Citrus Sinensis ID: 032366

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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--
Protein Sequence
MAGIGPITQDWEPVVIKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRGKK
Secondary Structure (PSIPRED)
cccccccccccccEEEccccccccccccHHHHHHHHHccccccccccccccccccccccccccccccccHHHHHccccccHHHHHHHHHHHHHccccHHHHHHHHcccHHHHHHHHcccccccHHHHHHHHHHHcccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccEEEcccccccHHcccHHHHHHHHHcccEEEEEEEEccccccccccccccccHHccccccccccccccHHHHHHHHHHHHHccccHHHHHHHHccccHHHHHHHcccccccHHHHHHHHHHHcccEcccc
Coil and Loop (DISEMBL)
magigpitqdwepvvikkkapnaatkkdEKVVNAARRAGADIETVRkshagtnkaassstslntrkldedtenlahdrvpSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEyesgkaipnqQILTKLERALgvklrgkk
Flexible Loop (DISEMBL)
magigpitqdwepvvikkkapnaatkkdekvvNAARragadietvrkshagtnkaassstslntrkldedtenlahdrvpsELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYEsgkaipnqqiltkleralgvklrgkk
Low Complexity Region (SEG)
MAGIGPITQDWEPVVIKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRGKK
Disordered region (IsUnstruct)
**********************************************************************************************************************************************
Disordered Region (DISOPRED)
****GPI*QDWEPVV*******************ARRAGAD********************************LAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG**
Disordered Region (DISEMBL)
MAGIGPITQDWEPVVIKKKA************NAARRAGADIETVRK*****************RKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRGKK
Disordered Region (DISPRO)
********QDWEPVVIKKK*P****************AGADIETVRKSHAG********************ENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR***
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAGIGPITQDWEPVVIKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAxxxxxxxxxxxxxxxxxxxxxKPQVIQEYESGKAIPNQQILTKLERALGVKLRGKK
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	142	2.2.26 [Sep-21-2011]
Q9LXT3	142	Multiprotein-bridging fac	yes	no	1.0	1.0	0.859	4e-67
Q9SJI8	142	Multiprotein-bridging fac	no	no	1.0	1.0	0.852	1e-65
Q9LV58	148	Multiprotein-bridging fac	no	no	0.964	0.925	0.517	1e-33
Q5ZMC0	148	Endothelial differentiati	yes	no	0.915	0.878	0.548	5e-32
O60869	148	Endothelial differentiati	yes	no	0.915	0.878	0.556	1e-31
Q3T0V7	148	Endothelial differentiati	yes	no	0.915	0.878	0.556	1e-31
Q6GPQ6	147	Endothelial differentiati	N/A	no	0.915	0.884	0.526	3e-31
P69736	148	Endothelial differentiati	yes	no	0.915	0.878	0.548	5e-31
Q9JMG1	148	Endothelial differentiati	yes	no	0.915	0.878	0.548	5e-31
Q6PBY3	146	Endothelial differentiati	yes	no	0.915	0.890	0.522	2e-30

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

 Score =  252 bits (644), Expect = 4e-67,   Method: Compositional matrix adjust.
 Identities = 122/142 (85%), Positives = 135/142 (95%)

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

Query: 61  SLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA 120
           SLNT+KLD+DTENL+HDRVP+ELKKAI+QAR +KKLTQSQLA LINEKPQVIQEYESGKA
Sbjct: 61  SLNTKKLDDDTENLSHDRVPTELKKAIMQARGEKKLTQSQLAHLINEKPQVIQEYESGKA 120

Query: 121 IPNQQILTKLERALGVKLRGKK 142
           IPNQQIL+KLERALG KLRGKK
Sbjct: 121 IPNQQILSKLERALGAKLRGKK 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 =  247 bits (631), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 121/142 (85%), Positives = 132/142 (92%)

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

Query: 61  SLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA 120
           SLNT+ LD+DTENL H+RVP+ELKKAI+QAR DKKLTQSQLAQ+INEKPQVIQEYESGKA
Sbjct: 61  SLNTKMLDDDTENLTHERVPTELKKAIMQARTDKKLTQSQLAQIINEKPQVIQEYESGKA 120

Query: 121 IPNQQILTKLERALGVKLRGKK 142
           IPNQQIL+KLERALG KLRGKK
Sbjct: 121 IPNQQILSKLERALGAKLRGKK 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 =  141 bits (355), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 72/139 (51%), Positives = 101/139 (72%), Gaps = 2/139 (1%)

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

Query: 63  NTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIP 122
           NT+KL+E+TE  A DRV +E++  I +AR +KK++Q+ LA+ INE+ QV+QEYE+GKA+P
Sbjct: 67  NTKKLEEETEPAAMDRVKAEVRLMIQKARLEKKMSQADLAKQINERTQVVQEYENGKAVP 126

Query: 123 NQQILTKLERALGVKLRGK 141
           NQ +L K+E+ LGVKLRGK
Sbjct: 127 NQAVLAKMEKVLGVKLRGK 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 =  135 bits (341), Expect = 5e-32,   Method: Compositional matrix adjust.
 Identities = 73/133 (54%), Positives = 93/133 (69%), Gaps = 3/133 (2%)

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  EDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILT 128
            +TE L HDRVP E+ K I Q R  K +TQ  LA  INEKPQVI +YESG+AIPN Q++ 
Sbjct: 63  RETEELHHDRVPLEVGKVIQQGRQSKGMTQKDLATKINEKPQVIADYESGRAIPNNQVMG 122

Query: 129 KLERALGVKLRGK 141
           K+ERA+G+KLRGK
Sbjct: 123 KIERAIGLKLRGK 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 =  134 bits (338), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 74/133 (55%), Positives = 92/133 (69%), Gaps = 3/133 (2%)

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  EDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILT 128
            +TE L HDRV  E+ K I Q R  K LTQ  LA  INEKPQVI +YESG+AIPN Q+L 
Sbjct: 63  RETEELHHDRVTLEVGKVIQQGRQSKGLTQKDLATKINEKPQVIADYESGRAIPNNQVLG 122

Query: 129 KLERALGVKLRGK 141
           K+ERA+G+KLRGK
Sbjct: 123 KIERAIGLKLRGK 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 =  134 bits (338), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 74/133 (55%), Positives = 92/133 (69%), Gaps = 3/133 (2%)

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  EDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILT 128
            +TE L HDRV  E+ K I Q R  K LTQ  LA  INEKPQVI +YESG+AIPN Q+L 
Sbjct: 63  RETEELHHDRVTLEVGKVIQQGRQSKGLTQKDLATKINEKPQVIADYESGRAIPNNQVLG 122

Query: 129 KLERALGVKLRGK 141
           K+ERA+G+KLRGK
Sbjct: 123 KIERAIGLKLRGK 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 =  133 bits (335), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 70/133 (52%), Positives = 91/133 (68%), Gaps = 3/133 (2%)

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  EDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILT 128
            +TE L HDRVP E+ K I Q R  K +TQ  LA  INEKPQVI +YE GKAIPN Q++ 
Sbjct: 63  RETEELHHDRVPLEVGKVIQQGRQGKGMTQKDLATKINEKPQVIADYECGKAIPNNQVMG 122

Query: 129 KLERALGVKLRGK 141
           K+ER +G+KLRGK
Sbjct: 123 KIERVIGLKLRGK 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 =  132 bits (333), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 73/133 (54%), Positives = 92/133 (69%), Gaps = 3/133 (2%)

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  EDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILT 128
            +TE L HDRV  E+ K I + R  K LTQ  LA  INEKPQVI +YESG+AIPN Q+L 
Sbjct: 63  RETEELHHDRVTLEVGKVIQRGRQSKGLTQKDLATKINEKPQVIADYESGRAIPNNQVLG 122

Query: 129 KLERALGVKLRGK 141
           K+ERA+G+KLRGK
Sbjct: 123 KIERAIGLKLRGK 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 =  132 bits (333), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 73/133 (54%), Positives = 92/133 (69%), Gaps = 3/133 (2%)

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  EDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILT 128
            +TE L HDRV  E+ K I + R  K LTQ  LA  INEKPQVI +YESG+AIPN Q+L 
Sbjct: 63  RETEELHHDRVTLEVGKVIQRGRQSKGLTQKDLATKINEKPQVIADYESGRAIPNNQVLG 122

Query: 129 KLERALGVKLRGK 141
           K+ERA+G+KLRGK
Sbjct: 123 KIERAIGLKLRGK 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 =  131 bits (329), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 69/132 (52%), Positives = 89/132 (67%), Gaps = 2/132 (1%)

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  DTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTK 129
           +TE L+H RVP E+ K I Q R +K LTQ  LA  INEKPQ+I EYE GKAIPN Q++ K
Sbjct: 63  ETEELSHQRVPLEVGKVIQQGRQNKGLTQKDLATKINEKPQIIAEYECGKAIPNNQVMGK 122

Query: 130 LERALGVKLRGK 141
           +ERA+G+KLRGK
Sbjct: 123 IERAIGLKLRGK 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	142
225446629	142	PREDICTED: multiprotein-bridging factor	1.0	1.0	0.866	4e-66
422779154	142	multiprotein bridging factor 1 [Vitis ps	1.0	1.0	0.859	7e-66
297817180	142	ATMBF1B/MBF1B [Arabidopsis lyrata subsp.	1.0	1.0	0.866	7e-66
15231105	142	multiprotein-bridging factor 1b [Arabido	1.0	1.0	0.859	3e-65
295913448	142	transcription factor [Lycoris longituba]	1.0	1.0	0.866	3e-65
297824233	142	ATMBF1A/MBF1A [Arabidopsis lyrata subsp.	1.0	1.0	0.845	6e-65
18406032	142	multiprotein bridging factor 1A [Arabido	1.0	1.0	0.852	9e-64
192910818	142	ethylene-responsive transcriptional coac	1.0	1.0	0.845	2e-63
359493778	142	PREDICTED: multiprotein-bridging factor	1.0	1.0	0.845	3e-63
20086364	140	putative multiprotein bridging factor 1	0.971	0.985	0.840	2e-61

>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 =  255 bits (652), Expect = 4e-66,   Method: Compositional matrix adjust.
 Identities = 123/142 (86%), Positives = 136/142 (95%)

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

Query: 61  SLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA 120
           SLNTRKLDE+TENLAHDRVP+ELKK+I+QAR DKKLTQSQLAQ+INEKPQ+IQEYESGKA
Sbjct: 61  SLNTRKLDEETENLAHDRVPTELKKSIMQARMDKKLTQSQLAQMINEKPQIIQEYESGKA 120

Query: 121 IPNQQILTKLERALGVKLRGKK 142
           IPNQQI+ KLERALGVKLRGKK
Sbjct: 121 IPNQQIIVKLERALGVKLRGKK 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 =  254 bits (649), Expect = 7e-66,   Method: Compositional matrix adjust.
 Identities = 122/142 (85%), Positives = 136/142 (95%)

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

Query: 61  SLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA 120
           SLNTRKLDE+TENLAHDRVP+ELKK+I+QAR DKKLTQSQLAQ+INEKPQ+IQEYESGKA
Sbjct: 61  SLNTRKLDEETENLAHDRVPTELKKSIMQARMDKKLTQSQLAQMINEKPQIIQEYESGKA 120

Query: 121 IPNQQILTKLERALGVKLRGKK 142
           IPNQQI+ KLERALGVKLRGKK
Sbjct: 121 IPNQQIIVKLERALGVKLRGKK 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 =  254 bits (649), Expect = 7e-66,   Method: Compositional matrix adjust.
 Identities = 123/142 (86%), Positives = 136/142 (95%)

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

Query: 61  SLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA 120
           SLNT+KLD+DTENL+HDRVP+ELKKAI+QAR +KKLTQSQLAQLINEKPQVIQEYESGKA
Sbjct: 61  SLNTKKLDDDTENLSHDRVPTELKKAIMQARGEKKLTQSQLAQLINEKPQVIQEYESGKA 120

Query: 121 IPNQQILTKLERALGVKLRGKK 142
           IPNQQIL+KLERALG KLRGKK
Sbjct: 121 IPNQQILSKLERALGAKLRGKK 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 =  252 bits (644), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 122/142 (85%), Positives = 135/142 (95%)

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

Query: 61  SLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA 120
           SLNT+KLD+DTENL+HDRVP+ELKKAI+QAR +KKLTQSQLA LINEKPQVIQEYESGKA
Sbjct: 61  SLNTKKLDDDTENLSHDRVPTELKKAIMQARGEKKLTQSQLAHLINEKPQVIQEYESGKA 120

Query: 121 IPNQQILTKLERALGVKLRGKK 142
           IPNQQIL+KLERALG KLRGKK
Sbjct: 121 IPNQQILSKLERALGAKLRGKK 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 =  252 bits (644), Expect = 3e-65,   Method: Compositional matrix adjust.
 Identities = 123/142 (86%), Positives = 135/142 (95%)

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

Query: 61  SLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA 120
           SLNTRKLDE+TENLAH+RVPSELKK+I+QAR DKK TQ+QLAQLINEKPQVIQEYESGKA
Sbjct: 61  SLNTRKLDEETENLAHERVPSELKKSIMQARMDKKYTQAQLAQLINEKPQVIQEYESGKA 120

Query: 121 IPNQQILTKLERALGVKLRGKK 142
           IPNQQI+ KLER LGVKLRGKK
Sbjct: 121 IPNQQIINKLERVLGVKLRGKK 142

Source: Lycoris longituba

Species: Lycoris longituba

Genus: Lycoris

Family: Amaryllidaceae

Order: Asparagales

Class: Liliopsida

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 =  251 bits (641), Expect = 6e-65,   Method: Compositional matrix adjust.
 Identities = 120/142 (84%), Positives = 135/142 (95%)

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

Query: 61  SLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA 120
           SLNT++LD+DTENL H+RVP+ELKKAI+QAR DKKLTQSQLAQ+INEKPQVIQEYESGKA
Sbjct: 61  SLNTKRLDDDTENLTHERVPTELKKAIMQARTDKKLTQSQLAQIINEKPQVIQEYESGKA 120

Query: 121 IPNQQILTKLERALGVKLRGKK 142
           IPNQQIL+KLERALG KLRGKK
Sbjct: 121 IPNQQILSKLERALGAKLRGKK 142

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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 =  247 bits (631), Expect = 9e-64,   Method: Compositional matrix adjust.
 Identities = 121/142 (85%), Positives = 132/142 (92%)

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

Query: 61  SLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA 120
           SLNT+ LD+DTENL H+RVP+ELKKAI+QAR DKKLTQSQLAQ+INEKPQVIQEYESGKA
Sbjct: 61  SLNTKMLDDDTENLTHERVPTELKKAIMQARTDKKLTQSQLAQIINEKPQVIQEYESGKA 120

Query: 121 IPNQQILTKLERALGVKLRGKK 142
           IPNQQIL+KLERALG KLRGKK
Sbjct: 121 IPNQQILSKLERALGAKLRGKK 142

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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 =  246 bits (629), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 120/142 (84%), Positives = 133/142 (93%)

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

Query: 61  SLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA 120
           SLNTRKLDE+TE L+H+RVPSELKK I++AR DKKLTQ+QLAQLINEKPQVIQEYESGKA
Sbjct: 61  SLNTRKLDEETETLSHERVPSELKKNIMKARMDKKLTQAQLAQLINEKPQVIQEYESGKA 120

Query: 121 IPNQQILTKLERALGVKLRGKK 142
           IPNQQI+ KLER LG KLRGKK
Sbjct: 121 IPNQQIIIKLERVLGAKLRGKK 142

Source: Elaeis guineensis

Species: Elaeis guineensis

Genus: Elaeis

Family: Arecaceae

Order: Arecales

Class: Liliopsida

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 =  245 bits (626), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 120/142 (84%), Positives = 133/142 (93%)

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

Query: 61  SLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA 120
           SLNTRKLDE+TENL H+RVP+ELKK+I+QAR DKKLTQ+QLAQ+INEKPQVIQEYESGKA
Sbjct: 61  SLNTRKLDEETENLTHERVPTELKKSIMQARLDKKLTQAQLAQMINEKPQVIQEYESGKA 120

Query: 121 IPNQQILTKLERALGVKLRGKK 142
           IPNQQI+TKLERALGVKLRGKK
Sbjct: 121 IPNQQIITKLERALGVKLRGKK 142

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|20086364|dbj|BAB88859.1| putative multiprotein bridging factor 1 [Nicotiana tabacum]

 Score =  239 bits (611), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 116/138 (84%), Positives = 129/138 (93%)

Query: 5   GPITQDWEPVVIKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNT 64
           G I QDWEPVVI+KKAP AA +KDEK VNAARR+GA+IET+RKS AGTNKAASSST+LNT
Sbjct: 3   GGIAQDWEPVVIRKKAPTAAARKDEKAVNAARRSGAEIETIRKSAAGTNKAASSSTTLNT 62

Query: 65  RKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQ 124
           RKLDEDTENLAH +VP+ELKKAI+QAR DKKLTQ+QLAQLINEKPQ+IQEYESGKAIPNQ
Sbjct: 63  RKLDEDTENLAHQKVPTELKKAIMQARQDKKLTQAQLAQLINEKPQIIQEYESGKAIPNQ 122

Query: 125 QILTKLERALGVKLRGKK 142
           QI++KLERALG KLRGKK
Sbjct: 123 QIISKLERALGAKLRGKK 140

Source: Nicotiana tabacum

Species: Nicotiana tabacum

Genus: Nicotiana

Family: Solanaceae

Order: Solanales

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	142
TAIR|locus:2098994	142	MBF1B "multiprotein bridging f	1.0	1.0	0.859	5.5e-61
TAIR|locus:2041509	142	MBF1A "multiprotein bridging f	1.0	1.0	0.852	6.4e-60
TAIR|locus:2091747	148	MBF1C "multiprotein bridging f	0.964	0.925	0.517	9.5e-34
UNIPROTKB|Q5ZMC0	148	EDF1 "Endothelial differentiat	0.915	0.878	0.548	4.7e-32
UNIPROTKB|Q3T0V7	148	EDF1 "Endothelial differentiat	0.915	0.878	0.556	4.7e-32
UNIPROTKB|E2R2F2	148	EDF1 "Uncharacterized protein"	0.915	0.878	0.556	4.7e-32
UNIPROTKB|O60869	148	EDF1 "Endothelial differentiat	0.915	0.878	0.556	4.7e-32
UNIPROTKB|A6N8P5	148	MBF1 "Multiprotein bridging fa	0.915	0.878	0.548	9.8e-32
MGI|MGI:1891227	148	Edf1 "endothelial differentiat	0.915	0.878	0.548	1.3e-31
RGD|1308073	148	Edf1 "endothelial differentiat	0.915	0.878	0.548	1.3e-31

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

 Score = 624 (224.7 bits), Expect = 5.5e-61, P = 5.5e-61
 Identities = 122/142 (85%), Positives = 135/142 (95%)

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

Query:    61 SLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA 120
             SLNT+KLD+DTENL+HDRVP+ELKKAI+QAR +KKLTQSQLA LINEKPQVIQEYESGKA
Sbjct:    61 SLNTKKLDDDTENLSHDRVPTELKKAIMQARGEKKLTQSQLAHLINEKPQVIQEYESGKA 120

Query:   121 IPNQQILTKLERALGVKLRGKK 142
             IPNQQIL+KLERALG KLRGKK
Sbjct:   121 IPNQQILSKLERALGAKLRGKK 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 = 614 (221.2 bits), Expect = 6.4e-60, P = 6.4e-60
 Identities = 121/142 (85%), Positives = 132/142 (92%)

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

Query:    61 SLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA 120
             SLNT+ LD+DTENL H+RVP+ELKKAI+QAR DKKLTQSQLAQ+INEKPQVIQEYESGKA
Sbjct:    61 SLNTKMLDDDTENLTHERVPTELKKAIMQARTDKKLTQSQLAQIINEKPQVIQEYESGKA 120

Query:   121 IPNQQILTKLERALGVKLRGKK 142
             IPNQQIL+KLERALG KLRGKK
Sbjct:   121 IPNQQILSKLERALGAKLRGKK 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 = 367 (134.2 bits), Expect = 9.5e-34, P = 9.5e-34
 Identities = 72/139 (51%), Positives = 101/139 (72%)

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

Query:    63 NTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIP 122
             NT+KL+E+TE  A DRV +E++  I +AR +KK++Q+ LA+ INE+ QV+QEYE+GKA+P
Sbjct:    67 NTKKLEEETEPAAMDRVKAEVRLMIQKARLEKKMSQADLAKQINERTQVVQEYENGKAVP 126

Query:   123 NQQILTKLERALGVKLRGK 141
             NQ +L K+E+ LGVKLRGK
Sbjct:   127 NQAVLAKMEKVLGVKLRGK 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 = 351 (128.6 bits), Expect = 4.7e-32, P = 4.7e-32
 Identities = 73/133 (54%), Positives = 93/133 (69%)

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 EDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILT 128
              +TE L HDRVP E+ K I Q R  K +TQ  LA  INEKPQVI +YESG+AIPN Q++ 
Sbjct:    63 RETEELHHDRVPLEVGKVIQQGRQSKGMTQKDLATKINEKPQVIADYESGRAIPNNQVMG 122

Query:   129 KLERALGVKLRGK 141
             K+ERA+G+KLRGK
Sbjct:   123 KIERAIGLKLRGK 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 = 351 (128.6 bits), Expect = 4.7e-32, P = 4.7e-32
 Identities = 74/133 (55%), Positives = 92/133 (69%)

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 EDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILT 128
              +TE L HDRV  E+ K I Q R  K LTQ  LA  INEKPQVI +YESG+AIPN Q+L 
Sbjct:    63 RETEELHHDRVTLEVGKVIQQGRQSKGLTQKDLATKINEKPQVIADYESGRAIPNNQVLG 122

Query:   129 KLERALGVKLRGK 141
             K+ERA+G+KLRGK
Sbjct:   123 KIERAIGLKLRGK 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 = 351 (128.6 bits), Expect = 4.7e-32, P = 4.7e-32
 Identities = 74/133 (55%), Positives = 92/133 (69%)

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 EDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILT 128
              +TE L HDRV  E+ K I Q R  K LTQ  LA  INEKPQVI +YESG+AIPN Q+L 
Sbjct:    63 RETEELHHDRVTLEVGKVIQQGRQSKGLTQKDLATKINEKPQVIADYESGRAIPNNQVLG 122

Query:   129 KLERALGVKLRGK 141
             K+ERA+G+KLRGK
Sbjct:   123 KIERAIGLKLRGK 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 = 351 (128.6 bits), Expect = 4.7e-32, P = 4.7e-32
 Identities = 74/133 (55%), Positives = 92/133 (69%)

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 EDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILT 128
              +TE L HDRV  E+ K I Q R  K LTQ  LA  INEKPQVI +YESG+AIPN Q+L 
Sbjct:    63 RETEELHHDRVTLEVGKVIQQGRQSKGLTQKDLATKINEKPQVIADYESGRAIPNNQVLG 122

Query:   129 KLERALGVKLRGK 141
             K+ERA+G+KLRGK
Sbjct:   123 KIERAIGLKLRGK 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 = 348 (127.6 bits), Expect = 9.8e-32, P = 9.8e-32
 Identities = 73/133 (54%), Positives = 92/133 (69%)

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 EDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILT 128
              +TE L HDRV  E+ K I Q R  K LTQ  LA  INEKPQVI +YESG+AIPN Q+L 
Sbjct:    63 RETEELHHDRVTLEVGKVIQQGRQSKGLTQKDLATKINEKPQVIADYESGRAIPNNQVLG 122

Query:   129 KLERALGVKLRGK 141
             K+ERA+G+KLRG+
Sbjct:   123 KIERAIGLKLRGR 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 = 347 (127.2 bits), Expect = 1.3e-31, P = 1.3e-31
 Identities = 73/133 (54%), Positives = 92/133 (69%)

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 EDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILT 128
              +TE L HDRV  E+ K I + R  K LTQ  LA  INEKPQVI +YESG+AIPN Q+L 
Sbjct:    63 RETEELHHDRVTLEVGKVIQRGRQSKGLTQKDLATKINEKPQVIADYESGRAIPNNQVLG 122

Query:   129 KLERALGVKLRGK 141
             K+ERA+G+KLRGK
Sbjct:   123 KIERAIGLKLRGK 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 = 347 (127.2 bits), Expect = 1.3e-31, P = 1.3e-31
 Identities = 73/133 (54%), Positives = 92/133 (69%)

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 EDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILT 128
              +TE L HDRV  E+ K I + R  K LTQ  LA  INEKPQVI +YESG+AIPN Q+L 
Sbjct:    63 RETEELHHDRVTLEVGKVIQRGRQSKGLTQKDLATKINEKPQVIADYESGRAIPNNQVLG 122

Query:   129 KLERALGVKLRGK 141
             K+ERA+G+KLRGK
Sbjct:   123 KIERAIGLKLRGK 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	0.5488	0.9154	0.8783	yes	no
O94700	MBF1_SCHPO	No assigned EC number	0.4117	0.9154	0.8783	yes	no
O60869	EDF1_HUMAN	No assigned EC number	0.5563	0.9154	0.8783	yes	no
Q9JMG1	EDF1_MOUSE	No assigned EC number	0.5488	0.9154	0.8783	yes	no
P0CO30	MBF1_CRYNJ	No assigned EC number	0.3873	0.8943	0.8466	yes	no
O14467	MBF1_YEAST	No assigned EC number	0.4130	0.9084	0.8543	yes	no
Q752P7	MBF1_ASHGO	No assigned EC number	0.4154	0.9366	0.875	yes	no
Q3T0V7	EDF1_BOVIN	No assigned EC number	0.5563	0.9154	0.8783	yes	no
Q9LXT3	MBF1B_ARATH	No assigned EC number	0.8591	1.0	1.0	yes	no
Q6PBY3	EDF1_DANRE	No assigned EC number	0.5227	0.9154	0.8904	yes	no
Q6BXQ8	MBF1_DEBHA	No assigned EC number	0.4532	0.9154	0.8666	yes	no
Q6FJN0	MBF1_CANGA	No assigned EC number	0.4172	0.9154	0.8609	yes	no
P69736	EDF1_RAT	No assigned EC number	0.5488	0.9154	0.8783	yes	no
Q9SJI8	MBF1A_ARATH	No assigned EC number	0.8521	1.0	1.0	no	no
Q4WX89	MBF1_ASPFU	No assigned EC number	0.3309	0.9084	0.8376	yes	no
Q8TG23	MBF1_YARLI	No assigned EC number	0.4154	0.9366	0.875	yes	no
Q6GPQ6	EDF1_XENLA	No assigned EC number	0.5263	0.9154	0.8843	N/A	no
Q6CIP4	MBF1_KLULA	No assigned EC number	0.4244	0.9154	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	142
pfam08523	70	pfam08523, MBF1, Multiprotein bridging factor 1	5e-20
COG1813	165	COG1813, COG1813, Predicted transcription factor,	3e-12
smart00530	56	smart00530, HTH_XRE, Helix-turn-helix XRE-family l	1e-10
pfam01381	55	pfam01381, HTH_3, Helix-turn-helix	3e-10
cd00093	58	cd00093, HTH_XRE, Helix-turn-helix XRE-family like	5e-10
TIGR00270	154	TIGR00270, TIGR00270, TIGR00270 family protein	1e-04
PHA01976	67	PHA01976, PHA01976, helix-turn-helix protein	1e-04
pfam12844	64	pfam12844, HTH_19, Helix-turn-helix domain	4e-04
TIGR03830	127	TIGR03830, CxxCG_CxxCG_HTH, putative zinc finger/h	0.002

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

 Score = 77.4 bits (191), Expect = 5e-20
 Identities = 35/72 (48%), Positives = 42/72 (58%), Gaps = 3/72 (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 DEDTENLAHDRV 79
          D +TE L   RV
Sbjct: 59 DRETEPLKPKRV 70

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

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

 Score = 60.1 bits (146), Expect = 3e-12
 Identities = 24/57 (42%), Positives = 35/57 (61%)

Query: 85  KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRGK 141
           + 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 = 1e-10
 Identities = 19/53 (35%), Positives = 30/53 (56%)

Query: 87  IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 139
           + + 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 = 3e-10
 Identities = 18/53 (33%), Positives = 29/53 (54%)

Query: 87  IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 139
           + + 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 = 51.4 bits (124), Expect = 5e-10
 Identities = 20/54 (37%), Positives = 31/54 (57%)

Query: 85  KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 138
           + + + 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 = 39.5 bits (92), Expect = 1e-04
 Identities = 19/55 (34%), Positives = 34/55 (61%)

Query: 87  IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRGK 141
           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 = 1e-04
 Identities = 16/52 (30%), Positives = 32/52 (61%)

Query: 87  IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 138
           +++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 = 36.0 bits (84), Expect = 4e-04
 Identities = 16/50 (32%), Positives = 27/50 (54%)

Query: 89  QARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 138
           + 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 = 0.002
 Identities = 12/50 (24%), Positives = 24/50 (48%), Gaps = 3/50 (6%)

Query: 86  AIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQ---QILTKLER 132
            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	142
KOG3398	135	consensus Transcription factor MBF1 [Transcription	99.97
PF08523	71	MBF1: Multiprotein bridging factor 1; InterPro: IP	99.83
PRK06424	144	transcription factor; Provisional	99.65
PHA01976	67	helix-turn-helix protein	99.63
PRK08359	176	transcription factor; Validated	99.59
TIGR03070	58	couple_hipB transcriptional regulator, y4mF family	99.56
TIGR00270	154	conserved hypothetical protein TIGR00270.	99.55
PF12844	64	HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_	99.54
PF01381	55	HTH_3: Helix-turn-helix; InterPro: IPR001387 This	99.52
COG1476	68	Predicted transcriptional regulators [Transcriptio	99.5
PRK09726	88	antitoxin HipB; Provisional	99.46
PF13560	64	HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_	99.45
PRK09706	135	transcriptional repressor DicA; Reviewed	99.43
COG1813	165	Predicted transcription factor, homolog of eukaryo	99.38
PRK09943	185	DNA-binding transcriptional repressor PuuR; Provis	99.34
PRK13890	120	conjugal transfer protein TrbA; Provisional	99.34
TIGR02607	78	antidote_HigA addiction module antidote protein, H	99.33
PRK08154	309	anaerobic benzoate catabolism transcriptional regu	99.3
TIGR02684	89	dnstrm_HI1420 probable addiction module antidote p	99.29
PRK10072	96	putative transcriptional regulator; Provisional	99.22
PF13443	63	HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3	99.19
TIGR02612	150	mob_myst_A mobile mystery protein A. Members of th	99.16
PRK04140	317	hypothetical protein; Provisional	99.12
smart00530	56	HTH_XRE Helix-turn-helix XRE-family like proteins.	99.11
cd00093	58	HTH_XRE Helix-turn-helix XRE-family like proteins.	99.04
TIGR03830	127	CxxCG_CxxCG_HTH putative zinc finger/helix-turn-he	99.0
PF13744	80	HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_	98.92
PRK10856	331	cytoskeletal protein RodZ; Provisional	98.91
PHA00542	82	putative Cro-like protein	98.89
COG3620	187	Predicted transcriptional regulator with C-termina	98.86
smart00352	75	POU Found in Pit-Oct-Unc transcription factors.	98.77
COG2944	104	Predicted transcriptional regulator [Transcription	98.74
PRK13355	517	bifunctional HTH-domain containing protein/aminotr	98.73
PRK02866	147	cyanate hydratase; Validated	98.72
COG3093	104	VapI Plasmid maintenance system antidote protein [	98.68
COG1709	241	Predicted transcriptional regulator [Transcription	98.64
TIGR00673	150	cynS cyanate hydratase. Alternate names include cy	98.57
COG1396	120	HipB Predicted transcriptional regulators [Transcr	98.39
COG1395	313	Predicted transcriptional regulator [Transcription	98.37
COG3655	73	Predicted transcriptional regulator [Transcription	98.35
PF07022	66	Phage_CI_repr: Bacteriophage CI repressor helix-tu	98.34
PF13413	62	HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_	98.19
PF08667	147	BetR: BetR domain; InterPro: IPR013975 CheY-like p	98.04
COG1426	284	Predicted transcriptional regulator contains Xre-l	97.96
COG5499	120	Predicted transcription regulator containing HTH d	97.95
cd01392	52	HTH_LacI Helix-turn-helix (HTH) DNA binding domain	97.92
TIGR01321	94	TrpR trp operon repressor, proteobacterial. This m	97.79
PHA01083	149	hypothetical protein	97.78
COG2522	119	Predicted transcriptional regulator [General funct	97.68
COG4800	170	Predicted transcriptional regulator with an HTH do	97.64
PF00356	46	LacI: Bacterial regulatory proteins, lacI family;	97.58
smart00354	70	HTH_LACI helix_turn _helix lactose operon represso	97.57
PF08965	118	DUF1870: Domain of unknown function (DUF1870); Int	97.55
PRK08099	399	bifunctional DNA-binding transcriptional repressor	97.32
COG3636	100	Predicted transcriptional regulator [Transcription	97.16
PF01710	119	HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Tr	97.13
COG5606	91	Uncharacterized conserved small protein [Function	97.01
PHA00675	78	hypothetical protein	96.99
TIGR03879	73	near_KaiC_dom probable regulatory domain. This mod	96.91
PF00157	75	Pou: Pou domain - N-terminal to homeobox domain; I	96.87
TIGR02147	271	Fsuc_second hypothetical protein, TIGR02147. This	96.84
PF13693	78	HTH_35: Winged helix-turn-helix DNA-binding; PDB:	96.77
PF13384	50	HTH_23: Homeodomain-like domain; PDB: 2X48_C.	96.7
PF02796	45	HTH_7: Helix-turn-helix domain of resolvase; Inter	96.62
PHA02591	83	hypothetical protein; Provisional	96.46
TIGR02293	133	TAS_TIGR02293 putative toxin-antitoxin system anti	96.34
PRK10014	342	DNA-binding transcriptional repressor MalI; Provis	96.25
PF13936	44	HTH_38: Helix-turn-helix domain; PDB: 2W48_A.	96.23
PF14549	60	P22_Cro: DNA-binding transcriptional regulator Cro	96.21
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	96.15
TIGR02844	80	spore_III_D sporulation transcriptional regulator	96.1
COG3423	82	Nlp Predicted transcriptional regulator [Transcrip	96.06
PRK09492	315	treR trehalose repressor; Provisional	96.01
PF04814	180	HNF-1_N: Hepatocyte nuclear factor 1 (HNF-1), N te	96.01
PRK03975	141	tfx putative transcriptional regulator; Provisiona	95.98
PRK09526	342	lacI lac repressor; Reviewed	95.92
TIGR01481	329	ccpA catabolite control protein A. Catabolite cont	95.88
PRK10703	341	DNA-binding transcriptional repressor PurR; Provis	95.88
TIGR02405	311	trehalos_R_Ecol trehalose operon repressor, proteo	95.88
TIGR00721	137	tfx DNA-binding protein, Tfx family. Tfx from Meth	95.86
PRK10727	343	DNA-binding transcriptional regulator GalR; Provis	95.71
PF08535	93	KorB: KorB domain; InterPro: IPR013741 This entry	95.65
cd00131	128	PAX Paired Box domain	95.6
PRK14987	331	gluconate operon transcriptional regulator; Provis	95.55
PRK10401	346	DNA-binding transcriptional regulator GalS; Provis	95.51
PF02001	106	DUF134: Protein of unknown function DUF134; InterP	95.51
PF05225	45	HTH_psq: helix-turn-helix, Psq domain; InterPro: I	95.49
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	95.48
PRK10344	92	DNA-binding transcriptional regulator Nlp; Provisi	95.46
cd04762	49	HTH_MerR-trunc Helix-Turn-Helix DNA binding domain	95.45
COG4197	96	Uncharacterized protein conserved in bacteria, pro	95.42
PRK01381	99	Trp operon repressor; Provisional	95.26
PRK08558	238	adenine phosphoribosyltransferase; Provisional	95.26
TIGR02531	88	yecD_yerC TrpR-related protein YerC/YecD. This mod	95.1
PRK10339	327	DNA-binding transcriptional repressor EbgR; Provis	95.06
COG1513	151	CynS Cyanate lyase [Inorganic ion transport and me	94.95
PF02376	87	CUT: CUT domain; InterPro: IPR003350 A class, also	94.94
PF06056	58	Terminase_5: Putative ATPase subunit of terminase	94.89
PF02954	42	HTH_8: Bacterial regulatory protein, Fis family; I	94.86
cd00569	42	HTH_Hin_like Helix-turn-helix domain of Hin and re	94.74
PF12728	51	HTH_17: Helix-turn-helix domain	94.73
PF05269	91	Phage_CII: Bacteriophage CII protein; InterPro: IP	94.65
TIGR01764	49	excise DNA binding domain, excisionase family. An	94.65
PF07037	122	DUF1323: Putative transcription regulator (DUF1323	94.62
COG1356	143	tfx Transcriptional regulator [DNA replication, re	94.62
KOG3802	398	consensus Transcription factor OCT-1, contains POU	94.58
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	94.53
PF01371	87	Trp_repressor: Trp repressor protein; InterPro: IP	94.43
PF01527	76	HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp	94.42
PRK13698	323	plasmid-partitioning protein; Provisional	94.31
cd04761	49	HTH_MerR-SF Helix-Turn-Helix DNA binding domain of	94.3
PF13518	52	HTH_28: Helix-turn-helix domain	94.2
cd04764	67	HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding dom	94.19
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	94.18
COG2944	104	Predicted transcriptional regulator [Transcription	93.99
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	93.79
cd04763	68	HTH_MlrA-like Helix-Turn-Helix DNA binding domain	93.78
PRK15418	318	transcriptional regulator LsrR; Provisional	93.69
PF13551	112	HTH_29: Winged helix-turn helix	93.69
PF00376	38	MerR: MerR family regulatory protein; InterPro: IP	93.66
TIGR00180	187	parB_part ParB-like partition proteins. This model	93.66
cd01104	68	HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain	93.65
cd01104	68	HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain	93.43
PF10668	60	Phage_terminase: Phage terminase small subunit; In	93.38
cd06171	55	Sigma70_r4 Sigma70, region (SR) 4 refers to the mo	93.29
COG2390	321	DeoR Transcriptional regulator, contains sigma fac	93.29
PRK09413	121	IS2 repressor TnpA; Reviewed	93.25
PRK04217	110	hypothetical protein; Provisional	93.25
COG1342	99	Predicted DNA-binding proteins [General function p	93.23
cd04764	67	HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding dom	93.2
smart00351	125	PAX Paired Box domain.	93.09
PF13542	52	HTH_Tnp_ISL3: Helix-turn-helix domain of transposa	93.02
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	92.98
PF08281	54	Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013	92.9
PF04552	160	Sigma54_DBD: Sigma-54, DNA binding domain; InterPr	92.84
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	92.79
COG2842	297	Uncharacterized ATPase, putative transposase [Gene	92.78
PF13411	69	MerR_1: MerR HTH family regulatory protein; PDB: 2	92.73
PF13613	53	HTH_Tnp_4: Helix-turn-helix of DDE superfamily end	92.7
cd04763	68	HTH_MlrA-like Helix-Turn-Helix DNA binding domain	92.62
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	92.62
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	92.59
PF13411	69	MerR_1: MerR HTH family regulatory protein; PDB: 2	92.54
TIGR01610	95	phage_O_Nterm phage replication protein O, N-termi	92.43
smart00422	70	HTH_MERR helix_turn_helix, mercury resistance.	92.41
cd04774	96	HTH_YfmP Helix-Turn-Helix DNA binding domain of th	92.39
smart00421	58	HTH_LUXR helix_turn_helix, Lux Regulon. lux regulo	92.32
TIGR03764	258	ICE_PFGI_1_parB integrating conjugative element, P	92.17
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	91.99
PF14590	166	DUF4447: Domain of unknown function (DUF4447); PDB	91.92
cd04784	127	HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain	91.72
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	91.7
cd01392	52	HTH_LacI Helix-turn-helix (HTH) DNA binding domain	91.66
smart00351	125	PAX Paired Box domain.	91.65
cd00131	128	PAX Paired Box domain	91.35
PF13545	76	HTH_Crp_2: Crp-like helix-turn-helix domain; PDB:	91.3
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	91.29
PF01418	77	HTH_6: Helix-turn-helix domain, rpiR family; Inter	91.26
PRK09744	75	DNA-binding transcriptional regulator DicC; Provis	91.22
PRK00118	104	putative DNA-binding protein; Validated	91.07
COG3415	138	Transposase and inactivated derivatives [DNA repli	90.8
smart00419	48	HTH_CRP helix_turn_helix, cAMP Regulatory protein.	90.68
PF11427	50	HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C	90.68
cd01105	88	HTH_GlnR-like Helix-Turn-Helix DNA binding domain	90.51
cd04773	108	HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding	90.31
PF07638	185	Sigma70_ECF: ECF sigma factor	90.31
PF05930	51	Phage_AlpA: Prophage CP4-57 regulatory protein (Al	90.24
PF13551	112	HTH_29: Winged helix-turn helix	90.17
PRK10072	96	putative transcriptional regulator; Provisional	90.07
cd04780	95	HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding dom	90.06
cd00592	100	HTH_MerR-like Helix-Turn-Helix DNA binding domain	90.05
KOG1168	385	consensus Transcription factor ACJ6/BRN-3, contain	90.03
PF13022	142	HTH_Tnp_1_2: Helix-turn-helix of insertion element	89.91
PF02042	52	RWP-RK: RWP-RK domain; InterPro: IPR003035 This do	89.81
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	89.77
cd01105	88	HTH_GlnR-like Helix-Turn-Helix DNA binding domain	89.52
cd04766	91	HTH_HspR Helix-Turn-Helix DNA binding domain of th	89.5
cd01106	103	HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain	89.48
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	89.33
COG2512	258	Predicted membrane-associated trancriptional regul	89.2
COG0789	124	SoxR Predicted transcriptional regulators [Transcr	89.08
cd01107	108	HTH_BmrR Helix-Turn-Helix DNA binding domain of th	89.01
cd04789	102	HTH_Cfa Helix-Turn-Helix DNA binding domain of the	88.83
cd04768	96	HTH_BmrR-like Helix-Turn-Helix DNA binding domain	88.82
PRK04132	846	replication factor C small subunit; Provisional	88.77
COG1522	154	Lrp Transcriptional regulators [Transcription]	88.77
cd04774	96	HTH_YfmP Helix-Turn-Helix DNA binding domain of th	88.75
cd04769	116	HTH_MerR2 Helix-Turn-Helix DNA binding domain of M	88.69
COG3311	70	AlpA Predicted transcriptional regulator [Transcri	88.65
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	88.63
TIGR02885	231	spore_sigF RNA polymerase sigma-F factor. Members	88.55
cd04765	99	HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding dom	88.54
cd04788	96	HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain	88.54
PF00356	46	LacI: Bacterial regulatory proteins, lacI family;	88.5
cd04772	99	HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding d	88.43
PHA01976	67	helix-turn-helix protein	88.29
TIGR03070	58	couple_hipB transcriptional regulator, y4mF family	88.25
PRK10458	467	DNA cytosine methylase; Provisional	88.2
cd04782	97	HTH_BltR Helix-Turn-Helix DNA binding domain of th	88.19
cd04775	102	HTH_Cfa-like Helix-Turn-Helix DNA binding domain o	88.11
PRK11891	429	aspartate carbamoyltransferase; Provisional	88.07
smart00497	53	IENR1 Intron encoded nuclease repeat motif. Repeat	87.89
cd04780	95	HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding dom	87.73
cd01107	108	HTH_BmrR Helix-Turn-Helix DNA binding domain of th	87.71
smart00422	70	HTH_MERR helix_turn_helix, mercury resistance.	87.69
cd04765	99	HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding dom	87.42
TIGR03697	193	NtcA_cyano global nitrogen regulator NtcA, cyanoba	87.34
PF00165	42	HTH_AraC: Bacterial regulatory helix-turn-helix pr	87.3
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	87.3
cd04766	91	HTH_HspR Helix-Turn-Helix DNA binding domain of th	87.25
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	87.23
cd01109	113	HTH_YyaN Helix-Turn-Helix DNA binding domain of th	87.19
cd04786	131	HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding dom	87.18
PRK11512	144	DNA-binding transcriptional repressor MarR; Provis	87.16
cd06170	57	LuxR_C_like C-terminal DNA-binding domain of LuxR-	87.12
PRK15043	243	transcriptional regulator MirA; Provisional	87.09
cd01279	98	HTH_HspR-like Helix-Turn-Helix DNA binding domain	87.04
PF13730	55	HTH_36: Helix-turn-helix domain	87.03
PF13011	85	LZ_Tnp_IS481: leucine-zipper of insertion element	86.99
TIGR03209	142	P21_Cbot clostridium toxin-associated regulator Bo	86.99
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	86.96
smart00354	70	HTH_LACI helix_turn _helix lactose operon represso	86.91
cd01282	112	HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding dom	86.9
PRK13413	200	mpi multiple promoter invertase; Provisional	86.8
cd04767	120	HTH_HspR-like_MBC Helix-Turn-Helix DNA binding dom	86.76
PRK08215	258	sporulation sigma factor SigG; Reviewed	86.69
cd01111	107	HTH_MerD Helix-Turn-Helix DNA binding domain of th	86.51
PRK05572	252	sporulation sigma factor SigF; Validated	86.4
PRK11169	164	leucine-responsive transcriptional regulator; Prov	86.23
COG1974	201	LexA SOS-response transcriptional repressors (RecA	86.22
COG2973	103	TrpR Trp operon repressor [Transcription]	86.2
TIGR02044	127	CueR Cu(I)-responsive transcriptional regulator. T	86.19
TIGR00122	69	birA_repr_reg BirA biotin operon repressor domain.	86.1
PF01710	119	HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Tr	86.03
COG1318	182	Predicted transcriptional regulators [Transcriptio	85.98
cd04788	96	HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain	85.93
PRK00215	205	LexA repressor; Validated	85.93
PRK12427	231	flagellar biosynthesis sigma factor; Provisional	85.88
cd04781	120	HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding dom	85.84
PRK06759	154	RNA polymerase factor sigma-70; Validated	85.68
PF13309	64	HTH_22: HTH domain	85.67
TIGR02395	429	rpoN_sigma RNA polymerase sigma-54 factor. A sigma	85.64
TIGR01636	134	phage_rinA phage transcriptional activator, RinA f	85.56
TIGR03001	244	Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxoco	85.55
cd01279	98	HTH_HspR-like Helix-Turn-Helix DNA binding domain	85.53
cd04783	126	HTH_MerR1 Helix-Turn-Helix DNA binding domain of t	85.43
TIGR02999	183	Sig-70_X6 RNA polymerase sigma factor, TIGR02999 f	85.39
PF00196	58	GerE: Bacterial regulatory proteins, luxR family;	85.27
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	85.22
PF00440	47	TetR_N: Bacterial regulatory proteins, tetR family	85.21
TIGR02392	270	rpoH_proteo alternative sigma factor RpoH. A sigma	85.19
cd01108	127	HTH_CueR Helix-Turn-Helix DNA binding domain of Cu	85.19
PRK07037	163	extracytoplasmic-function sigma-70 factor; Validat	84.83
PF07453	37	NUMOD1: NUMOD1 domain; InterPro: IPR010896 This he	84.77
TIGR02985	161	Sig70_bacteroi1 RNA polymerase sigma-70 factor, Ba	84.72
PRK12469	481	RNA polymerase factor sigma-54; Provisional	84.65
PRK10840	216	transcriptional regulator RcsB; Provisional	84.51
PRK09526	342	lacI lac repressor; Reviewed	84.41
cd04777	107	HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding dom	84.41
PRK11924	179	RNA polymerase sigma factor; Provisional	84.25
TIGR02393	238	RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter	84.2
PRK13832	520	plasmid partitioning protein; Provisional	84.19
PF01381	55	HTH_3: Helix-turn-helix; InterPro: IPR001387 This	84.16
PRK05932	455	RNA polymerase factor sigma-54; Reviewed	84.14
cd04767	120	HTH_HspR-like_MBC Helix-Turn-Helix DNA binding dom	84.13
TIGR02054	120	MerD mercuric resistence transcriptional repressor	84.11
PRK11161	235	fumarate/nitrate reduction transcriptional regulat	83.89
PRK14987	331	gluconate operon transcriptional regulator; Provis	83.88
TIGR02980	227	SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G	83.78
cd01110	139	HTH_SoxR Helix-Turn-Helix DNA binding domain of th	83.75
PRK09391	230	fixK transcriptional regulator FixK; Provisional	83.7
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	83.7
PRK11179	153	DNA-binding transcriptional regulator AsnC; Provis	83.54
PRK01905	77	DNA-binding protein Fis; Provisional	83.54
PRK13918	202	CRP/FNR family transcriptional regulator; Provisio	83.52
PRK00430	95	fis global DNA-binding transcriptional dual regula	83.43
PF09048	59	Cro: Cro; InterPro: IPR000655 Bacteriophage lambda	83.4
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	83.38
cd04785	126	HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding do	83.36
PHA01082	133	putative transcription regulator	83.31
cd04769	116	HTH_MerR2 Helix-Turn-Helix DNA binding domain of M	83.28
TIGR02989	159	Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodop	83.23
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	83.08
PRK09047	161	RNA polymerase factor sigma-70; Validated	83.04
PRK12529	178	RNA polymerase sigma factor; Provisional	83.04
cd04776	118	HTH_GnyR Helix-Turn-Helix DNA binding domain of th	83.02
PRK11753	211	DNA-binding transcriptional dual regulator Crp; Pr	83.01
PRK09652	182	RNA polymerase sigma factor RpoE; Provisional	82.84
PRK12519	194	RNA polymerase sigma factor; Provisional	82.83
PF09571	318	RE_XcyI: XcyI restriction endonuclease; InterPro:	82.83
COG2963	116	Transposase and inactivated derivatives [DNA repli	82.79
cd04770	123	HTH_HMRTR Helix-Turn-Helix DNA binding domain of H	82.75
smart00347	101	HTH_MARR helix_turn_helix multiple antibiotic resi	82.69
cd04787	133	HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain	82.67
PRK10727	343	DNA-binding transcriptional regulator GalR; Provis	82.54
PF00376	38	MerR: MerR family regulatory protein; InterPro: IP	82.46
PRK06986	236	fliA flagellar biosynthesis sigma factor; Validate	82.45
TIGR02937	158	sigma70-ECF RNA polymerase sigma factor, sigma-70	82.25
PRK10423	327	transcriptional repressor RbsR; Provisional	82.23
TIGR02047	127	CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional	82.22
PRK09514	140	zntR zinc-responsive transcriptional regulator; Pr	82.18
PRK10227	135	DNA-binding transcriptional regulator CueR; Provis	82.18
PRK09639	166	RNA polymerase sigma factor SigX; Provisional	82.17
PRK08583	257	RNA polymerase sigma factor SigB; Validated	82.08
PRK09642	160	RNA polymerase sigma factor SigW; Reviewed	81.94
PRK09954	362	putative kinase; Provisional	81.9
PF08822	165	DUF1804: Protein of unknown function (DUF1804); In	81.87
TIGR01950	142	SoxR redox-sensitive transcriptional activator Sox	81.78
PF06322	64	Phage_NinH: Phage NinH protein; InterPro: IPR01045	81.74
TIGR02043	131	ZntR Zn(II)-responsive transcriptional regulator.	81.64
TIGR02947	193	SigH_actino RNA polymerase sigma-70 factor, TIGR02	81.63
PRK15411	207	rcsA colanic acid capsular biosynthesis activation	81.49
PRK15002	154	redox-sensitivie transcriptional activator SoxR; P	81.45
PF04552	160	Sigma54_DBD: Sigma-54, DNA binding domain; InterPr	81.35
TIGR02366	176	DHAK_reg probable dihydroxyacetone kinase regulato	81.33
PF13560	64	HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_	81.32
PRK12523	172	RNA polymerase sigma factor; Reviewed	81.28
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	81.2
PRK06596	284	RNA polymerase factor sigma-32; Reviewed	81.06
PRK09645	173	RNA polymerase sigma factor SigL; Provisional	81.06
PRK12537	182	RNA polymerase sigma factor; Provisional	80.99
cd04782	97	HTH_BltR Helix-Turn-Helix DNA binding domain of th	80.97
TIGR02051	124	MerR Hg(II)-responsive transcriptional regulator.	80.94
PRK07122	264	RNA polymerase sigma factor SigF; Reviewed	80.89
cd00592	100	HTH_MerR-like Helix-Turn-Helix DNA binding domain	80.84
PRK13749	121	transcriptional regulator MerD; Provisional	80.8
PRK15320	251	transcriptional activator SprB; Provisional	80.75
cd07377	66	WHTH_GntR Winged helix-turn-helix (WHTH) DNA-bindi	80.62
cd04773	108	HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding	80.57
PRK09649	185	RNA polymerase sigma factor SigC; Reviewed	80.56
cd04790	172	HTH_Cfa-like_unk Helix-Turn-Helix DNA binding doma	80.55
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	80.28
PRK13919	186	putative RNA polymerase sigma E protein; Provision	80.28
PRK15002	154	redox-sensitivie transcriptional activator SoxR; P	80.01

>KOG3398 consensus Transcription factor MBF1 [Transcription]

Probab=99.97  E-value=9.4e-31  Score=185.20  Aligned_cols=132  Identities=68%  Similarity=0.951  Sum_probs=123.8

Q ss_pred             CCCCCcee-eccCCCCCccccCHHHHHHHHHcCCChhHHHhhhcCCCCCCCCCCCcccccchhhhccccCCcchHHHHHH
Q 032366            8 TQDWEPVV-IKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKA   86 (142)
Q Consensus         8 ~~~w~~~~-~~~~~~~~~~~~~~~~~~~a~r~G~~v~t~kk~~~g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~   86 (142)
                      .+|||||+ |+++. +..+.++++++|+|+|+|+.|+|+++|.+|.++.  .+.+++..++|++++++.+..+..+++..
T Consensus         1 ~~dw~~vt~~~~~~-~s~~~k~~~~vnaa~r~g~~v~t~~k~~~g~nkq--~~~~~~t~klD~etE~~~~~~v~~~Vg~a   77 (135)
T KOG3398|consen    1 TSDWDPVTVLKKKA-KAATLKDEKAVNAARRAGVDVETVKKFPAGLNKQ--HPSTQSTAKLDRETEELGHDRVPLEVGKA   77 (135)
T ss_pred             CCCcccceeeeccc-ccccccCHHHHHHHHHhcchhhhhhhhccccccc--CCcccchhhccccccccccccccHHHHHH
Confidence            47999985 66554 8889999999999999999999999999999985  45578899999999999999999999999


Q ss_pred             HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCCCC
Q 032366           87 IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRGKK  142 (142)
Q Consensus        87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~e~~  142 (142)
                      |...|.++||||++||.+++..++.|..||+|+.+|+..+|.+|.++|||.+++++
T Consensus        78 Iq~aR~~KgmsqkDLA~kInekpqVv~dyEsGrAIpNqqil~kmEraLgvKlrgk~  133 (135)
T KOG3398|consen   78 IQQARAQKGMSQKDLAQKINEKPQVIQDYESGRAIPNQQILSKMERALGVKLRGKN  133 (135)
T ss_pred             HHHHHHhccccHHHHHHHHccCchhhhhHhccccCchHHHHHHHHHHhceeccccc
Confidence            99999999999999999999999999999999999999999999999999999985

>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=99.83  E-value=5.2e-22  Score=129.51  Aligned_cols=70  Identities=51%  Similarity=0.774  Sum_probs=0.7

Q ss_pred             CCCCce-eeccCCCCCccccCHHHHHHHHHcCCChhHHHhhhcCCCCCCCCCCCcccccchhhhccccCCcc
Q 032366            9 QDWEPV-VIKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTENLAHDRV   79 (142)
Q Consensus         9 ~~w~~~-~~~~~~~~~~~~~~~~~~~~a~r~G~~v~t~kk~~~g~~~~~~~~~~~~~~kl~~~~~~~~~~~~   79 (142)
                      |||||| ||||+.|++++++++++||+|||+|..|+|++||.+|+|+ ++.+.++++.|||+++++|+++.+
T Consensus         1 qDWd~vtvi~kk~p~~~~~r~~~avNaArR~G~~v~T~KK~~~g~Nk-~~~~~~~n~~KLD~etE~~~~~kV   71 (71)
T PF08523_consen    1 QDWDPVTVIGKKGPRAKVARSESAVNAARRSGAVVETEKKYGAGNNK-HQHGEGQNAAKLDRETEELKHEKV   71 (71)
T ss_dssp             ---------------------------------------------------------------------S--
T ss_pred             CCCcccceecccCCCccccCCHHHHHHHHHcCCceEEEEeeeccccc-cCCCcccccccccccccccCCCCC
Confidence            799999 8999999999999999999999999999999999999999 667889999999999999998753

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=99.65  E-value=1.3e-15  Score=112.04  Aligned_cols=65  Identities=29%  Similarity=0.452  Sum_probs=61.7

Q ss_pred             cchHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCCCC
Q 032366           78 RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRGKK  142 (142)
Q Consensus        78 ~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~e~~  142 (142)
                      .+...|+.+|+.+|+++||||.+||+.+|+++++|++||+|+..|+.+.+.+|+++||+++.|++
T Consensus        80 ~~~~~~g~~Ir~lRe~~GLSQ~eLA~~iGvs~stIskiE~G~~~Ps~~~l~kLa~~Lgvsl~e~~  144 (144)
T PRK06424         80 DIVEDYAELVKNARERLSMSQADLAAKIFERKNVIASIERGDLLPDIKTARKLEKILGITLIEKA  144 (144)
T ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCCCCC
Confidence            34578999999999999999999999999999999999999999999999999999999999874

>PHA01976 helix-turn-helix protein

Probab=99.63  E-value=9.7e-16  Score=97.95  Aligned_cols=58  Identities=28%  Similarity=0.509  Sum_probs=56.3

Q ss_pred             HHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           82 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        82 ~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      .|+.+|+.+|..+|+||.+||+.+|+++++|++||+|...|+.+.+.+||++|||+++
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            5899999999999999999999999999999999999999999999999999999985

>PRK08359 transcription factor; Validated

Probab=99.59  E-value=7.7e-15  Score=110.93  Aligned_cols=63  Identities=17%  Similarity=0.245  Sum_probs=60.8

Q ss_pred             cchHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 032366           78 RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG  140 (142)
Q Consensus        78 ~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~e  140 (142)
                      .+...|+++|+++|+.+||||.+||+.+|+++++|++||+|+..|+.+++.+||++|+|++.+
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            577899999999999999999999999999999999999999999999999999999999875

>TIGR03070 couple_hipB transcriptional regulator, y4mF family

Probab=99.56  E-value=2.4e-14  Score=88.04  Aligned_cols=57  Identities=26%  Similarity=0.353  Sum_probs=54.9

Q ss_pred             HHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 032366           82 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL  138 (142)
Q Consensus        82 ~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl  138 (142)
                      .++.+|+.+|...||||.+||+.+|+|+++|++||+|+..|+.+.+.+|+++|||++
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            488999999999999999999999999999999999999999999999999999985

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.

>TIGR00270 conserved hypothetical protein TIGR00270

Probab=99.55  E-value=2.2e-14  Score=106.58  Aligned_cols=63  Identities=30%  Similarity=0.469  Sum_probs=60.1

Q ss_pred             cchHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 032366           78 RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG  140 (142)
Q Consensus        78 ~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~e  140 (142)
                      .+...|+.+|+.+|+++||||.+||+++|+++++|++||+|...|+.+.+.+|+++|||++.+
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            566789999999999999999999999999999999999999999999999999999999864

>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=99.54  E-value=1.2e-14  Score=92.07  Aligned_cols=56  Identities=34%  Similarity=0.484  Sum_probs=48.4

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      |++|+++|+.+|+||.+||+.+|+++++|++||+|+..|+...+.+||++|||+++
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            68999999999999999999999999999999999999999999999999999975

>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=99.52  E-value=2.2e-14  Score=88.21  Aligned_cols=53  Identities=34%  Similarity=0.494  Sum_probs=49.0

Q ss_pred             HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           87 IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      |+++|+++|+||.+||+.+|+|+++|++||+|+..|+.+.+.+||++|||+++
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            68899999999999999999999999999999999999999999999999875

; 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=99.50  E-value=5e-14  Score=90.94  Aligned_cols=56  Identities=29%  Similarity=0.431  Sum_probs=53.5

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 032366           85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG  140 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~e  140 (142)
                      .+|+.+|.+.|+||.+||+.+|||++||..||+|+..|+.....+||++|++++++
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            48999999999999999999999999999999999999999999999999998763

>PRK09726 antitoxin HipB; Provisional

Probab=99.46  E-value=3.7e-13  Score=90.97  Aligned_cols=60  Identities=25%  Similarity=0.361  Sum_probs=57.2

Q ss_pred             hHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           80 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      ...++.+|+.+|..+|+||.+||+.+||++++|++||+|...|+.+.+.+||++|||+++
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            457999999999999999999999999999999999999999999999999999999975

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

Probab=99.45  E-value=1e-13  Score=88.10  Aligned_cols=58  Identities=29%  Similarity=0.461  Sum_probs=50.4

Q ss_pred             HHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCCC
Q 032366           82 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA-IPNQQILTKLERALGVKLR  139 (142)
Q Consensus        82 ~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~-~p~~~~l~kLa~~Lgvsl~  139 (142)
                      .||..|+.+|...||||.++|+.+|+|+++|++||+|+. .|+.+.+.+||++||++++
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=99.43  E-value=4e-13  Score=97.18  Aligned_cols=59  Identities=25%  Similarity=0.294  Sum_probs=56.5

Q ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           81 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        81 ~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      ..++++|+.+|..+||||.+||+.+|||+++|++||+|...|+.+.+.+||++|||+++
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            45999999999999999999999999999999999999999999999999999999875

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

Probab=99.38  E-value=1.4e-12  Score=97.30  Aligned_cols=66  Identities=36%  Similarity=0.528  Sum_probs=62.4

Q ss_pred             CCcchHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCCC
Q 032366           76 HDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRGK  141 (142)
Q Consensus        76 ~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~e~  141 (142)
                      ...+..+++++|+.+|+.+||||++||++|+++.+.|.+||+|+..|+...+.+|.++|||.+.++
T Consensus        73 ~~elvedY~e~Ir~ARE~~G~SqedLA~ki~ek~svI~~iE~g~~~P~~~~akkLEk~LgIkL~e~  138 (165)
T COG1813          73 LPELVEDYGERIREAREKRGLSQEDLAAKLKEKVSVIRRIERGEATPNIKVAKKLEKLLGIKLVEK  138 (165)
T ss_pred             HHHHHHHHHHHHHHHHHHcCCCHHHHHHHhcccHHHHHHHHhcccCccHHHHHHHHHHhCceeeee
Confidence            346788999999999999999999999999999999999999999999999999999999999764

>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional

Probab=99.34  E-value=2.9e-12  Score=96.94  Aligned_cols=60  Identities=25%  Similarity=0.300  Sum_probs=57.3

Q ss_pred             hHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           80 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      .+.++.+|+.+|+++||||.+||+++|+|+++|++||+|+..|+...+.+||++|||+++
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            455899999999999999999999999999999999999999999999999999999975

>PRK13890 conjugal transfer protein TrbA; Provisional

Probab=99.34  E-value=4.1e-12  Score=90.71  Aligned_cols=60  Identities=15%  Similarity=0.295  Sum_probs=56.5

Q ss_pred             hHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           80 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      ...|+.+|+++|.++||||.+||+++|+|+++|++||+|+..|+.+++.+||++|||+++
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            356899999999999999999999999999999999999999999999999999999654

>TIGR02607 antidote_HigA addiction module antidote protein, HigA family

Probab=99.33  E-value=4.4e-12  Score=82.98  Aligned_cols=58  Identities=14%  Similarity=0.163  Sum_probs=54.7

Q ss_pred             HHHHHHH-HHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           82 ELKKAIV-QARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        82 ~~g~~Lk-~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      ..+++|+ .+|+++|+||.+||+.+|+|+++|++||+|...|+.+.+.+||++|||+++
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            3688899 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.

>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed

Probab=99.30  E-value=7.7e-12  Score=101.81  Aligned_cols=62  Identities=23%  Similarity=0.324  Sum_probs=58.9

Q ss_pred             cchHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           78 RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        78 ~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      .+...++++|+.+|+.+||||.+||+++|+|+++|++||+|+..|+.+.+.+||++|||+++
T Consensus        24 ~~~~~~g~rl~~~R~~~gltq~~lA~~~gvs~~~i~~~E~g~~~ps~~~l~~ia~~l~v~~~   85 (309)
T PRK08154         24 PFLAALGERVRTLRARRGMSRKVLAQASGVSERYLAQLESGQGNVSILLLRRVARALGCSLA   85 (309)
T ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHhCCCHH
Confidence            45577999999999999999999999999999999999999999999999999999999875

>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein

Probab=99.29  E-value=1.2e-11  Score=84.06  Aligned_cols=58  Identities=28%  Similarity=0.368  Sum_probs=54.2

Q ss_pred             hHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           80 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      ...++.+|+.+|+++||||  ||+++|||+++|++||+|+..|+.+.+.+||++||+++.
T Consensus        30 ~~~~~~~l~~~r~~~glSq--LAe~~GIs~stLs~iE~g~~~Ps~~tL~kI~~aLgi~l~   87 (89)
T TIGR02684        30 PAYIAHALGYIARARGMTQ--LARKTGLSRESLYKALSGKGNPTFDTILKVTKALGLKLT   87 (89)
T ss_pred             HHHHHHHHHHHHHHCChHH--HHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHcCCcee
Confidence            3458899999999999995  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.

>PRK10072 putative transcriptional regulator; Provisional

Probab=99.22  E-value=4.1e-11  Score=82.58  Aligned_cols=53  Identities=21%  Similarity=0.323  Sum_probs=49.5

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 032366           85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL  138 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl  138 (142)
                      ..|+.+|...||||.+||+.+|+|.++|++||+|++.|+...+. |+++|++++
T Consensus        36 ~eik~LR~~~glTQ~elA~~lGvS~~TVs~WE~G~r~P~~~~l~-Ll~~L~~~P   88 (96)
T PRK10072         36 TEFEQLRKGTGLKIDDFARVLGVSVAMVKEWESRRVKPSSAELK-LMRLIQANP   88 (96)
T ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH-HHHHHhhCH
Confidence            44999999999999999999999999999999999999998864 999999987

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

Probab=99.19  E-value=3e-11  Score=76.10  Aligned_cols=55  Identities=20%  Similarity=0.291  Sum_probs=42.5

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhCCCCCC
Q 032366           86 AIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK-AIPNQQILTKLERALGVKLRG  140 (142)
Q Consensus        86 ~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~-~~p~~~~l~kLa~~Lgvsl~e  140 (142)
                      +|+.++.++|+|+.+||+.+|+++++|++|.+|+ ..|+.+.+.+||++|||++++
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 689999999999999999753

>TIGR02612 mob_myst_A mobile mystery protein A

Probab=99.16  E-value=9.9e-11  Score=86.66  Aligned_cols=55  Identities=18%  Similarity=0.194  Sum_probs=51.4

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCC--CCHHHHHHHHHHhCCCCC
Q 032366           85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAI--PNQQILTKLERALGVKLR  139 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~--p~~~~l~kLa~~Lgvsl~  139 (142)
                      ..|+.+|..+||||.+||+++|||+++|++||+|...  |+.+.+.+||++|||++.
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            5799999999999999999999999999999999864  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).

>PRK04140 hypothetical protein; Provisional

Probab=99.12  E-value=2e-10  Score=94.14  Aligned_cols=61  Identities=25%  Similarity=0.302  Sum_probs=57.2

Q ss_pred             chHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           79 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      +....+++|+.+|+++||||.+||+.+|+|+++|++||+|+..|+.+.+.+|+++||+++.
T Consensus       123 ~v~i~GerLk~lRe~~GlSq~eLA~~lGVSr~tIskyE~G~~~Ps~e~~~kLa~~Lgv~l~  183 (317)
T PRK04140        123 YVKIDGDVLREAREELGLSLGELASELGVSRRTISKYENGGMNASIEVAIKLEEILDVPLT  183 (317)
T ss_pred             eehhhHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCChH
Confidence            4455799999999999999999999999999999999999999999999999999999864

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

Probab=99.11  E-value=3.7e-10  Score=66.41  Aligned_cols=53  Identities=36%  Similarity=0.543  Sum_probs=50.3

Q ss_pred             HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           87 IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      |+.+|...++|+.+||+.+|++..+|++|++|...|+.+.+.+|+++||+++.
T Consensus         2 i~~~~~~~~~s~~~la~~~~i~~~~i~~~~~~~~~~~~~~~~~i~~~~~~~~~   54 (56)
T smart00530        2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLD   54 (56)
T ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHhCCChh
Confidence            67789999999999999999999999999999999999999999999999875

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

Probab=99.04  E-value=1.2e-09  Score=64.69  Aligned_cols=55  Identities=36%  Similarity=0.529  Sum_probs=51.6

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      +.|+..+...|+|+.++|+.+|+++.+|++|++|...|+...+.+|++.||++++
T Consensus         2 ~~l~~~~~~~~~s~~~~a~~~~~~~~~v~~~~~g~~~~~~~~~~~i~~~~~~~~~   56 (58)
T cd00093           2 ERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLD   56 (58)
T ss_pred             hHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCChh
Confidence            4578889999999999999999999999999999999999999999999999875

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=99.00  E-value=1.1e-09  Score=77.73  Aligned_cols=58  Identities=26%  Similarity=0.324  Sum_probs=51.8

Q ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           81 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        81 ~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      ...+..|+.+|...|+||.+||+.+|+++++|++||+|...|+.. +..|.++|+++++
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            346778999999999999999999999999999999999988865 6778899999875

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=98.92  E-value=3e-09  Score=70.62  Aligned_cols=61  Identities=26%  Similarity=0.344  Sum_probs=49.3

Q ss_pred             chHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhCCCCC
Q 032366           79 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK-AIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~-~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      ....+...|.++|+++||||.++|+.+|++++.|+++++|+ ..++.+.+..++..||..++
T Consensus        15 ~k~~l~~~i~~~~~~~~ltQ~e~A~~lgisq~~vS~l~~g~~~~~sl~~L~~~l~aLG~~v~   76 (80)
T PF13744_consen   15 AKAQLMAAIRELREERGLTQAELAERLGISQPRVSRLENGKIDDFSLDTLLRYLEALGGRVE   76 (80)
T ss_dssp             HHHHHHHHHHHHHHCCT--HHHHHHHHTS-HHHHHHHHTT-GCC--HHHHHHHHHHTTEEEE
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHHCCChhHHHHHHcCcccCCCHHHHHHHHHHcCCeEE
Confidence            44567888999999999999999999999999999999986 56899999999999997653

>PRK10856 cytoskeletal protein RodZ; Provisional

Probab=98.91  E-value=2.9e-09  Score=87.80  Aligned_cols=60  Identities=20%  Similarity=0.211  Sum_probs=54.5

Q ss_pred             hHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCH------HHHHHHHHHhCCCCC
Q 032366           80 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQ------QILTKLERALGVKLR  139 (142)
Q Consensus        80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~------~~l~kLa~~Lgvsl~  139 (142)
                      .+.+|.+|+.+|+++||||.+||+++++++++|++||+|+..+..      .++..+|++|||+.+
T Consensus        12 ~~~~G~~Lr~aRe~~GlSq~~vA~~l~l~~~~I~~iE~g~~~~~~~~tf~RGyir~yA~~lgv~~~   77 (331)
T PRK10856         12 ALTTGERLRQAREQLGLTQQAVAERLCLKVSTVRDIEEDKAPADLASTFLRGYIRSYARLVHIPEE   77 (331)
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHCCCCCCChhHHHHHHHHHHHHHHHCcCHH
Confidence            345899999999999999999999999999999999999987766      458899999999875

>PHA00542 putative Cro-like protein

Probab=98.89  E-value=9.1e-09  Score=68.75  Aligned_cols=49  Identities=22%  Similarity=0.247  Sum_probs=45.0

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHh
Q 032366           86 AIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK-AIPNQQILTKLERAL  134 (142)
Q Consensus        86 ~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~-~~p~~~~l~kLa~~L  134 (142)
                      .+..++...|+||.+||+.+|||+++|++||+|. ..|+.+.+.+||+++
T Consensus        22 ~l~~~l~~~glTq~elA~~lgIs~~tIsr~e~g~~~~p~~~~l~ki~~~~   71 (82)
T PHA00542         22 ELVCALIRAGWSQEQIADATDVSQPTICRIYSGRHKDPRYSVVEKLRHLV   71 (82)
T ss_pred             HHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHHHHHH
Confidence            4667788999999999999999999999999999 479999999999886

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

Probab=98.86  E-value=6.8e-09  Score=77.52  Aligned_cols=52  Identities=23%  Similarity=0.319  Sum_probs=48.9

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q 032366           84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALG  135 (142)
Q Consensus        84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lg  135 (142)
                      .+-|++.|+++|+||++||++.|+|+++|.++|.|+..|....+.+|-++|.
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            4569999999999999999999999999999999999999999999988874

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

Probab=98.77  E-value=4.4e-08  Score=64.38  Aligned_cols=49  Identities=18%  Similarity=0.203  Sum_probs=42.1

Q ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHhC------CCHHHHHHHHcCCCCCCHHHHHHHH
Q 032366           81 SELKKAIVQARNDKKLTQSQLAQLIN------EKPQVIQEYESGKAIPNQQILTKLE  131 (142)
Q Consensus        81 ~~~g~~Lk~~R~~~glTQ~eLA~~lg------is~stIs~~E~G~~~p~~~~l~kLa  131 (142)
                      ..|+++|+..|...|+||.+||+.+|      +|+++|++||+|.-  +...+.+|-
T Consensus        10 e~~~~~lk~~R~~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es~~l--s~~n~~kl~   64 (75)
T smart00352       10 EAFAKTFKQRRIKLGFTQADVGLALGALYGPDFSQTTICRFEALQL--SFKNMCKLK   64 (75)
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhcccccCcCCHHHHHHHHhcCc--cHHHHHHHH
Confidence            46999999999999999999999999      59999999999864  555555553

>COG2944 Predicted transcriptional regulator [Transcription]

Probab=98.74  E-value=3e-08  Score=69.01  Aligned_cols=45  Identities=20%  Similarity=0.338  Sum_probs=40.7

Q ss_pred             HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHH
Q 032366           83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQIL  127 (142)
Q Consensus        83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l  127 (142)
                      -+..|+.+|+..||||.+||..+|+|.+||++||.|+..|+..-+
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            356799999999999999999999999999999999999975543

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

Probab=98.73  E-value=3.2e-08  Score=85.28  Aligned_cols=58  Identities=28%  Similarity=0.358  Sum_probs=55.0

Q ss_pred             HHHHHHHHHHHhCCCCHHHHHHHh-----CCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           82 ELKKAIVQARNDKKLTQSQLAQLI-----NEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        82 ~~g~~Lk~~R~~~glTQ~eLA~~l-----gis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      .|+++|+.+|+++|+||.+||+.+     +|++++|++||+|+..|+.+.+.+||++|||+++
T Consensus         3 ~~~~rL~~~r~~~g~tq~~la~~~~~~g~~vs~~~is~~e~g~~~p~~~~l~~la~~l~v~~~   65 (517)
T PRK13355          3 TFAERLKQAMKARGLKQEDLVHAAEARGVKLGKSHISQYVSGKTGPRRDVLPFLAAILGVSED   65 (517)
T ss_pred             hHHHHHHHHHHHCCCCHHHHHHHHHhccCCcCHHHHHHHHCCCCCCCHHHHHHHHHHhCcCHH
Confidence            588999999999999999999996     6999999999999999999999999999999975

>PRK02866 cyanate hydratase; Validated

Probab=98.72  E-value=7.6e-08  Score=70.92  Aligned_cols=59  Identities=22%  Similarity=0.254  Sum_probs=55.4

Q ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           81 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        81 ~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      .++.+.|..+|.++|||+.++|+.+|+|...+..+|.|+..++.+.+.+|+++||++.+
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            45788999999999999999999999999999999999999999999999999998754

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

Probab=98.68  E-value=7.1e-08  Score=67.05  Aligned_cols=57  Identities=18%  Similarity=0.257  Sum_probs=51.2

Q ss_pred             HHHHHHHH-HHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           83 LKKAIVQA-RNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        83 ~g~~Lk~~-R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      .|+.|++. .+..|+||.+||+.+||++.+|+++.+|++..+.+++.+|+++||.+++
T Consensus        10 PGEiL~eeflep~glt~~~lA~~lgV~r~~is~ling~~~iT~dmAlrL~k~fGtspe   67 (104)
T COG3093          10 PGEILREEFLEPLGLTQTELAEALGVTRNTISELINGRRAITADMALRLAKVFGTSPE   67 (104)
T ss_pred             chHHHHHHHhccccCCHHHHHHHhCCCHHHHHHHHcCCcCCCHHHHHHHHHHhCCCHH
Confidence            56667654 5667999999999999999999999999999999999999999999864

>COG1709 Predicted transcriptional regulator [Transcription]

Probab=98.64  E-value=2.7e-08  Score=77.39  Aligned_cols=56  Identities=27%  Similarity=0.444  Sum_probs=51.2

Q ss_pred             chHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCC-CCHHHHHHHHHHh
Q 032366           79 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAI-PNQQILTKLERAL  134 (142)
Q Consensus        79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~-p~~~~l~kLa~~L  134 (142)
                      +....|+.|+++|+..+.||.+||+.+|+|+|.|++||.|++. |....+.++-.+|
T Consensus        24 lS~~pge~lrKWR~~F~vSQ~elA~~l~vSpSVISDYE~GRRk~Pg~~~vkk~V~AL   80 (241)
T COG1709          24 LSEDPGETLRKWREIFNVSQTELARELGVSPSVISDYESGRRKSPGIAFVKKFVEAL   80 (241)
T ss_pred             ecCChhHHHHHHHHHhCccHHHHHHHhCCCcceeehhhccCccCccHHHHHHHHHHH
Confidence            4566899999999999999999999999999999999999987 8998888887665

>TIGR00673 cynS cyanate hydratase

Probab=98.57  E-value=3.4e-07  Score=67.65  Aligned_cols=56  Identities=16%  Similarity=0.174  Sum_probs=53.8

Q ss_pred             HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 032366           83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL  138 (142)
Q Consensus        83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl  138 (142)
                      +.+.|..+|.++|||++++|+.+|+|+..+..++.|+..++.+.+.+|+++||++.
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            77889999999999999999999999999999999999999999999999999874

Alternate names include cyanate lyase, cyanase and cyanate hydrolase.

>COG1396 HipB Predicted transcriptional regulators [Transcription]

Probab=98.39  E-value=2.7e-06  Score=54.21  Aligned_cols=56  Identities=30%  Similarity=0.520  Sum_probs=52.6

Q ss_pred             HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCC
Q 032366           83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA-IPNQQILTKLERALGVKL  138 (142)
Q Consensus        83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~-~p~~~~l~kLa~~Lgvsl  138 (142)
                      ++.+++.+|...|+||.++|..+|++..+++.||+|.. .|....+..++..|++..
T Consensus         2 ~~~~~~~~r~~~~~s~~~~a~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~   58 (120)
T COG1396           2 IGERLKELRKKKGLSQEELAERLGVSRSTISRIERGRSESPSLELLARLAAALGVSL   58 (120)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCCHHHHHHHHHHHCCCH
Confidence            67899999999999999999999999999999999999 899999999999988754

>COG1395 Predicted transcriptional regulator [Transcription]

Probab=98.37  E-value=9.1e-07  Score=72.15  Aligned_cols=57  Identities=19%  Similarity=0.330  Sum_probs=54.1

Q ss_pred             HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      -|+.|++.|.++|+|..+||..+|+|+.+|+.||+|...|+.+.+.+|.+.||.++-
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            478899999999999999999999999999999999999999999999999998763

>COG3655 Predicted transcriptional regulator [Transcription]

Probab=98.35  E-value=1.2e-06  Score=57.41  Aligned_cols=57  Identities=19%  Similarity=0.236  Sum_probs=50.9

Q ss_pred             HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCC-CCHHHHHHHHHHhCCCCC
Q 032366           83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAI-PNQQILTKLERALGVKLR  139 (142)
Q Consensus        83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~-p~~~~l~kLa~~Lgvsl~  139 (142)
                      +.-++...+.+++++..+||+.+|||.++++.+.+|+.. ...++|.+||++|+|.+-
T Consensus         3 i~~~l~~~l~~r~~~~~eLa~~igis~~~ls~l~~gk~k~I~~~tL~~iC~~LeCqpg   60 (73)
T COG3655           3 IAVRLDVMLADRKISLKELAEAIGISEANLSKLKTGKVKAIRLSTLEKICKALECQPG   60 (73)
T ss_pred             chHhHHHHHHHHhhhHHHHHHHHcccHHHHHHHHcCCcceeeHHHHHHHHHHcCCChh
Confidence            345677888999999999999999999999999988864 589999999999999875

>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=98.34  E-value=1.9e-07  Score=59.78  Aligned_cols=53  Identities=19%  Similarity=0.332  Sum_probs=38.7

Q ss_pred             HHHHHHHhCCCC-HHHHHHHhCCCHHHHH-HHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           86 AIVQARNDKKLT-QSQLAQLINEKPQVIQ-EYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        86 ~Lk~~R~~~glT-Q~eLA~~lgis~stIs-~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      .|+++++..|++ +.+||+.+|||+++|+ .|......| .+.+.+||..+||+++
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            467777777775 5699999999999999 898877777 9999999999999975

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=98.19  E-value=6.4e-06  Score=52.27  Aligned_cols=54  Identities=24%  Similarity=0.374  Sum_probs=40.3

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCC--CCCCH----HHHHHHHHHhCCCCC
Q 032366           86 AIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK--AIPNQ----QILTKLERALGVKLR  139 (142)
Q Consensus        86 ~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~--~~p~~----~~l~kLa~~Lgvsl~  139 (142)
                      +|+..|..+|+|..++|..++|+.+.|..+|+|.  ..|+.    ..+..+|++||++.+
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            4899999999999999999999999999999986  44553    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=98.04  E-value=1.8e-05  Score=58.41  Aligned_cols=59  Identities=15%  Similarity=0.218  Sum_probs=54.4

Q ss_pred             HHHHHHHHHHHHhCCCCH----HHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           81 SELKKAIVQARNDKKLTQ----SQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        81 ~~~g~~Lk~~R~~~glTQ----~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      ..+.++|+++...+|+.+    .+||+.||||.+++++-.+|+..++...+.+|++.||++++
T Consensus         4 ~~~~erV~~Ll~~~Gi~kr~~~s~LA~iL~Is~ssa~RKL~G~~~ftl~EI~~Ia~~fgvS~d   66 (147)
T PF08667_consen    4 QAIAERVRELLDRKGIPKRKHASELADILGISYSSAYRKLNGKSPFTLEEIKKIAKHFGVSPD   66 (147)
T ss_pred             HHHHHHHHHHHHHcCCcchhhHHHHHHHHCCCHHHHHHHhcCCCCCCHHHHHHHHHHhCcCHH
Confidence            458899999999999876    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 [].

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

Probab=97.96  E-value=1.3e-05  Score=64.93  Aligned_cols=58  Identities=21%  Similarity=0.357  Sum_probs=51.1

Q ss_pred             HHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC--CCC----HHHHHHHHHHhCCCCC
Q 032366           82 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA--IPN----QQILTKLERALGVKLR  139 (142)
Q Consensus        82 ~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~--~p~----~~~l~kLa~~Lgvsl~  139 (142)
                      ++|++||+.|+++|||+.|+|.+++|..++|..+|.|..  .|.    ...+...|++||++.+
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  333    3468899999999865

>COG5499 Predicted transcription regulator containing HTH domain [Transcription]

Probab=97.95  E-value=1.8e-05  Score=55.50  Aligned_cols=56  Identities=20%  Similarity=0.225  Sum_probs=52.0

Q ss_pred             HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      --+.|+.++...|+|+.+||..+| |.+.++++.+|++..+.+.+.+|.+-||++.+
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            456789999999999999999999 88999999999999999999999999999864

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

Probab=97.92  E-value=3.3e-05  Score=46.35  Aligned_cols=40  Identities=13%  Similarity=0.170  Sum_probs=33.2

Q ss_pred             HHHHHhCCCHHHHHHHHcCCCCCCHH---HHHHHHHHhCCCCC
Q 032366          100 QLAQLINEKPQVIQEYESGKAIPNQQ---ILTKLERALGVKLR  139 (142)
Q Consensus       100 eLA~~lgis~stIs~~E~G~~~p~~~---~l~kLa~~Lgvsl~  139 (142)
                      +||+.+|||+++|++|++|...++..   .+..+++.||+.+.
T Consensus         2 ~lA~~~gvs~~tvs~~l~g~~~vs~~~~~~i~~~~~~l~~~~~   44 (52)
T cd01392           2 DIARAAGVSVATVSRVLNGKPRVSEETRERVLAAAEELGYRPN   44 (52)
T ss_pred             cHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHHHhCCCCC
Confidence            79999999999999999999766544   45568888888764

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

>TIGR01321 TrpR trp operon repressor, proteobacterial

Probab=97.79  E-value=0.00012  Score=50.27  Aligned_cols=50  Identities=12%  Similarity=0.098  Sum_probs=38.7

Q ss_pred             HHHHHHHHHH--HhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHH
Q 032366           82 ELKKAIVQAR--NDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLE  131 (142)
Q Consensus        82 ~~g~~Lk~~R--~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa  131 (142)
                      .+..|++-.+  ...++||+++|+.+|||.+||++++++-...+++.-.-|.
T Consensus        40 ~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~sn~lk~~~~~~~~~l~   91 (94)
T TIGR01321        40 DLGDRIRIVNELLNGNMSQREIASKLGVSIATITRGSNNLKTMDPNFKQFLR   91 (94)
T ss_pred             HHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHHHhhcccCCHHHHHHHH
Confidence            4555655554  3578999999999999999999999998866666555444

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.

