cyanase N-terminal domain {Escherichia coli [TaxId	97.83
d2hsga1	57	Glucose-resistance amylase regulator CcpA, N-termi	97.6
d1efaa1	59	Lac repressor (LacR), N-terminal domain {Escherich	97.49
d1qpza1	57	Purine repressor (PurR), N-terminal domain {Escher	97.38
d1k78a1	63	Pax-5 {Human (Homo sapiens) [TaxId: 9606]}	97.22
d1e3oc2	75	Oct-1 {Human (Homo sapiens) [TaxId: 9606]}	97.2
d1uxda_	59	Fructose repressor (FruR), N-terminal domain {Esch	97.14
d1ic8a2	94	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Human (H	97.12
d1au7a2	72	Pit-1 {Rat (Rattus norvegicus) [TaxId: 10116]}	97.03
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	96.69
d2awia1	65	PrgX {Enterococcus faecalis [TaxId: 1351]}	96.61
d1nera_	74	Ner {Bacteriophage mu [TaxId: 10677]}	95.88
d1pdnc_	123	Paired protein (prd) {Fruit fly (Drosophila melano	95.85
d1vz0a1	93	Putative partitioning protein ParB/Spo0J {Thermus	95.69
d2jn6a1	89	Uncharacterized protein Cgl2762 {Corynebacterium g	95.54
d1hlva1	66	DNA-binding domain of centromere binding protein B	95.23
d2o4aa1	83	DNA-binding protein SATB1 {Human (Homo sapiens) [T	95.09
d2ppxa1	62	Uncharacterized protein Atu1735 {Agrobacterium tum	94.82
d2csfa1	88	DNA-binding protein SATB2 {Human (Homo sapiens) [T	94.79
d1gdta1	43	gamma,delta resolvase (C-terminal domain) {Escheri	94.72
d1r71a_	114	Transcriptional repressor protein KorB DNA-binding	94.59
d1z6ra1	70	Mlc protein N-terminal domain {Escherichia coli [T	94.58
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	94.57
d1i5za1	69	Catabolite gene activator protein (CAP), C-termina	94.41
d1s4ka_	120	Putative cytoplasmic protein YdiL {Salmonella typh	94.36
d1y7ya1	69	Restriction-modification controller protein C.AhdI	94.15
d1x2la1	87	Homeobox protein Cux-2, CUTL2 {Human (Homo sapiens	94.1
d1r69a_	63	434 C1 repressor, DNA-binding domain {Bacteriophag	93.84
d1s7ea2	80	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	93.54
d2croa_	65	cro 434 {Bacteriophage 434 [TaxId: 10712]}	93.52
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	93.51
d1jhga_	101	Trp repressor, TrpR {Escherichia coli [TaxId: 562]	93.41
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	93.27
d1wh6a_	101	Homeobox protein Cux-2, CUTL2 {Human (Homo sapiens	93.27
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	93.08
d1wh8a_	111	Homeobox protein Cux-2, CUTL2 {Human (Homo sapiens	93.05
d2r1jl1	66	P22 C2 repressor, DNA-binding domain {Salmonella b	93.01
d2ox6a1	162	Hypothetical protein SO3848 {Shewanella oneidensis	92.95
d1utxa_	66	Putative transcription regulator CylR2 {Enterococc	92.84
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	92.7
d2hoea1	62	N-acetylglucosamine kinase {Thermotoga maritima [T	92.59
d2ofya1	82	Putative transcriptional regulator RHA1_ro04071 {R	92.56
d2b5aa1	77	Regulatory protein C.BclI {Bacillus caldolyticus [	92.1
d3e5ua1	80	Chlorophenol reduction protein CprK {Desulfitobact	92.01
d2gaua1	81	Transcriptional regulator PG0396, C-terminal domai	91.89
d1lmb3_	87	lambda C1 repressor, DNA-binding domain {Bacteriop	91.81
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	91.63
d1zyba1	73	Probable transcription regulator BT4300, C-termina	91.54
d1ft9a1	80	CO-sensing protein CooA, C-terminal domain {Rhodos	91.36
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	91.05
d1or7a1	68	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	90.96
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	90.95
d1b0na2	68	SinR repressor, DNA-binding domain {Bacillus subti	90.85
d3ctaa1	85	Ta1064 (RFK), N-terminal domain {Thermoplasma acid	90.66
d1umqa_	60	Photosynthetic apparatus regulatory protein PprA (	90.57
d2ao9a1	120	Phage protein BC1890 {Bacillus cereus [TaxId: 1396	90.3
d2zcwa1	82	Transcriptional regulator TTHA1359, C-terminal dom	90.25
d1nr3a_	122	DNA-binding protein Tfx {Archaeon Methanobacterium	90.03
d1x57a1	78	Endothelial differentiation-related factor 1, EDF1	89.59
d1y9qa1	79	Probable transcriptional regulator VC1968, N-termi	89.4
d1rzsa_	61	cro p22 {Bacteriophage p22 [TaxId: 10754]}	89.23
d2bgca1	100	Listeriolysin regulatory protein PrfA, C-terminal	89.07
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	88.71
d1r8ea1	118	Transcription activator BmrR {Bacillus subtilis [T	88.54
d1q06a_	127	Transcriptional regulator CueR {Escherichia coli [	88.22
d1ku3a_	61	Sigma70 (SigA, RpoD) {Thermus aquaticus [TaxId: 27	88.2
d1j9ia_	68	Terminase gpNU1 subunit domain {Bacteriophage lamb	88.13
d1s7oa_	106	Hypothetical protein SPy1201 {Streptococcus pyogen	87.95
d1a04a1	67	Nitrate/nitrite response regulator (NarL) {Escheri	87.72
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	87.71
d1lnwa_	141	MexR repressor {Pseudomonas aeruginosa [TaxId: 287	87.35
d2o3fa1	83	Putative transcriptional regulator YbbH {Bacillus	87.31
d1r8da_	109	Multidrug transporter activator MtaN {Bacillus sub	86.77
d1r8da_	109	Multidrug transporter activator MtaN {Bacillus sub	86.67
d1etxa_	89	FIS protein {Escherichia coli [TaxId: 562]}	86.46
d1v7ba1	74	Transcriptional regulator Cgl2612 {Corynebacterium	86.22
d1xsva_	106	Hypothetical protein SAV1236 {Staphylococcus aureu	85.92
d2a61a1	139	Transcriptional regulator TM0710 {Thermotoga marit	85.59
d2p7vb1	68	Sigma70 (SigA, RpoD) {Escherichia coli [TaxId: 562	85.59
d1fsea_	67	Germination protein GerE {Bacillus subtilis [TaxId	85.43
d2i10a1	69	Putative transcriptional regulator RHA1_ro09068 {R	84.91
d1p4wa_	87	Transcriptional regulator RcsB {Erwinia amylovora	84.75
d1d1la_	61	cro lambda repressor {Bacteriophage lambda [TaxId:	84.64
d2icta1	87	Antitoxin HigA {Escherichia coli [TaxId: 562]}	84.33
d2ev0a1	61	Manganese transport regulator MntR {Bacillus subti	84.22
d2auwa1	67	Hypothetical protein NE0471 C-terminal domain {Nit	84.11
d1l3la1	65	Quorum-sensing transcription factor TraR, C-termin	83.93
d1lj9a_	144	Transcriptional regulator SlyA {Enterococcus faeca	83.9
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	83.89
d1pdnc_	123	Paired protein (prd) {Fruit fly (Drosophila melano	83.72
d1yioa1	70	Response regulatory protein StyR, C-terminal domai	83.49
d1r8ea1	118	Transcription activator BmrR {Bacillus subtilis [T	83.4
d2a6ca1	69	HTH-motif protein NE1354 {Nitrosomonas europaea [T	83.23
d1jt6a1	71	Multidrug binding protein QacR {Staphylococcus aur	83.22
d3broa1	135	Transcriptional regulator OEOE1854 {Oenococcus oen	83.21
d2g7sa1	74	Putative transcriptional regulator Atu0279 {Agroba	83.15
d1z0xa1	68	Transcriptional regulator EF0787 {Enterococcus fae	82.87
d1bl0a1	54	MarA {Escherichia coli [TaxId: 562]}	82.85
d2d6ya1	68	Putative regulator SCO4008 {Streptomyces coelicolo	82.71
d2fbqa1	79	Transcriptional regulator PsrA {Pseudomonas aerugi	82.33
d2etha1	140	Putative transcriptional regulator TM0816 {Thermot	81.99
d1t56a1	73	Ethr repressor {Mycobacterium tuberculosis [TaxId:	81.96
d2vkva1	62	Tetracyclin repressor (Tet-repressor, TetR) {Esche	81.86
d2isya1	63	Iron-dependent regulator IdeR {Mycobacterium tuber	81.63
d2o38a1	89	Hypothetical protein RPA3824 {Rhodopseudomonas pal	81.5
d2gfna1	77	Probable transcriptional regulator RHA1_ro04631 {R	81.4
d1ntca_	91	DNA-binding domain of NTRC {Salmonella typhimurium	81.32
d2fx0a1	73	Hemolysin II regulatory protein, HlyIIR {Bacillus	80.71
d1g2ha_	61	Transcriptional regulator TyrR, C-terminal domain	80.7
d2fq4a1	69	Transcriptional regulator BC3163 {Bacillus cereus	80.13
d1zs4a1	78	Regulatory protein cII {Bacteriophage lambda [TaxI	80.08
d1z91a1	137	Organic hydroperoxide resistance transcriptional r	80.07

>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=99.70  E-value=2.6e-17  Score=108.31  Aligned_cols=64  Identities=64%  Similarity=0.918  Sum_probs=60.7

Q ss_pred             cchHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCCC
Q 031871           87 RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRGK  150 (151)
Q Consensus        87 ~~~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~e~  150 (151)
                      .+.+.||.+|+.+|+.+||||.+||+.+|+|+++|++||+|...|+.+.+.+||++|||++++.
T Consensus         2 ~~~~~iG~~I~~~R~~~gltq~~lA~~~gis~~~is~~E~G~~~p~~~~l~~la~~l~v~l~~~   65 (78)
T d1x57a1           2 RVTLEVGKVIQQGRQSKGLTQKDLATKINEKPQVIADYESGRAIPNNQVLGKIERAIGLKLRGK   65 (78)
T ss_dssp             CCCCHHHHHHHHHHHTTTCCHHHHHHHHTSCHHHHHHHHHTCSCCCHHHHHHHHHHHTBCCSST
T ss_pred             cccHHHHHHHHHHHHHcCCChhHHHHcCCCCHHHHHHHHccCCCCCHHHHHHHHHHhCCccccc
Confidence            4567999999999999999999999999999999999999999999999999999999999754

>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=99.68  E-value=5.2e-17  Score=104.17  Aligned_cols=60  Identities=23%  Similarity=0.243  Sum_probs=58.0

Q ss_pred             HHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 031871           90 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG  149 (151)
Q Consensus        90 ~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~e  149 (151)
                      ..||++|+++|+.+||||.+||+.+|+|+++|++||+|+..|+.+.+.+||++|||++++
T Consensus         8 ~~~g~~ik~~R~~~gltq~~lA~~~gis~~~i~~~E~g~~~p~~~~l~~ia~~l~v~~~~   67 (69)
T d1y7ya1           8 VKFGQRLRELRTAKGLSQETLAFLSGLDRSYVGGVERGQRNVSLVNILKLATALDIEPRE   67 (69)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCSCCBHHHHHHHHHHTTSCGGG
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHhHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHhCcCHHH
Confidence            569999999999999999999999999999999999999999999999999999999875

>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=99.62  E-value=1.5e-16  Score=103.75  Aligned_cols=61  Identities=21%  Similarity=0.278  Sum_probs=58.2

Q ss_pred             chHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           88 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        88 ~~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      +...||.+|+.+|..+||||.+||+.+|+|+++|++||+|++.|+.+.+.+||++|||+++
T Consensus         7 ~~~~~g~~ik~~R~~~gltq~~lA~~~gis~~~i~~~e~g~~~p~~~~l~~ia~~l~v~~~   67 (77)
T d2b5aa1           7 IKRKFGRTLKKIRTQKGVSQEELADLAGLHRTYISEVERGDRNISLINIHKICAALDIPAS   67 (77)
T ss_dssp             HHHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCSCCBHHHHHHHHHHTTCCHH
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHH
Confidence            3567999999999999999999999999999999999999999999999999999999975

>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=99.61  E-value=7.6e-16  Score=100.81  Aligned_cols=61  Identities=20%  Similarity=0.310  Sum_probs=58.3

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG  149 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~e  149 (151)
                      ...|+.+|+.+|..+||||.+||+.+|+++++|++||+|+..|+.+.+.+||++|||++++
T Consensus         6 ~~~ig~~lr~~R~~~g~sq~~lA~~~gis~~~i~~~E~g~~~p~~~~l~~ia~~l~v~~~~   66 (79)
T d1y9qa1           6 KSQIANQLKNLRKSRGLSLDATAQLTGVSKAMLGQIERGESSPTIATLWKIASGLEASFSA   66 (79)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHSSCHHHHHHHHTTCSCCCHHHHHHHHHHHTCCSGG
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHCcchhHHHHHHcCCCCCCHHHHHHHHHHHCCCHHH
Confidence            4679999999999999999999999999999999999999999999999999999999863

>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=99.61  E-value=4e-16  Score=98.97  Aligned_cols=58  Identities=22%  Similarity=0.326  Sum_probs=56.1

Q ss_pred             HHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           91 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        91 ~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      .++++|+.+|+.+||||.+||+.+|+++++|++||+|+..|+.+.+.+||++|+|+++
T Consensus         3 ~ig~rik~~R~~~g~tq~~lA~~~gvs~~~i~~~e~g~~~p~~~~l~~ia~~l~v~~~   60 (66)
T d2r1jl1           3 LMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCSPD   60 (66)
T ss_dssp             CHHHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHTTSSCCBHHHHHHHHHHTTSCHH
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHH
Confidence            4799999999999999999999999999999999999999999999999999999975

>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=99.60  E-value=2.8e-16  Score=99.54  Aligned_cols=57  Identities=28%  Similarity=0.272  Sum_probs=53.5

Q ss_pred             HHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           91 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        91 ~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      .++++|+.+|+++||||.|||+.+|+++++|++||+|+..|+ +.+.+||++|||+++
T Consensus         3 ~i~~rlr~~R~~~gltq~~lA~~~gvs~~ti~~~E~g~~~~~-~~l~~ia~~l~v~~~   59 (65)
T d2croa_           3 TLSERLKKRRIALKMTQTELATKAGVKQQSIQLIEAGVTKRP-RFLFEIAMALNCDPV   59 (65)
T ss_dssp             SHHHHHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHTTCCSSC-TTHHHHHHHTTSCHH
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHCcCHhHHHHHHCCCCCCH-HHHHHHHHHhCCCHH
Confidence            489999999999999999999999999999999999998766 789999999999875