>PHA01083 hypothetical protein

Probab=97.78  E-value=4.8e-05  Score=56.01  Aligned_cols=54  Identities=17%  Similarity=0.242  Sum_probs=45.8

Q ss_pred             HHHHHHHhCCC-CHHHHHHHhCCCHHHHHHHHcC-CCCCCHHHHHHHHHHhCCCCC
Q 032366           86 AIVQARNDKKL-TQSQLAQLINEKPQVIQEYESG-KAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        86 ~Lk~~R~~~gl-TQ~eLA~~lgis~stIs~~E~G-~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      .|....+.+++ +-++||..+||+++.|++|-+| ++.++.+.+..||+.+|+++.
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            34455555555 4568999999999999999999 999999999999999999874

>COG2522 Predicted transcriptional regulator [General function prediction only]

Probab=97.68  E-value=0.00017  Score=51.47  Aligned_cols=45  Identities=20%  Similarity=0.327  Sum_probs=36.6

Q ss_pred             cchHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCC
Q 032366           78 RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIP  122 (142)
Q Consensus        78 ~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p  122 (142)
                      .+.+.+...|.+...+.|+||.++|+.+|+|++.||+|.+|++.+
T Consensus         5 ~vlPaiRa~lA~~L~eeG~Sq~~iA~LLGltqaAVS~Yls~krg~   49 (119)
T COG2522           5 EVLPAIRALLAKELIEEGLSQYRIAKLLGLTQAAVSQYLSGKRGS   49 (119)
T ss_pred             HHHHHHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHccCCch
Confidence            345567777755555559999999999999999999999998873

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

Probab=97.64  E-value=0.00027  Score=51.81  Aligned_cols=54  Identities=17%  Similarity=0.242  Sum_probs=49.2

Q ss_pred             hHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHh
Q 032366           80 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERAL  134 (142)
Q Consensus        80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~L  134 (142)
                      .+.|+.-|+.+..++|||..|||++.||+.+|+.++.+| +.|+.+++.+|-+.+
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            356899999999999999999999999999999999999 689999998887765

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

Probab=97.58  E-value=0.0003  Score=42.06  Aligned_cols=42  Identities=12%  Similarity=0.131  Sum_probs=32.9

Q ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHH---HHHHHHhCCCC
Q 032366           97 TQSQLAQLINEKPQVIQEYESGKAIPNQQIL---TKLERALGVKL  138 (142)
Q Consensus        97 TQ~eLA~~lgis~stIs~~E~G~~~p~~~~l---~kLa~~Lgvsl  138 (142)
                      |.+|+|+.+|+|.+||+++.+|....+.+..   ..+++.||..+
T Consensus         1 Ti~dIA~~agvS~~TVSr~ln~~~~vs~~tr~rI~~~a~~lgY~p   45 (46)
T PF00356_consen    1 TIKDIAREAGVSKSTVSRVLNGPPRVSEETRERILEAAEELGYRP   45 (46)
T ss_dssp             CHHHHHHHHTSSHHHHHHHHTTCSSSTHHHHHHHHHHHHHHTB-S
T ss_pred             CHHHHHHHHCcCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHCCCC
Confidence            6789999999999999999999987777654   44555666443

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 ....

>smart00354 HTH_LACI helix_turn _helix lactose operon repressor

Probab=97.57  E-value=0.00026  Score=45.53  Aligned_cols=44  Identities=14%  Similarity=0.138  Sum_probs=35.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCC
Q 032366           96 LTQSQLAQLINEKPQVIQEYESGKAIPNQQI---LTKLERALGVKLR  139 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~G~~~p~~~~---l~kLa~~Lgvsl~  139 (142)
                      +|+.|||+.+|+|.+||+++.+|....+.+.   +.++++.||..+.
T Consensus         1 ~t~~~iA~~~gvS~~TVSr~ln~~~~v~~~t~~~i~~~~~~~gy~~~   47 (70)
T smart00354        1 ATIKDVARLAGVSKATVSRVLNGNGRVSEETREKVLAAMEELGYIPN   47 (70)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCCCC
Confidence            4789999999999999999999987665554   5667777776543

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

Probab=97.55  E-value=0.00028  Score=50.26  Aligned_cols=50  Identities=18%  Similarity=0.172  Sum_probs=38.5

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhC--CCHHHHHHHHcCCCCCCHHHHHHHHHHh
Q 032366           85 KAIVQARNDKKLTQSQLAQLIN--EKPQVIQEYESGKAIPNQQILTKLERAL  134 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~lg--is~stIs~~E~G~~~p~~~~l~kLa~~L  134 (142)
                      -.|+.+|...+||+.|.|..++  ++..+..+||+|...++++++..|....
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            3589999999999999999999  9999999999999999999888876653

; PDB: 1S4K_A.

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

Probab=97.32  E-value=0.00047  Score=58.33  Aligned_cols=47  Identities=23%  Similarity=0.280  Sum_probs=43.2

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCCC
Q 032366           93 DKKLTQSQLAQLINEKPQVIQEYESGKA-IPNQQILTKLERALGVKLR  139 (142)
Q Consensus        93 ~~glTQ~eLA~~lgis~stIs~~E~G~~-~p~~~~l~kLa~~Lgvsl~  139 (142)
                      ..|+|..+||+++|+|.++++++|+|+. .|+.+.|.+|+++|||+..
T Consensus         1 ~~~~~~~~~~~~~~~~~~y~~~l~~~~~~~ps~~~~~~~~~~~~~~~~   48 (399)
T PRK08099          1 QQGCTLQQVADASGMTKGYLSQLLNAKIKSPSAQKLEALHRFLGLEFP   48 (399)
T ss_pred             CCCCcHHHHHHHhCCcHHHHHHHhcCCCCCccHHHHHHHHHHhCCChh
Confidence            3689999999999999999999999985 6999999999999999853

>COG3636 Predicted transcriptional regulator [Transcription]

Probab=97.16  E-value=0.0021  Score=44.30  Aligned_cols=54  Identities=17%  Similarity=0.211  Sum_probs=46.0

Q ss_pred             HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 032366           83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL  138 (142)
Q Consensus        83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl  138 (142)
                      +...+...-..+||||  +|++.|+|+..+.+-.+...+|+.+.+.+++++||+.+
T Consensus        39 i~~alg~var~~GMsq--vA~~aGlsRe~LYkaLS~~GNPtf~Til~V~kAlG~rl   92 (100)
T COG3636          39 IAAALGVVARSRGMSQ--VARKAGLSREGLYKALSPGGNPTFDTILAVLKALGLRL   92 (100)
T ss_pred             HHHHHHHHHHhcCHHH--HHHHhCccHHHHHHHhCCCCCCcHHHHHHHHHHcCcee
Confidence            3444445556678776  99999999999999999999999999999999999875

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

Probab=97.13  E-value=0.002  Score=45.62  Aligned_cols=73  Identities=19%  Similarity=0.236  Sum_probs=48.6

Q ss_pred             HHHHHHHHHcCCChhHHHhhhcCCCCCCCCCCCcccc-cchhhhccccCCcchHHHHHHHHHH-HHhCCCCHHHHHHHhC
Q 032366           29 EKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTR-KLDEDTENLAHDRVPSELKKAIVQA-RNDKKLTQSQLAQLIN  106 (142)
Q Consensus        29 ~~~~~~a~r~G~~v~t~kk~~~g~~~~~~~~~~~~~~-kl~~~~~~~~~~~~~~~~g~~Lk~~-R~~~glTQ~eLA~~lg  106 (142)
                      .+..++|++.||+..|+.+|.. ..........+.-. +++.               +.|+.. -...++|+.|+|+.+|
T Consensus        19 ~s~~eaa~~F~VS~~Tv~~W~k-~~~~G~~~~k~r~~~Kid~---------------~~L~~~v~~~pd~tl~Ela~~l~   82 (119)
T PF01710_consen   19 KSIREAAKRFGVSRNTVYRWLK-RKETGDLEPKPRGRKKIDR---------------DELKALVEENPDATLRELAERLG   82 (119)
T ss_pred             chHHHHHHHhCcHHHHHHHHHH-hcccccccccccccccccH---------------HHHHHHHHHCCCcCHHHHHHHcC
Confidence            4678899999999999999976 32211100111111 3321               123333 3457899999999999


Q ss_pred             CCHHHHHHHHc
Q 032366          107 EKPQVIQEYES  117 (142)
Q Consensus       107 is~stIs~~E~  117 (142)
                      ||.++|+....
T Consensus        83 Vs~~ti~~~Lk   93 (119)
T PF01710_consen   83 VSPSTIWRALK   93 (119)
T ss_pred             CCHHHHHHHHH
Confidence            99999999875

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 [].

>COG5606 Uncharacterized conserved small protein [Function unknown]

Probab=97.01  E-value=0.0016  Score=43.99  Aligned_cols=61  Identities=23%  Similarity=0.250  Sum_probs=51.8

Q ss_pred             chHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCCC
Q 032366           79 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA-IPNQQILTKLERALGVKLR  139 (142)
Q Consensus        79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~-~p~~~~l~kLa~~Lgvsl~  139 (142)
                      +...+...|..+.+..+|+|+++|+.+||+++.++.+-+|+. ..+.+.|.-+....|..++
T Consensus        25 ir~~l~~~i~~~i~q~~l~Q~qiae~lgV~qprvS~l~~gk~~~fs~dkLvtml~~~g~ei~   86 (91)
T COG5606          25 IRSALMMAIKQWIEQAALSQAQIAELLGVTQPRVSDLARGKIQDFSIDKLVTMLARAGQEID   86 (91)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHhcchhHhhHHHHHHHHHHcCCccc
Confidence            455688889999999999999999999999999999999985 4577778777777776554

>PHA00675 hypothetical protein

Probab=96.99  E-value=0.0028  Score=41.82  Aligned_cols=42  Identities=10%  Similarity=0.064  Sum_probs=35.9

Q ss_pred             chHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 032366           79 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA  120 (142)
Q Consensus        79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~  120 (142)
                      +...--+.|+.+++..|.|+.+||+.+|||+++|+.|.+|++
T Consensus        23 Lt~~qV~~IR~l~~r~G~s~~~IA~~fGVsrstV~~I~~gk~   64 (78)
T PHA00675         23 LTDAEVERIRELHEVEGMSYAVLAEKFEQSKGAIAKICRYER   64 (78)
T ss_pred             cCHHHHHHHHHHHHhcCccHHHHHHHhCCCHHHHHHHHccch
Confidence            334455678888888899999999999999999999999874

>TIGR03879 near_KaiC_dom probable regulatory domain

Probab=96.91  E-value=0.0052  Score=40.28  Aligned_cols=49  Identities=24%  Similarity=0.255  Sum_probs=36.1

Q ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHH
Q 032366           81 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLE  131 (142)
Q Consensus        81 ~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa  131 (142)
                      ......+.-.|...|+|+.|+|+.+|+|.++|..+.+..  +....+.+|+
T Consensus        18 ~~~r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~~--~~~~~~~~~~   66 (73)
T TIGR03879        18 SLAEAAAALAREEAGKTASEIAEELGRTEQTVRNHLKGE--TKAGGLVKLA   66 (73)
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcC--cccchHHHHH
Confidence            333444444477899999999999999999999999853  3445555554

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.

>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=96.87  E-value=0.0065  Score=40.00  Aligned_cols=50  Identities=18%  Similarity=0.166  Sum_probs=38.5

Q ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHhC------CCHHHHHHHHcCCCCCCHHHHHHHHH
Q 032366           81 SELKKAIVQARNDKKLTQSQLAQLIN------EKPQVIQEYESGKAIPNQQILTKLER  132 (142)
Q Consensus        81 ~~~g~~Lk~~R~~~glTQ~eLA~~lg------is~stIs~~E~G~~~p~~~~l~kLa~  132 (142)
                      ..|.+.++..|...|+||.+++..+|      .|+++|+++|+=  ..+...+.+|--
T Consensus        10 e~Fa~~fk~rRi~LG~TQ~dVg~al~~~~G~~~SQttI~RFE~L--~LS~kn~~klkP   65 (75)
T PF00157_consen   10 EQFAKEFKQRRIKLGYTQADVGAALGRLYGKEFSQTTICRFEAL--QLSFKNMCKLKP   65 (75)
T ss_dssp             HHHHHHHHHHHHHTT--HHHHHHHHHHHHSSGGSHHHHHHHHTT--TSCHHHHHHHHH
T ss_pred             HHHHHHHHHhhhhcccCHHHHhHHHHHhcCccccchhhhhhHhc--ccCHHHHHHHHH
Confidence            46889999999999999999988876      499999999974  356666655543

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 ....

>TIGR02147 Fsuc_second hypothetical protein, TIGR02147

Probab=96.84  E-value=0.0034  Score=50.68  Aligned_cols=46  Identities=15%  Similarity=0.241  Sum_probs=43.0

Q ss_pred             CCCHHHHHHHhCCCH-HHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 032366           95 KLTQSQLAQLINEKP-QVIQEYESGKAIPNQQILTKLERALGVKLRG  140 (142)
Q Consensus        95 glTQ~eLA~~lgis~-stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~e  140 (142)
                      .+|-.++|+.+|++. +.++.+++|++.++...+.+++++||.+..|
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 9999999999999999999999999998765

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.

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

Probab=96.77  E-value=0.0033  Score=41.70  Aligned_cols=52  Identities=15%  Similarity=0.095  Sum_probs=39.0

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      ..|+.....+|+|..+||+..|++.+|+++...   .|.+..-..||++|||++.
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            346667778999999999999999999999764   4567777889999999875

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

Probab=96.70  E-value=0.0037  Score=37.05  Aligned_cols=24  Identities=4%  Similarity=0.097  Sum_probs=19.3

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcC
Q 032366           95 KLTQSQLAQLINEKPQVIQEYESG  118 (142)
Q Consensus        95 glTQ~eLA~~lgis~stIs~~E~G  118 (142)
                      |+|..++|+.+|+|++||.+|.+-
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            999999999999999999999864

>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=96.62  E-value=0.0042  Score=36.59  Aligned_cols=33  Identities=9%  Similarity=0.172  Sum_probs=23.9

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .+.+.+++. .|+|..++|+.+|||++||.+|.+
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 569999999999999999999975

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 ....

>PHA02591 hypothetical protein; Provisional

Probab=96.46  E-value=0.0066  Score=40.22  Aligned_cols=31  Identities=16%  Similarity=0.295  Sum_probs=26.7

Q ss_pred             HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           87 IVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +.....+.|+||.++|+.+|+++.+|++|..
T Consensus        51 vA~eL~eqGlSqeqIA~~LGVsqetVrKYL~   81 (83)
T PHA02591         51 VTHELARKGFTVEKIASLLGVSVRKVRRYLE   81 (83)
T ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHh
Confidence            4455566899999999999999999999864

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

Probab=96.34  E-value=0.014  Score=42.07  Aligned_cols=49  Identities=8%  Similarity=0.055  Sum_probs=38.4

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHH
Q 032366           85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERA  133 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~  133 (142)
                      ..+..+....|+|+++++..+|+|++|++++-++...++.+.-.++.++
T Consensus        26 ~~~~~l~~~l~ls~~el~~~lgis~~Tl~R~~~~~~~Ls~~~serl~~l   74 (133)
T TIGR02293        26 GALDRLAHLLAIGKAEIFKATGIPKATLQRRKMAHQRLSSEESDRLARV   74 (133)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHhhcCCCCCHHHHHHHHHH
Confidence            3456667788999999999999999999999987666776655544443

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.

>PRK10014 DNA-binding transcriptional repressor MalI; Provisional

Probab=96.25  E-value=0.014  Score=46.74  Aligned_cols=46  Identities=20%  Similarity=0.126  Sum_probs=37.8

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHH---HHHhCCCCC
Q 032366           94 KKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKL---ERALGVKLR  139 (142)
Q Consensus        94 ~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kL---a~~Lgvsl~  139 (142)
                      ...|.+|+|+++|||++|||+..||+...+.++-.++   ++-||..+.
T Consensus         5 ~~~Ti~dIA~~agVS~~TVSr~Ln~~~~vs~~tr~~V~~~a~elgY~p~   53 (342)
T PRK10014          5 KKITIHDVALAAGVSVSTVSLVLSGKGRISTATGERVNQAIEELGFVRN   53 (342)
T ss_pred             CCCcHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCCcC
Confidence            3579999999999999999999999887777665544   778887653

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

Probab=96.23  E-value=0.0063  Score=35.74  Aligned_cols=30  Identities=7%  Similarity=0.119  Sum_probs=20.4

Q ss_pred             HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           87 IVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      |..+ .+.|+|+.++|+.+|+|++||+++.+
T Consensus        13 I~~l-~~~G~s~~~IA~~lg~s~sTV~relk   42 (44)
T PF13936_consen   13 IEAL-LEQGMSIREIAKRLGRSRSTVSRELK   42 (44)
T ss_dssp             HHHH-HCS---HHHHHHHTT--HHHHHHHHH
T ss_pred             HHHH-HHcCCCHHHHHHHHCcCcHHHHHHHh
Confidence            4544 46899999999999999999998753

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

Probab=96.21  E-value=0.013  Score=36.93  Aligned_cols=41  Identities=22%  Similarity=0.276  Sum_probs=29.1

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCC
Q 032366           93 DKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVK  137 (142)
Q Consensus        93 ~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvs  137 (142)
                      ..| ++..||+.||||+++|++|  +.. .+......|..+-+-.
T Consensus         8 ~~G-~~~~lAkalGVs~~aVs~W--~~~-IP~~ra~~Ie~~T~G~   48 (60)
T PF14549_consen    8 YFG-GQSKLAKALGVSPQAVSQW--GER-IPAERAYQIEKLTNGK   48 (60)
T ss_dssp             HHS-SHHHHHHHHTS-HHHHHHH--HTS---HHHHHHHHHHTTTS
T ss_pred             HHC-CHHHHHHHHCCCHHHHHHh--cCc-cCHHHHHHHHHHhCCc
Confidence            345 8999999999999999999  444 4556677777765543

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

Probab=96.15  E-value=0.019  Score=33.75  Aligned_cols=34  Identities=21%  Similarity=0.371  Sum_probs=26.7

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .+.|..+...-++|+.++|+.+|+|.++++++.+
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            4456777778889999999999999999998753

...

>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID

Probab=96.10  E-value=0.062  Score=35.77  Aligned_cols=50  Identities=10%  Similarity=0.093  Sum_probs=39.4

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhC
Q 032366           85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK-AIPNQQILTKLERALG  135 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~-~~p~~~~l~kLa~~Lg  135 (142)
                      ..+..++. ..+|..++|+.+|+|.+||++..++. ...+.+...++-++..
T Consensus        10 ~I~e~l~~-~~~ti~dvA~~~gvS~~TVsr~L~~~~~~Vs~~Tr~rV~~aa~   60 (80)
T TIGR02844        10 EIGKYIVE-TKATVRETAKVFGVSKSTVHKDVTERLPEINPELAEEVKEVLD   60 (80)
T ss_pred             HHHHHHHH-CCCCHHHHHHHhCCCHHHHHHHhcCCCCCCCHHHHHHHHHHHc
Confidence            33445566 78999999999999999999999975 6678887777766543

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.

>COG3423 Nlp Predicted transcriptional regulator [Transcription]

Probab=96.06  E-value=0.02  Score=37.83  Aligned_cols=52  Identities=17%  Similarity=0.188  Sum_probs=41.4

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 032366           86 AIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG  140 (142)
Q Consensus        86 ~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~e  140 (142)
                      -|....+.+|+|...|+.+.|+|++|+.+...-. -|..+  ..||++|||++.|
T Consensus        12 dI~A~Lkk~G~Sl~~LS~~agls~~tL~n~L~rp-~pkgE--riIA~algv~P~e   63 (82)
T COG3423          12 DIIAALKKKGTSLAALSREAGLSSSTLANALDRP-WPKGE--RIIADALGVPPEE   63 (82)
T ss_pred             HHHHHHHHccccHHHHHHHcCCCHHHHHHHHcCC-CchHH--HHHHHHhCCCHHH
Confidence            3556677799999999999999999999988543 34444  4578999999865

>PRK09492 treR trehalose repressor; Provisional

Probab=96.01  E-value=0.016  Score=45.93  Aligned_cols=44  Identities=14%  Similarity=0.113  Sum_probs=35.9

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHH---HHHHHHhCCCC
Q 032366           95 KLTQSQLAQLINEKPQVIQEYESGKAIPNQQIL---TKLERALGVKL  138 (142)
Q Consensus        95 glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l---~kLa~~Lgvsl  138 (142)
                      ..|.+|+|+++|||.+|||++.||....+.++-   .+.++.||..+
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            479999999999999999999999877776654   44577777654

>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=96.01  E-value=0.026  Score=43.01  Aligned_cols=57  Identities=16%  Similarity=0.120  Sum_probs=38.7

Q ss_pred             cchHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHh
Q 032366           78 RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERAL  134 (142)
Q Consensus        78 ~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~L  134 (142)
                      +-...+.+.||..+..++++|.++++.+|||++.|++|.+-....+...-..|-..|
T Consensus       114 ~D~~~VkeeIK~fl~~h~IsQ~~V~q~TGisQS~lSq~L~kGt~Mk~qKR~alY~Wy  170 (180)
T PF04814_consen  114 RDPWRVKEEIKAFLQQHNISQREVVQVTGISQSHLSQHLNKGTPMKEQKRRALYRWY  170 (180)
T ss_dssp             S-HHHHHHHHHHHHHHCT--CHHHHHHHT--HHHHHHHHCTB----HHHHHHHHHHH
T ss_pred             hCHHHHHHHHHHHHHHcCCcHHHHHHHhhhhHHHHHHHHHcCCCccHHHHHHHHHHH
Confidence            445568899999999999999999999999999999999755555655555554443

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=95.98  E-value=0.011  Score=43.38  Aligned_cols=45  Identities=16%  Similarity=0.283  Sum_probs=33.4

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHcCCCC-C--CHHHHHHHHHHhCCCC
Q 032366           93 DKKLTQSQLAQLINEKPQVIQEYESGKAI-P--NQQILTKLERALGVKL  138 (142)
Q Consensus        93 ~~glTQ~eLA~~lgis~stIs~~E~G~~~-p--~~~~l~kLa~~Lgvsl  138 (142)
                      ..|+||.|+|+.+|+|+++|+.+|++-.. .  ...++ ++++.|+-++
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            69999999999999999999999986321 1  12233 6666666554

>PRK09526 lacI lac repressor; Reviewed

Probab=95.92  E-value=0.015  Score=46.61  Aligned_cols=44  Identities=9%  Similarity=-0.005  Sum_probs=35.7

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCC
Q 032366           95 KLTQSQLAQLINEKPQVIQEYESGKAIPNQQI---LTKLERALGVKL  138 (142)
Q Consensus        95 glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~---l~kLa~~Lgvsl  138 (142)
                      ..|.+|+|+++|||.+|||++.||....+.++   +.++++-||..+
T Consensus         5 ~~ti~dIA~~aGVS~~TVSrvLn~~~~vs~~tr~rV~~~a~elgY~p   51 (342)
T PRK09526          5 PVTLYDVARYAGVSYQTVSRVLNQASHVSAKTREKVEAAMAELNYVP   51 (342)
T ss_pred             CCcHHHHHHHhCCCHHHHHHHhcCCCCCCHHHHHHHHHHHHHHCCCc
Confidence            46999999999999999999999987666554   556666777654

>TIGR01481 ccpA catabolite control protein A

Probab=95.88  E-value=0.019  Score=45.74  Aligned_cols=44  Identities=9%  Similarity=0.083  Sum_probs=35.9

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCC
Q 032366           96 LTQSQLAQLINEKPQVIQEYESGKAIPNQQI---LTKLERALGVKLR  139 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~G~~~p~~~~---l~kLa~~Lgvsl~  139 (142)
                      .|.+|+|+.+|||.+|||++.||....+.++   +.+.++-||..+.
T Consensus         2 ~ti~dIA~~agvS~~TVSrvLn~~~~vs~~tr~rV~~~a~~lgY~pn   48 (329)
T TIGR01481         2 VTIYDVAREAGVSMATVSRVVNGNPNVKPATRKKVLEVIKRLDYRPN   48 (329)
T ss_pred             CcHHHHHHHhCCCHHHHHHHhCCCCCCCHHHHHHHHHHHHHHCCCCC
Confidence            4789999999999999999999987776655   5556777877653

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

>PRK10703 DNA-binding transcriptional repressor PurR; Provisional

Probab=95.88  E-value=0.019  Score=46.04  Aligned_cols=43  Identities=7%  Similarity=-0.009  Sum_probs=35.4

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCHH---HHHHHHHHhCCCC
Q 032366           96 LTQSQLAQLINEKPQVIQEYESGKAIPNQQ---ILTKLERALGVKL  138 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~G~~~p~~~---~l~kLa~~Lgvsl  138 (142)
                      .|.+|+|+.+|+|.+|||++.+|+...+.+   .+.++++.||..+
T Consensus         2 ~Ti~dIA~~agVS~~TVSrvLn~~~~vs~~tr~~V~~~a~elgY~p   47 (341)
T PRK10703          2 ATIKDVAKRAGVSTTTVSHVINKTRFVAEETRNAVWAAIKELHYSP   47 (341)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHCCCc
Confidence            489999999999999999999998666655   4667777787655

>TIGR02405 trehalos_R_Ecol trehalose operon repressor, proteobacterial

Probab=95.88  E-value=0.021  Score=45.49  Aligned_cols=44  Identities=11%  Similarity=0.118  Sum_probs=35.2

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCC
Q 032366           96 LTQSQLAQLINEKPQVIQEYESGKAIPNQQI---LTKLERALGVKLR  139 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~G~~~p~~~~---l~kLa~~Lgvsl~  139 (142)
                      .|.+|+|+.+|+|++|||++.||....+.++   +.+.++-||..+.
T Consensus         2 ~ti~dIA~~agVS~sTVSr~Ln~~~~vs~~tr~rV~~~a~~lgY~pn   48 (311)
T TIGR02405         2 LTIKDIARLAGVGKSTVSRVLNNEPKVSIETRERVEQVIQQSGFVPS   48 (311)
T ss_pred             CcHHHHHHHhCCCHHHHHHHhCCCCCCCHHHHHHHHHHHHHHCCCcC
Confidence            5899999999999999999999987666555   4555777776553

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

>TIGR00721 tfx DNA-binding protein, Tfx family

Probab=95.86  E-value=0.021  Score=41.70  Aligned_cols=34  Identities=18%  Similarity=0.329  Sum_probs=28.4

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 032366           84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESG  118 (142)
Q Consensus        84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G  118 (142)
                      ...+-.+| ..|+||+|+|+.+|+|+++|+.+|+.
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            34444555 69999999999999999999999974

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

>PRK10727 DNA-binding transcriptional regulator GalR; Provisional

Probab=95.71  E-value=0.023  Score=45.82  Aligned_cols=44  Identities=9%  Similarity=0.064  Sum_probs=35.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCC
Q 032366           96 LTQSQLAQLINEKPQVIQEYESGKAIPNQQI---LTKLERALGVKLR  139 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~G~~~p~~~~---l~kLa~~Lgvsl~  139 (142)
                      .|.+|+|+++|||.+|||++.||+...+.++   +.+.++-||..+.
T Consensus         2 ~ti~dIA~~aGVS~~TVSrvLn~~~~Vs~~tr~rV~~~a~elgY~pn   48 (343)
T PRK10727          2 ATIKDVARLAGVSVATVSRVINNSPKASEASRLAVHSAMESLSYHPN   48 (343)
T ss_pred             CCHHHHHHHhCCCHHHHHHHhCCCCCCCHHHHHHHHHHHHHHCCCCC
Confidence            4889999999999999999999987676654   5556777776553

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

Probab=95.65  E-value=0.012  Score=39.65  Aligned_cols=25  Identities=12%  Similarity=0.145  Sum_probs=19.2

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           93 DKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        93 ~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +.||||.|+|+++|.|+++|+++..
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            4799999999999999999999876

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.

>cd00131 PAX Paired Box domain

Probab=95.60  E-value=0.069  Score=38.30  Aligned_cols=75  Identities=12%  Similarity=0.140  Sum_probs=47.1

Q ss_pred             HHHHHHHHcCCChhHHHhhhc-----CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHH-HHHHHhCCCCHHHHHH
Q 032366           30 KVVNAARRAGADIETVRKSHA-----GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAI-VQARNDKKLTQSQLAQ  103 (142)
Q Consensus        30 ~~~~~a~r~G~~v~t~kk~~~-----g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~L-k~~R~~~glTQ~eLA~  103 (142)
                      +.-..|++.|++..|+.+|-.     |...+.+.+ ++...++.            ......| ...+..-.+|..||++
T Consensus        35 s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~~g-g~rpr~~~------------~~~~~~i~~~v~~~p~~Tl~El~~  101 (128)
T cd00131          35 RPCDISRQLRVSHGCVSKILNRYYETGSIRPGAIG-GSKPRVAT------------PEVVKKIEIYKQENPGMFAWEIRD  101 (128)
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCCCCC-CCCCCcCC------------HHHHHHHHHHHHHCCCCCHHHHHH
Confidence            456679999999999999854     655543221 12122211            1111223 2456777899999998


Q ss_pred             Hh---CC-------CHHHHHHHHc
Q 032366          104 LI---NE-------KPQVIQEYES  117 (142)
Q Consensus       104 ~l---gi-------s~stIs~~E~  117 (142)
                      .+   |+       |.+||+++..
T Consensus       102 ~L~~~gv~~~~~~~s~stI~R~L~  125 (128)
T cd00131         102 RLLQEGVCDKSNVPSVSSINRILR  125 (128)
T ss_pred             HHHHcCCcccCCCCCHHHHHHHHH
Confidence            86   55       8888888754

>PRK14987 gluconate operon transcriptional regulator; Provisional

Probab=95.55  E-value=0.022  Score=45.58  Aligned_cols=44  Identities=7%  Similarity=0.083  Sum_probs=36.0

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCC
Q 032366           95 KLTQSQLAQLINEKPQVIQEYESGKAIPNQQI---LTKLERALGVKL  138 (142)
Q Consensus        95 glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~---l~kLa~~Lgvsl  138 (142)
                      ..|.+|+|+++|||.+|||++.||....+.++   +.++++-||..+
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            36999999999999999999999987666554   556677777654

>PRK10401 DNA-binding transcriptional regulator GalS; Provisional

Probab=95.51  E-value=0.033  Score=44.93  Aligned_cols=44  Identities=14%  Similarity=0.160  Sum_probs=35.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCC
Q 032366           96 LTQSQLAQLINEKPQVIQEYESGKAIPNQQI---LTKLERALGVKLR  139 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~G~~~p~~~~---l~kLa~~Lgvsl~  139 (142)
                      .|.+|+|+++|||.+|||++.||+...+.++   +.+.++.||..+.
T Consensus         2 ~ti~dIA~~aGVS~~TVSrvLn~~~~Vs~~tr~kV~~~a~elgY~pn   48 (346)
T PRK10401          2 ITIRDVARQAGVSVATVSRVLNNSALVSADTREAVMKAVSELGYRPN   48 (346)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCC
Confidence            5889999999999999999999987666554   5566777776553

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

Probab=95.51  E-value=0.041  Score=38.57  Aligned_cols=28  Identities=14%  Similarity=0.096  Sum_probs=24.7

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           90 ARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        90 ~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +..-.||||.+.|+.+|||++|+.++.+
T Consensus        52 L~D~egl~QeeaA~~MgVSR~T~~ril~   79 (106)
T PF02001_consen   52 LVDYEGLSQEEAAERMGVSRPTFQRILE   79 (106)
T ss_pred             HHHHcCCCHHHHHHHcCCcHHHHHHHHH
Confidence            3455799999999999999999999875

>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=95.49  E-value=0.036  Score=32.74  Aligned_cols=39  Identities=23%  Similarity=0.314  Sum_probs=29.8

Q ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 032366           81 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA  120 (142)
Q Consensus        81 ~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~  120 (142)
                      ..+...|...+... +|+.+.|+..||+++||.++-+|..
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            34677788877544 9999999999999999999998864

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.

>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=95.48  E-value=0.042  Score=32.61  Aligned_cols=33  Identities=12%  Similarity=0.215  Sum_probs=26.9

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ..|-.+|--.++|+.|+|+.+|+|.++|++++.
T Consensus        10 r~vi~~~y~~~~t~~eIa~~lg~s~~~V~~~~~   42 (50)
T PF04545_consen   10 REVIRLRYFEGLTLEEIAERLGISRSTVRRILK   42 (50)
T ss_dssp             HHHHHHHHTST-SHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHhcCCCCHHHHHHHHCCcHHHHHHHHH
Confidence            345556668899999999999999999999874

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 ....

>PRK10344 DNA-binding transcriptional regulator Nlp; Provisional

Probab=95.46  E-value=0.053  Score=36.89  Aligned_cols=51  Identities=14%  Similarity=0.055  Sum_probs=40.3

Q ss_pred             HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 032366           87 IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG  140 (142)
Q Consensus        87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~e  140 (142)
                      |......+|+|..+|+...|++.+|+.+-...   |-+.-=..||++|||.+.+
T Consensus        13 I~AaL~KrG~sLa~lsr~~Gls~~TL~nAL~r---p~PKgEriIA~aLGv~P~e   63 (92)
T PRK10344         13 IIAGLRKKGTSMAAESRRNGLSSSTLANALSR---PWPKGEMIIAKALGTDPWV   63 (92)
T ss_pred             HHHHHHHcCCcHHHHHHHcCCChHHHHHHHcC---CCchHHHHHHHHHCcCHHH
Confidence            55556668999999999999999999987753   3344445689999998864

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

Probab=95.45  E-value=0.028  Score=32.21  Aligned_cols=23  Identities=22%  Similarity=0.445  Sum_probs=20.9

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcC
Q 032366           96 LTQSQLAQLINEKPQVIQEYESG  118 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~G  118 (142)
                      +|..|+|+.+|||++||.+|++-
T Consensus         1 ~s~~e~a~~lgvs~~tl~~~~~~   23 (49)
T cd04762           1 LTTKEAAELLGVSPSTLRRWVKE   23 (49)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHc
Confidence            57899999999999999999863

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.

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

Probab=95.42  E-value=0.0089  Score=40.81  Aligned_cols=39  Identities=23%  Similarity=0.358  Sum_probs=35.7

Q ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q 032366           97 TQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALG  135 (142)
Q Consensus        97 TQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lg  135 (142)
                      .|+.||.+||+|+++|++|-+|.+.....-...|+++.+
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            588999999999999999999999888888888888877

>PRK01381 Trp operon repressor; Provisional

Probab=95.26  E-value=0.052  Score=37.57  Aligned_cols=57  Identities=14%  Similarity=0.080  Sum_probs=42.6

Q ss_pred             hHHHHHHHHHHHH--hCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCC
Q 032366           80 PSELKKAIVQARN--DKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGV  136 (142)
Q Consensus        80 ~~~~g~~Lk~~R~--~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgv  136 (142)
                      ...++.|++-.+.  .-++||.++|+.+|||.+||++--+--...+...-.-|...|.-
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            3457777776653  34599999999999999999998776555567777777666653

>PRK08558 adenine phosphoribosyltransferase; Provisional

Probab=95.26  E-value=0.064  Score=42.44  Aligned_cols=48  Identities=15%  Similarity=0.336  Sum_probs=37.5

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHh
Q 032366           85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERAL  134 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~L  134 (142)
                      ..|+.++..  +|.+||++.+|++.+.+++|-+|+..|+.+....|.+-|
T Consensus        15 ~~lr~lk~~--~ty~el~~~~g~p~~~l~RYv~g~~~P~~~~a~~~~~~l   62 (238)
T PRK08558         15 RVLRSLKKT--YTYEELSSITGLPESVLNRYVNGHVLPSVERAREIVEKL   62 (238)
T ss_pred             HHHHHHhcc--cCHHHHHHHHCCCHHHHHHHHcCCcCCCHHHHHHHHHHH
Confidence            344444443  699999999999999999999999999987655554433

>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD

Probab=95.10  E-value=0.047  Score=36.95  Aligned_cols=28  Identities=11%  Similarity=0.004  Sum_probs=25.3

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 032366           91 RNDKKLTQSQLAQLINEKPQVIQEYESG  118 (142)
Q Consensus        91 R~~~glTQ~eLA~~lgis~stIs~~E~G  118 (142)
                      ....|+|+.++|+.+|+|++||+++.+|
T Consensus        46 ll~~G~S~~eIA~~LgISrsTIyRi~R~   73 (88)
T TIGR02531        46 MLKQGKTYSDIEAETGASTATISRVKRC   73 (88)
T ss_pred             HHHCCCCHHHHHHHHCcCHHHHHHHHHh
Confidence            4567999999999999999999999985

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.

>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional

Probab=95.06  E-value=0.03  Score=44.82  Aligned_cols=44  Identities=9%  Similarity=0.054  Sum_probs=34.7

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCC--CCHH---HHHHHHHHhCCCCC
Q 032366           96 LTQSQLAQLINEKPQVIQEYESGKAI--PNQQ---ILTKLERALGVKLR  139 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~G~~~--p~~~---~l~kLa~~Lgvsl~  139 (142)
                      .|.+|+|+++|||.+|||+..||...  .+.+   .+.++++-||..+.
T Consensus         2 ~ti~dIA~~agVS~~TVSrvln~~~~~~vs~~tr~rV~~~a~~lgY~pn   50 (327)
T PRK10339          2 ATLKDIAIEAGVSLATVSRVLNDDPTLNVKEETKHRILEIAEKLEYKTS   50 (327)
T ss_pred             CCHHHHHHHhCCCHHhhhhhhcCCCCCCcCHHHHHHHHHHHHHhCCCCc
Confidence            48899999999999999999998752  4444   46666888887553

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

Probab=94.95  E-value=0.17  Score=36.84  Aligned_cols=59  Identities=19%  Similarity=0.160  Sum_probs=54.2

Q ss_pred             hHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 032366           80 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL  138 (142)
Q Consensus        80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl  138 (142)
                      ...+.+.|-...+.+|+|-.+|++.+|.+...+....-|....+.+.+.++++.||.+-
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            45678888889999999999999999999999999999999999999999999999764

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

Probab=94.94  E-value=0.29  Score=33.00  Aligned_cols=42  Identities=12%  Similarity=0.173  Sum_probs=33.6

Q ss_pred             chHHHHHHHHHHHHhCCCCHHHHHHHh-CCCHHHHHHHHcCCC
Q 032366           79 VPSELKKAIVQARNDKKLTQSQLAQLI-NEKPQVIQEYESGKA  120 (142)
Q Consensus        79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~l-gis~stIs~~E~G~~  120 (142)
                      ....+...|+..+...+++|+.||+.+ |.|+.+++.+.+.-.
T Consensus        10 dT~~I~~~ik~~L~~~~IsQ~~Fa~~vL~rsqgtlsdlL~~PK   52 (87)
T PF02376_consen   10 DTKEIARRIKEWLKRNNISQRVFAKKVLNRSQGTLSDLLRKPK   52 (87)
T ss_dssp             -HHHHHHHHHHHHHHTT--HHHHHHHTTSS-HHHHHHHHHSCC
T ss_pred             CHHHHHHHHHHHHHHcCCCHHHHHHHHhccChhHHHHHhCCCC
Confidence            345789999999999999999999976 999999999998443

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.

>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=94.89  E-value=0.073  Score=33.20  Aligned_cols=25  Identities=4%  Similarity=0.117  Sum_probs=23.5

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           93 DKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        93 ~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ..|+++.++|+.+|++.+||..|-.
T Consensus        11 ~~G~~~~eIA~~Lg~~~~TV~~W~~   35 (58)
T PF06056_consen   11 LQGWSIKEIAEELGVPRSTVYSWKD   35 (58)
T ss_pred             HcCCCHHHHHHHHCCChHHHHHHHH
Confidence            3699999999999999999999986

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

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

Probab=94.86  E-value=0.078  Score=30.60  Aligned_cols=32  Identities=22%  Similarity=0.114  Sum_probs=26.2

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHH
Q 032366           84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEY  115 (142)
Q Consensus        84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~  115 (142)
                      ...|.......+.++.+.|+.+|||++++.+-
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            35678888999999999999999999999864

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 ....

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

Probab=94.74  E-value=0.19  Score=25.98  Aligned_cols=23  Identities=9%  Similarity=0.186  Sum_probs=21.1

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHH
Q 032366           93 DKKLTQSQLAQLINEKPQVIQEY  115 (142)
Q Consensus        93 ~~glTQ~eLA~~lgis~stIs~~  115 (142)
                      ..+++..++|+.+|++.++|.+|
T Consensus        19 ~~~~s~~~ia~~~~is~~tv~~~   41 (42)
T cd00569          19 AAGESVAEIARRLGVSRSTLYRY   41 (42)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHh
Confidence            46889999999999999999987

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

>PF12728 HTH_17: Helix-turn-helix domain

Probab=94.73  E-value=0.054  Score=32.13  Aligned_cols=28  Identities=21%  Similarity=0.297  Sum_probs=23.9

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCC
Q 032366           96 LTQSQLAQLINEKPQVIQEYESGKAIPN  123 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~G~~~p~  123 (142)
                      ||..|+|+.+|||.++|.+|.+....|.
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            6889999999999999999987555543

>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=94.65  E-value=0.0054  Score=41.84  Aligned_cols=41  Identities=15%  Similarity=0.220  Sum_probs=31.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 032366           94 KKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL  138 (142)
Q Consensus        94 ~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl  138 (142)
                      ..++|..+|+.+|++.++|++|-.+    -...+..|+.+|+..+
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            4468999999999999999999654    2355666666666654

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.

>TIGR01764 excise DNA binding domain, excisionase family

Probab=94.65  E-value=0.062  Score=30.86  Aligned_cols=27  Identities=15%  Similarity=0.235  Sum_probs=23.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCC
Q 032366           96 LTQSQLAQLINEKPQVIQEYESGKAIP  122 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~G~~~p  122 (142)
                      ||..|+|+.+|+|+++|.+|.+....|
T Consensus         2 lt~~e~a~~lgis~~ti~~~~~~g~i~   28 (49)
T TIGR01764         2 LTVEEAAEYLGVSKDTVYRLIHEGELP   28 (49)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHcCCCC
Confidence            688999999999999999999754444

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).

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

Probab=94.62  E-value=0.035  Score=39.62  Aligned_cols=23  Identities=26%  Similarity=0.351  Sum_probs=21.4

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcC
Q 032366           96 LTQSQLAQLINEKPQVIQEYESG  118 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~G  118 (142)
                      ||.+|||+.+|++++||++|-+-
T Consensus         1 MT~eELA~~tG~srQTINrWvRk   23 (122)
T PF07037_consen    1 MTPEELAELTGYSRQTINRWVRK   23 (122)
T ss_pred             CCHHHHHHHhCccHHHHHHHHHh
Confidence            79999999999999999999863

The function of this family is unknown.

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

Probab=94.62  E-value=0.032  Score=40.34  Aligned_cols=28  Identities=25%  Similarity=0.372  Sum_probs=25.1

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 032366           91 RNDKKLTQSQLAQLINEKPQVIQEYESG  118 (142)
Q Consensus        91 R~~~glTQ~eLA~~lgis~stIs~~E~G  118 (142)
                      ..++|+||+++|+.+|.++..||.+|+.
T Consensus        19 lRekG~tQ~eIA~~L~TTraNvSaIEkr   46 (143)
T COG1356          19 LREKGLTQSEIARILKTTRANVSAIEKR   46 (143)
T ss_pred             hhhccccHHHHHHHHccchhhHHHHHHH
Confidence            3468999999999999999999999963

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

Probab=94.58  E-value=0.033  Score=47.02  Aligned_cols=49  Identities=18%  Similarity=0.160  Sum_probs=39.9

Q ss_pred             hHHHHHHHHHHHHhCCCCHHHHHHHhC------CCHHHHHHHHcCCCCCCHHHHHHH
Q 032366           80 PSELKKAIVQARNDKKLTQSQLAQLIN------EKPQVIQEYESGKAIPNQQILTKL  130 (142)
Q Consensus        80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lg------is~stIs~~E~G~~~p~~~~l~kL  130 (142)
                      .+.|++.+|..|..+|+||.|+.-.+|      .|++||.++|.=  ..+..++-||
T Consensus       208 LEqFAK~FKqRRIkLGfTQaDVGlALG~lyGn~FSQTTIcRFEAL--qLSFKNMCKL  262 (398)
T KOG3802|consen  208 LEQFAKTFKQRRIKLGFTQADVGLALGALYGNVFSQTTICRFEAL--QLSFKNMCKL  262 (398)
T ss_pred             HHHHHHHHHhheeccccchhHHHHHHHhhhCcccchhhhhHhHhh--ccCHHHHhhh
Confidence            456999999999999999999999998      699999999963  3445544444

>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=94.53  E-value=0.051  Score=33.15  Aligned_cols=38  Identities=11%  Similarity=0.140  Sum_probs=26.8

Q ss_pred             HHHHHHHHH-HHhCCCCHHHHHHHhCCCHHHHHHHHcCC
Q 032366           82 ELKKAIVQA-RNDKKLTQSQLAQLINEKPQVIQEYESGK  119 (142)
Q Consensus        82 ~~g~~Lk~~-R~~~glTQ~eLA~~lgis~stIs~~E~G~  119 (142)
                      ++.+.+.-+ +.+.|.++.++|+..||+.+||+.|.+.+
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            345555443 56789999999999999999999998653

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

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

Probab=94.43  E-value=0.14  Score=34.55  Aligned_cols=38  Identities=13%  Similarity=0.058  Sum_probs=31.1

Q ss_pred             hHHHHHHHHHHH--HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           80 PSELKKAIVQAR--NDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        80 ~~~~g~~Lk~~R--~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ...+..|++-++  ...|+||.++|+.+|+|..||++.-+
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            345777877654  55899999999999999999998754

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 ....

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

Probab=94.42  E-value=0.054  Score=34.51  Aligned_cols=40  Identities=18%  Similarity=0.230  Sum_probs=29.8

Q ss_pred             cchHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           78 RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        78 ~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .+..+|-..+-.....-|.|..++|+..||++++|.+|.+
T Consensus         6 ~ys~e~K~~~v~~~~~~g~sv~~va~~~gi~~~~l~~W~~   45 (76)
T PF01527_consen    6 RYSPEFKLQAVREYLESGESVSEVAREYGISPSTLYNWRK   45 (76)
T ss_dssp             ---HHHHHHHHHHHHHHHCHHHHHHHHHTS-HHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHCCCceEeeecccccccccccHHHH
Confidence            3455666666555566799999999999999999999985

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.

>PRK13698 plasmid-partitioning protein; Provisional

Probab=94.31  E-value=0.091  Score=43.51  Aligned_cols=43  Identities=16%  Similarity=0.044  Sum_probs=34.8

Q ss_pred             chHHHHHHH-HHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCC
Q 032366           79 VPSELKKAI-VQARNDKKLTQSQLAQLINEKPQVIQEYESGKAI  121 (142)
Q Consensus        79 ~~~~~g~~L-k~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~  121 (142)
                      -..+.+... +.+....|+||++||+.+|+|+++|++..+=-..
T Consensus       159 s~iE~A~ay~~~L~~~~~~tQeeLA~~lG~SRs~Vsn~Lrla~L  202 (323)
T PRK13698        159 SAYERGLRYASRLQNEFAGNISALADAENISRKIITRCINTAKL  202 (323)
T ss_pred             CHHHHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHHHcC
Confidence            344567766 5677889999999999999999999999875443

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

Probab=94.30  E-value=0.081  Score=30.71  Aligned_cols=23  Identities=30%  Similarity=0.417  Sum_probs=20.7

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcC
Q 032366           96 LTQSQLAQLINEKPQVIQEYESG  118 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~G  118 (142)
                      ||..|+|+.+||++++|..|++-
T Consensus         1 ~~~~e~a~~~gv~~~tlr~~~~~   23 (49)
T cd04761           1 YTIGELAKLTGVSPSTLRYYERI   23 (49)
T ss_pred             CcHHHHHHHHCcCHHHHHHHHHC
Confidence            57889999999999999999863

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.

>PF13518 HTH_28: Helix-turn-helix domain

Probab=94.20  E-value=0.12  Score=30.38  Aligned_cols=24  Identities=4%  Similarity=0.059  Sum_probs=22.1

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           94 KKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        94 ~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .|.|..++|+.+|||+++|.+|.+
T Consensus        11 ~g~s~~~~a~~~gis~~tv~~w~~   34 (52)
T PF13518_consen   11 EGESVREIAREFGISRSTVYRWIK   34 (52)
T ss_pred             cCCCHHHHHHHHCCCHhHHHHHHH
Confidence            477999999999999999999975

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

Probab=94.19  E-value=0.15  Score=31.94  Aligned_cols=22  Identities=27%  Similarity=0.567  Sum_probs=20.2

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +|..|+|+.+|||++||..||.
T Consensus         1 ~~i~evA~~~gvs~~tlR~~~~   22 (67)
T cd04764           1 YTIKEVSEIIGVKPHTLRYYEK   22 (67)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5778999999999999999986

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

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

Probab=94.18  E-value=0.064  Score=29.61  Aligned_cols=23  Identities=9%  Similarity=0.219  Sum_probs=17.7

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 032366           95 KLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        95 glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .||+.|+|+.+|+++.||++...
T Consensus         2 ~mtr~diA~~lG~t~ETVSR~l~   24 (32)
T PF00325_consen    2 PMTRQDIADYLGLTRETVSRILK   24 (32)
T ss_dssp             E--HHHHHHHHTS-HHHHHHHHH
T ss_pred             CcCHHHHHHHhCCcHHHHHHHHH
Confidence            47999999999999999998753

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 ....

>COG2944 Predicted transcriptional regulator [Transcription]

Probab=93.99  E-value=0.046  Score=38.16  Aligned_cols=24  Identities=38%  Similarity=0.414  Sum_probs=21.2

Q ss_pred             HHHHHHcCCChhHHHhhhcCCCCC
Q 032366           32 VNAARRAGADIETVRKSHAGTNKA   55 (142)
Q Consensus        32 ~~~a~r~G~~v~t~kk~~~g~~~~   55 (142)
                      =.-|+..|++++|+++||.|..+|
T Consensus        61 ~vFA~~L~vs~~Tv~~WEqGr~kP   84 (104)
T COG2944          61 PVFARYLGVSVSTVRKWEQGRKKP   84 (104)
T ss_pred             HHHHHHHCCCHHHHHHHHcCCcCC
Confidence            346889999999999999999985

>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=93.79  E-value=0.11  Score=31.16  Aligned_cols=32  Identities=16%  Similarity=0.167  Sum_probs=24.1

Q ss_pred             HHHHHHHhCC-CCHHHHHHHhCCCHHHHHHHHc
Q 032366           86 AIVQARNDKK-LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        86 ~Lk~~R~~~g-lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .|..+....+ +|..+||+.+|||+.||.+..+
T Consensus         5 il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~   37 (55)
T PF08279_consen    5 ILKLLLESKEPITAKELAEELGVSRRTIRRDIK   37 (55)
T ss_dssp             HHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHH
T ss_pred             HHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHH
Confidence            3455545554 9999999999999999998753

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 ....

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

Probab=93.78  E-value=0.25  Score=31.03  Aligned_cols=61  Identities=16%  Similarity=0.151  Sum_probs=38.1

Q ss_pred             HHHHHcCCChhHHHhhhc--CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHh
Q 032366           33 NAARRAGADIETVRKSHA--GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLI  105 (142)
Q Consensus        33 ~~a~r~G~~v~t~kk~~~--g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~l  105 (142)
                      +.|++.|++..|++.|+.  |-..+....  ..-..+..++         ...-..|+.++. .|+|..++++.+
T Consensus         5 e~A~~~gVs~~tlr~ye~~~gl~~~~r~~--~g~R~yt~~d---------i~~l~~i~~l~~-~g~~l~~i~~~l   67 (68)
T cd04763           5 EVALLTGIKPHVLRAWEREFGLLKPQRSD--GGHRLFNDAD---------IDRILEIKRWID-NGVQVSKVKKLL   67 (68)
T ss_pred             HHHHHHCcCHHHHHHHHHhcCCCCCCcCC--CCCcccCHHH---------HHHHHHHHHHHH-cCCCHHHHHHHh
Confidence            589999999999999974  544332211  1112222211         123345677776 999999998765

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

>PRK15418 transcriptional regulator LsrR; Provisional

Probab=93.69  E-value=0.14  Score=42.02  Aligned_cols=55  Identities=15%  Similarity=0.108  Sum_probs=40.7

Q ss_pred             HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc-----CC--------CCCCHHHHHHHHHHhCCC
Q 032366           83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES-----GK--------AIPNQQILTKLERALGVK  137 (142)
Q Consensus        83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~-----G~--------~~p~~~~l~kLa~~Lgvs  137 (142)
                      +--++..+=-..||||.|+|+++|+|+++|+++..     |-        .....+.-.+|.+.||+.
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            33455666667899999999999999999999974     32        112345667788888864

>PF13551 HTH_29: Winged helix-turn helix

Probab=93.69  E-value=0.46  Score=31.98  Aligned_cols=80  Identities=16%  Similarity=0.231  Sum_probs=49.0

Q ss_pred             HHHHHHHcCCChhHHHhhhcCCCCCCCCCCCcccccchh-hhccccCCc-chHHHHHHHHHHHHhC------CCCHHHHH
Q 032366           31 VVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDE-DTENLAHDR-VPSELKKAIVQARNDK------KLTQSQLA  102 (142)
Q Consensus        31 ~~~~a~r~G~~v~t~kk~~~g~~~~~~~~~~~~~~kl~~-~~~~~~~~~-~~~~~g~~Lk~~R~~~------glTQ~eLA  102 (142)
                      .-..|+..|++..|+.+|-.--...     +  +..+.. ....-.+.. +.++.-..|.++..+.      .+|..+|+
T Consensus        15 ~~~ia~~lg~s~~Tv~r~~~~~~~~-----G--~~~l~~~~~~~g~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~   87 (112)
T PF13551_consen   15 IAEIARRLGISRRTVYRWLKRYREG-----G--IEGLLPRKPRGGRPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELA   87 (112)
T ss_pred             HHHHHHHHCcCHHHHHHHHHHHHcc-----c--HHHHHhccccCCCCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHH
Confidence            5678999999999999887642220     0  111111 111112222 4555555666665553      48899999


Q ss_pred             HHh-------CCCHHHHHHHHc
Q 032366          103 QLI-------NEKPQVIQEYES  117 (142)
Q Consensus       103 ~~l-------gis~stIs~~E~  117 (142)
                      +.+       .+|.+||.+|..
T Consensus        88 ~~l~~~~~~~~~s~~ti~r~L~  109 (112)
T PF13551_consen   88 EWLIEEEFGIDVSPSTIRRILK  109 (112)
T ss_pred             HHHHHhccCccCCHHHHHHHHH
Confidence            865       689999998864

>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=93.66  E-value=0.096  Score=29.82  Aligned_cols=25  Identities=24%  Similarity=0.473  Sum_probs=20.1

Q ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCC
Q 032366           97 TQSQLAQLINEKPQVIQEYESGKAI  121 (142)
Q Consensus        97 TQ~eLA~~lgis~stIs~~E~G~~~  121 (142)
                      |..|+|+.+|||..||..||.-.-.
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            4578999999999999999985443

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 ....

>TIGR00180 parB_part ParB-like partition proteins

Probab=93.66  E-value=0.28  Score=37.05  Aligned_cols=53  Identities=19%  Similarity=0.130  Sum_probs=40.2

Q ss_pred             chHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHH
Q 032366           79 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLER  132 (142)
Q Consensus        79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~  132 (142)
                      ...+.+..+++++...|+|+.++|+.+|+|.++|+++..=-. .+.+.+..+..
T Consensus       104 t~~e~a~~~~~l~~~~g~s~~~iA~~lg~s~~~V~r~l~l~~-lp~~v~~~~~~  156 (187)
T TIGR00180       104 SPIEEAQAYKRLLEKFSMTQEDLAKKIGKSRAHITNLLRLLK-LPSEIQSAIPE  156 (187)
T ss_pred             CHHHHHHHHHHHHHHhCCCHHHHHHHHCcCHHHHHHHHHHHc-CCHHHHHHHHh
Confidence            344566677777777899999999999999999999987433 45566655554

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=93.65  E-value=0.12  Score=32.17  Aligned_cols=22  Identities=23%  Similarity=0.437  Sum_probs=20.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +|..|+|+.+||+++||..|++
T Consensus         1 ~s~~eva~~~gvs~~tlr~w~~   22 (68)
T cd01104           1 YTIGAVARLTGVSPDTLRAWER   22 (68)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5788999999999999999997

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

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

Probab=93.43  E-value=0.45  Score=29.49  Aligned_cols=61  Identities=21%  Similarity=0.183  Sum_probs=35.5

Q ss_pred             HHHHHcCCChhHHHhhhc--CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHh
Q 032366           33 NAARRAGADIETVRKSHA--GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLI  105 (142)
Q Consensus        33 ~~a~r~G~~v~t~kk~~~--g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~l  105 (142)
                      +.|++.|++..|+++|+.  |...+...  ...-..+..+         ....-..|+.++. .|+|..++.+.+
T Consensus         5 eva~~~gvs~~tlr~w~~~~g~~~~~r~--~~~~r~yt~~---------~v~~l~~i~~l~~-~g~~l~~i~~~~   67 (68)
T cd01104           5 AVARLTGVSPDTLRAWERRYGLPAPQRT--DGGHRLYSEA---------DVARLRLIRRLTS-EGVRISQAAALA   67 (68)
T ss_pred             HHHHHHCcCHHHHHHHHHhCCCCCCCcC--CCCCeecCHH---------HHHHHHHHHHHHH-CCCCHHHHHHHh
Confidence            579999999999999996  33221110  0011111111         1113345566665 899999888754

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

>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=93.38  E-value=0.11  Score=32.85  Aligned_cols=24  Identities=17%  Similarity=0.343  Sum_probs=21.9

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcC
Q 032366           95 KLTQSQLAQLINEKPQVIQEYESG  118 (142)
Q Consensus        95 glTQ~eLA~~lgis~stIs~~E~G  118 (142)
                      +++..++|+.+|||.+||+.|-+-
T Consensus        22 ~i~lkdIA~~Lgvs~~tIr~WK~~   45 (60)
T PF10668_consen   22 KIKLKDIAEKLGVSESTIRKWKSR   45 (60)
T ss_pred             CccHHHHHHHHCCCHHHHHHHhhh
Confidence            589999999999999999999763

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 [].

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

Probab=93.29  E-value=0.25  Score=28.23  Aligned_cols=29  Identities=10%  Similarity=0.184  Sum_probs=24.8

Q ss_pred             HHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           89 QARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        89 ~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .++-..|+|+.++|+.+|++.++|.++..
T Consensus        20 ~~~~~~~~~~~~ia~~~~~s~~~i~~~~~   48 (55)
T cd06171          20 LLRFGEGLSYEEIAEILGISRSTVRQRLH   48 (55)
T ss_pred             HHHHhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            44445899999999999999999999864

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

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

Probab=93.29  E-value=0.18  Score=41.66  Aligned_cols=57  Identities=18%  Similarity=0.171  Sum_probs=44.1

Q ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc-----CC--------CCCCHHHHHHHHHHhCCC
Q 032366           81 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES-----GK--------AIPNQQILTKLERALGVK  137 (142)
Q Consensus        81 ~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~-----G~--------~~p~~~~l~kLa~~Lgvs  137 (142)
                      ..+..++..+.-..||||.|+|+++|||+.+|+++..     |-        .....+.-.+|.+.||++
T Consensus        12 ~~l~~~~A~lYY~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~GiV~I~i~~~~~~~~~Le~~L~~~fgL~   81 (321)
T COG2390          12 ERLLARAAWLYYVEGLTQSEIAERLGISRATVSRLLAKAREEGIVKISINSPVEGCLELEQQLKERFGLK   81 (321)
T ss_pred             HHHHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCeEEEEeCCCCcchHHHHHHHHHhcCCC
Confidence            3456677778888999999999999999999999874     21        122455667888888876

>PRK09413 IS2 repressor TnpA; Reviewed

Probab=93.25  E-value=0.27  Score=34.67  Aligned_cols=40  Identities=23%  Similarity=0.166  Sum_probs=32.9

Q ss_pred             cchHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           78 RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        78 ~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ....+|-..+-....+.|.|..++|+.+|||+++|++|-+
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            4556676666666677899999999999999999999965

>PRK04217 hypothetical protein; Provisional

Probab=93.25  E-value=0.31  Score=34.29  Aligned_cols=32  Identities=9%  Similarity=0.055  Sum_probs=27.9

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           86 AIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        86 ~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .+-.++...|+|++++|+.+|+|.+||.++..
T Consensus        49 eai~l~~~eGlS~~EIAk~LGIS~sTV~r~L~   80 (110)
T PRK04217         49 EALRLVDYEGLTQEEAGKRMGVSRGTVWRALT   80 (110)
T ss_pred             HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            44566777899999999999999999999875

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

Probab=93.23  E-value=0.11  Score=35.71  Aligned_cols=28  Identities=18%  Similarity=0.054  Sum_probs=24.7

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           90 ARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        90 ~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +..-.||+|.|.|.++|||++|+.+..+
T Consensus        44 LvD~~~l~QeeAA~rMgISr~Tfwr~l~   71 (99)
T COG1342          44 LVDYEGLTQEEAALRMGISRQTFWRLLT   71 (99)
T ss_pred             HHhHhhccHHHHHHHhcccHHHHHHHHH
Confidence            4456899999999999999999999875

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

Probab=93.20  E-value=0.34  Score=30.24  Aligned_cols=62  Identities=18%  Similarity=0.199  Sum_probs=37.9

Q ss_pred             HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhC
Q 032366           33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLIN  106 (142)
Q Consensus        33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lg  106 (142)
                      +.|+..|++..|++.|+. |.... +...+ .-..++.++         ...-..|+.++. .|+|.+++...++
T Consensus         5 evA~~~gvs~~tlR~~~~~g~l~~-~~~~~-g~R~y~~~~---------l~~l~~i~~l~~-~g~~l~~i~~~l~   67 (67)
T cd04764           5 EVSEIIGVKPHTLRYYEKEFNLYI-PRTEN-GRRYYTDED---------IELLKKIKTLLE-KGLSIKEIKEILN   67 (67)
T ss_pred             HHHHHHCcCHHHHHHHHHhcCCCC-CCCCC-CceeeCHHH---------HHHHHHHHHHHH-CCCCHHHHHHHhC
Confidence            578999999999999985 44431 11111 112222111         123455677777 8999999987663

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.

>smart00351 PAX Paired Box domain

Probab=93.09  E-value=0.34  Score=34.44  Aligned_cols=38  Identities=11%  Similarity=0.236  Sum_probs=30.5

Q ss_pred             chHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           79 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +..++..+|-.+-. .|+|+.++|+.+|||++||++|.+
T Consensus        18 ~s~~~R~riv~~~~-~G~s~~~iA~~~gvs~~tV~kwi~   55 (125)
T smart00351       18 LPDEERQRIVELAQ-NGVRPCDISRQLCVSHGCVSKILG   55 (125)
T ss_pred             CCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHH
Confidence            45556666665544 799999999999999999999964

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

Probab=93.02  E-value=0.38  Score=28.39  Aligned_cols=38  Identities=8%  Similarity=0.119  Sum_probs=29.2

Q ss_pred             chHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           79 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +...+...|-.+.... .|.+++|+.+|+|.+||.++-+
T Consensus        12 ~T~~~~~~i~~~~~~~-~s~~~vA~~~~vs~~TV~ri~~   49 (52)
T PF13542_consen   12 ITKRLEQYILKLLRES-RSFKDVARELGVSWSTVRRIFD   49 (52)
T ss_pred             HHHHHHHHHHHHHhhc-CCHHHHHHHHCCCHHHHHHHHH
Confidence            4444555665555555 7999999999999999999864

>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=92.98  E-value=0.33  Score=29.75  Aligned_cols=24  Identities=13%  Similarity=0.192  Sum_probs=21.1

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           94 KKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        94 ~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ..+|+.+||+.+|+|+++++++.+
T Consensus        24 ~~~s~~ela~~~g~s~~tv~r~l~   47 (67)
T cd00092          24 LPLTRQEIADYLGLTRETVSRTLK   47 (67)
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHH
Confidence            459999999999999999988754

>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=92.90  E-value=0.29  Score=29.18  Aligned_cols=34  Identities=9%  Similarity=0.181  Sum_probs=24.3

Q ss_pred             HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      -.+.+-.++-..|+|..|+|+.+|+|.++|..+-
T Consensus        14 ~~r~i~~l~~~~g~s~~eIa~~l~~s~~~v~~~l   47 (54)
T PF08281_consen   14 RQREIFLLRYFQGMSYAEIAEILGISESTVKRRL   47 (54)
T ss_dssp             HHHHHHHHHHTS---HHHHHHHCTS-HHHHHHHH
T ss_pred             HHHHHHHHHHHHCcCHHHHHHHHCcCHHHHHHHH
Confidence            3445566777889999999999999999998764

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.

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

Probab=92.84  E-value=0.026  Score=42.19  Aligned_cols=46  Identities=15%  Similarity=0.120  Sum_probs=1.8

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 032366           93 DKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL  138 (142)
Q Consensus        93 ~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl  138 (142)
                      ..-||++++|+.+|++.||||+.-+|+..-++.-+.-|..+|...+
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            3458999999999999999999999998777766777777776654

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.

>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=92.79  E-value=0.3  Score=29.51  Aligned_cols=34  Identities=15%  Similarity=0.133  Sum_probs=27.9

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ...|..+...-++|+.+||+.+++++++++++-+
T Consensus         6 ~~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~   39 (59)
T PF01047_consen    6 FRILRILYENGGITQSELAEKLGISRSTVTRIIK   39 (59)
T ss_dssp             HHHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCCChhHHHHHHH
Confidence            3456777888999999999999999999998753

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 ....

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

Probab=92.78  E-value=0.36  Score=39.54  Aligned_cols=60  Identities=17%  Similarity=0.042  Sum_probs=47.2

Q ss_pred             chHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 032366           79 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL  138 (142)
Q Consensus        79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl  138 (142)
                      .....-+.+++.-+-.+++|+.+|..+|+|+.+|+.+.+|...-...+-.+|+.+|+-+.
T Consensus         3 ~n~~~~k~~k~f~e~~~~~q~~~a~gi~~~~~~vsk~L~g~~g~~~~~~a~ia~~le~~~   62 (297)
T COG2842           3 INFIEIKKLKEFAEFSGMCQKYLARGIGTSAPALSKYLNGYKGDYATNEAKIAAFLEKKG   62 (297)
T ss_pred             hhHHHHHHHHHHHHhhhhhHHHHHHHhccCchhHHHHhcCcCchHHHHHHHHHHHHcCCC
Confidence            345567889999999999999999999999999999999833223455667777776543

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

Probab=92.73  E-value=0.12  Score=32.24  Aligned_cols=22  Identities=27%  Similarity=0.517  Sum_probs=20.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +|..|+|+.+|||+++|..||+
T Consensus         1 yti~eva~~~gvs~~tlr~y~~   22 (69)
T PF13411_consen    1 YTIKEVAKLLGVSPSTLRYYER   22 (69)
T ss_dssp             EEHHHHHHHTTTTHHHHHHHHH
T ss_pred             CcHHHHHHHHCcCHHHHHHHHH
Confidence            4678999999999999999996

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

Probab=92.70  E-value=0.13  Score=31.08  Aligned_cols=28  Identities=14%  Similarity=-0.020  Sum_probs=24.3

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           90 ARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        90 ~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .+-+.|+++.+||...|||++|+++|-+
T Consensus        14 ~~LR~~~~~~~La~~FgIs~stvsri~~   41 (53)
T PF13613_consen   14 MYLRLNLTFQDLAYRFGISQSTVSRIFH   41 (53)
T ss_pred             HHHHcCCcHhHHhhheeecHHHHHHHHH
Confidence            3455789999999999999999999864

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

Probab=92.62  E-value=0.15  Score=32.02  Aligned_cols=22  Identities=32%  Similarity=0.510  Sum_probs=20.1

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ++..|+|+.+||++++|..||.
T Consensus         1 ~~i~e~A~~~gVs~~tlr~ye~   22 (68)
T cd04763           1 YTIGEVALLTGIKPHVLRAWER   22 (68)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            4678999999999999999985

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

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

Probab=92.62  E-value=0.19  Score=40.11  Aligned_cols=34  Identities=18%  Similarity=0.333  Sum_probs=28.7

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      -+.|-.+|-..++||+++|+.+|||++.|+++++
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            3445556677799999999999999999999985

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

Probab=92.59  E-value=0.19  Score=30.88  Aligned_cols=24  Identities=17%  Similarity=0.254  Sum_probs=21.2

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           94 KKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        94 ~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ++.|..+||+.+|||++|++...+
T Consensus        22 R~~tl~elA~~lgis~st~~~~LR   45 (53)
T PF04967_consen   22 RRITLEELAEELGISKSTVSEHLR   45 (53)
T ss_pred             CcCCHHHHHHHhCCCHHHHHHHHH
Confidence            568999999999999999998654

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

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

Probab=92.54  E-value=0.57  Score=29.12  Aligned_cols=62  Identities=18%  Similarity=0.242  Sum_probs=38.4

Q ss_pred             HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhC
Q 032366           33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLIN  106 (142)
Q Consensus        33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lg  106 (142)
                      +.|+..|++.+|++.|+. |...+..  ....-..++.+         ....-..|+.++. .|+|..++.+.+.
T Consensus         5 eva~~~gvs~~tlr~y~~~gll~~~~--~~~g~r~y~~~---------dv~~l~~i~~l~~-~G~sl~~I~~~l~   67 (69)
T PF13411_consen    5 EVAKLLGVSPSTLRYYEREGLLPPPR--DENGYRYYSEE---------DVERLREIKELRK-QGMSLEEIKKLLK   67 (69)
T ss_dssp             HHHHHTTTTHHHHHHHHHTTSSTTBE--STTSSEEE-HH---------HHHHHHHHHHHHH-TTTHHHHHHHHH-
T ss_pred             HHHHHHCcCHHHHHHHHHhcCccccc--ccCceeeccHH---------HHHHHHHHHHHHH-CcCCHHHHHHHHc
Confidence            579999999999999987 3332211  01111222222         1224556777777 9999999887763

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

Probab=92.43  E-value=0.28  Score=33.24  Aligned_cols=25  Identities=12%  Similarity=0.205  Sum_probs=22.2

Q ss_pred             HhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           92 NDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        92 ~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ....+||.|||+.+|+++.+|++..
T Consensus        44 ~~~~is~~eLa~~~g~sr~tVsr~L   68 (95)
T TIGR01610        44 KQDRVTATVIAELTGLSRTHVSDAI   68 (95)
T ss_pred             cCCccCHHHHHHHHCcCHHHHHHHH
Confidence            5678999999999999999999843

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

>smart00422 HTH_MERR helix_turn_helix, mercury resistance

Probab=92.41  E-value=0.24  Score=30.84  Aligned_cols=22  Identities=23%  Similarity=0.345  Sum_probs=20.1

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +|..++|+.+|||+++|..|+.
T Consensus         1 ~s~~eva~~~gvs~~tlr~~~~   22 (70)
T smart00422        1 YTIGEVAKLAGVSVRTLRYYER   22 (70)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5788999999999999999975

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

Probab=92.39  E-value=0.6  Score=31.70  Aligned_cols=67  Identities=15%  Similarity=0.193  Sum_probs=42.0

Q ss_pred             HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhCCCHH
Q 032366           33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQ  110 (142)
Q Consensus        33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~s  110 (142)
                      ..|++.|++..|++.|+. |-..+...  .-.-..++..         ....-..|..++...|++..++...+.....
T Consensus         5 e~a~~~gvs~~tLR~ye~~Gll~p~r~--~~g~R~Y~~~---------dv~~l~~I~~L~~~~G~~l~ei~~~l~~~~~   72 (96)
T cd04774           5 EVAKRLGLTKRTLKYYEEIGLVSPERS--EGRYRLYSEE---------DLKRLERILRLREVLGFSLQEVTHFLERPLE   72 (96)
T ss_pred             HHHHHHCcCHHHHHHHHHCCCCCCCcC--CCCCEEECHH---------HHHHHHHHHHHHHHcCCCHHHHHHHHhcccc
Confidence            578999999999999986 33322111  1111222221         1224556777788789999999888766544

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.

>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon

Probab=92.32  E-value=0.61  Score=27.08  Aligned_cols=25  Identities=16%  Similarity=0.226  Sum_probs=23.0

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           93 DKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        93 ~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ..|+|..++|+.+|+|+++|..+..
T Consensus        16 ~~g~s~~eia~~l~is~~tv~~~~~   40 (58)
T smart00421       16 AEGLTNKEIAERLGISEKTVKTHLS   40 (58)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            5799999999999999999998865

lux regulon (activates the bioluminescence operon

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

Probab=92.17  E-value=0.27  Score=39.54  Aligned_cols=42  Identities=21%  Similarity=0.218  Sum_probs=31.3

Q ss_pred             CCCCHHHHHHHhCC-----CHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q 032366           94 KKLTQSQLAQLINE-----KPQVIQEYESGKAIPNQQILTKLERALG  135 (142)
Q Consensus        94 ~glTQ~eLA~~lgi-----s~stIs~~E~G~~~p~~~~l~kLa~~Lg  135 (142)
                      .++||.+||+++|-     |+++|+++..=-....+.+...|+.-+|
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     9999999987544455555555554443

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.

>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=91.99  E-value=0.45  Score=27.57  Aligned_cols=30  Identities=13%  Similarity=0.224  Sum_probs=22.8

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHH
Q 032366           85 KAIVQARNDKKLTQSQLAQLINEKPQVIQE  114 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~  114 (142)
                      ..|..+......+..+||+.+|+|.++|.+
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            446677778889999999999999999875

...

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

Probab=91.92  E-value=1  Score=32.82  Aligned_cols=40  Identities=23%  Similarity=0.224  Sum_probs=31.1

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCH
Q 032366           85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQ  124 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~  124 (142)
                      -.|+.+|...|+|..++++..+.|..-|-.||.|....+.
T Consensus        10 ie~~ylr~slgl~~aqv~~l~k~se~dv~aweage~~~~~   49 (166)
T PF14590_consen   10 IEIKYLRLSLGLTTAQVAELTKASEADVLAWEAGEKPAPG   49 (166)
T ss_dssp             HHHHHHHHHTT--HHHHHHHHTS-HHHHHHHHTTSS---H
T ss_pred             HHHHHHHHHcCCCHHHHHHhhccCHHHhhhhhccCCcCch
Confidence            3478899999999999999999999999999999876553

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

Probab=91.72  E-value=0.35  Score=34.24  Aligned_cols=22  Identities=23%  Similarity=0.305  Sum_probs=20.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      |+..|||+.+|||..||.-||+
T Consensus         1 m~IgevA~~~gvs~~tLRyYe~   22 (127)
T cd04784           1 MKIGELAKKTGCSVETIRYYEK   22 (127)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5788999999999999999996

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.

>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=91.70  E-value=0.46  Score=28.78  Aligned_cols=34  Identities=18%  Similarity=0.211  Sum_probs=26.2

Q ss_pred             HHHHHHHHHhCC--CCHHHHHHHhCCCHHHHHHHHc
Q 032366           84 KKAIVQARNDKK--LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        84 g~~Lk~~R~~~g--lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ...|..+...-+  +|+.+||+.++++++++++..+
T Consensus         8 ~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~   43 (62)
T PF12802_consen    8 FRVLMALARHPGEELTQSELAERLGISKSTVSRIVK   43 (62)
T ss_dssp             HHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHH
T ss_pred             HHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            345566666666  9999999999999999998753

...

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

Probab=91.66  E-value=0.57  Score=27.44  Aligned_cols=21  Identities=33%  Similarity=0.510  Sum_probs=18.5

Q ss_pred             HHHHcCCChhHHHhhhcCCCC
Q 032366           34 AARRAGADIETVRKSHAGTNK   54 (142)
Q Consensus        34 ~a~r~G~~v~t~kk~~~g~~~   54 (142)
                      .|++.|++.+|+.+|+.|...
T Consensus         3 lA~~~gvs~~tvs~~l~g~~~   23 (52)
T cd01392           3 IARAAGVSVATVSRVLNGKPR   23 (52)
T ss_pred             HHHHHCcCHHHHHHHHcCCCC
Confidence            689999999999999988753

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

>smart00351 PAX Paired Box domain

Probab=91.65  E-value=0.86  Score=32.35  Aligned_cols=74  Identities=9%  Similarity=0.132  Sum_probs=44.4

Q ss_pred             HHHHHHHHcCCChhHHHhhhc-----CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHH-HHHhCCCCHHHHHH
Q 032366           30 KVVNAARRAGADIETVRKSHA-----GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQ-ARNDKKLTQSQLAQ  103 (142)
Q Consensus        30 ~~~~~a~r~G~~v~t~kk~~~-----g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~-~R~~~glTQ~eLA~  103 (142)
                      +.-..|++.|++..|+.+|-.     |...+.+.. +....+            ........|.. ....-.+|..+|++
T Consensus        35 s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~~g-g~rp~~------------~~~~~~~~I~~~~~~~p~~t~~el~~  101 (125)
T smart00351       35 RPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIG-GSKPKV------------ATPKVVKKIADYKQENPGIFAWEIRD  101 (125)
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcCCC-CCCCCc------------cCHHHHHHHHHHHHHCCCCCHHHHHH
Confidence            455689999999999999854     544432111 111111            22223333443 45666899999988


Q ss_pred             HhC-----C-----CHHHHHHHH
Q 032366          104 LIN-----E-----KPQVIQEYE  116 (142)
Q Consensus       104 ~lg-----i-----s~stIs~~E  116 (142)
                      .+.     +     |.+||.+|.
T Consensus       102 ~L~~~gv~~~~~~Ps~sti~~~l  124 (125)
T smart00351      102 RLLSEGVCDKDNVPSVSSINRIL  124 (125)
T ss_pred             HHHHcCCCcCCCCCChhhHHHhh
Confidence            772     2     677777664

>cd00131 PAX Paired Box domain

Probab=91.35  E-value=0.72  Score=33.00  Aligned_cols=39  Identities=8%  Similarity=0.267  Sum_probs=30.7

Q ss_pred             cchHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           78 RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        78 ~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .+..++..+|-.+- +.|+|+.++|+.+|||++||.+|-+
T Consensus        17 ~lS~d~R~rIv~~~-~~G~s~~~iA~~~~Vs~~tV~r~i~   55 (128)
T cd00131          17 PLPDSIRQRIVELA-QSGIRPCDISRQLRVSHGCVSKILN   55 (128)
T ss_pred             cCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            34455666666554 4799999999999999999999953

>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=91.30  E-value=0.27  Score=31.15  Aligned_cols=24  Identities=17%  Similarity=0.277  Sum_probs=21.2

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           94 KKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        94 ~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ..+|+.+||..+|+|+.++++..+
T Consensus        27 ~~lt~~~iA~~~g~sr~tv~r~l~   50 (76)
T PF13545_consen   27 LPLTQEEIADMLGVSRETVSRILK   50 (76)
T ss_dssp             EESSHHHHHHHHTSCHHHHHHHHH
T ss_pred             ecCCHHHHHHHHCCCHHHHHHHHH
Confidence            468999999999999999998753

...

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

Probab=91.29  E-value=0.52  Score=29.93  Aligned_cols=29  Identities=17%  Similarity=0.039  Sum_probs=23.1

Q ss_pred             HHHHHhCC--CCHHHHHHHhCCCHHHHHHHH
Q 032366           88 VQARNDKK--LTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        88 k~~R~~~g--lTQ~eLA~~lgis~stIs~~E  116 (142)
                      ..++..-+  +|+.+||+.+|++.+++++..
T Consensus        13 ~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L   43 (68)
T smart00550       13 EFLENSGDETSTALQLAKNLGLPKKEVNRVL   43 (68)
T ss_pred             HHHHHCCCCCcCHHHHHHHHCCCHHHHHHHH
Confidence            34444435  999999999999999998874

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

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

Probab=91.26  E-value=0.34  Score=31.43  Aligned_cols=42  Identities=14%  Similarity=0.192  Sum_probs=27.9

Q ss_pred             HHHHHHH-HHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCC
Q 032366           82 ELKKAIV-QARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPN  123 (142)
Q Consensus        82 ~~g~~Lk-~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~  123 (142)
                      .+.+.|. ....-..+|..+||+.+|+|+++|.++.+.-..-+
T Consensus        20 ~Ia~yil~~~~~~~~~si~elA~~~~vS~sti~Rf~kkLG~~g   62 (77)
T PF01418_consen   20 KIADYILENPDEIAFMSISELAEKAGVSPSTIVRFCKKLGFSG   62 (77)
T ss_dssp             HHHHHHHH-HHHHCT--HHHHHHHCTS-HHHHHHHHHHCTTTC
T ss_pred             HHHHHHHhCHHHHHHccHHHHHHHcCCCHHHHHHHHHHhCCCC
Confidence            3455553 34566789999999999999999999987433333

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.

>PRK09744 DNA-binding transcriptional regulator DicC; Provisional

Probab=91.22  E-value=0.75  Score=30.20  Aligned_cols=36  Identities=19%  Similarity=0.421  Sum_probs=27.2

Q ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q 032366           97 TQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALG  135 (142)
Q Consensus        97 TQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lg  135 (142)
                      +...+|+.+|||+++|++|  |+.+| ...+.+|..+-+
T Consensus        12 s~~kvA~aLGIs~~AVsQW--Ge~VP-e~rA~~ie~~T~   47 (75)
T PRK09744         12 SKTKLANAAGVRLASVAAW--GELVP-EGRAMRLQEASG   47 (75)
T ss_pred             cHHHHHHHHCCCHHHHHHH--hccCc-HHHHHHHHHHhC
Confidence            6778999999999999999  77665 344455655544

>PRK00118 putative DNA-binding protein; Validated

Probab=91.07  E-value=0.53  Score=32.78  Aligned_cols=33  Identities=9%  Similarity=0.090  Sum_probs=27.7

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +.+-.++...|+|..++|+.+|+|++||.++..
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            334466677899999999999999999999864

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

Probab=90.80  E-value=0.68  Score=33.85  Aligned_cols=36  Identities=14%  Similarity=0.205  Sum_probs=29.6

Q ss_pred             HHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           82 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        82 ~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ++..++-..-...|+|..++|+++|+|.+||.+|.+
T Consensus         8 ~~R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~   43 (138)
T COG3415           8 DLRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVR   43 (138)
T ss_pred             HHHHHHHHHHHHcCccHHHHHHHhCccHHHHHHHHH
Confidence            344555556667899999999999999999999975

>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein

Probab=90.68  E-value=0.37  Score=27.54  Aligned_cols=24  Identities=17%  Similarity=0.259  Sum_probs=20.9

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           94 KKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        94 ~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ..+|+.++|+.+|+|+++++++.+
T Consensus         7 ~~~s~~~la~~l~~s~~tv~~~l~   30 (48)
T smart00419        7 LPLTRQEIAELLGLTRETVSRTLK   30 (48)
T ss_pred             eccCHHHHHHHHCCCHHHHHHHHH
Confidence            458999999999999999988654

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

Probab=90.68  E-value=0.99  Score=27.37  Aligned_cols=35  Identities=11%  Similarity=0.242  Sum_probs=26.1

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCC
Q 032366           85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK  119 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~  119 (142)
                      +..-..+.+.|++..++|+.+|-|+..|.+|.++-
T Consensus        10 qaqid~m~qlG~s~~~isr~i~RSr~~Ir~yl~dP   44 (50)
T PF11427_consen   10 QAQIDVMHQLGMSLREISRRIGRSRTCIRRYLKDP   44 (50)
T ss_dssp             HHHHHHHHHTT--HHHHHHHHT--HHHHHHHHHSC
T ss_pred             HHHHHHHHHhchhHHHHHHHhCccHHHHHHHhcCh
Confidence            33446788999999999999999999999998753

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

Probab=90.51  E-value=0.48  Score=31.57  Aligned_cols=23  Identities=13%  Similarity=0.345  Sum_probs=21.2

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 032366           95 KLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        95 glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ++|..++|+.+|||.+||..||+
T Consensus         1 ~~ti~evA~~~gvs~~tLR~ye~   23 (88)
T cd01105           1 VIGIGEVSKLTGVSPRQLRYWEE   23 (88)
T ss_pred             CcCHHHHHHHHCcCHHHHHHHHH
Confidence            47889999999999999999986

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=90.31  E-value=0.46  Score=32.86  Aligned_cols=22  Identities=27%  Similarity=0.578  Sum_probs=20.6

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ||..++|+.+|||++||..||.
T Consensus         1 ~~i~eva~~~gvs~~tlR~ye~   22 (108)
T cd04773           1 MTIGELAHLLGVPPSTLRHWEK   22 (108)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5788999999999999999996

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.

>PF07638 Sigma70_ECF: ECF sigma factor

Probab=90.31  E-value=0.56  Score=35.20  Aligned_cols=32  Identities=13%  Similarity=0.199  Sum_probs=26.5

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      .++-.+|.-.|+|..|+|+.+|||+.||.+..
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            34445677789999999999999999998754

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

Probab=90.24  E-value=0.09  Score=31.58  Aligned_cols=28  Identities=18%  Similarity=0.268  Sum_probs=20.4

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCC
Q 032366           96 LTQSQLAQLINEKPQVIQEYESGKAIPN  123 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~G~~~p~  123 (142)
                      ++.+|+++.+|+|++||.++.+....|.
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            5678999999999999999998555553

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=90.17  E-value=0.5  Score=31.79  Aligned_cols=27  Identities=7%  Similarity=0.110  Sum_probs=23.2

Q ss_pred             HHhCCC-CHHHHHHHhCCCHHHHHHHHc
Q 032366           91 RNDKKL-TQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        91 R~~~gl-TQ~eLA~~lgis~stIs~~E~  117 (142)
                      ....|+ |..++|+.+|+|++||++|.+
T Consensus         7 l~~~g~~~~~~ia~~lg~s~~Tv~r~~~   34 (112)
T PF13551_consen    7 LLAEGVSTIAEIARRLGISRRTVYRWLK   34 (112)
T ss_pred             HHHcCCCcHHHHHHHHCcCHHHHHHHHH
Confidence            345688 599999999999999999874

>PRK10072 putative transcriptional regulator; Provisional

Probab=90.07  E-value=0.29  Score=33.56  Aligned_cols=27  Identities=22%  Similarity=0.245  Sum_probs=23.8

Q ss_pred             HHHHHHHHHcCCChhHHHhhhcCCCCC
Q 032366           29 EKVVNAARRAGADIETVRKSHAGTNKA   55 (142)
Q Consensus        29 ~~~~~~a~r~G~~v~t~kk~~~g~~~~   55 (142)
                      -++.+.|+..|++..|+.+|+.|...|
T Consensus        47 lTQ~elA~~lGvS~~TVs~WE~G~r~P   73 (96)
T PRK10072         47 LKIDDFARVLGVSVAMVKEWESRRVKP   73 (96)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCC
Confidence            356789999999999999999999874

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

Probab=90.06  E-value=1.7  Score=29.39  Aligned_cols=65  Identities=17%  Similarity=0.248  Sum_probs=40.8

Q ss_pred             HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhCC
Q 032366           33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINE  107 (142)
Q Consensus        33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgi  107 (142)
                      +.|++.|+++.|++-|+. |-..|.... ..+-..++.+         ....-..|+.++...|++..++++.+..
T Consensus         5 eva~~~gvs~~tlR~Ye~~GLl~p~~r~-~~g~r~Y~~~---------dv~~l~~I~~L~~~~G~~l~~I~~~l~~   70 (95)
T cd04780           5 ELSKRSGVSVATIKYYLREGLLPEGRRL-APNQAEYSEA---------HVERLRLIRALQQEGGLPISQIKEVLDA   70 (95)
T ss_pred             HHHHHHCcCHHHHHHHHHCCCCCCCcCC-CCCCeecCHH---------HHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            478999999999999998 444321111 1111222221         1124455666777789999999988764

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.

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

Probab=90.05  E-value=0.94  Score=30.39  Aligned_cols=22  Identities=23%  Similarity=0.406  Sum_probs=20.2

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +|..|+|+.+||++++|..|++
T Consensus         1 ~~~~eva~~~gi~~~tlr~~~~   22 (100)
T cd00592           1 YTIGEVAKLLGVSVRTLRYYEE   22 (100)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5778999999999999999986

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.