>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=99.60  E-value=6.8e-16  Score=98.49  Aligned_cols=57  Identities=25%  Similarity=0.302  Sum_probs=54.1

Q ss_pred             HHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCCC
Q 031871           92 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA-IPNQQILTKLERALGVKLR  148 (151)
Q Consensus        92 ~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~-~p~~~~l~kLa~~Lgv~l~  148 (151)
                      +|++|+.+|.++||||.+||+.+|+++++|++||+|.. .|+.+.+.+||++|||+++
T Consensus         2 ig~~ik~~R~~~gltq~~la~~~gis~~~i~~~E~g~~~~ps~~~l~~ia~~l~v~~~   59 (68)
T d1b0na2           2 IGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNLQTNPSIQFLEKVSAVLDVSVH   59 (68)
T ss_dssp             CHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCCSCCCHHHHHHHHHHHTCCHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcCCCCCCCHHHHHHHHHHHCCcHH
Confidence            58999999999999999999999999999999999975 6999999999999999874

>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=99.58  E-value=6.8e-16  Score=98.10  Aligned_cols=56  Identities=30%  Similarity=0.358  Sum_probs=53.4

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      +.+|+.+|.++||||.+||+.+|+|+++|++||+|+..|+.+.+.+||++|||+++
T Consensus         3 ~~ri~~lR~~~g~tq~elA~~~gis~~~is~~e~g~~~p~~~~l~~ia~~l~v~~~   58 (66)
T d1utxa_           3 INNLKLIREKKKISQSELAALLEVSRQTINGIEKNKYNPSLQLALKIAYYLNTPLE   58 (66)
T ss_dssp             EECHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHTTSCCCCHHHHHHHHHHTTSCHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHhcccCHHHHHHHHcCCCCCCHHHHHHHHHHHCCCHH
Confidence            34799999999999999999999999999999999999999999999999999975

>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=99.58  E-value=6.4e-16  Score=97.13  Aligned_cols=56  Identities=30%  Similarity=0.457  Sum_probs=53.1

Q ss_pred             HHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           92 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        92 ~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      |+++|+.+|+++||||.|||+.+|+++++|++||+|+. |+.+.+.+||++|||+++
T Consensus         2 ig~rik~~R~~~g~sq~elA~~~gvs~~~is~~E~g~~-~~~~~l~~ia~~l~v~~~   57 (63)
T d1r69a_           2 ISSRVKSKRIQLGLNQAELAQKVGTTQQSIEQLENGKT-KRPRFLPELASALGVSVD   57 (63)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHTTSC-SSCTTHHHHHHHTTCCHH
T ss_pred             HHHHHHHHHHHcCCcHHHHHHHhCcCHHHHHHHHCCCC-cCHHHHHHHHHHHCcCHH
Confidence            78999999999999999999999999999999999975 788899999999999875

>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=99.58  E-value=3.4e-15  Score=95.69  Aligned_cols=60  Identities=20%  Similarity=0.286  Sum_probs=57.3

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhCCCCC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK-AIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~-~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      ...++.+|+.+|+++||||.|||+.+|+++++|++||+|+ ..|+.+.+.+||.+||++++
T Consensus         4 ~~~l~~~i~~~r~~~gltq~elA~~~gv~~~~is~ie~g~~~~~s~~~L~~ia~~Lg~~i~   64 (69)
T d2a6ca1           4 RSQLLIVLQEHLRNSGLTQFKAAELLGVTQPRVSDLMRGKIDLFSLESLIDMITSIGLKVE   64 (69)
T ss_dssp             HHHHHHHHHHHHHTTTCCHHHHHHHHTSCHHHHHHHHTTCGGGCCHHHHHHHHHHTTCCCC
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHHcCHhHHHHHHcccccchhHHHHHHHHHHhCCCcE
Confidence            4578999999999999999999999999999999999998 78999999999999999987

>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=99.54  E-value=3.1e-15  Score=100.09  Aligned_cols=56  Identities=16%  Similarity=0.268  Sum_probs=54.1

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      |++|+++|+++||||.+||+.+||++++|++||+|++.|+.+.+.+|+++|||+++
T Consensus         3 Ge~lke~r~~~glsq~~LA~~lGvs~~~is~ie~g~~~~s~~~~~kla~~lgvs~~   58 (87)
T d2icta1           3 GDIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVIGSSPQ   58 (87)
T ss_dssp             HHHHHHHHHHHTCCHHHHHHHHTCCHHHHHHHHHTSSCCCHHHHHHHHHHTCSCHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHhhcHHHHHHHHHhccCCCHHHHHHHHHHHCcCHH
Confidence            78899999999999999999999999999999999999999999999999999864

>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=99.54  E-value=6.5e-15  Score=98.45  Aligned_cols=61  Identities=18%  Similarity=0.163  Sum_probs=57.0

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG  149 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~e  149 (151)
                      ...++..++.+|+++||||.+||+.+|+|+++|++||+|...|+.+.+.+||++|||++++
T Consensus        10 ~~~l~~~i~~~R~~~gltq~~lA~~lgis~~~is~~E~g~~~~s~~~l~~ia~~l~v~~~~   70 (87)
T d1lmb3_          10 ARRLKAIYEKKKNELGLSQESVADKMGMGQSGVGALFNGINALNAYNAALLAKILKVSVEE   70 (87)
T ss_dssp             HHHHHHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHTTSSCCCHHHHHHHHHHHTSCGGG
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHhCccHHHHHHHHhccCCCcHHHHHHHHHHHCCCHHH
Confidence            3567788888899999999999999999999999999999999999999999999999874

>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=99.49  E-value=2.2e-14  Score=96.20  Aligned_cols=60  Identities=17%  Similarity=0.102  Sum_probs=56.9

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhCCCCC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK-AIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~-~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      ...++.+|+++|+.+||||.+||+.+|+++++|++||+|+ ..|+.+.+.+|+.+||++++
T Consensus         9 k~~l~~~i~~~r~~~gltq~~lA~~~gis~~~is~ie~G~~~~~~~~~L~~ia~~Lg~~i~   69 (89)
T d2o38a1           9 KLRLAYALNAVIDRARLSQAAAAARLGINQPKVSALRNYKLEGFSVERLMTLLNALDQDVE   69 (89)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCCTTCCHHHHHHHHHHTTEEEE
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHHhhHhHHHHHHcCCCCCCcHHHHHHHHHHcCCCHH
Confidence            5789999999999999999999999999999999999998 67999999999999999864

>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=99.48  E-value=3e-14  Score=94.39  Aligned_cols=58  Identities=19%  Similarity=0.286  Sum_probs=54.0

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhCCCCC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK-AIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~-~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      ...||.+|+.+|+  ++||.|||+++|+|+++|++||+|+ ..|+.+.+.+||++|||+++
T Consensus        12 ~~~lG~~ir~~R~--~~t~~eLA~~~Gvs~~~ls~iE~G~~~~ps~~tl~kia~~L~v~~~   70 (82)
T d2ofya1          12 GQRLGELLRSARG--DMSMVTVAFDAGISVETLRKIETGRIATPAFFTIAAVARVLDLSLD   70 (82)
T ss_dssp             HHHHHHHHHHHHT--TSCHHHHHHHHTCCHHHHHHHHTTCCSSCBHHHHHHHHHHTTCCHH
T ss_pred             HHHHHHHHHHHHH--cCCHHHHHHHHcCCHHHHHHHHcCCcCCCCHHHHHHHHHHHCCCHH
Confidence            4679999999995  6899999999999999999999998 57999999999999999975

>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=99.35  E-value=6.5e-13  Score=83.26  Aligned_cols=49  Identities=22%  Similarity=0.332  Sum_probs=43.9

Q ss_pred             HHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q 031871           95 AIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALG  144 (151)
Q Consensus        95 ~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lg  144 (151)
                      +|+.+|+..||||++||+.+||++++|++||+|+..|+...+..|+ .++
T Consensus         3 ~ik~~R~~~gltQ~elA~~lGvs~~tvs~~E~G~~~P~~~~~~ll~-~l~   51 (62)
T d2ppxa1           3 RIKIIRRALKLTQEEFSARYHIPLGTLRDWEQGRSEPDQPARAYLK-IIA   51 (62)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTSSCCCHHHHHHHH-HHH
T ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHH-HHh
Confidence            6899999999999999999999999999999999999988776554 443

>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=99.18  E-value=3.8e-11  Score=76.37  Aligned_cols=44  Identities=11%  Similarity=0.177  Sum_probs=39.6

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHH
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQIL  136 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l  136 (151)
                      .++|+.+|+.+||||.+||+.+|||+.+|++||+|++.++..+.
T Consensus         3 ~e~~k~~R~~~gltQ~elA~~LGvs~~ti~~yE~G~r~iP~~v~   46 (67)
T d2auwa1           3 HEMFGDWMHRNNLSLTTAAEALGISRRMVSYYRTAHKIIPRTIW   46 (67)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHTTSSCCCHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHH
Confidence            47899999999999999999999999999999999987665543

>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=98.41  E-value=7.1e-07  Score=54.32  Aligned_cols=59  Identities=20%  Similarity=0.435  Sum_probs=54.8

Q ss_pred             HHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhCCCCC
Q 031871           90 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK-AIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        90 ~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~-~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      .-|.++|++.|++-.|....||..+|.++.++..||+|+ ...+...+-+|+.+||.++-
T Consensus         4 tgfae~lk~rreqvkmdhaalas~lgetpetvaawengeggeltltqlg~ia~~lgtsig   63 (71)
T d2bnma1           4 TGFAELLKDRREQVKMDHAALASLLGETPETVAAWENGEGGELTLTQLGRIAHVLGTSIG   63 (71)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTTCTTCBHHHHHHHHHHTTSCTG
T ss_pred             hhHHHHHHHHHHHHhhhHHHHHHHHcCCchHHHHhhcCCCceeeHHHHHHHHHHHccccc
Confidence            468999999999999999999999999999999999998 56899999999999998863

>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=97.83  E-value=3e-05  Score=50.64  Aligned_cols=59  Identities=14%  Similarity=0.123  Sum_probs=55.9

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL  147 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l  147 (151)
                      ..++.+.|-..+.++|+|-.++|+.+|.|...+...-.|....+.+.+.++++.||++-
T Consensus        11 r~~lte~Il~AK~~kgltw~~IA~~iG~s~vwvtaa~lGQ~~l~~~~A~~l~~~L~L~~   69 (86)
T d1dwka1          11 RLDLADAILLSKAKKDLSFAEIADGTGLAEAFVTAALLGQQALPADAARLVGAKLDLDE   69 (86)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHTTSSSCHHHHHHHHTTSSCCCHHHHHHHHHHHTCCH
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHhcCCCCCHHHHHHHHHHcCCCH
Confidence            46789999999999999999999999999999999999999999999999999999864

>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=97.60  E-value=7.4e-05  Score=45.06  Aligned_cols=44  Identities=14%  Similarity=0.120  Sum_probs=35.8

Q ss_pred             CcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHH---HHHhCCCC
Q 031871          104 KLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKL---ERALGVKL  147 (151)
Q Consensus       104 glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kL---a~~Lgv~l  147 (151)
                      ++|..|+|+.+|+|.+|||++.+|...++.++..+|   ++.||-.+
T Consensus         1 NvTi~dvA~~agvS~~TVSr~Ln~~~~Vs~~tr~rV~~aa~~lgY~p   47 (57)
T d2hsga1           1 NVTIYDVAREASVSMATVSRVVNGNPNVKPSTRKKVLETIERLGYRP   47 (57)
T ss_dssp             CCCHHHHHHHTTSCHHHHHHHHTTCTTSCHHHHHHHHHHHHHHTCCS
T ss_pred             CcCHHHHHHHHCcCHHHHHHHhCCCCcCCHHHHHHHHHHHHHHCcCC
Confidence            579999999999999999999999988877765554   55666543

>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=97.49  E-value=8.1e-05  Score=45.20  Aligned_cols=44  Identities=9%  Similarity=-0.030  Sum_probs=35.5

Q ss_pred             CcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH---HHHHHhCCCC
Q 031871          104 KLTQSQLAQLINEKPQVIQEYESGKAIPNQQILT---KLERALGVKL  147 (151)
Q Consensus       104 glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~---kLa~~Lgv~l  147 (151)
                      ..|..|+|+.+|+|++|||++.+|...++.++..   .+++.||-.+
T Consensus         2 ~~Ti~diA~~agvS~sTVSr~l~~~~~vs~~tr~rI~~~a~~lgY~p   48 (59)
T d1efaa1           2 PVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIP   48 (59)
T ss_dssp             CCCHHHHHHTTTSCHHHHHHHHTTCSSCCTHHHHHHHHHHHHHTCCC
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHCCCCcCCHHHHHHHHHHHHHHCCCc
Confidence            5799999999999999999999999877766554   4555666544

>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=97.38  E-value=0.00019  Score=43.22  Aligned_cols=42  Identities=10%  Similarity=0.029  Sum_probs=34.3

Q ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH---HHHHHhCCCC
Q 031871          106 TQSQLAQLINEKPQVIQEYESGKAIPNQQILT---KLERALGVKL  147 (151)
Q Consensus       106 TQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~---kLa~~Lgv~l  147 (151)
                      |..|+|+.+|+|.+|||++.+|...++.++..   .+++.||-.+
T Consensus         2 Ti~dvA~~agVS~sTVSr~ln~~~~vs~~tr~rV~~~a~~lgY~p   46 (57)
T d1qpza1           2 TIKDVAKRANVSTTTVSHVINKTRFVAEETRNAVWAAIKELHYSP   46 (57)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHHTCSCCCHHHHHHHHHHHHHHTCCC
T ss_pred             CHHHHHHHHCcCHHHHHHHHCCCCccCHHHHHHHHHHHHHHCCCC
Confidence            78999999999999999999998888776654   4566666554

>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=97.22  E-value=0.00054  Score=41.94  Aligned_cols=44  Identities=7%  Similarity=0.267  Sum_probs=39.8

Q ss_pred             hhccCCcchHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871           81 LYCTDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus        81 ~~~~~~~~~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E  125 (151)
                      .|+++..+..++.++|-++-+ .|+|..++|+.++||.+++++|-
T Consensus         8 ~~~~GrPls~DLR~Riv~~~~-~G~s~r~aA~rf~VS~s~v~k~l   51 (63)
T d1k78a1           8 VFVNGRPLPDVVRQRIVELAH-QGVRPCDISRQLRVSHGCVSKIL   51 (63)
T ss_dssp             BCCTTSCCCHHHHHHHHHHHH-TTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             cccCCCcCCHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHH
Confidence            477888899999999998865 79999999999999999999994