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

Probab=90.03  E-value=0.16  Score=41.56  Aligned_cols=38  Identities=18%  Similarity=0.221  Sum_probs=33.8

Q ss_pred             hHHHHHHHHHHHHhCCCCHHHHHHHhC---------CCHHHHHHHHc
Q 032366           80 PSELKKAIVQARNDKKLTQSQLAQLIN---------EKPQVIQEYES  117 (142)
Q Consensus        80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lg---------is~stIs~~E~  117 (142)
                      .+.|+++.++.|..+|.||.|+.+.+-         +|++||-++|+
T Consensus       219 LEaFAErFKQRRIKLGVTQADVG~ALAnLKiPGVGsLSQSTICRFES  265 (385)
T KOG1168|consen  219 LEAFAERFKQRRIKLGVTQADVGKALANLKIPGVGSLSQSTICRFES  265 (385)
T ss_pred             HHHHHHHHHhhhhhhcccHHHHHHHHHhCcCCCcccccccceeeeee
Confidence            456999999999999999999998772         68999999996

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

Probab=89.91  E-value=0.33  Score=35.65  Aligned_cols=25  Identities=12%  Similarity=0.252  Sum_probs=19.7

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCC
Q 032366           95 KLTQSQLAQLINEKPQVIQEYESGK  119 (142)
Q Consensus        95 glTQ~eLA~~lgis~stIs~~E~G~  119 (142)
                      ..|+.++|+.+||+++|+.+|-+..
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

>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=89.81  E-value=0.87  Score=27.85  Aligned_cols=31  Identities=6%  Similarity=-0.010  Sum_probs=26.8

Q ss_pred             HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           87 IVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +.+++.-..+++.+.|+.+||+.+++.+..+
T Consensus         7 ~~~L~~~fhlp~~eAA~~Lgv~~T~LKr~CR   37 (52)
T PF02042_consen    7 LEDLSQYFHLPIKEAAKELGVSVTTLKRRCR   37 (52)
T ss_pred             HHHHHHHhCCCHHHHHHHhCCCHHHHHHHHH
Confidence            5677888899999999999999998887765

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

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor

Probab=89.77  E-value=1  Score=25.86  Aligned_cols=26  Identities=19%  Similarity=0.247  Sum_probs=22.2

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           91 RNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        91 R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ....++|..++++.+++++++++++.
T Consensus        10 ~~~~~~s~~~l~~~l~~s~~tv~~~l   35 (53)
T smart00420       10 AQQGKVSVEELAELLGVSEMTIRRDL   35 (53)
T ss_pred             HHcCCcCHHHHHHHHCCCHHHHHHHH
Confidence            33467999999999999999998865

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

Probab=89.52  E-value=2.1  Score=28.39  Aligned_cols=63  Identities=14%  Similarity=0.119  Sum_probs=38.3

Q ss_pred             HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhC
Q 032366           33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLIN  106 (142)
Q Consensus        33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lg  106 (142)
                      +.|++.|++..|++.|+. |-..+..... -.-..+..++         -..-..|+.+|. .|+|.+++.+.+.
T Consensus         6 evA~~~gvs~~tLR~ye~~Gll~p~r~~~-~g~R~Ys~~d---------v~~l~~I~~Lr~-~G~sl~~i~~~l~   69 (88)
T cd01105           6 EVSKLTGVSPRQLRYWEEKGLIKSIRSDG-GGQRKYSLAD---------VDRLLVIKELLD-EGFTLAAAVEKLR   69 (88)
T ss_pred             HHHHHHCcCHHHHHHHHHCCCCCCCccCC-CCceecCHHH---------HHHHHHHHHHHH-CCCCHHHHHHHHH
Confidence            589999999999999976 4433211110 0112222211         123455666766 8999999888775

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.

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

Probab=89.50  E-value=2  Score=28.55  Aligned_cols=63  Identities=17%  Similarity=0.210  Sum_probs=40.3

Q ss_pred             HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhC
Q 032366           33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLIN  106 (142)
Q Consensus        33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lg  106 (142)
                      ..|...|+++.|++.|+. |-..|....  ..-..++..         .-..-..|+.++.+.|++..++...+.
T Consensus         6 e~A~~~gvs~~tLr~ye~~Gli~p~r~~--~g~R~y~~~---------dv~~l~~i~~L~~d~g~~l~~i~~~l~   69 (91)
T cd04766           6 VAAELSGMHPQTLRLYERLGLLSPSRTD--GGTRRYSER---------DIERLRRIQRLTQELGVNLAGVKRILE   69 (91)
T ss_pred             HHHHHHCcCHHHHHHHHHCCCcCCCcCC--CCCeeECHH---------HHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence            479999999999999986 333321110  111112211         122456677778889999999988876

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.

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

Probab=89.48  E-value=0.6  Score=31.81  Aligned_cols=22  Identities=18%  Similarity=0.342  Sum_probs=20.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +|..|+|+.+|||++||..||+
T Consensus         1 ~ti~eva~~~gvs~~tlR~ye~   22 (103)
T cd01106           1 YTVGEVAKLTGVSVRTLHYYDE   22 (103)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5788999999999999999986

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

>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=89.33  E-value=0.34  Score=28.93  Aligned_cols=25  Identities=16%  Similarity=0.191  Sum_probs=20.8

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           93 DKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        93 ~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ..++|..|||+.+|++++++.++.+
T Consensus        16 ~~~~t~~eia~~~gl~~stv~r~L~   40 (52)
T PF09339_consen   16 GGPLTLSEIARALGLPKSTVHRLLQ   40 (52)
T ss_dssp             BSCEEHHHHHHHHTS-HHHHHHHHH
T ss_pred             CCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3458999999999999999999864

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.

>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]

Probab=89.20  E-value=0.88  Score=36.55  Aligned_cols=41  Identities=12%  Similarity=0.136  Sum_probs=35.7

Q ss_pred             CcchHHHHHHHHHHHHhCC-CCHHHHHHHhCCCHHHHHHHHc
Q 032366           77 DRVPSELKKAIVQARNDKK-LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        77 ~~~~~~~g~~Lk~~R~~~g-lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ..+..+..+.|..++..-| ++|+||.+.+|.|++|++++.+
T Consensus       191 ~~L~~~e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~  232 (258)
T COG2512         191 YDLNEDEKEILDLIRERGGRITQAELRRALGLSKTTVSRILR  232 (258)
T ss_pred             CCCCHHHHHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHH
Confidence            4567778888999999998 9999999999999999998753

>COG0789 SoxR Predicted transcriptional regulators [Transcription]

Probab=89.08  E-value=0.64  Score=32.25  Aligned_cols=22  Identities=23%  Similarity=0.330  Sum_probs=20.4

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +|..++|+.+|||..||.-||.
T Consensus         1 ~~I~eva~~~gvs~~tLRyYE~   22 (124)
T COG0789           1 YTIGEVAKLTGVSVRTLRFYER   22 (124)
T ss_pred             CcHHHHHHHhCCCHHHHHHHHH
Confidence            5778999999999999999996

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

Probab=89.01  E-value=0.66  Score=32.00  Aligned_cols=22  Identities=23%  Similarity=0.382  Sum_probs=20.4

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ++..++|+.+|||++||.-||+
T Consensus         1 ~~i~eva~~~gis~~tlR~ye~   22 (108)
T cd01107           1 FTIGEFAKLSNLSIKALRYYDK   22 (108)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5778999999999999999997

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.

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

Probab=88.83  E-value=0.72  Score=31.56  Aligned_cols=22  Identities=27%  Similarity=0.256  Sum_probs=20.7

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ++..|+|+.+|||++||..||+
T Consensus         2 ~~i~eva~~~gvs~~tlR~ye~   23 (102)
T cd04789           2 YTISELAEKAGISRSTLLYYEK   23 (102)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            6889999999999999999996

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=88.82  E-value=0.71  Score=31.19  Aligned_cols=23  Identities=22%  Similarity=0.356  Sum_probs=20.8

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcC
Q 032366           96 LTQSQLAQLINEKPQVIQEYESG  118 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~G  118 (142)
                      +|..|+|+.+|||++||.-||+-
T Consensus         1 ~ti~eva~~~gvs~~tLRyye~~   23 (96)
T cd04768           1 LTIGEFAKLAGVSIRTLRHYDDI   23 (96)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC
Confidence            47889999999999999999973

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.

>PRK04132 replication factor C small subunit; Provisional

Probab=88.77  E-value=0.67  Score=43.06  Aligned_cols=43  Identities=28%  Similarity=0.461  Sum_probs=40.1

Q ss_pred             HHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 032366           98 QSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG  140 (142)
Q Consensus        98 Q~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~e  140 (142)
                      .+++|++.||...-+-.|..|++.|+.....+||++||+.++.
T Consensus       420 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  462 (846)
T PRK04132        420 RKEIAEKTGIRADRILEYIKGKRKPSLKNYIKIAKALGINLEK  462 (846)
T ss_pred             HHHHHHHhCCcHHHHHHHHhcCCCccHHHHHHHHHHhcccHHH
Confidence            5689999999999999999999999999999999999998763

>COG1522 Lrp Transcriptional regulators [Transcription]

Probab=88.77  E-value=0.86  Score=32.63  Aligned_cols=33  Identities=12%  Similarity=0.322  Sum_probs=27.5

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      .+.|+.+......++.+||+.+|+|++++.+.-
T Consensus        11 ~~IL~~L~~d~r~~~~eia~~lglS~~~v~~Ri   43 (154)
T COG1522          11 RRILRLLQEDARISNAELAERVGLSPSTVLRRI   43 (154)
T ss_pred             HHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHH
Confidence            455677888888999999999999999987643

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

Probab=88.75  E-value=0.74  Score=31.24  Aligned_cols=22  Identities=14%  Similarity=0.288  Sum_probs=20.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ++..++|+.+|+|.+||..||+
T Consensus         1 ~~I~e~a~~~gvs~~tLR~ye~   22 (96)
T cd04774           1 YKVDEVAKRLGLTKRTLKYYEE   22 (96)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5778999999999999999996

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.

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

Probab=88.69  E-value=0.72  Score=32.17  Aligned_cols=22  Identities=27%  Similarity=0.303  Sum_probs=20.7

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ||..++|+.+|||..||.-||.
T Consensus         1 ~~ige~a~~~gvs~~tLryYe~   22 (116)
T cd04769           1 MYIGELAQQTGVTIKAIRLYEE   22 (116)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5788999999999999999997

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.

>COG3311 AlpA Predicted transcriptional regulator [Transcription]

Probab=88.65  E-value=0.43  Score=30.99  Aligned_cols=31  Identities=19%  Similarity=0.184  Sum_probs=26.1

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH
Q 032366           96 LTQSQLAQLINEKPQVIQEYESGKAIPNQQI  126 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~G~~~p~~~~  126 (142)
                      |...|++..+|+|+++|.++.+....|.+..
T Consensus        14 lrl~ev~~~~GlSrstiYr~i~~~~FPkpvk   44 (70)
T COG3311          14 LRLPEVAQLTGLSRSTIYRLIKDGTFPKPVK   44 (70)
T ss_pred             hhHHHHHHHHCccHHHHHHHHccCCCCCCee
Confidence            4567899999999999999999888776543

>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism

Probab=88.63  E-value=0.97  Score=27.64  Aligned_cols=31  Identities=13%  Similarity=0.118  Sum_probs=25.2

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           86 AIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        86 ~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      .+..+.....+|-.+||+.+|||..||.+-.
T Consensus         5 Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl   35 (57)
T PF08220_consen    5 ILELLKEKGKVSVKELAEEFGVSEMTIRRDL   35 (57)
T ss_pred             HHHHHHHcCCEEHHHHHHHHCcCHHHHHHHH
Confidence            3455666777899999999999999998754

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

>TIGR02885 spore_sigF RNA polymerase sigma-F factor

Probab=88.55  E-value=0.9  Score=35.00  Aligned_cols=28  Identities=21%  Similarity=0.242  Sum_probs=24.7

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 032366           91 RNDKKLTQSQLAQLINEKPQVIQEYESG  118 (142)
Q Consensus        91 R~~~glTQ~eLA~~lgis~stIs~~E~G  118 (142)
                      |--.|+|+.++|+.+|+|+.+|+++++.
T Consensus       195 ~~~~~~t~~eIA~~lgis~~~V~~~~~~  222 (231)
T TIGR02885       195 RYFKDKTQTEVANMLGISQVQVSRLEKK  222 (231)
T ss_pred             HHHcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            4457999999999999999999999863

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.

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

Probab=88.54  E-value=0.53  Score=32.17  Aligned_cols=22  Identities=18%  Similarity=0.534  Sum_probs=20.1

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +|..|+|+.+|||.+||..||.
T Consensus         1 yti~EvA~~~gVs~~tLR~ye~   22 (99)
T cd04765           1 FSIGEVAEILGLPPHVLRYWET   22 (99)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            4778999999999999999985

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.

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

Probab=88.54  E-value=0.79  Score=30.97  Aligned_cols=22  Identities=14%  Similarity=0.256  Sum_probs=20.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      |+..++|+.+|+|..||..||+
T Consensus         1 m~i~eva~~~gvs~~tlR~ye~   22 (96)
T cd04788           1 WKIGELARRTGLSVRTLHHYDH   22 (96)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5788999999999999999996

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.

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

Probab=88.50  E-value=1.1  Score=26.58  Aligned_cols=21  Identities=33%  Similarity=0.439  Sum_probs=18.1

Q ss_pred             HHHHHcCCChhHHHhhhcCCC
Q 032366           33 NAARRAGADIETVRKSHAGTN   53 (142)
Q Consensus        33 ~~a~r~G~~v~t~kk~~~g~~   53 (142)
                      .-|+++|+++.|+.+...|..
T Consensus         4 dIA~~agvS~~TVSr~ln~~~   24 (46)
T PF00356_consen    4 DIAREAGVSKSTVSRVLNGPP   24 (46)
T ss_dssp             HHHHHHTSSHHHHHHHHTTCS
T ss_pred             HHHHHHCcCHHHHHHHHhCCC
Confidence            468999999999999987763

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 ....

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

Probab=88.43  E-value=0.79  Score=31.21  Aligned_cols=22  Identities=36%  Similarity=0.569  Sum_probs=20.1

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ++..|+|+.+|||.+||..||+
T Consensus         1 y~i~e~A~~~gvs~~tlR~Ye~   22 (99)
T cd04772           1 YRTVDLARAIGLSPQTVRNYES   22 (99)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            3678999999999999999996

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.

>PHA01976 helix-turn-helix protein

Probab=88.29  E-value=0.42  Score=29.59  Aligned_cols=26  Identities=19%  Similarity=0.131  Sum_probs=22.6

Q ss_pred             HHHHHHHHHcCCChhHHHhhhcCCCC
Q 032366           29 EKVVNAARRAGADIETVRKSHAGTNK   54 (142)
Q Consensus        29 ~~~~~~a~r~G~~v~t~kk~~~g~~~   54 (142)
                      -++-..|.+.|++.+|+.+||.|...
T Consensus        16 lt~~~lA~~~gvs~~~v~~~e~g~~~   41 (67)
T PHA01976         16 WSAPELSRRAGVRHSLIYDFEADKRL   41 (67)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCC
Confidence            35667899999999999999999875

>TIGR03070 couple_hipB transcriptional regulator, y4mF family

Probab=88.25  E-value=0.5  Score=27.87  Aligned_cols=25  Identities=20%  Similarity=0.310  Sum_probs=22.0

Q ss_pred             HHHHHHHHcCCChhHHHhhhcCCCC
Q 032366           30 KVVNAARRAGADIETVRKSHAGTNK   54 (142)
Q Consensus        30 ~~~~~a~r~G~~v~t~kk~~~g~~~   54 (142)
                      ++-..|.+.|++.+|+.+|+.|...
T Consensus        17 tq~~lA~~~gvs~~~vs~~e~g~~~   41 (58)
T TIGR03070        17 TQADLADLAGVGLRFIRDVENGKPT   41 (58)
T ss_pred             CHHHHHHHhCCCHHHHHHHHCCCCC
Confidence            4567899999999999999999864

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.

>PRK10458 DNA cytosine methylase; Provisional

Probab=88.20  E-value=1.7  Score=37.76  Aligned_cols=46  Identities=15%  Similarity=0.177  Sum_probs=35.0

Q ss_pred             HHHhCCCCHHHHHHHhC------CCHHHHHHHHcCCCCC---CHHHHHHHHHHhC
Q 032366           90 ARNDKKLTQSQLAQLIN------EKPQVIQEYESGKAIP---NQQILTKLERALG  135 (142)
Q Consensus        90 ~R~~~glTQ~eLA~~lg------is~stIs~~E~G~~~p---~~~~l~kLa~~Lg  135 (142)
                      .|...+++|++||+.++      .+..+|.+||+|+..|   +...+..|-..+.
T Consensus        24 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (467)
T PRK10458         24 EKLLEIYDVKTLAAQLNGVGENHWSRAILKRWLAGKSAWHRLSEAEFAHLQTLLP   78 (467)
T ss_pred             HHHHHhcCHHHHHHHHhhcccCccCHHHHHHHHcCCCCCCCccHHHHHHHHHhcc
Confidence            34556789999999997      7899999999998744   4455556665553

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

Probab=88.19  E-value=0.83  Score=30.91  Aligned_cols=22  Identities=23%  Similarity=0.403  Sum_probs=20.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +|..|+|+.+|||..||..||+
T Consensus         1 ~~i~eva~~~gvs~~tlR~ye~   22 (97)
T cd04782           1 FTTGEFAKLCGISKQTLFHYDK   22 (97)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5778999999999999999986

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.

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

Probab=88.11  E-value=0.85  Score=31.16  Aligned_cols=22  Identities=23%  Similarity=0.274  Sum_probs=20.7

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +|..|+|+.+|||++||..||+
T Consensus         2 ~~i~eva~~~gvs~~tLR~ye~   23 (102)
T cd04775           2 YTIGQMSRKFGVSRSTLLYYES   23 (102)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            6889999999999999999996

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

>PRK11891 aspartate carbamoyltransferase; Provisional

Probab=88.07  E-value=0.87  Score=39.17  Aligned_cols=35  Identities=11%  Similarity=0.136  Sum_probs=32.3

Q ss_pred             HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      -.+.|+.++.+.|||..+||+++|++..++.+|.-
T Consensus         4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~wl~   38 (429)
T PRK11891          4 QQAFLRDAMRRLNMTREAFANRIGVSRRALDTWLL   38 (429)
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHhCCcHHhHHhhcC
Confidence            45678999999999999999999999999999985

>smart00497 IENR1 Intron encoded nuclease repeat motif

Probab=87.89  E-value=0.87  Score=26.79  Aligned_cols=25  Identities=12%  Similarity=0.123  Sum_probs=22.4

Q ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCC
Q 032366           97 TQSQLAQLINEKPQVIQEYESGKAI  121 (142)
Q Consensus        97 TQ~eLA~~lgis~stIs~~E~G~~~  121 (142)
                      |+.+.|+.+|++.++|++..+|...
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).

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

Probab=87.73  E-value=0.94  Score=30.70  Aligned_cols=22  Identities=18%  Similarity=0.188  Sum_probs=20.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      |+..+||+.+|+|.++|..||+
T Consensus         1 m~I~eva~~~gvs~~tlR~Ye~   22 (95)
T cd04780           1 MRMSELSKRSGVSVATIKYYLR   22 (95)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5788999999999999999997

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.

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

Probab=87.71  E-value=3.1  Score=28.58  Aligned_cols=67  Identities=15%  Similarity=0.173  Sum_probs=38.2

Q ss_pred             HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhCCCH
Q 032366           33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEKP  109 (142)
Q Consensus        33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~  109 (142)
                      +.|++.|++++|++-|+. |-..|......-+-..++..+         ...-..|+.+|. .|++..++...+....
T Consensus         5 eva~~~gis~~tlR~ye~~GLi~p~~~~~~ngyR~Y~~~~---------i~~l~~I~~lr~-~G~sl~~i~~l~~~~~   72 (108)
T cd01107           5 EFAKLSNLSIKALRYYDKIGLLKPAYVDPDTGYRYYSAEQ---------LERLNRIKYLRD-LGFPLEEIKEILDADN   72 (108)
T ss_pred             HHHHHHCcCHHHHHHHHHcCCCCCCcCCCCCCccccCHHH---------HHHHHHHHHHHH-cCCCHHHHHHHHhcCC
Confidence            478999999999999997 333321110001111222111         112234555544 8999999888776544

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.

>smart00422 HTH_MERR helix_turn_helix, mercury resistance

Probab=87.69  E-value=4  Score=25.13  Aligned_cols=63  Identities=16%  Similarity=0.233  Sum_probs=35.9

Q ss_pred             HHHHHHcCCChhHHHhhhc-CCCCCC-CCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhC
Q 032366           32 VNAARRAGADIETVRKSHA-GTNKAA-SSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLIN  106 (142)
Q Consensus        32 ~~~a~r~G~~v~t~kk~~~-g~~~~~-~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lg  106 (142)
                      -+.|++.|++..|++.|+. |-..+. ....+  -..+..+         ....-..+..+|. .|++..+++..+.
T Consensus         4 ~eva~~~gvs~~tlr~~~~~gli~~~~~~~~g--~r~y~~~---------dl~~l~~i~~lr~-~g~~~~~i~~~l~   68 (70)
T smart00422        4 GEVAKLAGVSVRTLRYYERIGLLPPPIRTEGG--YRLYSDE---------DLERLRFIKRLKE-LGFSLEEIKELLE   68 (70)
T ss_pred             HHHHHHHCcCHHHHHHHHHCCCCCCCccCCCC--CEecCHH---------HHHHHHHHHHHHH-cCCCHHHHHHHHh
Confidence            3578999999999999976 333321 01000  0111111         1123445566665 8888888877664

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

Probab=87.42  E-value=2.9  Score=28.51  Aligned_cols=63  Identities=17%  Similarity=0.060  Sum_probs=36.5

Q ss_pred             HHHHHcCCChhHHHhhhc--CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhC
Q 032366           33 NAARRAGADIETVRKSHA--GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLIN  106 (142)
Q Consensus        33 ~~a~r~G~~v~t~kk~~~--g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lg  106 (142)
                      +.|+..|++.+|++.|+.  |...+....  .+-..+..++         -..-..|+.+....|++..++.+.++
T Consensus         5 EvA~~~gVs~~tLR~ye~~~gli~p~r~~--~g~R~Yt~~d---------i~~l~~I~~llr~~G~~l~~i~~~l~   69 (99)
T cd04765           5 EVAEILGLPPHVLRYWETEFPQLKPVKRA--GGRRYYRPKD---------VELLLLIKHLLYEKGYTIEGAKQALK   69 (99)
T ss_pred             HHHHHHCcCHHHHHHHHHHcCCCCCcCCC--CCCeeeCHHH---------HHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence            579999999999999974  444322211  1112222111         11223344444568899988888665

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.

>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial

Probab=87.34  E-value=1.5  Score=32.11  Aligned_cols=24  Identities=17%  Similarity=0.242  Sum_probs=21.0

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           94 KKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        94 ~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ..+||.|||..+|+++.+|++..+
T Consensus       142 ~~~t~~~iA~~lG~tretvsR~l~  165 (193)
T TIGR03697       142 LRLSHQAIAEAIGSTRVTITRLLG  165 (193)
T ss_pred             CCCCHHHHHHHhCCcHHHHHHHHH
Confidence            348999999999999999999653

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.

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

Probab=87.30  E-value=0.97  Score=25.59  Aligned_cols=27  Identities=19%  Similarity=0.212  Sum_probs=20.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 032366           94 KKLTQSQLAQLINEKPQVIQEYESGKA  120 (142)
Q Consensus        94 ~glTQ~eLA~~lgis~stIs~~E~G~~  120 (142)
                      .+++..++|..+|+|++++.+..+-..
T Consensus         7 ~~~~l~~iA~~~g~S~~~f~r~Fk~~~   33 (42)
T PF00165_consen    7 QKLTLEDIAEQAGFSPSYFSRLFKKET   33 (42)
T ss_dssp             SS--HHHHHHHHTS-HHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            468999999999999999999876443

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=87.30  E-value=1.7  Score=25.65  Aligned_cols=22  Identities=23%  Similarity=0.308  Sum_probs=19.1

Q ss_pred             CC-CHHHHHHHhCCCHHHHHHHH
Q 032366           95 KL-TQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        95 gl-TQ~eLA~~lgis~stIs~~E  116 (142)
                      .+ |+.+||+.+|+|+++|.+..
T Consensus        19 ~l~s~~~la~~~~vs~~tv~~~l   41 (60)
T smart00345       19 KLPSERELAAQLGVSRTTVREAL   41 (60)
T ss_pred             cCcCHHHHHHHHCCCHHHHHHHH
Confidence            35 89999999999999998754

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

Probab=87.25  E-value=0.97  Score=30.09  Aligned_cols=22  Identities=32%  Similarity=0.394  Sum_probs=20.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +|..++|+.+|||++||..||.
T Consensus         2 ~~i~e~A~~~gvs~~tLr~ye~   23 (91)
T cd04766           2 YVISVAAELSGMHPQTLRLYER   23 (91)
T ss_pred             cCHHHHHHHHCcCHHHHHHHHH
Confidence            5788999999999999999996

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.

>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis

Probab=87.23  E-value=1.1  Score=27.96  Aligned_cols=34  Identities=9%  Similarity=0.057  Sum_probs=27.6

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .+.+..+...-.+|..++|+.+|+++++++++.+
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            3445556678889999999999999999988753

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.

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

Probab=87.19  E-value=1  Score=31.22  Aligned_cols=22  Identities=18%  Similarity=0.268  Sum_probs=20.4

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +|..++|+.+|||++||..||+
T Consensus         1 ~~i~e~a~~~gvs~~tlr~ye~   22 (113)
T cd01109           1 YTIKEVAEKTGLSADTLRYYEK   22 (113)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5788999999999999999996

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.

>cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily

Probab=87.18  E-value=1  Score=32.42  Aligned_cols=22  Identities=23%  Similarity=0.268  Sum_probs=20.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      |+..|||+.+|||..||.-||+
T Consensus         1 m~Ige~a~~~gvs~~tLRyYE~   22 (131)
T cd04786           1 MKIGELAKRSGMAASRIRFYEA   22 (131)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5788999999999999999996

Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic su

>PRK11512 DNA-binding transcriptional repressor MarR; Provisional

Probab=87.16  E-value=1.9  Score=30.88  Aligned_cols=36  Identities=11%  Similarity=0.123  Sum_probs=27.8

Q ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           81 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        81 ~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ..-...|..+...-++||.+||+.++++++++++..
T Consensus        40 ~~q~~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l   75 (144)
T PRK11512         40 AAQFKVLCSIRCAACITPVELKKVLSVDLGALTRML   75 (144)
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHH
Confidence            333444555556678999999999999999998764

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

Probab=87.12  E-value=0.96  Score=26.37  Aligned_cols=25  Identities=8%  Similarity=0.169  Sum_probs=22.7

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           93 DKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        93 ~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ..|+|..++|+.+|+|.++|..+-.
T Consensus        13 ~~~~s~~eia~~l~~s~~tv~~~~~   37 (57)
T cd06170          13 AEGKTNKEIADILGISEKTVKTHLR   37 (57)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            4789999999999999999998864

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

>PRK15043 transcriptional regulator MirA; Provisional

Probab=87.09  E-value=0.94  Score=36.15  Aligned_cols=23  Identities=17%  Similarity=0.326  Sum_probs=21.1

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 032366           95 KLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        95 glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      -+|..++|+.+|||+.||..||+
T Consensus         3 ~ytIgeVA~~~GVs~~TLR~wEr   25 (243)
T PRK15043          3 LYTIGEVALLCDINPVTLRAWQR   25 (243)
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHH
Confidence            37899999999999999999983

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

Probab=87.04  E-value=1.1  Score=30.52  Aligned_cols=22  Identities=27%  Similarity=0.454  Sum_probs=20.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +|..++|+.+|||+++|..||+
T Consensus         2 ~~i~eva~~~gVs~~tLR~ye~   23 (98)
T cd01279           2 YPISVAAELLGIHPQTLRVYDR   23 (98)
T ss_pred             cCHHHHHHHHCcCHHHHHHHHH
Confidence            5788999999999999999986

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.

>PF13730 HTH_36: Helix-turn-helix domain

Probab=87.03  E-value=0.83  Score=27.20  Aligned_cols=21  Identities=19%  Similarity=0.188  Sum_probs=19.3

Q ss_pred             CHHHHHHHhCCCHHHHHHHHc
Q 032366           97 TQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        97 TQ~eLA~~lgis~stIs~~E~  117 (142)
                      |++.||+.+|+|+.||.++.+
T Consensus        27 S~~~la~~~g~s~~Tv~~~i~   47 (55)
T PF13730_consen   27 SQETLAKDLGVSRRTVQRAIK   47 (55)
T ss_pred             CHHHHHHHHCcCHHHHHHHHH
Confidence            899999999999999998754

>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481

Probab=86.99  E-value=2.9  Score=28.13  Aligned_cols=32  Identities=6%  Similarity=0.056  Sum_probs=26.6

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           86 AIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        86 ~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .|-..-.+.|++..++|+..|||..|..+|..
T Consensus        16 ~lv~~vv~~g~~~a~aA~~~gVS~~Ta~kW~~   47 (85)
T PF13011_consen   16 RLVRRVVEQGWPVAHAAAEFGVSRRTAYKWLA   47 (85)
T ss_pred             HHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHH
Confidence            34444557899999999999999999999974

>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR

Probab=86.99  E-value=1.1  Score=31.66  Aligned_cols=30  Identities=13%  Similarity=0.199  Sum_probs=24.7

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHH
Q 032366           84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQ  113 (142)
Q Consensus        84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs  113 (142)
                      .+.+-.++.-.|+|.+|+|+.+|+|.+||.
T Consensus       112 ~r~v~~l~~~~~~s~~EIA~~l~is~~tV~  141 (142)
T TIGR03209       112 QKKIIYMKFFEDMKEIDIAKKLHISRQSVY  141 (142)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCcCHHhhc
Confidence            344555667789999999999999999985

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.

>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=86.96  E-value=1.2  Score=27.38  Aligned_cols=30  Identities=13%  Similarity=0.113  Sum_probs=24.1

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHH
Q 032366           86 AIVQARNDKKLTQSQLAQLINEKPQVIQEY  115 (142)
Q Consensus        86 ~Lk~~R~~~glTQ~eLA~~lgis~stIs~~  115 (142)
                      .|+.+....++|..+||+.+|+++++++.-
T Consensus        15 Il~~L~~~~~~t~~ela~~l~~~~~t~s~h   44 (61)
T PF12840_consen   15 ILRLLASNGPMTVSELAEELGISQSTVSYH   44 (61)
T ss_dssp             HHHHHHHCSTBEHHHHHHHHTS-HHHHHHH
T ss_pred             HHHHHhcCCCCCHHHHHHHHCCCHHHHHHH
Confidence            344556888999999999999999998864

...

>smart00354 HTH_LACI helix_turn _helix lactose operon repressor

Probab=86.91  E-value=2.4  Score=26.84  Aligned_cols=50  Identities=22%  Similarity=0.348  Sum_probs=34.8

Q ss_pred             HHHHHHcCCChhHHHhhhcCCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHh
Q 032366           32 VNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLI  105 (142)
Q Consensus        32 ~~~a~r~G~~v~t~kk~~~g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~l  105 (142)
                      -+.|+++|++..|+.++..|...                        +.++..++|.+.-.+.|+.....+..+
T Consensus         4 ~~iA~~~gvS~~TVSr~ln~~~~------------------------v~~~t~~~i~~~~~~~gy~~~~~~~~~   53 (70)
T smart00354        4 KDVARLAGVSKATVSRVLNGNGR------------------------VSEETREKVLAAMEELGYIPNRVARSL   53 (70)
T ss_pred             HHHHHHHCCCHHHHHHHHCCCCC------------------------CCHHHHHHHHHHHHHhCCCCCHHHHHH
Confidence            35799999999999998876543                        234466667777777777655555443

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

Probab=86.90  E-value=1.1  Score=31.13  Aligned_cols=22  Identities=18%  Similarity=0.255  Sum_probs=20.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      |+..|+|+.+|||.+||..||+
T Consensus         1 m~i~eva~~~gvs~~tlR~Ye~   22 (112)
T cd01282           1 MRIGELAARTGVSVRSLRYYEE   22 (112)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHH
Confidence            5788999999999999999996

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.

>PRK13413 mpi multiple promoter invertase; Provisional

Probab=86.80  E-value=1.3  Score=33.50  Aligned_cols=32  Identities=16%  Similarity=0.221  Sum_probs=26.4

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 032366           86 AIVQARNDKKLTQSQLAQLINEKPQVIQEYESG  118 (142)
Q Consensus        86 ~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G  118 (142)
                      .+..+ ...|+|..++|+.+|||++||.+|.+.
T Consensus       164 ~i~~~-~~~g~s~~~iak~lgis~~Tv~r~~k~  195 (200)
T PRK13413        164 KIKKL-LDKGTSKSEIARKLGVSRTTLARFLKT  195 (200)
T ss_pred             HHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHh
Confidence            44444 356999999999999999999999864

>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators

Probab=86.76  E-value=3.1  Score=29.66  Aligned_cols=68  Identities=21%  Similarity=0.111  Sum_probs=43.3

Q ss_pred             HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHH
Q 032366           33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQV  111 (142)
Q Consensus        33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~st  111 (142)
                      ..|++.|++..|++-|+. |-..+...   ..-+.++.         .....-+.|+.++.+.|++..++...+..-+.-
T Consensus         6 eVA~~~GVs~~TLR~wE~~GLl~p~r~---~G~R~Ys~---------~dv~rL~~I~~L~~e~G~~l~eI~~~L~l~~~~   73 (120)
T cd04767           6 VVAELLNIHPETLRIWERHGLIKPARR---NGQRLYSN---------NDLKRLRFIKKLINEKGLNIAGVKQILSMYPCW   73 (120)
T ss_pred             HHHHHHCcCHHHHHHHHHCCCCCCcCC---CCcEEECH---------HHHHHHHHHHHHHHHcCCCHHHHHHHHHhCccc
Confidence            478899999999999976 44432110   11111111         122345667888888999999999887654333


Q ss_pred             H
Q 032366          112 I  112 (142)
Q Consensus       112 I  112 (142)
                      .
T Consensus        74 ~   74 (120)
T cd04767          74 S   74 (120)
T ss_pred             c
Confidence            3

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

>PRK08215 sporulation sigma factor SigG; Reviewed

Probab=86.69  E-value=1.3  Score=34.83  Aligned_cols=29  Identities=21%  Similarity=0.126  Sum_probs=25.0

Q ss_pred             HHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           89 QARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        89 ~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .+|--.|+|+.++|+.+|+|+++|+++++
T Consensus       219 ~~~~~~~~t~~eIA~~lgis~~~V~~~~~  247 (258)
T PRK08215        219 NLRFFQGKTQMEVAEEIGISQAQVSRLEK  247 (258)
T ss_pred             HHHHhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            33445699999999999999999999975

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

Probab=86.51  E-value=1.2  Score=30.86  Aligned_cols=22  Identities=23%  Similarity=0.241  Sum_probs=20.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +|..|+|+.+|||..||..||+
T Consensus         1 y~Ige~A~~~gvs~~tlR~ye~   22 (107)
T cd01111           1 YSISQLALDAGVSVHIVRDYLL   22 (107)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            4778999999999999999996

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,

>PRK05572 sporulation sigma factor SigF; Validated

Probab=86.40  E-value=1.4  Score=34.59  Aligned_cols=30  Identities=23%  Similarity=0.155  Sum_probs=25.4

Q ss_pred             HHHHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 032366           89 QARNDKKLTQSQLAQLINEKPQVIQEYESG  118 (142)
Q Consensus        89 ~~R~~~glTQ~eLA~~lgis~stIs~~E~G  118 (142)
                      .++-..|+|++++|+.+|+|+++|+++++.
T Consensus       212 ~l~~~~~~s~~eIA~~lgis~~~V~~~~~r  241 (252)
T PRK05572        212 YLRYFKDKTQSEVAKRLGISQVQVSRLEKK  241 (252)
T ss_pred             HHHHhCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            334457999999999999999999999863

>PRK11169 leucine-responsive transcriptional regulator; Provisional

Probab=86.23  E-value=1.1  Score=33.12  Aligned_cols=31  Identities=13%  Similarity=0.324  Sum_probs=26.3

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHH
Q 032366           84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQE  114 (142)
Q Consensus        84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~  114 (142)
                      .+.|..+...-.+|..+||+.+|+|++++.+
T Consensus        17 ~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~   47 (164)
T PRK11169         17 RNILNELQKDGRISNVELSKRVGLSPTPCLE   47 (164)
T ss_pred             HHHHHHhccCCCCCHHHHHHHHCcCHHHHHH
Confidence            3456777888899999999999999998765

>COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]

Probab=86.22  E-value=0.9  Score=35.19  Aligned_cols=48  Identities=15%  Similarity=0.115  Sum_probs=43.2

Q ss_pred             HHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCC
Q 032366           89 QARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVK  137 (142)
Q Consensus        89 ~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvs  137 (142)
                      +.+++.+.++.++++..|+++ ++..|.++-..++...+....++|+.+
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            467788899999999999999 999999999999999999999988764

>COG2973 TrpR Trp operon repressor [Transcription]

Probab=86.20  E-value=2.4  Score=29.38  Aligned_cols=55  Identities=16%  Similarity=0.137  Sum_probs=36.7

Q ss_pred             hHHHHHHHHHH--HHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHh
Q 032366           80 PSELKKAIVQA--RNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERAL  134 (142)
Q Consensus        80 ~~~~g~~Lk~~--R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~L  134 (142)
                      ...++.|++-.  ..+..+||.|++..+|+|-.+|.+=-|.-...+++.-.-|.+.|
T Consensus        43 Real~~Rv~Iv~eLL~ge~sQREi~~~LgvsiAtITRGSN~LK~~~~~~k~~L~~~l   99 (103)
T COG2973          43 REALGTRVRIVEELLRGELSQREIAQKLGVSIATITRGSNSLKTADPEFKQWLEKVL   99 (103)
T ss_pred             HHHHHHHHHHHHHHHhccccHHHHHHHhCcchhhhccchhhhccCCHHHHHHHHHHh
Confidence            34567666544  45568999999999999988887744333333555555555544

>TIGR02044 CueR Cu(I)-responsive transcriptional regulator

Probab=86.19  E-value=1.2  Score=31.58  Aligned_cols=22  Identities=27%  Similarity=0.443  Sum_probs=20.6

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      |+..|+|+.+|||..||.-||.
T Consensus         1 m~I~e~a~~~gvs~~tlRyYe~   22 (127)
T TIGR02044         1 MNIGQVAKLTGLSSKMIRYYEE   22 (127)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5788999999999999999997

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.

>TIGR00122 birA_repr_reg BirA biotin operon repressor domain

Probab=86.10  E-value=2.1  Score=26.82  Aligned_cols=27  Identities=7%  Similarity=0.155  Sum_probs=22.2

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           91 RNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        91 R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ..+..++..+||+.+|+|+++|++.-+
T Consensus         9 L~~~~~~~~eLa~~l~vS~~tv~~~l~   35 (69)
T TIGR00122         9 LADNPFSGEKLGEALGMSRTAVNKHIQ   35 (69)
T ss_pred             HHcCCcCHHHHHHHHCCCHHHHHHHHH
Confidence            345568899999999999999988653

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.

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

Probab=86.03  E-value=1.7  Score=30.48  Aligned_cols=37  Identities=5%  Similarity=0.102  Sum_probs=30.4

Q ss_pred             hHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           80 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +.+|.+++-...+. |.|..++|...+||.+||.+|.+
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            34577777665554 88999999999999999999965

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 [].

>COG1318 Predicted transcriptional regulators [Transcription]

Probab=85.98  E-value=1.2  Score=33.92  Aligned_cols=33  Identities=21%  Similarity=0.301  Sum_probs=30.2

Q ss_pred             HHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCC
Q 032366           89 QARNDKKLTQSQLAQLINEKPQVIQEYESGKAI  121 (142)
Q Consensus        89 ~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~  121 (142)
                      -+|...|+|..++|+.+|.+.+||.++..|...
T Consensus        55 ~arekag~Ti~EIAeelG~TeqTir~hlkgetk   87 (182)
T COG1318          55 LAREKAGMTISEIAEELGRTEQTVRNHLKGETK   87 (182)
T ss_pred             HHHHHccCcHHHHHHHhCCCHHHHHHHHhcchh
Confidence            457999999999999999999999999998764

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

Probab=85.93  E-value=6.5  Score=26.40  Aligned_cols=65  Identities=15%  Similarity=0.235  Sum_probs=38.5

Q ss_pred             HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhCCC
Q 032366           33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEK  108 (142)
Q Consensus        33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis  108 (142)
                      +.|++.|+++.|++-|+. |-..|.... .-.-..++.+         ....-..|+.+|. .|++.+++...++..
T Consensus         5 eva~~~gvs~~tlR~ye~~Gll~p~~r~-~~gyR~Y~~~---------~l~~l~~I~~lr~-~G~~l~eI~~~l~~~   70 (96)
T cd04788           5 ELARRTGLSVRTLHHYDHIGLLSPSQRT-EGGHRLYDRA---------DIRRLHQIIALRR-LGFSLREIGRALDGP   70 (96)
T ss_pred             HHHHHHCcCHHHHHHHHHCCCCCCCccC-CCCceeeCHH---------HHHHHHHHHHHHH-cCCCHHHHHHHHhCC
Confidence            479999999999999997 333321110 0111222211         1113344556654 799999999988654

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.

>PRK00215 LexA repressor; Validated

Probab=85.93  E-value=1.8  Score=32.78  Aligned_cols=35  Identities=14%  Similarity=0.182  Sum_probs=26.4

Q ss_pred             HHHHHHHHHHH--hCCCCHHHHHHHhCC-CHHHHHHHH
Q 032366           82 ELKKAIVQARN--DKKLTQSQLAQLINE-KPQVIQEYE  116 (142)
Q Consensus        82 ~~g~~Lk~~R~--~~glTQ~eLA~~lgi-s~stIs~~E  116 (142)
                      .+-..|.+.+.  ...+|+.|||+.+|+ ++++++++.
T Consensus         8 ~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l   45 (205)
T PRK00215          8 EILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHL   45 (205)
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHH
Confidence            34555665444  445699999999999 999999983

>PRK12427 flagellar biosynthesis sigma factor; Provisional

Probab=85.88  E-value=1.6  Score=34.08  Aligned_cols=29  Identities=7%  Similarity=0.155  Sum_probs=24.9

Q ss_pred             HHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           89 QARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        89 ~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .+|-..|+|++++|+.+|+|.+.|+++++
T Consensus       193 ~l~~~~~~t~~EIA~~lgis~~~V~q~~~  221 (231)
T PRK12427        193 HLYYQHEMSLKEIALVLDLTEARICQLNK  221 (231)
T ss_pred             HHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            34445699999999999999999999875

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

Probab=85.84  E-value=1.3  Score=31.06  Aligned_cols=22  Identities=18%  Similarity=0.273  Sum_probs=20.7

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ||..|+|+.+|||..||.-||+
T Consensus         1 m~IgevA~~~gvs~~tlRyYe~   22 (120)
T cd04781           1 LDIAEVARQSGLPASTLRYYEE   22 (120)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5789999999999999999997

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

>PRK06759 RNA polymerase factor sigma-70; Validated

Probab=85.68  E-value=1.9  Score=30.64  Aligned_cols=33  Identities=15%  Similarity=-0.089  Sum_probs=26.6

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +.+-.++--.|+|..|+|+.+|+|.++|..+..
T Consensus       112 r~ii~l~~~~~~s~~EIA~~l~is~~tV~~~~~  144 (154)
T PRK06759        112 KYIIFERFFVGKTMGEIALETEMTYYQVRWIYR  144 (154)
T ss_pred             HHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            334445566799999999999999999998753

>PF13309 HTH_22: HTH domain

Probab=85.67  E-value=2.5  Score=26.60  Aligned_cols=21  Identities=10%  Similarity=0.121  Sum_probs=18.5

Q ss_pred             CHHHHHHHhCCCHHHHHHHHc
Q 032366           97 TQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        97 TQ~eLA~~lgis~stIs~~E~  117 (142)
                      +-..+|+.+|||+.||.+|.+
T Consensus        44 av~~vA~~L~iS~~TVY~YLr   64 (64)
T PF13309_consen   44 AVEYVAEKLGISRATVYRYLR   64 (64)
T ss_pred             HHHHHHHHHCCCHHHHHHHcC
Confidence            677899999999999999853

>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor

Probab=85.64  E-value=0.27  Score=42.14  Aligned_cols=42  Identities=14%  Similarity=0.112  Sum_probs=34.2

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCC
Q 032366           95 KLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGV  136 (142)
Q Consensus        95 glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgv  136 (142)
                      =||++++|+.+|++.||||+.-+|+..-++.-+.-|-.+|.-
T Consensus       318 PLtlkdiA~~lglheSTVSRav~~Kyi~tp~Gi~~lk~FFs~  359 (429)
T TIGR02395       318 PLTLREVAEELGLHESTISRAINNKYLQTPRGVFELKYFFSR  359 (429)
T ss_pred             CCcHHHHHHHhCCCccchhhhhcCceEecCCceEEHHHhcCC
Confidence            489999999999999999999999976665555566666654

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

>TIGR01636 phage_rinA phage transcriptional activator, RinA family

Probab=85.56  E-value=3.9  Score=29.28  Aligned_cols=35  Identities=23%  Similarity=0.264  Sum_probs=30.0

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCC
Q 032366           95 KLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGV  136 (142)
Q Consensus        95 glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgv  136 (142)
                      .+|..++|..+|+|.+++.++.+       ..+.+||..||.
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            36999999999999999999864       568888888873

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.

>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1

Probab=85.55  E-value=1.4  Score=34.67  Aligned_cols=55  Identities=5%  Similarity=0.137  Sum_probs=38.5

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc-CCCCCCHHHHHHHHHHhCCCCC
Q 032366           85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES-GKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~-G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      +.+-.++.-.|+|.+|+|+.+|||.+||..... +........-..++.-|++...
T Consensus       167 R~v~~L~~~eg~S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~~~~~~~~~~~~~  222 (244)
T TIGR03001       167 RHLLRLHFVDGLSMDRIGAMYQVHRSTVSRWVAQARERLLERTRRRLAERLKLSSP  222 (244)
T ss_pred             HHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcc
Confidence            334445566899999999999999999987764 4444455555666666665443

This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.

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

Probab=85.53  E-value=4.9  Score=27.19  Aligned_cols=64  Identities=19%  Similarity=0.220  Sum_probs=39.9

Q ss_pred             HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhCC
Q 032366           33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINE  107 (142)
Q Consensus        33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgi  107 (142)
                      +.|++.|++..|++.|+. |-..|...  ...-..++.         .....-..|+.++...|++..++...+..
T Consensus         6 eva~~~gVs~~tLR~ye~~Gli~p~r~--~~g~R~Ys~---------~dv~~l~~I~~L~~~~G~~l~~i~~~l~l   70 (98)
T cd01279           6 VAAELLGIHPQTLRVYDRLGLVSPART--NGGGRRYSN---------NDLELLRQVQRLSQDEGFNLAGIKRIIEL   70 (98)
T ss_pred             HHHHHHCcCHHHHHHHHHCCCCCCCcC--CCCCeeECH---------HHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence            578999999999999976 32222110  001111111         11224556777788899999999988755

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.

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

Probab=85.43  E-value=0.97  Score=31.94  Aligned_cols=22  Identities=27%  Similarity=0.363  Sum_probs=20.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      |+..|+|+.+|||..||..||.
T Consensus         1 m~I~e~a~~~gvs~~tlR~Ye~   22 (126)
T cd04783           1 LTIGELAKAAGVNVETIRYYQR   22 (126)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5788999999999999999996

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.

>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family

Probab=85.39  E-value=1.9  Score=31.62  Aligned_cols=32  Identities=19%  Similarity=0.202  Sum_probs=26.5

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      +.+-.++.-.|+|.+|+|+.+|+|.+||....
T Consensus       140 r~v~~l~~~~g~s~~EIA~~lgis~~tVk~~l  171 (183)
T TIGR02999       140 AEVVELRFFAGLTVEEIAELLGVSVRTVERDW  171 (183)
T ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Confidence            34455567789999999999999999998765

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.

>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=85.27  E-value=0.94  Score=27.46  Aligned_cols=26  Identities=4%  Similarity=0.161  Sum_probs=21.8

Q ss_pred             HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           92 NDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        92 ~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ...|++..++|+.+|+|+.||..+-+
T Consensus        15 l~~G~~~~eIA~~l~is~~tV~~~~~   40 (58)
T PF00196_consen   15 LAQGMSNKEIAEELGISEKTVKSHRR   40 (58)
T ss_dssp             HHTTS-HHHHHHHHTSHHHHHHHHHH
T ss_pred             HHhcCCcchhHHhcCcchhhHHHHHH
Confidence            45799999999999999999988753

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 ....

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=85.22  E-value=1.7  Score=34.17  Aligned_cols=28  Identities=21%  Similarity=0.125  Sum_probs=24.4

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           90 ARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        90 ~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +|--.|+|++++|+.+|+|+.+|+++++
T Consensus       217 ~~~~~~~t~~eIA~~lgis~~~V~~~~~  244 (254)
T TIGR02850       217 MRFFEGKTQMEVAEEIGISQAQVSRLEK  244 (254)
T ss_pred             HHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3444699999999999999999999985

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.

>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=85.21  E-value=4.2  Score=23.49  Aligned_cols=32  Identities=6%  Similarity=0.102  Sum_probs=25.7

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           86 AIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        86 ~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .+-..+--.++|..++|+++|+|++++.++-.
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            34445556789999999999999999998754

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 ....

>TIGR02392 rpoH_proteo alternative sigma factor RpoH

Probab=85.19  E-value=1.6  Score=34.72  Aligned_cols=24  Identities=29%  Similarity=0.307  Sum_probs=22.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           94 KKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        94 ~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .++|++++|+.+|||+.+|+++++
T Consensus       235 ~~~t~~eIA~~lgvS~~~V~q~~~  258 (270)
T TIGR02392       235 DKLTLQELAAEYGVSAERIRQIEK  258 (270)
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHH
Confidence            379999999999999999999985

A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.

>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators

Probab=85.19  E-value=1.2  Score=31.50  Aligned_cols=22  Identities=23%  Similarity=0.382  Sum_probs=20.6

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ||..|+|+.+|||..||.-||+
T Consensus         1 m~I~e~a~~~gvs~~tlRyYe~   22 (127)
T cd01108           1 MNIGEAAKLTGLSAKMIRYYEE   22 (127)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5788999999999999999996

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

>PRK07037 extracytoplasmic-function sigma-70 factor; Validated

Probab=84.83  E-value=2.1  Score=30.68  Aligned_cols=30  Identities=13%  Similarity=0.107  Sum_probs=25.0

Q ss_pred             HHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           87 IVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      +-.++--.|+|.+|+|+.+|+|.++|....
T Consensus       117 v~~l~~~~~~s~~EIA~~lgis~~tV~~~l  146 (163)
T PRK07037        117 AFEMYRLHGETQKDIARELGVSPTLVNFMI  146 (163)
T ss_pred             HHHHHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence            334556679999999999999999999863

>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases []

Probab=84.77  E-value=1.3  Score=24.52  Aligned_cols=19  Identities=16%  Similarity=0.295  Sum_probs=17.5

Q ss_pred             CHHHHHHHhCCCHHHHHHH
Q 032366           97 TQSQLAQLINEKPQVIQEY  115 (142)
Q Consensus        97 TQ~eLA~~lgis~stIs~~  115 (142)
                      |..+.|+.+|+++++|+++
T Consensus        18 Si~eAa~~l~i~~~~I~~~   36 (37)
T PF07453_consen   18 SIREAARYLGISHSTISKY   36 (37)
T ss_pred             CHHHHHHHhCCCHHHHHHh
Confidence            7889999999999999876

>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1

Probab=84.72  E-value=2.2  Score=30.04  Aligned_cols=29  Identities=7%  Similarity=-0.044  Sum_probs=24.6

Q ss_pred             HHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           89 QARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        89 ~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .++--.|+|..|+|+.+|+|+++|.....
T Consensus       123 ~l~~~~~~~~~eIA~~lgis~~tv~~~~~  151 (161)
T TIGR02985       123 ILSRFEGKSYKEIAEELGISVKTVEYHIS  151 (161)
T ss_pred             HHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            34556799999999999999999988753

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.

>PRK12469 RNA polymerase factor sigma-54; Provisional

Probab=84.65  E-value=0.45  Score=41.46  Aligned_cols=44  Identities=14%  Similarity=0.118  Sum_probs=36.6

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 032366           95 KLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL  138 (142)
Q Consensus        95 glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl  138 (142)
                      =|+.+++|+.+|++.||||+.-+++..-++.-+..|-.+|.-.+
T Consensus       369 PLtlkdVAe~lglHeSTVSRa~~~KY~~tp~GifeLK~FFs~~v  412 (481)
T PRK12469        369 PLVLRDVAEELGLHESTISRATGNKYMATPRGTFEFKHFFPRKL  412 (481)
T ss_pred             CCcHHHHHHHhCCCcchhhHHhcCceeecCCceEeHHHhhcccc
Confidence            58999999999999999999999998777666666767776444

>PRK10840 transcriptional regulator RcsB; Provisional

Probab=84.51  E-value=2.9  Score=31.29  Aligned_cols=49  Identities=14%  Similarity=0.207  Sum_probs=32.1

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHcC---C-CCCCHHHHHHHHHHhCCCCCCC
Q 032366           93 DKKLTQSQLAQLINEKPQVIQEYESG---K-AIPNQQILTKLERALGVKLRGK  141 (142)
Q Consensus        93 ~~glTQ~eLA~~lgis~stIs~~E~G---~-~~p~~~~l~kLa~~Lgvsl~e~  141 (142)
                      ..|+|.+|+|+.+++|..||..+-+.   + ...+...+..++.-.-.++-+|
T Consensus       163 ~~G~s~~eIA~~l~iS~~TV~~h~~~i~~Kl~v~~~~~l~~~~~~~~~~~~~~  215 (216)
T PRK10840        163 AEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIALLNYLSSVTLSPADK  215 (216)
T ss_pred             HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCCCHHHHHHHHHHhcCCcccC
Confidence            47999999999999999999888742   1 2224333434443334454444

>PRK09526 lacI lac repressor; Reviewed

Probab=84.41  E-value=2.1  Score=34.19  Aligned_cols=50  Identities=20%  Similarity=0.294  Sum_probs=33.3

Q ss_pred             HHHHHHHcCCChhHHHhhhcCCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHH
Q 032366           31 VVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQL  104 (142)
Q Consensus        31 ~~~~a~r~G~~v~t~kk~~~g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~  104 (142)
                      --.-|+++|++++|+.+..+|...                        +.++..++|.+.-+++|+.....|+.
T Consensus         8 i~dIA~~aGVS~~TVSrvLn~~~~------------------------vs~~tr~rV~~~a~elgY~pn~~a~~   57 (342)
T PRK09526          8 LYDVARYAGVSYQTVSRVLNQASH------------------------VSAKTREKVEAAMAELNYVPNRVAQQ   57 (342)
T ss_pred             HHHHHHHhCCCHHHHHHHhcCCCC------------------------CCHHHHHHHHHHHHHHCCCcCHHHHH
Confidence            346799999999999999876432                        33445555666666666655555543

>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily

Probab=84.41  E-value=1.7  Score=29.80  Aligned_cols=22  Identities=14%  Similarity=0.214  Sum_probs=20.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      |+..+||+.+|+|..||.-||+
T Consensus         1 m~Ige~a~~~gvs~~tlRyYe~   22 (107)
T cd04777           1 MKIGKFAKKNNITIDTVRHYID   22 (107)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5788999999999999999996

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.

>PRK11924 RNA polymerase sigma factor; Provisional

Probab=84.25  E-value=2  Score=30.85  Aligned_cols=28  Identities=11%  Similarity=0.147  Sum_probs=24.2

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           90 ARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        90 ~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ++...|+++.++|+.+|+|+++|..+..
T Consensus       136 l~~~~~~~~~eIA~~lgis~~tv~~~~~  163 (179)
T PRK11924        136 LRYVEGLSYREIAEILGVPVGTVKSRLR  163 (179)
T ss_pred             HHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            3445799999999999999999998864

>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain

Probab=84.20  E-value=1.9  Score=33.48  Aligned_cols=25  Identities=20%  Similarity=0.244  Sum_probs=23.2

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           93 DKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        93 ~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ..++|++++|+.+|+|.++|++++.
T Consensus       194 ~~~~t~~EIA~~lgis~~~V~q~~~  218 (238)
T TIGR02393       194 GRPHTLEEVGKEFNVTRERIRQIES  218 (238)
T ss_pred             CCCccHHHHHHHHCCCHHHHHHHHH
Confidence            4689999999999999999999986

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.

>PRK13832 plasmid partitioning protein; Provisional

Probab=84.19  E-value=3.2  Score=36.56  Aligned_cols=49  Identities=14%  Similarity=0.049  Sum_probs=35.1

Q ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHH
Q 032366           81 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLE  131 (142)
Q Consensus        81 ~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa  131 (142)
                      .+..+.++.+. +.|+|+.++|+.+|+|+++|+++-.= ...++.++..++
T Consensus       105 iEea~AfkrLi-e~G~T~EeIA~~lG~S~~~V~rlllL-A~L~P~lLdal~  153 (520)
T PRK13832        105 VDQWRAIERLV-ALGWTEEAIAVALALPVRQIRKLRLL-ANVLPAMLDHMA  153 (520)
T ss_pred             HHHHHHHHHHH-hcCCCHHHHHHHHCCCHHHHHHHHHH-cCCCHHHHHHHH
Confidence            34566677776 79999999999999999999996542 123445554443

>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=84.16  E-value=0.93  Score=26.77  Aligned_cols=25  Identities=16%  Similarity=0.258  Sum_probs=20.3

Q ss_pred             HHHHHHHHcCCChhHHHhhhcCCCC
Q 032366           30 KVVNAARRAGADIETVRKSHAGTNK   54 (142)
Q Consensus        30 ~~~~~a~r~G~~v~t~kk~~~g~~~   54 (142)
                      ++-..|.+.|++..|+.+|+.|...
T Consensus        11 s~~~la~~~gis~~~i~~~~~g~~~   35 (55)
T PF01381_consen   11 SQKELAEKLGISRSTISRIENGKRN   35 (55)
T ss_dssp             -HHHHHHHHTS-HHHHHHHHTTSST
T ss_pred             CHHHHHHHhCCCcchhHHHhcCCCC
Confidence            4567899999999999999999665

; 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 ....

>PRK05932 RNA polymerase factor sigma-54; Reviewed

Probab=84.14  E-value=0.49  Score=40.89  Aligned_cols=43  Identities=12%  Similarity=0.139  Sum_probs=34.0

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCC
Q 032366           95 KLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVK  137 (142)
Q Consensus        95 glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvs  137 (142)
                      =||++++|+.+|++.||||+.-+|+..-++.-+.-|-.+|.-.
T Consensus       343 PLtlkdvAe~lglheSTVSRav~~Kyv~tp~Gi~~lk~FFs~~  385 (455)
T PRK05932        343 PLVLKDIAEELGMHESTISRATTNKYMATPRGIFELKYFFSSA  385 (455)
T ss_pred             CccHHHHHHHhCCCccchhhhhcCceeecCCceEEHHHhcccc
Confidence            4899999999999999999999999766555555555555433

>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators

Probab=84.13  E-value=1.7  Score=31.00  Aligned_cols=22  Identities=23%  Similarity=0.454  Sum_probs=20.6

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ++..++|+.+||+++||..||+
T Consensus         2 ysI~eVA~~~GVs~~TLR~wE~   23 (120)
T cd04767           2 YPIGVVAELLNIHPETLRIWER   23 (120)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            6789999999999999999986

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

>TIGR02054 MerD mercuric resistence transcriptional repressor protein MerD

Probab=84.11  E-value=1.9  Score=30.60  Aligned_cols=23  Identities=26%  Similarity=0.274  Sum_probs=21.7

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 032366           95 KLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        95 glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .+|..|||+.+|+|..||.-||+
T Consensus         3 ~~tI~elA~~~gvs~~tlR~Ye~   25 (120)
T TIGR02054         3 AYTISRLAEDAGVSVHVVRDYLL   25 (120)
T ss_pred             CCcHHHHHHHHCcCHHHHHHHHH
Confidence            58999999999999999999996

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.

>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional

Probab=83.89  E-value=2.3  Score=32.46  Aligned_cols=22  Identities=9%  Similarity=0.220  Sum_probs=20.2

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHH
Q 032366           95 KLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        95 glTQ~eLA~~lgis~stIs~~E  116 (142)
                      .+||++||..+|+++.+|++..
T Consensus       184 ~lt~~~iA~~lG~sr~tvsR~l  205 (235)
T PRK11161        184 TMTRGDIGNYLGLTVETISRLL  205 (235)
T ss_pred             cccHHHHHHHhCCcHHHHHHHH
Confidence            4899999999999999999965

>PRK14987 gluconate operon transcriptional regulator; Provisional

Probab=83.88  E-value=2.2  Score=34.04  Aligned_cols=50  Identities=18%  Similarity=0.244  Sum_probs=32.8

Q ss_pred             HHHHHHHcCCChhHHHhhhcCCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHH
Q 032366           31 VVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQL  104 (142)
Q Consensus        31 ~~~~a~r~G~~v~t~kk~~~g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~  104 (142)
                      --.-|+++|++++|+.+..+|...                        +.++..+++.++-+++|+.....|+.
T Consensus         8 i~dIA~~agVS~~TVSrvLn~~~~------------------------vs~~tr~rV~~~a~elgY~pn~~a~~   57 (331)
T PRK14987          8 LQDVADRVGVTKMTVSRFLRNPEQ------------------------VSVALRGKIAAALDELGYIPNRAPDI   57 (331)
T ss_pred             HHHHHHHhCCCHHHhhhhhCCCCC------------------------CCHHHHHHHHHHHHHhCCCccHHHHH
Confidence            346899999999999998865432                        23345555666666666655555543

>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily

Probab=83.78  E-value=2.2  Score=32.63  Aligned_cols=31  Identities=19%  Similarity=0.127  Sum_probs=25.6

Q ss_pred             HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           87 IVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +-.++-..|+|++++|+.+|+|+++|..+..
T Consensus       186 vl~l~y~~~~s~~eIA~~lgis~~~v~~~~~  216 (227)
T TIGR02980       186 ILLLRFFEDKTQSEIAERLGISQMHVSRLLR  216 (227)
T ss_pred             HHHHHHhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3334455799999999999999999999865

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.

>cd01110 HTH_SoxR Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator

Probab=83.75  E-value=1.7  Score=31.40  Aligned_cols=22  Identities=18%  Similarity=0.246  Sum_probs=20.8

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ||..|+|+.+|||.+||.-||+
T Consensus         2 ~~I~EvA~~~Gvs~~tLRyYE~   23 (139)
T cd01110           2 LSVGEVAKRSGVAVSALHFYEQ   23 (139)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            6889999999999999999996

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.

>PRK09391 fixK transcriptional regulator FixK; Provisional

Probab=83.70  E-value=2.2  Score=32.83  Aligned_cols=23  Identities=4%  Similarity=0.121  Sum_probs=20.2

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHH
Q 032366           94 KKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        94 ~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ..+||++||..+|+++.++++..
T Consensus       178 i~lt~~~IA~~lGisretlsR~L  200 (230)
T PRK09391        178 LPMSRRDIADYLGLTIETVSRAL  200 (230)
T ss_pred             ecCCHHHHHHHHCCCHHHHHHHH
Confidence            34899999999999999999854

>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=83.70  E-value=1.8  Score=25.23  Aligned_cols=26  Identities=19%  Similarity=0.170  Sum_probs=21.2

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           91 RNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        91 R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      .....++..||++.+|+++++|++..
T Consensus        11 L~~~~~~~~el~~~l~~s~~~vs~hL   36 (47)
T PF01022_consen   11 LSEGPLTVSELAEELGLSQSTVSHHL   36 (47)
T ss_dssp             HTTSSEEHHHHHHHHTS-HHHHHHHH
T ss_pred             HHhCCCchhhHHHhccccchHHHHHH
Confidence            33477899999999999999999864

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 ....

>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional

Probab=83.54  E-value=2.3  Score=30.95  Aligned_cols=31  Identities=13%  Similarity=0.214  Sum_probs=25.9

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHH
Q 032366           84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQE  114 (142)
Q Consensus        84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~  114 (142)
                      .+.|..+...-..|..+||+.+|+|++++.+
T Consensus        12 ~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~   42 (153)
T PRK11179         12 RGILEALMENARTPYAELAKQFGVSPGTIHV   42 (153)
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHH
Confidence            3445777777889999999999999998865

>PRK01905 DNA-binding protein Fis; Provisional

Probab=83.54  E-value=3.2  Score=26.95  Aligned_cols=34  Identities=12%  Similarity=0.039  Sum_probs=28.7

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ...|.......+-++.+.|+.+||+++++.+.-+
T Consensus        39 ~~~i~~aL~~~~gn~s~aAr~LGIsrstL~rklk   72 (77)
T PRK01905         39 KPLLEVVMEQAGGNQSLAAEYLGINRNTLRKKLQ   72 (77)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            3457788888899999999999999999887654

>PRK13918 CRP/FNR family transcriptional regulator; Provisional

Probab=83.52  E-value=1.2  Score=33.09  Aligned_cols=23  Identities=13%  Similarity=0.130  Sum_probs=20.5

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHH
Q 032366           94 KKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        94 ~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      .-+||.+||..+|+++.+|++..
T Consensus       148 ~~~t~~~iA~~lG~tretvsR~l  170 (202)
T PRK13918        148 IYATHDELAAAVGSVRETVTKVI  170 (202)
T ss_pred             ecCCHHHHHHHhCccHHHHHHHH
Confidence            35799999999999999999865

>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional

Probab=83.43  E-value=3  Score=28.36  Aligned_cols=33  Identities=6%  Similarity=0.008  Sum_probs=28.3

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ..|.......+..+.+.|+.+|||++++.+..+
T Consensus        58 ~~i~~aL~~~~gn~s~AAr~LGIsRsTL~rKLk   90 (95)
T PRK00430         58 PLLDMVMQYTRGNQTRAALMLGINRGTLRKKLK   90 (95)
T ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence            457778888899999999999999999887654

>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=83.40  E-value=1.1  Score=28.08  Aligned_cols=32  Identities=9%  Similarity=0.114  Sum_probs=23.7

Q ss_pred             HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 032366           87 IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA  120 (142)
Q Consensus        87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~  120 (142)
                      |.+.-.+.|  |.+.|+.+||+++.|++-.+-.+
T Consensus         6 L~eyv~~~G--Q~kaA~~lGV~Q~AIsKAlr~gR   37 (59)
T PF09048_consen    6 LAEYVKEHG--QAKAARALGVTQSAISKALRAGR   37 (59)
T ss_dssp             HHHHHHHHH--HHHHHHHHTS-HHHHHHHHHCT-
T ss_pred             HHHHHHHhC--hHHHHHHcCCcHHHHHHHHHcCC
Confidence            344555566  99999999999999999887443

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 ....

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=83.38  E-value=2.9  Score=27.07  Aligned_cols=23  Identities=17%  Similarity=0.140  Sum_probs=20.9

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHH
Q 032366           94 KKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        94 ~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      .++|..++|+.+|+++++++++.
T Consensus        19 ~~~t~~~ia~~l~i~~~tv~r~l   41 (91)
T smart00346       19 GGLTLAELAERLGLSKSTAHRLL   41 (91)
T ss_pred             CCcCHHHHHHHhCCCHHHHHHHH
Confidence            47999999999999999998874

>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators

Probab=83.36  E-value=1.9  Score=30.49  Aligned_cols=22  Identities=32%  Similarity=0.401  Sum_probs=20.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ||..++|+.+|||..||..||+
T Consensus         1 ~~I~e~a~~~gvs~~tlR~Ye~   22 (126)
T cd04785           1 LSIGELARRTGVNVETIRYYES   22 (126)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5788999999999999999996

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.

>PHA01082 putative transcription regulator

Probab=83.31  E-value=0.94  Score=32.55  Aligned_cols=40  Identities=18%  Similarity=0.282  Sum_probs=33.5

Q ss_pred             HhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH-HHHHH
Q 032366           92 NDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQI-LTKLE  131 (142)
Q Consensus        92 ~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~-l~kLa  131 (142)
                      -+.|+|.+|-|+.|--|..+|.+|-.|+..|+.-. +.++-
T Consensus        27 feCgLsveeaa~LCfKsVrtVk~WD~G~~IPPeCkRLMr~~   67 (133)
T PHA01082         27 FECGLSVEEAAKLCFKTVSEVKQWDAGEKIPPICKRLMRWH   67 (133)
T ss_pred             hccCccHHHHHHHHHHhHHHHhhccCCCcCChHHHHHHHHh
Confidence            47899999999999999999999999999887542 44443

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

Probab=83.28  E-value=6  Score=27.47  Aligned_cols=63  Identities=24%  Similarity=0.308  Sum_probs=37.0

Q ss_pred             HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhCC
Q 032366           33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINE  107 (142)
Q Consensus        33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgi  107 (142)
                      +.|++.|+++.|++-|+. |-..|.... + +-+.++..+         ...-..|+.+|. .|++.+++...+..
T Consensus         5 e~a~~~gvs~~tLryYe~~GLi~p~~~~-~-~yR~Y~~~d---------~~~l~~I~~lr~-~G~sl~eI~~~l~~   68 (116)
T cd04769           5 ELAQQTGVTIKAIRLYEEKGLLPSPKRS-G-NYRVYDAQH---------VECLRFIKEARQ-LGFTLAELKAIFAG   68 (116)
T ss_pred             HHHHHHCcCHHHHHHHHHCCCCCCCCCC-C-CceeeCHHH---------HHHHHHHHHHHH-cCCCHHHHHHHHhc
Confidence            478999999999999997 444421111 1 222222211         113334555544 88998888876643

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.

>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family

Probab=83.23  E-value=2.7  Score=29.90  Aligned_cols=32  Identities=13%  Similarity=0.256  Sum_probs=25.5

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ..+-.++.-.|++.+++|+.+|+|.++|....
T Consensus       117 r~v~~l~~~~g~~~~eIA~~l~is~~tv~~~l  148 (159)
T TIGR02989       117 RELLQLRYQRGVSLTALAEQLGRTVNAVYKAL  148 (159)
T ss_pred             HHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHH
Confidence            33444466689999999999999999998653

This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=83.08  E-value=2.8  Score=28.25  Aligned_cols=30  Identities=13%  Similarity=0.358  Sum_probs=24.0

Q ss_pred             HHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           87 IVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      |..+...-.+|..+||+.+|+|++++.+..
T Consensus         9 l~~L~~~~~~~~~~la~~l~~s~~tv~~~l   38 (108)
T smart00344        9 LEELQKDARISLAELAKKVGLSPSTVHNRV   38 (108)
T ss_pred             HHHHHHhCCCCHHHHHHHHCcCHHHHHHHH
Confidence            445555567999999999999999997654

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

>PRK09047 RNA polymerase factor sigma-70; Validated

Probab=83.04  E-value=2.6  Score=30.01  Aligned_cols=31  Identities=10%  Similarity=-0.007  Sum_probs=25.4

Q ss_pred             HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           87 IVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +-.++.-.|+|.+|+|+.+|+|.++|.....
T Consensus       114 v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~  144 (161)
T PRK09047        114 AFLLRYWEDMDVAETAAAMGCSEGSVKTHCS  144 (161)
T ss_pred             HHHHHHHhcCCHHHHHHHHCCCHHHHHHHHH
Confidence            3344556799999999999999999988754

>PRK12529 RNA polymerase sigma factor; Provisional

Probab=83.04  E-value=2.7  Score=30.98  Aligned_cols=33  Identities=15%  Similarity=0.191  Sum_probs=26.6

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +.+-.++.-.|+|.+|+|+.+|+|.+||.....
T Consensus       133 R~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~  165 (178)
T PRK12529        133 KQAFLMATLDGMKQKDIAQALDIALPTVKKYIH  165 (178)
T ss_pred             HHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            334455666899999999999999999987653

>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR

Probab=83.02  E-value=2  Score=30.14  Aligned_cols=22  Identities=32%  Similarity=0.492  Sum_probs=20.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ++..++|+.+|||..||.-||+
T Consensus         1 ~~Igeva~~~gvs~~tlRyYe~   22 (118)
T cd04776           1 YTISELAREFDVTPRTLRFYED   22 (118)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            4678999999999999999996

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.

>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional

Probab=83.01  E-value=1.3  Score=33.01  Aligned_cols=23  Identities=9%  Similarity=0.309  Sum_probs=20.8

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 032366           95 KLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        95 glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      -+||++||..+|+++.+|+++.+
T Consensus       168 ~~t~~~lA~~lG~tr~tvsR~l~  190 (211)
T PRK11753        168 KITRQEIGRIVGCSREMVGRVLK  190 (211)
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHH
Confidence            58999999999999999999764

>PRK09652 RNA polymerase sigma factor RpoE; Provisional

Probab=82.84  E-value=2.7  Score=30.28  Aligned_cols=29  Identities=10%  Similarity=0.109  Sum_probs=24.3

Q ss_pred             HHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           89 QARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        89 ~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .++.-.|+|.+++|+.+|+|.++|..+..
T Consensus       138 ~l~~~~~~s~~eIA~~lgis~~tV~~~l~  166 (182)
T PRK09652        138 TLREIEGLSYEEIAEIMGCPIGTVRSRIF  166 (182)
T ss_pred             HHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            34455799999999999999999987754

>PRK12519 RNA polymerase sigma factor; Provisional

Probab=82.83  E-value=2  Score=31.82  Aligned_cols=29  Identities=14%  Similarity=0.135  Sum_probs=24.7

Q ss_pred             HHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           89 QARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        89 ~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .++.-.|+|++|+|+.+|+|.++|..+..
T Consensus       151 ~l~~~~g~s~~EIA~~lgis~~tV~~~l~  179 (194)
T PRK12519        151 ELAYYEGLSQSEIAKRLGIPLGTVKARAR  179 (194)
T ss_pred             hhhhhcCCCHHHHHHHhCCCHHHHHHHHH
Confidence            34555799999999999999999998764

>PF09571 RE_XcyI: XcyI restriction endonuclease; InterPro: IPR019071 There are four classes of restriction endonucleases: types I, II,III and IV

Probab=82.83  E-value=0.8  Score=37.41  Aligned_cols=65  Identities=15%  Similarity=-0.002  Sum_probs=49.8

Q ss_pred             hccccCCcchHHHHHHHHHHHHhCCCCHHHHHHH-hCCCHHHHHHHH-cCCCCCC-HHHHHHHHHHhC
Q 032366           71 TENLAHDRVPSELKKAIVQARNDKKLTQSQLAQL-INEKPQVIQEYE-SGKAIPN-QQILTKLERALG  135 (142)
Q Consensus        71 ~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~-lgis~stIs~~E-~G~~~p~-~~~l~kLa~~Lg  135 (142)
                      ...|+++.+.+.....+-..|.-.|+||++|... .|.+..-+..+| +|...+. ...+.-||.+|+
T Consensus        61 ev~F~vP~vL~~nPrligYYRLL~g~SQK~~yr~~~gl~~g~f~~mE~kG~~~~~~~~~i~dLc~~~~  128 (318)
T PF09571_consen   61 EVVFAVPYVLEANPRLIGYYRLLLGYSQKSFYRMNKGLGFGKFKSMESKGKIPKAQEPDIQDLCVAFN  128 (318)
T ss_pred             eEEeechHHHhhCcHHHHHHHHHHcccHHHhcccccCccccchhhhhhcCCccccccccHHHHHHHHH
Confidence            4567777888888899999999999999999986 677777788999 5665543 334666776664

All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry represents the restriction endonuclease XcyI, which recognises and cleaves the double-stranded sequence C^CCGGG. ; GO: 0000287 magnesium ion binding, 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system

>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]

Probab=82.79  E-value=3.9  Score=28.12  Aligned_cols=40  Identities=15%  Similarity=0.081  Sum_probs=34.6

Q ss_pred             cchHHHHHHHHHHHHhCCCCHHHHHHHhCC-CHHHHHHHHc
Q 032366           78 RVPSELKKAIVQARNDKKLTQSQLAQLINE-KPQVIQEYES  117 (142)
Q Consensus        78 ~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgi-s~stIs~~E~  117 (142)
                      ....+|-..+-.+..+-|.|..++|+..|| +.+++.+|-.
T Consensus         7 ~~s~EfK~~iv~~~~~~g~sv~~vAr~~gv~~~~~l~~W~~   47 (116)
T COG2963           7 KYSPEFKLEAVALYLRGGDTVSEVAREFGIVSATQLYKWRI   47 (116)
T ss_pred             cCCHHHHHHHHHHHHhcCccHHHHHHHhCCCChHHHHHHHH
Confidence            466778888888999999999999999996 9999997754

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

Probab=82.75  E-value=2.1  Score=29.88  Aligned_cols=22  Identities=27%  Similarity=0.457  Sum_probs=20.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ||..|+|+.+|||..||.-||+
T Consensus         1 ~~I~eva~~~gvs~~tLRyYe~   22 (123)
T cd04770           1 MKIGELAKAAGVSPDTIRYYER   22 (123)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5788999999999999999996

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.

>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein

Probab=82.69  E-value=4.8  Score=26.00  Aligned_cols=37  Identities=14%  Similarity=0.126  Sum_probs=27.8

Q ss_pred             hHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           80 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ...-...|..+....++++.++|+.+++++++|++..
T Consensus         9 ~~~~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l   45 (101)
T smart00347        9 TPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVL   45 (101)
T ss_pred             CHHHHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHH
Confidence            3334445566666667999999999999999888764

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

Probab=82.67  E-value=2.1  Score=30.55  Aligned_cols=22  Identities=18%  Similarity=0.359  Sum_probs=20.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      |+..|||+.+|||..||.-||+
T Consensus         1 m~IgE~A~~~gvs~~TLRyYE~   22 (133)
T cd04787           1 MKVKELANAAGVTPDTVRFYTR   22 (133)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5788999999999999999996

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

>PRK10727 DNA-binding transcriptional regulator GalR; Provisional

Probab=82.54  E-value=2.4  Score=33.98  Aligned_cols=21  Identities=29%  Similarity=0.411  Sum_probs=18.1

Q ss_pred             HHHHHcCCChhHHHhhhcCCC
Q 032366           33 NAARRAGADIETVRKSHAGTN   53 (142)
Q Consensus        33 ~~a~r~G~~v~t~kk~~~g~~   53 (142)
                      .-|+++|++++|+.+..+|..
T Consensus         6 dIA~~aGVS~~TVSrvLn~~~   26 (343)
T PRK10727          6 DVARLAGVSVATVSRVINNSP   26 (343)
T ss_pred             HHHHHhCCCHHHHHHHhCCCC
Confidence            469999999999999987653

>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=82.46  E-value=1.2  Score=25.27  Aligned_cols=19  Identities=21%  Similarity=0.207  Sum_probs=15.9

Q ss_pred             HHHHHcCCChhHHHhhhcC
Q 032366           33 NAARRAGADIETVRKSHAG   51 (142)
Q Consensus        33 ~~a~r~G~~v~t~kk~~~g   51 (142)
                      +.|+.+|+++.|++.|+.-
T Consensus         4 e~A~~~gvs~~tlR~ye~~   22 (38)
T PF00376_consen    4 EVAKLLGVSPRTLRYYERE   22 (38)
T ss_dssp             HHHHHHTS-HHHHHHHHHT
T ss_pred             HHHHHHCCCHHHHHHHHHC
Confidence            4789999999999999973

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 ....

>PRK06986 fliA flagellar biosynthesis sigma factor; Validated

Probab=82.45  E-value=2.5  Score=32.66  Aligned_cols=33  Identities=6%  Similarity=0.203  Sum_probs=26.7

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +.+-.++-..|+|.+|+|+.+|+|.++|..+..
T Consensus       190 r~vl~l~~~~g~s~~EIA~~lgis~~tV~~~~~  222 (236)
T PRK06986        190 QLVLSLYYQEELNLKEIGAVLGVSESRVSQIHS  222 (236)
T ss_pred             HHHHHhHhccCCCHHHHHHHHCCCHHHHHHHHH
Confidence            333444556799999999999999999998864

>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family

Probab=82.25  E-value=2.9  Score=28.65  Aligned_cols=27  Identities=11%  Similarity=0.163  Sum_probs=23.5

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           91 RNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        91 R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .--.|+|..++|+.+|+|+++|.++.+
T Consensus       122 ~~~~g~s~~eIA~~l~~s~~~v~~~~~  148 (158)
T TIGR02937       122 RYLEGLSYKEIAEILGISVGTVKRRLK  148 (158)
T ss_pred             HHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            334699999999999999999998864

Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.

>PRK10423 transcriptional repressor RbsR; Provisional

Probab=82.23  E-value=3  Score=33.00  Aligned_cols=20  Identities=30%  Similarity=0.303  Sum_probs=17.1

Q ss_pred             HHHHHcCCChhHHHhhhcCC
Q 032366           33 NAARRAGADIETVRKSHAGT   52 (142)
Q Consensus        33 ~~a~r~G~~v~t~kk~~~g~   52 (142)
                      .-|+++|++++|+.+..+|.
T Consensus         3 dIA~~agVS~~TVSrvLn~~   22 (327)
T PRK10423          3 DVARLAGVSTSTVSHVINKD   22 (327)
T ss_pred             hHHHHhCCcHHHHHHHhCCC
Confidence            35899999999999998754

>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator

Probab=82.22  E-value=1.9  Score=30.60  Aligned_cols=22  Identities=27%  Similarity=0.321  Sum_probs=20.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      |+..++|+.+|||..||..||+
T Consensus         1 m~I~e~a~~~gvs~~tlR~Ye~   22 (127)
T TIGR02047         1 MKIGELAQKTGVSVETIRFYEK   22 (127)
T ss_pred             CcHHHHHHHHCcCHHHHHHHHH
Confidence            5788999999999999999996

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.

>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional

Probab=82.18  E-value=2.1  Score=30.93  Aligned_cols=22  Identities=27%  Similarity=0.465  Sum_probs=20.7

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ++..|+|+.+|||..||..||+
T Consensus         2 ~~I~e~a~~~gvs~~tlR~Ye~   23 (140)
T PRK09514          2 YRIGELAKLAEVTPDTLRFYEK   23 (140)
T ss_pred             CcHHHHHHHHCcCHHHHHHHHH
Confidence            6789999999999999999997

>PRK10227 DNA-binding transcriptional regulator CueR; Provisional

Probab=82.18  E-value=2  Score=30.98  Aligned_cols=22  Identities=23%  Similarity=0.385  Sum_probs=20.6

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      |+..|||+.+|+|..||.-||+
T Consensus         1 m~Ige~a~~~gvs~~tlRyYE~   22 (135)
T PRK10227          1 MNISDVAKITGLTSKAIRFYEE   22 (135)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5788999999999999999997

>PRK09639 RNA polymerase sigma factor SigX; Provisional

Probab=82.17  E-value=3  Score=29.95  Aligned_cols=32  Identities=9%  Similarity=0.149  Sum_probs=26.4

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +.+-.++. .|+|.+++|+.+|+|.++|.....
T Consensus       118 r~il~l~~-~g~s~~eIA~~lgis~~tV~~~i~  149 (166)
T PRK09639        118 RTVLLLRF-SGYSYKEIAEALGIKESSVGTTLA  149 (166)
T ss_pred             HHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHH
Confidence            34445566 999999999999999999998763

>PRK08583 RNA polymerase sigma factor SigB; Validated

Probab=82.08  E-value=2.8  Score=32.81  Aligned_cols=29  Identities=10%  Similarity=0.110  Sum_probs=25.0

Q ss_pred             HHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           89 QARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        89 ~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .++--.|+|++|+|+.+|+|..+|..+..
T Consensus       215 ~l~~~~g~s~~eIA~~l~is~~tV~~~~~  243 (257)
T PRK08583        215 QCTFIENLSQKETGERLGISQMHVSRLQR  243 (257)
T ss_pred             HHHHhCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            34456799999999999999999999874

>PRK09642 RNA polymerase sigma factor SigW; Reviewed

Probab=81.94  E-value=3.1  Score=29.77  Aligned_cols=32  Identities=9%  Similarity=0.035  Sum_probs=25.9

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      +.+-.++.-.|+|.+|+|+.+|+|.++|....
T Consensus       112 r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l  143 (160)
T PRK09642        112 RDVVLAHYLEEKSYQEIALQEKIEVKTVEMKL  143 (160)
T ss_pred             HHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHH
Confidence            33445566789999999999999999997654

>PRK09954 putative kinase; Provisional

Probab=81.90  E-value=3.3  Score=33.99  Aligned_cols=33  Identities=9%  Similarity=0.169  Sum_probs=28.0

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +.|+.+++...+|+.+||+.+|+|+++|.+..+
T Consensus         7 ~il~~l~~~~~~s~~~la~~l~~s~~~v~~~i~   39 (362)
T PRK09954          7 EILAILRRNPLIQQNEIADILQISRSRVAAHIM   39 (362)
T ss_pred             HHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            456777777789999999999999999988765

>PF08822 DUF1804: Protein of unknown function (DUF1804); InterPro: IPR014926 This entry is represented by Bacteriophage D3112, Orf24

Probab=81.87  E-value=4.2  Score=30.63  Aligned_cols=37  Identities=16%  Similarity=0.127  Sum_probs=32.4

Q ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           81 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        81 ~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .+....++.+-.--++|....|..+|||..|+.+|-.
T Consensus         5 ~e~R~~~R~~YV~~~~sLe~aA~~~gVs~~TarrWK~   41 (165)
T PF08822_consen    5 QETRDAVRRAYVFDRLSLEQAAAKCGVSYATARRWKR   41 (165)
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHH
Confidence            4566777888788899999999999999999999986

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR

Probab=81.78  E-value=2.3  Score=31.00  Aligned_cols=22  Identities=32%  Similarity=0.324  Sum_probs=20.8

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      |+..|+|+.+|||..||.-||+
T Consensus         2 ~~IgevA~~~Gvs~~tLRyYE~   23 (142)
T TIGR01950         2 LTVGELAKRSGVAVSALHFYES   23 (142)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            6889999999999999999996

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.

>PF06322 Phage_NinH: Phage NinH protein; InterPro: IPR010454 This entry is represented by Bacteriophage 933W, NinH

Probab=81.74  E-value=2.9  Score=26.47  Aligned_cols=24  Identities=17%  Similarity=0.311  Sum_probs=21.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCC
Q 032366           96 LTQSQLAQLINEKPQVIQEYESGK  119 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~G~  119 (142)
                      =+|.|+|+.+++++.||.+|-...
T Consensus        17 GnqtEvaR~l~c~R~TVrKY~~D~   40 (64)
T PF06322_consen   17 GNQTEVARRLGCNRATVRKYSRDK   40 (64)
T ss_pred             CcHHHHHHHhcccHHHHHHHhccc
Confidence            379999999999999999998654

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator

Probab=81.64  E-value=2.4  Score=30.23  Aligned_cols=22  Identities=23%  Similarity=0.377  Sum_probs=20.8

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ++..|+|+.+|||..||..||.
T Consensus         2 ~~I~e~a~~~gvs~~tlR~Ye~   23 (131)
T TIGR02043         2 FQIGELAKLCGVTSDTLRFYEK   23 (131)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            6789999999999999999996

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.

>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family

Probab=81.63  E-value=0.95  Score=33.73  Aligned_cols=49  Identities=10%  Similarity=0.158  Sum_probs=32.3

Q ss_pred             HHHhCCCCHHHHHHHhCCCHHHHHHHHc-CCCCCCHHHHHHHHHHhCCCCC
Q 032366           90 ARNDKKLTQSQLAQLINEKPQVIQEYES-GKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        90 ~R~~~glTQ~eLA~~lgis~stIs~~E~-G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      ++.-.|+|.+|+|+.+|+|.++|..... ++... ...+...+...|+.++
T Consensus       142 L~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~L-r~~l~~~~~~~~~~~~  191 (193)
T TIGR02947       142 LADVEGFAYKEIAEIMGTPIGTVMSRLHRGRKQL-RKQLVDVAGERGFGPR  191 (193)
T ss_pred             ehhhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH-HHHHHHHHhccccccc
Confidence            4556799999999999999999988764 32222 1223344444555554

This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.