>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=97.20  E-value=0.00061  Score=42.81  Aligned_cols=53  Identities=19%  Similarity=0.184  Sum_probs=44.2

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhC------CCHHHHHHHHcCCCCCCHHHHHHHHHHh
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLIN------EKPQVIQEYESGKAIPNQQILTKLERAL  143 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lg------is~s~Is~~E~G~~~p~~~~l~kLa~~L  143 (151)
                      .+.|+..++..|...|+||.|++..+|      .|+++|+++|+=  ..+...+.+|--+|
T Consensus         9 le~Fa~~fk~rRi~LG~TQ~dVG~al~~l~g~~~SQttIcRFE~l--~LS~kn~~kLkP~L   67 (75)
T d1e3oc2           9 LEQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEAL--NLSFKNMSKLKPLL   67 (75)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHHHHHSCCCCHHHHHHHHHT--CSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhccccHHHHHHHHHHHcCcchhHHHHHHHHHh--ccCHHHHHHHHHHH
Confidence            467999999999999999999999886      599999999984  46777777765443

>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=97.14  E-value=0.00043  Score=41.79  Aligned_cols=44  Identities=14%  Similarity=0.102  Sum_probs=36.5

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcCCCC---C---CHHHHHHHHHHhCCCCC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESGKAI---P---NQQILTKLERALGVKLR  148 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G~~~---p---~~~~l~kLa~~Lgv~l~  148 (151)
                      +|.+|+|+.+|+|.+|||++.||...   +   +.+.+..+++.||-.+.
T Consensus         1 vTl~diA~~agvS~sTVSrvLn~~~~~~~vs~~tr~rV~~~a~~lgY~pn   50 (59)
T d1uxda_           1 MKLDEIARLAGVSRTTASYVINGKAKQYRVSDKTVEKVMAVVREHNYHPN   50 (59)
T ss_dssp             CCHHHHHHHHTSCTTHHHHHHHTCGGGTTCTTTTHHHHHHHHHHHTCCCC
T ss_pred             CCHHHHHHHHCcCHHHHHHHHcCCCCcCcCCHHHHHHHHHHHHHHCCCcC
Confidence            58899999999999999999998642   2   56677888888887654

>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=97.12  E-value=0.0011  Score=43.46  Aligned_cols=51  Identities=10%  Similarity=0.072  Sum_probs=43.8

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHH
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKL  139 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kL  139 (151)
                      ...+.+-|+.....++++|..+|+.+|+|+++||.+.++....+...-..|
T Consensus        26 ~~~v~~~IK~Fl~~h~I~Q~~Va~~TGlsQS~iSq~L~~g~~M~~~KR~al   76 (94)
T d1ic8a2          26 PWRVAKMVKSYLQQHNIPQREVVDTTGLNQSHLSQHLNKGTPMKTQKRAAL   76 (94)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHCCCHHHHHHHHHSBCCCCHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCcHHHHHHHHcccHHHHHHHHhCCCCccHHHHHHH
Confidence            467889999999999999999999999999999999998876666544433

>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=97.03  E-value=0.00084  Score=41.82  Aligned_cols=53  Identities=15%  Similarity=0.105  Sum_probs=43.8

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhC------CCHHHHHHHHcCCCCCCHHHHHHHHHHh
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLIN------EKPQVIQEYESGKAIPNQQILTKLERAL  143 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lg------is~s~Is~~E~G~~~p~~~~l~kLa~~L  143 (151)
                      .+.|++.++..|...|+||.|++..+|      .|+++|+++|+=  ..+...+.+|--+|
T Consensus         5 le~Fa~~fk~rRi~LG~TQ~dVG~al~~l~g~~~SQttIcRFE~l--~LS~kn~~klkPiL   63 (72)
T d1au7a2           5 LEQFANEFKVRRIKLGYTQTNVGEALAAVHGSEFSQTTICRFENL--QLSFKNACKLKAIL   63 (72)
T ss_dssp             HHHHHHHHHHHHHHHTCCHHHHHHHHHHTTSSCCCHHHHHHHHTT--CSBHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccCccHHHHHHHHHHhcCcccchhHHHHHHhc--ccCHHHHHHHHHHH
Confidence            367999999999999999999999875      699999999984  46777777665443

>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=96.69  E-value=0.0022  Score=36.86  Aligned_cols=38  Identities=16%  Similarity=0.162  Sum_probs=29.6

Q ss_pred             chHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           88 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        88 ~~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      +..+-.+.++.++. .|.|..++|+.+|||++||.+|--
T Consensus         6 lt~~q~~~a~~l~~-~G~s~~~iA~~~gVSr~TiYry~p   43 (47)
T d1ijwc_           6 INKHEQEQISRLLE-KGHPRQQLAIIFGIGVSTLYRYFP   43 (47)
T ss_dssp             SCHHHHHHHHHHHH-TTCCHHHHHHHHTCCHHHHHHHSC
T ss_pred             CCHHHHHHHHHHHH-CCCCHHHHHHHHCcCHHHHHhhCC
Confidence            33444455666664 699999999999999999999863

>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=96.61  E-value=0.0042  Score=36.60  Aligned_cols=55  Identities=22%  Similarity=0.234  Sum_probs=49.6

Q ss_pred             HHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 031871           92 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL  147 (151)
Q Consensus        92 ~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l  147 (151)
                      +|..|+++|++.+.-|-+|-.-+ +|.+.+-++|...+.++.+.+.++++.||+..
T Consensus         3 ig~~lkqir~elnyhqidlysgi-msksiyikveadsrpisveel~kfserlginf   57 (65)
T d2awia1           3 IGSVLKQIRQELNYHQIDLYSGI-MSKSVYIKVEADSRPISVEELSKFSERLGVNF   57 (65)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHTTT-SCHHHHHHHHTTCSCCBHHHHHHHHHHHTSCH
T ss_pred             cchHHHHHHHHhhhhHhHHHhhh-cccceEEEEecCCCcccHHHHHHHHHHhCchH
Confidence            67889999999999999987644 68999999999999999999999999999864

>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=95.88  E-value=0.0085  Score=37.45  Aligned_cols=50  Identities=16%  Similarity=0.147  Sum_probs=41.8

Q ss_pred             HHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 031871           96 IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  148 (151)
Q Consensus        96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lgv~l~  148 (151)
                      |+.....+|+|..+|++..|++.+|+.....   .|....=..||++||+.+.
T Consensus        14 I~AaL~krG~sLa~lsr~~gls~stl~naL~---rp~pKgEriIA~aLg~~P~   63 (74)
T d1nera_          14 VIAGLKKRKLSLSALSRQFGYAPTTLANALE---RHWPKGEQIIANALETKPE   63 (74)
T ss_dssp             HHHHHTTSSCCHHHHHHHHSCCHHHHHHTTT---SSCHHHHHHHHHHTTSCHH
T ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc---CCChHHHHHHHHHHCcCHH
Confidence            5566667899999999999999999998654   5677777789999999864

>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=95.85  E-value=0.0066  Score=41.24  Aligned_cols=44  Identities=7%  Similarity=0.239  Sum_probs=39.5

Q ss_pred             hhccCCcchHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871           81 LYCTDDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus        81 ~~~~~~~~~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E  125 (151)
                      .|+++..+..++..+|-.+- +.|+++.++|+.++||+++|++|.
T Consensus        10 ~~~~GrpLs~dlR~rIv~~~-~~G~s~r~iA~~~~VS~~tV~k~l   53 (123)
T d1pdnc_          10 VFINGRPLPNNIRLKIVEMA-ADGIRPCVISRQLRVSHGCVSKIL   53 (123)
T ss_dssp             EEETTSCCCHHHHHHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             cccCCcCCCHHHHHHHHHHH-HhcCCHHHHHHHHCcCHHHHHHHH
Confidence            47888889999999999986 579999999999999999999983

>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=95.69  E-value=0.0077  Score=39.11  Aligned_cols=36  Identities=14%  Similarity=0.130  Sum_probs=29.8

Q ss_pred             HHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           90 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        90 ~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      .+-+..++.+. +.|+||.++|+++|.|+++|++.-+
T Consensus         6 iEeA~a~~~L~-e~g~t~~~iA~~~Gks~~~V~~~Lr   41 (93)
T d1vz0a1           6 VEEARGYQALL-EMGLTQEEVARRVGKARSTVANALR   41 (93)
T ss_dssp             HHHHHHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHH-HcCCCHHHHHHHHccchHHHHHHHH
Confidence            34456777887 5899999999999999999998754

>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=95.54  E-value=0.012  Score=37.39  Aligned_cols=40  Identities=15%  Similarity=0.175  Sum_probs=30.8

Q ss_pred             cchHHHHHHHHHHH-hcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           87 RVPSELKKAIVQAR-NDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        87 ~~~~~~~~~Lk~~R-~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      ....+|-..+-.+- ...|+|..++|+.+||++++|.+|-+
T Consensus         5 ~Ys~EfK~~aV~l~~~~~g~s~~~vA~~lGIs~~tl~~W~k   45 (89)
T d2jn6a1           5 TYSEEFKRDAVALYENSDGASLQQIANDLGINRVTLKNWII   45 (89)
T ss_dssp             CCCHHHHHHHHHHHTTGGGSCHHHHHHHHTSCHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHcCCCcHHHHHHHHCCCHHHHHHHHH
Confidence            34566666655444 34589999999999999999999953

>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=95.23  E-value=0.012  Score=35.89  Aligned_cols=44  Identities=20%  Similarity=0.351  Sum_probs=32.1

Q ss_pred             HHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q 031871           96 IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALG  144 (151)
Q Consensus        96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lg  144 (151)
                      |+.+-.-..++|.|+|+.+||+++||+.|-+.+     +.+....+.+|
T Consensus        17 i~~~e~g~k~sq~eIA~~fGv~~STvs~IlKnK-----~kil~~~~~~g   60 (66)
T d1hlva1          17 IQEVEENPDLRKGEIARRFNIPPSTLSTILKNK-----RAILASERKYG   60 (66)
T ss_dssp             HHHHHHCTTSCHHHHHHHHTCCHHHHHHHHHTH-----HHHHHHHHHHG
T ss_pred             HHHHHcCCcchHHHHHHHhCCChhHHHHHHHHH-----HHHHHHHHHcC
Confidence            444444455899999999999999999998853     44555555554

>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=95.09  E-value=0.015  Score=37.12  Aligned_cols=59  Identities=17%  Similarity=0.222  Sum_probs=47.1

Q ss_pred             chHHHHHHHHHHHhcCCcCHHHHHHH-hCCCHHHHHHHHcCCCCCC------HHHHHHHHHHhCCC
Q 031871           88 VPSELKKAIVQARNDKKLTQSQLAQL-INEKPQVIQEYESGKAIPN------QQILTKLERALGVK  146 (151)
Q Consensus        88 ~~~~~~~~Lk~~R~~~glTQ~eLA~~-lgis~s~Is~~E~G~~~p~------~~~l~kLa~~Lgv~  146 (151)
                      +..++..+|++..+.++++|+-||+. +|.|+.+++.+.+....++      .+.+.+|-..|+.+
T Consensus         2 ~T~eI~~~i~~eL~~~~IsQ~~Fak~vL~rSQgtlSdLL~~pkpw~~ls~sgre~f~Rm~~wL~lP   67 (83)
T d2o4aa1           2 VSSEIYQWVRDELKRAGISQAVFARVAFNRTQGLLSEILRKEEDPKTASQSLLVNLRAMQNFLQLP   67 (83)
T ss_dssp             CCTTHHHHHHHHHHHHTCCHHHHHHHHHSCCHHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHTSC
T ss_pred             ccHHHHHHHHHHHHHcCCCHHHHHHHHHccCcHHHHHHHcCCCCchhhhHHHHHHHHHHHHHHcCh
Confidence            34678899999999999999999996 7999999999998654442      34667777777654

>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=94.82  E-value=0.0082  Score=35.79  Aligned_cols=27  Identities=15%  Similarity=0.154  Sum_probs=23.8

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCccC
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNKAA   56 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~~~   56 (151)
                      ++-+.|++.|++.+|+.+||+|...|.
T Consensus        14 tQ~elA~~lGvs~~tvs~~E~G~~~P~   40 (62)
T d2ppxa1          14 TQEEFSARYHIPLGTLRDWEQGRSEPD   40 (62)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHTTSSCCC
T ss_pred             CHHHHHHHhCCCHHHHHHHHCCCCCCC
Confidence            456799999999999999999988763

>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=94.79  E-value=0.034  Score=35.72  Aligned_cols=58  Identities=21%  Similarity=0.231  Sum_probs=48.1

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHH-hCCCHHHHHHHHcCCCCCC------HHHHHHHHHHhCCC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQL-INEKPQVIQEYESGKAIPN------QQILTKLERALGVK  146 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~-lgis~s~Is~~E~G~~~p~------~~~l~kLa~~Lgv~  146 (151)
                      ...+..+|++..+.++++|+-||+. +|.|+.+++.+.+....|+      .+++.+|-..|+.+
T Consensus        12 T~~Ia~~i~~eL~~~~IsQ~~Fak~vL~rSQGtlSdLLrkpkp~~~~~~sg~e~~~rm~~wL~lP   76 (88)
T d2csfa1          12 TAAIYDEIQQEMKRAKVSQALFAKVAANKSQGWLCELLRWKENPSPENRTLWENLCTIRRFLNLP   76 (88)
T ss_dssp             CTHHHHHHHHHHHHHTCCHHHHHHHHTCCCHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHTSC
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHHccCcHHHHHHHcCCCCcchhhHHHHHHHHHHHHHHhCh
Confidence            4688999999999999999999996 7999999999998755442      45677777777654

>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=94.72  E-value=0.038  Score=30.82  Aligned_cols=33  Identities=12%  Similarity=0.195  Sum_probs=28.1

Q ss_pred             HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcC
Q 031871           94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESG  127 (151)
Q Consensus        94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G  127 (151)
                      +.+++++ ..|++-.++|+.+||++++|.++.+.
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            4567777 48999999999999999999998764

>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=94.59  E-value=0.033  Score=36.73  Aligned_cols=37  Identities=22%  Similarity=0.311  Sum_probs=31.9

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      +.+.+..++.+.. .|+|+.++|+++|.|+++|+++-.
T Consensus        16 p~e~A~a~~~l~~-~g~s~~eiA~~~G~s~~~V~~~l~   52 (114)
T d1r71a_          16 PREIADFIGRELA-KGKKKGDIAKEIGKSPAFITQHVT   52 (114)
T ss_dssp             HHHHHHHHHHHHH-TTCCHHHHHHHHTCCHHHHHHHHG
T ss_pred             HHHHHHHHHHHHH-hCCCHHHHHHHHCCcHHHHHHHHH
Confidence            4567888888865 599999999999999999999876