>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional

Probab=81.49  E-value=2  Score=32.84  Aligned_cols=26  Identities=12%  Similarity=0.064  Sum_probs=23.3

Q ss_pred             HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           92 NDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        92 ~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ...|+|.+|+|+++++|..||..+-+
T Consensus       149 la~G~snkeIA~~L~iS~~TVk~h~~  174 (207)
T PRK15411        149 WMAGQGTIQISDQMNIKAKTVSSHKG  174 (207)
T ss_pred             HHcCCCHHHHHHHcCCCHHHHHHHHH
Confidence            45799999999999999999998864

>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional

Probab=81.45  E-value=7.8  Score=28.66  Aligned_cols=64  Identities=14%  Similarity=0.215  Sum_probs=37.0

Q ss_pred             HHHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhCC
Q 032366           32 VNAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINE  107 (142)
Q Consensus        32 ~~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgi  107 (142)
                      =+.|++.|+++.|++-|+. |-..+... .+ .-+.++.++         ...-..|+.+ ...|||..++.+.+..
T Consensus        15 gevAk~~gvs~~TlRyYE~~GLi~~~r~-~~-g~R~Y~~~~---------i~~L~~I~~l-r~lG~sL~eIk~ll~~   79 (154)
T PRK15002         15 GEVAKRSGVAVSALHFYESKGLITSIRN-SG-NQRRYKRDV---------LRYVAIIKIA-QRIGIPLATIGEAFGV   79 (154)
T ss_pred             HHHHHHHCcCHHHHHHHHHCCCCCCccC-CC-CCEEECHHH---------HHHHHHHHHH-HHcCCCHHHHHHHHHH
Confidence            3579999999999999997 44443111 11 112222211         1112223333 4589999999987753

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

Probab=81.35  E-value=1.6  Score=32.66  Aligned_cols=90  Identities=14%  Similarity=0.199  Sum_probs=24.3

Q ss_pred             HHHHHcCCChhHHHhhhcCCCCCCCCCCCcccccchhhhccccCCc-chHHHHHHHHHHHH----hCCCCHHHHHHHh--
Q 032366           33 NAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTENLAHDR-VPSELKKAIVQARN----DKKLTQSQLAQLI--  105 (142)
Q Consensus        33 ~~a~r~G~~v~t~kk~~~g~~~~~~~~~~~~~~kl~~~~~~~~~~~-~~~~~g~~Lk~~R~----~~glTQ~eLA~~l--  105 (142)
                      ..|...|++++|+.+--.|+--.++.+.-+--..+......-.... ....+-..|+++-.    .+-+|-.+|++.+  
T Consensus        54 ~iA~~lgl~~STVSRav~~Ky~~t~~Gi~plk~fF~~~~~~~~~~~~S~~~ik~~i~~lI~~Ed~~~PlSD~~i~~~L~~  133 (160)
T PF04552_consen   54 DIADELGLHESTVSRAVKNKYIQTPRGIFPLKDFFSRSVSSGSGEEFSSEAIKARIKELIEEEDKKKPLSDQEIAELLKE  133 (160)
T ss_dssp             -------------------------------S-----SS--SS-SS---TTH-HHHHHHHTTS-TTS---HHHHHHHHTT
T ss_pred             HHHHHhCCCHhHHHHHHcCceeecCCeeeeHHHhccccccCCCCcccHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHH
Confidence            4688999999999998877664333332232233332211111111 11224445555543    4689999999999  


Q ss_pred             ---CCCHHHHHHHHcCCCCC
Q 032366          106 ---NEKPQVIQEYESGKAIP  122 (142)
Q Consensus       106 ---gis~stIs~~E~G~~~p  122 (142)
                         .||+.||.+|=..-..|
T Consensus       134 ~gi~isRRTVaKYR~~L~Ip  153 (160)
T PF04552_consen  134 EGIKISRRTVAKYREELGIP  153 (160)
T ss_dssp             TTS---HHHHHHHHHHHT-S
T ss_pred             cCCCccHHHHHHHHHHcCCC
Confidence               78999999986543344

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.

>TIGR02366 DHAK_reg probable dihydroxyacetone kinase regulator

Probab=81.33  E-value=4.3  Score=29.47  Aligned_cols=38  Identities=13%  Similarity=0.106  Sum_probs=30.5

Q ss_pred             HHHHHHHHHHHhCC---CCHHHHHHHhCCCHHHHHHHHcCC
Q 032366           82 ELKKAIVQARNDKK---LTQSQLAQLINEKPQVIQEYESGK  119 (142)
Q Consensus        82 ~~g~~Lk~~R~~~g---lTQ~eLA~~lgis~stIs~~E~G~  119 (142)
                      .+.+.+.++..++|   +|.+++++++|||++|+.++-..+
T Consensus         7 ~I~~a~~~Ll~~k~~~~ITV~~I~~~AgvsR~TFY~hF~dK   47 (176)
T TIGR02366         7 KIAKAFKDLMEVQAFSKISVSDIMSTAQIRRQTFYNHFQDK   47 (176)
T ss_pred             HHHHHHHHHHHHCCCccCCHHHHHHHhCCCHHHHHHHCCCH
Confidence            46666677777765   689999999999999999887655

The seed alignment for this family was built from a set of closely related uncharacterized proteins associated with operons for the type of bacterial dihydroxyacetone kinase that transfers PEP-derived phosphate from a phosphoprotein, as in phosphotransferase system transport, rather than from ATP. Members have a TetR transcriptional regulator domain (pfam00440) at the N-terminus and sequence homology throughout.

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

Probab=81.32  E-value=1.6  Score=26.94  Aligned_cols=25  Identities=24%  Similarity=0.292  Sum_probs=20.8

Q ss_pred             HHHHHHHHcCCChhHHHhhhcCCCC
Q 032366           30 KVVNAARRAGADIETVRKSHAGTNK   54 (142)
Q Consensus        30 ~~~~~a~r~G~~v~t~kk~~~g~~~   54 (142)
                      ++-..|.+.|++.+|+.+||.|...
T Consensus        16 s~~~lA~~~g~s~s~v~~iE~G~~~   40 (64)
T PF13560_consen   16 SQAQLADRLGVSQSTVSRIERGRRP   40 (64)
T ss_dssp             -HHHHHHHHTS-HHHHHHHHTTSSS
T ss_pred             CHHHHHHHHCcCHHHHHHHHCCCCC
Confidence            5667899999999999999999884

>PRK12523 RNA polymerase sigma factor; Reviewed

Probab=81.28  E-value=3.5  Score=30.05  Aligned_cols=32  Identities=9%  Similarity=0.170  Sum_probs=26.5

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      +.+-.++.-.|+|.+|+|+.+|+|.++|....
T Consensus       125 r~v~~L~~~~g~s~~EIA~~lgis~~tV~~~l  156 (172)
T PRK12523        125 RAAFLYNRLDGMGHAEIAERLGVSVSRVRQYL  156 (172)
T ss_pred             HHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence            34445566789999999999999999998875

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=81.20  E-value=3.1  Score=32.82  Aligned_cols=27  Identities=19%  Similarity=0.132  Sum_probs=23.8

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           91 RNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        91 R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +--.|+|++++|+.+|+|.++|+++..
T Consensus       215 ~y~~~~s~~eIA~~lgvs~~~V~~~~~  241 (256)
T PRK07408        215 VFLHDLTQKEAAERLGISPVTVSRRVK  241 (256)
T ss_pred             HHHCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            344699999999999999999999875

>PRK06596 RNA polymerase factor sigma-32; Reviewed

Probab=81.06  E-value=1.7  Score=34.97  Aligned_cols=24  Identities=21%  Similarity=0.210  Sum_probs=22.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           94 KKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        94 ~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .++|+.++|+.+|||+.+|+++++
T Consensus       247 ~~~Tl~EIA~~lgvS~~rVrqi~~  270 (284)
T PRK06596        247 DKSTLQELAAEYGVSAERVRQIEK  270 (284)
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHH
Confidence            379999999999999999999986

>PRK09645 RNA polymerase sigma factor SigL; Provisional

Probab=81.06  E-value=3.5  Score=29.91  Aligned_cols=31  Identities=10%  Similarity=0.073  Sum_probs=25.3

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           86 AIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        86 ~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      .+-.++.-.|+|.+|+|+.+|+|.++|....
T Consensus       125 ~vl~L~~~~g~s~~EIA~~lgis~~tV~~~l  155 (173)
T PRK09645        125 AVLVRSYYRGWSTAQIAADLGIPEGTVKSRL  155 (173)
T ss_pred             HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHH
Confidence            3444566679999999999999999997654

>PRK12537 RNA polymerase sigma factor; Provisional

Probab=80.99  E-value=3.3  Score=30.51  Aligned_cols=31  Identities=6%  Similarity=0.101  Sum_probs=25.5

Q ss_pred             HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           87 IVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +-.++.-.|+|.+|+|+.+|+|.++|..+..
T Consensus       141 i~~l~~~~~~s~~eIA~~lgis~~tV~~~l~  171 (182)
T PRK12537        141 CILHAYVDGCSHAEIAQRLGAPLGTVKAWIK  171 (182)
T ss_pred             HHHHHHHcCCCHHHHHHHHCCChhhHHHHHH
Confidence            3444566899999999999999999988753

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

Probab=80.97  E-value=6.2  Score=26.55  Aligned_cols=64  Identities=13%  Similarity=0.119  Sum_probs=36.1

Q ss_pred             HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhCC
Q 032366           33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINE  107 (142)
Q Consensus        33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgi  107 (142)
                      +.|++.|++..|++-|+. |-..|..... -.-+.++.++         ..--..|+.+ ...|++..++...+..
T Consensus         5 eva~~~gvs~~tlR~ye~~Gll~p~~~~~-~gyR~Y~~~~---------~~~l~~I~~l-r~~G~~l~eI~~~l~~   69 (97)
T cd04782           5 EFAKLCGISKQTLFHYDKIGLFKPEIVKE-NGYRYYTLEQ---------FEQLDIILLL-KELGISLKEIKDYLDN   69 (97)
T ss_pred             HHHHHHCcCHHHHHHHHHCCCCCCCccCC-CCCccCCHHH---------HHHHHHHHHH-HHcCCCHHHHHHHHhc
Confidence            579999999999999986 4444321110 1111111111         1122334444 4478999998887754

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.

>TIGR02051 MerR Hg(II)-responsive transcriptional regulator

Probab=80.94  E-value=1.8  Score=30.58  Aligned_cols=21  Identities=29%  Similarity=0.347  Sum_probs=19.2

Q ss_pred             CHHHHHHHhCCCHHHHHHHHc
Q 032366           97 TQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        97 TQ~eLA~~lgis~stIs~~E~  117 (142)
                      |..+||+.+|||+.||..||.
T Consensus         1 ~I~e~a~~~gvs~~tlR~Ye~   21 (124)
T TIGR02051         1 TIGELAKAAGVNVETIRYYER   21 (124)
T ss_pred             CHHHHHHHHCcCHHHHHHHHH
Confidence            457999999999999999996

This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.

>PRK07122 RNA polymerase sigma factor SigF; Reviewed

Probab=80.89  E-value=3  Score=33.15  Aligned_cols=29  Identities=17%  Similarity=0.143  Sum_probs=24.7

Q ss_pred             HHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           89 QARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        89 ~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .++--.|+|+.++|+.+|+|.++|.+++.
T Consensus       225 ~l~y~~~~t~~EIA~~lgis~~~V~~~~~  253 (264)
T PRK07122        225 VLRFFESMTQTQIAERVGISQMHVSRLLA  253 (264)
T ss_pred             HHHhcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            34445699999999999999999999875

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

Probab=80.84  E-value=9.5  Score=25.38  Aligned_cols=62  Identities=19%  Similarity=0.225  Sum_probs=36.3

Q ss_pred             HHHHHcCCChhHHHhhhcC-CCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhC
Q 032366           33 NAARRAGADIETVRKSHAG-TNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLIN  106 (142)
Q Consensus        33 ~~a~r~G~~v~t~kk~~~g-~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lg  106 (142)
                      +.|++.|++..|++.|+.- -..+....  ..-..++.+         ....-..++.++. .|++..+++..+.
T Consensus         5 eva~~~gi~~~tlr~~~~~Gll~~~~~~--~g~r~y~~~---------dv~~l~~i~~l~~-~g~~~~~i~~~l~   67 (100)
T cd00592           5 EVAKLLGVSVRTLRYYEEKGLLPPERSE--NGYRLYSEE---------DLERLRLIRRLRE-LGLSLKEIRELLD   67 (100)
T ss_pred             HHHHHHCcCHHHHHHHHHCCCcCCCcCC--CCCcccCHH---------HHHHHHHHHHHHH-cCCCHHHHHHHHh
Confidence            5788999999999999862 22211110  111111111         1124455666666 8888888887664

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.

>PRK13749 transcriptional regulator MerD; Provisional

Probab=80.80  E-value=2.8  Score=29.89  Aligned_cols=23  Identities=22%  Similarity=0.228  Sum_probs=21.4

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 032366           95 KLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        95 glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .||..|||+++|+|..||.-||.
T Consensus         3 ~~tIgelA~~~gvS~~tiR~YE~   25 (121)
T PRK13749          3 AYTVSRLALDAGVSVHIVRDYLL   25 (121)
T ss_pred             CCcHHHHHHHHCCCHHHHHHHHH
Confidence            47899999999999999999986

>PRK15320 transcriptional activator SprB; Provisional

Probab=80.75  E-value=2  Score=33.76  Aligned_cols=27  Identities=11%  Similarity=0.076  Sum_probs=23.9

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           91 RNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        91 R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ....|+|++|+|+.+++|.+||+.+-+
T Consensus       175 LLAkG~SNKEIAekL~LS~KTVSTYKn  201 (251)
T PRK15320        175 LLSSGHPAIELAKKFGLGTKTVSIYRK  201 (251)
T ss_pred             HHHcCCCHHHHHHHhccchhhHHHHHH
Confidence            346799999999999999999998864

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

Probab=80.62  E-value=7.5  Score=23.16  Aligned_cols=20  Identities=15%  Similarity=0.230  Sum_probs=17.6

Q ss_pred             CHHHHHHHhCCCHHHHHHHH
Q 032366           97 TQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        97 TQ~eLA~~lgis~stIs~~E  116 (142)
                      |..+||+.+|+|++++++..
T Consensus        27 ~~~~la~~~~is~~~v~~~l   46 (66)
T cd07377          27 SERELAEELGVSRTTVREAL   46 (66)
T ss_pred             CHHHHHHHHCCCHHHHHHHH
Confidence            49999999999999988754

This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is

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

Probab=80.57  E-value=9.9  Score=26.10  Aligned_cols=63  Identities=17%  Similarity=0.136  Sum_probs=35.2

Q ss_pred             HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhC
Q 032366           33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLIN  106 (142)
Q Consensus        33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lg  106 (142)
                      +.|++.|+++.|++.|+. |-..+.... .-.-..++.+         .-..-..|+.+| ..|++..++...+.
T Consensus         5 eva~~~gvs~~tlR~ye~~Gll~p~~~~-~~g~R~Y~~~---------dl~~l~~I~~lr-~~G~~l~~I~~~l~   68 (108)
T cd04773           5 ELAHLLGVPPSTLRHWEKEGLLSPDREP-ETGYRVYDPS---------DVRDARLIHLLR-RGGYLLEQIATVVE   68 (108)
T ss_pred             HHHHHHCcCHHHHHHHHHCCCCCCCcCC-CCCceeeCHH---------HHHHHHHHHHHH-HCCCCHHHHHHHHH
Confidence            578999999999999987 333321110 0011111111         111334455554 47889888877664

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.

>PRK09649 RNA polymerase sigma factor SigC; Reviewed

Probab=80.56  E-value=3.3  Score=30.73  Aligned_cols=33  Identities=9%  Similarity=-0.006  Sum_probs=27.1

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      .+.+-.++.-.|+|.+|+|+.+|+|.++|....
T Consensus       135 ~r~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l  167 (185)
T PRK09649        135 QREALLLTQLLGLSYADAAAVCGCPVGTIRSRV  167 (185)
T ss_pred             HhHHhhhHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence            344455667789999999999999999998765

>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators

Probab=80.55  E-value=2.6  Score=31.56  Aligned_cols=22  Identities=36%  Similarity=0.357  Sum_probs=20.7

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +|..|||+.+|||++||..||.
T Consensus         2 ~~I~evA~~~gvs~~tLRyYe~   23 (172)
T cd04790           2 LTISQLARQFGLSRSTLLYYER   23 (172)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            6889999999999999999996

Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain

>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family

Probab=80.28  E-value=4.3  Score=25.14  Aligned_cols=34  Identities=18%  Similarity=0.255  Sum_probs=24.0

Q ss_pred             HHHHHHHHH-HhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           83 LKKAIVQAR-NDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        83 ~g~~Lk~~R-~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      +-+.|-.+. .....+..+||+.+|+|+++++...
T Consensus         9 YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml   43 (60)
T PF01325_consen    9 YLKAIYELSEEGGPVRTKDIAERLGVSPPTVTEML   43 (60)
T ss_dssp             HHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHH
T ss_pred             HHHHHHHHHcCCCCccHHHHHHHHCCChHHHHHHH
Confidence            334444443 4456789999999999999998764

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 ....

>PRK13919 putative RNA polymerase sigma E protein; Provisional

Probab=80.28  E-value=3.8  Score=30.09  Aligned_cols=31  Identities=13%  Similarity=0.150  Sum_probs=25.5

Q ss_pred             HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           87 IVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +-.++.-.|+|.+|+|+.+|+|.++|.....
T Consensus       143 vl~l~~~~~~s~~eIA~~lgis~~~V~~~l~  173 (186)
T PRK13919        143 VIEVLYYQGYTHREAAQLLGLPLGTLKTRAR  173 (186)
T ss_pred             HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3344566899999999999999999987754

>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional

Probab=80.01  E-value=3.1  Score=30.81  Aligned_cols=27  Identities=26%  Similarity=0.252  Sum_probs=23.8

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           91 RNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        91 R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +...=|+..|+|+.+|||..||..||+
T Consensus         7 ~~~~~~~IgevAk~~gvs~~TlRyYE~   33 (154)
T PRK15002          7 RIKALLTPGEVAKRSGVAVSALHFYES   33 (154)
T ss_pred             hhcccccHHHHHHHHCcCHHHHHHHHH
Confidence            444558999999999999999999996

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	142
1x57_A	91	Solution Structures Of The Hth Domain Of Human Edf-		1e-17
2jvl_A	107	Nmr Structure Of The C-Terminal Domain Of Mbf1 Of T		2e-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 = 1e-17,   Method: Compositional matrix adjust.
 Identities = 42/67 (62%), Positives = 50/67 (74%)
Query: 75  AHDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERAL 134
           + DRV  E+ K I Q R  K LTQ  LA  INEKPQVI +YESG+AIPN Q+L K+ERA+
Sbjct: 6   SGDRVTLEVGKVIQQGRQSKGLTQKDLATKINEKPQVIADYESGRAIPNNQVLGKIERAI 65
Query: 135 GVKLRGK 141
           G+KLRGK
Sbjct: 66  GLKLRGK 72

>pdb|2JVL|A Chain A, Nmr Structure Of The C-Terminal Domain Of Mbf1 Of Trichoderm Length = 107

Iteration: 1
 Score = 54.7 bits (130), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 31/77 (40%), Positives = 44/77 (57%), Gaps = 2/77 (2%)
Query: 66  KLDEDTENLAHDRVPSELKKAIVQARN--DKKLTQSQLAQLINEKPQVIQEYESGKAIPN 123
           K+D   + +    V  E+ KAI Q R   +  +TQ++L + I E    +  YE G A P+
Sbjct: 18  KVDRSDDIIKPKTVGKEVGKAIEQGRQKFEPTMTQAELGKEIGETAATVASYERGTATPD 77
Query: 124 QQILTKLERALGVKLRG 140
           Q IL+K+ER L VKLRG
Sbjct: 78  QNILSKMERVLNVKLRG 94

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	142
2jvl_A	107	TRMBF1; coactivator, helix-turn-helix, Pro binding	3e-27
1x57_A	91	Endothelial differentiation-related factor 1; HMBF	5e-24
1adr_A	76	P22 C2 repressor; transcription regulation; NMR {E	1e-09
2r1j_L	68	Repressor protein C2; protein-DNA complex, helix-t	3e-09
2wiu_B	88	HTH-type transcriptional regulator HIPB; transfera	3e-08
1r69_A	69	Repressor protein CI; gene regulating protein; 2.0	7e-08
2p5t_A	158	Putative transcriptional regulator PEZA; postsegre	1e-07
3omt_A	73	Uncharacterized protein; structural genomics, PSI-	1e-07
1zug_A	71	Phage 434 CRO protein; gene regulating protein, tr	1e-07
3ivp_A	126	Putative transposon-related DNA-binding protein; A	2e-07
2kpj_A	94	SOS-response transcriptional repressor, LEXA; NESG	2e-07
3kxa_A	141	NGO0477 protein, putative uncharacterized protein;	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;	4e-07
3f6w_A	83	XRE-family like protein; helix-turn-helix, DNA bin	9e-07
3mlf_A	111	Transcriptional regulator; structural genomics, he	1e-06
4ghj_A	101	Probable transcriptional regulator; structural gen	1e-06
2ef8_A	84	C.ECOT38IS, putative transcription factor; helix-t	2e-06
3lfp_A	98	CSP231I C protein; transcriptional regulator, DNA	8e-06
2ewt_A	71	BLDD, putative DNA-binding protein; the DNA-bindin	1e-05
3o9x_A	133	Uncharacterized HTH-type transcriptional regulato;	1e-05
2bnm_A	198	Epoxidase; oxidoreductase, cupin, HTH, cation-depe	6e-05
1y7y_A	74	C.AHDI; helix-turn-helix, DNA-binding protein, tra	1e-04
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	1e-04
2l49_A	99	C protein; P2 bacteriophage, P2 C, direct repeats,	2e-04
3eus_A	86	DNA-binding protein; structural genomics, PSI2,MCS	2e-04
3f52_A	117	CLP gene regulator (CLGR); helix-turn-helix motif,	6e-04

>2jvl_A TRMBF1; coactivator, helix-turn-helix, Pro binding, transcription; NMR {Trichoderma reesei} Length = 107

 Score = 96.5 bits (240), Expect = 3e-27
 Identities = 33/95 (34%), Positives = 48/95 (50%), Gaps = 2/95 (2%)

Query: 50  AGTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARN--DKKLTQSQLAQLINE 107
           A   + A  +      K+D   + +    V  E+ KAI Q R   +  +TQ++L + I E
Sbjct: 2   AMDPEFAGGTEGQRLTKVDRSDDIIKPKTVGKEVGKAIEQGRQKFEPTMTQAELGKEIGE 61

Query: 108 KPQVIQEYESGKAIPNQQILTKLERALGVKLRGKK 142
               +  YE G A P+Q IL+K+ER L VKLRG  
Sbjct: 62  TAATVASYERGTATPDQNILSKMERVLNVKLRGAN 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 = 87.9 bits (218), Expect = 5e-24
 Identities = 42/72 (58%), Positives = 51/72 (70%)

Query: 71  TENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKL 130
           +   + DRV  E+ K I Q R  K LTQ  LA  INEKPQVI +YESG+AIPN Q+L K+
Sbjct: 2   SSGSSGDRVTLEVGKVIQQGRQSKGLTQKDLATKINEKPQVIADYESGRAIPNNQVLGKI 61

Query: 131 ERALGVKLRGKK 142
           ERA+G+KLRGK 
Sbjct: 62  ERAIGLKLRGKD 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: 82  ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGV 136
            + + 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 = 49.5 bits (119), Expect = 3e-09
 Identities = 13/55 (23%), Positives = 25/55 (45%)

Query: 82  ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGV 136
            + + 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: 78  RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVK 137
             P++L  A+   R     TQS+LA+ I  K   I  +E+           K+ ++L + 
Sbjct: 8   YSPTQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELS 67

Query: 138 L 138
           +
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 = 45.7 bits (109), Expect = 7e-08
 Identities = 17/50 (34%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 87  IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGV 136
           +   R    L Q++LAQ +    Q I++ E+GK     + L +L  ALGV
Sbjct: 6   VKSKRIQLGLNQAELAQKVGTTQQSIEQLENGKT-KRPRFLPELASALGV 54

>2p5t_A Putative transcriptional regulator PEZA; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae} Length = 158

 Score = 46.8 bits (111), Expect = 1e-07
 Identities = 11/54 (20%), Positives = 25/54 (46%)

Query: 83  LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGV 136
           + K I   R    LTQ + A+++      +  YE+G +  + +++  + +   V
Sbjct: 2   IGKNIKSLRKTHDLTQLEFARIVGISRNSLSRYENGTSSVSTELIDIICQKFNV 55

>3omt_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; 1.65A {Cytophaga hutchinsonii} Length = 73

 Score = 45.0 bits (107), Expect = 1e-07
 Identities = 9/53 (16%), Positives = 23/53 (43%)

Query: 87  IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 139
           +     +K  T   L + +++    + ++ +    P+ + L  +  AL V +R
Sbjct: 13  LKSVLAEKGKTNLWLTETLDKNKTTVSKWCTNDVQPSLETLFDIAEALNVDVR 65

>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 = 45.0 bits (107), Expect = 1e-07
 Identities = 15/56 (26%), Positives = 26/56 (46%), Gaps = 1/56 (1%)

Query: 81  SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGV 136
             L + + + R   K+TQ++LA     K Q IQ  E+G     + +  ++  AL  
Sbjct: 2   QTLSERLKKRRIALKMTQTELATKAGVKQQSIQLIEAGVTKRPRFLF-EIAMALNC 56

>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 = 46.0 bits (109), Expect = 2e-07
 Identities = 17/57 (29%), Positives = 28/57 (49%)

Query: 82  ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 138
            L  AI +AR  + LT+ Q+  +I   P+ +   E+    P+ Q+L  L   L V +
Sbjct: 12  ALGLAIKEARKKQGLTREQVGAMIEIDPRYLTNIENKGQHPSLQVLYDLVSLLNVSV 68

>2kpj_A SOS-response transcriptional repressor, LEXA; NESG, GFT, structural genomics, PSI-2, protein structure initiative; NMR {Eubacterium rectale atcc 33656} Length = 94

 Score = 45.1 bits (107), Expect = 2e-07
 Identities = 11/56 (19%), Positives = 20/56 (35%)

Query: 83  LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 138
             + +       + TQ ++A+ I   PQ    +  G AIP    +  L     +  
Sbjct: 10  FSENLNSYIAKSEKTQLEIAKSIGVSPQTFNTWCKGIAIPRMGKVQALADYFNINK 65

>3kxa_A NGO0477 protein, putative uncharacterized protein; NEW protein fold, OPPF, STRU genomics, oxford protein production facility; 2.80A {Neisseria gonorrhoeae} Length = 141

 Score = 46.0 bits (109), Expect = 2e-07
 Identities = 24/107 (22%), Positives = 35/107 (32%), Gaps = 5/107 (4%)

Query: 37  RAGADIETVRKSHAGTNKAASSSTSL-----NTRKLDEDTENLAHDRVPSELKKAIVQAR 91
           R    I+ V+     T  AA     +         +D     +A         +  V  R
Sbjct: 18  RINGQIKCVKPISPNTTPAAEHIEHVRKNPRRKAAMDRAAARIADKIALKAGGETFVSLR 77

Query: 92  NDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 138
             K  TQS+LA         +   E+ K     + + KL  ALGV  
Sbjct: 78  MKKGFTQSELATAAGLPQPYLSRIENSKQSLQDKTVQKLANALGVSP 124

>3op9_A PLI0006 protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG, transcription regulat; HET: MSE; 1.90A {Listeria innocua} Length = 114

 Score = 45.5 bits (108), Expect = 3e-07
 Identities = 11/55 (20%), Positives = 28/55 (50%)

Query: 82  ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGV 136
           +  + + + + +  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 = 44.2 bits (105), Expect = 3e-07
 Identities = 14/53 (26%), Positives = 24/53 (45%)

Query: 87  IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 139
           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 = 46.5 bits (110), Expect = 4e-07
 Identities = 11/59 (18%), Positives = 20/59 (33%)

Query: 78  RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGV 136
                LK    + +N+  L+Q  +A  +      +    +G    N      L + L V
Sbjct: 13  EDARRLKAIYEKKKNELGLSQESVADKMGMGQSGVGALFNGINALNAYNAALLAKILKV 71

>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 = 9e-07
 Identities = 11/63 (17%), Positives = 25/63 (39%)

Query: 76  HDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALG 135
           H+     L   +++AR+   +TQ +LA  +      + + E+ +   +        R +G
Sbjct: 8   HNARYQALLDLLLEARSAAGITQKELAARLGRPQSFVSKTENAERRLDVIEFMDFCRGIG 67

Query: 136 VKL 138
              
Sbjct: 68  TDP 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 = 43.5 bits (102), Expect = 1e-06
 Identities = 22/72 (30%), Positives = 29/72 (40%), Gaps = 3/72 (4%)

Query: 67  LDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQI 126
           +D  TENL      S   K + + R D  LTQ +L  L     + IQ  E         +
Sbjct: 11  VDLGTENLYFQ---SNAMKTLKELRTDYGLTQKELGDLFKVSSRTIQNMEKDSTNIKDSL 67

Query: 127 LTKLERALGVKL 138
           L+K   A  VK 
Sbjct: 68  LSKYMSAFNVKY 79

>4ghj_A Probable transcriptional regulator; structural genomics, niaid, national institute of allergy AN infectious diseases; HET: MSE; 1.75A {Vibrio vulnificus} Length = 101

 Score = 43.4 bits (102), Expect = 1e-06
 Identities = 20/83 (24%), Positives = 38/83 (45%), Gaps = 5/83 (6%)

Query: 57  SSSTSLNTRKL---DEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQ 113
           SS   L T  L       +++    +  E+   + QAR ++ LTQS++A++     + + 
Sbjct: 8   SSGVDLGTENLYFQSNAMKHVTAAALAEEIGDRLKQARLNRDLTQSEVAEIAGIARKTVL 67

Query: 114 EYESGKAIPNQQILTKLERALGV 136
             E GK   +  I+  +  AL +
Sbjct: 68  NAEKGKVQLD--IMIAILMALDL 88

>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 = 15/63 (23%), Positives = 28/63 (44%)

Query: 76  HDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALG 135
           HD     L + + + R +  L+QS+LA  +      I + ES +   +   L +L   + 
Sbjct: 4   HDHRYRCLVQLLTKLRKEASLSQSELAIFLGLSQSDISKIESFERRLDALELFELLEVVA 63

Query: 136 VKL 138
            +L
Sbjct: 64  SRL 66

>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 = 41.0 bits (96), Expect = 8e-06
 Identities = 12/52 (23%), Positives = 23/52 (44%), Gaps = 4/52 (7%)

Query: 89  QARNDKKLTQSQLAQLINEKPQV----IQEYESGKAIPNQQILTKLERALGV 136
            AR    ++Q +L  L           + +YE GK  P+ ++  +L + L +
Sbjct: 8   DARLRAGISQEKLGVLAGIDEASASARMNQYEKGKHAPDFEMANRLAKVLKI 59

>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 = 1e-05
 Identities = 12/52 (23%), Positives = 19/52 (36%), Gaps = 2/52 (3%)

Query: 89  QARNDKKLTQSQLAQLINE--KPQVIQEYESGKAIPNQQILTKLERALGVKL 138
             R  + L+   + +      K  V+  YE G      Q L +L    GV +
Sbjct: 15  AIRTQQGLSLHGVEEKSQGRWKAVVVGSYERGDRAVTVQRLAELADFYGVPV 66

>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 = 13/92 (14%), Positives = 32/92 (34%)

Query: 40  ADIETVRKSHAGTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQS 99
             ++ +   +    + +  +   +   + +     A     +   + IV+ R    LTQ 
Sbjct: 29  TVLKGIHGLYCVHCEESIMNKEESDAFMAQVKAFRASVNAETVAPEFIVKVRKKLSLTQK 88

Query: 100 QLAQLINEKPQVIQEYESGKAIPNQQILTKLE 131
           + +++          YE G A P+   +  L 
Sbjct: 89  EASEIFGGGVNAFSRYEKGNAQPHPSTIKLLR 120

>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 = 40.2 bits (94), Expect = 6e-05
 Identities = 12/63 (19%), Positives = 26/63 (41%), Gaps = 1/63 (1%)

Query: 77  DRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIP-NQQILTKLERALG 135
               +   + +   R   K+  + LA L+ E P+ +  +E+G+        L ++   LG
Sbjct: 5   KTASTGFAELLKDRREQVKMDHAALASLLGETPETVAAWENGEGGELTLTQLGRIAHVLG 64

Query: 136 VKL 138
             +
Sbjct: 65  TSI 67

>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: 85  KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 138
           + + + R  K L+Q  LA L       +   E G+   +   + KL  AL ++ 
Sbjct: 16  QRLRELRTAKGLSQETLAFLSGLDRSYVGGVERGQRNVSLVNILKLATALDIEP 69

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646} Length = 293

 Score = 39.4 bits (91), Expect = 1e-04
 Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 1/55 (1%)

Query: 85  KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR 139
             I + R  + LTQ QL++ I  + +V +  ESG   P+  IL  +   L + + 
Sbjct: 8   SEIKKIRVLRGLTQKQLSENICHQSEVSR-IESGAVYPSMDILQGIAAKLQIPII 61

>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 = 37.6 bits (87), Expect = 2e-04
 Identities = 13/50 (26%), Positives = 25/50 (50%)

Query: 81  SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKL 130
           + + + IV  R  + L++ QLA L       +  YESG++ P   ++  +
Sbjct: 3   NTISEKIVLMRKSEYLSRQQLADLTGVPYGTLSYYESGRSTPPTDVMMNI 52

>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 = 37.2 bits (86), Expect = 2e-04
 Identities = 13/53 (24%), Positives = 25/53 (47%)

Query: 83  LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALG 135
           L + + QAR D  LTQ+ LA+ +++    + + E+ +   +     K   A  
Sbjct: 15  LCQRLRQARLDAGLTQADLAERLDKPQSFVAKVETRERRLDVIEFAKWMAACE 67

>3f52_A CLP gene regulator (CLGR); helix-turn-helix motif, transcriptional ACTI human pathogen, transcription activator; 1.75A {Corynebacterium glutamicum} PDB: 3f51_A Length = 117

 Score = 36.2 bits (83), Expect = 6e-04
 Identities = 20/83 (24%), Positives = 37/83 (44%), Gaps = 1/83 (1%)

Query: 57  SSSTSLNTRKLDEDTENLAHDR-VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEY 115
            + T+L  + + E     A +  +   L  A+   R DK +T  +LA+     P  + E 
Sbjct: 2   VTYTTLLDKPISESAPRKAPEPLLREALGAALRSFRADKGVTLRELAEASRVSPGYLSEL 61

Query: 116 ESGKAIPNQQILTKLERALGVKL 138
           E G+   + ++L  +  ALG  +
Sbjct: 62  ERGRKEVSSELLASVCHALGASV 84

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	142
2jvl_A	107	TRMBF1; coactivator, helix-turn-helix, Pro binding	99.7
2ewt_A	71	BLDD, putative DNA-binding protein; the DNA-bindin	99.59
1x57_A	91	Endothelial differentiation-related factor 1; HMBF	99.59
3s8q_A	82	R-M controller protein; protein-DNA complex, helix	99.57
3qq6_A	78	HTH-type transcriptional regulator SINR; helix-tur	99.57
1y7y_A	74	C.AHDI; helix-turn-helix, DNA-binding protein, tra	99.57
3kz3_A	80	Repressor protein CI; five helix bundle, DNA-bindi	99.57
3g5g_A	99	Regulatory protein; transcriptional regulator, hel	99.55
3f6w_A	83	XRE-family like protein; helix-turn-helix, DNA bin	99.55
3b7h_A	78	Prophage LP1 protein 11; structural genomics, PSI2	99.55
2k9q_A	77	Uncharacterized protein; all helix, helix-turn-hel	99.55
2b5a_A	77	C.BCLI; helix-turn-helix motif, gene regulation; 1	99.54
3omt_A	73	Uncharacterized protein; structural genomics, PSI-	99.54
2a6c_A	83	Helix-turn-helix motif; putative transcriptional r	99.53
2r1j_L	68	Repressor protein C2; protein-DNA complex, helix-t	99.53
2kpj_A	94	SOS-response transcriptional repressor, LEXA; NESG	99.53
3eus_A	86	DNA-binding protein; structural genomics, PSI2,MCS	99.53
3ivp_A	126	Putative transposon-related DNA-binding protein; A	99.52
3vk0_A	114	NHTF, transcriptional regulator; HTH motif, XRE tr	99.52
1adr_A	76	P22 C2 repressor; transcription regulation; NMR {E	99.52
3t76_A	88	VANU, transcriptional regulator vanug; structural	99.52
2wiu_B	88	HTH-type transcriptional regulator HIPB; transfera	99.51
3lfp_A	98	CSP231I C protein; transcriptional regulator, DNA	99.51
3op9_A	114	PLI0006 protein; structural genomics, PSI-2, prote	99.51
1lmb_3	92	Protein (lambda repressor); protein-DNA complex, d	99.51
4ghj_A	101	Probable transcriptional regulator; structural gen	99.5
2xi8_A	66	Putative transcription regulator; HTH DNA-binding	99.49
3f52_A	117	CLP gene regulator (CLGR); helix-turn-helix motif,	99.49
3bs3_A	76	Putative DNA-binding protein; XRE-family, structur	99.48
1r69_A	69	Repressor protein CI; gene regulating protein; 2.0	99.48
3mlf_A	111	Transcriptional regulator; structural genomics, he	99.48
3trb_A	104	Virulence-associated protein I; mobIle and extrach	99.47
1zug_A	71	Phage 434 CRO protein; gene regulating protein, tr	99.45
2wus_R	112	RODZ, putative uncharacterized protein; structural	99.44
2l49_A	99	C protein; P2 bacteriophage, P2 C, direct repeats,	99.44
3fmy_A	73	HTH-type transcriptional regulator MQSA (YGIT/B302	99.44
2ef8_A	84	C.ECOT38IS, putative transcription factor; helix-t	99.43
2ict_A	94	Antitoxin HIGA; helix-turn-helix, structural genom	99.43
2o38_A	120	Hypothetical protein; alpha-beta, helix-turn-helix	99.43
1b0n_A	111	Protein (SINR protein); transcription regulator, a	99.43
2ppx_A	99	AGR_C_3184P, uncharacterized protein ATU1735; HTH-	99.42
3cec_A	104	Putative antidote protein of plasmid maintenance;	99.42
3fym_A	130	Putative uncharacterized protein; HTH DNA binding,	99.42
1y9q_A	192	Transcriptional regulator, HTH_3 family; transcrip	99.41
2bnm_A	198	Epoxidase; oxidoreductase, cupin, HTH, cation-depe	99.4
2eby_A	113	Putative HTH-type transcriptional regulator YBAQ;	99.39
2ofy_A	86	Putative XRE-family transcriptional regulator; tra	99.37
3kxa_A	141	NGO0477 protein, putative uncharacterized protein;	99.36
3r1f_A	135	ESX-1 secretion-associated regulator ESPR; helix-t	99.33
3bd1_A	79	CRO protein; transcription factor, helix-turn-heli	99.3
3qwg_A	123	ESX-1 secretion-associated regulator ESPR; N-termi	99.3
3u3w_A	293	Transcriptional activator PLCR protein; ternary co	99.29
3pxp_A	292	Helix-turn-helix domain protein; DNA-binding, basi	99.25
4ich_A	311	Transcriptional regulator; structural genomics, PS	99.21
3o9x_A	133	Uncharacterized HTH-type transcriptional regulato;	99.17
2awi_A	317	PRGX; repressor, pheromone, DNA binding, regulator	99.17
2p5t_A	158	Putative transcriptional regulator PEZA; postsegre	99.15
3bdn_A	236	Lambda repressor; repressor, allostery; HET: DNA;	99.15
2qfc_A	293	PLCR protein; TPR, HTH, transcription regulation;	99.13
2l1p_A	83	DNA-binding protein SATB1; PSI-biology, NESG, stru	99.12
1neq_A	74	DNA-binding protein NER; NMR {Enterobacteria phage	99.08
2fjr_A	189	Repressor protein CI; genetic switch, regulation,	99.03
2auw_A	170	Hypothetical protein NE0471; alpha-beta structure,	98.83
1dw9_A	156	Cyanate lyase; cyanate degradation, structural gen	98.67
1nr3_A	122	MTH0916, DNA-binding protein TFX; northeast struct	98.6
1rzs_A	61	Antirepressor, regulatory protein CRO; helix-turn-	98.46
1uxc_A	65	FRUR (1-57), fructose repressor; DNA-binding prote	98.3
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	98.26
1zx4_A	192	P1 PARB, plasmid partition PAR B protein, PARB; tr	98.25
3g7d_A	443	PHPD; non heme Fe(II) dioxygenase, cupin, biosynth	98.22
2l8n_A	67	Transcriptional repressor CYTR; bacterial gene rep	98.13
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	98.08
2pij_A	67	Prophage PFL 6 CRO; transcription factor, helix-tu	98.03
1s4k_A	120	Putative cytoplasmic protein YDIL; structural geno	97.98
2hin_A	71	GP39, repressor protein; transcription factor, dim	97.57
1jhf_A	202	LEXA repressor; LEXA SOS repressor, hydrolase; 1.8	97.53
2l0k_A	93	Stage III sporulation protein D; SPOIIID, solution	97.44
2cw1_A	65	SN4M; lambda CRO fold, de novo protein; NMR {Synth	97.33
1zs4_A	83	Regulatory protein CII; helix-turn-helix, transcri	97.14
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	96.96
1xwr_A	97	Regulatory protein CII; all-alpha fold, DNA bindin	96.9
2x48_A	55	CAG38821; archeal virus, viral protein; 2.60A {Sul	96.86
4ich_A	311	Transcriptional regulator; structural genomics, PS	96.84
2ao9_A	155	Phage protein; structural genomics, nine-fold NCS.	96.63
1jhg_A	101	Trp operon repressor; complex (regulatory protein-	96.46
1jko_C	52	HIN recombinase, DNA-invertase HIN; water-mediated	96.42
1u78_A	141	TC3 transposase, transposable element TC3 transpos	95.96
2hsg_A	332	Glucose-resistance amylase regulator; CCPA, transc	95.75
3kjx_A	344	Transcriptional regulator, LACI family; LACL famil	95.53
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	95.49
2w7n_A	101	TRFB transcriptional repressor protein; INCP, plas	95.4
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	95.39
2ovg_A	66	Phage lambda CRO; transcription factor, helix-turn	95.26
2jn6_A	97	Protein CGL2762, transposase; GFT PSI-2, protein s	95.14
3h5t_A	366	Transcriptional regulator, LACI family; DNA-depend	95.06
1e3o_C	160	Octamer-binding transcription factor 1; transcript	95.0
2csf_A	101	DNA-binding protein SATB2; CUT domain, special AT-	94.9
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	94.78
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	94.73
1x2l_A	101	CUT-like 2, homeobox protein CUX-2; CUT domain, hu	94.6
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	94.6
1u78_A	141	TC3 transposase, transposable element TC3 transpos	94.45
1j9i_A	68	GPNU1 DBD;, terminase small subunit; DNA binding d	94.43
2o20_A	332	Catabolite control protein A; CCPA, transcriptiona	94.08
1k78_A	149	Paired box protein PAX5; paired domain, ETS domain	93.89
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	93.76
2jml_A	81	DNA binding domain/transcriptional regulator; anti	93.71
3frw_A	107	Putative Trp repressor protein; structural genomic	93.57
2o8x_A	70	Probable RNA polymerase sigma-C factor; promoter r	93.54
3me5_A	482	Cytosine-specific methyltransferase; structural ge	93.54
1r71_A	178	Transcriptional repressor protein KORB; INCP, plas	93.53
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	93.48
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	93.43
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	93.33
3kor_A	119	Possible Trp repressor; putative DNA-binding Trp r	93.32
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	93.28
3eus_A	86	DNA-binding protein; structural genomics, PSI2,MCS	93.12
2k27_A	159	Paired box protein PAX-8; paired domain, solution	93.05
3h5o_A	339	Transcriptional regulator GNTR; transcription regu	93.03
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	92.98
1wh6_A	101	CUT-like 2, homeobox protein CUX-2; CUT domain, st	92.9
1vz0_A	230	PARB, chromosome partitioning protein PARB; nuclea	92.87
2ox6_A	166	Hypothetical protein SO3848; structural genomics,	92.84
3e7l_A	63	Transcriptional regulator (NTRC family); sigma43 a	92.75
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	92.72
1hlv_A	131	CENP-B, major centromere autoantigen B; helix-turn	92.68
3dbi_A	338	Sugar-binding transcriptional regulator, LACI FAM;	92.61
2jpc_A	61	SSRB; DNA binding protein, structural genomics, PS	92.57
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	92.45
2l8n_A	67	Transcriptional repressor CYTR; bacterial gene rep	92.37
2w48_A	315	Sorbitol operon regulator; SORC, activator, repres	92.36
1k78_A	149	Paired box protein PAX5; paired domain, ETS domain	92.34
2vz4_A	108	Tipal, HTH-type transcriptional activator TIPA; tr	92.32
1x3u_A	79	Transcriptional regulatory protein FIXJ; helix-tur	92.28
3jvd_A	333	Transcriptional regulators; structural genomics, P	92.27
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	92.23
3ulq_B	90	Transcriptional regulatory protein COMA; tetratric	92.16
3bil_A	348	Probable LACI-family transcriptional regulator; st	92.16
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	92.12
1uxc_A	65	FRUR (1-57), fructose repressor; DNA-binding prote	92.09
3e3m_A	355	Transcriptional regulator, LACI family; structural	92.09
2dk5_A	91	DNA-directed RNA polymerase III 39 kDa polypeptide	92.03
1wh8_A	111	CUT-like 2, homeobox protein CUX-2; CUT domain, st	91.98
2k27_A	159	Paired box protein PAX-8; paired domain, solution	91.94
1fse_A	74	GERE; helix-turn-helix DNA-binding protein transcr	91.75
3ctp_A	330	Periplasmic binding protein/LACI transcriptional;	91.73
1umq_A	81	Photosynthetic apparatus regulatory protein; DNA-b	91.73
1z4h_A	66	TORI, TOR inhibition protein; winged helix, revers	91.7
1jye_A	349	Lactose operon repressor; gene regulation, protein	91.61
2rn7_A	108	IS629 ORFA; helix, all alpha, unknown function, st	91.6
2jml_A	81	DNA binding domain/transcriptional regulator; anti	91.33
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	91.19
1wiz_A	101	DNA-binding protein SATB2; helix bundle, KIAA1034	91.18
3c57_A	95	Two component transcriptional regulatory protein;	91.1
1je8_A	82	Nitrate/nitrite response regulator protein NARL; p	91.01
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	90.87
1s7o_A	113	Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SP	90.65
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	90.65
3mky_B	189	Protein SOPB; partition, F plasmid, centromere, DN	90.47
1ntc_A	91	Protein (nitrogen regulation protein (NTRC)); heli	90.36
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	90.12
2o4a_A	93	DNA-binding protein SATB1; protein-DNA complex, tr	90.0
1sfx_A	109	Conserved hypothetical protein AF2008; structural	89.71
1xsv_A	113	Hypothetical UPF0122 protein SAV1236; helix-turn-h	89.6
2o3f_A	111	Putative HTH-type transcriptional regulator YBBH;	89.47
3op9_A	114	PLI0006 protein; structural genomics, PSI-2, prote	88.99
3r0a_A	123	Putative transcriptional regulator; structural gen	88.93
1r8d_A	109	Transcription activator MTAN; protein-DNA complex,	88.82
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	88.76
1eto_A	98	FIS, factor for inversion stimulation; transcripti	88.49
3mzy_A	164	RNA polymerase sigma-H factor; PSI, MCSG, structur	88.48
1g2h_A	61	Transcriptional regulatory protein TYRR homolog; p	88.35
3iwf_A	107	Transcription regulator RPIR family; transcription	87.98
3kz3_A	80	Repressor protein CI; five helix bundle, DNA-bindi	87.91
3t72_q	99	RNA polymerase sigma factor RPOD, DNA-directed RN	87.86
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	87.85
2pg4_A	95	Uncharacterized protein; structural genomics, join	87.71
3fmy_A	73	HTH-type transcriptional regulator MQSA (YGIT/B302	87.68
3gp4_A	142	Transcriptional regulator, MERR family; structural	87.37
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	87.34
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	87.29
2w25_A	150	Probable transcriptional regulatory protein; trans	87.07
3oop_A	143	LIN2960 protein; protein structure initiative, PSI	87.06
2rnj_A	91	Response regulator protein VRAR; HTH LUXR-type dom	86.96
3nrv_A	148	Putative transcriptional regulator (MARR/EMRR FAM;	86.86
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	86.85
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	86.73
3gp4_A	142	Transcriptional regulator, MERR family; structural	86.72
1ub9_A	100	Hypothetical protein PH1061; helix-turn-helix moti	86.71
2nnn_A	140	Probable transcriptional regulator; structural gen	86.69
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	86.65
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	86.64
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	86.63
1on2_A	142	Transcriptional regulator MNTR; helix-turn-helix,	86.54
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	86.51
3g3z_A	145	NMB1585, transcriptional regulator, MARR family; t	86.44
2r0q_C	209	Putative transposon TN552 DNA-invertase BIN3; site	86.44
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	86.31
2p5k_A	64	Arginine repressor; DNA-binding domain, winged hel	86.26
1q06_A	135	Transcriptional regulator CUER; MERR family transc	86.14
1p4w_A	99	RCSB; solution structure, DNA binding domain, DNA	86.12
3hh0_A	146	Transcriptional regulator, MERR family; protein st	86.04
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	86.0
1yse_A	141	DNA-binding protein SATB1; all helical, DNA-bindin	85.98
1or7_A	194	Sigma-24, RNA polymerase sigma-E factor; regulatio	85.87
2hr3_A	147	Probable transcriptional regulator; MCSG, structur	85.79
3hh0_A	146	Transcriptional regulator, MERR family; protein st	85.75
3omt_A	73	Uncharacterized protein; structural genomics, PSI-	85.74
1ft9_A	222	Carbon monoxide oxidation system transcription reg	85.73
2rdp_A	150	Putative transcriptional regulator MARR; PFAM PF01	85.56
1y0u_A	96	Arsenical resistance operon repressor, putative; s	85.54
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	85.53
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	85.45
1gdt_A	183	GD resolvase, protein (gamma delta resolvase); pro	85.41
2xi8_A	66	Putative transcription regulator; HTH DNA-binding	85.4
2oz6_A	207	Virulence factor regulator; winged helix, helix-tu	85.37
3lsg_A	103	Two-component response regulator YESN; structural	85.3
2qvo_A	95	Uncharacterized protein AF_1382; PSI, structural g	85.28
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	85.23
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	85.17
2a61_A	145	Transcriptional regulator TM0710; APC4350, MCSG, m	85.16
2ef8_A	84	C.ECOT38IS, putative transcription factor; helix-t	85.08
2r1j_L	68	Repressor protein C2; protein-DNA complex, helix-t	85.0
3ryp_A	210	Catabolite gene activator; CAMP receptor protein (	84.96
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	84.96
1u2w_A	122	CADC repressor, cadmium efflux system accessory pr	84.93
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	84.91
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	84.87
1r8d_A	109	Transcription activator MTAN; protein-DNA complex,	84.81
2wte_A	244	CSA3; antiviral protein, viral resistance, winged	84.7
4hbl_A	149	Transcriptional regulator, MARR family; HTH, trans	84.69
2zcw_A	202	TTHA1359, transcriptional regulator, FNR/CRP famil	84.67
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	84.57
2vz4_A	108	Tipal, HTH-type transcriptional activator TIPA; tr	84.56
3s8q_A	82	R-M controller protein; protein-DNA complex, helix	84.53
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	84.42
1ku9_A	152	Hypothetical protein MJ223; putative transcription	84.33
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	84.28
1y7y_A	74	C.AHDI; helix-turn-helix, DNA-binding protein, tra	84.21
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	84.19
2fbi_A	142	Probable transcriptional regulator; MARR, APC5816,	84.15
2fmy_A	220	COOA, carbon monoxide oxidation system transcripti	84.13
2eth_A	154	Transcriptional regulator, putative, MAR family; M	84.1
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	84.0
1lmb_3	92	Protein (lambda repressor); protein-DNA complex, d	83.97
3iwz_A	230	CAP-like, catabolite activation-like protein; XCC,	83.85
2fbh_A	146	Transcriptional regulator PA3341; MARR, transcript	83.81
3dv8_A	220	Transcriptional regulator, CRP/FNR family; cyclic	83.7
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	83.69
2pex_A	153	Transcriptional regulator OHRR; transcription regu	83.67
2b5a_A	77	C.BCLI; helix-turn-helix motif, gene regulation; 1	83.62
1j5y_A	187	Transcriptional regulator, biotin repressor famil;	83.56
4dyq_A	140	Gene 1 protein; GP1, octamer, DNA-binding, viral p	83.55
2qww_A	154	Transcriptional regulator, MARR family; YP_013417.	83.52
3f6w_A	83	XRE-family like protein; helix-turn-helix, DNA bin	83.5
3e97_A	231	Transcriptional regulator, CRP/FNR family; YP_6044	83.43
1adr_A	76	P22 C2 repressor; transcription regulation; NMR {E	83.39
3s2w_A	159	Transcriptional regulator, MARR family; structural	83.38
3kp7_A	151	Transcriptional regulator TCAR; multiple drug resi	83.36
3k0l_A	162	Repressor protein; helix-turn-helix, structural ge	83.35
2ofy_A	86	Putative XRE-family transcriptional regulator; tra	83.24
2zkz_A	99	Transcriptional repressor PAGR; protein-DNA, HTH m	83.14
3d0s_A	227	Transcriptional regulatory protein; CAMP receptor	83.1
4ev0_A	216	Transcription regulator, CRP family; CAMP binding,	83.08
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	83.06
3bj6_A	152	Transcriptional regulator, MARR family; helix-turn	83.0
2jrt_A	95	Uncharacterized protein; solution, structure, NESG	82.86
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	82.79
3hot_A	345	Transposable element mariner, complete CDS; protei	82.77
2k9q_A	77	Uncharacterized protein; all helix, helix-turn-hel	82.75
3b02_A	195	Transcriptional regulator, CRP family; structural	82.72
2k9s_A	107	Arabinose operon regulatory protein; activator, ar	82.54
3o9x_A	133	Uncharacterized HTH-type transcriptional regulato;	82.46
2ewt_A	71	BLDD, putative DNA-binding protein; the DNA-bindin	82.41
2obp_A	96	Putative DNA-binding protein; structural genomics,	82.41
1z05_A	429	Transcriptional regulator, ROK family; structural	82.37
1lj9_A	144	Transcriptional regulator SLYA; HTH DNA binding pr	82.33
2kpj_A	94	SOS-response transcriptional repressor, LEXA; NESG	82.25
3cjn_A	162	Transcriptional regulator, MARR family; silicibact	82.25
2gxg_A	146	146AA long hypothetical transcriptional regulator;	82.25
1z6r_A	406	MLC protein; transcriptional repressor, ROK family	82.23
1zyb_A	232	Transcription regulator, CRP family; NP_813211.1,	82.0
1s3j_A	155	YUSO protein; structural genomics, MARR transcript	82.0
2nyx_A	168	Probable transcriptional regulatory protein, RV14;	81.91
2h09_A	155	Transcriptional regulator MNTR; transcription regu	81.89
3la7_A	243	Global nitrogen regulator; activator, DNA-binding,	81.86
3i4p_A	162	Transcriptional regulator, ASNC family; PSI, struc	81.82
3kkc_A	177	TETR family transcriptional regulator; APC20805, s	81.8
2hoe_A	380	N-acetylglucosamine kinase; TM1224, structural gen	81.77
3bs3_A	76	Putative DNA-binding protein; XRE-family, structur	81.47
1r69_A	69	Repressor protein CI; gene regulating protein; 2.0	81.44
3dkw_A	227	DNR protein; CRP-FNR, HTH, beta barrel, dimerizati	81.29
2gau_A	232	Transcriptional regulator, CRP/FNR family; structu	81.24
2zhg_A	154	Redox-sensitive transcriptional activator SOXR; ox	81.21
2kko_A	108	Possible transcriptional regulatory protein (possi	81.14
3e6c_C	250	CPRK, cyclic nucleotide-binding protein; CPRK, hal	81.12
1zug_A	71	Phage 434 CRO protein; gene regulating protein, tr	81.08
3oou_A	108	LIN2118 protein; protein structure initiative, PSI	81.06
3qq6_A	78	HTH-type transcriptional regulator SINR; helix-tur	80.93
3g7d_A	443	PHPD; non heme Fe(II) dioxygenase, cupin, biosynth	80.91
3e6m_A	161	MARR family transcriptional regulator; APC88769, s	80.89
1b4a_A	149	Arginine repressor; helix turn helix; 2.50A {Geoba	80.87
3mn2_A	108	Probable ARAC family transcriptional regulator; st	80.86
3gpv_A	148	Transcriptional regulator, MERR family; protein st	80.85
4fx0_A	148	Probable transcriptional repressor protein; helix-	80.83
2ppx_A	99	AGR_C_3184P, uncharacterized protein ATU1735; HTH-	80.82
3fx3_A	237	Cyclic nucleotide-binding protein; helix_TURN_heli	80.76
4ghj_A	101	Probable transcriptional regulator; structural gen	80.65
3qkx_A	188	Uncharacterized HTH-type transcriptional regulato;	80.57
3b7h_A	78	Prophage LP1 protein 11; structural genomics, PSI2	80.55
3dcf_A	218	Transcriptional regulator of the TETR/ACRR family;	80.51
3kcc_A	260	Catabolite gene activator; helix-turn-helix, CAMP,	80.31
3fm5_A	150	Transcriptional regulator; MCSG, PF04017, PSI, MAR	80.26
2frh_A	127	SARA, staphylococcal accessory regulator A; winged	80.24
3cdh_A	155	Transcriptional regulator, MARR family; helix-turn	80.21
2l49_A	99	C protein; P2 bacteriophage, P2 C, direct repeats,	80.1
3jw4_A	148	Transcriptional regulator, MARR/EMRR family; DNA-b	80.02

>2jvl_A TRMBF1; coactivator, helix-turn-helix, Pro binding, transcription; NMR {Trichoderma reesei}

Probab=99.70  E-value=6.8e-17  Score=111.43  Aligned_cols=84  Identities=37%  Similarity=0.573  Sum_probs=79.2

Q ss_pred             CCCCcccccchhhhccccCCcchHHHHHHHHHHHH--hCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q 032366           58 SSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARN--DKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALG  135 (142)
Q Consensus        58 ~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~--~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lg  135 (142)
                      .+...+..+++++++.+.+..+.+.++.+|+.+|.  .+||||.+||+.+|+|+++|++||+|+..|+.+.+.+||++||
T Consensus        10 ~~~~~~~~~~d~~~~~~~~~~~~~~~g~~lk~~R~~~~~glsq~elA~~~gis~~~is~~E~G~~~p~~~~l~~ia~~l~   89 (107)
T 2jvl_A           10 GTEGQRLTKVDRSDDIIKPKTVGKEVGKAIEQGRQKFEPTMTQAELGKEIGETAATVASYERGTATPDQNILSKMERVLN   89 (107)
T ss_dssp             CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHTTSSSCCCHHHHHHHHTCCHHHHHHHTTTCSCCCHHHHHHHHHTTT
T ss_pred             CCcccccccccccccccCHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHC
Confidence            34568889999999999999999999999999999  9999999999999999999999999999999999999999999


Q ss_pred             CCCCCC
Q 032366          136 VKLRGK  141 (142)
Q Consensus       136 vsl~e~  141 (142)
                      |++++.
T Consensus        90 v~~~e~   95 (107)
T 2jvl_A           90 VKLRGA   95 (107)
T ss_dssp             CBSSSS
T ss_pred             cCHhhh
Confidence            999874

>2ewt_A BLDD, putative DNA-binding protein; the DNA-binding domain of BLDD; 1.81A {Streptomyces coelicolor}

Probab=99.59  E-value=3.7e-15  Score=94.09  Aligned_cols=62  Identities=21%  Similarity=0.267  Sum_probs=58.4

Q ss_pred             chHHHHHHHHHHHHhCCCCHHHHHHHhC--CCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 032366           79 VPSELKKAIVQARNDKKLTQSQLAQLIN--EKPQVIQEYESGKAIPNQQILTKLERALGVKLRG  140 (142)
Q Consensus        79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~lg--is~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~e  140 (142)
                      ....++.+|+.+|..+|+||.+||+.+|  +|+++|++||+|+..|+.+.+.+||++|||++++
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            3456999999999999999999999999  9999999999999999999999999999999864

>1x57_A Endothelial differentiation-related factor 1; HMBF1alpha, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.35.1.12

Probab=99.59  E-value=5.5e-15  Score=98.13  Aligned_cols=65  Identities=63%  Similarity=0.905  Sum_probs=60.8

Q ss_pred             CCcchHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 032366           76 HDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG  140 (142)
Q Consensus        76 ~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~e  140 (142)
                      .+.+.+.++.+|+.+|..+||||.+||+.+|+|+++|++||+|+..|+.+.+.+||++|||++++
T Consensus         7 ~~~~~~~~~~~l~~~r~~~glsq~~lA~~~gis~~~is~~e~g~~~p~~~~l~~la~~l~v~~~~   71 (91)
T 1x57_A            7 GDRVTLEVGKVIQQGRQSKGLTQKDLATKINEKPQVIADYESGRAIPNNQVLGKIERAIGLKLRG   71 (91)
T ss_dssp             SSCCCCHHHHHHHHHHHTTTCCHHHHHHHHTSCHHHHHHHHHTCSCCCHHHHHHHHHHHTBCCSS
T ss_pred             HHHHHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHHH
Confidence            34556679999999999999999999999999999999999999999999999999999999976

>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=99.57  E-value=5.7e-15  Score=96.03  Aligned_cols=61  Identities=23%  Similarity=0.145  Sum_probs=58.0

Q ss_pred             chHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           79 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      +...++.+|+.+|..+||||.+||+.+|+|+++|++||+|+..|+.+.+.+||++|||+++
T Consensus         8 ~~~~~g~~lk~~R~~~glsq~~lA~~~gis~~~i~~~e~g~~~~~~~~l~~ia~~l~v~~~   68 (82)
T 3s8q_A            8 LLSKVSFVIKKIRLEKGMTQEDLAYKSNLDRTYISGIERNSRNLTIKSLELIMKGLEVSDV   68 (82)
T ss_dssp             HHHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCCCCBHHHHHHHHHHTTCCHH
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHCCCCCCCHHHHHHHHHHHCcCHH
Confidence            4567999999999999999999999999999999999999999999999999999999874

>3qq6_A HTH-type transcriptional regulator SINR; helix-turn-helix motif, biofilm, repressor, SINI; 1.90A {Bacillus subtilis}

Probab=99.57  E-value=4e-15  Score=96.79  Aligned_cols=61  Identities=23%  Similarity=0.278  Sum_probs=57.0

Q ss_pred             chHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcC-CCCCCHHHHHHHHHHhCCCCC
Q 032366           79 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESG-KAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G-~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      ....|+.+|+.+|+++||||.+||+.+|||+++|++||+| +..|+.+.+.+||++|||+++
T Consensus         7 ~~~~~~~~ik~~R~~~gltq~elA~~~gis~~~is~~E~G~~~~p~~~~l~~ia~~l~v~~~   68 (78)
T 3qq6_A            7 HHHMIGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIERNLQTNPSIQFLEKVSAVLDVSVH   68 (78)
T ss_dssp             -CTTHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTSCCCCBHHHHHHHHHHHTCCHH
T ss_pred             CCCCccHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHHHHHHCcCHH
Confidence            3456999999999999999999999999999999999999 889999999999999999864

>1y7y_A C.AHDI; helix-turn-helix, DNA-binding protein, transcriptional regulator, transcription regulator; 1.69A {Aeromonas hydrophila} SCOP: a.35.1.3

Probab=99.57  E-value=9.6e-15  Score=92.58  Aligned_cols=62  Identities=23%  Similarity=0.207  Sum_probs=58.4

Q ss_pred             chHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 032366           79 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG  140 (142)
Q Consensus        79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~e  140 (142)
                      ....++.+|+.+|..+|+||.+||+.+|+|+++|++||+|+..|+.+.+.+||++|||++++
T Consensus        10 ~~~~~~~~l~~~r~~~g~s~~~lA~~~gis~~~i~~~e~g~~~~~~~~l~~l~~~l~~~~~~   71 (74)
T 1y7y_A           10 DLVKFGQRLRELRTAKGLSQETLAFLSGLDRSYVGGVERGQRNVSLVNILKLATALDIEPRE   71 (74)
T ss_dssp             HHHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCSCCBHHHHHHHHHHTTSCGGG
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHhCcCHHH
Confidence            34679999999999999999999999999999999999999999999999999999999863

>3kz3_A Repressor protein CI; five helix bundle, DNA-binding, transcription, transcription regulation; 1.64A {Enterobacteria phage lambda}

Probab=99.57  E-value=6.9e-15  Score=95.58  Aligned_cols=61  Identities=16%  Similarity=0.156  Sum_probs=58.0

Q ss_pred             hHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 032366           80 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG  140 (142)
Q Consensus        80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~e  140 (142)
                      .+.++.+|+.+|+++|+||.+||+.+|||+++|++||+|+..|+.+.+.+||++|||++++
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            4568999999999999999999999999999999999999999999999999999999864

>3g5g_A Regulatory protein; transcriptional regulator, helix-turn-helix, restriction- modification, transcription regulator; 2.80A {Enterobacter SP} PDB: 3fya_A

Probab=99.55  E-value=7.3e-15  Score=100.01  Aligned_cols=61  Identities=23%  Similarity=0.145  Sum_probs=58.2

Q ss_pred             chHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           79 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      +...++.+|+.+|+++||||.+||+.+||++++|++||+|+..|+.+.+.+||++|||+++
T Consensus        25 ~~~~ig~~lr~~R~~~gltq~elA~~~gis~~~is~iE~G~~~ps~~~l~~ia~~l~v~~~   85 (99)
T 3g5g_A           25 LLSKVSFVIKKIRLEKGMTQEDLAYKSNLDRTYISGIERNSRNLTIKSLELIMKGLEVSDV   85 (99)
T ss_dssp             HHHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCSCCBHHHHHHHHHHTTCCHH
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHHCcCHH
Confidence            4567999999999999999999999999999999999999999999999999999999875

>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=99.55  E-value=9.3e-15  Score=95.09  Aligned_cols=60  Identities=17%  Similarity=0.220  Sum_probs=57.1

Q ss_pred             hHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           80 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      .+.++.+|+.+|.++||||.+||+.+|+++++|++||+|+..|+.+.+.+||++|||+++
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            456899999999999999999999999999999999999999999999999999999874

>3b7h_A Prophage LP1 protein 11; structural genomics, PSI2, MCSG, protein structure initiative, midwest center for structural genomics; 2.00A {Lactobacillus plantarum WCFS1}

Probab=99.55  E-value=1.2e-14  Score=93.16  Aligned_cols=60  Identities=15%  Similarity=0.279  Sum_probs=57.2

Q ss_pred             hHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCCC
Q 032366           80 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA-IPNQQILTKLERALGVKLR  139 (142)
Q Consensus        80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~-~p~~~~l~kLa~~Lgvsl~  139 (142)
                      ...++.+|+.+|..+|+||.+||+.+|+|+++|++||+|+. .|+.+.+.+||++|||+++
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            45799999999999999999999999999999999999999 9999999999999999874

>2k9q_A Uncharacterized protein; all helix, helix-turn-helix, plasmid, structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides thetaiotaomicron}

Probab=99.55  E-value=4.1e-15  Score=95.91  Aligned_cols=58  Identities=22%  Similarity=0.236  Sum_probs=55.5

Q ss_pred             HHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           82 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        82 ~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      .++.+|+.+|..+||||.+||+++|||+++|++||+|+..|+.+.+.+||++|||+++
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            4789999999999999999999999999999999999999999999999999999874

>2b5a_A C.BCLI; helix-turn-helix motif, gene regulation; 1.54A {Bacillus caldolyticus} SCOP: a.35.1.3

Probab=99.54  E-value=1.5e-14  Score=92.41  Aligned_cols=61  Identities=21%  Similarity=0.278  Sum_probs=57.8

Q ss_pred             chHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           79 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      ....++.+|+.+|..+|+||.+||+.+|+|+++|++||+|+..|+.+.+.+||++|||+++
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            4567999999999999999999999999999999999999999999999999999999874

>3omt_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; 1.65A {Cytophaga hutchinsonii}

Probab=99.54  E-value=3.3e-15  Score=95.28  Aligned_cols=58  Identities=16%  Similarity=0.273  Sum_probs=55.1

Q ss_pred             HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 032366           83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG  140 (142)
Q Consensus        83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~e  140 (142)
                      ++++|+.+|.++|+||.+||+.+|||+++|++||+|+..|+.+.+.+||++|||++++
T Consensus         9 ~~~~l~~~r~~~glsq~~lA~~~gis~~~is~~e~g~~~~~~~~l~~ia~~l~v~~~~   66 (73)
T 3omt_A            9 IFNRLKSVLAEKGKTNLWLTETLDKNKTTVSKWCTNDVQPSLETLFDIAEALNVDVRE   66 (73)
T ss_dssp             CCBCHHHHHHHHTCCHHHHHHHTTCCHHHHHHHHTTSSCCCHHHHHHHHHHHTSCGGG
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHHH
Confidence            5678999999999999999999999999999999999999999999999999999863

>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=99.53  E-value=2.6e-14  Score=93.71  Aligned_cols=62  Identities=19%  Similarity=0.297  Sum_probs=58.4

Q ss_pred             cchHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCCC
Q 032366           78 RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA-IPNQQILTKLERALGVKLR  139 (142)
Q Consensus        78 ~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~-~p~~~~l~kLa~~Lgvsl~  139 (142)
                      .....++.+|+.+|.++||||.+||+.+|+|+++|++||+|+. .|+.+.+.+||++|||+++
T Consensus        14 ~~~~~~~~~l~~~r~~~glsq~elA~~~gis~~~is~~e~g~~~~~~~~~l~~la~~l~~~~~   76 (83)
T 2a6c_A           14 KMRSQLLIVLQEHLRNSGLTQFKAAELLGVTQPRVSDLMRGKIDLFSLESLIDMITSIGLKVE   76 (83)
T ss_dssp             HHHHHHHHHHHHHHHTTTCCHHHHHHHHTSCHHHHHHHHTTCGGGCCHHHHHHHHHHTTCCCC
T ss_pred             cccHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHHHHHcCCCeE
Confidence            4556799999999999999999999999999999999999998 5999999999999999986

>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=99.53  E-value=1.5e-14  Score=90.18  Aligned_cols=58  Identities=22%  Similarity=0.326  Sum_probs=55.7

Q ss_pred             HHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           82 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        82 ~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      .++.+|+.+|..+|+||.+||+.+|+|+++|++||+|+..|+.+.+.+||++|||+++
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            4899999999999999999999999999999999999999999999999999999874

>2kpj_A SOS-response transcriptional repressor, LEXA; NESG, GFT, structural genomics, PSI-2, protein structure initiative; NMR {Eubacterium rectale atcc 33656}

Probab=99.53  E-value=2.7e-14  Score=95.49  Aligned_cols=61  Identities=18%  Similarity=0.229  Sum_probs=58.0

Q ss_pred             chHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           79 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      ..+.++.+|+.+|..+|+||.+||+.+|+|+++|++||+|+..|+.+.+.+||++|||+++
T Consensus         6 ~~~~~~~~lk~~r~~~glsq~~lA~~~gis~~~is~~e~G~~~p~~~~l~~ia~~l~v~~~   66 (94)
T 2kpj_A            6 QKAIFSENLNSYIAKSEKTQLEIAKSIGVSPQTFNTWCKGIAIPRMGKVQALADYFNINKS   66 (94)
T ss_dssp             HHHHHHHHHHHHHTTSSSCHHHHHHHHTCCHHHHHHHHTTSCCCCHHHHHHHHHHHTCCTH
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhCCCCCCHHHHHHHHHHHCcCHH
Confidence            3567999999999999999999999999999999999999999999999999999999975

>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=2.9e-14  Score=94.18  Aligned_cols=58  Identities=22%  Similarity=0.142  Sum_probs=55.4

Q ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 032366           81 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL  138 (142)
Q Consensus        81 ~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl  138 (142)
                      ..|+.+|+.+|+.+||||.+||+.+|+|+++|++||+|+..|+.+.+.+||++|||+.
T Consensus        13 ~~~g~~l~~~R~~~gltq~elA~~~gis~~~is~~E~G~~~p~~~~l~~ia~~l~v~~   70 (86)
T 3eus_A           13 VYLCQRLRQARLDAGLTQADLAERLDKPQSFVAKVETRERRLDVIEFAKWMAACEGLD   70 (86)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHTTCCHHHHHHHHTTSSCCBHHHHHHHHHHTTCGG
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHCCCCCCCHHHHHHHHHHcCCCc
Confidence            4589999999999999999999999999999999999999999999999999999953

>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=99.52  E-value=3.5e-14  Score=99.58  Aligned_cols=60  Identities=28%  Similarity=0.372  Sum_probs=57.7

Q ss_pred             hHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           80 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      .+.||.+|+.+|..+||||.+||+.+|||+++|++||+|+..|+.+.+.+||++|||+++
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            457999999999999999999999999999999999999999999999999999999985

>3vk0_A NHTF, transcriptional regulator; HTH motif, XRE transcription factor, DNA binding protein; 1.88A {Neisseria meningitidis}

Probab=99.52  E-value=2.4e-14  Score=99.13  Aligned_cols=62  Identities=19%  Similarity=0.141  Sum_probs=58.8

Q ss_pred             cchHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           78 RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        78 ~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      .+...++.+|+.+|+.+||||.+||+.+|+|+++|++||+|+..|+.+.+.+||++|||+++
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            45667999999999999999999999999999999999999999999999999999999874

>1adr_A P22 C2 repressor; transcription regulation; NMR {Enterobacteria phage P22} SCOP: a.35.1.2

Probab=99.52  E-value=2.4e-14  Score=91.13  Aligned_cols=58  Identities=22%  Similarity=0.326  Sum_probs=55.7

Q ss_pred             HHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           82 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        82 ~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      .++.+|+.+|..+|+||.+||+.+|+|+++|++||+|+..|+.+.+.+||++|||+++
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            4899999999999999999999999999999999999999999999999999999874

>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=99.51  E-value=2.3e-14  Score=93.88  Aligned_cols=61  Identities=25%  Similarity=0.349  Sum_probs=57.8

Q ss_pred             chHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           79 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      ....++.+|+.+|..+|+||.+||+.+|+|+++|++||+|+..|+.+.+.+||++|||+++
T Consensus         9 ~~~~~~~~l~~~r~~~glsq~~lA~~~gis~~~i~~~e~g~~~~~~~~l~~i~~~l~~~~~   69 (88)
T 2wiu_B            9 SPTQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELSMT   69 (88)
T ss_dssp             SHHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHCGGGCBHHHHHHHHHHTTCEEE
T ss_pred             CHHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHH
Confidence            3567999999999999999999999999999999999999999999999999999999875

>3lfp_A CSP231I C protein; transcriptional regulator, DNA binding protein, helix-turn-H restriction-modification, transcription; 2.00A {Citrobacter SP} PDB: 3lis_A

Probab=99.51  E-value=2.2e-14  Score=96.60  Aligned_cols=58  Identities=22%  Similarity=0.389  Sum_probs=55.7

Q ss_pred             HHHHHHHHHHhCCCCHHHHHHHhCCCHHH----HHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 032366           83 LKKAIVQARNDKKLTQSQLAQLINEKPQV----IQEYESGKAIPNQQILTKLERALGVKLRG  140 (142)
Q Consensus        83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~st----Is~~E~G~~~p~~~~l~kLa~~Lgvsl~e  140 (142)
                      ++.+|+.+|.++||||.+||+.+|+|+++    |++||+|+..|+.+.+.+||++|||+++.
T Consensus         2 ~g~~lk~~R~~~glsq~~lA~~~gis~~~~~~~is~~E~g~~~p~~~~l~~la~~l~v~~~~   63 (98)
T 3lfp_A            2 LIRRLKDARLRAGISQEKLGVLAGIDEASASARMNQYEKGKHAPDFEMANRLAKVLKIPVSY   63 (98)
T ss_dssp             CHHHHHHHHHHHTCCHHHHHHHTTCCHHHHHHHHHHHHHTSSCCCHHHHHHHHHHHTSCGGG
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCcchhhhHHHHHHCCCCCCCHHHHHHHHHHHCcCHHH
Confidence            68899999999999999999999999999    99999999999999999999999999863

>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=2.5e-14  Score=98.62  Aligned_cols=60  Identities=18%  Similarity=0.403  Sum_probs=57.0

Q ss_pred             hHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           80 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      .+.++.+|+.+|+.+||||.+||+.+|+|+++|++||+|+..|+.+.+.+||++|||+++
T Consensus         7 ~~~~~~~l~~~r~~~glsq~~lA~~~gis~~~i~~~e~g~~~p~~~~l~~la~~l~v~~~   66 (114)
T 3op9_A            7 QHQFAENLSRLKKEHGLKNHQIAELLNVQTRTVAYYMSGETKPDIEKLIRLATYFHLSID   66 (114)
T ss_dssp             CCCHHHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHHTSSCCCHHHHHHHHHHHTCCHH
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHH
Confidence            345999999999999999999999999999999999999999999999999999999875

>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=99.51  E-value=4.6e-14  Score=93.45  Aligned_cols=62  Identities=18%  Similarity=0.145  Sum_probs=57.6

Q ss_pred             chHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 032366           79 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG  140 (142)
Q Consensus        79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~e  140 (142)
                      +...++..|+.+|.++|+||.+||+.+|+|+++|++||+|+..|+.+.+.+||++|||++++
T Consensus        14 ~~~~l~~~l~~~R~~~glsq~~lA~~~gis~~~is~~e~g~~~~~~~~l~~ia~~l~v~~~~   75 (92)
T 1lmb_3           14 DARRLKAIYEKKKNELGLSQESVADKMGMGQSGVGALFNGINALNAYNAALLAKILKVSVEE   75 (92)
T ss_dssp             HHHHHHHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHTTSSCCCHHHHHHHHHHHTSCGGG
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHCCCHHH
Confidence            34568889999999999999999999999999999999999999999999999999999863

>4ghj_A Probable transcriptional regulator; structural genomics, niaid, national institute of allergy AN infectious diseases; HET: MSE; 1.75A {Vibrio vulnificus}

Probab=99.50  E-value=6.7e-14  Score=96.08  Aligned_cols=59  Identities=25%  Similarity=0.344  Sum_probs=54.2

Q ss_pred             cchHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 032366           78 RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL  138 (142)
Q Consensus        78 ~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl  138 (142)
                      .+...+|++|+.+|+++||||.+||+++|||+++|++||+|+  ++++.+.+|+.+||+.+
T Consensus        32 ~l~~~lG~~ir~~R~~~glTQ~eLA~~~gvs~~~is~~E~G~--~~~~~l~~i~~aL~~~~   90 (101)
T 4ghj_A           32 ALAEEIGDRLKQARLNRDLTQSEVAEIAGIARKTVLNAEKGK--VQLDIMIAILMALDLTE   90 (101)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHTTC--CBHHHHHHHHHHTTCCG
T ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHcCCCHHHHHHHHCCC--CCHHHHHHHHHHcCCCc
Confidence            456779999999999999999999999999999999999996  56788999999999964

>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=99.49  E-value=1.5e-14  Score=89.61  Aligned_cols=57  Identities=30%  Similarity=0.369  Sum_probs=53.5

Q ss_pred             HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      ++.+|+.+|.++|+||.+||+.+|+|+++|++||+|+..|+.+.+.+||++|||+++
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            345789999999999999999999999999999999999999999999999999874

>3f52_A CLP gene regulator (CLGR); helix-turn-helix motif, transcriptional ACTI human pathogen, transcription activator; 1.75A {Corynebacterium glutamicum} PDB: 3f51_A

Probab=99.49  E-value=4.6e-14  Score=97.68  Aligned_cols=62  Identities=26%  Similarity=0.353  Sum_probs=58.7

Q ss_pred             cchHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           78 RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        78 ~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      .....|+.+|+.+|..+||||.+||+.+|||+++|++||+|+..|+.+.+.+||++|||+++
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            45567999999999999999999999999999999999999999999999999999999874

>3bs3_A Putative DNA-binding protein; XRE-family, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.65A {Bacteroides fragilis}

Probab=99.48  E-value=2.7e-14  Score=91.05  Aligned_cols=58  Identities=24%  Similarity=0.315  Sum_probs=55.3

Q ss_pred             HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 032366           83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG  140 (142)
Q Consensus        83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~e  140 (142)
                      ++.+|+.+|..+|+||.+||+.+|+|+++|++||+|+..|+.+.+.+||++|||++++
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            6788999999999999999999999999999999999999999999999999999863

>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=99.48  E-value=5.5e-14  Score=87.86  Aligned_cols=56  Identities=30%  Similarity=0.415  Sum_probs=53.0

Q ss_pred             HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      |+.+|+.+|..+|+||.+||+.+|+|+++|++||+|+..|+.. +.+||++|||+++
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            7899999999999999999999999999999999999888777 9999999999874

>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=1.5e-14  Score=100.33  Aligned_cols=61  Identities=28%  Similarity=0.349  Sum_probs=57.3

Q ss_pred             hHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 032366           80 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG  140 (142)
Q Consensus        80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~e  140 (142)
                      ...++.+|+.+|+.+||||.+||+.+|||+++|++||+|+..|+.+.+.+||++|||++++
T Consensus        21 ~~~~g~~Lk~~R~~~gltq~elA~~~gis~~~is~~E~G~~~ps~~~l~~ia~~l~v~~~~   81 (111)
T 3mlf_A           21 QSNAMKTLKELRTDYGLTQKELGDLFKVSSRTIQNMEKDSTNIKDSLLSKYMSAFNVKYDD   81 (111)
T ss_dssp             CCSSCEEHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHHCCTTCCHHHHHHHHHHHTCCGGG
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHhCcCHHH
Confidence            3457889999999999999999999999999999999999999999999999999999863

>3trb_A Virulence-associated protein I; mobIle and extrachromosomal element functions, DNA binding P; 2.00A {Coxiella burnetii}

Probab=99.47  E-value=1e-13  Score=95.46  Aligned_cols=58  Identities=12%  Similarity=0.127  Sum_probs=55.1

Q ss_pred             HHHHHHHH-HHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           82 ELKKAIVQ-ARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        82 ~~g~~Lk~-~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      ..|++|++ +|+++||||.+||+.+|||+++|++||+|+..|+.+.+.+||++|||+++
T Consensus        13 ~pG~~Lk~~lr~~~gltq~eLA~~lGis~~~is~ie~G~~~~s~~~~~kla~~lgvs~~   71 (104)
T 3trb_A           13 HPGEILAEELGFLDKMSANQLAKHLAIPTNRVTAILNGARSITADTALRLAKFFGTTPE   71 (104)
T ss_dssp             CHHHHHHHHHHHTTSCCHHHHHHHHTSCHHHHHHHHTTSSCCCHHHHHHHHHHHTCCHH
T ss_pred             CHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHH
Confidence            37999996 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=99.45  E-value=1.3e-13  Score=86.52  Aligned_cols=57  Identities=28%  Similarity=0.272  Sum_probs=52.3

Q ss_pred             HHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           82 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        82 ~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      .++.+|+.+|..+|+||.+||+.+|+|+++|++||+|+..|.. .+.+||++|||+++
T Consensus         3 ~~~~~l~~~r~~~glsq~~lA~~~gis~~~i~~~e~g~~~~~~-~l~~i~~~l~~~~~   59 (71)
T 1zug_A            3 TLSERLKKRRIALKMTQTELATKAGVKQQSIQLIEAGVTKRPR-FLFEIAMALNCDPV   59 (71)
T ss_dssp             SHHHHHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHTTCCSSCS-THHHHHHHTTSCHH
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCChH-HHHHHHHHHCCCHH
Confidence            4899999999999999999999999999999999999987654 49999999999874

>2wus_R RODZ, putative uncharacterized protein; structural protein, cell WALL morphogenesis, bacterial cytos bacterial actin; 2.90A {Thermotoga maritima}

Probab=99.44  E-value=1.1e-13  Score=96.46  Aligned_cols=60  Identities=15%  Similarity=0.235  Sum_probs=54.3

Q ss_pred             hHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCC------CHHHHHHHHHHhCCCCC
Q 032366           80 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIP------NQQILTKLERALGVKLR  139 (142)
Q Consensus        80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p------~~~~l~kLa~~Lgvsl~  139 (142)
                      .+.+|.+|+.+|+++||||.+||+.+|||+++|++||+|+..|      ....+.+||++|||+++
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            4579999999999999999999999999999999999998754      34678999999999874

>2l49_A C protein; P2 bacteriophage, P2 C, direct repeats, DNA-binding protein, binding protein; NMR {Enterobacteria phage P2} PDB: 2xcj_A

Probab=99.44  E-value=8.8e-14  Score=93.23  Aligned_cols=58  Identities=22%  Similarity=0.354  Sum_probs=55.1

Q ss_pred             HHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHH--hCCCCC
Q 032366           82 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERA--LGVKLR  139 (142)
Q Consensus        82 ~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~--Lgvsl~  139 (142)
                      .++.+|+.+|..+|+||.+||+.+|+|+++|++||+|+..|+.+.+.+||++  |+|+++
T Consensus         4 ~~~~~l~~~r~~~gltq~~lA~~~gis~~~is~~e~g~~~p~~~~l~~ia~~l~~~v~~~   63 (99)
T 2l49_A            4 TISEKIVLMRKSEYLSRQQLADLTGVPYGTLSYYESGRSTPPTDVMMNILQTPQFTKYTL   63 (99)
T ss_dssp             CTTHHHHHHHHHTTCCHHHHHHHHCCCHHHHHHHTTTSSCCCHHHHHHHHSSSSSSSSSS
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCHH
Confidence            4789999999999999999999999999999999999999999999999999  888775

>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=99.44  E-value=1.2e-13  Score=88.69  Aligned_cols=56  Identities=27%  Similarity=0.400  Sum_probs=52.9

Q ss_pred             HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      .+.+|+.+|+.+||||.+||+.+|||+++|++||+|+..|+...+ +|+++|+++++
T Consensus        12 ~g~~lr~~R~~~gltq~elA~~~gvs~~tis~~E~G~~~p~~~~~-~l~~~l~~~p~   67 (73)
T 3fmy_A           12 APEFIVKVRKKLSLTQKEASEIFGGGVNAFSRYEKGNAXPHPSTI-KLLRVLDKHPE   67 (73)
T ss_dssp             CHHHHHHHHHHTTCCHHHHHHHHCSCTTHHHHHHTTSSCCCHHHH-HHHHHHHHCGG
T ss_pred             CHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHcCCCCCCHHHH-HHHHHHCCCHH
Confidence            688999999999999999999999999999999999999999988 99999998765

>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=3.5e-13  Score=87.31  Aligned_cols=60  Identities=22%  Similarity=0.212  Sum_probs=52.5

Q ss_pred             hHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH----HHHHHhCCCCC
Q 032366           80 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILT----KLERALGVKLR  139 (142)
Q Consensus        80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~----kLa~~Lgvsl~  139 (142)
                      .+.++.+|+.+|..+||||.+||+.+|+|+++|++||+|+..|+.+.+.    .|+.+|||+++
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            4579999999999999999999999999999999999999999966554    45556699874

>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=99.43  E-value=2.3e-13  Score=90.70  Aligned_cols=58  Identities=16%  Similarity=0.248  Sum_probs=55.6

Q ss_pred             HHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           82 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        82 ~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      .++++|+.+|..+|+||.+||+.+|||+++|++||+|+..|+.+.+.+||++|||+++
T Consensus         8 ~~g~~l~~~r~~~gltq~~lA~~~gis~~~is~~e~g~~~~~~~~~~~i~~~l~v~~~   65 (94)
T 2ict_A            8 RPGDIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVIGSSPQ   65 (94)
T ss_dssp             CHHHHHHHHHHHHTCCHHHHHHHHTCCHHHHHHHHHTSSCCCHHHHHHHHHHTCSCHH
T ss_pred             ChhHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHH
Confidence            4899999999999999999999999999999999999999999999999999999864

>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=99.43  E-value=2.8e-13  Score=95.40  Aligned_cols=61  Identities=16%  Similarity=0.093  Sum_probs=57.3

Q ss_pred             chHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCCC
Q 032366           79 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA-IPNQQILTKLERALGVKLR  139 (142)
Q Consensus        79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~-~p~~~~l~kLa~~Lgvsl~  139 (142)
                      +...++.+|+.+|+++||||.+||+++|+|+++|++||+|+. .|+.+.+.+||++|||+++
T Consensus        37 ~~~~lg~~L~~~R~~~glTQ~eLA~~lGis~~~Is~iE~G~~~~~s~~~l~~ia~~Lgv~~~   98 (120)
T 2o38_A           37 TKLRLAYALNAVIDRARLSQAAAAARLGINQPKVSALRNYKLEGFSVERLMTLLNALDQDVE   98 (120)
T ss_dssp             HHHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCCTTCCHHHHHHHHHHTTEEEE
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHHHHHhCCCcE
Confidence            455789999999999999999999999999999999999998 8999999999999999864

>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=99.43  E-value=2.6e-13  Score=92.44  Aligned_cols=57  Identities=25%  Similarity=0.328  Sum_probs=54.7

Q ss_pred             HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcC-CCCCCHHHHHHHHHHhCCCCC
Q 032366           83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESG-KAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G-~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      |+.+|+.+|..+|+||.+||+.+|+|+++|++||+| ...|+.+.+.+||++|||+++
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            688999999999999999999999999999999999 899999999999999999874

>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=99.42  E-value=8.7e-14  Score=94.04  Aligned_cols=58  Identities=19%  Similarity=0.257  Sum_probs=52.5

Q ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           81 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        81 ~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      +.++.+|+.+|..+||||.+||+.+|||+++|++||+|+..|+.. +.+|+++|+|+++
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            468999999999999999999999999999999999999999988 7899999999864

>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=99.42  E-value=2.8e-13  Score=92.00  Aligned_cols=59  Identities=24%  Similarity=0.308  Sum_probs=56.0

Q ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           81 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        81 ~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      ..++.+|+.+|..+|+||.+||+.+|+|+++|++||+|+..|+.+.+.+||++|||+++
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            35899999999999999999999999999999999999999999999999999999864

>3fym_A Putative uncharacterized protein; HTH DNA binding, DNA binding protein; 1.00A {Staphylococcus aureus subsp}

Probab=99.42  E-value=1.4e-13  Score=98.00  Aligned_cols=58  Identities=14%  Similarity=0.161  Sum_probs=54.1

Q ss_pred             HHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCH------HHHHHHHHHhCCCCC
Q 032366           82 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQ------QILTKLERALGVKLR  139 (142)
Q Consensus        82 ~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~------~~l~kLa~~Lgvsl~  139 (142)
                      .+|++|+++|+++||||.|||+++|+|+++|++||+|+..|.+      ..+.+||++|||+++
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            4899999999999999999999999999999999999987765      779999999999875

>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=99.41  E-value=5.8e-13  Score=99.15  Aligned_cols=61  Identities=20%  Similarity=0.308  Sum_probs=58.1

Q ss_pred             chHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           79 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      +...++.+|+.+|+++||||.+||+++|+|+++|++||+|+..|+.+.+.+||++|||+++
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            3467999999999999999999999999999999999999999999999999999999986

>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=99.40  E-value=6.8e-13  Score=98.96  Aligned_cols=61  Identities=20%  Similarity=0.424  Sum_probs=58.2

Q ss_pred             chHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCCC
Q 032366           79 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA-IPNQQILTKLERALGVKLR  139 (142)
Q Consensus        79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~-~p~~~~l~kLa~~Lgvsl~  139 (142)
                      ..+.++.+|+.+|+++||||.+||+++|+|+++|++||+|+. .|+.+.+.+||++|||+++
T Consensus         7 ~~~~~g~~l~~~r~~~g~s~~~la~~~gis~~~ls~~e~g~~~~p~~~~l~~ia~~l~~~~~   68 (198)
T 2bnm_A            7 ASTGFAELLKDRREQVKMDHAALASLLGETPETVAAWENGEGGELTLTQLGRIAHVLGTSIG   68 (198)
T ss_dssp             HHHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTTCTTCBHHHHHHHHHHTTSCTG
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHHHHHhCCCHH
Confidence            456799999999999999999999999999999999999999 9999999999999999985

>2eby_A Putative HTH-type transcriptional regulator YBAQ; hypothetical protein, JW0472, structural genomics, NPPSFA; 2.25A {Escherichia coli}

Probab=99.39  E-value=4.4e-13  Score=92.15  Aligned_cols=58  Identities=9%  Similarity=0.139  Sum_probs=55.4

Q ss_pred             HHHHHHHH-HHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           82 ELKKAIVQ-ARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        82 ~~g~~Lk~-~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      .+|.+|+. +|..+|+||.+||+.+|+|+++|++||+|+..|+.+.+.+||++|||+++
T Consensus        10 ~~g~~l~~~~r~~~glsq~~lA~~~gis~~~is~~e~g~~~~~~~~l~~la~~l~~~~~   68 (113)
T 2eby_A           10 TPGDILLYEYLEPLDLKINELAELLHVHRNSVSALINNNRKLTTEMAFRLAKVFDTTVD   68 (113)
T ss_dssp             CHHHHHHHHTTTTTTCCHHHHHHHHTSCHHHHHHHHTTSSCCCHHHHHHHHHHHTCCHH
T ss_pred             ChHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHH
Confidence            48999998 99999999999999999999999999999999999999999999999864

>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=99.37  E-value=1.2e-12  Score=85.52  Aligned_cols=58  Identities=19%  Similarity=0.268  Sum_probs=54.5

Q ss_pred             hHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCCC
Q 032366           80 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA-IPNQQILTKLERALGVKLR  139 (142)
Q Consensus        80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~-~p~~~~l~kLa~~Lgvsl~  139 (142)
                      ...++.+|+.+|..+  ||.+||+.+|||+++|++||+|+. .|+.+.+.+||++|||+++
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            356999999999998  999999999999999999999998 8999999999999999864

>3kxa_A NGO0477 protein, putative uncharacterized protein; NEW protein fold, OPPF, STRU genomics, oxford protein production facility; 2.80A {Neisseria gonorrhoeae}

Probab=99.36  E-value=4.6e-13  Score=96.62  Aligned_cols=59  Identities=27%  Similarity=0.263  Sum_probs=55.6

Q ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           81 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        81 ~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      ..++.+|+.+|..+||||.+||+.+|+|+++|++||+|+..|+.+.+.+||++|||+++
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            44678899999999999999999999999999999999999999999999999999874

>3r1f_A ESX-1 secretion-associated regulator ESPR; helix-turn-helix, transcription factor, helix-turn-helix transcription factor; 2.50A {Mycobacterium tuberculosis}

Probab=99.33  E-value=2.7e-12  Score=92.10  Aligned_cols=59  Identities=10%  Similarity=0.184  Sum_probs=55.3

Q ss_pred             HHHHHHHHHHHH------hCCCCHHHHHHHhC-----CCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCCC
Q 032366           81 SELKKAIVQARN------DKKLTQSQLAQLIN-----EKPQVIQEYESGKA-IPNQQILTKLERALGVKLR  139 (142)
Q Consensus        81 ~~~g~~Lk~~R~------~~glTQ~eLA~~lg-----is~stIs~~E~G~~-~p~~~~l~kLa~~Lgvsl~  139 (142)
                      ..|+++|+.+|.      ..++||.+||+.+|     +|+++|++||+|++ .|+.+.+.+||++|||+++
T Consensus         6 ~~~~~RL~~L~~~~~~~~~~~~T~~elA~~~~~~G~~is~s~is~~E~G~r~~Ps~~~l~~iA~~f~V~~~   76 (135)
T 3r1f_A            6 TTFAARLNRLFDTVYPPGRGPHTSAEVIAALKAEGITMSAPYLSQLRSGNRTNPSGATMAALANFFRIKAA   76 (135)
T ss_dssp             CCHHHHHHHHHHHCCCTTSCCCCHHHHHHHHHTTTCCCCHHHHHHHHHTSSCCCCHHHHHHHHHHHTSCTH
T ss_pred             HHHHHHHHHHHHhhcccCCCCCCHHHHHHHHcccCCCcCHHHHHHHHCCCCCCCCHHHHHHHHHHhCCCHH
Confidence            359999999999      57899999999999     99999999999997 8999999999999999975

>3bd1_A CRO protein; transcription factor, helix-turn-helix, prophage, structural evolution, transcription; 1.40A {Xylella fastidiosa}

Probab=99.30  E-value=1.3e-12  Score=84.56  Aligned_cols=51  Identities=24%  Similarity=0.258  Sum_probs=48.4

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhC--CCC
Q 032366           86 AIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALG--VKL  138 (142)
Q Consensus        86 ~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lg--vsl  138 (142)
                      +|+.+|+.+| ||.+||+.+|||+++|++||+|+..| .+.+.+||++||  |++
T Consensus         3 ~l~~~r~~~g-sq~~lA~~lgvs~~~is~~e~g~~~p-~~~l~~ia~~l~~~v~~   55 (79)
T 3bd1_A            3 AIDIAINKLG-SVSALAASLGVRQSAISNWRARGRVP-AERCIDIERVTNGAVIC   55 (79)
T ss_dssp             HHHHHHHHHS-SHHHHHHHHTCCHHHHHHHHHHTCCC-GGGHHHHHHHTTTSSCH
T ss_pred             HHHHHHHHhC-CHHHHHHHHCCCHHHHHHHHHCCCCC-HHHHHHHHHHHCCCCcH
Confidence            6899999999 99999999999999999999999888 999999999999  874

>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=99.30  E-value=5.4e-12  Score=89.30  Aligned_cols=58  Identities=10%  Similarity=0.179  Sum_probs=54.6

Q ss_pred             HHHHHHHHHHH------hCCCCHHHHHHHhC-----CCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCCC
Q 032366           82 ELKKAIVQARN------DKKLTQSQLAQLIN-----EKPQVIQEYESGKA-IPNQQILTKLERALGVKLR  139 (142)
Q Consensus        82 ~~g~~Lk~~R~------~~glTQ~eLA~~lg-----is~stIs~~E~G~~-~p~~~~l~kLa~~Lgvsl~  139 (142)
                      .|+++|..++.      ..++||.+||+.+|     +|+++|++||+|++ .|+.+.+.+||++|||+++
T Consensus         5 ~~a~RL~~L~~~~~~~~~~~lT~~elA~~~~~~G~~iS~s~is~iE~G~r~~Ps~~~l~~iA~~f~V~~~   74 (123)
T 3qwg_A            5 TFAARLNRLFDTVYPPGRGPHTSAEVIAALKAEGITMSAPYLSQLRSGNRTNPSGATMAALANFFRIKAA   74 (123)
T ss_dssp             CHHHHHHHHHHHSSCTTTCSCCHHHHHHHHHHTTCCCCHHHHHHHHHTSSCCCCHHHHHHHHHHTTSCTH
T ss_pred             hHHHHHHHHHHhhccCCCCCCCHHHHHHHHcccCCCcCHHHHHHHHcCCCCCCCHHHHHHHHHHhCCCHH
Confidence            48999999999      66899999999998     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=99.29  E-value=3.7e-12  Score=98.61  Aligned_cols=58  Identities=28%  Similarity=0.348  Sum_probs=56.1

Q ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           81 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        81 ~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      ..+|.+|+.+|+++||||.+||+.+ ||+++|++||+|+..|+.+.+.+||++|||+++
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            4699999999999999999999999 999999999999999999999999999999985

>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=99.25  E-value=9.2e-12  Score=99.83  Aligned_cols=60  Identities=23%  Similarity=0.307  Sum_probs=57.1

Q ss_pred             HHHHHHHHHHHHh------CCCCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCCCC
Q 032366           81 SELKKAIVQARND------KKLTQSQLAQLINEKPQVIQEYESGKA-IPNQQILTKLERALGVKLRG  140 (142)
Q Consensus        81 ~~~g~~Lk~~R~~------~glTQ~eLA~~lgis~stIs~~E~G~~-~p~~~~l~kLa~~Lgvsl~e  140 (142)
                      ..||.+|+.+|++      +||||.|||+++|||+++|++||+|+. .|+.+.+.+||++|+|+++|
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            4699999999999      999999999999999999999999997 99999999999999999864

>4ich_A Transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, transcription RE; 1.95A {Saccharomonospora viridis}

Probab=99.21  E-value=1.1e-12  Score=103.51  Aligned_cols=60  Identities=15%  Similarity=0.201  Sum_probs=0.0

Q ss_pred             hHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           80 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      .+.++++|+.+|+++||||.+||+++|||+++|++||+|+..|+.+.+.+||++|||+++
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            356999999999999999999999999999999999999999999999999999999985

>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=99.17  E-value=2.3e-11  Score=85.86  Aligned_cols=55  Identities=27%  Similarity=0.390  Sum_probs=49.5

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      +.+|+.+|+.+||||.+||+.+|+|+++|++||+|+..|+... .+|+++|+++++
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 577888887654

>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=99.28  Aligned_cols=57  Identities=21%  Similarity=0.215  Sum_probs=55.1

Q ss_pred             HHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           82 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        82 ~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      .+|++|+.+|+++|+||.+||+.+ +|+++|++||+|+..|+.+.+.+||++|||+++
T Consensus         3 ~ig~~lk~~R~~~gltq~~la~~~-is~~~is~~E~g~~~~~~~~l~~i~~~l~v~~~   59 (317)
T 2awi_A            3 KIGSVLKQIRQELNYHQIDLYSGI-MSKSVYIKVEADSRPISVEELSKFSERLGVNFF   59 (317)
T ss_dssp             CHHHHHHHHHHHTTCCHHHHHTTT-SCHHHHHHHHTTCSCCBHHHHHHHHHHHTSCHH
T ss_pred             HHHHHHHHHHHHCCCCHHHHHHHh-cCHHHHHHHHCCCCCCCHHHHHHHHHHcCCCHH
Confidence            489999999999999999999999 999999999999999999999999999999875

>2p5t_A Putative transcriptional regulator PEZA; postsegregational killing system, phosphoryltransferase, HEL helix motif, transcription regulator; 3.20A {Streptococcus pneumoniae}

Probab=99.15  E-value=3.3e-12  Score=93.05  Aligned_cols=57  Identities=19%  Similarity=0.355  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      ++.+|+.+|...|+||.+||+++|+|+++|++||+|...|+.+.+.+||++|||++.
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

>3bdn_A Lambda repressor; repressor, allostery; HET: DNA; 3.91A {Enterobacteria phage lambda}

Probab=99.15  E-value=2e-11  Score=93.16  Aligned_cols=60  Identities=18%  Similarity=0.170  Sum_probs=57.2

Q ss_pred             hHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           80 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      .+.++++|+++|+++|+||.+||+.+|+|+++|++||+|+..|+.+.+.+||++|||+++
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

>2qfc_A PLCR protein; TPR, HTH, transcription regulation; 2.60A {Bacillus thuringiensis serovar ISRAELE35646}

Probab=99.13  E-value=1.2e-11  Score=95.62  Aligned_cols=58  Identities=28%  Similarity=0.348  Sum_probs=55.9

Q ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           81 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        81 ~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      +.+|.+|+.+|+.+||||.+||+.+ +|+++|++||+|+..|+.+.+.+||++|||+++
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            5699999999999999999999999 999999999999999999999999999999875

>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=4.6e-11  Score=78.56  Aligned_cols=55  Identities=15%  Similarity=0.135  Sum_probs=49.6

Q ss_pred             cchHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCC
Q 032366           78 RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGV  136 (142)
Q Consensus        78 ~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgv  136 (142)
                      .....+..+|+.+|.  ||+|.+||+.+|||++||+.||+|+..|+.+  .+||++||.
T Consensus        17 ~~~~~~~~kLK~il~--GikQ~eLAK~iGIsqsTLSaIenG~~~PsL~--~kIAk~fg~   71 (83)
T 2l1p_A           17 WSHTTVRNALKDLLK--DMNQSSLAKECPLSQSMISSIVNSTYYANVS--AAKCQEFGR   71 (83)
T ss_dssp             CCHHHHHHHHHHHHT--TSCHHHHHHHSSSCHHHHHHHHTCSSCCCCC--SHHHHHHHH
T ss_pred             hhHHHHHHHHHHHHH--hcCHHHHHHHcCCCHHHHHHHHcCCCCCCch--HHHHHHHHH
Confidence            344568889999998  9999999999999999999999999999988  799999974

>1neq_A DNA-binding protein NER; NMR {Enterobacteria phage MU} SCOP: a.35.1.2 PDB: 1ner_A

Probab=99.08  E-value=1.2e-10  Score=75.50  Aligned_cols=53  Identities=15%  Similarity=0.161  Sum_probs=45.4

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      ..+|+.++.++|+||.+||+.+|+|+++|++|+++   |.+.....||++|||+++
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   334445569999999975

>2fjr_A Repressor protein CI; genetic switch, regulation, cooperativity, transcription regulator; 1.95A {Enterobacteria phage 186} PDB: 2fkd_A

Probab=99.03  E-value=3.6e-10  Score=83.55  Aligned_cols=58  Identities=16%  Similarity=0.133  Sum_probs=53.3

Q ss_pred             chHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           79 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      -.+.++++|+++|..+  ||.+||+++|+|+++|++||+|...| .+.+.+||++|||+++
T Consensus         6 ~~~~~~~rl~~~r~~~--tq~elA~~~Gis~~~i~~~e~g~~~p-~~~l~~ia~~~~v~~~   63 (189)
T 2fjr_A            6 SNVDVLDRICEAYGFS--QKIQLANHFDIASSSLSNRYTRGAIS-YDFAAHCALETGANLQ   63 (189)
T ss_dssp             CHHHHHHHHHHHHTCS--SHHHHHHHTTCCHHHHHHHHHSSSCC-HHHHHHHHHHHCCCHH
T ss_pred             ccHHHHHHHHHHHhhc--CHHHHHHHhCcCHHHHHHHHhCCCCC-HHHHHHHHHHHCCCHH
Confidence            3467999999999877  99999999999999999999999999 9999999999999863

>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=98.83  E-value=8.9e-09  Score=76.60  Aligned_cols=46  Identities=11%  Similarity=0.157  Sum_probs=41.3

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHH
Q 032366           84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTK  129 (142)
Q Consensus        84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~k  129 (142)
                      .++|+.+|+++||||.++|+.+|||+++|++||+|++.++...+.+
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            4589999999999999999999999999999999998777776543

>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=98.67  E-value=5.5e-08  Score=71.29  Aligned_cols=59  Identities=14%  Similarity=0.126  Sum_probs=56.1

Q ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           81 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        81 ~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      ..+.++|..+|.++|||+++||+.+|+|...+..+|.|+..|+.+.+.+|+++||++.+
T Consensus        12 ~~~~~~I~~AK~~KGLTwe~IAe~iG~S~v~vtaa~lGQ~~ls~e~A~kLa~~LgL~~e   70 (156)
T 1dw9_A           12 LDLADAILLSKAKKDLSFAEIADGTGLAEAFVTAALLGQQALPADAARLVGAKLDLDED   70 (156)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHTTSSSCHHHHHHHHTTSSCCCHHHHHHHHHHTTCCHH
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHcCCCCCCHHHHHHHHHHhCcCHH
Confidence            56889999999999999999999999999999999999999999999999999998754

>1nr3_A MTH0916, DNA-binding protein TFX; northeast structural genomics consortium, reduced- dimensionality PSI; NMR {Methanothermobacterthermautotrophicus} SCOP: d.236.1.1

Probab=98.60  E-value=8.6e-11  Score=82.43  Aligned_cols=49  Identities=16%  Similarity=0.256  Sum_probs=45.4

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHcC------CCCCCHHHHHHHHHHhCCCCCC
Q 032366           91 RNDKKLTQSQLAQLINEKPQVIQEYESG------KAIPNQQILTKLERALGVKLRG  140 (142)
Q Consensus        91 R~~~glTQ~eLA~~lgis~stIs~~E~G------~~~p~~~~l~kLa~~Lgvsl~e  140 (142)
                      |+ +||||.+||+++|+|+++|++||+|      +..|+...+.+||..|+|++++
T Consensus         2 R~-~glTQ~eLA~~~Gvs~~~is~~E~G~~~~~~~~~p~~~~l~~la~~l~v~~~~   56 (122)
T 1nr3_A            2 RE-RGWSQKKIARELKTTRQNVSAIERKAMENIEKSRNTLDFVKSLKSPVRILCRR   56 (122)
T ss_dssp             CC-CSCSSCSTHHHHHHCCSSSCCHHHHHHTTCSSSSCHHHHHHHHCCCEEEEECC
T ss_pred             cc-cCCCHHHHHHHhCCCHHHHHHHHcCCCccchhcccCHHHHHHHHHHHcccccc
Confidence            55 8999999999999999999999999      8889999999999999998753

>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=98.46  E-value=2.6e-07  Score=57.15  Aligned_cols=41  Identities=20%  Similarity=0.233  Sum_probs=34.1

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 032366           95 KLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL  138 (142)
Q Consensus        95 glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl  138 (142)
                      ++||.+||+.+|||+++|++||  ...| ...+..|+++||..+
T Consensus        10 ~~tq~~lA~~lGvs~~~Vs~we--~~~p-~~~~~~i~~~~~g~v   50 (61)
T 1rzs_A           10 FGTQRAVAKALGISDAAVSQWK--EVIP-EKDAYRLEIVTAGAL   50 (61)
T ss_dssp             HSSHHHHHHHHTCCHHHHHHCC--SBCC-HHHHHHHHHHTTSCS
T ss_pred             cCCHHHHHHHhCCCHHHHHHHH--hhCC-HHHHHHHHHHHCCCc
Confidence            4699999999999999999999  3344 456669999999655

>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=98.30  E-value=1.6e-06  Score=54.59  Aligned_cols=44  Identities=16%  Similarity=0.162  Sum_probs=37.1

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCC---CCCHHHHHHH---HHHhCCCCC
Q 032366           96 LTQSQLAQLINEKPQVIQEYESGKA---IPNQQILTKL---ERALGVKLR  139 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~G~~---~p~~~~l~kL---a~~Lgvsl~  139 (142)
                      +|+.|||+.+|+|++||+++++|+.   .++.++..+|   ++.||..++
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   7887766654   556888765

>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo, protein-DNA, human disease; 3.20A {Homo sapiens}

Probab=98.26  E-value=2.9e-06  Score=65.35  Aligned_cols=52  Identities=12%  Similarity=0.054  Sum_probs=44.8

Q ss_pred             chHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHH
Q 032366           79 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKL  130 (142)
Q Consensus        79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kL  130 (142)
                      -...++..|+.+|..+||||.+||+.+|||+++|++||++....+...+..+
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            3467899999999999999999999999999999999997776676655444

>1zx4_A P1 PARB, plasmid partition PAR B protein, PARB; translation; HET: CIT; 2.98A {Enterobacteria phage P1} PDB: 2ntz_A

Probab=98.25  E-value=3.3e-07  Score=69.29  Aligned_cols=54  Identities=9%  Similarity=0.147  Sum_probs=50.0

Q ss_pred             hHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHH----------------HcCCCCCCHHHHHHHHHHh
Q 032366           80 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEY----------------ESGKAIPNQQILTKLERAL  134 (142)
Q Consensus        80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~----------------E~G~~~p~~~~l~kLa~~L  134 (142)
                      ..++|.++..+ ...|+||.++|+.+|||+++|+++                ++|...|+...|.++++.|
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            45689999998 789999999999999999999997                6899999999999999999

>3g7d_A PHPD; non heme Fe(II) dioxygenase, cupin, biosynthetic protein; 1.80A {Streptomyces viridochromogenes} PDB: 3gbf_A 3rzz_A

Probab=98.22  E-value=1.6e-06  Score=70.49  Aligned_cols=57  Identities=19%  Similarity=0.186  Sum_probs=53.2

Q ss_pred             HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCCC
Q 032366           83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA-IPNQQILTKLERALGVKLR  139 (142)
Q Consensus        83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~-~p~~~~l~kLa~~Lgvsl~  139 (142)
                      .+-.|+..|...|+||.+||++.||++..|+.+|+|+. .+..+.+.+|+++|+|+.+
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            47789999999999999999999999999999999999 5599999999999999875

>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=98.13  E-value=5e-06  Score=52.55  Aligned_cols=45  Identities=13%  Similarity=0.062  Sum_probs=38.2

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCC
Q 032366           95 KLTQSQLAQLINEKPQVIQEYESGKAIPNQQI---LTKLERALGVKLR  139 (142)
Q Consensus        95 glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~---l~kLa~~Lgvsl~  139 (142)
                      .+|+.|+|+.+|||++||+++++|...++.+.   +.++++.||..++
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            47999999999999999999999998788776   5556888988765

>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=98.08  E-value=1.3e-05  Score=60.66  Aligned_cols=50  Identities=8%  Similarity=0.030  Sum_probs=43.7

Q ss_pred             chHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH
Q 032366           79 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILT  128 (142)
Q Consensus        79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~  128 (142)
                      -+..|+..|+.++..+|+||.+||+.+|+|+++|++|++|...++.....
T Consensus        27 ~p~~l~~~Ik~~l~~~gitQ~~lA~~~GiSqs~ISr~l~~~~~~~~~kra   76 (194)
T 1ic8_A           27 DPWRVAKMVKSYLQQHNIPQREVVDTTGLNQSHLSQHLNKGTPMKTQKRA   76 (194)
T ss_dssp             CHHHHHHHHHHHHHHTTCCHHHHHHHHCCCHHHHHHHHHSBCCCCHHHHH
T ss_pred             CHHHHHHHHHHHHHHcCCCHHHHHHHhCCChHHHHHHHhcCccccccccc
Confidence            45568999999999999999999999999999999999988777665433

>2pij_A Prophage PFL 6 CRO; transcription factor, helix-turn-helix, structural evolution, transcription; 1.70A {Pseudomonas fluorescens}

Probab=98.03  E-value=5.4e-06  Score=51.10  Aligned_cols=38  Identities=16%  Similarity=0.122  Sum_probs=34.3

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCH
Q 032366           86 AIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQ  124 (142)
Q Consensus        86 ~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~  124 (142)
                      +|+.+|.+.| ||.++|+.+|+|+++|++||+|...|++
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 9999999999999999999999876643

>1s4k_A Putative cytoplasmic protein YDIL; structural genomics, MCSG, PSI, PROT structure initiative; 1.90A {Salmonella typhimurium} SCOP: a.35.1.6

Probab=97.98  E-value=2.8e-05  Score=54.32  Aligned_cols=49  Identities=16%  Similarity=0.233  Sum_probs=43.8

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhC--CCHHHHHHHHcCCCCCCHHHHHHHHH
Q 032366           84 KKAIVQARNDKKLTQSQLAQLIN--EKPQVIQEYESGKAIPNQQILTKLER  132 (142)
Q Consensus        84 g~~Lk~~R~~~glTQ~eLA~~lg--is~stIs~~E~G~~~p~~~~l~kLa~  132 (142)
                      +..|+.+|..+||||.|.|..++  +|..+..+||+|+...+++++..+..
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            44689999999999999999998  99999999999999998888776653

>2hin_A GP39, repressor protein; transcription factor, dimer interface, helix-turn-helix; 1.05A {Enterobacteria phage N15} PDB: 3qws_A

Probab=97.57  E-value=0.00013  Score=46.55  Aligned_cols=41  Identities=17%  Similarity=0.203  Sum_probs=33.6

Q ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 032366           97 TQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL  138 (142)
Q Consensus        97 TQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl  138 (142)
                      +|.+||+.||||+++|++|++|...| ......|..+-+-.+
T Consensus        12 ~~~~lA~~lGVs~~aVs~W~~g~~iP-~~~~~~Ie~~T~G~v   52 (71)
T 2hin_A           12 DVEKAAVGVGVTPGAVYQWLQAGEIP-PLRQSDIEVRTAYKL   52 (71)
T ss_dssp             SHHHHHHHHTSCHHHHHHHHHHTSCC-HHHHHHHHHHTTTSS
T ss_pred             CHHHHHHHHCCCHHHHHHHHhCCCCC-HHHHHHHHHHhCCcc
Confidence            69999999999999999999886544 666778887776544

>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=97.53  E-value=8.7e-05  Score=55.13  Aligned_cols=38  Identities=18%  Similarity=0.240  Sum_probs=35.3

Q ss_pred             hHHHHHHHHHHHHhCCC--CHHHHHHHhCCC-HHHHHHHHc
Q 032366           80 PSELKKAIVQARNDKKL--TQSQLAQLINEK-PQVIQEYES  117 (142)
Q Consensus        80 ~~~~g~~Lk~~R~~~gl--TQ~eLA~~lgis-~stIs~~E~  117 (142)
                      ...+.++|+++|+++|+  ||.+||+.+|++ +++|++|++
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            34689999999999999  999999999999 999999987

>2l0k_A Stage III sporulation protein D; SPOIIID, solution structure, DNA binding, bacillus subti transcription factor, transcription; NMR {Bacillus subtilis}

Probab=97.44  E-value=0.00016  Score=48.43  Aligned_cols=52  Identities=12%  Similarity=0.072  Sum_probs=43.9

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhCC
Q 032366           85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK-AIPNQQILTKLERALGV  136 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~-~~p~~~~l~kLa~~Lgv  136 (142)
                      ..|.++....++|..+||+.+|||.+||+++.++. ..++.++..++.++||.
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            44556666667999999999999999999999997 67889999999888764

>2cw1_A SN4M; lambda CRO fold, de novo protein; NMR {Synthetic} SCOP: k.46.1.1

Probab=97.33  E-value=0.00025  Score=44.44  Aligned_cols=34  Identities=18%  Similarity=0.117  Sum_probs=28.7

Q ss_pred             HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCC
Q 032366           87 IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIP  122 (142)
Q Consensus        87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p  122 (142)
                      |+.++...  ||.++|+.+|+|+++|++|+++.+..
T Consensus         7 Lk~l~~~~--sq~~~A~~Lgvsq~aVS~~~~~~r~i   40 (65)
T 2cw1_A            7 LKKFVEDK--NQEYAARALGLSQKLIEEVLKRGLPV   40 (65)
T ss_dssp             HHHHHTTS--CHHHHHHHSSSCHHHHHHHHHTTCCC
T ss_pred             HHHHHHHc--CHHHHHHHhCCCHHHHHHHHHhcCCc
Confidence            66677765  99999999999999999999865543

>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=97.14  E-value=0.00052  Score=45.09  Aligned_cols=40  Identities=13%  Similarity=0.096  Sum_probs=33.6

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 032366           95 KLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL  138 (142)
Q Consensus        95 glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl  138 (142)
                      -++|..+|+.+|++.++|++|.+|.    .+.+..|..+||..+
T Consensus        24 ~~gQ~~vAe~~GvdeStISR~k~~~----~~~~~~lLa~Lglkv   63 (83)
T 1zs4_A           24 MLGTEKTAEAVGVDKSQISRWKRDW----IPKFSMLLAVLEWGV   63 (83)
T ss_dssp             HHCHHHHHHHHTSCHHHHHHHHHHT----HHHHHHHHHHHTTCC
T ss_pred             HHhhHHHHHHhCCCHHHHhhhhhhH----HHHHHHHHHHhccCC
Confidence            3689999999999999999999974    556677777788765

>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=96.96  E-value=0.0028  Score=35.44  Aligned_cols=37  Identities=8%  Similarity=0.144  Sum_probs=28.4

Q ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 032366           81 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESG  118 (142)
Q Consensus        81 ~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G  118 (142)
                      ......+..+. ..|+|..++|+.+|||++||.+|.+.
T Consensus         8 ~~~~~~i~~~~-~~g~s~~~IA~~lgis~~Tv~~~~~~   44 (51)
T 1tc3_C            8 DTERAQLDVMK-LLNVSLHEMSRKISRSRHCIRVYLKD   44 (51)
T ss_dssp             HHHHHHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHHC
T ss_pred             HHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHhh
Confidence            33444444443 57999999999999999999999753

>1xwr_A Regulatory protein CII; all-alpha fold, DNA binding protein; 2.56A {Bacteriophage lambda} SCOP: a.35.1.9 PDB: 1zpq_A

Probab=96.90  E-value=5.5e-05  Score=51.21  Aligned_cols=45  Identities=16%  Similarity=0.154  Sum_probs=31.9

Q ss_pred             HhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 032366           92 NDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL  138 (142)
Q Consensus        92 ~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl  138 (142)
                      .-.+++|..||+.+||+.++|++|++|.. +....+..+. .|+|.+
T Consensus        20 ~la~~gq~~vA~~iGV~~StISR~k~~~~-~~~~~lLa~l-~l~v~~   64 (97)
T 1xwr_A           20 KIAMLGTEKTAEAVGVDKSQISRWKRDWI-PKFSMLLAVL-EWGVVD   64 (97)
T ss_dssp             HHHHHCHHHHHHHHTCCTTTHHHHHHHHH-HHHHHHHHHH-HHCCCH
T ss_pred             HHHHHhHHHHHHHhCCCHHHHHHHHhhhH-HHHHHHHHHH-hcCCCh
Confidence            34567999999999999999999999752 2333333333 566654

>2x48_A CAG38821; archeal virus, viral protein; 2.60A {Sulfolobus islandicus rod-shaped virusorganism_taxid}

Probab=96.86  E-value=0.0028  Score=37.16  Aligned_cols=35  Identities=14%  Similarity=0.193  Sum_probs=28.5

Q ss_pred             HHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           82 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        82 ~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .....+..+ ...|+|+.++|+.+|+|++||++|.+
T Consensus        19 ~~~~~i~~l-~~~g~s~~eIA~~lgis~~TV~~~l~   53 (55)
T 2x48_A           19 DLVSVAHEL-AKMGYTVQQIANALGVSERKVRRYLE   53 (55)
T ss_dssp             HHHHHHHHH-HHTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            344555555 46899999999999999999999874

>4ich_A Transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, transcription RE; 1.95A {Saccharomonospora viridis}

Probab=96.84  E-value=0.00065  Score=52.98  Aligned_cols=102  Identities=12%  Similarity=0.126  Sum_probs=27.2

Q ss_pred             eeccCCCCCccccCHHHHHHHHHcCCChhHHHhhhcCCCCCCCCCCCcccccchhhhc----cccCC-------------
Q 032366           15 VIKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTE----NLAHD-------------   77 (142)
Q Consensus        15 ~~~~~~~~~~~~~~~~~~~~a~r~G~~v~t~kk~~~g~~~~~~~~~~~~~~kl~~~~~----~~~~~-------------   77 (142)
                      .||.+-..-...++-++-..|.+.|++.+|+.+||.|...+..    ..+.++.....    .|-..             
T Consensus        30 ~~~~~l~~~r~~~g~t~~~la~~~g~s~~~is~~e~g~~~p~~----~~l~~ia~~l~~~~~~l~~~~~~~~~~~~~~~~  105 (311)
T 4ich_A           30 ELRRRVRGLIHSRPGAQREFAAAIGLDESKLSKSLNGTRRFSP----HELVRIAEHSGVTVNWLINGRDDARTVAAVPAP  105 (311)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             HHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCH----HHHHHHHHHHCCChhhhhcCCCccccccCCCCc
Confidence            3565544444455557778999999999999999999876422    22222222111    00000             


Q ss_pred             --------------cchHHHHHHHHHHHHhC---CCCHHHHHHHhCCCHHHHHHHHcCCC
Q 032366           78 --------------RVPSELKKAIVQARNDK---KLTQSQLAQLINEKPQVIQEYESGKA  120 (142)
Q Consensus        78 --------------~~~~~~g~~Lk~~R~~~---glTQ~eLA~~lgis~stIs~~E~G~~  120 (142)
                                    .....+-+...++-.+.   ++|..++|+.+|||+.+|++|-.++.
T Consensus       106 ~~~~~~~~~~~~~~~~r~~il~aa~~l~~~~G~~~~T~~~IA~~AGvs~gtlY~yF~sKe  165 (311)
T 4ich_A          106 TARSRSAPAGEPQSEARRRILETAWRLIARRGYHNVRIHDIASELGTSNATIHYHFPSKK  165 (311)
T ss_dssp             -----------CCHHHHHHHHHHHHHHHHHHCGGGCCHHHHHHHHTCCHHHHHHHCSSHH
T ss_pred             ccccCCCCCccchhhHHHHHHHHHHHHHHHcCCccCCHHHHHHHhCCCchhHHHhCCCHH
Confidence                          00011222223333333   57999999999999999999976653

>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=96.63  E-value=0.003  Score=46.03  Aligned_cols=38  Identities=13%  Similarity=0.205  Sum_probs=32.2

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCCH-HHHHHHHHHh
Q 032366           95 KLTQSQLAQLINEKPQVIQEYESGKAIPNQ-QILTKLERAL  134 (142)
Q Consensus        95 glTQ~eLA~~lgis~stIs~~E~G~~~p~~-~~l~kLa~~L  134 (142)
                      |+|+.++|+.+|||++||++|.+.  .|.. +.+.++++.|
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            899999999999999999999985  4653 6777777764

>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=96.46  E-value=0.0058  Score=41.46  Aligned_cols=41  Identities=15%  Similarity=0.112  Sum_probs=32.7

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q 032366           95 KLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALG  135 (142)
Q Consensus        95 glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lg  135 (142)
                      .+||.|+|+.+|+|++||+++-+.-...+.+.-..|...|.
T Consensus        58 e~TQREIA~~lGiS~stISRi~r~L~~l~~~~k~~l~~~l~   98 (101)
T 1jhg_A           58 EMSQRELKNELGAGIATITRGSNSLKAAPVELRQWLEEVLL   98 (101)
T ss_dssp             CSCHHHHHHHHCCCHHHHHHHHHHHHHSCHHHHHHHHHHHS
T ss_pred             CcCHHHHHHHHCCChhhhhHHHHHHHHccHHHHHHHHHHhc
Confidence            39999999999999999999965544556677667766664

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

Probab=96.42  E-value=0.0045  Score=35.12  Aligned_cols=33  Identities=18%  Similarity=0.184  Sum_probs=26.5

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCC
Q 032366           86 AIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK  119 (142)
Q Consensus        86 ~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~  119 (142)
                      .+..+. ..|+|..++|+.+|||++||.+|.+..
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 468999999999999999999998643

>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=95.96  E-value=0.05  Score=37.03  Aligned_cols=76  Identities=8%  Similarity=0.081  Sum_probs=50.2

Q ss_pred             HHHHHHHHcCCChhHHHhhhcCCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhC--C
Q 032366           30 KVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLIN--E  107 (142)
Q Consensus        30 ~~~~~a~r~G~~v~t~kk~~~g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lg--i  107 (142)
                      +.-..|+..|++..|+.+|-.-....     +..  ..     .-.+..+....-..|..+.....+|..+|+..+|  +
T Consensus        24 s~~~ia~~lgis~~Tv~r~~~~~~~~-----g~~--~~-----~gr~~~l~~~~~~~i~~~~~~~~~s~~~i~~~lg~~~   91 (141)
T 1u78_A           24 SLHEMSRKISRSRHCIRVYLKDPVSY-----GTS--KR-----APRRKALSVRDERNVIRAASNSCKTARDIRNELQLSA   91 (141)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHSGGGT-----TCC--CC-----CCCCCSSCHHHHHHHHHHHHHCCCCHHHHHHHTTCCS
T ss_pred             CHHHHHHHHCcCHHHHHHHHHccccc-----CCc--CC-----CCCCCcCCHHHHHHHHHHHhCCCCCHHHHHHHHCCCc
Confidence            34567899999999999997532220     000  00     0111233344445555556667899999999999  8


Q ss_pred             CHHHHHHHHc
Q 032366          108 KPQVIQEYES  117 (142)
Q Consensus       108 s~stIs~~E~  117 (142)
                      |.+||.+|..
T Consensus        92 s~~tV~r~l~  101 (141)
T 1u78_A           92 SKRTILNVIK  101 (141)
T ss_dssp             CHHHHHHHHH
T ss_pred             cHHHHHHHHH
Confidence            9999999985

>2hsg_A Glucose-resistance amylase regulator; CCPA, transcriptional regulator, transcription regulator; 2.50A {Bacillus megaterium} SCOP: a.35.1.5 c.93.1.1 PDB: 1rzr_G 2jcg_A 1zvv_A 3oqo_A* 3oqm_A* 3oqn_A*

Probab=95.75  E-value=0.017  Score=44.78  Aligned_cols=44  Identities=11%  Similarity=0.101  Sum_probs=35.9

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCC
Q 032366           95 KLTQSQLAQLINEKPQVIQEYESGKAIPNQQI---LTKLERALGVKL  138 (142)
Q Consensus        95 glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~---l~kLa~~Lgvsl  138 (142)
                      ..|.+|+|+++|||.+|||+..||....+.++   +.+.++.||..+
T Consensus         2 ~~ti~dvA~~agVS~~TVSrvln~~~~vs~~tr~rV~~aa~~lgY~p   48 (332)
T 2hsg_A            2 NVTIYDVAREASVSMATVSRVVNGNPNVKPSTRKKVLETIERLGYRP   48 (332)
T ss_dssp             CCCHHHHHHHTTSCHHHHHHHHTTCTTSCHHHHHHHHHHHHHHTCCS
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHCCCc
Confidence            36899999999999999999999987777665   445567787655

>3kjx_A Transcriptional regulator, LACI family; LACL family, protein structure initiative II(PSI II), NYSGXRC, structural genomics; 2.33A {Silicibacter pomeroyi}

Probab=95.53  E-value=0.019  Score=44.78  Aligned_cols=47  Identities=9%  Similarity=0.094  Sum_probs=37.2

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCC
Q 032366           93 DKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQI---LTKLERALGVKLR  139 (142)
Q Consensus        93 ~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~---l~kLa~~Lgvsl~  139 (142)
                      .+..|.+|+|+++|||.+|||+..||....+.++   +.+.++.||..+.
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            3458999999999999999999999987777665   5555677887654

>2elh_A CG11849-PA, LD40883P; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Drosophila melanogaster}

Probab=95.49  E-value=0.028  Score=36.24  Aligned_cols=39  Identities=10%  Similarity=0.089  Sum_probs=29.3

Q ss_pred             cchHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           78 RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        78 ~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .+..++-..+..+. ..|.|..++|+.+|||++||.+|.+
T Consensus        22 ~ys~e~k~~~v~~~-~~g~s~~~iA~~~gIs~sTl~rW~k   60 (87)
T 2elh_A           22 SLTPRDKIHAIQRI-HDGESKASVARDIGVPESTLRGWCK   60 (87)
T ss_dssp             SCCHHHHHHHHHHH-HHTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHH-HCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            34445544444444 3689999999999999999999974

>2w7n_A TRFB transcriptional repressor protein; INCP, plasmid, repressor, DNA-binding, transcription/DNA; HET: BRU; 1.85A {Escherichia coli}

Probab=95.40  E-value=0.033  Score=37.68  Aligned_cols=35  Identities=9%  Similarity=-0.021  Sum_probs=28.4

Q ss_pred             HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ....+..+--..|+||.++|+.+|+|+++|+++..
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            33445555667899999999999999999998764

>2glo_A Brinker CG9653-PA; protein-DNA complex, helix-turn-helix motif, transcription/DNA complex; NMR {Drosophila melanogaster}

Probab=95.39  E-value=0.036  Score=33.05  Aligned_cols=38  Identities=16%  Similarity=0.170  Sum_probs=29.6

Q ss_pred             chHHHHHHHHHHHHhCCCC----HHHHHHHhCCCHHHHHHHHc
Q 032366           79 VPSELKKAIVQARNDKKLT----QSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        79 ~~~~~g~~Lk~~R~~~glT----Q~eLA~~lgis~stIs~~E~  117 (142)
                      ...+|-..+.. ..+.|.|    ..++|+.+||++++|.+|..
T Consensus         6 ys~efK~~~~~-~~~~g~s~~~~~~~vA~~~gIs~~tl~~W~~   47 (59)
T 2glo_A            6 FTPHFKLQVLE-SYRNDNDCKGNQRATARKYNIHRRQIQKWLQ   47 (59)
T ss_dssp             CCHHHHHHHHH-HHHHCTTTTTCHHHHHHHTTSCHHHHHHHHT
T ss_pred             CCHHHHHHHHH-HHHcCCCcchHHHHHHHHHCcCHHHHHHHHH
Confidence            44566666633 3446789    99999999999999999975

>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=95.26  E-value=0.016  Score=36.12  Aligned_cols=31  Identities=13%  Similarity=0.038  Sum_probs=25.0

Q ss_pred             HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCC
Q 032366           87 IVQARNDKKLTQSQLAQLINEKPQVIQEYESGK  119 (142)
Q Consensus        87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~  119 (142)
                      |+++....  |+.++|+.|||++++|++|.++.
T Consensus         7 L~~~~~~~--s~t~aA~~L~vtQ~AVS~~ir~~   37 (66)
T 2ovg_A            7 LKDYAMRF--GQTKTAKDLGVYPSSINQAIHAG   37 (66)
T ss_dssp             HHHHHHHH--CHHHHHHHHTSCHHHHHHHHHHT
T ss_pred             HHHHHHHC--CHHHHHHHhCCCHHHHHHHHHhC
Confidence            44554444  99999999999999999998743

>2jn6_A Protein CGL2762, transposase; GFT PSI-2, protein structure, structural genomics, protein structure initiative; NMR {Corynebacterium glutamicum} SCOP: a.4.1.19

Probab=95.14  E-value=0.038  Score=35.96  Aligned_cols=39  Identities=13%  Similarity=0.168  Sum_probs=29.4

Q ss_pred             chHHHHHHHHHHHHhC-CCCHHHHHHHhCCCHHHHHHHHc
Q 032366           79 VPSELKKAIVQARNDK-KLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        79 ~~~~~g~~Lk~~R~~~-glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +..++-..+-.+.... |+|..++|+.+|||++||.+|.+
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            3445554454444445 89999999999999999999974

>3h5t_A Transcriptional regulator, LACI family; DNA-dependent, protein structure initiative II(PSI II), NYSGXRC, 11232D), structural genomics; 2.53A {Corynebacterium glutamicum}

Probab=95.06  E-value=0.02  Score=45.09  Aligned_cols=45  Identities=7%  Similarity=0.056  Sum_probs=36.1

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCC
Q 032366           93 DKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQI---LTKLERALGVK  137 (142)
Q Consensus        93 ~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~---l~kLa~~Lgvs  137 (142)
                      .+..|.+|+|+++|||.+|||+..||....+.++   +.+.++.||..
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            4557899999999999999999999987666554   55667777765

>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=95.00  E-value=0.025  Score=40.89  Aligned_cols=38  Identities=18%  Similarity=0.264  Sum_probs=35.5

Q ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHhCC------CHHHHHHHHcC
Q 032366           81 SELKKAIVQARNDKKLTQSQLAQLINE------KPQVIQEYESG  118 (142)
Q Consensus        81 ~~~g~~Lk~~R~~~glTQ~eLA~~lgi------s~stIs~~E~G  118 (142)
                      ..|+..++..|...|+||.+++..+|.      |+++|+++|.=
T Consensus        10 ~~~~~~~k~~r~~lg~tQ~~vg~~lg~l~g~~~sq~ti~rfE~l   53 (160)
T 1e3o_C           10 EQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEAL   53 (160)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHHSCCCCHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHhhccccCCCcCcccccccccc
Confidence            569999999999999999999999998      99999999975

>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=94.90  E-value=0.086  Score=35.45  Aligned_cols=60  Identities=20%  Similarity=0.231  Sum_probs=48.5

Q ss_pred             chHHHHHHHHHHHHhCCCCHHHHHHHh-CCCHHHHHHHHcCCCCCC------HHHHHHHHHHhCCCC
Q 032366           79 VPSELKKAIVQARNDKKLTQSQLAQLI-NEKPQVIQEYESGKAIPN------QQILTKLERALGVKL  138 (142)
Q Consensus        79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~l-gis~stIs~~E~G~~~p~------~~~l~kLa~~Lgvsl  138 (142)
                      +...+...|....+.++++|.-||+.+ +-|+.+++.+.+-+..|.      .+.|.+|-..|+.+.
T Consensus        18 ~Tk~i~~~I~~ELK~~~IsQa~FAk~vlnRsQGtLSelLR~~enPkP~~~~lW~~Lk~m~nWL~Lpe   84 (101)
T 2csf_A           18 ITAAIYDEIQQEMKRAKVSQALFAKVAANKSQGWLCELLRWKENPSPENRTLWENLCTIRRFLNLPQ   84 (101)
T ss_dssp             CCTHHHHHHHHHHHHHTCCHHHHHHHHTCCCHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHTSCH
T ss_pred             hHHHHHHHHHHHHHHcCCcHHHHHHHHHHhchhHHHHHHhcccCCCcchhhHHHHHHHHHHHHcCCH
Confidence            456799999999999999999999976 899999999998554554      366777777777653

>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA complex, SOX; 2.05A {Mus musculus}

Probab=94.78  E-value=0.033  Score=40.52  Aligned_cols=48  Identities=19%  Similarity=0.223  Sum_probs=39.2

Q ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHhCC------CHHHHHHHHcCCCCCCHHHHHHH
Q 032366           81 SELKKAIVQARNDKKLTQSQLAQLINE------KPQVIQEYESGKAIPNQQILTKL  130 (142)
Q Consensus        81 ~~~g~~Lk~~R~~~glTQ~eLA~~lgi------s~stIs~~E~G~~~p~~~~l~kL  130 (142)
                      ..|++.++..|...|+||.+++..+|.      |+++|+++|+=.  .+...+.+|
T Consensus        16 ~~fa~~fk~~ri~lg~tQ~~vg~alg~l~g~~~Sqtti~rFE~l~--ls~kn~~kl   69 (164)
T 2xsd_C           16 EQFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQ--LSFKNMCKL   69 (164)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHHSCCCCHHHHHHHHTTC--SBHHHHHHH
T ss_pred             HHHHHHHHHHHhhcCCcccccccccccccCCCcCcchhhhhhccC--CCHHHHHHc
Confidence            568999999999999999999999887      999999999643  344444443

>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=94.73  E-value=0.027  Score=40.21  Aligned_cols=48  Identities=15%  Similarity=0.156  Sum_probs=38.9

Q ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHhCC------CHHHHHHHHcCCCCCCHHHHHHH
Q 032366           81 SELKKAIVQARNDKKLTQSQLAQLINE------KPQVIQEYESGKAIPNQQILTKL  130 (142)
Q Consensus        81 ~~~g~~Lk~~R~~~glTQ~eLA~~lgi------s~stIs~~E~G~~~p~~~~l~kL  130 (142)
                      ..|+..++..|...|+||.+++..+|.      |+++|+++|+=.  .+...+.+|
T Consensus         6 ~~fa~~~k~~ri~lg~tQ~~vg~al~~l~g~~~Sqtti~rfe~l~--ls~knm~kL   59 (146)
T 1au7_A            6 EQFANEFKVRRIKLGYTQTNVGEALAAVHGSEFSQTTICRFENLQ--LSFKNACKL   59 (146)
T ss_dssp             HHHHHHHHHHHHHHTCCHHHHHHHHHHTTSSCCCHHHHHHHHTTC--SBHHHHHHH
T ss_pred             HHHHHHHHHHHHhccCcHHhhhhhcchhccCCCCcchHHHHhccC--CChHHHHhc
Confidence            468899999999999999999999987      999999999743  344444443

>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=94.60  E-value=0.075  Score=35.91  Aligned_cols=56  Identities=9%  Similarity=0.099  Sum_probs=43.3

Q ss_pred             hHHHHHHHHHHHHhCCCCHHHHHHH-hCCCHHHHHHHHcCCCCC---C---HHHHHHHHHHhC
Q 032366           80 PSELKKAIVQARNDKKLTQSQLAQL-INEKPQVIQEYESGKAIP---N---QQILTKLERALG  135 (142)
Q Consensus        80 ~~~~g~~Lk~~R~~~glTQ~eLA~~-lgis~stIs~~E~G~~~p---~---~~~l~kLa~~Lg  135 (142)
                      ...+...|++.....++||..||+. +|.++.+|+.+.+--..-   .   .+...++-..|.
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            4568999999999999999999998 899999999999854321   1   344555555544

>1pdn_C Protein (PRD paired); protein-DNA complex, double helix, PAX, paired domain, DNA-binding protein, gene regulation/DNA complex; HET: DNA; 2.50A {Drosophila melanogaster} SCOP: a.4.1.5

Probab=94.60  E-value=0.079  Score=35.09  Aligned_cols=38  Identities=8%  Similarity=0.239  Sum_probs=30.2

Q ss_pred             chHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           79 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +..++...|..+. ..|+|..++|+.+|+|++||.+|.+
T Consensus        18 ~s~~~r~~i~~~~-~~g~s~~~ia~~lgis~~Tv~~w~~   55 (128)
T 1pdn_C           18 LPNNIRLKIVEMA-ADGIRPCVISRQLRVSHGCVSKILN   55 (128)
T ss_dssp             CCHHHHHHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            4455656665555 4799999999999999999999964

>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=94.45  E-value=0.091  Score=35.68  Aligned_cols=38  Identities=8%  Similarity=0.159  Sum_probs=29.7

Q ss_pred             chHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           79 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +..+....|..+. ..|+|..++|+.+|+|++||.+|.+
T Consensus         7 ~s~~~r~~i~~~~-~~G~s~~~ia~~lgis~~Tv~r~~~   44 (141)
T 1u78_A            7 LSDTERAQLDVMK-LLNVSLHEMSRKISRSRHCIRVYLK   44 (141)
T ss_dssp             CCHHHHHHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3344555555555 5799999999999999999999974

>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=94.43  E-value=0.024  Score=34.93  Aligned_cols=23  Identities=22%  Similarity=0.432  Sum_probs=21.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcC
Q 032366           96 LTQSQLAQLINEKPQVIQEYESG  118 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~G  118 (142)
                      ||..|+|+.+|||++||.+|...
T Consensus         3 lt~~e~a~~LgvS~~Tl~rw~~~   25 (68)
T 1j9i_A            3 VNKKQLADIFGASIRTIQNWQEQ   25 (68)
T ss_dssp             EEHHHHHHHTTCCHHHHHHHTTT
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHC
Confidence            68899999999999999999974

>2o20_A Catabolite control protein A; CCPA, transcriptional regulator, helix-turn-helix, transcrip; 1.90A {Lactococcus lactis}

Probab=94.08  E-value=0.0091  Score=46.47  Aligned_cols=45  Identities=11%  Similarity=0.091  Sum_probs=0.0

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCC
Q 032366           94 KKLTQSQLAQLINEKPQVIQEYESGKAIPNQQI---LTKLERALGVKL  138 (142)
Q Consensus        94 ~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~---l~kLa~~Lgvsl  138 (142)
                      ...|.+|+|+++|||.+|||+..||....+.++   +.+.++.||..+
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            357999999999999999999999976555554   455566677544

>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=93.89  E-value=0.17  Score=35.07  Aligned_cols=39  Identities=8%  Similarity=0.236  Sum_probs=31.5

Q ss_pred             cchHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           78 RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        78 ~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .+..++...|..+. ..|+|..++|+.+|+|++||.+|.+
T Consensus        32 ~~s~e~r~~iv~~~-~~G~s~~~iA~~lgis~~TV~rw~~   70 (149)
T 1k78_A           32 PLPDVVRQRIVELA-HQGVRPCDISRQLRVSHGCVSKILG   70 (149)
T ss_dssp             CCCHHHHHHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            45566666666665 4799999999999999999999964

>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=93.76  E-value=0.37  Score=34.20  Aligned_cols=48  Identities=25%  Similarity=0.271  Sum_probs=39.4

Q ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHhCC------CHHHHHHHHcCCCCCCHHHHHHH
Q 032366           81 SELKKAIVQARNDKKLTQSQLAQLINE------KPQVIQEYESGKAIPNQQILTKL  130 (142)
Q Consensus        81 ~~~g~~Lk~~R~~~glTQ~eLA~~lgi------s~stIs~~E~G~~~p~~~~l~kL  130 (142)
                      ..|++.++..|...|+||.+++..+|.      |+++|+++|.-..  +...+.++
T Consensus         7 ~~fa~~f~~~ri~lg~tQ~~vg~al~~l~g~~~Sqsti~rfe~l~l--s~kn~~kl   60 (151)
T 3d1n_I            7 REFAKNFKIRRLSLGLTQTQVGQAMTATEGPAYSQSAISRFEKLDI--TPKSAQKL   60 (151)
T ss_dssp             HHHHHHHHHHHHTTTCCHHHHHHHHSCSSSCCCCHHHHHHHHTTCS--CHHHHHHH
T ss_pred             HHHHHHHHHHHhhcCCCcccHHHhhccccCCCCCccccccccCCCC--ChhHHHHh
Confidence            468999999999999999999999997      9999999997643  44444433

>2jml_A DNA binding domain/transcriptional regulator; anti-repressor, MERR, carotenogenesis; HET: DNA; NMR {Myxococcus xanthus}

Probab=93.71  E-value=0.17  Score=32.03  Aligned_cols=63  Identities=19%  Similarity=0.227  Sum_probs=38.5

Q ss_pred             HHHHHcCCChhHHHhhhc--CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHh
Q 032366           33 NAARRAGADIETVRKSHA--GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLI  105 (142)
Q Consensus        33 ~~a~r~G~~v~t~kk~~~--g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~l  105 (142)
                      +.|+..|+++.|++.|+.  |-..+.....+ .-..++.+         ....-..|+.+|...|+|.+++.+.+
T Consensus        10 e~A~~~gvs~~tlR~ye~~~gl~~p~r~~~~-g~R~Y~~~---------dl~~l~~I~~l~~~~G~sl~ei~~~l   74 (81)
T 2jml_A           10 TIARMTGIREATLRAWERRYGFPRPLRSEGN-NYRVYSRE---------EVEAVRRVARLIQEEGLSVSEAIAQV   74 (81)
T ss_dssp             HHHHTTSTTHHHHHHHHHHTCCSCCBSSSCS-SSCEECHH---------HHHHHHHHHHHHHHTSTHHHHHHHHH
T ss_pred             HHHHHHCcCHHHHHHHHHhCCCCCCcCCCCC-CeeecCHH---------HHHHHHHHHHHHHHCCCCHHHHHHHH
Confidence            578999999999999987  43332211100 11112211         11234557777768899999988765

>3frw_A Putative Trp repressor protein; structural genomics, APC21159, PSI-2, P structure initiative; 2.05A {Ruminococcus obeum atcc 29174} PDB: 3g1c_A

Probab=93.57  E-value=0.17  Score=34.49  Aligned_cols=37  Identities=14%  Similarity=0.065  Sum_probs=29.6

Q ss_pred             HHHHHHHHHH-HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           81 SELKKAIVQA-RNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        81 ~~~g~~Lk~~-R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ..++.|++-+ ....|+|+.++++.+|+|.+||+++-+
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            3466666544 355799999999999999999999765

>2o8x_A Probable RNA polymerase sigma-C factor; promoter recognition, transcription regulation, helix-turn-H motif, transcription; 3.00A {Mycobacterium tuberculosis}

Probab=93.54  E-value=0.14  Score=30.62  Aligned_cols=33  Identities=9%  Similarity=-0.010  Sum_probs=26.9

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ..+-.++-..|+|..++|+.+|+|.++|..+..
T Consensus        21 r~il~l~~~~g~s~~eIA~~lgis~~tv~~~~~   53 (70)
T 2o8x_A           21 REALLLTQLLGLSYADAAAVCGCPVGTIRSRVA   53 (70)
T ss_dssp             HHHHHHHHTSCCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            344455667899999999999999999998753

>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=93.54  E-value=0.11  Score=43.99  Aligned_cols=50  Identities=6%  Similarity=0.042  Sum_probs=33.5

Q ss_pred             HHHHHHHHhCCCCHHHHHHHh------CCCHHHHHHHHcCCCCC---CHHHHHHHHHHhCC
Q 032366           85 KAIVQARNDKKLTQSQLAQLI------NEKPQVIQEYESGKAIP---NQQILTKLERALGV  136 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~l------gis~stIs~~E~G~~~p---~~~~l~kLa~~Lgv  136 (142)
                      +.|++++.  -+||++||+.|      +++..+|.+||+|+..|   +...+..|-..+-.
T Consensus        21 ~~~~~~~~--~~~~~~~a~~l~~~~~~~~~~~~~~rw~~~~~~~~~~~~~~~~~l~~~~~~   79 (482)
T 3me5_A           21 AMLEKLLQ--IYDVKMLVAQLNGVGENHWSAAILKRALANDSAWHRLSEKEFAHLQTLLPK   79 (482)
T ss_dssp             HHHHHHHT--TSCHHHHHHHHHHTCSSCCCHHHHHHHHC-------CCTHHHHHHHTTSCC
T ss_pred             HHHHHHHH--HcCHHHHHHHHHhhccCCCCHHHHHHHHcCCCCCccccHHHHHHHHhhCCC
Confidence            44566555  48999999999      89999999999998766   34455556555544

>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=93.53  E-value=0.15  Score=37.60  Aligned_cols=49  Identities=16%  Similarity=0.201  Sum_probs=34.7

Q ss_pred             hHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHH
Q 032366           80 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKL  130 (142)
Q Consensus        80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kL  130 (142)
                      +.+.+..++.+... |+||.++|+++|+|+++|+++.+=-. .++.++..|
T Consensus        38 piE~A~a~~~L~~~-G~t~eeiA~~lG~s~s~V~~~LrLl~-Lp~~v~~~v   86 (178)
T 1r71_A           38 PREIADFIGRELAK-GKKKGDIAKEIGKSPAFITQHVTLLD-LPEKIADAF   86 (178)
T ss_dssp             HHHHHHHHHHHHHT-TCCHHHHHHHHTCCHHHHHHHHGGGS-CCHHHHHHH
T ss_pred             HHHHHHHHHHHHHc-CCCHHHHHHHHCcCHHHHHHHHHHHc-CCHHHHHHH
Confidence            34556666666654 99999999999999999999976322 333444443

>2p7v_B Sigma-70, RNA polymerase sigma factor RPOD; RSD, regulator of sigma 70, sigma 70 domain 4, transcription, regulation, helix-turn-helix; 2.60A {Escherichia coli} SCOP: a.4.13.2

Probab=93.48  E-value=0.12  Score=31.26  Aligned_cols=25  Identities=12%  Similarity=0.258  Sum_probs=22.7

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           93 DKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        93 ~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ..|+|.+|+|+.+|+|.++|..+..
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            4699999999999999999998864

>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=93.43  E-value=0.13  Score=36.95  Aligned_cols=48  Identities=19%  Similarity=0.225  Sum_probs=37.7

Q ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHhC------CCHHHHHHHHcCCCCCCHHHHHHH
Q 032366           81 SELKKAIVQARNDKKLTQSQLAQLIN------EKPQVIQEYESGKAIPNQQILTKL  130 (142)
Q Consensus        81 ~~~g~~Lk~~R~~~glTQ~eLA~~lg------is~stIs~~E~G~~~p~~~~l~kL  130 (142)
                      ..|+..++..|...|+||.+++..+|      +|+++|.++|.-.  .+...+.+|
T Consensus        13 ~~fa~~fk~~ri~lg~tq~~vg~al~~l~G~~~Sqtti~rfE~l~--ls~~nm~kL   66 (155)
T 3l1p_A           13 EQFAKLLKQKRITLGYTQADVGLTLGVLFGKVFSQTTISRFEALQ--LSLKNMSKL   66 (155)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHHSCCCCHHHHHHHHTTC--SCHHHHHHH
T ss_pred             HHHHHHHHhhhheecccHHHHHHHHHhhcCccccccccccccccc--CChhhHhhc
Confidence            46889999999999999999888754      7999999999753  344444443

>3hug_A RNA polymerase sigma factor; ECF sigma factor, zinc binding anti-sigma factor, oxidative transcription regulation; 2.35A {Mycobacterium tuberculosis}

Probab=93.33  E-value=0.14  Score=32.86  Aligned_cols=33  Identities=12%  Similarity=0.154  Sum_probs=27.4

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +.+-.++...|+|.+++|+.+|+|.++|..+..
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            344456677899999999999999999998764

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

Probab=93.32  E-value=0.14  Score=35.60  Aligned_cols=37  Identities=14%  Similarity=0.149  Sum_probs=28.8

Q ss_pred             HHHHHHHHHH-HhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 032366           82 ELKKAIVQAR-NDKKLTQSQLAQLINEKPQVIQEYESG  118 (142)
Q Consensus        82 ~~g~~Lk~~R-~~~glTQ~eLA~~lgis~stIs~~E~G  118 (142)
                      .+..|++-++ ...|+|+.++|+.+|+|..||+++-+.
T Consensus        61 aLs~R~eV~klL~~G~syreIA~~~g~S~aTIsRv~r~   98 (119)
T 3kor_A           61 SLSQRLQVAKMIKQGYTYATIEQESGASTATISRVKRS   98 (119)
T ss_dssp             HHHHHHHHHHHHHHTCCHHHHHHHHCCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            4566654442 446899999999999999999998764

>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=93.28  E-value=0.1  Score=33.10  Aligned_cols=32  Identities=9%  Similarity=0.017  Sum_probs=25.4

Q ss_pred             HHHHHHHHhC---CCCHHHHHHHhCCCHHHHHHHH
Q 032366           85 KAIVQARNDK---KLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        85 ~~Lk~~R~~~---glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ..|..++..-   ++|..+||+.+|+++++|++..
T Consensus        18 ~IL~~L~~~~~~~~~t~~eLA~~Lgvs~~tV~~~L   52 (77)
T 1qgp_A           18 RILKFLEELGEGKATTAHDLSGKLGTPKKEINRVL   52 (77)
T ss_dssp             HHHHHHHHHCSSSCEEHHHHHHHHCCCHHHHHHHH
T ss_pred             HHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHH
Confidence            3445556666   7999999999999999998764

>3eus_A DNA-binding protein; structural genomics, PSI2,MCSG, protein structure initiative, midwest center for structural genomic binding; 1.80A {Silicibacter pomeroyi}

Probab=93.12  E-value=0.07  Score=33.91  Aligned_cols=43  Identities=14%  Similarity=0.057  Sum_probs=30.4

Q ss_pred             HHHHHHHHcCCChhHHHhhhcCCCCCCCCCCCcccccchhhhccccCCcc
Q 032366           30 KVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTENLAHDRV   79 (142)
Q Consensus        30 ~~~~~a~r~G~~v~t~kk~~~g~~~~~~~~~~~~~~kl~~~~~~~~~~~~   79 (142)
                      ++-..|.+.|++.+|+.+||.|...       +.+..+..-...|..+..
T Consensus        29 tq~elA~~~gis~~~is~~E~G~~~-------p~~~~l~~ia~~l~v~~~   71 (86)
T 3eus_A           29 TQADLAERLDKPQSFVAKVETRERR-------LDVIEFAKWMAACEGLDV   71 (86)
T ss_dssp             CHHHHHHHTTCCHHHHHHHHTTSSC-------CBHHHHHHHHHHTTCGGG
T ss_pred             CHHHHHHHhCcCHHHHHHHHCCCCC-------CCHHHHHHHHHHcCCCcH
Confidence            4567899999999999999999876       344444444445554433

>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=93.05  E-value=0.12  Score=36.45  Aligned_cols=38  Identities=8%  Similarity=0.240  Sum_probs=30.4

Q ss_pred             chHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           79 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +..++...|..+. ..|+|..++|+.+|+|++||.+|.+
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            4455555665555 4699999999999999999999985

>3h5o_A Transcriptional regulator GNTR; transcription regulator, GNTR,chromobacterium violaceum, PSI, SGX, DNA-binding; 2.30A {Chromobacterium violaceum}

Probab=93.03  E-value=0.017  Score=44.97  Aligned_cols=45  Identities=11%  Similarity=0.010  Sum_probs=0.0

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHH---HHHHHHHHhCCCC
Q 032366           94 KKLTQSQLAQLINEKPQVIQEYESGKAIPNQQ---ILTKLERALGVKL  138 (142)
Q Consensus        94 ~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~---~l~kLa~~Lgvsl  138 (142)
                      +..|.+|+|+++|||.+|||+..||....+.+   .+.+.++.||..+
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            34789999999999999999999997655544   4555566666654

>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=92.98  E-value=0.2  Score=30.77  Aligned_cols=31  Identities=13%  Similarity=0.298  Sum_probs=25.5

Q ss_pred             HHHHHHh----CCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           87 IVQARND----KKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        87 Lk~~R~~----~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      |-.++--    .|+|..|+|+.+|+|.++|..+..
T Consensus        18 il~l~~~l~~~~~~s~~eIA~~l~is~~tV~~~~~   52 (73)
T 1ku3_A           18 VLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIEN   52 (73)
T ss_dssp             HHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHhcccCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            4444554    799999999999999999998764

>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=92.90  E-value=0.19  Score=33.94  Aligned_cols=61  Identities=10%  Similarity=0.128  Sum_probs=48.9

Q ss_pred             hHHHHHHHHHHHHhCCCCHHHHHH-HhCCCHHHHHHHHcCCCC---CC---HHHHHHHHHHhCCCCCC
Q 032366           80 PSELKKAIVQARNDKKLTQSQLAQ-LINEKPQVIQEYESGKAI---PN---QQILTKLERALGVKLRG  140 (142)
Q Consensus        80 ~~~~g~~Lk~~R~~~glTQ~eLA~-~lgis~stIs~~E~G~~~---p~---~~~l~kLa~~Lgvsl~e  140 (142)
                      ..++...|++++...+++|+.||+ .+|.++.+|+++.+.-..   .+   .+...++-..|..+.++
T Consensus        19 Tk~I~~~ike~L~~~~isQ~~FA~~ILgrsqgtlSdlL~~PKpW~~L~~~Gre~fiRM~nWL~l~e~q   86 (101)
T 1wh6_A           19 TLELTRQVKEKLAKNGICQRIFGEKVLGLSQGSVSDMLSRPKPWSKLTQKGREPFIRMQLWLSDQLGQ   86 (101)
T ss_dssp             HHHHHHHHHHHHHTTTCCHHHHHHHTTCCCHHHHHHHHHSCCCTTTCCHHHHHHHHHHHHHHHHTTCS
T ss_pred             HHHHHHHHHHHHHHcCCcHHHHHHHHHccCcCcHHHHhcCCCCHHHHhHHhHHHHHHHHHHhCCcHHH
Confidence            457999999999999999999999 779999999999985432   22   45677777777766554

>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=92.87  E-value=0.18  Score=38.38  Aligned_cols=48  Identities=15%  Similarity=0.075  Sum_probs=35.2

Q ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHH
Q 032366           81 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKL  130 (142)
Q Consensus        81 ~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kL  130 (142)
                      .+.+..++.+. +.|+|+.++|+.+|+|+++|+++..=- ..+.+++..+
T Consensus       121 ~E~a~~~~~l~-~~g~t~~~iA~~lG~s~~~V~~~l~l~-~l~~~v~~~l  168 (230)
T 1vz0_A          121 VEEARGYQALL-EMGLTQEEVARRVGKARSTVANALRLL-QLPPEALEAL  168 (230)
T ss_dssp             HHHHHHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHHGG-GSCHHHHHHH
T ss_pred             HHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHH-cCCHHHHHHH
Confidence            44566666666 789999999999999999999987632 2334444444

>2ox6_A Hypothetical protein SO3848; structural genomics, PSI-2, MCSG, Pro structure initiative; 1.70A {Shewanella oneidensis} SCOP: a.35.1.6

Probab=92.84  E-value=0.64  Score=32.81  Aligned_cols=40  Identities=18%  Similarity=0.266  Sum_probs=35.9

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHH
Q 032366           86 AIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQ  125 (142)
Q Consensus        86 ~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~  125 (142)
                      .|+.+|...|+|..++++..+.|..-|-.||.|....+.-
T Consensus        11 e~~ylr~slgl~~aqv~~l~k~se~dv~aweage~~~~~l   50 (166)
T 2ox6_A           11 EMSYLRQSLSLSAAQVGQLTNHSEAEVLAWENAETQAPEL   50 (166)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTSSCCCHH
T ss_pred             hHHHHHHHcCCCHHHHHHHhccCHHHhhhhhhcCCcCcch
Confidence            4788999999999999999999999999999999766543

>3e7l_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+ ATPase, response regulator, transcriptional activator, ATP-binding; 2.25A {Aquifex aeolicus} PDB: 4fth_A

Probab=92.75  E-value=0.23  Score=29.92  Aligned_cols=34  Identities=12%  Similarity=-0.036  Sum_probs=29.2

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ...|.......+.++.+.|+.+|||++++.+..+
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            3556788888999999999999999999998764

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

Probab=92.72  E-value=0.18  Score=32.44  Aligned_cols=30  Identities=10%  Similarity=-0.003  Sum_probs=23.7

Q ss_pred             HHHHHHhC---CCCHHHHHHHhCCCHHHHHHHH
Q 032366           87 IVQARNDK---KLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        87 Lk~~R~~~---glTQ~eLA~~lgis~stIs~~E  116 (142)
                      |..++..-   .+|..+||+.+|+|+++|.+..
T Consensus        16 L~~L~~~~pg~~~t~~eLA~~Lgvsr~tV~~~L   48 (81)
T 1qbj_A           16 LKFLEELGEGKATTAHDLSGKLGTPKKEINRVL   48 (81)
T ss_dssp             HHHHHHHCTTCCBCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHH
Confidence            34455555   6999999999999999988763

>1hlv_A CENP-B, major centromere autoantigen B; helix-turn-helix, protein-DNA complex, riken structural genomics/proteomics initiative, RSGI; 2.50A {Homo sapiens} SCOP: a.4.1.7 a.4.1.7 PDB: 1bw6_A

Probab=92.68  E-value=0.2  Score=33.92  Aligned_cols=42  Identities=17%  Similarity=0.230  Sum_probs=30.1

Q ss_pred             cchHHHHHHHHHHHHhCCC-CHHHHHHHhCCCHHHHHHHHcCC
Q 032366           78 RVPSELKKAIVQARNDKKL-TQSQLAQLINEKPQVIQEYESGK  119 (142)
Q Consensus        78 ~~~~~~g~~Lk~~R~~~gl-TQ~eLA~~lgis~stIs~~E~G~  119 (142)
                      .+..++-..+-.+-.+.|. ++.++|+.+||+++||++|.++.
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            3455565555544434454 56699999999999999998774

>3dbi_A Sugar-binding transcriptional regulator, LACI FAM; structural genomics, sugar-binding transcriptional regulator structure initiative, PSI-2; HET: MSE; 2.45A {Escherichia coli K12}

Probab=92.61  E-value=0.022  Score=44.33  Aligned_cols=43  Identities=14%  Similarity=0.101  Sum_probs=0.0

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCHH---HHHHHHHHhCCCC
Q 032366           96 LTQSQLAQLINEKPQVIQEYESGKAIPNQQ---ILTKLERALGVKL  138 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~G~~~p~~~---~l~kLa~~Lgvsl  138 (142)
                      .|.+|+|+.+|||.+|||+..||....+.+   .+.+.++.||..+
T Consensus         4 ~ti~diA~~agVS~~TVSrvln~~~~vs~~tr~rV~~~a~~lgY~p   49 (338)
T 3dbi_A            4 TTMLEVAKRAGVSKATVSRVLSGNGYVSQETKDRVFQAVEESGYRP   49 (338)
T ss_dssp             ----------------------------------------------
T ss_pred             CCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCc
Confidence            588999999999999999999997655444   4556677777654

>2jpc_A SSRB; DNA binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium}

Probab=92.57  E-value=0.15  Score=29.85  Aligned_cols=44  Identities=9%  Similarity=0.113  Sum_probs=30.2

Q ss_pred             HhCCCCHHHHHHHhCCCHHHHHHHHcCC----CCCCHHHHHHHHHHhC
Q 032366           92 NDKKLTQSQLAQLINEKPQVIQEYESGK----AIPNQQILTKLERALG  135 (142)
Q Consensus        92 ~~~glTQ~eLA~~lgis~stIs~~E~G~----~~p~~~~l~kLa~~Lg  135 (142)
                      ...|+|.+|+|+.+|+|.+||..+-..-    ...+...+..++...|
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            4679999999999999999999876421    2334444444444443

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

Probab=92.45  E-value=0.23  Score=31.10  Aligned_cols=30  Identities=7%  Similarity=0.023  Sum_probs=24.0

Q ss_pred             HHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           87 IVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      |..+.....+|..|||+.+|+|+++|+++.
T Consensus         6 l~~L~~~~~~s~~eLa~~lgvs~~tv~r~L   35 (81)
T 2htj_A            6 LEFLNRHNGGKTAEIAEALAVTDYQARYYL   35 (81)
T ss_dssp             HHHHHHSCCCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHcCCCCHHHHHHHHCcCHHHHHHHH
Confidence            334444567999999999999999998864

>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=92.37  E-value=0.17  Score=31.23  Aligned_cols=52  Identities=13%  Similarity=0.213  Sum_probs=32.6

Q ss_pred             HHHHHHHHcCCChhHHHhhhcCCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHh
Q 032366           30 KVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLI  105 (142)
Q Consensus        30 ~~~~~a~r~G~~v~t~kk~~~g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~l  105 (142)
                      +.-..|+++|+++.|+.++..|...                        +..+..++|.++-.++|+....+|..+
T Consensus        11 t~~diA~~aGVS~sTVSr~ln~~~~------------------------vs~~t~~rV~~~a~~lgY~pn~~a~~l   62 (67)
T 2l8n_A           11 TMKDVALKAKVSTATVSRALMNPDK------------------------VSQATRNRVEKAAREVGYLPQPMGRNV   62 (67)
T ss_dssp             CHHHHHHHTTCCHHHHHHTTTCCCC------------------------SCHHHHHHHHHHHHHHCCCC-------
T ss_pred             CHHHHHHHHCCCHHHHHHHHcCCCC------------------------CCHHHHHHHHHHHHHhCCCccHHHHHh
Confidence            3566899999999999999877542                        234456667666666677666555543

>2w48_A Sorbitol operon regulator; SORC, activator, repressor, DNA-binding, transcription, transcription regulator, transcription regulation; 3.20A {Klebsiella pneumoniae}

Probab=92.36  E-value=0.21  Score=39.32  Aligned_cols=36  Identities=22%  Similarity=0.209  Sum_probs=31.3

Q ss_pred             HHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           82 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        82 ~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .+..++..+....++||.+||+.+|||+.||++...
T Consensus         8 ~~~~~ia~l~~~~~~~~~ela~~l~vS~~tIrRdL~   43 (315)
T 2w48_A            8 RLIVKIAQLYYEQDMTQAQIARELGIYRTTISRLLK   43 (315)
T ss_dssp             HHHHHHHHHHHTSCCCHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            455677888888999999999999999999998764

>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=92.34  E-value=0.46  Score=32.80  Aligned_cols=77  Identities=10%  Similarity=0.109  Sum_probs=49.4

Q ss_pred             HHHHHHHHcCCChhHHHhhhc-----CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHH-hCCCCHHHHHH
Q 032366           30 KVVNAARRAGADIETVRKSHA-----GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARN-DKKLTQSQLAQ  103 (142)
Q Consensus        30 ~~~~~a~r~G~~v~t~kk~~~-----g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~-~~glTQ~eLA~  103 (142)
                      +.-..|+..|++..|+.+|-.     |...+... .+.            .+..+..++...|..+.. ...+|..+++.
T Consensus        50 s~~~iA~~lgis~~TV~rw~~~~~~~G~~~~~~r-~gr------------~~~~~~~~~~~~I~~~~~~~~~~s~~~i~~  116 (149)
T 1k78_A           50 RPCDISRQLRVSHGCVSKILGRYYETGSIKPGVI-GGS------------KPKVATPKVVEKIAEYKRQNPTMFAWEIRD  116 (149)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHHHHHHSCCCCCCC-CCC------------CCSSSCHHHHHHHHHHHHHCTTCCHHHHHH
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHcCCCCccCC-CCC------------CCCCCCHHHHHHHHHHHHhCcchhHHHHHH
Confidence            345578999999999999865     32211000 000            011233445555666544 45799999999


Q ss_pred             Hh--------C--CCHHHHHHHHcCC
Q 032366          104 LI--------N--EKPQVIQEYESGK  119 (142)
Q Consensus       104 ~l--------g--is~stIs~~E~G~  119 (142)
                      .+        |  +|.+||.+|....
T Consensus       117 ~l~~~~~~~~g~~~S~sTV~r~L~~~  142 (149)
T 1k78_A          117 RLLAERVCDNDTVPSVSSINRIIRTK  142 (149)
T ss_dssp             HHHHTTSSCTTTSCCHHHHHHHHHCC
T ss_pred             HHHHhcccccCCCcCHHHHHHHHHHH
Confidence            88        7  8999999998643

>2vz4_A Tipal, HTH-type transcriptional activator TIPA; transcription, resistance, antibiotic; 2.90A {Streptomyces lividans}

Probab=92.32  E-value=0.14  Score=34.19  Aligned_cols=26  Identities=15%  Similarity=0.317  Sum_probs=22.7

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc-CCC
Q 032366           95 KLTQSQLAQLINEKPQVIQEYES-GKA  120 (142)
Q Consensus        95 glTQ~eLA~~lgis~stIs~~E~-G~~  120 (142)
                      ++|..++|+.+|||..||..||. |--
T Consensus         1 ~~~i~e~A~~~gvs~~tLR~ye~~Gll   27 (108)
T 2vz4_A            1 SYSVGQVAGFAGVTVRTLHHYDDIGLL   27 (108)
T ss_dssp             CBCHHHHHHHHTCCHHHHHHHHHHTSS
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence            47899999999999999999996 543

>1x3u_A Transcriptional regulatory protein FIXJ; helix-turn-helix; NMR {Sinorhizobium meliloti}

Probab=92.28  E-value=0.72  Score=28.15  Aligned_cols=46  Identities=13%  Similarity=0.112  Sum_probs=35.6

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHc----CCCCCCHHHHHHHHHHhCCCC
Q 032366           93 DKKLTQSQLAQLINEKPQVIQEYES----GKAIPNQQILTKLERALGVKL  138 (142)
Q Consensus        93 ~~glTQ~eLA~~lgis~stIs~~E~----G~~~p~~~~l~kLa~~Lgvsl  138 (142)
                      ..|+|.+++|+.+|+|.++|..+..    --...+...+..++..+|+..
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            6899999999999999999987764    123456666777777777653

>3jvd_A Transcriptional regulators; structural genomics, PSI-2, sugar binding protein, transcrip regulation, protein structure initiative; 2.30A {Corynebacterium glutamicum}

Probab=92.27  E-value=0.025  Score=44.14  Aligned_cols=45  Identities=18%  Similarity=0.116  Sum_probs=0.0

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCC
Q 032366           94 KKLTQSQLAQLINEKPQVIQEYESGKAIPNQQI---LTKLERALGVKL  138 (142)
Q Consensus        94 ~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~---l~kLa~~Lgvsl  138 (142)
                      +..|.+|+|+++|||.+|||+..||....+.++   +.+.++.||..+
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            347899999999999999999999876555544   555566666654

>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=92.23  E-value=0.69  Score=30.30  Aligned_cols=74  Identities=11%  Similarity=0.105  Sum_probs=45.4

Q ss_pred             HHHHHHHcCCChhHHHhhhc-----CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHH-hCCCCHHHHHHH
Q 032366           31 VVNAARRAGADIETVRKSHA-----GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARN-DKKLTQSQLAQL  104 (142)
Q Consensus        31 ~~~~a~r~G~~v~t~kk~~~-----g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~-~~glTQ~eLA~~  104 (142)
                      .-..|++.|++..|+.+|-.     |...+.+. .+....            .+..++...|..+.. ...+|..+++..
T Consensus        36 ~~~ia~~lgis~~Tv~~w~~~~~~~g~~~~~~~-~g~~~~------------~l~~~~~~~i~~~~~~~~~~s~~~i~~~  102 (128)
T 1pdn_C           36 PCVISRQLRVSHGCVSKILNRYQETGSIRPGVI-GGSKPR------------IATPEIENRIEEYKRSSPGMFSWEIREK  102 (128)
T ss_dssp             HHHHHHHHTCCHHHHHHHHHHHHHHCCSSCCCC-SCCCCC------------SSCSTHHHHHHHTTTTCTTCCHHHHHHH
T ss_pred             HHHHHHHHCcCHHHHHHHHHHHHhhCCcccccC-CCCCCC------------cCCHHHHHHHHHHHHhCcchHHHHHHHH
Confidence            34579999999999999865     32221100 000111            122223445555543 357999999999


Q ss_pred             h---C-------CCHHHHHHHHc
Q 032366          105 I---N-------EKPQVIQEYES  117 (142)
Q Consensus       105 l---g-------is~stIs~~E~  117 (142)
                      +   |       +|.+||.+|..
T Consensus       103 l~~~g~~~~~~~~s~~tv~r~l~  125 (128)
T 1pdn_C          103 LIREGVCDRSTAPSVSAISRLVR  125 (128)
T ss_dssp             HHHTSSSCSTTCCCHHHHHHHC-
T ss_pred             HHHcCCccccCCcCHHHHHHHHH
Confidence            9   7       59999999865

>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=92.16  E-value=0.35  Score=31.30  Aligned_cols=37  Identities=11%  Similarity=0.118  Sum_probs=27.2

Q ss_pred             chHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           79 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +...-.+.|..+.  .|+|.+|+|+.+|+|..||..+..
T Consensus        30 Lt~rE~~Vl~l~~--~G~s~~eIA~~L~iS~~TV~~~~~   66 (90)
T 3ulq_B           30 LTPRECLILQEVE--KGFTNQEIADALHLSKRSIEYSLT   66 (90)
T ss_dssp             CCHHHHHHHHHHH--TTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCHHHHHHHHHHH--cCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3333334444433  899999999999999999988764

>3bil_A Probable LACI-family transcriptional regulator; structural genomics, unknown function, PSI-2, protein structure initiative; 2.50A {Corynebacterium glutamicum atcc 13032}

Probab=92.16  E-value=0.027  Score=44.29  Aligned_cols=43  Identities=12%  Similarity=0.088  Sum_probs=0.0

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCC
Q 032366           96 LTQSQLAQLINEKPQVIQEYESGKAIPNQQI---LTKLERALGVKL  138 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~G~~~p~~~~---l~kLa~~Lgvsl  138 (142)
                      .|.+|+|+++|||.+|||+..||....+.++   +.+.++.||..+
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            5899999999999999999999976555544   455566677544

>1tty_A Sigma-A, RNA polymerase sigma factor RPOD; helix-turn-helix, transcription; NMR {Thermotoga maritima} SCOP: a.4.13.2

Probab=92.12  E-value=0.28  Score=31.28  Aligned_cols=32  Identities=22%  Similarity=0.289  Sum_probs=26.1

Q ss_pred             HHHHHHHh----CCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           86 AIVQARND----KKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        86 ~Lk~~R~~----~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .+-.+|--    .|+|..++|+.+|+|.++|..+..
T Consensus        25 ~vl~l~~~l~~~~~~s~~EIA~~lgis~~tV~~~~~   60 (87)
T 1tty_A           25 MVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEV   60 (87)
T ss_dssp             HHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            34445554    799999999999999999999874

>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=92.09  E-value=0.1  Score=32.13  Aligned_cols=22  Identities=27%  Similarity=0.190  Sum_probs=19.5

Q ss_pred             HHHHHHcCCChhHHHhhhcCCC
Q 032366           32 VNAARRAGADIETVRKSHAGTN   53 (142)
Q Consensus        32 ~~~a~r~G~~v~t~kk~~~g~~   53 (142)
                      -+.|+++|++..|+.++..|..
T Consensus         4 ~diA~~aGVS~sTVSrvLng~~   25 (65)
T 1uxc_A            4 DEIARLAGVSRTTASYVINGKA   25 (65)
T ss_dssp             HHHHHHHTSCHHHHHHHHHTCT
T ss_pred             HHHHHHHCcCHHHHHHHHcCCC
Confidence            4579999999999999998865

>3e3m_A Transcriptional regulator, LACI family; structural genomics, DNA-binding, plasmid, transcription regulation, PSI-2; 1.60A {Silicibacter pomeroyi}

Probab=92.09  E-value=0.027  Score=44.19  Aligned_cols=45  Identities=7%  Similarity=0.048  Sum_probs=0.0

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHH---HHHHHHHHhCCCC
Q 032366           94 KKLTQSQLAQLINEKPQVIQEYESGKAIPNQQ---ILTKLERALGVKL  138 (142)
Q Consensus        94 ~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~---~l~kLa~~Lgvsl  138 (142)
                      +-.|.+|+|+++|||.+|||+..||....+.+   .+.+.++.||..+
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            44789999999999999999999988655554   4555666676654

>2dk5_A DNA-directed RNA polymerase III 39 kDa polypeptide; structural genomics, winged helix domain, NPPSFA; NMR {Homo sapiens} SCOP: a.4.5.85

Probab=92.03  E-value=0.15  Score=33.47  Aligned_cols=32  Identities=9%  Similarity=-0.056  Sum_probs=26.0

Q ss_pred             HHHHHHHH--hCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           85 KAIVQARN--DKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        85 ~~Lk~~R~--~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ..|+.+..  ..|++|++||+.++++.++|+++.
T Consensus        24 ~Vl~~I~~~g~~gi~qkeLa~~~~l~~~tvt~iL   57 (91)
T 2dk5_A           24 LVYQIIEDAGNKGIWSRDVRYKSNLPLTEINKIL   57 (91)
T ss_dssp             HHHHHHHHHCTTCEEHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHcCCCCcCHHHHHHHHCCCHHHHHHHH
Confidence            34555555  569999999999999999998865

>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=91.98  E-value=0.28  Score=33.61  Aligned_cols=41  Identities=12%  Similarity=0.178  Sum_probs=36.9

Q ss_pred             chHHHHHHHHHHHHhCCCCHHHHHH-HhCCCHHHHHHHHcCC
Q 032366           79 VPSELKKAIVQARNDKKLTQSQLAQ-LINEKPQVIQEYESGK  119 (142)
Q Consensus        79 ~~~~~g~~Lk~~R~~~glTQ~eLA~-~lgis~stIs~~E~G~  119 (142)
                      -...+...|+++....+++|+-||+ .+|.++.+|+++.+--
T Consensus        28 DTk~I~~~ikewL~~~~isQ~~FA~~ILgrsQgtlSdlL~~P   69 (111)
T 1wh8_A           28 DTYSITKRVKEVLTDNNLGQRLFGESILGLTQGSVSDLLSRP   69 (111)
T ss_dssp             CHHHHHHHHHHHHHHTTCCHHHHHHHTTCCCHHHHHHHHHSC
T ss_pred             CHHHHHHHHHHHHHHCCCcHHHHHHHHhccCcCcHHHHHcCC
Confidence            4567999999999999999999999 7899999999999754

>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=91.94  E-value=0.75  Score=32.15  Aligned_cols=79  Identities=8%  Similarity=0.002  Sum_probs=46.8

Q ss_pred             HHHHHHHcCCChhHHHhhhcCCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHH-hCCCCHHHHHHHh----
Q 032366           31 VVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARN-DKKLTQSQLAQLI----  105 (142)
Q Consensus        31 ~~~~a~r~G~~v~t~kk~~~g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~-~~glTQ~eLA~~l----  105 (142)
                      .-..|+..|++..|+.+|-.-....  +...+..    +  .--.+..+...+...|..+.. ...+|..+|+..+    
T Consensus        44 ~~~IA~~lgis~~TV~rwl~r~~~~--G~~~~~~----r--~gr~~~~~~~~~~~~I~~~~~~~~~~s~~~i~~~l~~~~  115 (159)
T 2k27_A           44 PCDISRQLRVSHGCVSKILGRYYET--GSIRPGV----I--GGSKPKVATPKVVEKIGDYKRQNPTMFAWEIRDRLLAEG  115 (159)
T ss_dssp             HHHHHHHHTCCSHHHHHHHCCSSTT--SCCCCCC----C--CCCCCCCCCTTHHHHHHHHHHHCSSSCHHHHHHHHHHHT
T ss_pred             HHHHHHHHCcCHHHHHHHHHHHHhc--CCccCCC----C--CCCCCCCCCHHHHHHHHHHHHHCccchHHHHHHHHHHhc
Confidence            3457889999999999997643221  0000000    0  000011222334455555544 4679999999987    


Q ss_pred             ------CCCHHHHHHHHc
Q 032366          106 ------NEKPQVIQEYES  117 (142)
Q Consensus       106 ------gis~stIs~~E~  117 (142)
                            .+|.+||.+|..
T Consensus       116 ~~~~~~~~S~sTV~r~L~  133 (159)
T 2k27_A          116 VCDNDTVPSVSSINRIIR  133 (159)
T ss_dssp             CSCTTTSCCHHHHHHHHH
T ss_pred             ccccCCccCHHHHHHHHH
Confidence                  489999998875

>1fse_A GERE; helix-turn-helix DNA-binding protein transcriptional regulat transcription; 2.05A {Bacillus subtilis} SCOP: a.4.6.2

Probab=91.75  E-value=0.51  Score=28.39  Aligned_cols=25  Identities=12%  Similarity=0.066  Sum_probs=22.8

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           93 DKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        93 ~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ..|+|..++|+.+|+|.++|..+..
T Consensus        24 ~~g~s~~eIA~~l~is~~tV~~~~~   48 (74)
T 1fse_A           24 VQDKTTKEIASELFISEKTVRNHIS   48 (74)
T ss_dssp             TTTCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            6899999999999999999988764

>3ctp_A Periplasmic binding protein/LACI transcriptional; structural genomics, protein structure initiative; HET: XLF; 1.41A {Alkaliphilus metalliredigens}

Probab=91.73  E-value=0.032  Score=43.29  Aligned_cols=43  Identities=7%  Similarity=0.042  Sum_probs=0.0

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCC
Q 032366           96 LTQSQLAQLINEKPQVIQEYESGKAIPNQQI---LTKLERALGVKL  138 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~G~~~p~~~~---l~kLa~~Lgvsl  138 (142)
                      .|.+|+|+++|||.+|||+..||....+.++   +.+.++.||..+
T Consensus         3 ~ti~diA~~agVS~~TVSrvln~~~~vs~~tr~rV~~~~~~lgY~p   48 (330)
T 3ctp_A            3 ANIREIAKRAGISIATVSRHLNNTGYVSEDAREKIQKVVDELNYTP   48 (330)
T ss_dssp             ----------------------------------------------
T ss_pred             CCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHhCCCc
Confidence            5889999999999999999999976555544   455566677554

>1z4h_A TORI, TOR inhibition protein; winged helix, reverse turn, protein binding, DNA binding protein; NMR {Escherichia coli}

Probab=91.70  E-value=0.064  Score=32.84  Aligned_cols=29  Identities=7%  Similarity=-0.013  Sum_probs=24.1

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCC
Q 032366           95 KLTQSQLAQLINEKPQVIQEYESGKAIPN  123 (142)
Q Consensus        95 glTQ~eLA~~lgis~stIs~~E~G~~~p~  123 (142)
                      =++..|+|+.+|+|++||.+|.+....|.
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            36889999999999999999997544443

>1jye_A Lactose operon repressor; gene regulation, protein stability, protein DNA-binding, transcription; 1.70A {Escherichia coli} SCOP: c.93.1.1 PDB: 1lbi_A 1lbg_A* 1lbh_A 1jyf_A 3edc_A 1efa_A* 1jwl_A* 2pe5_A* 1tlf_A* 2p9h_A* 2paf_A* 1cjg_A* 1l1m_A 1osl_A 2kei_A* 2kej_A* 2kek_A* 2bjc_A 1lqc_A 1lcc_A* ...