>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=94.58  E-value=0.034  Score=33.72  Aligned_cols=35  Identities=11%  Similarity=0.079  Sum_probs=30.7

Q ss_pred             HHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871           91 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus        91 ~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E  125 (151)
                      .....|+.+|....+|..|||+.+|+|.+||+++-
T Consensus         6 N~~~Il~~i~~~g~~sr~eLa~~~gLS~~Tvs~iv   40 (70)
T d1z6ra1           6 NAGAVYRLIDQLGPVSRIDLSRLAQLAPASITKIV   40 (70)
T ss_dssp             HHHHHHHHHHSSCSCCHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHH
Confidence            34566888899999999999999999999999874

>d1z05a1 a.4.5.63 (A:10-80) Transcriptional regulator VC2007 N-terminal domain {Vibrio cholerae [TaxId: 666]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: Transcriptional regulator VC2007 N-terminal domain
species: Vibrio cholerae [TaxId: 666]

Probab=94.57  E-value=0.031  Score=33.77  Aligned_cols=34  Identities=9%  Similarity=0.103  Sum_probs=29.4

Q ss_pred             HHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871           92 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus        92 ~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E  125 (151)
                      ....|..++..-.+|..|||+.+|+|++||+++-
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            4556777888889999999999999999999873

>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=94.41  E-value=0.038  Score=33.21  Aligned_cols=23  Identities=13%  Similarity=0.309  Sum_probs=20.5

Q ss_pred             CcCHHHHHHHhCCCHHHHHHHHc
Q 031871          104 KLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus       104 glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      .+||.|||..+|+++.+|++..+
T Consensus        29 ~lt~~~lA~~~G~sRetvsr~L~   51 (69)
T d1i5za1          29 KITRQEIGQIVGCSRETVGRILK   51 (69)
T ss_dssp             ECCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHH
Confidence            48999999999999999998743

>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=94.36  E-value=0.074  Score=35.57  Aligned_cols=47  Identities=17%  Similarity=0.243  Sum_probs=40.6

Q ss_pred             HHHHHHHhcCCcCHHHHHHHhC--CCHHHHHHHHcCCCCCCHHHHHHHH
Q 031871           94 KAIVQARNDKKLTQSQLAQLIN--EKPQVIQEYESGKAIPNQQILTKLE  140 (151)
Q Consensus        94 ~~Lk~~R~~~glTQ~eLA~~lg--is~s~Is~~E~G~~~p~~~~l~kLa  140 (151)
                      -.|+.+|...-||..|-|.-++  ++..+..+||+|+..++.+++..+.
T Consensus         6 ~ELQalR~if~mti~EaA~~I~~~~~s~tWQqWE~Gd~~IP~~Vi~~l~   54 (120)
T d1s4ka_           6 LELQALRRIFDMTIEECTIYITQDNNSATWQRWEAGDIPISPEIIARLK   54 (120)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHTSSSCCHHHHHHHHHTSSCCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHhHHHHHHHHhcCccHHHHHHHHcCCCCCCHHHHHHHH
Confidence            4588999999999999999765  7899999999999999988865553

>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=94.15  E-value=0.0045  Score=37.50  Aligned_cols=43  Identities=16%  Similarity=0.042  Sum_probs=31.0

Q ss_pred             CHHHHHHHHHcCCChhhHHhhhcCCCccCCCCccccccccccc
Q 031871           28 DEKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDED   70 (151)
Q Consensus        28 ~~~~~~~a~r~g~~v~t~~k~~~g~~~~~~~~~~~~~~kl~~~   70 (151)
                      +=++.+.|.+.|++.+++.+||.|...|..+.+.+.+..|+.+
T Consensus        22 gltq~~lA~~~gis~~~i~~~E~g~~~p~~~~l~~ia~~l~v~   64 (69)
T d1y7ya1          22 GLSQETLAFLSGLDRSYVGGVERGQRNVSLVNILKLATALDIE   64 (69)
T ss_dssp             TCCHHHHHHHHTCCHHHHHHHHTTCSCCBHHHHHHHHHHTTSC
T ss_pred             CCCHHHHHhHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHhCcC
Confidence            3356779999999999999999999876554444444444433

>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=94.10  E-value=0.042  Score=35.20  Aligned_cols=56  Identities=9%  Similarity=0.099  Sum_probs=44.7

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHH-hCCCHHHHHHHHcCCCCC---C---HHHHHHHHHHhC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQL-INEKPQVIQEYESGKAIP---N---QQILTKLERALG  144 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~-lgis~s~Is~~E~G~~~p---~---~~~l~kLa~~Lg  144 (151)
                      ..++..+|++..+.++++|.-||+. +|.|+.++|.+.+.-...   +   .+...+|-..|+
T Consensus        11 T~~i~~~v~~~L~~~~I~Q~~Fa~~VL~rsQGtlSdLL~~PKPW~kl~~~gR~~y~RM~~WL~   73 (87)
T d1x2la1          11 TAEIAFQVKEQLLKHNIGQRVFGHYVLGLSQGSVSEILARPKPWRKLTVKGKEPFIKMKQFLS   73 (87)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHTTCSCHHHHHHHHHCCCCGGGCCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHHhhChHHHHHHHhCCCChHHhhHHHHHHHHHHHHHhc
Confidence            3678999999999999999999997 699999999999854322   2   355666666665

>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=93.84  E-value=0.011  Score=34.84  Aligned_cols=29  Identities=10%  Similarity=0.242  Sum_probs=23.8

Q ss_pred             HHHHHHHHHcCCChhhHHhhhcCCCccCCC
Q 031871           29 EKVVNAARRAGADIETVRKSHAGTNKAASS   58 (151)
Q Consensus        29 ~~~~~~a~r~g~~v~t~~k~~~g~~~~~~~   58 (151)
                      -++.+.|++.|++..++.+||+|++ |..+
T Consensus        15 ~sq~elA~~~gvs~~~is~~E~g~~-~~~~   43 (63)
T d1r69a_          15 LNQAELAQKVGTTQQSIEQLENGKT-KRPR   43 (63)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHTTSC-SSCT
T ss_pred             CcHHHHHHHhCcCHHHHHHHHCCCC-cCHH
Confidence            3567899999999999999999975 4333

>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=93.54  E-value=0.043  Score=34.62  Aligned_cols=57  Identities=11%  Similarity=0.133  Sum_probs=47.0

Q ss_pred             HHHHHHHHHHHhcCCcCHHHHHHH-hCCCHHHHHHHHcCCC-----CCCHHHHHHHHHHhCCC
Q 031871           90 SELKKAIVQARNDKKLTQSQLAQL-INEKPQVIQEYESGKA-----IPNQQILTKLERALGVK  146 (151)
Q Consensus        90 ~~~~~~Lk~~R~~~glTQ~eLA~~-lgis~s~Is~~E~G~~-----~p~~~~l~kLa~~Lgv~  146 (151)
                      .++..+|++..+.++++|+-||+. +|.|+.++|.+.+...     ....+.+.+|-..|+.+
T Consensus         5 ~~I~~~i~~eL~~~~IsQ~~Fa~~vL~rsQGtlSdLL~kPKPW~~l~~gre~y~RM~~wL~~p   67 (80)
T d1s7ea2           5 KEVAQRITTELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLKSGRETFRRMWKWLQEP   67 (80)
T ss_dssp             HHHHHHHHHHHTSSCCCHHHHHHHTSSSCSSHHHHHTTSCCTTCCCSSCHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHHccChHHHHHHHcCCCChhhhcchhHHHHHHHHHHcCH
Confidence            578999999999999999999997 6999999999988322     12467788888887744

>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=93.52  E-value=0.014  Score=34.80  Aligned_cols=26  Identities=23%  Similarity=0.351  Sum_probs=22.8

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCcc
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNKA   55 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~~   55 (151)
                      ++.+.|++.|++.+|+.+||+|...|
T Consensus        18 tq~~lA~~~gvs~~ti~~~E~g~~~~   43 (65)
T d2croa_          18 TQTELATKAGVKQQSIQLIEAGVTKR   43 (65)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHTTCCSS
T ss_pred             CHHHHHHHHCcCHhHHHHHHCCCCCC
Confidence            46778999999999999999998754

>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=93.51  E-value=0.055  Score=32.15  Aligned_cols=31  Identities=19%  Similarity=0.162  Sum_probs=25.8

Q ss_pred             HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      +.|..+....-+|..|||+.+|||++||.+.
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            4456666667799999999999999999886

>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=93.41  E-value=0.052  Score=35.68  Aligned_cols=38  Identities=11%  Similarity=0.088  Sum_probs=32.4

Q ss_pred             hHHHHHHHHHHHhc-CC-cCHHHHHHHhCCCHHHHHHHHc
Q 031871           89 PSELKKAIVQARND-KK-LTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~-~g-lTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      ...++.|++-++.. .| +||.++|+.+|+|..||++.-+
T Consensus        41 ~~~la~R~~ia~~L~~G~~s~reI~~~~gvs~aTItR~s~   80 (101)
T d1jhga_          41 REALGTRVRIIEELLRGEMSQRELKNELGAGIATITRGSN   80 (101)
T ss_dssp             HHHHHHHHHHHHHHHHCCSCHHHHHHHHCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCcCHHHHHHHhCCChHHHHHHHH
Confidence            36789999888744 67 8999999999999999998755

>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=93.27  E-value=0.066  Score=31.84  Aligned_cols=34  Identities=12%  Similarity=0.262  Sum_probs=27.8

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      -..+-.++-..|+|+.|+|+.+|+|.++|.....
T Consensus        26 ~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~~~   59 (71)
T d1rp3a2          26 EKLVIQLIFYEELPAKEVAKILETSVSRVSQLKA   59 (71)
T ss_dssp             HHHHHHHHHTSCCCHHHHHHHTTSCHHHHHHHHH
T ss_pred             HHHHHHHHHhHhCCHHHHHHHHCCCHHHHHHHHH
Confidence            3445556677899999999999999999988654

>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=93.27  E-value=0.093  Score=34.39  Aligned_cols=56  Identities=9%  Similarity=0.099  Sum_probs=44.0

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHH-hCCCHHHHHHHHcCCCCCC------HHHHHHHHHHhC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQL-INEKPQVIQEYESGKAIPN------QQILTKLERALG  144 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~-lgis~s~Is~~E~G~~~p~------~~~l~kLa~~Lg  144 (151)
                      ..++..+|++..+.++++|+-||+. +|.|+.+++.+.+.-...+      .+...+|-..|.
T Consensus        19 T~~I~~~v~~eL~~~~IsQ~~Fa~~VL~rSQGtlSdLL~~PKPW~kl~~~gr~~y~RM~~wL~   81 (101)
T d1wh6a_          19 TLELTRQVKEKLAKNGICQRIFGEKVLGLSQGSVSDMLSRPKPWSKLTQKGREPFIRMQLWLS   81 (101)
T ss_dssp             HHHHHHHHHHHHHTTTCCHHHHHHHTTCCCHHHHHHHHHSCCCTTTCCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCCcHHHHHHHHHccChHHHHHHHhCCCCHHHHhHhhhHHHHHHHHHhc
Confidence            4789999999999999999999997 7999999999998543221      245556555554

>d1j5ya1 a.4.5.1 (A:3-67) Putative transcriptional regulator TM1602, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Biotin repressor-like
domain: Putative transcriptional regulator TM1602, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=93.08  E-value=0.098  Score=31.04  Aligned_cols=34  Identities=26%  Similarity=0.269  Sum_probs=26.7

Q ss_pred             HHHHHHHHHhcCC-cCHHHHHHHhCCCHHHHHHHH
Q 031871           92 LKKAIVQARNDKK-LTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus        92 ~~~~Lk~~R~~~g-lTQ~eLA~~lgis~s~Is~~E  125 (151)
                      ....|..++...+ +|..+||+.+|||..||.+.-
T Consensus         9 ~~~Il~~L~~~~~~vs~~~La~~l~VS~~TI~rdi   43 (65)
T d1j5ya1           9 LKSIVRILERSKEPVSGAQLAEELSVSRQVIVQDI   43 (65)
T ss_dssp             HHHHHHHHHHCSSCBCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHH
Confidence            3444666666555 899999999999999998854

>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=93.05  E-value=0.092  Score=34.95  Aligned_cols=56  Identities=11%  Similarity=0.127  Sum_probs=45.4

Q ss_pred             hHHHHHHHHHHHhcCCcCHHHHHHH-hCCCHHHHHHHHcCCCCC---C---HHHHHHHHHHhC
Q 031871           89 PSELKKAIVQARNDKKLTQSQLAQL-INEKPQVIQEYESGKAIP---N---QQILTKLERALG  144 (151)
Q Consensus        89 ~~~~~~~Lk~~R~~~glTQ~eLA~~-lgis~s~Is~~E~G~~~p---~---~~~l~kLa~~Lg  144 (151)
                      ...+..+|++..+.++++|+-||+. +|.|+.+++.+.+-....   +   .+...+|-..|+
T Consensus        29 T~~Ia~~v~~~L~~~~I~Q~~Fa~~VL~rSQGtlSdLL~~PKPW~kl~~~gR~~y~RM~~wL~   91 (111)
T d1wh8a_          29 TYSITKRVKEVLTDNNLGQRLFGESILGLTQGSVSDLLSRPKPWHKLSLKGREPFVRMQLWLN   91 (111)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHTTCCCHHHHHHHHHSCCCTTTSCHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHcCchHHHHHHHHHccChHHHHHHHhCCCChhHhhHHHHHHHHHHHHHhc
Confidence            4689999999999999999999997 799999999999854332   2   355666666665

>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=93.01  E-value=0.0077  Score=35.99  Aligned_cols=29  Identities=3%  Similarity=0.094  Sum_probs=24.5

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCccCCC
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNKAASS   58 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~~~~~   58 (151)
                      ++.+.|.+.|++.+|+.+||+|...|..+
T Consensus        18 tq~~lA~~~gvs~~~i~~~e~g~~~p~~~   46 (66)
T d2r1jl1          18 RQAALGKMVGVSNVAISQWERSETEPNGE   46 (66)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHTTSSCCBHH
T ss_pred             CHHHHHHHHCCCHHHHHHHHcCCCCCCHH
Confidence            45678999999999999999998876443

>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=92.95  E-value=0.21  Score=34.07  Aligned_cols=45  Identities=20%  Similarity=0.273  Sum_probs=38.1

Q ss_pred             HHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHH
Q 031871           95 AIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKL  139 (151)
Q Consensus        95 ~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kL  139 (151)
                      .|+-+|...|+|..++++..+.|..-+-.||.|+...+.-.-.+|
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            478899999999999999999999999999999977664433343

>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=92.84  E-value=0.0085  Score=35.92  Aligned_cols=41  Identities=7%  Similarity=-0.072  Sum_probs=30.0