Probab=91.61  E-value=0.033  Score=43.66  Aligned_cols=43  Identities=9%  Similarity=-0.007  Sum_probs=0.0

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCHH---HHHHHHHHhCCCC
Q 032366           96 LTQSQLAQLINEKPQVIQEYESGKAIPNQQ---ILTKLERALGVKL  138 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~G~~~p~~~---~l~kLa~~Lgvsl  138 (142)
                      .|.+|+|+++|||.+|||+..||....+.+   .+.+.++.||..+
T Consensus         4 ~ti~diA~~aGVS~~TVSrvLn~~~~vs~~tr~rV~~~a~~lgY~p   49 (349)
T 1jye_A            4 VTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIP   49 (349)
T ss_dssp             ----------------------------------------------
T ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHCCCc
Confidence            689999999999999999999987655544   4555566677544

>2rn7_A IS629 ORFA; helix, all alpha, unknown function, structural genomics, PSI-2, protein structure initiative; NMR {Shigella flexneri}

Probab=91.60  E-value=0.14  Score=33.68  Aligned_cols=22  Identities=18%  Similarity=0.271  Sum_probs=20.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .|..++|..+|||++||.+|.+
T Consensus        31 ~s~~~va~~~gIs~~tl~~W~~   52 (108)
T 2rn7_A           31 ATICSIAPKIGCTPETLRVWVR   52 (108)
T ss_dssp             HHHHHHHHHHTSCHHHHHHHHH
T ss_pred             ccHHHHHHHHCcCHHHHHHHHH
Confidence            7899999999999999999965

>2jml_A DNA binding domain/transcriptional regulator; anti-repressor, MERR, carotenogenesis; HET: DNA; NMR {Myxococcus xanthus}

Probab=91.33  E-value=0.11  Score=32.88  Aligned_cols=24  Identities=13%  Similarity=0.290  Sum_probs=21.9

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           94 KKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        94 ~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .-+|..|+|+.+|||.+||..||.
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            347889999999999999999997

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

Probab=91.19  E-value=0.22  Score=32.36  Aligned_cols=34  Identities=12%  Similarity=0.112  Sum_probs=26.4

Q ss_pred             HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ...+|-.+....|+|-.+||+.+|+|+++|.+..
T Consensus        18 ~~~~IL~lL~~~g~sa~eLAk~LgiSk~aVr~~L   51 (82)
T 1oyi_A           18 IVCEAIKTIGIEGATAAQLTRQLNMEKREVNKAL   51 (82)
T ss_dssp             HHHHHHHHHSSSTEEHHHHHHHSSSCHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHH
Confidence            4444545544788999999999999999988754

>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=91.18  E-value=0.41  Score=32.27  Aligned_cols=59  Identities=12%  Similarity=0.162  Sum_probs=46.5

Q ss_pred             hHHHHHHHHHHHHhCCCCHHHHHH-HhCCCHHHHHHHHcCCCCC------CHHHHHHHHHHhCCCC
Q 032366           80 PSELKKAIVQARNDKKLTQSQLAQ-LINEKPQVIQEYESGKAIP------NQQILTKLERALGVKL  138 (142)
Q Consensus        80 ~~~~g~~Lk~~R~~~glTQ~eLA~-~lgis~stIs~~E~G~~~p------~~~~l~kLa~~Lgvsl  138 (142)
                      ...+...|++..+..+++|.-||+ .+|.++.+++++.+.-..|      ..+...++-..|..+-
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            456899999999999999999999 5799999999999865312      2456667777776653

>3c57_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 1.70A {Mycobacterium tuberculosis} PDB: 1zlk_A 1zlj_A

Probab=91.10  E-value=0.37  Score=31.25  Aligned_cols=37  Identities=16%  Similarity=0.217  Sum_probs=27.4

Q ss_pred             chHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           79 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +...-.+.|.. + ..|+|.+|+|+.+|+|..||..+..
T Consensus        28 Lt~~e~~vl~l-~-~~g~s~~eIA~~l~is~~tV~~~l~   64 (95)
T 3c57_A           28 LTDQERTLLGL-L-SEGLTNKQIADRMFLAEKTVKNYVS   64 (95)
T ss_dssp             CCHHHHHHHHH-H-HTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCHHHHHHHHH-H-HcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            33333333443 4 7899999999999999999988753

>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=91.01  E-value=0.39  Score=30.27  Aligned_cols=43  Identities=5%  Similarity=-0.011  Sum_probs=29.8

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHcC----CCCCCHHHHHHHHHHhC
Q 032366           93 DKKLTQSQLAQLINEKPQVIQEYESG----KAIPNQQILTKLERALG  135 (142)
Q Consensus        93 ~~glTQ~eLA~~lgis~stIs~~E~G----~~~p~~~~l~kLa~~Lg  135 (142)
                      ..|+|.+|+|+.+|+|.+||..+...    -...+...+..++...|
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            68999999999999999999877641    12234444444444444

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

Probab=90.87  E-value=0.41  Score=29.24  Aligned_cols=29  Identities=10%  Similarity=0.048  Sum_probs=23.1

Q ss_pred             HHHHHh-CCCCHHHHHHHhCCCHHHHHHHH
Q 032366           88 VQARND-KKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        88 k~~R~~-~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ..+... ..+|..+||+.+|+|+++|.+..
T Consensus        17 ~~L~~~~~~~s~~eLA~~lglsr~tv~~~l   46 (67)
T 2heo_A           17 QVLSDDGGPVAIFQLVKKCQVPKKTLNQVL   46 (67)
T ss_dssp             HHHHHHCSCEEHHHHHHHHCSCHHHHHHHH
T ss_pred             HHHHHcCCCcCHHHHHHHHCcCHHHHHHHH
Confidence            334333 46999999999999999998865

>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=90.65  E-value=0.44  Score=32.22  Aligned_cols=32  Identities=6%  Similarity=0.083  Sum_probs=26.4

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           86 AIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        86 ~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .+-.++-..|+|..++|+.+|+|.+||..+..
T Consensus        29 ~vl~l~y~~g~s~~EIA~~lgiS~~tV~~~l~   60 (113)
T 1s7o_A           29 NYIELYYADDYSLAEIADEFGVSRQAVYDNIK   60 (113)
T ss_dssp             HHHHHHHHTCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            34445556899999999999999999998764

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

Probab=90.65  E-value=0.37  Score=30.79  Aligned_cols=32  Identities=13%  Similarity=0.276  Sum_probs=25.3

Q ss_pred             HHHHHHHH-hCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           85 KAIVQARN-DKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        85 ~~Lk~~R~-~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ..|..+.. ..++|+.+||+.+|+|+++|+++.
T Consensus        25 ~~l~~l~~~~~~~t~~ela~~l~is~~tv~~~l   57 (109)
T 2d1h_A           25 AVLLKMVEIEKPITSEELADIFKLSKTTVENSL   57 (109)
T ss_dssp             HHHHHHHHHCSCEEHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHH
Confidence            34444443 678999999999999999999864

>3mky_B Protein SOPB; partition, F plasmid, centromere, DNA binding protein- complex; HET: DNA; 2.86A {Escherichia coli} PDB: 3mkw_B* 3mkz_A*

Probab=90.47  E-value=0.48  Score=35.37  Aligned_cols=39  Identities=15%  Similarity=0.006  Sum_probs=29.8

Q ss_pred             HHHHHHHHHHHHh-CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 032366           81 SELKKAIVQARND-KKLTQSQLAQLINEKPQVIQEYESGK  119 (142)
Q Consensus        81 ~~~g~~Lk~~R~~-~glTQ~eLA~~lgis~stIs~~E~G~  119 (142)
                      -+.|.....+... ...+|++||+.+|||++.|+++.+--
T Consensus        27 yErg~~y~r~L~~g~~~~Q~~lA~~~giS~a~VSR~L~~A   66 (189)
T 3mky_B           27 YERGQRYASRLQNEFAGNISALADAENISRKIITRCINTA   66 (189)
T ss_dssp             HHHHHHHHHHHHTTTTTCHHHHHHHHTSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCcccCHHHHHHHHCCCHHHHHHHHHHh
Confidence            3456555555544 46899999999999999999998643

>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=90.36  E-value=0.29  Score=31.68  Aligned_cols=33  Identities=9%  Similarity=0.084  Sum_probs=28.1

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ...|.......+.++.+.|+.+|||++|+.+..
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            455677788889999999999999999998764

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

Probab=90.12  E-value=0.27  Score=31.35  Aligned_cols=34  Identities=15%  Similarity=0.134  Sum_probs=27.5

Q ss_pred             HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      +.+.+..++....++..|||+.+++|..||.+-.
T Consensus         4 L~~Il~~L~~~g~vsv~eLa~~l~VS~~TIRrdL   37 (78)
T 1xn7_A            4 LIQVRDLLALRGRMEAAQISQTLNTPQPMINAML   37 (78)
T ss_dssp             HHHHHHHHHHSCSBCHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHH
Confidence            4455666777788999999999999999998743

>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=90.00  E-value=0.44  Score=31.63  Aligned_cols=58  Identities=16%  Similarity=0.149  Sum_probs=45.6

Q ss_pred             HHHHHHHHHHHHhCCCCHHHHHH-HhCCCHHHHHHHHcCCCCC------CHHHHHHHHHHhCCCC
Q 032366           81 SELKKAIVQARNDKKLTQSQLAQ-LINEKPQVIQEYESGKAIP------NQQILTKLERALGVKL  138 (142)
Q Consensus        81 ~~~g~~Lk~~R~~~glTQ~eLA~-~lgis~stIs~~E~G~~~p------~~~~l~kLa~~Lgvsl  138 (142)
                      ..+...|++..+..++||.-||+ .+|.++.+++.+.+.-..|      ..+...++-..|..+.
T Consensus        10 ~~I~~~ik~~Lk~~~isQ~~FA~~VL~rsQgtLs~lL~~Pkdpw~~l~~Gre~f~rM~nWL~l~e   74 (93)
T 2o4a_A           10 SEIYQWVRDELKRAGISQAVFARVAFNRTQGLLSEILRKEEDPKTASQSLLVNLRAMQNFLQLPE   74 (93)
T ss_dssp             TTHHHHHHHHHHHHTCCHHHHHHHHHSCCHHHHHHHHHHCCCTTSCCHHHHHHHHHHHHHHTSCH
T ss_pred             HHHHHHHHHHHHHcCCcHHHHHHHHHHHhhhHHHHHHcCCCCcHHHHHHHHHHHHHHHHHhCCCH
Confidence            45888999999999999999999 6799999999999855422      2445667777776653

>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=89.71  E-value=0.79  Score=29.11  Aligned_cols=33  Identities=6%  Similarity=0.080  Sum_probs=26.7

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ...|..+....++|+.+||+.+|+++++|++..
T Consensus        23 ~~il~~l~~~~~~s~~ela~~l~is~~tv~~~l   55 (109)
T 1sfx_A           23 VRIYSLLLERGGMRVSEIARELDLSARFVRDRL   55 (109)
T ss_dssp             HHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHH
Confidence            344555556678999999999999999999875

>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=89.60  E-value=0.55  Score=31.62  Aligned_cols=33  Identities=12%  Similarity=0.107  Sum_probs=26.8

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ..+-.++-..|+|..|+|+.+|+|.++|..+..
T Consensus        31 r~vl~l~~~~g~s~~EIA~~lgiS~~tV~~~l~   63 (113)
T 1xsv_A           31 RNYLELFYLEDYSLSEIADTFNVSRQAVYDNIR   63 (113)
T ss_dssp             HHHHHHHHTSCCCHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            334455667899999999999999999987653

>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=89.47  E-value=0.59  Score=31.44  Aligned_cols=31  Identities=10%  Similarity=0.122  Sum_probs=25.6

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHcCCCCCC
Q 032366           93 DKKLTQSQLAQLINEKPQVIQEYESGKAIPN  123 (142)
Q Consensus        93 ~~glTQ~eLA~~lgis~stIs~~E~G~~~p~  123 (142)
                      -..+|..+||+.+|+|++||.++.+--..-.
T Consensus        37 ~~~~si~elA~~~~vS~aTv~Rf~kklG~~g   67 (111)
T 2o3f_A           37 AIESTVNEISALANSSDAAVIRLCXSLGLKG   67 (111)
T ss_dssp             HHTCCHHHHHHHTTCCHHHHHHHHHHTTCSS
T ss_pred             HHhcCHHHHHHHHCCCHHHHHHHHHHcCCCC
Confidence            3589999999999999999999997443333

>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=88.99  E-value=0.54  Score=30.94  Aligned_cols=25  Identities=24%  Similarity=0.146  Sum_probs=21.8

Q ss_pred             HHHHHHHHcCCChhHHHhhhcCCCC
Q 032366           30 KVVNAARRAGADIETVRKSHAGTNK   54 (142)
Q Consensus        30 ~~~~~a~r~G~~v~t~kk~~~g~~~   54 (142)
                      ++-..|.+.|++.+|+.+|+.|...
T Consensus        24 sq~~lA~~~gis~~~i~~~e~g~~~   48 (114)
T 3op9_A           24 KNHQIAELLNVQTRTVAYYMSGETK   48 (114)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHHTSSC
T ss_pred             CHHHHHHHHCcCHHHHHHHHcCCCC
Confidence            4556899999999999999999765

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

Probab=88.93  E-value=0.56  Score=31.79  Aligned_cols=33  Identities=9%  Similarity=0.117  Sum_probs=26.5

Q ss_pred             HHHHHHHHHhCC--CCHHHHHHHhCCCHHHHHHHH
Q 032366           84 KKAIVQARNDKK--LTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        84 g~~Lk~~R~~~g--lTQ~eLA~~lgis~stIs~~E  116 (142)
                      ...|..+....+  +|+.+||+.+|++++||++..
T Consensus        29 ~~il~~L~~~~~~~~t~~eLa~~l~~s~sTV~r~L   63 (123)
T 3r0a_A           29 LNVMKSFLNEPDRWIDTDALSKSLKLDVSTVQRSV   63 (123)
T ss_dssp             HHHHHHHHHSTTCCEEHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHH
Confidence            345556666666  999999999999999999864

>1r8d_A Transcription activator MTAN; protein-DNA complex, transcription/DNA complex; 2.70A {Bacillus subtilis} SCOP: a.6.1.3 PDB: 1jbg_A

Probab=88.82  E-value=0.43  Score=31.78  Aligned_cols=23  Identities=17%  Similarity=0.359  Sum_probs=21.2

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 032366           95 KLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        95 glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      -+|..++|+.+|||+.||..||+
T Consensus         2 ~~~i~e~A~~~gvs~~tLR~ye~   24 (109)
T 1r8d_A            2 KYQVKQVAEISGVSIRTLHHYDN   24 (109)
T ss_dssp             CBCHHHHHHHHSCCHHHHHHHHH
T ss_pred             CccHHHHHHHHCcCHHHHHHHHH
Confidence            37889999999999999999986

>2d5v_A Hepatocyte nuclear factor 6; transcription factor, transcription-DNA complex; 2.00A {Rattus norvegicus} PDB: 1s7e_A

Probab=88.76  E-value=0.9  Score=32.44  Aligned_cols=39  Identities=13%  Similarity=0.171  Sum_probs=35.0

Q ss_pred             hHHHHHHHHHHHHhCCCCHHHHHHHh-CCCHHHHHHHHcC
Q 032366           80 PSELKKAIVQARNDKKLTQSQLAQLI-NEKPQVIQEYESG  118 (142)
Q Consensus        80 ~~~~g~~Lk~~R~~~glTQ~eLA~~l-gis~stIs~~E~G  118 (142)
                      ...+...|+..+...+++|..||+.+ |+++.+++.+.+.
T Consensus         6 t~~i~~~i~~~l~~~~i~q~~fa~~ilg~sq~~ls~~l~~   45 (164)
T 2d5v_A            6 TKEVAQRITTELKRYSIPQAIFAQRVLCRSQGTLSDLLRN   45 (164)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHTSCCHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHcCCchHHHHHHHhcCCchhHHHHcCC
Confidence            45689999999999999999999965 9999999999964

>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=88.49  E-value=0.82  Score=30.29  Aligned_cols=34  Identities=6%  Similarity=-0.028  Sum_probs=28.7

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ...|.......+.++.+.|+.+|||++++.+..+
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            3556777888899999999999999999987654

>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=88.48  E-value=0.88  Score=30.92  Aligned_cols=27  Identities=7%  Similarity=0.096  Sum_probs=24.0

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           91 RNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        91 R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +.-.|+|..|+|+.+|+|.++|.....
T Consensus       120 ~~~~g~s~~EIA~~lgis~~tV~~~~~  146 (164)
T 3mzy_A          120 YLIRGYSYREIATILSKNLKSIDNTIQ  146 (164)
T ss_dssp             HHTTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence            466899999999999999999988764

>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=88.35  E-value=0.66  Score=27.75  Aligned_cols=33  Identities=12%  Similarity=0.049  Sum_probs=26.8

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ...|....... .++.+.|+.+|||++|+.+..+
T Consensus        23 r~~I~~aL~~~-gn~~~aA~~LGIsr~tL~rklk   55 (61)
T 1g2h_A           23 AQVLKLFYAEY-PSTRKLAQRLGVSHTAIANKLK   55 (61)
T ss_dssp             HHHHHHHHHHS-CSHHHHHHHTTSCTHHHHHHHH
T ss_pred             HHHHHHHHHHh-CCHHHHHHHhCCCHHHHHHHHH
Confidence            45566666667 6899999999999999988765

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

Probab=87.98  E-value=0.54  Score=31.55  Aligned_cols=36  Identities=11%  Similarity=0.188  Sum_probs=28.1

Q ss_pred             HHHHHH-HHHHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 032366           83 LKKAIV-QARNDKKLTQSQLAQLINEKPQVIQEYESG  118 (142)
Q Consensus        83 ~g~~Lk-~~R~~~glTQ~eLA~~lgis~stIs~~E~G  118 (142)
                      +++.|- ....-..+|..+||+.+|+|++||.++.+-
T Consensus        22 ia~yil~~~~~~~~~si~elA~~~~vS~aTv~Rf~kk   58 (107)
T 3iwf_A           22 IAQFILNYPHKVVNMTSQEIANQLETSSTSIIRLSKK   58 (107)
T ss_dssp             HHHHHHHCHHHHTTCCHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHHHHhCHHHHHHCCHHHHHHHHCCCHHHHHHHHHH
Confidence            444443 334557899999999999999999999873

>3kz3_A Repressor protein CI; five helix bundle, DNA-binding, transcription, transcription regulation; 1.64A {Enterobacteria phage lambda}

Probab=87.91  E-value=0.37  Score=29.75  Aligned_cols=25  Identities=20%  Similarity=0.221  Sum_probs=22.0

Q ss_pred             HHHHHHHHcCCChhHHHhhhcCCCC
Q 032366           30 KVVNAARRAGADIETVRKSHAGTNK   54 (142)
Q Consensus        30 ~~~~~a~r~G~~v~t~kk~~~g~~~   54 (142)
                      ++-..|.+.|++.+|+.+|+.|...
T Consensus        27 tq~~lA~~~gvs~~~is~~e~g~~~   51 (80)
T 3kz3_A           27 SYESVADKMGMGQSAVAALFNGINA   51 (80)
T ss_dssp             CHHHHHHHTTSCHHHHHHHHTTSSC
T ss_pred             CHHHHHHHhCcCHHHHHHHHcCCCC
Confidence            3557899999999999999999876

>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=87.86  E-value=0.85  Score=30.18  Aligned_cols=24  Identities=13%  Similarity=0.238  Sum_probs=22.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           94 KKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        94 ~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .++|..|+|+.+|+|.++|..++.
T Consensus        38 e~~s~~EIA~~lgiS~~tVr~~~~   61 (99)
T 3t72_q           38 TDYTLEEVGKQFDVTRERIRQIEA   61 (99)
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHH
Confidence            689999999999999999999875

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

Probab=87.85  E-value=0.4  Score=30.43  Aligned_cols=29  Identities=3%  Similarity=0.023  Sum_probs=22.9

Q ss_pred             HHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           88 VQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        88 k~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ..+....++|..+||+.+|+|+++|++..
T Consensus        31 ~~l~~~~~~s~~ela~~l~is~~tvs~~l   59 (99)
T 3cuo_A           31 CMLSGSPGTSAGELTRITGLSASATSQHL   59 (99)
T ss_dssp             HHHTTCCSEEHHHHHHHHCCCHHHHHHHH
T ss_pred             HHHHhCCCcCHHHHHHHHCcCHHHHHHHH
Confidence            33333347999999999999999998864

>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=87.71  E-value=0.76  Score=29.32  Aligned_cols=29  Identities=0%  Similarity=0.076  Sum_probs=22.2

Q ss_pred             HHHHHHhC-CCCHHHHHHHhCCCHHH-HHHH
Q 032366           87 IVQARNDK-KLTQSQLAQLINEKPQV-IQEY  115 (142)
Q Consensus        87 Lk~~R~~~-glTQ~eLA~~lgis~st-Is~~  115 (142)
                      |..+...- ++|+.+||+.+|+++++ +++.
T Consensus        21 L~~l~~~~~~~t~~eLa~~l~is~~t~vs~~   51 (95)
T 2pg4_A           21 LLEFEKKGYEPSLAEIVKASGVSEKTFFMGL   51 (95)
T ss_dssp             HHHHHHTTCCCCHHHHHHHHCCCHHHHHTTH
T ss_pred             HHHHHhcCCCCCHHHHHHHHCCCchHHHHHH
Confidence            34444444 79999999999999999 5554

>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=87.68  E-value=0.31  Score=29.84  Aligned_cols=25  Identities=12%  Similarity=0.210  Sum_probs=21.9

Q ss_pred             HHHHHHHHcCCChhHHHhhhcCCCC
Q 032366           30 KVVNAARRAGADIETVRKSHAGTNK   54 (142)
Q Consensus        30 ~~~~~a~r~G~~v~t~kk~~~g~~~   54 (142)
                      ++-..|.+.|++..|+.+||.|...
T Consensus        26 tq~elA~~~gvs~~tis~~E~G~~~   50 (73)
T 3fmy_A           26 TQKEASEIFGGGVNAFSRYEKGNAX   50 (73)
T ss_dssp             CHHHHHHHHCSCTTHHHHHHTTSSC
T ss_pred             CHHHHHHHhCcCHHHHHHHHcCCCC
Confidence            4566899999999999999999876

>3gp4_A Transcriptional regulator, MERR family; structural genomics, DNA-BI transcription regulator, PSI-2; 1.85A {Listeria monocytogenes str}

Probab=87.37  E-value=0.56  Score=32.96  Aligned_cols=26  Identities=19%  Similarity=0.254  Sum_probs=22.8

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc-CCC
Q 032366           95 KLTQSQLAQLINEKPQVIQEYES-GKA  120 (142)
Q Consensus        95 glTQ~eLA~~lgis~stIs~~E~-G~~  120 (142)
                      .+|..++|+.+|||+.||.-||. |--
T Consensus         2 ~~~I~e~A~~~gvs~~tLR~Ye~~GLl   28 (142)
T 3gp4_A            2 SLNIKEASEKSGVSADTIRYYERIGLI   28 (142)
T ss_dssp             CBCHHHHHHHHTSCHHHHHHHHHHTSS
T ss_pred             CCcHHHHHHHHCcCHHHHHHHHHCCCC
Confidence            47899999999999999999996 443

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

Probab=87.34  E-value=1.1  Score=29.67  Aligned_cols=37  Identities=11%  Similarity=0.178  Sum_probs=28.6

Q ss_pred             hHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           80 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ...-...|..+...-++|+.+||+.+|+++++|++..
T Consensus        28 ~~~~~~iL~~l~~~~~~~~~ela~~l~~s~~tvs~~l   64 (138)
T 3bpv_A           28 TDAQVACLLRIHREPGIKQDELATFFHVDKGTIARTL   64 (138)
T ss_dssp             CHHHHHHHHHHHHSTTCBHHHHHHHHTCCHHHHHHHH
T ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHH
Confidence            3334445666666678999999999999999998764

>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=87.29  E-value=1.3  Score=30.46  Aligned_cols=32  Identities=22%  Similarity=0.366  Sum_probs=26.0

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ..|..+.....+|..+||+.+|+|++++.+..
T Consensus         9 ~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l   40 (144)
T 2cfx_A            9 NIIEELKKDSRLSMRELGRKIKLSPPSVTERV   40 (144)
T ss_dssp             HHHHHHHHCSCCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHH
Confidence            34556666678999999999999999988754

>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=87.07  E-value=1.3  Score=30.65  Aligned_cols=32  Identities=19%  Similarity=0.098  Sum_probs=26.2

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ..|..+...-.+|..+||+.+|+|++++++..
T Consensus        11 ~iL~~L~~~~~~s~~ela~~lg~s~~tv~~~l   42 (150)
T 2w25_A           11 ILVRELAADGRATLSELATRAGLSVSAVQSRV   42 (150)
T ss_dssp             HHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHH
Confidence            44566666677999999999999999998754

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

Probab=87.06  E-value=1  Score=30.34  Aligned_cols=38  Identities=11%  Similarity=0.175  Sum_probs=29.5

Q ss_pred             chHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           79 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      +...-...|..+...-++|+.+||+.+++++++++++.
T Consensus        35 lt~~~~~iL~~l~~~~~~t~~eLa~~l~~~~~~vs~~l   72 (143)
T 3oop_A           35 VTPEQWSVLEGIEANEPISQKEIALWTKKDTPTVNRIV   72 (143)
T ss_dssp             SCHHHHHHHHHHHHHSSEEHHHHHHHHTCCHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCcCHHHHHHHHCCCHhhHHHHH
Confidence            33344455666666689999999999999999999864

>2rnj_A Response regulator protein VRAR; HTH LUXR-type domain, DNA binding domain, activator, antibiotic resistance, cytoplasm, DNA-binding; NMR {Staphylococcus aureus}

Probab=86.96  E-value=0.7  Score=29.45  Aligned_cols=25  Identities=12%  Similarity=0.114  Sum_probs=22.6

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           93 DKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        93 ~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ..|+|.+|+|+.+|+|.+||..+..
T Consensus        42 ~~g~s~~eIA~~l~is~~tV~~~l~   66 (91)
T 2rnj_A           42 AKGYSNQEIASASHITIKTVKTHVS   66 (91)
T ss_dssp             HTTCCTTHHHHHHTCCHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            6899999999999999999988764

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

Probab=86.86  E-value=1.2  Score=30.00  Aligned_cols=38  Identities=3%  Similarity=0.045  Sum_probs=29.5

Q ss_pred             chHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           79 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      +...-...|..+...-++|+.+||+.+|++++++++..
T Consensus        38 l~~~~~~iL~~l~~~~~~t~~ela~~l~~~~~tvs~~l   75 (148)
T 3nrv_A           38 IGMTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTV   75 (148)
T ss_dssp             CCHHHHHHHHHHHHSSSBCHHHHHHHHTCCHHHHHHHH
T ss_pred             CCHHHHHHHHHHHcCCCCCHHHHHHHHCCCHHHHHHHH
Confidence            33334455666666679999999999999999998864

>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=86.85  E-value=0.88  Score=30.68  Aligned_cols=37  Identities=8%  Similarity=0.069  Sum_probs=25.9

Q ss_pred             hHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           80 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ...-...|..+...-++|+.+||+.+|+++++++++.
T Consensus        36 t~~~~~vL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l   72 (142)
T 3ech_A           36 TPPDVHVLKLIDEQRGLNLQDLGRQMCRDKALITRKI   72 (142)
T ss_dssp             CHHHHHHHHHHHHTTTCCHHHHHHHHC---CHHHHHH
T ss_pred             CHHHHHHHHHHHhCCCcCHHHHHHHhCCCHHHHHHHH
Confidence            3334455666666679999999999999999988764

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

Probab=86.73  E-value=1.4  Score=29.28  Aligned_cols=34  Identities=12%  Similarity=0.038  Sum_probs=27.2

Q ss_pred             HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      -...|..+...-++|+.+||+.+|+++++|++..
T Consensus        33 ~~~iL~~l~~~~~~~~~ela~~l~is~~~vs~~l   66 (142)
T 3bdd_A           33 RYSILQTLLKDAPLHQLALQERLQIDRAAVTRHL   66 (142)
T ss_dssp             HHHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHH
Confidence            3445566666678999999999999999998764

>3gp4_A Transcriptional regulator, MERR family; structural genomics, DNA-BI transcription regulator, PSI-2; 1.85A {Listeria monocytogenes str}

Probab=86.72  E-value=2.6  Score=29.41  Aligned_cols=63  Identities=17%  Similarity=0.212  Sum_probs=37.6

Q ss_pred             HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhC
Q 032366           33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLIN  106 (142)
Q Consensus        33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lg  106 (142)
                      +.|++.|+++.|++-|+. |-..|.... .-.-+.++.+         ....-..|+.+| ..|+|..++.+.+.
T Consensus         7 e~A~~~gvs~~tLR~Ye~~GLl~p~~r~-~~g~R~Y~~~---------dl~~l~~I~~lr-~~G~sL~eIk~~l~   70 (142)
T 3gp4_A            7 EASEKSGVSADTIRYYERIGLIPPIHRN-ESGVRKFGAE---------DLRWILFTRQMR-RAGLSIEALIDYLA   70 (142)
T ss_dssp             HHHHHHTSCHHHHHHHHHHTSSCCCCBC-TTSCBCBCHH---------HHHHHHHHHHHH-HTTCCHHHHHHHHH
T ss_pred             HHHHHHCcCHHHHHHHHHCCCCCCCcCC-CCCCeeeCHH---------HHHHHHHHHHHH-HcCCCHHHHHHHHH
Confidence            478999999999999998 544431111 0011111111         112344566665 67999999987664

>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=86.71  E-value=0.58  Score=29.61  Aligned_cols=30  Identities=13%  Similarity=0.192  Sum_probs=24.2

Q ss_pred             HHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           87 IVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      |..+....++|..+||+.+|+++++|++..
T Consensus        22 L~~L~~~~~~~~~ela~~l~is~~tvs~~l   51 (100)
T 1ub9_A           22 MIFLLPRRKAPFSQIQKVLDLTPGNLDSHI   51 (100)
T ss_dssp             HHHHHHHSEEEHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHhcCCcCHHHHHHHHCcCHHHHHHHH
Confidence            444445567999999999999999998754

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

Probab=86.69  E-value=1.4  Score=29.23  Aligned_cols=38  Identities=18%  Similarity=0.161  Sum_probs=28.8

Q ss_pred             chHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           79 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      +...-...|..+...-++|+.+||+.+|++++++++..
T Consensus        36 l~~~~~~iL~~l~~~~~~t~~ela~~l~~~~~tvs~~l   73 (140)
T 2nnn_A           36 LTPTQWAALVRLGETGPCPQNQLGRLTAMDAATIKGVV   73 (140)
T ss_dssp             CCHHHHHHHHHHHHHSSBCHHHHHHHTTCCHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHH
Confidence            33334445566656668999999999999999998874

>1rp3_A RNA polymerase sigma factor sigma-28 (FLIA); transcription; 2.30A {Aquifex aeolicus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1sc5_A

Probab=86.65  E-value=0.91  Score=32.94  Aligned_cols=32  Identities=9%  Similarity=0.233  Sum_probs=26.4

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           86 AIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        86 ~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .+-.++--.|+|..|+|+.+|+|.++|..+..
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            34445556799999999999999999998763

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

Probab=86.64  E-value=0.34  Score=31.69  Aligned_cols=34  Identities=12%  Similarity=0.094  Sum_probs=26.8

Q ss_pred             HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      +.+.+..++..-.++..|||+.+++|..||.+..
T Consensus         4 L~~Il~~L~~~g~vsv~eLA~~l~VS~~TIRrDL   37 (87)
T 2k02_A            4 LMEVRDMLALQGRMEAKQLSARLQTPQPLIDAML   37 (87)
T ss_dssp             THHHHHHHHHSCSEEHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHH
Confidence            3444566677778999999999999999987643

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

Probab=86.63  E-value=1.6  Score=30.65  Aligned_cols=32  Identities=16%  Similarity=0.199  Sum_probs=26.1

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ..|..+.....+|..+||+.+|+|++++++..
T Consensus        14 ~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l   45 (162)
T 2p5v_A           14 KILQVLQENGRLTNVELSERVALSPSPCLRRL   45 (162)
T ss_dssp             HHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHH
Confidence            44566666677999999999999999988754

>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=86.54  E-value=1.5  Score=29.69  Aligned_cols=26  Identities=12%  Similarity=0.190  Sum_probs=22.3

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           91 RNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        91 R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ....++|+.+||+.+|+++++|++..
T Consensus        18 ~~~~~~~~~ela~~l~vs~~tvs~~l   43 (142)
T 1on2_A           18 EEKGYARVSDIAEALAVHPSSVTKMV   43 (142)
T ss_dssp             HHHSSCCHHHHHHHHTSCHHHHHHHH
T ss_pred             hhcCCCCHHHHHHHhCCCHHHHHHHH
Confidence            34578999999999999999988754

>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=86.51  E-value=1.4  Score=30.43  Aligned_cols=32  Identities=13%  Similarity=0.169  Sum_probs=26.4

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ..|..+.....+|..+||+.+|+|++++.+..
T Consensus        12 ~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l   43 (152)
T 2cg4_A           12 GILEALMGNARTAYAELAKQFGVSPETIHVRV   43 (152)
T ss_dssp             HHHHHHHHCTTSCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHH
Confidence            44566667778999999999999999988754

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

Probab=86.44  E-value=1.5  Score=29.57  Aligned_cols=38  Identities=11%  Similarity=0.053  Sum_probs=29.9

Q ss_pred             chHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           79 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      +...-...|..+...-++|+.+||+.+|+++++++++.
T Consensus        29 lt~~q~~iL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l   66 (145)
T 3g3z_A           29 LNYNLFAVLYTLATEGSRTQKHIGEKWSLPKQTVSGVC   66 (145)
T ss_dssp             CCHHHHHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHH
Confidence            34444556666766778999999999999999998874

>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=86.44  E-value=1.6  Score=31.96  Aligned_cols=36  Identities=14%  Similarity=0.235  Sum_probs=28.1

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCC
Q 032366           85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAI  121 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~  121 (142)
                      +.|.++. ..|+|..++|+.+|+|++||.++.+....
T Consensus       166 ~~i~~~~-~~G~s~~~Ia~~l~is~~tv~r~l~~~~~  201 (209)
T 2r0q_C          166 HRVVEML-EEGQAISKIAKEVNITRQTVYRIKHDNGL  201 (209)
T ss_dssp             HHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHTTCC-
T ss_pred             HHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHhcccc
Confidence            3444444 36999999999999999999999876543

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

Probab=86.31  E-value=1  Score=31.16  Aligned_cols=32  Identities=22%  Similarity=0.281  Sum_probs=26.0

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ..|..+.....+|..+||+.+|+|++++.+..
T Consensus        13 ~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l   44 (151)
T 2dbb_A           13 QLVKILSENSRLTYRELADILNTTRQRIARRI   44 (151)
T ss_dssp             HHHHHHHHCTTCCHHHHHHHTTSCHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHH
Confidence            34556666778999999999999999988754

>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=86.26  E-value=1.3  Score=25.85  Aligned_cols=27  Identities=11%  Similarity=0.176  Sum_probs=23.3

Q ss_pred             HHhCCCCHHHHHHHh-----CCCHHHHHHHHc
Q 032366           91 RNDKKLTQSQLAQLI-----NEKPQVIQEYES  117 (142)
Q Consensus        91 R~~~glTQ~eLA~~l-----gis~stIs~~E~  117 (142)
                      .....+|..+|++.+     +||.+||++..+
T Consensus        15 ~~~~~~t~~el~~~l~~~~~~vs~~Tv~R~L~   46 (64)
T 2p5k_A           15 TSNEIETQDELVDMLKQDGYKVTQATVSRDIK   46 (64)
T ss_dssp             HHSCCCSHHHHHHHHHHTTCCCCHHHHHHHHH
T ss_pred             HcCCCCCHHHHHHHHHHhCCCcCHHHHHHHHH
Confidence            445679999999999     999999998765

>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=86.14  E-value=0.85  Score=31.64  Aligned_cols=22  Identities=23%  Similarity=0.385  Sum_probs=20.6

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ||..++|+.+|||..||..||+
T Consensus         1 ~~I~e~A~~~gvs~~tLR~ye~   22 (135)
T 1q06_A            1 MNISDVAKITGLTSKAIRFYEE   22 (135)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            5788999999999999999997

>1p4w_A RCSB; solution structure, DNA binding domain, DNA binding protein; NMR {Erwinia amylovora} SCOP: a.4.6.2

Probab=86.12  E-value=1.7  Score=28.60  Aligned_cols=57  Identities=11%  Similarity=0.174  Sum_probs=37.2

Q ss_pred             cchHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcC----CCCCCHHHHHHHHHHhCC
Q 032366           78 RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESG----KAIPNQQILTKLERALGV  136 (142)
Q Consensus        78 ~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G----~~~p~~~~l~kLa~~Lgv  136 (142)
                      .+.+.-.+.|..+  ..|+|.+|+|+.+|+|..||..+...    -...+...+..++...|+
T Consensus        34 ~Lt~re~~Vl~l~--~~G~s~~EIA~~L~iS~~TV~~~l~ri~~KLgv~~r~elv~~a~~~gl   94 (99)
T 1p4w_A           34 RLSPKESEVLRLF--AEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVDNDIALLNYLSSVSM   94 (99)
T ss_dssp             SCCHHHHHHHHHH--HHTCCHHHHHHHHTSCHHHHHHHHHHHHHHHTCSSHHHHHHHHHHHTC
T ss_pred             CCCHHHHHHHHHH--HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHcCC
Confidence            4444444444332  36999999999999999999887642    123345555566655554

>3hh0_A Transcriptional regulator, MERR family; protein structure initiative II(PSI II), NYSGXRC, 11183J, structural genomics; 2.67A {Bacillus cereus atcc 14579}

Probab=86.04  E-value=2.3  Score=29.89  Aligned_cols=64  Identities=11%  Similarity=0.104  Sum_probs=37.4

Q ss_pred             HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhCC
Q 032366           33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINE  107 (142)
Q Consensus        33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgi  107 (142)
                      +.|++.|+++.|++-|+. |-..|..... -.-+.++.+         ....-..|+.+| ..|+|..++...+..
T Consensus         9 evA~~~Gvs~~tLR~ye~~GLl~p~~r~~-~g~R~Y~~~---------dl~~l~~I~~lr-~~G~sl~~I~~~l~~   73 (146)
T 3hh0_A            9 EFASVGDVTVRALRYYDKINLLKPSDYTE-GGHRLYTKD---------DLYVLQQIQSFK-HLGFSLGEIQNIILQ   73 (146)
T ss_dssp             HHHHHHTCCHHHHHHHHHTTSSCCSEECT-TSCEEBCHH---------HHHHHHHHHHHH-HTTCCHHHHHHHHTS
T ss_pred             HHHHHHCcCHHHHHHHHHCCCCCCCeECC-CCCEeeCHH---------HHHHHHHHHHHH-HcCCCHHHHHHHHHc
Confidence            579999999999999997 4444321100 011111111         111233455554 579999998887764

>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=86.00  E-value=1.6  Score=29.00  Aligned_cols=36  Identities=14%  Similarity=0.042  Sum_probs=27.4

Q ss_pred             HHHHHHHHHHHHhC--CCCHHHHHHHhCCCHHHHHHHH
Q 032366           81 SELKKAIVQARNDK--KLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        81 ~~~g~~Lk~~R~~~--glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ..-...|..+...-  ++|+.+||+.+|+++++|++..
T Consensus        34 ~~~~~iL~~l~~~~~~~~~~~ela~~l~~~~~tvs~~l   71 (141)
T 3bro_A           34 GTQMTIIDYLSRNKNKEVLQRDLESEFSIKSSTATVLL   71 (141)
T ss_dssp             HHHHHHHHHHHHTTTSCCBHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCCCcCHHHHHHHHCCCcchHHHHH
Confidence            33444556665555  7999999999999999988764

>1yse_A DNA-binding protein SATB1; all helical, DNA-binding domain, T-cell development; NMR {Homo sapiens} SCOP: a.35.1.7

Probab=85.98  E-value=0.59  Score=33.29  Aligned_cols=60  Identities=15%  Similarity=0.143  Sum_probs=45.6

Q ss_pred             cchHHHHHHHHHHHHhCCCCHHHHHH-HhCCCHHHHHHHHcCCCC------CCHHHHHHHHHHhCCC
Q 032366           78 RVPSELKKAIVQARNDKKLTQSQLAQ-LINEKPQVIQEYESGKAI------PNQQILTKLERALGVK  137 (142)
Q Consensus        78 ~~~~~~g~~Lk~~R~~~glTQ~eLA~-~lgis~stIs~~E~G~~~------p~~~~l~kLa~~Lgvs  137 (142)
                      .+..++.+.|++..+..+++|.-||+ .+|.++.+++++.+--..      ...+...++-..|..+
T Consensus        21 ~vt~~I~~~Ik~eLk~~~IsQ~~FA~~VL~rsQGtLS~LLr~PkdPW~~LksGRE~fiRM~NWL~Lp   87 (141)
T 1yse_A           21 EVSSEIYQWVRDELKRAGISQAVFARVAFNRTQGLLSEILRKEEDPKTASQSLLVNLRAMQNFLQLP   87 (141)
T ss_dssp             SCCTHHHHHHHHHHHHHTCCHHHHHHHHCCSCTTHHHHHHHHCCCGGGCCHHHHHHHHHHHHHHHSC
T ss_pred             cchHHHHHHHHHHHHHcCCCHHHHHHHHHHhhhhhHHHHHcCCCCcHHHHHHHHHHHHHHHHHhcCC
Confidence            56678999999999999999999999 558999999999875442      1234455555555443

>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=85.87  E-value=1.1  Score=31.55  Aligned_cols=32  Identities=9%  Similarity=0.114  Sum_probs=26.3

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           86 AIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        86 ~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .+-.++.-.|+|.+|+|+.+|+|.++|.....
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            34445666899999999999999999998764

>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=85.79  E-value=1.4  Score=29.58  Aligned_cols=34  Identities=12%  Similarity=0.024  Sum_probs=27.6

Q ss_pred             HHHHHHHHHH-hCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           83 LKKAIVQARN-DKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        83 ~g~~Lk~~R~-~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      -...|..+.. ..++|+.+||+.+|+++++|++..
T Consensus        37 ~~~iL~~l~~~~~~~~~~~la~~l~i~~~~vs~~l   71 (147)
T 2hr3_A           37 QLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALL   71 (147)
T ss_dssp             HHHHHHHHHHTTSCBCHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHH
Confidence            3455666666 678999999999999999988764

>3hh0_A Transcriptional regulator, MERR family; protein structure initiative II(PSI II), NYSGXRC, 11183J, structural genomics; 2.67A {Bacillus cereus atcc 14579}

Probab=85.75  E-value=0.89  Score=32.08  Aligned_cols=24  Identities=13%  Similarity=0.166  Sum_probs=22.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           94 KKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        94 ~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ..+|..|+|+.+|||.+||..||.
T Consensus         3 ~~~tI~evA~~~Gvs~~tLR~ye~   26 (146)
T 3hh0_A            3 LAWLISEFASVGDVTVRALRYYDK   26 (146)
T ss_dssp             CCBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCcHHHHHHHHCcCHHHHHHHHH
Confidence            358999999999999999999997

>3omt_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; 1.65A {Cytophaga hutchinsonii}

Probab=85.74  E-value=0.43  Score=28.75  Aligned_cols=25  Identities=12%  Similarity=-0.013  Sum_probs=21.8

Q ss_pred             HHHHHHHHcCCChhHHHhhhcCCCC
Q 032366           30 KVVNAARRAGADIETVRKSHAGTNK   54 (142)
Q Consensus        30 ~~~~~a~r~G~~v~t~kk~~~g~~~   54 (142)
                      ++-..|.+.|++..|+.+|+.|...
T Consensus        23 sq~~lA~~~gis~~~is~~e~g~~~   47 (73)
T 3omt_A           23 TNLWLTETLDKNKTTVSKWCTNDVQ   47 (73)
T ss_dssp             CHHHHHHHTTCCHHHHHHHHTTSSC
T ss_pred             CHHHHHHHHCcCHHHHHHHHcCCCC
Confidence            4567899999999999999999865

>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=85.73  E-value=1.6  Score=31.38  Aligned_cols=21  Identities=24%  Similarity=0.253  Sum_probs=19.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHH
Q 032366           96 LTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E  116 (142)
                      +||.+||..+|+|+.+|++..
T Consensus       164 ~t~~~lA~~lG~sr~tvsR~l  184 (222)
T 1ft9_A          164 FTVEEIANLIGSSRQTTSTAL  184 (222)
T ss_dssp             CCHHHHHHHHCSCHHHHHHHH
T ss_pred             CCHHHHHHHhCCcHHHHHHHH
Confidence            899999999999999999765

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

Probab=85.56  E-value=1.7  Score=29.30  Aligned_cols=36  Identities=11%  Similarity=0.002  Sum_probs=28.0

Q ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           81 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        81 ~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ..-...|..+...-++|+.+||+.+|+++++|++..
T Consensus        42 ~~~~~iL~~l~~~~~~t~~ela~~l~~~~~tvs~~l   77 (150)
T 2rdp_A           42 PPQFVALQWLLEEGDLTVGELSNKMYLACSTTTDLV   77 (150)
T ss_dssp             HHHHHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCCCchhHHHHH
Confidence            333445566666678999999999999999998864

>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=85.54  E-value=1.9  Score=27.49  Aligned_cols=24  Identities=13%  Similarity=0.135  Sum_probs=21.6

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           93 DKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        93 ~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ...++..+||+.+|+|+++|++..
T Consensus        41 ~~~~~~~eLa~~l~is~~tv~~~L   64 (96)
T 1y0u_A           41 DKGRSEEEIMQTLSLSKKQLDYHL   64 (96)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             cCCCCHHHHHHHHCcCHHHHHHHH
Confidence            567999999999999999999854

>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=85.53  E-value=1.3  Score=28.88  Aligned_cols=24  Identities=4%  Similarity=0.047  Sum_probs=21.5

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           93 DKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        93 ~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ..++|..+||+.+|+|+++|++..
T Consensus        37 ~~~~~~~ela~~l~is~stvs~~L   60 (106)
T 1r1u_A           37 VSEASVGHISHQLNLSQSNVSHQL   60 (106)
T ss_dssp             HCCBCHHHHHHHHTCCHHHHHHHH
T ss_pred             hCCCCHHHHHHHHCcCHHHHHHHH
Confidence            567999999999999999998854

>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=85.45  E-value=1.2  Score=30.72  Aligned_cols=31  Identities=10%  Similarity=0.049  Sum_probs=24.7

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           86 AIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        86 ~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      .|..+.....+|..+||+.+|+|++++++..
T Consensus         8 il~~L~~~~~~~~~ela~~lg~s~~tv~~~l   38 (150)
T 2pn6_A            8 ILKILQYNAKYSLDEIAREIRIPKATLSYRI   38 (150)
T ss_dssp             HHHHHTTCTTSCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHcCCCCHHHHHHHHCcCHHHHHHHH
Confidence            3455555567999999999999999988754

>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=85.41  E-value=1.5  Score=31.49  Aligned_cols=32  Identities=13%  Similarity=0.196  Sum_probs=26.1

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 032366           86 AIVQARNDKKLTQSQLAQLINEKPQVIQEYESG  118 (142)
Q Consensus        86 ~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G  118 (142)
                      .|.++. ..|+|..++|+.+|+|++||.+|.+.
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 46999999999999999999998764

>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=85.40  E-value=0.48  Score=27.49  Aligned_cols=25  Identities=8%  Similarity=-0.028  Sum_probs=21.6

Q ss_pred             HHHHHHHHcCCChhHHHhhhcCCCC
Q 032366           30 KVVNAARRAGADIETVRKSHAGTNK   54 (142)
Q Consensus        30 ~~~~~a~r~G~~v~t~kk~~~g~~~   54 (142)
                      ++-..|++.|++.+|+.+|+.|...
T Consensus        16 s~~~lA~~~gis~~~i~~~e~g~~~   40 (66)
T 2xi8_A           16 SQSELAALLEVSRQTINGIEKNKYN   40 (66)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHTTSCC
T ss_pred             CHHHHHHHHCcCHHHHHHHHcCCCC
Confidence            3456899999999999999999765

>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=85.37  E-value=0.64  Score=32.94  Aligned_cols=23  Identities=9%  Similarity=0.309  Sum_probs=20.6

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 032366           95 KLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        95 glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .+||.+||..+|+++.+|+++.+
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            48999999999999999998754

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

Probab=85.30  E-value=1.3  Score=28.48  Aligned_cols=26  Identities=12%  Similarity=0.086  Sum_probs=22.9

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 032366           94 KKLTQSQLAQLINEKPQVIQEYESGK  119 (142)
Q Consensus        94 ~glTQ~eLA~~lgis~stIs~~E~G~  119 (142)
                      ..++..+||+.+|+|+.+++++-+..
T Consensus        18 ~~~~~~~lA~~~~~S~~~l~r~fk~~   43 (103)
T 3lsg_A           18 SQFTLSVLSEKLDLSSGYLSIMFKKN   43 (103)
T ss_dssp             TTCCHHHHHHHTTCCHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence            37999999999999999999988643

>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=85.28  E-value=0.86  Score=29.17  Aligned_cols=21  Identities=10%  Similarity=-0.021  Sum_probs=19.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHH
Q 032366           96 LTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E  116 (142)
                      +|+.+||+.+++++++++++.
T Consensus        31 ~t~~eLa~~l~i~~~tvs~~l   51 (95)
T 2qvo_A           31 VYIQYIASKVNSPHSYVWLII   51 (95)
T ss_dssp             EEHHHHHHHSSSCHHHHHHHH
T ss_pred             cCHHHHHHHHCcCHHHHHHHH
Confidence            999999999999999988864

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

Probab=85.23  E-value=1.9  Score=29.54  Aligned_cols=33  Identities=6%  Similarity=-0.078  Sum_probs=26.1

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ...|..+...-++|+.+||+.+|+++++|+++.
T Consensus        52 ~~iL~~l~~~~~~t~~ela~~l~is~~tvs~~l   84 (162)
T 2fa5_A           52 WRVITILALYPGSSASEVSDRTAMDKVAVSRAV   84 (162)
T ss_dssp             HHHHHHHHHSTTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHH
Confidence            344555555678999999999999999988764

>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=85.17  E-value=1.4  Score=29.94  Aligned_cols=30  Identities=7%  Similarity=0.151  Sum_probs=24.1

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHH
Q 032366           86 AIVQARNDKKLTQSQLAQLINEKPQVIQEY  115 (142)
Q Consensus        86 ~Lk~~R~~~glTQ~eLA~~lgis~stIs~~  115 (142)
                      .|..+...-.+|..+||+.+|+|++++++.
T Consensus         9 il~~L~~~~~~~~~ela~~lg~s~~tv~~~   38 (141)
T 1i1g_A            9 ILEILEKDARTPFTEIAKKLGISETAVRKR   38 (141)
T ss_dssp             HHHHHHHCTTCCHHHHHHHHTSCHHHHHHH
T ss_pred             HHHHHHHcCCCCHHHHHHHHCcCHHHHHHH
Confidence            345555556799999999999999999874

>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=85.16  E-value=1.9  Score=28.78  Aligned_cols=34  Identities=6%  Similarity=0.012  Sum_probs=27.0

Q ss_pred             HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      -...|..+...-++|+.+||+.+|++++++++..
T Consensus        35 ~~~iL~~l~~~~~~~~~~la~~l~~s~~tvs~~l   68 (145)
T 2a61_A           35 QFDILQKIYFEGPKRPGELSVLLGVAKSTVTGLV   68 (145)
T ss_dssp             HHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHCCCchhHHHHH
Confidence            3444555555678999999999999999998764

>2ef8_A C.ECOT38IS, putative transcription factor; helix-turn-helix, DNA binding protein, transcription regulator; HET: CME; 1.95A {Enterobacteria phage P2}

Probab=85.08  E-value=2.1  Score=25.95  Aligned_cols=25  Identities=12%  Similarity=0.011  Sum_probs=21.8

Q ss_pred             HHHHHHHHcCCChhHHHhhhcCCCC
Q 032366           30 KVVNAARRAGADIETVRKSHAGTNK   54 (142)
Q Consensus        30 ~~~~~a~r~G~~v~t~kk~~~g~~~   54 (142)
                      ++-..|.+.|++..|+.+|+.|...
T Consensus        25 sq~~lA~~~gis~~~i~~~e~g~~~   49 (84)
T 2ef8_A           25 SQSELAIFLGLSQSDISKIESFERR   49 (84)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHTTSSC
T ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCC
Confidence            4567899999999999999999765

>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=85.00  E-value=0.52  Score=27.50  Aligned_cols=25  Identities=4%  Similarity=0.101  Sum_probs=21.5

Q ss_pred             HHHHHHHHcCCChhHHHhhhcCCCC
Q 032366           30 KVVNAARRAGADIETVRKSHAGTNK   54 (142)
Q Consensus        30 ~~~~~a~r~G~~v~t~kk~~~g~~~   54 (142)
                      ++-..|++.|++..|+.+|+.|...
T Consensus        20 s~~~lA~~~gis~~~i~~~e~g~~~   44 (68)
T 2r1j_L           20 RQAALGKMVGVSNVAISQWERSETE   44 (68)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHTTSSC
T ss_pred             CHHHHHHHHCCCHHHHHHHHcCCCC
Confidence            3456899999999999999999765

>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=84.96  E-value=0.7  Score=32.81  Aligned_cols=23  Identities=13%  Similarity=0.309  Sum_probs=20.8

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 032366           95 KLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        95 glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .+||.+||..+|+++.+|++..+
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            47999999999999999998764

>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=84.96  E-value=1.1  Score=29.87  Aligned_cols=37  Identities=14%  Similarity=0.169  Sum_probs=28.1

Q ss_pred             hHHHHHHHHHHHHhC--CCCHHHHHHHhCCCHHHHHHHH
Q 032366           80 PSELKKAIVQARNDK--KLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        80 ~~~~g~~Lk~~R~~~--glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ...-...|..+....  ++|+.+||+.+|+++++++++.
T Consensus        30 t~~~~~vL~~l~~~~~~~~t~~ela~~l~~~~~tvs~~l   68 (139)
T 3eco_A           30 TNEQGHTLGYLYAHQQDGLTQNDIAKALQRTGPTVSNLL   68 (139)
T ss_dssp             CHHHHHHHHHHHHSTTTCEEHHHHHHHHTCCHHHHHHHH
T ss_pred             CHHHHHHHHHHHhcCCCCcCHHHHHHHhCCCcccHHHHH
Confidence            333445566665554  8999999999999999999874

>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=84.93  E-value=0.96  Score=30.46  Aligned_cols=30  Identities=10%  Similarity=0.062  Sum_probs=24.2

Q ss_pred             HHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           87 IVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      |..+.....+|..+||+.+|+|+++|++..
T Consensus        48 L~~L~~~~~~s~~eLa~~l~is~stvs~~L   77 (122)
T 1u2w_A           48 TYALCQDEELCVCDIANILGVTIANASHHL   77 (122)
T ss_dssp             HHHHHHSSCEEHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHCCCcCHHHHHHHHCcCHHHHHHHH
Confidence            344444567999999999999999999865

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

Probab=84.91  E-value=1.6  Score=28.81  Aligned_cols=29  Identities=24%  Similarity=0.299  Sum_probs=23.1

Q ss_pred             HHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           87 IVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      |..+.. ..+|+.++|+.+|+++++|++..
T Consensus        38 l~~L~~-~~~s~~ela~~l~is~stvsr~l   66 (119)
T 2lkp_A           38 LTQLRN-GPLPVTDLAEAIGMEQSAVSHQL   66 (119)
T ss_dssp             HHHHHH-CCCCHHHHHHHHSSCHHHHHHHH
T ss_pred             HHHHHH-CCCCHHHHHHHHCcCHHHHHHHH
Confidence            334443 57999999999999999998854

>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=84.87  E-value=2  Score=29.68  Aligned_cols=32  Identities=22%  Similarity=0.224  Sum_probs=25.8

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ..|..+.....+|..+||+.+|+|++++++..
T Consensus        11 ~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l   42 (151)
T 2cyy_A           11 KIIKILQNDGKAPLREISKITGLAESTIHERI   42 (151)
T ss_dssp             HHHHHHHHCTTCCHHHHHHHHCSCHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHH
Confidence            44555666678999999999999999988753

>1r8d_A Transcription activator MTAN; protein-DNA complex, transcription/DNA complex; 2.70A {Bacillus subtilis} SCOP: a.6.1.3 PDB: 1jbg_A

Probab=84.81  E-value=3  Score=27.49  Aligned_cols=65  Identities=11%  Similarity=0.177  Sum_probs=36.6

Q ss_pred             HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhCCC
Q 032366           33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEK  108 (142)
Q Consensus        33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis  108 (142)
                      +.|+..|+++.|++.|+. |-..|.....+ .-..++.++         ...-..|+.+ ...|+|..++...+..+
T Consensus         7 e~A~~~gvs~~tLR~ye~~Gll~p~~~~~~-g~R~Y~~~d---------l~~l~~I~~l-~~~G~~l~~I~~~l~~~   72 (109)
T 1r8d_A            7 QVAEISGVSIRTLHHYDNIELLNPSALTDA-GYRLYSDAD---------LERLQQILFF-KEIGFRLDEIKEMLDHP   72 (109)
T ss_dssp             HHHHHHSCCHHHHHHHHHTTSSCCSEECTT-CCEEBCHHH---------HHHHHHHHHH-HHTTCCHHHHHHHHHCT
T ss_pred             HHHHHHCcCHHHHHHHHHCCCCCCCeECCC-CCeeeCHHH---------HHHHHHHHHH-HHCCCCHHHHHHHHhCC
Confidence            478999999999999976 44442110000 001111111         1122334544 35699999998887543

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

Probab=84.70  E-value=1.6  Score=33.28  Aligned_cols=35  Identities=14%  Similarity=0.139  Sum_probs=28.3

Q ss_pred             HHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           82 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        82 ~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      .-...|..+....++|+.+||+.+|++++|+++..
T Consensus       153 ~~~~IL~~L~~~~~~s~~eLA~~lglsksTv~r~L  187 (244)
T 2wte_A          153 EEMKLLNVLYETKGTGITELAKMLDKSEKTLINKI  187 (244)
T ss_dssp             HHHHHHHHHHHHTCBCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHH
Confidence            34455566666779999999999999999999874

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

Probab=84.69  E-value=1.3  Score=30.18  Aligned_cols=37  Identities=3%  Similarity=0.039  Sum_probs=29.3

Q ss_pred             hHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           80 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ...-...|..+...-++|+.+||+.+++++++|+++.
T Consensus        40 t~~q~~iL~~l~~~~~~~~~eLa~~l~~~~~~vs~~l   76 (149)
T 4hbl_A           40 TYSQYLVMLTLWEENPQTLNSIGRHLDLSSNTLTPML   76 (149)
T ss_dssp             CHHHHHHHHHHHHSSSEEHHHHHHHHTCCHHHHHHHH
T ss_pred             CHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHH
Confidence            3334455666666789999999999999999998864

>2zcw_A TTHA1359, transcriptional regulator, FNR/CRP family; stationary phase, DNA-binding, transcription regulation; 1.50A {Thermus thermophilus}

Probab=84.67  E-value=0.74  Score=32.76  Aligned_cols=22  Identities=14%  Similarity=0.205  Sum_probs=20.0

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +||.+||..+|+|+.+|++..+
T Consensus       147 ~t~~~lA~~lg~sr~tvsR~l~  168 (202)
T 2zcw_A          147 ATHDELAAAVGSVRETVTKVIG  168 (202)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCHHHHHHHhCCCHHHHHHHHH
Confidence            8999999999999999998753

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

Probab=84.57  E-value=2  Score=30.73  Aligned_cols=32  Identities=19%  Similarity=0.240  Sum_probs=26.0

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ..|..+.....+|..+||+.+|+|++++.+..
T Consensus        21 ~IL~~L~~~~~~s~~eLA~~lglS~~tv~~~l   52 (171)
T 2ia0_A           21 NILRLLKKDARLTISELSEQLKKPESTIHFRI   52 (171)
T ss_dssp             HHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHH
Confidence            34566666678999999999999999988753

>2vz4_A Tipal, HTH-type transcriptional activator TIPA; transcription, resistance, antibiotic; 2.90A {Streptomyces lividans}

Probab=84.56  E-value=3.7  Score=27.04  Aligned_cols=65  Identities=17%  Similarity=0.261  Sum_probs=37.9

Q ss_pred             HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhCCC
Q 032366           33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEK  108 (142)
Q Consensus        33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis  108 (142)
                      +.|+..|+++.|++.|+. |-..|.....+ .-..++.+         ....-..|+.+| ..|+|..++...+..+
T Consensus         6 e~A~~~gvs~~tLR~ye~~Gll~p~~r~~~-g~R~Y~~~---------dl~~l~~I~~lr-~~G~sl~~I~~~l~~~   71 (108)
T 2vz4_A            6 QVAGFAGVTVRTLHHYDDIGLLVPSERSHA-GHRRYSDA---------DLDRLQQILFYR-ELGFPLDEVAALLDDP   71 (108)
T ss_dssp             HHHHHHTCCHHHHHHHHHHTSSCCSEECSS-CCEEBCHH---------HHHHHHHHHHHH-HTTCCHHHHHHHHTC-
T ss_pred             HHHHHHCcCHHHHHHHHHCCCCCCCccCCC-CCeecCHH---------HHHHHHHHHHHH-HCCCCHHHHHHHHhCC
Confidence            578999999999999976 44443210000 01111111         111234455554 5799999999988754

>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=84.53  E-value=0.54  Score=28.91  Aligned_cols=25  Identities=8%  Similarity=0.061  Sum_probs=21.7

Q ss_pred             HHHHHHHHcCCChhHHHhhhcCCCC
Q 032366           30 KVVNAARRAGADIETVRKSHAGTNK   54 (142)
Q Consensus        30 ~~~~~a~r~G~~v~t~kk~~~g~~~   54 (142)
                      ++-..|.+.|++.+|+.+||.|...
T Consensus        26 sq~~lA~~~gis~~~i~~~e~g~~~   50 (82)
T 3s8q_A           26 TQEDLAYKSNLDRTYISGIERNSRN   50 (82)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHTTCCC
T ss_pred             CHHHHHHHhCcCHHHHHHHHCCCCC
Confidence            4567899999999999999999865

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

Probab=84.42  E-value=1.9  Score=28.86  Aligned_cols=36  Identities=17%  Similarity=0.243  Sum_probs=26.4

Q ss_pred             hHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           80 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ...-...|..+... ++|+.+||+.+|+++++|++..
T Consensus        37 t~~~~~iL~~l~~~-~~t~~eLa~~l~~s~~tvs~~l   72 (146)
T 3tgn_A           37 TNTQEHILMLLSEE-SLTNSELARRLNVSQAAVTKAI   72 (146)
T ss_dssp             CHHHHHHHHHHTTC-CCCHHHHHHHHTCCHHHHHHHH
T ss_pred             CHHHHHHHHHHHhC-CCCHHHHHHHHCCCHHHHHHHH
Confidence            33334445555444 4999999999999999998765

>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=84.33  E-value=1.1  Score=29.93  Aligned_cols=36  Identities=14%  Similarity=0.057  Sum_probs=26.4

Q ss_pred             HHHHHHHHHHH-HhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           81 SELKKAIVQAR-NDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        81 ~~~g~~Lk~~R-~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ......|.-+. ...++|+.+||+.+|++++++++..
T Consensus        26 ~~~~~il~~L~~~~~~~t~~ela~~l~~~~stvs~~l   62 (152)
T 1ku9_A           26 KSVGAVYAILYLSDKPLTISDIMEELKISKGNVSMSL   62 (152)
T ss_dssp             HHHHHHHHHHHHCSSCEEHHHHHHHHTCCHHHHHHHH
T ss_pred             hhHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHH
Confidence            33444444443 3468999999999999999988864

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

Probab=84.28  E-value=2.1  Score=28.75  Aligned_cols=24  Identities=13%  Similarity=0.129  Sum_probs=21.0

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           93 DKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        93 ~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ..++|+.+||+.+|+++++|++..
T Consensus        29 ~~~~s~~ela~~l~is~~tv~~~l   52 (139)
T 2x4h_A           29 GEGAKINRIAKDLKIAPSSVFEEV   52 (139)
T ss_dssp             TSCBCHHHHHHHHTCCHHHHHHHH
T ss_pred             CCCcCHHHHHHHhCCChHHHHHHH
Confidence            457899999999999999998754

>1y7y_A C.AHDI; helix-turn-helix, DNA-binding protein, transcriptional regulator, transcription regulator; 1.69A {Aeromonas hydrophila} SCOP: a.35.1.3

Probab=84.21  E-value=0.6  Score=27.80  Aligned_cols=25  Identities=20%  Similarity=0.108  Sum_probs=21.6

Q ss_pred             HHHHHHHHcCCChhHHHhhhcCCCC
Q 032366           30 KVVNAARRAGADIETVRKSHAGTNK   54 (142)
Q Consensus        30 ~~~~~a~r~G~~v~t~kk~~~g~~~   54 (142)
                      ++-..|++.|++.+++.+|+.|...
T Consensus        28 s~~~lA~~~gis~~~i~~~e~g~~~   52 (74)
T 1y7y_A           28 SQETLAFLSGLDRSYVGGVERGQRN   52 (74)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHTTCSC
T ss_pred             CHHHHHHHHCcCHHHHHHHHCCCCC
Confidence            4566899999999999999999865

>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=84.19  E-value=1.5  Score=31.85  Aligned_cols=35  Identities=9%  Similarity=-0.048  Sum_probs=26.9

Q ss_pred             HHHHHHHHHHHhCC--CCHHHHHHHhCCCHHHHHHHH
Q 032366           82 ELKKAIVQARNDKK--LTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        82 ~~g~~Lk~~R~~~g--lTQ~eLA~~lgis~stIs~~E  116 (142)
                      .+-+.|.+...+.|  .|+.|||+.+|++.+++.++.
T Consensus         9 ~il~~I~~~~~~~g~~~s~~eia~~lgl~~~tv~~~l   45 (196)
T 3k2z_A            9 KVLLFIEEFIEKNGYPPSVREIARRFRITPRGALLHL   45 (196)
T ss_dssp             HHHHHHHHHHHHHSSCCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHcCCCcHHHHHHH
Confidence            45566666655555  799999999999998887754

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

Probab=84.15  E-value=1.5  Score=29.19  Aligned_cols=34  Identities=15%  Similarity=0.008  Sum_probs=27.2

Q ss_pred             HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      -...|..+...-++|+.+||+.+|++++++++..
T Consensus        38 ~~~iL~~l~~~~~~t~~ela~~l~~s~~~vs~~l   71 (142)
T 2fbi_A           38 QWRVIRILRQQGEMESYQLANQACILRPSMTGVL   71 (142)
T ss_dssp             HHHHHHHHHHHCSEEHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHCCCHhHHHHHH
Confidence            3445566666678999999999999999988764

>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=84.13  E-value=1.3  Score=31.74  Aligned_cols=23  Identities=13%  Similarity=0.193  Sum_probs=20.8

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHH
Q 032366           94 KKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        94 ~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ..+||.+||..+|+|+.+|+++.
T Consensus       166 ~~~t~~~lA~~lg~sr~tvsR~l  188 (220)
T 2fmy_A          166 LGLNTEEIALMLGTTRQTVSVLL  188 (220)
T ss_dssp             CSSCHHHHHHHHTSCHHHHHHHH
T ss_pred             ccCCHHHHHHHhCCcHHHHHHHH
Confidence            46899999999999999999875

>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=84.10  E-value=2  Score=29.29  Aligned_cols=34  Identities=6%  Similarity=-0.031  Sum_probs=27.1

Q ss_pred             HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      -...|..+...-++|+.+||+.++++++++++..
T Consensus        46 ~~~iL~~l~~~~~~t~~ela~~l~is~~tvs~~l   79 (154)
T 2eth_A           46 ELYAFLYVALFGPKKMKEIAEFLSTTKSNVTNVV   79 (154)
T ss_dssp             HHHHHHHHHHHCCBCHHHHHHHTTSCHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHH
Confidence            3445566666668999999999999999998864

>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=84.00  E-value=2.1  Score=28.32  Aligned_cols=34  Identities=12%  Similarity=0.120  Sum_probs=27.1

Q ss_pred             HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      -...|..+...-++|+.+||+.+|+++++++++.
T Consensus        36 ~~~iL~~l~~~~~~~~~~la~~l~~~~~tvs~~l   69 (138)
T 1jgs_A           36 QFKVLCSIRCAACITPVELKKVLSVDLGALTRML   69 (138)
T ss_dssp             HHHHHHHHHHHSSBCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHCCChHHHHHHH
Confidence            3444556666678999999999999999998764

>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=83.97  E-value=1.2  Score=27.88  Aligned_cols=25  Identities=20%  Similarity=0.187  Sum_probs=21.6

Q ss_pred             HHHHHHHHcCCChhHHHhhhcCCCC
Q 032366           30 KVVNAARRAGADIETVRKSHAGTNK   54 (142)
Q Consensus        30 ~~~~~a~r~G~~v~t~kk~~~g~~~   54 (142)
                      ++-..|.+.|++..|+.+|+.|...
T Consensus        32 sq~~lA~~~gis~~~is~~e~g~~~   56 (92)
T 1lmb_3           32 SQESVADKMGMGQSGVGALFNGINA   56 (92)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHTTSSC
T ss_pred             CHHHHHHHHCcCHHHHHHHHcCCCC
Confidence            4566889999999999999999765

>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=83.85  E-value=0.82  Score=32.92  Aligned_cols=22  Identities=14%  Similarity=0.250  Sum_probs=20.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +||.+||..+|+++.+|++..+
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            7999999999999999998764

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

Probab=83.81  E-value=1.3  Score=29.68  Aligned_cols=32  Identities=19%  Similarity=0.225  Sum_probs=25.7

Q ss_pred             HHHHHH-HHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           85 KAIVQA-RNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        85 ~~Lk~~-R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ..|..+ ...-++|+.+||+.+|+++++++++.
T Consensus        41 ~iL~~l~~~~~~~t~~~la~~l~~s~~~vs~~l   73 (146)
T 2fbh_A           41 LVLLHLARHRDSPTQRELAQSVGVEGPTLARLL   73 (146)
T ss_dssp             HHHHHHHHCSSCCBHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHH
Confidence            345555 45678999999999999999998764

>3dv8_A Transcriptional regulator, CRP/FNR family; cyclic nucleotide-binding domain, structural genomics, joint for structural genomics; 2.55A {Eubacterium rectale atcc 33656}

Probab=83.70  E-value=0.85  Score=32.60  Aligned_cols=23  Identities=22%  Similarity=0.339  Sum_probs=21.0

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 032366           95 KLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        95 glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .+||.+||..+|+++.+|+++-+
T Consensus       169 ~~t~~~lA~~lg~sr~tvsR~l~  191 (220)
T 3dv8_A          169 KITHETIANHLGSHREVITRMLR  191 (220)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             cCCHHHHHHHhCCCHHHHHHHHH
Confidence            68999999999999999998763

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

Probab=83.69  E-value=1.4  Score=28.60  Aligned_cols=29  Identities=17%  Similarity=0.138  Sum_probs=23.7

Q ss_pred             HHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           87 IVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      |..+ ....+|..+||+.+|+|+++|++..
T Consensus        27 L~~L-~~~~~~~~ela~~l~is~~tv~~~l   55 (114)
T 2oqg_A           27 LTEL-GRADQSASSLATRLPVSRQAIAKHL   55 (114)
T ss_dssp             HHHH-HHSCBCHHHHHHHSSSCHHHHHHHH
T ss_pred             HHHH-HcCCCCHHHHHHHHCcCHHHHHHHH
Confidence            3344 5567999999999999999998864

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

Probab=83.67  E-value=1.7  Score=29.53  Aligned_cols=34  Identities=3%  Similarity=0.005  Sum_probs=27.1

Q ss_pred             HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      -...|..+...-++|+.+||+.+++++++|+++.
T Consensus        49 ~~~iL~~l~~~~~~t~~ela~~l~~s~~tvs~~l   82 (153)
T 2pex_A           49 QYLVMLVLWETDERSVSEIGERLYLDSATLTPLL   82 (153)
T ss_dssp             HHHHHHHHHHSCSEEHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHhCCCcCHHHHHHHhCCCcccHHHHH
Confidence            3445556666678999999999999999998764

>2b5a_A C.BCLI; helix-turn-helix motif, gene regulation; 1.54A {Bacillus caldolyticus} SCOP: a.35.1.3

Probab=83.62  E-value=0.64  Score=27.95  Aligned_cols=25  Identities=16%  Similarity=0.145  Sum_probs=21.6

Q ss_pred             HHHHHHHHcCCChhHHHhhhcCCCC
Q 032366           30 KVVNAARRAGADIETVRKSHAGTNK   54 (142)
Q Consensus        30 ~~~~~a~r~G~~v~t~kk~~~g~~~   54 (142)
                      ++-..|.+.|++.+|+.+|+.|...
T Consensus        25 sq~~lA~~~gis~~~i~~~e~g~~~   49 (77)
T 2b5a_A           25 SQEELADLAGLHRTYISEVERGDRN   49 (77)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHTTCSC
T ss_pred             CHHHHHHHHCCCHHHHHHHHCCCCC
Confidence            4566899999999999999999765

>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=83.56  E-value=1.7  Score=31.37  Aligned_cols=30  Identities=20%  Similarity=0.191  Sum_probs=23.2

Q ss_pred             HHHHHHh-CCCCHHHHHHHhCCCHHHHHHHH
Q 032366           87 IVQARND-KKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        87 Lk~~R~~-~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      |..++.. ..+|..+||+.+|+|++||.+..
T Consensus        27 l~~L~~~~~~~s~~eLa~~l~vS~~Ti~rdi   57 (187)
T 1j5y_A           27 VRILERSKEPVSGAQLAEELSVSRQVIVQDI   57 (187)
T ss_dssp             HHHHHHCSSCBCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHcCCCcCHHHHHHHHCcCHHHHHHHH
Confidence            3444443 34999999999999999998754

>4dyq_A Gene 1 protein; GP1, octamer, DNA-binding, viral protein; 1.50A {Shigella phage SF6} PDB: 4dyc_A 4dyr_A 3hef_A 4dzj_A 4dzp_A

Probab=83.55  E-value=1  Score=31.39  Aligned_cols=37  Identities=5%  Similarity=0.021  Sum_probs=29.2

Q ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHhCC-CHHHHHHHHcC
Q 032366           81 SELKKAIVQARNDKKLTQSQLAQLINE-KPQVIQEYESG  118 (142)
Q Consensus        81 ~~~g~~Lk~~R~~~glTQ~eLA~~lgi-s~stIs~~E~G  118 (142)
                      .++.+.|-.+. ..|.|..++|+..|| |.+||.+|.+-
T Consensus        15 ~e~~e~I~~~i-~~G~sl~~i~~~~~~ps~~T~~~W~~~   52 (140)
T 4dyq_A           15 PEVADDICSLL-SSGESLLKVCKRPGMPDKSTVFRWLAK   52 (140)
T ss_dssp             TTHHHHHHHHH-HTTCCHHHHHTSTTCCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHH-HCCCcHHHHHhcCCCCCHHHHHHHHHc
Confidence            34555555444 479999999999999 99999999864

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

Probab=83.52  E-value=1.6  Score=29.63  Aligned_cols=33  Identities=6%  Similarity=-0.067  Sum_probs=26.4

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ...|..+...-++|+.+||+.+++++++++++.
T Consensus        44 ~~iL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l   76 (154)
T 2qww_A           44 LAMINVIYSTPGISVADLTKRLIITGSSAAANV   76 (154)
T ss_dssp             HHHHHHHHHSTTEEHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHH
Confidence            344555556678999999999999999988864

>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=83.50  E-value=0.55  Score=28.89  Aligned_cols=25  Identities=20%  Similarity=0.198  Sum_probs=21.6

Q ss_pred             HHHHHHHHcCCChhHHHhhhcCCCC
Q 032366           30 KVVNAARRAGADIETVRKSHAGTNK   54 (142)
Q Consensus        30 ~~~~~a~r~G~~v~t~kk~~~g~~~   54 (142)
                      ++-..|.+.|++..|+.+||.|...
T Consensus        29 tq~elA~~~gis~~~is~~e~g~~~   53 (83)
T 3f6w_A           29 TQKELAARLGRPQSFVSKTENAERR   53 (83)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHTTSSC
T ss_pred             CHHHHHHHHCcCHHHHHHHHCCCCC
Confidence            4557899999999999999999765

>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=83.43  E-value=0.87  Score=32.94  Aligned_cols=24  Identities=4%  Similarity=0.034  Sum_probs=21.2

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           94 KKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        94 ~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ..+||.+||..+|+|+.+|+++.+
T Consensus       174 ~~~t~~~iA~~lg~sr~tvsR~l~  197 (231)
T 3e97_A          174 LPLGTQDIMARTSSSRETVSRVLK  197 (231)
T ss_dssp             ECCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             cCCCHHHHHHHhCCcHHHHHHHHH
Confidence            358999999999999999999753

>1adr_A P22 C2 repressor; transcription regulation; NMR {Enterobacteria phage P22} SCOP: a.35.1.2

Probab=83.39  E-value=0.66  Score=27.76  Aligned_cols=25  Identities=4%  Similarity=0.101  Sum_probs=21.5

Q ss_pred             HHHHHHHHcCCChhHHHhhhcCCCC
Q 032366           30 KVVNAARRAGADIETVRKSHAGTNK   54 (142)
Q Consensus        30 ~~~~~a~r~G~~v~t~kk~~~g~~~   54 (142)
                      ++-..|++.|++.+|+.+|+.|...
T Consensus        20 s~~~lA~~~gis~~~i~~~e~g~~~   44 (76)
T 1adr_A           20 RQAALGKMVGVSNVAISQWERSETE   44 (76)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHTTSSC
T ss_pred             CHHHHHHHHCcCHHHHHHHHcCCCC
Confidence            3456899999999999999999765

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

Probab=83.38  E-value=1.3  Score=30.52  Aligned_cols=31  Identities=6%  Similarity=0.109  Sum_probs=25.5

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           86 AIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        86 ~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      .|..+...-++|+.+||+.+++++++++++.
T Consensus        55 vL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l   85 (159)
T 3s2w_A           55 FLMRLYREDGINQESLSDYLKIDKGTTARAI   85 (159)
T ss_dssp             HHHHHHHSCSEEHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHCCCCCHHHHHHHHCCCHHHHHHHH
Confidence            3555555678999999999999999999864

>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=83.36  E-value=1.2  Score=30.31  Aligned_cols=33  Identities=9%  Similarity=0.036  Sum_probs=27.2

Q ss_pred             HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      -...|..+ ...++|+.+||+.+|++++++++..
T Consensus        40 q~~iL~~l-~~~~~t~~eLa~~l~~~~~~vs~~l   72 (151)
T 3kp7_A           40 QSHVLNML-SIEALTVGQITEKQGVNKAAVSRRV   72 (151)
T ss_dssp             HHHHHHHH-HHSCBCHHHHHHHHCSCSSHHHHHH
T ss_pred             HHHHHHHH-HcCCcCHHHHHHHHCCCHHHHHHHH
Confidence            34456666 7789999999999999999998764

>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=83.35  E-value=1.4  Score=30.45  Aligned_cols=37  Identities=19%  Similarity=0.106  Sum_probs=28.5

Q ss_pred             hHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           80 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ...-...|..+...-++|+.+||+.+|+++++|+++.
T Consensus        45 t~~q~~iL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l   81 (162)
T 3k0l_A           45 SLPQFTALSVLAAKPNLSNAKLAERSFIKPQSANKIL   81 (162)
T ss_dssp             CHHHHHHHHHHHHCTTCCHHHHHHHHTSCGGGHHHHH
T ss_pred             CHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHH
Confidence            3334455666666678999999999999999988764

>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=83.24  E-value=0.66  Score=28.77  Aligned_cols=24  Identities=38%  Similarity=0.487  Sum_probs=21.1

Q ss_pred             HHHHHHHHcCCChhHHHhhhcCCC
Q 032366           30 KVVNAARRAGADIETVRKSHAGTN   53 (142)
Q Consensus        30 ~~~~~a~r~G~~v~t~kk~~~g~~   53 (142)
                      ++-..|.+.|++.+|+.+||.|..
T Consensus        29 sq~~lA~~~gis~~~is~~E~g~~   52 (86)
T 2ofy_A           29 SMVTVAFDAGISVETLRKIETGRI   52 (86)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHTTCC
T ss_pred             CHHHHHHHhCCCHHHHHHHHcCCC
Confidence            345789999999999999999976

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

Probab=83.14  E-value=1.4  Score=28.45  Aligned_cols=29  Identities=14%  Similarity=0.205  Sum_probs=23.9

Q ss_pred             HHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           89 QARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        89 ~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .+.....++..+||+.+|+|++++++..+
T Consensus        35 ~l~~~~~~~~~ela~~l~is~stvs~hL~   63 (99)
T 2zkz_A           35 ELYKHKALNVTQIIQILKLPQSTVSQHLC   63 (99)
T ss_dssp             HHHHHSCEEHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHCCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            44455679999999999999999998653

>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=83.10  E-value=0.9  Score=32.77  Aligned_cols=22  Identities=27%  Similarity=0.424  Sum_probs=20.1

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHH
Q 032366           95 KLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        95 glTQ~eLA~~lgis~stIs~~E  116 (142)
                      .+||.+||..+|+|+.+|++..
T Consensus       177 ~~t~~~lA~~lg~sr~tvsR~l  198 (227)
T 3d0s_A          177 DLTQEEIAQLVGASRETVNKAL  198 (227)
T ss_dssp             CCCHHHHHHHHTSCHHHHHHHH
T ss_pred             CCCHHHHHHHhCCcHHHHHHHH
Confidence            5899999999999999999865

>4ev0_A Transcription regulator, CRP family; CAMP binding, winged helix-turn-helix motif, DNA binding, transcription activator; HET: CMP; 2.40A {Thermus thermophilus}

Probab=83.08  E-value=0.91  Score=32.33  Aligned_cols=40  Identities=15%  Similarity=0.307  Sum_probs=29.8

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc-----CC--------CCCCHHHHHHHHHHh
Q 032366           95 KLTQSQLAQLINEKPQVIQEYES-----GK--------AIPNQQILTKLERAL  134 (142)
Q Consensus        95 glTQ~eLA~~lgis~stIs~~E~-----G~--------~~p~~~~l~kLa~~L  134 (142)
                      .+||.+||..+|+++.+|++.-+     |-        ..++.+.|.++|..|
T Consensus       163 ~~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~~~~~~i~i~d~~~L~~~a~~l  215 (216)
T 4ev0_A          163 QIRHHELAALAGTSRETVSRVLHALAEEGVVRLGPGTVEVREAALLEEIAFGL  215 (216)
T ss_dssp             ECCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEETTEEEESCHHHHHHHHTTC
T ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEecCCEEEEeCHHHHHHHhhcc
Confidence            47999999999999999998763     21        235667777776543

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

Probab=83.06  E-value=1.8  Score=27.33  Aligned_cols=23  Identities=9%  Similarity=0.066  Sum_probs=19.7

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHH
Q 032366           94 KKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        94 ~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      .-.|..|||+.+|+|.+||.+..
T Consensus        23 ~~psv~EIa~~lgvS~~TVrr~L   45 (77)
T 2jt1_A           23 APVKTRDIADAAGLSIYQVRLYL   45 (77)
T ss_dssp             SCEEHHHHHHHHTCCHHHHHHHH
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHH
Confidence            45689999999999999987764

>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=83.00  E-value=1.7  Score=29.31  Aligned_cols=34  Identities=18%  Similarity=0.076  Sum_probs=26.8

Q ss_pred             HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      -...|..+...-++|+.+||+.+|++++++++..
T Consensus        42 ~~~iL~~l~~~~~~t~~ela~~l~~~~~~vs~~l   75 (152)
T 3bj6_A           42 QRAILEGLSLTPGATAPQLGAALQMKRQYISRIL   75 (152)
T ss_dssp             HHHHHHHHHHSTTEEHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHH
Confidence            3444555555668999999999999999988764

>2jrt_A Uncharacterized protein; solution, structure, NESG, PSI, target RHR5, structural genomics, protein structure initiative; NMR {Rhodobacter sphaeroides}

Probab=82.86  E-value=3.1  Score=27.33  Aligned_cols=40  Identities=18%  Similarity=0.116  Sum_probs=32.3

Q ss_pred             cchHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           78 RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        78 ~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .....+-..|-.....-++|..|+|++.+||++.|..|..
T Consensus        32 rWs~~~Kl~VV~~~~~g~~s~~e~arry~Is~s~i~~W~r   71 (95)
T 2jrt_A           32 RWVASRKAAVVKAVIHGLITEREALDRYSLSEEEFALWRS   71 (95)
T ss_dssp             CCCHHHHHHHHHHHHTTSSCHHHHHHHTTCCHHHHHHHHH
T ss_pred             ccCHHHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHH
Confidence            3445565666666677789999999999999999999985

>3hot_A Transposable element mariner, complete CDS; protein-DNA complex, synaptic complex, transposase, inverted DNA, DNA binding protein-DNA complex; HET: 5IU; 3.25A {Drosophila mauritiana} PDB: 3hos_A*

Probab=82.77  E-value=8.9  Score=29.49  Aligned_cols=27  Identities=26%  Similarity=0.276  Sum_probs=24.1

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           91 RNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        91 R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .....+|..+||+.++||.++|.++..
T Consensus        82 ~~~~~~t~~~ia~~l~vs~~tV~r~L~  108 (345)
T 3hot_A           82 DEDDAQTQKQLAEQLEVSQQAVSNRLR  108 (345)
T ss_dssp             HHCSCCCHHHHHHHTTSCHHHHHHHHH
T ss_pred             HhCccchHHHHHHHHCCCHHHHHHHHH
Confidence            456689999999999999999999985

>2k9q_A Uncharacterized protein; all helix, helix-turn-helix, plasmid, structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides thetaiotaomicron}

Probab=82.75  E-value=0.61  Score=28.40  Aligned_cols=25  Identities=8%  Similarity=0.093  Sum_probs=21.4

Q ss_pred             HHHHHHHHcCCChhHHHhhhcCCCC
Q 032366           30 KVVNAARRAGADIETVRKSHAGTNK   54 (142)
Q Consensus        30 ~~~~~a~r~G~~v~t~kk~~~g~~~   54 (142)
                      ++-..|.+.|++.+|+.+|+.|...
T Consensus        17 sq~~lA~~~gis~~~i~~~e~g~~~   41 (77)
T 2k9q_A           17 TAKSVAEEMGISRQQLCNIEQSETA   41 (77)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHTCCSC
T ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCC
Confidence            3456899999999999999999764

>3b02_A Transcriptional regulator, CRP family; structural genomics, riken structural genomics/proteomics in RSGI; 1.92A {Thermus thermophilus} PDB: 2zdb_A

Probab=82.72  E-value=0.73  Score=32.66  Aligned_cols=23  Identities=4%  Similarity=0.148  Sum_probs=20.3

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 032366           95 KLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        95 glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .+||.+||..+|+|+.+|++..+
T Consensus       139 ~~t~~~lA~~lg~sr~tvsR~l~  161 (195)
T 3b02_A          139 TVSHEEIADATASIRESVSKVLA  161 (195)
T ss_dssp             ECCHHHHHHTTTSCHHHHHHHHH
T ss_pred             cCCHHHHHHHhCCCHHHHHHHHH
Confidence            38999999999999999998753

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

Probab=82.54  E-value=3.4  Score=26.65  Aligned_cols=25  Identities=12%  Similarity=0.135  Sum_probs=22.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcC
Q 032366           94 KKLTQSQLAQLINEKPQVIQEYESG  118 (142)
Q Consensus        94 ~glTQ~eLA~~lgis~stIs~~E~G  118 (142)
                      ..+|..+||+.+|+|++++++.-+.
T Consensus        19 ~~~~~~~lA~~~~~S~~~l~r~fk~   43 (107)
T 2k9s_A           19 SNFDIASVAQHVCLSPSRLSHLFRQ   43 (107)
T ss_dssp             SSCCHHHHHHHTTSCHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHH
Confidence            4699999999999999999999864

>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=82.46  E-value=0.61  Score=31.65  Aligned_cols=26  Identities=12%  Similarity=0.234  Sum_probs=22.4

Q ss_pred             HHHHHHHHcCCChhHHHhhhcCCCCC
Q 032366           30 KVVNAARRAGADIETVRKSHAGTNKA   55 (142)
Q Consensus        30 ~~~~~a~r~G~~v~t~kk~~~g~~~~   55 (142)
                      ++-..|.+.|++..|+.+||.|...|
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            45678999999999999999998763

>2ewt_A BLDD, putative DNA-binding protein; the DNA-binding domain of BLDD; 1.81A {Streptomyces coelicolor}

Probab=82.41  E-value=0.65  Score=27.53  Aligned_cols=25  Identities=8%  Similarity=0.065  Sum_probs=21.4

Q ss_pred             HHHHHHHHcC--CChhHHHhhhcCCCC
Q 032366           30 KVVNAARRAG--ADIETVRKSHAGTNK   54 (142)
Q Consensus        30 ~~~~~a~r~G--~~v~t~kk~~~g~~~   54 (142)
                      ++-..|.+.|  ++.+++.+||.|...
T Consensus        23 sq~~lA~~~g~~is~~~i~~~e~g~~~   49 (71)
T 2ewt_A           23 SLHGVEEKSQGRWKAVVVGSYERGDRA   49 (71)
T ss_dssp             CHHHHHHHTTTSSCHHHHHHHHHTCSC
T ss_pred             CHHHHHHHHCCcCCHHHHHHHHCCCCC
Confidence            4456889999  999999999999765

>2obp_A Putative DNA-binding protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE; 1.70A {Ralstonia eutropha} SCOP: a.4.5.71

Probab=82.41  E-value=3.4  Score=27.27  Aligned_cols=38  Identities=8%  Similarity=0.142  Sum_probs=28.4

Q ss_pred             chHHHHHHHHHHHHh------CCCCHHHHHHHhCCCHHHHHHHH
Q 032366           79 VPSELKKAIVQARND------KKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        79 ~~~~~g~~Lk~~R~~------~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      +.......|..+...      ..+++.+||+.++++++++++..
T Consensus        14 l~~~q~~vL~~L~~~~~~~~g~~~s~~eLa~~l~l~~stLsR~l   57 (96)
T 2obp_A           14 IDPAIVEVLLVLREAGIENGATPWSLPKIAKRAQLPMSVLRRVL   57 (96)
T ss_dssp             CCHHHHHHHHHHHHHTSSTTCCCCBHHHHHHHHTCCHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHHhhCCCCCcCHHHHHHHhCCchhhHHHHH
Confidence            344455555655554      56999999999999999998764

>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=82.37  E-value=2  Score=34.84  Aligned_cols=33  Identities=9%  Similarity=0.118  Sum_probs=28.9

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ...|+.++....+|+.|||+.+|+|++||+++-
T Consensus        42 ~~il~~l~~~~~~sr~ela~~~gls~~tv~~~v   74 (429)
T 1z05_A           42 GRVYKLIDQKGPISRIDLSKESELAPASITKIT   74 (429)
T ss_dssp             HHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHH
Confidence            445777888889999999999999999999874

>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=82.33  E-value=1.4  Score=29.49  Aligned_cols=32  Identities=16%  Similarity=0.181  Sum_probs=25.5

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ..|..+...-++|+.+||+.+++++++|++..
T Consensus        33 ~iL~~l~~~~~~t~~~la~~l~~s~~~vs~~l   64 (144)
T 1lj9_A           33 LYLVRVCENPGIIQEKIAELIKVDRTTAARAI   64 (144)
T ss_dssp             HHHHHHHHSTTEEHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHCcCcCHHHHHHHHCCCHhHHHHHH
Confidence            33555555568999999999999999998864

>2kpj_A SOS-response transcriptional repressor, LEXA; NESG, GFT, structural genomics, PSI-2, protein structure initiative; NMR {Eubacterium rectale atcc 33656}

Probab=82.25  E-value=0.65  Score=29.54  Aligned_cols=25  Identities=16%  Similarity=0.169  Sum_probs=21.7

Q ss_pred             HHHHHHHHcCCChhHHHhhhcCCCC
Q 032366           30 KVVNAARRAGADIETVRKSHAGTNK   54 (142)
Q Consensus        30 ~~~~~a~r~G~~v~t~kk~~~g~~~   54 (142)
                      ++-..|++.|++.+|+.+|+.|...
T Consensus        24 sq~~lA~~~gis~~~is~~e~G~~~   48 (94)
T 2kpj_A           24 TQLEIAKSIGVSPQTFNTWCKGIAI   48 (94)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHTTSCC
T ss_pred             CHHHHHHHHCcCHHHHHHHHhCCCC
Confidence            4566899999999999999999765

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

Probab=82.25  E-value=1.9  Score=29.59  Aligned_cols=34  Identities=9%  Similarity=0.029  Sum_probs=26.9

Q ss_pred             HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      -...|..+...-++|+.+||+.+|+++++|+++.
T Consensus        54 ~~~iL~~l~~~~~~t~~ela~~l~is~~tvs~~l   87 (162)
T 3cjn_A           54 KMRALAILSAKDGLPIGTLGIFAVVEQSTLSRAL   87 (162)
T ss_dssp             HHHHHHHHHHSCSEEHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHCCChhHHHHHH
Confidence            3444555666678999999999999999998864

>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=82.25  E-value=2  Score=28.74  Aligned_cols=33  Identities=15%  Similarity=-0.067  Sum_probs=26.0

Q ss_pred             HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      -...|..+. ..++|+.+||+.+|+++++|++..
T Consensus        39 ~~~iL~~l~-~~~~~~~ela~~l~~s~~tvs~~l   71 (146)
T 2gxg_A           39 DFLVLRATS-DGPKTMAYLANRYFVTQSAITASV   71 (146)
T ss_dssp             HHHHHHHHT-TSCBCHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHh-cCCcCHHHHHHHhCCCchhHHHHH
Confidence            334455555 778999999999999999988764

>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=82.23  E-value=1.7  Score=34.83  Aligned_cols=33  Identities=12%  Similarity=0.087  Sum_probs=28.6

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ...|+.+|....+|..|||+.+|+|++||+++-
T Consensus        19 ~~il~~l~~~~~~sr~~la~~~~ls~~tv~~~v   51 (406)
T 1z6r_A           19 GAVYRLIDQLGPVSRIDLSRLAQLAPASITKIV   51 (406)
T ss_dssp             HHHHHHHHSSCSCCHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHH
Confidence            345677888888999999999999999999864

>1zyb_A Transcription regulator, CRP family; NP_813211.1, structural genomics, joint center for structura genomics, JCSG; 2.15A {Bacteroides thetaiotaomicron} SCOP: a.4.5.4 b.82.3.2

Probab=82.00  E-value=1  Score=32.81  Aligned_cols=23  Identities=17%  Similarity=0.242  Sum_probs=20.6

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 032366           95 KLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        95 glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .+||.+||..+|+++.+|+++.+
T Consensus       186 ~~t~~~lA~~lG~sr~tvsR~l~  208 (232)
T 1zyb_A          186 KVKMDDLARCLDDTRLNISKTLN  208 (232)
T ss_dssp             ECCHHHHHHHHTSCHHHHHHHHH
T ss_pred             cCCHHHHHHHhCCChhHHHHHHH
Confidence            38999999999999999998754

>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=82.00  E-value=1.6  Score=29.55  Aligned_cols=33  Identities=15%  Similarity=0.238  Sum_probs=26.3

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ...|..+...-++|+.+||+.+|+++++|++..
T Consensus        40 ~~iL~~l~~~~~~t~~ela~~l~~s~~tvs~~l   72 (155)
T 1s3j_A           40 LFVLASLKKHGSLKVSEIAERMEVKPSAVTLMA   72 (155)
T ss_dssp             HHHHHHHHHHSEEEHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHH
Confidence            344555555668999999999999999998765

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

Probab=81.91  E-value=2  Score=29.94  Aligned_cols=33  Identities=18%  Similarity=0.264  Sum_probs=26.5

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ...|..+...-++|+.+||+.+|+++++++++.
T Consensus        48 ~~iL~~L~~~~~~t~~eLa~~l~is~~tvs~~l   80 (168)
T 2nyx_A           48 FRTLVILSNHGPINLATLATLLGVQPSATGRMV   80 (168)
T ss_dssp             HHHHHHHHHHCSEEHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHH
Confidence            344555555678999999999999999998864

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

Probab=81.89  E-value=3.2  Score=28.52  Aligned_cols=34  Identities=12%  Similarity=0.099  Sum_probs=25.3

Q ss_pred             HHHHHHHH-HHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           83 LKKAIVQA-RNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        83 ~g~~Lk~~-R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      +...|..+ ....++|+.+||+.+|+|+++|++..
T Consensus        41 ~~~~i~~~l~~~~~~~~~~la~~l~vs~~tvs~~l   75 (155)
T 2h09_A           41 YVELISDLIREVGEARQVDMAARLGVSQPTVAKML   75 (155)
T ss_dssp             HHHHHHHHHHHHSCCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCcCHHHHHHHhCcCHHHHHHHH
Confidence            34444433 34467999999999999999998864

>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=81.86  E-value=1.1  Score=33.04  Aligned_cols=24  Identities=17%  Similarity=0.237  Sum_probs=21.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           94 KKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        94 ~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ..+||.+||..+|+++.+|+++.+
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            468999999999999999998764

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

Probab=81.82  E-value=1.9  Score=30.41  Aligned_cols=32  Identities=16%  Similarity=0.101  Sum_probs=25.7

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      +.|..+.....+|..+||+.+|+|++++.+-.
T Consensus         7 ~il~~L~~~~~~s~~~la~~lg~s~~tv~~rl   38 (162)
T 3i4p_A            7 KILRILQEDSTLAVADLAKKVGLSTTPCWRRI   38 (162)
T ss_dssp             HHHHHHTTCSCSCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHCCCCCHHHHHHHHCcCHHHHHHHH
Confidence            34566666778999999999999999987643

>3kkc_A TETR family transcriptional regulator; APC20805, structural genomics, PSI-2, protein structure initiative; 2.50A {Streptococcus agalactiae 2603V}

Probab=81.80  E-value=1.4  Score=30.01  Aligned_cols=39  Identities=13%  Similarity=0.166  Sum_probs=29.1

Q ss_pred             HHHHHHHHHHhCC---CCHHHHHHHhCCCHHHHHHHHcCCCC
Q 032366           83 LKKAIVQARNDKK---LTQSQLAQLINEKPQVIQEYESGKAI  121 (142)
Q Consensus        83 ~g~~Lk~~R~~~g---lTQ~eLA~~lgis~stIs~~E~G~~~  121 (142)
                      +-+...++-.++|   .|..++|+.+|||++++.++-.++..
T Consensus        17 Il~aa~~l~~~~G~~~~tv~~Ia~~agvs~~t~Y~~F~sK~~   58 (177)
T 3kkc_A           17 IYNAFISLLQENDYSKITVQDVIGLANVGRSTFYSHYESKEV   58 (177)
T ss_dssp             HHHHHHHHTTTSCTTTCCHHHHHHHHCCCHHHHTTTCSSTHH
T ss_pred             HHHHHHHHHHhCChhHhhHHHHHHHhCCcHhhHHHHcCCHHH
Confidence            4444445555555   59999999999999999998776643

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

Probab=81.77  E-value=1.4  Score=35.17  Aligned_cols=29  Identities=10%  Similarity=0.184  Sum_probs=26.2

Q ss_pred             HHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           87 IVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      |+.+| ...+|..|||+.+|+|++||+++-
T Consensus        26 l~~l~-~~~~sr~~la~~~gls~~tv~~~v   54 (380)
T 2hoe_A           26 LKRIM-KSPVSRVELAEELGLTKTTVGEIA   54 (380)
T ss_dssp             HHHHH-HSCBCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHH-cCCcCHHHHHHHHCcCHHHHHHHH
Confidence            67778 888999999999999999999874

>3bs3_A Putative DNA-binding protein; XRE-family, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.65A {Bacteroides fragilis}

Probab=81.47  E-value=0.77  Score=27.50  Aligned_cols=25  Identities=12%  Similarity=0.097  Sum_probs=21.9

Q ss_pred             HHHHHHHHcCCChhHHHhhhcCCCC
Q 032366           30 KVVNAARRAGADIETVRKSHAGTNK   54 (142)
Q Consensus        30 ~~~~~a~r~G~~v~t~kk~~~g~~~   54 (142)
                      ++-..|++.|++..|+.+|+.|...
T Consensus        25 s~~~lA~~~gis~~~i~~~e~g~~~   49 (76)
T 3bs3_A           25 TNRWLAEQMGKSENTISRWCSNKSQ   49 (76)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHTTSSC
T ss_pred             CHHHHHHHHCcCHHHHHHHHcCCCC
Confidence            4567899999999999999999775

>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=81.44  E-value=1  Score=26.27  Aligned_cols=25  Identities=16%  Similarity=0.371  Sum_probs=21.7

Q ss_pred             HHHHHHHHcCCChhHHHhhhcCCCC
Q 032366           30 KVVNAARRAGADIETVRKSHAGTNK   54 (142)
Q Consensus        30 ~~~~~a~r~G~~v~t~kk~~~g~~~   54 (142)
                      ++-..|.+.|++..|+.+|+.|...
T Consensus        16 sq~~lA~~~gis~~~i~~~e~g~~~   40 (69)
T 1r69_A           16 NQAELAQKVGTTQQSIEQLENGKTK   40 (69)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHTTSCS
T ss_pred             CHHHHHHHHCcCHHHHHHHHcCCCC
Confidence            3456899999999999999999775

>3dkw_A DNR protein; CRP-FNR, HTH, beta barrel, dimerization helix, homodimer, transcription regulator; 3.60A {Pseudomonas aeruginosa}

Probab=81.29  E-value=0.85  Score=32.76  Aligned_cols=24  Identities=8%  Similarity=0.163  Sum_probs=21.1

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           94 KKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        94 ~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ..+||.+||..+|+|+.+|+++-+
T Consensus       177 ~~~t~~~lA~~lg~sr~tvsR~l~  200 (227)
T 3dkw_A          177 IPVAKQLVAGHLSIQPETFSRIMH  200 (227)
T ss_dssp             CCSCTHHHHHHTTSCHHHHHHHHH
T ss_pred             ecCCHHHHHHHhCCCHHHHHHHHH
Confidence            357999999999999999998764

>2gau_A Transcriptional regulator, CRP/FNR family; structural genomics, porphyromona gingivalis, PSI, protein structure initiative; 1.90A {Porphyromonas gingivalis} SCOP: a.4.5.4 b.82.3.2

Probab=81.24  E-value=1.1  Score=32.45  Aligned_cols=24  Identities=25%  Similarity=0.094  Sum_probs=21.1

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           94 KKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        94 ~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ..+||.+||..+|+++.+|++..+
T Consensus       179 ~~~t~~~lA~~lg~sr~tvsR~l~  202 (232)
T 2gau_A          179 IYLSREELATLSNMTVSNAIRTLS  202 (232)
T ss_dssp             CCCCHHHHHHHTTSCHHHHHHHHH
T ss_pred             cccCHHHHHHHhCCCHHHHHHHHH
Confidence            468999999999999999998753

>2zhg_A Redox-sensitive transcriptional activator SOXR; oxidative stress, MERR family, activator; HET: DNA; 2.80A {Escherichia coli} PDB: 2zhh_A

Probab=81.21  E-value=1.5  Score=31.15  Aligned_cols=24  Identities=25%  Similarity=0.250  Sum_probs=22.2

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           94 KKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        94 ~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .-+|..++|+.+|||..||..||+
T Consensus        10 ~~~~i~e~A~~~gvs~~TLR~ye~   33 (154)
T 2zhg_A           10 ALLTPGEVAKRSGVAVSALHFYES   33 (154)
T ss_dssp             CCBCHHHHHHHHTSCHHHHHHHHH
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHH
Confidence            458999999999999999999986

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

Probab=81.14  E-value=1.5  Score=28.84  Aligned_cols=24  Identities=4%  Similarity=-0.089  Sum_probs=21.3

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           93 DKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        93 ~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ...+|..+||+.+|+++++|++..
T Consensus        36 ~~~~s~~eLa~~lgis~stvs~~L   59 (108)
T 2kko_A           36 QGERAVEAIATATGMNLTTASANL   59 (108)
T ss_dssp             TCCEEHHHHHHHHTCCHHHHHHHH
T ss_pred             cCCcCHHHHHHHHCcCHHHHHHHH
Confidence            467899999999999999998864

>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=81.12  E-value=1.2  Score=32.83  Aligned_cols=24  Identities=8%  Similarity=0.156  Sum_probs=21.2

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           94 KKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        94 ~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ..+||.+||..+|+|+.+|+++.+
T Consensus       176 ~~~t~~~iA~~lG~sr~tvsR~l~  199 (250)
T 3e6c_C          176 MPLSQKSIGEITGVHHVTVSRVLA  199 (250)
T ss_dssp             CCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCCHHHHHHHhCCcHHHHHHHHH
Confidence            468999999999999999998763

>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=81.08  E-value=1  Score=26.49  Aligned_cols=25  Identities=24%  Similarity=0.373  Sum_probs=21.6

Q ss_pred             HHHHHHHHcCCChhHHHhhhcCCCC
Q 032366           30 KVVNAARRAGADIETVRKSHAGTNK   54 (142)
Q Consensus        30 ~~~~~a~r~G~~v~t~kk~~~g~~~   54 (142)
                      ++-..|.+.|++.+|+.+|+.|...
T Consensus        18 sq~~lA~~~gis~~~i~~~e~g~~~   42 (71)
T 1zug_A           18 TQTELATKAGVKQQSIQLIEAGVTK   42 (71)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHTTCCS
T ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCC
Confidence            3456899999999999999999775

>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=81.06  E-value=2.9  Score=27.04  Aligned_cols=26  Identities=4%  Similarity=0.028  Sum_probs=23.0

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 032366           94 KKLTQSQLAQLINEKPQVIQEYESGK  119 (142)
Q Consensus        94 ~glTQ~eLA~~lgis~stIs~~E~G~  119 (142)
                      ..+|..+||+.+|+|+.+++++-+..
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            37999999999999999999998743

>3qq6_A HTH-type transcriptional regulator SINR; helix-turn-helix motif, biofilm, repressor, SINI; 1.90A {Bacillus subtilis}

Probab=80.93  E-value=0.79  Score=28.26  Aligned_cols=25  Identities=12%  Similarity=0.169  Sum_probs=20.9

Q ss_pred             HHHHHHHHcCCChhHHHhhhcC-CCC
Q 032366           30 KVVNAARRAGADIETVRKSHAG-TNK   54 (142)
Q Consensus        30 ~~~~~a~r~G~~v~t~kk~~~g-~~~   54 (142)
                      ++-..|.+.|++..++.+||.| ...
T Consensus        25 tq~elA~~~gis~~~is~~E~G~~~~   50 (78)
T 3qq6_A           25 SLSELAEKAGVAKSYLSSIERNLQTN   50 (78)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHTTSCCC
T ss_pred             CHHHHHHHHCcCHHHHHHHHcCCCCC
Confidence            4456899999999999999999 444

>3g7d_A PHPD; non heme Fe(II) dioxygenase, cupin, biosynthetic protein; 1.80A {Streptomyces viridochromogenes} PDB: 3gbf_A 3rzz_A

Probab=80.91  E-value=2.1  Score=34.93  Aligned_cols=54  Identities=24%  Similarity=0.236  Sum_probs=43.2

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCCC
Q 032366           86 AIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA-IPNQQILTKLERALGVKLR  139 (142)
Q Consensus        86 ~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~-~p~~~~l~kLa~~Lgvsl~  139 (142)
                      +|..++..+.+|-.|+|...|+....+.++..+.. .|.......||+.|+|.+.
T Consensus         7 rl~hwmnark~t~~e~~~~~~~~~~~~~~~l~~~~~e~~~~~~~~l~~~l~v~~~   61 (443)
T 3g7d_A            7 KLAHWMNARKYTAAQTADLAGLPLDDLRRLLGDEANEPDPAAATALAEALSVEPS   61 (443)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHTSCHHHHHHHC--------CHHHHHHHHHTTCCGG
T ss_pred             hHHHhhhhhccccHHHHhhcCCCHHHHHHHhcCcccCCCHHHHHHHHHHhcCChH
Confidence            57788889999999999999999999999998764 5778889999999999875

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

Probab=80.89  E-value=1.8  Score=29.88  Aligned_cols=33  Identities=18%  Similarity=0.045  Sum_probs=26.4

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ...|..+...-++|+.+||+.+|+++++++++.
T Consensus        56 ~~vL~~l~~~~~~t~~eLa~~l~~~~~~vs~~l   88 (161)
T 3e6m_A           56 LRLLSSLSAYGELTVGQLATLGVMEQSTTSRTV   88 (161)
T ss_dssp             HHHHHHHHHHSEEEHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHH
Confidence            344555555668999999999999999999864

>1b4a_A Arginine repressor; helix turn helix; 2.50A {Geobacillus stearothermophilus} SCOP: a.4.5.3 d.74.2.1 PDB: 1f9n_A

Probab=80.87  E-value=2.4  Score=30.19  Aligned_cols=33  Identities=15%  Similarity=0.106  Sum_probs=27.0

Q ss_pred             HHHHHH-HHhCCCCHHHHHHHh-----CCCHHHHHHHHc
Q 032366           85 KAIVQA-RNDKKLTQSQLAQLI-----NEKPQVIQEYES  117 (142)
Q Consensus        85 ~~Lk~~-R~~~glTQ~eLA~~l-----gis~stIs~~E~  117 (142)
                      ..|+++ ....-.||.||++.+     ++|++||++..+
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 556667999999999     999999999876

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

Probab=80.86  E-value=3.6  Score=26.55  Aligned_cols=26  Identities=15%  Similarity=0.095  Sum_probs=23.0

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 032366           94 KKLTQSQLAQLINEKPQVIQEYESGK  119 (142)
Q Consensus        94 ~glTQ~eLA~~lgis~stIs~~E~G~  119 (142)
                      ..+|..+||+.+|+|+.+++++-+-.
T Consensus        17 ~~~~~~~lA~~~~~s~~~l~r~fk~~   42 (108)
T 3mn2_A           17 RPITIEKLTALTGISSRGIFKAFQRS   42 (108)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            46999999999999999999998744

>3gpv_A Transcriptional regulator, MERR family; protein structure initiative II(PSI II), NYSGXRC, structural genomics; 1.90A {Bacillus thuringiensis serovarkonkukian}

Probab=80.85  E-value=1.5  Score=30.80  Aligned_cols=24  Identities=21%  Similarity=0.207  Sum_probs=22.4

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           94 KKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        94 ~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ..++..++|+.+|||..||..||.
T Consensus        15 ~~~~I~evA~~~gvs~~tLR~Ye~   38 (148)
T 3gpv_A           15 MYYTIGQVAKMQHLTISQIRYYDK   38 (148)
T ss_dssp             CCBCHHHHHHHTTCCHHHHHHHHH
T ss_pred             CceeHHHHHHHHCcCHHHHHHHHH
Confidence            358999999999999999999997

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

Probab=80.83  E-value=2.1  Score=29.54  Aligned_cols=22  Identities=27%  Similarity=0.240  Sum_probs=18.5

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHH
Q 032366           95 KLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        95 glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ++||.+||+.+++++++++++.
T Consensus        52 ~~t~~eLa~~l~~~~~tvsr~v   73 (148)
T 4fx0_A           52 DLTMSELAARIGVERTTLTRNL   73 (148)
T ss_dssp             --CHHHHHHHHTCCHHHHHHHH
T ss_pred             CcCHHHHHHHHCCChhhHHHHH
Confidence            4899999999999999998864

>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=80.82  E-value=1  Score=28.92  Aligned_cols=25  Identities=16%  Similarity=0.166  Sum_probs=22.1

Q ss_pred             HHHHHHHHcCCChhHHHhhhcCCCC
Q 032366           30 KVVNAARRAGADIETVRKSHAGTNK   54 (142)
Q Consensus        30 ~~~~~a~r~G~~v~t~kk~~~g~~~   54 (142)
                      ++-..|.+.|++..|+.+||.|...
T Consensus        45 sq~elA~~lgvs~~~is~~E~G~~~   69 (99)
T 2ppx_A           45 TQEEFSARYHIPLGTLRDWEQGRSE   69 (99)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHTTSSC
T ss_pred             CHHHHHHHhCcCHHHHHHHHcCCCC
Confidence            4567899999999999999999876

>3fx3_A Cyclic nucleotide-binding protein; helix_TURN_helix, CAMP regulatory protein, structural genomi 2, protein structure initiative; 2.20A {Ruegeria pomeroyi} PDB: 3h3z_A*

Probab=80.76  E-value=0.92  Score=32.94  Aligned_cols=24  Identities=17%  Similarity=0.141  Sum_probs=21.2

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           94 KKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        94 ~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ..+||.+||..+|+++.+|+++.+
T Consensus       177 l~~t~~~iA~~lg~sr~tvsR~l~  200 (237)
T 3fx3_A          177 LPYDKMLIAGRLGMKPESLSRAFS  200 (237)
T ss_dssp             CCSCTHHHHHHTTCCHHHHHHHHH
T ss_pred             ecCCHHHHHHHhCCCHHHHHHHHH
Confidence            357899999999999999999864

>4ghj_A Probable transcriptional regulator; structural genomics, niaid, national institute of allergy AN infectious diseases; HET: MSE; 1.75A {Vibrio vulnificus}

Probab=80.65  E-value=0.89  Score=30.10  Aligned_cols=39  Identities=23%  Similarity=0.243  Sum_probs=27.5

Q ss_pred             eccCCCCCccccCHHHHHHHHHcCCChhHHHhhhcCCCC
Q 032366           16 IKKKAPNAATKKDEKVVNAARRAGADIETVRKSHAGTNK   54 (142)
Q Consensus        16 ~~~~~~~~~~~~~~~~~~~a~r~G~~v~t~kk~~~g~~~   54 (142)
                      ||.+-...+..++=++-..|.++|++..|+.+||.|+..
T Consensus        37 lG~~ir~~R~~~glTQ~eLA~~~gvs~~~is~~E~G~~~   75 (101)
T 4ghj_A           37 IGDRLKQARLNRDLTQSEVAEIAGIARKTVLNAEKGKVQ   75 (101)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHTTCCB
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHcCCCHHHHHHHHCCCCC
Confidence            444333333344456677899999999999999999654

>3qkx_A Uncharacterized HTH-type transcriptional regulato; structural genomics, joint center for structural genomics; HET: MSE; 2.35A {Haemophilus influenzae}

Probab=80.57  E-value=2.2  Score=29.07  Aligned_cols=37  Identities=22%  Similarity=0.117  Sum_probs=27.8

Q ss_pred             HHHHHHHHHHhCC---CCHHHHHHHhCCCHHHHHHHHcCC
Q 032366           83 LKKAIVQARNDKK---LTQSQLAQLINEKPQVIQEYESGK  119 (142)
Q Consensus        83 ~g~~Lk~~R~~~g---lTQ~eLA~~lgis~stIs~~E~G~  119 (142)
                      +-+...++-.++|   .|..++|+.+|||++++.++-.++
T Consensus        13 Il~aa~~l~~~~G~~~~ti~~Ia~~agvs~~t~Y~~F~sK   52 (188)
T 3qkx_A           13 IFSATDRLMAREGLNQLSMLKLAKEANVAAGTIYLYFKNK   52 (188)
T ss_dssp             HHHHHHHHHHHSCSTTCCHHHHHHHHTCCHHHHHHHSSSH
T ss_pred             HHHHHHHHHHhcCcccCCHHHHHHHhCCCcchHHHHcCCH
Confidence            3334444444554   799999999999999999997655

>3b7h_A Prophage LP1 protein 11; structural genomics, PSI2, MCSG, protein structure initiative, midwest center for structural genomics; 2.00A {Lactobacillus plantarum WCFS1}

Probab=80.55  E-value=0.83  Score=27.48  Aligned_cols=24  Identities=25%  Similarity=0.297  Sum_probs=21.1

Q ss_pred             HHHHHHHHcCCChhHHHhhhcCCC
Q 032366           30 KVVNAARRAGADIETVRKSHAGTN   53 (142)
Q Consensus        30 ~~~~~a~r~G~~v~t~kk~~~g~~   53 (142)
                      ++-..|.+.|++.+|+.+|+.|..
T Consensus        22 sq~~lA~~~gis~~~i~~~e~g~~   45 (78)
T 3b7h_A           22 TINRVATLAGLNQSTVNAMFEGRS   45 (78)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHCTTC
T ss_pred             CHHHHHHHHCcCHHHHHHHHcCCC
Confidence            345689999999999999999987

>3dcf_A Transcriptional regulator of the TETR/ACRR family; YP_290855.1, structural genomics, joint center for structural genomics, JCSG; 2.50A {Thermobifida fusca YX}

Probab=80.51  E-value=2.1  Score=29.94  Aligned_cols=39  Identities=18%  Similarity=0.158  Sum_probs=29.4

Q ss_pred             HHHHHHHHHHHhCC---CCHHHHHHHhCCCHHHHHHHHcCCC
Q 032366           82 ELKKAIVQARNDKK---LTQSQLAQLINEKPQVIQEYESGKA  120 (142)
Q Consensus        82 ~~g~~Lk~~R~~~g---lTQ~eLA~~lgis~stIs~~E~G~~  120 (142)
                      .+-+...++-.+.|   +|..++|+.+|||+.+++++-.++.
T Consensus        35 ~Il~aa~~l~~~~G~~~~tv~~Ia~~agvs~~t~Y~~F~sK~   76 (218)
T 3dcf_A           35 QIIKVATELFREKGYYATSLDDIADRIGFTKPAIYYYFKSKE   76 (218)
T ss_dssp             HHHHHHHHHHHHTCTTTCCHHHHHHHHTCCHHHHHHHCSSHH
T ss_pred             HHHHHHHHHHHHcCcccCcHHHHHHHhCCCHHHHHHHcCCHH
Confidence            34444455555555   7899999999999999999976653

>3kcc_A Catabolite gene activator; helix-turn-helix, CAMP, CAMP-binding, DNA-binding nucleotide-binding, transcription, transcription regulation; HET: CMP; 1.66A {Escherichia coli}

Probab=80.31  E-value=1.3  Score=33.07  Aligned_cols=23  Identities=13%  Similarity=0.309  Sum_probs=20.7

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 032366           95 KLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        95 glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .+||.+||..+|+++.+|+++.+
T Consensus       217 ~lt~~~lA~~lG~sr~tvsR~l~  239 (260)
T 3kcc_A          217 KITRQEIGQIVGCSRETVGRILK  239 (260)
T ss_dssp             ECCHHHHHHHHTCCHHHHHHHHH
T ss_pred             cCCHHHHHHHhCCCHHHHHHHHH
Confidence            47999999999999999998764

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

Probab=80.26  E-value=2.5  Score=28.62  Aligned_cols=33  Identities=18%  Similarity=0.184  Sum_probs=25.0

Q ss_pred             HHHHHHHHHh-CCCCHHHHHHHhCCCHHHHHHHH
Q 032366           84 KKAIVQARND-KKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        84 g~~Lk~~R~~-~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ...|..+... .++|+.+||+.+++++++++++.
T Consensus        42 ~~vL~~l~~~~~~~t~~eLa~~l~i~~~tvs~~l   75 (150)
T 3fm5_A           42 YSVLVLACEQAEGVNQRGVAATMGLDPSQIVGLV   75 (150)
T ss_dssp             HHHHHHHHHSTTCCCSHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHhCCCCcCHHHHHHHHCCCHhHHHHHH
Confidence            3445555433 46899999999999999998864

>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=80.24  E-value=1.3  Score=29.71  Aligned_cols=34  Identities=9%  Similarity=0.036  Sum_probs=26.5

Q ss_pred             HHHHHHHHHHh--CCCCHHHHHHHhCCCHHHHHHHH
Q 032366           83 LKKAIVQARND--KKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        83 ~g~~Lk~~R~~--~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      -...|..+...  .++|+.+||+.+++++++++++.
T Consensus        39 q~~vL~~l~~~~~~~~t~~eLa~~l~~~~~tvs~~l   74 (127)
T 2frh_A           39 EFAVLTYISENKEKEYYLKDIINHLNYKQPQVVKAV   74 (127)
T ss_dssp             HHHHHHHHHHTCCSEEEHHHHHHHSSSHHHHHHHHH
T ss_pred             HHHHHHHHHhccCCCcCHHHHHHHHCCCHHHHHHHH
Confidence            34445555555  68999999999999999988764

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

Probab=80.21  E-value=1.9  Score=29.32  Aligned_cols=33  Identities=9%  Similarity=0.093  Sum_probs=25.9

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ...|..+...-++|+.+||+.+|+++++++++.
T Consensus        46 ~~iL~~l~~~~~~t~~ela~~l~i~~~tvs~~l   78 (155)
T 3cdh_A           46 WRVLACLVDNDAMMITRLAKLSLMEQSRMTRIV   78 (155)
T ss_dssp             HHHHHHHSSCSCBCHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHHCCCcCHHHHHHHHCCCHHHHHHHH
Confidence            344555555568999999999999999998764

>2l49_A C protein; P2 bacteriophage, P2 C, direct repeats, DNA-binding protein, binding protein; NMR {Enterobacteria phage P2} PDB: 2xcj_A

Probab=80.10  E-value=1.2  Score=28.19  Aligned_cols=25  Identities=16%  Similarity=0.137  Sum_probs=21.7

Q ss_pred             HHHHHHHHcCCChhHHHhhhcCCCC
Q 032366           30 KVVNAARRAGADIETVRKSHAGTNK   54 (142)
Q Consensus        30 ~~~~~a~r~G~~v~t~kk~~~g~~~   54 (142)
                      ++-..|.+.|++.+|+.+|+.|...
T Consensus        19 tq~~lA~~~gis~~~is~~e~g~~~   43 (99)
T 2l49_A           19 SRQQLADLTGVPYGTLSYYESGRST   43 (99)
T ss_dssp             CHHHHHHHHCCCHHHHHHHTTTSSC
T ss_pred             CHHHHHHHHCcCHHHHHHHHcCCCC
Confidence            4466899999999999999999765

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

Probab=80.02  E-value=1.5  Score=29.73  Aligned_cols=36  Identities=19%  Similarity=0.202  Sum_probs=21.7

Q ss_pred             HHHHHHHHHHHHh--CCCCHHHHHHHhCCCHHHHHHHH
Q 032366           81 SELKKAIVQARND--KKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        81 ~~~g~~Lk~~R~~--~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ..-...|..+...  -++|+.+||+.+++++++++++.
T Consensus        41 ~~q~~vL~~l~~~~~~~~t~~eLa~~l~~~~~~vs~~l   78 (148)
T 3jw4_A           41 SQQGRMIGYIYENQESGIIQKDLAQFFGRRGASITSML   78 (148)
T ss_dssp             HHHHHHHHHHHHHTTTCCCHHHHHHC------CHHHHH
T ss_pred             HHHHHHHHHHHhCCCCCCCHHHHHHHHCCChhHHHHHH
Confidence            3334555666555  78999999999999999888764

---

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	142
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	1e-09
d2b5aa1	77	a.35.1.3 (A:1-77) Regulatory protein C.BclI {Bacil	4e-09
d1utxa_	66	a.35.1.3 (A:) Putative transcription regulator Cyl	3e-08
d2r1jl1	66	a.35.1.2 (L:3-68) P22 C2 repressor, DNA-binding do	2e-07
d1y9qa1	79	a.35.1.8 (A:4-82) Probable transcriptional regulat	2e-07
d1b0na2	68	a.35.1.3 (A:1-68) SinR repressor, DNA-binding doma	9e-07
d2croa_	65	a.35.1.2 (A:) cro 434 {Bacteriophage 434 [TaxId: 1	5e-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	1e-04
d2icta1	87	a.35.1.3 (A:8-94) Antitoxin HigA {Escherichia coli	4e-04

>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 = 50.9 bits (122), Expect = 2e-10
 Identities = 13/57 (22%), Positives = 24/57 (42%)

Query: 82  ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 138
           +  + + + 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 = 49.3 bits (117), Expect = 1e-09
 Identities = 42/65 (64%), Positives = 49/65 (75%)

Query: 77  DRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGV 136
           DRV  E+ K I Q R  K LTQ  LA  INEKPQVI +YESG+AIPN Q+L K+ERA+G+
Sbjct: 1   DRVTLEVGKVIQQGRQSKGLTQKDLATKINEKPQVIADYESGRAIPNNQVLGKIERAIGL 60

Query: 137 KLRGK 141
           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 = 48.3 bits (115), Expect = 4e-09
 Identities = 13/57 (22%), Positives = 24/57 (42%)

Query: 82  ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 138
           +  + + + R  K ++Q +LA L       I E E G    +   + K+  AL +  
Sbjct: 10  KFGRTLKKIRTQKGVSQEELADLAGLHRTYISEVERGDRNISLINIHKICAALDIPA 66

>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 = 45.2 bits (107), Expect = 3e-08
 Identities = 17/56 (30%), Positives = 26/56 (46%)

Query: 83  LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 138
           +   +   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 = 43.7 bits (103), Expect = 2e-07
 Identities = 13/56 (23%), Positives = 25/56 (44%)

Query: 83  LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 138
           + + I   R   K+ Q+ L +++      I ++E  +  PN + L  L +AL    
Sbjct: 4   MGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCSP 59

>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 = 43.8 bits (103), Expect = 2e-07
 Identities = 12/58 (20%), Positives = 23/58 (39%)

Query: 81  SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 138
           S++   +   R  + L+    AQL      ++ + E G++ P    L K+   L    
Sbjct: 7   SQIANQLKNLRKSRGLSLDATAQLTGVSKAMLGQIERGESSPTIATLWKIASGLEASF 64

>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 = 9e-07
 Identities = 14/57 (24%), Positives = 25/57 (43%), Gaps = 1/57 (1%)

Query: 83  LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESG-KAIPNQQILTKLERALGVKL 138
           + + 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 = 39.8 bits (93), Expect = 5e-06
 Identities = 15/58 (25%), Positives = 26/58 (44%), Gaps = 1/58 (1%)

Query: 81  SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 138
             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 = 38.1 bits (88), Expect = 3e-05
 Identities = 11/56 (19%), Positives = 21/56 (37%)

Query: 83  LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 138
           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 = 36.8 bits (85), Expect = 5e-05
 Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 1/56 (1%)

Query: 83  LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL 138
           +   +   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 = 35.9 bits (83), Expect = 1e-04
 Identities = 11/44 (25%), Positives = 21/44 (47%)

Query: 87  IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKL 130
           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 = 34.9 bits (80), Expect = 4e-04
 Identities = 9/50 (18%), Positives = 22/50 (44%)

Query: 87  IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGV 136
           I ++ ++  ++  + A+ +   P       +GKA    ++  KL   +G 
Sbjct: 6   IQESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVIGS 55

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	142
d1x57a1	78	Endothelial differentiation-related factor 1, EDF1	99.72
d1y7ya1	69	Restriction-modification controller protein C.AhdI	99.69
d2b5aa1	77	Regulatory protein C.BclI {Bacillus caldolyticus [	99.63
d1y9qa1	79	Probable transcriptional regulator VC1968, N-termi	99.63
d2r1jl1	66	P22 C2 repressor, DNA-binding domain {Salmonella b	99.63
d2croa_	65	cro 434 {Bacteriophage 434 [TaxId: 10712]}	99.62
d1b0na2	68	SinR repressor, DNA-binding domain {Bacillus subti	99.61
d1r69a_	63	434 C1 repressor, DNA-binding domain {Bacteriophag	99.6
d1utxa_	66	Putative transcription regulator CylR2 {Enterococc	99.6
d2a6ca1	69	HTH-motif protein NE1354 {Nitrosomonas europaea [T	99.58
d1lmb3_	87	lambda C1 repressor, DNA-binding domain {Bacteriop	99.56
d2icta1	87	Antitoxin HigA {Escherichia coli [TaxId: 562]}	99.56
d2o38a1	89	Hypothetical protein RPA3824 {Rhodopseudomonas pal	99.5
d2ofya1	82	Putative transcriptional regulator RHA1_ro04071 {R	99.47
d2ppxa1	62	Uncharacterized protein Atu1735 {Agrobacterium tum	99.38
d2auwa1	67	Hypothetical protein NE0471 C-terminal domain {Nit	99.21
d2bnma1	71	Hydroxypropylphosphonic acid epoxidase Fom4, N-ter	98.29
d1dwka1	86	Cyanase N-terminal domain {Escherichia coli [TaxId	97.91
d2hsga1	57	Glucose-resistance amylase regulator CcpA, N-termi	97.57
d1efaa1	59	Lac repressor (LacR), N-terminal domain {Escherich	97.49
d1qpza1	57	Purine repressor (PurR), N-terminal domain {Escher	97.38
d1uxda_	59	Fructose repressor (FruR), N-terminal domain {Esch	97.33
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	97.13
d1ic8a2	94	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Human (H	97.11
d1e3oc2	75	Oct-1 {Human (Homo sapiens) [TaxId: 9606]}	97.06
d1au7a2	72	Pit-1 {Rat (Rattus norvegicus) [TaxId: 10116]}	96.93
d2awia1	65	PrgX {Enterococcus faecalis [TaxId: 1351]}	96.39
d1nera_	74	Ner {Bacteriophage mu [TaxId: 10677]}	96.27
d2jn6a1	89	Uncharacterized protein Cgl2762 {Corynebacterium g	95.87
d1vz0a1	93	Putative partitioning protein ParB/Spo0J {Thermus	95.85
d1gdta1	43	gamma,delta resolvase (C-terminal domain) {Escheri	95.77
d1hlva1	66	DNA-binding domain of centromere binding protein B	95.37
d1k78a1	63	Pax-5 {Human (Homo sapiens) [TaxId: 9606]}	95.25
d1r71a_	114	Transcriptional repressor protein KorB DNA-binding	95.15
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	94.92
d2o4aa1	83	DNA-binding protein SATB1 {Human (Homo sapiens) [T	94.9
d2csfa1	88	DNA-binding protein SATB2 {Human (Homo sapiens) [T	94.73
d1z6ra1	70	Mlc protein N-terminal domain {Escherichia coli [T	94.6
d1s4ka_	120	Putative cytoplasmic protein YdiL {Salmonella typh	94.42
d1i5za1	69	Catabolite gene activator protein (CAP), C-termina	94.2
d2ox6a1	162	Hypothetical protein SO3848 {Shewanella oneidensis	94.16
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	94.03
d2ppxa1	62	Uncharacterized protein Atu1735 {Agrobacterium tum	94.0
d1jhga_	101	Trp repressor, TrpR {Escherichia coli [TaxId: 562]	93.89
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	93.77
d1x2la1	87	Homeobox protein Cux-2, CUTL2 {Human (Homo sapiens	93.7
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	93.34
d1umqa_	60	Photosynthetic apparatus regulatory protein PprA (	93.33
d2hoea1	62	N-acetylglucosamine kinase {Thermotoga maritima [T	93.21
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	93.18
d1wh8a_	111	Homeobox protein Cux-2, CUTL2 {Human (Homo sapiens	93.15
d1pdnc_	123	Paired protein (prd) {Fruit fly (Drosophila melano	93.05
d3e5ua1	80	Chlorophenol reduction protein CprK {Desulfitobact	92.94
d1rzsa_	61	cro p22 {Bacteriophage p22 [TaxId: 10754]}	92.9
d1s7ea2	80	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	92.83
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	92.82
d2gaua1	81	Transcriptional regulator PG0396, C-terminal domai	92.68
d1qpza1	57	Purine repressor (PurR), N-terminal domain {Escher	92.66
d1zyba1	73	Probable transcription regulator BT4300, C-termina	92.4
d1ft9a1	80	CO-sensing protein CooA, C-terminal domain {Rhodos	92.4
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	92.23
d1or7a1	68	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	92.23
d1wh6a_	101	Homeobox protein Cux-2, CUTL2 {Human (Homo sapiens	92.21
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	92.14
d1r8ea1	118	Transcription activator BmrR {Bacillus subtilis [T	91.5
d2zcwa1	82	Transcriptional regulator TTHA1359, C-terminal dom	91.38
d2hsga1	57	Glucose-resistance amylase regulator CcpA, N-termi	91.04
d2ao9a1	120	Phage protein BC1890 {Bacillus cereus [TaxId: 1396	90.96
d1a04a1	67	Nitrate/nitrite response regulator (NarL) {Escheri	90.73
d1etxa_	89	FIS protein {Escherichia coli [TaxId: 562]}	90.61
d1lmb3_	87	lambda C1 repressor, DNA-binding domain {Bacteriop	90.49
d3ctaa1	85	Ta1064 (RFK), N-terminal domain {Thermoplasma acid	90.45
d2bgca1	100	Listeriolysin regulatory protein PrfA, C-terminal	90.41
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	90.39
d1s7oa_	106	Hypothetical protein SPy1201 {Streptococcus pyogen	90.3
d2croa_	65	cro 434 {Bacteriophage 434 [TaxId: 10712]}	89.65
d1pdnc_	123	Paired protein (prd) {Fruit fly (Drosophila melano	89.65
d2r1jl1	66	P22 C2 repressor, DNA-binding domain {Salmonella b	89.63
d1ku3a_	61	Sigma70 (SigA, RpoD) {Thermus aquaticus [TaxId: 27	89.6
d1nr3a_	122	DNA-binding protein Tfx {Archaeon Methanobacterium	89.28
d1j9ia_	68	Terminase gpNU1 subunit domain {Bacteriophage lamb	89.06
d1fsea_	67	Germination protein GerE {Bacillus subtilis [TaxId	89.03
d1b0na2	68	SinR repressor, DNA-binding domain {Bacillus subti	88.92
d1y7ya1	69	Restriction-modification controller protein C.AhdI	88.88
d1r8da_	109	Multidrug transporter activator MtaN {Bacillus sub	88.86
d2o3fa1	83	Putative transcriptional regulator YbbH {Bacillus	88.83
d1p4wa_	87	Transcriptional regulator RcsB {Erwinia amylovora	88.73
d1efaa1	59	Lac repressor (LacR), N-terminal domain {Escherich	88.72
d1l3la1	65	Quorum-sensing transcription factor TraR, C-termin	88.44
d1g2ha_	61	Transcriptional regulator TyrR, C-terminal domain	88.44
d1v7ba1	74	Transcriptional regulator Cgl2612 {Corynebacterium	88.39
d1xsva_	106	Hypothetical protein SAV1236 {Staphylococcus aureu	88.07
d1yioa1	70	Response regulatory protein StyR, C-terminal domai	87.97
d1r8ea1	118	Transcription activator BmrR {Bacillus subtilis [T	87.67
d2a61a1	139	Transcriptional regulator TM0710 {Thermotoga marit	87.65
d2p7vb1	68	Sigma70 (SigA, RpoD) {Escherichia coli [TaxId: 562	87.65
d1ntca_	91	DNA-binding domain of NTRC {Salmonella typhimurium	87.16
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	87.14
d1utxa_	66	Putative transcription regulator CylR2 {Enterococc	86.89
d1q06a_	127	Transcriptional regulator CueR {Escherichia coli [	86.63
d2auwa1	67	Hypothetical protein NE0471 C-terminal domain {Nit	86.42
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	86.37
d1x57a1	78	Endothelial differentiation-related factor 1, EDF1	86.33
d2ofya1	82	Putative transcriptional regulator RHA1_ro04071 {R	86.03
d1t56a1	73	Ethr repressor {Mycobacterium tuberculosis [TaxId:	85.92
d2i10a1	69	Putative transcriptional regulator RHA1_ro09068 {R	85.76
d1z0xa1	68	Transcriptional regulator EF0787 {Enterococcus fae	85.66
d2gfna1	77	Probable transcriptional regulator RHA1_ro04631 {R	85.65
d1r8da_	109	Multidrug transporter activator MtaN {Bacillus sub	85.57
d2vkva1	62	Tetracyclin repressor (Tet-repressor, TetR) {Esche	85.56
d2g7sa1	74	Putative transcriptional regulator Atu0279 {Agroba	85.51
d2d6ya1	68	Putative regulator SCO4008 {Streptomyces coelicolo	85.31
d2ev0a1	61	Manganese transport regulator MntR {Bacillus subti	85.03
d1jt6a1	71	Multidrug binding protein QacR {Staphylococcus aur	84.94
d3broa1	135	Transcriptional regulator OEOE1854 {Oenococcus oen	84.65
d2b5aa1	77	Regulatory protein C.BclI {Bacillus caldolyticus [	84.56
d2gena1	70	Probable transcriptional regulator PA1836 {Pseudom	84.51
d2fbqa1	79	Transcriptional regulator PsrA {Pseudomonas aerugi	83.99
d2fx0a1	73	Hemolysin II regulatory protein, HlyIIR {Bacillus	83.81
d1r69a_	63	434 C1 repressor, DNA-binding domain {Bacteriophag	83.67
d2id3a1	68	Putative transcriptional regulator SCO5951 {Strept	83.63
d1lnwa_	141	MexR repressor {Pseudomonas aeruginosa [TaxId: 287	83.48
d2o7ta1	78	Transcriptional regulator Cgl1640/Cg1846 {Coryneba	83.42
d1ui5a1	71	A-factor receptor homolog CprB {Streptomyces coeli	82.9
d2etha1	140	Putative transcriptional regulator TM0816 {Thermot	82.69
d1r1ua_	94	Metal-sensing transcriptional repressor CzrA {Stap	82.68
d2oi8a1	79	Putative regulatory protein Sco4313 {Streptomyces	82.53
d1lj9a_	144	Transcriptional regulator SlyA {Enterococcus faeca	82.33
d2id6a1	75	Transcriptional regulator TM1030 {Thermotoga marit	82.26
d1zs4a1	78	Regulatory protein cII {Bacteriophage lambda [TaxI	82.09
d1vi0a1	72	Hypothetical transcriptional regulator YsiA {Bacil	82.05
d1d1la_	61	cro lambda repressor {Bacteriophage lambda [TaxId:	82.02
d2fq4a1	69	Transcriptional regulator BC3163 {Bacillus cereus	81.91
d1pb6a1	72	Hypothetical transcriptional regulator YcdC {Esche	81.75
d1jgsa_	138	Multiple antibiotic resistance repressor, MarR {Es	81.61
d3c07a1	75	Putative transcriptional regulator SCO4850 {Strept	81.53
d2np5a1	69	Transcriptional regulator RHA1_ro04179 {Rhodococcu	81.5
d1bl0a1	54	MarA {Escherichia coli [TaxId: 562]}	81.49
d2hkua1	70	Putative transcriptional regulator RHA1_ro03468 {R	81.35
d2hyja1	75	Putative transcriptional regulator SCO4940 {Strept	81.28
d2icta1	87	Antitoxin HigA {Escherichia coli [TaxId: 562]}	81.07
d1ttya_	87	Sigma70 (SigA, RpoD) {Thermotoga maritima [TaxId:	81.04
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	81.0
d1q06a_	127	Transcriptional regulator CueR {Escherichia coli [	80.85
d2isya1	63	Iron-dependent regulator IdeR {Mycobacterium tuber	80.73
d1z91a1	137	Organic hydroperoxide resistance transcriptional r	80.23

>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=99.72  E-value=1.2e-17  Score=108.22  Aligned_cols=64  Identities=64%  Similarity=0.918  Sum_probs=60.8

Q ss_pred             cchHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCCC
Q 032366           78 RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRGK  141 (142)
Q Consensus        78 ~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~e~  141 (142)
                      .+.++||++|+.+|+.+||||.+||+.+|||+++|++||+|...|+.+.+.+||++|||++++.
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            4567899999999999999999999999999999999999999999999999999999999764

>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=99.69  E-value=3.3e-17  Score=103.47  Aligned_cols=60  Identities=23%  Similarity=0.243  Sum_probs=57.8

Q ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 032366           81 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG  140 (142)
Q Consensus        81 ~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~e  140 (142)
                      ..||++|+.+|+++||||.+||+.+|+|+++|++||+|+..|+.+.+.+||++|||++++
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            459999999999999999999999999999999999999999999999999999999875

>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=99.63  E-value=2.3e-16  Score=101.28  Aligned_cols=61  Identities=21%  Similarity=0.278  Sum_probs=57.9

Q ss_pred             chHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           79 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      +...||++|+.+|..+||||.+||+.+|+|+++|++||+|+..|+.+.+.+||++|||+++
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            3456999999999999999999999999999999999999999999999999999999975

>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=99.63  E-value=5.5e-16  Score=99.92  Aligned_cols=61  Identities=20%  Similarity=0.310  Sum_probs=58.0

Q ss_pred             hHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 032366           80 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG  140 (142)
Q Consensus        80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~e  140 (142)
                      ...|+.+|+.+|+.+||||.+||+.+|+|+++|++||+|+..|+.+.+.+||++|||++++
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            4568999999999999999999999999999999999999999999999999999999863

>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=99.63  E-value=2.4e-16  Score=98.43  Aligned_cols=58  Identities=22%  Similarity=0.326  Sum_probs=56.1

Q ss_pred             HHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           82 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        82 ~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      .+|++|+.+|+++||||.+||+.+|+|+++|++||+|+..|+.+.+.+||++|+|+++
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            3899999999999999999999999999999999999999999999999999999975

>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=99.62  E-value=3.2e-16  Score=97.77  Aligned_cols=57  Identities=28%  Similarity=0.272  Sum_probs=53.5

Q ss_pred             HHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           82 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        82 ~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      .++++|+.+|+++||||.+||+.+|||+++|++||+|+..|+ +.+.+||++|||+++
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 789999999999975

>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=99.61  E-value=5.3e-16  Score=97.49  Aligned_cols=57  Identities=25%  Similarity=0.302  Sum_probs=54.1

Q ss_pred             HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCCC
Q 032366           83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA-IPNQQILTKLERALGVKLR  139 (142)
Q Consensus        83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~-~p~~~~l~kLa~~Lgvsl~  139 (142)
                      +|++|+.+|.++||||.+||+.+|+|+++|++||+|.. .|+.+.+.+||++|||+++
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            68999999999999999999999999999999999975 6999999999999999874

>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=99.60  E-value=4.2e-16  Score=96.50  Aligned_cols=56  Identities=30%  Similarity=0.457  Sum_probs=53.1

Q ss_pred             HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      ++++|+.+|+++||||.|||+.+|||+++|++||+|+. |+.+.+.+||++|||+++
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            79999999999999999999999999999999999975 788899999999999975

>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=99.60  E-value=4.6e-16  Score=97.36  Aligned_cols=55  Identities=31%  Similarity=0.378  Sum_probs=53.0

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      .+|+.+|.++||||.+||+.+|||+++|++||+|+..|+.+.+.+||++|||+++
T Consensus         4 ~ri~~lR~~~g~tq~elA~~~gis~~~is~~e~g~~~p~~~~l~~ia~~l~v~~~   58 (66)
T d1utxa_           4 NNLKLIREKKKISQSELAALLEVSRQTINGIEKNKYNPSLQLALKIAYYLNTPLE   58 (66)
T ss_dssp             ECHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHTTSCCCCHHHHHHHHHHTTSCHH
T ss_pred             HHHHHHHHHcCCCHHHHHHhcccCHHHHHHHHcCCCCCCHHHHHHHHHHHCCCHH
Confidence            4699999999999999999999999999999999999999999999999999975

>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=3.6e-15  Score=94.09  Aligned_cols=60  Identities=20%  Similarity=0.286  Sum_probs=57.0

Q ss_pred             hHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhCCCCC
Q 032366           80 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK-AIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~-~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      ...++.+|+.+|+++||||.+||+.+||++++|++||+|+ ..|+.+.+.+||.+||++++
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            3568999999999999999999999999999999999998 68999999999999999987

>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=99.56  E-value=3.2e-15  Score=98.42  Aligned_cols=61  Identities=18%  Similarity=0.163  Sum_probs=56.7

Q ss_pred             hHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCCC
Q 032366           80 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLRG  140 (142)
Q Consensus        80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~e  140 (142)
                      ...++..|+.+|+++||||.+||+.+|+|+++|++||+|...|+.+.+.+||++|||++++
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            3457777888899999999999999999999999999999999999999999999999874

>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=99.56  E-value=2.3e-15  Score=99.19  Aligned_cols=57  Identities=16%  Similarity=0.250  Sum_probs=54.6

Q ss_pred             HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      -|++|+++|+++||||.+||+.+|||+++|++||+|++.|+.+.+.+|+++|||+++
T Consensus         2 PGe~lke~r~~~glsq~~LA~~lGvs~~~is~ie~g~~~~s~~~~~kla~~lgvs~~   58 (87)
T d2icta1           2 PGDIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVIGSSPQ   58 (87)
T ss_dssp             HHHHHHHHHHHHTCCHHHHHHHHTCCHHHHHHHHHTSSCCCHHHHHHHHHHTCSCHH
T ss_pred             cHHHHHHHHHHcCCCHHHHHHHHhhcHHHHHHHHHhccCCCHHHHHHHHHHHCcCHH
Confidence            378999999999999999999999999999999999999999999999999999864

>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=99.50  E-value=2e-14  Score=94.90  Aligned_cols=61  Identities=16%  Similarity=0.100  Sum_probs=57.1

Q ss_pred             chHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhCCCCC
Q 032366           79 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK-AIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~-~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      ....++.+|+++|+++||||.+||+.+|+++++|++||+|+ ..|+.+.+.+||.+||++++
T Consensus         8 ~k~~l~~~i~~~r~~~gltq~~lA~~~gis~~~is~ie~G~~~~~~~~~L~~ia~~Lg~~i~   69 (89)
T d2o38a1           8 TKLRLAYALNAVIDRARLSQAAAAARLGINQPKVSALRNYKLEGFSVERLMTLLNALDQDVE   69 (89)
T ss_dssp             HHHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCCTTCCHHHHHHHHHHTTEEEE
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHHHhhHhHHHHHHcCCCCCCcHHHHHHHHHHcCCCHH
Confidence            45678999999999999999999999999999999999998 67999999999999999874

>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=99.47  E-value=3.6e-14  Score=92.52  Aligned_cols=58  Identities=19%  Similarity=0.286  Sum_probs=53.6

Q ss_pred             hHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhCCCCC
Q 032366           80 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGK-AIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~-~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      ...||.+|+.+|+  ++||.|||+++|+|+++|++||+|+ ..|+.+.+.+||++|||+++
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            4579999999995  7899999999999999999999998 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=99.38  E-value=7.8e-13  Score=81.59  Aligned_cols=47  Identities=23%  Similarity=0.311  Sum_probs=43.1

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHH
Q 032366           86 AIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLER  132 (142)
Q Consensus        86 ~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~  132 (142)
                      +|+.+|+..||||++||+.+|||+++|++||+|+..|+...+..|+.
T Consensus         3 ~ik~~R~~~gltQ~elA~~lGvs~~tvs~~E~G~~~P~~~~~~ll~~   49 (62)
T d2ppxa1           3 RIKIIRRALKLTQEEFSARYHIPLGTLRDWEQGRSEPDQPARAYLKI   49 (62)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTSSCCCHHHHHHHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHH
Confidence            58999999999999999999999999999999999999887766643

>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=99.21  E-value=3.1e-11  Score=75.54  Aligned_cols=43  Identities=12%  Similarity=0.186  Sum_probs=38.9

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH
Q 032366           84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQI  126 (142)
Q Consensus        84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~  126 (142)
                      +++|+.+|+++||||.+||+.+|||+.+|++||+|++.++..+
T Consensus         3 ~e~~k~~R~~~gltQ~elA~~LGvs~~ti~~yE~G~r~iP~~v   45 (67)
T d2auwa1           3 HEMFGDWMHRNNLSLTTAAEALGISRRMVSYYRTAHKIIPRTI   45 (67)
T ss_dssp             HHHHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHTTSSCCCHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH
Confidence            4789999999999999999999999999999999998655554

>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=98.29  E-value=3e-06  Score=50.64  Aligned_cols=58  Identities=21%  Similarity=0.448  Sum_probs=53.7

Q ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCC
Q 032366           81 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA-IPNQQILTKLERALGVKL  138 (142)
Q Consensus        81 ~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~-~p~~~~l~kLa~~Lgvsl  138 (142)
                      .-|.++|++.|++-.|....||..+|..+.+|..||+|+. ..+...+-+|+.+||.++
T Consensus         4 tgfae~lk~rreqvkmdhaalas~lgetpetvaawengeggeltltqlg~ia~~lgtsi   62 (71)
T d2bnma1           4 TGFAELLKDRREQVKMDHAALASLLGETPETVAAWENGEGGELTLTQLGRIAHVLGTSI   62 (71)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTTCTTCBHHHHHHHHHHTTSCT
T ss_pred             hhHHHHHHHHHHHHhhhHHHHHHHHcCCchHHHHhhcCCCceeeHHHHHHHHHHHcccc
Confidence            3588999999999999999999999999999999999975 568999999999999986

>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=97.91  E-value=2.2e-05  Score=50.49  Aligned_cols=58  Identities=14%  Similarity=0.130  Sum_probs=54.8

Q ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 032366           81 SELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL  138 (142)
Q Consensus        81 ~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl  138 (142)
                      .++.+.|-..+.++|||..+||+.+|.|...+.....|....+.+.+.+|+++||++-
T Consensus        12 ~~lte~Il~AK~~kgltw~~IA~~iG~s~vwvtaa~lGQ~~l~~~~A~~l~~~L~L~~   69 (86)
T d1dwka1          12 LDLADAILLSKAKKDLSFAEIADGTGLAEAFVTAALLGQQALPADAARLVGAKLDLDE   69 (86)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHTTSSSCHHHHHHHHTTSSCCCHHHHHHHHHHHTCCH
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHhcCCCCCHHHHHHHHHHcCCCH
Confidence            4678899999999999999999999999999999999999999999999999999864

>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=97.57  E-value=9.8e-05  Score=43.78  Aligned_cols=44  Identities=11%  Similarity=0.101  Sum_probs=36.1

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCC
Q 032366           95 KLTQSQLAQLINEKPQVIQEYESGKAIPNQQI---LTKLERALGVKL  138 (142)
Q Consensus        95 glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~---l~kLa~~Lgvsl  138 (142)
                      ++|.+|+|+.+|+|.+||+++.+|....+.++   +...++.||..+
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            47899999999999999999999987777665   555566677654

>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=9.2e-05  Score=44.23  Aligned_cols=45  Identities=9%  Similarity=0.003  Sum_probs=36.6

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCC
Q 032366           95 KLTQSQLAQLINEKPQVIQEYESGKAIPNQQI---LTKLERALGVKLR  139 (142)
Q Consensus        95 glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~---l~kLa~~Lgvsl~  139 (142)
                      ..|..|+|+.+|+|.+||+++.+|....+.++   +..+++.||..+.
T Consensus         2 ~~Ti~diA~~agvS~sTVSr~l~~~~~vs~~tr~rI~~~a~~lgY~pn   49 (59)
T d1efaa1           2 PVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPN   49 (59)
T ss_dssp             CCCHHHHHHTTTSCHHHHHHHHTTCSSCCTHHHHHHHHHHHHHTCCCC
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHCCCCcCCHHHHHHHHHHHHHHCCCcC
Confidence            57999999999999999999999987776554   5666777776553

>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=0.0002  Score=42.38  Aligned_cols=43  Identities=9%  Similarity=0.027  Sum_probs=35.4

Q ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCC
Q 032366           97 TQSQLAQLINEKPQVIQEYESGKAIPNQQI---LTKLERALGVKLR  139 (142)
Q Consensus        97 TQ~eLA~~lgis~stIs~~E~G~~~p~~~~---l~kLa~~Lgvsl~  139 (142)
                      |.+|+|+.+|+|.+|||++.+|....+.+.   +..+++.||..+.
T Consensus         2 Ti~dvA~~agVS~sTVSr~ln~~~~vs~~tr~rV~~~a~~lgY~pn   47 (57)
T d1qpza1           2 TIKDVAKRANVSTTTVSHVINKTRFVAEETRNAVWAAIKELHYSPS   47 (57)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHHTCSCCCHHHHHHHHHHHHHHTCCCC
T ss_pred             CHHHHHHHHCcCHHHHHHHHCCCCccCHHHHHHHHHHHHHHCCCCC
Confidence            789999999999999999999987777665   5566777776653

>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=97.33  E-value=0.00022  Score=42.41  Aligned_cols=44  Identities=14%  Similarity=0.111  Sum_probs=37.2

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCCC------CCHHHHHHHHHHhCCCCC
Q 032366           96 LTQSQLAQLINEKPQVIQEYESGKAI------PNQQILTKLERALGVKLR  139 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~G~~~------p~~~~l~kLa~~Lgvsl~  139 (142)
                      +|.+|+|+.+|+|.+||+++.||...      -+.+.+..+++.||..+.
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            58899999999999999999998632      256778888999998765

>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=97.13  E-value=0.00073  Score=38.32  Aligned_cols=39  Identities=15%  Similarity=0.152  Sum_probs=30.4

Q ss_pred             cchHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           78 RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        78 ~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .+.++-.+.++.++. .|.|..++|+.+|||++||++|.-
T Consensus         5 ~lt~~q~~~a~~l~~-~G~s~~~iA~~~gVSr~TiYry~p   43 (47)
T d1ijwc_           5 AINKHEQEQISRLLE-KGHPRQQLAIIFGIGVSTLYRYFP   43 (47)
T ss_dssp             SSCHHHHHHHHHHHH-TTCCHHHHHHHHTCCHHHHHHHSC
T ss_pred             cCCHHHHHHHHHHHH-CCCCHHHHHHHHCcCHHHHHhhCC
Confidence            344444555666664 699999999999999999999963

>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=97.11  E-value=0.0016  Score=41.96  Aligned_cols=53  Identities=9%  Similarity=0.053  Sum_probs=44.3

Q ss_pred             cchHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHH
Q 032366           78 RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKL  130 (142)
Q Consensus        78 ~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kL  130 (142)
                      .-...+.+-|+.....++++|..+|+.+|+|++.||.+.++....+...-..|
T Consensus        24 ~d~~~v~~~IK~Fl~~h~I~Q~~Va~~TGlsQS~iSq~L~~g~~M~~~KR~al   76 (94)
T d1ic8a2          24 EDPWRVAKMVKSYLQQHNIPQREVVDTTGLNQSHLSQHLNKGTPMKTQKRAAL   76 (94)
T ss_dssp             SCHHHHHHHHHHHHHHTTCCHHHHHHHHCCCHHHHHHHHHSBCCCCHHHHHHH
T ss_pred             cCHHHHHHHHHHHHHHcCCcHHHHHHHHcccHHHHHHHHhCCCCccHHHHHHH
Confidence            34556889999999999999999999999999999999998776666554443

>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=97.06  E-value=0.0015  Score=40.36  Aligned_cols=50  Identities=18%  Similarity=0.192  Sum_probs=41.0

Q ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHhC------CCHHHHHHHHcCCCCCCHHHHHHHHH
Q 032366           81 SELKKAIVQARNDKKLTQSQLAQLIN------EKPQVIQEYESGKAIPNQQILTKLER  132 (142)
Q Consensus        81 ~~~g~~Lk~~R~~~glTQ~eLA~~lg------is~stIs~~E~G~~~p~~~~l~kLa~  132 (142)
                      ..|...++..|...|+||.+++..+|      .|+++|+++|+=  ..+...+.+|--
T Consensus        10 e~Fa~~fk~rRi~LG~TQ~dVG~al~~l~g~~~SQttIcRFE~l--~LS~kn~~kLkP   65 (75)
T d1e3oc2          10 EQFAKTFKQRRIKLGFTQGDVGLAMGKLYGNDFSQTTISRFEAL--NLSFKNMSKLKP   65 (75)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHHHHHSCCCCHHHHHHHHHT--CSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccccHHHHHHHHHHHcCcchhHHHHHHHHHh--ccCHHHHHHHHH
Confidence            45899999999999999999999886      699999999974  346666665543

>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=96.93  E-value=0.00057  Score=41.90  Aligned_cols=50  Identities=14%  Similarity=0.106  Sum_probs=40.8

Q ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHhC------CCHHHHHHHHcCCCCCCHHHHHHHHH
Q 032366           81 SELKKAIVQARNDKKLTQSQLAQLIN------EKPQVIQEYESGKAIPNQQILTKLER  132 (142)
Q Consensus        81 ~~~g~~Lk~~R~~~glTQ~eLA~~lg------is~stIs~~E~G~~~p~~~~l~kLa~  132 (142)
                      ..|.+.++..|...|+||.|++..+|      .|+++|+++|+=  ..+...+.+|--
T Consensus         6 e~Fa~~fk~rRi~LG~TQ~dVG~al~~l~g~~~SQttIcRFE~l--~LS~kn~~klkP   61 (72)
T d1au7a2           6 EQFANEFKVRRIKLGYTQTNVGEALAAVHGSEFSQTTICRFENL--QLSFKNACKLKA   61 (72)
T ss_dssp             HHHHHHHHHHHHHHTCCHHHHHHHHHHTTSSCCCHHHHHHHHTT--CSBHHHHHHHHH
T ss_pred             HHHHHHHHHHHhccCccHHHHHHHHHHhcCcccchhHHHHHHhc--ccCHHHHHHHHH
Confidence            46899999999999999999999875      799999999974  346666655543

>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=96.39  E-value=0.0088  Score=34.57  Aligned_cols=55  Identities=22%  Similarity=0.234  Sum_probs=49.1

Q ss_pred             HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 032366           83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKL  138 (142)
Q Consensus        83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl  138 (142)
                      +|..|++.|++.++-|-+|-.-+ +|.+.+-+.|...+..+.+.+.++++.||+..
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            67889999999999999987544 59999999999999899999999999999863

>d1nera_ a.35.1.2 (A:) Ner {Bacteriophage mu [TaxId: 10677]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: Ner
species: Bacteriophage mu [TaxId: 10677]

Probab=96.27  E-value=0.0042  Score=38.29  Aligned_cols=50  Identities=16%  Similarity=0.146  Sum_probs=42.4

Q ss_pred             HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCC
Q 032366           87 IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGVKLR  139 (142)
Q Consensus        87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgvsl~  139 (142)
                      |......+|+|..+|++..|++.+|+.+..   ..|.+..=..||++||+.+.
T Consensus        14 I~AaL~krG~sLa~lsr~~gls~stl~naL---~rp~pKgEriIA~aLg~~P~   63 (74)
T d1nera_          14 VIAGLKKRKLSLSALSRQFGYAPTTLANAL---ERHWPKGEQIIANALETKPE   63 (74)
T ss_dssp             HHHHHTTSSCCHHHHHHHHSCCHHHHHHTT---TSSCHHHHHHHHHHTTSCHH
T ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHH---cCCChHHHHHHHHHHCcCHH
Confidence            556666789999999999999999999865   45777888889999999874

>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=95.87  E-value=0.007  Score=37.97  Aligned_cols=40  Identities=15%  Similarity=0.175  Sum_probs=31.2

Q ss_pred             cchHHHHHHHHHHH-HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           78 RVPSELKKAIVQAR-NDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        78 ~~~~~~g~~Lk~~R-~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .++.+|-..+-.+- ...|+|..++|+.+||++++|.+|-+
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            45566766654443 34589999999999999999999974

>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=95.85  E-value=0.0087  Score=38.22  Aligned_cols=35  Identities=14%  Similarity=0.143  Sum_probs=29.5

Q ss_pred             HHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           82 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        82 ~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +-+..++.+. +.|+|+.++|+++|.|+++|++..+
T Consensus         7 EeA~a~~~L~-e~g~t~~~iA~~~Gks~~~V~~~Lr   41 (93)
T d1vz0a1           7 EEARGYQALL-EMGLTQEEVARRVGKARSTVANALR   41 (93)
T ss_dssp             HHHHHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHH-HcCCCHHHHHHHHccchHHHHHHHH
Confidence            3456677776 6899999999999999999998764

>d1gdta1 a.4.1.2 (A:141-183) gamma,delta resolvase (C-terminal domain) {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: gamma,delta resolvase (C-terminal domain)
species: Escherichia coli [TaxId: 562]

Probab=95.77  E-value=0.013  Score=32.32  Aligned_cols=33  Identities=12%  Similarity=0.195  Sum_probs=28.1

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 032366           85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYESG  118 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G  118 (142)
                      +.|++++ +.|++..++|+.+||++++|.++.+.
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            3566666 47999999999999999999998764

>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=95.37  E-value=0.011  Score=35.61  Aligned_cols=38  Identities=21%  Similarity=0.353  Sum_probs=29.1

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCC
Q 032366           94 KKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGV  136 (142)
Q Consensus        94 ~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgv  136 (142)
                      ..++|.++|+.+||+++||+.|.+.     -+.+....+.+|.
T Consensus        24 ~k~sq~eIA~~fGv~~STvs~IlKn-----K~kil~~~~~~g~   61 (66)
T d1hlva1          24 PDLRKGEIARRFNIPPSTLSTILKN-----KRAILASERKYGV   61 (66)
T ss_dssp             TTSCHHHHHHHHTCCHHHHHHHHHT-----HHHHHHHHHHHGG
T ss_pred             CcchHHHHHHHhCCChhHHHHHHHH-----HHHHHHHHHHcCc
Confidence            4489999999999999999999875     3445455555543

>d1k78a1 a.4.1.5 (A:19-81) Pax-5 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Pax-5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.25  E-value=0.025  Score=33.56  Aligned_cols=39  Identities=8%  Similarity=0.243  Sum_probs=33.7

Q ss_pred             cchHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           78 RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        78 ~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .++.++.++|-++-+ .|+|..++|+.++||.+++++|.+
T Consensus        14 Pls~DLR~Riv~~~~-~G~s~r~aA~rf~VS~s~v~k~l~   52 (63)
T d1k78a1          14 PLPDVVRQRIVELAH-QGVRPCDISRQLRVSHGCVSKILG   52 (63)
T ss_dssp             CCCHHHHHHHHHHHH-TTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHH
Confidence            456778888887754 799999999999999999999964

>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=95.15  E-value=0.022  Score=37.07  Aligned_cols=37  Identities=22%  Similarity=0.311  Sum_probs=31.4

Q ss_pred             hHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           80 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +.+.+..++.+.. .|+|+.++|+++|.|+++|+++..
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            4456777877764 699999999999999999999986

>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=94.92  E-value=0.029  Score=33.42  Aligned_cols=35  Identities=9%  Similarity=0.098  Sum_probs=29.9

Q ss_pred             HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ....|+.++..-.+|..|||+.+|+|++||+++.+
T Consensus         8 ~~~Il~~l~~~g~~sr~eLa~~~glS~~Tv~~~l~   42 (71)
T d1z05a1           8 AGRVYKLIDQKGPISRIDLSKESELAPASITKITR   42 (71)
T ss_dssp             HHHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHH
Confidence            34567778888899999999999999999998753

>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=94.90  E-value=0.021  Score=35.75  Aligned_cols=59  Identities=17%  Similarity=0.205  Sum_probs=46.4

Q ss_pred             chHHHHHHHHHHHHhCCCCHHHHHH-HhCCCHHHHHHHHcCCCCCC------HHHHHHHHHHhCCC
Q 032366           79 VPSELKKAIVQARNDKKLTQSQLAQ-LINEKPQVIQEYESGKAIPN------QQILTKLERALGVK  137 (142)
Q Consensus        79 ~~~~~g~~Lk~~R~~~glTQ~eLA~-~lgis~stIs~~E~G~~~p~------~~~l~kLa~~Lgvs  137 (142)
                      +..++.++|++..+.++++|+-||+ .+|.|+.+++.+.+....++      .+.+.+|-..|+.+
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            3456899999999999999999999 57999999999998654442      34566676666643

>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=94.73  E-value=0.035  Score=35.05  Aligned_cols=59  Identities=20%  Similarity=0.227  Sum_probs=47.6

Q ss_pred             chHHHHHHHHHHHHhCCCCHHHHHH-HhCCCHHHHHHHHcCCCCCC------HHHHHHHHHHhCCC
Q 032366           79 VPSELKKAIVQARNDKKLTQSQLAQ-LINEKPQVIQEYESGKAIPN------QQILTKLERALGVK  137 (142)
Q Consensus        79 ~~~~~g~~Lk~~R~~~glTQ~eLA~-~lgis~stIs~~E~G~~~p~------~~~l~kLa~~Lgvs  137 (142)
                      +..++.++|++..+.++++|+-||+ .+|.|+.+++.+.+....|.      .+.+.+|-..|+.+
T Consensus        11 ~T~~Ia~~i~~eL~~~~IsQ~~Fak~vL~rSQGtlSdLLrkpkp~~~~~~sg~e~~~rm~~wL~lP   76 (88)
T d2csfa1          11 ITAAIYDEIQQEMKRAKVSQALFAKVAANKSQGWLCELLRWKENPSPENRTLWENLCTIRRFLNLP   76 (88)
T ss_dssp             CCTHHHHHHHHHHHHHTCCHHHHHHHHTCCCHHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHTSC
T ss_pred             cHHHHHHHHHHHHHHcCCCHHHHHHHHHccCcHHHHHHHcCCCCcchhhHHHHHHHHHHHHHHhCh
Confidence            4567999999999999999999999 57999999999998654442      35677777777654

>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=94.60  E-value=0.03  Score=33.40  Aligned_cols=35  Identities=11%  Similarity=0.069  Sum_probs=30.5