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCccCCCCccccccccccc
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDED   70 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~~~~~~~~~~~~kl~~~   70 (151)
                      ++-+.|++.|++.+++.+|++|...|..+...+.+..++.+
T Consensus        16 tq~elA~~~gis~~~is~~e~g~~~p~~~~l~~ia~~l~v~   56 (66)
T d1utxa_          16 SQSELAALLEVSRQTINGIEKNKYNPSLQLALKIAYYLNTP   56 (66)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHTTSCCCCHHHHHHHHHHTTSC
T ss_pred             CHHHHHHhcccCHHHHHHHHcCCCCCCHHHHHHHHHHHCCC
Confidence            45678999999999999999999876544444444444443

>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=92.70  E-value=0.14  Score=30.27  Aligned_cols=31  Identities=23%  Similarity=0.395  Sum_probs=26.3

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHH
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQE  123 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~  123 (151)
                      ..-|..+.....+|..++|+.+|+|+++|.+
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            4456777788899999999999999998875

>d2hoea1 a.4.5.63 (A:10-71) N-acetylglucosamine kinase {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: N-acetylglucosamine kinase
species: Thermotoga maritima [TaxId: 2336]

Probab=92.59  E-value=0.082  Score=31.27  Aligned_cols=29  Identities=10%  Similarity=0.187  Sum_probs=24.6

Q ss_pred             HHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871           96 IVQARNDKKLTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus        96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E  125 (151)
                      |+.+++ ..+|..|||+.+|+|+++|+++-
T Consensus         5 l~~i~~-~pisr~eLa~~~gls~~TVs~~v   33 (62)
T d2hoea1           5 LKRIMK-SPVSRVELAEELGLTKTTVGEIA   33 (62)
T ss_dssp             HHHHHH-SCBCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHH-CCcCHHHHHHHHCcCHHHHHHHH
Confidence            566665 46999999999999999999874

>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=92.56  E-value=0.0098  Score=37.59  Aligned_cols=41  Identities=32%  Similarity=0.333  Sum_probs=27.9

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCC-ccCCCCccccccccccc
Q 031871           30 KVVNAARRAGADIETVRKSHAGTN-KAASSSTSLNTRKLDED   70 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~-~~~~~~~~~~~~kl~~~   70 (151)
                      +..+.|.++|++.+++.+||+|+. .|....+.+.+..|+.+
T Consensus        27 t~~eLA~~~Gvs~~~ls~iE~G~~~~ps~~tl~kia~~L~v~   68 (82)
T d2ofya1          27 SMVTVAFDAGISVETLRKIETGRIATPAFFTIAAVARVLDLS   68 (82)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHTTCCSSCBHHHHHHHHHHTTCC
T ss_pred             CHHHHHHHHcCCHHHHHHHHcCCcCCCCHHHHHHHHHHHCCC
Confidence            345799999999999999999974 44433333444444443

>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=92.10  E-value=0.012  Score=36.09  Aligned_cols=41  Identities=15%  Similarity=0.052  Sum_probs=29.5

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCccCCCCccccccccccc
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDED   70 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~~~~~~~~~~~~kl~~~   70 (151)
                      ++-..|.+.|++.+++.+|+.|...|..+.+.+....++.+
T Consensus        25 tq~~lA~~~gis~~~i~~~e~g~~~p~~~~l~~ia~~l~v~   65 (77)
T d2b5aa1          25 SQEELADLAGLHRTYISEVERGDRNISLINIHKICAALDIP   65 (77)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHTTCSCCBHHHHHHHHHHTTCC
T ss_pred             CHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCC
Confidence            55678999999999999999998766444434444444443

>d3e5ua1 a.4.5.4 (A:148-227) Chlorophenol reduction protein CprK {Desulfitobacterium hafniense [TaxId: 49338]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Chlorophenol reduction protein CprK
species: Desulfitobacterium hafniense [TaxId: 49338]

Probab=92.01  E-value=0.072  Score=32.68  Aligned_cols=23  Identities=9%  Similarity=0.147  Sum_probs=20.6

Q ss_pred             CCcCHHHHHHHhCCCHHHHHHHH
Q 031871          103 KKLTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus       103 ~glTQ~eLA~~lgis~s~Is~~E  125 (151)
                      ..+||.|||..+|+|+.++++.-
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            46899999999999999999874

>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=91.89  E-value=0.058  Score=33.06  Aligned_cols=39  Identities=26%  Similarity=0.158  Sum_probs=28.5

Q ss_pred             CCcCHHHHHHHhCCCHHHHHHHHc-----C-------C-CCCCHHHHHHHHH
Q 031871          103 KKLTQSQLAQLINEKPQVIQEYES-----G-------K-AIPNQQILTKLER  141 (151)
Q Consensus       103 ~glTQ~eLA~~lgis~s~Is~~E~-----G-------~-~~p~~~~l~kLa~  141 (151)
                      ..+||.|||..+|+|+.+|++.-+     |       . ...+.+.|.++|+
T Consensus        28 ~~lt~~eLA~~~G~sretvsr~L~~l~~~glI~~~~~~i~I~d~~~L~~~a~   79 (81)
T d2gaua1          28 IYLSREELATLSNMTVSNAIRTLSTFVSERMLALDGKRIKIIDCDRLQKTAR   79 (81)
T ss_dssp             CCCCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEEETTEEEESCHHHHHHHHH
T ss_pred             ecCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCEEEEcCHHHHHHHHh
Confidence            468999999999999999998732     1       1 1345666666664

>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=91.81  E-value=0.029  Score=35.41  Aligned_cols=43  Identities=19%  Similarity=0.181  Sum_probs=31.0

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCccCCCCcccccccccccch
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTE   72 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~~~~~~~~~~~~kl~~~~~   72 (151)
                      ++-+.|.+.|++.+++.+||+|.+.|..+.+.+...-|+.+.+
T Consensus        27 tq~~lA~~lgis~~~is~~E~g~~~~s~~~l~~ia~~l~v~~~   69 (87)
T d1lmb3_          27 SQESVADKMGMGQSGVGALFNGINALNAYNAALLAKILKVSVE   69 (87)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHTTSSCCCHHHHHHHHHHHTSCGG
T ss_pred             CHHHHHHHhCccHHHHHHHHhccCCCcHHHHHHHHHHHCCCHH
Confidence            4567899999999999999999997655444444444444433

>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=91.63  E-value=0.14  Score=30.13  Aligned_cols=31  Identities=13%  Similarity=0.243  Sum_probs=26.5

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHH
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQE  123 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~  123 (151)
                      .+-|..+.....+|..+||+.+|+|.+++..
T Consensus         8 ~~IL~~L~~~~r~s~~eiA~~l~ls~~~v~~   38 (63)
T d2cg4a1           8 RGILEALMGNARTAYAELAKQFGVSPETIHV   38 (63)
T ss_dssp             HHHHHHHHHCTTSCHHHHHHHHTSCHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHH
Confidence            3457778888999999999999999988765

>d1zyba1 a.4.5.4 (A:148-220) Probable transcription regulator BT4300, C-terminal domain {Bacteroides thetaiotaomicron [TaxId: 818]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Probable transcription regulator BT4300, C-terminal domain
species: Bacteroides thetaiotaomicron [TaxId: 818]

Probab=91.54  E-value=0.072  Score=32.50  Aligned_cols=22  Identities=18%  Similarity=0.240  Sum_probs=20.0

Q ss_pred             CcCHHHHHHHhCCCHHHHHHHH
Q 031871          104 KLTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus       104 glTQ~eLA~~lgis~s~Is~~E  125 (151)
                      .+||+|||..+|+++.+|++.-
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            5899999999999999999864

>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=91.36  E-value=0.076  Score=32.60  Aligned_cols=22  Identities=23%  Similarity=0.249  Sum_probs=20.1

Q ss_pred             CcCHHHHHHHhCCCHHHHHHHH
Q 031871          104 KLTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus       104 glTQ~eLA~~lgis~s~Is~~E  125 (151)
                      .+||+|+|..+|+++.++++..
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            5899999999999999999873

>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=91.05  E-value=0.18  Score=29.42  Aligned_cols=30  Identities=7%  Similarity=0.148  Sum_probs=25.0

Q ss_pred             HHHHHHHhcCCcCHHHHHHHhCCCHHHHHH
Q 031871           94 KAIVQARNDKKLTQSQLAQLINEKPQVIQE  123 (151)
Q Consensus        94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~  123 (151)
                      +-|..+.....+|..+||+.+|+|++++..
T Consensus         7 kIl~~L~~n~r~s~~~lA~~~gls~~~v~~   36 (60)
T d1i1ga1           7 IILEILEKDARTPFTEIAKKLGISETAVRK   36 (60)
T ss_dssp             HHHHHHHHCTTCCHHHHHHHHTSCHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHH
Confidence            345667778889999999999999998865

>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=90.96  E-value=0.18  Score=29.74  Aligned_cols=33  Identities=9%  Similarity=0.144  Sum_probs=27.5

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E  125 (151)
                      ...+-.+|.-.|+|+.|+|+.+|+|.++|...-
T Consensus        23 ~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l   55 (68)
T d1or7a1          23 LRMAITLRELDGLSYEEIAAIMDCPVGTVRSRI   55 (68)
T ss_dssp             HHHHHHHHHTTCCCHHHHHHHTTSCHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCHHHHHHHHCcCHHHHHHHH
Confidence            344556778889999999999999999998754

>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=90.95  E-value=0.19  Score=29.22  Aligned_cols=30  Identities=23%  Similarity=0.288  Sum_probs=25.5

Q ss_pred             HHHHHHHhcCCcCHHHHHHHhCCCHHHHHH
Q 031871           94 KAIVQARNDKKLTQSQLAQLINEKPQVIQE  123 (151)
Q Consensus        94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~  123 (151)
                      +-|..+.....+|..++|+.+|+|.++|..
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            446777778889999999999999988764

>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=90.85  E-value=0.017  Score=34.67  Aligned_cols=26  Identities=12%  Similarity=0.105  Sum_probs=22.4

Q ss_pred             HHHHHHHHHcCCChhhHHhhhcCCCc
Q 031871           29 EKVVNAARRAGADIETVRKSHAGTNK   54 (151)
Q Consensus        29 ~~~~~~a~r~g~~v~t~~k~~~g~~~   54 (151)
                      =++.+.|++.|++.+++.+||+|...
T Consensus        15 ltq~~la~~~gis~~~i~~~E~g~~~   40 (68)
T d1b0na2          15 YSLSELAEKAGVAKSYLSSIERNLQT   40 (68)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHTTCCS
T ss_pred             CCHHHHHHHHCCCHHHHHHHHcCCCC
Confidence            35677899999999999999999653

>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=90.66  E-value=0.12  Score=32.36  Aligned_cols=23  Identities=26%  Similarity=0.241  Sum_probs=20.5

Q ss_pred             CCcCHHHHHHHhCCCHHHHHHHH
Q 031871          103 KKLTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus       103 ~glTQ~eLA~~lgis~s~Is~~E  125 (151)
                      .++|+.+||+.+|+++++++++-
T Consensus        20 ~~lt~~eLa~~l~i~~~~vs~~l   42 (85)
T d3ctaa1          20 AYLTSSKLADMLGISQQSASRII   42 (85)
T ss_dssp             EECCHHHHHHHHTSCHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHH
Confidence            46999999999999999998863

>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=90.57  E-value=0.17  Score=29.60  Aligned_cols=34  Identities=15%  Similarity=0.045  Sum_probs=29.0

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      ...|.......+..+.+.|+.+|||++|+.+-..
T Consensus        22 r~~I~~aL~~~~gn~~~aA~~LGIsR~TL~rkmk   55 (60)
T d1umqa_          22 WEHIQRIYEMCDRNVSETARRLNMHRRTLQRILA   55 (60)
T ss_dssp             HHHHHHHHHHTTSCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCcHHHHHHHHCCCHHHHHHHHH
Confidence            4567888888999999999999999999987543

>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=90.30  E-value=0.099  Score=34.70  Aligned_cols=26  Identities=19%  Similarity=0.281  Sum_probs=22.3

Q ss_pred             CcCHHHHHHHhCCCHHHHHHHH-cCCC
Q 031871          104 KLTQSQLAQLINEKPQVIQEYE-SGKA  129 (151)
Q Consensus       104 glTQ~eLA~~lgis~s~Is~~E-~G~~  129 (151)
                      .-||.++|+.+|||+.++.+|- +.+.
T Consensus        36 kktqeqiAeelGisr~tLyrWrt~dk~   62 (120)
T d2ao9a1          36 KRTQDEMANELGINRTTLWEWRTKNQD   62 (120)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHHHCHH
T ss_pred             hhhHHHHHHHhChhHHHHHHHhhcchh
Confidence            4599999999999999999998 4443

>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=90.03  E-value=0.0029  Score=43.33  Aligned_cols=26  Identities=15%  Similarity=0.294  Sum_probs=23.4

Q ss_pred             hcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871          101 NDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus       101 ~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      .++||||+|+|+.+|.|++.|+-+|+
T Consensus         2 R~kGltQ~eIA~~LgTSraNIs~IEk   27 (122)
T d1nr3a_           2 RERGWSQKKIARELKTTRQNVSAIER   27 (122)
T ss_dssp             CCCSCSSCSTHHHHHHCCSSSCCHHH
T ss_pred             ccccCCHHHHHHHHCccHHHHHHHHH
Confidence            36899999999999999998888886

>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=89.59  E-value=0.021  Score=35.41  Aligned_cols=42  Identities=10%  Similarity=0.086  Sum_probs=31.0

Q ss_pred             cCHHHHHHHHHcCCChhhHHhhhcCCCccCCCCccccccccc
Q 031871           27 KDEKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLD   68 (151)
Q Consensus        27 ~~~~~~~~a~r~g~~v~t~~k~~~g~~~~~~~~~~~~~~kl~   68 (151)
                      ++-++-+.|...|++..++.+||.|...|..+.+.+....|+
T Consensus        18 ~gltq~~lA~~~gis~~~is~~E~G~~~p~~~~l~~la~~l~   59 (78)
T d1x57a1          18 KGLTQKDLATKINEKPQVIADYESGRAIPNNQVLGKIERAIG   59 (78)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHHHTCSCCCHHHHHHHHHHHT
T ss_pred             cCCChhHHHHcCCCCHHHHHHHHccCCCCCHHHHHHHHHHhC
Confidence            344667899999999999999999998765544444444443

>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=89.40  E-value=0.028  Score=34.47  Aligned_cols=41  Identities=10%  Similarity=0.105  Sum_probs=29.9