Q ss_pred             HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ....|+.++..-.+|..|||+.+|+|.+||+++-+
T Consensus         7 ~~~Il~~i~~~g~~sr~eLa~~~gLS~~Tvs~iv~   41 (70)
T d1z6ra1           7 AGAVYRLIDQLGPVSRIDLSRLAQLAPASITKIVH   41 (70)
T ss_dssp             HHHHHHHHHSSCSCCHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHH
Confidence            45567888999999999999999999999998754

>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=94.42  E-value=0.1  Score=34.32  Aligned_cols=47  Identities=17%  Similarity=0.243  Sum_probs=40.6

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhC--CCHHHHHHHHcCCCCCCHHHHHHHH
Q 032366           85 KAIVQARNDKKLTQSQLAQLIN--EKPQVIQEYESGKAIPNQQILTKLE  131 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~lg--is~stIs~~E~G~~~p~~~~l~kLa  131 (142)
                      -.|+.+|.-.-||..|-|.-++  ++..+..+||+|+...+.+++..|.
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            3588999999999999999765  6899999999999999988866554

>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=94.20  E-value=0.035  Score=32.80  Aligned_cols=23  Identities=13%  Similarity=0.309  Sum_probs=20.7

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 032366           95 KLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        95 glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .+||.|||..+|+|+.+|++..+
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            38999999999999999998754

>d2ox6a1 a.35.1.6 (A:5-166) Hypothetical protein SO3848 {Shewanella oneidensis [TaxId: 70863]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: YdiL-like
domain: Hypothetical protein SO3848
species: Shewanella oneidensis [TaxId: 70863]

Probab=94.16  E-value=0.13  Score=34.48  Aligned_cols=45  Identities=20%  Similarity=0.273  Sum_probs=37.9

Q ss_pred             HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHH
Q 032366           86 AIVQARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKL  130 (142)
Q Consensus        86 ~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kL  130 (142)
                      .|+.+|...|+|..++++..+.|..-|-.||.|....+.-...+|
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            478899999999999999999999999999999976654433333

>d1rp3a2 a.4.13.2 (A:164-234) Sigma factor sigma-28 (FliA) {Aquifex aeolicus [TaxId: 63363]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma factor sigma-28 (FliA)
species: Aquifex aeolicus [TaxId: 63363]

Probab=94.03  E-value=0.044  Score=32.16  Aligned_cols=34  Identities=12%  Similarity=0.262  Sum_probs=28.2

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .+.+-.++--.|+|+.|+|+.+|+|.++|.....
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            3445566777899999999999999999998753

>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=94.00  E-value=0.015  Score=33.98  Aligned_cols=26  Identities=15%  Similarity=0.164  Sum_probs=22.8

Q ss_pred             HHHHHHHHcCCChhHHHhhhcCCCCC
Q 032366           30 KVVNAARRAGADIETVRKSHAGTNKA   55 (142)
Q Consensus        30 ~~~~~a~r~G~~v~t~kk~~~g~~~~   55 (142)
                      ++-+.|.+.|++.+|+.+||.|...|
T Consensus        14 tQ~elA~~lGvs~~tvs~~E~G~~~P   39 (62)
T d2ppxa1          14 TQEEFSARYHIPLGTLRDWEQGRSEP   39 (62)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHTTSSCC
T ss_pred             CHHHHHHHhCCCHHHHHHHHCCCCCC
Confidence            45678999999999999999998874

>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=93.89  E-value=0.041  Score=35.58  Aligned_cols=52  Identities=12%  Similarity=0.074  Sum_probs=36.8

Q ss_pred             hHHHHHHHHHHHH-hCC-CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHH
Q 032366           80 PSELKKAIVQARN-DKK-LTQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLE  131 (142)
Q Consensus        80 ~~~~g~~Lk~~R~-~~g-lTQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa  131 (142)
                      ...++.|++-++. ..| +||.++++.+|+|..||++.-+--..-+...-..|.
T Consensus        41 ~~~la~R~~ia~~L~~G~~s~reI~~~~gvs~aTItR~s~~Lk~~~~~~k~~L~   94 (101)
T d1jhga_          41 REALGTRVRIIEELLRGEMSQRELKNELGAGIATITRGSNSLKAAPVELRQWLE   94 (101)
T ss_dssp             HHHHHHHHHHHHHHHHCCSCHHHHHHHHCCCHHHHHHHHHHHHHSCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCcCHHHHHHHhCCChHHHHHHHHHHHhCChHHHHHHH
Confidence            3458888888764 367 899999999999999999876533333334333333

>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=93.77  E-value=0.033  Score=32.69  Aligned_cols=32  Identities=19%  Similarity=0.129  Sum_probs=25.6

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      +.|..+....-+|..+||+.+|||++||.+..
T Consensus         9 ~iL~~L~~~~~~s~~eLa~~l~vS~~ti~r~i   40 (63)
T d1biaa1           9 KLIALLANGEFHSGEQLGETLGMSRAAINKHI   40 (63)
T ss_dssp             HHHHHHTTSSCBCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHCCcCCHHHHHHHHCcCHHHHHHHH
Confidence            34555555666899999999999999999864

>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=93.70  E-value=0.059  Score=33.92  Aligned_cols=56  Identities=9%  Similarity=0.099  Sum_probs=43.5

Q ss_pred             hHHHHHHHHHHHHhCCCCHHHHHHH-hCCCHHHHHHHHcCCCCC---C---HHHHHHHHHHhC
Q 032366           80 PSELKKAIVQARNDKKLTQSQLAQL-INEKPQVIQEYESGKAIP---N---QQILTKLERALG  135 (142)
Q Consensus        80 ~~~~g~~Lk~~R~~~glTQ~eLA~~-lgis~stIs~~E~G~~~p---~---~~~l~kLa~~Lg  135 (142)
                      ..++..+|++..+.++++|.-||+. +|.|+.+++.+.+.-...   +   .+...++-..|+
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            4568999999999999999999995 689999999999854322   2   245556666555

>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=93.34  E-value=0.087  Score=30.77  Aligned_cols=32  Identities=22%  Similarity=0.211  Sum_probs=25.6

Q ss_pred             HHHHHHHHhCC-CCHHHHHHHhCCCHHHHHHHH
Q 032366           85 KAIVQARNDKK-LTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        85 ~~Lk~~R~~~g-lTQ~eLA~~lgis~stIs~~E  116 (142)
                      ..|..++...+ +|..+||+.+|||..||.+..
T Consensus        11 ~Il~~L~~~~~~vs~~~La~~l~VS~~TI~rdi   43 (65)
T d1j5ya1          11 SIVRILERSKEPVSGAQLAEELSVSRQVIVQDI   43 (65)
T ss_dssp             HHHHHHHHCSSCBCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHH
Confidence            44555666555 899999999999999999865

>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=93.33  E-value=0.072  Score=30.89  Aligned_cols=34  Identities=15%  Similarity=0.045  Sum_probs=29.9

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .+.|.......+..+.+.|+.+|||++|+.+-..
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            4668888899999999999999999999987654

>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=93.21  E-value=0.06  Score=31.41  Aligned_cols=30  Identities=10%  Similarity=0.182  Sum_probs=25.1

Q ss_pred             HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           87 IVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      |+.+++ ..+|..|||+.+|+|.+||+++-+
T Consensus         5 l~~i~~-~pisr~eLa~~~gls~~TVs~~v~   34 (62)
T d2hoea1           5 LKRIMK-SPVSRVELAEELGLTKTTVGEIAK   34 (62)
T ss_dssp             HHHHHH-SCBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHH-CCcCHHHHHHHHCcCHHHHHHHHH
Confidence            556664 569999999999999999998753

>d2cfxa1 a.4.5.32 (A:1-63) Transcriptional regulator LrpC {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Transcriptional regulator LrpC
species: Bacillus subtilis [TaxId: 1423]

Probab=93.18  E-value=0.11  Score=30.19  Aligned_cols=31  Identities=23%  Similarity=0.395  Sum_probs=26.4

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHH
Q 032366           84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQE  114 (142)
Q Consensus        84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~  114 (142)
                      .+.|..+.....+|..+||+.+|+|+++|.+
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            3456777788889999999999999999875

>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=93.15  E-value=0.21  Score=32.63  Aligned_cols=57  Identities=11%  Similarity=0.108  Sum_probs=44.8

Q ss_pred             chHHHHHHHHHHHHhCCCCHHHHHHH-hCCCHHHHHHHHcCCCCC---C---HHHHHHHHHHhC
Q 032366           79 VPSELKKAIVQARNDKKLTQSQLAQL-INEKPQVIQEYESGKAIP---N---QQILTKLERALG  135 (142)
Q Consensus        79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~-lgis~stIs~~E~G~~~p---~---~~~l~kLa~~Lg  135 (142)
                      -..++.++|++..+.++++|.-||+. +|.|+.+++++.+.-...   +   .+...+|-..|+
T Consensus        28 DT~~Ia~~v~~~L~~~~I~Q~~Fa~~VL~rSQGtlSdLL~~PKPW~kl~~~gR~~y~RM~~wL~   91 (111)
T d1wh8a_          28 DTYSITKRVKEVLTDNNLGQRLFGESILGLTQGSVSDLLSRPKPWHKLSLKGREPFVRMQLWLN   91 (111)
T ss_dssp             CHHHHHHHHHHHHHHTTCCHHHHHHHTTCCCHHHHHHHHHSCCCTTTSCHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHcCchHHHHHHHHHccChHHHHHHHhCCCChhHhhHHHHHHHHHHHHHhc
Confidence            35679999999999999999999995 689999999999854332   2   345666666655

>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=93.05  E-value=0.097  Score=34.51  Aligned_cols=38  Identities=8%  Similarity=0.223  Sum_probs=32.8

Q ss_pred             cchHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           78 RVPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        78 ~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      .+..++..+|-.+- +.|+++.++|+.++||+++|++|.
T Consensus        16 pLs~dlR~rIv~~~-~~G~s~r~iA~~~~VS~~tV~k~l   53 (123)
T d1pdnc_          16 PLPNNIRLKIVEMA-ADGIRPCVISRQLRVSHGCVSKIL   53 (123)
T ss_dssp             CCCHHHHHHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             CCCHHHHHHHHHHH-HhcCCHHHHHHHHCcCHHHHHHHH
Confidence            45667888888875 579999999999999999999996

>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=92.94  E-value=0.041  Score=33.32  Aligned_cols=24  Identities=8%  Similarity=0.156  Sum_probs=21.1

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           94 KKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        94 ~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ..+||.|||..+|+|+.+|++..+
T Consensus        29 ~~lt~~elA~~~g~sretvsr~l~   52 (80)
T d3e5ua1          29 MPLSQKSIGEITGVHHVTVSRVLA   52 (80)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             eCCCHHHHHHHHCCCHHHHHHHHH
Confidence            358999999999999999998753

>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=92.90  E-value=0.035  Score=32.68  Aligned_cols=37  Identities=19%  Similarity=0.274  Sum_probs=28.0

Q ss_pred             CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCC
Q 032366           97 TQSQLAQLINEKPQVIQEYESGKAIPNQQILTKLERALGV  136 (142)
Q Consensus        97 TQ~eLA~~lgis~stIs~~E~G~~~p~~~~l~kLa~~Lgv  136 (142)
                      +...+|+.+|||++.|++|  |+..| ......|...-+-
T Consensus        12 ~~~k~A~algis~~AVsqW--Ge~VP-e~RA~~ie~~T~G   48 (61)
T d1rzsa_          12 TQRAVAKALGISDAAVSQW--KEVIP-EKDAYRLEIVTAG   48 (61)
T ss_dssp             SHHHHHHHHTCCHHHHHHC--CSBCC-HHHHHHHHHHTTS
T ss_pred             CHHHHHHHhCCCHHHHHHH--hccCc-HHHHHHHHHHhCC
Confidence            6778999999999999999  87766 4445566655443

>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=92.83  E-value=0.099  Score=32.31  Aligned_cols=58  Identities=10%  Similarity=0.126  Sum_probs=46.7

Q ss_pred             hHHHHHHHHHHHHhCCCCHHHHHHH-hCCCHHHHHHHHcCC-----CCCCHHHHHHHHHHhCCC
Q 032366           80 PSELKKAIVQARNDKKLTQSQLAQL-INEKPQVIQEYESGK-----AIPNQQILTKLERALGVK  137 (142)
Q Consensus        80 ~~~~g~~Lk~~R~~~glTQ~eLA~~-lgis~stIs~~E~G~-----~~p~~~~l~kLa~~Lgvs  137 (142)
                      ..++..+|++..+.++++|.-||+. +|.|+.+++.+.+.-     -.+..+...++-..|+-+
T Consensus         4 T~~I~~~i~~eL~~~~IsQ~~Fa~~vL~rsQGtlSdLL~kPKPW~~l~~gre~y~RM~~wL~~p   67 (80)
T d1s7ea2           4 TKEVAQRITTELKRYSIPQAIFAQRVLCRSQGTLSDLLRNPKPWSKLKSGRETFRRMWKWLQEP   67 (80)
T ss_dssp             SHHHHHHHHHHHTSSCCCHHHHHHHTSSSCSSHHHHHTTSCCTTCCCSSCHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHHccChHHHHHHHcCCCChhhhcchhHHHHHHHHHHcCH
Confidence            3568999999999999999999995 589999999999732     123567788888887743

>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=92.82  E-value=0.086  Score=30.65  Aligned_cols=31  Identities=13%  Similarity=0.243  Sum_probs=26.5

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHH
Q 032366           84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQE  114 (142)
Q Consensus        84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~  114 (142)
                      .+.|..+.....+|..+||+.+|+|.+++..
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            3456778888899999999999999998865

>d2gaua1 a.4.5.4 (A:152-232) Transcriptional regulator PG0396, C-terminal domain {Porphyromonas gingivalis [TaxId: 837]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: Transcriptional regulator PG0396, C-terminal domain
species: Porphyromonas gingivalis [TaxId: 837]

Probab=92.68  E-value=0.042  Score=33.20  Aligned_cols=39  Identities=26%  Similarity=0.123  Sum_probs=28.9

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc-----CC--------CCCCHHHHHHHHH
Q 032366           94 KKLTQSQLAQLINEKPQVIQEYES-----GK--------AIPNQQILTKLER  132 (142)
Q Consensus        94 ~glTQ~eLA~~lgis~stIs~~E~-----G~--------~~p~~~~l~kLa~  132 (142)
                      ..+||.|||..+|+|+.+|++..+     |-        ...+.+.|.++|+
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            358999999999999999998753     21        2346666666665

>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=92.66  E-value=0.067  Score=30.94  Aligned_cols=49  Identities=24%  Similarity=0.274  Sum_probs=37.2

Q ss_pred             HHHHHcCCChhHHHhhhcCCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHh
Q 032366           33 NAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLI  105 (142)
Q Consensus        33 ~~a~r~G~~v~t~kk~~~g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~l  105 (142)
                      .-|+++|+++.|+.+...|...                        +.++..++|.+..++.|+....+|..|
T Consensus         5 dvA~~agVS~sTVSr~ln~~~~------------------------vs~~tr~rV~~~a~~lgY~pn~~Ar~L   53 (57)
T d1qpza1           5 DVAKRANVSTTTVSHVINKTRF------------------------VAEETRNAVWAAIKELHYSPSAVARSL   53 (57)
T ss_dssp             HHHHHHTSCHHHHHHHHHTCSC------------------------CCHHHHHHHHHHHHHHTCCCCHHHHHH
T ss_pred             HHHHHHCcCHHHHHHHHCCCCc------------------------cCHHHHHHHHHHHHHHCCCCCHHHHHH
Confidence            4689999999999999876432                        445577778888888888777676654

>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=92.40  E-value=0.053  Score=32.59  Aligned_cols=23  Identities=17%  Similarity=0.242  Sum_probs=20.5

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 032366           95 KLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        95 glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .+||++||..+|+++.+|++..+
T Consensus        27 ~lt~~elA~~lg~sr~tvsr~l~   49 (73)
T d1zyba1          27 KVKMDDLARCLDDTRLNISKTLN   49 (73)
T ss_dssp             ECCHHHHHHHHTSCHHHHHHHHH
T ss_pred             ecCHHHHHHHHCCCHHHHHHHHH
Confidence            48999999999999999998753

>d1ft9a1 a.4.5.4 (A:134-213) CO-sensing protein CooA, C-terminal domain {Rhodospirillum rubrum [TaxId: 1085]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: CAP C-terminal domain-like
domain: CO-sensing protein CooA, C-terminal domain
species: Rhodospirillum rubrum [TaxId: 1085]

Probab=92.40  E-value=0.053  Score=32.84  Aligned_cols=22  Identities=23%  Similarity=0.249  Sum_probs=20.2

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHH
Q 032366           95 KLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        95 glTQ~eLA~~lgis~stIs~~E  116 (142)
                      .+||++||..+|+++.||++..
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            5899999999999999999875

>d1i1ga1 a.4.5.32 (A:2-61) LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: LprA
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=92.23  E-value=0.12  Score=29.76  Aligned_cols=31  Identities=6%  Similarity=0.124  Sum_probs=25.5

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHH
Q 032366           85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEY  115 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~  115 (142)
                      +.|..+.....+|..+||+.+|+|+++|.+-
T Consensus         7 kIl~~L~~n~r~s~~~lA~~~gls~~~v~~R   37 (60)
T d1i1ga1           7 IILEILEKDARTPFTEIAKKLGISETAVRKR   37 (60)
T ss_dssp             HHHHHHHHCTTCCHHHHHHHHTSCHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHH
Confidence            3456677778899999999999999988753

>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=92.23  E-value=0.12  Score=30.07  Aligned_cols=33  Identities=9%  Similarity=0.144  Sum_probs=27.6

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      .+.+-.++.-.|+|..|+|+.+|+|.++|...-
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            344556777889999999999999999998765

>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=92.21  E-value=0.12  Score=33.20  Aligned_cols=57  Identities=9%  Similarity=0.080  Sum_probs=43.4

Q ss_pred             chHHHHHHHHHHHHhCCCCHHHHHHH-hCCCHHHHHHHHcCCCCCC------HHHHHHHHHHhC
Q 032366           79 VPSELKKAIVQARNDKKLTQSQLAQL-INEKPQVIQEYESGKAIPN------QQILTKLERALG  135 (142)
Q Consensus        79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~-lgis~stIs~~E~G~~~p~------~~~l~kLa~~Lg  135 (142)
                      ...++..+|++..+.++++|.-||+. +|.|+.+++.+.+.-...+      .+...+|-..|+
T Consensus        18 dT~~I~~~v~~eL~~~~IsQ~~Fa~~VL~rSQGtlSdLL~~PKPW~kl~~~gr~~y~RM~~wL~   81 (101)
T d1wh6a_          18 DTLELTRQVKEKLAKNGICQRIFGEKVLGLSQGSVSDMLSRPKPWSKLTQKGREPFIRMQLWLS   81 (101)
T ss_dssp             CHHHHHHHHHHHHHTTTCCHHHHHHHTTCCCHHHHHHHHHSCCCTTTCCHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHcCCcHHHHHHHHHccChHHHHHHHhCCCCHHHHhHhhhHHHHHHHHHhc
Confidence            35679999999999999999999995 6899999999998543221      244555555544

>d2cyya1 a.4.5.32 (A:5-64) Putative transcriptional regulator PH1519 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Putative transcriptional regulator PH1519
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=92.14  E-value=0.13  Score=29.55  Aligned_cols=30  Identities=23%  Similarity=0.288  Sum_probs=25.6

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHH
Q 032366           85 KAIVQARNDKKLTQSQLAQLINEKPQVIQE  114 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~  114 (142)
                      +.|..+.....+|..+||+.+|+|.++|..
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            446777778889999999999999998865

>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=91.50  E-value=0.62  Score=29.67  Aligned_cols=74  Identities=9%  Similarity=0.050  Sum_probs=44.4

Q ss_pred             HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHH
Q 032366           33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINEKPQV  111 (142)
Q Consensus        33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~st  111 (142)
                      +.|+..|+++.|++-|+. |-..|......-.-+-++..+       +  ..-..|+.+| ..|+|.+++.+.+..+...
T Consensus         8 evA~~~gvs~~tlR~Ye~~GLl~P~~~r~~~gyR~Y~~~~-------l--~~l~~I~~lr-~~g~sl~eIk~~l~~~~~~   77 (118)
T d1r8ea1           8 EVSKLANVSIKALRYYDKIDLFKPAYVDPDTSYRYYTDSQ-------L--IHLDLIKSLK-YIGTPLEEMKKAQDLEMEE   77 (118)
T ss_dssp             HHHHHHTCCHHHHHHHHHTTSSCCSEECTTTCCEEEETGG-------G--GHHHHHHHHH-HTTCCHHHHHHHTTSCHHH
T ss_pred             HHHHHHCcCHHHHHHHHHcCCcccccccCCCCcccccHHH-------H--HHHHHHHHHH-HcCCCHHHHHHHHccCHHH
Confidence            478999999999999997 334432110000111122211       1  1334566665 4899999999988877665


Q ss_pred             HHHHH
Q 032366          112 IQEYE  116 (142)
Q Consensus       112 Is~~E  116 (142)
                      +..+.
T Consensus        78 ~~~~l   82 (118)
T d1r8ea1          78 LFAFY   82 (118)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            55543

>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=91.04  E-value=0.16  Score=29.23  Aligned_cols=49  Identities=18%  Similarity=0.287  Sum_probs=35.5

Q ss_pred             HHHHHcCCChhHHHhhhcCCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHh
Q 032366           33 NAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLI  105 (142)
Q Consensus        33 ~~a~r~G~~v~t~kk~~~g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~l  105 (142)
                      .-|+++|+++.|+.+...|...                        +.++..++|.+.-++.|+....+|..|
T Consensus         6 dvA~~agvS~~TVSr~Ln~~~~------------------------Vs~~tr~rV~~aa~~lgY~pn~~A~~L   54 (57)
T d2hsga1           6 DVAREASVSMATVSRVVNGNPN------------------------VKPSTRKKVLETIERLGYRPNAVARGL   54 (57)
T ss_dssp             HHHHHTTSCHHHHHHHHTTCTT------------------------SCHHHHHHHHHHHHHHTCCSCHHHHHH
T ss_pred             HHHHHHCcCHHHHHHHhCCCCc------------------------CCHHHHHHHHHHHHHHCcCCCHHHHHh
Confidence            4689999999999999875432                        445567777777777777665566544

>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=90.96  E-value=0.084  Score=34.49  Aligned_cols=25  Identities=20%  Similarity=0.296  Sum_probs=21.9

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHH-cCC
Q 032366           95 KLTQSQLAQLINEKPQVIQEYE-SGK  119 (142)
Q Consensus        95 glTQ~eLA~~lgis~stIs~~E-~G~  119 (142)
                      .-||.++|+.+|||+.++.+|- +.+
T Consensus        36 kktqeqiAeelGisr~tLyrWrt~dk   61 (120)
T d2ao9a1          36 KRTQDEMANELGINRTTLWEWRTKNQ   61 (120)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHHHCH
T ss_pred             hhhHHHHHHHhChhHHHHHHHhhcch
Confidence            4599999999999999999998 444

>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=90.73  E-value=0.12  Score=30.26  Aligned_cols=26  Identities=8%  Similarity=0.086  Sum_probs=22.8

Q ss_pred             HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           92 NDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        92 ~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ...|+|..++|+.+|+|..||..+..
T Consensus        18 l~~G~s~~eIA~~l~iS~~TV~~~~~   43 (67)
T d1a04a1          18 IAQGLPNKMIARRLDITESTVKVHVK   43 (67)
T ss_dssp             HHTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHhCCCHHHHHHHHCCCHHHHHHHHH
Confidence            34699999999999999999988764

>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=90.61  E-value=0.2  Score=31.15  Aligned_cols=34  Identities=3%  Similarity=-0.009  Sum_probs=29.3

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ...|..+....+..+.+.|+.+|||++|+.+..+
T Consensus        51 ~~~i~~aL~~~~gn~~~aA~~LGisR~tL~~klk   84 (89)
T d1etxa_          51 QPLLDMVMQYTRGNATRAALMMGINRGTLRKKLK   84 (89)
T ss_dssp             HHHHHHHHHHTTTCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCcHHHHHHHHCCCHHHHHHHHH
Confidence            4556788899999999999999999999987653

>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=90.49  E-value=0.14  Score=31.57  Aligned_cols=55  Identities=16%  Similarity=0.163  Sum_probs=35.6

Q ss_pred             HHHHHHHHcCCChhHHHhhhcCCCCCCCCCCCcccccchhhhccc--cCCcchHHHHHHHHHHH
Q 032366           30 KVVNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTENL--AHDRVPSELKKAIVQAR   91 (142)
Q Consensus        30 ~~~~~a~r~G~~v~t~kk~~~g~~~~~~~~~~~~~~kl~~~~~~~--~~~~~~~~~g~~Lk~~R   91 (142)
                      ++-..|.+.|++.+++.+||.|.+.       +.+..+..-...|  .+..+...+.+.+.+..
T Consensus        27 tq~~lA~~lgis~~~is~~E~g~~~-------~s~~~l~~ia~~l~v~~~~~~~~~~~~~~~~~   83 (87)
T d1lmb3_          27 SQESVADKMGMGQSGVGALFNGINA-------LNAYNAALLAKILKVSVEEFSPSIAREIYEMY   83 (87)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHTTSSC-------CCHHHHHHHHHHHTSCGGGTCHHHHHHHHHHH
T ss_pred             CHHHHHHHhCccHHHHHHHHhccCC-------CcHHHHHHHHHHHCCCHHHHChhHHHHHHHHH
Confidence            4567899999999999999999987       3344433333333  33455555666555443

>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=90.45  E-value=0.3  Score=29.83  Aligned_cols=34  Identities=24%  Similarity=0.237  Sum_probs=25.8

Q ss_pred             HHHHHHHHHh------CCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           84 KKAIVQARND------KKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        84 g~~Lk~~R~~------~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ...|..++..      -++|+.+||+.+|+++++++++.+
T Consensus         4 ~~~l~~l~~~~~~~~~~~lt~~eLa~~l~i~~~~vs~~l~   43 (85)
T d3ctaa1           4 YRAIKKIKEAAEASNRAYLTSSKLADMLGISQQSASRIII   43 (85)
T ss_dssp             HHHHHHHHHHTTTSSEEECCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHhhhccCCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            4445555543      368999999999999999988753

>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=90.41  E-value=0.11  Score=33.21  Aligned_cols=39  Identities=15%  Similarity=0.117  Sum_probs=29.3

Q ss_pred             CCCHHHHHHHhCCC-HHHHHHHHc-----CC--------CCCCHHHHHHHHHH
Q 032366           95 KLTQSQLAQLINEK-PQVIQEYES-----GK--------AIPNQQILTKLERA  133 (142)
Q Consensus        95 glTQ~eLA~~lgis-~stIs~~E~-----G~--------~~p~~~~l~kLa~~  133 (142)
                      .+||.|||..+|+| +.||++..+     |-        ..++.+.|.++|.-
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 899887653     11        24577778777754

>d2d1ha1 a.4.5.50 (A:1-109) Hypothetical transcriptional regulator ST1889 {Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: TrmB-like
domain: Hypothetical transcriptional regulator ST1889
species: Sulfolobus tokodaii [TaxId: 111955]

Probab=90.39  E-value=0.2  Score=31.65  Aligned_cols=36  Identities=11%  Similarity=0.153  Sum_probs=27.2

Q ss_pred             HHHHHHHHHHHHhCC-CCHHHHHHHhCCCHHHHHHHH
Q 032366           81 SELKKAIVQARNDKK-LTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        81 ~~~g~~Lk~~R~~~g-lTQ~eLA~~lgis~stIs~~E  116 (142)
                      ..-...|..+....| +|+.+||+.+|+++++|++..
T Consensus        21 ~~~~~iL~~L~~~~~~~t~~eLa~~~~i~~~tvs~~l   57 (109)
T d2d1ha1          21 DTDVAVLLKMVEIEKPITSEELADIFKLSKTTVENSL   57 (109)
T ss_dssp             HHHHHHHHHHHHHCSCEEHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCCCHHHHHHHHCccHhHHHHHH
Confidence            333445555655554 999999999999999998865

>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=90.30  E-value=0.22  Score=32.07  Aligned_cols=35  Identities=6%  Similarity=0.057  Sum_probs=29.3

Q ss_pred             HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      -.+.+-.++--.|||+.++|+.+|||+++|.....
T Consensus        20 ~qR~v~~L~y~~~ls~~EIA~~lgiS~~aV~~~l~   54 (106)
T d1s7oa_          20 KQMNYIELYYADDYSLAEIADEFGVSRQAVYDNIK   54 (106)
T ss_dssp             HHHHHHHHHHHTCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence            34556677888999999999999999999987664

>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=89.65  E-value=0.36  Score=27.61  Aligned_cols=25  Identities=24%  Similarity=0.373  Sum_probs=21.8

Q ss_pred             HHHHHHHHcCCChhHHHhhhcCCCC
Q 032366           30 KVVNAARRAGADIETVRKSHAGTNK   54 (142)
Q Consensus        30 ~~~~~a~r~G~~v~t~kk~~~g~~~   54 (142)
                      ++-..|.+.|++..|+.+||.|...
T Consensus        18 tq~~lA~~~gvs~~ti~~~E~g~~~   42 (65)
T d2croa_          18 TQTELATKAGVKQQSIQLIEAGVTK   42 (65)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHTTCCS
T ss_pred             CHHHHHHHHCcCHhHHHHHHCCCCC
Confidence            4566899999999999999999765

>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=89.65  E-value=0.64  Score=30.27  Aligned_cols=72  Identities=13%  Similarity=0.125  Sum_probs=42.7

Q ss_pred             HHHHHHHcCCChhHHHhhhc-----CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHH-HhCCCCHHHHHHH
Q 032366           31 VVNAARRAGADIETVRKSHA-----GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQAR-NDKKLTQSQLAQL  104 (142)
Q Consensus        31 ~~~~a~r~G~~v~t~kk~~~-----g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R-~~~glTQ~eLA~~  104 (142)
                      .-.+|++.|++.+|+.+|-.     |...+.+...++ ...            ..+.....|..+. ..-.+|..||.+.
T Consensus        35 ~r~iA~~~~VS~~tV~k~l~r~~~~G~~~~~~~~~~r-pr~------------~t~~~~~~I~~~~~~~P~~t~~El~~~  101 (123)
T d1pdnc_          35 PCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSK-PRI------------ATPEIENRIEEYKRSSPGMFSWEIREK  101 (123)
T ss_dssp             HHHHHHHHTCCHHHHHHHHHHHHHHCCSSCCCCSCCC-CCS------------SCSTHHHHHHHTTTTCTTCCHHHHHHH
T ss_pred             HHHHHHHHCcCHHHHHHHHHHHHccCCcCcCCCCCCC-CCC------------CCHHHHHHHHHHHHhCCCccHHHHHHH
Confidence            34689999999999999854     766543322111 111            1112334454443 3456788888776


Q ss_pred             h----------CCCHHHHHHH
Q 032366          105 I----------NEKPQVIQEY  115 (142)
Q Consensus       105 l----------gis~stIs~~  115 (142)
                      +          -.|.+||+++
T Consensus       102 L~~egv~~~~~~pSvStI~Ri  122 (123)
T d1pdnc_         102 LIREGVCDRSTAPSVSAISRL  122 (123)
T ss_dssp             HHHTSSSCSTTCCCHHHHHHH
T ss_pred             HHHcCCCCCCCCCChhhHhhc
Confidence            6          2367777765

>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=89.63  E-value=0.09  Score=30.43  Aligned_cols=25  Identities=4%  Similarity=0.101  Sum_probs=22.0

Q ss_pred             HHHHHHHHcCCChhHHHhhhcCCCC
Q 032366           30 KVVNAARRAGADIETVRKSHAGTNK   54 (142)
Q Consensus        30 ~~~~~a~r~G~~v~t~kk~~~g~~~   54 (142)
                      ++...|.+.|++.+|+.+||.|...
T Consensus        18 tq~~lA~~~gvs~~~i~~~e~g~~~   42 (66)
T d2r1jl1          18 RQAALGKMVGVSNVAISQWERSETE   42 (66)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHTTSSC
T ss_pred             CHHHHHHHHCCCHHHHHHHHcCCCC
Confidence            4566899999999999999999876

>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=89.60  E-value=0.34  Score=28.01  Aligned_cols=25  Identities=12%  Similarity=0.221  Sum_probs=23.0

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           93 DKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        93 ~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ...+|..++|+.+|||...|.+++.
T Consensus        26 ~~~~tl~eIa~~lgiS~erVrqi~~   50 (61)
T d1ku3a_          26 GREHTLEEVGAYFGVTRERIRQIEN   50 (61)
T ss_dssp             SSCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHH
Confidence            5679999999999999999999985

>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=89.28  E-value=0.0032  Score=42.39  Aligned_cols=25  Identities=16%  Similarity=0.302  Sum_probs=22.8

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           93 DKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        93 ~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ++||||.|+|+.+|.|++.|+-+|+
T Consensus         3 ~kGltQ~eIA~~LgTSraNIs~IEk   27 (122)
T d1nr3a_           3 ERGWSQKKIARELKTTRQNVSAIER   27 (122)
T ss_dssp             CCSCSSCSTHHHHHHCCSSSCCHHH
T ss_pred             cccCCHHHHHHHHCccHHHHHHHHH
Confidence            5899999999999999998888885

>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=89.06  E-value=0.089  Score=31.56  Aligned_cols=22  Identities=23%  Similarity=0.466  Sum_probs=20.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +++++||+.+|||..||..|-+
T Consensus         3 Vnk~~lA~iFGVS~~TI~~W~~   24 (68)
T d1j9ia_           3 VNKKQLADIFGASIRTIQNWQE   24 (68)
T ss_dssp             EEHHHHHHHTTCCHHHHHHHTT
T ss_pred             cCHHHHHHHhCCCHHHHHHHHH
Confidence            5789999999999999999975

>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=89.03  E-value=0.19  Score=29.21  Aligned_cols=26  Identities=12%  Similarity=0.026  Sum_probs=23.2

Q ss_pred             HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           92 NDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        92 ~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ...|+|.+|+|+.+|+|..||..+..
T Consensus        16 ~~~G~s~~eIA~~L~is~~TV~~~~~   41 (67)
T d1fsea_          16 LVQDKTTKEIASELFISEKTVRNHIS   41 (67)
T ss_dssp             HTTTCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHccCCHHHHHHHHCCCHHHHHHHHH
Confidence            45799999999999999999988764

>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=88.92  E-value=0.015  Score=34.38  Aligned_cols=26  Identities=12%  Similarity=0.105  Sum_probs=22.2

Q ss_pred             HHHHHHHHHcCCChhHHHhhhcCCCC
Q 032366           29 EKVVNAARRAGADIETVRKSHAGTNK   54 (142)
Q Consensus        29 ~~~~~~a~r~G~~v~t~kk~~~g~~~   54 (142)
                      =++-..|++.|++.+|+.+||.|...
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            35567899999999999999999754

>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=88.88  E-value=0.11  Score=30.38  Aligned_cols=26  Identities=19%  Similarity=0.068  Sum_probs=22.8

Q ss_pred             HHHHHHHHHcCCChhHHHhhhcCCCC
Q 032366           29 EKVVNAARRAGADIETVRKSHAGTNK   54 (142)
Q Consensus        29 ~~~~~~a~r~G~~v~t~kk~~~g~~~   54 (142)
                      =++-..|.+.|++.+++.+||.|...
T Consensus        23 ltq~~lA~~~gis~~~i~~~E~g~~~   48 (69)
T d1y7ya1          23 LSQETLAFLSGLDRSYVGGVERGQRN   48 (69)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHTTCSC
T ss_pred             CCHHHHHhHhCCCHHHHHHHHCCCCC
Confidence            35567899999999999999999876

>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=88.86  E-value=0.23  Score=31.46  Aligned_cols=23  Identities=17%  Similarity=0.359  Sum_probs=21.5

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHc
Q 032366           95 KLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        95 glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .+|..|||+.+|||+.||.-||+
T Consensus         2 ~ytI~e~A~~~gvs~~tlR~Ye~   24 (109)
T d1r8da_           2 KYQVKQVAEISGVSIRTLHHYDN   24 (109)
T ss_dssp             CBCHHHHHHHHSCCHHHHHHHHH
T ss_pred             cccHHHHHHHHCcCHHHHHHHHH
Confidence            47899999999999999999996

>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=88.83  E-value=0.16  Score=31.17  Aligned_cols=43  Identities=14%  Similarity=0.156  Sum_probs=31.1

Q ss_pred             HHHHHHH-HHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHH
Q 032366           83 LKKAIVQ-ARNDKKLTQSQLAQLINEKPQVIQEYESGKAIPNQQ  125 (142)
Q Consensus        83 ~g~~Lk~-~R~~~glTQ~eLA~~lgis~stIs~~E~G~~~p~~~  125 (142)
                      +++.|.. .-.-..+|..+||+.+|+|++||.++.+.-..-...
T Consensus        23 ia~yil~~~~~~~~~si~~lA~~~~vS~sTi~Rf~kklG~~gf~   66 (83)
T d2o3fa1          23 LADYILAHPHKAIESTVNEISALANSSDAAVIRLCKSLGLKGFQ   66 (83)
T ss_dssp             HHHHHHHCHHHHHTCCHHHHHHHTTCCHHHHHHHHHHTTCSSHH
T ss_pred             HHHHHHcCHHHHHHccHHHHHHHHCCCHHHHHHHHHHhCCCCHH
Confidence            4454433 344467999999999999999999999844444433

>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=88.73  E-value=0.46  Score=29.06  Aligned_cols=48  Identities=10%  Similarity=0.150  Sum_probs=37.4

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHcC----CCCCCHHHHHHHHHHhCCCCCC
Q 032366           93 DKKLTQSQLAQLINEKPQVIQEYESG----KAIPNQQILTKLERALGVKLRG  140 (142)
Q Consensus        93 ~~glTQ~eLA~~lgis~stIs~~E~G----~~~p~~~~l~kLa~~Lgvsl~e  140 (142)
                      ..|++.+++|+.+++|..||..+-+.    -...+...+...|..+|+-+-|
T Consensus        35 ~~G~s~~eIA~~l~iS~~TV~~~~~~i~~Kl~~~~~~~lv~~a~~~gl~~~~   86 (87)
T d1p4wa_          35 AEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVDNDIALLNYLSSVSMTPVD   86 (87)
T ss_dssp             HHTCCHHHHHHHHTSCHHHHHHHHHHHHHHHTCSSHHHHHHHHHHHTCSSCC
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCCCCHHHHHHHHHHcCCCCCC
Confidence            45999999999999999999887652    2355777777888888865443

>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=88.72  E-value=0.18  Score=29.18  Aligned_cols=50  Identities=18%  Similarity=0.267  Sum_probs=34.8

Q ss_pred             HHHHHHcCCChhHHHhhhcCCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHh
Q 032366           32 VNAARRAGADIETVRKSHAGTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLI  105 (142)
Q Consensus        32 ~~~a~r~G~~v~t~kk~~~g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~l  105 (142)
                      -+-|+++|+++.|+.++..|...                        +.++..++|.+.-+++|+....+|..|
T Consensus         6 ~diA~~agvS~sTVSr~l~~~~~------------------------vs~~tr~rI~~~a~~lgY~pn~~Ar~L   55 (59)
T d1efaa1           6 YDVAEYAGVSYQTVSRVVNQASH------------------------VSAKTREKVEAAMAELNYIPNRVAQQL   55 (59)
T ss_dssp             HHHHHTTTSCHHHHHHHHTTCSS------------------------CCTHHHHHHHHHHHHHTCCCCHHHHHH
T ss_pred             HHHHHHHCCCHHHHHHHHCCCCc------------------------CCHHHHHHHHHHHHHHCCCcCHHHHHH
Confidence            45789999999999999876543                        233456667776666666655555544

>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=88.44  E-value=0.23  Score=28.74  Aligned_cols=45  Identities=13%  Similarity=-0.002  Sum_probs=30.6

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHcCC----CCCCHHHHHHHHHHhC
Q 032366           91 RNDKKLTQSQLAQLINEKPQVIQEYESGK----AIPNQQILTKLERALG  135 (142)
Q Consensus        91 R~~~glTQ~eLA~~lgis~stIs~~E~G~----~~p~~~~l~kLa~~Lg  135 (142)
                      ....|+|-+|+|+.+|+|..||..+-+.-    ...+...+..+|.-+|
T Consensus        15 l~~~G~s~~eIA~~l~iS~~TV~~~~~~i~~Klgv~~r~~l~~~a~~~g   63 (65)
T d1l3la1          15 WIAVGKTMEEIADVEGVKYNSVRVKLREAMKRFDVRSKAHLTALAIRRK   63 (65)
T ss_dssp             HHTTTCCHHHHHHHHTCCHHHHHHHHHHHHHHHTCSSHHHHHHHHHHTT
T ss_pred             HHHhcCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCCCHHHHHHHHHHcC
Confidence            34569999999999999999998876421    2334444444544443

>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=88.44  E-value=0.62  Score=26.69  Aligned_cols=33  Identities=12%  Similarity=0.066  Sum_probs=26.6

Q ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           84 KKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        84 g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      .+.|.......| +..+.|+.+||+++|+.+-.+
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            455677777777 788999999999999987654

>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=88.39  E-value=0.12  Score=30.56  Aligned_cols=28  Identities=11%  Similarity=-0.034  Sum_probs=23.8

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 032366           93 DKKLTQSQLAQLINEKPQVIQEYESGKA  120 (142)
Q Consensus        93 ~~glTQ~eLA~~lgis~stIs~~E~G~~  120 (142)
                      -.++|..++|+.+|||+++|.++-.++.
T Consensus        22 ~~~~s~~~Ia~~agvs~~t~Y~~F~~K~   49 (74)
T d1v7ba1          22 LETLSYDSLAEATGLSKSGLIYHFPSRH   49 (74)
T ss_dssp             STTCCHHHHHHHHCSCHHHHHHHCSSHH
T ss_pred             ccccCHHHHHHHhCcCcchHhhhCCCHH
Confidence            3467999999999999999999976553

>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=88.07  E-value=0.36  Score=31.00  Aligned_cols=35  Identities=11%  Similarity=0.096  Sum_probs=29.3

Q ss_pred             HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      -.+.+-.+|--.|+|..|+|+.+|||+++|.....
T Consensus        22 ~QR~vl~L~~~e~ls~~EIA~~lgiS~~aV~~~l~   56 (106)
T d1xsva_          22 KQRNYLELFYLEDYSLSEIADTFNVSRQAVYDNIR   56 (106)
T ss_dssp             HHHHHHHHHHTSCCCHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCcHHHHHHHHCcCHHHHHHHHH
Confidence            34456678888999999999999999999987654

>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=87.97  E-value=0.25  Score=29.07  Aligned_cols=26  Identities=12%  Similarity=0.072  Sum_probs=22.7

Q ss_pred             HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           92 NDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        92 ~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ...|+|.+++|..+|+|..||..+-.
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            45699999999999999999988753

>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=87.67  E-value=0.19  Score=32.35  Aligned_cols=22  Identities=14%  Similarity=0.342  Sum_probs=20.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      +|..+||+.+|||..||.-||+
T Consensus         4 ytI~evA~~~gvs~~tlR~Ye~   25 (118)
T d1r8ea1           4 YSIGEVSKLANVSIKALRYYDK   25 (118)
T ss_dssp             EEHHHHHHHHTCCHHHHHHHHH
T ss_pred             ccHHHHHHHHCcCHHHHHHHHH
Confidence            5788999999999999999997

>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=87.65  E-value=0.54  Score=30.52  Aligned_cols=38  Identities=5%  Similarity=0.017  Sum_probs=30.3

Q ss_pred             hHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           80 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ...-...|..+...-++|+.+||+.+|+++++|+++.+
T Consensus        29 t~~q~~iL~~i~~~~~~t~~~la~~l~i~~~tvs~~l~   66 (139)
T d2a61a1          29 TPAQFDILQKIYFEGPKRPGELSVLLGVAKSTVTGLVK   66 (139)
T ss_dssp             CHHHHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHhCCCcccchHHHH
Confidence            34445566677677799999999999999999988753

>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=87.65  E-value=0.25  Score=29.34  Aligned_cols=24  Identities=13%  Similarity=0.238  Sum_probs=22.0

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           94 KKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        94 ~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ..+|..++|+.+|||+..|.++|.
T Consensus        24 ~~~tl~eI~~~lgiSrerVrqie~   47 (68)
T d2p7vb1          24 TDYTLEEVGKQFDVTRERIRQIEA   47 (68)
T ss_dssp             SCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CcCCHHHHHHHHCCCHHHHHHHHH
Confidence            348999999999999999999996

>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=87.16  E-value=0.29  Score=30.16  Aligned_cols=32  Identities=9%  Similarity=0.059  Sum_probs=27.8

Q ss_pred             HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           85 KAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        85 ~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ..|.......+..+.+.|+.+||+++|+.+-.
T Consensus        54 ~lI~~aL~~~~Gn~~~AA~~LGI~R~TL~~Kl   85 (91)
T d1ntca_          54 TLLTTALRHTQGHKQEAARLLGWGAATLTAKL   85 (91)
T ss_dssp             HHHHHHHHHTTTCTTHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHHhCCcHHHHHHHHCCCHHHHHHHH
Confidence            35788889999999999999999999998643

>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=87.14  E-value=0.23  Score=29.57  Aligned_cols=26  Identities=19%  Similarity=0.249  Sum_probs=22.9

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           91 RNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        91 R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      +...++|..|+|+.+|++++++.++.
T Consensus        16 ~~~~~~s~~eia~~~~~~~st~~rll   41 (75)
T d1mkma1          16 KNPGDVSVSEIAEKFNMSVSNAYKYM   41 (75)
T ss_dssp             HCSSCBCHHHHHHHTTCCHHHHHHHH
T ss_pred             hCCCCCCHHHHHHHHCcCHHHHHHHH
Confidence            34568999999999999999999985

>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=86.89  E-value=0.17  Score=29.29  Aligned_cols=25  Identities=8%  Similarity=-0.028  Sum_probs=21.9

Q ss_pred             HHHHHHHHcCCChhHHHhhhcCCCC
Q 032366           30 KVVNAARRAGADIETVRKSHAGTNK   54 (142)
Q Consensus        30 ~~~~~a~r~G~~v~t~kk~~~g~~~   54 (142)
                      ++-..|.+.|++.+|+.+|+.|...
T Consensus        16 tq~elA~~~gis~~~is~~e~g~~~   40 (66)
T d1utxa_          16 SQSELAALLEVSRQTINGIEKNKYN   40 (66)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHTTSCC
T ss_pred             CHHHHHHhcccCHHHHHHHHcCCCC
Confidence            4456799999999999999999876

>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=86.63  E-value=0.37  Score=31.27  Aligned_cols=22  Identities=23%  Similarity=0.385  Sum_probs=20.7

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHc
Q 032366           96 LTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~  117 (142)
                      |+..|||+.+|||..||.-||+
T Consensus         1 m~Ige~A~~~gvs~~TlR~Ye~   22 (127)
T d1q06a_           1 MNISDVAKITGLTSKAIRFYEE   22 (127)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH
Confidence            6788999999999999999996

>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=86.42  E-value=0.2  Score=29.75  Aligned_cols=25  Identities=16%  Similarity=0.119  Sum_probs=22.4

Q ss_pred             HHHHHHHHcCCChhHHHhhhcCCCC
Q 032366           30 KVVNAARRAGADIETVRKSHAGTNK   54 (142)
Q Consensus        30 ~~~~~a~r~G~~v~t~kk~~~g~~~   54 (142)
                      ++-..|.+.|++..|+.+||.|...
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            5677999999999999999999865

>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=86.37  E-value=0.76  Score=28.87  Aligned_cols=37  Identities=5%  Similarity=0.036  Sum_probs=29.3

Q ss_pred             hHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           80 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ...-...+..+...-.+|+.+||+.+|+++++|+.+.
T Consensus        19 t~~e~~v~~~L~~~g~~t~~eia~~~~i~~~~v~~~l   55 (109)
T d1sfxa_          19 KPSDVRIYSLLLERGGMRVSEIARELDLSARFVRDRL   55 (109)
T ss_dssp             CHHHHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHH
T ss_pred             CHHHHHHHHHHHhcCCCCHHHHHHHhCCCcchHHHHH
Confidence            3444555666677788999999999999999998765

>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=86.33  E-value=0.14  Score=30.82  Aligned_cols=29  Identities=10%  Similarity=0.108  Sum_probs=24.7

Q ss_pred             ccCHHHHHHHHHcCCChhHHHhhhcCCCC
Q 032366           26 KKDEKVVNAARRAGADIETVRKSHAGTNK   54 (142)
Q Consensus        26 ~~~~~~~~~a~r~G~~v~t~kk~~~g~~~   54 (142)
                      .++-++-..|...|++..++.+||.|...
T Consensus        17 ~~gltq~~lA~~~gis~~~is~~E~G~~~   45 (78)
T d1x57a1          17 SKGLTQKDLATKINEKPQVIADYESGRAI   45 (78)
T ss_dssp             TTTCCHHHHHHHHTSCHHHHHHHHHTCSC
T ss_pred             HcCCChhHHHHcCCCCHHHHHHHHccCCC
Confidence            34446778899999999999999999876

>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=86.03  E-value=0.24  Score=30.29  Aligned_cols=23  Identities=39%  Similarity=0.478  Sum_probs=20.4

Q ss_pred             HHHHHHcCCChhHHHhhhcCCCC
Q 032366           32 VNAARRAGADIETVRKSHAGTNK   54 (142)
Q Consensus        32 ~~~a~r~G~~v~t~kk~~~g~~~   54 (142)
                      -..|.++|++.+++.+||.|+..
T Consensus        29 ~eLA~~~Gvs~~~ls~iE~G~~~   51 (82)
T d2ofya1          29 VTVAFDAGISVETLRKIETGRIA   51 (82)
T ss_dssp             HHHHHHHTCCHHHHHHHHTTCCS
T ss_pred             HHHHHHHcCCHHHHHHHHcCCcC
Confidence            36899999999999999999754

>d1t56a1 a.4.1.9 (A:22-94) Ethr repressor {Mycobacterium tuberculosis [TaxId: 1773]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Ethr repressor
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=85.92  E-value=0.16  Score=29.72  Aligned_cols=26  Identities=15%  Similarity=0.092  Sum_probs=22.7

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 032366           94 KKLTQSQLAQLINEKPQVIQEYESGK  119 (142)
Q Consensus        94 ~glTQ~eLA~~lgis~stIs~~E~G~  119 (142)
                      .++|..++|+.+|||++++.++-.++
T Consensus        22 ~~~t~~~Ia~~agvs~~t~Y~~F~~K   47 (73)
T d1t56a1          22 ADISVDDLAKGAGISRPTFYFYFPSK   47 (73)
T ss_dssp             GGCCHHHHHHHHTCCHHHHHHHCSSH
T ss_pred             ccCCHHHHHHHhCCCHHHHHHHCcCH
Confidence            35799999999999999999997654

>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=85.76  E-value=0.85  Score=26.21  Aligned_cols=33  Identities=9%  Similarity=0.114  Sum_probs=27.1

Q ss_pred             HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCC
Q 032366           87 IVQARNDKKLTQSQLAQLINEKPQVIQEYESGK  119 (142)
Q Consensus        87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~  119 (142)
                      |-..+--.++|..++|+.+|+|+.++..+-.++
T Consensus        12 lf~~~G~~~~ti~~Ia~~agvs~~~~Y~~F~~K   44 (69)
T d2i10a1          12 LFWRQGYEGTSITDLTKALGINPPSLYAAFGSK   44 (69)
T ss_dssp             HHHHHTTTTCCHHHHHHHHTCCHHHHHHHHCSH
T ss_pred             HHHHHCcccCCHHHHHHHhCCChhHHHHHCcCH
Confidence            334455568899999999999999999998665

>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=85.66  E-value=0.11  Score=30.43  Aligned_cols=27  Identities=19%  Similarity=0.261  Sum_probs=23.2

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 032366           94 KKLTQSQLAQLINEKPQVIQEYESGKA  120 (142)
Q Consensus        94 ~glTQ~eLA~~lgis~stIs~~E~G~~  120 (142)
                      .++|..++|+.+|+|+++|.++-.++.
T Consensus        22 ~~~t~~~Ia~~agvs~~~iy~hF~~K~   48 (68)
T d1z0xa1          22 EQLSMRKVAKQLGVQAPAIYWYFKNKQ   48 (68)
T ss_dssp             GGCCHHHHHHHHTSCHHHHHTTCSSHH
T ss_pred             cccCHHHHHHHHCcchhHHHHhcCCHH
Confidence            468999999999999999999865543

>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=85.65  E-value=0.18  Score=29.93  Aligned_cols=27  Identities=15%  Similarity=0.176  Sum_probs=23.3

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 032366           94 KKLTQSQLAQLINEKPQVIQEYESGKA  120 (142)
Q Consensus        94 ~glTQ~eLA~~lgis~stIs~~E~G~~  120 (142)
                      .++|..++|+.+|+|++++.++-.++.
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            467999999999999999999976553

>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=85.57  E-value=1.3  Score=27.64  Aligned_cols=64  Identities=11%  Similarity=0.177  Sum_probs=37.9

Q ss_pred             HHHHHcCCChhHHHhhhc-CCCCCCCCCCCcccccchhhhccccCCcchHHHHHHHHHHHHhCCCCHHHHHHHhCC
Q 032366           33 NAARRAGADIETVRKSHA-GTNKAASSSTSLNTRKLDEDTENLAHDRVPSELKKAIVQARNDKKLTQSQLAQLINE  107 (142)
Q Consensus        33 ~~a~r~G~~v~t~kk~~~-g~~~~~~~~~~~~~~kl~~~~~~~~~~~~~~~~g~~Lk~~R~~~glTQ~eLA~~lgi  107 (142)
                      ..|+.+|+++.|++-|+. |-..|..... -.-+.++.+         ....-..|+.+| ..|+|..++.+.+..
T Consensus         7 e~A~~~gvs~~tlR~Ye~~GLl~p~~r~~-~gyR~Y~~~---------~~~~l~~I~~lr-~~G~sl~eI~~~l~~   71 (109)
T d1r8da_           7 QVAEISGVSIRTLHHYDNIELLNPSALTD-AGYRLYSDA---------DLERLQQILFFK-EIGFRLDEIKEMLDH   71 (109)
T ss_dssp             HHHHHHSCCHHHHHHHHHTTSSCCSEECT-TCCEEBCHH---------HHHHHHHHHHHH-HTTCCHHHHHHHHHC
T ss_pred             HHHHHHCcCHHHHHHHHHcCCcCCcccCC-cccccccHH---------HHHHHHHHHHHH-HcCCCHHHHHHHHhc
Confidence            478999999999999997 3333221110 111111111         111235566666 489999999887754

>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=85.56  E-value=0.16  Score=29.06  Aligned_cols=29  Identities=21%  Similarity=0.110  Sum_probs=24.6

Q ss_pred             HhCCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 032366           92 NDKKLTQSQLAQLINEKPQVIQEYESGKA  120 (142)
Q Consensus        92 ~~~glTQ~eLA~~lgis~stIs~~E~G~~  120 (142)
                      --.++|..++|+.+|||+++|..+-.++.
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            34568999999999999999999976653

>d2g7sa1 a.4.1.9 (A:3-76) Putative transcriptional regulator Atu0279 {Agrobacterium tumefaciens [TaxId: 358]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator Atu0279
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=85.51  E-value=0.33  Score=28.46  Aligned_cols=29  Identities=10%  Similarity=0.170  Sum_probs=24.2

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHcCC
Q 032366           91 RNDKKLTQSQLAQLINEKPQVIQEYESGK  119 (142)
Q Consensus        91 R~~~glTQ~eLA~~lgis~stIs~~E~G~  119 (142)
                      +--.++|..++|+.+|+|+++|.++-.++
T Consensus        20 ~G~~~~s~~~Ia~~agvs~~~iY~~F~sK   48 (74)
T d2g7sa1          20 GGYNSFSYADISQVVGIRNASIHHHFPSK   48 (74)
T ss_dssp             HCGGGCCHHHHHHHHCCCHHHHHHHCSSH
T ss_pred             hCccccCHHHHHHHHCcCcchHHHHCcCH
Confidence            33456899999999999999999996554

>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=85.31  E-value=0.69  Score=26.63  Aligned_cols=32  Identities=16%  Similarity=0.126  Sum_probs=26.5

Q ss_pred             HHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 032366           89 QARNDKKLTQSQLAQLINEKPQVIQEYESGKA  120 (142)
Q Consensus        89 ~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~  120 (142)
                      ..+--.++|..++|+++|+|++++.++-.++.
T Consensus        16 ~~~G~~~~ti~~Ia~~agvs~~~~Y~~F~~K~   47 (68)
T d2d6ya1          16 ARHGIAGARIDRIAAEARANKQLIYAYYGNKG   47 (68)
T ss_dssp             HHHTTTSCCHHHHHHHHTCCHHHHHHHHSSHH
T ss_pred             HHhCccccCHHHHHHHHCcchhHHHHHCcCHH
Confidence            33444678999999999999999999987763

>d2ev0a1 a.4.5.24 (A:2-62) Manganese transport regulator MntR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Iron-dependent repressor protein
domain: Manganese transport regulator MntR
species: Bacillus subtilis [TaxId: 1423]

Probab=85.03  E-value=1.3  Score=25.23  Aligned_cols=25  Identities=12%  Similarity=0.193  Sum_probs=21.4

Q ss_pred             HhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           92 NDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        92 ~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ..-..+..+||+.+|+|++++++..
T Consensus        18 ~~~~v~~~~iA~~L~vs~~SVs~mi   42 (61)
T d2ev0a1          18 EKGYARVSDIAEALAVHPSSVTKMV   42 (61)
T ss_dssp             HHSSCCHHHHHHHHTCCHHHHHHHH
T ss_pred             cCCCccHHHHHHHhCCCchhHHHHH
Confidence            4456889999999999999998764

>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=84.94  E-value=0.56  Score=27.14  Aligned_cols=29  Identities=10%  Similarity=0.004  Sum_probs=24.8

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHcCC
Q 032366           91 RNDKKLTQSQLAQLINEKPQVIQEYESGK  119 (142)
Q Consensus        91 R~~~glTQ~eLA~~lgis~stIs~~E~G~  119 (142)
                      +--.++|..++|+.+|||++++.++-.++
T Consensus        17 ~G~~~~s~~~Ia~~agvs~~~~y~~F~~K   45 (71)
T d1jt6a1          17 NGYNATTTGEIVKLSESSKGNLYYHFKTK   45 (71)
T ss_dssp             HCTTTCCHHHHHHHTTCCHHHHHHHHSSH
T ss_pred             hCccccCHHHHHHHHCcCHhHHHHHCcCH
Confidence            34457899999999999999999997665

>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=84.65  E-value=0.94  Score=29.01  Aligned_cols=38  Identities=13%  Similarity=0.057  Sum_probs=27.9

Q ss_pred             chHHHHHHHHHHHHhC--CCCHHHHHHHhCCCHHHHHHHH
Q 032366           79 VPSELKKAIVQARNDK--KLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        79 ~~~~~g~~Lk~~R~~~--glTQ~eLA~~lgis~stIs~~E  116 (142)
                      +...-...|..+....  ++|+.+||+.+++++++++++.
T Consensus        27 lt~~q~~vL~~l~~~~~~~it~~ela~~~~~~~~~vs~~l   66 (135)
T d3broa1          27 LTGTQMTIIDYLSRNKNKEVLQRDLESEFSIKSSTATVLL   66 (135)
T ss_dssp             CCHHHHHHHHHHHHTTTSCCBHHHHHHHHTCCHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCCCCCHHHHHHHHCcCHhHHHHHH
Confidence            3344445555555544  4999999999999999999764

>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=84.56  E-value=0.26  Score=29.16  Aligned_cols=25  Identities=16%  Similarity=0.145  Sum_probs=21.7

Q ss_pred             HHHHHHHHcCCChhHHHhhhcCCCC
Q 032366           30 KVVNAARRAGADIETVRKSHAGTNK   54 (142)
Q Consensus        30 ~~~~~a~r~G~~v~t~kk~~~g~~~   54 (142)
                      ++-..|.+.|++.+++.+|+.|...
T Consensus        25 tq~~lA~~~gis~~~i~~~e~g~~~   49 (77)
T d2b5aa1          25 SQEELADLAGLHRTYISEVERGDRN   49 (77)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHTTCSC
T ss_pred             CHHHHHHHHCCCHHHHHHHHcCCCC
Confidence            4556799999999999999999865

>d2gena1 a.4.1.9 (A:6-75) Probable transcriptional regulator PA1836 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Probable transcriptional regulator PA1836
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=84.51  E-value=0.29  Score=28.34  Aligned_cols=29  Identities=7%  Similarity=-0.099  Sum_probs=24.5

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHcCC
Q 032366           91 RNDKKLTQSQLAQLINEKPQVIQEYESGK  119 (142)
Q Consensus        91 R~~~glTQ~eLA~~lgis~stIs~~E~G~  119 (142)
                      .--.++|..++|+.+|+|++++.++-.++
T Consensus        16 ~G~~~~si~~Ia~~agvs~~t~Y~~F~sK   44 (70)
T d2gena1          16 HGVDATTIEMIRDRSGASIGSLYHHFGNK   44 (70)
T ss_dssp             HCTTTCCHHHHHHHHCCCHHHHHHHTCSH
T ss_pred             hCcccCCHHHHHHHHCcCHHHHHHHCCCH
Confidence            33467899999999999999999997654

>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=83.99  E-value=0.6  Score=27.49  Aligned_cols=28  Identities=4%  Similarity=-0.115  Sum_probs=24.1

Q ss_pred             HhCCCCHHHHHHHhCCCHHHHHHHHcCC
Q 032366           92 NDKKLTQSQLAQLINEKPQVIQEYESGK  119 (142)
Q Consensus        92 ~~~glTQ~eLA~~lgis~stIs~~E~G~  119 (142)
                      --.++|..+||+.+|+|+.+|.++-..+
T Consensus        21 G~~~~ti~~Ia~~agvs~~s~y~~F~~K   48 (79)
T d2fbqa1          21 GFAETSLRLITSKAGVNLAAVNYHFGSK   48 (79)
T ss_dssp             CSTTCCHHHHHHHHTSCHHHHHHHTCSH
T ss_pred             CcccccHHHHHHHHCcChhHHHHHCcCH
Confidence            3357899999999999999999997654

>d2fx0a1 a.4.1.9 (A:4-76) Hemolysin II regulatory protein, HlyIIR {Bacillus cereus [TaxId: 1396]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Hemolysin II regulatory protein, HlyIIR
species: Bacillus cereus [TaxId: 1396]

Probab=83.81  E-value=1  Score=26.29  Aligned_cols=28  Identities=14%  Similarity=0.140  Sum_probs=24.5

Q ss_pred             HhCCCCHHHHHHHhCCCHHHHHHHHcCC
Q 032366           92 NDKKLTQSQLAQLINEKPQVIQEYESGK  119 (142)
Q Consensus        92 ~~~glTQ~eLA~~lgis~stIs~~E~G~  119 (142)
                      --.++|..++|+.+|||+++|.++-.++
T Consensus        21 G~~~~si~~Ia~~agvs~~~~Y~~F~~K   48 (73)
T d2fx0a1          21 GYEGTSIQEIAKEAKVNVAMASYYFNGK   48 (73)
T ss_dssp             CTTTCCHHHHHHHHTSCHHHHHHHHTSH
T ss_pred             CcccCcHHHHHHHHCcChhHHHHHCcCH
Confidence            3367899999999999999999998765

>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=83.67  E-value=0.3  Score=27.74  Aligned_cols=24  Identities=13%  Similarity=0.342  Sum_probs=21.3

Q ss_pred             HHHHHHHHcCCChhHHHhhhcCCC
Q 032366           30 KVVNAARRAGADIETVRKSHAGTN   53 (142)
Q Consensus        30 ~~~~~a~r~G~~v~t~kk~~~g~~   53 (142)
                      ++-+.|++.|++..++.+||.|++
T Consensus        16 sq~elA~~~gvs~~~is~~E~g~~   39 (63)
T d1r69a_          16 NQAELAQKVGTTQQSIEQLENGKT   39 (63)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHTTSC
T ss_pred             cHHHHHHHhCcCHHHHHHHHCCCC
Confidence            556789999999999999999965

>d2id3a1 a.4.1.9 (A:13-80) Putative transcriptional regulator SCO5951 {Streptomyces coelicolor [TaxId: 1902]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator SCO5951
species: Streptomyces coelicolor [TaxId: 1902]

Probab=83.63  E-value=0.28  Score=28.41  Aligned_cols=26  Identities=8%  Similarity=-0.004  Sum_probs=22.9

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 032366           94 KKLTQSQLAQLINEKPQVIQEYESGK  119 (142)
Q Consensus        94 ~glTQ~eLA~~lgis~stIs~~E~G~  119 (142)
                      .++|..++|+.+|+|+++|.++-.++
T Consensus        25 ~~~t~~~Ia~~agvs~~~iY~~F~~k   50 (68)
T d2id3a1          25 DALDLGEIARRAGVGKTTVYRRWGTP   50 (68)
T ss_dssp             GGCCHHHHHHHHTCCHHHHHHHHCSH
T ss_pred             ccCCHHHHHHHHCcCHHHHHHHCcCH
Confidence            46799999999999999999997654

>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=83.48  E-value=0.8  Score=29.80  Aligned_cols=38  Identities=8%  Similarity=0.066  Sum_probs=30.0

Q ss_pred             hHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           80 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ...-...|..+-...|+|+.+||+.+++++++|+++.+
T Consensus        35 t~~q~~vL~~l~~~~~~t~~~la~~l~~~~~~vsr~l~   72 (141)
T d1lnwa_          35 TPPDVHVLKLIDEQRGLNLQDLGRQMCRDKALITRKIR   72 (141)
T ss_dssp             CHHHHHHHHHHHSSTTCBHHHHHHHTTCCHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHCCCCCHHHHHHHHCccHhHHHHHHH
Confidence            34445556666677789999999999999999998753

>d2o7ta1 a.4.1.9 (A:1-78) Transcriptional regulator Cgl1640/Cg1846 {Corynebacterium glutamicum [TaxId: 1718]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator Cgl1640/Cg1846
species: Corynebacterium glutamicum [TaxId: 1718]

Probab=83.42  E-value=0.24  Score=29.51  Aligned_cols=26  Identities=12%  Similarity=0.083  Sum_probs=22.8

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 032366           94 KKLTQSQLAQLINEKPQVIQEYESGK  119 (142)
Q Consensus        94 ~glTQ~eLA~~lgis~stIs~~E~G~  119 (142)
                      .++|..++|+.+|||.++|.++-.++
T Consensus        26 ~~~t~~~Ia~~agvs~~t~y~~F~sK   51 (78)
T d2o7ta1          26 DSLTMENIAEQAGVGVATLYRNFPDR   51 (78)
T ss_dssp             GGCCHHHHHHHHTCCHHHHHHHCSSH
T ss_pred             cccCHHHHHHHhCCCHHHHHHHCcCH
Confidence            56899999999999999999986544

>d1ui5a1 a.4.1.9 (A:5-75) A-factor receptor homolog CprB {Streptomyces coelicolor [TaxId: 1902]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: A-factor receptor homolog CprB
species: Streptomyces coelicolor [TaxId: 1902]

Probab=82.90  E-value=0.59  Score=27.11  Aligned_cols=29  Identities=14%  Similarity=0.004  Sum_probs=24.1

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHcCC
Q 032366           91 RNDKKLTQSQLAQLINEKPQVIQEYESGK  119 (142)
Q Consensus        91 R~~~glTQ~eLA~~lgis~stIs~~E~G~  119 (142)
                      .--.++|..++|+.+|+|++++.++-..+
T Consensus        21 ~G~~~~si~~Ia~~agvs~~~~y~~F~sK   49 (71)
T d1ui5a1          21 RGYESTTLSEIVAHAGVTKGALYFHFAAK   49 (71)
T ss_dssp             HCTTTCCHHHHHHHHTCCHHHHHHHCSSH
T ss_pred             hCccccCHHHHHHHHCcCHhHHHHHCcCH
Confidence            34457899999999999999999996543

>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=82.69  E-value=1.2  Score=28.73  Aligned_cols=35  Identities=6%  Similarity=-0.031  Sum_probs=28.6

Q ss_pred             HHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           82 ELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        82 ~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      .-...|..+...-++|+.+||+.++++++++++..
T Consensus        33 ~q~~iL~~l~~~~~~t~~~La~~l~i~~~~vs~~v   67 (140)
T d2etha1          33 TELYAFLYVALFGPKKMKEIAEFLSTTKSNVTNVV   67 (140)
T ss_dssp             HHHHHHHHHHHHCCBCHHHHHHHTTSCHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHH
Confidence            33455666677788999999999999999998865

>d1r1ua_ a.4.5.5 (A:) Metal-sensing transcriptional repressor CzrA {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: Metal-sensing transcriptional repressor CzrA
species: Staphylococcus aureus [TaxId: 1280]

Probab=82.68  E-value=0.52  Score=29.29  Aligned_cols=30  Identities=7%  Similarity=0.091  Sum_probs=23.8

Q ss_pred             HHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           87 IVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      |-.+.....++-.+|++.+|+|++++++-.
T Consensus        23 Il~~L~~~~~~v~el~~~l~~s~~~vS~HL   52 (94)
T d1r1ua_          23 IMELLSVSEASVGHISHQLNLSQSNVSHQL   52 (94)
T ss_dssp             HHHHHHHCCBCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHcCCccHHHHHHHHCCCHHHHHHHH
Confidence            333444567999999999999999999754

>d2oi8a1 a.4.1.9 (A:8-86) Putative regulatory protein Sco4313 {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 regulatory protein Sco4313
species: Streptomyces coelicolor [TaxId: 1902]

Probab=82.53  E-value=0.36  Score=28.58  Aligned_cols=29  Identities=14%  Similarity=0.264  Sum_probs=23.7

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHcCC
Q 032366           91 RNDKKLTQSQLAQLINEKPQVIQEYESGK  119 (142)
Q Consensus        91 R~~~glTQ~eLA~~lgis~stIs~~E~G~  119 (142)
                      +--.++|..++|+.+|||+.++.++-.++
T Consensus        25 ~G~~~~t~~~Ia~~agvs~~~~Y~~F~~k   53 (79)
T d2oi8a1          25 AGASALSLNAIAKRMGMSGPALYRYFDGR   53 (79)
T ss_dssp             HCTTSCCHHHHHHHTTCCHHHHHTTCSSH
T ss_pred             hCccccCHHHHHHHhCCCCCchhhhcCCH
Confidence            34456899999999999999999875544

>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=82.33  E-value=0.56  Score=30.77  Aligned_cols=35  Identities=14%  Similarity=0.132  Sum_probs=27.9

Q ss_pred             HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           83 LKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        83 ~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      -...|..+...-|+|+.+||+.+++++++++++.+
T Consensus        31 q~~iL~~i~~~~~~t~~~la~~l~i~~~tvs~~l~   65 (144)
T d1lj9a_          31 QYLYLVRVCENPGIIQEKIAELIKVDRTTAARAIK   65 (144)
T ss_dssp             HHHHHHHHHHSTTEEHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHHCccHhhHHHHHH
Confidence            34445566666789999999999999999988753

>d2id6a1 a.4.1.9 (A:1-75) Transcriptional regulator TM1030 {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator TM1030
species: Thermotoga maritima [TaxId: 2336]

Probab=82.26  E-value=0.39  Score=28.20  Aligned_cols=29  Identities=17%  Similarity=0.217  Sum_probs=24.6

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHcCC
Q 032366           91 RNDKKLTQSQLAQLINEKPQVIQEYESGK  119 (142)
Q Consensus        91 R~~~glTQ~eLA~~lgis~stIs~~E~G~  119 (142)
                      .--.++|..++|+.+|+|+++|.++-..+
T Consensus        19 ~G~~~~ti~~Ia~~agvs~~~iY~~F~~k   47 (75)
T d2id6a1          19 KGYDRATTDEIAEKAGVAKGLIFHYFKNK   47 (75)
T ss_dssp             HHHHHCCHHHHHHHHTCCTHHHHHHHSSH
T ss_pred             hCccccCHHHHHHHhCCCHHHHHHHCCCH
Confidence            34457899999999999999999997654

>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=82.09  E-value=0.33  Score=29.31  Aligned_cols=24  Identities=13%  Similarity=0.178  Sum_probs=21.7

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHcCC
Q 032366           96 LTQSQLAQLINEKPQVIQEYESGK  119 (142)
Q Consensus        96 lTQ~eLA~~lgis~stIs~~E~G~  119 (142)
                      +.|..+|+.+||..+.|++|.+|-
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            469999999999999999998874

>d1vi0a1 a.4.1.9 (A:6-77) Hypothetical transcriptional regulator YsiA {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Hypothetical transcriptional regulator YsiA
species: Bacillus subtilis [TaxId: 1423]

Probab=82.05  E-value=0.29  Score=28.49  Aligned_cols=27  Identities=19%  Similarity=0.091  Sum_probs=23.4

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHcCC
Q 032366           93 DKKLTQSQLAQLINEKPQVIQEYESGK  119 (142)
Q Consensus        93 ~~glTQ~eLA~~lgis~stIs~~E~G~  119 (142)
                      -.++|..+||+.+|||+.++.++-.++
T Consensus        19 ~~~~ti~~Ia~~agvs~~~~y~~F~~K   45 (72)
T d1vi0a1          19 YHQSQVSKIAKQAGVADGTIYLYFKNK   45 (72)
T ss_dssp             GGGCCHHHHHHHHTSCHHHHHHHCSSH
T ss_pred             cccccHHHHHHHHCcCHHHHHHHCcCH
Confidence            356899999999999999999987654

>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=82.02  E-value=0.7  Score=26.75  Aligned_cols=32  Identities=9%  Similarity=-0.044  Sum_probs=26.1

Q ss_pred             HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 032366           87 IVQARNDKKLTQSQLAQLINEKPQVIQEYESGKA  120 (142)
Q Consensus        87 Lk~~R~~~glTQ~eLA~~lgis~stIs~~E~G~~  120 (142)
                      |.+.-.+.|  |...|+.+|+.++.|++-....+
T Consensus         7 L~dyv~~~G--QaKaA~~LGv~Q~AIsKAira~R   38 (61)
T d1d1la_           7 LKDYAMRFG--QTKTAKDLGVYQSAINKAIHAGR   38 (61)
T ss_dssp             HHHHHHHHC--HHHHHHHHTCCTHHHHHHHHTTC
T ss_pred             HHHHHHHHC--hHHHHHHcCccHHHHHHHHhcCC
Confidence            455556677  99999999999999999887544

>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=81.91  E-value=1.6  Score=25.01  Aligned_cols=28  Identities=14%  Similarity=0.115  Sum_probs=23.3

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 032366           91 RNDKKLTQSQLAQLINEKPQVIQEYESG  118 (142)
Q Consensus        91 R~~~glTQ~eLA~~lgis~stIs~~E~G  118 (142)
                      +--.++|..++|+++|+|+++|.++-.+
T Consensus        20 ~G~~~~t~~~Ia~~agvs~~~~y~~F~~   47 (69)
T d2fq4a1          20 SGFKAVTVDKIAERAKVSKATIYKWWPN   47 (69)
T ss_dssp             HCTTTCCHHHHHHHHTCCHHHHHHHCSS
T ss_pred             hCcccCCHHHHHHHHCcCHHHHHHHCCC
Confidence            3345679999999999999999998544

>d1pb6a1 a.4.1.9 (A:14-85) Hypothetical transcriptional regulator YcdC {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Hypothetical transcriptional regulator YcdC
species: Escherichia coli [TaxId: 562]

Probab=81.75  E-value=0.59  Score=27.20  Aligned_cols=29  Identities=17%  Similarity=0.052  Sum_probs=24.2

Q ss_pred             HHhCCCCHHHHHHHhCCCHHHHHHHHcCC
Q 032366           91 RNDKKLTQSQLAQLINEKPQVIQEYESGK  119 (142)
Q Consensus        91 R~~~glTQ~eLA~~lgis~stIs~~E~G~  119 (142)
                      +--.++|..++|+.+|||++++.++-.++
T Consensus        20 ~G~~~~ti~~Ia~~agvs~~t~y~~F~~K   48 (72)
T d1pb6a1          20 FGFHGTRLEQIAELAGVSKTNLLYYFPSK   48 (72)
T ss_dssp             HCTTTCCHHHHHHHTTSCHHHHHHHSSSH
T ss_pred             hCccccCHHHHHHHhCCChHHHHHHCcCH
Confidence            33467899999999999999999997554

>d1jgsa_ a.4.5.28 (A:) Multiple antibiotic resistance repressor, MarR {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Multiple antibiotic resistance repressor, MarR
species: Escherichia coli [TaxId: 562]

Probab=81.61  E-value=1.4  Score=28.47  Aligned_cols=37  Identities=11%  Similarity=0.121  Sum_probs=28.9

Q ss_pred             hHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           80 PSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        80 ~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ...-...|..+...-++|+.+||+.+++++++++++.
T Consensus        33 t~~q~~vL~~l~~~~~~t~~ela~~~~i~~~~vs~~v   69 (138)
T d1jgsa_          33 TAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRML   69 (138)
T ss_dssp             CHHHHHHHHHHHHHSSBCHHHHHHHHTCCHHHHHHHH
T ss_pred             CHHHHHHHHhHHhCcCCCHHHHHHHHCCCHhHHHHHH
Confidence            3334555666666779999999999999999998754

>d3c07a1 a.4.1.9 (A:15-89) Putative transcriptional regulator SCO4850 {Streptomyces coelicolor [TaxId: 1902]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator SCO4850
species: Streptomyces coelicolor [TaxId: 1902]

Probab=81.53  E-value=0.36  Score=28.18  Aligned_cols=26  Identities=23%  Similarity=0.137  Sum_probs=22.7

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 032366           94 KKLTQSQLAQLINEKPQVIQEYESGK  119 (142)
Q Consensus        94 ~glTQ~eLA~~lgis~stIs~~E~G~  119 (142)
                      .++|..++|+.+|||++++.++-.++
T Consensus        24 ~~~t~~~Ia~~agvs~~~~y~~F~~k   49 (75)
T d3c07a1          24 DRTTMRAIAQEAGVSVGNAYYYFAGK   49 (75)
T ss_dssp             TTCCHHHHHHHHTSCHHHHHHHCSSH
T ss_pred             ccCCHHHHHHHHCcCHHHHHHHCcCH
Confidence            45799999999999999999996554

>d2np5a1 a.4.1.9 (A:9-77) Transcriptional regulator RHA1_ro04179 {Rhodococcus sp. [TaxId: 1831]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional regulator RHA1 ro04179
species: Rhodococcus sp. [TaxId: 1831]

Probab=81.50  E-value=0.62  Score=26.67  Aligned_cols=26  Identities=15%  Similarity=0.036  Sum_probs=22.6

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 032366           94 KKLTQSQLAQLINEKPQVIQEYESGK  119 (142)
Q Consensus        94 ~glTQ~eLA~~lgis~stIs~~E~G~  119 (142)
                      .++|..++|+.+|+|+++|..+-..+
T Consensus        20 ~~~ti~~Ia~~agvs~~~iy~~F~sK   45 (69)
T d2np5a1          20 EGASVREVAKRAGVSIGAVQHHFSTK   45 (69)
T ss_dssp             GGCCHHHHHHHHTCCHHHHHHHCSSH
T ss_pred             cccCHHHHHHHhCCCHHHHHHHCcCH
Confidence            46799999999999999999986543

>d1bl0a1 a.4.1.8 (A:9-62) MarA {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: AraC type transcriptional activator
domain: MarA
species: Escherichia coli [TaxId: 562]

Probab=81.49  E-value=0.47  Score=26.08  Aligned_cols=25  Identities=8%  Similarity=0.040  Sum_probs=22.4

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           93 DKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        93 ~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ...+|..+||+.+|+|++++.++-+
T Consensus        17 ~~~~tl~~lA~~~~~s~~~l~r~Fk   41 (54)
T d1bl0a1          17 ESPLSLEKVSERSGYSKWHLQRMFK   41 (54)
T ss_dssp             TSCCCCHHHHHHSSSCHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            3579999999999999999999876

>d2hkua1 a.4.1.9 (A:18-87) Putative transcriptional regulator RHA1_ro03468 {Rhodococcus sp. RHA1 [TaxId: 101510]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator RHA1 ro03468
species: Rhodococcus sp. RHA1 [TaxId: 101510]

Probab=81.35  E-value=0.62  Score=27.04  Aligned_cols=27  Identities=15%  Similarity=0.282  Sum_probs=23.9

Q ss_pred             CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 032366           94 KKLTQSQLAQLINEKPQVIQEYESGKA  120 (142)
Q Consensus        94 ~glTQ~eLA~~lgis~stIs~~E~G~~  120 (142)
                      .+.|..++|+.+|||..+|.++-.++.
T Consensus        19 ~~~t~~~Ia~~agvs~~~~Y~~F~~K~   45 (70)
T d2hkua1          19 EGVPITQICAAAGAHPNQVTYYYGSKE   45 (70)
T ss_dssp             TTSCHHHHHHHHTCCHHHHHHHHSSHH
T ss_pred             cCchHHHHHHHHCCChhhHHhcCCCHH
Confidence            479999999999999999999986653

>d2hyja1 a.4.1.9 (A:8-82) Putative transcriptional regulator SCO4940 {Streptomyces coelicolor [TaxId: 1902]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator SCO4940
species: Streptomyces coelicolor [TaxId: 1902]

Probab=81.28  E-value=0.2  Score=29.65  Aligned_cols=28  Identities=14%  Similarity=0.079  Sum_probs=23.4

Q ss_pred             HhCCCCHHHHHHHhCCCHHHHHHHHcCC
Q 032366           92 NDKKLTQSQLAQLINEKPQVIQEYESGK  119 (142)
Q Consensus        92 ~~~glTQ~eLA~~lgis~stIs~~E~G~  119 (142)
                      --.++|..++|+.+|+|+++|.++-.++
T Consensus        22 G~~~~t~~~Ia~~agvs~~~~Y~~F~~K   49 (75)
T d2hyja1          22 GLDGITIGRLAEELEMSKSGVHKHFGTK   49 (75)
T ss_dssp             CGGGCCHHHHHHHHTCCHHHHHTTCSSH
T ss_pred             CcccCcHHHHHHHHCcCHHHHHHHCcCH
Confidence            3356899999999999999999986544

>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=81.07  E-value=0.95  Score=27.45  Aligned_cols=25  Identities=16%  Similarity=0.105  Sum_probs=22.2

Q ss_pred             HHHHHHHHcCCChhHHHhhhcCCCC
Q 032366           30 KVVNAARRAGADIETVRKSHAGTNK   54 (142)
Q Consensus        30 ~~~~~a~r~G~~v~t~kk~~~g~~~   54 (142)
                      ++-..|++.|++.+|+.+|+.|+..
T Consensus        16 sq~~LA~~lGvs~~~is~ie~g~~~   40 (87)
T d2icta1          16 SLREFARAMEIAPSTASRLLTGKAA   40 (87)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHTSSC
T ss_pred             CHHHHHHHHhhcHHHHHHHHHhccC
Confidence            4567899999999999999999876

>d1ttya_ a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Sigma3 and sigma4 domains of RNA polymerase sigma factors
family: Sigma4 domain
domain: Sigma70 (SigA, RpoD)
species: Thermotoga maritima [TaxId: 2336]

Probab=81.04  E-value=0.68  Score=28.60  Aligned_cols=25  Identities=24%  Similarity=0.259  Sum_probs=22.8

Q ss_pred             hCCCCHHHHHHHhCCCHHHHHHHHc
Q 032366           93 DKKLTQSQLAQLINEKPQVIQEYES  117 (142)
Q Consensus        93 ~~glTQ~eLA~~lgis~stIs~~E~  117 (142)
                      ...+|..++|+.+|||+..|.++|.
T Consensus        36 ~~~~tl~eI~~~lgiSrERVRQie~   60 (87)
T d1ttya_          36 GKPKTLEEVGQYFNVTRERIRQIEV   60 (87)
T ss_dssp             SSCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             CCcCCHHHHHHHhCCCHHHHHHHHH
Confidence            3568999999999999999999996

>d1jhfa1 a.4.5.2 (A:2-72) LexA repressor, N-terminal DNA-binding domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: LexA repressor, N-terminal DNA-binding domain
domain: LexA repressor, N-terminal DNA-binding domain
species: Escherichia coli [TaxId: 562]

Probab=81.00  E-value=1.4  Score=25.77  Aligned_cols=35  Identities=20%  Similarity=0.235  Sum_probs=28.2

Q ss_pred             HHHHHHHHHHHhCCC--CHHHHHHHhCC-CHHHHHHHH
Q 032366           82 ELKKAIVQARNDKKL--TQSQLAQLINE-KPQVIQEYE  116 (142)
Q Consensus        82 ~~g~~Lk~~R~~~gl--TQ~eLA~~lgi-s~stIs~~E  116 (142)
                      .+-+.|+....+.|.  |..|+|+.+|+ |+++|.++.
T Consensus         9 ~vL~~I~~~~~~~G~~Ps~rei~~~~g~~S~stv~~~l   46 (71)
T d1jhfa1           9 EVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHL   46 (71)
T ss_dssp             HHHHHHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHcCCCCHHHHHHHH
Confidence            466677888777785  79999999999 899887764

>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=80.85  E-value=1.3  Score=28.38  Aligned_cols=18  Identities=17%  Similarity=0.261  Sum_probs=16.8

Q ss_pred             HHHHHcCCChhHHHhhhc
Q 032366           33 NAARRAGADIETVRKSHA   50 (142)
Q Consensus        33 ~~a~r~G~~v~t~kk~~~   50 (142)
                      +.|+++|+++.|++-|+.
T Consensus         5 e~A~~~gvs~~TlR~Ye~   22 (127)
T d1q06a_           5 DVAKITGLTSKAIRFYEE   22 (127)
T ss_dssp             HHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHCcCHHHHHHHHH
Confidence            579999999999999997

>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=80.73  E-value=2  Score=24.62  Aligned_cols=35  Identities=6%  Similarity=0.126  Sum_probs=25.5

Q ss_pred             HHHHHHHHHHH-hCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           82 ELKKAIVQARN-DKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        82 ~~g~~Lk~~R~-~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      ++-+.|-.+-. ....+..++|+.+|++++++++..
T Consensus         9 dYL~~I~~L~~~~~~v~~~~iA~~L~vs~~SVt~mv   44 (63)
T d2isya1           9 MYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTV   44 (63)
T ss_dssp             HHHHHHHHHHHTTCCCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCCcHHHHHHHhCCCchhHHHHH
Confidence            34455555533 344789999999999999998764

>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=80.23  E-value=0.73  Score=29.80  Aligned_cols=38  Identities=8%  Similarity=0.073  Sum_probs=30.3

Q ss_pred             chHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 032366           79 VPSELKKAIVQARNDKKLTQSQLAQLINEKPQVIQEYE  116 (142)
Q Consensus        79 ~~~~~g~~Lk~~R~~~glTQ~eLA~~lgis~stIs~~E  116 (142)
                      +...-...|..+...-++|+.+||+.++++++++++.-
T Consensus        31 Lt~~q~~vL~~l~~~~~~t~~~La~~~~i~~~~vsr~i   68 (137)
T d1z91a1          31 ITYPQYLALLLLWEHETLTVKKMGEQLYLDSGTLTPML   68 (137)
T ss_dssp             CCHHHHHHHHHHHHHSEEEHHHHHHTTTCCHHHHHHHH
T ss_pred             cCHHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHH
Confidence            33444555677777889999999999999999998864