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCccCCCCccccccccccc
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDED   70 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~~~~~~~~~~~~kl~~~   70 (151)
                      +.-+.|.+.|++.+++.+||+|...|......+....++.+
T Consensus        23 sq~~lA~~~gis~~~i~~~E~g~~~p~~~~l~~ia~~l~v~   63 (79)
T d1y9qa1          23 SLDATAQLTGVSKAMLGQIERGESSPTIATLWKIASGLEAS   63 (79)
T ss_dssp             CHHHHHHHHSSCHHHHHHHHTTCSCCCHHHHHHHHHHHTCC
T ss_pred             CHHHHHHHHCcchhHHHHHHcCCCCCCHHHHHHHHHHHCCC
Confidence            56778999999999999999998876444444444444443

>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=89.23  E-value=0.41  Score=28.36  Aligned_cols=36  Identities=19%  Similarity=0.304  Sum_probs=27.9

Q ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q 031871          106 TQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALG  144 (151)
Q Consensus       106 TQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l~kLa~~Lg  144 (151)
                      ++..+|+.+||+++.|++|  |+-.|. .....|...-+
T Consensus        12 ~~~k~A~algis~~AVsqW--Ge~VPe-~RA~~ie~~T~   47 (61)
T d1rzsa_          12 TQRAVAKALGISDAAVSQW--KEVIPE-KDAYRLEIVTA   47 (61)
T ss_dssp             SHHHHHHHHTCCHHHHHHC--CSBCCH-HHHHHHHHHTT
T ss_pred             CHHHHHHHhCCCHHHHHHH--hccCcH-HHHHHHHHHhC
Confidence            6788999999999999999  776554 44556666544

>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=89.07  E-value=0.15  Score=32.99  Aligned_cols=39  Identities=15%  Similarity=0.120  Sum_probs=29.0

Q ss_pred             CcCHHHHHHHhCCC-HHHHHHHHc------------CC-CCCCHHHHHHHHHH
Q 031871          104 KLTQSQLAQLINEK-PQVIQEYES------------GK-AIPNQQILTKLERA  142 (151)
Q Consensus       104 glTQ~eLA~~lgis-~s~Is~~E~------------G~-~~p~~~~l~kLa~~  142 (151)
                      .+||+|||..+|+| +.+|++.-+            ++ ..++.+.|.++|.-
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 889887632            12 23577778777753

>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=88.71  E-value=0.29  Score=31.29  Aligned_cols=32  Identities=13%  Similarity=0.287  Sum_probs=24.8

Q ss_pred             HHHHHHHHh-cCCcCHHHHHHHhCCCHHHHHHH
Q 031871           93 KKAIVQARN-DKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        93 ~~~Lk~~R~-~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ...|..+.. ...+|+.+||+.+|+++++|++.
T Consensus        24 ~~iL~~L~~~~~~~t~~eLa~~~~i~~~tvs~~   56 (109)
T d2d1ha1          24 VAVLLKMVEIEKPITSEELADIFKLSKTTVENS   56 (109)
T ss_dssp             HHHHHHHHHHCSCEEHHHHHHHHTCCHHHHHHH
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHCccHhHHHHH
Confidence            444555543 44599999999999999999886

>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=88.54  E-value=0.9  Score=29.29  Aligned_cols=73  Identities=10%  Similarity=0.038  Sum_probs=42.9

Q ss_pred             HHHHHHcCCChhhHHhhhc-CCCccCC-CCcccccccccccchhhhHHHHHhhccCCcchHHHHHHHHHHHhcCCcCHHH
Q 031871           32 VNAARRAGADIETVRKSHA-GTNKAAS-SSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQ  109 (151)
Q Consensus        32 ~~~a~r~g~~v~t~~k~~~-g~~~~~~-~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~~~~~~~~~Lk~~R~~~glTQ~e  109 (151)
                      -+.|+..|+++.|+|-|+. |-..|.. .+. ..-+--+.  .                ....-..|+.+|. .|+|.++
T Consensus         7 ~evA~~~gvs~~tlR~Ye~~GLl~P~~~r~~-~gyR~Y~~--~----------------~l~~l~~I~~lr~-~g~sl~e   66 (118)
T d1r8ea1           7 GEVSKLANVSIKALRYYDKIDLFKPAYVDPD-TSYRYYTD--S----------------QLIHLDLIKSLKY-IGTPLEE   66 (118)
T ss_dssp             HHHHHHHTCCHHHHHHHHHTTSSCCSEECTT-TCCEEEET--G----------------GGGHHHHHHHHHH-TTCCHHH
T ss_pred             HHHHHHHCcCHHHHHHHHHcCCcccccccCC-CCcccccH--H----------------HHHHHHHHHHHHH-cCCCHHH
Confidence            4689999999999999996 3233321 100 00011111  1                1122344666654 7999999


Q ss_pred             HHHHhCCCHHHHHHH
Q 031871          110 LAQLINEKPQVIQEY  124 (151)
Q Consensus       110 LA~~lgis~s~Is~~  124 (151)
                      +.+.+..+...+..+
T Consensus        67 Ik~~l~~~~~~~~~~   81 (118)
T d1r8ea1          67 MKKAQDLEMEELFAF   81 (118)
T ss_dssp             HHHHTTSCHHHHHHH
T ss_pred             HHHHHccCHHHHHHH
Confidence            988887776555443

>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=88.22  E-value=0.17  Score=33.51  Aligned_cols=24  Identities=21%  Similarity=0.322  Sum_probs=21.5

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcCC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESGK  128 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G~  128 (151)
                      |+..|||+.+|||..||.-||+-.
T Consensus         1 m~Ige~A~~~gvs~~TlR~Ye~~G   24 (127)
T d1q06a_           1 MNISDVAKITGLTSKAIRFYEEKG   24 (127)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHTT
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHcC
Confidence            678999999999999999998743

>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=88.20  E-value=0.47  Score=27.82  Aligned_cols=25  Identities=12%  Similarity=0.221  Sum_probs=23.2

Q ss_pred             cCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871          102 DKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus       102 ~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      ...+|..++|+.+|+|...|.++|.
T Consensus        26 ~~~~tl~eIa~~lgiS~erVrqi~~   50 (61)
T d1ku3a_          26 GREHTLEEVGAYFGVTRERIRQIEN   50 (61)
T ss_dssp             SSCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            5779999999999999999999986

>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=88.13  E-value=0.15  Score=31.07  Aligned_cols=23  Identities=22%  Similarity=0.463  Sum_probs=20.6

Q ss_pred             CcCHHHHHHHhCCCHHHHHHHHc
Q 031871          104 KLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus       104 glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      .+++++||+.+|||..||..|-+
T Consensus         2 ~Vnk~~lA~iFGVS~~TI~~W~~   24 (68)
T d1j9ia_           2 EVNKKQLADIFGASIRTIQNWQE   24 (68)
T ss_dssp             EEEHHHHHHHTTCCHHHHHHHTT
T ss_pred             ccCHHHHHHHhCCCHHHHHHHHH
Confidence            35789999999999999999965

>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=87.95  E-value=0.3  Score=31.88  Aligned_cols=34  Identities=6%  Similarity=0.079  Sum_probs=28.4

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      ...+-.++-..|||+.|+|+.+|+|+++|.....
T Consensus        21 qR~v~~L~y~~~ls~~EIA~~lgiS~~aV~~~l~   54 (106)
T d1s7oa_          21 QMNYIELYYADDYSLAEIADEFGVSRQAVYDNIK   54 (106)
T ss_dssp             HHHHHHHHHHTCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            4556667788899999999999999999987644

>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=87.72  E-value=0.25  Score=29.25  Aligned_cols=25  Identities=8%  Similarity=0.126  Sum_probs=21.9

Q ss_pred             cCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871          102 DKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus       102 ~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      ..|+|..++|+.+|+|+.||..+-.
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            3599999999999999999987654

>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=87.71  E-value=0.27  Score=29.74  Aligned_cols=26  Identities=19%  Similarity=0.249  Sum_probs=22.9

Q ss_pred             HhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871          100 RNDKKLTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus       100 R~~~glTQ~eLA~~lgis~s~Is~~E  125 (151)
                      +...++|..|+|+.+|++++++.++-
T Consensus        16 ~~~~~~s~~eia~~~~~~~st~~rll   41 (75)
T d1mkma1          16 KNPGDVSVSEIAEKFNMSVSNAYKYM   41 (75)
T ss_dssp             HCSSCBCHHHHHHHTTCCHHHHHHHH
T ss_pred             hCCCCCCHHHHHHHHCcCHHHHHHHH
Confidence            44578999999999999999999983

>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=87.35  E-value=0.78  Score=30.36  Aligned_cols=38  Identities=8%  Similarity=0.083  Sum_probs=30.5

Q ss_pred             chHHHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871           88 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus        88 ~~~~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E  125 (151)
                      +...-...|..+-...|+|+.+||+.+++++++|+++-
T Consensus        34 lt~~q~~vL~~l~~~~~~t~~~la~~l~~~~~~vsr~l   71 (141)
T d1lnwa_          34 LTPPDVHVLKLIDEQRGLNLQDLGRQMCRDKALITRKI   71 (141)
T ss_dssp             CCHHHHHHHHHHHSSTTCBHHHHHHHTTCCHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHCCCCCHHHHHHHHCccHhHHHHHH
Confidence            34444556677777888999999999999999999873

>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=87.31  E-value=0.23  Score=30.92  Aligned_cols=37  Identities=14%  Similarity=0.113  Sum_probs=28.9

Q ss_pred             HhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHH
Q 031871          100 RNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQIL  136 (151)
Q Consensus       100 R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p~~~~l  136 (151)
                      -.-..+|..+||+.+|+|+++|.++-+.-..-....+
T Consensus        32 ~~~~~~si~~lA~~~~vS~sTi~Rf~kklG~~gf~e~   68 (83)
T d2o3fa1          32 HKAIESTVNEISALANSSDAAVIRLCKSLGLKGFQDL   68 (83)
T ss_dssp             HHHHTCCHHHHHHHTTCCHHHHHHHHHHTTCSSHHHH
T ss_pred             HHHHHccHHHHHHHHCCCHHHHHHHHHHhCCCCHHHH
Confidence            3445799999999999999999999875555554443

>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=86.77  E-value=0.36  Score=30.98  Aligned_cols=24  Identities=17%  Similarity=0.282  Sum_probs=21.8

Q ss_pred             CcCHHHHHHHhCCCHHHHHHHHcC
Q 031871          104 KLTQSQLAQLINEKPQVIQEYESG  127 (151)
Q Consensus       104 glTQ~eLA~~lgis~s~Is~~E~G  127 (151)
                      .+|..|||+.+|+|+.+|.-||+-
T Consensus         2 ~ytI~e~A~~~gvs~~tlR~Ye~~   25 (109)
T d1r8da_           2 KYQVKQVAEISGVSIRTLHHYDNI   25 (109)
T ss_dssp             CBCHHHHHHHHSCCHHHHHHHHHT
T ss_pred             cccHHHHHHHHCcCHHHHHHHHHc
Confidence            478999999999999999999863

>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=86.67  E-value=0.56  Score=30.00  Aligned_cols=65  Identities=11%  Similarity=0.081  Sum_probs=37.9

Q ss_pred             HHHHHHcCCChhhHHhhhcCCC-ccCCCCcccccccccccchhhhHHHHHhhccCCcchHHHHHHHHHHHhcCCcCHHHH
Q 031871           32 VNAARRAGADIETVRKSHAGTN-KAASSSTSLNTRKLDEDTENLALLLSVLYCTDDRVPSELKKAIVQARNDKKLTQSQL  110 (151)
Q Consensus        32 ~~~a~r~g~~v~t~~k~~~g~~-~~~~~~~~~~~~kl~~~~~~~~~~~s~~~~~~~~~~~~~~~~Lk~~R~~~glTQ~eL  110 (151)
                      -+.|+.+|+++.|+|-|+.-.. .|..    +... =-+.   +..         .  ....-..|+.+|. .|+|.+++
T Consensus         6 ~e~A~~~gvs~~tlR~Ye~~GLl~p~~----r~~~-gyR~---Y~~---------~--~~~~l~~I~~lr~-~G~sl~eI   65 (109)
T d1r8da_           6 KQVAEISGVSIRTLHHYDNIELLNPSA----LTDA-GYRL---YSD---------A--DLERLQQILFFKE-IGFRLDEI   65 (109)
T ss_dssp             HHHHHHHSCCHHHHHHHHHTTSSCCSE----ECTT-CCEE---BCH---------H--HHHHHHHHHHHHH-TTCCHHHH
T ss_pred             HHHHHHHCcCHHHHHHHHHcCCcCCcc----cCCc-cccc---ccH---------H--HHHHHHHHHHHHH-cCCCHHHH
Confidence            4689999999999999996322 2211    1100 0010   000         0  1122355666764 79999999


Q ss_pred             HHHhCC
Q 031871          111 AQLINE  116 (151)
Q Consensus       111 A~~lgi  116 (151)
                      .+.+..
T Consensus        66 ~~~l~~   71 (109)
T d1r8da_          66 KEMLDH   71 (109)
T ss_dssp             HHHHHC
T ss_pred             HHHHhc
Confidence            887754

>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=86.46  E-value=0.42  Score=30.08  Aligned_cols=33  Identities=3%  Similarity=-0.011  Sum_probs=28.4

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E  125 (151)
                      ...|..+....+..+.+.|+.+||+++|+.+..
T Consensus        51 ~~~i~~aL~~~~gn~~~aA~~LGisR~tL~~kl   83 (89)
T d1etxa_          51 QPLLDMVMQYTRGNATRAALMMGINRGTLRKKL   83 (89)
T ss_dssp             HHHHHHHHHHTTTCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHHcCCcHHHHHHHHCCCHHHHHHHH
Confidence            556777888889999999999999999998754

>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=86.22  E-value=0.32  Score=28.93  Aligned_cols=34  Identities=9%  Similarity=-0.023  Sum_probs=26.8

Q ss_pred             HHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCC
Q 031871           96 IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA  129 (151)
Q Consensus        96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~  129 (151)
                      +-.-+--.++|..++|+.+|||++++..+-..+.
T Consensus        16 l~~~~G~~~~s~~~Ia~~agvs~~t~Y~~F~~K~   49 (74)
T d1v7ba1          16 YIGEYSLETLSYDSLAEATGLSKSGLIYHFPSRH   49 (74)
T ss_dssp             HHHHSCSTTCCHHHHHHHHCSCHHHHHHHCSSHH
T ss_pred             HHHHhCccccCHHHHHHHhCcCcchHhhhCCCHH
Confidence            3333455678999999999999999999866553

>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=85.92  E-value=0.52  Score=30.70  Aligned_cols=34  Identities=12%  Similarity=0.119  Sum_probs=28.5

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      ...+-.+|-..|+|..|+|+.+|+|+++|.....
T Consensus        23 QR~vl~L~~~e~ls~~EIA~~lgiS~~aV~~~l~   56 (106)
T d1xsva_          23 QRNYLELFYLEDYSLSEIADTFNVSRQAVYDNIR   56 (106)
T ss_dssp             HHHHHHHHHTSCCCHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCcHHHHHHHHCcCHHHHHHHHH
Confidence            4456668889999999999999999999987543

>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=85.59  E-value=0.69  Score=30.44  Aligned_cols=35  Identities=6%  Similarity=0.012  Sum_probs=28.0

Q ss_pred             HHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871           91 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus        91 ~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E  125 (151)
                      .-...|..+...-++|+.+||+.+|+++++|+++-
T Consensus        31 ~q~~iL~~i~~~~~~t~~~la~~l~i~~~tvs~~l   65 (139)
T d2a61a1          31 AQFDILQKIYFEGPKRPGELSVLLGVAKSTVTGLV   65 (139)
T ss_dssp             HHHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHhCCCcccchHHH
Confidence            34455666666678999999999999999998874

>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=85.59  E-value=0.34  Score=29.13  Aligned_cols=24  Identities=13%  Similarity=0.238  Sum_probs=22.2

Q ss_pred             CCcCHHHHHHHhCCCHHHHHHHHc
Q 031871          103 KKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus       103 ~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      ..+|+.++|+.+|+|+..|.++|.
T Consensus        24 ~~~tl~eI~~~lgiSrerVrqie~   47 (68)
T d2p7vb1          24 TDYTLEEVGKQFDVTRERIRQIEA   47 (68)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CcCCHHHHHHHHCCCHHHHHHHHH
Confidence            458999999999999999999987

>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=85.43  E-value=0.38  Score=28.29  Aligned_cols=44  Identities=9%  Similarity=0.026  Sum_probs=29.8

Q ss_pred             hcCCcCHHHHHHHhCCCHHHHHHHHcCC----CCCCHHHHHHHHHHhC
Q 031871          101 NDKKLTQSQLAQLINEKPQVIQEYESGK----AIPNQQILTKLERALG  144 (151)
Q Consensus       101 ~~~glTQ~eLA~~lgis~s~Is~~E~G~----~~p~~~~l~kLa~~Lg  144 (151)
                      ...|+|-+|+|+.+|+|..||..+-..-    ..-+...+...+..+|
T Consensus        16 ~~~G~s~~eIA~~L~is~~TV~~~~~~i~~Kl~v~~r~~lv~~a~~~G   63 (67)
T d1fsea_          16 LVQDKTTKEIASELFISEKTVRNHISNAMQKLGVKGRSQAVVELLRMG   63 (67)
T ss_dssp             HTTTCCHHHHHHHHTSCHHHHHHHHHHHHHHHTCSSHHHHHHHHHHTT
T ss_pred             HHccCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCCCHHHHHHHHHHcc
Confidence            3579999999999999999998775421    2234444444444444

>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=84.91  E-value=0.89  Score=26.53  Aligned_cols=37  Identities=8%  Similarity=0.081  Sum_probs=29.4

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCC
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA  129 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~  129 (151)
                      +..+-.-+--.++|..++|+.+|+|+.++..+-.++.
T Consensus         9 A~~lf~~~G~~~~ti~~Ia~~agvs~~~~Y~~F~~K~   45 (69)
T d2i10a1           9 AMELFWRQGYEGTSITDLTKALGINPPSLYAAFGSKR   45 (69)
T ss_dssp             HHHHHHHHTTTTCCHHHHHHHHTCCHHHHHHHHCSHH
T ss_pred             HHHHHHHHCcccCCHHHHHHHhCCChhHHHHHCcCHH
Confidence            3344445667789999999999999999999876653

>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=84.75  E-value=0.95  Score=27.98  Aligned_cols=47  Identities=11%  Similarity=0.155  Sum_probs=36.7

Q ss_pred             CCcCHHHHHHHhCCCHHHHHHHHcC----CCCCCHHHHHHHHHHhCCCCCC
Q 031871          103 KKLTQSQLAQLINEKPQVIQEYESG----KAIPNQQILTKLERALGVKLRG  149 (151)
Q Consensus       103 ~glTQ~eLA~~lgis~s~Is~~E~G----~~~p~~~~l~kLa~~Lgv~l~e  149 (151)
                      .|++.+++|+.+++|..||..+-+.    -...+...+...|..+|+-+-|
T Consensus        36 ~G~s~~eIA~~l~iS~~TV~~~~~~i~~Kl~~~~~~~lv~~a~~~gl~~~~   86 (87)
T d1p4wa_          36 EGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVDNDIALLNYLSSVSMTPVD   86 (87)
T ss_dssp             HTCCHHHHHHHHTSCHHHHHHHHHHHHHHHTCSSHHHHHHHHHHHTCSSCC
T ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCCCCHHHHHHHHHHcCCCCCC
Confidence            4999999999999999999877542    2455777788888888865433

>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=84.64  E-value=0.38  Score=28.39  Aligned_cols=34  Identities=9%  Similarity=-0.087  Sum_probs=26.6

Q ss_pred             HHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCCCC
Q 031871           96 IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIP  131 (151)
Q Consensus        96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~~p  131 (151)
                      |.+.-.+.|  |...|+.+|+.++.|++--+-.+.+
T Consensus         7 L~dyv~~~G--QaKaA~~LGv~Q~AIsKAira~R~I   40 (61)
T d1d1la_           7 LKDYAMRFG--QTKTAKDLGVYQSAINKAIHAGRKI   40 (61)
T ss_dssp             HHHHHHHHC--HHHHHHHHTCCTHHHHHHHHTTCCE
T ss_pred             HHHHHHHHC--hHHHHHHcCccHHHHHHHHhcCCeE
Confidence            344555667  9999999999999999987765543

>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=84.33  E-value=0.28  Score=30.52  Aligned_cols=40  Identities=10%  Similarity=0.010  Sum_probs=28.8

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCccCCCCcccccccccc
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDE   69 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~~~~~~~~~~~~kl~~   69 (151)
                      ++-..|++.|++.+|+.+|++|+..+..+...+....++.
T Consensus        16 sq~~LA~~lGvs~~~is~ie~g~~~~s~~~~~kla~~lgv   55 (87)
T d2icta1          16 SLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVIGS   55 (87)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHTSSCCCHHHHHHHHHHTCS
T ss_pred             CHHHHHHHHhhcHHHHHHHHHhccCCCHHHHHHHHHHHCc
Confidence            4567999999999999999999887544333333344443

>d2ev0a1 a.4.5.24 (A:2-62) Manganese transport regulator MntR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Iron-dependent repressor protein
domain: Manganese transport regulator MntR
species: Bacillus subtilis [TaxId: 1423]

Probab=84.22  E-value=1.1  Score=26.00  Aligned_cols=35  Identities=11%  Similarity=0.164  Sum_probs=24.8

Q ss_pred             HHHHHHHHH-HhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871           91 ELKKAIVQA-RNDKKLTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus        91 ~~~~~Lk~~-R~~~glTQ~eLA~~lgis~s~Is~~E  125 (151)
                      ++-+.|-.+ ......+..+||+.+|+++++++..-
T Consensus         7 dYLk~I~~l~~~~~~v~~~~iA~~L~vs~~SVs~mi   42 (61)
T d2ev0a1           7 DYIEQIYMLIEEKGYARVSDIAEALAVHPSSVTKMV   42 (61)
T ss_dssp             HHHHHHHHHHHHHSSCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCccHHHHHHHhCCCchhHHHHH
Confidence            333444333 33456789999999999999998763

>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=84.11  E-value=0.29  Score=29.42  Aligned_cols=25  Identities=16%  Similarity=0.119  Sum_probs=22.3

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCCCc
Q 031871           30 KVVNAARRAGADIETVRKSHAGTNK   54 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~~~   54 (151)
                      ++.++|.+.|++..|+.+||.|...
T Consensus        16 tQ~elA~~LGvs~~ti~~yE~G~r~   40 (67)
T d2auwa1          16 SLTTAAEALGISRRMVSYYRTAHKI   40 (67)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHTTSSC
T ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCC
Confidence            4678999999999999999999764

>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=83.93  E-value=0.51  Score=27.62  Aligned_cols=44  Identities=14%  Similarity=-0.012  Sum_probs=30.2

Q ss_pred             hcCCcCHHHHHHHhCCCHHHHHHHHcC----CCCCCHHHHHHHHHHhC
Q 031871          101 NDKKLTQSQLAQLINEKPQVIQEYESG----KAIPNQQILTKLERALG  144 (151)
Q Consensus       101 ~~~glTQ~eLA~~lgis~s~Is~~E~G----~~~p~~~~l~kLa~~Lg  144 (151)
                      ...|+|-+|+|+.+|+|..||..+-+.    -...+...+..+|..+|
T Consensus        16 ~~~G~s~~eIA~~l~iS~~TV~~~~~~i~~Klgv~~r~~l~~~a~~~g   63 (65)
T d1l3la1          16 IAVGKTMEEIADVEGVKYNSVRVKLREAMKRFDVRSKAHLTALAIRRK   63 (65)
T ss_dssp             HTTTCCHHHHHHHHTCCHHHHHHHHHHHHHHHTCSSHHHHHHHHHHTT
T ss_pred             HHhcCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCCCHHHHHHHHHHcC
Confidence            356999999999999999999876542    12334444555554444

>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=83.90  E-value=0.62  Score=31.03  Aligned_cols=33  Identities=15%  Similarity=0.155  Sum_probs=26.7

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E  125 (151)
                      ...|..+...-|+|+.+||+.+++++++++++-
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            344555666779999999999999999999863

>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=83.89  E-value=0.93  Score=28.88  Aligned_cols=34  Identities=6%  Similarity=0.068  Sum_probs=27.5

Q ss_pred             HHHHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           91 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        91 ~~~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      .-...+..+...-.+|+.+||+.+|+++++|+.+
T Consensus        21 ~e~~v~~~L~~~g~~t~~eia~~~~i~~~~v~~~   54 (109)
T d1sfxa_          21 SDVRIYSLLLERGGMRVSEIARELDLSARFVRDR   54 (109)
T ss_dssp             HHHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCCHHHHHHHhCCCcchHHHH
Confidence            3345566666777899999999999999998876

>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=83.72  E-value=2.1  Score=28.08  Aligned_cols=26  Identities=15%  Similarity=0.141  Sum_probs=20.1

Q ss_pred             HHHHHHHHcCCChhhHHhhhc-----CCCcc
Q 031871           30 KVVNAARRAGADIETVRKSHA-----GTNKA   55 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~-----g~~~~   55 (151)
                      +.-.+|++.|++.+|+.+|-.     |...|
T Consensus        34 s~r~iA~~~~VS~~tV~k~l~r~~~~G~~~~   64 (123)
T d1pdnc_          34 RPCVISRQLRVSHGCVSKILNRYQETGSIRP   64 (123)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHHHHHHCCSSC
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHccCCcCc
Confidence            345789999999999998854     65554

>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=83.49  E-value=0.53  Score=28.02  Aligned_cols=26  Identities=12%  Similarity=0.072  Sum_probs=22.2

Q ss_pred             hcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871          101 NDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus       101 ~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      ...|+|-.++|..+|+|..||..+-.
T Consensus        24 l~~G~s~~eIA~~l~iS~~TV~~~~~   49 (70)
T d1yioa1          24 TIRGLMNKQIAGELGIAEVTVKVHRH   49 (70)
T ss_dssp             HTTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            34699999999999999999987643

>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=83.40  E-value=0.33  Score=31.57  Aligned_cols=23  Identities=13%  Similarity=0.263  Sum_probs=21.1

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESG  127 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G  127 (151)
                      +|..|||+.+|||+.||.-||+-
T Consensus         4 ytI~evA~~~gvs~~tlR~Ye~~   26 (118)
T d1r8ea1           4 YSIGEVSKLANVSIKALRYYDKI   26 (118)
T ss_dssp             EEHHHHHHHHTCCHHHHHHHHHT
T ss_pred             ccHHHHHHHHCcCHHHHHHHHHc
Confidence            57889999999999999999974

>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=83.23  E-value=0.085  Score=31.55  Aligned_cols=41  Identities=15%  Similarity=0.016  Sum_probs=29.1

Q ss_pred             HHHHHHHHcCCChhhHHhhhcCC-CccCCCCccccccccccc
Q 031871           30 KVVNAARRAGADIETVRKSHAGT-NKAASSSTSLNTRKLDED   70 (151)
Q Consensus        30 ~~~~~a~r~g~~v~t~~k~~~g~-~~~~~~~~~~~~~kl~~~   70 (151)
                      ++.++|++.|++..++.+||.|+ ..|+.+.+.+.+..|+.+
T Consensus        21 tq~elA~~~gv~~~~is~ie~g~~~~~s~~~L~~ia~~Lg~~   62 (69)
T d2a6ca1          21 TQFKAAELLGVTQPRVSDLMRGKIDLFSLESLIDMITSIGLK   62 (69)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHTTCGGGCCHHHHHHHHHHTTCC
T ss_pred             CHHHHHHHHHcCHhHHHHHHcccccchhHHHHHHHHHHhCCC
Confidence            56789999999999999999997 444444444444444443

>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=83.22  E-value=0.78  Score=26.88  Aligned_cols=34  Identities=9%  Similarity=0.009  Sum_probs=27.3

Q ss_pred             HHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCC
Q 031871           96 IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA  129 (151)
Q Consensus        96 Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~  129 (151)
                      +-.-+--.++|..++|+.+|||++++..+-.++-
T Consensus        13 l~~~~G~~~~s~~~Ia~~agvs~~~~y~~F~~K~   46 (71)
T d1jt6a1          13 LFIKNGYNATTTGEIVKLSESSKGNLYYHFKTKE   46 (71)
T ss_dssp             HHHHHCTTTCCHHHHHHHTTCCHHHHHHHHSSHH
T ss_pred             HHHHhCccccCHHHHHHHHCcCHhHHHHHCcCHH
Confidence            3344556788999999999999999999876653

>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=83.21  E-value=1.2  Score=28.97  Aligned_cols=35  Identities=14%  Similarity=0.070  Sum_probs=26.0

Q ss_pred             HHHHHHHHHHHhc--CCcCHHHHHHHhCCCHHHHHHH
Q 031871           90 SELKKAIVQARND--KKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        90 ~~~~~~Lk~~R~~--~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ..-...|..+...  .++|+.+||+.+++++++++++
T Consensus        29 ~~q~~vL~~l~~~~~~~it~~ela~~~~~~~~~vs~~   65 (135)
T d3broa1          29 GTQMTIIDYLSRNKNKEVLQRDLESEFSIKSSTATVL   65 (135)
T ss_dssp             HHHHHHHHHHHHTTTSCCBHHHHHHHHTCCHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCCCHHHHHHHHCcCHhHHHHH
Confidence            3334445555544  3499999999999999999975

>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=83.15  E-value=0.5  Score=28.06  Aligned_cols=31  Identities=10%  Similarity=0.164  Sum_probs=25.3

Q ss_pred             HHhcCCcCHHHHHHHhCCCHHHHHHHHcCCC
Q 031871           99 ARNDKKLTQSQLAQLINEKPQVIQEYESGKA  129 (151)
Q Consensus        99 ~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~  129 (151)
                      -+--.++|..++|+.+|++++++..+-.++.
T Consensus        19 ~~G~~~~s~~~Ia~~agvs~~~iY~~F~sK~   49 (74)
T d2g7sa1          19 RGGYNSFSYADISQVVGIRNASIHHHFPSKS   49 (74)
T ss_dssp             HHCGGGCCHHHHHHHHCCCHHHHHHHCSSHH
T ss_pred             HhCccccCHHHHHHHHCcCcchHHHHCcCHH
Confidence            3445678999999999999999999866543

>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=82.87  E-value=0.16  Score=30.15  Aligned_cols=29  Identities=17%  Similarity=0.188  Sum_probs=24.0

Q ss_pred             cCCcCHHHHHHHhCCCHHHHHHHHcCCCC
Q 031871          102 DKKLTQSQLAQLINEKPQVIQEYESGKAI  130 (151)
Q Consensus       102 ~~glTQ~eLA~~lgis~s~Is~~E~G~~~  130 (151)
                      -.++|..++|+++|+|++++..+-.++..
T Consensus        21 ~~~~t~~~Ia~~agvs~~~iy~hF~~K~~   49 (68)
T d1z0xa1          21 LEQLSMRKVAKQLGVQAPAIYWYFKNKQA   49 (68)
T ss_dssp             GGGCCHHHHHHHHTSCHHHHHTTCSSHHH
T ss_pred             ccccCHHHHHHHHCcchhHHHHhcCCHHH
Confidence            35789999999999999999987665543

>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=82.85  E-value=0.39  Score=26.86  Aligned_cols=26  Identities=8%  Similarity=0.024  Sum_probs=22.5

Q ss_pred             cCCcCHHHHHHHhCCCHHHHHHHHcC
Q 031871          102 DKKLTQSQLAQLINEKPQVIQEYESG  127 (151)
Q Consensus       102 ~~glTQ~eLA~~lgis~s~Is~~E~G  127 (151)
                      ...+|..+||+.+|+|+++++++-+.
T Consensus        17 ~~~~tl~~lA~~~~~s~~~l~r~Fk~   42 (54)
T d1bl0a1          17 ESPLSLEKVSERSGYSKWHLQRMFKK   42 (54)
T ss_dssp             TSCCCCHHHHHHSSSCHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            35799999999999999999998653

>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=82.71  E-value=1  Score=26.26  Aligned_cols=37  Identities=16%  Similarity=0.089  Sum_probs=29.3

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCC
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA  129 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~  129 (151)
                      +..+-.-+--.++|..++|+++|+|++++..+-.++.
T Consensus        11 a~~l~~~~G~~~~ti~~Ia~~agvs~~~~Y~~F~~K~   47 (68)
T d2d6ya1          11 AVAEFARHGIAGARIDRIAAEARANKQLIYAYYGNKG   47 (68)
T ss_dssp             HHHHHHHHTTTSCCHHHHHHHHTCCHHHHHHHHSSHH
T ss_pred             HHHHHHHhCccccCHHHHHHHHCcchhHHHHHCcCHH
Confidence            3334444556789999999999999999999987764

>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=82.33  E-value=0.65  Score=27.76  Aligned_cols=32  Identities=3%  Similarity=-0.078  Sum_probs=26.2

Q ss_pred             HHHhcCCcCHHHHHHHhCCCHHHHHHHHcCCC
Q 031871           98 QARNDKKLTQSQLAQLINEKPQVIQEYESGKA  129 (151)
Q Consensus        98 ~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~~  129 (151)
                      .-+--.++|..++|+.+|+|+.++.++-..+.
T Consensus        18 ~~~G~~~~ti~~Ia~~agvs~~s~y~~F~~K~   49 (79)
T d2fbqa1          18 AEKGFAETSLRLITSKAGVNLAAVNYHFGSKK   49 (79)
T ss_dssp             HHHCSTTCCHHHHHHHHTSCHHHHHHHTCSHH
T ss_pred             HHhCcccccHHHHHHHHCcChhHHHHHCcCHH
Confidence            33455679999999999999999999876553

>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=81.99  E-value=0.79  Score=30.12  Aligned_cols=33  Identities=6%  Similarity=-0.004  Sum_probs=26.9

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E  125 (151)
                      ...|..+...-++|+.+||+.++++++++++.-
T Consensus        35 ~~iL~~l~~~~~~t~~~La~~l~i~~~~vs~~v   67 (140)
T d2etha1          35 LYAFLYVALFGPKKMKEIAEFLSTTKSNVTNVV   67 (140)
T ss_dssp             HHHHHHHHHHCCBCHHHHHHHTTSCHHHHHHHH
T ss_pred             HHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHH
Confidence            444566666678999999999999999998863

>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=81.96  E-value=0.28  Score=29.07  Aligned_cols=29  Identities=14%  Similarity=0.027  Sum_probs=24.0

Q ss_pred             hcCCcCHHHHHHHhCCCHHHHHHHHcCCC
Q 031871          101 NDKKLTQSQLAQLINEKPQVIQEYESGKA  129 (151)
Q Consensus       101 ~~~glTQ~eLA~~lgis~s~Is~~E~G~~  129 (151)
                      --.++|..++|+.+|||++++..+-.++.
T Consensus        20 G~~~~t~~~Ia~~agvs~~t~Y~~F~~K~   48 (73)
T d1t56a1          20 PLADISVDDLAKGAGISRPTFYFYFPSKE   48 (73)
T ss_dssp             CGGGCCHHHHHHHHTCCHHHHHHHCSSHH
T ss_pred             CcccCCHHHHHHHhCCCHHHHHHHCcCHH
Confidence            33468999999999999999999866553

>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=81.86  E-value=0.26  Score=28.53  Aligned_cols=29  Identities=21%  Similarity=0.110  Sum_probs=24.5

Q ss_pred             hcCCcCHHHHHHHhCCCHHHHHHHHcCCC
Q 031871          101 NDKKLTQSQLAQLINEKPQVIQEYESGKA  129 (151)
Q Consensus       101 ~~~glTQ~eLA~~lgis~s~Is~~E~G~~  129 (151)
                      --.++|..++|+.+|+|+++|..+-.++.
T Consensus        16 G~~~~s~~~Ia~~agvs~~tiy~~F~~K~   44 (62)
T d2vkva1          16 GIEGLTTRKLAQKLGVEQPTLYWHVKNKR   44 (62)
T ss_dssp             HHHHCCHHHHHHHHTSCHHHHHHHSCCHH
T ss_pred             CcccCCHHHHHHHhCCCHHHHHHHCCCHH
Confidence            34578999999999999999999876653

>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=81.63  E-value=1.8  Score=25.23  Aligned_cols=36  Identities=6%  Similarity=0.124  Sum_probs=26.0

Q ss_pred             HHHHHHHHHHH-hcCCcCHHHHHHHhCCCHHHHHHHH
Q 031871           90 SELKKAIVQAR-NDKKLTQSQLAQLINEKPQVIQEYE  125 (151)
Q Consensus        90 ~~~~~~Lk~~R-~~~glTQ~eLA~~lgis~s~Is~~E  125 (151)
                      ++.-+.|-.+- .....+..++|+.+|++++++++.-
T Consensus         8 EdYL~~I~~L~~~~~~v~~~~iA~~L~vs~~SVt~mv   44 (63)
T d2isya1           8 EMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTV   44 (63)
T ss_dssp             HHHHHHHHHHHHTTCCCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCCCcHHHHHHHhCCCchhHHHHH
Confidence            34445555553 3445789999999999999998763

>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=81.50  E-value=0.089  Score=33.14  Aligned_cols=43  Identities=19%  Similarity=0.083  Sum_probs=32.0

Q ss_pred             HHHHHHHHHcCCChhhHHhhhcCC-CccCCCCcccccccccccc
Q 031871           29 EKVVNAARRAGADIETVRKSHAGT-NKAASSSTSLNTRKLDEDT   71 (151)
Q Consensus        29 ~~~~~~a~r~g~~v~t~~k~~~g~-~~~~~~~~~~~~~kl~~~~   71 (151)
                      =++...|.+.|++-.|+.+||+|+ ..|..+.+.+.+..|+.+.
T Consensus        25 ltq~~lA~~~gis~~~is~ie~G~~~~~~~~~L~~ia~~Lg~~i   68 (89)
T d2o38a1          25 LSQAAAAARLGINQPKVSALRNYKLEGFSVERLMTLLNALDQDV   68 (89)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHTTCCTTCCHHHHHHHHHHTTEEE
T ss_pred             CCHHHHHHHHHhhHhHHHHHHcCCCCCCcHHHHHHHHHHcCCCH
Confidence            356789999999999999999997 4455555555566666543

>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=81.40  E-value=0.31  Score=29.22  Aligned_cols=27  Identities=15%  Similarity=0.176  Sum_probs=23.5

Q ss_pred             CCcCHHHHHHHhCCCHHHHHHHHcCCC
Q 031871          103 KKLTQSQLAQLINEKPQVIQEYESGKA  129 (151)
Q Consensus       103 ~glTQ~eLA~~lgis~s~Is~~E~G~~  129 (151)
                      .++|..++|+.+|+|++++..+-.++.
T Consensus        25 ~~~s~~~Ia~~agvs~~~lY~~F~~K~   51 (77)
T d2gfna1          25 SAVTTRAVAEESGWSTGVLNHYFGSRH   51 (77)
T ss_dssp             GGCCHHHHHHHHSSCHHHHHHHTSSHH
T ss_pred             cccCHHHHHHHHCCCHHHHHHHCcCHH
Confidence            467999999999999999999876554

>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=81.32  E-value=0.56  Score=29.17  Aligned_cols=31  Identities=10%  Similarity=0.090  Sum_probs=26.8

Q ss_pred             HHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           94 KAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        94 ~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ..|.......+..+.+.|+.+||+++|+.+-
T Consensus        54 ~lI~~aL~~~~Gn~~~AA~~LGI~R~TL~~K   84 (91)
T d1ntca_          54 TLLTTALRHTQGHKQEAARLLGWGAATLTAK   84 (91)
T ss_dssp             HHHHHHHHHTTTCTTHHHHHTTCCHHHHHHH
T ss_pred             HHHHHHHHHhCCcHHHHHHHHCCCHHHHHHH
Confidence            3577788888999999999999999999863

>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=80.71  E-value=1.6  Score=25.80  Aligned_cols=31  Identities=16%  Similarity=0.167  Sum_probs=26.2

Q ss_pred             HHHhcCCcCHHHHHHHhCCCHHHHHHHHcCC
Q 031871           98 QARNDKKLTQSQLAQLINEKPQVIQEYESGK  128 (151)
Q Consensus        98 ~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~  128 (151)
                      .-.--.++|..++|+.+|||++++..+-.++
T Consensus        18 ~~~G~~~~si~~Ia~~agvs~~~~Y~~F~~K   48 (73)
T d2fx0a1          18 GERGYEGTSIQEIAKEAKVNVAMASYYFNGK   48 (73)
T ss_dssp             HHHCTTTCCHHHHHHHHTSCHHHHHHHHTSH
T ss_pred             HHhCcccCcHHHHHHHHCcChhHHHHHCcCH
Confidence            3345577899999999999999999998765

>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=80.70  E-value=1.4  Score=25.44  Aligned_cols=33  Identities=12%  Similarity=0.066  Sum_probs=24.9

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHHHc
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  126 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~E~  126 (151)
                      ...|..+....| +..+.|+.+||+++++.+-.+
T Consensus        23 r~~I~~aL~~~g-n~~~aA~~Lgisr~tL~rKlk   55 (61)
T d1g2ha_          23 AQVLKLFYAEYP-STRKLAQRLGVSHTAIANKLK   55 (61)
T ss_dssp             HHHHHHHHHHSC-SHHHHHHHTTSCTHHHHHHHH
T ss_pred             HHHHHHHHHHCC-CHHHHHHHHCCCHHHHHHHHH
Confidence            445566656666 678999999999999987543

>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=80.13  E-value=1.6  Score=25.42  Aligned_cols=32  Identities=16%  Similarity=0.137  Sum_probs=25.3

Q ss_pred             HHHHhcCCcCHHHHHHHhCCCHHHHHHHHcCC
Q 031871           97 VQARNDKKLTQSQLAQLINEKPQVIQEYESGK  128 (151)
Q Consensus        97 k~~R~~~glTQ~eLA~~lgis~s~Is~~E~G~  128 (151)
                      -.-+--.++|..++|+++|++++++..+-.++
T Consensus        17 ~~~~G~~~~t~~~Ia~~agvs~~~~y~~F~~k   48 (69)
T d2fq4a1          17 LLESGFKAVTVDKIAERAKVSKATIYKWWPNK   48 (69)
T ss_dssp             HHHHCTTTCCHHHHHHHHTCCHHHHHHHCSSH
T ss_pred             HHHhCcccCCHHHHHHHHCcCHHHHHHHCCCH
Confidence            33345567899999999999999999975443

>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=80.08  E-value=0.48  Score=29.05  Aligned_cols=24  Identities=13%  Similarity=0.178  Sum_probs=21.6

Q ss_pred             cCHHHHHHHhCCCHHHHHHHHcCC
Q 031871          105 LTQSQLAQLINEKPQVIQEYESGK  128 (151)
Q Consensus       105 lTQ~eLA~~lgis~s~Is~~E~G~  128 (151)
                      +.|..+|+.+||..+.|++|-+|-
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            469999999999999999998863

>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=80.07  E-value=0.73  Score=30.28  Aligned_cols=32  Identities=9%  Similarity=0.123  Sum_probs=27.0

Q ss_pred             HHHHHHHHhcCCcCHHHHHHHhCCCHHHHHHH
Q 031871           93 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEY  124 (151)
Q Consensus        93 ~~~Lk~~R~~~glTQ~eLA~~lgis~s~Is~~  124 (151)
                      ...|..+...-++|+.+||+.++++++++++.
T Consensus        36 ~~vL~~l~~~~~~t~~~La~~~~i~~~~vsr~   67 (137)
T d1z91a1          36 YLALLLLWEHETLTVKKMGEQLYLDSGTLTPM   67 (137)
T ss_dssp             HHHHHHHHHHSEEEHHHHHHTTTCCHHHHHHH
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHH
Confidence            44466666678999999999999999999886